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|254780608|ref|YP_003065021.1| ribosomal large subunit
pseudouridine synthase C [Candidatus Liberibacter asiaticus str.
psy62]
         (346 letters)

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

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


Results from round 1


>gi|254780608|ref|YP_003065021.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Liberibacter asiaticus str. psy62]
 gi|254040285|gb|ACT57081.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Liberibacter asiaticus str. psy62]
          Length = 346

 Score =  724 bits (1870), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 346/346 (100%), Positives = 346/346 (100%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ
Sbjct: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ
Sbjct: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ
Sbjct: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF
Sbjct: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP
Sbjct: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL 346
           EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL
Sbjct: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL 346


>gi|315121808|ref|YP_004062297.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Liberibacter solanacearum CLso-ZC1]
 gi|313495210|gb|ADR51809.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Liberibacter solanacearum CLso-ZC1]
          Length = 336

 Score =  530 bits (1366), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 252/336 (75%), Positives = 292/336 (86%), Gaps = 1/336 (0%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  MT V+++++END ENMR DRWFK HYPHINF NLQK+LRSGQ+R+DK+RVK N+R+Q
Sbjct: 1   MLFMTCVKHIIIENDVENMRFDRWFKLHYPHINFGNLQKLLRSGQIRLDKRRVKSNDRVQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SGQVVRIPP+I+ L+H  +++  LDSSV+  K+S FLK+ILLYED+K+Y+FNKP GISVQ
Sbjct: 61  SGQVVRIPPIIDVLDHATEKRYSLDSSVDFLKNSAFLKNILLYEDNKLYIFNKPPGISVQ 120

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+ YHIDGFLKSW DSKGQKPRL HRLD+ETSGILVVARTRAAAQ LTESFRMRRI+
Sbjct: 121 GGSGVTYHIDGFLKSWSDSKGQKPRLIHRLDRETSGILVVARTRAAAQSLTESFRMRRIR 180

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIYWSLV G+P+NKKECI+ WL KK+ IGGDYV VV QNEKGA+YAISHFKVID F  KF
Sbjct: 181 KIYWSLVRGVPQNKKECISGWLFKKAKIGGDYVQVVDQNEKGAHYAISHFKVIDRFEYKF 240

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPH 299
           CWLEMQP+TGRTHQLRVHALH+G PIVGD KY  N  K  F++ IQNKLYLHARY+D PH
Sbjct: 241 CWLEMQPYTGRTHQLRVHALHVGHPIVGDKKYRINDSKEIFSNHIQNKLYLHARYIDFPH 300

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
           PEGGRLQITAPLP HM KTWDS GFKY++++ IKRL
Sbjct: 301 PEGGRLQITAPLPVHMAKTWDSFGFKYNQDIDIKRL 336


>gi|325292801|ref|YP_004278665.1| ribosomal large subunit pseudouridine synthase C [Agrobacterium sp.
           H13-3]
 gi|325060654|gb|ADY64345.1| ribosomal large subunit pseudouridine synthase C [Agrobacterium sp.
           H13-3]
          Length = 329

 Score =  379 bits (973), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 175/322 (54%), Positives = 235/322 (72%), Gaps = 3/322 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK HYP + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEADEAGMRLDRWFKIHYPGLGFGQLQKLLRSGQVRVDGGRVKTDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PPV + L   +K   I    +  +   + L  +LL+ED K+ VFNKPAGI+VQGGS
Sbjct: 61  MVRVPPVDSDLK--VKSGPIGSRDLKHSADGELLARMLLHEDDKVLVFNKPAGIAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HRLD++TSG+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 119 GVNRHIDGLLEAWTSPKGEKPRLVHRLDRDTSGVLVVARTRGAAQKLTAAFRERDTKKTY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+  ++ I+ WL+K+    GD + + K  E+GA++AIS+++VID  AQ   WL
Sbjct: 179 WALVRGVPRKHQDKISTWLVKEQTPDGDRMRIAKHGEEGADHAISYYRVIDTAAQNLAWL 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALHMG PI+GD KY  +    +F   +Q +L+LHAR++D+PHP G
Sbjct: 239 EMEPYTGRTHQLRVHALHMGHPIIGDPKYYIDDPNWDFPGGVQKRLHLHARHIDIPHPNG 298

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           GRL+++APLP HMV+TW+ LG 
Sbjct: 299 GRLRVSAPLPPHMVQTWNLLGL 320


>gi|159184771|ref|NP_354476.2| ribosomal large subunit pseudouridine synthase C [Agrobacterium
           tumefaciens str. C58]
 gi|159140059|gb|AAK87261.2| ribosomal large subunit pseudouridine synthase C [Agrobacterium
           tumefaciens str. C58]
          Length = 329

 Score =  377 bits (967), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 174/322 (54%), Positives = 234/322 (72%), Gaps = 3/322 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK HYP + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEADEAGMRLDRWFKIHYPGLGFGQLQKLLRSGQVRVDGGRVKTDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PPV + +    K   I    +  +   + L  +LL+ED K+ VFNKPAGI+VQGGS
Sbjct: 61  MVRVPPVDSDMK--TKTGPIGSKDLKHSADGELLARMLLHEDDKVLVFNKPAGIAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HRLD++TSG+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 119 GVNRHIDGLLEAWTSPKGEKPRLVHRLDRDTSGVLVVARTRGAAQKLTAAFRERDTKKTY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+  ++ I+ WL+K+    GD + + K  E+GA++AIS+++VID  AQ   WL
Sbjct: 179 WALVRGVPRKHQDKISTWLVKEQTPDGDRMRIAKHGEEGADHAISYYRVIDTAAQNLAWL 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALHMG PI+GD KY  +    +F   +Q +L+LHAR++D+PHP G
Sbjct: 239 EMEPYTGRTHQLRVHALHMGHPIIGDPKYYIDDPNWDFPGGVQKRLHLHARHIDIPHPNG 298

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           GRL+++APLP HMV+TW+ LG 
Sbjct: 299 GRLRVSAPLPPHMVQTWNLLGL 320


>gi|222086089|ref|YP_002544621.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221723537|gb|ACM26693.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 332

 Score =  372 bits (956), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 170/323 (52%), Positives = 237/323 (73%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK++RSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIEVEPDEAGMRLDRWFKVHFPGLGFGQLQKLMRSGQVRVDGGRVKTDARVQPGQ 60

Query: 64  VVRIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           +VR+PP+ ++A     K   I +  +  +  +D L  +LL+ED K++V NKPAG++VQGG
Sbjct: 61  IVRVPPLDVDAKG--PKSGPIGNKDMKHSSDADLLARMLLHEDEKVFVLNKPAGLAVQGG 118

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+  H+D  L++W   KG+KPRL HRLD++TSG+LVVARTR AAQ LT +FR R  +K 
Sbjct: 119 SGLTRHLDKMLEAWTSKKGEKPRLVHRLDRDTSGVLVVARTRGAAQKLTAAFRERDTKKT 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YWSLV G+P+  ++ I+ WL+K++   GD + + K  E GA++AI++++V++  AQ   W
Sbjct: 179 YWSLVKGVPRKHEDKISTWLVKEATADGDRMRIAKHGEDGADHAITYYRVLETAAQSLAW 238

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPE 301
           LEM+P+TGRTHQLRVHALHMG PI+GD KY  +    +F   +QN+L+LHAR++D+PHP 
Sbjct: 239 LEMEPYTGRTHQLRVHALHMGHPIIGDPKYFDDDHNWDFPGGVQNRLHLHARHIDIPHPN 298

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
           GGRL+ITAPLP HMV+TW+ LG 
Sbjct: 299 GGRLRITAPLPPHMVQTWNLLGL 321


>gi|190891935|ref|YP_001978477.1| RNA-pseudouridine synthase, ribosomal large subunit C [Rhizobium
           etli CIAT 652]
 gi|190697214|gb|ACE91299.1| RNA-pseudouridine synthase protein, ribosomal large subunit C
           [Rhizobium etli CIAT 652]
          Length = 330

 Score =  365 bits (938), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 168/322 (52%), Positives = 231/322 (71%), Gaps = 3/322 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEPDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+   ++  +K   I    +  +   D L  ++L+ED K+ V NKP GI+VQGGS
Sbjct: 61  TVRVPPL--DVDAKLKSGPIAGKDLKHSSDFDLLSRMVLHEDEKVIVLNKPPGIAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K Y
Sbjct: 119 GVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRERDTKKTY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+  ++ I+ WL+K++   GD + + K  E GA++AIS ++V++  AQ   WL
Sbjct: 179 WALVKGVPRKHEDKISTWLVKEATADGDRMRIAKHGEDGADHAISFYRVLETAAQNLAWL 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALH+G PI+GD KY  +    +F   IQ KL+LHAR++D+PHP G
Sbjct: 239 EMEPYTGRTHQLRVHALHIGHPIIGDPKYFDDDPNWDFPGGIQKKLHLHARHIDIPHPSG 298

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           GRL+++APLP HMV+TW+ LG 
Sbjct: 299 GRLRVSAPLPPHMVQTWNLLGL 320


>gi|241204807|ref|YP_002975903.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240858697|gb|ACS56364.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 330

 Score =  363 bits (931), Expect = 3e-98,   Method: Compositional matrix adjust.
 Identities = 171/324 (52%), Positives = 234/324 (72%), Gaps = 7/324 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEPDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDF--LKSILLYEDSKIYVFNKPAGISVQG 121
            VR+PP+   ++  +K   I  +  +L   SDF  L  ++L+ED K+ V NKP G++VQG
Sbjct: 61  TVRVPPM--DVDAKLKSGPI--AGKDLKHSSDFQLLSRMVLHEDDKVIVLNKPPGLAVQG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K
Sbjct: 117 GSGVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRERDTKK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            YW+LV G+P+  ++ I+ WL+K+    GD + + K  E GA++AIS ++V++  AQ   
Sbjct: 177 TYWALVKGVPRKHEDKISTWLVKEPTADGDRMRIAKHGEDGADHAISFYRVLETAAQNLA 236

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHP 300
           WLEM+P+TGRTHQLRVHALH+G PI+GD KY  +    +F   +Q KL+LHAR++D+PHP
Sbjct: 237 WLEMEPYTGRTHQLRVHALHIGHPIIGDPKYFDDDPNWDFPGGVQKKLHLHARHIDIPHP 296

Query: 301 EGGRLQITAPLPAHMVKTWDSLGF 324
            GGRL+I+APLPAHMV+TW+ LG 
Sbjct: 297 SGGRLRISAPLPAHMVQTWNLLGL 320


>gi|327191042|gb|EGE58095.1| RNA-pseudouridine synthase protein, ribosomal large subunit C
           [Rhizobium etli CNPAF512]
          Length = 330

 Score =  362 bits (930), Expect = 4e-98,   Method: Compositional matrix adjust.
 Identities = 166/322 (51%), Positives = 231/322 (71%), Gaps = 3/322 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEPDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+   ++  +K   I    +  +   + L  ++L+ED K+ V NKP GI+VQGGS
Sbjct: 61  TVRVPPL--DVDAKLKSGPIAGKDLKHSSDFELLSRMVLHEDDKVIVLNKPPGIAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K Y
Sbjct: 119 GVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRERDTKKTY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+  ++ I+ WL+K++   GD + + K  E GA++AIS ++V++  AQ   W+
Sbjct: 179 WALVKGVPRKHEDKISTWLVKEATADGDRMRIAKHGEDGADHAISFYRVLETAAQNLAWI 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALH+G PI+GD KY  +    +F   IQ KL+LHAR++D+PHP G
Sbjct: 239 EMEPYTGRTHQLRVHALHIGHPIIGDPKYFDDDPNWDFPGGIQKKLHLHARHIDIPHPSG 298

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           GRL+++APLP HMV+TW+ LG 
Sbjct: 299 GRLRVSAPLPPHMVQTWNLLGL 320


>gi|116252313|ref|YP_768151.1| ribosomal large subunit pseudouridine synthase C [Rhizobium
           leguminosarum bv. viciae 3841]
 gi|115256961|emb|CAK08055.1| putative ribosomal large subunit pseudouridine synthase C
           [Rhizobium leguminosarum bv. viciae 3841]
          Length = 330

 Score =  362 bits (930), Expect = 4e-98,   Method: Compositional matrix adjust.
 Identities = 165/322 (51%), Positives = 231/322 (71%), Gaps = 3/322 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEPDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+   ++  +K   I    +  +   + L  ++L+ED K+ V NKP G++VQGGS
Sbjct: 61  TVRVPPM--DVDAKLKSGPIAGKDLKHSTDFELLSRMVLHEDEKVIVLNKPPGLAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K Y
Sbjct: 119 GVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRERDTKKTY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+  ++ I+ WL+K+    GD + + K  E GA++AIS ++V++  AQ   WL
Sbjct: 179 WALVKGVPRKHEDKISTWLVKEPTADGDRMRIAKHGEDGADHAISFYRVLETAAQNLAWL 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALH+G PI+GD KY  +    +F   +Q KL+LHAR++D+PHP G
Sbjct: 239 EMEPYTGRTHQLRVHALHIGHPIIGDPKYFDDDPNWDFPGGVQKKLHLHARHIDIPHPSG 298

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           GRL+++APLP+HMV+TW+ LG 
Sbjct: 299 GRLRVSAPLPSHMVQTWNLLGL 320


>gi|227821788|ref|YP_002825758.1| ribosomal large subunit pseudouridine synthase C [Sinorhizobium
           fredii NGR234]
 gi|227340787|gb|ACP25005.1| ribosomal large subunit pseudouridine synthase C [Sinorhizobium
           fredii NGR234]
          Length = 330

 Score =  362 bits (928), Expect = 5e-98,   Method: Compositional matrix adjust.
 Identities = 164/323 (50%), Positives = 232/323 (71%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +++  V+ DE  MRLDRWFK HYP + F  LQK+LRSGQ+RVD  R K + R+Q GQ
Sbjct: 1   MAGIEHRQVDGDEAGMRLDRWFKVHYPGLGFGPLQKLLRSGQIRVDGARAKSDTRVQPGQ 60

Query: 64  VVRIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +R+PP+ ++A +   K   I    +  +   D L  ++L+ED+K+ V NKPAG++VQGG
Sbjct: 61  TIRVPPLGVDAKD--TKTGPIGGRDLRHSSDGDLLSRMVLHEDAKVIVLNKPAGLAVQGG 118

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG++ HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +KI
Sbjct: 119 SGVSRHIDKMLEAWTSQKGEKPRLVHRLDRDTSGVLVIARTRGAAQQLTAAFRERDTRKI 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YWSLV G+P+ +++ I+ WL+K+    GD + + K  + GA++AIS++++++   Q   W
Sbjct: 179 YWSLVKGVPRKREDRISTWLVKEQTPDGDRMRIAKHGDDGADHAISYYRIVEQAGQNLAW 238

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           LEM+P+TGRTHQLRVHA H+G PI+GD KY  A+    F   IQN+L+LHAR +D+PHP 
Sbjct: 239 LEMEPYTGRTHQLRVHAAHIGHPIIGDPKYFEADVNWTFPGGIQNRLHLHARCIDIPHPN 298

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
           GGRL++TAPLP HMV++W+ LG 
Sbjct: 299 GGRLKVTAPLPPHMVQSWNLLGL 321


>gi|15965142|ref|NP_385495.1| ribosomal large subunit pseudouridine synthase C protein
           [Sinorhizobium meliloti 1021]
 gi|307314392|ref|ZP_07593998.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti BL225C]
 gi|307322745|ref|ZP_07602066.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti AK83]
 gi|15074322|emb|CAC45968.1| Probable ribosomal large subunit pseudouridine synthase C
           [Sinorhizobium meliloti 1021]
 gi|306891605|gb|EFN22470.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti AK83]
 gi|306899090|gb|EFN29732.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti BL225C]
          Length = 330

 Score =  361 bits (927), Expect = 9e-98,   Method: Compositional matrix adjust.
 Identities = 165/322 (51%), Positives = 229/322 (71%), Gaps = 2/322 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +++  V++DE  MRLDRWFK H+P + F  LQK+LRSGQ+RVD  R K + RIQ GQ
Sbjct: 1   MAGIEHRQVDSDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQIRVDGARAKSDTRIQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP +       K   I    +  +   + L  ++L+ED+K+ V NKPAG++VQGGS
Sbjct: 61  TIRIPP-LGVDPKEAKSGPIGGRDLRQSPDGELLSRMVLHEDAKVIVLNKPAGLAVQGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HID  L++W   KG+KPRL HRLD++TSG+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 120 GVNRHIDKMLEAWTSQKGEKPRLVHRLDRDTSGVLVVARTRGAAQQLTAAFRERDTKKTY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD V + K  E GA++AIS++++++   Q   WL
Sbjct: 180 WALVRGVPRKREDKISTWLVKEPTPDGDRVRIAKHGEDGADHAISYYRIVEQAGQNLAWL 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA H+G PI+GD KY  A+    F   +QN+L+LHAR++D+PHP G
Sbjct: 240 EMEPYTGRTHQLRVHAAHIGHPIIGDPKYFEADVNWTFPGGMQNRLHLHARHIDIPHPNG 299

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           GRL+ITAPLP HMV++W+ LGF
Sbjct: 300 GRLKITAPLPQHMVQSWNLLGF 321


>gi|209549478|ref|YP_002281395.1| pseudouridine synthase [Rhizobium leguminosarum bv. trifolii
           WSM2304]
 gi|209535234|gb|ACI55169.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 329

 Score =  361 bits (926), Expect = 9e-98,   Method: Compositional matrix adjust.
 Identities = 168/323 (52%), Positives = 230/323 (71%), Gaps = 6/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEADEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64  VVRIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VR+PP+ ++A     K   I    +  +   + L  ++L+ED K+ V NKP GI+VQGG
Sbjct: 61  TVRVPPLDVDAK----KSGPIAGKDLKHSSDFELLSRMVLHEDDKVIVLNKPPGIAVQGG 116

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K 
Sbjct: 117 SGVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRERDTKKT 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+P+  ++ I+ WL+K+    GD + + K  E GA++AIS ++VI+  AQ   W
Sbjct: 177 YWALVKGVPRKHEDKISTWLVKEPTADGDRMRIAKHGEDGADHAISFYRVIETAAQNLAW 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPE 301
           LEM+P+TGRTHQLRVHALH+G PI+GD KY  +    +F   +Q KL+LHAR++D+PHP 
Sbjct: 237 LEMEPYTGRTHQLRVHALHIGHPIIGDPKYFDDDPNWDFPGGVQKKLHLHARHIDIPHPS 296

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
           GGRL+++APLP HMV+TW+ LG 
Sbjct: 297 GGRLRVSAPLPPHMVQTWNLLGL 319


>gi|222148667|ref|YP_002549624.1| ribosomal large subunit pseudouridine synthase C [Agrobacterium
           vitis S4]
 gi|221735653|gb|ACM36616.1| ribosomal large subunit pseudouridine synthase C [Agrobacterium
           vitis S4]
          Length = 330

 Score =  360 bits (923), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 164/325 (50%), Positives = 230/325 (70%), Gaps = 2/325 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ V  DE  MRLDRWFK HYP + F  LQK++RSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHITVGPDEAGMRLDRWFKIHYPGLGFGPLQKLMRSGQVRVDGGRVKTDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP ++      K   I    +      + L  +LL+ED K++V NKPAG++VQGGS
Sbjct: 61  VVRVPP-MDVDAKTPKSGPIASHDLKHAGDGELLARMLLHEDEKVFVLNKPAGLAVQGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HID  L++W   KG+KPRL HRLD++TSG+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 120 GLNRHIDQMLEAWTSKKGEKPRLVHRLDRDTSGVLVVARTRGAAQKLTAAFRERDTKKTY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+   + I+ W++K+    GD + + +  E GA++A+S+++V++  AQ   WL
Sbjct: 180 WALVKGVPRKHDDKISTWVVKEQTEDGDRMRIARHGEDGADHAVSYYRVLETAAQSLAWL 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLR+HALH+G PI+GD KY  +    +F   +Q +L+LHAR++D+PHP+G
Sbjct: 240 EMEPYTGRTHQLRLHALHIGHPIIGDPKYYIDDPNWDFPGGVQKRLHLHARHIDIPHPDG 299

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           GRL+ITAPLP HMV+TW+ LG   +
Sbjct: 300 GRLRITAPLPPHMVQTWNLLGLDME 324


>gi|150396240|ref|YP_001326707.1| RluA family pseudouridine synthase [Sinorhizobium medicae WSM419]
 gi|150027755|gb|ABR59872.1| pseudouridine synthase, RluA family [Sinorhizobium medicae WSM419]
          Length = 330

 Score =  355 bits (911), Expect = 5e-96,   Method: Compositional matrix adjust.
 Identities = 163/326 (50%), Positives = 231/326 (70%), Gaps = 8/326 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +++  V++DE  MRLDRWFK H+P + F  LQK+LRSGQ+RVD  R K + RIQ GQ
Sbjct: 1   MAGIEHRQVDSDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQIRVDGARAKSDTRIQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            +RIPP    L    KE+K   I    +  +   + L  ++L+ED+K+ V NKP G++VQ
Sbjct: 61  TIRIPP----LGVDPKEKKTGPIGGRDLRQSPDGELLSRMVLHEDAKVIVLNKPPGLAVQ 116

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+  HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +
Sbjct: 117 GGSGVNRHIDKMLEAWTSQKGEKPRLVHRLDRDTSGVLVIARTRGAAQQLTAAFRERDTK 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW+LV G+P+ +++ I+ W++K+    GD V + K  E GA++AIS +++++   Q  
Sbjct: 177 KTYWALVRGVPRKREDKISTWVVKEQTPDGDRVRIAKHGEDGADHAISFYRIVEQAGQNL 236

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
            WLEM+P+TGRTHQLRVHA H+G PI+GD KY  A+    F   +QN+L+LHAR++D+PH
Sbjct: 237 AWLEMEPYTGRTHQLRVHAAHIGHPIIGDPKYFEADVNWTFPGGMQNRLHLHARHIDIPH 296

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFK 325
           P GGRL++TAPLP HM+++W+ LGF+
Sbjct: 297 PNGGRLKVTAPLPQHMMQSWNLLGFE 322


>gi|86357851|ref|YP_469743.1| pseudouridylate synthase, ribosomal large subunit C protein
           [Rhizobium etli CFN 42]
 gi|86281953|gb|ABC91016.1| pseudouridylate synthase, ribosomal large subunit C protein
           [Rhizobium etli CFN 42]
          Length = 317

 Score =  354 bits (909), Expect = 8e-96,   Method: Compositional matrix adjust.
 Identities = 161/307 (52%), Positives = 226/307 (73%), Gaps = 3/307 (0%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ+VR+PP+   ++  +
Sbjct: 1   MRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQMVRVPPL--DVDAKL 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K   I    +  +   + L  ++L+ED K+ V NKP G++VQGGSG+A HID  L++W+ 
Sbjct: 59  KSGPIAGKDLKHSSDFELLSRMVLHEDEKVIVLNKPPGLAVQGGSGVARHIDQMLEAWIS 118

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K YWSLV G+P+  ++ I
Sbjct: 119 PKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRERDTKKTYWSLVKGVPRKHEDKI 178

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           + WL+K+    GD + + K  E GA++A+S+++V++  AQ+  WLEM+P+TGRTHQLRVH
Sbjct: 179 STWLVKEPTADGDRMRIAKHGEDGADHAVSYYRVVETAAQRLAWLEMEPYTGRTHQLRVH 238

Query: 259 ALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
           ALH+G PI+GD KY  +    +F   IQ +L+LHAR++D+PHP GGRL++TAPLP HMV+
Sbjct: 239 ALHIGHPIIGDPKYFDDDPNWDFPGGIQKRLHLHARHIDIPHPSGGRLRVTAPLPPHMVQ 298

Query: 318 TWDSLGF 324
           +W+ LGF
Sbjct: 299 SWNLLGF 305


>gi|163760834|ref|ZP_02167913.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE C [Hoeflea
           phototrophica DFL-43]
 gi|162281878|gb|EDQ32170.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE C [Hoeflea
           phototrophica DFL-43]
          Length = 329

 Score =  354 bits (908), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 165/325 (50%), Positives = 232/325 (71%), Gaps = 10/325 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  VQ   V+ DE  MRLDRWFK H+P + F  LQK+LRSGQ+RVD  RVK + R+Q GQ
Sbjct: 1   MAGVQLKQVDPDETGMRLDRWFKTHFPGLGFGQLQKLLRSGQIRVDGGRVKSDARLQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQ---KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            VRIPP+       + E+    +   ++      D L  +LL+EDSK+ VFNKPAG++VQ
Sbjct: 61  TVRIPPMG------VDEKGSAPLTAKTIRNRDDGDVLSQMLLHEDSKVLVFNKPAGLAVQ 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+  ++D  L++W + KG+KPRL HRLD++T+G+LVVARTR AAQ LT +FR R  +
Sbjct: 115 GGSGVTRNVDDMLEAWRNKKGEKPRLVHRLDRDTAGVLVVARTRGAAQALTAAFRERTTK 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW+LV G+P++++  I+ WL+K++   GD + V K  E GA++A+S++++I+  AQ  
Sbjct: 175 KTYWALVTGVPRDREGKISTWLVKEATDDGDRMRVAKHGEPGADHAVSYYRIIEKAAQNL 234

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPH 299
           CWLE++P+TGRTHQLRVH LH+G PI+GD KY  + K   F   +Q +L+L AR++ +PH
Sbjct: 235 CWLELEPYTGRTHQLRVHCLHLGHPILGDPKYYDHDKNREFPGGMQKRLHLLARHISVPH 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGF 324
           P+GGRL +TAPLP HMV++W+ LGF
Sbjct: 295 PDGGRLSVTAPLPPHMVQSWNLLGF 319


>gi|13470583|ref|NP_102152.1| ribosomal large subunit pseudouridine synthase C [Mesorhizobium
           loti MAFF303099]
 gi|14021325|dbj|BAB47938.1| ribosomal large subunit pseudouridine synthase C [Mesorhizobium
           loti MAFF303099]
          Length = 326

 Score =  353 bits (907), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 162/324 (50%), Positives = 233/324 (71%), Gaps = 8/324 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + VE  E  MRLDRWFK H+P + F +LQK+LRSGQ+RVD  RVK ++R++ GQ
Sbjct: 1   MAGVEQITVEAGEAGMRLDRWFKTHFPGLGFGHLQKLLRSGQIRVDGGRVKADSRVEPGQ 60

Query: 64  VVRIPPVINALNHIIK--EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           VVRIPP+      + K  E  +   S+     +D L  +L++ED K++VFNKPAG++VQG
Sbjct: 61  VVRIPPL-----EVDKKGESALTGHSIRNQGDADVLAKMLIHEDPKVFVFNKPAGLAVQG 115

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+  ++D  L++W + KG+KPRL HRLD++TSG+LVVARTR AA  L+E+FR R  +K
Sbjct: 116 GSGVTRNVDDMLEAWRNQKGEKPRLVHRLDRDTSGVLVVARTRLAAMKLSEAFRARETKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            YW+LV G+P  +++ I+ WL+K+    GD V V    EKGA++A+S++++I+  AQ   
Sbjct: 176 TYWALVKGVPPKREDKISTWLIKEPTEDGDRVRVAAHGEKGADHAVSYYRIIEQAAQTMT 235

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP 300
           WLEM+P+TGRTHQLRVHA ++GCPI+GD KY  A+   +F   IQN+L+LHAR + +PHP
Sbjct: 236 WLEMEPYTGRTHQLRVHAAYIGCPIIGDPKYFEADTNWDFPGGIQNRLHLHARRIIIPHP 295

Query: 301 EGGRLQITAPLPAHMVKTWDSLGF 324
           + G + +TAP+P HM ++W+ +GF
Sbjct: 296 DKGLIDVTAPMPPHMRQSWNLIGF 319


>gi|121602476|ref|YP_989029.1| RluA family pseudouridine synthase [Bartonella bacilliformis KC583]
 gi|120614653|gb|ABM45254.1| pseudouridine synthase, RluA family [Bartonella bacilliformis
           KC583]
          Length = 327

 Score =  353 bits (905), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 171/324 (52%), Positives = 233/324 (71%), Gaps = 8/324 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++   VE DE  MRLDRWFK HYP + F  LQKILRSGQVRVD  RVK N R+ +GQ
Sbjct: 1   MVNIKIKNVEEDENGMRLDRWFKVHYPGLGFGYLQKILRSGQVRVDGGRVKANMRLVTGQ 60

Query: 64  VVRIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +R+P   I +  +I    K++    +     D LK +LLYED KI+VFNKPAG++VQGG
Sbjct: 61  SIRVPSFFIESKRNISITSKVISQQDD----GDLLKKMLLYEDPKIFVFNKPAGLAVQGG 116

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+  H+DG L++W + KG+KPRL HRLD+ETSG+LVVAR+R+AAQ LT +FR R ++KI
Sbjct: 117 SGLTRHVDGMLEAWRNKKGEKPRLVHRLDRETSGLLVVARSRSAAQALTAAFRTREMKKI 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+P+ K+E I+ W+ K++   GD + V +  E  AN+A+S+++++D  A+   W
Sbjct: 177 YWALVRGVPRKKQEKISTWMAKETTAQGDKMRVCEHGELDANHAVSYYRILDTRARALSW 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHP 300
           LEM+P+TGRTHQLRVHA H+G PI+GD KY  +   N+  P  +QN+L+LHAR + +PHP
Sbjct: 237 LEMEPYTGRTHQLRVHASHIGHPIIGDSKYFFS-DSNWELPGGMQNRLHLHARRIRIPHP 295

Query: 301 EGGRLQITAPLPAHMVKTWDSLGF 324
            GG L ITAPLP HMV++++ L F
Sbjct: 296 SGGILDITAPLPPHMVQSFNLLAF 319


>gi|260468522|ref|ZP_05813689.1| pseudouridine synthase, RluA family [Mesorhizobium opportunistum
           WSM2075]
 gi|259028678|gb|EEW29987.1| pseudouridine synthase, RluA family [Mesorhizobium opportunistum
           WSM2075]
          Length = 326

 Score =  352 bits (903), Expect = 5e-95,   Method: Compositional matrix adjust.
 Identities = 160/324 (49%), Positives = 233/324 (71%), Gaps = 8/324 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + VE  E  MRLDRWFK H+P + F +LQK+LRSGQ+RVD  RVK ++R++ GQ
Sbjct: 1   MAGVEQITVEAGEAGMRLDRWFKTHFPGLGFGHLQKLLRSGQIRVDGGRVKADSRVEPGQ 60

Query: 64  VVRIPPVINALNHIIK--EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           VVR+PP+      + K  E  +   S+     +D L  +L++ED K++VFNKPAG++VQG
Sbjct: 61  VVRVPPL-----EVDKKGESPLTGHSIRNQGDADVLAKMLIHEDPKVFVFNKPAGLAVQG 115

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+  ++D  L++W + KG+KPRL HRLD++TSG+LVVARTR AA  L+E+FR R  +K
Sbjct: 116 GSGVTRNVDDMLEAWRNQKGEKPRLVHRLDRDTSGVLVVARTRLAAMKLSEAFRARETKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            YW+LV G+P  +++ I+ WL+K+    GD V +    EKGA++A+S++++I+  AQ   
Sbjct: 176 TYWALVKGVPPKREDKISTWLIKEPTPDGDRVRIAAHGEKGADHAVSYYRIIEQAAQTMT 235

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP 300
           WLEM+P+TGRTHQLRVHA ++GCPI+GD KY  A+   +F   IQN+L+LHAR + +PHP
Sbjct: 236 WLEMEPYTGRTHQLRVHAAYIGCPIIGDPKYFEADTNWDFPGGIQNRLHLHARRIVIPHP 295

Query: 301 EGGRLQITAPLPAHMVKTWDSLGF 324
           + G + +TAP+P HM ++W+ +GF
Sbjct: 296 DKGFIDVTAPMPPHMRQSWNLIGF 319


>gi|319783351|ref|YP_004142827.1| pseudouridine synthase, RluA family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317169239|gb|ADV12777.1| pseudouridine synthase, RluA family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 326

 Score =  351 bits (901), Expect = 9e-95,   Method: Compositional matrix adjust.
 Identities = 161/324 (49%), Positives = 231/324 (71%), Gaps = 8/324 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + VE  E  MRLDRWFK H+P + F +LQK+LRSGQ+RVD  RVK + R++ GQ
Sbjct: 1   MAGVEQITVEAGEAGMRLDRWFKTHFPGLGFGHLQKLLRSGQIRVDGGRVKADTRVEPGQ 60

Query: 64  VVRIPPVINALNHIIK--EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           +VR+PP+      + K  E  +   S+     +D L  +L++ED K++VFNKPAG++VQG
Sbjct: 61  MVRVPPL-----EVDKKGESALTGHSIRNQGDADVLSKMLIHEDPKVFVFNKPAGLAVQG 115

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+  ++D  L++W   KG+KPRL HRLD++TSG+LVVARTR AA  L+E+FR R  +K
Sbjct: 116 GSGVTRNVDDMLEAWRSPKGEKPRLVHRLDRDTSGVLVVARTRLAAMKLSEAFRARETKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            YW+LV G+P  +++ I+ WL+K+    GD V V    EKGA++A+S+++VI+  AQ   
Sbjct: 176 TYWALVKGVPPKREDKISTWLIKEPTPDGDRVRVAAHGEKGADHAVSYYRVIEQAAQTMT 235

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP 300
           WLEM+P+TGRTHQLRVHA ++GCPI+GD KY  A+   +F   IQN+L+LHAR + +PHP
Sbjct: 236 WLEMEPYTGRTHQLRVHAAYIGCPILGDPKYFEADTNWDFPGGIQNRLHLHARRIIIPHP 295

Query: 301 EGGRLQITAPLPAHMVKTWDSLGF 324
           + G + +TAP+P HM ++W+ +GF
Sbjct: 296 DKGVIDVTAPMPPHMRQSWNLIGF 319


>gi|153009413|ref|YP_001370628.1| RluA family pseudouridine synthase [Ochrobactrum anthropi ATCC
           49188]
 gi|151561301|gb|ABS14799.1| pseudouridine synthase, RluA family [Ochrobactrum anthropi ATCC
           49188]
          Length = 326

 Score =  346 bits (888), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 158/322 (49%), Positives = 227/322 (70%), Gaps = 4/322 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LRSGQVR+D  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDTGEAGMRLDRWFKVHYPGLGFGHLQKLLRSGQVRIDGSRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+      +     +   ++   +  D L  +LLYED K+YVFNKPAG++VQGGS
Sbjct: 61  TVRIPPLGVDEKAV---GPVTARTIRSQQDGDVLSQMLLYEDPKVYVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G++ H+DG L++W + KG+KPRL HR+D++TSG+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 118 GVSRHVDGMLEAWRNKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTTAFRERDTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+++    GD + V +  E  +++A+S++++I+       WL
Sbjct: 178 WALVKGVPRKREDKISTWLVREQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLTWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           G + +TAPLP HMV++W+ LGF
Sbjct: 298 GTIDVTAPLPPHMVQSWNLLGF 319


>gi|256061091|ref|ZP_05451246.1| pseudouridine synthase, RluA family protein [Brucella neotomae
           5K33]
 gi|261325093|ref|ZP_05964290.1| pseudouridine synthase [Brucella neotomae 5K33]
 gi|261301073|gb|EEY04570.1| pseudouridine synthase [Brucella neotomae 5K33]
          Length = 326

 Score =  345 bits (884), Expect = 7e-93,   Method: Compositional matrix adjust.
 Identities = 163/325 (50%), Positives = 227/325 (69%), Gaps = 10/325 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDASEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            VRIPP+       + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++VQ
Sbjct: 61  AVRIPPLG------VDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQ 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +
Sbjct: 115 GGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTK 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +N+A+S++++I+      
Sbjct: 175 KTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSNHAVSYYRIIEKAGNNL 234

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
            WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+
Sbjct: 235 AWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFLGGIQKRLHLHARRIRIPN 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGF 324
           P GG + +TAPLP HMV++W+ LGF
Sbjct: 295 PSGGIIDVTAPLPPHMVQSWNLLGF 319


>gi|239831992|ref|ZP_04680321.1| pseudouridine synthase, RluA family [Ochrobactrum intermedium LMG
           3301]
 gi|239824259|gb|EEQ95827.1| pseudouridine synthase, RluA family [Ochrobactrum intermedium LMG
           3301]
          Length = 326

 Score =  345 bits (884), Expect = 7e-93,   Method: Compositional matrix adjust.
 Identities = 159/325 (48%), Positives = 227/325 (69%), Gaps = 10/325 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LRSGQ+R+D  R K + R+Q+GQ
Sbjct: 1   MAVVEQKIVDTGEAGMRLDRWFKVHYPGLGFGHLQKLLRSGQIRIDGSRAKADTRVQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            VRIPP+       + E+    +   ++   +  D L  +LLYED K+YVFNKPAG++VQ
Sbjct: 61  TVRIPPLG------VDEKATGPVTARTIRSQQDGDVLSQMLLYEDPKVYVFNKPAGLAVQ 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+  HIDG L++W + KG+KPRL HR+D++TSG+LVVARTR AAQ LT +FR R  +
Sbjct: 115 GGSGVTRHIDGMLEAWRNKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTAAFRERDTK 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW+LV G+P+ +++ I+ WL+K     GD + V +  E  +++A+S++++I+      
Sbjct: 175 KTYWALVKGVPRKREDKISTWLVKDQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNL 234

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
            WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+
Sbjct: 235 TWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPN 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGF 324
           P GG + +TAPLP HMV++W+ LGF
Sbjct: 295 PSGGIIDVTAPLPPHMVQSWNLLGF 319


>gi|254719077|ref|ZP_05180888.1| ribosomal large subunit pseudouridine synthase C [Brucella sp.
           83/13]
 gi|265984067|ref|ZP_06096802.1| pseudouridine synthase [Brucella sp. 83/13]
 gi|306838360|ref|ZP_07471205.1| pseudouridine synthase, RluA family [Brucella sp. NF 2653]
 gi|306843875|ref|ZP_07476470.1| pseudouridine synthase, RluA family [Brucella sp. BO1]
 gi|264662659|gb|EEZ32920.1| pseudouridine synthase [Brucella sp. 83/13]
 gi|306275630|gb|EFM57354.1| pseudouridine synthase, RluA family [Brucella sp. BO1]
 gi|306406500|gb|EFM62734.1| pseudouridine synthase, RluA family [Brucella sp. NF 2653]
          Length = 326

 Score =  344 bits (883), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 163/325 (50%), Positives = 227/325 (69%), Gaps = 10/325 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LRSGQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRSGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            VRIPP+       + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++VQ
Sbjct: 61  AVRIPPLG------VDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQ 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +
Sbjct: 115 GGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTK 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+      
Sbjct: 175 KTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNL 234

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
            WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+
Sbjct: 235 AWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPN 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGF 324
           P GG + +TAPLP HMV++W+ LGF
Sbjct: 295 PSGGIIDVTAPLPPHMVQSWNLLGF 319


>gi|52430461|ref|YP_089633.1| ribosomal large subunit pseudouridine synthase C [Brucella suis
           1330]
 gi|47524242|gb|AAT34905.1| ribosomal large subunit pseudouridine synthase C [Brucella suis
           1330]
          Length = 326

 Score =  344 bits (883), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 164/326 (50%), Positives = 226/326 (69%), Gaps = 12/326 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLT----KHSDFLKSILLYEDSKIYVFNKPAGISV 119
            VRIPP       +  ++K  D     T    +  D L  +LLYED KI+VFNKPAG++V
Sbjct: 61  AVRIPP-------LGVDEKAADPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           QGGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  
Sbjct: 114 QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDT 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+     
Sbjct: 174 KKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNN 233

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP 298
             WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P
Sbjct: 234 LAWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIP 293

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGF 324
           +P GG + +TAPLP HMV++W+ LGF
Sbjct: 294 NPSGGIIDVTAPLPPHMVQSWNLLGF 319


>gi|17987266|ref|NP_539900.1| ribosomal large subunit pseudouridine synthase C [Brucella
           melitensis bv. 1 str. 16M]
 gi|225627477|ref|ZP_03785514.1| pseudouridine synthase, RluA family protein [Brucella ceti str.
           Cudo]
 gi|17982942|gb|AAL52164.1| ribosomal large subunit pseudouridine synthase c [Brucella
           melitensis bv. 1 str. 16M]
 gi|225617482|gb|EEH14527.1| pseudouridine synthase, RluA family protein [Brucella ceti str.
           Cudo]
          Length = 343

 Score =  343 bits (881), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 162/326 (49%), Positives = 227/326 (69%), Gaps = 10/326 (3%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
            M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+G
Sbjct: 17  FMAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAG 76

Query: 63  QVVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q VRIPP+       + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++V
Sbjct: 77  QAVRIPPLG------VDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV 130

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           QGGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  
Sbjct: 131 QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDT 190

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+     
Sbjct: 191 KKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNN 250

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP 298
             WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P
Sbjct: 251 LAWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIP 310

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGF 324
           +P GG + +TAPLP HMV++W+ LGF
Sbjct: 311 NPSGGIIDVTAPLPPHMVQSWNLLGF 336


>gi|254701751|ref|ZP_05163579.1| ribosomal large subunit pseudouridine synthase C [Brucella suis bv.
           5 str. 513]
 gi|261752304|ref|ZP_05996013.1| pseudouridine synthase [Brucella suis bv. 5 str. 513]
 gi|261742057|gb|EEY29983.1| pseudouridine synthase [Brucella suis bv. 5 str. 513]
          Length = 326

 Score =  343 bits (881), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 162/325 (49%), Positives = 227/325 (69%), Gaps = 10/325 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            VRIPP+       + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++VQ
Sbjct: 61  AVRIPPLG------VDEKAASPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQ 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +
Sbjct: 115 GGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTK 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+      
Sbjct: 175 KTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNL 234

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
            WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+
Sbjct: 235 AWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPN 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGF 324
           P GG + +TAPLP HMV++W+ LGF
Sbjct: 295 PSGGIIDVTAPLPPHMVQSWNLLGF 319


>gi|225852505|ref|YP_002732738.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           ATCC 23457]
 gi|254693715|ref|ZP_05155543.1| ribosomal large subunit pseudouridine synthase C [Brucella abortus
           bv. 3 str. Tulya]
 gi|254706805|ref|ZP_05168633.1| ribosomal large subunit pseudouridine synthase C [Brucella
           pinnipedialis M163/99/10]
 gi|254710085|ref|ZP_05171896.1| ribosomal large subunit pseudouridine synthase C [Brucella
           pinnipedialis B2/94]
 gi|254714086|ref|ZP_05175897.1| ribosomal large subunit pseudouridine synthase C [Brucella ceti
           M644/93/1]
 gi|254716858|ref|ZP_05178669.1| ribosomal large subunit pseudouridine synthase C [Brucella ceti
           M13/05/1]
 gi|256031581|ref|ZP_05445195.1| ribosomal large subunit pseudouridine synthase C [Brucella
           pinnipedialis M292/94/1]
 gi|256044659|ref|ZP_05447563.1| ribosomal large subunit pseudouridine synthase C [Brucella
           melitensis bv. 1 str. Rev.1]
 gi|256113553|ref|ZP_05454373.1| ribosomal large subunit pseudouridine synthase C [Brucella
           melitensis bv. 3 str. Ether]
 gi|256159719|ref|ZP_05457466.1| ribosomal large subunit pseudouridine synthase C [Brucella ceti
           M490/95/1]
 gi|256254981|ref|ZP_05460517.1| ribosomal large subunit pseudouridine synthase C [Brucella ceti
           B1/94]
 gi|256264005|ref|ZP_05466537.1| pseudouridine synthase [Brucella melitensis bv. 2 str. 63/9]
 gi|256369422|ref|YP_003106930.1| ribosomal large subunit pseudouridine synthase C [Brucella microti
           CCM 4915]
 gi|260168711|ref|ZP_05755522.1| ribosomal large subunit pseudouridine synthase C [Brucella sp.
           F5/99]
 gi|260564005|ref|ZP_05834491.1| pseudouridine synthase [Brucella melitensis bv. 1 str. 16M]
 gi|261213987|ref|ZP_05928268.1| pseudouridine synthase [Brucella abortus bv. 3 str. Tulya]
 gi|261218659|ref|ZP_05932940.1| pseudouridine synthase [Brucella ceti M13/05/1]
 gi|261222167|ref|ZP_05936448.1| pseudouridine synthase [Brucella ceti B1/94]
 gi|261314272|ref|ZP_05953469.1| pseudouridine synthase [Brucella pinnipedialis M163/99/10]
 gi|261317634|ref|ZP_05956831.1| pseudouridine synthase [Brucella pinnipedialis B2/94]
 gi|261321843|ref|ZP_05961040.1| pseudouridine synthase [Brucella ceti M644/93/1]
 gi|261758188|ref|ZP_06001897.1| pseudouridine synthase [Brucella sp. F5/99]
 gi|265988669|ref|ZP_06101226.1| pseudouridine synthase [Brucella pinnipedialis M292/94/1]
 gi|265991083|ref|ZP_06103640.1| pseudouridine synthase [Brucella melitensis bv. 1 str. Rev.1]
 gi|265994920|ref|ZP_06107477.1| pseudouridine synthase [Brucella melitensis bv. 3 str. Ether]
 gi|265998132|ref|ZP_06110689.1| pseudouridine synthase [Brucella ceti M490/95/1]
 gi|225640870|gb|ACO00784.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           ATCC 23457]
 gi|255999582|gb|ACU47981.1| ribosomal large subunit pseudouridine synthase C [Brucella microti
           CCM 4915]
 gi|260154021|gb|EEW89113.1| pseudouridine synthase [Brucella melitensis bv. 1 str. 16M]
 gi|260915594|gb|EEX82455.1| pseudouridine synthase [Brucella abortus bv. 3 str. Tulya]
 gi|260920751|gb|EEX87404.1| pseudouridine synthase [Brucella ceti B1/94]
 gi|260923748|gb|EEX90316.1| pseudouridine synthase [Brucella ceti M13/05/1]
 gi|261294533|gb|EEX98029.1| pseudouridine synthase [Brucella ceti M644/93/1]
 gi|261296857|gb|EEY00354.1| pseudouridine synthase [Brucella pinnipedialis B2/94]
 gi|261303298|gb|EEY06795.1| pseudouridine synthase [Brucella pinnipedialis M163/99/10]
 gi|261738172|gb|EEY26168.1| pseudouridine synthase [Brucella sp. F5/99]
 gi|262552600|gb|EEZ08590.1| pseudouridine synthase [Brucella ceti M490/95/1]
 gi|262766033|gb|EEZ11822.1| pseudouridine synthase [Brucella melitensis bv. 3 str. Ether]
 gi|263001867|gb|EEZ14442.1| pseudouridine synthase [Brucella melitensis bv. 1 str. Rev.1]
 gi|263094149|gb|EEZ18071.1| pseudouridine synthase [Brucella melitensis bv. 2 str. 63/9]
 gi|264660866|gb|EEZ31127.1| pseudouridine synthase [Brucella pinnipedialis M292/94/1]
          Length = 326

 Score =  343 bits (881), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 162/325 (49%), Positives = 227/325 (69%), Gaps = 10/325 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            VRIPP+       + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++VQ
Sbjct: 61  AVRIPPLG------VDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQ 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +
Sbjct: 115 GGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTK 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+      
Sbjct: 175 KTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNL 234

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
            WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+
Sbjct: 235 AWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPN 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGF 324
           P GG + +TAPLP HMV++W+ LGF
Sbjct: 295 PSGGIIDVTAPLPPHMVQSWNLLGF 319


>gi|326409020|gb|ADZ66085.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           M28]
 gi|326538730|gb|ADZ86945.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           M5-90]
          Length = 331

 Score =  343 bits (880), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 162/326 (49%), Positives = 227/326 (69%), Gaps = 10/326 (3%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
            M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+G
Sbjct: 5   FMAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAG 64

Query: 63  QVVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q VRIPP+       + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++V
Sbjct: 65  QAVRIPPLG------VDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV 118

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           QGGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  
Sbjct: 119 QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDT 178

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+     
Sbjct: 179 KKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNN 238

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP 298
             WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P
Sbjct: 239 LAWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIP 298

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGF 324
           +P GG + +TAPLP HMV++W+ LGF
Sbjct: 299 NPSGGIIDVTAPLPPHMVQSWNLLGF 324


>gi|237815424|ref|ZP_04594422.1| pseudouridine synthase, RluA family [Brucella abortus str. 2308 A]
 gi|237790261|gb|EEP64471.1| pseudouridine synthase, RluA family [Brucella abortus str. 2308 A]
          Length = 343

 Score =  343 bits (880), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 162/326 (49%), Positives = 227/326 (69%), Gaps = 10/326 (3%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
            M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+G
Sbjct: 17  FMAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAG 76

Query: 63  QVVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q VRIPP+       + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++V
Sbjct: 77  QAVRIPPLG------VDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV 130

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           QGGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  
Sbjct: 131 QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDT 190

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+     
Sbjct: 191 KKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNN 250

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP 298
             WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P
Sbjct: 251 LAWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIP 310

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGF 324
           +P GG + +TAPLP HMV++W+ LGF
Sbjct: 311 NPSGGIIDVTAPLPLHMVQSWNLLGF 336


>gi|260754735|ref|ZP_05867083.1| pseudouridine synthase [Brucella abortus bv. 6 str. 870]
 gi|260757958|ref|ZP_05870306.1| pseudouridine synthase [Brucella abortus bv. 4 str. 292]
 gi|260761781|ref|ZP_05874124.1| pseudouridine synthase [Brucella abortus bv. 2 str. 86/8/59]
 gi|260883756|ref|ZP_05895370.1| pseudouridine synthase [Brucella abortus bv. 9 str. C68]
 gi|297248324|ref|ZP_06932042.1| ribosomal large subunit pseudouridine synthase C [Brucella abortus
           bv. 5 str. B3196]
 gi|260668276|gb|EEX55216.1| pseudouridine synthase [Brucella abortus bv. 4 str. 292]
 gi|260672213|gb|EEX59034.1| pseudouridine synthase [Brucella abortus bv. 2 str. 86/8/59]
 gi|260674843|gb|EEX61664.1| pseudouridine synthase [Brucella abortus bv. 6 str. 870]
 gi|260873284|gb|EEX80353.1| pseudouridine synthase [Brucella abortus bv. 9 str. C68]
 gi|297175493|gb|EFH34840.1| ribosomal large subunit pseudouridine synthase C [Brucella abortus
           bv. 5 str. B3196]
          Length = 331

 Score =  343 bits (879), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 162/326 (49%), Positives = 227/326 (69%), Gaps = 10/326 (3%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
            M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+G
Sbjct: 5   FMAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAG 64

Query: 63  QVVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q VRIPP+       + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++V
Sbjct: 65  QAVRIPPLG------VDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV 118

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           QGGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  
Sbjct: 119 QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDT 178

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+     
Sbjct: 179 KKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNN 238

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP 298
             WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P
Sbjct: 239 LAWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIP 298

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGF 324
           +P GG + +TAPLP HMV++W+ LGF
Sbjct: 299 NPSGGIIDVTAPLPLHMVQSWNLLGF 324


>gi|62289923|ref|YP_221716.1| ribosomal large subunit pseudouridine synthase C [Brucella abortus
           bv. 1 str. 9-941]
 gi|82699851|ref|YP_414425.1| RNA-binding protein S4 [Brucella melitensis biovar Abortus 2308]
 gi|189024165|ref|YP_001934933.1| Pseudouridine synthase [Brucella abortus S19]
 gi|254689230|ref|ZP_05152484.1| Pseudouridine synthase [Brucella abortus bv. 6 str. 870]
 gi|254697365|ref|ZP_05159193.1| Pseudouridine synthase [Brucella abortus bv. 2 str. 86/8/59]
 gi|254730263|ref|ZP_05188841.1| Pseudouridine synthase [Brucella abortus bv. 4 str. 292]
 gi|256257480|ref|ZP_05463016.1| Pseudouridine synthase [Brucella abortus bv. 9 str. C68]
 gi|260545328|ref|ZP_05821069.1| pseudouridine synthase [Brucella abortus NCTC 8038]
 gi|62196055|gb|AAX74355.1| ribosomal large subunit pseudouridine synthase C [Brucella abortus
           bv. 1 str. 9-941]
 gi|82615952|emb|CAJ10975.1| RNA-binding S4:Pseudouridine synthase:Pseudouridine synthase,
           Rlu:Pseudouridine synthase, RluD [Brucella melitensis
           biovar Abortus 2308]
 gi|189019737|gb|ACD72459.1| Pseudouridine synthase [Brucella abortus S19]
 gi|260096735|gb|EEW80610.1| pseudouridine synthase [Brucella abortus NCTC 8038]
          Length = 326

 Score =  343 bits (879), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 162/325 (49%), Positives = 227/325 (69%), Gaps = 10/325 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            VRIPP+       + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++VQ
Sbjct: 61  AVRIPPLG------VDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQ 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +
Sbjct: 115 GGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTK 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+      
Sbjct: 175 KTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNL 234

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
            WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+
Sbjct: 235 AWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPN 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGF 324
           P GG + +TAPLP HMV++W+ LGF
Sbjct: 295 PSGGIIDVTAPLPLHMVQSWNLLGF 319


>gi|110634000|ref|YP_674208.1| ribosomal large subunit pseudouridine synthase C [Mesorhizobium sp.
           BNC1]
 gi|110284984|gb|ABG63043.1| ribosomal large subunit pseudouridine synthase C [Chelativorans sp.
           BNC1]
          Length = 327

 Score =  343 bits (879), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 155/322 (48%), Positives = 227/322 (70%), Gaps = 5/322 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V++ E  MRLDRWFK HYP + F  LQK+LR+GQVRVD  R K + R+Q+GQ
Sbjct: 1   MAGVEQIEVDSGEAGMRLDRWFKTHYPGLGFGQLQKLLRTGQVRVDGGRAKADTRVQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++R+PP+  A++H  K       ++     ++ L  +L++ED K++VFNKPAG++VQGGS
Sbjct: 61  MIRVPPL--AVDH--KGAPATIRTMRDRGDAEVLSQMLIHEDEKVFVFNKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+DG L++W + +G+KPRL HRLD++TSG+LVVARTR AA  LTESFR R  +KIY
Sbjct: 117 GVNRHVDGMLEAWRNKRGEKPRLVHRLDRDTSGVLVVARTRLAAVKLTESFRARETKKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+L+ G+PK  +  I+ WL++++   GD + + K  E GA++A+S +++++       WL
Sbjct: 177 WALIKGVPKKAEGRISTWLVRETTPDGDRMRIAKHGEPGADHAVSTYRLVEQAGTALSWL 236

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            M+P TGR HQLRVHA H+GCPI+GD KY  A+        IQN+L+LHAR + +PHP+G
Sbjct: 237 VMEPFTGRMHQLRVHAAHIGCPIIGDPKYFEADQNWELPGGIQNRLHLHARRIIIPHPDG 296

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           G + +TA +P HM ++W+ LGF
Sbjct: 297 GSIDVTAEMPPHMQQSWNLLGF 318


>gi|163843268|ref|YP_001627672.1| RluA family pseudouridine synthase [Brucella suis ATCC 23445]
 gi|163673991|gb|ABY38102.1| pseudouridine synthase, RluA family [Brucella suis ATCC 23445]
          Length = 326

 Score =  342 bits (877), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 161/325 (49%), Positives = 227/325 (69%), Gaps = 10/325 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            VRIPP+       + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++VQ
Sbjct: 61  AVRIPPLG------VDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQ 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LV+ARTR AAQ LT SFR R  +
Sbjct: 115 GGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVLARTRGAAQALTASFRERDTK 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+      
Sbjct: 175 KTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNL 234

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
            WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+
Sbjct: 235 AWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPN 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGF 324
           P GG + +TAPLP HMV++W+ LGF
Sbjct: 295 PSGGIIDVTAPLPPHMVQSWNLLGF 319


>gi|49475763|ref|YP_033804.1| ribosomal large subunit pseudouridine synthase c [Bartonella
           henselae str. Houston-1]
 gi|49238570|emb|CAF27811.1| Ribosomal large subunit pseudouridine synthase c [Bartonella
           henselae str. Houston-1]
          Length = 327

 Score =  342 bits (877), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 165/324 (50%), Positives = 226/324 (69%), Gaps = 8/324 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   VE DE  MRLDRWFK HYP + F +LQK+LRSGQ+R+D +RVK + R+  GQ
Sbjct: 1   MAGVEIKKVEVDESGMRLDRWFKAHYPGLGFGHLQKLLRSGQIRIDGRRVKADTRLLMGQ 60

Query: 64  VVRIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           VVRIPP+ +N +  +     + D ++        LK +LLYED KI+VFNKPAG++VQGG
Sbjct: 61  VVRIPPLPVNDMGSL----PVTDKTLRGQDDEVILKKMLLYEDPKIFVFNKPAGLAVQGG 116

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+  H+D  L+ W + KG+KPRL HRLD+ETSG+L+VAR+R AAQ LT +FR R  +K 
Sbjct: 117 SGLTRHVDSMLRVWRNKKGEKPRLVHRLDRETSGVLIVARSRGAAQALTTAFRTRETKKT 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K++ I+ W++K      D + V +  E  + +A+S+++V+D   +   W
Sbjct: 177 YWALVRGVPKKKQDKISTWMVKDISTQVDKMRVCEHGEPDSYHAVSYYRVVDTRGRALSW 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHP 300
           LEM+P+TGRTHQLRVHA HM  PI+GD KY  +   N+T P  IQN+L+LHAR + +PHP
Sbjct: 237 LEMEPYTGRTHQLRVHAAHMDHPIIGDAKYFFS-DSNWTLPGGIQNRLHLHARRIRIPHP 295

Query: 301 EGGRLQITAPLPAHMVKTWDSLGF 324
            GG L I APLP HMV++++ L F
Sbjct: 296 SGGILDIVAPLPPHMVQSFNLLAF 319


>gi|161618953|ref|YP_001592840.1| RluA family pseudouridine synthase [Brucella canis ATCC 23365]
 gi|254704293|ref|ZP_05166121.1| RluA family pseudouridine synthase [Brucella suis bv. 3 str. 686]
 gi|260566460|ref|ZP_05836930.1| pseudouridine synthase [Brucella suis bv. 4 str. 40]
 gi|261754961|ref|ZP_05998670.1| pseudouridine synthase [Brucella suis bv. 3 str. 686]
 gi|161335764|gb|ABX62069.1| pseudouridine synthase, RluA family [Brucella canis ATCC 23365]
 gi|260155978|gb|EEW91058.1| pseudouridine synthase [Brucella suis bv. 4 str. 40]
 gi|261744714|gb|EEY32640.1| pseudouridine synthase [Brucella suis bv. 3 str. 686]
          Length = 326

 Score =  342 bits (876), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 161/325 (49%), Positives = 226/325 (69%), Gaps = 10/325 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            VRIPP+       + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++VQ
Sbjct: 61  AVRIPPLG------VDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQ 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +
Sbjct: 115 GGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTK 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+      
Sbjct: 175 KTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNL 234

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
            WLEM+P+TGRTHQLRVHA ++G PI+GD KY   +    F   IQ +L+LHAR + +P+
Sbjct: 235 AWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEVDQNWEFPGGIQKRLHLHARRIRIPN 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGF 324
           P GG + +TAPLP HMV++W+ LGF
Sbjct: 295 PSGGIIDVTAPLPPHMVQSWNLLGF 319


>gi|49474373|ref|YP_032415.1| ribosomal large subunit pseudouridine synthase c [Bartonella
           quintana str. Toulouse]
 gi|49239877|emb|CAF26275.1| Ribosomal large subunit pseudouridine synthase c [Bartonella
           quintana str. Toulouse]
          Length = 327

 Score =  341 bits (875), Expect = 9e-92,   Method: Compositional matrix adjust.
 Identities = 167/326 (51%), Positives = 228/326 (69%), Gaps = 12/326 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   VE DE  MRLDRWFK +YP + F  LQK+LRSGQ+RVD  RVK + R+  GQ
Sbjct: 1   MAGVEIKKVEADESGMRLDRWFKVYYPGLGFGYLQKLLRSGQIRVDGGRVKADTRLLIGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSD---FLKSILLYEDSKIYVFNKPAGISVQ 120
           VVR+PP++      + E++ L  +  + +  D    LK +LLYEDSKI+VFNKPAG++VQ
Sbjct: 61  VVRVPPLL------VDEKESLPVTDKIIREQDDRVILKKMLLYEDSKIFVFNKPAGLAVQ 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+  H D  L+ W + KG+KPRL HRLD+ETSG+L+VAR+R AAQ LT +FR R  +
Sbjct: 115 GGSGLTRHFDSMLEVWRNKKGEKPRLVHRLDRETSGVLIVARSRGAAQTLTAAFRARETK 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW+LV G+PK K++ I+ W++K     GD + V +  E  +N+A+S+++V+D   +  
Sbjct: 175 KTYWALVRGVPKKKQDKISTWVVKDITAQGDKMCVCEHGEPDSNHAVSYYRVLDTRGRAL 234

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLP 298
            WLEM+P+TGRTHQLRVHA +M  PI+GD KY  +   N+  P  IQN+L+LHAR + +P
Sbjct: 235 SWLEMEPYTGRTHQLRVHAAYMDNPIIGDSKYFFS-DSNWKLPRGIQNRLHLHARRIRIP 293

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGF 324
           HP GG L ITAPLP HMV++++ L F
Sbjct: 294 HPSGGILDITAPLPPHMVQSFNLLAF 319


>gi|163868619|ref|YP_001609828.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           tribocorum CIP 105476]
 gi|161018275|emb|CAK01833.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           tribocorum CIP 105476]
          Length = 327

 Score =  340 bits (872), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 166/323 (51%), Positives = 226/323 (69%), Gaps = 6/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   VE DE  MRLDRWFK HYP + F  LQK+LRSGQ+RVD  RVK + R+  GQ
Sbjct: 1   MAGVEIKKVETDENGMRLDRWFKVHYPGLGFGALQKLLRSGQIRVDGGRVKADTRLCMGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+   L+++I    I D ++        LK +LLYED K++VFNKPAG++VQGGS
Sbjct: 61  SVRVPPL--PLDNMI-SLPITDKTLRGQDDGTILKKMLLYEDPKVFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HID  L+ W + KG+KPRL HRLD+ETSG+L+VAR+R AAQ LT +FR R  +K Y
Sbjct: 118 GLTRHIDSMLEVWRNKKGEKPRLVHRLDRETSGVLIVARSRGAAQALTAAFRERETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+PK K++ I+ W++K+    GD + V    E  +++A+S+++V+D   +   WL
Sbjct: 178 WALVRGVPKKKQDKISTWMVKEMTAQGDKMRVCDHGEPDSHHAVSYYRVLDTRGRTLSWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPE 301
           EM+P+TGRTHQLRVHA +M  PI+GD KY  +   N+T P  IQN+L+LHAR + +PHP 
Sbjct: 238 EMEPYTGRTHQLRVHAAYMDHPIIGDSKYFFS-DSNWTLPGGIQNRLHLHARRIRIPHPS 296

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
           GG L I APLP HMV++++ L F
Sbjct: 297 GGILDIIAPLPPHMVQSFNLLSF 319


>gi|294852409|ref|ZP_06793082.1| ribosomal large subunit pseudouridine synthase C [Brucella sp. NVSL
           07-0026]
 gi|294820998|gb|EFG37997.1| ribosomal large subunit pseudouridine synthase C [Brucella sp. NVSL
           07-0026]
          Length = 331

 Score =  340 bits (872), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 160/326 (49%), Positives = 226/326 (69%), Gaps = 10/326 (3%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
            M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+G
Sbjct: 5   FMAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAG 64

Query: 63  QVVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q VRIPP+       + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++V
Sbjct: 65  QAVRIPPLG------VDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV 118

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           QGGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  
Sbjct: 119 QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDT 178

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++++     
Sbjct: 179 KKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRILEKAGNN 238

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP 298
             WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P
Sbjct: 239 LAWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIP 298

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGF 324
           +P GG + + APLP HMV++W+ LGF
Sbjct: 299 NPSGGIIDVMAPLPPHMVQSWNLLGF 324


>gi|240850791|ref|YP_002972191.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           grahamii as4aup]
 gi|240267914|gb|ACS51502.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           grahamii as4aup]
          Length = 327

 Score =  339 bits (869), Expect = 4e-91,   Method: Compositional matrix adjust.
 Identities = 166/324 (51%), Positives = 226/324 (69%), Gaps = 8/324 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   VE DE  MRLDRWFK HYP + F  LQK+LRSGQ+R+D  RVK + R+  GQ
Sbjct: 1   MVGVEIKKVEVDENGMRLDRWFKVHYPGLGFGALQKLLRSGQIRLDGGRVKADTRLCMGQ 60

Query: 64  VVRIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VRIPP+ IN   ++     I D ++        LK +LLYED K++VFNKPAG++VQGG
Sbjct: 61  AVRIPPLPINDKANL----SITDKTLRGQDDETVLKKMLLYEDPKVFVFNKPAGLAVQGG 116

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+  H+D  L+ W + KG+KPRL HRLD+ETSG+L+VAR+R AAQ LT +FR R  +K 
Sbjct: 117 SGLTRHMDSMLEVWRNKKGEKPRLVHRLDRETSGVLIVARSRGAAQSLTAAFRARETKKT 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K++ I+ W++K+    GD + V +  E  A++A+S+++V+D   +   W
Sbjct: 177 YWALVRGVPKKKQDKISTWMVKEMTAQGDKMRVCEHGEPDAHHAVSYYRVLDTRGRALSW 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHP 300
           LEM+P+TGRTHQLRVHA +M  PI+GD KY  +   N+T P  IQN+L+LHAR + +PHP
Sbjct: 237 LEMEPYTGRTHQLRVHAAYMDHPIIGDTKYFFS-DSNWTLPGGIQNRLHLHARRIRIPHP 295

Query: 301 EGGRLQITAPLPAHMVKTWDSLGF 324
            GG L I APLP HMV++++ L F
Sbjct: 296 SGGILDIVAPLPPHMVQSFNLLSF 319


>gi|148560154|ref|YP_001258940.1| ribosomal large subunit pseudouridine synthase C [Brucella ovis
           ATCC 25840]
 gi|148371411|gb|ABQ61390.1| ribosomal large subunit pseudouridine synthase C [Brucella ovis
           ATCC 25840]
          Length = 318

 Score =  339 bits (869), Expect = 4e-91,   Method: Compositional matrix adjust.
 Identities = 159/317 (50%), Positives = 224/317 (70%), Gaps = 10/317 (3%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ VRIPP+ 
Sbjct: 1   MDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQAVRIPPLG 60

Query: 72  NALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                 + E+    +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGSG+  H
Sbjct: 61  ------VDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGSGVTRH 114

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           IDG L++W  +KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K YW+LV 
Sbjct: 115 IDGMLEAWRSTKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTYWALVK 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WLEM+P+
Sbjct: 175 GVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWLEMEPY 234

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P GG + +
Sbjct: 235 TGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSGGIIDV 294

Query: 308 TAPLPAHMVKTWDSLGF 324
           TAPLP HMV++W+ LGF
Sbjct: 295 TAPLPPHMVQSWNLLGF 311


>gi|114704677|ref|ZP_01437585.1| ribosomal large subunit pseudouridine synthase C [Fulvimarina
           pelagi HTCC2506]
 gi|114539462|gb|EAU42582.1| ribosomal large subunit pseudouridine synthase C [Fulvimarina
           pelagi HTCC2506]
          Length = 328

 Score =  337 bits (863), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 158/326 (48%), Positives = 224/326 (68%), Gaps = 10/326 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   V++DE  +RLDRWFK HYP + F  LQK+LRSGQ+RVD  R K + R+  GQ
Sbjct: 1   MAAVEQRRVDDDEAGLRLDRWFKLHYPGLAFGQLQKLLRSGQIRVDGGRAKSDTRVAPGQ 60

Query: 64  VVRIPPVIN----ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +VR+PP+      + NH +       +++      D L  +++YED K+ VFNKPAG++V
Sbjct: 61  MVRVPPLATDSKTSTNHPLTA-----NTIKGRPDGDVLSQMVIYEDEKVIVFNKPAGLAV 115

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           QGGSG+A H+D  L++W + KG+KPRL HRLD++TSGILVVARTR AA  LT++FR R  
Sbjct: 116 QGGSGVARHVDDMLEAWRNKKGEKPRLVHRLDRDTSGILVVARTRGAATALTKAFRERDT 175

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K+YW++V G+P  K+  I+ +L K+    GD + + +  ++GA++A+SH++VID  AQ 
Sbjct: 176 KKLYWAVVKGVPAKKEGRISTYLKKEQTPDGDRMRIARHGDEGADHALSHYRVIDQVAQN 235

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLP 298
           F WLE++PHTGRTHQLRVHA H+G PI+GD KY   +    F   +Q +L+LHAR + +P
Sbjct: 236 FAWLELEPHTGRTHQLRVHAAHIGHPILGDPKYFEHDTNWEFPGGVQMRLHLHARRLVIP 295

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGF 324
           HP GG +   APLP HM +T++  GF
Sbjct: 296 HPSGGMIDQIAPLPQHMRQTFNLFGF 321


>gi|304391488|ref|ZP_07373430.1| rRNA pseudouridylate synthase C [Ahrensia sp. R2A130]
 gi|303295717|gb|EFL90075.1| rRNA pseudouridylate synthase C [Ahrensia sp. R2A130]
          Length = 338

 Score =  336 bits (862), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 162/324 (50%), Positives = 224/324 (69%), Gaps = 4/324 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +T V    V+ DE  MRLDRWFK HYP + F  LQK+LRSGQVRVD  RVK  +R+++GQ
Sbjct: 3   LTGVSQKTVDEDEGGMRLDRWFKLHYPGVGFGKLQKLLRSGQVRVDGGRVKTASRLEAGQ 62

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVRIPP+ +A +   K   +  +++      D L+ ++LYED K+ VFNKP+G++VQGGS
Sbjct: 63  VVRIPPLDSAASD--KPLHMTSNTIRDRHDEDVLRDMILYEDKKVLVFNKPSGLAVQGGS 120

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           GI+  +D  L+S  D  GQKPRL HRLD++TSG+LVVA+TR AA  LT+SFR R  QK Y
Sbjct: 121 GISRSVDSMLESLRDKAGQKPRLCHRLDRDTSGVLVVAKTRGAAAALTKSFRQRTTQKTY 180

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV GIP+ K+  I+ +L+K+    GD + V K  E+ A++A+S ++VID   +   W+
Sbjct: 181 WALVRGIPRQKEGRISTYLVKEQTEDGDRMRVAKHGERHADHAVSFYRVIDSNPRTVSWV 240

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E+ PHTGRTHQLRVHA H+G PI+GD+KY +         IQ +L+LHAR + +PHP+  
Sbjct: 241 ELSPHTGRTHQLRVHADHIGHPIIGDNKYFSTENWEMPGGIQKRLHLHARRIRIPHPDEN 300

Query: 304 R--LQITAPLPAHMVKTWDSLGFK 325
           +  L +TAPLP HMV++W+   F+
Sbjct: 301 QPTLDVTAPLPPHMVQSWNLFAFE 324


>gi|90417736|ref|ZP_01225648.1| ribosomal large subunit pseudouridine synthase C [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90337408|gb|EAS51059.1| ribosomal large subunit pseudouridine synthase C [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 328

 Score =  334 bits (856), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 159/323 (49%), Positives = 224/323 (69%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   +E+DE  +RLDRWFK HYP + F +LQK+LRSGQVRVD  R K + R+Q GQ
Sbjct: 1   MASVEQRRIEDDEAGLRLDRWFKLHYPGLGFGHLQKLLRSGQVRVDGGRAKTDTRVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAGISVQGG 122
           +VRIPP+         +   L ++    KH D  L  +L+YED K++VFNKPAG++VQGG
Sbjct: 61  MVRIPPMSGDAGR--PKIGPLTANTMRDKHDDEVLSQMLIYEDEKVFVFNKPAGLAVQGG 118

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+  H+D  L++W   KG+KPRL HRLD++TSG+LVVARTR AA  LT++FR R  +K 
Sbjct: 119 SGLNRHVDKMLEAWRSRKGEKPRLVHRLDRDTSGVLVVARTRGAATALTKAFRERDTKKT 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+++ G+P   +  I+ +L+K+    GD +   K  E+GA++A++H++VI+  AQ F W
Sbjct: 179 YWAILKGVPVPHEGRISTFLVKEQTPDGDRMRTAKHGEEGADHALTHYRVIENLAQNFSW 238

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +EM+P+TGRTHQLRVHALH+G PI+GD KY   +    F   +Q +L+LHAR + +PHP 
Sbjct: 239 VEMEPYTGRTHQLRVHALHIGNPILGDPKYFEHDTNWEFPGGVQKRLHLHARRIVIPHPS 298

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
           GG +   APLP HM++T++  GF
Sbjct: 299 GGFIDQIAPLPPHMIQTFNLFGF 321


>gi|319407393|emb|CBI81044.1| ribosomal large subunit pseudouridine synthase C [Bartonella sp.
           1-1C]
          Length = 327

 Score =  331 bits (848), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 159/324 (49%), Positives = 226/324 (69%), Gaps = 8/324 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   VE DE  MRLDRWFK +YP + F  LQK+LRSGQ+RVD  RVK + R+  GQ
Sbjct: 1   MVSVKIKKVEADESGMRLDRWFKVYYPDVGFGYLQKLLRSGQIRVDGGRVKNDMRLVVGQ 60

Query: 64  VVRIPPVINALNHIIKEQK--ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            +R+PP++     I KE    +++  V        LK +LLYEDSKI+VFNKPAG++VQG
Sbjct: 61  SIRVPPLL-----IDKEDSFSVINKIVCGRDDDIILKDMLLYEDSKIFVFNKPAGLAVQG 115

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+  HID  L+ W + KG+KPRL HR+D+ETSGILVVAR+R AAQ LT +FR R  +K
Sbjct: 116 GSGLTRHIDNMLEVWRNKKGEKPRLVHRIDRETSGILVVARSRGAAQALTAAFRTRETKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            YW+LV G+P+ K++ I+ W++++    GD + V ++ +  +N+A+S+++V+D   +   
Sbjct: 176 TYWALVRGVPRKKQDKISTWMVREITAQGDKMRVCERRQPDSNHAVSYYRVLDTRGKALS 235

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHP 300
           WLEM+P+TGRTHQLRVHA ++  PI+GD KY  ++   +    +QN+L+LHAR + +PHP
Sbjct: 236 WLEMEPYTGRTHQLRVHAAYINHPIIGDSKYFFSDSNWDLPRGMQNRLHLHARRIRIPHP 295

Query: 301 EGGRLQITAPLPAHMVKTWDSLGF 324
            GG L +TAPLP HMV++++   F
Sbjct: 296 SGGVLDVTAPLPPHMVQSFNLFAF 319


>gi|319899068|ref|YP_004159161.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           clarridgeiae 73]
 gi|319403032|emb|CBI76587.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           clarridgeiae 73]
          Length = 327

 Score =  329 bits (843), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 158/323 (48%), Positives = 224/323 (69%), Gaps = 6/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++   VE DE  MRLDRWFK +YP++ F  LQK+LRSGQ+R+D  RVK + R+  GQ
Sbjct: 1   MVGIKIRKVEADESGMRLDRWFKIYYPNVGFGYLQKLLRSGQIRIDGGRVKNDMRLVVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP+            +++ ++        LK+ILLYEDSKI+VFNKPAG++VQGGS
Sbjct: 61  SIRVPPLFTDKKDGFP---VINKTICGQDDRITLKNILLYEDSKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+D  L++W + KG+KPRL HRLD+ETSGILVVAR+R AAQ LT +FR R  +K Y
Sbjct: 118 GLTRHVDSMLEAWRNKKGEKPRLVHRLDRETSGILVVARSRGAAQVLTAAFRARETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ K++ I+ W+ ++     D + V +  +  +N+AIS+++V+D   +   WL
Sbjct: 178 WALVRGVPRKKQDKISTWMAREITTQADKMRVCEHRQPDSNHAISYYRVLDTRGKSLSWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPE 301
           EM+P+TGRTHQLRVHA H+  PI+GD KY  +   N+  P  +QN+L+LHAR + +PHP 
Sbjct: 238 EMEPYTGRTHQLRVHAAHINHPIIGDSKYFFS-DSNWELPRGVQNRLHLHARRIRIPHPS 296

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
           GG L ITAPLP HMV++++   F
Sbjct: 297 GGILDITAPLPPHMVQSFNIFAF 319


>gi|319404393|emb|CBI77996.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           rochalimae ATCC BAA-1498]
          Length = 327

 Score =  329 bits (843), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 157/324 (48%), Positives = 227/324 (70%), Gaps = 8/324 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   VE DE  MRLDRWFK +YP + F  LQK+LRSGQ+RVD  RVK + R+  GQ
Sbjct: 1   MVGVKIKKVEADENGMRLDRWFKVYYPDVGFGYLQKLLRSGQIRVDGGRVKNDVRLVMGQ 60

Query: 64  VVRIPPVINALNHIIKEQK--ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            +R+PP++     I KE    +++  V    +   LK +LLYEDSKI+VFNKPAG++VQG
Sbjct: 61  SIRVPPLL-----IDKEDSFPVINKIVCGQDNDIILKDMLLYEDSKIFVFNKPAGLAVQG 115

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+  H+D  L+ W + KG+KPRL HR+D+ETSG+LVVAR+R AAQ LT +FR R  +K
Sbjct: 116 GSGLTRHVDSMLEVWRNKKGEKPRLVHRIDRETSGVLVVARSRGAAQALTAAFRTRETKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            YW+LV G+P+ K++ I+ W++++    GD + V ++ +  +N+A+S+++V+D   +   
Sbjct: 176 TYWALVRGVPRKKQDKISTWMVREITAQGDKMRVCERRQPDSNHAVSYYRVLDTRGKALS 235

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHP 300
           WLEM+P+TGRTHQLRVHA ++  PI+GD KY  ++   +    +QN+L+LHAR + +PHP
Sbjct: 236 WLEMEPYTGRTHQLRVHAAYINHPIIGDSKYFFSDSNWDLPGGMQNRLHLHARRIRIPHP 295

Query: 301 EGGRLQITAPLPAHMVKTWDSLGF 324
            GG L +TAPLP HMV++++   F
Sbjct: 296 SGGILDVTAPLPPHMVQSFNLFAF 319


>gi|319405867|emb|CBI79499.1| ribosomal large subunit pseudouridine synthase C [Bartonella sp. AR
           15-3]
          Length = 327

 Score =  328 bits (841), Expect = 8e-88,   Method: Compositional matrix adjust.
 Identities = 159/325 (48%), Positives = 226/325 (69%), Gaps = 10/325 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   V+ DE  MRLDRWFK +YP + F  LQK+LRSGQ+RVD +RVK + R+  GQ
Sbjct: 1   MVGVKIKKVKADESGMRLDRWFKVYYPDVGFGYLQKLLRSGQIRVDGRRVKNDVRLVVGQ 60

Query: 64  VVRIPPVINALNHIIKEQK--ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            +R+PP +     I KE    + +  +   +    LK +LLYEDSKI+VFNKPAG++VQG
Sbjct: 61  SIRVPPFL-----IDKEDSAPVFNKIIFGQEDEVILKDMLLYEDSKIFVFNKPAGLAVQG 115

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+  H+D  L+ W + KG+KPRL HR+D+ETSG+LVVAR+R AAQ LT +FR R  +K
Sbjct: 116 GSGLTRHVDSMLEVWRNKKGEKPRLVHRIDRETSGVLVVARSRGAAQALTAAFRTRETKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            YW+LV G+P+ K++ I+ W++++    GD V V ++ +  +N+A+S+++V+D   +   
Sbjct: 176 TYWALVRGVPRKKQDKISTWMVREITEQGDKVRVCERRQADSNHAVSYYRVLDTRGKALS 235

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPH 299
           WLEM+P+TGRTHQLRVHA +M  PI+GD KY      N+  P  +QN+L+LHAR + +PH
Sbjct: 236 WLEMEPYTGRTHQLRVHAAYMKHPIIGDSKYFFP-DSNWALPGGMQNRLHLHARRIRIPH 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGF 324
           P GG L ITAPLP HM+++++   F
Sbjct: 295 PSGGILDITAPLPPHMLQSFNLFAF 319


>gi|319408734|emb|CBI82391.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           schoenbuchensis R1]
          Length = 326

 Score =  327 bits (838), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 160/322 (49%), Positives = 224/322 (69%), Gaps = 10/322 (3%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   VE  E  MRLDRWFK HYP + F  LQK+LRSGQ+RVD +RVK + R+  GQ +R
Sbjct: 3   VEIKKVEEGESGMRLDRWFKVHYPGLAFGYLQKLLRSGQIRVDGRRVKTDIRLIVGQSIR 62

Query: 67  IP--PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +P   V N  N  + ++ I D +         L+ +LLY+D KI+V NKPAG++VQGGSG
Sbjct: 63  VPFLSVDNKKNLSVTDKTIHDQA-----KLAILEKMLLYKDPKIFVLNKPAGLAVQGGSG 117

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +  HIDG L+ W + KG+KPRL HRLD+ETSG+L++AR+R AAQ LT +FR R  +K YW
Sbjct: 118 LTCHIDGMLEVWRNKKGEKPRLVHRLDRETSGVLIIARSRGAAQALTAAFRARETKKTYW 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+P+ K++ I+ W++K++   GD + V +  E  +N+A+S+++V+D   +   WLE
Sbjct: 178 ALVRGVPRKKQDKISTWMVKETTAQGDKMRVCEHGEPDSNHAVSYYRVLDTRGRALSWLE 237

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEG 302
           M+P+TGRTHQLRVHA +M  PI+GD KY  +   N+  P  IQN+L+LHAR + +PHP G
Sbjct: 238 MEPYTGRTHQLRVHAAYMDHPIIGDSKYFFS-DNNWELPGGIQNRLHLHARRIRIPHPSG 296

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           G L I APLP HMV++++ L F
Sbjct: 297 GILDIIAPLPPHMVQSFNLLAF 318


>gi|118591144|ref|ZP_01548543.1| ribosomal large subunit pseudouridine synthase C [Stappia aggregata
           IAM 12614]
 gi|118436220|gb|EAV42862.1| ribosomal large subunit pseudouridine synthase C [Stappia aggregata
           IAM 12614]
          Length = 355

 Score =  317 bits (813), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 155/322 (48%), Positives = 216/322 (67%), Gaps = 3/322 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ ++   V  DE  MRLDRWFK+HYP + F +LQK+LR+GQVRVD KR + N RI  GQ
Sbjct: 17  MSAIEQKQVTADEAGMRLDRWFKSHYPGLGFGHLQKLLRTGQVRVDGKRAETNTRIAKGQ 76

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++RIPP+   L    K+     S+  +      ++ +LL+EDS++ V NKPAG++VQGGS
Sbjct: 77  MIRIPPLGVELPADDKKNAKPKSTKLIADDRKAIEDMLLFEDSQVMVLNKPAGLAVQGGS 136

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+DG L ++ D KG KPRL HRLD+ETSGI++VARTR AAQ LT++FR R  +KIY
Sbjct: 137 GLKRHLDGMLDAYTDRKGNKPRLVHRLDRETSGIILVARTRQAAQELTKAFRHRNTRKIY 196

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+++ G+PK  +  I+ +L +    G + + VV+Q E  A +A+S + V +   QK  W+
Sbjct: 197 WAILAGVPKPFQGRISTFLARND--GEERMQVVRQGEDEAQHAVSLYSVFEKSGQKLSWV 254

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
            M+P TGRTHQLR HA H+G PI+GD KY           IQN+L+L AR + +PHP G 
Sbjct: 255 TMKPVTGRTHQLRAHAAHIGHPIIGDDKYFNIENWELPGGIQNRLHLLARRIVIPHPSGH 314

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           G + ++APLP HM +TW+ LGF
Sbjct: 315 GTIDVSAPLPPHMQQTWNLLGF 336


>gi|328543393|ref|YP_004303502.1| Pseudouridine synthase [polymorphum gilvum SL003B-26A1]
 gi|326413138|gb|ADZ70201.1| Pseudouridine synthase [Polymorphum gilvum SL003B-26A1]
          Length = 334

 Score =  310 bits (793), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 213/322 (66%), Gaps = 3/322 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++   V  DE  MRLDRWFK+HYP + F +LQK+LR+GQVRVD KR     R+ +GQ
Sbjct: 1   MAAIELKTVTADEAGMRLDRWFKSHYPGLGFGHLQKLLRTGQVRVDGKRADSATRLATGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+   +     +     SS  +      ++ ++LYED ++ V NKPAG++VQGGS
Sbjct: 61  SVRVPPLGVVVAADDTKNARPKSSRLIADDRKAVEDMILYEDDQVMVLNKPAGLAVQGGS 120

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G++ H+DG L ++ + KG+KPRL HRLD+ETSG+L+VA+TR AAQ LT +FR R  +KIY
Sbjct: 121 GLSRHLDGMLDAFTNKKGEKPRLVHRLDRETSGVLLVAKTRKAAQELTRAFRQRSTRKIY 180

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+L+ G+PK ++  I+ +L +    G + + V +  +  A +A+S + V++  AQK  W+
Sbjct: 181 WALLAGVPKPRQGRISTYLARDE--GSEKMKVARHGDDEAQHAVSLYSVVEQSAQKLAWV 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
            ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP G 
Sbjct: 239 SLRPVTGRTHQLRAHAAHIGHPIVGDDKYFNIENWELPGGIQNRLHLLARRIVIPHPSGH 298

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           G + ++APLP HM ++W+ LGF
Sbjct: 299 GTIDVSAPLPPHMQQSWNLLGF 320


>gi|254500715|ref|ZP_05112866.1| pseudouridine synthase, RluA family [Labrenzia alexandrii DFL-11]
 gi|222436786|gb|EEE43465.1| pseudouridine synthase, RluA family [Labrenzia alexandrii DFL-11]
          Length = 340

 Score =  309 bits (792), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 152/323 (47%), Positives = 213/323 (65%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ ++   V  DE  MRLDRWFK HYP + F  LQK+LR+GQVRVD KR + N RI  GQ
Sbjct: 1   MSAIEQKKVTADEAGMRLDRWFKAHYPGLGFGRLQKLLRTGQVRVDGKRAESNTRIAKGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++RIPP+   L    K+     S+  +      ++ +LLYED+++ V NKPAG++VQGGS
Sbjct: 61  IIRIPPLGVELPADDKKNARPKSTKLIADDKKAIEDMLLYEDNQVMVLNKPAGLAVQGGS 120

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+DG L ++ D KG KPRL HRLD+ETSGI++VARTR AAQ LT++FR R  +K+Y
Sbjct: 121 GLKRHLDGMLDAFTDQKGNKPRLVHRLDRETSGIILVARTRQAAQELTKAFRHRNTRKVY 180

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCW 242
           W+++ G+PK  +  I+ +L +      + + VV+Q     A +A+S + V +   QK  W
Sbjct: 181 WTILAGVPKPHQGRISTFLARDEE--EERMQVVRQGGADDAQHAVSLYSVFEKSGQKLSW 238

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + M+P TGRTHQLR HA H+G PI+GD KY           IQN+L+L AR + +PHP G
Sbjct: 239 VTMKPVTGRTHQLRAHAAHIGHPIIGDDKYFNIENWELPGGIQNRLHLLARRIVIPHPSG 298

Query: 303 -GRLQITAPLPAHMVKTWDSLGF 324
            G++ ++APLP HM +TW+ LGF
Sbjct: 299 HGKIDVSAPLPPHMQQTWNLLGF 321


>gi|146341534|ref|YP_001206582.1| putative ribosomal large subunit pseudouridine synthase RluC-like
           protein [Bradyrhizobium sp. ORS278]
 gi|146194340|emb|CAL78364.1| putative ribosomal large subunit pseudouridine synthase RluC-like
           (23S RNA pseudouridylate synthase) (RNA-uridine
           isomerase) [Bradyrhizobium sp. ORS278]
          Length = 458

 Score =  308 bits (790), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 151/327 (46%), Positives = 219/327 (66%), Gaps = 7/327 (2%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ VVV  DE NMR+DR+ +  +P ++F ++Q+I+R G++RVD KR    +R++ G
Sbjct: 128 LPTKVQTVVVTADENNMRVDRFLEARFPGLSFSHIQRIVRKGELRVDGKRADSKDRLEEG 187

Query: 63  QVVRIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           Q VRIPP+ ++A     KE+  L  S    K  D LK++ LYED  + V NKPAG++VQG
Sbjct: 188 QSVRIPPLKLDA----PKERAGL--SEGERKTLDSLKAMTLYEDDDVLVLNKPAGLAVQG 241

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+  HID  L+   D+KGQKPRL HR+D+ETSG L++A+TR AA HLT +FR R  +K
Sbjct: 242 GSGMTRHIDQMLEVMRDAKGQKPRLVHRIDRETSGCLLIAKTRFAATHLTGAFRHRSARK 301

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +YW+LV G+PK K+  I+ +L K        + V    ++GA++A++++ V++  A K  
Sbjct: 302 VYWALVAGVPKPKQGRISTYLAKDEGEDDTIMRVAAHGDEGASHAVTYYAVVEASANKLA 361

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           W+ ++P TGRTHQLR H  H+G PIVGD KY      +    +QN+L+L AR + +PHP 
Sbjct: 362 WVSLKPVTGRTHQLRAHMAHIGHPIVGDPKYFNIENWSLPGGLQNRLHLLARRIVIPHPR 421

Query: 302 GGRLQITAPLPAHMVKTWDSLGFKYDR 328
           GG +  TAPLP HM+++W+ LG ++DR
Sbjct: 422 GGVIDATAPLPPHMLQSWNLLGLEHDR 448


>gi|148256356|ref|YP_001240941.1| ribosomal large subunit pseudouridine synthase C [Bradyrhizobium
           sp. BTAi1]
 gi|146408529|gb|ABQ37035.1| ribosomal large subunit pseudouridine synthase C [Bradyrhizobium
           sp. BTAi1]
          Length = 458

 Score =  308 bits (788), Expect = 9e-82,   Method: Compositional matrix adjust.
 Identities = 150/327 (45%), Positives = 217/327 (66%), Gaps = 7/327 (2%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ VVV  DE NMR+DR+ +  +P ++F ++Q+I+R G++RVD KR    +R++ G
Sbjct: 128 LPTKVQTVVVTADENNMRVDRFLEARFPGLSFSHIQRIVRKGELRVDGKRADSKDRLEEG 187

Query: 63  QVVRIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           Q VRIPP+ ++A     KE+  L  +   T  S  LK++ LYED  + V NKP G++VQG
Sbjct: 188 QTVRIPPLKLDA----PKERAGLSEAERKTLES--LKAMTLYEDDDVLVLNKPVGLAVQG 241

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+  HID  L+   D+KGQKPRL HR+D+ETSG L++A+TR AA HLT +FR R  +K
Sbjct: 242 GSGMTRHIDQMLEVMRDAKGQKPRLVHRIDRETSGCLLIAKTRFAATHLTGAFRSRSARK 301

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IYW+LV G+PK K+  I+ +L K        + V    ++GA++A++++ V++  A K  
Sbjct: 302 IYWALVAGVPKPKQGRISTYLAKDEGEDDTIMRVAAHGDEGASHAVTYYAVVEASANKLA 361

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           W+ ++P TGRTHQLR H  H+G PIVGD KY           +QN+L+L AR + +PHP 
Sbjct: 362 WVSLKPVTGRTHQLRAHMAHIGHPIVGDPKYFNIENWALPGGLQNRLHLLARRIVIPHPR 421

Query: 302 GGRLQITAPLPAHMVKTWDSLGFKYDR 328
           GG +  TAPLP HM+++W+ LG ++DR
Sbjct: 422 GGVIDATAPLPPHMLQSWNLLGLEHDR 448


>gi|307946319|ref|ZP_07661654.1| rRNA pseudouridylate synthase C [Roseibium sp. TrichSKD4]
 gi|307769983|gb|EFO29209.1| rRNA pseudouridylate synthase C [Roseibium sp. TrichSKD4]
          Length = 333

 Score =  307 bits (787), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 213/322 (66%), Gaps = 3/322 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ ++   V  DE  MRLDRWFK HYP + F  LQK+LR+GQVRVD KR + N RI  GQ
Sbjct: 1   MSAIEQKTVTADEAGMRLDRWFKAHYPGMGFGRLQKLLRTGQVRVDGKRAESNTRIAKGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+   L    K+     SS  +      ++ ++L+ED+ + V NKPAG++VQGGS
Sbjct: 61  TVRIPPLGVELPANDKKNAKPKSSKLMADDKAAIEDMMLFEDNHVMVLNKPAGLAVQGGS 120

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+DG L+++ + KG+KP+L HRLD+ETSGI++VA+TR AAQ LT++FR R  +KIY
Sbjct: 121 GLKRHLDGMLEAYTNKKGEKPKLVHRLDRETSGIILVAKTRKAAQELTKAFRHRNTRKIY 180

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+++ G+PK  +  I+ +L +   +  + + V +  +  A +A+S + V +  AQK  W+
Sbjct: 181 WAMLAGVPKPHQGRISTYLARSEEM--ERMRVARHGDDEAQHAVSLYSVFEKSAQKLSWV 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
            ++P TGRTHQLR HA H+G PI+GD KY           IQN+L+L AR + +PHP G 
Sbjct: 239 TLKPVTGRTHQLRAHAAHIGHPIIGDDKYFNIENWELPGGIQNRLHLLARRIVIPHPSGN 298

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           G + ++APLP HM +TW+ LGF
Sbjct: 299 GMIDVSAPLPPHMQQTWNLLGF 320


>gi|90424892|ref|YP_533262.1| pseudouridine synthase RluD [Rhodopseudomonas palustris BisB18]
 gi|90106906|gb|ABD88943.1| ribosomal large subunit pseudouridine synthase C [Rhodopseudomonas
           palustris BisB18]
          Length = 501

 Score =  302 bits (774), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 142/334 (42%), Positives = 218/334 (65%), Gaps = 16/334 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           + L T V+ VVV  DE NMR+DR+ +  YP ++F ++Q+I+R G++RVD KR    +R++
Sbjct: 168 VPLPTKVETVVVSADENNMRVDRFLEARYPGLSFSHIQRIVRKGELRVDGKRADSKDRLE 227

Query: 61  SGQVVRIPPV------INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
            GQ VRIPP+      +   N    EQK + +          L++++LYED+ + V NKP
Sbjct: 228 EGQTVRIPPLKLDAPKVGTGNLSEAEQKTMAA----------LRAMILYEDADVMVLNKP 277

Query: 115 AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           AG++VQGGSG   H+D  L+   D+KGQKPRL HRLD+ET+G L++A+TR AA  LT +F
Sbjct: 278 AGLAVQGGSGTTRHVDLMLEVMRDAKGQKPRLVHRLDKETAGCLLIAKTRFAATALTGAF 337

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R  +K+YW+LV G+PK K+  I+ +L K+       + + +  ++GA++A++++ V++
Sbjct: 338 RERSARKVYWALVAGVPKPKQGRISTYLAKEESEDDTIMRIAEHGDEGASHAVTYYAVVE 397

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
             A K  W+ ++P TGRTHQLR H  H+G  IVGD KY           +QN+L+L AR 
Sbjct: 398 TSASKLAWVSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNIENWQLPGGLQNRLHLLARR 457

Query: 295 MDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           + +PHP GG + ++APLP HM+++W+ LG ++DR
Sbjct: 458 IVIPHPRGGTIDVSAPLPPHMLQSWNLLGLEHDR 491


>gi|209884846|ref|YP_002288703.1| pseudouridine synthase, RluD [Oligotropha carboxidovorans OM5]
 gi|209873042|gb|ACI92838.1| pseudouridine synthase, RluD [Oligotropha carboxidovorans OM5]
          Length = 412

 Score =  302 bits (773), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 144/326 (44%), Positives = 216/326 (66%), Gaps = 5/326 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ VVV  DE NMR+DR+ + H+P ++F ++Q+I+R G++RV+ KR    +R+  G
Sbjct: 82  LPTKVQTVVVTADENNMRVDRFLEAHFPGLSFSHIQRIVRKGELRVNGKRADSKDRLNEG 141

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             VRIPP+      +   +   + S   +K  D L+ ++L+ED+ + V NKPAG++VQGG
Sbjct: 142 DNVRIPPL-----KLDAPKTGGNLSEAGSKVLDELRKMVLFEDADVMVLNKPAGLAVQGG 196

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+  H+DG L+   D+KGQ+PRL HRLD+ETSG L++A+TR AA  LT SFR R  +KI
Sbjct: 197 SGLTRHVDGMLEVMRDAKGQRPRLVHRLDRETSGCLLIAKTRFAASTLTGSFRHRSARKI 256

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K+ +     + +    ++GA +A++++ V++  AQK  W
Sbjct: 257 YWALVAGVPKPKQGRISTYLAKEENEEDSIMRIAAHGDEGAAHAVTYYAVVEASAQKLAW 316

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+G  IVGD KY           +QN+L+L AR + +PHP G
Sbjct: 317 VSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNKENWQLPGGLQNRLHLLARRIVIPHPRG 376

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDR 328
           G + +TAPLP HM+++W+ LG + DR
Sbjct: 377 GVIDVTAPLPPHMLQSWNLLGLEADR 402


>gi|240136939|ref|YP_002961408.1| Pseudouridine synthase, RluD [Methylobacterium extorquens AM1]
 gi|240006905|gb|ACS38131.1| Pseudouridine synthase, RluD [Methylobacterium extorquens AM1]
          Length = 463

 Score =  301 bits (771), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 139/329 (42%), Positives = 214/329 (65%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + V+ DE  MR+DR+    +P + F  +Q I+R G++RVD KR K N+R++ 
Sbjct: 130 TLASGVQTLTVDPDEAGMRIDRFLGARFPQLPFTRVQSIVRKGELRVDGKRAKPNDRLEP 189

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+   L+   +  +   S+  +   ++FL+S++LYED+ + + NKP G++VQG
Sbjct: 190 GSSVRVPPL--KLDQPTERPR---SAAKIDGDAEFLRSLILYEDADMMILNKPFGLAVQG 244

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L++     GQ+PRL HRLD++T+G L+VA+TR AA  L +SFR R  +K
Sbjct: 245 GSGTVRHVDGLLEALTGPDGQRPRLVHRLDKDTAGCLIVAKTRLAASTLAKSFRSRAARK 304

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+LV G+P+ ++  ++ +L+K      D  + V K  + GA++A++++  +D  AQK 
Sbjct: 305 IYWALVAGVPRTRQGRVSTYLVKDEPTDADARMRVAKHGDDGASHALTYYATVDQAAQKL 364

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP
Sbjct: 365 AWLSLKPVTGRTHQLRAHAAHIGHPIVGDPKYFDVENWELPGGIQNRLHLLARRIVIPHP 424

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 425 RTGQPVDVSAPLPPHMAQSWNLLGFDAAR 453


>gi|218528371|ref|YP_002419187.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
 gi|218520674|gb|ACK81259.1| pseudouridine synthase, RluA family [Methylobacterium
           chloromethanicum CM4]
          Length = 468

 Score =  301 bits (771), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 139/329 (42%), Positives = 214/329 (65%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + V+ DE  MR+DR+    +P + F  +Q I+R G++RVD KR K N+R++ 
Sbjct: 135 TLASGVQTLTVDPDEAGMRIDRFLGARFPQLPFTRVQSIVRKGELRVDGKRAKPNDRLEP 194

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+   L+   +  +   S+  +   ++FL+S++LYED+ + + NKP G++VQG
Sbjct: 195 GSSVRVPPL--KLDQPTERPR---SAAKIDGDAEFLRSLILYEDADMMILNKPFGLAVQG 249

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L++     GQ+PRL HRLD++T+G L+VA+TR AA  L +SFR R  +K
Sbjct: 250 GSGTVRHVDGLLEALTGPDGQRPRLVHRLDKDTAGCLIVAKTRLAASTLAKSFRSRAARK 309

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+LV G+P+ ++  ++ +L+K      D  + V K  + GA++A++++  +D  AQK 
Sbjct: 310 IYWALVAGVPRTRQGRVSTYLVKDEPTDADARMRVAKHGDDGASHALTYYATVDQAAQKL 369

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP
Sbjct: 370 AWLSLKPVTGRTHQLRAHAAHIGHPIVGDPKYFDVENWELPGGIQNRLHLLARRIVIPHP 429

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 430 RTGQPVDVSAPLPPHMAQSWNLLGFDAAR 458


>gi|163849730|ref|YP_001637773.1| RluA family pseudouridine synthase [Methylobacterium extorquens
           PA1]
 gi|163661335|gb|ABY28702.1| pseudouridine synthase, RluA family [Methylobacterium extorquens
           PA1]
          Length = 468

 Score =  301 bits (771), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 139/329 (42%), Positives = 214/329 (65%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + V+ DE  MR+DR+    +P + F  +Q I+R G++RVD KR K N+R++ 
Sbjct: 135 TLASGVQTLTVDPDEAGMRIDRFLGARFPQLPFTRVQSIVRKGELRVDGKRAKPNDRLEP 194

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+   L+   +  +   S+  +   ++FL+S++LYED+ + + NKP G++VQG
Sbjct: 195 GSSVRVPPL--KLDQPTERPR---SAAKIDGDAEFLRSLILYEDADMMILNKPFGLAVQG 249

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L++     GQ+PRL HRLD++T+G L+VA+TR AA  L +SFR R  +K
Sbjct: 250 GSGTVRHVDGLLEALTGPDGQRPRLVHRLDKDTAGCLIVAKTRLAASTLAKSFRSRAARK 309

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+LV G+P+ ++  ++ +L+K      D  + V K  + GA++A++++  +D  AQK 
Sbjct: 310 IYWALVAGVPRTRQGRVSTYLVKDEPTDADARMRVAKHGDDGASHALTYYATVDQAAQKL 369

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP
Sbjct: 370 AWLSLKPVTGRTHQLRAHAAHIGHPIVGDPKYFDVENWELPGGIQNRLHLLARRIVIPHP 429

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 430 RTGQPVDVSAPLPPHMAQSWNLLGFDAAR 458


>gi|254558792|ref|YP_003065887.1| pseudouridylate synthase [Methylobacterium extorquens DM4]
 gi|254266070|emb|CAX21822.1| pseudouridylate synthase [Methylobacterium extorquens DM4]
          Length = 468

 Score =  301 bits (770), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 139/329 (42%), Positives = 214/329 (65%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + V+ DE  MR+DR+    +P + F  +Q I+R G++RVD KR K N+R++ 
Sbjct: 135 TLASGVQTLTVDPDEAGMRIDRFLGARFPQLPFTRVQSIVRKGELRVDGKRAKPNDRLEP 194

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+   L+   +  +   S+  +   ++FL+S++LYED+ + + NKP G++VQG
Sbjct: 195 GSSVRVPPL--KLDQPTERPR---SAAKIDGDAEFLRSLILYEDADMMILNKPFGLAVQG 249

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L++     GQ+PRL HRLD++T+G L+VA+TR AA  L +SFR R  +K
Sbjct: 250 GSGTVRHVDGLLEALTGPDGQRPRLVHRLDKDTAGCLIVAKTRLAASTLAKSFRSRAARK 309

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+LV G+P+ ++  ++ +L+K      D  + V K  + GA++A++++  +D  AQK 
Sbjct: 310 IYWALVAGVPRTRQGRVSTYLVKDEPTDADARMRVAKHGDDGASHALTYYATVDQAAQKL 369

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP
Sbjct: 370 AWLSLKPVTGRTHQLRAHAAHIGHPIVGDPKYFDVENWELPGGIQNRLHLLARRIVIPHP 429

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 430 RTGQPVDVSAPLPPHMAQSWNLLGFDAAR 458


>gi|188579622|ref|YP_001923067.1| pseudouridine synthase [Methylobacterium populi BJ001]
 gi|179343120|gb|ACB78532.1| pseudouridine synthase, RluA family [Methylobacterium populi BJ001]
          Length = 446

 Score =  300 bits (768), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 140/332 (42%), Positives = 214/332 (64%), Gaps = 13/332 (3%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + V  DE  MR+DR+    +P + F  +Q I+R G++RVD KR K N+R++ 
Sbjct: 113 TLASGVQTLTVAPDEAGMRIDRFLGARFPQLPFTRVQSIVRKGELRVDGKRAKPNDRLEP 172

Query: 62  GQVVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           G  VR+PP        +K ++  D   S+  +   ++FL+S++LYED+ + + NKP G++
Sbjct: 173 GSSVRVPP--------LKLEQPTDRPRSAAKVVGDAEFLRSLILYEDADMMILNKPFGLA 224

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           VQGGSG   H+DG L++     GQ+PRL HRLD++T+G L+VA+TR AA  L +SFR R 
Sbjct: 225 VQGGSGTVRHVDGLLEALTGPDGQRPRLVHRLDKDTAGCLIVAKTRLAAATLAKSFRSRA 284

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFA 237
            +KIYW+LV G+P+ ++  ++ +L+K      D  + V K  ++GA++A++++  +D  A
Sbjct: 285 ARKIYWALVAGVPRTRQGRVSTYLVKDEPTDADARMRVAKHGDEGASHALTYYATVDQAA 344

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           QK  WL ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +
Sbjct: 345 QKLAWLSLKPVTGRTHQLRAHAAHIGHPIVGDPKYFDVENWELPGGIQNRLHLLARRIVI 404

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           PHP  G+ + ++APLP HM ++W+ LGF   R
Sbjct: 405 PHPRTGQPVDVSAPLPPHMAQSWNLLGFDAAR 436


>gi|115525546|ref|YP_782457.1| RluA family pseudouridine synthase [Rhodopseudomonas palustris
           BisA53]
 gi|115519493|gb|ABJ07477.1| ribosomal large subunit pseudouridine synthase C [Rhodopseudomonas
           palustris BisA53]
          Length = 458

 Score =  300 bits (767), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 147/331 (44%), Positives = 216/331 (65%), Gaps = 15/331 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ VVV  DE  MR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 128 LPTKVQTVVVTADENAMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 187

Query: 63  QVVRIPPV-INAL----NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           Q VRIPP+ ++A     N    EQK L +          LK+++LYED+ + V NKPAG+
Sbjct: 188 QSVRIPPLQLDAPKGGGNLSEAEQKTLAA----------LKAMILYEDADVMVLNKPAGL 237

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +VQGGSG   H+D  L+   DSKGQKPRL HRLD+ET+G L+VA+TR AA  LT SFR R
Sbjct: 238 AVQGGSGTTRHVDLMLEVMRDSKGQKPRLVHRLDKETAGCLLVAKTRFAATALTGSFRSR 297

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +K+YW+LV G+PK K+  I+ +L K        + V    ++GA++A++++ V++  A
Sbjct: 298 SARKVYWALVAGVPKPKQGRISTYLAKDESEDDSIMRVAAHGDEGASHAVTYYAVVETSA 357

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           QK  W+ ++P TGRTHQLR H  H+G  I+GD KY           +Q +L+L AR + +
Sbjct: 358 QKLAWVSLKPVTGRTHQLRAHMAHIGHAIIGDPKYFNIENWELPGGLQKRLHLLARRIAI 417

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           PHP GG + +TAPLP HM+++W+ LG ++DR
Sbjct: 418 PHPRGGVIDVTAPLPPHMLQSWNLLGLEHDR 448


>gi|298291467|ref|YP_003693406.1| pseudouridine synthase [Starkeya novella DSM 506]
 gi|296927978|gb|ADH88787.1| pseudouridine synthase, RluA family [Starkeya novella DSM 506]
          Length = 363

 Score =  300 bits (767), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 154/349 (44%), Positives = 215/349 (61%), Gaps = 33/349 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V+ DEE MRLDRWFK H+P ++F +LQK+LRSGQVRVD  RVK N R+ SGQ VR
Sbjct: 3   VETRRVDRDEEGMRLDRWFKTHFPELSFGHLQKLLRSGQVRVDGGRVKTNTRLSSGQSVR 62

Query: 67  IPPV-----INALNHIIKEQKILDSSV--------NLTKHSDF----------------- 96
           IPP+     ++A +HI  E+ I                + SD                  
Sbjct: 63  IPPLEEKPQLSAADHIEAEEAIARGEAPPRPPRNGEGARRSDLAAPAVKRASVDDKDAAA 122

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           LK++ L+ED  + V NKP G++VQGGSG   H+DG L++     GQKPRL HR+D++TSG
Sbjct: 123 LKAMTLFEDRDVLVLNKPYGLAVQGGSGTYRHVDGMLEALRGDDGQKPRLVHRIDKDTSG 182

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           IL+VA++R AA  L ++FR R  +K+YW+LV G+P+  +  I+ +L K      + + V 
Sbjct: 183 ILLVAKSRLAASTLAKTFRSRSARKVYWALVPGVPRPAQGRISTYLAKDE--AAERMRVA 240

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +  +  A++AIS++ V+D  AQK  WL M+P TGRTHQLR HA H+G PIVGD KY    
Sbjct: 241 RHGDDEASHAISYYAVVDHAAQKLSWLSMKPVTGRTHQLRAHAAHIGHPIVGDPKYFNVE 300

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
                  +QN+L+L AR + +PHP   +L  ++APLP HM ++W+ LGF
Sbjct: 301 NWPLPGGLQNRLHLLARRLVIPHPRADKLIDVSAPLPPHMQQSWNVLGF 349


>gi|86749455|ref|YP_485951.1| pseudouridine synthase RluD [Rhodopseudomonas palustris HaA2]
 gi|86572483|gb|ABD07040.1| ribosomal large subunit pseudouridine synthase C [Rhodopseudomonas
           palustris HaA2]
          Length = 453

 Score =  300 bits (767), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 146/331 (44%), Positives = 217/331 (65%), Gaps = 15/331 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T V+ VVV  DE  MR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 123 LPTKVETVVVTADENGMRVDRFLEGRFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 182

Query: 63  QVVRIPPV----INALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           Q VRIPP+      A  H+ + EQK L +          LK++ LYED+ + V NKPAG+
Sbjct: 183 QSVRIPPLKLDTPKAPGHLSEAEQKTLAA----------LKAMTLYEDADVLVLNKPAGL 232

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +VQGGSG   HID  L+   DSKGQKPRL HR+D+ET+G L+VA+TR AA  LT SFR R
Sbjct: 233 AVQGGSGTTKHIDLMLEVMRDSKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRHR 292

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +KIYW+LV G+PK K+  I+ +L K+       + + +  ++GA++A++++ V++  A
Sbjct: 293 SARKIYWALVAGVPKPKQGRISTYLAKEESEDDSIMRIAEHGDEGASHAVTYYAVVETSA 352

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           QK  W+ ++P TGRTHQLR H  H+G  IVGD KY           +Q +L+L AR + +
Sbjct: 353 QKLAWVSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNIENWQLPGGLQKRLHLLARRIVI 412

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           PHP GG + ++APLP HM+++W+ LG ++DR
Sbjct: 413 PHPRGGTIDVSAPLPPHMLQSWNLLGLEHDR 443


>gi|85715100|ref|ZP_01046084.1| pseudouridine synthase, RluD [Nitrobacter sp. Nb-311A]
 gi|85698015|gb|EAQ35888.1| pseudouridine synthase, RluD [Nitrobacter sp. Nb-311A]
          Length = 380

 Score =  299 bits (766), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 139/324 (42%), Positives = 216/324 (66%), Gaps = 5/324 (1%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T VQ V V  DE NMR+DR+ +  +P ++F ++Q+I+R G++RV+ +R    +R+  G  
Sbjct: 52  TRVQTVAVTADEANMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGRRADSKDRVSEGDK 111

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+      +   +  +  S   TK  D L+ ++L+ED+ + V NKPAG++VQGGSG
Sbjct: 112 VRIPPL-----RLDTPKAAVGLSDAETKIRDELRKMVLFEDADVMVLNKPAGLAVQGGSG 166

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++ HIDG L++  D+KGQ+PRL HRLD+ET+G L++ARTR AA  LT +FR R  +KIYW
Sbjct: 167 LSRHIDGMLETMRDAKGQRPRLVHRLDRETAGCLLIARTRFAATALTGAFRHRSARKIYW 226

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+PK K+  I+ +L K+ +     + V    ++GA++A++++ V++  AQK  W+ 
Sbjct: 227 ALVAGVPKPKQGRISTYLAKEENEEESIMRVAAHGDEGASHAVTYYAVVETSAQKLAWVS 286

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++P TGRTHQLR H  H+G  I+GD KY           +QN+L+L AR + +PHP GG 
Sbjct: 287 LKPVTGRTHQLRAHMAHVGHAIIGDPKYFNKENWQLPGGLQNRLHLLARRIVIPHPRGGV 346

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           + ++APLP HM+++W+ LG + +R
Sbjct: 347 IDVSAPLPPHMLQSWNLLGLEANR 370


>gi|75675586|ref|YP_318007.1| pseudouridine synthase, RluD [Nitrobacter winogradskyi Nb-255]
 gi|74420456|gb|ABA04655.1| ribosomal large subunit pseudouridine synthase C [Nitrobacter
           winogradskyi Nb-255]
          Length = 412

 Score =  298 bits (762), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 137/324 (42%), Positives = 215/324 (66%), Gaps = 5/324 (1%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T VQ V V  DE NMR+DR+ +  +P ++F ++Q+++R G++RV+ +R    +R+  G  
Sbjct: 84  TKVQTVAVTADEANMRVDRFLEARFPGLSFSHIQRVVRKGELRVNGRRADSKDRVSEGDK 143

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+      +   +  +  S   TK  D L+ ++L+ED+ + V NKPAG++VQGGSG
Sbjct: 144 VRIPPL-----KLDTPKAAVGLSDAETKIRDELRKMVLFEDADVMVLNKPAGLAVQGGSG 198

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++ HIDG L++  D+KGQ+PRL HRLD+ET+G L++A+TR AA  LT +FR R  +KIYW
Sbjct: 199 LSRHIDGMLETMRDAKGQRPRLVHRLDRETAGCLLIAKTRFAATALTGAFRHRSARKIYW 258

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+PK K+  I+ +L K+ +     + +    ++GA++A++++ V++  AQK  W+ 
Sbjct: 259 ALVAGVPKPKQGRISTYLAKEENEEESIMRIAAHGDEGASHAVTYYAVVETSAQKLAWVS 318

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++P TGRTHQLR H  H+G  I+GD KY           +QN+L+L AR + +PHP GG 
Sbjct: 319 LKPVTGRTHQLRAHMAHIGHAIIGDPKYFNKENWQLPGGLQNRLHLLARRIVIPHPRGGV 378

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           +  +APLP HM+++W+ LG + DR
Sbjct: 379 IDASAPLPPHMLQSWNLLGLEADR 402


>gi|299135225|ref|ZP_07028416.1| pseudouridine synthase, RluA family [Afipia sp. 1NLS2]
 gi|298590202|gb|EFI50406.1| pseudouridine synthase, RluA family [Afipia sp. 1NLS2]
          Length = 413

 Score =  296 bits (758), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 141/326 (43%), Positives = 216/326 (66%), Gaps = 5/326 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ VVV  DE NMR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 83  LPTKVQTVVVTADENNMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 142

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP+      +   +   + S   TK  + L+ ++L+ED+ + V NKPAG++VQGG
Sbjct: 143 QSVRIPPL-----KLDAPKTGGNLSEAATKTLEELRKMILFEDADVMVLNKPAGLAVQGG 197

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG++ H+D  L+   D+KGQ+PRL HRLD+ETSG L++A+TR AA  LT SFR R  +KI
Sbjct: 198 SGLSRHVDQMLEVMRDAKGQRPRLVHRLDRETSGCLLIAKTRFAASVLTGSFRHRSARKI 257

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K+ +     + + +  ++GA +A++++ V++  AQK  W
Sbjct: 258 YWALVAGVPKPKQGRISTYLAKEENEEDSIMRIAEHGDEGAAHAVTYYAVVEASAQKLAW 317

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+   IVGD KY           +Q +L+L AR + +PHP G
Sbjct: 318 VSLKPVTGRTHQLRAHMAHIDHAIVGDPKYFNKENWQLPGGLQKRLHLLARRIVIPHPRG 377

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDR 328
           G + +TAPLP HM+++W+ LG + DR
Sbjct: 378 GVIDVTAPLPPHMLQSWNLLGLEADR 403


>gi|192291994|ref|YP_001992599.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           TIE-1]
 gi|192285743|gb|ACF02124.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           TIE-1]
          Length = 455

 Score =  295 bits (755), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 144/331 (43%), Positives = 214/331 (64%), Gaps = 15/331 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T V+ V V  DE  MR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 125 LPTKVETVTVTADENGMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 184

Query: 63  QVVRIPPV----INALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           Q VRIPP+         H+ + EQK L +          LK++ L+ED+ + V NKPAG+
Sbjct: 185 QSVRIPPLKLDTPKLPGHLSEAEQKTLQT----------LKAMTLFEDADVLVLNKPAGL 234

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +VQGGSG   HID  L+   D+KGQKPRL HR+D+ET+G L+VA+TR AA  LT SFR R
Sbjct: 235 AVQGGSGTTRHIDQMLEVLRDAKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRHR 294

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +KIYW+LV G+PK K+  I+ +L K+       + V K  + GA++A++++ V++   
Sbjct: 295 SARKIYWALVAGVPKPKQGRISTYLAKEESEDDSIMRVAKHGDDGASHAVTYYAVVETSG 354

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           QK  W+ ++P TGRTHQLR H  H+G  IVGD KY           +QN+L+L AR + +
Sbjct: 355 QKLAWVSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNIENWQLPGGLQNRLHLLARRIVI 414

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           PHP GG + ++APLP HM+++W+ LG ++DR
Sbjct: 415 PHPRGGVIDVSAPLPPHMLQSWNLLGLEHDR 445


>gi|254470362|ref|ZP_05083766.1| ribosomal large subunit pseudouridine synthase C [Pseudovibrio sp.
           JE062]
 gi|211960673|gb|EEA95869.1| ribosomal large subunit pseudouridine synthase C [Pseudovibrio sp.
           JE062]
          Length = 349

 Score =  295 bits (754), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 143/320 (44%), Positives = 213/320 (66%), Gaps = 15/320 (4%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ D+  +RLDRWFK ++P + F  LQK+LR+ QVRVD KR + + R+++GQ +RIPP+ 
Sbjct: 25  VDEDDAGIRLDRWFKENFPELGFGRLQKLLRTKQVRVDGKRAEASTRLEAGQEIRIPPLG 84

Query: 72  NAL------NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
             L      N   + +K++DS        + ++ ++L+EDS + V NKPAG++VQGGSG+
Sbjct: 85  VELAADDRKNAKPRARKLVDSD------REAIEQMMLFEDSHVMVLNKPAGLAVQGGSGL 138

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG L ++ + KG KPRL HRLD+ETSGIL+VA+TR AAQ LT++FR R  +KIYW+
Sbjct: 139 KRHVDGMLDAFTNQKGDKPRLVHRLDRETSGILLVAKTRRAAQELTKAFRHRNTRKIYWA 198

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+PK ++  I+ +L +    G + + V +  +  A +A+S + V++   QK  W+ +
Sbjct: 199 MVAGVPKPRQGRISTYLARDE--GEERMRVARHGDDEAQHAVSLYNVVEQSGQKLAWVTL 256

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
           +P TGRTHQLR H+ H+G PI+GD KY           IQNKL+L AR + +PHP G G 
Sbjct: 257 KPVTGRTHQLRAHSAHIGHPIIGDPKYFNIQNWELPGGIQNKLHLLARRIVIPHPSGNGV 316

Query: 305 LQITAPLPAHMVKTWDSLGF 324
           + ++APLP HM +TW+ LG 
Sbjct: 317 IDVSAPLPPHMQQTWNLLGM 336


>gi|39936271|ref|NP_948547.1| pseudouridine synthase RluD [Rhodopseudomonas palustris CGA009]
 gi|39650126|emb|CAE28649.1| possible ribosomal large subunit pseudouridine synthase C
           [Rhodopseudomonas palustris CGA009]
          Length = 455

 Score =  295 bits (754), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 145/331 (43%), Positives = 213/331 (64%), Gaps = 15/331 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T V+ V V  DE  MR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 125 LPTKVETVTVTADENGMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 184

Query: 63  QVVRIPPV----INALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           Q VRIPP+         H+ + EQK L +          LK++ L+ED+ + V NKPAG+
Sbjct: 185 QSVRIPPLKLDTPKLPGHLSEAEQKTLQT----------LKAMTLFEDADVLVLNKPAGL 234

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +VQGGSG   HID  L+   DSKGQKPRL HR+D+ET+G L+VA+TR AA  LT SFR R
Sbjct: 235 AVQGGSGTTRHIDQMLEVLRDSKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRHR 294

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +KIYW+LV G+PK K+  I+ +L K        + V K  + GA++A++++ V++   
Sbjct: 295 SARKIYWALVAGVPKPKQGRISTYLAKDESEEDSIMRVAKHGDDGASHAVTYYAVVETSG 354

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           QK  W+ ++P TGRTHQLR H  H+G  IVGD KY           +QN+L+L AR + +
Sbjct: 355 QKLAWVSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNIENWQLPGGLQNRLHLLARRIVI 414

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           PHP GG + ++APLP HM+++W+ LG ++DR
Sbjct: 415 PHPRGGVIDVSAPLPPHMLQSWNLLGLEHDR 445


>gi|23012328|ref|ZP_00052441.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 456

 Score =  294 bits (753), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 137/329 (41%), Positives = 211/329 (64%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + V  DE  MR+DR+    +P + F  +Q I+R G++RVD KR K ++R++ 
Sbjct: 123 TLASGVQTLTVSPDEAGMRIDRFLGARFPQLPFTRVQSIVRKGELRVDGKRAKPSDRLEP 182

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+   L+      +   S   +   ++FL+S++LYED+ + + NKP G++VQG
Sbjct: 183 GSSVRVPPL--KLDQPTDRPR---SPNKVAGDAEFLRSLILYEDADMMILNKPFGLAVQG 237

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L++     GQ+PRL HRLD++T+G L++A+TR AA  L +SFR R  +K
Sbjct: 238 GSGTVRHVDGLLEALTGPDGQRPRLVHRLDKDTAGCLIIAKTRLAAATLAKSFRSRAARK 297

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+LV G+P+ ++  ++ +L+K      D  + V K  + GA++A++++  +D  AQK 
Sbjct: 298 IYWALVAGVPRTRQGRVSTYLVKDEPTDADARMRVAKHGDDGASHALTYYATVDQAAQKL 357

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP
Sbjct: 358 AWLSLKPVTGRTHQLRAHAAHIGHPIVGDPKYFDVENWELPGGIQNRLHLLARRIVIPHP 417

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 418 RTGQPVDVSAPLPPHMAQSWNLLGFDAAR 446


>gi|170747290|ref|YP_001753550.1| RluA family pseudouridine synthase [Methylobacterium radiotolerans
           JCM 2831]
 gi|170653812|gb|ACB22867.1| pseudouridine synthase, RluA family [Methylobacterium radiotolerans
           JCM 2831]
          Length = 471

 Score =  294 bits (753), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 138/329 (41%), Positives = 212/329 (64%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + VE DE  MR+DR+    +P + F  +Q I+R G++RVD KR K N+R++ 
Sbjct: 138 TLASGVQTLTVEPDEAGMRIDRFLTARFPLLPFTRVQTIVRKGELRVDGKRAKPNDRLEP 197

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+   L+   +  +   S+      + F++S++LYED+ + + NKP G++VQG
Sbjct: 198 GMSVRVPPL--RLDQPTERPR---SAAREQDDAAFIRSLILYEDADMMILNKPFGLAVQG 252

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L +     GQKPRL HRLD++T+G L++A+TR AA  L +SFR R  +K
Sbjct: 253 GSGTVRHVDGLLAALTGPDGQKPRLVHRLDKDTAGCLIIAKTRLAAATLAKSFRSRAARK 312

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+L  G+P+ ++  ++ +L K+     D  + V K  ++GA++A++++ ++D  AQK 
Sbjct: 313 IYWALTAGVPRVRQGRVSTYLAKEEPTDADARMRVAKHGDEGASHALTYYAMVDQAAQKL 372

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL  +P TGRTHQLR HA H+G PIVGD KY +         IQN+L+L AR + +PHP
Sbjct: 373 SWLSFKPVTGRTHQLRAHAAHIGHPIVGDPKYFSVENWELPGGIQNRLHLLARRIVIPHP 432

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 433 RTGKPVDVSAPLPPHMAQSWNLLGFDAAR 461


>gi|92117127|ref|YP_576856.1| pseudouridine synthase, RluD [Nitrobacter hamburgensis X14]
 gi|91800021|gb|ABE62396.1| ribosomal large subunit pseudouridine synthase C [Nitrobacter
           hamburgensis X14]
          Length = 411

 Score =  294 bits (752), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 140/324 (43%), Positives = 211/324 (65%), Gaps = 5/324 (1%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T VQ V V  DE NMR+DR+ +  +P ++F ++Q+++R G++RV+ KR    +R+  G  
Sbjct: 83  TKVQTVAVTADEANMRVDRFLEARFPGLSFSHIQRVVRKGELRVNGKRADSKDRLGEGDK 142

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+      +   +     S   TK  D L+ ++L+ED+ + V NKPAG++VQGGSG
Sbjct: 143 VRIPPL-----KLDTPKVAAGLSEAETKIRDELQKMVLFEDADVMVLNKPAGLAVQGGSG 197

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++ HIDG L+   D+KGQ+PRL HRLD+ET+G L+VA+TR AA  LT SFR R  +KIYW
Sbjct: 198 LSRHIDGMLEVMCDAKGQRPRLVHRLDRETAGCLLVAKTRFAATALTGSFRHRSARKIYW 257

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+PK K+  I+ +L K+       + +    ++GA++A++++ V++  AQK  W+ 
Sbjct: 258 ALVAGVPKPKQGRISTYLAKEESEEDSIMRIAAHGDEGASHAVTYYAVVETSAQKLAWVS 317

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++P TGRTHQLR H  H+   IVGD KY           +Q +L+L AR + +PHP GG 
Sbjct: 318 LKPVTGRTHQLRAHMAHIDHAIVGDPKYFNKENWQLPGGLQKRLHLLARRIVIPHPRGGV 377

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           + +TAPLP HM+++W+ LG + DR
Sbjct: 378 IDVTAPLPPHMLQSWNLLGLEADR 401


>gi|91977597|ref|YP_570256.1| pseudouridine synthase RluD [Rhodopseudomonas palustris BisB5]
 gi|91684053|gb|ABE40355.1| ribosomal large subunit pseudouridine synthase C [Rhodopseudomonas
           palustris BisB5]
          Length = 444

 Score =  294 bits (752), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 145/331 (43%), Positives = 212/331 (64%), Gaps = 15/331 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T V+ VVV  DE NMR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 114 LPTKVETVVVTADENNMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 173

Query: 63  QVVRIPPV----INALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           Q VRIPP+         H+ + EQK L +          LK + LYED+ + V NKP G+
Sbjct: 174 QSVRIPPLKLDTPKLPGHLSEAEQKTLQA----------LKEMTLYEDADVLVLNKPLGL 223

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +VQGGSG   HID  L+   DSKGQKPRL HR+D+ET+G L+VA+TR AA  LT SFR R
Sbjct: 224 AVQGGSGTTRHIDLMLEVMRDSKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRSR 283

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +KIYW+LV G+PK K+  I+ +L K        + V    + GA++A++++ V++  A
Sbjct: 284 SARKIYWALVAGVPKPKQGRISTYLAKDESEDDSIMRVAAHGDDGASHAVTYYAVVETSA 343

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            K  W+ ++P TGRTHQLR H  H+G  I+GD KY           +QN+L+L AR + +
Sbjct: 344 TKLAWVSLKPVTGRTHQLRAHMAHIGHAIIGDPKYFNIENWKLPGGLQNRLHLLARRIVI 403

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           PHP GG + ++APLP HM+++W+ LG ++DR
Sbjct: 404 PHPRGGVIDVSAPLPPHMLQSWNLLGLEHDR 434


>gi|306840487|ref|ZP_07473246.1| pseudouridine synthase, RluA family [Brucella sp. BO2]
 gi|306289502|gb|EFM60720.1| pseudouridine synthase, RluA family [Brucella sp. BO2]
          Length = 284

 Score =  293 bits (751), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 137/283 (48%), Positives = 198/283 (69%), Gaps = 10/283 (3%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILL 102
           +RVD  R K + RIQ+GQ VRIPP+       + E+    +   ++   +  D L  +LL
Sbjct: 1   MRVDGGRAKADTRIQAGQAVRIPPLG------VDEKAAGPMTAKTIRNQQDGDVLSQMLL 54

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED K++VFNKPAG++VQGGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVAR
Sbjct: 55  YEDPKVFVFNKPAGLAVQGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVAR 114

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           TR AAQ LT SFR R  +K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  
Sbjct: 115 TRGAAQALTASFRERDTKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPD 174

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFT 281
           +++A+S++++I+       WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F 
Sbjct: 175 SDHAVSYYRIIEKAGNNLAWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFP 234

Query: 282 SPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
             IQ +L+LHAR++ +P+P GG + +TAPLP HMV++W+ LGF
Sbjct: 235 GGIQKRLHLHARHIRIPNPSGGIIDVTAPLPPHMVQSWNLLGF 277


>gi|316933564|ref|YP_004108546.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           DX-1]
 gi|315601278|gb|ADU43813.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           DX-1]
          Length = 455

 Score =  293 bits (750), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 144/331 (43%), Positives = 212/331 (64%), Gaps = 15/331 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T V+ V V  DE  MR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 125 LPTKVETVTVTADENGMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 184

Query: 63  QVVRIPPV----INALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           Q VRIPP+         H+ + EQK L +          L+ + L+ED+ + V NKPAG+
Sbjct: 185 QSVRIPPLKLDTPKLPGHLSEAEQKTLQA----------LRDMTLFEDADVLVLNKPAGL 234

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +VQGGSG   HID  L+   DSKGQKPRL HR+D+ET+G L+VA+TR AA  LT SFR R
Sbjct: 235 AVQGGSGTTRHIDQMLEVLRDSKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRHR 294

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +KIYW+LV G+PK K+  I+ +L K        + V K  + GA++A++++ V++   
Sbjct: 295 SARKIYWALVAGVPKPKQGRISTYLAKDESEEDSIMRVAKHGDDGASHAVTYYAVVETSG 354

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           QK  W+ ++P TGRTHQLR H  H+G  IVGD KY           +QN+L+L AR + +
Sbjct: 355 QKLAWVSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNIENWQLPGGLQNRLHLLARRIVI 414

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           PHP GG + ++APLP HM+++W+ LG ++DR
Sbjct: 415 PHPRGGVIDVSAPLPPHMLQSWNLLGLEHDR 445


>gi|27380477|ref|NP_772006.1| ribosomal large subunit pseudouridine synthase C [Bradyrhizobium
           japonicum USDA 110]
 gi|27353641|dbj|BAC50631.1| bll5366 [Bradyrhizobium japonicum USDA 110]
          Length = 405

 Score =  293 bits (749), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 140/326 (42%), Positives = 208/326 (63%), Gaps = 5/326 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ V V  DE NMR+DR+ +  +P ++F ++Q+++R G++RVD KRV   +R++ G
Sbjct: 75  LPTKVQTVTVTADENNMRVDRFLEARFPGLSFSHIQRVVRKGELRVDGKRVDSKDRLEEG 134

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP+      +   + + + S    K    LK + +YED  + V NKP G++VQGG
Sbjct: 135 QSVRIPPL-----KLDAPKAVGELSEAAQKTLKALKEMTIYEDDDVLVLNKPFGLAVQGG 189

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   HID  L+   DSKGQKPRL HR+D++TSG L++A+TR AA HLT +FR R  +K+
Sbjct: 190 SGTTRHIDQMLEVMRDSKGQKPRLVHRIDKDTSGCLLIAKTRFAASHLTGAFRSRSARKV 249

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K+       + + +  ++GA++A++++ V++    K  W
Sbjct: 250 YWALVPGLPKPKQGRISTFLAKEESEDDTIMRIAQHGDEGASHAVTYYAVVETAGNKLTW 309

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+G PIVGD KY           +QN+L+L AR + +PHP G
Sbjct: 310 VSLKPVTGRTHQLRAHMEHIGHPIVGDPKYFNIENWQLPGGLQNRLHLLARRIVIPHPRG 369

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDR 328
           G +  TAPLP HM ++W+ LG    R
Sbjct: 370 GVIDATAPLPPHMQQSWNLLGLDASR 395


>gi|300023017|ref|YP_003755628.1| pseudouridine synthase [Hyphomicrobium denitrificans ATCC 51888]
 gi|299524838|gb|ADJ23307.1| pseudouridine synthase, RluA family [Hyphomicrobium denitrificans
           ATCC 51888]
          Length = 327

 Score =  282 bits (722), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 144/336 (42%), Positives = 216/336 (64%), Gaps = 24/336 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V + E +MRLDRWF+ H+P + +  LQK+LRSGQVRV+ KR + N+R+ +G  +R
Sbjct: 3   VETITVADGEADMRLDRWFRVHFPEVGYTYLQKLLRSGQVRVNSKRAQANDRLSAGAEIR 62

Query: 67  IPPVINALNHIIKEQKILDSS----VNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQG 121
           +P        I++E K L  +    + ++K   D ++ ++L+ED  + V NKP G++VQG
Sbjct: 63  VPA-------IVREPKKLSPTGRPALGVSKGDRDAIEKMILFEDDHVLVLNKPFGLAVQG 115

Query: 122 GSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G+G   HIDG L+   D   G++PRL HRLD++T+G+L+VA+TR AA  L  +F+ R   
Sbjct: 116 GTGTKKHIDGMLEGMADRFGGERPRLVHRLDRDTTGVLLVAKTREAAAKLGRTFQTRSAA 175

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQK 239
           K YW+LV G+PK  +  +   L+K S   GD V   +  E+  A +A +H+ V+D  A K
Sbjct: 176 KTYWALVKGVPKPPQGKVEAALVKASGPDGDRVRKARPGEQDAAMHATTHYSVVDRAAHK 235

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMD 296
             W+ ++P TGR HQLR H   +G PIVGD+KY    +G+   P +N   KL+LHAR + 
Sbjct: 236 AAWVSLKPVTGRQHQLRAHMHLIGHPIVGDNKY----EGDVHMPAENIEKKLHLHARRLV 291

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLY 331
           +PHP+GG+ + +TAPLPAHM+ +WD LGF  D N++
Sbjct: 292 IPHPKGGKTIDVTAPLPAHMLASWDLLGF--DVNMF 325


>gi|154248685|ref|YP_001419643.1| RluA family pseudouridine synthase [Xanthobacter autotrophicus Py2]
 gi|154162770|gb|ABS69986.1| pseudouridine synthase, RluA family [Xanthobacter autotrophicus
           Py2]
          Length = 364

 Score =  281 bits (719), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 151/356 (42%), Positives = 211/356 (59%), Gaps = 37/356 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V    V  DE  MRLDRWFK H+P ++F +LQK++R+GQVRVD  RVK ++R++ GQ VR
Sbjct: 3   VAMKTVAEDEAGMRLDRWFKVHFPDLSFGHLQKLVRTGQVRVDGGRVKTSSRVEPGQSVR 62

Query: 67  IPPVIN---------------------------ALNHIIKEQKILDSSVNLTKHSD---- 95
           IPP+ +                           A        K   S+    +  D    
Sbjct: 63  IPPLGDEPQDEPAGKPGAAGKASEAGRVSAGGEASGTTEAPAKPRQSASAAKRKEDEDRA 122

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           FLKSI L+ED  + V NKP G++VQGGSG   H+DG L+   D  GQKPRL HR+D++TS
Sbjct: 123 FLKSITLFEDKDVMVLNKPYGLAVQGGSGTYRHMDGILEVLRDKDGQKPRLVHRIDKDTS 182

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L+VA+TR AA  L +SFR R  +K+YW++V G+PK K+  I+ +L +      + + V
Sbjct: 183 GCLLVAKTRFAASVLAKSFRSREARKVYWAVVPGVPKPKQGRISTYLARDEDE--EKMRV 240

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +  E  A++AI+++ V+D  AQK  WL ++P TGRTHQLR H  H+G PIVGD KY   
Sbjct: 241 ARHGEDEASHAITYYAVVDQAAQKMSWLSLKPVTGRTHQLRAHLAHIGHPIVGDPKYFDI 300

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF---KYD 327
                   +QN+L+L AR + +PHP G G + ++APLP HM +++  LGF   +YD
Sbjct: 301 ENWELPGGLQNRLHLLARRLVIPHPRGQGLIDVSAPLPHHMAQSFAVLGFDASQYD 356


>gi|220926865|ref|YP_002502167.1| RluA family pseudouridine synthase [Methylobacterium nodulans ORS
           2060]
 gi|219951472|gb|ACL61864.1| pseudouridine synthase, RluA family [Methylobacterium nodulans ORS
           2060]
          Length = 457

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 137/331 (41%), Positives = 205/331 (61%), Gaps = 12/331 (3%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L T VQ + V  DE  MR+DR+    +P + F  +Q ++R G++RV+ KR K  +R++ 
Sbjct: 125 ALATGVQMLEVTPDEAGMRIDRFLSARFPQLPFTRIQSLVRKGELRVNGKRAKAADRVEP 184

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKIYVFNKPAGISV 119
           G  VR+PP        +K      S       SD  FL+S++LYED  + V NKP G++V
Sbjct: 185 GASVRVPP--------LKLDAPPSSPSPARAESDLAFLRSLVLYEDQDMMVLNKPFGLAV 236

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           QGGSG   H+DG L++     GQKPRL HRLD++T+G LVVA++R AA  L ++FR R  
Sbjct: 237 QGGSGTKRHVDGLLEALRTPDGQKPRLVHRLDKDTAGCLVVAKSRLAAATLAKTFRSRAA 296

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQ 238
           +KIYW+L  G+P+ ++  I+ +L K+     D  + V +  ++GA++A++++ V+D   Q
Sbjct: 297 RKIYWALAAGVPRVRQGRISTYLAKEEMGDADARMRVAQHGDEGASHALTYYAVVDQAGQ 356

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           K  WL ++P TGRTHQLR HA H+G P+VGD KY           +QN+L+L AR + +P
Sbjct: 357 KLSWLSLKPVTGRTHQLRAHAAHIGHPLVGDPKYFDIENWELPGGLQNRLHLLARRIVIP 416

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           HP   + + +TAPLP HM ++W+ LGF   R
Sbjct: 417 HPRTNKPVDVTAPLPPHMAQSWNLLGFDASR 447


>gi|170744410|ref|YP_001773065.1| RluA family pseudouridine synthase [Methylobacterium sp. 4-46]
 gi|168198684|gb|ACA20631.1| pseudouridine synthase, RluA family [Methylobacterium sp. 4-46]
          Length = 469

 Score =  280 bits (717), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 134/329 (40%), Positives = 204/329 (62%), Gaps = 8/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L T VQ + V  DE  MR+DR+    +P + F  +Q ++R G++RV+ KR K  +R++ 
Sbjct: 137 ALATGVQTLEVTPDEAGMRIDRFLSARFPQLPFTRIQSLVRKGELRVNGKRAKAADRVEP 196

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+       +   K   S         +L+S++LYED  + V NKP G++VQG
Sbjct: 197 GASVRVPPLK------LDAAKPGPSPARAESDLAYLRSLVLYEDQDMMVLNKPYGLAVQG 250

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L++     GQKPRL HRLD++T+G LV+A+TR AA  L ++FR R  +K
Sbjct: 251 GSGTKRHVDGLLEALRAPDGQKPRLVHRLDKDTAGCLVIAKTRLAAATLAKTFRSRAARK 310

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+L  G+PK ++  ++ +L K+     D  + V +  ++GA++A++++ V+D   QK 
Sbjct: 311 IYWALAAGVPKVRQGRVSTYLAKEEVGEADARMRVAQHGDEGASHALTYYAVVDQAGQKL 370

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL ++P TGRTHQLR HA H+G P+VGD KY           +QN+L+L AR + +PHP
Sbjct: 371 SWLSLKPVTGRTHQLRAHAAHIGHPLVGDPKYFDIENWELPGGLQNRLHLLARRIVIPHP 430

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
              + + +TAPLP HM ++W+ LGF   R
Sbjct: 431 RTNKPVDVTAPLPPHMAQSWNLLGFDAGR 459


>gi|158424148|ref|YP_001525440.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
 gi|158331037|dbj|BAF88522.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
          Length = 384

 Score =  277 bits (709), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 140/354 (39%), Positives = 214/354 (60%), Gaps = 35/354 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V  DE +MRLDRWFK H+P ++F +LQK++R+GQVRVD  RVK + R+  GQ VR
Sbjct: 25  VELKQVTEDEADMRLDRWFKTHFPDLSFGHLQKLVRTGQVRVDGGRVKTSTRLSPGQSVR 84

Query: 67  IPPV--------------INALNHIIKEQ---------------KILDSSVNLTKHSDFL 97
           +PP+                    +  E+               ++  ++      ++FL
Sbjct: 85  VPPLGDDAAPAASPAQSKTKGEGAVAGEEGGFAGSGSPFAPAAHQVRAAARREQTDAEFL 144

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +SI+L+ED  + V NKP+GI+VQGGSG   HIDG L +     GQKPRL HR+D++T+G 
Sbjct: 145 RSIILFEDKDVLVLNKPSGIAVQGGSGTFRHIDGMLDALRAKDGQKPRLVHRIDKDTAGC 204

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+ R +A  L ++FR R  +KIYW+LV G+PK ++  I+ +L ++     + + V +
Sbjct: 205 LLIAKNRLSAAQLAKNFRSREARKIYWALVPGVPKPRQGRISTYLAREE--AEERMRVAR 262

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+ A++A++++ V++  AQK  WL ++P TGRTHQ+R H  H+  PIVGD KY     
Sbjct: 263 HGEEDASHAVTYYAVVEHAAQKMSWLSLKPVTGRTHQIRAHLAHIHHPIVGDPKYFNIEN 322

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF---KYD 327
                 +QN+L+L AR + +PHP G G + ++APLP HM ++W  LGF   +YD
Sbjct: 323 WELPGGLQNRLHLLARRLVIPHPRGEGMIDVSAPLPPHMAQSWAVLGFDATQYD 376


>gi|83593991|ref|YP_427743.1| ribosomal large subunit pseudouridine synthase C [Rhodospirillum
           rubrum ATCC 11170]
 gi|83576905|gb|ABC23456.1| ribosomal large subunit pseudouridine synthase C [Rhodospirillum
           rubrum ATCC 11170]
          Length = 330

 Score =  277 bits (708), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 137/318 (43%), Positives = 197/318 (61%), Gaps = 5/318 (1%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V V  DE+  RLDRWFK  YP +    L+K+LR+GQ+RVD KRVK   R+++GQ VR
Sbjct: 3   VETVAVTQDEDGSRLDRWFKRRYPALTHGRLEKLLRTGQIRVDGKRVKSGERLEAGQQVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+ +           +            L+  +L+ED+ + V NK AG++VQGG+G  
Sbjct: 63  VPPLGDEAPSPSSSGHAVPRPAA-EGEIRALRRAILHEDAHLIVINKEAGLAVQGGTGTP 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +H+DG L+S  D  G+ PRL HRLD++TSG+LV+ART+AAA+ LT +FR R   K+YW++
Sbjct: 122 HHLDGMLESLADG-GETPRLVHRLDKDTSGVLVLARTQAAARALTSAFRSREALKVYWAI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G P   +  I   L K +   G+ + +   NE+    A++ F+V+D  A+   W+E+ 
Sbjct: 181 VVGRPPMLQGTIKGALAKVAGGRGERMEI---NEEEGKRAVTDFRVVDQAAKACAWVELH 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P TGRTHQLRVH L MG PI+GD KY         + +  +++LHAR + LPHP GG L+
Sbjct: 238 PRTGRTHQLRVHCLEMGTPILGDGKYGGPGAFLEGTELPKRMHLHARALALPHPAGGVLE 297

Query: 307 ITAPLPAHMVKTWDSLGF 324
           I AP P H V++  +LGF
Sbjct: 298 IIAPPPPHFVESLKTLGF 315


>gi|182678295|ref|YP_001832441.1| RluA family pseudouridine synthase [Beijerinckia indica subsp.
           indica ATCC 9039]
 gi|182634178|gb|ACB94952.1| pseudouridine synthase, RluA family [Beijerinckia indica subsp.
           indica ATCC 9039]
          Length = 350

 Score =  276 bits (707), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 138/342 (40%), Positives = 205/342 (59%), Gaps = 31/342 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + + V+ DEE MRLDRWFK   P ++  +L KI+R+GQVRVD  RVK   R+ +GQ VR
Sbjct: 3   AKTLTVDTDEEGMRLDRWFKRRLPDLSLSHLNKIVRTGQVRVDGARVKTATRLAAGQSVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP       +   ++ L+    ++  +  L+ ++L+ED  + V NKP G++VQGGSG+ 
Sbjct: 63  VPP-------LDLPERPLEKPAIVSADAQALREMILFEDRDLMVLNKPFGLAVQGGSGMT 115

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +HID  L S  + +G +P L HRLD++TSG+L+VA+TR  A  L E FR R+ +KIYW++
Sbjct: 116 HHIDKMLASLPNERGDRPVLVHRLDRDTSGVLLVAKTRRMAAELGEIFRSRQARKIYWAV 175

Query: 187 VWGIPKNKKECIANWLLK---------------KSHIGGDYVHVVKQNEKGANYAISHFK 231
           V G+PK  +  I+ +L K               ++  G + + V K  E+ A ++++++ 
Sbjct: 176 VEGVPKPAQGRISLYLAKGEGMEDKRGPHGRDAEARAGLEKMRVAKHGEEDARHSVTYYA 235

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN---------FTS 282
           ++D    +  WL M+P TGRTHQLR HA  +G PI+GD KY    K +            
Sbjct: 236 IVDKVPSRLAWLSMKPITGRTHQLRAHAEAIGHPIIGDPKYGLKPKDDPRRNDPNRAIPE 295

Query: 283 PIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
            ++ KL+L AR + LPHP GG L +TAPLP HM KT+D  GF
Sbjct: 296 GVERKLHLLARRLILPHPRGGILDVTAPLPPHMQKTFDLFGF 337


>gi|296114939|ref|ZP_06833585.1| pseudouridine synthase, RluA family protein [Gluconacetobacter
           hansenii ATCC 23769]
 gi|295978497|gb|EFG85229.1| pseudouridine synthase, RluA family protein [Gluconacetobacter
           hansenii ATCC 23769]
          Length = 325

 Score =  275 bits (704), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 137/328 (41%), Positives = 200/328 (60%), Gaps = 18/328 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS++T    + V +DE ++RLDRWF+ HYPH+    LQK+ R+GQ+RVD  RV  + R+ 
Sbjct: 1   MSVVT----LTVSDDEADIRLDRWFRRHYPHLTQGALQKLCRTGQIRVDGGRVTTSTRLA 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            GQ VR+PP+  A        + LD      +    ++ +++Y D ++ V NKPAGI+VQ
Sbjct: 57  PGQAVRVPPIPQASRPAPVTHRTLDD-----RQVREIRKMVIYSDDQVIVLNKPAGIAVQ 111

Query: 121 GGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           GG GI +HIDG L    +     +PRL HR+D++TSG+L++ART   A  L  SFR R +
Sbjct: 112 GGPGITHHIDGLLDGLREQPDDPRPRLVHRIDRDTSGLLLLARTPGVAAKLAASFRSRDV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K+YW++  G P      +   L +     G  + V  + +K A +A+S ++V+D   +K
Sbjct: 172 RKVYWAVTVGRPTPASGIVDQPLTRLGAGAGAIMVVAGRRDKDAVHALSEYEVLDAAGRK 231

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMD 296
             WL + P TGRTHQLRVH   +G PI+GD KY    A+ +G       ++L+LHAR +D
Sbjct: 232 LSWLALSPLTGRTHQLRVHCEALGTPILGDPKYGDDRAHVEG-----FPDQLHLHARMLD 286

Query: 297 LPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           LPHP GGRL ++A LPAHM +T+  LGF
Sbjct: 287 LPHPAGGRLVVSADLPAHMKETFRQLGF 314


>gi|329114604|ref|ZP_08243363.1| Ribosomal large subunit pseudouridine synthase C [Acetobacter
           pomorum DM001]
 gi|326696084|gb|EGE47766.1| Ribosomal large subunit pseudouridine synthase C [Acetobacter
           pomorum DM001]
          Length = 328

 Score =  275 bits (703), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 138/323 (42%), Positives = 198/323 (61%), Gaps = 12/323 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V   V E DE+ +RLDR+F+ HYPH+    LQK+ R+GQ+RV+ KRV+ + R++ GQ
Sbjct: 1   MSVVNRTVSE-DEDGIRLDRYFRRHYPHLTQGALQKLCRTGQIRVEGKRVEASTRLEPGQ 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+  A        + LD      K +  ++ +++Y+D  + V NKPAG++VQGG 
Sbjct: 60  TVRVPPIPMAAKPARDVPRPLDE-----KLAREIRKMVVYQDKHVIVLNKPAGLAVQGGP 114

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           GI  HID  L    +    +PRL HR+D++TSG+L++ART   A  L  SFR R ++KIY
Sbjct: 115 GITKHIDMMLDGLREEDDPRPRLVHRIDKDTSGLLLLARTPGVAAKLAASFRGRDVKKIY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++V G P      I   L +     G       + +  A +A S ++V+D  A+KF WL
Sbjct: 175 WAVVVGRPDPLSGEIDQPLARLGAGPGSITVAADRKDADAQFARSVYEVLDSAARKFSWL 234

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E+ P TGRTHQLRVH   +G PI+GD KY   A     FT    ++L+LHAR +D+PHP 
Sbjct: 235 ELSPLTGRTHQLRVHCESLGTPILGDPKYGGAAAHPSGFT----DRLHLHARMLDMPHPA 290

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
           GGRL ++A LP HM +T+ +LGF
Sbjct: 291 GGRLTVSAELPPHMRETFRTLGF 313


>gi|162148058|ref|YP_001602519.1| ribosomal large subunit pseudouridine synthase A [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209542674|ref|YP_002274903.1| RluA family pseudouridine synthase [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|161786635|emb|CAP56217.1| putative ribosomal large subunit pseudouridine synthase A
           [Gluconacetobacter diazotrophicus PAl 5]
 gi|209530351|gb|ACI50288.1| pseudouridine synthase, RluA family [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 325

 Score =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 137/328 (41%), Positives = 197/328 (60%), Gaps = 16/328 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS++T    + V  DE ++RLDRWF+ HYPH+    LQK+ R+GQVRVD KR + + R+ 
Sbjct: 1   MSVVT----LTVSEDEADIRLDRWFRRHYPHLTQGALQKLCRTGQVRVDGKRAETSTRLL 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            GQ VR+PP+  A       + +LD    L +    ++ +++Y D ++ V NKPAG+ VQ
Sbjct: 57  PGQAVRVPPIPGASRPAPPPRPVLDE--RLVRE---IRGMVIYSDDQVIVLNKPAGLPVQ 111

Query: 121 GGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           GG GI +H+D  L    D     +PRL HR+D++TSG+L++ART   A  L  SFR R +
Sbjct: 112 GGPGIIHHVDAMLDGLKDQDDDPRPRLVHRIDRDTSGLLLLARTPGVAAKLAASFRGRDV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K YW++V G P      I   L +     G    V  + +  A +A+S ++V+D   +K
Sbjct: 172 RKTYWAIVVGRPSPASGVIDQPLARLGAGPGALTVVASRKDADAAHALSEYEVLDAAGRK 231

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDL 297
             WL + P TGRTHQLRVH   +G PI+GD KY     G+   P    ++L+LHAR +DL
Sbjct: 232 LSWLALSPLTGRTHQLRVHCEALGTPILGDPKY----GGDTAHPEGFVDRLHLHARTLDL 287

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           PHP GGRL ++A LP+HM +T+  LGF 
Sbjct: 288 PHPAGGRLVVSADLPSHMRETFRQLGFS 315


>gi|258542797|ref|YP_003188230.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256633875|dbj|BAH99850.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256636934|dbj|BAI02903.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-03]
 gi|256639987|dbj|BAI05949.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-07]
 gi|256643043|dbj|BAI08998.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-22]
 gi|256646098|dbj|BAI12046.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-26]
 gi|256649151|dbj|BAI15092.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-32]
 gi|256652138|dbj|BAI18072.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-01-42C]
 gi|256655195|dbj|BAI21122.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-12]
          Length = 328

 Score =  270 bits (691), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 136/323 (42%), Positives = 195/323 (60%), Gaps = 12/323 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V   V E DE  +RLDR+F+ HYPH+    LQK+ R+GQ+RV+ KRV+ + R++ GQ
Sbjct: 1   MSVVNRTVSE-DEAGIRLDRYFRRHYPHLTQGALQKLCRTGQIRVEGKRVEASTRLEPGQ 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+  A        + LD      K +  ++ +++Y+D  +   NKPAG++VQGG 
Sbjct: 60  TVRVPPIPMAAKPARDVPRPLDE-----KLAREIRKMVVYQDKHVIALNKPAGLAVQGGP 114

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           GI  H+D  L    +    +PRL HR+D++TSG+L++ART   A  L  SFR R ++KIY
Sbjct: 115 GITKHVDMMLDGLREEDDPRPRLVHRIDKDTSGLLLLARTPGVAAKLAASFRGRDVKKIY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++V G P      I   L +     G       + +  A  A S ++V+D  A+KF WL
Sbjct: 175 WAVVVGRPDPLSGEIDQPLARLGAGPGSITVAADRKDADAQSARSVYEVLDSAARKFSWL 234

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E+ P TGRTHQLRVH   +G PI+GD KY   A     FT    ++L+LHAR +D+PHP 
Sbjct: 235 ELSPLTGRTHQLRVHCESLGTPILGDPKYGGAAAHPSGFT----DRLHLHARMLDMPHPA 290

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
           GGRL ++A LP HM +T+ +LGF
Sbjct: 291 GGRLTVSAELPPHMRETFRTLGF 313


>gi|330993253|ref|ZP_08317189.1| Ribosomal large subunit pseudouridine synthase C [Gluconacetobacter
           sp. SXCC-1]
 gi|329759655|gb|EGG76163.1| Ribosomal large subunit pseudouridine synthase C [Gluconacetobacter
           sp. SXCC-1]
          Length = 322

 Score =  270 bits (690), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 133/316 (42%), Positives = 190/316 (60%), Gaps = 8/316 (2%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V +DE ++RLDRWF+ HYPH+    LQK+ R+GQVRVD +R     R++ GQ VR+PP
Sbjct: 3   LTVSDDEADIRLDRWFRRHYPHLTQGALQKLCRTGQVRVDGRRATAATRLEPGQAVRVPP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           + NA        K LD+     +    +  +++Y D  + V NKPAGI+VQGG GI +HI
Sbjct: 63  IPNASRPPPLAVKPLDA-----RQVREINQMVIYRDDHVIVLNKPAGIAVQGGPGITHHI 117

Query: 130 DGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           D  L    DS    +PRL HR+D++TSG+L+VART   A  L  +FR R + K+YW++V 
Sbjct: 118 DALLDGLRDSPDDPRPRLVHRIDRDTSGLLLVARTPGVAAKLAAAFRGRDVHKVYWAVVV 177

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G P      I   L +     G    V ++ +  A +A+S ++V+D  A+K  WL + P 
Sbjct: 178 GRPSPATGIIDQPLTRLGAGAGAISVVAERGDADAVHALSEYEVLDAAARKMSWLALSPL 237

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT 308
           TGRTHQLRVH   +G PI+GD KY  +      +   ++L+LHAR ++LPHP GG L + 
Sbjct: 238 TGRTHQLRVHCEALGNPILGDPKYGGDVA--HVAGFADRLHLHARRLELPHPAGGTLVVE 295

Query: 309 APLPAHMVKTWDSLGF 324
           A LP HM +T+  +GF
Sbjct: 296 ADLPPHMRETFRQIGF 311


>gi|217976287|ref|YP_002360434.1| pseudouridine synthase, RluA family [Methylocella silvestris BL2]
 gi|217501663|gb|ACK49072.1| pseudouridine synthase, RluA family [Methylocella silvestris BL2]
          Length = 349

 Score =  269 bits (687), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 144/353 (40%), Positives = 206/353 (58%), Gaps = 37/353 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS+ TY     V  DE+ +RLDRWFK   P ++  +L KI+R+GQVRVD  RVK   R+ 
Sbjct: 1   MSVQTYE----VAEDEDGLRLDRWFKRRIPALSLSHLNKIVRTGQVRVDGARVKTATRLA 56

Query: 61  SGQVVRIPPVINALN-HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            GQ VR+PP    LN     E  +   S    +    L+ ++L+ED  + V NKP G++V
Sbjct: 57  QGQNVRVPP----LNLEAAPEAPVFRISEEDQRD---LRQMILFEDKDLMVLNKPYGLAV 109

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           QGGSG+  HIDG L S  + +G +P L HRLD++TSG+L++A+TR  A  L E FR R+ 
Sbjct: 110 QGGSGMRRHIDGMLASLPNERGDRPVLVHRLDRDTSGVLLIAKTRKMAADLGEIFRSRQA 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGG-------------DYVHVVKQNEKGANYA 226
           QKIYW+LV G+PK  +  I+ +L K   +               + + V K  ++ A ++
Sbjct: 170 QKIYWALVEGVPKPAQGKISLFLAKGEGMDARGPRRSDEERASMEKMRVAKHGDEDAQHS 229

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------- 279
           ++++  +D F+ +  WL M+P TGRTHQLR HA  +G PI+GD KY    K +       
Sbjct: 230 VTYYATVDTFSPRAAWLSMKPITGRTHQLRAHAEAIGHPIIGDPKYGLRPKTDPRRNDPL 289

Query: 280 --FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF---KYD 327
                 I+ KL+L AR + LPHP GG L +TAPLP HM  ++++ GF   +YD
Sbjct: 290 RAIPETIERKLHLLARRLVLPHPRGGVLDVTAPLPPHMANSFETFGFDVKQYD 342


>gi|58040098|ref|YP_192062.1| ribosomal large subunit pseudouridine synthase C [Gluconobacter
           oxydans 621H]
 gi|58002512|gb|AAW61406.1| Ribosomal large subunit pseudouridine synthase C [Gluconobacter
           oxydans 621H]
          Length = 335

 Score =  266 bits (681), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 133/339 (39%), Positives = 193/339 (56%), Gaps = 10/339 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    +V E DE ++RLDRWF+ HYP++    LQK+ R GQ+RV+  RV+ N R+  GQ
Sbjct: 1   MTVTNRIVTE-DEADIRLDRWFRRHYPNLTQGALQKLCRKGQIRVEGGRVQTNTRLIPGQ 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+ +         K           +  ++ +++YED  + V +KP+G++ QGG 
Sbjct: 60  SVRIPPLPDV-------DKPAPLPPPDPMLAREIRKMVIYEDEHLLVLDKPSGLATQGGP 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           GI  H+D  L       G +PRL HR+D++TSGIL++ART   A  L  +FR R ++K Y
Sbjct: 113 GITKHVDMMLDGLRTEGGDRPRLVHRIDRDTSGILLIARTPGVAAKLAAAFRGRDVEKTY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++V G P  +   I   L K    G   V    ++E+ A  A + ++ +D   +K  WL
Sbjct: 173 WAVVVGRPSPESGIIDQPLAKIGAGGAALVIAASRDEEDAASAKTEYETLDAAGKKLSWL 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++ P TGRTHQLRVH   +G PI+GD +Y    K        ++L+LHAR +D+PHP GG
Sbjct: 233 KLSPLTGRTHQLRVHTESIGTPILGDPRYGG--KAAHPEGFIDRLHLHARQLDIPHPAGG 290

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECK 342
           RL +TAPLP HM +T+ +LGF        KR+      K
Sbjct: 291 RLIVTAPLPPHMRETFRTLGFVPGETPAPKRVRGGSSSK 329


>gi|296444792|ref|ZP_06886755.1| pseudouridine synthase, RluA family [Methylosinus trichosporium
           OB3b]
 gi|296257740|gb|EFH04804.1| pseudouridine synthase, RluA family [Methylosinus trichosporium
           OB3b]
          Length = 365

 Score =  265 bits (677), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 138/352 (39%), Positives = 203/352 (57%), Gaps = 34/352 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + VQ + V  DE  +RLDRWFK  +P +   +L KI R G+VRVD KRV    R++  Q 
Sbjct: 12  SPVQTLTVTEDEAGLRLDRWFKRRFPALALSHLAKICRKGEVRVDGKRVDTATRLEQDQK 71

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+PP+   L        IL +S    + +  L  + LYED+ + V NKP G++VQGGSG
Sbjct: 72  IRVPPL--KLEAAAAAPTILRAS---PEDARALADMTLYEDASLLVLNKPYGLAVQGGSG 126

Query: 125 IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +  HIDG L+S   +KG  +P L HRLD++TSG+L++A+ R  A  L E FR R+ +KIY
Sbjct: 127 MTRHIDGMLESL--AKGDTRPVLVHRLDRDTSGVLLIAKNRRTAADLGEIFRSRQAKKIY 184

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDY-----------------VHVVKQNEKGANYA 226
           W+LV G+PK  +  ++ +L K + +G D                  + V +  ++GA ++
Sbjct: 185 WALVEGVPKPAQGRVSLYLAKGAAMGDDRPPRPGSERREAADAREKMRVARHGDEGAQHS 244

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------- 279
           ++++ +++  A +  WL M+P TGRTHQLR HA  + CPI GD KY    +         
Sbjct: 245 LTYYAIVEKAAPRCAWLSMKPLTGRTHQLRAHAEAIACPIFGDPKYGHRPEDEVRRRDPM 304

Query: 280 --FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
                 ++ KL+L AR + LP+P+GG L +TAPLPAHM  +WD  GF   R 
Sbjct: 305 RAMPEGLERKLHLLARRLILPNPKGGTLDVTAPLPAHMQTSWDVFGFDASRQ 356


>gi|296535679|ref|ZP_06897854.1| ribosomal large subunit pseudouridine synthase C [Roseomonas
           cervicalis ATCC 49957]
 gi|296264003|gb|EFH10453.1| ribosomal large subunit pseudouridine synthase C [Roseomonas
           cervicalis ATCC 49957]
          Length = 331

 Score =  262 bits (670), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 137/332 (41%), Positives = 200/332 (60%), Gaps = 14/332 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q+  V   + + RLDRWF+ H+P +    LQK+LR+GQ+RVD KR + N R+  GQ +R
Sbjct: 8   IQHRTVHAADADSRLDRWFRRHFPQLTQGALQKMLRTGQIRVDGKRAEANTRLARGQEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+         E    D  V+  + +  L++++LY D  I   NKP G+ VQGG  I 
Sbjct: 68  IPPLPEG---PAPEPVARDRQVS-AEDAKALEAMILYRDDYIIALNKPHGLPVQGGPNIK 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            H+DG L +    K ++PRL HRLD++TSG++++AR  +AA  L ++FR R  +K YW++
Sbjct: 124 KHLDGMLDALTFEKEERPRLVHRLDRDTSGVILLARDASAAGFLAKAFRGRDAEKTYWAI 183

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G P+ +   I +  L K   G     VV    +   +AI+ F  +D   +   WLE++
Sbjct: 184 VVGQPQYQGGRI-DMRLAKQGGGPMGERVVPAEGRDGAHAITEFDTVDVARRHATWLELR 242

Query: 247 PHTGRTHQLRVH-ALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           P TGRTHQLRVH A  + CPI+GD KY    A+ +G     + N L+LHAR + +PHPEG
Sbjct: 243 PLTGRTHQLRVHCAAALSCPILGDGKYGGQAAHLEG-----MSNALHLHARRIVVPHPEG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           G L++TAPLP HM++++ +LGF   RN   KR
Sbjct: 298 GTLEVTAPLPPHMLESFATLGFDKPRNTAPKR 329


>gi|323138142|ref|ZP_08073215.1| pseudouridine synthase, RluA family [Methylocystis sp. ATCC 49242]
 gi|322396604|gb|EFX99132.1| pseudouridine synthase, RluA family [Methylocystis sp. ATCC 49242]
          Length = 351

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 140/337 (41%), Positives = 197/337 (58%), Gaps = 28/337 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V    V  DE  MR+DRWFK  YP +   +L KI R G+VRVD KRV+ + R++ GQ VR
Sbjct: 10  VSTTTVTEDEAGMRVDRWFKRRYPTLALSHLAKICRKGEVRVDGKRVETSTRLEEGQKVR 69

Query: 67  IPPV-INALNH-IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +PP+ I A     +K     D+          LK++ L+ED  + V NKP G++ QGGSG
Sbjct: 70  VPPLRIEAPEAPAVKRASPEDAQA--------LKAMTLFEDKDVLVLNKPWGLATQGGSG 121

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              H+DG L+S       +P L HRLD++TSG+L+VA+TR  A  L E FR R+ +KIYW
Sbjct: 122 QKRHVDGMLESLARGD-SRPVLVHRLDRDTSGVLLVAKTRRMAADLGEIFRSRQAKKIYW 180

Query: 185 SLVWGIPKNKKECIANWLLK-----KSHIGG---DYVHVVKQNEKGANYAISHFKVIDCF 236
           +LV G+PK  +  ++ +L K     K+  GG   + + V K  E  A ++++++ ++D  
Sbjct: 181 ALVEGVPKPAQGRVSLYLAKGAGMEKARGGGRDLEKMRVAKHGEADAQHSLTYYAIVDKV 240

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN---------FTSPIQNK 287
           A +  WL M+P TGRTHQLR HA  +G PI GD KY    + +             ++ K
Sbjct: 241 APRCAWLSMKPLTGRTHQLRAHAEAIGHPIFGDPKYGRRPEDDVRRRDPLRAMPDGLERK 300

Query: 288 LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           L+L AR + LPHP GG L +TAPLP HM K+W+  GF
Sbjct: 301 LHLLARRLVLPHPRGGTLDVTAPLPPHMQKSWELFGF 337


>gi|83858519|ref|ZP_00952041.1| ribosomal large subunit pseudouridine synthase C [Oceanicaulis
           alexandrii HTCC2633]
 gi|83853342|gb|EAP91194.1| ribosomal large subunit pseudouridine synthase C [Oceanicaulis
           alexandrii HTCC2633]
          Length = 325

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 134/331 (40%), Positives = 204/331 (61%), Gaps = 14/331 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ V V  DE+ MR+DRWFK H+PH++   ++K+LR+GQ+RVD  R K N R+ +GQ
Sbjct: 1   MSGVQTVEVTRDEDEMRVDRWFKKHFPHVSHGMIEKLLRTGQIRVDGGRAKGNQRLSAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+ +A     +EQ  +       + + F +S+++YED ++   NKP G++VQGGS
Sbjct: 61  SVRVPPMPDAGE--PREQGSI-----TRQDAQFARSLVIYEDKQMIALNKPPGLAVQGGS 113

Query: 124 GIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +  H+D  L+++   KG QKPRL HRLD++TSG+LVVA+T  +A+ L   F+ R ++K 
Sbjct: 114 KVTMHLDHLLQAF--GKGDQKPRLVHRLDKDTSGVLVVAKTAQSAKRLARLFQTRDVKKT 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFAQKFC 241
           YW++  G+P  +   I  ++ KKS  G   + V  +  E+GA +A++ + V D    +  
Sbjct: 172 YWAICLGLPAPRAGEIKGFM-KKSMEGDRELMVGARHGEEGAQHALTRYAVADNAGARAS 230

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           W+ ++P TGRTHQLRVH   MG  I GD KY  ++       +  KL+LHAR +++P   
Sbjct: 231 WVVLRPETGRTHQLRVHMQAMGHSIYGDGKYTCDYPD--PEGLSRKLHLHARKIEIPREG 288

Query: 302 GGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
              L I A LP HM  ++D+LGF    NL +
Sbjct: 289 QKPLVIEADLPKHMADSFDALGFNPGDNLML 319


>gi|288958958|ref|YP_003449299.1| ribosomal large subunit pseudouridine synthase C [Azospirillum sp.
           B510]
 gi|288911266|dbj|BAI72755.1| ribosomal large subunit pseudouridine synthase C [Azospirillum sp.
           B510]
          Length = 354

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 132/325 (40%), Positives = 197/325 (60%), Gaps = 11/325 (3%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V  DE +MRLDRWFK H+P +N   LQK+LR+GQVR+D KR + ++R+ +GQ VR
Sbjct: 21  VEIRTVTADEADMRLDRWFKRHFPDVNHSYLQKLLRTGQVRIDGKRAETSSRLAAGQGVR 80

Query: 67  IPPV------INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           IPP+      +   NH   +       ++  K    L++++LY D+ +   NKPAG++VQ
Sbjct: 81  IPPLAAWAAPVKGPNHGSNQGAGKPKGMS-DKQIAELQALVLYRDADVIAINKPAGLAVQ 139

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GG+G + H+D  L +      ++P+L HRLD++TSG+L++ART  AA  LTE FR   ++
Sbjct: 140 GGTGTSKHLDAMLDALRFDGNERPKLVHRLDKDTSGVLLLARTTFAASKLTELFRGSAVR 199

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIYW++  G+P   +  I   L K+   GG +   V +N++    A++ + V +   ++ 
Sbjct: 200 KIYWAVTVGVPTPYQGKIDLALAKE---GGPHGERVAENKEEGKRAVTVYSVQENVGKQA 256

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++ M P TGRTHQLRVH   +G PI+GD KY         + +  KL+LHAR + LPHP
Sbjct: 257 AFVAMWPLTGRTHQLRVHMAAVGTPILGDGKYAGQGAFLAGAEVAKKLHLHARRLILPHP 316

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGF 324
            GG+ + +TAPLP HM  TW   GF
Sbjct: 317 RGGKTIDVTAPLPDHMQATWKYFGF 341


>gi|149187024|ref|ZP_01865331.1| pseudouridylate synthase [Erythrobacter sp. SD-21]
 gi|148829313|gb|EDL47757.1| pseudouridylate synthase [Erythrobacter sp. SD-21]
          Length = 376

 Score =  256 bits (655), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 131/326 (40%), Positives = 195/326 (59%), Gaps = 12/326 (3%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     V+   VE D++ +RLDRWFK H P I F  + K  R+GQ+RVD  R K ++R+ 
Sbjct: 1   MKTSDEVRNFTVEADDDGIRLDRWFKRHLPQIGFGTVSKWARTGQIRVDGSRAKPDDRLA 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK-IYVFNKPAGISV 119
            GQ +R+PP  +A +   K+++       LTK        +L E +K   V NKP G++ 
Sbjct: 61  QGQQIRVPPGGDAPHKKPKQKR------ELTKAEIEQAEAMLIEQTKSALVINKPPGLAT 114

Query: 120 QGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           QGG+    H+DG L ++++  + Q+PRL HRLD++TSGIL+VART  +A   ++ F  R 
Sbjct: 115 QGGTNTFNHVDGLLDAYMEEGEEQRPRLVHRLDKDTSGILLVARTPGSAAFFSKRFSGRS 174

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            +KIYW+LV G+P  ++  I   L K+   GG+ +HV   + +G   A + ++V++   +
Sbjct: 175 AKKIYWALVVGVPDIRQGVIEAPLAKQPGSGGEKMHV---DHEGGAPAKTKYRVVESAGK 231

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           K  WLE+QP TGRTHQLRVH   MG PIVGD KY    +   T  +  K++LHAR + + 
Sbjct: 232 KVAWLELQPMTGRTHQLRVHCAAMGHPIVGDGKYGGK-EAFLTGSVSRKMHLHARRLIID 290

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGF 324
            P+GG+L +TA LP H   + + +GF
Sbjct: 291 SPDGGKLDVTAELPEHFAASMEQIGF 316


>gi|296284584|ref|ZP_06862582.1| pseudouridylate synthase [Citromicrobium bathyomarinum JL354]
          Length = 388

 Score =  256 bits (653), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 125/317 (39%), Positives = 186/317 (58%), Gaps = 10/317 (3%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           QY V E+DE  +RLDRWFK H P + F  + +  R+GQ+RVD  R K ++R+  GQV+RI
Sbjct: 15  QYTVAEDDE-GVRLDRWFKRHLPEVGFATVARWARTGQIRVDGARAKPDDRLTQGQVLRI 73

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP   A       ++ L             +++++ E     V NKP G++ QGGS    
Sbjct: 74  PPGNPARAKTPPRRRELTEDQKAQ-----ARAMVIKETPNAIVLNKPPGLATQGGSKTFS 128

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           H+DG L ++V+  G +PRL HRLD++TSG+L++ART  +A   ++ F  R  +K+YW+LV
Sbjct: 129 HVDGLLDAFVEGDGPRPRLVHRLDKDTSGVLLIARTPGSAAAFSKRFAGRSAKKVYWALV 188

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+P+     I   L K+   GG+ +HV   + +G   A + ++V++    +  WLE++P
Sbjct: 189 VGVPEQHVGEIDAPLAKQPGTGGEKMHV---DTEGGQPAKTRYRVVERAGNRAAWLELEP 245

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQLRVH   MG PIVGD KY    +   T  +  K++LHAR + +  P GG+L +
Sbjct: 246 LTGRTHQLRVHCAAMGHPIVGDGKYGGQ-EAFLTGSVSRKMHLHARRLIISQPGGGQLDV 304

Query: 308 TAPLPAHMVKTWDSLGF 324
           TA LP H   T + +GF
Sbjct: 305 TAELPEHFAATMEQMGF 321


>gi|154253208|ref|YP_001414032.1| RluA family pseudouridine synthase [Parvibaculum lavamentivorans
           DS-1]
 gi|154157158|gb|ABS64375.1| pseudouridine synthase, RluA family [Parvibaculum lavamentivorans
           DS-1]
          Length = 330

 Score =  255 bits (651), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 131/321 (40%), Positives = 190/321 (59%), Gaps = 5/321 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V  + V  +E+ +RLDRWFK  +P +    L+K+LR+GQVRVD  R K N R+ +GQ
Sbjct: 1   MNQVSQLDVTEEEDGVRLDRWFKRRFPMLTHGRLEKLLRTGQVRVDGARAKANARLATGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP    L     +Q            ++ L++ ++Y+D  + V NKP G++VQGG+
Sbjct: 61  VVRVPP----LGEDADKQAPKAVHAPSVDDAEMLRANVIYKDKSVLVLNKPVGLAVQGGT 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG L + +    ++PRL HRLD++TSG+LV+ART  AA  L ++F+ +  QKIY
Sbjct: 117 KTERHLDGMLDALIFDAKERPRLVHRLDRDTSGVLVLARTAKAAAALAQAFKQKDAQKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P  ++  I   L K+     + V   K+ ++GA  A++HF  +   A    W+
Sbjct: 177 WALVVGVPVPRQGTIDLALSKQGGPRAERVFAAKRGDEGARDAVTHFSTVSTAAHTLAWV 236

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              P TGRTHQ+R HA  +  PIVGD KY      +    I  KL+LHAR +D+ HP+GG
Sbjct: 237 AFMPLTGRTHQIRAHAAAIETPIVGDGKY-GGVNAHPGGEIPRKLHLHARSIDIAHPDGG 295

Query: 304 RLQITAPLPAHMVKTWDSLGF 324
           RL + A LP HM  +W  LGF
Sbjct: 296 RLHVEADLPPHMKTSWKLLGF 316


>gi|87200850|ref|YP_498107.1| ribosomal large subunit pseudouridine synthase C [Novosphingobium
           aromaticivorans DSM 12444]
 gi|87136531|gb|ABD27273.1| ribosomal large subunit pseudouridine synthase C [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 436

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 128/321 (39%), Positives = 186/321 (57%), Gaps = 10/321 (3%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   +  D+   RLDRWFK H P + F  + +  R+GQ+R+D KR   + R+++GQ++R
Sbjct: 11  VRQFTIGKDDAGARLDRWFKRHLPQVGFATVSRWARTGQIRIDGKRADVDTRLEAGQILR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PP       +    K   +   LT+      +S++L +D    V NKP G++ QGGSG 
Sbjct: 71  VPP--GNATPVGTPGKGERARKPLTEEQIQLAESMVLEKDRAAIVLNKPPGLATQGGSGT 128

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG L ++V+    +PRL HRLD++TSG+L++ART  +A   ++ F  R  +KIYW+
Sbjct: 129 HEHVDGLLDAYVNEGEARPRLVHRLDKDTSGVLLIARTPGSAAFFSKRFSCRSARKIYWA 188

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G+P  K   I   L K+   GG+ + V +  +     A S ++VI        W+E+
Sbjct: 189 LVVGVPDVKDGLIELPLAKQPGTGGEKMMVDESGQ--GQSARSRYRVISRAGNAAAWVEL 246

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           QP TGRTHQLRVH   +G PIVGD KY   A F    T  I  K++LHAR + + HPEG 
Sbjct: 247 QPLTGRTHQLRVHMAAIGHPIVGDGKYGGQAAF---LTGSISRKMHLHARRLRIEHPEGD 303

Query: 304 RLQITAPLPAHMVKTWDSLGF 324
            + +TAPLPAH   +  SLGF
Sbjct: 304 MIDVTAPLPAHFAASMASLGF 324


>gi|254294409|ref|YP_003060432.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254042940|gb|ACT59735.1| pseudouridine synthase, RluA family [Hirschia baltica ATCC 49814]
          Length = 343

 Score =  253 bits (645), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 125/326 (38%), Positives = 195/326 (59%), Gaps = 11/326 (3%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V + E ++RLDRW K  +P +    ++K+LR G+VRVD  R K + R++ GQVVR
Sbjct: 8   VLQIPVGDTEGDVRLDRWLKRRFPGLTQGQVEKLLRKGEVRVDGSRAKSSTRLEPGQVVR 67

Query: 67  IPPVIN---ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +PP+ +      H  KE+++  S     + ++ ++S++LYED  +YV NKP+G++VQGG+
Sbjct: 68  VPPMPSTDQGKKHPQKEEEVYVSP----RDAELIQSLILYEDEDVYVLNKPSGLAVQGGT 123

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG   +       KPRL HRLD++TSG+LV+A+T  +A  +++ FR R + KIY
Sbjct: 124 KTLRHVDGMANALTRPGQDKPRLVHRLDKDTSGLLVLAKTAQSAAEMSKHFRSRELDKIY 183

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--QNEKGANYAISHFKVIDCFAQKFC 241
           W++V G+P   +  +  W++K    G D   +      +KGA +AI+ FKV+    Q+  
Sbjct: 184 WAVVKGVPNPNEGELRGWMMKAHGPGQDKELMTAGVHGQKGAVFAITDFKVVSTAGQRAS 243

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           W+ ++P TGR HQLR H   +G  I+GD KY  + +     P    L+LHAR + +P   
Sbjct: 244 WVALKPSTGRKHQLRYHMSEIGNSILGDAKYTCDRETPAGLP--PGLHLHARALRMPRRR 301

Query: 302 GGRLQITAPLPAHMVKTWDSLGFKYD 327
           G  +++ APLP HM KT+D  GF  D
Sbjct: 302 GSDVEVIAPLPEHMKKTFDFFGFSED 327


>gi|89070524|ref|ZP_01157813.1| ribosomal large subunit pseudouridine synthase C [Oceanicola
           granulosus HTCC2516]
 gi|89043831|gb|EAR50029.1| ribosomal large subunit pseudouridine synthase C [Oceanicola
           granulosus HTCC2516]
          Length = 348

 Score =  250 bits (638), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 129/338 (38%), Positives = 191/338 (56%), Gaps = 22/338 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + VE DE +MRLDRW +  +P +    ++K+ R G++R+D  RVK N RI  GQ
Sbjct: 1   MSGVQTITVEADEADMRLDRWLRARFPQLTQGRIEKMCRKGELRIDGGRVKSNTRIAPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+         E +         + ++ +++ +LY D  + V NKP G+  QGGS
Sbjct: 61  QVRVPPLPPP-----GEVRPAGRDEPSAQDAEMMRAAVLYRDDHLIVLNKPPGLPTQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG   +      +KPRL HRLD++TSGIL++ARTRAAA+ LT++FR R  +KIY
Sbjct: 116 RQTRHVDGLSAALTFGLEEKPRLVHRLDKDTSGILLLARTRAAAKGLTDAFRSRETRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNE----KGANYAISHFKVIDC 235
           W+ V G+P  +   +   L+K+   G     + +  +  +E      A  A++ + VI+ 
Sbjct: 176 WAAVAGVPHPRMGTVKYGLVKQPGHGARGENEKMRCIHPDEVLRTPDAKRAVTDYAVIET 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNK 287
            A++  W+ + P TGRTHQLR H   +G PI GD KY  + + N            I  K
Sbjct: 236 LARRAAWVALVPVTGRTHQLRAHMAELGHPIAGDGKYGGSGQENLGDGWGAGLGGDISRK 295

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
           L LHAR + L HP  G R+  TAPLP HM +TW+ +G+
Sbjct: 296 LQLHARSLSLTHPVSGARMTFTAPLPDHMARTWEYVGW 333


>gi|312114370|ref|YP_004011966.1| pseudouridine synthase [Rhodomicrobium vannielii ATCC 17100]
 gi|311219499|gb|ADP70867.1| pseudouridine synthase, RluA family [Rhodomicrobium vannielii ATCC
           17100]
          Length = 326

 Score =  249 bits (637), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 133/329 (40%), Positives = 199/329 (60%), Gaps = 15/329 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   V  D++ +RLDRW K +YP +    +QK++R+GQVRVD  RVK ++R+ +GQ VR
Sbjct: 3   IEKRAVRTDDDGLRLDRWLKKNYPTLPHTLVQKLVRTGQVRVDGGRVKADSRLSTGQEVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +P       +    Q  L     L+K   DF++ ++++E+ ++++ NKP GI+VQGG+  
Sbjct: 63  VPTHFAEPEN--APQPSLKPPPGLSKADRDFIERMIVFENDEMFILNKPFGIAVQGGTKT 120

Query: 126 AYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             HIDG L    D   G++PRL HRLD++T+GIL VA+ R  A  L   F+ R +QKIYW
Sbjct: 121 TRHIDGLLAGMADRFGGERPRLVHRLDRDTTGILAVAKDRQTAARLGRLFQTRSVQKIYW 180

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFCWL 243
           ++  GIPK  +  +   L+K S   GD V   +  E+  A +A + + VID  A    W+
Sbjct: 181 AITRGIPKPTQGKVEAALVKASGPDGDRVRKARPGEQELAQHATTFYSVIDR-AANMAWV 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQN---KLYLHARYMDLPH 299
            ++P TGR HQLR H   +G PI+GD KY     G+ T  PI+N   KL+LHAR + L  
Sbjct: 240 SLKPVTGRQHQLRAHMDILGTPILGDQKY-----GDGTEIPIENIERKLHLHARRLTLKD 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           P+ G + I+APLP+H+ +T++ LGF   R
Sbjct: 295 PKLGEIDISAPLPSHIAQTFELLGFDAGR 323


>gi|332187840|ref|ZP_08389574.1| pseudouridine synthase, RluA family protein [Sphingomonas sp. S17]
 gi|332012190|gb|EGI54261.1| pseudouridine synthase, RluA family protein [Sphingomonas sp. S17]
          Length = 363

 Score =  249 bits (636), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 127/346 (36%), Positives = 198/346 (57%), Gaps = 10/346 (2%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +  +V+   V  D++ +RLDRWFK H P  +F  + K  R+GQ+RVD  R    +RI +G
Sbjct: 1   MTDFVRQFTVGYDDDGIRLDRWFKRHLPDTSFTTVAKWARTGQLRVDGARATPGDRITAG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           QV+R+PP   A     K  +    ++     + F + +++++D    V NKP G++ QGG
Sbjct: 61  QVLRVPPAEPAPAESAKPSR--PRNILSEDEAAFAREMVIHKDRDALVLNKPPGLATQGG 118

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +    H+DG L +       +P+L HRLD++TSG L+VAR   +A    ++F  R  +KI
Sbjct: 119 TKTTTHVDGLLDALQFEAEGRPKLVHRLDKDTSGALLVARNARSAAFFAKAFSGRTAKKI 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+P  +   I   + K+   GG+ +HV ++N + A    S ++VI+    + CW
Sbjct: 179 YWALVVGVPSIEDGTIELPIAKQPGTGGEKMHVDEENGQAAR---SRYRVIERAGNRCCW 235

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +E+QP TGRTHQLRVH   +G PIVGD KY   A F    T  I  K++LHAR + + HP
Sbjct: 236 VELQPFTGRTHQLRVHMAAIGHPIVGDGKYGGAAAF---LTGGISRKMHLHARRIRVDHP 292

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL 346
           +GGR+  TA LP+H  ++ + LGF   R   + +   +    +++L
Sbjct: 293 DGGRIDQTAELPSHFAESMNQLGFDEIRGDVLPQEEDRGPPPKDVL 338


>gi|163739478|ref|ZP_02146888.1| Pseudouridine synthase, RluD [Phaeobacter gallaeciensis BS107]
 gi|163740271|ref|ZP_02147665.1| ribosomal large subunit pseudouridine synthase C [Phaeobacter
           gallaeciensis 2.10]
 gi|161386129|gb|EDQ10504.1| ribosomal large subunit pseudouridine synthase C [Phaeobacter
           gallaeciensis 2.10]
 gi|161387231|gb|EDQ11590.1| Pseudouridine synthase, RluD [Phaeobacter gallaeciensis BS107]
          Length = 348

 Score =  249 bits (636), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 133/343 (38%), Positives = 196/343 (57%), Gaps = 25/343 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  D+ + R+DRW +  +PH++   ++K+ R G++R+D  RVK N+R+ +GQ
Sbjct: 1   MSGVQMITVSEDDADQRIDRWLRRLFPHVSQGRIEKMCRKGELRLDGGRVKANSRVAAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKIYVFNKPAGISVQG 121
           VVR+PP+  +      + K  ++       +D   ++  ++Y+D  + V NKPAG++VQG
Sbjct: 61  VVRVPPLGAS------DLKPAEAPSYRISEADAKMIRGCVIYKDDAVIVLNKPAGLAVQG 114

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG   +      +KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K
Sbjct: 115 GSGTTKHVDGLSAALQFDAEEKPRLVHRLDKDTSGVLVLARTRLAAQSLTAAFRHRATRK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVI 233
           IYW+LV G+P      I   L+K    G    G+ +  +  NE     GA  + +H+  +
Sbjct: 175 IYWALVAGVPTPYLGEIKCGLVKAPGHGKSGEGEKMIAIHSNEVDSTPGAKRSHTHYATL 234

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQ 285
              A +  W+ M+P TGRTHQLR H   +G PI GD KY  + + N            I 
Sbjct: 235 YRVASRAAWVAMEPITGRTHQLRAHMAEIGHPIAGDGKYGGSSQENLGDGWGAQLGGIIS 294

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            KL+LH R M   HP   + L ITAPLP HM  +WD+ G+  D
Sbjct: 295 KKLHLHCRRMAFEHPTTKKPLSITAPLPDHMKDSWDTFGWSED 337


>gi|326388341|ref|ZP_08209937.1| ribosomal large subunit pseudouridine synthase C [Novosphingobium
           nitrogenifigens DSM 19370]
 gi|326207073|gb|EGD57894.1| ribosomal large subunit pseudouridine synthase C [Novosphingobium
           nitrogenifigens DSM 19370]
          Length = 436

 Score =  249 bits (635), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 128/322 (39%), Positives = 183/322 (56%), Gaps = 14/322 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+  VV  D++ +RLDRWFK H P + F  + +  R+GQ+RVD KR   + R+  GQ +R
Sbjct: 10  VRQFVVGRDDDGVRLDRWFKRHLPQVGFATVSRWARTGQIRVDGKRADVDTRLVPGQTLR 69

Query: 67  IPP--VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +PP       +   + +K L       +     + I+L +D    V NKP G++ QGGSG
Sbjct: 70  VPPGGTQAPGSRGPRTRKPL-----TEEEMALAERIVLTQDRAAIVLNKPPGLATQGGSG 124

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              H+DG L ++      +PRL HRLD++TSG+L++ART  +A + +  F  R  +KIYW
Sbjct: 125 THSHVDGLLDAYAGDNDPRPRLVHRLDKDTSGVLLIARTPGSAAYFSRHFSGRSAKKIYW 184

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV GIP+     I   L K+   GG+ + V +  E     A + ++VID    +  W+E
Sbjct: 185 ALVMGIPEINDGYIDLPLAKQPGTGGEKMMVDESGE--GQTARTRYRVIDRAGNRAAWVE 242

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +QP TGRTHQLRVH   +G PIVGD KY   A F    +  I  KL+LHAR + +PHPEG
Sbjct: 243 LQPLTGRTHQLRVHMAAIGHPIVGDGKYGGQAAF---LSGSISRKLHLHARRLLIPHPEG 299

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
             + + APLP H   +   LGF
Sbjct: 300 DTIDVVAPLPEHFAASLAQLGF 321


>gi|85707668|ref|ZP_01038734.1| pseudouridylate synthase [Erythrobacter sp. NAP1]
 gi|85689202|gb|EAQ29205.1| pseudouridylate synthase [Erythrobacter sp. NAP1]
          Length = 395

 Score =  249 bits (635), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 125/325 (38%), Positives = 193/325 (59%), Gaps = 16/325 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V +D++ +RLDRWFK + P I F  + +  R+GQVRVD  RVK  +R+++GQV+R
Sbjct: 8   VRQFTVSDDDDGIRLDRWFKRNLPKIGFATISRWARTGQVRVDGGRVKPEDRLEAGQVLR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP         K ++ L       +     +++++ E     V NKP G++ QGGS   
Sbjct: 68  VPPGGEDQKRGPKPRRPL-----TEEEIAEARAMVIRETPSAIVLNKPPGLATQGGSKTT 122

Query: 127 YHIDGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            H+DG L ++VD + +   +PRL HRLD++TSG+L++ART  +A   +  F  R  +K+Y
Sbjct: 123 KHVDGLLDAFVDDQEEDAPRPRLVHRLDKDTSGVLLIARTPGSAATYSRKFSGRSARKVY 182

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ ++  I   L K+   GG+ +HV   +E+G   A + ++V++    +  W+
Sbjct: 183 WALVVGVPEVREGTIDAPLAKQPGTGGEKMHV---DEEGGQIAKTRYRVVERAGTRAAWV 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-- 301
           E++P TGRTHQLRVH   +G PIVGD KY        T  I  K++LHAR + +  PE  
Sbjct: 240 ELEPLTGRTHQLRVHLAAIGHPIVGDGKYGGQ-DAFLTGAISRKMHLHARRLIIGTPESK 298

Query: 302 --GGRLQITAPLPAHMVKTWDSLGF 324
             GG+L +TA LP H   + +SLGF
Sbjct: 299 GAGGKLDVTADLPEHFATSMESLGF 323


>gi|163796887|ref|ZP_02190844.1| Pseudouridine synthase, RluD [alpha proteobacterium BAL199]
 gi|159177876|gb|EDP62425.1| Pseudouridine synthase, RluD [alpha proteobacterium BAL199]
          Length = 331

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 125/323 (38%), Positives = 188/323 (58%), Gaps = 8/323 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V  D+ + RLDRWFK ++P +  V+L K+LR+GQVRVD +RVK   R+++GQ
Sbjct: 1   MKAVETRIVAQDDGDQRLDRWFKRYFPTLGHVHLTKLLRTGQVRVDGRRVKAGERLEAGQ 60

Query: 64  VVRIPP--VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            +RIPP  V  A    +K +          + ++ L+ ++L+ D  +   NKPAG++VQG
Sbjct: 61  TIRIPPMDVPAASAEAVKAKP---GGKGDAETAEQLRRLILHTDRDVLAINKPAGLAVQG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSGI  H+DG L   +    ++PRL HRLD++TSG+L+V R+  AA+ LTE+FR +   K
Sbjct: 118 GSGITKHVDGALDGLMFDAKERPRLVHRLDKDTSGVLLVGRSYQAARRLTEAFRAKSAMK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IYW+LV G PK     I   + K     G+ + +  +N K    A + +  ++    K  
Sbjct: 178 IYWALVVGEPKPNAGSIEGAIGKLPGRAGEKMAIDLENGK---RAFTRYVTVERLGGKVT 234

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           W+ + P TGRTHQLRVH   +G PI+GD KY           +  KL+LHAR + +P  +
Sbjct: 235 WVALFPVTGRTHQLRVHMAELGTPILGDGKYGGAEAFLQGEGVSRKLHLHARAIRIPDAK 294

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
           G  +++ APL  HM ++W   G 
Sbjct: 295 GRPVEVIAPLADHMARSWAFFGL 317


>gi|99080132|ref|YP_612286.1| ribosomal large subunit pseudouridine synthase C [Ruegeria sp.
           TM1040]
 gi|99036412|gb|ABF63024.1| ribosomal large subunit pseudouridine synthase C [Ruegeria sp.
           TM1040]
          Length = 348

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 130/341 (38%), Positives = 197/341 (57%), Gaps = 21/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  D+   R+DRW +  +PH+N   ++K+ R G++R+D  RVK N R+++GQ
Sbjct: 1   MSGVQMITVTEDDGGQRIDRWLRRLFPHVNQGRIEKMCRKGELRLDGGRVKANTRVEAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+  +     + + +  S  +    +  ++  ++Y+D  + V NKPAG++VQGGS
Sbjct: 61  VVRVPPLAESDMKPAEARPVKISDAD----AKMIRDCVIYKDDDVLVINKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG  ++       KPRL HRLD++TSG+LV+AR R AAQ LT +FR +  +KIY
Sbjct: 117 GTTKHVDGLSEALRFDAEDKPRLVHRLDKDTSGLLVLARNRKAAQGLTAAFRHKNTRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLK-----KSHIGGDYVHVVKQN---EKGANYAISHFKVIDC 235
           W+LV G+P      I   L+K     KS  G   + V  ++     GA  A +++  +  
Sbjct: 177 WALVAGVPTPYLGEIKTGLVKAPGHGKSGEGEKMIPVDPRDVDATPGAKRAHTYYATLYR 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ M+P TGRTHQLR H   MG PI+GD KY  + + N            I  K
Sbjct: 237 VASRASWVAMEPVTGRTHQLRAHMAGMGHPIIGDGKYGGSGQENLGDGWGAQIGGLISKK 296

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR +   HP  G+ + +TA LP HM ++WD+ G+  D
Sbjct: 297 LHLHARRLQFEHPVTGKVVTVTAALPDHMKESWDTFGWTED 337


>gi|259416795|ref|ZP_05740715.1| ribosomal large subunit pseudouridine synthase C [Silicibacter sp.
           TrichCH4B]
 gi|259348234|gb|EEW60011.1| ribosomal large subunit pseudouridine synthase C [Silicibacter sp.
           TrichCH4B]
          Length = 348

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 130/341 (38%), Positives = 197/341 (57%), Gaps = 21/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  D+   R+DRW +  +PH+N   ++K+ R G++R+D  RVK N R+++GQ
Sbjct: 1   MSGVQMITVTEDDGGQRIDRWLRRLFPHVNQGRIEKMCRKGELRLDGGRVKANTRVEAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+  +     + + +  S  +    +  ++  ++Y+D  + V NKPAG++VQGGS
Sbjct: 61  VVRVPPLAKSDMKPAEARPVKISDAD----AKMIRDCVVYKDDDVLVINKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG  ++       KPRL HRLD++TSG+LV+AR R AAQ LT +FR +  +KIY
Sbjct: 117 GTTKHVDGLSEALRFDAEDKPRLVHRLDKDTSGLLVLARNRKAAQGLTAAFRHKNTRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLK-----KSHIGGDYVHVVKQN---EKGANYAISHFKVIDC 235
           W+LV G+P      I   L+K     KS  G   + V  ++     GA  A +++  +  
Sbjct: 177 WALVAGVPTPYLGEIKTGLVKAPGHGKSGEGEKMIPVDPRDVDATPGAKRAHTYYATLYR 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ M+P TGRTHQLR H   MG PI+GD KY  + + N            I  K
Sbjct: 237 VASRASWVAMEPVTGRTHQLRAHMAGMGHPIIGDGKYGGSGQENLGDGWGAQIGGLISKK 296

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR +   HP  G+ + +TA LP HM ++WD+ G+  D
Sbjct: 297 LHLHARRLQFEHPVTGKVVTVTAALPDHMKESWDTFGWTED 337


>gi|114327246|ref|YP_744403.1| ribosomal large subunit pseudouridine synthase C [Granulibacter
           bethesdensis CGDNIH1]
 gi|114315420|gb|ABI61480.1| ribosomal large subunit pseudouridine synthase C [Granulibacter
           bethesdensis CGDNIH1]
          Length = 366

 Score =  246 bits (629), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 127/323 (39%), Positives = 190/323 (58%), Gaps = 16/323 (4%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP-- 69
           V +DE ++RLDRWF+ HYP +  V +QK+ R+GQ+RVD  R +   R+Q GQ VRIPP  
Sbjct: 39  VTDDEADIRLDRWFRRHYPSLTQVAIQKMCRTGQIRVDGARAEAATRLQPGQSVRIPPLK 98

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V +A     +  + LD           L+S +LY+D  + V NKP+G+  QGG GI  H+
Sbjct: 99  VPSAAEQEGEGPRALDPI-----QQKELESWILYKDDHLIVLNKPSGLPSQGGPGITRHL 153

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           DG L      +  +PRL HRLD++TSG++V+AR+   A  L   FR R  +K+YW++V G
Sbjct: 154 DGLLDGLRFGRDDRPRLVHRLDRDTSGVIVIARSPGVAAKLAALFRTRETEKVYWAVVAG 213

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            P   +  I   LL+++    + V +  + ++    AI+ ++ +D  A+K  WLE++P T
Sbjct: 214 RPVPVEGRIDRPLLRQND-RNEPVVLADRKDRDKVTAITDYRTLDHAARKLAWLELRPLT 272

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCA----NFKG----NFTSPIQNKLYLHARYMDLPHPE 301
           GR HQLRVH   M  PI+GD +Y +    + +G         +  +L+LHAR + LPHP 
Sbjct: 273 GRMHQLRVHCAAMDAPILGDERYGSWRNTDERGVRNTALVEGLSRRLHLHARRLSLPHPA 332

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
           GG L + A L  HM +T+++LGF
Sbjct: 333 GGMLSVEADLSPHMAETFETLGF 355


>gi|89053115|ref|YP_508566.1| ribosomal large subunit pseudouridine synthase C [Jannaschia sp.
           CCS1]
 gi|88862664|gb|ABD53541.1| ribosomal large subunit pseudouridine synthase C [Jannaschia sp.
           CCS1]
          Length = 354

 Score =  246 bits (628), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 126/339 (37%), Positives = 196/339 (57%), Gaps = 18/339 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + +  D+ + RLDRWF+  +PH+    ++K+ R G++RVD  RVK N R++ GQ
Sbjct: 1   MSGVQTLEIGPDDGDQRLDRWFRRIFPHVPQGRIEKMCRKGEIRVDGGRVKSNTRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAGISVQGG 122
           +VR+PP+ +A +        ++++  ++   +  +++ ++Y D  I   NKPAG+  QGG
Sbjct: 61  MVRVPPLPDAADPKADPANWVNNASRISDADEKMIRAAVIYRDDHIIAINKPAGLPTQGG 120

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +G + H+DG  ++       KPRL HRLD++TSG+L++ARTR  A+ LT++FR+R  +KI
Sbjct: 121 TGQSRHVDGLAEALKFGLEDKPRLVHRLDKDTSGVLLMARTRMGAKALTDAFRLRSTRKI 180

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVID 234
           YW+ V G P  +   I   L+K    G     + +  V  +E     GA  A + + V+ 
Sbjct: 181 YWAAVAGSPLPRMGTIKLGLVKAPGHGRGGENEKMRAVPVDEIAQVDGAKRAETDYAVMS 240

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQN 286
               + CW  + P TGRTHQLR H   +G PI+GD KY  + + N            I  
Sbjct: 241 NLGGRVCWCALVPITGRTHQLRAHMAEIGHPIIGDGKYGGSGQENLGDGWGAQLGGEISR 300

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
           KL+LHAR +   HP  G ++ + APLP HM KTWD+LG+
Sbjct: 301 KLHLHARSLSFRHPMTGAQVNLVAPLPEHMAKTWDTLGW 339


>gi|254449547|ref|ZP_05062984.1| ribosomal large subunit pseudouridine synthase C [Octadecabacter
           antarcticus 238]
 gi|198263953|gb|EDY88223.1| ribosomal large subunit pseudouridine synthase C [Octadecabacter
           antarcticus 238]
          Length = 347

 Score =  244 bits (624), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 136/341 (39%), Positives = 195/341 (57%), Gaps = 26/341 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE + RLDRW K  +  +    ++K+ R G++RVD  RVK N R++ GQ
Sbjct: 1   MSRVQNLTVGPDEGDQRLDRWIKRRFAQLQQGGIEKMCRKGEIRVDGGRVKSNTRVEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VRIPP+ +A        ++ D   ++TK     ++  ++Y+D  + V NKPAG+  QGG
Sbjct: 61  TVRIPPLPDA-------DEVDDRPRDMTKADIQLIQGCVIYKDDHVIVLNKPAGLPTQGG 113

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           S    H+DG  ++      ++PRL HRLD++TSG+LV+ARTR AA+ LTE+FR R  +KI
Sbjct: 114 SKQLRHVDGMAEALRFGYDERPRLVHRLDKDTSGVLVLARTRMAAKSLTEAFRHRNTEKI 173

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDY-------VHVVKQNEK-GANYAISHFKVID 234
           YW+LV G+P  K   I   L+K+   GG         VH    ++  GA  A++++ V+ 
Sbjct: 174 YWALVAGVPIPKLGSIKYGLVKQGGHGGKGDNERMKCVHPKDVDKTFGAKRALTNYTVLT 233

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---------NFKGNFTSPIQ 285
             A +  W+ + P TGRTHQLR H   +G PIVGD KY A          +       I 
Sbjct: 234 SLADRTAWVALTPVTGRTHQLRAHIAEIGHPIVGDGKYGAAAVQDNPGDGWGAGMGEEIG 293

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            KL+LHAR + + HPE G+ L I A LP HM KTW   G++
Sbjct: 294 RKLHLHARSLRIEHPETGKELWIKASLPQHMEKTWGFFGWE 334


>gi|114570313|ref|YP_756993.1| ribosomal large subunit pseudouridine synthase C [Maricaulis maris
           MCS10]
 gi|114340775|gb|ABI66055.1| ribosomal large subunit pseudouridine synthase C [Maricaulis maris
           MCS10]
          Length = 330

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 125/327 (38%), Positives = 192/327 (58%), Gaps = 18/327 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + VE  E+  R+DRWFK  +PH++ + +QK+ R GQ+RVD  RVK ++R+  GQ
Sbjct: 1   MSGVQTIKVEATEDGSRVDRWFKRRFPHVSAIMVQKLCRKGQIRVDGGRVKGDSRVHEGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKIYVFNKPAGISVQG 121
            +RIPP+                 VN     D  ++KS+++Y+D ++  FNKPAG++VQG
Sbjct: 61  EIRIPPLPEPGER---------PPVNRMSDEDIAYVKSLVIYQDDELIAFNKPAGLAVQG 111

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GS    H+DG L ++ +    +PRL HRLD++TSGIL+V +   A   L ++F+  + +K
Sbjct: 112 GSKTTRHLDGMLDAFGEGL-DRPRLVHRLDKDTSGILIVGKGPKATARLAKAFQSHKTRK 170

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGD----YVHVVKQNEKGANYAISHFKVIDCFA 237
            YW++  G+PK K   I  ++ K +  G D     +      ++GA +A++ + VI    
Sbjct: 171 TYWAIAIGVPKPKMGEIKGFMRKAAASGVDSERETMVAAGHGDEGAQHALTRYVVIGEAG 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           QK  W+ ++P TGRTHQLRVH   MG  I+GD KY  +        +  +L LHAR +++
Sbjct: 231 QKASWVALRPVTGRTHQLRVHLAAMGTAILGDKKYTCHRPA--PEDLGRRLCLHARRLEI 288

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGF 324
           P P G  L +TA LP  + K +D+LGF
Sbjct: 289 PRPGGKPLVLTADLPPALKKIYDTLGF 315


>gi|46201801|ref|ZP_00054336.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 324

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 130/324 (40%), Positives = 197/324 (60%), Gaps = 14/324 (4%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +E  +RLDRWFK H+P +    L+K LR+G VRVD KR K N R+++GQ +R+PP
Sbjct: 1   MTVAEEESEIRLDRWFKRHFPTVGHGLLEKWLRAGNVRVDGKRAKSNQRLEAGQAIRVPP 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            + A    ++E K +   V   K +  L+  +LY D  +   NKP G++VQGG+G+A   
Sbjct: 61  -LPADEAPVREAKPV---VVDEKIARMLRDAVLYMDDDVIALNKPPGLAVQGGTGMA--- 113

Query: 130 DGFLKSWVDS---KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           D  L +W+D+      +P+L HRLD++TSG+L++ RT  AA  L  +F+ R  +K YW+L
Sbjct: 114 DKHLDAWLDALCFGAGRPKLVHRLDKDTSGVLLLGRTANAASKLAAAFKSRSARKCYWAL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+P+  +  I   L K     G+ + V K+  K   +A+++++V+D   ++  WLEM+
Sbjct: 174 VAGVPRYPQGRIDAPLAKLPGKAGEKMAVDKEEGK---HAVTYYRVVDSTLKRAAWLEME 230

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           P TGRTHQLR H L +G PI+GD KY         + +  KL+LHAR + LPHP  G+ L
Sbjct: 231 PRTGRTHQLRAHCLLLGTPIMGDGKYGGQDALIEGTGVSRKLHLHARAVRLPHPRTGKML 290

Query: 306 QITAPLPAHMVKTWDSLGFKYDRN 329
           ++ APLP H+  ++D  GF   R+
Sbjct: 291 EVAAPLPPHIKASFDFFGFTESRS 314


>gi|144899540|emb|CAM76404.1| ribosomal large subunit pseudouridine synthase C [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 333

 Score =  243 bits (621), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 132/323 (40%), Positives = 188/323 (58%), Gaps = 7/323 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  VQ + V  D+ ++RLDRWFK HYP +    L+K LR+GQVRVD KR K N R+  G 
Sbjct: 1   MNSVQILAVAEDDADIRLDRWFKRHYPTVGHGLLEKWLRTGQVRVDGKRAKANQRLSPGL 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PPV        K            K +  L+  +LY D  +   NKPAGI+VQGG+
Sbjct: 61  HIRVPPVPE--GEAPKANPENRRPAVDEKIARMLRDAVLYMDDDVIALNKPAGIAVQGGT 118

Query: 124 GIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    HID +L + +  +  +PRL HRLD++TSG+L++ R+  AA  L  +F+ R  +K 
Sbjct: 119 GTGDKHIDAWLDALMFDRDDRPRLVHRLDKDTSGVLLLGRSANAAAKLAAAFKSRAARKC 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK ++  I   L K     G+ + V   +E     A++ ++V+D   +K  W
Sbjct: 179 YWALVVGVPKLRQGRIDAALAKLPGRAGEKMAV---DEDEGKRAVTWYRVVDNALRKAAW 235

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           LEM+P TGRTHQLR H   MG PI+GD KY         + +  K++LHAR + +PHP  
Sbjct: 236 LEMEPRTGRTHQLRAHTALMGTPIMGDGKYGGTEAFISGTGVSRKMHLHARAVRIPHPRT 295

Query: 303 GR-LQITAPLPAHMVKTWDSLGF 324
           G+ L + APLP HM K+++  GF
Sbjct: 296 GKELVVVAPLPEHMEKSFEFFGF 318


>gi|254476979|ref|ZP_05090365.1| pseudouridine synthase, RluD [Ruegeria sp. R11]
 gi|214031222|gb|EEB72057.1| pseudouridine synthase, RluD [Ruegeria sp. R11]
          Length = 348

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 129/343 (37%), Positives = 195/343 (56%), Gaps = 25/343 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  D+   R+DRW +  +PH++   ++K+ R G++R+D  RVK ++R+++GQ
Sbjct: 1   MSGVQMITVTEDDAGQRIDRWLRRLFPHVSQGRIEKMCRKGELRLDGGRVKASSRVEAGQ 60

Query: 64  VVRIPPVINA--LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            VR+PP+  +         ++I D+   +      ++  ++Y+D  + V NKPAG++VQG
Sbjct: 61  TVRVPPLPASDLKPAEAPSRRISDADAKM------IRGCVIYKDDAVIVLNKPAGLAVQG 114

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG  ++      +KPRL HRLD++TSG+LV+ARTR AAQ LT +FR    +K
Sbjct: 115 GSGTTKHVDGLSEALKFDAEEKPRLVHRLDKDTSGVLVLARTRQAAQALTAAFRHHATRK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVI 233
           IYW+LV G+P      I   L+K    G    G+ +  +  NE     GA  + + +  +
Sbjct: 175 IYWALVAGVPTPYLGEIKCGLVKAPGHGKSGEGEKMIAIHSNEVDSTPGAKRSHTQYATL 234

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQ 285
              A +  W+ M+P TGRTHQLR H   +G PI GD KY  + + N            I 
Sbjct: 235 YRVASRAAWVAMEPITGRTHQLRAHMAEIGHPIAGDGKYGGSGQENLGDGWGAQLGGIIS 294

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            KL+LH R M   HP   + L ITAPLP HM ++WD+ G+  D
Sbjct: 295 KKLHLHCRRMAFEHPTTKKPLSITAPLPEHMKESWDTFGWSED 337


>gi|148555622|ref|YP_001263204.1| ribosomal large subunit pseudouridine synthase C [Sphingomonas
           wittichii RW1]
 gi|148500812|gb|ABQ69066.1| ribosomal large subunit pseudouridine synthase C [Sphingomonas
           wittichii RW1]
          Length = 368

 Score =  243 bits (619), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 123/326 (37%), Positives = 190/326 (58%), Gaps = 6/326 (1%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS     +   V  D+  +RLDRWFK H P  +F  + +  R+GQ+RVD KR    +RI+
Sbjct: 1   MSGADDSRQFTVGEDDHGIRLDRWFKRHMPDTSFNIVSRWARTGQLRVDGKRAAPGDRIE 60

Query: 61  SGQVVRIPPVINALNHIIKE-QKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGIS 118
           +GQV+R+PP   A      + Q+       LT+    F +S+++++D +  V NKP G++
Sbjct: 61  AGQVIRLPPAEIAAAATAAKAQRPARPRAPLTEEEIAFARSLVIHQDRQAIVINKPPGLA 120

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            QGG+    H+D  L +       +P+L HRLD++TSG+L++ART  AA H  ++F  R 
Sbjct: 121 TQGGTKTDIHVDRLLDALQFDAESRPKLVHRLDKDTSGVLLLARTSRAAAHFAKAFSSRT 180

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            +K+YW++  G+P      I   + K+   GG+ +HV   +EK  + A + ++VI+    
Sbjct: 181 ARKVYWAIATGVPSIDDGMIELPIAKQPGTGGEKMHV---DEKEGSPARTRYRVIERAGN 237

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           + CW+E+QPHTGRTHQLRVH   +G PIVGD KY    +   +  I  K++LHAR + + 
Sbjct: 238 RACWVELQPHTGRTHQLRVHLAAIGHPIVGDGKY-GGAEAFLSGTISRKMHLHARRLRVD 296

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGF 324
           HP+GG L + A  P H+  +  +LGF
Sbjct: 297 HPDGGTLDVIAEPPEHITDSLRNLGF 322


>gi|85373096|ref|YP_457158.1| pseudouridylate synthase [Erythrobacter litoralis HTCC2594]
 gi|84786179|gb|ABC62361.1| pseudouridylate synthase [Erythrobacter litoralis HTCC2594]
          Length = 399

 Score =  242 bits (618), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 126/339 (37%), Positives = 193/339 (56%), Gaps = 17/339 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   VE D+E +RLDRWFK + P + F  + +  R+GQ+RVD KR +  +R+ +GQV+R
Sbjct: 10  VRQFTVEADDEGVRLDRWFKRNLPQVGFGTISRWARTGQLRVDGKRARPEDRLAAGQVLR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP         + +K L       +     + +++ E     V NKP G++ QGG+   
Sbjct: 70  IPPGGEDPERNPRARKPLSP-----EQVRMAQDMVIKETKSAIVLNKPPGLATQGGTKTT 124

Query: 127 YHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            H+DG L ++VD +   +PRL HRLD++TSG+L++ART  +A   ++ F  R  +K+YW+
Sbjct: 125 KHVDGLLDAFVDGEDDPRPRLVHRLDKDTSGVLLIARTPGSAAAYSKRFAGRSAKKVYWA 184

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G+P   +  I   L K+   GG+ +HV ++N      A + ++V++    + CW+E+
Sbjct: 185 LVVGVPDLHEGEIDAPLAKQPGTGGEKMHVDEEN---GQPAKTRYRVVERAGNRACWVEL 241

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP----- 300
           +P TGRTHQLRVH   MG PIVGD KY        T  +  K++LHAR + +  P     
Sbjct: 242 EPMTGRTHQLRVHMAAMGHPIVGDGKYGGQ-DAFLTGSVSRKMHLHARRLIIAQPAENGK 300

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQD 339
            GG+L +TA LP H   + + LGF  D +L   R   +D
Sbjct: 301 SGGKLDVTADLPEHFAASMEQLGF--DISLSKARPLRED 337


>gi|260432477|ref|ZP_05786448.1| ribosomal large subunit pseudouridine synthase C [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260416305|gb|EEX09564.1| ribosomal large subunit pseudouridine synthase C [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 347

 Score =  242 bits (617), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 132/342 (38%), Positives = 196/342 (57%), Gaps = 24/342 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + VE  + + RLDRW +  +PH++   ++K+ R G++RVD  RVK + R+Q+GQ
Sbjct: 1   MSGVQMITVEPGDGDQRLDRWLRRLFPHVSQGRIEKMCRKGELRVDGGRVKGSTRLQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQ-KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           VVR+PP+ +  +     + ++ D+   +      ++S ++Y D  +   NKP G+ VQGG
Sbjct: 61  VVRVPPLPDPDHKPAPTRPRVTDADAKM------IQSCVIYRDDHVLALNKPHGLPVQGG 114

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG A H+DG  ++      + PRL HRLD++TSG+L++ARTR AA+ LT +FR R  +KI
Sbjct: 115 SGQARHVDGLAEALRFGYDENPRLVHRLDKDTSGVLLMARTREAAKGLTAAFRHRNTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVID 234
           YW+LV G+P      I   L+K    G    G+ +  V  NE     GA  A + +  + 
Sbjct: 175 YWALVAGVPTPYLGEIKTGLVKAPGHGKQGEGEKMIAVHLNEIDSTPGAKRAHTLYATLF 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQN 286
             A +  W+ M+P TGRTHQLR H   +G PI+GD KY  + + N            I  
Sbjct: 235 RVASRASWVAMEPVTGRTHQLRAHMAAIGHPIIGDGKYGGSGQENLGDGWGAQLGGVISK 294

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           KL+LHAR     HP  G+ + I APLP HM  +WD+LG+  D
Sbjct: 295 KLHLHARTASFKHPMTGKQVTINAPLPPHMKDSWDTLGWTED 336


>gi|84685385|ref|ZP_01013283.1| ribosomal large subunit pseudouridine synthase C [Maritimibacter
           alkaliphilus HTCC2654]
 gi|84666542|gb|EAQ13014.1| ribosomal large subunit pseudouridine synthase C [Rhodobacterales
           bacterium HTCC2654]
          Length = 350

 Score =  242 bits (617), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 130/341 (38%), Positives = 192/341 (56%), Gaps = 22/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRWFK  +PH+    ++K+ R G++RVD  RVK + R++ GQ
Sbjct: 1   MSRVQTITVAEGDGDQRLDRWFKRQFPHVPQGRVEKMCRKGEIRVDGGRVKASTRVEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+ +       E+          K +  ++  ++Y D  I   NKP G+  QGGS
Sbjct: 61  EVRIPPLPDP-----GERPAAPRPSVTDKDAQMIRDCVIYRDDHIIALNKPPGLPTQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  +        KPRL HRLD++TSG+L++ARTR  A+ LT++FR R  +KIY
Sbjct: 116 KQTRHVDGLAEVLTFGYDDKPRLVHRLDKDTSGVLLLARTRQVAKDLTDAFRHRNTRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W++V G+P  +K  +   L+K    G    G+ +  +  +E    +GA  A + + VI+ 
Sbjct: 176 WAVVAGVPLPRKGTVKWGLVKAPGHGGQGEGEKMLCIHPSEVAKVEGAKRAETDYVVIEN 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNK 287
            AQ+  W+ + P TGRTHQLR H   MG PIVGD KY  + + N            I  K
Sbjct: 236 LAQRAAWVGLTPITGRTHQLRAHMAEMGHPIVGDGKYGGSGQENLGDGWGAMLGGEISKK 295

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR +++ HP   + + I A LP HM +TW+ LGF+ D
Sbjct: 296 LHLHARSIEIEHPVTKKPIFIEAALPEHMARTWEQLGFRVD 336


>gi|254466117|ref|ZP_05079528.1| pseudouridine synthase, RluD [Rhodobacterales bacterium Y4I]
 gi|206687025|gb|EDZ47507.1| pseudouridine synthase, RluD [Rhodobacterales bacterium Y4I]
          Length = 348

 Score =  242 bits (617), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 128/341 (37%), Positives = 199/341 (58%), Gaps = 21/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  D+   R+DRW +  +PH+N   ++K+ R G++R+D  RVK ++R+++GQ
Sbjct: 1   MSGVQMITVSEDDGGQRIDRWLRRLFPHVNQGRIEKMCRKGELRLDGARVKASSRVEAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+ ++     + + +  S  +    +  ++S ++Y D  + V NKPAG++VQGGS
Sbjct: 61  VVRVPPLADSDLKPAEPRAMKISDAD----AKMIQSCVIYRDDDVIVLNKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG  ++      +KP+L HR+D++TSG+LV+AR R AAQ LT +FR +  +KIY
Sbjct: 117 GTTKHVDGLAEALKFGLEEKPKLVHRIDKDTSGVLVLARNRKAAQGLTAAFRHKNTRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLK-----KSHIGGDYVHVVKQ---NEKGANYAISHFKVIDC 235
           W+LV G+P      I N L+K     KS  G   ++V  +   +  GA  A + +  +  
Sbjct: 177 WALVAGVPTPYLGEIKNGLVKAPGHGKSGEGEKMINVHPRDIDDTPGAKRAHTLYATLYR 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ M+P TGRTHQLR H   MG PI GD KY  + + N            I  K
Sbjct: 237 VASRAAWVAMEPITGRTHQLRAHMSGMGHPIAGDGKYGGSGQENMGDGWGAQIGGVISKK 296

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR M   HP   + + + APLP HM ++W++ G+  D
Sbjct: 297 LHLHARRMVFEHPVTRKPVSVVAPLPEHMKESWETFGWSED 337


>gi|254459621|ref|ZP_05073037.1| pseudouridine synthase, RluA family [Rhodobacterales bacterium
           HTCC2083]
 gi|206676210|gb|EDZ40697.1| pseudouridine synthase, RluA family [Rhodobacteraceae bacterium
           HTCC2083]
          Length = 347

 Score =  241 bits (614), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 126/341 (36%), Positives = 198/341 (58%), Gaps = 24/341 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ +++E D+ + RLDR+ K  +P +    ++K+ R G++R+D  RVK N+R+++G 
Sbjct: 1   MSRVQTIIIEEDDGDQRLDRFLKRKFPQVTQGMIEKMCRKGELRLDGGRVKANSRVETGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+ ++       +    S V+    + F++S ++Y+D  +   NKPAG+ VQGG+
Sbjct: 61  QLRIPPLPDS----AAPKHAAPSKVSAAD-TKFIRSCVIYKDDHVIALNKPAGLPVQGGT 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G A H+DG L + +    ++P+L HRLD++TSG+L++ RTR A   LT SFR R  +KIY
Sbjct: 116 GHARHVDGLLDALMYDFEERPKLVHRLDKDTSGVLILGRTRRATADLTASFRHRNTRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+ + G+P  +   I   L+K    G    G+ +  +   E    +GA  A++ + V++ 
Sbjct: 176 WAAIAGVPNPRMGTIKYGLMKAPGHGARGEGEKMICIHPREVDQTEGAKRALTDYAVLET 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNK 287
             Q+  W  + P TGRTHQLR H   MG P+VGD KY  + + N            +  K
Sbjct: 236 AGQRTSWCALIPITGRTHQLRAHMSEMGHPVVGDGKYGGSGQENLGDGWGSQLGGDLSKK 295

Query: 288 LYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR + + HP     L ITAPLP HM +TWD+  F +D
Sbjct: 296 LHLHARSLQIEHPSTKATLHITAPLPDHMQRTWDT--FAWD 334


>gi|254436973|ref|ZP_05050467.1| pseudouridine synthase, RluA family [Octadecabacter antarcticus
           307]
 gi|198252419|gb|EDY76733.1| pseudouridine synthase, RluA family [Octadecabacter antarcticus
           307]
          Length = 347

 Score =  241 bits (614), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 132/341 (38%), Positives = 195/341 (57%), Gaps = 26/341 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE + RLDRW K  + H+    ++K+ R G++RVD  RVK N R++ GQ
Sbjct: 1   MSRVQNLTVGLDEGDQRLDRWIKRRFAHLQQGGIEKMCRKGEIRVDGGRVKTNTRVEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +RIPP+ +A        ++ +   ++TK     ++  ++Y+D  +   NKPAG+  QGG
Sbjct: 61  KIRIPPLPDA-------NEVDERPRDMTKADIQLIQGCVIYKDDHVIALNKPAGLPTQGG 113

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           S    H+DG  ++      +KPRL HRLD++TSG+L++ARTR AA+ LT++FR R  +KI
Sbjct: 114 SKQLRHVDGMAEALRFGYDEKPRLVHRLDKDTSGVLILARTRMAAKSLTDAFRHRNTEKI 173

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDY-------VHVVKQNEK-GANYAISHFKVID 234
           YW+LV G+P  K   +   L+K+   GG         VH    ++  GA  A++++ V+ 
Sbjct: 174 YWALVAGVPIPKLGSVKYGLVKQGGHGGKGDNERMKCVHPKDVDKTFGAKRALTNYTVLT 233

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---------NFKGNFTSPIQ 285
             A +  W+ + P TGRTHQLR H   +G PIVGD KY A          +       I 
Sbjct: 234 SLADRTAWVALTPVTGRTHQLRAHMAEIGHPIVGDGKYGAQAVQDNPGDGWGAGMGEEIG 293

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            KL+LHAR + + HPE G+ L I A LP HM KTW   G++
Sbjct: 294 RKLHLHARSLRIEHPETGKELWIKASLPPHMGKTWSFFGWE 334


>gi|56695430|ref|YP_165778.1| ribosomal large subunit pseudouridine synthase C [Ruegeria pomeroyi
           DSS-3]
 gi|56677167|gb|AAV93833.1| ribosomal large subunit pseudouridine synthase C [Ruegeria pomeroyi
           DSS-3]
          Length = 347

 Score =  240 bits (613), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 132/342 (38%), Positives = 193/342 (56%), Gaps = 24/342 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRWF+  +PH+    ++K+ R G++RVD  R K   R++ GQ
Sbjct: 1   MSGVQMITVGEGDGDQRLDRWFRRMFPHVGQGRIEKMCRKGELRVDGARAKPATRLEVGQ 60

Query: 64  VVRIPPVINALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VRIPP+          + ++ DS   L      +++ +L+ D  I V NKPAG++VQGG
Sbjct: 61  QVRIPPLPAPGERPEPVKSRVSDSDAKL------IRACVLHRDDDIIVLNKPAGLAVQGG 114

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   H+DG  ++      + PRL HRLD++TSG+LV+ARTR AA  LT +FR R  +KI
Sbjct: 115 SGQTRHVDGLSEALRFGNDENPRLVHRLDKDTSGVLVLARTREAAARLTAAFRHRNTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVID 234
           YW+LV G+P      I   L+K    G    G+ ++VV  +E     GA  A +++  + 
Sbjct: 175 YWALVAGVPTPYLGEIKTGLVKAGGHGARGEGEKMNVVHLSELDATPGAKRAHTYYATLY 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQN 286
             A +  W+ M+P TGRTHQLR H   +G PI+GD KY  + + N            I  
Sbjct: 235 RVAGRASWVAMEPVTGRTHQLRAHMAGIGHPIIGDGKYGGSGQENLGDGWGAQLGGIISK 294

Query: 287 KLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
           KL+LHAR +   HP    ++  TAPLP HM ++WD+ G+  D
Sbjct: 295 KLHLHARSLSFEHPSTRKKVTFTAPLPEHMRESWDTFGWTED 336


>gi|83854943|ref|ZP_00948473.1| ribosomal large subunit pseudouridine synthase C [Sulfitobacter sp.
           NAS-14.1]
 gi|83941466|ref|ZP_00953928.1| ribosomal large subunit pseudouridine synthase C [Sulfitobacter sp.
           EE-36]
 gi|83842786|gb|EAP81953.1| ribosomal large subunit pseudouridine synthase C [Sulfitobacter sp.
           NAS-14.1]
 gi|83847286|gb|EAP85161.1| ribosomal large subunit pseudouridine synthase C [Sulfitobacter sp.
           EE-36]
          Length = 349

 Score =  240 bits (612), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 133/338 (39%), Positives = 192/338 (56%), Gaps = 25/338 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ++VVE  + + RLDRWFK  +P I    ++K+ R G +RVD  RVK + R++ GQ
Sbjct: 1   MSRVQHLVVEEGDGDQRLDRWFKRTFPLIGQGLIEKMCRKGDIRVDGGRVKASTRLEVGQ 60

Query: 64  VVRIPPVINA-LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VRIPP+ +       K  +I ++         F++S ++Y D  I   NKP G+ VQGG
Sbjct: 61  TVRIPPLPDEKAPPPPKRTRISEADTK------FIRSCVIYRDDHIIALNKPPGLPVQGG 114

Query: 123 SGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           SG +  H+D    + +    +KPRL HRLD++TSG+L++ARTR+ A  LT SFR R  +K
Sbjct: 115 SGQSDRHVDALADALMFELDEKPRLVHRLDKDTSGVLIMARTRSIAAALTASFRHRETRK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVV----KQNEKGANYAISHFKVI 233
           IYW+ V G+P  +   I   L+K    G    G+ ++ V     +  +GA  A + +  +
Sbjct: 175 IYWAAVAGVPHPRNGTIKFGLVKAFGHGARGEGEKMYCVHPKDMETTEGAKRATTDYATL 234

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQ 285
               ++ CW+ + P TGRTHQLR H   +G PIVGD KY  + + N            I 
Sbjct: 235 AQAGKRTCWMALIPVTGRTHQLRAHMAEIGHPIVGDGKYGGSGQENMGDGWGAQLGGDIS 294

Query: 286 NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            KL+LHAR + L HP    RL +TAPLP HM +TWD+ 
Sbjct: 295 KKLHLHARSLTLEHPVTKARLNLTAPLPDHMARTWDTF 332


>gi|149913096|ref|ZP_01901630.1| hypothetical protein RAZWK3B_03870 [Roseobacter sp. AzwK-3b]
 gi|149813502|gb|EDM73328.1| hypothetical protein RAZWK3B_03870 [Roseobacter sp. AzwK-3b]
          Length = 348

 Score =  240 bits (612), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 129/336 (38%), Positives = 188/336 (55%), Gaps = 25/336 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRW + H+PH++   ++K+ R G++RVD  RVK + R++ GQ
Sbjct: 1   MSGVQTLTVTEGDADQRLDRWLRRHFPHVSQGRIEKLCRKGELRVDGGRVKASTRLEVGQ 60

Query: 64  VVRIPPVINA--LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            VRIPP+ +   ++      +I D+   +      ++S ++Y D  I   NKP G+ VQG
Sbjct: 61  QVRIPPLPDPGQIDSASPHSRISDADARM------IQSAVIYRDDHIIALNKPPGLPVQG 114

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GS    H+DG   +      +KPRL HRLD++TSG+L++AR+RA A+ LT  FR R  +K
Sbjct: 115 GSKQTRHVDGLADALRFGAEEKPRLVHRLDKDTSGVLILARSRAVAKTLTAGFRHRDTRK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVK----QNEKGANYAISHFKVI 233
           IYW+ V G+P  +   I   L+K    G    G+ +  +      +  GA  A + F VI
Sbjct: 175 IYWAAVAGVPSPRMGTIRFGLVKAPGHGAQGEGEKMLCLHPEAVDSTPGAKRATTDFAVI 234

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQ 285
           +    +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            I 
Sbjct: 235 ESAGARCAWVALVPVTGRTHQLRAHMAEIGHPIVGDGKYGGSGQENMGDGWGAQLGGEIS 294

Query: 286 NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
            KL+LHAR + L HP    RL +TAPLP HM +TWD
Sbjct: 295 RKLHLHARSLTLEHPVSRARLHLTAPLPDHMKRTWD 330


>gi|16126223|ref|NP_420787.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus CB15]
 gi|221234996|ref|YP_002517432.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus NA1000]
 gi|13423445|gb|AAK23955.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus CB15]
 gi|220964168|gb|ACL95524.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus NA1000]
          Length = 331

 Score =  240 bits (612), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 127/322 (39%), Positives = 185/322 (57%), Gaps = 12/322 (3%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V+  E+ +RLDRWFK  +PH+N + L K+ RSGQVRVD  R K + ++ +G  +R
Sbjct: 6   VRTLYVDAGEDGVRLDRWFKRRWPHLNHIQLNKLFRSGQVRVDGSRAKADTKLAAGSQIR 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+ +A +   K  K+    V       + KS++LYED ++   NKPAG++VQGG+   
Sbjct: 66  VPPLPDAPDPSDK-NKLSARDVA------YAKSLVLYEDEEVLALNKPAGLAVQGGTKTT 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            HID  L +W +    +PRL HRLD++TSG+L++ +T +AA  L+ +F  R+ QK YW++
Sbjct: 119 KHIDKLLSAWGEGV-DRPRLVHRLDRDTSGVLLLGKTPSAAARLSGAFAKRKAQKTYWAI 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G P +  E +    L K  +G   + V  Q  +  A  A + F  I     +  W+ +
Sbjct: 178 VAGNP-HPTEGVMELHLAKRGVGDRELVVPAQPKDPDAQPAETEFVTISRAGPRVTWMAL 236

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +PHTGRTHQLR H   MG PI+GD KY        +  +  KL LHAR + LPHP  G L
Sbjct: 237 RPHTGRTHQLRAHMKAMGHPILGDPKYGDEKSAPLSEGL--KLQLHARSILLPHPSAGML 294

Query: 306 QITAPLPAHMVKTWDSLGFKYD 327
            I APL   M + +   GF  D
Sbjct: 295 HIEAPLSPEMKEGFRKFGFSED 316


>gi|126737039|ref|ZP_01752774.1| ribosomal large subunit pseudouridine synthase C [Roseobacter sp.
           SK209-2-6]
 gi|126721624|gb|EBA18327.1| ribosomal large subunit pseudouridine synthase C [Roseobacter sp.
           SK209-2-6]
          Length = 348

 Score =  239 bits (610), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 128/345 (37%), Positives = 195/345 (56%), Gaps = 29/345 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  ++++ R+DRW +  +PH+N   ++K+ R G++R+D  RVK + R+ +GQ
Sbjct: 1   MSGVQMITVTEEDDDQRIDRWLRRLFPHVNQGRIEKMCRKGELRLDGGRVKASTRVATGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSD----FLKSILLYEDSKIYVFNKPAGISV 119
           VVR+PP        +    +  +    TK SD     ++  ++Y+D  + V NKPAG++V
Sbjct: 61  VVRVPP--------LPASDLKPAEPRATKISDADAKMIRGCVIYKDDDVIVLNKPAGLAV 112

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           QGGSG   H+DG  ++      +KPRL HRLD++TSG+LV+AR R AAQ LT +FR +  
Sbjct: 113 QGGSGTTRHVDGLSEALRLEAEEKPRLVHRLDKDTSGVLVLARNRKAAQALTAAFRHKNT 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIG--GDYVHVVK------QNEKGANYAISHFK 231
           +KIYW+LV G+P      I   L+K    G  G+   ++        +  GA  A +H+ 
Sbjct: 173 RKIYWALVAGVPTPYLGEIKTGLVKAPGHGRSGEGEKMIPVHPRDIDDTPGAKRAHTHYA 232

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-------- 283
            +   A +  W+ M+P TGRTHQLR H   +G PI GD KY  + + N            
Sbjct: 233 TLYRVASRASWVAMEPITGRTHQLRAHMAAIGHPIAGDGKYGGSGQENLGDGWGAQLGGI 292

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           I  KL+LHAR +   HP   + + + A LP HM ++WD+LG+  D
Sbjct: 293 ISKKLHLHARRLVFEHPVSHKPISVEAELPEHMKESWDTLGWTED 337


>gi|126724897|ref|ZP_01740740.1| Pseudouridine synthase, RluD [Rhodobacterales bacterium HTCC2150]
 gi|126706061|gb|EBA05151.1| Pseudouridine synthase, RluD [Rhodobacterales bacterium HTCC2150]
          Length = 347

 Score =  238 bits (608), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 129/339 (38%), Positives = 188/339 (55%), Gaps = 24/339 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  +E   RLDRW + H+P ++   ++K+ R G++RVD  RVK N R+  GQ
Sbjct: 1   MSAVQTIAVGENEAEQRLDRWMRRHFPDLSQGQVEKMCRKGEIRVDGGRVKANTRVTQGQ 60

Query: 64  VVRIPPVINALNHII-KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           ++RIPP+ +    +   E KI D+   L      +  +++Y+D  I   NKP GI VQGG
Sbjct: 61  LIRIPPLKDGPKKVYYDEPKISDADRKL------MMDMVIYKDDYIIALNKPPGIPVQGG 114

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   HIDG  ++      +KPRL HRLD++TSG+L++AR + +A  LT  FR R  +KI
Sbjct: 115 SGQKRHIDGLSEALRFDSDEKPRLVHRLDKDTSGVLLLARNQRSASELTAVFRSRESRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKK----SHIGGDYVHVVKQNE----KGANYAISHFKVID 234
           YW+ V G+P  K   I   L+K        GG+ +  +   +     GA  A + + V+ 
Sbjct: 175 YWAAVGGVPHPKMGTIRFGLVKAPGHGPSGGGEKMICIHPRDIDKTDGAKRATTDYAVMT 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQN 286
             A++  W+ + P TGRTHQLR H   +G PI+GD KY  + + N            I  
Sbjct: 235 TLARRSAWMALVPVTGRTHQLRAHMAELGHPIIGDGKYGGSGQENLGDGWGAQLGGDISK 294

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
            L+LHAR + L HP  G RL + A LP HM  TW ++G+
Sbjct: 295 NLHLHARSLTLKHPVTGARLHLVAELPRHMAATWKTVGW 333


>gi|56551335|ref|YP_162174.1| RluA family pseudouridine synthase [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241760988|ref|ZP_04759077.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|260753046|ref|YP_003225939.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis NCIMB
           11163]
 gi|56542909|gb|AAV89063.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241374607|gb|EER64068.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|258552409|gb|ACV75355.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
          Length = 374

 Score =  237 bits (605), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 126/341 (36%), Positives = 203/341 (59%), Gaps = 12/341 (3%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+  VV++D++ +RLDRWF+ H P   F  + +  R+GQ+R+D +R    +R+ +GQ +R
Sbjct: 5   VRNFVVDDDDDGIRLDRWFQRHLPDTGFARIARWTRTGQIRLDGRRATPGSRVMAGQSIR 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PP   A  ++   +    S   LT+   +F +S++++ D    V NKPAG++ QGG+  
Sbjct: 65  VPP---AEPNLQDNRPTKPSRPELTEAEIEFAQSLVIHRDKAAIVVNKPAGLATQGGTKT 121

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            YH+DG L +       +P+L HRLD++TSG+L++AR+   A + +++F  R   K+YW+
Sbjct: 122 HYHLDGLLDALQFEAPSRPKLVHRLDKDTSGVLLLARSANNAGYFSKAFSGRTAHKVYWA 181

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G+P   +  I   L ++   GG+ +HV ++N  GA  A + ++VI+      CWLE+
Sbjct: 182 LVVGVPSITEGLIDLPLARQPGSGGEKMHVDEEN--GAT-AKTLYRVIERAGNAACWLEL 238

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QP TGRTHQLR H   +G PIVGD KY    +   T  +  K++LHAR + +PHP+G  L
Sbjct: 239 QPLTGRTHQLRAHLSAIGFPIVGDGKYGGK-EAFLTGGVSRKMHLHARRLVIPHPDGSNL 297

Query: 306 QITAPLPAHMVKTWDSLGFK----YDRNLYIKRLYSQDECK 342
            + A LP H +++   LGF     YDR L  +++  ++  K
Sbjct: 298 DVHADLPEHFLESMSLLGFDLENGYDRPLGGEKVIDKEAEK 338


>gi|84499811|ref|ZP_00998099.1| ribosomal large subunit pseudouridine synthase C [Oceanicola
           batsensis HTCC2597]
 gi|84392955|gb|EAQ05166.1| ribosomal large subunit pseudouridine synthase C [Oceanicola
           batsensis HTCC2597]
          Length = 347

 Score =  237 bits (605), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 128/342 (37%), Positives = 193/342 (56%), Gaps = 24/342 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  ++   RLDRW +  +P +    ++K+ R G +RVDK RVK + R+++GQ
Sbjct: 1   MSGVQMLTVAPEDAGQRLDRWLRRLFPQVTQGRIEKMCRKGDLRVDKGRVKSSTRLEAGQ 60

Query: 64  VVRIPPVI-NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           VVR+PP+  +A         + ++   L      ++  +L+ D  I   NKPAG+  QGG
Sbjct: 61  VVRVPPLPESAAPEPAPRDAVSEADARL------IRDCVLWSDDHIVALNKPAGLPTQGG 114

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           S  + H+DG  ++ V +  +KPRL HRLD++TSG+L++ARTR AAQ LT + R ++ +KI
Sbjct: 115 SKQSRHVDGLSQALVPAGAEKPRLVHRLDKDTSGVLLLARTRVAAQGLTAALRHKQTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGD-------YVHVVK-QNEKGANYAISHFKVID 234
           YW+LV G+P      I   L+K    G          VH  + +   GA  A + +  + 
Sbjct: 175 YWALVAGVPTPYLGEIRYGLVKAPGHGKGGEGEKMIAVHPAEVEGTPGAKRAHTLYATLY 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQN 286
             A +  W+ ++P TGRTHQLR H   +G PI+GD KY  + + N            I  
Sbjct: 235 RVASRASWVALEPLTGRTHQLRAHLAEIGHPIIGDGKYGGSGQENLGDGWGAQLGGIISR 294

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           KL+LHAR M   HP  G+ + +TAPLP HM ++WD+LG+  D
Sbjct: 295 KLHLHARSMTFEHPVTGKPVTVTAPLPDHMAESWDTLGWAED 336


>gi|310816979|ref|YP_003964943.1| RluA family pseudouridine synthase [Ketogulonicigenium vulgare Y25]
 gi|308755714|gb|ADO43643.1| RluA family pseudouridine synthase [Ketogulonicigenium vulgare Y25]
          Length = 347

 Score =  237 bits (604), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 128/336 (38%), Positives = 194/336 (57%), Gaps = 19/336 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   E ++RLDRW +  +P++    ++K+ R G++RVD  RVK N R++ GQ
Sbjct: 1   MSGVQTITVAEGEGDLRLDRWLRKKFPNLTQGQIEKMCRKGELRVDGGRVKSNARLEDGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKH-SDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VRIPP    L   I++Q  +     +T+  ++ +++ +L++D  I V NKP G+  QGG
Sbjct: 61  NVRIPP----LGAEIEQQAPMAVRTRVTRSDAEMIQAAVLWKDEHIIVLNKPPGLPSQGG 116

Query: 123 SGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           SG+   H+DG  ++ +     +P+L HRLD++TSG+L++ART   A+ L+E+ R R ++K
Sbjct: 117 SGLGDRHVDGLTEALMFGYKDRPKLVHRLDKDTSGLLLLARTDRVARALSEALRHRNVRK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK----QNEKGANYAISHFKVIDCFA 237
           IYW+ V GIP      +   L+K    G + +H V        +GA  A + + V D   
Sbjct: 177 IYWAAVAGIPTPWAGSVKYGLVKMGRRGDEKMHCVHPAAVATTEGAKRAHTDYAVQDQAG 236

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLY 289
           Q+  W+ + P TGRTHQLR H   +G PI+GD KY  +   N            +QNKL+
Sbjct: 237 QRMAWMALVPITGRTHQLRAHMAEIGHPIIGDGKYGGSNAENAGDGWGAGIGGGVQNKLH 296

Query: 290 LHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
           LHAR + + HP     L + APLPAHM  TWD LG+
Sbjct: 297 LHARTLIIEHPITKETLTLQAPLPAHMQSTWDYLGW 332


>gi|307294362|ref|ZP_07574206.1| pseudouridine synthase, RluA family [Sphingobium chlorophenolicum
           L-1]
 gi|306880513|gb|EFN11730.1| pseudouridine synthase, RluA family [Sphingobium chlorophenolicum
           L-1]
          Length = 432

 Score =  237 bits (604), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 117/319 (36%), Positives = 185/319 (57%), Gaps = 8/319 (2%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V  D++ +RLDRWF+ H P + F  + +  R+GQ+RVD  R    +RI  GQ +R
Sbjct: 67  VRQFRVGADDDGIRLDRWFQRHLPDVGFNTVSRWARTGQLRVDGARAAPGDRIAEGQSIR 126

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PP         K +++      LT     F + I+++ D++  V NKP G++ QGG+  
Sbjct: 127 VPPAEPKAAETAKPKRV---RPQLTDDQIAFAQGIVIHRDAQAIVINKPPGLATQGGTKT 183

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG L +      Q+P+L HRLD++TSG L++ART  +A    ++F  R  +K+YW+
Sbjct: 184 DDHVDGLLDALEYELDQRPKLVHRLDKDTSGALLIARTARSAAFFAKAFSSRTARKVYWA 243

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+P  +   +   + K+   GG+ +HV   +E+    + S ++VI+    +  W+E+
Sbjct: 244 IVMGVPSIEDGMVELPIAKQPGTGGEKMHV---DEEEGLPSRSRYRVIERAGNRAAWVEL 300

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QP+TGRTHQLRVH   +G PIVGD KY    +   +  I  K++LHAR + + HP+GGR+
Sbjct: 301 QPYTGRTHQLRVHMAAIGHPIVGDGKYGGK-EAFLSGTISRKMHLHARRIRVDHPDGGRV 359

Query: 306 QITAPLPAHMVKTWDSLGF 324
            + A LP H   +  SLGF
Sbjct: 360 DVRAELPEHFAASLASLGF 378


>gi|148259184|ref|YP_001233311.1| RluA family pseudouridine synthase [Acidiphilium cryptum JF-5]
 gi|326402337|ref|YP_004282418.1| pseudouridine synthase [Acidiphilium multivorum AIU301]
 gi|146400865|gb|ABQ29392.1| ribosomal large subunit pseudouridine synthase C [Acidiphilium
           cryptum JF-5]
 gi|325049198|dbj|BAJ79536.1| pseudouridine synthase [Acidiphilium multivorum AIU301]
          Length = 324

 Score =  235 bits (600), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 126/318 (39%), Positives = 190/318 (59%), Gaps = 7/318 (2%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V V  D+ +MRLDR+ ++ +P +    +QK  R+GQVRVD KR + +  + +GQ VR
Sbjct: 3   VRIVTVGPDQADMRLDRFLRSLHPGLTQGAIQKFCRTGQVRVDGKRAEASTHLAAGQAVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV        + Q ++ +  ++ +    L + +L+ D+ + V +KPAG++ QGG GIA
Sbjct: 63  IPPVPETPAPKPR-QTVVANEWDVKE----LNARILHRDADVLVIDKPAGLATQGGKGIA 117

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            H+DG L +      ++PRL HRLD++TSG+LV+AR   AA  L  +FR R ++K YW++
Sbjct: 118 RHLDGMLDALRFDAAERPRLVHRLDRDTSGVLVLARNAFAANRLAAAFRGRDMEKTYWAI 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+P   +  I   L +     G       ++++ A  AI+ ++ +D   +KF WLE+ 
Sbjct: 178 VVGLPIPMEGQIDLPLARIGGAQGARTRPADRDDEDAAKAITDYRTLDHAGRKFSWLELH 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P TGRTHQLR H   +G PI+GD  Y  +    F      +L+LHAR + LPHP GGRL 
Sbjct: 238 PLTGRTHQLRAHCAAIGTPILGDAPYGEHLA--FAEGFPRQLHLHARRLVLPHPRGGRLS 295

Query: 307 ITAPLPAHMVKTWDSLGF 324
           + A LPAHM  T+ +LGF
Sbjct: 296 VEAELPAHMKTTFATLGF 313


>gi|126736635|ref|ZP_01752375.1| Pseudouridine synthase, RluD [Roseobacter sp. CCS2]
 gi|126713948|gb|EBA10819.1| Pseudouridine synthase, RluD [Roseobacter sp. CCS2]
          Length = 351

 Score =  234 bits (598), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 131/349 (37%), Positives = 194/349 (55%), Gaps = 41/349 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ  V+  D+ + RLDR+ +  +PH+    ++K+ R G+VRVD  RVK N+R++ GQ
Sbjct: 1   MSGVQTRVIGPDDGDQRLDRYLRRLFPHLTQGRIEKMCRKGEVRVDGGRVKSNSRVEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKH------SDFLKSILLYEDSKIYVFNKPAGI 117
            +RIPP        +  ++   ++ +L KH      +  ++S ++Y+D  I   NKP G+
Sbjct: 61  KIRIPP--------LPTEEEAAAAASLAKHGVTKADAKLIQSCVIYKDDHIIAINKPHGL 112

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           + QGG+    H+DG  ++ +    +KPRL HRLD++TSG+L++ARTR  A+ LTE+ + R
Sbjct: 113 ATQGGTNTTRHVDGLSEALMFDYDEKPRLVHRLDKDTSGVLLLARTRMMAKQLTENLKHR 172

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------------GAN 224
             +KIYW+ V G+P  +   I   L+K    G        +NEK             GA 
Sbjct: 173 ETRKIYWAAVAGVPHPRAGTIKYGLVKAPGHGRG-----GENEKMRCVHPRDLDSVEGAK 227

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF---- 280
            A S + V+D  A +  W  + P TGRTHQLR H   +G PIVGD KY  + + N     
Sbjct: 228 RATSDYAVMDTLASRAAWCALVPITGRTHQLRAHMAEIGHPIVGDGKYGGSGQENLGDGW 287

Query: 281 ----TSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLGF 324
                S I  KL+LHAR + + HP  G  L +TAPLP HM  TWD +G+
Sbjct: 288 GAGMGSEIGRKLHLHARSLTIEHPATGATLHLTAPLPEHMQNTWDFVGW 336


>gi|294675889|ref|YP_003576504.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           capsulatus SB 1003]
 gi|294474709|gb|ADE84097.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           capsulatus SB 1003]
          Length = 355

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 131/341 (38%), Positives = 190/341 (55%), Gaps = 20/341 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE   RLDRW K  +P +    ++K+ R+GQ+RVD  RVK ++RI  G 
Sbjct: 1   MSSVQLIKVTEDEGESRLDRWLKKKFPVLTQGAVEKMCRTGQLRVDGGRVKASDRIGPGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKIYVFNKPAGISVQG 121
            VR+PP+  A     + +            +D   +++ +L++D  I   NKPAG+  QG
Sbjct: 61  EVRVPPLPEAGAKAPESRSEARRDATQISPADEKMIQAAVLWKDEHIIALNKPAGLPSQG 120

Query: 122 GSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GSG    H+DG L++       +P++ HRLD++TSG+L++ART   A+ L+ESFR++  +
Sbjct: 121 GSGQGDRHVDGLLEALKFGYKDRPKMVHRLDKDTSGVLLIARTDRVARALSESFRLKTTR 180

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKS--HIGGDY-----VHVVKQNEK-GANYAISHFKV 232
           KIYW+ V G+P  KK  I   L+K      GG+      +H  K +    A  A + F V
Sbjct: 181 KIYWAAVAGVPSPKKGTIRYGLVKAPGHGRGGEGEKMLCIHPSKVDATPDAKRATTDFAV 240

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPI 284
           ID    +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            I
Sbjct: 241 IDGLGSRVSWVGLVPITGRTHQLRAHMAELGHPIVGDGKYGGSGQENLGDGWGSQLGGEI 300

Query: 285 QNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
             KL+LHAR +   HP    R+ +TAPLP HMV+TW +LG+
Sbjct: 301 SRKLHLHARTISFDHPITKKRITLTAPLPDHMVRTWKTLGW 341


>gi|85703848|ref|ZP_01034951.1| ribosomal large subunit pseudouridine synthase C [Roseovarius sp.
           217]
 gi|85671168|gb|EAQ26026.1| ribosomal large subunit pseudouridine synthase C [Roseovarius sp.
           217]
          Length = 347

 Score =  234 bits (597), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 127/335 (37%), Positives = 188/335 (56%), Gaps = 24/335 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ  VV  D+ + RLDRW +  +PH+  V ++K+ R G+VRVD  RVK   R++ GQ
Sbjct: 1   MSGVQTRVVGPDDGDQRLDRWIRRLFPHVGQVQIEKMCRKGEVRVDGGRVKPATRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VRIPP+ +       +++   +   ++   +  ++S ++Y D  +   NKP G+ VQGG
Sbjct: 61  SVRIPPLPDT------DERPTGALARISPADAKMIQSCVIYRDDHVIALNKPPGLPVQGG 114

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           S    H+DG  ++      +KPRL HRLD++TSG+L++ARTR AA+ LT +FR R  +KI
Sbjct: 115 SKQTRHVDGLAEALRFGAEEKPRLVHRLDKDTSGVLLLARTREAAKGLTAAFRHRNTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVID 234
           YW+ V G+P  +   +   L+K    G    G+ +  V   E     GA  A + + VI+
Sbjct: 175 YWAAVAGVPTPRMGTVRYGLVKAPGHGAKGEGEKMICVHPREVESTPGAKPATTDYAVIE 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQN 286
               +  W+ + P TGRTHQLR H   +G P+VGD KY  + + N            +  
Sbjct: 235 AAGARTSWMALIPVTGRTHQLRAHMAEIGHPVVGDGKYGGSGQENLGDGWGAQLGGDVSR 294

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
           KL+LHAR + + HP     L ITAPLP HM +TWD
Sbjct: 295 KLHLHARSLKIEHPVSRAILHITAPLPEHMQRTWD 329


>gi|302382665|ref|YP_003818488.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
 gi|302193293|gb|ADL00865.1| pseudouridine synthase, RluA family [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 350

 Score =  234 bits (596), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 121/320 (37%), Positives = 187/320 (58%), Gaps = 12/320 (3%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            Q + V   E+ +RLDRWF+  +PH++ + +QK+ R GQ+RVD  R+K   R+ +G  VR
Sbjct: 24  AQILYVAEAEDGIRLDRWFRRRWPHLSNIQVQKMARGGQIRVDGARIKPEGRLTAGAAVR 83

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+   +     E   L +  ++     F KS+++YED  +   NKP G++VQGG+   
Sbjct: 84  VPPIPEPIVRAPGEHMAL-TPADIA----FAKSMVIYEDDLVIALNKPWGLAVQGGTKTT 138

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            H+D  L +W +   ++PRL HRLD++TSG+L++ +   AA+ L  +F  R+ +K YW++
Sbjct: 139 RHVDRLLSAWGEGM-ERPRLVHRLDRDTSGVLLLGKGPEAAKRLAGAFARRQAKKTYWAI 197

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           V G+PK     I +  LKKS I  DY  +      + GA  A + + VI   AQ+  W+ 
Sbjct: 198 VMGLPKPADGQI-SVHLKKSGIN-DYEIMRPADPKDPGAEPAETAYAVISHAAQRASWMA 255

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++P TGRTHQLR H   +G PI+GD KY  +     + P+  KL LHAR ++L HP GG 
Sbjct: 256 LRPFTGRTHQLRAHMKAIGHPILGDPKYGDDASTQLSGPL--KLQLHARRIELDHPAGGT 313

Query: 305 LQITAPLPAHMVKTWDSLGF 324
           L + AP+ A +   ++  GF
Sbjct: 314 LVVEAPISAELRAGFEHFGF 333


>gi|294011526|ref|YP_003544986.1| ribosomal large subunit pseudouridine synthase C [Sphingobium
           japonicum UT26S]
 gi|292674856|dbj|BAI96374.1| ribosomal large subunit pseudouridine synthase C [Sphingobium
           japonicum UT26S]
          Length = 436

 Score =  234 bits (596), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 114/318 (35%), Positives = 183/318 (57%), Gaps = 6/318 (1%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V  D++ +RLDRWF+ H P + F  + +  R+GQ+RVD  R    +RI  GQ +R
Sbjct: 71  VRQFRVGADDDGIRLDRWFQRHLPDVGFNTVSRWARTGQLRVDGARAAPGDRIAEGQSIR 130

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP         K +++     +      F + ++++ D++  V NKP G++ QGG+   
Sbjct: 131 VPPAEPKAPETAKPRRVRPQLTD--DQMAFAQGLVIHRDAQAIVINKPPGLATQGGTKTD 188

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            H+DG L +      Q+P+L HRLD++TSG L++ART  +A +  ++F  R  +K+YW++
Sbjct: 189 DHVDGLLDALEFDLDQRPKLVHRLDKDTSGALLIARTARSAAYFAKAFSSRTARKVYWAI 248

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+P  +   I   + K+   GG+ +HV   +E+    + S ++VI+    +  W+E+Q
Sbjct: 249 VMGVPSIEDGMIELPIAKQPGTGGEKMHV---DEEEGLPSRSRYRVIERAGNRAAWVELQ 305

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P+TGRTHQLRVH   +G PIVGD KY        +  I  K++LHAR + + HP+GG + 
Sbjct: 306 PYTGRTHQLRVHMAAIGHPIVGDGKYGGK-DAFLSGTISRKMHLHARRIRVDHPDGGPVD 364

Query: 307 ITAPLPAHMVKTWDSLGF 324
           + A LP H   +  SLGF
Sbjct: 365 VRAELPEHFAASLASLGF 382


>gi|329889168|ref|ZP_08267511.1| pseudouridine synthase, RluA family protein [Brevundimonas diminuta
           ATCC 11568]
 gi|328844469|gb|EGF94033.1| pseudouridine synthase, RluA family protein [Brevundimonas diminuta
           ATCC 11568]
          Length = 331

 Score =  234 bits (596), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 123/322 (38%), Positives = 186/322 (57%), Gaps = 10/322 (3%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  DE+++RLDRWFK  +PH+  + ++K+ RSGQ+RVD  RVK  +R+ +G  VR
Sbjct: 5   VQTLYVAEDEDDIRLDRWFKRRWPHLTHIQVEKMARSGQIRVDGSRVKPQDRLTAGAAVR 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+ +A       +K  D      +   + KS++LYED  +   NKP G++VQGG+   
Sbjct: 65  VPPLPDA-----NPRKPGDLHELSERDIAYAKSLVLYEDHMVIALNKPHGLAVQGGTKTT 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            HID  L +W +    +PRL HRLD++TSG+L++ +   AA+ L  +F  R+ +K YW++
Sbjct: 120 KHIDRLLSAWGEGM-DRPRLVHRLDRDTSGVLLLGKGPEAAKRLAGAFARRQAKKTYWAI 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGG-DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G PK     I +  LKK+ I   + +   +  +     A + F  I   A +  W+ +
Sbjct: 179 VIGNPKPSAGQI-DMALKKTGINDFEMMRPAEPKDPKGEPAETAFATISRAAHRAAWMAL 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +P TGRTHQLR H   +G PI+GD KY  +     + P+  KL LHAR ++L HP GG+L
Sbjct: 238 RPFTGRTHQLRAHMAAIGHPILGDPKYGDDKSRELSGPL--KLQLHARRIELDHPGGGKL 295

Query: 306 QITAPLPAHMVKTWDSLGFKYD 327
            + APL   M   ++  GF  D
Sbjct: 296 IVEAPLSPEMKAGFNHFGFSED 317


>gi|197104733|ref|YP_002130110.1| ribosomal large subunit pseudouridine synthase C [Phenylobacterium
           zucineum HLK1]
 gi|196478153|gb|ACG77681.1| ribosomal large subunit pseudouridine synthase C [Phenylobacterium
           zucineum HLK1]
          Length = 325

 Score =  234 bits (596), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 129/323 (39%), Positives = 185/323 (57%), Gaps = 14/323 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V+  EE +RLDRWFK  +PH+N + +QK+ RSGQ+RVD  R K + R+ +G 
Sbjct: 1   MREVRTLYVDKGEEGVRLDRWFKRRWPHLNHIQIQKLTRSGQIRVDGARAKPDTRLSAGS 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+           + +  LD      + + + +S+++YED  +   NKP+G++VQGG+
Sbjct: 61  QVRV--PPLPDAPPPRAKGELDP-----REAAYARSLVIYEDEDVLALNKPSGLAVQGGT 113

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               HIDG L +W +   ++PRL HRLD++TSG+LV+ +T  AA  L  +F  RR QKIY
Sbjct: 114 KTTRHIDGLLSAWGEGL-ERPRLVHRLDRDTSGVLVLGKTPGAAAKLAGAFAKRRTQKIY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFC 241
           W+LV G+PK  +  +   L KK    GD   +V  + K   A  A + F  +   A K  
Sbjct: 173 WALVAGLPKPGQGVLELPLAKKGV--GDREMMVPADPKDPRAETAETEFVTLARAADKVA 230

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           W+ + PHTGRTHQLR H L MG PI+GD KY        +  +  KL LHAR + LPHP 
Sbjct: 231 WMALWPHTGRTHQLRAHMLAMGHPILGDPKYKTEASEALSGGL--KLQLHARRLVLPHPS 288

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
            G L + AP+   M   ++  GF
Sbjct: 289 RGTLMLEAPIGKEMKAGFERFGF 311


>gi|159042871|ref|YP_001531665.1| ribosomal large subunit pseudouridine synthase C [Dinoroseobacter
           shibae DFL 12]
 gi|157910631|gb|ABV92064.1| ribosomal large subunit pseudouridine synthase C [Dinoroseobacter
           shibae DFL 12]
          Length = 348

 Score =  233 bits (595), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 126/338 (37%), Positives = 192/338 (56%), Gaps = 21/338 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE + RLDRW +  +PH+    ++K+ R G++RVD  RVK   R+Q+GQ
Sbjct: 1   MSGVQTLTVGVDEGDQRLDRWLRRRFPHLGQGRIEKMCRKGELRVDGGRVKPATRLQTGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+        +  +   S  +     + L+  ++Y D+ I   NKPAG+ VQGGS
Sbjct: 61  AVRVPPLPAPGEITARPARARISDAD----REMLQGTVIYRDADILALNKPAGLPVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   HIDG  ++      + PRL HRLD++TSG+L++ARTR +A  LT +FR R+ +KIY
Sbjct: 117 GQERHIDGMAEALQFELDEPPRLVHRLDKDTSGVLLMARTRRSAAALTAAFRARQTRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+ V G+P+ +   +   L+K    G    G+ +  +   +      A  A + + V+  
Sbjct: 177 WAAVAGVPQPQLGTVRYALMKAPGHGKRGEGEKMLCIDPRQMDAHPDAKRATTDYAVLSA 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNK 287
             ++  W  + P TGRTHQLR H   +G PI+GD KY  + + N            +  K
Sbjct: 237 LGRRVAWCVLVPITGRTHQLRAHMAELGHPIIGDGKYGGSGQENLGDGWGAQLGGEMSKK 296

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
           L+LHAR++ L HP  G +L +TAPLP HM +TW++LG+
Sbjct: 297 LHLHARHLSLTHPVTGAQLSLTAPLPPHMARTWEALGW 334


>gi|254419979|ref|ZP_05033703.1| pseudouridine synthase, RluA family [Brevundimonas sp. BAL3]
 gi|196186156|gb|EDX81132.1| pseudouridine synthase, RluA family [Brevundimonas sp. BAL3]
          Length = 341

 Score =  233 bits (594), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 122/328 (37%), Positives = 186/328 (56%), Gaps = 22/328 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V  DE+ +RLDRWF+  +PH++ + +QK+ RSGQ+RVD  R+K   R+ +G  VR
Sbjct: 15  VLTIYVAEDEDGIRLDRWFRRRWPHLSNIQVQKMARSGQIRVDGARIKPEGRLTAGAAVR 74

Query: 67  IPPVINALN------HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +PP+ +  +      H + E+ I            F KS++LYED  +   NKP G++VQ
Sbjct: 75  VPPIPDDTSRQAGDLHTLSERDIA-----------FAKSLVLYEDDMVIAINKPHGLAVQ 123

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GG+  + H+D  L +W +    +PRL HRLD++TSG+L++ +   AA+ L  +F  R+ +
Sbjct: 124 GGTKTSRHVDRLLSAWGEGM-DRPRLVHRLDRDTSGVLLLGKGPEAAKRLAGAFARRQAK 182

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGG-DYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           K YW++V G PK     I +  LKK+ I   + +    + +  A  A + F  I   + +
Sbjct: 183 KTYWAIVIGNPKPYSGQI-DMPLKKTGINDFEMMRPADRKDPKAEPAETAFSTISRASHR 241

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
             W+ ++P TGRTHQLR H   +G PI+GD KY        + P+  KL LHAR ++L H
Sbjct: 242 AAWMALRPFTGRTHQLRAHMAGIGHPILGDPKYGDEKSRELSGPL--KLQLHARSIELDH 299

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFKYD 327
           P GG L++TAPL   M   +   GF  D
Sbjct: 300 PRGGLLKVTAPLSPEMKAGFAHFGFSED 327


>gi|163733779|ref|ZP_02141221.1| ribosomal large subunit pseudouridine synthase C [Roseobacter
           litoralis Och 149]
 gi|161392890|gb|EDQ17217.1| ribosomal large subunit pseudouridine synthase C [Roseobacter
           litoralis Och 149]
          Length = 346

 Score =  233 bits (593), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 133/341 (39%), Positives = 189/341 (55%), Gaps = 22/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE + RLDRWFK  +P I+   ++K+ R G++RVD  RVK   R++ GQ
Sbjct: 1   MSAVQTLTVGEDEGDQRLDRWFKKQFPLISQGRVEKMCRKGEIRVDGGRVKAATRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP    L        +  S+V+    +  ++S ++Y D  I   NKPAG+  QGGS
Sbjct: 61  QVRIPP----LPDTAAPAPVARSAVSAAD-AKLIQSCVIYRDDHIIAINKPAGLPTQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG  ++       KPRL HRLD++TSG+L++ARTR AA+ LT + R +  +KIY
Sbjct: 116 GQTRHVDGLSEALKFGFEDKPRLVHRLDKDTSGVLLLARTRMAAKALTTAMRHKETRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+LV G+P      I   L+K    G    G+ +  +   E     GA  A + +  +  
Sbjct: 176 WALVAGVPTPYLGEIRYALVKAPGHGRRGEGEKMIALPPREVDETPGAKRAHTLYATLYR 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
              +  W+ M+P TGRTHQLRVH   +G PIVGD KY  + + N            I  K
Sbjct: 236 VGSRASWVAMEPITGRTHQLRVHMAEIGHPIVGDGKYGGSGQENMGDGWGAQLGGVISKK 295

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR M   HPE  + + ITA +P HM ++WD+ G+  D
Sbjct: 296 LHLHARMMRFEHPETRKPVTITADMPDHMKQSWDTFGWTED 336


>gi|254486362|ref|ZP_05099567.1| 23S rRNA pseudouridylate synthase [Roseobacter sp. GAI101]
 gi|214043231|gb|EEB83869.1| 23S rRNA pseudouridylate synthase [Roseobacter sp. GAI101]
          Length = 349

 Score =  233 bits (593), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 129/338 (38%), Positives = 191/338 (56%), Gaps = 25/338 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ +++E  + + RLDRWFK  +P I+   ++K+ R G +RV+  RVK + R++ GQ
Sbjct: 1   MSRVQNLIIEQGDGDQRLDRWFKRMFPLISQGRIEKMCRKGDIRVNGGRVKASTRLEVGQ 60

Query: 64  VVRIPPVINA-LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +RIPP+ +       K  +I D+         F++S ++Y D  I   NKP G+ VQGG
Sbjct: 61  EIRIPPLPDTEAPPPPKRTRISDADAK------FIRSCVIYRDDYIIALNKPPGLPVQGG 114

Query: 123 SGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           SG +  H+D    + +    +KPRL HRLD++TSG+L++ARTR+ A  LT SFR R+ +K
Sbjct: 115 SGQSDRHVDALADALMFDLDEKPRLVHRLDKDTSGVLIMARTRSIAADLTSSFRHRQTRK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVI 233
           IYW+ V G+P  K   I   L+K    G    G+ ++ V   +    +GA  A + +  +
Sbjct: 175 IYWAAVAGVPHPKNGTIKFGLVKAFGHGARGEGEKMYCVHPKDMDTTEGAKRATTDYATL 234

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQ 285
                + CW+ + P TGRTHQLR H   +G PIVGD KY  + + N            I 
Sbjct: 235 AQAGTRTCWVALIPVTGRTHQLRAHMAEIGHPIVGDGKYGGSGQENMGDGWGAQLGGDIS 294

Query: 286 NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            KL+LHAR + L HP     L + AP+P HMV+TWD+ 
Sbjct: 295 KKLHLHARSLTLEHPVTKATLNLIAPMPDHMVRTWDTF 332


>gi|295688947|ref|YP_003592640.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
 gi|295430850|gb|ADG10022.1| pseudouridine synthase, RluA family [Caulobacter segnis ATCC 21756]
          Length = 332

 Score =  232 bits (591), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 129/328 (39%), Positives = 187/328 (57%), Gaps = 12/328 (3%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    V+ + V+  E+ +RLDRWFK  +PH+N + L K+ RSGQVRVD  R K + ++ 
Sbjct: 1   MSTTKEVRTLYVDAGEDGVRLDRWFKRRWPHLNHIQLNKLFRSGQVRVDGSRAKADTKLA 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  +R+PP+ +A +   K  K+    V       + KS++LYED ++   NKPAG++VQ
Sbjct: 61  AGSQIRVPPLPDAPDPADK-NKLSARDVA------YAKSLVLYEDEEVLALNKPAGLAVQ 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GG+    HID  L +W +    +PRL HRLD++TSG+L++ +T +AA  L+ +F  R+ Q
Sbjct: 114 GGTKTTKHIDKLLSAWGEGV-DRPRLVHRLDRDTSGVLLLGKTPSAAARLSGAFAKRKAQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQK 239
           K YW++V G P +  E +    L K  +G   + V  Q  +  A  A + F  I     +
Sbjct: 173 KTYWAIVAGNP-HPTEGVMELHLAKRGVGDRELVVPAQPKDADAQPAETEFVTISRAGPR 231

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
             W+ ++PHTGRTHQLR H   MG PI+GD KY        +  +  KL LHAR + LPH
Sbjct: 232 VTWMALRPHTGRTHQLRAHMKAMGHPILGDPKYGDEKSAPLSEGL--KLQLHARSILLPH 289

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFKYD 327
           P  G L I APL   M + +   GF  D
Sbjct: 290 PSAGMLHIEAPLSPEMKEGFRKFGFSED 317


>gi|254512315|ref|ZP_05124382.1| ribosomal large subunit pseudouridine synthase C [Rhodobacteraceae
           bacterium KLH11]
 gi|221536026|gb|EEE39014.1| ribosomal large subunit pseudouridine synthase C [Rhodobacteraceae
           bacterium KLH11]
          Length = 347

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 127/343 (37%), Positives = 197/343 (57%), Gaps = 26/343 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRW +  +PH++   ++K+ R G++RVD  RVK + R++ GQ
Sbjct: 1   MSGVQMITVAEGDGDQRLDRWLRRLFPHVSQGRIEKMCRKGELRVDGGRVKASTRLEVGQ 60

Query: 64  VVRIPPVINALNH--IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           VVR+PP+ +A +H   +   ++ D+   +      ++S ++Y+D ++   NKP G+ VQG
Sbjct: 61  VVRVPPLPDA-DHKPAVVRHRVSDADAKM------IQSCVIYKDDQVLALNKPHGLPVQG 113

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+D   ++      + PRL HRLD++TSG+L++ARTR AA+ LT +FR R  +K
Sbjct: 114 GSGQTRHVDSLSEALRFGYDENPRLVHRLDKDTSGVLLMARTRDAAKALTAAFRHRNTRK 173

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVI 233
           IYW+LV G+P      I   L+K S  G    G+ +  +  +E     GA  A + +  +
Sbjct: 174 IYWALVAGVPTPYLGEIKTGLVKASGHGKQGEGEKMIALHPSEVNDTPGAKRAHTLYATL 233

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQ 285
              A +  W+ M+P TGRTHQLR H   +G PI+GD KY  + + N            I 
Sbjct: 234 YRVAGRAAWVAMEPVTGRTHQLRAHMAAIGHPIIGDGKYGGSGQENLGDGWGAQLGGIIS 293

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            KL+LHAR +   HP   + + + APLP HM  +WD+LG+  D
Sbjct: 294 KKLHLHARSLSFEHPITRKPVSLAAPLPDHMKHSWDTLGWTED 336


>gi|86135800|ref|ZP_01054379.1| ribosomal large subunit pseudouridine synthase C [Roseobacter sp.
           MED193]
 gi|85826674|gb|EAQ46870.1| ribosomal large subunit pseudouridine synthase C [Roseobacter sp.
           MED193]
          Length = 348

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 127/343 (37%), Positives = 191/343 (55%), Gaps = 25/343 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   +++ R+DRW +  +PH+N   ++K+ R G++R+D  RVK N R+ +GQ
Sbjct: 1   MSGVQMITVAEADDDQRIDRWLRRLFPHVNQGRIEKMCRKGELRLDGGRVKANTRVAAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKIYVFNKPAGISVQG 121
           VVR+PP+  +      + K     V     +D   ++  ++Y+D  + V NKPAG++VQG
Sbjct: 61  VVRVPPLAES------DLKPAAPRVARISETDAKMIRGCVIYKDDDVIVLNKPAGLAVQG 114

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG   +      +KPRL HRLD++TSG+LV+AR R AA+ LT +FR R  +K
Sbjct: 115 GSGTTKHVDGLADALRFDAEEKPRLVHRLDKDTSGVLVLARNRLAAKSLTAAFRHRNTRK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH----VVKQNE----KGANYAISHFKVI 233
           IYW+LV G+P      I   L+K    G          V  NE     GA  A +++  +
Sbjct: 175 IYWALVAGVPTPYLGEIKAGLVKAGGHGAGGEGEKMIAVHPNEIDRTPGAKRAHTYYATL 234

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQ 285
              A +  W+ M+P TGRTHQLR H   +G PI+GD KY  + + N            I 
Sbjct: 235 YRVAGRASWVAMEPVTGRTHQLRAHMAEIGHPIIGDGKYGGSGQENLGDGWGAQLGGVIS 294

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            KL+LHAR +   HP   + + + A LP+HM  +W++ G+  D
Sbjct: 295 KKLHLHARRLVFEHPTTKKDIVMMAELPSHMKDSWETFGWTED 337


>gi|149203330|ref|ZP_01880300.1| Pseudouridine synthase, RluD [Roseovarius sp. TM1035]
 gi|149143163|gb|EDM31202.1| Pseudouridine synthase, RluD [Roseovarius sp. TM1035]
          Length = 347

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 126/335 (37%), Positives = 187/335 (55%), Gaps = 24/335 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ  +V  D+ + RLDRW +  +PH+  V ++K+ R G++RVD  RVK   R++ GQ
Sbjct: 1   MSGVQTRIVGPDDGDQRLDRWVRRLFPHVGQVQIEKMCRKGELRVDGGRVKPATRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VRIPP+ +       +++   +   ++   +  ++S ++Y D  I   NKP G+ VQGG
Sbjct: 61  SVRIPPLPDT------DERPTGALARISPADAKMIQSCVIYRDDHIIALNKPPGLPVQGG 114

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           S    H+DG  ++       KPRL HRLD++TSG+L++ARTR AA+ LT +FR R  +KI
Sbjct: 115 SKQLRHVDGLAEALRFGAEDKPRLVHRLDKDTSGVLLLARTREAAKGLTAAFRHRNTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVID 234
           YW+ V G+P  +   I   L+K    G    G+ +  +   +     GA  A + + VI+
Sbjct: 175 YWAAVAGVPTPRMGTIRFGLVKAPGHGAKGEGEKMLCLHPRDIDATPGAKPATTDYAVIE 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQN 286
               +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            +  
Sbjct: 235 AAGARTAWMALIPVTGRTHQLRAHMAEIGHPIVGDGKYGGSGQENLGDGWGAQLGGDVSR 294

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
           KL+LHAR + + HP     L ITAPLP HM +TWD
Sbjct: 295 KLHLHARSLKIEHPVSRAILHITAPLPEHMARTWD 329


>gi|167645622|ref|YP_001683285.1| RluA family pseudouridine synthase [Caulobacter sp. K31]
 gi|167348052|gb|ABZ70787.1| pseudouridine synthase, RluA family [Caulobacter sp. K31]
          Length = 329

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 124/328 (37%), Positives = 183/328 (55%), Gaps = 10/328 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V+  E+ +RLDRWFK  +PH+N + L K+ RSGQVRVD  R K + ++ +G 
Sbjct: 1   MREVRTLFVDAGEDGVRLDRWFKRRWPHLNHIQLNKLFRSGQVRVDGSRAKADTKLAAGS 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+P  +       ++QK+    +       F KS++LYED ++   NKPAG++VQGG+
Sbjct: 61  QIRVP-PLPDAPDPDEKQKLSPRDIA------FAKSLVLYEDEEVLALNKPAGLAVQGGT 113

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              +HID  L +W +    +P+L HRLD++TSG+L++ +T AAA  L+ SF  R+ QK Y
Sbjct: 114 KTTHHIDKLLSAWGEGV-NRPKLVHRLDRDTSGVLLLGKTPAAAARLSGSFAKRKAQKTY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++V G P   +  I   L K+     + V   +  +     A + F  I     +  W+
Sbjct: 173 WAIVAGNPHPTEGVIELHLAKRGVGDRELVVPAEPKDPDGQPAETEFVSISRAGPRVTWM 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++PHTGRTHQLR H   +G PI+GD KY  +     +  +  KL LHAR + LPHP  G
Sbjct: 233 ALRPHTGRTHQLRAHMKAIGHPILGDPKYSDDKALQLSEGL--KLQLHARSIVLPHPSVG 290

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNLY 331
            L I APL   M   +   GF  D   Y
Sbjct: 291 TLAIQAPLSPEMKAGFAKFGFSEDEAEY 318


>gi|126728208|ref|ZP_01744024.1| ribosomal large subunit pseudouridine synthase C [Sagittula
           stellata E-37]
 gi|126711173|gb|EBA10223.1| ribosomal large subunit pseudouridine synthase C [Sagittula
           stellata E-37]
          Length = 347

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 128/344 (37%), Positives = 194/344 (56%), Gaps = 28/344 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRW K  +PH+    ++K+ R G++R+D  R K ++R+++G 
Sbjct: 1   MSRVQTITVGPGDGDQRLDRWLKRLFPHVAQSRIEKMCRKGELRLDGGRCKASSRVETGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLT---KHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            VRIPP        + E   +DS+   +   K ++ +++ +L++D  I   NKP G++ Q
Sbjct: 61  QVRIPP--------LPEPGQVDSAPKPSFNEKDAEMIRACVLWKDDHIIALNKPPGLATQ 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG   H+DG  ++      +KPRL HRLD++TSG+L++ARTRA A+ LTE+ R R  +
Sbjct: 113 GGSGQTRHVDGLSEALTFGMDEKPRLVHRLDKDTSGVLLLARTRAVAKALTEAIRHREAR 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKV 232
           KIYW+LV G+P      I   L+K    G     + +  V   E    +GA  A + +  
Sbjct: 173 KIYWALVAGVPTPYLGEIKYGLVKAPGHGKGGEAEKMRCVHPKEIATTEGAKRAHTLYAT 232

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------I 284
           +   A +  W+ M+P TGRTHQLR H   +G PI+GD KY  + + N            I
Sbjct: 233 LYRVAGRASWVAMEPVTGRTHQLRAHMAEIGHPIIGDGKYGGSGQENLGDGWGAQLGGII 292

Query: 285 QNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
             KL+LHAR + L HP        TAPLP HM ++WD+LG++ D
Sbjct: 293 SKKLHLHARSLTLLHPVTKTPFTATAPLPEHMKQSWDTLGWEED 336


>gi|94497617|ref|ZP_01304185.1| pseudouridylate synthase [Sphingomonas sp. SKA58]
 gi|94422834|gb|EAT07867.1| pseudouridylate synthase [Sphingomonas sp. SKA58]
          Length = 394

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 116/312 (37%), Positives = 184/312 (58%), Gaps = 8/312 (2%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           QY V  +D+  +RLDRWF+ H P + F  + +  R+GQ+RVD  R    +RI  GQ++R+
Sbjct: 89  QYRVAADDD-GIRLDRWFQRHLPDVGFNLVSRWSRTGQLRVDGARAAPGDRISEGQMIRV 147

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           PP     +   + ++     V+LT     + + ++++ D++  V NKP G++ QGG+   
Sbjct: 148 PPAEQKPDAADRPKRA--RIVDLTPDEISYAQDMVIHRDAQAIVINKPPGLATQGGTKTD 205

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            H+D  L + +     +P+L HRLD++TSG L++ART  AA H  ++F  R  +K+YW+L
Sbjct: 206 EHVDKLLDALLFDAESRPKLVHRLDKDTSGALLLARTSRAAAHFAKAFSSRTARKVYWAL 265

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+P  +   I   + K+   GG+ +HV   +E+    A S ++VI+    +  W+E+Q
Sbjct: 266 VMGVPSIEDGMIELPIAKQPGTGGEKMHV---DEEEGLPARSRYRVIERAGNRAAWIELQ 322

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P+TGRTHQLRVH   +G PIVGD KY        +  I  K++LHAR + + HP+GGR+ 
Sbjct: 323 PYTGRTHQLRVHMAAIGHPIVGDGKYGGK-DAFLSGTISRKMHLHARRIRVDHPDGGRVD 381

Query: 307 ITAPLPAHMVKT 318
           +TA LP H   +
Sbjct: 382 MTAELPTHFANS 393


>gi|83950496|ref|ZP_00959229.1| ribosomal large subunit pseudouridine synthase C [Roseovarius
           nubinhibens ISM]
 gi|83838395|gb|EAP77691.1| ribosomal large subunit pseudouridine synthase C [Roseovarius
           nubinhibens ISM]
          Length = 346

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 123/322 (38%), Positives = 180/322 (55%), Gaps = 17/322 (5%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           + + RLDRW +  +PH+    ++K+ R G++RVD  RVK ++R+Q GQ VRIPP+    +
Sbjct: 7   DADQRLDRWLRRLFPHLGQGRIEKMCRKGELRVDGGRVKSSHRLQVGQSVRIPPIPAPDD 66

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
              K       S    + +  +++ ++Y D  I   NKP G+ VQGGS    H+DG  ++
Sbjct: 67  SEDKAAPPRPRSRVSDEDAAMIRAAVIYRDDHIIALNKPPGLPVQGGSKQTRHVDGLAEA 126

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 +KPRL HRLD++TSG+L++ARTR  A  LT +FR R  +KIYW+ V G+P  + 
Sbjct: 127 LRFDLDEKPRLVHRLDKDTSGVLILARTRQMAADLTAAFRHRNTRKIYWAAVAGVPLPRM 186

Query: 196 ECIANWLLKKSHIGGDY-------VHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
             +   L+K    G          +H  +  N  GA +A S + V++   Q+  W+ + P
Sbjct: 187 GTVKYGLVKAPGHGKGGEGEKMLCIHPREVDNTPGAKHATSDYAVLENAGQRTAWMALVP 246

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLPH 299
            TGRTHQLR H   +G PIVGD KY  + + N            +  KL+LHAR + + H
Sbjct: 247 VTGRTHQLRAHMAELGHPIVGDGKYGGSGQENLGDGWGAQLGGDVSRKLHLHARSLTIRH 306

Query: 300 PE-GGRLQITAPLPAHMVKTWD 320
           P  G RL +TAPLP HM +TWD
Sbjct: 307 PATGARLHLTAPLPDHMARTWD 328


>gi|255263430|ref|ZP_05342772.1| ribosomal large subunit pseudouridine synthase C [Thalassiobium sp.
           R2A62]
 gi|255105765|gb|EET48439.1| ribosomal large subunit pseudouridine synthase C [Thalassiobium sp.
           R2A62]
          Length = 347

 Score =  228 bits (582), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 124/341 (36%), Positives = 193/341 (56%), Gaps = 28/341 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ ++V   + + R+DRW +  +PH++   ++K+ R G +RVD  RVK N R++ GQ
Sbjct: 1   MSGVQKIIVAEGDGDQRVDRWLRRLFPHVSQGRIEKMCRKGDLRVDGGRVKSNTRVEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKIYVFNKPAGISVQG 121
            VR+PP+ +A        +I    V     +D   ++S+++Y+D  I   NKP+GI+ QG
Sbjct: 61  EVRVPPLPDA-------DEITAGPVTKITSADAEMMRSLVIYKDDHIIALNKPSGIASQG 113

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GS    H+DG  ++      +KPRL HRLD++TSG+ ++ARTR  A+ ++++F+ R  +K
Sbjct: 114 GSKQVRHLDGLAEALKFDYFEKPRLVHRLDRDTSGVFIMARTREIAKAMSDAFKERETRK 173

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHI---GGDY-----VHVVK-QNEKGANYAISHFKV 232
           IYW+ V G+P      +  W L KS     GG+      +H  + ++  GA  A + + +
Sbjct: 174 IYWAAVGGVPHPAMGTV-RWGLIKSGGHGRGGENEKMRCIHPREVEHTPGAKRATTDYAL 232

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPI 284
           +D    +  W+ + P TGRTHQLR H   MG PI+GD KY  + + N            I
Sbjct: 233 LDRLGSRAAWIALVPVTGRTHQLRAHMAEMGHPIIGDGKYGGSGQENLGDGWGAGMGEEI 292

Query: 285 QNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
             KL+LHAR +   HP  G R+ +TA LP HM  TWD +G+
Sbjct: 293 GRKLHLHARSLSFTHPATGKRVNLTASLPEHMKHTWDFVGW 333


>gi|209963759|ref|YP_002296674.1| RNA pseudouridine synthase [Rhodospirillum centenum SW]
 gi|209957225|gb|ACI97861.1| RNA pseudouridine synthase [Rhodospirillum centenum SW]
          Length = 336

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 132/326 (40%), Positives = 198/326 (60%), Gaps = 10/326 (3%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+  +V +DE  +RLDRWFK HYP ++ + LQK+LR+GQVRVD KR + + R+  GQ VR
Sbjct: 9   VETRLVGDDEGEVRLDRWFKRHYPLLSHIQLQKLLRTGQVRVDGKRAEASTRLLPGQSVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+ +A        K     V+  + +  L++ +L+ D  + V +KPAG++ QGG+   
Sbjct: 69  IPPLPDAPPPDAVRPKA-RPEVD-ERAAKELRARVLFRDHDVIVLDKPAGLATQGGTNQV 126

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            H+D  L +       +P+L HRLD++TSG LV+AR+ AAA  LT +FR R  +KIYW++
Sbjct: 127 KHLDAMLDALKFEAEGRPKLVHRLDKDTSGCLVLARSAAAAAKLTAAFRSREARKIYWAV 186

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G+PK  K  I   + K++   G+ + V   +E    +AI+++ V++   ++  ++ + 
Sbjct: 187 TVGVPKPMKGRIDLPVAKEAGTRGERMTV---DEDEGVHAITYYTVLEHAHKQAAFVALW 243

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF---TSPIQNKLYLHARYMDLPHPEGG 303
           P TGRTHQLRVH   +G PI+GD KY    +G F      +  +L+LHAR + LPHP GG
Sbjct: 244 PRTGRTHQLRVHMAALGTPILGDGKYAG--QGAFLEGAGDLPRQLHLHARRIILPHPRGG 301

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRN 329
            + +TAPLP HM   WD  GF+  R 
Sbjct: 302 VIDVTAPLPKHMRPAWDYFGFEDKRK 327


>gi|146278539|ref|YP_001168698.1| RluA family pseudouridine synthase [Rhodobacter sphaeroides ATCC
           17025]
 gi|145556780|gb|ABP71393.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides ATCC 17025]
          Length = 346

 Score =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 128/340 (37%), Positives = 188/340 (55%), Gaps = 24/340 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  VQ + V  DE   RLDRWFK  +PH+    ++K+ R+GQVRVD  R K ++R+  G 
Sbjct: 1   MKSVQLLTVTADEGEQRLDRWFKRRFPHVTQGAVEKMCRTGQVRVDGARAKASDRVAEGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP+ +      +  ++  S   +      ++  ++Y+D+ I V NKPAG+  QGGS
Sbjct: 61  EIRVPPLPDPDAPRPQASRVTKSDEQM------IQDCVIYKDNDIIVLNKPAGLPSQGGS 114

Query: 124 GIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    H+DG  ++      ++P+L HRLD++TSG+LV+ART   A+ L+ESFR R  +KI
Sbjct: 115 GQGERHVDGLTEALKFGYKERPKLVHRLDKDTSGVLVLARTDRVARALSESFRHRNTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNEKG----ANYAISHFKVID 234
           YW+LV G+P  K+  I   L+K +  G    G+ +  +   + G    A  A + F  + 
Sbjct: 175 YWALVAGVPSPKQGSIKYALMKAAGHGRGGEGEKMLCIHPAKVGDYPEAKRAQTDFFTLW 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQN 286
               +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            +  
Sbjct: 235 FLGTRCAWMALSPITGRTHQLRAHMAELGHPIVGDGKYGGSSQENAGDGWGAQIGGEVSR 294

Query: 287 KLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
           KL+LHAR + + HP    L   TAPLP HM KTW  L +K
Sbjct: 295 KLHLHARSLTIEHPIRKELVTFTAPLPPHMAKTWKLLDWK 334


>gi|84515664|ref|ZP_01003025.1| ribosomal large subunit pseudouridine synthase C [Loktanella
           vestfoldensis SKA53]
 gi|84510106|gb|EAQ06562.1| ribosomal large subunit pseudouridine synthase C [Loktanella
           vestfoldensis SKA53]
          Length = 351

 Score =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 124/344 (36%), Positives = 191/344 (55%), Gaps = 31/344 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V    +  D+ + RLDR+ +  +PH+    ++K+ R G++RVD  RVK + R++ GQ
Sbjct: 1   MSGVHTRTIGPDDGDQRLDRYLRRLFPHLTQGRIEKLCRKGELRVDGGRVKTSTRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKH------SDFLKSILLYEDSKIYVFNKPAGI 117
            VRIPP        +  ++   ++  L +H      +  ++S ++Y D  I   NKP G+
Sbjct: 61  KVRIPP--------LPTEQEAAAAATLARHGVTKADAKLIQSCVIYRDDHIIAINKPHGL 112

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           + QGG+    H+DG  ++ +    +KPRL HRLD++TSG+L++ARTR  A+ LTE+ + R
Sbjct: 113 ATQGGTNTTRHVDGMAEALMFGYDEKPRLVHRLDRDTSGVLLLARTRMMAKQLTENLKHR 172

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISH 229
             +KIYW+ V G+P  +   I   L+K    G     + +  V  NE    +GA  A S 
Sbjct: 173 ETRKIYWAAVAGVPHPRAGTIKYGLVKAPGHGKGGENEKMRCVHPNEIASTEGAKRATSD 232

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------T 281
           + V+D  A +  W  + P TGRTHQLR H   +G PI+GD KY  + + N          
Sbjct: 233 YAVMDTLASRAAWCALVPITGRTHQLRAHMAEIGHPIIGDGKYGGSGQENLGDGWGASMG 292

Query: 282 SPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           S I  K++LHAR + + HP  G+ L +TA LP HM  TWD +G+
Sbjct: 293 SEIGRKMHLHARSLTIEHPATGKTLHLTADLPEHMQNTWDFVGW 336


>gi|77462289|ref|YP_351793.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides 2.4.1]
 gi|332560170|ref|ZP_08414492.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides WS8N]
 gi|77386707|gb|ABA77892.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides 2.4.1]
 gi|332277882|gb|EGJ23197.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides WS8N]
          Length = 346

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 127/340 (37%), Positives = 188/340 (55%), Gaps = 24/340 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE   RLDRWFK  +PH+    ++K+ R+GQVRVD  R K ++R+  G 
Sbjct: 1   MSSVQLLKVTADEGEQRLDRWFKRRFPHVTQGAVEKMCRTGQVRVDGARAKASDRVAEGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP+ +      +  ++  S   +      ++  ++Y D+ I V NKPAG+  QGGS
Sbjct: 61  EIRVPPLPDPDAPRPQASRVTKSDEQM------IQDCVIYRDNDIIVLNKPAGLPSQGGS 114

Query: 124 GIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    H+DG  ++      ++P+L HRLD++TSG+LV+ART   A+ L+ESFR R  +KI
Sbjct: 115 GQGERHVDGLTEALKFGYKERPKLVHRLDKDTSGVLVLARTDRVARALSESFRHRNTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNEKG----ANYAISHFKVID 234
           YW+LV G+P  K+  I   L+K    G    G+ +  +   + G    A  A + F  + 
Sbjct: 175 YWALVAGVPSPKQGSIKYALMKAPGHGRGGEGEKMLCIHPAKVGDYPEAKRAQTDFFTLW 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQN 286
               +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            +  
Sbjct: 235 FLGSRCAWMALSPITGRTHQLRAHMAELGHPIVGDGKYGGSGQENLGDGWGAQIGGEMSR 294

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           KL+LHAR + + HP +   +  TAPLP HM KTW  L +K
Sbjct: 295 KLHLHARSLTIEHPIKKDLVTFTAPLPGHMAKTWKLLDWK 334


>gi|260428027|ref|ZP_05782006.1| ribosomal large subunit pseudouridine synthase C [Citreicella sp.
           SE45]
 gi|260422519|gb|EEX15770.1| ribosomal large subunit pseudouridine synthase C [Citreicella sp.
           SE45]
          Length = 351

 Score =  227 bits (578), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 125/341 (36%), Positives = 188/341 (55%), Gaps = 18/341 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + +   + + RLDRW K H+PH+    ++K+ R G++RVD  RVK + R++ GQ
Sbjct: 1   MSRVQTITIGPGDGDQRLDRWLKRHFPHLAQGRIEKMCRKGEIRVDGGRVKASTRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+                 V+    +  ++  ++++D  I   NKP G+ VQGGS
Sbjct: 61  QVRIPPLPEPDAVNAAPAAAPKPRVS-DADTKLIQDAVIWKDDHIIALNKPPGLPVQGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  ++      +KPRL HRLD++TSG+L++ARTRA AQ LT + R ++ +KIY
Sbjct: 120 KTTRHVDGLSEALRFGLDEKPRLVHRLDKDTSGVLLLARTRAVAQALTAAIRHKQTRKIY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W++V G+P      I   L+K    G    G+ +  V   +    +GA  A + +  +  
Sbjct: 180 WAVVAGVPTPYLGEIRYALVKAPGHGSSGEGEKMICVHPRDVDRTEGAKRAHTLYATLYR 239

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ ++P TGRTHQLR H   +G PI+GD KY  + + N            I  K
Sbjct: 240 VAGRASWVALEPITGRTHQLRAHMAEIGHPIIGDGKYGGSGQENLGDGWGAQLGGVISKK 299

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR M   HP    R+ +TAPLP HM  TW++LG+  D
Sbjct: 300 LHLHARSMTFEHPVTHKRVTVTAPLPEHMKHTWETLGWTED 340


>gi|126461165|ref|YP_001042279.1| RluA family pseudouridine synthase [Rhodobacter sphaeroides ATCC
           17029]
 gi|126102829|gb|ABN75507.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides ATCC 17029]
          Length = 346

 Score =  225 bits (574), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 126/340 (37%), Positives = 187/340 (55%), Gaps = 24/340 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE   RLDRWFK  +PH+    ++K+ R+GQVRVD  R K ++R+  G 
Sbjct: 1   MSSVQLLKVTADEGEQRLDRWFKRRFPHVTQGAVEKMCRTGQVRVDGARAKASDRVAEGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP+ +      +  ++  S   +      ++  ++Y D+ I V NKP G+  QGGS
Sbjct: 61  EIRVPPLPDPDAPRPQASRVTKSDEQM------IQDCVIYRDNDIIVLNKPPGLPSQGGS 114

Query: 124 GIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    H+DG  ++      ++P+L HRLD++TSG+LV+ART   A+ L+ESFR R  +KI
Sbjct: 115 GQGERHVDGLTEALKFGYKERPKLVHRLDKDTSGVLVLARTDRVARALSESFRHRNTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNEKG----ANYAISHFKVID 234
           YW+LV G+P  K+  I   L+K    G    G+ +  +   + G    A  A + F  + 
Sbjct: 175 YWALVAGVPSPKQGSIKYALMKAPGHGRGGEGEKMLCIHPAKVGDYPEAKRAQTDFFTLW 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQN 286
               +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            +  
Sbjct: 235 FLGSRCAWMALSPITGRTHQLRAHMAELGHPIVGDGKYGGSGQENLGDGWGAQIGGEMSR 294

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           KL+LHAR + + HP +   +  TAPLP HM KTW  L +K
Sbjct: 295 KLHLHARSLTIEHPIKKDLVTFTAPLPGHMAKTWKLLDWK 334


>gi|110678758|ref|YP_681765.1| ribosomal large subunit pseudouridine synthase C [Roseobacter
           denitrificans OCh 114]
 gi|109454874|gb|ABG31079.1| ribosomal large subunit pseudouridine synthase C [Roseobacter
           denitrificans OCh 114]
          Length = 346

 Score =  225 bits (573), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 129/342 (37%), Positives = 185/342 (54%), Gaps = 24/342 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE + RLDRWFK  +P I+   ++K+ R G++RVD  RVK   R++ GQ
Sbjct: 1   MSAVQTLTVGEDEGDQRLDRWFKKQFPLISQGRVEKMCRKGEIRVDGGRVKAATRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP    L        +  S+V+    +  ++S ++Y D  I   NKPAG+  QGGS
Sbjct: 61  QVRIPP----LPDTAAPAPVARSAVS-AADARMIQSCVIYRDDHIIAINKPAGLPTQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG  ++       KPRL HRLD++TSG+L++ARTR AA+ LT + R +  +KIY
Sbjct: 116 GQTRHVDGLAEALKFGFEDKPRLVHRLDKDTSGVLLLARTRMAAKALTTAMRHKETRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK---------QNEKGANYAISHFKVID 234
           W+LV G+P      I  + L K+   G      K             GA  A + +  + 
Sbjct: 176 WALVAGVPTPYLGEI-RYALVKAQGRGRGGEGEKMIALPPREVDETPGAKRAHTLYATLY 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQN 286
               +  W+ M+P TGRTHQLR H   +G PI+GD KY  + + N            I  
Sbjct: 235 RVGSRASWVAMEPITGRTHQLRAHMAEIGHPIIGDGKYGGSGQENMGDGWGAQLGGVISK 294

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           KL+LHAR M   HPE  + + ITA +P HM ++W++ G+  D
Sbjct: 295 KLHLHARMMRFEHPETRKPVTITADMPDHMKQSWETFGWTED 336


>gi|114771239|ref|ZP_01448659.1| ribosomal large subunit pseudouridine synthase C [alpha
           proteobacterium HTCC2255]
 gi|114548164|gb|EAU51051.1| ribosomal large subunit pseudouridine synthase C [alpha
           proteobacterium HTCC2255]
          Length = 348

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 124/340 (36%), Positives = 190/340 (55%), Gaps = 23/340 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V++D ++ RLDR+ +  +P +    ++K+ R G+ RVD  RVK + R+  GQ
Sbjct: 1   MSGVQIIEVDDDGQDQRLDRFLRRTFPELGQGRIEKMCRKGECRVDGSRVKASTRLSVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VR+PP+ +      K+     ++  +TK  +  ++  +LY+D  I   NKPAG++VQGG
Sbjct: 61  TVRVPPLPDT-----KDMPRDTATAKITKADAQMIRDAVLYKDDYIIAINKPAGLAVQGG 115

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   H+DG   +       KP+L HRLD++TSG+L++ART  AA  LT++F+ R  +KI
Sbjct: 116 SGQMRHVDGLSAALKFDLENKPKLVHRLDKDTSGVLLLARTGLAASGLTKAFQSRETRKI 175

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVID 234
           YW+ V G P  K   I   L+K    G    G+ +  +  +E      A +A + + V++
Sbjct: 176 YWAAVAGCPHPKIGTIKYGLIKAGGHGPNGSGEKMQCIHPSEVTDMPDAKHATTDYTVLE 235

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQN 286
              ++  W+ + P TGRTHQLR H   +G PIVGD KY  N + N            I  
Sbjct: 236 DVGKRASWVALVPITGRTHQLRAHMAELGNPIVGDGKYGTNTQTNDGDGWGAQLGGDISR 295

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           K++LHAR +   HP     + ITA LP HM KTW + G++
Sbjct: 296 KMHLHARSITFTHPITKKEIHITAELPDHMEKTWTTFGWE 335


>gi|221638143|ref|YP_002524405.1| Ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides KD131]
 gi|221158924|gb|ACL99903.1| Ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides KD131]
          Length = 343

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 125/337 (37%), Positives = 186/337 (55%), Gaps = 24/337 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V  DE   RLDRWFK  +PH+    ++K+ R+GQVRVD  R K ++R+  G  +R
Sbjct: 1   MQLLKVTADEGEQRLDRWFKRRFPHVTQGAVEKMCRTGQVRVDGARAKASDRVAEGMEIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+ +      +  ++  S   +      ++  ++Y D+ I V NKPAG+  QGGSG  
Sbjct: 61  VPPLPDPDAPRPQASRVTKSDEQM------IQDCVIYRDNDIIVLNKPAGLPSQGGSGQG 114

Query: 127 Y-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG  ++      ++P+L HRLD++TSG+LV+ART   A+ L+ESFR R  +KIYW+
Sbjct: 115 ERHVDGLTEALKFGYKERPKLVHRLDKDTSGVLVLARTDRVARALSESFRHRNTRKIYWA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNEKG----ANYAISHFKVIDCFA 237
           LV G+P  K+  I   L+K    G    G+ +  +   + G    A  A + F  +    
Sbjct: 175 LVAGVPSPKQGSIKYALMKAPGHGRGGEGEKMLCIHPAKVGDYPEAKRAQTDFFTLWFLG 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLY 289
            +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            +  KL+
Sbjct: 235 SRCAWMALSPITGRTHQLRAHMAELGHPIVGDGKYGGSGQENLGDGWGAQIGGEMSRKLH 294

Query: 290 LHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           LHAR + + HP +   +  TAPLP HM KTW  L +K
Sbjct: 295 LHARSLTIEHPIKKDLVTFTAPLPGHMAKTWKLLDWK 331


>gi|329851361|ref|ZP_08266118.1| pseudouridine synthase, RluA family protein [Asticcacaulis
           biprosthecum C19]
 gi|328840207|gb|EGF89779.1| pseudouridine synthase, RluA family protein [Asticcacaulis
           biprosthecum C19]
          Length = 334

 Score =  223 bits (567), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 120/323 (37%), Positives = 188/323 (58%), Gaps = 6/323 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   V+ + V   E+ +R+DR+FK  +PH+N V L K+LRSGQVRVD  RVK + R+ +G
Sbjct: 1   MSNEVKTLYVAEGEDGIRVDRFFKRRWPHVNHVQLNKLLRSGQVRVDGGRVKADTRLATG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VR+PP+    +   ++++  + S    +   + +S++LYED  +   NKP+G++VQGG
Sbjct: 61  QTVRVPPLPAVPDQDQQKRERAELSPQEIR---YARSLVLYEDEDVIAINKPSGLAVQGG 117

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +    H+D  L +W +   ++PRL HRLD++TSG+L++ ++ +AA  L  +F  RR  K 
Sbjct: 118 TKTKNHVDRLLSAWGEGL-ERPRLVHRLDRDTSGVLLLGKSPSAAARLAGAFAKRRANKT 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G PK ++  I   L+KK     + V      E GA  A + +  I     +  W
Sbjct: 177 YWALVVGNPKPEEGYIDTPLIKKGFHDREIVQPADPKEPGAEPAETEYVTIGRAGPRVAW 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++PHTGRTHQLR H   +G  I+GD KY  +   + +  +   L LH R ++LPHP  
Sbjct: 237 MGLRPHTGRTHQLRAHMQAIGHSILGDPKYGNDESRSLSEGL--GLQLHHRRIELPHPTQ 294

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G L + APL   +   +D  GF+
Sbjct: 295 GTLIVEAPLDPVIKAGFDRFGFE 317


>gi|163745572|ref|ZP_02152932.1| ribosomal large subunit pseudouridine synthase C [Oceanibulbus
           indolifex HEL-45]
 gi|161382390|gb|EDQ06799.1| ribosomal large subunit pseudouridine synthase C [Oceanibulbus
           indolifex HEL-45]
          Length = 348

 Score =  221 bits (562), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 128/343 (37%), Positives = 192/343 (55%), Gaps = 25/343 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRWFK  +P IN   ++K+ R G++RVD  RVK N R+++GQ
Sbjct: 1   MSRVQTITVAVGDGDQRLDRWFKRMFPQINQGLIEKMCRKGEIRVDGGRVKANTRLEAGQ 60

Query: 64  VVRIPPVINALNHII-KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VR+PP+ ++      K  +I D+   +      +++ ++Y D  +   NKP G++VQGG
Sbjct: 61  EVRVPPLPDSAPPPPPKRTRITDADAKM------IRNCVIYRDEHVIALNKPPGLAVQGG 114

Query: 123 SGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           SG A  H+D   ++ +    +KPRL HRLD++TSG+L++ARTR AA+ LT + R R  +K
Sbjct: 115 SGQADRHVDALSEALIFDAEEKPRLVHRLDRDTSGVLLLARTRLAAKALTAAMRHRETRK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVI 233
           IYW++V G+P      +   L+K    G    G+ +  V   +     GA  A + +  +
Sbjct: 175 IYWAIVAGVPTPYLGEVKYGLVKAGGHGRSGEGEKMIAVHPRDMDATPGAKRAHTLYATL 234

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQ 285
                +  W+ M+P TGRTHQLR H   +G PIVGD KY  + + N            I 
Sbjct: 235 FRVGSRASWVAMEPVTGRTHQLRAHMAEIGHPIVGDGKYGGSGQENLGDGWGAQLGGIIS 294

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            KL+LHAR M   HP   + + ITA LP HM  +WD+ G+  D
Sbjct: 295 KKLHLHARMMRFEHPHTRKPVTITAELPEHMAHSWDTFGWTED 337


>gi|304319748|ref|YP_003853391.1| Ribosomal large subunit pseudouridine synthase C [Parvularcula
           bermudensis HTCC2503]
 gi|303298651|gb|ADM08250.1| Ribosomal large subunit pseudouridine synthase C [Parvularcula
           bermudensis HTCC2503]
          Length = 324

 Score =  220 bits (560), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 114/327 (34%), Positives = 184/327 (56%), Gaps = 12/327 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           ++ VQ V V + E   RLDRW K  +P +    +QK LR GQVR++  RVK ++R++SG+
Sbjct: 5   VSGVQEVTVTSAEAGQRLDRWMKRRFPGVTQGQVQKWLRKGQVRLNGGRVKADHRVESGE 64

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+          + ++  +      ++ ++ +++YED  I   NKPAG++VQGG+
Sbjct: 65  VVRVPPIDPEAAAPPPSRPVVGPA-----EAEMMRGLVIYEDDDILALNKPAGLAVQGGA 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               HIDG L  + + +  +PRL HRLD++T G+L++A++RA A  L+ +F+  RI K Y
Sbjct: 120 KTLIHIDGMLDVFGEGEA-RPRLVHRLDRDTGGVLLLAKSRAVAATLSLAFQQHRIGKTY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++  G+P      I   + K    G + +   +Q +     A++ ++ ++   QK  +L
Sbjct: 179 WAITKGVPHPLFGRIDMRIEKAGEPGREKMRGTEQGQS----ALTDYQTVETAGQKAAFL 234

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++PHTGRTHQ+RVH   +G PIVGD KY     G     + N+++L  R M +P     
Sbjct: 235 ALRPHTGRTHQIRVHLSAIGTPIVGDRKYGG--AGAVLEGLPNQMHLFCRQMHVPRRGRP 292

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNL 330
            L +TA L   M  +W   GF    +L
Sbjct: 293 PLVVTADLTGGMATSWSIFGFSRPDDL 319


>gi|103487583|ref|YP_617144.1| pseudouridine synthase, RluD [Sphingopyxis alaskensis RB2256]
 gi|98977660|gb|ABF53811.1| ribosomal large subunit pseudouridine synthase C [Sphingopyxis
           alaskensis RB2256]
          Length = 405

 Score =  219 bits (558), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 120/323 (37%), Positives = 186/323 (57%), Gaps = 15/323 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ- 63
           T +   V+  +++ +RLDRWFK H P      L +  RSGQ+ +D ++   ++RI  GQ 
Sbjct: 6   TPLDDAVIGEEDDGIRLDRWFKRHRPGTPHALLARWARSGQLTLDGRKADVSDRIAVGQR 65

Query: 64  -VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V+ +PPV        K++ + ++ V L +      S+L++ D+   V NK  G++ QGG
Sbjct: 66  LVMPVPPVEAEARPARKDRPLTEADVALAE------SMLIHRDASAIVLNKLPGLATQGG 119

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   +H+DG L +       +P+L HRLD++TSG L++ART  AA    +SF  R  +K 
Sbjct: 120 TKTEHHVDGLLDALKYDAPVRPKLVHRLDKDTSGALLIARTPRAAAWFAKSFSNRSAKKT 179

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G+P   +  I   L K+   GG+ +HV   ++ G   + + ++VID       W
Sbjct: 180 YWAIVVGVPDIAQGEIDLPLAKQPGSGGEKMHV---HDSGL-ASKTRYRVIDRAGNSAAW 235

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-TSPIQNKLYLHARYMDLPHPE 301
           +E+QP TGRTHQLRVH   +G PIVGD KY    KG F T  I  KL+LH+R + + HP+
Sbjct: 236 VELQPLTGRTHQLRVHMAAIGHPIVGDGKYGG--KGAFLTGTISRKLHLHSRRLRIDHPD 293

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
           GG + ++A +P H   + D+LGF
Sbjct: 294 GGVIDVSADVPDHFAASLDALGF 316


>gi|315500130|ref|YP_004088933.1| pseudouridine synthase, rlua family [Asticcacaulis excentricus CB
           48]
 gi|315418142|gb|ADU14782.1| pseudouridine synthase, RluA family [Asticcacaulis excentricus CB
           48]
          Length = 335

 Score =  218 bits (556), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 120/318 (37%), Positives = 185/318 (58%), Gaps = 6/318 (1%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V   E+ +R+D++FK  +PH+N + L K+LRSGQVRVD  R K + R+ +GQ VR
Sbjct: 5   VKILYVAEGEDGVRIDKFFKRRWPHLNHIQLNKLLRSGQVRVDGARAKADTRLSTGQSVR 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+ +A +   +EQ+  + +    +   + KS++LYED  +   NKP+G++VQGG+   
Sbjct: 65  VPPLPDAPS---EEQQKRERAELSPQEVRYAKSLVLYEDEDVIAINKPSGLAVQGGTKTK 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            HID  L +W +   ++PRL HRLD++TSG+L++ ++ +AA  L  +F  R+  K YW+L
Sbjct: 122 NHIDRLLSAWGEGL-ERPRLVHRLDRDTSGVLLLGKSPSAAARLAGAFAKRKAYKTYWAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G P  K+  I   L+KK     + V      E GA  A + +  I   A +  W+ ++
Sbjct: 181 VAGTPDPKEGVIDVPLVKKGINDREMVMPADPKEPGAEAAETEYVTISRAAHRLAWMALR 240

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           PHTGRTHQLR H   +G  I+GD KY        +  +   L LH R +++PHP  G L 
Sbjct: 241 PHTGRTHQLRAHMQAIGHCILGDPKYKDEKSIALSEGL--GLQLHHRRIEIPHPTHGTLI 298

Query: 307 ITAPLPAHMVKTWDSLGF 324
           + APL   +   +D  GF
Sbjct: 299 VEAPLDPVIQAGFDRYGF 316


>gi|114766871|ref|ZP_01445793.1| ribosomal large subunit pseudouridine synthase C [Pelagibaca
           bermudensis HTCC2601]
 gi|114540917|gb|EAU43977.1| ribosomal large subunit pseudouridine synthase C [Roseovarius sp.
           HTCC2601]
          Length = 350

 Score =  216 bits (551), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 123/341 (36%), Positives = 182/341 (53%), Gaps = 19/341 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRW K  +PH+    ++K+ R G++RVD  R K   R++ GQ
Sbjct: 1   MSRVQTITVGPGDGDQRLDRWLKRQFPHLQQGRIEKMCRKGELRVDGGRCKAATRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+           K    +      +  ++  ++Y D  I   NKP G+ VQGGS
Sbjct: 61  QVRVPPLPEPGETPAPAAK--PKATVSDADAKMIRDAVIYRDDHIIALNKPPGLPVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  ++      +KPRL HRLD++TSG+L++ARTR  AQ LT + R ++ +KIY
Sbjct: 119 KQERHVDGLAEALRFDYDEKPRLVHRLDKDTSGVLLLARTREIAQALTGAIRHKQTRKIY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W++V G+P      I   L+K    G    G+ +  V   E     GA  A + +  +  
Sbjct: 179 WAVVAGVPTPYLGEIRFGLVKAPGHGKSGEGEKMICVHPREMDRTPGAKRAHTLYATLYR 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ ++P TGRTHQLR H   +G PI+GD KY  + + N            I  K
Sbjct: 239 VAGRASWVALEPITGRTHQLRAHMAEIGHPIIGDGKYGGSGQENLGDGWGAQLGGVISKK 298

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR M   HP   + + +TA LPAHM  TW++LG+  D
Sbjct: 299 LHLHARSMTFLHPVTKKPVTVTASLPAHMANTWETLGWAED 339


>gi|119383542|ref|YP_914598.1| RluA family pseudouridine synthase [Paracoccus denitrificans
           PD1222]
 gi|119373309|gb|ABL68902.1| ribosomal large subunit pseudouridine synthase C [Paracoccus
           denitrificans PD1222]
          Length = 348

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 126/340 (37%), Positives = 183/340 (53%), Gaps = 25/340 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE   R+DRW K  +P +    ++K+ R+GQ+RVD  RVK N RI+ GQ
Sbjct: 1   MSGVQTIRVGEDEGEQRIDRWLKKRFPQLTQGAVEKMCRTGQLRVDGGRVKANTRIEPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+          +  +  S      ++ ++S +L+ D  I   NKP G+  QGGS
Sbjct: 61  EVRVPPLPEGAPPPAAPKASVKQS-----DAEMIQSCVLWRDEHIIALNKPPGLPSQGGS 115

Query: 124 GIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    H+DG   + +     +P+L HRLD++TSG+L++ART   A+ L+E+FR R  +KI
Sbjct: 116 GQGDRHVDGLTTALMFGYKDRPKLVHRLDKDTSGVLLLARTDRIARALSEAFRHRLTRKI 175

Query: 183 YWSLVWGIPKNKKECIANWLLKK---------SHIGGDYVHVVKQNEKGANYAISHFKVI 233
           YW+ V G+P  +   I   L+K            +   +   V   E GA  A + + V+
Sbjct: 176 YWAAVAGVPHPRMGSIKYGLVKAPGRGRGGEGEKMMAVHPSAVAATE-GAKRAHTDYAVL 234

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQ 285
           D    +  W+ M P TGRTHQLR H   +G PIVGD KY  + + N            I 
Sbjct: 235 DALGGRVSWVAMVPVTGRTHQLRAHMAEIGHPIVGDGKYGGSGQENLGDGWGAQLGGEIS 294

Query: 286 NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
            KL+LHAR +   HP   +L  +TAPLP HM +TW +LG+
Sbjct: 295 RKLHLHARMIRFEHPITKKLITVTAPLPEHMSRTWKTLGW 334


>gi|114797120|ref|YP_759725.1| RluA family pseudouridine synthase [Hyphomonas neptunium ATCC
           15444]
 gi|114737294|gb|ABI75419.1| pseudouridine synthase, RluA family [Hyphomonas neptunium ATCC
           15444]
          Length = 349

 Score =  216 bits (549), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 118/334 (35%), Positives = 186/334 (55%), Gaps = 27/334 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V + E   RLDRW K    +     ++K+LR+GQ+RV+  R K N R+ +   VR P +
Sbjct: 9   TVSDKETGARLDRWIKRRM-NATQGQVEKLLRTGQIRVNGSRAKANTRLVTADEVRFP-I 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
             A +     +K  ++     +  +FL+SI+++ED  +   NKPAG++VQGGSG   H+D
Sbjct: 67  FAAED--AGARKAANAKQISEEDREFLRSIIIHEDDDMLAINKPAGLAVQGGSGQGRHVD 124

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G + + +D  G +P L HRLD++TSG+L++A+  AAA  LTE FR R + K+YW++  G+
Sbjct: 125 GLI-AGMDVDGHRPVLVHRLDKDTSGVLLLAKHPAAAARLTELFRSREMDKVYWAVTVGV 183

Query: 191 PKNKKECIANWLLK------------------KSHIGGDYVHVVK--QNEKGANYAISHF 230
           P  +   I  W++K                       GD   +++  Q  +GA ++I+ +
Sbjct: 184 PSPQAGQIRCWMVKGVPDINEPSGYRPVDPYATKRRDGDRERMIRSAQGVEGARHSITDY 243

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
            V+     K  W+ M+P TGR HQLR H L M   I+GD+KY +  +      +   L+L
Sbjct: 244 VVVSTAGPKAAWVAMRPETGRMHQLRFHMLEMNTSILGDYKYKS--RREVPQGLAEGLHL 301

Query: 291 HARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           HAR + +P   G  ++I APLP HM +T+++LGF
Sbjct: 302 HARALIIPREHGKPIKIVAPLPPHMKETFETLGF 335


>gi|260577148|ref|ZP_05845125.1| pseudouridine synthase, RluA family [Rhodobacter sp. SW2]
 gi|259020622|gb|EEW23941.1| pseudouridine synthase, RluA family [Rhodobacter sp. SW2]
          Length = 349

 Score =  203 bits (516), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 121/337 (35%), Positives = 183/337 (54%), Gaps = 23/337 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V+ + V  DE   RLDRWFK  +P +    ++K+ R+GQVRVD  R K ++R+  G 
Sbjct: 1   MSAVKLLTVSGDEGEQRLDRWFKRRFPQLTQGAVEKMCRTGQVRVDGARAKASDRVVPGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP+ ++        + L   V+    +  ++S +L++D  I V NKP G+  QGGS
Sbjct: 61  EIRVPPLPDSE----APSRPLRDGVSAAD-TKMIQSCVLFKDEHIIVLNKPPGLPSQGGS 115

Query: 124 GIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    H+DG  ++      ++P+L HRLD++TSG+L++ART   A+ L+E+FR R  +KI
Sbjct: 116 GQGDRHVDGLTEALKFGYKERPKLVHRLDKDTSGVLILARTDRVARALSEAFRHRNTRKI 175

Query: 183 YWSLVWGIPKNKKECIANWLLKKS--HIGGD-----YVHVVKQNE-KGANYAISHFKVID 234
           YW+LV G+P  ++  I   L+K      GG+      +H  K  +   A  A + + V+ 
Sbjct: 176 YWALVAGVPHPRQGSIKYALMKAPGHGRGGEGEKMLCIHPAKTADYPDAKRAQTDYFVLW 235

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQN 286
               +  W+ ++P TGRTHQLR H   MG PI+GD KY      N            I  
Sbjct: 236 FLGSRLSWVALEPITGRTHQLRAHMAEMGHPILGDGKYGGGGADNLGDGWGAQVGGDISR 295

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           KL+LHAR + + HP     +   A LP HM KTW + 
Sbjct: 296 KLHLHARSLSVEHPITKAMMTFVAQLPEHMAKTWKTF 332


>gi|1568620|gb|AAB09035.1| orfEU5; uncharacterized orf upstream of txpA similar to H.
           influenzae HI0412 [Bartonella bacilliformis]
          Length = 221

 Score =  199 bits (506), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 105/196 (53%), Positives = 137/196 (69%), Gaps = 5/196 (2%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           +++M  ++   VE DE  MRLDRWFK HYP + F  LQKILRSGQVRVD  RVK N R+ 
Sbjct: 30  VTVMVNIKIKNVEEDENGMRLDRWFKVHYPGLGFGYLQKILRSGQVRVDGGRVKANMRLV 89

Query: 61  SGQVVRIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +GQ +R+P   I +  +I    K++          D LK +LLYED KI+VFNKPAG++V
Sbjct: 90  TGQSIRVPSFFIESKRNISITSKVISQQ----DDGDLLKKMLLYEDPKIFVFNKPAGLAV 145

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           QGGSG+  H+DG L++W + KG+KPRL HRLD+ETSG+LVVAR+  AAQ LT +FR R +
Sbjct: 146 QGGSGLTRHVDGMLEAWRNKKGEKPRLVHRLDRETSGLLVVARSXXAAQALTAAFRTREM 205

Query: 180 QKIYWSLVWGIPKNKK 195
           +KIYW+LV   P  K+
Sbjct: 206 KKIYWALVRRXPXKKQ 221


>gi|281204012|gb|EFA78208.1| Probable ribosomal large subunit pseudouridine synthase C protein
           [Polysphondylium pallidum PN500]
          Length = 702

 Score =  196 bits (499), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 133/379 (35%), Positives = 192/379 (50%), Gaps = 68/379 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV------DKKRVKFNNRIQ 60
           V   VVE D + MR+DRW  NHYP I    L K +RS ++ V      ++K+V+ N+R+ 
Sbjct: 325 VATKVVE-DLDGMRVDRWVSNHYPVITHSLLCKWIRSNKISVSDSLNGERKQVELNDRLV 383

Query: 61  SGQVVRIPPVINALNHIIKEQKILD--SSVNLTKHSDF----LKSILLYEDSKIYVFNKP 114
           +GQ V +P  + AL    KEQ++ D        + SD     ++  +LY+D ++ + NKP
Sbjct: 384 TGQWVNVP--MKAL----KEQRLADRKEPTKYARLSDEEIKEIRDSVLYKDDQLLIINKP 437

Query: 115 AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            G+SVQGG+G+  H+D  +        + PRL HRLD+ETSGIL++ARTR AA  + + F
Sbjct: 438 QGLSVQGGTGLKKHLDMMMSHLKFELEEAPRLCHRLDRETSGILILARTRKAATAMADKF 497

Query: 175 RM---RR------------------------------------------IQKIYWSLVWG 189
            M   RR                                          I+K YW+L+  
Sbjct: 498 EMKLKRRTTRQDRDKKDKQKKDGSGSGSSSKKDKDRSGGEDEELRDDNGIRKTYWALLTS 557

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            P  K+  I   L K    G + V   K+   GA  AI+ +KV++       ++ + P T
Sbjct: 558 TPNPKEGRIRAPLKKVVQDGEEMVIATKETGDGAKLAITEYKVVESSLTNASFVSLWPET 617

Query: 250 GRTHQLRVH-ALHMGCPIVGDHKYCANFKGNFTSPIQNK--LYLHARYMDLPHPEGG-RL 305
           GRTHQLRVH A  +  PIVGD KY  N    F S +  K  L+LHAR ++  HPE   ++
Sbjct: 618 GRTHQLRVHCASILSSPIVGDKKYGKNDSVAFQSVLGKKIPLHLHARRVEFFHPETNKKI 677

Query: 306 QITAPLPAHMVKTWDSLGF 324
            + APLP ++  +WD LGF
Sbjct: 678 DVVAPLPKNLENSWDMLGF 696


>gi|58698525|ref|ZP_00373428.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Drosophila ananassae]
 gi|225630144|ref|YP_002726935.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia sp. wRi]
 gi|225677282|ref|ZP_03788264.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Muscidifurax uniraptor]
 gi|58534967|gb|EAL59063.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Drosophila ananassae]
 gi|225590674|gb|EEH11919.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Muscidifurax uniraptor]
 gi|225592125|gb|ACN95144.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia sp. wRi]
          Length = 307

 Score =  196 bits (498), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 110/322 (34%), Positives = 182/322 (56%), Gaps = 16/322 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++  ++ +++E+D  N+RLDR+ +  +P +    ++K LR G ++VD  + K ++R+ SG
Sbjct: 1   MLQSIKTILIEDD--NVRLDRYIRRIFPDLKQSVIEKSLRKGLIKVDDCKAKSSDRVNSG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q + +   +N + +   ++K  +  VNL      L+  +LYED  I   NKPAG+ VQGG
Sbjct: 59  QTITLKH-LNYIENANSDRKYNEKLVNL------LRENILYEDEYILAINKPAGVIVQGG 111

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             +   +   L      +G+  ++ HRLD++TSG+++ AR    A++L E F+ RR++K 
Sbjct: 112 VKVKISMSDLLDQI--REGETFKIVHRLDRDTSGVIIFARNANVARYLMEEFKGRRVKKT 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L  GIP +K     ++ L K ++ G    VV +N      A +HF +I        +
Sbjct: 170 YLALTSGIP-SKDSGTIDYPLVKKYVSGQEKVVVDEN--SPQNATTHFSIIAKSKHNVAY 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L++QP TGRTHQLR H  H+ CPI+GD KY    K  F   I NK++LH+  + L  P  
Sbjct: 227 LKLQPITGRTHQLRAHLAHINCPILGDGKYGG--KKAFIDGIANKIHLHSHSLSLKLPNN 284

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
             + ITAP+  H+ K+ ++L F
Sbjct: 285 KEITITAPITKHIEKSIEALFF 306


>gi|190570815|ref|YP_001975173.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Culex quinquefasciatus Pel]
 gi|213019659|ref|ZP_03335464.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Culex quinquefasciatus JHB]
 gi|190357087|emb|CAQ54492.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Culex quinquefasciatus Pel]
 gi|212994700|gb|EEB55343.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Culex quinquefasciatus JHB]
          Length = 307

 Score =  195 bits (495), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 114/318 (35%), Positives = 181/318 (56%), Gaps = 16/318 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++VE++  N+RLDR+ +  +P++    ++K LR G ++VD    K ++R+ SGQ + 
Sbjct: 5   IKTILVEDN--NVRLDRYIRRIFPNLKQSAIEKSLRKGLIKVDNCTAKSSDRVSSGQTI- 61

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              +I  L++I  E    D   N  K  + L+  +LYED  I   NKPAG+ VQGG  + 
Sbjct: 62  ---MIRYLDYI--ENTNSDCKYN-EKLVNLLRENILYEDEYILAINKPAGVIVQGGIKVK 115

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             I   L    + +  K  + HRLD++TSG+++ AR  + A++L E F+ RRI+K Y +L
Sbjct: 116 ISISDLLDQIREREIFK--IVHRLDRDTSGVIIFARNASVAKYLMEEFKGRRIKKTYLAL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            +GIP +K     ++ L K +I G    VV  +E     A +HF +I        +L++Q
Sbjct: 174 TFGIP-SKDNGTIDYPLVKKYISGQEKVVV--DEDSPQNATTHFLIIARLKHNVAYLKLQ 230

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P TGRTHQLR H  H+ CPI+GD KY    K  F   + N+++LH+  + L  P    + 
Sbjct: 231 PITGRTHQLRAHLAHINCPILGDGKYGG--KKAFIDGVANQIHLHSYSLSLKLPNNKEVT 288

Query: 307 ITAPLPAHMVKTWDSLGF 324
           ITAP+P H+ K+ ++L F
Sbjct: 289 ITAPVPKHIEKSIEALSF 306


>gi|218678850|ref|ZP_03526747.1| RNA-pseudouridine synthase protein, ribosomal large subunit C
           [Rhizobium etli CIAT 894]
          Length = 174

 Score =  195 bits (495), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 91/174 (52%), Positives = 122/174 (70%), Gaps = 2/174 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEPDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+   ++  +K   I    +  +   + L  ++L+ED K+ V NKP GI+VQGGS
Sbjct: 61  TVRVPPL--DVDAKVKSGPIAGRDLKHSSDFELLSRMVLHEDDKVIVLNKPPGIAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R
Sbjct: 119 GVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRER 172


>gi|42520290|ref|NP_966205.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Drosophila melanogaster]
 gi|42410028|gb|AAS14139.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Drosophila melanogaster]
          Length = 307

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 109/322 (33%), Positives = 182/322 (56%), Gaps = 16/322 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++  ++ +++E+D  N+RLDR+ +  +P +    ++K LR G ++V+  + K ++R+ SG
Sbjct: 1   MLQSIKTILIEDD--NVRLDRYIRRIFPDLKQSVIEKSLRKGLIKVNDCKAKSSDRVNSG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q + +   +N + +   ++K  +  VNL      L+  +LYED  I   NKPAG+ VQGG
Sbjct: 59  QTITLKH-LNYIENANSDRKYNEKLVNL------LRENILYEDEYILAINKPAGVIVQGG 111

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             +   +   L      +G+  ++ HRLD++TSG+++ AR    A++L E F+ RR++K 
Sbjct: 112 VKVKISMSDLLDQI--REGETFKIVHRLDRDTSGVIIFARNANVARYLMEEFKGRRVKKT 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L  GIP +K     ++ L K ++ G    VV +N      A +HF +I        +
Sbjct: 170 YLALTSGIP-SKDSGTIDYPLVKKYVSGQEKVVVDEN--SPQNATTHFSIIAKSKHNVAY 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L++QP TGRTHQLR H  H+ CPI+GD KY    K  F   I NK++LH+  + L  P  
Sbjct: 227 LKLQPITGRTHQLRAHLAHINCPILGDGKYGG--KKAFIDGIANKIHLHSHSLSLKLPNN 284

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
             + ITAP+  H+ K+ ++L F
Sbjct: 285 KEITITAPITKHIEKSIEALFF 306


>gi|218658410|ref|ZP_03514340.1| RNA-pseudouridine synthase protein, ribosomal large subunit C
           [Rhizobium etli IE4771]
          Length = 161

 Score =  179 bits (455), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 84/159 (52%), Positives = 112/159 (70%), Gaps = 2/159 (1%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ VR+PP+   ++
Sbjct: 5   KPGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQTVRVPPL--DVD 62

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
             +K   I    +  +   + L  ++L+ED K+ V NKP GI+VQGGSG+A HID  L++
Sbjct: 63  AKLKSGPIAGKDLKHSSDFELLSRMVLHEDEKVIVLNKPPGIAVQGGSGVARHIDQMLEA 122

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +F
Sbjct: 123 WTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAF 161


>gi|88798806|ref|ZP_01114389.1| ribosomal large subunit pseudouridine synthase C [Reinekea sp.
           MED297]
 gi|88778569|gb|EAR09761.1| ribosomal large subunit pseudouridine synthase C [Reinekea sp.
           MED297]
          Length = 313

 Score =  179 bits (455), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 109/303 (35%), Positives = 168/303 (55%), Gaps = 19/303 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  VQ++ V  D    RLD + + +  ++    + +I+R G+VRV+KKR K + ++  G 
Sbjct: 1   MAKVQFIEVSADRAEQRLDNFLRYYLNNVPKSRIYRIIRKGEVRVNKKRAKPDTKLSEGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PPV  A   I   Q     S  L K  D     +++EDS +   NKP+G++V GGS
Sbjct: 61  VVRVPPVTMAEKTIENPQ----PSAGLRKALDH---AIVFEDSALLAVNKPSGLAVHGGS 113

Query: 124 GIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQ 180
           G+     G +++    +  +P   L HRLD++TSG+++VA+ R +   L + FR + R++
Sbjct: 114 GLKL---GLIEALRAQRESEPFLELVHRLDRDTSGVVLVAKKRKSLTLLQDEFRQKTRVR 170

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           K YW LV G  P       A  L  +    G+    V+ N K +    +HF+V+  + Q 
Sbjct: 171 KTYWCLVKGHWPDGCSVVDAPLLRHEESASGERRVSVQANGKPSR---THFRVLKQY-QD 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
             W+E  P TGRTHQ+RVH  ++GCPI+GD KY  +   +  S +  N+L+LHA  + LP
Sbjct: 227 CAWVEALPITGRTHQIRVHCQYVGCPILGDDKYQDSEAESLASKLGLNRLFLHAAQLTLP 286

Query: 299 HPE 301
           HPE
Sbjct: 287 HPE 289


>gi|330962632|gb|EGH62892.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. maculicola str. ES4326]
          Length = 318

 Score =  179 bits (454), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 113/321 (35%), Positives = 183/321 (57%), Gaps = 21/321 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  IPPV-----RVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSGLS 122

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y +
Sbjct: 123 FGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMA 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     ++ +   LLK +   G+   +V+ NE+G   A++ FKV+  F      +E 
Sbjct: 181 LVRGNWATAQKQVRAPLLKSNLRSGE--RMVEVNEEGKE-ALTLFKVLRRFGDFATMVEA 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPE 301
           +P TGRTHQ+RVH LH G  I GD KY      NF+  I++    +L+LHA  + +P P+
Sbjct: 238 KPVTGRTHQIRVHTLHAGHAIAGDTKYGDE---NFSREIRDLGGKRLFLHAYMLTVPMPD 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G +L + AP+     KT + L
Sbjct: 295 GSKLNVQAPVDEMWAKTVERL 315


>gi|270157796|ref|ZP_06186453.1| RluA family pseudouridine synthase [Legionella longbeachae D-4968]
 gi|289163935|ref|YP_003454073.1| Ribosomal large subunit pseudouridine synthase [Legionella
           longbeachae NSW150]
 gi|269989821|gb|EEZ96075.1| RluA family pseudouridine synthase [Legionella longbeachae D-4968]
 gi|288857108|emb|CBJ10923.1| Ribosomal large subunit pseudouridine synthase [Legionella
           longbeachae NSW150]
          Length = 318

 Score =  179 bits (454), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 111/295 (37%), Positives = 168/295 (56%), Gaps = 18/295 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V Y  + N+EE  RLD +       +   ++ +I+R+G+VRV+KKR + N+R+ +G 
Sbjct: 1   MSEVSYKEISNEEEGQRLDNYLIRVLKGVPKSHIYRIIRAGEVRVNKKRAQINSRLHAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPPV       + E K +    NL K    L+  +++EDS + V NKPAGI+V GGS
Sbjct: 61  SVRIPPV------RVSEPKEVFVGNNLAKR---LQESIIFEDSSLLVINKPAGIAVHGGS 111

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G++  +   L+    S      L HRLD+ETSG L++A+ R+  + +      R +QK Y
Sbjct: 112 GLSLGVIEALRK-TRSDLAYLELIHRLDKETSGCLLLAKKRSVLRAIHALLEAREVQKTY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           W+L+    + KK  I    L+K+ +  G+ +  VK+  K +  A   FK+++ + Q  CW
Sbjct: 171 WALLTHRWEGKKRVIVQAALEKNILKSGERIVKVKEEGKASETA---FKLLENYEQA-CW 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--PIQNKLYLHARYM 295
           +E  P TGRTHQ+RVH+ H+G  IVGD KY A   G        QN+L+LHAR +
Sbjct: 227 VEASPKTGRTHQIRVHSAHLGHVIVGDKKYGA-LAGQVEGIDNQQNRLFLHARSI 280


>gi|260767405|ref|ZP_05876343.1| ribosomal large subunit pseudouridine synthase C [Vibrio furnissii
           CIP 102972]
 gi|260617640|gb|EEX42821.1| ribosomal large subunit pseudouridine synthase C [Vibrio furnissii
           CIP 102972]
          Length = 316

 Score =  179 bits (453), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 111/321 (34%), Positives = 185/321 (57%), Gaps = 16/321 (4%)

Query: 1   MSLM-TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS M T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++
Sbjct: 1   MSEMRTQVQFIDIDEDMAGQRIDNFLRNQLKSIPKSVVYRILRKGEVRVNKKRVKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VR+PPV       +KE ++   S  L K ++ L+  +LYED  + V NKP+G +V
Sbjct: 61  EAGDIVRVPPVTID----VKEDEVAAPSTKLNKVAE-LEHCILYEDDHMLVLNKPSGTAV 115

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL++A+ R+A + L   FR + +
Sbjct: 116 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLIAKKRSALRQLQSQFREKTV 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y++LV G  K++ + +   LLK      +   +V+ N  G   + + FK+++ FA  
Sbjct: 175 QKYYFALVMGEWKSQCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKILEKFADA 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  ++G PI  D +Y       +T+    ++L+LHA  +   
Sbjct: 229 -TLVQASPITGRTHQIRVHTQYVGHPIAWDDRYGDRRFDAYTAQFGIDRLFLHAANIQFA 287

Query: 299 HPEGG-RLQITAPLPAHMVKT 318
           HP  G +++I APL A + K 
Sbjct: 288 HPASGEKMEINAPLDAKLEKA 308


>gi|260773154|ref|ZP_05882070.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           metschnikovii CIP 69.14]
 gi|260612293|gb|EEX37496.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           metschnikovii CIP 69.14]
          Length = 318

 Score =  178 bits (452), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 112/321 (34%), Positives = 183/321 (57%), Gaps = 17/321 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T VQ+V ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++ +G  
Sbjct: 9   TQVQFVDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLAAGDS 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RIPPV   +N    + +    S+ L + ++ L++ ++YED  + + NKP+G +V GGSG
Sbjct: 69  IRIPPVTMEVN----DSEPAAPSIKLNRVAE-LEACIVYEDDHLLILNKPSGTAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK Y+
Sbjct: 124 LKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYF 182

Query: 185 SLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G  P N K  + N  L K+ I      +V+ N  G   + + F+V++ FAQ    L
Sbjct: 183 ALVMGRWPANVK--VVNAPLLKNEINS----IVRVNPNG-KPSETRFRVLEQFAQA-TLL 234

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPE- 301
           +  P TGRTHQ+RVH  + G PI  D +Y       + S    N+L+LHA  +   HP  
Sbjct: 235 QASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYVSQFSINRLFLHAANIQFMHPAT 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G ++ I+APL A + +    +
Sbjct: 295 GDKMDISAPLDASLERALGQM 315


>gi|315179570|gb|ADT86484.1| ribosomal large subunit pseudouridine synthase C [Vibrio furnissii
           NCTC 11218]
          Length = 316

 Score =  178 bits (452), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 111/321 (34%), Positives = 185/321 (57%), Gaps = 16/321 (4%)

Query: 1   MSLM-TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS M T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++
Sbjct: 1   MSEMRTQVQFIDIDEDMAGQRIDNFLRNQLKSIPKSVVYRILRKGEVRVNKKRVKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VR+PPV       +KE ++   S  L K ++ L+  +LYED  + V NKP+G +V
Sbjct: 61  EAGDIVRVPPVTID----VKEDEVAAPSTKLNKVAE-LEHCILYEDDHMLVLNKPSGTAV 115

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL++A+ R+A + L   FR + +
Sbjct: 116 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLIAKKRSALRQLQSQFREKTV 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y++LV G  K++ + +   LLK      +   +V+ N  G   + + FK+++ FA  
Sbjct: 175 QKYYFALVMGEWKSQCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKILEKFADA 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  ++G PI  D +Y       +T+    ++L+LHA  +   
Sbjct: 229 -TLVQASPITGRTHQIRVHTQYVGHPIAWDDRYGDRRFDAYTAQFGIDRLFLHAANIQFT 287

Query: 299 HPEGG-RLQITAPLPAHMVKT 318
           HP  G +++I APL A + K 
Sbjct: 288 HPASGEKMEINAPLDAKLEKA 308


>gi|153827554|ref|ZP_01980221.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MZO-2]
 gi|149738478|gb|EDM52874.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MZO-2]
          Length = 315

 Score =  178 bits (451), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 110/317 (34%), Positives = 184/317 (58%), Gaps = 17/317 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G      EC + N  L K+ +      +V+ N  G + + + F++++ FA+  
Sbjct: 177 YYYALVMG--HWDAECKVVNAPLLKNEVNS----IVRVNPNGKS-SETRFRILEKFAEA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   H
Sbjct: 229 TLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVH 288

Query: 300 PEG-GRLQITAPLPAHM 315
           P    +L+I APL AH+
Sbjct: 289 PASEKKLEIHAPLEAHL 305


>gi|71735436|ref|YP_273876.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|257487558|ref|ZP_05641599.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tabaci ATCC 11528]
 gi|298486212|ref|ZP_07004275.1| Ribosomal large subunit pseudouridine synthase C [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|71555989|gb|AAZ35200.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|298159219|gb|EFI00277.1| Ribosomal large subunit pseudouridine synthase C [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|320325303|gb|EFW81370.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. glycinea str. B076]
 gi|320327712|gb|EFW83720.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330877844|gb|EGH11993.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330891478|gb|EGH24139.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. mori str. 301020]
 gi|330985584|gb|EGH83687.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. lachrymans str. M301315]
          Length = 318

 Score =  178 bits (451), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 112/321 (34%), Positives = 183/321 (57%), Gaps = 21/321 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  IPPV-----RVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSGLS 122

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y +
Sbjct: 123 FGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMA 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     ++ +   L+K +   G+   +V+ NE+G   A++ FKV+  F      +E 
Sbjct: 181 LVRGNWATAQKQVRAPLMKSNLRSGE--RMVEVNEEGKE-ALTIFKVLRRFGDFATMVEA 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPE 301
           +P TGRTHQ+RVH LH G  I GD KY      NF+  I++    +L+LHA  + +P P+
Sbjct: 238 KPVTGRTHQIRVHTLHAGHAIAGDTKYGDE---NFSREIRDLGGKRLFLHAYMLTVPMPD 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G +L + AP+     KT + L
Sbjct: 295 GSKLNVQAPVDEMWAKTVERL 315


>gi|289624528|ref|ZP_06457482.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aesculi str. NCPPB3681]
 gi|330869277|gb|EGH03986.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aesculi str. 0893_23]
          Length = 318

 Score =  177 bits (450), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 112/321 (34%), Positives = 183/321 (57%), Gaps = 21/321 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  IPPV-----RVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSGLS 122

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y +
Sbjct: 123 FGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMA 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     ++ +   L+K +   G+   +V+ NE+G   A++ FKV+  F      +E 
Sbjct: 181 LVRGNWATAQKQVRAPLMKSNLRSGE--RMVEVNEEGKK-ALTIFKVLRRFGDFATMVEA 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPE 301
           +P TGRTHQ+RVH LH G  I GD KY      NF+  I++    +L+LHA  + +P P+
Sbjct: 238 KPVTGRTHQIRVHTLHAGHAIAGDTKYGDE---NFSREIRDLGGKRLFLHAYMLTVPMPD 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G +L + AP+     KT + L
Sbjct: 295 GSKLNVQAPVDEMWAKTVERL 315


>gi|229528953|ref|ZP_04418343.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           12129(1)]
 gi|229332727|gb|EEN98213.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           12129(1)]
          Length = 315

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 110/317 (34%), Positives = 183/317 (57%), Gaps = 17/317 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G      EC + N  L K+ +      +V+ N  G   + + F++++ FA+  
Sbjct: 177 YYYALVMG--HWDAECKVVNAPLLKNEVNS----IVRVNSNG-KPSETRFRILEKFAEA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   H
Sbjct: 229 TLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVH 288

Query: 300 PEG-GRLQITAPLPAHM 315
           P    +L+I APL AH+
Sbjct: 289 PASEKKLEIHAPLEAHL 305


>gi|330966256|gb|EGH66516.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 318

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 112/321 (34%), Positives = 183/321 (57%), Gaps = 21/321 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  IPPV-----RVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSGLS 122

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y +
Sbjct: 123 FGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMA 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     ++ +   LLK +   G+   +V+ NE+G   A++ FKV+  F      +E 
Sbjct: 181 LVRGNWATAQKQVRAPLLKSNLRSGE--RMVEVNEEGKE-ALTLFKVLRRFGDFATMVEA 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPE 301
           +P TGRTHQ+RVH LH G  I GD KY      +F+  I++    +L+LHA  + +P P+
Sbjct: 238 KPVTGRTHQIRVHTLHAGHAIAGDTKYGDE---SFSREIRDLGGKRLFLHAYMLTVPMPD 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G +L + AP+     KT + L
Sbjct: 295 GSKLNVQAPVDEMWAKTVERL 315


>gi|170660217|ref|YP_001740053.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213969773|ref|ZP_03397908.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato T1]
 gi|301382849|ref|ZP_07231267.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato Max13]
 gi|302062845|ref|ZP_07254386.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato K40]
 gi|302131353|ref|ZP_07257343.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato NCPPB 1108]
 gi|118201620|gb|ABK79683.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213925581|gb|EEB59141.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato T1]
 gi|330878259|gb|EGH12408.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
 gi|331019164|gb|EGH99220.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. lachrymans str. M302278PT]
          Length = 318

 Score =  177 bits (449), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 112/321 (34%), Positives = 183/321 (57%), Gaps = 21/321 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  IPPV-----RVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSGLS 122

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y +
Sbjct: 123 FGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMA 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     ++ +   LLK +   G+   +V+ NE+G   A++ FKV+  F      +E 
Sbjct: 181 LVRGNWATAQKQVRAPLLKSNLRSGE--RMVEVNEEGKE-ALTLFKVLRRFGDFATMVEA 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPE 301
           +P TGRTHQ+RVH LH G  I GD KY      +F+  I++    +L+LHA  + +P P+
Sbjct: 238 KPVTGRTHQIRVHTLHAGHAIAGDTKYGDE---SFSREIRDLGGKRLFLHAYMLTVPMPD 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G +L + AP+     KT + L
Sbjct: 295 GSKLNVQAPVDEMWAKTVERL 315


>gi|153216570|ref|ZP_01950521.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           1587]
 gi|229513684|ref|ZP_04403146.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           TMA 21]
 gi|229521940|ref|ZP_04411357.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           TM 11079-80]
 gi|229524038|ref|ZP_04413443.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           bv. albensis VL426]
 gi|254226963|ref|ZP_04920527.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           V51]
 gi|254286849|ref|ZP_04961802.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           AM-19226]
 gi|124114199|gb|EAY33019.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           1587]
 gi|125620503|gb|EAZ48873.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           V51]
 gi|150423140|gb|EDN15088.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           AM-19226]
 gi|229337619|gb|EEO02636.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           bv. albensis VL426]
 gi|229340865|gb|EEO05870.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           TM 11079-80]
 gi|229348865|gb|EEO13822.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           TMA 21]
          Length = 315

 Score =  177 bits (448), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 110/317 (34%), Positives = 183/317 (57%), Gaps = 17/317 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G      EC + N  L K+ +      +V+ N  G   + + F++++ FA+  
Sbjct: 177 YYYALVMG--HWDAECKVVNAPLLKNEVNS----IVRVNPNG-KPSETRFRILEKFAEA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   H
Sbjct: 229 TLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVH 288

Query: 300 PEG-GRLQITAPLPAHM 315
           P    +L+I APL AH+
Sbjct: 289 PASEKKLEIHAPLEAHL 305


>gi|15642030|ref|NP_231662.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|121729883|ref|ZP_01682310.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           V52]
 gi|147673109|ref|YP_001217555.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O395]
 gi|227082155|ref|YP_002810706.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           M66-2]
 gi|229507883|ref|ZP_04397388.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           BX 330286]
 gi|229511882|ref|ZP_04401361.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
 gi|229519018|ref|ZP_04408461.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC9]
 gi|229607428|ref|YP_002878076.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MJ-1236]
 gi|254849115|ref|ZP_05238465.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MO10]
 gi|255745223|ref|ZP_05419172.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholera
           CIRS 101]
 gi|262167652|ref|ZP_06035355.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC27]
 gi|298497942|ref|ZP_07007749.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MAK 757]
 gi|14423896|sp|Q9KQH0|RLUC_VIBCH RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|9656573|gb|AAF95176.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|121628373|gb|EAX60874.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           V52]
 gi|146314992|gb|ABQ19531.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O395]
 gi|227010043|gb|ACP06255.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           M66-2]
 gi|227013925|gb|ACP10135.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O395]
 gi|229343707|gb|EEO08682.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC9]
 gi|229351847|gb|EEO16788.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
 gi|229355388|gb|EEO20309.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           BX 330286]
 gi|229370083|gb|ACQ60506.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MJ-1236]
 gi|254844820|gb|EET23234.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MO10]
 gi|255737053|gb|EET92449.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholera
           CIRS 101]
 gi|262023857|gb|EEY42555.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC27]
 gi|297542275|gb|EFH78325.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MAK 757]
          Length = 315

 Score =  177 bits (448), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 110/317 (34%), Positives = 183/317 (57%), Gaps = 17/317 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G      EC + N  L K+ +      +V+ N  G   + + F++++ FA+  
Sbjct: 177 YYYALVMG--HWDAECKVVNAPLLKNEVNS----IVRVNPNG-KPSETRFRILEKFAEA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   H
Sbjct: 229 TLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVH 288

Query: 300 PEG-GRLQITAPLPAHM 315
           P    +L+I APL AH+
Sbjct: 289 PASEKKLEIHAPLEAHL 305


>gi|289649339|ref|ZP_06480682.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aesculi str. 2250]
          Length = 318

 Score =  177 bits (448), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 112/321 (34%), Positives = 183/321 (57%), Gaps = 21/321 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  IPPV-----RVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSGLS 122

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y +
Sbjct: 123 FGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMA 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     ++ +   L+K +   G+   +V+ NE+G   A++ FKV+  F      +E 
Sbjct: 181 LVRGNWATAQKQVRAPLMKSNLRSGE--RMVEVNEEGKE-ALTIFKVLRRFGDFATMVEA 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPE 301
           +P TGRTHQ+RVH LH G  I GD KY      NF+  I++    +L+LHA  + +P P+
Sbjct: 238 KPVTGRTHQIRVHTLHAGHAIAGDTKYGDE---NFSREIRDLGGKRLFLHAYMLTVPMPD 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G +L + AP+     KT + L
Sbjct: 295 GCKLNVQAPVDEMWAKTVERL 315


>gi|153830613|ref|ZP_01983280.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           623-39]
 gi|148873911|gb|EDL72046.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           623-39]
          Length = 315

 Score =  176 bits (447), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 110/317 (34%), Positives = 183/317 (57%), Gaps = 17/317 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQXKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G      EC + N  L K+ +      +V+ N  G   + + F++++ FA+  
Sbjct: 177 YYYALVMG--HWDAECKVVNAPLLKNEVNS----IVRVNPNG-KPSETRFRILEKFAEA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   H
Sbjct: 229 TLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVH 288

Query: 300 PEG-GRLQITAPLPAHM 315
           P    +L+I APL AH+
Sbjct: 289 PASEKKLEIHAPLEAHL 305


>gi|153820359|ref|ZP_01973026.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           NCTC 8457]
 gi|126509095|gb|EAZ71689.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           NCTC 8457]
          Length = 310

 Score =  176 bits (447), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 110/314 (35%), Positives = 182/314 (57%), Gaps = 17/314 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++G V
Sbjct: 1   TQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEAGDV 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V GGSG
Sbjct: 61  VRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHGGSG 115

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK Y+
Sbjct: 116 LHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYY 174

Query: 185 SLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G      EC + N  L K+ +      +V+ N  G   + + F++++ FA+    +
Sbjct: 175 ALVMG--HWDAECKVVNAPLLKNEVNS----IVRVNPNG-KPSETRFRILEKFAEA-TLV 226

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEG 302
           +  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP  
Sbjct: 227 QASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVHPAS 286

Query: 303 -GRLQITAPLPAHM 315
             +L+I APL AH+
Sbjct: 287 EKKLEIHAPLEAHL 300


>gi|331012623|gb|EGH92679.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 318

 Score =  176 bits (447), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 112/321 (34%), Positives = 182/321 (56%), Gaps = 21/321 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  IPPV-----RVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSGLS 122

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y +
Sbjct: 123 FGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMA 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     ++ +   L+K +   G+ +  V  NE+G   A++ FKV+  F      +E 
Sbjct: 181 LVRGNWATAQKQVRAPLMKSNLRSGERMGEV--NEEGKE-ALTIFKVLRRFGDFATMVEA 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPE 301
           +P TGRTHQ+RVH LH G  I GD KY      NF+  I++    +L+LHA  + +P P+
Sbjct: 238 KPVTGRTHQIRVHTLHAGHAIAGDTKYGDE---NFSREIRDLGGKRLFLHAYMLTVPMPD 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G +L + AP+     KT + L
Sbjct: 295 GSKLNVQAPVDEMWAKTVERL 315


>gi|260776340|ref|ZP_05885235.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260607563|gb|EEX33828.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 314

 Score =  176 bits (447), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 108/323 (33%), Positives = 186/323 (57%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N    I    + +ILR G+VRV+KKR+K   ++++
Sbjct: 3   EIRTKVQFVDIDEDMAGQRIDNFLRNQLKSIPKSMVYRILRKGEVRVNKKRIKAEYKLKA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV      I ++Q  +  S  L K ++ L+ ++++ED  + + NKP+G +V G
Sbjct: 63  GDLVRIPPVT-----IEEKQDEVAPSTKLNKVAE-LEHMIIHEDEHMLILNKPSGTAVHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 117 GSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  K+  + +   LLK      +   +V+ N +G   + + FK+I+ FA+   
Sbjct: 176 YYFALVMGQWKSSCKVVNAPLLK-----NEVNSIVRVNPQG-KPSETRFKIIEKFAEA-T 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  ++L+LHA  +   HP
Sbjct: 229 LIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKFKHP 288

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                ++++AP+ A + K   SL
Sbjct: 289 SNDEWMEVSAPMEAKLEKALASL 311


>gi|327481320|gb|AEA84630.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           stutzeri DSM 4166]
          Length = 317

 Score =  176 bits (446), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 110/326 (33%), Positives = 181/326 (55%), Gaps = 19/326 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  + VQ + V  +    R+D + +     +    + +ILR G+VRV+K R+K   ++Q+
Sbjct: 6   SQTSGVQILEVAPELAGQRIDNFLRTQLRGVPKTLIYRILRKGEVRVNKGRIKPEYKLQA 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VR+PP+  A      E + L   +      + L+S ++YED  + V NKPAGI+V G
Sbjct: 66  GDLVRVPPLRLAERD---EPEPLAQGL-----LERLESAIVYEDKALIVLNKPAGIAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG++Y +   L+  +    ++  L HRLD++TSG+L+VA+ R+  +HL ++ R   + K
Sbjct: 118 GSGLSYGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMVAKKRSMLRHLHQALRGDGVDK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G     K+ ++  LLK +   G+ +  V ++ K    A++ F+V+  F     
Sbjct: 177 RYMALVRGRWDTSKKQVSAPLLKNTLRSGERMVEVTEDGK---EALTLFRVLRRFGDFAT 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDL 297
            +E +P TGRTHQ+RVHA H G  I GD KY      +FT  ++     +L+LHA  + +
Sbjct: 234 LVEAKPVTGRTHQIRVHARHAGHSIAGDSKYGDE---DFTREVRELGGKRLFLHAYALKV 290

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLG 323
           P P+GG L + AP+     +T + LG
Sbjct: 291 PLPDGGELSLEAPVDEVWARTLERLG 316


>gi|66044884|ref|YP_234725.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           B728a]
 gi|289671959|ref|ZP_06492849.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. syringae FF5]
 gi|63255591|gb|AAY36687.1| Pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           B728a]
 gi|330900159|gb|EGH31578.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. japonica str. M301072PT]
 gi|330952677|gb|EGH52937.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae Cit 7]
 gi|330973866|gb|EGH73932.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aceris str. M302273PT]
 gi|330975220|gb|EGH75286.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aptata str. DSM 50252]
          Length = 318

 Score =  176 bits (446), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 112/321 (34%), Positives = 182/321 (56%), Gaps = 21/321 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  IPPV-----RVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSGLS 122

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y +
Sbjct: 123 FGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMA 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G      + +   L+K +   G+   +V+ NE+G   A++ FKV+  F      +E 
Sbjct: 181 LVRGNWATALKQVRAPLMKSNLRSGE--RMVEVNEEGKE-ALTIFKVLRRFGDFATMVEA 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPE 301
           +P TGRTHQ+RVH LH G  I GD KY      NF+  I++    +L+LHA  + +P P+
Sbjct: 238 KPVTGRTHQIRVHTLHAGHAIAGDTKYGDE---NFSREIRDLGGKRLFLHAYMLTVPMPD 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G +L + AP+     KT + L
Sbjct: 295 GSKLNVQAPVDDMWAKTVERL 315


>gi|258621208|ref|ZP_05716242.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM573]
 gi|258586596|gb|EEW11311.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM573]
          Length = 316

 Score =  176 bits (445), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 110/317 (34%), Positives = 181/317 (57%), Gaps = 17/317 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKTIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEAPPPSTKLNKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G      EC + N  L K+ +      +V+ N  G   + + F++++ FA+  
Sbjct: 177 YYYALVMG--HWDSECKVVNAPLLKNEVNS----IVRVNPNG-KPSETRFRILEKFAEA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   H
Sbjct: 229 TLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAKFGIERLFLHAANIQFVH 288

Query: 300 PEG-GRLQITAPLPAHM 315
           P    +L+I APL AH+
Sbjct: 289 PASEEKLEIHAPLEAHL 305


>gi|297579532|ref|ZP_06941460.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC385]
 gi|297537126|gb|EFH75959.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC385]
          Length = 315

 Score =  176 bits (445), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 109/317 (34%), Positives = 183/317 (57%), Gaps = 17/317 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G      EC + N  L K+ +      +V+ N  G   + + F++++ FA+  
Sbjct: 177 YYYALVMG--HWDAECKVVNAPLLKNEVNS----IVRVNPNG-KPSETRFRILEKFAEA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   H
Sbjct: 229 TLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIQRLFLHAANIQFVH 288

Query: 300 PEG-GRLQITAPLPAHM 315
           P    +L+I APL +H+
Sbjct: 289 PASEKKLEIHAPLESHL 305


>gi|117925074|ref|YP_865691.1| ribosomal large subunit pseudouridine synthase C [Magnetococcus sp.
           MC-1]
 gi|117608830|gb|ABK44285.1| ribosomal large subunit pseudouridine synthase C [Magnetococcus sp.
           MC-1]
          Length = 328

 Score =  175 bits (444), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 114/326 (34%), Positives = 176/326 (53%), Gaps = 20/326 (6%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V+ V V+ +    RLD++ K+ +P + F  +Q+++R+GQVRV+K R + + R+  G  
Sbjct: 8   TAVRTVQVDEEYAGSRLDKFLKSQFPSVPFSLIQRLMRTGQVRVNKGRARGDRRLAFGDW 67

Query: 65  VRIPPVI----NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           VR+PPV       L H  KE KIL  S ++   +       L+ D  I V NKPAGI V 
Sbjct: 68  VRLPPVTPPTAEELEHPNKE-KILHQSADVEART-------LHRDGWILVLNKPAGIPVH 119

Query: 121 GGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           GGSG  + +   +++ ++  G   +  L HRLD+ETSG+L+      A + LTE+ R  +
Sbjct: 120 GGSGHQWGVVDAVRASLEKLGIEAQAELCHRLDKETSGLLLFGLRPRAVRLLTEAMRENQ 179

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y +LV G+P  ++  I   L K +  GG+ + VV   E+G   A++H++V+  +  
Sbjct: 180 VTKTYLTLVQGVPAARQGVINQPLSKGNVRGGERMVVV---EQGGQRAVTHYRVLRSYGV 236

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDL 297
               LE+Q  TGRTHQ+RVH   +G P+ GD KY    F          +L+LHA  +  
Sbjct: 237 A-SLLEVQLETGRTHQIRVHMQWLGHPVAGDGKYGDKAFNKWMRERGLKRLFLHASELAF 295

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL 322
            HPE   +L   APL   + +  + L
Sbjct: 296 RHPENEQKLAYQAPLDDELTRVLEGL 321


>gi|237800339|ref|ZP_04588800.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. oryzae str. 1_6]
 gi|331023196|gb|EGI03253.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. oryzae str. 1_6]
          Length = 318

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 111/321 (34%), Positives = 182/321 (56%), Gaps = 21/321 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V V  +    R+D +   +   +    + +I+R G+VRV+K R K   ++Q+G +VR
Sbjct: 11  VQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRIVRKGEVRVNKGRTKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  IPPV-----RVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSGLS 122

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y +
Sbjct: 123 FGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMA 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     ++ +   LLK +   G+   +V+ NE+G   A++ FKV+  F      +E 
Sbjct: 181 LVRGNWAAAQKQVRAPLLKSNLRSGE--RMVEVNEEGKE-ALTIFKVLRRFGDFATMVEA 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPE 301
           +P TGRTHQ+RVH LH G  I GD KY      NF+  I++    +L+LHA  + +P P+
Sbjct: 238 KPVTGRTHQIRVHTLHAGHAIAGDTKYGDE---NFSREIRDLGGKRLFLHAYMLTVPMPD 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G +L + AP+     +T + L
Sbjct: 295 GSKLNVQAPVDEMWARTVERL 315


>gi|323499352|ref|ZP_08104328.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           sinaloensis DSM 21326]
 gi|323315537|gb|EGA68572.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           sinaloensis DSM 21326]
          Length = 314

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 108/323 (33%), Positives = 184/323 (56%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V +++D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++Q+
Sbjct: 3   EIRTKVQFVDIDDDMAGQRIDNFLRNQLKSIPKSMVYRILRKGEVRVNKKRVKAEYKLQA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV      I ++ + +  S  L K ++ L+ +++YED  + + NKP+G +V G
Sbjct: 63  GDLVRIPPVT-----IEEKAEEVAPSTKLNKVAE-LEHMIIYEDEHMLILNKPSGTAVHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K
Sbjct: 117 GSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  K+  + +   LLK      +   +V+ N  G   + + FK+I+ F++   
Sbjct: 176 FYFALVMGQWKSSCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKIIEKFSEA-T 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  ++L+LHA  +   HP
Sbjct: 229 LIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKFQHP 288

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                ++I AP+ A + K    L
Sbjct: 289 SNDEWMEINAPMEAKLEKALAGL 311


>gi|258625453|ref|ZP_05720346.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM603]
 gi|258582257|gb|EEW07113.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM603]
          Length = 316

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 109/317 (34%), Positives = 180/317 (56%), Gaps = 17/317 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKTIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEATPPSTKLNKVAE-LEHCIVYEDEHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G      EC + N  L K+ +      +V+ N  G   + + F++++ F +  
Sbjct: 177 YYYALVMG--HWDPECKVVNAPLLKNEVNS----IVRVNPNG-KPSETRFRILEKFTEA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   H
Sbjct: 229 TLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAKFGIERLFLHAANIQFVH 288

Query: 300 PEG-GRLQITAPLPAHM 315
           P    +L+I APL AH+
Sbjct: 289 PASEEKLEIHAPLEAHL 305


>gi|302187286|ref|ZP_07263959.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. syringae 642]
          Length = 318

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 111/321 (34%), Positives = 182/321 (56%), Gaps = 21/321 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  IPPV-----RVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSGLS 122

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y +
Sbjct: 123 FGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMA 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G      + +   L+K +   G+   +V+ N++G   A++ FKV+  F      +E 
Sbjct: 181 LVRGNWATALKQVRAPLMKSNLRSGE--RMVEVNDEGKE-ALTIFKVLRRFGDFATMVEA 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPE 301
           +P TGRTHQ+RVH LH G  I GD KY      NF+  I++    +L+LHA  + +P P+
Sbjct: 238 KPVTGRTHQIRVHTLHAGHAIAGDTKYGDE---NFSREIRDLGGKRLFLHAYMLTVPMPD 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G +L + AP+     KT + L
Sbjct: 295 GSKLNVQAPVDDMWAKTVERL 315


>gi|218709011|ref|YP_002416632.1| ribosomal large subunit pseudouridine synthase C [Vibrio splendidus
           LGP32]
 gi|218322030|emb|CAV18069.1| Ribosomal large subunit pseudouridine synthase C [Vibrio splendidus
           LGP32]
          Length = 314

 Score =  174 bits (441), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 111/325 (34%), Positives = 183/325 (56%), Gaps = 20/325 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N   +I    + +I+R G+VRV+KKR+K   ++++
Sbjct: 3   EIRTQVQFVDIDEDMAGQRIDNFLRNQLKNIPKSMIYRIVRKGEVRVNKKRIKAEYKLKA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDS--SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           G +VRIPPV         E+K  ++  S  L K S+ L+  ++YED  + + NKP+G +V
Sbjct: 63  GDLVRIPPV-------TIEEKTEENVPSTKLNKVSE-LEQCIIYEDDHMLILNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +    +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y++LV G  KN  + +   LLK      +   +V+ N  G   + + FKV++ F Q+
Sbjct: 174 QKYYFALVMGEWKNSCKVVNAPLLK-----NEVNSIVRVNPNG-KASETRFKVLEKF-QE 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
              ++  P TGRTHQ+RVHA + G PI  D +Y       +T  +  N+L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHAQYTGHPIAWDDRYGDRRFDAYTGKVGLNRLFLHAANIKFI 286

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSL 322
           HP    ++ I+AP+   + K    L
Sbjct: 287 HPGSEEKMDISAPMERRLEKALTGL 311


>gi|238920268|ref|YP_002933783.1| 23S rRNA pseudouridylate synthase C [Edwardsiella ictaluri 93-146]
 gi|238869837|gb|ACR69548.1| ribosomal large subunit pseudouridine synthase C [Edwardsiella
           ictaluri 93-146]
          Length = 320

 Score =  174 bits (441), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 113/320 (35%), Positives = 178/320 (55%), Gaps = 14/320 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V+ V +  DE   R+D + +N    +    + +I+R G+VRV+KKR+K   ++++G  
Sbjct: 6   TSVKLVTIAADEAGQRIDNFLRNQLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLEAGDQ 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S  L K +  L   +LYED  + V NKP+G +V GGSG
Sbjct: 66  VRIPPV------RVAERDEAPVSARLDKVA-ALNGCILYEDDYLLVLNKPSGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD+ETSG+L+VA+ R+A + L E  R + +QK Y 
Sbjct: 119 LSFGVIEGLRA-LRPEARFLELVHRLDRETSGVLLVAKKRSALRSLHEQLREKGMQKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + +   LLK +   G+   VV+ N +G   + + FKV + FA     ++
Sbjct: 178 ALVRGQWQSHCKVVQAPLLKNTLQSGE--RVVRVNAEG-KPSETRFKVEERFANA-TLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D +Y   +F         N+L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHTLHAGHPIAFDDRYGDRDFDRELADTGLNRLFLHAAALRFVHPHSG 293

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             L++ APL A +    ++L
Sbjct: 294 ETLRVEAPLDAALRHCLNAL 313


>gi|86147922|ref|ZP_01066226.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio sp. MED222]
 gi|85834247|gb|EAQ52401.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio sp. MED222]
          Length = 314

 Score =  174 bits (440), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 111/325 (34%), Positives = 183/325 (56%), Gaps = 20/325 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N   +I    + +I+R G+VRV+KKR+K   ++++
Sbjct: 3   EIRTQVQFVDIDEDMAGQRIDNFLRNQLKNIPKSMIYRIVRKGEVRVNKKRIKAEYKLKA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDS--SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           G +VRIPPV         E+K  ++  S  L K S+ L+  ++YED  + + NKP+G +V
Sbjct: 63  GDLVRIPPV-------TIEEKTEENVPSTKLNKVSE-LEQCIIYEDDHMLILNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +    +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y++LV G  KN  + +   LLK      +   +V+ N  G   + + FKV++ F Q+
Sbjct: 174 QKYYFALVMGEWKNSCKVVNAPLLK-----NEVNSIVRVNPNG-KASETRFKVLEKF-QE 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
              ++  P TGRTHQ+RVHA + G PI  D +Y       +T  +  N+L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHAQYTGHPIAWDDRYGDRRFDAYTGKVGLNRLFLHAANIKFI 286

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSL 322
           HP    ++ I+AP+   + K    L
Sbjct: 287 HPGSEEKIDISAPMERRLEKALTGL 311


>gi|84394338|ref|ZP_00993060.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio splendidus 12B01]
 gi|84375031|gb|EAP91956.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio splendidus 12B01]
          Length = 314

 Score =  174 bits (440), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 112/326 (34%), Positives = 183/326 (56%), Gaps = 22/326 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N   +I    + +I+R G+VRV+KKR+K   ++++
Sbjct: 3   EIRTQVQFVDIDEDMAGQRIDNFLRNQLKNIPKSMIYRIVRKGEVRVNKKRIKAEYKLKA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDS--SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           G +VRIPPV         E+K  ++  S  L K S+ L+  ++YED  + + NKP+G +V
Sbjct: 63  GDLVRIPPV-------TIEEKTEENVPSTKLNKVSE-LEQCIIYEDDHMLILNKPSGTAV 114

Query: 120 QGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            GGSG+ +  I+       DS+  +  L HR+D++TSGIL+VA+ R+A +HL   FR + 
Sbjct: 115 HGGSGLKFGAIEALRALRPDSRFLE--LVHRIDRDTSGILLVAKKRSALRHLQAQFREKT 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           +QK Y++LV G  KN  + +   LLK      +   +V+ N  G   + + FKV++ F Q
Sbjct: 173 VQKYYFALVMGEWKNSCKVVNAPLLK-----NEVNSIVRVNPNG-KASETRFKVLEKF-Q 225

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDL 297
               ++  P TGRTHQ+RVHA + G PI  D +Y       +T  +  N+L+LHA  +  
Sbjct: 226 DATLVQASPITGRTHQIRVHAQYTGHPIAWDDRYGDRRFDAYTGKVGLNRLFLHAANIKF 285

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSL 322
            HP    ++ I+AP+   + +    L
Sbjct: 286 THPGSEEKIDISAPMEKRLERALTGL 311


>gi|269962047|ref|ZP_06176401.1| ribosomal large subunit pseudouridine synthase C [Vibrio harveyi
           1DA3]
 gi|269833131|gb|EEZ87236.1| ribosomal large subunit pseudouridine synthase C [Vibrio harveyi
           1DA3]
          Length = 355

 Score =  174 bits (440), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 108/323 (33%), Positives = 181/323 (56%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++++
Sbjct: 45  EIRTQVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKA 104

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV      + K++  +  S  L K ++ L+  +++ED  + V NKP+G +V G
Sbjct: 105 GDLVRIPPVT-----VEKKEDDVAPSTKLNKVAE-LEDKIIFEDDHLLVLNKPSGTAVHG 158

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K
Sbjct: 159 GSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFRGKTVKK 217

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  KN  + +   LLK      +   +V+ N  G   + + FKV++ F Q   
Sbjct: 218 FYFALVMGEWKNSCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKVLEKFEQA-T 270

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  N+L+LHA  +   HP
Sbjct: 271 LIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGLNRLFLHAANIKFQHP 330

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                ++I AP+ A + K    L
Sbjct: 331 SNDEWMEINAPMEAKLEKVLAGL 353


>gi|330811001|ref|YP_004355463.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327379109|gb|AEA70459.1| Ribosomal large subunit pseudouridine synthase C [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 322

 Score =  174 bits (440), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 115/322 (35%), Positives = 182/322 (56%), Gaps = 23/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 15  VQLLEVSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PPV       + E+   D  V L +     L++ ++YED  + V NKPAGI+V GGSG+
Sbjct: 75  VPPVR------VPER---DEPVPLAQGLLQRLEASIIYEDKALIVINKPAGIAVHGGSGL 125

Query: 126 AYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E  R   + K Y 
Sbjct: 126 NFGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHEQLRGDGVDKRYM 183

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  +   + +   LLK +   G+   +V+ NE+G   A++ FKV+  F      +E
Sbjct: 184 ALVRGRWETSIKQVRAPLLKSNLRSGE--RMVEVNEEGKE-ALTVFKVLRRFDDFATLIE 240

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHP 300
            +P TGRTHQ+RVH LH G  I GD KY  +   +FT  I++    +L+LHA  + +P P
Sbjct: 241 AKPVTGRTHQIRVHTLHAGHCIAGDSKYGDD---DFTKEIRDLGGKRLFLHAYMLTVPLP 297

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
           +GG L++ AP+     KT + L
Sbjct: 298 DGGELKLQAPVDDMWAKTVERL 319


>gi|157375768|ref|YP_001474368.1| lysozyme [Shewanella sediminis HAW-EB3]
 gi|157318142|gb|ABV37240.1| Lysozyme [Shewanella sediminis HAW-EB3]
          Length = 325

 Score =  174 bits (440), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 111/320 (34%), Positives = 181/320 (56%), Gaps = 13/320 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + VQ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +
Sbjct: 14  SKVQLVTIDEDNVGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQDGDI 73

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PPV  A     KE++    S  L+K S  L+  +L+ED  + V NKPAG++V GGSG
Sbjct: 74  VRVPPVRMA----DKEERP-GPSAKLSKVSQ-LEDRILFEDKHLIVLNKPAGLAVHGGSG 127

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + I   ++S   ++ +   L HRLD++TSG+L++A+ R+A +HL +  R +++QK Y 
Sbjct: 128 VDFGIIEAMRSLRPTQ-KFLELAHRLDKDTSGVLLIAKKRSALRHLHDQLRFKKMQKDYQ 186

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  + + + I   LLK +   G+   +V+ N++G     + FK+I  + Q    ++
Sbjct: 187 ALVKGTWQARDKAIKAPLLKLTLKSGE--RIVRVNQEGKECE-TRFKIIQRY-QGSTLVQ 242

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY    +  +  +   N+L+LHA  +   HP   
Sbjct: 243 ASPVTGRTHQIRVHCQYTGHPIACDEKYSEQKYDDSIRALGLNRLFLHAAQLRFTHPGTE 302

Query: 304 RLQIT-APLPAHMVKTWDSL 322
            + I  APL   ++KT D L
Sbjct: 303 EVMIVKAPLDPVLIKTLDKL 322


>gi|323495017|ref|ZP_08100106.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           brasiliensis LMG 20546]
 gi|323310674|gb|EGA63849.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           brasiliensis LMG 20546]
          Length = 319

 Score =  173 bits (439), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 107/323 (33%), Positives = 183/323 (56%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V +++D    R+D + +NH   I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTKVQFVDIDDDMAGQRIDNFLRNHLKSIPKSMVYRILRKGEVRVNKKRVKAEYKLKA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV      I ++ + +  S  L K ++ L+ +++YED  + + NKP+G +V G
Sbjct: 63  GDLVRIPPVT-----IEEKAQEVAPSTKLNKVAE-LEHMIIYEDDHMLILNKPSGTAVHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K
Sbjct: 117 GSGLKFGAIEALRA-LRPEARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  K+  + +   LLK      +   +V+ N  G   + + FK+++ FA    
Sbjct: 176 FYFALVMGQWKSSCKVVNAPLLK-----NEVNSIVRVNPNG-KASETRFKILEKFADA-T 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  ++L+LHA  +   HP
Sbjct: 229 LIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKFQHP 288

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                ++I AP+   + K    L
Sbjct: 289 SNDEWMEINAPMEPKLEKVLKGL 311


>gi|148977658|ref|ZP_01814234.1| 23S rRNA ribosomal pseudouridine synthase [Vibrionales bacterium
           SWAT-3]
 gi|145963173|gb|EDK28441.1| 23S rRNA ribosomal pseudouridine synthase [Vibrionales bacterium
           SWAT-3]
          Length = 314

 Score =  173 bits (439), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 109/325 (33%), Positives = 184/325 (56%), Gaps = 20/325 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N   +I    + +I+R G+VRV+KKR+K   ++++
Sbjct: 3   EIRTQVQFVDIDEDMAGQRIDNFLRNQLKNIPKSMIYRIVRKGEVRVNKKRIKAEYKLKA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDS--SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           G +VRIPPV         E+K+ ++  S  L K S+ L+  ++YED  + + NKP+G +V
Sbjct: 63  GDLVRIPPV-------TIEEKVEENVPSTKLNKVSE-LEQCIIYEDDHMLILNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPEARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y++LV G  KN  + +   LLK      +   +V+ N  G   + + FKV++ F + 
Sbjct: 174 QKYYFALVMGEWKNSCKVVNAPLLK-----NEVNSIVRVNPNG-KASETRFKVLEKF-KD 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  ++L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKFT 286

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSL 322
           HP    ++ I+AP+ A + K    L
Sbjct: 287 HPGSEEKMDISAPIEARLEKALTGL 311


>gi|170720703|ref|YP_001748391.1| RluA family pseudouridine synthase [Pseudomonas putida W619]
 gi|169758706|gb|ACA72022.1| pseudouridine synthase, RluA family [Pseudomonas putida W619]
          Length = 333

 Score =  173 bits (438), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 112/322 (34%), Positives = 184/322 (57%), Gaps = 21/322 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K RVK   +IQ+G +VR
Sbjct: 26  VQLIEVAPELAGQRIDNFLITALKGVPRTLVYRILRKGEVRVNKGRVKPEYKIQAGDIVR 85

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + +  +    +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 86  VPPV-----RLPERDEPAPVAQGLLQR---LEAAIVYEDKALIVMNKPAGIAVHGGSGLS 137

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y +L
Sbjct: 138 FGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYMAL 196

Query: 187 VWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G  P +KK+  A  LLK +   G+   +V+ N++G   A++ F+V+  F +    +E 
Sbjct: 197 VRGHWPTSKKQVNAP-LLKSNLRSGE--RMVEVNDEGKE-ALTLFRVLRRFGEFATIVEA 252

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPE 301
           +P TGRTHQ+RVH LH G  I GD KY      +F+  I++    +L+LHA  + +P P+
Sbjct: 253 RPITGRTHQIRVHTLHAGHMIAGDSKYGDE---DFSREIRDLGGKRLFLHAYALTVPLPD 309

Query: 302 GGRLQITAPLPAHMVKTWDSLG 323
           GG L++ AP+     KT + LG
Sbjct: 310 GGELKLEAPVDEVWAKTVERLG 331


>gi|254508499|ref|ZP_05120618.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus 16]
 gi|219548611|gb|EED25617.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus 16]
          Length = 314

 Score =  173 bits (438), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 107/323 (33%), Positives = 182/323 (56%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V +++D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++Q+
Sbjct: 3   EIRTKVQFVDIDDDMAGQRIDNFLRNQLKSIPKSMVYRILRKGEVRVNKKRVKAEYKLQA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV      + ++   +  S  L K ++ L+ +++YED  + + NKP+G +V G
Sbjct: 63  GDLVRIPPVT-----MEEKTDEIAPSTKLNKVAE-LEHMIIYEDDHMLILNKPSGTAVHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  K +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K
Sbjct: 117 GSGLKFGAIEALRA-LRPKARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  K+  + +   LLK      +   +V+ N  G   + + FK+I+ F+    
Sbjct: 176 FYFALVMGQWKSSCKVVNAPLLK-----NEVNSIVRVNPNG-KASETRFKIIEKFSDA-T 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  ++L+LHA  +   HP
Sbjct: 229 LVQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKFQHP 288

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                ++I AP+ A + +    L
Sbjct: 289 SNDEWMEINAPMEAKLERVLAGL 311


>gi|262170983|ref|ZP_06038661.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           MB-451]
 gi|261892059|gb|EEY38045.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           MB-451]
          Length = 316

 Score =  172 bits (437), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 108/317 (34%), Positives = 179/317 (56%), Gaps = 17/317 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKTIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEATPPSTKLNKVAE-LEHCIVYEDEHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G      EC + N  L K+ +      +V+ N  G   + + F++++ F +  
Sbjct: 177 YYYALVMG--HWDPECKVVNAPLLKNEVNS----IVRVNPNG-KPSETRFRILEKFTEA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   H
Sbjct: 229 TLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAKFGIERLFLHAANIQFVH 288

Query: 300 PEG-GRLQITAPLPAHM 315
           P    +L+I APL  H+
Sbjct: 289 PASEEKLEIHAPLEVHL 305


>gi|262166132|ref|ZP_06033869.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM223]
 gi|262025848|gb|EEY44516.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM223]
          Length = 316

 Score =  172 bits (437), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 108/317 (34%), Positives = 180/317 (56%), Gaps = 17/317 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKTIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEATPPSTKLNKVAE-LEHCIVYEDEHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G      EC + N  L K+ +      +V+ N  G   + + F++++ F +  
Sbjct: 177 YYYALVMG--HWDPECKVVNAPLLKNEVNS----IVRVNPNG-KPSETRFRILEKFTEA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   H
Sbjct: 229 TLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAKFGIERLFLHAANIQFVH 288

Query: 300 PEG-GRLQITAPLPAHM 315
           P    +L+I APL A++
Sbjct: 289 PASEEKLEIHAPLEAYL 305


>gi|163803777|ref|ZP_02197632.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio sp. AND4]
 gi|159172418|gb|EDP57289.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio sp. AND4]
          Length = 314

 Score =  172 bits (436), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 109/325 (33%), Positives = 183/325 (56%), Gaps = 20/325 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++++
Sbjct: 3   EIRTKVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILD--SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           G +VRIPPV         EQK +D   S  L K ++ L+ ++++ED  + V NKP+G +V
Sbjct: 63  GDLVRIPPV-------TVEQKEVDVAPSTKLNKVAE-LEHMIIFEDEHMLVLNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A ++L   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRYLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y++LV G  KN  + +   LLK      +   +V+ N KG   + + FK+++ F Q 
Sbjct: 174 KKFYFALVMGEWKNSCKVVNAPLLK-----NEVNSIVRVNPKG-KPSETRFKILEKFEQA 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  ++L+LHA  +   
Sbjct: 228 -TLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKFQ 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP     ++I AP+ A + K    L
Sbjct: 287 HPSNDEWMEINAPMEAKLEKALAGL 311


>gi|294085986|ref|YP_003552746.1| pseudouridine synthase [Candidatus Puniceispirillum marinum
           IMCC1322]
 gi|292665561|gb|ADE40662.1| pseudouridine synthase, RluA family [Candidatus Puniceispirillum
           marinum IMCC1322]
          Length = 335

 Score =  172 bits (436), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 102/326 (31%), Positives = 172/326 (52%), Gaps = 22/326 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++  +  DE+  RLDR  +   P +    ++K+LR+G +R+D  + K  +R+  GQ +R+
Sbjct: 11  RFETISEDEDGSRLDRVLRRLIPGLAQGQIEKMLRNGLIRIDGAKAKSASRVAVGQQIRL 70

Query: 68  PPVINALNHI------IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           P  I+AL  +      +  + +   S+           +++ E       NKP+G++VQG
Sbjct: 71  PISIDALATVKPAANKMSAKALGAPSIGGAPLQKTFDDMVIGEGKGWLALNKPSGLAVQG 130

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G+G   H+DG L +     G + RL HR+D++TSG+L++A+T  +A+ LT++F    I+K
Sbjct: 131 GTGTKQHVDGMLAALAARGGDRLRLVHRIDKDTSGVLLLAKTLQSARSLTDAFHKHAIEK 190

Query: 182 IYWSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            Y +L  G+P  +   K+ I       S + G     +  ++ G   A + F+ +D   +
Sbjct: 191 TYLALCMGLPPEEGAVKQAI-------SKLPGKSGERMVADDDG-QSAHTLFRRVDHAGR 242

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           K   + ++P TGRTHQLR+H   +G  I GD KY      +    +  +L+LHA  + LP
Sbjct: 243 KLTLMALRPLTGRTHQLRIHMALIGHVICGDGKY-GGVDAHPGGMVARQLHLHAWQLKLP 301

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGF 324
               G+L ITAP   HMV + D+LG 
Sbjct: 302 D---GKL-ITAPPSPHMVTSLDALGL 323


>gi|170726386|ref|YP_001760412.1| RluA family pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169811733|gb|ACA86317.1| pseudouridine synthase, RluA family [Shewanella woodyi ATCC 51908]
          Length = 319

 Score =  172 bits (436), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 107/318 (33%), Positives = 179/318 (56%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +VR
Sbjct: 10  VQLVTIDEDHVGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQDGDIVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + ++ +    S NL+K S  L+  +L+ED  + V NKPAG++V GGSG+ 
Sbjct: 70  VPPV-----RVSEKDERPGPSANLSKVSQ-LEERILFEDKHLIVLNKPAGLAVHGGSGVD 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + I   ++S   ++ +   L HRLD++TSG+L++A+ R+A +HL +  R +++QK Y +L
Sbjct: 124 FGIIEAMRSLRPTQ-KFLELAHRLDKDTSGVLLIAKKRSALRHLHDQLRFKKMQKDYQAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + + + I   LLK +   G+   +V+ N++G     + FK++  + Q    ++  
Sbjct: 183 VKGTWQARDKAIKAPLLKLTLKSGE--RIVRVNQEGKECE-TRFKILQRY-QGSTLVQAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           P TGRTHQ+RVH  + G PI  D KY    +  +  +   N+L+LHA  +   HP    +
Sbjct: 239 PVTGRTHQIRVHCQYTGHPIACDEKYSEQKYDDSMRALGLNRLFLHAAQLRFTHPGNEEV 298

Query: 306 QIT-APLPAHMVKTWDSL 322
            I  APL   + +T D L
Sbjct: 299 MIVKAPLDPVLTQTLDKL 316


>gi|330502588|ref|YP_004379457.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           mendocina NK-01]
 gi|328916874|gb|AEB57705.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           mendocina NK-01]
          Length = 317

 Score =  172 bits (436), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 116/328 (35%), Positives = 183/328 (55%), Gaps = 25/328 (7%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  + VQ + V  +    R+D + +     +    + +ILR G+VRV+K R+K   ++Q+
Sbjct: 6   SPTSGVQLIEVAPELAGQRIDNFLRAQLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQA 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PP+  A      E + L   +      + L++ ++YED  + V NKPAGI+V G
Sbjct: 66  GDVVRVPPLRLAER---DEPEPLAQGL-----LERLEAAIVYEDKALIVLNKPAGIAVHG 117

Query: 122 GSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GSG+ Y  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E  R   + 
Sbjct: 118 GSGLNYGVIEAFRQLRPDAKDLE--LVHRLDRDTSGLLMIAKKRSMLRHLHEQLRGDGVD 175

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHI--GGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           K Y +LV G     K+ + N  L+KS++  G   V V  + ++    A++ F+V+  F +
Sbjct: 176 KRYMALVRGHWATAKKQV-NAPLQKSNLRSGERMVEVDGEGKE----ALTLFRVLRRFGE 230

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARY 294
               +E +P TGRTHQ+RVHA H G  I GD KY  +    FT  I+     +L+LHA  
Sbjct: 231 FATLVEAKPVTGRTHQIRVHAKHAGHSIAGDSKYGDD---GFTREIRELGGKRLFLHAYE 287

Query: 295 MDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           + +P PEGG L++ AP+     KT + L
Sbjct: 288 LHVPLPEGGVLKLEAPVDEMWAKTLERL 315


>gi|156975190|ref|YP_001446096.1| rRNA ribosomal pseudouridine synthase [Vibrio harveyi ATCC
           BAA-1116]
 gi|156526784|gb|ABU71870.1| hypothetical protein VIBHAR_02917 [Vibrio harveyi ATCC BAA-1116]
          Length = 339

 Score =  172 bits (435), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 107/323 (33%), Positives = 182/323 (56%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++++
Sbjct: 28  EIRTKVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKA 87

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV      + K++  +  S  L K ++ L+ ++++ED  + V NKP+G +V G
Sbjct: 88  GDLVRIPPVT-----VEKKEDDVAPSTKLNKVAE-LEHMIIFEDDHMLVLNKPSGTAVHG 141

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K
Sbjct: 142 GSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKK 200

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  KN  + +   LLK      +   +V+ N  G   + + FKV++ F Q   
Sbjct: 201 FYFALVMGEWKNSCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKVLERFEQA-T 253

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  ++L+LHA  +   HP
Sbjct: 254 LIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGLDRLFLHAANIKFQHP 313

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                ++I AP+ A + K    L
Sbjct: 314 SNDEWMEINAPMEAKLEKVLVGL 336


>gi|218512946|ref|ZP_03509786.1| RNA-pseudouridine synthase protein, ribosomal large subunit C
           [Rhizobium etli 8C-3]
          Length = 303

 Score =  172 bits (435), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 83/191 (43%), Positives = 118/191 (61%), Gaps = 10/191 (5%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           RVK + R+Q GQ VR+PP+   ++  +K   I    +  +   D L  ++L+ED K+ V 
Sbjct: 2   RVKSDARVQPGQTVRVPPL--DVDAKLKSGPIAGKDLKHSSDFDLLSRMVLHEDEKVIVL 59

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           NKP GI+VQGGSG+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT
Sbjct: 60  NKPPGIAVQGGSGVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLT 119

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
            +FR R  +K YW+LV G+P+  ++ I+ WL+K++   GD + + K   K A        
Sbjct: 120 AAFRERDTKKTYWALVKGVPRKHEDKISTWLVKEATADGDRMRIAKTRRKTAPTMR---- 175

Query: 232 VIDCFAQKFCW 242
               F    CW
Sbjct: 176 ----FPSTACW 182


>gi|262404383|ref|ZP_06080938.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. RC586]
 gi|262349415|gb|EEY98553.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. RC586]
          Length = 315

 Score =  172 bits (435), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 107/317 (33%), Positives = 179/317 (56%), Gaps = 17/317 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKTIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEATPPSTKLNKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G      EC + N  L K+ +      +V+ N  G   + + F++++ F +  
Sbjct: 177 YYYALVMG--HWDAECKVVNAPLLKNEVNS----IVRVNPNG-KPSETRFRILEKFTEA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   H
Sbjct: 229 TLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAKFGIERLFLHAANIQFVH 288

Query: 300 PEG-GRLQITAPLPAHM 315
           P    +++I APL  H+
Sbjct: 289 PASEEKMEIHAPLEEHL 305


>gi|221135371|ref|ZP_03561674.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase [Glaciecola sp. HTCC2999]
          Length = 316

 Score =  172 bits (435), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 115/307 (37%), Positives = 178/307 (57%), Gaps = 30/307 (9%)

Query: 5   TYVQYVVVENDEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           T+ Q   VE D E    R+D + K H   +    + +ILR G+VRV+KKR+K   ++Q+ 
Sbjct: 6   TFQQVSFVEIDPELAGQRIDNFLKTHLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLQAH 65

Query: 63  QVVRIPPVINALNHIIKEQKILDS----SVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
            V+R+PP+           ++ D+    +V L K +  ++  ++YED +I V NKP+G++
Sbjct: 66  DVIRVPPI-----------RVSDAPEPVNVKLDKVA-VMQDYIIYEDDRIMVINKPSGLA 113

Query: 119 VQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           V GGSG+++  I+G      D+K  +  L HR+D++TSGIL+VA+ R+A +HL E  R +
Sbjct: 114 VHGGSGLSFGLIEGLRALRPDAKFME--LVHRIDRDTSGILLVAKRRSALRHLHEQLRDK 171

Query: 178 RIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           ++QK Y +LVWG  P+N+ +  A  LLK     G+   +V  N +G   + + ++V+  F
Sbjct: 172 KMQKRYHALVWGQWPENRFKVKAP-LLKNVLKSGE--RIVNVNPEG-KPSETRYRVLQAF 227

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARY 294
           AQ    +E  P TGRTHQ+RVH LH G PI GD KY  +  GN     Q   +L+LHA  
Sbjct: 228 AQT-TLVEASPITGRTHQIRVHCLHAGFPIGGDPKYN-DIDGNAQLATQGLKRLFLHAHS 285

Query: 295 MDLPHPE 301
           +   HP+
Sbjct: 286 LSFIHPK 292


>gi|269139453|ref|YP_003296154.1| 23S rRNA pseudouridylate synthase [Edwardsiella tarda EIB202]
 gi|267985114|gb|ACY84943.1| 23S rRNA pseudouridylate synthase [Edwardsiella tarda EIB202]
 gi|304559348|gb|ADM42012.1| Ribosomal large subunit pseudouridine synthase C [Edwardsiella
           tarda FL6-60]
          Length = 320

 Score =  172 bits (435), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 111/311 (35%), Positives = 174/311 (55%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +N    +    + +I+R G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKLVTIAADEAGQRIDNFLRNQLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLEAGDQVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+     S  L K +  L   +LYED  + V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAERDEAPVSARLDKVA-ALNDCILYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD+ETSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRETSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK +   G+   VV+ N +G   + + FKV + FA     ++  
Sbjct: 180 VRGQWQSHCKVVQAPLLKNTLQSGE--RVVRVNAEG-KPSETRFKVEERFANA-TLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y   +F         N+L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTLHAGHPIAFDDRYGDRDFDRELADTGLNRLFLHAAALRFVHPHSGET 295

Query: 305 LQITAPLPAHM 315
           L++ APL A +
Sbjct: 296 LRVEAPLDAAL 306


>gi|146306651|ref|YP_001187116.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           mendocina ymp]
 gi|145574852|gb|ABP84384.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           mendocina ymp]
          Length = 332

 Score =  171 bits (434), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 114/328 (34%), Positives = 184/328 (56%), Gaps = 25/328 (7%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  + VQ + V  D    R+D + +     +    + +ILR G+VRV+K R+K   ++Q+
Sbjct: 21  SPTSGVQLIEVAPDFAGQRIDNFLRTQLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQA 80

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VR+PP+      + +  +    +  L +    L++ ++YED  + V NKPAGI+V G
Sbjct: 81  GDIVRVPPL-----RLAERDEPEPVAQGLLER---LEAAIVYEDKALIVLNKPAGIAVHG 132

Query: 122 GSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GSG+ Y  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R   + 
Sbjct: 133 GSGLNYGVIEAFRQLRPDAKDLE--LVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVD 190

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHI--GGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           K Y +LV G     K+ + N  L+KS++  G   V V  + ++    A++ F+V+  F  
Sbjct: 191 KRYMALVRGHWATAKKQV-NAPLQKSNLRSGERMVEVDGEGKE----ALTLFRVLRRFGD 245

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARY 294
               +E +P TGRTHQ+RVHA H G  I GD KY  +   +FT  I+     +L+LHA  
Sbjct: 246 FATLVEAKPVTGRTHQIRVHAKHAGHCIAGDSKYGDD---DFTREIRELGGKRLFLHAYE 302

Query: 295 MDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           + +P PEGG L++ AP+     KT + L
Sbjct: 303 LHVPLPEGGVLKLEAPVDDMWAKTLERL 330


>gi|27366288|ref|NP_761816.1| ribosomal large subunit pseudouridine synthase C [Vibrio vulnificus
           CMCP6]
 gi|320156795|ref|YP_004189174.1| ribosomal large subunit pseudouridine synthase C [Vibrio vulnificus
           MO6-24/O]
 gi|34395774|sp|Q8D8G1|RLUC_VIBVU RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|27362489|gb|AAO11343.1| Ribosomal large subunit pseudouridine synthase C [Vibrio vulnificus
           CMCP6]
 gi|319932107|gb|ADV86971.1| ribosomal large subunit pseudouridine synthase C [Vibrio vulnificus
           MO6-24/O]
          Length = 315

 Score =  171 bits (434), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 112/323 (34%), Positives = 179/323 (55%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ V ++ D    R+D + +N    +    + +I+R G+VRV+KKRVK   ++ +
Sbjct: 3   EIRTKVQIVDIDEDMAGQRIDNFLRNQLKDVPKSMIYRIVRKGEVRVNKKRVKAEYKLAA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVRIPPV      + K+      S  L K ++ L+ +++YED  + V NKP+G +V G
Sbjct: 63  GDVVRIPPVT-----LEKKDPETAPSTKLNKVAE-LQDLIIYEDDHLLVLNKPSGTAVHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 117 GSGLKFGAIEALRA-LRPEARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  KN  + +   LLK      +   +V+ N  G   + + FKVI+ F Q   
Sbjct: 176 YYFALVMGEWKNSCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKVIEKFPQA-T 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T+    N+L+LHA  +   HP
Sbjct: 229 LVQASPITGRTHQIRVHTQYSGHPIAWDDRYGDRRFDAYTAQHGLNRLFLHAANIRFTHP 288

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
              + ++I AP+   + K   SL
Sbjct: 289 ATEQPMEINAPMGEQLEKVVQSL 311


>gi|148549014|ref|YP_001269116.1| RluA family pseudouridine synthase [Pseudomonas putida F1]
 gi|148513072|gb|ABQ79932.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           putida F1]
          Length = 333

 Score =  171 bits (433), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 111/318 (34%), Positives = 178/318 (55%), Gaps = 15/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K RVK   +IQ+G +VR
Sbjct: 26  VQLIEVAPELAGQRIDNFLITALKGVPKTLVYRILRKGEVRVNKGRVKPEYKIQAGDIVR 85

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + +  +    +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 86  VPPV-----RLPERDEPAPVAQGLLQR---LEAAIVYEDKALIVMNKPAGIAVHGGSGLS 137

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y +L
Sbjct: 138 FGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYMAL 196

Query: 187 VWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G  P +KK+  A  LLK +   G+   +V+ N++G   A++ F+V+  F      +E 
Sbjct: 197 VRGHWPTSKKQVNAP-LLKSNLRSGE--RMVEVNDEGKE-ALTLFRVLRRFGDFATIVEA 252

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +P TGRTHQ+RVH LH G  I GD KY   +F          +L+LHA  + +P P+GG 
Sbjct: 253 RPITGRTHQIRVHTLHAGHMIAGDSKYGDEDFSREIRELGGKRLFLHAYALTVPLPDGGE 312

Query: 305 LQITAPLPAHMVKTWDSL 322
           L++ AP+     KT D L
Sbjct: 313 LKLEAPVDEVWAKTVDRL 330


>gi|73666929|ref|YP_302945.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia canis
           str. Jake]
 gi|72394070|gb|AAZ68347.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia canis
           str. Jake]
          Length = 308

 Score =  171 bits (432), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 114/324 (35%), Positives = 176/324 (54%), Gaps = 32/324 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +Y  V+ D++++R+D++ +     I    ++K LR G V +D  +VK N RI++G V+ I
Sbjct: 4   KYYTVKEDDQDVRVDKFVR-RVLKIPQSLVEKFLRKGIVLLDNAKVKSNTRIKTGNVIYI 62

Query: 68  PPVINALNHIIKEQ----KI--LDSS--VNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
                  N II E+    +I   DSS  +NL  +S      +LYED  + + NKPAG+SV
Sbjct: 63  K-----CNTIIGEEIHTKRICKTDSSYLINLISNS------ILYEDDDVLIINKPAGVSV 111

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           QGG+ +   I   L    D  G+  R+ HRLD++TSGIL++AR   A++ +   F+ RR+
Sbjct: 112 QGGTKVRISISDILDKIRD--GESMRIVHRLDKDTSGILMLARNARASRLIMHEFKNRRV 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +L  GIPKN    I + + KK H   ++   +         AI+ F V+      
Sbjct: 170 EKKYLALTQGIPKNDVGEINHSITKKKH---NFYENIGTGNSIFQEAITSFFVLKKLPYD 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLP 298
              LE++P TGR HQ+R+H  H+GC I+GD KY     G F + + N  L LHA ++ + 
Sbjct: 227 IGLLELKPKTGRKHQIRIHLSHIGCSIIGDKKY-----GKFCNHVLNDHLQLHAHFLSID 281

Query: 299 HPEGGRLQITAPLPAHMVKTWDSL 322
                +L  TAP+P +M  T  +L
Sbjct: 282 -IGNKKLSFTAPMPDYMKDTIMNL 304


>gi|304409811|ref|ZP_07391431.1| pseudouridine synthase, RluA family [Shewanella baltica OS183]
 gi|307304167|ref|ZP_07583920.1| pseudouridine synthase, RluA family [Shewanella baltica BA175]
 gi|304352329|gb|EFM16727.1| pseudouridine synthase, RluA family [Shewanella baltica OS183]
 gi|306913065|gb|EFN43488.1| pseudouridine synthase, RluA family [Shewanella baltica BA175]
          Length = 319

 Score =  170 bits (430), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 110/318 (34%), Positives = 179/318 (56%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +VR
Sbjct: 10  VQLITIDEDHFEQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQIGDIVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V GGSG+ 
Sbjct: 70  IPPV-----RVAEPDNRTAPSPNLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHGGSGVD 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+S +  + +   L HRLD++TSG+L+VA+ R+A +HL +  R +++QK Y +L
Sbjct: 124 YGVIEALRS-LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    + + +   LLK +   G+   +V+ N +G   + + FK++  + Q    ++  
Sbjct: 183 VKGEWSAQDKAVKQPLLKITLKSGE--RIVRVNAEG-KPSETRFKIMQRY-QGCTLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH    G PI  D KY    F G+  S    +L+LHA  +   HPE    
Sbjct: 239 PVTGRTHQIRVHCQFAGHPIACDDKYSEQGFDGSMRSLGLARLFLHAAELMFIHPENDEV 298

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++++APL  ++ +  D L
Sbjct: 299 MRVSAPLDENLSQLLDKL 316


>gi|28898835|ref|NP_798440.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|153839692|ref|ZP_01992359.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus AQ3810]
 gi|260361710|ref|ZP_05774737.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus K5030]
 gi|260879491|ref|ZP_05891846.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus AN-5034]
 gi|260898210|ref|ZP_05906706.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus Peru-466]
 gi|34395766|sp|Q87N15|RLUC_VIBPA RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|28807054|dbj|BAC60324.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|149746785|gb|EDM57773.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus AQ3810]
 gi|308088378|gb|EFO38073.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus Peru-466]
 gi|308093528|gb|EFO43223.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus AN-5034]
 gi|308111282|gb|EFO48822.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus K5030]
 gi|328474606|gb|EGF45411.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus 10329]
          Length = 315

 Score =  170 bits (430), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 104/323 (32%), Positives = 183/323 (56%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++++
Sbjct: 3   EIRTQVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV      + K+++ +  S  L K ++ L+ +++YED  + + NKP+G +V G
Sbjct: 63  GDLVRIPPVT-----VEKKEEDVAPSTKLNKVAE-LEHMIIYEDDHMLILNKPSGTAVHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K
Sbjct: 117 GSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  K+  + +   LLK      +   +V+ N  G   + + FK+++ F Q   
Sbjct: 176 FYFALVMGQWKSSCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKILEKFEQA-T 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  ++L+LHA  +   HP
Sbjct: 229 LIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQLGLDRLFLHAANIKFQHP 288

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                ++I AP+ + + K    L
Sbjct: 289 SNDEWMEINAPMESKLEKVLVGL 311


>gi|317492376|ref|ZP_07950805.1| RluA family pseudouridine synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316919715|gb|EFV41045.1| RluA family pseudouridine synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 318

 Score =  170 bits (430), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 111/320 (34%), Positives = 175/320 (54%), Gaps = 14/320 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V+ V +  DE   R+D + +N    +    + +I+R G+VRV+KKR+K   ++QSG  
Sbjct: 6   TSVKLVTIAADEAGQRIDNFLRNQLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQSGDE 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       I E+     S  L K +  L   +++ED  + V NKP+G +V GGSG
Sbjct: 66  VRIPPV------RIAERDEAPVSAKLDKVA-ALNDCIIFEDDYLLVLNKPSGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD+ETSG+L+VA+ R+A + L E  RM+ +QK Y 
Sbjct: 119 LSFGVIEGLRA-LRPEARFLELVHRLDRETSGVLLVAKKRSALRALHEQLRMKGMQKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + +   LLK     G+   +V+ N +G   + + FKV + F +    ++
Sbjct: 178 ALVRGQWQSHCKVVQAPLLKNILQSGE--RIVRVNAEG-KPSETRFKVEERF-ENATLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D +Y    F         ++L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHTLHAGHPIAFDDRYGDREFDSELKGTGLDRLFLHAAALRFEHPNTG 293

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             +++ APL   +    D L
Sbjct: 294 ETMRVEAPLDKKLRHCLDVL 313


>gi|319425978|gb|ADV54052.1| pseudouridine synthase, RluA family [Shewanella putrefaciens 200]
          Length = 330

 Score =  170 bits (430), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 110/318 (34%), Positives = 178/318 (55%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +VR
Sbjct: 21  VQLITIDEDHFEQRIDNFLMTALKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQMGDIVR 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V GGSG+ 
Sbjct: 81  IPPV-----RVAESDNRTAPSANLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHGGSGVD 134

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+S +  + +   L HRLD++TSG+L+VA+ R+A +HL +  R +++QK Y +L
Sbjct: 135 YGVIEALRS-LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQKDYLAL 193

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    + + +   LLK +   G+   +V+ N +G   + + FK++  + Q    ++  
Sbjct: 194 VKGEWSAQDKVVKQPLLKITLKSGE--RIVRVNAEG-KPSETRFKIMQRY-QGCTLVKAS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HPE    
Sbjct: 250 PVTGRTHQIRVHCQFAGHPIACDDKYSEQGFDDSMRSLGLTRLFLHAAELMFIHPENDEV 309

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++I+APL  ++ +  D L
Sbjct: 310 MRISAPLDENLSQLLDKL 327


>gi|313499940|gb|ADR61306.1| RluA family pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 318

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 110/318 (34%), Positives = 178/318 (55%), Gaps = 15/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K RVK   +IQ+G +VR
Sbjct: 11  VQLIEVAPELAGQRIDNFLITALKGVPKTLVYRILRKGEVRVNKGRVKPEYKIQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + +  +    +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  VPPV-----RLPERDEPAPVAQGLLQR---LEAAIVYEDKALIVMNKPAGIAVHGGSGLS 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y +L
Sbjct: 123 FGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYMAL 181

Query: 187 VWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G  P +KK+  A  LLK +   G+   +V+ N++G   A++ F+V+  F      +E 
Sbjct: 182 VRGHWPTSKKQVNAP-LLKSNLRSGE--RMVEVNDEGKE-ALTLFRVLRRFGDFATIVEA 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +P TGRTHQ+RVH LH G  I GD KY   +F          +L+LHA  + +P P+GG 
Sbjct: 238 RPITGRTHQIRVHTLHAGHMIAGDSKYGDEDFSREIRELGGKRLFLHAYALTVPLPDGGE 297

Query: 305 LQITAPLPAHMVKTWDSL 322
           L++ AP+     KT + L
Sbjct: 298 LKLEAPVDEVWAKTVERL 315


>gi|113868540|ref|YP_727029.1| pseudouridylate synthase, 23S RNA-specific [Ralstonia eutropha H16]
 gi|113527316|emb|CAJ93661.1| pseudouridylate synthase, 23S RNA-specific [Ralstonia eutropha H16]
          Length = 334

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 116/329 (35%), Positives = 177/329 (53%), Gaps = 35/329 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV ++   E  R+D +       +   ++ ++LRSG+VRV+K R+    R+QSG VVR
Sbjct: 21  VAYVTIDEGSEGQRIDNFLLKVAKGVPKSHIYRVLRSGEVRVNKGRIDATYRLQSGDVVR 80

Query: 67  IPPVINALNHIIKEQKILDSS-VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           IPP+           ++ +S+  +  +H    +  +L+ED+++ V NKPAG++V GGSG+
Sbjct: 81  IPPM-----------RVANSAQSDNAQHVPAGEFPVLFEDAQLLVINKPAGVAVHGGSGV 129

Query: 126 AYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A+  I+   +S  ++K  +  L HRLD+ETSGILV+A+ R+A  HL E  R   + K Y+
Sbjct: 130 AFGVIEQLRRSRPEAKFLE--LVHRLDRETSGILVLAKKRSALVHLHEQIRGSAMDKRYF 187

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           + V G   N ++ +   L K S   G+   V  Q +  A++ +  F  ++ F Q F  LE
Sbjct: 188 ACVAGEFPNARQHVKLPLYKYSTPDGER-RVRVQADGLASHTV--FNRVEAF-QGFTLLE 243

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT----------SPIQNKLYLHARY 294
            +  TGRTHQ+RVH  H G PIVGD KY     G+F+           P   +++LHA  
Sbjct: 244 AELKTGRTHQIRVHLAHSGFPIVGDEKY-----GDFSLNKALARSGARPGLKRMFLHAHR 298

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP  G  L + APLP   V     L
Sbjct: 299 LVFIHPATGEPLAVEAPLPDECVGFLQQL 327


>gi|149192304|ref|ZP_01870513.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio shilonii AK1]
 gi|148833857|gb|EDL50885.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio shilonii AK1]
          Length = 315

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 106/300 (35%), Positives = 175/300 (58%), Gaps = 15/300 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V +++D    R+D + +N   +I    + +I+R G+VRV+KKRVK   ++Q+
Sbjct: 3   EIRTKVQFVDIDDDMAGQRIDNFLRNQLKNIPKSVVYRIVRKGEVRVNKKRVKAEYKLQA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VRIPPV      I ++Q+    S  L K ++ L+S ++YED  + + NKP+GI+V G
Sbjct: 63  GDSVRIPPVT-----IEEKQEEAPISTKLNKVAE-LESQIIYEDDHMLILNKPSGIAVHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 117 GSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  K K  C    ++K   +  +   +V+ N  G   + + FKV++ F Q   
Sbjct: 176 YYFALVMG--KWKPSC---RVVKAPLLKNEVNSIVRVNPNG-KPSETRFKVLESFEQA-T 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T+ +  ++L+LHA  +   HP
Sbjct: 229 LIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTAKVGLDRLFLHAANIVFMHP 288


>gi|77460386|ref|YP_349893.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens Pf0-1]
 gi|77384389|gb|ABA75902.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens Pf0-1]
          Length = 320

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 111/322 (34%), Positives = 179/322 (55%), Gaps = 22/322 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLLEVSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PPV       + E+   D  V L +     L++ ++YED  + V NKPAGI+V GGSG+
Sbjct: 71  VPPVR------VPER---DEPVPLAQGLLQRLEASIVYEDKALIVINKPAGIAVHGGSGL 121

Query: 126 AYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            Y  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y 
Sbjct: 122 NYGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G      + +   L K +   G+   +V+ +E+    +++ FKV+  F      +E
Sbjct: 180 ALVRGNWATSIKQVRAALGKSNLRSGE--RMVEVDEEEGKESVTVFKVLRRFGDFATLIE 237

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHP 300
            +P TGRTHQ+RVH LH G  I GD KY  +   NF+  I++    +L+LHA  + +P P
Sbjct: 238 AKPITGRTHQIRVHTLHAGHCIAGDTKYGDD---NFSKEIRDLGGKRLFLHAYMLTVPLP 294

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
           +GG L++ AP+     KT + L
Sbjct: 295 DGGELKLQAPVDEMWAKTVERL 316


>gi|294636835|ref|ZP_06715170.1| ribosomal large subunit pseudouridine synthase [Edwardsiella tarda
           ATCC 23685]
 gi|291089978|gb|EFE22539.1| ribosomal large subunit pseudouridine synthase [Edwardsiella tarda
           ATCC 23685]
          Length = 320

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 110/313 (35%), Positives = 174/313 (55%), Gaps = 14/313 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V+ V +  DE   R+D + +N    +    + +I+R G+VRV+KKR+K   ++++G  
Sbjct: 6   TSVKLVTIAADEAGQRIDNFLRNQLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLEAGDE 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S  L K +  L   +LYED  + V NKP+G +V GGSG
Sbjct: 66  VRIPPV------RVAERDEAPVSARLDKVA-ALNDCVLYEDDYLMVLNKPSGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD+ETSG+L+VA+ R+A + L E  R + +QK Y 
Sbjct: 119 LSFGVIEGLRA-LRPEARFLELVHRLDRETSGVLLVAKKRSALRSLHEQLREKGMQKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + +   LLK     G+   +V+ N +G   + + FKV + FA     ++
Sbjct: 178 ALVRGHWQSHCKVVQAPLLKNILQSGE--RIVRVNAEG-KPSETRFKVEERFANA-TLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D +Y   +F         N+L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHTLHAGHPIAFDDRYGDRDFDRELAETGLNRLFLHAAALRFVHPHSG 293

Query: 304 R-LQITAPLPAHM 315
             +++ APL A +
Sbjct: 294 ETMRVEAPLDAAL 306


>gi|167032492|ref|YP_001667723.1| RluA family pseudouridine synthase [Pseudomonas putida GB-1]
 gi|166858980|gb|ABY97387.1| pseudouridine synthase, RluA family [Pseudomonas putida GB-1]
          Length = 333

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 107/318 (33%), Positives = 173/318 (54%), Gaps = 15/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K RVK   +IQ+G +VR
Sbjct: 26  VQLIEVAPELAGQRIDNFLITALKGVPKTLVYRILRKGEVRVNKGRVKPEYKIQAGDIVR 85

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + +  +    +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 86  VPPV-----RLPERDEPAPVAQGLLQR---LEAAIVYEDKALIVMNKPAGIAVHGGSGLS 137

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y +L
Sbjct: 138 FGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYMAL 196

Query: 187 VWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G  P +KK+  A  L      G   V V  + ++    A++ F+V+  F +    +E 
Sbjct: 197 VRGHWPTSKKQVNAPLLKSNLRSGERMVEVSDEGKE----ALTLFRVLRRFGEFATIVEA 252

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +P TGRTHQ+RVH LH G  I GD KY   +F          +L+LHA  + +P P+GG 
Sbjct: 253 RPITGRTHQIRVHTLHAGHMIAGDSKYGDEDFSREIRELGGKRLFLHAYALTVPLPDGGE 312

Query: 305 LQITAPLPAHMVKTWDSL 322
           L++ AP+     KT + L
Sbjct: 313 LKLEAPVDEVWAKTIERL 330


>gi|113970739|ref|YP_734532.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           MR-4]
 gi|114047966|ref|YP_738516.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           MR-7]
 gi|113885423|gb|ABI39475.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           MR-4]
 gi|113889408|gb|ABI43459.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           MR-7]
          Length = 329

 Score =  169 bits (429), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 107/307 (34%), Positives = 177/307 (57%), Gaps = 13/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + ++ D  + R+D +       +    + +I+R G+VRV+KKR+K   ++Q G VVR
Sbjct: 20  VQLITIDEDHLDQRIDNFLITVLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQIGDVVR 79

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + ++      S NL+K S  L+  +L+ED+ + V NKPAGI+V GGSG+ 
Sbjct: 80  VPPV-----RMAEQDNRTAPSANLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHGGSGVD 133

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+S +  + +   L HRLD++TSG+L+VA+ R+A +HL +  R +++QK Y +L
Sbjct: 134 YGVIEALRS-LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHDQLRQKKMQKDYLAL 192

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    + + +   LLK +   G+   +V+ N +G     + FK++  + Q    ++  
Sbjct: 193 VKGEWSAQDKVVKQPLLKLTLKSGE--RIVRVNGEGKPSE-TRFKIVQRY-QGCTLVQAS 248

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  +MG PI  D KY    F  +  +   ++L+LHA  +   HPE    
Sbjct: 249 PVTGRTHQIRVHCQYMGHPIACDEKYSEQTFDDSMRALGLSRLFLHAAELMFIHPENDEV 308

Query: 305 LQITAPL 311
           ++++APL
Sbjct: 309 MRVSAPL 315


>gi|325275825|ref|ZP_08141690.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas sp.
           TJI-51]
 gi|324099044|gb|EGB97025.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas sp.
           TJI-51]
          Length = 318

 Score =  169 bits (428), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 107/317 (33%), Positives = 176/317 (55%), Gaps = 13/317 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K RVK   +IQ+G +VR
Sbjct: 11  VQLIEVAPELAGQRIDNFLITALKGVPKTLVYRILRKGEVRVNKGRVKPEYKIQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + +  +    +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  VPPV-----RLPERDEPAPVAQGLLQR---LEAAIVYEDKALIVMNKPAGIAVHGGSGLS 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y +L
Sbjct: 123 FGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYMAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     K+ +   LLK +   G+   +V+ N++G   A++ F+V+  F      +E +
Sbjct: 182 VRGHWPTAKKQVNAPLLKSNLRSGE--RMVEVNDEGKE-ALTLFRVLRRFGDFATIVEAR 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           P TGRTHQ+RVH LH G  I GD+KY   +F          +L+LHA  + +P P+GG L
Sbjct: 239 PITGRTHQIRVHTLHAGHMIAGDNKYGDEDFSREIRELGGKRLFLHAYALTVPLPDGGEL 298

Query: 306 QITAPLPAHMVKTWDSL 322
           ++ AP+     KT + L
Sbjct: 299 KLEAPVDEVWAKTVERL 315


>gi|119478176|ref|ZP_01618232.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [marine gamma
           proteobacterium HTCC2143]
 gi|119448685|gb|EAW29929.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [marine gamma
           proteobacterium HTCC2143]
          Length = 328

 Score =  169 bits (428), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 107/301 (35%), Positives = 171/301 (56%), Gaps = 26/301 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V +     R+D +   H   +    + +ILR G+VRV+K RVK   R+  G ++R
Sbjct: 16  VTFLEVTDAHAGQRIDNFLLRHLKGVPKSRIYRILRKGEVRVNKSRVKAEYRLCDGDLLR 75

Query: 67  IPPVINALNHIIKEQKILDS-SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           IPPV       I + K  +S SV+L++    L + +LYED ++ + NKP+G++V GGSGI
Sbjct: 76  IPPVR------ISDAKPAESVSVSLSR---LLSNSILYEDDRLLIINKPSGLAVHGGSGI 126

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +   L+  +  + +   L HRLD++TSG +++A+ R+  +HL E  R  +I K Y +
Sbjct: 127 SQGLIEALR-VLRPEARFLELVHRLDRDTSGCVMIAKKRSMLRHLHEQLRSGKIDKRYLA 185

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G    K+  +   LLK S   G+  V+V  + +K    +I+ F V++ +AQ    +E
Sbjct: 186 LVSGRWPQKRRVVNEPLLKNSLQSGERMVNVAPEGKK----SITEFSVVERYAQA-TLVE 240

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY-----CANFKGNFTSPIQNKLYLHARYMDLPH 299
            +P TGRTHQ+RVHA + GCP++GD KY     C +FK         +L+LHA  + +P 
Sbjct: 241 AKPITGRTHQIRVHAQYAGCPLLGDDKYGNPAACRDFKKRGL----RRLFLHAASLKVPL 296

Query: 300 P 300
           P
Sbjct: 297 P 297


>gi|99034362|ref|ZP_01314387.1| hypothetical protein Wendoof_01000811 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 264

 Score =  169 bits (428), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 98/277 (35%), Positives = 153/277 (55%), Gaps = 14/277 (5%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           VD  + K ++R+ SGQ + +   +N + +   ++K  +  VNL      L+  +LYED  
Sbjct: 1   VDDCKAKSSDRVNSGQTITLKH-LNYIENANSDRKYNEKLVNL------LRENILYEDEY 53

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I   NKPAG+ VQGG  +   +   L      +G+  ++ HRLD++TSG+++ AR    A
Sbjct: 54  ILAINKPAGVIVQGGVKVKISMSDLLDQI--REGETFKIVHRLDRDTSGVIIFARNANVA 111

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           ++L E F+ RR++K Y +L  GIP +K     ++ L K ++ G    VV +N      A 
Sbjct: 112 RYLMEEFKGRRVKKTYLALTSGIP-SKDSGTIDYPLVKKYVSGQEKVVVDEN--SPQNAT 168

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +HF +I        +L++QP TGRTHQLR H  H+ CPI+GD KY    K  F   I NK
Sbjct: 169 THFSIIAKSKHNVAYLKLQPITGRTHQLRAHLAHINCPILGDGKYGG--KKAFIDGIANK 226

Query: 288 LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           ++LH+  + L  P    + ITAP+  H+ K+ ++L F
Sbjct: 227 IHLHSHSLSLKLPNNKEITITAPITKHIEKSIEALFF 263


>gi|104780776|ref|YP_607274.1| 23S rRNA pseudouridylate synthase [Pseudomonas entomophila L48]
 gi|95109763|emb|CAK14468.1| 23S rRNA pseudouridylate synthase [Pseudomonas entomophila L48]
          Length = 318

 Score =  169 bits (428), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 108/319 (33%), Positives = 181/319 (56%), Gaps = 17/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLIEVAPELAGQRIDNFLITALKGVPKTLVYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + +  +    +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  VPPV-----RLPERDEPAPVAQGLLQR---LEAAIVYEDKALIVMNKPAGIAVHGGSGLS 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y +L
Sbjct: 123 FGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYMAL 181

Query: 187 VWGI-PKNKKECIANWLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           V G  P +KK+   N  L+KS++  G+   +V+ N++G   A++ F+V+  F +    +E
Sbjct: 182 VRGHWPTSKKQV--NAPLQKSNLRSGE--RMVEVNDEGKE-ALTMFRVLRRFGEFATIVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   +F          +L+LHA  + +P P+GG
Sbjct: 237 ARPITGRTHQIRVHTLHAGHMIAGDSKYGDEDFSREIRELGGKRLFLHAYQLTVPLPDGG 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
            L++ AP+     KT + L
Sbjct: 297 ELKLEAPVDEVWAKTVERL 315


>gi|120599252|ref|YP_963826.1| RluA family pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|146292674|ref|YP_001183098.1| RluA family pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|120559345|gb|ABM25272.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           W3-18-1]
 gi|145564364|gb|ABP75299.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           putrefaciens CN-32]
          Length = 330

 Score =  169 bits (428), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 110/318 (34%), Positives = 178/318 (55%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +VR
Sbjct: 21  VQLITIDEDHFEQRIDNFLMTALKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQMGDIVR 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V GGSG+ 
Sbjct: 81  IPPV-----RVAESDNRTAPSANLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHGGSGVD 134

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+S +  + +   L HRLD++TSG+L+VA+ R+A +HL +  R +++QK Y +L
Sbjct: 135 YGVIEALRS-LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQKDYLAL 193

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    + + +   LLK +   G+   +V+ N +G   + + FK++  + Q    ++  
Sbjct: 194 VKGEWSAQDKVVKQPLLKITLKSGE--RIVRVNAEG-KPSETRFKIMQRY-QGCTLVKAS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HPE    
Sbjct: 250 PVTGRTHQIRVHCQFAGHPIACDDKYSEQGFDDSMRSLGLTRLFLHAAELMFIHPENDDV 309

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++I+APL  ++ +  D L
Sbjct: 310 MRISAPLDENLSQLLDKL 327


>gi|167623698|ref|YP_001673992.1| RluA family pseudouridine synthase [Shewanella halifaxensis
           HAW-EB4]
 gi|167353720|gb|ABZ76333.1| pseudouridine synthase, RluA family [Shewanella halifaxensis
           HAW-EB4]
          Length = 319

 Score =  169 bits (428), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 107/318 (33%), Positives = 176/318 (55%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++  G +VR
Sbjct: 10  VQMVTIDEDHVGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLADGDIVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + + +     S  LTK S  L+  +L+ED  + V NKP+GI+V GGSG+ 
Sbjct: 70  IPPV-----RVSESEGRPGPSAKLTKVSQ-LEERILFEDKYLIVLNKPSGIAVHGGSGVE 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++S + ++ +   L HRLD+ETSG+L++A+ R+A +HL +  R +++QK Y +L
Sbjct: 124 FGVIEAMRS-LRTQQKFLELVHRLDKETSGVLLIAKKRSALRHLHDQLRYKKMQKDYVAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK +   G+   +V+ N++G     + FK++  ++     ++  
Sbjct: 183 VRGEWQSHDKVIKAPLLKLTLKSGE--RIVRVNKEGKESE-TRFKILQRYSDS-TLVQAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH    G PI  D KY    F  +  +   N+L+LHA  +   HPE    
Sbjct: 239 PVTGRTHQIRVHCQFAGHPIACDEKYSEQKFDDSMRAQGLNRLFLHAAQLKFTHPETEEV 298

Query: 305 LQITAPLPAHMVKTWDSL 322
           +Q+ APL   +  T   L
Sbjct: 299 MQVKAPLDTILESTLKKL 316


>gi|127512523|ref|YP_001093720.1| RluA family pseudouridine synthase [Shewanella loihica PV-4]
 gi|126637818|gb|ABO23461.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           loihica PV-4]
          Length = 329

 Score =  169 bits (427), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 109/312 (34%), Positives = 168/312 (53%), Gaps = 17/312 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +  V+ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G 
Sbjct: 17  LNKVELVTIDEDNLGQRIDNFLVTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQDGD 76

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VRIPPV      +   +     S  LTK S  L+  +L+ED  I V NKPAGI+V GGS
Sbjct: 77  IVRIPPV-----RVSASEDKPGPSAKLTKVSQ-LEGRILFEDKAIIVLNKPAGIAVHGGS 130

Query: 124 GIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G+ +   G +++    + Q+    L HRLD+ETSG+L++A+ R A +HL +  R +++QK
Sbjct: 131 GVDF---GVIEAMRSLRPQQKFLELVHRLDKETSGVLLIAKKRRALKHLHDQLRYKKMQK 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  +N  + I   LLK +   G+ +  V Q  K +    + FK++  + Q   
Sbjct: 188 DYMALVRGEWQNHDKVINAPLLKLTLKSGERIVRVNQEGKPSE---TRFKIMQRY-QGAT 243

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP
Sbjct: 244 LVQASPVTGRTHQIRVHCQYAGHPIACDEKYSEQKFDDAMRELGLNRLFLHAAQLKFTHP 303

Query: 301 EGGR-LQITAPL 311
                +Q+ APL
Sbjct: 304 VSEEVMQVKAPL 315


>gi|157962324|ref|YP_001502358.1| RluA family pseudouridine synthase [Shewanella pealeana ATCC
           700345]
 gi|157847324|gb|ABV87823.1| pseudouridine synthase, RluA family [Shewanella pealeana ATCC
           700345]
          Length = 319

 Score =  169 bits (427), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 107/318 (33%), Positives = 176/318 (55%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++  G +VR
Sbjct: 10  VQLVTIDEDHVGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLADGDIVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + + +     S  LTK S  L+  +L+ED  + V NKP+GI+V GGSG+ 
Sbjct: 70  IPPV-----RVSESEGRPGPSAKLTKVSQ-LEERILFEDKYLIVLNKPSGIAVHGGSGVE 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++S + ++ +   L HRLD+ETSG+L++A+ R+A +HL +  R +++QK Y +L
Sbjct: 124 FGVIEAMRS-LRTQQKFLELVHRLDKETSGVLLIAKKRSALRHLHDQLRYKKMQKDYVAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK +   G+   +V+ N++G     + FK++  + +    ++  
Sbjct: 183 VRGEWQSHDKVIKAPLLKLTLKSGE--RIVRVNKEGKESE-TRFKILQRY-EDSTLVQAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH    G PI  D KY    F  +  +   N+L+LHA  +   HPE    
Sbjct: 239 PVTGRTHQIRVHCQFAGHPIACDEKYSEQKFDDSMRAQGLNRLFLHAAQLKFTHPETEEV 298

Query: 305 LQITAPLPAHMVKTWDSL 322
           +Q+ APL   +  T   L
Sbjct: 299 MQVKAPLDTILESTLKKL 316


>gi|307611132|emb|CBX00776.1| ribosomal large subunit pseudouridine synthase [Legionella
           pneumophila 130b]
          Length = 315

 Score =  169 bits (427), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 108/297 (36%), Positives = 168/297 (56%), Gaps = 22/297 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V Y  + ++E+  RLD +       +   ++ +I+R G+VR++KKR + N+R+Q G 
Sbjct: 1   MSEVSYKEIGSEEDGQRLDNYLIRILKGVPKSHIYRIIRGGEVRINKKRAQANSRLQIGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+       + + K +  S NL K    LK  +++EDS + V NKPAGI+V GGS
Sbjct: 61  SIRIPPI------RMTDSKEIFVSDNLAKR---LKDSIIFEDSSLLVINKPAGIAVHGGS 111

Query: 124 GIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G++   I+   K+  D       L HRLD+ETSG L++A+ R+  + +      R +QKI
Sbjct: 112 GLSLGVIEALRKTRHDL--SYLELVHRLDRETSGCLLLAKKRSTLRAIQALLEAREVQKI 169

Query: 183 YWSLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           YW+L+   W     KK  I   L K +   G+ V  V+++ K +    + FK+++ + Q 
Sbjct: 170 YWALLTHRW--DGKKKITITAPLEKNTLKSGERVVSVQKDGKASE---TDFKLLENYHQA 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGNFTSPIQNKLYLHARYM 295
            CW+E  P TGRTHQ+RVH+ + G  IVGD KY +   +       QN+LYLHAR +
Sbjct: 225 -CWVEASPKTGRTHQIRVHSAYFGHVIVGDEKYGSKVGEVEGIDYQQNRLYLHARSI 280


>gi|37526730|ref|NP_930074.1| 23S rRNA pseudouridylate synthase C [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|36786162|emb|CAE15214.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 319

 Score =  169 bits (427), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 107/311 (34%), Positives = 175/311 (56%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +++DE   R+D +       +    + +I+R G+VR++K R+K   ++ +G VVR
Sbjct: 8   VQFVTIDDDEAGQRVDNFLLARLKGVPKSMIYRIVRKGEVRINKGRIKPEYKLSAGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++ +  S  L K +  L   +LYED  I V NKPAG +V GGSG++
Sbjct: 68  IPPV------RVAERQAVPVSAKLDKVA-ALDDCILYEDDHILVLNKPAGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+  +  + +   L HRLD++TSGIL++A+ R+A + L E  R++++QK Y +L
Sbjct: 121 FGVIEGLR-VLRPEAKFLELVHRLDRDTSGILLIAKKRSALRALHEQLRLKQMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+   +VK N +G   + + FKV + FA     ++  
Sbjct: 180 VRGQWPSHCKVVQAPLLKNILQSGE--RIVKVNSEG-KPSETRFKVEERFANA-TLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D++Y    F    ++   N+L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTQYAGHPIAFDNRYGDKVFDSQLSATGLNRLFLHASVIKFTHPSTGET 295

Query: 305 LQITAPLPAHM 315
           L++ AP+   +
Sbjct: 296 LRLEAPMDEQL 306


>gi|37679452|ref|NP_934061.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio vulnificus YJ016]
 gi|37198196|dbj|BAC94032.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio vulnificus YJ016]
          Length = 315

 Score =  168 bits (426), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 110/323 (34%), Positives = 179/323 (55%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ V ++ D    R+D + +N    +    + +I+R G+VRV+KKRVK   ++ +
Sbjct: 3   EIRTKVQIVDIDEDMAGQRIDNFLRNQLKDVPKSMIYRIVRKGEVRVNKKRVKAEYKLAA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV      + K+      S  L K ++ L+ +++YED  + V NKP+G +V G
Sbjct: 63  GDIVRIPPVT-----LEKKDPETAPSTKLNKVAE-LQDLIIYEDDHLLVLNKPSGTAVHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 117 GSGLKFGAIEALRA-LRPEARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  +N  + +   LLK      +   +V+ N  G   + + FKVI+ F Q   
Sbjct: 176 YYFALVMGEWENSCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKVIEKFPQA-T 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T+    N+L+LHA  +   HP
Sbjct: 229 LVQASPITGRTHQIRVHTQYSGHPIAWDDRYGDRRFDAYTAQHGLNRLFLHAANIRFTHP 288

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
              + ++I AP+   + K   SL
Sbjct: 289 ATEQIMEINAPMGELLEKVVQSL 311


>gi|262276054|ref|ZP_06053863.1| ribosomal large subunit pseudouridine synthase C [Grimontia
           hollisae CIP 101886]
 gi|262219862|gb|EEY71178.1| ribosomal large subunit pseudouridine synthase C [Grimontia
           hollisae CIP 101886]
          Length = 318

 Score =  168 bits (426), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 103/318 (32%), Positives = 177/318 (55%), Gaps = 16/318 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ + +D    R+D + +N   ++    + ++LR G+VRV+KKR+K   ++Q+G V+R
Sbjct: 8   VQFIDISDDIAGQRIDNFLRNRLKNVPKSMIYRVLRKGEVRVNKKRIKPEYKLQAGDVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      I +  +    S  L + ++  K + +YED  + V NKP+G +V GGSG+ 
Sbjct: 68  VPPI-----KIPETAQAEAPSTKLNRVAELEKCV-IYEDDHMLVLNKPSGTAVHGGSGLH 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +     ++S +    +   L HR+D++TSGIL++A+ R+A +HL   FR + +QK Y++L
Sbjct: 122 FGAIEAMRS-LRPDARFLELVHRIDRDTSGILLIAKKRSALRHLQAQFREKTVQKYYFAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G  K   + +   LLK      +   +V+ N  G   + + FKV++ F Q    ++  
Sbjct: 181 TMGNWKPSMKKVTAPLLK-----NEVNSIVRVNPDG-KPSETRFKVLEQFDQA-TLVQAS 233

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA ++G P+  D +Y       +T     N+L+LHA  +   HP  G  
Sbjct: 234 PITGRTHQIRVHAQYVGHPLAWDDRYGDPRFDAYTKKFGLNRLFLHAANIKFTHPGSGEM 293

Query: 305 LQITAPLPAHMVKTWDSL 322
           + I+AP+   + KT + L
Sbjct: 294 MDISAPMDKQLEKTLEGL 311


>gi|89094316|ref|ZP_01167257.1| ribosomal large subunit pseudouridine synthase C [Oceanospirillum
           sp. MED92]
 gi|89081375|gb|EAR60606.1| ribosomal large subunit pseudouridine synthase C [Oceanospirillum
           sp. MED92]
          Length = 321

 Score =  168 bits (426), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 112/321 (34%), Positives = 171/321 (53%), Gaps = 17/321 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V++V + ++    R+D +            + +I+R G+VRV+KKR+K   R+  G +
Sbjct: 10  TQVRFVEITDNNAGQRIDNFLITALKGAPKSLVYRIVRKGEVRVNKKRIKPEYRLALGDL 69

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV  A       +K   + V+ ++ SD L+  +LYED  + V NKP+GI+V GGSG
Sbjct: 70  VRIPPVRLA-------EKAPPAKVS-SRLSDQLEQAVLYEDDDLIVVNKPSGIAVHGGSG 121

Query: 125 IAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           I+    G ++S+   + Q     L HRLD++TSG +++A+ R+  + + +S +   I KI
Sbjct: 122 ISL---GLIESFRQMRPQCKFLELVHRLDRDTSGCILIAKKRSTLKLMHDSLKKSTITKI 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G    +K  I   L K     G+   VVK    G    ++ +KV+  F ++   
Sbjct: 179 YHALVVGSWSERKRRIDAPLKKNELKSGE--RVVKVTADGKE-CLTEYKVLQRFGREATL 235

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPE 301
           +E +P TGRTHQ+RVH    G PIVGD KY  +            +L+LHA  +  P P 
Sbjct: 236 VEARPITGRTHQIRVHCQFAGHPIVGDEKYGVDEVNAEMREKGFKRLFLHAAELRFPLPS 295

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           GGR  + APL   + K   SL
Sbjct: 296 GGRQVVKAPLEMPLQKAIKSL 316


>gi|294141325|ref|YP_003557303.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           violacea DSS12]
 gi|293327794|dbj|BAJ02525.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           violacea DSS12]
          Length = 319

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 107/318 (33%), Positives = 174/318 (54%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +VR
Sbjct: 10  VQLITIDEDHLGQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQDGDIVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      I         S  LTK S  L+  +++ED  I V NKP+GI+V GGSG+ 
Sbjct: 70  IPPV-----RISDRSDRPGPSAKLTKVSQ-LEDRIVFEDKSIIVLNKPSGIAVHGGSGVD 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++S   ++ +   L HRLD++TSG+L++A+ R+A +HL +  R +++QK Y +L
Sbjct: 124 FGVIEAMRSLRPTQ-KFLELVHRLDKDTSGVLLIAKKRSALRHLHDQLRFKKMQKDYQAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + + + I   LLK +   G+   +V+ N++G     + FK++  + Q    ++  
Sbjct: 183 VKGTWQARDKVIKAPLLKLTLKSGE--RIVRVNQEGKECE-TRFKILQRY-QGATLVQAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           P TGRTHQ+RVH  + G PI  D KY    F  +      N+L+LHA  +   HP    +
Sbjct: 239 PVTGRTHQIRVHCQYAGHPIACDDKYSEQRFDDSMRVHGLNRLFLHAAQLRFIHPGTEEV 298

Query: 306 QIT-APLPAHMVKTWDSL 322
            +  APL   + +T D L
Sbjct: 299 MVVQAPLDPVLTETLDKL 316


>gi|163751081|ref|ZP_02158312.1| RluC [Shewanella benthica KT99]
 gi|161329242|gb|EDQ00241.1| RluC [Shewanella benthica KT99]
          Length = 319

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 107/318 (33%), Positives = 174/318 (54%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +VR
Sbjct: 10  VQLVTIDEDHLGQRIDNYLMTKLKGVPKSRIYRIVRKGEVRVNKKRIKPEYKLQDGDIVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      +  +      S  LTK S  L+  +++ED  I V NKP+GI+V GGSG+ 
Sbjct: 70  IPPV-----RVSDKSDRPGPSAKLTKVSQ-LEDRIVFEDKFIIVLNKPSGIAVHGGSGVD 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   +++   ++ +   L HRLD++TSG+L++A+ R+A +HL +  R +++QK Y +L
Sbjct: 124 FGVIEAMRALRPTQ-KFLELVHRLDKDTSGVLLIAKKRSALRHLHDQLRFKKMQKDYQAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + + + I   LLK +   G+   +V+ N++G     + FK++  + Q    ++  
Sbjct: 183 VKGTWQARDKVIKAPLLKLTLKSGE--RIVRVNQEGKECE-TRFKILQRY-QGATLVQAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP    +
Sbjct: 239 PVTGRTHQIRVHCQYAGHPIACDDKYSEQRFDDTMRVHGLNRLFLHAAQLRFTHPGTEEI 298

Query: 306 QIT-APLPAHMVKTWDSL 322
            I  APL   + +T D L
Sbjct: 299 MIVQAPLDPVLTETLDKL 316


>gi|160874866|ref|YP_001554182.1| RluA family pseudouridine synthase [Shewanella baltica OS195]
 gi|160860388|gb|ABX48922.1| pseudouridine synthase, RluA family [Shewanella baltica OS195]
          Length = 329

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 109/318 (34%), Positives = 177/318 (55%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +VR
Sbjct: 20  VQLITIDEDHFEQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQIGDIVR 79

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V GGSG+ 
Sbjct: 80  IPPV-----RVAEPDNRTAPSPNLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHGGSGVD 133

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+S +  + +   L HRLD++TSG+L+VA+ R+A +HL +  R +++QK Y +L
Sbjct: 134 YGVIEALRS-LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQKDYLAL 192

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    + + +   LLK +   G+   +V+ N +G     + FK++  + Q    ++  
Sbjct: 193 VKGEWSAQDKAVKQPLLKITLKSGE--RIVRVNAEGKPSE-TRFKIMQRY-QGCTLVKAS 248

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HPE    
Sbjct: 249 PVTGRTHQIRVHCQFAGHPIACDDKYSEQAFDDSMRSLGLTRLFLHAAELMFIHPENDEV 308

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++++APL  ++ +  D L
Sbjct: 309 MRVSAPLDENLSQLLDKL 326


>gi|315267102|gb|ADT93955.1| pseudouridine synthase, RluA family [Shewanella baltica OS678]
          Length = 319

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 109/318 (34%), Positives = 178/318 (55%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +VR
Sbjct: 10  VQLITIDEDHFEQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQIGDIVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V GGSG+ 
Sbjct: 70  IPPV-----RVAEPDNRTAPSPNLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHGGSGVD 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+S +  + +   L HRLD++TSG+L+VA+ R+A +HL +  R +++QK Y +L
Sbjct: 124 YGVIEALRS-LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    + + +   LLK +   G+   +V+ N +G   + + FK++  + Q    ++  
Sbjct: 183 VKGEWSAQDKAVKQPLLKITLKSGE--RIVRVNAEG-KPSETRFKIMQRY-QGCTLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HPE    
Sbjct: 239 PVTGRTHQIRVHCQFAGHPIACDDKYSEQAFDDSMRSLGLTRLFLHAAELMFIHPENDEV 298

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++++APL  ++ +  D L
Sbjct: 299 MRVSAPLDENLSQLLDKL 316


>gi|126173940|ref|YP_001050089.1| RluA family pseudouridine synthase [Shewanella baltica OS155]
 gi|125997145|gb|ABN61220.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           baltica OS155]
          Length = 329

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 109/318 (34%), Positives = 177/318 (55%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +VR
Sbjct: 20  VQLITIDEDHFEQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQIGDIVR 79

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V GGSG+ 
Sbjct: 80  IPPV-----RVAEPDNRTAPSPNLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHGGSGVD 133

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+S +  + +   L HRLD++TSG+L+VA+ R+A +HL +  R +++QK Y +L
Sbjct: 134 YGVIEALRS-LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQKDYLAL 192

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    + + +   LLK +   G+   +V+ N +G     + FK++  + Q    ++  
Sbjct: 193 VKGEWSAQDKAVKQPLLKITLKSGE--RIVRVNAEGKPSE-TRFKIMQRY-QGCTLVKAS 248

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HPE    
Sbjct: 249 PVTGRTHQIRVHCQFAGHPIACDDKYSEQGFDDSMRSLGLTRLFLHAAELMFIHPENDEV 308

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++++APL  ++ +  D L
Sbjct: 309 MRVSAPLDENLSQLLDKL 326


>gi|54295134|ref|YP_127549.1| ribosomal large subunit pseudouridine synthase [Legionella
           pneumophila str. Lens]
 gi|53754966|emb|CAH16454.1| Ribosomal large subunit pseudouridine synthase [Legionella
           pneumophila str. Lens]
          Length = 315

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 108/297 (36%), Positives = 168/297 (56%), Gaps = 22/297 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V Y  + ++E+  RLD +       +   ++ +I+R G+VR++KKR + N+R+Q G 
Sbjct: 1   MSEVSYKEIGSEEDGQRLDNYLIRILKGVPKSHIYRIIRGGEVRINKKRAQANSRLQIGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+       + + K +  S NL K    LK  +++EDS + V NKPAGI+V GGS
Sbjct: 61  SIRIPPI------RMTDSKEIFVSDNLAKR---LKDSIIFEDSSLLVINKPAGIAVHGGS 111

Query: 124 GIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G++   I+   K+  D       L HRLD+ETSG L++A+ R+  + +      R +QKI
Sbjct: 112 GLSLGVIEALRKTRHDL--SYLELVHRLDRETSGCLLLAKKRSTLRAIHALLEAREVQKI 169

Query: 183 YWSLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           YW+L+   W     KK  I   L K +   G+ V  V+++ K +    + FK+++ + Q 
Sbjct: 170 YWALLTHRW--DGKKKITITAPLEKNTLKSGERVVSVQKDGKASE---TDFKLLENYHQA 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGNFTSPIQNKLYLHARYM 295
            CW+E  P TGRTHQ+RVH+ + G  IVGD KY +   +       QN+LYLHAR +
Sbjct: 225 -CWVEASPKTGRTHQIRVHSAYFGHVIVGDEKYGSKVGEVEGIDYQQNRLYLHARSI 280


>gi|54298185|ref|YP_124554.1| ribosomal large subunit pseudouridine synthase [Legionella
           pneumophila str. Paris]
 gi|53751970|emb|CAH13394.1| Ribosomal large subunit pseudouridine synthase [Legionella
           pneumophila str. Paris]
          Length = 315

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 108/297 (36%), Positives = 168/297 (56%), Gaps = 22/297 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V Y  + ++E+  RLD +       +   ++ +I+R G+VR++KKR + N+R+Q G 
Sbjct: 1   MSEVSYKEIGSEEDGQRLDNYLIRILKGVPKSHIYRIIRGGEVRINKKRAQANSRLQIGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+       + + K +  S NL K    LK  +++EDS + V NKPAGI+V GGS
Sbjct: 61  SIRIPPI------RMTDSKEIFVSDNLAKR---LKDSIIFEDSSLLVINKPAGIAVHGGS 111

Query: 124 GIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G++   I+   K+  D       L HRLD+ETSG L++A+ R+  + +      R +QKI
Sbjct: 112 GLSLGVIEALRKTRHDL--SYLELVHRLDRETSGCLLLAKKRSTLRAIQALLEAREVQKI 169

Query: 183 YWSLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           YW+L+   W     KK  I   L K +   G+ V  V+++ K +    + FK+++ + Q 
Sbjct: 170 YWALLTHRW--DGKKKITITAPLEKNTLKSGERVVSVQKDGKASE---TDFKLLENYHQA 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGNFTSPIQNKLYLHARYM 295
            CW+E  P TGRTHQ+RVH+ + G  IVGD KY +   +       QN+LYLHAR +
Sbjct: 225 -CWVEASPKTGRTHQIRVHSAYFGHVIVGDGKYGSKVGEVEGIDYQQNRLYLHARSI 280


>gi|332141130|ref|YP_004426868.1| ribosomal large subunit pseudouridine synthase C [Alteromonas
           macleodii str. 'Deep ecotype']
 gi|327551152|gb|AEA97870.1| ribosomal large subunit pseudouridine synthase C [Alteromonas
           macleodii str. 'Deep ecotype']
          Length = 313

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 112/320 (35%), Positives = 177/320 (55%), Gaps = 19/320 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++V V+ D    R+D + +     +    + +ILR G+VRV+K RVK   ++Q+  +VR
Sbjct: 9   VRFVTVDADLAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKGRVKPEYKLQADDIVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +        K LD    L  H       +L+ED +I V NKP+G++V GGSG++
Sbjct: 69  IPPVRVSEGAPAPSPK-LDKIAALESH-------ILFEDDRILVMNKPSGMAVHGGSGLS 120

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+G      D+K  +  L HRLD++TSG +++A+ R+A +H+ E  R  ++ K Y +
Sbjct: 121 FGLIEGLRALRPDAKFME--LVHRLDRDTSGCILIAKKRSALRHMHEQLRTGKMDKRYNA 178

Query: 186 LVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G  PKN+ +  A  L K     G+ +  V  + K +    + +++++ +A     +E
Sbjct: 179 LVAGEWPKNRFKVKAP-LRKNVLQSGERMVSVSDDGKPSE---TRYRILEEYAGA-TLVE 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
             P TGRTHQ+RVH LH G PI  D KY  A+F  +      N+L+LHAR + L HP   
Sbjct: 234 ASPITGRTHQIRVHCLHAGHPIACDPKYGDADFDASMRQKGLNRLFLHARSISLLHPATE 293

Query: 303 GRLQITAPLPAHMVKTWDSL 322
            R+  +APL   +  T ++L
Sbjct: 294 ERVTFSAPLDPILSNTLNAL 313


>gi|117921007|ref|YP_870199.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           ANA-3]
 gi|117613339|gb|ABK48793.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           ANA-3]
          Length = 329

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 105/307 (34%), Positives = 177/307 (57%), Gaps = 13/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + ++ D  + R+D +       +    + +I+R G+VRV+KKR+K   ++Q G VVR
Sbjct: 20  VQLITIDEDHLDQRIDNFLITVLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQIGDVVR 79

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + ++      S NL++ S  L+  +L+ED+ + V NKPAGI+V GGSG+ 
Sbjct: 80  VPPV-----RMAEQDNRTAPSANLSRVSQ-LEDRILHEDNHLIVLNKPAGIAVHGGSGVD 133

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+S +  + +   L HRLD++TSG+L+VA+ R+A +H+ +  R +++QK Y +L
Sbjct: 134 YGVIEALRS-LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHMHDQLRYKKMQKDYLAL 192

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    + + +   LLK +   G+   +V+ N +G   + + FK++  + Q    ++  
Sbjct: 193 VKGEWSAQDKVVKQPLLKLTLKSGE--RIVRVNAEG-KPSETRFKIVQRY-QGCTLVQAS 248

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  +MG PI  D KY    F  +  +    +L+LHA  +   HPE    
Sbjct: 249 PVTGRTHQIRVHCQYMGHPIACDEKYSEQAFDDSMRALGLTRLFLHAAELMFIHPENDEV 308

Query: 305 LQITAPL 311
           ++++APL
Sbjct: 309 MRVSAPL 315


>gi|119775123|ref|YP_927863.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119767623|gb|ABM00194.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           amazonensis SB2B]
          Length = 330

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 107/328 (32%), Positives = 176/328 (53%), Gaps = 23/328 (7%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           ++ T VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++ +
Sbjct: 15  TVPTQVQLISIDEDGAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLAA 74

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PPV      + ++      S NL + +  L+  +L+ED +I V NKPAGI+V G
Sbjct: 75  GDEVRVPPV-----RVAEKDYRTAPSANLNRVAQ-LEDRILFEDKQIIVLNKPAGIAVHG 128

Query: 122 GSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           GSG+ Y +   L+S       +P      L HRLD++TSG+L++A+ R A +HL +  R 
Sbjct: 129 GSGVDYGVIESLRSL------RPTCKFLELVHRLDRDTSGVLLIAKKRMALRHLHDQLRN 182

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           +++QK+Y +LV G  +     +   LLK +   G+   +V+ N +G   + + F+V+  F
Sbjct: 183 KQMQKVYQALVRGQWQEHDRVVKAPLLKITLKSGE--RIVRVNSEG-KPSETRFRVLRRF 239

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYM 295
            +    +E  P TGRTHQ+RVH  + G PI  D KY    F     +    +L+LHA  +
Sbjct: 240 DEA-SLVEASPVTGRTHQIRVHCQYQGHPIACDDKYSEQKFDDAMRAKGLQRLFLHAAQL 298

Query: 296 DLPHPEG-GRLQITAPLPAHMVKTWDSL 322
              HPE   ++ + APL   +    D+L
Sbjct: 299 TFTHPESETQMTVQAPLDGDLTAVLDAL 326


>gi|226943601|ref|YP_002798674.1| Pseudouridine synthase, RluC [Azotobacter vinelandii DJ]
 gi|226718528|gb|ACO77699.1| Pseudouridine synthase, RluC [Azotobacter vinelandii DJ]
          Length = 278

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 101/278 (36%), Positives = 165/278 (59%), Gaps = 21/278 (7%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFL 97
           +ILR G+VRV+K R+K   ++Q+G +VR+PP+  A           D  V L +   + L
Sbjct: 4   RILRKGEVRVNKGRIKPEYKLQAGDLVRVPPLRLAER---------DEPVPLAQGLLERL 54

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++ +++ED  + V NKPAGI+V GGSG+++ +   L+  +  + +   L HRLD++TSG+
Sbjct: 55  EAAIVHEDKSLIVLNKPAGIAVHGGSGLSHGVIEALRQ-LRPEARDLELVHRLDRDTSGL 113

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+ R+  +HL E+ R   + K Y +LV G   + ++ ++  L K +   G+   +V+
Sbjct: 114 LMIAKKRSMLRHLHEALRGDGVDKRYLALVRGAWPSARKQVSAPLQKNTLRSGE--RMVE 171

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +E+G   A++ F+V+  F      +E +P TGRTHQ+RVHA H G PI GD KY     
Sbjct: 172 VDEEG-REALTLFRVLRRFGDFATLVEAKPVTGRTHQIRVHARHAGHPIAGDAKYGDE-- 228

Query: 278 GNFTSPIQ----NKLYLHARYMDLPHPEGGRLQITAPL 311
             FT  I+     +L+LHA  + +P PEGG L++ AP+
Sbjct: 229 -TFTREIRALGGKRLFLHAYSLAVPLPEGGELRLEAPV 265


>gi|194290175|ref|YP_002006082.1| ribosomal large subunit pseudouridine synthase c [Cupriavidus
           taiwanensis LMG 19424]
 gi|193224010|emb|CAQ70019.1| Ribosomal large subunit pseudouridine synthase C [Cupriavidus
           taiwanensis LMG 19424]
          Length = 333

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 116/329 (35%), Positives = 168/329 (51%), Gaps = 36/329 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV ++   E  R+D +       +   ++ ++LRSG+VRV+K R+    R+QSG VVR
Sbjct: 21  VAYVTIDEGSEGQRIDNFLLKVAKGVPKSHIYRVLRSGEVRVNKGRIDATYRLQSGDVVR 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++      S        +F    +L+ED+ + V NKPAG++V GGSG+A
Sbjct: 81  IPP--------MRVASAAQSGAAPVPAGEF---PVLFEDAHLLVINKPAGVAVHGGSGVA 129

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    S+ Q     L HRLD+ETSGILV+A+ R+A  HL E  R   + K Y+
Sbjct: 130 F---GVIEQLRRSRPQAKFLELVHRLDRETSGILVLAKKRSALVHLHEQIRGNTMDKRYY 186

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           + V G   N ++ +   L K S   G+   V  Q +  A++ +  F  ++ F   F  LE
Sbjct: 187 ACVAGEFLNARQHVKLPLYKYSTPDGER-RVRVQADGLASHTV--FNRVEAFP-GFTLLE 242

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT----------SPIQNKLYLHARY 294
            +  TGRTHQ+RVH  H G PIVGD KY     G+FT           P   +++LHA  
Sbjct: 243 AELKTGRTHQIRVHLAHSGFPIVGDEKY-----GDFTLNKSLARSGAKPGIKRMFLHAHR 297

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP  G  L + APLP   V     L
Sbjct: 298 LVFIHPATGEPLSVEAPLPDECVGFLQQL 326


>gi|312882470|ref|ZP_07742211.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           caribbenthicus ATCC BAA-2122]
 gi|309369870|gb|EFP97381.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           caribbenthicus ATCC BAA-2122]
          Length = 315

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 103/323 (31%), Positives = 183/323 (56%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V +++D    R+D + +N    +    + +ILR G+VRV+KKRVK   ++Q+
Sbjct: 3   EIRTKVQFVDIDDDMAGQRIDNFLRNQLKAVPKSMVYRILRKGEVRVNKKRVKAEYKLQA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VR+PPV      + +++  +  S  L K ++ L+ ++++ED  + V NKP+G +V G
Sbjct: 63  GDIVRVPPVT-----LSEKEDNVALSTKLNKVAE-LEEMIIFEDDHLLVLNKPSGTAVHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K
Sbjct: 117 GSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  K++ + +   LLK      +   +V+ N  G   + + FK+++ FA    
Sbjct: 176 YYYALVMGEWKSQCKVVNAPLLK-----NEVNSIVRVNPNG-KASETRFKILEKFANA-T 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  +   HP
Sbjct: 229 LIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKAGLDRLFLHAANIQFVHP 288

Query: 301 -EGGRLQITAPLPAHMVKTWDSL 322
                ++++AP+   + K    L
Sbjct: 289 GSDNMIELSAPMGEKLEKVLGLL 311


>gi|217973818|ref|YP_002358569.1| RluA family pseudouridine synthase [Shewanella baltica OS223]
 gi|217498953|gb|ACK47146.1| pseudouridine synthase, RluA family [Shewanella baltica OS223]
          Length = 319

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 109/318 (34%), Positives = 178/318 (55%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +VR
Sbjct: 10  VQLITIDEDHFEQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQIGDIVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V GGSG+ 
Sbjct: 70  IPPV-----RVAEPDNRTAPSPNLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHGGSGVD 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+S +  + +   L HRLD++TSG+L+VA+ R+A +HL +  R +++QK Y +L
Sbjct: 124 YGVIEALRS-LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    + + +   LLK +   G+   +V+ N +G   + + FK++  + Q    ++  
Sbjct: 183 VKGEWSAQDKAVKQPLLKITLKSGE--RIVRVNAEG-KPSETRFKIMQRY-QGCTLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HPE    
Sbjct: 239 PVTGRTHQIRVHCQFAGHPIACDDKYSEQGFDDSMRSLGLARLFLHAAELMFIHPENDEV 298

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++++APL  ++ +  D L
Sbjct: 299 MRVSAPLDENLSQLLDKL 316


>gi|114562667|ref|YP_750180.1| pseudouridine synthase, RluA family protein [Shewanella
           frigidimarina NCIMB 400]
 gi|114333960|gb|ABI71342.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           frigidimarina NCIMB 400]
          Length = 318

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 107/318 (33%), Positives = 180/318 (56%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+YV ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +VR
Sbjct: 9   VEYVTIDEDHFEQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQIGDIVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + ++      S NL++ S  L+  +++ED+ + V NKPAGI+V GGSG+ 
Sbjct: 69  VPPV-----RVAEKDNRKAPSPNLSRVSQ-LEDRIIHEDNHLIVLNKPAGIAVHGGSGVD 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+S +  + +   L HRLD++TSG+L+VA+ R+A +HL E  R + +QK Y +L
Sbjct: 123 YGVIEGLRS-LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHEQLRSKTMQKDYLAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + +   LLK +   G+   +V+ N++G   + + +K++  + Q    ++  
Sbjct: 182 VRGEWQASDKVVKAPLLKITLKSGE--RIVRVNKEGKE-SETRYKIMQRY-QGCTLVKAS 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G  I  D KY    F  +  +   ++L+LHA  +   HPE    
Sbjct: 238 PVTGRTHQIRVHCQYAGHAIACDDKYSEQQFDDSMRALGLDRLFLHAAELKFTHPENDEI 297

Query: 305 LQITAPLPAHMVKTWDSL 322
           +Q+ APL   ++ T D L
Sbjct: 298 MQVKAPLDPVLLSTLDKL 315


>gi|239994407|ref|ZP_04714931.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase [Alteromonas macleodii ATCC
           27126]
          Length = 313

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 112/320 (35%), Positives = 175/320 (54%), Gaps = 19/320 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++V VE D    R+D + +     +    + +ILR G+VRV+K RVK   ++Q+  ++R
Sbjct: 9   VRFVTVEADLAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKGRVKPEYKLQADDLIR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +        K LD   +L  H       +L+ED +I V NKP+G++V GGSG++
Sbjct: 69  IPPVRVSEGAPAPSPK-LDKIASLESH-------ILFEDDRILVINKPSGMAVHGGSGLS 120

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+G      D+K  +  L HRLD++TSG +++A+ R+A +H+ E  R  ++ K Y +
Sbjct: 121 FGLIEGLRALRPDAKFME--LVHRLDRDTSGCILIAKKRSALRHMHEQLRTGKMDKRYNA 178

Query: 186 LVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G  PK + +  A  L K     G+ +  V  + K +    + +++++ +A     +E
Sbjct: 179 LVAGEWPKTRFKVKA-ALRKNVLQSGERMVSVSDDGKPSE---TRYRILEEYAGA-TLVE 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
             P TGRTHQ+RVH LH G PI  D KY  A+F         N+L+LHAR + L HP   
Sbjct: 234 ASPITGRTHQIRVHCLHAGHPIACDPKYGDADFDAAMRQKGLNRLFLHARSISLLHPATE 293

Query: 303 GRLQITAPLPAHMVKTWDSL 322
            R+  TAPL   +  T  +L
Sbjct: 294 ERVTFTAPLDDTLSNTLKAL 313


>gi|269967347|ref|ZP_06181408.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           alginolyticus 40B]
 gi|269828055|gb|EEZ82328.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           alginolyticus 40B]
          Length = 368

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 103/323 (31%), Positives = 180/323 (55%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++++
Sbjct: 57  EIRTKVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKA 116

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV      + K+   +  S  L K ++ L++++++ED  + + NKP+G +V G
Sbjct: 117 GDLVRIPPVT-----VEKKDDDVAPSTKLNKVAE-LENMIIFEDDHMLILNKPSGTAVHG 170

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K
Sbjct: 171 GSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKK 229

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  K+  + +   LLK      +   +V+ N  G   + + FK+++ F Q   
Sbjct: 230 FYLALVMGQWKSSCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKILEKFEQA-T 282

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  ++L+LHA  +   HP
Sbjct: 283 LIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGLDRLFLHAANIKFQHP 342

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                ++I AP+   + K    L
Sbjct: 343 SNDEWMEINAPMEPKLEKVLAGL 365


>gi|262393762|ref|YP_003285616.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. Ex25]
 gi|262337356|gb|ACY51151.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. Ex25]
          Length = 314

 Score =  167 bits (422), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 103/323 (31%), Positives = 179/323 (55%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++++
Sbjct: 3   EIRTKVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV      + K+   +  S  L K ++ L+ ++++ED  + + NKP+G +V G
Sbjct: 63  GDLVRIPPVT-----VEKKDDDVAPSTKLNKVAE-LEDMIIFEDDHMLILNKPSGTAVHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K
Sbjct: 117 GSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  K+  + +   LLK      +   +V+ N  G   + + FK+++ F Q   
Sbjct: 176 FYLALVMGQWKSSCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKILEKFEQA-T 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  ++L+LHA  +   HP
Sbjct: 229 LIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGLDRLFLHAANIKFQHP 288

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                ++I AP+   + K    L
Sbjct: 289 SNDEWMEINAPMEPKLEKVLAGL 311


>gi|148359833|ref|YP_001251040.1| ribosomal large subunit (23S rRNA) pseudouridine synthase C
           [Legionella pneumophila str. Corby]
 gi|296107879|ref|YP_003619580.1| ribosomal large subunit pseudouridine synthase C [Legionella
           pneumophila 2300/99 Alcoy]
 gi|148281606|gb|ABQ55694.1| ribosomal large subunit (23S rRNA) pseudouridine synthase C
           [Legionella pneumophila str. Corby]
 gi|295649781|gb|ADG25628.1| ribosomal large subunit pseudouridine synthase C [Legionella
           pneumophila 2300/99 Alcoy]
          Length = 315

 Score =  167 bits (422), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 108/297 (36%), Positives = 167/297 (56%), Gaps = 22/297 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V Y  + ++E   RLD +       +   ++ +I+R G+VR++KKR + N+R+Q G 
Sbjct: 1   MSEVSYKEIGSEENGQRLDNYLIRILKGVPKSHIYRIIRGGEVRINKKRAQANSRLQIGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+       + + K +  S NL K    LK  +++EDS + V NKPAGI+V GGS
Sbjct: 61  SIRIPPI------RMTDSKEIFVSDNLAKR---LKDSIIFEDSSLLVINKPAGIAVHGGS 111

Query: 124 GIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G++   I+   K+  D       L HRLD+ETSG L++A+ R+  + +      R +QKI
Sbjct: 112 GLSLGVIEALRKTRHDL--SYLELVHRLDRETSGCLLLAKKRSTLRAIQALLEAREVQKI 169

Query: 183 YWSLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           YW+L+   W     KK  I   L K +   G+ V  V+++ K +    + FK+++ + Q 
Sbjct: 170 YWALLTHRW--DGKKKITITAPLEKNTLKSGERVVSVQKDGKASE---TDFKLLENYHQA 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGNFTSPIQNKLYLHARYM 295
            CW+E  P TGRTHQ+RVH+ + G  IVGD KY +   +       QN+LYLHAR +
Sbjct: 225 -CWVEASPKTGRTHQIRVHSAYFGHVIVGDGKYGSKVGEVEGIDYQQNRLYLHARSI 280


>gi|254229869|ref|ZP_04923274.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. Ex25]
 gi|151937638|gb|EDN56491.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. Ex25]
          Length = 345

 Score =  167 bits (422), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 103/323 (31%), Positives = 179/323 (55%), Gaps = 16/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++++
Sbjct: 34  EIRTKVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKA 93

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV      + K+   +  S  L K ++ L+ ++++ED  + + NKP+G +V G
Sbjct: 94  GDLVRIPPVT-----VEKKDDDVAPSTKLNKVAE-LEDMIIFEDDHMLILNKPSGTAVHG 147

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K
Sbjct: 148 GSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKK 206

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  K+  + +   LLK      +   +V+ N  G   + + FK+++ F Q   
Sbjct: 207 FYLALVMGQWKSSCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKILEKFEQA-T 259

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  ++L+LHA  +   HP
Sbjct: 260 LIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGLDRLFLHAANIKFQHP 319

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                ++I AP+   + K    L
Sbjct: 320 SNDEWMEINAPMEPKLEKVLAGL 342


>gi|52842505|ref|YP_096304.1| ribosomal large subunit (23S rRNA) pseudouridine synthase C
           [Legionella pneumophila subsp. pneumophila str.
           Philadelphia 1]
 gi|52629616|gb|AAU28357.1| ribosomal large subunit (23S rRNA) pseudouridine synthase C
           [Legionella pneumophila subsp. pneumophila str.
           Philadelphia 1]
          Length = 317

 Score =  167 bits (422), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 108/297 (36%), Positives = 167/297 (56%), Gaps = 22/297 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V Y  + ++E   RLD +       +   ++ +I+R G+VR++KKR + ++R+Q G 
Sbjct: 3   MSEVSYKEIGSEENGQRLDNYLIRILKGVPKSHIYRIIRGGEVRINKKRAQASSRLQIGD 62

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+       + + K +  S NL K    LK  +++EDS + V NKPAGI+V GGS
Sbjct: 63  SIRIPPIR------MTDSKEIFVSDNLAKR---LKDSIIFEDSSLLVINKPAGIAVHGGS 113

Query: 124 GIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G++   I+   K+  D       L HRLD+ETSG L++A+ R+  + +      R +QKI
Sbjct: 114 GLSLGVIEALRKTRHDL--SYLELVHRLDRETSGCLLLAKKRSTLRAIQALLEAREVQKI 171

Query: 183 YWSLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           YW+L+   W     KK  I   L K +   G+ V  V+++ K +    + FK+++ + Q 
Sbjct: 172 YWALLTHRW--DGKKKITITAPLEKNTLKSGERVVSVQKDGKASE---TDFKLLENYHQA 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGNFTSPIQNKLYLHARYM 295
            CW+E  P TGRTHQ+RVH+ + G  IVGD KY A   +       QN+LYLHAR +
Sbjct: 227 -CWVEASPKTGRTHQIRVHSAYFGHVIVGDEKYGAKVGEVEGIDYQQNRLYLHARSI 282


>gi|237746016|ref|ZP_04576496.1| ribosomal large subunit pseudouridine synthase C [Oxalobacter
           formigenes HOxBLS]
 gi|229377367|gb|EEO27458.1| ribosomal large subunit pseudouridine synthase C [Oxalobacter
           formigenes HOxBLS]
          Length = 340

 Score =  166 bits (421), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 123/333 (36%), Positives = 177/333 (53%), Gaps = 35/333 (10%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S M  V+ +    +E+  R+D +    +  +   ++ +ILRSG++RV+KKRV    RI++
Sbjct: 23  SQMRQVRLITATENEDGQRIDNYLFRTFKGVPKSHVYRILRSGEIRVNKKRVDQTYRIRT 82

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G ++RIPPV  A      EQK         KH       +LYED  + V NKPAG++V G
Sbjct: 83  GDIIRIPPVKTA------EQK--------EKHIPPAGFDILYEDDSVLVINKPAGVAVHG 128

Query: 122 GSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GSG++Y +   L++     G K   L HRLD+ETSGILV+A+ R+A   L E  R   + 
Sbjct: 129 GSGVSYGVIEQLRAM--RPGAKFLELVHRLDKETSGILVLAKKRSALTRLHEQIRDGSVD 186

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQK 239
           K Y +LV G  KN ++ +   LLK     G+    V+ +E G A++ I  F V+  +   
Sbjct: 187 KRYQALVHGDWKNPRQHVRLPLLKYHTAEGE--RRVRVDESGQASHTI--FNVLKHYPD- 241

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-------KGNFTSPIQNKLYLHA 292
           F  LE +  TGRTHQ+RVH    G  I GD KY  +F       KG        +++LHA
Sbjct: 242 FTLLEAELKTGRTHQIRVHLASSGFVIAGDDKY-GDFELNRQLQKGKKGEDALKRMFLHA 300

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMV---KTWDS 321
             +   HPE G+ L I+APLP   +   KT +S
Sbjct: 301 YKITFIHPETGKPLTISAPLPDECIGYLKTLES 333


>gi|209695670|ref|YP_002263599.1| ribosomal large subunit pseudouridine synthase C (rRNA uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Aliivibrio salmonicida LFI1238]
 gi|208009622|emb|CAQ79918.1| ribosomal large subunit pseudouridine synthase C (rRNA uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Aliivibrio salmonicida LFI1238]
          Length = 315

 Score =  166 bits (421), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 109/322 (33%), Positives = 179/322 (55%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +++D    R+D +      ++    + +I+R G+VRV+KKR+K   +IQ G +VR
Sbjct: 8   VQFVEIDDDFAGQRIDNYLLARLKNVPKSMIYRIVRKGEVRVNKKRIKPEYKIQEGDIVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +   +   SV L K S+ L+S ++YED  + + NKP+G +V GGSG+ 
Sbjct: 68  IPPV-----KLPESTAVELPSVKLAKVSE-LESCIIYEDDHLLILNKPSGTAVHGGSGLK 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +     L++ +    +   L HR+D++TSGIL++A+ R+A + L E FR + +QK Y++L
Sbjct: 122 FGAIEALRA-LRPDARYLELVHRIDRDTSGILLIAKKRSALRRLQEQFRNKTVQKYYFAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K+  + +   LLK      +   +V+ N  G   + + FK+++ F Q    ++  
Sbjct: 181 VMGHWKSTCKVVNVPLLK-----NEVNSIVRVNPNGKP-SETRFKILEKFEQA-TLIQAS 233

Query: 247 PHTGRTHQLRVHALHMGCPI-----VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           P TGRTHQ+RVHA H G PI      GD ++ A + G F     ++L+LHA  +   HP 
Sbjct: 234 PITGRTHQIRVHAQHAGHPIGWDDRYGDRRFDA-YTGQFG---LDRLFLHAANIKFTHPS 289

Query: 302 GGRL-QITAPLPAHMVKTWDSL 322
              L  I+AP+   + +    L
Sbjct: 290 TEELMDISAPMEKRLERVLTGL 311


>gi|330829706|ref|YP_004392658.1| 23S rRNA pseudouridylate synthase C [Aeromonas veronii B565]
 gi|328804842|gb|AEB50041.1| 23S rRNA pseudouridylate synthase C [Aeromonas veronii B565]
          Length = 327

 Score =  166 bits (421), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 103/311 (33%), Positives = 176/311 (56%), Gaps = 15/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +E + +  R+D + K     +    + +ILR G+VRV+KKR+K   ++ +G  VR
Sbjct: 21  VQLLTIEAEHDGQRIDNFLKTQLKGVPKSLIYRILRKGEVRVNKKRIKPEYKLCAGDEVR 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + ++ ++  +++ + +    L+S +L+ED  + V NKP+G++V GGSG++
Sbjct: 81  VPPV-----RVAEKNELPSANLGVIQR---LESQILFEDDAMIVLNKPSGMAVHGGSGLS 132

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ ++K Y +L
Sbjct: 133 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRVKTMRKQYLAL 191

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + +   L K     G+ V  V  + K +    + F+++  FA+    +E  
Sbjct: 192 VRGKWQAHVKVVNAPLRKNDLQSGERVVRVSADGKPSE---TRFRIVRQFAEA-TLVECS 247

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D KY  A F     S    +L+LHA  +   HP  GR 
Sbjct: 248 PITGRTHQIRVHTLHAGHPIACDDKYGEAAFDEKMRSQGLKRLFLHAWKLSFTHPADGRE 307

Query: 305 LQITAPLPAHM 315
           +Q+ APL   +
Sbjct: 308 MQVEAPLAPEL 318


>gi|226330541|ref|ZP_03806059.1| hypothetical protein PROPEN_04459 [Proteus penneri ATCC 35198]
 gi|225201336|gb|EEG83690.1| hypothetical protein PROPEN_04459 [Proteus penneri ATCC 35198]
          Length = 317

 Score =  166 bits (421), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 106/314 (33%), Positives = 174/314 (55%), Gaps = 16/314 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     VQ+V ++ DE   R+D +       +    + +I+R G+VRV+K R+K   ++ 
Sbjct: 1   MKSFNQVQFVTIDGDEAGQRIDNFLLARLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLN 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  +RIPPV       + E++ +  S  L K S  L + +LYED  + + NKP+G +V 
Sbjct: 61  AGDSIRIPPV------RVSEKEEVAVSPKLDKVS-ALANCILYEDDHLMLINKPSGTAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HRLD++TSG+L++A+ R+A + L E  R++++Q
Sbjct: 114 GGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLIAKKRSALRALHEQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + +   LLK     G+ V  V    K +    + FKV + F  +F
Sbjct: 173 KDYLALVRGQWQSHTKVVQAPLLKNILQSGERVVKVSNEGKPSE---TRFKVEERF--EF 227

Query: 241 CWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP 298
             L +  P TGRTHQ+RVH LH G PI  D +Y   +F         N+L+LHA  +   
Sbjct: 228 ATLVKASPVTGRTHQIRVHTLHAGHPIAFDDRYGDRDFDSQLVGTKLNRLFLHASSLTFT 287

Query: 299 HPE-GGRLQITAPL 311
           HP  G +++I AP+
Sbjct: 288 HPSTGDQMRIEAPM 301


>gi|284007272|emb|CBA72588.1| 23S rRNA pseudouridylate synthase C [Arsenophonus nasoniae]
          Length = 315

 Score =  166 bits (421), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 106/317 (33%), Positives = 174/317 (54%), Gaps = 14/317 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M +   VQ+V ++NDE   R+D +       +    + +I+R G+VR++  R+K   +IQ
Sbjct: 1   MKIQNQVQFVTIDNDEAGQRIDNFLLTRLKGVPKSMIYRIIRKGEVRINSGRIKPEYKIQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G ++RIPPV  A     K+Q ++ + ++       L   +LYED  + V NKP+G++V 
Sbjct: 61  AGDLIRIPPVRQAE----KQQTVISAKLDKVAA---LSDCILYEDDHLLVLNKPSGMAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+ + I   L+  +  + +   L HRLD+ETSG+L++A+ R+A + L +  R++++Q
Sbjct: 114 GGSGVNFGIIEALR-ILRPEARFLELVHRLDRETSGVLLIAKKRSALRVLHQQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G   +  + I   LLK     G+   +VK    G  Y+ +HFK+ + F+   
Sbjct: 173 KQYLALVKGQWPSHIKVIQAPLLKNILQSGE--RIVKVGTDG-KYSETHFKIEERFSNA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVHA +   PI  D++Y   +F          +L+LHA  + L H
Sbjct: 229 TLVKASPITGRTHQIRVHAQYAKHPIACDNRYGDLDFDQQLAITGLKRLFLHASSLILIH 288

Query: 300 PEG-GRLQITAPLPAHM 315
           P    RL   APL   +
Sbjct: 289 PSSEERLTFNAPLDQQL 305


>gi|197284738|ref|YP_002150610.1| 23S rRNA pseudouridylate synthase C [Proteus mirabilis HI4320]
 gi|227357743|ref|ZP_03842092.1| ribosomal large subunit pseudouridine synthase C [Proteus mirabilis
           ATCC 29906]
 gi|194682225|emb|CAR41940.1| ribosomal large subunit pseudouridine synthase C [Proteus mirabilis
           HI4320]
 gi|227162072|gb|EEI47086.1| ribosomal large subunit pseudouridine synthase C [Proteus mirabilis
           ATCC 29906]
          Length = 317

 Score =  166 bits (420), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 108/314 (34%), Positives = 176/314 (56%), Gaps = 16/314 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     VQ+V ++ DE   R+D +       +    + +I+R G+VRV+K R+K   ++ 
Sbjct: 1   MKSFNQVQFVTIDGDEAGQRIDNFLLARLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLA 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  +RIPPV       + E++    S  L K S   + IL YED  + + NKP+G +V 
Sbjct: 61  AGDSIRIPPVR------VAEKEEHAVSPKLEKVSALAECIL-YEDEHVMLINKPSGTAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HRLD++TSG+L++A+ R+A + L E  R++++Q
Sbjct: 114 GGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLIAKKRSALRSLHEQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + +   LLK     G+   VVK + +G   + + FKV + F  +F
Sbjct: 173 KDYLALVRGQWQSHTKVVQAPLLKNILQSGE--RVVKVSSEG-KPSETRFKVEERF--EF 227

Query: 241 CWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP 298
             L +  P TGRTHQ+RVH LH G PI  D +Y   +F     S   N+L+LHA  +   
Sbjct: 228 ATLVKASPVTGRTHQIRVHTLHAGHPIAFDDRYGDRDFDTQLASTKLNRLFLHASSLTFI 287

Query: 299 HPEGG-RLQITAPL 311
           HP  G +++I AP+
Sbjct: 288 HPSTGEKMRIEAPM 301


>gi|91793653|ref|YP_563304.1| pseudouridine synthase, RluD [Shewanella denitrificans OS217]
 gi|91715655|gb|ABE55581.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           denitrificans OS217]
          Length = 318

 Score =  166 bits (420), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 112/321 (34%), Positives = 180/321 (56%), Gaps = 15/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T VQ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G V
Sbjct: 7   TQVQLVTIDEDHFEQRIDNYLITALKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQIGDV 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV      + ++      S NL++ S  L++ +++ED  + V NKPAGI+V GGSG
Sbjct: 67  VRIPPV-----RMAEKDYRTAPSANLSRVS-VLETRIIHEDKHLIVLNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           I + +   L+S +  + +   L HRLD++TSG+L+VA+ R+A +HL +  R + +QK Y 
Sbjct: 121 IDFGVIEGLRS-LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHDQLRNKTMQKDYL 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL- 243
           +LV G  + K + I   LLK +   G+   +V+ N +G   + + F+++  +    C L 
Sbjct: 180 ALVRGEWQAKDKSIKAPLLKITLASGE--RIVRVNAEG-KASETRFRIMQRY--DGCTLV 234

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +  P TGRTHQ+RVH    G  I  D KY   +F  +      N+L+LHA  +   HPE 
Sbjct: 235 KASPVTGRTHQIRVHCQFAGHAIACDDKYSEQSFDDSMRVHGLNRLFLHAAELKFIHPEN 294

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
              +Q+ APL  ++ +T + L
Sbjct: 295 DEVMQVQAPLDENLSQTLEKL 315


>gi|153000233|ref|YP_001365914.1| RluA family pseudouridine synthase [Shewanella baltica OS185]
 gi|151364851|gb|ABS07851.1| pseudouridine synthase, RluA family [Shewanella baltica OS185]
          Length = 329

 Score =  166 bits (419), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 108/318 (33%), Positives = 177/318 (55%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +VR
Sbjct: 20  VQLITIDEDHFEQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQIGDIVR 79

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V GGSG+ 
Sbjct: 80  IPPV-----RVAEPDNRTAPSPNLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHGGSGVD 133

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+S +  + +   L HRLD++TSG+L+VA+ R+A +HL +  R +++QK Y +L
Sbjct: 134 YGVIEALRS-LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQKDYLAL 192

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    + + +   LLK +   G+   +V+ N +G     + FK++  + Q    ++  
Sbjct: 193 VKGEWSAQDKAVKQPLLKITLKSGE--RIVRVNAEGKPSE-TRFKIMQRY-QGCTLVKAS 248

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HPE    
Sbjct: 249 PVTGRTHQIRVHCQFAGHPIACDDKYSEQGFDDSMRSLGLTRLFLHAAELMFIHPENDEV 308

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++++APL  ++ +  + L
Sbjct: 309 MRVSAPLDENLSQLLNKL 326


>gi|269102256|ref|ZP_06154953.1| ribosomal large subunit pseudouridine synthase C [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268162154|gb|EEZ40650.1| ribosomal large subunit pseudouridine synthase C [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 344

 Score =  166 bits (419), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 110/329 (33%), Positives = 181/329 (55%), Gaps = 22/329 (6%)

Query: 1   MSLMTYV----QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN 56
           ++LMT V    Q++ + +D    R+D + +    ++    + +ILR G+VRV+KKR+K  
Sbjct: 27  ITLMTEVKPKVQFIEISDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPE 86

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
            ++Q G +VR+PPV      I +++     S NL K ++ L+S ++YED  + V NKP+G
Sbjct: 87  YKLQDGDLVRVPPV-----SIPEKEDQAPISTNLNKVAE-LESCIIYEDDHLLVLNKPSG 140

Query: 117 ISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +V GGSG+ +  I+       D++  +  L HR+D++TSGIL+VA+ R+A + L E FR
Sbjct: 141 TAVHGGSGLKFGAIEALRALRPDARFLE--LVHRIDRDTSGILLVAKKRSALRRLQEQFR 198

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            + +QK Y++LV G  K   + +   LLK      +   +V+ N  G   + + FKV++ 
Sbjct: 199 NKTVQKYYFALVMGEWKASCKKVTAPLLK-----NEVNSIVRVNPNG-KPSDTRFKVLER 252

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARY 294
           F Q    ++  P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  
Sbjct: 253 FHQA-TLVQASPVTGRTHQIRVHCQYTGHPIAWDDRYGDPRFDAYTKKTGLNRLFLHAAN 311

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP     ++I AP+   + +  + L
Sbjct: 312 IQFTHPSTDEAMEINAPMEPKLERCLEKL 340


>gi|146311257|ref|YP_001176331.1| 23S rRNA pseudouridylate synthase C [Enterobacter sp. 638]
 gi|145318133|gb|ABP60280.1| ribosomal large subunit pseudouridine synthase C [Enterobacter sp.
           638]
          Length = 315

 Score =  166 bits (419), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 108/308 (35%), Positives = 173/308 (56%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V + +DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++++G  VR
Sbjct: 8   VKMVAIADDEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A     +E++ +   +N       L + +LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPVRVAE----REEEAVSPHLNKVA---ALTNAILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+   +V+ N +G   + + FKV + +  +FC L   
Sbjct: 180 VRGQWQSHVKVVQAPLLKNILQSGE--RIVRVNSEG-KPSETRFKVEERY--EFCTLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
            P TGRTHQ+RVH LH G PI  D +Y    F         ++L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTLHAGHPIAFDDRYGDREFDKQLAGTGLSRLFLHAAALKFTHPGTGE 294

Query: 304 RLQITAPL 311
            +++ APL
Sbjct: 295 EMRVEAPL 302


>gi|71892188|ref|YP_277920.1| ribosomal large subunit (23S) pseudouridine synthase C [Candidatus
           Blochmannia pennsylvanicus str. BPEN]
 gi|71796294|gb|AAZ41045.1| ribosomal large subunit (23S) pseudouridine synthase C [Candidatus
           Blochmannia pennsylvanicus str. BPEN]
          Length = 338

 Score =  166 bits (419), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 99/308 (32%), Positives = 173/308 (56%), Gaps = 14/308 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ + ++    R+D +   +        + KI+R+G +R++KKR+KF  ++Q G ++R
Sbjct: 8   VHFIRISSNSSGQRIDNFLYTYLKVAPKSMIYKIIRTGAIRINKKRIKFQYKLQIGDLLR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        I+  KI   ++   +   FL++I++YED  +   NKP G++  GGSG+ 
Sbjct: 68  IPP--------IRGIKINRFNMKYMEEVAFLQNIIIYEDDYLLALNKPTGVAAHGGSGLK 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  K Q   L HRLD+ETSG+L+VA+ R A  +L E  R++ ++K Y +L
Sbjct: 120 FGVIEGLRA-LRPKAQFLELVHRLDRETSGVLLVAKRRTALVYLHEQLRLQNMKKEYLAL 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G      + ++  L KK+ +      VV  + +   ++ +HF++ + F     +L ++
Sbjct: 179 VHGRWNVNLQIVSVPLFKKNTLLNS-SRVVYIDSENGKFSTTHFQIKEYFDNVATFLAIK 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEG-G 303
           P TGRTHQ+RVH  +   PIVGD++Y  +++ N  F     N+L+LHA  +   HP+   
Sbjct: 238 PITGRTHQIRVHTQYASHPIVGDNRY-GDYQSNTRFKRFGFNRLFLHASILRFIHPKTKK 296

Query: 304 RLQITAPL 311
           +  I APL
Sbjct: 297 KFHIHAPL 304


>gi|256822394|ref|YP_003146357.1| RluA family pseudouridine synthase [Kangiella koreensis DSM 16069]
 gi|256795933|gb|ACV26589.1| pseudouridine synthase, RluA family [Kangiella koreensis DSM 16069]
          Length = 316

 Score =  166 bits (419), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 112/327 (34%), Positives = 179/327 (54%), Gaps = 32/327 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V V  +E   R+D +       +   ++ K+LR G+VRV+K R+K   +I+ G  VR
Sbjct: 9   VQFVEVHAEEAGQRIDNFLLKKLKGVPKSHIYKMLRKGEVRVNKGRIKAEYKIKEGDSVR 68

Query: 67  IPPV--INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +PPV   N    +  +  I+            L+S +LYED ++ V NKP G++V GGSG
Sbjct: 69  LPPVKTTNTATEVPVKLNIVQE----------LESAILYEDKRLIVLNKPHGMAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +++   G +++    + + P   L HRLD++TSG L++A+ R+  + L E  + + + K 
Sbjct: 119 MSF---GVIEALRALRPEAPFLELVHRLDRDTSGCLLIAKKRSTLRFLHEQLQKKLMSKQ 175

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           YW+LV G    K + I ++ L K+H+  G+ V  V +N K    +++ F V++ F + F 
Sbjct: 176 YWALVEGKWPAKLKHI-DFPLAKNHLKSGERVVRVTENGKP---SLTSFNVVEVF-KNFS 230

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-----CANFKGNFTSPIQNKLYLHARYMD 296
            +  +P TGRTHQ+RVHA   G P+VGD KY        FK    S    +L+LHA  + 
Sbjct: 231 LVSAEPVTGRTHQIRVHAQQAGHPLVGDPKYGNDDVTEQFKRQGLS---GRLFLHAYSLT 287

Query: 297 LP-HPEGGRLQITAPLPAHMVKTWDSL 322
               PE   +++ APLPA + KT + L
Sbjct: 288 FKVTPEDKAIRVEAPLPADLQKTLEYL 314


>gi|227326844|ref|ZP_03830868.1| 23S rRNA pseudouridylate synthase C [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 318

 Score =  166 bits (419), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 108/318 (33%), Positives = 173/318 (54%), Gaps = 14/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  DE   R+D +   H   +    + +ILR G+VR++KKRVK   ++  G V+R
Sbjct: 8   VQFVTISADEAGQRVDNFLHTHLKGVPKSMVYRILRKGEVRINKKRVKPEYKLLDGDVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A      E+     S +L K +  L   ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRQA------ERDETPVSASLGKVA-ALAECIIYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +V+ N  G   + + FK+ + F +    +   
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILQSGE--RIVRVNSDGKQ-SETRFKIEERF-EHATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA H G PI  D +Y    F          +L+LHA+ +   HP  G  
Sbjct: 236 PVTGRTHQIRVHAQHAGHPIAFDDRYGDREFDQQLADTGLKRLFLHAQALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSL 322
           L++ APL + + +    L
Sbjct: 296 LRVEAPLDSGLRRCLQVL 313


>gi|227111672|ref|ZP_03825328.1| 23S rRNA pseudouridylate synthase C [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 318

 Score =  166 bits (419), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 108/318 (33%), Positives = 173/318 (54%), Gaps = 14/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  DE   R+D +   H   +    + +ILR G+VR++KKRVK   ++  G V+R
Sbjct: 8   VQFVTISADEAGQRIDNFLHTHLKGVPKSMVYRILRKGEVRINKKRVKPEYKLLDGDVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A      E+     S +L K +  L   ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRQA------ERDETPVSASLGKVA-ALAECIIYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +V+ N  G   + + FK+ + F +    +   
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILQSGE--RIVRVNSDG-KPSETRFKIEERF-EHATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA H G PI  D +Y    F          +L+LHA+ +   HP  G  
Sbjct: 236 PVTGRTHQIRVHAQHAGHPIAFDDRYGDREFDQQLADTGLKRLFLHAQALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSL 322
           L++ APL + + +    L
Sbjct: 296 LRVEAPLDSGLRRCLQVL 313


>gi|291085563|ref|ZP_06353360.2| ribosomal large subunit pseudouridine synthase [Citrobacter youngae
           ATCC 29220]
 gi|291071302|gb|EFE09411.1| ribosomal large subunit pseudouridine synthase [Citrobacter youngae
           ATCC 29220]
          Length = 331

 Score =  165 bits (418), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 111/319 (34%), Positives = 175/319 (54%), Gaps = 16/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   +++ G +VR
Sbjct: 22  VKTVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEDGDIVR 81

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A     +E+ I   S NL K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 82  IPPVRVADR---EEEAI---SPNLQKVA-ALTDVILYEDDHILVLNKPSGTAVHGGSGLS 134

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 135 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 193

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 194 VRGQWQSHVKSVQAPLLKNILQSGERIVRVNQEGKPSE---TRFKVEERYA--FATLVRC 248

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +   HP  G 
Sbjct: 249 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLADTGLNRLFLHAAALKFTHPGTGE 308

Query: 305 -LQITAPLPAHMVKTWDSL 322
            ++I AP+   + ++ + L
Sbjct: 309 VMRIEAPMDKQLKRSLEVL 327


>gi|90413248|ref|ZP_01221243.1| putative 23S rRNA ribosomal pseudouridinesynthase [Photobacterium
           profundum 3TCK]
 gi|90325800|gb|EAS42258.1| putative 23S rRNA ribosomal pseudouridinesynthase [Photobacterium
           profundum 3TCK]
          Length = 314

 Score =  165 bits (418), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 105/318 (33%), Positives = 178/318 (55%), Gaps = 16/318 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ + +D    R+D + +    ++    + +ILR G+VRV+KKR+K   ++Q G ++R
Sbjct: 8   VQFIDITDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDLIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      + ++      S  L+K ++ L+S ++YED  + V NKP+G +V GGSG+ 
Sbjct: 68  VPPIF-----LPEQADQAPISTKLSKVAE-LESCVIYEDDHLLVLNKPSGTAVHGGSGLK 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + +QK Y++L
Sbjct: 122 FGAIEALRA-LRPDARYLELVHRIDRDTSGILLVAKKRSALRKLQEQFREKTVQKYYFAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K   + +   LLK      + +  V QN K ++   + FKV++ F +    ++  
Sbjct: 181 VMGEWKASCKKVTAPLLKNE---VNSIVRVNQNGKASD---TRFKVLERF-EHATLVQAS 233

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +   HP     
Sbjct: 234 PVTGRTHQIRVHCQYEGHPIAWDDRYGDPRFDAYTKKTGLNRLFLHAANIKFTHPSTDEP 293

Query: 305 LQITAPLPAHMVKTWDSL 322
           + I+APL A + ++ D+L
Sbjct: 294 VDISAPLDALLTRSLDNL 311


>gi|261346051|ref|ZP_05973695.1| ribosomal large subunit pseudouridine synthase [Providencia
           rustigianii DSM 4541]
 gi|282565938|gb|EFB71473.1| ribosomal large subunit pseudouridine synthase [Providencia
           rustigianii DSM 4541]
          Length = 318

 Score =  165 bits (417), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 106/313 (33%), Positives = 172/313 (54%), Gaps = 14/313 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     VQ++ + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q
Sbjct: 1   MKTENQVQFIDISDDEAGQRIDNFLLGKLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +   VR+PPV       + E++    S  L K +  L   +LYED  I V NKP+G +V 
Sbjct: 61  ANDQVRVPPVR------VAERENAPISAKLDKVA-ALADCILYEDESILVINKPSGTAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R++++Q
Sbjct: 114 GGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRALHEQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + +   LLK     G+   +V+ N +G   + + FKV + F    
Sbjct: 173 KDYLALVRGNWQSHMKVVQAPLLKNILQSGE--RIVRVNSEG-KPSETRFKVEERF-DNA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH LH G PI  D +Y    F    T     +L+LHA  +   H
Sbjct: 229 TLVKASPVTGRTHQIRVHTLHAGHPIAFDDRYGDKQFDSQLTGTGLKRLFLHANALTFTH 288

Query: 300 PEGG-RLQITAPL 311
           P+ G  +++ APL
Sbjct: 289 PKTGEEMRVVAPL 301


>gi|212635834|ref|YP_002312359.1| pseudouridine synthase RluD [Shewanella piezotolerans WP3]
 gi|212557318|gb|ACJ29772.1| Pseudouridine synthase, RluD [Shewanella piezotolerans WP3]
          Length = 308

 Score =  165 bits (417), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 105/315 (33%), Positives = 177/315 (56%), Gaps = 13/315 (4%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G VVRIPP
Sbjct: 2   VTIDEDHTGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQDGDVVRIPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V      + + +     S  LTK S  L++ ++YED  I V NKP+GI+V GGSG+ + +
Sbjct: 62  V-----RVSESEGRPGPSAKLTKVSQ-LENRIIYEDKFIIVLNKPSGIAVHGGSGVDFGV 115

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++S + ++ +   L HRLD++TSG+L++A+ R+A +HL +  R +++QK Y +LV G
Sbjct: 116 IEAMRS-LRTQQKFLELVHRLDKDTSGLLLIAKKRSALKHLHDQLRYKKMQKDYLALVRG 174

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +   + +   LLK +   G+   +V+ N++G   + + FK++  ++     ++  P T
Sbjct: 175 EWQKHDKAVKAPLLKLTLKSGE--RIVRVNKEGKE-SETRFKIMQRYSDA-TLVQASPIT 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           GRTHQ+RVH  + G PI  D KY    F  +  +   N+L+LHA  +   HP+    +Q+
Sbjct: 231 GRTHQIRVHCQYAGHPIACDEKYSEQKFDDSMRAHGLNRLFLHAAQLRFIHPDTDEVMQV 290

Query: 308 TAPLPAHMVKTWDSL 322
            APL   +  T   L
Sbjct: 291 KAPLDPILESTLSKL 305


>gi|229592115|ref|YP_002874234.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens SBW25]
 gi|229363981|emb|CAY51520.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens SBW25]
          Length = 319

 Score =  165 bits (417), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 110/322 (34%), Positives = 180/322 (55%), Gaps = 23/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLLEVSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PPV       + E+   D  V L +     L++ +++ED+K+ V NKP GI+V GGSG+
Sbjct: 71  VPPVR------VPER---DEPVPLAQGLLQRLEASIVFEDNKLIVINKPCGIAVHGGSGL 121

Query: 126 AYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y 
Sbjct: 122 NFGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHTALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   +  + +   L K +   G+   +V+ +E+G   A++ FKV+  F      +E
Sbjct: 180 ALVRGNWASSIKSVRAPLQKSNLRSGE--RMVEVDEEGKE-ALTLFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHP 300
            +P TGRTHQ+RVH LH G  I GD KY       F+  I++    +L+LHA  + +P P
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHCIAGDTKYGDE---GFSKEIRDLGGKRLFLHAYMLTVPLP 293

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
           +GG L++ AP+     KT + L
Sbjct: 294 DGGELKLQAPVDEMWAKTVERL 315


>gi|237808945|ref|YP_002893385.1| pseudouridine synthase, RluA family [Tolumonas auensis DSM 9187]
 gi|237501206|gb|ACQ93799.1| pseudouridine synthase, RluA family [Tolumonas auensis DSM 9187]
          Length = 314

 Score =  165 bits (417), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 104/318 (32%), Positives = 175/318 (55%), Gaps = 15/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ ++ +++  R+D + K     +    + +ILR G+VRV+KKR+K   ++  G  +R
Sbjct: 8   VQFITIDAEQDGQRIDNFLKTQLKGVPKSLIYRILRKGEVRVNKKRIKPEYKLCVGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A  + +   K+   SV    H       ++YED  I V NKP+G++V GGSG++
Sbjct: 68  VPPVRVAEENELPSSKL--GSVQALAHQ------IIYEDEAIIVLNKPSGLAVHGGSGLS 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A +HL E  R++ ++K Y +L
Sbjct: 120 FGVIEGLRA-LRPESRFLELVHRLDRDTSGLLLVAKKRSALKHLHEQLRVKTMRKQYLAL 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + +   LLK     G+   +V+ N +G   + + F+++  FA     +   
Sbjct: 179 VRGQWQPHVKAVNAPLLKNILQSGE--RIVRVNSEG-KPSETRFQIMQKFAHATLVM-AS 234

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D KY   +F         ++L+LHA  +   HP  G+ 
Sbjct: 235 PITGRTHQIRVHTLHAGHPIACDDKYGERDFDEQVKKAGLHRLFLHAYRLTFTHPVTGKE 294

Query: 305 LQITAPLPAHMVKTWDSL 322
           + + APL   +    D L
Sbjct: 295 MSVEAPLDKELQSALDRL 312


>gi|332288916|ref|YP_004419768.1| 23S rRNA pseudouridylate synthase C [Gallibacterium anatis UMN179]
 gi|330431812|gb|AEC16871.1| 23S rRNA pseudouridylate synthase C [Gallibacterium anatis UMN179]
          Length = 321

 Score =  164 bits (416), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 107/307 (34%), Positives = 177/307 (57%), Gaps = 13/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +E DEE  R+D +       +    + +I+R G+VRV+K R+K   ++Q G VVR
Sbjct: 13  VQLLTIEPDEELQRIDNYLLTKLKGVPKSLIYRIIRKGEVRVNKGRIKPEYKLQVGDVVR 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      I ++      S  L K  + L+  +L+ED ++ + NKP+GI+V GGSG++
Sbjct: 73  IPPV-----RISEKSNTAPLSTKLNK-VNALEQQILFEDDQLLILNKPSGIAVHGGSGLS 126

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A ++L +  R + IQK Y +L
Sbjct: 127 FGVIEALRA-LRPQAKFLELVHRLDRDTSGILLVAKKRSALRNLHQQLREKTIQKDYLAL 185

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +VK +++G   + + FKV + F +    ++  
Sbjct: 186 VRGEWQSHCKVVKAPLLKNELSSGE--RIVKVSDQG-KPSETRFKVEERF-KIATLVKAS 241

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY +       +P+   +L+LHA  +   HP+ G +
Sbjct: 242 PVTGRTHQIRVHTQYAGHPIAFDSKYGSKEFDQLLAPLGLQRLFLHAASIRFTHPKSGEQ 301

Query: 305 LQITAPL 311
           + I+APL
Sbjct: 302 MVISAPL 308


>gi|237731018|ref|ZP_04561499.1| 23S rRNA pseudouridylate synthase [Citrobacter sp. 30_2]
 gi|226906557|gb|EEH92475.1| 23S rRNA pseudouridylate synthase [Citrobacter sp. 30_2]
          Length = 331

 Score =  164 bits (416), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 111/319 (34%), Positives = 174/319 (54%), Gaps = 16/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   +++ G +VR
Sbjct: 22  VKTVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEDGDIVR 81

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A     +E+ I   S NL K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 82  IPPVRVAER---EEEAI---SPNLQKVA-ALTDVILYEDDHILVLNKPSGTAVHGGSGLS 134

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 135 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 193

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 194 VRGQWQSHVKTVQAPLLKNILQSGERIVRVNQEGKPSE---TRFKVEERYA--FATLVRC 248

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +   HP  G 
Sbjct: 249 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLADTGLNRLFLHAAALKFTHPGTGE 308

Query: 305 -LQITAPLPAHMVKTWDSL 322
            ++I AP+   + +  + L
Sbjct: 309 VMRIEAPMDKQLKRCLEVL 327


>gi|312962573|ref|ZP_07777063.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens WH6]
 gi|311283153|gb|EFQ61744.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens WH6]
          Length = 319

 Score =  164 bits (416), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 110/322 (34%), Positives = 180/322 (55%), Gaps = 23/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLLEVSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PPV       + E+   D  V L +     L++ +++ED+K+ V NKP GI+V GGSG+
Sbjct: 71  VPPVR------VPER---DEPVPLAQGLLQRLEASIVFEDNKLIVINKPCGIAVHGGSGL 121

Query: 126 AYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y 
Sbjct: 122 NFGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHTALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   +  + +   L K +   G+   +V+ +E+G   A++ FKV+  F      +E
Sbjct: 180 ALVRGNWASSIKSVRAPLQKSNLRSGE--RMVEVDEEGKE-ALTLFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHP 300
            +P TGRTHQ+RVH LH G  I GD KY       F+  I++    +L+LHA  + +P P
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHCIAGDTKYGDE---GFSKEIRDLGGKRLFLHAYMLTVPLP 293

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
           +GG L++ AP+     KT + L
Sbjct: 294 DGGELKLQAPVDEMWAKTVERL 315


>gi|89900510|ref|YP_522981.1| pseudouridine synthase RluD [Rhodoferax ferrireducens T118]
 gi|89345247|gb|ABD69450.1| Pseudouridine synthase, RluD [Rhodoferax ferrireducens T118]
          Length = 346

 Score =  164 bits (416), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 105/321 (32%), Positives = 169/321 (52%), Gaps = 20/321 (6%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+ D    RLD +   H   +   ++ +I+RSG+VRV+K R   + R+ +G  VR+PP
Sbjct: 19  IRVDEDAAGQRLDNFLMRHLKGVPKTHVYRIIRSGEVRVNKGRASADARLAAGDTVRLPP 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  +     K + +  +  +     DF    +L+ED ++ V +KPAG++V GGSG+++ +
Sbjct: 79  LRISERVAEKAEAMTQAMAHGAPARDF---PILFEDEQLLVIDKPAGVAVHGGSGVSFGV 135

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+     + +   L HRLD++TSGIL++A+ R+A   L   FR R   K Y +LV G
Sbjct: 136 IEQLR-MARPEAKFLELVHRLDRDTSGILLIAKKRSALTRLQSQFRERETGKTYLALVAG 194

Query: 190 I-PKNKK---ECIANWLLK----KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
             P N+K   + +  +LL      +  G   V VV +++     +++  KV +  A  F 
Sbjct: 195 HWPANRKVLDKPLYKYLLPGKDGSAGEGERRVKVVSRDDPNGMPSVTLVKVRETTATSFT 254

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYM 295
            LE+   TGRTHQ+RVH    G PI GD KY  +F  N         P   +++LHA  +
Sbjct: 255 LLEVTIKTGRTHQIRVHLASEGYPIAGDDKY-GDFGLNKKLLQSGPRPGLKRMFLHAWRL 313

Query: 296 DLPHPEGG-RLQITAPLPAHM 315
              HP  G R+++ APLP  +
Sbjct: 314 QFNHPASGERMELLAPLPTEL 334


>gi|88658198|ref|YP_507572.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           chaffeensis str. Arkansas]
 gi|88599655|gb|ABD45124.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           chaffeensis str. Arkansas]
          Length = 307

 Score =  164 bits (415), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 104/311 (33%), Positives = 170/311 (54%), Gaps = 21/311 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV--V 65
           +Y +VE D+ N+R+D++ +     I    ++K LR G V +D  +VK + RI++G V  V
Sbjct: 4   KYYIVEEDDHNIRIDKFIR-RILKIPQSLVEKFLRKGVVLLDNTKVKSDVRIKAGNVICV 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R   VI     I   +KI  +  +   H   +++ ++YED  + + NKPAGISVQGG+ +
Sbjct: 63  RYDRVIYERKQI---RKICKADSDFLVH--LIRNSVVYEDDDVLIINKPAGISVQGGTKV 117

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              I   +    D  G+  ++ HRLD++TSGIL++AR    ++ +   F+ RR++K Y +
Sbjct: 118 KISISDIVDKIRD--GESMKIVHRLDKDTSGILMLARNARISRLIMHEFKNRRVEKKYLA 175

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L  GIPKN    I + ++K        + + K N+     A++ F V+         LE+
Sbjct: 176 LTQGIPKNDIGQINHSIIKNKR----SLSLDKVNDSYLQEAVTSFSVLKKLPYGIGLLEL 231

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-KLYLHARYMDLPHPEGGR 304
           +P TGR HQ+R+H  H+GC I+GD KY     G F   + N  L LHA ++ +   E  +
Sbjct: 232 KPITGRKHQIRIHLSHIGCSIIGDKKY-----GKFCEHVLNDNLQLHAYFLSINIGE-KK 285

Query: 305 LQITAPLPAHM 315
           +  T P+P++M
Sbjct: 286 IDFTVPVPSYM 296


>gi|50120723|ref|YP_049890.1| 23S rRNA pseudouridylate synthase C [Pectobacterium atrosepticum
           SCRI1043]
 gi|49611249|emb|CAG74695.1| ribosomal large subunit pseudouridine synthase C [Pectobacterium
           atrosepticum SCRI1043]
          Length = 318

 Score =  164 bits (415), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  DE   R+D +   H   +    + +ILR G+VR++KKRVK   ++  G V+R
Sbjct: 8   VQFVTISADEAGQRIDNFLHTHLKGVPKSMVYRILRKGEVRINKKRVKPEYKLLDGDVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A      E+     S +L K +  L   ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRQA------ERDETPVSASLGKVA-ALAECIIYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +V+ N +G   + + FK+ + F +    +   
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILQSGE--RIVRVNSEG-KASETRFKIEERF-EHATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA + G PI  D +Y    F          +L+LHA+ +   HP  G  
Sbjct: 236 PVTGRTHQIRVHAQYAGHPIAFDDRYGDREFDRQLAGSGLKRLFLHAQALRFEHPNTGET 295

Query: 305 LQITAPL 311
           L++ APL
Sbjct: 296 LRVEAPL 302


>gi|212712798|ref|ZP_03320926.1| hypothetical protein PROVALCAL_03895 [Providencia alcalifaciens DSM
           30120]
 gi|212684490|gb|EEB44018.1| hypothetical protein PROVALCAL_03895 [Providencia alcalifaciens DSM
           30120]
          Length = 318

 Score =  164 bits (415), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 104/313 (33%), Positives = 169/313 (53%), Gaps = 14/313 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     VQ++ + +DE   R+D +  +    +    + +I+R G+VRV+K R+K   ++ 
Sbjct: 1   MKTENQVQFIDISDDEAGQRIDNFLLSKLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLL 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  VR+PPV       + E++    S  L K +  L   +LYED  I V NKP+G +V 
Sbjct: 61  EGDQVRVPPVR------VAERETAPVSAKLDKVA-ALADCILYEDESILVINKPSGTAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R++++Q
Sbjct: 114 GGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRALHEQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + +   LLK     G+ +  V    K +    + FKV + F +  
Sbjct: 173 KDYLALVRGNWQSHTKVVQAPLLKNILQSGERIVRVSSEGKPSE---TRFKVEERF-ENA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH LH G PI  D +Y    F          +L+LHA  +   H
Sbjct: 229 TLVKASPVTGRTHQIRVHTLHAGHPIAFDDRYGDKQFDSQLADTGLKRLFLHAYALKFTH 288

Query: 300 PEGG-RLQITAPL 311
           P+ G  +++ APL
Sbjct: 289 PKSGEEMRVVAPL 301


>gi|54308380|ref|YP_129400.1| putative 23S rRNA ribosomal pseudouridinesynthase [Photobacterium
           profundum SS9]
 gi|46912808|emb|CAG19598.1| putative 23S rRNA ribosomal pseudouridinesynthase [Photobacterium
           profundum SS9]
          Length = 307

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 102/318 (32%), Positives = 178/318 (55%), Gaps = 16/318 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q++ + +D    R+D + +    ++    + +ILR G+VRV+KKR+K   ++Q G ++R
Sbjct: 1   MQFIDITDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDLIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      + +++     S  L+K ++ L+S ++YED  + V NKP+G +V GGSG+ 
Sbjct: 61  VPPIF-----MPEQENQAPISTKLSKVAE-LESCVIYEDDHLLVLNKPSGTAVHGGSGLK 114

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + ++K Y++L
Sbjct: 115 FGAIEALRA-LRPDARYLELVHRIDRDTSGILLVAKKRSALRKLQEQFREKTVKKYYFAL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K   + +   LLK      +   +V+ N  G   + + FKV++ F +    ++  
Sbjct: 174 VMGEWKASSKKVTAPLLK-----NEVNSIVRVNPNG-KASDTRFKVLERF-EHATLVQAS 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +   HP     
Sbjct: 227 PVTGRTHQIRVHCQYEGHPIAWDDRYGDPRFDAYTKKTGLNRLFLHAANIKFTHPSTDEP 286

Query: 305 LQITAPLPAHMVKTWDSL 322
           + I+APL A + ++ D+L
Sbjct: 287 VDISAPLDALLTRSLDNL 304


>gi|311280008|ref|YP_003942239.1| pseudouridine synthase, RluA family [Enterobacter cloacae SCF1]
 gi|308749203|gb|ADO48955.1| pseudouridine synthase, RluA family [Enterobacter cloacae SCF1]
          Length = 341

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 109/312 (34%), Positives = 170/312 (54%), Gaps = 16/312 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++++G  VR
Sbjct: 34  VKMVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLEAGDEVR 93

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 94  IPPV------RVAEREEDAVSPHLQKVA-ALSDVILYEDDHILVLNKPSGTAVHGGSGLS 146

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 147 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGMQKDYLAL 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V    K +    + FKV + FA  F  L   
Sbjct: 206 VRGQWQSHTKVVQAPLLKNILQSGERIVRVSSEGKPSE---TRFKVEERFA--FATLVRC 260

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  H G PI  D +Y    F         N+L+LHA  +   HP  G 
Sbjct: 261 SPVTGRTHQIRVHTQHAGHPIAFDDRYGDREFDKQLAGTGLNRLFLHAAALKFTHPGTGE 320

Query: 305 -LQITAPLPAHM 315
            +++ AP+ A +
Sbjct: 321 TMRVEAPMDAQL 332


>gi|261822069|ref|YP_003260175.1| 23S rRNA pseudouridylate synthase C [Pectobacterium wasabiae
           WPP163]
 gi|261606082|gb|ACX88568.1| pseudouridine synthase, RluA family [Pectobacterium wasabiae
           WPP163]
          Length = 318

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 107/318 (33%), Positives = 174/318 (54%), Gaps = 14/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  DE   R+D +   H   +    + +ILR G+VR++KKRVK   ++  G V+R
Sbjct: 8   VQFVTISADEAGQRIDNFLHTHLKGVPKSLVYRILRKGEVRINKKRVKPEYKLLDGDVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A      E+     S +L K +   + I +YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRQA------ERDETPVSASLGKVAALTECI-IYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +V+ N +G   + + FK+ + F +    +   
Sbjct: 180 VRGQWQSHCKAVQAPLLKNILQSGE--RIVRVNSEG-KPSETRFKIEERF-EHATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA + G PI  D +Y    F          +L+LHA+ +   HP  G  
Sbjct: 236 PVTGRTHQIRVHAQYAGHPIAFDDRYGDREFDQQLADTGLKRLFLHAQALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSL 322
           L++ APL + + +    L
Sbjct: 296 LRVEAPLDSGLRRCLQVL 313


>gi|310767299|gb|ADP12249.1| 23S rRNA pseudouridylate synthase C [Erwinia sp. Ejp617]
          Length = 320

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 108/308 (35%), Positives = 173/308 (56%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VHFIAISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++  + S  L K +  L++ ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEENVSPKLAKVA-ALEAAIIYEDDYLLVMNKPSGTAVHGGSGLS 120

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+G      D++  +  L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +
Sbjct: 121 FGVIEGLRALRPDARFLE--LVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   +  + +   LLK     G+   VVK + +G   + + FKV + +A     ++ 
Sbjct: 179 LVRGQWPSHVKAVRAPLLKNILQSGE--RVVKVSSEG-KPSETLFKVEERYAIA-TLVKA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH LH G PI  D +Y    F    +S    +L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTLHAGHPIAFDDRYGETEFDQQLSSTGLKRLFLHAAALRFTHPNTGE 294

Query: 305 -LQITAPL 311
            +++ APL
Sbjct: 295 IMRVEAPL 302


>gi|94311375|ref|YP_584585.1| ribosomal large subunit pseudouridine synthase C [Cupriavidus
           metallidurans CH34]
 gi|93355227|gb|ABF09316.1| 23S rRNA pseudouridylate synthase [Cupriavidus metallidurans CH34]
          Length = 338

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 111/324 (34%), Positives = 174/324 (53%), Gaps = 26/324 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV V+   E  R+D +       +   ++ ++LRSG+VRV+K RV    R+Q+G VVR
Sbjct: 23  VAYVTVDESSEGQRIDNFLLKVAKGVPKSHIYRVLRSGEVRVNKGRVDATYRLQNGDVVR 82

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+           ++ + +          +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 83  IPPM-----------RVAEKAAPTGGFVPAGEFPVLFEDAALLVIDKPAGVAVHGGSGVA 131

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   ++  ++K  +  L HRLD+ETSGILV+A+ R+   HL E  R   + K Y++
Sbjct: 132 FGVIEQLRRARPEAKFLE--LVHRLDRETSGILVLAKKRSVLVHLHEQIRGNGMDKRYFA 189

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G   N ++ +   L K S   G+   V  Q +  A++ +  F  ++ F   +  LE 
Sbjct: 190 CVAGEFPNTRQHVKLPLYKYSTPDGER-RVRVQADGLASHTV--FNRMEAF-DGYTLLEA 245

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMDLPH 299
           +  TGRTHQ+RVH   +G PIVGD KY  +F  N       T P   +++LHA  + L H
Sbjct: 246 ELKTGRTHQIRVHLQSIGFPIVGDDKY-GDFALNKALSRSGTKPGLKRMFLHAHRLTLTH 304

Query: 300 P-EGGRLQITAPLPAHMVKTWDSL 322
           P  G  + ++APLPA  V+    L
Sbjct: 305 PVTGAPMTVSAPLPAECVEFLQQL 328


>gi|300723637|ref|YP_003712942.1| 23S rRNA pseudouridylate synthase [Xenorhabdus nematophila ATCC
           19061]
 gi|297630159|emb|CBJ90796.1| 23S rRNA pseudouridylate synthase [Xenorhabdus nematophila ATCC
           19061]
          Length = 318

 Score =  164 bits (414), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 108/308 (35%), Positives = 170/308 (55%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +++DE   R+D +       +    + +ILR G+VR++K RVK   ++  G  +R
Sbjct: 8   VQFVTIDDDEAGQRIDNFLLARLKGVPKSMIYRILRKGEVRINKGRVKPEYKLTVGDTIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+       + E++    S  L K +  L   +LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPI------RVSEKQEPPVSAKLDKVA-ALAECILYEDDHILVINKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL++A+ R+A + L E  R++++QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRALHEQLRLKQMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+   VVK + +G   + + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHCKVVEAPLLKNILQSGE--RVVKVSSEG-KPSETRFKVEERYA--FATLVRA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH LH G PI  D +Y    F         N+L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTLHAGHPIAFDDRYGDRAFDAQLAETNLNRLFLHASSLKFTHPSMGE 294

Query: 305 -LQITAPL 311
            L+  AP+
Sbjct: 295 TLRFEAPM 302


>gi|183599498|ref|ZP_02960991.1| hypothetical protein PROSTU_02977 [Providencia stuartii ATCC 25827]
 gi|188021745|gb|EDU59785.1| hypothetical protein PROSTU_02977 [Providencia stuartii ATCC 25827]
          Length = 317

 Score =  164 bits (414), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 107/313 (34%), Positives = 169/313 (53%), Gaps = 14/313 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     VQ++ + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++ 
Sbjct: 1   MKTQNQVQFIDISDDEAGQRIDNFLLAKLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLI 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  VR+PPV       + E++    S  L K S  L   +LYED  I V NKP+G +V 
Sbjct: 61  AGDQVRVPPVR------VAEREEAPVSAKLDKVS-ALADCILYEDDAILVINKPSGTAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R++++Q
Sbjct: 114 GGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRALHEQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + I   LLK     G+ V  V    K +    + FKV + F    
Sbjct: 173 KDYLALVRGHWQSHTKVIQAPLLKNILQSGERVVRVSPEGKPSE---TRFKVEERF-DNA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH LH G PI  D++Y    F          +L+LHA  +   H
Sbjct: 229 TLVKASPVTGRTHQIRVHTLHAGHPIAFDNRYGDKQFDSQLADTGLKRLFLHASALKFTH 288

Query: 300 PEGG-RLQITAPL 311
           P+ G  +++ APL
Sbjct: 289 PKTGEEMRLQAPL 301


>gi|84779551|dbj|BAE74328.1| ribosomal large subunit pseudouridine synthase C [Sodalis
           glossinidius str. 'morsitans']
          Length = 328

 Score =  163 bits (413), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 111/312 (35%), Positives = 171/312 (54%), Gaps = 16/312 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ +  DE   R+D + + +   +    + +I+R G+VRV+KKRVK   ++Q+   VR
Sbjct: 18  VHFITISADEAGQRIDNFLRTYLKGVPKSMIYRIVRKGEVRVNKKRVKPEYKLQNDDEVR 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +      +++    S  L K +  L   +LYED  + + NKPAG +V GGSG++
Sbjct: 78  IPPVRRS------DEEHAPISTGLDKVA-ALNEAVLYEDDHLLILNKPAGTAVHGGSGLS 130

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+G      D++  +  L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +
Sbjct: 131 FGVIEGLRALRPDARFLE--LVHRLDRDTSGVLLVAKKRSALRALHEQLRAKGMQKDYLA 188

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  ++  + IA  LLK     G+   +V+ N +G   + + FKV + F      +  
Sbjct: 189 LVRGQWQSHVKTIAAPLLKNILASGE--RIVRVNSEG-KPSETCFKVEERFTLAM-LVRA 244

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVHA H G PI  D +Y    F         N+L+LHA  +   HP  G 
Sbjct: 245 SPVTGRTHQIRVHAQHAGHPIAFDDRYGDGMFDQQLKGCGLNRLFLHAAALRFDHPGSGE 304

Query: 305 -LQITAPLPAHM 315
            L+I APL A +
Sbjct: 305 TLRIDAPLDASL 316


>gi|253688887|ref|YP_003018077.1| pseudouridine synthase, RluA family [Pectobacterium carotovorum
           subsp. carotovorum PC1]
 gi|251755465|gb|ACT13541.1| pseudouridine synthase, RluA family [Pectobacterium carotovorum
           subsp. carotovorum PC1]
          Length = 318

 Score =  163 bits (413), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 109/318 (34%), Positives = 173/318 (54%), Gaps = 14/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  DE   R+D +   H   +    + +ILR G+VR++KKRVK   ++  G V+R
Sbjct: 8   VQFVTISADEAGQRVDNFLHTHLKGVPKSMVYRILRKGEVRINKKRVKPEYKLLDGDVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A      E+     S +L K +  L   ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRQA------ERDETPVSASLGKVA-ALAECIIYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   VV+ N +G   + + FKV + F +    +   
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILQSGE--RVVRVNSEG-KPSETRFKVEERF-EHATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D +Y    F          +L+LHA+ +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDEQLADTGLKRLFLHAQALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSL 322
           L+I APL   + +   +L
Sbjct: 296 LRIEAPLDNGLRRCLQAL 313


>gi|162382793|ref|YP_454733.2| 23S rRNA pseudouridylate synthase C [Sodalis glossinidius str.
           'morsitans']
          Length = 318

 Score =  163 bits (413), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 111/312 (35%), Positives = 171/312 (54%), Gaps = 16/312 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ +  DE   R+D + + +   +    + +I+R G+VRV+KKRVK   ++Q+   VR
Sbjct: 8   VHFITISADEAGQRIDNFLRTYLKGVPKSMIYRIVRKGEVRVNKKRVKPEYKLQNDDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +      +++    S  L K +  L   +LYED  + + NKPAG +V GGSG++
Sbjct: 68  IPPVRRS------DEEHAPISTGLDKVA-ALNEAVLYEDDHLLILNKPAGTAVHGGSGLS 120

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+G      D++  +  L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +
Sbjct: 121 FGVIEGLRALRPDARFLE--LVHRLDRDTSGVLLVAKKRSALRALHEQLRAKGMQKDYLA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  ++  + IA  LLK     G+   +V+ N +G   + + FKV + F      +  
Sbjct: 179 LVRGQWQSHVKTIAAPLLKNILASGE--RIVRVNSEG-KPSETCFKVEERFTLAM-LVRA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVHA H G PI  D +Y    F         N+L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHAQHAGHPIAFDDRYGDGMFDQQLKGCGLNRLFLHAAALRFDHPGSGE 294

Query: 305 -LQITAPLPAHM 315
            L+I APL A +
Sbjct: 295 TLRIDAPLDASL 306


>gi|259908803|ref|YP_002649159.1| 23S rRNA pseudouridylate synthase C [Erwinia pyrifoliae Ep1/96]
 gi|224964425|emb|CAX55934.1| 23S rRNA pseudouridylate synthase [Erwinia pyrifoliae Ep1/96]
 gi|283478783|emb|CAY74699.1| pseudouridylate synthase [Erwinia pyrifoliae DSM 12163]
          Length = 320

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 108/319 (33%), Positives = 177/319 (55%), Gaps = 16/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VHFIAISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++  + S  L K +  L++ +++ED  + V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEENVSPKLAKVA-ALEAAIIFEDDYLLVMNKPSGTAVHGGSGLS 120

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+G      D++  +  L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +
Sbjct: 121 FGVIEGLRALRPDARFLE--LVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   +  + +   LLK     G+   VVK + +G   + + FKV + +A     ++ 
Sbjct: 179 LVRGQWPSHVKAVRAPLLKNILQSGE--RVVKVSSEG-KPSETLFKVEERYAIA-TLVKA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH LH G PI  D +Y    F    +S    +L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTLHAGHPIALDDRYGETEFDQQLSSTGLKRLFLHAAALRFTHPNTGE 294

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++ APL   + +   +L
Sbjct: 295 IMRVEAPLDEQLKRCLAAL 313


>gi|157146217|ref|YP_001453536.1| 23S rRNA pseudouridylate synthase C [Citrobacter koseri ATCC
           BAA-895]
 gi|157083422|gb|ABV13100.1| hypothetical protein CKO_01974 [Citrobacter koseri ATCC BAA-895]
          Length = 317

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 108/308 (35%), Positives = 170/308 (55%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH LH G PI  D +Y    F         ++L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTLHAGHPIAFDDRYGDREFDKQLAGTGLSRLFLHAAALKFTHPGTGE 294

Query: 305 -LQITAPL 311
            ++I AP+
Sbjct: 295 VMRIEAPM 302


>gi|304413613|ref|ZP_07395057.1| 23S rRNA pseudouridylate synthase [Candidatus Regiella insecticola
           LSR1]
 gi|304283704|gb|EFL92098.1| 23S rRNA pseudouridylate synthase [Candidatus Regiella insecticola
           LSR1]
          Length = 294

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 108/275 (39%), Positives = 160/275 (58%), Gaps = 15/275 (5%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           +I+R G+VRV+K R+K   ++Q+G  VRIPPV       + E++    SV L K S  L 
Sbjct: 15  RIVRKGEVRVNKGRIKPEYKLQNGDRVRIPPVR------VAERETRTLSVKLNKISS-LP 67

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L+ED  + + NKP GI+V GGSG+ + +   L++ +  + +   L HRLD++TSG+L
Sbjct: 68  DRILFEDDALLILNKPFGIAVHGGSGVDFGVIEALRA-LRPEARFLELVHRLDRDTSGVL 126

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++A+ R+A + L E  R+++IQK Y +LV G  P + K+  A  L      GG    VVK
Sbjct: 127 LIAKKRSALRALHEQLRLKKIQKDYLALVKGHWPSSCKKVQAPLLKNVLQNGG---RVVK 183

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANF 276
            + +G   + +HFKV + F +    L+  P TGRTHQ+RVH LH G PI  D++Y    F
Sbjct: 184 VSSEG-KVSETHFKVEERF-EYATLLKASPITGRTHQIRVHTLHSGHPIAFDNRYGDREF 241

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
             +      N+L+LHA  +   HP GG L I APL
Sbjct: 242 DRHLQDTGLNRLFLHAATLCCQHPLGGTLSIEAPL 276


>gi|253989177|ref|YP_003040533.1| 23S rRNA pseudouridylate synthase C [Photorhabdus asymbiotica
           subsp. asymbiotica ATCC 43949]
 gi|253780627|emb|CAQ83789.1| 23S rRNA pseudouridine synthase [Photorhabdus asymbiotica]
          Length = 319

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 104/311 (33%), Positives = 170/311 (54%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +++DE   R+D +       +    + +I+R G+VRV+K RVK   ++ +G VVR
Sbjct: 8   VQFVTIDDDEAGQRVDNFLLARLKGVPKSMIYRIVRKGEVRVNKGRVKPEYKLSAGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++ +  S  L K +  L   +LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAERQEIAVSAKLHKVA-ALDGCILYEDDYILVINKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+  +  + +   L HRLD++TSGIL++A+ R+  + L E  R++++QK Y +L
Sbjct: 121 FGVIEGLR-VLRPEAKFLELVHRLDRDTSGILLIAKKRSVLRALHEQLRLKQMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V    K +    + FK+ + F      +   
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILQSGERIVKVSGEGKPSE---TRFKIEERFTNA-TLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA ++G PI  D +Y    F    +    N+L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHAQYVGHPIAFDDRYGDKTFDSQLSDTGLNRLFLHASALKFTHPSTGET 295

Query: 305 LQITAPLPAHM 315
           L++ AP+   +
Sbjct: 296 LRLEAPMDGQL 306


>gi|188534161|ref|YP_001907958.1| 23S rRNA pseudouridylate synthase C [Erwinia tasmaniensis Et1/99]
 gi|188029203|emb|CAO97075.1| 23S rRNA pseudouridylate synthase [Erwinia tasmaniensis Et1/99]
          Length = 320

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 107/308 (34%), Positives = 173/308 (56%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  +R
Sbjct: 8   VHFIAISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++  + S  L K +  L++ ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREDDNVSPKLAKVA-ALEAAIIYEDDYLLVMNKPSGTAVHGGSGLS 120

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+G      D++  +  L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +
Sbjct: 121 FGVIEGLRALRPDARFLE--LVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   +  + +   LLK     G+   VVK + +G   + + FKV + +A     ++ 
Sbjct: 179 LVRGQWPSHVKAVRAPLLKNILQSGE--RVVKVSSEG-KPSETLFKVEERYAIA-TLVKA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH LH G PI  D +Y  A F    +     +L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTLHAGHPIAFDDRYGEAEFDQQLSGTGLKRLFLHAAALRFTHPNTGE 294

Query: 305 -LQITAPL 311
            +++ APL
Sbjct: 295 VMRVEAPL 302


>gi|254429310|ref|ZP_05043017.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881]
 gi|196195479|gb|EDX90438.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881]
          Length = 317

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 102/308 (33%), Positives = 170/308 (55%), Gaps = 19/308 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +V ++      RLD +   H   +    + +I+RSG+VR++K R K   R+ SG VVR
Sbjct: 11  VTFVTIDEGRHGQRLDNFLFTHLKGVPKSRVYRIIRSGEVRINKGRAKQTTRLASGDVVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  +       +     +V+    ++ L+   +YED ++++FNKP+G++V GGSG++
Sbjct: 71  IPPIRTS-------ESAAPPAVS-EGLAERLRRACVYEDDQLFIFNKPSGLAVHGGSGVS 122

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              I+     + D K  +  L HRLD++TSG+++VAR R+  + L    +  +++K YW 
Sbjct: 123 LGLIEALRVMYPDEKEME--LVHRLDRDTSGLIMVARRRSFLRKLQRLMQGGQVEKRYWL 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L  G  K K+  +   LLK  +     V V ++ +     +++H+++++ FAQ    +E 
Sbjct: 181 LCQGF-KGKERTLDAPLLKMMNGNERIVRVSREGKP----SVTHYRLLERFAQA-QLVEA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
              TGRTHQ+RVH+   G P++GD KY  A  +       + +L LHAR +   HP  G 
Sbjct: 235 TLETGRTHQIRVHSQFGGFPLLGDDKYGIAKGEALLAEIGRRRLCLHARTLVFVHPNTGK 294

Query: 304 RLQITAPL 311
           RL +TAPL
Sbjct: 295 RLTVTAPL 302


>gi|156934429|ref|YP_001438345.1| 23S rRNA pseudouridylate synthase C [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156532683|gb|ABU77509.1| hypothetical protein ESA_02260 [Cronobacter sakazakii ATCC BAA-894]
          Length = 317

 Score =  162 bits (411), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 108/307 (35%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V V  D+   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAVSADQAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALSDVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A ++L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRYLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + FA     +   
Sbjct: 180 VRGQWQSHVKNVQAPLLKNILQSGERIVRVNQEGKPSE---TRFKVEERFAIA-TLVRCS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D +Y    F     S   N+L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTQYAGHPIAFDDRYGDRAFDAQLASTGLNRLFLHAAALRFEHPGTGET 295

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 296 MRIEAPL 302


>gi|292487948|ref|YP_003530825.1| pseudouridylate synthase [Erwinia amylovora CFBP1430]
 gi|292899167|ref|YP_003538536.1| ribosomal large subunit pseudouridine synthase C [Erwinia amylovora
           ATCC 49946]
 gi|291199015|emb|CBJ46126.1| ribosomal large subunit pseudouridine synthase C [Erwinia amylovora
           ATCC 49946]
 gi|291553372|emb|CBA20417.1| pseudouridylate synthase [Erwinia amylovora CFBP1430]
          Length = 320

 Score =  162 bits (411), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 105/307 (34%), Positives = 173/307 (56%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  +R
Sbjct: 8   VHFIAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++  + S  L K +  L++ ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEENVSPKLAKVAA-LEAAIIYEDDYLLVMNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+   VVK + +G   + + FKV + +A     ++  
Sbjct: 180 VRGQWPSHVKAVRAPLLKNILQSGE--RVVKVSSEG-KPSETLFKVEERYAIA-TLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y  A F    +     +L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTLHAGHPIAFDDRYGEAGFDQQLSGTGLKRLFLHAAALRFTHPNTGEI 295

Query: 305 LQITAPL 311
           +++ APL
Sbjct: 296 MRVEAPL 302


>gi|167645618|ref|YP_001683281.1| pseudouridine synthase [Caulobacter sp. K31]
 gi|167348048|gb|ABZ70783.1| pseudouridine synthase [Caulobacter sp. K31]
          Length = 286

 Score =  162 bits (411), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 90/251 (35%), Positives = 139/251 (55%), Gaps = 7/251 (2%)

Query: 78  IKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           + + K  D+ +NLT     F KS++++ED  ++V NKPAG+S QGG   A+ +D  L + 
Sbjct: 30  VAKPKASDTPINLTPEEIAFTKSLVIHEDDSVFVLNKPAGLSSQGGRIQAHTLDDLLWAL 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIPKNKK 195
                 +PRL HRLD++TSG+++ ART+ AA  L ++   +R +K YW++V  G P+ + 
Sbjct: 90  ARRDRPRPRLIHRLDRDTSGVILTARTKPAATFLGKALMGKRFRKTYWAIVTPGAPEPRG 149

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I + L ++S     Y+ V + +   A  A S ++ +    +    +E+ P TGR HQL
Sbjct: 150 GQIDSPLRRESIGREAYMRVCEADHPDAETARSRYRTL-AATEGAALVELSPDTGRMHQL 208

Query: 256 RVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
           RVH   +G PI GD +Y      G    P   +L LHA  +  PHPEGG  +I+AP+P  
Sbjct: 209 RVHMASIGRPIAGDSRYGGALMLGGAPVP---RLMLHAANLVFPHPEGGERRISAPIPDD 265

Query: 315 MVKTWDSLGFK 325
           M      LG +
Sbjct: 266 MRAILAKLGLE 276


>gi|312172072|emb|CBX80329.1| pseudouridylate synthase [Erwinia amylovora ATCC BAA-2158]
          Length = 320

 Score =  162 bits (411), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 105/307 (34%), Positives = 173/307 (56%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  +R
Sbjct: 8   VHFIAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++  + S  L K +  L++ ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEENVSPKLAKVAA-LEAAIIYEDDYLLVMNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+   VVK + +G   + + FKV + +A     ++  
Sbjct: 180 VRGQWPSHVKAVRAPLLKNILQSGE--RVVKVSSEG-KPSETLFKVEERYAIA-TLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y  A F    +     +L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTLHAGHPIAFDDRYGEAGFDQQLSGTGLKRLFLHAAALRFTHPNTGEI 295

Query: 305 LQITAPL 311
           +++ APL
Sbjct: 296 MRVEAPL 302


>gi|320538809|ref|ZP_08038486.1| putative 23S rRNA pseudouridylate synthase [Serratia symbiotica
           str. Tucson]
 gi|320031154|gb|EFW13156.1| putative 23S rRNA pseudouridylate synthase [Serratia symbiotica
           str. Tucson]
          Length = 319

 Score =  162 bits (411), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 102/307 (33%), Positives = 166/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + + +DE   R+D +       +    + +I+R G+VRV+K+R+K   ++ +G +VR
Sbjct: 8   VQVITISDDEAGQRIDNFLLARLKGVPKSMIYRIVRKGEVRVNKRRIKAEYKLAAGDLVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A   ++     LD  V LT       + +LYED  + + NKP+G +V GGSG++
Sbjct: 68  VPPVRIAEREVVPVSAKLDKVVALT-------NCILYEDDHLLILNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L + +  + +   L HRLD++TSG+L+VA+ R+A + L E  RM+ +QK Y +L
Sbjct: 121 FGVIEGLHA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRMKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V    K +    + FKV +   +    ++  
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILHSGERIVRVSSEGKSSE---TRFKV-EARYEFATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F          +L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDRQLLGTGLKRLFLHAAALHFEHPATGET 295

Query: 305 LQITAPL 311
           ++I AP+
Sbjct: 296 VRIEAPM 302


>gi|307822685|ref|ZP_07652916.1| pseudouridine synthase, RluA family [Methylobacter tundripaludum
           SV96]
 gi|307736289|gb|EFO07135.1| pseudouridine synthase, RluA family [Methylobacter tundripaludum
           SV96]
          Length = 319

 Score =  162 bits (411), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 108/313 (34%), Positives = 162/313 (51%), Gaps = 15/313 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S+   VQ V +  +  + RLD +       +    + +I+R G+VRV+K RV    R+ +
Sbjct: 7   SVTPKVQLVEITEENCDQRLDNFLIARLKGVPKSRIYRIVRKGEVRVNKGRVDVKYRLVA 66

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV  A      E+  +   +        L+  +L+ED    + NKPAG +V G
Sbjct: 67  GDIVRIPPVRVAER---SEESYVPQGLQAA-----LQQGILFEDEGFLIVNKPAGFAVHG 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG++  I   L+  +  +     L HRLD++TSG L++A+ R+A + L E FR   I K
Sbjct: 119 GSGVSSGIIEGLR-LIRPEAHFLELVHRLDKDTSGCLIIAKKRSALKLLHELFRDNHIHK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L+ G    KK  +   LLK    GG+ + V+ Q+ K A    + F+ +  F+    
Sbjct: 178 TYLALLAGQWARKKLVVTAPLLKNVAKGGERMVVISQSGKEAE---TLFRRVKLFSDS-T 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
            +E  P TGRTHQ+RVHA  +G PIVGD +Y   +    F      +++LHA  +   HP
Sbjct: 234 LVEASPKTGRTHQIRVHAASLGHPIVGDERYGRDDINRGFKGRGYKRMFLHAEKLKFQHP 293

Query: 301 EGGR-LQITAPLP 312
             G  L I APLP
Sbjct: 294 VTGEPLTILAPLP 306


>gi|262043217|ref|ZP_06016352.1| ribosomal large subunit pseudouridine synthase C [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|259039444|gb|EEW40580.1| ribosomal large subunit pseudouridine synthase C [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
          Length = 331

 Score =  162 bits (410), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 108/308 (35%), Positives = 170/308 (55%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V    DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++++G  VR
Sbjct: 22  VKMVATAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLEAGDEVR 81

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 82  IPPV------RVAEREEEAVSPHLQKVA-ALSEVILYEDDHILVLNKPSGTAVHGGSGLS 134

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 135 YGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGMQKDYLAL 193

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +  +F  L   
Sbjct: 194 VRGQWQSHTKVVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERY--EFATLVRC 248

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  + G PI  D +Y    F    ++   N+L+LHA  +   HP  G 
Sbjct: 249 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLSATGLNRLFLHAAALKFTHPGSGE 308

Query: 305 -LQITAPL 311
            +++ APL
Sbjct: 309 VMRVEAPL 316


>gi|152969638|ref|YP_001334747.1| 23S rRNA pseudouridylate synthase C [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|329999760|ref|ZP_08303517.1| rRNA pseudouridylate synthase [Klebsiella sp. MS 92-3]
 gi|150954487|gb|ABR76517.1| 23S rRNA pseudouridylate synthase [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|328538217|gb|EGF64365.1| rRNA pseudouridylate synthase [Klebsiella sp. MS 92-3]
          Length = 331

 Score =  162 bits (409), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 107/308 (34%), Positives = 171/308 (55%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++++G  VR
Sbjct: 22  VKMVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLEAGDEVR 81

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 82  IPPV------RVAEREEEAVSPHLQKVA-ALSEVILYEDDHILVLNKPSGTAVHGGSGLS 134

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 135 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGMQKDYLAL 193

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +  +F  L   
Sbjct: 194 VRGQWQSHTKVVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERY--EFATLVRC 248

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  + G PI  D +Y    F    ++   N+L+LHA  +   HP  G 
Sbjct: 249 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLSATGLNRLFLHAAALKFTHPGSGE 308

Query: 305 -LQITAPL 311
            +++ APL
Sbjct: 309 VMRVEAPL 316


>gi|290475862|ref|YP_003468754.1| 23S rRNA pseudouridylate synthase [Xenorhabdus bovienii SS-2004]
 gi|289175187|emb|CBJ81990.1| 23S rRNA pseudouridylate synthase [Xenorhabdus bovienii SS-2004]
          Length = 318

 Score =  162 bits (409), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 105/299 (35%), Positives = 167/299 (55%), Gaps = 15/299 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +++DE   R+D +       +    + +ILR G+VRV+K R+K   ++ +  V+R
Sbjct: 8   VQFVTIDDDEAGQRIDNFLLARLKGVPKSMIYRILRKGEVRVNKGRIKPEYKLAAADVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       I E++    S  L K     + I LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RIAEKQQPPVSAKLGKVVALAECI-LYEDDYILVINKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L++A+ R+A + L E  R++++QK Y++L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLIAKKRSALRTLHEQLRLKQMQKDYFAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+   +VK + +G   + + FKV + +  +F  L   
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILQSGE--RIVKVSSEG-KPSETRFKVEERY--EFATLVRA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            P TGRTHQ+RVH LH G PI  D +Y    F    T    N+L+LHA  +   HP  G
Sbjct: 235 SPITGRTHQIRVHTLHAGHPIAFDDRYGDRAFDAQLTETGLNRLFLHASSLKFTHPSTG 293


>gi|152979496|ref|YP_001345125.1| 23S rRNA pseudouridylate synthase C [Actinobacillus succinogenes
           130Z]
 gi|150841219|gb|ABR75190.1| pseudouridine synthase, RluA family [Actinobacillus succinogenes
           130Z]
          Length = 319

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 102/311 (32%), Positives = 177/311 (56%), Gaps = 15/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G ++R
Sbjct: 10  VKMLQISDDEAGQRIDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQAGDIIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      I +++  + + +N       L+  +++ED  + V NKP+GI+V GGSG++
Sbjct: 70  VPPV-----RISEKETPVSTKLNKVAQ---LEQQIIFEDDCLLVLNKPSGIAVHGGSGLS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +    +   L HRLD++TSGIL+VA+ R+  ++L E  R++ +QK Y +L
Sbjct: 122 FGVIEGLRA-LRPHARFLELVHRLDRDTSGILLVAKKRSVLRNLHEQLRLKTVQKDYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK    GG+   +V+ +E+G   + + F V + +A     ++  
Sbjct: 181 VRGQWQSHVKAVKAPLLKNELSGGE--RMVRVSEQG-KPSETRFSVEERYADA-TLVKAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA + G PI  D KY   NF     +   N+L+LHA  +   HP+ G  
Sbjct: 237 PVTGRTHQIRVHAQYAGHPIAMDDKYGDRNFDAGMAALGLNRLFLHAANIRFEHPKTGEP 296

Query: 305 LQITAPLPAHM 315
           L++ APL   M
Sbjct: 297 LRLNAPLDDKM 307


>gi|238894120|ref|YP_002918854.1| 23S rRNA pseudouridylate synthase C [Klebsiella pneumoniae
           NTUH-K2044]
 gi|238546436|dbj|BAH62787.1| 23S rRNA pseudouridylate synthase [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 317

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 107/308 (34%), Positives = 171/308 (55%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++++G  VR
Sbjct: 8   VKMVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALSEVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +  +F  L   
Sbjct: 180 VRGQWQSHTKVVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERY--EFATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  + G PI  D +Y    F    ++   N+L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLSATGLNRLFLHAAALKFTHPGSGE 294

Query: 305 -LQITAPL 311
            +++ APL
Sbjct: 295 VMRVEAPL 302


>gi|322833656|ref|YP_004213683.1| pseudouridine synthase, RluA family [Rahnella sp. Y9602]
 gi|321168857|gb|ADW74556.1| pseudouridine synthase, RluA family [Rahnella sp. Y9602]
          Length = 320

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 107/313 (34%), Positives = 174/313 (55%), Gaps = 18/313 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + + +DE   R+D +       +    + +I+R G+VRV+KKR+K   ++ +G  VR
Sbjct: 8   VQLIPISDDEAGQRIDNFLLKILKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLIAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E+     S  L K +  L   +LYED  + + NKP+G +V GGSG++
Sbjct: 68  VPPV------RVAERDEAPVSAKLDKVA-ALADCILYEDDHLLILNKPSGTAVHGGSGLS 120

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+G      D++  +  L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +
Sbjct: 121 FGVIEGLRALRPDARFLE--LVHRLDRDTSGVLLVAKKRSALRSLHEQLRVKSMQKDYLA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-E 244
           LV G   +  + +   LLK     G+   +V+ N +G   + + FK+ + +  +F  L +
Sbjct: 179 LVRGEWPSHCKVVQAPLLKNILQSGE--RIVRVNAEG-KPSETRFKIEERY--EFATLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVHALH G PI  D +Y   +F    +    N+L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHALHAGHPIAFDDRYGERDFDAKLSGTGLNRLFLHAAALRFEHPNTG 293

Query: 304 R-LQITAPLPAHM 315
             ++I AP+ A +
Sbjct: 294 ETMRIEAPMDAKL 306


>gi|110833922|ref|YP_692781.1| ribosomal large subunit pseudouridine synthase C [Alcanivorax
           borkumensis SK2]
 gi|110647033|emb|CAL16509.1| Ribosomal large subunit pseudouridine synthase C [Alcanivorax
           borkumensis SK2]
          Length = 317

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 103/310 (33%), Positives = 168/310 (54%), Gaps = 23/310 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +V ++      RLD +   H   +    + +I+RSG+VRV+K R K   R+ +G VVR
Sbjct: 11  VTFVTIDEGRHGQRLDNFLFTHLKGVPKSRVYRIIRSGEVRVNKGRAKQTTRLCTGDVVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKH---SDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +PP+           +  DS+         ++ L+   +YED +++VFNKPAG++V GGS
Sbjct: 71  VPPI-----------RTSDSTAPAAVSEGLAERLRRACVYEDDQLFVFNKPAGLAVHGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G++  +   L+     + ++  L HRLD++TSG+++VAR R+  + L    +  +I+K Y
Sbjct: 120 GVSLGLIEALRVMFPQE-RELELVHRLDRDTSGLIMVARRRSFLRKLQRLMQGGQIEKRY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W L  G  K K+  +   LLK  +     V V ++ +     +++HF++++ FAQ    +
Sbjct: 179 WLLCQGF-KGKERTLDAPLLKMMNGNERIVRVSREGKP----SVTHFRLLERFAQA-QLV 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           E    TGRTHQ+RVH+   G  ++GD KY  A  +       + +L LHAR +   HP  
Sbjct: 233 EATLETGRTHQIRVHSQFGGFALLGDSKYGIAKGEALLAEIGRRRLCLHARTLVFVHPNT 292

Query: 303 G-RLQITAPL 311
           G RL +TAPL
Sbjct: 293 GKRLTVTAPL 302


>gi|238791866|ref|ZP_04635503.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           intermedia ATCC 29909]
 gi|238728970|gb|EEQ20487.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           intermedia ATCC 29909]
          Length = 327

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 15  VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       I E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 75  VPPVR------IAEREEVQISAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 128 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 186

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   VVK + +G   + + FKV + F +    ++  
Sbjct: 187 VRGQWQSHCKAVQAPLLKNILQSGE--RVVKVSSEG-KPSETRFKVEERF-EHATLVKAS 242

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 243 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNSGET 302

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 303 MRIEAPL 309


>gi|117620828|ref|YP_856764.1| ribosomal large subunit pseudouridine synthase C [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117562235|gb|ABK39183.1| ribosomal large subunit pseudouridine synthase C [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 327

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 107/311 (34%), Positives = 170/311 (54%), Gaps = 15/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +E + E  R+D + K     +    + +ILR G+VRV+KKR+K   ++ +G  VR
Sbjct: 21  VQLLTIEAEHEGQRIDNFLKTQLKGVPKSLIYRILRKGEVRVNKKRIKPEYKLCTGDEVR 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A  + +        S NL      L+S +L+ED  + V NKP+G++V GGSG++
Sbjct: 81  VPPVRVAEKNEL-------PSANLGS-IQRLESQILFEDDAMIVLNKPSGMAVHGGSGLS 132

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ ++K Y +L
Sbjct: 133 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRVKTMRKQYLAL 191

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + +   L K     G+ V  V  + K +    + F++   FA+    +E  
Sbjct: 192 VRGQWQPHVKVVNAPLRKNDLQSGERVVRVSSDGKPSE---TRFRIARQFAEA-TLVECS 247

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  H G PI  D KY  A F     S    +L+LHA  +   HP  GR 
Sbjct: 248 PITGRTHQIRVHTQHAGHPIACDDKYGEAAFDDKMRSHGLKRLFLHAWKLSFIHPADGRE 307

Query: 305 LQITAPLPAHM 315
           +Q+ APL   +
Sbjct: 308 MQVEAPLAPEL 318


>gi|52425679|ref|YP_088816.1| 23S rRNA pseudouridylate synthase C [Mannheimia succiniciproducens
           MBEL55E]
 gi|52307731|gb|AAU38231.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 325

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 106/311 (34%), Positives = 174/311 (55%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G  VR
Sbjct: 15  VKMLQISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDTVR 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A     KEQ  + + +N       L+  +++ED  + V NKP+GI+V GGSG++
Sbjct: 75  IPPVRVAE----KEQAPISNKLNKVAA---LEKQIIFEDDCLLVLNKPSGIAVHGGSGLS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+S +  + +   L HR+D++TSGIL+VA+ R+A ++L E  R++ ++K Y +L
Sbjct: 128 FGVIEALRS-LRPEARFLELVHRIDRDTSGILLVAKKRSALRNLHEQLRIKTVKKDYLAL 186

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK    GG+   +V+ NE+G   + + F + + +      +   
Sbjct: 187 VRGQWQSHVKVIRAPLLKNELSGGE--RIVRVNEQG-KPSETRFAIEERYPTA-TLVRAS 242

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP+ G  
Sbjct: 243 PVTGRTHQIRVHTQYAGHPIALDDKYGDKEFDQQMQKLGLNRLFLHAYSIKFEHPKSGEE 302

Query: 305 LQITAPLPAHM 315
           L++TAPL  +M
Sbjct: 303 LRLTAPLDENM 313


>gi|170717346|ref|YP_001784455.1| 23S rRNA pseudouridylate synthase C [Haemophilus somnus 2336]
 gi|168825475|gb|ACA30846.1| pseudouridine synthase, RluA family [Haemophilus somnus 2336]
          Length = 326

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 111/318 (34%), Positives = 175/318 (55%), Gaps = 14/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  DE   R+D +       +    + +ILR G+VRV+K R+K   ++QSG +VR
Sbjct: 13  VKILTINEDESGQRIDNFLLAKLKSVPKSLIYRILRKGEVRVNKGRIKPEYKLQSGDIVR 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       I E++    S  L K +   + I ++ED+ + V NKP+G++V GGSG+ 
Sbjct: 73  IPPV------RIAEKEHTPISKKLNKVAQLEQQI-IFEDNYLLVLNKPSGLAVHGGSGLN 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +     L++ +  + +   L HRLD++TSGIL++A+ R+A + L E  R + IQK Y +L
Sbjct: 126 FGAIEALRT-LRPEARFLELVHRLDRDTSGILLIAKKRSALRSLHEQLREKTIQKEYLAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   +VK +E+G   + + F V + +      ++  
Sbjct: 185 VRGHWQSHCKMIQAPLLKSELTSGE--RIVKVSEQG-KPSETKFSVEERY-NNATLVKAS 240

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY   NF    T+   N+L+LHA  +   HP+ G R
Sbjct: 241 PITGRTHQIRVHTQYAGHPIALDDKYGDKNFNQQMTALGLNRLFLHAFAICFEHPKTGER 300

Query: 305 LQITAPLPAHMVKTWDSL 322
           L++ APL   M     +L
Sbjct: 301 LRLVAPLDLAMKNILQAL 318


>gi|322616557|gb|EFY13466.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322620502|gb|EFY17366.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322622496|gb|EFY19341.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322629647|gb|EFY26422.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322632633|gb|EFY29379.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322636872|gb|EFY33575.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322646483|gb|EFY42993.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322650020|gb|EFY46438.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322653945|gb|EFY50268.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322658477|gb|EFY54739.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322663335|gb|EFY59537.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322670069|gb|EFY66209.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322674867|gb|EFY70958.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322676663|gb|EFY72730.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322682585|gb|EFY78604.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322686662|gb|EFY82641.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323195776|gb|EFZ80952.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323198332|gb|EFZ83436.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323204846|gb|EFZ89840.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323209187|gb|EFZ94124.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323213429|gb|EFZ98225.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323217853|gb|EGA02568.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323222141|gb|EGA06525.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323224914|gb|EGA09172.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323229655|gb|EGA13778.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323232880|gb|EGA16976.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323240615|gb|EGA24657.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323242929|gb|EGA26950.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323247713|gb|EGA31657.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323252621|gb|EGA36459.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323258851|gb|EGA42504.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323266949|gb|EGA50434.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323269990|gb|EGA53439.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
          Length = 317

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 108/319 (33%), Positives = 173/319 (54%), Gaps = 16/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLADTGLNRLFLHAAALKFTHPGTGE 294

Query: 305 -LQITAPLPAHMVKTWDSL 322
            ++I AP+   + +  + L
Sbjct: 295 VMRIEAPMDKQLKRCLEVL 313


>gi|288936150|ref|YP_003440209.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|290510796|ref|ZP_06550166.1| ribosomal large subunit pseudouridine synthase C [Klebsiella sp.
           1_1_55]
 gi|288890859|gb|ADC59177.1| pseudouridine synthase, RluA family [Klebsiella variicola At-22]
 gi|289777512|gb|EFD85510.1| ribosomal large subunit pseudouridine synthase C [Klebsiella sp.
           1_1_55]
          Length = 331

 Score =  161 bits (407), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 107/308 (34%), Positives = 170/308 (55%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++++G  VR
Sbjct: 22  VKMVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLEAGDEVR 81

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 82  IPPV------RVAEREEEAVSPHLQKVA-ALSEVILYEDDHILVLNKPSGTAVHGGSGLS 134

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 135 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGMQKDYLAL 193

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +  +F  L   
Sbjct: 194 VRGQWQSHTKVVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERY--EFATLVRC 248

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  + G PI  D +Y    F    +    N+L+LHA  +   HP  G 
Sbjct: 249 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLSGTGLNRLFLHAAALKFTHPGSGE 308

Query: 305 -LQITAPL 311
            +++ APL
Sbjct: 309 VMRVEAPL 316


>gi|251789227|ref|YP_003003948.1| pseudouridine synthase, RluA family [Dickeya zeae Ech1591]
 gi|247537848|gb|ACT06469.1| pseudouridine synthase, RluA family [Dickeya zeae Ech1591]
          Length = 320

 Score =  161 bits (407), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 109/311 (35%), Positives = 170/311 (54%), Gaps = 22/311 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ +  +E   R+D + +     +    + +ILR G+VRV+KKR+K   ++Q G  VR
Sbjct: 8   VQFLTISAEEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +      E++    S +L K S  L   +LYED  + + NKP+G +V GGSG++
Sbjct: 68  IPPVRQS------EREEAAVSASLDKVS-ALADCILYEDDHLLLLNKPSGTAVHGGSGLS 120

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+G      D++  +  L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +
Sbjct: 121 FGVIEGLRALRPDARFLE--LVHRLDRDTSGVLLVAKKRSALRSLHEQLRGKGMQKDYLA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV---IDCFAQKFCW 242
           LV G  ++  + +   LLK     G+   +V+ N +G   + + FKV    DC       
Sbjct: 179 LVRGQWQSHCKSVQAPLLKNVLQSGE--RIVRVNSEG-KPSETLFKVEERFDCAT----L 231

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +   P TGRTHQ+RVH  + G PI  D +Y   +F    T     +L+LHA+ +   HP 
Sbjct: 232 VRASPVTGRTHQIRVHTQYAGHPIAFDDRYGDRDFDAQLTGTGLKRLFLHAQALRFEHPH 291

Query: 302 GGR-LQITAPL 311
            G  L+I APL
Sbjct: 292 TGEMLRIEAPL 302


>gi|268589209|ref|ZP_06123430.1| ribosomal large subunit pseudouridine synthase [Providencia
           rettgeri DSM 1131]
 gi|291315465|gb|EFE55918.1| ribosomal large subunit pseudouridine synthase [Providencia
           rettgeri DSM 1131]
          Length = 319

 Score =  161 bits (407), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 104/313 (33%), Positives = 173/313 (55%), Gaps = 14/313 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+    VQ++ + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++ 
Sbjct: 1   MNTQNQVQFIDISDDEAGQRIDNFLLTKLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLV 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  VR+PPV       + E++    S  L K +  L + +L+ED  + V NKP+G +V 
Sbjct: 61  EGDQVRVPPVR------VAERETAPVSAKLDKVA-ALANCILFEDDVLLVLNKPSGTAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R++++Q
Sbjct: 114 GGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRALHEQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + +   LLK     G+   VVK + +G   + + FKV + F    
Sbjct: 173 KDYLALVRGNWQSHMKVVQAPLLKNILQSGE--RVVKVSSEG-KPSETRFKVEERF-DNA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH L+ G PI  D +Y    F         N+L+LHA  +   H
Sbjct: 229 TLIKASPVTGRTHQIRVHTLYAGHPIAFDDRYGDKQFDSQLAGTGLNRLFLHASALKFTH 288

Query: 300 PE-GGRLQITAPL 311
           P+ G  +++ APL
Sbjct: 289 PKTGDEMRLQAPL 301


>gi|331005269|ref|ZP_08328661.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC1989]
 gi|330420946|gb|EGG95220.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC1989]
          Length = 362

 Score =  161 bits (407), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 105/346 (30%), Positives = 183/346 (52%), Gaps = 35/346 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ ++      R+D +  +    +    + +ILR G+VRV+K RVK   ++  G VVR
Sbjct: 28  VQFITIDAGNTAQRIDNFLLSRLKGVPKSRIYRILRKGEVRVNKGRVKPEYKLCDGDVVR 87

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      + +  +    S  L   S  L+  +L+E+  + V NKP+G++V GGSGI+
Sbjct: 88  VPPI-----RVSQRDEPPQPSQKL---STLLEDSILFENDDLMVVNKPSGLAVHGGSGIS 139

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              I+ F +   D++  +  L HRLD++TSG +++A+ R++ +++ +  R  RIQKIY +
Sbjct: 140 LGLIESFRQMRPDNRFLE--LVHRLDRDTSGCIMIAKKRSSLRYIQQELREGRIQKIYRA 197

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCF-------- 236
           LV G   N+++ + + L+K     G+ V  + Q E +GA  + + + VI  +        
Sbjct: 198 LVDGRWPNRRKNVTSPLVKNQLSSGERVVRIAQPETEGAKASRTEYNVIQRYQYTANSHG 257

Query: 237 ------------AQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTS 282
                        ++ C L E +P TGRTHQ+RVH   +GC I+GD KYC       +  
Sbjct: 258 ECNGGQNGGQFDGRRECTLVEAKPITGRTHQIRVHCQSVGCAIIGDDKYCDGEINKYYRG 317

Query: 283 PIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
               +L+LHA  +    P+G  + + APL + ++  + ++  K DR
Sbjct: 318 AGLKRLFLHAFQLTFCLPDGSSVSVEAPLGSDLLPVFKNIQ-KSDR 362


>gi|59712354|ref|YP_205130.1| 23S rRNA pseudouridylate synthase [Vibrio fischeri ES114]
 gi|59480455|gb|AAW86242.1| 23S rRNA pseudouridylate synthase [Vibrio fischeri ES114]
          Length = 315

 Score =  161 bits (407), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 110/323 (34%), Positives = 178/323 (55%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +++D    R+D +      ++    + +I+R G+VRV+KKR+K   ++Q G VVR
Sbjct: 8   VQFVDIDDDFAGQRIDNFLLARLKNVPKSMIYRIVRKGEVRVNKKRIKPEYKLQEGDVVR 67

Query: 67  IPPVINALNHIIKEQKILD-SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           IPPV       + E    D  +V L K ++ L+  ++YED  + + NKP+G +V GGSG+
Sbjct: 68  IPPVK------VPESTAPDLPNVKLGKVAE-LEHCIIYEDDHVLILNKPSGTAVHGGSGL 120

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + +QK Y++
Sbjct: 121 KFGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRRLQEQFRNKTVQKYYFA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  KN  + +   LLK      +   +V+ N  G   + + FKV++ F Q    ++ 
Sbjct: 180 LVMGQWKNSCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKVLEKFEQA-TLIQA 232

Query: 246 QPHTGRTHQLRVHALHMGCPI-----VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            P TGRTHQ+RVH  + G PI      GD ++ A + G F     ++L+LHA  +   HP
Sbjct: 233 SPITGRTHQIRVHTQYTGHPIGWDDRYGDRRFDA-YTGQFG---LDRLFLHAANIKFTHP 288

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
               L  I+AP+ A + +    L
Sbjct: 289 ATEELMDISAPMGAKLERVLKGL 311


>gi|304312939|ref|YP_003812537.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium HdN1]
 gi|301798672|emb|CBL46904.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium HdN1]
          Length = 311

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 103/319 (32%), Positives = 173/319 (54%), Gaps = 16/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q++ VE +    R+D +       +    + + LR G+VRV+K R+K + R+Q G ++R
Sbjct: 1   MQWLEVEAEYAGQRIDNFLVARLKGVPKSVIYRCLRKGEVRVNKGRIKPDYRVQGGDLIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKH-SDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           IPP        ++  +  D  +++ +   + L+  +LYED  + V NKPAG++V GGSG+
Sbjct: 61  IPP--------LRRSEQSDDEIHVGERIRNLLEGAILYEDEGLIVLNKPAGMAVHGGSGV 112

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +   L++ +    +   L HRLD++TSG L+VA+ R+  + L E  +   I+K+YW+
Sbjct: 113 SVGVIEALRA-IRPLSRHLELVHRLDRDTSGCLMVAKKRSRLRVLHEQLQAGEIRKVYWA 171

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  K K   I   L K    GG+ +  V Q  K ++   + F ++  F ++   +E 
Sbjct: 172 LVEGRWKGKFRRIDAPLQKFGEQGGERIVKVSQQGKPSS---TEFVLLRHF-EETSLVEA 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-QNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVHA   G PIVGD KY    +  +   +   +++LHA+ +++P  + G+
Sbjct: 228 SPLTGRTHQIRVHAQFAGHPIVGDDKYENKERARYFRDLGAGRMFLHAKSLEIPSDQ-GK 286

Query: 305 LQITAPLPAHMVKTWDSLG 323
           +   APL        D LG
Sbjct: 287 MVFDAPLDTAFQSFIDQLG 305


>gi|260597456|ref|YP_003210027.1| 23S rRNA pseudouridylate synthase C [Cronobacter turicensis z3032]
 gi|260216633|emb|CBA29938.1| Ribosomal large subunit pseudouridine synthase C [Cronobacter
           turicensis z3032]
          Length = 333

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 105/307 (34%), Positives = 168/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  D+   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 24  VKIVAISADQAGQRIDNFLRTQLKGVPKSLIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 83

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 84  IPPV------RVAEREEEAVSPHLQKVA-ALSDVILYEDDHILVLNKPSGTAVHGGSGLS 136

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 137 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGMQKDYLAL 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + FA     +   
Sbjct: 196 VRGQWQSHVKTVQAPLLKNILQSGERIVRVNQEGKPSE---TRFKVEERFASA-TLVRCS 251

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH    G PI  D +Y    F     S   N+L+LHA  +   HP  G  
Sbjct: 252 PVTGRTHQIRVHTQFAGHPIAFDDRYGDRTFDAQLASTGLNRLFLHAAALRFEHPGTGET 311

Query: 305 LQITAPL 311
           +++ AP+
Sbjct: 312 MRVEAPM 318


>gi|113460859|ref|YP_718926.1| 23S rRNA pseudouridylate synthase C [Haemophilus somnus 129PT]
 gi|112822902|gb|ABI24991.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           somnus 129PT]
          Length = 326

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 110/311 (35%), Positives = 172/311 (55%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  DE   R+D +       +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 13  VKILTINEDESGQRIDNFLLAKLKSVPKSLIYRILRKGEVRVNKGRIKPEYKLQNGDIVR 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       I E++    S  L K +   + I+ +ED+ + V NKP+G++V GGSG+ 
Sbjct: 73  IPPVR------IAEKEHTPISKKLNKVAQLEQQII-FEDNYLLVLNKPSGLAVHGGSGLN 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +     L++ +  + +   L HRLD++TSGIL++A+ R+A + L E  R + IQK Y +L
Sbjct: 126 FGAIEALRT-LRPEARFLELVHRLDRDTSGILLIAKKRSALRSLHEQLREKTIQKEYLAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   +VK NE+G     + F V + +      ++  
Sbjct: 185 VRGHWQSHCKMIQAPLLKNELTSGE--RIVKVNEQGKPSE-TKFSVEERY-NNATLVKAS 240

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY   NF    T+   N+L+LHA  +   HP+ G R
Sbjct: 241 PITGRTHQIRVHTQYAGHPIALDDKYGDKNFDQQMTALGLNRLFLHAFAICFEHPKTGER 300

Query: 305 LQITAPLPAHM 315
           L++ APL   M
Sbjct: 301 LRLVAPLDLAM 311


>gi|206577057|ref|YP_002239295.1| ribosomal large subunit pseudouridine synthase C [Klebsiella
           pneumoniae 342]
 gi|206566115|gb|ACI07891.1| ribosomal large subunit pseudouridine synthase C [Klebsiella
           pneumoniae 342]
          Length = 317

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 107/308 (34%), Positives = 170/308 (55%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++++G  VR
Sbjct: 8   VKMVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALSEVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +  +F  L   
Sbjct: 180 VRGQWQSHTKVVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERY--EFATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  + G PI  D +Y    F    +    N+L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLSGTGLNRLFLHAAALKFTHPGSGE 294

Query: 305 -LQITAPL 311
            +++ APL
Sbjct: 295 VMRVEAPL 302


>gi|317047700|ref|YP_004115348.1| RluA family pseudouridine synthase [Pantoea sp. At-9b]
 gi|316949317|gb|ADU68792.1| pseudouridine synthase, RluA family [Pantoea sp. At-9b]
          Length = 318

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 109/308 (35%), Positives = 168/308 (54%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  +    R+D + +     +    + +ILR G+VRV+KKR+K   +++ G  +R
Sbjct: 8   VQFVAITAENAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEEGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A     +EQ +   S  L K +    +I LYED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRVAER---EEQAV---SPKLEKVASLADAI-LYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G   +  + +   LLK     G+ V  V    K +    + FKV + F   F  L + 
Sbjct: 180 VRGDWPSHLKVVQAPLLKNILQSGERVVRVSAEGKPSE---TRFKVEERFG--FATLVKA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH LH G PI  D +Y    F+    +   ++L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTLHAGHPIAFDDRYGDREFERQLAATGLSRLFLHAAALTFTHPNTGE 294

Query: 305 -LQITAPL 311
            L++ APL
Sbjct: 295 TLRMEAPL 302


>gi|237748406|ref|ZP_04578886.1| ribosomal large subunit pseudouridine synthase C [Oxalobacter
           formigenes OXCC13]
 gi|229379768|gb|EEO29859.1| ribosomal large subunit pseudouridine synthase C [Oxalobacter
           formigenes OXCC13]
          Length = 339

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 117/339 (34%), Positives = 178/339 (52%), Gaps = 30/339 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           +S    V+ V V  +++  R+D +       +   ++ +ILRSG+VRV+KKR+    R+Q
Sbjct: 22  ISSFQQVRQVTVTENDDGQRIDNFLFRTCKGVPKSHIYRILRSGEVRVNKKRIDQTYRLQ 81

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  +RIPP+  A     +E+ +  +S +           +LYED  I V NKPAG++V 
Sbjct: 82  EGDTIRIPPIKVAER---EEKHVPGASFD-----------ILYEDDSILVINKPAGVAVH 127

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG++Y +   L++      +   L HRLD+ETSGILV+A+ R+A   L E  R   I 
Sbjct: 128 GGSGVSYGVIEQLRA-ARPNARFLELVHRLDKETSGILVLAKKRSALVKLHEQIREGSID 186

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQK 239
           K Y +LV G  KN+++ +   LLK     G+    V+ +  G A++ I  F V+  F + 
Sbjct: 187 KRYQALVKGDWKNQRQHVKLPLLKYHTADGE--RRVRVDAGGLASHTI--FNVLKRFPE- 241

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-------KGNFTSPIQNKLYLHA 292
           F  LE +  TGRTHQ+RVH    G  I GD KY  +F       KG        +++LHA
Sbjct: 242 FTLLEAELKTGRTHQIRVHLASSGHVIAGDDKY-GDFELNREIQKGKKGEDALKRMFLHA 300

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
             +   HPE G+ L ++APLP         L  + D+++
Sbjct: 301 YKITFIHPETGKPLTVSAPLPDECSGYLKGLDAENDKDV 339


>gi|261868551|ref|YP_003256473.1| 23S rRNA pseudouridylate synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413883|gb|ACX83254.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 319

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 108/311 (34%), Positives = 170/311 (54%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ V +DE   RLD +       +    + +I+R G+VRV+K R K   ++ +  VVR
Sbjct: 10  VQFLTVSDDEAGQRLDNFLLARLKGVPKSLIYRIVRKGEVRVNKARSKPEYKLLADDVVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A       +K  D+  N       L+  +++ED+ + V NKP+GI+V GGSG+ 
Sbjct: 70  IPPVRVA-------EKAQDTISNKLTKVAQLEQHIIFEDNYLLVLNKPSGIAVHGGSGLD 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +    +   L HRLD++TSGIL+VA+ R+A ++L E  R + +QK Y +L
Sbjct: 123 FGVIEALRA-LRPAARFLELVHRLDRDTSGILLVAKKRSALRNLHEQLREKTVQKDYLAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK    GG+   +VK +E+G   + + F V + +      ++  
Sbjct: 182 VRGQWQSHCKVVQAPLLKNELAGGE--RIVKVSEQG-KPSETRFSVEERYTNA-TLIKAS 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F  +      N+L+LHA  +   HP  G  
Sbjct: 238 PVTGRTHQIRVHTQYAGHPIAFDSKYGDKEFDQHMVELGLNRLFLHAYTIRFEHPHSGET 297

Query: 305 LQITAPLPAHM 315
           L++TAPL   M
Sbjct: 298 LRLTAPLEEKM 308


>gi|254482018|ref|ZP_05095260.1| pseudouridine synthase, RluA family [marine gamma proteobacterium
           HTCC2148]
 gi|214037708|gb|EEB78373.1| pseudouridine synthase, RluA family [marine gamma proteobacterium
           HTCC2148]
          Length = 318

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 104/318 (32%), Positives = 167/318 (52%), Gaps = 16/318 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+++ V+ +    RLD +       +    L + LR G++RV+K RVK + R+ +G +VR
Sbjct: 11  VRHLTVDENSSGQRLDNFLTRELKGVPRTRLYRALRKGEIRVNKGRVKADYRLVTGDLVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++     D        S+ LK  ++YED  + V +KP+G++V GGSG+ 
Sbjct: 71  IPP--------LRTPAPSDPPTIPRYWSEQLKQRVIYEDGGLLVVDKPSGLAVHGGSGLN 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+  + S+ +   L HRLD++TSG+++VAR  A  + L    R   + K Y +L
Sbjct: 123 FGMIESLRQ-IRSEDRYLELVHRLDRDTSGLIMVARKPAILRELHRQLREDHVDKRYLAL 181

Query: 187 VWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G  P++K    A         G   V V K+ ++    +I+ F V++ F +    +E 
Sbjct: 182 VAGKWPRSKVRVDAPLQKNVLQSGERMVRVAKEGKR----SITDFTVVERF-KGATLVEA 236

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR 304
           +P TGRTHQ+RVHALH G P++GD KY +         I   +L+LHAR +    P  GR
Sbjct: 237 KPVTGRTHQIRVHALHAGFPLLGDSKYGSPKGEALCEQIGLKRLFLHARALRFKLPGVGR 296

Query: 305 LQITAPLPAHMVKTWDSL 322
           +++ APL   +    D L
Sbjct: 297 MELEAPLDKDLEMALDKL 314


>gi|330805203|ref|XP_003290575.1| hypothetical protein DICPUDRAFT_81306 [Dictyostelium purpureum]
 gi|325079283|gb|EGC32890.1| hypothetical protein DICPUDRAFT_81306 [Dictyostelium purpureum]
          Length = 583

 Score =  160 bits (405), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 118/396 (29%), Positives = 180/396 (45%), Gaps = 87/396 (21%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP-------------HINFVNLQKILRSGQVRVDKKRV 53
           V+Y V   D E MR+DRW  +  P              I +   ++  ++    + + ++
Sbjct: 192 VKYYVTR-DMEGMRVDRWISHKLPILPHSLVCKWLRNKIIYKENEEFKQNSTSELKRHKM 250

Query: 54  KFNNRIQSGQVVRIPPV------INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           KFN++++ G  +  P        +  +N   K  ++ D  +   K S      +LY+D  
Sbjct: 251 KFNDKVEVGSWIYFPSQALLDQHMADINEPTKYTRLSDDEIKEIKES------VLYKDEH 304

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + V NKP G+SVQGGSG+  H+D  L      K + P+L HRLD+ TSGIL++ R+R AA
Sbjct: 305 LLVLNKPQGLSVQGGSGLKKHLDMMLNHLRFEKSENPKLVHRLDKATSGILILGRSRLAA 364

Query: 168 QHLTESFRMRR---------------------------------------------IQKI 182
             + E F ++                                              I+K 
Sbjct: 365 TAMAEKFELKLVSSKKKEKEKFNKDNERENKKNSSKKKKDTKDEEIDDDEDLENKGIKKT 424

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           YW+L+ G PK  +E      LKK  IGG+   +  +K  + GA  AI+ +KVI       
Sbjct: 425 YWALIAGAPK-PREGRIRAPLKKVMIGGEEKVIPALKIGD-GAKLAITEYKVIQSSLDNQ 482

Query: 241 CWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLH 291
            ++ + P TGRTHQLRVH A  +  PI+GD KY           F  + +S +  KL+LH
Sbjct: 483 SFVALWPETGRTHQLRVHCASVLNAPIIGDTKYGNKLVNESIKTFLNSASSSL--KLHLH 540

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           AR +   HP   + + I APLP  + ++W   GF Y
Sbjct: 541 ARRIQFIHPFTNKPIDIIAPLPPSLKESWKKFGFNY 576


>gi|300704630|ref|YP_003746233.1| ribosomal large subunit pseudouridine synthase c [Ralstonia
           solanacearum CFBP2957]
 gi|299072294|emb|CBJ43627.1| Ribosomal large subunit pseudouridine synthase C [Ralstonia
           solanacearum CFBP2957]
          Length = 350

 Score =  160 bits (405), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 109/324 (33%), Positives = 174/324 (53%), Gaps = 23/324 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D +  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 29  VAYVEIGEDAQGQRIDNFLMRLAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 88

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      I +       +      ++F    +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 89  IPPL-----RIAQPSAEQVEAARAVPAAEF---TILHEDTHLLVIDKPAGVAVHGGSGVA 140

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   +S  D+K  +  L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++
Sbjct: 141 FGVIEQLRRSRPDAKFLE--LVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFA 198

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G+  ++++ I   L K +   G+   V  Q +   ++ I  F  +  F   +  LE 
Sbjct: 199 AVKGVWPHQRQHIKAPLFKYTTPEGER-RVRVQADGQPSHTI--FNKVGVFG-PYTLLEA 254

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMDLPH 299
           +  TGRTHQ+RVH  H G PI+GD KY  +F  N        SP   +++LHA  + L H
Sbjct: 255 ELKTGRTHQIRVHLAHAGFPILGDDKY-GDFALNKALSRANASPRLARMFLHAHTLRLTH 313

Query: 300 PEGGRL-QITAPLPAHMVKTWDSL 322
           P+ G +    APLPA      D+L
Sbjct: 314 PQSGEIVTFKAPLPAECAAFLDAL 337


>gi|27904809|ref|NP_777935.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
 gi|34395769|sp|Q89AH2|RLUC_BUCBP RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|27904207|gb|AAO27040.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
          Length = 315

 Score =  160 bits (404), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 106/310 (34%), Positives = 173/310 (55%), Gaps = 23/310 (7%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           ++ +  + E  R+D + +  +  + F  + KI+R+GQ+R++KKR+  N +++ G  VRIP
Sbjct: 10  FLNITENSEKQRIDNFLRKTFKRLPFNLICKIIRTGQIRINKKRINQNYKLKLGDSVRIP 69

Query: 69  PVINALNHIIKEQKILDSSVNL-TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P        I  Q   +  + L T+ S    +++LYED+   + NKP+G+SV  GSGI Y
Sbjct: 70  P--------ITIQSDSNKKIKLNTRLSIIFNNMILYEDNYFLILNKPSGMSVHSGSGINY 121

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L+  +    +   L HRLD++TSG+L++A+ R+  ++L E  R ++I+K Y +LV
Sbjct: 122 GMIENLR-ILRPYNRYLDLVHRLDRDTSGVLIIAKKRSILRNLHEQLREKKIKKKYVALV 180

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+  +  + I+  LLK S       ++VK + KG   +I+HF +   +  K   + + P
Sbjct: 181 HGVWPDILKSISKPLLKTSSRKNK--NIVKIDPKGKE-SITHFNIKKKYT-KNTLISITP 236

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEG 302
            TGRTHQ+RVH LH+  PIV D KY         K  F     N+L LHA  ++  HP+ 
Sbjct: 237 ITGRTHQIRVHLLHLNYPIVLDAKYGIKKLDYFIKNKFNI---NRLLLHAESINFFHPKR 293

Query: 303 GR-LQITAPL 311
            + + ITAPL
Sbjct: 294 KKNILITAPL 303


>gi|325267840|ref|ZP_08134490.1| ribosomal large subunit pseudouridine synthase C [Kingella
           denitrificans ATCC 33394]
 gi|324980721|gb|EGC16383.1| ribosomal large subunit pseudouridine synthase C [Kingella
           denitrificans ATCC 33394]
          Length = 326

 Score =  160 bits (404), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 107/328 (32%), Positives = 172/328 (52%), Gaps = 25/328 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V+  E   RLD +       +   ++ +I+R+G+VRV+K R K   RIQ+G ++R
Sbjct: 9   VNHICVQEHESAQRLDNYLIKILKGVPKSHIHRIIRAGEVRVNKGRAKPETRIQTGDLIR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A       +K   SS+       F    ++YED  + V NKP+G++V GGSG++
Sbjct: 69  IPPVRTA-------EKTAKSSLQPVPARHFE---IVYEDDALLVVNKPSGVAVHGGSGVS 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E  R    +KIYW+L
Sbjct: 119 FGVIEQLRR-ARPEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEMLRNDHPKKIYWAL 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G  +     +   L+K +   G+ +  V   E G + A + F+V+D F+ +       
Sbjct: 178 GVGTWQPALRHVRLPLVKYTGAAGEKMVRVGSAEDGQS-AHTVFRVLDTFSGERPHSVGV 236

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +E    TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 237 SALSLVEATLKTGRTHQIRVHMQASGCPIAGDERY-GDYQANRRLQKLGLKRMFLHAYSL 295

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +L HP  G +L + A LP  + +  D L
Sbjct: 296 ELDHPLTGEKLVLQAALPDDLQRFLDGL 323


>gi|320179214|gb|EFW54172.1| 23S rRNA pseudouridylate synthase C [Shigella boydii ATCC 9905]
          Length = 319

 Score =  160 bits (404), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 109/310 (35%), Positives = 171/310 (55%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHP-E 301
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 302 GGRLQITAPL 311
           GG ++I AP+
Sbjct: 295 GGVMRIEAPM 304


>gi|270261338|ref|ZP_06189611.1| ribosomal large subunit pseudouridine synthase C [Serratia
           odorifera 4Rx13]
 gi|270044822|gb|EFA17913.1| ribosomal large subunit pseudouridine synthase C [Serratia
           odorifera 4Rx13]
          Length = 320

 Score =  160 bits (404), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 103/307 (33%), Positives = 169/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++ +G VVR
Sbjct: 8   VQLITISDDEAGQRIDNFLLARLKGVPKSMIYRIVRKGEVRVNKGRIKAEYKLAAGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S  L K +  L   +LYED  + + NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEAPVSAKLDKVA-ALADCILYEDDHLLLLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +V+ N +G   + + FKV + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNILQSGE--RIVRVNSEG-KPSETRFKVEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y    F          +L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHTLHAGHPIAFDDRYGDREFDRQLAGTGLKRLFLHAAALRFEHPGTGET 295

Query: 305 LQITAPL 311
           ++I AP+
Sbjct: 296 MRIEAPM 302


>gi|293390568|ref|ZP_06634902.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951102|gb|EFE01221.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 319

 Score =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 110/316 (34%), Positives = 173/316 (54%), Gaps = 24/316 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ V +DE   RLD +       +    + +I+R G+VRV+K R K   ++++  VVR
Sbjct: 10  VQFLTVSDDEAGQRLDNFLLARLKGVPKSLIYRIVRKGEVRVNKGRSKPEYKLRADDVVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+     S  LTK +  L+  +++ED+ + V NKP+GI+V GGSG+ 
Sbjct: 70  IPPVR------VAEKAQATISNKLTKVAQ-LEQHIIFEDNYLLVLNKPSGIAVHGGSGLD 122

Query: 127 YHIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + +   L++       +P      L HRLD++TSGIL+VA+ R+A ++L E  R + +QK
Sbjct: 123 FGVIEALRAL------RPAACFLELVHRLDRDTSGILLVAKKRSALRNLHEQLREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  ++  + +   LLK    GG+   +VK +E+G   + + F V + +     
Sbjct: 177 DYLALVRGQWQSHCKVVQAPLLKNELAGGE--RIVKVSEQG-KPSETRFSVEERYTNA-T 232

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D KY    F  +      N+L+LHA  +   HP
Sbjct: 233 LIKASPVTGRTHQIRVHTQYAGHPIAFDSKYGDKEFDQHMVELGLNRLFLHAYAIRFEHP 292

Query: 301 EGGR-LQITAPLPAHM 315
             G  L++TAPL   M
Sbjct: 293 HSGETLRLTAPLEEKM 308


>gi|261493033|ref|ZP_05989574.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261496687|ref|ZP_05993066.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261307656|gb|EEY08980.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261311310|gb|EEY12472.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 320

 Score =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 105/307 (34%), Positives = 168/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q   +VR
Sbjct: 11  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQPDDLVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E+     S  L K ++ L+S +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPVR------VAEKNEAPISTKLNKVAE-LESQILYEDDSMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+   +V+ +E+G   + + F + + +A     ++  
Sbjct: 183 VRGQWQAHTKVIKAPLLKNELASGE--RIVRVSEEG-KPSETRFSIEERYANA-TLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY    F          +L+LHA  +   HP+ G  
Sbjct: 239 PITGRTHQIRVHTQYAGHPIALDDKYGDVEFDSKMKEVGLQRLFLHAHAIRFEHPKTGEE 298

Query: 305 LQITAPL 311
           + ITAPL
Sbjct: 299 MVITAPL 305


>gi|308186402|ref|YP_003930533.1| pseudouridylate synthase [Pantoea vagans C9-1]
 gi|308056912|gb|ADO09084.1| putative pseudouridylate synthase [Pantoea vagans C9-1]
          Length = 318

 Score =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 106/308 (34%), Positives = 165/308 (53%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +V +  +    R+D + +     +    + +I+R G+VRV+KKRVK   +++ G  VR
Sbjct: 8   VHFVAITAENAGQRIDNFLRTQLKGVPKSMIYRIVRKGEVRVNKKRVKPEYKLEEGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+     S  L K +    +I L+ED  + V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAERDEDAVSPKLAKVASLADAI-LFEDESLLVMNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G   +  + +   LLK     G+ V  V    K +    + FKV + F  +F  L + 
Sbjct: 180 VRGNWPSHLKVVQAPLLKNILQSGERVVRVSSEGKASE---TRFKVEERF--EFATLVKA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH LH G PI  D +Y   +F     S    +L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTLHAGHPIAFDDRYGERDFDSQLASTGLKRLFLHAAALTFTHPATGE 294

Query: 305 -LQITAPL 311
            +++ APL
Sbjct: 295 VMRVEAPL 302


>gi|187928001|ref|YP_001898488.1| pseudouridine synthase [Ralstonia pickettii 12J]
 gi|187724891|gb|ACD26056.1| pseudouridine synthase, RluA family [Ralstonia pickettii 12J]
          Length = 344

 Score =  159 bits (402), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 110/315 (34%), Positives = 170/315 (53%), Gaps = 27/315 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D E  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 29  VAYVEIGEDAEGQRIDNFLMRVAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 88

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A              V   +     +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 89  IPPLRIA------------QQVEAARPVPAAEFTILHEDTHLLVIDKPAGVAVHGGSGVA 136

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   +S  D+K  +  L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++
Sbjct: 137 FGVIEQLRQSRPDAKFLE--LVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFA 194

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G+  +K++ I + L K +   G+   V  Q +  A++ I  F  +  F   +  LE 
Sbjct: 195 AVKGVWPHKRQHIKSPLHKYTTPEGER-RVRVQADGQASHTI--FNKVGVFG-PYTLLEA 250

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMDLPH 299
           +  TGRTHQ+RVH  H G PI+GD KY  +F  N        SP   +++LHA  + L H
Sbjct: 251 ELKTGRTHQIRVHLAHAGFPILGDDKY-GDFALNKALSRANASPRLARMFLHAHRLQLTH 309

Query: 300 PEGGR-LQITAPLPA 313
           P  G  +   APLPA
Sbjct: 310 PHSGEVVTFNAPLPA 324


>gi|161503726|ref|YP_001570838.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160865073|gb|ABX21696.1| hypothetical protein SARI_01811 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 317

 Score =  159 bits (402), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 107/308 (34%), Positives = 170/308 (55%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  + V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + FA  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERFA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
            P TGRTHQ+RVH  ++G PI  D +Y    F         ++L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTQYVGHPIAFDDRYGDREFDKQLAGTGLSRLFLHAAALKFTHPGTGD 294

Query: 304 RLQITAPL 311
            L+I AP+
Sbjct: 295 VLRIEAPM 302


>gi|66808785|ref|XP_638115.1| hypothetical protein DDB_G0285543 [Dictyostelium discoideum AX4]
 gi|60466557|gb|EAL64609.1| hypothetical protein DDB_G0285543 [Dictyostelium discoideum AX4]
          Length = 718

 Score =  159 bits (402), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 109/346 (31%), Positives = 167/346 (48%), Gaps = 74/346 (21%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILD--SSVNLTKHSD----FLKS 99
           V++ + ++KFN+++Q G  +  P        +I +Q+I D        + SD     ++ 
Sbjct: 375 VQLKRHKLKFNDKVQVGSWIYFPA------QVILDQQIADIKDPQKYARLSDQEIKEIRE 428

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +LY+D  I V NKP G+SVQGG+G+  H+D  L      K + P+L HRLD+ TSGIL+
Sbjct: 429 SVLYKDEHIIVLNKPQGLSVQGGTGLNKHLDMMLSHLRFEKDENPKLVHRLDRNTSGILI 488

Query: 160 VARTRAAAQHLTESFRMRR----------------------------------------- 178
           + R++ AA  +T+ F ++                                          
Sbjct: 489 LGRSKLAASAMTKKFELKLVKENKKDKDDNNNNKNNKNNNKNDSKRLFREKEVFNNNKNK 548

Query: 179 ----------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-DYVHVVKQNEKGANYAI 227
                     I+K YW+L+   P   KE      LKK  +GG + V        GA  AI
Sbjct: 549 DEENENYSKGIKKTYWALLGSTP-TPKEGRIRAPLKKVVVGGFEKVVPTLTTGDGAKIAI 607

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYC-----ANFKGNFT 281
           + +KV++    K C++ + P TGRTHQLRVH A  +  PI+GD KY      +N K    
Sbjct: 608 TEYKVLESSLTKHCFISLWPETGRTHQLRVHCASVLNTPIIGDPKYGDKESDSNLKDLL- 666

Query: 282 SPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKY 326
            P  +KL+LHAR ++  HP    ++ I+APLP  +V+ W ++GF Y
Sbjct: 667 -PYPSKLHLHARRIEFIHPFTNKKIDISAPLPRELVQNWKTMGFNY 711


>gi|332993476|gb|AEF03531.1| ribosomal large subunit pseudouridine synthase C [Alteromonas sp.
           SN2]
          Length = 314

 Score =  159 bits (402), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 109/319 (34%), Positives = 172/319 (53%), Gaps = 17/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++V VE D    R+D + +     +    + +ILR G+VRV+K RVK   ++ +  VVR
Sbjct: 9   VRFVTVEPDLAGQRVDNFLRTQLKGVPKSMIYRILRKGEVRVNKGRVKPEYKLVADDVVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +       +     S  L K +  L+S +L+ED +I V NKP+GI+V GGSG++
Sbjct: 69  IPPVRVS-------EGTPGPSPKLDKIA-ALESQILFEDERIIVINKPSGIAVHGGSGLS 120

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+G      D+   +  L HRLD++TSG +++A+ R+A +H+ E  R  ++ K Y +
Sbjct: 121 FGLIEGLRALRPDANFME--LVHRLDRDTSGCILIAKKRSALRHMHEQLRTGKMDKRYQA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   + +  +   L K     G+ +  V ++ K +    + ++++  F      +E 
Sbjct: 179 LVAGQWPDNRFKVKAPLRKNVLQSGERMVSVSEDGKPSE---TRYRILQKF-DTATLVEA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
            P TGRTHQ+RVH LH   PI  D KY  A F  +      N+L+LHA  + L HP    
Sbjct: 235 SPITGRTHQIRVHCLHAEHPIACDPKYGDAEFDESMRQKGLNRLFLHAHSISLIHPGTEE 294

Query: 304 RLQITAPLPAHMVKTWDSL 322
           R++ TAPL A +  T  +L
Sbjct: 295 RVKFTAPLDATLTNTLKAL 313


>gi|207725237|ref|YP_002255633.1| ribosomal large subunit pseudouridine synthase c protein [Ralstonia
           solanacearum MolK2]
 gi|207743612|ref|YP_002260004.1| ribosomal large subunit pseudouridine synthase c protein [Ralstonia
           solanacearum IPO1609]
 gi|206590471|emb|CAQ37433.1| ribosomal large subunit pseudouridine synthase c protein [Ralstonia
           solanacearum MolK2]
 gi|206595011|emb|CAQ61938.1| ribosomal large subunit pseudouridine synthase c protein [Ralstonia
           solanacearum IPO1609]
          Length = 352

 Score =  159 bits (402), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 108/324 (33%), Positives = 173/324 (53%), Gaps = 23/324 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D +  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 31  VAYVEIGEDAQGQRIDNFLMRLAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 90

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      I +       +      ++F    +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 91  IPPL-----RIAQPSAEQVEAARAVPAAEF---TILHEDTHLLVIDKPAGVAVHGGSGVA 142

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   +S  D+K  +  L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++
Sbjct: 143 FGVIEQLRRSRPDAKFLE--LVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFA 200

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G+  ++++ I   L K +   G+   V  Q +   ++ I  F  +  F   +  LE 
Sbjct: 201 AVKGVWPHQRQHIKAPLFKYTTPEGER-RVRVQADGQPSHTI--FNRVGVFG-PYTLLEA 256

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF------TSPIQNKLYLHARYMDLPH 299
           +  TGRTHQ+RVH  H G PI+GD KY  +F  N        SP   +++LHA  + L H
Sbjct: 257 ELKTGRTHQIRVHLAHAGFPILGDDKY-GDFALNKALSRANASPRLARMFLHAHTLRLTH 315

Query: 300 PEGGRL-QITAPLPAHMVKTWDSL 322
           P+ G +    APLPA      D+ 
Sbjct: 316 PQSGEIVTFKAPLPAECAAFLDAF 339


>gi|78485049|ref|YP_390974.1| pseudouridine synthase, RluD [Thiomicrospira crunogena XCL-2]
 gi|78363335|gb|ABB41300.1| ribosomal large subunit pseudouridine synthase C [Thiomicrospira
           crunogena XCL-2]
          Length = 312

 Score =  159 bits (402), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 104/310 (33%), Positives = 178/310 (57%), Gaps = 22/310 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+++ V +++   R+D +   HY ++    + +I+R G+VRV+K RVK N R+  G  VR
Sbjct: 3   VRFIEVTSEDAGQRVDNFLMRHYRNVPKTLIYRIIRKGEVRVNKGRVKQNTRLNDGDTVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      + ++ ++   +  + +  D     +LYED+ + V NKP+GI+V GGSGI 
Sbjct: 63  VPPI-----RVPEKTEVTVPTNQMQRIEDS----ILYEDNDLLVINKPSGIAVHGGSGIQ 113

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   +++ +    ++  L HR+D++TSG +++A+  +  + L E  R  ++ K Y +L
Sbjct: 114 WGLIEIVRA-LRPLAKRLELVHRIDRDTSGCILLAKKASVLKALHEQIRENKMTKEYLAL 172

Query: 187 V---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           V   W  PK   E I   LLK +   G+   VVK +++G   ++S+F+V++ + Q+   +
Sbjct: 173 VAHHW--PKG-LEKIDLPLLKNTLKSGE--RVVKVSDEG-KPSVSYFRVVERY-QECDLV 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEG 302
            ++  TGRTHQ+RVHAL  GCP+VGD KY        F +    +L LHA+Y+   HP  
Sbjct: 226 AVRLKTGRTHQIRVHALSQGCPLVGDDKYGEKETNKIFRAKGMKRLALHAQYLGFEHPVT 285

Query: 303 GR-LQITAPL 311
              L+I APL
Sbjct: 286 EEWLKIEAPL 295


>gi|170768204|ref|ZP_02902657.1| ribosomal large subunit pseudouridine synthase C [Escherichia
           albertii TW07627]
 gi|170122970|gb|EDS91901.1| ribosomal large subunit pseudouridine synthase C [Escherichia
           albertii TW07627]
          Length = 319

 Score =  159 bits (401), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 109/310 (35%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++ +G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLDAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEDAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F   FT      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQFTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|107102524|ref|ZP_01366442.1| hypothetical protein PaerPA_01003588 [Pseudomonas aeruginosa PACS2]
          Length = 318

 Score =  159 bits (401), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 113/315 (35%), Positives = 175/315 (55%), Gaps = 20/315 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S +T VQ + V  +    R+D +            + +ILR G+VRV+K R+K + R+Q+
Sbjct: 6   SPITGVQLLDVPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRIKPDYRLQA 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQ 120
           G  VR+PP+  A           D    L +   + +++ ++YED  + V NKPAGI+V 
Sbjct: 66  GDQVRVPPLRLAER---------DEPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVH 116

Query: 121 GGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           GGSG+ A  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R  +I
Sbjct: 117 GGSGVSAGVIEVFRQLRPDAKDIE--LVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKI 174

Query: 180 -QKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             K Y +LV G  P  KK   A  LLK +   G+   +V+ N +G + A++ F+V+  F 
Sbjct: 175 VDKRYHALVRGHWPAGKKNVRAP-LLKNNLRSGE--RMVEVNVEGKD-ALTEFRVLRRFG 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMD 296
                +E +P TGRTHQ+RVHA H G  I GD KY   +F          +L+LHA  + 
Sbjct: 231 DFATLVEARPITGRTHQIRVHAKHAGHAIAGDPKYGDEDFSREIRELGGKRLFLHAAQLR 290

Query: 297 LPHPEGGRLQITAPL 311
           +P P+G  L++ AP+
Sbjct: 291 VPLPDGQVLELEAPV 305


>gi|254361221|ref|ZP_04977365.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|153092712|gb|EDN73761.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
          Length = 320

 Score =  159 bits (401), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 168/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R K   ++Q   +VR
Sbjct: 11  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRNKPEYKLQPDDLVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E+     S  L K ++ L+S +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPVR------VAEKNEAPISTKLNKVAE-LESQILYEDESMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+   +V+ +E+G   + + F + + +A     ++  
Sbjct: 183 VRGQWQAHTKVIKAPLLKNELASGE--RIVRVSEEG-KPSETRFSIEERYANA-TLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F          +L+LHA  +   HP+ G  
Sbjct: 239 PITGRTHQIRVHTQYAGHPIALDDKYGDAEFDSKMKEVGLQRLFLHAHAIRFEHPKTGEE 298

Query: 305 LQITAPL 311
           + ITAPL
Sbjct: 299 MVITAPL 305


>gi|83748464|ref|ZP_00945486.1| Ribosomal large subunit pseudouridine synthase C [Ralstonia
           solanacearum UW551]
 gi|83724875|gb|EAP72031.1| Ribosomal large subunit pseudouridine synthase C [Ralstonia
           solanacearum UW551]
          Length = 350

 Score =  159 bits (401), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 108/324 (33%), Positives = 173/324 (53%), Gaps = 23/324 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D +  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 29  VAYVEIGEDAQGQRIDNFLMRLAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 88

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      I +       +      ++F    +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 89  IPPL-----RIAQPSAEQVEAARAVPAAEF---TILHEDTHLLVIDKPAGVAVHGGSGVA 140

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   +S  D+K  +  L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++
Sbjct: 141 FGVIEQLRRSRPDAKFLE--LVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFA 198

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G+  ++++ I   L K +   G+   V  Q +   ++ I  F  +  F   +  LE 
Sbjct: 199 AVKGVWPHQRQHIKAPLFKYTTPEGER-RVRVQADGQPSHTI--FNRVGVFG-PYTLLEA 254

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF------TSPIQNKLYLHARYMDLPH 299
           +  TGRTHQ+RVH  H G PI+GD KY  +F  N        SP   +++LHA  + L H
Sbjct: 255 ELKTGRTHQIRVHLAHAGFPILGDDKY-GDFALNKALSRANASPRLARMFLHAHTLRLTH 313

Query: 300 PEGGRL-QITAPLPAHMVKTWDSL 322
           P+ G +    APLPA      D+ 
Sbjct: 314 PQSGEIVTFKAPLPAECAAFLDAF 337


>gi|323937826|gb|EGB34090.1| RluA family protein pseudouridine synthase [Escherichia coli E1520]
          Length = 319

 Score =  159 bits (401), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 171/310 (55%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y  + F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDSEFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|145628779|ref|ZP_01784579.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 22.1-21]
 gi|145640373|ref|ZP_01795957.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae R3021]
 gi|144979249|gb|EDJ88935.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 22.1-21]
 gi|145274959|gb|EDK14821.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 22.4-21]
          Length = 322

 Score =  159 bits (401), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 105/313 (33%), Positives = 175/313 (55%), Gaps = 14/313 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+  +  S NL K +  L++ +L+ED  + V NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDVPISKNLNKVT-ALENQILFEDDCLIVLNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+   +V+ +E+G   + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGE--RIVRVSEQG-KPSETRFSIEERYTNA-TLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHM 315
             L+  APL   M
Sbjct: 299 ETLRFNAPLDHQM 311


>gi|120554793|ref|YP_959144.1| RluA family pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120324642|gb|ABM18957.1| ribosomal large subunit pseudouridine synthase C [Marinobacter
           aquaeolei VT8]
          Length = 317

 Score =  158 bits (400), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 102/303 (33%), Positives = 171/303 (56%), Gaps = 16/303 (5%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           + T VQ++ V+ D    R+D +       +    + +I+R G+VRV+K RVK ++R+  G
Sbjct: 1   MATEVQWITVDEDMAGQRVDNFLLARLRGVPKSIVYRIVRKGEVRVNKGRVKPDSRLNPG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VVRIPP++        EQ    S V        +++ +++E+ ++ V NKP+GI+V GG
Sbjct: 61  DVVRIPPLVQQAR---AEQPKPGSRVQ-----GVMEAAVVFENDEMLVVNKPSGIAVHGG 112

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+++ +   L+S   ++ +   L HRLD++TSG+++VA+ R+A + L +  R +RI+K 
Sbjct: 113 SGLSFGLIEVLRS-ARTEARFLELVHRLDRDTSGLVMVAKKRSALRFLQDELRQKRIRKY 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G      + +A  LL+     G+    V+ +E+G + +++ F  +  F Q +  
Sbjct: 172 YHALVVGSWPENVDRVAEPLLRFEMPNGE--RRVRVSEEGKS-SLTLFTCLQRF-QGYSL 227

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +E  P TGRTHQ+RVH+   G PI GD KY   A+ K  F +    +L LHAR ++   P
Sbjct: 228 VEASPVTGRTHQIRVHSAWAGHPIAGDDKYMDDASLKA-FRAIGGQRLMLHARALEFSLP 286

Query: 301 EGG 303
             G
Sbjct: 287 GSG 289


>gi|218689038|ref|YP_002397250.1| 23S rRNA pseudouridylate synthase C [Escherichia coli ED1a]
 gi|306814065|ref|ZP_07448238.1| 23S rRNA pseudouridylate synthase C [Escherichia coli NC101]
 gi|218426602|emb|CAR07430.1| 23S rRNA pseudouridylate synthase [Escherichia coli ED1a]
 gi|305852702|gb|EFM53150.1| 23S rRNA pseudouridylate synthase C [Escherichia coli NC101]
          Length = 319

 Score =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDGEFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|283784875|ref|YP_003364740.1| ribosomal large subunit pseudouridine synthase C [Citrobacter
           rodentium ICC168]
 gi|282948329|emb|CBG87914.1| ribosomal large subunit pseudouridine synthase C [Citrobacter
           rodentium ICC168]
          Length = 317

 Score =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 106/312 (33%), Positives = 171/312 (54%), Gaps = 16/312 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  +R
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKNVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  + G PI  D +Y    F     +   ++L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLAATGLSRLFLHAAALKFTHPGTGE 294

Query: 305 -LQITAPLPAHM 315
            L+I AP+   +
Sbjct: 295 VLRIEAPMDGQL 306


>gi|215486297|ref|YP_002328728.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O127:H6 str.
           E2348/69]
 gi|312968838|ref|ZP_07783045.1| pseudouridine synthase, RluA family protein [Escherichia coli
           2362-75]
 gi|331682589|ref|ZP_08383208.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli H299]
 gi|215264369|emb|CAS08726.1| 23S rRNA pseudouridy late synthase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|312286240|gb|EFR14153.1| pseudouridine synthase, RluA family protein [Escherichia coli
           2362-75]
 gi|331080220|gb|EGI51399.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli H299]
          Length = 319

 Score =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 109/310 (35%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       I E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RIAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|309781165|ref|ZP_07675902.1| ribosomal large subunit pseudouridine synthase C [Ralstonia sp.
           5_7_47FAA]
 gi|308919986|gb|EFP65646.1| ribosomal large subunit pseudouridine synthase C [Ralstonia sp.
           5_7_47FAA]
          Length = 344

 Score =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 109/315 (34%), Positives = 170/315 (53%), Gaps = 27/315 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  + E  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 29  VAYVEIGEEAEGQRIDNFLMRVAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 88

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A              V   +     +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 89  IPPLRIA------------QQVEAARPVPAAEFTILHEDTHLLVIDKPAGVAVHGGSGVA 136

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   +S  D+K  +  L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++
Sbjct: 137 FGVIEQLRQSRPDAKFLE--LVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFA 194

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G+  +K++ I + L K +   G+   V  Q +  A++ I  F  +  F   +  LE 
Sbjct: 195 AVKGVWPHKRQHIKSPLYKYTTPEGER-RVRVQADGQASHTI--FNKVGVFG-PYTLLEA 250

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMDLPH 299
           +  TGRTHQ+RVH  H G PI+GD KY  +F  N        SP   +++LHA  + L H
Sbjct: 251 ELKTGRTHQIRVHLAHAGFPILGDDKY-GDFALNKVLSRANASPRLARMFLHAHRLQLTH 309

Query: 300 PEGGR-LQITAPLPA 313
           P  G  +   APLPA
Sbjct: 310 PHSGEVVTFNAPLPA 324


>gi|15598171|ref|NP_251665.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PAO1]
 gi|116050977|ref|YP_790198.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|218890827|ref|YP_002439691.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa LESB58]
 gi|254235949|ref|ZP_04929272.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa C3719]
 gi|296388532|ref|ZP_06878007.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PAb1]
 gi|34395830|sp|Q9HZM9|RLUC_PSEAE RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|9949074|gb|AAG06363.1|AE004723_7 ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PAO1]
 gi|115586198|gb|ABJ12213.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|126167880|gb|EAZ53391.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa C3719]
 gi|218771050|emb|CAW26815.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa LESB58]
          Length = 318

 Score =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 113/315 (35%), Positives = 174/315 (55%), Gaps = 20/315 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  T VQ + V  +    R+D +            + +ILR G+VRV+K R+K + R+Q+
Sbjct: 6   SPTTGVQLLDVPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRIKPDYRLQA 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQ 120
           G  VR+PP+  A           D    L +   + +++ ++YED  + V NKPAGI+V 
Sbjct: 66  GDQVRVPPLRLAER---------DEPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVH 116

Query: 121 GGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           GGSG+ A  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R  +I
Sbjct: 117 GGSGVSAGVIEVFRQLRPDAKDIE--LVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKI 174

Query: 180 -QKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             K Y +LV G  P  KK   A  LLK +   G+   +V+ N +G + A++ F+V+  F 
Sbjct: 175 VDKRYHALVRGHWPAGKKNVRAP-LLKNNLRSGE--RMVEVNVEGKD-ALTEFRVLRRFG 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMD 296
                +E +P TGRTHQ+RVHA H G  I GD KY   +F          +L+LHA  + 
Sbjct: 231 DFATLVEARPITGRTHQIRVHAKHAGHAIAGDPKYGDEDFSREIRELGGKRLFLHAAQLR 290

Query: 297 LPHPEGGRLQITAPL 311
           +P P+G  L++ AP+
Sbjct: 291 VPLPDGQVLELEAPV 305


>gi|304397213|ref|ZP_07379092.1| pseudouridine synthase, RluA family [Pantoea sp. aB]
 gi|304355362|gb|EFM19730.1| pseudouridine synthase, RluA family [Pantoea sp. aB]
          Length = 318

 Score =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 106/308 (34%), Positives = 164/308 (53%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +V +  +    R+D + +     +    + +I+R G+VRV+KKRVK   +++ G  VR
Sbjct: 8   VHFVAITAENAGQRIDNFLRTQLKGVPKSMIYRIVRKGEVRVNKKRVKPEYKLEEGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+     S  L K +    +I L+ED  + V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAERDEDAVSPKLAKVASLADAI-LFEDESLLVMNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G   +  + +   LLK     G+ V  V    K +    + FKV + F   F  L + 
Sbjct: 180 VRGNWPSHLKVVQAPLLKNILQSGERVVRVSSEGKASE---TRFKVEERF--DFATLVKA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH LH G PI  D +Y   +F     S    +L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTLHAGHPIAFDDRYGERDFDSQLASTGLKRLFLHAAALTFTHPGTGE 294

Query: 305 -LQITAPL 311
            +++ APL
Sbjct: 295 VMRVEAPL 302


>gi|300922611|ref|ZP_07138711.1| pseudouridine synthase, RluA family [Escherichia coli MS 182-1]
 gi|300421088|gb|EFK04399.1| pseudouridine synthase, RluA family [Escherichia coli MS 182-1]
          Length = 319

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARVLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|241662583|ref|YP_002980943.1| pseudouridine synthase [Ralstonia pickettii 12D]
 gi|240864610|gb|ACS62271.1| pseudouridine synthase, RluA family [Ralstonia pickettii 12D]
          Length = 344

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 109/315 (34%), Positives = 170/315 (53%), Gaps = 27/315 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  + E  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 29  VAYVEIGEEAEGQRIDNFLMRVAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 88

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A              V   +     +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 89  IPPLRIA------------QQVEAARPVPAAEFAILHEDTHLLVIDKPAGVAVHGGSGVA 136

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   +S  D+K  +  L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++
Sbjct: 137 FGVIEQLRQSRPDAKFLE--LVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFA 194

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G+  +K++ I + L K +   G+   V  Q +  A++ I  F  +  F   +  LE 
Sbjct: 195 AVKGVWPHKRQHIKSPLYKYTTPEGER-RVRVQADGQASHTI--FNKVGVFG-PYTLLEA 250

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMDLPH 299
           +  TGRTHQ+RVH  H G PI+GD KY  +F  N        SP   +++LHA  + L H
Sbjct: 251 ELKTGRTHQIRVHLAHAGFPILGDDKY-GDFALNKALSRANASPRLARMFLHAHRLQLTH 309

Query: 300 PEGGR-LQITAPLPA 313
           P  G  +   APLPA
Sbjct: 310 PHSGEVVTFNAPLPA 324


>gi|49083776|gb|AAT51141.1| PA2975 [synthetic construct]
          Length = 319

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 113/315 (35%), Positives = 174/315 (55%), Gaps = 20/315 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  T VQ + V  +    R+D +            + +ILR G+VRV+K R+K + R+Q+
Sbjct: 6   SPTTGVQLLDVPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRIKPDYRLQA 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQ 120
           G  VR+PP+  A           D    L +   + +++ ++YED  + V NKPAGI+V 
Sbjct: 66  GDQVRVPPLRLAER---------DEPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVH 116

Query: 121 GGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           GGSG+ A  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R  +I
Sbjct: 117 GGSGVSAGVIEVFRQLRPDAKDIE--LVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKI 174

Query: 180 -QKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             K Y +LV G  P  KK   A  LLK +   G+   +V+ N +G + A++ F+V+  F 
Sbjct: 175 VDKRYHALVRGHWPAGKKNVRAP-LLKNNLRSGE--RMVEVNVEGKD-ALTEFRVLRRFG 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMD 296
                +E +P TGRTHQ+RVHA H G  I GD KY   +F          +L+LHA  + 
Sbjct: 231 DFATLVEARPITGRTHQIRVHAKHAGHAIAGDPKYGDEDFSREIRELGGKRLFLHAAQLR 290

Query: 297 LPHPEGGRLQITAPL 311
           +P P+G  L++ AP+
Sbjct: 291 VPLPDGQVLELEAPV 305


>gi|145299036|ref|YP_001141877.1| ribosomal large subunit pseudouridine synthase C [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142851808|gb|ABO90129.1| ribosomal large subunit pseudouridine synthase C [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 327

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 109/312 (34%), Positives = 168/312 (53%), Gaps = 17/312 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +E + E  R+D + K     +    + +ILR G+VRV+KKR+K   ++  G  VR
Sbjct: 21  VQLLTIEAEHEGQRIDNFLKTQLKGVPKSLIYRILRKGEVRVNKKRIKPEYKLCPGDEVR 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A  + +        S NL      L+S +L+ED  + V NKP+G++V GGSG++
Sbjct: 81  VPPVRVAEKNEL-------PSANLGS-IQRLESQILFEDDAMIVLNKPSGMAVHGGSGLS 132

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+G      D++  +  L HRLD++TSG+L+VA+ R+A + L E  R++ ++K Y +
Sbjct: 133 FGVIEGLRALRPDARFLE--LVHRLDRDTSGVLLVAKKRSALRSLHEQLRVKTMRKQYLA 190

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  +   + +   L K     G+ V  V  + K +    + F++   FA+    +E 
Sbjct: 191 LVRGQWQPHVKVVNAPLRKNDLQSGERVVRVSSDGKPSE---TRFRIARQFAEA-TLVEC 246

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  H G PI  D KY  A F     S    +L+LHA  +   HP  GR
Sbjct: 247 SPITGRTHQIRVHTQHAGHPIACDDKYGEAAFDEKMRSQGLKRLFLHAWKLTFTHPVDGR 306

Query: 305 -LQITAPLPAHM 315
            + I APL   +
Sbjct: 307 EVLIEAPLAPEL 318


>gi|300716227|ref|YP_003741030.1| 23S rRNA pseudouridylate synthase [Erwinia billingiae Eb661]
 gi|299062063|emb|CAX59179.1| 23S rRNA pseudouridylate synthase [Erwinia billingiae Eb661]
          Length = 320

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 168/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+K R+K   ++ +G  +R
Sbjct: 8   VRMVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKGRIKPEYKLVAGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A     +E+ I   S  L K +    +I +YED  I V NKP+G +V GGSG++
Sbjct: 68  IPPVRVAER---EEEAI---SPKLDKVAALAHAI-VYEDDYILVMNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+   +V+ N +G   + + FKV + +A     ++  
Sbjct: 180 VRGSWPSHIKAVQAPLLKNILQSGE--RIVRVNSEG-KPSETRFKVEERYAHA-TLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y   +F          +L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHTLHAGHPIAFDDRYGERDFDAQLAGTGLKRLFLHAAALKFTHPNTGEV 295

Query: 305 LQITAPL 311
           +++ APL
Sbjct: 296 MRVEAPL 302


>gi|238749676|ref|ZP_04611181.1| Ribosomal large subunit pseudouridine synthase C [Yersinia rohdei
           ATCC 43380]
 gi|238712331|gb|EEQ04544.1| Ribosomal large subunit pseudouridine synthase C [Yersinia rohdei
           ATCC 43380]
          Length = 319

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 103/307 (33%), Positives = 165/307 (53%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A    I+    LD    L          +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRVAERDEIQVSAKLDKVAALA-------DCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + +   LLK     G+   +VK + +G   + + FK+ + F +    ++  
Sbjct: 180 VRGQWQPHCKAVQAPLLKNIMQSGE--RMVKVSSEG-KPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDPEFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPL 311
           +++ APL
Sbjct: 296 MRVEAPL 302


>gi|197336060|ref|YP_002156569.1| ribosomal large subunit pseudouridine synthase C [Vibrio fischeri
           MJ11]
 gi|197317550|gb|ACH66997.1| ribosomal large subunit pseudouridine synthase C [Vibrio fischeri
           MJ11]
          Length = 315

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 109/323 (33%), Positives = 177/323 (54%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +++D    R+D +      ++    + +I+R G+VRV+KKR+K   ++Q G VVR
Sbjct: 8   VQFVDIDDDFAGQRIDNFLLARLKNVPKSMIYRIVRKGEVRVNKKRIKPEYKLQEGDVVR 67

Query: 67  IPPVINALNHIIKEQKILD-SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           IPPV       + E    D  +V L K ++ L+  ++YED  + + NKP+G +V GGSG+
Sbjct: 68  IPPVK------VPESTAPDLPNVKLGKVAE-LEHCIIYEDDHVLILNKPSGTAVHGGSGL 120

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + +QK Y++
Sbjct: 121 KFGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRRLQEQFRNKTVQKYYFA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  KN  + +   LLK      +   +V+ N  G   + + FKV++ F Q    ++ 
Sbjct: 180 LVMGQWKNSCKVVNAPLLK-----NEVNSIVRVNPNG-KPSETRFKVLEKFEQA-TLIQA 232

Query: 246 QPHTGRTHQLRVHALHMGCPI-----VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            P TGRTHQ+RVH  + G  I      GD ++ A + G F     ++L+LHA  +   HP
Sbjct: 233 SPITGRTHQIRVHTQYTGHSIGWDDRYGDRRFDA-YTGQFG---LDRLFLHAANIKFTHP 288

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
               L  I+AP+ A + +    L
Sbjct: 289 ATEELMDISAPMEAKLERVLKGL 311


>gi|15602857|ref|NP_245929.1| 23S rRNA pseudouridylate synthase C [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|20139710|sp|Q9CM51|RLUC_PASMU RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|12721319|gb|AAK03076.1| RluC [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 326

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 107/318 (33%), Positives = 173/318 (54%), Gaps = 14/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  DE   R+D +       +    + +ILR G+VRV+K R+K   ++Q+  +VR
Sbjct: 14  VKMLTISEDEAGQRIDNYLLAKLKGVPKSLIYRILRKGEVRVNKGRIKPEYKLQANDIVR 73

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E++    S  L K S   K IL +ED  + V NKP+GI+V GGSG++
Sbjct: 74  VPPVR------VSEKEHAPISTKLNKVSQLEKQIL-FEDECLLVLNKPSGIAVHGGSGLS 126

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +    +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 127 FGVIEALRT-LRPDARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKTVQKDYLAL 185

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +V+ +E+G   + + F + + + +    ++  
Sbjct: 186 VRGQWQSHCKVVKAPLLKNELSSGE--RIVRVSEQG-KPSETRFSIEERY-EYATLVKAS 241

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY   +F    T     +L+LHA  +   HP+ G  
Sbjct: 242 PVTGRTHQIRVHTQYAGHPIALDDKYGDKHFDEQMTQLGLTRLFLHAFSIRFEHPKTGET 301

Query: 305 LQITAPLPAHMVKTWDSL 322
           L+I APL   M K   +L
Sbjct: 302 LRINAPLDPEMKKILGAL 319


>gi|109898450|ref|YP_661705.1| RluA family pseudouridine synthase [Pseudoalteromonas atlantica
           T6c]
 gi|109700731|gb|ABG40651.1| ribosomal large subunit pseudouridine synthase C [Pseudoalteromonas
           atlantica T6c]
          Length = 318

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 107/323 (33%), Positives = 176/323 (54%), Gaps = 19/323 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ +E D E  R+D + +     +    + +I+R G++RV+KKRVK   ++Q+   +R
Sbjct: 10  VQFIDIEPDLEGQRIDNFLRTLLKGVPKSLIYRIVRKGEIRVNKKRVKPEYKLQAHDQLR 69

Query: 67  IPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           IPP+ ++  N     +  LD   +L  H       +L+ED  + V NKP+G++V GGSG+
Sbjct: 70  IPPIRVSEPNEAPSTK--LDKVASLESH-------ILFEDDLLIVLNKPSGMAVHGGSGL 120

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L++ +  + +   L HRLD++TSG LV+A+ R+A ++L E  R +++ K Y +
Sbjct: 121 SFGVIEALRA-LRPQARFLELVHRLDRDTSGCLVIAKKRSALKNLHEQLRDKKMDKRYQA 179

Query: 186 LVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G  P+N+ +  A  LLK     G+ +  V    K +    + F+V+D F+     +E
Sbjct: 180 LVVGEWPENRYKVNAP-LLKNILKSGERLVSVDTEGKPSE---TRFRVLDRFSGA-TLVE 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
             P TGRTHQ+RVH LH G PI  D KY  + F G        +L+LHA  +   HP+  
Sbjct: 235 ASPITGRTHQIRVHCLHAGHPIACDDKYGDSEFTGLMNQKGLKRLFLHAYSLAFIHPKTE 294

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
            R+   APL   + +    L  +
Sbjct: 295 DRVSFQAPLDKQLNRALSVLEIR 317


>gi|313108160|ref|ZP_07794295.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa 39016]
 gi|310880797|gb|EFQ39391.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa 39016]
          Length = 326

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 113/315 (35%), Positives = 174/315 (55%), Gaps = 20/315 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  T VQ + V  +    R+D +            + +ILR G+VRV+K R+K + R+Q+
Sbjct: 14  SPTTGVQLLDVPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRIKPDYRLQA 73

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQ 120
           G  VR+PP+  A           D    L +   + +++ ++YED  + V NKPAGI+V 
Sbjct: 74  GDQVRVPPLRLAER---------DEPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVH 124

Query: 121 GGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           GGSG+ A  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL E+ R  +I
Sbjct: 125 GGSGVSAGVIEVFRQLRPDAKDIE--LVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKI 182

Query: 180 -QKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             K Y +LV G  P  KK   A  LLK +   G+   +V+ N +G + A++ F+V+  F 
Sbjct: 183 VDKRYHALVRGHWPAGKKNVRAP-LLKNNLRSGE--RMVEVNVEGKD-ALTEFRVLRRFG 238

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMD 296
                +E +P TGRTHQ+RVHA H G  I GD KY   +F          +L+LHA  + 
Sbjct: 239 DFATLVEARPITGRTHQIRVHAKHAGHAIAGDPKYGDEDFSREIRELGGKRLFLHAAQLR 298

Query: 297 LPHPEGGRLQITAPL 311
           +P P+G  L++ AP+
Sbjct: 299 VPLPDGQVLELEAPV 313


>gi|291617029|ref|YP_003519771.1| RluC [Pantoea ananatis LMG 20103]
 gi|291152059|gb|ADD76643.1| RluC [Pantoea ananatis LMG 20103]
          Length = 318

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 105/308 (34%), Positives = 166/308 (53%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +V +  +    R+D + +     +    + +I+R G+VRV+KKR+K   +++ G  VR
Sbjct: 8   VHFVAITAENAGQRIDNFLRTQLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLEEGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+     S  L K +    +I L+ED  + V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAERDEEAVSPKLAKVASLANAI-LFEDDHLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G   +  + +   LLK     G+ +  V  + K +    + FKV + F   F  L + 
Sbjct: 180 VQGNWPSHLKVVQAPLLKNILQSGERMVRVSSDGKPSE---TRFKVEERF--DFATLVKA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH LH G PI  D +Y    F    +S   N+L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTLHAGHPIAFDDRYGDRAFDSQLSSTGLNRLFLHAAALTFTHPNTGE 294

Query: 305 -LQITAPL 311
            L++ APL
Sbjct: 295 TLRMEAPL 302


>gi|197249745|ref|YP_002146857.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197213448|gb|ACH50845.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
          Length = 319

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLKK    G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKKILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|323967027|gb|EGB62453.1| RluA family protein pseudouridine synthase [Escherichia coli M863]
 gi|323976541|gb|EGB71629.1| RluA family protein pseudouridine synthase [Escherichia coli
           TW10509]
 gi|327253484|gb|EGE65122.1| pseudouridine synthase, RluA family protein [Escherichia coli
           STEC_7v]
          Length = 319

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDEHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|168767745|ref|ZP_02792752.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4486]
 gi|189363263|gb|EDU81682.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4486]
          Length = 319

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKREYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|331646343|ref|ZP_08347446.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli M605]
 gi|330910900|gb|EGH39410.1| pseudouridylate synthase, 23S RNA-specific [Escherichia coli AA86]
 gi|331045095|gb|EGI17222.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli M605]
          Length = 319

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|90579091|ref|ZP_01234901.1| putative 23S rRNA ribosomal pseudouridinesynthase [Vibrio angustum
           S14]
 gi|90439924|gb|EAS65105.1| putative 23S rRNA ribosomal pseudouridinesynthase [Vibrio angustum
           S14]
          Length = 314

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 101/318 (31%), Positives = 173/318 (54%), Gaps = 16/318 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ + +D    R+D + +    ++    + +ILR G+VRV+KKR+K   ++Q G +VR
Sbjct: 8   VQFIEISDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDLVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + ++++    S  L K ++ L+  ++YED  + + NKP+G +V GGSG+ 
Sbjct: 68  VPPVF-----VPEKEEQAPVSTKLNKVAE-LEHCIIYEDDHMLILNKPSGTAVHGGSGLK 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + +QK Y++L
Sbjct: 122 FGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRQLQEQFRNKTVQKYYFAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K     +   LLK      +   +V+ N +G   + + FKV++ F Q    ++  
Sbjct: 181 VMGEWKANCRKVTAPLLK-----NEVNSIVRVNPQG-KASDTRFKVLERFPQA-TLVQAS 233

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D +Y    F          +L+LHA  +   HP     
Sbjct: 234 PVTGRTHQIRVHCQYEGHPIAWDDRYGDPRFDAYTKKTGLGRLFLHAANIKFTHPSTDEG 293

Query: 305 LQITAPLPAHMVKTWDSL 322
           + I+AP+   + +  + L
Sbjct: 294 MDISAPMEPVLERCLEKL 311


>gi|16129049|ref|NP_415604.1| 23S rRNA pseudouridine synthase; specific to U955, U2504, and U2580
           [Escherichia coli str. K-12 substr. MG1655]
 gi|24112492|ref|NP_707002.1| 23S rRNA pseudouridylate synthase C [Shigella flexneri 2a str. 301]
 gi|30062620|ref|NP_836791.1| 23S rRNA pseudouridylate synthase C [Shigella flexneri 2a str.
           2457T]
 gi|89107932|ref|AP_001712.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12
           substr. W3110]
 gi|91210238|ref|YP_540224.1| 23S rRNA pseudouridylate synthase C [Escherichia coli UTI89]
 gi|110641262|ref|YP_668992.1| 23S rRNA pseudouridylate synthase C [Escherichia coli 536]
 gi|117623272|ref|YP_852185.1| 23S rRNA pseudouridylate synthase C [Escherichia coli APEC O1]
 gi|157156049|ref|YP_001462319.1| 23S rRNA pseudouridylate synthase C [Escherichia coli E24377A]
 gi|157160612|ref|YP_001457930.1| 23S rRNA pseudouridylate synthase C [Escherichia coli HS]
 gi|170020519|ref|YP_001725473.1| 23S rRNA pseudouridylate synthase C [Escherichia coli ATCC 8739]
 gi|170080737|ref|YP_001730057.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           str. K-12 substr. DH10B]
 gi|188495899|ref|ZP_03003169.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           53638]
 gi|209918340|ref|YP_002292424.1| 23S rRNA pseudouridylate synthase C [Escherichia coli SE11]
 gi|218553663|ref|YP_002386576.1| 23S rRNA pseudouridylate synthase C [Escherichia coli IAI1]
 gi|218557967|ref|YP_002390880.1| 23S rRNA pseudouridylate synthase C [Escherichia coli S88]
 gi|218694619|ref|YP_002402286.1| 23S rRNA pseudouridylate synthase C [Escherichia coli 55989]
 gi|218700411|ref|YP_002408040.1| 23S rRNA pseudouridylate synthase C [Escherichia coli IAI39]
 gi|237706929|ref|ZP_04537410.1| ribosomal large subunit pseudouridine synthase C [Escherichia sp.
           3_2_53FAA]
 gi|238900340|ref|YP_002926136.1| 23S rRNA pseudouridylate synthase [Escherichia coli BW2952]
 gi|253773891|ref|YP_003036722.1| 23S rRNA pseudouridylate synthase C [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254161192|ref|YP_003044300.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B str.
           REL606]
 gi|256018658|ref|ZP_05432523.1| 23S rRNA pseudouridylate synthase C [Shigella sp. D9]
 gi|256023217|ref|ZP_05437082.1| 23S rRNA pseudouridylate synthase C [Escherichia sp. 4_1_40B]
 gi|260843326|ref|YP_003221104.1| 23S rRNA pseudouridylate synthase rluC [Escherichia coli O103:H2
           str. 12009]
 gi|260854569|ref|YP_003228460.1| 23S rRNA pseudouridylate synthase rluC [Escherichia coli O26:H11
           str. 11368]
 gi|260867449|ref|YP_003233851.1| 23S rRNA pseudouridylate synthase rluC [Escherichia coli O111:H-
           str. 11128]
 gi|293409451|ref|ZP_06653027.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B354]
 gi|293414379|ref|ZP_06657028.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B185]
 gi|293433375|ref|ZP_06661803.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B088]
 gi|300816787|ref|ZP_07097007.1| pseudouridine synthase, RluA family [Escherichia coli MS 107-1]
 gi|300821134|ref|ZP_07101283.1| pseudouridine synthase, RluA family [Escherichia coli MS 119-7]
 gi|300902476|ref|ZP_07120458.1| pseudouridine synthase, RluA family [Escherichia coli MS 84-1]
 gi|300928363|ref|ZP_07143897.1| pseudouridine synthase, RluA family [Escherichia coli MS 187-1]
 gi|300938652|ref|ZP_07153381.1| pseudouridine synthase, RluA family [Escherichia coli MS 21-1]
 gi|300948672|ref|ZP_07162753.1| pseudouridine synthase, RluA family [Escherichia coli MS 116-1]
 gi|300956251|ref|ZP_07168560.1| pseudouridine synthase, RluA family [Escherichia coli MS 175-1]
 gi|300982570|ref|ZP_07176192.1| pseudouridine synthase, RluA family [Escherichia coli MS 200-1]
 gi|301023272|ref|ZP_07187069.1| pseudouridine synthase, RluA family [Escherichia coli MS 69-1]
 gi|301029700|ref|ZP_07192754.1| pseudouridine synthase, RluA family [Escherichia coli MS 196-1]
 gi|301304976|ref|ZP_07211078.1| pseudouridine synthase, RluA family [Escherichia coli MS 124-1]
 gi|301644499|ref|ZP_07244494.1| pseudouridine synthase, RluA family [Escherichia coli MS 146-1]
 gi|307137721|ref|ZP_07497077.1| 23S rRNA pseudouridylate synthase C [Escherichia coli H736]
 gi|307310137|ref|ZP_07589787.1| pseudouridine synthase, RluA family [Escherichia coli W]
 gi|312971222|ref|ZP_07785400.1| pseudouridine synthase, RluA family protein [Escherichia coli
           1827-70]
 gi|331641629|ref|ZP_08342764.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli H736]
 gi|331667486|ref|ZP_08368350.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli TA271]
 gi|331676876|ref|ZP_08377572.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli H591]
 gi|332279727|ref|ZP_08392140.1| ribosomal large subunit pseudouridine synthase C [Shigella sp. D9]
 gi|76363884|sp|P0AA39|RLUC_ECOLI RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|92090792|sp|P0AA40|RLUC_SHIFL RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|1787327|gb|AAC74170.1| 23S rRNA pseudouridine synthase; specific to U955, U2504, and U2580
           [Escherichia coli str. K-12 substr. MG1655]
 gi|4062660|dbj|BAA35894.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K12
           substr. W3110]
 gi|24051379|gb|AAN42709.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
 gi|30040866|gb|AAP16597.1| hypothetical protein S1170 [Shigella flexneri 2a str. 2457T]
 gi|91071812|gb|ABE06693.1| hypothetical protein UTI89_C1211 [Escherichia coli UTI89]
 gi|110342854|gb|ABG69091.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           536]
 gi|115512396|gb|ABJ00471.1| conserved hypothetical protein [Escherichia coli APEC O1]
 gi|157066292|gb|ABV05547.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           HS]
 gi|157078079|gb|ABV17787.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           E24377A]
 gi|169755447|gb|ACA78146.1| pseudouridine synthase, RluA family [Escherichia coli ATCC 8739]
 gi|169888572|gb|ACB02279.1| Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           str. K-12 substr. DH10B]
 gi|188491098|gb|EDU66201.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           53638]
 gi|209911599|dbj|BAG76673.1| 23S rRNA pseudouridylate synthase [Escherichia coli SE11]
 gi|218351351|emb|CAU97057.1| 23S rRNA pseudouridylate synthase [Escherichia coli 55989]
 gi|218360431|emb|CAQ97985.1| 23S rRNA pseudouridylate synthase [Escherichia coli IAI1]
 gi|218364736|emb|CAR02426.1| 23S rRNA pseudouridylate synthase [Escherichia coli S88]
 gi|218370397|emb|CAR18202.1| 23S rRNA pseudouridylate synthase [Escherichia coli IAI39]
 gi|226898139|gb|EEH84398.1| ribosomal large subunit pseudouridine synthase C [Escherichia sp.
           3_2_53FAA]
 gi|238859760|gb|ACR61758.1| 23S rRNA pseudouridylate synthase [Escherichia coli BW2952]
 gi|242376889|emb|CAQ31607.1| 23S rRNA pseudouridine synthase [Escherichia coli BL21(DE3)]
 gi|253324935|gb|ACT29537.1| pseudouridine synthase, RluA family [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253973093|gb|ACT38764.1| 23S rRNA pseudouridylate synthase [Escherichia coli B str. REL606]
 gi|253977307|gb|ACT42977.1| 23S rRNA pseudouridylate synthase [Escherichia coli BL21(DE3)]
 gi|257753218|dbj|BAI24720.1| 23S rRNA pseudouridylate synthase rluC [Escherichia coli O26:H11
           str. 11368]
 gi|257758473|dbj|BAI29970.1| 23S rRNA pseudouridylate synthase rluC [Escherichia coli O103:H2
           str. 12009]
 gi|257763805|dbj|BAI35300.1| 23S rRNA pseudouridylate synthase rluC [Escherichia coli O111:H-
           str. 11128]
 gi|260449775|gb|ACX40197.1| pseudouridine synthase, RluA family [Escherichia coli DH1]
 gi|281600502|gb|ADA73486.1| Ribosomal large subunit pseudouridine synthase C [Shigella flexneri
           2002017]
 gi|291324194|gb|EFE63616.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B088]
 gi|291434437|gb|EFF07410.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B185]
 gi|291469919|gb|EFF12403.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B354]
 gi|294492107|gb|ADE90863.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           IHE3034]
 gi|299877388|gb|EFI85599.1| pseudouridine synthase, RluA family [Escherichia coli MS 196-1]
 gi|300307151|gb|EFJ61671.1| pseudouridine synthase, RluA family [Escherichia coli MS 200-1]
 gi|300316920|gb|EFJ66704.1| pseudouridine synthase, RluA family [Escherichia coli MS 175-1]
 gi|300397117|gb|EFJ80655.1| pseudouridine synthase, RluA family [Escherichia coli MS 69-1]
 gi|300405508|gb|EFJ89046.1| pseudouridine synthase, RluA family [Escherichia coli MS 84-1]
 gi|300451827|gb|EFK15447.1| pseudouridine synthase, RluA family [Escherichia coli MS 116-1]
 gi|300456437|gb|EFK19930.1| pseudouridine synthase, RluA family [Escherichia coli MS 21-1]
 gi|300463621|gb|EFK27114.1| pseudouridine synthase, RluA family [Escherichia coli MS 187-1]
 gi|300526433|gb|EFK47502.1| pseudouridine synthase, RluA family [Escherichia coli MS 119-7]
 gi|300530561|gb|EFK51623.1| pseudouridine synthase, RluA family [Escherichia coli MS 107-1]
 gi|300839694|gb|EFK67454.1| pseudouridine synthase, RluA family [Escherichia coli MS 124-1]
 gi|301077163|gb|EFK91969.1| pseudouridine synthase, RluA family [Escherichia coli MS 146-1]
 gi|306909855|gb|EFN40349.1| pseudouridine synthase, RluA family [Escherichia coli W]
 gi|307627444|gb|ADN71748.1| 23S rRNA pseudouridylate synthase C [Escherichia coli UM146]
 gi|309701358|emb|CBJ00659.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           ETEC H10407]
 gi|310336424|gb|EFQ01610.1| pseudouridine synthase, RluA family protein [Escherichia coli
           1827-70]
 gi|313650461|gb|EFS14868.1| pseudouridine synthase, RluA family protein [Shigella flexneri 2a
           str. 2457T]
 gi|315060363|gb|ADT74690.1| 23S rRNA pseudouridylate synthase [Escherichia coli W]
 gi|315135718|dbj|BAJ42877.1| 23S rRNA pseudouridylate synthase C [Escherichia coli DH1]
 gi|315253886|gb|EFU33854.1| pseudouridine synthase, RluA family [Escherichia coli MS 85-1]
 gi|315287423|gb|EFU46834.1| pseudouridine synthase, RluA family [Escherichia coli MS 110-3]
 gi|323156893|gb|EFZ43027.1| pseudouridine synthase, RluA family protein [Escherichia coli
           EPECa14]
 gi|323163696|gb|EFZ49517.1| pseudouridine synthase, RluA family protein [Escherichia coli
           E128010]
 gi|323175240|gb|EFZ60853.1| pseudouridine synthase, RluA family protein [Escherichia coli
           LT-68]
 gi|323175683|gb|EFZ61277.1| pseudouridine synthase, RluA family protein [Escherichia coli 1180]
 gi|323185792|gb|EFZ71153.1| pseudouridine synthase, RluA family protein [Escherichia coli 1357]
 gi|323379076|gb|ADX51344.1| pseudouridine synthase, RluA family [Escherichia coli KO11]
 gi|323942555|gb|EGB38722.1| RluA family protein pseudouridine synthase [Escherichia coli E482]
 gi|323947612|gb|EGB43616.1| RluA family protein pseudouridine synthase [Escherichia coli H120]
 gi|323953228|gb|EGB49094.1| RluA family protein pseudouridine synthase [Escherichia coli H252]
 gi|323957910|gb|EGB53622.1| RluA family protein pseudouridine synthase [Escherichia coli H263]
 gi|323962685|gb|EGB58263.1| RluA family protein pseudouridine synthase [Escherichia coli H489]
 gi|323973325|gb|EGB68514.1| RluA family protein pseudouridine synthase [Escherichia coli TA007]
 gi|324007925|gb|EGB77144.1| pseudouridine synthase, RluA family [Escherichia coli MS 57-2]
 gi|324013284|gb|EGB82503.1| pseudouridine synthase, RluA family [Escherichia coli MS 60-1]
 gi|324117343|gb|EGC11250.1| RluA family protein pseudouridine synthase [Escherichia coli E1167]
 gi|331038427|gb|EGI10647.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli H736]
 gi|331065071|gb|EGI36966.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli TA271]
 gi|331075565|gb|EGI46863.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli H591]
 gi|332102079|gb|EGJ05425.1| ribosomal large subunit pseudouridine synthase C [Shigella sp. D9]
 gi|332342633|gb|AEE55967.1| pseudouridine synthase RluC [Escherichia coli UMNK88]
 gi|332758246|gb|EGJ88569.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           4343-70]
 gi|332759613|gb|EGJ89918.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           2747-71]
 gi|332761433|gb|EGJ91717.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           K-671]
 gi|332767695|gb|EGJ97888.1| 23S rRNA pseudouridine synthase [Shigella flexneri 2930-71]
 gi|333004896|gb|EGK24416.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           VA-6]
 gi|333005699|gb|EGK25217.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           K-218]
 gi|333008291|gb|EGK27765.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           K-272]
 gi|333019472|gb|EGK38755.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           K-304]
 gi|333019781|gb|EGK39053.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           K-227]
          Length = 319

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|331652138|ref|ZP_08353157.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli M718]
 gi|320200981|gb|EFW75565.1| 23S rRNA pseudouridylate synthase C [Escherichia coli EC4100B]
 gi|331050416|gb|EGI22474.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli M718]
 gi|332089150|gb|EGI94259.1| pseudouridine synthase, RluA family protein [Shigella boydii
           5216-82]
 gi|332092815|gb|EGI97883.1| pseudouridine synthase, RluA family protein [Shigella dysenteriae
           155-74]
          Length = 319

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|296102896|ref|YP_003613042.1| 23S rRNA pseudouridylate synthase C [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295057355|gb|ADF62093.1| 23S rRNA pseudouridylate synthase C [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 306

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 107/309 (34%), Positives = 170/309 (55%), Gaps = 16/309 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V + +DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++++G  VRIPP
Sbjct: 2   VAIADDEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLEAGDEVRIPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A     +E++++  S  L K +  L  ++LYED  I V NKP+G +V GGSG+++ +
Sbjct: 62  VRVAE----REEEVV--SPKLQKVA-ALSDVILYEDDHILVLNKPSGTAVHGGSGLSFGV 114

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +LV G
Sbjct: 115 IEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRG 173

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPH 248
             ++  + +   LLK     G+ +  V Q  K +    + FKV + +  +F  L    P 
Sbjct: 174 QWQSHVKVVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERY--EFATLVRCSPV 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
           TGRTHQ+RVH    G PI  D +Y    F         ++L+LHA  +   HP  G  ++
Sbjct: 229 TGRTHQIRVHTQFAGHPIAFDDRYGDREFDKQLAGTGLSRLFLHAAALKFTHPNTGETIR 288

Query: 307 ITAPLPAHM 315
           I APL   +
Sbjct: 289 IEAPLDEQL 297


>gi|327393480|dbj|BAK10902.1| ribosomal large subunit pseudouridine synthase C RluC [Pantoea
           ananatis AJ13355]
          Length = 318

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 105/308 (34%), Positives = 166/308 (53%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +V +  +    R+D + +     +    + +I+R G+VRV+KKR+K   +++ G  VR
Sbjct: 8   VHFVAITAENAGQRIDNFLRTQLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLEEGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+     S  L K +    +I L+ED  + V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAERDEEAVSPKLAKVASLANAI-LFEDDHLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPESRFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G   +  + +   LLK     G+ +  V  + K +    + FKV + F   F  L + 
Sbjct: 180 VQGNWPSHLKVVQAPLLKNILQSGERMVRVSSDGKPSE---TRFKVEERF--DFATLVKA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH LH G PI  D +Y    F    +S   N+L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTLHAGHPIAFDDRYGDRAFDSQLSSTGLNRLFLHAAALTFTHPNTGE 294

Query: 305 -LQITAPL 311
            L++ APL
Sbjct: 295 TLRMEAPL 302


>gi|261339387|ref|ZP_05967245.1| ribosomal large subunit pseudouridine synthase [Enterobacter
           cancerogenus ATCC 35316]
 gi|288318188|gb|EFC57126.1| ribosomal large subunit pseudouridine synthase [Enterobacter
           cancerogenus ATCC 35316]
          Length = 315

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 106/312 (33%), Positives = 172/312 (55%), Gaps = 16/312 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  D+   R+D + +     +    + +ILR G+VRV+KKRVK   ++++G  +R
Sbjct: 8   VKMVAIAEDDAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLEAGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A     +E++++  S  L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPVRVAE----REEEVV--SPKLQKVA-ALSDVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +  +F  L   
Sbjct: 180 VRGQWQSHVKVVQAPLLKNILQSGERIVRVNQEGKPSE---TRFKVEERY--EFATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  + G PI  D +Y    F         ++L+LHA  +   HP  G 
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLAGTGLSRLFLHAAALKFTHPNTGE 294

Query: 305 -LQITAPLPAHM 315
            ++I APL   +
Sbjct: 295 VIRIEAPLDEQL 306


>gi|15801203|ref|NP_287220.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7
           EDL933]
 gi|15830718|ref|NP_309491.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           Sakai]
 gi|195935476|ref|ZP_03080858.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           EC4024]
 gi|208807624|ref|ZP_03249961.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4206]
 gi|208816352|ref|ZP_03257531.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4045]
 gi|209400210|ref|YP_002269931.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4115]
 gi|217328324|ref|ZP_03444406.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. TW14588]
 gi|218704495|ref|YP_002412014.1| 23S rRNA pseudouridylate synthase C [Escherichia coli UMN026]
 gi|254792468|ref|YP_003077305.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           TW14359]
 gi|261227010|ref|ZP_05941291.1| Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. FRIK2000]
 gi|261256244|ref|ZP_05948777.1| Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. FRIK966]
 gi|293404372|ref|ZP_06648366.1| 23S rRNA pseudouridylate synthase C [Escherichia coli FVEC1412]
 gi|298380151|ref|ZP_06989756.1| 23S rRNA pseudouridylate synthase C [Escherichia coli FVEC1302]
 gi|300899606|ref|ZP_07117845.1| pseudouridine synthase, RluA family [Escherichia coli MS 198-1]
 gi|331662494|ref|ZP_08363417.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli TA143]
 gi|34395798|sp|Q8X8J3|RLUC_ECO57 RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|12514630|gb|AAG55832.1|AE005319_1 orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]
 gi|13360928|dbj|BAB34887.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|208727425|gb|EDZ77026.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4206]
 gi|208733000|gb|EDZ81688.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4045]
 gi|209161610|gb|ACI39043.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4115]
 gi|209773278|gb|ACI84951.1| hypothetical protein ECs1464 [Escherichia coli]
 gi|209773280|gb|ACI84952.1| hypothetical protein ECs1464 [Escherichia coli]
 gi|209773282|gb|ACI84953.1| hypothetical protein ECs1464 [Escherichia coli]
 gi|209773284|gb|ACI84954.1| hypothetical protein ECs1464 [Escherichia coli]
 gi|209773286|gb|ACI84955.1| hypothetical protein ECs1464 [Escherichia coli]
 gi|217318751|gb|EEC27177.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. TW14588]
 gi|218431592|emb|CAR12471.1| 23S rRNA pseudouridylate synthase [Escherichia coli UMN026]
 gi|254591868|gb|ACT71229.1| Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. TW14359]
 gi|281178195|dbj|BAI54525.1| 23S rRNA pseudouridylate synthase [Escherichia coli SE15]
 gi|291428958|gb|EFF01983.1| 23S rRNA pseudouridylate synthase C [Escherichia coli FVEC1412]
 gi|298279849|gb|EFI21357.1| 23S rRNA pseudouridylate synthase C [Escherichia coli FVEC1302]
 gi|300356877|gb|EFJ72747.1| pseudouridine synthase, RluA family [Escherichia coli MS 198-1]
 gi|320189769|gb|EFW64425.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           EC1212]
 gi|320637537|gb|EFX07337.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           G5101]
 gi|320643098|gb|EFX12299.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H- str.
           493-89]
 gi|320648556|gb|EFX17211.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H- str.
           H 2687]
 gi|320653870|gb|EFX21944.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320659350|gb|EFX26919.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|320664485|gb|EFX31636.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           LSU-61]
 gi|326339308|gb|EGD63122.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           1125]
 gi|326344731|gb|EGD68479.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           1044]
 gi|331060916|gb|EGI32880.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli TA143]
          Length = 319

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|170684091|ref|YP_001744093.1| 23S rRNA pseudouridylate synthase C [Escherichia coli SMS-3-5]
 gi|170521809|gb|ACB19987.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           SMS-3-5]
 gi|222032839|emb|CAP75578.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           LF82]
 gi|312945648|gb|ADR26475.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O83:H1 str.
           NRG 857C]
          Length = 319

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 171/310 (55%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F  + T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRHLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|315634769|ref|ZP_07890051.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           segnis ATCC 33393]
 gi|315476321|gb|EFU67071.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           segnis ATCC 33393]
          Length = 349

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 109/311 (35%), Positives = 171/311 (54%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ + +DE   RLD +       +    + +I+R G+VRV+K R K   ++Q+  VVR
Sbjct: 40  VQFLTISDDEAGQRLDNFLLARLKGVPKSLIYRIVRKGEVRVNKGRSKPEYKLQAEDVVR 99

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+     S  LTK +  L+  +++ED+ + V NKP+GI+V GGSG+ 
Sbjct: 100 IPPVR------VAEKAQETVSHKLTKVAQ-LEQHIIFEDNYLLVLNKPSGIAVHGGSGLD 152

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A +HL E  R + IQK Y +L
Sbjct: 153 FGVIEALRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRHLHEQLREKTIQKEYLAL 211

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +VK +E+G   + + F V + +      ++  
Sbjct: 212 VRGQWQSHCKVVQAPLLKNELSSGE--RIVKVSEQGKP-SETRFSVEERYVNA-TLVKAS 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP  G  
Sbjct: 268 PVTGRTHQIRVHTQYAGHPIALDSKYGDKVFDQQMAELGLNRLFLHAYSIRFEHPHSGET 327

Query: 305 LQITAPLPAHM 315
           L++TA L   M
Sbjct: 328 LRLTAQLDEKM 338


>gi|329297204|ref|ZP_08254540.1| 23S rRNA pseudouridylate synthase C [Plautia stali symbiont]
          Length = 319

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/307 (35%), Positives = 167/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  +  + R+D + +     +    + +ILR G+VRV+KKRVK   +++ G  VR
Sbjct: 8   VQFVAITAENADQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLEDGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A     +EQ +   S  L K +  L+S +LYED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVAER---EEQAV---SPKLDKVA-ALESCILYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + + K Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMLKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+ V  V    K +    + FKV + F      ++  
Sbjct: 180 VRGDWPSHLKVVQAPLLKNILQSGERVVRVSAEGKPSE---TRFKVEERFGLA-TLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTLHGGHPIAFDDRYGDREFDRQLAPTGLSRLFLHAAALTFTHPNTGES 295

Query: 305 LQITAPL 311
           L++ APL
Sbjct: 296 LRMEAPL 302


>gi|309796571|ref|ZP_07690978.1| pseudouridine synthase, RluA family [Escherichia coli MS 145-7]
 gi|308119883|gb|EFO57145.1| pseudouridine synthase, RluA family [Escherichia coli MS 145-7]
          Length = 319

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPAYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|82777302|ref|YP_403651.1| 23S rRNA pseudouridylate synthase C [Shigella dysenteriae Sd197]
 gi|309788155|ref|ZP_07682761.1| pseudouridine synthase, RluA family protein [Shigella dysenteriae
           1617]
 gi|81241450|gb|ABB62160.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
 gi|308924007|gb|EFP69508.1| pseudouridine synthase, RluA family protein [Shigella dysenteriae
           1617]
 gi|323190599|gb|EFZ75871.1| pseudouridine synthase, RluA family protein [Escherichia coli
           RN587/1]
          Length = 319

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDYILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|26247226|ref|NP_753266.1| 23S rRNA pseudouridylate synthase C [Escherichia coli CFT073]
 gi|227886557|ref|ZP_04004362.1| 23S rRNA pseudouridylate synthase C [Escherichia coli 83972]
 gi|300974389|ref|ZP_07172601.1| pseudouridine synthase, RluA family [Escherichia coli MS 45-1]
 gi|301051128|ref|ZP_07197959.1| pseudouridine synthase, RluA family [Escherichia coli MS 185-1]
 gi|331657147|ref|ZP_08358109.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli TA206]
 gi|34395779|sp|Q8FIP7|RLUC_ECOL6 RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|26107627|gb|AAN79826.1|AE016759_100 Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           CFT073]
 gi|227836761|gb|EEJ47227.1| 23S rRNA pseudouridylate synthase C [Escherichia coli 83972]
 gi|300297212|gb|EFJ53597.1| pseudouridine synthase, RluA family [Escherichia coli MS 185-1]
 gi|300410632|gb|EFJ94170.1| pseudouridine synthase, RluA family [Escherichia coli MS 45-1]
 gi|307553087|gb|ADN45862.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           ABU 83972]
 gi|315291063|gb|EFU50426.1| pseudouridine synthase, RluA family [Escherichia coli MS 153-1]
 gi|315296716|gb|EFU56011.1| pseudouridine synthase, RluA family [Escherichia coli MS 16-3]
 gi|331055395|gb|EGI27404.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli TA206]
          Length = 319

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSYVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|16760064|ref|NP_455681.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|29142165|ref|NP_805507.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|213163779|ref|ZP_03349489.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213425012|ref|ZP_03357762.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
 gi|213580589|ref|ZP_03362415.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213646390|ref|ZP_03376443.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|289829597|ref|ZP_06547152.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|34395803|sp|Q8Z7J7|RLUC_SALTI RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|25322405|pir||AE0641 pseudouridylate synthase (EC 4.2.1.70) - Salmonella enterica subsp.
           enterica serovar Typhi (strain CT18)
 gi|16502358|emb|CAD08312.1| ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70)
           [Salmonella enterica subsp. enterica serovar Typhi]
 gi|29137794|gb|AAO69356.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Typhi str. Ty2]
          Length = 319

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 109/321 (33%), Positives = 173/321 (53%), Gaps = 18/321 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   +++SG  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLESGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHARYMDLPHP-E 301
            P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGT 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G  ++I AP+   + +  + L
Sbjct: 295 GDVMRIEAPMDKQLKRCLEVL 315


>gi|327484563|gb|AEA78970.1| Ribosomal large subunit pseudouridine synthase C LSU Psi955,
           Psi2504 and Psi2580 [Vibrio cholerae LMA3894-4]
          Length = 321

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 95/271 (35%), Positives = 160/271 (59%), Gaps = 15/271 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G      EC + N  L K+ +      +V+ N  G   + + F++++ FA+  
Sbjct: 177 YYYALVMG--HWDAECKVVNAPLLKNEVNS----IVRVNSNG-KPSETRFRILEKFAEA- 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             ++  P TGRTHQ+RVH  +MG PI  D +
Sbjct: 229 TLVQASPVTGRTHQIRVHTQYMGHPIAWDDR 259


>gi|74311647|ref|YP_310066.1| 23S rRNA pseudouridylate synthase C [Shigella sonnei Ss046]
 gi|73855124|gb|AAZ87831.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|323165595|gb|EFZ51382.1| pseudouridine synthase, RluA family protein [Shigella sonnei 53G]
          Length = 319

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 107/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L++A+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLIAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|329889164|ref|ZP_08267507.1| RNA pseudouridylate synthase family protein [Brevundimonas diminuta
           ATCC 11568]
 gi|328844465|gb|EGF94029.1| RNA pseudouridylate synthase family protein [Brevundimonas diminuta
           ATCC 11568]
          Length = 241

 Score =  157 bits (397), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 84/227 (37%), Positives = 134/227 (59%), Gaps = 6/227 (2%)

Query: 88  VNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           V+LT+     ++S +++ED+ +  FNKP+G+S QGG   A  +D  L ++  S G++P L
Sbjct: 7   VSLTEDEIAAVRSWVVHEDAHLIAFNKPSGLSSQGGRIQANTLDDLLWAFARSNGKRPEL 66

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG+++ A+T+ AA    ++ +MR+ QK Y +LV   P+ K   I +  L++ 
Sbjct: 67  VHRLDRDTSGVILAAKTKPAAGFFGKAMQMRKFQKTYLALVAAAPEPKSGRITS-ALRRE 125

Query: 207 HIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            IG + Y+ VV  +  GA  A S ++ +   ++    +E+ P TGR HQLRVH   +G P
Sbjct: 126 EIGRESYMRVVDFDAPGAQGAASGYRTL-ASSEDGAVVELSPETGRMHQLRVHMASIGRP 184

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           +VGD +Y       F      +L LHA  +  PHP+GGR+ + AP P
Sbjct: 185 LVGDVRYGGAL--TFAGRAAPRLMLHAAKLSFPHPDGGRVTVEAPEP 229


>gi|324017411|gb|EGB86630.1| pseudouridine synthase, RluA family [Escherichia coli MS 117-3]
          Length = 319

 Score =  157 bits (397), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQVPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|160900713|ref|YP_001566295.1| RluA family pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160366297|gb|ABX37910.1| pseudouridine synthase, RluA family [Delftia acidovorans SPH-1]
          Length = 362

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 108/325 (33%), Positives = 166/325 (51%), Gaps = 29/325 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V++D    RLD +   H   +   ++ +I+RSG+VR++K RV    R+ +G +VR
Sbjct: 50  VRLIEVDDDSAGQRLDNFLIRHLKGVPKTHVYRIIRSGEVRINKGRVSAETRVSTGDIVR 109

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +       +K+ + +       DF     L ED  +   +KPAG++V GGSG++
Sbjct: 110 IPPVRIS-------EKVAEKAERPAPARDFPS---LLEDEHLIAIDKPAGVAVHGGSGVS 159

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    ++ Q     L HRLD+ETSGIL+VA+ R+A  HL + FR R   K Y 
Sbjct: 160 F---GVIEQLRQARPQSRFLELVHRLDRETSGILLVAKKRSALTHLQDQFRERETGKTYL 216

Query: 185 SLVWGI-PKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK--- 239
           +LV G  P N K  I   L K     G+  V V   ++     +++  +V    A +   
Sbjct: 217 ALVQGTWPANHK-VIDLPLHKYLQADGERRVRVTTADDPDGMRSVTLVRVRSTLAPQPLL 275

Query: 240 ----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHAR 293
                  LE+   TGRTHQ+RVH    G PI GD KY  +F  N     Q   +++LHA 
Sbjct: 276 GLPAMSLLEVTIKTGRTHQIRVHLSSQGHPIAGDDKY-GDFDLNRRLQKQGLKRMFLHAW 334

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVK 317
            +   HP  G R+++ A LP  + +
Sbjct: 335 RLQFTHPASGERVELRAELPEELAR 359


>gi|315618256|gb|EFU98846.1| pseudouridine synthase, RluA family protein [Escherichia coli 3431]
          Length = 319

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 170/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEVGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|56413826|ref|YP_150901.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197362749|ref|YP_002142386.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|56128083|gb|AAV77589.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Paratyphi A str. ATCC
           9150]
 gi|197094226|emb|CAR59731.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Paratyphi A str.
           AKU_12601]
          Length = 319

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 109/321 (33%), Positives = 173/321 (53%), Gaps = 18/321 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   +++SG  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLESGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LHPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHARYMDLPHP-E 301
            P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGT 294

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G  ++I AP+   + +  + L
Sbjct: 295 GDVMRIEAPMDKQLKRCLEVL 315


>gi|152986000|ref|YP_001347558.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PA7]
 gi|150961158|gb|ABR83183.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PA7]
          Length = 318

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 106/313 (33%), Positives = 170/313 (54%), Gaps = 16/313 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  T VQ + V  +    R+D +            + +ILR G+VRV+K R+K + R+Q+
Sbjct: 6   SPTTGVQLLDVPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRIKPDYRLQA 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQ 120
           G  VR+PP+  A           D    L +   + +++ ++YED  + V NKPAGI+V 
Sbjct: 66  GDQVRVPPLRLAER---------DEPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVH 116

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI- 179
           GGSG++  +    +  +  + +   L HRLD++TSG+L++A+ R+  +HL E+ R  +I 
Sbjct: 117 GGSGVSAGVIEVFRQ-LRPEARDIELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKIV 175

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G     K+ I   LLK +   G+   +V+ N +G + A++ F+V+  F   
Sbjct: 176 DKRYHALVRGHWPAGKKNIRAPLLKNNLRSGE--RMVEVNVEGKD-ALTEFRVLRRFGDF 232

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP 298
              +E +P TGRTHQ+RVHA H G  I GD KY   +F          +L+LHA  + +P
Sbjct: 233 ATLVEARPITGRTHQIRVHAKHAGHAIAGDPKYGDEDFSREIRELGGKRLFLHAAQLRVP 292

Query: 299 HPEGGRLQITAPL 311
            P+G  L++ AP+
Sbjct: 293 LPDGQVLELEAPV 305


>gi|73541961|ref|YP_296481.1| ribosomal large subunit pseudouridine synthase C [Ralstonia
           eutropha JMP134]
 gi|72119374|gb|AAZ61637.1| ribosomal large subunit pseudouridine synthase C [Ralstonia
           eutropha JMP134]
          Length = 352

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 116/322 (36%), Positives = 169/322 (52%), Gaps = 42/322 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV ++   E  R+D +       +   ++ ++LRSG+VRV+K RV    R+Q G VVR
Sbjct: 21  VAYVTIDEGAEGQRIDNFLLKVSKGVPKSHIYRVLRSGEVRVNKGRVDATYRLQIGDVVR 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKH----SDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           IPP+           ++ + S   T+H    +DF    +L+ED+ + V NKPAG++V GG
Sbjct: 81  IPPM-----------RVAEPS-QTTRHPVPAADF---PVLFEDAHLLVINKPAGVAVHGG 125

Query: 123 SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           SG+A+   G ++    ++ Q     L HRLD+ETSGILV+A+ R+A   L E  R   + 
Sbjct: 126 SGVAF---GVIEQLRKARPQAKFLELVHRLDRETSGILVLAKKRSALVDLHEQIRGNSMD 182

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH--FKVIDCFAQ 238
           K Y++ V G   N ++ +   L K S   G+    V+  E G     SH  F  ++ F  
Sbjct: 183 KRYFACVAGEFPNNRQHVKLPLYKYSTPDGE--RRVRVQEDGLP---SHTVFSRVEAFP- 236

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHA 292
            F  LE +  TGRTHQ+RVH  H G PI+GD KY  +F  N         P   +++LHA
Sbjct: 237 GFTLLEAELKTGRTHQIRVHLAHSGYPIIGDEKY-GDFALNKQLARAGARPGIKRMFLHA 295

Query: 293 RYMDLPHPEGGR--LQITAPLP 312
             +   HP G R  L + APLP
Sbjct: 296 HRLTFVHP-GTREPLVVAAPLP 316


>gi|145630415|ref|ZP_01786196.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae R3021]
 gi|145638677|ref|ZP_01794286.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittII]
 gi|229844426|ref|ZP_04464566.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae 6P18H1]
 gi|144984150|gb|EDJ91587.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae R3021]
 gi|145272272|gb|EDK12180.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittII]
 gi|229812675|gb|EEP48364.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae 6P18H1]
 gi|309750170|gb|ADO80154.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae R2866]
          Length = 322

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 104/313 (33%), Positives = 174/313 (55%), Gaps = 14/313 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRIKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+   +V+ +E+G   + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGE--RIVRVSEQG-KPSETRFSIEERYINA-TLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHM 315
             L+  APL   M
Sbjct: 299 ETLRFNAPLDHQM 311


>gi|145636319|ref|ZP_01791988.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittHH]
 gi|145270484|gb|EDK10418.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittHH]
          Length = 322

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 104/313 (33%), Positives = 174/313 (55%), Gaps = 14/313 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRIKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+   +V+ +E+G   + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGE--RIVRVSEQG-KPSETRFSIEERYINA-TLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHM 315
             L+  APL   M
Sbjct: 299 ETLRFNAPLDHQM 311


>gi|149376750|ref|ZP_01894508.1| 23S rRNA pseudouridylate synthase C [Marinobacter algicola DG893]
 gi|149358989|gb|EDM47455.1| 23S rRNA pseudouridylate synthase C [Marinobacter algicola DG893]
          Length = 313

 Score =  156 bits (395), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 102/307 (33%), Positives = 174/307 (56%), Gaps = 17/307 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ VVV+ D    R+D +       +    + +I+R G+VRV+K RVK + R+ +G  VR
Sbjct: 1   MRKVVVDEDNHGQRVDNYLMAQIRDVPRSIIYRIIRKGEVRVNKGRVKPDTRLNTGDEVR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV        KE+      V  ++    ++S +++E+ ++ V NKP+GI+V GGSG+ 
Sbjct: 61  IPPVTR------KEKPA--QVVPGSRVQGVMQSAVVFENDQMLVVNKPSGIAVHGGSGLD 112

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++    + +   L HRLD++TSG+++VA+ R+A ++L +  R +RI+K Y +L
Sbjct: 113 FGLIEVLRA-ARPEARFLELVHRLDRDTSGLVMVAKKRSALRYLQDELRHKRIRKHYHAL 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G      + ++  LL+     G+    V+ ++ G + +++ F+V++ F+  +  +E  
Sbjct: 172 VAGDWPGSVKKVSEPLLRFELGSGE--RRVRVDDAGKD-SLTRFRVLESFS-GYTLVEAS 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMD--LPHPEGG 303
           P TGRTHQ+RVH+   G PI GD KY  +     F S    +L LHAR +D  LP P G 
Sbjct: 228 PVTGRTHQIRVHSAWAGHPIAGDDKYMDDVSLRAFRSAGGQRLMLHARALDFTLP-PSGE 286

Query: 304 RLQITAP 310
            + + AP
Sbjct: 287 SVHLEAP 293


>gi|284920910|emb|CBG33973.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           042]
          Length = 319

 Score =  156 bits (395), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 108/310 (34%), Positives = 169/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y  L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLVL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|260582324|ref|ZP_05850117.1| pseudouridylate synthase [Haemophilus influenzae NT127]
 gi|319898067|ref|YP_004136264.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae F3031]
 gi|260094692|gb|EEW78587.1| pseudouridylate synthase [Haemophilus influenzae NT127]
 gi|309972429|gb|ADO95630.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae R2846]
 gi|317433573|emb|CBY81957.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae F3031]
          Length = 322

 Score =  156 bits (395), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 104/313 (33%), Positives = 174/313 (55%), Gaps = 14/313 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+   +V+ +E+G   + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGE--RIVRVSEQG-KPSETRFSIEERYINA-TLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHM 315
             L+  APL   M
Sbjct: 299 ETLRFNAPLDHQM 311


>gi|146282969|ref|YP_001173122.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           stutzeri A1501]
 gi|145571174|gb|ABP80280.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           stutzeri A1501]
          Length = 266

 Score =  156 bits (395), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 97/280 (34%), Positives = 159/280 (56%), Gaps = 19/280 (6%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           ++K R+K   ++Q+G +VR+PP+  A      E + L   +      + L+S ++YED  
Sbjct: 1   MNKGRIKPEYKLQAGDLVRVPPLRLAER---DEPEPLAQGL-----LERLESAIVYEDKA 52

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + V NKPAGI+V GGSG++Y +   L+  +    ++  L HRLD++TSG+L+VA+ R+  
Sbjct: 53  LIVLNKPAGIAVHGGSGLSYGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMVAKKRSML 111

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           +HL ++ R   + K Y +LV G     K+ ++  LLK +   G+ +  V ++ K    A+
Sbjct: 112 RHLHQALRGDGVDKRYMALVRGRWDTSKKQVSAPLLKNTLRSGERMVEVTEDGK---EAL 168

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN- 286
           + F+V+  F      +E +P TGRTHQ+RVHA H G  I GD KY      +FT  ++  
Sbjct: 169 TLFRVLRRFGDFATLVEAKPVTGRTHQIRVHARHAGHSIAGDSKYGDE---DFTREVREL 225

Query: 287 ---KLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
              +L+LHA  + +P P+GG L + AP+     +T + LG
Sbjct: 226 GGKRLFLHAYALKVPLPDGGELTLEAPVDEVWARTLERLG 265


>gi|241758991|ref|ZP_04757103.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           flavescens SK114]
 gi|241320812|gb|EER57045.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           flavescens SK114]
          Length = 328

 Score =  156 bits (394), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 103/323 (31%), Positives = 172/323 (53%), Gaps = 27/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   EE  RLD +       +   ++ +I+R+G+VR++KKR K +NRIQ+G  VR
Sbjct: 9   VSLIAVAEHEEGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDNRIQAGDTVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      I ++Q+  +S     +  D     ++YED  + V NKP+GI+V GGSG++
Sbjct: 69  IPPI-----RIAEKQRPSESQAAPAREFD-----IVYEDDALLVINKPSGIAVHGGSGVS 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++     + +   L HRLD++TSG+L++A+ R+A   L E+ R    +KIY +L
Sbjct: 119 FGVIEQIR-RARPEARYLELVHRLDKDTSGLLMIAKKRSALVKLHEAIRNDHPKKIYLAL 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--------- 237
             G   N +  +   L K  + G     +V+ +E G + A + F+V++ F+         
Sbjct: 178 GVGRLPNNRFHVKLPLFK--YTGAQGEKMVRVSEDGQS-AHTIFRVLNRFSDGLLHQVGL 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
               ++E    TGRTHQ+RVH     CPI GD +Y  +++ N         +++LHA  +
Sbjct: 235 SDLTFVEATLKTGRTHQIRVHLQSQDCPIAGDERY-GDYQANKRLQKLGLKRMFLHASEL 293

Query: 296 DLPHP-EGGRLQITAPLPAHMVK 317
            L HP  G +L +  PLP  + +
Sbjct: 294 HLAHPLTGEKLILKTPLPQELAQ 316


>gi|325497607|gb|EGC95466.1| 23S rRNA pseudouridylate synthase C [Escherichia fergusonii ECD227]
          Length = 317

 Score =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 104/307 (33%), Positives = 168/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++ +G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLAAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEDAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A     +   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYAIA-TLVRCS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D +Y    F     +   ++L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLANTGLSRLFLHAAALKFTHPGTGEV 295

Query: 305 LQITAPL 311
           ++I AP+
Sbjct: 296 MRIEAPM 302


>gi|242239020|ref|YP_002987201.1| pseudouridine synthase [Dickeya dadantii Ech703]
 gi|242131077|gb|ACS85379.1| pseudouridine synthase, RluA family [Dickeya dadantii Ech703]
          Length = 319

 Score =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 103/307 (33%), Positives = 164/307 (53%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ + ++E   R+D + +     +    + +ILR G+VR++KKRVK   ++  G  VR
Sbjct: 8   VQFMTISSEEAGQRIDNFLRVRLKGVPKSMIYRILRKGEVRINKKRVKPEYKLLDGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +      E+ + + S +L K S  L   +LYED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRQS------ERDVPEVSASLDKVSS-LTHCILYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRALHEQLRSKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V    K +       +  DC       ++  
Sbjct: 180 VRGQWQSHCKSVQAPLLKNILKSGERIVRVNGEGKPSETLFKVEERFDCAT----LVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA + G PI  D +Y    F          +L+LHA  + L HP  G  
Sbjct: 236 PVTGRTHQIRVHAQYAGHPIAFDDRYGDRAFDQQLADTGLKRLFLHAHALRLEHPHTGET 295

Query: 305 LQITAPL 311
           L+  APL
Sbjct: 296 LRFEAPL 302


>gi|114797784|ref|YP_761328.1| pseudouridine synthase family protein [Hyphomonas neptunium ATCC
           15444]
 gi|114737958|gb|ABI76083.1| pseudouridine synthase family protein [Hyphomonas neptunium ATCC
           15444]
          Length = 244

 Score =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 87/233 (37%), Positives = 136/233 (58%), Gaps = 8/233 (3%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +   +S+L++ED+ I  FNKP G++ QGGS +   +D  L ++  S G++PRL HRLDQ 
Sbjct: 15  AALARSLLIHEDAAILGFNKPPGMASQGGSSVGQSLDDLLWAFAKSNGKRPRLVHRLDQG 74

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDY 212
           TSG+++ ART+ AA  L+ +F  R  QK Y +LV G +P  +   I   L+K    G   
Sbjct: 75  TSGVMLTARTQPAAAFLSAAFAGRDAQKTYLALVKGKLPPAEHGVIDASLVKVEEGGRPR 134

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + + K + KGA  A + + V+    +    +++ P TGR HQ+RVH + +GCPI+GD  Y
Sbjct: 135 MILAKPSRKGAQPARTGWAVL-ARNEDHALMQLTPETGRMHQIRVHLMSLGCPILGDGLY 193

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
               +G  T+P   ++ LHA  +++PHPEGG L + AP+P       +  G +
Sbjct: 194 G---EGQATAP---RVMLHAARLEVPHPEGGTLTLEAPVPEDFRAAAEKAGLQ 240


>gi|218549187|ref|YP_002382978.1| 23S rRNA pseudouridylate synthase C [Escherichia fergusonii ATCC
           35469]
 gi|218356728|emb|CAQ89356.1| 23S rRNA pseudouridylate synthase [Escherichia fergusonii ATCC
           35469]
 gi|324113880|gb|EGC07854.1| RluA family protein pseudouridine synthase [Escherichia fergusonii
           B253]
          Length = 331

 Score =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 104/307 (33%), Positives = 168/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++ +G  VR
Sbjct: 22  VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLAAGDEVR 81

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 82  IPPV------RVAEREEDAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 134

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 135 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 193

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A     +   
Sbjct: 194 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYAIA-TLVRCS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D +Y    F     +   ++L+LHA  +   HP  G  
Sbjct: 250 PVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLANTGLSRLFLHAAALKFTHPGTGEV 309

Query: 305 LQITAPL 311
           ++I AP+
Sbjct: 310 MRIEAPM 316


>gi|205353078|ref|YP_002226879.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205272859|emb|CAR37786.1| ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70)
           [Salmonella enterica subsp. enterica serovar Gallinarum
           str. 287/91]
 gi|326628157|gb|EGE34500.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 319

 Score =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 107/310 (34%), Positives = 169/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARLLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|82702194|ref|YP_411760.1| pseudouridine synthase, RluD [Nitrosospira multiformis ATCC 25196]
 gi|82410259|gb|ABB74368.1| ribosomal large subunit pseudouridine synthase C [Nitrosospira
           multiformis ATCC 25196]
          Length = 328

 Score =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 105/329 (31%), Positives = 172/329 (52%), Gaps = 37/329 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++  + +  R+D +      ++   ++ ++LRSGQVR++ KR   +  +QSG +VRIPPV
Sbjct: 4   IIGEESKGQRIDNFLIKRLKNVPKSHVYRLLRSGQVRINSKRAPPDYHLQSGDIVRIPPV 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                  +  +K+            F+   +L+ED  +   NKP G++V GGSGI++ + 
Sbjct: 64  RTVEKSALPPKKL--------SKPGFIAFQVLFEDDALIAVNKPPGVAVHGGSGISFGVI 115

Query: 131 GFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             L++      Q P      L HRLD+ETSG+L++A+ RAA   L    RM  ++K Y +
Sbjct: 116 EQLRA------QHPDWRFLELAHRLDRETSGVLLLAKNRAALVELHRQLRMGEVEKHYLT 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKFCW 242
           LV G  +N ++ +   L K    GG+    V+++   +KG   A + F + + + Q F  
Sbjct: 170 LVKGRWRNGRQSVRLSLRKYLTPGGERRVAVEKDADEKKGGMSAHTVFILRESW-QSFSL 228

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT--------SPIQNKLYLHARY 294
           LE +  TGRTHQ+RVH  ++G PI GD KY     G+F          P   +++LHA  
Sbjct: 229 LEAELKTGRTHQIRVHLAYLGFPIAGDDKY-----GDFVLNKDIARRVPGLGRMFLHAWA 283

Query: 295 MDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           ++  HP    +L++ APLP  + K  D +
Sbjct: 284 VEFTHPVTHEKLRLEAPLPDDLQKFLDVM 312


>gi|319638921|ref|ZP_07993679.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317399825|gb|EFV80488.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 328

 Score =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 103/323 (31%), Positives = 172/323 (53%), Gaps = 27/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   EE  RLD +       +   ++ +I+R+G+VR++KKR K +NRIQ+G  VR
Sbjct: 9   VSLIAVAEHEEGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDNRIQAGDTVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A     ++Q+  +S     +  D     ++YED  + V NKP+G++V GGSG++
Sbjct: 69  IPPIRTA-----EKQRPSESQAAPAREFD-----IVYEDDALLVINKPSGVAVHGGSGVS 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++     + +   L HRLD++TSG+L++A+ R+A   L E+ R    +KIY +L
Sbjct: 119 FGVIEQIR-RARPEARYLELVHRLDKDTSGLLMIAKKRSALVKLHEAIRNDHPKKIYLAL 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--------- 237
             G   N +  +   L K  + G     +V+ +E G + A + F+V++ F+         
Sbjct: 178 GVGRLPNDRFHVKLPLFK--YTGAQDEKMVRVSEDGQS-AHTIFRVLNRFSDGLLHQVGL 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +E    TGRTHQ+RVH     CPI GD +Y  +++ N         +++LHA  +
Sbjct: 235 SDLTLVEATLKTGRTHQIRVHLQSQDCPIAGDERY-GDYQANKRLQKLGLKRMFLHASEL 293

Query: 296 DLPHP-EGGRLQITAPLPAHMVK 317
            L HP  G +L + APLP  + +
Sbjct: 294 HLAHPLTGEKLILKAPLPQELAQ 316


>gi|297519884|ref|ZP_06938270.1| 23S rRNA pseudouridylate synthase C [Escherichia coli OP50]
          Length = 319

 Score =  156 bits (394), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 107/310 (34%), Positives = 169/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+V + R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVTKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|16764542|ref|NP_460157.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|168237272|ref|ZP_02662330.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|168244787|ref|ZP_02669719.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|168822633|ref|ZP_02834633.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|194444187|ref|YP_002040440.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194448791|ref|YP_002045185.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194738103|ref|YP_002114185.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197263790|ref|ZP_03163864.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|198244450|ref|YP_002215951.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|204930731|ref|ZP_03221604.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|207857306|ref|YP_002243957.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|238910994|ref|ZP_04654831.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|34395808|sp|Q8ZQ16|RLUC_SALTY RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|16419703|gb|AAL20116.1| 23S rRNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|194402850|gb|ACF63072.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194407095|gb|ACF67314.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|194713605|gb|ACF92826.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|197242045|gb|EDY24665.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197289855|gb|EDY29216.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|197938966|gb|ACH76299.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|204320190|gb|EDZ05394.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205336408|gb|EDZ23172.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|205340990|gb|EDZ27754.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|206709109|emb|CAR33442.1| ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70)
           [Salmonella enterica subsp. enterica serovar Enteritidis
           str. P125109]
 gi|261246398|emb|CBG24207.1| ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70)
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. D23580]
 gi|301157727|emb|CBW17219.1| ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70)
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. SL1344]
 gi|312912174|dbj|BAJ36148.1| 23S rRNA pseudouridine synthase C [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|321223804|gb|EFX48867.1| Ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|323129456|gb|ADX16886.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|326623699|gb|EGE30044.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332988077|gb|AEF07060.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 319

 Score =  155 bits (393), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 107/310 (34%), Positives = 169/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|89073417|ref|ZP_01159941.1| putative 23S rRNA ribosomal pseudouridine synthase [Photobacterium
           sp. SKA34]
 gi|89050904|gb|EAR56378.1| putative 23S rRNA ribosomal pseudouridine synthase [Photobacterium
           sp. SKA34]
          Length = 314

 Score =  155 bits (393), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 100/318 (31%), Positives = 172/318 (54%), Gaps = 16/318 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ + +D    R+D + +    ++    + +ILR G+VRV+KKR+K   ++Q G +VR
Sbjct: 8   VQFIDISDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDLVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV      + ++++    S  L K ++ L+  ++YED  + + NKP+G +V GGSG+ 
Sbjct: 68  VPPVF-----VPEKEEQAPVSTKLNKVAE-LEHCIIYEDDHLLILNKPSGTAVHGGSGLK 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + +QK Y++L
Sbjct: 122 FGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRQLQEQFRNKTVQKYYFAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K     +   LLK      +   +V+ N +G   + + FKV++ F      ++  
Sbjct: 181 VMGEWKANCRKVTAPLLK-----NEVNSIVRVNPQG-KASDTRFKVLERFPLA-TLVQAS 233

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D +Y    F          +L+LHA  +   HP     
Sbjct: 234 PVTGRTHQIRVHCQYEGHPIAWDDRYGDPRFDAYTKKTGLGRLFLHAANIKFTHPSTDEA 293

Query: 305 LQITAPLPAHMVKTWDSL 322
           + I+AP+   + +  + L
Sbjct: 294 MDISAPMEPALERCLEKL 311


>gi|225075563|ref|ZP_03718762.1| hypothetical protein NEIFLAOT_00576 [Neisseria flavescens
           NRL30031/H210]
 gi|224953108|gb|EEG34317.1| hypothetical protein NEIFLAOT_00576 [Neisseria flavescens
           NRL30031/H210]
          Length = 328

 Score =  155 bits (393), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 102/323 (31%), Positives = 173/323 (53%), Gaps = 27/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   EE  RLD +       +   ++ +I+R+G+VR++KKR K +NRIQ+G  VR
Sbjct: 9   VSLIAVAEHEEGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDNRIQAGDTVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      I ++Q+  +S     +  +     ++YED  + V NKP+G++V GGSG++
Sbjct: 69  IPPI-----RIAEKQRPSESQAAPAREFE-----IVYEDDALLVINKPSGVAVHGGSGVS 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++     + +   L HRLD++TSG+L++A+ R+A   L E+ R    +KIY +L
Sbjct: 119 FGVIEQIR-RARPEARYLELVHRLDKDTSGLLMIAKKRSALVKLHEAIRNDHPKKIYLAL 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--------- 237
             G   N +  +   L K  + G     +V+ +E G + A + F+V++ F+         
Sbjct: 178 GVGRLPNDRFHVKLPLFK--YTGAQGEKMVRVSEDGQS-AHTIFRVLNRFSDGLLHQVGL 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
               ++E    TGRTHQ+RVH     CPI GD +Y  +++ N         +++LHA  +
Sbjct: 235 SDLTFVEATLKTGRTHQIRVHLQSQDCPIAGDERY-GDYQANKRLQKLGLKRMFLHASEL 293

Query: 296 DLPHP-EGGRLQITAPLPAHMVK 317
            L HP  G +L + APLP  + +
Sbjct: 294 HLAHPLTGEKLILKAPLPQELAQ 316


>gi|254785800|ref|YP_003073229.1| ribosomal large subunit pseudouridine synthase C [Teredinibacter
           turnerae T7901]
 gi|237685873|gb|ACR13137.1| ribosomal large subunit pseudouridine synthase C [Teredinibacter
           turnerae T7901]
          Length = 314

 Score =  155 bits (393), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 101/318 (31%), Positives = 171/318 (53%), Gaps = 15/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  + +D    R+D +            + +I+R G+VRV+K RVK   ++  G +VR
Sbjct: 5   VQFFTITDDNAGQRIDNFLVARLKGAPKSLIYRIIRRGEVRVNKGRVKPERKLAVGDLVR 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      + +      +  +L      L+  +LYE  ++ V NKP+G++V GGSG+ 
Sbjct: 65  VPPI-----RLAEPDAPTPAGKSLLLA---LEDAVLYETDQLLVVNKPSGLAVHGGSGVN 116

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQKIYWS 185
             +   ++  + +K     L HRLD+ETSG +++AR R+  ++L + FR  +++ K Y +
Sbjct: 117 LGLIEAIRQ-LKAKDTALELVHRLDRETSGCILIARKRSMLRYLQDLFRGEKQVDKRYQA 175

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   N+   +   LLK     G+   +V+ + +G   + + F V++ F +    +E 
Sbjct: 176 LVKGRWPNRAHSVNVPLLKGEVGNGE--RIVRASPEG-KPSRTEFDVLERF-ESATLIEA 231

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +P TGRTHQ+RVHA + G P+VGD KY  + F    +     +L+LHA Y+ +P P+G  
Sbjct: 232 RPITGRTHQIRVHAQYKGHPLVGDDKYGDDEFNKVMSQFGSRRLFLHAGYLGVPMPDGEY 291

Query: 305 LQITAPLPAHMVKTWDSL 322
           L+  APLP  +  T   L
Sbjct: 292 LEFRAPLPDDLQATLKQL 309


>gi|261253417|ref|ZP_05945990.1| ribosomal large subunit pseudouridine synthase C [Vibrio orientalis
           CIP 102891]
 gi|260936808|gb|EEX92797.1| ribosomal large subunit pseudouridine synthase C [Vibrio orientalis
           CIP 102891]
          Length = 300

 Score =  155 bits (393), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 100/306 (32%), Positives = 173/306 (56%), Gaps = 18/306 (5%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D + +N    I    + +ILR G+VRV+KKR+K   ++++G +VRIPPV      I +
Sbjct: 5   RIDNFLRNQLKSIPKSMVYRILRKGEVRVNKKRIKAEYKLKAGDLVRIPPVT-----IEE 59

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + +    S  L K ++ L+ ++++ED  + + NKP+G +V GGSG+ +     L++ +  
Sbjct: 60  KPEEAAPSTKLNKVAE-LEYMIIHEDDHMLILNKPSGTAVHGGSGLKFGAIEALRA-LRP 117

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-I 198
           + +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K Y++LV G  + K  C +
Sbjct: 118 EARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKKFYFALVMG--QWKANCKV 175

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N  L K+ +      +V+ N  G   + + FK+++ FA+    ++  P TGRTHQ+RVH
Sbjct: 176 VNAPLLKNEVNS----IVRVNPNG-KPSETRFKILEKFAEA-TLIQASPITGRTHQIRVH 229

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
             + G PI  D +Y       +T  +  ++L+LHA  +   HP     ++I AP+   + 
Sbjct: 230 TQYTGHPIAWDDRYGDRRFDAYTGQVGLDRLFLHAANIKFQHPSNDEWMEINAPMEPKLE 289

Query: 317 KTWDSL 322
           K    L
Sbjct: 290 KALVGL 295


>gi|332525768|ref|ZP_08401915.1| RluA family pseudouridine synthase [Rubrivivax benzoatilyticus JA2]
 gi|332109325|gb|EGJ10248.1| RluA family pseudouridine synthase [Rubrivivax benzoatilyticus JA2]
          Length = 305

 Score =  155 bits (392), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 101/312 (32%), Positives = 167/312 (53%), Gaps = 23/312 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V+ +    RLD +   H   +   ++ +++RSG+VRV+K R   + R+ +G  +R
Sbjct: 1   MQRITVDEESAGQRLDNFLLRHLKGVPKTHVYRVIRSGEVRVNKGRASADTRVAAGDEIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+  A       +K   ++V   +        +L+ED  +    KPAG++V GGSG++
Sbjct: 61  VPPMRIA-------EKPAAAAVPAREFP------VLFEDEHLLAIAKPAGVAVHGGSGVS 107

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              I+   ++  D++  +  L HRLD+ETSG+L++A+ R+A   L + FR R   K Y +
Sbjct: 108 SGVIEQLRRARPDARFLE--LVHRLDKETSGVLLLAKKRSALTALQDQFRARDTGKNYLA 165

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G+   K + +   L K +   G+ +V VV  +   A  +I+  + +      +  LE
Sbjct: 166 LVVGVWPKKLKVLDLALHKGTDAAGERHVRVVAADAPDARRSITVVRSVRAVG-PYSLLE 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPE 301
           +   TGRTHQ+RVH  H G PIVGD KY  +F  N T   +    +++LHA  +   HP 
Sbjct: 225 IGLKTGRTHQIRVHLAHSGHPIVGDPKY-GDFALNKTVAREKRFARMFLHAVELAFDHPA 283

Query: 302 GG-RLQITAPLP 312
            G R+ + APLP
Sbjct: 284 SGERITLHAPLP 295


>gi|149911608|ref|ZP_01900220.1| ribosomal large subunit pseudouridine synthase C [Moritella sp.
           PE36]
 gi|149805329|gb|EDM65342.1| ribosomal large subunit pseudouridine synthase C [Moritella sp.
           PE36]
          Length = 317

 Score =  155 bits (392), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 103/319 (32%), Positives = 171/319 (53%), Gaps = 16/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +V +  D +  R+D + +     +    + +I+R G+VRV+K R+K   ++Q   +VR
Sbjct: 9   VAFVTITEDYQGQRIDNFLRTKLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLQPEDIVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E + +  S NL      L+S ++YED  + V NKP+G++V GGSG++
Sbjct: 69  IPPV------RVSETEAISPSANLDS-VRALESQIIYEDDYLIVINKPSGMAVHGGSGLS 121

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+G      DS+  +  L HRLD++TSG L+VA+ R+  + L E  R++ ++K Y +
Sbjct: 122 FGLIEGLRAIRPDSRFLE--LVHRLDRDTSGCLLVAKKRSTLKALHEQLRLKTMRKDYQA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G        +   LLK +   G+   +V+ + +G   + + F +I  + +    ++ 
Sbjct: 180 LVAGAWPRSSRIVNAPLLKNTVSSGE--RLVRVDSEGKE-SQTRFSIIQRY-EHGTLVQA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVHALH G PI  D KY   +F  +       +L+LHA  +   +P    
Sbjct: 236 SPITGRTHQIRVHALHAGHPIACDDKYGDKDFTKHMNGLGLKRLFLHAARLQFFNPGTQE 295

Query: 305 LQ-ITAPLPAHMVKTWDSL 322
            Q + APL   +V+  + L
Sbjct: 296 TQEVEAPLDMALVRALEKL 314


>gi|53804453|ref|YP_113936.1| ribosomal large subunit pseudouridine synthase C [Methylococcus
           capsulatus str. Bath]
 gi|53758214|gb|AAU92505.1| ribosomal large subunit pseudouridine synthase C [Methylococcus
           capsulatus str. Bath]
          Length = 316

 Score =  155 bits (392), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 97/307 (31%), Positives = 168/307 (54%), Gaps = 21/307 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V+ +    R+D +  +    +   ++ +ILR+GQVR++  R K   R+  G VVRI
Sbjct: 13  RLIEVDAETAGQRIDNFLFSRLKGVPKSHVYRILRTGQVRINGGRSKAQQRLNEGDVVRI 72

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP+             L  +      + +L++ +L+ED  + V NKPAG++V GGSG+ +
Sbjct: 73  PPLR------------LAEAPEAGIPTPWLENRILHEDEDLLVVNKPAGMAVHGGSGLRF 120

Query: 128 H-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             I+G   +  D++  +  L HRLD++TSG L++A+ R+A + L E FR   + K Y +L
Sbjct: 121 GVIEGLRAAREDARFLE--LVHRLDRDTSGCLLIAKRRSALRQLHEQFRGEGVDKTYLAL 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G+   +++ +   LLK     G+   +VK + +G   AI+ F+ ++  +     +E +
Sbjct: 179 FSGVWARRRQVVDAPLLKNVLQSGE--RMVKISSEG-KAAITEFRRLEPLSGA-TLVEAR 234

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA  +G P+ GD +Y   +   +F      +++LHA  +   HP  GR 
Sbjct: 235 PVTGRTHQIRVHARSLGHPLAGDERYGDPSLNQDFRQRGLKRMFLHAATLAFTHPRNGRE 294

Query: 305 LQITAPL 311
           +++ APL
Sbjct: 295 IRVEAPL 301


>gi|330446422|ref|ZP_08310074.1| 23S rRNA pseudouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328490613|dbj|GAA04571.1| 23S rRNA pseudouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 314

 Score =  155 bits (392), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 99/307 (32%), Positives = 170/307 (55%), Gaps = 16/307 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ + +D    R+D + +    ++    + +ILR G+VRV+KKR+K   ++Q G +VR
Sbjct: 8   VQFIDINDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDLVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      + ++++    S  L K ++ L+  ++YED  + + NKP+G +V GGSG+ 
Sbjct: 68  VPPIF-----VPEKEEQEQVSTKLNKVAE-LEHCIIYEDDHMLILNKPSGTAVHGGSGLK 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + +QK Y++L
Sbjct: 122 FGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRKLQEQFRNKTVQKYYFAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K   + +   LLK      +   +V+ N +G   + + FKV++ F Q    ++  
Sbjct: 181 VMGEWKASCKKVTAPLLK-----NEVNSIVRVNPQG-KPSDTRFKVLERFPQA-TLVQAS 233

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D +Y    F          +L+LHA  +   HP     
Sbjct: 234 PVTGRTHQIRVHCQYEGHPIAWDDRYGDPRFDAYTKKTGLGRLFLHAANIKFTHPNTDEM 293

Query: 305 LQITAPL 311
           + I+AP+
Sbjct: 294 MDISAPM 300


>gi|161614588|ref|YP_001588553.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|162139595|ref|YP_216121.2| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|168467142|ref|ZP_02700984.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|224584309|ref|YP_002638107.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|161363952|gb|ABX67720.1| hypothetical protein SPAB_02338 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|195630420|gb|EDX49046.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|224468836|gb|ACN46666.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Paratyphi C strain
           RKS4594]
 gi|322714174|gb|EFZ05745.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 319

 Score =  155 bits (392), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 107/310 (34%), Positives = 169/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHARYMDLPHP-E 301
            P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGT 294

Query: 302 GGRLQITAPL 311
           G  ++I AP+
Sbjct: 295 GDVMRIEAPM 304


>gi|267992961|gb|ACY87846.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|320086374|emb|CBY96147.1| pseudouridylate synthase [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
          Length = 347

 Score =  155 bits (392), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 107/310 (34%), Positives = 169/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 36  VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 95

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 96  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 148

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 149 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 207

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 208 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 262

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  +   HP  
Sbjct: 263 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGT 322

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 323 GEVMRIEAPM 332


>gi|82544448|ref|YP_408395.1| 23S rRNA pseudouridylate synthase C [Shigella boydii Sb227]
 gi|110805101|ref|YP_688621.1| 23S rRNA pseudouridylate synthase C [Shigella flexneri 5 str. 8401]
 gi|187732109|ref|YP_001880745.1| 23S rRNA pseudouridylate synthase C [Shigella boydii CDC 3083-94]
 gi|300918689|ref|ZP_07135269.1| pseudouridine synthase, RluA family [Escherichia coli MS 115-1]
 gi|81245859|gb|ABB66567.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|110614649|gb|ABF03316.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|187429101|gb|ACD08375.1| ribosomal large subunit pseudouridine synthase C [Shigella boydii
           CDC 3083-94]
 gi|300414163|gb|EFJ97473.1| pseudouridine synthase, RluA family [Escherichia coli MS 115-1]
 gi|320186966|gb|EFW61679.1| 23S rRNA pseudouridylate synthase C [Shigella flexneri CDC 796-83]
 gi|332094085|gb|EGI99137.1| pseudouridine synthase, RluA family protein [Shigella boydii
           3594-74]
          Length = 319

 Score =  155 bits (392), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 107/310 (34%), Positives = 169/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V    ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRSQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|200389528|ref|ZP_03216139.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|199601973|gb|EDZ00519.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
          Length = 319

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 107/310 (34%), Positives = 169/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFMHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|70729172|ref|YP_258908.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens Pf-5]
 gi|68343471|gb|AAY91077.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens Pf-5]
          Length = 318

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 107/322 (33%), Positives = 172/322 (53%), Gaps = 23/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K R+K   ++Q+G    
Sbjct: 11  VQLLEVSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAG---- 66

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                + +          D  V L +     L++ +++ED  + V NKPAGI+V GGSG+
Sbjct: 67  -----DVVRVPPVRVPERDEPVPLAQGLLQRLEASIVFEDKALIVINKPAGIAVHGGSGL 121

Query: 126 AYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            +  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y 
Sbjct: 122 NFGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G      + +   LLK +   G+   +V+ NE+G   A++ FKV+  F      +E
Sbjct: 180 ALVRGHWATAVKQVRAPLLKSNLRSGE--RMVEVNEEGKE-ALTVFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHP 300
            +P TGRTHQ+RVH LH G  I GD KY  +   +FT  I+     +L+LHA  + +P P
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHCIAGDSKYGDD---DFTREIRELGGKRLFLHAYMLTVPLP 293

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
           +GG L++ AP+     KT + L
Sbjct: 294 DGGELKLQAPVDEMWAKTVERL 315


>gi|308049100|ref|YP_003912666.1| ribosomal large subunit pseudouridine synthase C [Ferrimonas
           balearica DSM 9799]
 gi|307631290|gb|ADN75592.1| ribosomal large subunit pseudouridine synthase C [Ferrimonas
           balearica DSM 9799]
          Length = 320

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 102/318 (32%), Positives = 170/318 (53%), Gaps = 13/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  D    R+D + +     +    + ++LR G+VRV+KKR+K   ++  G  +R
Sbjct: 12  VQWVDITEDHAGQRIDNFLRTFLKGVPKSLIYRLLRKGEVRVNKKRIKPEYKLADGDQIR 71

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I P+      + +  + +  S  L K +  L+S ++YED  + V NKP+GI+V GGSGI 
Sbjct: 72  IAPI-----RVSERDETVAPSAKLEKVAQ-LESQIVYEDKVMLVINKPSGIAVHGGSGIN 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++   ++ Q   L HRLD+ TSG+L+VA+ R+A +HL +  R + ++K Y +L
Sbjct: 126 FGVIEALRALRPNERQL-ELVHRLDRATSGLLMVAKRRSALKHLQDQLREKTMRKQYLAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    K   +   LLK +   G+ +  V    K +    + F++++ FA+    +E  
Sbjct: 185 VKGQWNPKTRAVQAPLLKNTLGTGERLVRVDAAGKPSE---TRFRIVENFAEG-TLVECS 240

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
           P TGRTHQ+RVH  H G PI  D +Y  + F         ++L+LHA  +   HP E   
Sbjct: 241 PITGRTHQIRVHTQHAGHPIACDERYGDDEFDVLMRKKGLDRLFLHAFRLSFTHPVEEVT 300

Query: 305 LQITAPLPAHMVKTWDSL 322
           + + APL   +    ++L
Sbjct: 301 MTVEAPLDNKLEAALEAL 318


>gi|311695112|gb|ADP97985.1| pseudouridine synthase, RluA family [marine bacterium HP15]
          Length = 352

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 100/306 (32%), Positives = 172/306 (56%), Gaps = 15/306 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V V+ D E  R+D +       +    + +++R G+VRV+K RVK ++R+++G  VR
Sbjct: 39  VQWVTVDEDNEGQRVDNFLLAQLRGVPKSIIYRVIRKGEVRVNKGRVKPDSRVRTGDQVR 98

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+        KE+   D     ++    ++S +++E+ ++ V NKP+GI+V GGSG++
Sbjct: 99  IPPITR------KEKP--DQVAPGSRVQGVMESAVVFENEQMLVVNKPSGIAVHGGSGLS 150

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+S      +   L HRLD++TSG+++VA+ R+A ++L +  R +RI+K Y +L
Sbjct: 151 FGLIEVLRS-ARPTAKFLELVHRLDRDTSGLIMVAKKRSALRYLQDELRQKRIRKHYHAL 209

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G      + +   LL+     G+    VK +  G   +++ F+ ++ +A  +  +E  
Sbjct: 210 VAGDWPASVDRVDVPLLRYEMPNGE--RRVKVDAAG-KASLTTFRCLEHYA-GYSLVEAS 265

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH+   G PI GD KY  +     F S    +L LHAR ++   P  G  
Sbjct: 266 PITGRTHQIRVHSAWAGHPIAGDDKYMDDVSLKAFRSIGGQRLMLHARALEFTLPVSGEA 325

Query: 305 LQITAP 310
           +++ AP
Sbjct: 326 MRLEAP 331


>gi|299067008|emb|CBJ38203.1| Ribosomal large subunit pseudouridine synthase C [Ralstonia
           solanacearum CMR15]
          Length = 346

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 106/327 (32%), Positives = 176/327 (53%), Gaps = 23/327 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D +  R+D +       +   ++ +ILRSG+VRV+K R+    R+  G +VR
Sbjct: 25  VAYVEIGEDAQGQRIDNFLMRLAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLNLGDLVR 84

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      + ++      +      ++F    +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 85  IPPL-----RVAQQSPGQAEAARAVPAAEF---TILHEDTHLLVIDKPAGVAVHGGSGVA 136

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   +S  ++K  +  L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++
Sbjct: 137 FGVIEQLRRSRPEAKFLE--LVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFA 194

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G+  ++++ I + L K +   G+   V  Q +   ++ +  F  +  F   +  LE 
Sbjct: 195 AVKGVWPHQRQHIKSPLFKYTTPEGER-RVRVQADGQPSHTV--FNRVGVFG-PYTLLEA 250

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMDLPH 299
           +  TGRTHQ+RVH  H G PI+GD KY  +F  N        SP   +++LHA  + L H
Sbjct: 251 ELKTGRTHQIRVHLAHAGFPILGDDKY-GDFALNKALSRANASPRLARMFLHAHTLRLTH 309

Query: 300 PEGGRL-QITAPLPAHMVKTWDSLGFK 325
           P+ G +    APLPA      ++L  K
Sbjct: 310 PQSGEIVTFKAPLPAECAAFLNALSPK 336


>gi|167855918|ref|ZP_02478667.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parasuis 29755]
 gi|219871480|ref|YP_002475855.1| 23S rRNA pseudouridylate synthase C [Haemophilus parasuis SH0165]
 gi|167852955|gb|EDS24220.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parasuis 29755]
 gi|219691684|gb|ACL32907.1| 23S rRNA pseudouridylate synthase C [Haemophilus parasuis SH0165]
          Length = 319

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 107/321 (33%), Positives = 173/321 (53%), Gaps = 14/321 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  + +DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q+  +VR
Sbjct: 11  VQFFTISDDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQADDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPVRVA------EKNEAPISTKLNKVAE-LEHQILYEDEVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGLLLVAKKRSALRSLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   +V+ +E+G   + + F VI+        ++  
Sbjct: 183 VRGQWQSHVKVIKAPLLKNELASGE--RIVRVSEEG-KPSETRF-VIEERYPIATLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGDREFDQKMQQAGLNRLFLHAHSIRFVHPKTGEE 298

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           + +TAPL   +      L  K
Sbjct: 299 MVVTAPLDKQLKAVLAKLRVK 319


>gi|157827593|ref|YP_001496657.1| ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           OSU 85-389]
 gi|157802897|gb|ABV79620.1| Ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           OSU 85-389]
          Length = 310

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 94/308 (30%), Positives = 163/308 (52%), Gaps = 13/308 (4%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++  N     RLD++ +  YP +    ++K LR  Q+ V+ K+ + + R+  G  + I  
Sbjct: 11  IITVNSPIASRLDKYLRRLYPLLTQGVIEKALRQKQIIVNSKKAEASLRVVEGDEIFIHD 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
             N    I +  K++ +   +T         L+YED  I   NKPAG++ QGGS I   +
Sbjct: 71  KFNL--PIAQPTKLVFTDAEITLAKKITTEYLIYEDDNIIAINKPAGLATQGGSKINLSV 128

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           D  LK +++S+G   +L HRLD+ETSG+L++A+   ++  L ++F+ + ++K Y ++ +G
Sbjct: 129 DSALK-YLNSQGADFKLVHRLDKETSGLLLIAKNYVSSVKLHDAFKEKLVEKTYLAVTYG 187

Query: 190 IP-KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
            P K++ E   N  ++KS   G    +   N+     AI+++K++         +E  P 
Sbjct: 188 KPIKDQGEVKTN--IEKSK--GSIPKITDINDNNGKLAITYYKLLKSLTNNLFLVEFIPI 243

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGR HQLR+HA  +GCPI GD+KY      +   P    ++LHA  + L     G+ + +
Sbjct: 244 TGRMHQLRLHAKLLGCPIFGDNKYG----NDKLMPYSKYMFLHANNIVLSKKVFGKEVNL 299

Query: 308 TAPLPAHM 315
            A LP++ 
Sbjct: 300 EAKLPSYF 307


>gi|62127337|gb|AAX65040.1| 23S rRNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
          Length = 347

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 107/310 (34%), Positives = 169/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 36  VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 95

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 96  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 148

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 149 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 207

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 208 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 262

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHARYMDLPHP-E 301
            P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  +   HP  
Sbjct: 263 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGT 322

Query: 302 GGRLQITAPL 311
           G  ++I AP+
Sbjct: 323 GDVMRIEAPM 332


>gi|328865280|gb|EGG13666.1| putative ribosomal large subunit pseudouridine synthase C protein
           [Dictyostelium fasciculatum]
          Length = 720

 Score =  154 bits (390), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 113/388 (29%), Positives = 174/388 (44%), Gaps = 84/388 (21%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV---------------DKKRVKFNNRI 59
           D   MR+DRW +  +P +    + K+LR   +                 DK+ ++ ++R 
Sbjct: 334 DLAKMRVDRWLRIQFPVMTHSLICKLLRKEVITATDEFHQNGLDDVAASDKRVLEQSDRT 393

Query: 60  QSGQVVRIPPVINALNHIIKEQKILD--SSVNLTKHSDF----LKSILLYEDSKIYVFNK 113
           ++G  + IP          KEQ++ D  S     + SD     +++ +LY+D  + V NK
Sbjct: 394 EAGSWIYIPA------KYAKEQRVADRESPEKYIRLSDAEIAAIRNSILYKDDDLLVINK 447

Query: 114 PAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           P G+SVQGG+G+  H+D  L        + PRL HRLD++TSGIL++ R R A   + + 
Sbjct: 448 PPGLSVQGGTGLKKHLDMMLSHLKFEADETPRLVHRLDKDTSGILILGRNRTATTAMADK 507

Query: 174 F--RMRR-------------------------------------------IQKIYWSLVW 188
           F  +++R                                           I K YW+L+ 
Sbjct: 508 FEQKLKRRSDREVKKEKKDKKDDSNNNNNNNYSSKKTTKTTVEEMKDDNSIIKTYWALLT 567

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
             P  ++  I   L K    G + V   K+   GA  AI+ ++VI+       ++ + P 
Sbjct: 568 STPNPREGRIRAPLQKIVENGQEKVVATKETGNGAKLAITEYRVIENSMADTSFVALWPE 627

Query: 249 TGRTHQLRVH-ALHMGCPIVGDHKYCANFKGNFTSPIQN------KLYLHARYMDLPHP- 300
           TGRTHQLRVH A  +G PI+GD KY        T+P +N       L+LHAR +   HP 
Sbjct: 628 TGRTHQLRVHCASILGSPIIGDVKYGGK---KSTAPFENVFDKNIPLHLHARRVQFYHPI 684

Query: 301 -EGGRLQITAPLPAHMVKTWDSLGFKYD 327
                + + APLP  +  +W  LGF  D
Sbjct: 685 NTNKLVDVIAPLPPTLQDSWSILGFNPD 712


>gi|330815964|ref|YP_004359669.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           gladioli BSR3]
 gi|327368357|gb|AEA59713.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           gladioli BSR3]
          Length = 342

 Score =  154 bits (390), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 108/326 (33%), Positives = 169/326 (51%), Gaps = 26/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  V V  +    R+D +       +   ++ +ILRSG+VRV+K R+    R+  G VVR
Sbjct: 25  VSMVEVGEEAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAYGDVVR 84

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A     +E   + ++          +  +++ED  + V NKPAG++V GGSG++
Sbjct: 85  IPPIRIAAADPSRESVPVPAA----------EFAVVFEDEAMLVINKPAGVAVHGGSGVS 134

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y++ 
Sbjct: 135 FGVIEQLRE-ARPEARFLELVHRLDRETSGILMIAKKRSALVGLHEQIRDNRMDKRYYAA 193

Query: 187 V---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           V   W     ++  +   L K S   G+   V  Q++   ++ +  F +ID ++  + +L
Sbjct: 194 VHGEWAADWGRRRAVKVPLFKYSTPDGER-RVRVQDDGLPSHTV--FNLIDRWSD-YAFL 249

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMDL 297
           E +  TGRTHQ+RVH  H+G PIVGD KY  +F  N         P   +++LHA  + L
Sbjct: 250 EAELKTGRTHQIRVHLAHLGLPIVGDAKY-GDFALNKALARANARPSLKRMFLHAYRLKL 308

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLP    +  D L
Sbjct: 309 AHPLSGETLQFDAPLPDECRRFLDQL 334


>gi|91205071|ref|YP_537426.1| ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           RML369-C]
 gi|122425980|sp|Q1RJX7|RLUC_RICBR RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|91068615|gb|ABE04337.1| Ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           RML369-C]
          Length = 301

 Score =  154 bits (390), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 94/308 (30%), Positives = 163/308 (52%), Gaps = 13/308 (4%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++  N     RLD++ +  YP +    ++K LR  Q+ V+ K+ + + R+  G  + I  
Sbjct: 2   IITVNSPIASRLDKYLRRLYPLLTQGVIEKALRQKQIIVNSKKAEASLRVVEGDEIFIHD 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
             N    I +  K++ +   +T         L+YED  I   NKPAG++ QGGS I   +
Sbjct: 62  KFNL--PIAQPTKLVFTDAEITLAKKITTEYLIYEDDNIIAINKPAGLATQGGSKINLSV 119

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           D  LK +++S+G   +L HRLD+ETSG+L++A+   ++  L ++F+ + ++K Y ++ +G
Sbjct: 120 DSALK-YLNSQGADFKLVHRLDKETSGLLLIAKNYVSSVKLHDAFKEKLVEKTYLAVTYG 178

Query: 190 IP-KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
            P K++ E   N  ++KS   G    +   N+     AI+++K++         +E  P 
Sbjct: 179 KPIKDQGEVKTN--IEKSK--GSIPKITDINDNNGKLAITYYKLLKSLTNNLFLVEFIPI 234

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGR HQLR+HA  +GCPI GD+KY      +   P    ++LHA  + L     G+ + +
Sbjct: 235 TGRMHQLRLHAKLLGCPIFGDNKYG----NDKLMPYSKYMFLHANNIVLSKKVFGKEVNL 290

Query: 308 TAPLPAHM 315
            A LP++ 
Sbjct: 291 EAKLPSYF 298


>gi|221068709|ref|ZP_03544814.1| pseudouridine synthase, RluA family [Comamonas testosteroni KF-1]
 gi|220713732|gb|EED69100.1| pseudouridine synthase, RluA family [Comamonas testosteroni KF-1]
          Length = 346

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 111/323 (34%), Positives = 166/323 (51%), Gaps = 27/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V+ D    RLD +   H   +   ++ +I+RSG+VR++K RV    R+Q G VVR
Sbjct: 34  VRLIEVDEDSAGQRLDNFLMRHLKGVPKTHVYRIIRSGEVRINKGRVSAETRVQPGDVVR 93

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +        K+ + +       DF     L +D  +   +KPAG++V GGSG++
Sbjct: 94  LPPVRIS-------DKVAEKAERPAPAKDFPA---LLDDEHMLALSKPAGVAVHGGSGVS 143

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   ++  D+K  +  L HRLD+ETSGIL+VA+ R+A  +L + FR R   K Y +
Sbjct: 144 FGVIEQLRQARPDAKFLE--LVHRLDRETSGILLVAKKRSALINLQDQFRERETGKTYLA 201

Query: 186 LVWGI-PKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK---- 239
           LV G  P NKK  I   L K     G+  V V   ++     +I+  KV      +    
Sbjct: 202 LVQGAWPANKK-VIDLPLHKYLQADGERRVRVTTADDPDGMRSITLVKVRKLIEPRPLQG 260

Query: 240 ---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARY 294
                 LE+   TGRTHQ+RVH    G PIVGD KY  +F  N     Q   +++LHA  
Sbjct: 261 LPAMSLLEVTIKTGRTHQIRVHLSSQGHPIVGDDKY-GDFDLNRRVQKQGLKRMFLHAWR 319

Query: 295 MDLPHPEGG-RLQITAPLPAHMV 316
           +   HP  G R+++ A LP  + 
Sbjct: 320 LQFNHPASGERVELRAELPPELA 342


>gi|240948340|ref|ZP_04752726.1| 23S rRNA pseudouridylate synthase C [Actinobacillus minor NM305]
 gi|240297379|gb|EER47920.1| 23S rRNA pseudouridylate synthase C [Actinobacillus minor NM305]
          Length = 320

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 103/307 (33%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  + +DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q+  +VR
Sbjct: 11  VQFFTISDDEAGQRLDNFLLTKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQADDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPV------RVAEKNEAPISTKLNKVAE-LEHQILYEDDVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSG+L+VA+ R+  ++L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGLLLVAKKRSVLRNLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   +V+ +E+G   + + F VI+        ++  
Sbjct: 183 VRGQWQSHVKVIKAPLLKNELASGE--RIVRVSEEG-KPSETRF-VIEERYPTATLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGDREFDQKMQQAGLNRLFLHAHSIRFVHPKTGEE 298

Query: 305 LQITAPL 311
           + +TAPL
Sbjct: 299 MVVTAPL 305


>gi|254420499|ref|ZP_05034223.1| RNA pseudouridine synthase family [Brevundimonas sp. BAL3]
 gi|196186676|gb|EDX81652.1| RNA pseudouridine synthase family [Brevundimonas sp. BAL3]
          Length = 241

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 83/231 (35%), Positives = 136/231 (58%), Gaps = 9/231 (3%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++S +++ED+ +  F+KP+G+S QGG   A+ +D  L ++  S G++P L HRLD++TSG
Sbjct: 17  VRSWVIHEDAHVIAFSKPSGLSSQGGRIQAHTLDDLLWAFARSNGKRPELVHRLDRDTSG 76

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHV 215
           +++ A+T+ AA  L ++ +MRR +K Y +L+   P+     I +  L++  IG + Y+ V
Sbjct: 77  VILAAKTKPAAGFLGKALQMRRFRKQYLALLSAAPEPASGTI-DAPLRREEIGRESYMRV 135

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  +  GA  + S ++ +    Q    +E++P TGR HQLRVH  H+G P++GD +Y   
Sbjct: 136 VAFDAPGAQGSQSRYRTLAANDQG-AVVELEPLTGRMHQLRVHMAHLGRPLIGDVRYG-- 192

Query: 276 FKGNFTSPI--QNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
             G  T+ +    +L LHA  +  PHPEGG   + AP PA       +LG 
Sbjct: 193 --GALTTEVGPAPRLMLHALKLSFPHPEGGTTTVEAPPPADFAGLRSALGL 241


>gi|168264021|ref|ZP_02685994.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|205347383|gb|EDZ34014.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
          Length = 319

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 107/310 (34%), Positives = 168/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   +++ G  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEVGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|254245933|ref|ZP_04939254.1| Ribosomal large subunit pseudouridine synthase C [Burkholderia
           cenocepacia PC184]
 gi|124870709|gb|EAY62425.1| Ribosomal large subunit pseudouridine synthase C [Burkholderia
           cenocepacia PC184]
          Length = 341

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 110/340 (32%), Positives = 169/340 (49%), Gaps = 43/340 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + ++ +    R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 24  VSMIEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVR 83

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A   + +    +    N           +LYED  + V +KPAG++V GGSG+A
Sbjct: 84  VPPVRVAAADLARADTPVVPPANFD---------VLYEDDAMLVIDKPAGVAVHGGSGVA 134

Query: 127 YHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           +   G ++     +  +PR     L HRLD+ETSGIL++A+ R A   L E  R  R+ K
Sbjct: 135 F---GVIEQM---RQARPRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDK 188

Query: 182 IY-------WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            Y       W   WG    ++  +   L K S   G+   V  Q++  A++ +  F ++D
Sbjct: 189 RYFACAHGEWQPDWG----RRRAVKAPLFKYSTPEGER-RVRVQDDGLASHTV--FNLVD 241

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKL 288
            +   +  +E +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   ++
Sbjct: 242 RWPD-YVLVEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANAQPSLKRM 299

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
           +LHA  + L HP  G  LQ  APLPA   +  D L    D
Sbjct: 300 FLHAHRLKLAHPLTGEALQFDAPLPAECRRFLDQLSALRD 339


>gi|93005114|ref|YP_579551.1| pseudouridine synthase, RluD [Psychrobacter cryohalolentis K5]
 gi|92392792|gb|ABE74067.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter
           cryohalolentis K5]
          Length = 343

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 106/317 (33%), Positives = 171/317 (53%), Gaps = 31/317 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V Y+ V   + + RLD +  N    +   ++ K++RS ++RV+ KR K ++R+Q   VVR
Sbjct: 38  VNYLEVTRHQHDQRLDNFLLNRLKGLPKPHIYKMIRSDEIRVNNKRCKAHDRVQREDVVR 97

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL---LYEDSKIYVFNKPAGISVQGGS 123
           I PV+ A     +E+ I+         ++F KS+L   +YED  + V NKP+GI+V GGS
Sbjct: 98  IAPVVLA----TREKPIIS--------TEFAKSLLARVVYEDEGLIVLNKPSGIAVHGGS 145

Query: 124 GIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G+A+   G +++  +  G+K   L HR+D++TSG+L++++ R+A + L +    + IQK 
Sbjct: 146 GLAF---GVIEAMREVTGKKYLELVHRIDKDTSGLLMISKKRSALKVLQQHLVDKTIQKH 202

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQK 239
           Y  +  G P   ++ I   LL+ +   G+    V   +     + +   V   F    Q 
Sbjct: 203 YLCIAKGQPALNEQRIDASLLRYTLASGERRVKVDTQDPQTKESQTDIVVHGRFMIAEQP 262

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E +P TGRTHQ+RVH  H+G  I+GD KY  + K        ++L LHA  +D+P 
Sbjct: 263 VSLIEAKPLTGRTHQIRVHLAHIGHAILGDDKYHVHDKSGV-----HRLCLHAWRLDIP- 316

Query: 300 PEGGRLQITAPLPAHMV 316
              G   ITAPLP  M+
Sbjct: 317 ---GYETITAPLPEEML 330


>gi|264677097|ref|YP_003277003.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
 gi|262207609|gb|ACY31707.1| pseudouridine synthase, RluA family [Comamonas testosteroni CNB-2]
          Length = 346

 Score =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 111/323 (34%), Positives = 166/323 (51%), Gaps = 27/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V+ D    RLD +   H   +   ++ +I+RSG+VR++K RV    R+Q G VVR
Sbjct: 34  VRLIEVDEDSAGQRLDNFLMRHLKGVPKTHVYRIIRSGEVRINKGRVSAETRVQPGDVVR 93

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +        K+ + +       DF     L +D  +   +KPAG++V GGSG++
Sbjct: 94  LPPVRIS-------DKVAEKAERPAPAKDFPA---LLDDEHMIALSKPAGVAVHGGSGVS 143

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   ++  D+K  +  L HRLD+ETSGIL+VA+ R+A  +L + FR R   K Y +
Sbjct: 144 FGVIEQLRQARPDAKFLE--LVHRLDRETSGILLVAKKRSALINLQDQFRERETGKTYLA 201

Query: 186 LVWGI-PKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK---- 239
           LV G  P NKK  I   L K     G+  V V   ++     +I+  KV      +    
Sbjct: 202 LVQGAWPANKK-VIDLPLHKYLQADGERRVRVTTADDPDGMRSITLVKVRKLIEPRPLQG 260

Query: 240 ---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARY 294
                 LE+   TGRTHQ+RVH    G PIVGD KY  +F  N     Q   +++LHA  
Sbjct: 261 LPAMSLLEVTIKTGRTHQIRVHLSSQGHPIVGDDKY-GDFDLNRRVQKQGLKRMFLHAWR 319

Query: 295 MDLPHPEGG-RLQITAPLPAHMV 316
           +   HP  G R+++ A LP  + 
Sbjct: 320 LQFNHPASGERVELRAELPPELA 342


>gi|17545760|ref|NP_519162.1| ribosomal large subunit pseudouridine synthase C protein [Ralstonia
           solanacearum GMI1000]
 gi|17428054|emb|CAD14743.1| probable ribosomal large subunit pseudouridine synthase c protein
           [Ralstonia solanacearum GMI1000]
          Length = 331

 Score =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 106/315 (33%), Positives = 171/315 (54%), Gaps = 23/315 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D +  R+D +       +   ++ +ILRSG+VRV+K R+    R+  G +VR
Sbjct: 10  VAYVEIGEDAQGQRIDNFLMRLAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLNLGDLVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      I ++      +      ++F    +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 70  IPPL-----RIAQQSPGQAEAARAVPAAEF---TILHEDTHLLVIDKPAGVAVHGGSGVA 121

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   +S  ++K  +  L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++
Sbjct: 122 FGVIEQLRRSRPEAKFLE--LVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G+  ++++ I   L K S   G+   V  Q +   ++ +  F  +  F   +  LE 
Sbjct: 180 AVKGVWPHQRQHIKAPLFKYSTPEGER-RVRVQADGQPSHTV--FNRVGVFG-PYTLLEA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMDLPH 299
           +  TGRTHQ+RVH  H G PI+GD KY  +F  N        SP   +++LHA  + L H
Sbjct: 236 ELKTGRTHQIRVHLAHAGFPILGDDKY-GDFALNKALSRANASPRLARMFLHAHTLRLTH 294

Query: 300 PEGGRL-QITAPLPA 313
           P+ G +    APLPA
Sbjct: 295 PQSGEIVTFKAPLPA 309


>gi|107022188|ref|YP_620515.1| pseudouridine synthase, RluD [Burkholderia cenocepacia AU 1054]
 gi|116689134|ref|YP_834757.1| RluA family pseudouridine synthase [Burkholderia cenocepacia
           HI2424]
 gi|105892377|gb|ABF75542.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           cenocepacia AU 1054]
 gi|116647223|gb|ABK07864.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           cenocepacia HI2424]
          Length = 334

 Score =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 110/340 (32%), Positives = 169/340 (49%), Gaps = 43/340 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + ++ +    R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 17  VSMIEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVR 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A   + +    +    N           +LYED  + V +KPAG++V GGSG+A
Sbjct: 77  VPPVRVAAADLARADTPVVPPANFD---------VLYEDDAMLVIDKPAGVAVHGGSGVA 127

Query: 127 YHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           +   G ++     +  +PR     L HRLD+ETSGIL++A+ R A   L E  R  R+ K
Sbjct: 128 F---GVIEQM---RQARPRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDK 181

Query: 182 IY-------WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            Y       W   WG    ++  +   L K S   G+   V  Q++  A++ +  F ++D
Sbjct: 182 RYFACAHGEWQPDWG----RRRAVKAPLFKYSTPEGER-RVRVQDDGLASHTV--FNLVD 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKL 288
            +   +  +E +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   ++
Sbjct: 235 RWPD-YVLVEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANAQPSLKRM 292

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
           +LHA  + L HP  G  LQ  APLPA   +  D L    D
Sbjct: 293 FLHAHRLKLAHPLTGEALQFDAPLPAECRRFLDQLSALRD 332


>gi|223041614|ref|ZP_03611813.1| ribosomal large subunit pseudouridine synthase [Actinobacillus
           minor 202]
 gi|223017589|gb|EEF16001.1| ribosomal large subunit pseudouridine synthase [Actinobacillus
           minor 202]
          Length = 320

 Score =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 104/307 (33%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q+  +VR
Sbjct: 11  VQFFSISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQADDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPVR------VAEKNEAPISTKLNKVAE-LEHQILYEDDVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSG+L+VA+ R+A ++L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGLLLVAKKRSALRNLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   +V+ +E+G   + + F VI+        ++  
Sbjct: 183 VRGQWQSHVKVIKAPLLKNELASGE--RIVRVSEEG-KPSETRF-VIEERYPTATLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGDREFDQKMQQAGLNRLFLHAHSIRFVHPKTGEE 298

Query: 305 LQITAPL 311
           + +TAPL
Sbjct: 299 MIVTAPL 305


>gi|145632659|ref|ZP_01788393.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 3655]
 gi|144986854|gb|EDJ93406.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 3655]
          Length = 322

 Score =  154 bits (388), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 103/313 (32%), Positives = 173/313 (55%), Gaps = 14/313 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKSRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+   +V+ +E+G   + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGE--RIVRVSEQG-KPSETRFSIEERYINA-TLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHM 315
             L+  A L   M
Sbjct: 299 ETLRFNASLDHQM 311


>gi|16272361|ref|NP_438574.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae Rd
           KW20]
 gi|260580525|ref|ZP_05848353.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae RdAW]
 gi|1175639|sp|P44433|RLUC_HAEIN RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|1573385|gb|AAC22071.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|260092867|gb|EEW76802.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae RdAW]
          Length = 322

 Score =  154 bits (388), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 103/313 (32%), Positives = 173/313 (55%), Gaps = 14/313 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+   +V+ +E+G   + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQASLLKNELSSGE--RIVRVSEQG-KPSETRFSIEERYINA-TLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHM 315
             L+  A L   M
Sbjct: 299 ETLRFNASLDHQM 311


>gi|254467985|ref|ZP_05081391.1| ribosomal large subunit pseudouridine synthase C [beta
           proteobacterium KB13]
 gi|207086795|gb|EDZ64078.1| ribosomal large subunit pseudouridine synthase C [beta
           proteobacterium KB13]
          Length = 306

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 106/318 (33%), Positives = 179/318 (56%), Gaps = 20/318 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q++ ++   E+ R+D +    +  +   ++ KI+R+G+VRV+KKRVK   +++   VVR
Sbjct: 6   IQHIDIDESSEDQRIDNFLFKTFKDVPKNHIFKIIRNGEVRVNKKRVKTLYKLKINDVVR 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      I K++K         K SD  K  ++YED  + V NKP+G++V GGSGI 
Sbjct: 66  IPPI----EFIEKKEK---------KPSDNFKPHIIYEDEWLLVVNKPSGLAVHGGSGID 112

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++  +  + +   L HR+D+ TSG++V+A+ R+A + + E FR ++I+K Y   
Sbjct: 113 FGLIEHMRH-IKPEYKFLELVHRIDKNTSGVIVIAKKRSALRSMQELFRNKKIKKNYLVA 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +KK+ ++  L KK    G +V+VV+   +G   + S F ++    QK   L  Q
Sbjct: 172 VKGNWDSKKKEVSLRLEKKQTSEGHHVNVVEDPLRG-KLSKSIFYLVKQM-QKQSLLSAQ 229

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHP-EGG 303
             TGRTHQ+RV    +G P++GD KY  +F  N    S    +++LHA  +   HP    
Sbjct: 230 IITGRTHQIRVQLAFLGFPVLGDDKY-GDFALNKKLQSSGLKRMFLHAHKLSFFHPFTEE 288

Query: 304 RLQITAPLPAHMVKTWDS 321
           ++++TA LP  + K +D 
Sbjct: 289 KVELTADLPIELRKFFDE 306


>gi|206559376|ref|YP_002230137.1| ribosomal large subunit pseudouridine synthase C 2 [Burkholderia
           cenocepacia J2315]
 gi|206561222|ref|YP_002231987.1| ribosomal large subunit pseudouridine synthase C 1 [Burkholderia
           cenocepacia J2315]
 gi|198035414|emb|CAR51290.1| ribosomal large subunit pseudouridine synthase C 2 [Burkholderia
           cenocepacia J2315]
 gi|198037264|emb|CAR53186.1| ribosomal large subunit pseudouridine synthase C 1 [Burkholderia
           cenocepacia J2315]
          Length = 334

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 107/335 (31%), Positives = 166/335 (49%), Gaps = 33/335 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + ++ +    R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 17  VSMIEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVR 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A   + +    +    N           +LYED  + V +KPAG++V GGSG+A
Sbjct: 77  VPPVRVAAADLARADTPVVPPANFD---------VLYEDDAMLVIDKPAGVAVHGGSGVA 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--- 183
           + +   ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y   
Sbjct: 128 FGVIEQMRQ-ARPRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFAC 186

Query: 184 ----WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
               W   WG    ++  +   L K S   G+   V  Q +  A++ +  F ++D +   
Sbjct: 187 AHGEWQPDWG----RRRAVKAPLFKYSTPEGER-RVRVQEDGLASHTV--FNLVDRWPN- 238

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHAR 293
           +  +E +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   +++LHA 
Sbjct: 239 YVLVEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANAQPSLKRMFLHAH 297

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
            + L HP  G  LQ  APLPA   +  D L    D
Sbjct: 298 RLKLAHPLTGEALQFDAPLPAECRRFLDQLSALRD 332


>gi|91789509|ref|YP_550461.1| pseudouridine synthase RluD [Polaromonas sp. JS666]
 gi|91698734|gb|ABE45563.1| Pseudouridine synthase, RluD [Polaromonas sp. JS666]
          Length = 378

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 105/335 (31%), Positives = 177/335 (52%), Gaps = 34/335 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+ D    RLD +   H   +   ++ +I+RSG+VR++K R + + R+++G +VR+PP
Sbjct: 31  VTVDEDYAGQRLDNFLIRHLKGVPKTHVYRIIRSGEVRINKGRAQADTRLEAGDIVRLPP 90

Query: 70  VINALNHIIKEQKILD------SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V  +     K Q + +      +S  +  ++   +  +L+ED  +   +KPAG++V GGS
Sbjct: 91  VRTSERADQKAQAMAEEVARHGASSTVGGYAPSREFPVLFEDDFLLAIDKPAGVAVHGGS 150

Query: 124 GIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G+++   G ++    ++ Q     L HRLD+ETSGIL++A+ R A + L E FR R   K
Sbjct: 151 GVSF---GVIEQLRMARPQADFLELVHRLDRETSGILLIAKRRMALKLLQEQFRERETDK 207

Query: 182 IYWSLVWGI-PKNKK---ECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCF 236
           +Y +LV G  P N +   + +  +LL      G+  V VV  +      +++  KV   F
Sbjct: 208 VYLALVSGNWPANHRVIDKALHKYLLPGGAGEGERRVKVVPNDHPDGMRSVTLVKVKSAF 267

Query: 237 A-------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-------- 281
           A         F  LE+   TGRTHQ+RVH  + G PI GD KY  +F+ N +        
Sbjct: 268 AALPAAPGTPFTLLEVTIKTGRTHQIRVHLANEGHPIAGDDKY-GDFELNKSLQKSVAGG 326

Query: 282 SPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           +P++ +++LHA  +   HP+  + + +  PLP  +
Sbjct: 327 APLK-RMFLHAWSLKFNHPKTRKTIHLETPLPDEL 360


>gi|194472684|ref|ZP_03078668.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194459048|gb|EDX47887.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
          Length = 319

 Score =  153 bits (387), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 106/310 (34%), Positives = 168/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH  +   PI  D +Y    F    T       +L+LHA  +   HP  
Sbjct: 235 SPVTGRTHQIRVHTQYASHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|145634591|ref|ZP_01790300.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittAA]
 gi|148825307|ref|YP_001290060.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittEE]
 gi|148827612|ref|YP_001292365.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittGG]
 gi|229846499|ref|ZP_04466607.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae 7P49H1]
 gi|319775660|ref|YP_004138148.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae F3047]
 gi|329122287|ref|ZP_08250875.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           aegyptius ATCC 11116]
 gi|145268136|gb|EDK08131.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittAA]
 gi|148715467|gb|ABQ97677.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae PittEE]
 gi|148718854|gb|ABQ99981.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae PittGG]
 gi|229810592|gb|EEP46310.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae 7P49H1]
 gi|317450251|emb|CBY86467.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae F3047]
 gi|327473848|gb|EGF19265.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           aegyptius ATCC 11116]
          Length = 322

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 103/313 (32%), Positives = 173/313 (55%), Gaps = 14/313 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+   +V+ +E+G   + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGE--RIVRVSEQG-KPSETRFSIEERYINA-TLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHM 315
             L+  A L   M
Sbjct: 299 ETLRFNASLDHQM 311


>gi|291282106|ref|YP_003498924.1| Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O55:H7 str. CB9615]
 gi|290761979|gb|ADD55940.1| Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O55:H7 str. CB9615]
          Length = 319

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 106/310 (34%), Positives = 168/310 (54%), Gaps = 18/310 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEG 302
            P  GRTHQ+RVH  + G PI  D +Y    F    T      N+ +LHA  +   HP  
Sbjct: 235 SPVAGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRPFLHAAALKFTHPGT 294

Query: 303 GR-LQITAPL 311
           G  ++I AP+
Sbjct: 295 GEVMRIEAPM 304


>gi|238897665|ref|YP_002923344.1| 23S rRNA pseudouridylate synthase [Candidatus Hamiltonella defensa
           5AT (Acyrthosiphon pisum)]
 gi|229465422|gb|ACQ67196.1| 23S rRNA pseudouridylate synthase [Candidatus Hamiltonella defensa
           5AT (Acyrthosiphon pisum)]
          Length = 281

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 104/277 (37%), Positives = 161/277 (58%), Gaps = 14/277 (5%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           L +ILR G+VRV+KKR+K   ++ +G ++RIPP+  A   II+ + I   S+   K    
Sbjct: 2   LYRILRKGEVRVNKKRIKPCYKLLTGDMLRIPPIKTA---IIQNKPI---SIKCNKVVAL 55

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
            +SIL +ED  I + NKP+G +V GGSG+++ +   L++    + +   L HRLD+ETSG
Sbjct: 56  AQSIL-FEDPDILILNKPSGTAVHGGSGLSFGVIEALRALRPDQ-RFLHLVHRLDRETSG 113

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           IL+VA+   A + L E  R++ ++K Y +LV G      + I   L K     G+   +V
Sbjct: 114 ILMVAKKPYALRSLNEQLRLKTMKKEYLALVAGDWPLSCKLIQAPLQKNILQNGE--RIV 171

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-AN 275
           K + +G   + +HF++ + F      ++++P TGRTHQ+RVHALH G PIV D +Y    
Sbjct: 172 KVSHQGKE-SQTHFEIEERFTNT-TLMKVRPLTGRTHQIRVHALHAGHPIVFDDRYGDPE 229

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           F+        N+L+LHA  ++  HP  G  +QI APL
Sbjct: 230 FEKKLKGCHLNRLFLHALSLEFVHPHSGETIQIKAPL 266


>gi|260912693|ref|ZP_05919179.1| ribosomal large subunit pseudouridine synthase C [Pasteurella
           dagmatis ATCC 43325]
 gi|260633071|gb|EEX51236.1| ribosomal large subunit pseudouridine synthase C [Pasteurella
           dagmatis ATCC 43325]
          Length = 381

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 101/311 (32%), Positives = 171/311 (54%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  +E   R+D +       +    + +ILR G+VRV+K R+K   ++Q+  +VR
Sbjct: 74  VKMLTISEEEAGQRIDNYLLAKLKGVPKSLIYRILRKGEVRVNKGRIKPEYKLQASDIVR 133

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +     KEQ  + + +N       L++ +L+ED  + V NKP+GI+V GGSG+ 
Sbjct: 134 VPPVRVSE----KEQAPVSTKLNKVNQ---LENQILFEDDCLLVLNKPSGIAVHGGSGLN 186

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A ++L E  R + +QK Y +L
Sbjct: 187 FGVIEALRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRNLHEQLREKTVQKDYLAL 245

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +V+ +E+G     + F + + + +    ++  
Sbjct: 246 VRGQWQSHCKVVKAPLLKNELSSGE--RIVRVSEQGKPSE-TRFSIEERY-ENATLVKAS 301

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F    +     +L+LHA  +   HP+ G  
Sbjct: 302 PVTGRTHQIRVHTQYAGHPIAFDDKYGDKQFDEQMSEIGLKRLFLHAFSIRFEHPKSGET 361

Query: 305 LQITAPLPAHM 315
           L+I APL   M
Sbjct: 362 LRINAPLDDEM 372


>gi|68249014|ref|YP_248126.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae
           86-028NP]
 gi|68057213|gb|AAX87466.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 86-028NP]
          Length = 331

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 103/313 (32%), Positives = 173/313 (55%), Gaps = 14/313 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 20  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 79

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 80  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 132

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 133 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 191

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+   +V+ +E+G   + + F + + +      ++
Sbjct: 192 ALVRGQWQSHIKVIQAPLLKNELSSGE--RIVRVSEQG-KPSETRFSIEERYINA-TLVK 247

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 248 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 307

Query: 304 R-LQITAPLPAHM 315
             L+  A L   M
Sbjct: 308 ETLRFNASLDHQM 320


>gi|170732422|ref|YP_001764369.1| RluA family pseudouridine synthase [Burkholderia cenocepacia MC0-3]
 gi|169815664|gb|ACA90247.1| pseudouridine synthase, RluA family [Burkholderia cenocepacia
           MC0-3]
          Length = 316

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 106/332 (31%), Positives = 166/332 (50%), Gaps = 33/332 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++ +    R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR+PP
Sbjct: 2   IEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A   + +    +    N           +LYED  + V +KPAG++V GGSG+A+ +
Sbjct: 62  VRVAAADLARADTPVVPPANFD---------VLYEDDAMLVIDKPAGVAVHGGSGVAFGV 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY------ 183
              ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y      
Sbjct: 113 IEQMRQ-ARPRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFACAHG 171

Query: 184 -WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            W   WG    ++  +   L K S   G+   V  Q++  A++ +  F ++D +   +  
Sbjct: 172 EWQPDWG----RRRAVKAPLFKYSTPEGER-RVRVQDDGLASHTV--FNLVDRWPD-YVL 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMD 296
           +E +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   +++LHA  + 
Sbjct: 224 VEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANAQPSLKRMFLHAHRLK 282

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
           L HP  G  LQ  APLPA   +  D L    D
Sbjct: 283 LAHPLTGEALQFDAPLPAECRRFLDQLSALRD 314


>gi|301169114|emb|CBW28711.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae 10810]
          Length = 322

 Score =  153 bits (386), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 103/313 (32%), Positives = 173/313 (55%), Gaps = 14/313 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDETGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+   +V+ +E+G   + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGE--RIVRVSEQG-KPSETRFSIEERYINA-TLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHM 315
             L+  A L   M
Sbjct: 299 ETLRFNASLDHQM 311


>gi|58617049|ref|YP_196248.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Gardel]
 gi|58416661|emb|CAI27774.1| Ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Gardel]
          Length = 305

 Score =  152 bits (385), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 97/314 (30%), Positives = 162/314 (51%), Gaps = 28/314 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +Y  ++ D   +R+DR+ +     I    ++K LR+  + +D  +VK N ++  G V+ +
Sbjct: 3   KYYTIQEDNLGVRIDRFIRKEL-RIPQSLIEKFLRNRIILLDGLKVKSNTKLNVGNVIYV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSG 124
                  N  I  ++  D  V        ++ I   ++YED  + V NKP+G+SVQGGS 
Sbjct: 62  Q------NECIISKEKKDKKVCKLASESLVRLICDNIVYEDDNVLVINKPSGVSVQGGSK 115

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   I   L S     G+  ++ HRLD+ TSGIL++AR    ++ +   F+ R+++K Y 
Sbjct: 116 VKISISDVLDSI--RIGESMKIVHRLDKSTSGILMLARNSRVSRLIMNEFKDRKVKKKYL 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L  GIP +    I   ++KK H        +++N      A++ F  +         L+
Sbjct: 174 ALTCGIPDDDCGQIDYPIVKKKH-----GITLEKNMSFVQQAVTMFSTLRKLPNDIGLLD 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +QP TGR HQ+R+H  H+GCPIVGD KY   C N   N+       L LHA ++ + + +
Sbjct: 229 LQPITGRKHQIRIHLSHIGCPIVGDVKYGKICDNISNNY-------LQLHAYFLSI-NID 280

Query: 302 GGRLQITAPLPAHM 315
           G  + IT P+P++M
Sbjct: 281 GKEISITIPMPSYM 294


>gi|226951907|ref|ZP_03822371.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ATCC 27244]
 gi|294649166|ref|ZP_06726607.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           haemolyticus ATCC 19194]
 gi|226837447|gb|EEH69830.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ATCC 27244]
 gi|292824964|gb|EFF83726.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           haemolyticus ATCC 19194]
          Length = 310

 Score =  152 bits (385), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 102/319 (31%), Positives = 171/319 (53%), Gaps = 25/319 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  ++  R+D +       +    + +++R GQVRV+KKR+K   R+Q G  +R
Sbjct: 10  VTWFDVDEHQDGQRIDNFLFTRLKGVPKSRIYRLIREGQVRVNKKRIKAETRLQIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAAPVSDSVAQSLLSRVVYEDEGLLVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           Y   G +++   + G+K   L HR+D++TSG++++++ R+  + L +  R  +IQK Y +
Sbjct: 123 Y---GLIEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDLLREHKIQKTYAA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +V G     K+ I   LL+     G+  V V K+ +       + +KV + F +    + 
Sbjct: 180 IVKGQVSLDKQLIDAPLLRYELANGERRVRVTKEGKPSK----TEWKVAERF-KTATLVH 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGG 303
             P +GRTHQ+RVH L +G P++GD KY  N    ++ P   +L LHA  +++P +P   
Sbjct: 235 ASPLSGRTHQIRVHGLSIGHPLIGDDKYGHNTA--YSGPEARRLCLHAMRLEIPNYP--- 289

Query: 304 RLQITAPLPAHMVKTWDSL 322
              I AP+P  M +  D L
Sbjct: 290 --TIEAPMPEDMQQLIDEL 306


>gi|288940468|ref|YP_003442708.1| RluA family pseudouridine synthase [Allochromatium vinosum DSM 180]
 gi|288895840|gb|ADC61676.1| pseudouridine synthase, RluA family [Allochromatium vinosum DSM
           180]
          Length = 346

 Score =  152 bits (385), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 106/326 (32%), Positives = 174/326 (53%), Gaps = 29/326 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           QYV V+   +  R+D +       +   +L ++LR G+VRV+K RVK   R+ +G VVRI
Sbjct: 37  QYVQVDTQADGQRIDNFLLRILKGVPRSHLYRLLRRGEVRVNKGRVKAEYRLCAGDVVRI 96

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP+   L       +  ++ +        L+  +++ED ++ V +KP+G++V GGSG++Y
Sbjct: 97  PPI--RLGESAPPARAPEAQLA------RLEGAIIHEDERLLVIDKPSGLAVHGGSGLSY 148

Query: 128 HIDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
              G ++S    + G++  L HRLD++TSG LVV + R+A + L    R   + K Y +L
Sbjct: 149 ---GLIESLRQLRPGRELELVHRLDRDTSGCLVVCKRRSALRELHALIREGGLDKRYLAL 205

Query: 187 VWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCW 242
           + G +P  + E + +  LKK+ +      +V+ + +G   A + F+ +  FA   Q    
Sbjct: 206 ILGELP--RAELLVDAPLKKNVLSSGE-RLVRVDAQGGKEARTRFRRLKRFAIDGQALTL 262

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CAN--FKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVHA H+G P+ GD KY    AN   KG        +L+LHA  +  
Sbjct: 263 VEAELITGRTHQIRVHAAHLGTPLAGDDKYGDEAANQRLKGYGL----KRLFLHASALSF 318

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
                 R L++  PLP  + +  D+L
Sbjct: 319 KLECMARPLRLECPLPDELQQVLDAL 344


>gi|323261040|gb|EGA44633.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
          Length = 295

 Score =  152 bits (385), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 102/293 (34%), Positives = 161/293 (54%), Gaps = 15/293 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDL 297
            P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  + L
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLADTGLNRLFLHAAALKL 287


>gi|300691996|ref|YP_003752991.1| ribosomal large subunit pseudouridine synthase C [Ralstonia
           solanacearum PSI07]
 gi|299079056|emb|CBJ51718.1| Ribosomal large subunit pseudouridine synthase C [Ralstonia
           solanacearum PSI07]
          Length = 346

 Score =  152 bits (385), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 104/316 (32%), Positives = 170/316 (53%), Gaps = 25/316 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D +  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 25  VAYVEIGEDAQGQRIDNFLMRLAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 84

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      I ++      +      ++F    +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 85  IPPL-----RIAQQSAQQAEAARAVPAAEF---TILHEDTHLLVIDKPAGVAVHGGSGVA 136

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    S+ +     L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y+
Sbjct: 137 F---GVIEQLRQSRPEAKFLELVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYF 193

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           + V G+  ++++ I   L K +   G+   V  Q +   ++ +  F  +  F   +  LE
Sbjct: 194 AAVKGLWPHQRQHIKAPLFKYTTPEGER-RVRVQADGQPSHTV--FNKVGVFG-PYTLLE 249

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMDLP 298
            +  TGRTHQ+RVH  H G PI+GD KY  +F  N        SP   +++LHA  + L 
Sbjct: 250 AELKTGRTHQIRVHLAHAGFPILGDDKY-GDFALNKALSRANASPRLARMFLHAHTLRLT 308

Query: 299 HPEGGRL-QITAPLPA 313
           HP+ G +    APLPA
Sbjct: 309 HPQSGEIVTFKAPLPA 324


>gi|74317581|ref|YP_315321.1| ribosomal large subunit pseudouridine synthase C [Thiobacillus
           denitrificans ATCC 25259]
 gi|74057076|gb|AAZ97516.1| pseudouridine synthase, RluD [Thiobacillus denitrificans ATCC
           25259]
          Length = 322

 Score =  152 bits (384), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 104/319 (32%), Positives = 167/319 (52%), Gaps = 16/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + ++   ++ RLD +       +    + K++R G+VR++  RV    R++ G  VR
Sbjct: 11  VRRLKIDEGADDQRLDNYLMARLKGVPKSRIYKLVRGGEVRINGGRVDVGYRLKVGDEVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A         ++  + +L +    L  ++LY D  +   NKPAG++V GGSGI+
Sbjct: 71  IPPVRMA-------APVITPATHLPQGGLRLLPLILYRDDALIALNKPAGMAVHGGSGIS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L+  +  + +   L HRLD+ETSG+L+VA  R A   L  + R  +I+K Y +L
Sbjct: 124 RGVIEQLRLEL-PECRYMELVHRLDRETSGVLLVALKRRALVGLHAAMRDGKIEKRYLTL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   N  + +   L K+    G+    V+   + A+   + F+ +  +A+ F  LE +
Sbjct: 183 VAGRWPNPLQHVKLPLHKRVTEEGEKRVTVRDTGQTAH---TIFRRLRGYAE-FTLLEAE 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHP-EGG 303
             TGRTHQ+RVH  H+G PI GD KY  +F+ N         +++LHA  +   HP  G 
Sbjct: 239 LKTGRTHQIRVHTSHLGFPIAGDDKY-GDFELNKRLAKRGLKRMFLHAAKLAFAHPISGE 297

Query: 304 RLQITAPLPAHMVKTWDSL 322
           R+ I APLPA +    D+L
Sbjct: 298 RMTIEAPLPADLATFLDTL 316


>gi|295677198|ref|YP_003605722.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1002]
 gi|295437041|gb|ADG16211.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1002]
          Length = 349

 Score =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 108/324 (33%), Positives = 169/324 (52%), Gaps = 40/324 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 25  VSLIEIDDRSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVR 84

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGI 125
           +PP+           ++  S+              +L+ED  + V +KPAG++V GGSG+
Sbjct: 85  VPPI-----------RVAQSNQAAAHVPVPAAGFQILFEDEHLLVIDKPAGVAVHGGSGV 133

Query: 126 AYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           A+   G ++   +++ Q     L HRLD+ETSGIL++A+ RAA  +L E  R  R+ K Y
Sbjct: 134 AF---GVIEQMREARPQAKFLELVHRLDRETSGILMLAKKRAALVNLHEQIRDNRMDKRY 190

Query: 184 WSLV-------WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           ++ V       WG  +  KE +  +L      G   V V  Q +  A++ I  F ++D +
Sbjct: 191 YACVHGEWASDWGRRRAVKEPLHKYLTSD---GERRVRV--QTDGLASHTI--FNLVDRW 243

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYL 290
              +  LE +  TGRTHQ+RVH  H+G PIVGD KY  +F  N         P   +++L
Sbjct: 244 PD-YALLEAELKTGRTHQIRVHLQHLGLPIVGDAKY-GDFALNKALARANAKPGIKRMFL 301

Query: 291 HARYMDLPHPE-GGRLQITAPLPA 313
           HA  + L HP  G  LQ+ APLPA
Sbjct: 302 HAYRLKLTHPATGAPLQLEAPLPA 325


>gi|269958889|ref|YP_003328678.1| ribosomal large subunit pseudouridine synthase C [Anaplasma
           centrale str. Israel]
 gi|269848720|gb|ACZ49364.1| ribosomal large subunit pseudouridine synthase C [Anaplasma
           centrale str. Israel]
          Length = 299

 Score =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 100/314 (31%), Positives = 165/314 (52%), Gaps = 25/314 (7%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +VE     +R+DR+ +   P +    ++++LR G++ ++  +V+ + R+ +G V+ I   
Sbjct: 6   LVEEACFGVRVDRYLRGLLPGVTQSFIERLLRRGEILLNNTKVRSSARVSNGDVLSIK-- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            +A   +++E++I    +      D + + +LYED  +   NKPAG+SVQGGS +   I 
Sbjct: 64  -HADRIVMREKEI--RRLQHVPLLDLISNNILYEDQNVIAINKPAGVSVQGGSKVGVSIG 120

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L       G   R+ HRLD++TSG+LV+AR    A+ L   FR RR+QK Y ++  G+
Sbjct: 121 DLLDKI--RPGGCCRIVHRLDKDTSGVLVLARDLDVARCLAREFRERRVQKEYIAITKGV 178

Query: 191 PKNKK-ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           P +   E       K     G+     +  EK A    S  +V+  FA     + ++P T
Sbjct: 179 PHSASGEVNTPIFYKVQSATGE-----RMLEKDAKTFFSVTRVLGNFA----VVLLRPVT 229

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHPEGGRLQIT 308
           GR HQLR+H   +GCPIVGD KYC         P++ + L+LHA  +      G +L I+
Sbjct: 230 GRKHQLRIHMSQIGCPIVGDSKYCK------CGPVEKETLHLHASLLTF-ELMGRKLSIS 282

Query: 309 APLPAHMVKTWDSL 322
           A +P +M +  ++L
Sbjct: 283 AGMPGYMEEKINTL 296


>gi|87118928|ref|ZP_01074826.1| ribosomal large subunit pseudouridine synthase C [Marinomonas sp.
           MED121]
 gi|86165319|gb|EAQ66586.1| ribosomal large subunit pseudouridine synthase C [Marinomonas sp.
           MED121]
          Length = 322

 Score =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 94/293 (32%), Positives = 169/293 (57%), Gaps = 15/293 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   ++ +  + R+D +       +    +  +LR G++RV+KKRVK + RI SG +VR
Sbjct: 14  VKINTIDENNHDQRIDNYLMAQLKGVPKGRIYNLLRKGEIRVNKKRVKPDTRIYSGDIVR 73

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I P++      ++  K  ++S    K    ++S ++YED+ + V NKP+G++V GGSG+ 
Sbjct: 74  IAPIV------VEPPK--EASPVPHKLMQLIESRIVYEDAGLMVVNKPSGLAVHGGSGLN 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWS 185
           + +   ++  + SK +   L HRLD++TSG++++++ R+  + L  + R +  +QK Y +
Sbjct: 126 FGLVEVVRQ-LRSKEKSIELVHRLDRDTSGLIMISKKRSVLKQLHAALREKEGVQKTYQA 184

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV+G    +K+ +   LLK     G+   +VK + +G   +++ FK++  F + +  +E 
Sbjct: 185 LVYGSWPKRKQQVNAPLLKNELKSGE--RIVKVHTEGKE-SLTRFKLLRQF-EGYSLVEC 240

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDL 297
           +P TGRTHQ+RVH LH G PIVGD KY  + +      +   +L LHA  +D+
Sbjct: 241 EPVTGRTHQIRVHTLHAGYPIVGDDKYSPSEQNKEAKGLGFKRLCLHAAKLDI 293


>gi|126668127|ref|ZP_01739089.1| ribosomal large subunit pseudouridine synthase C [Marinobacter sp.
           ELB17]
 gi|126627397|gb|EAZ98032.1| ribosomal large subunit pseudouridine synthase C [Marinobacter sp.
           ELB17]
          Length = 331

 Score =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 102/330 (30%), Positives = 180/330 (54%), Gaps = 21/330 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +V V+ D +  RLD +       +    + +I+R G+VR++K RVK + R+++G  VR
Sbjct: 15  VLWVTVDEDNDGQRLDNFLMAQLRGVPKSIIYRIVRKGEVRINKGRVKPDTRVKTGDQVR 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       ++++K+  ++    +    +++ +++E+ ++ V NKP+GI+V GGSG++
Sbjct: 75  IPPV-------VRKEKVPQAAPG-DRVQAVIEAAVVFENEQLLVVNKPSGIAVHGGSGLS 126

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++    + +   L HRLD++TSG+++VA+ R+A ++L +  R R I+K Y +L
Sbjct: 127 FGLIEVLRAG-RPQARFLELVHRLDRDTSGLVMVAKKRSALRYLQDELRHRHIRKHYHAL 185

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        +A  LL+     G+    VK +  G   +++ F+ ++ +   +  +E  
Sbjct: 186 VSGDWPAGMGKVAQPLLRYEMPNGE--RRVKVDSSGKE-SLTLFRCLERY-DGYSLVEAS 241

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHP---- 300
           P TGRTHQ+RVHA   G PI GD KY   A+ K  F +   ++L LHAR ++L  P    
Sbjct: 242 PVTGRTHQIRVHATFAGHPIAGDDKYMDDASLKA-FRALGGSRLMLHARALELSLPPDSD 300

Query: 301 -EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
            +   L++ AP           L  +  RN
Sbjct: 301 GQSPALKLEAPYDNAFAAALQKLAARTGRN 330


>gi|329894956|ref|ZP_08270755.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC3088]
 gi|328922685|gb|EGG30020.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC3088]
          Length = 321

 Score =  152 bits (384), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 95/307 (30%), Positives = 164/307 (53%), Gaps = 15/307 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +V Y  ++ DE   RLD +    +  +    + K +R G+VRV+K R     ++  G  +
Sbjct: 12  HVVYHQIDADEAGQRLDNFLLRWFAQVPKSRVYKAIRGGEVRVNKGRANAMYKLLEGDDI 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKH-SDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           RIPP        + E+ +      + KH  D ++  +LYED+   + NKP+G++V GGSG
Sbjct: 72  RIPP--------LGERALQMEGALVAKHWLDSVERGVLYEDADFMIINKPSGLAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + Y +   L+  +  + ++  L HRLD++TSG +++A+  +A +HL    R R++ K Y 
Sbjct: 124 LKYGLIEVLRQ-LRPEARRLELVHRLDRDTSGCIMIAKKNSALRHLHALLRDRKLTKRYH 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV+G     +  +   L K +   G+   +V+ NE+G   A + F  ++ +      +E
Sbjct: 183 ALVFGKWPRAQRLVDAPLKKFALASGE--RIVRVNEEGQK-AKTEFATLNRYP-GLTLVE 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVHA H+G  ++GD KY         + +   +L+LHA  ++L  P G 
Sbjct: 239 AKPITGRTHQIRVHAAHLGHCLLGDDKYAHEAAQELAASVGLKRLFLHAASLELVAPSGK 298

Query: 304 RLQITAP 310
            L ++AP
Sbjct: 299 SLTVSAP 305


>gi|332306496|ref|YP_004434347.1| pseudouridine synthase, RluA family [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332173825|gb|AEE23079.1| pseudouridine synthase, RluA family [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 318

 Score =  152 bits (383), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 107/322 (33%), Positives = 174/322 (54%), Gaps = 23/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ +E D E  R+D + +     +    + +I+R G++RV+KKRVK   ++Q+   +R
Sbjct: 10  VQFIEIEPDLEGQRIDNFLRTLLKGVPKSLIYRIVRKGEIRVNKKRVKPEYKLQAHDQLR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  +  +     K LD   +L  H       +L+ED  + V NKP+G++V GGSG++
Sbjct: 70  IPPIRVSEPNAAPSTK-LDKVASLESH-------ILFEDDLLIVLNKPSGMAVHGGSGLS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG LV+A+ R+A ++L E  R +++ K Y +L
Sbjct: 122 FGVIEALRA-LRPQARFLELVHRLDRDTSGCLVIAKKRSALKNLHEQLRDKKMDKRYHAL 180

Query: 187 VWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G  P+N+ +  A  LLK     G+ +  V    K +    + F+V++ +      +E 
Sbjct: 181 VVGEWPENRYKVNAP-LLKNILKSGERLVSVDSEGKPSE---TRFRVLERYVGA-TLVEA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK----LYLHARYMDLPHPE 301
            P TGRTHQ+RVH LH   PI  D KY     G FT  +  K    L+LHA  +   HP+
Sbjct: 236 SPITGRTHQIRVHCLHAVHPIACDDKYG---DGEFTELMNKKGLKRLFLHAYSLAFIHPK 292

Query: 302 G-GRLQITAPLPAHMVKTWDSL 322
              R+   APL   + K   +L
Sbjct: 293 TEERVSFQAPLDQQLNKALSAL 314


>gi|291614218|ref|YP_003524375.1| pseudouridine synthase, RluA family [Sideroxydans lithotrophicus
           ES-1]
 gi|291584330|gb|ADE11988.1| pseudouridine synthase, RluA family [Sideroxydans lithotrophicus
           ES-1]
          Length = 312

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 110/312 (35%), Positives = 167/312 (53%), Gaps = 23/312 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ ++   E  R+D +   H   +   ++ +ILR G+VRV+KKRV    R+Q G ++R
Sbjct: 9   VSWLEIDEGSEGQRIDNFLFRHLKGVPKSHVYRILR-GEVRVNKKRVDQTYRLQLGDILR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A       +K     V  T+        +LYED  +   NKP+G +V GGSG++
Sbjct: 68  IPPIRVA-------EKPESEYVPATEFP------ILYEDEALLAINKPSGTAVHGGSGVS 114

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+S    + +   L HRLD+ETSG+L+VA+ R+A   L E  R     K Y++L
Sbjct: 115 FGVIEQLRS-ARPQAKLLELVHRLDRETSGVLLVAKKRSALTGLHEIMREGNSDKRYFAL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  KN K+ +   L K     G+   +V+++ + A++ I  F +   + + F  LE Q
Sbjct: 174 VLGQWKNAKQHVKLPLHKFDTPQGEKRVMVREDGQ-ASHTI--FTLQQSWPE-FTLLEAQ 229

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGGR 304
             TGRTHQ+RVH  H+G PI GD KY  +F  N         +++LHA  +   HP  G 
Sbjct: 230 LKTGRTHQIRVHLSHLGFPIAGDDKY-GDFARNKELAKRGLKRMFLHAHSIAFNHPLTGE 288

Query: 305 -LQITAPLPAHM 315
            L ITAPLP  +
Sbjct: 289 PLSITAPLPPEL 300


>gi|71064834|ref|YP_263561.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter
           arcticus 273-4]
 gi|71037819|gb|AAZ18127.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter
           arcticus 273-4]
          Length = 338

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 105/317 (33%), Positives = 171/317 (53%), Gaps = 31/317 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V Y+ V   + + RLD +  N    +   ++ K++RS ++RV+ KR K ++R+Q   VVR
Sbjct: 33  VNYLEVTRHQHDQRLDNFLLNRLKGLPKPHIYKMIRSDEIRVNNKRCKAHDRVQREDVVR 92

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL---LYEDSKIYVFNKPAGISVQGGS 123
           I PV+ A     +E+ I+         ++F KS+L   +YED  + V NKP+GI+V GGS
Sbjct: 93  IAPVVLA----TREKPIIS--------TEFAKSLLARVVYEDEGLIVLNKPSGIAVHGGS 140

Query: 124 GIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G+ +   G +++  +  G+K   L HR+D++TSG+L++++ R+A + L +    + IQK 
Sbjct: 141 GLDF---GVIEAMREVTGKKYLELVHRIDKDTSGLLMISKKRSALKVLQQHLVDKTIQKH 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QK 239
           Y  +  G P   ++ I   LL+ +   G+    V   +     + +   V   F    Q 
Sbjct: 198 YLCIAKGQPALNEQRIDAPLLRYTLASGERRVKVDAQDPQTKESQTDIVVHGRFTIAEQP 257

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E +P TGRTHQ+RVH  H+G  I+GD+KY  + K        ++L LHA  +D+P 
Sbjct: 258 VSLIEAKPLTGRTHQIRVHLAHIGHAILGDNKYHVHDKSGV-----HRLCLHAWRLDIP- 311

Query: 300 PEGGRLQITAPLPAHMV 316
              G   ITAPLP  M+
Sbjct: 312 ---GYDTITAPLPDEML 325


>gi|302382659|ref|YP_003818482.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
 gi|302193287|gb|ADL00859.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
          Length = 248

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 86/232 (37%), Positives = 136/232 (58%), Gaps = 8/232 (3%)

Query: 84  LDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           L + V+LT+     ++S +++ED+ +  F KPAG+S QGG   A+ +D  L ++  S G+
Sbjct: 3   LRTPVSLTEDEIAAVRSWVIHEDASVIAFAKPAGLSSQGGRIQAHTLDDLLWAFARSNGK 62

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +P L HRLD++TSG+++ A+T+ AA  L ++ +  R+ K Y +LV   P+  +  I N  
Sbjct: 63  RPELVHRLDRDTSGVILAAKTKPAASFLGKAIQAHRLTKTYLALVSAAPEPPQGDI-NVP 121

Query: 203 LKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L +  IG + Y+ V   + KGA  + S ++ +   +     +E+QP TGR HQLRVH  H
Sbjct: 122 LVRQEIGRESYMRVAAFDTKGAQGSRSRYRTL-ASSDDGALVELQPFTGRMHQLRVHMAH 180

Query: 262 MGCPIVGDHKYCANF-KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           +G P++GD +Y      G   +P   +L LHA  +  PHPEGG   +TA LP
Sbjct: 181 IGRPLIGDVRYGGALTAGGRAAP---RLMLHAVSLTFPHPEGGERTVTAGLP 229


>gi|262374097|ref|ZP_06067374.1| 23S rRNA pseudouridylate synthase [Acinetobacter junii SH205]
 gi|262311108|gb|EEY92195.1| 23S rRNA pseudouridylate synthase [Acinetobacter junii SH205]
          Length = 310

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 102/319 (31%), Positives = 170/319 (53%), Gaps = 25/319 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +E  R+D +       +    + +++R GQVRV+KKR+K   R+  G  +R
Sbjct: 10  VTWFDVDEHQEGQRIDNFLFTRLKGVPKSRIYRLIREGQVRVNKKRIKAETRLSIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK    +      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETDAPVSDGVAQSLLSRVVYEDEGLLVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           Y   G +++   + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y +
Sbjct: 123 Y---GLIEAMRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDLLREHKIKKTYAA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +V G     ++ I   LL+     G+  V V K+ +       + +KVI+ F +    + 
Sbjct: 180 IVKGQVSLDQQLIDAPLLRYELANGERRVRVTKEGKPSK----TEWKVIERF-KAATLVH 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGG 303
             P +GRTHQ+RVH L +G P++GD KY  N    +T P   +L LHA  +D+P +P   
Sbjct: 235 ASPLSGRTHQIRVHGLSIGHPLIGDDKYGHNTA--YTGPEARRLCLHAMRLDIPNYP--- 289

Query: 304 RLQITAPLPAHMVKTWDSL 322
              I AP+P  M +  + L
Sbjct: 290 --TIEAPMPEDMQQVINEL 306


>gi|118594941|ref|ZP_01552288.1| Pseudouridine synthase, RluD [Methylophilales bacterium HTCC2181]
 gi|118440719|gb|EAV47346.1| Pseudouridine synthase, RluD [Methylophilales bacterium HTCC2181]
          Length = 324

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 108/322 (33%), Positives = 174/322 (54%), Gaps = 25/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+Y ++    E  ++D +      ++   ++ K+LRSGQVRV+KKR+K + R+  G  VR
Sbjct: 9   VRYELIGEGSEGQKIDNFLIKTLKNVPKSHIYKLLRSGQVRVNKKRIKTDFRLSLGDSVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP  +  + +     I      L + S      +++ED  + V NKP G++V GGSGI+
Sbjct: 69  IPPFTSPKSEVKTPISIKPEQALLIEKS------IIHEDDALIVINKPCGLAVHGGSGIS 122

Query: 127 YHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           Y +   L KS  D++  +  L HR+D+ETSGI+++A+ R     + +  R + I K Y  
Sbjct: 123 YGLIELLRKSRPDARFLE--LVHRIDKETSGIILIAKKRPVLVDIHKQMRDKSIHKKYQV 180

Query: 186 LVWGIPKNKKECIANWLLKKS-HIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCW 242
           +V G  + K+  +   L+K S   G   V V+ Q +   G+  + S F +   F Q F  
Sbjct: 181 IVNGKWQKKQLIVDLNLIKTSDEEGQKKVRVISQEDVVGGSKVSRSVFFLKQAFDQ-FSC 239

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------KLYLHARYMD 296
           LE++  TGRTHQ+RVH  H+G  IVGD KY     G+F+   ++      +++LHA  + 
Sbjct: 240 LEVKLVTGRTHQIRVHLSHLGFSIVGDDKY-----GDFSLNKRHAKLGFKRMFLHACELG 294

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
             HP  G  + +TAP+P+  +K
Sbjct: 295 FRHPLSGEDIFLTAPIPSDFIK 316


>gi|332184772|gb|AEE27026.1| Ribosomal large subunit pseudouridine synthase [Francisella cf.
           novicida 3523]
          Length = 307

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 103/316 (32%), Positives = 171/316 (54%), Gaps = 13/316 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V +D  + R+D +  + +  +    + + +R G++RV+KKRVK  +RI +G 
Sbjct: 1   MNKVELIEVPDDVIDQRIDNFLLSRFSCLPKSLIYRWIRKGELRVNKKRVKQTSRISAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           GI   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GINSGLVERLRQ-LRPKARRLDLVHRLDKETSGCVILAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G   +KK    +  LK++    D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHG-HWDKKIITIDLPLKRTETK-DGQRVVKVDSKDGKRALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDL-PHPE 301
           E++  TGRTHQ+RVH   MG PIV D KY  N K  +      +KL LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFNTKDQSLLEKGVDKLLLHAGKLEFYDEKQ 289

Query: 302 GGRLQITAPLPAHMVK 317
             ++ +TA L +   K
Sbjct: 290 NKQISVTAALDSRFEK 305


>gi|171057282|ref|YP_001789631.1| RluA family pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170774727|gb|ACB32866.1| pseudouridine synthase, RluA family [Leptothrix cholodnii SP-6]
          Length = 322

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 109/328 (33%), Positives = 165/328 (50%), Gaps = 28/328 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++  V+      RLD +            + +I+RSG+VRV+K R   + R+  G  VR
Sbjct: 11  VRHFQVDEAGAGQRLDNFLMRELKGAPKTLVYRIIRSGEVRVNKGRAGADTRLAIGDDVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP        ++  +  D + +     +F    +L ED  +    KPAG++V GGSG++
Sbjct: 71  VPP--------LRLSERPDPAESTVPPREF---PILLEDEHLLAIAKPAGVAVHGGSGVS 119

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    ++ Q     L HRLD+ETSGIL+VA+ R+A   L + FR R   K Y 
Sbjct: 120 F---GVIEQLRRARPQARFLELVHRLDKETSGILLVAKKRSALTALQDQFRQRDTGKTYA 176

Query: 185 SLVWGI-PKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           +LV G  P+NKK  I   L K +  GG+  V  V  +      +IS  +V+  F   +  
Sbjct: 177 ALVIGDWPENKK-VIDVALHKYTDAGGERRVRAVAADHPDGRRSISLVQVLKRF-DGYTL 234

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQ-NKLYLHARYM 295
           L++   TGRTHQ+RVH    G PIVGD KY       A  +G   +  +  +++LHAR +
Sbjct: 235 LDVTIKTGRTHQIRVHLQQAGHPIVGDDKYGDFALNKAMARGEAVAGCRFERMFLHARRL 294

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSL 322
              HP  G R+++ A LPA      DS 
Sbjct: 295 AFDHPASGERIELEAALPAECATLLDSF 322


>gi|152996325|ref|YP_001341160.1| RluA family pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150837249|gb|ABR71225.1| pseudouridine synthase, RluA family [Marinomonas sp. MWYL1]
          Length = 323

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 103/323 (31%), Positives = 170/323 (52%), Gaps = 30/323 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+YV ++++    R+D +       +    +  +LR G++RV+KKR K + R+Q+  VVR
Sbjct: 14  VRYVTIDDNNTGQRIDNFLVTFLKGVPKGKIYNLLRKGEIRVNKKRTKPDYRLQNEDVVR 73

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I P++ A           D  V   +    ++S ++YED  + V NKP+G++V GGSG++
Sbjct: 74  IAPIVIAPES--------DKPVLSDRLKSEIESRIVYEDKGLIVINKPSGLAVHGGSGLS 125

Query: 127 YHIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQ 180
           + +   ++        +P      L HRLD++TSG+++VA+ RA  + L  + R +  +Q
Sbjct: 126 FGLVEVIRQM------RPLEKFIELVHRLDRDTSGLIMVAKKRAVLKELHTALREKEGVQ 179

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV+G    +K  +   LLK     G+ V  V  + K    +++ FK++  F + +
Sbjct: 180 KTYLALVYGSWPKRKLQVNAPLLKNELQSGERVVRVHTDGK---ESLTRFKLVRQF-EGY 235

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             +E +P TGRTHQ+RVH  + G PIVGD KY        T  +   +L LHA  +D+  
Sbjct: 236 SLVECEPVTGRTHQIRVHTQYAGYPIVGDEKYSPAESLKETRALGFKRLCLHATRLDI-M 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSL 322
             G R+   APL     K W +L
Sbjct: 295 LNGERMLFEAPLD----KEWQTL 313


>gi|167586609|ref|ZP_02378997.1| pseudouridine synthase, RluA family protein [Burkholderia ubonensis
           Bu]
          Length = 334

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 110/332 (33%), Positives = 170/332 (51%), Gaps = 27/332 (8%)

Query: 8   QYVVVENDE--ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Q  +VE DE     R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +V
Sbjct: 16  QVSMVEIDETAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAHGDIV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + +     D+ V    H D     +L+ED  + V +KPAG++V GGSG+
Sbjct: 76  RVPPVRMAAADLARA----DTPVVPPAHFD-----VLFEDDAMLVIDKPAGVAVHGGSGV 126

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   L+     + +   L HRLD+ETSG+L++A+ RAA   L E  R  R+ K Y++
Sbjct: 127 AFGVIEQLRQ-ARPRAKFLELVHRLDRETSGVLMLAKKRAALVGLHEMIRENRMDKRYFA 185

Query: 186 LV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V   W     ++  +   L K +   G+   V  Q++   ++ +  F +++ +   +  
Sbjct: 186 CVHGEWQSDWGRRRAVKAPLFKYTTPEGER-RVRVQDDGLPSHTV--FNLVERWPD-YAL 241

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMD 296
           +E +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   +++LHA  + 
Sbjct: 242 VEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALSRANAQPSLKRMFLHAHRLR 300

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
           L HP  G  LQ  APLP    +  D L    D
Sbjct: 301 LAHPLTGEALQFDAPLPDECRRFLDQLSALRD 332


>gi|319792202|ref|YP_004153842.1| pseudouridine synthase, rlua family [Variovorax paradoxus EPS]
 gi|315594665|gb|ADU35731.1| pseudouridine synthase, RluA family [Variovorax paradoxus EPS]
          Length = 365

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 108/327 (33%), Positives = 169/327 (51%), Gaps = 33/327 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ V+ +    RLD +   H   +   ++ +I+RSG+VR++K RV+   RI+ G V+R
Sbjct: 32  IKFITVDAESAGQRLDNFLFRHLKGVPKTHVYRIIRSGEVRINKGRVQAETRIEVGDVLR 91

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +        +  + + +     +F    +L ED  +   +KPAG++V GGSG++
Sbjct: 92  LPPVRIS-------PRAEEGATSPAPAREF---PVLLEDDAVLAIDKPAGVAVHGGSGVS 141

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + +   L++     G K   L HRLD+ETSGIL+VA+ R+A   L + FR R   K Y +
Sbjct: 142 FGVIEQLRTA--RPGAKFLELVHRLDRETSGILLVAKKRSALVALQDQFRERETGKTYLA 199

Query: 186 LVWGI-PKNKK---ECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVIDCF-- 236
           LV G  P NKK     +A +LL      G     V VV ++   A  AI+  +V+     
Sbjct: 200 LVEGDWPANKKVLDAPLAKYLLPDGSGAGAGERRVRVVAKDHPDAMRAITLVRVLARLTL 259

Query: 237 ---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ----NKLY 289
              A     L +   TGRTHQ+RVH    G  I GD KY  +F+   T  +Q     +++
Sbjct: 260 PGDATPLSLLAVTIKTGRTHQIRVHLASAGHAIAGDDKY-GDFERQRT--LQKLGLKRMF 316

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHM 315
           LHA  +   HP GG R+ + A LP  +
Sbjct: 317 LHAWRLQFNHPAGGERVALQADLPPEL 343


>gi|51473455|ref|YP_067212.1| pseudouridine synthase [Rickettsia typhi str. Wilmington]
 gi|81692307|sp|Q68XB2|RLUC_RICTY RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|51459767|gb|AAU03730.1| Pseudouridine synthase [Rickettsia typhi str. Wilmington]
          Length = 303

 Score =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 92/304 (30%), Positives = 158/304 (51%), Gaps = 19/304 (6%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD++ K  YP +    ++K LR  QV V+ ++ + N R++ G  + I    N    + 
Sbjct: 11  FRLDKYLKRLYPSLTQGVIEKALRQKQVTVNFQKAEANLRVKEGDTIFINDYFNL--PVT 68

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + + ++ +   +      L   L+YED  +   NKPA ++ QGGS I   ID  LK +++
Sbjct: 69  QHETLVFADAEIKLAKKILTDYLIYEDDHLIAINKPASLATQGGSKINLSIDSALK-YLN 127

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +G   +L HRLD+ETSG+L++A+   ++  L ++F+ + + K Y+++ +G P      +
Sbjct: 128 YQGADFKLVHRLDKETSGLLLIAKNYLSSVKLHDAFKEKLVIKKYFAITYGRP------V 181

Query: 199 ANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
            N  + KS+IG   G    +   +      AI+++K++         +E  P TGR HQL
Sbjct: 182 KNVGIVKSNIGKSKGRMFKITDIDSDNGKLAITYYKLLKSLNNNLFLIEFMPVTGRMHQL 241

Query: 256 RVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           R+HA  +GCPI+GD KY     GN    P    ++LHA  + L     G  +++ A LP 
Sbjct: 242 RLHAQLLGCPILGDDKY-----GNKEVMPYSKYMFLHANNIYLSESIVGKEIKLEAKLPF 296

Query: 314 HMVK 317
           +  +
Sbjct: 297 YFTR 300


>gi|157825473|ref|YP_001493193.1| ribosomal large subunit pseudouridine synthase C [Rickettsia akari
           str. Hartford]
 gi|157799431|gb|ABV74685.1| ribosomal large subunit pseudouridine synthase C [Rickettsia akari
           str. Hartford]
          Length = 303

 Score =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 96/296 (32%), Positives = 159/296 (53%), Gaps = 15/296 (5%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R+ +G  + I    N      +
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNAQKAEASLRVNAGDKIFIKDKFNLPVKSPE 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +    D+ + L +        L+YED  +   NKPAG++ QGGS I   ID  LK +++ 
Sbjct: 72  KLVFTDAEIKLAQKITI--DYLIYEDDNLIAINKPAGLATQGGSKINLSIDSALK-YLNY 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKECI 198
           KG   +L HRLD+ETSG+L++A+   ++  L ++F+ + I K Y ++ +G P KN  E  
Sbjct: 129 KGADFKLVHRLDKETSGLLLIAKNYLSSVKLHDAFKEKLIVKTYCAITYGKPIKNVGEVR 188

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +N  ++KS   G    +   + + A  AI+++K++         +E  P TGR HQLR+H
Sbjct: 189 SN--IEKSK--GSTPKITDIDSENAKLAITYYKLLKSLDNNLFLIEFTPVTGRMHQLRLH 244

Query: 259 ALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
           +  +GCPIVGD+KY     GN    P    ++LH+  M L     G  +++ A LP
Sbjct: 245 SKLLGCPIVGDNKY-----GNKEIMPYSKYMFLHSNNMCLSEKIFGQEIKLEAKLP 295


>gi|313201079|ref|YP_004039737.1| RluA family pseudouridine synthase [Methylovorus sp. MP688]
 gi|312440395|gb|ADQ84501.1| pseudouridine synthase, RluA family [Methylovorus sp. MP688]
          Length = 312

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 108/326 (33%), Positives = 167/326 (51%), Gaps = 38/326 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+      R+D +       +   ++ +ILRSG+VRV+ KR+    R+Q G +VR+PP
Sbjct: 2   LTVDEGSAGQRIDNFLTKTLKGVPKSHVYRILRSGEVRVNSKRIDATYRLQLGDLVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +       ++ Q + + S  +       +  +++ED  + V +KPAG +V GGSG++  +
Sbjct: 62  IR------VQPQPVAEESRPVAAR---FEEAVIFEDEAMLVIDKPAGFAVHGGSGVSRGV 112

Query: 130 DGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              L+       ++P      L HRLD+ETSG+L+VA+ R+A   L E+ R   + K Y 
Sbjct: 113 IEQLRL------ERPHAKFLELVHRLDRETSGVLMVAKKRSALVGLHEAMRANHMDKRYL 166

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQKFCWL 243
            LV G  K KK+ +   L K  H+  +    V   E+G N   I H K    + + F  L
Sbjct: 167 MLVSGDWKEKKKRVVLALQK--HVTANGERKVTVEEEGQNSETIFHLK--KSYGE-FTLL 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT--SPIQ----NKLYLHARYMDL 297
           E Q  TGRTHQLRV   H+G PI GD KY     G+F     +Q     +++LH+    +
Sbjct: 222 EAQLITGRTHQLRVQLAHLGFPIAGDDKY-----GDFALNKALQKRGLKRMFLHSAETGI 276

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSL 322
            HP  G +L++ APLPA +     SL
Sbjct: 277 RHPLSGDKLKLIAPLPAALQAFLTSL 302


>gi|332535383|ref|ZP_08411176.1| ribosomal large subunit pseudouridine synthase C [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332035211|gb|EGI71720.1| ribosomal large subunit pseudouridine synthase C [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 319

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 102/315 (32%), Positives = 168/315 (53%), Gaps = 16/315 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D    R+D +   H   +    + K+LR G+VRV+KKR+K   ++Q   V+R
Sbjct: 9   VTYVTINEDHLGQRIDNFLITHLKGVPKSAIYKLLRKGEVRVNKKRIKPVYKLQLDDVLR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I P+      + + ++ + S ++       L++ +L+ED  + V NKP+G++V GGSG++
Sbjct: 69  IAPI-----RVAEREEFVPSKLDKVTR---LENDILFEDKYLIVINKPSGMAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++ +  + +   L HRLD++TSG L++A+ R+    L E  R + ++K YW+L
Sbjct: 121 YGLIEALRA-LRPEERSLELVHRLDRDTSGCLLIAKRRSVLTALHEQLREKTMEKNYWAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G   +K + +   L K +   G+ V  V   E   ++  + FKV++ F    C L + 
Sbjct: 180 VEGQWDSKTKNVTEGLRKNTLKSGERVVRVDNTEGKPSH--TRFKVLERFND--CSLVQA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
            P TGRTHQ+RVH    G PI  D KY    F  +      N+L+LHA  +   HP+   
Sbjct: 236 SPVTGRTHQIRVHTQCKGHPIACDDKYGDQGFDESMRKVGLNRLFLHAHDLSFYHPKNET 295

Query: 304 RLQITAPLPAHMVKT 318
            ++I APL   +  T
Sbjct: 296 TMRIEAPLDKTLKNT 310


>gi|323526881|ref|YP_004229034.1| RluA family pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323383883|gb|ADX55974.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1001]
          Length = 345

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 104/322 (32%), Positives = 172/322 (53%), Gaps = 36/322 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 21  VSVIEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVR 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+  A +     Q  + S+          +  +++ED  + V +KPAG++V GGSG+A
Sbjct: 81  VPPIRVAQHDEAAAQAPVPSA----------QFKIIFEDEHLLVIDKPAGVAVHGGSGVA 130

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++   +++ Q     L HRLD+ETSGIL++A+ R+A  +L +  R  R+ K Y+
Sbjct: 131 F---GVIEQMREARPQAKFLELVHRLDRETSGILMLAKKRSALVNLHDQIRENRMDKRYY 187

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK----GANYAISH--FKVIDCFAQ 238
           + V G      E  ++W  +++     + +V    E+     A+   SH  F +ID + +
Sbjct: 188 ACVHG------EWASDWGRRRAVREPLHKYVTADGERRVRVQADGLASHTVFNLIDRWPE 241

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHA 292
            +  LE +  TGRTHQ+RVH  H+  PIVGD KY  +F  N         P   +++LHA
Sbjct: 242 -YALLEAELKTGRTHQIRVHLQHLELPIVGDAKY-GDFALNKALARANAKPALKRMFLHA 299

Query: 293 RYMDLPHPE-GGRLQITAPLPA 313
             + L HP  G  LQ+ APLPA
Sbjct: 300 YRLKLTHPATGAPLQLEAPLPA 321


>gi|120609862|ref|YP_969540.1| RluA family pseudouridine synthase [Acidovorax citrulli AAC00-1]
 gi|120588326|gb|ABM31766.1| pseudouridine synthase, RluA family [Acidovorax citrulli AAC00-1]
          Length = 399

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 105/325 (32%), Positives = 167/325 (51%), Gaps = 33/325 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++V V+ +    RLD +       +   ++ +I+RSG+VR++K R   + R+++G VVR
Sbjct: 81  VRWVEVDAESAGQRLDNFLIRELKGVPKTHVYRIIRSGEVRINKGRAAADTRVEAGDVVR 140

Query: 67  IPPVINALNHIIKEQKILDS-SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PPV           +I D  +    + +   +  LL ED  +   +KPAG++V GGSG+
Sbjct: 141 VPPV-----------RISDKVAAKAERPAPAREFPLLLEDEHLVALDKPAGVAVHGGSGV 189

Query: 126 AYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++   G ++    ++ Q     L HRLD+ETSGIL+VA+ R+A  HL + FR R   K Y
Sbjct: 190 SF---GVIEQLRQARPQARFLELVHRLDRETSGILLVAKKRSALTHLQDQFRERETGKTY 246

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK--- 239
            +LV G    + + I   L K     G+  V V  +++     +I+  KV      +   
Sbjct: 247 LALVSGEWPERLKVIDAPLHKYLQADGERRVRVTTEDDPDGMRSITLVKVRSRVPARPAE 306

Query: 240 ----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLH 291
                  LE+   TGRTHQ+RVH    G PIVGD KY  +F  +    +Q     +++LH
Sbjct: 307 GLPAMALLEVTIKTGRTHQIRVHLASRGHPIVGDDKY-GDF--DLNRRVQKHGLRRMFLH 363

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHM 315
           A  +   HP  G R+++ A LPA +
Sbjct: 364 AWRLQFSHPASGERIELHAELPAEL 388


>gi|222111813|ref|YP_002554077.1| RluA family pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221731257|gb|ACM34077.1| pseudouridine synthase, RluA family [Acidovorax ebreus TPSY]
          Length = 339

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 111/322 (34%), Positives = 164/322 (50%), Gaps = 31/322 (9%)

Query: 11  VVENDEENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           +VE D E+   RLD +   H   +   ++ +I+RSG+VR++K R   + R+  G +VR+P
Sbjct: 23  IVEVDAESAGQRLDNFLIRHLKGVPKTHVYRIIRSGEVRLNKGRTSADARVAPGDLVRLP 82

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           PV  +        K+LD +       +F    +L ED  +   +KPAG +V GGSG+++ 
Sbjct: 83  PVRVS-------DKVLDKAERPAPAREF---PILLEDEHLIAIDKPAGTAVHGGSGVSF- 131

Query: 129 IDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             G ++    ++ Q     L HRLD+ETSGIL+VA+ R+A  HL + FR R   K Y +L
Sbjct: 132 --GVIEQLRQARPQARFLELVHRLDRETSGILLVAKKRSALTHLQDQFRGRETGKTYLAL 189

Query: 187 VWGI-PKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK----- 239
           V G  P NKK  I   L K     G+  V V   ++     +++  KV    A +     
Sbjct: 190 VTGHWPANKK-VIDTPLHKYLQEDGERRVRVTTPDDPDGMRSVTLVKVRSQLAPRPLQGL 248

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYM 295
                LE+   TGRTHQ+RVH    G PI GD KY  +F  N     Q   +++LHA  +
Sbjct: 249 PAMSLLEVTIKTGRTHQIRVHLSSQGHPIAGDDKY-GDFDLNRRLQKQGLKRMFLHAWRL 307

Query: 296 DLPHPEGG-RLQITAPLPAHMV 316
              HP  G RL++ A LP  + 
Sbjct: 308 QFDHPASGERLELRAELPPELT 329


>gi|251793109|ref|YP_003007835.1| 23S rRNA pseudouridylate synthase C [Aggregatibacter aphrophilus
           NJ8700]
 gi|247534502|gb|ACS97748.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           aphrophilus NJ8700]
          Length = 319

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 107/311 (34%), Positives = 172/311 (55%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ + +DE   RLD +       +    + +I+R G+VRV+K R K   ++Q+  VVR
Sbjct: 10  VQFLTINDDEAGQRLDNFLLARLKGVPKSLIYRIVRKGEVRVNKGRSKPEYKLQADDVVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A     K Q+ +  S  LTK +   + I+ +ED+ + V NKP+GI+V GGSG+ 
Sbjct: 70  IPPVRVAE----KAQETI--SNKLTKVAQLEQQII-FEDNYLLVLNKPSGIAVHGGSGLD 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A ++L +  R + +QK Y +L
Sbjct: 123 FGVIEALRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRNLHKQLREKTVQKEYLAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +VK +E+G   + + F V + +      ++  
Sbjct: 182 VRGQWQSHCKVVQAPLLKNELSSGE--RIVKVSEQG-KPSETRFSVEERYVNA-TLVKAS 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F          +L+LHA  +   HP  G  
Sbjct: 238 PVTGRTHQIRVHTQYAGHPIALDSKYGDKVFNQQMAELGLTRLFLHAYSIRFEHPHTGET 297

Query: 305 LQITAPLPAHM 315
           L++TA L  +M
Sbjct: 298 LRLTAQLDNYM 308


>gi|253998975|ref|YP_003051038.1| RluA family pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|253985654|gb|ACT50511.1| pseudouridine synthase, RluA family [Methylovorus sp. SIP3-4]
          Length = 333

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 107/326 (32%), Positives = 166/326 (50%), Gaps = 38/326 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+      R+D +       +   ++ +ILRSG+VRV+ KR+    R+Q G +VR+PP
Sbjct: 23  LTVDEGSAGQRIDNFLTKTLKGVPKSHVYRILRSGEVRVNSKRIDATYRLQLGDLVRVPP 82

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +      + +E + + +           +  +++ED  + V +KPAG +V GGSG++  +
Sbjct: 83  IRVQPQPVAEETRPVAAR---------FEEAVIFEDEAMLVIDKPAGFAVHGGSGVSRGV 133

Query: 130 DGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              L+       ++P      L HRLD+ETSG+L+VA+ R+A   L E+ R   + K Y 
Sbjct: 134 IEQLRL------ERPHAKFLELVHRLDRETSGVLMVAKKRSALVGLHEAMRANHMDKRYL 187

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQKFCWL 243
            LV G  K KK+ +   L K  H+  +    V   E+G N   I H K    + + F  L
Sbjct: 188 MLVSGDWKEKKKRVVLALQK--HVTANGERKVTVEEEGQNSETIFHLK--KSYGE-FTLL 242

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT--SPIQ----NKLYLHARYMDL 297
           E Q  TGRTHQLRV   H+G PI GD KY     G+F     +Q     +++LH+    +
Sbjct: 243 EAQLITGRTHQLRVQLAHLGFPIAGDDKY-----GDFALNKALQKRGLKRMFLHSAETGI 297

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSL 322
            HP  G +L++ APLPA +     SL
Sbjct: 298 RHPLSGDKLKLIAPLPAALQAFLTSL 323


>gi|56460456|ref|YP_155737.1| pseudouridylate synthase Rlu family protein [Idiomarina loihiensis
           L2TR]
 gi|56179466|gb|AAV82188.1| Predicted pseudouridylate synthase, Rlu family [Idiomarina
           loihiensis L2TR]
          Length = 315

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 100/323 (30%), Positives = 179/323 (55%), Gaps = 15/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           ++   V++  V  +E   R+D +       +    + +I+R G+VR +KKR+K + +++ 
Sbjct: 3   TIQQEVRWHTVSAEESGQRIDNFLIAQLRGVPKSLVYRIVRKGEVRANKKRIKPDYKLKE 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G ++RIPPV       + E+  L S+ NL + +  L+  +LYED  + + NKP+G++V G
Sbjct: 63  GDLIRIPPVK------VNERPDLPSA-NLEQVA-ALEHAILYEDDALMLINKPSGVAVHG 114

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ + +   L++ +  K +   L HR+D++TSG+L+VA+ R+  + L E  R + + K
Sbjct: 115 GSGLQFGLIEGLRA-LRPKEKSLELVHRIDRDTSGLLLVAKKRSVLRSLHEQLRNKEMNK 173

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  + +   +   L K +   G+   +V+ + +G   +++ F++   + ++  
Sbjct: 174 QYLALVRGQWQKRVRSVEAPLKKNTLKSGE--RIVRVDAEG-KASLTRFRIQQRY-KEGT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            +E  P TGRTHQ+RVHALH G PI  D KY   +F    +    N+L+LHA  +   HP
Sbjct: 230 LVEASPVTGRTHQIRVHALHAGHPIAKDPKYGDTDFDNTMSRLGLNRLFLHAWQLRFLHP 289

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G+ +   APL  ++ +T   L
Sbjct: 290 VTGKEVAFEAPLDDNLQQTLKQL 312


>gi|16125533|ref|NP_420097.1| ribosomal large subunit pseudouridine synthase D [Caulobacter
           crescentus CB15]
 gi|221234280|ref|YP_002516716.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus NA1000]
 gi|13422619|gb|AAK23265.1| ribosomal large subunit pseudouridine synthase D [Caulobacter
           crescentus CB15]
 gi|220963452|gb|ACL94808.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus NA1000]
          Length = 270

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 83/228 (36%), Positives = 126/228 (55%), Gaps = 5/228 (2%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +S +LYED  I V NKPAG+S QGG   A+ +D  L ++      +P+L HRLD++TSG+
Sbjct: 33  QSWVLYEDETIIVLNKPAGLSSQGGRIKAHTLDDLLWAFARPNRPRPKLVHRLDRDTSGV 92

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+T+ AA  L ++   +R +K Y ++V G P+ K   I + L ++S     Y+ V +
Sbjct: 93  ILTAKTKPAAAMLGKALEAKRFRKSYLAIVAGAPEPKGGMIDSPLRRESIGREAYMRVCE 152

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +   A  A S ++ +         +E+ P TGR HQLRVH   +G P+ GD +Y     
Sbjct: 153 PDHPDAETARSRYRTL-AHNGLAALVELSPDTGRMHQLRVHMASIGRPLAGDSRYGGALM 211

Query: 278 -GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
            G   +P   +L LHA  +  PHP GG  +I APLP   V   ++LG 
Sbjct: 212 LGGVPAP---RLMLHAASLAFPHPLGGERKILAPLPPDFVSMLEALGL 256


>gi|323144879|ref|ZP_08079445.1| rRNA pseudouridylate synthase C [Succinatimonas hippei YIT 12066]
 gi|322415346|gb|EFY06114.1| rRNA pseudouridylate synthase C [Succinatimonas hippei YIT 12066]
          Length = 335

 Score =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 103/323 (31%), Positives = 166/323 (51%), Gaps = 23/323 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V Y  V  D+   RLD +       +    + +ILR G+VRV+KKR + + ++ +G  +R
Sbjct: 27  VSYKTVTADDAGQRLDNYLLRILKGVPRSMIYRILRRGEVRVNKKRAEPSYKLCAGDEIR 86

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +   +I     L S  NL       K  + +E+  + V +KPAGI+  GGSGI 
Sbjct: 87  VPPVRVSTAPVIIPSANLHSVQNL-------KDRICFENEALIVVDKPAGIAAHGGSGIE 139

Query: 127 YHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + +   L++       +P      L HRLD+ETSG L+VA+ R+A ++L E FR R I+K
Sbjct: 140 FGLIEALRAL------RPEFSFLELAHRLDRETSGCLIVAKRRSALRNLHEQFRSRVIKK 193

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G    + + +   L++     G+   +V+ N K    + + F +++       
Sbjct: 194 RYLTLVPGKWDRRLKLVEAPLVRNELRSGE--RMVEVNFKSGAPSATGFDIVEELNDATL 251

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
              M PHTGRTHQ+RVH  ++  P+ GD KY +  F     +    +++LHA  +    P
Sbjct: 252 MAAM-PHTGRTHQIRVHCAYVKHPVGGDVKYGSEEFNDRLKALGLKRMFLHAAKITFTDP 310

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G+ L++ APLP  + K  + L
Sbjct: 311 VSGKLLKVEAPLPDELRKIVEIL 333


>gi|21672612|ref|NP_660679.1| ribosomal large subunit pseudouridine synthase [Buchnera aphidicola
           str. Sg (Schizaphis graminum)]
 gi|25091178|sp|Q8K9J8|RLUC_BUCAP RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|21623244|gb|AAM67890.1| ribosomal large subunit pseudouridine synthase [Buchnera aphidicola
           str. Sg (Schizaphis graminum)]
          Length = 314

 Score =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 101/322 (31%), Positives = 179/322 (55%), Gaps = 18/322 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V  + +  D  N R+D + +    ++    + +I+R+G++R++KKR+K + +++ G  
Sbjct: 6   TSVSIIYINEDMINQRIDNFLQKKLKNVPRSMIYRIIRTGKIRINKKRIKPDYKLKIGDK 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RIPP+      I+ E+K   SS+  T++   L + +LYED+ + + NKP+GI+V GGSG
Sbjct: 66  LRIPPI-----KILCEKK---SSLLTTEYKKNLLNNILYEDNYLLIINKPSGIAVHGGSG 117

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           I   +  + +  +    +   L HR+D++TSG+L++A+ R +   L +  R +++QK Y 
Sbjct: 118 INLGVIEYFRK-IRPLEKFLELVHRIDRDTSGVLMLAKKRRSLLSLHKQIREKKVQKKYI 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL- 243
           +LV G+       ++  LL K+H+      ++   E     A ++FK+   +   F  L 
Sbjct: 177 ALVHGLWPLSLRKVSEPLL-KTHLKNKQRKILINKE--GKPAETYFKIKKQYL--FTTLV 231

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQ-NKLYLHARYMDLPHPE 301
            + P TGRTHQ+RVH LH G PI+ D +Y   +   N  +  + N+L LHA  ++  HPE
Sbjct: 232 SITPKTGRTHQIRVHTLHAGHPILFDKRYGKRDLDCNIKNKTKINRLLLHATSINFIHPE 291

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
            G ++ I APL  +     ++L
Sbjct: 292 TGKKMHIVAPLDVYFKNYLNTL 313


>gi|315126331|ref|YP_004068334.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
 gi|315014845|gb|ADT68183.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
          Length = 319

 Score =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 101/309 (32%), Positives = 167/309 (54%), Gaps = 18/309 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +V +  D    R+D +   H   +    + KILR G+VRV+KKR+K   ++Q   V+R
Sbjct: 9   VTFVTINEDHLGQRIDNFLITHLKGVPKSAVYKILRKGEVRVNKKRIKPVYKLQLDDVIR 68

Query: 67  IPPVINALNHIIKEQKILDSSVN-LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           IPP+      + + ++ + S ++ +T+  D+    +L+ED  + V NKP+G++V GGSG+
Sbjct: 69  IPPI-----RVSEREEFVPSKLDKVTRLEDY----ILFEDKYLMVINKPSGMAVHGGSGL 119

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +Y +   L+  +  + +   L HRLD++TSG L++A+ R+    L E  R + ++K YW+
Sbjct: 120 SYGLIEALR-VLRPEERSLELVHRLDRDTSGCLLIAKRRSVLTALHEQLREKTMEKNYWA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-E 244
           LV G   +K + +   L K +   G+ V  V   E   ++  + FKV++ F    C L +
Sbjct: 179 LVEGQWDSKTKNVTEGLRKNTLKSGERVVRVDNTEGKPSH--TRFKVLERFND--CSLVQ 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
             P TGRTHQ+RVH    G  I  D KY    F  +      N+L+LHA  +   HP+  
Sbjct: 235 ASPVTGRTHQIRVHTQCQGHAIACDDKYGDQGFDESMRKRGLNRLFLHAHDLSFYHPKNE 294

Query: 303 GRLQITAPL 311
             +++ APL
Sbjct: 295 TTMRVEAPL 303


>gi|33151828|ref|NP_873181.1| 23S rRNA pseudouridylate synthase C [Haemophilus ducreyi 35000HP]
 gi|34395752|sp|P59835|RLUC_HAEDU RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|33148049|gb|AAP95570.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           ducreyi 35000HP]
          Length = 320

 Score =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 105/317 (33%), Positives = 168/317 (52%), Gaps = 16/317 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           ++   VQ+  + +DE   RLD +       +    + +I+R G+VRV+K RVK + ++Q 
Sbjct: 6   TISANVQFFTISDDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRVKPDYKLQH 65

Query: 62  GQVVRIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
             +VRIP V +   N      K L+    L +H       +LYED  + V NKP+GI V 
Sbjct: 66  NDIVRIPLVRVTPKNEAPISTK-LNKVAELEQH-------ILYEDDVMLVLNKPSGIGVH 117

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +Q
Sbjct: 118 GGSGLSFGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRALHEQLREKVVQ 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  +     I   LLK     G+   +VK +E+G   + + F + + +    
Sbjct: 177 KDYLALVRGQWQAHINVIKAPLLKNELQSGE--RIVKVSEQG-KPSETRFSIEERYPNA- 232

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +   H
Sbjct: 233 TLIKASPITGRTHQIRVHTQYAGHPIACDDRYGDQAFDAKLKQAGLNRLFLHAHSIRFEH 292

Query: 300 PEGG-RLQITAPLPAHM 315
           P+   ++ ITAPL  H+
Sbjct: 293 PKTAEQMFITAPLDHHL 309


>gi|88859600|ref|ZP_01134240.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas tunicata D2]
 gi|88818617|gb|EAR28432.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas tunicata D2]
          Length = 320

 Score =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 102/320 (31%), Positives = 172/320 (53%), Gaps = 18/320 (5%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T V +  V  D +  R+D +       +    + +ILR G+VRV+KKR+K   ++  G
Sbjct: 5   LGTQVIFHTVTEDHDGQRIDNFLITKLKGVPKSAIYRILRKGEVRVNKKRIKPIYKLNIG 64

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             VRIPP+  A     ++++ +  ++++      L+  +L+ED  + V NKPAG++V GG
Sbjct: 65  DEVRIPPIKMA-----EQEEFVPKNLDVISR---LEDAILFEDKYLIVINKPAGMAVHGG 116

Query: 123 SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           SG++Y   G +++    + Q+    L HRLD++TSG L++++ R+  + L E  R + +Q
Sbjct: 117 SGLSY---GLIEAMRTLRPQETALELVHRLDRDTSGCLLISKKRSVLKSLHEQLREKTMQ 173

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW+LV G   +K + +   L K +   G+ V  V   E  A++  + F+V++ F +  
Sbjct: 174 KNYWALVSGEWLSKDKNVTEPLRKNTLQSGERVVRVDHEEGKASH--TRFRVLERF-RDG 230

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH    G PI  D KY    F         N+L+LHA  +   H
Sbjct: 231 TLVQASPVTGRTHQIRVHTQCKGHPIACDDKYGDTEFDQKMKGFGLNRLFLHAHDLTFYH 290

Query: 300 PEGGR-LQITAPLPAHMVKT 318
           P+  + + + APL   + +T
Sbjct: 291 PKLEQDMTVEAPLDETLKRT 310


>gi|332977603|gb|EGK14371.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter sp.
           1501(2011)]
          Length = 364

 Score =  150 bits (378), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 105/318 (33%), Positives = 168/318 (52%), Gaps = 31/318 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V ++ V   +   R+D +       +   ++ K++RS +VR++ KR K  + ++ G V
Sbjct: 60  SQVNHLEVTRHQHGQRVDNFLLARLKGMPRAHIYKMIRSDEVRINNKRCKPYDNLERGDV 119

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL---LYEDSKIYVFNKPAGISVQG 121
           VRI PV  A     +E+ ++           F KS+L   +YED  + V NKP+G++V G
Sbjct: 120 VRIAPVRLA----TREKPVISEG--------FAKSLLERVVYEDEGLIVLNKPSGMAVHG 167

Query: 122 GSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GSG+ +   G +++  D+  +K   L HR+D++TSG+L++A+ R+  + L E  R + IQ
Sbjct: 168 GSGLDF---GVIEAMRDATSKKYLELVHRIDKDTSGLLMIAKKRSTLKVLQEYLREKTIQ 224

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---A 237
           K Y  +V G P      I   LL+ +   G+    V +N   A  + +  KV+  F    
Sbjct: 225 KHYLCIVKGQPALNDISIDAPLLRYTLASGERRVRVDKNSPDAKTSQTTCKVLARFEING 284

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    +E  PHTGRTHQ+RVH  ++G PI+GD KY        TS ++ +L LHA  +D+
Sbjct: 285 EPVSLIEAMPHTGRTHQIRVHLAYLGHPILGDDKYHI----QDTSGVR-RLCLHAWQLDI 339

Query: 298 PHPEGGRLQITAPLPAHM 315
           P  E     I APLP  M
Sbjct: 340 PEYE----TIKAPLPEDM 353


>gi|148652292|ref|YP_001279385.1| RluA family pseudouridine synthase [Psychrobacter sp. PRwf-1]
 gi|148571376|gb|ABQ93435.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter sp.
           PRwf-1]
          Length = 364

 Score =  150 bits (378), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 110/328 (33%), Positives = 175/328 (53%), Gaps = 32/328 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V  ++   R+D +       +   ++ K++RS +VR++ KR K  + ++ G VVR
Sbjct: 62  VNHLEVTRNQHGQRIDNFLLARLKGMPRAHIYKMIRSDEVRINNKRCKPYDNLERGDVVR 121

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL---LYEDSKIYVFNKPAGISVQGGS 123
           I PV  A     +E+ ++           F KS+L   +YED  + V NKP+G++V GGS
Sbjct: 122 IAPVKLA----TREKPVISEG--------FAKSLLERVVYEDEGLIVLNKPSGMAVHGGS 169

Query: 124 GIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G+ +   G +++  D+  +K   L HR+D++TSG+L++A+ R+  + L E  R + IQK 
Sbjct: 170 GLDF---GVIEAMRDATSKKYLELVHRIDKDTSGLLMIAKKRSTLKVLQEYLREKTIQKH 226

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQK 239
           Y  LV G P   +  I   LL+ +   G+    V +    A  + +  KV+  F    + 
Sbjct: 227 YLCLVKGQPALNEFEIDAPLLRYTVANGERRVKVDKANPEAKLSQTTCKVLARFKMNGEP 286

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E  PHTGRTHQ+RVH  ++G PI+GD KY  N K   TS ++ +L LHA  +D+P 
Sbjct: 287 VSLIEAMPHTGRTHQIRVHLAYLGHPILGDDKY--NIKD--TSGVR-RLCLHAWQLDVPE 341

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            E     I APLP  M ++     FK D
Sbjct: 342 YE----VIKAPLPEDM-QSLLPADFKLD 364


>gi|325981765|ref|YP_004294167.1| pseudouridine synthase, RluA family [Nitrosomonas sp. AL212]
 gi|325531284|gb|ADZ26005.1| pseudouridine synthase, RluA family [Nitrosomonas sp. AL212]
          Length = 326

 Score =  150 bits (378), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 114/343 (33%), Positives = 178/343 (51%), Gaps = 41/343 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  +T +    V+ D ++ R+D +    + ++   +L +++RSGQVRV+ KR+  N R++
Sbjct: 1   MESITSITKERVKEDGDDQRIDNFLFKRFRNVPKNHLYQLVRSGQVRVNGKRIDANYRLR 60

Query: 61  SGQVVRIPPVINALNHIIKEQKI-LDSSVNLTKHS--DFLKSILLYEDSKIYVFNKPAGI 117
            G +VRIPPV           KI    S+N T  +  +F     LYED  +   +KP+G+
Sbjct: 61  LGDMVRIPPV-----------KIETKDSLNRTAITCLNFFSFTHLYEDDAVLAIDKPSGM 109

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTE 172
           +V GGS +++ +   L++      Q P      L HRLD+ETSG+L++A+ R+A   L  
Sbjct: 110 AVHGGSNVSFGVIEQLRA------QNPSWKFLELVHRLDRETSGVLLLAKKRSALVELHR 163

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISH-- 229
             R   ++K Y  +V G  +N K+ +   L K     G+  V VV     G     SH  
Sbjct: 164 QIREGLVEKHYLVMVKGKWRNAKQHVRLILDKYVTASGERRVAVVTSIRPGNKPMPSHSI 223

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNF 280
           FK +D     F  L+ Q  TGRTHQ+RVH  H+G PI+GD KY  NF+         G+ 
Sbjct: 224 FK-LDKSWDNFSLLDAQIKTGRTHQIRVHLAHLGFPILGDDKY-GNFEINKRLAKGGGDG 281

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            S +  +++LHA  + + HP  G R+ + +PL + + K  D L
Sbjct: 282 KSKLM-RMFLHAHSLQITHPVSGQRINLRSPLSSDLQKFIDDL 323


>gi|149926440|ref|ZP_01914701.1| pseudouridine synthase [Limnobacter sp. MED105]
 gi|149824803|gb|EDM84017.1| pseudouridine synthase [Limnobacter sp. MED105]
          Length = 335

 Score =  150 bits (378), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 106/322 (32%), Positives = 173/322 (53%), Gaps = 28/322 (8%)

Query: 10  VVVENDE--ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           V++E DE  ++ RLD +  N    +   ++ +I+RSG+VR+++KR +   ++  G VVR+
Sbjct: 13  VLLEIDEKHQDQRLDNFLCNVCKGVPKSHVFRIIRSGEVRINRKRAEAKTKLCVGDVVRV 72

Query: 68  PPVINALNHIIKEQKILDS---SVNLTKHSDFLKSI----LLYEDSKIYVFNKPAGISVQ 120
           PP+       + E++ LDS   S  L K +  LK+     +L+ED  + V NKP+G++V 
Sbjct: 73  PPIK------VVEKQDLDSLSLSAGLNK-TQLLKAAADLPILFEDEHLLVVNKPSGMAVH 125

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG ++ +   +++      Q   L HR+D+ETSGIL++++ R+A + L E  R R  +
Sbjct: 126 GGSGSSFGLIECIRALRAETHQDLELVHRIDRETSGILIISKKRSALRKLQEQLRARSWK 185

Query: 181 KIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-- 237
           K Y +LV G  P+  ++     L  +S      V V    ++  + A + FKVI C+   
Sbjct: 186 KYYKTLVLGHWPEALRQVDLPLLKTQSSEKEARVFV----DESGDKACTKFKVIQCYKSS 241

Query: 238 -QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARY 294
              F  ++ Q  TGRTHQ+RVH      PI GD +Y  NF+ N     Q   +++LHA  
Sbjct: 242 YSSFTLIQAQILTGRTHQIRVHTSANKFPIAGDDRY-GNFEMNKQLARQGLKRMFLHAAR 300

Query: 295 MDLPHPEGGR-LQITAPLPAHM 315
           + L HP     + + APL   +
Sbjct: 301 LQLVHPATNETIVLEAPLAPEL 322


>gi|326316005|ref|YP_004233677.1| pseudouridine synthase, RluA family [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323372841|gb|ADX45110.1| pseudouridine synthase, RluA family [Acidovorax avenae subsp.
           avenae ATCC 19860]
          Length = 343

 Score =  150 bits (378), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 105/324 (32%), Positives = 167/324 (51%), Gaps = 31/324 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++V V+ +    RLD +       +   ++ +I+RSG+VR++K R   + RI++G VVR
Sbjct: 25  VRWVEVDAESAGQRLDNFLIRELKGVPKTHVYRIIRSGEVRINKGRAAADTRIEAGDVVR 84

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +        K+   +       +F    LL ED  +   +KPAG++V GGSG++
Sbjct: 85  VPPVRIS-------DKVAARAERPAPAREF---PLLLEDEHLIALDKPAGVAVHGGSGVS 134

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    ++ Q     L HRLD+ETSGIL+VA+ R+A  HL + FR R   K Y 
Sbjct: 135 F---GVIEQLRQARPQARFLELVHRLDRETSGILLVAKKRSALTHLQDQFRERETGKTYL 191

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK---- 239
           +LV G    + + I   L K   + G+  V V  +++     +I+  KV      +    
Sbjct: 192 ALVSGEWPERLKVIDAPLHKYLQVDGERRVRVTTEDDPDGMRSITLVKVRSRIPARPAEG 251

Query: 240 ---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHA 292
                 LE+   TGRTHQ+RVH    G PI+GD KY  +F  +    +Q     +++LHA
Sbjct: 252 LPAMALLEVTIKTGRTHQIRVHLASRGHPILGDDKY-GDF--DLNRRVQKHGLRRMFLHA 308

Query: 293 RYMDLPHPEGG-RLQITAPLPAHM 315
             +   HP  G R+++ A LPA +
Sbjct: 309 WRLQFSHPASGERVELHAELPADL 332


>gi|307544580|ref|YP_003897059.1| 23S rRNA pseudouridylate synthase C [Halomonas elongata DSM 2581]
 gi|307216604|emb|CBV41874.1| 23S rRNA pseudouridylate synthase C [Halomonas elongata DSM 2581]
          Length = 315

 Score =  150 bits (378), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 103/307 (33%), Positives = 161/307 (52%), Gaps = 15/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V V   +   R+D +            + +I+R G+VRV+KKRVK ++R+ +G VVR
Sbjct: 7   VQWVEVTEGQAGQRVDNFLMTRLKGAPRSLIYRIVRKGEVRVNKKRVKADSRLATGDVVR 66

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A    ++E  + D+  NL      L   +L E     V NKP+G++V GGSG+ 
Sbjct: 67  IPPLKLAPREAVRE--VSDNLRNL------LAGSVLLEGRDWLVLNKPSGLAVHGGSGVK 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L+  V        L HRLD++TSG L++A++R A   L  + +   + K Y +L
Sbjct: 119 IGLIEALRQ-VREDLDFLELVHRLDRDTSGCLLLAKSRTALLTLNTALKRHEMTKRYLAL 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    +++ ++  L +     G+    V  N K    A + F V + FA     +E +
Sbjct: 178 VAGRWPARRDFVSARLDRFDAGNGERRVRVDANGK---VARTRFAVRETFAGA-TLMEAE 233

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA H G P++GD KY +       +    ++L+LHA  +  P P  G+ 
Sbjct: 234 PVTGRTHQIRVHAAHAGHPLLGDDKYGSREGQRLAARWDLSRLFLHASELTFPEPTSGKP 293

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 294 VKIRAPL 300


>gi|241763829|ref|ZP_04761874.1| pseudouridine synthase, RluA family [Acidovorax delafieldii 2AN]
 gi|241366873|gb|EER61287.1| pseudouridine synthase, RluA family [Acidovorax delafieldii 2AN]
          Length = 336

 Score =  150 bits (378), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 107/325 (32%), Positives = 163/325 (50%), Gaps = 25/325 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +   + V V+ D    RLD +   H   +   ++ +I+RSG+VR++K R   + R+ +G 
Sbjct: 19  LPAARLVEVDEDSAGQRLDNFLLRHLKGVPKTHVYRIIRSGEVRINKGRANADTRLAAGD 78

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PPV  +        K+ + +       +F    +L ED  +   +KPAG++V GGS
Sbjct: 79  VVRLPPVRIS-------DKVAEKAERPAPAREF---PVLLEDEHVIALDKPAGVAVHGGS 128

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+++ +   L+       +   L HRLD+ETSGIL+VA+ R+A  HL + FR R   K Y
Sbjct: 129 GVSFGVIEQLRQ-ARPAARFLELVHRLDRETSGILLVAKKRSALTHLQDQFRERETGKTY 187

Query: 184 WSLVWGI-PKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK-- 239
            +LV G  P NKK  I   L K     G+  V V   ++     +++  KV      +  
Sbjct: 188 LALVTGDWPANKK-VIDLPLHKYLQADGERRVRVTTADDPDGMRSVTLVKVRQAVPARPM 246

Query: 240 -----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHA 292
                   LE+   TGRTHQ+RVH    G PIVGD KY  +F  N     Q   +++LHA
Sbjct: 247 QGLPAMSLLEVTIKTGRTHQIRVHLASQGHPIVGDDKY-GDFDLNKRLQKQGMRRMFLHA 305

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMV 316
             +   HP  G R+ + A LP+ + 
Sbjct: 306 WRLQFMHPASGERVVLHAALPSELA 330


>gi|329120429|ref|ZP_08249095.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327462113|gb|EGF08441.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 435

 Score =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 100/320 (31%), Positives = 171/320 (53%), Gaps = 27/320 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V   E   RLD +       +   ++ +++R+G+VR++KKR K  +RI +G +VRIPP
Sbjct: 117 LAVAEHEAGQRLDNYLIKILKGVPKSHIWRMIRAGEVRLNKKRCKPESRIAAGDIVRIPP 176

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V      + + QK  + +    +  D     ++YED  + V +KPAG++V GGSG+++ +
Sbjct: 177 V-----RVAERQKPSEKAAAPAREFD-----IVYEDDALLVIDKPAGVAVHGGSGVSFGV 226

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++     + +   L HRLD++TSG+L++A+ R+A   L E+ R    +KIY +L  G
Sbjct: 227 IEQIRR-ARPEARYLELVHRLDKDTSGLLMIAKKRSALVKLHEAIRNDHPKKIYLALGAG 285

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---------QKF 240
             +N +  +   L K +   G+   +V+ +E G + A + FKV++ F+            
Sbjct: 286 RLENDRFHVRLPLFKYTGAAGE--KMVRVSEDG-HSAHTVFKVLNRFSDGLLHRVGLSNL 342

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLP 298
             +E    TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  + L 
Sbjct: 343 TLVEATLKTGRTHQIRVHMQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHAAELHLD 401

Query: 299 HP-EGGRLQITAPLPAHMVK 317
           HP  G +L + APLP  + +
Sbjct: 402 HPLTGEKLVLKAPLPQDLAQ 421


>gi|319941549|ref|ZP_08015875.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
 gi|319804919|gb|EFW01761.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
          Length = 339

 Score =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 105/328 (32%), Positives = 171/328 (52%), Gaps = 32/328 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV++  D +  RLD +       +   ++ +++R+G+VRV KKR K   ++  G VVR
Sbjct: 25  VSYVLIGEDADGQRLDNFLFRIAKGVPKGHVYRVIRAGEVRVSKKRAKAETKLMLGDVVR 84

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL--LYEDSKIYVFNKPAGISVQGGSG 124
           IPP+           ++          +   + +L  LYED  I +  KPAGI+  GGSG
Sbjct: 85  IPPM-----------RVAQKPAGTPPAAPLAQGVLPVLYEDRHILIVLKPAGIAAHGGSG 133

Query: 125 IAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           I+Y   G ++    ++ ++P   L HRLD+ETSG +V+A+TR A   + +  +   ++K 
Sbjct: 134 ISY---GLIERLRATRPEEPMLELCHRLDKETSGAIVIAKTRKALVRMHDLMKEGGVEKH 190

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  LV G   N+++ +   L +     G+    V+ + +G + A + F V++ F     +
Sbjct: 191 YKLLVKGDWVNERQHVKVPLERYLLPSGE--RRVRASSEGMS-AHTIFTVLERFGS-VTY 246

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-------GNFTSPIQNKLYLHARYM 295
           L+ +  TGRTHQ+RVHAL  G P+ GD KY  +F        G   +P++ +++LHA  +
Sbjct: 247 LDAELKTGRTHQIRVHALSQGFPLAGDDKY-GDFAFNRECTHGLLGAPLK-RMFLHAWKL 304

Query: 296 DLPHPEGGRL-QITAPLPAHMVKTWDSL 322
              HP  G L  ITAPLP  +     +L
Sbjct: 305 RFAHPVTGELVDITAPLPEELSAVISAL 332


>gi|119469426|ref|ZP_01612365.1| 23S rRNA pseudouridylate synthase [Alteromonadales bacterium TW-7]
 gi|119447290|gb|EAW28559.1| 23S rRNA pseudouridylate synthase [Alteromonadales bacterium TW-7]
          Length = 320

 Score =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 99/308 (32%), Positives = 164/308 (53%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +V +  D    R+D +   H   +    + KILR G+VRV+KKR+K   ++Q   ++R
Sbjct: 9   VSFVTINEDHLGQRIDNFLITHLKGVPKSAIYKILRKGEVRVNKKRIKPVYKLQLDDIIR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      + + ++ + S ++       L+  +L+ED  + V NKP+G++V GGSG++
Sbjct: 69  IPPI-----KVAEREEFVPSKLDKVTR---LEDDILFEDKYLIVINKPSGMAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+  +  + +   L HRLD++TSG L++++ R+    L E  R + ++K YW+L
Sbjct: 121 YGLIEALR-VLRPEERNLELVHRLDRDTSGCLLISKRRSVLTSLHEQLREKTMEKNYWAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G    K + +   L K +   G+ V  V   E   ++  + FKV++ F +  C L + 
Sbjct: 180 VDGQWDGKTKNVTEGLRKNTLKSGERVVRVDNVEGKPSH--TRFKVLERFNE--CSLVQA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
            P TGRTHQ+RVH    G PI  D KY    F         N+L+LHA  +   HP+   
Sbjct: 236 SPVTGRTHQIRVHTQCKGHPIACDDKYGDQAFDAGMRKVGLNRLFLHAHDLSFYHPKNET 295

Query: 304 RLQITAPL 311
            +++ APL
Sbjct: 296 TMRVEAPL 303


>gi|30249427|ref|NP_841497.1| rluC; ribosomal large subunit pseudouridine synthase C
           [Nitrosomonas europaea ATCC 19718]
 gi|30138790|emb|CAD85367.1| rluC; ribosomal large subunit pseudouridine synthase C
           [Nitrosomonas europaea ATCC 19718]
          Length = 343

 Score =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 108/320 (33%), Positives = 166/320 (51%), Gaps = 35/320 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++   E+ R+D +       I   ++ ++LRSGQVRV+ KR+  + R+Q G  VRIPPVI
Sbjct: 29  IDETAESQRIDNFLIRSLKGIPRRHIYQLLRSGQVRVNSKRIDASYRLQLGDKVRIPPVI 88

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            ++  +        SS  + +   F    +LY+D  + V +KPAGI+V GGSGI++   G
Sbjct: 89  RSVKPV--------SSQGVYRTDRF---NILYQDDHLLVIDKPAGIAVHGGSGISH---G 134

Query: 132 FLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++     +GQ P      L HRLD+ETSGIL++AR R +   L    R   ++K Y +L
Sbjct: 135 VIEQL---RGQHPDWKFLELVHRLDRETSGILLLARKRQSLLELHRQIREGTVEKHYLTL 191

Query: 187 VWGIPKNKKECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           V G  KN  + +   L K     G+    V   + ++  A  A + F +   + + F  L
Sbjct: 192 VRGKWKNSVQNVRLPLNKYLTAAGERRVAVAAGRNDQDKAQQAHTLFTLQKAW-EDFSLL 250

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-------KGNFTSPIQNKLYLHARYMD 296
           + +  TGRTHQ+RVH  H+G PI GD KY  +F       K +    +  +++LHA    
Sbjct: 251 DAELKTGRTHQIRVHLAHLGFPIAGDDKY-GDFGLNKQLQKDDGKGQVLRRMFLHASAFT 309

Query: 297 LPHP-EGGRLQITAPLPAHM 315
             HP  G  L++ APLP  +
Sbjct: 310 CTHPVTGDLLRLEAPLPDEL 329


>gi|209517244|ref|ZP_03266089.1| pseudouridine synthase, RluA family [Burkholderia sp. H160]
 gi|209502380|gb|EEA02391.1| pseudouridine synthase, RluA family [Burkholderia sp. H160]
          Length = 349

 Score =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 107/324 (33%), Positives = 167/324 (51%), Gaps = 40/324 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 25  VSLLEIDDSSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVR 84

Query: 67  IPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PP+ +   N       +     ++           L+ED  + V +KPAG++V GGSG+
Sbjct: 85  VPPIRVAQPNEAAAHVPVPAGGFHI-----------LFEDEHLLVIDKPAGVAVHGGSGV 133

Query: 126 AYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           A+   G ++   +++ Q     L HRLD+ETSGIL++A+ RAA  +L E  R  R+ K Y
Sbjct: 134 AF---GVIEQMREARPQAKFLELVHRLDRETSGILMLAKKRAALVNLHEQIRENRMDKRY 190

Query: 184 -------WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
                  W+  WG  +  KE +  +L      G   V V  Q +  A++ I  F ++D +
Sbjct: 191 YACVHGEWATDWGRRRAVKEPLHKYLTAD---GERRVRV--QADGLASHTI--FNLVDRW 243

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYL 290
              +  LE +  TGRTHQ+RVH  H+  PIVGD KY  +F  N         P   +++L
Sbjct: 244 PD-YALLEAELKTGRTHQIRVHLQHLALPIVGDAKY-GDFALNKALARANAKPGIKRMFL 301

Query: 291 HARYMDLPHPE-GGRLQITAPLPA 313
           HA  + L HP  G  LQ+ APLPA
Sbjct: 302 HAYRLKLTHPATGAPLQLEAPLPA 325


>gi|121605976|ref|YP_983305.1| RluA family pseudouridine synthase [Polaromonas naphthalenivorans
           CJ2]
 gi|120594945|gb|ABM38384.1| pseudouridine synthase, RluA family [Polaromonas naphthalenivorans
           CJ2]
          Length = 398

 Score =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 104/341 (30%), Positives = 170/341 (49%), Gaps = 31/341 (9%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           + +     V V+ D    RLD +       +   ++ +I+RSG+VRV+K R   + R+++
Sbjct: 44  TALPQATLVTVDEDYAGQRLDNFLIRQLKGVPKTHVYRIIRSGEVRVNKGRAHADTRVEA 103

Query: 62  GQVVRIPPV---------INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
           G +VR+PPV           A+  ++ E     +S  +  ++   +  +L+ED  +   +
Sbjct: 104 GDIVRLPPVRTSERAEQKAQAMQSVMTEVARHGASSTVGGYAPAAEFPILFEDDFLLAID 163

Query: 113 KPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           KPAG++V GGSG+++ I   L+     +     L HRLD+ETSGIL++A+ R A + L E
Sbjct: 164 KPAGVAVHGGSGVSFGIIEQLR-MARPEADFLELVHRLDRETSGILLIAKRRMALKLLQE 222

Query: 173 SFRMRRIQKIYWSLVWGI-PKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            FR R   K+Y +LV G  P N++   + +  +LL     G   V +V  +   A  +++
Sbjct: 223 QFRERETDKVYLALVSGNWPANQRVIDKALHKYLLPN---GERRVKIVANDHPDAMRSVT 279

Query: 229 HFKVIDCFAQ-------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------AN 275
             KV    A         F  LE+   TGRTHQ+RVH    G PI GD KY       A 
Sbjct: 280 LVKVKTPIAANPLAPATPFTLLEVTIKTGRTHQIRVHLAGEGHPIAGDDKYGDFELNKAL 339

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            + +  S    +++LHA  +   HP+  + +Q+ A LP  +
Sbjct: 340 QRSSAGSASLKRMFLHAWSLKFNHPKTRKAVQLQASLPEEL 380


>gi|114775485|ref|ZP_01451053.1| ribosomal large subunit pseudouridine synthase C [Mariprofundus
           ferrooxydans PV-1]
 gi|114553596|gb|EAU55977.1| ribosomal large subunit pseudouridine synthase C [Mariprofundus
           ferrooxydans PV-1]
          Length = 315

 Score =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 106/319 (33%), Positives = 171/319 (53%), Gaps = 22/319 (6%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  DE+  RLDR    H    +   + +++R G VR++KKR K    + +G  V +P 
Sbjct: 11  LTIGADEDGSRLDRVLSRHLGAGHRALILRLIRKGNVRLNKKRCKPETHVAAGDQVFLPV 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +   + +  E+  + +S+ L K +      +LYED  + V NKPAG+ V GGSG   H 
Sbjct: 71  SLREPDTM--ERAPVSASL-LGKMASI---PVLYEDDSLLVVNKPAGMVVHGGSG---HE 121

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            G +++   S+G    RL HRLD++TSG+L++A+   A + LTESFR R +QK Y++L+ 
Sbjct: 122 AGLIEALKQSRGLDDLRLAHRLDRDTSGVLLMAKHLDALRRLTESFRERDMQKTYFALIA 181

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ---KFCWLEM 245
           G P      +++ L K    GG+   +V  +E+G   +++ ++V+  + +    +  + +
Sbjct: 182 GHPYAHAGRMSSNLAKGVVRGGE--RMVVDSEEG-KASVTDYQVMIEYERHGFPYAMVAL 238

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGR 304
            PH+GRTHQLRV   H G PI+GD KY    +   + S     L LHA  +   HP  G+
Sbjct: 239 NPHSGRTHQLRVQLQHEGHPILGDGKYGEKAQLAAYKSLGGKGLMLHAWRLRFTHPVSGK 298

Query: 305 -LQITAPLPAHMVKTWDSL 322
            L+  AP P      W +L
Sbjct: 299 SLECKAPWP----DNWSAL 313


>gi|34497273|ref|NP_901488.1| pseudouridine synthase [Chromobacterium violaceum ATCC 12472]
 gi|34103129|gb|AAQ59492.1| pseudouridine synthase [Chromobacterium violaceum ATCC 12472]
          Length = 312

 Score =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 102/320 (31%), Positives = 165/320 (51%), Gaps = 23/320 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V+ ++   RLD + +     +   ++ +ILRSG+VRV+K RV  + R+ +G ++R
Sbjct: 9   VTFLEVDAEDAGQRLDNYLQRLLKGVPKSHIYRILRSGEVRVNKGRVDASYRVAAGDMLR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+           ++ + +      + F    ++YED  + V +KPAG++V GGSG++
Sbjct: 69  IPPI-----------RVAERAEKTVPAATF---PVVYEDDALLVIDKPAGVAVHGGSGVS 114

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD+ETSG+L++A+ R+A   L +  R     K Y +L
Sbjct: 115 FGVIEQLRR-AHPEWRYLELVHRLDRETSGLLMLAKKRSALTRLHDMMRDNVPDKRYLAL 173

Query: 187 VWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
             G  P+N K+      L K H       V         YA ++F +   + + F  +E 
Sbjct: 174 ATGHWPENVKQV--KLPLYKFHTPDGERRVKIAEGDDGQYAHTNFSIQQRYTE-FTLVEA 230

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHP-EG 302
              TGRTHQ+RVH    GC I GD KY  +F  N         +++LHA+ + LPHP  G
Sbjct: 231 HLRTGRTHQIRVHMQANGCAIAGDEKY-GDFAYNKELARRGLKRMFLHAKSLTLPHPLTG 289

Query: 303 GRLQITAPLPAHMVKTWDSL 322
             L++ APLP  + K   SL
Sbjct: 290 ATLKLEAPLPPELQKFLKSL 309


>gi|257093130|ref|YP_003166771.1| RluA family pseudouridine synthase [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257045654|gb|ACV34842.1| pseudouridine synthase, RluA family [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 328

 Score =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 120/342 (35%), Positives = 180/342 (52%), Gaps = 43/342 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           +S  +  Q ++ EN E   RLD         +   ++  I+RSGQVRV+ +R + + R+Q
Sbjct: 4   VSKSSVTQALITEN-EHGQRLDNLLLKQCKGVPKSHVYSIVRSGQVRVNGRRAEVSYRLQ 62

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSS---VNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           +G V+RIPP+  A     +EQ+I+  +   V+L          +LYED  + + +KPAGI
Sbjct: 63  TGDVLRIPPLRIAR----REQEIVAGAEFNVDLP---------VLYEDDGLLIIDKPAGI 109

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTE 172
           +V GGSG ++ +   L+       Q+P+     L HRLD+ETSGIL+V + R+A   L E
Sbjct: 110 AVHGGSGESFGVIEALRR------QRPQARFLELAHRLDRETSGILLVGKKRSALLALHE 163

Query: 173 SFR-----MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYA 226
            FR      R   K Y  LV G   +    +   LLK     G+    V+ +E G A++ 
Sbjct: 164 MFRDGGGGGRGADKRYQVLVAGRWMDPVRNVRVPLLKYLQPSGE--RRVRVSEAGKASHT 221

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPI 284
           +  F+++  + + F  LE    TGRTHQ+RVH  H+G P+ GD KY  +F  N       
Sbjct: 222 V--FRLLARW-EHFSLLEAHLKTGRTHQIRVHLAHLGYPVAGDEKY-GDFALNRVLARDG 277

Query: 285 QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
             +++LHA  M LP+P  GR L + APLP  + +  DSL  K
Sbjct: 278 LKRMFLHAWTMRLPNPLDGRDLVVEAPLPVVLRRFLDSLSAK 319


>gi|114320585|ref|YP_742268.1| ribosomal large subunit pseudouridine synthase C [Alkalilimnicola
           ehrlichii MLHE-1]
 gi|114226979|gb|ABI56778.1| ribosomal large subunit pseudouridine synthase C [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 327

 Score =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 101/323 (31%), Positives = 157/323 (48%), Gaps = 22/323 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V+ V +  ++   R+D +       +    + ++LRSGQVRVD KR K   R+ +G+
Sbjct: 12  MSGVRQVRIGPEDAGQRVDNFLMRQLKGVPRSLIYRLLRSGQVRVDGKRTKPPRRLATGE 71

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPPV         + +    +    +    L   +LYED ++ V +KP+G++V GGS
Sbjct: 72  TVRIPPV---------QTRAPQEATPPARLQGELAQRILYEDDRLLVIDKPSGLAVHGGS 122

Query: 124 GIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G+A+   G ++    ++   P   L HRLD+ TSG L+VA+ R+A + L E  R   + K
Sbjct: 123 GLAW---GLIEVLRQARPSAPFLELVHRLDRATSGCLMVAKRRSALRELHEQLRTGAVHK 179

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L+ G        +   L ++S   G  V V    +     A + F+ +        
Sbjct: 180 RYLALLTGALGRGPIPVEAPLERRSGPAGG-VRVASHGK----LARTVFRAV-ARPGGMT 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
             E    TGRTHQ+RVHA H+G PI GD +Y           +   +L+LHA  ++L  P
Sbjct: 234 LAEADIATGRTHQIRVHAAHLGMPIAGDDRYGERAVNRRLRGLGLKRLFLHAHRLELSAP 293

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G+ L I APLP  +      L
Sbjct: 294 GTGQPLSIEAPLPDELAAVVAQL 316


>gi|186475584|ref|YP_001857054.1| RluA family pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184192043|gb|ACC70008.1| pseudouridine synthase, RluA family [Burkholderia phymatum STM815]
          Length = 353

 Score =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 107/321 (33%), Positives = 170/321 (52%), Gaps = 35/321 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + +++     R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +VR
Sbjct: 20  VSMLEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAHGDLVR 79

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+       I +      ++  + H D     +L+ED  + V +KPAG++V GGSG+A
Sbjct: 80  VPPIR------IAKSDEPAHALAPSAHFD-----ILFEDDHLLVIDKPAGVAVHGGSGVA 128

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++    + +   L HRLD+ETSG+L++A+ RAA  +L E  R  R+ K Y++ 
Sbjct: 129 FGVIEQLRA-ARPQAKFLELVHRLDRETSGVLMLAKKRAALVNLHEQIRENRMDKRYYAC 187

Query: 187 V-------WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           V       WG  +  KE +  +LL     G   V V  Q +   ++ +  F +I+ +   
Sbjct: 188 VHGEWASDWGRRRAVKEPLHKYLLPD---GERRVRV--QPDGLPSHTV--FNLIERWPD- 239

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------KLYLHAR 293
           +  LE +  TGRTHQ+RVH  H+G PIVGD KY  +F  N      N      +++LHA 
Sbjct: 240 YALLEAELKTGRTHQIRVHLAHLGLPIVGDAKY-GDFALNKALARANANLGLKRMFLHAY 298

Query: 294 YMDLPHPEGGR-LQITAPLPA 313
            + L HP  G+ +Q  APLPA
Sbjct: 299 RLKLTHPASGQTVQFDAPLPA 319


>gi|77360755|ref|YP_340330.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875666|emb|CAI86887.1| 23S rRNA pseudouridylate synthase, in E. coli modifies positions
           955, 2504, and 2580 in 23 S ribosomal RNA
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 319

 Score =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 99/308 (32%), Positives = 166/308 (53%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D    R+D +   H   +    + K+LR G+VRV+KKR+K   ++Q   V+R
Sbjct: 9   VTYVTINEDHLGQRIDNFLITHLKGVPKSAIYKLLRKGEVRVNKKRIKPVYKLQLEDVLR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I P+      + + ++ + S ++       L++ +++ED  + V NKP+G++V GGSG++
Sbjct: 69  IAPI-----RVAEREEFVPSKLDKVTR---LENDIIFEDKYLIVINKPSGMAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+  +  + +   L HRLD++TSG L++A+ R+    L E  R + ++K YW+L
Sbjct: 121 YGLIEALR-VLRPEERSLELVHRLDRDTSGCLLIAKRRSVLTALHEQLREKTMEKNYWAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G   +K + +   L K +   G+ V  V   E   ++  + FKV++ F +  C L + 
Sbjct: 180 VDGQWDSKTKNVTEGLRKNTLKSGERVVRVDNTEGKPSH--TRFKVLERFNE--CSLVQA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
            P TGRTHQ+RVH    G PI  D KY    F  +      N+L+LHA  +   HP+   
Sbjct: 236 SPVTGRTHQIRVHTQCKGHPIACDDKYGDEEFDNSMRKTGLNRLFLHAHDLTFYHPKNET 295

Query: 304 RLQITAPL 311
            +++ APL
Sbjct: 296 TMRVEAPL 303


>gi|134295142|ref|YP_001118877.1| RluA family pseudouridine synthase [Burkholderia vietnamiensis G4]
 gi|134138299|gb|ABO54042.1| pseudouridine synthase, RluA family [Burkholderia vietnamiensis G4]
          Length = 334

 Score =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 106/335 (31%), Positives = 164/335 (48%), Gaps = 33/335 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + ++ +    R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +VR
Sbjct: 17  VSMIEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLALGDLVR 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A   + + +  +                +LYED  + V NKPAG++V GGSG+A
Sbjct: 77  VPPVRVAAADLARAETPIVPPAQFD---------VLYEDDAMLVINKPAGVAVHGGSGVA 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--- 183
           + +   ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y   
Sbjct: 128 FGVIEQMRQ-ARPRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFAC 186

Query: 184 ----WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
               W   WG    ++  +   L K S   G+   V  Q++   ++ +  F +I+ +   
Sbjct: 187 GHGQWQPDWG----RRRVVKAPLFKYSTAEGER-RVRVQDDGLPSHTV--FNLIERWPD- 238

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHAR 293
           +  +E +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   +++LHA 
Sbjct: 239 YALVEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANAQPSLKRMFLHAY 297

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            + L HP  G  LQ  APLP    +  D L    D
Sbjct: 298 RLKLAHPLSGEPLQFDAPLPDECRRFLDQLSALRD 332


>gi|551786|gb|AAA23442.1| orfX [Escherichia coli]
          Length = 285

 Score =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 102/290 (35%), Positives = 160/290 (55%), Gaps = 17/290 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHA 292
            P TGRTHQ+RVH  + G PI  D +Y    F    T      N+L+LHA
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHA 284


>gi|90407030|ref|ZP_01215220.1| Predicted pseudouridylate synthase, Rlu family protein
           [Psychromonas sp. CNPT3]
 gi|90311901|gb|EAS39996.1| Predicted pseudouridylate synthase, Rlu family protein
           [Psychromonas sp. CNPT3]
          Length = 303

 Score =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 105/317 (33%), Positives = 168/317 (52%), Gaps = 22/317 (6%)

Query: 11  VVENDEENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           ++E  +EN   R+D + + H   +    + +I+R G+VRV+KKR+K + ++Q G +VRIP
Sbjct: 1   MLEISQENAKQRIDNFLRLHLKGVPKSLIYRIIRKGEVRVNKKRIKPDYKLQPGDIVRIP 60

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
           PV      +  E  +    +N       L+S ++YED  + + NKP+GI+V GGSG+++ 
Sbjct: 61  PV-----KVSAENPLPSPKLNAIAQ---LESRIVYEDDALLILNKPSGIAVHGGSGLSFG 112

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            I+G      D++  +  L HRLD+ TSG L++A+ R+  + L E  R + + K Y +LV
Sbjct: 113 AIEGLRALRPDARFLE--LVHRLDKATSGCLLIAKKRSMLRALHEQLRNKTMNKQYLALV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    K   +   LLK S        VVK +  G   A + FK++  +      +E  P
Sbjct: 171 KGSWDKKDRSVKEPLLKDSQNS-----VVKVSALG-KQAETRFKIMQRY-HGATLVEASP 223

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPE-GGRL 305
            TGRTHQ+RVH    G  I GD +Y A  F     +   N+L+LHA ++   HP    ++
Sbjct: 224 VTGRTHQIRVHCACKGHNIAGDDRYGAPEFSKKMQALGLNRLFLHAAHITFYHPVLEKKM 283

Query: 306 QITAPLPAHMVKTWDSL 322
            ++APL A +    + L
Sbjct: 284 TVSAPLCAPLAALLEKL 300


>gi|67459415|ref|YP_247039.1| ribosomal large subunit pseudouridine synthase [Rickettsia felis
           URRWXCal2]
 gi|75536169|sp|Q4UKQ3|RLUC_RICFE RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|67004948|gb|AAY61874.1| Ribosomal large subunit pseudouridine synthase [Rickettsia felis
           URRWXCal2]
          Length = 305

 Score =  149 bits (375), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 99/308 (32%), Positives = 165/308 (53%), Gaps = 25/308 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R++ G  + I    +  N  +K
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNSQKAEASLRVKGGDKIFIN---DKFNLPVK 68

Query: 80  EQKIL---DSSVNLTKH--SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           + + L   D+ + L K   +D+L    +YED  +   NKPAG++ QGGS I   ID  LK
Sbjct: 69  QPEKLVFTDAEIKLAKKITTDYL----IYEDDNLIAINKPAGLATQGGSKINLSIDSALK 124

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KN 193
            +++ KG   +L HRLD+ETSG+L++A+   +   L ++F+ + + K Y+++ +G P KN
Sbjct: 125 -YLNYKGADFKLVHRLDKETSGLLLIAKNYLSNVKLHDAFKEKLVVKTYFAVTYGKPIKN 183

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E  +N  ++KS   G    +     +    AI+++K++         +E  P TGR H
Sbjct: 184 VGEVRSN--IEKSK--GSTPKITDIYSENGKLAITYYKLLKSLDNNLFLIEFTPVTGRMH 239

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           QLR+HA  +GCPIVGD KY     GN    P    ++LHA  + L     G+ + + A L
Sbjct: 240 QLRLHAKLLGCPIVGDDKY-----GNKEIMPYSKYMFLHANNICLSEKIFGKEINLEAKL 294

Query: 312 PAHMVKTW 319
           P +    +
Sbjct: 295 PFYFTDKF 302


>gi|169634491|ref|YP_001708227.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii SDF]
 gi|169153283|emb|CAP02389.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii]
          Length = 310

 Score =  149 bits (375), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 100/318 (31%), Positives = 168/318 (52%), Gaps = 23/318 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   ++  G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLAIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAAPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           Y   G +++   + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y +
Sbjct: 123 Y---GLIEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +V G     K+ I   L +     G+  V V K+ +       + + V + F +    + 
Sbjct: 180 IVKGQVSLDKQLIDAPLFRYELANGERRVRVSKEGKPSK----TEWVVAERF-KNATLVH 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P +GRTHQ+RVH L +G P+VGD KY  N    +T P   +L LHA  +D+P    G 
Sbjct: 235 ASPLSGRTHQIRVHGLSIGHPLVGDDKYGHNTA--YTGPEARRLCLHAMRLDIP----GY 288

Query: 305 LQITAPLPAHMVKTWDSL 322
             I APLP  M +  ++L
Sbjct: 289 PTIEAPLPEDMTQLLEAL 306


>gi|307730549|ref|YP_003907773.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1003]
 gi|307585084|gb|ADN58482.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1003]
          Length = 345

 Score =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 105/323 (32%), Positives = 171/323 (52%), Gaps = 38/323 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 21  VSVIEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVR 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+  A +     Q  + S+          +  +++ED  + V +KPAG++V GGSG+A
Sbjct: 81  VPPIRVAQHDEAAAQAPVPSA----------QFKIIFEDEHLLVIDKPAGVAVHGGSGVA 130

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++   +++ Q     L HRLD+ETSGIL++A+ R+A  +L +  R  ++ K Y+
Sbjct: 131 F---GVIEQMREARPQAKFLELVHRLDRETSGILMLAKKRSALVNLHDQIRENKMDKRYY 187

Query: 185 SLV-------WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           + V       WG  +  KE +  +L      G   V V  Q +  A++ +  F +ID + 
Sbjct: 188 ACVHGDWASDWGRRRAVKEPLHKYLTAD---GERRVRV--QADGLASHTV--FNLIDRWP 240

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLH 291
             +  LE +  TGRTHQ+RVH  H+  PIVGD KY  +F  N         P   +++LH
Sbjct: 241 D-YALLEAELKTGRTHQIRVHLQHLELPIVGDAKY-GDFALNKALARANAKPGLKRMFLH 298

Query: 292 ARYMDLPHPE-GGRLQITAPLPA 313
           A  + L HP  G  LQ+ APLPA
Sbjct: 299 AYRLKLTHPATGAPLQLEAPLPA 321


>gi|92113717|ref|YP_573645.1| ribosomal large subunit pseudouridine synthase C [Chromohalobacter
           salexigens DSM 3043]
 gi|91796807|gb|ABE58946.1| ribosomal large subunit pseudouridine synthase C [Chromohalobacter
           salexigens DSM 3043]
          Length = 315

 Score =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 98/307 (31%), Positives = 162/307 (52%), Gaps = 15/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V V   +   R+D + +          + +I+R G++RV+KKRVK + R++ G +VR
Sbjct: 7   VQWVEVSEGQVGQRIDNFLRTRLKGAPKSLIYRIVRKGEIRVNKKRVKADYRLELGDLVR 66

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A    ++E  + D   NL      L   +L E     V NKPAG++V GGSG+ 
Sbjct: 67  IPPLRLAPEEAVRE--VSDGLRNL------LAGSVLVEGPAWLVINKPAGLAVHGGSGVK 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L+   D       L HRLD++TSG L++A++R A   L ++ +  ++ K Y +L
Sbjct: 119 IGLIEALRQVRDDL-DFLELVHRLDRDTSGCLLLAKSRTALVTLNQALKAHQMDKQYLAL 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    ++E ++  L +     G+    V+ + +G   + + F V + F+ +   +E +
Sbjct: 178 VQGRWPTRREFVSARLDRFD--AGNGERRVRVDSQG-KVSRTRFAVREAFS-RVTLIEAE 233

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA H G  ++GD KY           ++  +L+LH+  +  P P  GR 
Sbjct: 234 PVTGRTHQIRVHAAHAGHALLGDDKYGTREGARLARELKLERLFLHSNALTFPEPSSGRP 293

Query: 305 LQITAPL 311
           + + APL
Sbjct: 294 VHVKAPL 300


>gi|183179760|ref|ZP_02957971.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MZO-3]
 gi|183013171|gb|EDT88471.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MZO-3]
          Length = 267

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 95/271 (35%), Positives = 157/271 (57%), Gaps = 17/271 (6%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           ++KKRVK   ++++G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  
Sbjct: 1   MNKKRVKAEYKLEAGDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDH 55

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + + NKP+G +V GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A 
Sbjct: 56  LLILNKPSGTAVHGGSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSAL 114

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           +HL   FR + +QK Y++LV G      EC + N  L K+ +      +V+ N  G   +
Sbjct: 115 RHLQAQFREKTVQKYYYALVMG--HWDAECKVVNAPLLKNEVNS----IVRVNPNG-KPS 167

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ- 285
            + F++++ FA+    ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+    
Sbjct: 168 ETRFRILEKFAEA-TLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGI 226

Query: 286 NKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
            +L+LHA  +   HP    +L+I APL AH+
Sbjct: 227 ERLFLHAANIQFVHPASEKKLEIHAPLEAHL 257


>gi|170695400|ref|ZP_02886545.1| pseudouridine synthase, RluA family [Burkholderia graminis C4D1M]
 gi|170139591|gb|EDT07774.1| pseudouridine synthase, RluA family [Burkholderia graminis C4D1M]
          Length = 345

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 106/323 (32%), Positives = 172/323 (53%), Gaps = 38/323 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 21  VSVIEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVR 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      + +  + + S+      ++F    +++ED  + V +KPAG++V GGSG+A
Sbjct: 81  VPPI-----RVAQHDETVPSAP--VPSAEFR---IIFEDEHLLVIDKPAGVAVHGGSGVA 130

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    S+ Q     L HRLD+ETSGIL++A+ R+A  +L +  R  R+ K Y+
Sbjct: 131 F---GVIEQMRQSRPQAKFLELVHRLDRETSGILMLAKKRSALVNLHDQIRENRMDKRYY 187

Query: 185 SLV-------WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           + V       WG  +  KE +  +L      G   V V  Q +  A++ +  F +ID + 
Sbjct: 188 ACVHGEWASDWGRRRAVKEPLHKYLTAD---GERRVRV--QADGLASHTV--FNLIDRWP 240

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLH 291
             +  LE +  TGRTHQ+RVH  H+  PIVGD KY  +F  N         P   +++LH
Sbjct: 241 D-YALLEAELKTGRTHQIRVHLQHLELPIVGDAKY-GDFALNKALARSNAKPGLKRMFLH 298

Query: 292 ARYMDLPHPE-GGRLQITAPLPA 313
           A  + L HP  G  LQ+ APLPA
Sbjct: 299 AYRLKLTHPATGAPLQLEAPLPA 321


>gi|298370246|ref|ZP_06981562.1| ribosomal large subunit pseudouridine synthase C [Neisseria sp.
           oral taxon 014 str. F0314]
 gi|298281706|gb|EFI23195.1| ribosomal large subunit pseudouridine synthase C [Neisseria sp.
           oral taxon 014 str. F0314]
          Length = 332

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 99/321 (30%), Positives = 171/321 (53%), Gaps = 25/321 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RIQ+G ++R
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIQAGDLLR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A     ++Q+  ++ V      +F    ++YED  + V NKP+G +V GGSG++
Sbjct: 71  IPPVRTA-----EKQRPSENRVQAAPAREF---DIVYEDDALLVINKPSGTAVHGGSGVS 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++     + +   L HRLD++TSG+L++A+ R+A   L E+ R  R +KIY +L
Sbjct: 123 FGVIEQIR-RARPEARYLELVHRLDKDTSGLLMIAKKRSALVRLHEAIRNDRPKKIYLAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G  +N +  +   L K +   G+ +  V ++ + A+     F+V++ F+         
Sbjct: 182 GVGRLENDRFHVKLPLFKYTGAQGEKMVRVSEDGQSAHTV---FRVLNRFSDGLLHQAGL 238

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +E    TGRTHQ+RVH     CPI GD +Y  +++ N         +++LHA  +
Sbjct: 239 SHLTLVEATLKTGRTHQIRVHLQSQHCPIAGDERY-GDYQANKRLQKLGLKRMFLHASEL 297

Query: 296 DLPHP-EGGRLQITAPLPAHM 315
            L HP  G +L + A LP  +
Sbjct: 298 HLDHPLTGEKLVLKADLPQEL 318


>gi|315498200|ref|YP_004087004.1| pseudouridine synthase [Asticcacaulis excentricus CB 48]
 gi|315416212|gb|ADU12853.1| pseudouridine synthase [Asticcacaulis excentricus CB 48]
          Length = 286

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 86/249 (34%), Positives = 134/249 (53%), Gaps = 7/249 (2%)

Query: 79  KEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + QK +D  + L+     ++KS+L++ED  I  FNKP+ +S QGG G  +++D  L ++ 
Sbjct: 41  RNQKAIDRPLKLSDEEVVWVKSMLIHEDGVIMGFNKPSNLSSQGGRGNFHNLDDMLWAFA 100

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            S G KPRL HRLD++TSGI++ A+TR +A  +  +   R + K Y  +V      K E 
Sbjct: 101 RSNGNKPRLLHRLDRDTSGIILAAKTRTSAAFVGNAIAARDVHKAYVCIVANPHNLKDEG 160

Query: 198 IANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           + +  L++  IG + Y  +   +   A  A + ++V+         ++ +P TGR HQ+R
Sbjct: 161 VIDAPLRREEIGREAYSRICDPHHPDALTARTIYRVV-SRTDTSALVQCEPFTGRMHQIR 219

Query: 257 VHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           VH  H+GCPI GD +Y           P   +L LHAR +D PHP+GGR +  AP    +
Sbjct: 220 VHMAHLGCPIAGDVRYGGALSLDGLRVP---RLMLHARAIDFPHPDGGRRRWEAPPSPDI 276

Query: 316 VKTWDSLGF 324
                 LG 
Sbjct: 277 QALCKGLGL 285


>gi|292490642|ref|YP_003526081.1| pseudouridine synthase [Nitrosococcus halophilus Nc4]
 gi|291579237|gb|ADE13694.1| pseudouridine synthase, RluA family [Nitrosococcus halophilus Nc4]
          Length = 325

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 111/314 (35%), Positives = 172/314 (54%), Gaps = 21/314 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V ++ ++   R+D +  +    +    + + LR G+VRV+K RV  + R++ G  VR
Sbjct: 12  VRLVEIQLEQAGQRIDNFLLSQLKGVPKSRIYRCLRRGEVRVNKSRVASSYRLEQGDQVR 71

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+   ++H   ++ +  S ++L      ++S LLYED  + + NKPAGI+V  GS I+
Sbjct: 72  IPPL--RVSHPSVKEPVAPSLLHL------IESSLLYEDKHLLILNKPAGIAVHSGSSIS 123

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           Y   G +++    + + P   L HRLD+ETSG L+VA+TR+    L    R + I K Y 
Sbjct: 124 Y---GVIETLRHLRPEAPFLELVHRLDRETSGCLMVAKTRSTLLALQSMQREQLIHKRYL 180

Query: 185 SLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G  P+N  + +   LLK     G+   VVK +  G   A SHF     + ++   +
Sbjct: 181 ALVKGRWPRNIGQ-VNLPLLKNILQSGE--RVVKVSATG-KPAASHFHPKQLY-KEATLM 235

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           E+   TGRTHQ+RVHA H+G P+ GD KY    F     +    +L+LHA  +    PEG
Sbjct: 236 EITLETGRTHQIRVHAAHLGHPLGGDEKYGDPAFNKRLRNLGLRRLFLHADQLSFTPPEG 295

Query: 303 GR-LQITAPLPAHM 315
            + L+ITAPLP  +
Sbjct: 296 KKLLKITAPLPEEL 309


>gi|219682262|ref|YP_002468646.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. Tuc7 (Acyrthosiphon pisum)]
 gi|219621995|gb|ACL30151.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. Tuc7 (Acyrthosiphon pisum)]
 gi|311086084|gb|ADP66166.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. LL01 (Acyrthosiphon pisum)]
 gi|311086657|gb|ADP66738.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. TLW03 (Acyrthosiphon pisum)]
 gi|311087242|gb|ADP67322.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. JF99 (Acyrthosiphon pisum)]
 gi|311087761|gb|ADP67840.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. JF98 (Acyrthosiphon pisum)]
          Length = 314

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 96/314 (30%), Positives = 173/314 (55%), Gaps = 28/314 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + +  +  N R+D + ++ +  +    + +I+R+G++R++KKR+K + +++ G +++
Sbjct: 8   ISIIYINKEMLNQRIDNFMRSKFKSVPKSMIYRIIRTGKIRINKKRIKPHYKLKIGDILK 67

Query: 67  IPPVINALNHIIKEQKILDSSVNL---TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           IPP+           KIL    N      HS  L + +LYEDS + + NKP+GI+V GGS
Sbjct: 68  IPPI-----------KILCDIKNTFFPLNHSTNLLNRILYEDSHLLIINKPSGIAVHGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+ + +  + +  +    +   L HR+D++TSG+L++A+ R +   L E  R ++I+K Y
Sbjct: 117 GLNFGVIEYFRK-LRPLNKFLELVHRIDRDTSGVLILAKKRTSLVSLHEQLREKKIKKEY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G+  +  + I+  LLK        + ++ +  K +    ++F++   F+     L
Sbjct: 176 IALVHGLWPDHIKKISEPLLKIQFKNKQKMVLIDKKGKPSE---TYFQIKKKFSSS-TLL 231

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-----NKLYLHARYMDLP 298
            + P TGRTHQ+RVHALH G PI  D +Y  N   N  + I+     N+L LH+  +   
Sbjct: 232 SIIPKTGRTHQIRVHALHAGHPIFFDKRYGKN---NLDADIKNNHKINRLLLHSSGVHFI 288

Query: 299 HPE-GGRLQITAPL 311
           HP+ G ++ I APL
Sbjct: 289 HPKNGNKIYIKAPL 302


>gi|165977322|ref|YP_001652915.1| 23S rRNA pseudouridylate synthase C [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|165877423|gb|ABY70471.1| ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
          Length = 321

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 108/307 (35%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q   VVR
Sbjct: 11  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQPDDVVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPVRVA------EKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+   +V+ +E+G   + +HF + + +A     ++  
Sbjct: 183 VRGQWQAHTKVIKAPLLKNELASGE--RIVRVSEEG-KPSETHFSIEERYANA-TLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 298

Query: 305 LQITAPL 311
           + ITAPL
Sbjct: 299 MLITAPL 305


>gi|302878469|ref|YP_003847033.1| pseudouridine synthase, RluA family [Gallionella capsiferriformans
           ES-2]
 gi|302581258|gb|ADL55269.1| pseudouridine synthase, RluA family [Gallionella capsiferriformans
           ES-2]
          Length = 319

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 106/344 (30%), Positives = 173/344 (50%), Gaps = 38/344 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ ++   E  R+D +   H   +   ++ +ILR G+VRV+KKRV    R++ G ++R
Sbjct: 9   VTFLTIDESGEEQRIDNFLFRHLKGVPKSHVYRILR-GEVRVNKKRVDQTYRLKLGDLLR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A    + E  I             L+  ++YED  + + NKP+G++V GGSG++
Sbjct: 68  IPPVRVAQKQEVDEVYI-----------PALELPVIYEDDALVIINKPSGLAVHGGSGVS 116

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    ++ Q     L HRLD+ETSG+L++A+ R+A   + E  R     K Y 
Sbjct: 117 F---GVIEQMRRARPQAKFLELVHRLDRETSGVLLLAKKRSALTAMHEIMREGVSDKRYL 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   N ++ +   L K     G+   +V++  + ++   S    +      +  LE
Sbjct: 174 TLVLGQWNNARQHVKLPLFKFDTPQGEKRVMVREGGQASHTIFS----LQKNWPGYSLLE 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEG 302
            Q  TGRTHQ+RVH  H+G PI GD KY  +F  N     Q   +++LHA  +   HP  
Sbjct: 230 AQLKTGRTHQIRVHLSHLGFPIAGDDKY-GDFARNRELMKQGLKRMFLHAHSISFSHPLT 288

Query: 303 GR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNI 345
           G  + I+APLP  +               +I +L +Q+  K N+
Sbjct: 289 GEPMHISAPLPPELAS-------------FIAKLDAQEAAKDNL 319


>gi|187924897|ref|YP_001896539.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187716091|gb|ACD17315.1| pseudouridine synthase, RluA family [Burkholderia phytofirmans
           PsJN]
          Length = 341

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 105/323 (32%), Positives = 171/323 (52%), Gaps = 38/323 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 17  VSMIEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVR 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP        I+  +  +++      +   K  +++ED  + V +KPAG++V GGSG+A
Sbjct: 77  VPP--------IRVAQPSETATQAPVPAAHFK--IIFEDEHLLVIDKPAGVAVHGGSGVA 126

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++   +++ Q     L HRLD+ETSGIL++A+ R+A  +L E  R  ++ K Y+
Sbjct: 127 F---GVIEQMREARPQAKFLELVHRLDRETSGILMLAKKRSALVNLHEQIRENKMDKRYY 183

Query: 185 SLV-------WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           + V       WG  +  KE +  +L      G   V V  Q +  A++ +  F +ID + 
Sbjct: 184 ACVHGDWASDWGRRRAVKEPLHKYLTAD---GERRVRV--QPDGLASHTV--FNLIDRWP 236

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLH 291
           + +  LE +  TGRTHQ+RVH  H+  PIVGD KY  +F  N         P   +++LH
Sbjct: 237 E-YALLEAELKTGRTHQIRVHLQHLELPIVGDAKY-GDFALNKALARANAKPGLKRMFLH 294

Query: 292 ARYMDLPHPE-GGRLQITAPLPA 313
           A  + L HP  G  LQ  APLPA
Sbjct: 295 AYRLKLTHPATGAPLQFEAPLPA 317


>gi|56416692|ref|YP_153766.1| ribosomal large subunit pseudouridine synthase [Anaplasma marginale
           str. St. Maries]
 gi|222475057|ref|YP_002563472.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Florida]
 gi|255003036|ref|ZP_05278000.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Puerto Rico]
 gi|255004159|ref|ZP_05278960.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Virginia]
 gi|56387924|gb|AAV86511.1| ribosomal large subunit pseudouridine synthase [Anaplasma marginale
           str. St. Maries]
 gi|222419193|gb|ACM49216.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Florida]
          Length = 296

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 99/315 (31%), Positives = 164/315 (52%), Gaps = 27/315 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +VE     +R+DR+ +   P +    ++++LR G++ ++  + K + R+ +G V+ I   
Sbjct: 6   LVEGTCFEVRVDRYLRGLLPGVTQSFIERLLRRGEILLNNTKAKSSTRVSNGDVLSIK-- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            +A    ++E++I   ++      D +   +LYED  I   NKPAG+SVQGGS +   ID
Sbjct: 64  -HADRIALREKEI--RALQHVPLLDLISGSILYEDKNIIAINKPAGVSVQGGSKVKVSID 120

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L       G+  R+ HRLD++TSG+LV+AR    A++L   FR RR++K Y ++  G+
Sbjct: 121 DVLDKI--KPGECCRIVHRLDKDTSGVLVLARNLDVARYLAREFRERRVKKEYIAVTRGV 178

Query: 191 PKNKKECIANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQP 247
           P+     ++  +  K  S  G   +      EK A    S  +++ DC       + ++P
Sbjct: 179 PQPASGEVSTPIFYKVRSATGESMI------EKEAKTFFSVMRILGDC-----AVVLLRP 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGR HQLR+H   +GCPIVGD+KY    K +     +  L+LHA  +      G  L I
Sbjct: 228 VTGRKHQLRIHMSQIGCPIVGDNKY---HKCDLAE--KEMLHLHASLLTF-ELMGRTLSI 281

Query: 308 TAPLPAHMVKTWDSL 322
            A +P +M +  + L
Sbjct: 282 AANVPRYMEEKINPL 296


>gi|57239048|ref|YP_180184.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Welgevonden]
 gi|58578991|ref|YP_197203.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Welgevonden]
 gi|57161127|emb|CAH58040.1| putative ribosomal large subunit pseudouridine synthase C
           [Ehrlichia ruminantium str. Welgevonden]
 gi|58417617|emb|CAI26821.1| Ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Welgevonden]
          Length = 305

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 97/312 (31%), Positives = 160/312 (51%), Gaps = 24/312 (7%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +Y  ++ D   +R+DR+ +     I    ++K LR+  + +D  +VK N ++  G V+ +
Sbjct: 3   KYYTIQEDNLGVRIDRFIRKEL-RIPQSLIEKFLRNRIILLDGLKVKSNTKLNVGNVIYV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSG 124
                  N  I  ++  D  V        +K I   ++YED  + V NKP+G+SVQGGS 
Sbjct: 62  Q------NECIISKEKKDKKVCKFASESLVKLICDNIVYEDDNVLVINKPSGVSVQGGSK 115

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   I   L S     G+  ++ HRLD+ TSGIL++AR    ++ +   F+ R+++K Y 
Sbjct: 116 VKISISDVLDSI--RIGESMKIVHRLDKSTSGILMLARNARVSRLIMNEFKDRKVKKKYL 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L  GIP +    I   ++KK H        +++N      A++ F  +         L+
Sbjct: 174 ALTCGIPDDDFGQIDYPIVKKKH-----GITLEKNMSFMQQAVTMFSTLRKLPNDIGLLD 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHPEGG 303
           +QP TGR HQ+R+H   +GCPIVGD KY     G     I N  L LHA ++ + + +G 
Sbjct: 229 LQPITGRKHQIRIHLSRIGCPIVGDVKY-----GKICDSISNDYLQLHAYFLSI-NIDGK 282

Query: 304 RLQITAPLPAHM 315
            + IT P+P++M
Sbjct: 283 EISITIPMPSYM 294


>gi|115351042|ref|YP_772881.1| RluA family pseudouridine synthase [Burkholderia ambifaria AMMD]
 gi|115281030|gb|ABI86547.1| pseudouridine synthase, RluA family [Burkholderia ambifaria AMMD]
          Length = 334

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 105/335 (31%), Positives = 163/335 (48%), Gaps = 33/335 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + ++ +    R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +VR
Sbjct: 17  VSMLEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDIVR 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A   + +    +                +LYED  + V NKPAG++V GGSG+A
Sbjct: 77  VPPVRVAAADLARADTPIVPPAQFE---------VLYEDDAMLVINKPAGVAVHGGSGVA 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--- 183
           + +   ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y   
Sbjct: 128 FGVIEQMRQ-ARPRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFAC 186

Query: 184 ----WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
               W   WG    ++  +   L K S   G+   V  Q++   ++ +  F +++ +   
Sbjct: 187 GHGEWQSDWG----RRRAVKAPLFKYSTAEGER-RVRVQDDGLPSHTV--FNLLERWPD- 238

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHAR 293
           +  +E +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   +++LHA 
Sbjct: 239 YALVEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANAQPSLKRMFLHAH 297

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            + L HP  G  LQ  APLP    +  D L    D
Sbjct: 298 RLKLAHPLTGEPLQFDAPLPDECRRFLDQLSALRD 332


>gi|260220730|emb|CBA28584.1| Ribosomal large subunit pseudouridine synthase C [Curvibacter
           putative symbiont of Hydra magnipapillata]
          Length = 361

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 109/334 (32%), Positives = 164/334 (49%), Gaps = 29/334 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ V V+ D    RLD +       +   ++ +I+RSG+VRV+K R   + R+  G V
Sbjct: 18  SQVKSVTVDEDSAGQRLDNFLMRELKGVPKTHVYRIIRSGEVRVNKGRASADTRLAVGDV 77

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+PPV  +     K   + +         DF    +L+ED      +KPAG++V GGSG
Sbjct: 78  IRLPPVRTSERAEQKTAAMAEQVGRFVPAKDF---PVLFEDDHFLAVDKPAGVAVHGGSG 134

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L+     K     L HRLD+ETSGIL+VA+ R+A ++L + FR R   K Y 
Sbjct: 135 VSFGVIEQLR-MARPKATFLELVHRLDRETSGILLVAKKRSALKNLQDQFRERETGKTYL 193

Query: 185 SLVWGI-PKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-------- 232
           +LV G  P NKK   + +  +LL     G   V VV ++   A  ++S  KV        
Sbjct: 194 ALVAGQWPANKKVLDKSLQKYLLAD---GERRVRVVAKDHPDAMPSLSLVKVHSVTPAAR 250

Query: 233 -IDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---- 286
                 QK +  LE+   TGRTHQ+RVH    G  IVGD KY  +F  N      +    
Sbjct: 251 TAQTPQQKVYSLLEVTIKTGRTHQIRVHLASEGMGIVGDDKY-GDFDLNKALARDDGALA 309

Query: 287 --KLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
             +++LHA      HP  G R+ +   LP  + +
Sbjct: 310 LKRMFLHAWRFQCNHPATGERVVLQTGLPPELAR 343


>gi|169797345|ref|YP_001715138.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii AYE]
 gi|184156731|ref|YP_001845070.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|213155841|ref|YP_002317886.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           baumannii AB0057]
 gi|215484783|ref|YP_002327018.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB307-0294]
 gi|260556236|ref|ZP_05828455.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           baumannii ATCC 19606]
 gi|301345638|ref|ZP_07226379.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB056]
 gi|301511837|ref|ZP_07237074.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB058]
 gi|301597322|ref|ZP_07242330.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB059]
 gi|332852954|ref|ZP_08434464.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6013150]
 gi|332867958|ref|ZP_08437946.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6013113]
 gi|332873142|ref|ZP_08441099.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6014059]
 gi|169150272|emb|CAM88169.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii AYE]
 gi|183208325|gb|ACC55723.1| Pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|213055001|gb|ACJ39903.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           baumannii AB0057]
 gi|213987620|gb|ACJ57919.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB307-0294]
 gi|260410291|gb|EEX03590.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           baumannii ATCC 19606]
 gi|322506621|gb|ADX02075.1| rluC [Acinetobacter baumannii 1656-2]
 gi|323516497|gb|ADX90878.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332728890|gb|EGJ60245.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6013150]
 gi|332733659|gb|EGJ64818.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6013113]
 gi|332738654|gb|EGJ69524.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6014059]
          Length = 310

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 98/319 (30%), Positives = 172/319 (53%), Gaps = 25/319 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   ++  G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLAIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKH-SDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           + P        I+ ++  +++V ++   +  L S ++YED  + V NKP+GI+V GGSG+
Sbjct: 70  VAP--------IRYEQKDETAVPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAVHGGSGV 121

Query: 126 AYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           AY   G +++   + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y 
Sbjct: 122 AY---GLIEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYA 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++V G     K+ I   L +     G+  V V K+ +       + + V + F +    +
Sbjct: 179 AIVKGQVSLDKQLIDAPLFRYELANGERRVRVSKEGKPSK----TEWVVAERF-KNATLV 233

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              P +GRTHQ+RVH L +G P+VGD KY  N    +T P   +L LHA  +D+P    G
Sbjct: 234 HASPLSGRTHQIRVHGLSIGHPLVGDDKYGHNTA--YTGPEARRLCLHAMRLDIP----G 287

Query: 304 RLQITAPLPAHMVKTWDSL 322
              I APLP  M +  ++L
Sbjct: 288 YPTIEAPLPEDMTQLLEAL 306


>gi|172060047|ref|YP_001807699.1| RluA family pseudouridine synthase [Burkholderia ambifaria MC40-6]
 gi|171992564|gb|ACB63483.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MC40-6]
          Length = 316

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 104/332 (31%), Positives = 163/332 (49%), Gaps = 33/332 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++ +    R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +VR+PP
Sbjct: 2   IEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDIVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A   + +    +                +LYED  + V NKPAG++V GGSG+A+ +
Sbjct: 62  VRVAAADLARADTPIVPPAQFE---------VLYEDDAMLVINKPAGVAVHGGSGVAFGV 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY------ 183
              ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y      
Sbjct: 113 IEQMRQ-ARPRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFACGHG 171

Query: 184 -WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            W   WG    ++  +   L K S   G+   V  Q++   ++ +  F +++ + + +  
Sbjct: 172 EWQSDWG----RRRAVKAPLFKYSTAEGER-RVRVQDDGLPSHTV--FNLLERWPE-YAL 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMD 296
           +E +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   +++LHA  + 
Sbjct: 224 VEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANAQPSLKRMFLHAHRLK 282

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L HP  G  LQ  APLP    +  D L    D
Sbjct: 283 LAHPLTGEPLQFDAPLPDECRRFLDQLSALRD 314


>gi|33519868|ref|NP_878700.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Blochmannia floridanus]
 gi|33504213|emb|CAD83475.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Blochmannia floridanus]
          Length = 322

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 103/316 (32%), Positives = 165/316 (52%), Gaps = 31/316 (9%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D +   +   +    + +++R G+VRV+KKR+KF  R++ G +++IP         IK
Sbjct: 21  RVDNFLSFYLKTVPKSMIYRMIRIGKVRVNKKRIKFQYRLKIGDLLKIPA--------IK 72

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             KI  S +       FL++ ++YED  + V NKP+GISV GG      ++      +D+
Sbjct: 73  YVKIRQSCMCNISEMMFLQNTVIYEDEHLLVLNKPSGISVHGGGDNKLQLN-----IIDA 127

Query: 140 -KGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            +  +P+     L HRLD++TSG+L++A++R     L E  R+++IQK Y ++V+G    
Sbjct: 128 LRMLRPKIRFLWLVHRLDRDTSGLLLIAKSRIVLIKLHEQLRLQKIQKTYLAIVYGSWDT 187

Query: 194 KKECIANWLLKKSHIGGDYV---HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
               I+  L KK     DY+   +VV  + K    A + F+V + F      L + P TG
Sbjct: 188 HITSISAPLFKKK----DYIKNINVVFIDSKFGKLAQTCFQVKERFKNIATLLNIIPITG 243

Query: 251 RTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
           RTHQ+RVH  +  CPI+GDH Y        F     N+L+LHA  +   HP    ++ I+
Sbjct: 244 RTHQIRVHTQYAQCPIIGDHVYGKQKVNVQFKKLGWNRLFLHASTLCFIHPCTEEKMNIS 303

Query: 309 APLPAHMVKTWDSLGF 324
           AP+       +D L F
Sbjct: 304 APVDQSF---YDCLSF 316


>gi|78065696|ref|YP_368465.1| pseudouridine synthase, RluD [Burkholderia sp. 383]
 gi|77966441|gb|ABB07821.1| Pseudouridine synthase, RluD [Burkholderia sp. 383]
          Length = 334

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 110/333 (33%), Positives = 173/333 (51%), Gaps = 29/333 (8%)

Query: 8   QYVVVENDEENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Q  ++E DE ++  R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +V
Sbjct: 16  QVSMLEIDESSVGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDIV 75

Query: 66  RIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           R+PPV + A +    E  I+  +     H D     +L+ED  + V NKPAG++V GGSG
Sbjct: 76  RVPPVRVAAADLARAEATIVPPA-----HFD-----VLFEDDAMLVINKPAGVAVHGGSG 125

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +A+ +   ++     + +   L HRLD+ETSG+L++A+ R A   L E  R  ++ K Y+
Sbjct: 126 VAFGVIEQMRQ-ARPRAKFLELVHRLDRETSGVLMLAKKRTALVGLHEQIRENKMDKRYF 184

Query: 185 SLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           + V   W     ++  +   L K S   G+   V  Q++   ++ +  F ++D + + + 
Sbjct: 185 ACVHGEWQSDWGRRRAVKAPLFKYSTPEGER-RVRVQDDGLPSHTV--FNLVDLWPE-YA 240

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYM 295
            LE +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   +++LHA  +
Sbjct: 241 LLEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANAQPSLKRMFLHAYRL 299

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
            L HP  G  LQ  APLP    +  D L    D
Sbjct: 300 RLAHPLTGEALQFDAPLPDECRRFLDQLSALRD 332


>gi|301328545|ref|ZP_07221606.1| pseudouridine synthase, RluA family [Escherichia coli MS 78-1]
 gi|300844937|gb|EFK72697.1| pseudouridine synthase, RluA family [Escherichia coli MS 78-1]
          Length = 283

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 102/278 (36%), Positives = 157/278 (56%), Gaps = 18/278 (6%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           +ILR G+VRV+KKR+K   ++++G  VRIPPV       + E++    S +L K +  L 
Sbjct: 4   RILRKGEVRVNKKRIKPEYKLEAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALA 56

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            ++LYED  I V NKP+G +V GGSG+++ +   L++ +  + +   L HRLD++TSG+L
Sbjct: 57  DVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVL 115

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+ R+A + L E  R + +QK Y +LV G  ++  + +   LLK     G+ +  V Q
Sbjct: 116 LVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQ 175

Query: 219 NEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANF 276
             K +    + FKV + +A  F  L    P TGRTHQ+RVH  + G PI  D +Y    F
Sbjct: 176 EGKPSE---TRFKVEERYA--FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREF 230

Query: 277 KGNFTSPIQ--NKLYLHARYMDLPHPEGGR-LQITAPL 311
               T      N+L+LHA  +   HP  G  ++I AP+
Sbjct: 231 DRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPM 268


>gi|119945867|ref|YP_943547.1| pseudouridine synthase, RluA family protein [Psychromonas
           ingrahamii 37]
 gi|119864471|gb|ABM03948.1| ribosomal large subunit pseudouridine synthase C [Psychromonas
           ingrahamii 37]
          Length = 312

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 101/316 (31%), Positives = 172/316 (54%), Gaps = 20/316 (6%)

Query: 11  VVENDEENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           ++E  +EN   R+D + + H   +    + +I+R G+VRV+KKR+K + ++Q+G  VRIP
Sbjct: 10  ILEITQENAQQRIDNYLRLHLKGVPKSMIYRIVRKGEVRVNKKRIKPDYKLQTGDFVRIP 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           PV      + KE  +    +N       L+S ++YED  + + NKP+G++V GGSG+ + 
Sbjct: 70  PV-----RVAKENALPSPKLNKIAR---LESQIVYEDDGLIILNKPSGLAVHGGSGLDFG 121

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           I   L++ +  + +   L HRLD+ TSG L++A+ R+  + L E  R + + K Y +LV 
Sbjct: 122 IIEGLRA-LRPESRFLELVHRLDKATSGCLLIAKKRSMLRALHEQLRNKTMNKQYHALVK 180

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+ + K   +   LLKK+        +VK +E G   + + FK++  + Q    +E  P 
Sbjct: 181 GVWEKKWRSVTAPLLKKAQDS-----IVKVSELG-KASETRFKILQRY-QGATLVEASPV 233

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
           TGRTHQ+RVH+   G  I  D +Y    F     +   N+L+LHA ++   HP    ++ 
Sbjct: 234 TGRTHQIRVHSASKGHNIACDDRYGDEQFSKEMQALGLNRLFLHAAHITFFHPVLEKQMT 293

Query: 307 ITAPLPAHMVKTWDSL 322
           ++APL + +    + L
Sbjct: 294 VSAPLCSELTLLLEKL 309


>gi|170700219|ref|ZP_02891235.1| pseudouridine synthase, RluA family [Burkholderia ambifaria
           IOP40-10]
 gi|170134852|gb|EDT03164.1| pseudouridine synthase, RluA family [Burkholderia ambifaria
           IOP40-10]
          Length = 316

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 106/332 (31%), Positives = 164/332 (49%), Gaps = 33/332 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++ +    R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +VR+PP
Sbjct: 2   IEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDIVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A   + +     D+ +    H +     +LYED  + V NKPAG++V GGSG+A+ +
Sbjct: 62  VRVAAADLARA----DTPIVPPAHFE-----VLYEDDAMLVINKPAGVAVHGGSGVAFGV 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY------ 183
              ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y      
Sbjct: 113 IEQMRQ-ARPRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFACGHG 171

Query: 184 -WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            W   WG    ++  +   L K S   G+    V   + G   + + F +++ +   +  
Sbjct: 172 EWQSDWG----RRRAVKAPLFKYSTAEGERRVRV---QDGGLPSHTVFNLLERWPD-YAL 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMD 296
           +E +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   +++LHA  + 
Sbjct: 224 VEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANAQPSLKRMFLHAHRLK 282

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L HP  G  LQ  APLP    +  D L    D
Sbjct: 283 LAHPLTGEPLQFDAPLPDECRRFLDQLSALRD 314


>gi|257454043|ref|ZP_05619317.1| ribosomal large subunit pseudouridine synthase C [Enhydrobacter
           aerosaccus SK60]
 gi|257448521|gb|EEV23490.1| ribosomal large subunit pseudouridine synthase C [Enhydrobacter
           aerosaccus SK60]
          Length = 365

 Score =  147 bits (371), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 103/323 (31%), Positives = 171/323 (52%), Gaps = 36/323 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V Y+ V   + + R+D +       +   ++  ++RS ++RV+ KR K ++++Q   VVR
Sbjct: 56  VNYLTVTRQQHDQRVDNFLLGRLKGLPRSHVYNMIRSDEIRVNGKRCKPHDKLQRNDVVR 115

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL---LYEDSKIYVFNKPAGISVQGGS 123
           I P+  A     +E+ ++          DF +S+L   +YED  + V NKP+G++V GGS
Sbjct: 116 IAPIKLA----TREKPVISP--------DFAQSLLERIVYEDEGLIVLNKPSGMAVHGGS 163

Query: 124 GIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G ++   G +++  ++ G+K   L HR+D++TSG+L++A+ R+  + L E  R + +QK 
Sbjct: 164 GESF---GVIEAMREATGKKYLELVHRIDKDTSGLLMIAKKRSTLKTLQEHLREKTLQKT 220

Query: 183 YWSLVWGIPKNKKECIANWLLK---------KSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           Y  LV G   ++ + I   LLK         KS      V V  ++ K +   I+  +  
Sbjct: 221 YLCLVVGWISSETQTIDKPLLKYTLPATQEGKSGERRVKVDVKSEDSKPSQTQINVLQKF 280

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGNFTSPIQNKLYLHA 292
           +   QK   +E +P TGRTHQ+RVH   +G P++GD KY  N  KG+    +  +L LHA
Sbjct: 281 ELNGQKVSLIEAKPLTGRTHQIRVHLASIGHPLLGDDKYNPNVAKGDK---MVRRLCLHA 337

Query: 293 RYMDLPHPEGGRLQITAPLPAHM 315
             + +P  E     ITA LP  M
Sbjct: 338 YQLAIPEYE----TITAELPVDM 356


>gi|322515396|ref|ZP_08068389.1| ribosomal large subunit pseudouridine synthase C [Actinobacillus
           ureae ATCC 25976]
 gi|322118578|gb|EFX90808.1| ribosomal large subunit pseudouridine synthase C [Actinobacillus
           ureae ATCC 25976]
          Length = 356

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 108/307 (35%), Positives = 172/307 (56%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  + +DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q   VVR
Sbjct: 46  VQFFTISDDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQENDVVR 105

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E+     S  L K ++  + IL YED  + V NKP+GI+V GGSG++
Sbjct: 106 VPPVRVA------EKNEAPISTKLNKVAELEQQIL-YEDDVMLVINKPSGIAVHGGSGLS 158

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A ++L E  R + +QK Y +L
Sbjct: 159 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRNLHEQLREKVVQKDYLAL 217

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   +VK +E+G   + + F + + +A     ++  
Sbjct: 218 VRGQWQSHVKVIRAPLLKNELASGE--RIVKVSEEG-KLSETRFAIEERYANA-TLVKAS 273

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +   ++L+LHA  +   HP+ G  
Sbjct: 274 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAVGLHRLFLHAYSIRFEHPKTGEE 333

Query: 305 LQITAPL 311
           + ITAPL
Sbjct: 334 MLITAPL 340


>gi|319763867|ref|YP_004127804.1| pseudouridine synthase, rlua family [Alicycliphilus denitrificans
           BC]
 gi|330823869|ref|YP_004387172.1| RluA family pseudouridine synthase [Alicycliphilus denitrificans
           K601]
 gi|317118428|gb|ADV00917.1| pseudouridine synthase, RluA family [Alicycliphilus denitrificans
           BC]
 gi|329309241|gb|AEB83656.1| pseudouridine synthase, RluA family [Alicycliphilus denitrificans
           K601]
          Length = 339

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 109/324 (33%), Positives = 165/324 (50%), Gaps = 35/324 (10%)

Query: 11  VVENDEENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           +VE D E+   RLD +   H   +   ++ +I+RSG+VR++K R   + R+ +G  VR+P
Sbjct: 23  IVEVDAESAGQRLDNFLIRHLKGVPKTHVYRIIRSGEVRLNKGRTSADARVAAGDRVRLP 82

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           PV  +        K+ D +       +F    +L ED  +   +KPAG++V GGSG+++ 
Sbjct: 83  PVRVS-------DKVQDKAERPAPAREF---PILLEDEHLIALDKPAGVAVHGGSGVSF- 131

Query: 129 IDGFLKSWVDSKGQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             G ++    ++ Q+ R   L HRLD+ETSGIL+VA+ R+A +HL + FR R   K Y +
Sbjct: 132 --GVIEQLRQAR-QEARFLELVHRLDRETSGILLVAKRRSALKHLQDQFRERETGKTYLA 188

Query: 186 LVWGI-PKNKKECIANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--- 239
           LV G  P NKK  + +  L K     G   V V    +     +I+  KV      +   
Sbjct: 189 LVPGAWPANKK--VIDLPLHKYLQEDGERRVRVTTPQDSDGMRSITLVKVHSHLPARPLQ 246

Query: 240 ----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHAR 293
                  LE+   TGRTHQ+RVH    G PI GD KY  +F  N     Q   +++LHA 
Sbjct: 247 GLPAMSLLEVTIKTGRTHQIRVHLASQGHPIAGDDKY-GDFDLNRRLQKQGLRRMFLHAW 305

Query: 294 YMDLPHPEGG-RLQITAPLPAHMV 316
            +   HP  G R+++ A LP  + 
Sbjct: 306 RLQFDHPASGERMELRAELPPELA 329


>gi|254994901|ref|ZP_05277091.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Mississippi]
          Length = 296

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 99/315 (31%), Positives = 164/315 (52%), Gaps = 27/315 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +VE     +R+DR+ +   P +    ++++LR G++ ++  + K + R+ +G V+ I   
Sbjct: 6   LVEGTCFEVRVDRYLRGLLPGVTQSFIERLLRRGEILLNNTKAKSSTRVSNGDVLSIK-- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            +A    ++E++I   ++      D +   +LYED  I   NKPAG+SVQGGS +   ID
Sbjct: 64  -HADRIALREKEI--HALQHVPLLDLISGSILYEDKNIIAINKPAGVSVQGGSKVKVSID 120

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L       G+  R+ HRLD++TSG+LV+AR    A++L   FR RR++K Y ++  G+
Sbjct: 121 DVLDKI--KPGECCRIVHRLDKDTSGVLVLARNLDVARYLAREFRERRVKKEYIAVTRGV 178

Query: 191 PKNKKECIANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQP 247
           P+     ++  +  K  S  G   +      EK A    S  +++ DC       + ++P
Sbjct: 179 PQPASGEVSTPIFYKVRSATGESMI------EKEAKTFFSVMRILGDC-----AVVLLRP 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGR HQLR+H   +GCPIVGD+KY    K +     +  L+LHA  +      G  L I
Sbjct: 228 VTGRKHQLRIHMSQIGCPIVGDNKY---HKCDLAE--KEMLHLHASLLTF-ELMGRTLSI 281

Query: 308 TAPLPAHMVKTWDSL 322
            A +P +M +  + L
Sbjct: 282 AANVPRYMEEKINPL 296


>gi|157803478|ref|YP_001492027.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           canadensis str. McKiel]
 gi|157784741|gb|ABV73242.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           canadensis str. McKiel]
          Length = 303

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 96/306 (31%), Positives = 165/306 (53%), Gaps = 25/306 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R+  G  + I    +  N  +K
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQIIVNARKAEASLRVIDGDKIFIS---DKFNLPVK 68

Query: 80  EQKIL---DSSVNLTKH--SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           + + L   D+ + L K   +D+L    +YED  +   NKPAG++ QGGS I   ID  LK
Sbjct: 69  QPEKLVFTDAEIKLAKKITTDYL----IYEDDNLIAINKPAGLATQGGSKINLSIDSALK 124

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KN 193
            +++ KG   +L HRLD+ETSG+L++A+   ++    ++F+ + + K Y+++ +G P KN
Sbjct: 125 -YLNYKGADFKLVHRLDKETSGLLLIAKNYLSSIKFHDAFKDKLVVKTYFAVTYGKPIKN 183

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E  +N  ++KS   G    +   + +    AI+++K++         +E  P TG+ H
Sbjct: 184 VGEVRSN--IEKSK--GSTRKITDIDSENGKLAITYYKLLKSLDNNLFLIEFTPITGKMH 239

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
           QLR+HA  +GCPI+GD KY     GN    P    ++LHA ++ L     G  + + A L
Sbjct: 240 QLRLHAKLLGCPILGDDKY-----GNKEIMPYSQYMFLHANHICLSEKVFGTEINLEAKL 294

Query: 312 PAHMVK 317
           P +  +
Sbjct: 295 PFYFTR 300


>gi|299771717|ref|YP_003733743.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. DR1]
 gi|298701805|gb|ADI92370.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. DR1]
          Length = 310

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 98/317 (30%), Positives = 167/317 (52%), Gaps = 21/317 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R  QVRV+KKRVK   +++ G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIRESQVRVNKKRVKAETKLEIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAAPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAVHGGSGMA 122

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           Y   G +++   + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y +
Sbjct: 123 Y---GLIEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKQLQDMLREHKIRKTYAA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G     K+ I   LL+     G+    V ++ K +    + + V + F +    +  
Sbjct: 180 IVKGQVSLDKQLIDAPLLRYELANGERRVRVTKDGKPSK---TEWVVAERF-KNATLVHA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            P +GRTHQ+RVH L +G P++GD KY       +T P   +L LHA  +D+P    G  
Sbjct: 236 SPLSGRTHQIRVHGLSIGHPLIGDDKY--GHTTEYTGPEARRLCLHAMRLDIP----GYP 289

Query: 306 QITAPLPAHMVKTWDSL 322
            I APLP  M +   +L
Sbjct: 290 PIEAPLPEDMTQLLKAL 306


>gi|238650483|ref|YP_002916335.1| hypothetical protein RPR_02200 [Rickettsia peacockii str. Rustic]
 gi|238624581|gb|ACR47287.1| hypothetical protein RPR_02200 [Rickettsia peacockii str. Rustic]
          Length = 303

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 91/301 (30%), Positives = 161/301 (53%), Gaps = 15/301 (4%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R++ G  + I    N    + +
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNSQKAEASLRVKGGDKIFINDKFNL--PVKQ 69

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            +K++ +   +   +      L+Y D  +   NKPAG++ QGG+ I   ID  LK +++ 
Sbjct: 70  PEKLVFTDAEIKLATKITTDYLIYADDNLIAINKPAGLATQGGTKINLSIDSALK-YLNY 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKECI 198
           KG   +L HRLD++TSG+L++A+   ++  L ++F+ + + K Y+++ +G P KN  E  
Sbjct: 129 KGTDFKLVHRLDKKTSGLLLIAKNYLSSVKLHDAFKEKLVVKTYFAVTYGKPIKNVGEVR 188

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +N  ++KS   G    +   + +    AI+++KV+         +E  P TGR HQLR+H
Sbjct: 189 SN--IEKSK--GSTPKITDIDSENGKLAITYYKVLKSLDNNLFLIEFTPVTGRMHQLRLH 244

Query: 259 ALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           A  +GCPI+GD KY     GN    P    ++LHA  + L     G  +++ A LP +  
Sbjct: 245 AKLLGCPILGDDKY-----GNKEIMPYSKYMFLHANNICLSEKIFGQEIKLDAKLPFYFT 299

Query: 317 K 317
           +
Sbjct: 300 R 300


>gi|157964329|ref|YP_001499153.1| ribosomal large subunit pseudouridine synthase [Rickettsia
           massiliae MTU5]
 gi|157844105|gb|ABV84606.1| Ribosomal large subunit pseudouridine synthase [Rickettsia
           massiliae MTU5]
          Length = 306

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 97/306 (31%), Positives = 167/306 (54%), Gaps = 25/306 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R++ G  + I    +  N  +K
Sbjct: 15  RLDKYLKRLYPLLTQGVIEKALRQKQITVNSQKTEASLRVKGGDKIFIN---DKFNLPVK 71

Query: 80  EQKIL---DSSVNLTKH--SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           + + L   D+ + L K   +D+L    +Y D  +   NK AG++ QGGS I   ID  LK
Sbjct: 72  QPEKLVFTDAEIKLAKKITTDYL----IYADDNLIAINKLAGLATQGGSKINLSIDSALK 127

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KN 193
            +++ KG   +L HRLD+ETSG+L++A+   ++  L ++F+ + + K Y+++ +G P KN
Sbjct: 128 -YLNYKGADFKLVHRLDKETSGLLLIAKNYLSSVKLHDAFKEKLVVKTYFAVTYGKPIKN 186

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E  +N  ++KS   G    +   + + +  AI+++KV+         +E  P TGR H
Sbjct: 187 VGEVRSN--IEKSK--GSTPKITNIDSENSKLAITYYKVLKSLDNNLFLIEFTPVTGRMH 242

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           QLR+HA  +GCPI+GD KY     GN    P    ++LHA  + L     G+ +++ A L
Sbjct: 243 QLRLHARLLGCPILGDDKY-----GNKEIMPYSKYMFLHANNICLSEKIFGKEIKLEAKL 297

Query: 312 PAHMVK 317
           P +  +
Sbjct: 298 PFYFTR 303


>gi|239947789|ref|ZP_04699542.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           endosymbiont of Ixodes scapularis]
 gi|239922065|gb|EER22089.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           endosymbiont of Ixodes scapularis]
          Length = 303

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 98/306 (32%), Positives = 168/306 (54%), Gaps = 25/306 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++V+ + R++ G  + I    +  N  +K
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNSQKVEASLRVKGGDKIFIN---DKFNLPVK 68

Query: 80  EQKIL---DSSVNLTKH--SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           + K L   D+ + L K   +D+L    +YED  +   NKPAG++ QGGS I   ID  LK
Sbjct: 69  QPKKLVFTDAEIKLAKKITTDYL----IYEDDNLIAINKPAGLATQGGSKIKLSIDSALK 124

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KN 193
            +++ KG   +L HRLD+ETSG+L++A+   ++  L + F+ + + K Y+++ +G P KN
Sbjct: 125 -YLNYKGADFKLVHRLDKETSGLLLIAKNYLSSVKLHDVFKEKLVVKTYFAVTYGKPIKN 183

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E  +N  ++KS      +  +  + +    AI+++K++         +E  P TGR H
Sbjct: 184 VGEVRSN--IEKSKRSTPKITDI--DSENGKLAITYYKLLKPLDNNLFLIEFTPVTGRMH 239

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           QLR+H+  +GCPI+GD KY     GN    P    ++LHA  + L     G+ +++ A L
Sbjct: 240 QLRLHSKLLGCPILGDDKY-----GNKEIMPYSKYMFLHANNICLYEKIFGKEIKLEAKL 294

Query: 312 PAHMVK 317
           P +  +
Sbjct: 295 PFYFTR 300


>gi|238762184|ref|ZP_04623156.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           kristensenii ATCC 33638]
 gi|238699531|gb|EEP92276.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           kristensenii ATCC 33638]
          Length = 319

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 104/307 (33%), Positives = 167/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A    I+    LD    L          +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVAEREEIQVSAKLDKVAALA-------DCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +VK + +G   + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGE--RMVKVSSEG-KPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F G       ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDGQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 296 MRIEAPL 302


>gi|16331032|ref|NP_441760.1| hypothetical protein slr1629 [Synechocystis sp. PCC 6803]
 gi|3915482|sp|P74346|Y1629_SYNY3 RecName: Full=Uncharacterized RNA pseudouridine synthase slr1629;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|1653527|dbj|BAA18440.1| slr1629 [Synechocystis sp. PCC 6803]
          Length = 327

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 103/313 (32%), Positives = 156/313 (49%), Gaps = 39/313 (12%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQ--VVRIPPVINAL 74
            +RLD+W     P ++    QK++ SGQV+ +    +  N I ++G   VV IP +I   
Sbjct: 31  GVRLDKWLAEQLPELSRSRCQKLIESGQVQRNGLVCQDKNLILKTGDRLVVNIPELIPL- 89

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG--- 131
             ++ +   LD               +LYED ++ + NKPAG+ V  G G   H DG   
Sbjct: 90  -DVVAQNIPLD---------------ILYEDEQLIIINKPAGLVVHPGPG---HPDGTVV 130

Query: 132 --FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              L    D  G    Q+P + HRLD++T+G +VVA+T  A  +L    + +  +++YW 
Sbjct: 131 NALLAHCPDLAGIGGVQRPGIVHRLDKDTTGAMVVAKTELALHNLQVQLKEKTARRLYWG 190

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V+G PK  +  +   L    H G      +   EKG   A++H+++++       WLE 
Sbjct: 191 IVYGSPKEIQGTVN--LPVGRHPGDRQKMGIVPVEKGGREAVTHWRLLERIG-NHSWLEF 247

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH+  MG P+VGD+ Y +    N   P Q    LHA  + L HP  G  
Sbjct: 248 QLETGRTHQIRVHSKQMGHPLVGDNLYTSPGSVNVNLPGQ---ALHAHQLSLIHPVSGEI 304

Query: 305 LQITAPLPAHMVK 317
           +   AP+PAH  K
Sbjct: 305 ITAIAPMPAHFEK 317


>gi|171317151|ref|ZP_02906353.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MEX-5]
 gi|171097718|gb|EDT42548.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MEX-5]
          Length = 316

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 103/327 (31%), Positives = 161/327 (49%), Gaps = 33/327 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++ +    R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +VR+PP
Sbjct: 2   IEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDIVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A   + +    +                +LYED  + V NKPAG++V GGSG+A+ +
Sbjct: 62  VRVAAADLARADTPIVPPAQFE---------VLYEDDAMLVINKPAGVAVHGGSGVAFGV 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY------ 183
              ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y      
Sbjct: 113 IEQMRQ-ARPRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFACGHG 171

Query: 184 -WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            W   WG    ++  +   L K S   G+   V  Q++   ++ +  F +++ +   +  
Sbjct: 172 EWQSDWG----RRRAVKAPLFKYSTAEGER-RVRVQDDGLPSHTV--FNLLERWPD-YAL 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMD 296
           +E +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   +++LHA  + 
Sbjct: 224 VEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANAQPSLKRMFLHAHRLK 282

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
           L HP  G  LQ  APLP    +  D L
Sbjct: 283 LAHPLTGEPLQFDAPLPDECRRFLDQL 309


>gi|239814386|ref|YP_002943296.1| pseudouridine synthase, RluA family [Variovorax paradoxus S110]
 gi|239800963|gb|ACS18030.1| pseudouridine synthase, RluA family [Variovorax paradoxus S110]
          Length = 370

 Score =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 102/323 (31%), Positives = 162/323 (50%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ V+ +    RLD +   H   +   ++ +I+RSG+VR++K R +   RI++G V+R
Sbjct: 38  IKFITVDAESAGQRLDNFLFRHLKGVPKTHVYRIIRSGEVRINKGRAQAETRIEAGDVLR 97

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP       I    +  + +       +F    +L ED  +   +KPAG++V GGSG++
Sbjct: 98  LPP-------IRISPRAEEGATPPAPAREF---PVLLEDDAVLAIDKPAGVAVHGGSGVS 147

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + +   L++     G K   L HRLD+ETSGIL+VA+ R+A   L + FR R   K Y +
Sbjct: 148 FGVIEQLRTA--RPGAKFLELVHRLDRETSGILLVAKKRSALVALQDQFRERETGKTYLA 205

Query: 186 LVWGI-PKNKK---ECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDCF--- 236
           LV G  P NKK     +A +LL     G     V VV ++   A  A++  +V+      
Sbjct: 206 LVEGAWPANKKVLDAPLAKYLLPGDGAGAGERRVRVVAKDHPDAMRAVTLVRVLARLTLP 265

Query: 237 --AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHAR 293
             A     L +   TGRTHQ+RVH    G  I GD KY    +      +   +++LHA 
Sbjct: 266 GDAAPLSLLAVTIKTGRTHQIRVHLASAGHAIAGDDKYGDFERQRVLQKLGLKRMFLHAW 325

Query: 294 YMDLPHPEGG-RLQITAPLPAHM 315
            +   HP  G R+ + A LP  +
Sbjct: 326 RLQFNHPATGERVALQAGLPPEL 348


>gi|294787877|ref|ZP_06753121.1| ribosomal large subunit pseudouridine synthase C [Simonsiella
           muelleri ATCC 29453]
 gi|294484170|gb|EFG31853.1| ribosomal large subunit pseudouridine synthase C [Simonsiella
           muelleri ATCC 29453]
          Length = 334

 Score =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 100/323 (30%), Positives = 169/323 (52%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V+  +   RLD +       +   ++Q+I+RSG+VR++K R K ++RIQ G VVR
Sbjct: 15  VNHLTVQEHDAEQRLDNYLIKILKGVPKSHIQRIIRSGEVRLNKGRAKPDSRIQIGDVVR 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A       +K+        K+    +  +++ED  + V NKPAG++V GGSG++
Sbjct: 75  IPPIRVA-------EKLPPHFSGSLKNIPAREFDIVFEDDALIVINKPAGVAVHGGSGVS 127

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    ++  +    L HRLD++TSG+L++A+ R A   L E  R    +K+Y 
Sbjct: 128 F---GVIEQLRQARPNESYLELVHRLDKDTSGLLMIAKKRRALVKLHEMLRNDHPKKVYL 184

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA------- 237
           +L  G  + +   I   ++K +   G+ + V   NE+    A + F+V++ F+       
Sbjct: 185 ALGVGTWQPENRHIKLPIVKYTGAAGEKM-VRVGNEEDGQSAYTIFRVLNTFSGSLTHSV 243

Query: 238 --QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHAR 293
                  ++    TGRTHQ+RVH     CPI GD +Y  +++ N         +++LHA 
Sbjct: 244 GISALSLVQATLKTGRTHQIRVHMQSQDCPIAGDERY-GDYQANKRLQKLGLKRMFLHAY 302

Query: 294 YMDLPHP-EGGRLQITAPLPAHM 315
            + L HP  G RL + A LPA +
Sbjct: 303 ELILDHPISGERLHLKAELPAEL 325


>gi|271500125|ref|YP_003333150.1| pseudouridine synthase, RluA family [Dickeya dadantii Ech586]
 gi|270343680|gb|ACZ76445.1| pseudouridine synthase, RluA family [Dickeya dadantii Ech586]
          Length = 320

 Score =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 107/314 (34%), Positives = 171/314 (54%), Gaps = 20/314 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ +  +E   R+D + +     +    + +ILR G+VRV+KKRVK   ++  G  +R
Sbjct: 8   VQFLTISAEEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLLDGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +      E++    S +L K S  L + +LYED  + + NKP+G +V GGSG++
Sbjct: 68  IPPVRQS------EREEAAVSASLDKVS-ALANCILYEDDYLLLLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRAKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV---IDCFAQKFCWL 243
           V G  ++  + +   LLK     G+   +V+ N +G   + + FKV    DC       +
Sbjct: 180 VRGQWQSHCKSVQAPLLKNVLQSGE--RIVRVNSEG-KPSETLFKVEERFDC----ATLV 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
              P TGRTHQ+RVH  H G PI  D +Y   +F          +L+LHA+ +   HP  
Sbjct: 233 RASPITGRTHQIRVHTQHAGHPIAFDDRYGDRDFDAQLADTGLKRLFLHAQALRFEHPHT 292

Query: 303 GR-LQITAPLPAHM 315
           G  L+I APL A +
Sbjct: 293 GETLRIEAPLDAGL 306


>gi|229586508|ref|YP_002845009.1| Ribosomal large subunit pseudouridine synthase [Rickettsia africae
           ESF-5]
 gi|228021558|gb|ACP53266.1| Ribosomal large subunit pseudouridine synthase [Rickettsia africae
           ESF-5]
          Length = 303

 Score =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 96/306 (31%), Positives = 166/306 (54%), Gaps = 25/306 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R++ G  + I    +  N  +K
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNAQKAEASLRVKGGDKIFIN---DKFNLPVK 68

Query: 80  EQKIL---DSSVNLTKH--SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           + + L   D+ + L K   +D+L    +Y D  +   NKPAG++ QGG+ I   ID  LK
Sbjct: 69  QPEKLVFTDAEIKLAKKITTDYL----IYADDNLIAINKPAGLATQGGTKINLSIDSALK 124

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KN 193
            +++ KG   +L HRLD++TSG+L++A+   ++  L ++F+ + + K Y+++ +G P KN
Sbjct: 125 -YLNYKGADFKLVHRLDKKTSGLLLIAKNYLSSVKLHDAFKEKLVVKTYFAVTYGKPIKN 183

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E  +N  ++KS   G  + +   + +    AI+++KV+         +E  P TGR H
Sbjct: 184 VGEVRSN--IEKSK--GSTLKITDIDSENGKLAITYYKVLKSLDNNLFLIEFTPVTGRMH 239

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           QLR+HA  +GCPI+GD KY     GN    P    ++LHA  + L     G   ++ A L
Sbjct: 240 QLRLHAKLLGCPILGDDKY-----GNKEIMPYSKYMFLHANNICLSEKIFGQESKLEAKL 294

Query: 312 PAHMVK 317
           P +  +
Sbjct: 295 PFYFTR 300


>gi|303256986|ref|ZP_07343000.1| ribosomal large subunit pseudouridine synthase C [Burkholderiales
           bacterium 1_1_47]
 gi|302860477|gb|EFL83554.1| ribosomal large subunit pseudouridine synthase C [Burkholderiales
           bacterium 1_1_47]
          Length = 334

 Score =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 106/321 (33%), Positives = 167/321 (52%), Gaps = 27/321 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+   +  RLD +  +    +    + +++RSG+VRV+K R   + R+QSG  VRIPP+ 
Sbjct: 23  VDESNDGQRLDNFLLSQLKGVPKSLIYRVVRSGEVRVNKGRAHVDTRLQSGDEVRIPPI- 81

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
               +  KE +     + L++        +L+ED  I V +KPAG++  GGSGI+Y   G
Sbjct: 82  ---RYTEKESEHSAPPLKLSEMPP-----ILFEDQNIMVVDKPAGMASHGGSGISY---G 130

Query: 132 FLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            ++    S+ + P   L HRLD+ TSG+LV+A+TR A   L E  R   + K Y +LV G
Sbjct: 131 LIERMRASRPELPFLELVHRLDRGTSGVLVLAKTRKALVRLHEMIREGEMHKTYQALVKG 190

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +N ++     L K     G+    V       +++I  F++ + F      +E+   T
Sbjct: 191 DWQNDRQHAKFPLFKYVTPSGERRVRVDPENGLPSHSI--FRLKERFG-PVSLVEVDLLT 247

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFK-------GNFTSPIQNKLYLHARYMDLPHP-E 301
           GRTHQ+RVHA  +G P+VGD KY  +F        G+   P + +++LH+  +   HP  
Sbjct: 248 GRTHQIRVHAAELGFPLVGDEKY-GDFAFNDEVAHGSLGVPFK-RMFLHSGKICFHHPIT 305

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G  L+I APLP   V+  + L
Sbjct: 306 GEELEIEAPLPKDCVELIEVL 326


>gi|332162113|ref|YP_004298690.1| 23S rRNA pseudouridylate synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|325666343|gb|ADZ42987.1| 23S rRNA pseudouridylate synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
          Length = 319

 Score =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 104/307 (33%), Positives = 167/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +  N    +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLNKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A    I+    LD    L          +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVAEREEIQVSAKLDKVAALA-------DCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +VK + +G   + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGE--RMVKVSSEG-KPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDSQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 296 MRIEAPL 302


>gi|226939996|ref|YP_002795069.1| RluC [Laribacter hongkongensis HLHK9]
 gi|226714922|gb|ACO74060.1| RluC [Laribacter hongkongensis HLHK9]
          Length = 312

 Score =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 96/319 (30%), Positives = 165/319 (51%), Gaps = 20/319 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  + +DE   RLD W       +   ++ +I+R G+VR++K R + + R+++G VVR
Sbjct: 9   VTFHTITDDEAGQRLDNWLIKILKGVPKSHVYRIVRGGEVRINKGRCQVDQRVETGDVVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+       I E+      V            +++ED  + V +KP G++V GGSG++
Sbjct: 69  IPPI------RIAERPAATRPVPAAAFP------VVFEDDALLVIDKPCGVAVHGGSGVS 116

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++    + +   L HRLD++TSG+L++A+ R+A   L +  R   + K Y +L
Sbjct: 117 FGVIEQLRA-ARPQAKFLELVHRLDRDTSGLLLIAKKRSALVALHDMIRRNMLDKRYLAL 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G     ++ +   L K +   G+    V+ +E G   + + F+++  FA     +E  
Sbjct: 176 GVGRWNPARKSVKKPLTKYTLPDGE--RRVRVDEAGGQASHTDFRIVRSFA-GHTLIEAT 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR 304
             TGRTHQ+RVH     CPI GD KY  ++  N     Q   +++LHA  + L HP  G+
Sbjct: 233 LQTGRTHQIRVHMQSADCPIAGDDKY-GDYATNKDLARQGLKRMFLHAWQLRLQHPLTGQ 291

Query: 305 -LQITAPLPAHMVKTWDSL 322
            L+  APLP  + +  ++L
Sbjct: 292 LLEFRAPLPDELNRFIETL 310


>gi|15616954|ref|NP_240167.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. APS (Acyrthosiphon pisum)]
 gi|219681707|ref|YP_002468093.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. 5A (Acyrthosiphon pisum)]
 gi|257471403|ref|ZP_05635402.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. LSR1 (Acyrthosiphon pisum)]
 gi|11387076|sp|P57430|RLUC_BUCAI RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|25322330|pir||E84970 pseudouridylate synthase (EC 4.2.1.70) [imported] - Buchnera sp.
           (strain APS)
 gi|10039019|dbj|BAB13053.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. APS (Acyrthosiphon pisum)]
 gi|219624550|gb|ACL30705.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. 5A (Acyrthosiphon pisum)]
          Length = 314

 Score =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 95/314 (30%), Positives = 173/314 (55%), Gaps = 28/314 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + +  +  N R+D + ++ +  +    + +I+R+G++R++KKR+K + +++ G +++
Sbjct: 8   ISIIYINKEMLNQRIDNFMRSKFKSVPKSMIYRIIRTGKIRINKKRIKPHYKLKIGDILK 67

Query: 67  IPPVINALNHIIKEQKILDSSVNL---TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           IPP+           KIL    N      HS  L + +LYEDS + + NKP+GI+V GGS
Sbjct: 68  IPPI-----------KILCDIKNTFFPLNHSTNLLNRILYEDSHLLIINKPSGIAVHGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+ + +  + +  +    +   L HR+D++TSG+L++A+ R +   L E  R ++I+K Y
Sbjct: 117 GLNFGVIEYFRK-LRPLNKFLELVHRIDRDTSGVLILAKKRTSLVSLHEQLREKKIKKEY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G+  +  + I+  LLK        + ++ +  K +    ++F++   F+     L
Sbjct: 176 IALVHGLWPDHIKKISEPLLKIQFKNKQKMVLIDKKGKPSE---TYFQIKKKFSSS-TLL 231

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-----NKLYLHARYMDLP 298
            + P TGRTHQ+RVHALH G PI  D +Y  N   +  + I+     N+L LH+  +   
Sbjct: 232 SIIPKTGRTHQIRVHALHAGHPIFFDKRYGKN---DLDADIKNNHKINRLLLHSSGVHFI 288

Query: 299 HPE-GGRLQITAPL 311
           HP+ G ++ I APL
Sbjct: 289 HPKNGNKIYIKAPL 302


>gi|225025072|ref|ZP_03714264.1| hypothetical protein EIKCOROL_01961 [Eikenella corrodens ATCC
           23834]
 gi|224942164|gb|EEG23373.1| hypothetical protein EIKCOROL_01961 [Eikenella corrodens ATCC
           23834]
          Length = 323

 Score =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 100/334 (29%), Positives = 171/334 (51%), Gaps = 40/334 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V Y+ V+      RLD +       +   ++ +I+R G+VRV+KKR   ++R+ +G  VR
Sbjct: 9   VNYLSVDEAAAGQRLDNFLIRLLKGVPKSHIHRIIRGGEVRVNKKRAAADSRLAAGDEVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A      E  +     +           +++ED  + V +KP+G++V GGSG++
Sbjct: 69  IPPIRLAQKAEQAEAAVPPREFD-----------IVFEDEHLLVVDKPSGVAVHGGSGVS 117

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    ++ Q     L HRLD++TSG+LVVA+ R+A   L E++R  + +K+Y 
Sbjct: 118 F---GVIEQLRRARPQARYLELVHRLDKDTSGLLVVAKKRSALVKLHEAWRNDKPKKVYL 174

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA------- 237
           +L  G        +   L K +   G+   +V+ +E+G + A + F+V++ F        
Sbjct: 175 ALGMGAWPQGVRQVKLPLFKYTGAAGE--KMVRVSEEGQS-AHTLFRVLESFGGAPLHAV 231

Query: 238 --QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLY 289
                  +E    TGRTHQ+RVH     CPI GD +Y     G++T+  +       +++
Sbjct: 232 GLSALSLMEATLRTGRTHQIRVHMQSQNCPIAGDERY-----GDYTANRRLKKLGLKRMF 286

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           LHA  ++L HP  G  L +TAPLP  + +  + L
Sbjct: 287 LHAHRLELEHPASGETLVLTAPLPEELRQMLEGL 320


>gi|326795265|ref|YP_004313085.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326546029|gb|ADZ91249.1| pseudouridine synthase, RluA family [Marinomonas mediterranea
           MMB-1]
          Length = 324

 Score =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 98/314 (31%), Positives = 172/314 (54%), Gaps = 26/314 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V++V ++ +    R+D +       +    +  +LR G++RV+KKR K + R+QSG +
Sbjct: 14  TKVRFVDIDENNHGQRIDNFLITELKGLPKGKIYNLLRKGEIRVNKKRTKPDYRLQSGDI 73

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRI P+      ++ E+   D           ++S ++YED  + V NKP+G++V GGSG
Sbjct: 74  VRIAPL------VLPERA--DKPTVAEGLKAQIESRIIYEDKGLLVVNKPSGLAVHGGSG 125

Query: 125 IAYHIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR- 178
           +++ +   ++        +P      L HRLD++TSG++++A+ R+  + L E+ R +  
Sbjct: 126 LSFGLVEVVRQM------RPLEKFVELVHRLDRDTSGLIMIAKRRSVLKLLHEALREKSG 179

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           +QK Y +LV G    +K+ +   LLK     G+   VV+ N +G   +++ F ++  F +
Sbjct: 180 VQKTYLALVHGAWSKRKQKVDAPLLKNELKSGE--RVVRVNPEGKE-SLTRFNLVREF-E 235

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDL 297
            F  ++ +P TGRTHQ+RVH    G  IVGD KY ++     T  +   +L LHA  +++
Sbjct: 236 GFSLIQCEPVTGRTHQIRVHTQFAGHSIVGDDKYTSSELNKQTKEMGFKRLCLHATRLEI 295

Query: 298 PHPEGGRLQITAPL 311
            + EG +L + APL
Sbjct: 296 DY-EGEKLILEAPL 308


>gi|296158256|ref|ZP_06841088.1| pseudouridine synthase, RluA family [Burkholderia sp. Ch1-1]
 gi|295891592|gb|EFG71378.1| pseudouridine synthase, RluA family [Burkholderia sp. Ch1-1]
          Length = 323

 Score =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 103/319 (32%), Positives = 168/319 (52%), Gaps = 38/319 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR+PP
Sbjct: 2   IEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +      + +  +    +     H       +++ED  + V +KPAG++V GGSG+A+  
Sbjct: 62  I-----RVAQPSEAAAQAPVPAAHFK-----IIFEDEHLLVIDKPAGVAVHGGSGVAF-- 109

Query: 130 DGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            G ++   +++ Q     L HRLD+ETSGIL++A+ R+A  +L E  R  ++ K Y++ V
Sbjct: 110 -GVIEQMREARPQAKFLELVHRLDRETSGILMLAKKRSALVNLHEQIRENKMDKRYYACV 168

Query: 188 -------WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
                  WG  +  KE +  +L      G   V V  Q +  A++ +  F +ID + + +
Sbjct: 169 HGEWASDWGRRRAVKEPLHKYLTAD---GERRVRV--QPDGLASHTV--FNLIDRWPE-Y 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARY 294
             LE +  TGRTHQ+RVH  H+G PIVGD KY  +F  N         P   +++LHA  
Sbjct: 221 ALLEAELKTGRTHQIRVHLQHLGLPIVGDAKY-GDFALNKALARANAKPGLKRMFLHAYR 279

Query: 295 MDLPHPEGGR-LQITAPLP 312
           + L HP  G  LQ  APLP
Sbjct: 280 LKLTHPATGEPLQFDAPLP 298


>gi|262280824|ref|ZP_06058607.1| 23S rRNA pseudouridylate synthase [Acinetobacter calcoaceticus
           RUH2202]
 gi|262257724|gb|EEY76459.1| 23S rRNA pseudouridylate synthase [Acinetobacter calcoaceticus
           RUH2202]
          Length = 310

 Score =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 97/317 (30%), Positives = 169/317 (53%), Gaps = 21/317 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R  QVRV+KKRVK   +++ G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIRESQVRVNKKRVKAETKLEIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P+     +  K++     S N+ +    L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAPI----RYEQKDETTAPVSDNVAQS---LLSRIVYEDEGLLVVNKPSGIAVHGGSGMA 122

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           Y   G +++   + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y +
Sbjct: 123 Y---GLIEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G     K+ I   LL+     G+    V ++ K +    + + V + F +    +  
Sbjct: 180 IVKGQVSLDKQLIDAPLLRYELANGERRVRVTKDGKPSK---TEWVVAERF-KNATLIHA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            P +GRTHQ+RVH L +G P++GD KY       +T P   +L LHA  +D+P    G  
Sbjct: 236 SPLSGRTHQIRVHGLSIGHPLIGDDKY--GHTTAYTGPEARRLCLHAMRLDIP----GYP 289

Query: 306 QITAPLPAHMVKTWDSL 322
            I APLP  M +   +L
Sbjct: 290 PIEAPLPEDMTQLLKAL 306


>gi|71280214|ref|YP_269010.1| ribosomal large subunit pseudouridine synthase C [Colwellia
           psychrerythraea 34H]
 gi|71145954|gb|AAZ26427.1| ribosomal large subunit pseudouridine synthase C [Colwellia
           psychrerythraea 34H]
          Length = 360

 Score =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 98/318 (30%), Positives = 173/318 (54%), Gaps = 14/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+++ +++++   R+D +       +   +L +++R G++RV+KKR+K   ++     VR
Sbjct: 52  VRFITIDSEDAGQRIDNFLLRTLKGVPKSHLYRLMRKGEIRVNKKRIKPVYKLLIDDEVR 111

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I P+      + +E+  + + +++  +   L+  +L+ED ++ V NKP+G++V GGSG++
Sbjct: 112 IAPI-----RVSEEKDAVSTGLHIVAN---LEKQILFEDDRLIVINKPSGMAVHGGSGLS 163

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG L+VA+ R+  +HL E FR + +QK Y +L
Sbjct: 164 FGLIEALRA-LRPEARMLELVHRLDRDTSGCLMVAKKRSTLRHLHEQFRDKNVQKFYHAL 222

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    K   + + L K     G+ V VV  N+ G     + F+V++ + +    +   
Sbjct: 223 VKGHWPTKLTRVTDALKKNDLKSGERV-VVVDNQLGKESE-TRFRVLERY-RGATLVRAF 279

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH    G  I  D KY    F     S    +L+LHA  ++  HP    R
Sbjct: 280 PVTGRTHQIRVHCQTSGHSIAMDAKYGHEEFDEQMKSKGLKRLFLHAASIEFTHPNTEQR 339

Query: 305 LQITAPLPAHMVKTWDSL 322
           L+I APL A + K    L
Sbjct: 340 LKIEAPLEASLEKLLSKL 357


>gi|160872397|ref|ZP_02062529.1| ribosomal large subunit pseudouridine synthase C [Rickettsiella
           grylli]
 gi|159121196|gb|EDP46534.1| ribosomal large subunit pseudouridine synthase C [Rickettsiella
           grylli]
          Length = 315

 Score =  146 bits (368), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 99/322 (30%), Positives = 168/322 (52%), Gaps = 16/322 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +QY+ +  D    RLD +  +    +    L +I+R G++R+ KKRVK + R+Q G 
Sbjct: 1   MQTIQYLTITKDYSGQRLDNFLISRLKGLPKSRLYRIIRKGELRIYKKRVKPDYRLQEGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++R+PP+  +L+ +  ++K+L+      K + FL+  +++ED  + V NKP+G++V GGS
Sbjct: 61  IIRVPPL--SLSGLPTKKKVLNE-----KQAKFLEKTIIFEDKHLLVLNKPSGMAVHGGS 113

Query: 124 GIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           GI    I+ F    +  + +   L HRLD+ETSG L++A+ R+  + L E  R+  I+K 
Sbjct: 114 GITLGVIEAF--RLIRPQLKFLELVHRLDRETSGCLLMAKKRSILKELHELLRLNGIKKT 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G        +A  L K     G+   +V+   +G   +++ F +   ++     
Sbjct: 172 YIALVSGHWPPSLLSVAEPLYKNQRQSGE--RMVRVQPEGKR-SLTKFSIQQYYSDS-TL 227

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +   P TGRTHQ+RVHA  +  PI+GD KY               +L+LHA  +    P 
Sbjct: 228 VTATPITGRTHQIRVHAQCVNHPIIGDEKYGNKEINKKMRQLGCKRLFLHASELVFTLPS 287

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + L + A LP  + +  + L
Sbjct: 288 QEKTLTLQAKLPEDLNRLLNQL 309


>gi|90415859|ref|ZP_01223792.1| Predicted pseudouridylate synthase, Rlu family protein [marine
           gamma proteobacterium HTCC2207]
 gi|90332233|gb|EAS47430.1| Predicted pseudouridylate synthase, Rlu family protein [marine
           gamma proteobacterium HTCC2207]
          Length = 324

 Score =  145 bits (367), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 101/328 (30%), Positives = 167/328 (50%), Gaps = 25/328 (7%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  + V YV +  ++   RLD +       +    + ++LR G+VRV+K RVK  +R++ 
Sbjct: 15  SQFSQVSYVDIGPEQAGQRLDNFLIKILKGVPKSRIYRLLRKGEVRVNKGRVKAESRLKE 74

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VR+PP+       + E+  + +     K   +L   +L+ED  + + NKP+G++V G
Sbjct: 75  GDIVRLPPI------RVAERGEMPAVGRQLKQ--YLADNILFEDDGLLIINKPSGLAVHG 126

Query: 122 GSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           GSG++    G +++    + + P      L HRLD++TSG L++A+ RA    L +  + 
Sbjct: 127 GSGVSL---GAIEAL---RAEHPELRFLELVHRLDRDTSGCLMLAKKRAVLLALQQDMQR 180

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I+K Y +L  G     K  I   L K +   G+ +  V  + K    +++HFK +  +
Sbjct: 181 NYIEKRYTALSKGRWPKGKNTINAPLRKNTLQSGERMVRVDASGKA---SVTHFKSLQQY 237

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYM 295
                 L+++  TGRTHQ+RVH      PI GD KY          P+   +L+LHARY+
Sbjct: 238 PSA-TLLDIKLETGRTHQIRVHCQFAEQPIAGDPKYGDEHFNESLKPLGLKRLFLHARYL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP  G  +++ APLPA + K    L
Sbjct: 297 RFKHPLSGDWVEVEAPLPADLEKVLTKL 324


>gi|332529427|ref|ZP_08405386.1| pseudouridine synthase RluD [Hylemonella gracilis ATCC 19624]
 gi|332041073|gb|EGI77440.1| pseudouridine synthase RluD [Hylemonella gracilis ATCC 19624]
          Length = 322

 Score =  145 bits (367), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 103/321 (32%), Positives = 171/321 (53%), Gaps = 25/321 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+ +    RLD +       +   ++ +I+RSG+VRV+K R     R+QSG  VR+PP
Sbjct: 1   MTVDEESAGQRLDNFLLRQLKGVPKTHVYRIIRSGEVRVNKGRANAETRVQSGDAVRLPP 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  +     K + +        +  +F    +L+ED  +   +KPAG++V GGSG+++ +
Sbjct: 61  LRLSERAADKAEAMAHGGGAPGR--EF---PVLFEDEAVLAVDKPAGVAVHGGSGVSFGV 115

Query: 130 DGFLKS---WVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              L++   +  + G K   L HRLD+ETSGIL++A+ R+A + L + FR R   K Y +
Sbjct: 116 IEQLRTARGYGQAGGAKFLELVHRLDRETSGILLLAKKRSALKALQDQFRERETGKTYLA 175

Query: 186 LVWGI-PKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           LV G  P++KK   + +  +LL+    G   V VV +++     A++  KV    +    
Sbjct: 176 LVSGRWPQSKKVLDKPLHKYLLED---GERRVRVVAKDDPEGMRAVTLVKVRQA-SDTHS 231

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-----FTSPIQNKLYLHARYMD 296
            LE+   TGRTHQ+RVH    G  I GD KY  +F+ N       SP++ +++LHA  + 
Sbjct: 232 LLEVTIKTGRTHQIRVHLASEGHAIAGDDKY-GDFELNRVLQKGASPLK-RMFLHAWRLQ 289

Query: 297 LPHP-EGGRLQITAPLPAHMV 316
             HP  G R+++ + LP  + 
Sbjct: 290 FTHPVSGERIELMSALPTDLT 310


>gi|253996195|ref|YP_003048259.1| RluA family pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253982874|gb|ACT47732.1| pseudouridine synthase, RluA family [Methylotenera mobilis JLW8]
          Length = 340

 Score =  145 bits (367), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 106/326 (32%), Positives = 173/326 (53%), Gaps = 33/326 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           ++ ++   E  R+D +       +   ++ +ILRSG+VRV+KKR+  + R+  G VVR+P
Sbjct: 23  FLTIDEASEGQRIDNFLTKTLKGVPKSHVYRILRSGEVRVNKKRIDADFRLSLGDVVRVP 82

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P  +         +  +S+V +T  S F ++++ YED  + V +K AG +V GGSGI+  
Sbjct: 83  PTRST------AVEKTESAVPVT--SKFEQAVI-YEDDAMLVIDKAAGFAVHGGSGISRG 133

Query: 129 IDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +   L+       ++PR     L HRLD+ETSG+L++A+ R+A   L E+ R  +  K Y
Sbjct: 134 VIEQLRL------ERPRAKFLELVHRLDRETSGVLMLAKKRSALVALHEAIRNNQTDKRY 187

Query: 184 WSLV---WGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGA-NYAISHFKVIDCFAQ 238
             LV   W  PK +    +  ++L       + V  V +++ G    + + F+++  F+ 
Sbjct: 188 LVLVQGEWLEPKKRVVLDLQKYVLPNGERRVNVVTDVSKDKFGERQTSETMFRLLKNFSH 247

Query: 239 ----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHA 292
               KF  LE Q  TGRTHQLRV   H+G PIVGD KY  +F  N         +++LH+
Sbjct: 248 PVIGKFSLLEAQLVTGRTHQLRVQLAHLGFPIVGDDKY-GDFDLNKFLAKHGLKRMFLHS 306

Query: 293 RYMDLPHP-EGGRLQITAPLPAHMVK 317
               + HP    +L++ AP+PA + K
Sbjct: 307 SVTKIRHPLTAEKLELIAPVPAELNK 332


>gi|260549179|ref|ZP_05823400.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter sp.
           RUH2624]
 gi|260407907|gb|EEX01379.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter sp.
           RUH2624]
          Length = 310

 Score =  145 bits (367), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 96/319 (30%), Positives = 172/319 (53%), Gaps = 25/319 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   ++  G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLAIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKH-SDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           + P        I+ ++  +++V ++   +  L S ++YED  + V NKP+GI+V GGSG+
Sbjct: 70  VAP--------IRYEQKDETAVPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAVHGGSGV 121

Query: 126 AYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           AY   G +++   + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y 
Sbjct: 122 AY---GLIEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYA 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++V G     K+ I   L +     G+  V V K+ +       + + V + F +    +
Sbjct: 179 AIVKGQVSLDKQLIDAPLFRYELANGERRVRVSKEGKPSK----TEWVVAERF-KNATLV 233

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              P +GRTHQ+RVH L +G P++GD KY  N    +  P   +L LHA  +D+P    G
Sbjct: 234 HASPLSGRTHQIRVHGLSIGHPLLGDDKYGHNTA--YAGPEARRLCLHAMRLDIP----G 287

Query: 304 RLQITAPLPAHMVKTWDSL 322
              I APLP  M++  ++L
Sbjct: 288 YPTIEAPLPEDMIQLLEAL 306


>gi|297538696|ref|YP_003674465.1| RluA family pseudouridine synthase [Methylotenera sp. 301]
 gi|297258043|gb|ADI29888.1| pseudouridine synthase, RluA family [Methylotenera sp. 301]
          Length = 343

 Score =  145 bits (366), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 109/334 (32%), Positives = 168/334 (50%), Gaps = 49/334 (14%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           ++ V+   E  R+D +       +   ++ +ILRSG+VRV+KKR+  + R+  G VVR+P
Sbjct: 27  FLTVDEASEGQRVDNFLTKTLKGVPKSHVYRILRSGEVRVNKKRIDADFRLTIGDVVRVP 86

Query: 69  PV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P+    + H+       +++V     S F  +I +YED  I V +KPAG +V GGSG++ 
Sbjct: 87  PIRATIVEHV-------ETAVPAV--SKFENTI-IYEDDAILVIDKPAGFAVHGGSGVSR 136

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   ++     K +   L HRLD+ETSG+L++A+ R+A   L E+ R  +  K Y  LV
Sbjct: 137 GVIEQMR-LERPKAKFLELVHRLDRETSGVLMLAKKRSALVALHEAIRNNQTDKRYLMLV 195

Query: 188 WGIPKNKKECIANWLLKKSHI-----------GGDYVHVV------KQNEKGANYAISHF 230
            G           WL  K  +           G   V+VV      K NE+  +  +  F
Sbjct: 196 RG----------EWLEAKKRVVLDLQKYLLPNGERRVNVVTDVSKDKYNERQTSETM--F 243

Query: 231 KVIDCFAQ----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPI 284
           K++  ++     KF  LE Q  TGRTHQLRV   H+G  IVGD KY  +F  N       
Sbjct: 244 KLLKNYSHPVLGKFSLLEAQLVTGRTHQLRVQLAHLGFQIVGDDKY-GDFAVNKSLVKSG 302

Query: 285 QNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
             +++LH+    + HP    +L++ APLP  + K
Sbjct: 303 LKRMFLHSSVTKIRHPLTNDKLELVAPLPPELSK 336


>gi|261364850|ref|ZP_05977733.1| ribosomal large subunit pseudouridine synthase [Neisseria mucosa
           ATCC 25996]
 gi|288566895|gb|EFC88455.1| ribosomal large subunit pseudouridine synthase [Neisseria mucosa
           ATCC 25996]
          Length = 332

 Score =  145 bits (366), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 101/323 (31%), Positives = 171/323 (52%), Gaps = 25/323 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RIQ+G ++R
Sbjct: 11  VSLITVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIQTGDLLR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A     ++Q+   SS N  +     +  ++YED  + V +KPAG++V GGSG++
Sbjct: 71  IPPVRTA-----EKQR---SSENRAQAVPAREFDIIYEDDALLVIDKPAGVAVHGGSGVS 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++     + +   L HRLD++TSG+L++A+ R+A   L E+ R    +KIY +L
Sbjct: 123 FGVIEQIR-RARPEARYLELVHRLDKDTSGLLMIAKKRSALVKLHEAIRNDHPKKIYLAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   N    +   L K  + G     +V+ +E G + A + F V++ F+         
Sbjct: 182 GVGKLPNDSFHVKLPLFK--YTGAQGEKMVRVSEDGQS-AHTIFHVLNRFSDDLLHQVGL 238

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                ++    TGRTHQ+RVH     CPI GD +Y  +++ N         +++LHA  +
Sbjct: 239 SHLTLVQATLKTGRTHQIRVHLQSQQCPIAGDERY-GDYQANKRLQKLGLKRMFLHAAEL 297

Query: 296 DLPHP-EGGRLQITAPLPAHMVK 317
            L HP  G +L + APLP  + +
Sbjct: 298 HLNHPLTGEKLILKAPLPQELAQ 320


>gi|303252739|ref|ZP_07338900.1| 23S rRNA pseudouridylate synthase C [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|302648389|gb|EFL78584.1| 23S rRNA pseudouridylate synthase C [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
          Length = 321

 Score =  145 bits (366), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 108/307 (35%), Positives = 169/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q   VVR
Sbjct: 11  VQFFTISEDEVGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQPDDVVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPVRVA------EKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+   +V+ +EKG   + + F + + +A     ++  
Sbjct: 183 VRGQWQAHTKVIKAPLLKNELASGE--RIVRVSEKG-KPSETRFSIEERYANA-TLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 298

Query: 305 LQITAPL 311
           + ITAPL
Sbjct: 299 MLITAPL 305


>gi|262370010|ref|ZP_06063337.1| 23S rRNA pseudouridylate synthase [Acinetobacter johnsonii SH046]
 gi|262315049|gb|EEY96089.1| 23S rRNA pseudouridylate synthase [Acinetobacter johnsonii SH046]
          Length = 312

 Score =  145 bits (366), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 97/310 (31%), Positives = 165/310 (53%), Gaps = 21/310 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   ++  G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLSIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK  +++    K +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDENAAPVSDKVAQSLLSRVVYEDEGLMVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           Y   G ++    + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y +
Sbjct: 123 Y---GLIEGLRAATGKKYLELIHRIDRDTSGLVMISKKRSVLKSLQDMLREHKIKKTYAA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+    K+ I   L +     G+    V+ + +G   + + + V + F      +  
Sbjct: 180 VVKGVVSLDKQLIDAPLHRYELANGE--RRVRVSSEGKE-SKTQWNVAERFMHA-TLVYA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            P +GRTHQ+RVH L +G P+VGD KY    +  +  P   +L LHA  +D+P    G  
Sbjct: 236 SPLSGRTHQIRVHGLSIGHPLVGDDKY--GHETEYKGPKPRRLCLHAMRLDIP----GYA 289

Query: 306 QITAPLPAHM 315
            I APLP  M
Sbjct: 290 PIEAPLPEDM 299


>gi|91784729|ref|YP_559935.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           xenovorans LB400]
 gi|91688683|gb|ABE31883.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           xenovorans LB400]
          Length = 323

 Score =  145 bits (366), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 102/319 (31%), Positives = 169/319 (52%), Gaps = 38/319 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR+PP
Sbjct: 2   IEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +      + +  +    +     H       +++ED  + V +KPAG++V GGSG+A+  
Sbjct: 62  I-----RVAQPSEAAAQAPVPAAHFR-----IIFEDEHLLVIDKPAGVAVHGGSGVAF-- 109

Query: 130 DGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            G ++   +++ Q     L HRLD+ETSGIL++A+ R+A  +L E  R  ++ K Y++ V
Sbjct: 110 -GVIEQMREARPQAKFLELVHRLDRETSGILMLAKKRSALVNLHEQIRENKMDKRYYACV 168

Query: 188 -------WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
                  WG  +  +E +  +L      G   V V  Q +  A++ +  F +ID + + +
Sbjct: 169 HGEWASDWGRRRAVREPLHKYLTAD---GERRVRV--QPDGLASHTV--FNLIDRWPE-Y 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARY 294
             LE +  TGRTHQ+RVH  H+G PIVGD KY  +F  N        +P   +++LHA  
Sbjct: 221 ALLEAELKTGRTHQIRVHLQHLGLPIVGDAKY-GDFALNKALARANANPGLKRMFLHAYR 279

Query: 295 MDLPHPEGGR-LQITAPLP 312
           + L HP  G  LQ  APLP
Sbjct: 280 LKLTHPATGEPLQFEAPLP 298


>gi|307248951|ref|ZP_07530961.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|306854562|gb|EFM86755.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
          Length = 326

 Score =  145 bits (366), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 108/307 (35%), Positives = 169/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q   VVR
Sbjct: 16  VQFFTISEDEVGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQPDDVVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 76  VPPVRVA------EKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 128

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 129 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 187

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+   +V+ +EKG   + + F + + +A     ++  
Sbjct: 188 VRGQWQAHTKVIKAPLLKNELASGE--RIVRVSEKG-KPSETRFSIEERYANA-TLVKAS 243

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 244 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 303

Query: 305 LQITAPL 311
           + ITAPL
Sbjct: 304 MLITAPL 310


>gi|88705138|ref|ZP_01102850.1| Ribosomal large subunit pseudouridine synthase C [Congregibacter
           litoralis KT71]
 gi|88700833|gb|EAQ97940.1| Ribosomal large subunit pseudouridine synthase C [Congregibacter
           litoralis KT71]
          Length = 309

 Score =  145 bits (366), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 100/312 (32%), Positives = 162/312 (51%), Gaps = 20/312 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V+Y+ V+   E  RLD +     P +    L + +R G++RV+K RVK + R+  G 
Sbjct: 1   MSAVRYLTVDERGEGQRLDNYVLRECPAVPKTRLYRAMRKGEIRVNKGRVKPDRRLALGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+           +  +         + L + +++ED  +   NKP+GI+V GGS
Sbjct: 61  VVRLPPLSTP--------EPRERGAAPPGWQERLGARVVFEDEHLLAINKPSGIAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQK 181
           G+ + +   L++     G K   L HRLD+ETSG+++VA+  AA + L E  R + +I K
Sbjct: 113 GLQFGLIETLRTM--RPGAKFLELVHRLDRETSGLILVAKKPAALRALHELLRQKGKIDK 170

Query: 182 IYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y +L  G  P++ +   A     +   G   V V K  +     +I+ F++   F+   
Sbjct: 171 RYLALAEGAWPRHLRLVEAPLKRFERQSGERQVKVAKDGKP----SITEFRIKRSFSAA- 225

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             +E +P TGRTHQ+RVHALH G P++GD KY +         +   +L+LHA+ +    
Sbjct: 226 TLVEARPLTGRTHQIRVHALHGGHPLLGDGKYQSEKGEGLARKLGLKRLFLHAQSLSF-E 284

Query: 300 PEGGRLQITAPL 311
               R ++TAPL
Sbjct: 285 LNDQRYELTAPL 296


>gi|238783756|ref|ZP_04627775.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           bercovieri ATCC 43970]
 gi|238715307|gb|EEQ07300.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           bercovieri ATCC 43970]
          Length = 319

 Score =  145 bits (366), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVA------EREEIQISAKLDKVA-VLADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   VVK + +G   + + FKV + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGE--RVVKVSSEG-KPSETRFKVEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 296 MRIEAPL 302


>gi|124265850|ref|YP_001019854.1| ribosomal large subunit pseudouridine synthase C [Methylibium
           petroleiphilum PM1]
 gi|124258625|gb|ABM93619.1| ribosomal large subunit pseudouridine synthase C [Methylibium
           petroleiphilum PM1]
          Length = 320

 Score =  145 bits (366), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 97/318 (30%), Positives = 164/318 (51%), Gaps = 28/318 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ V  D    RLD +       +   ++ +I+RSG+VRV++ R   + R+ +G  +R
Sbjct: 1   MRHLTVGEDGAGQRLDNYLVKTLKGVPKTHVYRIIRSGEVRVNRGRAAADTRLAAGDELR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A            +        +F    +++ED  + V +KPAG++V GGSG++
Sbjct: 61  LPPVRMATP----------AEREAAPPREF---PVVHEDEHLLVIDKPAGVAVHGGSGVS 107

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    ++ Q     L HRLD+ETSG+L++A+ R+A   L + FR R   K Y 
Sbjct: 108 F---GVIEQLRRARPQAKFLELVHRLDRETSGLLLLAKKRSALTRLQDQFRARETGKTYA 164

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G    + + I   L K     G+  V V   +++    +I+  +V   +A  +  L
Sbjct: 165 ALVPGAWPARHKVIDAPLHKYLDGAGERRVRVTGADDEDGQRSITLVQVAAAYA-GYTLL 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQ-NKLYLHARYMD 296
           ++   TGRTHQ+RVH  H G  IVGD KY       A  +G     ++ ++++LHAR + 
Sbjct: 224 DVTIKTGRTHQIRVHLAHAGHAIVGDDKYGDFALNKAFARGEAVPAVKFDRMFLHARRLR 283

Query: 297 LPHPEGGR-LQITAPLPA 313
             HP  G  +++ A LPA
Sbjct: 284 FEHPASGETIELEAALPA 301


>gi|322641590|gb|EFY38228.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
          Length = 274

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 95/267 (35%), Positives = 151/267 (56%), Gaps = 14/267 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F  L   
Sbjct: 180 VRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--FATLVRC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY 272
            P TGRTHQ+RVH  + G PI  D +Y
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRY 261


>gi|170023919|ref|YP_001720424.1| 23S rRNA pseudouridylate synthase C [Yersinia pseudotuberculosis
           YPIII]
 gi|169750453|gb|ACA67971.1| pseudouridine synthase, RluA family [Yersinia pseudotuberculosis
           YPIII]
          Length = 320

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVA------EREEVQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKSMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   VVK + +G   + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAIQAPLLKNIMQSGE--RVVKVSSEG-KPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPE-GGR 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNTGAT 295

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 296 MRIEAPL 302


>gi|190151234|ref|YP_001969759.1| ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|307246812|ref|ZP_07528878.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307251150|ref|ZP_07533072.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|307253568|ref|ZP_07535436.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|307255795|ref|ZP_07537597.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|307257984|ref|ZP_07539737.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|307260247|ref|ZP_07541955.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|307264584|ref|ZP_07546167.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
 gi|189916365|gb|ACE62617.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|306852283|gb|EFM84522.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|306856816|gb|EFM88950.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|306858948|gb|EFM90993.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|306861258|gb|EFM93250.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|306863531|gb|EFM95461.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|306865694|gb|EFM97574.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|306870113|gb|EFN01874.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
          Length = 326

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 107/307 (34%), Positives = 169/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q   VVR
Sbjct: 16  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQPDDVVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 76  VPPVRVA------EKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 128

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 129 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 187

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+   +V+ +E+G   + + F + + +A     ++  
Sbjct: 188 VRGQWQAHTKVIKAPLLKNELASGE--RIVRVSEEG-KPSETRFSIEERYANA-TLVKAS 243

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 244 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 303

Query: 305 LQITAPL 311
           + ITAPL
Sbjct: 304 MLITAPL 310


>gi|46143747|ref|ZP_00134463.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
          Length = 326

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 107/307 (34%), Positives = 169/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q   VVR
Sbjct: 16  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQPDDVVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 76  VPPVRVA------EKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 128

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 129 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLRKKVVQKDYLAL 187

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+   +V+ +E+G   + + F + + +A     ++  
Sbjct: 188 VRGQWQAHTKVIKAPLLKNELASGE--RIVRVSEEG-KPSETRFSIEERYANA-TLVKAS 243

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 244 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 303

Query: 305 LQITAPL 311
           + ITAPL
Sbjct: 304 MLITAPL 310


>gi|332284960|ref|YP_004416871.1| ribosomal large subunit pseudouridine synthase C [Pusillimonas sp.
           T7-7]
 gi|330428913|gb|AEC20247.1| ribosomal large subunit pseudouridine synthase C [Pusillimonas sp.
           T7-7]
          Length = 322

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 104/320 (32%), Positives = 168/320 (52%), Gaps = 24/320 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++V + +++   R+D +       +   +L K +RSG+VRV+K R+  + R++ G  VR
Sbjct: 19  VRFVEIGDEQAGQRIDNFLLRICKGVPKSHLYKAIRSGEVRVNKGRIAADYRLELGDTVR 78

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+   L    + +++  +   +           ++ED  + V NKPAG++V GGSG++
Sbjct: 79  VPPL--RLPRPDEPRRVPPAVFPV-----------VFEDEAMVVVNKPAGVAVHGGSGVS 125

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    ++   P   L HRLD+ETSG+L++A+ R A   L +  R    +K Y 
Sbjct: 126 F---GVIEQLRAARPDAPFLELAHRLDRETSGLLIIAKKRKALLGLHDMMREGGGRKHYQ 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   N K+ +   LLK     G+    V    K A+  I+  K       ++  L 
Sbjct: 183 ALVVGDWVNDKQHLRQPLLKWLTASGERRVKVDAQGKVAHTIITLQKRYG----RYSLLG 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +  TGRTHQ+RVH    G PIVGD KY ++  +  F     N+++LHA  ++LPHP  G
Sbjct: 239 AELRTGRTHQIRVHLASCGYPIVGDDKYGSDEVRAYFAGLGLNRMFLHACRLELPHPLTG 298

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             L +TA LP   +KT D L
Sbjct: 299 EPLVLTADLPPVCLKTLDYL 318


>gi|255021322|ref|ZP_05293370.1| Ribosomal large subunit pseudouridine synthase C [Acidithiobacillus
           caldus ATCC 51756]
 gi|254969185|gb|EET26699.1| Ribosomal large subunit pseudouridine synthase C [Acidithiobacillus
           caldus ATCC 51756]
          Length = 316

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 99/309 (32%), Positives = 160/309 (51%), Gaps = 20/309 (6%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  +E   RLD +       +   ++ KILRSG+VRV+K R + +  +  G V+R+PPV 
Sbjct: 11  VTAEEAGQRLDNFLLRVLKGVPRSHIYKILRSGEVRVNKGRARPHYHLHLGDVLRLPPVR 70

Query: 72  NALNHII---KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           +A    +    EQ  +D           L+  +L+ED ++ V +KPAG++V GGSGI Y 
Sbjct: 71  SADPAAVPRLPEQLAVD-----------LRERVLFEDDRVLVLDKPAGMAVHGGSGIRYG 119

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +   L+  +    ++  L HRLD++TSG L++++ R+A + L ++ R   + K Y +LV 
Sbjct: 120 VIEALRQ-LRPDLRELELVHRLDRDTSGCLLLSKRRSALRSLHQALREEAMDKRYLALVG 178

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  K  +  +   L K     G+ +  V +++ G       ++  D         E+   
Sbjct: 179 GRWKGAERVVKLPLRKNILQSGERIVRVDEDQ-GKPARTRFYREEDLGIATLLRAELD-- 235

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-Q 306
           TGRTHQ+RVH   +G P  GD KY    F G   +    +L+LHA ++  PHP   R+ +
Sbjct: 236 TGRTHQIRVHLQAIGHPTAGDSKYGDETFNGAMRALGLRRLFLHAAFLAFPHPRDERIVR 295

Query: 307 ITAPLPAHM 315
           + APLPA +
Sbjct: 296 VEAPLPADL 304


>gi|126209339|ref|YP_001054564.1| 23S rRNA pseudouridylate synthase C [Actinobacillus
           pleuropneumoniae L20]
 gi|126098131|gb|ABN74959.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
          Length = 321

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 107/307 (34%), Positives = 169/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q   VVR
Sbjct: 11  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQPDDVVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPVRVA------EKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLRKKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+   +V+ +E+G   + + F + + +A     ++  
Sbjct: 183 VRGQWQAHTKVIKAPLLKNELASGE--RIVRVSEEG-KPSETRFSIEERYANA-TLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 298

Query: 305 LQITAPL 311
           + ITAPL
Sbjct: 299 MLITAPL 305


>gi|332975054|gb|EGK11960.1| ribosomal large subunit pseudouridine synthase C [Kingella kingae
           ATCC 23330]
          Length = 334

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 101/329 (30%), Positives = 174/329 (52%), Gaps = 25/329 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ ++  E   RLD +       +   ++ +I+R+G+VRV+K RVK + RI++  +VR
Sbjct: 9   VNHITIQEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRVNKGRVKPDYRIENKDLVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+       I E+ +  S  N    +      +++ED  + V NKP+G++V GGSG++
Sbjct: 69  IPPI------RIAEKDVSGSLKNAPIPAREFD--IVFEDDAMIVINKPSGVAVHGGSGVS 120

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   +S  D+K  +  L HRLD++TSG+L++A+ R+A   L E  R    +KIY +
Sbjct: 121 FGVIEQLRQSRPDAKYLE--LVHRLDRDTSGLLMIAKKRSALVKLHEMLRNDHPKKIYLA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-------- 237
           L  G  + +   +   L+K +   G+ +  V  +  G + A + F+V++ F+        
Sbjct: 179 LGVGTWQPENRHVKLPLIKYTGANGEKMVRVGSDADGQS-AHTIFRVLNTFSGSLMHSVG 237

Query: 238 -QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARY 294
                 +E    TGRTHQ+RVH     CPI GD +Y  +++ N         +++LHA  
Sbjct: 238 ISALSLVEATLKTGRTHQIRVHMQSQNCPIAGDERY-GDYQANKRLQKLGLKRMFLHAFV 296

Query: 295 MDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           ++L HP  G +L + A LP  +    D+L
Sbjct: 297 LELNHPLTGEKLHLKADLPKELQNLLDNL 325


>gi|303249693|ref|ZP_07335898.1| 23S rRNA pseudouridylate synthase C [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|302651505|gb|EFL81656.1| 23S rRNA pseudouridylate synthase C [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
          Length = 321

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 107/307 (34%), Positives = 169/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q   VVR
Sbjct: 11  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQPDDVVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPVRVA------EKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+   +V+ +E+G   + + F + + +A     ++  
Sbjct: 183 VRGQWQAHTKVIKAPLLKNELASGE--RIVRVSEEG-KPSETRFSIEERYANA-TLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 298

Query: 305 LQITAPL 311
           + ITAPL
Sbjct: 299 MLITAPL 305


>gi|45442052|ref|NP_993591.1| 23S rRNA pseudouridylate synthase C [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108807929|ref|YP_651845.1| 23S rRNA pseudouridylate synthase C [Yersinia pestis Antiqua]
 gi|108812199|ref|YP_647966.1| 23S rRNA pseudouridylate synthase C [Yersinia pestis Nepal516]
 gi|145599137|ref|YP_001163213.1| 23S rRNA pseudouridylate synthase C [Yersinia pestis Pestoides F]
 gi|149366507|ref|ZP_01888541.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           CA88-4125]
 gi|161484824|ref|NP_669067.2| 23S rRNA pseudouridylate synthase C [Yersinia pestis KIM 10]
 gi|162420400|ref|YP_001607836.1| 23S rRNA pseudouridylate synthase C [Yersinia pestis Angola]
 gi|165938469|ref|ZP_02227026.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166214606|ref|ZP_02240641.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167427006|ref|ZP_02318759.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|218928727|ref|YP_002346602.1| 23S rRNA pseudouridylate synthase C [Yersinia pestis CO92]
 gi|229841579|ref|ZP_04461738.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229843691|ref|ZP_04463834.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229894436|ref|ZP_04509618.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Pestoides A]
 gi|229902524|ref|ZP_04517643.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Nepal516]
 gi|270490299|ref|ZP_06207373.1| pseudouridine synthase, RluA family [Yersinia pestis KIM D27]
 gi|294504206|ref|YP_003568268.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Z176003]
 gi|34395806|sp|Q8ZFU1|RLUC_YERPE RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|45436915|gb|AAS62468.1| ribosomal large subunit pseudouridine synthaseC [Yersinia pestis
           biovar Microtus str. 91001]
 gi|108775847|gb|ABG18366.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Nepal516]
 gi|108779842|gb|ABG13900.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Antiqua]
 gi|115347338|emb|CAL20236.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           CO92]
 gi|145210833|gb|ABP40240.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Pestoides F]
 gi|149290881|gb|EDM40956.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           CA88-4125]
 gi|162353215|gb|ABX87163.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Angola]
 gi|165913584|gb|EDR32204.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166204213|gb|EDR48693.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167053985|gb|EDR63813.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|229680570|gb|EEO76667.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Nepal516]
 gi|229689299|gb|EEO81362.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229697945|gb|EEO87992.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229703455|gb|EEO90472.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Pestoides A]
 gi|262366257|gb|ACY62814.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           D182038]
 gi|270338803|gb|EFA49580.1| pseudouridine synthase, RluA family [Yersinia pestis KIM D27]
 gi|294354665|gb|ADE65006.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Z176003]
 gi|320014732|gb|ADV98303.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Medievalis str. Harbin 35]
          Length = 320

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVA------EREEVQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKSMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   VVK + +G   + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAIQAPLLKNIMQSGE--RVVKVSSEG-KPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHALHAGHPIAFDDRYGYREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 296 MRIEAPL 302


>gi|134095276|ref|YP_001100351.1| 23S rRNA pseudouridylate synthase [Herminiimonas arsenicoxydans]
 gi|133739179|emb|CAL62228.1| Ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Herminiimonas arsenicoxydans]
          Length = 326

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 106/321 (33%), Positives = 165/321 (51%), Gaps = 30/321 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            +  +E   R+D +       +   ++ ++LRSG+VRV+K R+    R+  G VVRIPP+
Sbjct: 22  TISEEEAGQRIDNFLLRICKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLTEGDVVRIPPI 81

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-I 129
                      +I + + +    ++F    +L ED+ + V +KPAG++V GGSG++Y  I
Sbjct: 82  -----------RIAEKAPSTAPGAEFK---ILLEDNHLLVIDKPAGVAVHGGSGVSYGVI 127

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +    +  D+K  +  L HRLD++TSG+LV+A+ R+A  +L E  R     K Y  LV G
Sbjct: 128 EQLRAARPDAKFLE--LVHRLDRDTSGVLVLAKKRSALTNLHEQIRGGEPDKRYLVLVHG 185

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             KN ++ I   L K S   G+   V  Q +   ++ I  F +I  + + F  LE +  T
Sbjct: 186 DWKNARQHIKLALHKYSTADGER-RVRVQADGMESHTI--FNLIQRYGE-FALLEAELKT 241

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANF-------KGNFTSPIQNKLYLHARYMDLPHPEG 302
           GRTHQ+RVH    G  I GD KY  +F       K N       +++LHA  +   HPE 
Sbjct: 242 GRTHQIRVHLASSGFAIAGDDKY-GDFALNRELQKANGERVALKRMFLHAHQITFIHPES 300

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
           G+ + + APLP    +   SL
Sbjct: 301 GKPVTLNAPLPPECERFLKSL 321


>gi|165925607|ref|ZP_02221439.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|166008246|ref|ZP_02229144.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|167402395|ref|ZP_02307858.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167421825|ref|ZP_02313578.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|165922716|gb|EDR39867.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165992628|gb|EDR44929.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166960310|gb|EDR56331.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167048228|gb|EDR59636.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|262362323|gb|ACY59044.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           D106004]
          Length = 327

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 15  VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 75  VPPVRVA------EREEVQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 128 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKSMQKDYLAL 186

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   VVK + +G   + + FK+ + F +    ++  
Sbjct: 187 VRGQWQSHCKAIQAPLLKNIMQSGE--RVVKVSSEG-KPSETRFKIEERF-EHATLVKAS 242

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 243 PVTGRTHQIRVHALHAGHPIAFDDRYGYREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 302

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 303 MRIEAPL 309


>gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudouridine synthase C [Herbaspirillum
           seropedicae SmR1]
 gi|300073996|gb|ADJ63395.1| ribosomal large subunit pseudouridine synthase C protein
           [Herbaspirillum seropedicae SmR1]
          Length = 355

 Score =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 98/313 (31%), Positives = 163/313 (52%), Gaps = 26/313 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + + ++E   R+D +       +   ++ ++LRSG+VRV+K R+    R+  G VVR
Sbjct: 33  VQLLTISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLAEGDVVR 92

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+           ++ +    +   ++F    +L EDS + V +KPAG++V GGSG++
Sbjct: 93  VPPI-----------RVAEKQETVVPGAEFR---ILLEDSHLLVIDKPAGVAVHGGSGVS 138

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    + +   L HRLD++TSG+L++A+ R+A  +L +  R     K Y++L
Sbjct: 139 YGVIEQLRA-ARPQAKFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTL 197

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  KN ++ +   L K S   G+    V+ + + ++   S  +    FA     LE +
Sbjct: 198 VQGDWKNARQHVKLPLFKYSTPDGERRVRVQADGQPSHTVFSLLRRFGDFA----LLEAE 253

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH    G PIVGD KY       A  K +       +++LHA  +   HP
Sbjct: 254 LKTGRTHQIRVHLSSSGFPIVGDDKYGDFALNKALQKADGRRIAFKRMFLHAWRISFRHP 313

Query: 301 EGG-RLQITAPLP 312
           E G  + + A LP
Sbjct: 314 ESGDTVTLKAGLP 326


>gi|224825744|ref|ZP_03698848.1| pseudouridine synthase, RluA family [Lutiella nitroferrum 2002]
 gi|224601968|gb|EEG08147.1| pseudouridine synthase, RluA family [Lutiella nitroferrum 2002]
          Length = 310

 Score =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 105/319 (32%), Positives = 164/319 (51%), Gaps = 24/319 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V   E   R+D +       +   ++ +ILRSG+VRV+K R+    R+Q+   +R
Sbjct: 9   VTFYTVGEAESGQRIDNFLVRLLKGVPKSHIYRILRSGEVRVNKGRIDAAYRLQADDQIR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV           ++ +   N    + F    ++YED+ + V +KPAGI+V GGSG++
Sbjct: 69  LPPV-----------RVAERQENDAPATTF---PVIYEDNALLVIDKPAGIAVHGGSGVS 114

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  I+   K++ + +  +  L HRLD+ETSG+L++A+ R+A   L +  R     K Y +
Sbjct: 115 FGVIEQLRKAYPEYRFLE--LVHRLDRETSGLLMLAKKRSALLKLHDMMRSSTPDKRYLA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L  G  ++ K  +   L K ++  G+    V  N + A+   + FKV + FA  F  +E 
Sbjct: 173 LGVGRWQDDKH-VKLPLFKFTNAEGERRVRVADNGQSAH---TIFKVQERFAD-FTLVEA 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +  TGRTHQ+RVH    G PI GD KY  A            +++LHA  + LPHP  G 
Sbjct: 228 RLRTGRTHQIRVHMAASGHPIAGDDKYGDAALNRELGRRGLRRMFLHAASLSLPHPLTGE 287

Query: 305 -LQITAPLPAHMVKTWDSL 322
            L   APLP  +    DSL
Sbjct: 288 PLSFQAPLPPELAHFLDSL 306


>gi|238022130|ref|ZP_04602556.1| hypothetical protein GCWU000324_02036 [Kingella oralis ATCC 51147]
 gi|237866744|gb|EEP67786.1| hypothetical protein GCWU000324_02036 [Kingella oralis ATCC 51147]
          Length = 328

 Score =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 101/334 (30%), Positives = 170/334 (50%), Gaps = 39/334 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V   E   RLD +       +   ++ +I+R G+VRV+K R K + R+ +G  VR
Sbjct: 9   VNHISVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRGGEVRVNKGRAKPDYRVAAGDCVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI------LLYEDSKIYVFNKPAGISVQ 120
           IPP+           ++ + +V     SD LK++      +++ED  + V NKP+GI+V 
Sbjct: 69  IPPI-----------RVAEKNV-----SDSLKTVPPREFEIIFEDDALLVINKPSGIAVH 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L+     +     L HRLD++TSG+L++A+ R+A   L E  R    +
Sbjct: 113 GGSGVSFGVIEQLR-QARPEANYLELVHRLDKDTSGLLMIAKKRSALVKLHEMLRNDHPK 171

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--- 237
           KIY +L  G  + +   +   L+K +   G+   +V+  ++G + A + F+V+D F+   
Sbjct: 172 KIYLALGVGAWQPENRHVRLPLVKYTGAAGE--KMVRVGDEGQS-AHTIFRVLDTFSGCL 228

Query: 238 ------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLY 289
                      +E    TGRTHQ+RVH    GCPI GD +Y  +++ N         +++
Sbjct: 229 THSVGISALSLVEATLKTGRTHQIRVHMQASGCPIAGDERY-GDYQANRRLQKLGLKRMF 287

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           LHA  + L HP  G  L + A LP  + +    L
Sbjct: 288 LHAHRLVLAHPLSGETLDLVAGLPEELERVLGRL 321


>gi|239500866|ref|ZP_04660176.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB900]
          Length = 310

 Score =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 96/319 (30%), Positives = 171/319 (53%), Gaps = 25/319 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   ++  G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLAIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKH-SDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           + P        I+ ++  +++V ++   +  L S ++YED  + V NKP+GI+V GGSG+
Sbjct: 70  VAP--------IRYEQKDETAVPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAVHGGSGV 121

Query: 126 AYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           AY   G +++   + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y 
Sbjct: 122 AY---GLIEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYA 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++V G     K+ I   L +     G+  V V K+ +       + + V + F +    +
Sbjct: 179 AIVKGQVSLDKQLIDAPLFRYELANGERRVRVSKEGKPSK----TEWVVAERF-KNATLV 233

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              P +GRTHQ+RVH L +G P++GD KY  N    +  P   +L LHA  +D+P    G
Sbjct: 234 HASPLSGRTHQIRVHGLSIGHPLLGDDKYGHNTA--YAGPEARRLCLHAMRLDIP----G 287

Query: 304 RLQITAPLPAHMVKTWDSL 322
              I APLP  M +  ++L
Sbjct: 288 YPTIEAPLPEDMTQLLEAL 306


>gi|238754377|ref|ZP_04615733.1| Ribosomal large subunit pseudouridine synthase C [Yersinia ruckeri
           ATCC 29473]
 gi|238707410|gb|EEP99771.1| Ribosomal large subunit pseudouridine synthase C [Yersinia ruckeri
           ATCC 29473]
          Length = 320

 Score =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 108/308 (35%), Positives = 172/308 (55%), Gaps = 16/308 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E++    S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVA------EREDAPVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
           V G  ++  + +   LLK     G+   VVK + +G   + + FKV + F  + C L + 
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGE--RVVKVSSEG-KPSETRFKVEERF--EHCTLVKA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVHALH G PI  D +Y   +F         ++L+LHA  +   HP+ G 
Sbjct: 235 SPITGRTHQIRVHALHAGHPIAFDDRYGDRDFDLQLKGTGLHRLFLHAAALRFAHPDTGE 294

Query: 305 -LQITAPL 311
            ++I APL
Sbjct: 295 TMRIEAPL 302


>gi|296136842|ref|YP_003644084.1| pseudouridine synthase, RluA family [Thiomonas intermedia K12]
 gi|295796964|gb|ADG31754.1| pseudouridine synthase, RluA family [Thiomonas intermedia K12]
          Length = 329

 Score =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 97/320 (30%), Positives = 159/320 (49%), Gaps = 30/320 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V +  E  RLD +   H   +   ++ +I+RSG+VRV+  R   + ++QS   VR
Sbjct: 9   VRLLQVGDAGEGQRLDNFLARHLKGVPLSHIHRIVRSGEVRVNGGRASADQKLQSSDQVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A               +  + +  L+  +++ED  +   NKP G++V GGSG++
Sbjct: 69  IPPVRVA-------------QPDTPRSAPALQFPIVFEDDFLLAINKPEGVAVHGGSGVS 115

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++      +   L HRLD++TSG+L++A+ R+A   L  + R R   K Y +L
Sbjct: 116 FGVIEALRA-ARPTAKFLELVHRLDRDTSGLLLIAKKRSALTTLHAALRERHADKRYLAL 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-------QK 239
           V G+       I   L K     G+    V+ + +    + + F+  + FA         
Sbjct: 175 VAGLWTRGAVMIEAPLHKYLLANGE--RRVRVDAQQGQESRTQFRSQEQFALPGLGPWGG 232

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQNKLYLHAR 293
              ++ +  TGRTHQ+RVH  H G PIVGD KY  +       +G    P   +++LHA 
Sbjct: 233 LSLMQARLLTGRTHQIRVHLAHCGHPIVGDDKYGDDSLNALLARGQAGVPPFRRMFLHAE 292

Query: 294 YMDLPHPEGG-RLQITAPLP 312
            + + HP  G RL++ APLP
Sbjct: 293 SLTIAHPASGERLELRAPLP 312


>gi|157370141|ref|YP_001478130.1| 23S rRNA pseudouridylate synthase C [Serratia proteamaculans 568]
 gi|157321905|gb|ABV41002.1| pseudouridine synthase, RluA family [Serratia proteamaculans 568]
          Length = 320

 Score =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 104/311 (33%), Positives = 168/311 (54%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISDDEAGQRIDNFLLARLKGVPKSMIYRIVRKGEVRVNKGRIKAEYKLAPGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E++    S  L K +  L   +LYED  + + NKP+G +V GGSG++
Sbjct: 68  VPPVRVA------EREDAPVSAKLDKVA-ALAHCILYEDDHLLLLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V    K +    + FKV + F +    ++  
Sbjct: 180 VRGEWQSHCKAVQAPLLKNILQSGERIVRVSSEGKPSE---TRFKVEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F          +L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDRQLAGTGLKRLFLHAAALRFEHPGTGET 295

Query: 305 LQITAPLPAHM 315
           ++I AP+ A +
Sbjct: 296 MRIEAPMDAEL 306


>gi|51596800|ref|YP_070991.1| 23S rRNA pseudouridylate synthase C [Yersinia pseudotuberculosis IP
           32953]
 gi|186895871|ref|YP_001872983.1| 23S rRNA pseudouridylate synthase C [Yersinia pseudotuberculosis
           PB1/+]
 gi|51590082|emb|CAH21716.1| ribosomal large subunit pseudouridine synthase C [Yersinia
           pseudotuberculosis IP 32953]
 gi|186698897|gb|ACC89526.1| pseudouridine synthase, RluA family [Yersinia pseudotuberculosis
           PB1/+]
          Length = 320

 Score =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVA------EREEVQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKSMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   VVK + +G   + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAIQAPLLKNIMQSGE--RVVKVSSEG-KPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 296 IRIEAPL 302


>gi|157828222|ref|YP_001494464.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           rickettsii str. 'Sheila Smith']
 gi|165932925|ref|YP_001649714.1| hypothetical protein RrIowa_0413 [Rickettsia rickettsii str. Iowa]
 gi|157800703|gb|ABV75956.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           rickettsii str. 'Sheila Smith']
 gi|165908012|gb|ABY72308.1| hypothetical protein RrIowa_0413 [Rickettsia rickettsii str. Iowa]
          Length = 303

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 95/306 (31%), Positives = 165/306 (53%), Gaps = 25/306 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + +  ++ G  + I    +  N  +K
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNSQKAEASLSVKGGDKIFIN---DKFNLPVK 68

Query: 80  EQKIL---DSSVNLTKH--SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           + + L   D+ + L K   +D+L    +Y D  +   NKPAG++ QGG+ I   ID  LK
Sbjct: 69  QPEKLVFTDAEIKLAKKITTDYL----IYADDNLIAINKPAGLATQGGTKINLSIDSALK 124

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KN 193
            +++ KG   +L HRLD++TSG+L++A+   ++  L ++F+ + + K Y+++ +G P KN
Sbjct: 125 -YLNYKGTDFKLVHRLDKKTSGLLLIAKNYLSSVKLHDAFKEKLVVKTYFAVTYGKPIKN 183

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E  +N  ++KS   G    +   + +    AI+++KV+         +E  P TGR H
Sbjct: 184 VGEVRSN--IEKSK--GSTPKITDIDSENGKLAITYYKVLKSLDNNLFLIEFTPVTGRMH 239

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
           QLR+HA  +GCPI+GD KY     GN    P    ++LHA  + L     G  +++ A L
Sbjct: 240 QLRLHAKLLGCPILGDDKY-----GNKAIMPYSKYMFLHAHNICLSEKIFGQEIKLEAKL 294

Query: 312 PAHMVK 317
           P +  +
Sbjct: 295 PFYFTR 300


>gi|21958555|gb|AAM85318.1|AE013778_4 hypothetical protein y1750 [Yersinia pestis KIM 10]
          Length = 341

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 29  VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 88

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 89  VPPVRVA------EREEVQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 141

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 142 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKSMQKDYLAL 200

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   VVK + +G   + + FK+ + F +    ++  
Sbjct: 201 VRGQWQSHCKAIQAPLLKNIMQSGE--RVVKVSSEG-KPSETRFKIEERF-EHATLVKAS 256

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 257 PVTGRTHQIRVHALHAGHPIAFDDRYGYREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 316

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 317 MRIEAPL 323


>gi|307262378|ref|ZP_07544024.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|306867926|gb|EFM99756.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
          Length = 326

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 107/307 (34%), Positives = 168/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q   VVR
Sbjct: 16  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQPDDVVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 76  VPPVRVA------EKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 128

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  +     L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 129 FGVIEALRA-LRPQAHFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 187

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+   +V+ +E+G   + + F + + +A     ++  
Sbjct: 188 VRGQWQAHTKVIKAPLLKNELASGE--RIVRVSEEG-KPSETRFSIEERYANA-TLVKAS 243

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 244 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 303

Query: 305 LQITAPL 311
           + ITAPL
Sbjct: 304 MLITAPL 310


>gi|293610198|ref|ZP_06692499.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292827430|gb|EFF85794.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 310

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 97/318 (30%), Positives = 167/318 (52%), Gaps = 23/318 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   +++ G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLEIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAAPVSDSVAQSLLSRVVYEDEGLLVINKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           Y   G +++   + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y +
Sbjct: 123 Y---GLIEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +V G     K+ I   L +     G+  V V K+ +       + + V + F +    + 
Sbjct: 180 IVKGQVSLDKQLIDAPLFRYELANGERRVRVSKEGKPSK----TEWVVAERF-KNATLVH 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P +GRTHQ+RVH L +G P++GD KY       ++ P   +L LHA  +D+P    G 
Sbjct: 235 ASPLSGRTHQIRVHGLSIGHPLLGDDKY--GHTTEYSGPQARRLCLHAMRLDIP----GY 288

Query: 305 LQITAPLPAHMVKTWDSL 322
             I APLP  M +   +L
Sbjct: 289 PPIEAPLPEDMTQLLKAL 306


>gi|153948793|ref|YP_001400547.1| 23S rRNA pseudouridylate synthase C [Yersinia pseudotuberculosis IP
           31758]
 gi|152960288|gb|ABS47749.1| ribosomal large subunit pseudouridine synthase C [Yersinia
           pseudotuberculosis IP 31758]
          Length = 320

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 170/307 (55%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVA------EREEVQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKSMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   VVK + +G   + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAIQAPLLKNIMQSGE--RVVKVSSEG-KPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHALHAGHPIAFDDRYGDRAFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 296 IRIEAPL 302


>gi|123441934|ref|YP_001005917.1| 23S rRNA pseudouridylate synthase C [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122088895|emb|CAL11702.1| ribosomal large subunit pseudouridine synthase C [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|318606162|emb|CBY27660.1| ribosomal large subunit pseudouridine synthase C; LSU Psi955,
           Psi2504 and Psi2580 [Yersinia enterocolitica subsp.
           palearctica Y11]
          Length = 319

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 103/307 (33%), Positives = 166/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A    I+    LD    L          +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVAEREEIQVSAKLDKVAALA-------DCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +VK + +G   + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGE--RMVKVSSEG-KPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDSQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 296 MRIEAPL 302


>gi|238795959|ref|ZP_04639471.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           mollaretii ATCC 43969]
 gi|238720164|gb|EEQ11968.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           mollaretii ATCC 43969]
          Length = 319

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 104/307 (33%), Positives = 166/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A    I+    LD    L          +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVAEREEIQVSAKLDKVAALA-------DCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L++A+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLIAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   VVK + +G   + + FKV + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGE--RVVKVSSEG-KPSETRFKVEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 296 MRIEAPL 302


>gi|330999175|ref|ZP_08322894.1| rRNA pseudouridylate synthase [Parasutterella excrementihominis YIT
           11859]
 gi|329575375|gb|EGG56919.1| rRNA pseudouridylate synthase [Parasutterella excrementihominis YIT
           11859]
          Length = 389

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 106/321 (33%), Positives = 166/321 (51%), Gaps = 27/321 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+   +  RLD +  +    +    + +++RSG+VRV+K R   + R+QSG  VRIPP+ 
Sbjct: 78  VDESNDGQRLDNFLLSQLKGVPKSLIYRVVRSGEVRVNKGRAHVDTRLQSGDEVRIPPI- 136

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
               +  KE +     + L++        +L+ED  I V +KPAG++  GGSGI+Y   G
Sbjct: 137 ---RYTEKESEHSAPPLKLSEMPP-----ILFEDQNIMVVDKPAGMASHGGSGISY---G 185

Query: 132 FLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            ++    S+ + P   L HRLD+ TSG+LV+A+TR A   L E  R   + K Y +LV G
Sbjct: 186 LIERMRASRPELPFLELVHRLDRGTSGVLVLAKTRKALVRLHEMIREGEMHKAYQALVKG 245

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +N ++     L K     G+    V       +++I  F++ + F      +E+   T
Sbjct: 246 DWQNDRQHAKFPLFKYVTPSGERRVRVDPENGLPSHSI--FRLKERFG-PVSLVEVDLLT 302

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFK-------GNFTSPIQNKLYLHARYMDLPHP-E 301
           GRTHQ+RVHA  +G P+VGD KY  +F        G    P + +++LH+  +   HP  
Sbjct: 303 GRTHQIRVHAAELGFPLVGDEKY-GDFAFNDEVAHGLLGVPFK-RMFLHSGKICFHHPIT 360

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G  L+I APLP   V+  + L
Sbjct: 361 GEELEIEAPLPKDCVELIEVL 381


>gi|134301269|ref|YP_001121237.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis WY96-3418]
 gi|134049046|gb|ABO46117.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis WY96-3418]
          Length = 309

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 99/316 (31%), Positives = 168/316 (53%), Gaps = 13/316 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIEVTEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G   +KK    +  LK++    D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHG-HWDKKIIKIDLPLKRTET-KDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDL-PHPE 301
           E++  TGRTHQ+RVH   MG PIV D KY    K         ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVK 317
             ++ +TA L +   K
Sbjct: 290 NKQISVTAALDSRFEK 305


>gi|56707234|ref|YP_169130.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis SCHU S4]
 gi|110669704|ref|YP_666261.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis FSC198]
 gi|118498217|ref|YP_899267.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. novicida U112]
 gi|194324401|ref|ZP_03058174.1| pseudouridine synthase, RluA family [Francisella tularensis subsp.
           novicida FTE]
 gi|224456294|ref|ZP_03664767.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|254369904|ref|ZP_04985913.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica FSC022]
 gi|254369919|ref|ZP_04985927.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis FSC033]
 gi|254375025|ref|ZP_04990505.1| ribosomal large subunit pseudouridine synthase C [Francisella
           novicida GA99-3548]
 gi|254874072|ref|ZP_05246782.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|56603726|emb|CAG44688.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis SCHU S4]
 gi|110320037|emb|CAL08071.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis FSC198]
 gi|118424123|gb|ABK90513.1| ribosomal large subunit pseudouridine synthase C [Francisella
           novicida U112]
 gi|151568165|gb|EDN33819.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis FSC033]
 gi|151572743|gb|EDN38397.1| ribosomal large subunit pseudouridine synthase C [Francisella
           novicida GA99-3548]
 gi|157122874|gb|EDO66991.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica FSC022]
 gi|194321466|gb|EDX18951.1| pseudouridine synthase, RluA family [Francisella tularensis subsp.
           novicida FTE]
 gi|254840071|gb|EET18507.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|282158342|gb|ADA77733.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis NE061598]
          Length = 309

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 99/316 (31%), Positives = 168/316 (53%), Gaps = 13/316 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIEVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G   +KK    +  LK++    D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHG-HWDKKIIKIDLPLKRTET-KDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDL-PHPE 301
           E++  TGRTHQ+RVH   MG PIV D KY    K         ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVK 317
             ++ +TA L +   K
Sbjct: 290 NKQISVTAALDSRFEK 305


>gi|156503277|ref|YP_001429342.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica FTNF002-00]
 gi|290954356|ref|ZP_06558977.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica URFT1]
 gi|295312220|ref|ZP_06803020.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica URFT1]
 gi|156253880|gb|ABU62386.1| pseudouridine synthase, Rlu family protein [Francisella tularensis
           subsp. holarctica FTNF002-00]
          Length = 309

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 99/316 (31%), Positives = 168/316 (53%), Gaps = 13/316 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIDVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMTVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G   +KK    +  LK++    D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHG-HWDKKIIKIDLPLKRTET-KDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDL-PHPE 301
           E++  TGRTHQ+RVH   MG PIV D KY    K         ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVK 317
             ++ +TA L +   K
Sbjct: 290 NKQISVTAALDSRFEK 305


>gi|88607689|ref|YP_505141.1| ribosomal large subunit pseudouridine synthase C [Anaplasma
           phagocytophilum HZ]
 gi|88598752|gb|ABD44222.1| ribosomal large subunit pseudouridine synthase C [Anaplasma
           phagocytophilum HZ]
          Length = 297

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 94/306 (30%), Positives = 161/306 (52%), Gaps = 24/306 (7%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+ ++  P +    ++K+LR G++R++  +   ++R+Q G  V I  V + +    
Sbjct: 1   MRLDRYVRSILPGVPQALVEKLLRKGEIRLNSSKALASSRVQRGDTVSIRNV-DKIASRS 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           KE K +     L   SD +    +Y+D  I   NKPAG++VQGG+ ++  +   L   + 
Sbjct: 60  KEAKEVHDDALLRLVSDNI----IYKDENIIAINKPAGVNVQGGTKVSISLSDLLNKII- 114

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             G++  + HRLD++TSG+L++AR ++ A+ L+E  R RR++K Y ++  G+P   K  I
Sbjct: 115 -PGEQLHIVHRLDRDTSGVLIIARGQSIARILSEELRFRRVRKEYIAVTKGVPAFSKGEI 173

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +  K   G     + K+       A + F V+   +++   + + P TGR HQLR+H
Sbjct: 174 TMPIYCKKQSGVGETLIPKE-------AKTVFSVLQS-SKRHAVMLLSPVTGRKHQLRIH 225

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
                CPI+GD KY  +      + +Q  N L+LHA        +   + I AP+P +M+
Sbjct: 226 LSQFCCPIIGDTKYSKD------TEVQQHNSLHLHAFRTSFQLFD-REIVIKAPVPEYMI 278

Query: 317 KTWDSL 322
            T + L
Sbjct: 279 ATINEL 284


>gi|319779244|ref|YP_004130157.1| Ribosomal large subunit pseudouridine synthase C [Taylorella
           equigenitalis MCE9]
 gi|317109268|gb|ADU92014.1| Ribosomal large subunit pseudouridine synthase C [Taylorella
           equigenitalis MCE9]
          Length = 310

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 106/312 (33%), Positives = 163/312 (52%), Gaps = 21/312 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +  V+YV V++  +  R+D +       +   ++ K +RSGQVRV+K RV    RI +G 
Sbjct: 5   LPSVKYVQVDDSSDGQRIDNFLIKFSKGVPKSHIYKAIRSGQVRVNKGRVNSECRIHTGD 64

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP       + +EQ     S   T++ D     +++ED    + NKPAG++V GGS
Sbjct: 65  EIRIPPF-----RLPQEQP---KSFIPTRNFD-----IIFEDDYFLIINKPAGVAVHGGS 111

Query: 124 GIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G++Y  I+    S  DSK  +  L HRLD+ETSG+L++A+ R+A   L +  R  ++ K 
Sbjct: 112 GVSYGVIEQIRTSRPDSKFLE--LVHRLDKETSGLLIIAKKRSALVALQDMIRQSKLHKS 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y++L+ G    K + I   L K     G+    VK + +   YA S  + ++   + F  
Sbjct: 170 YYALIKGNWPEKLKDIKLPLYKYLTPQGE--RRVKVDAENGKYAHSKVRKVEKVGE-FEL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP- 300
           L +Q  TGRTHQ+RVH    G PIVGD KY  +        +  N+++LHA  +   HP 
Sbjct: 227 LSVQILTGRTHQIRVHLRSSGFPIVGDEKYGDDALTLHVKKLGFNRMFLHAYILSFVHPI 286

Query: 301 EGGRLQITAPLP 312
              RL+    LP
Sbjct: 287 TEKRLEFKIDLP 298


>gi|15892267|ref|NP_359981.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           conorii str. Malish 7]
 gi|20139551|sp|Q92IS6|RLUC_RICCN RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|15619407|gb|AAL02882.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           conorii str. Malish 7]
          Length = 303

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 96/306 (31%), Positives = 164/306 (53%), Gaps = 25/306 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R++ G  + I    +  N  +K
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNAQKAEASLRVKGGDKIFIN---DKFNLPVK 68

Query: 80  EQKIL---DSSVNLTKH--SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           + + L   D+ + L K   +D+L    +Y D  +   NKPAG++ QGG+ I   ID  LK
Sbjct: 69  QPEKLVFTDAEIKLAKKITTDYL----IYADDNLIAINKPAGLATQGGTKINLSIDSALK 124

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KN 193
            +++ KG   +L HRLD++TSG+L++A+   ++  L  +F+ + + K Y+++ +G P KN
Sbjct: 125 -YLNYKGADFKLVHRLDKKTSGLLLIAKNYLSSVKLHNAFKEKLVVKTYFAVTYGKPIKN 183

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E  +N  ++KS   G    +   + +    AI+++KV+         +E  P TGR H
Sbjct: 184 VGEVRSN--IEKSK--GSTPKITDIDSENGKLAITYYKVLKSLDNNLFLIEFTPVTGRMH 239

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           QLR+HA  +GCPI+GD KY     GN    P    ++LHA  + L     G   ++ A L
Sbjct: 240 QLRLHAKLLGCPILGDDKY-----GNKEIMPYSKYMFLHANNICLSEKIFGQESKLEAKL 294

Query: 312 PAHMVK 317
           P +  +
Sbjct: 295 PFYFTR 300


>gi|332678953|gb|AEE88082.1| Ribosomal large subunit pseudouridine synthase C [Francisella cf.
           novicida Fx1]
          Length = 309

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 99/316 (31%), Positives = 168/316 (53%), Gaps = 13/316 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIEVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G   +KK    +  LK++    D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHG-HWDKKIIKIDLPLKRTET-KDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDL-PHPE 301
           E++  TGRTHQ+RVH   MG PIV D KY    K         ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAGKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVK 317
             ++ +TA L +   K
Sbjct: 290 NKQISVTAALDSRFEK 305


>gi|89257067|ref|YP_514429.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica LVS]
 gi|115315423|ref|YP_764146.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica OSU18]
 gi|167009454|ref|ZP_02274385.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           FSC200]
 gi|254368306|ref|ZP_04984325.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica 257]
 gi|89144898|emb|CAJ80243.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica LVS]
 gi|115130322|gb|ABI83509.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           OSU18]
 gi|134254115|gb|EBA53209.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica 257]
          Length = 309

 Score =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 99/316 (31%), Positives = 168/316 (53%), Gaps = 13/316 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIDVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G   +KK    +  LK++    D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHG-HWDKKIIKIDLPLKRTET-KDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDL-PHPE 301
           E++  TGRTHQ+RVH   MG PIV D KY    K         ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVK 317
             ++ +TA L +   K
Sbjct: 290 NKQISVTAALDSRFEK 305


>gi|15604128|ref|NP_220643.1| hypothetical protein RP258 [Rickettsia prowazekii str. Madrid E]
 gi|14423907|sp|Q9ZDR7|RLUC_RICPR RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|3860820|emb|CAA14720.1| unknown [Rickettsia prowazekii]
 gi|292571856|gb|ADE29771.1| Ribosomal large subunit pseudouridine synthase [Rickettsia
           prowazekii Rp22]
          Length = 303

 Score =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 90/304 (29%), Positives = 155/304 (50%), Gaps = 19/304 (6%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD++ K  YP +    ++K LR  Q+ V+ ++ + N R++ G  + I    N    + 
Sbjct: 11  FRLDKYLKRLYPLLTQGVIEKALRQKQITVNFQKAEANLRVKVGDTIFINDYFNL--PVT 68

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + + ++ +   +      L   L+YED  +   NKPA ++ QGGS I   ID  LK +++
Sbjct: 69  QHETLVFADAEIKLAKKILTDYLIYEDDHLIAINKPASLATQGGSKINLSIDSALK-YLN 127

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +G   +L HRLD+ETSG+L++A+   ++  L  +F+ + + K Y+++ +G P      +
Sbjct: 128 YQGADFKLVHRLDKETSGLLLIAKNYLSSVKLHNAFKEKLVIKKYFAITYGRP------V 181

Query: 199 ANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
            N    KS+IG        +   +      AI+++K++         +E  P TGR HQL
Sbjct: 182 KNVGTVKSNIGKSKRRLSKIANIDSDDGKLAITYYKLLKSLNNNLFLIEFMPVTGRMHQL 241

Query: 256 RVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           R+HA  +GCPI+GD KY     GN    P    ++LHA  + L     G  +++ A LP 
Sbjct: 242 RLHAQLLGCPILGDDKY-----GNKEIMPYSKYMFLHANNIYLSETIVGKEIKLEAKLPF 296

Query: 314 HMVK 317
           +  +
Sbjct: 297 YFTR 300


>gi|254373560|ref|ZP_04989047.1| hypothetical protein FTCG_01516 [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|151571285|gb|EDN36939.1| hypothetical protein FTCG_01516 [Francisella novicida GA99-3549]
          Length = 309

 Score =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 99/316 (31%), Positives = 168/316 (53%), Gaps = 13/316 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIEVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G   +KK    +  LK++    D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHG-HWDKKIIRIDLPLKRTET-KDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDL-PHPE 301
           E++  TGRTHQ+RVH   MG PIV D KY    K         ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAGKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVK 317
             ++ +TA L +   K
Sbjct: 290 NKQISVTAALDSRFEK 305


>gi|208780244|ref|ZP_03247586.1| pseudouridine synthase, RluA family [Francisella novicida FTG]
 gi|208743893|gb|EDZ90195.1| pseudouridine synthase, RluA family [Francisella novicida FTG]
          Length = 309

 Score =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 99/316 (31%), Positives = 168/316 (53%), Gaps = 13/316 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIEVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G   +KK    +  LK++    D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHG-HWDKKIIKIDLPLKRTET-KDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDL-PHPE 301
           E++  TGRTHQ+RVH   MG PIV D KY    K         ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDRGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVK 317
             ++ +TA L +   K
Sbjct: 290 NKQISVTAALDSRFEK 305


>gi|187931011|ref|YP_001890995.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. mediasiatica FSC147]
 gi|187711920|gb|ACD30217.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. mediasiatica FSC147]
          Length = 309

 Score =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 100/316 (31%), Positives = 168/316 (53%), Gaps = 13/316 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIEVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQISRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +S+V G   +KK    +  LK++    D   VVK + K    A++    +      F  L
Sbjct: 172 YSIVHG-HWDKKIIKIDLPLKRTETK-DGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDL-PHPE 301
           E++  TGRTHQ+RVH   MG PIV D KY    K         ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVK 317
             ++ +TA L +   K
Sbjct: 290 NKQISVTAALDSRFEK 305


>gi|197104730|ref|YP_002130107.1| ribosomal large subunit pseudouridine synthase D [Phenylobacterium
           zucineum HLK1]
 gi|196478150|gb|ACG77678.1| ribosomal large subunit pseudouridine synthase D [Phenylobacterium
           zucineum HLK1]
          Length = 243

 Score =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 81/231 (35%), Positives = 121/231 (52%), Gaps = 6/231 (2%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            ++S++LYED+ I   NKPAG+S QGG G    +D  L ++      +PRL HRLD++TS
Sbjct: 16  LVRSLVLYEDADILALNKPAGLSSQGGRGQVNTLDELLWAFAKPGKARPRLIHRLDRDTS 75

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKECIANWLLKKSHIGGDYVH 214
           G+++ A+T+ AA  L ++   R   K Y ++V  G P   K  I   L +       Y+ 
Sbjct: 76  GVILTAKTKPAAGFLGKALMKRAFSKTYLAIVTPGAPVPAKGVIDRPLRRVEEGREAYMR 135

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V + +   A  A S ++ +    +    +E+ P TGR HQLRVH   +G PI GD +Y  
Sbjct: 136 VCEPDHPDAEAAASRYRTLK-EGEGAALVELSPETGRMHQLRVHLAAVGRPIAGDARYGG 194

Query: 275 NFK-GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
               G    P   +L LHAR +  PHP GG  ++ A  P+ M +   +LG 
Sbjct: 195 ALMVGGRPVP---RLMLHARALAFPHPAGGTKRLEAEPPSDMAELIQALGL 242


>gi|329850247|ref|ZP_08265092.1| RNA pseudouridylate synthase family protein [Asticcacaulis
           biprosthecum C19]
 gi|328840562|gb|EGF90133.1| RNA pseudouridylate synthase family protein [Asticcacaulis
           biprosthecum C19]
          Length = 267

 Score =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 78/219 (35%), Positives = 126/219 (57%), Gaps = 7/219 (3%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++KS+++YED+ I  FNKP+G+S QGG G  +++D  + ++  S G++P+L HRLD++TS
Sbjct: 42  WVKSMVIYEDADIMGFNKPSGLSSQGGRGDGHNLDDMMWAFAKSNGKRPKLVHRLDRDTS 101

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVH 214
           GIL+VA+T+ A   L ++   R   K Y ++V G     +  + +  L++  +G + +  
Sbjct: 102 GILLVAKTQPAVSFLGKAMIRRAFDKTYLAIVSGAELPDRFTV-DAPLRREEVGREAWSR 160

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V   +   A  A + F+V+         ++  PHTGR HQ+RVH  H+G PI GD +Y  
Sbjct: 161 VCAPDHPDALTAQTTFEVLK-RGDDAALIQCSPHTGRMHQIRVHLAHLGTPIAGDVRYGG 219

Query: 275 NFK-GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
               G    P   +L LHA  +  PHP GG   ++AP+P
Sbjct: 220 ALSVGGRGVP---RLMLHALSLTFPHPAGGDKTLSAPIP 255


>gi|313679572|ref|YP_004057311.1| ribosomal large subunit pseudouridine synthase d [Oceanithermus
           profundus DSM 14977]
 gi|313152287|gb|ADR36138.1| ribosomal large subunit pseudouridine synthase D [Oceanithermus
           profundus DSM 14977]
          Length = 306

 Score =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 89/237 (37%), Positives = 129/237 (54%), Gaps = 22/237 (9%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQ--KPRLTHR 149
           ++ L   +LYED  + V NKPAG+      G+     ++  L  WV+  G+  +P + HR
Sbjct: 71  AEDLTVEILYEDEDMVVVNKPAGMVTHPAPGVTRGTLVNALLGRWVEPGGEPVRPGIVHR 130

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ETSG++VVAR  AA + L ++F+ R + K Y +L  G+P N    IA        IG
Sbjct: 131 LDKETSGVIVVARHEAALRRLADAFKQRFVFKRYVALTEGVPANTT-VIAP-------IG 182

Query: 210 GDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              VH  K +  G  A YA + F+V+   A+    +E +PHTGRTHQ+RVH  H+  PI 
Sbjct: 183 RHPVHRFKMHTGGIKARYAETDFEVV-ATAEGRALVEARPHTGRTHQIRVHLKHLHTPIW 241

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            D  Y         SP   +L LHA  + +PHP+ G+ L  TAP+P  M + W++ G
Sbjct: 242 ADPLY------GKPSPFIGRLALHAYELRVPHPKSGKILSFTAPVPEDMARGWEAAG 292


>gi|238758384|ref|ZP_04619561.1| Ribosomal large subunit pseudouridine synthase C [Yersinia aldovae
           ATCC 35236]
 gi|238703288|gb|EEP95828.1| Ribosomal large subunit pseudouridine synthase C [Yersinia aldovae
           ATCC 35236]
          Length = 322

 Score =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 104/307 (33%), Positives = 165/307 (53%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLVDGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A    ++    LD    L          +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVAEREEVQLSPKLDKVAALA-------DCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKNMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + +   LLK     G+   VVK + +G   + + FKV + F +    ++  
Sbjct: 180 VRGQWQAHCKAVQAPLLKNIMQSGE--RVVKVSSEG-KPSETRFKVEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNSGET 295

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 296 MRIEAPL 302


>gi|293396582|ref|ZP_06640858.1| ribosomal large subunit pseudouridine synthase C [Serratia
           odorifera DSM 4582]
 gi|291420846|gb|EFE94099.1| ribosomal large subunit pseudouridine synthase C [Serratia
           odorifera DSM 4582]
          Length = 319

 Score =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 103/307 (33%), Positives = 167/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++ +G VVR
Sbjct: 8   VQLITISDDEAGQRIDNFLLARLKGVPKSMIYRIVRKGEVRVNKGRIKAEYKLAAGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E++    S  L K +  L + +LYED  + + NKP+G +V GGSG++
Sbjct: 68  VPPVRVA------EREEAPVSAKLDKVA-ALANCILYEDDHLLLLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V    K +    + FKV + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNILQSGERIVRVSSEGKPSE---TRFKVEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y    F          +L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHTLHAGHPIAFDDRYGDREFDRQLAGTGLKRLFLHAAALRFEHPGTGET 295

Query: 305 LQITAPL 311
           L+I AP+
Sbjct: 296 LRIEAPM 302


>gi|253583482|ref|ZP_04860680.1| pseudouridylate synthase [Fusobacterium varium ATCC 27725]
 gi|251834054|gb|EES62617.1| pseudouridylate synthase [Fusobacterium varium ATCC 27725]
          Length = 290

 Score =  143 bits (360), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 97/311 (31%), Positives = 167/311 (53%), Gaps = 25/311 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V+ + E++RLD++ +  Y +I    + K +R+G+++V+ K+ K N R+Q    +++   
Sbjct: 4   IVDKEFEDVRLDKFLRKKYENIPLTEIFKGIRTGKIKVNGKKSKENYRLQLNDKIKVF-- 61

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
               +   KE+K+L+      +  + +K  ++YED  I +FNK   + +  GSG  + I 
Sbjct: 62  --FKDGETKEEKLLEIE---DREIEKIKKSIVYEDENILIFNKKNNMVMHKGSGYDFGIS 116

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             LK ++  K       +R+D+ TSG+++ A++  AA+ L E  R R I+K Y+ LV GI
Sbjct: 117 ELLKGYL--KNPNFNFVNRIDKATSGLIIGAKSLVAARELAEEIRNRNIEKKYYILVEGI 174

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            KN++  I ++L K      D V  V++ E+GA  +IS+FK I  + +    LE    +G
Sbjct: 175 IKNREFTIKSYLKKIE----DKVIEVEEFEEGAKESISYFK-IKKYGKDCTLLEGTLGSG 229

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLRV   +MG  I+GD KY    KG      +  +YL + Y+ +       ++I  P
Sbjct: 230 RTHQLRVQLANMGNAIIGDVKYG---KGK-----EKMMYLFSHYLKIKKY---GIEIDLP 278

Query: 311 LPAHMVKTWDS 321
           +P   +K   S
Sbjct: 279 IPEEYIKRLGS 289


>gi|238789119|ref|ZP_04632908.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           frederiksenii ATCC 33641]
 gi|238722883|gb|EEQ14534.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           frederiksenii ATCC 33641]
          Length = 319

 Score =  142 bits (359), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 103/307 (33%), Positives = 166/307 (54%), Gaps = 14/307 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLLDGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A    I+    LD    L          +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVAEREEIQVSAKLDKVAALA-------DCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +VK + +G   + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGE--RMVKVSSEG-KPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPL 311
           ++I APL
Sbjct: 296 MRIEAPL 302


>gi|319787308|ref|YP_004146783.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317465820|gb|ADV27552.1| pseudouridine synthase, RluA family [Pseudoxanthomonas suwonensis
           11-1]
          Length = 319

 Score =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 106/330 (32%), Positives = 168/330 (50%), Gaps = 35/330 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + V V  D +  RLD +            + K++RSGQVRV+  R K   ++  G  VR
Sbjct: 10  ARTVTVPEDRDGQRLDNFLLGQLKGAPRSLVYKLVRSGQVRVNGGRAKAERKLAGGDEVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      +  E +    +  L +    +++ +++ED++I V +KP+G++  GGSGI+
Sbjct: 70  IPPV-----RVETEAERGTPAPGLLQR---MEASIVFEDARILVIDKPSGVASHGGSGIS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT----ESFRMRRIQKI 182
           +     L++     GQ   L HRLD++TSGILVVA+ R+A   L     E      I+K 
Sbjct: 122 FGAIETLRAL--RPGQTLELAHRLDRDTSGILVVAKKRSALAELQALMREGGSGGGIRKR 179

Query: 183 YWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC-FA 237
           Y +L+ G +P       A       H+G   G   HV  Q  +    ++SHF+ ++    
Sbjct: 180 YLTLLAGRMPDGTMSVDAPL-----HVGLRQGGERHV--QVNQAGKPSVSHFRALERRGG 232

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARY 294
           Q +C + ++  TGRTHQ+RVHA H+G P+ GD KY     N +    + ++ +L+LHA  
Sbjct: 233 QSYCEVRIE--TGRTHQIRVHAQHIGHPVAGDDKYGDPEVNRRLRDKAGLR-RLFLHAAS 289

Query: 295 MDLPHPEGGRLQIT--APLPAHMVKTWDSL 322
           ++    + GR   T  APLP  + +  D L
Sbjct: 290 LEFAL-DAGRTPYTLNAPLPPELREVLDRL 318


>gi|254252865|ref|ZP_04946183.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           dolosa AUO158]
 gi|124895474|gb|EAY69354.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           dolosa AUO158]
          Length = 341

 Score =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 107/328 (32%), Positives = 164/328 (50%), Gaps = 29/328 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + ++      R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +VR
Sbjct: 24  VSMIQIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAYGDLVR 83

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV         +    D+ V    H D     +LYED  + V +KPAG++V GGSG++
Sbjct: 84  VPPV----RVAAADLARADAPVVPPAHFD-----VLYEDDAMLVIDKPAGVAVHGGSGVS 134

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD+ETSG+L++A+ RAA   L E  R  RI K Y++ 
Sbjct: 135 FGVIEQLRQ-ARPRAKFLELVHRLDRETSGVLMLAKKRAALVGLHEQIRENRIDKRYFAC 193

Query: 187 V---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH--FKVIDCFAQKFC 241
           V   W     ++  +   L K +   G+    V+  E G     SH  F +++ +   + 
Sbjct: 194 VHGDWQAEWGRRRAVKAPLFKYTTPEGE--RRVRVQEDGLP---SHTVFNLVERWPD-YA 247

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYM 295
            +E +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   +++LHA  +
Sbjct: 248 LVEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANAQPSLKRMFLHAHRL 306

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            + HP  G  LQ  APLP    +  D L
Sbjct: 307 RVAHPLTGEALQFDAPLPDDCRRFLDQL 334


>gi|299532487|ref|ZP_07045877.1| pseudouridine synthase, RluA family protein [Comamonas testosteroni
           S44]
 gi|298719434|gb|EFI60401.1| pseudouridine synthase, RluA family protein [Comamonas testosteroni
           S44]
          Length = 294

 Score =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 105/302 (34%), Positives = 157/302 (51%), Gaps = 27/302 (8%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
           H   +   ++ +I+RSG+VR++K RV    R+Q G VVR+PPV  +       +K+ + +
Sbjct: 3   HLKGVPKTHVYRIIRSGEVRINKGRVSAETRVQPGDVVRLPPVRIS-------EKVSEKA 55

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRL 146
                  DF     L +D  +   +KPAG++V GGSG+++  I+   ++  D+K  +  L
Sbjct: 56  ERPAPAKDFPA---LLDDEHMLALSKPAGVAVHGGSGVSFGVIEQLRQARPDAKFLE--L 110

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKK 205
            HRLD+ETSGIL+VA+ R+A  +L + FR R   K Y +LV G  P NKK  I   L K 
Sbjct: 111 VHRLDRETSGILLVAKKRSALINLQDQFRERETGKTYLALVQGAWPANKK-VIDLPLHKY 169

Query: 206 SHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK-------FCWLEMQPHTGRTHQLRV 257
               G+  V V   ++     +I+  KV      +          LE+   TGRTHQ+RV
Sbjct: 170 LQADGERRVRVTTADDPDGMRSITLVKVRKLIEPRPLQGLPAMSLLEVTIKTGRTHQIRV 229

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAH 314
           H    G PIVGD KY  +F  N     Q   +++LHA  +   HP  G R+++ A LP  
Sbjct: 230 HLSSQGHPIVGDDKY-GDFDLNRRVQKQGLKRMFLHAWRLQFNHPASGERVELRAELPPE 288

Query: 315 MV 316
           + 
Sbjct: 289 LA 290


>gi|54114079|gb|AAV29673.1| NT02FT1763 [synthetic construct]
          Length = 309

 Score =  142 bits (359), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 99/316 (31%), Positives = 167/316 (52%), Gaps = 13/316 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELFEVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G   +KK    +  LK++    D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHG-HWDKKIIKIDLPLKRTETK-DGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDL-PHPE 301
           E++  TGRTHQ+RVH   MG PIV D KY    K         ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVK 317
             ++ +TA L +   K
Sbjct: 290 NKQISVTAALDSRFEK 305


>gi|94676891|ref|YP_588880.1| ribosomal large subunit pseudouridine synthase C [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
 gi|94220041|gb|ABF14200.1| ribosomal large subunit pseudouridine synthase C [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
          Length = 322

 Score =  142 bits (358), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 102/305 (33%), Positives = 157/305 (51%), Gaps = 20/305 (6%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV-INAL 74
           E   R+D + +     +    + +I+R G+VR++KKR+K   ++QSG  +R+PPV  N +
Sbjct: 17  EAGQRIDNFLRTKLKGVPKSLIYRIIRKGEVRINKKRIKPQYKLQSGDQIRLPPVWRNNI 76

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFL 133
             +   Q          K    L   +LYED  I V NKPAG +V GG  +++  I+G  
Sbjct: 77  TQLFSPQ---------LKKVAVLADTILYEDDYILVLNKPAGTAVHGGYKLSFGVIEGLR 127

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             W  +K  +  L HRLD++TSG L+VA+ R+A + + E  RM+ I K Y +LV G    
Sbjct: 128 ALWPFAKFLE--LIHRLDRDTSGALLVAKKRSALRLMHEQLRMKNINKHYLALVRG-QWE 184

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               +   L+KK    G   H+V+ +  G   + + FK+ + F      +   P TGRTH
Sbjct: 185 SDTVVEVPLMKKIQSNGK--HIVQVSSDG-KMSKTFFKIEENFTIA-TLVNASPITGRTH 240

Query: 254 QLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           Q+RVH+ + G PI  D +Y  N F         ++L+LHA  +   HP  G  L+I APL
Sbjct: 241 QIRVHSQYAGHPIAFDDRYGDNEFDQQLKKCGLSRLFLHAVALSFKHPISGEILRIEAPL 300

Query: 312 PAHMV 316
              ++
Sbjct: 301 DESLL 305


>gi|225873450|ref|YP_002754909.1| pseudouridine synthase, RluA family [Acidobacterium capsulatum ATCC
           51196]
 gi|225793546|gb|ACO33636.1| pseudouridine synthase, RluA family [Acidobacterium capsulatum ATCC
           51196]
          Length = 355

 Score =  142 bits (358), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 106/352 (30%), Positives = 162/352 (46%), Gaps = 60/352 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q+  V  +    RLD W     P ++   ++ +L  GQV VD  + + + +++ G+ V 
Sbjct: 26  IQHFTVPAEAAGQRLDAWLTTQLPDVSRSRVKLLLDDGQVTVDSLKERASLKLRGGESVE 85

Query: 67  I-----PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           +     PP + A+   I     LD               ++YED  + V NKPAG+ V  
Sbjct: 86  VRGEPAPPPLRAMAEDIP----LD---------------IIYEDKDLIVVNKPAGMMVHA 126

Query: 122 GSG----------IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHL 170
           GSG          +   + G  +    + G  +P + HRLD+ETSG+++VAR  AA Q L
Sbjct: 127 GSGATDSARNRGTLVNALLGRQEKLSKTGGDLRPGIVHRLDKETSGLIIVARNDAAHQRL 186

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            E F  R I K Y +LV G     +  I N  + +  I      +  +  +GA  AISH+
Sbjct: 187 AEMFSQREIHKTYLALVHGHIAEDRGTI-NAAIARDVI--RRTRMTTRRTEGARTAISHY 243

Query: 231 KV---IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +V   I+    KF  + ++  TGRTHQ+RVH   +G P+VGD  Y A        P+ N+
Sbjct: 244 RVQRRIETRWGKFTLVSVRIETGRTHQIRVHLSSIGHPVVGDTHYGAPT--TIVLPVANR 301

Query: 288 L----------------YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                            +LHA  +  PHP   + L + APLPA +V   + L
Sbjct: 302 ARRKQLPAPEGLSLPRNFLHAAELKFPHPRSEKPLHLEAPLPAELVAFLEQL 353


>gi|262375074|ref|ZP_06068308.1| 23S rRNA pseudouridylate synthase [Acinetobacter lwoffii SH145]
 gi|262310087|gb|EEY91216.1| 23S rRNA pseudouridylate synthase [Acinetobacter lwoffii SH145]
          Length = 318

 Score =  142 bits (358), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 96/310 (30%), Positives = 161/310 (51%), Gaps = 20/310 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  ++  R+D +  +    +    + +++R GQVRV+KKR+K   ++  G  +R
Sbjct: 10  VTWFEVDEHQDGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLAIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++    K +  L + ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDESAAPVSDKVAQGLLARVIYEDEGLMVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           Y   G ++    + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y +
Sbjct: 123 Y---GLIEGLRAATGKKYLELIHRIDRDTSGLVMISKKRSVLKTLQDMLREHKIKKTYAA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G     K+ I   L +     G+    V   E     + + + V + F      +  
Sbjct: 180 VVKGQVSLDKQLIDAPLHRYELANGERRVCVSPKE--GKESKTQWNVQERFMHA-TLVYA 236

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            P +GRTHQ+RVH L +G P+VGD KY    +  +  P   +L LHA  +D+P    G  
Sbjct: 237 SPLSGRTHQIRVHGLSIGHPLVGDEKY--GHETEYRGPKPRRLCLHAMRLDIP----GYP 290

Query: 306 QITAPLPAHM 315
            I APLP  M
Sbjct: 291 AIEAPLPEDM 300


>gi|163846479|ref|YP_001634523.1| RluA family pseudouridine synthase [Chloroflexus aurantiacus
           J-10-fl]
 gi|222524258|ref|YP_002568729.1| pseudouridine synthase, RluA family [Chloroflexus sp. Y-400-fl]
 gi|172045876|sp|Q45826|Y901_CHLAA RecName: Full=Uncharacterized RNA pseudouridine synthase Caur_0901;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|163667768|gb|ABY34134.1| pseudouridine synthase, RluA family [Chloroflexus aurantiacus
           J-10-fl]
 gi|222448137|gb|ACM52403.1| pseudouridine synthase, RluA family [Chloroflexus sp. Y-400-fl]
          Length = 316

 Score =  142 bits (357), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 103/315 (32%), Positives = 156/315 (49%), Gaps = 38/315 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--I 67
           VVV   +   R+DR+     P ++   +Q+++  G V  D +  + +  ++ G V++  I
Sbjct: 17  VVVPPTQTAERIDRFLAGAMPDLSRAQVQRLIEQGFVLYDGRSPRASQPVRPGAVIQLTI 76

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
           PP I     ++ E   LD               ++YED+ I V NKPAG+ V    G   
Sbjct: 77  PPPIP--TELVAEPIPLD---------------VVYEDADIAVINKPAGMVVHPAPGHPR 119

Query: 126 AYHIDGFLKSWVDSK--GQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++  L  + D    G+ +P + HRLD++TSG+LV+AR   A + L +  + RR++KI
Sbjct: 120 GTLVNALLARYPDLAIGGELRPGIVHRLDRDTSGLLVIARHDQAMRSLVDQQQARRMRKI 179

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFC 241
           Y +LV G P       A        IG D    ++         A +H++++D F   + 
Sbjct: 180 YQALVIGRPPETGTIDAP-------IGRDPRDRLRMAVVPDGRPARTHYRLLDTFG-DYS 231

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE+Q  TGRTHQ+RVH  H+G PIVGD  Y         S    + +LHA Y+ L HP 
Sbjct: 232 LLEVQLETGRTHQIRVHLRHLGYPIVGDPVYGPRRSHLHLS----RQFLHAAYLGLVHPR 287

Query: 302 GGRLQ-ITAPLPAHM 315
            GR Q  TAPLPA +
Sbjct: 288 SGRWQEFTAPLPADL 302


>gi|307131541|ref|YP_003883557.1| Ribosomal large subunit pseudouridine synthase C [Dickeya dadantii
           3937]
 gi|306529070|gb|ADM99000.1| Ribosomal large subunit pseudouridine synthase C [Dickeya dadantii
           3937]
          Length = 318

 Score =  142 bits (357), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 103/314 (32%), Positives = 167/314 (53%), Gaps = 20/314 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ V ++E   R+D + +     +    + +ILR G+VRV+KKR+K   ++  G  VR
Sbjct: 8   VQFLTVSSEEAGQRIDNFLRTRLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLLDGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +      E++    S +L K S  +  IL  +   + + NKP+G +V GGSG++
Sbjct: 68  IPPVRQS------EREEPAVSASLDKVSALVDCILYED-DYLLLLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRGKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV---IDCFAQKFCWL 243
           V G  ++  + +   LLK     G+   +V+ N +G   + + FKV    DC       +
Sbjct: 180 VRGQWQSHCKAVQAPLLKNVLQSGE--RIVRVNSEG-KPSETLFKVEERFDCAT----LV 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
              P TGRTHQ+RVH  + G PI  D +Y    F          +L+LHA  +   HP  
Sbjct: 233 RASPITGRTHQIRVHTQYAGHPIAFDDRYGDREFDAQLAGTGLKRLFLHALALRFEHPHT 292

Query: 303 GR-LQITAPLPAHM 315
           G  ++I APL A +
Sbjct: 293 GETMRIEAPLDAGL 306


>gi|294341011|emb|CAZ89406.1| Ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Thiomonas sp. 3As]
          Length = 329

 Score =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 97/320 (30%), Positives = 159/320 (49%), Gaps = 30/320 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V +  E  RLD +   H   +   ++ +I+RSG+VRV+  R   + ++QS   VR
Sbjct: 9   VRLLQVGDAGEGQRLDNFLARHLKGVPRSHIHRIVRSGEVRVNGGRASADQKLQSSDQVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A               +  + +  L+  +++ED  +   NKP G++V GGSG++
Sbjct: 69  IPPVRVA-------------QPDAPRAAPALQFPVVFEDDFLLAINKPEGVAVHGGSGVS 115

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++      +   L HRLD++TSG+L++A+ R+A   L  + R R   K Y +L
Sbjct: 116 FGVIEALRA-ARPTAKFLELVHRLDRDTSGLLLIAKKRSALTTLHAALRERHADKRYLAL 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-------QK 239
           V G+       I   L K     G+    V+ + +    + + F+  + FA         
Sbjct: 175 VAGLWTRGAVMIEAPLHKYLLANGE--RRVRVDVQQGQESRTQFRSQEQFALPGLGPWGG 232

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQNKLYLHAR 293
              ++ +  TGRTHQ+RVH  H G PIVGD KY  +       +G    P   +++LHA 
Sbjct: 233 LSLMQARLLTGRTHQIRVHLAHCGHPIVGDDKYGDDSLNALLARGQAGVPPFRRMFLHAE 292

Query: 294 YMDLPHPEGG-RLQITAPLP 312
            + + HP  G RL++ APLP
Sbjct: 293 SLAIAHPASGERLELRAPLP 312


>gi|238026595|ref|YP_002910826.1| Pseudouridine synthase, RluA family protein [Burkholderia glumae
           BGR1]
 gi|237875789|gb|ACR28122.1| Pseudouridine synthase, RluA family protein [Burkholderia glumae
           BGR1]
          Length = 316

 Score =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 103/323 (31%), Positives = 163/323 (50%), Gaps = 26/323 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V  D    R+D +       +   ++ +ILRSG+VRV+K R+    R+  G VVRIPP
Sbjct: 2   VEVGEDAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGDVVRIPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  A     +E   + +          ++  +L+ED  +   NKPAG++V GGSG+++ +
Sbjct: 62  IRVAAADPAREAAPVPA----------VEFEILFEDEALIAINKPAGVAVHGGSGVSFGV 111

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-- 187
              +++      +   L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y++    
Sbjct: 112 IEQMRA-ARPNAKFLELVHRLDRETSGILMLAKKRSALVALHEQIRENRMDKRYYACAHG 170

Query: 188 -WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            W     ++  +   L K S   G+   V  Q++   ++ +  F +I+ +   +  +E +
Sbjct: 171 DWAADWGRRRAVKVPLFKYSTAEGER-RVRVQDDGLPSHTV--FNLIERWPD-YALVEAE 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH  H+G PI GD KY  +F  N         P   +++LHA  + L HP
Sbjct: 227 LKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANARPSLKRMFLHAYRLKLAHP 285

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  LQ  APLP    +  D L
Sbjct: 286 LSGEPLQFDAPLPDECRRFLDQL 308


>gi|90021267|ref|YP_527094.1| ribosomal large subunit pseudouridine synthase C [Saccharophagus
           degradans 2-40]
 gi|89950867|gb|ABD80882.1| ribosomal large subunit pseudouridine synthase C [Saccharophagus
           degradans 2-40]
          Length = 321

 Score =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 105/317 (33%), Positives = 164/317 (51%), Gaps = 26/317 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ V  DE   RLD +       +    + +++R G+VRV+K R K   ++  G VVR
Sbjct: 5   VQFLTVSEDEAGQRLDNYLLARLKGVPKSLIYRVIRKGEVRVNKGRAKPERKLAGGDVVR 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL----LYEDSKIYVFNKPAGISVQGG 122
           +PPV  A             S      S  LK +L    + ++    V NKPAG++V GG
Sbjct: 65  VPPVRVA------------ESPEPVPISKTLKGVLDNAVIADEPGYLVVNKPAGLAVHGG 112

Query: 123 SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRI 179
           SG+     G +++   +  Q     L HRLD++TSG ++VA+ R+  ++L E FR  +RI
Sbjct: 113 SGVTL---GLIEALRQAFPQYSYLELVHRLDRDTSGCILVAKKRSMLRYLQELFRGEKRI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G   +++  +   LL+K    G+ +  V  + K +    + F V+  F + 
Sbjct: 170 HKRYLALVIGRWPSRRNLVDAPLLRKELQSGERIVRVSLDGKPSK---TEFNVVQRFGES 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +E +P TGRTHQ+RVHA H G P+VGD KY    F  +      N+L+LHA  +   
Sbjct: 227 ATLVEARPITGRTHQIRVHAQHQGHPLVGDPKYGNEVFDLSVKKLGVNRLFLHAAGLSFK 286

Query: 299 HPEGGRLQITAPLPAHM 315
           + +G ++ I  PLPA +
Sbjct: 287 NADGEQVNIEVPLPAEL 303


>gi|290979858|ref|XP_002672650.1| predicted protein [Naegleria gruberi]
 gi|284086228|gb|EFC39906.1| predicted protein [Naegleria gruberi]
          Length = 624

 Score =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 102/343 (29%), Positives = 163/343 (47%), Gaps = 54/343 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIP 68
           + V  + ++MRLD++       INF  +QKI R  Q+  +   VK NN R+  G +++IP
Sbjct: 279 LTVSQEHDDMRLDKFLTKTLA-INFGLIQKITRKKQLFKNGIAVKENNERVFKGDIIKIP 337

Query: 69  P--------------VINALNHIIKEQKILDS---------------------------S 87
                          +        K Q+  D                             
Sbjct: 338 KDFIDSEKRQEIDEHITGKREQFNKAQRETDKIDRDDEMDTISSETLGNPIYSKNGGKMK 397

Query: 88  VNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW--VDSKGQKP 144
           + LT+   + ++S +L+++ +I   NKP GI VQGGS   +HID  L +   +D    +P
Sbjct: 398 LELTQEQIEEIRSWILFKNDEIIALNKPYGICVQGGSNQTFHIDALLDALTGLDGFNVRP 457

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI--QKIYWSLVWGIPKNKKECIANWL 202
           +L HRLD++T+G+L+VAR RA A  + +  +   +  +K YW++  G+P      I   +
Sbjct: 458 KLVHRLDRDTTGVLIVARNRAGAIRMQQWLQESTVPLKKCYWAVTVGVPTPTTGRIKMVI 517

Query: 203 -LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
            ++K   G + V  V      +  ++S +K ID    K  W+ + P TGR HQLRVH A 
Sbjct: 518 DIQKDANGVEKVVPVDNKTDSSKISVSEYKTIDHMTDKLAWVALYPVTGRKHQLRVHCAS 577

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNK----LYLHARYMDLPH 299
            +G PI+GD+KY      + T  + +K    L+LH R M LP+
Sbjct: 578 ALGAPILGDYKYGEGVPESLTHVVPDKSLKRLHLHHRAMKLPY 620


>gi|312795518|ref|YP_004028440.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           rhizoxinica HKI 454]
 gi|312167293|emb|CBW74296.1| Ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70)
           [Burkholderia rhizoxinica HKI 454]
          Length = 336

 Score =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 100/321 (31%), Positives = 160/321 (49%), Gaps = 34/321 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V++     R+D +       +   ++ +ILRSG+VRV+K RV  + R++ G +VR
Sbjct: 17  VSWLNVDDASAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDASYRLEHGDIVR 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP        I+  +   S V+    +      +LYED  +   +KPAGI+V GGSG++
Sbjct: 77  VPP--------IRVAQPAHSPVSAPAAT----FPVLYEDDCLIALDKPAGIAVHGGSGVS 124

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--- 183
           + +   +++      +   L HRLD+ETSG+L++A+ RAA   L E  R  R+ K Y   
Sbjct: 125 FGVIEQMRA-ARPGARMLELVHRLDRETSGVLLLAKKRAALVGLHEQIREGRLDKRYLAC 183

Query: 184 ----WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
               W   WG+ +  K  +  +L       G+    V+ +  G++   +  + +      
Sbjct: 184 ARGAWPADWGVRRAVKAPLHKYLTAD----GERRVRVQPDGLGSHTVFNLRQRLG----D 235

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARY 294
           +  LE +  TGRTHQ+RVH  H+G PIVGD KY       N       P   +++LHA  
Sbjct: 236 YLLLEAELKTGRTHQIRVHLAHLGLPIVGDDKYGDFSLNKNLARPGVRPGLRRMFLHAWR 295

Query: 295 MDLPHP-EGGRLQITAPLPAH 314
           + + HP  G  L   APLPA 
Sbjct: 296 LSIQHPASGAPLSFEAPLPAE 316


>gi|152981207|ref|YP_001353037.1| ribosomal large subunit pseudouridine synthase C [Janthinobacterium
           sp. Marseille]
 gi|151281284|gb|ABR89694.1| ribosomal large subunit pseudouridine synthase C [Janthinobacterium
           sp. Marseille]
          Length = 339

 Score =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 104/325 (32%), Positives = 168/325 (51%), Gaps = 30/325 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V + +++   R+D +       +   ++ ++LRSG+VRV+K R+    R+  G +VR
Sbjct: 31  VQLVTINDEDAGQRIDNFLLRICKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLVEGDIVR 90

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+           +I + + +    ++F    +L ED+ + V +KPAG++V GGSG++
Sbjct: 91  IPPI-----------RIAEKAPSTAPGAEFK---ILLEDNHLLVIDKPAGVAVHGGSGVS 136

Query: 127 YH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           Y  I+    +  D+K  +  L HRLD++TSG+LV+A+ R+A  +L E  R     K Y  
Sbjct: 137 YGVIEQLRAARPDAKFLE--LVHRLDRDTSGVLVLAKKRSALTNLHEQIRGGEPDKRYLV 194

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  KN ++ I   L K +   G+   V  Q +   ++ +  F +I  +   F  LE 
Sbjct: 195 LVHGDWKNARQHIKLPLHKYTTPEGER-RVRVQADGMESHTV--FNLIQRYG-PFSLLEA 250

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANF-------KGNFTSPIQNKLYLHARYMDLP 298
           +  TGRTHQ+RVH    G  I GD KY  +F       K +       +++LHA  +   
Sbjct: 251 ELKTGRTHQIRVHLASSGFAIAGDDKY-GDFALNRDLQKADGERVALKRMFLHAHQITFI 309

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HPE G+ + + APLP    +   SL
Sbjct: 310 HPESGKPVTLNAPLPPECERFLKSL 334


>gi|301155711|emb|CBW15179.1| 23S rRNA pseudouridylate synthase [Haemophilus parainfluenzae T3T1]
          Length = 326

 Score =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 107/311 (34%), Positives = 173/311 (55%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  DE   R+D +       +    + +ILR G+VRV+K R+K   ++Q+G VVR
Sbjct: 13  VKMLTISEDEAGQRIDNYLLAKLKGVPKSLIYRILRKGEVRVNKGRIKPEYKLQNGDVVR 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +      E+     S NL K +  L+S +L+ED  + V NKP+GI+V GGSG+ 
Sbjct: 73  VPPVRVS------EKNTAPISKNLNKVAS-LESHILFEDDCLLVLNKPSGIAVHGGSGLN 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A ++L E  R++ +QK Y +L
Sbjct: 126 FGVIEALRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRNLHEQLRVKTVQKDYLAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +VK +E+G   + + F + + + Q    ++  
Sbjct: 185 VRGQWQSHVKVVQAPLLKNELASGE--RIVKVSEQG-KPSETRFSIEERY-QNATLVKAS 240

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP+ G  
Sbjct: 241 PVTGRTHQIRVHTQYAGHPIALDDKYGDKEFDKYMQDLGLNRLFLHAFSIRFEHPKTGET 300

Query: 305 LQITAPLPAHM 315
           L++ A L   M
Sbjct: 301 LRLNAQLDEKM 311


>gi|77166295|ref|YP_344820.1| pseudouridine synthase, RluD [Nitrosococcus oceani ATCC 19707]
 gi|254435147|ref|ZP_05048654.1| pseudouridine synthase, RluA family [Nitrosococcus oceani AFC27]
 gi|76884609|gb|ABA59290.1| ribosomal large subunit pseudouridine synthase C [Nitrosococcus
           oceani ATCC 19707]
 gi|207088258|gb|EDZ65530.1| pseudouridine synthase, RluA family [Nitrosococcus oceani AFC27]
          Length = 324

 Score =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 105/311 (33%), Positives = 166/311 (53%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  ++   R+D +  +    +    + + LR G+VRV+K R+  + R+Q G  VR
Sbjct: 12  VRILKIHLEQAGQRIDNFLFSQLKGVPKSRIYRCLRKGEVRVNKSRIASSYRLQQGDQVR 71

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+   ++H   ++ I  S + L K+S        YED ++ + NKPA I V GGSG++
Sbjct: 72  VPPL--RVSHSPLKRPIAHSLLLLIKNSLL------YEDKELLMLNKPARIPVHGGSGVS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y I   L+  +  +     L HRLD+ETSG L+VA+TR+A   L    + + I K Y +L
Sbjct: 124 YGIIEALR-ILRPEAAFLELVHRLDRETSGCLMVAKTRSALLTLQAMQQKQLIHKRYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + +   LLK  +I      +VK N  G   AISHF     +  +   +E+ 
Sbjct: 183 VKGRWRKNVQRVDLPLLK--NILRSEERIVKVNSAG-KPAISHFYPKLFYGGEATLMEVT 239

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
             TGRTHQ+RVHA H+G P+ GD KY  ++F         ++L+LHA  +    PEG + 
Sbjct: 240 LETGRTHQIRVHAAHLGHPLGGDEKYGDSSFNKQLRCMGLHRLFLHASQLTFTLPEGKKT 299

Query: 305 LQITAPLPAHM 315
           ++  APLP  +
Sbjct: 300 IKAAAPLPKEL 310


>gi|85713201|ref|ZP_01044230.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
 gi|85692974|gb|EAQ30943.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
          Length = 315

 Score =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 95/295 (32%), Positives = 156/295 (52%), Gaps = 14/295 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  V  DE   R+D +       +    + +ILR G+VRV+KKR K + +I++G  +R
Sbjct: 8   VQWHDVARDEAGQRIDNFLIARLRGVPKSLVYRILRKGEVRVNKKRTKPDYKIKAGDAIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +    +   K       L K ++ L+  ++YED    + NKP+G++V GGSG+ 
Sbjct: 68  IPPVKVSPKPELPSPK-------LAKVAE-LEQAIVYEDDAFMIVNKPSGLAVHGGSGLN 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  +     L HRLD++TSG++++A+ R+  + L    R + + K Y +L
Sbjct: 120 FGLIEGLRA-LRPQDNALELVHRLDRDTSGLIMIAKKRSVLKVLHAQLRDKEMNKQYLAL 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +     +   L K +   G+ +  V    K ++   + F++   +A+    +E  
Sbjct: 179 VRGQWQKNVRNVEAPLKKNTLKSGERIVRVDAEGKPSH---TRFRINQRYAEA-TLVEAS 234

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP 300
           P TGRTHQ+RVHALH G PI GD KY  A+F          +L+LHA  +   HP
Sbjct: 235 PVTGRTHQIRVHALHAGHPIAGDPKYGDASFNERMQQGGLTRLFLHAWQLSFKHP 289


>gi|319943487|ref|ZP_08017769.1| ribosomal large subunit pseudouridine synthase C [Lautropia
           mirabilis ATCC 51599]
 gi|319743302|gb|EFV95707.1| ribosomal large subunit pseudouridine synthase C [Lautropia
           mirabilis ATCC 51599]
          Length = 343

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 102/343 (29%), Positives = 164/343 (47%), Gaps = 30/343 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+  T +Q++ V+   E  RLD +       +    + +++R G+VRVD +RVK   R+ 
Sbjct: 10  MAQTTPIQWLTVDEGHEGQRLDNYLLAMLRGVPKTRIYRMIRKGEVRVDGRRVKAEQRVA 69

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ VR+PP+ +     + +  +           D     +L+ED  + V +K  G++V 
Sbjct: 70  AGERVRVPPLAS-----VPQTALRPGPARGGPKLDDRHIRILFEDEHLLVVDKSEGLAVH 124

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSGI+  +   L++     GQ   L HRLD++TSG+LV+A+ R+A   L   F    ++
Sbjct: 125 GGSGISAGLIERLRA-TRPPGQFLELAHRLDRDTSGLLVIAKRRSALLALHRMFAAGEVK 183

Query: 181 KIYWSLV---WGIPKNKKECIANWLLKK--SHIGGDYVHVVKQNEKGAN----YAISHFK 231
           K Y ++V   WG P   +  +  + L +  +  G   V V  Q +  A          F 
Sbjct: 184 KRYLAIVKGHWGRP---RPVLVQFPLLRYLTPAGERRVRVDVQGQPSATRFRRLQALDFG 240

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT------SPIQ 285
                      LE +  TGRTHQ+RVH  H G PI+GD KY     G+FT          
Sbjct: 241 GTPGLPPHGALLECELLTGRTHQIRVHLAHGGHPILGDEKY-----GDFTLNKVLDDMGA 295

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           N+++LHA ++++ HP+    L + AP+PA         G   D
Sbjct: 296 NRMFLHAFHLEMKHPKKEEMLVLDAPMPAAFEALLARFGVTAD 338


>gi|187477608|ref|YP_785632.1| ribosomal large subunit pseudouridine synthase C [Bordetella avium
           197N]
 gi|115422194|emb|CAJ48718.1| ribosomal large subunit pseudouridine synthase C [Bordetella avium
           197N]
          Length = 319

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 105/313 (33%), Positives = 161/313 (51%), Gaps = 28/313 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V V+  +E  RLD +       +   ++ K +R G+VRV+K R+  + R+  G VVR
Sbjct: 17  VRMVEVDAGQEGQRLDNFLLRLCKGVPKSHIYKAIRGGEVRVNKGRISADYRLVVGDVVR 76

Query: 67  IPPVINALNHIIKEQKILDSS-VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PP+           ++ D         S+F    ++YED  + V NKPAG++V GGSG+
Sbjct: 77  VPPL-----------RLPDPGQPKPVPASEF---PVVYEDDAMLVINKPAGVAVHGGSGV 122

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L++    + +   L HRLD+ETSG+L++A+ R+A   L    R  R  K Y +
Sbjct: 123 SFGVIEQLRA-ARPEARFLELVHRLDRETSGLLMIAKKRSALLALHAMLREGRGSKRYLA 181

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CW 242
           LV G   N ++ I   L K +   G+    V  + + A+  IS         Q+F     
Sbjct: 182 LVEGDWVNDRQHIRLALSKWTTQSGERRVKVDPDGQTAHTVIS-------LKQRFGDYSL 234

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPE 301
           +E +  TGRTHQ+RVH    G PIVGD KY  +  +  F     N+++LHA  + L HP 
Sbjct: 235 VEAELRTGRTHQIRVHLAASGFPIVGDDKYGTDETRALFARQGFNRMFLHAYQLTLDHPL 294

Query: 302 GGR-LQITAPLPA 313
            G  L +TA LPA
Sbjct: 295 TGEPLSLTAELPA 307


>gi|261856344|ref|YP_003263627.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261836813|gb|ACX96580.1| pseudouridine synthase, RluA family [Halothiobacillus neapolitanus
           c2]
          Length = 346

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 105/301 (34%), Positives = 157/301 (52%), Gaps = 24/301 (7%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           +ILR+G+VRV+ +R K   R+ +G  VRIPP+   L    +E   + S+  L + +D   
Sbjct: 55  RILRTGEVRVNSQRAKPTTRLATGDEVRIPPL--KLQSPSQESAGVISANWLARAAD--- 109

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            +++YED  +   NKPAG++V GGS I + +   ++      G+K  L HR+D++TSG+L
Sbjct: 110 -MIVYEDEALLAVNKPAGLAVHGGSNIPFGLIELMRQHT-GLGEKLELAHRIDRDTSGLL 167

Query: 159 VVARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++A+TRA    L   FR     +K Y ++V G   +K + +   L K    G    H V+
Sbjct: 168 ILAKTRATLHSLQTQFRPEGHAEKQYLAIVHGHWPDKLKRVDAPLEKWQ--GEGESHRVQ 225

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-- 275
            N +G   A++HF V+    +    L  Q  TGRTHQ+RVH  H   PIVGD KY     
Sbjct: 226 VNPQGKE-AVTHFAVL-AANKNATLLRAQLETGRTHQIRVHTAHENHPIVGDEKYGQREW 283

Query: 276 ----FKGNFTSPIQN-KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
               F     S  +   L LHA  + L HP+  + LQ+TAP+P      W SL  + +  
Sbjct: 284 DKRLFPSTGASARRRPPLLLHAYRLMLTHPQTEQPLQLTAPIP----DKWRSLAQQLNLT 339

Query: 330 L 330
           L
Sbjct: 340 L 340


>gi|121998031|ref|YP_001002818.1| RluA family pseudouridine synthase [Halorhodospira halophila SL1]
 gi|121589436|gb|ABM62016.1| ribosomal large subunit pseudouridine synthase C [Halorhodospira
           halophila SL1]
          Length = 325

 Score =  140 bits (352), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 104/330 (31%), Positives = 166/330 (50%), Gaps = 25/330 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++  V  DE   R+D +       +    + ++LR GQVRVD  R K   R+ +G+VVR
Sbjct: 8   VRHHQVLADEAGQRIDNFLLRQLKGVPRSRVYRLLRKGQVRVDGGRAKPTRRLSAGEVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDF-LKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           IPPV        + Q    +S  L    +  L+  +LYED ++ V +KP+G++V GGS +
Sbjct: 68  IPPVSG------QRQTSQPASGGLPDGLEARLRRGVLYEDERLLVLDKPSGLAVHGGSTV 121

Query: 126 AYHIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                G +++    +G +P      L HRLDQETSG L++A+ R+  + L E  R  +++
Sbjct: 122 RL---GLVEAL---RGLRPDLPFIELVHRLDQETSGCLMLAKRRSTLRRLHEQLRQGKVE 175

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L+ G  +       +  L++   G      V+ +++G   A++ F     + Q  
Sbjct: 176 KHYTTLLVGPLRGVTPLRVDAPLERL-PGAPRERQVRVSKQG-RAAVTEFLRKQSWPQA- 232

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLP 298
             +  +  TGRTHQ+RVHA H+G P+ GD +Y  +   N T       +L+LHA  + L 
Sbjct: 233 TLVTARLETGRTHQIRVHARHIGHPVAGDERY-GDRGANATMRDYGLRRLFLHASSLRLQ 291

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           HP+ G  L I APL   +    + L    D
Sbjct: 292 HPDTGEPLCIEAPLSDELKAVLERLSHSQD 321


>gi|145588577|ref|YP_001155174.1| RluA family pseudouridine synthase [Polynucleobacter necessarius
           subsp. asymbioticus QLW-P1DMWA-1]
 gi|145046983|gb|ABP33610.1| ribosomal large subunit pseudouridine synthase C [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 339

 Score =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 106/318 (33%), Positives = 162/318 (50%), Gaps = 23/318 (7%)

Query: 15  DEENMRLD----RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E   RLD    RW K     +   ++ +I+RSG+VRV+KKR +   R+  G VVR+PPV
Sbjct: 27  EEAGQRLDNYLLRWAKG----VPKSHVYRIIRSGEVRVNKKRAEPTTRLVEGDVVRVPPV 82

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
             A    +       +      +SD  K  +L+ED  + + NKPAG++V GGSGIA    
Sbjct: 83  RIAEPAQMAAVNTAQTKSRAQGYSD--KMPILFEDEALLIVNKPAGLAVHGGSGIAL--- 137

Query: 131 GFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           G +++   ++ +     L HRLD++TSG+L++A+ R+A   L    R  +  K Y+ L  
Sbjct: 138 GVIETLRITRPELKFLELVHRLDRDTSGVLLLAKKRSALVELHRQIREGQTDKRYYLLAH 197

Query: 189 G-IPKNKKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           G I +  +     + L K  +  G+    V  +   ++ A+   +V           E Q
Sbjct: 198 GEIEQGAQVMQLKYPLHKYLLANGERRVRVDPDGLPSHTALRVTQVFKREGAAITLAEAQ 257

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
             TGRTHQ+RVH L +G  I+GD KY   F+         +LYLHA      HP  G ++
Sbjct: 258 LKTGRTHQIRVHLLKLGHAILGDDKY--GFEDQDKLLKSKRLYLHAHLAGFTHPRTGEKM 315

Query: 306 QITAPLP---AHMVKTWD 320
           +I +PLP   A M+KT+D
Sbjct: 316 RIESPLPSEFAAMMKTFD 333


>gi|328952411|ref|YP_004369745.1| pseudouridine synthase, RluA family [Desulfobacca acetoxidans DSM
           11109]
 gi|328452735|gb|AEB08564.1| pseudouridine synthase, RluA family [Desulfobacca acetoxidans DSM
           11109]
          Length = 331

 Score =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 102/329 (31%), Positives = 158/329 (48%), Gaps = 40/329 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE +EE +RLD +     P  +   LQ+ +++G V+V+++  + +  ++ G  V + P  
Sbjct: 20  VEAEEEGLRLDHFLVRKMPSFSRARLQRWIKAGLVQVNQEERQPHYHMRKGDRVAVSPPE 79

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--I 129
               H+  E   L                +LYED  +   NKP G++V  G+G +    +
Sbjct: 80  VQRWHLAPEPIPLK---------------ILYEDEDLLALNKPPGLTVHPGAGQSSGTLV 124

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G    Q+P L HRLD++TSG++VVA+T  A Q L + F+ RR+ K Y +
Sbjct: 125 NALLHHCPDLGGIGDVQRPGLVHRLDKDTSGVMVVAKTDRAHQALIKQFKNRRVDKRYLA 184

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYV--HVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           LVWG   +N+ E        +  IG      H +    +    A + ++ +  +   F W
Sbjct: 185 LVWGRFSENQGEI-------EEEIGRHPTQRHKMAVTSRRGRPAATSWRRLQEYPGPFSW 237

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTS--PIQNKLYLHARY 294
           LE++ HTGRTHQ+RVH   +G P+VGD  Y A            T   P+  +  LHA  
Sbjct: 238 LELKLHTGRTHQIRVHLSSLGHPVVGDKIYGAGDRRLLVLPPELTELRPLVRRQALHAWK 297

Query: 295 MDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           + L HP     L + APLP  + K  D L
Sbjct: 298 LHLKHPCRDLELDLEAPLPEDLQKILDFL 326


>gi|282600817|ref|ZP_06257758.1| ribosomal large subunit pseudouridine synthase [Subdoligranulum
           variabile DSM 15176]
 gi|282571024|gb|EFB76559.1| ribosomal large subunit pseudouridine synthase [Subdoligranulum
           variabile DSM 15176]
          Length = 302

 Score =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 80/262 (30%), Positives = 135/262 (51%), Gaps = 30/262 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++    YP +    L K LR  +++++ K+   + R+Q+G V+R+          +
Sbjct: 12  VRLDKYLMEQYPSLGLGRLNKALRENKIKLNGKKQPLSTRVQNGDVIRL---------FL 62

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS--- 135
           K++++ D  +          ++ +YED  I V NKPAGI V G +      D  LK    
Sbjct: 63  KDEQLEDRPLP--------SAVFVYEDEDILVVNKPAGIEVDGPAA-----DTLLKRVQT 109

Query: 136 --WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 K     L HRLD  TSG++++A+ +A    LT++ + R I+K Y  + +G P+ 
Sbjct: 110 TLAAAGKAGHAVLCHRLDTGTSGLVLLAKNQATELFLTQAIKARTIEKRYLCVTFGRPQP 169

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               + ++LLK +  G   V ++     GA   I+ ++ +   + +   LE++  TGRTH
Sbjct: 170 PAALMHDYLLKDAERG--VVKIITSPASGAKEVITGYETL-AVSGRLALLEVELVTGRTH 226

Query: 254 QLRVHALHMGCPIVGDHKYCAN 275
           Q+R H  H+GCPI+GD KY  N
Sbjct: 227 QIRAHLAHIGCPILGDSKYGNN 248


>gi|21242847|ref|NP_642429.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21108337|gb|AAM36965.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 328

 Score =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 105/334 (31%), Positives = 163/334 (48%), Gaps = 39/334 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDF---LKSILLYEDSKIYVFNKPAGISVQGGS 123
           IPPV           +I D        S F   L++ +++ED+++   NKP+G++  GGS
Sbjct: 76  IPPV-----------RINDEDDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGS 124

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------R 177
           GI++     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R
Sbjct: 125 GISFGAIETLRAL--RPNQSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGR 182

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVI 233
            I K Y +L+ G +P       A       HIG   G   HV  Q       ++SHFK++
Sbjct: 183 GITKRYLTLLVGRMPDGVMTVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFKLL 235

Query: 234 DC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYL 290
           +      +C + ++  TGRTHQ+RVHA H+G P+ GD KY  A+        +   +L+L
Sbjct: 236 ERRGGHSYCEVRIE--TGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFL 293

Query: 291 HARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSLG 323
           HA  ++     G    + +APL   + +  D LG
Sbjct: 294 HAASLEFALDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|295688944|ref|YP_003592637.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
 gi|295430847|gb|ADG10019.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
          Length = 271

 Score =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 136/269 (50%), Gaps = 13/269 (4%)

Query: 78  IKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           + + K ++  + LT       +S +LYED  I V +KPAG+S QGG   A+ +D  L ++
Sbjct: 12  VAKPKAVECPITLTPDEIATAQSWVLYEDEAIIVLDKPAGLSSQGGRIKAHTLDDLLWAF 71

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIPKNKK 195
                 +PRL HRLD++TSG+++ A+T+  A  L E+   +R +K Y ++V  G P+ K 
Sbjct: 72  AKPGKARPRLIHRLDRDTSGVILTAKTKPGAAFLGEAMMAKRFRKSYLAIVAPGAPEPKG 131

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I + L ++S     Y+ V   +   A  A S ++ +         +E+ P TGR HQL
Sbjct: 132 GMIDSPLRRESIGREAYMRVCAPDHPEAETARSRYRTL-AANATAALVELSPDTGRMHQL 190

Query: 256 RVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
           RVH   +G P+ GD +Y      G    P   +L LHA  +  PHP GG  ++ APLP+ 
Sbjct: 191 RVHMASIGRPLAGDSRYGGALMLGGVAVP---RLMLHAAKLTFPHPLGGERKVMAPLPSD 247

Query: 315 MVKTWDSLGFKYDRNLYIKRLYSQDECKQ 343
            V    +L      +L I    + D   Q
Sbjct: 248 FVAMLKAL------DLPIPEQPASDAVDQ 270


>gi|330720408|gb|EGG98730.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC2047]
          Length = 330

 Score =  139 bits (350), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 93/312 (29%), Positives = 163/312 (52%), Gaps = 17/312 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ +  D    R+D +       +    + +I+R G+VRV+K R+K + ++QSG VVR
Sbjct: 24  VQFLEITEDSAGQRIDNFLCARLKGVPRTRIYRIVRKGEVRVNKGRIKADYKLQSGDVVR 83

Query: 67  IPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PP+ +   N + +  K L  +         L+  +LYED  + + NKP+G++V GGSGI
Sbjct: 84  VPPIRVAEANELPQAGKGLKEA---------LEQAVLYEDDSLLIINKPSGLAVHGGSGI 134

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +   L+  +  + +   L HRLD++TSG ++VA+ R+  ++L +  R   + K Y +
Sbjct: 135 KLGLIETLRQ-LRPEARFLELVHRLDRDTSGCVMVAKKRSMLRYLHDLLRTNGVTKHYQA 193

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G    +K  +   L K +   G+ + V   + K    +++ ++V   F+  +  ++ 
Sbjct: 194 LVVGKWPTRKHKVDVPLQKNTLQSGERMVVADPDGKP---SLTRYEVRQRFS-GYTLVQA 249

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P +GRTHQ+RVH    G  I GD KY   +      +    +L+LHA  +    PE G+
Sbjct: 250 YPVSGRTHQIRVHCQFAGHSIAGDDKYTDEDTNKRLKAMGLRRLFLHAESLAFKLPETGK 309

Query: 305 -LQITAPLPAHM 315
            L++ APL   +
Sbjct: 310 LLRVEAPLDEQL 321


>gi|313667509|ref|YP_004047793.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           lactamica ST-640]
 gi|313004971|emb|CBN86399.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           lactamica 020-06]
          Length = 330

 Score =  139 bits (350), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 96/323 (29%), Positives = 161/323 (49%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIAVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRAAEKEMPSERRAAVPAREFD---------IVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V ++ + A+     F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVRLPLFKYTGAQGEKMVRVSEDGQAAHTV---FRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVK 317
            L HP  G  L + A LP  + +
Sbjct: 297 HLNHPLTGEPLVLKAELPPDLAQ 319


>gi|77358713|ref|YP_338279.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           RSA 493]
 gi|161830459|ref|YP_001596417.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           RSA 331]
 gi|212213029|ref|YP_002303965.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           CbuG_Q212]
 gi|71066703|gb|AAZ22625.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           RSA 493]
 gi|161762326|gb|ABX77968.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           RSA 331]
 gi|212011439|gb|ACJ18820.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           CbuG_Q212]
          Length = 308

 Score =  139 bits (350), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 107/319 (33%), Positives = 164/319 (51%), Gaps = 25/319 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V +++     RLD +       +    + + +R G+VRV+K+RV  + R+  G +VRIPP
Sbjct: 6   VTIDDAHAGQRLDNFLITRLKGVPSTRIYRAIRKGEVRVNKRRVGADYRLVVGDLVRIPP 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A     K+   +D  + ++     L+  +LYE++ + V +KPAG+ V GGSGI   +
Sbjct: 66  VQMAAP---KKPATVDEKLLIS-----LEMRILYEEADLLVIDKPAGLPVHGGSGIQGGV 117

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+  +  K +   L HRLD+ETSG L+VA+ R+    L      R++ K Y  LV G
Sbjct: 118 IEALR-IMRPKVRLLELVHRLDRETSGCLMVAKKRSTLVALHTLLTQRKVIKQYLLLVKG 176

Query: 190 IPKNKKECIANWLLKKSHI--GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
             +   EC     LKK+ +  G   V V    EK    A++ F+ +  F Q    +E +P
Sbjct: 177 QWQGG-ECRVEVPLKKNRLQSGERMVKV----EKEGKSAVTVFRPLKIFEQA-SLIEAKP 230

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPEGG 303
            TGRTHQ+RVHA H+G PI GD KY       F   ++N    +L+LH+  + L   E  
Sbjct: 231 LTGRTHQIRVHAAHLGYPIAGDEKYGDKV---FNREMRNYGLRRLFLHSAGI-LCQWEDK 286

Query: 304 RLQITAPLPAHMVKTWDSL 322
           RL + A L + ++K    L
Sbjct: 287 RLGVCAILDSELMKCLTQL 305


>gi|325579066|ref|ZP_08149022.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325159301|gb|EGC71435.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 326

 Score =  139 bits (350), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 106/311 (34%), Positives = 172/311 (55%), Gaps = 14/311 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  DE   R+D +       +    + +ILR G+VRV+K R+K   ++Q+G VVR
Sbjct: 13  VKMLTISEDEAGQRIDNYLLAKLKGVPKSLIYRILRKGEVRVNKGRIKPEYKLQNGDVVR 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +      E+     S NL K +  L+S +L+ED  + V NKP+GI+V GGSG+ 
Sbjct: 73  VPPVRVS------EKNTAPISKNLNKVAS-LESHILFEDDCLLVLNKPSGIAVHGGSGLN 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+  ++L E  R++ +QK Y +L
Sbjct: 126 FGVIEALRA-LRPEARFLELVHRLDRDTSGILLVAKKRSTLRNLHEQLRVKTVQKDYLAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+   +VK +E+G   + + F + + + Q    ++  
Sbjct: 185 VRGQWQSHVKVVQAPLLKNELASGE--RIVKVSEQG-KPSETRFAIEERY-QNATLVKAS 240

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP+ G  
Sbjct: 241 PVTGRTHQIRVHTQYAGHPIALDDKYGDKEFDKYMQDLGLNRLFLHAFSIRFEHPKTGET 300

Query: 305 LQITAPLPAHM 315
           L++ A L   M
Sbjct: 301 LRLNAQLDEKM 311


>gi|166712251|ref|ZP_02243458.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 328

 Score =  139 bits (350), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 105/331 (31%), Positives = 164/331 (49%), Gaps = 33/331 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+   D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPPVR------VNEEG--DKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRAL--RPNQNLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC- 235
           K Y SL+ G +P       A       HIG   G   HV  Q       ++SHFK+++  
Sbjct: 186 KRYLSLLIGRMPDGVMSVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFKLLERR 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHAR 293
               +C  E++  TGRTHQ+RVHA H+G P+ GD KY  A+        +   +L+LHA 
Sbjct: 239 GGHSYC--EVRIETGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAA 296

Query: 294 YMDLPHPEGGRLQI-TAPLPAHMVKTWDSLG 323
            ++     G    + +APL   + +  D LG
Sbjct: 297 SLEFALDAGQTPYVLSAPLAPELAEALDQLG 327


>gi|91227385|ref|ZP_01261774.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio alginolyticus
           12G01]
 gi|91188649|gb|EAS74939.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio alginolyticus
           12G01]
          Length = 268

 Score =  139 bits (350), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 89/279 (31%), Positives = 156/279 (55%), Gaps = 16/279 (5%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           +RV+KKR+K   ++++  +VRIPPV      + K+   +  S  L K ++ L++++++ED
Sbjct: 1   MRVNKKRIKAEYKLKARDLVRIPPVT-----VEKKDDDVAPSTKLNKVAE-LENMIIFED 54

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
             + + NKP+G +V GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+
Sbjct: 55  DHMLILNKPSGTAVHGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRS 113

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           A +HL   FR + ++K Y +LV G  K+  + +   LLK      +   +V+ N  G   
Sbjct: 114 ALRHLQAQFREKTVKKFYLALVMGQWKSSCKVVNAPLLK-----NEVNSIVRVNPNG-KP 167

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           + + FK+++ F Q    ++  P TGRTHQ+RVH  + G PI  D +Y       +T  + 
Sbjct: 168 SETRFKILEKFEQA-TLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVG 226

Query: 286 -NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            ++L+LHA  +   HP     ++I AP+   + K    L
Sbjct: 227 LDRLFLHAANIKFQHPSNDEWMEINAPMEPKLEKVLAGL 265


>gi|325927798|ref|ZP_08189023.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           perforans 91-118]
 gi|325541788|gb|EGD13305.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           perforans 91-118]
          Length = 328

 Score =  139 bits (350), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 104/331 (31%), Positives = 164/331 (49%), Gaps = 33/331 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       I E+   D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPPVR------INEEG--DKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRAL--RPNQSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC- 235
           K Y +L+ G +P       A       HIG   G   HV  Q       ++SHFK+++  
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFKLLERR 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHAR 293
               +C + ++  TGRTHQ+RVHA H+G P+ GD KY  A+        +   +L+LHA 
Sbjct: 239 GGHSYCEVRIE--TGRTHQIRVHAQHLGHPVAGDEKYGEADVNKRLRDQLGLKRLFLHAA 296

Query: 294 YMDLPHPEGGRLQI-TAPLPAHMVKTWDSLG 323
            ++     G    + +APL   + +  D LG
Sbjct: 297 SLEFALDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|326568395|gb|EGE18475.1| RluA family pseudouridine synthase [Moraxella catarrhalis BC7]
          Length = 382

 Score =  139 bits (349), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 94/307 (30%), Positives = 168/307 (54%), Gaps = 25/307 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V ++ V N+++  R+D +       +   +L K++RS ++R++ KR K ++++  G V
Sbjct: 58  SRVNFLTVTNNQDGQRVDNFLLARLKGLPRSHLYKLIRSDEIRINGKRCKAHDKLYMGDV 117

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+ P+  +    ++E  I+   +     +  L   +++ED+ + V NKP G++V GGSG
Sbjct: 118 VRVAPIRLS----VREAPIISEEL-----AKGLLERIIFEDNGLIVLNKPHGMAVHGGSG 168

Query: 125 IAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++   G +++   + G+K   L HR+D++TSG+L++A+ R+  + L E FR + IQK Y
Sbjct: 169 ESF---GIIEAMRLAMGKKYLELIHRIDKDTSGLLLIAKKRSTLKILQEQFRKKTIQKRY 225

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNE-KGANYA---ISHFKVIDCFAQ 238
             LV G  +  +  I   LL+ +   G+  V V   NE K   YA   ++  K +  F +
Sbjct: 226 LCLVMGHVQADEMVIDVPLLRYTLANGERRVKVAHLNEQKAGEYAKASLTKIKTLLRFKK 285

Query: 239 KFCWLEM---QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             C + +    P TGRTHQ+RVH  H+G  ++GD KY    + N  +P   +L LHA  +
Sbjct: 286 DGCPVSLVLAMPATGRTHQIRVHMAHIGHALLGDDKY----QNNPLAPKVGRLCLHAWQL 341

Query: 296 DLPHPEG 302
            + + +G
Sbjct: 342 GMTNDDG 348


>gi|154707769|ref|YP_001424927.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           Dugway 5J108-111]
 gi|161349250|ref|ZP_02096635.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           'MSU Goat Q177']
 gi|165920598|ref|ZP_02219569.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           RSA 334]
 gi|212218908|ref|YP_002305695.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           CbuK_Q154]
 gi|154357055|gb|ABS78517.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           Dugway 5J108-111]
 gi|164601538|gb|EDQ95142.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           'MSU Goat Q177']
 gi|165916800|gb|EDR35404.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           RSA 334]
 gi|212013170|gb|ACJ20550.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           CbuK_Q154]
          Length = 308

 Score =  139 bits (349), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 107/319 (33%), Positives = 164/319 (51%), Gaps = 25/319 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V +++     RLD +       +    + + +R G+VRV+K+RV  + R+  G +VRIPP
Sbjct: 6   VTIDDAHAGQRLDNFLITRLKGVPSTRIYRAIRKGEVRVNKRRVGADYRLVVGDLVRIPP 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A     K+   +D  + ++     L+  +LYE++ + V +KPAG+ V GGSGI   +
Sbjct: 66  VQMAAP---KKPATVDEKLLIS-----LEMRILYEEADLLVIDKPAGLPVHGGSGIQGGL 117

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+  +  K +   L HRLD+ETSG L+VA+ R+    L      R++ K Y  LV G
Sbjct: 118 IEALR-IMRPKVRLLELVHRLDRETSGCLMVAKKRSTLVALHTLLTQRKVIKQYLLLVKG 176

Query: 190 IPKNKKECIANWLLKKSHI--GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
             +   EC     LKK+ +  G   V V    EK    A++ F+ +  F Q    +E +P
Sbjct: 177 QWQGG-ECRVEVPLKKNRLQSGERMVKV----EKEGKSAVTVFRPLKIFEQA-SLIEAKP 230

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPEGG 303
            TGRTHQ+RVHA H+G PI GD KY       F   ++N    +L+LH+  + L   E  
Sbjct: 231 LTGRTHQIRVHAAHLGYPIAGDEKYGDKV---FNREMRNYGLRRLFLHSAGI-LCQWEDK 286

Query: 304 RLQITAPLPAHMVKTWDSL 322
           RL + A L + ++K    L
Sbjct: 287 RLGVCAILDSELMKCLTQL 305


>gi|310778176|ref|YP_003966509.1| pseudouridine synthase [Ilyobacter polytropus DSM 2926]
 gi|309747499|gb|ADO82161.1| pseudouridine synthase [Ilyobacter polytropus DSM 2926]
          Length = 289

 Score =  139 bits (349), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 98/290 (33%), Positives = 155/290 (53%), Gaps = 25/290 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           + RLD++ +  Y  IN   + K++R G+++V+ K+VK N R+Q G +V++      +   
Sbjct: 11  DTRLDKYIRKKYEGINLTEIFKLIRKGRIKVNGKKVKQNYRLQDGDIVKVF----YMGGE 66

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
              +K +D S    K ++++K  ++YED  + +FNK   + +  GSG  Y +   LKS+ 
Sbjct: 67  TAVKKFIDLS---PKETEYIKKGIVYEDEDVLLFNKSPNMVMHKGSGHDYGLSEMLKSYY 123

Query: 138 DSKGQKPRLT--HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               Q+   T  +R+D+ TSG+++ A+     + L+E  R   I K Y+ LV G    ++
Sbjct: 124 ----QREDFTFINRIDKATSGLIIGAKNLPMTRKLSEDMRDGNINKRYYILVEGRVDREE 179

Query: 196 ECIANWLLKKSHIGGDYVHVV--KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             I ++L K         HVV  ++ EKGA  +IS+FKV+    +    LE    TGRTH
Sbjct: 180 FQIKSYLKKTD------THVVELEKYEKGAKESISYFKVVQR-GKNRTILEGTLGTGRTH 232

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFT--SPIQNKLYLHARYMDLPHPE 301
           QLRVH  ++G PIVGD KY  N +G     S     L L  + +DLP PE
Sbjct: 233 QLRVHLANLGHPIVGDAKYGENTRGEMCLFSHYTEILSLGIK-VDLPLPE 281


>gi|300112960|ref|YP_003759535.1| RluA family pseudouridine synthase [Nitrosococcus watsonii C-113]
 gi|299538897|gb|ADJ27214.1| pseudouridine synthase, RluA family [Nitrosococcus watsonii C-113]
          Length = 324

 Score =  139 bits (349), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 104/321 (32%), Positives = 167/321 (52%), Gaps = 14/321 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  ++   R+D +  +H   +    + + LR G+VRV+K R+  + R+Q G  VR
Sbjct: 12  VRILEIHLEQVGQRIDNFLFSHLKGVPKSRIYRCLRRGEVRVNKSRITSSYRLQQGDQVR 71

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+   ++H   ++ I    + L K+S      LLYED ++ + +KPAGI V GGSG++
Sbjct: 72  IPPL--RVSHPPLKRPIAHFLLFLIKNS------LLYEDKELLILDKPAGIPVHGGSGVS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y I   L++ +  +     L HRLD+ETSG L++A+TR     L    + + I K Y +L
Sbjct: 124 YGIIEVLRA-LRPEATFLELVHRLDRETSGCLMIAKTRGTLLTLQAMQQKQLIHKRYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + +   LLK  +I      +VK +  G   A S F     +  +   +E+ 
Sbjct: 183 VKGRWRKNVQRVDLPLLK--NISRSKERIVKVSPAGKPAA-SRFYPKLFYRDEATLVEVA 239

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
             TGRTHQ+RVHA H+G P+ GD KY  + F          +L+LHA  +    PEG + 
Sbjct: 240 LETGRTHQIRVHATHLGHPLGGDEKYGDSTFNKRLRYLGLRRLFLHASQLIFTLPEGKKT 299

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           ++  APLP  +    ++   K
Sbjct: 300 IKTIAPLPEELNAVMEAYAIK 320


>gi|296113828|ref|YP_003627766.1| RluA family pseudouridine synthase [Moraxella catarrhalis RH4]
 gi|295921522|gb|ADG61873.1| RluA family pseudouridine synthase [Moraxella catarrhalis RH4]
 gi|326562171|gb|EGE12499.1| RluA family pseudouridine synthase [Moraxella catarrhalis 7169]
 gi|326564465|gb|EGE14691.1| RluA family pseudouridine synthase [Moraxella catarrhalis 46P47B1]
 gi|326565646|gb|EGE15809.1| RluA family pseudouridine synthase [Moraxella catarrhalis 12P80B1]
 gi|326572296|gb|EGE22291.1| RluA family pseudouridine synthase [Moraxella catarrhalis BC8]
 gi|326574310|gb|EGE24257.1| RluA family pseudouridine synthase [Moraxella catarrhalis O35E]
 gi|326574892|gb|EGE24822.1| RluA family pseudouridine synthase [Moraxella catarrhalis 101P30B1]
 gi|326576218|gb|EGE26133.1| RluA family pseudouridine synthase [Moraxella catarrhalis CO72]
          Length = 382

 Score =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 94/307 (30%), Positives = 167/307 (54%), Gaps = 25/307 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V ++ V N+++  R+D +       +   +L K++RS ++R++ KR K ++++  G V
Sbjct: 58  SRVNFLTVTNNQDGQRVDNFLLARLKGLPRSHLYKLIRSDEIRINGKRCKAHDKLYMGDV 117

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+ P+  +    ++E  I+   +     +  L   +++ED  + V NKP G++V GGSG
Sbjct: 118 VRVAPIRLS----VREAPIISEEL-----AKGLLERIIFEDDGLIVLNKPHGMAVHGGSG 168

Query: 125 IAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++   G +++   + G+K   L HR+D++TSG+L++A+ R+  + L E FR + IQK Y
Sbjct: 169 ESF---GIIEAMRLAMGKKYLELIHRIDKDTSGLLLIAKKRSTLKILQEQFRKKTIQKRY 225

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNE-KGANYA---ISHFKVIDCFAQ 238
             LV G  +  +  I   LL+ +   G+  V V   NE K   YA   ++  K +  F +
Sbjct: 226 LCLVMGHVQADEMVIDVPLLRYTLANGERRVKVAHLNEQKAGEYAKASLTKIKTLLRFKK 285

Query: 239 KFCWLEM---QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             C + +    P TGRTHQ+RVH  H+G  ++GD KY    + N  +P   +L LHA  +
Sbjct: 286 DGCPVSLVLAMPATGRTHQIRVHMAHIGHALLGDDKY----QNNPLAPKVGRLCLHAWQL 341

Query: 296 DLPHPEG 302
            + + +G
Sbjct: 342 GMTNDDG 348


>gi|254514408|ref|ZP_05126469.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium NOR5-3]
 gi|219676651|gb|EED33016.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium NOR5-3]
          Length = 309

 Score =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 91/297 (30%), Positives = 152/297 (51%), Gaps = 17/297 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V+++ V+   +  RLD +     P I    L + +R G++RV+K R K + R+  G 
Sbjct: 1   MSGVRFLTVDERSDGQRLDNYILRECPGIPKTRLYRAMRKGEIRVNKGRAKPDQRLMLGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+              +         + L + +++ED  +   NKP+GI+V GGS
Sbjct: 61  RVRLPPLSTPPPR--------EPGAAPPGWQERLATSVVFEDDHLLAINKPSGIAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKI 182
           G+ + +   L++ +    +   L HRLD+ETSG+++VA+  AA + L E  R + +I K 
Sbjct: 113 GLQFGLIETLRA-MRPHARFLELVHRLDRETSGLVLVAKKPAALRALHEQLRAQGKIDKR 171

Query: 183 YWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y +L  G  P++ +   A     +   G   V V K+ +     + + F++ + FA    
Sbjct: 172 YLALAEGAWPRHLRLVEAPLQRFERKSGERMVKVAKEGK----ASTTEFRIRESFAD-VT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDL 297
            LE +P TGRTHQ+RVHA H G  ++GD KY       +T  +Q  +L+LHA  +  
Sbjct: 227 LLEARPLTGRTHQIRVHAQHAGHALLGDGKYQTANGEAYTRKLQLKRLFLHAESLSF 283


>gi|326567130|gb|EGE17252.1| RluA family pseudouridine synthase [Moraxella catarrhalis BC1]
          Length = 382

 Score =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 94/307 (30%), Positives = 167/307 (54%), Gaps = 25/307 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V ++ V N+++  R+D +       +   +L K++RS ++R++ KR K ++++  G V
Sbjct: 58  SRVNFLTVTNNQDGQRVDNFLLARLKGLPRSHLYKLIRSDEIRINGKRCKAHDKLYMGDV 117

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+ P+  +    ++E  I+   +     +  L   +++ED  + V NKP G++V GGSG
Sbjct: 118 VRVAPIRLS----VREAPIISEEL-----AKGLLERIIFEDDGLIVLNKPHGMAVHGGSG 168

Query: 125 IAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++   G +++   + G+K   L HR+D++TSG+L++A+ R+  + L E FR + IQK Y
Sbjct: 169 ESF---GIIEAMRLAMGKKYLELIHRIDKDTSGLLLIAKKRSTLKILQEQFRKKTIQKRY 225

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNE-KGANYA---ISHFKVIDCFAQ 238
             LV G  +  +  I   LL+ +   G+  V V   NE K   YA   ++  K +  F +
Sbjct: 226 LCLVMGHVQADEMVIDVPLLRYTLANGERRVKVAHLNEQKAGEYAKASLTKIKTLLRFKK 285

Query: 239 KFCWLEM---QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             C + +    P TGRTHQ+RVH  H+G  ++GD KY    + N  +P   +L LHA  +
Sbjct: 286 DGCPVSLVLAMPATGRTHQIRVHMAHIGHALLGDDKY----QNNPLAPKVGRLCLHAWQL 341

Query: 296 DLPHPEG 302
            + + +G
Sbjct: 342 GMTNDDG 348


>gi|241667739|ref|ZP_04755317.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25015]
 gi|254876283|ref|ZP_05248993.1| ribosomal large subunit pseudouridine synthase C [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|254842304|gb|EET20718.1| ribosomal large subunit pseudouridine synthase C [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
          Length = 309

 Score =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 92/290 (31%), Positives = 154/290 (53%), Gaps = 13/290 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  VQ + V +D    R+D +  + +  +    + + +R G++RV+KKRVK   R+ +G 
Sbjct: 1   MNKVQLIEVTDDVIEQRIDNFLISKFSRLPKSLIYRWIRKGELRVNKKRVKQTTRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L   ++  K+  S      H DFL+  +LYE     V +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEENLEIAKVSKS------HLDFLEQRILYETDDYIVVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKERKVNKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++LV G    K + I   L +     G    +VK +++    A++    +      +  L
Sbjct: 172 YALVHGHWDEKVDAIDLPLSRTETKDGQ--RIVKVDKREGKRALTRILAVQKIGD-YSLL 228

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHA 292
           E++  TGRTHQ+RVH   MG PIV D KY          +   +KL LHA
Sbjct: 229 EIKLETGRTHQIRVHTRAMGHPIVADKKYGYMIDDEKLLAKGVDKLLLHA 278


>gi|78047980|ref|YP_364155.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
 gi|78036410|emb|CAJ24101.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
          Length = 328

 Score =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 103/331 (31%), Positives = 164/331 (49%), Gaps = 33/331 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       I E+   D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPPVR------INEEG--DKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRAL--RPNQSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC- 235
           K Y +L+ G +P       A       HIG   G   HV  Q       ++SHF++++  
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFRLLERR 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHAR 293
               +C + ++  TGRTHQ+RVHA H+G P+ GD KY  A+        +   +L+LHA 
Sbjct: 239 GGHSYCEVRIE--TGRTHQIRVHAQHLGHPVAGDEKYGEADVNKRLRDQLGLKRLFLHAA 296

Query: 294 YMDLPHPEGGRLQI-TAPLPAHMVKTWDSLG 323
            ++     G    + +APL   + +  D LG
Sbjct: 297 SLEFALDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|167627177|ref|YP_001677677.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017]
 gi|167597178|gb|ABZ87176.1| Lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017]
          Length = 309

 Score =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 93/291 (31%), Positives = 156/291 (53%), Gaps = 15/291 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  VQ + V +D    R+D +  + +  +    + + +R G++RV+KKRVK   R+ +G 
Sbjct: 1   MNKVQLIEVADDVIEQRIDNFLISKFSRLPKSLIYRWIRKGELRVNKKRVKQTTRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L   ++  K+  S      H DFL+  +LYE     V +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEENLEIAKVSKS------HLDFLEQRILYETDDYIVVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKERKVNKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++LV G    K + I   L +     G    +VK +++    A++    +      +  L
Sbjct: 172 YALVHGHWDEKVDAIDLPLSRTETKDGQ--RIVKVDKREGKRALTRILAVQKIGD-YSLL 228

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHK--YCANFKGNFTSPIQNKLYLHA 292
           E++  TGRTHQ+RVH   MG PIV D K  Y  + K      + +KL LHA
Sbjct: 229 EIKLETGRTHQIRVHTRAMGHPIVADKKYGYMVDDKKLLAKGV-DKLLLHA 278


>gi|289805597|ref|ZP_06536226.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 274

 Score =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 99/283 (34%), Positives = 155/283 (54%), Gaps = 18/283 (6%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           +VRV+KKR+K   +++SG  VRIPPV       + E++    S +L K +  L  ++LYE
Sbjct: 1   EVRVNKKRIKPEYKLESGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYE 53

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  I V NKP+G +V GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R
Sbjct: 54  DDHILVLNKPSGTAVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKR 112

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           +A + L E  R + +QK Y +LV G  ++  + +   LLK     G+ +  V Q  K + 
Sbjct: 113 SALRSLHEQLREKGMQKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE 172

Query: 225 YAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTS 282
              + FKV + +A  F  L    P TGRTHQ+RVH  + G PI  D +Y    F    T 
Sbjct: 173 ---TRFKVEERYA--FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTE 227

Query: 283 PIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                 +L+LHA  +   HP  G  ++I AP+   + +  + L
Sbjct: 228 AGTGLKRLFLHAAALKFTHPGTGDVMRIEAPMDKQLKRCLEVL 270


>gi|309379094|emb|CBX22225.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 330

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 96/323 (29%), Positives = 160/323 (49%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIAVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPAREFD---------IVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  + + A+     F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVRLPLFKYTGAQGEKMVRVSGDGQAAHTV---FRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVK 317
            L HP  G  L + A LP  + +
Sbjct: 297 HLNHPLTGEPLALKAELPPDLAQ 319


>gi|296313302|ref|ZP_06863243.1| ribosomal large subunit pseudouridine synthase [Neisseria
           polysaccharea ATCC 43768]
 gi|296840180|gb|EFH24118.1| ribosomal large subunit pseudouridine synthase [Neisseria
           polysaccharea ATCC 43768]
          Length = 330

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 98/323 (30%), Positives = 162/323 (50%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A       +K + S       +   +++  YED  + V NKP+G++V GGSG++
Sbjct: 71  IPPVRVA-------EKEMPSERRAAVPARVFEAV--YEDDALLVVNKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V ++ + A+     F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSEDGQAAHTV---FRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVK 317
            L HP  G  L + A LP  + +
Sbjct: 297 HLNHPLTGEPLVLKAELPPDLAQ 319


>gi|326504872|dbj|BAK06727.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 472

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 107/375 (28%), Positives = 167/375 (44%), Gaps = 77/375 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           RW +   P +    +QK+ R  +V+ +    + ++   S +  R+  V +A +H++    
Sbjct: 95  RWVRRCCPDLPASLVQKLFRLRKVKKNAVTAETSSTHASAEQFRLRRV-SAKDHLLPGDT 153

Query: 83  ILDSSVNLTKHS--------------DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           +    VN+ + S              DFL+S+ +Y+D  I V NKP G+ VQGG GI   
Sbjct: 154 LF-LPVNIQESSVAEKARKFDNRNEIDFLRSLEIYKDKAIIVVNKPPGMPVQGGVGIKNS 212

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR---------- 178
           ID     + ++    PRL HRLD++ SG+LV+ RT+ +A  L   FR +           
Sbjct: 213 IDVLAPMFEENSSDAPRLVHRLDRDCSGVLVLGRTQLSASILHAIFREKTADALADGTQQ 272

Query: 179 -IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVID 234
            +Q+ Y +LV G P++ K  ++  L K     G    +  +   N      A++ ++VI+
Sbjct: 273 VLQRKYVALVMGTPRHPKGLLSAPLAKVLLQDGKSERLTVRAGPNTTSVQDALTEYRVIE 332

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNFTS-PI-------- 284
              Q F WLE+ P TGR HQLRVH    +G PIVGD+KY      ++T  P+        
Sbjct: 333 SCPQGFTWLELFPLTGRKHQLRVHCAEVLGTPIVGDYKYGRQAHQDWTPLPVSQTVDKEL 392

Query: 285 --------------------QNKLYLHARYMDLPHPEGG-----------------RLQI 307
                               Q +L+LH + M LP                      +L  
Sbjct: 393 LRKQRLPFGLVLGGGSIAEQQPQLHLHCKQMMLPDISAAVQGLQSEDADRDFSDLEKLSF 452

Query: 308 TAPLPAHMVKTWDSL 322
            APLP HM  +W+ L
Sbjct: 453 VAPLPLHMRLSWEVL 467


>gi|254448155|ref|ZP_05061618.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium HTCC5015]
 gi|198262281|gb|EDY86563.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium HTCC5015]
          Length = 321

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 99/325 (30%), Positives = 172/325 (52%), Gaps = 24/325 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            Q + V ++    R+D +   ++  +    + ++LR G+VRV+  R K   +++SG ++R
Sbjct: 12  TQKLTVPDEAVGQRIDNFLMGYWKGVPRSRVYRVLRKGEVRVNGGRKKPIYKLKSGDLLR 71

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       I+ Q   ++ V      +  + IL +ED ++ V NKP+G++   GSG+ 
Sbjct: 72  LPPVR------IEPQG--ETEVPAGAWREIAQRIL-FEDERLLVINKPSGMAAHAGSGVP 122

Query: 127 YHI-DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + I +   +   D  G++  L HRLD+ETSG L++A+ R+    L +SFR R   K Y +
Sbjct: 123 FGIAEAVHQHHCD--GKRTELVHRLDRETSGCLLLAKGRSVLNVLQDSFRQRETHKQYLA 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCW 242
           L+ G  K  +    +  L+K+ + G+ + VV +  K    A+S F+ +  +    +    
Sbjct: 181 LLVGDLKGSRRV--DLALQKTKLSGEAMVVVDEAGKS---ALSDFEPLAHYPWNDRTLTL 235

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHP 300
             +  HTGRTHQ+RVHA  +G P++GD KY  + + N  +  Q   +L+LHA  +  P  
Sbjct: 236 ARVTIHTGRTHQIRVHARALGLPLLGDDKY-GDERLNRDAKRQGLKRLFLHAESIRFPL- 293

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFK 325
           EG  L   APL A + +  ++L  +
Sbjct: 294 EGQTLYFEAPLDADLEQFINALPMR 318


>gi|261378098|ref|ZP_05982671.1| ribosomal large subunit pseudouridine synthase C [Neisseria cinerea
           ATCC 14685]
 gi|269145550|gb|EEZ71968.1| ribosomal large subunit pseudouridine synthase C [Neisseria cinerea
           ATCC 14685]
          Length = 330

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 98/323 (30%), Positives = 162/323 (50%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A       +K + S       +   +++  YED  + V NKP+G++V GGSG++
Sbjct: 71  IPPVRVA-------EKEMPSERRAAVPARVFEAV--YEDDALLVVNKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V ++ + A+     F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSEDGQAAHTV---FRVLSRFSDGILHSVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVK 317
            L HP  G  L + A LP  + +
Sbjct: 297 HLNHPLTGEPLVLKAELPPDLAQ 319


>gi|297830600|ref|XP_002883182.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297329022|gb|EFH59441.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 477

 Score =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 115/389 (29%), Positives = 172/389 (44%), Gaps = 78/389 (20%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVR------VDK------ 50
           L++    V    D       RW     P +    +QK+ R  QVR      VD       
Sbjct: 74  LLSDGDSVKASTDNSKTTALRWILRCRPDLPRTLVQKLFRLRQVRRQMSLSVDGHELQRS 133

Query: 51  --KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSK 107
             KRV     +  G  + +P  ++  N           S   ++    F+ S++LY+D  
Sbjct: 134 QLKRVAAKESLNVGDRIYLPLSVD--NDTPPTPPAKKESFQCSEEERKFVCSLVLYKDPA 191

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAA 166
           I V NKP G++VQGGSGI   ID    + +   K + PRL HRLD++ SG+LV+ART+ A
Sbjct: 192 IIVLNKPHGLAVQGGSGIKTSIDELAATCLTFDKSESPRLVHRLDRDCSGLLVLARTQTA 251

Query: 167 AQHLTESFR--------------MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-- 210
           A  L   FR              ++ +++ Y +LV G P+ +K  I+  L K     G  
Sbjct: 252 ATVLHSIFREKTCGASAYGVKKNIKSLKRKYMALVIGCPRRQKGQISAPLRKVVVDDGKS 311

Query: 211 DYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVG 268
           D + V    E     +AI+ +KVI+     + WLE++P TGR HQLRVH    +G PI+G
Sbjct: 312 DRITVNDNGELVSTQHAITEYKVIESSPHGYTWLELRPLTGRKHQLRVHCAEVLGTPILG 371

Query: 269 DHKYC--------------------------ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           D+KY                            +  G   S  Q  L+LH++ +DLP+   
Sbjct: 372 DYKYGWQAHKAREPFVSSETTPTKPSSSPFGLDLDGGDVSSKQPHLHLHSKQIDLPNISQ 431

Query: 303 --GRLQIT--------------APLPAHM 315
              ++Q++              APLP+HM
Sbjct: 432 LLEKMQVSSDSDISDLDSLKFDAPLPSHM 460


>gi|218295180|ref|ZP_03496016.1| pseudouridine synthase, RluA family [Thermus aquaticus Y51MC23]
 gi|218244383|gb|EED10908.1| pseudouridine synthase, RluA family [Thermus aquaticus Y51MC23]
          Length = 307

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 85/247 (34%), Positives = 127/247 (51%), Gaps = 30/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQ------KPRLTHRLDQ 152
           +LYED  + V NKP G+      G+     ++  L  + + K        +P + HRLD+
Sbjct: 74  ILYEDEDLLVLNKPPGLLTHPAPGVYTGTVVNALLGRYYEPKAVERPEMVRPGIVHRLDK 133

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLK--KSHI 208
           +TSG+LVVA+   A + L+++FR R + K Y +L  G PK       I    ++  K H+
Sbjct: 134 DTSGVLVVAKHGGALEALSQAFRDRLVMKRYLALTEGHPKEGTLIAPIGRHPVERHKMHV 193

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           GG              YA +HF+V+   A     +E +PHTGRTHQ+RVH  H+  PI+G
Sbjct: 194 GG----------VAPRYAETHFQVL-ATAGPHALVEARPHTGRTHQIRVHLKHLRAPILG 242

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           D  Y         SP+  +  LHA  + LPHP  GR L+  AP+PA M + W++LG  + 
Sbjct: 243 DEVYGKK------SPVIPRQALHAYELRLPHPRTGRILEFLAPVPADMARAWEALGGAWP 296

Query: 328 RNLYIKR 334
             + + R
Sbjct: 297 EGIALNR 303


>gi|294664687|ref|ZP_06730020.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
 gi|292605540|gb|EFF48858.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
          Length = 328

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 103/334 (30%), Positives = 162/334 (48%), Gaps = 39/334 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDF---LKSILLYEDSKIYVFNKPAGISVQGGS 123
           IPPV           +  D        S F   L++ +++ED+++   NKP+G++  GGS
Sbjct: 76  IPPV-----------RTNDEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGS 124

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------R 177
           GI++     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R
Sbjct: 125 GISFGAIETLRAL--RPNQSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGR 182

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVI 233
            I K Y +L+ G +P       A       HIG   G   HV  Q       ++SHF+++
Sbjct: 183 GITKRYLTLLVGRMPDGVMTVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFRLL 235

Query: 234 DC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYL 290
           +      +C + ++  TGRTHQ+RVHA H+G P+ GD KY  A+        +   +L+L
Sbjct: 236 ERRGGHSYCEVRIE--TGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFL 293

Query: 291 HARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSLG 323
           HA  ++     G    + +APL   + +  D LG
Sbjct: 294 HAASLEFALDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|190575132|ref|YP_001972977.1| putative ribosomal large subunit pseudouridine synthase C
           [Stenotrophomonas maltophilia K279a]
 gi|190013054|emb|CAQ46686.1| putative ribosomal large subunit pseudouridine synthase C
           [Stenotrophomonas maltophilia K279a]
          Length = 324

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 102/337 (30%), Positives = 162/337 (48%), Gaps = 50/337 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   ++++G  VR
Sbjct: 16  VRMITVPADRAGQRLDNFLLGQLKGAPRSLVYKLVRSGQVRVNGGRAKAERKLEAGDEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGS 123
           +PPV           ++ +    +     F++ +   +++ED+++   NKP G++  GGS
Sbjct: 76  VPPV-----------RLTEEGDKVGPPEAFMRRLEQAIVFEDARLLALNKPTGVASHGGS 124

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR---IQ 180
           GI++     L++     GQ   L HRLD++TSG+L+VA+ R+A   L    R      I+
Sbjct: 125 GISFGAIETLRAL--RPGQTLELVHRLDRDTSGLLIVAKKRSALSELQALLREDHGAGIR 182

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC-F 236
           K Y +L+ G   +    +   L    H+G   G   HV  Q       +ISHF+V++   
Sbjct: 183 KRYLTLLAGRMPDGVMTVDAPL----HVGLRQGGERHV--QVNAIGKESISHFRVLERRG 236

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK--------- 287
              +C  E++  TGRTHQ+RVHA H+G P+ GD KY          P  NK         
Sbjct: 237 GHSYC--EVRIETGRTHQIRVHAQHLGHPVAGDDKYG--------DPAVNKRLREQIGLK 286

Query: 288 -LYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
            L+LHA  ++    +G     + APL   +V+  D L
Sbjct: 287 RLFLHAASLEFALDDGKSPYVLNAPLADELVEALDRL 323


>gi|218767110|ref|YP_002341622.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis Z2491]
 gi|121051118|emb|CAM07389.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis Z2491]
 gi|254672162|emb|CBA04981.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis alpha275]
          Length = 330

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 98/323 (30%), Positives = 162/323 (50%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K  + G     +V+ +E G + A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFK--YTGAQGEKMVRVSEDGQS-AHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVK 317
            L HP  G  L + A LP  + +
Sbjct: 297 HLNHPLTGEPLVLKAELPPDLAQ 319


>gi|161870862|ref|YP_001600036.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis 053442]
 gi|161596415|gb|ABX74075.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis 053442]
 gi|325141211|gb|EGC63711.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis CU385]
 gi|325145393|gb|EGC67670.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M01-240013]
          Length = 330

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 98/323 (30%), Positives = 162/323 (50%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K  + G     +V+ +E G + A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFK--YTGAQGEKMVRVSEDGQS-AHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVK 317
            L HP  G  L + A LP  + +
Sbjct: 297 HLNHPLTGEPLVLKAELPPDLAQ 319


>gi|114331690|ref|YP_747912.1| pseudouridine synthase, RluA family protein [Nitrosomonas eutropha
           C91]
 gi|114308704|gb|ABI59947.1| ribosomal large subunit pseudouridine synthase C [Nitrosomonas
           eutropha C91]
          Length = 354

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 103/328 (31%), Positives = 154/328 (46%), Gaps = 51/328 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+   E  R+D +       I   ++ ++LRSGQVRV+ KR+    R+     VRIPPV+
Sbjct: 40  VDETAEGQRIDNFLIKALKDIPRRHIYQLLRSGQVRVNSKRIDAGYRLLLNDKVRIPPVL 99

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                I ++        +            LY+D  + V NKPAG +V GGSGI+Y +  
Sbjct: 100 KLAKPISRQAPYRAEQFDT-----------LYQDDYLLVINKPAGTAVHGGSGISYGVIE 148

Query: 132 FLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            L+       Q+P      L HRLD+ETSG+L++AR R     L +  R   ++K Y +L
Sbjct: 149 QLRK------QRPDWKFLELVHRLDRETSGVLLLARKRQTLLELHKQIREGTVRKHYLTL 202

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS---HFKVIDCFA------ 237
           V G  KN  + +   L         Y ++  + E+    A     H KV   +       
Sbjct: 203 VRGKWKNSLQNVRLPL---------YKYLTAEGERRVAIATGRNDHDKVQQAYTLFALQK 253

Query: 238 --QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-------KGNFTSPIQNKL 288
             + F  L+ +  TGRTHQ+RVH  H+G PI GD KY  +F       K + +  +  ++
Sbjct: 254 NWEAFSLLDAELKTGRTHQIRVHLAHLGFPIAGDDKY-GDFGLNRQLQKDDGSGLVLKRM 312

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHM 315
           +LHA      HP  G  L++ APLP  +
Sbjct: 313 FLHASVFVCTHPVTGELLRLEAPLPDEL 340


>gi|325918635|ref|ZP_08180739.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325535142|gb|EGD07034.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 328

 Score =  137 bits (344), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 102/329 (31%), Positives = 159/329 (48%), Gaps = 39/329 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VRIPPV 
Sbjct: 21  VPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVRIPPV- 79

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFL---KSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                     ++ +        S FL   ++ +++ED+++   NKP+G++  GGSGI++ 
Sbjct: 80  ----------RVTEEGDKAAPPSSFLARLEAAIVFEDARLLALNKPSGVASHGGSGISFG 129

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQKI 182
               L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I K 
Sbjct: 130 AIETLRAL--RPNQTLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITKR 187

Query: 183 YWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC-FA 237
           Y +L+ G +P       A       HIG   G   HV  Q       ++SHFK+++    
Sbjct: 188 YLTLLVGRMPDGVMTVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFKLLERRGG 240

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHARYM 295
             +C + ++  TGRTHQ+RVHA H+G P+ GD KY  A         +   +L+LHA  +
Sbjct: 241 HSYCEVRIE--TGRTHQIRVHAQHLGHPVAGDDKYGEAEVNKRLRDQLGLKRLFLHAASL 298

Query: 296 DLPHPEGGRLQI-TAPLPAHMVKTWDSLG 323
           +     G    + +APL   + +  D LG
Sbjct: 299 EFALDAGKTPYVLSAPLAPELAEALDRLG 327


>gi|167570710|ref|ZP_02363584.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           oklahomensis C6786]
          Length = 335

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 108/330 (32%), Positives = 160/330 (48%), Gaps = 32/330 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + +++     R+D +       +   ++ +ILRSG+VRV+K RV    R+  G V  
Sbjct: 17  VSLIEIDDGAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAHGDV-- 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V      +        +       + F    +L+ED  I   NKPAG++V GGSG+A
Sbjct: 75  ---VRVPPVRVAAADLARAAGPGPVPAAAFE---ILFEDDAIIALNKPAGVAVHGGSGVA 128

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    ++       L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y+
Sbjct: 129 F---GVIEQMRHARPHAKFLELVHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRYF 185

Query: 185 SLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH--FKVIDCFAQK 239
           + V   W     ++  +   L K S   G+    V+  E G     SH  F ++DC+   
Sbjct: 186 ACVHGEWAPDWGRRRAVKAPLFKYSTPDGE--RRVRVQEDGLP---SHTVFNLVDCWPD- 239

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHAR 293
           +  LE +  TGRTHQ+RVH  H+G PIVGD KY  +F  N         P   +++LHA 
Sbjct: 240 YALLEAELKTGRTHQIRVHLAHLGLPIVGDAKY-GDFALNKALARANAVPSLKRMFLHAH 298

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            + L HP  G  LQ  APLPA   +  D L
Sbjct: 299 RLRLAHPLTGEPLQFDAPLPAECRQFLDQL 328


>gi|94970372|ref|YP_592420.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Koribacter versatilis Ellin345]
 gi|94552422|gb|ABF42346.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Koribacter versatilis Ellin345]
          Length = 333

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 102/350 (29%), Positives = 169/350 (48%), Gaps = 56/350 (16%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   Q++ V  D+ N+RLD++  +H P ++   +Q ++   ++ VD K  K + +++  +
Sbjct: 1   MDGAQHIQVSADDANIRLDQYLVSHLPDVSRARVQALIDDEKILVDGKSSKPSYKLRGSE 60

Query: 64  VVRI-----PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           V+ +     PP + A    I E   LD               ++YED  + V NKPAG+ 
Sbjct: 61  VIDVVGEYQPPPLRA----IPEDIPLD---------------VVYEDDDLAVINKPAGMM 101

Query: 119 VQGGSGIAYH-------IDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAA 167
           V  G+G           ++  L   ++  +  G  +P + HRLD+ETSG++VVA+   A 
Sbjct: 102 VHVGAGATEEERNRGTLVNALLYRFRALSEVGGDMRPGIVHRLDKETSGLIVVAKNDVAH 161

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-- 225
           + L E F  RR+ K Y +LV G PK  K  I         I  D     +   +G+    
Sbjct: 162 RKLAEQFSSRRVHKKYVALVHGWPKKLKGTI------NLPIARDMSRRTRMTTRGSGGRD 215

Query: 226 AISHFKV---IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
           A+SH++V   I+    KF  +E++  TGRTHQ+RVH   +G P+VGD  Y A  +   T 
Sbjct: 216 ALSHYEVKEKIESPYGKFALVEVKIETGRTHQIRVHMASLGHPVVGDTLYGAPGELRVTK 275

Query: 283 PIQN---------KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            ++          + +LHA  ++L  P  G+ L+    +PA +    ++L
Sbjct: 276 ALKGMPSKMASLERNFLHAAEIELQQPATGKALRFVTKVPAALEDFAETL 325


>gi|261391734|emb|CAX49183.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C; rRNA pseudouridylate synthase C) [Neisseria
           meningitidis 8013]
          Length = 330

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 96/323 (29%), Positives = 161/323 (49%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V ++ + A+     F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVRLPLFKYTGAQGEKMVRVSEDGQSAHTV---FRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVK 317
            L HP  G  L + A LP  + +
Sbjct: 297 HLNHPLTGEPLVLKAELPPDLAQ 319


>gi|289665912|ref|ZP_06487493.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 328

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 103/331 (31%), Positives = 162/331 (48%), Gaps = 33/331 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+   D +         L++ +++ED+++   NKP G++  GGSGI+
Sbjct: 76  IPPVR------VNEEG--DKAAPPPSFMARLEAAIVFEDARLLALNKPTGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRAL--RPNQSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC- 235
           K Y +L+ G +P       A       HIG   G   HV  Q       ++SHFK+++  
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFKLLERR 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHAR 293
               +C + ++  TGRTHQ+RVHA H+G P+ GD KY  A+        +   +L+LHA 
Sbjct: 239 GGHSYCEVRIE--TGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAA 296

Query: 294 YMDLPHPEGGRLQI-TAPLPAHMVKTWDSLG 323
            ++     G    + +APL   + +  D LG
Sbjct: 297 SLEFALDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|294625341|ref|ZP_06703977.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
 gi|292600359|gb|EFF44460.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
          Length = 328

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 103/334 (30%), Positives = 162/334 (48%), Gaps = 39/334 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLRGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDF---LKSILLYEDSKIYVFNKPAGISVQGGS 123
           IPPV           +  D        S F   L++ +++ED+++   NKP+G++  GGS
Sbjct: 76  IPPV-----------RTNDEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGS 124

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------R 177
           GI++     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R
Sbjct: 125 GISFGAIETLRAL--RPNQSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGR 182

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVI 233
            I K Y +L+ G +P       A       HIG   G   HV  Q       ++SHF+++
Sbjct: 183 GITKRYLTLLVGRMPDGVMTVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFRLL 235

Query: 234 DC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYL 290
           +      +C + ++  TGRTHQ+RVHA H+G P+ GD KY  A+        +   +L+L
Sbjct: 236 ERRGGHSYCEVRIE--TGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFL 293

Query: 291 HARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSLG 323
           HA  ++     G    + +APL   + +  D LG
Sbjct: 294 HAASLEFALDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|294668132|ref|ZP_06733239.1| ribosomal large subunit pseudouridine synthase [Neisseria elongata
           subsp. glycolytica ATCC 29315]
 gi|291309840|gb|EFE51083.1| ribosomal large subunit pseudouridine synthase [Neisseria elongata
           subsp. glycolytica ATCC 29315]
          Length = 297

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 93/294 (31%), Positives = 158/294 (53%), Gaps = 25/294 (8%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           ++ +I+R+G+VR++KKR K ++RIQ+G ++RIPPV  A     ++Q+  ++        +
Sbjct: 5   HIHRIIRAGEVRLNKKRCKPDSRIQTGDLLRIPPVRTA-----EKQRPSENRAQAAPARE 59

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           F    ++YED  + V +KPAG +V GGSG+++ +   ++     + +   L HRLD++TS
Sbjct: 60  F---TIIYEDDALLVIDKPAGTAVHGGSGVSFGVIEQIR-RARPEARYLELVHRLDKDTS 115

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A+ R A   L E+ R    QKIY +L  G   N    +   L K  + G     +
Sbjct: 116 GLLMIAKKRNALVKLHEAIRNDHPQKIYLALGVGKLPNDSFHVKLPLFK--YTGAQGEKM 173

Query: 216 VKQNEKGANYAISHFKVIDCFAQK---------FCWLEMQPHTGRTHQLRVHALHMGCPI 266
           V+ +E G + A + F+V++ F+              ++    TGRTHQ+RVH     CPI
Sbjct: 174 VRVSEDGQS-AHTIFRVLNRFSDGLLHQVGLSHLTLVQATLKTGRTHQIRVHLQSQQCPI 232

Query: 267 VGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
            GD +Y  +++ N         +++LHA  + L HP  G  L + A LP  + +
Sbjct: 233 AGDERY-GDYQANKRLQKLGLKRMFLHAAELHLDHPLTGEPLHLKAELPQELAQ 285


>gi|188577474|ref|YP_001914403.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           oryzae pv. oryzae PXO99A]
 gi|188521926|gb|ACD59871.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           oryzae pv. oryzae PXO99A]
          Length = 313

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 103/326 (31%), Positives = 160/326 (49%), Gaps = 33/326 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VRIPPV 
Sbjct: 6   VPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVRIPPVR 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                 + E+   D +   +     L++ +++ED+++   NKP+G++  GGSGI++    
Sbjct: 66  ------VNEEG--DKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGISFGAIE 117

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQKIYWS 185
            L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I K Y S
Sbjct: 118 TLRAL--RPNQNLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITKRYLS 175

Query: 186 LVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC-FAQKF 240
           L+ G +P       A       HIG   G   HV  Q       ++SHF +++      +
Sbjct: 176 LLIGRMPDGVMSVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFTLLERRGGHSY 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHARYMDLP 298
           C  E++  TGRTHQ+RVHA H+G P+ GD KY  A+        +   +L+LHA  ++  
Sbjct: 229 C--EVRIETGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAASLEFA 286

Query: 299 HPEGGRLQI-TAPLPAHMVKTWDSLG 323
              G    + +APL   + +  D LG
Sbjct: 287 LDAGQTPYVLSAPLAPELAEALDQLG 312


>gi|15230381|ref|NP_188575.1| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|75274073|sp|Q9LT72|PUS4_ARATH RecName: Full=RNA pseudourine synthase 4, mitochondrial; AltName:
           Full=RNA pseudouridylate synthase 4; AltName:
           Full=RNA-uridine isomerase 4; Flags: Precursor
 gi|11994467|dbj|BAB02469.1| unnamed protein product [Arabidopsis thaliana]
 gi|110737723|dbj|BAF00800.1| hypothetical protein [Arabidopsis thaliana]
 gi|134031916|gb|ABO45695.1| At3g19440 [Arabidopsis thaliana]
 gi|332642719|gb|AEE76240.1| RNA pseudourine synthase 4 [Arabidopsis thaliana]
          Length = 477

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 113/390 (28%), Positives = 173/390 (44%), Gaps = 80/390 (20%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVR------VDK------ 50
           L++    V    D       RW     P +    +QK+ R  QVR      VD       
Sbjct: 74  LLSDGDSVKSSTDNSKTTALRWILRCRPDLPRTLVQKLFRLRQVRREMSMSVDGDELQRS 133

Query: 51  --KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSK 107
             KRV     +  G  + +P  ++  N   +       S   + +   F+ S++LY+D  
Sbjct: 134 QLKRVAAKESLNVGDRIYLPLSVD--NDTPQTPPAKKESFQCSDEERKFVCSLVLYKDPA 191

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAA 166
           I V NKP G++VQGGSGI   ID    S +   K + PRL HRLD++ SG+LV+ART+ A
Sbjct: 192 IIVLNKPHGLAVQGGSGIKTSIDELAASCLKFDKSESPRLVHRLDRDCSGLLVLARTQTA 251

Query: 167 AQHLTESFR--------------MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           A  L   FR              ++ +++ Y +LV G P  ++  I+  L +K  +    
Sbjct: 252 ATVLHSIFREKTTGASAYGVKKNVKSLKRKYMALVIGCPPRQRGQISAPL-RKVVVDDGK 310

Query: 213 VHVVKQNEKG----ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIV 267
              +  N+ G      +AI+ ++VI+     + WLE++P TGR HQLRVH    +G PIV
Sbjct: 311 SERITVNDNGELVSTQHAITEYRVIESSPHGYTWLELRPLTGRKHQLRVHCAEVLGTPIV 370

Query: 268 GDHKYC--------------------------ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           GD+KY                            +  G   S  Q  L+LH++ +DLP+  
Sbjct: 371 GDYKYGWQAHKAREPFVSSENNPTKQSSSPFGLDLDGGDVSSKQPHLHLHSKQIDLPNIS 430

Query: 302 G--GRLQIT--------------APLPAHM 315
               ++Q++              APLP+HM
Sbjct: 431 QLLEKMQVSSDSDISDLDSLKFDAPLPSHM 460


>gi|58582695|ref|YP_201711.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84624582|ref|YP_451954.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|58427289|gb|AAW76326.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84368522|dbj|BAE69680.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 328

 Score =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 102/331 (30%), Positives = 163/331 (49%), Gaps = 33/331 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRMLKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+   D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPPVR------VNEEG--DKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRAL--RPNQNLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC- 235
           K Y +L+ G +P       A       HIG   G   HV  Q       ++SHF +++  
Sbjct: 186 KRYLTLLIGRMPDGVMSVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFTLLERR 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHAR 293
               +C + ++  TGRTHQ+RVHA H+G P+ GD KY  A+        +   +L+LHA 
Sbjct: 239 GGHSYCEVRIE--TGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAA 296

Query: 294 YMDLPHPEGGRLQI-TAPLPAHMVKTWDSLG 323
            ++     G    + +APL   + +  D LG
Sbjct: 297 SLEFALDAGQTPYVLSAPLAPELAEALDQLG 327


>gi|192359429|ref|YP_001982148.1| pseudouridine synthase Rlu family protein [Cellvibrio japonicus
           Ueda107]
 gi|190685594|gb|ACE83272.1| pseudouridine synthase, RluA family subfamily [Cellvibrio japonicus
           Ueda107]
          Length = 349

 Score =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 104/333 (31%), Positives = 174/333 (52%), Gaps = 35/333 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+++ ++ +    RLD +       +    +  ++R G+VRV+K R + + ++ +G +VR
Sbjct: 35  VRFLTIDAELAGQRLDNFLMAQLKGVPKSRIYNLVRKGEVRVNKGRSRPDYKLCAGDLVR 94

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A   +    K  +  V L   S      +L+E+  + V NKP G++V GGSG+ 
Sbjct: 95  VPPVRTAEARVAAPAKAGNQLVALLDQS------VLFENEGLLVINKPPGLAVHGGSGVN 148

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR---RIQKIY 183
             +   L+  +  + +   L HRLD++TSG ++VA+ R+  +HL  + R +   +I+K+Y
Sbjct: 149 LGLIETLRQ-MRPEARYLELVHRLDRDTSGCIMVAKKRSYLRHLQAALRDKVEGQIEKVY 207

Query: 184 WSLVWGI-PKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            +LV G  P    +   N  L ++ +G D  YV V    +     +++ F VI  + Q F
Sbjct: 208 CALVVGHWPARLHQV--NAPLLRTEVGADERYVRVHPDGKP----SLTLFNVIQRY-QGF 260

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMD 296
             +E +P TGRTHQ+RVHA H G  +VGD KY  +   +    ++N    +L+LHA  + 
Sbjct: 261 TLVEARPVTGRTHQIRVHARHAGHGLVGDEKYGDD---DINLHMRNQGIKRLFLHASSLG 317

Query: 297 LPHPEGGRLQIT---APLP---AHMVKTWDSLG 323
              P  G  Q+T   APLP   A  +   +SLG
Sbjct: 318 FCLP--GEAQMTWVEAPLPQDLAQPLSCLESLG 348


>gi|50083692|ref|YP_045202.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ADP1]
 gi|49529668|emb|CAG67380.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ADP1]
          Length = 310

 Score =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 94/307 (30%), Positives = 165/307 (53%), Gaps = 23/307 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +       +    + +++R GQVRV+KKR+K  +++  G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFTRLKGVPKSRIYRLIREGQVRVNKKRIKAESKLSIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK    +    + +  L + ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDESDAPVSDQVAKSLLNRVVYEDEGLLVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           Y   G +++   + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y +
Sbjct: 123 Y---GLIEAMRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDLLREHKIRKTYAA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G     ++ I   LL+     G+  V V K+ +       + ++V + F ++   + 
Sbjct: 180 LVKGQVSLDQQLIDAPLLRYELSNGERRVRVSKEGKPSK----TEWRVAERF-KEATLVY 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P +GRTHQ+RVH L +G P+VGD KY    +  ++ P   +L LHA  +++P    G 
Sbjct: 235 ASPLSGRTHQIRVHGLSIGHPLVGDDKY--GHQTVYSGPEARRLCLHAMRLEIP----GY 288

Query: 305 LQITAPL 311
             I APL
Sbjct: 289 PVIEAPL 295


>gi|255321251|ref|ZP_05362417.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           radioresistens SK82]
 gi|262380064|ref|ZP_06073219.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           radioresistens SH164]
 gi|255301805|gb|EET81056.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           radioresistens SK82]
 gi|262298258|gb|EEY86172.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           radioresistens SH164]
          Length = 312

 Score =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 94/311 (30%), Positives = 168/311 (54%), Gaps = 23/311 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K  +++  G  VR
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAESKLAIGDQVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           + P        I+ +   ++ V ++ K +  L S ++YED  + V NKP+GI+V GGSG+
Sbjct: 70  VAP--------IRFEPKDETPVPVSDKVAQGLLSRVIYEDEGLMVVNKPSGIAVHGGSGV 121

Query: 126 AYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           AY   G ++    + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y 
Sbjct: 122 AY---GLIEGLRAATGKKYLELVHRIDRDTSGLVMISKKRSVLKTLQDLLREHKIKKTYA 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G     ++ I   L +     G+    V+ +++G + + + + V + F      + 
Sbjct: 179 AIVKGQVSLDQQLIDAPLYRYELANGE--RRVRVSKEGKD-SKTQWNVAERFMHA-TLVY 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P +GRTHQ+RVH L +G P+VGD KY    +  +  P   +L LHA  +++P    G 
Sbjct: 235 ASPLSGRTHQIRVHGLSIGHPLVGDDKY--GHETEYKGPKPRRLCLHAIRLEIP----GY 288

Query: 305 LQITAPLPAHM 315
             I APLP  M
Sbjct: 289 PTIEAPLPEDM 299


>gi|326566216|gb|EGE16368.1| RluA family pseudouridine synthase [Moraxella catarrhalis 103P14B1]
          Length = 382

 Score =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 91/307 (29%), Positives = 166/307 (54%), Gaps = 25/307 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V ++ V N+++  R+D +       +   +L K++RS ++R++ KR K ++++  G V
Sbjct: 58  SRVNFLTVTNNQDGQRVDNFLLARLKGLPRSHLYKLIRSDEIRINGKRCKAHDKLYMGDV 117

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+ P+  +    ++E  I+   +     +  L   +++ED  + V NKP G++V GGSG
Sbjct: 118 VRVAPIRLS----VREAPIISEEL-----AKGLLERIIFEDDGLIVLNKPHGMAVHGGSG 168

Query: 125 IAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++   G +++   + G+K   L HR+D++TSG+L++A+ R+  + L E FR + I K Y
Sbjct: 169 ESF---GIIEAMRLAMGKKYLELIHRIDKDTSGLLLIAKKRSTLKILQEQFRTKTIHKQY 225

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGAN----YAISHFKVIDCFAQ 238
             LV G  +  +  I   LL+ +   G+  V V   NE+ A      +++  K +  F +
Sbjct: 226 LCLVMGHVQADEMVIDVPLLRYTLANGERRVKVAHLNEQKAGEHAKASLTKIKTLLRFKK 285

Query: 239 KFCWLEM---QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             C + +    P TGRTHQ+RVH  H+G  ++GD KY    + N  +P   +L LHA  +
Sbjct: 286 DGCPVSLVLAMPATGRTHQIRVHMAHIGHALLGDDKY----QNNPLAPKVGRLCLHAWQL 341

Query: 296 DLPHPEG 302
            + + +G
Sbjct: 342 GMTNDDG 348


>gi|225428918|ref|XP_002282614.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|296090438|emb|CBI40257.3| unnamed protein product [Vitis vinifera]
          Length = 476

 Score =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 108/384 (28%), Positives = 166/384 (43%), Gaps = 90/384 (23%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDK-----------------KRVKFNNRIQSGQVV 65
           +W     P +    +QK+ R  QVR +                  KRV   + +  G  +
Sbjct: 97  KWVVRCCPQLPRSLVQKLFRLRQVRRESYNMITSDIGVQNQEHRLKRVAAKDLMNLGDQI 156

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +P  +        E    D  +N      F+ ++ LY+D  I V NKP G+ VQGG GI
Sbjct: 157 LLPITVEEFPSEKHEYHCNDEEIN------FVHNLELYKDPAIIVVNKPPGLPVQGGIGI 210

Query: 126 AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR--------- 175
              +D    +++     + PRL HRLD+++SGIL++ RT+ +A  L   FR         
Sbjct: 211 KRSLDELAATYLRYDCSEPPRLVHRLDRDSSGILIMGRTQTSATILHSIFREKTFGASNN 270

Query: 176 -----MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG--DYVHVVKQNEK-GANYAI 227
                 R +Q+ YW+LV G P+  +  I+  L K     G  + + +V   +   + +AI
Sbjct: 271 DIDTKKRILQRRYWALVIGSPRRPRGLISAPLGKVVVDDGKSERITIVDNVQTMSSQHAI 330

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC------------A 274
           + ++VI      + WLE+ P TGR HQLRVH    +G PIVGD+KY             +
Sbjct: 331 TEYRVIKSSCHGYTWLELSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQAHRKWKQLFQS 390

Query: 275 NFKGNFTSPIQNK--------------------LYLHARYMDLPH--------------- 299
           N + N    + N+                    L+LH + M LP+               
Sbjct: 391 NIEKNLDENLSNRKTHPFGLDLESGSILDKQPHLHLHCKQMVLPNVSLALQNLQLSAECD 450

Query: 300 -PEGGRLQITAPLPAHMVKTWDSL 322
             E   L+  APLP+HM ++WD L
Sbjct: 451 LSELESLEFVAPLPSHMQRSWDIL 474


>gi|254521304|ref|ZP_05133359.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219718895|gb|EED37420.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 307

 Score =  135 bits (341), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 104/332 (31%), Positives = 160/332 (48%), Gaps = 46/332 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD +            + K++RSGQVRV+  R K   ++++G  VR+PP
Sbjct: 2   ITVPADRAGQRLDNFLLGQLKGAPRSLVYKLVRSGQVRVNGGRAKAERKLEAGDEVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V      + +E    D +         L+  +++ED+++   NKP G++  GGSGI++  
Sbjct: 62  V-----RLTEEG---DKAGPPEAFMRRLEQAIVFEDARLLALNKPTGVASHGGSGISFGA 113

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR---IQKIYWSL 186
              L++     GQ   L HRLD++TSG+L+VA+ R+A   L    R      I+K Y +L
Sbjct: 114 IETLRAL--RPGQTLELVHRLDRDTSGLLIVAKKRSALSELQALLREDHGAGIRKRYLTL 171

Query: 187 VWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC-FAQKFC 241
           + G +P       A       H+G   G   HV  Q       +ISHF+V++      +C
Sbjct: 172 LTGRMPDGVMTVDAPL-----HVGLRQGGERHV--QVNAIGKESISHFRVLERRGGHSYC 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK----------LYLH 291
             E++  TGRTHQ+RVHA H+G P+ GD KY          P+ NK          L+LH
Sbjct: 225 --EVRIETGRTHQIRVHAQHLGHPVAGDDKYG--------DPVVNKRLREQIGLKRLFLH 274

Query: 292 ARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           A  ++    +G     + APL   +V+  D L
Sbjct: 275 AASLEFALDDGKSPYVLNAPLADELVEALDRL 306


>gi|15676125|ref|NP_273256.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis MC58]
 gi|7225419|gb|AAF40655.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis MC58]
 gi|316985120|gb|EFV64072.1| pseudouridine synthase, RluA family protein [Neisseria meningitidis
           H44/76]
 gi|325143210|gb|EGC65550.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis 961-5945]
 gi|325197484|gb|ADY92940.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis G2136]
 gi|325199409|gb|ADY94864.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis H44/76]
          Length = 330

 Score =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 96/323 (29%), Positives = 160/323 (49%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  + + A+     F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSADGQSAHTV---FRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVK 317
            L HP  G  L + A LP  + +
Sbjct: 297 HLNHPLTGEPLVLKAELPPDLAQ 319


>gi|83719070|ref|YP_442774.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis E264]
 gi|83652895|gb|ABC36958.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis E264]
          Length = 391

 Score =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 97/318 (30%), Positives = 150/318 (47%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRVD    K    +  G  + +      L  ++ 
Sbjct: 65  RLDKALAQLFPEFSRSRLQQWIESERVRVDGAPAKIRQAVPLGATIEL------LPDLLP 118

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 119 EQ--------LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 170

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG  +   E
Sbjct: 171 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWG--QMPDE 228

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 229 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTPWERQPVSAIHCDLETGRTH 286

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 287 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPATGRSMQWRA 346

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 347 PLPADLAALVDALGFGAD 364


>gi|198283980|ref|YP_002220301.1| RluA family pseudouridine synthase [Acidithiobacillus ferrooxidans
           ATCC 53993]
 gi|218668096|ref|YP_002426617.1| ribosomal large subunit pseudouridine synthase C [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198248501|gb|ACH84094.1| pseudouridine synthase, RluA family [Acidithiobacillus ferrooxidans
           ATCC 53993]
 gi|218520309|gb|ACK80895.1| ribosomal large subunit pseudouridine synthase C [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 317

 Score =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 99/306 (32%), Positives = 161/306 (52%), Gaps = 14/306 (4%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V + E   RLD +       +   ++ KILRSG+VRV+K R + +  +  G V+R+PPV 
Sbjct: 11  VTDAEAGQRLDNFLLRVMKGVPRSHIYKILRSGEVRVNKGRARPHYHLAEGDVLRLPPVR 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A           D +V        L++ +LYEDS + V +KP+G++V GGSG+++ +  
Sbjct: 71  VAAPS--------DPAVLPAYLQGQLEAAVLYEDSHLLVLDKPSGLAVHGGSGLSWGVIE 122

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L+  +    ++  L HRLD++TSG L+ ++ R+A + L E+ R   ++K Y  L  G  
Sbjct: 123 ALRQ-LRPDARELELVHRLDRDTSGCLIFSKKRSALRALHEALRAGLMEKRYLVLAAGDW 181

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           + +   +   L K +   G+ +  V   E  A +  +HF  ++ F +    L+    TGR
Sbjct: 182 QGEARSVRLALRKNTLQSGERMVRVDPVEGKAAH--THFLPLERF-RGAVLLQADLDTGR 238

Query: 252 THQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           THQ+RVH   +G  + GD KY  A F     +    +L+LHA  +   HP+ GR ++I A
Sbjct: 239 THQIRVHLQAIGHAVAGDEKYGDAAFNQRLRALGLRRLFLHAALVAFRHPQDGRPMRIEA 298

Query: 310 PLPAHM 315
           PLPA +
Sbjct: 299 PLPADL 304


>gi|257138984|ref|ZP_05587246.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis E264]
          Length = 385

 Score =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 97/318 (30%), Positives = 150/318 (47%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRVD    K    +  G  + +      L  ++ 
Sbjct: 59  RLDKALAQLFPEFSRSRLQQWIESERVRVDGAPAKIRQAVPLGATIEL------LPDLLP 112

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 113 EQ--------LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 164

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG  +   E
Sbjct: 165 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWG--QMPDE 222

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 223 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTPWERQPVSAIHCDLETGRTH 280

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 281 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPATGRSMQWRA 340

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 341 PLPADLAALVDALGFGAD 358


>gi|237736831|ref|ZP_04567312.1| tRNA pseudouridine synthase A [Fusobacterium mortiferum ATCC 9817]
 gi|229420693|gb|EEO35740.1| tRNA pseudouridine synthase A [Fusobacterium mortiferum ATCC 9817]
          Length = 292

 Score =  135 bits (341), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 89/307 (28%), Positives = 162/307 (52%), Gaps = 22/307 (7%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ + E++RLD++ +   P +    + K +R G+++V+ K+ K N R+Q   VV++  V
Sbjct: 4   LIDKEYEDVRLDKFLRKKLPDMALTEIFKCIRVGKIKVNGKKSKENYRLQLNDVVKLFFV 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           + +            +S    K    +K  ++YED ++ + NK A + +  GSG  Y + 
Sbjct: 64  VESKECDKNNNINKINSEKFEK----IKKYIVYEDDRVLILNKKANMVMHKGSGHEYGVS 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             LK ++++        +R+D+ TSG++V A++    + L+E  R R++ K Y+ LV G 
Sbjct: 120 EILKEYLNNPN--FNFVNRIDKATSGLVVGAKSLVVTRELSEEIRERKVDKKYYILVEGK 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K ++  I ++L K      D V  ++Q E+GA  ++S FKV++ + +    LE    +G
Sbjct: 178 VKRREFQIKSYLKKLE----DKVVELEQYEEGAKESLSFFKVVE-YGKNCTLLEGTLGSG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLRV    MG PI+GD KY    KG      +  +YL + Y+ +   E   ++I  P
Sbjct: 233 RTHQLRVQLASMGNPIIGDSKYG---KGK-----EKMMYLFSHYLKI---EKYGIEIDLP 281

Query: 311 LPAHMVK 317
           +P   ++
Sbjct: 282 IPKEYIQ 288


>gi|301629906|ref|XP_002944074.1| PREDICTED: ribosomal large subunit pseudouridine synthase C-like
           [Xenopus (Silurana) tropicalis]
          Length = 541

 Score =  135 bits (340), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 105/337 (31%), Positives = 160/337 (47%), Gaps = 38/337 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V+ +    RLD +       +   ++ +I+RSG+VRV++ R     R+  G  VR+
Sbjct: 27  RLVAVDAESSGQRLDNFLLRQLKGVPKTHVYRIIRSGEVRVNRGRASAGTRVAEGDQVRL 86

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIA 126
           PPV       + E+  L +      H    ++  LL ED ++   +KPAG++V GGSG++
Sbjct: 87  PPVR------VSEKVALKAG-----HPAPARAFALLLEDEQLIAIDKPAGVAVHGGSGVS 135

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    ++ Q P   L HRLD+ETSGIL+VA+ R+A   L + FR R   K Y 
Sbjct: 136 F---GVIEQLRQARPQAPFLELVHRLDRETSGILLVAKKRSALHQLQDQFRERATGKTYL 192

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK---- 239
           +LV G      + I   L K     G+  V V          A++  K+      +    
Sbjct: 193 ALVQGSWPAAHKVIDLPLHKYLLPDGERRVRVTTPENPDGMRALTLVKLRAHLPPRPLQG 252

Query: 240 ---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARY 294
                 LE+   TGRTHQ+RVH    G PIVGD KY  +F  N   P Q   +++LHA  
Sbjct: 253 LPAMTLLEVTIKTGRTHQIRVHLASQGHPIVGDDKY-GDFDLNKRLPQQGLKRMFLHAWR 311

Query: 295 MDLP-HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
           +  P  P          +P H  + +D + F +D  L
Sbjct: 312 LHPPWEPT---------MPDHRPRRFDLIAFDWDGTL 339


>gi|121611690|ref|YP_999497.1| RluA family pseudouridine synthase [Verminephrobacter eiseniae
           EF01-2]
 gi|121556330|gb|ABM60479.1| pseudouridine synthase, RluA family [Verminephrobacter eiseniae
           EF01-2]
          Length = 334

 Score =  135 bits (340), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 95/308 (30%), Positives = 150/308 (48%), Gaps = 26/308 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + V V+      RLD +       +   ++ +I+RSGQVR++K R   + R+Q+G +VR
Sbjct: 22  ARLVQVDGASAGQRLDNFLLRQLKGVPKTHVYRIIRSGQVRINKGRAHADTRVQAGDMVR 81

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGI 125
           +PP+           +I D+     +H    +   +L+ED  +   +KPAG++V GGSG+
Sbjct: 82  LPPL-----------RISDAVAQKAEHPAPAREFPILWEDEHLIAIDKPAGVAVHGGSGV 130

Query: 126 AYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++   G ++    ++   P   L HRLD+ETSGIL+VA+ R+A  HL    R R   K Y
Sbjct: 131 SF---GVIEQLRQARPDAPFLELVHRLDRETSGILLVAKKRSALTHLQAQLRARTTGKTY 187

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK--- 239
            +LV G     +  I   L K     G+  V V   ++     +I+  +    +  +   
Sbjct: 188 LALVAGAWPAHQRVIDLPLHKYLQADGERRVRVTTADDPHGMRSITLVRPRGSWPARAGL 247

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYM 295
                LE+   TGRTHQ+RVH    G  I GD KY  +F+ N     Q   +++LHA  +
Sbjct: 248 PALQLLEVTIKTGRTHQIRVHLASQGHAIAGDDKY-GDFELNKRMQKQGLKRMFLHAWRL 306

Query: 296 DLPHPEGG 303
              HP  G
Sbjct: 307 QFKHPASG 314


>gi|121634072|ref|YP_974317.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis FAM18]
 gi|120865778|emb|CAM09507.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis FAM18]
 gi|308388417|gb|ADO30737.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis alpha710]
 gi|319411317|emb|CBY91728.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C; rRNA pseudouridylate synthase C) [Neisseria
           meningitidis WUE 2594]
 gi|325133121|gb|EGC55793.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M6190]
 gi|325139089|gb|EGC61635.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis ES14902]
          Length = 330

 Score =  135 bits (340), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 96/318 (30%), Positives = 158/318 (49%), Gaps = 26/318 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  + + A+     F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSADGQSAHTV---FRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLP 312
            L HP  G  L + A LP
Sbjct: 297 HLNHPLTGEPLVLKAELP 314


>gi|289668996|ref|ZP_06490071.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 328

 Score =  135 bits (340), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 101/330 (30%), Positives = 162/330 (49%), Gaps = 31/330 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+   D +         L++ +++ED+++   NKP G++  GGSGI+
Sbjct: 76  IPPVR------VNEEG--DKAAPPPSFMARLEAAIVFEDARLLALNKPTGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+++VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRAL--RPNQSLELVHRLDRDTSGLVIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC-F 236
           K Y +L+ G   +    +   L    HIG   G   HV  Q       ++SHFK+++   
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPL----HIGLRQGGERHV--QVNAIGKPSLSHFKLLERRG 239

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHARY 294
              +C + ++  TGRTHQ+RVHA H+G P+ GD KY  A+        +   +L+LHA  
Sbjct: 240 GHSYCEVRIE--TGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAAS 297

Query: 295 MDLPHPEGGRLQI-TAPLPAHMVKTWDSLG 323
           ++     G    + +APL   + +  D LG
Sbjct: 298 LEFALDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|194015066|ref|ZP_03053683.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus pumilus ATCC 7061]
 gi|194014092|gb|EDW23657.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus pumilus ATCC 7061]
          Length = 304

 Score =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 93/322 (28%), Positives = 159/322 (49%), Gaps = 36/322 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  ++ + RLD++     P  +   +Q+ ++ G + V+ K+VK N ++Q+G  +++  
Sbjct: 6   IAVSEEQTSERLDKFLSTTEPEWSRTQVQQWVKDGLIEVNGKQVKANYKVQAGDQIKVE- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                   I E ++LD        ++ +   + YED+ + V NKP G+ V    G     
Sbjct: 65  --------IPEPEVLDVE------AEPMDLDIYYEDADVLVVNKPRGMVVHPAPGHVSGT 110

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y
Sbjct: 111 LVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRKY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYV--HVVKQNEKGANYAISHFKVIDCFAQKFC 241
            ++V GI ++    I       + IG D      +   ++ A  A++HF VI+ F Q F 
Sbjct: 171 TAVVHGIIQHDTGTI------DAPIGRDKKDRQSMTVTKESAKQAVTHFDVIERF-QDFT 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E +  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   HP 
Sbjct: 224 VVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPRKTVDF-----NGQLLHAGVLGFDHPR 278

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++ TAP+PA M    DSL
Sbjct: 279 TGEYIEFTAPIPADMQAFIDSL 300


>gi|254805759|ref|YP_003083980.1| ribosomal large subunit pseudouridine synthase [Neisseria
           meningitidis alpha14]
 gi|254669301|emb|CBA08284.1| ribosomal large subunit pseudouridine synthase [Neisseria
           meningitidis alpha14]
          Length = 330

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 96/323 (29%), Positives = 159/323 (49%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +              +YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFEA---------VYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  + + A+     F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSADGQSAHTV---FRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVK 317
            L HP  G  L + A LP  + +
Sbjct: 297 HLNHPLTGEPLVLKAELPPDLAQ 319


>gi|325921639|ref|ZP_08183476.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           gardneri ATCC 19865]
 gi|325547873|gb|EGD18890.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           gardneri ATCC 19865]
          Length = 328

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 102/331 (30%), Positives = 161/331 (48%), Gaps = 33/331 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPQDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+   D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPPVR------VNEEG--DKAAPPSAFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   +    R       R I 
Sbjct: 128 FGAIETLRAL--RPNQTLELVHRLDRDTSGLLIVAKKRSALTEMQALMREDDRVQGRGIT 185

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC- 235
           K Y +L+ G +P       A       HIG   G   HV  Q       ++SHFK+++  
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFKLLERR 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHAR 293
               +C + ++  TGRTHQ+RVHA H+G P+ GD KY  A         +   +L+LHA 
Sbjct: 239 GGHSYCEVRIE--TGRTHQIRVHAQHLGHPVAGDDKYGEAEVNKRLRDQLGLKRLFLHAA 296

Query: 294 YMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
            ++     G     + APL   +    D LG
Sbjct: 297 SLEFALDAGKAPYVLNAPLAPELADALDRLG 327


>gi|91775675|ref|YP_545431.1| pseudouridine synthase, RluD [Methylobacillus flagellatus KT]
 gi|91709662|gb|ABE49590.1| Pseudouridine synthase, RluD [Methylobacillus flagellatus KT]
          Length = 326

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 104/324 (32%), Positives = 164/324 (50%), Gaps = 28/324 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + ++   E  R+D +       +   ++ +ILRSG+VRV+ KRV  + ++  G  VR
Sbjct: 16  VNLLTIDEASEGQRVDNFLAKILKGVPKSHIYRILRSGEVRVNSKRVDSSCKLNLGDQVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A             SV   + S F  +I+ +ED  + V +KPAG +V GGSGI+
Sbjct: 76  VPPVRMAQPQA--------ESVARPQASRFEGAII-FEDEALLVIDKPAGFAVHGGSGIS 126

Query: 127 YHIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             +   L+       ++P      L HRLD+ETSG+L++A+ R A  +L ++ R  +  K
Sbjct: 127 RGVIEQLRL------ERPHAKFLELVHRLDRETSGVLLLAKKRVALVNLHDAIRNNQTDK 180

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y  LV G   ++K  +   L K     G+    V+   + ++      K +     +F 
Sbjct: 181 RYLVLVHGKWTDQKRRVKLPLHKFVLPSGERRVAVQDGGQNSDTIFYLRKPLG----EFT 236

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPH 299
            LE Q  TGRTHQLRV   H+G PI GD KY  +F  N +   +   +++LH+   +L H
Sbjct: 237 LLEAQLVTGRTHQLRVQLSHLGFPIAGDDKY-GDFALNKSLQKRGLKRMFLHSAETNLRH 295

Query: 300 P-EGGRLQITAPLPAHMVKTWDSL 322
           P  G +L++ APLP  + K  + L
Sbjct: 296 PVSGEKLKLIAPLPDELNKFIEML 319


>gi|254491706|ref|ZP_05104885.1| pseudouridine synthase, RluA family [Methylophaga thiooxidans
           DMS010]
 gi|224463184|gb|EEF79454.1| pseudouridine synthase, RluA family [Methylophaga thiooxydans
           DMS010]
          Length = 318

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 94/313 (30%), Positives = 160/313 (51%), Gaps = 19/313 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ +   +   R+D +       +    + + +R G+VRV+K R+K   +IQ+G +VR
Sbjct: 11  VQFIEISPSQAGQRIDNFLLTLEKGVPKSRIYRAIRKGEVRVNKGRIKQTYKIQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+  A       ++   + V+ +     L+ I+ +ED  + V NKP+G++V  GS I 
Sbjct: 71  VPPLRVA-------EREAPTHVSESLRQQLLQDII-FEDDSMLVLNKPSGLAVHAGSQIQ 122

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               G ++++   K +     L HRLD++TSG L++A++R +  +L +     +I K Y 
Sbjct: 123 V---GVIEAFRIIKPELAFLELVHRLDRDTSGCLLLAKSRDSLLNLQQQMLSDQIDKRYL 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L+ GI  N +E +   LLK +   G+   +VK    G        +  D    +    E
Sbjct: 180 TLLKGILPNAEELVEQPLLKNTVSSGE--RMVKVTPDGKRAKTLFIRQQDLSLAQLT--E 235

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++ +TGRTHQ+RVHA     P+ GD KY    F     S    +L+LHA  + + HP  G
Sbjct: 236 VKLYTGRTHQIRVHAAWTQHPVAGDDKYGDREFNKTLKSFGLKRLFLHAWRLGIRHPVSG 295

Query: 304 R-LQITAPLPAHM 315
             +Q+ APLP  +
Sbjct: 296 EPMQLEAPLPTAL 308


>gi|167836421|ref|ZP_02463304.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis MSMB43]
          Length = 344

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 98/321 (30%), Positives = 149/321 (46%), Gaps = 34/321 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRVD    K    +  G  + +      L  ++ 
Sbjct: 18  RLDKALAQLFPEFSRSRLQQWIESDRVRVDGAPAKIRQPVPLGATIEL------LPDLLP 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 72  EQ--------LAFTPEPVPLSIVYEDEAIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 123

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG   +K  
Sbjct: 124 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWGQMPDKGT 183

Query: 197 CIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTG 250
             A        IG D      +          A +HF+ +D      Q    +     TG
Sbjct: 184 IDAP-------IGRDPRERTRMAVVTGAAGKPARTHFRAVDTTLWERQPVSAIHCDLETG 236

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQ 306
           RTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q
Sbjct: 237 RTHQIRVHCAHVGHPLLGDPVYGRARGKRSVTPLPGGFARQALHAWRLGLVHPATGRTMQ 296

Query: 307 ITAPLPAHMVKTWDSLGFKYD 327
             APLPA +    ++LGF  D
Sbjct: 297 WRAPLPADLAALVEALGFGAD 317


>gi|325129115|gb|EGC51964.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis N1568]
          Length = 330

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 96/318 (30%), Positives = 157/318 (49%), Gaps = 26/318 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +              +YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFEA---------VYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  + + A+     F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSADGQSAHTV---FRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLP 312
            L HP  G  L + A LP
Sbjct: 297 HLNHPLTGEPLVLKAELP 314


>gi|167581726|ref|ZP_02374600.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis TXDOH]
          Length = 389

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 97/318 (30%), Positives = 150/318 (47%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRVD    K    +  G  + +      L  ++ 
Sbjct: 63  RLDKALAQLFPEFSRSRLQQWIESERVRVDGAPAKIRQAVPLGATIEL------LPDLLP 116

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 117 EQ--------LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 168

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG  +   E
Sbjct: 169 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWG--QMPDE 226

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 227 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTH 284

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 285 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPATGRSMQWRA 344

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 345 PLPADLAALVDALGFGAD 362


>gi|167619842|ref|ZP_02388473.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis Bt4]
          Length = 385

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 97/318 (30%), Positives = 150/318 (47%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRVD    K    +  G  + +      L  ++ 
Sbjct: 59  RLDKALAQLFPEFSRSRLQQWIESERVRVDGAPAKIRQAVPLGATIEL------LPDLLP 112

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 113 EQ--------LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 164

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG  +   E
Sbjct: 165 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWG--QMPDE 222

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 223 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTH 280

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 281 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPATGRSMQWRA 340

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 341 PLPADLAALVDALGFGAD 358


>gi|194366450|ref|YP_002029060.1| RluA family pseudouridine synthase [Stenotrophomonas maltophilia
           R551-3]
 gi|194349254|gb|ACF52377.1| pseudouridine synthase, RluA family [Stenotrophomonas maltophilia
           R551-3]
          Length = 324

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 103/334 (30%), Positives = 160/334 (47%), Gaps = 44/334 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   ++++G  VR
Sbjct: 16  VRMITVPADRAGQRLDNFLLGQLKGAPRSLVYKLVRSGQVRVNGGRAKAERKLEAGDEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E+   D +         L+  +++ED+++   NKP G++  GGSGI+
Sbjct: 76  VPPVR------LSEEG--DKAGPPEAFMRRLEQAIVFEDARLLALNKPTGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR---IQKIY 183
           +     L++     GQ   L HRLD++TSG+L+VA+ R+A   L    R      I+K Y
Sbjct: 128 FGAIETLRAL--RPGQTLELVHRLDRDTSGLLIVAKKRSALSELQALLREDHGAGIRKRY 185

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC-FAQK 239
            +L+ G   +    +   L    H+G   G   HV  Q       +ISHF+V++      
Sbjct: 186 LTLLAGRMPDGVMTVDAPL----HVGLRQGGERHV--QVNAIGKESISHFRVLERRGGHS 239

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK----------LY 289
           +C + ++  TGRTHQ+RVHA H+G P+ GD KY          P  NK          L+
Sbjct: 240 YCEVRIE--TGRTHQIRVHAQHLGHPVAGDDKYG--------DPAVNKRLREQIGLKRLF 289

Query: 290 LHARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
           LHA  ++     G    +  APL   +V+  D L
Sbjct: 290 LHAASLEFALDAGKTPYVLNAPLADELVEALDRL 323


>gi|325203319|gb|ADY98772.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M01-240355]
 gi|325205289|gb|ADZ00742.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M04-240196]
          Length = 330

 Score =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 95/323 (29%), Positives = 160/323 (49%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  + + A+     F+ ++ F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSADGQSAHTV---FRALNRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVK 317
            L HP  G  L + A LP  + +
Sbjct: 297 HLNHPLTGEPLVLKAELPPDLAQ 319


>gi|71899934|ref|ZP_00682081.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|71730297|gb|EAO32381.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
          Length = 330

 Score =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 102/330 (30%), Positives = 167/330 (50%), Gaps = 31/330 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ VVV  +    RLD +  +    +    + K++RSGQVRV+  RVK   ++  G  VR
Sbjct: 18  VRIVVVPAEHSGQRLDNFLLSKLKGVPRSLIYKLVRSGQVRVNGGRVKAERKLDGGDEVR 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      +I+++ I+  S         +++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 78  LPPL-----RLIQDRAIVAPSAAFLAR---MEAAIVFEDARLLALNKPSGMASHGGSGIS 129

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--------RR 178
           Y +   ++  +    Q+  L HRLD++TSG+L++A+ RAA   L    R         R 
Sbjct: 130 YGVIEAMR--ILRPKQELELVHRLDRDTSGLLIMAKKRAALIELQALMREASVNGKEGRG 187

Query: 179 IQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CF 236
           I K Y +L+ G +P       A   +   H G  +V V    +     + S F++++   
Sbjct: 188 IAKRYLTLLSGRMPNGVMSVDAPLHINLRHGGERHVRVHHDGKP----SKSRFRLLERRG 243

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHAR 293
            Q +C  E+   TGRTHQ+RVHA H+G P+ GD KY     N K      +Q +L+LHA 
Sbjct: 244 GQSYC--EVLIETGRTHQIRVHAQHLGHPVTGDDKYGDQEVNRKLRDQIGLQ-RLFLHAV 300

Query: 294 YMDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
            ++     G    +  APL   +V   D L
Sbjct: 301 SLEFALDAGSTPYVLNAPLAEDLVAALDRL 330


>gi|33597841|ref|NP_885484.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           parapertussis 12822]
 gi|33602743|ref|NP_890303.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           bronchiseptica RB50]
 gi|33574270|emb|CAE38602.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           parapertussis]
 gi|33577185|emb|CAE35742.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           bronchiseptica RB50]
          Length = 321

 Score =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 96/319 (30%), Positives = 163/319 (51%), Gaps = 22/319 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  + +  R+D +       +   ++ K +R G+VRV+K R+    R+  G VVR
Sbjct: 19  VRMLAIGPEHDGQRIDNFLLRLCKGVPKSHIYKAIRGGEVRVNKGRISAEYRLVEGDVVR 78

Query: 67  IPPVINALNHIIKEQKILD-SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PP+           ++ D  +      ++F    ++YED  + V +KPAG++V GGSG+
Sbjct: 79  VPPL-----------RLPDPGAARPVPGAEF---PVVYEDDALLVIDKPAGVAVHGGSGV 124

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L++    + +   L HRLD+ETSG+L++A+ R+A   L    R  +  K Y +
Sbjct: 125 SFGVIEQLRA-ARPQARFLELVHRLDRETSGLLMLAKKRSALLALHAMLREGKGDKHYLA 183

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   N ++ I   L K +   G+    V Q  + A+  ++  K    ++     ++ 
Sbjct: 184 LVEGDWVNDRQHIRLALTKWTTQSGERRVRVDQAGQAAHTIVTLRKRFGGYS----LVDA 239

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
           +  TGRTHQ+RVH    G PIVGD KY  +  +  F      +++LHA  + LPHP  G 
Sbjct: 240 ELRTGRTHQIRVHLASSGFPIVGDDKYGTDETRAAFARRGFGRMFLHAHQLTLPHPLTGE 299

Query: 304 RLQITAPLPAHMVKTWDSL 322
            L++TA LP   +K    L
Sbjct: 300 TLRLTADLPPACLKLLKQL 318


>gi|226501200|ref|NP_001151637.1| LOC100285271 [Zea mays]
 gi|195648278|gb|ACG43607.1| RNA binding protein [Zea mays]
          Length = 439

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 95/316 (30%), Positives = 146/316 (46%), Gaps = 41/316 (12%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVR----------VDKKRVKFNNRIQSG 62
           E    N    RW ++  PH+    +QK+ R  +V+           D   ++   R  S 
Sbjct: 75  EGACSNATAIRWVRHCCPHVPASLVQKLFRLRKVKKNLVTADTSSTDSITLQLRLRRVSA 134

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHS--DFLKSILLYEDSKIYVFNKPAGISVQ 120
           +   +P  I  L   I+E  + + +      +  DFL+ + +Y+D  I V NKP G+ VQ
Sbjct: 135 KDELVPGDILFLPVNIQESSVTEKTKKFGNKNEIDFLRDLEIYKDRAIIVLNKPPGMPVQ 194

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-- 178
           GG GI   ID     + +   + PRL HRLD++ SG+LV+ RT+ +A  +   FR +   
Sbjct: 195 GGVGIKNSIDILAPMFENGSSEVPRLVHRLDRDCSGVLVLGRTQFSASLMHAIFREKTAD 254

Query: 179 ---------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV---KQNEKGANYA 226
                    +Q+ Y +LV G P++ K  ++  L K     G    +      N      A
Sbjct: 255 ALGDGTQQVLQRKYVALVIGRPRHPKGLLSAPLAKVVLQDGRSERLTVCAGSNTASVQDA 314

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNFTSPIQ 285
           ++ ++VI+ F Q + WLE+ P TGR HQLRVH    +G PIVGD+KY             
Sbjct: 315 LTEYRVIESFPQGYTWLELFPRTGRKHQLRVHCAEVLGTPIVGDYKYGRQ---------- 364

Query: 286 NKLYLHARYMDLPHPE 301
                H  +M LP P+
Sbjct: 365 ----AHQNWMPLPMPQ 376


>gi|59802102|ref|YP_208814.1| RluC [Neisseria gonorrhoeae FA 1090]
 gi|194099977|ref|YP_002003116.1| RluC [Neisseria gonorrhoeae NCCP11945]
 gi|239997984|ref|ZP_04717908.1| RluC [Neisseria gonorrhoeae 35/02]
 gi|240015038|ref|ZP_04721951.1| RluC [Neisseria gonorrhoeae DGI18]
 gi|240113908|ref|ZP_04728398.1| RluC [Neisseria gonorrhoeae MS11]
 gi|240116640|ref|ZP_04730702.1| RluC [Neisseria gonorrhoeae PID18]
 gi|240122106|ref|ZP_04735068.1| RluC [Neisseria gonorrhoeae PID24-1]
 gi|240124728|ref|ZP_04737614.1| RluC [Neisseria gonorrhoeae SK-92-679]
 gi|240129077|ref|ZP_04741738.1| RluC [Neisseria gonorrhoeae SK-93-1035]
 gi|254494662|ref|ZP_05107833.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae 1291]
 gi|260439599|ref|ZP_05793415.1| RluC [Neisseria gonorrhoeae DGI2]
 gi|268593835|ref|ZP_06128002.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae 35/02]
 gi|268599970|ref|ZP_06134137.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae MS11]
 gi|268602307|ref|ZP_06136474.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae PID18]
 gi|268683306|ref|ZP_06150168.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae SK-92-679]
 gi|268687455|ref|ZP_06154317.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae SK-93-1035]
 gi|291042839|ref|ZP_06568580.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae DGI2]
 gi|293398142|ref|ZP_06642347.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae F62]
 gi|59718997|gb|AAW90402.1| putative ribosomal large subunit pseudouridine synthase C
           [Neisseria gonorrhoeae FA 1090]
 gi|193935267|gb|ACF31091.1| RluC [Neisseria gonorrhoeae NCCP11945]
 gi|226513702|gb|EEH63047.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae 1291]
 gi|268547224|gb|EEZ42642.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae 35/02]
 gi|268584101|gb|EEZ48777.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae MS11]
 gi|268586438|gb|EEZ51114.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae PID18]
 gi|268623590|gb|EEZ55990.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae SK-92-679]
 gi|268627739|gb|EEZ60139.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae SK-93-1035]
 gi|291013273|gb|EFE05239.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae DGI2]
 gi|291611405|gb|EFF40475.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae F62]
 gi|317165428|gb|ADV08969.1| RluC [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 330

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 95/308 (30%), Positives = 154/308 (50%), Gaps = 25/308 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +    + +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKGYIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V NKP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFE---------VVYEDDALLVVNKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K  + G     +V+ +E G + A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFK--YTGAQGEKMVRVSEDGQS-AHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGG 303
            L HP  G
Sbjct: 297 HLNHPLTG 304


>gi|260893452|ref|YP_003239549.1| pseudouridine synthase, RluA family [Ammonifex degensii KC4]
 gi|260865593|gb|ACX52699.1| pseudouridine synthase, RluA family [Ammonifex degensii KC4]
          Length = 331

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 96/332 (28%), Positives = 156/332 (46%), Gaps = 60/332 (18%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE +E  +RLD +   + P  +   LQ+++  G V+V  ++VK + +++ G+ + +    
Sbjct: 9   VEEEEAGVRLDVYLARNLPENSRSYLQRLINEGYVQVGGRKVKPSYKVKPGEEILV---- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------- 124
                       L  +  L    + +   ++YED  + V NKP G+ V  G+G       
Sbjct: 65  -----------FLPPAETLEVEPEPIPLEIIYEDEDLLVVNKPRGMVVHPGAGHKRGTLV 113

Query: 125 --IAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             + YH      I+G L+         P + HRLD++TSG+L+VA+  AA   L+   + 
Sbjct: 114 NALLYHCRSLSGINGVLR---------PGIVHRLDKDTSGLLMVAKNDAAHLSLSAQLKE 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           RR+ K YW+LV+G  K  +  I   + +          V      G   A++H++V++ F
Sbjct: 165 RRVLKEYWALVYGEVKPAQGRIEAPIGRHPRYRQKMAVVA-----GGRPAVTHYEVVEYF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLH 291
              +  L ++P TGRTHQ+RVH  ++G PIVGD KY         +G F         LH
Sbjct: 220 P-GYTLLRVRPETGRTHQIRVHLHYLGHPIVGDLKYGPARPHLGLEGQF---------LH 269

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           A  +   HP  G  L+  APLP  + +    L
Sbjct: 270 AGVLGFTHPRTGEFLRFEAPLPPELERVLAEL 301


>gi|258544039|ref|ZP_05704273.1| ribosomal large subunit pseudouridine synthase C [Cardiobacterium
           hominis ATCC 15826]
 gi|258520667|gb|EEV89526.1| ribosomal large subunit pseudouridine synthase C [Cardiobacterium
           hominis ATCC 15826]
          Length = 311

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 97/315 (30%), Positives = 154/315 (48%), Gaps = 25/315 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           ++ V ++ V  D+   RLD + +  YP +    + ++LR G+VRV+KKR K   R+ +G 
Sbjct: 3   VSRVHFLTVTADDAGQRLDNFLRKRYPALPKSRIYQMLRRGEVRVNKKRAKPELRVAAGD 62

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP+ +A       Q +           + +   +LYED    + NKPAGI+V GGS
Sbjct: 63  ELRLPPLADATR---PPQDV------PAFWCERIAGAVLYEDDDFLMLNKPAGIAVHGGS 113

Query: 124 GIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              Y  ID   + W     +   L HRLD++TSG+LV+ + RAA        +   ++K 
Sbjct: 114 EQPYGVIDAVRQVWGAGYAE---LAHRLDRDTSGVLVLGKNRAALAGFQALMQAGGVEKR 170

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  LV G        +   L K    GG+ + V   + + A    + F+++  FA     
Sbjct: 171 YLCLVDGHWNPATREVRLHLAKAQLQGGERMVVGAADGQEAR---TRFRLLQTFADA-SL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK----LYLHARYMDLP 298
           LE    TGRTHQ+RV   H G  I GD KY    K +F   ++ +    ++LHA ++   
Sbjct: 227 LEATLDTGRTHQIRVSVQHRGHGIAGDDKYG---KRDFNRAMRKRGYKGMFLHAAHIAFA 283

Query: 299 HPEGGRLQITAPLPA 313
           + +   + + APLPA
Sbjct: 284 Y-DARAIAVEAPLPA 297


>gi|240017486|ref|ZP_04724026.1| RluC [Neisseria gonorrhoeae FA6140]
 gi|240118863|ref|ZP_04732925.1| RluC [Neisseria gonorrhoeae PID1]
 gi|268604570|ref|ZP_06138737.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae PID1]
 gi|268588701|gb|EEZ53377.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae PID1]
          Length = 330

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 95/308 (30%), Positives = 154/308 (50%), Gaps = 25/308 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +    + +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKGYIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V NKP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFE---------VVYEDDALLVVNKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K  + G     +V+ +E G + A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFK--YTGAQGEKMVRVSEDGQS-AHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGG 303
            L HP  G
Sbjct: 297 HLNHPLTG 304


>gi|71275230|ref|ZP_00651517.1| Pseudouridine synthase, RluD [Xylella fastidiosa Dixon]
 gi|71899549|ref|ZP_00681705.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|170731225|ref|YP_001776658.1| pseudouridylate synthase [Xylella fastidiosa M12]
 gi|71164039|gb|EAO13754.1| Pseudouridine synthase, RluD [Xylella fastidiosa Dixon]
 gi|71730678|gb|EAO32753.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|167966018|gb|ACA13028.1| pseudouridylate synthase [Xylella fastidiosa M12]
          Length = 330

 Score =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 101/330 (30%), Positives = 167/330 (50%), Gaps = 31/330 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ VVV  +    RLD +  +    +    + K++RSGQVRV+  RVK   ++  G  VR
Sbjct: 18  VRIVVVPAEHSGQRLDNFLLSKLKGVPRSLIYKLVRSGQVRVNGGRVKAERKLDGGDEVR 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      +I+++ I+  S         +++ +++ED+++   NKP+G++  GGSG++
Sbjct: 78  LPPL-----RLIQDRAIVAPSAAFLAR---MEAAIVFEDARLLALNKPSGMASHGGSGVS 129

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--------RR 178
           Y +   ++  +    Q+  L HRLD++TSG+L++A+ RAA   L    R         R 
Sbjct: 130 YGVIEAMR--ILRPKQELELVHRLDRDTSGLLIMAKKRAALIELQALMREASVNGKEGRG 187

Query: 179 IQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CF 236
           I K Y +L+ G +P       A   +   H G  +V V    +     + S F++++   
Sbjct: 188 IAKRYLTLLSGRMPNGVMSVDAPLHINLRHGGERHVRVHHDGKP----SKSRFRLLERRG 243

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHAR 293
            Q +C  E+   TGRTHQ+RVHA H+G P+ GD KY     N K      +Q +L+LHA 
Sbjct: 244 GQSYC--EVLIETGRTHQIRVHAQHLGHPVTGDDKYGDQEVNRKLRDQIGLQ-RLFLHAV 300

Query: 294 YMDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
            ++     G    +  APL   +V   D L
Sbjct: 301 SLEFALDAGSTPYVLNAPLAEDLVAALDRL 330


>gi|240124400|ref|ZP_04737356.1| RluC [Neisseria gonorrhoeae PID332]
 gi|268683027|ref|ZP_06149889.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae PID332]
 gi|268623311|gb|EEZ55711.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae PID332]
          Length = 330

 Score =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 95/308 (30%), Positives = 154/308 (50%), Gaps = 25/308 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +    + +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKGYIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V NKP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFE---------VVYEDDALLVVNKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K  + G     +V+ +E G + A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFK--YTGAQGEKMVRVSEDGQS-AHTVFRVLSHFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGG 303
            L HP  G
Sbjct: 297 HLNHPLTG 304


>gi|240081627|ref|ZP_04726170.1| RluC [Neisseria gonorrhoeae FA19]
 gi|268597722|ref|ZP_06131889.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae FA19]
 gi|268551510|gb|EEZ46529.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae FA19]
          Length = 330

 Score =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 95/308 (30%), Positives = 153/308 (49%), Gaps = 25/308 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +    + +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKGYIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V NKP+G++V GGSG+ 
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFE---------VVYEDDALLVVNKPSGVAVHGGSGVG 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K  + G     +V+ +E G + A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFK--YTGAQGEKMVRVSEDGQS-AHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGG 303
            L HP  G
Sbjct: 297 HLNHPLTG 304


>gi|285018394|ref|YP_003376105.1| pseudouridine synthase (rna-uridine isomerase) (rna pseudouridylate
           synthase) protein [Xanthomonas albilineans GPE PC73]
 gi|283473612|emb|CBA16115.1| probable pseudouridine synthase (rna-uridine isomerase) (rna
           pseudouridylate synthase) protein [Xanthomonas
           albilineans]
          Length = 330

 Score =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 100/333 (30%), Positives = 164/333 (49%), Gaps = 33/333 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + V  D    R+D +            + K++RSGQVRV+  R K   +++ G  
Sbjct: 16  SAVRILKVPEDRAGQRVDNFLLGQLKGAPRSLIYKLMRSGQVRVNGGRTKAERKLEVGDE 75

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV        + Q+  + +       + L++ ++YED+++   NKP+G++  GGSG
Sbjct: 76  VRIPPV--------RLQEEGEKTAPPAAFMERLEAAIVYEDARLLALNKPSGVASHGGSG 127

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RR 178
           I++     L++   +  Q   L HRLD++TSG+L+VA+ R+A   L    R       R 
Sbjct: 128 ISFGAIETLRALRPN--QTLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDQVQGRG 185

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC 235
           I K Y +L+ G   +    +   L    HIG   G   HV  Q       ++SHF++++ 
Sbjct: 186 IGKRYLTLLVGRLPDGTMTVEVPL----HIGLRQGGERHV--QVHAAGKPSLSHFRMLER 239

Query: 236 -FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHA 292
                +C + ++  TGRTHQ+RVHA H+G P+ GD KY            I   +L+LHA
Sbjct: 240 RGGHSYCEVRIE--TGRTHQIRVHAQHLGYPVAGDDKYGDPEVNKRLREHIGLKRLFLHA 297

Query: 293 RYMDLPHPEGGRLQ--ITAPLPAHMVKTWDSLG 323
             ++    +GG+    + APL   + +    LG
Sbjct: 298 ASLEFTL-DGGKAPYLLNAPLADELSEALSRLG 329


>gi|304389009|ref|ZP_07371056.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis ATCC 13091]
 gi|304337143|gb|EFM03330.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis ATCC 13091]
 gi|325131027|gb|EGC53753.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis OX99.30304]
 gi|325135123|gb|EGC57750.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M13399]
 gi|325137030|gb|EGC59626.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M0579]
 gi|325202968|gb|ADY98422.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M01-240149]
 gi|325207234|gb|ADZ02686.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis NZ-05/33]
          Length = 330

 Score =  133 bits (335), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 95/323 (29%), Positives = 159/323 (49%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  + + A+     F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSADGQSAHTV---FRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVK 317
            L HP  G  L +   LP  + +
Sbjct: 297 HLNHPLTGEPLVLKVGLPPDLAQ 319


>gi|284052171|ref|ZP_06382381.1| ribosomal large subunit pseudouridine synthase D [Arthrospira
           platensis str. Paraca]
 gi|291568935|dbj|BAI91207.1| probable pseudouridine synthase [Arthrospira platensis NIES-39]
          Length = 308

 Score =  133 bits (335), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 98/324 (30%), Positives = 154/324 (47%), Gaps = 41/324 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-------KKRVKFNNRI 59
           ++ +  E D EN RLDRW       ++   LQ ++ SG V V+       K  V+  +RI
Sbjct: 3   IELICEEQDGENQRLDRWLSERVQQLSRSRLQALISSGHVWVNNSPCTSKKATVQIGDRI 62

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q    V IPP I        E K  +  +++           LYED ++ + NKPAG+ V
Sbjct: 63  Q----VEIPPAIPL------ELKATNIPLDI-----------LYEDEELLIINKPAGLVV 101

Query: 120 QGGSGIAYH--IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G A    ++  L       G    Q+P + HRLD++T+G + +A+T  A QHL   
Sbjct: 102 HPAPGHANDTLVNALLAHCETLAGIGGVQRPGIVHRLDKDTTGAIAIAKTDHAHQHLQAQ 161

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + +  ++ Y  +++G+PK     I +  + + H     + +V +++ G   AI+ ++V 
Sbjct: 162 IQAKTARRQYLGIIYGVPKTTSGVI-DQPIGRHHSDRKKMAIVPEHQ-GGRSAITRWQVQ 219

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           +     +  +E +  TGRTHQ+RVH+  +G PIVGD  Y          P Q    LHA 
Sbjct: 220 ERLG-NYTLIEFELETGRTHQIRVHSASIGHPIVGDRVYGKGRSVGVNLPGQ---ALHAW 275

Query: 294 YMDLPHPEGGRL-QITAPLPAHMV 316
            + L HP  G L +  APLP  M 
Sbjct: 276 KLTLQHPTSGELIEAIAPLPHTMT 299


>gi|94499595|ref|ZP_01306132.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [Oceanobacter sp. RED65]
 gi|94428349|gb|EAT13322.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [Oceanobacter sp. RED65]
          Length = 318

 Score =  133 bits (335), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 104/326 (31%), Positives = 172/326 (52%), Gaps = 22/326 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  V  D    R+D +  +         + +I+R G+VRV+K R+K   +++ G VVR
Sbjct: 9   VQFEEVTADYVGQRIDNFLMSRIKGAPKSLVYRIIRKGEVRVNKGRIKPEYKVKLGDVVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV        K +   D++      ++ ++  +L+ED      NKP G++V GGSGI+
Sbjct: 69  IPPV--------KVKAEGDAAPISKDMAEGIEQSILFEDDYFLAVNKPRGMAVHGGSGIS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF-RMRRIQKIYWS 185
             +   L++ +  K ++  L HRLD++TSG+++VA+ R A     +   R + +QK Y +
Sbjct: 121 LGLIEVLRN-LRPKAKRLELVHRLDRDTSGVILVAKRRTALVAFHKMLQRKQGMQKRYLA 179

Query: 186 LVWGI-PKNKKECIANWLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           LV+G  PK+ K+      LKK+ +  G+ +  V Q+ K ++   S    I+   + +  +
Sbjct: 180 LVYGNWPKHLKDV--EVPLKKNELKSGERLVKVAQDGKPSHTRYS----IERKFKGYTLV 233

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKLYLHARYMDLPHPE 301
             +P TGRTHQ+RVH    G  IVGD KY  +   +G      + +L+LHA+ +   HPE
Sbjct: 234 NAEPVTGRTHQIRVHCQFSGHNIVGDEKYATDEELQGARQQGAR-RLFLHAQSLRFKHPE 292

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFKY 326
            G ++ I APL     +   SL  K+
Sbjct: 293 TGEKMTIQAPLDEAFEQFLSSLDAKH 318


>gi|328542559|ref|YP_004302668.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [polymorphum gilvum SL003B-26A1]
 gi|326412305|gb|ADZ69368.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Polymorphum gilvum SL003B-26A1]
          Length = 346

 Score =  133 bits (334), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 99/329 (30%), Positives = 159/329 (48%), Gaps = 48/329 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPV 70
           V  ++   RLD     H   ++   +Q ++RSG+V VD  + V+   R+  G  +     
Sbjct: 25  VGAEDAGKRLDAVLAAHLADLSRTRVQALIRSGEVTVDGGKIVEPKYRVNEGATL----- 79

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
             AL         L          + +  +++YED  + V +KPAG+ V  G+G      
Sbjct: 80  --ALG--------LPEPEEAEPKGEDIPLVVVYEDDDLIVIDKPAGLVVHPGAGNWTGTL 129

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRI 179
           ++  ++   DS       ++P + HRLD+ETSG+LVVA+T AA + L+E F    R   +
Sbjct: 130 VNALIRHCGDSLSGIGGVRRPGIVHRLDKETSGLLVVAKTDAAHKGLSEQFADHGRSGPL 189

Query: 180 QKIYWSLVWGIPKNKKECI-ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++ Y +LVWG P   +  + AN  L +S      + VV+    G  +A++H++V++ F  
Sbjct: 190 ERAYAALVWGAPATLRGTVDAN--LARSDANRQKISVVRN---GGRHAVTHWQVLERFGP 244

Query: 239 K-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQN---- 286
                    LE +  TGRTHQ+RVH  H+G P++GD  Y A F+     F  PI+     
Sbjct: 245 ADQPAVASLLECRLETGRTHQIRVHMAHIGHPLIGDQIYGAGFRTKANRFPEPIRTHVGG 304

Query: 287 --KLYLHARYMDLPHPEGGR-LQITAPLP 312
             +  LHA  +   HP  G  L+  +P P
Sbjct: 305 FPRQALHAGLLAFAHPRTGETLRFESPYP 333


>gi|224105621|ref|XP_002313876.1| predicted protein [Populus trichocarpa]
 gi|222850284|gb|EEE87831.1| predicted protein [Populus trichocarpa]
          Length = 324

 Score =  133 bits (334), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 99/295 (33%), Positives = 141/295 (47%), Gaps = 68/295 (23%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQE 153
           +F++ + LY+D+ I V NKP G+ VQGG GI   +D    S   S   + PRL HRLD++
Sbjct: 31  NFIRGLELYKDAAIIVVNKPPGMPVQGGIGIKRSLDELSASCFSSDYSEPPRLVHRLDRD 90

Query: 154 TSGILVVARTRAAAQHLTESFR-------------MRRI-QKIYWSLVWGIPKNKKECIA 199
            SGILV+ RT+ +A  L   FR              RRI Q+ YW+LV G P+  K  I+
Sbjct: 91  CSGILVMGRTQTSATVLHAIFREKTLAASNDDVGNKRRILQRKYWALVIGSPRRPKGLIS 150

Query: 200 NWLLKKSHIGG--DYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             L K     G  D + VV+ ++   + +A++ ++VI+  +  F WLE+ P TGR HQLR
Sbjct: 151 APLGKVVVDNGKSDRITVVENSQNLSSQHAVTQYRVIES-SHGFTWLELSPLTGRKHQLR 209

Query: 257 VHALH-MGCPIVGDHKYC------------ANFKGNFT--------------------SP 283
           VH    +G PIVGD+KY             +N + N                      S 
Sbjct: 210 VHCAEVLGTPIVGDYKYAWQAHRNWKQLQWSNIEDNSNDKSLSEKILPFALDLDSGSISE 269

Query: 284 IQNKLYLHARYMDLPH----------------PEGGRLQITAPLPAHMVKTWDSL 322
              +L+LH + M LP                  +   L+  APLP +M K+WD L
Sbjct: 270 KHPRLHLHCKQMVLPDVSKALQDVQLSSDYDFSQLASLKFDAPLPPYMKKSWDIL 324


>gi|83644955|ref|YP_433390.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83632998|gb|ABC28965.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 315

 Score =  133 bits (334), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 92/299 (30%), Positives = 152/299 (50%), Gaps = 19/299 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + V +++  +  RLD +       +    + KI+R G+VR++K R K   +++ G  VR
Sbjct: 12  ARVVTIDSGSDGQRLDNFLVRELKGVPKGKIYKIIRKGEVRINKGRCKPETKLKDGDQVR 71

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  +    + E  I    + L   S       L+E+ ++ + NKP G++V GGSG++
Sbjct: 72  IPPIRVSEGDSL-EPVIPAGLIELVSQS------TLFENDELLIINKPCGVAVHGGSGVS 124

Query: 127 YHIDGFLKSWVDSKGQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           + +   L++      Q  R   L HRLD++TSG+LV+A+ R A     +  +  R++KIY
Sbjct: 125 FGVIEILRA----ARQDIRFLELAHRLDRDTSGVLVLAKKRRALVQFHDMLKTGRVEKIY 180

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            + V G     K  I   L K     G+ +  V ++ K +    + F+V+   A +   +
Sbjct: 181 HAWVCGKWPKHKSVITAPLKKNVLRSGERMVNVSEDGKPSE---TRFRVLYSGAGR-TLV 236

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPE 301
           E QP TGRTHQ+RVHA   G PI+GD KYC +        +   +L LHA  + +  P+
Sbjct: 237 EAQPITGRTHQIRVHAKFAGHPIIGDDKYCDSETNRVYRDMGVKRLCLHAYSLRMSWPD 295


>gi|163856053|ref|YP_001630351.1| ribosomal large subunit pseudouridine synthase C [Bordetella petrii
           DSM 12804]
 gi|163259781|emb|CAP42082.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           petrii]
          Length = 322

 Score =  133 bits (334), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 100/319 (31%), Positives = 162/319 (50%), Gaps = 22/319 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V V  + +  R+D +       +   ++ K +R G+VRV+K R++ + R+ +G VVR
Sbjct: 20  VRLVEVGPEHDGQRIDNFLVRLCKGVPKSHIYKAIRGGEVRVNKGRIQADYRVAAGDVVR 79

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+          +            ++F    ++YED  + V +KPAG++V GGSG++
Sbjct: 80  VPPL----------RLPAPGESRPVPGAEF---PVVYEDEALLVVDKPAGVAVHGGSGVS 126

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++    + +   L HRLD+ETSG+L++A+ R+A   L    R  R  K Y +L
Sbjct: 127 FGVIEQLRA-ARPQARFLELAHRLDRETSGLLMIAKKRSALLALHAMLREGRGDKHYLAL 185

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFCWLEM 245
           V G   N ++ I   L K +   G+    V+ +  G A + I   K        +  ++ 
Sbjct: 186 VEGDWVNDRQHIRLALTKWTTQSGE--RRVRPDPDGQAAHTIVTLK---QRLGGYSLVDA 240

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +  TGRTHQ+RVH    G PIVGD KY  +  +  F     N+++LHA  + LPHP    
Sbjct: 241 ELRTGRTHQIRVHLAASGFPIVGDDKYGTDETRARFARLGFNRMFLHAHQLTLPHPLTQE 300

Query: 305 -LQITAPLPAHMVKTWDSL 322
            L++TA LPA   K    L
Sbjct: 301 PLRLTAELPAACRKLLQQL 319


>gi|146328747|ref|YP_001209889.1| ribosomal large subunit pseudouridine synthase, RluC [Dichelobacter
           nodosus VCS1703A]
 gi|146232217|gb|ABQ13195.1| ribosomal large subunit pseudouridine synthase, RluC [Dichelobacter
           nodosus VCS1703A]
          Length = 313

 Score =  132 bits (333), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 98/315 (31%), Positives = 164/315 (52%), Gaps = 26/315 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V   +   R+D + + ++P +    + ++LR G+VR +KKRVK  ++I +G V+R
Sbjct: 9   VHFMTVSAADAGQRVDNFIRKYHPALPKSRIYQMLRKGEVRRNKKRVKPTDKICAGDVIR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+INA        +  D ++ +      +++ +LYED    + NKPAGI V GGSG  
Sbjct: 69  LPPIINA--------QRADVAIPIYWQKR-IEAAVLYEDDHFLILNKPAGIVVHGGSGHE 119

Query: 127 YHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + +   ++S W ++  +   L HRLD +TSG+LV+ + R A      +     ++K YW+
Sbjct: 120 FGVIDVVRSIWGENYAE---LAHRLDGDTSGVLVLGKHRQALNAFQTAMNEGTVEKRYWA 176

Query: 186 LVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G+  + + E + +  L K+ +       V + E  A +A + F V+  + Q    +E
Sbjct: 177 LVDGVWTREEAEVVVH--LTKAPLNVREKMQVSELE-NAQFARTWFYVLQRW-QDATLME 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK----LYLHARYMDLPHP 300
               TGRTHQ+RV A H    I GD KY    K  F   ++ K    L+LHAR +   + 
Sbjct: 233 AVLDTGRTHQIRVSAAHCQHAIAGDKKYG---KREFNDLVRKKGFHGLFLHAREIKFCY- 288

Query: 301 EGGRLQITAPLPAHM 315
           +   + + APL   M
Sbjct: 289 QNQTIHVMAPLTEAM 303


>gi|189349901|ref|YP_001945529.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           multivorans ATCC 17616]
 gi|189333923|dbj|BAG42993.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           multivorans ATCC 17616]
          Length = 334

 Score =  132 bits (333), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 106/331 (32%), Positives = 165/331 (49%), Gaps = 25/331 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + ++      R+D +       +   ++ +ILRSG+VRV+K RV    R+  G VVR
Sbjct: 17  VSMIQIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDVVR 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A   + +    +                +L+ED  + V +KPAG++V GGSG+A
Sbjct: 77  VPPVRVAAADLARADAPIVPPAQFD---------VLFEDDAMLVIDKPAGVAVHGGSGVA 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD+ETSG+L++A+ R A   L E  R  RI K Y++ 
Sbjct: 128 FGVIEQLRQ-ARPRAKFLELVHRLDRETSGVLMLAKKRTALVALHEQIRENRIDKRYFAC 186

Query: 187 V---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           V   W     ++  +   L K +   G+   V  Q++  A++ +  F +++ +   +  +
Sbjct: 187 VHGEWQADWGRRRAVKAPLFKYTTADGER-RVRVQDDGLASHTV--FNLVERWPD-YALV 242

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMDL 297
           E +  TGRTHQ+RVH  H+G PIVGD KY  +F  N         P   +++LHA  + L
Sbjct: 243 EAELKTGRTHQIRVHLAHLGLPIVGDAKY-GDFALNKALARANAQPSLKRMFLHAHRLRL 301

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
            HP  G  LQ  APLPA      D L    D
Sbjct: 302 AHPLSGDALQFDAPLPAECRHFLDQLSALRD 332


>gi|28199848|ref|NP_780162.1| pseudouridylate synthase [Xylella fastidiosa Temecula1]
 gi|182682599|ref|YP_001830759.1| RluA family pseudouridine synthase [Xylella fastidiosa M23]
 gi|28057969|gb|AAO29811.1| pseudouridylate synthase [Xylella fastidiosa Temecula1]
 gi|182632709|gb|ACB93485.1| pseudouridine synthase, RluA family [Xylella fastidiosa M23]
 gi|307578881|gb|ADN62850.1| pseudouridylate synthase [Xylella fastidiosa subsp. fastidiosa
           GB514]
          Length = 330

 Score =  132 bits (333), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 101/330 (30%), Positives = 166/330 (50%), Gaps = 31/330 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ VVV  +    RLD +  +    +    + K++RSGQVRV+  RVK   ++  G  VR
Sbjct: 18  VRIVVVPAEHSGQRLDNFLLSKLKGVPRSLIYKLVRSGQVRVNGGRVKAERKLDGGDEVR 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      +I+++ I+  S         +++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 78  LPPL-----RLIQDRAIVAPSAAFLAR---MEAAIVFEDARLLALNKPSGMASHGGSGIS 129

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--------RR 178
           Y +   ++  +    Q+  L HRLD++TSG+L++A+ RA    L    R         R 
Sbjct: 130 YGVIEAMR--ILRPKQELELVHRLDRDTSGLLIMAKKRAVLIELQALMREASVNGKEGRG 187

Query: 179 IQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CF 236
           I K Y +L+ G +P       A   +   H G  +V V    +     + S F++++   
Sbjct: 188 IAKRYLTLLSGRMPNGVMSVDAPLHINLRHGGERHVRVHHDGKP----SKSRFRLLERRG 243

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHAR 293
            Q +C  E+   TGRTHQ+RVHA H+G P+ GD KY     N K      +Q +L+LHA 
Sbjct: 244 GQSYC--EVLIETGRTHQIRVHAQHLGHPVTGDDKYGDQEVNRKLRDQIGLQ-RLFLHAV 300

Query: 294 YMDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
            ++     G    +  APL   +V   D L
Sbjct: 301 SLEFALDAGSTPYVLNAPLAEDLVAALDRL 330


>gi|33591688|ref|NP_879332.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           pertussis Tohama I]
 gi|33571331|emb|CAE44806.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           pertussis Tohama I]
 gi|332381081|gb|AEE65928.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           pertussis CS]
          Length = 316

 Score =  132 bits (333), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 95/318 (29%), Positives = 161/318 (50%), Gaps = 20/318 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  + +  R+D +       +   ++ K +R G+VRV+K R+    R+  G VVR
Sbjct: 14  VRMLAIGPEHDGQRIDNFLLRLCKGVPKSHIYKAIRGGEVRVNKGRISAEYRLVEGDVVR 73

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+           ++ D     T+     +  ++YED  + V +KPAG++V GGSG++
Sbjct: 74  VPPL-----------RLPDPGA--TRPVPGAEFPVVYEDDALLVIDKPAGVAVHGGSGVS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++    + +   L HRLD+ETSG+L++A+ R+A   L    R  +  K Y +L
Sbjct: 121 FGVIEQLRA-ARPQARFLELVHRLDRETSGLLMLAKKRSALLALHAMLREGKGDKHYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   N ++ I   L K +   G+    V Q  + A+  ++  K    ++     ++ +
Sbjct: 180 VEGDWVNDRQHIRLALTKWTTQSGERRVRVDQAGQAAHTIVTLRKRFGGYS----LVDAE 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
             TGRTHQ+RVH    G PIVGD K   +  +  F      +++LHA  + LPHP  G  
Sbjct: 236 LRTGRTHQIRVHLASSGFPIVGDDKCGTDEIRAAFARRGFGRMFLHAHQLTLPHPLTGET 295

Query: 305 LQITAPLPAHMVKTWDSL 322
           L++TA LP   +K    L
Sbjct: 296 LRLTADLPPACLKLLKQL 313


>gi|254294411|ref|YP_003060434.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254042942|gb|ACT59737.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
          Length = 272

 Score =  132 bits (333), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 122/234 (52%), Gaps = 7/234 (2%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           D++  +LL ED  I  FNKP+G++ Q  S      D  L+ +V   G++PR+ HRLD  T
Sbjct: 32  DYMDELLLGEDDSILAFNKPSGLACQTRSPADRTFDALLQVYVKRNGKRPRMLHRLDMLT 91

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--Y 212
           SG+++ ART+ A     ++F  R   K Y ++V G    K E + +  L++     +   
Sbjct: 92  SGVIIAARTKPATSFFQQTFERREAYKSYLAIVRGPAFEKSEGVIDAHLQRYQKEPNLAL 151

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +     + +GA  A + + V+      + +L + P TGRTHQLRVH  H G PI+ D  Y
Sbjct: 152 MRPCDVDGEGAQDARTRYLVLSS-QNDYHFLLLTPETGRTHQLRVHLEHFGRPILADPYY 210

Query: 273 CAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
             +  +G++      +L LHA  +  PHP+GG + I A +P  M +   +L  +
Sbjct: 211 GTDALEGSYQP---ARLMLHAYRLLTPHPDGGEIDIIADVPDDMKECLTALSLE 261


>gi|254670429|emb|CBA06026.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis alpha153]
          Length = 330

 Score =  132 bits (333), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 96/323 (29%), Positives = 159/323 (49%), Gaps = 26/323 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +              +YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFEA---------VYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLR-RARPEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G+ K   +     L    + G     +V+ +  G + A + F+V+  F+         
Sbjct: 181 --GVGKLPDDNFHVRLPLSKYTGAQGEKMVRVSADGQS-AHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                +     TGRTHQ+RVH    GCPI GD +Y  +++ N         +++LHA  +
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERY-GDYQANRRLQKLGLKRMFLHASEL 296

Query: 296 DLPHPEGGR-LQITAPLPAHMVK 317
            L HP  G  L +   LP  + +
Sbjct: 297 HLNHPLTGEPLVLKVGLPPDLAQ 319


>gi|261400963|ref|ZP_05987088.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           lactamica ATCC 23970]
 gi|269209209|gb|EEZ75664.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           lactamica ATCC 23970]
          Length = 295

 Score =  132 bits (333), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 91/294 (30%), Positives = 152/294 (51%), Gaps = 26/294 (8%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           ++ +I+R+G+VR++KKR K ++RI  G  VRIPPV  A   +  E++    +        
Sbjct: 5   HIHRIIRAGEVRLNKKRCKPDSRIAEGDTVRIPPVRVAEKEMPSERRAAVPAREFD---- 60

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
                ++YED  + V +KP+G++V GGSG+++ +   L+     + +   L HRLD++TS
Sbjct: 61  -----IVYEDDALLVIDKPSGVAVHGGSGVSFGVIEQLR-RARPEARYLELVHRLDKDTS 114

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+VA+ R+A   L E+ R    +KIY +L  G   +    I   L K +   G+ +  
Sbjct: 115 GLLMVAKKRSALVKLHEAIRNDHPKKIYLALGVGKLPDDNFHIKLPLFKYTGAQGEKMVR 174

Query: 216 VKQNEKGANYAISHFKVIDCFAQK---------FCWLEMQPHTGRTHQLRVHALHMGCPI 266
           V ++ + A+     F+V+  F+              +     TGRTHQ+RVH    GCPI
Sbjct: 175 VSEDGQSAHTV---FRVLSRFSDGILHGVGLSHLTLVRATLKTGRTHQIRVHLQSQGCPI 231

Query: 267 VGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
            GD +Y  +++ N         +++LHA  + L HP  G  L + A LP  + +
Sbjct: 232 AGDERY-GDYQANRRLQKLGLKRMFLHASELHLNHPLTGEPLVLKAELPPDLAQ 284


>gi|86605450|ref|YP_474213.1| RluA family pseudouridine synthase [Synechococcus sp. JA-3-3Ab]
 gi|86553992|gb|ABC98950.1| pseudouridine synthase, RluA family [Synechococcus sp. JA-3-3Ab]
          Length = 310

 Score =  132 bits (333), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 100/324 (30%), Positives = 163/324 (50%), Gaps = 44/324 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSG 62
           M  ++ V V   ++ +RLDR      P ++   LQ+++R GQV ++ +     +R +Q+G
Sbjct: 1   MAEIRRVTVTEKQQGLRLDRGLAEQLPELSRSRLQQLIRQGQVWLNGQPCLDKDRPLQAG 60

Query: 63  Q--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
               VRIPP       +  E+  LD               +LYED  + V NKP G+ V 
Sbjct: 61  DQIEVRIPPATP--TPLQPERIPLD---------------ILYEDEDLLVINKPRGLVVH 103

Query: 121 GGSGIAYHIDGFLK----------SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
              G   H  G L           S ++ + Q+P + HRLD++T+G LV+A+   A QHL
Sbjct: 104 PAPG---HASGTLVHALLAHCPRLSGINGE-QRPGIVHRLDKDTTGALVIAKHDQAHQHL 159

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
               + +  ++IY  +V+G P   +  I+   + +  +    + VV   +  A  A++H+
Sbjct: 160 QAQIQAKTARRIYLGVVFGRPAQSQGTISAP-IGRHPVDRQKMAVVPPGQGRA--AVTHW 216

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLY 289
           +V++     +  ++ +  TGRTHQ+RVHA H+  PIVGD  Y      + TSP++ +   
Sbjct: 217 QVLERLG-NYTLMQFELETGRTHQIRVHAAHLRLPIVGDPLYTQ----SKTSPVKLSGQA 271

Query: 290 LHARYMDLPHPEGGR-LQITAPLP 312
           LHA  +   HP  G+ LQ+TAPLP
Sbjct: 272 LHAWKLSFVHPRTGQPLQVTAPLP 295


>gi|13473214|ref|NP_104781.1| pseudouridine synthase [Mesorhizobium loti MAFF303099]
 gi|14023962|dbj|BAB50567.1| pseudouridine synthase [Mesorhizobium loti MAFF303099]
          Length = 329

 Score =  132 bits (332), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 99/337 (29%), Positives = 160/337 (47%), Gaps = 50/337 (14%)

Query: 10  VVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRI 67
           +VV  D    RLD+W      P ++   +Q ++R G V VD K      R + +G+ V I
Sbjct: 2   LVVGADAAGQRLDQWLAASLGPDMSRSRVQMLIRQGAVSVDGKPADETKRKMSAGESVSI 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           +          + +   +LYED  + V NKPAG+ V  G+G   
Sbjct: 62  ---------------AMPEPEPAAPQGEAIALDVLYEDDALIVINKPAGLVVHPGAGNWT 106

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RM 176
              ++  +    DS       ++P + HRLD+ETSG++VVA+T  A + L+E+F    R 
Sbjct: 107 GTLVNALIHHCGDSLSGIGGVRRPGIVHRLDKETSGVMVVAKTDRAHKALSEAFADHGRT 166

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVID 234
             +++ Y +LVWGIP+     +   L + +    D V   VV +    A +A++HF V +
Sbjct: 167 GDLERAYLALVWGIPQRPTGTVDAPLGRAA----DRVRRAVVPEGRDDARHAVTHFAVQE 222

Query: 235 CFA---QKFC---WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQ 285
            F    Q+F     +E +  TGRTHQ+RVH  H+G P++GD  Y   F+        P++
Sbjct: 223 RFGENQQEFATASLVECRLETGRTHQIRVHMAHIGHPVIGDPDYGQAFRTKANRLPEPLK 282

Query: 286 NKL------YLHARYMDLPHPEGG-RLQITAPLPAHM 315
           +++       LHA  +   HP+    ++  AP+P  M
Sbjct: 283 SQVKAFSRQALHAWLLAFRHPDTHLTMRFEAPIPRDM 319


>gi|171463176|ref|YP_001797289.1| pseudouridine synthase, RluA family [Polynucleobacter necessarius
           subsp. necessarius STIR1]
 gi|171192714|gb|ACB43675.1| pseudouridine synthase, RluA family [Polynucleobacter necessarius
           subsp. necessarius STIR1]
          Length = 335

 Score =  132 bits (332), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 104/327 (31%), Positives = 165/327 (50%), Gaps = 25/327 (7%)

Query: 7   VQYVVVENDEENMRLD----RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           V   ++  +E   RLD    RW K     +   ++ +I+RSG+VRV+KKR +   R+  G
Sbjct: 20  VHLQIIGPEEAGQRLDNYLLRWAKG----VPKSHVYRIIRSGEVRVNKKRAEPTTRLIEG 75

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VVR+PPV   +    +   +  +      H    K  +L+ED  + + NKPAG++V GG
Sbjct: 76  DVVRLPPV--RIAEPAQMAAVNSAQTKFRAHGYSDKMPILFEDEALLIVNKPAGLAVHGG 133

Query: 123 SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           SGIA    G +++   ++ +     L HRLD++TSG+L +A+ R+A   L    R  +  
Sbjct: 134 SGIAL---GVIETLRITRPELKFLELVHRLDRDTSGVLFLAKKRSALVELHRQIREDQAD 190

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           K Y+ L  G I +  +     + L K  +  G+    V  +   ++ A+   K +     
Sbjct: 191 KRYYLLAHGEIVQGAQTMQLKYPLHKYLLPNGERRVRVDPDGLPSHTALRVTKALKREGA 250

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDL 297
                E Q  TGRTHQ+RVH   +G  I+GD KY   F+ +    I++K LYLHA     
Sbjct: 251 AITLAEAQLKTGRTHQIRVHLQKLGHAILGDDKY--GFE-DLDKVIKSKRLYLHAHLAGF 307

Query: 298 PHPEGG-RLQITAPLPAH---MVKTWD 320
            HP  G +++I +PLP     M+KT++
Sbjct: 308 THPRTGEKMRIESPLPPEFTAMMKTFE 334


>gi|144897601|emb|CAM74465.1| Pseudouridylate synthase [Magnetospirillum gryphiswaldense MSR-1]
          Length = 230

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 84/232 (36%), Positives = 127/232 (54%), Gaps = 11/232 (4%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           D L + +LY D+ + + +KPAG++V  G+   ++H+   L+       + P L HRLD++
Sbjct: 4   DELLARVLYRDAMVLIIDKPAGLAVHAGARDGSHHLMDLLEPLRFGLPRNPELAHRLDRD 63

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG LV+ R R A   L E F     QK YW++V G P  +   I   L K     G + 
Sbjct: 64  TSGCLVLGRHRKALARLGEIFAGSEAQKTYWAVVVGKPPAESGIIDKRLKKLERRHG-WR 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            VV  ++KG + A++ ++V+     +  W+E +P TGRTHQ+RVH   +GCPIVGD  Y 
Sbjct: 123 MVV--DDKGQD-AVTEYRVLGGNG-RLSWIEAKPRTGRTHQIRVHLAAIGCPIVGDSTY- 177

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPH-PEGGRLQITAPLPAHMVKTWDSLGF 324
                +  SP    L+LHAR + LP+ P+   +   AP+PAHM+      G+
Sbjct: 178 GRGTADLVSP---HLHLHARSITLPYNPKKSPITAQAPVPAHMIDALIQCGW 226


>gi|209525222|ref|ZP_03273765.1| pseudouridine synthase, RluA family [Arthrospira maxima CS-328]
 gi|209494407|gb|EDZ94719.1| pseudouridine synthase, RluA family [Arthrospira maxima CS-328]
          Length = 308

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 96/324 (29%), Positives = 149/324 (45%), Gaps = 41/324 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-------KKRVKFNNRI 59
           ++ +  + D EN RLD+W       ++   LQ ++ SG V ++       K  V+  +RI
Sbjct: 3   IELICEDKDGENQRLDKWLSERVHQLSRSRLQALISSGHVWINNSPCTSKKATVQIGDRI 62

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q    V IPP I        E K  +  +++           LYED ++ + NKPAG+ V
Sbjct: 63  Q----VEIPPAIPL------ELKATNIPLDI-----------LYEDEELLIINKPAGLVV 101

Query: 120 QGGSGIAYH--IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G      ++  L       G    Q+P + HRLD++T+G + +A+T  A QHL   
Sbjct: 102 HPAPGHENDTLVNALLAHCETLAGIGGVQRPGIVHRLDKDTTGAIAIAKTDHAHQHLQAQ 161

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + +  ++ Y  +++G+PK     I   + +  H        +    +G   AI+H+KV 
Sbjct: 162 IQAKTARRQYLGIIYGVPKTTSGVIDQPIGR--HPSDRQKMAIVPQHQGGRSAITHWKVK 219

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           +     +  +E +  TGRTHQ+RVH+  MG PIVGD  Y          P Q    LHA 
Sbjct: 220 ERLG-NYTLIEFELETGRTHQIRVHSASMGHPIVGDRVYGKGRSVGVNLPGQ---ALHAW 275

Query: 294 YMDLPHPEGGRL-QITAPLPAHMV 316
            + L HP  G L +  APLP  M 
Sbjct: 276 KLTLQHPTSGELIEAIAPLPHTMT 299


>gi|15839195|ref|NP_299883.1| pseudouridylate synthase [Xylella fastidiosa 9a5c]
 gi|9107828|gb|AAF85403.1|AE004067_10 pseudouridylate synthase [Xylella fastidiosa 9a5c]
          Length = 330

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 100/329 (30%), Positives = 166/329 (50%), Gaps = 29/329 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ VVV  +    RLD +  +    +    + K++RSGQVRV+  RVK   ++  G  +R
Sbjct: 18  VRIVVVPAEHSGQRLDNFLLSKLKGVPRSLIYKLVRSGQVRVNGGRVKAERKLDGGDEIR 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      +I+++ I+  S         +++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 78  LPPL-----RLIQDRAIVAPSAAFLAR---MEAAIVFEDARLLALNKPSGMASHGGSGIS 129

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--------RR 178
           Y +   ++  +    Q+  L HRLD++TSG+L++A+ RAA   L    R         R 
Sbjct: 130 YGVIEAMR--ILRPKQELELVHRLDRDTSGLLIMAKKRAALIELQALMREASVNGKEGRG 187

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FA 237
           I K Y +L+ G   N    +   L      GG+    V  + K +    S F++++    
Sbjct: 188 IAKRYLTLLSGRMPNGVMSVDAPLHINLRQGGERHVRVHHDGKPSK---SRFRLLERRGG 244

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARY 294
           Q +C  E+   TGRTHQ+RVHA H+G P+ GD KY     N +      +Q +L+LHA  
Sbjct: 245 QSYC--EVLIETGRTHQIRVHAQHLGHPVTGDDKYGDQEVNRRLRDQIGLQ-RLFLHAVS 301

Query: 295 MDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
           ++     G    +  APL   +V   D L
Sbjct: 302 LEFALDAGSTPYVLNAPLAEDLVAALDRL 330


>gi|157692226|ref|YP_001486688.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
 gi|157680984|gb|ABV62128.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
          Length = 304

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 94/325 (28%), Positives = 159/325 (48%), Gaps = 42/325 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  ++ + RLD++     P  +   +Q+ ++ G + V+ K+VK N ++Q+G  +++  
Sbjct: 6   IAVSEEQTSERLDKFLSTSEPEWSRTQVQQWVKDGLIEVNGKQVKANYKVQAGDQIKVE- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                   I E + LD        ++ +   + YED+ + V NKP G+ V    G     
Sbjct: 65  --------IPEPEALDVE------AEAMDLDIYYEDADVLVVNKPRGMVVHPAPGHVSGT 110

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y
Sbjct: 111 LVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRKY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++V GI ++    I       + IG D      + V K++ K    A++HF VI+ F  
Sbjct: 171 TAVVHGIIQHDTGTI------DAPIGRDKKDRQSMTVTKESSK---QAVTHFDVIERF-D 220

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   
Sbjct: 221 DFTVVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPRKTVDF-----NGQLLHAGVLGFD 275

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  G  ++ TAP+PA M    DSL
Sbjct: 276 HPRTGEYIEFTAPVPADMRGFIDSL 300


>gi|237653101|ref|YP_002889415.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|237624348|gb|ACR01038.1| pseudouridine synthase, RluA family [Thauera sp. MZ1T]
          Length = 319

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 100/324 (30%), Positives = 161/324 (49%), Gaps = 31/324 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++  ++      R+D +       +   ++ +ILRSG+VRV+ +RV+   R+Q G  VR
Sbjct: 11  VRHERIDEAAAGQRIDNYLLRIAKGVPKSHVYRILRSGEVRVNGRRVQQTYRLQEGDEVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A               +           ++YED  + V +KP+G +V GGSG++
Sbjct: 71  IPPIRIA------------EPTHAAPAPAGKPLPVVYEDEALLVIDKPSGKAVHGGSGVS 118

Query: 127 YHIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           Y +   L+       Q+P      L HRLD+ETSG+L+VA+ R+A   L +  R   ++K
Sbjct: 119 YGVIEQLRV------QRPELRMLELAHRLDRETSGLLIVAKKRSALTALHDMMREGSVEK 172

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   N  + +   L K     G+    V    K A+   S  +++  + + + 
Sbjct: 173 RYLTLVPGRWSNPLQHVKVPLHKYLTAEGERRVRVADEGKAAH---SIVRLVRRW-RDYS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPH 299
            LE++  TGRTHQ+RVH  H+G  + GD KY  +F  N    ++   +++LHA  + L H
Sbjct: 229 LLEVELKTGRTHQIRVHLAHLGFALCGDDKY-GDFALNKRLEVEGLRRMFLHAAKLRLAH 287

Query: 300 P-EGGRLQITAPLPAHMVKTWDSL 322
           P  G  L   +PLPA +    D L
Sbjct: 288 PLTGAPLAFDSPLPADLQTFLDRL 311


>gi|83312904|ref|YP_423168.1| putative pseudouridine synthase in lpd 3'region [Magnetospirillum
           magneticum AMB-1]
 gi|82947745|dbj|BAE52609.1| Hypothetical pseudouridine synthase in lpd 3'region
           [Magnetospirillum magneticum AMB-1]
          Length = 229

 Score =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 77/232 (33%), Positives = 127/232 (54%), Gaps = 12/232 (5%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           D + S +LY+D  + V +KPAG++V  G     H++ +L +      + P+L HRLD++T
Sbjct: 4   DEILSRVLYKDQDVIVLDKPAGLAVHAGPNSPDHLELYLGALAFGWAEMPKLAHRLDRDT 63

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L++ R   A + L + F  RR++K+YWS+  G P      +   LLK S  G  +  
Sbjct: 64  SGCLILGRHAKAIKRLGKMFEHRRVEKVYWSVSHGSPAADSGTVDAPLLKVSARGQGW-- 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +K +  G   +I+ + V+   +    W+E +P TGRTHQ+R+HA ++GCP++GD  Y  
Sbjct: 122 RIKVDPAG-QPSITDWSVLG-RSDGLSWIEWRPRTGRTHQIRIHAQYLGCPLLGDAYYGP 179

Query: 275 NFKGNFTSPIQNKLYLHARYMDLP--HPEGGRLQITAPLPAHMVKTWDSLGF 324
           + +         +L+L AR +  P   P    +++TAP P HMV+     G+
Sbjct: 180 DPEPKV------RLHLLARAVAFPALAPSKDPVRVTAPPPEHMVEALRRCGW 225


>gi|288871585|ref|ZP_06410236.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           hathewayi DSM 13479]
 gi|288862917|gb|EFC95215.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           hathewayi DSM 13479]
          Length = 304

 Score =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 95/321 (29%), Positives = 158/321 (49%), Gaps = 44/321 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q  VVE +++ +R+D++     P ++   LQK+L++  V V  K VK N +  +G ++ +
Sbjct: 3   QQFVVEEEDKAIRIDKYLSERCPELSRSYLQKLLKAEAVFVGGKPVKSNYKTAAGDLIEL 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                    I+ E+  LD               +LYEDS I + NKP G+ V   +G   
Sbjct: 63  EVPEAVEPKIVPEEMDLD---------------ILYEDSDIILINKPKGMVVHPAAG--- 104

Query: 128 HIDGFLKSWV------DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           H  G L + +      D  G     +P + HR+D +T+G+L+V +   A   + E  ++ 
Sbjct: 105 HYSGTLVNGLMAHCRADLSGINGVMRPGIVHRIDMDTTGVLIVCKNDMAHNSIAEQLKVH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDC 235
            I + Y+++V G+ K  +  ++        IG   V   K   NEK    A++H++V++ 
Sbjct: 165 SITRKYYAVVHGVMKEDEGTVSGP------IGRHPVDRKKMCINEKNGRDAVTHYRVLER 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARY 294
           F Q F ++E +  TGRTHQ+RVH   +G P++GD  Y     G    P +     LHA  
Sbjct: 219 FRQ-FTYVECRLETGRTHQIRVHMASIGHPLLGDAVY-----GPAKCPYKLTGQTLHAGV 272

Query: 295 MDLPHPEGGR-LQITAPLPAH 314
           + + HP  G  ++ TAPLP +
Sbjct: 273 LGIVHPRTGEYMEFTAPLPEY 293


>gi|255555275|ref|XP_002518674.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223542055|gb|EEF43599.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 536

 Score =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 104/346 (30%), Positives = 160/346 (46%), Gaps = 74/346 (21%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G++    KRV   + +  G  + +P  + AL    ++QK         K ++F++ + LY
Sbjct: 196 GEMEHKTKRVAAKDLMNVGDRIFLPISVQALP--FEKQKCHCGE----KEANFIRGLELY 249

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVAR 162
           +D  I V NKP G+ VQGG GI    D    S +     + PRL HRLD+++SGILV+ R
Sbjct: 250 KDEAIIVVNKPPGMPVQGGIGIKSSFDELAASCLSYDYSEPPRLVHRLDRDSSGILVMGR 309

Query: 163 TRAAAQHLTESFR-------------MRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           T+ +   L   FR              RRI Q+ YW+LV G P+ +K  I+  L K    
Sbjct: 310 TQTSTMVLHSVFREKTFAASNHDIGERRRILQRKYWALVIGSPRRQKGIISAPLGKVVVD 369

Query: 209 GG--DYVHVVKQNEKGA-NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGC 264
            G  D + VV+  E  +  +A++ ++V++  +  + WLE+ P TGR HQLRVH    +G 
Sbjct: 370 DGKSDRITVVENAESTSFQHAVTQYRVMES-SHGYAWLELSPITGRKHQLRVHCAEVLGT 428

Query: 265 PIVGDHKY-------------------------CA-------NFKGNFTSPIQNKLYLHA 292
           PIVGD+KY                         C        + +    S    +L+LH 
Sbjct: 429 PIVGDYKYGWQVHRKWKQLPFPNLEKISNENALCKKILPFGIDLESGSISEKHPRLHLHC 488

Query: 293 RYMDLPHPEGG----------------RLQITAPLPAHMVKTWDSL 322
           + M LP                      +++ APLP++M ++WD L
Sbjct: 489 KQMVLPDVSQALRGVQTSSNYDFSDLKSIELDAPLPSYMQRSWDIL 534


>gi|293603991|ref|ZP_06686404.1| ribosomal large subunit pseudouridine synthase C [Achromobacter
           piechaudii ATCC 43553]
 gi|292817595|gb|EFF76663.1| ribosomal large subunit pseudouridine synthase C [Achromobacter
           piechaudii ATCC 43553]
          Length = 301

 Score =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 98/309 (31%), Positives = 159/309 (51%), Gaps = 28/309 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+++    RLD +       +   ++ K +R G+VRV+K R+  + RI +G +VRIPP
Sbjct: 2   VEVDDEHAGQRLDNFLMRLCKGVPKTHIYKAIRGGEVRVNKGRISVDYRIVAGDIVRIPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
           +   L    K + +  +              +++ED  + V +KPAG++V GGSG+++  
Sbjct: 62  L--RLPDPGKPRPVPGAEFP-----------VVFEDDALLVVDKPAGVAVHGGSGVSFGV 108

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           I+    +  D+K  +  L HRLD+ETSG+L+VA+ R+A   L    R  +  K Y +LV 
Sbjct: 109 IEQLRAARPDAKFLE--LVHRLDRETSGLLMVAKKRSALLALHAMLREGKGDKHYLALVE 166

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEM 245
           G   N ++ I   L K +   G+    V  + + A+  I+         Q+F     ++ 
Sbjct: 167 GDWVNDRQHIKLGLSKWTTQSGERRVKVDPDGQTAHTIIT-------LKQRFGGYSLVDA 219

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
           +  TGRTHQ+RVH    G PIVGD KY   + +  F+     +++LHA  + L HP  G 
Sbjct: 220 ELRTGRTHQIRVHLAASGFPIVGDDKYGHDDVRAEFSRMGFGRMFLHAHQLTLAHPVTGE 279

Query: 304 RLQITAPLP 312
            + +TA LP
Sbjct: 280 SMTLTAELP 288


>gi|161525362|ref|YP_001580374.1| RluA family pseudouridine synthase [Burkholderia multivorans ATCC
           17616]
 gi|221201329|ref|ZP_03574368.1| pseudouridine synthase, RluA family [Burkholderia multivorans
           CGD2M]
 gi|221208809|ref|ZP_03581807.1| pseudouridine synthase, RluA family [Burkholderia multivorans CGD2]
 gi|221214111|ref|ZP_03587084.1| pseudouridine synthase, RluA family [Burkholderia multivorans CGD1]
 gi|160342791|gb|ABX15877.1| pseudouridine synthase, RluA family [Burkholderia multivorans ATCC
           17616]
 gi|221166288|gb|EED98761.1| pseudouridine synthase, RluA family [Burkholderia multivorans CGD1]
 gi|221171265|gb|EEE03714.1| pseudouridine synthase, RluA family [Burkholderia multivorans CGD2]
 gi|221178597|gb|EEE11005.1| pseudouridine synthase, RluA family [Burkholderia multivorans
           CGD2M]
          Length = 316

 Score =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 105/328 (32%), Positives = 164/328 (50%), Gaps = 25/328 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++      R+D +       +   ++ +ILRSG+VRV+K RV    R+  G VVR+PP
Sbjct: 2   IQIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDVVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A   + +    +                +L+ED  + V +KPAG++V GGSG+A+ +
Sbjct: 62  VRVAAADLARADAPIVPPAQFD---------VLFEDDAMLVIDKPAGVAVHGGSGVAFGV 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-- 187
              L+     + +   L HRLD+ETSG+L++A+ R A   L E  R  RI K Y++ V  
Sbjct: 113 IEQLRQ-ARPRAKFLELVHRLDRETSGVLMLAKKRTALVALHEQIRENRIDKRYFACVHG 171

Query: 188 -WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            W     ++  +   L K +   G+   V  Q++  A++ +  F +++ +   +  +E +
Sbjct: 172 EWQADWGRRRAVKAPLFKYTTADGER-RVRVQDDGLASHTV--FNLVERWPD-YALVEAE 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH  H+G PIVGD KY  +F  N         P   +++LHA  + L HP
Sbjct: 228 LKTGRTHQIRVHLAHLGLPIVGDAKY-GDFALNKALARANAQPSLKRMFLHAHRLRLAHP 286

Query: 301 -EGGRLQITAPLPAHMVKTWDSLGFKYD 327
             G  LQ  APLPA      D L    D
Sbjct: 287 LSGDALQFDAPLPAECRHFLDQLSALRD 314


>gi|257468012|ref|ZP_05632108.1| tRNA pseudouridine synthase A [Fusobacterium ulcerans ATCC 49185]
 gi|317062298|ref|ZP_07926783.1| rRNA pseudouridylate synthase C [Fusobacterium ulcerans ATCC 49185]
 gi|313687974|gb|EFS24809.1| rRNA pseudouridylate synthase C [Fusobacterium ulcerans ATCC 49185]
          Length = 290

 Score =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 93/311 (29%), Positives = 161/311 (51%), Gaps = 25/311 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V+ + E++RLD++ +  Y  I    + K +R+G+++V+ K+ K N R+Q    +++   
Sbjct: 4   IVDKEFEDVRLDKFLRKKYEDIPLTEIFKGIRTGKIKVNGKKSKENYRLQLNDEIKVF-- 61

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                   KE+K+L+      K  + +K  ++YE+  + +FNK   + +  GSG  + I 
Sbjct: 62  --FKGGETKEEKLLEVE---DKEIEKIKKSIVYENENVLIFNKKNNMVMHKGSGYDFGIS 116

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             LK ++  K       +R+D+ TSG+++ A++   A+ L E  R R I K Y+ LV G 
Sbjct: 117 ELLKGYL--KNPNFNFVNRIDKATSGLIIGAKSLVTARELAEEIRNRNIDKRYYILVEGK 174

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K+K+  I ++L K      D V  V++ E+GA  ++S FKV   + +    LE    +G
Sbjct: 175 VKDKEFTIKSYLKKIE----DKVIEVEKFEEGAKESLSFFKV-KKYGKDCTLLEGTLGSG 229

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLRV   +MG  I+GD KY    KG      +  +YL + Y+ +       ++I  P
Sbjct: 230 RTHQLRVQLANMGNAIIGDTKYG---KGK-----EKIMYLFSHYLKINKY---GIEIDLP 278

Query: 311 LPAHMVKTWDS 321
           +P   +K   S
Sbjct: 279 IPDEYIKRLGS 289


>gi|269836533|ref|YP_003318761.1| pseudouridine synthase, RluA family [Sphaerobacter thermophilus DSM
           20745]
 gi|269785796|gb|ACZ37939.1| pseudouridine synthase, RluA family [Sphaerobacter thermophilus DSM
           20745]
          Length = 313

 Score =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 96/323 (29%), Positives = 159/323 (49%), Gaps = 41/323 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PP 69
           V  +E+  RLDR        I+    Q ++++G V V+ +  +   RI  G  + I  PP
Sbjct: 16  VAAEEDGERLDRLIAARVAEISRSYAQSLVKAGDVYVNGEPARPARRIHEGDTIEILLPP 75

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V                  +LT   +++   ++YED  + +F+KPAG+      G   H 
Sbjct: 76  V--------------PEPDDLT--PEYIPVPVIYEDDDVIIFDKPAGLVTHPAPG---HE 116

Query: 130 DGFLKSWVDS---------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G L + V +          G++P + HRLD++TSG++VVA+   A ++L + ++ R + 
Sbjct: 117 HGTLVNVVKALRPDVPLLMGGKRPGIVHRLDKDTSGLIVVAKNEEARRYLVQQWQQRDVV 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G+ +  +  I +  + +       + VV         A++HF+V++ F +  
Sbjct: 177 KRYIALVHGVIRENEGTI-DAPISRDPRNRKRMAVVPNGRP----AVTHFRVLERF-RDA 230

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L +Q  TGRTHQ+RVH L +G PIVGD  Y    K  F  PI  + +LHA Y+    P
Sbjct: 231 TLLNVQIETGRTHQIRVHMLFIGHPIVGDQMYG---KRPFRIPIARQ-FLHASYLKFSLP 286

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E GR +++   LPA + +  + L
Sbjct: 287 ESGRPIEVETALPADLREVLERL 309


>gi|21231531|ref|NP_637448.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66768413|ref|YP_243175.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|21113212|gb|AAM41372.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66573745|gb|AAY49155.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
          Length = 327

 Score =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 103/339 (30%), Positives = 160/339 (47%), Gaps = 49/339 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRTGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +E    D +   +     L++ +++ED+++   NKP G++  GGSGI+
Sbjct: 76  IPPV-----RLTEEG---DKAAPPSAFQARLEAAIVFEDARLLALNKPTGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRAL--RPNQTLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVDGRSIT 185

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC- 235
           K Y +L+ G +P       A       HIG   G   HV  Q       ++SHF++++  
Sbjct: 186 KRYLTLLVGRMPDGVMSVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFRLLERR 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-------- 287
               +C + ++  TGRTHQ+RVHA H+G  + GD KY          P  NK        
Sbjct: 239 GGHSYCEVRIE--TGRTHQIRVHAQHLGHAVAGDDKYG--------DPEVNKRLRDQVGL 288

Query: 288 --LYLHARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSLG 323
             L+LHA  ++     G    +  APL   + +  D LG
Sbjct: 289 RRLFLHAASLEFALDNGKTPYVLNAPLAPELAEALDRLG 327


>gi|188991778|ref|YP_001903788.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. B100]
 gi|167733538|emb|CAP51742.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris]
          Length = 327

 Score =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 100/331 (30%), Positives = 159/331 (48%), Gaps = 33/331 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRTGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +E    D +   +     L++ +++ED+++   NKP G++  GGSGI+
Sbjct: 76  IPPV-----RLTEEG---DKAAPPSAFQARLEAAIVFEDARLLALNKPTGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRAL--RPNQTLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVDGRSIT 185

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDC- 235
           K Y +L+ G +P       A       HIG   G   HV  Q       ++SHF++++  
Sbjct: 186 KRYLTLLVGRMPDGVMSVDAPL-----HIGLRQGGERHV--QVNAIGKPSLSHFRLLERR 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHAR 293
               +C + ++  TGRTHQ+RVHA H+G  + GD KY            +   +L+LHA 
Sbjct: 239 GGHSYCEVRIE--TGRTHQIRVHAQHLGHAVAGDDKYGDPEVNKRLRDQVGLRRLFLHAA 296

Query: 294 YMDLPHPEGGRLQI-TAPLPAHMVKTWDSLG 323
            ++     G    +  APL   + +  D LG
Sbjct: 297 SLEFSLDNGKTPYVLNAPLAPELAEALDRLG 327


>gi|317401917|gb|EFV82523.1| pseudouridine synthase [Achromobacter xylosoxidans C54]
          Length = 321

 Score =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 97/311 (31%), Positives = 158/311 (50%), Gaps = 26/311 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V V  +    RLD +       +   ++ K +R G+VRV+K R+  + R+  G +VR
Sbjct: 19  VRMVEVGAEHAGQRLDNYLMRLCKGVPKTHIYKAIRGGEVRVNKGRISVDYRVAEGDMVR 78

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+   L    K + +  +   +           ++ED  + V +KPAG++V GGSG++
Sbjct: 79  IPPL--RLPDPGKPRPVPAAEFPV-----------VFEDDAMLVVDKPAGVAVHGGSGVS 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++    + +   L HRLD+ETSG+L+VA+ R+A   L    R  R  K Y++L
Sbjct: 126 FGVIEQLRA-ARPEAKFLELVHRLDRETSGLLMVAKKRSALLALHAMLREGRSDKHYYAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWL 243
           V G   N ++ I   L K +   G+    V  + + A+  I+         Q+F     +
Sbjct: 185 VEGDWVNDRQHIKLSLSKWTTQSGERRVKVDPDGQTAHTIIT-------LKQRFGRYSLV 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + +  TGRTHQ+RVH    G PIVGD KY  +  +  F+     +++LHA  + L HP  
Sbjct: 238 DAELRTGRTHQIRVHLAASGFPIVGDDKYGHDEVRAEFSRMGFGRMFLHAHQLTLNHPLT 297

Query: 303 GR-LQITAPLP 312
           G  + +TA LP
Sbjct: 298 GEPMTLTAELP 308


>gi|300087236|ref|YP_003757758.1| RluA family pseudouridine synthase [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
 gi|299526969|gb|ADJ25437.1| pseudouridine synthase, RluA family [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
          Length = 301

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 96/317 (30%), Positives = 152/317 (47%), Gaps = 39/317 (12%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D E  RLDR+     P  +  +LQ+++R G V V+ +  +  + ++ G  V +       
Sbjct: 14  DREGWRLDRYLAEKLPDRSRASLQELIREGFVTVNGRPARPASPLKPGDRVTVE------ 67

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                    L      T  ++ +   ++YED  + V +KPAG++     G   H  G L 
Sbjct: 68  ---------LPPPAPTTATAEDIPLTVIYEDEDLAVIDKPAGLTTHPAPG---HPAGTLL 115

Query: 135 SWV--------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +        DS   +P + HRLD++TSG++VVAR+R A   L++ FR R + K+Y +L
Sbjct: 116 NALLSRFPELRDSGLDRPGIVHRLDKDTSGLMVVARSRQAHARLSDQFRNREVTKVYLAL 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G      E I    + +       + V +Q  +    A S FKVI  F +    LE++
Sbjct: 176 VRGC-VEPAEGIIEAAIGRHRTQRKKMTVSEQGRE----ARSRFKVIRRF-RNHTLLEVR 229

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
            +TGRTHQ+RVH   +G P++GD  Y A       SP   + +LHA  +   HP  GR +
Sbjct: 230 IYTGRTHQIRVHLAAIGHPVIGDATYGAE------SPDFPRQFLHAHRLGFRHPTDGRKM 283

Query: 306 QITAPLPAHMVKTWDSL 322
             T+ LPA +    + L
Sbjct: 284 SFTSELPADLAGPLERL 300


>gi|220909998|ref|YP_002485309.1| RluA family pseudouridine synthase [Cyanothece sp. PCC 7425]
 gi|219866609|gb|ACL46948.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7425]
          Length = 313

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 97/319 (30%), Positives = 158/319 (49%), Gaps = 42/319 (13%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-------KKRVKFNNRIQSGQVVRIPPV 70
           N RLDR+     P ++   +Q+++  GQV V+       K+ V+  +RIQ    + +PP 
Sbjct: 9   NERLDRYLAAQLPDLSRSRIQQLIEQGQVYVNGQLCQAKKQIVQVGDRIQ----LELPPP 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           + A    + E   LD               +LYED ++ + NKPAG+ V    G      
Sbjct: 65  VAA--EPLPEHIPLD---------------ILYEDDQLLIVNKPAGLVVHPAPGHSGGTL 107

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D  G    Q+P + HRLD++TSG + +A+T  A +HL    + +  ++ Y 
Sbjct: 108 VNALLAHCGDLPGIGGVQRPGIVHRLDKDTSGAIAIAKTELAHRHLQAQIKAKTARREYL 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +V+G+PK     I +  + +  +    + VV  ++KG + A++H+++ +     F  L+
Sbjct: 168 GVVYGVPKTSSGRI-DLPIGRHPVDRKKMAVVA-SDKGRS-AVTHWQIQERLG-NFTLLQ 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
            Q  TGRTHQ+RVH   +G PIVGD  Y +   G+ T        LHA  + L HP  G 
Sbjct: 224 FQLETGRTHQIRVHIAQLGHPIVGDPLYSS---GHATGVNLTGQALHAWKLALQHPVTGA 280

Query: 304 RLQITAPLPAHMVKTWDSL 322
            + +TAPLP  + K  + L
Sbjct: 281 TIAVTAPLPPELTKLLEVL 299


>gi|53720057|ref|YP_109043.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei K96243]
 gi|53725726|ref|YP_102318.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           mallei ATCC 23344]
 gi|67641115|ref|ZP_00439900.1| pseudouridine synthase, RluA family [Burkholderia mallei GB8 horse
           4]
 gi|121600497|ref|YP_993794.1| RluA family pseudouridine synthase [Burkholderia mallei SAVP1]
 gi|124385930|ref|YP_001028742.1| RluA family pseudouridine synthase [Burkholderia mallei NCTC 10229]
 gi|126448075|ref|YP_001081352.1| RluA family pseudouridine synthase [Burkholderia mallei NCTC 10247]
 gi|126452060|ref|YP_001067109.1| RluA family pseudouridine synthase [Burkholderia pseudomallei
           1106a]
 gi|134277927|ref|ZP_01764642.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 305]
 gi|167000755|ref|ZP_02266562.1| pseudouridine synthase, RluA family [Burkholderia mallei PRL-20]
 gi|167739572|ref|ZP_02412346.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 14]
 gi|167825182|ref|ZP_02456653.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 9]
 gi|167846678|ref|ZP_02472186.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei B7210]
 gi|167895267|ref|ZP_02482669.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 7894]
 gi|167911901|ref|ZP_02498992.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 112]
 gi|167919896|ref|ZP_02506987.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei BCC215]
 gi|217420690|ref|ZP_03452195.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 576]
 gi|226199879|ref|ZP_03795429.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pakistan 9]
 gi|237813217|ref|YP_002897668.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           MSHR346]
 gi|242315815|ref|ZP_04814831.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106b]
 gi|254178644|ref|ZP_04885299.1| pseudouridine synthase, RluA family [Burkholderia mallei ATCC
           10399]
 gi|254184188|ref|ZP_04890778.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1655]
 gi|254191223|ref|ZP_04897727.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pasteur 52237]
 gi|254195717|ref|ZP_04902143.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei S13]
 gi|254199211|ref|ZP_04905577.1| pseudouridine synthase, RluA family [Burkholderia mallei FMH]
 gi|254205518|ref|ZP_04911870.1| pseudouridine synthase, RluA family [Burkholderia mallei JHU]
 gi|254259234|ref|ZP_04950288.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1710a]
 gi|254357685|ref|ZP_04973958.1| pseudouridine synthase, RluA family [Burkholderia mallei
           2002721280]
 gi|52210471|emb|CAH36454.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei K96243]
 gi|52429149|gb|AAU49742.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           mallei ATCC 23344]
 gi|121229307|gb|ABM51825.1| pseudouridine synthase, RluA family [Burkholderia mallei SAVP1]
 gi|124293950|gb|ABN03219.1| pseudouridine synthase, RluA family [Burkholderia mallei NCTC
           10229]
 gi|126225702|gb|ABN89242.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106a]
 gi|126240945|gb|ABO04038.1| pseudouridine synthase, RluA family [Burkholderia mallei NCTC
           10247]
 gi|134251577|gb|EBA51656.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 305]
 gi|147748807|gb|EDK55881.1| pseudouridine synthase, RluA family [Burkholderia mallei FMH]
 gi|147752961|gb|EDK60026.1| pseudouridine synthase, RluA family [Burkholderia mallei JHU]
 gi|148026812|gb|EDK84833.1| pseudouridine synthase, RluA family [Burkholderia mallei
           2002721280]
 gi|157938895|gb|EDO94565.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pasteur 52237]
 gi|160699683|gb|EDP89653.1| pseudouridine synthase, RluA family [Burkholderia mallei ATCC
           10399]
 gi|169652462|gb|EDS85155.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei S13]
 gi|184214719|gb|EDU11762.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1655]
 gi|217396102|gb|EEC36119.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 576]
 gi|225927935|gb|EEH23972.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pakistan 9]
 gi|237503168|gb|ACQ95486.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           MSHR346]
 gi|238521978|gb|EEP85425.1| pseudouridine synthase, RluA family [Burkholderia mallei GB8 horse
           4]
 gi|242139054|gb|EES25456.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106b]
 gi|243063307|gb|EES45493.1| pseudouridine synthase, RluA family [Burkholderia mallei PRL-20]
 gi|254217923|gb|EET07307.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1710a]
          Length = 335

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 108/331 (32%), Positives = 163/331 (49%), Gaps = 34/331 (10%)

Query: 8   QYVVVENDEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Q  ++E DE     R+D +       +   ++ +ILRSG+VRV+K R+    R+  G VV
Sbjct: 16  QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGDVV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                      +        +       ++F    +L+ED  I V NKPAG++V GGSG+
Sbjct: 76  -----RVPPVRVAAADLARAAGPAPVPAAEFE---ILFEDDAIIVLNKPAGVAVHGGSGV 127

Query: 126 AYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           A+   G ++    ++       L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y
Sbjct: 128 AF---GVIEQMRHARPHAKFLELAHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRY 184

Query: 184 WSLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH--FKVIDCFAQ 238
           ++ V   W     ++  +   L K +   G+    V+  E G     SH  F ++D +  
Sbjct: 185 FACVHGDWAADWGRRRVVKAPLFKYATPDGE--RRVRVQEDGLP---SHTVFNLVDRWPD 239

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHA 292
            +  +E +  TGRTHQ+RVH  H+G PIVGD KY       A  + N    I+ +++LHA
Sbjct: 240 -YALVEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARANAVPSIK-RMFLHA 297

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             + L HP  G  LQ  APLPA   +  D L
Sbjct: 298 HRLRLAHPLTGEPLQFDAPLPAECRQFIDQL 328


>gi|56478533|ref|YP_160122.1| ribosomal large subunit pseudouridine synthase C [Aromatoleum
           aromaticum EbN1]
 gi|56314576|emb|CAI09221.1| ribosomal large subunit pseudouridine synthase C [Aromatoleum
           aromaticum EbN1]
          Length = 318

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 96/312 (30%), Positives = 160/312 (51%), Gaps = 31/312 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+      R+D +       +   ++ +ILRSG+VRV+  RV    R+     +RIPP+ 
Sbjct: 14  VDEAAAGQRIDNYLLRICKGVPKSHVYRILRSGEVRVNGGRVAPTYRLAENDEIRIPPIR 73

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A            ++       + L   +++ED  + V +KP+G +V GGSG+++ +  
Sbjct: 74  LAEK----------TTSGPAPAGEPLP--VVFEDEALLVVDKPSGKAVHGGSGVSFGVIE 121

Query: 132 FLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            L+S      Q+P      L HR+D+ETSG+LV+A+ R+A   L +  R  R++K Y +L
Sbjct: 122 QLRS------QRPDARLLELAHRIDRETSGLLVIAKKRSALTALHDMMREGRVEKRYLTL 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   N  + I   L K     G+    V  + K ++   S  +++  ++ +F  LE++
Sbjct: 176 VPGRWANPLQHIKEPLFKYLTAEGERRVRVSGDGKASH---SIVRLVRRWS-RFSLLEVE 231

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHP-EGG 303
             TGRTHQ+RVH  H+G P+ GD KY  +F  N +   +   +++LHA  +   HP  G 
Sbjct: 232 LKTGRTHQIRVHLAHLGFPLCGDDKY-GDFALNKSLEAEGLKRMFLHAARLSFAHPLTGE 290

Query: 304 RLQITAPLPAHM 315
            + +TA LPA +
Sbjct: 291 AITLTADLPAEL 302


>gi|167562573|ref|ZP_02355489.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           oklahomensis EO147]
 gi|167569756|ref|ZP_02362630.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           oklahomensis C6786]
          Length = 395

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 94/318 (29%), Positives = 148/318 (46%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRVD    K    +  G  + +      L  ++ 
Sbjct: 69  RLDKALAQLFPEFSRSRLQQWIESERVRVDGALAKIRQPVPLGATIEL------LPDLLP 122

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  + V +KPAG+ V   +G      ++G L  + 
Sbjct: 123 EQ--------LAFAPEPVPLSVVYEDDTLVVIDKPAGLVVHPAAGNWSGTLLNGLLHRYA 174

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 175 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALAWG--QMPAE 232

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 233 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTAMWARQPVSAIHCDLETGRTH 290

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 291 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPATGRTMQWRA 350

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLP  +    D+LGF  D
Sbjct: 351 PLPDDLAALVDALGFGSD 368


>gi|116626305|ref|YP_828461.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Solibacter usitatus Ellin6076]
 gi|116229467|gb|ABJ88176.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 296

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 94/316 (29%), Positives = 150/316 (47%), Gaps = 44/316 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI----PPVI 71
           +   R+D+W   H P  +   +Q+ ++S +VRV+   VK +  +++   V +    PP +
Sbjct: 9   DTGQRIDQWLHAHLPDFSRSRIQEWIKSARVRVNGAAVKTSYTLRAADAVEVEPADPPPL 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
           NA    I  +                   +LYED+ +   +KPAG+ V  G+G+     +
Sbjct: 69  NATAEDIPLR-------------------ILYEDADVVAIDKPAGMVVHAGAGVHSGTLV 109

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L  +    G     +P + HRLD+ TSG+L+VA+  AA Q L   F  R I+K+Y +
Sbjct: 110 NALLHRFATLSGVGGPLRPGIVHRLDRFTSGVLLVAKNDAAHQKLAAQFSGREIEKVYLA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN--YAISHFKVIDCFAQKFCWL 243
           LV G  K +   I      +  I  D VH  +   + A    A S ++V+  F   F  L
Sbjct: 170 LVHGTVKPETGRI------ERPIARDPVHRARMTARLAEGRAAWSEYRVLRRFPD-FTLL 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E++  TGRTHQ+RVH   +  P+VGD  Y     G    P+  + +LHA  +    P G 
Sbjct: 223 EVRIGTGRTHQIRVHLASIRHPVVGDTLY-----GAPAQPLLGRYFLHAHRIRFHLPSGR 277

Query: 304 RLQITAPLPAHMVKTW 319
            + I +PLP  + + W
Sbjct: 278 EMLIESPLPPDL-EAW 292


>gi|239617850|ref|YP_002941172.1| pseudouridine synthase, RluA family [Kosmotoga olearia TBF 19.5.1]
 gi|239506681|gb|ACR80168.1| pseudouridine synthase, RluA family [Kosmotoga olearia TBF 19.5.1]
          Length = 299

 Score =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 100/311 (32%), Positives = 159/311 (51%), Gaps = 38/311 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHI- 77
           RLD++ ++  P +   ++ K+LR G VRV+ KR+K  +  +  G VV       A+N+  
Sbjct: 18  RLDKFLRHVLPDLKLSSIYKLLRKGNVRVNGKRIKAPSYELSLGDVV-------AVNYRG 70

Query: 78  -IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
            I+  K L  S  L  H+  +K  +LYED      +KPAG++V  G G  I   I+G L 
Sbjct: 71  NIEYLKRLKESRELIPHNLPIK--ILYEDESFLAVDKPAGLAVHPGKGVQIVTLIEGLL- 127

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           ++    G KP L HRLD+ TSG+L+VA++  AA+ LT  FR +RI K Y +LV G+P+  
Sbjct: 128 AYGKRNGFKPFLVHRLDKHTSGVLLVAKSPQAARELTAMFREKRIDKRYVTLVKGLPEKS 187

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  + + +     +  +  ++VK+   G +                 +LE++  TG+ HQ
Sbjct: 188 RAYLKDVI---DGLREESEYIVKKAYSGCS-----------------FLEVRLFTGKKHQ 227

Query: 255 LRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLY-LHARYMDLPHPEGGR-LQITAPL 311
           +R     +G P+VGD  Y    F  NF    + K Y LH   M   HP+ G  +++ + L
Sbjct: 228 IRRQMAKIGHPVVGDDVYGDREFNRNFKKRYELKRYFLHCMKMGFIHPKTGHYVEVLSEL 287

Query: 312 PAHMVKTWDSL 322
           P  + K  + L
Sbjct: 288 PDDLKKVLEKL 298


>gi|126439038|ref|YP_001059822.1| RluA family pseudouridine synthase [Burkholderia pseudomallei 668]
 gi|167903651|ref|ZP_02490856.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei NCTC 13177]
 gi|126218531|gb|ABN82037.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 668]
          Length = 335

 Score =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 105/331 (31%), Positives = 160/331 (48%), Gaps = 34/331 (10%)

Query: 8   QYVVVENDEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Q  ++E DE     R+D +       +   ++ +ILRSG+VRV+K R+    R+  G   
Sbjct: 16  QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGD-- 73

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                       ++      +           +  +L+ED  I V NKPAG++V GGSG+
Sbjct: 74  ------VVRVPPVRVAAADLARAAGPAPVPAAEFEILFEDDAIIVLNKPAGVAVHGGSGV 127

Query: 126 AYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           A+   G ++    ++       L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y
Sbjct: 128 AF---GVIEQMRHARPHAKFLELAHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRY 184

Query: 184 WSLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH--FKVIDCFAQ 238
           ++ V   W     ++  +   L K +   G+    V+  E G     SH  F ++D +  
Sbjct: 185 FACVHGDWAADWGRRRVVRAPLFKYATPDGE--RRVRVQEDGLP---SHTVFNLVDRWPD 239

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHA 292
            +  +E +  TGRTHQ+RVH  H+G PIVGD KY       A  + N    I+ +++LHA
Sbjct: 240 -YALVEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARANAVPSIK-RMFLHA 297

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             + L HP  G  LQ  APLPA   +  D L
Sbjct: 298 HRLRLAHPLTGEPLQFDAPLPAECRQFIDQL 328


>gi|95929105|ref|ZP_01311850.1| Pseudouridine synthase, RluD [Desulfuromonas acetoxidans DSM 684]
 gi|95135006|gb|EAT16660.1| Pseudouridine synthase, RluD [Desulfuromonas acetoxidans DSM 684]
          Length = 350

 Score =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 100/336 (29%), Positives = 157/336 (46%), Gaps = 45/336 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E  +   RLDR+     P +    L+K++  G VRV+ + VK   +++ G+ V +    
Sbjct: 9   IEPGQAAERLDRFLTRQLPELTRSQLKKLVDDGLVRVNDQTVKAGAKLRGGETVCV---- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                       L  + ++    + L   +LYEDS + V NK AG+ V   +G   H  G
Sbjct: 65  -----------TLPQAQSVETLPEDLPLTVLYEDSDLIVINKAAGMVVHPAAG---HSSG 110

Query: 132 FLKSWV-----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            L + +     D  G     +P + HRLD++TSG++V  +      HL   F+   IQ+ 
Sbjct: 111 TLVNALLYHCHDLSGVGGELRPGIVHRLDKDTSGVMVATKNDVTHNHLAAQFKDHSIQRR 170

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCF-AQK 239
           Y +LV G  +N +  I       + IG    H  K   KG     A++H+KV+  + A +
Sbjct: 171 YVALVHGQVQNARGTI------DAPIGRHPTHRKKMTSKGRGGRRAVTHWKVLRRYDADR 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--NKLY------LH 291
              LEM+  TGRTHQ+RVH   M  P+VGD  Y    + N  + ++  N+++      LH
Sbjct: 225 LSLLEMRLETGRTHQIRVHLSEMNLPLVGDPLYGNRTRANGINDLEVRNRVHALHRQALH 284

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           AR +   HP  G  L+ T+ LP  +      L  KY
Sbjct: 285 ARLLGFIHPRTGDYLEFTSDLPGDLASIVAFLDDKY 320


>gi|311104735|ref|YP_003977588.1| ribosomal large subunit pseudouridine synthase C [Achromobacter
           xylosoxidans A8]
 gi|310759424|gb|ADP14873.1| ribosomal large subunit pseudouridine synthase C [Achromobacter
           xylosoxidans A8]
          Length = 325

 Score =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 96/309 (31%), Positives = 158/309 (51%), Gaps = 22/309 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V V+ ++   RLD +       +   ++ K +R G+VR++K R   + R+  G VVR
Sbjct: 23  VRMVEVDAEQAGQRLDNFLARLCKGVPKTHIYKAIRGGEVRINKGRTSADYRVAEGDVVR 82

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+   L    K + +  +   +           ++ED  + V +KPAG++V GGSG++
Sbjct: 83  IPPL--RLPDPGKPRPVPGAEFPV-----------VFEDEALLVVDKPAGVAVHGGSGVS 129

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + +   L++     G K   L HRLD+ETSG+L+VA+ R+A   L    R  +  K Y +
Sbjct: 130 FGVIEQLRAA--RPGAKFLELVHRLDRETSGLLMVAKKRSALLALHAMLREGKGDKHYLA 187

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   N ++ I   L K +   G+    V  + + A+  ++  + +  ++     ++ 
Sbjct: 188 LVEGDWVNDRQHIKLGLSKWTTQSGERRVKVDPDGQSAHTIVTLKQRLGGYS----LVDA 243

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +  TGRTHQ+RVH    G PIVGD KY  +  +  F      +++LHA  + L HP  G 
Sbjct: 244 ELRTGRTHQIRVHLAASGFPIVGDDKYGRDEVRAEFARMGFGRMFLHAHQLTLAHPVTGE 303

Query: 305 -LQITAPLP 312
            L +TA LP
Sbjct: 304 PLTLTAELP 312


>gi|254282586|ref|ZP_04957554.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium NOR51-B]
 gi|219678789|gb|EED35138.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium NOR51-B]
          Length = 315

 Score =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 96/320 (30%), Positives = 160/320 (50%), Gaps = 21/320 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + V V  +E   RLD +       +    L + +R G+VRV+K R K + R+++G  VR
Sbjct: 8   ARLVTVTEEESGQRLDNYLLRTLQGVPKTRLYRAVRKGEVRVNKGRAKVDLRLKAGDTVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP       ++  Q    + V+         SI+L + + +   NKP+G++V GGSG+ 
Sbjct: 68  LPP-------LVASQPKGPAPVSGRWRKAIGGSIVL-DTADLLALNKPSGLAVHGGSGVD 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L++    + +   L HRLD++TSG+++VA+  +  + L    R   I K Y  L
Sbjct: 120 VGLIESLRAMFPEQ-RYLELVHRLDRDTSGLILVAKRASVLRDLHAQLRDGEIDKRYQCL 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G      + +   L + S   G+    V  + K    +++ F+V++ F Q    LE +
Sbjct: 179 VSGRWPAYLKQVDGPLERYSLASGERRVRVSVDGK---PSLTRFRVLERF-QDATLLEAK 234

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-QNKLYLHA---RYMDLPHPEG 302
           P +GRTHQ+RVHAL  G PI+GD KY        T+ +  N+L+LHA   R+    HP  
Sbjct: 235 PVSGRTHQIRVHALQAGHPILGDAKYSNAESEALTAAVTANRLFLHAESLRFKLGDHP-- 292

Query: 303 GRLQITAPLPAHMVKTWDSL 322
              +++APL + +    + L
Sbjct: 293 --CELSAPLDSSLRAVLERL 310


>gi|167581129|ref|ZP_02374003.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           thailandensis TXDOH]
          Length = 335

 Score =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 107/331 (32%), Positives = 161/331 (48%), Gaps = 34/331 (10%)

Query: 8   QYVVVENDEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Q  ++E DE     R+D +       +   ++ +ILRSG+VRV+K R+    R+  G VV
Sbjct: 16  QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGDVV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                      +        +       ++F    +L+ED  I   NKPAG++V GGSG+
Sbjct: 76  -----RVPPVRVAAADLARAAGSAPVPAAEFE---ILFEDDAIIALNKPAGVAVHGGSGV 127

Query: 126 AYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           A+   G ++    ++       L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y
Sbjct: 128 AF---GVIEQMRHARPHAKFLELVHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRY 184

Query: 184 WSLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH--FKVIDCFAQ 238
           ++ V   W     ++  +   L K +   G+    V+  E G     SH  F ++D +  
Sbjct: 185 FACVHGDWAADWGRRRAVKAPLFKYATPDGE--RRVRVQEDGLP---SHTVFNLVDRWPD 239

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHA 292
            +  +E +  TGRTHQ+RVH  H+G PIVGD KY  +F  N         P   +++LHA
Sbjct: 240 -YALVEAELKTGRTHQIRVHLAHLGLPIVGDAKY-GDFALNKALARASAVPSIKRMFLHA 297

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             + L HP  G  LQ  APLPA   +  D L
Sbjct: 298 HRLRLAHPLTGEPLQFDAPLPAECRQFLDQL 328


>gi|167619213|ref|ZP_02387844.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           thailandensis Bt4]
 gi|257138436|ref|ZP_05586698.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           thailandensis E264]
          Length = 335

 Score =  129 bits (325), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 107/331 (32%), Positives = 161/331 (48%), Gaps = 34/331 (10%)

Query: 8   QYVVVENDEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Q  ++E DE     R+D +       +   ++ +ILRSG+VRV+K R+    R+  G VV
Sbjct: 16  QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGDVV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                      +        +       ++F    +L+ED  I   NKPAG++V GGSG+
Sbjct: 76  -----RVPPVRVAAADLARAAGPAPVPAAEFE---ILFEDDAIIALNKPAGVAVHGGSGV 127

Query: 126 AYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           A+   G ++    ++       L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y
Sbjct: 128 AF---GVIEQMRHARPHAKFLELVHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRY 184

Query: 184 WSLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH--FKVIDCFAQ 238
           ++ V   W     ++  +   L K +   G+    V+  E G     SH  F ++D +  
Sbjct: 185 FACVHGDWAADWGRRRAVKAPLFKYATPDGE--RRVRVQEDGLP---SHTVFNLVDRWPD 239

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHA 292
            +  +E +  TGRTHQ+RVH  H+G PIVGD KY  +F  N         P   +++LHA
Sbjct: 240 -YALVEAELKTGRTHQIRVHLAHLGLPIVGDAKY-GDFALNKALARASAVPSIKRMFLHA 297

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             + L HP  G  LQ  APLPA   +  D L
Sbjct: 298 HRLRLAHPLTGEPLQFDAPLPAECRQFLDQL 328


>gi|76810444|ref|YP_334298.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 1710b]
 gi|76579897|gb|ABA49372.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 1710b]
          Length = 477

 Score =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 105/330 (31%), Positives = 160/330 (48%), Gaps = 32/330 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + ++      R+D +       +   ++ +ILRSG+VRV+K R+    R+  G VV 
Sbjct: 159 VSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGDVV- 217

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                     +        +       ++F    +L+ED  I V NKPAG++V GGSG+A
Sbjct: 218 ----RVPPVRVAAADLARAAGPAPVPAAEFE---ILFEDDAIIVLNKPAGVAVHGGSGVA 270

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    ++       L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y+
Sbjct: 271 F---GVIEQMRHARPHAKFLELAHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRYF 327

Query: 185 SLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH--FKVIDCFAQK 239
           + V   W     ++  +   L K +   G+    V+  E G     SH  F ++D +   
Sbjct: 328 ACVHGDWAADWGRRRVVKAPLFKYATPDGE--RRVRVQEDGLP---SHTVFNLVDRWPD- 381

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHAR 293
           +  +E +  TGRTHQ+RVH  H+G PIVGD KY  +F  N         P   +++LHA 
Sbjct: 382 YALVEAELKTGRTHQIRVHLAHLGLPIVGDAKY-GDFALNKALARANAVPSIKRMFLHAH 440

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            + L HP  G  LQ  APLPA   +  D L
Sbjct: 441 RLRLAHPLTGEPLQFDAPLPAECRQFIDQL 470


>gi|254497897|ref|ZP_05110662.1| ribosomal large subunit (23S rRNA) pseudouridine synthase C
           [Legionella drancourtii LLAP12]
 gi|254352895|gb|EET11665.1| ribosomal large subunit (23S rRNA) pseudouridine synthase C
           [Legionella drancourtii LLAP12]
          Length = 263

 Score =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 89/241 (36%), Positives = 134/241 (55%), Gaps = 20/241 (8%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           + +G V+RIPP+  +      E K +     L K    LK  +++ED+   V NKP+GI+
Sbjct: 1   MHAGDVIRIPPIRTS------EAKEVFVGDALAKR---LKDCIIFEDACFLVINKPSGIA 51

Query: 119 VQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           V GGSG++   I+   K+  D       L HRLD+ETSG L++A+ R+  + +      R
Sbjct: 52  VHGGSGLSLGVIEALRKTRQDLA--YLELIHRLDKETSGCLLLAKKRSTLRAMHALLEAR 109

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +QK YW+L+    + KK+   +  L+K+ I      VV  N++G     + FK+++ + 
Sbjct: 110 EVQKTYWALLTHRWEGKKQVTVHAALEKN-ILKSGERVVSVNDEGKASETT-FKLLENY- 166

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARY 294
           Q+ CW+E  P TGRTHQ+RVH+ H+G  IVGD KY A   G     I N   +LYLHAR 
Sbjct: 167 QQACWVEASPKTGRTHQIRVHSAHLGHVIVGDEKYGA-LAGEVEG-IDNRHRRLYLHARS 224

Query: 295 M 295
           +
Sbjct: 225 I 225


>gi|88608500|ref|YP_506438.1| ribosomal large subunit pseudouridine synthase C [Neorickettsia
           sennetsu str. Miyayama]
 gi|88600669|gb|ABD46137.1| ribosomal large subunit pseudouridine synthase C [Neorickettsia
           sennetsu str. Miyayama]
          Length = 305

 Score =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 100/313 (31%), Positives = 156/313 (49%), Gaps = 23/313 (7%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +VEND    RLD++ ++ +       LQK LR   VR++   VK +  +  G  + +   
Sbjct: 5   IVENDCR--RLDKYLRDTFGQFPQSALQKALRKKAVRLNNSVVKASAAVLKGDSLTLSA- 61

Query: 71  INALNHIIKEQKILDSSVNL--TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            N L  +   ++I   S  +  +K  +F+ S++LYED  +   +KP G  VQ G GI   
Sbjct: 62  -NFLQILSSPREIPSDSSKVVDSKFVEFIASLMLYEDENVLAISKPFGFPVQSGYGITAS 120

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           ID  +KS       + R+ HRLD+ T+G+L+ A+T  AA+ L   F  R ++K Y ++V 
Sbjct: 121 IDNAMKSI----NPEYRVVHRLDKHTTGVLIFAKTLDAARELWRLFSNRLVKKSYLAIVI 176

Query: 189 GIPKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFCWLE 244
           G  K KK   +C  N +L K         V++ N  G   +AI+ F VI  F +    +E
Sbjct: 177 GELKEKKGVVDCYINKVLFKGE------EVMQCNNIGNGEHAITQFHVIKKF-KNTSLIE 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           + P TGR HQ+R     +G P++ D KY    K      +  KL LHA  ++     G  
Sbjct: 230 LFPLTGRKHQIRSQMASIGHPVLNDGKY-GRRKAFLEWSVNKKLCLHACEIEF-ELFGKV 287

Query: 305 LQITAPLPAHMVK 317
           +++TA LP H  +
Sbjct: 288 IKVTAELPVHFAE 300


>gi|258511286|ref|YP_003184720.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478012|gb|ACV58331.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 314

 Score =  129 bits (325), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 93/336 (27%), Positives = 169/336 (50%), Gaps = 43/336 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPH----INFVNLQKILRSGQVRVDKK-RVKF 55
           M    +VQY V   D    RLDRW  +        ++   +Q+ L  G +R  +  R+K 
Sbjct: 1   MRPAIHVQYEVSAEDA-GERLDRWLTDRLQEDDIEVSRTQVQRWLDDGFIRRARPGRLKA 59

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           ++ +++G +  +          + E++ L+   +     D +  ++ YED  + V +KP 
Sbjct: 60  SDPVEAGDLYEVD---------VPEEEPLELVPD-----DGVPFVVAYEDDDVIVVDKPR 105

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAA 166
           G+ V  G+G   H+ G L + + ++G          +P + HR+D++TSG++V A++  A
Sbjct: 106 GVVVHPGAG---HMRGTLVNGLLARGTPLCTLAGALRPGVVHRIDKDTSGLVVFAKSDRA 162

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
            + L E+FR   +++ Y ++  G   +++  I   + +      D   +  +  +G   A
Sbjct: 163 YRALVEAFRAHDVEREYVAIAHGRMPHREGTIDMPIARDP---ADRQRMAVR--QGGKRA 217

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++HF+V++ FA K+ +L ++  TGRTHQ+RVH   +G PI GD  Y        T PI  
Sbjct: 218 VTHFEVLESFA-KYSYLRLRLETGRTHQIRVHLAAIGHPIAGDPVYGP----RHTLPIDG 272

Query: 287 KLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           +  LHAR +   HP+G RL+  + +P+ M +  D L
Sbjct: 273 Q-ALHARTLGFTHPDGRRLRFESAVPSDMARLLDGL 307


>gi|269468168|gb|EEZ79867.1| pseudouridylate synthase, 23S RNA-specific [uncultured SUP05
           cluster bacterium]
          Length = 303

 Score =  129 bits (324), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 95/310 (30%), Positives = 152/310 (49%), Gaps = 25/310 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+   E  RLD +   H   +   ++ +++R G+VRV+K R K   ++Q   VVR
Sbjct: 3   VSFKTVDEFSEGQRLDNYLLKHLKGVPKSHIYRVIRKGEVRVNKGRKKAEYKLQLDDVVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP I     I   Q ++  S+        L   +LYED  + + NKP+G++V  GSG+A
Sbjct: 63  IPP-IRVSESI---QVVVSDSLK-----QLLSDAILYEDKGLLIINKPSGLAVHSGSGVA 113

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
               G +++      +   L HRLD+ TSG+L++A+ R+  ++L E     +++K Y +L
Sbjct: 114 V---GVIEALRGMYKEPVELVHRLDRSTSGVLLIAKKRSVLKNLHEQLSQHQMEKRYTAL 170

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ---KFCWL 243
           V G    K+  I   L + S         V  + KG   A+SHF+ +  F     +   +
Sbjct: 171 VKGTWSKKRHTIDAPLYQNS-------RGVVIDAKGKQ-AVSHFQPLKNFHNDEFEASLV 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEG 302
           E+   TGR HQ+R HA + G  I  D KY    F     +    +L+LHA  +   +P  
Sbjct: 223 EVLIETGRMHQIRAHAKYAGHSIAFDDKYGDKIFDTQVKAKGLKRLFLHAHQLTFANPLT 282

Query: 303 GRLQ-ITAPL 311
             +Q + APL
Sbjct: 283 SEIQKVKAPL 292


>gi|222641041|gb|EEE69173.1| hypothetical protein OsJ_28343 [Oryza sativa Japonica Group]
          Length = 465

 Score =  129 bits (324), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 95/335 (28%), Positives = 150/335 (44%), Gaps = 70/335 (20%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKI 108
           +RV   +++  G ++ +P  +N     +KE  + + +      ++  FL+ + +Y+D  I
Sbjct: 133 RRVSAKDQLMPGDILFLP--VN-----LKESSVAEKTKKFDNRNEINFLRGLEIYKDEAI 185

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V NKP G+ VQGG GI   ID     + ++  + PRL HRLD++ SGILV+ R + +  
Sbjct: 186 IVVNKPPGMPVQGGVGIKNSIDVLASMFEENSSEAPRLVHRLDRDCSGILVLGRNQLSTS 245

Query: 169 HLTESFRMRR-----------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV- 216
            L   FR +            +Q+ Y +LV G P++ K  ++  L K     G    +  
Sbjct: 246 MLHAIFREKTADALADGTQHVLQRKYVALVIGTPRHPKGLLSAPLAKILLQDGKSERLTI 305

Query: 217 --KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC 273
               N      A++ ++VI+   Q + WLE+ P TGR HQLRVH    +G PIVGD+KY 
Sbjct: 306 RASSNAASVQDALTEYRVIESCPQGYTWLELFPRTGRKHQLRVHCAEVLGTPIVGDYKYG 365

Query: 274 AN-----------------------------FKGNFTSPIQNKLYLHARYMDLP------ 298
                                            G   +  Q +L+LH + M LP      
Sbjct: 366 RQAHQKWMPLPLPRTIDEELLRKRKLPFGLVVGGGSIAEEQPQLHLHCKQMVLPDVSVAL 425

Query: 299 --------HPEGG---RLQITAPLPAHMVKTWDSL 322
                   +P+     +L   APLP HM  +W+ L
Sbjct: 426 HRLQSSDVNPDFSDLEKLNFVAPLPLHMRLSWEIL 460


>gi|83719283|ref|YP_442243.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           thailandensis E264]
 gi|83653108|gb|ABC37171.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           thailandensis E264]
          Length = 477

 Score =  129 bits (324), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 104/330 (31%), Positives = 159/330 (48%), Gaps = 32/330 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + ++      R+D +       +   ++ +ILRSG+VRV+K R+    R+  G VV 
Sbjct: 159 VSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGDVV- 217

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                     +        +       ++F    +L+ED  I   NKPAG++V GGSG+A
Sbjct: 218 ----RVPPVRVAAADLARAAGPAPVPAAEFE---ILFEDDAIIALNKPAGVAVHGGSGVA 270

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++    ++       L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y+
Sbjct: 271 F---GVIEQMRHARPHAKFLELVHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRYF 327

Query: 185 SLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH--FKVIDCFAQK 239
           + V   W     ++  +   L K +   G+    V+  E G     SH  F ++D +   
Sbjct: 328 ACVHGDWAADWGRRRAVKAPLFKYATPDGE--RRVRVQEDGLP---SHTVFNLVDRWPD- 381

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHAR 293
           +  +E +  TGRTHQ+RVH  H+G PIVGD KY  +F  N         P   +++LHA 
Sbjct: 382 YALVEAELKTGRTHQIRVHLAHLGLPIVGDAKY-GDFALNKALARASAVPSIKRMFLHAH 440

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            + L HP  G  LQ  APLPA   +  D L
Sbjct: 441 RLRLAHPLTGEPLQFDAPLPAECRQFLDQL 470


>gi|218201639|gb|EEC84066.1| hypothetical protein OsI_30347 [Oryza sativa Indica Group]
          Length = 465

 Score =  129 bits (324), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 95/335 (28%), Positives = 150/335 (44%), Gaps = 70/335 (20%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKI 108
           +RV   +++  G ++ +P  +N     +KE  + + +      ++  FL+ + +Y+D  I
Sbjct: 133 RRVSAKDQLMPGDILFLP--VN-----LKESSVAEKTKKFDNRNEINFLRGLEIYKDEAI 185

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V NKP G+ VQGG GI   ID     + ++  + PRL HRLD++ SGILV+ R + +  
Sbjct: 186 IVVNKPPGMPVQGGVGIKNSIDVLASMFEENSSEAPRLVHRLDRDCSGILVLGRNQLSTS 245

Query: 169 HLTESFRMRR-----------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV- 216
            L   FR +            +Q+ Y +LV G P++ K  ++  L K     G    +  
Sbjct: 246 MLHAIFREKTADALADGTQHVLQRKYVALVIGTPRHPKGLLSAPLAKILLQDGKSERLTV 305

Query: 217 --KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC 273
               N      A++ ++VI+   Q + WLE+ P TGR HQLRVH    +G PIVGD+KY 
Sbjct: 306 RASSNAASVQDALTEYRVIESCPQGYTWLELFPRTGRKHQLRVHCAEVLGTPIVGDYKYG 365

Query: 274 AN-----------------------------FKGNFTSPIQNKLYLHARYMDLP------ 298
                                            G   +  Q +L+LH + M LP      
Sbjct: 366 RQAHQKWMPLPLPRTIDEELLRKRKLPFGLVVGGGSIAEEQPQLHLHCKQMVLPDVSVAL 425

Query: 299 --------HPEGG---RLQITAPLPAHMVKTWDSL 322
                   +P+     +L   APLP HM  +W+ L
Sbjct: 426 HRLQSSDVNPDFSDLEKLNFVAPLPLHMRLSWEIL 460


>gi|167837371|ref|ZP_02464254.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           thailandensis MSMB43]
          Length = 335

 Score =  129 bits (324), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 110/331 (33%), Positives = 166/331 (50%), Gaps = 34/331 (10%)

Query: 8   QYVVVENDEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Q  ++E DE     R+D +       +   ++ +ILRSG+VRV+K R+    R+  G VV
Sbjct: 16  QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGDVV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + +   +        +        +L+ED  I   NKPAG++V GGSG+
Sbjct: 76  RVPPVRVAAADLARAAGLAPVPAAAFE--------ILFEDDAIIALNKPAGVAVHGGSGV 127

Query: 126 AYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           A+   G ++    ++       L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y
Sbjct: 128 AF---GVIEQMRHARPHAKFLELAHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRY 184

Query: 184 WSLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH--FKVIDCFAQ 238
           ++ V   W     ++  +   L K +   G+    V+  E G     SH  F ++D +  
Sbjct: 185 FACVHGDWAADWGRRRTVKAPLFKYATPDGE--RRVRVQEDGLP---SHTVFNLVDRWPD 239

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHA 292
            +  +E +  TGRTHQ+RVH  H+G PIVGD KY  +F  N        +P   +++LHA
Sbjct: 240 -YALVEAELKTGRTHQIRVHLAHLGLPIVGDAKY-GDFALNKALSRANAAPSIKRMFLHA 297

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +   HP  G  LQ  APLPA   +  D L
Sbjct: 298 HRLRFAHPLTGEPLQFDAPLPAECRQFLDQL 328


>gi|219849171|ref|YP_002463604.1| pseudouridine synthase, RluA family [Chloroflexus aggregans DSM
           9485]
 gi|219543430|gb|ACL25168.1| pseudouridine synthase, RluA family [Chloroflexus aggregans DSM
           9485]
          Length = 310

 Score =  129 bits (323), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 97/323 (30%), Positives = 157/323 (48%), Gaps = 40/323 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV--VRI 67
           ++V ++    R+DR+     P ++   +Q+++  G V    +  + +  +  G +  V I
Sbjct: 17  LIVPSEASGQRIDRFLAASMPDLSRTQVQRLIEQGMVLYAGRPTRASQPLHPGTIIHVTI 76

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
           PP +     ++ E   LD               ++YED+ + V NKPAG+ V    G   
Sbjct: 77  PPPVPV--ELMPESIPLD---------------IVYEDADVAVINKPAGMVVHPAPGHPR 119

Query: 126 AYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++  L  + D   S   +P + HRLD++TSG+LV+AR  AA + L E  + RR++KI
Sbjct: 120 GTLVNALLARYPDLAISGEVRPGIVHRLDRDTSGLLVIARHDAALRALVEQQQARRMRKI 179

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFC 241
           Y +LV G P       A        IG D    ++         A +H++VI  F   + 
Sbjct: 180 YQALVVGRPPVCGTIDAP-------IGRDPRDRLRMAVVADGRPARTHYRVIATFG-DYS 231

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            LE+Q  TGRTHQ+RVH  H+G PIVGD  Y     G   S ++  + +LHA  +   HP
Sbjct: 232 LLEVQLETGRTHQIRVHLRHLGYPIVGDPVY-----GPRRSHLRLTRQFLHAGQLGFFHP 286

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G+  + TAPLP+ +    +++
Sbjct: 287 RDGQWREFTAPLPSDLSSVLNAM 309


>gi|320449663|ref|YP_004201759.1| ribosomal large subunit pseudouridine synthase D [Thermus
           scotoductus SA-01]
 gi|320149832|gb|ADW21210.1| ribosomal large subunit pseudouridine synthase D [Thermus
           scotoductus SA-01]
          Length = 308

 Score =  129 bits (323), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 100/337 (29%), Positives = 162/337 (48%), Gaps = 49/337 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           VV    E +RLD+        ++    Q+ +  G+V+V +K V K + R++  +V+ +PP
Sbjct: 4   VVRFRMEGVRLDQAVAEAC-GVSRSRAQEWIAQGRVQVGEKVVEKPSYRLKGEEVLVVPP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                     E+K   +  +L          +LYED  + V NKPAG+      G+    
Sbjct: 63  ----------EEKPFVAPQDLA-------IPVLYEDEDLLVLNKPAGLLTHPAPGVYTGT 105

Query: 128 HIDGFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            ++  L  +         +  +P + HRLD++TSG+LVVA+   A + L  +FR R + K
Sbjct: 106 VVNALLGRYFPLQEAERPEEVRPGIVHRLDKDTSGVLVVAKHGGALEALARAFRDRLVMK 165

Query: 182 IYWSLVWGIPKNKK--ECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            Y ++  G PK       I    ++  K H+GG              YA + F+++   A
Sbjct: 166 RYLAITEGHPKEGTLIAPIGRHPVERHKMHVGG----------IAPRYAETEFRIL-ATA 214

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +E +PHTGRTHQ+RVH  ++  PI+GD  Y         SP   +  LHA  + +
Sbjct: 215 GPYALVEARPHTGRTHQIRVHLKYLRAPILGDELY------GRPSPHIPRQALHAYELRI 268

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
           PHP  GR L+  AP+P  MVK W +LG ++   + ++
Sbjct: 269 PHPRTGRFLEFRAPVPRDMVKAWGALGGEWPEGIILE 305


>gi|289208370|ref|YP_003460436.1| pseudouridine synthase [Thioalkalivibrio sp. K90mix]
 gi|288944001|gb|ADC71700.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. K90mix]
          Length = 328

 Score =  129 bits (323), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 92/315 (29%), Positives = 155/315 (49%), Gaps = 26/315 (8%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +  RLD +       +    + +++R G +RVD +R K   R+  G  VR+P     L+ 
Sbjct: 24  DGQRLDNFLLRELKGVPKSLIYRLVRKGAIRVDGRRAKVTQRLSVGSEVRVP----DLDR 79

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
               ++ +   V      D L+  +L+ED ++ V +KP+G++V GGSG+A+ I   ++  
Sbjct: 80  PEAVERDIPPGV-----LDRLRRSILHEDDQVLVLDKPSGLAVHGGSGLAFGIIEAMRQL 134

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               G +  L HRLD+ETSG L++A++R+  Q    + R  R++K Y +L  G   + + 
Sbjct: 135 --RPGSELELGHRLDRETSGCLLLAKSRSGLQDFHAALREGRVEKRYLALQVGAFPSDQP 192

Query: 197 CIANWLLKKSHIGGDYVHVVKQNE----KGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            + +  +  S  G D    ++  E    + A  AIS F  ++ +   F   E++  TGRT
Sbjct: 193 IVCDEPIASSR-GPDGKRRMRAGEDADPESARSAISQFVPLERYG-SFQLAEVRIGTGRT 250

Query: 253 HQLRVHALHMGCPIVGDHKYC---AN--FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           HQ+RVH   +G P+ GDH Y    AN   +G        +L+LHA+ +            
Sbjct: 251 HQIRVHGQAIGHPVGGDHDYGLPDANRVLRGAGL----KRLFLHAQALQYEDSASESHVY 306

Query: 308 TAPLPAHMVKTWDSL 322
           +APLP  +    D+L
Sbjct: 307 SAPLPDELQSILDAL 321


>gi|153823924|ref|ZP_01976591.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
 gi|126518556|gb|EAZ75779.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
          Length = 224

 Score =  129 bits (323), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 69/188 (36%), Positives = 117/188 (62%), Gaps = 6/188 (3%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWG 189
            Y++LV G
Sbjct: 177 YYYALVMG 184


>gi|289522930|ref|ZP_06439784.1| ribosomal large subunit pseudouridine synthase D [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289503954|gb|EFD25118.1| ribosomal large subunit pseudouridine synthase D [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 299

 Score =  129 bits (323), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 78/211 (36%), Positives = 117/211 (55%), Gaps = 15/211 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSW---VDSKGQKPRLTHRLDQETS 155
           +LYED+ I + +KPA + V    G  Y   + G +  +    DS  ++P + HRLD  TS
Sbjct: 76  VLYEDADIIIIDKPAPLVVHPAVGHWYGTLVHGLVYRYPELADSDMRRPGIVHRLDAGTS 135

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V+AR   + Q LT++F+ R ++K Y +LV+G P  +K  IA      S IG    + 
Sbjct: 136 GLMVIARNLFSKQKLTDAFKARSVKKEYLALVYGSPNKEKGTIA------SPIGRHPKNR 189

Query: 216 VKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +K     G   A++ ++V+     KF +L    HTGRTHQ+RVH   MGCPIVGD  Y  
Sbjct: 190 LKMAVVSGGREAVTEYEVL-WSNDKFSFLRCTIHTGRTHQIRVHLKDMGCPIVGDRLYGC 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           N K  +    +++ +LHA  +  PHP  GR+
Sbjct: 249 NLKAEWVP--KDRFFLHAWKLAFPHPRDGRI 277


>gi|121601705|ref|YP_988611.1| RluA family pseudouridine synthase [Bartonella bacilliformis KC583]
 gi|120613882|gb|ABM44483.1| pseudouridine synthase, RluA family [Bartonella bacilliformis
           KC583]
          Length = 336

 Score =  129 bits (323), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 102/338 (30%), Positives = 161/338 (47%), Gaps = 49/338 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           + + D    R+D+W   HY + ++   LQ ++R G +++D K V +   +I+S Q + + 
Sbjct: 5   ITDEDALGQRIDQWLAKHYQNELSRSRLQTLIREGYLKIDGKLVTEPKTKIKSNQTIEL- 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
             I  LN+   E + +   +             L+ED  I V NKPAG+ V  G G    
Sbjct: 64  -TIPTLNNAYPEGEAIPLHI-------------LFEDDHIIVVNKPAGLVVHPGHGNWTG 109

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF----R 175
                + YH    L      +  +P + HRLD+ TSG++VVA+   A + L+  F    R
Sbjct: 110 TLVNALIYHCGDSLSGIGGVR--RPGIVHRLDKNTSGVIVVAKNDLAHKGLSAQFSDHGR 167

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              + + Y +L+WG P N+   +    L ++        V+  +   A +A++HF VI+ 
Sbjct: 168 TGVLDRRYHALIWGSP-NRNIGVITASLGRARYDRTKQAVIHSHNIYARHAVTHFSVIEK 226

Query: 236 F---AQKFCW---LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQ- 285
           +   A K  +   LE +  TGRTHQ+RVH  H+G P+VGD  Y   FK     F S I+ 
Sbjct: 227 YQTCADKIPFASLLECRLETGRTHQIRVHMAHIGHPLVGDTVYGNAFKTKSNRFDSTIKE 286

Query: 286 -----NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
                N+  LHA  +   HP  G  +  +APLP  M +
Sbjct: 287 AIDLFNRQALHAASLTFEHPAKGNIMSFSAPLPQDMAE 324


>gi|221212790|ref|ZP_03585766.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Burkholderia multivorans CGD1]
 gi|221167003|gb|EED99473.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Burkholderia multivorans CGD1]
          Length = 400

 Score =  129 bits (323), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 96/319 (30%), Positives = 147/319 (46%), Gaps = 35/319 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +VRVD    K    +  G  + + P       ++ 
Sbjct: 70  RLDKALAQLFPEFSRSRLQSWIDAQRVRVDGAPAKIRQPVPLGATIELVP------DLLP 123

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 124 EQ--------LAFTPEPVPLDIVYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYG 175

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG   ++ 
Sbjct: 176 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGAMPDEG 235

Query: 196 ECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVID-CFAQK--FCWLEMQPHT 249
              A        IG D     +           A +HF+ +D C  Q+     ++    T
Sbjct: 236 TIDAP-------IGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLET 288

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHP-EGGRL 305
           GRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  G  +
Sbjct: 289 GRTHQIRVHCSHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPVTGSAM 348

Query: 306 QITAPLPAHMVKTWDSLGF 324
           Q   PLP  M    D+LGF
Sbjct: 349 QWRCPLPDDMTALVDALGF 367


>gi|302035761|ref|YP_003796083.1| 23S rRNA pseudouridine synthase [Candidatus Nitrospira defluvii]
 gi|300603825|emb|CBK40157.1| 23S rRNA pseudouridine synthase [Candidatus Nitrospira defluvii]
          Length = 321

 Score =  129 bits (323), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 84/325 (25%), Positives = 156/325 (48%), Gaps = 32/325 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV   E + R+D +  N  P  +   LQ+++  G++ ++ + ++ + +I+ G  +R+  
Sbjct: 11  IVVTGGESSKRIDVFLANRDPTFSRSALQRLIGEGRILINGQTIRPSQKIKPGDRIRLE- 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                   +   + LD         + +   +L+ED+++ V +KPAG+ V    G     
Sbjct: 70  --------VPRPEPLDLK------PEAIPFDILHEDAELLVLHKPAGLVVHPAPGNWSGT 115

Query: 125 ----IAYHI--DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               + +H    G   S +  K ++P L HRLD+ETSG++V+A+T  A + L   F++  
Sbjct: 116 LVNALLHHFATSGVTPSHIGGK-ERPGLVHRLDKETSGVMVIAKTDQAHRALAAQFKLHT 174

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I ++Y +L+WG+PK     I   + + +     +     + +  A    + ++V + + +
Sbjct: 175 ITRVYEALIWGVPKKGHGLIELAIGRDTKERKKFSARTTKPKPSA----TDYQVEERYGK 230

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              ++ + P TGRTHQLRVH   +  PI+GD  Y      +       ++ LHAR +   
Sbjct: 231 IAAYVRLFPRTGRTHQLRVHLTSIDHPILGDKTYGGAKVMSVAGVTIPRVMLHARTLGFT 290

Query: 299 HPEGGRL-QITAPLPAHMVKTWDSL 322
           HP GG   +   P P  M +  D L
Sbjct: 291 HPNGGEYHEFDVPCPPDMEQVQDLL 315


>gi|206900407|ref|YP_002249968.1| ribosomal large subunit pseudouridine synthase C [Dictyoglomus
           thermophilum H-6-12]
 gi|206739510|gb|ACI18568.1| ribosomal large subunit pseudouridine synthase C [Dictyoglomus
           thermophilum H-6-12]
          Length = 226

 Score =  129 bits (323), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 76/212 (35%), Positives = 122/212 (57%), Gaps = 16/212 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTH 148
           +DFL   ++YED+ + V NKPAGI VQG    +  +    K+++  K +KP      + H
Sbjct: 2   ADFLNLEVIYEDNHLLVVNKPAGILVQGDITKSTTLLEISKAYIKEKYKKPGNVFLAIVH 61

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+  SG+++ AR   +A  L+E+FR R+++K Y +L  GI K KK  I+  LL    +
Sbjct: 62  RLDKPVSGVVIFARNSKSAGRLSEAFRERKVEKEYIALCKGIFKVKKGTISESLL---WV 118

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +    V Q++K  N AI+H++V++ F +    + + P TGR HQLR H  ++G PI+G
Sbjct: 119 EKERKARVSQDDKSKN-AITHYEVLEEF-KNLSLVRLIPETGRKHQLRAHLSYIGHPILG 176

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           D KY            +++++LH + M +PHP
Sbjct: 177 DEKYGGG------RIFKDRIFLHCKKMAVPHP 202


>gi|322437152|ref|YP_004219364.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX9]
 gi|321164879|gb|ADW70584.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX9]
          Length = 371

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 95/334 (28%), Positives = 155/334 (46%), Gaps = 51/334 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP--PVINALN 75
            MRLD +     P I+   +Q ++ +GQV+VD    K   +++ G+ + I   P +  L 
Sbjct: 58  GMRLDAYLAQALPDISRARVQILIEAGQVKVDGAVPKAKAKLKGGETIEIEGQPQLEPL- 116

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----------- 124
           H I E   L                ++YED  + V NKPAG+ V  G+G           
Sbjct: 117 HAIPEDIPLQ---------------IVYEDEYLAVVNKPAGMMVHAGAGSTDDERNRGTL 161

Query: 125 ---IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + +H+     S     G+ +P + HRLD++TSG++VVA+     + L E F  RR+ 
Sbjct: 162 VNAVLFHMGKTADSLSGVGGELRPGIVHRLDKQTSGLIVVAKDDVTHRRLGEMFSERRVS 221

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN--YAISHFKV---IDC 235
           K Y +L  G  K     ++  + +      D V  ++   +  +   A+SHF V   +D 
Sbjct: 222 KTYLTLAHGELKKADTTVSLPIAR------DLVRRIRMTTRRGDGRSAVSHFHVLERLDT 275

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----SPIQ-NKLY 289
              KF ++E++  TGRTHQ+RVH   +G P+VGD  Y A      T      P++  + +
Sbjct: 276 PYGKFTFVEVKIETGRTHQIRVHLQSLGHPVVGDTLYGAPHVVRLTKEPNVEPLELERNF 335

Query: 290 LHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           LHA  +   HP     ++  APL   +V+  + +
Sbjct: 336 LHAARLAFVHPRTEEEMEFEAPLAEELVEFLEKI 369


>gi|167563550|ref|ZP_02356466.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           oklahomensis EO147]
          Length = 247

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 89/236 (37%), Positives = 125/236 (52%), Gaps = 24/236 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +L+ED  I   NKPAG++V GGSG+A+   G ++    ++       L HRLD+ETSGIL
Sbjct: 15  ILFEDDAIIALNKPAGVAVHGGSGVAF---GVIEQMRHARPHAKFLELVHRLDRETSGIL 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---WGIPKNKKECIANWLLKKSHIGGDYVHV 215
           ++A+ R+A   L E  R  R+ K Y++ V   W     ++  +   L K S   G+    
Sbjct: 72  MLAKKRSALVGLHEQIRENRMDKRYFACVHGEWAPDWGRRRAVKAPLFKYSTPDGE--RR 129

Query: 216 VKQNEKGANYAISH--FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           V+  E G     SH  F ++DC+   +  LE +  TGRTHQ+RVH  H+G PIVGD KY 
Sbjct: 130 VRVQEDGLP---SHTVFNLVDCWPD-YALLEAELKTGRTHQIRVHLAHLGLPIVGDAKY- 184

Query: 274 ANFKGN------FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +F  N         P   +++LHA  + L HP  G  LQ  APLPA   +  D L
Sbjct: 185 GDFALNKALARANAVPSLKRMFLHAHRLRLAHPLTGEPLQFDAPLPAECRQFLDQL 240


>gi|288962105|ref|YP_003452400.1| ribosomal large subunit pseudouridine synthase C [Azospirillum sp.
           B510]
 gi|288914371|dbj|BAI75856.1| ribosomal large subunit pseudouridine synthase C [Azospirillum sp.
           B510]
          Length = 257

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 64/194 (32%), Positives = 107/194 (55%), Gaps = 4/194 (2%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I DS  + +  +  L++ +L+ D   +V +KPAG++V     I  H++ +L    ++ G+
Sbjct: 2   IPDSPPSASLSAGQLRARVLHRDELCFVIDKPAGLAVHKAGRITDHLELYLPHLAEADGE 61

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P+L HRLD++T+G L++ RT  A +   + F    ++K YW++  G+P+     I   L
Sbjct: 62  PPKLAHRLDRDTAGCLILGRTPWALKRFGQMFAAGHVEKTYWAVADGVPEAGSGVIDLPL 121

Query: 203 LK----KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           LK    KS  G          +     A++ ++V+   A   CWLE++P TGRTHQ+RVH
Sbjct: 122 LKRIEPKSPSGAGRSSWTILPDPAGQPAVTEYRVLGTAADGRCWLELRPRTGRTHQIRVH 181

Query: 259 ALHMGCPIVGDHKY 272
              +GCP+VG+  Y
Sbjct: 182 CAAIGCPLVGEPFY 195


>gi|167587072|ref|ZP_02379460.1| pseudouridine synthase, RluA family protein [Burkholderia ubonensis
           Bu]
          Length = 401

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 147/319 (46%), Gaps = 35/319 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +VRVD    K    +  G  + + P       ++ 
Sbjct: 70  RLDKALAQLFPEFSRSRLQSWIDAQRVRVDGAPAKIRQPVPLGATIELAP------DLLP 123

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 124 EQ--------LAFTPEPVPLDIVYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYG 175

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG   ++ 
Sbjct: 176 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPDEG 235

Query: 196 ECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVID-CFAQK--FCWLEMQPHT 249
              A        IG D     +           A +HF+ +D C  Q+     ++    T
Sbjct: 236 TIDAP-------IGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLET 288

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-L 305
           GRTHQ+RVH  H G P++GD  Y         +P+ +   +  LHA  + L HP  G+ +
Sbjct: 289 GRTHQIRVHCAHAGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGLVHPVSGKTM 348

Query: 306 QITAPLPAHMVKTWDSLGF 324
           Q   PLP  M     +LGF
Sbjct: 349 QWRCPLPDDMTALVAALGF 367


>gi|319781137|ref|YP_004140613.1| pseudouridine synthase, RluA family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317167025|gb|ADV10563.1| pseudouridine synthase, RluA family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 346

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 97/337 (28%), Positives = 159/337 (47%), Gaps = 50/337 (14%)

Query: 10  VVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRI 67
           +V + D    RLD+W      P ++   +Q ++R G V VD K +    R +  G+ V +
Sbjct: 19  LVADADAAGQRLDQWLAARLGPDMSRSRVQMLIRQGAVSVDGKLIDETKRKMAPGESVSV 78

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           +          + +   +LYED ++ V NKPAG+ V  G+G   
Sbjct: 79  ---------------TMPEPEPAEPQGENIALDVLYEDDELIVINKPAGLVVHPGAGNWT 123

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----M 176
              ++  +    DS       ++P + HRLD+ETSG++VVA+T  A + L+E+F      
Sbjct: 124 GTLVNALIHHCGDSLSGIGGVRRPGIVHRLDKETSGVMVVAKTDRAHKSLSEAFADHGLT 183

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVID 234
             +++ Y +LVWGIP+     +   L + +    D V   VV +    A +A++HF V +
Sbjct: 184 GDLERAYLALVWGIPQRPTGRVDAPLGRAA----DRVRRAVVPEGRDDARHAVTHFAVQE 239

Query: 235 CFA---QKFC---WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQ 285
            F    Q+F     +E +  TGRTHQ+RVH  H+G P++GD  Y   F+        P++
Sbjct: 240 RFGESQQEFATASMVECRLETGRTHQIRVHMAHIGHPVIGDPDYGQAFRTKANRLPEPLK 299

Query: 286 NKL------YLHARYMDLPHPEGG-RLQITAPLPAHM 315
           +++       LHA  +   HP     ++  APLP  M
Sbjct: 300 SQVKAFPRQALHAWLLAFRHPTTHLTMRFEAPLPRDM 336


>gi|319898406|ref|YP_004158499.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           clarridgeiae 73]
 gi|319402370|emb|CBI75909.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           clarridgeiae 73]
          Length = 335

 Score =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 99/344 (28%), Positives = 158/344 (45%), Gaps = 50/344 (14%)

Query: 12  VENDEENM---RLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + N  EN    R+D+W    Y   I+   LQ ++R G +++D            GQ+++ 
Sbjct: 5   ITNTNENACGQRIDQWLAKQYKGEISRSRLQTLIREGHLKID------------GQLIKE 52

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
           P      N II  + I+ +  +     + L   + +ED  + V NKPAG+ V  G+G   
Sbjct: 53  PKTKLKSNQII--ELIIPAPNDARPQGEALALDIFFEDDHVIVINKPAGLVVHPGNGNWT 110

Query: 125 ------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF---- 174
                 + YH    L      K  +P + HRLD++TSG++V+A+   A ++L   F    
Sbjct: 111 GTLVNALIYHCSDSLSGIGGIK--RPGIVHRLDKDTSGVMVIAKNDIAHRNLNAQFADHG 168

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R   + + Y +++WG P      I  +L + SH       VV      A +AI+HF +++
Sbjct: 169 RTSALDRRYHAIIWGSPNRNIATIDTFLARSSHDRTKRA-VVHSEHANARHAITHFSLLE 227

Query: 235 CFAQ-----KFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSP-IQ 285
            +        F   LE +  TGRTHQ+RVH  H+G P++GD  Y   F  K N   P I+
Sbjct: 228 KYGTCNDTTPFASLLECRLETGRTHQIRVHMAHIGHPLIGDKVYGNAFKTKSNVLDPVIK 287

Query: 286 NKL------YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           NK+       LHA  +   HP  G  +  ++P P  +    + L
Sbjct: 288 NKIDQFNRQALHATSLTFEHPVNGEIMSFSSPFPKDLADLINHL 331


>gi|255659722|ref|ZP_05405131.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
 gi|260848296|gb|EEX68303.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
          Length = 308

 Score =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 102/330 (30%), Positives = 156/330 (47%), Gaps = 40/330 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IP 68
           V   D++  RLDR+     P ++  ++QK++  GQ  V  +  K N ++Q+G+ V   +P
Sbjct: 7   VYTADQDGERLDRFLTRMEPTLSRAHVQKVIAEGQALVSGRVRKANYKLQAGEKVTFHLP 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                     K  +IL   + L          +LYEDS I V NK  G+ V   +GI   
Sbjct: 67  EA--------KPVEILPEDIPLD---------ILYEDSDIIVINKARGMVVHPATGIYTG 109

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D  G     +P + HRLD++TSG++V A+  AA   L E  R +   +I
Sbjct: 110 TLVNALLYHCKDLSGINGEIRPGIVHRLDKDTSGVMVAAKNDAAHLDLAEQIRTKAAHRI 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++V G  + +   I      K  IG    D   +   +E G   A++HF+V++ F   
Sbjct: 170 YRAIVCGNIREEAGVI------KGDIGRHPTDRKKMAIVHEHG-KPAVTHFRVLERFGA- 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +E +  TGRTHQ+RVH   +G P++GD KY       F    Q    LH+  + L H
Sbjct: 222 YTLVECRLETGRTHQIRVHMASIGHPVLGDPKYGPRKACPFAIKGQA---LHSLQLTLTH 278

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           P     +  TAPLP  M K   +L  K+ R
Sbjct: 279 PRTREVMTFTAPLPEDMEKILKALRAKFQR 308


>gi|22299081|ref|NP_682328.1| ribosomal large subunit pseudouridine synthase D
           [Thermosynechococcus elongatus BP-1]
 gi|22295263|dbj|BAC09090.1| ribosomal large subunit pseudouridine synthase D
           [Thermosynechococcus elongatus BP-1]
          Length = 308

 Score =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 96/315 (30%), Positives = 156/315 (49%), Gaps = 38/315 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD +    +P  +    Q++++ G VR++ +   + N  +  G+V+ +           
Sbjct: 15  RLDTFLAQQHPEFSRSRWQQLIQQGHVRLNGQVCDRKNQPLSGGEVLEV----------- 63

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSW 136
               +L +   L    + L   +LYED ++ + NKP  + V    G ++   + G L   
Sbjct: 64  ----VLPTPEPLDLVPEPLPLSILYEDEELLILNKPVDLVVHPAPGHSHGTLVHGLLAHC 119

Query: 137 VDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            D  G    Q+P + HRLD++TSG++VVA+T  A  HL +  + R++Q+ Y  +V+G P+
Sbjct: 120 PDLTGIGGVQRPGIVHRLDKDTSGVMVVAKTEFALHHLQQQLKTRQMQRHYLGVVYGQPR 179

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGR 251
             +  +   L +  H        V   EKG   AI+H+ V + F  + C L E +  TGR
Sbjct: 180 EDRGTVITPLGR--HPVDRKKMAVVPPEKGRT-AITHWYVKERF--RHCALVEFRLETGR 234

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---YLHARYMDLPHPEGGR-LQI 307
           THQ+RVHA H+G P++GD  Y         SP++ KL    LHA  + L HP  G+ +  
Sbjct: 235 THQIRVHAAHLGWPLLGDPLYGRG------SPLKVKLPGQALHAYRLQLQHPRSGQEIVA 288

Query: 308 TAPLPAHMVKTWDSL 322
            APLP H+ +    L
Sbjct: 289 IAPLPDHLERLLQRL 303


>gi|56750446|ref|YP_171147.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 6301]
 gi|81299921|ref|YP_400129.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 7942]
 gi|56685405|dbj|BAD78627.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 6301]
 gi|81168802|gb|ABB57142.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 7942]
          Length = 313

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 98/311 (31%), Positives = 154/311 (49%), Gaps = 46/311 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRV-----DKKR--VKFNNRIQSGQVVRIPPVIN 72
           RLDRW    +PH++   LQK++ +GQ+RV     D+KR   +  +R++    + +PP   
Sbjct: 16  RLDRWLAQQWPHLSRARLQKLIAAGQLRVNGEVCDQKRWQPRLGDRLE----LEMPPT-E 70

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
           A+  +  E+  LD               +LYED+ + + NK  G+ V   +G      + 
Sbjct: 71  AIA-LAPEEIPLD---------------ILYEDADLLIVNKAVGMVVHPAAGHDTGTLVH 114

Query: 131 GFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             L    DS       Q+P + HRLD++T+G +VVA+T AA   L +  R +  Q+ Y  
Sbjct: 115 ALLAHCGDSLTGIGGEQRPGIVHRLDKDTTGAMVVAKTEAALLSLQDQIRQKTAQREYLG 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V+G P+     +   + +  H+       V   E+G  +A++H++V +     +  L  
Sbjct: 175 VVFGSPRQDSGQVEEPIGR--HLRDRKRMAVVPIERGGRWALTHWQVRERLG-NYALLHY 231

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGG 303
           +  TGRTHQ+RVH+ HMG P+VGD  Y     GN  S   N     LHA  + L HP  G
Sbjct: 232 RLATGRTHQIRVHSHHMGHPLVGDPLY-----GNGRSLGVNLQGQALHAWRLSLQHPRTG 286

Query: 304 R-LQITAPLPA 313
             + + APLPA
Sbjct: 287 EVIAVEAPLPA 297


>gi|71907635|ref|YP_285222.1| ribosomal large subunit pseudouridine synthase C [Dechloromonas
           aromatica RCB]
 gi|71847256|gb|AAZ46752.1| ribosomal large subunit pseudouridine synthase C [Dechloromonas
           aromatica RCB]
          Length = 334

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 108/341 (31%), Positives = 162/341 (47%), Gaps = 30/341 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +V V  +E   RLD +       +   ++ +ILRSG+VRV+ KRV    R+  G  +R
Sbjct: 9   VTHVEVGEEELGQRLDNFLIRRCKGVPKSHIYRILRSGEVRVNSKRVDATYRLCVGDNIR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A     +  +     V+L          ++YED  + + +KP GI+V GGSG++
Sbjct: 69  IPPIRIAERPQNEVDEAAKERVDLP---------IIYEDEAMLIIDKPEGIAVHGGSGVS 119

Query: 127 YHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI-- 179
           + +   L+       Q+P+     L HRLD+ETSG+L+V + R A   L + FR      
Sbjct: 120 FGVIEALRR------QRPQAKFLELAHRLDRETSGVLLVGKKRLALTALHDMFREHGAGA 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y  LV G   N  + +   L K    GG+    V    K ++     F+++  + + 
Sbjct: 174 DKRYLVLVKGRWMNNTQHVKLPLHKYLTEGGERRVSVDAQGKASHTV---FRLLARWPEA 230

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDL 297
              LE Q  TGRTHQ+RVH  H+G PI+GD KY  +F  N         ++ LHA  M  
Sbjct: 231 -SLLEAQLKTGRTHQIRVHLAHLGFPILGDEKY-GDFALNKALKRDGLKRMALHAWRMVF 288

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            HP     L+  APLP  +     +L  +  R    + L S
Sbjct: 289 QHPLTAVPLECIAPLPEGVGNYIAALDGQSPREFSAENLES 329


>gi|307944601|ref|ZP_07659941.1| ribosomal large subunit pseudouridine synthase D [Roseibium sp.
           TrichSKD4]
 gi|307772350|gb|EFO31571.1| ribosomal large subunit pseudouridine synthase D [Roseibium sp.
           TrichSKD4]
          Length = 341

 Score =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 94/328 (28%), Positives = 156/328 (47%), Gaps = 46/328 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPV 70
           V+ D+   RLD         ++   +Q +++ G+V VD +K V+  +R+  GQ + +   
Sbjct: 20  VDADDHGKRLDAVLAGQIASLSRNRIQTLIKGGEVTVDGRKIVEPKHRVNEGQTLTL--- 76

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                        L    +     + +   ++YED  + V +KPAG+ V  G+G      
Sbjct: 77  ------------TLPEPEDPDPKGENIPLSIIYEDDHLIVVDKPAGLVVHPGAGNLTGTL 124

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRI 179
           ++  +    DS       ++P + HR+D++TSG+LVVA+T  A Q L+E F    +   +
Sbjct: 125 VNALIHHCGDSLSGIGSVKRPGIVHRIDKDTSGLLVVAKTDQAHQGLSEQFADHGKTGPL 184

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +LVWG P + K  I N  L +S      + VVK       +AI+ ++V + F +K
Sbjct: 185 ERAYSALVWGAPSSLKGTI-NANLARSQANRQKIAVVK---TAGRHAITRWQVKERFGEK 240

Query: 240 -----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN---FTSPIQNKL--- 288
                   +E +  TGRTHQ+RVH  H+G P++GD  Y A FK        P++  +   
Sbjct: 241 DTEALASLMECRLETGRTHQIRVHMAHIGHPLIGDMDYGAGFKTKTKRLEDPLKTTINTF 300

Query: 289 ---YLHARYMDLPHPEGGR-LQITAPLP 312
               LHA  +   HP  G  L+  +P P
Sbjct: 301 TRQALHAGLLAFAHPVSGETLRFESPFP 328


>gi|161524654|ref|YP_001579666.1| RluA family pseudouridine synthase [Burkholderia multivorans ATCC
           17616]
 gi|189350589|ref|YP_001946217.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans ATCC 17616]
 gi|160342083|gb|ABX15169.1| pseudouridine synthase, RluA family [Burkholderia multivorans ATCC
           17616]
 gi|189334611|dbj|BAG43681.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans ATCC 17616]
          Length = 400

 Score =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 147/319 (46%), Gaps = 35/319 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +VRVD    K    +  G  + + P       ++ 
Sbjct: 70  RLDKALAQLFPEFSRSRLQSWIDAQRVRVDGAPAKIRQPVPLGATIELVP------DLLP 123

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 124 EQ--------LAFTPEPVPLDIVYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYG 175

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG   ++ 
Sbjct: 176 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGAMPDEG 235

Query: 196 ECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVID-CFAQK--FCWLEMQPHT 249
              A        IG D      +          A +HF+ +D C  Q+     ++    T
Sbjct: 236 TIDAP-------IGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLET 288

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHP-EGGRL 305
           GRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  G  +
Sbjct: 289 GRTHQIRVHCSHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPVTGSAM 348

Query: 306 QITAPLPAHMVKTWDSLGF 324
           Q   PLP  M    ++LGF
Sbjct: 349 QWRCPLPDDMTALVEALGF 367


>gi|261222782|ref|ZP_05937063.1| ribosomal large subunit pseudouridine synthase D [Brucella ceti
           B1/94]
 gi|260921366|gb|EEX88019.1| ribosomal large subunit pseudouridine synthase D [Brucella ceti
           B1/94]
          Length = 347

 Score =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 92/342 (26%), Positives = 159/342 (46%), Gaps = 49/342 (14%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           T ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G
Sbjct: 12  TRLKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREG 71

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I               +L          + +   +LYED  + V NKPAG+ V  G
Sbjct: 72  MNIAI---------------VLSEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPG 116

Query: 123 SG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           +G         + YH    L      +  +P + HRLD++TSG++VVA+   A +HL+E 
Sbjct: 117 NGNWTGTLVNALIYHCGDSLSGIGGIR--RPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQ 174

Query: 174 F----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           F    R   +++ Y +LVWG+ +  +  +  +L  +SH       VV +  + A +AI+H
Sbjct: 175 FADHGRTGDLERAYLALVWGMTERPQGTVDAYL-GRSHRDRTKQAVVHEEREDARHAITH 233

Query: 230 FKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNF 280
           +  ++ F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K      
Sbjct: 234 YATVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKL 293

Query: 281 TSPIQNKL------YLHARYMDLPHPEGGRL-QITAPLPAHM 315
             P++  +       LHA  +   HP    L +  APLP  M
Sbjct: 294 PEPLKEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDM 335


>gi|17986660|ref|NP_539294.1| ribosomal large subunit pseudouridine synthase D [Brucella
           melitensis bv. 1 str. 16M]
 gi|225853117|ref|YP_002733350.1| pseudouridine synthase [Brucella melitensis ATCC 23457]
 gi|17982277|gb|AAL51558.1| ribosomal large subunit pseudouridine synthase d [Brucella
           melitensis bv. 1 str. 16M]
 gi|225641482|gb|ACO01396.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           ATCC 23457]
          Length = 347

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 91/340 (26%), Positives = 160/340 (47%), Gaps = 45/340 (13%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           T ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G
Sbjct: 12  TRLKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREG 71

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I               +L          + +   +LYED  + V NKPAG+ V  G
Sbjct: 72  MNIAI---------------VLPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPG 116

Query: 123 SG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF- 174
           +G      ++  +    DS       ++P + HRLD++TSG++VVA+   A +HL+E F 
Sbjct: 117 NGNWTGTLVNALIYQCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFA 176

Query: 175 ---RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              R   +++ Y +LVWG+ +  +  +  +L  +SH       VV +  + A +AI+H+ 
Sbjct: 177 DHGRTGDLERAYLALVWGMTERPQGTVDAYL-GRSHRDRTKQAVVHEEREDARHAITHYA 235

Query: 232 VIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTS 282
            ++ F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        
Sbjct: 236 TVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPE 295

Query: 283 PIQNKL------YLHARYMDLPHPEGGRL-QITAPLPAHM 315
           P++  +       LHA  +   HP    L +  APLP  M
Sbjct: 296 PLKEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDM 335


>gi|37519642|ref|NP_923019.1| pseudouridine synthase [Gloeobacter violaceus PCC 7421]
 gi|35210633|dbj|BAC88014.1| glr0073 [Gloeobacter violaceus PCC 7421]
          Length = 310

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 96/323 (29%), Positives = 152/323 (47%), Gaps = 38/323 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+ D+  MRLDRW       ++   +Q ++  G V ++ +  +  + + SG  V +  
Sbjct: 11  LTVQPDQSAMRLDRWLAEQVADLSRARIQALIDQGLVLLNNRPCRPRDLVHSGDAVAL-- 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            I A   +  E + +   +             +YED ++ V +KP G+ V    G +   
Sbjct: 69  TIPAPEPLAIEARPIALDI-------------VYEDEELIVIDKPRGLVVHPAPGHSDDT 115

Query: 129 -IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    +  G     +P + HRLD++T+G+LVVA+T  A QHL    + +  ++ Y
Sbjct: 116 LVNALLAHCRNLSGINGVLRPGIVHRLDKDTTGLLVVAKTDRAHQHLQTQIQAKTARRDY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC 241
            +++ G P      I       + IG   VH  K   + KG   A +H++V++     F 
Sbjct: 176 LAIIAGAPAETTGTI------DAPIGRHPVHRQKMAVHPKG-RPARTHWRVLERLG-NFT 227

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            +E    TGRTHQ+RVH LH G PI GD  Y     G+   P   N   LHA  +   HP
Sbjct: 228 LVEFSLQTGRTHQIRVHCLHKGWPIAGDPLY-----GSVKVPATLNGQALHAFRLGFEHP 282

Query: 301 -EGGRLQITAPLPAHMVKTWDSL 322
             G RL   +P+PA MVK  D+L
Sbjct: 283 VTGERLTFESPMPAEMVKLLDAL 305


>gi|296123932|ref|YP_003631710.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
 gi|296016272|gb|ADG69511.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
          Length = 345

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 96/331 (29%), Positives = 152/331 (45%), Gaps = 36/331 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + VE      R+D +    YP+ + V  Q+ +  G+V V+   VK + R++   V+    
Sbjct: 17  LTVEARAHGWRIDHYLSRLYPNFSRVAFQRTIEEGKVLVNGLPVKISRRLRVNDVIEFSL 76

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                  +  E   LD               +LY+D  + V NK A + V  G G     
Sbjct: 77  PAEPDQRVQPEDIPLD---------------ILYDDEYLCVINKTANMIVHPGRGNYRGT 121

Query: 125 IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +A  +     S  D  GQ +  + HRLD++TSG+LVVA+     QHL+  F  R ++K Y
Sbjct: 122 LAGALQFHFDSLSDVAGQYRAGIVHRLDRDTSGVLVVAKDNTVHQHLSRQFEERSVEKEY 181

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++VWG  +   + +  + ++ S    + + V    +  A  A + ++V   F + F ++
Sbjct: 182 HAIVWGEMQFDADYVETY-VRVSFRNRERMMVCPPGD-NARQAATFYEVQQRF-RGFTYV 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY----CANFKGNFTSPIQ-------NKLYLHA 292
           ++QP TGRTHQLRVH  H+G PI+ D  Y    C           +       ++  LHA
Sbjct: 239 KLQPQTGRTHQLRVHMHHLGHPIIADRLYEGKTCVKLSDILPETPEEADETLIDRQALHA 298

Query: 293 RYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           R +   HP    R+   APLPA   KT D+L
Sbjct: 299 RRLAFNHPVTKKRMVFEAPLPADFQKTLDTL 329


>gi|307154024|ref|YP_003889408.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7822]
 gi|306984252|gb|ADN16133.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7822]
          Length = 305

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 97/323 (30%), Positives = 156/323 (48%), Gaps = 33/323 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVR-- 66
           + ++ ++  +RLD W     P ++   LQ ++  G +R++ K       ++Q G ++   
Sbjct: 3   ITLQVEQGKLRLDVWLAQKIPDLSRSRLQNLIEQGNLRLNGKICTDKKTKVQQGDLLYLF 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           IPPV   LN +  E+  LD               +LYED ++ + NKPAG+ V    G  
Sbjct: 63  IPPV-EPLN-LQPEEIPLD---------------VLYEDEQLIIINKPAGLVVHPAPGHE 105

Query: 125 IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L    +  G    Q+P + HRLD++T+G LV+A+T  A QHL    + +  +
Sbjct: 106 KGTLVNALLSHCSNLAGIGGVQRPGIVHRLDKDTTGALVIAKTDYAHQHLQAQLKAKTAR 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y  +V+G+PK     I N  + +  I    + VV   EKG   AI+H+++ +     +
Sbjct: 166 REYLGVVYGVPKTGSGTI-NLPIGRHPIERKKMAVVPL-EKGGRVAITHWEIRERLGN-Y 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +  +  TGRTHQ+RVH+  MG PIVGD  Y +   G       +   LHA  + L HP
Sbjct: 223 TLIHFRLETGRTHQIRVHSTAMGHPIVGDPVYSS---GRSIGVNLDGQVLHAWKLTLEHP 279

Query: 301 -EGGRLQITAPLPAHMVKTWDSL 322
             G  ++  APLP    K    L
Sbjct: 280 LSGAIIEAIAPLPETFTKLLSVL 302


>gi|239832765|ref|ZP_04681094.1| pseudouridine synthase, RluA family [Ochrobactrum intermedium LMG
           3301]
 gi|239825032|gb|EEQ96600.1| pseudouridine synthase, RluA family [Ochrobactrum intermedium LMG
           3301]
          Length = 402

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 95/342 (27%), Positives = 157/342 (45%), Gaps = 49/342 (14%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           T V+ +  ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G
Sbjct: 67  TRVKELTTDSDATGKRLDQWLAAALGPDLSRSRVQSLIAEGHVTIDGVPARETKQKLREG 126

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +          I E   LD               +LYED  + V NKPAG+ V  G
Sbjct: 127 MTIAVVLPEPEPAEPIAENIPLD---------------ILYEDDDLIVINKPAGLVVHPG 171

Query: 123 SG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           +G         + YH    L        ++P + HRLD++TSG++VVA+   + +HL+E 
Sbjct: 172 NGNWTGTLVNALIYHCGDSLSGI--GGIRRPGIVHRLDKDTSGVMVVAKNDLSHRHLSEQ 229

Query: 174 F----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           F    R   +++ Y +LVWG+ +  +  I +  L +SH       VV +    A +AI+H
Sbjct: 230 FADHGRTGDLERAYLALVWGMTERPQGYI-DAHLGRSHRDRTKQAVVNEERDDARHAITH 288

Query: 230 FKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNF 280
           +  ++ F  +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K      
Sbjct: 289 YATVEKFGPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKL 348

Query: 281 TSPIQNKL------YLHARYMDLPHPEGGRL-QITAPLPAHM 315
             P++  +       LHA  +   HP  G L +  AP+P  M
Sbjct: 349 PEPLKEAVRGFHRQALHAFLLAFTHPSSGELMRFEAPVPEDM 390


>gi|221198059|ref|ZP_03571105.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans CGD2M]
 gi|221204383|ref|ZP_03577400.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans CGD2]
 gi|221175240|gb|EEE07670.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans CGD2]
 gi|221181991|gb|EEE14392.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans CGD2M]
          Length = 399

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 147/319 (46%), Gaps = 35/319 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +VRVD    K    +  G  + + P       ++ 
Sbjct: 70  RLDKALAQLFPEFSRSRLQSWIDAQRVRVDGAPAKIRQPVPLGATIELVP------DLLP 123

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 124 EQ--------LAFTPEPVPLDIVYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYG 175

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG   ++ 
Sbjct: 176 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGAMPDEG 235

Query: 196 ECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVID-CFAQK--FCWLEMQPHT 249
              A        IG D     +           A +HF+ +D C  Q+     ++    T
Sbjct: 236 TIDAP-------IGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLET 288

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHP-EGGRL 305
           GRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  G  +
Sbjct: 289 GRTHQIRVHCSHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPVTGSAM 348

Query: 306 QITAPLPAHMVKTWDSLGF 324
           Q   PLP  M    ++LGF
Sbjct: 349 QWRCPLPDDMTALVEALGF 367


>gi|52430462|ref|YP_089634.1| ribosomal large subunit pseudouridine synthase D [Brucella suis
           1330]
 gi|161619586|ref|YP_001593473.1| RluA family pseudouridine synthase [Brucella canis ATCC 23365]
 gi|163845235|ref|YP_001622890.1| RluA family pseudouridine synthase [Brucella suis ATCC 23445]
 gi|237816033|ref|ZP_04595029.1| pseudouridine synthase, RluA family [Brucella abortus str. 2308 A]
 gi|256370063|ref|YP_003107574.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella microti CCM 4915]
 gi|294850907|ref|ZP_06791583.1| ribosomal large subunit pseudouridine synthase D [Brucella sp. NVSL
           07-0026]
 gi|297248929|ref|ZP_06932637.1| ribosomal large subunit pseudouridine synthase D [Brucella abortus
           bv. 5 str. B3196]
 gi|47524301|gb|AAT34906.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella suis 1330]
 gi|161336397|gb|ABX62702.1| pseudouridine synthase, RluA family [Brucella canis ATCC 23365]
 gi|163675958|gb|ABY40068.1| pseudouridine synthase, RluA family [Brucella suis ATCC 23445]
 gi|237788696|gb|EEP62908.1| pseudouridine synthase, RluA family [Brucella abortus str. 2308 A]
 gi|256000226|gb|ACU48625.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella microti CCM 4915]
 gi|294821550|gb|EFG38546.1| ribosomal large subunit pseudouridine synthase D [Brucella sp. NVSL
           07-0026]
 gi|297174062|gb|EFH33419.1| ribosomal large subunit pseudouridine synthase D [Brucella abortus
           bv. 5 str. B3196]
          Length = 347

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 92/342 (26%), Positives = 159/342 (46%), Gaps = 49/342 (14%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           T ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G
Sbjct: 12  TRLKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREG 71

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I               +L          + +   +LYED  + V NKPAG+ V  G
Sbjct: 72  MNIAI---------------VLPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPG 116

Query: 123 SG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           +G         + YH    L      +  +P + HRLD++TSG++VVA+   A +HL+E 
Sbjct: 117 NGNWTGTLVNALIYHCGDSLSGIGGIR--RPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQ 174

Query: 174 F----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           F    R   +++ Y +LVWG+ +  +  +  +L  +SH       VV +  + A +AI+H
Sbjct: 175 FADHGRTGDLERAYLALVWGMTERPQGTVDAYL-GRSHRDRTKQAVVHEEREDARHAITH 233

Query: 230 FKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNF 280
           +  ++ F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K      
Sbjct: 234 YATVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKL 293

Query: 281 TSPIQNKL------YLHARYMDLPHPEGGRL-QITAPLPAHM 315
             P++  +       LHA  +   HP    L +  APLP  M
Sbjct: 294 PEPLKEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDM 335


>gi|118602128|ref|YP_903343.1| ribosomal large subunit pseudouridine synthase C [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
 gi|118567067|gb|ABL01872.1| ribosomal large subunit pseudouridine synthase C [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
          Length = 303

 Score =  126 bits (317), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 103/321 (32%), Positives = 157/321 (48%), Gaps = 39/321 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           + + +V+   E  RLD +       +   ++ +++R G VRV+K R K + ++    +VR
Sbjct: 3   ISFQIVDEFSEGQRLDNYLLKILKGVPKSHICRVIRKGWVRVNKGRKKVSYKLILNDIVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  +   IIK   I DS   L      L    LYED  + + NKP+G+SV  GSG+ 
Sbjct: 63  IPPIKVS---IIKSIYISDSLKKL------LIDAKLYEDKGLLIINKPSGLSVHSGSGVD 113

Query: 127 YHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             I   L+       +KP  L HRLD+ TSG+L++A+ R+  ++L E      ++K Y +
Sbjct: 114 VGIIEALRQIY----KKPIELVHRLDRATSGVLLIAKKRSVLKNLHEQLSQHTVEKRYTA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ---KFCW 242
           LV G+   K   I   L + S     Y+ V   + KG  YAISHF+ +  F+        
Sbjct: 170 LVKGVWSKKCHTIDAPLYQNSR----YIMV---DAKG-KYAISHFQPLKNFSDGGFSASL 221

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-------ANFKGNFTSPIQNKLYLHARYM 295
           +E+   TGRTHQ+RVHA + G  +  D KY          FKG        +L+LHA   
Sbjct: 222 VEISIETGRTHQIRVHAKYAGHALACDDKYGDKEFDRQVKFKG------LKRLFLHAHQF 275

Query: 296 DLPHPEGGRLQ-ITAPLPAHM 315
              +P    +Q + A LP  +
Sbjct: 276 IFTNPLTNDIQKVNASLPVEL 296


>gi|166367953|ref|YP_001660226.1| ribosomal large subunit pseudouridine synthase D [Microcystis
           aeruginosa NIES-843]
 gi|166090326|dbj|BAG05034.1| ribosomal large subunit pseudouridine synthase D [Microcystis
           aeruginosa NIES-843]
          Length = 308

 Score =  126 bits (317), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 90/301 (29%), Positives = 148/301 (49%), Gaps = 27/301 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD W  +H P ++   LQK++  G ++++ + +  N   + GQ  R+            
Sbjct: 14  RLDAWMGSHLPDLSRSRLQKLIEQGYIQLNGQ-ICTNKNTKVGQGDRL------------ 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            +  +  S  L   ++ ++  +LYED  + + NKPA + V    G      ++  L    
Sbjct: 61  -KITIPDSQPLELTAEAIELDILYEDDYLIIINKPADLVVHPAPGHESGTLVNALLHHCP 119

Query: 138 DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +  G    Q+P + HRLD++T+G +V+A+T  A QHL    + +  ++ Y +LV G+PK+
Sbjct: 120 NLAGIGGIQRPGIVHRLDKDTTGAIVIAKTDQAHQHLQAQLKTKTARREYIALVHGVPKS 179

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +   I   L    H        +   EKG   A++H++V +     +  +E +  TGRTH
Sbjct: 180 ETGTID--LPIGRHRSDRQKMAIIAVEKGGRNAVTHWQVKERLG-NYTLMEFRLETGRTH 236

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Q+RVH+ H+G PI+GD  Y +        P Q    LHA  + L HP  G  L+  APLP
Sbjct: 237 QIRVHSSHIGHPILGDPLYSSGRSIGINLPGQ---LLHAHRLILVHPVTGESLEAIAPLP 293

Query: 313 A 313
           A
Sbjct: 294 A 294


>gi|187923831|ref|YP_001895473.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187715025|gb|ACD16249.1| pseudouridine synthase, RluA family [Burkholderia phytofirmans
           PsJN]
          Length = 431

 Score =  126 bits (317), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 98/348 (28%), Positives = 159/348 (45%), Gaps = 30/348 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV ++    RLD+     +P  +   LQ  + + +VR+D K  K    +  G  + + P
Sbjct: 68  VVVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAKIRQPVPLGATIELVP 127

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +L   +  T     L+  ++YED  + V NKPAG+ V   +G     
Sbjct: 128 ------------DLLPEQLAFTPEPVPLE--IVYEDDTLVVINKPAGMVVHPAAGNWSGT 173

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++G L  + D+    PR  + HRLD+ETSG++VVART  A   L    + R +++ Y +
Sbjct: 174 VLNGLLYRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLA 233

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCW 242
           LVWG     +E   +  + +       + VV         A +HF+ +D      Q    
Sbjct: 234 LVWG--NMPEEGTIDAPIGRDPRERTRMAVV--TSASGKPARTHFRRVDSAIWQRQPVTA 289

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPH 299
           +     TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L H
Sbjct: 290 IHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGLIH 349

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGF-KYDRNLYIKRLYSQDECKQNI 345
           P+ GR +Q  A  PA M     +LG  + D   + +  Y +D+   ++
Sbjct: 350 PQTGRTMQWRADAPADMEALSAALGLGRDDAGEFDETYYEEDDYDASL 397


>gi|254719684|ref|ZP_05181495.1| RluA family pseudouridine synthase [Brucella sp. 83/13]
 gi|265984699|ref|ZP_06097434.1| pseudouridine synthase [Brucella sp. 83/13]
 gi|306840039|ref|ZP_07472826.1| pseudouridine synthase, RluA family [Brucella sp. NF 2653]
 gi|264663291|gb|EEZ33552.1| pseudouridine synthase [Brucella sp. 83/13]
 gi|306404853|gb|EFM61145.1| pseudouridine synthase, RluA family [Brucella sp. NF 2653]
          Length = 334

 Score =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 91/340 (26%), Positives = 159/340 (46%), Gaps = 49/340 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMN 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L          + +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF- 174
                    + YH    L      +  +P + HRLD++TSG++VVA+   A +HL+E F 
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGIR--RPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFA 163

Query: 175 ---RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              R   +++ Y +LVWG+ +  +  +  +L  +SH       VV++  + A +AI+H+ 
Sbjct: 164 DHGRTGDLERAYLALVWGMTERPQGTVDAYL-GRSHRDRTKQAVVREEREDARHAITHYA 222

Query: 232 VIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTS 282
            ++ F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        
Sbjct: 223 TVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPE 282

Query: 283 PIQNKL------YLHARYMDLPHPEGGRL-QITAPLPAHM 315
           P++  +       LHA  +   HP    L +  APLP  M
Sbjct: 283 PLKQAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPDDM 322


>gi|325522995|gb|EGD01421.1| RluA family pseudouridine synthase [Burkholderia sp. TJI49]
          Length = 279

 Score =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 96/297 (32%), Positives = 152/297 (51%), Gaps = 34/297 (11%)

Query: 11  VVENDEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           ++E DE     R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +VR+P
Sbjct: 1   MIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDLVRVP 60

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           PV         +    D+ V    H D     +LYED  + V +KPAG++V GGSG+A+ 
Sbjct: 61  PV----RVAAADLARADAPVVPPAHFD-----VLYEDDAMLVIDKPAGVAVHGGSGVAFG 111

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY----- 183
           +   L+     + +   L HRLD+ETSG+L++A+ R+A   L E  R  R+ K Y     
Sbjct: 112 VIEQLRQ-ARPRAKFLELVHRLDRETSGVLMLAKKRSALVGLHEQIRENRMDKRYYACGH 170

Query: 184 --WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
             W   WG    ++  +   L K +   G+   V  Q++  A++ +  F +++ +   + 
Sbjct: 171 GEWQPDWG----RRRAVKAPLFKYTTPEGER-RVRVQDDGLASHTV--FNLVERWPD-YA 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHA 292
            +E +  TGRTHQ+RVH  H+G PI GD KY  +F  N         P   +++LHA
Sbjct: 223 LVEAELKTGRTHQIRVHLAHLGLPIAGDAKY-GDFALNKALARANAQPSLKRMFLHA 278


>gi|262340910|ref|YP_003283765.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase D) [Blattabacterium sp. (Blattella germanica)
           str. Bge]
 gi|262272247|gb|ACY40155.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase D) [Blattabacterium sp. (Blattella germanica)
           str. Bge]
          Length = 342

 Score =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 94/333 (28%), Positives = 161/333 (48%), Gaps = 48/333 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++   +++ +R+D++ KN+  +I+   +QK   SG++ V+K  VK N +I+    V I  
Sbjct: 12  IITNKNQKEIRIDKFLKNYIQNISRNQIQKWTTSGKILVNKNIVKKNYKIKPLDFVEIEI 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
            I ++   ++ + I    +NL          +LYED  + V NKPAG+ V  G       
Sbjct: 72  SIPSVLDHLEYKNITAEKINLD---------ILYEDEDVLVVNKPAGMVVHPGFGNETGT 122

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              GI YH+     +  +    +  L HRLD++TSG+LV A+   + +HL + F  R IQ
Sbjct: 123 LIHGIKYHLTN--SNLNNFNLYRCGLVHRLDKDTSGLLVFAKNEYSQKHLFQQFYSRTIQ 180

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGAN---YAISHFKV 232
           + Y +L+WG    +K  I  +      IG D      + ++KQ  +  N   ++++H+KV
Sbjct: 181 RKYIALIWGNLIEEKGTITGF------IGRDPKNRKKMTILKQENQEFNKGKFSVTHYKV 234

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY----------CANFKGNFTS 282
           ++ F +   ++     TG+THQ+R H  H+G P+  D  Y          C+N    F +
Sbjct: 235 LERF-KYLTYVSCNIKTGKTHQIRAHFKHLGHPLFHDSIYGGNRIFMKKKCSNQNIEFLN 293

Query: 283 P---IQNKLYLHARYMDLPHPEGGRLQITAPLP 312
               I  +  LHA  +   HP  G+     P+P
Sbjct: 294 TCLKILQRQALHAISLSFIHPRNGKCHFLCPIP 326


>gi|217421724|ref|ZP_03453228.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 576]
 gi|217395466|gb|EEC35484.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 576]
          Length = 395

 Score =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 93/318 (29%), Positives = 145/318 (45%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRV     K    +  G  + + P +        
Sbjct: 69  RLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIELLPELLPEQLAFT 128

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            + +  S              ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 129 PEPVPLS--------------IVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 174

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 175 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWG--RMPDE 232

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 233 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTH 290

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 291 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPASGRSMQWRA 350

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 351 PLPADLAALVDALGFGAD 368


>gi|167893970|ref|ZP_02481372.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei 7894]
 gi|167918689|ref|ZP_02505780.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei BCC215]
 gi|237812527|ref|YP_002896978.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei MSHR346]
 gi|254179573|ref|ZP_04886172.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1655]
 gi|184210113|gb|EDU07156.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1655]
 gi|237504431|gb|ACQ96749.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei MSHR346]
          Length = 389

 Score =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 93/318 (29%), Positives = 145/318 (45%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRV     K    +  G  + + P +        
Sbjct: 63  RLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIELLPELLPEQLAFT 122

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            + +  S              ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 123 PEPVPLS--------------IVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 168

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 169 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWG--RMPDE 226

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 227 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTH 284

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 285 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPASGRSMQWRA 344

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 345 PLPADLAALVDALGFGAD 362


>gi|53723511|ref|YP_102984.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           mallei ATCC 23344]
 gi|76810454|ref|YP_333728.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei 1710b]
 gi|52426934|gb|AAU47527.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           mallei ATCC 23344]
 gi|76579907|gb|ABA49382.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei 1710b]
          Length = 395

 Score =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 93/318 (29%), Positives = 145/318 (45%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRV     K    +  G  + + P +        
Sbjct: 69  RLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIELLPELLPEQLAFT 128

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            + +  S              ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 129 PEPVPLS--------------IVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 174

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 175 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWG--RMPDE 232

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 233 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTH 290

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 291 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPASGRSMQWRA 350

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 351 PLPADLAALVDALGFGAD 368


>gi|226197455|ref|ZP_03793032.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pakistan 9]
 gi|225930834|gb|EEH26844.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pakistan 9]
          Length = 389

 Score =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 93/318 (29%), Positives = 145/318 (45%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRV     K    +  G  + + P +        
Sbjct: 63  RLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIELLPELLPEQLAFT 122

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            + +  S              ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 123 PEPVPLS--------------IVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 168

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 169 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWG--RMPDE 226

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 227 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTH 284

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 285 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPASGRSMQWRA 344

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 345 PLPADLAALVDALGFGAD 362


>gi|67641328|ref|ZP_00440109.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           mallei GB8 horse 4]
 gi|121600453|ref|YP_993132.1| RluA family pseudouridine synthase [Burkholderia mallei SAVP1]
 gi|124385530|ref|YP_001026092.1| RluA family pseudouridine synthase [Burkholderia mallei NCTC 10229]
 gi|126448439|ref|YP_001080638.1| RluA family pseudouridine synthase [Burkholderia mallei NCTC 10247]
 gi|134277051|ref|ZP_01763766.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 305]
 gi|167902420|ref|ZP_02489625.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei NCTC 13177]
 gi|254177619|ref|ZP_04884274.1| pseudouridine synthase, RluA family [Burkholderia mallei ATCC
           10399]
 gi|254199929|ref|ZP_04906295.1| pseudouridine synthase, RluA family [Burkholderia mallei FMH]
 gi|254206262|ref|ZP_04912614.1| pseudouridine synthase, RluA family [Burkholderia mallei JHU]
 gi|254260754|ref|ZP_04951808.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1710a]
 gi|254358323|ref|ZP_04974596.1| pseudouridine synthase, RluA family [Burkholderia mallei
           2002721280]
 gi|121229263|gb|ABM51781.1| pseudouridine synthase, RluA family [Burkholderia mallei SAVP1]
 gi|124293550|gb|ABN02819.1| pseudouridine synthase, RluA family [Burkholderia mallei NCTC
           10229]
 gi|126241309|gb|ABO04402.1| pseudouridine synthase, RluA family [Burkholderia mallei NCTC
           10247]
 gi|134250701|gb|EBA50780.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 305]
 gi|147749525|gb|EDK56599.1| pseudouridine synthase, RluA family [Burkholderia mallei FMH]
 gi|147753705|gb|EDK60770.1| pseudouridine synthase, RluA family [Burkholderia mallei JHU]
 gi|148027450|gb|EDK85471.1| pseudouridine synthase, RluA family [Burkholderia mallei
           2002721280]
 gi|160698658|gb|EDP88628.1| pseudouridine synthase, RluA family [Burkholderia mallei ATCC
           10399]
 gi|238522242|gb|EEP85688.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           mallei GB8 horse 4]
 gi|254219443|gb|EET08827.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1710a]
          Length = 389

 Score =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 93/318 (29%), Positives = 145/318 (45%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRV     K    +  G  + + P +        
Sbjct: 63  RLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIELLPELLPEQLAFT 122

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            + +  S              ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 123 PEPVPLS--------------IVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 168

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 169 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWG--RMPDE 226

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 227 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTH 284

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 285 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPASGRSMQWRA 344

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 345 PLPADLAALVDALGFGAD 362


>gi|167910661|ref|ZP_02497752.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei 112]
          Length = 389

 Score =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 93/318 (29%), Positives = 145/318 (45%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRV     K    +  G  + + P +        
Sbjct: 63  RLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIELLPELLPEQLAFT 122

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            + +  S              ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 123 PEPVPLS--------------IVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 168

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 169 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWG--RMPDE 226

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 227 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTH 284

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 285 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPASGRSMQWRA 344

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 345 PLPADLAALVDALGFGAD 362


>gi|254297450|ref|ZP_04964903.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           406e]
 gi|157806772|gb|EDO83942.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           406e]
          Length = 389

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 93/318 (29%), Positives = 145/318 (45%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRV     K    +  G  + + P +        
Sbjct: 63  RLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIELLPELLPEQLAFT 122

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            + +  S              ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 123 PEPVPLS--------------IVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 168

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 169 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALAWG--RMPDE 226

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 227 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTH 284

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 285 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPASGRSMQWRA 344

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 345 PLPADLAALVDALGFGAD 362


>gi|53719166|ref|YP_108152.1| putative ribosomal large subunit pseudouridine synthase D
           [Burkholderia pseudomallei K96243]
 gi|126454439|ref|YP_001066469.1| RluA family pseudouridine synthase [Burkholderia pseudomallei
           1106a]
 gi|242316335|ref|ZP_04815351.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106b]
 gi|52209580|emb|CAH35533.1| putative ribosomal large subunit pseudouridine synthase D
           [Burkholderia pseudomallei K96243]
 gi|126228081|gb|ABN91621.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106a]
 gi|242139574|gb|EES25976.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106b]
          Length = 395

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 93/318 (29%), Positives = 145/318 (45%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRV     K    +  G  + + P +        
Sbjct: 69  RLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIELLPELLPEQLAFT 128

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            + +  S              ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 129 PEPVPLS--------------IVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 174

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 175 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALAWG--RMPDE 232

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 233 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTH 290

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 291 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPASGRSMQWRA 350

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 351 PLPADLAALVDALGFGAD 368


>gi|254189036|ref|ZP_04895547.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pasteur 52237]
 gi|157936715|gb|EDO92385.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pasteur 52237]
          Length = 395

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 93/318 (29%), Positives = 145/318 (45%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRV     K    +  G  + + P +        
Sbjct: 69  RLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIELLPELLPEQLAFT 128

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            + +  S              ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 129 PEPVPLS--------------IVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 174

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 175 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALAWG--RMPDE 232

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 233 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTH 290

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 291 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPASGRSMQWRA 350

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 351 PLPADLAALVDALGFGAD 368


>gi|254708671|ref|ZP_05170482.1| RluA family pseudouridine synthase [Brucella pinnipedialis B2/94]
 gi|254714518|ref|ZP_05176329.1| RluA family pseudouridine synthase [Brucella ceti M644/93/1]
 gi|254717416|ref|ZP_05179227.1| RluA family pseudouridine synthase [Brucella ceti M13/05/1]
 gi|256030197|ref|ZP_05443811.1| RluA family pseudouridine synthase [Brucella pinnipedialis
           M292/94/1]
 gi|256160371|ref|ZP_05458061.1| RluA family pseudouridine synthase [Brucella ceti M490/95/1]
 gi|256255579|ref|ZP_05461115.1| RluA family pseudouridine synthase [Brucella ceti B1/94]
 gi|261219246|ref|ZP_05933527.1| pseudouridine synthase [Brucella ceti M13/05/1]
 gi|261316161|ref|ZP_05955358.1| pseudouridine synthase [Brucella pinnipedialis B2/94]
 gi|261322307|ref|ZP_05961504.1| pseudouridine synthase [Brucella ceti M644/93/1]
 gi|265987225|ref|ZP_06099782.1| pseudouridine synthase [Brucella pinnipedialis M292/94/1]
 gi|265998740|ref|ZP_06111297.1| pseudouridine synthase [Brucella ceti M490/95/1]
 gi|260924335|gb|EEX90903.1| pseudouridine synthase [Brucella ceti M13/05/1]
 gi|261294997|gb|EEX98493.1| pseudouridine synthase [Brucella ceti M644/93/1]
 gi|261295384|gb|EEX98880.1| pseudouridine synthase [Brucella pinnipedialis B2/94]
 gi|262553429|gb|EEZ09198.1| pseudouridine synthase [Brucella ceti M490/95/1]
 gi|264659422|gb|EEZ29683.1| pseudouridine synthase [Brucella pinnipedialis M292/94/1]
          Length = 334

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 91/340 (26%), Positives = 158/340 (46%), Gaps = 49/340 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMN 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L          + +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLSEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF- 174
                    + YH    L      +  +P + HRLD++TSG++VVA+   A +HL+E F 
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGIR--RPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFA 163

Query: 175 ---RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              R   +++ Y +LVWG+ +  +  +  +L  +SH       VV +  + A +AI+H+ 
Sbjct: 164 DHGRTGDLERAYLALVWGMTERPQGTVDAYL-GRSHRDRTKQAVVHEEREDARHAITHYA 222

Query: 232 VIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTS 282
            ++ F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        
Sbjct: 223 TVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPE 282

Query: 283 PIQNKL------YLHARYMDLPHPEGGRL-QITAPLPAHM 315
           P++  +       LHA  +   HP    L +  APLP  M
Sbjct: 283 PLKEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDM 322


>gi|258515575|ref|YP_003191797.1| pseudouridine synthase, RluA family [Desulfotomaculum acetoxidans
           DSM 771]
 gi|257779280|gb|ACV63174.1| pseudouridine synthase, RluA family [Desulfotomaculum acetoxidans
           DSM 771]
          Length = 305

 Score =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 92/316 (29%), Positives = 150/316 (47%), Gaps = 35/316 (11%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD +  N YP I+   LQ+++  G V ++ K+V    +I+ G  + +        
Sbjct: 11  EIGQRLDVYLSNCYPDISRSQLQRLIAQGLVEINGKKVAAKYKIKPGDYINL-------- 62

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                   +   V ++  ++ +   + +ED  + V NKP G+ V    G      ++  L
Sbjct: 63  -------TIPDPVGVSVEAENIALDIYFEDEDVIVINKPRGMVVHPAEGNYTGTMVNALL 115

Query: 134 KSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D  G     +P + HRLD++TSG+L+VA+   A  +L      R + + Y +LV G
Sbjct: 116 YHCRDLSGINGVLRPGIVHRLDKDTSGLLMVAKNDLAHNNLAAQLEKRLVNRRYLALVHG 175

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
             K     +       + IG D     K    ++ +  A++HFKV+  F  ++  LE++ 
Sbjct: 176 NLKQDAGTV------DAPIGRDACSRQKMAVTDRNSRSAVTHFKVLKRFG-RYTLLELKL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++G  +VGD KY  + K +F    Q   +LHA  +   HP  G+ L+
Sbjct: 229 ETGRTHQIRVHMKYIGYQVVGDPKYGPS-KPHFNLDGQ---FLHACLLGFAHPRTGKYLE 284

Query: 307 ITAPLPAHMVKTWDSL 322
             APLP  +VK    L
Sbjct: 285 FNAPLPDILVKVLAEL 300


>gi|126438505|ref|YP_001059203.1| RluA family pseudouridine synthase [Burkholderia pseudomallei 668]
 gi|167738292|ref|ZP_02411066.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei 14]
 gi|167815478|ref|ZP_02447158.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei 91]
 gi|167845428|ref|ZP_02470936.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei B7210]
 gi|126217998|gb|ABN81504.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 668]
          Length = 389

 Score =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 93/318 (29%), Positives = 145/318 (45%), Gaps = 28/318 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRV     K    +  G  + + P +        
Sbjct: 63  RLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIELLPELLPEQLAFT 122

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            + +  S              ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 123 PEPVPLS--------------IVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 168

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 169 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALAWG--RMPDE 226

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 227 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTH 284

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITA 309
           Q+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  GR +Q  A
Sbjct: 285 QIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLVHPASGRSMQWRA 344

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    D+LGF  D
Sbjct: 345 PLPADLAALVDALGFGAD 362


>gi|256045267|ref|ZP_05448161.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           bv. 1 str. Rev.1]
 gi|256114226|ref|ZP_05454971.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           bv. 3 str. Ether]
 gi|256263395|ref|ZP_05465927.1| ribosomal large subunit pseudouridine synthase [Brucella melitensis
           bv. 2 str. 63/9]
 gi|260565840|ref|ZP_05836323.1| ribosomal large subunit pseudouridine synthase [Brucella melitensis
           bv. 1 str. 16M]
 gi|265991692|ref|ZP_06104249.1| pseudouridine synthase [Brucella melitensis bv. 1 str. Rev.1]
 gi|265995529|ref|ZP_06108086.1| pseudouridine synthase [Brucella melitensis bv. 3 str. Ether]
 gi|260151213|gb|EEW86308.1| ribosomal large subunit pseudouridine synthase [Brucella melitensis
           bv. 1 str. 16M]
 gi|262766813|gb|EEZ12431.1| pseudouridine synthase [Brucella melitensis bv. 3 str. Ether]
 gi|263002648|gb|EEZ15051.1| pseudouridine synthase [Brucella melitensis bv. 1 str. Rev.1]
 gi|263093392|gb|EEZ17461.1| ribosomal large subunit pseudouridine synthase [Brucella melitensis
           bv. 2 str. 63/9]
 gi|326409663|gb|ADZ66728.1| pseudouridine synthase [Brucella melitensis M28]
 gi|326539370|gb|ADZ87585.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           M5-90]
          Length = 334

 Score =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 90/338 (26%), Positives = 159/338 (47%), Gaps = 45/338 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMN 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L          + +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF--- 174
                 ++  +    DS       ++P + HRLD++TSG++VVA+   A +HL+E F   
Sbjct: 106 NWTGTLVNALIYQCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADH 165

Query: 175 -RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R   +++ Y +LVWG+ +  +  +  +L  +SH       VV +  + A +AI+H+  +
Sbjct: 166 GRTGDLERAYLALVWGMTERPQGTVDAYL-GRSHRDRTKQAVVHEEREDARHAITHYATV 224

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPI 284
           + F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        P+
Sbjct: 225 EKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPEPL 284

Query: 285 QNKL------YLHARYMDLPHPEGGRL-QITAPLPAHM 315
           +  +       LHA  +   HP    L +  APLP  M
Sbjct: 285 KEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDM 322


>gi|315498779|ref|YP_004087583.1| pseudouridine synthase, rlua family [Asticcacaulis excentricus CB
           48]
 gi|315416791|gb|ADU13432.1| pseudouridine synthase, RluA family [Asticcacaulis excentricus CB
           48]
          Length = 334

 Score =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 101/338 (29%), Positives = 152/338 (44%), Gaps = 53/338 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--I 67
           +V+ +D    RLDR      P ++   LQ ++  G +  D + +          + R  +
Sbjct: 22  LVLTSDMAGDRLDRALLPLLPDLSRARLQALISDGHLSHDGQTIADGKHKARAGLYRLFV 81

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P  ++A    I E + L   V             LYED+ + V NKPAG++     G A 
Sbjct: 82  PAPVSA----IPEAQNLPLEV-------------LYEDAHLIVVNKPAGMAAHPAPGTA- 123

Query: 128 HIDGFL---------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             DG L         +S     G  +P + HRLD++TSG++V A++ AA + L+E F   
Sbjct: 124 --DGTLVNALLFHCGESLSGIGGVLRPGIVHRLDKDTSGVMVAAKSDAAHRGLSELFSRH 181

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF- 236
            I + Y +LV G PK     +   + +  H     + V+K    G   AISH++ ++ F 
Sbjct: 182 DIDRAYEALVRGAPKTASGTVTTRIGRSPH-DRKKMAVLKS---GGREAISHYRTLNSFG 237

Query: 237 ------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-- 288
                 A+  C LE    TGRTHQ+RVH  ++GCP +GD  Y +       +     L  
Sbjct: 238 GEKPVAARVRCTLE----TGRTHQIRVHMAYLGCPCLGDPVYGSGAPHRAVAEALKTLSF 293

Query: 289 ---YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
               LHA ++   HP  G RL   APLPA M     +L
Sbjct: 294 ARQALHAAHLGFVHPVTGERLAFEAPLPADMADLLSAL 331


>gi|260461536|ref|ZP_05809783.1| pseudouridine synthase, RluA family [Mesorhizobium opportunistum
           WSM2075]
 gi|259032606|gb|EEW33870.1| pseudouridine synthase, RluA family [Mesorhizobium opportunistum
           WSM2075]
          Length = 334

 Score =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 98/343 (28%), Positives = 158/343 (46%), Gaps = 50/343 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNR-IQS 61
           M     +V   D    RLD+W      P ++   +Q ++R G V ++ K V    R +  
Sbjct: 1   MEAPTVLVTGADAAGQRLDQWLAASLGPDMSRSRVQMLIRQGAVSINGKPVDETKRKMLP 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G+ V +            E   LD               +LYED  + V NKPAG+ V  
Sbjct: 61  GESVSVAMPEPEPAEPQGENIALD---------------VLYEDDALIVINKPAGLVVHP 105

Query: 122 GSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G+G      ++  +    DS       ++P + HRLD+ETSG++VVA+T  A + L+E+F
Sbjct: 106 GAGNWTGTLVNALIHHCGDSLSGIGGVRRPGIVHRLDKETSGVMVVAKTDRAHKALSEAF 165

Query: 175 R----MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAIS 228
                   +++ Y +LVWGIP+     +   L + +    D V   VV +    A +A++
Sbjct: 166 ADHGLTGDLERAYLALVWGIPQRPTGTVDAPLGRAA----DRVRRAVVPEGRDDARHAVT 221

Query: 229 HFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GN 279
           HF V + F +K         +E +  TGRTHQ+RVH  H+G P++GD  Y   F+     
Sbjct: 222 HFAVQERFGEKQQEFATASLVECRLETGRTHQIRVHMAHIGHPVIGDPDYGQAFRTKANR 281

Query: 280 FTSPIQNKL------YLHARYMDLPHPEGG-RLQITAPLPAHM 315
              P+++++       LHA  +   HP+    ++  AP+P  M
Sbjct: 282 LPEPLKSQVKAFSRQALHAWLLAFRHPDTHLTMRFEAPIPRDM 324


>gi|254796911|ref|YP_003081748.1| ribosomal large subunit pseudouridine synthase C [Neorickettsia
           risticii str. Illinois]
 gi|254590147|gb|ACT69509.1| ribosomal large subunit pseudouridine synthase C [Neorickettsia
           risticii str. Illinois]
          Length = 305

 Score =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 99/313 (31%), Positives = 155/313 (49%), Gaps = 23/313 (7%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VVEND    RLD++ ++ +       LQK LR   V+++   VK +  +  G  + +   
Sbjct: 5   VVENDCR--RLDKYLRDTFGPFPQSALQKALRKKAVKLNNVVVKASAAVLKGDSLTLSA- 61

Query: 71  INALNHIIKEQKILDSSVNL--TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            N L  +   ++I   S  +  +K   F+ S++LYED  +   +KP G  VQ G GI   
Sbjct: 62  -NFLQILSSPREIPSDSSKVVDSKFVKFIASLMLYEDENVLAIDKPFGFPVQSGYGITTS 120

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           ID  +KS       + R+ HRLD+ T+G+L+ A+T  AA+ L   F  R ++K Y ++V 
Sbjct: 121 IDNAMKSI----NPEYRVVHRLDKHTTGVLIFAKTLDAARELWRLFSNRLVKKRYLAIVI 176

Query: 189 GIPKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFCWLE 244
           G  K KK   +C  N +L K         V++ N  G   +AI+ F VI  F +    +E
Sbjct: 177 GELKEKKGAVDCYINKVLFKGE------EVMQCNHIGNGEHAITQFHVIKKF-KNASLIE 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           + P TGR HQ+R     +G P++ D KY    +      +  KL LHA  ++     G  
Sbjct: 230 LFPLTGRKHQIRSQMASIGHPVLNDGKY-GRREAFLECSVNKKLCLHACEIEF-ELFGKI 287

Query: 305 LQITAPLPAHMVK 317
           +++TA LP H  +
Sbjct: 288 IKVTAELPVHFAE 300


>gi|302386409|ref|YP_003822231.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
 gi|302197037|gb|ADL04608.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
          Length = 304

 Score =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 94/316 (29%), Positives = 156/316 (49%), Gaps = 38/316 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q  VV  +E  +R+DR+  +    I+   LQK+L+   V V++K VK N ++ +G     
Sbjct: 3   QEYVVAPEEAGVRIDRYLSDRCQDISRSYLQKLLKEQSVLVEEKPVKSNYKVNAGDR--- 59

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I+      KE +I    + L          ++YED  I + NKP G+ V   +G   
Sbjct: 60  ---ISVFFPESKEPEIQPEDIPLN---------IIYEDKDIILINKPKGMVVHPAAG--- 104

Query: 128 HIDGFLKSWVDSKGQ----------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           H  G L + + S  +          +P + HR+D +T+G+L+V +   A   ++E  +  
Sbjct: 105 HYSGTLVNGLMSHCRSELSGINGVMRPGIVHRIDMDTTGVLIVCKNDMAHSSISEQLKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I + Y ++V G+ K + E   N  + +  +    + +   NEK    A++H++V++ F 
Sbjct: 165 SITRKYAAIVHGVLK-EDEGTVNAPIGRHPVDRKKMSI---NEKNGREAVTHYRVLERFK 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q F ++E Q  TGRTHQ+RVH   +G P++GD  Y  + K  F    Q    LHA  + +
Sbjct: 221 Q-FTYIECQLETGRTHQIRVHMASIGHPLLGDSVYGPS-KCPFRLTGQT---LHAGILGI 275

Query: 298 PHPEGGR-LQITAPLP 312
            HP  G  ++ TAPLP
Sbjct: 276 IHPRTGEYMEFTAPLP 291


>gi|62290527|ref|YP_222320.1| ribosomal large subunit pseudouridine synthase D [Brucella abortus
           bv. 1 str. 9-941]
 gi|82700443|ref|YP_415017.1| ribosomal large subunit pseudouridine synthase [Brucella melitensis
           biovar Abortus 2308]
 gi|148558837|ref|YP_001259509.1| ribosomal large subunit pseudouridine synthase D [Brucella ovis
           ATCC 25840]
 gi|189024749|ref|YP_001935517.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella abortus S19]
 gi|254689825|ref|ZP_05153079.1| RluA family pseudouridine synthase [Brucella abortus bv. 6 str.
           870]
 gi|254694317|ref|ZP_05156145.1| RluA family pseudouridine synthase [Brucella abortus bv. 3 str.
           Tulya]
 gi|254697973|ref|ZP_05159801.1| RluA family pseudouridine synthase [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254700318|ref|ZP_05162146.1| RluA family pseudouridine synthase [Brucella suis bv. 5 str. 513]
 gi|254703437|ref|ZP_05165265.1| RluA family pseudouridine synthase [Brucella suis bv. 3 str. 686]
 gi|254708478|ref|ZP_05170306.1| RluA family pseudouridine synthase [Brucella pinnipedialis
           M163/99/10]
 gi|254730859|ref|ZP_05189437.1| RluA family pseudouridine synthase [Brucella abortus bv. 4 str.
           292]
 gi|256061695|ref|ZP_05451832.1| RluA family pseudouridine synthase [Brucella neotomae 5K33]
 gi|256258078|ref|ZP_05463614.1| RluA family pseudouridine synthase [Brucella abortus bv. 9 str.
           C68]
 gi|260547225|ref|ZP_05822963.1| ribosomal large subunit pseudouridine synthase [Brucella abortus
           NCTC 8038]
 gi|260568746|ref|ZP_05839214.1| ribosomal large subunit pseudouridine synthase [Brucella suis bv. 4
           str. 40]
 gi|260755356|ref|ZP_05867704.1| pseudouridine synthase [Brucella abortus bv. 6 str. 870]
 gi|260758578|ref|ZP_05870926.1| pseudouridine synthase [Brucella abortus bv. 4 str. 292]
 gi|260762410|ref|ZP_05874747.1| pseudouridine synthase [Brucella abortus bv. 2 str. 86/8/59]
 gi|260884372|ref|ZP_05895986.1| pseudouridine synthase [Brucella abortus bv. 9 str. C68]
 gi|261214623|ref|ZP_05928904.1| pseudouridine synthase [Brucella abortus bv. 3 str. Tulya]
 gi|261315976|ref|ZP_05955173.1| pseudouridine synthase [Brucella pinnipedialis M163/99/10]
 gi|261325700|ref|ZP_05964897.1| pseudouridine synthase [Brucella neotomae 5K33]
 gi|261750812|ref|ZP_05994521.1| pseudouridine synthase [Brucella suis bv. 5 str. 513]
 gi|261754066|ref|ZP_05997775.1| pseudouridine synthase [Brucella suis bv. 3 str. 686]
 gi|62196659|gb|AAX74959.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella abortus bv. 1 str. 9-941]
 gi|82616544|emb|CAJ11622.1| Prenyl group binding site (CAAX box):RNA-binding S4:Pseudouridine
           synthase:Pseudouridine synthase, Rlu:Pseudouridine
           synthase [Brucella melitensis biovar Abortus 2308]
 gi|148370094|gb|ABQ60073.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella ovis ATCC 25840]
 gi|189020321|gb|ACD73043.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella abortus S19]
 gi|260095590|gb|EEW79468.1| ribosomal large subunit pseudouridine synthase [Brucella abortus
           NCTC 8038]
 gi|260154130|gb|EEW89212.1| ribosomal large subunit pseudouridine synthase [Brucella suis bv. 4
           str. 40]
 gi|260668896|gb|EEX55836.1| pseudouridine synthase [Brucella abortus bv. 4 str. 292]
 gi|260672836|gb|EEX59657.1| pseudouridine synthase [Brucella abortus bv. 2 str. 86/8/59]
 gi|260675464|gb|EEX62285.1| pseudouridine synthase [Brucella abortus bv. 6 str. 870]
 gi|260873900|gb|EEX80969.1| pseudouridine synthase [Brucella abortus bv. 9 str. C68]
 gi|260916230|gb|EEX83091.1| pseudouridine synthase [Brucella abortus bv. 3 str. Tulya]
 gi|261301680|gb|EEY05177.1| pseudouridine synthase [Brucella neotomae 5K33]
 gi|261305002|gb|EEY08499.1| pseudouridine synthase [Brucella pinnipedialis M163/99/10]
 gi|261740565|gb|EEY28491.1| pseudouridine synthase [Brucella suis bv. 5 str. 513]
 gi|261743819|gb|EEY31745.1| pseudouridine synthase [Brucella suis bv. 3 str. 686]
          Length = 334

 Score =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 91/340 (26%), Positives = 158/340 (46%), Gaps = 49/340 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMN 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L          + +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF- 174
                    + YH    L      +  +P + HRLD++TSG++VVA+   A +HL+E F 
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGIR--RPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFA 163

Query: 175 ---RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              R   +++ Y +LVWG+ +  +  +  +L  +SH       VV +  + A +AI+H+ 
Sbjct: 164 DHGRTGDLERAYLALVWGMTERPQGTVDAYL-GRSHRDRTKQAVVHEEREDARHAITHYA 222

Query: 232 VIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTS 282
            ++ F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        
Sbjct: 223 TVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPE 282

Query: 283 PIQNKL------YLHARYMDLPHPEGGRL-QITAPLPAHM 315
           P++  +       LHA  +   HP    L +  APLP  M
Sbjct: 283 PLKEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDM 322


>gi|306844672|ref|ZP_07477257.1| pseudouridine synthase, RluA family [Brucella sp. BO1]
 gi|306274844|gb|EFM56614.1| pseudouridine synthase, RluA family [Brucella sp. BO1]
          Length = 334

 Score =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 90/337 (26%), Positives = 158/337 (46%), Gaps = 49/337 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMN 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L          + +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF- 174
                    + YH    L      +  +P + HRLD++TSG++VVA+   A +HL+E F 
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGIR--RPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFA 163

Query: 175 ---RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              R   +++ Y +LVWG+ +  +  +  +L  +SH       VV++  + A +AI+H+ 
Sbjct: 164 DHGRTGDLERAYLALVWGMTERPQGTVDAYL-GRSHRDRTKQAVVREEREDARHAITHYA 222

Query: 232 VIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTS 282
            ++ F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        
Sbjct: 223 TVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPE 282

Query: 283 PIQNKL------YLHARYMDLPHPEGGRL-QITAPLP 312
           P++  +       LHA  +   HP    L +  APLP
Sbjct: 283 PLKKAVQGFHRQALHAWLLAFTHPITEELMRFEAPLP 319


>gi|302035759|ref|YP_003796081.1| 23S rRNA pseudouridine synthase [Candidatus Nitrospira defluvii]
 gi|300603823|emb|CBK40155.1| 23S rRNA pseudouridine synthase [Candidatus Nitrospira defluvii]
          Length = 320

 Score =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 87/300 (29%), Positives = 141/300 (47%), Gaps = 30/300 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++   E+  RLD +     P ++   LQ+++ +G VRV+    K + RI++G V+     
Sbjct: 6   IISAGEQPKRLDVFLVQREPKLSRAALQRMITAGWVRVNSHIAKSSQRIRAGDVIVFDTP 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
             A   I  E + L+               +L+ED    V NKPAGI      G  +  +
Sbjct: 66  QPAPLRIAGETQQLE---------------VLFEDHACLVLNKPAGIVTHPSPG--HWSN 108

Query: 131 GFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             L + +D          P + HRLD++TSG++VVA+T  A + L+E F    I + Y +
Sbjct: 109 TLLNALLDHCARGGGAATPGVVHRLDKDTSGVMVVAKTEEAHRKLSEQFERHSITRQYEA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWL 243
           LV G+P   +  I      ++ +G D  H  + + +      A++ ++V + F +    L
Sbjct: 169 LVVGVPAQSEGRI------EAALGPDRHHPKRTSTQTLQPKPAVTDYRVEEVFDKVAARL 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            + PHTGRTHQ+R H   +G PI+GD  Y     G        ++ LHAR +   HP  G
Sbjct: 223 VLSPHTGRTHQIRAHLHVIGHPILGDRSYGGERVGAIAGYEIPRVMLHARTLGFRHPATG 282


>gi|118581597|ref|YP_902847.1| RluA family pseudouridine synthase [Pelobacter propionicus DSM
           2379]
 gi|118504307|gb|ABL00790.1| ribosomal large subunit pseudouridine synthase D [Pelobacter
           propionicus DSM 2379]
          Length = 315

 Score =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 93/332 (28%), Positives = 159/332 (47%), Gaps = 43/332 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           +V   D E +RLD +  +         +Q+++ SG + VD + V+ + +++ G+ + I  
Sbjct: 3   LVFPVDSEPVRLDLFLSSQLASETRSTIQRLIESGNIMVDGREVRPSLKLKGGESISIQL 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P  + A        + L  S+ L          +LYED  + V NKPAG+ V  G G + 
Sbjct: 63  PEPVAA--------RPLPESIPLE---------VLYEDGDLIVINKPAGMVVHPGPGNSS 105

Query: 128 H--IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HRLD+ TSG++VVA+   + Q L+  F +  I++
Sbjct: 106 GTLVNALLAHCTDLSGIGGELRPGIVHRLDKGTSGVMVVAKNDRSHQALSAQFSVHSIKR 165

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQK 239
           IY +LV+G P+     +      +  IG      ++++   +   +A++ ++V   +  +
Sbjct: 166 IYQALVYGSPQQDSGRL------EGQIGRHPTDRLRRSGLARQGKHAVTRWRVRGRYG-R 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLY-------LH 291
            C +E++  TGRTHQ+RVH    G P++GD  Y    +  N T P   KL        LH
Sbjct: 219 ICLMELRLETGRTHQIRVHMSEAGFPLLGDPLYPDGGRFNNLTDPRLRKLITTLARQALH 278

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           AR +   HP  G  L+ +  +PA M    + L
Sbjct: 279 ARTLGFIHPASGNYLEFSVDMPADMAALLEYL 310


>gi|254495420|ref|ZP_05108344.1| ribosomal large subunit pseudouridine synthase D [Polaribacter sp.
           MED152]
 gi|85819775|gb|EAQ40932.1| ribosomal large subunit pseudouridine synthase D [Polaribacter sp.
           MED152]
          Length = 345

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 94/336 (27%), Positives = 158/336 (47%), Gaps = 67/336 (19%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--- 67
           V  + +E +R+D++  N   +     +Q+  ++G V V+   VK N++++   VVR+   
Sbjct: 21  VAADGQEPLRVDKFLMNFIENATRNKVQQAAKAGNVLVNDIAVKSNHKVKPKDVVRVVLA 80

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---- 122
            PP   A N ++ E   LD               ++YED  + V NKPAG+ V  G    
Sbjct: 81  YPP---AENLLVAEDIPLD---------------IIYEDDAVIVVNKPAGMVVHPGHGNY 122

Query: 123 -----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                +G+ +HI+    +      ++P L HR+D++TSG+LVVA+T  A  HL++ F  R
Sbjct: 123 SGTLVNGLIHHIENLPTN----SNERPGLVHRIDKDTSGLLVVAKTEFAMAHLSKQFFDR 178

Query: 178 RIQKIYWSLVWG--------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
             +++Y++LVWG        I  N    + N L       GD+            +A++H
Sbjct: 179 TTERLYYALVWGNIEEDEGRIEGNIGRSLKNRLQMAVFPDGDF----------GKHAVTH 228

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSP 283
           FKV++        ++ +  TGRTHQ+R H  H+G  +  D +Y  +   KG     +   
Sbjct: 229 FKVLERLTY-VTLVQCKLETGRTHQIRAHFKHIGHTLFNDERYGGDEILKGTTFTKYKQF 287

Query: 284 IQN------KLYLHARYMDLPHPEGGR-LQITAPLP 312
           +QN      +  LHA+ +   HP  G  L   + +P
Sbjct: 288 VQNCFKVLPRQALHAKTLGFTHPTTGEFLSFNSEIP 323


>gi|225628223|ref|ZP_03786257.1| pseudouridine synthase, RluA family protein [Brucella ceti str.
           Cudo]
 gi|260167874|ref|ZP_05754685.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Brucella sp. F5/99]
 gi|261757311|ref|ZP_06001020.1| ribosomal large subunit pseudouridine synthase [Brucella sp. F5/99]
 gi|225616069|gb|EEH13117.1| pseudouridine synthase, RluA family protein [Brucella ceti str.
           Cudo]
 gi|261737295|gb|EEY25291.1| ribosomal large subunit pseudouridine synthase [Brucella sp. F5/99]
          Length = 334

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 91/340 (26%), Positives = 158/340 (46%), Gaps = 49/340 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIAYGHVTIDGAPARETKQKLREGMN 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L          + +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLSEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF- 174
                    + YH    L      +  +P + HRLD++TSG++VVA+   A +HL+E F 
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGIR--RPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFA 163

Query: 175 ---RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              R   +++ Y +LVWG+ +  +  +  +L  +SH       VV +  + A +AI+H+ 
Sbjct: 164 DHGRTGDLERAYLALVWGMTERPQGTVDAYL-GRSHRDRTKQAVVHEEREDARHAITHYA 222

Query: 232 VIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTS 282
            ++ F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        
Sbjct: 223 TVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPE 282

Query: 283 PIQNKL------YLHARYMDLPHPEGGRL-QITAPLPAHM 315
           P++  +       LHA  +   HP    L +  APLP  M
Sbjct: 283 PLKEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDM 322


>gi|310828904|ref|YP_003961261.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           limosum KIST612]
 gi|308740638|gb|ADO38298.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           limosum KIST612]
          Length = 307

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 93/322 (28%), Positives = 154/322 (47%), Gaps = 37/322 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD +     P  +   ++ +L  G V+VD  + K + +++  +++ +    
Sbjct: 8   VSEEKAGVRLDAYCAEQEPDFSRGYIKNLLNEGAVKVDGGQKKASYKLKGKEIITMEIPE 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------- 124
            A + I  E   L+               ++YED  + V NKP G+ V    G       
Sbjct: 68  PAESTIEPENIPLE---------------IIYEDEDVIVVNKPKGMVVHPAPGSPSGTLV 112

Query: 125 -IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H  G L +   +   +P + HR+D++TSG+L+VA+  AA Q+LTE  +   I + Y
Sbjct: 113 NALMHHTGALSNI--NGVYRPGIIHRIDKDTSGLLMVAKNNAAHQNLTEQLKAHTITRQY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVIDCFAQKFC 241
            +LV GI +N +  I   + +      D V   VVK+N K    A++HF+ +  +A+ + 
Sbjct: 171 KALVKGIMENNRGTIDMPIGRHPK---DRVRMAVVKENSK---EAVTHFETLKRYAEGYT 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++ +  TGRTHQ+RVH   +G PI GD  Y  + K  F +  Q    LHA  +   HP 
Sbjct: 225 LMQFRLETGRTHQIRVHMQAIGYPIAGDPLYKGDKKNPFKTEGQ---CLHAELLGFKHPR 281

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++ +APLP       D L
Sbjct: 282 TGEYMEFSAPLPEAFQAILDGL 303


>gi|83589720|ref|YP_429729.1| ribosomal large subunit pseudouridine synthase D [Moorella
           thermoacetica ATCC 39073]
 gi|83572634|gb|ABC19186.1| ribosomal large subunit pseudouridine synthase D [Moorella
           thermoacetica ATCC 39073]
          Length = 306

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 95/324 (29%), Positives = 154/324 (47%), Gaps = 38/324 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIP 68
           VVV  +    R+D W     P ++   +Q++L +G++ +    R+K N R++ G+ VR+ 
Sbjct: 3   VVVPPEARGRRIDAWLAGELPEVSRSRIQQLLEAGEITLALPGRLKANYRLRGGERVRV- 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIA 126
                          L     L    + +   +LYED  I V NKP G+ V    GS   
Sbjct: 62  --------------RLPEPTLLAARPEAIPLDILYEDEDIIVVNKPQGMVVHPAPGSEGG 107

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D  G     +P + HRLD++TSGILV A+  AA + L    +   +++I
Sbjct: 108 TLVNALLYHCGDLSGINGVLRPGIVHRLDKDTSGILVAAKNDAAHRGLAAQIKDHSMKRI 167

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y +LV G    P+ + E      + +  +    + V  +N +    A++H++V++ F   
Sbjct: 168 YLALVHGEVAEPRGRVEAP----IGRHPVDRQRMAVTLKNSR---PAVTHYRVVEHFP-G 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  LE +  TGRTHQ+RVH   +G P+VGD KY    +  F  P Q    LHA  +   H
Sbjct: 220 YTLLEARLETGRTHQIRVHMAFIGHPVVGDPKYGPR-RCPFAVPGQ---LLHAGCLGFVH 275

Query: 300 P-EGGRLQITAPLPAHMVKTWDSL 322
           P  G  L+ T P P+  ++  + L
Sbjct: 276 PVRGDYLEFTTPPPSIFLQVLEQL 299


>gi|188580214|ref|YP_001923659.1| pseudouridine synthase, RluA family [Methylobacterium populi BJ001]
 gi|179343712|gb|ACB79124.1| pseudouridine synthase, RluA family [Methylobacterium populi BJ001]
          Length = 345

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 101/331 (30%), Positives = 153/331 (46%), Gaps = 48/331 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV-INALNHII 78
           RLDR     +  ++   LQ ++R G V+ D            G VVR P   + A + I 
Sbjct: 36  RLDRVLARAFDDLSRARLQALVRDGLVQCD------------GAVVRDPARKVGAGSRI- 82

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----- 133
                + + +      + L   +++ED  + V +KPAG+ V   +G   H DG L     
Sbjct: 83  --DLTVPAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPAAG---HEDGTLVNRLI 137

Query: 134 ----KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYW 184
                S     G ++P + HRLD++TSG+LVVA+   A Q L+  F    R   +++ Y 
Sbjct: 138 AHCGASLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQFADHGRSGALERAYL 197

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--FCW 242
           +LVWG+P+ +   I   L +  H   + + VV+  E     AI+H++V    A       
Sbjct: 198 ALVWGVPEPRAGTIRANLARSRH-NREKIAVVRDGE--GREAITHYRVEALPAADGVTAL 254

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKL------YLHAR 293
           L  +  TGRTHQ+RVH  H G P++GD  Y   FK        P ++ L       LHA 
Sbjct: 255 LRCRLETGRTHQIRVHLSHRGHPLLGDAVYGGAFKTKAARLAEPARDALTALARQALHAA 314

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            +   HP  G RL+  +PLPA   +   +LG
Sbjct: 315 ELGFLHPRSGERLRFESPLPADFSRLLAALG 345


>gi|119357434|ref|YP_912078.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           phaeobacteroides DSM 266]
 gi|119354783|gb|ABL65654.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           phaeobacteroides DSM 266]
          Length = 350

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 97/330 (29%), Positives = 155/330 (46%), Gaps = 61/330 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++      +     +Q+ +  G+V V+ K VK N +I+S  +++I  +      + 
Sbjct: 34  MRIDKYLTQQVENATRNKVQEAITEGRVLVNGKPVKSNYKIKSCDLIQITFLRPPAPEMA 93

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E   +D               ++YED+ + V NK AG+ V    G         I +HI
Sbjct: 94  PENIPID---------------IIYEDADLMVVNKEAGMVVHPAFGNWTGTLANAILHHI 138

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G     +D   Q+P + HRLD++TSG++++A+   A Q L   F  R+++KIY +LVWG
Sbjct: 139 -GNDTGELDCSLQRPGIVHRLDKDTSGLIIIAKNPLALQRLARQFAQRQVEKIYHALVWG 197

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEK----------GANYAISHFKVIDCFAQK 239
           +P+     I      K++IG       K+N K             +AI+ + VI+   + 
Sbjct: 198 VPEPASGTI------KTNIGRS-----KKNRKVMTTYPFEGIDGKHAITDYAVIEDL-RY 245

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY------------CANFKGNFTSPIQNK 287
           F  + ++ HTGRTHQ+RVH  H+G PI+GD  Y              +F  N    I  +
Sbjct: 246 FSLVSIKLHTGRTHQIRVHLQHLGHPILGDTVYGGASIRTLPFSKSESFIKNLLEIIPRQ 305

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
             LHA+ +    P     L  TAPLP  M+
Sbjct: 306 -ALHAQTLRFTQPLTHEPLSFTAPLPGDMI 334


>gi|296157780|ref|ZP_06840614.1| pseudouridine synthase, RluA family [Burkholderia sp. Ch1-1]
 gi|295892026|gb|EFG71810.1| pseudouridine synthase, RluA family [Burkholderia sp. Ch1-1]
          Length = 431

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 97/350 (27%), Positives = 161/350 (46%), Gaps = 30/350 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV ++    RLD+     +P  +   LQ  + + +VR+D K  K    +  G  + +
Sbjct: 66  RSVVVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAKIRQPVPLGATIEL 125

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 126 VP------DLLPEQ--------LAFTPEPVPLAIVYEDDTLVVINKPAGMVVHPAAGNWS 171

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + D+    PR  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 172 GTLLNGLLYRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 231

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKF 240
            +LVWG     +E   +  + +       + VV         A +HF+ +D      Q  
Sbjct: 232 LALVWG--NMPEEGTIDAPIGRDPRERTRMAVV--TSASGKPARTHFRRVDSAIWERQPV 287

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L
Sbjct: 288 TAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGGFARQALHAWRLGL 347

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF-KYDRNLYIKRLYSQDECKQNI 345
            HP+ GR +Q  A +P  M     +LG  + D   + +  Y +D+ + ++
Sbjct: 348 IHPKTGRTMQWRADVPEDMEALSAALGLGRDDAGEFDETYYEEDDYEASL 397


>gi|262199978|ref|YP_003271187.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262083325|gb|ACY19294.1| pseudouridine synthase, RluA family [Haliangium ochraceum DSM
           14365]
          Length = 303

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 90/321 (28%), Positives = 149/321 (46%), Gaps = 39/321 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-I 59
           MS+        V +++   RLD+      P ++    + +L  G V VD+ RVK  +R +
Sbjct: 1   MSIRARTVRFEVADEDVGKRLDQLLAARVPELSRRMARTLLDIGGVFVDRTRVKVASRKL 60

Query: 60  QSGQVVRI---PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           + GQ V +     +  A   + KE +  DS           +  +++ED  + V +KPAG
Sbjct: 61  RPGQSVEVHLGGALERATKEVGKEARKRDSRA-------LPRFKIVFEDRDLVVVDKPAG 113

Query: 117 ISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +     S      D G L + +  + ++  + HR+D +TSG+LV A+TR A QHL+E FR
Sbjct: 114 LL----SAPTPESDLGNLAALLRERRERVYVVHRIDLQTSGLLVFAKTRRANQHLSERFR 169

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             +I++ Y ++V G P      I   L  +                    A +H +V+  
Sbjct: 170 EHQIERAYTAVVAGAPVEDTFTIDLPLRGR-------------------RATTHLQVLQR 210

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             ++   L+ +  TGRTHQ+R+H L  G P++GD +Y        T P   ++ LHAR +
Sbjct: 211 IGERAAVLDARLETGRTHQIRLHCLQRGYPVLGDPQYGERMSDELTPP---RMALHARVL 267

Query: 296 DLPHPEGGRL-QITAPLPAHM 315
              HP  G   +  + LPA +
Sbjct: 268 GFEHPRSGEARRFESELPADL 288


>gi|117924690|ref|YP_865307.1| pseudouridine synthase [Magnetococcus sp. MC-1]
 gi|117608446|gb|ABK43901.1| pseudouridine synthase [Magnetococcus sp. MC-1]
          Length = 255

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 80/238 (33%), Positives = 120/238 (50%), Gaps = 9/238 (3%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           T  ++ L+S LLY D  + + NKPAGI V  G G   +++           + P L HRL
Sbjct: 5   TITANDLESRLLYRDGLLLIINKPAGIPVHAGPGGGANLEALFGGLRFGLPKAPALAHRL 64

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG LV+ R   A   L + F   ++QK YW++V G P   +  +   L K S    
Sbjct: 65  DRDTSGCLVLGRHAKALSKLGKLFSQGKVQKTYWAVVQGGPPQAQGSMDFPLYKISTAQQ 124

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  VV   +     +++ ++V+   A    WLE+ P TGRTHQ+RVH  H+G PI GD 
Sbjct: 125 GWRMVVDPEQ--GKSSLTLYRVLGRSA-THSWLELTPKTGRTHQIRVHCAHVGLPIEGDL 181

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
           +Y     G   S  Q  L+LHAR + LP       + ++AP P  M    +  G++ +
Sbjct: 182 QY-----GAAPSEPQLTLHLHARQIILPISASKAPINVSAPPPRAMRGLLEQCGYRAE 234


>gi|85859994|ref|YP_462196.1| ribosomal large subunit pseudouridine synthase D [Syntrophus
           aciditrophicus SB]
 gi|85723085|gb|ABC78028.1| ribosomal large subunit pseudouridine synthase D [Syntrophus
           aciditrophicus SB]
          Length = 324

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 87/298 (29%), Positives = 150/298 (50%), Gaps = 39/298 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHIIK 79
           L  +    YP  +   ++K+LR G +R + K V  ++ ++ +G VV I    N    I  
Sbjct: 46  LIEFLAEQYPDSSRTRIKKLLRHGNIRCNNKPVTLHSHKLSAGDVVEI----NTYGGIAA 101

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI---SVQGGSGIAYHIDGFLKSW 136
           +                L   +L+ED  +    KP GI   S  G + + + +   LK  
Sbjct: 102 KAG--------------LPFPVLFEDQHVIAVEKPVGIATFSADGSASVQWIVAQALKE- 146

Query: 137 VDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             S+G+      HRLD+E SG+L+ A+++ A  H+ E ++    +K Y++LV G P++  
Sbjct: 147 -HSRGKIHAFAVHRLDKEVSGVLLFAKSKMAMDHIKEKWK--EAEKRYYALVEGKPESPD 203

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I +WL++        VH  +++ K A ++++H+++I    Q +  L+++  TGR +Q+
Sbjct: 204 GTIESWLVEDH---AQKVHSTRESSK-AKFSVTHYRIIKQVNQ-YTLLDVKLQTGRKNQI 258

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           RVH   +GCPI GD KY A       +    ++ LHA Y+  PHP  G R+ I +P+P
Sbjct: 259 RVHLSDIGCPIAGDRKYGA------AADFVRRIRLHAYYLSFPHPVTGERISIESPMP 310


>gi|91783470|ref|YP_558676.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           xenovorans LB400]
 gi|91687424|gb|ABE30624.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           xenovorans LB400]
          Length = 438

 Score =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 96/350 (27%), Positives = 157/350 (44%), Gaps = 29/350 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +VV ++    RLD+     +P  +   LQ  + + +VR+D K  K    +  G  + +
Sbjct: 66  RSIVVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAKIRQPVPLGATIEL 125

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
            P             +L   +  T     L+  ++YED  + V NKPAG+ V   +G   
Sbjct: 126 VP------------DLLPEQLAFTPEPVPLE--IIYEDDTLVVINKPAGMVVHPAAGNWS 171

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + D+    PR  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 172 GTLLNGLLYRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 231

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKF 240
            +LVWG     +E   +  + +       + VV         A +HF+ +D      Q  
Sbjct: 232 LALVWG--NMPEEGTIDAPIGRDPRERTRMAVV--TSAAGKPARTHFRRVDSAIWERQPV 287

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L
Sbjct: 288 TAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGGFARQALHAWRLGL 347

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL 346
            HP+ GR +Q  A +P  M     +LG   D        Y +++  + +L
Sbjct: 348 IHPKTGRTMQWRADVPEDMEALSAALGLGRDDAGEFDETYYEEDDYEALL 397


>gi|217966766|ref|YP_002352272.1| pseudouridine synthase [Dictyoglomus turgidum DSM 6724]
 gi|217335865|gb|ACK41658.1| pseudouridine synthase [Dictyoglomus turgidum DSM 6724]
          Length = 226

 Score =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 73/217 (33%), Positives = 118/217 (54%), Gaps = 26/217 (11%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTH 148
           +D L+  ++YED+ + V NKPAG+ VQG    +  +    K+++  K QK       + H
Sbjct: 2   ADLLRPEIIYEDNHLLVVNKPAGVLVQGDITKSTTLLEISKAYIKEKYQKAGNVFLAIVH 61

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL----- 203
           RLD+  SG+++ AR   +A  L+E+FR R+++K Y ++  GI K KK  I   L      
Sbjct: 62  RLDKPVSGVVIFARNSKSAGRLSEAFRERKVEKEYLAICEGIFKIKKGTINESLFWDERE 121

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +K+ I          N+  +  AI+H++V++ F +    + + P TGR HQLR H  ++G
Sbjct: 122 RKAKIS---------NKAESRVAITHYEVLEEF-KNLSLVRLIPETGRKHQLRAHLSYIG 171

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            PI+GD KY            ++K++LH R M +PHP
Sbjct: 172 HPILGDEKYGG------VRIFKDKIFLHCRRMRIPHP 202


>gi|296120899|ref|YP_003628677.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
 gi|296013239|gb|ADG66478.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
          Length = 269

 Score =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 76/244 (31%), Positives = 119/244 (48%), Gaps = 24/244 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           L+  +L ED  +    KPAG+  QG       ++ ++K+W+  K  KP      + HRLD
Sbjct: 18  LEPQILLEDGPLLAIWKPAGLLTQGVPQGLPTLENWVKNWIREKYAKPGNVYLGIPHRLD 77

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +  SG+++ AR   AA  L E FR RR++K Y ++V G+P      + N+LLK       
Sbjct: 78  RPVSGVMLFARNSKAAARLAEVFRDRRVKKTYTAVVEGMPPQTTGRLTNYLLKDPQAA-- 135

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +  +V +   G+  AI  ++++   A +   LE++  TGR HQ+RV    MGCP+VGD +
Sbjct: 136 HSQIVAEGTPGSKSAILDYRLLGTVAGRSL-LEIELQTGRMHQIRVQMAAMGCPVVGDQE 194

Query: 272 YCANFKGNFTSPI---------------QNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           Y     G+ T+                   ++ LHA  + +PHP     + I AP PA  
Sbjct: 195 YQTPQAGDTTTRTVEEQSTTNLTTQPRGSERIALHASQIIVPHPIRFDEVTIHAPFPAEW 254

Query: 316 VKTW 319
              W
Sbjct: 255 ASYW 258


>gi|159029548|emb|CAO87700.1| rluD [Microcystis aeruginosa PCC 7806]
          Length = 308

 Score =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 89/301 (29%), Positives = 146/301 (48%), Gaps = 27/301 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD W  +  P ++   LQK++  G ++++ + +  N   + GQ  R+            
Sbjct: 14  RLDAWMGSQLPDLSRSRLQKLIEQGYIQLNGQ-ICTNKNTKVGQGDRL------------ 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            +  +  S  L   ++ +   +LYED  + + NKPA + V    G      ++  L    
Sbjct: 61  -KITIPDSQPLQLSAEAIDLDILYEDEYLIIINKPADLVVHPAPGHESGTLVNALLHHCP 119

Query: 138 DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +  G    Q+P + HRLD++T+G +V+A+T  A QHL    + +  ++ Y +LV G+PK+
Sbjct: 120 NLAGIGGIQRPGIVHRLDKDTTGAIVIAKTDQAHQHLQAQLKTKTARREYMALVHGVPKS 179

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +   I   L    H        +   EKG   A++H++V +     +  +E +  TGRTH
Sbjct: 180 ETGTID--LPISRHRSDRQKMAIIAVEKGGRNAVTHWQVKERLG-NYTLMEFRLETGRTH 236

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Q+RVH+ H+G PI+GD  Y +        P Q    LHA  + L HP  G  L+  APLP
Sbjct: 237 QIRVHSSHIGHPILGDPLYSSGRSIGINLPGQ---LLHAYRLILIHPVTGESLEAIAPLP 293

Query: 313 A 313
           A
Sbjct: 294 A 294


>gi|254252275|ref|ZP_04945593.1| Pseudouridine synthase RluD [Burkholderia dolosa AUO158]
 gi|124894884|gb|EAY68764.1| Pseudouridine synthase RluD [Burkholderia dolosa AUO158]
          Length = 400

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 95/329 (28%), Positives = 146/329 (44%), Gaps = 35/329 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V       RLD+     +P  +   LQ  + + +VR+D    K    +  G  + + P
Sbjct: 59  VAVPASLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRIDGAPAKIRQPVPLGATIELVP 118

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                  ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 119 ------DLLPEQ--------LAFTPEPVPLDVVYEDDALVVINKPAGVVVHPAAGNWSGT 164

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++G L  + D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++
Sbjct: 165 ILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFA 224

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFA---QK 239
           LVWG         A        IG D     +           A +HF+ +D      Q 
Sbjct: 225 LVWGTMPEAGTIDAP-------IGRDPRERTRMAVVTGASGKPARTHFRTVDTCVWQRQP 277

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMD 296
              ++    TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + 
Sbjct: 278 VSAIQCDLETGRTHQIRVHCSHVGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLG 337

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           L HP  G+ +Q   PLP  M     +LGF
Sbjct: 338 LVHPVTGKAMQWRCPLPDDMNALVAALGF 366


>gi|319408111|emb|CBI81764.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           schoenbuchensis R1]
          Length = 340

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 102/352 (28%), Positives = 165/352 (46%), Gaps = 50/352 (14%)

Query: 11  VVENDEENMRLDRWF-KNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVR-- 66
           + +      R+D+W  K ++  ++   LQ ++R G ++VD + +K    ++Q  Q +   
Sbjct: 5   ITDESALGQRIDQWLAKKYHNELSRSRLQTLIREGYLKVDGQLIKEPKTKLQPNQTIELI 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           IPP+ N   H+  E  +LD               +L+ED  + V NKPAG+ V  G+G  
Sbjct: 65  IPPLKNV--HLEGEAIVLD---------------ILFEDDHVIVINKPAGLVVHPGNGNW 107

Query: 125 IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----R 175
               ++  +    DS       ++P + HRLD+ TSG++VVA+   A + L+  F    R
Sbjct: 108 TGTLVNALIHHCGDSLSGIGGVKRPGIVHRLDKNTSGVMVVAKNDFAHKSLSAQFSDHGR 167

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              + + Y +L+W  P+     I   L +  H       VV+     A +AI+HF +++ 
Sbjct: 168 TCALDRRYHALIWNAPRRNIGTIDVPLGRSPHNRIKQT-VVRHQNVHARHAITHFSLLEK 226

Query: 236 F-----AQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQN 286
           +     A+ F   LE +  TGRTHQ+RVH  H+G P+VGD  Y   FK       S I+N
Sbjct: 227 YKTCADAEPFASLLECRLETGRTHQIRVHMAHIGHPLVGDTVYGNAFKTKANTLNSTIKN 286

Query: 287 KL------YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLY 331
            +       LHA  +   HP  G  +  ++P P  M +  +    K D N Y
Sbjct: 287 AIDQFNRQALHAVSLTFEHPAKGEIMSFSSPPPQDMAELINHFK-KLDWNFY 337


>gi|167720581|ref|ZP_02403817.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei DM98]
          Length = 247

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 87/236 (36%), Positives = 126/236 (53%), Gaps = 24/236 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +L+ED  I V NKPAG++V GGSG+A+   G ++    ++       L HRLD+ETSGIL
Sbjct: 15  ILFEDDAIIVLNKPAGVAVHGGSGVAF---GVIEQMRHARPHAKFLELAHRLDRETSGIL 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---WGIPKNKKECIANWLLKKSHIGGDYVHV 215
           ++A+ R+A   L E  R  R+ K Y++ V   W     ++  +   L K +   G+    
Sbjct: 72  MLAKKRSALVGLHEQIRENRMDKRYFACVHGDWAADWGRRRVVKAPLFKYATPDGE--RR 129

Query: 216 VKQNEKGANYAISH--FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           V+  E G     SH  F ++D +   +  +E +  TGRTHQ+RVH  H+G PIVGD KY 
Sbjct: 130 VRVQEDGLP---SHTVFNLVDRWPD-YALVEAELKTGRTHQIRVHLAHLGLPIVGDAKYG 185

Query: 274 ------ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 A  + N    I+ +++LHA  + L HP  G  LQ  APLPA   +  D L
Sbjct: 186 DFALNKALARANAVPSIK-RMFLHAHRLRLAHPLTGEPLQFDAPLPAECRQFIDQL 240


>gi|167816774|ref|ZP_02448454.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 91]
          Length = 248

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 87/236 (36%), Positives = 126/236 (53%), Gaps = 24/236 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +L+ED  I V NKPAG++V GGSG+A+   G ++    ++       L HRLD+ETSGIL
Sbjct: 16  ILFEDDAIIVLNKPAGVAVHGGSGVAF---GVIEQMRHARPHAKFLELAHRLDRETSGIL 72

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---WGIPKNKKECIANWLLKKSHIGGDYVHV 215
           ++A+ R+A   L E  R  R+ K Y++ V   W     ++  +   L K +   G+    
Sbjct: 73  MLAKKRSALVGLHEQIRENRMDKRYFACVHGDWAADWGRRRVVKAPLFKYATPDGE--RR 130

Query: 216 VKQNEKGANYAISH--FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           V+  E G     SH  F ++D +   +  +E +  TGRTHQ+RVH  H+G PIVGD KY 
Sbjct: 131 VRVQEDGLP---SHTVFNLVDRWPD-YALVEAELKTGRTHQIRVHLAHLGLPIVGDAKYG 186

Query: 274 ------ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 A  + N    I+ +++LHA  + L HP  G  LQ  APLPA   +  D L
Sbjct: 187 DFALNKALARANAVPSIK-RMFLHAHRLRLAHPLTGEPLQFDAPLPAECRQFIDQL 241


>gi|119503335|ref|ZP_01625419.1| ribosomal large subunit pseudouridine synthase C [marine gamma
           proteobacterium HTCC2080]
 gi|119460981|gb|EAW42072.1| ribosomal large subunit pseudouridine synthase C [marine gamma
           proteobacterium HTCC2080]
          Length = 320

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 95/318 (29%), Positives = 162/318 (50%), Gaps = 18/318 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++ VV  +E   RLD + +     +    + + +R G+VRVDK RVK + R+++G  VR
Sbjct: 18  VEWRVVLPEEAGQRLDNFLQRVRGGVPKTRIYRAIRKGEVRVDKGRVKPDTRLEAGVSVR 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      + ++ +   ++   T+    L++ ++ E+S + V NKP G++V GGSGI 
Sbjct: 78  IPPL-----RVPEKAEAAGAAGWRTR----LRASIIREESTLLVVNKPPGLAVHGGSGIN 128

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L++  ++  +   L HRLD++TSG+L+VAR  +  ++L    R   I K Y  L
Sbjct: 129 VGLIETLRAMYETD-RYLELVHRLDRDTSGLLLVARRASTLRNLHVLLRSNGIDKRYLCL 187

Query: 187 VWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G  P + K   A         G   V V     +    +++ F+V+  ++     +E 
Sbjct: 188 VNGRWPAHLKRVDAPLEKFALPSGERRVKVAATGRQ----SLTTFRVVRRWSSA-TLVEA 242

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR 304
           +P TGRTHQ+RVH  H G PI+GD KY           +   +L+LHA  ++    +   
Sbjct: 243 KPVTGRTHQIRVHCQHAGFPILGDAKYADEAAVRIADKLGLKRLFLHAASLNF-RLDDQN 301

Query: 305 LQITAPLPAHMVKTWDSL 322
             + A LP  + +  D++
Sbjct: 302 YSLEAGLPTELERLLDAI 319


>gi|119897905|ref|YP_933118.1| ribosomal large subunit pseudouridine synthase C [Azoarcus sp.
           BH72]
 gi|119670318|emb|CAL94231.1| ribosomal large subunit pseudouridine synthase C [Azoarcus sp.
           BH72]
          Length = 319

 Score =  123 bits (309), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 94/314 (29%), Positives = 159/314 (50%), Gaps = 31/314 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++  ++      R+D +       +   ++ +ILR G+VRV+ +RV+   R+  G  VR
Sbjct: 10  VRHERIDEASAGQRIDNFLLRLAKGVPKSHVYRILRGGEVRVNGRRVQPTYRLALGDEVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+           ++ + + +    +     + ++ED  + V +KP+G +V GGSG++
Sbjct: 70  VPPL-----------RLAEPTRSAPAPAGKPLPV-VFEDDALLVVDKPSGKAVHGGSGVS 117

Query: 127 YHIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           Y +   L++      Q+P      L HRLD+ETSG+L+VA+ R+A   L +  R  +++K
Sbjct: 118 YGVIEQLRT------QRPELRMLELAHRLDRETSGLLIVAKKRSALTALHDMMREGQVEK 171

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   N  + +   LLK     G+    V    K A+   S  +++  +A  + 
Sbjct: 172 RYLTLVPGRWMNPMQHVKAPLLKYLTPEGERRVRVSDEGKPAH---SIVRLVQRWAD-YS 227

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPH 299
            LE++  TGRTHQ+RVH  H+G P+ GD KY  +F  N         +++LHA  +   H
Sbjct: 228 LLEVELKTGRTHQIRVHLTHLGFPLCGDDKY-GDFALNKRLEGEGLRRMFLHAASLRFHH 286

Query: 300 PEGGR-LQITAPLP 312
           P  G  L   A LP
Sbjct: 287 PLTGELLAFEAALP 300


>gi|170692348|ref|ZP_02883511.1| pseudouridine synthase, RluA family [Burkholderia graminis C4D1M]
 gi|170142778|gb|EDT10943.1| pseudouridine synthase, RluA family [Burkholderia graminis C4D1M]
          Length = 450

 Score =  123 bits (309), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 97/342 (28%), Positives = 156/342 (45%), Gaps = 30/342 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV ++    RLD+     +P  +   LQ  + + +VR+D K  K    +  G  + + P
Sbjct: 68  VVVPDELAGERLDKVLARLFPEFSRNRLQSWIEAERVRIDGKPAKIRQPVPLGATIELVP 127

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +L   +  T     L+  ++YED  + V NKPAG+ V   +G     
Sbjct: 128 ------------DLLPEQLAFTPEPVPLE--IVYEDDTLVVINKPAGMVVHPAAGNWSGT 173

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++G L  + D+    PR  + HRLD+ETSG++VVART  A   L    + R +++ Y +
Sbjct: 174 VLNGLLYRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLA 233

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCW 242
           LVWG     +E   +  + +       + VV         A +HF+ +D      Q    
Sbjct: 234 LVWG--NMPEEGTIDAPIGRDPRERTRMAVVTG--ASGKPARTHFRRVDTAIWQRQPVTA 289

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---YLHARYMDLPH 299
           +     TGRTHQ+RVH  H+G P++GD  Y         +P+  +     LHA  + L H
Sbjct: 290 IHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGEFARQALHAWRLGLIH 349

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGF-KYDRNLYIKRLYSQD 339
           P+ GR +Q  A +PA +     +LG  + D   + +  Y +D
Sbjct: 350 PKTGRTMQWRADVPADIAALSAALGLGRDDAGEFDETYYEED 391


>gi|86608591|ref|YP_477353.1| RluA family pseudouridine synthase [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86557133|gb|ABD02090.1| pseudouridine synthase, RluA family [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 317

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 93/321 (28%), Positives = 158/321 (49%), Gaps = 44/321 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           ++ + V   ++ +RLDR      P ++   LQ+++R GQV ++ +  +  +R +Q+G  V
Sbjct: 11  IRQIRVTEKQQGLRLDRGLAEQLPELSRSRLQQLIRQGQVWLNGQPCRDKDRPLQAGDEV 70

Query: 66  --RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
             RIPP       +  E   LD               +LYED  + V NKP G+ V    
Sbjct: 71  EVRIPPATP--TALQPEPIPLD---------------ILYEDDDLLVINKPRGLVVHPAP 113

Query: 124 GIAYHIDGFLK----------SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           G   H  G L           S ++ + Q+P + HRLD++T+G LV+A+   A QHL   
Sbjct: 114 G---HASGTLVHALLAHCPRLSGINGE-QRPGIVHRLDKDTTGALVIAKHDQAHQHLQAQ 169

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + +  +++Y  +V+G P   +  ++   + +  +    + V+   +     A++H++V+
Sbjct: 170 IQAKTARRLYLGVVFGRPAQSQGTVSAP-IGRHPVDRQKMAVLTPGQ--GRVAVTHWQVL 226

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHA 292
           +     +  ++ +  TGRTHQ+RVHA H+  PIVGD  Y      + TSP++     LHA
Sbjct: 227 ERLG-NYTLMQFELETGRTHQIRVHAAHLRLPIVGDPLYTQ----SKTSPVKLGGQALHA 281

Query: 293 RYMDLPHPEGGR-LQITAPLP 312
             +    P  G+ LQ TAPLP
Sbjct: 282 WKLSFVQPRTGQPLQFTAPLP 302


>gi|291528977|emb|CBK94563.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale M104/1]
          Length = 312

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 91/328 (27%), Positives = 160/328 (48%), Gaps = 46/328 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V++++E  RLD++  + YP I+    Q+IL+  Q+ V+ K  K N R+++  +V +  + 
Sbjct: 8   VQSEQEGERLDKYLSSIYPDISRSFFQRILKENQILVNDKPQKANYRLKTDDIVDV-TIP 66

Query: 72  NALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
           +A+   I  Q I LD               +LYED  + V NKP G+ V   +G      
Sbjct: 67  DAVQTPILPQDIPLD---------------ILYEDDDVLVVNKPKGMVVHPSAGHYSDTL 111

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              I YH    L S ++ +  +P + HR+D +T+G L+V +   +   ++E  +     +
Sbjct: 112 VNAIMYHCKDSL-SGINGE-IRPGIVHRIDMDTTGSLIVCKNDESHIKISEQIKHHSCNR 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY  +V G  KN +  I   + +  +        +  NEK    A++H+KV++ F   + 
Sbjct: 170 IYVGIVCGNVKNDEGTIEGAIGRNPNDRKK----MAINEKNGKPAVTHYKVLERFGD-YT 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL------YLHARYM 295
           +++ +  TGRTHQ+RVH   +  P++GD  Y +       SP +N+        LHA+ +
Sbjct: 225 YMQFKLETGRTHQIRVHMASINHPLLGDMLYSS------YSPTKNRFKGLEGQCLHAKTI 278

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP+ G  ++  APLP +     + L
Sbjct: 279 GFVHPKTGEYMEFDAPLPKYFANLLEVL 306


>gi|220927321|ref|YP_002502623.1| RluA family pseudouridine synthase [Methylobacterium nodulans ORS
           2060]
 gi|219951928|gb|ACL62320.1| pseudouridine synthase, RluA family [Methylobacterium nodulans ORS
           2060]
          Length = 337

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 104/354 (29%), Positives = 160/354 (45%), Gaps = 60/354 (16%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQS 61
           + + V+   +   E   RLDR     +P ++   LQ ++R G VR+D   ++    R+  
Sbjct: 1   MESEVRVAEIPAGEAPERLDRALARTWPDLSRSRLQGLIREGGVRLDGAEIRDAAVRVAG 60

Query: 62  GQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           GQ   V +PP   A                 T  ++    I+ YED  + V +KP G+ V
Sbjct: 61  GQTVAVTVPPARPA-----------------TPEAEERALIIPYEDDDLIVIDKPPGLVV 103

Query: 120 QGGSGIAYHIDGFL---------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQH 169
               G   H  G L          S     G ++P + HRLD++TSG+LVVA+   A   
Sbjct: 104 HPAPG---HDSGTLVNALIAHCGASLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDMAHAA 160

Query: 170 LTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           L+  F    R  ++++ Y +LVWG+P+ +   I +  L +S    + + VV+  EKG  +
Sbjct: 161 LSLQFADHGRSGQLERAYLALVWGVPEPRAGRI-DAALARSDSNREKIAVVRP-EKG-RH 217

Query: 226 AISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--K 277
           AI+H++       +       C LE    TGRTHQ+RVH  H G P++GD  Y A F  K
Sbjct: 218 AITHYRTEAVLGVREPVGLVRCRLE----TGRTHQIRVHLAHRGHPLLGDATYGAAFRTK 273

Query: 278 GNFTSP-------IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                P          +  LHA  +   HP     L+  +PLPA + +   +LG
Sbjct: 274 AARLEPEARAALDALGRQALHAAVLGFVHPRTNAFLRFESPLPADLARLVAALG 327


>gi|332521351|ref|ZP_08397807.1| pseudouridine synthase, RluA family [Lacinutrix algicola 5H-3-7-4]
 gi|332043079|gb|EGI79277.1| pseudouridine synthase, RluA family [Lacinutrix algicola 5H-3-7-4]
          Length = 345

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 95/335 (28%), Positives = 159/335 (47%), Gaps = 57/335 (17%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--- 67
           + +  +  +R+D+W  N   +     +Q   + G + V+ + VK N +++   V+++   
Sbjct: 22  IADKGQAPLRIDKWLMNKVENATRNKIQAAAKEGNIYVNDQPVKSNYKVKPLDVIKVLFE 81

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
            PP  N L   + E   LD               ++YED  + V NKPAG+ V  G G  
Sbjct: 82  HPPFENLL---VGEDLPLD---------------IVYEDDTLLVVNKPAGMVVHPGHGNY 123

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  + YH D   K+  D    +P L HR+D++TSG+LVVA+T  A  HL++ F+ +
Sbjct: 124 SGTLINALIYHFDNLPKNSSD----RPGLVHRIDKDTSGLLVVAKTEHAMAHLSKQFKDK 179

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             ++ Y ++VWG + +++     N      +   + V++    +KG   A++H+KV++  
Sbjct: 180 TSEREYVAIVWGNMEEDEGTIEGNIGRHPKNRLQNTVYMDDDADKGKP-AVTHYKVLERL 238

Query: 237 AQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS-------- 282
                  C LE    TGRTHQ+RVH  H+G  +  D +Y      KG  FT         
Sbjct: 239 TYVTLVSCKLE----TGRTHQIRVHMKHIGHTLFNDERYGGERILKGTTFTKYKQFVDNC 294

Query: 283 -PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             +  +  LHA+ +   HPE G+ +Q   P+P  M
Sbjct: 295 FKVLPRQALHAKTLGFEHPETGKIMQFNTPVPDDM 329


>gi|88802386|ref|ZP_01117913.1| ribosomal large subunit pseudouridine synthase D [Polaribacter
           irgensii 23-P]
 gi|88781244|gb|EAR12422.1| ribosomal large subunit pseudouridine synthase D [Polaribacter
           irgensii 23-P]
          Length = 346

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 95/336 (28%), Positives = 159/336 (47%), Gaps = 67/336 (19%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--- 67
           V    +E +R+D++  N   +     LQ+  ++G V V++  VK N++++   VVRI   
Sbjct: 21  VASAGQEPLRVDKFLMNFIENATRSKLQQAAKAGNVLVNEISVKSNHKVKPNDVVRIVLA 80

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---- 122
            PP   A + ++ E   LD               ++YED  + V NKPAG+ V  G    
Sbjct: 81  YPP---AESLLVAEDIPLD---------------IIYEDDTVIVVNKPAGMVVHPGHGNY 122

Query: 123 -----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                +G+ +HI+    +   +  ++P L HR+D++TSG+LVVA+T  A  +L+  F  R
Sbjct: 123 SGTLVNGLIHHIE----NLPTNSNERPGLVHRIDKDTSGLLVVAKTEFAMANLSRQFFER 178

Query: 178 RIQKIYWSLVWG--------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
             +++Y++LVWG        I  N    + N L       GD+            +A+SH
Sbjct: 179 TTERLYYALVWGNVAEDEGRIEGNIGRSLKNRLQMAVFPDGDF----------GKHAVSH 228

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---- 282
           +KV++        +E +  TGRTHQ+R H  H+G  +  D +Y  +   KG  FT     
Sbjct: 229 YKVLERLTY-VTLVECKLETGRTHQIRAHFKHIGHTLFNDERYGGDGVLKGTTFTKYKQF 287

Query: 283 -----PIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                 +  +  LHA+ +   HP+ G  +Q  + +P
Sbjct: 288 VHNCFKVLPRQALHAKTLGFTHPKTGVFMQFNSEIP 323


>gi|51246582|ref|YP_066466.1| ribosomal large subunit pseudouridine synthase D [Desulfotalea
           psychrophila LSv54]
 gi|50877619|emb|CAG37459.1| related to ribosomal large subunit pseudouridine synthase D
           [Desulfotalea psychrophila LSv54]
          Length = 327

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 96/317 (30%), Positives = 156/317 (49%), Gaps = 47/317 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV-----R 66
           V  ++   RLD++     P ++   +    +   V VD +  K + R++ G+ V     +
Sbjct: 23  VSYNQRGTRLDQFLAFSLPDVSRALITLSNKKELVLVDDEVKKSSYRLKEGETVTCALWQ 82

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
            PP+       ++ Q++           DF     +YED  + V +KP GI V  G+G  
Sbjct: 83  APPLS------LEPQQV-----------DFES---IYEDDSLLVLSKPPGIVVHPGNGNT 122

Query: 125 IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + G L    +  G     +P + HRLD++TSG +VVA+   + + L +SF+ R++ 
Sbjct: 123 EGTLVHGLLYHCREIGGVGDAIRPGIVHRLDKDTSGAMVVAKDERSLRTLVDSFKERQVY 182

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQ 238
           K+Y +LV GIPK  +  I       + IG   VH  K   +E+   +A ++++V++ F  
Sbjct: 183 KVYHALVCGIPKKYEGRIV------APIGRHSVHRQKMAISERTGKFAATNWQVVEVFET 236

Query: 239 K---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           K   +  L +   TGRTHQ+RVH   +GCPI GD  Y +  +    +P   +  LHA  +
Sbjct: 237 KDGPYSLLRVHIETGRTHQIRVHMSSIGCPIAGDQVYGSKRQ----NPAFARQMLHASRL 292

Query: 296 DLPHPEGGR-LQITAPL 311
            LPHP  GR +  TAPL
Sbjct: 293 RLPHPVTGRTMSFTAPL 309


>gi|307729591|ref|YP_003906815.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1003]
 gi|307584126|gb|ADN57524.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1003]
          Length = 430

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 96/344 (27%), Positives = 154/344 (44%), Gaps = 29/344 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV ++    RLD+     +P  +   LQ  + + +VR+D K  K    +  G  + +
Sbjct: 66  RTVVVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAKIRQPVPLGASIEL 125

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
            P             +L   +  T     L+  +++ED  + V NKPAG+ V   +G   
Sbjct: 126 VP------------DLLPEQLAFTPEPVPLE--IVFEDDTLVVINKPAGMVVHPAAGNWS 171

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + D+    PR  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 172 GTVLNGLLYRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 231

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKF 240
            +LVWG     +E   +  + +       + VV         A +HF+ +D      Q  
Sbjct: 232 LALVWG--NMPEEGTIDAPIGRDPRERTRMAVV--TGASGKPARTHFRRVDTAIWQRQPV 287

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---YLHARYMDL 297
             +     TGRTHQ+RVH  H+G P++GD  Y         +P+  +     LHA  + L
Sbjct: 288 TAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGEFARQALHAWRLGL 347

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
            HP+ GR +Q  A +P  M     +LG   D        Y +D+
Sbjct: 348 IHPKTGRSMQWRADVPEDMAALSAALGLGRDDAGEFDDTYYEDD 391


>gi|288960501|ref|YP_003450841.1| ribosomal large subunit pseudouridine synthase D [Azospirillum sp.
           B510]
 gi|288912809|dbj|BAI74297.1| ribosomal large subunit pseudouridine synthase D [Azospirillum sp.
           B510]
          Length = 226

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 115/226 (50%), Gaps = 13/226 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  + + +KPAG+ V  G     +++    +      + P L HRLD++TSG L++
Sbjct: 10  ILYRDGLMLILDKPAGLPVHAGPAGGPNLERHFDALRFGFPKPPSLAHRLDRDTSGCLIL 69

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   A + +   F+  ++ K YW++V G P      I   L K S+  G +  V   + 
Sbjct: 70  GRHAKALRKIGILFQNGKVDKTYWAVVAGGPPQDSGRIELPLAKISNKTGGWRIVGSPD- 128

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A++ + V+   A    WLE+ PHTGRTHQ+RVH   +GCP++GD +Y        
Sbjct: 129 --GQSAVTDY-VVRGQADGLTWLELTPHTGRTHQIRVHCASIGCPLIGDPQY-------- 177

Query: 281 TSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGFK 325
             P    L+LH+R + LP +P+   +   AP+P HM    ++ GF 
Sbjct: 178 GGPEGKPLHLHSRAISLPLYPKRDPVGAVAPVPPHMRAALEACGFS 223


>gi|68536967|ref|YP_251672.1| pseudouridylate synthase [Corynebacterium jeikeium K411]
 gi|68264566|emb|CAI38054.1| pseudouridylate synthase [Corynebacterium jeikeium K411]
          Length = 313

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 93/322 (28%), Positives = 158/322 (49%), Gaps = 24/322 (7%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q ++V + + + RLD++ ++H   +    L +++R+ Q+ V+  + K + R  +G  VR+
Sbjct: 7   QTLIVSDSQADRRLDKYIRSHVKGVPATVLFRLMRTKQITVNGAKCKPDQRTVAGDKVRL 66

Query: 68  PP--VINALNHIIKEQKILDS-SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           P   V  A      ++K  +  +  L++H       +++ED  + V NKPA I+V  GSG
Sbjct: 67  PALEVARAKPPPAGDRKAAEQLARRLSRH-------IVFEDDALLVVNKPANIAVHVGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--RRIQKI 182
           +   +   L+  +  K ++  L HRLD+ETSG+L+VA+     +HL E  R     IQ+ 
Sbjct: 120 VKAGVIEALRV-LRPKEKELELAHRLDKETSGLLIVAKKSKMLRHLQELLRTGGEDIQRY 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G  K          +     G   V     + +   +A +   V   +      
Sbjct: 179 YLAVVSGGVKRTGRQTQRIEVPLRKTGAATV----VDSRAGQWAETKMWVKKPWGTAGTL 234

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHP 300
           +E+Q  TGR HQ+RVH  H+G PI+GD +Y  N   N  +  +    L LHA  + +P P
Sbjct: 235 VEVQLLTGRKHQIRVHLQHLGHPIIGDSRY-GNPAANRAAAEKGVRMLMLHACRLVVPLP 293

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
           +G  L + AP+P      W+ L
Sbjct: 294 DGEVLDLHAPMPP----AWNKL 311


>gi|218438495|ref|YP_002376824.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
 gi|218171223|gb|ACK69956.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7424]
          Length = 306

 Score =  122 bits (307), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 100/325 (30%), Positives = 155/325 (47%), Gaps = 41/325 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV------DKKR-VKFNNRIQSGQV 64
           +E ++  +RLDRW     P ++   LQ ++  G +++      DKK  VK  +R+     
Sbjct: 5   LEVEQGKLRLDRWLAQKLPDLSRSRLQTLIEQGNLQLNGTICTDKKTLVKSGDRLH---- 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + IPPV           K LD      +  D    IL YED ++ + NKPAG+ V    G
Sbjct: 61  LLIPPV-----------KPLD-----LQPQDIPLDIL-YEDDQLIIINKPAGLVVHPSPG 103

Query: 125 --IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 ++  L    +  G    Q+P + HRLD++T+G LVVA+T  A  HL +  + + 
Sbjct: 104 HEQGTLVNALLSHCSNLAGIGGVQRPGIVHRLDKDTTGALVVAKTDYAHHHLQQQLKAKT 163

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y  +V+G+PK     I N  + +  I    + VV   EKG   AI+H+++++    
Sbjct: 164 ARREYLGIVYGVPKTTSGKI-NLSIGRHPIERKKMAVVPL-EKGGREAITHWEILERLG- 220

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +  +  TGRTHQ+RVH   M  PIVGD  Y +          Q    LHA  + L 
Sbjct: 221 NYSLIYFRLETGRTHQIRVHCQAMNHPIVGDPVYSSGRSIGVNLAGQ---ALHAWKLTLE 277

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  G  ++  APLP+   K  + L
Sbjct: 278 HPLSGEIIETIAPLPSTFTKLLEVL 302


>gi|254559695|ref|YP_003066790.1| ribosomal large subunit pseudouridine synthase D [Methylobacterium
           extorquens DM4]
 gi|254266973|emb|CAX22773.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Methylobacterium
           extorquens DM4]
          Length = 330

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 103/347 (29%), Positives = 159/347 (45%), Gaps = 54/347 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + +V++      RLDR     +  ++   LQ ++R G VR D            G VVR
Sbjct: 8   ARSLVLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCD------------GIVVR 55

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL----LYEDSKIYVFNKPAGISVQGG 122
            P         +     +D SV     ++ L   L    ++ED  + V +KPAG+ V   
Sbjct: 56  DP------ARKVGAGSRIDLSVPAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPA 109

Query: 123 SGIAYHIDGFLKS------WVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           +G   H DG L +       V   G    ++P + HRLD++TSG+LVVA+   A Q L+ 
Sbjct: 110 AG---HEDGTLVNRLIAHCGVSLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSA 166

Query: 173 SF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            F    R   +++ Y +LVW +P+ +   I   L +  H   + + VV++ E     AI+
Sbjct: 167 QFADHGRSGALERAYLALVWNVPEPRAGTIRANLARSRH-NREKIAVVREGE--GREAIT 223

Query: 229 HFKVIDCFAQKFCWLEMQPH--TGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSP 283
           H++V D   +      ++ H  TGRTHQ+RVH  H G P++GD  Y   FK      + P
Sbjct: 224 HYRVEDVHGEGGVTALLRCHLETGRTHQIRVHLSHRGHPLLGDRVYGGAFKTKAARLSEP 283

Query: 284 IQNKL------YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            +  L       LHA  +   HP  G RL+  +PLP    +   +LG
Sbjct: 284 ARAALDALGRQALHAVELGFLHPRSGERLRFESPLPEDFSRLLAALG 330


>gi|167041971|gb|ABZ06708.1| putative RNA pseudouridylate synthase [uncultured marine
           microorganism HF4000_141E02]
          Length = 320

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 87/291 (29%), Positives = 148/291 (50%), Gaps = 15/291 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V+V  D++ MRLD +       +    + +++R G+VR++ KR K  +R+     VRIPP
Sbjct: 10  VIVSRDDDGMRLDNYLIKIIKGMPKSRIYRMIRKGEVRINSKRAKPRSRVHVNDTVRIPP 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDF--LKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              ALN    E K   SSV   +  DF  + +I+++E+    + NKP+G++V GGSGI  
Sbjct: 70  Y--ALN----EPKTNVSSV---RKDDFRRINNIVIFENDSFLLVNKPSGLAVHGGSGIHL 120

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L+S+ + + +   L HRLD++TSG L+V++ ++  + L E FR  ++QK Y  L+
Sbjct: 121 GLIELLRSFREQRNEHLELVHRLDKDTSGCLLVSKKKSKLRKLHEYFREGKVQKTYLGLM 180

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        I   L   S      + V    +     A + F +++ +       +++P
Sbjct: 181 VGKFTQTVYEIDQPLKIISTPENGRLAV---PDDSGTKAKTKFFLMEKYKNS-ALFKIEP 236

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            TG+THQ+R HA +M  P+  D +Y        +     +L+LHA  +  P
Sbjct: 237 ITGKTHQIRAHAKYMKTPLAADQRYGIQPDQIVSEFGLTRLFLHAESITFP 287


>gi|149200603|ref|ZP_01877608.1| 23S rRNA/tRNA pseudouridine synthase [Lentisphaera araneosa
           HTCC2155]
 gi|149136305|gb|EDM24753.1| 23S rRNA/tRNA pseudouridine synthase [Lentisphaera araneosa
           HTCC2155]
          Length = 323

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 101/337 (29%), Positives = 152/337 (45%), Gaps = 36/337 (10%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Y    VV+   E  RLDR+     P  +   LQK L+ G   + +   K N R+ S  V+
Sbjct: 7   YTHSWVVDEFNECQRLDRYISQQLPEYSRTFLQKSLKDGAFELVRSGAKINARM-SENVI 65

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
               V   +     E  +L   + L          ++YED  I V NKPAG+ V  G+G 
Sbjct: 66  EGDFVHYKMPEEADESTLLPEDIELD---------IIYEDDDILVVNKPAGMVVHPGAGN 116

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                    +   +D F  S +D    +P + HRLD+ETSG+++VA++      L+ SF 
Sbjct: 117 YTGTLVNALLGRDLDTF--SAMDDGSSRPGIVHRLDKETSGVIIVAKSAKNLDKLSRSFA 174

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK-QNEKGAN---YAISHFK 231
            R ++K Y +L  G  +  ++ I       SHIG    +  K +N   +N    AISH+K
Sbjct: 175 RRDVEKYYVALCRGTIRVGRDTIT------SHIGRSRSNRQKMENTNDSNRGKEAISHYK 228

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V+         ++++  TGRTHQ+RVH   +  P+VGD  Y         SP  ++  LH
Sbjct: 229 VL-ADNNGATLVKLKIDTGRTHQIRVHMSGINHPVVGDKLYGVRRLDEKESP--DRHILH 285

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           A    + HP     +  TAPL        D  G ++D
Sbjct: 286 AWRTRIIHPGTQEIMTFTAPLHDDFKSVCDKFGIEFD 322


>gi|254448982|ref|ZP_05062436.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium HTCC5015]
 gi|198261376|gb|EDY85667.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium HTCC5015]
          Length = 353

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 97/345 (28%), Positives = 163/345 (47%), Gaps = 51/345 (14%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T+   + + ++    RLD+     +P  +   LQ+ L+ G + +D + +   +++  G++
Sbjct: 6   THHHQLSIPDEHAGQRLDKVLSALFPDFSRSRLQQWLKDGCITLDGQVLPGKHKVDGGEL 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R             EQ+ L  +V        +  ++LYED  I V +KPAG+ V   +G
Sbjct: 66  LRAD---------FPEQEDLSGAVEAQD----IPLVVLYEDDDILVVDKPAGMVVHPAAG 112

Query: 125 IAYHIDGFLKS----WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              + DG L++    +       PR  + HRLD++TSG+LVVAR  +A Q L    + R 
Sbjct: 113 ---NPDGTLQNALLFYAPELAGVPRSGIVHRLDKDTSGLLVVARNHSAHQSLVAQLQERS 169

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-- 236
           + +IY ++V+G+P +      N      H G      V+Q   G   A++H++V   +  
Sbjct: 170 VSRIYEAIVFGVPVSGGRVEGNI---GRHPGDRKKMAVRQ--VGGKEAVTHYRVEAKYRH 224

Query: 237 -AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY------ 289
            +   C LE    TGRTHQ+RVH  H+G P+VGD  Y    +      I++ L       
Sbjct: 225 HSHVRCQLE----TGRTHQIRVHMSHIGFPLVGDPVYGGRLR--LPGDIEDSLLACLKRF 278

Query: 290 ----LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
               LHA  + L HP  G  ++  +P+P  M    D L F+ + +
Sbjct: 279 DRQALHAAELGLIHPRSGEAMRWESPMPEDM----DELLFELEND 319


>gi|148244244|ref|YP_001218938.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Vesicomyosocius okutanii HA]
 gi|146326071|dbj|BAF61214.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 303

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 94/320 (29%), Positives = 155/320 (48%), Gaps = 37/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  ++   +  RLD +       +   ++ +++R G+VRV+K R K   ++    +VR
Sbjct: 3   VSFQTIDEFSQGQRLDNYLLKILKGVPKSHIYRVIRKGEVRVNKGRKKSEYKLNLDDIVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+       +   K + +S  L K    L + +LYED  + + NKP+G++V  GSG+ 
Sbjct: 63  IPPIK------VSTTKSMYTSDGLKK---ILTNAILYEDKGLLIINKPSGLAVHSGSGVN 113

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
               G +++      +   L HRLD+ TSG+L+VA+ R   ++L E      I+K Y +L
Sbjct: 114 V---GVIEALRQMYKEPIELVHRLDRATSGVLLVAKKRLVLKNLHEQLNQHTIEKHYIAL 170

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKF--CWL 243
           V G+   K   I   L   S          K + KG  Y++SHF  +  F  + F    +
Sbjct: 171 VKGVWSKKIHTINAPLYNNS-------RYTKVDAKG-KYSVSHFHPLKNFNIENFSASLV 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-------ANFKGNFTSPIQNKLYLHARYMD 296
            +   TGRTHQ+RVHA ++G  +  D+KY          FKG        +L+LH+  + 
Sbjct: 223 NISIETGRTHQIRVHAKYVGHALACDNKYGDKEFDRQVKFKG------LKRLFLHSNQLI 276

Query: 297 LPHPEGGRLQ-ITAPLPAHM 315
             +P    +Q + APLP  +
Sbjct: 277 FINPLTNDIQKVNAPLPIEL 296


>gi|134295824|ref|YP_001119559.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           vietnamiensis G4]
 gi|134138981|gb|ABO54724.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           vietnamiensis G4]
          Length = 401

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 93/319 (29%), Positives = 145/319 (45%), Gaps = 35/319 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +V +D    K    +  G  + + P       ++ 
Sbjct: 70  RLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAKIRQPVPLGAKIELVP------DLLP 123

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L   ++ +   ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 124 EQ--------LAFAAEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWSGTLLNGLLHRYG 175

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG    + 
Sbjct: 176 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEEG 235

Query: 196 ECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFA---QKFCWLEMQPHT 249
              A        IG D     +           A +HF+ +D      Q    ++    T
Sbjct: 236 TIDAP-------IGRDPRERTRMAVVTGASGKPARTHFRTVDTCVWQRQPVSAIQCDLET 288

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-L 305
           GRTHQ+RVH  H G P++GD  Y         +P+ N   +  LHA  + L HP  G+ +
Sbjct: 289 GRTHQIRVHCSHAGHPLLGDPVYGRARGKRSVTPLPNGFARQALHAWRLGLVHPVTGKTM 348

Query: 306 QITAPLPAHMVKTWDSLGF 324
           Q   PLP  M +   +LGF
Sbjct: 349 QWRCPLPDDMNELVAALGF 367


>gi|317154635|ref|YP_004122683.1| RluA family pseudouridine synthase [Desulfovibrio aespoeensis
           Aspo-2]
 gi|316944886|gb|ADU63937.1| pseudouridine synthase, RluA family [Desulfovibrio aespoeensis
           Aspo-2]
          Length = 305

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 90/299 (30%), Positives = 138/299 (46%), Gaps = 17/299 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M   Q+V V   E   +L ++ +      +    +Q+ +R GQVRVDK R K  +RI++G
Sbjct: 1   MHSAQFVTVTPAESGQKLLQFLERRLDGAVPRTAIQRWIRKGQVRVDKGRSKPFDRIEAG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP           +             +F+     Y+D ++ V  KPAG++V GG
Sbjct: 61  QTVRIPPYEPG-------ETGGGKPAAPGGPLEFV-----YDDDRMLVIAKPAGLAVHGG 108

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            GI+  + G L +       KP L HRLD++TSG+L+ ART  A + L + F    I K+
Sbjct: 109 DGISDSVAGRLAAAFADADFKPTLAHRLDRDTSGLLLAARTYDALRDLNDRFAAGTIGKL 168

Query: 183 YWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V G  +      + + L K+   G + V  V+        A++    +    +K  
Sbjct: 169 YLTWVTGRWREPGTVLLEDQLEKRGAPGSEKVEPVRDGS--GKEALARVACL-LAGEKRS 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            L ++  TGRTHQ+RV     G P+ GD KY    +          L L  + + LP P
Sbjct: 226 LLAVRLLTGRTHQIRVQLASRGHPVAGDGKYGPARQRTSLRLHCFALRLDGQTLTLPPP 284


>gi|220934527|ref|YP_002513426.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. HL-EbGR7]
 gi|219995837|gb|ACL72439.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. HL-EbGR7]
          Length = 323

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 106/328 (32%), Positives = 159/328 (48%), Gaps = 22/328 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  + V  V V + +   RLD +       +   ++ ++LR G+VRV+K R K   R+Q 
Sbjct: 6   SPPSKVTLVRVGSGQAGQRLDNFLLGQLKGVPKSHVYRLLRKGEVRVNKGRAKPEYRLQE 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VRIPPV  A +     Q  L   +     ++ L+  +L ED  + V NKPAG++V G
Sbjct: 66  GDQVRIPPVRQAASPPDDSQMPLPGEL-----AETLRRAVLLEDEDLLVLNKPAGLAVHG 120

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           GSG+     G +++    +  +PR     L HRLD+ETSG LV+A+ R A     E+ + 
Sbjct: 121 GSGVKL---GLIEAM---RRLRPRADFLELAHRLDRETSGCLVLAKRREALLAFHEALKS 174

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + K Y +L+ G+ +     I+  L +K       V  V+ +E G  +A S F     F
Sbjct: 175 GGVDKHYVTLLAGVWQGGPRRISETLARKGPR--TQVRKVEVDEDG-KHAESFFFPRRHF 231

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYM 295
                 + ++  TGRTHQ+RVHA H G P+ GD +Y    F          + +LHA  +
Sbjct: 232 VDA-TLMGVEIGTGRTHQIRVHAAHEGFPVAGDSQYGDFEFNRRMKRLGLKRQFLHAETL 290

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
               P   R  QI APLPA +    + L
Sbjct: 291 RFHLPGHERPYQIQAPLPADLEAVLERL 318


>gi|163867809|ref|YP_001609013.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           tribocorum CIP 105476]
 gi|161017460|emb|CAK01018.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           tribocorum CIP 105476]
          Length = 334

 Score =  122 bits (307), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 97/337 (28%), Positives = 154/337 (45%), Gaps = 47/337 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V +    + RLD+W    Y  + +   LQ ++R G +++D            GQ ++ P 
Sbjct: 6   VTDEGALDQRLDQWLAKQYHDVLSRSRLQTLIREGCLKID------------GQFIKEPK 53

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                N II+ +  + +  +    ++ +   +LYED  + V NKPAG+ V  G+G     
Sbjct: 54  TKLKPNQIIELE--MPNLRDAEPSAEAIALDILYEDDHVIVINKPAGLVVHPGNGNWTGT 111

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RM 176
               + YH    L      K  +P + HRLD+ TSG++VVA+   A + L+  F    R 
Sbjct: 112 LVNALIYHCGNSLSGIGGVK--RPGVVHRLDKNTSGVMVVAKNDLAHKSLSAQFSDHGRT 169

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + + Y +L+WG P      I   L +  H       V KQ    A +A++HF +++ +
Sbjct: 170 CALDRRYHALIWGTPHRNVWTIDASLGRSPHNRTKQAVVHKQTPH-ARHAVTHFSLLEKY 228

Query: 237 AQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQ--- 285
                       LE +  TGRTHQ+RVH  H+G P++GD  Y   F  K N  +P     
Sbjct: 229 GTHADSTSFASLLECRLETGRTHQIRVHMAHIGHPLIGDTVYGNAFKTKSNTLNPTLKNA 288

Query: 286 ----NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
               N+  LHA  +   HP  G+ +  +APLP  M +
Sbjct: 289 IDQFNRHALHAASLTFEHPSSGKVISFSAPLPQDMAQ 325


>gi|325528651|gb|EGD05737.1| RluA family pseudouridine synthase [Burkholderia sp. TJI49]
          Length = 359

 Score =  122 bits (306), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 93/319 (29%), Positives = 145/319 (45%), Gaps = 35/319 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +VR+D    K    +  G  + + P       ++ 
Sbjct: 28  RLDKALAQLFPEFSRSRLQSWIDAQRVRIDGAPAKIRQPVPLGATIELVP------DLLP 81

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 82  EQ--------LAFTPEPVPLDVVYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYG 133

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG+     
Sbjct: 134 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGMMPEDG 193

Query: 196 ECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHT 249
              A        IG D      +          A +HF+ +D      Q    ++    T
Sbjct: 194 TIDAP-------IGRDPRERTRMAVVTGASGKPARTHFRTVDTCVWQRQPVSAIQCDLET 246

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-L 305
           GRTHQ+RVH  H+G P++GD  Y         + + N   +  LHA  + L HP  G+ +
Sbjct: 247 GRTHQIRVHCSHVGHPLLGDPVYGRARGKRSVAALPNGFARQALHAWRLGLIHPVTGKAM 306

Query: 306 QITAPLPAHMVKTWDSLGF 324
           Q   PLP  M    ++LGF
Sbjct: 307 QWRCPLPDDMNALVEALGF 325


>gi|23015589|ref|ZP_00055361.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 327

 Score =  122 bits (306), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 91/327 (27%), Positives = 155/327 (47%), Gaps = 44/327 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQ--VVRI 67
            VE +E   RLDRW     P ++   ++ ++  G+V +D   +   + R++ GQ   V +
Sbjct: 13  AVEPEEAATRLDRWLAARLPELSRTRIKALIEDGRVSLDATTISDASLRVKPGQCFTVEV 72

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP   A      E +  D ++++           +YED  + V +KPAG+ V    G   
Sbjct: 73  PPDAPA------EPEAQDIALSV-----------VYEDEDLIVIDKPAGMVVHPAPGNPD 115

Query: 128 H--IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++  L    +S       ++P + HR+D++TSG+LV A+T AA + L   F    ++
Sbjct: 116 ETLVNALLAHCGESLAGIGGVKRPGIVHRIDKDTSGLLVAAKTDAAHRGLAAQFAEHSLE 175

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + YW+LVWG P  ++  I   + +  +     + VVK    G   A++ ++V+  FA   
Sbjct: 176 RAYWALVWGTPSPRQGEIEGNIGRNPN-DRKKMAVVKS---GGKPALTRYRVLKSFAGGA 231

Query: 241 CWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN----FTSPIQNKL------Y 289
             L E +  TGRTHQ+RVH    G P++GD  Y    +G+        ++  L       
Sbjct: 232 VSLVECRLATGRTHQIRVHMTAQGHPLIGDPVY-GRIRGSRKVVLPPEVKESLTTFPRQA 290

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHM 315
           LHA  +   HP  G  ++  +P+PA +
Sbjct: 291 LHAYLLGFSHPTKGYEVRFESPIPADI 317


>gi|297583963|ref|YP_003699743.1| RluA family pseudouridine synthase [Bacillus selenitireducens
           MLS10]
 gi|297142420|gb|ADH99177.1| pseudouridine synthase, RluA family [Bacillus selenitireducens
           MLS10]
          Length = 307

 Score =  122 bits (306), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 98/321 (30%), Positives = 153/321 (47%), Gaps = 42/321 (13%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINA 73
           DE+  RLD+W  +     +    Q  ++ G V V+ +  K N +++ G VVR+  P +  
Sbjct: 9   DEQGKRLDKWLTDQSDDWSRSLTQSWIQEGYVTVNDETSKANYKLKIGDVVRVKVPEVEE 68

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
           L  I  E   LD               ++YED  + V NKPAG+ V    G      ++G
Sbjct: 69  LE-ITAEDLDLD---------------IVYEDQDVIVVNKPAGMVVHPAPGHPSGTLVNG 112

Query: 132 FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV
Sbjct: 113 LMYHCQDLSGINGVARPGIVHRIDKDTSGLLMVAKHDKAHESLVDQLKNKTTIRQYEALV 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVID---CFAQKFCW 242
            G   ++K  +       + IG D     K    E+ A  A++HF+VI+    +    C 
Sbjct: 173 VGTIPHEKGTV------DAPIGRDPQDRQKMTVTEENARDAVTHFQVIERMNGYTHVLCE 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-E 301
           LE    TGRTHQ+RVH  ++G PIVGD KY    K +F+   Q    LHAR +   HP  
Sbjct: 227 LE----TGRTHQIRVHMKYIGYPIVGDPKYGPRKKHDFSIEGQ---ALHARTLGFVHPVT 279

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G ++   A +P    +T D +
Sbjct: 280 GEQMTFEAEVPERFKETLDQM 300


>gi|332981610|ref|YP_004463051.1| ribosomal large subunit pseudouridine synthase D [Mahella
           australiensis 50-1 BON]
 gi|332699288|gb|AEE96229.1| ribosomal large subunit pseudouridine synthase D [Mahella
           australiensis 50-1 BON]
          Length = 304

 Score =  122 bits (306), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 92/318 (28%), Positives = 159/318 (50%), Gaps = 32/318 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +D+ + RLD +    +      ++Q ++++G + V+ + +K   +++ G ++++    
Sbjct: 8   VTSDKADQRLDTFLAESFEQWTRSHIQNLIKNGNITVNGQHIKSGYKLKDGDIIKVE--- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
                 + E + +D      +  D   +IL YED  I V NKP G+ V   +G   A  +
Sbjct: 65  ------VPELRPID-----IQPEDIPLNIL-YEDEDIIVINKPQGMVVHPAAGNYSATLV 112

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSG+LVVA+   A   L +  + +   + Y +
Sbjct: 113 NALLAHCKDLSGINGEIRPGIVHRIDKDTSGVLVVAKNDMAHVALAQQIKEKTAIRKYVA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L+ G  K     I N  + +       + VV     G   A++HFKV++ F  ++  +E 
Sbjct: 173 LLEGDIKEDTGVI-NAPIARHPTDRKKMAVVS----GGRSAVTHFKVLERFG-RYTLIEA 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +  TGRTHQ+RVH  ++G P+VGD  Y    K  F   ++ +L LHA+Y+   HP  GR 
Sbjct: 227 RLETGRTHQIRVHMAYIGHPVVGDPVYGYR-KQAFA--LKGQL-LHAQYLGFVHPRTGRY 282

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++  APLP + V   D L
Sbjct: 283 MEFCAPLPDYFVDIIDKL 300


>gi|296446414|ref|ZP_06888358.1| pseudouridine synthase [Methylosinus trichosporium OB3b]
 gi|296256049|gb|EFH03132.1| pseudouridine synthase [Methylosinus trichosporium OB3b]
          Length = 229

 Score =  122 bits (306), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 85/239 (35%), Positives = 123/239 (51%), Gaps = 22/239 (9%)

Query: 99  SILLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           S LLY D  + V +KPAG+ V    +GG  +  H D           + P L HRLD++T
Sbjct: 3   SRLLYRDGLMLVVDKPAGLPVHRGPRGGDNLEDHFDALRFGLP----RPPALAHRLDRDT 58

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG LV+ R R A + L + FR  RI+K YW++V G P +    I   L +     G ++ 
Sbjct: 59  SGCLVLGRHRKALERLGKLFRDGRIEKTYWAVVEGAPADDAGEIDMALGRLDSTRGWWM- 117

Query: 215 VVKQNEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              + +     A +H++ +    D   +   +LE++P TGRTHQLRVH   MG PI+GD 
Sbjct: 118 ---RPDPLGLPAQTHWRALARGQDTEGRDIAFLELKPRTGRTHQLRVHMQAMGWPILGDP 174

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDR 328
            Y     G+        L+LHAR + +P  +G   + +TAP+P HM  T D+LG    R
Sbjct: 175 VY-----GHGKREGAPPLHLHARAIVVPIRDGHESVAVTAPVPPHMRGTLDTLGCDETR 228


>gi|253577879|ref|ZP_04855151.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850197|gb|EES78155.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 304

 Score =  122 bits (306), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 92/331 (27%), Positives = 161/331 (48%), Gaps = 56/331 (16%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPP 69
           V + +  +R+DR+       ++   +QK+L+  ++ V+   VK N ++Q G    V +P 
Sbjct: 8   VSDGQSGIRIDRYLSEMNEELSRSYIQKLLKEQKITVNGSAVKANYKVQEGDEISVAVPD 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                   IKE  IL   + L          +LYED  + + NKP G+ V   +G   H 
Sbjct: 68  --------IKEPDILPEDIPLD---------ILYEDDDVLIVNKPKGMVVHPSAG---HT 107

Query: 130 DGFLKSWV-----DSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            G L + +     D+        +P + HR+D++T+G L+V +   A ++L E  +   I
Sbjct: 108 SGTLVNAIMFHCKDNLSGINGVLRPGIVHRIDKDTTGALLVCKNDNAHRNLAEQLKEHSI 167

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-----AISHFKVID 234
           ++ Y ++V G+ K  +  I   + +         H + + +   NY     A++H+KV++
Sbjct: 168 RRRYRAIVAGVLKEDEGTIEGPIGR---------HPIDRKKMAVNYKNGKDAVTHYKVLE 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHA 292
            F +   ++E +  TGRTHQ+RVH   +G P++GD  Y     G+  +P  +Q +  LHA
Sbjct: 219 RF-KNATYVECRLETGRTHQIRVHMTSIGHPLLGDEVY-----GSGKNPYHLQGQT-LHA 271

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +   HP  G  ++ TAPLP + VK  + L
Sbjct: 272 MILGFVHPSTGEYMEFTAPLPEYFVKLLEKL 302


>gi|240137515|ref|YP_002961986.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Methylobacterium
           extorquens AM1]
 gi|240007483|gb|ACS38709.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Methylobacterium
           extorquens AM1]
          Length = 330

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 100/343 (29%), Positives = 158/343 (46%), Gaps = 46/343 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + +V++      RLDR     +  ++   LQ ++R G VR D            G VVR
Sbjct: 8   ARSLVLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCD------------GIVVR 55

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            P     +    +    + + +      + L   +++ED  + V +KPAG+ V   +G  
Sbjct: 56  DP--ARKVGAGCRINLSVPAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPAAG-- 111

Query: 127 YHIDGFLKS------WVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF-- 174
            H DG L +       V   G    ++P + HRLD++TSG+LVVA+   A Q L+  F  
Sbjct: 112 -HEDGTLVNRLIAHCGVSLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQFAD 170

Query: 175 --RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
             R   +++ Y +LVW +P+ +   I   L +  H   + + VV+  E     AI+H++V
Sbjct: 171 HGRSGALERAYLALVWNVPEPRAGTIRANLARSRH-NREKIAVVRDGE--GREAITHYRV 227

Query: 233 IDCFAQKFCWLEMQPH--TGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQNK 287
            D   +      ++ H  TGRTHQ+RVH  H G P++GD  Y   FK      + P +  
Sbjct: 228 EDVHGEGGVTALLRCHLETGRTHQIRVHLSHRGHPLLGDAVYGGAFKTKAARLSEPARAA 287

Query: 288 L------YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           L       LHA  +   HP  G RL+  +PLPA   +   +LG
Sbjct: 288 LDVLGRQALHAVELGFLHPRSGERLRFESPLPADFSRLLAALG 330


>gi|108758809|ref|YP_633659.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108462689|gb|ABF87874.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 306

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 94/312 (30%), Positives = 145/312 (46%), Gaps = 29/312 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q V V  +    RLDR+     P IN    + ++ SG VR+  KR +   ++  G+ + +
Sbjct: 4   QKVQVPREAAGERLDRFLSKQVPGINLERARALIDSGAVRIRGKRCQPTRKLWGGEEIEL 63

Query: 68  P-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
             P   A +    E  +L                +L++DS + + NKP GI V+   G A
Sbjct: 64  ERPEPRAASVAASEGPVLP---------------VLHDDSALVIVNKPPGIVVEP-EGRA 107

Query: 127 YHIDGFL---KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + G L   +   D +G  +P + HRLD+ETSG L  ART  AA  L  SF+ +R+ K 
Sbjct: 108 ASVVGLLAAQRPPFDVEGLAQPGVVHRLDRETSGCLAFARTDTAAAALLRSFQEKRVDKR 167

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G P  +      +    +    D      +       A+S F+V + FA     
Sbjct: 168 YWTLVLGQPPAQGRLEGPY----ARDPADPRRFTTRVPSARRAALS-FEVRERFADA-AL 221

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           LE+   TGRTHQ+RV     G P++ D  Y     + +  +    +  LHA  ++LP P 
Sbjct: 222 LEVDLDTGRTHQVRVQLSEAGFPVLADSLYGPPEARAHAAARALGRQALHAFTLELPSPA 281

Query: 302 GGR-LQITAPLP 312
            G+ +++ APLP
Sbjct: 282 TGQPVRVEAPLP 293


>gi|153008568|ref|YP_001369783.1| RluA family pseudouridine synthase [Ochrobactrum anthropi ATCC
           49188]
 gi|151560456|gb|ABS13954.1| pseudouridine synthase, RluA family [Ochrobactrum anthropi ATCC
           49188]
          Length = 334

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 94/340 (27%), Positives = 156/340 (45%), Gaps = 49/340 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ +  ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELTTDSDATGKRLDQWLAAALGPELSRSRVQSLIAEGHVTIDGAPAREAKQKLREGMT 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I          I E   LD               +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAIVLPEPEPAEPIAENIPLD---------------ILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF- 174
                    + YH    L      +  +P + HRLD++TSG++VVA+   + +HL+E F 
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGIR--RPGIVHRLDKDTSGVMVVAKNDRSHRHLSEQFA 163

Query: 175 ---RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              R   +++ Y +LVWG+ +  +  I +  L +SH       VV +  + A +AI+H+ 
Sbjct: 164 DHGRTGDLERAYLALVWGMTERPQGFI-DAHLGRSHRDRTKQAVVNEEREDARHAITHYV 222

Query: 232 VIDCFA------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTS 282
            ++ FA           +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        
Sbjct: 223 TVEKFAPLEDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPE 282

Query: 283 PIQNKL------YLHARYMDLPHPEGGRL-QITAPLPAHM 315
           P++  +       LHA  +   HP    L +  AP+P  M
Sbjct: 283 PLKEAVRGFHRQALHAWLLAFTHPATEELMRFEAPVPEDM 322


>gi|170752009|ref|YP_001758269.1| RluA family pseudouridine synthase [Methylobacterium radiotolerans
           JCM 2831]
 gi|170658531|gb|ACB27586.1| pseudouridine synthase, RluA family [Methylobacterium radiotolerans
           JCM 2831]
          Length = 334

 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 100/335 (29%), Positives = 157/335 (46%), Gaps = 53/335 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RLDR     +P ++   LQ ++R+GQV+ D           SG+V        A  
Sbjct: 15  EGGVRLDRALVALFPDLSRARLQDLIRTGQVQRDG----LPALDPSGKVA-------AGA 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-- 133
           HI+        +  + + +D     ++YED  + V +KPAG+ V    G   H  G L  
Sbjct: 64  HIVLRVPPAAPAEPVAEAADL---PIVYEDDDLIVIDKPAGLVVHPAPG---HESGTLVN 117

Query: 134 -------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQK 181
                   S     G ++P + HRLD++TSG++VVA+   A Q LT  F    R   +++
Sbjct: 118 ALIAHCGASLSGIGGVRRPGIVHRLDKDTSGLIVVAKNDTAHQGLTAQFADHGRSGPLER 177

Query: 182 IYWSLVWGIPKNKKECI-ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y ++VWG+P+ +   I AN  L +S    + + VV  ++    +A++H+ V + + +  
Sbjct: 178 AYAAVVWGLPQPRAGTIQAN--LARSRFHREKIAVV--SDASGRHAVTHYAVAEAYGEAA 233

Query: 241 ---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKL------ 288
              C LE    TGRTHQ+RVH  H G P++GD  Y   F+      +S  +  L      
Sbjct: 234 LVRCRLE----TGRTHQIRVHLAHRGHPLLGDTVYGGAFRTKAARLSSEARAALTALGRQ 289

Query: 289 YLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
            LHA  +   HP  G  L+  +PLP  M     +L
Sbjct: 290 ALHAELLGFSHPRTGTTLRFESPLPPDMTALVQAL 324


>gi|221633017|ref|YP_002522242.1| pseudouridine synthase, RluA family [Thermomicrobium roseum DSM
           5159]
 gi|221156507|gb|ACM05634.1| pseudouridine synthase, RluA family [Thermomicrobium roseum DSM
           5159]
          Length = 322

 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 94/323 (29%), Positives = 156/323 (48%), Gaps = 41/323 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PP 69
           +   E   RLD+   +    ++   +Q++++ G + V+ +  K   R++ G  + +  PP
Sbjct: 15  ISEREHGERLDKLIASRVTGMSRSFVQQLMKRGAILVNGEPCKPAQRVRYGDRLEVYLPP 74

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V              +   +L    +FL   ++YED  I VF+KP GI      G   H 
Sbjct: 75  V--------------EPPTDL--EPEFLPIPVIYEDDDIIVFDKPPGIVTHPAPG---HE 115

Query: 130 DGFLKSWVDS--------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            G L + + +           +P + HRLD++TSG+LVVA+T AA   L E ++ R + K
Sbjct: 116 HGTLVNALKAIRPDLQVQPSHRPGIVHRLDKDTSGLLVVAKTEAARLALLEQWQSRSVVK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKF 240
            Y +LV G+ +     I       + I  D V   K         AI+HF+V++ F +  
Sbjct: 176 KYTALVHGVVEPDSGTI------DAPISRDPVERTKMAVVSWGRPAITHFRVLERF-RCA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L++   TGRTHQ+RVH   +G P+VGD +Y  +    F  P+  + +LHARY+   HP
Sbjct: 229 TLLDVTIETGRTHQIRVHCAFIGHPVVGDSQYGGHRP--FCVPVPRQ-FLHARYLRFVHP 285

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G+ +++  PLP  +    ++L
Sbjct: 286 TTGQAIELETPLPYDLRTVLEAL 308


>gi|170703044|ref|ZP_02893871.1| pseudouridine synthase, RluA family [Burkholderia ambifaria
           IOP40-10]
 gi|170132052|gb|EDT00553.1| pseudouridine synthase, RluA family [Burkholderia ambifaria
           IOP40-10]
          Length = 365

 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 94/320 (29%), Positives = 146/320 (45%), Gaps = 37/320 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +V +D    K    +  G  + + P          
Sbjct: 28  RLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAKIRQPVPLGARIELVP---------- 77

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +L   +  T     L  I  YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 78  --DLLPEQLAFTPEPVPLDVI--YEDDALLVINKPAGVVVHPAAGNWSGTILNGLLHRYG 133

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG +P++ 
Sbjct: 134 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEDG 193

Query: 195 KECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVID-CFAQK--FCWLEMQPH 248
                      + IG D      +          A +HF+ +D C  Q+     ++    
Sbjct: 194 T--------IDAPIGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLE 245

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR- 304
           TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L HP  G+ 
Sbjct: 246 TGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPDGFARQALHAWRLGLVHPLTGKT 305

Query: 305 LQITAPLPAHMVKTWDSLGF 324
           +Q   PLP  M     +LGF
Sbjct: 306 MQWRCPLPEDMNALIAALGF 325


>gi|209965860|ref|YP_002298775.1| RNA pseudouridine synthase, putative [Rhodospirillum centenum SW]
 gi|209959326|gb|ACI99962.1| RNA pseudouridine synthase, putative [Rhodospirillum centenum SW]
          Length = 239

 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 123/237 (51%), Gaps = 16/237 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---LTHRLDQE 153
           +++ LLY D  + + +KPAGI+V GG G  +  D   + +   +   PR   L HRLD++
Sbjct: 6   IQARLLYRDGLMLILDKPAGIAVHGGPGSRHGADNLERYFEHLRFGLPRPPALAHRLDRD 65

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDY 212
           TSG LV+ R   A + L   F+  RI K YW++V G P+     I   LLK++    G  
Sbjct: 66  TSGCLVLGRHPKALRKLGLLFQDGRIGKTYWAVVRGGPEGDAGTIDKALLKRTDARRGWK 125

Query: 213 VHVVKQNEKGANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           +  +      A  A++ ++V+   +        WLE+ P TGRTHQ+R H   MGCP++G
Sbjct: 126 MIALPPGTPEAQEAVTDWRVMGRGSLPKIGDLAWLELHPRTGRTHQIRAHCAAMGCPVLG 185

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
           D  Y   ++          L+LH+R + +P +     + +TAP+P H+ +   + G+
Sbjct: 186 DPVYGGRYE-------AEPLHLHSRAISVPVYATKPAVAVTAPVPPHLREALAACGW 235


>gi|187734524|ref|YP_001876636.1| pseudouridine synthase, RluA family [Akkermansia muciniphila ATCC
           BAA-835]
 gi|187424576|gb|ACD03855.1| pseudouridine synthase, RluA family [Akkermansia muciniphila ATCC
           BAA-835]
          Length = 323

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 94/321 (29%), Positives = 147/321 (45%), Gaps = 49/321 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRI 67
           +  ++ +  +RLD++   H P ++   +Q +++SG V V+    K  N +  G    VRI
Sbjct: 3   LTTDDADGKIRLDQYLAAHLPELSRSRIQSLIKSGDVLVNGSPAKPKNPVSRGDSITVRI 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
           P    A      E +  D  +++           LYED  + V NK +G+ V   +G   
Sbjct: 63  PEPEPA------EAQPQDIPLDI-----------LYEDEDVVVINKESGMVVHPAAGNPD 105

Query: 126 AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G    ++P + HRLD++TSG LV+A+   A Q LT  F  R  +K
Sbjct: 106 GTIVNALLHHCGDLSGIGGVERPGIVHRLDKDTSGCLVIAKNDGAHQSLTAQFAARSTEK 165

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFAQ 238
            Y ++V GIP      +       +HIG   V+ +K    N      AI+ + ++ C   
Sbjct: 166 RYLAVVQGIPSQSSGTVF------THIGRHPVNRLKMAVVNPGSGKAAITDYDLL-CADP 218

Query: 239 K------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                   C L    HTGRTHQ+RVH L++G P++GD  Y    +         +L LHA
Sbjct: 219 STDSSLVLCTL----HTGRTHQIRVHMLYLGHPLIGDPIYAKPARQKAKP---GRLMLHA 271

Query: 293 RYMDLPHPEGG-RLQITAPLP 312
             +   HP  G R+   AP+P
Sbjct: 272 WRLGFDHPRTGKRMDFEAPVP 292


>gi|171320446|ref|ZP_02909479.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MEX-5]
 gi|171094306|gb|EDT39380.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MEX-5]
          Length = 369

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 94/320 (29%), Positives = 146/320 (45%), Gaps = 37/320 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +V +D    K    +  G  + + P          
Sbjct: 28  RLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAKIRQPVPLGARIELVP---------- 77

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +L   +  T     L  I  YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 78  --DLLPEQLAFTPEPVPLDVI--YEDDALLVINKPAGVVVHPAAGNWSGTILNGLLHRYG 133

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG +P++ 
Sbjct: 134 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEDG 193

Query: 195 KECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVID-CFAQK--FCWLEMQPH 248
                      + IG D      +          A +HF+ +D C  Q+     ++    
Sbjct: 194 T--------IDAPIGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLE 245

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR- 304
           TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L HP  G+ 
Sbjct: 246 TGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPDGFARQALHAWRLGLVHPLTGKT 305

Query: 305 LQITAPLPAHMVKTWDSLGF 324
           +Q   PLP  M     +LGF
Sbjct: 306 MQWRCPLPDDMNALIAALGF 325


>gi|1491643|emb|CAA61435.1| ORFA [Chloroflexus aurantiacus J-10-fl]
          Length = 253

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 83/222 (37%), Positives = 118/222 (53%), Gaps = 19/222 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSK--GQ-KPRLTHRLDQETS 155
           ++YED+ I V NKPAG+ V    G      ++  L  + D    G+ +P + HRLD++TS
Sbjct: 30  VVYEDADIAVINKPAGMVVHPAPGHPRGTLVNALLARYPDLAIGGELRPGIVHRLDRDTS 89

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LV+AR   A + L +  + RR++KIY +LV G P       A        IG D    
Sbjct: 90  GLLVIARHDQAMRSLVDQQQARRMRKIYQALVIGRPPETGTIDAP-------IGRDPRDR 142

Query: 216 VKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           ++         A +H++++D F   +  LE+Q  TGRTHQ+RVH  H+G PIVGD  Y  
Sbjct: 143 LRMAVVPDGRPARTHYRLLDTFG-DYSLLEVQLETGRTHQIRVHLRHLGYPIVGDPVYGP 201

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHM 315
                  S    + +LHA Y+ L HP  GR Q  TAPLPA +
Sbjct: 202 RRSHLHLS----RQFLHAAYLGLVHPRSGRWQEFTAPLPADL 239


>gi|332883200|gb|EGK03483.1| hypothetical protein HMPREF9456_01550 [Dysgonomonas mossii DSM
           22836]
          Length = 225

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 118/228 (51%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I + NK     VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VLYEDNHIIIINKTVSEIVQGDKTGDKPLSEIVKEYLKEKYNKPGNVFCGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ A+T  A   L E F+ ++I K YW++V  +PK  +  + N+L++       Y + 
Sbjct: 63  GIVIFAKTSKALSRLNEMFKNKQIDKTYWAIVKNMPKEPEGTLRNYLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V++    +  AI H+K+I   + ++  LE+   TGR HQ+RV    MGCPI GD KY   
Sbjct: 123 VEK--PNSKLAILHYKLI-ARSDRYNLLEVGLETGRHHQIRVQLSKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
             G   S     + LHAR +   HP    L ++TAPLP   +  W +L
Sbjct: 177 --GFDRSNPDGGISLHARKVSFLHPVSKELIEVTAPLPKDTL--WQAL 220


>gi|240850017|ref|YP_002971410.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           grahamii as4aup]
 gi|240267140|gb|ACS50728.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           grahamii as4aup]
          Length = 334

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 94/341 (27%), Positives = 157/341 (46%), Gaps = 55/341 (16%)

Query: 11  VVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +      RLD+W    Y ++ +   LQ ++R G +++D            GQ ++ P 
Sbjct: 6   ITDEGALGQRLDQWLAKQYHNVFSRSRLQTLIREGYLKID------------GQFIKEPK 53

Query: 70  VINALNHIIKEQKILDSSV----NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
                   ++ ++I++ ++    +    ++ +   +L+ED  I V NKPAG+ V  G+G 
Sbjct: 54  TK------LRPKQIIELAMPDLRDAEPSAEAIALDILFEDDHIIVINKPAGLVVHPGNGN 107

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF-- 174
                   + YH    L      K  +P + HRLD+ TSG+++VA+   A + L+  F  
Sbjct: 108 WTGTLVNALIYHCGNSLSGIGGVK--RPGIVHRLDKNTSGVMIVAKNDLAHKSLSAQFSD 165

Query: 175 --RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
             R   + + Y +L+WG P      I   L +  H       + KQN   A +A++HF +
Sbjct: 166 HGRTCALDRRYHALIWGTPHRNVWTIDASLGRSPHNRTKQAVIHKQNPY-ARHAVTHFSL 224

Query: 233 IDCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSP 283
           ++ +            LE +  TGRTHQ+RVH  H+G P++GD  Y   FK     F   
Sbjct: 225 LEKYGSHADSTSFASLLECRLETGRTHQIRVHMAHIGHPLIGDTVYGNAFKTKSNAFNPT 284

Query: 284 IQNKL------YLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           I+N +       LHA  +   HP  G+ +  +APLP  M K
Sbjct: 285 IRNAIDQFNRQALHAASLSFEHPSTGKVMSFSAPLPQDMAK 325


>gi|238924093|ref|YP_002937609.1| pseudouridine synthase, RluA family [Eubacterium rectale ATCC
           33656]
 gi|238875768|gb|ACR75475.1| pseudouridine synthase, RluA family [Eubacterium rectale ATCC
           33656]
 gi|291524836|emb|CBK90423.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale DSM 17629]
          Length = 312

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 90/328 (27%), Positives = 160/328 (48%), Gaps = 46/328 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V++++E  RLD++  + YP I+    Q+IL+  Q+ V+ K  K N R+++  +V +  + 
Sbjct: 8   VQSEQEGERLDKYLSSIYPDISRSFFQRILKENQILVNDKPQKANYRLKTDDIVDV-TIP 66

Query: 72  NALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
           +A+   I  Q I LD               +LYED  + V NKP G+ V   +G      
Sbjct: 67  DAVQTPILPQDIPLD---------------ILYEDDDVLVVNKPKGMVVHPSAGHYSDTL 111

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              I YH    L S ++ +  +P + HR+D +T+G L+V +   +   ++E  +     +
Sbjct: 112 VNAIMYHCKDSL-SGINGE-IRPGIVHRIDMDTTGSLIVCKNDESHIKISEQIKDHSCNR 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY  +V G  K+ +  I   + +  +        +  NEK    A++H+KV++ F   + 
Sbjct: 170 IYVGIVCGNVKDDEGTIEGAIGRNPNDRKK----MAINEKNGKPAVTHYKVLERFGD-YT 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL------YLHARYM 295
           +++ +  TGRTHQ+RVH   +  P++GD  Y +       SP +N+        LHA+ +
Sbjct: 225 YMQFKLETGRTHQIRVHMASINHPLLGDMLYSS------YSPTKNRFKGLEGQCLHAKTI 278

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP+ G  ++  APLP +     + L
Sbjct: 279 GFVHPKTGEYMEFDAPLPKYFANLLEVL 306


>gi|25026884|ref|NP_736938.1| putative ribosomal large subunit pseudouridine synthase C
           [Corynebacterium efficiens YS-314]
 gi|259506052|ref|ZP_05748954.1| ribosomal large subunit pseudouridine synthase C [Corynebacterium
           efficiens YS-314]
 gi|23492164|dbj|BAC17138.1| putative ribosomal large subunit pseudouridine synthase C
           [Corynebacterium efficiens YS-314]
 gi|259166340|gb|EEW50894.1| ribosomal large subunit pseudouridine synthase C [Corynebacterium
           efficiens YS-314]
          Length = 304

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 92/318 (28%), Positives = 162/318 (50%), Gaps = 29/318 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T+V+  + E      RLD++ + H   +    + + LR+G+++V+ ++ K + R Q G +
Sbjct: 10  TFVEVEIPEA-HAGRRLDKYLRAHLKGVPASLIFRQLRTGKIKVNGRKAKPDYRTQPGDM 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +++      L   + E     +S+  TK  + + + +++ED+ + V NKPA I+V  G+G
Sbjct: 69  LKM------LQMDLPENLPPPASLP-TKLLNQIDNGIIHEDADLIVLNKPADIAVHTGTG 121

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--RRIQKI 182
           +A  +   L+     +     L HRLD ETSG+L+VA+T A  +H+ +  R   R + + 
Sbjct: 122 VAGGVIEALRQLRPGEADL-ELAHRLDHETSGLLMVAKTPAMLRHIQQLLREDDRALSRR 180

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  LV G   +    +   L +           V+ +  G + A++ F+V   F  +   
Sbjct: 181 YALLVRGRWPDHLTAVDAPLQRTDT-------TVRVHPDGQS-ALTFFEVERRFGNRATL 232

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           ++ +  TGR HQ+RVHA H G PI+GD KY  + +   T      L+LHA  + +P P+G
Sbjct: 233 VKARLTTGRKHQIRVHARHAGHPIIGDRKY-GDPRARATH-----LFLHAAELTVPMPDG 286

Query: 303 GRLQITAPLPAHMVKTWD 320
              + +APLP +    WD
Sbjct: 287 MTREFSAPLPTN----WD 300


>gi|117925422|ref|YP_866039.1| ribosomal large subunit pseudouridine synthase D [Magnetococcus sp.
           MC-1]
 gi|117609178|gb|ABK44633.1| ribosomal large subunit pseudouridine synthase D [Magnetococcus sp.
           MC-1]
          Length = 332

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 96/339 (28%), Positives = 155/339 (45%), Gaps = 47/339 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIP 68
            ++  D+   RLD+    H+P +    LQ+ ++  +V VD +  K  + +++ GQ + I 
Sbjct: 12  TLLHADDAGQRLDKALCCHFPDLTRSTLQRWIKEERVIVDHEVAKLPSQKVRVGQHIIIY 71

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--- 125
           P     +  + E+  L+               +L+ED  + V NKPAG+ V  G+G+   
Sbjct: 72  PSEPEPSTALPEEIALE---------------ILFEDEHLIVLNKPAGMVVHPGAGVNHG 116

Query: 126 ------AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                  YH            G     +P + HRLD+ETSGI+V A+   A  HL+  F 
Sbjct: 117 TLVNALLYHCGTPDNPHGGLSGIGGVIRPGIVHRLDKETSGIMVAAKQDHAHIHLSRQFE 176

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVI 233
            R I + Y +L  GIP+  +  I      +  IG   +H  K    E+G   A + +KV+
Sbjct: 177 QRTIGRRYLALTRGIPQPAQGRI------EGAIGRHPIHRTKMAVVEQGGRAAATRYKVL 230

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLY--- 289
           +   Q F  +  +  +GRTHQ+RVH  H+G P+VGD  Y A  K  +   P+  + +   
Sbjct: 231 EPLGQ-FALIRCRLESGRTHQIRVHMTHIGHPLVGDPLYGAQHKAPSHWPPLHRQRFDQF 289

Query: 290 ----LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
               LHA  +   HP  G  +    P PA   + +++L 
Sbjct: 290 QRQALHAHTLTFIHPHTGEEMSFKRPPPADFRQLYETLA 328


>gi|330817148|ref|YP_004360853.1| Pseudouridine synthase RluD [Burkholderia gladioli BSR3]
 gi|327369541|gb|AEA60897.1| Pseudouridine synthase RluD [Burkholderia gladioli BSR3]
          Length = 398

 Score =  121 bits (304), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 96/337 (28%), Positives = 150/337 (44%), Gaps = 47/337 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV +     RLD+     +P  +   LQ  +   +VRVD    K    +  G  + +
Sbjct: 57  RVVVVPDSLAGERLDKALAQLFPEFSRSRLQGWIDEQRVRVDGAPAKVRQPVPLGATIEL 116

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
            P       ++ EQ        L    + +   ++YED  + V +KPAG+ V   +G   
Sbjct: 117 VP------DLLPEQ--------LAFAPEPVPLSIVYEDEALVVIDKPAGLVVHPAAGNWS 162

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + ++    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 163 GTLLNGLLHRYGEAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 222

Query: 184 WSLVWG-IPKNKKECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVIDCFA-- 237
           ++LVWG +P++            + IG D      +          A +HF+ +D     
Sbjct: 223 FALVWGRMPESGT--------IDAPIGRDPRERTRMAVVTGASGKPARTHFRCVDTVLWQ 274

Query: 238 -QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKL 288
            Q    +     TGRTHQ+RVH  H G P++GD  Y         A   G F      + 
Sbjct: 275 NQPVSAIHCDLETGRTHQIRVHCAHTGHPLLGDPVYGRARGKRSVAALPGGFA-----RQ 329

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            LHA  + L HP  GR +Q   P+P  + +   +LGF
Sbjct: 330 ALHAWRLGLVHPLTGRSMQWRCPVPDDIAELAAALGF 366


>gi|257416242|ref|ZP_05593236.1| pseudouridylate synthase [Enterococcus faecalis AR01/DG]
 gi|257158070|gb|EEU88030.1| pseudouridylate synthase [Enterococcus faecalis ARO1/DG]
          Length = 301

 Score =  121 bits (304), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 94/319 (29%), Positives = 157/319 (49%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 11  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                E ++LD        ++ +   ++YED+ + V NKP G+ V   +G   H +G L 
Sbjct: 65  -----EPEVLDMV------AEDIPLTIVYEDNDVIVVNKPQGMVVHPSAG---HPNGTLV 110

Query: 135 SWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + +              +P + HR+D++TSG+L+VA++  A + L +  + +   + Y +
Sbjct: 111 NALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKSDQAHESLAKQLKEKTSLRKYVA 170

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 171 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DTFTLVE 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 224 LQLETGRTHQIRVHMKYIGYPLAGDTLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 278

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 279 QLVFEAPLPEVFEKTLHQL 297


>gi|223984556|ref|ZP_03634687.1| hypothetical protein HOLDEFILI_01982 [Holdemania filiformis DSM
           12042]
 gi|223963484|gb|EEF67865.1| hypothetical protein HOLDEFILI_01982 [Holdemania filiformis DSM
           12042]
          Length = 307

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 90/312 (28%), Positives = 152/312 (48%), Gaps = 36/312 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++VE  ++ +RLD++        +    Q+++    VR+D   VK + ++++G  + +  
Sbjct: 6   LIVEEQDQGVRLDKYLSTAMDDCSRSRAQQLIDEEAVRIDDLPVKNSYKVKAGDEIEV-- 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                   + E++ L++          +   ++YED  + V NKP G+ V  G G   H 
Sbjct: 64  -------TLPEEEALEA------QPQEMALNVVYEDHDVIVINKPKGLVVHPGPGNPDHT 110

Query: 129 -IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G L    D  G     +P + HR+D++TSG++V  +   A Q L +    +   + Y
Sbjct: 111 LVNGLLWHCHDLSGINGVLRPGIVHRIDKDTSGLIVACKNDNAHQSLAKQLAEKTAGRQY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC 241
           ++LV G+  ++   I       + IG D     K    EK +  AI+HFKV++ F   + 
Sbjct: 171 YALVHGVINHEYGTI------DAPIGRDEKDRQKMAVTEKNSRPAITHFKVVERF-DNYT 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH  ++G PIVGD KY        T P Q ++ LHA  +   HP 
Sbjct: 224 LVSCRLETGRTHQIRVHMQYIGFPIVGDPKYSL----RKTLPTQGQM-LHAYQLSFTHPS 278

Query: 302 GG-RLQITAPLP 312
            G R+   APLP
Sbjct: 279 TGERMTFEAPLP 290


>gi|222054127|ref|YP_002536489.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
 gi|221563416|gb|ACM19388.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
          Length = 319

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 93/340 (27%), Positives = 156/340 (45%), Gaps = 48/340 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT ++  V EN E   RLD +       +    +Q+++ SG + V+    K + +++ G+
Sbjct: 1   MTDIELTVPENTEAE-RLDSYIARTVETLTRAAVQRLMESGMITVNGMPPKPSLKLKGGE 59

Query: 64  VVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            ++I  PP + A                     + +   +LYED  + V NK AG+ V  
Sbjct: 60  QLKIAVPPPVEA-----------------GPAPENIPLEILYEDRDLVVVNKGAGMVVHP 102

Query: 122 GSGIAYH--IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G+G +    ++  L    D  G     +P + HR+D++TSGILVVA+  A+   L+E FR
Sbjct: 103 GAGNSGGTLVNALLGHCTDLSGIGGELRPGIVHRIDKDTSGILVVAKNDASHLALSEQFR 162

Query: 176 MRRIQKIYWSLVWGIPKNK----KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              I++IY ++V+G PK      +  I    + +  + G   H          +A++H++
Sbjct: 163 EHSIKRIYIAIVYGSPKTDSGRLESIIGRHPVDRKRMSGKARH--------GKHAVTHWR 214

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLY- 289
           VI  +    C + ++  TGRTHQ+RVH    G P+VGD  Y    +  +   P+  +L  
Sbjct: 215 VIGRYP-GMCLIRLRLETGRTHQIRVHLSEAGHPLVGDEVYGGGARLDSVKDPVLRRLIR 273

Query: 290 ------LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 LHA+ +   HP     L+    LP  M    + L
Sbjct: 274 ELGRQALHAKTLGFVHPSTKEYLEFDTDLPRDMATIVEHL 313


>gi|78066563|ref|YP_369332.1| ribosomal large subunit pseudouridine synthase D [Burkholderia sp.
           383]
 gi|77967308|gb|ABB08688.1| ribosomal large subunit pseudouridine synthase D [Burkholderia sp.
           383]
          Length = 402

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 93/316 (29%), Positives = 148/316 (46%), Gaps = 29/316 (9%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +V VD    K    +  G  +++ P       ++ 
Sbjct: 70  RLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAPAKIRQPVPLGAKIQLVP------DLLP 123

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 124 EQ--------LAFTPEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYG 175

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG     +
Sbjct: 176 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGT--MPE 233

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQK--FCWLEMQPHTGRT 252
           E   +  + +       + VV         A +HF+ +D C  Q+     ++    TGRT
Sbjct: 234 EGTIDAPIGRDPRERTRMAVV--TGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRT 291

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQIT 308
           HQ+RVH  H G P++GD  Y         +P+ +   +  LHA  + L HP  G+ +Q  
Sbjct: 292 HQIRVHCAHAGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGLVHPVTGKAMQWR 351

Query: 309 APLPAHMVKTWDSLGF 324
            PLP  M     +LGF
Sbjct: 352 CPLPDDMNTLVAALGF 367


>gi|303326647|ref|ZP_07357089.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Desulfovibrio sp. 3_1_syn3]
 gi|302862635|gb|EFL85567.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Desulfovibrio sp. 3_1_syn3]
          Length = 524

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 89/302 (29%), Positives = 147/302 (48%), Gaps = 32/302 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ--VVR 66
           +++  D    RLDR  ++  P ++   LQK + +G+  VD   V + + + + GQ  ++ 
Sbjct: 6   LLITADTAGRRLDRVLRDAAPGLSRAALQKAVLAGRCLVDGLPVSRPDAKTRPGQRVLLE 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP  NAL+    E+  L+               LL++D  + V NKPAG++V       
Sbjct: 66  LPPTENALS---PEEGHLE---------------LLWQDESLVVCNKPAGLTVHPCPSCP 107

Query: 127 YH-----IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            H     + G        +G +P + HRLD++TSG+L+VA T  A   L+ +F  R + K
Sbjct: 108 EHTLVQRLLGRFPQLGRLEGLRPGIVHRLDKDTSGLLLVALTEPARLALSAAFARREVHK 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G+P  + EC     L +       + V+ +   G     +  ++ +   Q+  
Sbjct: 168 EYLALVSGLPPEQGECREP--LGRHPTAKIKMAVLPETRGGKPAHTTWKRLWNTPDQRVS 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L ++ HTGRTHQ+RVH  H+G P++GD  Y A       +P Q    LHA ++   HP+
Sbjct: 226 LLAVRIHTGRTHQIRVHLAHLGHPLLGDKLY-APAPVRELAPRQ---MLHAWHLAFSHPD 281

Query: 302 GG 303
            G
Sbjct: 282 SG 283


>gi|21674122|ref|NP_662187.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           tepidum TLS]
 gi|21647279|gb|AAM72529.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           tepidum TLS]
          Length = 329

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 94/318 (29%), Positives = 140/318 (44%), Gaps = 39/318 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+DR+      +     +QK +   +V V+ K VK N RI+S   + I           
Sbjct: 12  MRIDRYLTQQVENATRNKVQKAIEEQRVLVNGKPVKSNYRIKSCDHIHI----------- 60

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
                L          D   SIL YED  + V +K AG+ V    G         I +H+
Sbjct: 61  ---TFLRPPAPELAPEDIPISIL-YEDDDLMVIDKEAGMVVHPAFGNWTGTLANAILHHL 116

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G     +D    +P + HRLD++TSG+++VA+   A   L   F  R+++K+Y ++VWG
Sbjct: 117 -GKDADDLDKTEMRPGIVHRLDKDTSGLIIVAKNPVALHKLATQFARRQVEKVYKAIVWG 175

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +P N         + +SH     +           +AI+ + V++  A  F  ++M  HT
Sbjct: 176 VP-NPPSGTIKTNIGRSHKNRKVMANFPFEGAEGKHAITDYLVVEDLAY-FALMDMTLHT 233

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNF----TSPIQNKLY-------LHARYMDLP 298
           GRTHQ+RVH  H+G PI+GD  Y            + P  + L        LHA  +   
Sbjct: 234 GRTHQIRVHLQHLGHPILGDQTYGGATPRTLPFSKSEPFTHNLLELMGRQALHAETLRFR 293

Query: 299 HPEGGR-LQITAPLPAHM 315
            P  G  L  TAPLP  M
Sbjct: 294 QPTTGEPLAFTAPLPEDM 311


>gi|218528997|ref|YP_002419813.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
 gi|218521300|gb|ACK81885.1| pseudouridine synthase, RluA family [Methylobacterium
           chloromethanicum CM4]
          Length = 343

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 103/347 (29%), Positives = 158/347 (45%), Gaps = 54/347 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + +V++      RLDR     +  ++   LQ ++R G VR D            G VVR
Sbjct: 21  ARSLVLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCD------------GIVVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL----LYEDSKIYVFNKPAGISVQGG 122
            P         +     +D SV     ++ L   L    ++ED  + V +KPAG+ V   
Sbjct: 69  DP------ARKVGAGCRIDLSVPAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPA 122

Query: 123 SGIAYHIDGFL---------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           +G   H DG L          S     G ++P + HRLD++TSG+LVVA+   A Q L+ 
Sbjct: 123 AG---HEDGTLVNRLIAHCGASLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSA 179

Query: 173 SF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            F    R   +++ Y +LVW +P+ +   I   L +  H   + + VV++ E     AI+
Sbjct: 180 QFADHGRSGALERAYLALVWNVPEPRAGTIRANLARSRH-NREKIAVVREGE--GREAIT 236

Query: 229 HFKVIDCFAQKFCWLEMQPH--TGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSP 283
           H++V D   +      ++ H  TGRTHQ+RVH  H G P++GD  Y   FK      + P
Sbjct: 237 HYRVEDVHGEGGVTALLRCHLETGRTHQIRVHLSHRGHPLLGDAVYGGAFKTKAARLSEP 296

Query: 284 IQNKL------YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            +  L       LHA  +   HP  G RL+  +PLP    +   +LG
Sbjct: 297 ARAALDALGRQALHAVELGFLHPRSGERLRFESPLPEDFSRLLAALG 343


>gi|294055321|ref|YP_003548979.1| pseudouridine synthase, RluA family [Coraliomargarita akajimensis
           DSM 45221]
 gi|293614654|gb|ADE54809.1| pseudouridine synthase, RluA family [Coraliomargarita akajimensis
           DSM 45221]
          Length = 312

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 94/327 (28%), Positives = 152/327 (46%), Gaps = 44/327 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +  ++ R D+ F + +  I+   LQ+   +GQV  D + +    +I  G ++R     
Sbjct: 10  VPDGIQSGRADKLFASKFEDISRARLQRAFDAGQVSFDGEAIDKRFKINRGGLLR----- 64

Query: 72  NALNHIIKEQKILDS-SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---- 126
                      +LD    N+      +   ++YEDS + V +KP G+    GSG      
Sbjct: 65  ----------AVLDEPDANVGPRPVDMPLEIVYEDSCMVVVSKPVGMVTHPGSGTGEDTL 114

Query: 127 -----YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                +H  G L S      ++P + HRLD+ETSG++ VA+T  A   L  +F  R   K
Sbjct: 115 VHALLHHTGGQLSSV--GAPERPGIVHRLDKETSGLIAVAKTDLAHHKLASAFSERNTYK 172

Query: 182 IYWSLVWGIPKNK----KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            Y +LV G P       +E I    + ++ +       V+ N + A+   + + V + F 
Sbjct: 173 RYRALVLGSPMRSSGTVREPIGRHPVVRTRM------AVQPNGRDAH---TDWTVDERFG 223

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMD 296
            +   +    HTGRTHQ+RVH  H   P++GD  Y   FK N    I   ++ LH+  + 
Sbjct: 224 DRAALISCVIHTGRTHQIRVHMSHERLPLLGDTTY--GFKPNRLKGISVPRVMLHSTELH 281

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
           LPHPE G+ L++ APLP    +  ++L
Sbjct: 282 LPHPETGKLLELNAPLPQDFERVIEAL 308


>gi|323526134|ref|YP_004228287.1| RluA family pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323383136|gb|ADX55227.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1001]
          Length = 426

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 98/347 (28%), Positives = 157/347 (45%), Gaps = 40/347 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV ++    RLD+     +P  +   LQ  + + +VR+D K  K    +  G  + + P
Sbjct: 68  VVVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAKIRQPVPLGATIELVP 127

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                  ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 128 ------DLLPEQ--------LAFTPEPVPLDIVYEDDTLVVINKPAGMVVHPAAGNWSGT 173

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++G L  + D+    PR  + HRLD+ETSG++VVART  A   L    + R +++ Y +
Sbjct: 174 VLNGLLYRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLA 233

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCW 242
           LVWG     +E   +  + +       + VV         A +HF+ +D      Q    
Sbjct: 234 LVWG--NMPEEGTIDAPIGRDPRERTRMAVVTG--ASGKPARTHFRRVDTALWQRQPVTA 289

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARY 294
           +     TGRTHQ+RVH  H+G P++GD  Y         A   G+F      +  LHA  
Sbjct: 290 IHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVAPLPGDFA-----RQALHAWR 344

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGF-KYDRNLYIKRLYSQD 339
           + L HP+ GR +Q  A +P  +     +LG  + D   + +  Y +D
Sbjct: 345 LGLIHPKTGRTMQWRADVPEDIAALSAALGLGRDDAGEFDETYYEED 391


>gi|170077579|ref|YP_001734217.1| 23S rRNA-specific pseudouridylate synthase [Synechococcus sp. PCC
           7002]
 gi|169885248|gb|ACA98961.1| 23S rRNA-specific pseudouridylate synthase [Synechococcus sp. PCC
           7002]
          Length = 308

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 89/314 (28%), Positives = 147/314 (46%), Gaps = 46/314 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVD-------KKRVKFNNRIQSGQVVRIP-PVI 71
           RLD+W     P ++   LQ+++  GQV+++       K ++K  +R+    +++IP P  
Sbjct: 16  RLDQWLAQQLPELSRSRLQRLIEQGQVQLNEAPCQSKKTKLKVGDRL----ILKIPAPAT 71

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            AL     E   LD               +L+ED    + NKPAG+ V    G      +
Sbjct: 72  MALA---PEAMDLD---------------ILFEDEHFLIVNKPAGMVVHPAPGNYTGTLV 113

Query: 130 DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            G L    ++       Q+P + HRLD++T+G + +A+T  A QHL    + +  ++ Y 
Sbjct: 114 HGLLAHCGENLAGIGGVQRPGIVHRLDKDTTGAIAIAKTDQAHQHLQAQIKAKTARREYM 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +V+G P+N         + + H G      V +       A++H+++++     +  L 
Sbjct: 174 GIVYGCPRNDAAGTIEAPIAR-HKGDRKKMAVDET---GRPAVTHWEIMERLG-NYSLLY 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
            +  TGRTHQ+RVH+ HMG PI+GD  Y +N    F         LHAR + + HP  G 
Sbjct: 229 YKLETGRTHQIRVHSAHMGNPIIGDPLYTSN---KFDKVKLTGQALHARKLIVKHPVTGE 285

Query: 304 RLQITAPLPAHMVK 317
            ++  APLP    K
Sbjct: 286 TIEAIAPLPTEFEK 299


>gi|310823803|ref|YP_003956161.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309396875|gb|ADO74334.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 321

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 94/325 (28%), Positives = 164/325 (50%), Gaps = 36/325 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E D   MRLD++ +    ++   +L K++R  +VRV+ KR +    + +G V+ I    
Sbjct: 6   IEEDSVGMRLDKYLRKRLANMPTSHLFKMIRVKKVRVNGKRAQPEQLLAAGDVIAIRG-- 63

Query: 72  NALNHIIKEQKILDSSVNLTK------HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                   EQ++L  +    +        D  + ++L ED  +   +KP+G++V  GSGI
Sbjct: 64  -------DEQQLLGPAPGGERLPPPPPPVDPSELVILLEDDWMMAVDKPSGMAVHTGSGI 116

Query: 126 -AYHIDGFLKSWVDSKGQKPRLT----HRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +  ++++++  K  +   T    HRLD+ETSG+++VA+ R A  H TE F   R +
Sbjct: 117 TGGTLVDYVRAYLGPKAVRNDFTASPAHRLDRETSGVILVAKRRPAMVHFTEVFTESRAR 176

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFA 237
           K Y +LV G +P++    + +  L +     +      +  +G N   A++ +KVI   +
Sbjct: 177 KRYVTLVKGKMPQD--SGVIDLPLSEHQQTAE-----SKARRGVNMQEALTRWKVIRQSS 229

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARY 294
           +    L     TGRTHQ+R H   +G P+ GD KY  +F  N     +    +L+LHA  
Sbjct: 230 EA-ALLSCAIETGRTHQIRRHLAAVGHPVAGDRKY-GDFAFNRDVRARWGLKRLFLHAER 287

Query: 295 MDLPHPE-GGRLQITAPLPAHMVKT 318
           ++ PHP+ GG++ + A LP  +  T
Sbjct: 288 IEFPHPQHGGKVTVEARLPPELKDT 312


>gi|167041415|gb|ABZ06167.1| putative RNA pseudouridylate synthase [uncultured marine
           microorganism HF4000_006O13]
          Length = 320

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 83/291 (28%), Positives = 149/291 (51%), Gaps = 15/291 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V+V  D++ MRLD +       +    + +++R G+VR++ KR K  +R+     VRIPP
Sbjct: 10  VIVSRDDDGMRLDNYLIKIIKGMPKSRIYRMIRKGEVRINSKRAKPRSRVHVNDTVRIPP 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDF--LKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                 + + E K   SSV   +  DF  + +I+++E+    + NKP+G++V GGSGI  
Sbjct: 70  ------YAVNEPKTNVSSV---RKDDFRRINNIVIFENDSFLLVNKPSGLAVHGGSGIHL 120

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L+S+ + + +   L HRLD++TSG L+V++ ++  + L E FR  +++K Y  L+
Sbjct: 121 GLIELLRSFREKRNEHLELVHRLDKDTSGCLLVSKKKSKLRKLHEYFREGKVKKTYLGLM 180

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        I   L   +      + V   + K A    + F +++ +       +++P
Sbjct: 181 VGKFTQTVYEIDQPLKIITTPENGRLAVPDDSGKKAK---TKFFLMEKYKNS-ALFKIEP 236

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            TG+THQ+R HA +M  P+  D++Y        +     +L+LHA  +  P
Sbjct: 237 ITGKTHQIRAHAKYMKTPLAADNRYGIQPDQIVSEFGLTRLFLHAESITFP 287


>gi|115372593|ref|ZP_01459900.1| ribosomal large subunit pseudouridine synthase C [Stigmatella
           aurantiaca DW4/3-1]
 gi|115370314|gb|EAU69242.1| ribosomal large subunit pseudouridine synthase C [Stigmatella
           aurantiaca DW4/3-1]
          Length = 330

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 94/325 (28%), Positives = 164/325 (50%), Gaps = 36/325 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E D   MRLD++ +    ++   +L K++R  +VRV+ KR +    + +G V+ I    
Sbjct: 15  IEEDSVGMRLDKYLRKRLANMPTSHLFKMIRVKKVRVNGKRAQPEQLLAAGDVIAIRG-- 72

Query: 72  NALNHIIKEQKILDSSVNLTK------HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                   EQ++L  +    +        D  + ++L ED  +   +KP+G++V  GSGI
Sbjct: 73  -------DEQQLLGPAPGGERLPPPPPPVDPSELVILLEDDWMMAVDKPSGMAVHTGSGI 125

Query: 126 -AYHIDGFLKSWVDSKGQKPRLT----HRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +  ++++++  K  +   T    HRLD+ETSG+++VA+ R A  H TE F   R +
Sbjct: 126 TGGTLVDYVRAYLGPKAVRNDFTASPAHRLDRETSGVILVAKRRPAMVHFTEVFTESRAR 185

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFA 237
           K Y +LV G +P++    + +  L +     +      +  +G N   A++ +KVI   +
Sbjct: 186 KRYVTLVKGKMPQDS--GVIDLPLSEHQQTAE-----SKARRGVNMQEALTRWKVIRQSS 238

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARY 294
           +    L     TGRTHQ+R H   +G P+ GD KY  +F  N     +    +L+LHA  
Sbjct: 239 EA-ALLSCAIETGRTHQIRRHLAAVGHPVAGDRKY-GDFAFNRDVRARWGLKRLFLHAER 296

Query: 295 MDLPHPE-GGRLQITAPLPAHMVKT 318
           ++ PHP+ GG++ + A LP  +  T
Sbjct: 297 IEFPHPQHGGKVTVEARLPPELKDT 321


>gi|260909666|ref|ZP_05916361.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 472 str. F0295]
 gi|260636225|gb|EEX54220.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 472 str. F0295]
          Length = 349

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 94/342 (27%), Positives = 164/342 (47%), Gaps = 58/342 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+DR+      H +   +QK   SG V V+++ VK N +++ G V+ +  
Sbjct: 24  IVVDKGQVPVRIDRFMTERLQHSSRNRIQKAADSGFVHVNERPVKSNYKVRPGDVITL-- 81

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
           +++  +H            + T  ++ +   ++YED  + V NKPAG+ V  G+G     
Sbjct: 82  MLDRPHH------------DTTIEAEEIPLDVVYEDEALMVINKPAGMVVHPGAGNFNGT 129

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H+        D+   +  L HR+D++TSG+LVVA+T  A + L   F  +   
Sbjct: 130 LINAVAWHLRNM--PSFDANDPEVGLVHRIDKDTSGLLVVAKTPEAKRKLGLQFFNKTTH 187

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDY---------VHVVKQNEKGANYAISHFK 231
           + Y +LVW          AN+   +  I G+          + V   + +    A++H++
Sbjct: 188 RSYNALVW----------ANFAENEGRIEGNIGRDPRDRLRMAVFPPDSEMGKPAVTHYR 237

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQ 285
           V++ F     ++E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S     IQ
Sbjct: 238 VLERFGY-VTFVECILETGRTHQIRAHMKHIGHPMFGDERYGGTEILRGERSSTYKAYIQ 296

Query: 286 N------KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
           N      +  LHAR +   HP  G ++  T+P+P  M +  D
Sbjct: 297 NCFKLCPRQALHARTLGFVHPNTGQQMDFTSPMPQDMEQLLD 338


>gi|224541418|ref|ZP_03681957.1| hypothetical protein CATMIT_00580 [Catenibacterium mitsuokai DSM
           15897]
 gi|224525664|gb|EEF94769.1| hypothetical protein CATMIT_00580 [Catenibacterium mitsuokai DSM
           15897]
          Length = 306

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 95/330 (28%), Positives = 157/330 (47%), Gaps = 36/330 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q +  E +E+ +RLD+   NH P  +   +QK +++GQV V+    K N +++   V++
Sbjct: 3   IQSITPELEEKGLRLDKVILNHMPDRSRTEIQKWIKAGQVIVNDNVEKANYKVEEEDVIQ 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +         I  E   LD               ++YED  + V NKP G+ V   +GI 
Sbjct: 63  VTLPDPQSTEIRPEDIPLD---------------IIYEDEDVIVVNKPTGMIVHPSAGIY 107

Query: 126 -AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L    D        +P + HR+D+ETSG+L+VA+   A + L++      + 
Sbjct: 108 SGTLVNALLYHCHDLSAINGITRPGIVHRIDKETSGLLMVAKNDNAHRSLSKQLEEHSVV 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQ 238
           + Y +LV G+  +    I      ++ IG D     K     K A  AI++FKV++ +  
Sbjct: 168 RRYVALVHGVINHNVGRI------EAPIGRDSKDRKKMAVTSKNAKDAITNFKVLERY-D 220

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E +  TGRTHQ+RVH  ++G P+ GD +Y   F+ +  +   N  YLHAR +   
Sbjct: 221 DMTLIECRLETGRTHQIRVHMQYIGHPVYGDPQY--GFRNDDNT---NGQYLHARVLGFV 275

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           HP     +   APLP    +    LG +Y+
Sbjct: 276 HPRTNEHMYFEAPLPDFFEEKIKELGGEYN 305


>gi|256964973|ref|ZP_05569144.1| pseudouridylate synthase [Enterococcus faecalis HIP11704]
 gi|256955469|gb|EEU72101.1| pseudouridylate synthase [Enterococcus faecalis HIP11704]
 gi|295113102|emb|CBL31739.1| ribosomal large subunit pseudouridine synthase D [Enterococcus sp.
           7L76]
          Length = 301

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 94/319 (29%), Positives = 156/319 (48%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 11  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                E ++LD        ++ +   ++YED+ + V NKP G+ V   +G   H +G L 
Sbjct: 65  -----EPEVLDMV------AEDIPLTIVYEDNDVIVVNKPQGMVVHPSAG---HPNGTLV 110

Query: 135 SWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + +              +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 111 NALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 170

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 171 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 224 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 278

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 279 QLVFEAPLPEVFEKTLHQL 297


>gi|172060753|ref|YP_001808405.1| RluA family pseudouridine synthase [Burkholderia ambifaria MC40-6]
 gi|171993270|gb|ACB64189.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MC40-6]
          Length = 407

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 93/320 (29%), Positives = 149/320 (46%), Gaps = 37/320 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +V +D    K    +  G  + + P       ++ 
Sbjct: 70  RLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAKIRQPVPLGARIELVP------DLLP 123

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 124 EQ--------LAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWSGTILNGLLHRYG 175

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG +P++ 
Sbjct: 176 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEDG 235

Query: 195 KECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVID-CFAQK--FCWLEMQPH 248
                      + IG D     +           A +HF+ +D C  Q+     ++    
Sbjct: 236 T--------IDAPIGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLE 287

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR- 304
           TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L HP  G+ 
Sbjct: 288 TGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPDGFARQALHAWRLGLVHPLTGKT 347

Query: 305 LQITAPLPAHMVKTWDSLGF 324
           +Q   PLP  M     +LGF
Sbjct: 348 MQWRCPLPDDMNALIAALGF 367


>gi|115351782|ref|YP_773621.1| RluA family pseudouridine synthase [Burkholderia ambifaria AMMD]
 gi|115281770|gb|ABI87287.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           ambifaria AMMD]
          Length = 405

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 93/320 (29%), Positives = 149/320 (46%), Gaps = 37/320 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +V +D    K    +  G  + + P       ++ 
Sbjct: 70  RLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAKIRQPVPLGARIELVP------DLLP 123

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 124 EQ--------LAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWSGTILNGLLHRYG 175

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG +P++ 
Sbjct: 176 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEDG 235

Query: 195 KECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVID-CFAQK--FCWLEMQPH 248
                      + IG D      +          A +HF+ +D C  Q+     ++    
Sbjct: 236 T--------IDAPIGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLE 287

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR- 304
           TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L HP  G+ 
Sbjct: 288 TGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPDGFARQALHAWRLGLVHPLTGKT 347

Query: 305 LQITAPLPAHMVKTWDSLGF 324
           +Q   PLP  M     +LGF
Sbjct: 348 MQWRCPLPDDMNALIAALGF 367


>gi|163852141|ref|YP_001640184.1| pseudouridine synthase [Methylobacterium extorquens PA1]
 gi|163663746|gb|ABY31113.1| pseudouridine synthase [Methylobacterium extorquens PA1]
          Length = 239

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 79/229 (34%), Positives = 116/229 (50%), Gaps = 19/229 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           LLY D+ + V +KPAG+ V    +GG  +  H+D           ++P  THRLD++TSG
Sbjct: 20  LLYRDALMLVIDKPAGLPVHPGPKGGPTLTDHLDALRFGLP----RRPEATHRLDRDTSG 75

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R   A   L   F   ++ K YW+LV G P+  +  I   L K+S    D     
Sbjct: 76  CLVLGRHAKALARLNRLFADGKVDKTYWALVEGGPEAMEGRIDLPLAKRSD---DPRSWW 132

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + +     +++ ++V+    +  CWLE++P TGRTHQLRVH   MG PI GD  Y    
Sbjct: 133 MKTDPAGAPSLTFYRVLG-RTEGLCWLELKPVTGRTHQLRVHCAAMGWPIRGDAIYGGAG 191

Query: 277 KGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
           +          L LHAR + LP +P+   + + AP PAHM    ++ G 
Sbjct: 192 RDG------PGLQLHARGLSLPLYPKREAIAVEAPAPAHMRAGLEACGM 234


>gi|110635475|ref|YP_675683.1| ribosomal large subunit pseudouridine synthase D [Mesorhizobium sp.
           BNC1]
 gi|110286459|gb|ABG64518.1| ribosomal large subunit pseudouridine synthase D [Chelativorans sp.
           BNC1]
          Length = 343

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 92/335 (27%), Positives = 156/335 (46%), Gaps = 45/335 (13%)

Query: 10  VVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRI 67
           ++ +   E  RLD+W      P  +   +Q ++R G V ++ + V    R + +G+   I
Sbjct: 15  LLADEKAEGNRLDQWLAARLAPDFSRSRIQALIREGAVTLNGRTVAEPKRKVAAGEFYCI 74

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           L          + +   +LYED  + V +KPAG+ V  G G   
Sbjct: 75  ---------------TLPEPEAPEPQGEDIPLDILYEDEALIVIDKPAGLVVHPGPGNWT 119

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RM 176
              ++  +    D+       ++P + HRLD++TSG++VVA+T  A + L E+F    + 
Sbjct: 120 GTLVNALIHHCGDTLSGIGGVRRPGIVHRLDRDTSGVMVVAKTDQAHRVLAEAFADHGQD 179

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             +++ Y +LVWG+P+ +   + +  L +S        VV Q    A +A++H+ V++ +
Sbjct: 180 GDLERAYVALVWGVPR-RISGLVDAPLGRSASDRTLRAVVPQGRADARHAVTHYTVLERY 238

Query: 237 A------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKL 288
                  Q    +E +  TGRTHQ+RVH  H+G P+VGD  Y   F  K N   P   ++
Sbjct: 239 GTGTPEEQIAALVECRLETGRTHQIRVHMAHIGHPLVGDPAYGRAFRTKANRLPPALAEM 298

Query: 289 Y-------LHARYMDLPHPEGGR-LQITAPLPAHM 315
                   LHAR +   HP  G+ ++  A +PA M
Sbjct: 299 VAAFPRQALHARLLAFRHPVSGKIMRFEAAIPADM 333


>gi|288929438|ref|ZP_06423283.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 317 str. F0108]
 gi|288329540|gb|EFC68126.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 317 str. F0108]
          Length = 349

 Score =  120 bits (302), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 94/342 (27%), Positives = 164/342 (47%), Gaps = 58/342 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+DR+      H +   +QK   +G V V+++ VK N +++ G V+ +  
Sbjct: 24  IVVDRGQVPVRIDRFMTERLQHSSRNRIQKAADAGFVHVNERPVKSNYKVRPGDVITL-- 81

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
           +++  +H            + T  ++ +   ++YED  + V NKPAG+ V  G+G     
Sbjct: 82  MLDRPHH------------DTTIEAEDIPLDVVYEDDALMVINKPAGMVVHPGAGNFHGT 129

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H+        D+   +  L HR+D++TSG+LVVA+T  A + L   F  +   
Sbjct: 130 LINAVAWHLRNM--PSFDANDPEVGLVHRIDKDTSGLLVVAKTPEAKRKLGLQFFNKTTH 187

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDY---------VHVVKQNEKGANYAISHFK 231
           + Y +LVW          AN+   +  I G+          + V   + +    A++H++
Sbjct: 188 RSYNALVW----------ANFAEDEGRIEGNIGRDPRDRLRMAVFPPDSETGKPAVTHYR 237

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQ 285
           V++ F     ++E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S     IQ
Sbjct: 238 VLERFGY-VTFVECILETGRTHQIRAHMKHIGHPMFGDERYGGTEILRGERSSTYKAYIQ 296

Query: 286 N------KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
           N      +  LHAR +   HP  G ++  T+PLP  M +  D
Sbjct: 297 NCFKLCPRQALHARTLGFVHPTTGQQMDFTSPLPQDMEQLLD 338


>gi|295676473|ref|YP_003604997.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1002]
 gi|295436316|gb|ADG15486.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1002]
          Length = 416

 Score =  120 bits (302), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 96/332 (28%), Positives = 149/332 (44%), Gaps = 35/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV N+    RLD+     +P  +   LQ  + + +VRVD K  K    +  G  + + P
Sbjct: 70  VVVPNELAGERLDKVLAKVFPEFSRSRLQSWIEAQRVRVDGKPAKIRQPVPLGATIELVP 129

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +L   +  T     L+  ++YED  + V NKPAG+ V   +G     
Sbjct: 130 ------------DLLPEQLAFTPEPVPLE--IVYEDDTLVVINKPAGMVVHPAAGNWSGT 175

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++G L  + ++    PR  + HRLD+ETSG++VVART  A   L    + R +++ Y +
Sbjct: 176 VLNGLLHRYGETAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLA 235

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVIDCFA---QK 239
           LVWG   ++    A        IG D      +          A +HF+ +       Q 
Sbjct: 236 LVWGNMPDEGTIDAP-------IGRDPRERTRMAVVTGAAGKPARTHFRRVASAIWQRQP 288

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMD 296
              +     TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + 
Sbjct: 289 VTAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLG 348

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L HP+ GR +Q  A +PA +     +LG   D
Sbjct: 349 LIHPKTGRSMQWRADVPADIEALSAALGLGRD 380


>gi|291546177|emb|CBL19285.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus sp.
           SR1/5]
          Length = 304

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 95/330 (28%), Positives = 153/330 (46%), Gaps = 52/330 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            VE +E  +R+DR+       ++   LQK+L+ GQ+ V +K  K N +++    + +   
Sbjct: 7   TVEKEESGIRIDRYLAEKDSGLSRSFLQKLLKEGQITVGEKAAKSNYKVRENDRIHLEIP 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            ++   I+ E   LD               +LYED  + + NKP G+ V   +G   H  
Sbjct: 67  DSSEPDIVPEDIPLD---------------ILYEDEDVLIVNKPKGMVVHPAAG---HYQ 108

Query: 131 GFLKSWV-----DSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G L + V     DS        +P + HR+D++T+G L+V +   A + L E  +   I+
Sbjct: 109 GTLVNAVMAHCGDSLSGINGVMRPGIVHRIDKDTTGALLVCKNDIAHRDLAEQLKCHSIR 168

Query: 181 KIYWSLVWGIPKNKKECIANWL------LKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + Y ++V G  K  +  I   +       KK  I          N K    AI+H+KV++
Sbjct: 169 RRYRAVVQGNLKEDEGTIEGPIGRHPTDRKKMAI----------NHKNGKDAITHYKVLE 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHAR 293
            F +   ++E +  TGRTHQ+RVH   +G P++GD  Y     G+  +P       LHA 
Sbjct: 219 RFGEA-TYVECRLETGRTHQIRVHMASIGHPLLGDTVY-----GSSRNPYHLEGQALHAM 272

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +   HP  G  ++ TAPLP + VK    L
Sbjct: 273 ILGFVHPRTGEYMEFTAPLPEYFVKLLTKL 302


>gi|107029027|ref|YP_626122.1| pseudouridine synthase, RluD [Burkholderia cenocepacia AU 1054]
 gi|116689814|ref|YP_835437.1| RluA family pseudouridine synthase [Burkholderia cenocepacia
           HI2424]
 gi|254248088|ref|ZP_04941409.1| Pseudouridine synthase, RluD [Burkholderia cenocepacia PC184]
 gi|105898191|gb|ABF81149.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           cenocepacia AU 1054]
 gi|116647903|gb|ABK08544.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           cenocepacia HI2424]
 gi|124872864|gb|EAY64580.1| Pseudouridine synthase, RluD [Burkholderia cenocepacia PC184]
          Length = 402

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 94/319 (29%), Positives = 145/319 (45%), Gaps = 35/319 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +V VD    K    +  G  + + P       ++ 
Sbjct: 70  RLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAPAKIRQPVPLGAKIALVP------DLLP 123

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ        L    + +   ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 124 EQ--------LAFTPEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYG 175

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG    + 
Sbjct: 176 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEEG 235

Query: 196 ECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVID-CFAQK--FCWLEMQPHT 249
              A        IG D     +           A +HF+ +D C  Q+     ++    T
Sbjct: 236 TIDAP-------IGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLET 288

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-L 305
           GRTHQ+RVH  H G P++GD  Y         +P+ +   +  LHA  + L HP  G+ +
Sbjct: 289 GRTHQIRVHCAHAGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGLVHPVTGKAM 348

Query: 306 QITAPLPAHMVKTWDSLGF 324
           Q   PLP  M     +LGF
Sbjct: 349 QWRCPLPDDMNTLVAALGF 367


>gi|307273068|ref|ZP_07554314.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|306510053|gb|EFM79077.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|315147417|gb|EFT91433.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4244]
 gi|315150758|gb|EFT94774.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0012]
          Length = 310

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 94/319 (29%), Positives = 156/319 (48%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 20  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 73

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                E ++LD        ++ +   ++YED+ + V NKP G+ V   +G   H +G L 
Sbjct: 74  -----EPEVLDMV------AEDIPLTIVYEDNDVIVVNKPQGMVVHPSAG---HPNGTLV 119

Query: 135 SWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + +              +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 120 NALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 179

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 180 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 233 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 287

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 288 QLVFEAPLPEVFEKTLHQL 306


>gi|163850438|ref|YP_001638481.1| RluA family pseudouridine synthase [Methylobacterium extorquens
           PA1]
 gi|163662043|gb|ABY29410.1| pseudouridine synthase, RluA family [Methylobacterium extorquens
           PA1]
          Length = 343

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 103/347 (29%), Positives = 157/347 (45%), Gaps = 54/347 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + +V++      RLDR     +  ++   LQ ++R G VR D            G VVR
Sbjct: 21  ARSLVLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCD------------GIVVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL----LYEDSKIYVFNKPAGISVQGG 122
            P         +     +D SV     ++ L   L    ++ED  + V +KPAG+ V   
Sbjct: 69  DP------ARKVGAGCRIDLSVPAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPA 122

Query: 123 SGIAYHIDGFL---------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           +G   H DG L          S     G ++P + HRLD++TSG+LVVA+   A Q L+ 
Sbjct: 123 AG---HEDGTLVNRLIAHCGASLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSA 179

Query: 173 SF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            F    R   +++ Y +LVW +P+ +   I   L +  H   + + VV+  E     AI+
Sbjct: 180 QFADHGRSGALERAYLALVWNVPEPRAGTIRANLARSRH-NREKIAVVRDGE--GREAIT 236

Query: 229 HFKVIDCFAQKFCWLEMQPH--TGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSP 283
           H++V D   +      ++ H  TGRTHQ+RVH  H G P++GD  Y   FK      + P
Sbjct: 237 HYRVEDVHGEGGVTALLRCHLETGRTHQIRVHLSHRGHPLLGDAVYGGAFKTKAARLSEP 296

Query: 284 IQNKL------YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            +  L       LHA  +   HP  G RL+  +PLP    +   +LG
Sbjct: 297 ARAALDALGRQALHAVELGFLHPRSGERLRFESPLPEDFSRLLAALG 343


>gi|260435696|ref|ZP_05789666.1| pseudouridylate synthase, 23S rRNA-specific [Synechococcus sp. WH
           8109]
 gi|260413570|gb|EEX06866.1| pseudouridylate synthase, 23S rRNA-specific [Synechococcus sp. WH
           8109]
          Length = 333

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 93/308 (30%), Positives = 143/308 (46%), Gaps = 32/308 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +     +   +QK + +G VRV+ K  K    ++ G  V++  PP    L++
Sbjct: 37  MRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKTGKAKTPLRQGDEVQLWMPPP-EPLSY 95

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E   LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 96  LKPEPMDLD---------------VLFEDDHLIVLNKPAGLTVHPAPGNKDGTLVNGLLH 140

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y+++V G+
Sbjct: 141 HCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVRLQVQIQKRIASREYFAVVHGV 200

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +       Y  V  +N     YA +H+ +++     +  L  +  TG
Sbjct: 201 PAGDSGTIVGPIGRHPADRKKYAVVSSEN---GRYACTHWTLVERLGD-YSLLRFKLDTG 256

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  HM  P+VGD  Y    K     P Q    LHA  + L HP    R+   A
Sbjct: 257 RTHQIRVHCAHMNHPVVGDPTYSRCRKLPIELPGQA---LHAVQLGLDHPITRERMVFEA 313

Query: 310 PLPAHMVK 317
           PLP  M K
Sbjct: 314 PLPPVMEK 321


>gi|78213965|ref|YP_382744.1| ribosomal large subunit pseudouridine synthase D [Synechococcus sp.
           CC9605]
 gi|78198424|gb|ABB36189.1| Pseudouridine synthase, RluD [Synechococcus sp. CC9605]
          Length = 333

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 93/308 (30%), Positives = 142/308 (46%), Gaps = 32/308 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +     +   +QK + +G VRV+ K  K    ++ G  V++  PP    L +
Sbjct: 37  MRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKTGKAKTPLRQGDEVQLWMPPP-EPLPY 95

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E   LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 96  LKPEPMDLD---------------VLFEDDHLIVLNKPAGLTVHPAPGNKDGTLVNGLLH 140

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y+++V G+
Sbjct: 141 HCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVRLQVQIQKRIASREYFAVVHGV 200

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +       Y  V  +N     YA +H+ +++     +  L  +  TG
Sbjct: 201 PGGDSGTIVGAIGRHPADRKKYAVVSSEN---GRYACTHWTLVERLGD-YSLLRFKLDTG 256

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  HM  P+VGD  Y    K     P Q    LHA  + L HP    R+   A
Sbjct: 257 RTHQIRVHCAHMNHPVVGDPTYSRCRKLPIELPGQA---LHAVQLGLDHPITRERMMFEA 313

Query: 310 PLPAHMVK 317
           PLP  M K
Sbjct: 314 PLPPVMEK 321


>gi|227553528|ref|ZP_03983577.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|255972642|ref|ZP_05423228.1| pseudouridylate synthase [Enterococcus faecalis T1]
 gi|255975694|ref|ZP_05426280.1| pseudouridylate synthase [Enterococcus faecalis T2]
 gi|256762651|ref|ZP_05503231.1| pseudouridylate synthase [Enterococcus faecalis T3]
 gi|256961775|ref|ZP_05565946.1| pseudouridylate synthase [Enterococcus faecalis Merz96]
 gi|257079163|ref|ZP_05573524.1| pseudouridylate synthase [Enterococcus faecalis JH1]
 gi|257085033|ref|ZP_05579394.1| pseudouridylate synthase [Enterococcus faecalis Fly1]
 gi|257419447|ref|ZP_05596441.1| pseudouridylate synthase [Enterococcus faecalis T11]
 gi|257422461|ref|ZP_05599451.1| pseudouridylate synthase [Enterococcus faecalis X98]
 gi|294779380|ref|ZP_06744781.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|227177333|gb|EEI58305.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|255963660|gb|EET96136.1| pseudouridylate synthase [Enterococcus faecalis T1]
 gi|255968566|gb|EET99188.1| pseudouridylate synthase [Enterococcus faecalis T2]
 gi|256683902|gb|EEU23597.1| pseudouridylate synthase [Enterococcus faecalis T3]
 gi|256952271|gb|EEU68903.1| pseudouridylate synthase [Enterococcus faecalis Merz96]
 gi|256987193|gb|EEU74495.1| pseudouridylate synthase [Enterococcus faecalis JH1]
 gi|256993063|gb|EEU80365.1| pseudouridylate synthase [Enterococcus faecalis Fly1]
 gi|257161275|gb|EEU91235.1| pseudouridylate synthase [Enterococcus faecalis T11]
 gi|257164285|gb|EEU94245.1| pseudouridylate synthase [Enterococcus faecalis X98]
 gi|294453509|gb|EFG21910.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|323480881|gb|ADX80320.1| pseudouridine synthase, RluA family protein [Enterococcus faecalis
           62]
          Length = 301

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 157/319 (49%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 11  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                E ++LD        ++ +   ++YED+ + V NKP G+ V   +G         +
Sbjct: 65  -----EPEVLDMV------AEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNAL 113

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H D  L +  D    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 114 LHHAD-HLSAINDVV--RPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 170

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 171 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 224 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 278

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 279 QLVFEAPLPEVFEKTLHQL 297


>gi|304393319|ref|ZP_07375247.1| ribosomal large subunit pseudouridine synthase D [Ahrensia sp.
           R2A130]
 gi|303294326|gb|EFL88698.1| ribosomal large subunit pseudouridine synthase D [Ahrensia sp.
           R2A130]
          Length = 365

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 97/351 (27%), Positives = 167/351 (47%), Gaps = 54/351 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++V + ++  R+D++   + P  ++   +Q ++R G V ++ +  +  + +I +G V
Sbjct: 35  MEVLIVSHVDDGKRVDKFISANAPDDLSRARVQALVRQGNVTINGELPRGTSTKISNGDV 94

Query: 65  VR--IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           VR  +PP  +A+     E   LD               +L+ED  + V  KPAG+ V   
Sbjct: 95  VRFLMPPPEDAIPQ--PENIPLD---------------ILHEDDDLIVLIKPAGMVVHPA 137

Query: 123 SG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            G         + +H DG L      K  +P + HRLD++TSG++VVA++  A   L E 
Sbjct: 138 PGNWSGTLVNALLHHCDGNLSGIGGVK--RPGIVHRLDKDTSGVMVVAKSYRAHIDLQEQ 195

Query: 174 F----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           F    R   +++ YW+L WG P   K  + + L+ +         VV++    A +AI+H
Sbjct: 196 FADHGRTGPLERAYWALAWGAPPRMKGKV-DTLIGRHPTRRVQRAVVEEGAPDAKHAITH 254

Query: 230 FKVIDCFAQK-------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
           ++V+  F             +E +  TGRTHQ+RVH  H+G P++GD +Y   +      
Sbjct: 255 YEVVKRFEDAERSGEAMASLIECKLETGRTHQIRVHLTHLGNPLLGDPEYGRAYANRIVR 314

Query: 283 -PIQ--------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            P +        N+  LHAR +   HP  G  ++ TA   + M    DS+G
Sbjct: 315 LPHKAQSLFAEFNRQALHARTLGFRHPATGETMRFTAEPTSDMQALIDSIG 365


>gi|57239260|ref|YP_180396.1| pseudouridylate synthase [Ehrlichia ruminantium str. Welgevonden]
 gi|58579223|ref|YP_197435.1| SfhB protein homolog (peudouridylate synthase) [Ehrlichia
           ruminantium str. Welgevonden]
 gi|57161339|emb|CAH58262.1| ribosomal large subunit pseudouridine synthase D [Ehrlichia
           ruminantium str. Welgevonden]
 gi|58417849|emb|CAI27053.1| SfhB protein homolog (peudouridylate synthase) [Ehrlichia
           ruminantium str. Welgevonden]
          Length = 324

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 88/311 (28%), Positives = 146/311 (46%), Gaps = 41/311 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++N EEN RLD++                     ++++  R K    IQ+ ++     
Sbjct: 6   IFIQNGEENKRLDKFI-------------------ALKLNISRNKVQQLIQNNKIYLFNK 46

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKS------ILLYEDSKIYVFNKPAGISVQGGS 123
           ++   NHI K   I   ++   +H+  +         +LYED  I + NK  GI+V  G+
Sbjct: 47  IVKDNNHITKVNDIYYINMPTQEHNCSITPNINIPITILYEDQDIIIINKEPGITVHPGA 106

Query: 124 GIAYH--IDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++G +  +  +     K  +P + HRLD++TSG++V+AR   +   L++    
Sbjct: 107 GTKDDTLVNGLIAHYGSTLSYIGKASRPGIVHRLDKDTSGLMVIARNEHSYYFLSDLLSK 166

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           ++I+K Y ++VWGIP  K   I N +  KS+     +  V  +      AI+ +  I  F
Sbjct: 167 KQIKKEYLAVVWGIPNPKCNIIKNHIDTKSN--NKQMMTVTHSRNKGKLAITEYNTIQTF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQNKL---Y 289
           A     ++ + +TGRTHQ+RVH  ++G  I+GD KY  N     K    S I N L    
Sbjct: 225 ASIATLVKCRIYTGRTHQIRVHMSYIGNSIIGDQKYGKNDSKIAKYAQQSTIINTLKRQA 284

Query: 290 LHARYMDLPHP 300
           LHA  +   HP
Sbjct: 285 LHAHKLGFIHP 295


>gi|257082401|ref|ZP_05576762.1| pseudouridylate synthase [Enterococcus faecalis E1Sol]
 gi|256990431|gb|EEU77733.1| pseudouridylate synthase [Enterococcus faecalis E1Sol]
          Length = 301

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 157/319 (49%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 11  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                E ++LD        ++ +   ++YED+ + V NKP G+ V   +G         +
Sbjct: 65  -----EPEVLDMV------AEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNAL 113

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H D  L +  D    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 114 LHHAD-HLSAINDVV--RPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 170

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 171 LVHGVIPHDKGEI--NTPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 224 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 278

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 279 QLVFEAPLPEVFEKTLHQL 297


>gi|299136326|ref|ZP_07029510.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX8]
 gi|298602450|gb|EFI58604.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX8]
          Length = 446

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 96/340 (28%), Positives = 160/340 (47%), Gaps = 43/340 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   VE   + MRLD +     P I+   +  ++  GQV VD    K   +++ G+++ 
Sbjct: 118 VRSFTVEPAAKEMRLDAYLAKAIPDISRARVVLLIEKGQVTVDGNPGKGKQKLKGGEMIE 177

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I              +       L    + +   ++YED  + V +K AG+ V  G+G +
Sbjct: 178 I--------------EGEPRPEPLHAQPEDIPLTIVYEDDDLAVVDKAAGMMVHAGAGDS 223

Query: 127 YHIDGFL---------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               G L         KS     G  +P + HRLD++TSG++VVA+  +  + L+E F  
Sbjct: 224 ERNRGTLVNALLFHMGKSLSQVSGDLRPGIVHRLDKQTSGLIVVAKNDSTHRKLSEMFSE 283

Query: 177 RRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKV 232
           RR++K+Y +LV  W  P    +      L    I  D V  ++   +  G   A+SH++V
Sbjct: 284 RRLRKVYLALVHGWIAPATGAQDSGTIQLP---ISRDLVRRIRMTTRRSGGRSAVSHWRV 340

Query: 233 IDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL- 288
           ++  +    KF  +E++  TGRTHQ+RVH   +G P+VGD  Y A  + N     Q ++ 
Sbjct: 341 LEKISGPYGKFSLVEVRIETGRTHQIRVHMQAIGHPVVGDFLYGAPHRINPIGGPQAEVE 400

Query: 289 -------YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
                  +LHA  ++  HP  G +L + A LP  +V+  +
Sbjct: 401 GFALERNFLHAAELEFVHPRTGEKLALDAALPEELVQVLE 440


>gi|159902752|ref|YP_001550096.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9211]
 gi|159887928|gb|ABX08142.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9211]
          Length = 327

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 94/304 (30%), Positives = 145/304 (47%), Gaps = 34/304 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDRW  +     +   +QK +  G V+V++K  K    ++ G  +++          +
Sbjct: 27  MRLDRWLVSQRSEQSRARIQKFINEGLVKVNEKIGKAKTPLRQGDEIKLWLPPPEPLPYL 86

Query: 79  KEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKS 135
           K +KI LD               +LYED  + V NK AGI+V    G  +   ++G L  
Sbjct: 87  KPEKISLD---------------ILYEDKYLIVINKQAGIAVHPAPGNKFGTLVNGLLHH 131

Query: 136 WVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +VVA+T+ A  +L +  + R   +IY ++V G+P
Sbjct: 132 CNDLPGISGKLRPGIVHRLDKDTTGCIVVAKTQEALVNLQKQIQTRVASRIYLAIVHGVP 191

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K  K  I   + +  H      + V  NE  A YA +H+++ +     +  L  +  TGR
Sbjct: 192 KGDKGTIIGAIGR--HPVDRKKYAVVTNEM-ARYACTHWELKERLGD-YSLLSFKLDTGR 247

Query: 252 THQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-T 308
           THQ+RVH  H G PI+GD  Y  C       +S +     LHA  + L HP      +  
Sbjct: 248 THQIRVHCAHFGHPILGDQTYSRCKKLPNGVSSQV-----LHAVKLGLKHPHNNETMLFE 302

Query: 309 APLP 312
           APLP
Sbjct: 303 APLP 306


>gi|291087665|ref|ZP_06572048.1| ribosomal large subunit pseudouridine synthase D [Clostridium sp.
           M62/1]
 gi|291074400|gb|EFE11764.1| ribosomal large subunit pseudouridine synthase D [Clostridium sp.
           M62/1]
          Length = 300

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 94/328 (28%), Positives = 159/328 (48%), Gaps = 48/328 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  + + +R+D++       ++   LQK+L+S  V VDK+ VK + ++ +G+ +     
Sbjct: 1   MVPAEAQGVRIDKFLSEACDGLSRSYLQKLLKSELVEVDKRTVKNSYKLSAGEKIEFEVP 60

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
             A   I  E   LD               ++YEDS I + NKP G+ V   +G      
Sbjct: 61  EAAEPEIKAEDIPLD---------------IIYEDSDIILVNKPKGMVVHPAAGHYSQTL 105

Query: 125 ---IAYHI-DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + YH  DG   S ++    +P + HR+D +T+G+L+V +   A   + E  ++  I 
Sbjct: 106 VNGLMYHCRDGL--SGINGV-LRPGIVHRIDMDTTGVLIVCKNDFAHNAIAEQLKVHSIT 162

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQ 238
           + Y+++V G+ +  +  +       + IG   V   K   N K    A++H++V++ F Q
Sbjct: 163 RKYFAIVHGVIQEDEGTV------DAPIGRHPVDRKKMSINRKNGKEAVTHYRVLERFRQ 216

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---YLHARYM 295
            F ++E Q  TGRTHQ+RVH   +G P++GD  Y         S I  KL    LHA  +
Sbjct: 217 -FTYVECQLETGRTHQIRVHMASIGHPLLGDSVYGP-------SKIPFKLQGQTLHAGVL 268

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            + HP  G  ++ +APLP +  +  D L
Sbjct: 269 GIVHPRTGNYMEFSAPLPEYFSELLDKL 296


>gi|170733153|ref|YP_001765100.1| RluA family pseudouridine synthase [Burkholderia cenocepacia MC0-3]
 gi|169816395|gb|ACA90978.1| pseudouridine synthase, RluA family [Burkholderia cenocepacia
           MC0-3]
          Length = 360

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 141/319 (44%), Gaps = 35/319 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +V VD    K    +  G  + + P          
Sbjct: 28  RLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAPAKIRQPVPLGAKIALVP---------- 77

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +L   +  T     L  I  YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 78  --DLLPEQLAFTPEPVPLDVI--YEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYG 133

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG      
Sbjct: 134 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEAG 193

Query: 196 ECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVID-CFAQK--FCWLEMQPHT 249
              A        IG D      +          A +HF+ +D C  Q+     ++    T
Sbjct: 194 TIDAP-------IGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLET 246

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-L 305
           GRTHQ+RVH  H G P++GD  Y         +P+ +   +  LHA  + L HP  G+ +
Sbjct: 247 GRTHQIRVHCAHAGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGLVHPVTGKAM 306

Query: 306 QITAPLPAHMVKTWDSLGF 324
           Q   PLP  M     +LGF
Sbjct: 307 QWRCPLPDDMNTLVAALGF 325


>gi|58617275|ref|YP_196474.1| SfhB protein homolog (peudouridylate synthase) [Ehrlichia
           ruminantium str. Gardel]
 gi|58416887|emb|CAI28000.1| SfhB protein homolog (peudouridylate synthase) [Ehrlichia
           ruminantium str. Gardel]
          Length = 324

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 87/311 (27%), Positives = 147/311 (47%), Gaps = 41/311 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++N EEN RLD++                     ++++  R +    IQ+ ++     
Sbjct: 6   IFIQNGEENKRLDKFIA-------------------LKLNISRNRVQQLIQNNKIYLFNK 46

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKS------ILLYEDSKIYVFNKPAGISVQGGS 123
           ++   NHI K   I   ++   +H+  +         +LYED  I + NK  GI+V  G+
Sbjct: 47  IVKDNNHITKVNDIYYINMPTQEHNCSITPNINIPITILYEDQDIIIINKEPGITVHPGA 106

Query: 124 GIAYH--IDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++G +  +  +     K  +P + HRLD++TSG++V+AR   +   L++    
Sbjct: 107 GTKDDTLVNGLIAHYGSTLSYIGKASRPGIVHRLDKDTSGLMVIARNEHSYYFLSDLLSK 166

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           ++I+K Y ++VWGIP  K   I N +  KS+     +  V  ++     AI+ +  I  F
Sbjct: 167 KQIKKEYLAVVWGIPNPKCNIIKNHIDTKSN--NKQMMTVTHSQNKGKLAITEYNTIQTF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQNKL---Y 289
           A     ++ + +TGRTHQ+RVH  ++G  I+GD KY  N     K    S I N L    
Sbjct: 225 ASIATLVKCRIYTGRTHQIRVHMSYIGNSIIGDQKYGKNDSKIAKYAQQSTIINTLKRQA 284

Query: 290 LHARYMDLPHP 300
           LHA  +   HP
Sbjct: 285 LHAHKLGFIHP 295


>gi|227518911|ref|ZP_03948960.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|229549858|ref|ZP_04438583.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|293383481|ref|ZP_06629394.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecalis R712]
 gi|293388864|ref|ZP_06633350.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecalis S613]
 gi|307269533|ref|ZP_07550872.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|307277912|ref|ZP_07558996.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
 gi|307289260|ref|ZP_07569216.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|312901873|ref|ZP_07761138.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
 gi|312907690|ref|ZP_07766681.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|312910308|ref|ZP_07769155.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
 gi|312951652|ref|ZP_07770547.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|227073600|gb|EEI11563.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|229305127|gb|EEN71123.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|291079272|gb|EFE16636.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecalis R712]
 gi|291081789|gb|EFE18752.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecalis S613]
 gi|306499969|gb|EFM69330.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|306505309|gb|EFM74495.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
 gi|306514153|gb|EFM82729.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|310626718|gb|EFQ10001.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|310630369|gb|EFQ13652.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|311289581|gb|EFQ68137.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
 gi|311291066|gb|EFQ69622.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
 gi|315152327|gb|EFT96343.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0031]
 gi|315156128|gb|EFU00145.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0043]
 gi|315158230|gb|EFU02247.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0312]
 gi|315162361|gb|EFU06378.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0645]
 gi|315163874|gb|EFU07891.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1302]
 gi|315169613|gb|EFU13630.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1342]
 gi|315172438|gb|EFU16455.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1346]
 gi|315576067|gb|EFU88258.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309B]
 gi|315580642|gb|EFU92833.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309A]
 gi|327535286|gb|AEA94120.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecalis OG1RF]
 gi|329571882|gb|EGG53560.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1467]
          Length = 310

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 157/319 (49%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 20  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 73

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                E ++LD        ++ +   ++YED+ + V NKP G+ V   +G         +
Sbjct: 74  -----EPEVLDMV------AEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNAL 122

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H D  L +  D    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 123 LHHAD-HLSAINDVV--RPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 179

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 180 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 233 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 287

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 288 QLVFEAPLPEVFEKTLHQL 306


>gi|72383396|ref|YP_292751.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. NATL2A]
 gi|72003246|gb|AAZ59048.1| ribosomal large subunit pseudouridine synthase D [Prochlorococcus
           marinus str. NATL2A]
          Length = 326

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 95/306 (31%), Positives = 148/306 (48%), Gaps = 38/306 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IPPVINALNH 76
           MRLDRW  +     +  ++QK + +G  RV+ K  K    ++ G +++  +PP    L +
Sbjct: 27  MRLDRWLVSQRAEQSRAHIQKFIEAGFARVNGKTGKAKTPVRPGDIIQLWVPPP-EPLPY 85

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E+  LD               +LYED  + V NK AGI+V    G      ++G + 
Sbjct: 86  LKPEEIDLD---------------ILYEDDHLIVINKTAGIAVHPAPGNKSGTLVNGLIH 130

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +VVA+T+ A   L    + R   + Y ++V G 
Sbjct: 131 HCPDLPGIGGKLRPGIVHRLDKDTTGCIVVAKTQEALVKLQIQIQKRVASRNYIAVVHGA 190

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            KN +  I   + +       Y  V   +E+   YA +H+K+I      F  L+ +  TG
Sbjct: 191 IKNNEGMIVGSIGRHPKDRKKYAVV---DEESGRYACTHWKLIKNLGN-FSLLKFKLDTG 246

Query: 251 RTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGRLQ 306
           RTHQ+RVH+ H+G PI+GD  Y  C         PI+     LHA  + L HP    +++
Sbjct: 247 RTHQIRVHSAHIGHPIIGDQTYSRCKKL------PIKLGGQALHAIELGLIHPITLEKMK 300

Query: 307 ITAPLP 312
            TAPLP
Sbjct: 301 FTAPLP 306


>gi|182680419|ref|YP_001834565.1| pseudouridine synthase [Beijerinckia indica subsp. indica ATCC
           9039]
 gi|182636302|gb|ACB97076.1| pseudouridine synthase [Beijerinckia indica subsp. indica ATCC
           9039]
          Length = 234

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 82/233 (35%), Positives = 126/233 (54%), Gaps = 13/233 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L++ LLY D  + V +KPAGI V  G     +++ F         ++P L HRLD++TSG
Sbjct: 6   LQARLLYRDGMMLVLDKPAGIPVHKGPKGGDNLEAFFDDLRFGLPRRPALAHRLDRDTSG 65

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R   A + L   F+  +I K YWS+V G P   +  I   L ++    G ++ V 
Sbjct: 66  CLVLGRHHKALEKLGLLFKQGKIAKTYWSVVLGGPTEDEGLIDLPLGRRDAERGWWMKV- 124

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-AN 275
             + +GA  A + + V+   +   C L ++P TGRTHQLRVH    G PI+GD  Y  A+
Sbjct: 125 --DPEGAP-AQTRWTVL-ARSADHCLLALKPLTGRTHQLRVHCAAQGFPILGDPVYGPAD 180

Query: 276 FKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            KG  T      L+LHAR +++P +     +++ AP+PAHM     +LG++ +
Sbjct: 181 HKGGET------LHLHARAIEIPLYKNKEAIKVEAPVPAHMRPALMALGWREE 227


>gi|302389579|ref|YP_003825400.1| ribosomal large subunit pseudouridine synthase D
           [Thermosediminibacter oceani DSM 16646]
 gi|302200207|gb|ADL07777.1| ribosomal large subunit pseudouridine synthase D
           [Thermosediminibacter oceani DSM 16646]
          Length = 307

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 96/329 (29%), Positives = 160/329 (48%), Gaps = 49/329 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RI 67
           ++V+ D+   RLD +       ++   +QK +  G V+V+++ VK + +++ G V+   I
Sbjct: 7   ILVQEDDAKKRLDVFLSGVINDLSRSYIQKGIEEGWVKVNERIVKPHYKLKKGDVIVADI 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
           P                 S   L+   + +   +++ED  I V NKP G+ V    G   
Sbjct: 67  P-----------------SPKPLSLEPENIPLDIIHEDRDIIVVNKPRGMVVYPAPGNYS 109

Query: 126 AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HRLD++TSG++VVA+   A + L   F+ + ++K
Sbjct: 110 GTLVNALLYHTKDLSGINGVMRPGIVHRLDKDTSGVIVVAKNDMAHRELAMQFKNKLVKK 169

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNE-----KGANYAISHFKVIDC 235
            Y ++VWG IP+++          ++ IG    H  K+ E     K    AI+HFKV++ 
Sbjct: 170 TYLAVVWGNIPEDRATI-------EAPIGR---HPAKRVEMAVTAKNGKEAITHFKVLER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARY 294
           F + F ++E+   TGRTHQ+RVH   +G P+VGD  Y         SP   N   LHA  
Sbjct: 220 F-EDFTFIEVNIETGRTHQIRVHMSFIGHPVVGDPLYSRK-----KSPFNINGQALHAYR 273

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + L HP  G  +   AP+P  + +  ++L
Sbjct: 274 LGLNHPRTGEFMTFEAPIPQDITEILNTL 302


>gi|160942600|ref|ZP_02089845.1| hypothetical protein FAEPRAM212_00074 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446079|gb|EDP23082.1| hypothetical protein FAEPRAM212_00074 [Faecalibacterium prausnitzii
           M21/2]
          Length = 316

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 70/263 (26%), Positives = 131/263 (49%), Gaps = 19/263 (7%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD +    YP +    L K LR  +++++ K+   + R+ +G  +++      L+ ++ 
Sbjct: 13  RLDNYLTQQYPALTPGRLNKALRENKIKLNGKKQPLSTRVMAGDEIKL----FILDDVLD 68

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             + ++        +    + ++Y+  +I + NKPAG++V G           L  +++ 
Sbjct: 69  ADRRVEGPAWKNART---PAQVVYDCPQILIVNKPAGVAVDGPEDDTLLNRALL--YLNK 123

Query: 140 KGQ-------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +G+        P L HRLD  TSG++++A+T  A +    + + R +QK Y  + +G P 
Sbjct: 124 QGEYKENDLYTPALCHRLDTGTSGLVIIAKTPEAEELFLSAIKNREVQKTYLCVTFGRPM 183

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                +  +LLK +  G   V +V+  + GA    + ++ I   + +   L++Q  TGRT
Sbjct: 184 PPDATLGGYLLKDADRG--IVKIVEDKQPGAKEVETRYETI-AVSGRLALLKVQLITGRT 240

Query: 253 HQLRVHALHMGCPIVGDHKYCAN 275
           HQ+R H   +GCPI+GD KY  N
Sbjct: 241 HQIRAHMASIGCPILGDSKYGNN 263


>gi|148262954|ref|YP_001229660.1| RluA family pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146396454|gb|ABQ25087.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           uraniireducens Rf4]
          Length = 320

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 94/336 (27%), Positives = 158/336 (47%), Gaps = 40/336 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ +  EN E   RLD +       +     Q+++ +GQ+ VD    K + +++ G+
Sbjct: 1   MENVELIFPENSEIE-RLDSFIARSVNGMTRATAQRLIEAGQITVDGHPQKPSLKLKGGE 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +            E   L+               +L+ED  + V NK AG+ V  G+
Sbjct: 60  RLMVTIPPPVAAEPAAETIPLE---------------ILFEDRNLVVVNKAAGMVVHPGA 104

Query: 124 GIAYH--IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G +    ++  L    D  G     +P + HR+D++TSG+LVVA++ AA Q L E F+  
Sbjct: 105 GNSGGTLVNALLGHCTDLSGIGGELRPGIVHRIDKDTSGVLVVAKSDAAHQSLAEQFKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDC 235
            I+++Y +LV+G PK+ K  +      +SHIG   V   + + K     +A++H++V+  
Sbjct: 165 TIKRVYLALVYGAPKDDKGRL------ESHIGRHPVDRKRMSGKAKHGKHAVTHWRVVGR 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLY----- 289
           + +    L ++  TGRTHQ+RVH    G P+VGD  Y    +    +  +  KL      
Sbjct: 219 Y-RGITLLRLRLETGRTHQIRVHLSEAGYPLVGDDVYGGGSRLATVSDTLLRKLIKDLGR 277

Query: 290 --LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             LHA+ +   HP  G  L+    LP  M +  + L
Sbjct: 278 QALHAKTLGFIHPVTGEYLEFDTELPDDMARIVEYL 313


>gi|222874381|gb|EEF11512.1| predicted protein [Populus trichocarpa]
          Length = 304

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 82/269 (30%), Positives = 143/269 (53%), Gaps = 30/269 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 57  VSMIEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVR 116

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      + +  +    +     H       +++ED  + V +KPAG++V GGSG+A
Sbjct: 117 VPPI-----RVAQPSEAAAQAPVPAAHFR-----IIFEDEHLLVIDKPAGVAVHGGSGVA 166

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   G ++   +++ Q     L HRLD+ETSGIL++A+ R+A  +L E  R  ++ K Y+
Sbjct: 167 F---GVIEQMREARPQAKFLELVHRLDRETSGILMLAKKRSALVNLHEQIRENKMDKRYY 223

Query: 185 SLV-------WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           + V       WG  +  +E +  +L      G   V V  Q +  A++ +  F +ID + 
Sbjct: 224 ACVHGEWASDWGRRRAVREPLHKYLTAD---GERRVRV--QPDGLASHTV--FNLIDRWP 276

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           + +  LE +  TGRTHQ+RVH  H+G PI
Sbjct: 277 E-YALLEAELKTGRTHQIRVHLQHLGLPI 304


>gi|206560228|ref|YP_002230992.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           cenocepacia J2315]
 gi|198036269|emb|CAR52165.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           cenocepacia J2315]
          Length = 361

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 141/319 (44%), Gaps = 35/319 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + + +V VD    K    +  G  + + P          
Sbjct: 28  RLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAPAKIRQPVPLGAKIALVP---------- 77

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +L   +  T     L  I  YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 78  --DLLPEQLAFTPEPVPLDVI--YEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYG 133

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D+    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVWG      
Sbjct: 134 DAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEAG 193

Query: 196 ECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVID-CFAQK--FCWLEMQPHT 249
              A        IG D      +          A +HF+ +D C  Q+     ++    T
Sbjct: 194 TIDAP-------IGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLET 246

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-L 305
           GRTHQ+RVH  H G P++GD  Y         +P+ +   +  LHA  + L HP  G+ +
Sbjct: 247 GRTHQIRVHCAHAGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGLVHPVTGKAM 306

Query: 306 QITAPLPAHMVKTWDSLGF 324
           Q   PLP  M     +LGF
Sbjct: 307 QWRCPLPDDMNALVAALGF 325


>gi|124006632|ref|ZP_01691464.1| pseudouridine synthase, RluD [Microscilla marina ATCC 23134]
 gi|123987787|gb|EAY27478.1| pseudouridine synthase, RluD [Microscilla marina ATCC 23134]
          Length = 360

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 88/333 (26%), Positives = 161/333 (48%), Gaps = 43/333 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +E +R+D++  +  P+I     Q  +R G V+V+ + VK N +++   ++ I  
Sbjct: 40  IVVDKGQEPVRIDKFLMDRVPNITRNKTQNAIREGFVKVNDQEVKPNYKVRPEDIIII-- 97

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
              +L    +E +++   + +          ++YED  + V +K AG+ V          
Sbjct: 98  ---SLPEPPRESEVVPEDIPIN---------IVYEDDDLLVVHKEAGMVVHPAYNNWTGT 145

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             + +AYH     K+  +++  +P L HR+D++TSG+LVVA++  A QHL + F    I+
Sbjct: 146 LVNALAYH----FKNLPENRDGRPGLVHRIDKDTSGLLVVAKSEHALQHLAKQFFDHTIE 201

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y++LVWG PK +   I +  L +S           + + G  +A++H+KV+    +  
Sbjct: 202 RTYYALVWGEPKQEAGTI-DVNLGRSLKDRRVTAAFPEGDFG-RHAVTHYKVLKNL-RYV 258

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKL 288
             ++    TGRTHQ+R H  H+G P+  D  Y  +   KG   S           +  + 
Sbjct: 259 SLVQCNLETGRTHQIRAHMKHLGHPLFNDATYGGDKILKGTVFSKYRAFVENCFKVMPRQ 318

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            LHA+ +   HP   + +Q  + LP    K  +
Sbjct: 319 ALHAKSLGFVHPTTQKFIQFDSELPKDFQKAME 351


>gi|257069409|ref|YP_003155664.1| pseudouridine synthase, RluA family [Brachybacterium faecium DSM
           4810]
 gi|256560227|gb|ACU86074.1| pseudouridine synthase, RluA family [Brachybacterium faecium DSM
           4810]
          Length = 318

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 156/321 (48%), Gaps = 27/321 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + ++V+ +    RLD++ ++    +    L ++LR G++RV+ ++ + N R+Q+G  + 
Sbjct: 15  ARTLIVDVEHAGRRLDKFLRSRVKGVPAGLLFRLLRQGKLRVNGRKAQQNYRLQAGDEIT 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P    AL               L +    L+   L+ED  + + +KPAG++V  G+ + 
Sbjct: 75  VP----ALRIDADAAPPPAVPPALIQQ---LRGTALHEDEDLLIIDKPAGVAVHRGTDVP 127

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--IQKI 182
               G + +    + + P   L HRLD+ TSG+L +A++ +  ++L +  R R   I++ 
Sbjct: 128 A---GVIDALRQLRPELPDLELIHRLDRSTSGVLALAKSPSMLRYLHDLLRDREDEIERR 184

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G    +   +   L ++ +       VV   +     A +H  V   F  +   
Sbjct: 185 YLALVAGHWPAETTILDAPLRREEN------RVVVDPD--GQRAETHVAVAQRFGNRATL 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPE 301
           LE++  TGR HQ+RVH  H G PI GD +Y  + F     S     L+LHA  + +P P+
Sbjct: 237 LEVRLLTGRKHQIRVHLQHAGHPIAGDDRYGDDAFNRRAASLGGTGLHLHAAELVIPRPD 296

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G  L +TAP P    + W+ L
Sbjct: 297 GTTLAVTAPTP----RRWEQL 313


>gi|227823294|ref|YP_002827266.1| putative ribosomal large subunit pseudouridine synthase D
           [Sinorhizobium fredii NGR234]
 gi|227342295|gb|ACP26513.1| putative ribosomal large subunit pseudouridine synthase D
           [Sinorhizobium fredii NGR234]
          Length = 352

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 82/244 (33%), Positives = 125/244 (51%), Gaps = 33/244 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQE 153
           +LYED  + V  KPAG+ V  G+G      ++  +    DS       ++P + HRLD+E
Sbjct: 102 VLYEDDDLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGGVRRPGIVHRLDKE 161

Query: 154 TSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           TSG++VVA+  AA +HL++ F    R   +++ Y ++VWG P+  K  I N  L ++   
Sbjct: 162 TSGVMVVAKNDAAHRHLSDQFADHGRTGPLERAYQAVVWGRPRQLKGTI-NAALGRA--- 217

Query: 210 GDYVH--VVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALH 261
           GD     V ++    A  AI+H++V++ + +K         +E    TGRTHQ+RVH  H
Sbjct: 218 GDRTKRAVKREESDDAREAITHYEVVERYHEKPDGTCLAATVECHLETGRTHQIRVHMAH 277

Query: 262 MGCPIVGDHKYCANF--KGNFTSPIQ-------NKLYLHARYMDLPHPEGG-RLQITAPL 311
           +G P++GD  Y A F  K N             ++  LHA  +   HP  G  +   APL
Sbjct: 278 IGNPLIGDPDYGAAFRTKANLLPETARSVVNRFSRQALHAFMLQFEHPSSGDTMHFEAPL 337

Query: 312 PAHM 315
           PA M
Sbjct: 338 PADM 341


>gi|15643702|ref|NP_228748.1| ribosomal large subunit pseudouridine synthase C [Thermotoga
           maritima MSB8]
 gi|222100610|ref|YP_002535178.1| Pseudouridine synthase [Thermotoga neapolitana DSM 4359]
 gi|4981478|gb|AAD36021.1|AE001757_14 ribosomal large subunit pseudouridine synthase C [Thermotoga
           maritima MSB8]
 gi|221573000|gb|ACM23812.1| Pseudouridine synthase [Thermotoga neapolitana DSM 4359]
          Length = 304

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 97/314 (30%), Positives = 152/314 (48%), Gaps = 36/314 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHII 78
           RLD++ +N    +    + K++R G+V V++KRVK  +  ++ G VV +   +N  N   
Sbjct: 13  RLDKFLRNQLKDVPLSVIYKLIRKGKVYVNRKRVKDPSFDLEEGDVVELR-YVNLENLPK 71

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSW 136
           + +K   + V +       K  +LYED    V NKP  I++  G G+  A  I+G L  +
Sbjct: 72  RSEKKDLTPVPM-------KLDVLYEDDHYLVLNKPPNIAIHPGKGVHVATLIEGLL-YY 123

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              KG  P L HRLD+ETSG+LVVA+ R AA+ LTE F+ R I+K Y +LV G+P+N  +
Sbjct: 124 GQEKGFSPFLVHRLDKETSGLLVVAKNREAARILTELFKGRNIEKEYVTLVRGVPENNMK 183

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                           + +    ++  +  +S   + D        L ++ HTGR HQ+R
Sbjct: 184 ----------------ITIPLDGQEAVSEIVSVKPLKDV-----SLLRVKIHTGRKHQIR 222

Query: 257 VHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGRLQITAPLPA 313
            H   +G P+VGD  Y   +F   F       + +LH+  M    P         APLP 
Sbjct: 223 RHLSQIGFPVVGDDTYGDRHFNREFRKRYGLKRQFLHSYRMKFIDPWTEEEKDFRAPLPD 282

Query: 314 HMVKTWDSLGFKYD 327
            ++   + L  + D
Sbjct: 283 DLLSVLNLLEERSD 296


>gi|257090036|ref|ZP_05584397.1| pseudouridylate synthase [Enterococcus faecalis CH188]
 gi|256998848|gb|EEU85368.1| pseudouridylate synthase [Enterococcus faecalis CH188]
          Length = 301

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 157/319 (49%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 11  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                E ++LD        ++ +   ++YED+ + V NKP G+ V   +G         +
Sbjct: 65  -----EPEVLDMI------AEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNAL 113

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H D  L +  D    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 114 LHHAD-HLSAINDVV--RPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 170

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 171 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 224 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 278

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 279 QLVFEAPLPEVFEKTLHQL 297


>gi|78185708|ref|YP_378142.1| pseudouridine synthase, RluD [Synechococcus sp. CC9902]
 gi|78170002|gb|ABB27099.1| ribosomal large subunit pseudouridine synthase D [Synechococcus sp.
           CC9902]
          Length = 339

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 97/308 (31%), Positives = 146/308 (47%), Gaps = 32/308 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +     +   +QK + +G VRV+ K+ K    ++ G  V++  PP    L +
Sbjct: 40  MRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKQGKAKTPLREGDQVQLWMPPP-EPLPY 98

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  +   LD               +L+ED  I V NK AG++V    G      ++G L 
Sbjct: 99  LKPQPMDLD---------------VLFEDEHIIVLNKSAGLTVHPAPGNKDGTLVNGLLH 143

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++TSG +VVA+++ A   L    + R   + Y+++V G+
Sbjct: 144 HCPDLPGISGKLRPGIVHRLDKDTSGCIVVAKSQEALVKLQVQIQKRVASREYFAVVHGV 203

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +  H      + V  +E G  YA +H+ +I+ F   +  L  +  TG
Sbjct: 204 PDGDSGTIIGAVGR--HPVDRKKYAVVSDESG-RYARTHWTLIERFGD-YSLLRFKLDTG 259

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  H+  P+VGD  Y    K     P Q    LHA  + L HP  G R+   A
Sbjct: 260 RTHQIRVHCAHINHPVVGDPTYSRCRKLPLDLPGQA---LHAVQLGLDHPITGERMVFEA 316

Query: 310 PLPAHMVK 317
           PLP  M K
Sbjct: 317 PLPPVMEK 324


>gi|225378086|ref|ZP_03755307.1| hypothetical protein ROSEINA2194_03746 [Roseburia inulinivorans DSM
           16841]
 gi|225210087|gb|EEG92441.1| hypothetical protein ROSEINA2194_03746 [Roseburia inulinivorans DSM
           16841]
          Length = 303

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 99/328 (30%), Positives = 160/328 (48%), Gaps = 50/328 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPP 69
           VE + E  RLD++    +P  +    QK+++ G V V+ K  K N R+++  +V   IP 
Sbjct: 8   VEYEYEGERLDKYVSILFPEQSRSFFQKLIKDGNVSVNDKVQKANYRLKTEDLVTVEIPD 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
            +        E +IL   + L          +LYED  + V NKP G+ V   +G     
Sbjct: 68  AV--------ETQILPEDIPLD---------ILYEDDDLLVVNKPKGMVVHPSAGHYSGT 110

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               I YH    L S ++ +  +P + HR+D +T+G L+V +   +   + E  +   + 
Sbjct: 111 LVNAIMYHCKDSL-SGINGE-IRPGIVHRIDMDTTGSLIVCKNDESHVFIAEQIKEHSVN 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQ 238
           + Y  +V+G+ ++ +  I       + IG   V   K   NEK    AI+H+KV++ F  
Sbjct: 169 RRYRGIVYGVVRDDEGTI------HAPIGRHPVDRKKMAINEKNGKDAITHYKVLERF-D 221

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMD 296
           K+ ++E +  TGRTHQ+RVH   +G P++GD  Y      N  SP  +Q +  LHA  + 
Sbjct: 222 KYTYMEFKLETGRTHQIRVHMASIGHPLLGDTLYS-----NGKSPYKLQGQT-LHAMTIG 275

Query: 297 LPHPEGGR--LQITAPLPAHMVKTWDSL 322
             HP G R  ++I+APLP +  K    L
Sbjct: 276 FIHP-GTREYMEISAPLPEYFEKILRDL 302


>gi|281413199|ref|YP_003347278.1| pseudouridine synthase, RluA family [Thermotoga naphthophila
           RKU-10]
 gi|281374302|gb|ADA67864.1| pseudouridine synthase, RluA family [Thermotoga naphthophila
           RKU-10]
          Length = 304

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 97/317 (30%), Positives = 148/317 (46%), Gaps = 42/317 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHII 78
           RLD++ +N    +    + K++R G+V V+KKRVK  +  ++ G VV +   +N  N   
Sbjct: 13  RLDKFLRNQLKDVPLSVIYKLIRKGKVYVNKKRVKDPSFELEEGDVVELR-YVNLENLPK 71

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSW 136
           + +K   + V +       K  +LYED    V NKP  I++  G G+  A  I+G L  +
Sbjct: 72  RSEKKDLTPVPM-------KLDVLYEDDHYLVLNKPPNIAIHPGKGVHVATLIEGLL-HY 123

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              KG  P L HRLD++TSG+LVVA+ R AA+ LTE F+ R I+K Y +LV G+P+N  +
Sbjct: 124 GQEKGFSPFLVHRLDKDTSGLLVVAKNREAARILTELFKGRNIEKEYVTLVRGVPENNMK 183

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                                        A+S    +    +    L ++ HTGR HQ+R
Sbjct: 184 LTIPL--------------------DGQEAVSEIVSVKPL-KDVSLLRVKIHTGRKHQIR 222

Query: 257 VHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
            H   +G P+VGD  Y        F+  +    Q   +LH+  M    P         AP
Sbjct: 223 RHLSQIGFPVVGDDTYGDRHFNIEFRKRYGLKRQ---FLHSYRMKFIDPWTEEEKDFRAP 279

Query: 311 LPAHMVKTWDSLGFKYD 327
           LP  ++   + L  + D
Sbjct: 280 LPDDLLSVLNLLKERSD 296


>gi|320102981|ref|YP_004178572.1| RluA family pseudouridine synthase [Isosphaera pallida ATCC 43644]
 gi|319750263|gb|ADV62023.1| pseudouridine synthase, RluA family [Isosphaera pallida ATCC 43644]
          Length = 432

 Score =  120 bits (300), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 91/334 (27%), Positives = 157/334 (47%), Gaps = 42/334 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIP 68
           VV++  E  RLD +  + +P  +   +QK++ +  V V+ K  + + +++ G  V  R+P
Sbjct: 99  VVKSKLEGRRLDTYLTSRFPDYSRSVIQKVIDANAVMVNGKPARASQKVREGDFVSLRLP 158

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AY 127
            + +          I    + LT         ++YED  + + +KPAG+    G G  + 
Sbjct: 159 ELWDG--------TIPAQDIPLT---------VIYEDQWLSIIDKPAGMVTHPGKGNWSG 201

Query: 128 HIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +   L+   D+  Q     +P + HRLD++T+G+L+VAR       L + F  R I+K 
Sbjct: 202 TVVNALQHRYDTLSQLAGSTRPGVVHRLDRDTTGLLIVARDDTIHGKLAQLFETRTIEKE 261

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++  GIP+  ++ I   L    H        ++    G   A + ++V++ F  +F  
Sbjct: 262 YLAICSGIPERDRDWIDQPL--GPHPTVREKMAIRGEADGGRPARTFYEVVERF-DRFAL 318

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTS----------PIQNKLY 289
           +  QP TGRTHQ+RVH  H+G PI+ D  Y       +G+              +  +  
Sbjct: 319 VRCQPLTGRTHQIRVHLTHVGLPILADKLYSGRDRITRGDLLGWQARGDDHDHVLLTRQA 378

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           LHA  +   HP  G  L+I +PLP  M +T ++L
Sbjct: 379 LHAHRLKFLHPATGEPLEIRSPLPPDMAETLETL 412


>gi|86132824|ref|ZP_01051415.1| pseudouridine synthase, RluA family [Dokdonia donghaensis MED134]
 gi|85816530|gb|EAQ37717.1| pseudouridine synthase, RluA family [Dokdonia donghaensis MED134]
          Length = 347

 Score =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 95/338 (28%), Positives = 157/338 (46%), Gaps = 71/338 (21%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  N   +     +QK  ++G ++V+ K VK N ++++G VVR         
Sbjct: 28  QEPLRVDKFLMNFVENATRNKIQKAAKNGSIQVNNKVVKQNYKVKAGDVVRA-----MFE 82

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           H   E  +    + L          ++YED  + V NKPAG+ V  G G         + 
Sbjct: 83  HPPHEFLLTPEDIPLD---------IIYEDDDLLVVNKPAGMVVHPGHGNYSGTLINALI 133

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +HID    +  ++  ++P L HR+D++TSG+LVVA+T  A  HL++ F  +  ++ Y ++
Sbjct: 134 HHID----NLPNNSSERPGLVHRIDKDTSGLLVVAKTEHAMTHLSKQFFNKTTEREYVAI 189

Query: 187 VWG------------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           VWG            I ++ K  + N + K               E+    A++H+KV++
Sbjct: 190 VWGNVVDDEGTIEGNIGRHPKNRLQNTVFKDD------------EEEQGKPAVTHYKVLE 237

Query: 235 CFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS------ 282
                 Q  C LE    TGRTHQ+RVH  ++G  +  D +Y  N   KG +FT       
Sbjct: 238 RLGYVTQVACKLE----TGRTHQIRVHMKYIGHTLFNDERYGGNAILKGTSFTKYKQFVE 293

Query: 283 ---PIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMV 316
               I  +  LHA+ +   HP  G  +    P+P  M 
Sbjct: 294 NCFKILPRQALHAKTLGFVHPTTGEYKRFETPVPEDMA 331


>gi|225567968|ref|ZP_03776993.1| hypothetical protein CLOHYLEM_04041 [Clostridium hylemonae DSM
           15053]
 gi|225163256|gb|EEG75875.1| hypothetical protein CLOHYLEM_04041 [Clostridium hylemonae DSM
           15053]
          Length = 304

 Score =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 96/331 (29%), Positives = 161/331 (48%), Gaps = 48/331 (14%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV--V 65
           ++  VEN EE  R+DR+        +   +QK+++   + V+ K VK N R+  G +  V
Sbjct: 3   EFFTVEN-EEGERIDRYLAEMLSDRSRSYIQKLIKDSHILVNNKPVKANYRLSCGDMLEV 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            IP          KE  IL   + L          +LYED+ I + NKP  + V    G 
Sbjct: 62  TIPSA--------KEPDILPEDIPLH---------ILYEDADIIIVNKPKQMVVHPAPG- 103

Query: 126 AYHIDGFLKSWV------DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             H  G L + +      +  G     +P + HR+D +T+G L+V +   A Q L+E  +
Sbjct: 104 --HYSGTLVNALMFHCGRELSGINGMMRPGIVHRIDMDTTGSLIVCKNDMAHQALSEQLK 161

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I++IY ++V G  K ++  ++  + +           +  + K A  A++H+KV++ 
Sbjct: 162 KHSIRRIYEAVVHGGFKEEEGTVSAPIGRHP----TDRKRMSTHAKNAREAVTHYKVLER 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQNKLYLHA 292
           F + + +++ +  TGRTHQ+RVH   +G PIVGD  Y      F G     +Q +  LHA
Sbjct: 218 FGE-YSYIQCELETGRTHQIRVHMSSIGHPIVGDMVYGPRRCPFPG-----LQGQT-LHA 270

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + + + HP  G  L++ APLP + V+  + L
Sbjct: 271 KTLGIIHPRTGEYLEVEAPLPQYFVELLEKL 301


>gi|55980377|ref|YP_143674.1| ribosomal large subunit pseudouridine synthase D [Thermus
           thermophilus HB8]
 gi|55771790|dbj|BAD70231.1| ribosomal large subunit pseudouridine synthase D [Thermus
           thermophilus HB8]
          Length = 308

 Score =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 80/244 (32%), Positives = 121/244 (49%), Gaps = 32/244 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVD--SKGQ----KPRLTHRLDQ 152
           +LYED  +   NKP G+      G+     ++  L  +     KG     +P + HRLD+
Sbjct: 74  ILYEDEDVLALNKPPGLLTHPAPGVYSGTVVNLLLARYYGPVEKGPPELVRPGIVHRLDK 133

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-----LLKKSH 207
           +TSG+LVVA+     + L  +FR R + K Y ++  G P+     IA          K H
Sbjct: 134 DTSGVLVVAKHGGVLEGLARAFRDRLVMKRYLAITEGHPREGV-LIAPIGRHPRERHKMH 192

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +GG            A YA + F+V+   A  +  +E +PHTGRTHQ+RVH  ++G PI+
Sbjct: 193 VGG----------LAARYAETEFQVL-ATAGPYALVEARPHTGRTHQIRVHLKYLGAPIL 241

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           GD  Y         SP   +  LHA  + +PHP  GR L++ AP+P  M   W++LG ++
Sbjct: 242 GDELY------GRKSPHIGRQALHAYELRIPHPRTGRILELLAPVPQDMAAAWEALGGRW 295

Query: 327 DRNL 330
              +
Sbjct: 296 PEEV 299


>gi|312903470|ref|ZP_07762650.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
 gi|310633346|gb|EFQ16629.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
 gi|315577834|gb|EFU90025.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0630]
          Length = 310

 Score =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 157/319 (49%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 20  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 73

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                E ++LD        ++ +   ++YED+ + V NKP G+ V   +G         +
Sbjct: 74  -----EPEVLDMI------AEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNAL 122

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H D  L +  D    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 123 LHHAD-HLSAINDVV--RPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 179

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 180 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 233 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 287

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 288 QLVFEAPLPEVFEKTLHQL 306


>gi|332799431|ref|YP_004460930.1| pseudouridine synthase, RluA family [Tepidanaerobacter sp. Re1]
 gi|332697166|gb|AEE91623.1| pseudouridine synthase, RluA family [Tepidanaerobacter sp. Re1]
          Length = 308

 Score =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 101/315 (32%), Positives = 153/315 (48%), Gaps = 38/315 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVRIPP 69
            V  D+E  RLD +  +         L+K +  G ++V+   VK N R+ Q  Q++   P
Sbjct: 8   TVTRDDEKKRLDIFLADKLQDSRSF-LKKGIVEGWIKVNGSIVKPNYRLRQEDQIIVTVP 66

Query: 70  VINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
              AL  +I  + I LD               +++ED  I V NKP G+ V    G    
Sbjct: 67  --QALQPLIDPEDIPLD---------------IIFEDRDIVVINKPRGMVVYPAPGNYSG 109

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             I+  L    D   +    +P + HRLD++TSG++VVA+   A  +L++  + R ++K+
Sbjct: 110 TLINALLNHTKDLSARGGTMRPGIVHRLDKDTSGVIVVAKNDTAHINLSKQLKSREVKKV 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +  K  I N  + +  I    + V  +N K    AI+HFKV++ F + F +
Sbjct: 170 YQTLVWGKVQEDKATI-NAPIGRHPIKRKEMAVTTKNSK---EAITHFKVLERFDE-FTF 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHPE 301
           LE+   TGRTHQ+RVH   +G PIVGD  Y          P + K   LHA  +   HP 
Sbjct: 225 LEVAIETGRTHQIRVHMKFIGHPIVGDPIYSRK-----KVPFEIKGQALHAYKLGFCHPS 279

Query: 302 GGR-LQITAPLPAHM 315
             + ++  APLP  M
Sbjct: 280 NNQYMEFEAPLPDDM 294


>gi|319405172|emb|CBI78777.1| ribosomal large subunit pseudouridine synthase D [Bartonella sp. AR
           15-3]
          Length = 333

 Score =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 95/346 (27%), Positives = 159/346 (45%), Gaps = 48/346 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            Q++  EN     R+D+W    Y   ++   LQ ++R G +++D            GQ++
Sbjct: 2   AQHITNEN-ACGQRIDQWLAKQYKEELSRSRLQTLIREGYLKID------------GQLI 48

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           + P +    N II  +  + +  +     + L   +L+ED+ + V NKPAG+ V  G+G 
Sbjct: 49  KEPKIKLKSNQII--ELTIPTPNDARPQGEALALDILFEDNHVIVINKPAGLVVHPGNGN 106

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF-- 174
                   + YH    L      K  +P + HRLD++TSG++V+A+   A ++L   F  
Sbjct: 107 WTGTLVNALIYHCSDSLSGIGGIK--RPGIVHRLDKDTSGVMVIAKNDLAHRNLNAQFAD 164

Query: 175 --RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
             R   + + Y +++WG P N+     +  L +S        VV      A  AI+HF +
Sbjct: 165 HGRTSALDRRYHAVIWGSP-NRNIVTIDTFLARSSRDRTKRSVVHSEHAHARRAITHFSL 223

Query: 233 IDCFA------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSP- 283
           ++ +            LE +  TGRTHQ+RVH  H+G P++GD  Y   F  K N   P 
Sbjct: 224 LEKYGACNDATSLASLLECRLETGRTHQIRVHMAHIGHPLIGDKVYGNAFKTKSNTLDPE 283

Query: 284 IQ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           I+      N+  LHA  +   HP   + +  ++P P  +    +SL
Sbjct: 284 IKNIIDQFNRQALHATSLTFEHPANRKIMSFSSPFPKDLTNLINSL 329


>gi|126664287|ref|ZP_01735278.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BAL38]
 gi|126623707|gb|EAZ94404.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BAL38]
          Length = 346

 Score =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 86/316 (27%), Positives = 153/316 (48%), Gaps = 43/316 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D++  N   +     +Q+   +G + V+   VK N ++++G VVR+      L H  
Sbjct: 29  LRVDKFLMNMIENTTRNKIQQAAENGSILVNDVAVKSNYKVKAGDVVRL-----VLAHPT 83

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            EQ +   ++ L          ++YED ++ V NKPAG+ V  G G         +AYH 
Sbjct: 84  YEQLLTPENIPLD---------IVYEDDQLLVINKPAGMVVHPGHGNYSGTLVNALAYHF 134

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +    +      ++P L HR+D++T+G+LVVA+T  A  +L++ F  +  ++ Y +LVWG
Sbjct: 135 ENLPMN----SSERPGLVHRIDKDTTGLLVVAKTELAMAYLSKQFAEKTSEREYVALVWG 190

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +  +  +   + +  H        V ++++    A++H+KV++ F      +  Q  T
Sbjct: 191 NIEEDEGTVEGNIGR--HDTNRMRMAVHESDEKGKPAVTHYKVLERFGY-VTLVSCQLET 247

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---------PIQNKLYLHARYMDL 297
           GRTHQ+RVH  H+G  +  D +Y  +   KG  FT           +  +  LHA+ +  
Sbjct: 248 GRTHQIRVHMKHIGHTLFNDERYGGDSILKGTTFTKYKQFVDNCFKVLPRQALHAKTLGF 307

Query: 298 PHPEGGR-LQITAPLP 312
            HP     L+   P+P
Sbjct: 308 EHPITKEFLRFNTPIP 323


>gi|288553139|ref|YP_003425074.1| large ribosomal pseudouridine synthesis protein [Bacillus
           pseudofirmus OF4]
 gi|288544299|gb|ADC48182.1| large ribosomal pseudouridine synthesis protein [Bacillus
           pseudofirmus OF4]
          Length = 304

 Score =  119 bits (299), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 92/322 (28%), Positives = 160/322 (49%), Gaps = 38/322 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SG 62
           M  +Q+ ++E ++ N R+D++        +   +Q+ ++ GQV+V+ K  K N ++Q   
Sbjct: 1   MEEIQWTILEENK-NERIDKFLTAQNGEWSRSQVQQWIKDGQVQVNGKATKSNYKMQVED 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           QV    P    L+ +I E   LD               ++YED+ + V NKP G+ V   
Sbjct: 60  QVTLSIPEPEELD-VIAEDIPLD---------------VVYEDADVIVVNKPRGMVVHPA 103

Query: 123 SG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L    + 
Sbjct: 104 PGHYTGTLVNALLYHCKDLSGINGVIRPGIVHRIDKDTSGLLMVAKNDHAHESLVSQLKA 163

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV--HVVKQNEKGANYAISHFKVID 234
           +  ++ Y ++V G+  ++   I      ++ IG D      +   E  +  A++HF V++
Sbjct: 164 KTTKRHYKAIVHGVIPHQHGTI------EAPIGRDKKDRQSMTVTEDNSRDAVTHFTVLE 217

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
           CF + F +++ +  TGRTHQ+RVH  ++G P+ GD KY    K   T  I+ +  LHA  
Sbjct: 218 CF-KDFTYVQCELETGRTHQIRVHMKYIGYPLAGDPKYGPKKK---TLEIEGQA-LHAAT 272

Query: 295 MDLPHPEGG-RLQITAPLPAHM 315
           +   HP  G  L+ +AP+P  M
Sbjct: 273 LGFTHPRTGEELEFSAPIPEDM 294


>gi|46198348|ref|YP_004015.1| ribosomal large subunit pseudouridine synthase D [Thermus
           thermophilus HB27]
 gi|46195970|gb|AAS80388.1| ribosomal large subunit pseudouridine synthase D [Thermus
           thermophilus HB27]
          Length = 300

 Score =  119 bits (299), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 80/244 (32%), Positives = 121/244 (49%), Gaps = 32/244 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVD--SKGQ----KPRLTHRLDQ 152
           +LYED  +   NKP G+      G+     ++  L  +     KG     +P + HRLD+
Sbjct: 66  ILYEDEDVLALNKPPGLLTHPAPGVYSGTVVNLLLARYYGPVEKGPPELVRPGIVHRLDK 125

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-----LLKKSH 207
           +TSG+LVVA+     + L  +FR R + K Y ++  G P+     IA          K H
Sbjct: 126 DTSGVLVVAKHGGVLEGLARAFRDRLVMKRYLAITEGHPREGV-LIAPIGRHPRERHKMH 184

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +GG            A YA + F+V+   A  +  +E +PHTGRTHQ+RVH  ++G PI+
Sbjct: 185 VGG----------LAARYAETEFQVL-ATAGPYALVEARPHTGRTHQIRVHLKYLGAPIL 233

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           GD  Y         SP   +  LHA  + +PHP  GR L++ AP+P  M   W++LG ++
Sbjct: 234 GDELY------GRKSPHIGRQALHAYELRIPHPRTGRILELLAPVPQDMAAAWEALGGRW 287

Query: 327 DRNL 330
              +
Sbjct: 288 PEEV 291


>gi|332292606|ref|YP_004431215.1| pseudouridine synthase, RluA family [Krokinobacter diaphorus
           4H-3-7-5]
 gi|332170692|gb|AEE19947.1| pseudouridine synthase, RluA family [Krokinobacter diaphorus
           4H-3-7-5]
          Length = 347

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 92/330 (27%), Positives = 153/330 (46%), Gaps = 47/330 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  N   +     +QK  ++G ++V+   VK N ++++G VVR         
Sbjct: 28  QEPLRVDKFLMNFVENATRNKIQKAAKNGSIQVNNIVVKQNYKVKAGDVVRA-----MFE 82

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           H   E  +    +++          ++YED ++ V NKPAG+ V  G G         + 
Sbjct: 83  HPPHEFLLTPEDIDID---------VVYEDDQLMVVNKPAGMVVHPGHGNYSGTLINALI 133

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +H+D    +  D    +P L HR+D++TSG+LVVA+T  A  HL++ F  +  ++ Y ++
Sbjct: 134 HHVDNLPNNSSD----RPGLVHRIDKDTSGLLVVAKTEQAMTHLSKQFFNKTTEREYVAI 189

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWL 243
           VWG   + +  I   + +             ++E     A++H+KVI+         C L
Sbjct: 190 VWGNVVDDEGTIEGNIGRHPKNRLQNTVFYGEDEDQGKPAVTHYKVIERLGYVTLVSCKL 249

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---------PIQNKLYLH 291
           E    TGRTHQ+RVH  H+G  +  D +Y  N   KG  FT           I  +  LH
Sbjct: 250 E----TGRTHQIRVHMKHIGHTLFNDERYGGNAILKGTTFTKYKQFVDNCFKILPRQALH 305

Query: 292 ARYMDLPHPEGGRLQ-ITAPLPAHMVKTWD 320
           A+ +   HP  G  +    P+P  M    D
Sbjct: 306 AKTLGFVHPTTGEYKRFETPVPEDMTGCID 335


>gi|257087008|ref|ZP_05581369.1| pseudouridylate synthase [Enterococcus faecalis D6]
 gi|256995038|gb|EEU82340.1| pseudouridylate synthase [Enterococcus faecalis D6]
          Length = 301

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 94/319 (29%), Positives = 155/319 (48%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 11  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                E ++LD        ++ +   ++YED+ + V NKP G+ V    G   H +G L 
Sbjct: 65  -----EPEVLDMV------AEDIPLTIVYEDNDVIVVNKPQGMVVHPSVG---HPNGTLV 110

Query: 135 SWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + +              +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 111 NALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 170

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 171 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 224 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 278

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 279 QLVFEAPLPEVFEKTLHQL 297


>gi|108759922|ref|YP_634049.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108463802|gb|ABF88987.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 318

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 89/316 (28%), Positives = 157/316 (49%), Gaps = 26/316 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E D   MRLD+  +   P++   +L K++R+ +VRV+ KR +    +  G V+ I    
Sbjct: 6   IEADTAGMRLDKHLRKRLPNVPVSHLFKMIRTKKVRVNGKRAQPEQLLSEGDVLTIR--- 62

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHID 130
                ++  ++              L  ++L ED  +   +KP+G++V  GSGI    + 
Sbjct: 63  GDEQQLVGAERPKVDPPPPPVDPSRL--VILREDDWLMAVDKPSGMAVHTGSGITGGTLV 120

Query: 131 GFLKSWVDSKGQKPRLT----HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++++++  K  +        HRLD+ETSG+++VA+ R A  H TE F     +K Y +L
Sbjct: 121 DYVRAYLGPKAVRNDFAASPAHRLDRETSGVILVAKRRPAMVHFTEVFTHGLSRKRYLTL 180

Query: 187 VWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQKFCWL 243
           V G +P++    + +  L +     +      +  +G N   A++ +KV+   ++    L
Sbjct: 181 VKGKMPRD--SGVIDLPLSEHQQTAE-----SKARRGVNMQAAVTRWKVVKQSSEA-ALL 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP 300
                TGRTHQ+R H   +G P+ GD KY  +F  N     +    +L+LHA  ++ PHP
Sbjct: 233 SCAIETGRTHQIRRHLAAIGHPVAGDKKY-GDFAFNRDVRARWGLKRLFLHAERIEFPHP 291

Query: 301 EGG-RLQITAPLPAHM 315
           EGG ++ + APL   +
Sbjct: 292 EGGAKVAVEAPLAVEL 307


>gi|304437216|ref|ZP_07397176.1| ribosomal large subunit pseudouridine synthase D [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369708|gb|EFM23373.1| ribosomal large subunit pseudouridine synthase D [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 300

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 95/327 (29%), Positives = 153/327 (46%), Gaps = 53/327 (16%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVI 71
           +D+   RLD +     P ++    Q+++  G V VD +R K N ++  G+ V   IPP  
Sbjct: 6   SDQAGERLDVFLVRQLPTLSRSYAQRLVAEGHVTVDGERRKANFKLSGGESVACTIPPA- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                  +  +I   ++ L          +LYED+ I V NKP G+ V   +G+     +
Sbjct: 65  -------EAVEIRAENIPLN---------VLYEDADIIVINKPRGMVVHPAAGVYTGTLV 108

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HRLD++TSG++V A+   A   L    R +  ++ Y +
Sbjct: 109 NALLHHCSDLSGINGDLRPGIVHRLDKDTSGVMVAAKNDMAHHFLARQIRDKEARREYRA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDY---------VHVVKQNEKGANYAISHFKVIDCF 236
           +V+G          N + +   I GD          + +V++N K A    +HF+V++ F
Sbjct: 169 IVYG----------NIVERAGVITGDIGRHPTDRKKMAIVRENGKPAT---THFEVLERF 215

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              + ++  +  TGRTHQ+RVH   +G P+VGD KY A  K  F    Q    LH+  + 
Sbjct: 216 GD-YTFVACRLETGRTHQIRVHMTSIGHPLVGDTKYTAK-KNPFAIAGQ---ALHSLTLT 270

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWDSL 322
           L HP     +  TAPL A M +   +L
Sbjct: 271 LTHPRTQAEMTFTAPLSADMDEILHTL 297


>gi|78189580|ref|YP_379918.1| pseudouridine synthase, RluD [Chlorobium chlorochromatii CaD3]
 gi|78171779|gb|ABB28875.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           chlorochromatii CaD3]
          Length = 363

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 91/345 (26%), Positives = 154/345 (44%), Gaps = 65/345 (18%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---- 67
           V   +  MR+D +      +     +Q+ +  G+V V+ K VK N R++S  V+ +    
Sbjct: 41  VSRTQSPMRIDVYLTQQVENATRNKVQEAIEEGRVVVNGKCVKANYRLKSCDVIEVTFLR 100

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
           PP            ++   ++ +          ++YED  + V NK  G+ V    G   
Sbjct: 101 PPA----------PELAPEAIPIA---------IMYEDDDLMVINKEPGMVVHPAFGNWT 141

Query: 125 ------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 I +H+ G     +D+   +P + HRLD++TSG++++A+   A   L   F  R+
Sbjct: 142 GTLANAILHHL-GNSAEALDASEMRPGIVHRLDKDTSGLIIIAKNPIALHKLARQFAERK 200

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK----VID 234
           + KIY +L WG+PK     I       ++IG  +    K  +  AN+     +    + D
Sbjct: 201 VGKIYKALTWGVPKQASGTIT------TNIGRSH----KNRKVMANFPFEGLEGKTAITD 250

Query: 235 -CFAQKFCW---LEMQPHTGRTHQLRVHALHMGCPIVGDHKY------------CANFKG 278
            C  +   W   + ++ HTGRTHQ+RVH  H+G PIVGD  Y              +F  
Sbjct: 251 YCVEENLEWFSVMSLRLHTGRTHQIRVHLQHLGLPIVGDVTYGGATPRALPFSKSEHFVK 310

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           N    +  +  LHA  +   HP  G  + ++APLP  M++  + +
Sbjct: 311 NLLE-LLPRQALHAETLTFHHPTTGEEITLSAPLPEDMLQALEKI 354


>gi|170744872|ref|YP_001773527.1| RluA family pseudouridine synthase [Methylobacterium sp. 4-46]
 gi|168199146|gb|ACA21093.1| pseudouridine synthase, RluA family [Methylobacterium sp. 4-46]
          Length = 336

 Score =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 96/335 (28%), Positives = 152/335 (45%), Gaps = 56/335 (16%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHII 78
           RLDR     +P ++   LQ ++R G VR+D   ++    ++  GQ V +           
Sbjct: 18  RLDRALARLWPDLSRNRLQGLIREGGVRLDGAEIRDGAVKVAGGQRVAV----------- 66

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----- 133
                +  ++  T  +      ++YED  + V +KPAG+ V    G   H DG L     
Sbjct: 67  ----AVPQALPATPAAQARDLAIVYEDDDLIVIDKPAGLVVHPAPG---HPDGTLVNALI 119

Query: 134 ----KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYW 184
                S     G ++P + HRLD++TSG+LVVA+   A   L+  F    R   +++ Y 
Sbjct: 120 AHCGASLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHAGLSLQFADHGRSGMLERAYL 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK------VIDCFAQ 238
           +LVWG+P  +   I +  L +S    + + VV+  +    +A++H++        +   Q
Sbjct: 180 ALVWGVPAPRNGTI-DAALARSERNREKIAVVRPEQ--GRHAVTHYRTEAVLGAREPVGQ 236

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSP-------IQNKLY 289
             C LE    TGRTHQ+RVH  H G P++GD  Y A F  K     P          +  
Sbjct: 237 IRCRLE----TGRTHQIRVHLAHRGHPLLGDRTYGAAFRTKAARLDPEAREALDALGRQA 292

Query: 290 LHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           LHA  +   HP     L+  +PLPA + +   +LG
Sbjct: 293 LHAAVLGFVHPRSHAVLRFESPLPADLARLVAALG 327


>gi|193212389|ref|YP_001998342.1| pseudouridine synthase, RluA family [Chlorobaculum parvum NCIB
           8327]
 gi|193085866|gb|ACF11142.1| pseudouridine synthase, RluA family [Chlorobaculum parvum NCIB
           8327]
          Length = 349

 Score =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 87/323 (26%), Positives = 148/323 (45%), Gaps = 49/323 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI----PPVINAL 74
           MR+DR+      ++    +Q  +  G+V V+ K VK N R++S   + +    PP     
Sbjct: 34  MRIDRYLTQQVENMTRNKVQAAIEEGRVLVNGKPVKSNYRVKSCDHIHLTFLRPPA---- 89

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                  ++    + +T         +LYED  + V +K AG+ V    G         I
Sbjct: 90  ------PELAPEDIPIT---------ILYEDDDLMVIDKEAGMVVHPAFGNWTGTLANAI 134

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H+ G     +D    +P + HRLD++TSG++++A+   A   L   F  R+++K+Y +
Sbjct: 135 LHHL-GKDADELDKTEMRPGIVHRLDKDTSGLIIIAKNPTALHKLARQFANRQVEKVYKA 193

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +VWG+PK +   I    + +SH     +           +AI+ ++V++     F  +++
Sbjct: 194 IVWGVPKAESGTIKTN-IGRSHKNRKVMANFPYEGAEGKHAITDYQVVEDLGY-FSLMDV 251

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY------------CANFKGNFTSPIQNKLYLHAR 293
             HTGRTHQ+RVH  H+G  I+GD  Y               F  N    + ++  LHA+
Sbjct: 252 TLHTGRTHQIRVHLQHLGHSILGDETYGGATPRTLPFSKSEPFTRNLLE-LMSRQALHAQ 310

Query: 294 YMDLPHPEGGR-LQITAPLPAHM 315
            +    P  G  L  +APLP  M
Sbjct: 311 TLRFRQPTTGEPLSFSAPLPEDM 333


>gi|294011927|ref|YP_003545387.1| ribosomal large subunit pseudouridine synthase D [Sphingobium
           japonicum UT26S]
 gi|292675257|dbj|BAI96775.1| ribosomal large subunit pseudouridine synthase D [Sphingobium
           japonicum UT26S]
          Length = 320

 Score =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 87/342 (25%), Positives = 164/342 (47%), Gaps = 45/342 (13%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV----DKKRVKFN 56
           +S ++ ++  + E  ++ MRLD+      P ++   L+ ++  GQV        +    +
Sbjct: 2   VSGVSIIEATIGEA-QDGMRLDKALAELVPDLSRERLKALIAEGQVTGRPAHAGRSPNPS 60

Query: 57  NRIQSGQVVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
            ++ +GQ   I  PP +        E + +   + L          +++ED+ + V +KP
Sbjct: 61  MKVAAGQAFAIVLPPPM--------EAEAVAQDIPLA---------IVHEDADLIVIDKP 103

Query: 115 AGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
           AG+ V   +G         + +H  G L         +P + HR+D++TSG+LVVA++  
Sbjct: 104 AGLVVHPAAGNLDGTLVNALLHHCQGRLSGI--GGVARPGIVHRIDKDTSGLLVVAKSDR 161

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           A + L + F+   I ++Y ++V+G+P+     + +W+ +      D   +    E    +
Sbjct: 162 AHEGLAQQFKAHSIDRLYAAIVYGVPQPAAGTVDSWIGRSD---ADRKKMAVHREGRGKH 218

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           A++H++ ++   +    +E +  TGRTHQ+RVH  H+G P++GD  Y    KG F S ++
Sbjct: 219 AVTHYRTMERL-RGAAMVECRLETGRTHQVRVHMAHLGHPLIGDPVYGRERKG-FKSILE 276

Query: 286 ----NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
               N+  LHA+ +   HP  G  L   + LPA M +    L
Sbjct: 277 TLGFNRQALHAKRLGFIHPVTGEALSFDSKLPADMQELLSEL 318


>gi|3915406|sp|O50310|Y723_CHLP8 RecName: Full=Uncharacterized RNA pseudouridine synthase Cpar_0723;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2661852|emb|CAB06297.1| hypothetical protein [Prosthecochloris vibrioformis]
          Length = 327

 Score =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 87/323 (26%), Positives = 148/323 (45%), Gaps = 49/323 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI----PPVINAL 74
           MR+DR+      ++    +Q  +  G+V V+ K VK N R++S   + +    PP     
Sbjct: 12  MRIDRYLTQQVENMTRNKVQAAIEEGRVLVNGKPVKSNYRVKSCDHIHLTFLRPPA---- 67

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                  ++    + +T         +LYED  + V +K AG+ V    G         I
Sbjct: 68  ------PELAPEDIPIT---------ILYEDDDLMVIDKEAGMVVHPAFGNWTGTLANAI 112

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H+ G     +D    +P + HRLD++TSG++++A+   A   L   F  R+++K+Y +
Sbjct: 113 LHHL-GKDADELDKTEMRPGIVHRLDKDTSGLIIIAKNPTALHKLARQFANRQVEKVYKA 171

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +VWG+PK +   I    + +SH     +           +AI+ ++V++     F  +++
Sbjct: 172 IVWGVPKAESGTIKTN-IGRSHKNRKVMANFPYEGAEGKHAITDYQVVEDLGY-FSLMDV 229

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN------------FKGNFTSPIQNKLYLHAR 293
             HTGRTHQ+RVH  H+G  I+GD  Y               F  N    + ++  LHA+
Sbjct: 230 TLHTGRTHQIRVHLQHLGHSILGDETYGGATPRTLPFSKSEPFTRNLLE-LMSRQALHAQ 288

Query: 294 YMDLPHPEGGR-LQITAPLPAHM 315
            +    P  G  L  +APLP  M
Sbjct: 289 TLRFRQPTTGEPLSFSAPLPEDM 311


>gi|254473085|ref|ZP_05086483.1| ribosomal large subunit pseudouridine synthase D [Pseudovibrio sp.
           JE062]
 gi|211957806|gb|EEA93008.1| ribosomal large subunit pseudouridine synthase D [Pseudovibrio sp.
           JE062]
          Length = 349

 Score =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 92/342 (26%), Positives = 159/342 (46%), Gaps = 50/342 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           +  E ++   RLD     H    +   LQ ++R+GQV++ ++ V +   R+ +G  + + 
Sbjct: 26  ITPEPEDTGRRLDAVLAAHIDDFSRNRLQALIRAGQVQIGQRTVLEPKYRVCAGDTITL- 84

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
                   I+ E +  +         + +   ++YED  + V +KPAG+ V  G+G    
Sbjct: 85  --------IVPEPEAAEP------QPEDIPLTIVYEDEDLIVIDKPAGLVVHPGAGNPTG 130

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF----R 175
                + +H    L      K  +P + HR+D++T+G+LV+A+   A Q L   F    R
Sbjct: 131 TLVNALIHHCGSSLSGIGGVK--RPGIVHRIDKDTTGLLVIAKNDMAHQGLAAQFADHGR 188

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              +++ Y +LVWG P   K  + +  L +S      + V+K    G  +AI+H++V + 
Sbjct: 189 TGPLERAYKALVWGAPTAAKGTV-DANLARSTANRQKISVLK---TGGRHAITHWQVQER 244

Query: 236 F-----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQNK 287
           F     A     +E +  TGRTHQ+RVH  H+G P++GD  Y + F+     F  P++ +
Sbjct: 245 FGPQDEAAVASLIECRLETGRTHQIRVHMSHIGNPLIGDMDYGSGFRTKYNKFHEPLKTQ 304

Query: 288 L------YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           L       LHA  +   HP     ++  + LPA       SL
Sbjct: 305 LAEFKRQALHAGLLAFAHPRTQEFMKFESELPADFAGILQSL 346


>gi|257439373|ref|ZP_05615128.1| ribosomal large subunit pseudouridine synthase C [Faecalibacterium
           prausnitzii A2-165]
 gi|257198248|gb|EEU96532.1| ribosomal large subunit pseudouridine synthase C [Faecalibacterium
           prausnitzii A2-165]
          Length = 316

 Score =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 71/263 (26%), Positives = 130/263 (49%), Gaps = 19/263 (7%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD +    +P +N   L K LR  +++++ K+   + R+ +G  +++      L+ ++ 
Sbjct: 13  RLDNYLMQQFPALNPGRLNKALRENKIKLNGKKQPLSTRVMAGDEIKL----FILDEVLD 68

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             K ++             + ++Y+  +I V NKPAG++V G           L  +++ 
Sbjct: 69  ADKRVEGPAWKNARG---PAQVIYDCPQILVVNKPAGLAVDGPEDDTLLNRALL--YLNQ 123

Query: 140 KGQ-------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +G+        P L HRLD  TSG++++A+T  A Q   E  + R ++K Y  + +G P 
Sbjct: 124 QGEYKENDLYTPALCHRLDTGTSGLVIIAKTPEAEQLFLEVIKNREVKKTYLCVTFGRPT 183

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                +  +LLK +  G   V +V   + GA    + ++ +   + +   L+++  TGRT
Sbjct: 184 PPDGTLGGYLLKDADRG--IVKIVPDKQPGAKDVETQYETV-AVSGRLALLKVRLITGRT 240

Query: 253 HQLRVHALHMGCPIVGDHKYCAN 275
           HQ+R H   +GCPI+GD KY  N
Sbjct: 241 HQIRAHMASIGCPILGDSKYGNN 263


>gi|56964104|ref|YP_175835.1| pseudouridine synthase [Bacillus clausii KSM-K16]
 gi|56910347|dbj|BAD64874.1| pseudouridine synthase [Bacillus clausii KSM-K16]
          Length = 302

 Score =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 93/319 (29%), Positives = 153/319 (47%), Gaps = 42/319 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++  +    R+D+   + +   +   +Q+ +  G V V++K VK N+++Q G  V +   
Sbjct: 5   IITKEHHEQRIDKVVVDLHGQASRTAVQRWINEGAVLVNEKEVKTNSKVQQGDKVTL--- 61

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                   +E ++L   + L          ++YEDS + V NKP G+ V    G   H  
Sbjct: 62  ---TEPAAQEVELLGEDIPLD---------VVYEDSDVIVVNKPRGLVVHPAPG---HES 106

Query: 131 GFL--------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G L        K      G+ +P + HR+D++TSG+++ A+  AA +HL    + +  ++
Sbjct: 107 GTLVNALLFHCKDLSGINGEIRPGIVHRIDKDTSGLIMAAKHDAAHEHLAAQLKAKTTER 166

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQK 239
            Y ++V G+  + K  I       + IG D     K      N   A++HF + + F Q 
Sbjct: 167 RYKAIVHGVIPHAKGTI------DAPIGRDPKDRQKMAVTHVNSRPAVTHFSLEETFKQ- 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           + ++  +  TGRTHQ+RVH  ++G P+ GD KY        T PI N   LHA  +   H
Sbjct: 220 YSYISCELETGRTHQIRVHFNYIGHPLAGDPKYGP----KKTLPI-NGQALHAETLGFTH 274

Query: 300 PEGG-RLQITAPLPAHMVK 317
           P  G RL+ +APLPA M K
Sbjct: 275 PRTGERLRFSAPLPAEMEK 293


>gi|320530727|ref|ZP_08031771.1| pseudouridine synthase, RluA family [Selenomonas artemidis F0399]
 gi|320137014|gb|EFW28952.1| pseudouridine synthase, RluA family [Selenomonas artemidis F0399]
          Length = 301

 Score =  119 bits (298), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 94/310 (30%), Positives = 146/310 (47%), Gaps = 35/310 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVIN 72
           D    RLD +      + +   +Q+++  G VRVD  RVK N +++SG+ +   +PP   
Sbjct: 7   DSTGERLDVFLARQMENCSRSYVQRLITDGNVRVDGARVKPNYKLRSGEEICCTVPPAEE 66

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
            +  I  E   LD               +LYED  I V NK  G+ V   +G      ++
Sbjct: 67  VV--IAAEDIPLD---------------VLYEDEDIIVINKERGMVVHPAAGNLTGTLVN 109

Query: 131 GFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             L    D  G     +P + HRLD++TSG++V A+   A   L +  R +  ++ Y +L
Sbjct: 110 ALLFRCRDLSGINGELRPGIVHRLDKDTSGVMVAAKNDMAHHFLAQQIRSKAARREYRAL 169

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    +   I   +  +       + +V+    G   A +HF+V++ F   + ++   
Sbjct: 170 VHGNIAERAGVITGDI-GRHPTDRKRMAIVRS---GGKSATTHFEVLERFGD-YTFVSCV 224

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRL 305
             TGRTHQ+RVH   +G P+VGD KY A  K  F    Q    LH+  + L HP  G ++
Sbjct: 225 LETGRTHQIRVHMTSIGHPLVGDAKYTA-MKNPFGIHGQ---ALHSHILTLVHPRTGAQM 280

Query: 306 QITAPLPAHM 315
           + TAPLPA M
Sbjct: 281 RFTAPLPADM 290


>gi|315027878|gb|EFT39810.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2137]
          Length = 310

 Score =  119 bits (298), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 94/319 (29%), Positives = 155/319 (48%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 20  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 73

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                E ++LD        ++ +   ++YED+ + V NKP G+ V    G   H +G L 
Sbjct: 74  -----EPEVLDMV------AEDIPLTIVYEDNDVIVVNKPQGMVVHPSVG---HPNGTLV 119

Query: 135 SWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + +              +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 120 NALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 179

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 180 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 233 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 287

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 288 QLVFEAPLPEVFEKTLHQL 306


>gi|209522216|ref|ZP_03270853.1| pseudouridine synthase, RluA family [Burkholderia sp. H160]
 gi|209497345|gb|EDZ97563.1| pseudouridine synthase, RluA family [Burkholderia sp. H160]
          Length = 419

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 95/332 (28%), Positives = 150/332 (45%), Gaps = 35/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV ++    RLD+     +P  +   LQ  + + +VRVD K  K    +  G  + + P
Sbjct: 70  VVVPDELAGERLDKVVAKVFPEFSRSRLQSWIEAERVRVDGKPAKIRQPVPLGATIELEP 129

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                  ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 130 ------DLLPEQ--------LAFTPEPVPLDIVYEDDTLVVINKPAGMVVHPAAGNWSGT 175

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++G L  + ++    PR  + HRLD+ETSG++VVART  A   L    + R +++ Y +
Sbjct: 176 VLNGLLYRYGEAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLA 235

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVIDCFA---QK 239
           LVWG   ++    A        IG D      +          A +HF+ +       Q 
Sbjct: 236 LVWGNMPDEGTIDAP-------IGRDPRERTRMAVVTGAAGKPARTHFRRVTSAIWQRQP 288

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMD 296
              +     TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + 
Sbjct: 289 VTAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLG 348

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L HP+ GR +Q  A +PA +     +LG   D
Sbjct: 349 LIHPKTGRSMQWRADVPADIEALSAALGLGRD 380


>gi|221309420|ref|ZP_03591267.1| hypothetical protein Bsubs1_08546 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221313745|ref|ZP_03595550.1| hypothetical protein BsubsN3_08482 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221318669|ref|ZP_03599963.1| hypothetical protein BsubsJ_08416 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221322942|ref|ZP_03604236.1| hypothetical protein BsubsS_08522 [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|255767360|ref|NP_389429.3| pseudouridylate synthase [Bacillus subtilis subsp. subtilis str.
           168]
 gi|254763395|sp|Q45480|YLYB_BACSU RecName: Full=Uncharacterized RNA pseudouridine synthase ylyB;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|1373157|gb|AAB57767.1| orf-X; hypothetical protein; Method: conceptual translation
           supplied by author [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|225184987|emb|CAB13420.3| pseudouridylate synthase [Bacillus subtilis subsp. subtilis str.
           168]
          Length = 303

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 93/323 (28%), Positives = 152/323 (47%), Gaps = 39/323 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIP 68
           +    ++++ R+D++  +     +   +Q+ ++ GQV V+   VK N +IQ G QV    
Sbjct: 6   ITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSAVKANYKIQPGDQVTVTV 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
           P   AL+ ++ E   LD               + YED  + V NKP G+ V    G    
Sbjct: 66  PEPEALD-VLAEPMDLD---------------IYYEDQDVLVVNKPRGMVVHPAPGHLTG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + 
Sbjct: 110 TLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRK 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYV--HVVKQNEKGANYAISHFKVIDCFAQKF 240
           Y ++V G+  +    I       + IG D      +     G N A++HF V++ F Q F
Sbjct: 170 YTAVVHGLISHDDGTI------DAPIGRDKKDRQSMTVTRDGKN-AVTHFHVLERF-QDF 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E Q  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   HP
Sbjct: 222 TLVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDF-----NGQALHAGVLGFDHP 276

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  ++  APLP  M +  ++L
Sbjct: 277 RTGEYVEFEAPLPEDMAELIENL 299


>gi|87123536|ref|ZP_01079387.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9917]
 gi|86169256|gb|EAQ70512.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9917]
          Length = 329

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 95/308 (30%), Positives = 142/308 (46%), Gaps = 32/308 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +     +   +QK + +G VRV+ K  K    ++ G  V++  PP    L +
Sbjct: 37  MRLDRWLVSQRSEQSRARIQKFIDAGFVRVNGKTGKAKTPLRQGDAVQLWMPPP-EPLPY 95

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E   LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 96  LKPEPMDLD---------------VLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLH 140

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y ++V G+
Sbjct: 141 HCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQLQIQKRIASREYLAVVHGV 200

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P+     I   + +       Y  V  +N     YA +H+ + +  A  +  L  +  TG
Sbjct: 201 PRGDSGTIVGAIGRHPADRKKYAVVSGEN---GRYACTHWSLQERLAD-YSLLRFKLDTG 256

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  HM  P+VGD  Y    K     P Q    LHA  + L HP    RL   A
Sbjct: 257 RTHQIRVHCAHMNHPVVGDPTYSRCRKLPVELPGQA---LHAFQLGLDHPITRERLLFEA 313

Query: 310 PLPAHMVK 317
           PLP  M K
Sbjct: 314 PLPPVMEK 321


>gi|292669557|ref|ZP_06602983.1| ribosomal large subunit pseudouridine synthase D [Selenomonas noxia
           ATCC 43541]
 gi|292648766|gb|EFF66738.1| ribosomal large subunit pseudouridine synthase D [Selenomonas noxia
           ATCC 43541]
          Length = 302

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 94/330 (28%), Positives = 157/330 (47%), Gaps = 53/330 (16%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IP 68
           +   D    RLD +     P ++    Q+++   +V VD    K N +++ G+ V   +P
Sbjct: 4   IFSADCAGERLDVFLVRKMPDLSRSYAQRLIEEKRVTVDGTPRKANYKLRGGECVACDLP 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           PV        +E  +   ++ L          +LYED+ I V NKP G+ V   +GI+  
Sbjct: 64  PV--------EEVSVRAENIPLD---------ILYEDADIIVVNKPRGMVVHPAAGISGG 106

Query: 129 --IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D  G     +P + HRLD++TSG++  A+  AA + L E  + +  ++ 
Sbjct: 107 TLVNALLYHCRDLSGINGALRPGIVHRLDKDTSGVMAAAKNDAAHRSLAEQIQKKEARRE 166

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDY---------VHVVKQNEKGANYAISHFKVI 233
           Y ++V+G          N   +   I GD          + +V++N K   +A +HF+V+
Sbjct: 167 YRAIVYG----------NIAERAGIITGDIGRHPTDRKRMAIVRENGK---HATTHFEVL 213

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F   + ++  +  TGRTHQ+RVH   +G P+VGD KY +  K  F    Q    LH+ 
Sbjct: 214 ERFG-GYTFVACRLETGRTHQIRVHMTSIGHPLVGDAKYTSK-KNPFAIAGQ---ALHSL 268

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            + L HP  G  +  TAPLPA + +   +L
Sbjct: 269 TLTLAHPRSGEEMAFTAPLPADIEEILCAL 298


>gi|313675894|ref|YP_004053890.1| ribosomal large subunit pseudouridine synthase d [Marivirga
           tractuosa DSM 4126]
 gi|312942592|gb|ADR21782.1| ribosomal large subunit pseudouridine synthase D [Marivirga
           tractuosa DSM 4126]
          Length = 231

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 72/231 (31%), Positives = 121/231 (52%), Gaps = 17/231 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LT 147
           + +FL+ I++YED+ + V NKP+G+ VQG       I    K ++  K  KP        
Sbjct: 3   YQEFLQ-IVMYEDNHLLVVNKPSGMLVQGDQTGDTPISEHAKEYIAKKYDKPGKVFCGTP 61

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HR+D+  SG LV+ART  A + +++ F    + K YW++    P   ++ I +WL K S+
Sbjct: 62  HRIDRPVSGTLVLARTSKALERVSKLFHDGEVDKTYWAITEKRPPKTEDTITHWLKKDSN 121

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               + H+   ++KG   +   ++++     +   +E++PHTGR HQ+RV    +GCPI+
Sbjct: 122 KNLTHAHM--SDKKGGLKSTLSYRLVRALGDR-NLIEVKPHTGRPHQIRVQLARIGCPII 178

Query: 268 GDHKYCANFKGNFTSPIQN-KLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           GD KY       F  P ++  + LHAR +   HP +     + +P+P   V
Sbjct: 179 GDVKY------GFPKPTKDGSIALHARAISFVHPVKKEPFNVVSPIPKAFV 223


>gi|256619215|ref|ZP_05476061.1| pseudouridylate synthase [Enterococcus faecalis ATCC 4200]
 gi|256853277|ref|ZP_05558647.1| pseudouridylate synthase [Enterococcus faecalis T8]
 gi|300860210|ref|ZP_07106297.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|256598742|gb|EEU17918.1| pseudouridylate synthase [Enterococcus faecalis ATCC 4200]
 gi|256711736|gb|EEU26774.1| pseudouridylate synthase [Enterococcus faecalis T8]
 gi|300849249|gb|EFK76999.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
          Length = 301

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 156/319 (48%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 11  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                E + LD        ++ +   ++YED+ + V NKP G+ V   +G         +
Sbjct: 65  -----EPEALDMV------AEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNAL 113

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H D  L +  D    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 114 LHHAD-HLSAINDVV--RPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 170

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 171 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 224 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 278

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 279 QLVFEAPLPEVFEKTLHQL 297


>gi|83312285|ref|YP_422549.1| pseudouridylate synthase, 23S RNA-specific [Magnetospirillum
           magneticum AMB-1]
 gi|82947126|dbj|BAE51990.1| Pseudouridylate synthase, 23S RNA-specific [Magnetospirillum
           magneticum AMB-1]
          Length = 505

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 93/323 (28%), Positives = 149/323 (46%), Gaps = 41/323 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RI 59
           M +   +    VE +E   RLDRW     P ++   ++ ++  G+V +++  +   + R+
Sbjct: 181 MPVTQRLTPPAVEPEEAGTRLDRWLALRLPELSRTRIKGLMEDGRVSLEETTISDASLRV 240

Query: 60  QSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           + GQ  VV +PP   A              + LT         ++YED  + V +KPAG+
Sbjct: 241 KPGQCFVVDVPPDAPAQPE--------PQDIALT---------VVYEDEDLIVIDKPAGM 283

Query: 118 SVQGGSGIAYH--IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHL 170
            V    G      ++  L    +S       ++P + HR+D++TSG+LV A+T AA + L
Sbjct: 284 VVHPAPGNPDETLVNALLAHCGESLAGIGGVKRPGIVHRIDKDTSGLLVAAKTDAAHRGL 343

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              F    +++ YW+LVWG P  ++  I   + +  +     + VVK    G   A++ +
Sbjct: 344 ATQFAAHTLERAYWALVWGTPSPRQGEIEGNIGRNPN-DRKKMAVVK---SGGKPALTRY 399

Query: 231 KVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSP---- 283
           +V+  FA     L E +  TGRTHQ+RVH    G P+VGD  Y      KG    P    
Sbjct: 400 RVLKSFAGGAVSLVECRLATGRTHQIRVHMTTQGHPLVGDPVYGRIRGHKGVVLPPEVKT 459

Query: 284 --IQ-NKLYLHARYMDLPHPEGG 303
             IQ  +  LHA  +   HP  G
Sbjct: 460 ALIQFPRQALHAYLLGFSHPTKG 482


>gi|218781210|ref|YP_002432528.1| pseudouridine synthase, RluA family [Desulfatibacillum alkenivorans
           AK-01]
 gi|218762594|gb|ACL05060.1| pseudouridine synthase, RluA family [Desulfatibacillum alkenivorans
           AK-01]
          Length = 321

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 94/325 (28%), Positives = 153/325 (47%), Gaps = 33/325 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+N E+  RLD +   H  +++     +++R G V VDK   K +  ++ G++V +    
Sbjct: 11  VQNKEQGQRLDAFVPVHCKNLSRNACARLIRQGLVTVDKSVKKPSYVLKPGEMVSV---- 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--I 129
                 + E +  D    + +  D     +LYED  I   NKP G+ V    G + +  +
Sbjct: 67  -----TVPEPETADI---VAQDMDL---AILYEDRDIVAVNKPPGMVVHPAPGHSSNTLV 115

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G    Q+P + HRLD+ETSG+++ A+  AA   L+E    RR++K Y +
Sbjct: 116 NALLAHCKDLSGIGGVQRPGIVHRLDKETSGVILAAKNDAAHAGLSEQLAQRRVEKFYLA 175

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L  G+ K     I +  L +       +HV          A+S + V + F     ++++
Sbjct: 176 LAHGVIKEDTGVI-DLPLARHPSDRKRMHV--STPAKGREALSLWTVKERFLDA-TYVKV 231

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFT------SPIQNKLYLHARYMDLP 298
           Q  TGRTHQ+RVH   +  P++GD  Y    K G         +P   +  LHA  +   
Sbjct: 232 QIKTGRTHQIRVHLAALHHPVIGDTVYGGRKKRGRLPASVLGKAPPPERQMLHAHIVSFT 291

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSL 322
           HP  G +L +TAPLP  M +  ++L
Sbjct: 292 HPVTGEKLTLTAPLPQDMAQLLEAL 316


>gi|225181681|ref|ZP_03735121.1| pseudouridine synthase, RluA family [Dethiobacter alkaliphilus AHT
           1]
 gi|225167662|gb|EEG76473.1| pseudouridine synthase, RluA family [Dethiobacter alkaliphilus AHT
           1]
          Length = 312

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 92/300 (30%), Positives = 143/300 (47%), Gaps = 33/300 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI- 67
           ++ V+      RLD     H   +    +QK++    V+VD K  K N R+++G+ V + 
Sbjct: 5   FITVDEVLAGERLDVAVSRHVEELTRARVQKLIAEDYVQVDGKPQKANYRLRAGETVEVT 64

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            P V  A   I  E+  LD               +LYED  + V NKP G+ +   +G A
Sbjct: 65  VPEVKPA--EIAAEKIDLD---------------ILYEDQDVLVLNKPKGLVIHPAAGHA 107

Query: 127 YH--IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L    D  G     +P + HRLD++TSG++VVA+   A   L+  F+   + 
Sbjct: 108 GGTLVNALLHHCDDLSGIGGEARPGIVHRLDKDTSGVMVVAKNDRAHLSLSRQFKAHSVT 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G P  ++  I   + +  H        +   EKG   A++HFKV+D F + +
Sbjct: 168 REYVAIVHGEPAVEQGTIDAAIAR--HPKERKKMALTTAEKG-RRAVTHFKVLDRFGE-Y 223

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            +L ++  TGRTHQ+RVH   +G P+VGD  Y    K  F    Q    LHAR +   HP
Sbjct: 224 SYLALRLETGRTHQIRVHLSSLGHPVVGDPVYGYK-KQKFKLSGQA---LHARLLGFNHP 279


>gi|94497522|ref|ZP_01304091.1| Pseudouridine synthase, RluD [Sphingomonas sp. SKA58]
 gi|94422939|gb|EAT07971.1| Pseudouridine synthase, RluD [Sphingomonas sp. SKA58]
          Length = 317

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 90/340 (26%), Positives = 164/340 (48%), Gaps = 43/340 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRI 59
           M L   +    +   +  +RLDR   +  P ++   L+ ++  GQV      R+  + ++
Sbjct: 1   MVLGDSIIEATIGPAQHGLRLDRALADLLPDLSRERLKTLIGDGQVHSAPVGRISGSMKV 60

Query: 60  QSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
             GQ   + +PP +  L+ + ++       + LT         +++ED+ + V +KPAG+
Sbjct: 61  AEGQRFTITLPPPV-PLDTVAQD-------IPLT---------IVHEDADLLVVDKPAGL 103

Query: 118 SVQGGSGIAYHIDGFLKSWV--DSKGQ--------KPRLTHRLDQETSGILVVARTRAAA 167
            V   +G   ++DG L + +     GQ        +P + HR+D++TSG+LVVA+T  A 
Sbjct: 104 VVHPAAG---NLDGTLVNALLHHCAGQLSGIGGVARPGIVHRIDKDTSGLLVVAKTDRAH 160

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           + L   F+   I++ Y ++ +GIP      + +W+ +      D   +    E    +A+
Sbjct: 161 EGLARQFKDHSIERAYAAITYGIPVPPAGTVDSWIGRSD---ADRKKMAVHREGRGKHAV 217

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN- 286
           +H++ +D   +    +E +  TGRTHQ+RVH  H+G P++GD  Y    KG F S ++  
Sbjct: 218 THYRTLDRL-RGAALVECRLETGRTHQVRVHMAHIGHPLIGDPVYGRERKG-FKSILETL 275

Query: 287 ---KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              +  LHAR +   HP     L   + LPA + +   +L
Sbjct: 276 GFRRQALHARMLGFIHPVTDEPLMFESALPADVQELLSAL 315


>gi|78100963|pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli
           Pseudouridine Synthase Rluc
 gi|78100964|pdb|1XPI|B Chain B, Crystal Structure Of The Catalytic Domain Of E. Coli
           Pseudouridine Synthase Rluc
          Length = 231

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 122/220 (55%), Gaps = 11/220 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L  ++LYED  I V NKP+G +V GGSG+++ +   L++ +  + +   L HRLD++TSG
Sbjct: 3   LADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSG 61

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+VA+ R+A + L E  R + +QK Y +LV G  ++  + +   LLK     G+ +  V
Sbjct: 62  VLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRV 121

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-A 274
            Q  K +    + FKV + +A  F  L    P TGRTHQ+RVH  + G PI  D +Y   
Sbjct: 122 SQEGKPSE---TRFKVEERYA--FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDR 176

Query: 275 NFKGNFTSPIQ--NKLYLHARYMDLPHPEGGR-LQITAPL 311
            F    T      N+L+LHA  +   HP  G  ++I AP+
Sbjct: 177 EFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPM 216


>gi|291484098|dbj|BAI85173.1| hypothetical protein BSNT_02552 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 303

 Score =  119 bits (297), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 91/322 (28%), Positives = 150/322 (46%), Gaps = 37/322 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIP 68
           +    ++++ R+D++  +     +   +Q+ ++ GQV V+   VK N +IQ G QV    
Sbjct: 6   ITASEEQKSERIDKFLASSENDWSRTQVQQWVKDGQVVVNGSAVKANYKIQPGDQVTVTV 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
           P   AL+ ++ E   LD               + YED  + V NKP G+ V    G    
Sbjct: 66  PEPEALD-VLAEPMDLD---------------IYYEDQDVLVVNKPRGMVVHPAPGHLTG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + 
Sbjct: 110 TLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRK 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFC 241
           Y ++V G+  +    I       + IG D          +    A++HF V++ F Q F 
Sbjct: 170 YTAVVHGLISHDDGTI------DAPIGRDKKDRQSMTVTRDGKSAVTHFHVLERF-QDFT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E Q  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   HP 
Sbjct: 223 LVECQLETGRTHQIRVHMRYIGFPLAGDPKYGPRKTIDF-----NGQALHAGVLGFDHPR 277

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++  APLP  M +  ++L
Sbjct: 278 TGEYVEFEAPLPEDMAELIENL 299


>gi|328950026|ref|YP_004367361.1| pseudouridine synthase, RluA family [Marinithermus hydrothermalis
           DSM 14884]
 gi|328450350|gb|AEB11251.1| pseudouridine synthase, RluA family [Marinithermus hydrothermalis
           DSM 14884]
          Length = 318

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 93/331 (28%), Positives = 152/331 (45%), Gaps = 39/331 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V    E +RLD+         +    Q  + +G VRVD   V    +   G+ V +  
Sbjct: 4   VEVRFSAEGVRLDQAVAERT-GASRAKAQAWIAAGYVRVDGVPVTKPGKRLKGETVEVVA 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
             +    +  EQ+ L+               +LYED  + V NKP G++     G+    
Sbjct: 63  PPDPPPRVAPEQRDLE---------------ILYEDEDMVVVNKPPGMATHPAPGLTSGT 107

Query: 129 -IDGFLKSWVDS--KGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            ++  +  +  +  +G+     +P + HRLD++TSG++VV R  AA + L ++F+ R + 
Sbjct: 108 LVNALMGRYAQAAVEGEPPEQVRPGIVHRLDRDTSGVIVVGRHDAAVRRLADAFKNRFVF 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++  G P    E      + +  +    +HV   N + A    S    +D  A   
Sbjct: 168 KRYVAITVGQP---PEMTLVAPIGRHPVERHKMHVSGVNARYAETDFSLLATVDGHA--- 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             ++ +PHTGRTHQ+RVH  H+  PI+GD  Y         SP  ++  LHA  + +PHP
Sbjct: 222 -LVDARPHTGRTHQIRVHLKHLYAPILGDELY------GKPSPYISRQALHAYELRIPHP 274

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
             GR +   AP+P  MV  W++LG ++   L
Sbjct: 275 RSGRIMTFVAPVPRDMVAAWEALGGRWPDGL 305


>gi|229545666|ref|ZP_04434391.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|307275817|ref|ZP_07556956.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|307291840|ref|ZP_07571711.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|229309234|gb|EEN75221.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|306497106|gb|EFM66652.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|306507509|gb|EFM76640.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|315029545|gb|EFT41477.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4000]
 gi|315032018|gb|EFT43950.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0017]
 gi|315144961|gb|EFT88977.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2141]
 gi|315168880|gb|EFU12897.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1341]
          Length = 310

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 156/319 (48%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 20  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 73

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                E + LD        ++ +   ++YED+ + V NKP G+ V   +G         +
Sbjct: 74  -----EPEALDMV------AEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNAL 122

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H D  L +  D    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 123 LHHAD-HLSAINDVV--RPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 179

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 180 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 233 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 287

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 288 QLVFEAPLPEVFEKTLHQL 306


>gi|325474713|gb|EGC77899.1| RNA pseudouridylate synthase [Treponema denticola F0402]
          Length = 244

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 81/241 (33%), Positives = 126/241 (52%), Gaps = 24/241 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGI 157
           +LYED  I + NK A + V        A  +D  L+     KG+ K    HRLD+ETSG+
Sbjct: 8   ILYEDKDILIVNKSADLLVGADRWDSEAPRLDKILEELYKDKGERKIYPVHRLDKETSGL 67

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK-KSHIGGDYVHVV 216
           ++ A    A + L + F+ R+I+KIY ++  GIP+ +     N+  + K  I GD +H  
Sbjct: 68  IIYALNAEAHKILNDDFQNRKIEKIYHAVSAGIPQEE-----NFKTEAKLRIDGDKLHRT 122

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--- 273
             +EK    +++ F ++  F+ +FC LE +P TGRTHQ+R H  H+G PI+ D+ Y    
Sbjct: 123 VIDEKKGKESLTEFSLLKKFS-RFCLLEARPITGRTHQIRAHLKHLGLPILCDNLYGNGE 181

Query: 274 --------ANFKGN--FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                    N++GN     PI ++L LHA  +   HP    +++I+A  P  M    + L
Sbjct: 182 PVYISALKKNWRGNKYEERPIISRLALHAHSLKFFHPISKEKIEISASCPKDMAGLINQL 241

Query: 323 G 323
           G
Sbjct: 242 G 242


>gi|321315311|ref|YP_004207598.1| pseudouridylate synthase [Bacillus subtilis BSn5]
 gi|320021585|gb|ADV96571.1| pseudouridylate synthase [Bacillus subtilis BSn5]
          Length = 303

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 93/323 (28%), Positives = 152/323 (47%), Gaps = 39/323 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIP 68
           +    ++++ R+D++  +     +   +Q+ ++ GQV V+   VK N +IQ G QV    
Sbjct: 6   ITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSAVKANYKIQPGDQVTVTV 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
           P   AL+ ++ E   LD               + YED  + V NKP G+ V    G    
Sbjct: 66  PEPEALD-VLAEPLDLD---------------IYYEDQDVLVVNKPRGMVVHPAPGHLTG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + 
Sbjct: 110 TLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRK 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYV--HVVKQNEKGANYAISHFKVIDCFAQKF 240
           Y ++V G+  +    I       + IG D      +     G N A++HF V++ F Q F
Sbjct: 170 YTAVVHGLISHDDGTI------DAPIGRDKKDRQSMTVTRDGKN-AVTHFHVLERF-QDF 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E Q  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   HP
Sbjct: 222 TLVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDF-----NGQALHAGVLGFDHP 276

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  ++  APLP  M +  ++L
Sbjct: 277 RTGEYVEFEAPLPEDMAELIENL 299


>gi|220904866|ref|YP_002480178.1| pseudouridine synthase, RluA family [Desulfovibrio desulfuricans
           subsp. desulfuricans str. ATCC 27774]
 gi|219869165|gb|ACL49500.1| pseudouridine synthase, RluA family [Desulfovibrio desulfuricans
           subsp. desulfuricans str. ATCC 27774]
          Length = 525

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 95/326 (29%), Positives = 150/326 (46%), Gaps = 44/326 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD---KKRVKFNNRIQ 60
           M+ +Q  +    +   RLDR      P ++   LQK++++G   VD   +KR     R+ 
Sbjct: 1   MSRLQLKITAG-QAGKRLDRILGATVPELSRAALQKVVQAGCCTVDGLPEKRPAAKMRM- 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-----LLYEDSKIYVFNKPA 115
            GQ V                     +++L +H D L+       LL++D  + V NKPA
Sbjct: 59  -GQTV---------------------TLDLPEHPDRLQPEEGHLELLWQDDHLVVCNKPA 96

Query: 116 GISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           G++V          +   + G        +GQ+P + HRLD++TSG+LVVA T A    L
Sbjct: 97  GLTVHPCPSCPEQTLVQRLLGRFPQLSRLEGQRPGIVHRLDKDTSGLLVVALTEADCLAL 156

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
             +F  R++ K Y +LV G+P  + +C     L +       + VV +++ G N      
Sbjct: 157 AAAFAERQVHKEYLALVSGLPPLEGQCREP--LGRHPTAKIKMAVVPEDQGGRNAFTEWR 214

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           ++ +        L ++ HTGRTHQ+RVH  H+G P++GD  Y      N  +P Q    L
Sbjct: 215 RLWNTDDGSVSLLAVRIHTGRTHQIRVHMTHLGYPLLGDRLYAPKAVQNM-APRQ---ML 270

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHM 315
           HA  +   HP  G  ++ T P P  M
Sbjct: 271 HAWRLGFTHPASGEDMRFTCPPPHDM 296


>gi|85860531|ref|YP_462733.1| ribosomal large subunit pseudouridine synthase D [Syntrophus
           aciditrophicus SB]
 gi|85723622|gb|ABC78565.1| ribosomal large subunit pseudouridine synthase D [Syntrophus
           aciditrophicus SB]
          Length = 333

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 96/327 (29%), Positives = 159/327 (48%), Gaps = 50/327 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRI--P 68
           V   E  +RLD +  +H    +   LQ+++ SG+V +  K  ++ + ++++G +V +  P
Sbjct: 12  VTATESGLRLDLFLASHESGFSRARLQRLIESGRVTISGKAAIRASQKLRTGDIVMLEEP 71

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P            +++   + L+         +LYED  + V +KPAG+ V   +G   H
Sbjct: 72  PATPL--------ELIPQDIPLS---------ILYEDHDLLVLDKPAGLVVHPAAG---H 111

Query: 129 IDGFLKSWV-----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           + G L + +     D  G     +P + HRLD++TSG+LVVA+T AA Q L   F+  ++
Sbjct: 112 VSGTLVNALLFHCRDLAGIGGVMRPGIVHRLDKDTSGLLVVAKTDAAHQGLALQFKKHQV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCFA 237
            K Y +LV+G P+ K   I         +G   V   K + K      A + +++ + F 
Sbjct: 172 GKTYQALVYGDPREKTGQI------DLPVGRHPVERKKMSTKSRRGKEAATRWRIAERFG 225

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSP-IQNKL------Y 289
                L +   TGRTHQ+RVH   +G P+VGD  Y ++ +    T P ++ +L       
Sbjct: 226 VA-TLLNVDIVTGRTHQIRVHLAAIGHPVVGDAVYGSSKRATTLTDPAVKGRLKEMSRQA 284

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHM 315
           LHA  +   HP   + L+  APLPA M
Sbjct: 285 LHAARLSFTHPVTHKILEFHAPLPADM 311


>gi|306841397|ref|ZP_07474100.1| pseudouridine synthase, RluA family [Brucella sp. BO2]
 gi|306288582|gb|EFM59931.1| pseudouridine synthase, RluA family [Brucella sp. BO2]
          Length = 294

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 78/244 (31%), Positives = 125/244 (51%), Gaps = 32/244 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  + V NKPAG+ V  G+G         + YH    L      +  +P + HRLD
Sbjct: 42  ILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLSGIGGIR--RPGIVHRLD 99

Query: 152 QETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           ++TSG++VVA+   A +HL+E F    R   +++ Y +LVWG+ +  +  +  +L  +SH
Sbjct: 100 KDTSGVMVVAKNNRAHRHLSEQFADHGRTGDLERAYLALVWGMTERPQGTVDAYL-GRSH 158

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALH 261
                  VV++  + A +AI+H+  ++ F+ +         +E +  TGRTHQ+RVH  H
Sbjct: 159 RDRTKQAVVREEREDARHAITHYATVEKFSPREDATALASLVECRLETGRTHQIRVHMAH 218

Query: 262 MGCPIVGDHKYCANFK---GNFTSPIQNKL------YLHARYMDLPHPEGGRL-QITAPL 311
           +G P+VGD  Y + +K        P++  +       LHA  +   HP    L +  APL
Sbjct: 219 IGHPLVGDMDYGSAYKTKANKLPEPLKQAVQGFHRQALHAWLLAFTHPITEELMRFEAPL 278

Query: 312 PAHM 315
           P  M
Sbjct: 279 PDDM 282


>gi|296331122|ref|ZP_06873596.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305674277|ref|YP_003865949.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
 gi|296151766|gb|EFG92641.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305412521|gb|ADM37640.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
          Length = 303

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 93/323 (28%), Positives = 152/323 (47%), Gaps = 39/323 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIP 68
           +    ++++ R+D++  +     +   +Q+ ++ GQV V+   VK N +IQ G QV    
Sbjct: 6   ITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSPVKSNYKIQPGDQVTVTV 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
           P   AL+ ++ E   LD               + YED  + V NKP G+ V    G    
Sbjct: 66  PEPEALD-VLAEPMDLD---------------IYYEDQDVLVVNKPRGMVVHPAPGHLTG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + 
Sbjct: 110 TLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRK 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYV--HVVKQNEKGANYAISHFKVIDCFAQKF 240
           Y ++V G+  +    I       + IG D      +     G N A++HF V++ F Q F
Sbjct: 170 YTAVVHGLISHDDGTI------DAPIGRDKKDRQSMTVTRDGKN-AVTHFHVLERF-QDF 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E Q  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   HP
Sbjct: 222 TLVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDF-----NGQALHAGILGFDHP 276

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  ++  APLP  M +  ++L
Sbjct: 277 RTGEYVEFEAPLPEDMAELIENL 299


>gi|329769635|ref|ZP_08261039.1| hypothetical protein HMPREF0433_00803 [Gemella sanguinis M325]
 gi|328838390|gb|EGF87999.1| hypothetical protein HMPREF0433_00803 [Gemella sanguinis M325]
          Length = 299

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 89/312 (28%), Positives = 155/312 (49%), Gaps = 38/312 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D++ +N    ++  N+Q ++  G ++VD   VK N +++   V+ I           K
Sbjct: 15  RIDKFLQNELSDLSRTNIQNLISEGYIKVDGNTVKTNYKLKESNVITID---------YK 65

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-- 137
           E + LD    + K    +   ++YED+ + + NKP G+ V   +G   H DG L + +  
Sbjct: 66  EPEELD----VVKQD--IPVDIVYEDNDLLIVNKPKGMVVHPSAG---HKDGTLVNALLY 116

Query: 138 -----DSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                   G  +P + HR+D++TSG+L+VA+   A   L+E    + +++ Y++LV G  
Sbjct: 117 HCELSSINGTIRPGIVHRIDKDTSGLLIVAKNDKAHVKLSEMIANKEVKRKYYALVHGSI 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K+    I   + +      +   V+ + +     +I+HFKVID F +K+  +E +  TGR
Sbjct: 177 KHDYGTIDAPIARNPKERKEMA-VIDEGKP----SITHFKVIDRF-EKYTLIECELETGR 230

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  ++  P+VGD  Y      N      N   LH++ ++  HP  G  L     
Sbjct: 231 THQIRVHMKYINHPLVGDPVYGPRKTLN-----TNGQSLHSKSIEFNHPITGEHLYFETE 285

Query: 311 LPAHMVKTWDSL 322
           +P++MV T   L
Sbjct: 286 IPSYMVDTMAKL 297


>gi|303249294|ref|ZP_07335526.1| pseudouridine synthase, RluA family [Desulfovibrio fructosovorans
           JJ]
 gi|302489300|gb|EFL49257.1| pseudouridine synthase, RluA family [Desulfovibrio fructosovorans
           JJ]
          Length = 323

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 89/301 (29%), Positives = 142/301 (47%), Gaps = 28/301 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           + T VQ   V   E   +L ++        +    LQK +R+GQVR+D KR K  +R+ +
Sbjct: 1   MKTPVQNFTVAEAEGGQKLLQYLARRLDGAVPPTALQKFIRTGQVRIDGKRCKPFDRVAA 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           GQ+VR+PP      + IKE +   +     +  D     +L+ED +I V  KPAG+ V  
Sbjct: 61  GQIVRMPP------YEIKEPRNSPAKTAAPRGHDL---DILHEDDEILVIVKPAGLPVHP 111

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG  + +   L++       +P   HRLD++T+G+L+VA++  A + + E+       K
Sbjct: 112 GSGHPFALTSILRARYPDAPFRPTPAHRLDRDTTGVLLVAKSYRALRAIHEAMTTGTAHK 171

Query: 182 IYWSLVWGI----PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            Y + VWG       N    + + L K+   G + V    +   G   A+   +++    
Sbjct: 172 DYLAWVWGEWTLGEANDWVTLRDRLAKEGGPGRERV----EPSAGGKDAVCKVRLLGVM- 226

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +E++  TGRT Q+R      G PIVGD KY     G    P++    LHA  + L
Sbjct: 227 DTASLVEVRLETGRTQQIRAQLASRGAPIVGDPKY-----GGGPPPMR----LHAWRVVL 277

Query: 298 P 298
           P
Sbjct: 278 P 278


>gi|239908533|ref|YP_002955275.1| pseudouridine synthase [Desulfovibrio magneticus RS-1]
 gi|239798400|dbj|BAH77389.1| pseudouridine synthase [Desulfovibrio magneticus RS-1]
          Length = 339

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 96/330 (29%), Positives = 148/330 (44%), Gaps = 54/330 (16%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           + T VQ++ V   E   +L ++      P +    LQK +R+GQVR+D KR K  +R+  
Sbjct: 1   MKTPVQHITVTAAEAGQKLLQYLARRLGPGLPLAALQKCIRTGQVRLDGKRCKPFDRVAQ 60

Query: 62  GQVVRIPP-------------VINALNHIIKEQ--------KILDSSVNLTKHSDFLKSI 100
           GQVVR+PP                 L  +   +        K   S+ + T         
Sbjct: 61  GQVVRVPPFELDEAGPAGGALGAPELAAVPTGRPKPGPLSVKTSPSAAHRTGGRAMPALE 120

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED ++ V  KPAG+ V  GSG  + +   L +       KP   HRLD++T+G+L+V
Sbjct: 121 ILHEDDELLVVVKPAGLPVHPGSGHTFALTTLLHAHAPHAPFKPTPAHRLDRDTTGLLLV 180

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK-----------SHIG 209
           A++    + L E+ +   ++K Y++ VWG           WLL +           +  G
Sbjct: 181 AKSYRRLRALHEAMQDGTLRKDYFAWVWG----------KWLLGEENEWVTMRDALAKSG 230

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           G     V   E G   A++  ++I   A     +E++  TGRTHQ+R      G P+VGD
Sbjct: 231 GPGRERVTAGEDG-KEAVAKVRLIS-RAPTASLVEVRLETGRTHQIRAQLASRGYPLVGD 288

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
            KY     G   +P    L LHA  + LP 
Sbjct: 289 AKY-----GGGPTP----LRLHAWRVILPE 309


>gi|124024982|ref|YP_001014098.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. NATL1A]
 gi|123960050|gb|ABM74833.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. NATL1A]
          Length = 326

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 93/306 (30%), Positives = 149/306 (48%), Gaps = 38/306 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IPPVINALNH 76
           MRLDRW  +     +  ++QK + +G  RV+ K  K    ++ G +++  +PP    L +
Sbjct: 27  MRLDRWLVSQRAEQSRAHVQKFIEAGFARVNGKTGKAKTPVRPGDIIQLWVPPP-EPLPY 85

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E+  LD               +LYED  + V NK AG++V    G      ++G + 
Sbjct: 86  LKPEEIDLD---------------ILYEDDHLIVINKTAGMAVHPAPGNKSGTLVNGLIH 130

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +VVA+T+ A   L    + R   + Y ++V G 
Sbjct: 131 HCPDLPGIGGKLRPGIVHRLDKDTTGCIVVAKTQEALVKLQIQIQKRVASRNYIAVVHGA 190

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K+ +  I   + +       Y  V   +E+   YA +H+K+I+     F  L+ +  TG
Sbjct: 191 IKDNEGMIVGSIGRHPKDRKKYAVV---DEESGRYACTHWKLIENLGN-FSLLKFKLDTG 246

Query: 251 RTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGRLQ 306
           RTHQ+RVH+ H+G PI+GD  Y  C         PI+     LHA  + L HP    +++
Sbjct: 247 RTHQIRVHSAHIGHPIIGDQTYSRCKKL------PIKLGGQALHAIELGLIHPITLEKMK 300

Query: 307 ITAPLP 312
            TAPLP
Sbjct: 301 FTAPLP 306


>gi|332707717|ref|ZP_08427744.1| ribosomal large subunit pseudouridine synthase D [Lyngbya majuscula
           3L]
 gi|332353420|gb|EGJ32933.1| ribosomal large subunit pseudouridine synthase D [Lyngbya majuscula
           3L]
          Length = 320

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 90/322 (27%), Positives = 148/322 (45%), Gaps = 41/322 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVD-------KKRVKFNNRIQSGQVVRIPPVIN 72
           RLD +     P ++   +QK++  G V+V+       K +V+  +RI             
Sbjct: 26  RLDSYIAQQTPDLSRSRIQKLIEQGNVQVNDHVCISKKAKVQLGDRI------------- 72

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
             +  I + K L+         + +   +LYED  + + NKPAG+ V    G      ++
Sbjct: 73  --SLTIPDPKPLE------LQPEVIPLDILYEDDVLIIINKPAGLVVHPAPGHESGTLVN 124

Query: 131 GFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             L       G    Q+P + HRLD++T+G + +A+T  A  HL    + +  Q+ Y  +
Sbjct: 125 ALLAHCPKLTGIGGVQRPGIVHRLDKDTTGAIAIAKTDQAHGHLQAQLQAKTAQRQYLGV 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G P  +   I N  + +  +    + VV   EKG   AI+H++V +     +  +  Q
Sbjct: 185 VYGAPSAESGTI-NQPIGRHPVDRKKMAVVP-VEKGGRPAITHWQVRERLG-NYTLMHFQ 241

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH+ ++G PIVGD  Y +        P Q    LHA  + L HP  G  +
Sbjct: 242 LETGRTHQIRVHSSYIGHPIVGDTVYSSARSVGVNLPGQA---LHAWRLQLQHPVSGEWI 298

Query: 306 QITAPLPAHMVKTWDSLGFKYD 327
           +  AP P  ++K  D L  ++ 
Sbjct: 299 EFVAPPPLALIKLLDVLRLRFS 320


>gi|284039250|ref|YP_003389180.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283818543|gb|ADB40381.1| pseudouridine synthase [Spirosoma linguale DSM 74]
          Length = 248

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 73/205 (35%), Positives = 105/205 (51%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + + NK  GI VQG       +   LK ++  K  KP      L HRLD+  S
Sbjct: 8   VVYEDNHLLIVNKDPGILVQGDRTGDITLLDVLKDYIKEKYNKPGEVFLGLVHRLDRPVS 67

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ART  A + + E FR R++QK YW++V   P    + + NWL+K      + V V
Sbjct: 68  GLVVFARTSKALERMNEIFRKRQVQKTYWAVVRRKPPKDSDKLVNWLIKDEQ--KNQVTV 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +  A   ++V+    + +  LE+ P TGR HQ+R    HMGCPI GD KY   
Sbjct: 126 YDYEVPKSQKAELSYRVLGKINEHYL-LEVNPITGRPHQIRSQLAHMGCPIRGDIKY--- 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G   +    K+YLHAR +   HP
Sbjct: 182 --GYDRAVADKKIYLHARRLYFIHP 204


>gi|118588308|ref|ZP_01545717.1| Prenyl group binding site (CAAX box):RNA-binding S4:Pseudouridine
           synthase:Pseudouridine synthase, Rlu:Pseudouridine
           [Stappia aggregata IAM 12614]
 gi|118439014|gb|EAV45646.1| Prenyl group binding site (CAAX box):RNA-binding S4:Pseudouridine
           synthase:Pseudouridine synthase, Rlu:Pseudouridine
           [Stappia aggregata IAM 12614]
          Length = 341

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 93/340 (27%), Positives = 155/340 (45%), Gaps = 46/340 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIP 68
           + V+  +   RLD     H   ++   +Q +++SG V V   K V+   R+  G  + + 
Sbjct: 18  LTVDAADAGKRLDAVLATHLEALSRNRIQSLIKSGDVTVGGAKIVEPKYRVNEGDALTL- 76

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                          L  + +     + +   +++ED  + V +KPAG+ V  G+G    
Sbjct: 77  --------------TLPQAEDPEPKGEDIPVTVVFEDEHLIVVDKPAGLVVHPGAGNWTG 122

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMR 177
             ++  +    DS       ++P + HR+D++TSG+LVVA+T  A + L   F    R  
Sbjct: 123 TLVNALIHHCGDSLSGIGGVKRPGIVHRIDKDTSGLLVVAKTDQAHKGLAAQFADHGRTG 182

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LVWG P   K  I N  L +S      + VVK + +    AI+H++V + F 
Sbjct: 183 PLERAYSALVWGAPSGLKGTI-NANLARSQANRQKIAVVKTSGR---QAITHWQVKERFG 238

Query: 238 QK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQN--- 286
                     LE +  TGRTHQ+RVH  H+G P++GD  Y + FK        P+++   
Sbjct: 239 NAEQPALASLLECRLETGRTHQIRVHMAHIGHPLIGDDDYGSGFKTKANRLEEPLKSLVN 298

Query: 287 ---KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              +  LHA  +   HP  G+ L+  +P PA        L
Sbjct: 299 GFHRQALHAGLLAFEHPVNGKTLRFESPYPADFANLLSGL 338


>gi|237744439|ref|ZP_04574920.1| tRNA pseudouridine synthase A [Fusobacterium sp. 7_1]
 gi|229431668|gb|EEO41880.1| tRNA pseudouridine synthase A [Fusobacterium sp. 7_1]
          Length = 292

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 88/309 (28%), Positives = 158/309 (51%), Gaps = 27/309 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++Y++ E D E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G ++ 
Sbjct: 2   IEYIIDE-DYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDIIF 60

Query: 67  I--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           I  P      N    E+K ++ S  + K    LK ++++E+  ++V NKP G  V  GSG
Sbjct: 61  IFLPETFKEQN----EEKFIEIS-QIRKEK--LKQMIVFENDNLFVINKPLGDVVHKGSG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +    +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+
Sbjct: 114 HDISLLEEFRSYYSNNN--INFVNRIDKLTSGLVIGAKNIKTAREIAKEIQTGNIVKKYY 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  +     + N+L K      + V V    ++G   +I++FK I  +  K+  LE
Sbjct: 172 ILVNGKIEKDNFILENYLKKDE----ERVIVSDIEKEGYKKSITYFKKIKEY-DKYTLLE 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQLR    H+G  IVGD KY  N K       ++ +YL + Y+ +       
Sbjct: 227 AELKTGRTHQLRAQLDHLGNNIVGDTKYGKNEK-------EDIMYLFSYYLKIDLY---N 276

Query: 305 LQITAPLPA 313
           L+I   +P 
Sbjct: 277 LEIKLDMPV 285


>gi|33866856|ref|NP_898415.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Synechococcus sp. WH 8102]
 gi|33639457|emb|CAE08841.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Synechococcus sp. WH 8102]
          Length = 331

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 92/306 (30%), Positives = 140/306 (45%), Gaps = 32/306 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +     +   +QK + +G VRV+ K  K    ++ G  V++  PP    L +
Sbjct: 37  MRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKTGKAKTPLRQGDEVQMWMPPP-EPLPY 95

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E   LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 96  LKPEPMALD---------------VLFEDDHLIVINKPAGLTVHPAPGNKDGTLVNGLLH 140

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y ++V G+
Sbjct: 141 HCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQQALVRLQGQIQKRIASREYLAVVHGV 200

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +       Y  V   N+    YA +H+ + +     +  L  +  TG
Sbjct: 201 PGGDSGTIVGAIGRHPADRKKYAVV---NDDSGRYACTHWTLQERLGD-YSLLRFKLDTG 256

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  H+  P+VGD  Y    K     P Q    LHA  + L HP  G R+   A
Sbjct: 257 RTHQIRVHCAHINHPVVGDPTYSRCRKLPMELPGQA---LHAFQLGLDHPISGERMAFQA 313

Query: 310 PLPAHM 315
           PLP  M
Sbjct: 314 PLPPVM 319


>gi|229824104|ref|ZP_04450173.1| hypothetical protein GCWU000282_01408 [Catonella morbi ATCC 51271]
 gi|229786458|gb|EEP22572.1| hypothetical protein GCWU000282_01408 [Catonella morbi ATCC 51271]
          Length = 309

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 91/317 (28%), Positives = 157/317 (49%), Gaps = 36/317 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+   +  P  +   +QKI++ G V V+ +  K N +++  + +    ++   N  ++
Sbjct: 14  RLDKVLTDLLPGESRSTIQKIIKDGLVSVNGQEQKANFKLKGDETL----LVARRNLAVE 69

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYHID 130
           E  + +           +   ++YED  I V NKPAG+ V            +G+ ++++
Sbjct: 70  EDSLPEPEA--------MDLDIIYEDEDILVINKPAGLVVHPSKGHLKGTLVNGLLHYLN 121

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G L +  D    +P + HR+D++TSG+LVVA+  AA Q L +      +++ Y +LV G 
Sbjct: 122 GNLSTGSDF--YRPGIVHRIDKDTSGLLVVAKHNAAHQALADQLLNHDMRRSYIALVHGQ 179

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            K  +  I   L +      D  + ++    K   YA++ F+V++ F +    L+++  T
Sbjct: 180 VKAPQGTIEAPLQR------DPANRLRWTVAKEGKYALTRFQVMENF-ENATLLDLELET 232

Query: 250 GRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQ+RVH   +G P+VGD  Y     + KG+    +  +L LHA  + L HP  G  L
Sbjct: 233 GRTHQIRVHLEFIGHPLVGDPVYRKGLDHIKGSLVHDMTGQL-LHAYALKLQHPRSGEWL 291

Query: 306 QITAPLPAHMVKTWDSL 322
           +  APLP    +  D L
Sbjct: 292 EFKAPLPRRFEEALDQL 308


>gi|187779872|ref|ZP_02996345.1| hypothetical protein CLOSPO_03468 [Clostridium sporogenes ATCC
           15579]
 gi|187773497|gb|EDU37299.1| hypothetical protein CLOSPO_03468 [Clostridium sporogenes ATCC
           15579]
          Length = 305

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 96/324 (29%), Positives = 154/324 (47%), Gaps = 44/324 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE + +N+RLD +    +   +   LQ I+  G V V+ K  K N +++ G  +++    
Sbjct: 8   VEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIKVN--- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                 I E K+L          + +K  ++YED  + V NKP  + V    G+     +
Sbjct: 65  ------IPEPKLLQIE------PEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLV 112

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+   I ++Y +
Sbjct: 113 NALLSHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           LV GI K+ +  I      ++ IG   V  +K    K   YA++H+KVI+ F +    +E
Sbjct: 173 LVEGIIKDGQGTI------EAPIGRHPVDRIKMAVVKDGRYAVTHYKVIERF-KNHTLVE 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLHARYMDLPH 299
            +  TGRTHQ+RVH  H+  P+VGD  Y       N KG           LHA+ +   H
Sbjct: 226 CKLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLKGQM---------LHAKLLGFIH 276

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G+ ++  + LP +  K    L
Sbjct: 277 PTTGQYVEFESQLPEYFKKIIKIL 300


>gi|300871781|ref|YP_003786654.1| pseudouridine synthase [Brachyspira pilosicoli 95/1000]
 gi|300689482|gb|ADK32153.1| pseudouridine synthase [Brachyspira pilosicoli 95/1000]
          Length = 238

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 81/233 (34%), Positives = 125/233 (53%), Gaps = 12/233 (5%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDGFLKSWVDSKGQK- 143
           NL + ++F+   LLYED+ I V  KP  I  Q    G +    +I  ++K   + +G   
Sbjct: 3   NLEQITNFIN--LLYEDNHIIVAVKPPNIPTQADNTGDTSFFENIKDYIKLKYNKQGNVF 60

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+  SG++V A+T  AA  L+E+ R R  QK Y+ +V GI   K+  + N+L+
Sbjct: 61  LGLVHRLDRPVSGVMVFAKTSKAASRLSEAIRNRNFQKTYYCVVKGILLEKENTLENYLI 120

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           KK++  G+   VV +N K A  AI H+KV+ +   +    L+++  TGR HQ+RV   ++
Sbjct: 121 KKTNKLGNIAMVVFENTKNAKKAILHYKVLKEDNIKNLSLLKIELETGRFHQIRVQLSNL 180

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAH 314
           G  I GD KY +  K +        L L A+ +  PHP +   + I A LP +
Sbjct: 181 GHAIYGDRKYGSYIKYDRDDV---PLALFAKSIKFPHPTKNEEIFIEANLPDY 230


>gi|163755786|ref|ZP_02162904.1| ribosomal large subunit pseudouridine synthase D [Kordia algicida
           OT-1]
 gi|161324307|gb|EDP95638.1| ribosomal large subunit pseudouridine synthase D [Kordia algicida
           OT-1]
          Length = 346

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 93/339 (27%), Positives = 158/339 (46%), Gaps = 54/339 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--- 67
             E  ++ +R+D++  N         +Q+  + G + V+ K VK N +++   V+++   
Sbjct: 23  TAEKGQQPLRVDKYLMNFIEGATRNKIQQAAKDGNIFVNGKPVKSNYKVKGNDVIKVLFA 82

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
            PP  N L   + E   +D               ++YED  + V NKPAG+ V  G G  
Sbjct: 83  HPPYENLL---VGEDIPID---------------IVYEDDDLLVVNKPAGMVVHPGHGNY 124

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  + YH D   K+      ++P L HR+D++TSG+LVVA+T  A  HL + F  +
Sbjct: 125 SGTLINALIYHFDNLPKN----SNERPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDK 180

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             ++IY++LVWG + +++     N      +   + V   +  +KG   A++H+KV++  
Sbjct: 181 TSERIYYALVWGNVEEDEGTVEGNIGRHPKNRLQNTVFFGEDADKGKP-AVTHYKVLERL 239

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---------PI 284
                 +  Q  TGRTHQ+RVH  H+G  +  D +Y      KG  FT           I
Sbjct: 240 GY-VTLVSCQLETGRTHQIRVHMKHIGHTLFNDERYGGERILKGTTFTKYKQFVENCFKI 298

Query: 285 QNKLYLHARYMDLPHPEGG-RLQITAPLP---AHMVKTW 319
             +  LHA+ +   HP  G ++   + +P   A  ++ W
Sbjct: 299 LPRQALHAKTLGFIHPRTGEKMSFNSEVPSDIAECIEKW 337


>gi|144898737|emb|CAM75601.1| Pseudouridylate synthase [Magnetospirillum gryphiswaldense MSR-1]
          Length = 226

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 69/227 (30%), Positives = 118/227 (51%), Gaps = 13/227 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            D +K+ +L++D  + V +KPAG++V  G     H++ +L +        PRL HRLD++
Sbjct: 3   EDEIKARILFKDQDVIVLDKPAGLAVHAGPNSPDHLELYLDALKFGWSMAPRLAHRLDRD 62

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG L++ R   + + L + F   R++K YW++V G P      I+  + K +  GG  +
Sbjct: 63  TSGCLLLGRHDKSIKRLGKMFMQGRVEKAYWTVVHGTPPEDTGEISAPIHKVTGKGGWRI 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +    +     A++ ++V+        W+E  P TGRTHQ+RVH  H+GCP+ GD  Y 
Sbjct: 123 II----DAAGQPAVTRWRVLG-RGDGLSWIECTPLTGRTHQIRVHMKHLGCPVRGDVYYG 177

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR--LQITAPLPAHMVKT 318
            + +          L+L +  + +P    G+  ++  AP P HMV+ 
Sbjct: 178 PDPESEL------GLHLQSHAIGVPPLSTGKDWIRAEAPPPPHMVQA 218


>gi|154249509|ref|YP_001410334.1| RluA family pseudouridine synthase [Fervidobacterium nodosum
           Rt17-B1]
 gi|154153445|gb|ABS60677.1| pseudouridine synthase, RluA family [Fervidobacterium nodosum
           Rt17-B1]
          Length = 317

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 95/310 (30%), Positives = 156/310 (50%), Gaps = 47/310 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHII 78
           R+D++ +    ++    + K LR+G+V+++ K+VK  + ++  G V+ +           
Sbjct: 29  RVDKFLRKMLKNVPLSAIYKFLRTGKVKINGKKVKDPSTKLNIGDVIEL----------- 77

Query: 79  KEQKILDSSVNLTKHSDFLKSI-----LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDG 131
               I +S  N ++    LK +     ++YED  I   NKPAG+SV  G  +     I+G
Sbjct: 78  ----IEESLDNYSREYLELKPVKMDLDIIYEDELIIAINKPAGVSVHPGKNVNKPSIIEG 133

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +  +    G +P L HRLD+ETSG+L+VA+ R+ A+ L+E    R ++KIY +LV+G  
Sbjct: 134 LI-HYGKENGFEPFLVHRLDKETSGVLIVAKDRSVARELSEIISSRNVEKIYNALVFG-- 190

Query: 192 KNKKECIANWLLKKSHIGGDYV-HVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHT 249
           K +K  I   +      G D V H++          I +F+V ++  + +  +LE++  T
Sbjct: 191 KVQKVTINTPI-----DGQDAVSHII---------PIEYFRVKLNGISVELSFLEVEIET 236

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKL-YLHARYMDLPHPEGGRLQ 306
           GR HQ+R H   + CPIVGD  Y  NF+ N  F+     K  +LH + M      G    
Sbjct: 237 GRKHQIRKHLSSINCPIVGDKDY-GNFRLNREFSKNFGLKRHFLHCKQMKFVF-NGRNYN 294

Query: 307 ITAPLPAHMV 316
           I A LP  + 
Sbjct: 295 ILAQLPKDLT 304


>gi|110639847|ref|YP_680057.1| ribosomal large subunit pseudouridine synthase D [Cytophaga
           hutchinsonii ATCC 33406]
 gi|110282528|gb|ABG60714.1| ribosomal large subunit pseudouridine synthase D [Cytophaga
           hutchinsonii ATCC 33406]
          Length = 348

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 90/336 (26%), Positives = 157/336 (46%), Gaps = 47/336 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV +  +  MR+D++  +   +     +Q  +    V+V+ K  K + +++ G V+ I  
Sbjct: 25  VVCDPGQSLMRIDKFLMSRIQYATRSRIQYGIEIDSVKVNDKSTKASYKVRPGDVITI-- 82

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
              +L H  +E  ++   + L          ++YED +I + NK  G+ V    G     
Sbjct: 83  ---SLPHPPREDVLIPEDIPLD---------IVYEDDQILIVNKKPGMVVHPAHGNWTGT 130

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +AYH +  L + V+ K  +P L HR+D++TSG+LV+A+T  A   + + F    I+
Sbjct: 131 LVNALAYHFEN-LPTHVNGK-IRPGLIHRIDKDTSGLLVIAKTDYAMTFMAKQFADHSIE 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---A 237
           + Y+++ WG+P  K   I N+L + +      +    +NE+    AI+H+K +  +   A
Sbjct: 189 RTYYAICWGVPDPKSGTIKNYLGRSTK--DRKLVTTYENEEDGKLAITHYKTLAAYHYVA 246

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQN----- 286
              C LE    TGRTHQ+R H   +G  +  D  Y  N        G +   ++N     
Sbjct: 247 LIQCNLE----TGRTHQIRAHMKSIGHSLFNDMSYGGNSVVKGTVTGKYKQFVENCFKLL 302

Query: 287 -KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            +  LHA+ +   HP    ++Q  + LPA M    D
Sbjct: 303 PRQALHAKTLGFIHPTTKEKMQFDSELPADMQAVLD 338


>gi|282900595|ref|ZP_06308537.1| Pseudouridine synthase, RluD [Cylindrospermopsis raciborskii
           CS-505]
 gi|281194395|gb|EFA69350.1| Pseudouridine synthase, RluD [Cylindrospermopsis raciborskii
           CS-505]
          Length = 326

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 93/320 (29%), Positives = 150/320 (46%), Gaps = 39/320 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV---VRIPPVIN 72
           ++  RLDR+  +  P ++   +Q ++  G V+V+ K     N    G     V IPPV  
Sbjct: 30  QKTQRLDRYLSSVIPDLSRSRIQDLIEQGYVQVNGKVCYSKNITLDGGEYLEVEIPPVQA 89

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG- 131
           A   ++ +   LD               +LYED ++ + NKPAG+ V    G   H++G 
Sbjct: 90  A--QLVAQDIPLD---------------ILYEDEQLLILNKPAGLVVHPAPG---HLEGT 129

Query: 132 ----FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                L    +  G    Q+P + HRLD++T+G + +A+T  A + L    + +  ++ Y
Sbjct: 130 LVHALLAHCPNLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKQLQLQLQSKIARREY 189

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             +V+G PK++   I   L    H        +   E+G   AI+++ + +     +  +
Sbjct: 190 LGVVYGAPKSESGTID--LPIGRHPQQRKKMAIVPVEQGGRNAITNWHIKERLG-NYTLI 246

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             Q  TGRTHQ+RVH+  MG PIVGD  Y +        P Q    LHA  + L HP  G
Sbjct: 247 HFQLETGRTHQIRVHSAKMGHPIVGDPVYSSGRSVGVNLPGQA---LHAWQLKLQHPTSG 303

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             +++TAPLP  + K  + L
Sbjct: 304 EWVEVTAPLPDSLTKLIEVL 323


>gi|225011533|ref|ZP_03701971.1| pseudouridine synthase, RluA family [Flavobacteria bacterium
           MS024-2A]
 gi|225004036|gb|EEG42008.1| pseudouridine synthase, RluA family [Flavobacteria bacterium
           MS024-2A]
          Length = 346

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 90/320 (28%), Positives = 149/320 (46%), Gaps = 51/320 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI----PPVINAL 74
           +R+D++      ++    +Q+  ++G + VD   VK N +++ G  V++    PP  N L
Sbjct: 33  LRVDKFLMARVENVTRSKIQQAAKAGSIFVDGNEVKSNYKVKGGDKVKVLFSHPPYENLL 92

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGI 125
              + E   LD               +++ED  + V NKP G+ V  G         +G+
Sbjct: 93  ---VPEDMPLD---------------IVFEDDILVVVNKPPGMVVHPGHGNYSGTLLNGL 134

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            YH D   K+      ++P L HR+D++TSG+LV+A+T  A  HL + F  +  ++ Y +
Sbjct: 135 LYHFDQLPKN----SNERPGLVHRIDKDTSGLLVIAKTEQAMTHLAKQFFDKTSERKYSA 190

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LVWG  K ++  I   + +  H        V ++      A +HFKVI+ F      +E 
Sbjct: 191 LVWGDVKEEEGTIEGAIGR--HPKNRLQMAVFEDNSQGKEAKTHFKVIERFGY-VTLIEC 247

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---------PIQNKLYLHAR 293
           Q  TGRTHQ+R H   +G  +  D +Y  +   KG +FT           +  +  LHA+
Sbjct: 248 QLETGRTHQIRAHLKFIGHTLFNDARYGGDKILKGTSFTKYKQFVENCFALLPRQALHAQ 307

Query: 294 YMDLPHPEGG-RLQITAPLP 312
            +   HP  G ++    PLP
Sbjct: 308 TLGFIHPSSGEKMLFETPLP 327


>gi|282896340|ref|ZP_06304362.1| Pseudouridine synthase, RluD [Raphidiopsis brookii D9]
 gi|281198836|gb|EFA73715.1| Pseudouridine synthase, RluD [Raphidiopsis brookii D9]
          Length = 323

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 91/320 (28%), Positives = 151/320 (47%), Gaps = 39/320 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV---VRIPPVIN 72
           ++  RLDR+  +  P ++   +Q ++  G V+V+ K     N    G     V +PPV  
Sbjct: 27  QKTQRLDRYLSSVIPDLSRSRIQDLIEQGYVQVNGKVCYSKNITLDGGEYLEVEVPPVQA 86

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG- 131
           A   ++ +   LD               +LYED ++ + NKPAG+ V    G   H++G 
Sbjct: 87  A--QLVAQDIPLD---------------ILYEDEQLLILNKPAGLVVHPAPG---HLEGT 126

Query: 132 ----FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                L    +  G    Q+P + HRLD++T+G + +A+T  A + L    + +  ++ Y
Sbjct: 127 LVHALLAHCPNLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKQLQLQLQSKTARREY 186

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             +V+G PK++   +   L    H        +   E+G   AI+++ + +     +  +
Sbjct: 187 LGVVYGAPKSESGTMD--LPIGRHPQQRKKMAIVPVEQGGRNAITNWYIKERLG-NYTLI 243

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             Q  TGRTHQ+RVH+  MG PIVGD  Y +        P Q    LHA  + L HP  G
Sbjct: 244 HFQLETGRTHQIRVHSAKMGHPIVGDPVYSSGRSVGVNLPGQA---LHAWQLKLQHPTSG 300

Query: 304 R-LQITAPLPAHMVKTWDSL 322
           + +++TAPLP  + K  + L
Sbjct: 301 KWVEVTAPLPDSLTKLIEVL 320


>gi|238927877|ref|ZP_04659637.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
 gi|238884210|gb|EEQ47848.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
          Length = 299

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 93/327 (28%), Positives = 153/327 (46%), Gaps = 53/327 (16%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVI 71
           +D    RLD +     P ++    Q+++  G V VD +R K N ++   ++V   +PP  
Sbjct: 5   SDRVGERLDVFLVRQMPALSRSYAQRLIAGGNVAVDGERRKANFKLSGAEMVVCTLPPA- 63

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                  +E +I    + L          +LYED+ I V NK  G+ V   +G+     +
Sbjct: 64  -------EETEICAEDIPLD---------ILYEDADIIVINKRRGMVVHPAAGVHTGTLV 107

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HRLD++TSG++V A+   A  +L    R +  ++ Y +
Sbjct: 108 NALLHHCSDLSGINGALRPGIVHRLDKDTSGVMVAAKNDMAHHYLARQIRDKEARREYRA 167

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDY---------VHVVKQNEKGANYAISHFKVIDCF 236
           +V+G          N + +   I GD          + +V++N + A    +HF+V++ F
Sbjct: 168 IVYG----------NIVERAGVITGDIGRHPTDRKKMAIVRENGRPAT---THFEVLERF 214

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              + ++  +  TGRTHQ+RVH   +G P+VGD KY A  K  F    Q    LH+  + 
Sbjct: 215 GD-YTFVACRLETGRTHQIRVHMTSIGHPLVGDTKYTAK-KNPFAITGQ---ALHSLTLT 269

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWDSL 322
           L HP     +  TAPLPA M +   +L
Sbjct: 270 LTHPRTQEEMTFTAPLPADMEEILHTL 296


>gi|154252611|ref|YP_001413435.1| RluA family pseudouridine synthase [Parvibaculum lavamentivorans
           DS-1]
 gi|154156561|gb|ABS63778.1| pseudouridine synthase, RluA family [Parvibaculum lavamentivorans
           DS-1]
          Length = 482

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 96/343 (27%), Positives = 151/343 (44%), Gaps = 45/343 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + V V  ++   RLD++                   G       R +    I+ GQV R
Sbjct: 134 TRAVTVTAEDAGARLDKYLTEALGDKG---------EGDAPATLSRARMRQLIEQGQVSR 184

Query: 67  -----IPPVINALNHIIKEQKILDSSVNL-TKHSDFLKSI---LLYEDSKIYVFNKPAGI 117
                 P ++   ++ +K  + L  SV   T      ++I   ++YED+ + V  KPAG+
Sbjct: 185 EEKAGAPKLLTDPSYRVKAGERLSVSVPPPTPAKPAGQAIPLEIVYEDADLIVVMKPAGL 244

Query: 118 SVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V    G         +  H    L      K  +P + HRLD+ETSG++VVA+T  A Q
Sbjct: 245 VVHPAPGNPDMTLVNALVAHCGETLSGIGGEK--RPGIVHRLDKETSGLMVVAKTDRAHQ 302

Query: 169 HLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GA 223
            L+  F    R  ++ + Y +L WG+P+ +K  +   + + SH       V  + E+ G 
Sbjct: 303 GLSAQFAAHGRDGKLTRAYTALTWGVPQTRKGTVDANIARSSHNRSKMATVRDRGEETGG 362

Query: 224 NYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT- 281
             AI+H+ V   +A      +E +  TGRTHQ+RVH   +G P++GD  Y    K   + 
Sbjct: 363 RIAITHYTVKTDYADGLVAEVECRLETGRTHQIRVHMTALGHPLLGDATYGTGMKSRKSK 422

Query: 282 -SPIQ-------NKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
            SP         N+  LHA ++   HP  G ++   APLP  M
Sbjct: 423 LSPEAQAALERLNRQALHAHHLGFEHPVAGEKMSFDAPLPEDM 465


>gi|218530900|ref|YP_002421716.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
 gi|218523203|gb|ACK83788.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
          Length = 239

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 79/229 (34%), Positives = 116/229 (50%), Gaps = 19/229 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           LLY D+ + V +KPAG+ V    +GG  +  H+D           ++P   HRLD++TSG
Sbjct: 20  LLYRDALMLVIDKPAGLPVHPGPKGGPTLTDHLDALRFGLP----RRPEAAHRLDRDTSG 75

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R   A   L   F   R+ K YW+LV G P+  +  I   L K+S    D     
Sbjct: 76  CLVLGRHAKALARLNRLFADGRVDKTYWALVEGGPEAMEGRIDLPLAKRSD---DPRSWW 132

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + +     +++ ++V+   ++   WLE++P TGRTHQLRVH   MG PI GD  Y +  
Sbjct: 133 MKTDPAGAPSLTLYRVLG-QSEGLSWLELKPVTGRTHQLRVHCAAMGWPIRGDAIYGSAG 191

Query: 277 KGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
           +          L LHAR + LP +P+   + + AP PAHM    D+ G 
Sbjct: 192 RDG------PGLQLHARGLSLPLYPKREAIAVEAPAPAHMRAGLDACGM 234


>gi|260494008|ref|ZP_05814139.1| pseudouridylate synthase [Fusobacterium sp. 3_1_33]
 gi|260198154|gb|EEW95670.1| pseudouridylate synthase [Fusobacterium sp. 3_1_33]
          Length = 304

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 87/308 (28%), Positives = 158/308 (51%), Gaps = 27/308 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++Y++ E D E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G ++ 
Sbjct: 2   IEYIIDE-DYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDIIF 60

Query: 67  I--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           I  P +    N    E+K ++ S       + LK ++++E+  ++V NKP G  V  GSG
Sbjct: 61  IFLPEIFKEKN----EEKFIEIS---QIRKEKLKQMIVFENDNLFVINKPLGDVVHKGSG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +    +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+
Sbjct: 114 HDISLLEEFRSYYSNNN--INFVNRIDKLTSGLVIGAKNIKTAREVAKEIQAGNIVKKYY 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  +     + N+L K      + V V    ++G   +I++FK I  +  K+  LE
Sbjct: 172 ILVNGKIEKDNFILENYLKKDE----ERVIVSDIEKEGYKKSITYFKKIKEY-DKYTLLE 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQLR    H+G  IVGD KY  N K       ++ +YL + Y+ +       
Sbjct: 227 AELKTGRTHQLRAQLNHLGNNIVGDIKYGKNEK-------EDIMYLFSYYLKIDLY---N 276

Query: 305 LQITAPLP 312
           L+I   +P
Sbjct: 277 LEIKLEIP 284


>gi|254431057|ref|ZP_05044760.1| pseudouridylate synthase, 23S rRNA-specific [Cyanobium sp. PCC
           7001]
 gi|197625510|gb|EDY38069.1| pseudouridylate synthase, 23S rRNA-specific [Cyanobium sp. PCC
           7001]
          Length = 320

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 92/304 (30%), Positives = 142/304 (46%), Gaps = 32/304 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW     P  +   +QK + +G VRV+    +    ++ G  V +  PP    L +
Sbjct: 22  MRLDRWLVAQRPEQSRARIQKFIEAGYVRVNGVTGRAKTPLRHGDRVEVWMPPP-EPLPY 80

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           ++ +   LD               +LYED+ + V NKPAG++V    G      ++G L 
Sbjct: 81  LVAQAMPLD---------------VLYEDAHLIVLNKPAGLTVHPAPGNKDGTLVNGLLH 125

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +VVA+++ A  +L    + R   + Y  +V G 
Sbjct: 126 HCPDLPGIGGELRPGIVHRLDKDTTGCIVVAKSQEALVNLQVQIQKRIASRDYLGVVHGQ 185

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      +   + +       Y  V   ++    +A +H++V +     +  L  +  TG
Sbjct: 186 PAADHGTVIGAIGRHPADRKKYAVV---SDASGRHACTHWQVQERLGD-YALLRFKLDTG 241

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH+ HMG PIVGD  Y    +     P Q    LHA  + L HP    RL + A
Sbjct: 242 RTHQIRVHSAHMGHPIVGDPVYSRCRRLPLALPGQA---LHAVRLGLDHPITRERLVLEA 298

Query: 310 PLPA 313
           PLPA
Sbjct: 299 PLPA 302


>gi|308173508|ref|YP_003920213.1| pseudouridylate synthase [Bacillus amyloliquefaciens DSM 7]
 gi|307606372|emb|CBI42743.1| pseudouridylate synthase [Bacillus amyloliquefaciens DSM 7]
 gi|328553560|gb|AEB24052.1| pseudouridylate synthase [Bacillus amyloliquefaciens TA208]
 gi|328911647|gb|AEB63243.1| pseudouridylate synthase [Bacillus amyloliquefaciens LL3]
          Length = 304

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 91/322 (28%), Positives = 155/322 (48%), Gaps = 36/322 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+ ++++ R+D++  +   + +   +Q+ ++ G V V+ K VK N ++Q G       
Sbjct: 6   ITVQPEQKSERIDKFLASTGENWSRTQVQQWVKEGLVSVNGKSVKANYKMQPG------- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
             + +N  I E + LD    L +  D     + YED  + V NKP G+ V    G     
Sbjct: 59  --DQVNVTIPEPEELDV---LAEPMDL---DIYYEDQDVLVVNKPRGMVVHPAPGHVTGT 110

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y
Sbjct: 111 LVNGLMAHCNDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYV--HVVKQNEKGANYAISHFKVIDCFAQKFC 241
            ++V G+  +    I       + IG D      +    +G+  A++HF V++ F Q F 
Sbjct: 171 TAVVHGVISHDDGTI------DAPIGRDKKDRQSMTVTREGSKNAVTHFHVLERF-QDFT 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E +  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   HP 
Sbjct: 224 LVECRLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTVDF-----NGQALHAGILGFDHPR 278

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++  APLP  M K  + L
Sbjct: 279 TGEYMEFEAPLPEDMKKLIELL 300


>gi|284929127|ref|YP_003421649.1| ribosomal large subunit pseudouridine synthase D [cyanobacterium
           UCYN-A]
 gi|284809586|gb|ADB95291.1| ribosomal large subunit pseudouridine synthase D [cyanobacterium
           UCYN-A]
          Length = 316

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 90/323 (27%), Positives = 158/323 (48%), Gaps = 35/323 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRI-PPVIN 72
           +++  R+DRW   H  +I+   +QK++++G + ++ K  K    ++ +G  + +  P   
Sbjct: 8   EDKGDRIDRWLSKHILNISRARIQKLIQAGNIILNNKICKTKKEQLIAGDCLEVFVPSPK 67

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
            L  +I E   LD               +LYED  + + NK AG+ V    G      + 
Sbjct: 68  KL-ELIPEAIPLD---------------VLYEDKYLIIINKVAGMVVHPSPGHENGTLVH 111

Query: 131 GFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             L    D  G    Q+P + HRLD++T+G +V+A+T    QHL +  R R +++ Y ++
Sbjct: 112 ALLHHCRDLSGIGEVQRPGIVHRLDKDTTGTIVIAKTDFVHQHLQKQIRDRVVEREYLAI 171

Query: 187 VWGIPKNKK--ECIANWLLKKSHIGGDYVH----VVKQNEKGANYAISHFKVIDCFAQKF 240
           + G+ KN++  + + N  +    IG   +      V  +EK    A++++K+++     +
Sbjct: 172 IHGVLKNRENNDNVVNKGVIDLPIGRHLIDRKKMAVMPSEKNGRKAVTYWKILERLGN-Y 230

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +  +  TGRTHQ+RVH+  +GCPI+GD  Y +N   N     Q    LHA  + L HP
Sbjct: 231 SMVNFKLGTGRTHQIRVHSSFLGCPILGDPLYSSNHSFNINLSGQ---ALHAHKLSLIHP 287

Query: 301 -EGGRLQITAPLPAHMVKTWDSL 322
               +++ITA  P    K   +L
Sbjct: 288 VSSNKIEITANPPIEFTKLLKTL 310


>gi|298492053|ref|YP_003722230.1| pseudouridine synthase, RluA family ['Nostoc azollae' 0708]
 gi|298233971|gb|ADI65107.1| pseudouridine synthase, RluA family ['Nostoc azollae' 0708]
          Length = 329

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 97/348 (27%), Positives = 160/348 (45%), Gaps = 62/348 (17%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-------KKRVKFN 56
           MT +  +V +N +   RLD +  +   +++   LQ+++  G V ++       K  VK  
Sbjct: 21  MTVINLLVSQNTQ---RLDLYLSSELQNLSRSRLQQLIEQGHVLLNDQVCTSKKVNVKVG 77

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           +RI     V IP         ++  K++   + L          +LYED ++ + NKPAG
Sbjct: 78  DRI----CVEIPS--------LQPLKLVAEDIPLD---------ILYEDEQLLILNKPAG 116

Query: 117 ISVQGGSGIAYHIDG-----FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAA 167
           + V    G   H+DG      L    +  G    Q+P + HRLD++T+G + +A+T  A 
Sbjct: 117 LVVHPAPG---HLDGTLVNALLAHCANLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAY 173

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           QHL    + +  ++ Y  +V+G+PK +   I   L    H        +   E+G   AI
Sbjct: 174 QHLQAQLQAKTARREYLGVVYGVPKTESGIIN--LPISRHPQDRKKMAIVPTEQGGRTAI 231

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFT 281
           +H+++ +  +  +  +  Q  TGRTHQ+RVH+  +G PIVGD  Y A      N  G+  
Sbjct: 232 THWQIRERLS-NYTLIHFQLETGRTHQIRVHSAKIGHPIVGDSVYGAGRSVGVNLAGH-- 288

Query: 282 SPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
                   LHA  + L HP  G  +Q+TA  P       + L  + +R
Sbjct: 289 -------ALHAWQLKLQHPISGDWIQVTASPPQTFTTLLEVLRRRSER 329


>gi|317968170|ref|ZP_07969560.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp.
           CB0205]
          Length = 325

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 94/308 (30%), Positives = 141/308 (45%), Gaps = 32/308 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRIPPVINALNH 76
           MRLDRW     P  +   +QK + +G VRV+    R K   R+     + +PP    L +
Sbjct: 22  MRLDRWLVAQRPEQSRARIQKFIDAGYVRVNGVTGRAKTPLRLNDTVELWMPPP-EPLPY 80

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +I +   LD               +LYED  + V NKPAG++V    G      ++G L 
Sbjct: 81  LIPQDIPLD---------------VLYEDEHLIVLNKPAGLTVHPAPGNKDGTLVNGLLH 125

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +VVA+++ A   L    + R   + Y ++V G 
Sbjct: 126 HCPDLPGIGGEMRPGIVHRLDKDTTGCIVVAKSQEALVKLQVQIQKRVASREYLAVVHGA 185

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +       Y  V   ++    +A +H+ +++     +  +  +  TG
Sbjct: 186 PAGDNGTIVGAIGRHPADRKKYAVV---HDGSGRHACTHWTLLERLGD-YALMRFKLDTG 241

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  H+G PIVGD  Y    K   T P Q    LHA  + L HP    R+   A
Sbjct: 242 RTHQIRVHCAHIGHPIVGDPVYSRCRKLPLTLPGQA---LHAFQLGLDHPIRKDRMLFEA 298

Query: 310 PLPAHMVK 317
           PLP  M K
Sbjct: 299 PLPEVMEK 306


>gi|192288803|ref|YP_001989408.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           TIE-1]
 gi|192282552|gb|ACE98932.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           TIE-1]
          Length = 334

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 96/342 (28%), Positives = 151/342 (44%), Gaps = 51/342 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIP 68
           VVV  DE + RLDR      P ++   L+ ++  G+V +    V+        G+ + I 
Sbjct: 11  VVVAGDEGSQRLDRVLAARCPELSRSRLKALILDGRVAIAGTPVRDPAYHASPGETITID 70

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                      E   LD               ++YED+ I V NKP G+ V   +G  + 
Sbjct: 71  VPPPVPAEPAGEAIALD---------------IVYEDADIIVLNKPRGLVVHPAAG--HE 113

Query: 129 IDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----R 175
               + + +   G         ++P + HRLD++T+G++V A+   A Q L+  F    R
Sbjct: 114 TGTLVNALIAHCGASLSGIGGVRRPGIVHRLDKDTTGLMVAAKNDKAHQSLSAQFADHGR 173

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              +++ Y + VWG+P  K   I   + +  H        V+Q   G   AI+H++V++ 
Sbjct: 174 TGELRRGYLAFVWGVPGRKYGTIDAPIDRHPH--AREKMAVRQ---GGREAITHWEVLEN 228

Query: 236 FAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQ--- 285
           FA K        +  Q  TGRTHQ+RVH  H+G P++GD  Y  +F  K N  +P     
Sbjct: 229 FAGKDGKPVAALIACQLETGRTHQIRVHLAHLGHPLLGDDVYGPHFKTKANQLAPAGRAA 288

Query: 286 ----NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                +  LHA  + L HP  G  L   +PLPA +     +L
Sbjct: 289 LAGLGRQALHAYLLTLEHPSTGEVLTWESPLPADLAHLQAAL 330


>gi|168014236|ref|XP_001759658.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162689197|gb|EDQ75570.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 283

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 90/274 (32%), Positives = 133/274 (48%), Gaps = 58/274 (21%)

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVAR 162
           +D++I V NKP+G++VQGGS +   +D  +++ +  +  + PRL HRLD+ETSG LV+ R
Sbjct: 1   QDAEIIVINKPSGLAVQGGSDVVKSLDSMMEAALSYNYNEGPRLVHRLDKETSGALVLGR 60

Query: 163 TRAAAQHLTESFRMRRIQKI-------YWSLVWGIPKNKKECIANWLLKKSHIGG--DYV 213
           T  +   L    R  + +KI       Y +LV G+P+ K+  I+  L K     G  D +
Sbjct: 61  THQSTVFLQALLR-NKTEKISQAPGRCYLALVIGVPEKKEGRISAPLAKVVSDSGKLDKM 119

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALH-MGCPIVGDHK 271
            VV  +   A  AI+ +KV+       C WLE++P TGR HQ+RVH    +G PIVGD+K
Sbjct: 120 RVVHGSHPNAQEAITDYKVLGSSLFAGCSWLELRPLTGRKHQIRVHCAEVLGMPIVGDYK 179

Query: 272 Y-------------CANFKGNFTSPIQNK--------LYLHARYMDLPH----------- 299
           Y               + K +     ++         L+LH R + LP            
Sbjct: 180 YGWRALRLWPPTDRTEDTKSSVLGLRESGHVWSSKPYLHLHCRQLILPDVAQAFKSQSRE 239

Query: 300 ----PEGGR---------LQITAPLPAHMVKTWD 320
                 G R         L+I APLP HMV +W+
Sbjct: 240 RSSAQTGARVSGSQFAEPLEIIAPLPPHMVVSWN 273


>gi|210612741|ref|ZP_03289456.1| hypothetical protein CLONEX_01658 [Clostridium nexile DSM 1787]
 gi|210151434|gb|EEA82442.1| hypothetical protein CLONEX_01658 [Clostridium nexile DSM 1787]
          Length = 305

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 90/335 (26%), Positives = 159/335 (47%), Gaps = 54/335 (16%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q V VE +    R+D++    +P ++   +QK+++ G V  + K VK N ++       
Sbjct: 2   IQTVTVEKEFSGNRVDKFLSEQFPDLSRSYIQKLIKDGHVTANGKIVKANYKL------- 54

Query: 67  IPPVINALNHI------IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
                NAL+ +      ++E  I+  ++ +          +LYED  I + NKP G+ V 
Sbjct: 55  -----NALDTLALDKPELQEPDIVPENIPID---------ILYEDEDILIVNKPKGMVVH 100

Query: 121 GGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
             +G         + YH    L     +   +P + HR+D +T+G L+V +     Q L 
Sbjct: 101 PSAGHYSGTLVNALMYHCKDQLSGI--NGIMRPGIVHRIDMDTTGSLLVCKNDFVHQDLA 158

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISH 229
           E  +   IQ+IY ++V G+ K  +  I       + IG   +   K   N K   +A++H
Sbjct: 159 EQLKEHSIQRIYHAIVHGVIKEDEGTI------DAPIGRHPIERKKMSVNYKNGKHAVTH 212

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKL 288
           +KVI+ F + + +++ +  TGRTHQ+RVH  H+  P++GD  Y     G    P +    
Sbjct: 213 YKVIERF-KNYTYIKCRLETGRTHQIRVHMAHIRHPLLGDAVY-----GPAKCPFKLQGQ 266

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            LHA+ + + HP     +++ APLP + +   + L
Sbjct: 267 TLHAKTLGIVHPRTHEYIEVDAPLPDYFISLLNKL 301


>gi|307293091|ref|ZP_07572937.1| pseudouridine synthase, RluA family [Sphingobium chlorophenolicum
           L-1]
 gi|306881157|gb|EFN12373.1| pseudouridine synthase, RluA family [Sphingobium chlorophenolicum
           L-1]
          Length = 316

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 86/325 (26%), Positives = 157/325 (48%), Gaps = 44/325 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---PPVIN 72
           ++ MRLD+      P ++   L+ ++  GQV    +    + ++  GQ   I   PPV  
Sbjct: 16  QDGMRLDKALAELVPDLSRERLKALIVDGQVTSSGRAPNPSLKVTMGQAFAIALPPPV-- 73

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                  E + +  ++ L          +++ED+ + V +KPAG+ V   +G   ++DG 
Sbjct: 74  -------EAEAVAQNIPLA---------IVHEDADLIVIDKPAGLVVHPAAG---NLDGT 114

Query: 133 LKSWV--DSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           L + +    +GQ        +P + HR+D++TSG+LVVA++  A + L + F    I ++
Sbjct: 115 LVNALLHHCQGQLSGIGGVARPGIVHRIDKDTSGLLVVAKSDRAHEGLAQQFAAHSIDRL 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V+G P+     + +W+ +      D   +    E    +A++H++ ++   +    
Sbjct: 175 YAAIVYGAPQPAAGTVDSWIGRSD---ADRKKMAVCREGRGKHAVTHYRTLEKL-RGAAL 230

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLP 298
           +E +  TGRTHQ+RVH   +G P++GD  Y    KG F S ++     +  LHA+ +   
Sbjct: 231 VECRLETGRTHQVRVHMTQLGHPLIGDPVYGKERKG-FKSILETLGFKRQALHAKRLGFI 289

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSL 322
           HP  G  L   + LPA M +    L
Sbjct: 290 HPVTGEALSFDSQLPADMQELLSEL 314


>gi|88801297|ref|ZP_01116825.1| ribosomal large subunit pseudouridine synthase D [Polaribacter
           irgensii 23-P]
 gi|88781955|gb|EAR13132.1| ribosomal large subunit pseudouridine synthase D [Polaribacter
           irgensii 23-P]
          Length = 228

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 75/227 (33%), Positives = 113/227 (49%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ I + NK AG   QG       +   +K ++  K  KP        HRLD+ TS
Sbjct: 10  VLFEDNHIIIINKRAGDITQGDKTGDKPLSDVIKEYIKEKYNKPGEVFIGTVHRLDRPTS 69

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ ART  A   L +  R + I K YW+LV   P    + I N+L K +     +V+ 
Sbjct: 70  GIVIFARTSKALTRLNKMLRDKVIDKTYWALVKNAPIKATDTITNFLKKDTKKNKSFVY- 128

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+  +G   A+ H+K++    + +C LE+   TGR HQ+R    H+G  I GD KY A+
Sbjct: 129 -KKEIEGCKKAVLHYKILQKL-ESYCLLEIDLETGRHHQIRTQLSHIGSVIKGDLKYGAS 186

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
                 S     + LHAR +   HP     + ITAP P  ++  W++
Sbjct: 187 -----RSNKDGSISLHARKIKFTHPVSKEEIAITAPTPKDII--WNA 226


>gi|148544158|ref|YP_001271528.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri DSM 20016]
 gi|184153530|ref|YP_001841871.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227364587|ref|ZP_03848648.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM2-3]
 gi|325682298|ref|ZP_08161815.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
 gi|148531192|gb|ABQ83191.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri DSM 20016]
 gi|183224874|dbj|BAG25391.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227070424|gb|EEI08786.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM2-3]
 gi|324978137|gb|EGC15087.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
          Length = 303

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 93/314 (29%), Positives = 149/314 (47%), Gaps = 42/314 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+   +H+   +   +Q  +  G V V+ K+VK   ++  G  V+I P       +  
Sbjct: 16  RIDKQLGHHFDQFSRSQIQHWIEDGHVLVNGKQVKPKYKLLVGDHVQIIPEEPQKIDLAP 75

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL--KS 135
           E   LD               ++YED  + V NKP G+ V    G   H  ++  L    
Sbjct: 76  EDIPLD---------------IVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHSP 120

Query: 136 WVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                G+ +P + HR+D++TSG+L+VA+   A + LT   + +  ++ Y +LV G+ K  
Sbjct: 121 LSTINGEFRPGIVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKED 180

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVIDCFAQKFCWLEMQPHT 249
           K  I   L +           +K  +K A      +A++HF V++ F + +  +  Q  T
Sbjct: 181 KGTIDAPLGRS----------LKDRKKQAVVVDGRHAVTHFNVLERF-KNYTLVACQLET 229

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+ GD  Y     G   +   N  YLHAR +   HP  G+ +  T
Sbjct: 230 GRTHQIRVHMKYIGHPLAGDPLY-----GPRKTLAGNGQYLHARLLGFKHPRTGKEMVFT 284

Query: 309 APLPAHMVKTWDSL 322
           APLPA+ VK  + L
Sbjct: 285 APLPAYFVKMLEHL 298


>gi|256959131|ref|ZP_05563302.1| pseudouridylate synthase [Enterococcus faecalis DS5]
 gi|256949627|gb|EEU66259.1| pseudouridylate synthase [Enterococcus faecalis DS5]
          Length = 301

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 94/319 (29%), Positives = 156/319 (48%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 11  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                E ++LD        ++ +   ++YED+ + V NKP  + V   +G         +
Sbjct: 65  -----EPEVLDMV------AEDIPLTIVYEDNDVIVVNKPQDMVVHPSAGHPKGTLVNAL 113

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H D  L +  D    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 114 LHHAD-HLSAINDVV--RPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 170

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 171 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 224 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 278

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 279 QLVFEAPLPEVFEKTLHQL 297


>gi|116074038|ref|ZP_01471300.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9916]
 gi|116069343|gb|EAU75095.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9916]
          Length = 343

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 95/313 (30%), Positives = 144/313 (46%), Gaps = 32/313 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +     +   +QK + +G VRV+ K  K    ++ G  V++  PP    L +
Sbjct: 40  MRLDRWLVSQRSEQSRARIQKFIDAGFVRVNGKTGKAKTPLRDGDEVQLWMPPP-EPLPY 98

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E   LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 99  LKPEPMDLD---------------VLFEDDHLIVINKPAGLTVHPAPGNKDGTLVNGLLH 143

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y ++V G+
Sbjct: 144 HCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQVQIQKRIASREYMAVVHGL 203

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P+     I   + +  H      + V   E G  YA +H+ +++     +  L  +  TG
Sbjct: 204 PQGDSGSIVGAIGR--HPADRKKYAVVSGESG-RYACTHWTLVERLGD-YSLLRFKLDTG 259

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  HM  P+VGD  Y    K     P Q    LHA  + L HP    R+   A
Sbjct: 260 RTHQIRVHCAHMNHPVVGDPTYSRCRKLPIDLPGQA---LHAFQLGLDHPITRERMVFEA 316

Query: 310 PLPAHMVKTWDSL 322
           PLP  M K    L
Sbjct: 317 PLPPVMEKLLSVL 329


>gi|323343928|ref|ZP_08084155.1| ribosomal large subunit pseudouridine synthase D [Prevotella oralis
           ATCC 33269]
 gi|323095747|gb|EFZ38321.1| ribosomal large subunit pseudouridine synthase D [Prevotella oralis
           ATCC 33269]
          Length = 355

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 96/337 (28%), Positives = 163/337 (48%), Gaps = 58/337 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +E +R+D++      H +   +Q+   +G V V+ + VK N +++   V+ +  
Sbjct: 25  LVVDKGQEPLRIDKYMSEKLQHSSRNRIQRAADAGFVHVNDRPVKSNYKVRPLDVITL-- 82

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
           +++   H        DS++     ++ +   +++EDS++ V NKPAG+ V  G G     
Sbjct: 83  MLDRPRH--------DSTIE----AEDIPLDIVFEDSELMVINKPAGLVVHPGVGNFHGT 130

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+   LKS+ D    +  L HR+D++TSG+LV+A+T  A   L   F  +   
Sbjct: 131 LVNAIAWHLKD-LKSF-DPNDPEVGLVHRIDKDTSGLLVIAKTPMAKTKLGLQFFNKTTH 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------VVKQNEKGANYAISHFK 231
           + Y +LVWG          N+   +  I G+            V   + +    A++H++
Sbjct: 189 RSYNALVWG----------NFTEDEGRIEGNIARDPKDRLRMTVFAPDSEIGKSAVTHYR 238

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQ 285
           VI+ F      +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S     IQ
Sbjct: 239 VIERFGY-VTLVECILETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSTYRAFIQ 297

Query: 286 N------KLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           N      +  LHAR +   HP  G ++  T+ LPA M
Sbjct: 298 NCFKLCSRQALHARTLGFAHPVTGKQMDFTSELPADM 334


>gi|116072001|ref|ZP_01469269.1| Pseudouridine synthase, RluD [Synechococcus sp. BL107]
 gi|116065624|gb|EAU71382.1| Pseudouridine synthase, RluD [Synechococcus sp. BL107]
          Length = 339

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 96/308 (31%), Positives = 146/308 (47%), Gaps = 32/308 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +     +   +QK + +G VRV+ K+ K    ++ G  V++  PP    L +
Sbjct: 40  MRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKQGKAKTPLREGDQVQLWMPPP-EPLPY 98

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  +   LD               +L+ED  I V NK AG++V    G      ++G L 
Sbjct: 99  LRPQPMDLD---------------VLFEDEHIIVLNKSAGLTVHPAPGNKDGTLVNGLLH 143

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++TSG +VVA+++ A   L    + R   + Y+++V G+
Sbjct: 144 HCPDLPGISGKLRPGIVHRLDKDTSGCIVVAKSQEALVKLQVQIQKRVASREYFAVVHGV 203

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +  H      + V  +E G  YA +H+ +++ F   +  L  +  TG
Sbjct: 204 PNGDSGTIIGAVGR--HPVDRKKYAVVSDESG-RYARTHWFLVERFGD-YSLLRFKLDTG 259

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  H+  P+VGD  Y    K     P Q    LHA  + L HP  G R+   A
Sbjct: 260 RTHQIRVHCAHINHPVVGDPTYSRCRKLPVDLPGQA---LHAVQLGLDHPITGERMVFEA 316

Query: 310 PLPAHMVK 317
           PLP  M K
Sbjct: 317 PLPPVMEK 324


>gi|194468025|ref|ZP_03074011.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
 gi|194452878|gb|EDX41776.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
          Length = 303

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 94/312 (30%), Positives = 147/312 (47%), Gaps = 38/312 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+   +H+   +   +Q  +  G V V+ K+VK   ++  G  V+I P       +  
Sbjct: 16  RIDKQLGHHFDQFSRSQIQHWIEDGHVLVNGKQVKPKYKLLVGDHVQIIPEEPQKIDLAP 75

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL--KS 135
           E   LD               ++YED  + V NKP G+ V    G   H  ++  L    
Sbjct: 76  EDIPLD---------------IVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHSP 120

Query: 136 WVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                G+ +P + HR+D++TSG+L+VA+   A + LT   + +  ++ Y +LV G+ K  
Sbjct: 121 LSTINGEFRPGIVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKED 180

Query: 195 KECIANWL---LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K  I   L   LK     G  V           +A++HF V++ F + +  +  Q  TGR
Sbjct: 181 KGTIDAPLGRSLKDRKKQGVVV--------DGRHAVTHFNVLERF-KNYTLVACQLETGR 231

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P+ GD  Y     G   +   N  YLHAR +   HP  G+ +  TAP
Sbjct: 232 THQIRVHMKYIGHPLAGDPLY-----GPRKTLAGNGQYLHARLLGFKHPRTGKEMVFTAP 286

Query: 311 LPAHMVKTWDSL 322
           LPA+ VK  + L
Sbjct: 287 LPAYFVKMLEHL 298


>gi|42528076|ref|NP_973174.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
 gi|41819121|gb|AAS13093.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
          Length = 244

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 79/240 (32%), Positives = 122/240 (50%), Gaps = 22/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGI 157
           +LYED  I + NK AG+ V        A  +D  L+     KG+ K    HRLD+ETSG+
Sbjct: 8   ILYEDKDILIVNKNAGLLVGADRWDSEAPRLDKILEELYKDKGERKIYPVHRLDKETSGL 67

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A    A + L + F+ R+I+KIY ++  GIP+ +       L     I GD +H   
Sbjct: 68  IIYALNAEAHKTLNDDFQNRKIEKIYHAVSAGIPQEENFKAEEKL----RIDGDKLHRTV 123

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV-------GDH 270
            +EK    +++ F ++  F+ +FC LE +P TGRTHQ+R H  H+G PI+       G+ 
Sbjct: 124 IDEKKGKESLTEFSLLKRFS-RFCLLEARPITGRTHQIRAHLKHLGLPILCDNLYGNGEP 182

Query: 271 KYCANFKGNFTS------PIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
            Y +  K N+        PI ++L LHA  +   HP    +++I+A  P  M    + L 
Sbjct: 183 VYISALKKNWRGDKYEERPIISRLALHAHSLKFFHPISKEKIEISADYPKDMAGLINQLS 242


>gi|315037134|gb|EFT49066.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0027]
          Length = 310

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 94/319 (29%), Positives = 156/319 (48%), Gaps = 45/319 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G   VV IP      
Sbjct: 20  EKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIVVTIP------ 73

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                E ++LD        ++ +   ++YED+ + V NKP  + V   +G         +
Sbjct: 74  -----EPEVLDMV------AEDIPLTIVYEDNDVIVVNKPQDMVVHPSAGHPKGTLVNAL 122

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H D  L +  D    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +
Sbjct: 123 LHHAD-HLSAINDVV--RPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVA 179

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G IP +K E   N  + +S +      V++    G   A++HF V++ F   F  +E
Sbjct: 180 LVHGVIPHDKGEI--NAPIGRSKVDRKMQAVIE----GGKEAVTHFTVLERF-DAFTLVE 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G 
Sbjct: 233 LQLETGRTHQIRVHMKYIGYPLAGDPLY-----GPKKTLPGNGQFLHAKLLGFTHPTTGE 287

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L   APLP    KT   L
Sbjct: 288 QLVFEAPLPEVFEKTLHQL 306


>gi|251772724|gb|EES53286.1| Ribosomal large subunit pseudouridine synthase, RluA family
           [Leptospirillum ferrodiazotrophum]
          Length = 313

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 94/322 (29%), Positives = 144/322 (44%), Gaps = 35/322 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV--VRIPP 69
           V+  E   RLD +        +   +QKIL  G + V+ +    + +I+   +  V IPP
Sbjct: 4   VDPGESKKRLDHFLAQTCLPFSRSRIQKILDEGLITVNGRIEPASYKIRGADIITVHIPP 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
              A +    E+  LD               +LYED  + V NKP  + V    G     
Sbjct: 64  --PAPSEDAPEEMDLD---------------ILYEDEFLLVINKPPSLVVHPAPGHPNGT 106

Query: 125 IAYHIDGFLKSWVDSKGQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           +   + G L      +G+ P    L HRLDQ TSG+LVV +      HL E FR R + K
Sbjct: 107 LLNGLLGHLSREEAGEGEGPARAGLVHRLDQNTSGLLVVGKKSEVVDHLMEQFRGRTVSK 166

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L  GIP +++  I   + + +   GD       +  G   + + ++V+  + + + 
Sbjct: 167 SYIALAIGIPPSRRGLIDAPIGRSN---GDRKKFAVTS--GGKPSQTRYRVMTAYREGYS 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            L++   TGRTHQ+RVH  H+G P+ GD  Y    KG   + +  ++ LHA  +   HP 
Sbjct: 222 LLDITLLTGRTHQIRVHMQHLGYPLAGDPVY--KKKGRKDNLLFPRIMLHAANLGFTHPI 279

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
            G  L+  APLP  M      L
Sbjct: 280 TGEELKFHAPLPPDMQGALSQL 301


>gi|163794483|ref|ZP_02188454.1| Pseudouridylate synthase, 23S RNA-specific [alpha proteobacterium
           BAL199]
 gi|159180207|gb|EDP64730.1| Pseudouridylate synthase, 23S RNA-specific [alpha proteobacterium
           BAL199]
          Length = 349

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 86/327 (26%), Positives = 149/327 (45%), Gaps = 42/327 (12%)

Query: 20  RLDRWF------KNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72
           R+DRW       +   P ++   L+ ++  G++ V+   +   ++ ++ G   RI     
Sbjct: 37  RIDRWLARCLEDRETDPPLSRNRLKTLILDGRLFVNGATITDPSSPVKPGATYRI----- 91

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--ID 130
                     + +++  + +  D L   ++YED+ + V +KPAG++V    G      ++
Sbjct: 92  ---------DVPEATPAIPEAQD-LPLTVVYEDAALIVIDKPAGMTVHPAPGAPKDTLVN 141

Query: 131 GFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             +    DS       ++P + HR+D++TSG+LVVA+T AA   L   F    I + Y +
Sbjct: 142 ALIAHCGDSLSGIGGVKRPGIVHRIDKDTSGLLVVAKTDAAHHALAARFADHSIDRAYRA 201

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L WG P      I   + +      D + +  + E     A++HF+ +  F +    LE 
Sbjct: 202 LCWGRPIPPAGRIEGAIGRHPR---DRIRMAVRPEGSGKAAVTHFRTVRAFNEAATLLEC 258

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKLY------LHARYMD 296
           +  TGRTHQ+RVH  H+G P+VGD  Y        G      +++L+      LHA  + 
Sbjct: 259 RLETGRTHQIRVHLTHIGHPLVGDPVYGRGRSAKLGGLPEETRDRLHGFSRQALHAAVLG 318

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSL 322
             HP  G  L+  +PLP  +    D L
Sbjct: 319 FNHPITGEPLRFESPLPEDLAALIDDL 345


>gi|124024488|ref|YP_001018795.1| pseudouridylate synthase specific to ribosomal large subunit
           [Prochlorococcus marinus str. MIT 9303]
 gi|123964774|gb|ABM79530.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9303]
          Length = 324

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 92/303 (30%), Positives = 142/303 (46%), Gaps = 32/303 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +     +  ++QK + +G VRV+    +    ++ G  V++  PP    L +
Sbjct: 28  MRLDRWLVSQRSEQSRSHIQKFIEAGLVRVNGITGRAKTPLRQGDEVQLWMPPP-EPLPY 86

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
           +  E   LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 87  LQPEAMHLD---------------VLFEDRHLIVINKPAGLTVHPAPGNRNGTLVNGLLH 131

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +V+A+++ A   L +  + R   + Y ++V G 
Sbjct: 132 HCSDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQQQIQKRIASRNYLAVVHGA 191

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P   +  I   + +       Y  V    E G  +A +H+ +++     +  L  Q  TG
Sbjct: 192 PTGDQGTIVAAIGRHPVDRKKYAVV---TEDGGRHACTHWTLVERLGD-YSLLRFQLDTG 247

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  H+G PIVGD  Y    K     P Q    LHA  + L HP  G R+   A
Sbjct: 248 RTHQIRVHCAHIGHPIVGDPIYSRCRKLPIDLPGQ---ILHAVQLGLDHPLTGERMVFEA 304

Query: 310 PLP 312
           PLP
Sbjct: 305 PLP 307


>gi|325954148|ref|YP_004237808.1| pseudouridine synthase [Weeksella virosa DSM 16922]
 gi|323436766|gb|ADX67230.1| pseudouridine synthase, RluA family [Weeksella virosa DSM 16922]
          Length = 362

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 85/328 (25%), Positives = 155/328 (47%), Gaps = 41/328 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +  +R+D++      +     +Q+   +G + V+   VK N +++ G  ++I  
Sbjct: 22  ITVDKGQSLLRIDKFLMIRIENATRNKIQQAAENGNILVNNLPVKSNYKVKPGDFIQI-- 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L +  +E KI+   + L          +++ED ++ V +KPAG+ V  G G     
Sbjct: 80  ---MLENPPREHKIIAEDLPLN---------IVFEDDQVLVIDKPAGMVVHPGHGNYSGT 127

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + +H D      + ++ ++P L HR+D++TSG+LV+A+T  A  HL   F      
Sbjct: 128 LVNALKFHFDNL--PSMSAELERPGLVHRIDKDTSGLLVIAKTEQAMNHLALQFANHTTT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG     +  I   + +  H+       V ++     +A++H+KV++  +   
Sbjct: 186 RKYNALVWGNVTEDEGTITGHIGR--HLKDRMQMAVFEDGSQGKHAVTHYKVLERLSY-V 242

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN------KL 288
             +E Q  TGRTHQ+R H  ++G P+  D +Y  N   KG     +   ++N      + 
Sbjct: 243 TLVECQLETGRTHQIRTHFKYIGHPLFNDERYGGNKILKGTTFTKYKQFVENCFNICPRQ 302

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHM 315
            LHAR +   HP  G  ++  A LP  M
Sbjct: 303 ALHARTLGFTHPTTGEFMEFEATLPNDM 330


>gi|283780614|ref|YP_003371369.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
 gi|283439067|gb|ADB17509.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
          Length = 355

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 94/337 (27%), Positives = 154/337 (45%), Gaps = 49/337 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR--VKFNNRIQSGQVVRI 67
           +VVE  E + RLD++        + + L++++ +G V ++  R  VK   R+ +G  V I
Sbjct: 39  LVVEEREADGRLDQFLALRLHRYSRMQLRRVIDAGGVLLNGSRAKVKVAYRVSTGDRVSI 98

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                          +L    +   + + +   +L+ED  +   NKP G+ V    G   
Sbjct: 99  ---------------VLPEMPSAGPNPEKIPLDILFEDEHLIAVNKPPGMVVHPARG--- 140

Query: 128 HIDGFLKSWV--------DSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           H  G L S +           GQ +P + HRLD++TSG+++VA+T      L   F  R 
Sbjct: 141 HWSGTLTSALAFHFQQLSTVGGQHRPGIVHRLDRDTSGVIIVAKTDPVHFSLAAQFADRT 200

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH----VVKQNEKGANYAISHFKVID 234
             K Y+++  G+P   ++ ++        IG    H     ++     +  A + F V++
Sbjct: 201 TAKEYFAITAGVPDRDRDVVSQP------IGIHPFHREKMAIRPGHSTSRDAETMFHVLE 254

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--------FKGNFTSPIQN 286
            FAQ    +E  P TGRTHQ+RVH  H+  P++ D  Y            +   T  + N
Sbjct: 255 RFAQ-HAAVECLPKTGRTHQIRVHLAHVRTPVLCDKLYGGRAEITQGELVRDGSTEVVLN 313

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           +  LHAR + + HP+ G RL I APLPA + +  D L
Sbjct: 314 RQALHARKLSINHPKTGERLTIEAPLPADLQRVLDLL 350


>gi|134299530|ref|YP_001113026.1| RluA family pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134052230|gb|ABO50201.1| ribosomal large subunit pseudouridine synthase D [Desulfotomaculum
           reducens MI-1]
          Length = 306

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 93/311 (29%), Positives = 152/311 (48%), Gaps = 35/311 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIP 68
           +V+ +    RLD +  N    I+   +QK++  G V VD K  + N++++  + +  +IP
Sbjct: 7   IVDGENAKCRLDVFLANQCQDISRSYIQKLIEDGLVTVDGKPARANHKLRVEETIHMQIP 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
           P         +E K+   ++ L          + YEDS + V NKP G+ V    G    
Sbjct: 67  PA--------EELKVEPENIPLD---------IYYEDSHVIVVNKPRGMVVHPAEGNIAG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D  G     +P + HRLD++TSG+++ A+   A Q L    + R + + 
Sbjct: 110 TLVNALLYHCHDLSGINGIMRPGIVHRLDKDTSGLIMAAKHDQAHQSLARQLKDRTVTRR 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV    K     I N  + +       + VV++N K A   ++HF+V++ F   +  
Sbjct: 170 YQALVHHNIKGDFGTI-NAPIGRDPRDRQKMAVVERNSKNA---VTHFQVLERFGD-YTL 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+RVH  ++G P+VGD KY  + K +F    Q    LHA+ +   HP  
Sbjct: 225 IECRLETGRTHQIRVHMAYIGFPLVGDPKYGPS-KSHFHLDGQ---LLHAKVLGFLHPVS 280

Query: 303 GR-LQITAPLP 312
           G  L+  APLP
Sbjct: 281 GEYLEFIAPLP 291


>gi|190893167|ref|YP_001979709.1| RNA-pseudouridylate synthase, ribosomal large subunit D [Rhizobium
           etli CIAT 652]
 gi|190698446|gb|ACE92531.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli CIAT 652]
          Length = 354

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 93/349 (26%), Positives = 160/349 (45%), Gaps = 53/349 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQV 64
           ++ V+  ++    RLD W         +   ++ +++ GQV +  + +    R +++G  
Sbjct: 24  IRKVLTADETAEGRLDAWLTAQLGEEFSRSRIKVLIKDGQVSMRGQLITDPQRKVRAGDS 83

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
             I                L    + T   + +   +LYED  + V +KPAG+ V  GSG
Sbjct: 84  FEI---------------TLPEPEDPTPQGEDIPLDILYEDDDLIVISKPAGLVVHPGSG 128

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF- 174
                    + +H    L        ++P + HRLD++T+G++VVA+   A +HL+  F 
Sbjct: 129 NWTGTLVNALIHHCGATLSGI--GGVRRPGIVHRLDKDTTGVMVVAKNDVAHRHLSLQFA 186

Query: 175 ---RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISH 229
              R   +++ Y ++VWG P++    +   L + +   GD     V + + + A+ AI+H
Sbjct: 187 DHGRTMPLERAYRAIVWGRPRSLTGTVDAPLGRAT---GDRTRRAVKRPDSQDADEAITH 243

Query: 230 FKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFT 281
           ++VI+ F +          +E +  TGRTHQ+RVH  H+G P++GD  Y A F  K N  
Sbjct: 244 YEVIERFHETPDATALASLVECRLETGRTHQIRVHMAHIGHPLLGDTVYGAGFRTKANLL 303

Query: 282 SPIQNKLY-------LHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
                K+        LHA  +   HP  G L     PLP  MV+  ++L
Sbjct: 304 PEDIRKVVNRFDRQALHAFMLQFEHPRSGELMHFEVPLPDDMVELVEAL 352


>gi|319406711|emb|CBI80344.1| ribosomal large subunit pseudouridine synthase D [Bartonella sp.
           1-1C]
          Length = 333

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 93/344 (27%), Positives = 159/344 (46%), Gaps = 44/344 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            Q++  EN     R+D+W    Y   ++   LQ ++R G +++D            GQ++
Sbjct: 2   TQHITSEN-ACGQRIDQWLAKQYKGELSRSRLQTLIREGYLKID------------GQLI 48

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           + P      N II  +  + +  +     + +   +L+ED+ I V NKPAG+ V  G+G 
Sbjct: 49  KEPKTKLKSNQII--ELTIPTPNDAQPQGEAIALDILFEDNHIIVINKPAGLVVHPGNGN 106

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF---- 174
                ++G +    DS       ++P + HRLD++TSG++V+A++  A ++L   F    
Sbjct: 107 WTGTLVNGLIYHCRDSLSGIGGIKRPGIVHRLDKDTSGVMVIAKSDFAHRNLNAQFADHG 166

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R   + + Y +++WG P      I  +L + S        VV      A  AI+H  +++
Sbjct: 167 RTSPLDRRYHAVIWGSPNRNIATIDTFLARSSRDRTKRT-VVHSEHAHARRAITHISLLE 225

Query: 235 CFA------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSP-IQ 285
            +            LE +  TGRTHQ+RVH  H+G P++GD  Y   F  K N   P I+
Sbjct: 226 KYGTCNDATSLASLLECRLETGRTHQIRVHMSHIGHPLIGDKVYGNAFKTKSNTLDPDIK 285

Query: 286 ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 N+  LHA  +   HP   + +  ++P P  +V   + L
Sbjct: 286 NIIDQFNRQALHATSLTFEHPANSQIMSFSSPFPKDLVDLLNHL 329


>gi|261417496|ref|YP_003251179.1| pseudouridine synthase, RluA family [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261373952|gb|ACX76697.1| pseudouridine synthase, RluA family [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302326984|gb|ADL26185.1| ribosomal large subunit pseudouridine synthase D [Fibrobacter
           succinogenes subsp. succinogenes S85]
          Length = 424

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 78/272 (28%), Positives = 138/272 (50%), Gaps = 33/272 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +VE      R+D++      +++  ++QK++ +G+V+V   +V  N R+++G  V +   
Sbjct: 4   IVEEKHNGERIDKFLVGVMENVSRTDVQKLIEAGEVKVGGGKVSKNFRVETGMAVVV--- 60

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---- 126
                     +K+++   +  +  D   +I+ YED  I V NKP  + V  G+G++    
Sbjct: 61  ----------EKMIEKESSTLEPEDIPLNIV-YEDDDIVVINKPRNLVVHPGNGVSKGTL 109

Query: 127 -----YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                YH    L +   +   +P + HRLD++T G++VVA+  AA +HL      R + +
Sbjct: 110 AAALLYHFKENLSTV--NGPLRPGIVHRLDKDTPGLMVVAKNDAAHRHLAHQLETRTLHR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKF 240
            Y +LVWG P++ +  I       + IG +  + +K    KG   + +H+     FA   
Sbjct: 168 TYNALVWGCPRDLEGTI------DAPIGRNPKNRLKMAVVKGGKESRTHYVAKQFFAIA- 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             LE+Q  +GRTHQ+RVH+ + G P+VGD  Y
Sbjct: 221 TLLELQLESGRTHQIRVHSRYTGHPVVGDPLY 252


>gi|194476821|ref|YP_002049000.1| Pseudouridine synthase, RluD [Paulinella chromatophora]
 gi|171191828|gb|ACB42790.1| Pseudouridine synthase, RluD [Paulinella chromatophora]
          Length = 315

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 96/319 (30%), Positives = 146/319 (45%), Gaps = 34/319 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---PPV 70
           +D   MRLDRW     P  +   +QK + +G VRV+  +      ++ G  V+I   PP 
Sbjct: 17  SDLVPMRLDRWLALKRPEQSRSRIQKFIYAGLVRVNGIKSSTKTPLRQGDQVQIWMPPP- 75

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-- 128
            + L ++I +   LD               +L+ED  + V NKPA ++V    G  Y   
Sbjct: 76  -DLLPYLIPQHIPLD---------------ILFEDQYLIVVNKPADLTVHPAPGNKYGTL 119

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++G L    D  G     +P + HRLD+ T+G +V+A+T+     L    + R + + Y 
Sbjct: 120 VNGLLFHCSDLMGIGGEMRPGVVHRLDKSTTGCIVIAKTKEILAALQLQIQNRVVSREYI 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +V G+P   K  I   L +  H      + V  NEKG  YA +H+ +I+ +   +  L 
Sbjct: 180 GIVHGVPATNKGTIIGKLGR--HPVNRKRYAVLVNEKG-RYACTHWCLIERWGD-YSLLR 235

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
            +  TGRTHQ+R+H  H+G PI+GD  Y    +        N   LHA  +   HP    
Sbjct: 236 FKLDTGRTHQIRIHCSHIGYPIIGDQYYSKQRRLPLAF---NGQALHAVELSFNHPVNSD 292

Query: 304 RLQITAPLPAHMVKTWDSL 322
           R+   APLP    K   S 
Sbjct: 293 RMVFHAPLPKIFEKLLTSF 311


>gi|300867006|ref|ZP_07111676.1| conserved hypothetical protein [Oscillatoria sp. PCC 6506]
 gi|300334989|emb|CBN56842.1| conserved hypothetical protein [Oscillatoria sp. PCC 6506]
          Length = 319

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 98/315 (31%), Positives = 150/315 (47%), Gaps = 52/315 (16%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-------KKRVKFNNRIQSGQVVRIPPV 70
           + RLD W  N  P ++   +Q ++  G V V+       K+ VK  +RI     + IP  
Sbjct: 23  SQRLDLWLSNELPDLSRSRIQNLILQGNVTVNDLICKSKKENVKNGDRIH----IAIP-- 76

Query: 71  INALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +A    +K + I LD               +LYED  + + NKPAG+ V   +G   H 
Sbjct: 77  -DAEPLDLKPEAIPLD---------------ILYEDESLIIINKPAGLVVHPAAG---HP 117

Query: 130 DGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            G L + + +           +P + HRLD++TSG +VVA+T  A QHL    + +  ++
Sbjct: 118 GGTLVNALLAHCPLAEIGGVLRPGIVHRLDKDTSGAIVVAKTDFAHQHLQAQLKAKTARR 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y  +V+G  K +   I +  + +  +    + VV   EKG   A++H+++ +     + 
Sbjct: 178 EYLGVVYGTLKTENGTI-DLPIGRHSVDRKKMAVVTI-EKGGRSAVTHWQIQERLGN-YT 234

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKLYLHARYMDLPH 299
            +  Q  TGRTHQ+RVHA  +G PIVGD  Y +N     N T        LHA  + L H
Sbjct: 235 LIHFQLETGRTHQIRVHAAQIGHPIVGDPVYSSNHDIGVNLTGQ-----ALHAWRLKLQH 289

Query: 300 PEGGRL-QITAPLPA 313
           P  G L +  APLPA
Sbjct: 290 PVSGELIEAIAPLPA 304


>gi|46202662|ref|ZP_00208608.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 227

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 79/233 (33%), Positives = 117/233 (50%), Gaps = 17/233 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L + +LY D  + + +KPAG+ V  G     H+  FL        Q P L HRLD+ETSG
Sbjct: 5   LVARVLYRDPAVLIIDKPAGLMVHAGPKGGEHLGLFLDQLRFGLAQSPELAHRLDRETSG 64

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ RTR A   L + F      K YW++V G P+  +  I ++ LKK      +   V
Sbjct: 65  CLVLGRTRKALAGLGDLFAKGLADKTYWAVVVGKPREDQGVI-DYALKKREKKFGWRMEV 123

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            +N      +++ ++++     +  WLE +P TGRTHQ+R H   +G P+VGD  Y    
Sbjct: 124 DRN---GLASVTQWRLLGTDG-RLSWLECRPLTGRTHQIRAHCAAIGHPLVGDAIY---- 175

Query: 277 KGNFTSPIQ-NKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKT-----WDSL 322
            G  T  +  ++L LH+R + LP H     +   AP+P HM        WD+L
Sbjct: 176 -GRGTGTLAGDRLMLHSRNIVLPFHAGKPPIAAKAPVPEHMRAVLEGCGWDTL 227


>gi|254477672|ref|ZP_05091058.1| ribosomal large subunit pseudouridine synthase D [Ruegeria sp. R11]
 gi|214031915|gb|EEB72750.1| ribosomal large subunit pseudouridine synthase D [Ruegeria sp. R11]
          Length = 344

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 95/358 (26%), Positives = 156/358 (43%), Gaps = 62/358 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           +++V+ EN  +  RLD+      P    ++   L +++ +GQ+ VD K V     R++ G
Sbjct: 6   IEFVIAENPPK--RLDKAVSRDVPEEATLSRTRLARLIEAGQLEVDGKIVTDAKARVEEG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I       +HI  E   L+               +++ED  + V NKPAG+ V   
Sbjct: 64  ATISITVEEAEDSHIGPEDIPLE---------------VIFEDDDLIVINKPAGMVVHPA 108

Query: 123 SGIAYH--IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G      ++  L    D+       ++P + HR+D+ETSG+LVVA++ AA Q L   F 
Sbjct: 109 PGTPSGTLVNALLHHCGDNLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQFE 168

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------------G 222
              +++ Y ++ +G+P      +   +   S   G+ + +  Q  +             G
Sbjct: 169 KHTVERYYRAVCYGVPDGNDPRL-RGVKGASFEPGNILKLTTQLARHKTDRQKQAVLFQG 227

Query: 223 ANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +AI+  +++D F          CWLE    TGRTHQ+RVH  H G  +VGD  Y    
Sbjct: 228 GRHAITRARIVDSFGTPPVVALIECWLE----TGRTHQIRVHMAHAGHGLVGDPVYGGKR 283

Query: 277 K-------GNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           K           + +Q   +  LHA  +   HP  G  ++  APLP  M    D+L  
Sbjct: 284 KLAAKALSTQAAAAVQGFPRQALHAAVLGFVHPVSGEDMRFEAPLPQDMATLLDTLAL 341


>gi|189346997|ref|YP_001943526.1| pseudouridine synthase, RluA family [Chlorobium limicola DSM 245]
 gi|189341144|gb|ACD90547.1| pseudouridine synthase, RluA family [Chlorobium limicola DSM 245]
          Length = 354

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 92/335 (27%), Positives = 148/335 (44%), Gaps = 59/335 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++      +     +Q+ +   +V V+ + VK N RI+S   + I  +      + 
Sbjct: 38  MRIDKYLTQQVENATRNKVQEAIEEERVLVNGRPVKSNYRIKSCDTILITFLRPPAPELA 97

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E   +D               ++YEDS + V NK  G+ V    G         I +HI
Sbjct: 98  PEDIPID---------------IVYEDSDLMVVNKEPGMVVHPAFGNWTGTLANAILHHI 142

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G     +D+   +P + HRLD++TSG++++A+   A   L   F MR++QKIY ++VWG
Sbjct: 143 -GRDAESLDASELRPGIVHRLDKDTSGLIIIAKNPTALHRLARQFAMRQVQKIYKAIVWG 201

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHF----KVIDCFAQK----F 240
           +P  +   I       ++IG       K+N K  ANY          + D   ++    F
Sbjct: 202 VPDPRSGTIL------TNIGRS-----KKNRKIMANYPYEGLDGKHAITDYLVEENLHWF 250

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY------------CANFKGNFTSPIQNKL 288
             + +  HTGRTHQ+R H  H G PI+GD  Y              +F  N    I  + 
Sbjct: 251 SVVSLTLHTGRTHQIRAHMQHTGNPILGDETYGGTVIRTLPFSKSESFVTNLLE-IMPRQ 309

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
            LHA  +    P    +L  ++PLP  M +T + +
Sbjct: 310 ALHAETLSFSQPTTHEKLTFSSPLPTDMQRTLEKI 344


>gi|282857614|ref|ZP_06266832.1| ribosomal large subunit pseudouridine synthase D [Pyramidobacter
           piscolens W5455]
 gi|282584552|gb|EFB89902.1| ribosomal large subunit pseudouridine synthase D [Pyramidobacter
           piscolens W5455]
          Length = 315

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 99/327 (30%), Positives = 155/327 (47%), Gaps = 39/327 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +   +E  RLD   +  +P +    + K  R G VR++ KR + N+R+  GQ V +P   
Sbjct: 7   ISRHDEGRRLDSVLRGMWPGVPLGAMMKYFRKGAVRLEGKRCQPNDRVLEGQHVWVP--- 63

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI----SVQGGSGIAY 127
                  +E   +  +         L   ++Y D  + V NKPAG+     V+G   +  
Sbjct: 64  ------WEEPGTVGRAEMPDGTPRRLPLDVIYSDRCVMVVNKPAGLLSQPDVKGEDSVVT 117

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              G+    VD +   P+L HRLD+ TSG++ +A      + L E F+ RR  K YW++V
Sbjct: 118 RALGYA---VDPE-FPPQLVHRLDRNTSGVMALALDGPTTRALMECFKARRADKRYWAIV 173

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            G +P+  +  I   LLK +        +V+ + KG   A++ +K +   +  F   E+ 
Sbjct: 174 IGELPERGR--IDVPLLKDAD-----KKLVRVDPKG-ERAVTEYKRLTS-SGAFSLAEVH 224

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMD-------L 297
             TGRTHQ+RVH  H+G P++GD KY  +F  KG   S    +  LHAR +        L
Sbjct: 225 LLTGRTHQIRVHMNHVGHPLLGDVKY-GDFGSKGQLRSLGVKRPMLHARSLTLNGLPAFL 283

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGF 324
            H EG   +  AP P  + +  + LGF
Sbjct: 284 SHLEGKTFR--APAPDDLRRVMEKLGF 308


>gi|170751707|ref|YP_001757967.1| pseudouridine synthase [Methylobacterium radiotolerans JCM 2831]
 gi|170658229|gb|ACB27284.1| pseudouridine synthase [Methylobacterium radiotolerans JCM 2831]
          Length = 224

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 73/223 (32%), Positives = 117/223 (52%), Gaps = 20/223 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           LLY D+ + V +KPAG+ V    +GG  +  H+D           ++P   HRLD++TSG
Sbjct: 11  LLYRDALLLVIDKPAGLPVHPGPRGGETLTDHLDALRFGLP----RRPEAAHRLDRDTSG 66

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            L + R   A   L + F    ++K YW++V G P  ++  I   L ++S    D     
Sbjct: 67  CLALGRHAKALARLGKLFSGSAVEKTYWAIVAGGPAGEEGSIDLPLARRSD---DPRSWW 123

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + +   + +++H++V+   A    WLE++P TGRTHQLRVH    G PI+GD  Y    
Sbjct: 124 MKADPAGDPSLTHWRVLG-RAGGRTWLELKPVTGRTHQLRVHCAASGWPILGDAVYGGAP 182

Query: 277 KGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKT 318
           +G       + L+LHAR + +P +P+   + +TAP P H+ + 
Sbjct: 183 RG-------SALHLHARALSIPLYPKRDAIAVTAPPPPHIAEA 218


>gi|58584466|ref|YP_198039.1| pseudouridylate synthase, 23S RNA-specific [Wolbachia endosymbiont
           strain TRS of Brugia malayi]
 gi|58418782|gb|AAW70797.1| Pseudouridylate synthases, 23S RNA-specific [Wolbachia endosymbiont
           strain TRS of Brugia malayi]
          Length = 389

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 73/221 (33%), Positives = 122/221 (55%), Gaps = 12/221 (5%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           + N+RLDR+ +  +P++    ++K LR G ++V+  + K ++R+ SGQ++     I  L+
Sbjct: 11  DNNVRLDRYIRRIFPNLKQSVIEKSLRRGLIKVNDCKAKSSDRVNSGQII----TIKYLD 66

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           +I  E    D   N  K  + L+S +LYED  I   NKPAG+ VQGG  +   I   L  
Sbjct: 67  YI--ENANSDCKHN-EKLVELLRSNILYEDEYILAINKPAGVIVQGGIKVKISISDLLDQ 123

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               +G+  ++ HRLD++TSG ++ AR    A++L E F+ RR++K Y +L  GIP +K 
Sbjct: 124 V--REGETFKIVHRLDRDTSGAIIFARNANVARYLMEEFKGRRVKKTYLALTSGIP-SKN 180

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + ++ L K ++ G    V+ +N      A + F +I  F
Sbjct: 181 RGVIDYPLVKKYVSGQEKVVIDKN--SPQDATTRFSIIAKF 219



 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 43/122 (35%), Positives = 66/122 (54%), Gaps = 8/122 (6%)

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCF------AQKFCWLEMQPHTGRTHQLRVHAL 260
           H+    +   K + K A+Y     K +D         +   +L++QP TGRTHQLR H  
Sbjct: 266 HLSAPILVSSKTDHKQAHYTTFSIKKLDSSIMCRNDTRSVAYLKLQPITGRTHQLRTHLA 325

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           ++ CPI+GD KY    K  F   I +K++LH+  + L  P   ++ ITAPLP H+ K+ +
Sbjct: 326 YINCPILGDGKYGG--KKAFVDGIASKIHLHSYSLSLKLPNNKKITITAPLPEHIKKSIE 383

Query: 321 SL 322
           +L
Sbjct: 384 AL 385


>gi|240146315|ref|ZP_04744916.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis L1-82]
 gi|257201556|gb|EEU99840.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis L1-82]
          Length = 310

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 97/335 (28%), Positives = 160/335 (47%), Gaps = 57/335 (17%)

Query: 12  VENDEENMRLDRWFK---------NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +E + E  RLD++           ++ P  +F   QK++R G V+V+    K N R++  
Sbjct: 8   IEAEYEGERLDKYLSVIFEQSKTSSNAPSRSF--FQKLIRDGHVKVNDSIAKANYRLRMD 65

Query: 63  QVV--RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            +V   IP  +        E  IL   + L          +LYED  + V NKP G+ V 
Sbjct: 66  DLVCVEIPDAV--------ETPILPEDIPLD---------ILYEDDDLLVVNKPKGMVVH 108

Query: 121 GGSGIAYHIDGFLKSWV-----DS----KGQ-KPRLTHRLDQETSGILVVARTRAAAQHL 170
             +G   H  G L + +     DS     G+ +P + HR+D +T+G L+V +   +   +
Sbjct: 109 PSAG---HYSGTLVNAIMFHCKDSLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHIKI 165

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAIS 228
            E  +   + + Y  +V+G+ K+ +  I       + IG    +  K   NEK    AI+
Sbjct: 166 AEQIKEHSVNRRYRGIVYGVVKDDEGTI------NAPIGRHPTNRKKMAINEKNGKPAIT 219

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
           H+KV++ F+  + ++E +  TGRTHQ+RVH   +G P++GD  Y +  K  F +  Q   
Sbjct: 220 HYKVLERFSN-YTYMEFKLETGRTHQIRVHMASIGHPLLGDTVYSSG-KSPFKTQGQT-- 275

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            LHA  +   HP     ++I+APLP + +K   SL
Sbjct: 276 -LHAMTIGFIHPHTNEYMEISAPLPEYFLKILKSL 309


>gi|319403704|emb|CBI77289.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           rochalimae ATCC BAA-1498]
          Length = 333

 Score =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 94/344 (27%), Positives = 156/344 (45%), Gaps = 44/344 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            Q++  EN     R+D+W    Y   ++   LQ ++R G +++D            GQ++
Sbjct: 2   TQHITNEN-ACGQRIDQWLAKQYKGELSRSRLQTLIREGYLKID------------GQLI 48

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           + P      N II  +  + +        + L   +L+ED+ I V NKPAG+ V  G+G 
Sbjct: 49  KEPKTKLKSNQII--ELTIPTPNEAQPQGEALVLDILFEDNHIIVINKPAGLVVHPGNGN 106

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF---- 174
                ++G +    DS       ++P + HRLD++TSG++V+A+   A ++L   F    
Sbjct: 107 WTGTLVNGLIYHCRDSLSGIGGIKRPGIVHRLDKDTSGVMVIAKNDLAHRNLNAQFADHG 166

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R   + + Y +++WG P      I  +L + S        VV      A  AI+HF +++
Sbjct: 167 RTSALDRRYHAVIWGSPNRNIATIDTFLARSSRDRTKRT-VVHSEYAHARRAITHFSLLE 225

Query: 235 CFA------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSP-IQ 285
            +            LE +  TGRTHQ+RVH  H+G P++GD  Y   F  K N   P I+
Sbjct: 226 KYGTCNDTTSLASLLECRLETGRTHQIRVHMSHIGHPLIGDKVYGNAFKTKSNTLDPEIK 285

Query: 286 NKL------YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           N +       LHA  +   HP     +  ++P P  +    + L
Sbjct: 286 NTIDQFNRQALHATSLTFEHPANSEIMSFSSPFPKDLADLLNHL 329


>gi|227529323|ref|ZP_03959372.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           vaginalis ATCC 49540]
 gi|227350751|gb|EEJ41042.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           vaginalis ATCC 49540]
          Length = 305

 Score =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 95/315 (30%), Positives = 153/315 (48%), Gaps = 33/315 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+   +H   I+   LQK +  G V V+ ++VK   ++  G  V + P         K
Sbjct: 16  RIDKELAHHLTDISRSQLQKWIEDGNVTVNGEKVKPKYKLVVGDRVVVQPK--------K 67

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL--KS 135
            QKI     N+          ++YED  + V NKP G+ V    G   H  ++  L    
Sbjct: 68  PQKIDLEPENIPLD-------IVYEDDDVIVVNKPQGMVVHPAPGHPNHTLVNALLYHSP 120

Query: 136 WVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                G+ +P + HR+D++TSG+L++A+   A + L    + +  ++ Y +LV G+ K +
Sbjct: 121 LSTINGEFRPGIVHRIDKDTSGLLMIAKNDLAHRSLAAQLKAKTNEREYVALVHGVIKEE 180

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I +  L +S        VV+       +A++HFKV++ F Q +  +  +  TGRTHQ
Sbjct: 181 RGTI-DAPLGRSKKDRKKQAVVED----GRHAVTHFKVLELF-QHYTLVSCRLETGRTHQ 234

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH  ++G P+ GD  Y     G   +   N  YLHAR +   HP  G+ +  T+PLP 
Sbjct: 235 IRVHMKYIGHPLAGDPLY-----GPRKTLPGNGQYLHARLLGFKHPRTGKQMTFTSPLPE 289

Query: 314 HMVKTWDSLGFKYDR 328
           +  K  D L  K DR
Sbjct: 290 YFQKMIDHLE-KTDR 303


>gi|218290459|ref|ZP_03494579.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|218239480|gb|EED06675.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
          Length = 314

 Score =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 91/336 (27%), Positives = 168/336 (50%), Gaps = 43/336 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPH----INFVNLQKILRSGQVRVDKK-RVKF 55
           M    +VQY V   D    RLDRW  +        ++   +Q+ +  G VR  +  R+K 
Sbjct: 1   MRPAIHVQYEVSAEDA-GERLDRWLTDRLQEDEIEVSRTQVQRWISDGCVRRARPGRLKA 59

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           ++ +++G +  +          + E++ ++ + +       +   + YED  + V +KP 
Sbjct: 60  SDPVEAGDLYEVD---------VPEEEPMELAPDAG-----VPFAVAYEDDDVVVVDKPR 105

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAA 166
           G+ V  G+G   H+ G L + + ++G          +P + HR+D++TSG++V A++  A
Sbjct: 106 GVVVHPGAG---HMRGTLVNGLLARGTQLCTLAGAMRPGVVHRIDKDTSGLVVFAKSDRA 162

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
            + L E+FR   +++ Y ++  G   +++  I   + +      D   +  +  +G   A
Sbjct: 163 YRWLVEAFRAHDVEREYVAIAHGRMSHREGTIDMPIARDP---ADRQRMAVR--QGGKRA 217

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++HF+V++ FA K+ +L ++  TGRTHQ+RVH   +G PI GD  Y        T PI  
Sbjct: 218 VTHFEVLESFA-KYSYLRLRLETGRTHQIRVHLAAIGHPIAGDPVYGP----RHTLPIDG 272

Query: 287 KLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           +  LHAR +   HP+G RL+  + +P+ M +  D L
Sbjct: 273 QA-LHARTLGFTHPDGRRLRFESAIPSDMARLLDGL 307


>gi|223939777|ref|ZP_03631648.1| pseudouridine synthase, RluA family [bacterium Ellin514]
 gi|223891553|gb|EEF58043.1| pseudouridine synthase, RluA family [bacterium Ellin514]
          Length = 318

 Score =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 94/331 (28%), Positives = 152/331 (45%), Gaps = 41/331 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   VE    + RLD + +  +P ++   +Q+++  G ++V+ + +K  +  ++G+++ +
Sbjct: 7   ESFTVEVSLPSERLDTFLRERFPAVSRGTIQRLIEQGHIKVNGQTIKPTHHPRAGELIEV 66

Query: 68  --PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
             P    A      E +  D  +++           ++EDS + V NK  G+ V   +G 
Sbjct: 67  YWPEARPA------EARPEDIPLDI-----------IFEDSDLLVLNKAPGLVVHPAAGH 109

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                   + +H +G L         +P + HRLD+ETSG LVVA+  AA   L E F  
Sbjct: 110 EEHTLVNALLHHCEGQLSGI--GGVARPGIVHRLDKETSGCLVVAKNDAAHMALAEQFSG 167

Query: 177 RRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           R ++K Y ++V G + +N  E  A+     +H     V      +     A + +KV + 
Sbjct: 168 RTLEKTYLAIVCGEVVRNSGEIRASIARHPTHRKRMTV-----TDGSGREAWTSYKVRER 222

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF---TSPIQNKLYLHA 292
           F+    WLE   HTGRTHQ+RVH  H+G PIVGD  Y           T     +  LHA
Sbjct: 223 FSGA-TWLEALLHTGRTHQIRVHFQHLGYPIVGDATYGTRQNKRLIEVTGYAAPRQMLHA 281

Query: 293 RYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             +   HP +G +L   AP PA       SL
Sbjct: 282 WKLSFLHPCKGKKLSFEAPWPADFQTALASL 312


>gi|220929832|ref|YP_002506741.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|220000160|gb|ACL76761.1| pseudouridine synthase [Clostridium cellulolyticum H10]
          Length = 223

 Score =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 69/205 (33%), Positives = 109/205 (53%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  KP  I VQ  +     +   LK ++  K  KP      L HRLD+   
Sbjct: 5   IVYEDNHLLVVEKPVNIPVQADNSKDIDMLTLLKQYLKEKYNKPGEVYLGLVHRLDRPVG 64

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T   A  L++  R R  +K Y ++V G+P+ +K+ + N+LLK S    + VHV
Sbjct: 65  GVMVFAKTSKCASRLSDQIRTRTFKKTYLAIVRGVPQKQKDELRNFLLKDS--SENMVHV 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           VK+  + A  AI  ++V+    +    L++Q HTGR HQ+RV   H G P+ GD +Y   
Sbjct: 123 VKEGTRDAKEAILDYEVLKSNGE-LSLLQIQLHTGRPHQIRVQLSHSGYPLYGDQRY--- 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G + +    ++ L A  + L HP
Sbjct: 179 --GIYVNKPGQQIALWASSLTLEHP 201


>gi|169831112|ref|YP_001717094.1| RluA family pseudouridine synthase [Candidatus Desulforudis
           audaxviator MP104C]
 gi|169637956|gb|ACA59462.1| pseudouridine synthase, RluA family [Candidatus Desulforudis
           audaxviator MP104C]
          Length = 309

 Score =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 90/331 (27%), Positives = 148/331 (44%), Gaps = 41/331 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +    VE ++E  RLD +     P ++   +QK++    V V+ +  + ++R++ G 
Sbjct: 1   MATLNRYTVEEEDEQTRLDVFLAGQNPELSRARIQKLISLELVTVNGRPARASHRVRGGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V              E K+ D      +  + +   + +ED  + V NKP G+ V    
Sbjct: 61  CV--------------ELKVPDPETPRIE-PEAIPLEVCFEDPDVLVVNKPRGLVVHPAV 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HRLD++TSG+L+VA+  AA   L    + R
Sbjct: 106 GHYSGTLVNALLHHCRDLSGINGILRPGIVHRLDRDTSGLLMVAKNDAAHLALAGQLKDR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G P+ +   +   + +      D   +      G   A +H++V+  F 
Sbjct: 166 AVLRRYTALVHGRPRRETGTVDAPIGRHPR---DRQRMAVTPRSG-RAARTHYRVVRRF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHA 292
            KF  LE+   TGRTHQ+RVH  H+G P+VGD KY         +G F         LHA
Sbjct: 221 DKFSLLELTLDTGRTHQIRVHMAHVGHPLVGDLKYGHARPELGLEGQF---------LHA 271

Query: 293 RYMDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
             +   HP  G + +  APLP+ +    + L
Sbjct: 272 GTLGFRHPRTGEVLVFEAPLPSELAAVLERL 302


>gi|154685962|ref|YP_001421123.1| YlyB [Bacillus amyloliquefaciens FZB42]
 gi|154351813|gb|ABS73892.1| YlyB [Bacillus amyloliquefaciens FZB42]
          Length = 304

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 92/325 (28%), Positives = 157/325 (48%), Gaps = 42/325 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+ ++++ R+D++  +   + +   +Q+ ++ G V V+ K VK N ++Q G       
Sbjct: 6   ITVQPEQKSERIDKFLASTGENWSRTQVQQWVKEGLVSVNGKSVKANYKMQPG------- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
             + +N  I E + LD    L +  D     + YED  + V NKP G+ V    G     
Sbjct: 59  --DQVNVTIPEPEELDV---LAEPMDL---DIYYEDQDVLVVNKPRGMVVHPAPGHVTGT 110

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y
Sbjct: 111 LVNGLMAHCNDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++V G+  +    I       + IG D      + V +++ K A   ++HF V++ F Q
Sbjct: 171 TAVVHGVISHDDGTI------DAPIGRDKKDRQSMTVTRESSKNA---VTHFHVLERF-Q 220

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   
Sbjct: 221 DFTLVECRLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDF-----NGQALHAGILGFD 275

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  G  ++  APLP  M K  + L
Sbjct: 276 HPRTGEYMEFEAPLPEDMKKLIEDL 300


>gi|320538536|ref|ZP_08038397.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
 gi|320144643|gb|EFW36398.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
          Length = 228

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 77/228 (33%), Positives = 120/228 (52%), Gaps = 30/228 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+E+  +++ NKPAGISVQGG+GI+  I   L+    +K       HRLD+ETSG+L++
Sbjct: 11  VLFENDSLFIINKPAGISVQGGAGISNCIIDILERQCAAKLFP---VHRLDKETSGVLLI 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T  AA   ++  + + I K Y ++ +  P  ++  I   L                 E
Sbjct: 68  AKTSQAAAEYSKILQAKTIVKEYRAVCFYAPPKQRGSIRTPL----------------RE 111

Query: 221 KGAN-YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            G    A++ ++V+    +   +L +  HTGR HQ+R+H   +GCPI+ D KY  +FK N
Sbjct: 112 NGTEKTAVTDYRVLK-KTENHSYLSLALHTGRKHQIRIHLASLGCPIILDDKY-GDFKQN 169

Query: 280 FTSPIQ-----NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
               +Q      K+ L A  + LP  +G   QI APLPAHM +  + L
Sbjct: 170 --KALQKAFGIKKMQLSAYSLTLPL-DGKSRQIIAPLPAHMTEALEKL 214


>gi|304383942|ref|ZP_07366399.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
 gi|304335020|gb|EFM01293.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
          Length = 357

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 92/342 (26%), Positives = 161/342 (47%), Gaps = 57/342 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV++ +  +R+D++      H +   +Q    +G + V+ K VK N +++   VV +  
Sbjct: 28  TVVDSGQMPVRIDKYLFEKMQHSSRNRIQNAADAGFIHVNGKPVKSNYKVRPSDVVTL-- 85

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
           +++   H            + T   + +   ++YED+ + V NKPAG+ V  G+G     
Sbjct: 86  MLDRPQH------------DTTIEPEEMPLEVVYEDNDLMVINKPAGLVVHPGAGNFHGT 133

Query: 125 IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   +  +LK         P   L HR+D++TSG+L++A+T  A   L   F  +   + 
Sbjct: 134 LVNALAWYLKDLDTYDPNDPEVGLVHRIDKDTSGLLLIAKTPEAKSKLGVQFLNKTTHRS 193

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------VVKQNEKGANYAISHFKVI 233
           Y +LVWG          N+  ++  I G+            V+  + +    A++H+KV+
Sbjct: 194 YVALVWG----------NFTDEEGRIEGNIARDPKDRLRMTVLPSDSEMGKPAVTHYKVL 243

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQNK 287
           + F     W+E    TGRTHQ+R H  ++G P+ GD +Y      +GN +S     +QN 
Sbjct: 244 ERFGYT-TWIECVLETGRTHQIRAHMKYIGHPLFGDERYGGTEILRGNRSSTYKAFVQNG 302

Query: 288 L------YLHARYMDLPHPEGGR-LQITAPLP---AHMVKTW 319
           L       LHA+ +   HP  GR +  T+PLP   + ++K W
Sbjct: 303 LKICPRQALHAQTLGFIHPTTGRQMDFTSPLPEDLSALLKRW 344


>gi|329957415|ref|ZP_08297890.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
 gi|328522292|gb|EGF49401.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
          Length = 223

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 71/219 (32%), Positives = 114/219 (52%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKLYLKEKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E F+   ++K YW++V   P+ ++  + N+L++       Y + 
Sbjct: 63  GLVIFAKTSKALTRLNEMFKNSEVKKTYWAVVKNQPREQEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   +Q +C LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPNSKKAILHYRLI-AKSQNYCLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
             G+  S     + LHAR++   HP    L ++ AP+P 
Sbjct: 177 --GSPRSNPDGSICLHARFVRFVHPVSKELIEVEAPVPG 213


>gi|315038468|ref|YP_004032036.1| pseudouridine synthase [Lactobacillus amylovorus GRL 1112]
 gi|325956884|ref|YP_004292296.1| pseudouridine synthase [Lactobacillus acidophilus 30SC]
 gi|312276601|gb|ADQ59241.1| pseudouridine synthase [Lactobacillus amylovorus GRL 1112]
 gi|325333449|gb|ADZ07357.1| pseudouridine synthase [Lactobacillus acidophilus 30SC]
 gi|327183663|gb|AEA32110.1| pseudouridine synthase [Lactobacillus amylovorus GRL 1118]
          Length = 302

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 82/306 (26%), Positives = 154/306 (50%), Gaps = 44/306 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           ++E  +E+ RLD++     P ++   ++++++   + V++K+ K + ++Q+G  + +  P
Sbjct: 6   LLEVKDEHGRLDKFVSEQIPDLSRTRVKELIQDDNILVNQKKEKVSYKVQAGDQIEVNVP 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
            +  L+ ++ E   LD               ++YED  + V NKP G+ V    G     
Sbjct: 66  AVKPLD-VVPEDIPLD---------------IVYEDDDVIVVNKPQGMVVHPAPGHSDHT 109

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH     KS    +G +P + HR+D++TSG+L++A+   A + L +    +  +
Sbjct: 110 LVNALLYHTKDLAKS---PEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNK 166

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           +IYW++V G    +   I +  + ++      + VV++ +K    AI+HFKV+  F + +
Sbjct: 167 RIYWAIVHGNFSEENGTI-DAPIGRNPYDRKKMAVVERGKK----AITHFKVLKQF-KGY 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLP 298
             +E Q  TGRTHQ+RVH  ++G  + GD  Y      KGN         +LHA+ +   
Sbjct: 221 SLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPRKTLKGNGQ-------FLHAKVLGFK 273

Query: 299 HPEGGR 304
           HP  G+
Sbjct: 274 HPRTGK 279


>gi|170017468|ref|YP_001728387.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
 gi|169804325|gb|ACA82943.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
          Length = 307

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 94/324 (29%), Positives = 155/324 (47%), Gaps = 39/324 (12%)

Query: 10  VVVENDEENMRLDRWF-KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           + +E   E  R+D    K   P+   V L + L+ G + V++ +VK + ++ SG ++ I 
Sbjct: 5   ITLEITNETGRIDAVLAKKSLPYSRTV-LAEWLQDGHIVVNQTQVKRSYKVNSGDLITIL 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P       II E   LD               ++YED+ + V NKP G+ V   +G   H
Sbjct: 64  PPAVQNTEIIAENMPLD---------------IIYEDNDLLVVNKPQGMVVHPAAG---H 105

Query: 129 IDGFLKSWV--------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             G L + +         +   +P + HR+D++TSG+L+VA+   A Q L+E  +  + +
Sbjct: 106 TSGTLVNALLYHAPLSTINGSFRPGIVHRIDRDTSGLLMVAKNDKAHQALSEQLKAHKNE 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQK 239
           +IY++LV G        I   L +        V   KQ  + G   AI+HF+V+  +   
Sbjct: 166 RIYYALVRGEFSEDSGTINAPLARHK------VDRKKQAVQAGGREAITHFEVVTRYV-G 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  L+++  TGRTHQ+RVH  ++G PI+GD  Y +  K        N   LHA+ + L  
Sbjct: 219 YTLLKIRLETGRTHQIRVHMTYIGHPIIGDPVYGSAQK--LPHVTLNGQMLHAKTLSLTQ 276

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G  L   + LP++  K+  +L
Sbjct: 277 PTTGELLTFDSELPSYFTKSLATL 300


>gi|33864373|ref|NP_895933.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9313]
 gi|33641153|emb|CAE22283.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9313]
          Length = 324

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 92/303 (30%), Positives = 142/303 (46%), Gaps = 32/303 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +     +  ++QK + +G VRV+    +    ++ G  V +  PP    L +
Sbjct: 28  MRLDRWLVSQRSEQSRSHIQKFIEAGLVRVNGITGRAKTPLRQGDEVELWMPPP-EPLPY 86

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
           +  E+  LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 87  LQPEEMPLD---------------VLFEDRHLIVINKPAGLTVHPAPGNRNGTLVNGLLH 131

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +V+A+++ A   L E  + R   + Y ++V G 
Sbjct: 132 HCSDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQEQIQKRIASRNYLAVVHGA 191

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P   +  I   + +       Y  V    E G  +A +H+ +++  A  +  L  +  TG
Sbjct: 192 PSGDQGTIVAAIGRHPVDRKKYAVV---TEDGGRHACTHWTLVERLAD-YSLLRFKLDTG 247

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  H+G PIVGD  Y    K     P Q    LHA  + L HP    R+   A
Sbjct: 248 RTHQIRVHCAHIGHPIVGDPIYSRCRKLPMDLPGQ---ILHAVQLGLDHPLTRERMIFEA 304

Query: 310 PLP 312
           PLP
Sbjct: 305 PLP 307


>gi|125973425|ref|YP_001037335.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           thermocellum ATCC 27405]
 gi|256004403|ref|ZP_05429384.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281417627|ref|ZP_06248647.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|125713650|gb|ABN52142.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           thermocellum ATCC 27405]
 gi|255991687|gb|EEU01788.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281409029|gb|EFB39287.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|316940339|gb|ADU74373.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           1313]
          Length = 303

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 93/328 (28%), Positives = 162/328 (49%), Gaps = 40/328 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--V 64
           ++ +++ ++E  +R+D W        +   +QK++  G + V+ K VK N +I+     +
Sbjct: 1   MEEIILVSNESGIRIDAWLCGKVKDYSRSYIQKLINDGMILVNGKPVKSNYKIKQNDEIL 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
            RIP           E ++LD        ++ +   +LYED  I V +KP G+ V   +G
Sbjct: 61  ARIP-----------EPQVLDVV------AEDIDVPILYEDEHIIVVDKPKGMVVHPAAG 103

Query: 125 --IAYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  LK    +        +P + HR+D++TSG+LVVA++ AA + L+E  +  
Sbjct: 104 NYSGTLVNALLKHCGTNLSNINGIIRPGIVHRIDKDTSGVLVVAKSNAAHEGLSEKLKDH 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDC 235
            I+++Y ++V GI +     I       + IG   V   K   N K    A++ FKV++ 
Sbjct: 164 DIERVYIAVVHGIIREDYGKI------DAPIGRHPVDRKKMAVNTKNGRRAVTRFKVLER 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F +   ++E    TGRTHQ+RVH  ++G PI+GD  Y    + N    I N   LHA+ +
Sbjct: 218 F-KDATYIEATLETGRTHQIRVHMSYIGFPIIGDTVYG---RKNDIYNI-NGQALHAKKL 272

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSL 322
              HP +G  ++  +PLP +  +  + L
Sbjct: 273 GFVHPIKGEYMEFESPLPEYFKELLEKL 300


>gi|158320450|ref|YP_001512957.1| RluA family pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158140649|gb|ABW18961.1| pseudouridine synthase, RluA family [Alkaliphilus oremlandii
           OhILAs]
          Length = 308

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 99/337 (29%), Positives = 159/337 (47%), Gaps = 56/337 (16%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--P 68
           V+E D +N RLD +    Y  ++   +QK+++   ++V+ K  K    I+ G  + I  P
Sbjct: 8   VLEEDVDN-RLDLYISEQYEELSRSYIQKLIKDHHIKVNGKIEKAKYMIKLGDEIEINLP 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
            V        +E  I   ++ LT         ++YED  + V +KP G+ V    G    
Sbjct: 67  QV--------EEVTIEPENIPLT---------IVYEDEDVIVVDKPQGMVVHPAPGNYSG 109

Query: 125 -----IAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                + +H    L    D  G  +P + HR+D++TSG+LVVA+  AA + L E FR   
Sbjct: 110 TLVNALLFHCKNQLS---DVNGPMRPGIVHRIDKDTSGLLVVAKNNAAHEILAEQFRAHT 166

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFA 237
             + Y ++V G  + K+  +       + IG   V  +K+       +A++HFKV++ F 
Sbjct: 167 NTRKYHAIVVGNIREKEAAV------DAPIGRHPVDRLKRAVMNDGKHAVTHFKVLEVF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLHA 292
           + F ++E +  TGRTHQ+RVH  ++G P+VGD  Y A     N KG           LHA
Sbjct: 220 RDFTYIEAKLETGRTHQIRVHLSYIGNPLVGDPLYGAKSSKFNLKGQI---------LHA 270

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           +     HP+    ++ T+ LP +  K    L   Y R
Sbjct: 271 KVFGFIHPKTKEYMEFTSDLPEYFNKVLRVLRNNYSR 307


>gi|325283365|ref|YP_004255906.1| pseudouridine synthase, RluA family [Deinococcus proteolyticus MRP]
 gi|324315174|gb|ADY26289.1| pseudouridine synthase, RluA family [Deinococcus proteolyticus MRP]
          Length = 319

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 91/304 (29%), Positives = 139/304 (45%), Gaps = 50/304 (16%)

Query: 41  LRSGQVRVD-KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           + +G+V V+ K   K +++++ G+ + I P   A   +  EQ  LD              
Sbjct: 36  IAAGRVEVEGKAATKASHKLRGGEALHISPPPPADLSVQPEQVPLD-------------- 81

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL------------KSWVDSK-GQKPRL 146
            +LYED  +   NKP G+      G+   + G L            +S  DS  G +P +
Sbjct: 82  -VLYEDDALIAVNKPPGMVTHPAPGV---VSGTLVNALLGRLELPQQSDHDSPAGYRPGI 137

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG++VVA+T  A   L+ SF+ R  QK+Y ++  G  K +     +     +
Sbjct: 138 VHRLDKDTSGVIVVAKTVQAHAALSASFKARETQKVYLAIAAGEWKAQTPAKVD-----A 192

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVI------DCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            IG   V   K    GAN   +  + +      D   +    +  +P TGRTHQ+RVH  
Sbjct: 193 PIGRHPVQRQKMTVGGANPRDAQTRFVPLSHHPDGHGRTLALVRCEPRTGRTHQIRVHLA 252

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           H+G PIVGD  Y    +         +  LHA  + LPHP     L +TAP P  ++  W
Sbjct: 253 HLGSPIVGDAVYGRESQA------MPRQALHAWQLTLPHPVTQEPLHLTAPPPDDLLDAW 306

Query: 320 DSLG 323
            +LG
Sbjct: 307 VALG 310


>gi|313207050|ref|YP_004046227.1| ribosomal large subunit pseudouridine synthase d [Riemerella
           anatipestifer DSM 15868]
 gi|312446366|gb|ADQ82721.1| ribosomal large subunit pseudouridine synthase D [Riemerella
           anatipestifer DSM 15868]
 gi|315022556|gb|EFT35583.1| ribosomal large subunit pseudouridine synthase D [Riemerella
           anatipestifer RA-YM]
          Length = 352

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 93/340 (27%), Positives = 162/340 (47%), Gaps = 55/340 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+ ++E +R+D++      + +   + +  R+G V V+   VK N R++ G  V +  
Sbjct: 31  LVVDKNQEPLRIDKYLLIFRQNSSRNKISQTCRAGNVVVNGTPVKQNYRVKPGDKVSV-- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L H  +E  I+   + +          ++YED  + V +K AG+ V  G G     
Sbjct: 89  ---LLTHPPRENVIVPQDIPIN---------IVYEDDDLLVVDKEAGMVVHPGFGNWDGT 136

Query: 125 ----IAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               +AYH +   LK+ +D  G    L HR+D++TSG+LV+A+   A   L + F  R  
Sbjct: 137 LVNALAYHFEKNGLKTDLDRVG----LVHRIDKDTSGLLVIAKNEYAMSFLAKQFFERTT 192

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH----VVKQNEKGANYAISHFKVIDC 235
           +++YW+ VWG        I      K HIG D  +     V ++     +A++H+KV++ 
Sbjct: 193 KRLYWAFVWGNLAEDTGTI------KGHIGRDLKNRMQMAVYEDGSLGKHAVTHYKVLER 246

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG----NFTSPIQN--- 286
           F +   W+E +  TGRTHQ+R H  H+G  +  D +Y  +   +G     +   ++N   
Sbjct: 247 F-RYMTWVECKLETGRTHQIRAHFRHIGHTLFNDERYEGHQILRGINLPKYKQFVKNVFE 305

Query: 287 ---KLYLHARYMDLPHPEGGR-LQITAPLPAHM---VKTW 319
              +  LHA  +   HP   + +   +P+P  M   V+ W
Sbjct: 306 VLPRHALHAHTLGFTHPTTKKEMYFESPMPQDMQQAVEKW 345


>gi|269121652|ref|YP_003309829.1| pseudouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268615530|gb|ACZ09898.1| pseudouridine synthase, RluA family [Sebaldella termitidis ATCC
           33386]
          Length = 305

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 93/333 (27%), Positives = 162/333 (48%), Gaps = 48/333 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++ E  EE  RLD +       +    +Q++++ G + V+ K+ K + +++    + 
Sbjct: 1   MEKIIFEISEEGKRLDLYIAER-TELTRTRIQQLIKDGNINVNNKKSKPSYKVEKNDFIE 59

Query: 67  IPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +         II ++K +D    ++N+          +LYEDS I V +K AGI V    
Sbjct: 60  M---------IIPDEKEIDLVPENINIK---------ILYEDSDIAVIDKEAGIVVHPSH 101

Query: 124 G---------IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           G         + YHI    K      G+ +P + HRLD++TSG+L++A+   A   L+E 
Sbjct: 102 GHESGTLVNAVMYHI----KDLSGINGEIRPGIVHRLDKDTSGLLIIAKNDTAHLRLSEM 157

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F    I+K Y +++ G   NK+      L+ +       + VVK N K    AI++F+V+
Sbjct: 158 FGSSGIRKTYIAILKG-KINKESGKLETLIGRDPKDRKKMAVVKTNGK---TAITYFQVL 213

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D   +KF  +++   TGRTHQ+RVH  ++G P++GD  Y  + K      I  +  LHA 
Sbjct: 214 DK-NEKFSLVKVNIQTGRTHQIRVHMKYLGYPVLGDSVYGRDNK------IAGRQMLHAY 266

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            ++  HP   + ++I + LP    K     G +
Sbjct: 267 KLEFLHPVTQKAMKIISELPQDFEKALKETGLE 299


>gi|227544604|ref|ZP_03974653.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri CF48-3A]
 gi|300910266|ref|ZP_07127726.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
 gi|227185411|gb|EEI65482.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri CF48-3A]
 gi|300892914|gb|EFK86274.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
          Length = 303

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 95/314 (30%), Positives = 152/314 (48%), Gaps = 42/314 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+   +H+   +   +Q  +  G V V+ ++VK   ++  G  V+I P         +
Sbjct: 16  RIDKQLGHHFDQFSRSQIQHWIEDGHVLVNGEQVKPKYKLLVGDHVQIIPE--------E 67

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL--KS 135
            QKI     +LT     L   ++YED  + V NKP G+ V    G   H  ++  L    
Sbjct: 68  PQKI-----DLTPEDIPLD--IVYEDDDVIVVNKPQGMVVHPAPGHPNHTLVNALLYHSP 120

Query: 136 WVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                G+ +P + HR+D++TSG+L+VA+   A + LT   + +  ++ Y +LV G+ K  
Sbjct: 121 LSTINGEFRPGIVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKED 180

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVIDCFAQKFCWLEMQPHT 249
           K  I   L +           +K  +K A      +AI+HF V++ F + +  +  Q  T
Sbjct: 181 KGTIDAPLGRS----------LKDRKKQAVVVDGRHAITHFNVLERF-KNYTLVACQLET 229

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+ GD  Y     G   +   N  YLHAR +   HP  G+ +  T
Sbjct: 230 GRTHQIRVHMKYIGHPLAGDPLY-----GPRKTLAGNGQYLHARLLGFKHPRTGKEMVFT 284

Query: 309 APLPAHMVKTWDSL 322
           APLPA+  K  + L
Sbjct: 285 APLPAYFTKMLEHL 298


>gi|148270918|ref|YP_001245378.1| RluA family pseudouridine synthase [Thermotoga petrophila RKU-1]
 gi|147736462|gb|ABQ47802.1| ribosomal large subunit pseudouridine synthase C [Thermotoga
           petrophila RKU-1]
          Length = 304

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 101/324 (31%), Positives = 150/324 (46%), Gaps = 38/324 (11%)

Query: 12  VENDEENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIP 68
           VE  +EN   RLD++ +N    +    + K++R G+V V+ KRVK  +  ++ G VV   
Sbjct: 3   VEVTKENFYRRLDKFLRNQLKDVPLSVIYKLIRKGKVYVNGKRVKDPSFDLEEGDVVEF- 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
             +N  N   + +K   + V        +K  +LYE     V NKP  I++  G G  +A
Sbjct: 62  RYVNLENLPKRSEKKDLTPVP-------MKLDVLYEGKHYLVLNKPPNIAIHPGKGVHVA 114

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             I+G L  +   KG  P L HRLD++TSG+LVVA+ R AA+ LTE F+ R I+K Y +L
Sbjct: 115 TLIEGLL-HYGQEKGFSPFLVHRLDKDTSGLLVVAKDREAARILTELFKDRNIEKEYVTL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G P+N  +                             AIS    +    +    L ++
Sbjct: 174 VRGTPENNMKITIPL--------------------DGQEAISEIVSVKSL-RDVSLLRVK 212

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQ-NKLYLHARYMDLPHP-EGG 303
            HTGR HQ+R H   +G P+VGD  Y   +F   F       +L+LH+  M    P    
Sbjct: 213 IHTGRKHQIRRHLSQIGFPVVGDDTYGDRHFNREFRKRYGLKRLFLHSYRMKFIDPWTEE 272

Query: 304 RLQITAPLPAHMVKTWDSLGFKYD 327
                APLP  ++   + L  + D
Sbjct: 273 EKDFRAPLPDDLLSVLNFLEERSD 296


>gi|325335513|gb|ADZ11787.1| Pseudouridylate synthase, 23S RNA-specific [Riemerella
           anatipestifer RA-GD]
          Length = 354

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 93/340 (27%), Positives = 162/340 (47%), Gaps = 55/340 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+ ++E +R+D++      + +   + +  R+G V V+   VK N R++ G  V +  
Sbjct: 33  LVVDKNQEPLRIDKYLLIFRQNSSRNKISQTCRAGNVVVNGTPVKQNYRVKPGDKVSV-- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L H  +E  I+   + +          ++YED  + V +K AG+ V  G G     
Sbjct: 91  ---LLTHPPRENVIVPQDIPIN---------IVYEDDDLLVVDKEAGMVVHPGFGNWDGT 138

Query: 125 ----IAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               +AYH +   LK+ +D  G    L HR+D++TSG+LV+A+   A   L + F  R  
Sbjct: 139 LVNALAYHFEKNGLKTDLDRVG----LVHRIDKDTSGLLVIAKNEYAMSFLAKQFFERTT 194

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH----VVKQNEKGANYAISHFKVIDC 235
           +++YW+ VWG        I      K HIG D  +     V ++     +A++H+KV++ 
Sbjct: 195 KRLYWAFVWGNLAEDTGTI------KGHIGRDLKNRMQMAVYEDGSLGKHAVTHYKVLER 248

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG----NFTSPIQN--- 286
           F +   W+E +  TGRTHQ+R H  H+G  +  D +Y  +   +G     +   ++N   
Sbjct: 249 F-RYMTWVECKLETGRTHQIRAHFRHIGHTLFNDERYEGHQILRGINLPKYKQFVKNVFE 307

Query: 287 ---KLYLHARYMDLPHPEGGR-LQITAPLPAHM---VKTW 319
              +  LHA  +   HP   + +   +P+P  M   V+ W
Sbjct: 308 VLPRHALHAHTLGFTHPTTKKEMYFESPMPQDMQQAVEKW 347


>gi|298292787|ref|YP_003694726.1| pseudouridine synthase [Starkeya novella DSM 506]
 gi|296929298|gb|ADH90107.1| pseudouridine synthase [Starkeya novella DSM 506]
          Length = 250

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 119/228 (52%), Gaps = 17/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +L+ D  + V +KPAG++V    +GG  +A H+D       ++    P L HRLD++TSG
Sbjct: 15  VLHRDGMMLVIDKPAGLAVHKGPKGGETLADHLDALRFGLPNA----PELAHRLDKDTSG 70

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R R A   L ++F    + K Y ++V G+P   +  I   L K+S   G ++ V 
Sbjct: 71  CLVLGRHRKALADLGKAFADGTVGKTYMAVVRGVPAEPRGRIELKLSKRSPTRGWWMAVD 130

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              ++    AIS ++ I    +    L + P TGRTHQLRVH   +G PI+GD  Y    
Sbjct: 131 PNGQE----AISEWETI-AAGEGLAVLVLSPLTGRTHQLRVHMNAIGHPILGDSIYG--- 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
            G    P    L+LH+R + +P  +G  + + APLP H+  T +  GF
Sbjct: 183 -GASRLPGGPILHLHSRRVVIPQRKGEAIDVRAPLPPHIRATIERAGF 229


>gi|256027210|ref|ZP_05441044.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
 gi|289765187|ref|ZP_06524565.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
 gi|289716742|gb|EFD80754.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
          Length = 304

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 86/308 (27%), Positives = 157/308 (50%), Gaps = 27/308 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++Y++ E D E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G ++ 
Sbjct: 2   IEYIIDE-DYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDIIF 60

Query: 67  I--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           I  P      N    E+K ++ S       + LK ++++++  ++V NKP G  V  GSG
Sbjct: 61  IFLPETFKEQN----EEKFIELS---QVRKEKLKQMIVFQNDNLFVINKPLGDVVHKGSG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +    +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+
Sbjct: 114 HDISLLEEFRSYYSNNN--INFVNRIDKLTSGLVIGAKNIKTAREIAKEIQTGNIVKKYY 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  +     + N+L K      + V V    ++G   +I++FK I  +  K+  LE
Sbjct: 172 ILVNGKIEKDNFILENYLKKDE----ERVIVSDIEKEGYKKSITYFKKIKEY-DKYTLLE 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQLR    H+G  IVGD KY  N K       ++ +YL + Y+ +       
Sbjct: 227 AELKTGRTHQLRAQLNHLGNNIVGDTKYGKNEK-------EDIMYLFSYYLKIDLY---N 276

Query: 305 LQITAPLP 312
           L+I   +P
Sbjct: 277 LEIKLEIP 284


>gi|88707052|ref|ZP_01104748.1| Ribosomal large subunit pseudouridine synthase D [Congregibacter
           litoralis KT71]
 gi|88698702|gb|EAQ95825.1| Ribosomal large subunit pseudouridine synthase D [Congregibacter
           litoralis KT71]
          Length = 312

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 88/300 (29%), Positives = 148/300 (49%), Gaps = 38/300 (12%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RLD+     +P  +   LQ  +RSG++R+D  + +  + I+ G+V+ +    NA    
Sbjct: 2   GARLDQAAAQLFPEFSRARLQSWIRSGELRLDGTKGRPRDAIRGGEVLSL----NA---- 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
                 L+S V+ T  ++ L   ++YED ++ V +KPAG+ V  G+G      ++  L  
Sbjct: 54  -----ELESEVSWT--AEALPLEIVYEDEELLVIDKPAGLVVHPGAGNHNGTLVNALLNH 106

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             D +   PR  + HRLD+ETSG+LVVA T  A + L    + + +Q+ Y+++V G+P  
Sbjct: 107 RPDLEA-IPRGGIVHRLDKETSGLLVVAATLNAHRSLVAQLQKKDVQREYFAIVRGVPSG 165

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                      ++ IG       K      G   A++H+++   FAQ +  L++Q  TGR
Sbjct: 166 GGRV-------EAAIGRHPRQRTKMAVVAAGGKPAVTHYRIARRFAQ-YTALDVQLETGR 217

Query: 252 THQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDLPHPEGG 303
           THQ+RVH  H G P++GD  Y    +          + ++   +  LHA+ +   HP  G
Sbjct: 218 THQIRVHMAHRGYPLLGDPVYGGRLQLPRGASERLAAALRGFRRQALHAQRLSFVHPGSG 277


>gi|258593870|emb|CBE70211.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [NC10 bacterium 'Dutch sediment']
          Length = 314

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 97/323 (30%), Positives = 150/323 (46%), Gaps = 42/323 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++ +     +RLDR+       +    +Q+++++G+V VD +  K +     GQ + 
Sbjct: 6   IRELIADISAGGLRLDRYLSTAT-GLPRSQIQRLIKAGRVLVDGRCPKASAIAHPGQQIS 64

Query: 67  I---PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +   PP  + L     E   LD               +LYED+ + V NKPAG+ V    
Sbjct: 65  LSIPPPQPSTLT---PEPIPLD---------------ILYEDTDMLVLNKPAGLVVHPAP 106

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      +   L    D  G    ++P + HRLD+ETSG++VVA+T  A   L   F+ R
Sbjct: 107 GHHSGTLVHAILYHCPDLPGIGEERRPGIVHRLDKETSGVMVVAKTDTAMASLATQFKGR 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           R+QK Y +LV G  K  +  IA  + +      D   +  +  KG   A+++++VI    
Sbjct: 167 RVQKTYIALVHGEVKQPQGQIAADIGRHER---DRKRMAVRTRKG-REAVTNYRVIKRLG 222

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-------CANFKGNFTSPIQNKLYL 290
                LE+QP TGRTHQ+RVH   +G P+VGD  Y       C           +  L L
Sbjct: 223 -GLTLLELQPQTGRTHQIRVHLSAIGHPVVGDKVYGGRREKKCRVLSVECRVKTERHL-L 280

Query: 291 HARYMDLPHPEGGR-LQITAPLP 312
           HA  + L HP     ++  APLP
Sbjct: 281 HAWKLGLFHPRTDVWMEFEAPLP 303


>gi|94984711|ref|YP_604075.1| pseudouridine synthase, RluD [Deinococcus geothermalis DSM 11300]
 gi|94554992|gb|ABF44906.1| Pseudouridine synthase, RluD [Deinococcus geothermalis DSM 11300]
          Length = 341

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 81/291 (27%), Positives = 130/291 (44%), Gaps = 37/291 (12%)

Query: 54  KFNNRIQSGQVVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           K + +++ G+ +R+  PP  +A   +  E   LD               +LYED  +   
Sbjct: 67  KASLKLKGGETLRVQVPPPPDAT--VSPEAVPLD---------------VLYEDEHLIAV 109

Query: 112 NKPAGISVQGGSGIAYH--IDGFL--------KSWVDSKGQKPRLTHRLDQETSGILVVA 161
           NKP G+      G+     ++  L           V   G +P + HRLD++TSG++VVA
Sbjct: 110 NKPPGMVTHPAPGVTSGTLVNALLGRLTLPEQPGAVGPDGYRPGIVHRLDKDTSGVIVVA 169

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +T  A   L  +F+ R   K Y ++  G+ K +     N  + +       + V     +
Sbjct: 170 KTVEAHARLAAAFKDRSTHKTYLAIAAGMWKAQGPVSVNAPVGRHPTARQRMTVGGVGPR 229

Query: 222 GANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            A    +      D   +    +  QPHTGRTHQ+RVH  H+G PI+GD  Y        
Sbjct: 230 EAQTLFTPLATHPDGHGRTLALVRAQPHTGRTHQIRVHLAHLGSPILGDAVY------GR 283

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
            S +  +  LHA+++ LPHP  G  L + AP+P  +++ W +LG      L
Sbjct: 284 ASAVMPRHALHAQFLTLPHPVTGETLHLHAPVPDDLLRAWVALGGAVPAEL 334


>gi|302391670|ref|YP_003827490.1| ribosomal large subunit pseudouridine synthase D [Acetohalobium
           arabaticum DSM 5501]
 gi|302203747|gb|ADL12425.1| ribosomal large subunit pseudouridine synthase D [Acetohalobium
           arabaticum DSM 5501]
          Length = 308

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 95/333 (28%), Positives = 169/333 (50%), Gaps = 42/333 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR- 66
           +Y++ +ND +  RLD++       ++   +QK++ +G+V V+K+  K + R+Q G  V+ 
Sbjct: 6   EYIIDDNDVD-QRLDKFLAYQNEELSRSYIQKLIDNGEVTVNKEEKKNSYRLQVGDEVKL 64

Query: 67  -IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            IP          +E +I   S+ L          ++ ED  I V NK A + V    G 
Sbjct: 65  IIPQP--------EEVEIKPESIPLE---------VIAEDEDIVVINKQADLVVHPAPGH 107

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                   + YH D    S ++ +  +P + HRLD++TSG +V A+   A ++L + F+ 
Sbjct: 108 KQGTLVNALLYHCDNL--SGINGE-IRPGIVHRLDKDTSGAIVAAKNDQAHRNLVKQFKE 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           RR +KIY +LV G  K+ K  I +  + +       + V K+N K    A++ F+V++ F
Sbjct: 165 RRTEKIYLALVEGNIKHNKAKI-DAAIGRDPYNRKRMAVTKRNSK---QAVTRFEVLERF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              + W++++  TGRTHQ+RVH  ++  P+VGD  Y  N K        ++  LHA  + 
Sbjct: 221 GN-YTWVKLKLETGRTHQIRVHMSYIDNPVVGDRLYGYN-KQQLNV---HRQLLHAYQLG 275

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             HP   + ++ TA +P+ + +  + L  + +R
Sbjct: 276 FNHPRRNKWVEFTAEMPSDIKQILEKLRSEKNR 308


>gi|86358939|ref|YP_470831.1| pseudouridylate synthase, ribosomal large subunit D protein
           [Rhizobium etli CFN 42]
 gi|86283041|gb|ABC92104.1| pseudouridylate synthase, ribosomal large subunit D protein
           [Rhizobium etli CFN 42]
          Length = 354

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 95/347 (27%), Positives = 158/347 (45%), Gaps = 49/347 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQV 64
           ++ V+  ++    RLD W         +   ++ +++ GQV +  ++V    R ++ G  
Sbjct: 24  IRKVLTADETAEGRLDAWLTAQVGEDFSRSRIKALIKDGQVSLRGEQVTDPQRKVRVGDS 83

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
             I                L    + T   + +   +L+ED  + V +KPAG+ V  GSG
Sbjct: 84  FEI---------------TLPEPEDPTPKGEDIPLEILHEDDDLIVISKPAGLVVHPGSG 128

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF--- 174
                 ++  +    D+       ++P + HRLD++T+G++VVA+   A +HL+  F   
Sbjct: 129 NWTGTLVNALIHHCGDTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDVAHRHLSLQFADH 188

Query: 175 -RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFK 231
            R   +++ Y ++VWG P+     I   L + +   GD     V + + + A+ AI+H++
Sbjct: 189 GRTMPLERAYRAVVWGRPRTLSGTIDAPLGRAT---GDRTRRAVKRPDSQDADAAITHYE 245

Query: 232 VIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSP 283
           VI+ F +          +E    TGRTHQ+RVH  H+G P+VGD  Y A F  K N    
Sbjct: 246 VIERFQENPDATALASLVECHLETGRTHQIRVHMAHIGHPLVGDTVYGAGFRTKANLLPE 305

Query: 284 IQNKLY-------LHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
              K+        LHA  +   HP  G L     PLP  MVK   +L
Sbjct: 306 EIRKVVNGFGRQALHAFMLQFEHPRTGELMHFEVPLPDDMVKLVAAL 352


>gi|186683943|ref|YP_001867139.1| RluA family pseudouridine synthase [Nostoc punctiforme PCC 73102]
 gi|186466395|gb|ACC82196.1| pseudouridine synthase, RluA family [Nostoc punctiforme PCC 73102]
          Length = 345

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 89/326 (27%), Positives = 148/326 (45%), Gaps = 47/326 (14%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-------RVKFNNRIQSGQVVR 66
            D +  R+DR+     P ++   +Q+++  G V+++ K        VK  +RI     + 
Sbjct: 44  TDTKGDRIDRFLSQELPDLSRSRIQQLIEQGNVQLNDKVCTSKKINVKLGDRI----TLE 99

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IP          +  ++L   + L          +LYED ++ + NKPAG+ V    G  
Sbjct: 100 IPEA--------QPLELLAEDIPLD---------ILYEDDQLLILNKPAGLVVHPAPG-- 140

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            H DG L + + +           Q+P + HRLD++T+G + +A+T  A  HL    + +
Sbjct: 141 -HPDGTLVNALLAHCPNLPGIGGVQRPGIVHRLDKDTTGAIAIAKTEVAHHHLQAQLKAK 199

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++ Y  +V+G PK +   I   L    H        +   E+G   A++H++V++   
Sbjct: 200 TARREYLGVVYGAPKVESGTID--LPIGRHPQDRKKMAIMPIEQGGRSAVTHWQVLERLG 257

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  +  Q  TGRTHQ+RVH+  +G PIVGD  Y +          Q    LHA  + L
Sbjct: 258 -NFTLIRFQLETGRTHQIRVHSAKIGHPIVGDPIYSSGHSVGVNLSGQ---ALHAWRLRL 313

Query: 298 PHPEGGRL-QITAPLPAHMVKTWDSL 322
            HP  G + ++TA  P    K  + L
Sbjct: 314 QHPLSGEMIEVTATPPTQFTKLLEML 339


>gi|148262258|ref|YP_001228964.1| RluA family pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146395758|gb|ABQ24391.1| pseudouridine synthase, RluA family [Geobacter uraniireducens Rf4]
          Length = 296

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 85/324 (26%), Positives = 155/324 (47%), Gaps = 40/324 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIP 68
           VVV  D   MRLD   K  +P ++   +++I+  G   + +  V+  +R ++ G ++ + 
Sbjct: 5   VVVGADHAGMRLDDGAKELFPQLSKTQIRRIIDWGGCTICEALVRVASRPLREGDLIAL- 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----S 123
                   +++ ++ ++ S        + K  LL+ED+     NK AGI+ Q        
Sbjct: 64  -------GVMEPERCVEIS--------YRKEDLLFEDANYLAVNKAAGINSQRTPYQLKG 108

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + Y ++ ++KS + SK +  R+ HRLD+ TSG++   + + AA H++   +  +++K+Y
Sbjct: 109 TVEYAVETYMKS-LGSK-EPARVIHRLDRGTSGVMFFPKDKRAATHISFLLKEGKVEKVY 166

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++V G+P  ++  +   + K +     Y   +   E     A + F+VI    +    L
Sbjct: 167 WAMVAGVPDEEQWTVDAPIAKLNKF--RYGVALPGRE-----ARTAFRVI-AVGKGATLL 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E  P TGRTHQ+RVH +H   PI+GD  Y  +           ++ LH R M     +G 
Sbjct: 219 EALPFTGRTHQIRVHLVHSNLPIIGDTTYGGD--------TAARMMLHCRSMAFTSRDGK 270

Query: 304 RLQITAPLPAHMVKTWDSLGFKYD 327
            +Q  APL    +K     G + +
Sbjct: 271 PVQAIAPLDEGFLKACRDFGIETE 294


>gi|108759583|ref|YP_629678.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108463463|gb|ABF88648.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 310

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 88/292 (30%), Positives = 140/292 (47%), Gaps = 28/292 (9%)

Query: 36  NLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
             + ++  G V V  KR +  N R+ +GQVV +         +++E     S ++    +
Sbjct: 31  GARGLVEVGAVYVAGKRSRDANARLTAGQVVTV---------VLEEGG--QSPLSEAPPA 79

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQE 153
             L+  +LYED+ +   +KPAG+S Q   G    +   L   V +K G+   L HRLD+E
Sbjct: 80  PELR--VLYEDADVIAVDKPAGVSAQPTEG---RVGDSLVDLVGAKLGRPAGLVHRLDRE 134

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKECIANWLLKKSHIGGDY 212
           TSG+ V  +T  A   L   FR  R +K Y +    G+P +    +   L K     G +
Sbjct: 135 TSGVTVFGKTAEATSALAAEFREGRARKRYVAATGPGLPPSG--TVDLPLSKDPSRPGRW 192

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                 N      A++ F  +      FC +E+ PHTGRTHQLR H   +G PI+GD +Y
Sbjct: 193 RATRAAN---GVPALTDFHTLSS-GPAFCVVELLPHTGRTHQLRAHLTALGAPILGDARY 248

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
               +         +  LHA+ ++L HP  G+ L+I AP+P  +++ + + G
Sbjct: 249 GGAARAEGVE--APRCLLHAQALELGHPRTGKLLRIEAPVPEDLMRFFLAAG 298


>gi|167761774|ref|ZP_02433901.1| hypothetical protein BACSTE_00112 [Bacteroides stercoris ATCC
           43183]
 gi|167700410|gb|EDS16989.1| hypothetical protein BACSTE_00112 [Bacteroides stercoris ATCC
           43183]
          Length = 223

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 73/219 (33%), Positives = 114/219 (52%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKLYLKEKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E FR   ++K YW++V   P+  +  + N+L++       Y + 
Sbjct: 63  GLVVFAKTSKALARLNEMFRNSEVKKTYWAVVKNRPRESEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   +Q +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPNSKKAILHYRLI-ARSQNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
             G+  S     + LHAR++   HP   +L ++ AP+PA
Sbjct: 177 --GSPRSNPDGSICLHARFVRFVHPVSKKLIEVEAPVPA 213


>gi|153953824|ref|YP_001394589.1| pseudouridine synthase [Clostridium kluyveri DSM 555]
 gi|219854440|ref|YP_002471562.1| hypothetical protein CKR_1097 [Clostridium kluyveri NBRC 12016]
 gi|146346705|gb|EDK33241.1| Predicted pseudouridine synthase [Clostridium kluyveri DSM 555]
 gi|219568164|dbj|BAH06148.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 305

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 92/331 (27%), Positives = 156/331 (47%), Gaps = 47/331 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +V +DEEN+RLD +   H    +   +Q ++    V V+ +  K N + ++G  ++
Sbjct: 3   IRNFLVNDDEENLRLDLFICKHIQDKSRSYIQNLIEDNLVEVNHRMKKSNYKTKTGDNIK 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +                L  +V L    + +K  +LYEDS + V NKP G+ V   SG+ 
Sbjct: 63  VS---------------LPDAVELNIKGEDIKLDILYEDSDVIVVNKPQGMIVHPASGVY 107

Query: 126 -AYHIDGFLK-SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  L     D  G     +P + HR+D++TSGILV+A+   +   L+E  +   +
Sbjct: 108 TGTLVNALLNHCREDLSGINGIARPGIVHRIDKDTSGILVIAKNDMSHNKLSEQLKDHSM 167

Query: 180 QKIYWSLVWGIPKNKKECIANWLL--KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + Y +LV GI K +K  +   +   KK  I    V       +G   A++H++VI  F 
Sbjct: 168 TREYIALVEGIIKEEKGSLDKPIGRHKKDKIKMAVV-------EGGKRAVTHYEVIKRF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLHA 292
           +++  ++    TGRTHQ+RVH  ++G P+VGD  Y       N KG           LHA
Sbjct: 220 KEYTLVKCILETGRTHQIRVHMCYLGHPVVGDPVYGYKKQKFNLKGQL---------LHA 270

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + +   HP  G  ++    +P +  +  D L
Sbjct: 271 QKLGFIHPGTGTYMEFQVEVPEYFKRIIDIL 301


>gi|213961970|ref|ZP_03390235.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           sputigena Capno]
 gi|213955323|gb|EEB66640.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           sputigena Capno]
          Length = 350

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 88/313 (28%), Positives = 153/313 (48%), Gaps = 56/313 (17%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  N   +     +Q+  + G + V+ + VK N+R+++  VV++      L+
Sbjct: 34  QEPLRVDKFLMNFVENATRNKVQQAAKQGNIFVNGEPVKANHRVKANDVVKV-----LLS 88

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           H   E  ++  ++ L          ++YED  + V NKPAG+ V  G G         + 
Sbjct: 89  HPPHEDLLVPENIPLN---------IVYEDDALLVVNKPAGMVVHPGHGNYSGTLINALV 139

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH +       ++   +P L HR+D++TSG+LV+A+T  A  HLT+ F  +  Q+ Y +L
Sbjct: 140 YHFE----HLPNNSSNRPGLVHRIDKDTSGLLVIAKTEEAMLHLTQQFFYKTTQREYIAL 195

Query: 187 VWGIPKNKKECIANWLLKKSHIG---GDYVHV-VKQNEKGANYAISHFKVIDCFAQKF-- 240
           VWG  +  +  +      + HIG    D + + V  +      A++H+KV++ F      
Sbjct: 196 VWGNIEEDEGTV------RGHIGRHLKDRLQMDVFPDGSHGKEAVTHYKVLERFGYVTLV 249

Query: 241 -CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN------K 287
            C LE    TGRTHQ+RVH  H+G  +  D +Y  +   KG     +   ++N      +
Sbjct: 250 SCRLE----TGRTHQIRVHLKHIGHTLFNDERYGGDKILKGTTFAKYKQFVENCFAVLPR 305

Query: 288 LYLHARYMDLPHP 300
             LHA+ +   HP
Sbjct: 306 QALHAKTLGFEHP 318


>gi|311068067|ref|YP_003972990.1| pseudouridylate synthase [Bacillus atrophaeus 1942]
 gi|310868584|gb|ADP32059.1| pseudouridylate synthase [Bacillus atrophaeus 1942]
          Length = 303

 Score =  116 bits (290), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 89/316 (28%), Positives = 154/316 (48%), Gaps = 35/316 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINA 73
           ++++ R+D++  +     +   +Q+ ++ G + V+   VK N ++Q G  V++  P   A
Sbjct: 11  EQKSERIDKFLASAEKDWSRTQVQQWVKDGHIEVNGSPVKANYKMQPGDQVKVTVPEPEA 70

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
           L+ ++ E   LD               + YED  + V NKP G+ V    G      ++G
Sbjct: 71  LD-VLAEPMDLD---------------IYYEDQDVLVVNKPRGMVVHPAPGHVTGTLVNG 114

Query: 132 FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y ++V
Sbjct: 115 LMAHCKDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVHKTVTRKYMAVV 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI  +    I +  + +       + VV++   G N A++HF V++ F Q F  +E Q 
Sbjct: 175 HGIISHDDGTI-DAPIGRDKKDRQSMTVVRE---GKN-AVTHFHVLERF-QDFTLVECQL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   HP   + ++
Sbjct: 229 ETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDF-----NGQALHAGILGFQHPRTDKYIE 283

Query: 307 ITAPLPAHMVKTWDSL 322
             APLP  M K  ++L
Sbjct: 284 FEAPLPGDMTKLIENL 299


>gi|49473932|ref|YP_031974.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           quintana str. Toulouse]
 gi|49239435|emb|CAF25784.1| Ribosomal large subunit pseudouridine synthase D [Bartonella
           quintana str. Toulouse]
          Length = 334

 Score =  116 bits (290), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 97/335 (28%), Positives = 155/335 (46%), Gaps = 61/335 (18%)

Query: 20  RLDRWF-KNHYPHINFVNLQKILRSGQVRVD-------KKRVKFNNRIQSGQVVRIPPVI 71
           RLD+W  K ++  ++   LQ ++R G +++D       K ++K N  I+    + IP   
Sbjct: 15  RLDQWLTKQYHSALSRSRLQALIREGYLKIDGQLIHEPKTKLKPNQMIE----LTIP--- 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------- 124
                I+++ K    ++ L          +L+ED  + V NK AG+ V  G+G       
Sbjct: 68  -----ILRDAKPSGEAIKLD---------ILFEDDHVIVINKQAGLVVHPGNGNLTGTLV 113

Query: 125 --IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMRR 178
             + YH    L      K  +P + HRLD+ TSGI+VVA+   A ++L+  F    R   
Sbjct: 114 NALIYHCGDSLSGIGGVK--RPGIVHRLDKNTSGIMVVAKNDLAHKNLSAQFSDHGRTSA 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA- 237
           + + Y +L+WG P      I   L +  H       +  QN   A +A++HF +++ +  
Sbjct: 172 LDRRYHALIWGSPNRNVWKIDAPLGRSPHNRTKQAVIYSQNPH-ARHAVTHFSLLEKYGI 230

Query: 238 ----QKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQ----- 285
                 F   LE +  TGRTHQ+RVH  H+G P+VGD  Y      K N   PI      
Sbjct: 231 CSDKTSFASLLECRLETGRTHQIRVHMAHIGHPLVGDTVYGNACKTKSNMLKPIIKNAID 290

Query: 286 --NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
             N+  LHA  +   HP  G+ +  ++P+P  M +
Sbjct: 291 QFNRQALHAASLTFEHPATGKIMSFSSPIPQDMAE 325


>gi|160902202|ref|YP_001567783.1| RluA family pseudouridine synthase [Petrotoga mobilis SJ95]
 gi|160359846|gb|ABX31460.1| pseudouridine synthase, RluA family [Petrotoga mobilis SJ95]
          Length = 319

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 93/319 (29%), Positives = 161/319 (50%), Gaps = 43/319 (13%)

Query: 12  VENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VE ++E  RLD +     P  I+   +Q  +  GQ+ V+  + K + +++ G  ++I   
Sbjct: 8   VEREDEQKRLDIYIAQKMPIEISRNLIQNAITKGQITVNGSQKKPHYKVKQGDEIQID-- 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI------SVQGGS- 123
            + L    KE+ IL  ++ L          +LYED ++ V NKPAG+      S++ G+ 
Sbjct: 66  FHELVEETKEENILPENIPLN---------ILYEDEELIVINKPAGLIVHPTPSIKTGTL 116

Query: 124 --GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + +H+    K+  D    +  + HRLD+ETSG+LVVA+   +   L++ F+ R+  K
Sbjct: 117 VNALMHHVKDLDKTMQDP--NRLGIVHRLDKETSGVLVVAKNAFSHHLLSKEFKERKTMK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFA 237
            Y ++V G  K +KE   N  L +        H + ++++   Y    AI+ +K +  F 
Sbjct: 175 YYLAIVEGTLK-EKEGEINLPLGR--------HPILRHKRAVVYNGKEAITEYKTLKEFG 225

Query: 238 Q--KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARY 294
                 W+ ++  TGRTHQ+RVH  ++G P++GD  Y  N  + N   P+  ++ LHA  
Sbjct: 226 DLATLVWIRLR--TGRTHQIRVHFKYIGNPLIGDSLYGKNKIEKNLQIPVGRQM-LHALK 282

Query: 295 MDLPHPEGGR-LQITAPLP 312
           +   HP+    ++  APLP
Sbjct: 283 LGFYHPKTKEWMEFLAPLP 301


>gi|299821727|ref|ZP_07053615.1| ribosomal large subunit pseudouridine synthase [Listeria grayi DSM
           20601]
 gi|299817392|gb|EFI84628.1| ribosomal large subunit pseudouridine synthase [Listeria grayi DSM
           20601]
          Length = 302

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 95/326 (29%), Positives = 149/326 (45%), Gaps = 46/326 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  E+ MR+D++        +  ++Q++L+ GQV VD + VK N + Q G +V +  
Sbjct: 6   VEVKETEKGMRIDKFLAEKASK-SRSSVQQLLKDGQVTVDGEVVKPNYKCQLGDIVEMEE 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
               +  I  E   LD               + YED  + V NKP G+ V   +G     
Sbjct: 65  RAPEVIEIEAEDIPLD---------------IYYEDEDLLVVNKPEGMVVHPSAGHYTGT 109

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HR+D++TSG+L+VA+  AA + L    + +   + Y
Sbjct: 110 LVNALLYHCKDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDAAHESLASQLKAKTSHREY 169

Query: 184 WSLVWGIPKNKKECI------ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +LV G   ++K  I      A    +K  + GD              A +HF+V++ F 
Sbjct: 170 VALVHGDIAHQKGTIEAPIGRAKDDRQKMAVVGD-----------GKEARTHFEVLERFG 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  +  Q  TGRTHQ+RVH  ++G P+ GD KY     G   +   N  YLHA+ +  
Sbjct: 219 D-FTLITCQLDTGRTHQIRVHLKYIGHPLAGDPKY-----GPKNTLPGNGQYLHAKKLGF 272

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL 322
            HP     L   +PLPA   +  + L
Sbjct: 273 VHPRTKEELSFESPLPADFEEVLEKL 298


>gi|172057958|ref|YP_001814418.1| RluA family pseudouridine synthase [Exiguobacterium sibiricum
           255-15]
 gi|171990479|gb|ACB61401.1| pseudouridine synthase, RluA family [Exiguobacterium sibiricum
           255-15]
          Length = 307

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 90/311 (28%), Positives = 153/311 (49%), Gaps = 47/311 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHI 77
           R+D+W        +   +Q  L++G V VD + VK N ++   +  +VRIP  +      
Sbjct: 17  RIDKWLAEQQ-DWSRSQVQDWLKAGHVEVDGRIVKPNYKMSGTEEILVRIPEAV------ 69

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E ++L   + L          ++YEDS + V NKP G+ V   +G   H+ G L + +
Sbjct: 70  --ELEVLPEDIPLD---------VVYEDSDVIVINKPKGMVVHPAAG---HVSGTLVNAL 115

Query: 138 -----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                D  G    ++P + HR+D++TSG+L+VA+   A + L +  + +  +++Y +LV 
Sbjct: 116 LHHCQDLSGINGVKRPGIVHRIDKDTSGLLMVAKNDLAHESLAQQLKDKTTERLYIALVH 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           G   ++   I      ++ +G D      +   +K +  A++HF+V++ + + F  +E +
Sbjct: 176 GEIPHELGTI------EAPVGRDKNDRQRMTVTDKNSKAAVTHFRVLERY-EGFTVVECK 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  +   HP  G  L
Sbjct: 229 LETGRTHQIRVHMRYIGFPLAGDPKY-----GPRKTMKMNGQALHAAVLGFKHPRTGEML 283

Query: 306 QITAPLPAHMV 316
              APLP  M 
Sbjct: 284 HFEAPLPEEMT 294


>gi|169827034|ref|YP_001697192.1| putative RNA pseudouridine synthase ylyB [Lysinibacillus sphaericus
           C3-41]
 gi|168991522|gb|ACA39062.1| Hypothetical RNA pseudouridine synthase ylyB [Lysinibacillus
           sphaericus C3-41]
          Length = 303

 Score =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 90/319 (28%), Positives = 149/319 (46%), Gaps = 38/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT V Y + E  ++  R+D+   +     +   +   +  G ++V+   VK   ++++G 
Sbjct: 1   MTEVTYTI-EEQQQGERIDKALSSLQSEWSRTQIGNWISDGNIKVNGDAVKAKYKVKAGD 59

Query: 64  VVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           V+ I  P    L+ +I E   LD               ++YED+ + V NKP G+ V   
Sbjct: 60  VIAIDVPEAEPLD-VIAENLALD---------------IVYEDADVLVVNKPKGMVVHPA 103

Query: 123 SG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L +    
Sbjct: 104 PGHMTGTLVNGLMYQCKDLSGINGIMRPGIVHRIDKDTSGLLMVAKNDVAHESLVDQLVN 163

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDC 235
           + + + Y +LV G   + K  I       + IG D     KQ       +A++HF V++ 
Sbjct: 164 KTVTRKYIALVHGHIAHDKGTI------DAPIGRDQKDRQKQAIVDNGKHAVTHFHVVER 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F   +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +F   +     LHA  +
Sbjct: 218 FGD-YTLVECRLETGRTHQIRVHMNYIGFPLVGDPKYGPKKTIDFGGQV-----LHAATL 271

Query: 296 DLPHPEGGR-LQITAPLPA 313
              HP  G  L+   PLPA
Sbjct: 272 GFNHPSSGEYLEFETPLPA 290


>gi|17228018|ref|NP_484566.1| hypothetical protein alr0522 [Nostoc sp. PCC 7120]
 gi|9957317|gb|AAG09315.1| hypothetical protein [Nostoc sp. PCC 7120]
 gi|17129867|dbj|BAB72480.1| alr0522 [Nostoc sp. PCC 7120]
          Length = 312

 Score =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 85/311 (27%), Positives = 147/311 (47%), Gaps = 33/311 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV---KFNNRIQSGQVVRIP 68
           +E +E++ R+DR+     P ++   +Q+++  G+V+V+ K     K N ++     + +P
Sbjct: 7   LEVEEDSARIDRYLAEELPDLSRSRIQQLIEQGKVQVNGKVCTSKKINLKVGDRITLEVP 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                             +  L   ++ +   +LYED ++ + NKPAG+ V    G ++ 
Sbjct: 67  -----------------EAQPLEIQAEDIPLDILYEDDQLLILNKPAGLVVHPAPGHSHG 109

Query: 129 --IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D  G    Q+P + HRLD++T+G + +A+T  A +H+    + +  ++ 
Sbjct: 110 TLVNALLAHCPDLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKHIQAQLQAKTARRE 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  +V+G PK     +   L    H        V   E+G   AI+H+++ +     F  
Sbjct: 170 YLGVVYGAPKTASGKVD--LPIGRHPQDRKKMAVVPIEEGGRSAITHWQIQERLG-NFTL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-E 301
           +  Q  TGRTHQ+RVH+  MG PIVGD  Y +        P Q    LHA  + L HP  
Sbjct: 227 IHFQLETGRTHQIRVHSAKMGHPIVGDPVYGSGRSVGVNLPGQ---ALHAWRLRLQHPIT 283

Query: 302 GGRLQITAPLP 312
           G  ++ TA  P
Sbjct: 284 GDWVEATATPP 294


>gi|49475182|ref|YP_033223.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           henselae str. Houston-1]
 gi|49237987|emb|CAF27192.1| Ribosomal large subunit pseudouridine synthase D [Bartonella
           henselae str. Houston-1]
          Length = 334

 Score =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 95/335 (28%), Positives = 158/335 (47%), Gaps = 43/335 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + + +    RLD+W    Y ++ +   LQ ++R G ++VD            GQ+++ P 
Sbjct: 6   ITDENALGQRLDQWLAKQYHNVLSRSRLQALIREGYLKVD------------GQLIKEPK 53

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                N II  +  + +  +     + +   +L+ED  + V NKPAG+ V  G+G     
Sbjct: 54  TKLKSNQII--ELTMPALRDAEPSGEAIALDILFEDDHVIVINKPAGLVVHPGNGNWTGT 111

Query: 128 HIDGFL----KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMRR 178
            ++  +    KS     G ++P + HRLD+ TSG++VVA+   A + L+  F    R   
Sbjct: 112 LVNALIHHCGKSLSGIGGVKRPGIVHRLDKNTSGVMVVAKNDLAHKSLSAQFFDHGRTSA 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-- 236
           + + Y +L+WG P      I   + +  H       V  Q    A +A++HF +++ +  
Sbjct: 172 LDRRYHALIWGSPNRNVWTIDAPVGRSPHNRTKQAVVYNQCLH-ARHAVTHFSLLEQYGT 230

Query: 237 -AQKFCW---LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKL- 288
            A K  +   LE +  TGRTHQ+RVH  H+G P+VGD  Y   FK       S I+N + 
Sbjct: 231 CADKTPFASLLECRLETGRTHQIRVHMAHIGHPLVGDTVYGNAFKTKSNTLNSIIKNAID 290

Query: 289 -----YLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
                 LHA  +   HP  G+ +  ++PLP  M +
Sbjct: 291 QFNRQALHAANLTFEHPATGKIMSFSSPLPQDMAE 325


>gi|300691371|ref|YP_003752366.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Ralstonia solanacearum PSI07]
 gi|299078431|emb|CBJ51083.2| Ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Ralstonia solanacearum PSI07]
          Length = 358

 Score =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 93/326 (28%), Positives = 147/326 (45%), Gaps = 34/326 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+      P  +   LQ+ + +G VRV    V+    +  G  V + P          
Sbjct: 51  RLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVRPRAAVCGGDRVEVVP---------- 100

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            Q+  D S  + +  D     ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 101 -QRAADESAFVAEPIDL---DVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYP 156

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           ++  + PR  + HRLD+ETSG++VVART  A   L    + R +++ Y +LVWG  +  +
Sbjct: 157 EA-AELPRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWG--ETPE 213

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---VIDCFAQKFCWLEMQPHTGRT 252
               +  + +     D   +          A +HFK   V+D    +   +  Q  TGRT
Sbjct: 214 AGTIDAPIGRDP--RDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLVRCQLETGRT 271

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YLHARYMDLPHPEGGR- 304
           HQ+RVH    G P++GD  Y  NF+      I+  L        LHA  + L HP  G+ 
Sbjct: 272 HQIRVHFESEGHPLLGDPVYTRNFRRGQPQTIKAPLPVPFARQALHAVRLGLVHPASGQS 331

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNL 330
           +   A +P  + +  D+L    D +L
Sbjct: 332 IHWHAGVPDDLAELMDALEMDPDADL 357


>gi|83312510|ref|YP_422774.1| putative pseudouridine synthase in lpd 3'region [Magnetospirillum
           magneticum AMB-1]
 gi|82947351|dbj|BAE52215.1| Hypothetical pseudouridine synthase in lpd 3'region
           [Magnetospirillum magneticum AMB-1]
          Length = 225

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 74/226 (32%), Positives = 115/226 (50%), Gaps = 12/226 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LLY D  + + +KPAG++V  G     H+  +L +      ++P L HRLD+ETSG LV+
Sbjct: 7   LLYRDPAVLIIDKPAGLAVHAGPKGGEHLMLYLDALSFGLKRRPELAHRLDRETSGCLVL 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            RT  A   L E F      K YW++V G P+  +  I   L K+    G  + V    +
Sbjct: 67  GRTSKALAGLGELFAKGLADKTYWAVVVGKPREDQGVIDYALKKREKKFGWRMEV----D 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    +++ ++++     +  WLE +P TGRTHQ+R H   +G P+VGD  Y     G  
Sbjct: 123 RTGLASVTQWRLLGSDG-RLSWLECRPLTGRTHQIRAHCAAIGHPLVGDSIY-----GRG 176

Query: 281 TSPIQ-NKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
           T  +  ++L LH+R + LP H     +   AP+P HM+      G+
Sbjct: 177 TGTLAGDRLMLHSRRIVLPFHAGKPPIAAEAPVPEHMLSVLKGCGW 222


>gi|317129279|ref|YP_004095561.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
 gi|315474227|gb|ADU30830.1| pseudouridine synthase, RluA family [Bacillus cellulosilyticus DSM
           2522]
          Length = 305

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 86/315 (27%), Positives = 155/315 (49%), Gaps = 38/315 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           + ++E  +R+D++  +H+P  +   +Q+ +    ++V+   +K   ++++G         
Sbjct: 6   ITSEENGVRIDKFISDHFPQWSRTIIQQWIVDNHIQVNGTPIKSKYKVKAG--------- 56

Query: 72  NALNHI-IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
              +HI I+E       + L   ++ L   ++YED  + V NKP G+ V    G      
Sbjct: 57  ---DHIEIREP----DPIPLEIPAENLNLDIIYEDGDVLVVNKPRGMVVHPAPGHYTGTL 109

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    + +  ++ Y+
Sbjct: 110 VNGLMYHCHDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDRAHESLVNQLKNKETKRRYY 169

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---C 241
           ++V GI  + K  I   + +      +    +   EK +  A++HF+V++ F +     C
Sbjct: 170 AIVSGIIPHDKGTIDAPIGRNP----EDRQSMMVTEKNSRDAVTHFQVVERFYRHTLVSC 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE    TGRTHQ+RVH  ++G PIVGD KY    K  F  PI+ +  LHA  +   HP 
Sbjct: 226 ELE----TGRTHQIRVHLKYIGFPIVGDPKYGPRKKQKF--PIEGQA-LHAELLGFQHPS 278

Query: 302 GGRLQ-ITAPLPAHM 315
              L+    P+P  M
Sbjct: 279 TNELKTFQVPMPHDM 293


>gi|291536189|emb|CBL09301.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis M50/1]
          Length = 310

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 95/333 (28%), Positives = 161/333 (48%), Gaps = 53/333 (15%)

Query: 12  VENDEENMRLDRWFK---------NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +E + E  RLD++           ++ P  +F   QK++R G V+V+    K N R++  
Sbjct: 8   IEAEYEGERLDKYLSVIFEQSKTSSNAPSRSF--FQKLIRDGHVKVNDSIAKANYRLRMD 65

Query: 63  QVV--RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            +V   IP  +        E  IL   + L          +LYED  + V NKP G+ V 
Sbjct: 66  DLVCVEIPDAV--------ETPILPEDIPLD---------ILYEDDDLLVVNKPKGMVVH 108

Query: 121 GGSGIAYHIDGFLKSWV-----DS----KGQ-KPRLTHRLDQETSGILVVARTRAAAQHL 170
             +G   H  G L + +     DS     G+ +P + HR+D +T+G L+V +   +   +
Sbjct: 109 PSAG---HYSGTLVNAIMFHCKDSLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHVKI 165

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            E  +   + + Y  +V+G+ K+ +  I N  + +       + + K+N K A   I+H+
Sbjct: 166 AEQIKEHSVNRRYRGIVYGVVKDDEGTI-NAPIGRHPTNRKKMAINKKNGKPA---ITHY 221

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           KV++ F+  + ++E +  TGRTHQ+RVH   +G P++GD  Y +  K  F +  Q    L
Sbjct: 222 KVLERFSN-YTYMEFKLETGRTHQIRVHMASIGHPLLGDTVYSSG-KSPFKTQGQT---L 276

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           HA  +   HP     ++I+APLP + +K   SL
Sbjct: 277 HAMTIGFIHPHTNEYMEISAPLPEYFLKILKSL 309


>gi|186475732|ref|YP_001857202.1| RluA family pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184192191|gb|ACC70156.1| pseudouridine synthase, RluA family [Burkholderia phymatum STM815]
          Length = 436

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 93/332 (28%), Positives = 149/332 (44%), Gaps = 37/332 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +V VD +  K    +  G  + +
Sbjct: 81  RVVTVPPGLAGERLDKVLAKVFPEFSRSRLQSWIEAQRVHVDGQPAKIRQPVPLGASIEL 140

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
            P       ++ EQ        L   ++ +   ++YED  + V NKPAG+ V   +G   
Sbjct: 141 VP------DLLPEQ--------LAFTAEPVPLDVVYEDDTLVVINKPAGLVVHPAAGNWS 186

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + D+    PR  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 187 GTVLNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 246

Query: 184 WSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFA-- 237
            +LVWG +P +            + IG D     +           A +HF+ ID     
Sbjct: 247 LALVWGNMPDDGT--------IDAPIGRDPRERTRMAVVTGAAGKPARTHFRRIDSTVWE 298

Query: 238 -QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHAR 293
            Q    +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA 
Sbjct: 299 RQPVSAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGGFARQALHAW 358

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            + L HP+ GR +Q  A +P  + +  ++LG 
Sbjct: 359 RLALVHPKTGRTMQWRADVPGDIAELSEALGL 390


>gi|313115842|ref|ZP_07801276.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310621840|gb|EFQ05361.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 298

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 69/255 (27%), Positives = 128/255 (50%), Gaps = 19/255 (7%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
            YP +N   L K LR  +++++ K+   + R+ +G  +++      L+ ++   + +D  
Sbjct: 3   QYPALNPGRLNKALRENKIKLNGKKQPLSTRVMAGDEIKL----FILDEVLDADRRVDGP 58

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ----- 142
                      + ++Y+  +I + NKPAG++V G           L  +++ +G+     
Sbjct: 59  AWKNARG---PAQVVYDCPQIVIVNKPAGLAVDGPEDDTLLNRTLL--YLNQQGEYKEND 113

Query: 143 --KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P L HRLD  TSG+++VA+T  A +    + + R ++K Y  + +G P      +  
Sbjct: 114 LYTPALCHRLDTGTSGLVIVAKTPEAEELFLAAIKNREVKKTYLCVTFGRPMPPDATLGG 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           +LLK +  G   V +V++ + GA    + ++ I   + +   L++Q  TGRTHQ+R H  
Sbjct: 174 YLLKDADRG--IVKIVEEKQPGAKEVETRYETI-AVSGRLALLKVQLITGRTHQIRAHMA 230

Query: 261 HMGCPIVGDHKYCAN 275
            +GCPI+GD KY  N
Sbjct: 231 SIGCPILGDSKYGNN 245


>gi|154249782|ref|YP_001410607.1| RluA family pseudouridine synthase [Fervidobacterium nodosum
           Rt17-B1]
 gi|154153718|gb|ABS60950.1| pseudouridine synthase, RluA family [Fervidobacterium nodosum
           Rt17-B1]
          Length = 314

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 91/313 (29%), Positives = 154/313 (49%), Gaps = 35/313 (11%)

Query: 12  VENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-PP 69
           V + E   RLD++     P  I+   +Q+ +++G+V V+    K + +++SG ++ +  P
Sbjct: 5   VTSRENGWRLDKFVMEKTPEWISRTFIQRAIKNGEVLVNGTSKKPSYKVKSGDIITLNAP 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               +  I+ E   LD               ++YED  I V NK  GI       I  H 
Sbjct: 65  EAPEIPEILPEDIPLD---------------IIYEDRDILVINKQPGIITHP---IPSHT 106

Query: 130 DGFLKSWV-----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G + + V     D +G     +P + HRLD++TSG++V+A+   A Q LT+ F+ R  +
Sbjct: 107 SGTIVNGVLYHCKDLQGIGGVLRPGIVHRLDKDTSGVMVIAKNDLAHQSLTKQFKDRLTE 166

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y  LV G+PK K+  I   + +   +    V +   N +    A++H+KV+  F    
Sbjct: 167 KLYICLVKGVPKRKEGDIEINIARNPVL---RVKMTVTNSEYGKPALTHYKVVREFGDIA 223

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +   P TGRTHQ+RVH  ++G P++GD  Y    K +    I+ ++ LHA  +   HP
Sbjct: 224 ALVFAYPKTGRTHQIRVHMKYIGHPLMGDEVY-GRAKEDEIFGIKRQM-LHALSLSFYHP 281

Query: 301 EGG-RLQITAPLP 312
             G +++  A +P
Sbjct: 282 RTGEKVKFIAKIP 294


>gi|257866108|ref|ZP_05645761.1| pseudouridylate synthase [Enterococcus casseliflavus EC30]
 gi|257872439|ref|ZP_05652092.1| pseudouridylate synthase [Enterococcus casseliflavus EC10]
 gi|257800042|gb|EEV29094.1| pseudouridylate synthase [Enterococcus casseliflavus EC30]
 gi|257806603|gb|EEV35425.1| pseudouridylate synthase [Enterococcus casseliflavus EC10]
          Length = 302

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 86/321 (26%), Positives = 156/321 (48%), Gaps = 47/321 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINA 73
           EE  R+D+      P+ +   +Q+ L+   V +  + V+ N ++++G   ++++P     
Sbjct: 11  EEKGRVDKVLAERLPNHSRSQIQQWLKEDAVTLKGETVRANYKVKAGDHLIIQVP----- 65

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
                 E +++D         + +   ++Y+D+ + V NKP G+ V   +G         
Sbjct: 66  ------EPEVVDL------QPENIPLTIVYQDADVAVINKPQGMVVHPSAGHPNGTLVNA 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + YH+D    S ++    +P + HR+D++TSG+L++A+   A + L +  + +   + Y 
Sbjct: 114 LLYHMDDL--STINDV-VRPGIVHRIDKDTSGLLMIAKNDQAHESLAKQLKDKTSLRKYV 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   ++K  I N  + +S +      V++  +     A++HF V++ F Q F  +E
Sbjct: 171 ALVHGTISHEKGTI-NAPIGRSKVNRKMQAVIENGKP----AVTHFTVLERFEQ-FTLVE 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +Q  TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP  
Sbjct: 225 LQLETGRTHQIRVHMQYIGFPLAGDPLYGPKRTLKGNGQ-------FLHAKLLGFTHPTT 277

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
           G  L   APLP     T   L
Sbjct: 278 GESLVFEAPLPELFADTLKKL 298


>gi|332879773|ref|ZP_08447463.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
 gi|332682292|gb|EGJ55199.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
          Length = 353

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 91/329 (27%), Positives = 158/329 (48%), Gaps = 57/329 (17%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  N   +     +Q+  + G + V+ + VK N+R+++   V++        
Sbjct: 39  QEPLRVDKFLMNFVENATRNKVQQAAKQGNIFVNGQPVKSNHRVKANDEVKV-----YFA 93

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           H   E  ++  ++ L          ++YED  + V NKPAG+ V  G G         + 
Sbjct: 94  HPPHEDLLIPENIPLQ---------IVYEDDSLLVVNKPAGMVVHPGHGNYSGTLINALV 144

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH +    +  ++   +P L HR+D++TSG+LV+A+T  A  HLT+ F  +  ++ Y +L
Sbjct: 145 YHFE----NLPNNSSNRPGLVHRIDKDTSGLLVIAKTEEAMLHLTQQFFHKTTEREYIAL 200

Query: 187 VWGIPKNKKECIANWLLKKSHIG---GDYVHV-VKQNEKGANYAISHFKVIDCFAQKF-- 240
           VWG  +  +  +      + HIG    D + + V  +      A++H+KV++ F      
Sbjct: 201 VWGNVEADEGTV------RGHIGRHLKDRLQMDVFPDGSHGKEAVTHYKVLERFGYVTLV 254

Query: 241 -CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN------K 287
            C LE    TGRTHQ+RVH  H+G  +  D +Y  +   KG     +   + N      +
Sbjct: 255 SCRLE----TGRTHQIRVHMKHIGHTLFNDERYGGDKILKGTTFAKYKQFVDNCFSVLPR 310

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             LHA+ +   HP  G  L+  + LPA M
Sbjct: 311 QALHAKTLGFEHPVSGEYLRFDSELPADM 339


>gi|148285150|ref|YP_001249240.1| ribosomal large subunit pseudouridine synthase [Orientia
           tsutsugamushi str. Boryong]
 gi|146740589|emb|CAM81239.1| ribosomal large subunit pseudouridine synthase [Orientia
           tsutsugamushi str. Boryong]
          Length = 312

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 84/309 (27%), Positives = 150/309 (48%), Gaps = 19/309 (6%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + + N     RLD++ K  Y H+    +++ +R G ++V+  + K   +++   ++ I  
Sbjct: 3   ITISNCLVTTRLDKFLKRKYSHLTQGVIERGIRKGHIKVNDAKSKAKLQVKDNDILTIAD 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHS---DFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            + + ++    +       N+   +     + +  + E S   + NKPA +  QGGS I+
Sbjct: 63  YLTSCSNQKHIKLKKKVKDNVGVKALAHKIVNNYKIAETSDYIIINKPALLPTQGGSKIS 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +D  +K    S     +L HRLD+ET+G+L++A+    A  L+++F    I+K Y ++
Sbjct: 123 LSLDDAIKYLNKSFYYDFKLVHRLDRETTGLLIIAKNHGTAIKLSQAFLHHSIEKEYIAI 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEM 245
           + G+P      I   + K     GD    + + + G   +I+ ++V       +   +  
Sbjct: 183 LQGVPSQLSGEIITNITKT----GDR---MIETQNGGKVSITKYQVKAISINSQLSLVSF 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLP-HPEGG 303
            P TGRTHQLRVHA  +G PI+GD KY  +N   N++      L LHA  + +P H  G 
Sbjct: 236 IPVTGRTHQLRVHAAKIGYPIIGDKKYNISNTYYNYS------LKLHAAKICIPKHLFGN 289

Query: 304 RLQITAPLP 312
           +    APLP
Sbjct: 290 QRIYYAPLP 298


>gi|172039934|ref|YP_001799648.1| pseudouridylate synthase C [Corynebacterium urealyticum DSM 7109]
 gi|171851238|emb|CAQ04214.1| pseudouridylate synthase C [Corynebacterium urealyticum DSM 7109]
          Length = 313

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 88/323 (27%), Positives = 158/323 (48%), Gaps = 26/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q ++V + + + RLD++ ++    +    L +++R+ Q+ V+  + K + R  +G  V +
Sbjct: 7   QTLIVSDSQADRRLDKYIRSQVKGVPATVLFRMMRTKQITVNGAKCKPDQRTVAGDKVHL 66

Query: 68  PP--VINALNHIIKEQKILDS-SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           P   V  A      ++K  +  +  L++H       +++ED  + + NKPA I+V  GSG
Sbjct: 67  PALEVAEAKPKPAGDRKAAEQLARRLSRH-------IVFEDDDLLIVNKPANIAVHVGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--RRIQKI 182
           +   +   L+  +  + ++  L HRLD+ETSG+L+VA+     +HL    R     IQ+ 
Sbjct: 120 VKAGVIEALR-VLRPEDKELELAHRLDKETSGLLIVAKNSKMLRHLQSLLREGGEDIQRY 178

Query: 183 YWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           Y ++  G+ K   K+    +  L+K+  G   V     + +    A +   V   + +  
Sbjct: 179 YLAVAGGVLKKSGKQARRIDAPLRKT--GAATV----VDRRAGQQAETKLWVKKPWGRAG 232

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPH 299
             +E+Q  TGR HQ+RVH  H+G PI+GD +Y         +    + L LHA  + +P 
Sbjct: 233 TLVEVQLLTGRKHQIRVHLQHLGHPIIGDSRYGDKAANQAAAEKGVRMLMLHASRLVIPL 292

Query: 300 PEGGRLQITAPLPAHMVKTWDSL 322
           P G  L + AP+P      W+ L
Sbjct: 293 PSGEELDVQAPMPP----AWNKL 311


>gi|148243331|ref|YP_001228488.1| pseudouridylate synthases, 23S RNA-specific [Synechococcus sp.
           RCC307]
 gi|147851641|emb|CAK29135.1| Pseudouridylate synthases, 23S RNA-specific [Synechococcus sp.
           RCC307]
          Length = 316

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 89/303 (29%), Positives = 138/303 (45%), Gaps = 32/303 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +  P  +   +QK + +G VRV+    +    ++ G  +++  PP    L +
Sbjct: 22  MRLDRWLVSQRPEQSRARIQKFIEAGYVRVNGTTGRAKTPLRHGDEIKLWMPPP-EPLPY 80

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E   LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 81  LQPEPMDLD---------------VLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLH 125

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y ++V G+
Sbjct: 126 HCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQQALVKLQVQIQKRVASREYLAVVHGV 185

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P  +   I   + +       Y  V   N     YA +H+ + +     +  L  +  TG
Sbjct: 186 PAGESGTIVGAIGRHPVDRKKYAVVSSDN---GRYACTHWSLQERLGD-YSLLRFKLDTG 241

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  H   P+VGD  Y    K     P Q    LHA  + L HP  G R+   A
Sbjct: 242 RTHQIRVHCAHRNHPVVGDPTYSRCRKLPIELPGQA---LHAVQLGLDHPITGERMVFEA 298

Query: 310 PLP 312
           PLP
Sbjct: 299 PLP 301


>gi|288574921|ref|ZP_06393278.1| pseudouridine synthase, RluA family [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570662|gb|EFC92219.1| pseudouridine synthase, RluA family [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 340

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 90/312 (28%), Positives = 147/312 (47%), Gaps = 42/312 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVR 66
           + ++V  D + +RLD  F + +  ++   +Q+++R G V+V   KRVK +  + +G+ +R
Sbjct: 33  EEILVPPDMDGVRLD-AFLSDFLGVSRTFIQRVIRDGYVKVFQGKRVKPSRSVLAGESLR 91

Query: 67  --IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
             +PP         +   ++   V+ +         ++YED  I V +KPAG+ V    G
Sbjct: 92  FKLPPP--------QRMDLVPEPVDFS---------VVYEDEDIIVVDKPAGVVVHPAPG 134

Query: 125 --IAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 + G L  + D    +   +P + HRLD  TSG+L VAR   +   L  SFR R+
Sbjct: 135 HWRGTLVHGLLYRYPDIGTINDVVRPGIVHRLDSTTSGLLAVARNTESLNELQSSFRDRK 194

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD----YVHVVKQNEKGANYAISHFKVID 234
           + K Y +L  G        +   +   + IG D    Y   V  + K A   +       
Sbjct: 195 VGKFYLALSDG------RVVGEEISLDAPIGRDRNNRYRMTVTDDGKNARTDVYPLWNRG 248

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHAR 293
            ++   C L    H+GRTHQ+RVH  H+G P+VGD  Y    K     P ++ +++LHA 
Sbjct: 249 RYSFLICEL----HSGRTHQIRVHLRHLGAPLVGDELYGFRKKARKNDPLLEGRVFLHAW 304

Query: 294 YMDLPHPEGGRL 305
            + LPHP  G +
Sbjct: 305 KLVLPHPRTGEI 316


>gi|227878615|ref|ZP_03996537.1| pseudouridylate synthase [Lactobacillus crispatus JV-V01]
 gi|256843219|ref|ZP_05548707.1| pseudouridine synthase [Lactobacillus crispatus 125-2-CHN]
 gi|256850423|ref|ZP_05555851.1| pseudouridine synthase [Lactobacillus crispatus MV-1A-US]
 gi|293380626|ref|ZP_06626679.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
 gi|295692991|ref|YP_003601601.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|312977447|ref|ZP_07789195.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           crispatus CTV-05]
 gi|227861792|gb|EEJ69389.1| pseudouridylate synthase [Lactobacillus crispatus JV-V01]
 gi|256614639|gb|EEU19840.1| pseudouridine synthase [Lactobacillus crispatus 125-2-CHN]
 gi|256712820|gb|EEU27813.1| pseudouridine synthase [Lactobacillus crispatus MV-1A-US]
 gi|290922813|gb|EFD99762.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
 gi|295031097|emb|CBL50576.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|310895878|gb|EFQ44944.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           crispatus CTV-05]
          Length = 303

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 83/305 (27%), Positives = 150/305 (49%), Gaps = 44/305 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           +E   E  RLD++     P ++   ++++++   + V+ K  K + +IQ+G  + +  P 
Sbjct: 7   LEVKNEKGRLDKFVSEQIPDLSRTRVKELVKDQNILVNGKVEKVSYKIQAGDKIEVNIPA 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
           +  L+ +I E   LD               ++YED  + V NKP G+ V    G      
Sbjct: 67  VKPLD-VIPENIPLD---------------IVYEDDDVIVVNKPQGMVVHPAPGHPDHTL 110

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + YH     +S    +G +P + HR+D++TSG+L++A+T  A + L +    +  ++
Sbjct: 111 VNALLYHTKALAQS---PEGFRPGIVHRIDKDTSGLLMIAKTAKARESLEDQLAHKTNKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +YW++V G    +   I +  + ++      + VV+  +K    AI+HFKV++ F + + 
Sbjct: 168 LYWAIVHGNFAEENGVI-DAPIGRNPYDRKKMAVVETGKK----AITHFKVLEQF-KDYS 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPH 299
            +E Q  TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   H
Sbjct: 222 LIECQLETGRTHQIRVHLDYIGHPVAGDPLYGPRKTLKGHGQ-------FLHAKVLGFKH 274

Query: 300 PEGGR 304
           P  G 
Sbjct: 275 PSTGE 279


>gi|88657737|ref|YP_507302.1| ribosomal large subunit pseudouridine synthase A [Ehrlichia
           chaffeensis str. Arkansas]
 gi|88599194|gb|ABD44663.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Ehrlichia chaffeensis str. Arkansas]
          Length = 337

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 84/314 (26%), Positives = 150/314 (47%), Gaps = 41/314 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +++ +EN RLD++  +                   +++  R +    I+  +++    
Sbjct: 20  IFIKSGDENNRLDKFIAS-------------------KLNISRNQVQQLIKDSKILLFDT 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSD------FLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +I   NHI K   I + S+ +   SD      ++   ++YED  I + NK  GI+V  G+
Sbjct: 61  IIRDNNHITKVNDIYNISIPIKTISDTITPNHYIPISVVYEDHDIIIINKAPGITVHPGA 120

Query: 124 GIAYH--IDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G   +  ++  +  + +S     K  +P + HRLD++TSG++V+A+   +   L++    
Sbjct: 121 GTNNNTLVNALVAHYGNSLSHVGKATRPGIIHRLDKDTSGLMVIAKNEKSYYFLSDLLLK 180

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           ++I+K Y ++VWG+P  K   I N++  K +     + V     KG   AI+ ++    F
Sbjct: 181 KQIKKEYLAVVWGLPNPKSNTIKNYICVKPN-NKQMMTVTHLPHKGK-LAITEYQTQKSF 238

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQNKL---Y 289
           +     ++ + HTGRTHQ+RVH  ++G  I+GD KY  N     K    S I N L    
Sbjct: 239 SNIASLIKCRIHTGRTHQIRVHMSYIGNSIIGDQKYGKNNSKSVKYAKQSTIINTLKRQA 298

Query: 290 LHARYMDLPHPEGG 303
           LHA  +   HP   
Sbjct: 299 LHAYKLGFTHPTSN 312


>gi|294674881|ref|YP_003575497.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Prevotella ruminicola 23]
 gi|294472042|gb|ADE81431.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Prevotella ruminicola 23]
          Length = 347

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 93/341 (27%), Positives = 160/341 (46%), Gaps = 60/341 (17%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  +  +R+D++   H PH +   +Q+   +G + V++K VK N +++ G ++ +    
Sbjct: 25  VDKGQVPIRIDKYLVEHQPHSSRNRIQQAADAGFIHVNEKPVKSNYKVRPGDIITL---- 80

Query: 72  NALNHIIKEQKILDSS-VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                      +LD    + T   + +   ++YED+ + V NKPAG+ V  G G      
Sbjct: 81  -----------MLDRPHYDTTIEPEDIPLEVVYEDADLMVINKPAGMVVHPGCGNFNGTL 129

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              IA+H+   L S+ D    +  L HR+D++TSG+LVVA+T  A   L + F  +   +
Sbjct: 130 VNAIAWHLKD-LASY-DPNDPEVGLVHRIDKDTSGLLVVAKTPDAKTSLGKQFFNKTTHR 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDY---------VHVVKQNEKGANYAISHFKV 232
            Y +LVWG          N++  +  I G+          + V   + +    A++H+KV
Sbjct: 188 SYNALVWG----------NFVEDEGRIEGNIGRDPKDRLRMEVFPPDSEIGKPAVTHYKV 237

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQN 286
           ++ +      +E    TGRTHQ+R H  H+G P+  D +Y      +G  T+     IQN
Sbjct: 238 MERYGY-VTLVECILETGRTHQIRAHMKHIGHPLFADERYGGTELLRGERTASYKAYIQN 296

Query: 287 ------KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
                 +  LHA+ +   HP  G+ +  T+  PA M    D
Sbjct: 297 CFKLCPRQVLHAKTLGFVHPTTGKQMDFTSEWPADMAALID 337


>gi|227892505|ref|ZP_04010310.1| pseudouridylate synthase [Lactobacillus ultunensis DSM 16047]
 gi|227865626|gb|EEJ73047.1| pseudouridylate synthase [Lactobacillus ultunensis DSM 16047]
          Length = 305

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 82/306 (26%), Positives = 154/306 (50%), Gaps = 44/306 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           ++E  +E+ RLD++     P ++   ++++++   + V+ K  K + ++Q+G  V +  P
Sbjct: 6   LLEVKDEHGRLDKFVSEQVPDLSRTRVKELIQDKNILVNNKSEKVSYKVQAGDCVLVNVP 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
            +  L+ ++ E   LD               ++YED  + V NKP G+ V    G     
Sbjct: 66  AVKPLD-VVPENIPLD---------------IVYEDDDVIVVNKPQGMVVHPAPGHPDHT 109

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH     +S    +G +P + HR+D++TSG+L++A+   A + L +    +  +
Sbjct: 110 LVNALLYHTKDLAQS---PEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNK 166

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           +IYW++V G    +   I + L+ ++      + VV+  +K    A++HFKV++ F + F
Sbjct: 167 RIYWAIVHGNFGEEGGTI-DALIGRNPYDRKKMAVVENGKK----AVTHFKVLEQF-KGF 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLP 298
             +E Q  TGRTHQ+RVH  ++G  + GD  Y      KG+         +LHA+ +   
Sbjct: 221 SLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPRKTLKGHGQ-------FLHAKVLGFR 273

Query: 299 HPEGGR 304
           HP+ G+
Sbjct: 274 HPQSGK 279


>gi|225419732|ref|ZP_03762035.1| hypothetical protein CLOSTASPAR_06070 [Clostridium asparagiforme
           DSM 15981]
 gi|225041622|gb|EEG51868.1| hypothetical protein CLOSTASPAR_06070 [Clostridium asparagiforme
           DSM 15981]
          Length = 303

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 91/331 (27%), Positives = 158/331 (47%), Gaps = 55/331 (16%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IPP 69
           V +++  +R+D++  +    ++   LQK+L+SGQV V  + VK +  +Q G ++   +P 
Sbjct: 6   VTDEDGGVRIDKYLTSVCEGLSRSYLQKLLKSGQVLVGGQGVKASYAVQEGDLIELEVPE 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +        E +IL   ++L          +LYED  I + NKP G+ V   +G   H 
Sbjct: 66  AV--------EPEILAEPMDLD---------VLYEDEDIILINKPKGMVVHPAAGHYTHT 108

Query: 129 -IDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            ++G L      +GQ        +P + HR+D +T+G+++  +   A   L E  +   I
Sbjct: 109 LVNGLLDHC---RGQLSGINGVMRPGIVHRIDMDTTGVIIACKNDLAHSCLAEQLKEHSI 165

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-----AISHFKVID 234
            + Y ++V G+ K  +  +   + +         H V++ +   NY     A++H+KV+ 
Sbjct: 166 TRRYQAIVHGVVKEDEGTVDAPIGR---------HPVERKKMSINYNNGREAVTHYKVLR 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHA 292
            F Q +  +E +  TGRTHQ+RVH   +  P++GD  Y     G    PI       LHA
Sbjct: 217 RFRQ-YTHVECRLETGRTHQIRVHMASIHHPLLGDAVY-----GPARCPIPGLQGQTLHA 270

Query: 293 RYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
             + + HP  G  ++ TAPLP +  K   +L
Sbjct: 271 GVLGIRHPRTGAYMEFTAPLPDYFAKLLRTL 301


>gi|160914264|ref|ZP_02076485.1| hypothetical protein EUBDOL_00274 [Eubacterium dolichum DSM 3991]
 gi|158433891|gb|EDP12180.1| hypothetical protein EUBDOL_00274 [Eubacterium dolichum DSM 3991]
          Length = 303

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 85/323 (26%), Positives = 155/323 (47%), Gaps = 42/323 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  D ++ R+D++       ++   +  ++  G + V+            G+V+R    +
Sbjct: 8   VAEDADSQRIDKYLSMVVEDLSRSRIASLIEEGSILVN------------GEVIRAKYKV 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
              +HI       +  + L    + ++  + YED  + V NKP GI V   +G      +
Sbjct: 56  KPADHITAA---FEDEMALEAAPEKMELDIRYEDHDVIVINKPKGIVVHPANGNQSGTLV 112

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +G L    D  G     +P + HR+D++T+G+L+VA+   A   L++  + + + ++Y++
Sbjct: 113 NGLLYHCKDLSGINGVLRPGIVHRIDKDTTGLLIVAKNDKAHASLSKQLQNKSVNRLYYA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           LV G+ +++   I       + IG D      + V+  N K A    +HF+V++ FA K+
Sbjct: 173 LVHGVIEHEFGTI------DAPIGRDPKDRQKMAVIATNSKPAR---THFRVVERFA-KY 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E +  TGRTHQ+RVH  ++G P+VGD KY  +++    +   N   LHA  +   HP
Sbjct: 223 TLVECRLETGRTHQIRVHMQYIGHPVVGDEKY--SYRKTMKT---NGQLLHAHQLTFLHP 277

Query: 301 EGG-RLQITAPLPAHMVKTWDSL 322
               R+ + APLP       + L
Sbjct: 278 TTNERITVEAPLPKQFADILEEL 300


>gi|116253506|ref|YP_769344.1| ribosomal large subunit pseudouridine synthase D [Rhizobium
           leguminosarum bv. viciae 3841]
 gi|115258154|emb|CAK09255.1| putative ribosomal large subunit pseudouridine synthase D
           [Rhizobium leguminosarum bv. viciae 3841]
          Length = 341

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 95/346 (27%), Positives = 159/346 (45%), Gaps = 53/346 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV-RIP 68
           V+  ++    RLD W                  + QV  +  R +    I+ GQV+ R  
Sbjct: 14  VLTADETAEGRLDAWL-----------------TAQVGEEFSRSRIKALIKDGQVLLRGE 56

Query: 69  PVINALNHIIKEQKI---LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           PV +    +         L    + T   + +   +L+ED  + V +KP+G+ V  G+G 
Sbjct: 57  PVTDPQRKVRTGDSFELTLPEPEDPTPQGEDIPLDILHEDDDVIVISKPSGLVVHPGAGN 116

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF---- 174
                ++  +    D+       ++P + HRLD++T+G++VVA+   A +HL+  F    
Sbjct: 117 WTGTLVNALIHHCSDTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHG 176

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKV 232
           R   +++ Y ++VWG P+     +   L + +   GD     V + + + A+ AI+H++V
Sbjct: 177 RTMPLERAYQAIVWGRPRTLSGTVDAPLGRAT---GDRTRRAVKRPDSQDADEAITHYQV 233

Query: 233 IDCFAQK-----FCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPI 284
           I+ F +K     F  L E +  TGRTHQ+RVH  H+G P++GD  Y A F  K N     
Sbjct: 234 IERFHEKPDATAFASLVECRLETGRTHQIRVHMAHIGHPLLGDTVYGAGFKTKANLLPEE 293

Query: 285 QNKLY-------LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             K+        LHA  +   HP  G  +    PLP  MV+  ++L
Sbjct: 294 IRKVVNGFGRQALHAFMLQFEHPRTGEIMHFEVPLPDDMVELVEAL 339


>gi|23012044|ref|ZP_00052228.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 238

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 81/233 (34%), Positives = 120/233 (51%), Gaps = 21/233 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           LLY D+ + V +KPAG+ V    +GG  +  H+D           ++P   HRLD++TSG
Sbjct: 20  LLYRDALMLVIDKPAGLPVHPGPKGGPTLTDHLDSLRFGLP----RRPEAAHRLDRDTSG 75

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R   A   L   F   ++ K YW+LV G P   +  I   L ++S     +   +
Sbjct: 76  CLVLGRHAKALARLNRLFADSKVDKSYWALVEGGPSETEGRIDLPLARRSDDPRSWW--M 133

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-AN 275
           K +  GA  +++ ++V+    +   WLE++P TGRTHQLRVH   MG PI GD  Y  A+
Sbjct: 134 KTDPAGAP-SLTLYRVLG-RTEGLSWLELKPVTGRTHQLRVHCAAMGWPIRGDAIYGQAD 191

Query: 276 FKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            +G         L LHAR + LP +P+   + + AP PAHM     + G + D
Sbjct: 192 RQG-------PGLQLHARSLSLPLYPKRDAIAVEAPAPAHMQAGLVACGMRAD 237


>gi|282881100|ref|ZP_06289787.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
 gi|281304904|gb|EFA96977.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
          Length = 355

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 93/328 (28%), Positives = 161/328 (49%), Gaps = 40/328 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+ ++E +R+D++      H +   +QK   +G V V+ + VK N +++   V+ +  
Sbjct: 25  VVVDKNQEPLRIDKYMFERLKHSSRNRIQKAADAGFVHVNDQPVKSNYKVRPLDVITL-- 82

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
           +++A  H        DS++     ++ +   ++YED+++ V NKPAG+ V  G+G     
Sbjct: 83  MLDAPQH--------DSTIE----AEEIPLNIVYEDTEVMVVNKPAGMVVHPGAGNFHGT 130

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H+        D+      L HR+D++TSG+LV+A+T  A   L   F  +   
Sbjct: 131 LINAVAWHLKDL--PTFDANDPAVGLVHRIDKDTSGLLVIAKTPDAKTKLGLQFFNKTTH 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG   N++E      + +       + V   +      AI+H++V++ F    
Sbjct: 189 RSYHALVWG-NFNEEEGRIEGNIARDPKDRLRMCVFPPDSAVGKTAITHYRVLERFGY-V 246

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQNKL------ 288
             +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S     IQN L      
Sbjct: 247 TLIECILETGRTHQIRAHMKHIGHPLFGDERYGGMEILRGQRSSTYKAFIQNCLSLCHRQ 306

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHM 315
            LHA+ +   HP+  R +  T+ LP  M
Sbjct: 307 ALHAKTLGFVHPKTNREMNFTSDLPEDM 334


>gi|222149596|ref|YP_002550553.1| ribosomal large subunit pseudouridine synthase RluD subfamily
           [Agrobacterium vitis S4]
 gi|221736578|gb|ACM37541.1| ribosomal large subunit pseudouridine synthase RluD subfamily
           [Agrobacterium vitis S4]
          Length = 342

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 78/244 (31%), Positives = 123/244 (50%), Gaps = 33/244 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQE 153
           +LYED  + V +KPAG+ V  G+G      ++  +    DS       ++P + HRLD+E
Sbjct: 92  VLYEDKDLIVLSKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGGVKRPGIVHRLDKE 151

Query: 154 TSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           TSG++VVA+   A +HL + F    R   +++ Y +LVWG P+  +  I   L +     
Sbjct: 152 TSGVMVVAKNDIAHRHLADQFADHGRSGPLERAYQALVWGRPRGLRGTIDAALGR----A 207

Query: 210 GDYVH--VVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALH 261
           GD     V +++   A  AI+H++V++ + +K         +E +  TGRTHQ+RVH  H
Sbjct: 208 GDRTKRTVKREDTDDAREAITHYQVMERYGEKPDATCLASLVECRLETGRTHQIRVHMAH 267

Query: 262 MGCPIVGDHKYCANF--KGNFTSPIQNKLY-------LHARYMDLPHPEGGR-LQITAPL 311
           +G P++GD +Y A F  K N        +        LHA  +   HP  G  +   AP+
Sbjct: 268 IGHPLIGDPEYGAAFKTKANLLPDAAKAIVTNFHRQALHAYLLAFEHPTTGDVMHFAAPI 327

Query: 312 PAHM 315
           P  M
Sbjct: 328 PDDM 331


>gi|149173826|ref|ZP_01852455.1| ribosomal large subunit pseudouridine synthase [Planctomyces maris
           DSM 8797]
 gi|148847356|gb|EDL61690.1| ribosomal large subunit pseudouridine synthase [Planctomyces maris
           DSM 8797]
          Length = 342

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 96/345 (27%), Positives = 155/345 (44%), Gaps = 60/345 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD------KKRVKFNNRIQSGQ 63
           + VE      R+D +    YP+   V  Q  ++   V V+       +R++ N+R+    
Sbjct: 19  ITVEARAHGWRIDHYLCRLYPNYTRVLFQTAIKQEAVLVNGLPVKAARRMRVNDRVS--- 75

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+P + +  N +  E   +D               ++YED  I + NKP+ + V  G 
Sbjct: 76  -VRLPELPD--NRLPPEDIPID---------------IVYEDDWIAIINKPSDMIVHPGK 117

Query: 124 G---------IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           G         + YH D       D  GQ +P + HRLD+ TSGI+VVA+       L+  
Sbjct: 118 GNYAGTLAGALQYHFDQL----SDVAGQYRPGIVHRLDRNTSGIMVVAKDNQVHAKLSAQ 173

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  R +QK Y ++VWG  +   + I  ++    H       +V      A  A ++++VI
Sbjct: 174 FEKRDVQKEYRAIVWGRMEFDTDYIDTFMC--VHPRAREKMIVCDEGGNARNAFTYYEVI 231

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---------------ANFKG 278
           + + Q F ++ ++P TGRTHQLRVH  H+G  IV D  Y                A+   
Sbjct: 232 ERY-QAFTYVRLKPRTGRTHQLRVHMQHIGHSIVADRVYGGHKSLKMKSLGIQAEADAAE 290

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +  +  +  LHA  ++  HP+ G+ ++  APLP  M  T  +L
Sbjct: 291 LESDVLIERQALHAYCLEFFHPQSGKPMKFEAPLPEDMQNTLAAL 335


>gi|209550662|ref|YP_002282579.1| pseudouridine synthase [Rhizobium leguminosarum bv. trifolii
           WSM2304]
 gi|209536418|gb|ACI56353.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 341

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 93/346 (26%), Positives = 156/346 (45%), Gaps = 53/346 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV-VRIP 68
           V+  ++    RLD W                  + QV  +  R +    I+ GQV +R  
Sbjct: 14  VLTADETAEGRLDAWL-----------------TAQVGEEFSRSRIKALIKDGQVSLRGE 56

Query: 69  PVINALNHIIKEQKI---LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           PV +    +         L    + T   + +   +L+ED  + V +KP+G+ V  GSG 
Sbjct: 57  PVTDPQRKVRNGDSFEITLPEPEDPTPQGEDIPLDILHEDEDLIVISKPSGLVVHPGSGN 116

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF---- 174
                ++  +    D+       ++P + HRLD++T+G++VVA+   A +HL+  F    
Sbjct: 117 WTGTLVNALIHHCGDTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHG 176

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKV 232
           R   +++ Y ++VWG P++    +   L + +   GD     V + +   A+ AI+H++V
Sbjct: 177 RTMPLERAYQAVVWGRPRSLTGTVDAPLGRAT---GDRTRRAVKRPDSHDADEAITHYEV 233

Query: 233 IDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ- 285
           I+ F +          +E    TGRTHQ+RVH  H+G P++GD  Y A FK       + 
Sbjct: 234 IERFQENPDATALASLVECHLETGRTHQIRVHMAHIGHPLLGDTVYGAGFKTKANRLPEE 293

Query: 286 --------NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
                   N+  LHA  +   HP  G L     PLP  MV+  ++L
Sbjct: 294 VRKVVNGFNRQALHAFMLQFEHPRTGELMHFEVPLPDDMVELVEAL 339


>gi|39938617|ref|NP_950383.1| pseudouridylate synthase [Onion yellows phytoplasma OY-M]
 gi|39721726|dbj|BAD04216.1| pseudouridylate synthases [Onion yellows phytoplasma OY-M]
          Length = 303

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 97/324 (29%), Positives = 158/324 (48%), Gaps = 42/324 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++   E   RLD +   H  ++N    QK++ + QV V+ K  K +  +++  ++ +   
Sbjct: 8   LISASEAFQRLDHFLLTHI-NLNKSQCQKLILAQQVLVNSKPAKKSYLLKAQDLITV--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA------GISVQGGS- 123
                 II + +    SVNL    + L   ++YED  + V NKPA       +S Q  + 
Sbjct: 64  ------IIPQTQ---ESVNLQTPQN-LNLDIIYEDPYLAVINKPANLVAHPSLSFQETTL 113

Query: 124 --GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             G+ Y       S VD+  Q+P + HRLD+ T+G+L++A+    +  L  +F+ R+I K
Sbjct: 114 VNGLLYQFATL--SHVDT--QRPGIVHRLDKNTTGLLIIAKNNDVSDKLQIAFQQRKITK 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK-QNEKGANYAISHFKVIDCFAQKF 240
           IYW+L+ G  ++K          K  IG +  + +K Q       A++HFK +  F+  F
Sbjct: 170 IYWALIEGFLEDKGTI-------KLPIGRNPHNRLKMQVIPDGKTAVTHFKTLQRFSH-F 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E    TGRTHQLR H   +  PI+GD  Y +    +  +P+    +LHA+ +   HP
Sbjct: 222 SLMEFNLETGRTHQLRAHFSFLKRPIIGDLLYGS---SHHITPLGQ--FLHAKMLKFNHP 276

Query: 301 -EGGRLQITAPLPAHMVKTWDSLG 323
                L + APLPA+  K   SL 
Sbjct: 277 ITNQNLILEAPLPANFEKLLQSLN 300


>gi|88809823|ref|ZP_01125329.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 7805]
 gi|88786207|gb|EAR17368.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 7805]
          Length = 327

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 93/313 (29%), Positives = 144/313 (46%), Gaps = 32/313 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +     +   +QK + +G VRV+ +  K    ++ G  V++  PP    L +
Sbjct: 34  MRLDRWLVSQRREQSRARIQKFIDAGLVRVNGRTGKAKTPLRQGDEVQLWMPPP-EPLPY 92

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E   LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 93  LKPEAMDLD---------------VLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLH 137

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y ++V G+
Sbjct: 138 HCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQVQIQKRIASREYLAVVHGV 197

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +  H      + V   E G  +A +H+ + +     +  L  +  TG
Sbjct: 198 PSGDSGTIVGAIGR--HPVDRKKYAVVSTESG-RFACTHWSLQERLGD-YSLLRFKLDTG 253

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  HM  P+VGD  Y    K     P Q    LHA  + L HP    R+   A
Sbjct: 254 RTHQIRVHCAHMNHPVVGDPTYSRCRKLPIELPGQ---ALHAFQLGLDHPISRERMLFEA 310

Query: 310 PLPAHMVKTWDSL 322
           PLP  MV+  + L
Sbjct: 311 PLPGVMVRLLNKL 323


>gi|170759197|ref|YP_001786899.1| RluA family pseudouridine synthase [Clostridium botulinum A3 str.
           Loch Maree]
 gi|169406186|gb|ACA54597.1| pseudouridine synthase, RluA family [Clostridium botulinum A3 str.
           Loch Maree]
          Length = 305

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 97/324 (29%), Positives = 152/324 (46%), Gaps = 44/324 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE + +N+RLD      +   +   LQ I+  G V V+ K  K N +++ G  + I    
Sbjct: 8   VEKEFDNVRLDLCLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIEIN--- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                 I E K+L          + +K  ++YED  + V NKP  + V    G+     +
Sbjct: 65  ------IPEPKLLQIE------PEDVKLDVIYEDKDVIVVNKPQEMVVHPAPGVYSGTLV 112

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+   I ++Y +
Sbjct: 113 NALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           LV GI KN++  I      ++ IG   V  +K    K   +A++H+KVI  F +    +E
Sbjct: 173 LVEGIIKNEQGTI------EAPIGRHPVDRIKMAVVKDGRHAVTHYKVIKRF-KNHTLVE 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLHARYMDLPH 299
            +  TGRTHQ+RVH  H+  P+VGD  Y       N KG           LHA+ +   H
Sbjct: 226 CRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLKGQM---------LHAKLLGFIH 276

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G+ ++  + LP +  K    L
Sbjct: 277 PTTGQYVEFESELPEYFKKIIKIL 300


>gi|119946871|ref|YP_944551.1| pseudouridine synthase, RluA family protein [Psychromonas
           ingrahamii 37]
 gi|119865475|gb|ABM04952.1| ribosomal large subunit pseudouridine synthase D [Psychromonas
           ingrahamii 37]
          Length = 322

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 96/329 (29%), Positives = 161/329 (48%), Gaps = 44/329 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V + +   RLD+   + +P  +   +++ + +  V++D + + +   ++ +GQ V +  V
Sbjct: 11  VTDQQLGFRLDQAVASLFPDYSRTRIKEWILADMVKIDGEVINRPREKVYTGQTVGVQAV 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +     + K QKI              K  ++YED  I V NKPAG+ V  G+G   + D
Sbjct: 71  LED-EVVFKAQKI--------------KLEIVYEDDDILVINKPAGLVVHPGAG---NPD 112

Query: 131 G-FLKSWVDSKGQ---KPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G  L + +    Q    PR  + HRLD++T+G++VVA+T  A  HL  S + R I + Y 
Sbjct: 113 GTVLNALLHHFPQIIEVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVTSLQAREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCW 242
           ++  G               ++ IG D VH VK   N  G  +A++H++V + + +    
Sbjct: 173 AIAMG-------GFTAGGFVEAPIGRDKVHRVKMAVNSTGGKHALTHYRVSEKY-RAHTR 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQN-----KLYLHARY 294
           L ++  TGRTHQ+RVH +H+G  + GD  Y       KG   + +       +  LHA  
Sbjct: 225 LRLRLETGRTHQIRVHMMHIGHVLTGDPVYGGRPRPPKGASEALLATLRGFRRQALHATM 284

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + L HP  G  ++  APLPA M +  ++L
Sbjct: 285 LRLAHPITGEIMEWHAPLPADMAELAEAL 313


>gi|323702053|ref|ZP_08113721.1| pseudouridine synthase, RluA family [Desulfotomaculum nigrificans
           DSM 574]
 gi|323532935|gb|EGB22806.1| pseudouridine synthase, RluA family [Desulfotomaculum nigrificans
           DSM 574]
          Length = 307

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 93/313 (29%), Positives = 154/313 (49%), Gaps = 41/313 (13%)

Query: 13  ENDEENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIP 68
           E D+EN   RLD +       ++   +Q+++  GQV V+    K N +++ G    V +P
Sbjct: 7   EVDQENAKSRLDVFLSGQCHDLSRSYIQRLIEEGQVTVNDLPTKANYKLRVGDRVAVEVP 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
           P         +E +++   + L          + YED+ + V NKP G+ V    G    
Sbjct: 67  PA--------EELQVVPEPIPLD---------IYYEDNDVIVVNKPRGMVVHPAEGNTSG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D  G     +P + HRLD++TSG+++VA+   A   L +  + R + + 
Sbjct: 110 TLVNALLYHCRDLSGINGVLRPGIVHRLDKDTSGLIMVAKNDLAHNSLAQQLKDRTVTRR 169

Query: 183 YWSLVWGIPKNKKECIA--NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           Y +LV     N +E +   N  + +       + VV++N K    A++H++V++ F Q +
Sbjct: 170 YRALVH---NNIREEVGTVNAPIGRDPRDRQRMAVVERNSKP---AVTHYRVLERFGQ-Y 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E +  TGRTHQ+RVH  ++G P+VGD KY    K +F    Q    LHA  +   HP
Sbjct: 223 TLVECRLETGRTHQIRVHMAYIGHPVVGDPKYGPT-KPHFDLDGQ---LLHAGVLGFKHP 278

Query: 301 EGGR-LQITAPLP 312
             G+ L+ TAPLP
Sbjct: 279 TTGQYLEFTAPLP 291


>gi|167758164|ref|ZP_02430291.1| hypothetical protein CLOSCI_00502 [Clostridium scindens ATCC 35704]
 gi|167664061|gb|EDS08191.1| hypothetical protein CLOSCI_00502 [Clostridium scindens ATCC 35704]
          Length = 304

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 95/329 (28%), Positives = 154/329 (46%), Gaps = 44/329 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++  VEN ++  R+DR+        +   +QK+++   V V++K VK N R+  G  V I
Sbjct: 3   EFFTVEN-QDGERIDRYLSEELADRSRSYIQKLIKENYVTVNQKPVKANYRLSLGDRVEI 61

Query: 68  --PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
             P          KE  I    + L          +LYED  I + NKP  + V    G 
Sbjct: 62  DLPEA--------KEPDIRPEDIPLD---------ILYEDKDIIIVNKPKQMVVHPAPGH 104

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                   + YH    L     +   +P + HR+D +T+G LV  +   A Q L+   + 
Sbjct: 105 YSQTLVNALMYHCGSDLSGI--NGTMRPGIVHRIDMDTTGSLVACKNDMAHQSLSRQLKE 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVID 234
             I++IY ++V G   N KE    +    + IG       K +   +    A++H++V++
Sbjct: 163 HSIRRIYVAIVHG---NIKE---EYGTVNAPIGRHPTERKKMSIHSRNGREAVTHYQVLE 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F   + ++  +  TGRTHQ+RVH   +G P++GD  Y    K  F  P+Q +  LHAR 
Sbjct: 217 RFGD-YTYIRCELETGRTHQIRVHMASLGHPLLGDGVYGPK-KCPF-PPLQGQT-LHART 272

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + + HP  G  L++ APLPA+ ++  D L
Sbjct: 273 LGIIHPRTGEYLEVNAPLPAYFIELLDKL 301


>gi|318040686|ref|ZP_07972642.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp.
           CB0101]
          Length = 404

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 89/303 (29%), Positives = 142/303 (46%), Gaps = 32/303 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW     P  +   +QK + SG VRV+    +    ++    V +  PP    L +
Sbjct: 22  MRLDRWLVAQRPEQSRARIQKFIESGYVRVNGVTGRAKTPLRQSDTVELWMPPP-EPLPY 80

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           ++ ++  LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 81  LMPQEIPLD---------------VLFEDEHLIVLNKPAGLTVHPAPGNKDGTLVNGLLH 125

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +VVA+++ A   L    + R   + Y ++V G+
Sbjct: 126 HCPDLPGISGKLRPGIVHRLDKDTTGCIVVAKSQEALVKLQVQIQKRIASREYLAVVHGV 185

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P  +   I   + +  H      + V  ++ G  +A +H+ +++     +  +  +  TG
Sbjct: 186 PAAEHGTIVGAIGR--HPADRKKYAVVHDDSG-RHACTHWTLVERLGD-YSLMRFKLDTG 241

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  H+G PIVGD  Y    K     P Q    LHA  + L HP    R+   A
Sbjct: 242 RTHQIRVHCAHIGHPIVGDPVYSRCRKLPMALPGQA---LHAFQLGLDHPISRERMLFEA 298

Query: 310 PLP 312
           PLP
Sbjct: 299 PLP 301


>gi|220915194|ref|YP_002490498.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219953048|gb|ACL63432.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 339

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 96/331 (29%), Positives = 162/331 (48%), Gaps = 32/331 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD+  +     +   ++ K+ R+ +VRV+ +R K +  +  G VV    
Sbjct: 4   LTVTADAAGQRLDKLVRKALRDVPLSHVYKMFRTRKVRVNGQRGKADQLVAEGDVV---- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGI--A 126
           VI        E+++L  +           +  +L+ED+ +   +KPAG++   G+GI  A
Sbjct: 60  VIRG-----DEERLLAKAAPAAPGGAPRVTFGVLHEDADLLAVDKPAGLAAHPGTGIEGA 114

Query: 127 YHID---GFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-RRIQ 180
             ++   G+LK+  D      KP   HRLD++TSG+++VA+ R A   LTE+F     + 
Sbjct: 115 TLVEMARGYLKTPDDLPPTEFKPSPAHRLDRDTSGVVLVAKHRKAMVRLTETFTSGEGVH 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQ 238
           K Y +LV G  K  +E     L    H        +    +G N+  A++ +KV+   A+
Sbjct: 175 KTYLALVKG--KMPREAGTIDLPLSEHEQTSKSKAM----RGVNFQEALTRWKVVSA-AK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYM 295
           +   L +   TGRTHQ+R H   +G P+ GD +Y  +F  N T+  +    ++ LHA  +
Sbjct: 228 EISLLAVTIETGRTHQIRRHLEAVGHPVAGDRRY-GDFAFNRTARTRWGLRRMGLHAWKL 286

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           ++PHP  G  L++ AP PA + +       K
Sbjct: 287 EVPHPLTGAPLRLEAPFPAELAEVLSRANLK 317


>gi|126649705|ref|ZP_01721941.1| YlyB [Bacillus sp. B14905]
 gi|126593424|gb|EAZ87369.1| YlyB [Bacillus sp. B14905]
          Length = 303

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 90/319 (28%), Positives = 149/319 (46%), Gaps = 38/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT V Y + E  ++  R+D+   +     +   +   +  G ++V+   VK   ++++G 
Sbjct: 1   MTQVTYTI-EEQQQGERIDKALSSLQSEWSRTQIGNWVSDGNIKVNGDAVKPKYKVKAGD 59

Query: 64  VVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           V+ I  P    L+ +I E   LD               ++YED+ + V NKP G+ V   
Sbjct: 60  VIAIDVPEAEPLD-VIAENLALD---------------IVYEDADVLVVNKPKGMVVHPA 103

Query: 123 SG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L +    
Sbjct: 104 PGHLTGTLVNGLMYQCKDLSGINGIMRPGIVHRIDKDTSGLLMVAKNDVAHESLVDQLVN 163

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDC 235
           + + + Y +LV G   + K  I       + IG D     KQ       +A++HF V++ 
Sbjct: 164 KTVTRKYIALVHGHIAHDKGTI------DAPIGRDQKDRQKQAIVDNGKHAVTHFHVVER 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F   +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +F   +     LHA  +
Sbjct: 218 FGD-YTLVECRLETGRTHQIRVHMNYIGFPLVGDPKYGPKKTIDFGGQV-----LHAATL 271

Query: 296 DLPHPEGGR-LQITAPLPA 313
              HP  G  L+   PLPA
Sbjct: 272 GFNHPSSGEYLEFETPLPA 290


>gi|148653370|ref|YP_001280463.1| RluA family pseudouridine synthase [Psychrobacter sp. PRwf-1]
 gi|148572454|gb|ABQ94513.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter sp.
           PRwf-1]
          Length = 420

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 92/326 (28%), Positives = 150/326 (46%), Gaps = 34/326 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V  ++   R+D+   + +   +   LQ  L+SG + V+    K   R++ G +VR+   
Sbjct: 108 TVTQEQAGQRIDKLAADMFTEHSRAQLQDWLKSGNLTVNDHNEKAKYRVKIGDIVRLEAK 167

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           +        EQ   D   ++       K  ++YED  + V NKP G+ V  G+G      
Sbjct: 168 L--------EQHGSDQPEDI-------KLDIIYEDDSVIVINKPVGMVVHPGAGNWSGTL 212

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           ++G L  + + +   PR  L HR+D+ TSG+LV+ +T+AA   L E  + + + + Y  +
Sbjct: 213 VNGLLYHYPN-QAHLPRAGLVHRIDKNTSGLLVIGKTKAAQLELQEQLKDKSVYRHYQCV 271

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEM 245
           V G        +A      + IG       K         AI+H   I   +  +  L++
Sbjct: 272 VAG----DAPSLARQRTIDAPIGRHRTQRTKMTVTSTGKTAITHIMKITPLSDTYSLLDV 327

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQN--KLYLHARYMDL 297
           +  TGRTHQ+RVH  H+G PI+GD  Y       A         IQ+  +  LHA  +  
Sbjct: 328 RLETGRTHQIRVHLSHIGHPIIGDDIYGNRQQLRAGLTPEQRQAIQSFPRQALHAYKLGF 387

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HPE G  +++TAPLP  +V+   +L
Sbjct: 388 IHPETGESIELTAPLPQDIVELAHTL 413


>gi|39933445|ref|NP_945721.1| pseudouridine synthase RluD [Rhodopseudomonas palustris CGA009]
 gi|39647291|emb|CAE25812.1| possible pseudouridine synthases [Rhodopseudomonas palustris
           CGA009]
          Length = 407

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 94/342 (27%), Positives = 152/342 (44%), Gaps = 51/342 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIP 68
           VVV  DE + RLDR      P ++   L+ ++  G+V +    V+        G+ + I 
Sbjct: 84  VVVAGDEGSQRLDRVLAARCPELSRSRLKALILDGRVAIAGTPVRDPAYHASPGETITID 143

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                      E   LD               ++YED+ I V NKP G+ V   +G  + 
Sbjct: 144 VPPPVPAEPAGEAIALD---------------IVYEDADIIVLNKPRGLVVHPAAG--HE 186

Query: 129 IDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----R 175
               + + +   G         ++P + HRLD++T+G++V A+   A Q L+  F    R
Sbjct: 187 TGTLVNALIAHCGASLSGIGGVRRPGIVHRLDKDTTGLMVAAKNDKAHQSLSAQFADHGR 246

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              +++ Y + VWG+P  K   I   + +  H        V+Q+ +    AI+H++V++ 
Sbjct: 247 TGELRRGYLAFVWGVPGRKYGTIDAPIDRHPH--AREKMAVRQSGR---EAITHWEVLEN 301

Query: 236 FAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQ--- 285
           F+ K        +  Q  TGRTHQ+RVH  H+G P++GD  Y  +F  K N  +P     
Sbjct: 302 FSGKDGKPVAALIACQLETGRTHQIRVHLAHLGHPLLGDDVYGPHFKTKANQLAPAGRAA 361

Query: 286 ----NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                +  LHA  + L HP  G  L   +PLPA +     +L
Sbjct: 362 LAGLGRQALHAYLLTLEHPSTGEVLTWESPLPADLAHLQAAL 403


>gi|295132692|ref|YP_003583368.1| ribosomal large subunit pseudouridine synthase D [Zunongwangia
           profunda SM-A87]
 gi|294980707|gb|ADF51172.1| ribosomal large subunit pseudouridine synthase D [Zunongwangia
           profunda SM-A87]
          Length = 352

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 92/332 (27%), Positives = 156/332 (46%), Gaps = 49/332 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           + E  +  +R+D++  N+        +QK  + G + V+   VK N ++++G VV++   
Sbjct: 26  IAEKGQNPLRVDKYLMNYIEKATRNKIQKAAKDGNIYVNDVPVKQNYKVKAGDVVQV--- 82

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                H   E  +   ++ L          ++YED  + V NKPAG+ V  G G      
Sbjct: 83  --MFEHPPYEFLLTPENIPLD---------IVYEDDTLLVVNKPAGMVVHPGHGNYSGTL 131

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + YH +    +  D    +P L HR+D++TSG+LV+A+T  A  HL++ F  +  ++
Sbjct: 132 INALVYHFENLPNNSSD----RPGLVHRIDKDTSGLLVIAKTEHAMAHLSKQFFDKTSER 187

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y ++VWG + +++     N      +   + V+  +  EKG   A++H KV++ F    
Sbjct: 188 EYIAIVWGNVEEDEGTVEGNIGRHPKNRLQNTVYEGEDAEKGKP-AVTHLKVLERFGYVT 246

Query: 241 ---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---------PIQ 285
              C LE    TGRTHQ+RVH  H+G  +  D +Y      KG  FT           I 
Sbjct: 247 LVACKLE----TGRTHQIRVHMKHIGHTLFNDERYGGEKILKGTTFTKYKQFVENCFKIL 302

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
            +  LHA+ +   HP+ G  +   + LP  M+
Sbjct: 303 PRQALHAKTLGFTHPKTGEWMSFNSDLPEDML 334


>gi|17546347|ref|NP_519749.1| ribosomal large subunit pseudouridine synthase D protein [Ralstonia
           solanacearum GMI1000]
 gi|34395802|sp|Q8XYX8|RLUD_RALSO RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|17428644|emb|CAD15330.1| probable ribosomal large subunit pseudouridine synthase d protein
           [Ralstonia solanacearum GMI1000]
          Length = 358

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 95/341 (27%), Positives = 154/341 (45%), Gaps = 36/341 (10%)

Query: 7   VQYVVVENDEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           ++ ++VE  E     RLD+      P  +   LQ+ + +G VRV    V+    +  G  
Sbjct: 36  IEPIIVEIPEALHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVRPRAAVCGGDR 95

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + + P           Q+  D +  + +  D     ++YED  + V NKPAG+ V   +G
Sbjct: 96  IEVVP-----------QRADDENAFVAEPVDL---DVVYEDDTLLVINKPAGLVVHPAAG 141

Query: 125 --IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 ++G L  +  + G  PR  + HRLD+ETSG++VVART  A   L    + R ++
Sbjct: 142 NWSGTVLNGLLHRYPQAAG-LPRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVK 200

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---VIDCFA 237
           + Y +LVWG  +  +    +  + +     D   +          A +HFK   V+D   
Sbjct: 201 RTYLALVWG--ETPEAGTIDAPIGRDP--RDRTRMAIIETASGKPARTHFKTLDVVDLGR 256

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YL 290
            +   ++ Q  TGRTHQ+RVH    G P++GD  Y  NF+      I+  L        L
Sbjct: 257 AQVSLVQCQLETGRTHQIRVHFESEGHPLLGDPVYTRNFRRGRPQTIKAPLPAPFARQAL 316

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           HA  + L HP  G+ +   A +P  + +  D+L    D +L
Sbjct: 317 HAVRLGLVHPASGQSVHWHAGVPDDLAELMDALEMDPDVDL 357


>gi|309778048|ref|ZP_07672988.1| ribosomal large subunit pseudouridine synthase D
           [Erysipelotrichaceae bacterium 3_1_53]
 gi|308914185|gb|EFP59985.1| ribosomal large subunit pseudouridine synthase D
           [Erysipelotrichaceae bacterium 3_1_53]
          Length = 304

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/325 (26%), Positives = 155/325 (47%), Gaps = 43/325 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++   +E  +R+D++       ++   +Q +L+ G + V++K  K N +++         
Sbjct: 6   IIAAAEEAGVRIDKYISEQ-EELSRSRVQSLLQEGLILVNEKPAKANYKVK--------- 55

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
              A +HI       D  + L    + ++  + YED  + V NKP  I V   +G     
Sbjct: 56  ---AQDHITA---CFDDEMELEARPEAMELDVRYEDEDVIVINKPKNIVVHPAAGNQTGT 109

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G L    D  G     +P + HR+D++T+G+L+VA+   A   L++  + + + ++Y
Sbjct: 110 LVNGLLYHCKDLSGINGTLRPGIIHRIDKDTTGLLIVAKNDLAHASLSKQLQSKTVNRLY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDY-----VHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++LV G+ ++    I       + IG D      + V   N K A    +HF+VI+ F +
Sbjct: 170 YALVHGVIQHDFGTI------DAPIGRDVKDRQKMAVTSTNSKDAR---THFQVIERF-E 219

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +E +  TGRTHQ+RVH  ++G P+VGD KY  +++    +   N   LHA  +   
Sbjct: 220 NYTLVECRLETGRTHQIRVHMQYIGHPVVGDEKY--SYRKTMQT---NGQLLHAHQLTFQ 274

Query: 299 HPEGGRL-QITAPLPAHMVKTWDSL 322
           HP  G +  + A LP       + L
Sbjct: 275 HPRTGEMITVEAELPKQFADILEEL 299


>gi|145219868|ref|YP_001130577.1| ribosomal large subunit pseudouridine synthase D [Prosthecochloris
           vibrioformis DSM 265]
 gi|145206032|gb|ABP37075.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           phaeovibrioides DSM 265]
          Length = 349

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 91/329 (27%), Positives = 145/329 (44%), Gaps = 39/329 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++      +     +Q+ +  G+V V+ K VK N RI+S  ++             
Sbjct: 34  MRIDQYLSRQVENATRNKVQEAIEDGRVLVNDKVVKSNYRIKSCDLI------------- 80

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E   L          D   +I+ YEDS++ V NK  G+ V    G         I +HI
Sbjct: 81  -EMTFLRPPAPELAPEDIPIAIV-YEDSELMVINKEPGMVVHPAFGNWTGTLANAILHHI 138

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G     +D    +P + HRLD++TSG++++A+   A   L + F  R++ K Y +LVWG
Sbjct: 139 -GENAGSLDESELRPGIVHRLDKDTSGLIIIAKNPTALHRLAKQFADRKVVKTYKALVWG 197

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +P   +  I   + +         +   + E+G   AI+ +++ +     F  L +  HT
Sbjct: 198 VPATPEGTIRTNIGRSRKDRKVMANFPYEGEEGKT-AITDYRLEEDL-HWFSLLSLTLHT 255

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-----IQNKL------YLHARYMDLP 298
           GRTHQ+R H  H+G  I+ D  Y      N   P     ++N L       LHA  +   
Sbjct: 256 GRTHQIRAHMQHLGHQILSDATYGGASIRNLDFPKSESFVRNLLDLLPRQALHAESLSFQ 315

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HP  G  +   APLP  M +  D +   Y
Sbjct: 316 HPTTGETISFHAPLPLDMAQAIDKIRVIY 344


>gi|150397811|ref|YP_001328278.1| RluA family pseudouridine synthase [Sinorhizobium medicae WSM419]
 gi|150029326|gb|ABR61443.1| pseudouridine synthase, RluA family [Sinorhizobium medicae WSM419]
          Length = 343

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 79/251 (31%), Positives = 126/251 (50%), Gaps = 33/251 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQE 153
           +LYED  + V  KPAG+ V  G+G      ++  +    DS       ++P + HRLD++
Sbjct: 92  VLYEDQDLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGGVKRPGIVHRLDKD 151

Query: 154 TSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           TSG++VVA+  AA +HL++ F    R   +++ Y ++VWG P+  K  I   L +     
Sbjct: 152 TSGVMVVAKNDAAHRHLSDQFADHGRNGPLERAYRAVVWGRPRQLKGTIDAPLGR----A 207

Query: 210 GDYVH--VVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALH 261
           GD     V + +   A  AI+H++V+D + +K         +E    TGRTHQ+RVH  H
Sbjct: 208 GDRTKRAVKRDDSDDAREAITHYEVVDRYHEKPDGTSLASAVECHLETGRTHQIRVHMAH 267

Query: 262 MGCPIVGDHKYCANFKGN---FTSPIQNKL------YLHARYMDLPHPEGGR-LQITAPL 311
           +G P++GD  Y A F+        P +  +       LHA  +   HP  G  +   A +
Sbjct: 268 IGHPLIGDPDYGAAFRTKANLLPEPARTAVNRFPRQALHAFMLQFEHPSTGETMHFEAAV 327

Query: 312 PAHMVKTWDSL 322
           P+ M +  D+L
Sbjct: 328 PSDMQELVDAL 338


>gi|300703940|ref|YP_003745542.1| ribosomal large subunit pseudouridine synthase d [Ralstonia
           solanacearum CFBP2957]
 gi|299071603|emb|CBJ42927.1| Ribosomal large subunit pseudouridine synthase D [Ralstonia
           solanacearum CFBP2957]
          Length = 370

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 92/326 (28%), Positives = 147/326 (45%), Gaps = 34/326 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+      P  +   LQ+ + +G VRV    V+    +  G  + + P          
Sbjct: 63  RLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVRPRAAVCGGDRIEVVP---------- 112

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            Q+  D +  + +  D     ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 113 -QRAADENAFVAEPIDL---DVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYP 168

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + G  PR  + HRLD+ETSG++VVART  A   L    + R +++ Y +LVWG  +  +
Sbjct: 169 QAAGL-PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWG--ETPE 225

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---VIDCFAQKFCWLEMQPHTGRT 252
               +  + +     D   +          A +HFK   VID    +   ++ Q  TGRT
Sbjct: 226 AGTIDAPIGRDP--RDRTRMAIIETASGKPARTHFKTLDVIDLGRAQVSLVQCQLETGRT 283

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YLHARYMDLPHPEGGR- 304
           HQ+RVH    G P++GD  Y  NF+      I+  L        LHA  + + HP  G+ 
Sbjct: 284 HQIRVHFESEGHPLLGDPVYTRNFRRGRPQTIKAPLPIPFARQALHAVRLGIVHPASGQS 343

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNL 330
           +   A +P  + +  D+L    D +L
Sbjct: 344 MHWHAGVPDDLAELMDALEMDPDADL 369


>gi|313896045|ref|ZP_07829599.1| pseudouridine synthase, RluA family [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312975470|gb|EFR40931.1| pseudouridine synthase, RluA family [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 301

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 98/319 (30%), Positives = 144/319 (45%), Gaps = 53/319 (16%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVIN 72
           D    RLD +      + +   +Q+++  G VRVD   VK N +++SG+ +   +PP   
Sbjct: 7   DCAGERLDVFLARQIENCSRSYVQRLITDGNVRVDGAPVKPNYKLRSGEEICCTVPPAEE 66

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
            +  I  E   LD               +LYED  I V NK  G+ V   +G      ++
Sbjct: 67  VV--IAAEDIPLD---------------VLYEDEDIIVINKARGMVVHPAAGNLTGTLVN 109

Query: 131 GFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             L    D  G     +P + HRLD++TSG++V A+   A   L +  R +  ++ Y +L
Sbjct: 110 ALLFRCRDLSGINGELRPGIVHRLDKDTSGVMVAAKNDMAHHFLAQQIRSKDARREYRAL 169

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK------GANYAISHFKVIDCFAQKF 240
           V G          N   +   I GD        ++      G   A +HF+V++ F    
Sbjct: 170 VHG----------NIAERAGVITGDIGRHPTDRKRMAIVRSGGKSATTHFEVLERFGDYT 219

Query: 241 ---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
              C LE    TGRTHQ+RVH   +G P+VGD KY A  K  F    Q    LH+  + L
Sbjct: 220 LVSCVLE----TGRTHQIRVHMTSIGHPLVGDAKYTA-MKNPFGIHGQ---ALHSHILTL 271

Query: 298 PHPE-GGRLQITAPLPAHM 315
            HP  G +++ TAPLPA M
Sbjct: 272 AHPRTGAQMRFTAPLPADM 290


>gi|153875465|ref|ZP_02003256.1| ribosomal large subunit pseudouridine synthase D [Beggiatoa sp. PS]
 gi|152068071|gb|EDN66744.1| ribosomal large subunit pseudouridine synthase D [Beggiatoa sp. PS]
          Length = 321

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 93/308 (30%), Positives = 150/308 (48%), Gaps = 34/308 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+   + +P  +   LQ+ +R G V V+    +  ++++ G+ ++I            
Sbjct: 19  RLDKALADLFPDYSRARLQQWIRGGYVLVNSISWRAKDKVKGGEDIQI------------ 66

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVD 138
               L+  V+    +  L   LLYED  I V NKPAG+ V  G+G   + +   L ++  
Sbjct: 67  -TAQLEEEVSWQPQT--LPLTLLYEDKDILVVNKPAGLIVHPGAGHQQNTLVNALLNYAP 123

Query: 139 SKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              Q PR  + HRLD++TSG+LVVAR+  A +HL E  + R   + Y ++V G   +   
Sbjct: 124 ELAQLPRAGIVHRLDKDTSGVLVVARSLPAHKHLVEQLQNREFLREYKAIVIGALISGST 183

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             A   + +       + VVK+ +     AI+H++V+  + +   ++ +Q  TGRTHQ+R
Sbjct: 184 VDAP--IGRHPTQRTRMAVVKKGKP----AITHYRVLQRY-RVHTFIRVQLETGRTHQIR 236

Query: 257 VHALHMGCPIVGDHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQI 307
           VH  H   P++GD  Y        N    F   ++   +  LHA  + L HP  G  +Q 
Sbjct: 237 VHLAHKHYPLIGDSVYGGRLQIPPNSSDTFKEALRTFPRQALHAERLGLTHPISGEMMQW 296

Query: 308 TAPLPAHM 315
           TAPLP  M
Sbjct: 297 TAPLPDDM 304


>gi|262046428|ref|ZP_06019390.1| pseudouridine synthase [Lactobacillus crispatus MV-3A-US]
 gi|260573299|gb|EEX29857.1| pseudouridine synthase [Lactobacillus crispatus MV-3A-US]
          Length = 303

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 83/305 (27%), Positives = 150/305 (49%), Gaps = 44/305 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           +E   E  RLD++     P ++   ++++++   + V+ K  K + +IQ+G  + +  P 
Sbjct: 7   LEVKNEKGRLDKFVSEQIPDLSRTRVKELVKDQNILVNGKVEKVSYKIQAGDKIEVNIPA 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
           +  L+ +I E   LD               ++YED  + V NKP G+ V    G      
Sbjct: 67  VKPLD-VIPENIPLD---------------IVYEDDDVIVVNKPQGMVVHPAPGHPDHTL 110

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + YH     +S    +G +P + HR+D++TSG+L++A+T  A + L +    +  ++
Sbjct: 111 VNALLYHSKALAQS---PEGFRPGIVHRIDKDTSGLLMIAKTAKARESLEDQLAHKTNKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +YW++V G    +   I +  + ++      + VV+  +K    AI+HFKV++ F + + 
Sbjct: 168 LYWAIVHGNFAEENGVI-DAPIGRNPYDRKKMAVVETGKK----AITHFKVLEQF-KDYS 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPH 299
            +E Q  TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   H
Sbjct: 222 LIECQLETGRTHQIRVHLDYIGHPVAGDPLYGPRKTLKGHGQ-------FLHAKVLGFKH 274

Query: 300 PEGGR 304
           P  G 
Sbjct: 275 PSTGE 279


>gi|254419052|ref|ZP_05032776.1| pseudouridine synthase, RluA family [Brevundimonas sp. BAL3]
 gi|196185229|gb|EDX80205.1| pseudouridine synthase, RluA family [Brevundimonas sp. BAL3]
          Length = 339

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 95/332 (28%), Positives = 143/332 (43%), Gaps = 56/332 (16%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQ-VVRIPPVIN 72
           D   +RLD+     +P ++   LQ +L  G VR D   +   + + Q G  VV +PPV  
Sbjct: 27  DAPGVRLDKALAEAFPTLSRARLQALLAEGAVRRDGLVLTAGSAKAQPGLYVVALPPVAP 86

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
           A                 T   + +   +LYED+ + V +KPAG++     G      ++
Sbjct: 87  A-----------------TPQPEAIPLTVLYEDADLIVIDKPAGMAAHPAPGCETGTLVN 129

Query: 131 GFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             L    DS        +P + HRLD++TSG++V A+T  A Q L+  F    I++ Y +
Sbjct: 130 ALLAHCGDSLSGIGGVARPGIVHRLDKDTSGVMVAAKTDRAHQGLSALFATHDIERTYIA 189

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDY--VHVVKQNEKGANYAISHFKVIDCF------- 236
           L  G P   +  I   + + +   GD   + V+K    G   AI+ + V   F       
Sbjct: 190 LTRGAPSPSRGRIETRIGRST---GDRKKIAVLK---AGGREAITDYVVQAIFGEPAKAS 243

Query: 237 -----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-----N 286
                A+  C L    HTGRTHQ+RVH    G PI+GD  Y +         +       
Sbjct: 244 GAPLAARVACTL----HTGRTHQIRVHLSSKGSPILGDATYGSGSPAAAVRAVVAEAGLA 299

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           +  LHA  +   HP  G  L+   P PA MV+
Sbjct: 300 RQALHAAVLGFVHPVTGETLRFETPPPADMVR 331


>gi|160890006|ref|ZP_02071009.1| hypothetical protein BACUNI_02440 [Bacteroides uniformis ATCC 8492]
 gi|270294676|ref|ZP_06200878.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|156860394|gb|EDO53825.1| hypothetical protein BACUNI_02440 [Bacteroides uniformis ATCC 8492]
 gi|270276143|gb|EFA22003.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 223

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 71/218 (32%), Positives = 113/218 (51%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKQYLKEKYSKPGNVFIGVAHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E F+   ++K YW++V  +P+ ++  + N+L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFKNSEVKKTYWAVVKNLPREEEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   G+  AI H+++I   +Q +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPGSKKAILHYRLIG-RSQNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             G+  S     + LHARY+   HP    L ++ AP+P
Sbjct: 177 --GSPRSNPDGSICLHARYIRFVHPVSKELIEVEAPVP 212


>gi|121533717|ref|ZP_01665544.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
 gi|121307708|gb|EAX48623.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
          Length = 309

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 93/321 (28%), Positives = 153/321 (47%), Gaps = 35/321 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIP 68
           + E+ ++  RLD +     P ++  ++Q+I+ +G+V V+ K  K N ++       +R+P
Sbjct: 12  IAEDVDKGKRLDLFLVERLPELSRTHIQRIIAAGEVTVNGKAGKANYKLAPADYVTIRLP 71

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                     K  +I   +++L          +LYED  I V NKP G+ V   +G    
Sbjct: 72  EP--------KPAEIKAEAISLD---------ILYEDEDIIVINKPRGMVVHPAAGNYEG 114

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L+      G     +P + HRLD++TSG+++VA+T  A   L    + R   + 
Sbjct: 115 TLVNALLRHCDRLSGINGVSRPGIVHRLDKDTSGVMMVAKTDRAHLDLARQIKERTAGRK 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G  K + + I N  + +       + VV  N K    AI+ F+V++ F   +  
Sbjct: 175 YVAIVHGNIK-ENQGIINAPIGRHPTDRKKMAVVFTNSK---EAITTFQVLERFGD-YTL 229

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-E 301
           +E +  TGRTHQ+RVH  ++G P+VGD KY    +  F    Q    LHA  +   HP  
Sbjct: 230 VECRLFTGRTHQIRVHMAYIGHPVVGDPKYGPG-RQRFAIMGQ---ALHAAELTFQHPVT 285

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G R+  T PLP  M    + L
Sbjct: 286 GERMSFTVPLPDDMRAILEEL 306


>gi|257875741|ref|ZP_05655394.1| pseudouridylate synthase [Enterococcus casseliflavus EC20]
 gi|257809907|gb|EEV38727.1| pseudouridylate synthase [Enterococcus casseliflavus EC20]
          Length = 302

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/321 (26%), Positives = 156/321 (48%), Gaps = 47/321 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINA 73
           EE  R+D+      P+ +   +Q+ L+   V +  + V+ N ++++G   ++++P     
Sbjct: 11  EEKGRVDKVLAERLPNHSRSQIQQWLKEDAVTLMGETVRANYKVKAGDHLIIQVP----- 65

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
                 E +++D         + +   ++Y+D+ + V NKP G+ V   +G         
Sbjct: 66  ------EPEVVDL------QPENIPLTIVYQDADVAVINKPQGMVVHPSAGHPNGTLVNA 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + YH+D    S ++    +P + HR+D++TSG+L++A+   A + L +  + +   + Y 
Sbjct: 114 LLYHMDDL--STINDV-VRPGIVHRIDKDTSGLLMIAKNDQAHESLAKQLKDKTSLRKYV 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   ++K  I N  + +S +      V++  +     A++HF V++ F Q F  +E
Sbjct: 171 ALVHGTISHEKGTI-NAPIGRSKVNRKMQAVIENGKP----AVTHFTVLERFEQ-FTLVE 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +Q  TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP  
Sbjct: 225 LQLETGRTHQIRVHMQYIGFPLAGDPLYGPKRTLKGNGQ-------FLHAKLLGFTHPTT 277

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
           G  L   APLP     T   L
Sbjct: 278 GESLVFEAPLPELFADTLKKL 298


>gi|197120482|ref|YP_002132433.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196170331|gb|ACG71304.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 339

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 95/331 (28%), Positives = 162/331 (48%), Gaps = 32/331 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD+  +     +   ++ K+ R+ +VRV+ +R K +  +  G VV    
Sbjct: 4   LTVTADAAGQRLDKLVRKALRDVPLSHVYKMFRTRKVRVNGQRGKADQLVAEGDVV---- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGI--A 126
           VI        E+++L  +           +  +L+ED+ +   +KPAG++   G+GI  A
Sbjct: 60  VIRG-----DEERLLAKAAPAAPGGAPRVTFGVLHEDADLLAVDKPAGLAAHPGTGIEGA 114

Query: 127 YHID---GFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-RRIQ 180
             ++   G+L++  D      KP   HRLD++TSG+++VA+ R A   LTE+F     + 
Sbjct: 115 TLVEMARGYLRTPDDLPPTEFKPSPAHRLDRDTSGVVLVAKHRKAMVRLTETFTSGEGVH 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQ 238
           K Y +LV G  K  +E     L    H        +    +G N+  A++ +KV+   A+
Sbjct: 175 KTYLALVKG--KMPREAGTIDLPLSEHEQTSRSKAL----RGVNFQEALTRWKVVSA-AK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYM 295
           +   L +   TGRTHQ+R H   +G P+ GD +Y  +F  N T+  +    ++ LHA  +
Sbjct: 228 EISLLAVTIETGRTHQIRRHLEAVGHPVAGDRRY-GDFAFNRTARTRWGLRRMGLHAWKL 286

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           ++PHP  G  L++ AP PA + +       K
Sbjct: 287 EVPHPLTGAPLRLEAPFPAELAEVLSRANLK 317


>gi|310820541|ref|YP_003952899.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309393613|gb|ADO71072.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 315

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 100/335 (29%), Positives = 150/335 (44%), Gaps = 50/335 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + VE  +   R+D  F      ++   L+++   G VRV+ + VK    + +GQ      
Sbjct: 9   LTVEPTKAGQRVD-LFVGEALGLSRAKLKRLFEEGAVRVNGRAVKKGLLVSAGQ------ 61

Query: 70  VINALNHIIKE------QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ--- 120
                 HI+ E      + + D+   L         ++L+ED+ + V +KPAG       
Sbjct: 62  ------HILVEWEEETREAVPDTGFPL---------VVLHEDAALVVVDKPAGRPSHPLK 106

Query: 121 -GGSG------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            G +G      IA + +    S    +G    L HRLD ETSG+L+ ARTR A Q L  +
Sbjct: 107 PGETGTVANALIARYPECAQASEDAREGG---LCHRLDIETSGVLLAARTREAWQRLRTA 163

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  R + K Y +LV G   ++ E          H   D V      E+GA  A S F+V 
Sbjct: 164 FSGREVDKHYVALVTGPLADEGEIEIPLRHHPRHP--DRVEPALPGEEGAREAHSLFQV- 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
              +  F  +E++  TG  HQ+R H   +G P+VGD  Y     G    P  ++ +LHAR
Sbjct: 221 QARSGDFSLVEVRILTGVLHQVRAHLAGIGAPLVGDSLY-----GGREEPGLSRFFLHAR 275

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            +   HPE G RLQ+ +PLP  + +     G   D
Sbjct: 276 ALGFTHPETGQRLQVESPLPQELAEVLRHHGLSAD 310


>gi|77920540|ref|YP_358355.1| suppressor of ftsH mutation [Pelobacter carbinolicus DSM 2380]
 gi|77546623|gb|ABA90185.1| ribosomal large subunit pseudouridine synthase D [Pelobacter
           carbinolicus DSM 2380]
          Length = 326

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/331 (25%), Positives = 151/331 (45%), Gaps = 39/331 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+     P ++   L+K++  G+V +D    K  ++++ G+ + +            
Sbjct: 17  RLDRFLVEQLPELSRSQLKKLIDDGRVLLDGAAAKPGSKLKGGETLTV------------ 64

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              + D S       D +  ++LYED  + V +KP G+ V    G      ++  L    
Sbjct: 65  --DVPDPSPAEAVSED-IPLVILYEDRHLIVIDKPPGMVVHPAPGHYQGTLVNALLHHCQ 121

Query: 138 DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           D  G     +P + HRLD++TSG++V  +T +A Q L   F+   I + Y +L+ G+   
Sbjct: 122 DLSGIGGELRPGIVHRLDKDTSGVMVATKTDSAHQSLAAQFKAHSITRRYIALIHGVLTG 181

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCF-AQKFCWLEMQPHTG 250
            +  I         IG    H  K +   +   +A++H++V+  F   +   +E+   TG
Sbjct: 182 DRGSIDRP------IGRHPTHRKKMSTTCRTGRHAVTHWRVLRRFDDDRLTLVELALETG 235

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEG 302
           RTHQ+RVH      P++GD  Y  + +    +  Q         +  LHAR +   HPE 
Sbjct: 236 RTHQIRVHFSEQQHPLLGDPVYGGSGRLKTINDPQLLKRAKALGRQALHARLLGFQHPET 295

Query: 303 GR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           G+ L+ ++PLP  +    D L  KY +  ++
Sbjct: 296 GKYLEFSSPLPEDLRSVIDYLTEKYGQPPFV 326


>gi|328957532|ref|YP_004374918.1| pseudouridylate synthase [Carnobacterium sp. 17-4]
 gi|328673856|gb|AEB29902.1| pseudouridylate synthase [Carnobacterium sp. 17-4]
          Length = 301

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 88/325 (27%), Positives = 150/325 (46%), Gaps = 53/325 (16%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +EE+ RLD+   +  P I   ++Q+ ++ G V V+ +++K N ++Q G  + I       
Sbjct: 10  NEESGRLDKVLTDLLPSITRSHIQQWIKEGNVSVNGEKMKANYKVQPGDEIAI------- 62

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGF 132
                   +    V+L   ++ +   ++Y+D  + V NK  G+ V   +G      ++  
Sbjct: 63  --------VEPELVSLEVLAEDIPIEIVYQDEDVVVVNKAQGMVVHPSAGHQTGTLVNAL 114

Query: 133 LKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +    D  G     +P + HR+D++TSG+L+VA+  AA + L    + +   + Y +LV 
Sbjct: 115 MHHITDLSGINGTIRPGIVHRIDKDTSGLLMVAKNDAAHEKLAAQLKDKTSLREYIALVH 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK------GANYAISHFKVIDCFAQKFCW 242
           G+  ++K  I   L +            KQ+ K      G   A++HF V++ F + F  
Sbjct: 175 GVIPHEKGTIDAPLGRS-----------KQDRKKQDIIDGGRAAVTHFTVLERF-KDFTL 222

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY----CANFKGNFTSPIQNKLYLHARYMDLP 298
           + ++  TGRTHQ+RVH  ++G P+ GD  Y        KG F         LHA  +   
Sbjct: 223 VSLKLETGRTHQIRVHMKYIGYPLAGDPIYGPRKTLEGKGQF---------LHATTLGFK 273

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  G  L   APLP     T + L
Sbjct: 274 HPTSGEFLTFEAPLPKLFEDTLNDL 298


>gi|78186656|ref|YP_374699.1| pseudouridine synthase, RluD [Chlorobium luteolum DSM 273]
 gi|78166558|gb|ABB23656.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           luteolum DSM 273]
          Length = 354

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/329 (26%), Positives = 147/329 (44%), Gaps = 39/329 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++      +     +Q+ +  G+V V+ K VK N R++S   + +  +      + 
Sbjct: 38  MRIDQYLTRQVENATRNKVQEAIEDGRVLVNGKSVKSNYRVKSCDSIEMTFLRPPAPELA 97

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E   +D               ++YEDS + V NK  G+ V    G         I +H 
Sbjct: 98  PEDIPID---------------IVYEDSDLMVVNKAPGMVVHPAFGNWTGTLANAILHHF 142

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G     +++   +P + HRLD++TSG+++VAR   A   L   F  R++ K+Y +++WG
Sbjct: 143 -GTDAEELETDELRPGIVHRLDKDTSGLIIVARNPTALHRLARQFADRKVSKLYTAILWG 201

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +P+ ++  I   + +         +   +  +G   AI+ ++V +     F   E+  HT
Sbjct: 202 VPEPQEGTIHTNIGRSRRDRKVMANFPYEGLEGKT-AITDYRVTENL-HWFSLAELTLHT 259

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-----IQNKL------YLHARYMDLP 298
           GRTHQ+R H  H+G  I+GD  Y          P     ++N L       LHA  +   
Sbjct: 260 GRTHQIRAHMQHLGHQILGDTTYGGASLRTLDFPRSESFVKNLLDLLPRQALHAASLSFH 319

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            P  GR L  TAPLP  M +  + +   Y
Sbjct: 320 QPTTGRPLSFTAPLPEDMAQALEKIRVIY 348


>gi|284036309|ref|YP_003386239.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283815602|gb|ADB37440.1| pseudouridine synthase, RluA family [Spirosoma linguale DSM 74]
          Length = 348

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 81/326 (24%), Positives = 150/326 (46%), Gaps = 43/326 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+DR+  +   +     +Q  + +  VRV+ K  K + +I+   ++ +  
Sbjct: 20  IVVDKGQSLLRIDRFLMDRLQNATRTKIQAGIDAESVRVNDKPTKASYKIKPSDIITV-- 77

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
              +L H  +E  +   ++ +          +++ED  + V NKPAG+ V    G     
Sbjct: 78  ---SLPHPPRETDLKPENIPIN---------IVFEDDDLLVINKPAGMVVHPAHGNWDGT 125

Query: 125 ----IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + YH      S     G+ +P L HR+D++TSG++V+A+T  A  +L   F    I
Sbjct: 126 LVNALVYHFQNLPTS---RHGEVRPGLVHRIDKDTSGLMVIAKTEFAMTYLARQFFEHTI 182

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +L WG+P  +   I  ++ +   I    V  +  +E    +A++H+  ++     
Sbjct: 183 ERTYNALTWGVPNPQIGTITGFIGRS--IKDRKVQAIYDDESKGKWAVTHYTTLEDLGY- 239

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF------KGNFTSPIQNKL----- 288
              +E +  TGRTHQ+R H  H+G P+  D  Y  +        G++ + ++N       
Sbjct: 240 VALVECKLETGRTHQIRAHFKHIGNPLFNDAMYGGDRILRGTPVGSYKAFVENAFKLLPR 299

Query: 289 -YLHARYMDLPHPEGGR-LQITAPLP 312
             LHAR +   HP     LQ  + LP
Sbjct: 300 QALHARSLGFKHPRTKEWLQFDSNLP 325


>gi|187928999|ref|YP_001899486.1| pseudouridine synthase [Ralstonia pickettii 12J]
 gi|309782614|ref|ZP_07677336.1| ribosomal large subunit pseudouridine synthase D [Ralstonia sp.
           5_7_47FAA]
 gi|187725889|gb|ACD27054.1| pseudouridine synthase, RluA family [Ralstonia pickettii 12J]
 gi|308918589|gb|EFP64264.1| ribosomal large subunit pseudouridine synthase D [Ralstonia sp.
           5_7_47FAA]
          Length = 370

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/299 (28%), Positives = 138/299 (46%), Gaps = 33/299 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+      P  +   LQ+ + +G VR+  + V+    I  G  + + P          
Sbjct: 63  RLDKALAKLLPDYSRSRLQQWIDAGAVRLRGEVVRPRAAISGGDRIEVVP---------- 112

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            Q+  D +  + +  D     ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 113 -QRAADENAFVAEPIDL---DVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYP 168

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D+  + PR  + HRLD++TSG++VVART  A   L    + R +++ Y +LVWG  +  +
Sbjct: 169 DAV-ELPRAGIVHRLDKDTSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWG--ETPE 225

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---VIDCFAQKFCWLEMQPHTGRT 252
           E   +  + +     D   +          A +HFK   V+D    +   +  Q  TGRT
Sbjct: 226 EATIDAPIGRDP--RDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLVRCQLETGRT 283

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YLHARYMDLPHPEGGR 304
           HQ+RVH    G P++GD  Y  NF+      I+ +L        LHA  + L HP  G+
Sbjct: 284 HQIRVHFESEGHPLLGDPVYTRNFRRGQPQTIKAQLPVPFTRQALHAVRLGLVHPASGK 342


>gi|154245827|ref|YP_001416785.1| pseudouridine synthase [Xanthobacter autotrophicus Py2]
 gi|154159912|gb|ABS67128.1| pseudouridine synthase [Xanthobacter autotrophicus Py2]
          Length = 264

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 78/232 (33%), Positives = 115/232 (49%), Gaps = 14/232 (6%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LY D  + + +KP G+ V    +GG  +A H+D           + P L HRLD++TSG
Sbjct: 21  VLYRDGMMLIIDKPHGLPVHAGPKGGETLADHLDALRFGLP----RAPELAHRLDKDTSG 76

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R   A   L + F    + K Y ++  G P      I   L K+S   G ++  V
Sbjct: 77  CLVLGRHAKALALLGKLFANGSVGKTYLAVTQGSPAEDAGRIDQPLAKRSPHRGWWMQAV 136

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            +   GA  AI+ ++V+   A  F  + + P TGRTHQLR H  ++G PI GD    A +
Sbjct: 137 PKGTPGAQEAITDYRVLH-RAGGFAVMALSPVTGRTHQLRAHLSNLGHPIFGD----AIY 191

Query: 277 KGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            G    P    L+LH+R + +P    G  +  +APLP H+ +T  SLG   D
Sbjct: 192 GGASRLPGGPTLHLHSRRIVVPLKANGPAVAASAPLPPHICETLSSLGLSPD 243


>gi|161507611|ref|YP_001577565.1| pseudouridine synthase [Lactobacillus helveticus DPC 4571]
 gi|160348600|gb|ABX27274.1| pseudouridine synthase [Lactobacillus helveticus DPC 4571]
          Length = 303

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/314 (27%), Positives = 156/314 (49%), Gaps = 47/314 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           VEN  E  RLD++     P ++   ++++++  ++ V+ K  K + +IQ+G  + I  P 
Sbjct: 9   VEN--EYGRLDKFISEQIPDLSRTRVKELVKEKEILVNHKVEKVSYKIQAGDKIEINVPA 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
           +  L+ ++ E   LD               ++YED  + V NKP G+ V    G      
Sbjct: 67  VKPLD-VVPENIPLD---------------IVYEDEVVIVVNKPQGMVVHPAPGHPDHTL 110

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + YH     +S    +G +P + HR+D++TSG+L++A+   A + L +    +  ++
Sbjct: 111 VNALLYHTQDLAQS---PEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IYW++V G    ++  + +  + ++      + VV+  +K    A++HFKV+  F + + 
Sbjct: 168 IYWAIVHG-DFGEENGVIDAPIGRNPYDRKKMAVVENGKK----AVTHFKVLKQF-KGYS 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPH 299
            +E Q  TGRTHQ+RVH  ++G  + GD  Y      KGN         +LHA+ +   H
Sbjct: 222 LIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPRKTLKGNGQ-------FLHAKVLGFKH 274

Query: 300 PEGGR-LQITAPLP 312
           P  G+ L+ TA  P
Sbjct: 275 PRTGKWLEFTAEPP 288


>gi|330993274|ref|ZP_08317210.1| Ribosomal large subunit pseudouridine synthase D [Gluconacetobacter
           sp. SXCC-1]
 gi|329759676|gb|EGG76184.1| Ribosomal large subunit pseudouridine synthase D [Gluconacetobacter
           sp. SXCC-1]
          Length = 323

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 95/336 (28%), Positives = 149/336 (44%), Gaps = 46/336 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP- 68
           V+   D+   R DR+       ++   ++ ++ SG +            +++G  +R P 
Sbjct: 10  VIATADDAGQRTDRFIATATGALSRSRVKALMESGHL------------LRNGSPLRDPA 57

Query: 69  -PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            PV   + + I     L  ++  T     +   +LYED  + V +KPAG+ V    G   
Sbjct: 58  EPVRAGMCYEIH----LPPAIPATPQGQDIALDILYEDRDLIVLDKPAGMVVHPAPG--- 110

Query: 128 HIDGFL---------KSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           + DG L         +S     G+K P + HRLD++TSGI+V A+T  A Q L+ +F  R
Sbjct: 111 NEDGTLVNALLAHCGESLTGIGGEKRPGIVHRLDKDTSGIMVAAKTELAHQALSLAFAER 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           RI + Y ++ WG+P   +      + +      D   +      G   A++H++VI+ F 
Sbjct: 171 RIDRAYQAICWGLPVPAQGSFDGAIGRDRR---DRKRMAVIANGGGKQALTHYRVIETFH 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC----ANFKGNFTSPIQNKL----- 288
                +E +  TGRTHQ+RVH  H G  +VGD  Y     A  +G   +     L     
Sbjct: 228 GGLAHVECRLATGRTHQIRVHFAHAGHALVGDPVYLRRIPAAARGLPVAARDAALDFPRQ 287

Query: 289 YLHARYMDLPHPEGGR--LQITAPLPAHMVKTWDSL 322
            LHAR +   HP  G   L  TAP PA       S+
Sbjct: 288 ALHARRLGFVHPRSGEQLLFETAP-PADFTTLLGSI 322


>gi|170741578|ref|YP_001770233.1| pseudouridine synthase [Methylobacterium sp. 4-46]
 gi|168195852|gb|ACA17799.1| pseudouridine synthase [Methylobacterium sp. 4-46]
          Length = 228

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 76/231 (32%), Positives = 113/231 (48%), Gaps = 17/231 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           S +LY D+ + V +KPAG+ V    +GG  +  H+D           ++P   HRLD++T
Sbjct: 8   SRVLYRDALVLVIDKPAGLPVHPGPKGGETLVQHLDALRFGLP----RRPEAAHRLDRDT 63

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L + R   A   L + F     +K YW+LV G P  ++  I   L ++S    D   
Sbjct: 64  SGCLALGRHAKALARLGQLFAQGHARKTYWALVDGAPAAEEGEIDLALARRSE---DPRS 120

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              + +   + A++ +++     +   WLE++P TGRTHQLRVH   MG PI GD  Y A
Sbjct: 121 WWMRADPAGDPALTRWRLRGRSPEGGAWLELEPVTGRTHQLRVHCAAMGWPIRGDAVYGA 180

Query: 275 NFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
             +          L LHAR + LP +P    +   AP+P HM     + GF
Sbjct: 181 APRRGGPG-----LQLHARSLSLPLYPRKPPVTAEAPVPPHMRAGLAACGF 226


>gi|153810897|ref|ZP_01963565.1| hypothetical protein RUMOBE_01281 [Ruminococcus obeum ATCC 29174]
 gi|149833293|gb|EDM88375.1| hypothetical protein RUMOBE_01281 [Ruminococcus obeum ATCC 29174]
          Length = 304

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 91/326 (27%), Positives = 160/326 (49%), Gaps = 46/326 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPP 69
           +++ E+N+R+D++     P ++   LQK+L+ G V V+ + VK N + Q G   ++ IP 
Sbjct: 8   IDSSEKNVRIDKYLAECCPDLSRSYLQKLLKDGAVSVNTRIVKANYKTQPGDHVILNIPD 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +      I  E   LD               +LYED  + V NKP  + V   +G   H+
Sbjct: 68  LQTP--DIKPENIPLD---------------ILYEDQWLMVVNKPKDMVVHPSAG---HM 107

Query: 130 DGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +G L + V +             +P + HR+D++T+G L++ +     ++L E  +   I
Sbjct: 108 EGTLVNAVMAHCGDNLSGINGVMRPGIVHRIDKDTTGALLICKDDMVHRNLAEQLKEHSI 167

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y ++V G  K + E   +  + +  I    + +   N K    A++H+KV++ F Q 
Sbjct: 168 KRRYRAIVQGNIK-EDEGTVDAPIGRHPIDRKKMAI---NHKNGKEAVTHYKVLERFGQT 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDL 297
             ++E +  TGRTHQ+RVH   +G P++GD  Y     G+  +P  +Q +  LHA  +  
Sbjct: 224 -TYIECRLETGRTHQIRVHMASLGHPLLGDTVY-----GSSKNPYHLQGQA-LHAMILGF 276

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  ++  AP+P +  K  D L
Sbjct: 277 IHPVTGEYMEFEAPIPEYFSKLLDKL 302


>gi|52080148|ref|YP_078939.1| pseudouridine synthase [Bacillus licheniformis ATCC 14580]
 gi|52785525|ref|YP_091354.1| YlyB [Bacillus licheniformis ATCC 14580]
 gi|319646073|ref|ZP_08000303.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
 gi|52003359|gb|AAU23301.1| Pseudouridine synthase [Bacillus licheniformis ATCC 14580]
 gi|52348027|gb|AAU40661.1| YlyB [Bacillus licheniformis ATCC 14580]
 gi|317391823|gb|EFV72620.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
          Length = 304

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/320 (26%), Positives = 150/320 (46%), Gaps = 32/320 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  + +  R+D++        +   +Q+ ++  +V V+   VK N ++Q G  V +  
Sbjct: 6   MTVHEEHKGERIDKYLTAVEADWSRTQVQQWIKEDRVLVNGNAVKANYKVQEGDAVSVQ- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                   + E + LD +      ++ +   + YED  + V NKP G+ V    G     
Sbjct: 65  --------VPEPEPLDVT------AEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGT 110

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y
Sbjct: 111 LVNGLMAHCDDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G+  +    I +  + +       + V ++N K   +A++HF+VI+ F   F  +
Sbjct: 171 TALVHGVIPHDHGTI-DAPIGRDKKDRQSMTVTRENGK---HAVTHFEVIERF-DDFTVV 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E Q  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   HP  G
Sbjct: 226 ECQLETGRTHQIRVHMKYIGFPLAGDPKYGPKKTVDF-----NGQVLHAGVLGFDHPRTG 280

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             ++  APLP  M    D +
Sbjct: 281 EYVEFEAPLPDDMKNLLDKI 300


>gi|83745881|ref|ZP_00942938.1| Ribosomal large subunit pseudouridine synthase D [Ralstonia
           solanacearum UW551]
 gi|207743017|ref|YP_002259409.1| ribosomal large subunit pseudouridine synthase d protein [Ralstonia
           solanacearum IPO1609]
 gi|83727571|gb|EAP74692.1| Ribosomal large subunit pseudouridine synthase D [Ralstonia
           solanacearum UW551]
 gi|206594414|emb|CAQ61341.1| ribosomal large subunit pseudouridine synthase d protein [Ralstonia
           solanacearum IPO1609]
          Length = 370

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 92/326 (28%), Positives = 146/326 (44%), Gaps = 34/326 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+      P  +   LQ+ + +G VRV    V+    +  G  + + P          
Sbjct: 63  RLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVRPREAVCGGDRIEVVP---------- 112

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            Q+  D +  + +  D     ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 113 -QRAADENAFVAEPIDL---DVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYP 168

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + G  PR  + HRLD+ETSG++VVART  A   L    + R +++ Y +LVWG  +  +
Sbjct: 169 QAAGL-PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWG--ETPE 225

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---VIDCFAQKFCWLEMQPHTGRT 252
               +  + +     D   +          A +HFK   VID    +   ++ Q  TGRT
Sbjct: 226 AGTIDAPIGRDP--RDRTRMAIIETASGKPARTHFKTLDVIDLGRAQVSLVQCQLETGRT 283

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YLHARYMDLPHPEGGR- 304
           HQ+RVH    G P++GD  Y  NF+      I+  L        LHA  + + HP  G+ 
Sbjct: 284 HQIRVHFESEGHPLLGDPVYTRNFRRGQPQTIKAPLPVPFARQALHAVRLGIVHPASGQS 343

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNL 330
           +   A +P  +    D+L    D +L
Sbjct: 344 MHWHAGVPDDLADLMDALEMDSDVDL 369


>gi|83592447|ref|YP_426199.1| ribosomal large subunit pseudouridine synthase D [Rhodospirillum
           rubrum ATCC 11170]
 gi|83575361|gb|ABC21912.1| ribosomal large subunit pseudouridine synthase D [Rhodospirillum
           rubrum ATCC 11170]
          Length = 343

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 86/320 (26%), Positives = 147/320 (45%), Gaps = 39/320 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI-- 67
            V+ +    RLD+W     P ++   LQ+++   +V V+ + + + + R++ GQ VR+  
Sbjct: 28  AVDAEAAGQRLDKWLATVIPTLSRARLQQLIGEKRVSVNGQTIGEGSRRVKPGQTVRVEE 87

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP I A                 T   + +   ++YED  + V +K AG+ V  G G   
Sbjct: 88  PPPIAA-----------------TPQPEAIALTVVYEDDDLIVIDKAAGMVVHPGPGNPD 130

Query: 128 H--IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           H  ++  L     S       ++P + HRLD++TSG+++ A+T  A   L E F    + 
Sbjct: 131 HTLVNALLAHCGPSLSGIGGERRPGIVHRLDKDTSGLMIAAKTDLAHHGLAEQFACHSLT 190

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y  LVWG P+     I +  L +       + VV    +G   A++H++V+       
Sbjct: 191 REYLCLVWGRPRPAAGSI-DAPLGRHPTQRKKMAVVS---RGGKRALTHYRVVGDVEGIA 246

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQ--NKLYLHAR 293
             ++    TGRTHQ+RVH  H+G P++GD  Y          G+ +  I    +  LH+ 
Sbjct: 247 SIVKCTLSTGRTHQVRVHMAHIGHPLLGDAVYGHRNIPKKLPGDLSERIARLTRQALHSF 306

Query: 294 YMDLPHPEGGR-LQITAPLP 312
           ++   HP  G  L+  + LP
Sbjct: 307 HLGFLHPRTGESLEFLSELP 326


>gi|68171180|ref|ZP_00544587.1| Pseudouridine synthase, RluD [Ehrlichia chaffeensis str. Sapulpa]
 gi|67999411|gb|EAM86053.1| Pseudouridine synthase, RluD [Ehrlichia chaffeensis str. Sapulpa]
          Length = 323

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 84/311 (27%), Positives = 149/311 (47%), Gaps = 41/311 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +++ +EN RLD++  +                   +++  R +    I+  +++    
Sbjct: 6   IFIKSGDENNRLDKFIAS-------------------KLNISRNQVQQLIKDSKILLFDT 46

Query: 70  VINALNHIIKEQKILDSSVNLTKHSD------FLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +I   NHI K   I + S+     SD      ++   ++YED  I + NK  GI+V  G+
Sbjct: 47  IIRDNNHITKVNDIYNISIPTKTISDTITPNHYIPISVVYEDHDIIIINKAPGITVHPGA 106

Query: 124 GIAYH--IDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G   +  ++  +  + +S     K  +P + HRLD++TSG++V+A+   +   L++    
Sbjct: 107 GTNNNTLVNALVAHYGNSLSHVGKATRPGIIHRLDKDTSGLMVIAKNEKSYYFLSDLLLK 166

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           ++I+K Y ++VWG+P  K   I N++  K +     + V     KG   AI+ ++    F
Sbjct: 167 KQIKKEYLAVVWGLPNPKSNTIKNYICVKPN-NKQMMTVTHLPHKGK-LAITEYQTQKSF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQNKL---Y 289
           +     ++ + HTGRTHQ+RVH  ++G  I+GD KY  N     K    S I N L    
Sbjct: 225 SNIASLIKCRIHTGRTHQIRVHMSYIGNSIIGDQKYGKNNSKSVKYAKQSTIINTLKRQA 284

Query: 290 LHARYMDLPHP 300
           LHA  +   HP
Sbjct: 285 LHAYKLGFTHP 295


>gi|189184769|ref|YP_001938554.1| ribosomal large subunit pseudouridine synthase C [Orientia
           tsutsugamushi str. Ikeda]
 gi|189181540|dbj|BAG41320.1| ribosomal large subunit pseudouridine synthase C [Orientia
           tsutsugamushi str. Ikeda]
          Length = 312

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 85/299 (28%), Positives = 145/299 (48%), Gaps = 19/299 (6%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  Y H+    +++ +R G ++V+  + K   +++   V+ I   +   ++   
Sbjct: 13  RLDKFLKRKYSHLTQGVIERGIRKGHIKVNDAKSKAKLQVKDNDVLTIADYLTTCSNQKH 72

Query: 80  EQKILDSSVNLTKHS---DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            +       N+   +     +    + E S   + NKPA +  QGGS I+  +D  +K  
Sbjct: 73  IKLKKKVKDNVGVKALAHKIVNDYKIAETSDYIIINKPALLPTQGGSKISLSLDDAIKYL 132

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             S     +L HRLD+ETSG+L++A+    A  L+++F    I+K Y +++ G+P     
Sbjct: 133 NKSFYYDFKLVHRLDRETSGLLIIAKNHKTAIKLSQAFLHHSIEKEYTAILQGVPSQLSG 192

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
            I   + K     GD    + + + G   +I+ ++V       +   +   P TGRTHQL
Sbjct: 193 EIITNITKT----GDR---MLETQNGGKVSITKYQVKAVSMNSQLSLVSFIPVTGRTHQL 245

Query: 256 RVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLP 312
           RVHA  +G PI+GD KY  +N   N++      L LHA  + +P H  G +    APLP
Sbjct: 246 RVHAAKIGHPIIGDKKYNISNTYYNYS------LKLHAAKICIPKHMFGDQRIYYAPLP 298


>gi|150002980|ref|YP_001297724.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           vulgatus ATCC 8482]
 gi|254883622|ref|ZP_05256332.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           4_3_47FAA]
 gi|294775614|ref|ZP_06741123.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|319642310|ref|ZP_07996968.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_40A]
 gi|149931404|gb|ABR38102.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           vulgatus ATCC 8482]
 gi|254836415|gb|EET16724.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           4_3_47FAA]
 gi|294450556|gb|EFG19047.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|317386033|gb|EFV66954.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_40A]
          Length = 223

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 78/234 (33%), Positives = 119/234 (50%), Gaps = 18/234 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
           I++YED+ I V NK +   VQG       +   +K ++  K  KP      +THRLD+  
Sbjct: 2   IVVYEDNHIIVVNKTSSEIVQGDKTGDTPLSEMVKQYLKEKYNKPGNVFIGVTHRLDRPV 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V A+T  A   L E FR   ++K YW++V   PK  +  + ++L++       Y +
Sbjct: 62  SGLVVFAKTSKALPRLNEMFRNGEVKKTYWAIVKECPKETEGELVHYLVRNEKQNKSYAY 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              +  K +  A+ H+K+I   +Q +  LE+   TGR HQ+R     MGCPI GD KY  
Sbjct: 122 --DKEVKNSKKAVLHYKLIG-HSQNYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY-- 176

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYD 327
              G   S     + LHAR +   HP    + Q+TAP+P   +  W+  GF+ D
Sbjct: 177 ---GFPRSNPDGSICLHARTVQFVHPVSKEMIQLTAPVPEGNL--WN--GFEMD 223


>gi|207724162|ref|YP_002254560.1| ribosomal large subunit pseudouridine synthase d protein [Ralstonia
           solanacearum MolK2]
 gi|206589372|emb|CAQ36334.1| ribosomal large subunit pseudouridine synthase d protein [Ralstonia
           solanacearum MolK2]
          Length = 370

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 92/326 (28%), Positives = 147/326 (45%), Gaps = 34/326 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+      P  +   LQ+ + +G VRV    V+    +  G  + + P          
Sbjct: 63  RLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVRPRAAVCGGDRIEVVP---------- 112

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            Q+  D +  + +  D     ++YED  + V NKPAG+ V   +G      ++G L  + 
Sbjct: 113 -QRAADENAFVAEPIDL---DVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYP 168

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + G  PR  + HRLD+ETSG++VVART  A   L    + R +++ Y +LVWG  +  +
Sbjct: 169 QAAGL-PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWG--ETPE 225

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---VIDCFAQKFCWLEMQPHTGRT 252
               +  + +     D   +          A +HFK   VID    +   ++ Q  TGRT
Sbjct: 226 AGTIDAPIGRDP--RDRTRMAIIETASGKPARTHFKTLDVIDLGRAQVSLVQCQLETGRT 283

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YLHARYMDLPHPEGGR- 304
           HQ+RVH    G P++GD  Y  NF+      I+  L        LHA  + + HP  G+ 
Sbjct: 284 HQIRVHFESEGHPLLGDPVYTRNFRRGQPQTIKAPLPIPFARQALHAVRLGIVHPASGQS 343

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNL 330
           +   A +P  + +  D+L    D +L
Sbjct: 344 MHWHAGVPDDLAELMDALEMDSDVDL 369


>gi|295396961|ref|ZP_06807083.1| ribosomal large subunit pseudouridine synthase D [Aerococcus
           viridans ATCC 11563]
 gi|294974814|gb|EFG50519.1| ribosomal large subunit pseudouridine synthase D [Aerococcus
           viridans ATCC 11563]
          Length = 322

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 90/324 (27%), Positives = 153/324 (47%), Gaps = 37/324 (11%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---PPVIN 72
           E+ +RLD++  N +   +   ++K ++   V V+ K  K +  + +G ++ +    P   
Sbjct: 20  EDGLRLDQFVTNQFTDESRTTIKKWIKDKLVTVNGKVAKASQSLVNGDLIGVEKPAPAEA 79

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------S 123
                + E+  LD               +++ED  I V NKPA + V            +
Sbjct: 80  EEFKPVAEKMALD---------------IVFEDDDILVVNKPANLVVHPSVNHPTNTLVN 124

Query: 124 GIAYHI-DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G+ YH+ +   +  V  +  +P + HRLD++T+G+LVVA+++AA ++LT+     ++ +I
Sbjct: 125 GLLYHVQENGSQLAVGRESFRPGIVHRLDKDTTGLLVVAKSQAALENLTKQVANHQMTRI 184

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  LV+G        I   + +       +    + NE G  +A++HF V   +   +  
Sbjct: 185 YAGLVYGEIFEAGGTIDAPIRRHEKDRLKF----ETNEAG-RHAVTHFTVKHRYV-GYTL 238

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-E 301
           +  Q  TGRTHQ+RVHA  +  PIV D  Y   +K  F S   N   LHA  ++L HP  
Sbjct: 239 VNFQLETGRTHQIRVHANFINHPIVDDPLYARQYKERFFS--DNGQLLHAHRLELEHPVT 296

Query: 302 GGRLQITAPLPAHMVKTWDSLGFK 325
           G  +   AP+P H  +    L FK
Sbjct: 297 GEHMVFDAPIPDHFQEVLHQLTFK 320


>gi|260063592|ref|YP_003196672.1| ribosomal large subunit pseudouridine synthase D [Robiginitalea
           biformata HTCC2501]
 gi|88783037|gb|EAR14210.1| ribosomal large subunit pseudouridine synthase D [Robiginitalea
           biformata HTCC2501]
          Length = 343

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 94/337 (27%), Positives = 155/337 (45%), Gaps = 61/337 (18%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--- 67
             +  ++ +R+D++      +     +Q+  R G +R +++ +K N R++ G  +R+   
Sbjct: 22  TADTGQKPLRVDKFLMTRIRNATRNKIQQAARDGNIRANEQVIKQNYRVKPGDTIRVLFE 81

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
            PP  N L   + E   LD               ++YED  + V NKPAG+ V  G G  
Sbjct: 82  HPPYENLL---LPEDIPLD---------------IVYEDEVLLVVNKPAGMVVHPGHGNY 123

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  + +H+D    +       +P L HR+D+ETSG+LV+A+T AA  +L   F  +
Sbjct: 124 TGTLVNALVHHLDQLPLN----SDNRPGLVHRIDKETSGLLVIAKTEAAMANLARQFFDK 179

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKV--- 232
             ++ Y +LVWG   +    +   + +  K+ +    + V     +G   A++H++V   
Sbjct: 180 TTRREYLALVWGNVADDSGTVEGPIGRNPKNRL---QMQVFPDGSQGKE-AVTHYRVEER 235

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS------- 282
           +       C LE    TGRTHQ+RVH  H+G  I  D +Y  +   KG +FT        
Sbjct: 236 LGYVTLVSCRLE----TGRTHQIRVHMQHIGHTIFNDSRYGGDRILKGTSFTKYKQFVEN 291

Query: 283 --PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
              I  +  LHAR +   HP  G+ L   AP+P  M 
Sbjct: 292 AFKILPRQALHARTLGFTHPLSGKELDFEAPVPEDMA 328


>gi|148240684|ref|YP_001226071.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp. WH
           7803]
 gi|147849223|emb|CAK24774.1| Pseudouridylate synthase, 23S RNA-specific [Synechococcus sp. WH
           7803]
          Length = 333

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 92/308 (29%), Positives = 139/308 (45%), Gaps = 32/308 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +     +   +QK + +G VRV+    K    ++ G  V++  PP    L +
Sbjct: 37  MRLDRWLVSQRSEQSRARIQKFIDAGYVRVNGNTGKAKTPLRQGDEVQLWMPPP-EPLPY 95

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E   LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 96  LKPEAMDLD---------------VLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLH 140

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y ++V G+
Sbjct: 141 HCPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQVQIQKRIASREYLAVVHGV 200

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +       Y  V  +N     YA +H+ + +     +  L  +  TG
Sbjct: 201 PAGDSGTIVGAIGRHPADRKKYAVVSGEN---GRYACTHWSLQERLGD-YSLLRFKLDTG 256

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  HM  P+VGD  Y    K     P Q    LHA  + L HP    R+   A
Sbjct: 257 RTHQIRVHCAHMNHPVVGDPTYSRCRKLPIELPGQA---LHAFQLGLDHPITRERMLFEA 313

Query: 310 PLPAHMVK 317
           PLP  M K
Sbjct: 314 PLPPVMDK 321


>gi|194334247|ref|YP_002016107.1| RluA family pseudouridine synthase [Prosthecochloris aestuarii DSM
           271]
 gi|194312065|gb|ACF46460.1| pseudouridine synthase, RluA family [Prosthecochloris aestuarii DSM
           271]
          Length = 347

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 91/332 (27%), Positives = 147/332 (44%), Gaps = 53/332 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D +      +     +Q+ +   +V V+ K +K N RI+S   + +  +      + 
Sbjct: 34  MRIDVYLAQQVENATRNKVQEAIAEHRVLVNGKTIKSNYRIKSLDSIEVTFLRPPAPELA 93

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E   +D               ++YED  + V NK + + V    G         I +HI
Sbjct: 94  PEDIPID---------------IIYEDEDLMVVNKASDMVVHPAFGNWTGTLANAILHHI 138

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G     +D    +P + HRLD+ TSG++++A+   A   L   F  R+++K Y ++VWG
Sbjct: 139 -GKEAGDLDCSDMRPGIVHRLDKNTSGLIIIAKNSTALHRLARQFANRQVEKKYQAIVWG 197

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNE-----KGANYAISHFKVID--CFAQKFCW 242
           +P+     I      K++IG    +           K    AI+ ++V    C+   F  
Sbjct: 198 VPEPATGLI------KTNIGRSVRNRKVMTSYPFEGKDGKTAITEYRVQQSLCY---FSL 248

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-----TSPIQNKL------YLH 291
           +E+  HTGRTHQ+RVH  H+G PI+GD  Y  +   N       S ++N L       LH
Sbjct: 249 VEVTLHTGRTHQIRVHMQHLGHPILGDETYGGSSIRNLPFSKSESFVKNLLETIPRQALH 308

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A  +    P  G RL  TAPLP  M+   + +
Sbjct: 309 AESLTFTQPTTGERLSFTAPLPEDMLTALEKI 340


>gi|241206033|ref|YP_002977129.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859923|gb|ACS57590.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 341

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 95/348 (27%), Positives = 159/348 (45%), Gaps = 57/348 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV-VRIP 68
           V+  ++    RLD W                  + QV  +  R +    I+ GQV +R  
Sbjct: 14  VLTADESAEGRLDAWL-----------------TAQVGEEFSRSRIKALIKDGQVFLRGE 56

Query: 69  PVINALNHIIKEQKI---LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           PV +    +         L    + T   + +   +L+ED  + V +KP+G+ V  G+G 
Sbjct: 57  PVTDPQRKVRTGDSFELTLPEPEDPTPQGEDIPLDILHEDDDVIVISKPSGLVVHPGAGN 116

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF-- 174
                   + +H    L      +  +P + HRLD++T+G++VVA+   A +HL+  F  
Sbjct: 117 WTGTLVNALIHHCSNTLSGIGGVR--RPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFAD 174

Query: 175 --RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHF 230
             R   +++ Y ++VWG P++    +   L + +   GD     V + + + A+ AI+H+
Sbjct: 175 HGRTMPLERAYQAVVWGRPRSLSGMVDAPLGRAT---GDRTRRAVKRPDSQDADEAITHY 231

Query: 231 KVIDCFAQK-----FCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTS 282
           +V++ F +K     F  L E +  TGRTHQ+RVH  H+G P++GD  Y A F  K N   
Sbjct: 232 QVVERFHEKPDATAFASLVECRLETGRTHQIRVHMAHIGHPLLGDTVYGAGFKTKANLLP 291

Query: 283 PIQNKLY-------LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
               K+        LHA  +   HP  G  +    PLP  MV+  ++L
Sbjct: 292 EEIRKIVNGFGRQALHAFMLQFEHPRTGEIMHFEVPLPDDMVELVEAL 339


>gi|260663035|ref|ZP_05863928.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
 gi|260552656|gb|EEX25656.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
          Length = 304

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 87/305 (28%), Positives = 144/305 (47%), Gaps = 32/305 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            D    R+D+   +H+P  +   L++ +  G V V+ + VK   ++Q+G  V I P    
Sbjct: 11  TDGMTGRIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAGDRVVIEP---- 66

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDG 131
                      ++ V +    + +   ++YED  + V NKP G+ V    G   H  ++ 
Sbjct: 67  -----------ETPVEIDLEPENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNA 115

Query: 132 FL--KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +         G+ +P + HR+D++TSG+L+VA+T  A + LT   + +   + Y +LV 
Sbjct: 116 LMYHAPLSSINGELRPGIVHRIDKDTSGLLMVAKTDRAHRSLTAQLKEKSNLREYVALVH 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+ K  +  I   L +          VV     G  +AI+HF+V+  + Q +  +  +  
Sbjct: 176 GVIKENEGTIDAPLARSPKDRKKQAVVV-----GGRHAITHFRVLKRY-QHYTLVACRLE 229

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
           TGRTHQ+RVH  ++  P+ GD  Y        T P   + YLHAR +   HP  G  +  
Sbjct: 230 TGRTHQIRVHMKYINHPLAGDPLYGP----RKTLPGHGQ-YLHARLLGFEHPVTGEEMVF 284

Query: 308 TAPLP 312
           TAPLP
Sbjct: 285 TAPLP 289


>gi|269791933|ref|YP_003316837.1| pseudouridine synthase [Thermanaerovibrio acidaminovorans DSM 6589]
 gi|269099568|gb|ACZ18555.1| pseudouridine synthase [Thermanaerovibrio acidaminovorans DSM 6589]
          Length = 302

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 97/321 (30%), Positives = 143/321 (44%), Gaps = 36/321 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  D+E  RLDR  +  +P +N       +R GQVR+D +RV  + R+  GQ + +P   
Sbjct: 6   IPPDQEGRRLDRLIREWWPEVNMGLRMGAIRRGQVRLDGRRVPCSQRLLEGQELTVP--- 62

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ--GGSGIAYHI 129
                  +E +   S          L   +++ D ++ V NKPAG   Q  GG G +   
Sbjct: 63  -----WDQEPRRSGSGTPCPAEGRELPRWVIHWDRRLLVANKPAGWICQPGGGRGTSLPE 117

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           + +    VD   + P  +HRLD  T+G+++V    A  + L   FR   I+K+YW+LV G
Sbjct: 118 EVWRLLGVD---RGPVPSHRLDVNTTGVVLVPLDGALGRELHRLFREGTIRKLYWALVRG 174

Query: 190 IPKNKKECIANWL--LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                  C+   L  L  S  G   V      +  A   +    V   F+     +E++ 
Sbjct: 175 T------CVGEALVDLPLSKDGRGNVTPSPSGQP-ARSVVRPLAVRGGFSL----VEVEL 223

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL- 305
            TGR HQ RVH  H+G PI+GD +Y   F+G        +  LHAR + LP  E  G L 
Sbjct: 224 LTGRQHQARVHLAHLGLPILGDVRYGVRFRG------VGRTMLHARRVLLPFGESLGDLA 277

Query: 306 --QITAPLPAHMVKTWDSLGF 324
                APL   M +    LG 
Sbjct: 278 GAAFEAPLYPDMAEAARRLGL 298


>gi|160901794|ref|YP_001567375.1| RluA family pseudouridine synthase [Petrotoga mobilis SJ95]
 gi|160359438|gb|ABX31052.1| pseudouridine synthase, RluA family [Petrotoga mobilis SJ95]
          Length = 303

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 86/256 (33%), Positives = 133/256 (51%), Gaps = 34/256 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVRIPPVINALNHII 78
           RLD + + +YP I    +  ++R G V+V++KRVK NN I + G  V+I         I+
Sbjct: 15  RLDTFIRKNYPEIKLGAIYGLIRKGFVKVNEKRVKKNNYILEIGDNVKI---------IL 65

Query: 79  KEQKI--LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
            E K+  L      +  +  +   ++YED  + V NKPA +SV  GS   +A  I+G + 
Sbjct: 66  DENKLEELSRPTQPSLKARPVSFDIIYEDKDLLVINKPAKVSVHPGSKEEMATIIEGVMH 125

Query: 135 SWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
               S+G+ +P L HRLD+ TSG++VVA+ +  A+ LT+  + R  +K Y +L+ G    
Sbjct: 126 Y---SRGEFEPHLVHRLDKLTSGVMVVAKNKQTARELTQLIKSRETRKYYLTLLVG---- 178

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                   L KKS   G+ V  V    K A    +  K  D F + +  +E++ +TGR H
Sbjct: 179 -------NLNKKS---GELVSTVYG--KTAQLKFNLKKKFDLFGELYSLVEIELYTGRKH 226

Query: 254 QLRVHALHMGCPIVGD 269
           Q+RV    +G PI GD
Sbjct: 227 QIRVQFADLGFPIAGD 242


>gi|238917079|ref|YP_002930596.1| lysozyme [Eubacterium eligens ATCC 27750]
 gi|238872439|gb|ACR72149.1| lysozyme [Eubacterium eligens ATCC 27750]
          Length = 310

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 85/328 (25%), Positives = 155/328 (47%), Gaps = 40/328 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--V 64
           VQ ++ E +++  R+D++       ++   +QK+L  G + VD K VK N ++   +   
Sbjct: 5   VQNLIAEPEDKGTRIDKYLSQELEDVSRSRIQKLLDDGDITVDDKCVKSNYKLNGTEHIT 64

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + IP +I          +IL  ++ L          ++YED  + + +KP G+ V   +G
Sbjct: 65  ITIPELIVP--------QILPENIPLN---------IIYEDDDVILIDKPKGMVVHPAAG 107

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                    + YH    L     +   +P + HR+D  T+G++V  +   A   +     
Sbjct: 108 HYTGTVVNALMYHCRDNLSGI--NGVMRPGIVHRIDMNTTGVIVACKNDKAHNDIAAQLA 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           +  I + Y+ +V    K ++E   +  + ++      + V ++N K   +A++H++V++ 
Sbjct: 166 VHSITRKYYCIVHNRFK-EEEGTVDAPIGRNPKDRKMMAVDRKNGK---HAVTHYRVLEN 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F  K+ ++E Q  TGRTHQ+RVH   +G PI+GD  YC    G     +Q +  LHA  +
Sbjct: 222 F-DKYSFIECQLETGRTHQIRVHMASIGHPILGDDVYCHARSG---YKLQGQT-LHAGVL 276

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP  G  ++  APLP +  K    L
Sbjct: 277 GFIHPSTGEYMEFKAPLPGYFEKLLKDL 304


>gi|262195687|ref|YP_003266896.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262079034|gb|ACY15003.1| pseudouridine synthase, RluA family [Haliangium ochraceum DSM
           14365]
          Length = 322

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 89/328 (27%), Positives = 148/328 (45%), Gaps = 40/328 (12%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72
           +DE   RLD++       ++   +++++  G V+VD   V K   ++Q G+ V +     
Sbjct: 18  DDEPRARLDQFLTACELALSRSQVKRLIDEGAVQVDGAEVRKPGFKLQGGEAVEV----- 72

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                      L +   L      +   + YED  I V +KPAG+ V    G   H DG 
Sbjct: 73  ----------ALPAPQPLAAEPQAIPLDICYEDEHIIVVDKPAGLVVHPAPG---HPDGT 119

Query: 133 LKSWV-----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           L + +     D  G     +P + HRLD++TSG++V  +T  A   + E+F+  R+++ Y
Sbjct: 120 LVNALLAHCHDLSGIGGALRPGIVHRLDKDTSGVMVATKTEIAHHAMVETFQAHRLERAY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFC 241
            ++V   P+  +  I+         G   VH  K + +      AI+ ++V   F +   
Sbjct: 180 LAVVAPPPEPPRGTISTLH------GRHPVHRKKFSGRVSRGKQAITQYRVERVFGRLAA 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---YLHARYMDLP 298
            +  Q  TGRTHQ+RVH   MG P++GD  Y   ++    +P+   L    LHA  +   
Sbjct: 234 EVRCQLETGRTHQIRVHLSEMGAPLIGDVLYGRRYRDGVLAPLARALGRQALHATLLAFA 293

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           HP  G  L+   P PA M    ++L  +
Sbjct: 294 HPVTGAPLRFERPPPADMQTLIEALAAR 321


>gi|166031852|ref|ZP_02234681.1| hypothetical protein DORFOR_01553 [Dorea formicigenerans ATCC
           27755]
 gi|166028305|gb|EDR47062.1| hypothetical protein DORFOR_01553 [Dorea formicigenerans ATCC
           27755]
          Length = 302

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 93/328 (28%), Positives = 150/328 (45%), Gaps = 40/328 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            +Y  VEN EE  R+DR+     P  +   LQK+++   ++V+ K VK N R+  G  V 
Sbjct: 2   TEYFTVEN-EEGDRIDRYLAEEMPERSRSYLQKLIKEQYIKVNNKPVKANYRLVLGDRVE 60

Query: 67  --IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
             IP          KE  I   ++ L          +LYED  + V NKP  + V    G
Sbjct: 61  VCIPEA--------KEPDIEPENIPLD---------ILYEDEDVIVVNKPKQMVVHPAPG 103

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                    + YH    L     +   +P + HR+D +T+G L++ +   A Q L     
Sbjct: 104 HYSGTLVNALMYHCGNELSGI--NGTSRPGIVHRIDMDTTGSLIICKNDMAHQSLAVQLE 161

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I +IY ++V G  K ++E   N  + +       + +   + K A  AI+H+KV+  
Sbjct: 162 EHSINRIYEAIVHGNIK-EEEGTVNAPIGRHPTDRKKMSI---HAKNARNAITHYKVLKR 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F   + +++ +  TGRTHQ+RVH   +G P++GD  Y    K  F+  +     LHAR +
Sbjct: 218 FGD-YTYIQCKLETGRTHQIRVHMASIGHPLLGDQVYGPK-KCPFSKLVGQT--LHARTL 273

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP     +++ APLP + +   + L
Sbjct: 274 GFIHPRTNEYIEVNAPLPDYFLNLLEKL 301


>gi|315607390|ref|ZP_07882389.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
 gi|315250947|gb|EFU30937.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
          Length = 367

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 94/341 (27%), Positives = 153/341 (44%), Gaps = 56/341 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +  +R+D++     PH +   +Q    +G +RV+ + VK N +++ G VV +  
Sbjct: 37  IEVDAGQAPVRIDKFLTEKNPHQSRNRIQSAADAGFIRVNGRPVKSNYKVRPGDVVTL-- 94

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I+   + L          ++YED  + V NKPAG+ V  G+G     
Sbjct: 95  ---MLDRPKHDTSIVPEDIPLA---------VVYEDDGLMVINKPAGMVVHPGAGNFTGT 142

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +AY++        D+   +  L HR+D++TSG+LVVA+T  A   L + F  +   
Sbjct: 143 LINAVAYYLKDL--PTFDANSPEVGLVHRIDKDTSGLLVVAKTPEAKTCLGKQFFNKTTH 200

Query: 181 KIYWSLVWG--------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           + Y +LVWG        I  N      N L  K    G  +            A++H++V
Sbjct: 201 RSYNALVWGNIVDDEGRIEGNIARDPRNRLRMKVFAPGSGI---------GKSAVTHYRV 251

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQN 286
           ++ F      +E +  TGRTHQ+R H  H+G P+ GD  Y      +G  +S     IQN
Sbjct: 252 LERFGYT-TLVECRLETGRTHQIRAHMKHIGHPLFGDETYGGTEILRGQRSSTYKAFIQN 310

Query: 287 ------KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
                 +  LHAR +   HP  GR +  ++  PA      D
Sbjct: 311 CFKLCPRQALHARTLGFVHPVSGRQMDFSSEWPADFAALID 351


>gi|241663187|ref|YP_002981547.1| pseudouridine synthase [Ralstonia pickettii 12D]
 gi|240865214|gb|ACS62875.1| pseudouridine synthase, RluA family [Ralstonia pickettii 12D]
          Length = 370

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 89/314 (28%), Positives = 143/314 (45%), Gaps = 35/314 (11%)

Query: 7   VQYVVVENDEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
            + ++VE  E     RLD+      P  +   LQ+ + +G VR+  + V+    I  G  
Sbjct: 48  AEPIIVEIPEAMHGERLDKALAKLLPDYSRSRLQQWIDAGAVRLHGEVVRPRAAISGGDR 107

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + + P           Q+  D +  + +  D     ++YED  + V NKPAG+ V   +G
Sbjct: 108 IEVVP-----------QRAADENAFVAEPIDL---DVVYEDDTLLVINKPAGLVVHPAAG 153

Query: 125 --IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 ++G L  + D+  + PR  + HRLD++TSG++VVART  A   L    + R ++
Sbjct: 154 NWSGTVLNGLLHRYPDAV-ELPRAGIVHRLDKDTSGLMVVARTLPAQTDLVRQLQARTVK 212

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---VIDCFA 237
           + Y +LVWG  +  +E   +  + +     D   +          A +HFK   V+D   
Sbjct: 213 RTYLALVWG--ETPEEATIDAPIGRDP--RDRTRMAIIETASGKPARTHFKTLDVVDLGR 268

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YL 290
            +   +  Q  TGRTHQ+RVH    G P++GD  Y  NF+      I+  L        L
Sbjct: 269 AQVSLVRCQLETGRTHQIRVHFESEGHPLLGDPVYTRNFRRGQPQTIKAPLPVPFARQAL 328

Query: 291 HARYMDLPHPEGGR 304
           HA  + L HP  G+
Sbjct: 329 HAVRLGLVHPASGK 342


>gi|251797854|ref|YP_003012585.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247545480|gb|ACT02499.1| pseudouridine synthase, RluA family [Paenibacillus sp. JDR-2]
          Length = 315

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 95/333 (28%), Positives = 155/333 (46%), Gaps = 69/333 (20%)

Query: 20  RLDRWFKN--HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVINALN 75
           R+D++  +  +   I+   +Q+ ++SG V V++  VK N ++ SG  V  R+P   +A  
Sbjct: 25  RIDKFVTDSLNEDSISRTQVQEWIKSGAVLVNQNTVKPNYKLSSGDHVGIRVPEPEDAA- 83

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
            I+ E   LD               ++YED+ + V NKP G+ V    G         + 
Sbjct: 84  -IVAEDIPLD---------------IVYEDADVIVINKPRGMVVHPAPGHSSGTVVNALM 127

Query: 127 YH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           YH      I+G L+         P + HR+D++TSG+L+ A+   A   L E  +   + 
Sbjct: 128 YHCKDLSGINGVLR---------PGIVHRIDKDTSGLLMAAKNDLAHVSLAEQLKDHSVS 178

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVIDCFA 237
           + Y +LV G +P ++    A        IG D     +    ++ + +A++HF V++  A
Sbjct: 179 RKYIALVHGNLPHDQGTIDAP-------IGRDQNDRKLFTVTDRNSKHAVTHFAVLERIA 231

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQNKLYLHAR 293
             +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y  N     KG           LHA 
Sbjct: 232 DDYTIVELQLETGRTHQIRVHMKYIGYPLAGDPMYGRNKTVALKGQ---------ALHAA 282

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +   HP  G  L+  AP+PA M    +SL  +
Sbjct: 283 VLGFKHPRTGEFLEFEAPIPADMEHVINSLRLR 315


>gi|147678153|ref|YP_001212368.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI]
 gi|146274250|dbj|BAF59999.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI]
          Length = 312

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 93/319 (29%), Positives = 151/319 (47%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V    V  ++   RLD +       +    +QK++  G   V+ +R + + R++ G 
Sbjct: 1   MLTVNSFQVGEEDAGKRLDLFLAGEMEGLTRTYVQKLIAEGMASVNGQRGRASYRVKPGD 60

Query: 64  VVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           VV +  P    L  I KE   L+               + YED+ + V NKP G+ V   
Sbjct: 61  VVVLQVPEPEGLE-IKKEPIPLE---------------VYYEDADVIVINKPRGMVVHPA 104

Query: 123 SG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++  L    D  G     +P + HRLD++TSG+++VA+   A   L    + 
Sbjct: 105 DGNYSGTLVNALLYHCSDLSGINGVMRPGIVHRLDKDTSGLIMVAKNDTAHLSLARQLKE 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVID 234
           R+I + Y +LV G+ K +   +       + IG D     K    +K A  A++ ++V++
Sbjct: 165 RQITRRYLALVHGLLKEQSGMV------DAPIGRDPRDRKKMAVLQKNAKQAVTRYRVLE 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F + + ++E+   TGRTHQ+RVH  ++G P+VGD KY  + + +F    Q   +LHA  
Sbjct: 219 RF-KGYTYIELMLETGRTHQIRVHMSYIGHPVVGDLKYGPS-RPHFGLEGQ---FLHAAV 273

Query: 295 MDLPHPEGGR-LQITAPLP 312
           +   HP  G  LQ  APLP
Sbjct: 274 LGFHHPRTGEYLQFEAPLP 292


>gi|241890118|ref|ZP_04777416.1| ribosomal large subunit pseudouridine synthase D [Gemella
           haemolysans ATCC 10379]
 gi|241863740|gb|EER68124.1| ribosomal large subunit pseudouridine synthase D [Gemella
           haemolysans ATCC 10379]
          Length = 299

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 85/312 (27%), Positives = 153/312 (49%), Gaps = 38/312 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D++ +     ++  N+Q ++  G ++VD   +K N +++ G V+ I           K
Sbjct: 15  RIDKFLQQELTDVSRTNIQNLISEGYIKVDGNNIKTNYKLKEGNVITID---------YK 65

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E + LD    + K    +   ++YED+ + + NK  G+ V    G   H DG L + +  
Sbjct: 66  EPEELD----VVKQD--IPVDIVYEDNDLIIVNKAKGMVVHPSVG---HKDGTLVNALLF 116

Query: 140 KGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             +        +P + HR+D++TSG+L+VA+   A   L+E    + +++ Y++LV G  
Sbjct: 117 HSELSSINGTIRPGIVHRIDKDTSGLLIVAKNDKAHVKLSEMIANKDVKRKYYALVHGSI 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K+    I   + +      +   ++ + +     +I+HFKVID F +K+  +E +  TGR
Sbjct: 177 KHDYGTIDAPIARNPKERKEMA-IIDEGKP----SITHFKVIDRF-EKYTLIECELETGR 230

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  ++  P+VGD  Y      N      N   LH++ ++  HP  G  L     
Sbjct: 231 THQIRVHMKYINHPLVGDPVYGPRKTLN-----TNGQALHSKSIEFNHPITGEHLYFETE 285

Query: 311 LPAHMVKTWDSL 322
           +P +MV+T   L
Sbjct: 286 IPEYMVETMSKL 297


>gi|158426220|ref|YP_001527512.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
 gi|158333109|dbj|BAF90594.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
          Length = 319

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 78/234 (33%), Positives = 117/234 (50%), Gaps = 14/234 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           L + LL+ D  + V +KPAG+ V    +GG  +  H++G          + P L HRLD+
Sbjct: 82  LAARLLHRDGMVLVLDKPAGLPVHPGPKGGETLHDHLNGLRFGLP----RAPELAHRLDK 137

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG LV+ R   A   L   F   +  K Y ++  G P  +   I   L K+S   G +
Sbjct: 138 DTSGCLVLGRHGKALALLNRLFAEGQADKTYVAVTRGAPAEETGRIDQPLAKRSPHRGWW 197

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +  V +   G   A++ ++V+    +    + + P TGRTHQLR H  H+G PI+GD  Y
Sbjct: 198 MQAVPKGTPGGLEAVTDWRVL-ARTEGLAVMALSPVTGRTHQLRAHLSHIGFPILGDSIY 256

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
                G    P    L+LH+R + LP  + G  +   APLP HMV+T  +LG +
Sbjct: 257 ----GGASRLPGGPMLHLHSRRIVLPVAKNGPAIDARAPLPPHMVETLTALGLE 306


>gi|254780610|ref|YP_003065023.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Candidatus Liberibacter asiaticus str. psy62]
 gi|254040287|gb|ACT57083.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Candidatus Liberibacter asiaticus str. psy62]
          Length = 340

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 81/252 (32%), Positives = 121/252 (48%), Gaps = 30/252 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  I V NKPAG+ V    G         + YH    L S    K  +P + HRLD
Sbjct: 92  ILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVK--RPGIVHRLD 149

Query: 152 QETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           ++T+G++VVA+   A Q L+E F    +  R+++ Y+++VWGIP      I N  L +  
Sbjct: 150 KDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPL-PDSGIINAPLGRCK 208

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMG 263
                  V   ++K A+ AI+H++ I+ + +        L+    TGRTHQ+RVH  H G
Sbjct: 209 SNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKG 268

Query: 264 CPIVGDHKYCANFK-------GNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPA 313
            P++GD  Y   FK        N  S I +  +  LHA  +   HP   + +    P+P 
Sbjct: 269 NPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPE 328

Query: 314 HMVKTWDSLGFK 325
            M+     L  K
Sbjct: 329 DMLTVIRKLNEK 340


>gi|299535889|ref|ZP_07049209.1| putative RNA pseudouridine synthase ylyB [Lysinibacillus fusiformis
           ZC1]
 gi|298728641|gb|EFI69196.1| putative RNA pseudouridine synthase ylyB [Lysinibacillus fusiformis
           ZC1]
          Length = 303

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 92/328 (28%), Positives = 154/328 (46%), Gaps = 56/328 (17%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT V Y + E  ++  R+D+   +     +   +   +  G ++V+   VK   ++++G 
Sbjct: 1   MTQVTYTI-EEQQQGERIDKALSSLQSEWSRTQIGNWISDGVIKVNGDAVKAKYKVKAGD 59

Query: 64  VVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-- 120
           ++ I  P +  L+ ++ E   LD               ++YED+ + V NKP G+ V   
Sbjct: 60  IIAIDVPEVEELD-VVPENLDLD---------------IVYEDADVLVVNKPKGMVVHPA 103

Query: 121 ----GGS---GIAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
               GG+   G+ YH      I+G L+         P + HR+D++TSG+L+VA+   A 
Sbjct: 104 PGHMGGTLVNGLMYHCKDLSGINGVLR---------PGIVHRIDKDTSGLLMVAKNDTAH 154

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYA 226
           + L      + + + Y +LV G   + K  I       + IG D     KQ       +A
Sbjct: 155 ESLVNQLVNKTVTRKYIALVHGHIAHDKGTI------DAPIGRDQKDRQKQAVVDNGKHA 208

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++HF+V++ F   +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +F   +  
Sbjct: 209 VTHFQVVERFGD-YTLVECRLETGRTHQIRVHMNYIGFPLVGDPKYGPKKTIDFGGQV-- 265

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPA 313
              LHA  +   HP  G  L+   PLPA
Sbjct: 266 ---LHAATLGFDHPSSGEYLEFETPLPA 290


>gi|288925171|ref|ZP_06419106.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           D17]
 gi|288337936|gb|EFC76287.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           D17]
          Length = 358

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 94/341 (27%), Positives = 153/341 (44%), Gaps = 56/341 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +  +R+D++     PH +   +Q    +G +RV+ + VK N +++ G VV +  
Sbjct: 28  IEVDAGQAPVRIDKFLTEKNPHQSRNRIQSAADAGFIRVNGRPVKSNYKVRPGDVVTL-- 85

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I+   + L          ++YED  + V NKPAG+ V  G+G     
Sbjct: 86  ---MLDRPKHDTSIVPEDIPLA---------VVYEDDGLMVINKPAGMVVHPGAGNFTGT 133

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +AY++        D+   +  L HR+D++TSG+LVVA+T  A   L + F  +   
Sbjct: 134 LINAVAYYLKDL--PTFDANSPEVGLVHRIDKDTSGLLVVAKTPEAKTCLGKQFFNKTTH 191

Query: 181 KIYWSLVWG--------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           + Y +LVWG        I  N      N L  K    G  +            A++H++V
Sbjct: 192 RSYNALVWGNIVDDEGRIEGNIARDPRNRLRMKVFAPGSGI---------GKSAVTHYRV 242

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQN 286
           ++ F      +E +  TGRTHQ+R H  H+G P+ GD  Y      +G  +S     IQN
Sbjct: 243 LERFGYT-TLVECRLETGRTHQIRAHMKHIGHPLFGDETYGGTEILRGQRSSTYKAFIQN 301

Query: 287 ------KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
                 +  LHAR +   HP  GR +  ++  PA      D
Sbjct: 302 CFKLCPRQALHARTLGFVHPVSGRQMDFSSEWPADFAALID 342


>gi|308178003|ref|YP_003917409.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
 gi|307745466|emb|CBT76438.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
          Length = 321

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 83/311 (26%), Positives = 157/311 (50%), Gaps = 23/311 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +V++++    R++++ ++    +    + K++R GQ+RV+ K+V+   R+ +   + 
Sbjct: 18  IETIVIDSEHTGRRIEKYLRSALKSMPAGQMFKLMRKGQLRVNGKKVQEGYRLAANDKIT 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P    A +     +  ++    L K    L++ +++ED  + V +KPAGI V  G+   
Sbjct: 78  LP----AFHAQPTREPRIEVPPALLKR---LRNTVVHEDEDVLVIDKPAGIPVHKGTD-- 128

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMR--RIQKI 182
            +  G ++++   + + P   L+HRLD++TSG+LV+A+T +  ++L E  R R   I++ 
Sbjct: 129 -NPAGVIEAFRQLRPELPDLELSHRLDRDTSGLLVLAKTPSILRYLHEMLRDREDEIERH 187

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G        I   LL+ +    D +      ++         +V     ++   
Sbjct: 188 YLALVAGSWNEDTAVIHTPLLRLA----DRMVADPTGQRAETRVWVQQRV----GKRATI 239

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           L++Q  TGR HQ+RVH    G PI GD +Y  A F           L+LHA  + +P P+
Sbjct: 240 LDVQLMTGRKHQIRVHLQSEGHPIAGDDRYGFAKFNSRVEQLGGRGLFLHATKLVIPKPD 299

Query: 302 GGRLQITAPLP 312
           G  L + AP+P
Sbjct: 300 GQELVVEAPMP 310


>gi|297621148|ref|YP_003709285.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
 gi|297376449|gb|ADI38279.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
          Length = 287

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 118/219 (53%), Gaps = 19/219 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +L+ED  + ++NKP+G++        + +  F  S+         L HRLD+ET+G 
Sbjct: 78  RDAILFEDDHLLIYNKPSGMNSD-----EFGLGKFFPSFP--------LIHRLDKETTGC 124

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       + E F+ ++I K Y ++V G+P NK+E +    + +       +    
Sbjct: 125 IMFAKYPKVKNRMIELFKGKKISKHYLAVVDGVP-NKREGVEESFIGQISSNPGSIKWGN 183

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + K   +A + + +I+   ++   L+MQP TGRTHQLRVHA  MG PI+GD +YC +FK
Sbjct: 184 VSPKQGQHAKTQW-MIEKRGKEAALLKMQPITGRTHQLRVHAAQMGHPILGDFRYCRHFK 242

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            ++     ++  LHA  +  PHP     L+I AP+PA M
Sbjct: 243 CSYQP---SRTLLHAYTLHFPHPILDAYLKIKAPIPADM 278


>gi|291295265|ref|YP_003506663.1| pseudouridine synthase RluA family [Meiothermus ruber DSM 1279]
 gi|290470224|gb|ADD27643.1| pseudouridine synthase, RluA family [Meiothermus ruber DSM 1279]
          Length = 327

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 87/254 (34%), Positives = 121/254 (47%), Gaps = 39/254 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI-----------AYHIDGFLKSWVDSKG-----QKP 144
           +LYED  + V NKPAG+      G+            + +D  L    +  G     QKP
Sbjct: 75  ILYEDPDLIVINKPAGMITHPAPGVYSGTLVNAILGRFGLDLSLGESEEEGGLLLQAQKP 134

Query: 145 RL-----THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            L      HRLD+ TSG++VVAR  AA + L E+F  R + K Y +L  GIP+       
Sbjct: 135 ELIRPGIVHRLDKGTSGVIVVARHEAAHRRLAEAFAGRSVYKRYIALTVGIPREG----- 189

Query: 200 NWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
              L  + IG   V   + +  G  A +A + F+V+   A+    +    HTGRTHQ+RV
Sbjct: 190 ---LLSAPIGRHPVDRTRMHVGGVAARHAQTEFEVL-AVAEPHALVSAILHTGRTHQIRV 245

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H  H+  PI+GD  Y         S +  +  LHA  + L HP  G+ L   AP+PA MV
Sbjct: 246 HLKHLHAPILGDEVY------GKPSELIARQALHAYELRLQHPRTGKYLHFVAPIPADMV 299

Query: 317 KTWDSLGFKYDRNL 330
             W SLG  +  +L
Sbjct: 300 WAWVSLGGAWPEDL 313


>gi|329766891|ref|ZP_08258419.1| hypothetical protein HMPREF0428_00116 [Gemella haemolysans M341]
 gi|328837616|gb|EGF87241.1| hypothetical protein HMPREF0428_00116 [Gemella haemolysans M341]
          Length = 299

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 82/312 (26%), Positives = 149/312 (47%), Gaps = 38/312 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D++ +     ++  N+Q ++  G ++VD   +K N +++ G V+ I         ++K
Sbjct: 15  RIDKFLQQELTDVSRTNIQNLISEGYIKVDGNNIKTNYKLKDGNVITIEYKEPEELDVVK 74

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +   +D               ++YED  + + NK  G+ V    G   H DG L + +  
Sbjct: 75  QDIPID---------------IVYEDDDLIIVNKAKGMVVHPSVG---HKDGTLVNALLF 116

Query: 140 KGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             +        +P + HR+D++TSG+L+VA+   A   L+E    + +++ Y++LV G  
Sbjct: 117 HSELSSINGTIRPGIVHRIDKDTSGLLIVAKNDKAHVKLSEMIANKDVKRKYYALVHGSI 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K+    I   + +      +   V+ +       +I+HFKV+D F +K+  +E +  TGR
Sbjct: 177 KHDYGTIDAPIARNPKERKEMA-VIDE----GKLSITHFKVVDRF-EKYTLIECELETGR 230

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  ++  P+VGD  Y      N      N   LH++ ++  HP  G  L     
Sbjct: 231 THQIRVHMKYINHPLVGDPVYGPRKTLN-----TNGQALHSKSIEFNHPITGEHLYFETE 285

Query: 311 LPAHMVKTWDSL 322
           +P +MV+T   L
Sbjct: 286 IPEYMVETMSKL 297


>gi|197128104|gb|ACH44602.1| putative RIKEN cDNA 2410001E19 [Taeniopygia guttata]
          Length = 283

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 72/201 (35%), Positives = 112/201 (55%), Gaps = 23/201 (11%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHR 149
           +  LK   LY++ +I V +KP G+ V GG GI   I   L    K   + K +   L HR
Sbjct: 14  AKILKQRTLYQNEEIVVIDKPYGLPVHGGPGIKNCIADVLPILAKMLENMKAEPLHLCHR 73

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----------IPKNKKECIA 199
           LD+ET+G++V+AR++ AA+ +   F+ R+++KIYW++V G          IP  +KE  +
Sbjct: 74  LDKETTGVMVLARSKEAAEKIRLLFKTRQVEKIYWAIVLGDPDPVEGVVEIPIVEKEVQS 133

Query: 200 NWLLKKSHIGGDYV------HVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           +    K  +  +Y        V+K +  + A  A++ ++ + C A     LE+QP TG  
Sbjct: 134 HQSHYKMTLAPNYRLCPEDGKVMKTRGSRHAERAVTRYRRL-CAASACSLLELQPVTGVK 192

Query: 253 HQLRVH-ALHMGCPIVGDHKY 272
           HQ+RVH A  +GCPI+GDHKY
Sbjct: 193 HQIRVHLAYGLGCPILGDHKY 213


>gi|146300375|ref|YP_001194966.1| RluA family pseudouridine synthase [Flavobacterium johnsoniae
           UW101]
 gi|146154793|gb|ABQ05647.1| ribosomal large subunit pseudouridine synthase D [Flavobacterium
           johnsoniae UW101]
          Length = 347

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 86/308 (27%), Positives = 141/308 (45%), Gaps = 42/308 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D++     P+     +Q     G + V+   VK N +++   V+ I      L+H  
Sbjct: 30  LRIDKYLMYLIPNATRNKIQNAATDGNIFVNDIPVKSNYKVKPFDVITI-----MLSHPP 84

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E  IL   + L          ++YED  + + NK  G+ V  G G         +A+H 
Sbjct: 85  FENHILPEDIPLN---------IVYEDDALLLINKEPGMVVHPGHGNYTGTLVNALAHHF 135

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           D    +      ++P L HR+D++TSG+LVVA+T AA  HL + F  +  ++ Y +LVWG
Sbjct: 136 DNLPMN----SSERPGLVHRIDKDTSGLLVVAKTEAAMTHLAKQFEAKTTEREYIALVWG 191

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               +   I   L +  H+       V  + +    AI+H+KV++ F      +  +  T
Sbjct: 192 NVAAESGTIEGNLAR--HLKDRMQMAVFADPEIGKPAITHYKVLERFGY-VTLISCKLET 248

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN------KLYLHARYMDL 297
           GRTHQ+R H  H+G P+  D +Y  +   KG     +   I+N      +  LHA+ +  
Sbjct: 249 GRTHQIRAHMKHIGHPLFNDERYGGHLILKGTTFTKYKQFIENCFKALPRQALHAKTLGF 308

Query: 298 PHPEGGRL 305
            HP  G L
Sbjct: 309 VHPNTGEL 316


>gi|326692704|ref|ZP_08229709.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           argentinum KCTC 3773]
          Length = 308

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 92/323 (28%), Positives = 157/323 (48%), Gaps = 37/323 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +   ++  R+D    N     +   L   ++SG+V V+ +RVK + ++ +G V+ I P
Sbjct: 5   ITINITDQTGRIDAILANQNLPYSRTVLANWVQSGEVLVNGQRVKRSYKVAAGDVISIQP 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  I+ E   LD               ++YED+ + V NKP G+ V   +G   H 
Sbjct: 65  PAVQPTEIVAEAMPLD---------------IVYEDADLLVVNKPQGMVVHPAAG---HT 106

Query: 130 DGFLKSWV-------DSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            G L + +          G+ +P + HR+D++TSG+L+VA+   A Q L+   +  +  +
Sbjct: 107 SGTLVNGLLHHAPLSTINGEFRPGIVHRIDRDTSGLLMVAKNDQAHQALSAQLKAHKNDR 166

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKF 240
           IY++LV G      E   N     + I    +   KQ  ++G   A++HF+VI  +   +
Sbjct: 167 IYYALVRG------EFEENTGTINAPIARHAIDRKKQAVQEGGREAVTHFEVIARYV-GY 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L+++  TGRTHQ+RVH  ++G PIVGD  Y    K +  + +  +L LHA+ + L  P
Sbjct: 220 TLLKVRLETGRTHQIRVHLTYIGHPIVGDPVYGGAQKLSGVN-LAGQL-LHAKTLSLTQP 277

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  L   + LPA+  +   +L
Sbjct: 278 TTGENLIFDSELPAYFEQALATL 300


>gi|320105613|ref|YP_004181203.1| RluA family pseudouridine synthase [Terriglobus saanensis SP1PR4]
 gi|319924134|gb|ADV81209.1| pseudouridine synthase, RluA family [Terriglobus saanensis SP1PR4]
          Length = 441

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 98/363 (26%), Positives = 163/363 (44%), Gaps = 74/363 (20%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD +     P I+   +Q ++  GQVRVD K  K   ++  G+ + I          
Sbjct: 86  GLRLDAYLAKAMPDISRGRVQLLIEQGQVRVDGKTAKNKLKLLGGERIEI---------- 135

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-------ID 130
             E +   + +        LK  ++YED  + V +KPAG+ V  GSG+          ++
Sbjct: 136 --EGEPRPAPLKAMAEDIPLK--IVYEDEHMAVIDKPAGMMVHAGSGLTDDARSGGTLVN 191

Query: 131 GFLKSW---VDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             L  +   + S G   +P + HRLD++TSG+++VA+     + L E F  R ++K Y +
Sbjct: 192 ALLHHFNVNLSSVGGELRPGIVHRLDKQTSGLIMVAKNDRTHRALGEMFSDRSLEKRYLA 251

Query: 186 LVWG------------------IPKNKKECIA---------NWLLKKSHIGGDYVHVVKQ 218
           LV G                  +P  +              +W+  +S      +H  ++
Sbjct: 252 LVHGEVGAKARGNAERDHGTINLPIGRDPIRRTRMTTRSRQSWMTTESPGTPSKLHPEER 311

Query: 219 NEKG------ANYAISHFKV---IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                     A  A+SH++V   +D  A KF  LE+   TGRTHQ+RVH   +G P+VGD
Sbjct: 312 EPMKEPKLYEARAAVSHYEVLERLDTSAGKFTLLEVLIETGRTHQIRVHMQAIGHPVVGD 371

Query: 270 HKYCANFK---------GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
             Y A  +         G+  +  +N  +LHA+ + L HP  G  L++ A +PA +++  
Sbjct: 372 TLYGAPARIVGLHRPEDGDGATLPRN--FLHAKELHLAHPITGEDLELEAEIPADLIELL 429

Query: 320 DSL 322
           + L
Sbjct: 430 NRL 432


>gi|317481349|ref|ZP_07940417.1| RNA pseudouridylate synthase [Bacteroides sp. 4_1_36]
 gi|316902445|gb|EFV24331.1| RNA pseudouridylate synthase [Bacteroides sp. 4_1_36]
          Length = 223

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 113/218 (51%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKQYLKEKYSKPGNVFIGVAHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E F+   ++K YW++V  +P+ ++  + N+L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFKNSEVKKTYWAVVKNLPREEEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   G+  AI H+++I   +Q +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPGSKKAILHYRLIG-RSQNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             G+  S     + LHARY+   HP     +++ AP+P
Sbjct: 177 --GSPRSNPDGSICLHARYIRFVHPVSKEPIEVEAPVP 212


>gi|116492705|ref|YP_804440.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           pentosaceus ATCC 25745]
 gi|116102855|gb|ABJ67998.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           pentosaceus ATCC 25745]
          Length = 300

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 80/304 (26%), Positives = 143/304 (47%), Gaps = 35/304 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q+  V +D+E+ RLD+   NHYP +    +Q +++  Q+ V++       ++    V+ +
Sbjct: 3   QFSFVVSDQESGRLDKVVTNHYPDLTRSKIQNLIKQEQILVNQAPTTNRYKVSENDVIDV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           L   V ++   + +   +++ED  + V NKP G+ V    G   
Sbjct: 63  ---------------TLPDPVEVSVKPEKMNLDIVFEDDDVIVVNKPQGMVVHPAPGHEN 107

Query: 126 AYHIDGFLK--SWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++G L         G+ +P + HR+D++TSG+L+VA+   A   L+   + +  Q+ 
Sbjct: 108 GTLVNGLLDHAPLATVNGELRPGIVHRIDKDTSGLLMVAKNDQAMLSLSAQLKAKTNQRK 167

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G  K +   I N  + +S      + +V+        A++HFKV++ F   +  
Sbjct: 168 YLAIVHGNFKEEAGTI-NAPIGRSKKDRKKMAIVEDGRP----AVTHFKVLERFTD-YTL 221

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHP 300
           +E +  TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP
Sbjct: 222 IECELETGRTHQIRVHLKYIGHPVAGDPLYGPRNTLKGNGQ-------FLHAKLLGFKHP 274

Query: 301 EGGR 304
             G 
Sbjct: 275 RTGE 278


>gi|170289613|ref|YP_001739851.1| RluA family pseudouridine synthase [Thermotoga sp. RQ2]
 gi|170177116|gb|ACB10168.1| pseudouridine synthase, RluA family [Thermotoga sp. RQ2]
          Length = 304

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 131/265 (49%), Gaps = 51/265 (19%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK---FNNRIQSGQVVRIPPVINALNH 76
           RLD++ +N         + K++R G+V V+ KRV+   F+  ++ G  V I  V      
Sbjct: 13  RLDKFLRNTLKDFPLSTIYKLIRKGKVYVNGKRVRDPGFD--LEEGDTVEIKYV------ 64

Query: 77  IIKEQKILDSSVNLTKHSDF-------LKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                    +  NL K SD        +K  +++E+    V NKPAGI++  G G+  A 
Sbjct: 65  ---------NLENLPKRSDKKDLTPVPMKLDIIHENDNYLVLNKPAGIAIHPGKGVHVAT 115

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            I+G L  +   +G +P L HRLD++TSG+L+VA+ R AA+ LTE FR R ++K Y +LV
Sbjct: 116 LIEGLL-YYGQEQGFEPFLVHRLDKDTSGLLIVAKNREAARVLTEMFRGRNMEKEYIALV 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+P+N      N  +     G + V  +   +   N ++   K+               
Sbjct: 175 KGVPEN------NLKITIPLDGQEAVSEIVSVKPLKNVSLLRVKI--------------- 213

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
           HTGR HQ+R H   +G P+VGD  Y
Sbjct: 214 HTGRKHQIRRHLSQIGFPVVGDDTY 238


>gi|325263923|ref|ZP_08130656.1| ribosomal large subunit pseudouridine synthase D [Clostridium sp.
           D5]
 gi|324030961|gb|EGB92243.1| ribosomal large subunit pseudouridine synthase D [Clostridium sp.
           D5]
          Length = 305

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 90/320 (28%), Positives = 150/320 (46%), Gaps = 46/320 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINALN 75
            +R+D++     P +   ++QK++ +G V V +K VK N +  +     VRIP     + 
Sbjct: 14  GIRIDKFLAEAIPDVTRSHIQKLISTGLVTVGQKAVKANYKTALNDEIAVRIPE--PEIP 71

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
            I  E   LD               +LYED+ I + NKP G+ V    G         + 
Sbjct: 72  DIQPEDIPLD---------------ILYEDNDILIVNKPKGMVVHPAPGHYSNTLVNAVM 116

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH    L S ++    +P + HR+D +T+G L++ +   A Q L E  +   I + Y ++
Sbjct: 117 YHCRDNL-SGINGVA-RPGIVHRIDMDTTGSLIICKNDTAHQALAEQLKEHHITRKYHAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLE 244
           V G  K   + +       + IG   V   K + +      A++H+KV++ F + + ++E
Sbjct: 175 VHGNLKEDSQTV------DAPIGRHPVDRKKMSTRAPHGRQAVTHYKVLERFGE-YTYIE 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGG 303
            +  TGRTHQ+RVH   +G PIVGD  Y     G    P +     LHA+ + + HP  G
Sbjct: 228 CELETGRTHQIRVHMASIGHPIVGDTVY-----GPAKCPFKLQGQTLHAKILGITHPSTG 282

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             ++  APLP + ++  + L
Sbjct: 283 EYMEFDAPLPEYFLELLNKL 302


>gi|282879373|ref|ZP_06288116.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
 gi|281298486|gb|EFA90912.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
          Length = 355

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 91/339 (26%), Positives = 159/339 (46%), Gaps = 52/339 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +E +R+D++      H +   +QK   +G V V+ + VK N +++   V+ +  
Sbjct: 25  IVVDKGQEPLRVDKYMFERLKHSSRNRIQKAADAGFVHVNDQPVKSNYKVRPLDVITLML 84

Query: 70  VINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
                +H I+ + I LD               ++YEDS + V NK  G+ V  G+G    
Sbjct: 85  DAPQHDHTIEAEDIPLD---------------IVYEDSDLMVVNKAPGMVVHPGAGNFHG 129

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                +A+H+     +  D+      L HR+D++TSG+LV+A+T  A   L   F  +  
Sbjct: 130 TLINAVAWHLKDL--TSFDANDPAVGLVHRIDKDTSGLLVIAKTPVAKTKLGLQFFNKTT 187

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVID 234
            + Y +LVWG    ++  I      + +IG D      ++V   + +    A++H+++++
Sbjct: 188 HRSYNALVWGNFNEEEGRI------EGNIGRDPRDRLRMNVFPPDSEIGKSAVTHYRILE 241

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP--------- 283
            F      +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S          
Sbjct: 242 RFGY-VTLVECILETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSTYKAFIQNCF 300

Query: 284 -IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            + N+  LHA+ +   HP  GR +  T+ LP  M +  D
Sbjct: 301 KVCNRQALHAKTLGFVHPTTGRQMDFTSDLPNDMQQLLD 339


>gi|226313367|ref|YP_002773261.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226096315|dbj|BAH44757.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
          Length = 309

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 92/326 (28%), Positives = 160/326 (49%), Gaps = 46/326 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIP 68
            V+  ++N R+D++        +   +Q  ++ G+V V+ + +K N ++Q+   V  R+P
Sbjct: 13  TVDPADKNERIDKFITLQNEDWSRSQVQAWVKEGRVTVNGEPIKNNYKLQAEDEVTLRVP 72

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
           P         KE  I    ++L          ++YEDS + V NKP G+ V    G    
Sbjct: 73  PP--------KEMAIQPEEMSLD---------IVYEDSDVVVVNKPRGLVVHPAPGHYSG 115

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G L    D  G     +P + HR+D++TSG+L+VA+   A   L E  +   + + 
Sbjct: 116 TLVNGLLAHCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDKAHMGLAEQLKAHTVNRK 175

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFA 237
           Y +LV G+  ++   I      ++ IG D      + VV +N K    A++HF V++ F 
Sbjct: 176 YVALVHGVIPHEMGTI------EAPIGRDPKNRQQMAVVFENSKP---AVTHFIVLERF- 225

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +++  +E++  TGRTHQ+RVH  ++  P+ GD KY     G   +   +   LHA+ +  
Sbjct: 226 KEYTMVELKLETGRTHQIRVHMKYIDYPLAGDPKY-----GPKNTLELDGQALHAKTLGF 280

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL 322
            HP  G +L+  AP+P  M+   + L
Sbjct: 281 IHPRTGEQLEFEAPMPKEMLDVIEVL 306


>gi|295109999|emb|CBL23952.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           obeum A2-162]
          Length = 304

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 92/324 (28%), Positives = 154/324 (47%), Gaps = 42/324 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+    N+R+DR+  +  P  +   +QK+L+  QV V+ + +K N + QSG  +      
Sbjct: 8   VDASANNIRIDRYLADQCPEHSRSYIQKLLKEEQVLVNGRVIKANYKTQSGDYIEFHIPD 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
             +  I+ E   LD               +LYED  + V NKP  + V   +G   H  G
Sbjct: 68  PEVPDILPENIPLD---------------ILYEDDYVLVVNKPKDMVVHPSAG---HTSG 109

Query: 132 FLKSWVDSK-GQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            L + V +  G+         +P + HR+D++T+G L++ +     + L E  +   I++
Sbjct: 110 TLVNAVMAHCGEHLSGINGVLRPGIVHRIDKDTTGALLICKDDVVHRDLAEQLKEHSIKR 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G  K + E   N  + +       + +   N K    AI+H+KV++ F Q   
Sbjct: 170 RYRAVVQGNLK-EDEGTVNAPVGRHPTDRKKMAI---NHKNGKEAITHYKVLERFGQA-T 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPH 299
           ++E +  TGRTHQ+RVH   +G P++GD  Y     G+  +P  +Q +  LHA  +   H
Sbjct: 225 YIECRLETGRTHQIRVHMASLGHPLLGDTVY-----GSSKNPYHLQGQA-LHAMILGFVH 278

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G  L+  APLP +  K  + L
Sbjct: 279 PITGEYLEFEAPLPEYFSKLLEKL 302


>gi|300023530|ref|YP_003756141.1| pseudouridine synthase [Hyphomicrobium denitrificans ATCC 51888]
 gi|299525351|gb|ADJ23820.1| pseudouridine synthase, RluA family [Hyphomicrobium denitrificans
           ATCC 51888]
          Length = 344

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 90/335 (26%), Positives = 154/335 (45%), Gaps = 50/335 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           +    ++   RLDRW       ++   +Q ++R G V       +    ++ G   R+  
Sbjct: 13  LTAAAEDAGQRLDRWLAQKIEDLSRARIQALIRDGYVSDGGTIREARTPVKPGITYRVEL 72

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP          E  +   ++ L+         ++YED+ + V +KP G+ V   +G A 
Sbjct: 73  PPA--------SEPDVAGETLPLS---------IVYEDADLIVIDKPTGLVVHPAAGHAS 115

Query: 128 H--IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RM 176
              ++  +    DS       ++P + HRLD++TSG+LVVA+T AA Q L + F    R 
Sbjct: 116 GTLVNALIAHCGDSLSGIGGVKRPGIVHRLDKDTSGLLVVAKTDAAHQGLADQFKSHGRD 175

Query: 177 RRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R+ + Y + VWG +P  K    A   L +S      + VV+  E G   A +H++V+  
Sbjct: 176 GRLFRSYLAFVWGRLPLPKGTISAR--LGRSQANRTKIAVVR-GEAG-RSATTHYEVLQV 231

Query: 236 FAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ----- 285
           F  +        + +   TGRTHQ+RVH  H+G P++GD  Y + F+    S  +     
Sbjct: 232 FPGERSTGDVSLVRLVLETGRTHQIRVHLAHIGHPVLGDAVYGSGFRTRLASLKEAARAA 291

Query: 286 ----NKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
               ++  LHA  ++  HP    +L+ ++ LPA +
Sbjct: 292 ASELSRQALHAETLEFEHPTSLKKLKFSSELPADL 326


>gi|188582089|ref|YP_001925534.1| pseudouridine synthase [Methylobacterium populi BJ001]
 gi|179345587|gb|ACB80999.1| pseudouridine synthase [Methylobacterium populi BJ001]
          Length = 249

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 78/229 (34%), Positives = 116/229 (50%), Gaps = 19/229 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LY D+ + V +KPAG+ V    +GG  +  H+D           ++P   HRLD++TSG
Sbjct: 20  ILYRDALMLVIDKPAGLPVHPGPKGGPTLTDHLDALRFGLP----RRPEAAHRLDRDTSG 75

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R   A   L   F   +  K YW+LV G P   +  I   L K+S     +   +
Sbjct: 76  CLVLGRHARALARLNRLFADGKADKTYWALVEGGPDEAEGRIDLPLAKRSDDPRSWW--M 133

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K +  GA  +++ ++V+   A    WLE++P TGRTHQLRVH   MG PI GD  Y +  
Sbjct: 134 KTDPAGAP-SLTLYRVLG-RADGLSWLELKPVTGRTHQLRVHCAAMGWPIRGDAIYGSAG 191

Query: 277 KGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
           +          L LHAR + LP +P+   +++ AP P HM    ++ G 
Sbjct: 192 RAG------PGLQLHARALSLPLYPKRDAIRVEAPAPMHMRAGLEACGM 234


>gi|323700246|ref|ZP_08112158.1| pseudouridine synthase, RluA family [Desulfovibrio sp. ND132]
 gi|323460178|gb|EGB16043.1| pseudouridine synthase, RluA family [Desulfovibrio desulfuricans
           ND132]
          Length = 305

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 80/289 (27%), Positives = 135/289 (46%), Gaps = 30/289 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M   Q VVV   E   +L ++ +      +    +QK +R+GQVRVDK R K  +R+++G
Sbjct: 1   MPETQSVVVSQAESGQKLLQFLERRLSGEVPRSAIQKWIRTGQVRVDKGRKKPFDRLEAG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP     +  + E   L                + YED+++    KPAG++  GG
Sbjct: 61  QTVRIPPYAPGQDKQVSEAGGL---------------AVAYEDAELLAVAKPAGLAAHGG 105

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            G+   +   L++   +    P L HRLD++TSG+L+ A++ A  + L + F    + K+
Sbjct: 106 DGVDDSVVARLRAMYRNADFMPTLAHRLDRDTSGLLLAAKSYAVLRELNDLFASNGVAKV 165

Query: 183 YWSLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y + V   W  P      + + + K+   G + V            A++    +   ++ 
Sbjct: 166 YLAWVDGRWDEPDGT--LLEDVMEKRGAPGAERVRT-----GSGKTALARVTGL-VSSRD 217

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQ 285
              + ++  TGRTHQ+RV     G  ++GD KY    A  KG+   P++
Sbjct: 218 RSLVAVRLLTGRTHQIRVQLASRGHAVIGDRKYGAPSARGKGSSRGPMR 266


>gi|296133340|ref|YP_003640587.1| pseudouridine synthase, RluA family [Thermincola sp. JR]
 gi|296031918|gb|ADG82686.1| pseudouridine synthase, RluA family [Thermincola potens JR]
          Length = 321

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 84/305 (27%), Positives = 145/305 (47%), Gaps = 35/305 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D +    + H++   +QK++  G + V+  RVK N ++++G++VR+            
Sbjct: 34  RIDVYLAGIFDHLSRSFIQKLIGDGYITVNGTRVKANYKLKAGELVRVE----------- 82

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
               +  +  L   ++ +   +LYED  + V NKP G+ V    G      ++  L    
Sbjct: 83  ----IPYTEELEVSAEPIPLEILYEDRDVIVINKPQGMVVHPAPGNYSGTLVNALLWHCK 138

Query: 138 DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           D  G     +P + HRLD++TSG+++ A+       L +  + R + + Y +L+ G+   
Sbjct: 139 DLSGINGVMRPGIVHRLDKDTSGVIMAAKNDETHASLAKQIKDRTVTRRYLALIHGVIPE 198

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
               I      ++ IG D     K     K +  A++H+KV++ F  K+ ++E +  TGR
Sbjct: 199 PAGII------EAPIGRDPKDRKKMAVTTKNSKPAVTHYKVLERF-NKYTFVECKLETGR 251

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++  P+VGD  Y    K  F    Q    LHA  +   HP  G  L+  AP
Sbjct: 252 THQIRVHMAYLKYPVVGDPVY-GPAKNEFG---QTGQLLHAHILGFHHPRTGEYLEFKAP 307

Query: 311 LPAHM 315
           LP + 
Sbjct: 308 LPEYF 312


>gi|114321699|ref|YP_743382.1| ribosomal large subunit pseudouridine synthase D [Alkalilimnicola
           ehrlichii MLHE-1]
 gi|114228093|gb|ABI57892.1| ribosomal large subunit pseudouridine synthase D [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 313

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 98/331 (29%), Positives = 157/331 (47%), Gaps = 46/331 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++++  +   RLD+      P  +   +Q+ +R G VR++    +  +++ +GQ V I  
Sbjct: 9   ILIDEQQTGQRLDQALAALLPDYSRSRIQQWIREGAVRLEGTAPRPRDKVAAGQQVTI-- 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  + +EQ++    + L          + YED  + V +KPAG+ V  G+G   + 
Sbjct: 67  ----RAELEEEQRVSAEPIPLR---------IQYEDRHLLVIDKPAGLVVHPGAG---NR 110

Query: 130 DGFLKSWV---DSK-GQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +G L++ +   D +  + PR  + HRLD++TSG++VVAR+ AA   L    + R +++ Y
Sbjct: 111 EGTLQNALLHHDPQLAELPRSGIVHRLDKDTSGLMVVARSLAAHTALVAQLQARSVRREY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF--- 240
            +LV G P       A   + +       + VV   E+G   A +H++V +  A      
Sbjct: 171 LALVNGCPVAGGTVEAP--IGRHPRDRKRMAVV---ERG-RPATTHYRVEERLAAHTLLR 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHA 292
           C+LE    TGRTHQ+RVH  H G P+VGD  Y    +     T   +  L       LHA
Sbjct: 225 CFLE----TGRTHQIRVHMAHAGYPLVGDPVYGGRLRLPPRATEAQRQALRAFQRQALHA 280

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
             + L HPE G RL   APLP  M      L
Sbjct: 281 ARLALDHPESGERLSWEAPLPEDMAALLACL 311


>gi|325916249|ref|ZP_08178530.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325537543|gb|EGD09258.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 331

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 92/343 (26%), Positives = 160/343 (46%), Gaps = 40/343 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +V ++    R D      +P  +   L + ++SG   +D +  +  + ++ G+ V+
Sbjct: 13  IRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGEMARPRDTLRGGESVQ 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V+    H   +   L                +LYED ++ V +KPAG+ V  G+G  
Sbjct: 73  LQVVLETQTHAAPQDIPLS---------------VLYEDDQVLVIDKPAGLVVHPGAG-- 115

Query: 127 YHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            + DG L + +     +    PR  + HRLD+ETSG++VVART  A   L E    R + 
Sbjct: 116 -NPDGTLVNALLFRDPALSAVPRAGVVHRLDKETSGVMVVARTVQAQTALVEQLSARDVH 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G   +     AN  + + H        V+ + +    A++H+++ + F +  
Sbjct: 175 RQYLAVVVGALVSG--GTANAPIDR-HPRDRLKMAVRDDGRD---AVTHYRLRERF-RAH 227

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHA 292
             LE +  TGRTHQ+RVH  H+  PIVGD  Y    K     T  + ++L       LHA
Sbjct: 228 TALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDDLVHELRTFKRQALHA 287

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
             ++  HP  G+ ++ TAP+PA + +   +L     R   + R
Sbjct: 288 ETLEFLHPVSGQPVRATAPVPADLQRLMTALREDSARAAELAR 330


>gi|331091117|ref|ZP_08339959.1| hypothetical protein HMPREF9477_00602 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330405339|gb|EGG84875.1| hypothetical protein HMPREF9477_00602 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 307

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 88/330 (26%), Positives = 159/330 (48%), Gaps = 52/330 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++  +E  MR+D +      +++   +QK+++  ++ V+   VK N ++ +  +V++   
Sbjct: 7   IINQEENGMRIDVFLSKKMDNVSRSYIQKLIKEKEISVNGMAVKANYKVSANDIVQL--T 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           I  L+    E  IL  ++ L          +LYED+ I + NKP G+ V        H  
Sbjct: 65  IPDLS----EPDILPENIPLD---------ILYEDADILIVNKPKGMVVHPSPS---HYT 108

Query: 131 GFLKSWV------DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G L + +      D  G     +P + HR+D +T+G L+V +   A Q L E  ++  I+
Sbjct: 109 GTLVNALMYYCKDDLSGINGVMRPGIVHRIDMDTTGSLLVCKNDFAHQKLAEDLKVHNIK 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-----AISHFKVIDC 235
           +IY ++V G+ K  +  +   + +         H + + +   NY     A++H++V+  
Sbjct: 169 RIYHAIVHGVIKEDEGTVEGPIGR---------HPIDRKKMSINYKNGKPAVTHYRVLKR 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHAR 293
           F+  + ++E Q  TGRTHQ+RVH   +   +VGD  Y     G   SP  +Q +  LHA+
Sbjct: 220 FSN-YTYIECQLETGRTHQIRVHMASIHHALVGDTVY-----GPAKSPFHLQGQT-LHAK 272

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            + + HP     L+I APLP +     + L
Sbjct: 273 ILGIHHPRTNEYLEIDAPLPEYFTDLLEKL 302


>gi|282892065|ref|ZP_06300542.1| hypothetical protein pah_c205o103 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498107|gb|EFB40449.1| hypothetical protein pah_c205o103 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 319

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 92/316 (29%), Positives = 147/316 (46%), Gaps = 37/316 (11%)

Query: 11  VVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++  E  +RLD+   + Y  + +    Q ++  G V ++ + VK   +   G  V +  
Sbjct: 13  IIQEMEAGIRLDKVLADRYKSNGSRTYFQMLIEKGLVLLNGEPVKKRFKPNVGDDVELFF 72

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                  +I EQ  L+               +LYED  + + NKP G+ V    G     
Sbjct: 73  AAAPEIDLIPEQIPLN---------------ILYEDEHLLIINKPVGMVVHPAPGNWTGT 117

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH  G+  S       +P + HRLD+ETSG+LV A+T +  Q L E F  R++ 
Sbjct: 118 FVNALLYHC-GYSLSDASVDSIRPGIVHRLDKETSGVLVAAKTLSVQQKLMELFAARQVY 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW++  G P N   C  NW + +  I    +  V+++ K A       +V      + 
Sbjct: 177 KEYWAICLGNPGN---CELNWPIGRHPIHRKQM-TVREDGKEALTFCETLEV----GNEI 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           C  ++   TGRTHQ+RVH  H G PI+GD  Y +  + N     + ++ LHAR +   HP
Sbjct: 229 CLAKLILSTGRTHQIRVHLKHKGHPILGDSIYGSK-QVNMRYRAERQM-LHARKLAFIHP 286

Query: 301 -EGGRLQITAPLPAHM 315
               ++++ APLPA M
Sbjct: 287 ITQQKIEVEAPLPADM 302


>gi|289450514|ref|YP_003475442.1| putative rRNA pseudouridylate synthase C [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
 gi|289185061|gb|ADC91486.1| putative rRNA pseudouridylate synthase C [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
          Length = 327

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 81/292 (27%), Positives = 136/292 (46%), Gaps = 28/292 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ N++   ++ R     YP +     QK LR+  + +D KR+K +   ++GQ +RI   
Sbjct: 5   IINNEQSGKKVVRILTTLYPTVPAYIFQKALRNKDLMLDGKRLKNDVTAEAGQTLRI--- 61

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                  +K++ +  +S N  + +      ++YED  I + NKP G++V  G     H  
Sbjct: 62  ------YVKDEVLAQASDNTDRKNQLPSYTVVYEDKNIILINKPQGLTVHPGKNTPPHST 115

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              K   D   +   L HRLD+ T G+++VA+ +     + E+   +++ K Y  LV GI
Sbjct: 116 LIEKLRADYNDENLTLCHRLDRNTGGLVLVAKNKVTLGKINEALAEQQVIKRYRCLVRGI 175

Query: 191 P-----------KNKKECIANWLLKKSHIGGDYVHVVKQNEK---GANYAISH-FKVIDC 235
           P            +  E  A W  K ++    ++H  +Q +       Y + H F  +  
Sbjct: 176 PDIGRDVYISDGDSMHELNAFW-EKPANSDEVFIHDEQQADDLPICTRYRVLHIFTALAA 234

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
             +    LE++  TGRTHQ+R H  H+G PI+GD KY  N    F S  +NK
Sbjct: 235 DGEPISELEVELVTGRTHQIRAHLAHIGHPILGDGKYGRN---EFNSQFKNK 283


>gi|225027663|ref|ZP_03716855.1| hypothetical protein EUBHAL_01922 [Eubacterium hallii DSM 3353]
 gi|224954977|gb|EEG36186.1| hypothetical protein EUBHAL_01922 [Eubacterium hallii DSM 3353]
          Length = 319

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 86/322 (26%), Positives = 150/322 (46%), Gaps = 36/322 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVR 66
           Y  V  ++E MRLD++        +   +QK+++ G+V V  K+ K   R  ++   V+ 
Sbjct: 21  YYTVMEEQEGMRLDQFLAGELKEHSRSYIQKLIKEGRVTVGDKKEKPGCRLKVEDNVVIC 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +PP        +KE ++L   ++L          ++YED  + + NKP  + V    G  
Sbjct: 81  VPP--------LKELEVLPEKMDLD---------IIYEDEDVILINKPKDMVVHPCPGRY 123

Query: 125 IAYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++G L    D+        +P + HR+D++T+G+LVV +   A + L E  +   I
Sbjct: 124 TGTLVNGLLYHCRDNLSGINGVLRPGIVHRIDKDTTGVLVVCKNDMAHKSLAEQLKEHSI 183

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V+     ++E   +  + +S      + V  +N K    A++H+KV+     +
Sbjct: 184 TRKYEAIVYN-NFTQEEGTVDAPIGRSPADRKKMAVEPKNGK---RAVTHYKVLSHLNHQ 239

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           F  +E Q  TGRTHQ+RVH   +  P++GD  Y        T        LHAR +   H
Sbjct: 240 FNHIECQLETGRTHQIRVHMASIRHPLLGDTTYGPKNAMGLTGQC-----LHARVLGFIH 294

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  ++  APLP +  K  +
Sbjct: 295 PRTGEYVEFEAPLPEYFQKLLE 316


>gi|126327383|ref|XP_001372198.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4, [Monodelphis domestica]
          Length = 364

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 90/314 (28%), Positives = 148/314 (47%), Gaps = 41/314 (13%)

Query: 51  KRVKFNNRIQSGQVVRIP--PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKI 108
           ++++   + Q  +   +P  PV   ++ +I+  K L + V+    S  LK  +L++D  +
Sbjct: 48  EKLRTEKQEQKAKEKEVPRDPVQRRVHELIRYTKQLQN-VHPNVLSKALKRGILHQDKDL 106

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
            V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G++++AR +
Sbjct: 107 IVINKPYGLPVHGGPGVKSCITDILPILAKMLFGHKAEPLHLCHRLDKETTGVMILARDK 166

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------- 214
             A  + E F+ R++ K YW++  G+P      I   +++K   G    H          
Sbjct: 167 EMAHQVQELFKTRQVTKKYWAICVGVPMPSAGMIDIPIIEKEVQGQQQHHKMTLAPNYRL 226

Query: 215 -----VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVG 268
                V  +  + A+ A++ ++V+         LE+QP TG  HQLRVH A  +GCP++G
Sbjct: 227 ENGKTVKVRPNRHAHIAVTQYRVLSS-TLTCALLELQPVTGVKHQLRVHLAFGLGCPVLG 285

Query: 269 DHKYCANFK---GNFTSPIQNK------------LYLHARYMDLPH--PEGGRLQITAPL 311
           DHKY    K      +  I  K            L+LHA+ + LP   PE   L +   L
Sbjct: 286 DHKYSDWNKLAPQKLSVGILKKLGLEQAKTRYLPLHLHAQQLTLPPLGPESEELNLVCKL 345

Query: 312 PAHMVKTWDSLGFK 325
           P + + +   LG +
Sbjct: 346 PRYFLHSLLRLGLE 359


>gi|229541180|ref|ZP_04430240.1| pseudouridine synthase, RluA family [Bacillus coagulans 36D1]
 gi|229325600|gb|EEN91275.1| pseudouridine synthase, RluA family [Bacillus coagulans 36D1]
          Length = 303

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 97/330 (29%), Positives = 154/330 (46%), Gaps = 47/330 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  + + ++E+ E N RLD+   +     +   +Q+ ++ G + V+ K+ K N R+Q+G 
Sbjct: 1   MEKMDHTILEH-EANERLDKMVSSIREEWSRSQVQQWIKDGDITVNGKKEKANYRLQTGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V I      L  I  E   LD               + YED+ + V NKP G+ V   +
Sbjct: 60  LVEIEVPEPELPDIEPEDLHLD---------------IYYEDADVLVVNKPKGMVVHPSN 104

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHFTGTLVNGLMYHCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDYAHEKLAAQLSEK 164

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVH----VVKQNEKGANYAISHFKV 232
            + + Y++LV G IP       A        IG D        V  N K A   ++HF V
Sbjct: 165 TVTRKYFALVHGNIPHEAGTIDAP-------IGRDPADRQRMAVVDNGKDA---VTHFHV 214

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++ F  ++ ++E +  TGRTHQ+RVH  ++G P+ GD KY      +F         LHA
Sbjct: 215 LERF-DRYTFIECRLETGRTHQIRVHMKYIGHPLAGDPKYGPKKTIDFGGQA-----LHA 268

Query: 293 RYMDLPHPEGGR-LQITAPLP---AHMVKT 318
             +   HP  G  L   APLP   AH++ T
Sbjct: 269 GVLGFCHPRTGETLTFEAPLPDDFAHLLNT 298


>gi|326799397|ref|YP_004317216.1| pseudouridine synthase [Sphingobacterium sp. 21]
 gi|326550161|gb|ADZ78546.1| pseudouridine synthase [Sphingobacterium sp. 21]
          Length = 232

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 115/226 (50%), Gaps = 14/226 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGI 157
           +LYED  +   NKP+G  V+  +     ++  L +++  K  K    R  HRLD+  SG+
Sbjct: 11  ILYEDEHLVAINKPSGYLVEASAKEKRALEEMLSAYLSEKHHKDIQTRAVHRLDRRVSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A+T  A + +   F+ R ++K YW++V   P    + + +WL +       Y H   
Sbjct: 71  LLFAKTTVALEGMIALFKARLVEKTYWAIVANPPLVPSDKLVHWLTRDKEQNISYTH--N 128

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           + +  +  A   +++++  A  F  +E+ P TGRTHQ+R     +GCPIVGD+KY     
Sbjct: 129 EPQPHSVKAELAYRLLEK-ADDFFLIEVYPFTGRTHQIRAQLAAIGCPIVGDYKY----- 182

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           G      +  + LHA+ +  PHP   R + + AP+P    + W+S 
Sbjct: 183 GFPREKPRRAIALHAKQLRFPHPIDHRSVYLEAPIPD--AQLWNSF 226


>gi|153853142|ref|ZP_01994551.1| hypothetical protein DORLON_00536 [Dorea longicatena DSM 13814]
 gi|149753928|gb|EDM63859.1| hypothetical protein DORLON_00536 [Dorea longicatena DSM 13814]
          Length = 272

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 91/304 (29%), Positives = 144/304 (47%), Gaps = 46/304 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           ++ G V+V++K VK N R+  G  V +         I+ E   LD               
Sbjct: 1   MKEGYVKVNQKPVKSNYRLSFGDSVEVTLPEAKEPDIVPENIPLD--------------- 45

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  I + NKP  + V    G         + YH    L     +   +P + HR+D
Sbjct: 46  ILYEDQDIIMINKPKQMVVHPAPGHYSGTLVNALMYHCGDELSGI--NGCMRPGIVHRID 103

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +T+G LVV +   A Q L+E  ++  I++IY ++V G   N KE              D
Sbjct: 104 MDTTGSLVVCKNDKAHQSLSEQLKVHSIRRIYVAIVHG---NIKEDSGTVNAPIGRHPTD 160

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              +    + G + A++H+KV++ F   + +++ +  TGRTHQ+RVH   +G P+VGD  
Sbjct: 161 RKKMSTHCKNGRD-AVTHYKVLERFGD-YTYIQCELETGRTHQIRVHMASIGHPLVGDEV 218

Query: 272 YCAN---FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           Y      FKG     +Q +  LHAR + + HP  G+ L++ APLP + ++  D L     
Sbjct: 219 YGPKKCPFKG-----LQGQT-LHARTLGIIHPTTGKYLEVNAPLPEYFIELLDRL----- 267

Query: 328 RNLY 331
           RN+Y
Sbjct: 268 RNIY 271


>gi|110597884|ref|ZP_01386166.1| Pseudouridine synthase, RluD [Chlorobium ferrooxidans DSM 13031]
 gi|110340461|gb|EAT58947.1| Pseudouridine synthase, RluD [Chlorobium ferrooxidans DSM 13031]
          Length = 349

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 89/319 (27%), Positives = 137/319 (42%), Gaps = 41/319 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++      +     +Q+ +  G+V V++KRVK N RI+S   ++I  +      + 
Sbjct: 34  MRIDQYLTRQVENATRNKVQEAIEEGRVLVNEKRVKSNYRIKSCDTIQITFLRPPAPELA 93

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E   +D               ++YED  + V NK  G+ V    G         I +HI
Sbjct: 94  PEDIPID---------------IIYEDEDLMVINKKPGMVVHPAFGNWTGTLANAILHHI 138

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G     +D    +P + HRLD+ TSG+++VA+   A   L   F  R++ KIY ++VWG
Sbjct: 139 -GIGAEELDKSSLRPGIVHRLDKNTSGLIIVAKNPVALHRLARQFADRQVVKIYKAIVWG 197

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +P  +   I    + +S      +       K    AI+ + V +     F  L +  HT
Sbjct: 198 VPAEQSGTITTN-IGRSKKDRKVMANFPYEGKDGKTAITDYSVTENL-HWFSLLSLTLHT 255

Query: 250 GRTHQLRVHALHMGCPIVGDHKY------------CANFKGNFTSPIQNKLYLHARYMDL 297
           GRTHQ+R H  H+G  I+GD  Y               F  N    +  +  LHA  +  
Sbjct: 256 GRTHQIRAHMQHLGHQILGDETYGGAVLRTLPFSRSEGFVRNLLE-LLPRQALHAATLSF 314

Query: 298 PHPEGGR-LQITAPLPAHM 315
             P     L  TAPLP  M
Sbjct: 315 HQPTTREPLSFTAPLPEDM 333


>gi|319950238|ref|ZP_08024165.1| pseudouridine synthase, RluA family protein [Dietzia cinnamea P4]
 gi|319436142|gb|EFV91335.1| pseudouridine synthase, RluA family protein [Dietzia cinnamea P4]
          Length = 297

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 88/281 (31%), Positives = 138/281 (49%), Gaps = 23/281 (8%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           L K+LR G++RV+ +R + N R+  G V+ +P    A+        +      L    D 
Sbjct: 6   LFKLLRQGRLRVNGRRAEQNYRLAEGDVIDLP----AMQAGAPATTVTRPPTALL---DR 58

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETS 155
           +   +LYEDS + V +KPAG++V  GS +   +   L+    D  G +  L HRLD++TS
Sbjct: 59  MAKTVLYEDSNLLVVDKPAGVAVHRGSDMPAGVIETLRFLCPDLPGLE--LGHRLDRDTS 116

Query: 156 GILVVARTRAAAQHLTESFRMRR--IQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDY 212
           G+LV+ +T    +HL E  R R   I++ Y ++V G  P N     A    + + +    
Sbjct: 117 GVLVLTKTPPMLRHLHEMLRDREKEIERHYLAIVAGQWPANLGVLEAPLRRRDADV---- 172

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             VV         A +H +V          ++++  TGR HQ+RVH  H G PI GD +Y
Sbjct: 173 --VVDPR---GQRAETHVRVRRRVGDWATLVDVRLFTGRKHQIRVHLQHAGHPIAGDDRY 227

Query: 273 C-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
               F     S   + L+LHA  M +P P+G  + ++AP+P
Sbjct: 228 GDPRFDSVVASRGGSGLHLHAARMVIPLPDGRDVVVSAPMP 268


>gi|78044742|ref|YP_360337.1| ribosomal large subunit pseudouridine synthase A [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77996857|gb|ABB15756.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Carboxydothermus hydrogenoformans Z-2901]
          Length = 305

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 93/321 (28%), Positives = 152/321 (47%), Gaps = 52/321 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           VVV ++   +RLD++        ++   ++K++  G+V V+    K + +++ G+++ + 
Sbjct: 7   VVVNSEYSGLRLDKFLAEQEELELSRSFIKKLIEEGKVTVNGLHRKASYKVRGGEIIAV- 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
                         +L     L+   + +   ++YED  + V NK AG+ V    G    
Sbjct: 66  --------------LLPPPRELSVKPEEIPLDIVYEDEDLVVVNKKAGMVVHPAEGNWDG 111

Query: 125 -----IAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                + YH      I G L+         P + HRLD++TSG+LVVA+   A Q L E 
Sbjct: 112 TLVNALLYHCQNLSGIGGVLR---------PGIVHRLDKDTSGLLVVAKNDLAHQSLAEQ 162

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + ++  + YW++V G  KNK+  I   L    H        V  N K A      +KV+
Sbjct: 163 IKEKKAVREYWTIVHGYLKNKEGIID--LPIGRHPRDRQKMAVVSNGKTAQTV---YKVL 217

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-YLHA 292
           + F + F  ++ +  TGRTHQ+RVH  ++G P++GD KY     G+  +P   K   LHA
Sbjct: 218 EEFNKGFTLIQAKLLTGRTHQIRVHFSYLGHPVLGDPKY-----GHQNNPFGVKRQMLHA 272

Query: 293 RYMDLPHPEGGR-LQITAPLP 312
             +   HP  G  L+ TAPLP
Sbjct: 273 IKLSFIHPRSGELLEFTAPLP 293


>gi|323486916|ref|ZP_08092232.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323399779|gb|EGA92161.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 305

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 89/332 (26%), Positives = 156/332 (46%), Gaps = 51/332 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV-- 65
           +Y+V E     +R+D++     P      LQK+L+S  V V+ K VK + +  +G  V  
Sbjct: 4   EYIVPEKSS-GLRIDKFLTESCPDYTRSFLQKLLKSELVEVNGKPVKSSYKTAAGDTVTF 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +P  + A   I  ++  LD               +LYED  + + NKP G+ V   +G 
Sbjct: 63  EVPEAVEA--EITAQEMPLD---------------ILYEDEDVILINKPKGMVVHPAAG- 104

Query: 126 AYHIDGFLKSWVD----------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             H +G L + +           +   +P + HR+D +T+G+L+V +   A   + E  +
Sbjct: 105 --HYEGTLVNGLMHHCREQLSGINGVMRPGIVHRIDMDTTGVLIVCKNDLAHNSIAEQLK 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKV 232
           +  I + Y+++V+G  K+ +  I   +       G + +  K+   N K    A++H+KV
Sbjct: 163 VHSITRKYYAVVFGSLKDDEGTIHAPI-------GRHPNDRKKMSINSKNGKDAVTHYKV 215

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLH 291
           ++ F   +  +E +  TGRTHQ+RVH   +G P++GD  Y     G    P +     LH
Sbjct: 216 LERF-HGYTLVECRLETGRTHQIRVHMASIGHPLLGDQVY-----GPAKQPFRLQGQTLH 269

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           A  +   HP  G  ++ +APLP +  +  + L
Sbjct: 270 AGVLGFLHPRTGEYMEFSAPLPKYFEELLEKL 301


>gi|315224831|ref|ZP_07866652.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           ochracea F0287]
 gi|314945234|gb|EFS97262.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           ochracea F0287]
          Length = 352

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 86/322 (26%), Positives = 153/322 (47%), Gaps = 43/322 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  N   +     +Q+  + G + V+ + VK N+R+++   V++        
Sbjct: 35  QEPLRVDKFLMNFVENATRNKVQQAAKQGNIFVNGEPVKSNHRVKANDEVKV-----LFP 89

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           H   E  ++  ++ L          ++YED  + V NKPAGI V  G G         + 
Sbjct: 90  HPPHEDLLVPENIPLN---------IVYEDDSLLVVNKPAGIVVHPGHGNYSGTLINALV 140

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH +    +  ++   +P L HR+D++TSG+LVVA+T  A  HLT+ F  +  Q+ Y +L
Sbjct: 141 YHFE----NLPNNSSNRPGLVHRIDKDTSGLLVVAKTEEAMLHLTQQFFNKTTQREYIAL 196

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           VWG  +  +  +   + +  H+       V  +      A++H+KV++ F      +  +
Sbjct: 197 VWGNIEEDEGTVCGHIGR--HLKDRLQMDVFPDGSHGKEAVTHYKVLERFGY-VTLISCK 253

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN------KLYLHARY 294
             TGRTHQ+RVH  H+G  +  D +Y  +   KG     +   ++N      +  LHA+ 
Sbjct: 254 LETGRTHQIRVHLKHIGHTLFNDERYGGDKILKGTTFAKYKQFVENCFAVLPRQALHAKT 313

Query: 295 MDLPHPEGGR-LQITAPLPAHM 315
           +   HP   + L   + LP  M
Sbjct: 314 LGFEHPITHKYLSFDSELPNDM 335


>gi|325570254|ref|ZP_08146120.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           casseliflavus ATCC 12755]
 gi|325156737|gb|EGC68911.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           casseliflavus ATCC 12755]
          Length = 302

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 88/322 (27%), Positives = 156/322 (48%), Gaps = 49/322 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIP-PVIN 72
           EE  R+D+      P  +   +Q+ L+   V ++ + V+ N ++++G   V+++P P + 
Sbjct: 11  EEKGRVDKVLAERLPDHSRSQVQQWLKEDAVTLEGETVRANYKVKAGDHLVIQVPEPEVV 70

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-------- 124
            L            ++ LT         ++Y+D+ + V NKP G+ V   +G        
Sbjct: 71  GLE---------PENIPLT---------IVYQDADVAVINKPQGMVVHPSAGHPNGTLVN 112

Query: 125 -IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + YH+D    S ++    +P + HR+D++TSG+L++A+   A + L +  + +   + Y
Sbjct: 113 ALLYHMDDL--STINDV-VRPGIVHRIDKDTSGLLMIAKNDQAHESLAKQLKDKTSLRKY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G   ++K  I N  + +S +      V++  +     A++HF V++ F Q F  +
Sbjct: 170 VALVHGNISHEKGTI-NAPIGRSKVNRKMQAVIENGKP----AVTHFTVLERFDQ-FTLV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E+Q  TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP 
Sbjct: 224 ELQLETGRTHQIRVHMQYIGFPLAGDPIYGPKRTLKGNGQ-------FLHAKLLGFAHPA 276

Query: 302 GGRLQI-TAPLPAHMVKTWDSL 322
            G   +  APLP     T   L
Sbjct: 277 TGESMVFEAPLPELFADTLKKL 298


>gi|325108531|ref|YP_004269599.1| pseudouridine synthase [Planctomyces brasiliensis DSM 5305]
 gi|324968799|gb|ADY59577.1| pseudouridine synthase, RluA family [Planctomyces brasiliensis DSM
           5305]
          Length = 336

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 86/337 (25%), Positives = 163/337 (48%), Gaps = 38/337 (11%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V++ V+  +E ++RLD W  +H    +    QK +++G++RV+ ++VK + R++ G+ 
Sbjct: 12  TQVEHEVL-AEEVDLRLDAWLSSHSAGHSRSQWQKAIQAGEIRVNGQKVKPSYRLRIGE- 69

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
                         K    L            +   +LY+D  + V NKPA + V  G  
Sbjct: 70  --------------KISGQLKVVAAPVVAPAPIALDILYQDEHLVVVNKPAHLIVHPGKA 115

Query: 125 -----IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                +A  +        ++ G+ +P + HRLD++TSG++V+A      ++L+  F  R 
Sbjct: 116 NYGGTLANALVHHFNQLSETGGEHRPGIVHRLDRDTSGVIVIALNNRVHENLSAQFADRT 175

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y ++VWG  +   + I   +  ++H       +V   +  A  A + ++ ++ F +
Sbjct: 176 VEKEYRAIVWGKVEFDADIIETHV--RTHSKHREKMIVCGPDPEARQATTFYETLERF-R 232

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY--------- 289
            F +L++ P TGRTHQLRVH  ++  PIV D  Y  + +   +  +++K +         
Sbjct: 233 GFSYLKLLPKTGRTHQLRVHLQYLRHPIVADRLYGGHPQLALSELLESKEHMTEDRVLIE 292

Query: 290 ---LHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
              LHA  +   HP    R++  +P+P  M +T D++
Sbjct: 293 RQALHAHRLQFTHPVTEERVEFISPIPDDMQRTLDAM 329


>gi|237740738|ref|ZP_04571219.1| tRNA pseudouridine synthase A [Fusobacterium sp. 2_1_31]
 gi|229422755|gb|EEO37802.1| tRNA pseudouridine synthase A [Fusobacterium sp. 2_1_31]
          Length = 295

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 81/315 (25%), Positives = 161/315 (51%), Gaps = 32/315 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV--VRIP 68
           +++ + E +R+DR+ + H  +I    + K+LR  +++V+ K+V  + R+  G +  V +P
Sbjct: 5   IIDEEYETVRIDRFLRKHLKNIALSEIYKMLRKAKIKVNNKKVSQDYRLVLGDIIFVFLP 64

Query: 69  PVINALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                      E+K  ++ + L +   + LKS++ YE+  +++ NK  G  +  GSG   
Sbjct: 65  ESF--------EEKNEETFIELNEIRKEELKSMIAYENENLFIINKNLGDVIHKGSGHDI 116

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +    +S+  +   K    +R+D+ TSG+++ A+    A+ + +  ++  I K Y+ LV
Sbjct: 117 SLLEEFRSYYSN--NKINFVNRIDKLTSGLVIGAKNIKTAREIAKEIQLGNILKKYYILV 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQKFCWLEM 245
           +G  + ++  + N+L K      D   V+  + +  +Y  +I+H+K I+     +  LE 
Sbjct: 175 YGKIEKEEFILENYLKK------DEEKVIVSDVEKEDYKKSITHYKRING-DNDYTLLEA 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +  TGRTHQLR    H+G  IVGD KY  N K       ++ +YL + Y+ +   +   L
Sbjct: 228 ELKTGRTHQLRAQLNHLGHTIVGDTKYGKNIK-------EDIMYLFSYYLKIDLYD---L 277

Query: 306 QITAPLPAHMVKTWD 320
           ++   +P   +K ++
Sbjct: 278 ELELRIPNFFLKKYN 292


>gi|194336853|ref|YP_002018647.1| pseudouridine synthase, RluA family [Pelodictyon
           phaeoclathratiforme BU-1]
 gi|194309330|gb|ACF44030.1| pseudouridine synthase, RluA family [Pelodictyon
           phaeoclathratiforme BU-1]
          Length = 349

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 92/329 (27%), Positives = 146/329 (44%), Gaps = 47/329 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI----PPVINAL 74
           MR+D++      +     +Q+ +  G+V V++ RVK N RI+S  V+ +    PP     
Sbjct: 34  MRIDQYLTQQVENATRNKVQEAIEEGRVLVNENRVKSNYRIKSCDVIEMTFLRPP----- 88

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                       +  LT  +  ++  ++YED  + V NK AG+ V    G         I
Sbjct: 89  ------------APELTAENIPIE--IIYEDCDLMVVNKKAGMVVHPAFGNWTGTLANAI 134

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +HI G     +D    +P + HRLD+ TSG+++VA+   A   L   F  R++ K+Y +
Sbjct: 135 LHHI-GMDAEELDQAELRPGIVHRLDKNTSGLIIVAKNPIALHRLARQFAERKVIKVYKA 193

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +VWG+P      I   + +         +   + E G   AI+ + V++   Q F  L +
Sbjct: 194 IVWGVPDPAAGTITTNIGRSKKDRKVMANFPFEGEYGKT-AITDYSVMENL-QWFSLLSL 251

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----SPIQNKL------YLHARY 294
           + HTGRTHQ+R H  H+G  I+GD  Y              S ++N L       LHA  
Sbjct: 252 RLHTGRTHQIRAHLQHLGHQILGDVTYGGTILRTLPFSKSESFVKNLLELLPRQALHAET 311

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +    P     L  TAP+P  M    D +
Sbjct: 312 LSFHQPISHEPLSFTAPMPEDMQHALDKI 340


>gi|320333612|ref|YP_004170323.1| RluA family pseudouridine synthase [Deinococcus maricopensis DSM
           21211]
 gi|319754901|gb|ADV66658.1| pseudouridine synthase, RluA family [Deinococcus maricopensis DSM
           21211]
          Length = 323

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 87/306 (28%), Positives = 138/306 (45%), Gaps = 58/306 (18%)

Query: 43  SGQVRVDKK-RVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +G+VRV+ +   K + +++ G+  +V +PP +  L H+  E   LD              
Sbjct: 37  AGRVRVNGQVTTKSSLKLRGGETLIVDVPPPV--LAHVEPENVPLD-------------- 80

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWV--------DSKGQKPRLTHR 149
            +LYED  +   NKP G++     G+     ++  L               G +P + HR
Sbjct: 81  -VLYEDDALIAINKPPGMTTHPAPGVTTGTLVNALLGRMPLPEQDGARGPDGYRPGIVHR 139

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK---- 205
           LD++TSG++VVA+T  A   L ++F+ R  +K Y +L  G          +W  +K    
Sbjct: 140 LDKDTSGVIVVAKTVEAHAKLADAFKARETRKTYLALAGG----------SWSAQKPLNI 189

Query: 206 -SHIGGDYVHVVKQNEKGANYAISHFKVIDCFA------QKFCWLEMQPHTGRTHQLRVH 258
            + IG   V   +    G N   +  + +   A      Q    +  +P TGRTHQLRVH
Sbjct: 190 DAPIGRHPVDRQRMTVGGVNPREAQTRFVPLAAHPNGRGQTLALVRCEPRTGRTHQLRVH 249

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
             H G PI+GD  Y         S +  +  LHA  + +PHP  G  L + AP+P  M++
Sbjct: 250 LQHAGSPILGDAVY------GRASDVMPRQALHAWALVIPHPTTGEPLHLHAPVPDDMLQ 303

Query: 318 TWDSLG 323
            W + G
Sbjct: 304 AWVAFG 309


>gi|167630173|ref|YP_001680672.1| pseudouridine synthase, rlua family [Heliobacterium modesticaldum
           Ice1]
 gi|167592913|gb|ABZ84661.1| pseudouridine synthase, rlua family [Heliobacterium modesticaldum
           Ice1]
          Length = 369

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 95/322 (29%), Positives = 148/322 (45%), Gaps = 52/322 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V   E + R+D W        +  + Q  ++ G V +D   +K N R++ G V+ + P
Sbjct: 38  LTVTPAEADSRVDVWLVQKGLVPSRSHGQNWIKEGLVTLDGGPLKANYRLRPGDVIEVAP 97

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                  I+ E   L+               ++++D+ I V NKPAG+ V    G     
Sbjct: 98  PAPEAVEILPEDIPLE---------------IIFQDADIAVINKPAGLVVHPAEGHWSGT 142

Query: 125 ----IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + YHI    K      G+ +P + HR+D++TSG+LVVA+   A  HLTE  +  R+
Sbjct: 143 LVNALLYHI----KDLSGINGELRPGIVHRIDKDTSGLLVVAKNDRAHIHLTEQVKDHRV 198

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVID 234
           ++ Y ++V G+   +   +      ++ IG D     K  ++     G   AI+HF+V+ 
Sbjct: 199 RREYLAVVHGVIGAETGRV------EAPIGRDP----KDRQRMAVIAGGKSAITHFRVLA 248

Query: 235 CFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
            +  Q F  L  +  TGRTHQ+RVH  H+G P+ GD KY    K  F    Q    LHA 
Sbjct: 249 RYPEQGFSLLHCRLETGRTHQIRVHLAHIGHPVAGDPKYGPR-KAAFGLTGQ---ALHAW 304

Query: 294 YMDLPHPEGG---RLQITAPLP 312
            ++  HP  G   R Q   P P
Sbjct: 305 KLEFVHPRSGEPMRFQADPPEP 326


>gi|320160390|ref|YP_004173614.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
 gi|319994243|dbj|BAJ63014.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
          Length = 310

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 96/329 (29%), Positives = 157/329 (47%), Gaps = 45/329 (13%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV-- 65
           +V      +  RLD++   H+P ++   +Q ++R G VRV  K V K    +++G+ V  
Sbjct: 6   FVFTCEPHQEGRLDKFLVAHFPELSRSQIQGLIRDGFVRVSGKTVQKTGFLVEAGKEVEI 65

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           RIPP                   +L      L+ I  +E+  + + NKPAG+ V   +G 
Sbjct: 66  RIPP---------------PQPTSLEPEPIPLEVI--FENQDLLLVNKPAGMVVHPSAGH 108

Query: 125 -IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                +   L    + +G    ++P + HRLD++TSG++++A+   A + L + FR+R++
Sbjct: 109 DRGTLVHAALAHIPELEGIHGEERPGVVHRLDKDTSGLILLAKNDRAHRWLQDQFRLRKV 168

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH----VVKQNEKGANYAISHFKVIDC 235
           QK Y +LV G P      I      ++ IG D  +     V   EKG   A+S +   + 
Sbjct: 169 QKTYLALVDGRPPTPTGRI------EAPIGRDPKNRQRMAVVPPEKGRE-AVSEYFTREV 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARY 294
           F      LE+ P TGRTHQ+RVH   +GCP+ GD  Y     G+  + +  N+ +LHA  
Sbjct: 222 FP-SHTLLEVHPLTGRTHQIRVHLAFIGCPVAGDLIY-----GHKHATVSLNRHFLHAYR 275

Query: 295 MDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           + +  P E       APLP+ + +    L
Sbjct: 276 LTIQLPGESSPRTFEAPLPSELEQVLQVL 304


>gi|260438385|ref|ZP_05792201.1| ribosomal large subunit pseudouridine synthase D [Butyrivibrio
           crossotus DSM 2876]
 gi|292808971|gb|EFF68176.1| ribosomal large subunit pseudouridine synthase D [Butyrivibrio
           crossotus DSM 2876]
          Length = 316

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 85/302 (28%), Positives = 147/302 (48%), Gaps = 48/302 (15%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSD 95
           +QK++ +G V V+ K  K   +I    ++++  P +  +N I+ E   LD          
Sbjct: 43  IQKLIEAGNVCVNDKNTKTGYKISYNDLIKVMIPYLEDIN-IVAENIPLD---------- 91

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRL 146
                ++YED  I + NKP G+ V   +G         + YH    L     +   +P +
Sbjct: 92  -----IVYEDDDIILVNKPKGMVVHPSAGHYTGTLVNALMYHCSNNLSGI--NGVMRPGI 144

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HR+D++T+GI+V  +  AA   L+E  +   I + Y+++     K K+  +       +
Sbjct: 145 VHRIDKDTTGIIVACKNDAAHISLSEQLKEHNITRYYYAICHNCFKEKEGTV------DA 198

Query: 207 HIGGDYVHVVKQNEKGANY-----AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            IG    H V++ +   NY     A++H++V++ F + F +++ +  TGRTHQ+RVH   
Sbjct: 199 PIGR---HPVERKKMAINYKNGKKAVTHYEVLENF-RNFAYIKCKLETGRTHQIRVHMAS 254

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           +  P++GD+ YC N K  F    Q    LHA  +   HP  G+ ++ +APLP +  K  D
Sbjct: 255 ISHPLLGDNVYC-NAKCPFELEGQT---LHAGVLGFIHPRTGKYMEFSAPLPEYFEKILD 310

Query: 321 SL 322
            L
Sbjct: 311 IL 312


>gi|157363878|ref|YP_001470645.1| RluA family pseudouridine synthase [Thermotoga lettingae TMO]
 gi|157314482|gb|ABV33581.1| pseudouridine synthase, RluA family [Thermotoga lettingae TMO]
          Length = 298

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 103/329 (31%), Positives = 156/329 (47%), Gaps = 59/329 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           + VE  E N+RLD +     P  I+   +Q+ ++ G+V V+    K N R++ G VV+I 
Sbjct: 1   MTVEKSEVNLRLDLFLLQRIPKAISRSFVQRAIKEGKVTVNDVIRKPNYRVKFGDVVKIS 60

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
              NA +  I+ + I              +  ++YED  I V NKPAG+ V     I  H
Sbjct: 61  IPSNAQSISIEPEPI--------------QIGVIYEDEDIIVVNKPAGMIVHP---IPSH 103

Query: 129 IDGFLKSWV-----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             G L + +     D KG     +P + HRLD++TSG++VVA+   A  +L+  F+ R++
Sbjct: 104 NSGTLVNALLYHCKDLKGIGGELRPGIVHRLDKDTSGVMVVAKNDFAHHNLSNQFKDRKV 163

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV-----HVVKQNEKGAN----YAISHF 230
            K+Y +LV G              K  H+ GD       H V + +  A+     A++H+
Sbjct: 164 FKMYLALVSG--------------KVEHLEGDIQISIARHPVLRTKMAASEIGRIAVTHY 209

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           KVI  F      +   P TGRTHQ+RVH   +  PI+GD  Y    KG+  S    +  L
Sbjct: 210 KVIKYFEHATLLMAF-PKTGRTHQIRVHMKCINHPILGDKLYG---KGSGAS----RQML 261

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           HA  +   HP     ++  APLP    +T
Sbjct: 262 HATKLGFYHPRTHEWIEFIAPLPEDFKET 290


>gi|237737691|ref|ZP_04568172.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           mortiferum ATCC 9817]
 gi|229419571|gb|EEO34618.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           mortiferum ATCC 9817]
          Length = 318

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 96/323 (29%), Positives = 156/323 (48%), Gaps = 41/323 (12%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVI 71
           END+   R+D++            +QKI+ +G V +  K++ K  N+++  +++    V+
Sbjct: 13  ENDK-GKRIDKFLNELIDDATRSYVQKIIDNGLVEIQGKKITKSGNKLKGTEII----VV 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------- 124
           N     I E ++LD    LT     L   ++YEDS I V NK   + V    G       
Sbjct: 68  N-----IPEDEVLD----LTPEDIPLD--IIYEDSDIVVINKAPNLVVHPAHGNYSGTLV 116

Query: 125 --IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + YHI     S ++    +P + HRLD++TSG++VVA+   A   L+E F+ + ++KI
Sbjct: 117 NALLYHIKDL--STINGV-IRPGIVHRLDKDTSGVIVVAKNDEAHGKLSEMFKEKTLEKI 173

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  +  GI K K   I   + + S    D   +   NE G   AIS+++VID   +    
Sbjct: 174 YVCIAKGIFKEKSGRIKTLIGRDSR---DRKKMAVVNENGK-IAISNYEVIDE-GKNHSL 228

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-E 301
           ++++  TGRTHQ+RVH  H+  PI+GD  Y     G       ++  LHA  +   HP +
Sbjct: 229 VKVRIETGRTHQIRVHMKHLNHPIMGDTTYGNGNDG------ADRQMLHAYRLKFIHPTK 282

Query: 302 GGRLQITAPLPAHMVKTWDSLGF 324
              + + APLP    +    +G 
Sbjct: 283 NTEMTVIAPLPEDFKRAAKHVGV 305


>gi|238027090|ref|YP_002911321.1| Pseudouridine synthase RluD [Burkholderia glumae BGR1]
 gi|237876284|gb|ACR28617.1| Pseudouridine synthase RluD [Burkholderia glumae BGR1]
          Length = 400

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 139/307 (45%), Gaps = 28/307 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +VRVD +  K    +  G  + +
Sbjct: 57  RLVAVPPALAGERLDKALAQLFPEFSRSRLQSWIEAQRVRVDGEPAKVRQPVPLGATIEL 116

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P       ++ EQ        L    + +   ++YED  + V +KPAG+ V   +G   
Sbjct: 117 VP------DLLPEQ--------LAFTPEPVPLAIVYEDEALVVIDKPAGLVVHPAAGNWN 162

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + ++    PR  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 163 GTLLNGLLHRYGEAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 222

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKF 240
           ++LVWG  +       +  + +       + VV         A +HF+ +D      Q  
Sbjct: 223 FALVWG--RTPASGTIDAPIGRDPRERTRMAVV--TGASGKPARTHFRTVDSVLWQNQPV 278

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H+G P++GD  Y         + + +   +  LHA  + L
Sbjct: 279 SAIQCDLETGRTHQIRVHCAHLGHPLLGDPVYGRARGKRSVAALPDGFARQALHAWRLGL 338

Query: 298 PHPEGGR 304
            HP  GR
Sbjct: 339 VHPVTGR 345


>gi|49259509|pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of
           Pseudouridine Synthase Rluc From Escherichia Coli
 gi|49259510|pdb|1V9K|B Chain B, The Crystal Structure Of The Catalytic Domain Of
           Pseudouridine Synthase Rluc From Escherichia Coli
          Length = 228

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 78/216 (36%), Positives = 118/216 (54%), Gaps = 11/216 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++ YED  I V NKP+G +V GGSG+++ +   L++ +  + +   L HRLD++TSG+L+
Sbjct: 3   VIXYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLL 61

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+ R+A + L E  R +  QK Y +LV G  ++  + +   LLK     G+ +  V Q 
Sbjct: 62  VAKKRSALRSLHEQLREKGXQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFK 277
            K +    + FKV + +A  F  L    P TGRTHQ+RVH  + G PI  D +Y    F 
Sbjct: 122 GKPSE---TRFKVEERYA--FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFD 176

Query: 278 GNFTSPIQ--NKLYLHARYMDLPHPEGGRL-QITAP 310
              T      N+L+LHA  +   HP  G + +I AP
Sbjct: 177 RQLTEAGTGLNRLFLHAAALKFTHPGTGEVXRIEAP 212


>gi|163790745|ref|ZP_02185172.1| hypothetical protein CAT7_01150 [Carnobacterium sp. AT7]
 gi|159874046|gb|EDP68123.1| hypothetical protein CAT7_01150 [Carnobacterium sp. AT7]
          Length = 309

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 91/295 (30%), Positives = 144/295 (48%), Gaps = 36/295 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALN 75
           E M L  +  +   H +  +++ IL  GQV VD+K  K +N  +  GQVV I        
Sbjct: 29  EPMELLPFLLSVMTHTSRNSVKSILTRGQVTVDEKMTKKHNFPLLPGQVVAI-------- 80

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG---ISVQGGSGIAYHIDGF 132
                     S+    K +  +   +LYED  I V +K AG   I+ +    +  H    
Sbjct: 81  ---------QSNKAAIKETALIGMTILYEDDAIIVIDKEAGLLSIAAKFAQELTAHRQ-- 129

Query: 133 LKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           L ++V  + Q  R+   HRLD++TSG++V A+T    Q + E+++    ++IY +LV G+
Sbjct: 130 LINYVKQENQNNRIYVVHRLDRDTSGVMVFAKTEKIKQDMQENWKEIVKERIYTALVEGV 189

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +  +  I  WL +   +    VH     + G   AI+H+K I    + F  LE +  TG
Sbjct: 190 VREDEGTIKTWLTESKAMK---VHSATY-DNGGKLAITHYKKIRN-NEDFTLLEARLETG 244

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           R +Q+RVH   +G P+ GD KY A      ++P++ +L LHA  + L HP  G L
Sbjct: 245 RKNQIRVHMETLGHPVAGDKKYGAT-----SNPLK-RLGLHATTLALIHPTTGEL 293


>gi|148379448|ref|YP_001253989.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 3502]
 gi|153934249|ref|YP_001383827.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           ATCC 19397]
 gi|153935171|ref|YP_001387377.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           Hall]
 gi|148288932|emb|CAL83019.1| putative ribosomal large subunit pseudouridine synthase
           [Clostridium botulinum A str. ATCC 3502]
 gi|152930293|gb|ABS35793.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 19397]
 gi|152931085|gb|ABS36584.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           Hall]
 gi|322805794|emb|CBZ03359.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum H04402 065]
          Length = 305

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 94/324 (29%), Positives = 153/324 (47%), Gaps = 44/324 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE + +N+RLD +    +   +   LQ I+  G V V+ K  K N +++ G  + +    
Sbjct: 8   VEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIEVN--- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                 I E K+L          + +K  ++YED  + V NKP  + V    G+     +
Sbjct: 65  ------IPEPKLLQIE------PEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLV 112

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+   I ++Y +
Sbjct: 113 NALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           LV GI K+++  I      ++ IG   V  +K    K   +A++H+KVI+ F +    +E
Sbjct: 173 LVEGIIKDEQGTI------EAPIGRHPVDRIKMAVVKDGRHAVTHYKVIERF-KNHTLVE 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLHARYMDLPH 299
            +  TGRTHQ+RVH  H+  P+VGD  Y       N KG           LHA+ +   H
Sbjct: 226 CRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLKGQM---------LHAKLLGFIH 276

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P   + ++  + LP +  K    L
Sbjct: 277 PTTRQYVEFESELPEYFKKIIKIL 300


>gi|146283956|ref|YP_001174109.1| pseudouridine synthase [Pseudomonas stutzeri A1501]
 gi|145572161|gb|ABP81267.1| pseudouridine synthase [Pseudomonas stutzeri A1501]
 gi|327482283|gb|AEA85593.1| pseudouridine synthase [Pseudomonas stutzeri DSM 4166]
          Length = 324

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 94/339 (27%), Positives = 156/339 (46%), Gaps = 48/339 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  D    RLD+     +   +   L   ++ G + VD   ++  + + +G V+ +    
Sbjct: 15  VPFDLGGQRLDQVAAQLFSEHSRSRLAAWIKDGLLTVDGAVLRPRDTVHAGAVLELSAEQ 74

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    + +   LD               ++YED +I V +KPAG+ V   +G   H DG
Sbjct: 75  QAQGEWVAQDIPLD---------------IVYEDDQILVIDKPAGLVVHPAAG---HADG 116

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L E  + R + +IY +
Sbjct: 117 TLLNALLHHVPDLINVPRAGIVHRLDKDTTGLMVVAKTLQAQTRLVEQLQARSVSRIYEA 176

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+        A   + +       + VV    +G   A+SH++V++ F +    + +
Sbjct: 177 IVIGVIITGGTVDAP--IGRHGQQRQRMAVV----EGGKPAVSHYRVLERF-RSHTHVRV 229

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-----------KLYLHARY 294
           +  TGRTHQ+RVH  H+G P+VGD  Y   F+     P  N           +  LHAR+
Sbjct: 230 KLETGRTHQIRVHMTHLGYPLVGDPLYAGRFR---IPPAANPTLVQTLREFPRQALHARF 286

Query: 295 MDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           ++L HP  G R++  +PLP   V  W     + DR  ++
Sbjct: 287 LELDHPVTGQRMKWESPLPDDFV--WLLTLLQQDREAFV 323


>gi|83955695|ref|ZP_00964275.1| ribosomal large subunit pseudouridine synthase D [Sulfitobacter sp.
           NAS-14.1]
 gi|83839989|gb|EAP79165.1| ribosomal large subunit pseudouridine synthase D [Sulfitobacter sp.
           NAS-14.1]
          Length = 344

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 94/361 (26%), Positives = 158/361 (43%), Gaps = 60/361 (16%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M++ Q      D    RLD+      P   +++   L ++L  G V+VD   V    +R 
Sbjct: 1   MSHRQITFTIADSPPPRLDKALARDVPEDANLSRTRLGRLLEQGAVQVDGTVVTDPRSRA 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++GQ + +       +HI+ E+  L+               +++ED+ + V NKPAG+ V
Sbjct: 61  EAGQQITVDVEEAEDSHILAEEIPLE---------------VVFEDADLIVINKPAGMVV 105

Query: 120 QG--GSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               GS     ++  L    D        ++P + HR+D++TSG+LVVA++ AA   L +
Sbjct: 106 HPAPGSPSGTLVNALLAHCGDDLSGVGGMKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAK 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK----------- 221
            F    +++ Y +LV+G+P +  +     +   S   G+ + +  Q  +           
Sbjct: 166 QFEKHTVERYYQALVYGVP-DANDPRLRGVKGASFEPGNILKLTTQLARHRTDRQRQAVF 224

Query: 222 --GANYAISHFKVI------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             G  +A++  + +      +  A   CWLE    TGRTHQ+RVH  H G  +VGD  Y 
Sbjct: 225 FQGGRHAVTRARTVARLGNPEVLALMECWLE----TGRTHQIRVHMAHAGHALVGDPTYG 280

Query: 274 AN---FKGNFTSPIQNKL------YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
                 KG  +      +       LHA  +   HP  G  ++  APLP  M     +LG
Sbjct: 281 GKRKLAKGAVSDAAAEAVRSFPRQALHAAVLGFDHPVTGDYVRFEAPLPGDMTDLLGALG 340

Query: 324 F 324
           +
Sbjct: 341 Y 341


>gi|295425512|ref|ZP_06818204.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           amylolyticus DSM 11664]
 gi|295064803|gb|EFG55719.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           amylolyticus DSM 11664]
          Length = 302

 Score =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 81/313 (25%), Positives = 152/313 (48%), Gaps = 46/313 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    + VEN  E  RLD++  +    ++   +++++  G + V++K  K + +++ G 
Sbjct: 1   MTKKYELTVEN--EKGRLDKYLADKIDDLSRTRVKELIDDGLILVNQKVEKASYKVKDGD 58

Query: 64  VVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            + +  P +  L+ +I E   LD               ++YED+ + V NKP G+ V   
Sbjct: 59  AIEVTVPAVKPLD-VIPENIPLD---------------IIYEDNDVIVVNKPQGMVVHPA 102

Query: 123 SG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           +G         + YH      S    +G +P + HR+D++TSG+L++A+     + L + 
Sbjct: 103 AGHPDHTLVNALLYHTKDLASS---PEGFRPGIVHRIDKDTSGLLMIAKNSQVRESLEDQ 159

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
              +  +++Y ++V G    ++  I   + +  H       V      G  +A++HFKVI
Sbjct: 160 LAHKTNKRLYLAIVHGNFAEEEGTIDAPIARNPHDRKKMGVVA-----GGKHAVTHFKVI 214

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLH 291
           + F + +  ++ +  TGRTHQ+RVH  ++G P+ GD  Y +    KGN         +LH
Sbjct: 215 EQF-KGYSLIQCKLETGRTHQIRVHLSYIGHPVAGDPLYGSRKTLKGNGQ-------FLH 266

Query: 292 ARYMDLPHPEGGR 304
           A+ +   HP+ G+
Sbjct: 267 AQVLGFKHPKTGK 279


>gi|295698595|ref|YP_003603250.1| ribosomal large subunit pseudouridine synthase C [Candidatus Riesia
           pediculicola USDA]
 gi|291157274|gb|ADD79719.1| ribosomal large subunit pseudouridine synthase C [Candidatus Riesia
           pediculicola USDA]
          Length = 331

 Score =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 84/294 (28%), Positives = 155/294 (52%), Gaps = 16/294 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+ +    R+D +       +    + +++R G++RVD  +V  + R+Q   +++IP 
Sbjct: 17  IFVDENSLFQRIDNFLIKRLKRVPKRLIYRLIRIGKIRVDDSKVNPSYRVQKEDLIKIPI 76

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDF-LKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            ++            D S+++ + + + +K  +LYEDS+I V NKP+GI+V  GS  ++ 
Sbjct: 77  SLSYSQ---------DKSISIQRKNFYWIKKRILYEDSEILVLNKPSGIAVHSGSKFSFG 127

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           I   L+  V  + +   L HR+D+ETSGIL++A++R   Q + + F  ++I K Y  LV 
Sbjct: 128 IIEILRE-VYFQSKYLELIHRIDKETSGILLIAKSRNILQLIQKQFCSQKIFKKYIVLVH 186

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+  +K + I+ +L KK     +    +K+N + +    + F++ + FA  F  +   P 
Sbjct: 187 GVWPSKIKRISCFLEKKISQKKEKKIEIKKNGRMSE---TLFQIKERFAS-FTLMLATPI 242

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           TGR HQ+R+H   +  PIV D +Y       N       +L+LH+  + + HP+
Sbjct: 243 TGRKHQIRLHTKKINHPIVLDKRYGNRKLDRNLKESGLKRLFLHSSSITMNHPK 296


>gi|257058664|ref|YP_003136552.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8802]
 gi|256588830|gb|ACU99716.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8802]
          Length = 318

 Score =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 88/309 (28%), Positives = 148/309 (47%), Gaps = 32/309 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN--NRIQSGQVVRIPPVINALNHI 77
           R+D W   +   I+  +LQK++  G + ++ + V  N   ++ SG  +++         +
Sbjct: 21  RIDLWLSQNLDQISRSHLQKLIEQGNIYLNNQ-VCLNKKTKVNSGDRLQVFLPPPEPLEL 79

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
             E   LD               +LYED  + + NK AG+ V    G      + G L  
Sbjct: 80  QPEPIPLD---------------ILYEDDSLIIINKSAGLVVHPAPGHTTGTLVHGLLYH 124

Query: 136 WVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             +  G    Q+P + HRLD++T+G +VVA+T  A QHL    + +  ++ Y  +V+G+P
Sbjct: 125 CPNLVGIGGIQRPGIVHRLDKDTTGAIVVAKTDYAHQHLQAQLKAKTARREYLGVVYGVP 184

Query: 192 KNKK--ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +++   +   N  + + H G      V   E G   AI+H+++++     +  +E +  T
Sbjct: 185 RHEDTHQGTINVPIGR-HRGDRKKMAVVPVENGGREAITHWQIVERLG-NYTLVEFRLET 242

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
           GRTHQ+RVH+ ++G PIVGD  Y +   G       +   LHA  + L HP  G  ++  
Sbjct: 243 GRTHQIRVHSSYIGHPIVGDPLYSS---GGSVGVNLSGQALHAYRLILEHPVTGNTIEAI 299

Query: 309 APLPAHMVK 317
           APLPA   K
Sbjct: 300 APLPAEFTK 308


>gi|297566959|ref|YP_003685931.1| pseudouridine synthase, RluA family [Meiothermus silvanus DSM 9946]
 gi|296851408|gb|ADH64423.1| pseudouridine synthase, RluA family [Meiothermus silvanus DSM 9946]
          Length = 315

 Score =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 121/247 (48%), Gaps = 41/247 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA------------YHIDGFLKSWVDSKGQKPR--- 145
           +LYED  + V NKPAG+      G+               + G L + ++ +   PR   
Sbjct: 75  ILYEDQDLVVVNKPAGMITHPAPGVTSGTLVNAILGRYAELRGVLATQLEDEEAPPRPEL 134

Query: 146 ----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KECIA 199
               + HRLD++TSG+++VAR  AA + L+E+FR R + K Y ++  G PK       I 
Sbjct: 135 IRPGIVHRLDKDTSGVILVARHEAAHRRLSEAFRGRSVYKRYLAITVGHPKEGTFAAPIG 194

Query: 200 NWLLKKS--HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
              + ++  H+GG              YA + F+++   A ++  +    HTGRTHQ+RV
Sbjct: 195 RHPVDRTRMHVGG----------IAPRYAETDFEIL-AIAGEYALVSAILHTGRTHQIRV 243

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +  PI+GD  Y         S +  +  LHA  + + HP  G+ L+ TAP+PA M 
Sbjct: 244 HLKALHAPILGDDVY------GKPSGLIARQALHAYELRIQHPRSGKYLEFTAPVPADMA 297

Query: 317 KTWDSLG 323
             W++LG
Sbjct: 298 GAWEALG 304


>gi|317121731|ref|YP_004101734.1| ribosomal large subunit pseudouridine synthase D [Thermaerobacter
           marianensis DSM 12885]
 gi|315591711|gb|ADU51007.1| ribosomal large subunit pseudouridine synthase D [Thermaerobacter
           marianensis DSM 12885]
          Length = 321

 Score =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 92/327 (28%), Positives = 151/327 (46%), Gaps = 48/327 (14%)

Query: 11  VVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRI 67
           VV       RLD +        +    +Q+++RS Q+RV+ +  + + R++ G+  VV +
Sbjct: 18  VVPASAAGERLDVFLAGQDSLELTRSAIQRLIRSQQIRVNGRPARPSRRLEPGEEVVVEL 77

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P    A + ++ E   LD               ++YED+ + V NKP G  V    G   
Sbjct: 78  P--APAPSGVVAEPLPLD---------------VVYEDADVVVLNKPRGWVVHPAPG--- 117

Query: 128 HIDG-----FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           H  G      L  + + +G     +P + HRLD++T+G+LVVAR+  A + L    + R 
Sbjct: 118 HPQGTLANALLARYPEMEGVGGPGRPGIVHRLDRDTTGLLVVARSPLAYRELVRQLKERG 177

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + + Y +LV G P+  +E   +  + +  +    + V+     G   A +HF+V++   +
Sbjct: 178 VHREYLALVRGSPE-VREGTVDAPIGRHPVDRKRMAVLP---GGGRPARTHFEVVERAGR 233

Query: 239 KF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARY 294
                CWL+    TGRTHQ+RVH   +G P+ GD  Y     +G      Q    LHA  
Sbjct: 234 YTLLRCWLD----TGRTHQIRVHLAFIGLPVAGDPVYGGRRAEGELGLEGQA---LHATR 286

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWD 320
           +  PHP  GR +  T P PA   +  +
Sbjct: 287 LAFPHPRDGRPMDFTVPPPADFQRALE 313


>gi|182677345|ref|YP_001831491.1| RluA family pseudouridine synthase [Beijerinckia indica subsp.
           indica ATCC 9039]
 gi|182633228|gb|ACB94002.1| pseudouridine synthase, RluA family [Beijerinckia indica subsp.
           indica ATCC 9039]
          Length = 346

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 90/324 (27%), Positives = 150/324 (46%), Gaps = 57/324 (17%)

Query: 11  VVENDEENMRLDRWF----KNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVV 65
           VV  +E   RLDR+     +     ++ + ++ ++  G V VD + R+  +  +++GQ++
Sbjct: 19  VVGAEEAGQRLDRFLAERTETGAAFLSRMRIKTLIEQGHVSVDGEARLTASASVRAGQII 78

Query: 66  R--IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
              +PP         KE   +   + L          ++YED+ + V +KPAG+ V   +
Sbjct: 79  ELAVPPA--------KEAVPVAQDLPLN---------IVYEDAGLVVLDKPAGLVVHPAA 121

Query: 124 GIAYHIDGFL---------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           G   H  G L         +S     G ++P + HRLD++TSG+LV A+T A  Q L   
Sbjct: 122 G---HAQGTLVNALMAHCGESLSGIGGVKRPGIVHRLDKDTSGLLVAAKTDAVHQGLARL 178

Query: 174 F----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           F    +   + + Y + VWG+P  +   I   L + +    D       +E    +A++H
Sbjct: 179 FADHGQNLHLVREYLAFVWGVPARQSGRIEAALGRHAQ---DRERQAVVSEDVGRHAVTH 235

Query: 230 FKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN---FTS 282
           ++V++ F +K       +  Q  TGRTHQ+RVH  H+G P++GD  Y   FK      + 
Sbjct: 236 WEVLEVFQRKGKPVASLIACQLETGRTHQIRVHMAHIGHPLLGDPLYGKGFKSKSAILSP 295

Query: 283 PIQNKL------YLHARYMDLPHP 300
           P Q  L       LHA  +   HP
Sbjct: 296 PAQEALRQLGRQALHAAQLGFEHP 319


>gi|104783634|ref|YP_610132.1| 23S rRNA pseudouridine synthase [Pseudomonas entomophila L48]
 gi|95112621|emb|CAK17349.1| 23S rRNA pseudouridine synthase [Pseudomonas entomophila L48]
          Length = 320

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 89/318 (27%), Positives = 151/318 (47%), Gaps = 44/318 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + + SG ++ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFSEYSRSRLSSWIKDGRLTVDGAVLRPRDTVHSGSILALEAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    + +   LD               ++YED +I V NKPAG+ V   +G   H DG
Sbjct: 71  EAQGEWVAQDIELD---------------IVYEDDQILVINKPAGLVVHPAAG---HPDG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A  +L +  + R + +IY  
Sbjct: 113 TLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTLQAQTNLVDQLQKRSVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +V G+       IA   +       GG+   +   +  G   A+SH++V+  F +    +
Sbjct: 173 IVVGV------VIAGGKIDAPIGRHGGERQRMAVTD--GGKPAVSHYRVLKRF-RSHTHV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYM 295
            ++  TGRTHQ+RVH  H+G P+VGD  Y   F+            ++N  +  LHAR++
Sbjct: 224 RVKLETGRTHQIRVHMAHVGYPLVGDQTYGVRFRIPPAASVAMVEAVKNFPRQALHARFL 283

Query: 296 DLPHPEGG-RLQITAPLP 312
            L HP  G R++  +PLP
Sbjct: 284 ALDHPTTGERMEWASPLP 301


>gi|329114084|ref|ZP_08242848.1| Ribosomal large subunit pseudouridine synthase D [Acetobacter
           pomorum DM001]
 gi|326696623|gb|EGE48300.1| Ribosomal large subunit pseudouridine synthase D [Acetobacter
           pomorum DM001]
          Length = 337

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 87/342 (25%), Positives = 145/342 (42%), Gaps = 61/342 (17%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V  ++   R+DR+       ++   ++ ++  G ++ D            G  +R P  
Sbjct: 22  TVTPEQAGERIDRFLAAIMETLSRSRIKSLIEEGHLKCD------------GVCIREPAA 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           I      +K +  +  +       + +   +LYED  + V +KPAG+ V    G      
Sbjct: 70  IARAG--MKVELTIPPAAPAVPQGEDISFTVLYEDDDLIVLDKPAGLVVHPAPGNETGTL 127

Query: 129 IDGFLKSWVDS-KG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++G +    +S KG    ++P + HRLD++TSG++V A+T  A Q L+E F  RRI + Y
Sbjct: 128 VNGLIAHCGESLKGIGGERRPGIVHRLDKDTSGVMVAAKTEMAHQALSEDFAARRIDRTY 187

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE----------KGANYAISHFKVI 233
            +  WG+P N  E             GD+   + +++          KG  +A++H++ +
Sbjct: 188 LAFCWGLP-NPAE-------------GDFEGAIGRDKRDRKRMALTPKGGKWALTHYRTL 233

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY------------CANFKGNFT 281
             F      +  +  TGRTHQ+RVH    G P++GD  Y             A       
Sbjct: 234 QAFGTGAALVACKLATGRTHQIRVHFSANGHPLIGDPLYLRRIPAASRVLPSAARAAALD 293

Query: 282 SPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            P Q    LHA  +   HP  G +L    P+P  M     SL
Sbjct: 294 FPRQ---ALHAARLGFIHPRTGEKLLFETPMPEDMQALERSL 332


>gi|227514877|ref|ZP_03944926.1| pseudouridylate synthase [Lactobacillus fermentum ATCC 14931]
 gi|227086724|gb|EEI22036.1| pseudouridylate synthase [Lactobacillus fermentum ATCC 14931]
          Length = 291

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 85/299 (28%), Positives = 143/299 (47%), Gaps = 32/299 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+   +H+P  +   L++ +  G V V+ + VK   ++Q+G  V I P          
Sbjct: 4   RIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAGDRVVIKP---------- 53

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL--KS 135
                ++ V +    + +   ++YED  + V NKP G+ V    G   H  ++  +    
Sbjct: 54  -----ETPVEIDLEPENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALMYYAP 108

Query: 136 WVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                G+ +P + HR+D++TSG+L+VA+T  A + LT   + +   + Y +LV G+ K  
Sbjct: 109 LSSINGELRPGIVHRIDKDTSGLLMVAKTDRAHRSLTAQLKEKSNLREYVALVHGVIKEN 168

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I   L +          VV     G  +A++HF+V+  + Q +  +  +  TGRTHQ
Sbjct: 169 EGTIDAPLARSPKDRKKQAVVV-----GGRHAVTHFRVLKRY-QHYTLVACRLETGRTHQ 222

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +RVH  ++  P+ GD  Y        T P   + YLHAR +   HP  G  +  TAPLP
Sbjct: 223 IRVHMKYINHPLAGDPLYGP----RKTLPGHGQ-YLHARLLGFEHPVTGEEMVFTAPLP 276


>gi|326335706|ref|ZP_08201892.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           sp. oral taxon 338 str. F0234]
 gi|325692135|gb|EGD34088.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           sp. oral taxon 338 str. F0234]
          Length = 345

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 91/331 (27%), Positives = 160/331 (48%), Gaps = 61/331 (18%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  N   + +   +Q+  + G + V+   VK N+R+++   V++        
Sbjct: 29  QEPLRVDKFLMNFVENASRNKVQQAAKDGNIFVNGVAVKSNHRVKANDEVKV-----MFA 83

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIA 126
           H   E  ++   + L          ++YED ++ + NKPAG+ V  G         +G+ 
Sbjct: 84  HPPHEYLLVPELIPLN---------IVYEDEELIIINKPAGLVVHPGHGNYQGTLINGLI 134

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH +   K+  D    +P L HR+D++TSG+LVVA+T  A  HL + F  +  ++ Y +L
Sbjct: 135 YHFEQLPKNSSD----RPGLVHRIDKDTSGLLVVAKTEEAMNHLAKQFFNKTSEREYIAL 190

Query: 187 VWG-IPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           VWG IP+++            HIG        + V     +G   AI+H+KV++ F    
Sbjct: 191 VWGNIPEDEGTITG-------HIGRHPKNRLQMTVFPDGSEGKE-AITHYKVLERFGYVT 242

Query: 241 ---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQN----- 286
              C LE    TGRTHQ+R H  ++G P+  D +Y  +   KG  ++     ++N     
Sbjct: 243 LVSCRLE----TGRTHQIRAHFTYIGHPLFNDERYGGDKILKGTTSTKYKQFVENCFKVL 298

Query: 287 -KLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            +  LHA+ + +  P  G+ L+  + +P  M
Sbjct: 299 PRQALHAKTLGIEKPSTGQMLRFDSEIPQDM 329


>gi|315640856|ref|ZP_07895955.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           italicus DSM 15952]
 gi|315483395|gb|EFU73892.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           italicus DSM 15952]
          Length = 302

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 93/323 (28%), Positives = 155/323 (47%), Gaps = 51/323 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           EE  R+D+       + +   +Q  L+   V++D   VK N ++Q G  + I        
Sbjct: 11  EEKGRIDKVLAEKLANYSRSQIQLWLKEACVKIDGVVVKANYKVQKGDRITIQ------- 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
             I E + LD        ++ L   ++YED+ + V NKP G+ V   +G         + 
Sbjct: 64  --IPEPETLDLI------AENLPLEIVYEDADVAVINKPQGMVVHPSAGHPNGTLVNALI 115

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH++    S ++    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +L
Sbjct: 116 YHLNSL--SSINGV-IRPGIVHRIDKDTSGLLMVAKNDQAHEDLAKQLKDKTSLRKYVAL 172

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYV----HVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           V G+  + K  I      ++ IG   V      V  N K A   ++HF+V++ + + +  
Sbjct: 173 VHGVIPHDKGVI------RAPIGRSTVDRKMQAVVDNGKDA---VTHFQVLERY-EDYTL 222

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHP 300
           +E+Q  TGRTHQ+RVH  ++G P+VGD  Y      KGN         +LHA+ +   HP
Sbjct: 223 VELQLETGRTHQIRVHMQYIGYPLVGDPVYGLKRTIKGNGQ-------FLHAKLLGFTHP 275

Query: 301 EGG-RLQITAPLPAHMVKTWDSL 322
             G ++   APLP    KT   L
Sbjct: 276 STGEKMVFEAPLPEIFKKTLAKL 298


>gi|39995193|ref|NP_951144.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           sulfurreducens PCA]
 gi|39981955|gb|AAR33417.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           sulfurreducens PCA]
 gi|298504197|gb|ADI82920.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           sulfurreducens KN400]
          Length = 322

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 85/330 (25%), Positives = 148/330 (44%), Gaps = 43/330 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  + E  RLD++       I     Q+++  G+V VD +  K + +++ G+        
Sbjct: 12  VPTEGEAERLDQFVARSVQGITRSAAQRLIEEGRVTVDDRLEKPSLKLRGGE-------- 63

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
                  +    +         ++ +  ++L+ED  + V +KPAG+ V   +G      +
Sbjct: 64  -------RVVVTVPPPAPAVPEAEEIPLVVLHEDGDVVVVDKPAGMVVHPAAGNPGGTLV 116

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSG+LVVA++  A + L+  F    ++++Y +
Sbjct: 117 NALLAHCTDLSGIGGEIRPGIVHRIDKDTSGVLVVAKSDRAHESLSRQFHDHTVKRVYLA 176

Query: 186 LVWGIPKNKKECIANWLLK----KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           LV+G P+  K  I   + +    +  + G   H          +A++H++V   F     
Sbjct: 177 LVYGSPREDKGRIEGAIGRHPTDRKKMSGAARH--------GKHAVTHWRVAARFT-GVT 227

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKL-------YLHAR 293
            L ++  TGRTHQ+RVH    G P+VGD  Y    +  N   P+  KL        LHA+
Sbjct: 228 LLRLRLETGRTHQIRVHMAEAGFPLVGDEVYGGAGRINNLRDPVLRKLIRELGRQALHAK 287

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +   HP  G  L+    LP  M +  D L
Sbjct: 288 TLGFVHPVTGEYLEFDTELPEDMARIIDYL 317


>gi|166713128|ref|ZP_02244335.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzicola BLS256]
          Length = 331

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 90/343 (26%), Positives = 159/343 (46%), Gaps = 40/343 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +V ++    R D      +P  +   L + ++SG   +D    +  + ++ G+ V+
Sbjct: 13  IRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGGESVQ 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V+    H   +   L                +LYED+++ V +KPAG+ V  G+G  
Sbjct: 73  VQVVLETQTHAAPQDIALS---------------VLYEDAQVLVIDKPAGLVVHPGAG-- 115

Query: 127 YHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            + DG L + +     +    PR  + HRLD++TSG++VVART  A   L E    R + 
Sbjct: 116 -NPDGTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSARDVH 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G   +     AN  + + H        V+ + +    A++H+++ + F +  
Sbjct: 175 RQYLAVVVGALVSG--GTANAPIDR-HPRDRLKMAVRDDGRD---AVTHYRLRERF-RAH 227

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHA 292
             LE +  TGRTHQ+RVH  H+  PIVGD  Y    K     T  + ++L       LHA
Sbjct: 228 TALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQALHA 287

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
             ++  HP  G  ++ +AP+PA + +   +L     R   + R
Sbjct: 288 ETLEFLHPVSGEPVRASAPVPADLQRLMTALREDSARAAELAR 330


>gi|299066639|emb|CBJ37832.1| Ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Ralstonia solanacearum CMR15]
          Length = 353

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 95/341 (27%), Positives = 153/341 (44%), Gaps = 36/341 (10%)

Query: 7   VQYVVVENDEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           ++ +VVE  E     RLD+      P  +   LQ+ + +G VRV    V+    +  G  
Sbjct: 31  IEPIVVEIPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVRPRAAVCGGDR 90

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + + P           Q+  D +  + +  D     ++YED  + V NKPAG+ V   +G
Sbjct: 91  IEVVP-----------QRADDENAFVAEPIDL---DVVYEDDTLLVINKPAGLVVHPAAG 136

Query: 125 --IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 ++G L  +  + G  PR  + HRLD+ETSG++VVART  A   L    + R ++
Sbjct: 137 NWSGTVLNGLLHRYPQAAG-LPRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVK 195

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---VIDCFA 237
           + Y +LVWG  +  +    +  + +     D   +          A +HFK   V+D   
Sbjct: 196 RTYLALVWG--ETPEAGTIDAPIGRDP--RDRTRMAIIETASGKPARTHFKTLDVVDLGR 251

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YL 290
            +   ++ Q  TGRTHQ+RVH    G P++GD  Y  NF+      I+  L        L
Sbjct: 252 AQVSLVQCQLETGRTHQIRVHFESEGHPLLGDPVYTRNFRRGRPQTIKAPLPAPFARQAL 311

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNL 330
           HA  + L HP  G  +   A +P  + +  ++L    D +L
Sbjct: 312 HAVRLGLVHPASGHSVHWHAGVPDDLAELMEALEMDPDVDL 352


>gi|86156486|ref|YP_463271.1| ribosomal large subunit pseudouridine synthase C [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|85772997|gb|ABC79834.1| ribosomal large subunit pseudouridine synthase C [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 339

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 95/331 (28%), Positives = 160/331 (48%), Gaps = 32/331 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD+  +     +   ++ K+ R+ +VRV+  R K +  +  G VV    
Sbjct: 4   LTVSADAAGQRLDKLVRKALRDVPLSHVYKMFRTRKVRVNGARGKADQVVAEGDVV---- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGI--A 126
           VI        E+++L  +           +  +L+ED+ +   +KPAG++   G+GI  A
Sbjct: 60  VIRG-----DEERLLAKAAPAAPGGAPRVTFGVLHEDADLLAVDKPAGLAAHPGTGIEGA 114

Query: 127 YHID---GFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-RRIQ 180
             ++   G+LK+  D      KP   HRLD++TSG+++VA+ R A   L E+F     + 
Sbjct: 115 TLVEMARGYLKTPDDLPPTEFKPSPAHRLDRDTSGVVLVAKHRKAMVRLGETFTTGEGVH 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQ 238
           K Y +LV G  K  +E     L    H        +    +G N+  A++ +KV+   A+
Sbjct: 175 KTYLALVKG--KMPREAGTIDLPLSEHEQTSKSKAM----RGVNFQEALTRWKVVSA-AK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYM 295
           +   L +   TGRTHQ+R H   +G P+ GD +Y  +F  N T+  +    ++ LHA  +
Sbjct: 228 EISLLAVTIETGRTHQIRRHLEAVGHPVAGDRRY-GDFAFNRTARTRWGLRRMGLHAWRL 286

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           ++PHP  G  L++ AP PA + +       K
Sbjct: 287 EVPHPLTGAPLRLEAPFPAELAEVLSRANLK 317


>gi|326204205|ref|ZP_08194065.1| pseudouridine synthase [Clostridium papyrosolvens DSM 2782]
 gi|325985716|gb|EGD46552.1| pseudouridine synthase [Clostridium papyrosolvens DSM 2782]
          Length = 223

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 67/205 (32%), Positives = 108/205 (52%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  KP  I VQ  +     +   LK ++  K  KP      L HRLD+   
Sbjct: 5   IIYEDNHLLVVEKPVNIPVQADNTKDTDMLTLLKKYLKEKYNKPGEVYLGLVHRLDRPVG 64

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  L+E  R R  +K+Y +++ G+PK +K  + N+L+K S    + V+V
Sbjct: 65  GVMVFAKTSKAASRLSEQVRTRTFKKVYLAVIRGVPKEQKTKLRNFLVKDS--SENMVYV 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           VK+  K A  A+  ++V+         ++++ HTGR HQ+RV   H G P+ GD +Y   
Sbjct: 123 VKEGTKDAKEAVLEYEVLKSDGL-LSMIKVKLHTGRPHQIRVQLSHSGYPLYGDQRY--- 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G   +    ++ L A  + L HP
Sbjct: 179 --GITVNKPGQQIALWASSLTLEHP 201


>gi|254303145|ref|ZP_04970503.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148323337|gb|EDK88587.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 289

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 87/308 (28%), Positives = 156/308 (50%), Gaps = 27/308 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++Y++ E + E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G +V 
Sbjct: 2   IEYIIDE-EYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLILGDIVF 60

Query: 67  I--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           I  P      N    E+K ++ S    +  + LK ++++E+  ++V NK  G  V  GSG
Sbjct: 61  IFLPENFKENN----EEKFIELS---QERKEKLKEMIVFENDSLFVINKLLGDVVHKGSG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +    +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+
Sbjct: 114 HDISLLEEFRSYYSNNN--INFVNRIDKLTSGLVIGAKNIKTAREVAKEIQSGNIVKKYY 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  +     I N+L K      + V V    + G   +I++FK I  +  K+  LE
Sbjct: 172 ILVNGKIEKNDFIIENYLKKDE----EKVIVSDVEKDGYKKSITYFKKIKEY-NKYTLLE 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQLR    H+G  IVGD KY  N K       ++ +YL + Y+ +       
Sbjct: 227 AELKTGRTHQLRAQLNHIGNNIVGDTKYGKNEK-------EDLMYLFSYYLKIDLY---N 276

Query: 305 LQITAPLP 312
           L+I   +P
Sbjct: 277 LEIKLEIP 284


>gi|212690568|ref|ZP_03298696.1| hypothetical protein BACDOR_00054 [Bacteroides dorei DSM 17855]
 gi|237709607|ref|ZP_04540088.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           9_1_42FAA]
 gi|237725250|ref|ZP_04555731.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D4]
 gi|265754237|ref|ZP_06089426.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_33FAA]
 gi|212666917|gb|EEB27489.1| hypothetical protein BACDOR_00054 [Bacteroides dorei DSM 17855]
 gi|229436516|gb|EEO46593.1| ribosomal large subunit pseudouridine synthase D [Bacteroides dorei
           5_1_36/D4]
 gi|229456243|gb|EEO61964.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           9_1_42FAA]
 gi|263234946|gb|EEZ20501.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_33FAA]
          Length = 223

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 76/233 (32%), Positives = 119/233 (51%), Gaps = 18/233 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK +   VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VVYEDNHIVVVNKTSSEIVQGDKTGDTPLSEMVKQYLKEKYNKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E FR   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVVFAKTSKALPRLNEMFRNGEVKKTYWAIVKECPKETEGELVHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K +  A+ H+K+I   +Q +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVKNSKKAVLHYKLIG-HSQNYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYD 327
             G+  S     + LHAR +   HP    + ++TAP+P   +  W+  GF+ D
Sbjct: 177 --GSPRSNPDGSICLHARTVQFVHPVSKEMIRLTAPVPEGNL--WN--GFEID 223


>gi|317495177|ref|ZP_07953547.1| RluA family pseudouridine synthase [Gemella moribillum M424]
 gi|316914599|gb|EFV36075.1| RluA family pseudouridine synthase [Gemella moribillum M424]
          Length = 299

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 85/312 (27%), Positives = 153/312 (49%), Gaps = 38/312 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D++ +     ++  N+Q ++  G ++VD K +K N +++ G  + I           K
Sbjct: 15  RIDKFLQKELSELSRTNIQNLISEGYIKVDGKEIKTNFKLKDGNEITIE---------YK 65

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E + LD    + K    +   ++YEDS + V NK  G+ V   +G   H DG L + +  
Sbjct: 66  EPEELD----VVKQD--IPVDIVYEDSDLIVVNKAKGMVVHPSAG---HRDGTLVNALLF 116

Query: 140 KGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             +        +P + HR+D++TSG+LVVA+   A   L+E    + +++ Y++LV G  
Sbjct: 117 HSELSSINGTIRPGIVHRIDKDTSGLLVVAKNDKAHVKLSEMIANKDVKRKYYALVHGSI 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K+    I   + +      +   ++ + +     +I+HFKV++ F +K+  +E +  TGR
Sbjct: 177 KHDYGTIDAPIARNPKERKEMA-IIDEGKP----SITHFKVVERF-EKYTLIECELETGR 230

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  ++  P+VGD  Y      N      N   LH++ ++  HP  G  L    P
Sbjct: 231 THQIRVHMKYINHPLVGDPVYGPRKTLN-----ANGQALHSKSIEFNHPITGEHLYFETP 285

Query: 311 LPAHMVKTWDSL 322
           +P +M+     L
Sbjct: 286 IPQYMLDIMAKL 297


>gi|254500895|ref|ZP_05113046.1| pseudouridine synthase, RluA family [Labrenzia alexandrii DFL-11]
 gi|222436966|gb|EEE43645.1| pseudouridine synthase, RluA family [Labrenzia alexandrii DFL-11]
          Length = 341

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 89/330 (26%), Positives = 159/330 (48%), Gaps = 46/330 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           + V+ ++   R+D    +H   ++   +Q ++++G V +   ++ +   R+  G  + + 
Sbjct: 18  LTVDPEDAGKRIDAVLASHLETLSRNRIQSLIKAGDVSIGGAKIGEPKYRVNEGDEITL- 76

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                    + E +  D      K  D   S++ +ED+ + V +KPAG+ V  G+G    
Sbjct: 77  --------HLPEPEDPDP-----KGEDIPLSVV-FEDAHVIVIDKPAGLVVHPGAGNWTG 122

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMR 177
             ++  +    DS       ++P + HR+D++TSG+LVVA+T  A Q L   F    R  
Sbjct: 123 TLVNALIHHCGDSLSGIGGVKRPGIVHRIDKDTSGLLVVAKTDQAHQGLAAQFADHGRTG 182

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LVWG P + K  I +  L +S      + VVK + +   +AI+H++V + F 
Sbjct: 183 PLERAYSALVWGAPSSLKGTI-DANLARSQANRQKMAVVKTSGR---HAITHWQVKERFG 238

Query: 238 QK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQN--- 286
                     +E +  TGRTHQ+RVH  H+G P++GD  Y + FK        P+++   
Sbjct: 239 AADQPPLASLMECRLETGRTHQIRVHMAHIGHPLLGDDDYGSGFKTKINRLEEPLKSLVG 298

Query: 287 ---KLYLHARYMDLPHPEGGR-LQITAPLP 312
              +  LHA  +   HP  G  L+  +P P
Sbjct: 299 GFTRQALHAGLLAFEHPVSGETLRFESPYP 328


>gi|71083779|ref|YP_266499.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter ubique HTCC1062]
 gi|91763185|ref|ZP_01265149.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter ubique HTCC1002]
 gi|71062892|gb|AAZ21895.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter ubique HTCC1062]
 gi|91717598|gb|EAS84249.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter ubique HTCC1002]
          Length = 304

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 88/286 (30%), Positives = 148/286 (51%), Gaps = 29/286 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V++   +MR+DRW +N+  +     ++K L+SG+V+++ K++K ++++++G        I
Sbjct: 7   VDSTFNDMRIDRWIRNNLGNYPQGLIEKSLKSGKVKINNKKIKSSHKVKTGDT------I 60

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           +  N   KE  I+  ++      + +K    +++  +    V NK +GISVQGG+    +
Sbjct: 61  DLFNFDFKET-IVQKTIKFVPSEEVIKENEELIIDNNDDFIVLNKSSGISVQGGTKSKKN 119

Query: 129 -IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +D F +S +  +  KP   HRLD++TSG+ ++A+ R +AQ LT  FR+R++ K Y ++ 
Sbjct: 120 LVDIFARSEI-FQDTKPFSVHRLDKDTSGVFIMAKHRQSAQLLTSLFRLRKVHKTYLAIC 178

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQ 246
            G            L K S    D +     + +    A + +KV+D      C L EM+
Sbjct: 179 HG-----------ELQKDSGEWNDDLTRYDNDREVVEKARTLYKVLD--KNSICSLVEMK 225

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           P TGR HQLR     +GCPI GD KY      N    I   L LH+
Sbjct: 226 PITGRKHQLRKQLYAVGCPIYGDQKYKF---SNTDKAINKNLMLHS 268


>gi|300775211|ref|ZP_07085073.1| ribosomal large subunit pseudouridine synthase D [Chryseobacterium
           gleum ATCC 35910]
 gi|300505951|gb|EFK37087.1| ribosomal large subunit pseudouridine synthase D [Chryseobacterium
           gleum ATCC 35910]
          Length = 357

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 91/339 (26%), Positives = 160/339 (47%), Gaps = 53/339 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V++ +E +R+D++   +  + +   + +  R+G V V+   VK N R++ G  + +  
Sbjct: 37  ITVDSKQEPLRIDKFLLIYRQNSSRNKISQTCRAGNVIVNGVAVKQNYRVKPGDQISV-- 94

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L H  +E  I+   + +          ++YED  + V +K AG+ V  G G     
Sbjct: 95  ---LLAHPPRENVIIPQDIPVN---------IIYEDDDLVVVDKEAGMVVHPGFGNWDGT 142

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +AYH   F K+   S   +  L HR+D++TSG+LV+A+   A   L + F  R  +
Sbjct: 143 LVNALAYH---FEKNGEKSDLDRVGLVHRIDKDTSGLLVIAKNEYALSFLAKQFFNRTTK 199

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNEKGANYAISHFKVIDCF 236
           ++YW+ VWG  +  +  I      + HIG          V ++     +A++H+KV++ F
Sbjct: 200 RLYWAFVWGNLQEDEGTI------RGHIGRHPKNRMQMSVYEDGSQGKHAVTHYKVLERF 253

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG----NFTSPIQN---- 286
            +   W+E +  TGRTHQ+R H  H+G  +  D +Y  +   +G     +   I+N    
Sbjct: 254 -KYMTWVECKLETGRTHQIRAHFRHIGHTLFNDERYEGHTPLRGVNLPKYKQFIKNVFEI 312

Query: 287 --KLYLHARYMDLPHPEGGR-LQITAPLPAHM---VKTW 319
             +  LHA  +   HP   + L   +P+P  M   VK W
Sbjct: 313 LPRHALHAHTLGFIHPTTKKELYFESPMPKDMADAVKKW 351


>gi|254518704|ref|ZP_05130760.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
 gi|226912453|gb|EEH97654.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
          Length = 305

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 87/337 (25%), Positives = 158/337 (46%), Gaps = 52/337 (15%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  + + + E +   +R+D++  N     +   +Q ++ SG + V+ K VK N ++++  
Sbjct: 1   MDELVFKITEEENIGIRIDKYLSNIIEGKSRSFIQGLIDSGAILVNNKEVKSNYKLRNHD 60

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
             +V +P  I        E  +    ++L          ++YED  + V NKP G+ V  
Sbjct: 61  EIIVSMPEPI--------ELDVEPEDIDLN---------IVYEDEDVIVLNKPQGVVVHP 103

Query: 122 GSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++G L    D  G     +P + HR+D++TSGILV+A+   A  HL + F+
Sbjct: 104 APGNYSGTLVNGLLYHCKDLSGINGVIRPGIVHRIDKDTSGILVIAKNDDAHNHLAKQFK 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK---------GANYA 226
              I++ Y++LV G              K S I G     + +N+K             A
Sbjct: 164 NHSIKREYYALVEG--------------KFSKIEGTVDKPIGRNKKDRLKMAIMEDGKRA 209

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++H+ V++ +      ++    TGRTHQ+RVH   +G P+VGD  Y +N K  F   +Q 
Sbjct: 210 VTHYNVLEQYNNGTALVKCTLETGRTHQIRVHMASIGHPLVGDPLYNSNKKQKFK--LQG 267

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           ++ LHA+ +   HP     ++  + LP + ++  +++
Sbjct: 268 QV-LHAKTLGFIHPRSNEYIEFDSELPKYYLELLENI 303


>gi|78224625|ref|YP_386372.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           metallireducens GS-15]
 gi|78195880|gb|ABB33647.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           metallireducens GS-15]
          Length = 319

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 84/322 (26%), Positives = 149/322 (46%), Gaps = 35/322 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   + E  RLD++       +    +Q+++  G+V VD K  K + +++ G+ +     
Sbjct: 8   IAPGEGEAGRLDQFVARSVEGMTRSTVQRLIDEGRVTVDGKVEKPSLKLRGGERI----- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                        +         ++ +  ++L+EDS + V NK AG+ V  G+G      
Sbjct: 63  ----------VVAVPPPAPAVPEAEEIPLVILHEDSDLVVVNKSAGMVVHPGAGTPGGTL 112

Query: 129 IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D  G     +P + HR+D++T+G+LVVA+   + + L   FR   I++IY 
Sbjct: 113 VNALLAHCTDLSGIGGEIRPGIVHRIDKDTTGVLVVAKNDRSHEGLARQFREHTIKRIYL 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV+G PK     I   + +      D + +  + + G  +A++H+KV+  +      L 
Sbjct: 173 ALVFGSPKTDTGRIEGAIGRHPT---DRLRMSGKAKHG-KHAVTHWKVLARYP-GMTLLR 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLY-------LHARYMD 296
           ++  TGRTHQ+RVH    G P+VGD  Y    + N    P+  KL        LHA+ + 
Sbjct: 228 LRLETGRTHQIRVHLAESGHPLVGDEVYGGAGRANDLRDPVLKKLVRELGRQALHAKTLG 287

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
             HP  G  ++    LP  M +
Sbjct: 288 FIHPASGSYVEFDTELPDDMAR 309


>gi|15966478|ref|NP_386831.1| putative ribosomal large subunit pseudouridine synthase protein
           [Sinorhizobium meliloti 1021]
 gi|307300485|ref|ZP_07580265.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti BL225C]
 gi|307318350|ref|ZP_07597785.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti AK83]
 gi|15075749|emb|CAC47304.1| Putative ribosomal large subunit pseudouridine synthase
           [Sinorhizobium meliloti 1021]
 gi|306896032|gb|EFN26783.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti AK83]
 gi|306904651|gb|EFN35235.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti BL225C]
          Length = 343

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 124/244 (50%), Gaps = 33/244 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQE 153
           +LYED+ + V  KPAG+ V  G+G      ++  +    DS       ++P + HRLD++
Sbjct: 92  VLYEDADLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGGVKRPGIVHRLDKD 151

Query: 154 TSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           TSG++VVA+  AA +HL++ F    R   +++ Y ++VWG P+  K  I   L +     
Sbjct: 152 TSGVMVVAKNDAAHRHLSDQFADHGRNGPLERAYRAVVWGRPRQLKGKIDAPLGR----A 207

Query: 210 GDYVH--VVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALH 261
           GD     V +++   A  AI+H++V++ + +K         +E    TGRTHQ+RVH  H
Sbjct: 208 GDRTKRAVKREDSDDAREAITHYEVVERYHEKPDGTSLASTVECHLETGRTHQIRVHMAH 267

Query: 262 MGCPIVGDHKYCANFKGN---FTSPIQNKL------YLHARYMDLPHPEGGR-LQITAPL 311
           +G P++GD  Y A F+        P +  +       LHA  +   HP  G  +    P+
Sbjct: 268 IGHPLIGDPDYGAAFRTKANLLPEPARAAVNRFPRQALHAFMLQFEHPATGETMHFETPV 327

Query: 312 PAHM 315
           PA M
Sbjct: 328 PADM 331


>gi|172038237|ref|YP_001804738.1| pseudouridine synthase [Cyanothece sp. ATCC 51142]
 gi|171699691|gb|ACB52672.1| pseudouridine synthase [Cyanothece sp. ATCC 51142]
          Length = 314

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 91/330 (27%), Positives = 158/330 (47%), Gaps = 52/330 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-------KKRVKFNNRIQSG 62
           + VEN  +  RLD W  N    I+  ++Q+++  G + ++       K +VK  +R+Q  
Sbjct: 5   LTVEN--KGNRLDLWLSNQLTDISRSHIQRLIEQGNIILNNEVCTNKKIKVKIGDRLQ-- 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +P           E K L+         + L   +LYED ++ + NKPA + V   
Sbjct: 61  --INLP-----------EPKPLELK------PEPLPLDILYEDEQLIIINKPANLVVHPA 101

Query: 123 SG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      + G L    +  G    Q+P + HRLD++T+G +VVA+T  A Q+L    + 
Sbjct: 102 PGHETGTLVHGLLYHCSNLAGIGGVQRPGIVHRLDKDTTGAMVVAKTDFAHQNLQAQIKN 161

Query: 177 RRIQKIYWSLVWGIPKNKKE------CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
           +  ++ Y  +++G+  N+++       I N  + +  I    + VV   ++G   AI+H+
Sbjct: 162 KTAKREYLGIIYGVLTNQEDKENSHQGIINLPIGRHPIDRKKMAVVPLEKRGRE-AITHW 220

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKL 288
           ++++     +  ++    TGRTHQ+RVH+ + G PIVGD  Y  N   K N +       
Sbjct: 221 EILERLGN-YSLVKFTLETGRTHQIRVHSSYYGNPIVGDPLYSTNRSLKMNLSGQ----- 274

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            LHA  + L HP    +++  APLP  + K
Sbjct: 275 ALHAHKLTLTHPITSEKIEAIAPLPDELTK 304


>gi|323466424|gb|ADX70111.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 310

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 86/314 (27%), Positives = 155/314 (49%), Gaps = 47/314 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           VEN  E  RLD++     P ++   ++++++  ++ V+ K  K + +IQ+G  + I  P 
Sbjct: 16  VEN--EYGRLDKFVSEQIPDLSRTRVKELVKEKEILVNHKVEKVSYKIQAGDKIEINVPA 73

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
           +  L+ ++ E   LD               ++YED  + V NKP G+ V    G      
Sbjct: 74  VKPLD-VVPENIPLD---------------IVYEDEDVIVVNKPQGMVVHPAPGHPDHTL 117

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + YH     +S    +G +P + HR+D++TSG+L++A+   A + L +    +  ++
Sbjct: 118 VNALLYHTQDLAQS---PEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNKR 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IYW++V G    ++  + +  + ++      + VV+  +K    A++HFKV+  F + + 
Sbjct: 175 IYWAIVHG-NFGEENGVIDAPIGRNPYDRKKMAVVENGKK----AVTHFKVLRQF-KGYS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPH 299
            +E Q  TGRTHQ+RVH  ++G  + GD  Y      KGN         +LHA+ +   H
Sbjct: 229 LIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPRKTLKGNGQ-------FLHAKVLGFKH 281

Query: 300 PEGGR-LQITAPLP 312
           P  G+ L+ T   P
Sbjct: 282 PRTGKWLEFTVEPP 295


>gi|297183890|gb|ADI20012.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium EB000_65A11]
          Length = 318

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 90/330 (27%), Positives = 156/330 (47%), Gaps = 47/330 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  D    RLD      +P  +   LQ  +++G++ VD ++ K  +++  G++V     
Sbjct: 10  IVPEDLAFNRLDHVASALFPQYSRSRLQTWIKNGELVVDGQKRKSKDKVTGGELV----- 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                       I  S++  T  +  +   + YED  + V NKP+G+ V  G+G   + D
Sbjct: 65  -----------AIQSSAIETTYEAQAIPLNVAYEDEHLLVVNKPSGLVVHPGAG---NFD 110

Query: 131 GFLKSWVDSKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + +    ++    PR  + HRLD++T+G+LVVA+T     HL +  + R + +IY 
Sbjct: 111 GTLLNGLLHHAEQLNGIPRAGIVHRLDKDTTGLLVVAKTLTTQHHLVQQLQARSVSRIYD 170

Query: 185 SLVWG-IPKNKK--ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++V+G + ++ K  + I     +++ +             G   AI+H+KV+  F +   
Sbjct: 171 AVVYGSLTRSGKVDQPIGRHTTQRTKMA---------IRPGGKPAITHYKVVRNFGE-HS 220

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHAR 293
            +E+   TGRTHQ+RVH   +  P++GD+ Y   FK   +  S +   L       LHAR
Sbjct: 221 HIELALETGRTHQIRVHMQSISHPLIGDNTYGGGFKEPAHKDSGLLKALREFKRPALHAR 280

Query: 294 YMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
            + L HP     +   A +P  M    D L
Sbjct: 281 ELKLIHPATEEEMHWCAEIPVDMQTLLDDL 310


>gi|158335489|ref|YP_001516661.1| RluA family pseudouridine synthase [Acaryochloris marina MBIC11017]
 gi|158305730|gb|ABW27347.1| pseudouridine synthase, RluA family [Acaryochloris marina
           MBIC11017]
          Length = 328

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 89/318 (27%), Positives = 144/318 (45%), Gaps = 38/318 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHII 78
           R+DRW  N    ++  ++QK++  G V+++ K        +Q G  V +        HI 
Sbjct: 14  RIDRWLANQVDSLSRSHIQKLIEQGHVQINHKICTSKKYALQIGDQVEV--------HIP 65

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSW 136
             Q        L    + +   +L+ED  + + NKPAG+ V    G A    + G L   
Sbjct: 66  APQP-------LALEPEPMDLEILFEDDHLLIVNKPAGLVVHPAPGHATGTLVHGLLAHC 118

Query: 137 VDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            D +G         ++P + HRLD++T+G ++VA+T  A QHL      +   + Y  LV
Sbjct: 119 QDGQGSTLSGIGGVERPGIVHRLDKDTTGAIMVAKTNQAHQHLQAQIAAKTALREYVGLV 178

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G P      +   + +  H        V   E+G   A++H++++      +  ++ + 
Sbjct: 179 YGRPSALTGRMEFPIGR--HRSDRIKMAVVPEEQGGKVAVTHWQILQPLG-NYALVKFRL 235

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHPE-GGR 304
            TGRTHQ+RVH   MG PIVGD  Y    + K N +  +     LHA  + L HP     
Sbjct: 236 ETGRTHQIRVHCAQMGWPIVGDPLYSRGRSLKVNLSGQV-----LHAWRLSLKHPVFHTE 290

Query: 305 LQITAPLPAHMVKTWDSL 322
           + + APLP   VK  + L
Sbjct: 291 ISVQAPLPIDFVKLLNRL 308


>gi|312127570|ref|YP_003992444.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311777589|gb|ADQ07075.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           hydrothermalis 108]
          Length = 299

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 93/318 (29%), Positives = 163/318 (51%), Gaps = 47/318 (14%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           RLDR+         +FV  QKI+  G V V++ +V K   +++SG ++++         +
Sbjct: 9   RLDRYLSEALSKTRSFV--QKIIEEGNVLVNQTQVLKPAYKVKSGDIIKV---------V 57

Query: 78  IKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
           I E K   I+   +N+          ++YED  + V NKP G+ V  G+G         +
Sbjct: 58  IPEPKQLSIVAQDINIE---------VVYEDEHLAVINKPRGMVVHPGAGNFENTLVNAL 108

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   G L S   +   +P + HRLD++TSG+LVVA+T  A   L+E+ +  +I++IY++
Sbjct: 109 LHKFRGRLSSI--NGVIRPGIVHRLDKDTSGLLVVAKTDEAHVKLSEALKSHQIKRIYYA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G+ K     I N  + +  +    + VV   ++    A+++F+V++ F  K+ ++++
Sbjct: 167 ICEGVLKEDSGVI-NAPIGRHPVNRLKMAVVPNGKE----AVTYFEVLERF-DKYTFVKL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +  TGRTHQ+RVH  ++G P++GD  Y    K  F    Q    LHA  ++  HP     
Sbjct: 221 RLKTGRTHQIRVHMSYIGYPLLGDGTY-GRAKNEFGVEGQ---VLHAGEIEFVHPITSEV 276

Query: 305 LQITAPLPAHMVKTWDSL 322
           L  +A LP + +K  + L
Sbjct: 277 LHFSAELPEYFLKILNIL 294


>gi|307243485|ref|ZP_07525636.1| pseudouridine synthase, RluA family [Peptostreptococcus stomatis
           DSM 17678]
 gi|306493129|gb|EFM65131.1| pseudouridine synthase, RluA family [Peptostreptococcus stomatis
           DSM 17678]
          Length = 310

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 92/329 (27%), Positives = 157/329 (47%), Gaps = 51/329 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---- 67
           V+ D    RLD +  + Y  I+   +QK+++ G V V+++  K + +++ G  + I    
Sbjct: 13  VDQDSAGKRLDVFIADQYQDISRSYVQKLIKDGLVLVNEEVKKASYKLEEGDRMEIAMPE 72

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
           P V+  L   I     LD               ++YED  + + NKP G+ V    G   
Sbjct: 73  PEVLEVLAQDID----LD---------------IVYEDDDLLIVNKPQGMVVHPAPGNPD 113

Query: 125 ------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 I YH    L S   +   +P + HR+D+ TSG+LVVA+  A+ Q L + F++  
Sbjct: 114 GTLVNAIMYHCKDKLSSI--NGVIRPGIVHRIDKNTSGLLVVAKNNASHQGLADQFKLHS 171

Query: 179 IQKIYWSLVWGIPKNKKECIANW--LLKKSHIGGDYVHVVKQN--EKGANYAISHFKVID 234
           I + Y  +  G          NW  +    +IG +    +K    + G  +A++HF VI+
Sbjct: 172 ITREYEMVCIG--------GVNWDQMTIDKNIGRNPKDRLKMAVLDTGGRHAVTHFTVIE 223

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              + + +++ +  TGRTHQ+RVH+ ++  PI+GD  Y    K    S ++ +  LHAR 
Sbjct: 224 HL-EGYTYMKAKLETGRTHQIRVHSNYLRHPILGDTLYGYQVKK--FSKLEGQT-LHARK 279

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP  G  ++ T+ LP +  K  D++
Sbjct: 280 LGFVHPRTGEYMEFTSDLPDYFKKILDTI 308


>gi|189499996|ref|YP_001959466.1| pseudouridine synthase, RluA family [Chlorobium phaeobacteroides
           BS1]
 gi|189495437|gb|ACE03985.1| pseudouridine synthase, RluA family [Chlorobium phaeobacteroides
           BS1]
          Length = 346

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 88/333 (26%), Positives = 149/333 (44%), Gaps = 41/333 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V   ++ MR+D +      +     +Q+ +   +VRV+ K VK N +I+S   + I  + 
Sbjct: 27  VAQTQKPMRIDVYLAQQVENATRNKVQEAISEHRVRVNGKTVKANYKIKSLDSIEITFLR 86

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------- 124
                +  E   +D               ++YED+ + V NK  G+ V    G       
Sbjct: 87  PPAPELAPEDIPVD---------------IIYEDNDLMVINKAPGMVVHPAFGNWTGTLA 131

Query: 125 --IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             I +H+ G     +D+   +P + HRLD+ TSG+++VA+   A   L + F  R+++K 
Sbjct: 132 NAILHHL-GTDAEKLDTTELRPGIVHRLDKNTSGLIIVAKHATALHRLAKQFAERQVEKK 190

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++VWG+P+   E I    + +S      +       K    A++ ++V++   + F  
Sbjct: 191 YQAIVWGVPE-PPEGIVKTNIGRSIRDRKVMTSYDFEGKEGKTAVTEYRVVENL-RYFSL 248

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY------------CANFKGNFTSPIQNKLYL 290
           +EM  HTGRTHQ+RVH  H+  PI+GD  Y              +F  N    I  +  L
Sbjct: 249 VEMILHTGRTHQIRVHLKHINAPILGDETYGGAGVQSLPFSKSESFVKNLLERIPRQ-AL 307

Query: 291 HARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           HA  +    P    R+ ++AP P  M    D +
Sbjct: 308 HAASLSFFQPTTRERITLSAPQPEDMQAALDKI 340


>gi|167771408|ref|ZP_02443461.1| hypothetical protein ANACOL_02774 [Anaerotruncus colihominis DSM
           17241]
 gi|167666048|gb|EDS10178.1| hypothetical protein ANACOL_02774 [Anaerotruncus colihominis DSM
           17241]
          Length = 306

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 91/326 (27%), Positives = 153/326 (46%), Gaps = 39/326 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Y   E  +  +R DRW  +    +     +QK+     VRV +K V  N+R++ G+   I
Sbjct: 5   YYTSEESDAGVRADRWLASAAEGLLTRSAIQKLCDCKAVRVGEKPVSKNDRLRGGETFII 64

Query: 68  P-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
             P    L+ + ++  I                 ++YED  + V NKP G+ V    G  
Sbjct: 65  DVPDAQPLDIVPQDIPIE----------------IVYEDGDLLVVNKPKGMVVHPAPGHP 108

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  + YH  G L S   +   +P + HR+D++TSG+L+VA+  AA   L E  +  
Sbjct: 109 NGTLVNALLYHCQGRLSSI--NGVIRPGIVHRIDKDTSGLLIVAKNDAAHGTLAEQIKNH 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              +IY ++V+G   +  E   +  + +S      + V  +N +GA   ++H++V++   
Sbjct: 167 SFTRIYNAVVYG-GFSTDEGTVDAPIGRSQNDRKKMCVTDRNARGA---VTHYRVLERLG 222

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            +F WL++   TGRTHQ+RVH  ++G P+ GD  Y    +   TS   +   LHAR +  
Sbjct: 223 -RFTWLKLCLETGRTHQIRVHMAYIGHPVAGDPIYGP--QKTITS--LHGQCLHARVIGF 277

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL 322
            HP  G  ++ ++ LP +      SL
Sbjct: 278 HHPRTGVYMEFSSELPDYFSTFLTSL 303


>gi|220924284|ref|YP_002499586.1| pseudouridine synthase [Methylobacterium nodulans ORS 2060]
 gi|219948891|gb|ACL59283.1| pseudouridine synthase [Methylobacterium nodulans ORS 2060]
          Length = 228

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 75/232 (32%), Positives = 116/232 (50%), Gaps = 19/232 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           S +LY D+ + V +KPAG+ V    +GG  +  H+D           ++P   HRLD++T
Sbjct: 8   SRVLYRDALVLVIDKPAGLPVHPGPRGGETLVQHLDALRFGLP----RRPEAAHRLDRDT 63

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L + R   A   L   F    ++K YW+LV G+P  ++  I   L ++S    D   
Sbjct: 64  SGCLALGRHAKALARLGGLFAGCEVRKTYWALVEGMPAAEEGAIDLPLARRSD---DPRS 120

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-C 273
              + +   + A++ +++         WLE++P TGRTHQLRVH   MG PI GD  Y  
Sbjct: 121 WWMKPDPAGDPALTRWRLRGRGPDGSAWLELEPVTGRTHQLRVHCAAMGWPIRGDAIYGV 180

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
           A  +G         L LHAR + LP +P+   + + AP+P H+     + G+
Sbjct: 181 APRQGG------PGLQLHARALTLPLYPKKPAIAVAAPVPPHIRPGLSACGW 226


>gi|154494935|ref|ZP_02033940.1| hypothetical protein PARMER_03979 [Parabacteroides merdae ATCC
           43184]
 gi|154085485|gb|EDN84530.1| hypothetical protein PARMER_03979 [Parabacteroides merdae ATCC
           43184]
          Length = 225

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 72/219 (32%), Positives = 109/219 (49%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I   NK     VQG       +   LK+W+  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIAVNKTCREIVQGDKTGDTPLSDMLKAWLKEKYCKPGNVFVGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR+  ++K YW++V   P  ++  + NWL++       Y + 
Sbjct: 63  GVVLFAKTSKALARLNEMFRVGEVKKTYWAIVKNCPPAEEGELVNWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  A+ H+KVI   +  +  L +   TGR HQ+R     MGCPI GD KY   
Sbjct: 123 TERT--NAKKAVLHYKVI-ARSDNYYLLAIDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
             G   S     + LH+R  +  HP   + + I AP+PA
Sbjct: 177 --GFPRSNPDGGISLHSRSAEFIHPVSKQPVSIVAPVPA 213


>gi|49066398|gb|AAT49291.1| putative bacteriocin [Prevotella nigrescens]
 gi|242332477|tpg|DAA06525.1| TPA_exp: NigA [Prevotella nigrescens]
          Length = 363

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 93/340 (27%), Positives = 161/340 (47%), Gaps = 53/340 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +E +R+D++      H +   +QK   +G + V+   VK N +++   V+ +  
Sbjct: 36  VEVDKGQEAVRIDKFLFERMQHSSRNRIQKAADAGSIYVNGTPVKSNYKVRPNDVITL-- 93

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I+   + L          ++YED++I V NKPAG+ V  G+G     
Sbjct: 94  ---MLDRPKHDNTIVAEDMPLN---------VVYEDNEIMVINKPAGLVVHPGAGNFRGT 141

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+   LK++ D       L HR+D++TSG+L++A+T  A   L + F  +   
Sbjct: 142 LINAIAWHLRD-LKNF-DPNDPAVGLVHRIDKDTSGLLLIAKTPDAKTFLGKQFFNKTTH 199

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-----VHVVKQNEKGANYAISHFKVIDC 235
           + Y +LVWG     +  I      + +IG D      + V   +      A++H+KV++ 
Sbjct: 200 RSYVALVWGNFTEDEGRI------EGNIGRDSKDRLRMKVFDTDSGIGKPAVTHYKVLER 253

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ-------- 285
           F      +E    TGRTHQ+R H  H+G P+ GD +Y      +G  TS  +        
Sbjct: 254 FGYT-TLIECILETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRTSAYRAYIQNCFK 312

Query: 286 --NKLYLHARYMDLPHPEGG-RLQITAPLP---AHMVKTW 319
             N+  LHA+ +   HP  G ++  T+ LP   + +++ W
Sbjct: 313 LCNRQALHAKTLGFVHPRTGEQMDFTSELPDDLSSVIEKW 352


>gi|323691964|ref|ZP_08106213.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
 gi|323503973|gb|EGB19786.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
          Length = 305

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 89/332 (26%), Positives = 156/332 (46%), Gaps = 51/332 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV-- 65
           +Y+V E     +R+D++     P      LQK+L+S  V V+ K VK + +  +G  V  
Sbjct: 4   EYIVPEKSS-GLRIDKFLTEICPDYTRSFLQKLLKSELVEVNGKPVKSSYKTAAGDTVTF 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +P  + A   I  ++  LD               +LYED  + + NKP G+ V   +G 
Sbjct: 63  EVPEAVEA--EITAQEMPLD---------------ILYEDEDVILINKPKGMVVHPAAG- 104

Query: 126 AYHIDGFLKSWVD----------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             H +G L + +           +   +P + HR+D +T+G+L+V +   A   + E  +
Sbjct: 105 --HYEGTLVNGLMHHCREQLSGINGVMRPGIVHRIDMDTTGVLIVCKNDLAHNSIAEQLK 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKV 232
           +  I + Y+++V+G  K+ +  I   +       G + +  K+   N K    A++H+KV
Sbjct: 163 VHSITRKYYAVVFGSLKDDEGTIHAPI-------GRHPNDRKKMSINSKNGKDAVTHYKV 215

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLH 291
           ++ F   +  +E +  TGRTHQ+RVH   +G P++GD  Y     G    P +     LH
Sbjct: 216 LERF-HGYTLVECRLETGRTHQIRVHMASIGHPLLGDQVY-----GPAKQPFRLQGQTLH 269

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           A  +   HP  G  ++ +APLP +  +  + L
Sbjct: 270 AGVLGFLHPRTGEYMEFSAPLPKYFEELLEKL 301


>gi|297180914|gb|ADI17118.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0070_03O15]
 gi|297181510|gb|ADI17697.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0130_23I23]
          Length = 305

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 94/324 (29%), Positives = 160/324 (49%), Gaps = 43/324 (13%)

Query: 15  DEENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           DEEN   R+D +    +  ++   +Q ++  G+V V+ K V  + + +    + I   + 
Sbjct: 9   DEENANNRIDIFLSRKFDSLSRGIVQGLIDEGKVLVNGKTVDRDYKTKVDDQIEIEFDLE 68

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
             N        L   +NL          +++E++ + + +K AG++V  G+G   +  I+
Sbjct: 69  TNN------ADLPQDINLN---------IVFENNDLLIIDKHAGLTVHPGAGQKDSTLIN 113

Query: 131 GFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           G L  + D K + PR  + HRLD++TSG++++ART  +  +LT+  + R+I++ Y++LV 
Sbjct: 114 GLLYMYPDQK-KIPRYGVVHRLDKDTSGLMIIARTLESHTNLTDLIQTRKIKRNYYALVH 172

Query: 189 GIPKNKKECIANWLLKKS---HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           G P      IA   + K    H     +  VK+   G   AI+HFKV   F + F  L++
Sbjct: 173 GQP------IAGNTIDKPIGRHPKNRLLFCVKE---GGREAITHFKVHKKF-KNFSLLDV 222

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQ-----NKLYLHARYMDLP 298
              TGRTHQ+RVH  H+G PI GD  YC   N+K +  + I       +  LHA  ++  
Sbjct: 223 SLETGRTHQIRVHMQHIGHPIAGDQSYCRIKNWKNSTENEINALNSLGRQSLHAYKLEFT 282

Query: 299 HPEGGRLQITAPLPAHMVKTWDSL 322
           + E       + +P  + K  D L
Sbjct: 283 YEEKD-FSFLSNIPEELQKVIDQL 305


>gi|254415358|ref|ZP_05029119.1| pseudouridine synthase, RluA family [Microcoleus chthonoplastes PCC
           7420]
 gi|196177833|gb|EDX72836.1| pseudouridine synthase, RluA family [Microcoleus chthonoplastes PCC
           7420]
          Length = 330

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 83/293 (28%), Positives = 138/293 (47%), Gaps = 26/293 (8%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           N E + RLDR+     P ++   +QK++  G V       + N+ + + +   I P  ++
Sbjct: 8   NQENSDRLDRYLAQQLPDLSRSRIQKLIEEGNV-------QLNHNLCTSKKATIQPG-DS 59

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
           ++  I + K LD         + +   +LYED +I + NKPA + V    G      ++ 
Sbjct: 60  IHLTIPDAKPLDLK------PEAIPLDILYEDDQILIVNKPANLVVHPAPGHENGTLVNA 113

Query: 132 FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    +  G    Q+P + HRLD++T+G + +A+T  A  HL    + +  ++ Y  +V
Sbjct: 114 LLAHCPNLAGIGGVQRPGIVHRLDKDTTGAIAIAKTDHAHHHLQAQLKAKTARRDYLGVV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G P  +   I N+ + + H        V   EKG   AI+H+++ +     +  +  Q 
Sbjct: 174 YGSPATETGTI-NFPIGR-HPSDRKKMAVVPLEKGGRSAITHWQIKERLG-NYTLIHFQL 230

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            TGRTHQ+RVH  H+G PI+GD  Y          P Q    LHA  + L HP
Sbjct: 231 ETGRTHQIRVHTAHIGHPIIGDPVYSKGRDIGVNLPGQ---ALHAWRLQLQHP 280


>gi|87300810|ref|ZP_01083652.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 5701]
 gi|87284681|gb|EAQ76633.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 5701]
          Length = 315

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 93/303 (30%), Positives = 138/303 (45%), Gaps = 32/303 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRIPPVINALNH 76
           MRLDRW     P  +   +QK + +G VRV+    R K   R+            + +  
Sbjct: 22  MRLDRWLVAQRPEQSRARIQKFIDAGYVRVNGVTGRAKTPLRLH-----------DEVQL 70

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
            +   + L   +      D     +L+ED+ + V NKPAG++V    G      ++G L 
Sbjct: 71  WMPPPEPLPYLLPQPIPLD-----VLFEDAHLIVLNKPAGLTVHPAPGNRDGTLVNGLLH 125

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +VVA+++ A   L    + R   + Y ++V G 
Sbjct: 126 HCPDLPGIGGEMRPGIVHRLDKDTTGCIVVAKSQEALVRLQVQIQKRVASREYLAVVHGA 185

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +  H      + V   EKG  +A +H+ +I+     +  L  +  TG
Sbjct: 186 PAASSGTIVGAIGR--HPADRKKYAVVAEEKG-RFACTHWTLIERLGD-YSLLRFRLDTG 241

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  H+G PIVGD  Y    K     P Q    LHA  + L HP  G RL   A
Sbjct: 242 RTHQIRVHCAHIGHPIVGDVTYSRCRKLPLELPGQA---LHAVALGLDHPISGERLAFEA 298

Query: 310 PLP 312
           PLP
Sbjct: 299 PLP 301


>gi|73667158|ref|YP_303174.1| ribosomal large subunit pseudouridine synthase D [Ehrlichia canis
           str. Jake]
 gi|72394299|gb|AAZ68576.1| ribosomal large subunit pseudouridine synthase D [Ehrlichia canis
           str. Jake]
          Length = 323

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 92/328 (28%), Positives = 159/328 (48%), Gaps = 37/328 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN---RIQSGQVVR 66
           + ++ +E N RLD+   N   + +   +Q++++  +V +    +  NN   ++    ++ 
Sbjct: 6   IFIKIEEANNRLDKLIANKL-NTSRNQVQQLIKDSKVSLFNNIITDNNHTTKVNDIYIIN 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IP      N II    I  S              +LYED  I + NK +GI+V  G+G  
Sbjct: 65  IPTK-EISNTIIPNHSIPIS--------------VLYEDHDIIIINKTSGITVHPGAGTK 109

Query: 127 YH--IDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            +  ++  +  + ++     K  +P + HRLD++TSG++V+A+   +   L+E    ++I
Sbjct: 110 NNTLVNALVAHYGNALSTVGKATRPGIIHRLDKDTSGLMVIAKNEKSYYFLSELLLKKQI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++VWG P  K   I N++  K +     + V   + KG   AI+ +K    F+  
Sbjct: 170 KKEYLAVVWGSPNPKNNTIQNYICVKPN-NKQMMAVTHLSHKGK-LAITEYKTKQNFSNI 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQNKL---YLHA 292
              ++ + HTGRTHQ+RVH  H+G  I+GD KY  N     K    S I N L    LHA
Sbjct: 228 ASLIKCRIHTGRTHQIRVHMSHIGNSIIGDQKYGKNNSKITKYAKQSTIINTLKRQALHA 287

Query: 293 RYMDLPHP-EGGRLQITAPLPAHMVKTW 319
             +   HP +   ++  A +P H ++T 
Sbjct: 288 YKLGFIHPTKNTYIEFRADIP-HDIQTL 314


>gi|294782109|ref|ZP_06747435.1| tRNA pseudouridine synthase A [Fusobacterium sp. 1_1_41FAA]
 gi|294480750|gb|EFG28525.1| tRNA pseudouridine synthase A [Fusobacterium sp. 1_1_41FAA]
          Length = 296

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 159/313 (50%), Gaps = 27/313 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ + E +R+DR+ + H  +I    + K+LR  +++V+ K+V  + R+  G ++ +   
Sbjct: 5   IIDEEYETVRIDRFLRKHLKNIALSEIYKMLRKAKIKVNNKKVSQDYRLILGDIIFV--- 61

Query: 71  INALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
              L    KE+   ++ + L +   + LKS++ YE+  +++ NK  G  +  GSG    +
Sbjct: 62  --FLPENFKEKNEDETFIELNEIRKEKLKSMITYENENLFIINKNLGDVIHKGSGHDISL 119

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               +++  +   K    +R+D+ TSG+++ A+    A+ + +  ++  I K Y+ LV+G
Sbjct: 120 LEEFRAYYSN--NKVNFVNRIDKLTSGLVIGAKNIKTAREIAKEIQLGNITKKYYILVYG 177

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQKFCWLEMQP 247
             + ++  + N+L K      D   V+  + +  +Y  +I+H+K I+     +  LE + 
Sbjct: 178 KIEKEEFILENYLKK------DEEKVIVSDIEKEDYKKSITHYKRING-NDDYTLLEAEL 230

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQLR    H+G  IVGD KY  N K       +  +YL + Y+ +   +   L++
Sbjct: 231 KTGRTHQLRAQLNHIGHTIVGDTKYGKNIK-------EETMYLFSYYLKIDLYD---LEL 280

Query: 308 TAPLPAHMVKTWD 320
              +P    K ++
Sbjct: 281 EMGIPDFFFKKYN 293


>gi|170723708|ref|YP_001751396.1| RluA family pseudouridine synthase [Pseudomonas putida W619]
 gi|169761711|gb|ACA75027.1| pseudouridine synthase, RluA family [Pseudomonas putida W619]
          Length = 352

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 96/336 (28%), Positives = 150/336 (44%), Gaps = 42/336 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   V+  + +  G ++ +    
Sbjct: 43  VPSELGGQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDTVHGGSMLALEAEQ 102

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    I E   LD               ++YED +I V NKPAG+ V   +G   H  G
Sbjct: 103 EAQGEWIAEDIELD---------------IVYEDDQIMVINKPAGLVVHPAAG---HASG 144

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L E  + R + +IY  
Sbjct: 145 TLLNALLHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTLQAQTKLVEQLQSRTVSRIYEC 204

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+     +  A       H G      V +   G   A+SH++V+  F +    + +
Sbjct: 205 IVIGVVTAGGKINAPI---GRHGGARQRMAVTE---GGKPAVSHYRVLKRF-RSHTHVRV 257

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKLYLHARYMDL 297
           +  TGRTHQ+RVH  H+G P+VGD  Y   F+     SP          +  LHAR++ L
Sbjct: 258 KLETGRTHQIRVHMAHVGFPLVGDQTYGGRFRIPPAASPTMVEAVKTFPRQALHARFLAL 317

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            HP  G R++  + LP   V  W       DR  +I
Sbjct: 318 DHPTTGERMEWASELPDDFV--WLLSLLNQDREAFI 351


>gi|258647058|ref|ZP_05734527.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           tannerae ATCC 51259]
 gi|260853174|gb|EEX73043.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           tannerae ATCC 51259]
          Length = 360

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 93/341 (27%), Positives = 155/341 (45%), Gaps = 51/341 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV +  ++ +R+D++   H P  +   +Q+  ++G + ++ +  K N R++   VV +  
Sbjct: 33  VVADKGQQLLRVDKFLMAHLPDTSRNRIQQAAKAGFIHINGRPEKSNYRVKPHDVVTL-- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    E  I   ++ L          ++YED  + V NK AG+ V  G G     
Sbjct: 91  ---LLDRPRYENLIEPENIPLD---------IVYEDEALIVVNKSAGLVVHPGFGNYTGT 138

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +AYH    LK   D     P   L HR+D++TSG+LV+A+T  A   L   F  + 
Sbjct: 139 LVNALAYH----LKDVADYDPNDPGVGLVHRIDKDTSGLLVIAKTPDAKSKLGVQFFNKT 194

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVIDCF 236
            ++ Y +LVWG  K  +  I   + +  H   D +   V   +      A++H+KV+  F
Sbjct: 195 TRRRYEALVWGNVKTDEGRIEGNIARDPH---DRLQMAVFAPDSGIGKPAVTHYKVLKRF 251

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQN---- 286
                 +E Q  TGRTHQ+R H  H+G P+  D +Y  +        G + S I+N    
Sbjct: 252 GY-VTLIECQLETGRTHQIRTHMRHIGHPLFNDARYGGDKVLRGTTSGAYNSFIRNCFEI 310

Query: 287 --KLYLHARYMDLPHPEGGRLQITAPLPAH----MVKTWDS 321
             +  LHAR +   HP  G     + LP      +++ W++
Sbjct: 311 CPRQALHARTLGFKHPTTGEEMDFSVLPPQDFNGLIEKWET 351


>gi|146074929|ref|XP_001462641.1| pseudouridylate synthase-like protein [Leishmania infantum]
 gi|134066719|emb|CAM65179.1| pseudouridylate synthase-like protein [Leishmania infantum JPCM5]
 gi|322496043|emb|CBZ31115.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 413

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 96/360 (26%), Positives = 165/360 (45%), Gaps = 44/360 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV----RVDKKR-VKFNNRIQS 61
           +QY VV  D    R+D +   H+P  ++  ++++++ G +    +  KKR  +  +R++ 
Sbjct: 55  LQYHVVTQDWFGQRVDDFVMQHHPEWDYETVKRLVQQGHIYRYRKNGKKRYTRLTDRLEF 114

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNL------------------TKHSDFLKSILLY 103
            ++V +P          + Q    S V L                   K  +  + ++L+
Sbjct: 115 DELVVVP-----TASFWERQLAPPSGVELQSSSTSQQQERRQKFHLSAKTREMAQEMVLF 169

Query: 104 EDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           ++  + V NKP+G+ +      +A +I   L +W  +  QKP + H LD ETSG +V+AR
Sbjct: 170 KNEHVIVINKPSGVPIMPTHDPLAMNITDLLPAWRYTNTQKPVICHNLDTETSGCVVLAR 229

Query: 163 TRAAAQHLTESFRMRRI-QKIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNE 220
           +  A + L   F  R +   +YW    G P  N      ++ ++K   GGD +       
Sbjct: 230 SANAHRMLGRMFVKRVVPNSVYWGFAVGKPPVNFGRIRMHFEIQKGQ-GGDVIVARPTPT 288

Query: 221 KGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK- 277
             +   I+ F V++  A +F  ++   P T R HQ R+ A H +  P++GD KY      
Sbjct: 289 ADSKVGIAEF-VVNASALEFGSFISFYPLTTRRHQERIMAAHALRAPLLGDAKYGGESAF 347

Query: 278 ----GNFTSPIQN--KLYLHARYMDLPHPEGGR--LQITAPLPAHMVKTWDSLGFKYDRN 329
                 F  P +    L+LH R + LP+  G    + +TAPLP HM KT+  LG+  D +
Sbjct: 348 PHSLSLFWDPARKDVPLHLHHRKIQLPYKNGAGEFVCVTAPLPPHMEKTFKRLGWPVDAD 407


>gi|332884260|gb|EGK04528.1| hypothetical protein HMPREF9456_00855 [Dysgonomonas mossii DSM
           22836]
          Length = 355

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 93/344 (27%), Positives = 156/344 (45%), Gaps = 64/344 (18%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V +  +  +R+D++   H   ++   +Q+   +  + V+   VK N RI+   V+ +   
Sbjct: 32  VADKGQGMIRVDKYLAMHIVGVSRNRIQQAAEADCILVNNTPVKSNYRIKPLDVISV--- 88

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
              +N   +E +I+   + L          ++YED  + V NKP G+ V  G G      
Sbjct: 89  --VMNRPPRELEIIPEDIPLD---------VVYEDEDLMVINKPPGLVVHPGFGNYQGTM 137

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              IAY     LK   +   + PRL   HR+D++TSG+++VA+   A  HL+  F  +  
Sbjct: 138 VNAIAYR----LKDTPEYDSKDPRLGIVHRIDKDTSGLILVAKNAYAKTHLSAQFFNKTT 193

Query: 180 QKIYWSLVWG--------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           ++ Y +LVWG        I  N    + N +L       DY            +A++H+K
Sbjct: 194 KRQYIALVWGNISDDEGRIEANIGRSLKNRMLMTVFPEADY----------GKHAVTHYK 243

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQ 285
           V++        ++ +  TGRTHQ+RVH  H+G  +  D +Y  N   KG     +   +Q
Sbjct: 244 VLERLGY-VTLIQCRLETGRTHQIRVHMKHIGYTLFNDERYGGNEILKGTNFAKYKQFVQ 302

Query: 286 N------KLYLHARYMDLPHPEGGR-LQITAPLP---AHMVKTW 319
           N      +  LHA+ +   HP  G+ L   APLP   + +V+ W
Sbjct: 303 NCFNICPRQALHAQTLGFVHPRTGQELMFEAPLPDDMSQLVEKW 346


>gi|229496851|ref|ZP_04390560.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           endodontalis ATCC 35406]
 gi|229316262|gb|EEN82186.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           endodontalis ATCC 35406]
          Length = 359

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 91/333 (27%), Positives = 156/333 (46%), Gaps = 50/333 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+D++  +   H +   +Q    +G + V +  +K N +++ G V+ +  
Sbjct: 35  IVVDKGQTPLRIDKFLVDKLEHSSRHRIQLAAEAGYLFVGETPIKSNYKVRPGDVITL-- 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L     E+ I+   + L          ++YED+ + V NKPAG+ V  G+G     
Sbjct: 93  ---RLARPPHERGIVAEDIPLE---------VVYEDNDLLVVNKPAGMVVHPGNGNYTGT 140

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +AY+     K   D+      L HR+D++TSG+LVVA+   A   L + F  +  +
Sbjct: 141 LVNALAYYFRDDPK--YDANDPNVGLVHRIDKDTSGLLVVAKRPEAKTALGKQFFEKTSE 198

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDC 235
           + Y +LVWG  K  +  I      + +IG D      + V   N      AI+H++V++ 
Sbjct: 199 RSYRALVWGAFKESEGRI------EGNIGRDPRDRTRMSVFPPNSDEGKNAITHYRVLET 252

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP---------- 283
           FA    ++E +  TGRTHQ+R H   +  P+ GD KY  +   +G  +S           
Sbjct: 253 FA-FVSYIECRLETGRTHQIRAHMKSINHPLFGDEKYGGSEILRGRPSSSYLSFARHMLE 311

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           +  +  LHAR +   HP  G  ++  AP+P  M
Sbjct: 312 LCPRQALHARTLGFTHPLTGEFMRFEAPIPRDM 344


>gi|148269598|ref|YP_001244058.1| RluA family pseudouridine synthase [Thermotoga petrophila RKU-1]
 gi|147735142|gb|ABQ46482.1| ribosomal large subunit pseudouridine synthase D [Thermotoga
           petrophila RKU-1]
          Length = 311

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 92/309 (29%), Positives = 155/309 (50%), Gaps = 29/309 (9%)

Query: 12  VENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VE  EE  RLD++ K   P  I+   +QK ++ G+V+V+ +  K + +++ G++V +   
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSLIQKAIKEGKVKVNGQIKKPSYKLKEGEIVEV--- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
              L    +E  +    + L          +LYED  I V +KP  + V           
Sbjct: 63  --DLPEKPQEATVQPEEIELK---------VLYEDRDIVVIDKPGDMIVHPVPSKLSGTL 111

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D +G     +P + HRLD+ETSG++VVA+   A Q L++ F+ R+++K Y 
Sbjct: 112 VNALLNHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYI 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  K K E + +  L +  +    + VV+  ++    AI+ ++V+  F      + 
Sbjct: 172 LLVKGRVK-KDEGVVDLPLARHPVLRIKMAVVETGKE----AITEYRVLKRFDDVATLVL 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P TGRTHQ+RVH   +G PI+GD  Y    K +    I+ ++ LHA  +   HP  G+
Sbjct: 227 AFPKTGRTHQIRVHMKSLGHPIMGDKIY-GKPKEDEIFGIKRQM-LHALKLGFFHPRTGK 284

Query: 305 -LQITAPLP 312
            ++  +PLP
Sbjct: 285 WMEFVSPLP 293


>gi|256819393|ref|YP_003140672.1| pseudouridine synthase, RluA family [Capnocytophaga ochracea DSM
           7271]
 gi|256580976|gb|ACU92111.1| pseudouridine synthase, RluA family [Capnocytophaga ochracea DSM
           7271]
          Length = 352

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 85/322 (26%), Positives = 153/322 (47%), Gaps = 43/322 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  N   +     +Q+  + G + V+ + VK N+R+++   V++        
Sbjct: 35  QEPLRVDKFLMNFVENATRNKVQQAAKQGNIFVNGEPVKSNHRVKANDEVKV-----LFP 89

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           H   E  ++  ++ L          ++YED  + V NKPAG+ V  G G         + 
Sbjct: 90  HPPHEDLLVPENIPLN---------IVYEDDSLLVVNKPAGMVVHPGHGNYSGTLINALV 140

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH +    +  ++   +P L HR+D++TSG+LVVA+T  A  HLT+ F  +  Q+ Y +L
Sbjct: 141 YHFE----NLPNNSSNRPGLVHRIDKDTSGLLVVAKTEEAMLHLTQQFFNKTTQREYIAL 196

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           VWG  +  +  +   + +  H+       V  +      A++H+KV++ F      +  +
Sbjct: 197 VWGNIEEDEGTVCGHIGR--HLKDRLQMDVFPDGSHGKEAVTHYKVLERFGY-VTLISCK 253

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN------KLYLHARY 294
             TGRTHQ+RVH  H+G  +  D +Y  +   KG     +   ++N      +  LHA+ 
Sbjct: 254 LETGRTHQIRVHLKHIGHTLFNDERYGGDKILKGTTFAKYKQFVENCFAVLPRQALHAKT 313

Query: 295 MDLPHPEGGR-LQITAPLPAHM 315
           +   HP   + L   + LP  M
Sbjct: 314 LGFEHPITHKYLSFDSELPNDM 335


>gi|289667068|ref|ZP_06488143.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. musacearum NCPPB4381]
          Length = 331

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 91/348 (26%), Positives = 160/348 (45%), Gaps = 40/348 (11%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L   ++  +V ++    R D      +P  +   L + ++SG   +D    +  + ++ 
Sbjct: 8   ALEPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRG 67

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G+ V++  V+    H   +   L                +LYED ++ V +KPAG+ V  
Sbjct: 68  GESVQVQVVLETQTHAAPQDIPLS---------------VLYEDEQVLVIDKPAGLVVHP 112

Query: 122 GSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G+G   + DG L + +     +    PR  + HRLD++TSG++VVART  A   L E   
Sbjct: 113 GAG---NPDGTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLS 169

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + + Y ++V G   +     AN  + + H        V+ + +    A++H+++ + 
Sbjct: 170 ARDVHRQYLAVVVGALVSG--GTANAPIDR-HPRDRLKMAVRDDGRD---AVTHYRLRER 223

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL----- 288
           F +    LE +  TGRTHQ+RVH  H+  PIVGD  Y    K     T  + ++L     
Sbjct: 224 F-RAHTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKR 282

Query: 289 -YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
             LHA  ++  HP  G  ++ +AP+PA + +   +L     R   + R
Sbjct: 283 QALHAETLEFRHPVSGEPVRASAPVPADLQRLMTALREDSARAAEMAR 330


>gi|257878226|ref|ZP_05657879.1| pseudouridylate synthase [Enterococcus faecium 1,230,933]
 gi|257880994|ref|ZP_05660647.1| pseudouridylate synthase [Enterococcus faecium 1,231,502]
 gi|257889576|ref|ZP_05669229.1| pseudouridylate synthase [Enterococcus faecium 1,231,410]
 gi|257892484|ref|ZP_05672137.1| pseudouridylate synthase [Enterococcus faecium 1,231,408]
 gi|258616265|ref|ZP_05714035.1| hypothetical protein EfaeD_11195 [Enterococcus faecium DO]
 gi|260559776|ref|ZP_05831955.1| pseudouridylate synthase [Enterococcus faecium C68]
 gi|293559348|ref|ZP_06675890.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1162]
 gi|293569846|ref|ZP_06680933.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1071]
 gi|294621730|ref|ZP_06700894.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium U0317]
 gi|314939741|ref|ZP_07846963.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|314941758|ref|ZP_07848635.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|314948303|ref|ZP_07851695.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
 gi|314952391|ref|ZP_07855398.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|314991990|ref|ZP_07857443.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|314995712|ref|ZP_07860802.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|257812454|gb|EEV41212.1| pseudouridylate synthase [Enterococcus faecium 1,230,933]
 gi|257816652|gb|EEV43980.1| pseudouridylate synthase [Enterococcus faecium 1,231,502]
 gi|257825936|gb|EEV52562.1| pseudouridylate synthase [Enterococcus faecium 1,231,410]
 gi|257828863|gb|EEV55470.1| pseudouridylate synthase [Enterococcus faecium 1,231,408]
 gi|260074000|gb|EEW62323.1| pseudouridylate synthase [Enterococcus faecium C68]
 gi|291587594|gb|EFF19471.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1071]
 gi|291598739|gb|EFF29792.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium U0317]
 gi|291606712|gb|EFF36104.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1162]
 gi|313590103|gb|EFR68948.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313593425|gb|EFR72270.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|313595508|gb|EFR74353.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|313599436|gb|EFR78279.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|313640970|gb|EFS05550.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|313645284|gb|EFS09864.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
          Length = 303

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 92/322 (28%), Positives = 155/322 (48%), Gaps = 51/322 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E+ R+D+   N +   +   +Q  L++G V V+ + VK N +++ G  + +         
Sbjct: 11  ESGRIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVKANYKVKQGDEITV--------- 61

Query: 77  IIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
           +I E + LD    ++ LT         ++YED  + V NKP G+ V   +G         
Sbjct: 62  LIPEPETLDVVPENIPLT---------IVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNA 112

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + YHI     S ++    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y 
Sbjct: 113 LMYHIKDL--STINGV-IRPGIVHRIDKDTSGLLMVAKNDQAHESLAQQLKDKTSLRKYV 169

Query: 185 SLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G IP  K    A     K +     +  ++++ K A   ++HF V++ F + F  +
Sbjct: 170 ALVHGEIPHEKGTINAPIGRSKEN---RKMQAIREDGKSA---VTHFTVLERF-EGFTLV 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E++  TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP 
Sbjct: 223 ELKLETGRTHQIRVHMKYIGYPLAGDPVYGPKKTLKGNGQ-------FLHAQMLGFTHPT 275

Query: 302 GGRLQI-TAPLPAHMVKTWDSL 322
                I  APLP    KT + L
Sbjct: 276 TNEKMIFEAPLPEVFEKTLEKL 297


>gi|10129882|dbj|BAB13516.1| pseudouridine synthase homolog [Sinorhizobium meliloti]
          Length = 264

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 124/244 (50%), Gaps = 33/244 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQE 153
           +LYED+ + V  KPAG+ V  G+G      ++  +    DS       ++P + HRLD++
Sbjct: 13  VLYEDADLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGGVKRPGIVHRLDKD 72

Query: 154 TSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           TSG++VVA+  AA +HL++ F    R   +++ Y ++VWG P+  K  I   L +     
Sbjct: 73  TSGVMVVAKNDAAHRHLSDQFADHGRNGPLERAYRAVVWGRPRQLKGKIDAPLGR----A 128

Query: 210 GDYVH--VVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALH 261
           GD     V +++   A  AI+H++V++ + +K         +E    TGRTHQ+RVH  H
Sbjct: 129 GDRTKRAVKREDSDDAREAITHYEVVERYHEKPDGTSLASTVECHLETGRTHQIRVHMAH 188

Query: 262 MGCPIVGDHKYCANFKGN---FTSPIQNKL------YLHARYMDLPHPEGGR-LQITAPL 311
           +G P++GD  Y A F+        P +  +       LHA  +   HP  G  +    P+
Sbjct: 189 IGHPLIGDPDYGAAFRTKANLLPEPARAAVNRFPRQALHAFMLQFEHPATGETMHFETPV 248

Query: 312 PAHM 315
           PA M
Sbjct: 249 PADM 252


>gi|260101276|ref|ZP_05751513.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           helveticus DSM 20075]
 gi|260084917|gb|EEW69037.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           helveticus DSM 20075]
          Length = 306

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 86/314 (27%), Positives = 155/314 (49%), Gaps = 47/314 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           VEN  E  RLD++     P ++   ++++++  ++ V+ K  K + +IQ+G  + I  P 
Sbjct: 12  VEN--EYGRLDKFISEQIPDLSRTRVKELVKEKEILVNHKVEKVSYKIQAGDKIEINVPA 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
           +  L+ ++ E   LD               ++YED  + V NKP G+ V    G      
Sbjct: 70  VKPLD-VVPENIPLD---------------IVYEDEVVIVVNKPQGMVVHPAPGHPDHTL 113

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + YH     +S    +G +P + HR+D++TSG+L++A+   A + L +    +  ++
Sbjct: 114 VNALLYHTQDLAQS---PEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNKR 170

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IYW++V G    ++  + +  + ++      + VV+  +K    A++HFKV+  F + + 
Sbjct: 171 IYWAIVHG-NFGEENGVIDAPIGRNLYDRKKMAVVENGKK----AVTHFKVLKQF-KGYS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPH 299
            +E Q  TGRTHQ+RVH  ++G  + GD  Y      KGN         +LHA+ +   H
Sbjct: 225 LIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPRKTLKGNGQ-------FLHAKVLGFKH 277

Query: 300 PEGGR-LQITAPLP 312
           P  G+ L+ T   P
Sbjct: 278 PRTGKWLEFTVEPP 291


>gi|302670833|ref|YP_003830793.1| pseudouridine synthase RluA family protein [Butyrivibrio
           proteoclasticus B316]
 gi|302395306|gb|ADL34211.1| pseudouridine synthase RluA family [Butyrivibrio proteoclasticus
           B316]
          Length = 309

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 150/318 (47%), Gaps = 40/318 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIP 68
           +V ++ + MR+D+        ++   ++K++   +V  + K VK +  +      V+ IP
Sbjct: 11  IVTDEYDGMRIDKLISELIDSLSRTYIKKLIDDKKVSCNGKVVKASFHVSENDEIVMEIP 70

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
           P+   +  I+ +   LD               ++YED+ + V NKP  + V   +G    
Sbjct: 71  PI--EIPQILPQDIPLD---------------IIYEDNDVVVVNKPKDMVVHPAAGHYKD 113

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                I YH    L     +   +P + HR+D++T+G +++ +   A Q + E  +   I
Sbjct: 114 TLVNAIMYHCKDNLSGI--NGVMRPGIVHRIDKDTTGSVIICKNDNAHQSIAEQLKEHSI 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            ++Y ++ +G+ K + E      + +S      + VV     G  YA +H++V+  F + 
Sbjct: 172 NRVYHAICYGVIK-EDEGDVTAPIGRSVNDRKKMAVVP----GGKYASTHYRVLKRFPED 226

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F ++E +  TGRTHQ+RVH  H+G P++GD  Y +     F +   N   LHA+ +   
Sbjct: 227 GFTYIECKLQTGRTHQIRVHMSHIGHPLLGDEVYASGRHSKFKT---NGQCLHAKTLGFI 283

Query: 299 HPEGGR-LQITAPLPAHM 315
           HP  G  ++  APLP + 
Sbjct: 284 HPVSGEYIETDAPLPEYF 301


>gi|15643228|ref|NP_228272.1| hypothetical protein TM0462 [Thermotoga maritima MSB8]
 gi|4980971|gb|AAD35547.1|AE001724_5 conserved hypothetical protein [Thermotoga maritima MSB8]
          Length = 311

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 92/309 (29%), Positives = 154/309 (49%), Gaps = 29/309 (9%)

Query: 12  VENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VE  EE  RLD++ K   P  I+   +QK ++ G+V+V+ +  K + +++ G++V +   
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSMIQKAIKEGKVKVNGQIKKPSYKLKEGEIVEV--- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
              L    +E  +    + L          +LYED  I V +KP  + V           
Sbjct: 63  --DLPEKPQEATVQPEEIELK---------VLYEDRDIIVIDKPGDMIVHPVPSKLSGTL 111

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D +G     +P + HRLD+ETSG++VVA+   A Q L++ F+ R+++K Y 
Sbjct: 112 VNALLHHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYI 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  KN  E + +  L +  +    + VV+  ++    AI+ ++V+  F      + 
Sbjct: 172 LLVKGKMKN-DEGVIDLPLARHPVLRIKMAVVETGKE----AITEYRVLKRFDDVATLVL 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P TGRTHQ+RVH   +G PI+GD  Y    K +    I+ ++ LHA  +   HP  G 
Sbjct: 227 AFPKTGRTHQIRVHMKSLGHPIMGDKIY-GKPKEDEIFGIKRQM-LHALKLGFFHPRTGE 284

Query: 305 -LQITAPLP 312
            ++  +PLP
Sbjct: 285 WMEFVSPLP 293


>gi|86144060|ref|ZP_01062398.1| ribosomal large subunit pseudouridine synthase D [Leeuwenhoekiella
           blandensis MED217]
 gi|85829520|gb|EAQ47984.1| ribosomal large subunit pseudouridine synthase D [Leeuwenhoekiella
           blandensis MED217]
          Length = 344

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 87/325 (26%), Positives = 157/325 (48%), Gaps = 49/325 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  N         +Q+  ++G ++V+   VK N+++++  VVR+        
Sbjct: 28  QEPLRVDKFLMNFIEKATRNKIQQAAKNGNIQVNGAVVKQNHKVKANDVVRV-----LFE 82

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           H   E  +    + L          +++ED  + V NKPAG+ V  G G         + 
Sbjct: 83  HPPYEFLLTPEDIPLD---------IVFEDDTLLVVNKPAGMVVHPGHGNYSGTLINALI 133

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH D   +   +S G +P L HR+D++TSG+LVVA+T  A  HL + F  +  ++ Y ++
Sbjct: 134 YHFDNLPE---NSSG-RPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTSEREYIAI 189

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKF-CWL 243
           VWG  +  +  +   + +  H      + V ++      A++H+KV++   +  K  C L
Sbjct: 190 VWGNVEEDQGTVEGHIGR--HPKNRMQNTVYEDGDQGKEAVTHYKVLERLGYVTKISCKL 247

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN------KLYLH 291
           E    TGRTHQ+RVH  H+G  +  D +Y  +   KG     +   ++N      +  LH
Sbjct: 248 E----TGRTHQIRVHMKHIGHTLFNDERYGGDAILKGTTFTKYKQFVENCFKVLPRQALH 303

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHM 315
           A+ +   HP+ G  ++  + +P  M
Sbjct: 304 AKTLGFEHPKTGEWMRFDSAIPEDM 328


>gi|262198126|ref|YP_003269335.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262081473|gb|ACY17442.1| pseudouridine synthase, RluA family [Haliangium ochraceum DSM
           14365]
          Length = 369

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 89/337 (26%), Positives = 148/337 (43%), Gaps = 44/337 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+  VV+ D    RLD + K   P ++   LQ ++R     V  +++K +  + SG V+ 
Sbjct: 34  VRRFVVDEDSAGFRLDHYLKRQIPRLSRTKLQDVIRHQLEPVRGRQLKPSASVHSGDVI- 92

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                  ++   + +     ++ +           LY D  + V +KPAG+ V   +   
Sbjct: 93  ------VMSRRARPEPPCPRTIGV-----------LYSDPHMLVIDKPAGLPVHASA--R 133

Query: 127 YHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   +   +   GQ  ++ HRLD+ETSG LVVAR +  A  L  +F  +R  K Y +
Sbjct: 134 FYFNTLTRVLGERFPGQPMQICHRLDRETSGALVVARGKPEAARLKGAFADKRAHKTYLA 193

Query: 186 LVWGIPK---------NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           LVWG P           + + I +  L         + +  +   GA  +++  +V++  
Sbjct: 194 LVWGDPPWPDGAWDSAPEDDAIIDLPLGLVADESARIKIRMEVRAGALPSLTRVRVLE-R 252

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-------CANFKGNFTSPIQNKL- 288
             +   +   P TGR HQ+R H    G PIVGD  Y        A      T  +  ++ 
Sbjct: 253 RGRAALVRCLPLTGRQHQIRAHLAACGHPIVGDKLYAHGDDVFAAYCDRGMTPELLERVR 312

Query: 289 ----YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
                LHA  + LPHP EG +++  +PLPA M    D
Sbjct: 313 LPRQALHAAAIALPHPFEGRQVRAESPLPADMRAFLD 349


>gi|218245618|ref|YP_002370989.1| RluA family pseudouridine synthase [Cyanothece sp. PCC 8801]
 gi|218166096|gb|ACK64833.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8801]
          Length = 318

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 90/310 (29%), Positives = 147/310 (47%), Gaps = 34/310 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D W   +   I+  +LQK++  G + ++ + V  N + +     R+            
Sbjct: 21  RIDLWLSQNLDQISRSHLQKLIEQGNIYLNNQ-VCLNKKTKVNLGDRL------------ 67

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL------ 133
            Q  L     L    + +   +LYED  + + NK AG+ V    G   H  G L      
Sbjct: 68  -QVFLPPPEPLELQPEPIPLDILYEDDSLIIINKSAGLVVHPAPG---HTSGTLVHGLLY 123

Query: 134 --KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              + V   G Q+P + HRLD++T+G +VVA+T  A QHL    + +  ++ Y  +V+G+
Sbjct: 124 HCPNLVGIGGVQRPGIVHRLDKDTTGAIVVAKTDYAHQHLQAQLKAKTARREYLGVVYGV 183

Query: 191 PKNKK--ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           P++K   +   N  + + H G      V   E G   AI+H+++++     +  +E +  
Sbjct: 184 PRHKDTHQGTINVPIGR-HRGDRKKMAVVPVENGGREAITHWQIVERLG-NYTLVEFRLE 241

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
           TGRTHQ+RVH+ ++G PIVGD  Y +   G       +   LHA  + L HP  G  ++ 
Sbjct: 242 TGRTHQIRVHSSYIGHPIVGDPLYSS---GGSVGVNLSGQALHAYRLILEHPVTGNTIEA 298

Query: 308 TAPLPAHMVK 317
            APLPA   K
Sbjct: 299 IAPLPAEFTK 308


>gi|75909134|ref|YP_323430.1| ribosomal large subunit pseudouridine synthase D [Anabaena
           variabilis ATCC 29413]
 gi|75702859|gb|ABA22535.1| ribosomal large subunit pseudouridine synthase D [Anabaena
           variabilis ATCC 29413]
          Length = 312

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 82/311 (26%), Positives = 146/311 (46%), Gaps = 33/311 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV---KFNNRIQSGQVVRIP 68
           +E +E + R+DR+     P ++   +Q+++  G+V+V+ K     K N ++     + +P
Sbjct: 7   LEVEENSARIDRYLAEELPDLSRSRIQQLIEQGKVQVNGKVCTSKKINLKVGDRITLEVP 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                             +  L   ++ +   +LYED ++ + NKPAG+ V    G ++ 
Sbjct: 67  -----------------EAQPLELQAEDIPLDILYEDDQLLILNKPAGLVVHPAPGHSHG 109

Query: 129 --IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L       G    Q+P + HRLD++T+G + +A+T  A +H+    + +  ++ 
Sbjct: 110 TLVNALLAHCPHLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKHIQAQLQTKTARRE 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  +V+G PK     +   L    H        +   E+G   AI+H+++ +     F  
Sbjct: 170 YLGVVYGAPKTSSGKVD--LPIGRHPQDRKKMAIVPVEEGGRSAITHWQIQERLG-NFTL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-E 301
           +  Q  TGRTHQ+RVH+  +G PIVGD  Y +        P Q    LHA  + L HP  
Sbjct: 227 IHFQLETGRTHQIRVHSAKIGHPIVGDPVYGSGRSVGVNLPGQ---ALHAWRLRLQHPIT 283

Query: 302 GGRLQITAPLP 312
           G  +++TA  P
Sbjct: 284 GDWVEVTATPP 294


>gi|312131061|ref|YP_003998401.1| ribosomal large subunit pseudouridine synthase d [Leadbetterella
           byssophila DSM 17132]
 gi|311907607|gb|ADQ18048.1| ribosomal large subunit pseudouridine synthase D [Leadbetterella
           byssophila DSM 17132]
          Length = 240

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 74/218 (33%), Positives = 111/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V NK AG+ V   S     ++ ++K ++  K  KP        HRLD+  S
Sbjct: 6   VIYEDNHLIVVNKAAGVLVHSDSTGDKTLEDYVKEYIKDKYNKPGEVFLGTVHRLDRPVS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ ART  A   + E F+ R+IQK YW++    P+ K   + +WL K S    +    
Sbjct: 66  GVVIFARTSKALTRMNELFKKRQIQKTYWAITMRKPEKKSGRLTHWLRKDS--VQNKTEA 123

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +   +GA  A   ++ +     K   +E+ P TGR HQ+RV    MG PI GD KY + 
Sbjct: 124 FESEVEGAQRADLDYRYVGTL-NKHHLIEVNPITGRPHQIRVQLASMGTPIKGDVKYGSP 182

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            KGN    I    +LHAR +   HP +   L I AP+P
Sbjct: 183 -KGNADGSI----FLHARRVYFIHPVKKEPLVIKAPVP 215


>gi|121593575|ref|YP_985471.1| ribosomal large subunit pseudouridine synthase D [Acidovorax sp.
           JS42]
 gi|120605655|gb|ABM41395.1| ribosomal large subunit pseudouridine synthase D [Acidovorax sp.
           JS42]
          Length = 334

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 95/331 (28%), Positives = 153/331 (46%), Gaps = 31/331 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           ++ VVV  ++   RLD+      P  +   LQ++L  G VR++ + V K  +R++ G  +
Sbjct: 27  LREVVVGAEQHAQRLDKALAELVPEFSRSYLQQLLLQGCVRLNGREVQKPASRVKVGDRI 86

Query: 66  RIPPVINALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
            +       +   + EQ  LD               ++YED  I V +KPAG+ V    G
Sbjct: 87  AVEMRPTQQSQAFRPEQWPLD---------------VVYEDEHILVIHKPAGLVVHPAPG 131

Query: 125 --IAYHIDGFLKSWVDSKG-QKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                 ++  L    D++  Q PR  + HRLD++TSG++VVAR+R+A   L      R +
Sbjct: 132 NWSGTLLNALLGR--DAQAMQVPRAGIVHRLDKDTSGLMVVARSRSAMDALVRMIAAREV 189

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y +L WG          +  + +       + VV   +     A + F +ID   ++
Sbjct: 190 SRQYVALGWGGWTGAAHRSVHAPIGRDPRNRLRMAVVDLAQHPGKEARTDFDLIDA-NEE 248

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
            C +    HTGRTHQ+RVH   +  P+V D    A + G    P+  +  LHA  +   H
Sbjct: 249 VCLVRCTLHTGRTHQIRVHMASIRHPLVAD----ALYGGALAGPMHRQ-ALHAFRLAFVH 303

Query: 300 P-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           P  G  L+  APLP  M +  D  G +Y+R+
Sbjct: 304 PVTGAALEFHAPLPEDMAQALDFWGLRYNRS 334


>gi|322487770|emb|CBZ23011.1| pseudouridylate synthase-like protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 414

 Score =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 95/360 (26%), Positives = 161/360 (44%), Gaps = 43/360 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV----RVDKKR-VKFNNRIQS 61
           +QY VV  D    R+D +   H+P  ++  ++++++ G +    +  KKR  +  +R++ 
Sbjct: 55  LQYHVVTQDWFGQRVDDFVTQHHPEWDYETVKRLVQQGHIYRYRKNGKKRYTRLTDRLEF 114

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNL-------------------TKHSDFLKSILL 102
            ++V +P          + Q    S V L                    K  +  + ++L
Sbjct: 115 DELVVVP-----TASFWERQLAPPSGVELQSSSTSQRQQERRQTFHLSAKAREMAQEMVL 169

Query: 103 YEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +++  + V NKP+G+ +      +A +I   L +W  +  QKP + H LD ETSG +V+A
Sbjct: 170 FKNEHVVVINKPSGVPIMPTHDPLAMNITDLLPAWRYTNTQKPIICHNLDTETSGCVVLA 229

Query: 162 RTRAAAQHLTESFRMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           R+  A + L   F  R +   +YW    G P      I      +   GGD +       
Sbjct: 230 RSSNAHRMLGRMFVKRVVPNSVYWGFAVGKPPVNFGRIRMHFEVQKGQGGDVIVARPTPT 289

Query: 221 KGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK- 277
             +   I+ F V++  A +F  ++   P T R HQ R+ A H +  P++GD KY      
Sbjct: 290 ADSKVGIAEF-VVNASALEFGSFISFYPLTTRRHQERIMAAHALRAPLLGDAKYGGESAF 348

Query: 278 ----GNFTSPIQN--KLYLHARYMDLPHPEGGR--LQITAPLPAHMVKTWDSLGFKYDRN 329
                 F  P +    L+LH R + LP+  G    + +TAPLP HM KT+  LG+  D +
Sbjct: 349 PHSLSLFWDPARKDVPLHLHHRKIQLPYKNGAGEFVCVTAPLPPHMEKTFKRLGWPVDAD 408


>gi|149202314|ref|ZP_01879287.1| Pseudouridine synthase, RluD [Roseovarius sp. TM1035]
 gi|149144412|gb|EDM32443.1| Pseudouridine synthase, RluD [Roseovarius sp. TM1035]
          Length = 342

 Score =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 99/359 (27%), Positives = 158/359 (44%), Gaps = 60/359 (16%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M   Q V    D+   RLD+      P    ++   L ++L  G VRV+   V +   R+
Sbjct: 1   MGLDQLVFRIGDDPPQRLDKALVRDVPEAAVLSRTRLARLLEEGAVRVNGAVVSEAKARV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G ++ I       +H+  E   L+               ++YED  + V NKPAG+ V
Sbjct: 61  QAGDLIEIVVPEARESHMAPEAIALE---------------VVYEDDDLIVVNKPAGMVV 105

Query: 120 --QGGSGIAYHIDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               GS     ++  L    DS       ++P + HR+D+ETSG+LVVA++ AA Q L  
Sbjct: 106 HPAPGSPEGTLVNALLHHCGDSLSGVGGAKRPGIVHRIDKETSGLLVVAKSDAAHQGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV---------KQNE--- 220
            F    +++ Y ++V+G+P+     +   L   S   G+ + +          +Q +   
Sbjct: 166 QFEAHSVERQYRAVVYGVPEASDPRL-RGLRGISFEPGNILRIATRLARHKTDRQRQAVL 224

Query: 221 -KGANYAISHFKVIDCF------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +G  +A++  +VI+ F      A   CWLE    TGRTHQ+RVH  + G  ++GD  Y 
Sbjct: 225 FEGGRHAVTRARVIESFGTPGVAALMECWLE----TGRTHQIRVHMAYAGHGLIGDPVYG 280

Query: 274 ANFK---------GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
              K         G   +    +  LHA  +   HP  G  L+  A LP  M+    +L
Sbjct: 281 GRRKLKEKALLPAGVAAAQEFPRQALHAAVLGFVHPGTGAALRFEADLPQDMLALLSAL 339


>gi|75676616|ref|YP_319037.1| pseudouridine synthase, RluD [Nitrobacter winogradskyi Nb-255]
 gi|74421486|gb|ABA05685.1| ribosomal large subunit pseudouridine synthase D [Nitrobacter
           winogradskyi Nb-255]
          Length = 351

 Score =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 146/321 (45%), Gaps = 43/321 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV  DE  +RLDR    H P ++   L+ ++ +G V + KK      R + G V    P
Sbjct: 17  VVVTGDEGAVRLDRVLAVHSPDLSRSRLKSLILAGHVSIVKK-ASVAERTE-GPV----P 70

Query: 70  VINALNHIIKEQKI---LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           V +   H+     I   +  +++     + +   ++YED  + V NKP G+ V   +G  
Sbjct: 71  VRDPAYHVAPGDTITIHVPPAISAKPQGEAIALDIIYEDDDLIVINKPKGLVVHPAAG-- 128

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESF--- 174
           +H    + + +   G+         +P + HRLD++T+G++V A+  AA + L   F   
Sbjct: 129 HHTGTLVNALIAHCGETLSGIGGVCRPGIVHRLDKDTTGLMVAAKNDAAHKSLGAQFADH 188

Query: 175 -RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R   +++ Y + VWG+P N+     +  + +      Y         G   AI+H++V 
Sbjct: 189 GRTGAMRRGYLAFVWGLP-NRSHGTVDAPIDRH----PYAREKMAVRAGGREAITHWEVR 243

Query: 234 DCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTS 282
             F  +        L  Q  TGRTHQ+RVH  H+G P++GD  Y  +F+      G   +
Sbjct: 244 QAFNGRDGKPVAALLACQLATGRTHQIRVHLAHVGHPLMGDGVYGPHFRTKVSHLGERAA 303

Query: 283 PIQNKL---YLHARYMDLPHP 300
              + L    LHA  + L HP
Sbjct: 304 AALSALGRQALHASLLVLEHP 324


>gi|300173082|ref|YP_003772248.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299887461|emb|CBL91429.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 308

 Score =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 90/294 (30%), Positives = 144/294 (48%), Gaps = 41/294 (13%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           L++G + V+  +VK   ++ +G  + I  P VI     II E   LD             
Sbjct: 36  LQTGHILVNGVQVKRAYKVTTGDTITILQPEVIT--TEIIAEDIPLD------------- 80

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-------DSKGQ-KPRLTHRL 150
             ++YED  I V NKP G+ V   +G   H  G L + +          G+ +P + HR+
Sbjct: 81  --IIYEDDDILVVNKPQGMVVHPAAG---HSSGTLVNALLFHAPLSTINGEFRPGIVHRI 135

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+   A Q L+   +  +  +IY++LV G      E + N     + I  
Sbjct: 136 DRDTSGLLMVAKNDQAHQGLSAQLKAHKNDRIYYALVRG------EFVENSGTINAPINR 189

Query: 211 DYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             V   KQ  ++G   AI+HF+VI+ +   +  L+++  TGRTHQ+RVH  ++G P+VGD
Sbjct: 190 HKVDRKKQAVQEGGREAITHFEVIERYV-GYTLLKVRLETGRTHQIRVHMTYIGHPVVGD 248

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
             Y +    N      N   LHA+ + L  P+ G  L+  + LPA+      +L
Sbjct: 249 PVYGS--AQNLAGVKLNGQMLHAKTLSLTQPKTGEELRFDSALPAYFKDALATL 300


>gi|220928062|ref|YP_002504971.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|219998390|gb|ACL74991.1| pseudouridine synthase, RluA family [Clostridium cellulolyticum
           H10]
          Length = 304

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 90/318 (28%), Positives = 150/318 (47%), Gaps = 36/318 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +R+D W   +    +   +QK+   G V  +  +VK N R+++   +++       
Sbjct: 9   DTDGVRIDSWLAGNLEDYSRSYIQKLCLDGNVWANGIQVKSNYRVKTDDNIKVN------ 62

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGF 132
              + E +ILD         + +   ++YED  I V NKP G+ V    G      ++  
Sbjct: 63  ---VPEAEILDVE------PEDIPLDIVYEDKHIIVINKPKGMVVHPAVGNYTGTLVNAL 113

Query: 133 LKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +K   DS        +P + HR+D++TSG+LVVA++  A + L+E  +   I++ Y +LV
Sbjct: 114 MKHCGDSLSDINGVIRPGIVHRIDKDTSGLLVVAKSNIAHERLSEKLKTHDIKREYIALV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEM 245
            GI       I       + IG + V   K   N +    AI+HFKV++ F Q   +LE+
Sbjct: 174 DGIIYENSGKI------DAPIGRNPVERKKMCVNTENGRNAITHFKVLERF-QNATYLEL 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
           +  TGRTHQ+RVH  ++  PI+GD  Y    K  + +  Q    LHA  +   HP  G  
Sbjct: 227 KLETGRTHQIRVHMAYINHPIIGDMVY-GRRKQKYKTKGQ---VLHAWRLSFQHPITGEE 282

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++    +P +  +    L
Sbjct: 283 VKFETAVPEYFQRILSQL 300


>gi|297568585|ref|YP_003689929.1| pseudouridine synthase, RluA family [Desulfurivibrio alkaliphilus
           AHT2]
 gi|296924500|gb|ADH85310.1| pseudouridine synthase, RluA family [Desulfurivibrio alkaliphilus
           AHT2]
          Length = 324

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 97/327 (29%), Positives = 150/327 (45%), Gaps = 35/327 (10%)

Query: 11  VVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           VV   E   RLD            +    LQ ++R G+VRV+   V+    ++ G +++ 
Sbjct: 12  VVAPHEAGRRLDLVLATRAAGSAELTRSRLQSLIRQGRVRVESAGVEAGP-LKPGMLLKA 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              ++      +  +++   V  T          LYED  I V  KP G+ V    G   
Sbjct: 71  GDRVDLQVPPPEATELVAEEVEFTP---------LYEDEDILVLVKPPGLVVHPADG--- 118

Query: 128 HIDGFL--------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           H  G L        ++     GQ +P + HRLD++TSG LVVA+   A  +L + F+ R 
Sbjct: 119 HRQGTLVHGLLHHCRNLSGISGQLRPGIVHRLDKDTSGCLVVAKNDLAHHNLVQQFKGRE 178

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCF 236
           ++K Y +L+ GI     E     +L    IG   VH  K     +G   A++H++V   F
Sbjct: 179 VEKTYQALLRGI---LAEDTGQVVLP---IGRHPVHRKKMAVRREGGREAVTHWRVRQRF 232

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           +  +  +E+   TGRTHQ+RVH   +G P+ GD  Y  N + +    I ++ +LHA  + 
Sbjct: 233 SAGYTLVELLLETGRTHQIRVHMAALGHPLAGDRLYGRNPEKDMPYGI-DRQWLHAWRLA 291

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
             HP  G RL  TAPL   +  + D L
Sbjct: 292 FNHPRSGRRLTFTAPLWVDLQASLDRL 318


>gi|118101844|ref|XP_001231937.1| PREDICTED: hypothetical protein [Gallus gallus]
          Length = 344

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 69/202 (34%), Positives = 111/202 (54%), Gaps = 25/202 (12%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHR 149
           +  L+   +Y+D ++ V NKP G+ V GG G+   I   L    K  V+ K +   L HR
Sbjct: 71  AKALRQRAVYQDEEVVVLNKPYGLPVHGGPGVKNCIADVLPILAKMLVNMKAEPLHLCHR 130

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----------IPKNKKECIA 199
           LD+ET+G++V+AR + AA  +   F+ R+++KIYW++  G          IP  ++E  +
Sbjct: 131 LDKETTGVMVLARNKEAADRIRLLFKTRQVEKIYWAISVGSPDPAEGIVEIPMVEREVQS 190

Query: 200 NWLLKKSHIGGDY--------VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           +    K  +  +Y        V  +++N + A  A++ ++V+   +     LE+QP TG 
Sbjct: 191 HQPHFKMTLAPNYRMSPEDGKVLKIRKN-RNAESAVTQYRVL-ASSSACSLLELQPITGV 248

Query: 252 THQLRVH-ALHMGCPIVGDHKY 272
            HQLRVH A  +GCPI+GDHKY
Sbjct: 249 KHQLRVHLAYGLGCPILGDHKY 270


>gi|83941136|ref|ZP_00953598.1| ribosomal large subunit pseudouridine synthase D [Sulfitobacter sp.
           EE-36]
 gi|83846956|gb|EAP84831.1| ribosomal large subunit pseudouridine synthase D [Sulfitobacter sp.
           EE-36]
          Length = 344

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 93/361 (25%), Positives = 158/361 (43%), Gaps = 60/361 (16%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M++ Q      D    RLD+      P   +++   L ++L  G V+VD   V    +R 
Sbjct: 1   MSHRQITFTIADSPPPRLDKALARDVPEDANLSRTRLGRLLEQGAVQVDGTVVTDPRSRA 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++GQ + +       +HI+ E+  L+               +++ED+ + V NKPAG+ V
Sbjct: 61  EAGQQITVDVEEAEDSHILAEEIPLE---------------VVFEDADLIVINKPAGMVV 105

Query: 120 QG--GSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               GS     ++  L    D        ++P + HR+D++TSG+LVVA++ AA   L +
Sbjct: 106 HPAPGSPSGTLVNALLAHCGDDLSGVGGMKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAK 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK----------- 221
            F    +++ Y +LV+G+P +  +     +   S   G+ + +  Q  +           
Sbjct: 166 QFEKHTVERYYQALVYGVP-DANDPRLRGVKGASFEPGNILKLTTQLARHRTDRQRQAVF 224

Query: 222 --GANYAISHFKVI------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             G  +A++  + +      +  A   CWLE    TGRTHQ+RVH  H G  +VGD  Y 
Sbjct: 225 FQGGRHAVTRARTVARLGNPEVLALMECWLE----TGRTHQIRVHMAHAGHALVGDPTYG 280

Query: 274 AN---FKGNFTSPIQNKL------YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
                 KG  +      +       LHA  +   HP  G  ++  APLP  M     ++G
Sbjct: 281 GKRKLAKGAVSDAAAEAVRSFPRQALHAAVLGFDHPVTGDYVRFEAPLPGDMTDLLGAVG 340

Query: 324 F 324
           +
Sbjct: 341 Y 341


>gi|258543199|ref|YP_003188632.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256634277|dbj|BAI00253.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256637337|dbj|BAI03306.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-03]
 gi|256640389|dbj|BAI06351.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-07]
 gi|256643446|dbj|BAI09401.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-22]
 gi|256646501|dbj|BAI12449.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-26]
 gi|256649554|dbj|BAI15495.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-32]
 gi|256652540|dbj|BAI18474.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-01-42C]
 gi|256655598|dbj|BAI21525.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-12]
          Length = 337

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 88/344 (25%), Positives = 145/344 (42%), Gaps = 68/344 (19%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ- 63
           T V + V   ++   R+DR+       ++   ++ ++  G +  D   ++    I     
Sbjct: 17  TAVSFTVTP-EQAGERIDRFLAATMETLSRSRIKSLIEEGHLACDGVCIREPAAIARAGM 75

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
             V+ IPP   A+                    + +   +LYED  + V +KPAG+ V  
Sbjct: 76  EVVLTIPPAAPAV-----------------PQGEDISFTVLYEDDDLIVLDKPAGLVVHP 118

Query: 122 GSG--IAYHIDGFLKSWVDS-KG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             G      ++G +    +S KG    ++P + HRLD++TSG++V A+T  A Q L+E F
Sbjct: 119 APGNETGTLVNGLIAHCGESLKGIGGERRPGIVHRLDKDTSGVMVAAKTEMAHQALSEDF 178

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE----------KGAN 224
             RRI + Y +  WG+P N  E             GD+   + +++          KG  
Sbjct: 179 AARRIDRAYLAFCWGLP-NPAE-------------GDFEGAIGRDKRDRKRMALTPKGGK 224

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY------------ 272
           +A++H++ +  F      +  +  TGRTHQ+RVH    G P++GD  Y            
Sbjct: 225 WALTHYRTLQAFGTGAALVACKLATGRTHQIRVHFSANGHPLIGDPLYLRRIPAASRVLP 284

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
            A        P Q    LHA  +   HP  G +L    P+P  M
Sbjct: 285 SAARAAALDFPRQ---ALHAARLGFIHPRTGEKLLFETPMPEDM 325


>gi|153940691|ref|YP_001390824.1| RluA family pseudouridine synthase [Clostridium botulinum F str.
           Langeland]
 gi|152936587|gb|ABS42085.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           Langeland]
 gi|295318893|gb|ADF99270.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           230613]
          Length = 305

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 94/324 (29%), Positives = 152/324 (46%), Gaps = 44/324 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE + +N+RLD +    +   +   LQ I+  G V V+ K  K N +++ G  + +    
Sbjct: 8   VEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIEVN--- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                 I E K+L          + +K  ++YED  + V NKP  + V    G+     +
Sbjct: 65  ------IPEPKLLQIE------PEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLV 112

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+   I ++Y +
Sbjct: 113 NALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           LV GI K ++  I      ++ IG   V  +K    K   +A++H+KVI+ F +    +E
Sbjct: 173 LVEGIIKYEQGTI------EAPIGRHPVDRIKMAVVKDGRHAVTHYKVIERF-KNHTLVE 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLHARYMDLPH 299
            +  TGRTHQ+RVH  H+  P+VGD  Y       N KG           LHA+ +   H
Sbjct: 226 CRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLKGQM---------LHAKLLGFIH 276

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P   + ++  + LP +  K    L
Sbjct: 277 PTTRQYVEFESELPEYFKKIIKIL 300


>gi|298208169|ref|YP_003716348.1| ribosomal large subunit pseudouridine synthase D [Croceibacter
           atlanticus HTCC2559]
 gi|83848090|gb|EAP85960.1| ribosomal large subunit pseudouridine synthase D [Croceibacter
           atlanticus HTCC2559]
          Length = 356

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/334 (26%), Positives = 150/334 (44%), Gaps = 54/334 (16%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  N   +     +QK  + G + V+   VK N ++++G  V++        
Sbjct: 37  QEPLRVDKFLMNFIENATRNKIQKAAKEGNIYVNDAVVKQNYKVKAGDEVKV-----LFE 91

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           H   E  +    + L          +++ED  + V NKPAG+ V  G G         + 
Sbjct: 92  HPPYEMLLTPEDIPLN---------IVHEDDDVLVVNKPAGMVVHPGHGNYSGTLINALV 142

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +H D       ++   +P L HR+D++TSG+LVVA+T  A  HL++ F  +   + Y +L
Sbjct: 143 FHFDNL----PNNSSNRPGLVHRIDKDTSGLLVVAKTEHAMTHLSKQFFNKTSSREYIAL 198

Query: 187 VWGIPKNKKECIANWLLKKSHIG-------GDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           VWG  ++ +  I      + HIG        + V +    ++    A++H+KVI+     
Sbjct: 199 VWGNVEDDQGTI------EGHIGRHPKNRLQNTVFLEDDADEKGKPAVTHYKVIERLGY- 251

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------K 287
              L  +  TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +
Sbjct: 252 VTLLSCKLETGRTHQIRVHLKHIGHTLFNDERYGGDKILKGTHFSKYKQFVDNCFKTLPR 311

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             LHA+ +   HP  G  L   + +P  +    D
Sbjct: 312 QALHAKTLGFEHPVSGEWLSFDSEIPKDISDCVD 345


>gi|218661228|ref|ZP_03517158.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli IE4771]
          Length = 260

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 79/253 (31%), Positives = 124/253 (49%), Gaps = 36/253 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           + +ED  I V +KPAG+ V  G G         + YH    L        ++P + HRLD
Sbjct: 11  IFHEDDDIIVISKPAGLVVHPGPGNWTGTLVNALIYHCGDTLSGI--GGVRRPGIVHRLD 68

Query: 152 QETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           ++T+G++VVA+   A +HL+  F    R   +++ Y ++VWG P++    +   L + + 
Sbjct: 69  KDTTGVMVVAKNDVAHRHLSLQFADHGRTMPLERAYQAIVWGRPRSLTGTVDAPLGRAT- 127

Query: 208 IGGDYVH--VVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHA 259
             GD     V + +   A+ AI+H++VI+ F +          +E +  TGRTHQ+RVH 
Sbjct: 128 --GDRTRRAVKRPDSHDADEAITHYEVIERFHETPDATALAALVECRLETGRTHQIRVHM 185

Query: 260 LHMGCPIVGDHKYCANF--KGNFTSPIQNKLY-------LHARYMDLPHPEGGRL-QITA 309
            H+G P++GD  Y A F  K N       K+        LHA  +   HP  G L     
Sbjct: 186 AHIGHPLLGDTVYGAGFRTKANLLPEEIRKVVNGFDRQALHAFMLQFEHPRSGDLMHFEV 245

Query: 310 PLPAHMVKTWDSL 322
           PLP  MV+  ++L
Sbjct: 246 PLPEDMVELVEAL 258


>gi|90422129|ref|YP_530499.1| pseudouridine synthase RluD [Rhodopseudomonas palustris BisB18]
 gi|90104143|gb|ABD86180.1| ribosomal large subunit pseudouridine synthase D [Rhodopseudomonas
           palustris BisB18]
          Length = 391

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 89/338 (26%), Positives = 149/338 (44%), Gaps = 47/338 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V  DE  +RLDR      P ++   L+ ++ +GQVR+         R          P
Sbjct: 60  VTVAGDEGAVRLDRVLALRAPELSRSRLKALILAGQVRL---------RPADASAALPTP 110

Query: 70  VINALNHIIKEQKI---LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + +   H+     I   +  +V      + +   ++YED  I V +KP G+ V   +G  
Sbjct: 111 LRDPAYHVEAGDTITIDVPPAVAAEPAGEAIALDIVYEDDDIIVIDKPKGLVVHPAAG-- 168

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF--- 174
           +     + + +   G         ++P + HRLD++T+G++VVA+   A + L+E F   
Sbjct: 169 HETGTLVNALIAHCGNSLSGIGGVRRPGIVHRLDKDTTGLMVVAKNDKAHKSLSEQFADH 228

Query: 175 -RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R   +++ Y + +WG P N+     +  + +     + + V      G   A++H++V 
Sbjct: 229 GRTNEMRRGYKAFIWGAP-NRPHGTVDAPIDRHPFAREKMAV----RDGGREAVTHWEVE 283

Query: 234 DCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT------- 281
           D F  +        L  Q  TGRTHQ+RVH  H+G P++GD  Y  +FK           
Sbjct: 284 DTFLGRGGKPVVSLLACQLETGRTHQIRVHLAHIGHPLLGDGVYGPHFKTKANALNLPAQ 343

Query: 282 --SPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
                  +  LHA  + L HP  G  L+ TA LPA + 
Sbjct: 344 AALAALGRQALHAYLLALEHPVSGEILEWTAELPADLA 381


>gi|15806790|ref|NP_295512.1| ribosomal large subunit pseudouridine synthase D [Deinococcus
           radiodurans R1]
 gi|6459564|gb|AAF11343.1|AE002020_2 ribosomal large subunit pseudouridine synthase D [Deinococcus
           radiodurans R1]
          Length = 338

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 83/306 (27%), Positives = 140/306 (45%), Gaps = 46/306 (15%)

Query: 41  LRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           + +G V +D +   K + +++ G+ +R+ P       +  E   LD              
Sbjct: 52  IEAGLVEIDGRAASKASQKLRGGEALRVSPPPLPSAQVEPEDVPLD-------------- 97

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-------------KSWVDSKGQKPRL 146
            +++ED  +   NKP G+      G+   I G L             + +    G +P +
Sbjct: 98  -VIFEDEHLIAINKPPGMVTHPAPGV---ISGTLVNALLGRMSLPEQQDFDGPDGYRPGI 153

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG++VVA+T AA   L  +F+ R  +K Y ++  G  K ++    +  + + 
Sbjct: 154 VHRLDKDTSGVIVVAKTVAAHARLAAAFKDRETKKTYLAIAAGAWKAERPVQVDAPIGRH 213

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHALHM 262
            I    + V      GA  A + F  +D       +    +  QP TGRTHQ+RVH  H+
Sbjct: 214 QIQRQRMTV---GGAGAREAQTLFTPLDAHPDGHGRTLALVRAQPRTGRTHQIRVHLAHL 270

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           G PI+GD  Y         S I  +  LHA+++++PHP  G  L + A +P  ++  W  
Sbjct: 271 GSPILGDAVY------GRASEIMPRHALHAQFLEVPHPVSGDILHLQAAVPEDLLGAWVG 324

Query: 322 LGFKYD 327
           LG ++D
Sbjct: 325 LGGRWD 330


>gi|220931776|ref|YP_002508684.1| ribosomal large subunit pseudouridine synthase D [Halothermothrix
           orenii H 168]
 gi|219993086|gb|ACL69689.1| ribosomal large subunit pseudouridine synthase D [Halothermothrix
           orenii H 168]
          Length = 308

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 94/329 (28%), Positives = 163/329 (49%), Gaps = 45/329 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IPP 69
           V ++EE  R+D++       ++   +QK++ + +V V+ + VK + ++  G  +R  IPP
Sbjct: 10  VSSEEEGKRIDKYLSKLNKDLSRSYIQKLIDNDKVLVNGESVKRSFKVNRGDHIRLIIPP 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                    ++  I    ++L          ++YED  I V NK AG+ V    G     
Sbjct: 70  P--------EDSGIKPVEMDLD---------IIYEDKDILVLNKNAGLVVHPAPGNHENT 112

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                IAY  +    S V+    +P + HRLD++TSG++V+A+   + + L E F+ R+ 
Sbjct: 113 LVNALIAYCDNLSTISGVN----RPGIVHRLDKDTSGVMVIAKNDISHRKLVEQFKQRKT 168

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +L+ G    K+  I   + +  H     + V ++N K    A+++FKV++ F + 
Sbjct: 169 KKYYRTLLKGELPYKEGKIDAPIGRDPH-DRKKMAVTRKNSKK---AVTYFKVLEFF-RD 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
             ++E++  TGRTHQ+RVH  +MG P+VGD  Y     G   + +Q  +  LHA  +   
Sbjct: 224 HSYVEVELKTGRTHQIRVHFSYMGFPVVGDSIY-----GKKRNRLQATRQLLHAYRLGFY 278

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HP   + ++  A LP    K  D L  K+
Sbjct: 279 HPRNDKWVEYKASLPDDFKKALDILENKF 307


>gi|228940981|ref|ZP_04103539.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar berliner ATCC 10792]
 gi|228973912|ref|ZP_04134487.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar thuringiensis str. T01001]
 gi|228980501|ref|ZP_04140811.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis Bt407]
 gi|228779321|gb|EEM27578.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis Bt407]
 gi|228785778|gb|EEM33782.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar thuringiensis str. T01001]
 gi|228818660|gb|EEM64727.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar berliner ATCC 10792]
 gi|326941662|gb|AEA17558.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar chinensis CT-43]
          Length = 302

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 89/318 (27%), Positives = 151/318 (47%), Gaps = 37/318 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAAEQKNERIDKFVTGINNEWSRSQVQQWIKDDVVTVNGKAVKVNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          I E + LD         + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITV---------TIPEPEALDI------QPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDC 235
            + + Y ++V G+  + K  I       + IG D      +  +E G N A++HF+V++ 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTI------DAPIGRDKKERQSMTVDENGKN-AVTHFQVLER 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  +
Sbjct: 219 F-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGIL 272

Query: 296 DLPHPEGGR-LQITAPLP 312
              HP  G  +Q  AP+P
Sbjct: 273 GFDHPRTGEYIQFEAPIP 290


>gi|288962534|ref|YP_003452829.1| ribosomal large subunit pseudouridine synthase D [Azospirillum sp.
           B510]
 gi|288914800|dbj|BAI76285.1| ribosomal large subunit pseudouridine synthase D [Azospirillum sp.
           B510]
          Length = 363

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 75/269 (27%), Positives = 127/269 (47%), Gaps = 27/269 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           + +     RLD+      P ++   +Q +L  G VR D + +   + R++ GQ+  +   
Sbjct: 46  IPDTAAGQRLDKALSAGLPDLSRSRVQALLEQGCVRGDGRTITDPSQRVKYGQIFELRMP 105

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
            +A    + +   LD               ++YED+ + V +KPAG+ V   +G      
Sbjct: 106 GSAAAEPLPQDIPLD---------------VVYEDADVLVVDKPAGLVVHPAAGNPDGTL 150

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L    DS       ++P + HRLD++TSG++VVA+   A   L++ F  R + + Y
Sbjct: 151 VNALLAHCGDSLSGIGGVRRPGIVHRLDKDTSGLMVVAKNDRAHHGLSDQFSDRTLSRTY 210

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LVWG+P N  +      + +S      + VV    K A    + ++V+  F      +
Sbjct: 211 LALVWGVP-NPTQGRIEGNIGRSSADRKKMAVVTGGGKPAG---TKYRVVKSFGMAASLV 266

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           E    TGRTHQ+RVH  H+G P+VGD  Y
Sbjct: 267 ECVLETGRTHQIRVHLTHIGHPLVGDPLY 295


>gi|257884651|ref|ZP_05664304.1| pseudouridylate synthase [Enterococcus faecium 1,231,501]
 gi|261207803|ref|ZP_05922488.1| pseudouridylate synthase [Enterococcus faecium TC 6]
 gi|289566255|ref|ZP_06446687.1| RNA pseudouridine synthase ylyB [Enterococcus faecium D344SRF]
 gi|294616594|ref|ZP_06696370.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1636]
 gi|257820489|gb|EEV47637.1| pseudouridylate synthase [Enterococcus faecium 1,231,501]
 gi|260078186|gb|EEW65892.1| pseudouridylate synthase [Enterococcus faecium TC 6]
 gi|289161962|gb|EFD09830.1| RNA pseudouridine synthase ylyB [Enterococcus faecium D344SRF]
 gi|291590544|gb|EFF22277.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1636]
          Length = 303

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 92/322 (28%), Positives = 155/322 (48%), Gaps = 51/322 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E+ R+D+   N +   +   +Q  L++G V V+ + VK N +++ G  + +         
Sbjct: 11  ESGRIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVKANYKVKQGDEITV--------- 61

Query: 77  IIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
           +I E + LD    ++ LT         ++YED  + V NKP G+ V   +G         
Sbjct: 62  LIPEPETLDVVPENIPLT---------IVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNA 112

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + YHI     S ++    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y 
Sbjct: 113 LMYHIKDL--STINGV-IRPGIVHRIDKDTSGLLMVAKNDQAHESLAQQLKDKTSLRKYV 169

Query: 185 SLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G IP  K    A     K +     +  ++++ K A   ++HF V++ F + F  +
Sbjct: 170 ALVHGEIPHEKGTINAPIGRSKEN---RKMQAIREDGKPA---VTHFTVLERF-EGFTLV 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E++  TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP 
Sbjct: 223 ELKLETGRTHQIRVHMKYIGYPLAGDPVYGPKKTLKGNGQ-------FLHAQMLGFTHPT 275

Query: 302 GGRLQI-TAPLPAHMVKTWDSL 322
                I  APLP    KT + L
Sbjct: 276 TNEKMIFEAPLPEVFEKTLEKL 297


>gi|296127625|ref|YP_003634877.1| pseudouridine synthase [Brachyspira murdochii DSM 12563]
 gi|296019441|gb|ADG72678.1| pseudouridine synthase [Brachyspira murdochii DSM 12563]
          Length = 237

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 74/208 (35%), Positives = 114/208 (54%), Gaps = 15/208 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +YED+ I V  KP  I VQG  +G     D  +K ++  K  K       L HRLD+  S
Sbjct: 14  IYEDNHIIVAVKPPNIPVQGDITGDLSFFDN-IKDYIKIKYNKKGNVFLGLVHRLDRPVS 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  AA  L+E+ R R+ +K Y+++V GI  +K+  + N+L+KK++  G+   V
Sbjct: 73  GIMVFAKTSKAASRLSEAIRDRKFEKTYYAVVNGILLDKEGMLENYLIKKTNKLGNIAQV 132

Query: 216 VKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V +N K A  A   ++VI +   +    L+++  TGR HQ+RV   ++G  I GD KY  
Sbjct: 133 VFENTKNAKIAKLKYEVIKEDLIKNLSLLKIELETGRFHQIRVQLSNIGHTIYGDRKY-- 190

Query: 275 NFKGNFTSPIQNK--LYLHARYMDLPHP 300
              GN+    ++   L L A+ +  PHP
Sbjct: 191 ---GNYIKYDRDNVPLALFAKSLRFPHP 215


>gi|85714567|ref|ZP_01045554.1| pseudouridine synthase, RluD [Nitrobacter sp. Nb-311A]
 gi|85698452|gb|EAQ36322.1| pseudouridine synthase, RluD [Nitrobacter sp. Nb-311A]
          Length = 351

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 89/326 (27%), Positives = 141/326 (43%), Gaps = 43/326 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV  +E + RLDR    H P ++   L+ ++ +G V V KK         SG     P 
Sbjct: 17  VVVTGNEGSARLDRVLAVHSPDLSRSRLKSLILAGHVSVVKKASAAER--TSGP----PS 70

Query: 70  VINALNHIIKEQKI---LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           V +   H+     I   +   ++     + +   ++YED+ + V NKP G+ V  G+G  
Sbjct: 71  VSDPAYHVAPGDTITIRVPPPISAKPQGEAIALDIVYEDNDLIVINKPKGLVVHPGAGHQ 130

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF--- 174
                  +  H  G L         +P + HRLD++T+G++V A+  AA + L+  F   
Sbjct: 131 AGTLVNALIAHCGGSLSGI--GGVCRPGIVHRLDKDTTGLMVAAKNDAAHKSLSTQFADH 188

Query: 175 -RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R   +++ Y + VWG+P      I   + +       Y         G   AI+H+ V+
Sbjct: 189 GRTGAMRRGYLAFVWGLPNRPHGTIDAPIDRHP-----YAREKMAVRAGGREAITHWDVV 243

Query: 234 DCFAQKF-----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSP--- 283
             F           L  +  TGRTHQ+RVH  H G P++GD  Y ++F  K N   P   
Sbjct: 244 QAFDDPAGKSVAALLACRLATGRTHQIRVHLAHAGHPLMGDGVYGSHFRTKANHLGPRAA 303

Query: 284 ----IQNKLYLHARYMDLPHPEGGRL 305
                  +  LHA  + + HP  G +
Sbjct: 304 AALSALGRQALHASLLVIEHPRTGEI 329


>gi|119476934|ref|ZP_01617215.1| Pseudouridine synthase, RluD [marine gamma proteobacterium
           HTCC2143]
 gi|119449741|gb|EAW30978.1| Pseudouridine synthase, RluD [marine gamma proteobacterium
           HTCC2143]
          Length = 318

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 89/298 (29%), Positives = 140/298 (46%), Gaps = 38/298 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RLD+     +P  +   LQ  ++SG++ VD +  K   ++QSG+++ +  V+     
Sbjct: 16  EGSRLDQIAAQLFPDYSRARLQIWIKSGELTVDGEAKKSREKLQSGELLELRAVVE---- 71

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLK 134
              E++    S++L          ++YED  + V NKPAG+ V  GSG A    ++  L 
Sbjct: 72  --DEERWDAESMDLD---------IVYEDEALLVVNKPAGLVVHPGSGNASGTLLNALLA 120

Query: 135 SWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              D     PR  + HRLD++TSGI+VVA+T AA   L    + R + ++Y ++V+G   
Sbjct: 121 HLPDI-ASVPRAGIVHRLDKDTSGIMVVAKTLAAQNSLVNQLQARTVSRVYEAVVFG--- 176

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                +    + ++ IG       K      G   A +H+++I  F    C +     TG
Sbjct: 177 ----SLTGGGVVRADIGRHPRQRTKMAVLAIGGKEATTHYRLIKRF-NNHCHIRCMLETG 231

Query: 251 RTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLHARYMDLPHP 300
           RTHQ+RVH  H+   +VGD  Y       KG     I       +  LHAR + L HP
Sbjct: 232 RTHQIRVHMAHIKHALVGDPVYAGRPRIPKGASEELINGLRGFGRQALHARKLSLIHP 289


>gi|294617890|ref|ZP_06697499.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1679]
 gi|291595835|gb|EFF27119.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1679]
          Length = 303

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 92/322 (28%), Positives = 155/322 (48%), Gaps = 51/322 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E+ R+D+   N +   +   +Q  L++G V V+ + VK N +++ G  + +         
Sbjct: 11  ESGRIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVKANYKVKQGDEITV--------- 61

Query: 77  IIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
           +I E + LD    ++ LT         ++YED  + V NKP G+ V   +G         
Sbjct: 62  LIPEPETLDVVPENIPLT---------IVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNA 112

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + YHI     S ++    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y 
Sbjct: 113 LIYHIKDL--STINGV-IRPGIVHRIDKDTSGLLMVAKNDQAHESLAQQLKDKTSLRKYV 169

Query: 185 SLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G IP  K    A     K +     +  ++++ K A   ++HF V++ F + F  +
Sbjct: 170 ALVHGEIPHEKGTINAPIGRSKEN---RKMQAIREDGKPA---VTHFTVLERF-EGFTLV 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E++  TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP 
Sbjct: 223 ELKLETGRTHQIRVHMKYIGYPLAGDPVYGPKKTLKGNGQ-------FLHAQMLGFTHPT 275

Query: 302 GGRLQI-TAPLPAHMVKTWDSL 322
                I  APLP    KT + L
Sbjct: 276 TNEKMIFEAPLPEVFEKTLEKL 297


>gi|153003089|ref|YP_001377414.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152026662|gb|ABS24430.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 298

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 97/318 (30%), Positives = 151/318 (47%), Gaps = 33/318 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVRIP 68
           +VV + +   RLDR+       ++    ++ L SG V +D +R K + R+ Q+GQ V   
Sbjct: 6   LVVASADGGERLDRFIAARG-GVSRGAARRALDSGGVFLDGRRCKVSGRLLQAGQKV--- 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            V+N          + ++       S   ++ LLY D  +   +KPAG+  Q        
Sbjct: 62  -VVN----------LEEAGRAAPARSALERARLLYADQDLVAVDKPAGVPSQ----PTLT 106

Query: 129 ID-GFLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            D G L   V D  G    L HRLD+ETSG+ V+ART AAA  L E+FR    +K Y +L
Sbjct: 107 TDRGTLPELVSDLLGAPVTLVHRLDRETSGVTVLARTAAAAAALAEAFRTGTPEKTYLAL 166

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
               P      I   L K     G     +++ +   + A + ++ +         +E +
Sbjct: 167 CARPPAPPDGRIDAPLGKDPARAG-----LRRVDPRGDAAATRYRTLRA-GPLAALVEAR 220

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPE-GGR 304
           P TGRTHQ+RVH  H+G P++GD +Y    + G    P   ++ LHAR +++ HP  G R
Sbjct: 221 PETGRTHQIRVHLAHLGAPLLGDPRYGGPRRVGEVAIP---RVMLHARRLEIDHPATGAR 277

Query: 305 LQITAPLPAHMVKTWDSL 322
           L + AP+P  +     +L
Sbjct: 278 LLLEAPVPEDLRAAEGAL 295


>gi|303237207|ref|ZP_07323777.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
 gi|302482594|gb|EFL45619.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
          Length = 221

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 113/228 (49%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I +  K +G  VQG       +   +K+W+  K  KP      + HRLD+  S
Sbjct: 3   VLYEDNHIIIVYKESGEIVQGDKTGDKPLSETVKAWLKEKYAKPGNVFVGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  A   L E FR   ++K YW++V   P+  +  I N+LL+       Y + 
Sbjct: 63  GIVVFAKTSKALSRLNEMFRKGEVKKTYWAMVQNSPQKLEGTIENYLLRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +  +KGA  AI  +K I    +++  LE+   TGR HQ+R    +MGC I GD KY A 
Sbjct: 122 -EYEKKGAKKAILKYKTIGQ-TERYTLLEVNLMTGRHHQIRCQLANMGCVIKGDLKYGAK 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     + L +  ++  HP   + + + +PLP   V  WDS 
Sbjct: 180 -----RSNPDGSISLLSHSVEFIHPVSKQPISVVSPLPQEAV--WDSF 220


>gi|303238885|ref|ZP_07325416.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
 gi|302593518|gb|EFL63235.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
          Length = 308

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 90/319 (28%), Positives = 153/319 (47%), Gaps = 36/319 (11%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ++E  +R+D W  +     +   +QK+L  G V V+   VK N +I+S   + +      
Sbjct: 12  SEESGVRIDAWISSRLKEYSRSYIQKLLNDGHVLVNGSLVKSNYKIKSSDEITVQ----- 66

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
               I E ++LD         + ++  +LYED  + V NKP G+ V   +G      ++ 
Sbjct: 67  ----IPEPEVLDIV------PENIEIPVLYEDEHVLVVNKPKGMVVHPAAGNYSGTLVNA 116

Query: 132 FLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            +    DS        +P + HR+D++TSG+LVVA++  A + L+   +   I ++Y +L
Sbjct: 117 LMDYCGDSLSSINGVIRPGIVHRIDKDTSGVLVVAKSNEAHEKLSLKLKDHDINRVYVAL 176

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLE 244
           V GI + +   I       + IG   V   K   N      A+++FKV++ F +    +E
Sbjct: 177 VHGIIREESGKI------DAPIGRHPVDRKKMAVNTNNGRRAVTYFKVLERF-KDATLVE 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
           ++  TGRTHQ+RVH  ++G PI+GD  Y    K  +    Q    LHA+ +   HP +  
Sbjct: 230 VKLETGRTHQIRVHMSYIGYPIIGDTVYGKK-KDKYDIGGQA---LHAKTLGFVHPVKNE 285

Query: 304 RLQITAPLPAHMVKTWDSL 322
            ++  A LP +  K  + L
Sbjct: 286 YMEFEAELPEYFKKLLEEL 304


>gi|289662940|ref|ZP_06484521.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. vasculorum NCPPB702]
          Length = 331

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 91/347 (26%), Positives = 159/347 (45%), Gaps = 40/347 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L   ++  +V ++    R D      +P  +   L + ++SG   +D    +  + ++ G
Sbjct: 9   LEPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +   L                +LYED ++ V +KPAG+ V  G
Sbjct: 69  ESVQVQVVLETQTHAAPQDIPLS---------------VLYEDEQVLVIDKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +     +    PR  + HRLD++TSG++VVART  A   L E    
Sbjct: 114 AG---NPDGTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSA 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + + Y ++V G   +     AN  + + H        V+ + +    A++H+++ + F
Sbjct: 171 RDVHRQYLAVVVGALVSG--GTANAPIDR-HPRDRLKMAVRDDGRD---AVTHYRLRERF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------ 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y    K     T  + ++L      
Sbjct: 225 -RAHTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQ 283

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  ++  HP  G  ++ +AP+PA + +   +L     R   + R
Sbjct: 284 ALHAETLEFLHPVSGEPVRASAPVPADLQRLMTALREDSARAAEMAR 330


>gi|224083652|ref|XP_002197702.1| PREDICTED: RNA pseudouridylate synthase domain containing 4
           [Taeniopygia guttata]
          Length = 351

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 72/201 (35%), Positives = 112/201 (55%), Gaps = 23/201 (11%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHR 149
           +  LK   LY++ +I V +KP G+ V GG GI   I   L    K   + K +   L HR
Sbjct: 82  AKILKQKTLYQNEEIVVIDKPYGLPVHGGPGIKNCIADVLPILAKMLENMKTEPLHLCHR 141

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----------IPKNKKECIA 199
           LD+ET+G++V+AR++ AA+ +   F+ R+++KIYW++V G          IP  +KE  +
Sbjct: 142 LDKETTGVMVLARSKEAAEKIRLLFKTRQVEKIYWAIVLGDPDPVEGVVEIPIVEKEVQS 201

Query: 200 NWLLKKSHIGGDYV------HVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           +    K  +  +Y        V+K +  + A  A++ ++ + C A     LE+QP TG  
Sbjct: 202 HQSHYKMTLAPNYRLCPEDGKVMKIRGHRHAERAVTRYRRL-CAASACSLLELQPITGVK 260

Query: 253 HQLRVH-ALHMGCPIVGDHKY 272
           HQ+RVH A  +GCPI+GDHKY
Sbjct: 261 HQIRVHLAYGLGCPILGDHKY 281


>gi|71744254|ref|XP_803639.1| pseudouridylate synthase [Trypanosoma brucei TREU927]
 gi|70830922|gb|EAN76427.1| pseudouridylate synthase, putative [Trypanosoma brucei]
          Length = 406

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 96/348 (27%), Positives = 165/348 (47%), Gaps = 38/348 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV-----RVDKKRVKFNNRIQS 61
           +QY VV  +    R+D +   HYP  ++  ++++++ G +        KK  +  +R++ 
Sbjct: 56  LQYHVVTQEWFGERVDSFLTCHYPQWDYETIKRLVQQGHIYRYRKNGKKKFTRLTDRLEF 115

Query: 62  GQVVRIPPVINALNHIIKEQKILDSS----VNLTKHS-DFLKSILLYEDSKIYVFNKPAG 116
            +++ +P        +     +L+ +      L+  + +   +++L+++  + V NKP G
Sbjct: 116 DELLVVPTRAFWEKQLAPPSGVLEETDGPKFKLSATAREMAHNMVLFKNEHVIVINKPHG 175

Query: 117 ISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           + +          I   L +W  +   KP + H LD+ETSG +V+ARTR A + L   F 
Sbjct: 176 LPMMPTDDPQEMSIAAMLPAWKFTNVAKPVVCHNLDRETSGCVVLARTRNAHRMLGRMFV 235

Query: 176 MRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIG------GDYVHVVKQNEKGANYAIS 228
            R +   +YWS   G P        N+   + H        GD +       K +  AI+
Sbjct: 236 KRVVPNSVYWSFCVGKP------TVNYGRVRMHFDITRGNKGDIIVARPSPTKTSKVAIA 289

Query: 229 HFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC--ANFKGN---FT 281
            F V++  A +F  ++   P T R HQ R+ A H + CP++GD KY   A F  +   F 
Sbjct: 290 EF-VVNASALEFGSFISFYPLTTRRHQERIMAAHALRCPVLGDAKYGGDAAFPSSLSLFW 348

Query: 282 SPIQNK---LYLHARYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGF 324
            P +NK   L+LH R + LP+    G  + +TAPLP  M KT+  LG+
Sbjct: 349 DP-ENKGLPLHLHHRKIQLPYKNTAGEFICVTAPLPTQMEKTFKKLGW 395


>gi|325661581|ref|ZP_08150205.1| hypothetical protein HMPREF0490_00939 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325472108|gb|EGC75322.1| hypothetical protein HMPREF0490_00939 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 310

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 97/325 (29%), Positives = 154/325 (47%), Gaps = 50/325 (15%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI--QS 61
           M   +Y   +ND   MR+D++     P ++   LQK+++  +V V+ + VK N ++  + 
Sbjct: 1   MEERRYTAEKNDL--MRIDKFLSEKLPDLSRSYLQKLIKEKEVLVNGQPVKANYKLSLED 58

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V IP         +KE  IL   + L          +LYED  I V NKP G+ V  
Sbjct: 59  HISVTIPE--------LKEPDILPEQIPLD---------ILYEDEDILVVNKPKGMVVHP 101

Query: 122 GSGIAYHIDGFLKSWV--DSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLT 171
            +G   H  G L + +    K Q        +P + HR+D +T+G L+V +   A Q L 
Sbjct: 102 SAG---HYSGTLVNALMFHCKDQLSGINGVMRPGIVHRIDMDTTGSLIVCKNDFAHQSLA 158

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISH 229
           E  +   I + Y ++V G+ K     I       + IG   V   K   N K   +A++H
Sbjct: 159 EQLKDHTITRKYHAIVHGVLKEDNGTI------DAPIGRHPVERKKMSVNYKNGKHAVTH 212

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKL 288
           ++V+  F +KF ++E Q  TGRTHQ+RVH   +  P++GD  Y     G   SP++    
Sbjct: 213 YRVLKRF-EKFTYVECQLETGRTHQIRVHMASIRHPLLGDAVY-----GPAKSPMKLQGQ 266

Query: 289 YLHARYMDLPHPEGGR-LQITAPLP 312
            LHA+ + + HP   + ++  A LP
Sbjct: 267 TLHAKILGIIHPRTSQYMEFNAELP 291


>gi|169335052|ref|ZP_02862245.1| hypothetical protein ANASTE_01458 [Anaerofustis stercorihominis DSM
           17244]
 gi|169257790|gb|EDS71756.1| hypothetical protein ANASTE_01458 [Anaerofustis stercorihominis DSM
           17244]
          Length = 301

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 82/328 (25%), Positives = 163/328 (49%), Gaps = 39/328 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +++V E +++N+R D++  +     +  +L+K+ + G+V ++ ++VK + ++ +G+
Sbjct: 1   MEIKEFIVTE-EKQNIRCDKFLSDKLEDFSRESLKKLFKEGEVFLNDEKVKPSRKLIAGE 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++          + E ++LD        ++ +   ++YED  + + +KP G+ V   +
Sbjct: 60  RVKVN---------LPEPEVLDVI------AENIPINIVYEDEDVVIVDKPQGMVVHPAN 104

Query: 124 G---------IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           G         + YH+    K      G  +P + HR+D++TSG+L++A+   A  HL   
Sbjct: 105 GNHSGTLVNALMYHV----KDLSSINGVIRPGIVHRIDKDTSGLLIIAKNDNAHNHLAVQ 160

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+   I + Y ++  GI       I +  + +  I    + V + N K    A++HF VI
Sbjct: 161 FKEHSINRRYKTICHGIIHENSGTI-DAPIGRDKIKRKEMCVTQSNSK---RAVTHFDVI 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             +  K+ +L++   TGRTHQ+RVH  ++  P++GD  Y   F      P + +L LHA 
Sbjct: 217 KRY-DKYTFLDVHLETGRTHQIRVHLKYISHPVIGDKVY--GFNSQIDRPFKGQL-LHAY 272

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            +   HP+    ++  + LP +  +  D
Sbjct: 273 KLGFIHPKTNEYMEFNSELPDYFYELLD 300


>gi|146306004|ref|YP_001186469.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           mendocina ymp]
 gi|145574205|gb|ABP83737.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           mendocina ymp]
          Length = 324

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 92/337 (27%), Positives = 159/337 (47%), Gaps = 42/337 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  ++   RLD+     +   +   L   ++ G++ VD    +  + + +G  +    V
Sbjct: 14  IVPFEQGGQRLDQVAAQLFGEFSRSRLSTWIKDGRLTVDGAVARPRDTVHAGSTL----V 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           ++A      E    D  +N+           +YED  + V +KPAG+ V   +G   H D
Sbjct: 70  LDAEQEAQGEWVAQDIELNI-----------VYEDEHLLVIDKPAGLVVHPAAG---HAD 115

Query: 131 GFLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L +     V      PR  + HRLD++T+G++VVA+T  A  +L E  + R + +IY 
Sbjct: 116 GTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTLQAQTNLVEQLQKRSVSRIYE 175

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +  G+        A   + +S      + V      G   AISH++V++ + +    + 
Sbjct: 176 CICIGVITAGGTIDAP--IGRSSSQRQRMAVTD----GGKPAISHYRVLERY-RSHTHVR 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQN-----KLYLHARYMD 296
           ++  TGRTHQ+RVH  H+G P+VGD  Y   F+       S +Q+     +  LHAR+++
Sbjct: 229 VKLETGRTHQIRVHMSHVGYPLVGDPVYAGRFRIPPAASQSLVQSLKEFPRQALHARFLE 288

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           L HP  G R++  +PLP  +V  W     + DR  ++
Sbjct: 289 LDHPATGKRMKWESPLPDDLV--WLLTLLRQDREAFV 323


>gi|71651380|ref|XP_814369.1| pseudouridylate synthase-like protein [Trypanosoma cruzi strain CL
           Brener]
 gi|70879335|gb|EAN92518.1| pseudouridylate synthase-like protein, putative [Trypanosoma cruzi]
          Length = 448

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 92/347 (26%), Positives = 161/347 (46%), Gaps = 29/347 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV----RVDKKR-VKFNNRIQS 61
           VQY V+  D    R+D +   H+P  ++  ++ +++ G +    +  KKR  +  +R++ 
Sbjct: 97  VQYHVITQDWFGQRVDTFLTQHHPEWSYETMKTLVQQGHIYRYRKNGKKRFTRITDRLEF 156

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHS------DFLKSILLYEDSKIYVFNKPA 115
            +++ +P  +     +     +L  S   T         +   +++L+++  + V NKP 
Sbjct: 157 DELLVVPTPVFYERQLAPPTGVLQESNKPTHFKLSSQVREMAHNMVLFKNEHVIVINKPH 216

Query: 116 GISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G+ +   S     +I   L +W  +   KP + H LD+ETSG +V+AR++ A + L   F
Sbjct: 217 GVPMMPTSDPQEMNIAAMLSAWKYTNSTKPIVCHNLDKETSGCVVLARSKNAHRMLARMF 276

Query: 175 RMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             R +   +YW    G P      I           GD +       K +   I+ F V+
Sbjct: 277 VKRVVPNSVYWGFCVGKPSVNFGRIRMHFEMTRGTKGDIIVARPSPTKTSKVGIAEF-VV 335

Query: 234 DCFAQKF-CWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNFTSPI------Q 285
           +  A +F  ++   P T R HQ R+ A H +  P++GD KY    +  F S +      +
Sbjct: 336 NASALEFGSFISFYPLTTRRHQERIMAAHALRSPLLGDAKYGG--ESAFPSSMSLFWDPE 393

Query: 286 NK---LYLHARYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGFKYD 327
           +K   L+LH R + LP+    G  + +TAPLP HM KT+  LG+  D
Sbjct: 394 DKGLPLHLHHRKIQLPYKNSTGEFVCVTAPLPIHMEKTFKKLGWPCD 440


>gi|261331103|emb|CBH14092.1| pseudouridylate synthase, putative [Trypanosoma brucei gambiense
           DAL972]
          Length = 406

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 96/348 (27%), Positives = 165/348 (47%), Gaps = 38/348 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV-----RVDKKRVKFNNRIQS 61
           +QY VV  +    R+D +   HYP  ++  ++++++ G +        KK  +  +R++ 
Sbjct: 56  LQYHVVTQEWFGERVDSFLTCHYPQWDYETIKRLVQQGHIYRYRKNGKKKFTRLTDRLEF 115

Query: 62  GQVVRIPPVINALNHIIKEQKILDSS----VNLTKHS-DFLKSILLYEDSKIYVFNKPAG 116
            +++ +P        +     +L+ +      L+  + +   +++L+++  + V NKP G
Sbjct: 116 DELLVVPTRAFWEKQLAPPSGVLEETDGPKFKLSATAREMAHNMVLFKNEHVIVINKPHG 175

Query: 117 ISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           + +          I   L +W  +   KP + H LD+ETSG +V+ARTR A + L   F 
Sbjct: 176 LPMMPTDDPQEMSIAAMLPAWKFTNVAKPVVCHNLDRETSGCVVLARTRNAHRMLGRMFV 235

Query: 176 MRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIG------GDYVHVVKQNEKGANYAIS 228
            R +   +YWS   G P        N+   + H        GD +       K +  AI+
Sbjct: 236 KRVVPNSVYWSFCVGKP------TVNYGRVRMHFDITRGNKGDIIVARPSPTKTSKVAIA 289

Query: 229 HFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC--ANFKGN---FT 281
            F V++  A +F  ++   P T R HQ R+ A H + CP++GD KY   A F  +   F 
Sbjct: 290 EF-VVNASALEFGSFISFYPLTTRRHQERIMAAHALRCPVLGDAKYGGDAAFPSSLSLFW 348

Query: 282 SPIQNK---LYLHARYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGF 324
            P +NK   L+LH R + LP+    G  + +TAPLP  M KT+  LG+
Sbjct: 349 DP-ENKGLPLHLHHRKIQLPYKNTAGEFICVTAPLPTQMEKTFKKLGW 395


>gi|71276441|ref|ZP_00652717.1| Pseudouridine synthase, RluD [Xylella fastidiosa Dixon]
 gi|71901554|ref|ZP_00683637.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|170730991|ref|YP_001776424.1| pseudouridylate synthase [Xylella fastidiosa M12]
 gi|71162757|gb|EAO12483.1| Pseudouridine synthase, RluD [Xylella fastidiosa Dixon]
 gi|71728678|gb|EAO30826.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|167965784|gb|ACA12794.1| Pseudouridylate synthase [Xylella fastidiosa M12]
          Length = 331

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 94/347 (27%), Positives = 160/347 (46%), Gaps = 42/347 (12%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L  + +   V +     R D      +P  +   L + ++SG V ++   V+  + +  G
Sbjct: 9   LAGFSRQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVRPRDPVYGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           +VVR+  V +     + +   LD               +LYED  ++V NKPAG+ V  G
Sbjct: 69  EVVRLQVVPDIRTDAVPQDIPLD---------------ILYEDEHVFVLNKPAGLIVHPG 113

Query: 123 SGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +     +    PR  + HRLD++TSG++VVART  A   L E    
Sbjct: 114 AG---NPDGTLVNALLHRDPALAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSS 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R++ + Y ++V  +         N  +++ H        V    K    A++H+++ + F
Sbjct: 171 RQVHRQYLAVV--VSALVSGGTVNAAIER-HPRDRLRMAVSDTGK---EAVTHYRLRERF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQ-----NKL 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y  +    KG   + +       + 
Sbjct: 225 -RAHTALECRLDTGRTHQIRVHMAHLRHPIVGDRLYGGSLKLPKGGTDALVAMLRGFKRQ 283

Query: 289 YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  ++  HP G   ++I AP+P  + +   +L  + D  L+ +R
Sbjct: 284 ALHAEVLEFLHPVGALPVRIVAPVPEDLCQLLAAL--REDSALFFER 328


>gi|159900009|ref|YP_001546256.1| pseudouridine synthase [Herpetosiphon aurantiacus ATCC 23779]
 gi|159893048|gb|ABX06128.1| pseudouridine synthase [Herpetosiphon aurantiacus ATCC 23779]
          Length = 560

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 74/224 (33%), Positives = 110/224 (49%), Gaps = 12/224 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D +I V NKP G++     G     D         + +   +  RLD++TSG+++ 
Sbjct: 5   ILYRDEQILVINKPTGVATHAPQGDLALTDVERALRAQLQLEYLAIHQRLDRDTSGVMLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A   AA  +L  +F    I+K Y +LV+G+P   +  I   L   +  G   + V   ++
Sbjct: 65  ALDPAANANLATAFAEHTIEKTYQALVYGVPIQTQGVIDAAL---APAGDGMIQVASAHD 121

Query: 221 KGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           + A  AI+H++V +    Q+F  LE+QP TGRTHQLRVH   +G PIVGD  Y       
Sbjct: 122 RRAQSAITHYRVLVSSPDQRFSLLELQPKTGRTHQLRVHCECLGHPIVGDPLYD------ 175

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +    +L LHA  +   HP   + L I AP PA   +    L
Sbjct: 176 -VARAAPRLMLHASELRFTHPLTQQPLHIQAPTPALFTRVAQGL 218


>gi|222110296|ref|YP_002552560.1| RluA family pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221729740|gb|ACM32560.1| pseudouridine synthase, RluA family [Acidovorax ebreus TPSY]
          Length = 334

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 94/330 (28%), Positives = 151/330 (45%), Gaps = 31/330 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           ++ VVV  ++   RLD+      P  +   LQ++L  G VR++ + V K  +R+++G  +
Sbjct: 27  LREVVVGAEQHAQRLDKALAELVPEFSRSYLQQLLLQGCVRLNGREVQKPASRVKAGDRI 86

Query: 66  RIPPVINALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
            +       +   + EQ  LD               ++YED  I V +KPAG+ V    G
Sbjct: 87  AVEMRPTQQSQAFRPEQWPLD---------------VVYEDEHILVIHKPAGLVVHPAPG 131

Query: 125 --IAYHIDGFLKSWVDSKG-QKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                 ++  L    D++  Q PR  + HRLD++TSG++VVAR+R+A   L      R +
Sbjct: 132 NWSGTLLNALLGR--DAQAMQVPRAGIVHRLDKDTSGLMVVARSRSAMDALVRMIAAREV 189

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y +L WG          +  + +       + VV   +     A + F +ID   ++
Sbjct: 190 SRQYVALGWGGWTGAAHRSVHAPIGRDPRNRLRMAVVDLAQHPGKEARTDFDLIDA-NEE 248

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
            C +    HTGRTHQ+RVH   +  P+V D  Y     G       ++  LHA  +   H
Sbjct: 249 VCLVRCTLHTGRTHQIRVHMASIRHPLVADVLYGGAMAGPM-----HRQALHAFRLAFVH 303

Query: 300 P-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           P  G  L+  APLP  M +  D  G +Y+R
Sbjct: 304 PVTGAPLEFHAPLPEDMTQALDFWGLRYNR 333


>gi|259503429|ref|ZP_05746331.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           antri DSM 16041]
 gi|259168507|gb|EEW53002.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           antri DSM 16041]
          Length = 303

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 95/323 (29%), Positives = 151/323 (46%), Gaps = 35/323 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +D    R+D+   +H+   +   LQK +  G V+V+ + VK   ++  G  V I P    
Sbjct: 9   DDTLTGRVDKALAHHFRQFSRSQLQKWIADGNVQVNGEAVKAKAKLAVGDQVVIKPEAPQ 68

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDG 131
              ++ E+  LD               ++YED  + V NKP G+ V    G   H  ++ 
Sbjct: 69  KIDLVPEKIPLD---------------IVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNA 113

Query: 132 FLKSWVDSK--GQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            L     S   G+ +P + HR+D++TSG+L+VA+   A + L    + +  Q+ Y +LV 
Sbjct: 114 LLYHCPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDLAHRSLAAQLKAKTNQREYVALVH 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQP 247
           G+ K     +       + IG       KQ       +A++HFKV++ F + +  +  + 
Sbjct: 174 GVIKQDAGTV------DAPIGRSKKDRKKQAIVSDGRHAVTHFKVLERF-RHYTLVSCRL 226

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH   +G P+ GD  Y        T P + + YLHAR +   HP  G+ L 
Sbjct: 227 ETGRTHQIRVHMKSIGHPLAGDPLYGP----RKTLPGRGQ-YLHARLLGFKHPRTGQELV 281

Query: 307 ITAPLPAHMVKTWDSLGFKYDRN 329
            T PLP +  +  D L  K D N
Sbjct: 282 FTVPLPDYFQQMVDKLK-KTDSN 303


>gi|309792569|ref|ZP_07687031.1| RluA family pseudouridine synthase [Oscillochloris trichoides DG6]
 gi|308225383|gb|EFO79149.1| RluA family pseudouridine synthase [Oscillochloris trichoides DG6]
          Length = 299

 Score =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 88/311 (28%), Positives = 152/311 (48%), Gaps = 32/311 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PP 69
           +E      RLDR+     P ++   +Q ++ +GQV V+ + V+ ++ ++ G +V +  PP
Sbjct: 1   MEAQAAGHRLDRFVAQALPDLSRSFVQHLIAAGQVLVNAQAVRPSHALRHGDLVSVTVPP 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                    +   ++  ++ L          ++YED+ + V  KPAG+ V    G     
Sbjct: 61  A--------QPVALVPEAIPLH---------VVYEDADVVVVEKPAGMVVHPAPGHPNGT 103

Query: 128 HIDGFLKSWVDSK---GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            ++  L  + D +     +P + HRLD  TSG+LVVAR   A +HLT     R+++KIY 
Sbjct: 104 LVNALLARYPDMQVGGDLRPGIVHRLDAGTSGLLVVARHDQALRHLTALQHARQMRKIYL 163

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G  K  +  I   + +  H   D + +          A +H++V +     +  LE
Sbjct: 164 AVAEGRFKQAEGLIDAPVGRHPH---DRLRMAVTPT--GREARTHYRVCEELG-NYTLLE 217

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++  TGRTHQ+RVH  H+G PI+GD  Y    KG  T  ++ + +LHA  +     +G  
Sbjct: 218 LRLETGRTHQIRVHLQHLGRPILGDPLYGVR-KGRPTFGLERQ-FLHAHCLGFQLLDGSW 275

Query: 305 LQITAPLPAHM 315
            + T+PLPA +
Sbjct: 276 REFTSPLPADL 286


>gi|331084859|ref|ZP_08333947.1| hypothetical protein HMPREF0987_00250 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330410953|gb|EGG90375.1| hypothetical protein HMPREF0987_00250 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 301

 Score =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 97/325 (29%), Positives = 154/325 (47%), Gaps = 50/325 (15%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI--QS 61
           M   +Y   +ND   MR+D++     P ++   LQK+++  +V V+ + VK N ++  + 
Sbjct: 1   MEERRYTTEKNDL--MRIDKFLSEKLPDLSRSYLQKLIKEKEVLVNGQPVKANYKLSLED 58

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V IP         +KE  IL   + L          +LYED  I V NKP G+ V  
Sbjct: 59  HISVMIPE--------LKEPDILPEQIPLD---------ILYEDEDILVVNKPKGMVVHP 101

Query: 122 GSGIAYHIDGFLKSWV--DSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLT 171
            +G   H  G L + +    K Q        +P + HR+D +T+G L+V +   A Q L 
Sbjct: 102 SAG---HYSGTLVNALMFHCKDQLSGINGVMRPGIVHRIDMDTTGSLIVCKNDFAHQSLA 158

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISH 229
           E  +   I + Y ++V G+ K     I       + IG   V   K   N K   +A++H
Sbjct: 159 EQLKDHTITRKYHAIVHGVLKEDNGTI------DAPIGRHPVERKKMSVNYKNGKHAVTH 212

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKL 288
           ++V+  F +KF ++E Q  TGRTHQ+RVH   +  P++GD  Y     G   SP++    
Sbjct: 213 YRVLKRF-EKFTYVECQLETGRTHQIRVHMASIRHPLLGDAIY-----GPAKSPMKLQGQ 266

Query: 289 YLHARYMDLPHPEGGR-LQITAPLP 312
            LHA+ + + HP   + ++  A LP
Sbjct: 267 TLHAKILGIIHPRTSQYMEFNAELP 291


>gi|330995872|ref|ZP_08319768.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
 gi|329574403|gb|EGG55974.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
          Length = 363

 Score =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 94/333 (28%), Positives = 157/333 (47%), Gaps = 48/333 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIP 68
           +  ++ ++ MR+D++   H  + +   LQ+      + V+ + VK + +++   ++V + 
Sbjct: 37  LTADSGQKPMRIDKFLMEHLYNTSRNRLQRAAEQEFILVNGRPVKSSYKVKPLDEIVILL 96

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
                 N II E   LD               ++YED  + V +KPAG+ V  G G    
Sbjct: 97  DRPKYENEIIPEDIPLD---------------IVYEDEDLMVVDKPAGLVVHPGCGNYTG 141

Query: 125 -----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                IA+H    LK   D     P   L HR+D++TSG+LVVA+   A  HL   F  +
Sbjct: 142 TLVNAIAWH----LKDNPDYDPNDPTVGLVHRIDKDTSGLLVVAKNADAKTHLGRQFFNK 197

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCF 236
             Q++Y +LVWG  ++++  I   + +  H        V   + G   +A++H++V++ F
Sbjct: 198 TTQRLYNALVWGSFQDEEGRIEGNIAR--HPKDRMQMAVFPPDSGIGKHAVTHYRVLENF 255

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN---- 286
                 +E +  TGRTHQ+R H  H+G P+  D +Y  N   +G     +   IQN    
Sbjct: 256 -NYVTLVECRLETGRTHQIRAHMKHIGHPLFNDERYGGNEILRGTQFSKYKQFIQNCFAV 314

Query: 287 --KLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
             +  LHAR +   HP  G+ +  T+ LPA M 
Sbjct: 315 CPRQALHARTLGFIHPRSGQEMYFTSELPADMT 347


>gi|281411684|ref|YP_003345763.1| pseudouridine synthase, RluA family [Thermotoga naphthophila
           RKU-10]
 gi|281372787|gb|ADA66349.1| pseudouridine synthase, RluA family [Thermotoga naphthophila
           RKU-10]
          Length = 311

 Score =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 92/309 (29%), Positives = 154/309 (49%), Gaps = 29/309 (9%)

Query: 12  VENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VE  EE  RLD++ K   P  I+   +QK ++ G+V+V+ +  K + +++ G++V +   
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSMIQKAIKEGKVKVNGQIKKPSYKLKEGEIVEV--- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
              L    +E  +    + L          +LYED  I V +KP  + V           
Sbjct: 63  --DLPEKPQEATVQPEEIELK---------VLYEDRDIVVIDKPRDMIVHPVPSKLSGTL 111

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D +G     +P + HRLD+ETSG++VVA+   A Q L++ F+ R+++K Y 
Sbjct: 112 VNALLNHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYI 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  K K E + +  L +  +    + VV+  ++    AI+ ++V+  F      + 
Sbjct: 172 LLVKGRVK-KDEGVVDLPLARHPVLRIKMAVVETGKE----AITEYRVLKRFDDVATLVL 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P TGRTHQ+RVH   +G PI+GD  Y    K +    I+ ++ LHA  +   HP  G 
Sbjct: 227 AFPKTGRTHQIRVHMKSLGHPIMGDKIY-GKPKEDEIFGIKRQM-LHALKLGFFHPRTGE 284

Query: 305 -LQITAPLP 312
            ++  +PLP
Sbjct: 285 WMEFVSPLP 293


>gi|312875944|ref|ZP_07735934.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311797425|gb|EFR13764.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 300

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 90/315 (28%), Positives = 166/315 (52%), Gaps = 41/315 (13%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           RLD++         +FV  QKI+  G V V++ +V K   +++SG ++++         +
Sbjct: 9   RLDKYLSEALSKTRSFV--QKIIEEGNVWVNQTQVLKPAYKVKSGDIIKV---------V 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH 128
           I E K       L+  +  +   ++YED  + V NKP G+ V  G+G         + + 
Sbjct: 58  IPEPK------QLSLVAQDIDIEVVYEDEHLAVINKPCGMVVHPGTGNFENTLVNALLHK 111

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             G L S   +   +P + HRLD++TSG+L+VA+T  A   L+E+ +  +I++IY+++  
Sbjct: 112 FSGRLSSI--NGVIRPGIVHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICE 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+ K     I N  + +  +    + VV   ++    A+++F+V++ F  K+ +++++  
Sbjct: 170 GVLKEDSGVI-NAPIGRHPVNRLKMAVVPNGKE----AVTYFEVLERF-DKYTFIKLRLK 223

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  ++G P++GD  Y    K  F   +Q ++ LHA  ++  HP   + L  
Sbjct: 224 TGRTHQIRVHMSYIGYPLLGDSSY-GRAKNEFG--VQGQV-LHAGEIEFVHPITSKVLHF 279

Query: 308 TAPLPAHMVKTWDSL 322
           +A LP + V+  + L
Sbjct: 280 SADLPEYFVEILNML 294


>gi|304404034|ref|ZP_07385696.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
 gi|304347012|gb|EFM12844.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
          Length = 324

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 91/326 (27%), Positives = 149/326 (45%), Gaps = 44/326 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           VVE DE   RLD++    +    ++   +Q+ ++SG V V+    K  +R+++G V+ + 
Sbjct: 26  VVEVDEAGERLDKYVTESFADSAVSRTQIQEWIKSGAVLVNGTEAKAKHRLEAGDVITVE 85

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                   II E   L+               ++YED  + V NK  G+ V    G  +H
Sbjct: 86  VPEPEPAEIIAEPIPLN---------------IVYEDEDVIVINKQRGLVVHPAPG--HH 128

Query: 129 ----IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  +    D  G     +P + HR+D++TSG+L+ A+  AA   L+   +   + 
Sbjct: 129 SGTVVNALMYHCQDLSGINGSIRPGIVHRIDKDTSGLLMAAKNDAAHASLSAQLKEHTVT 188

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVIDCFA 237
           + Y +LV G +P ++    A        IG D     +    +K + +A++HF VI+   
Sbjct: 189 RKYIALVHGNLPHDRGTVDAP-------IGRDSRDRKMFAVTDKNSKHAVTHFSVIERL- 240

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  LE+Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   N   LHA  +  
Sbjct: 241 DDYTVLELQLETGRTHQIRVHMKYIGHPLAGDPMY-----GRSKTVALNGQALHAAILGF 295

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP     L+  AP+P  M     SL
Sbjct: 296 NHPRTNEYLEFEAPIPEDMENVLHSL 321


>gi|294669553|ref|ZP_06734620.1| hypothetical protein NEIELOOT_01452 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291308466|gb|EFE49709.1| hypothetical protein NEIELOOT_01452 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 372

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 90/313 (28%), Positives = 147/313 (46%), Gaps = 47/313 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD       P  +   L   ++ G V V+ K  K  +++  G+ + +          
Sbjct: 38  GLRLDAALAKLLPDYSRSRLADWIKEGAVSVNGKPAKPKDKLIGGEKLAV---------- 87

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
               +I +S+  L    + +   ++YED  + V NKPAG+ V   +G      ++G L +
Sbjct: 88  ----QIRESNETLAFTPEAMDLDIIYEDDSVIVLNKPAGLVVHPAAGNWSGTLLNGLL-A 142

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PK 192
              +    PR  + HRLD++TSG++VVA+T  A  HL +  + R +++IY ++  GI P 
Sbjct: 143 HCPALQNIPRAGIVHRLDKDTSGLMVVAKTLPAQNHLVQQLQTRTVKRIYRAVADGIVPF 202

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           + K         ++ IG D  + VK    + G   A++H KV++ + Q   ++E    TG
Sbjct: 203 DGK--------IETQIGRDPHNRVKMAVVKFGGKEAVTHVKVLERY-QAHSYIECALETG 253

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----------YLHARYMDLPHP 300
           RTHQ+RVH      P+ GD  Y     GN   P  + +           LHA  +   HP
Sbjct: 254 RTHQIRVHMREAKHPLAGDPVY-----GNPRHPCSDTVKTEIKALARQALHAYRLSFIHP 308

Query: 301 E-GGRLQITAPLP 312
           + GG +Q  APLP
Sbjct: 309 QNGGEMQFEAPLP 321


>gi|261749573|ref|YP_003257259.1| ribosomal large subunit pseudouridine synthase D [Blattabacterium
           sp. (Periplaneta americana) str. BPLAN]
 gi|261497666|gb|ACX84116.1| ribosomal large subunit pseudouridine synthase D [Blattabacterium
           sp. (Periplaneta americana) str. BPLAN]
          Length = 344

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 88/358 (24%), Positives = 171/358 (47%), Gaps = 53/358 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---- 67
           VE  ++ +R+D++ +    +I+   +QK   SG++ V++  +K N +I+   +V      
Sbjct: 10  VEKYQKTIRIDKFLRKSIQNISRNQIQKATNSGKILVNQCIIKKNYKIKPFDLVEAEIYY 69

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----- 122
           PP++++     + + I+  ++ L          +LYED  I V NK AG+ V  G     
Sbjct: 70  PPILDS-----EYKNIIAENIPLN---------ILYEDEDILVINKAAGMVVHPGFGNEK 115

Query: 123 ----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                GI YH         + +  +  L HR+D++T+G+LV+A+   A ++L + F  + 
Sbjct: 116 GTLIHGIKYHFKN------NHQLYRLGLVHRIDKDTTGLLVLAKNEYAQKYLFQQFISKT 169

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           IQ+ Y +LVWG  + ++  I+ ++ +  +     + + ++N   + Y+++H+KV++ F +
Sbjct: 170 IQRKYLALVWGNIQKQEGTISGFIGRDPN-NRKRMTLFQRNFYRSRYSVTHYKVLERF-K 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP-----------IQ 285
              ++     TG+THQ+RVH  ++G P+  D  Y  +  F   + S            + 
Sbjct: 228 YLTYVSCNLETGKTHQIRVHFKYLGHPLFNDSTYGGDKIFMKKYLSKKSIDFFKDSLNLL 287

Query: 286 NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQ 343
            +  LHA  +   HP+  +   T  +P    K    L     RN Y      ++E K+
Sbjct: 288 KRQALHAGSLSFIHPKNRKCHFTCSIPEDFKKVLQKL-----RNQYFITRSPEEEYKR 340


>gi|149566907|ref|XP_001518233.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4, partial [Ornithorhynchus anatinus]
          Length = 301

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 81/271 (29%), Positives = 130/271 (47%), Gaps = 42/271 (15%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG---FLKSWVDSKGQKP-RLTHR 149
           +  LK  +LY+D ++ V +KP G+ V GG GI   I      L   +D    +P  L HR
Sbjct: 29  AKVLKDGILYQDKELVVIDKPYGLPVHGGPGIQRCITDVLPILAKMLDGFRAEPLHLCHR 88

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--- 206
           LD+ET+G++V+AR+R  A  +   F+MR++ K YW++  G+P + +  +   +++K    
Sbjct: 89  LDKETTGVMVLARSRDVAHQVQGQFKMRQVAKTYWAVCVGVPVHSEGVVDIPIVEKEVQS 148

Query: 207 -------------HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                        H+  D   V ++  + A+ A++ ++ +         LE++P TG  H
Sbjct: 149 QQQHHKMTLAPNYHL-EDGKMVKRRVSRDADSAVTQYRTLS-GTTSCTLLELRPITGVKH 206

Query: 254 QLRVH-ALHMGCPIVGDHKYC--ANFKGNFTSPIQNK-------------LYLHARYMDL 297
           QLRVH A  +GCPI+GDHKY            P+  K             L+LHA+ + L
Sbjct: 207 QLRVHLAFGLGCPILGDHKYSNWNKLAPQKLPPVILKSLGLEQRKSRYIPLFLHAQRLTL 266

Query: 298 PHPEGGR---LQITAPLPAHMVKTWDSLGFK 325
           P   G R   L +  P  A   +    LG +
Sbjct: 267 P-ALGNRSRDLDLECPPSAFFERCLSRLGLE 296


>gi|71653582|ref|XP_815426.1| pseudouridylate synthase-like protein [Trypanosoma cruzi strain CL
           Brener]
 gi|70880480|gb|EAN93575.1| pseudouridylate synthase-like protein, putative [Trypanosoma cruzi]
          Length = 407

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 92/345 (26%), Positives = 159/345 (46%), Gaps = 25/345 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV----RVDKKR-VKFNNRIQS 61
           VQY V+  D    R+D +   H+P  ++  ++ +++ G +    +  KKR  +  +R++ 
Sbjct: 56  VQYHVITQDWFGQRVDTFLTQHHPEWSYETMKTLVQQGHIYRYRKNGKKRFTRITDRLEF 115

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLT------KHSDFLKSILLYEDSKIYVFNKPA 115
            +++ +P  +     +     +L  S   T      +  +   +++L+++  + V NKP 
Sbjct: 116 DELLVVPTPVFYERQLAPPTGVLQESKKPTHFKLSSQVREMAHNMVLFKNEHVIVINKPH 175

Query: 116 GISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G+ +   S     +I   L +W  +   KP + H LD+ETSG +V+AR++ A + L   F
Sbjct: 176 GVPMMPTSDPQEMNIAAMLSAWKYTNSTKPIVCHNLDKETSGCVVLARSKNAHRMLARMF 235

Query: 175 RMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             R +   +YW    G P      I           GD +       K +   I+ F V+
Sbjct: 236 VKRVVPNSVYWGFCVGKPSVNFGRIRMHFEMTRGTKGDIIVARPSPTKTSKVGIAEF-VV 294

Query: 234 DCFAQKF-CWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCAN--FKGN---FTSPIQN 286
           +  A +F  ++   P T R HQ R+ A H +  P++GD KY     F  +   F  P   
Sbjct: 295 NASALEFGSFISFYPLTTRRHQERIMAAHALRSPLLGDAKYGGESAFPSSMSLFWDPEDK 354

Query: 287 --KLYLHARYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGFKYD 327
              L+LH R + LP+    G  + +TAPLP HM KT+  LG+  D
Sbjct: 355 GLPLHLHHRKIQLPYKNSTGEFVCVTAPLPIHMEKTFKKLGWPCD 399


>gi|113931514|ref|NP_001039205.1| RNA pseudouridylate synthase domain-containing protein 4 [Xenopus
           (Silurana) tropicalis]
 gi|123892314|sp|Q28C59|RUSD4_XENTR RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 4
 gi|89268931|emb|CAJ83700.1| RNA pseudouridylate synthase domain containing 4 [Xenopus
           (Silurana) tropicalis]
          Length = 324

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 85/292 (29%), Positives = 137/292 (46%), Gaps = 48/292 (16%)

Query: 77  IIKEQKILDSSVNLTKHSDF--------LKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           I  E+K+L+ +   T   +         LKS ++ ED ++ + NKP G+ V GG  +   
Sbjct: 19  IRAERKVLEGAARETSRKNAPTIVYLRELKSQVVREDPELVLVNKPHGLPVHGGPTVERS 78

Query: 129 IDGFLKSWVDS----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   L +        K +  +L HRLD++T+G L++ART  AA+ + ++ R R + ++YW
Sbjct: 79  VASLLPALAKHHFGWKAEPLKLCHRLDRDTTGALILARTTEAAERVQQALREREVHRVYW 138

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHV-------VKQNEKG----------ANYAI 227
           +L  G P + +E I +  + +    G   H         + +E+G          A+ A+
Sbjct: 139 ALCLGTP-SPREGILDIPIMEKETSGPQKHYKMALSPRFRVSEEGAVERVRVPRSAHEAV 197

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYC-----ANFKG--- 278
           + ++ +   A     +E+ P TG  HQLRVH AL + CPI+GDHKY      A  K    
Sbjct: 198 TRYRTLGA-ASGASLVELHPITGVKHQLRVHLALGLNCPILGDHKYSHWGRLAPQKPPDS 256

Query: 279 -----NFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                  T P      L+LHA  + LP  +G   + +  PLP    KT   L
Sbjct: 257 VLRALGLTVPQARTLSLHLHAVQLTLPSSDGSTPIVLQCPLPYTFRKTLRKL 308


>gi|307297764|ref|ZP_07577570.1| pseudouridine synthase, RluA family [Thermotogales bacterium
           mesG1.Ag.4.2]
 gi|306917024|gb|EFN47406.1| pseudouridine synthase, RluA family [Thermotogales bacterium
           mesG1.Ag.4.2]
          Length = 312

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 85/309 (27%), Positives = 151/309 (48%), Gaps = 36/309 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHII 78
           RLDR  +     +   ++ K+LR G VRV+  +++  + +++ G  V++       +   
Sbjct: 33  RLDRVLRKELSDLKLSSIYKLLRRGNVRVNGNKIRDGSWKMEIGDKVQV-----VFSGDP 87

Query: 79  KEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFLKS 135
            + K L+ S  LT KH   +   +L+ED  I   +KP+GISV  G GI     ++G + +
Sbjct: 88  SKLKRLEESRELTPKH---IPLDILFEDDLIVAVDKPSGISVHPGKGIQIITLVEGLM-A 143

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +SKG  PR  HRLD+ TSG+++ A++  AA+ L++ FR R ++K Y++LV G P+ + 
Sbjct: 144 YGNSKGFVPRPVHRLDKHTSGVILFAKSPEAARELSKLFRERGVEKGYFTLVKGFPEKRG 203

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           + ++    ++          V++     +YA +    ID F            TG+ HQ+
Sbjct: 204 KLVS----QREKFVESLAFTVEK-----SYATTSLLWIDLF------------TGKKHQI 242

Query: 256 RVHALHMGCPIVGDHKYCAN-FKGNFTSPIQ-NKLYLHARYMDLPHPEGGRLQITAPLPA 313
           R      G P+VGD  Y    F  +F       + +LH   +     +G  ++I + LP 
Sbjct: 243 RRQLSEAGYPVVGDDVYGDRLFNRDFKKETGLRRYFLHCSRLSFARNDGKEIEIISELPG 302

Query: 314 HMVKTWDSL 322
            + +    L
Sbjct: 303 DLKRVLGCL 311


>gi|296876327|ref|ZP_06900379.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 15912]
 gi|296432617|gb|EFH18412.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 15912]
          Length = 296

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 86/289 (29%), Positives = 142/289 (49%), Gaps = 37/289 (12%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV----NLTKHSDFLKSILLYEDSK 107
           R   N +I+ G+V+ +   +    + +KE  I+   V     ++  ++ L   ++YED  
Sbjct: 24  RAVANEQIKEGKVL-VNGTVKKAKYTVKEGDIIQYEVPEVEEVSYEAEDLPLDIVYEDQD 82

Query: 108 IYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           + V NKP G+ V   +G         + YHI     S ++ +  +P + HR+D++TSG+L
Sbjct: 83  VVVVNKPQGMVVHPSAGHTSGTLVNALLYHIKDL--SGINGE-LRPGIVHRIDKDTSGLL 139

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+   A   L E  + ++  + YW++V G   N +  I      ++ IG       KQ
Sbjct: 140 MVAKNDQAHVALAEELKDKKSLRKYWAIVHGNLPNDRGMI------EAPIGRSEKDRKKQ 193

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-- 274
               KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y    
Sbjct: 194 AVTAKG-KPAVTRFQVLERFGN-YTLVELQLETGRTHQIRVHMAYIGHPVAGDPAYGPKK 251

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             KG          +LHAR +   HP  G  L+ TA +PA   KT + L
Sbjct: 252 TLKGQGQ-------FLHARTLGFTHPRTGETLEFTAEVPAIFEKTLEDL 293


>gi|330811803|ref|YP_004356265.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327379911|gb|AEA71261.1| Ribosomal large subunit pseudouridine synthase D [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 320

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 91/336 (27%), Positives = 154/336 (45%), Gaps = 42/336 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G ++ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVHGGAILELTAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    + +   LD               ++YED  I V NKPAG+ V   +G   H DG
Sbjct: 71  EAQGEWVAQDIALD---------------IVYEDDDILVINKPAGLVVHPAAG---HADG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  
Sbjct: 113 TLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+     +   N  + +       + V++    G   A+SH++V++ F +    + +
Sbjct: 173 IVIGVVTAGGKI--NAPIGRHGQQRQRMAVME----GGKQAVSHYRVLERF-RSHTHVRV 225

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDL 297
           +  TGRTHQ+RVH  H+  P+VGD  Y   F+            ++N  +  LHAR+++L
Sbjct: 226 KLETGRTHQIRVHMAHINFPLVGDPAYGGRFRIPPAASQTMVESLKNFPRQALHARFLEL 285

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            HP  G R+   +PLP   V  W     K DR  +I
Sbjct: 286 DHPTTGKRMSWESPLPDDFV--WLLTLLKQDREAFI 319


>gi|256845300|ref|ZP_05550758.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_36A2]
 gi|256718859|gb|EEU32414.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_36A2]
          Length = 290

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 86/308 (27%), Positives = 157/308 (50%), Gaps = 27/308 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++Y++ E D E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G +V 
Sbjct: 2   IEYIIDE-DYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDIVF 60

Query: 67  I--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           I  P      N    E+K ++  +N  +    LK ++++E+  ++V NK  G  V  GSG
Sbjct: 61  IFLPESFKENN----EKKFIE--LNQVRKEK-LKQMIVFENENLFVINKSLGDVVHKGSG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +    +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+
Sbjct: 114 HDISLLEEFRSYYSNNN--INFVNRIDRLTSGLVIGAKNIKTARDIAKEIQAGNIVKKYY 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  +     + N+L K      + V V    ++G   +I++FK I  +  ++  LE
Sbjct: 172 ILVNGKIEKDNFILENYLKKDE----EKVIVSDIEKEGYKKSITYFKKIKEY-DRYTLLE 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQLR    H+G  IVGD KY  N K       ++ +YL + Y+ +       
Sbjct: 227 AELKTGRTHQLRAQLNHIGNNIVGDTKYGRNEK-------EDIMYLFSYYLKIDLY---N 276

Query: 305 LQITAPLP 312
           L+I   +P
Sbjct: 277 LEIKLEIP 284


>gi|262195124|ref|YP_003266333.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262078471|gb|ACY14440.1| pseudouridine synthase, RluA family [Haliangium ochraceum DSM
           14365]
          Length = 345

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 94/326 (28%), Positives = 143/326 (43%), Gaps = 58/326 (17%)

Query: 22  DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ---VVRIPPVINALNHII 78
           D+    H+P  +   +  +   G+VRV+ ++VK    + +G    + R+P     L    
Sbjct: 28  DKLVGEHFPAASRRRVTALFADGRVRVNGRKVKKGAIVPAGAEIALTRLPVADEELVPQA 87

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             + +LD               LLYED  I V +KPAG+        A   D    + V 
Sbjct: 88  NHELVLD---------------LLYEDDAIAVVSKPAGLPSHPLR--AGERDTLANALVA 130

Query: 139 ------SKGQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                 + G  PR   L HRLD +TSG+LV ART+ A   L  +F    ++K Y +L +G
Sbjct: 131 HYPECAAIGADPREAGLAHRLDIDTSGVLVAARTQKAWHALRAAFGSGAVEKHYLALTFG 190

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------- 242
            P + +  +A  L+++    G   H V +++ G        +  D    +  W       
Sbjct: 191 APSSGEMDVA--LVQR----GRRAHPVFRDDAGFGGFGGRGERGDALPARTTWRIERRFG 244

Query: 243 ----LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-------ANFKGNFTS----PIQNK 287
               L  + HTGR HQ+RVH    G PI+GD  Y        A  + +  +    P   +
Sbjct: 245 PACLLLCRAHTGRMHQIRVHLALAGAPIIGDSLYAPAPETLSAAEREDLAALSEHPEATR 304

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLP 312
            +LHA  + +PHPE GR L+I APLP
Sbjct: 305 HFLHASAVTIPHPETGRALRIEAPLP 330


>gi|28211276|ref|NP_782220.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           tetani E88]
 gi|28203716|gb|AAO36157.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           tetani E88]
          Length = 307

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 90/323 (27%), Positives = 155/323 (47%), Gaps = 32/323 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +V+ + EN RLD +   +    +   ++K+     + V+ +  K N +++ G +V+
Sbjct: 5   IEKFLVKEEFENERLDLFIVENLKDKSRSFIKKLSDDKGIMVNDEIKKVNYKVKCGDIVK 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +         + KE+ I     N+  +       +LYED  I V NKP G+ V  G G  
Sbjct: 65  VL--------LPKEEGIYLEKENMDLN-------ILYEDEDIIVINKPQGMVVHPGVGNT 109

Query: 125 IAYHIDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++G L   KS  +  G+ +P + HR+D++TSGILV+A+T  A +HL    +   + 
Sbjct: 110 KGTLVNGLLAHCKSLSNINGEERPGIVHRIDKDTSGILVIAKTNRAHEHLANQLKDHSML 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           ++Y +L  G+ K     I   L +      D +     +E     A++H+KVI+ +    
Sbjct: 170 RVYMALTEGVIKEDMGTIDKDLGRNP---SDRIKFAVVDE--GKRAVTHYKVINRYNNN- 223

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E +  TGRTHQ+RVH  ++G PIVGD  Y    +  F    Q    LHA+ +   HP
Sbjct: 224 SLIECRLETGRTHQIRVHMSYIGHPIVGDPTYGYK-RQKFKLKGQ---MLHAKKLGFIHP 279

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  ++  + +P    K  + L
Sbjct: 280 TNGEYMEFDSEIPEEFKKILEIL 302


>gi|153814897|ref|ZP_01967565.1| hypothetical protein RUMTOR_01112 [Ruminococcus torques ATCC 27756]
 gi|317500410|ref|ZP_07958634.1| pseudouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089583|ref|ZP_08338482.1| hypothetical protein HMPREF1025_02065 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145847928|gb|EDK24846.1| hypothetical protein RUMTOR_01112 [Ruminococcus torques ATCC 27756]
 gi|316898165|gb|EFV20212.1| pseudouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330404951|gb|EGG84489.1| hypothetical protein HMPREF1025_02065 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 303

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 89/332 (26%), Positives = 152/332 (45%), Gaps = 64/332 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI----PPV 70
           D    R+DR+   +  +++   +QK+L+ G++ V++  VK N +I     + +    P V
Sbjct: 9   DRSGERIDRFLSENLENLSRSYIQKLLKDGKISVNQSSVKPNYKISENDKIEVFIPDPEV 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
           ++    I+ E   LD               +LYEDS I + NKP  + V    G      
Sbjct: 69  LD----ILPENIPLD---------------ILYEDSDILIVNKPKNMVVHPAPGHYEHTL 109

Query: 125 ---IAYH-------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              + YH       I+G L+         P + HR+D +T+G L++ +   A Q + E  
Sbjct: 110 VNAVMYHCKDNLSGINGILR---------PGIVHRIDMDTTGSLLICKNDKAHQIIAEQL 160

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN--YAISHFKV 232
           +   I + Y ++V G  K     +       + IG   +   K + K  N  +A++H+ V
Sbjct: 161 KEHSITRRYHAIVHGKIKEDNGVV------NAPIGRHPIDRKKMSTKAKNGKHAVTHYTV 214

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLH 291
           +  F + + ++E +  TGRTHQ+RVH   +G PI+GD  Y     G    P +     LH
Sbjct: 215 LRRF-KDYTYIECELETGRTHQIRVHMASIGHPILGDSMY-----GPSKCPFKLQGQTLH 268

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           A+ + + HP  G+ +++ APLP +  K    L
Sbjct: 269 AKVLGITHPSTGKYIEVDAPLPEYFNKLLKQL 300


>gi|124003349|ref|ZP_01688199.1| ribosomal large subunit pseudouridine synthase C [Microscilla
           marina ATCC 23134]
 gi|123991447|gb|EAY30878.1| ribosomal large subunit pseudouridine synthase C [Microscilla
           marina ATCC 23134]
          Length = 250

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 70/205 (34%), Positives = 109/205 (53%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ + + NK  G+ VQG       +  ++K ++  K  KP      + HR+D+  S
Sbjct: 15  VLYEDNHLIIVNKKGGMLVQGDKTGDKTLGDWVKEYIKEKYDKPGAVFLGIPHRIDRPVS 74

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+++ART  A + + + F+ R+IQK YW++V   P  ++  + +WL K      + V  
Sbjct: 75  GIVILARTSKALERMNQLFKTRKIQKTYWAIVKRKPAEEEGKLVHWLKKDG--AKNVVTA 132

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   GA  A + +KV+      +  LE+ P TGR HQ+RV    MGCPI GD KY   
Sbjct: 133 HDEPVDGAQKAETRYKVLGNLNDHWL-LEVNPITGRPHQIRVQLASMGCPIRGDIKYGFP 191

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
            K     P +N ++LHAR +   HP
Sbjct: 192 RK----DPDKN-IHLHARRVYFMHP 211


>gi|332664097|ref|YP_004446885.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
 gi|332332911|gb|AEE50012.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
          Length = 237

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 80/231 (34%), Positives = 119/231 (51%), Gaps = 27/231 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LY+++++  FNKPAGI  Q    G   +    + F KS V       +L HRLD+  SG
Sbjct: 21  VLYKNNQLIAFNKPAGIPTQTDKTGDKSLLQLAEIFTKSAV-------QLVHRLDRPASG 73

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I++V++T  A  +L E FR R+IQK Y ++V  +P   K  + +W+ K     G     V
Sbjct: 74  IVLVSKTAKALANLNEQFRNRQIQKTYLAVVEALPAEPKGRLEHWIWKN----GQTNRSV 129

Query: 217 KQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              EKG   A  AI  ++++   + ++  LE++  TGR HQ+R     MGC I GD KY 
Sbjct: 130 ISTEKGHANAQEAILEYQLLGS-SDRYHLLEVKLLTGRHHQIRAQLAAMGCIIKGDVKYG 188

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           A       S     ++LHA  +   HP     + +TAPLP   V  WD++G
Sbjct: 189 ARRSNKDRS-----IHLHAWKLSFQHPVSHETVVLTAPLPVDAV--WDAMG 232


>gi|58337436|ref|YP_194021.1| pseudouridine synthase [Lactobacillus acidophilus NCFM]
 gi|58254753|gb|AAV42990.1| pseudouridine synthase [Lactobacillus acidophilus NCFM]
          Length = 302

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 81/297 (27%), Positives = 146/297 (49%), Gaps = 44/297 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHII 78
           RLD++       ++   ++++++   + V++K  K + +IQ G  + I  P +  L+ I+
Sbjct: 15  RLDKFISEQLSDLSRTRVKELIQDQNILVNEKVEKVSYKIQDGDKIEITVPAVKPLD-IV 73

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E   LD               ++YED  + V NKP G+ V    G         + YH 
Sbjct: 74  AENIPLD---------------IVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHT 118

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               +S    +G +P + HR+D++TSG+L++A+   A + L +    +  ++IYW++V G
Sbjct: 119 QDLAQS---PEGFRPGIVHRIDKDTSGLLMIAKNATARESLEQQLANKTNKRIYWAIVHG 175

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               ++  I +  + ++      + VV+  +K    AI+HFKV+  F + +  +E Q  T
Sbjct: 176 NFSEEQGSI-DAPIGRNPYDRKKMAVVENGKK----AITHFKVLKQF-KGYSLIECQLET 229

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GRTHQ+RVH  ++G  + GD  Y      KGN         +LHA+ +   HP+ G+
Sbjct: 230 GRTHQIRVHLDYIGHAVAGDPLYGPRKTLKGNGQ-------FLHAKILGFKHPKTGK 279


>gi|332828139|gb|EGK00855.1| hypothetical protein HMPREF9455_02820 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 225

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 73/228 (32%), Positives = 114/228 (50%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I + NK     VQG       +   +K ++  K  KP      +THRLD+ TS
Sbjct: 3   VLYEDNHIIIVNKTVSEIVQGDKTGDKPLSEIVKEYLKEKYNKPGNVFCGVTHRLDRPTS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V ++T  A   L + F+ + I K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GIVVFSKTSKALPRLNDMFKNKEISKTYWAVVKNAPKQPEGTLKHYLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    +  AI H+K+I   + K+  LE+   TGR HQ+R     +G PI GD KY A 
Sbjct: 123 TEK--PNSKLAILHYKLI-ARSDKYSLLEIDLETGRHHQIRCQLAKIGSPIKGDLKYGAE 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
                 S     + LHAR +   HP    L ++TAP+P   +  W +L
Sbjct: 180 -----RSNPDGGISLHARKISFIHPVSKELIEVTAPVPEDNL--WQAL 220


>gi|293553487|ref|ZP_06674115.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1039]
 gi|291602364|gb|EFF32588.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1039]
          Length = 303

 Score =  110 bits (275), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 91/322 (28%), Positives = 156/322 (48%), Gaps = 51/322 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E+ R+D+   N +   +   +Q  L++G V V+ + VK N +++ G  + +         
Sbjct: 11  ESGRIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVKANYKVKQGDDITV--------- 61

Query: 77  IIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
           +I E + LD    ++ LT         ++YED  + V NKP G+ V   +G         
Sbjct: 62  LIPEPETLDVVPENIPLT---------IVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNA 112

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + YHI     S ++    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y 
Sbjct: 113 LMYHIKDL--STINGV-IRPGIVHRIDKDTSGLLMVAKNDQAHESLAQQLKDKTSLRKYV 169

Query: 185 SLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G IP  K    A     K +     +  ++++ K A   ++HF V++ F + F  +
Sbjct: 170 ALVHGEIPHEKGTINAPIGRSKEN---RKMQAIREDGKPA---VTHFTVLERF-EGFTLV 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E++  TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP 
Sbjct: 223 ELKLETGRTHQIRVHMKYIGYPLAGDPVYGPKKTLKGNGQ-------FLHAQMLGFTHPT 275

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
              ++   APLP    KT + L
Sbjct: 276 TNEKMFFEAPLPEVFEKTLEKL 297


>gi|189468453|ref|ZP_03017238.1| hypothetical protein BACINT_04850 [Bacteroides intestinalis DSM
           17393]
 gi|189436717|gb|EDV05702.1| hypothetical protein BACINT_04850 [Bacteroides intestinalis DSM
           17393]
          Length = 223

 Score =  110 bits (275), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 109/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSEIVKQYLKEKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E F+   ++K YW++V   PK  +  + N+L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFKTSEVKKTYWAIVKNAPKEPEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   +  +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPKSKKAILHYRLIGK-SDNYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             G   S     + LHAR +   HP    + ++ AP+P
Sbjct: 177 --GFARSNPDGSICLHARRISFVHPVSKEMIEVEAPVP 212


>gi|268611664|ref|ZP_06145391.1| RluA family pseudouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 304

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 86/331 (25%), Positives = 155/331 (46%), Gaps = 42/331 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ +  + V + +   R+D++  ++   +    +Q ++  G++ V  K V  N +++ G 
Sbjct: 1   MSDIITLNVSDSDRGARIDKFISDNVEELTRSAVQGLMEKGKILVSGKSVSKNYKLRDGD 60

Query: 64  VVRI----PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            V +    P  ++AL     E   LD               ++YEDS + V NKP G+ V
Sbjct: 61  TVEVEIPEPEPMDAL----PEDIPLD---------------IVYEDSDLLVVNKPKGMVV 101

Query: 120 QGGSG--IAYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    DS        +P + HR+D+ TSG+L+VA+  AA  HL E
Sbjct: 102 HPAHGNHSGTLVNALLHHCGDSLSGINGVIRPGIVHRIDKNTSGLLIVAKNDAAHLHLAE 161

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
             ++    + Y ++  G  K  +  I +  + +       + V  +N +    A++H+ V
Sbjct: 162 QIKVHSFTREYEAVASGYFKETEGTI-DAPIGRHKTDRKKMCVTTENSRN---AVTHYSV 217

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           I  +   +  + ++  TGRTHQ+RVH  ++G P++GD  Y   +KG     I+ +  LHA
Sbjct: 218 IRQYG-GYAHVRLRLETGRTHQIRVHLAYIGHPVLGDDVYGKAYKG-----IEGQC-LHA 270

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           R +   HP  G  ++ T+ LP + V   + L
Sbjct: 271 RKIGFIHPTTGEYMEFTSELPDYFVSILNKL 301


>gi|239623975|ref|ZP_04667006.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239522006|gb|EEQ61872.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 314

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/324 (25%), Positives = 153/324 (47%), Gaps = 49/324 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E ++R+DR+     P ++   +QK+L+SGQV V+            G++++   V+ A +
Sbjct: 22  ESDVRIDRYLAETCPELSRSYIQKLLKSGQVLVN------------GRLIKASYVVTADD 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           HI   +  +  +V     ++ +   +LYED  I + NKP G+ V   +G         + 
Sbjct: 70  HI---EVDVPEAVEPEIEAEPMDLDILYEDQDIILVNKPKGMVVHPAAGHYSHTLVNGLM 126

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH    L     +   +P + HR+D +T+G+L+V +   A   +    +   I + Y ++
Sbjct: 127 YHCKNQLSGI--NGVMRPGIVHRIDMDTTGVLIVCKNDMAHNSIAAQLKEHSITRRYQAI 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-----AISHFKVIDCFAQKFC 241
           V G+ K  +  +   + +         H  ++ +   NY     A++H++V+  F Q + 
Sbjct: 185 VHGVIKEDEGTVDAPIGR---------HQTERKKMCINYNNGRNAVTHYQVLRRFEQ-YT 234

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL--YLHARYMDLPH 299
           ++E +  TGRTHQ+RVH   +  P++GD  Y     G    P+       LHA  + + H
Sbjct: 235 YVECRLETGRTHQIRVHMASLHHPLLGDKVY-----GPAKCPVPGLTGQTLHAGVLGIVH 289

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G  ++ TAPLP +  +   +L
Sbjct: 290 PRTGEYMEFTAPLPEYFERLLRNL 313


>gi|229098363|ref|ZP_04229309.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-29]
 gi|228685068|gb|EEL39000.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-29]
          Length = 302

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 91/329 (27%), Positives = 152/329 (46%), Gaps = 39/329 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKEND 60

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V IP          +E  I    +NL          + YED+ + V NKP G+ V  
Sbjct: 61  EITVTIPDP--------EELDIQAEDMNLE---------IYYEDADVLVVNKPRGMVVHP 103

Query: 122 GSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L     
Sbjct: 104 APGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLV 163

Query: 176 MRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V+D
Sbjct: 164 AKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVLD 217

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  
Sbjct: 218 RF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGI 271

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP  G  +Q  AP+P    +T + L
Sbjct: 272 LGFDHPRTGEYIQFEAPIPEVFEETLNIL 300


>gi|163790406|ref|ZP_02184837.1| Pseudouridylate synthase, 23S rRNA-specific [Carnobacterium sp.
           AT7]
 gi|159874310|gb|EDP68383.1| Pseudouridylate synthase, 23S rRNA-specific [Carnobacterium sp.
           AT7]
          Length = 301

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 90/323 (27%), Positives = 153/323 (47%), Gaps = 51/323 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINAL 74
           EE  RLD+      P I   ++Q+ ++ G V V+ + +K N ++Q S ++V I P + +L
Sbjct: 11  EETGRLDKVLTELLPSITRSHIQQWIKEGNVTVNGENLKANYKVQPSDEIVIIEPELVSL 70

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                  ++L   + +          ++Y+D  + V NK  G+ V   +G         +
Sbjct: 71  -------EVLAEDIPIE---------IVYQDEDVVVVNKAQGMVVHPSAGHQTGTLVNAL 114

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            YHI     S ++    +P + HR+D++TSG+L+VA+  +A + L    + +   + Y +
Sbjct: 115 MYHIKDL--SGINGT-IRPGIVHRIDKDTSGLLMVAKNDSAHEKLAAQLKDKTSLREYIA 171

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           LV G+  ++K  I       + +G   V   KQ+   G   A++HF V++ F + F  + 
Sbjct: 172 LVHGVIPHEKGTI------DAPLGRSKVDRKKQDIIDGGREAVTHFTVLERF-KDFTLVS 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY----CANFKGNFTSPIQNKLYLHARYMDLPHP 300
           ++  TGRTHQ+RVH  ++G P+ GD  Y        KG F         LHA+ +   HP
Sbjct: 225 LKLETGRTHQIRVHMKYIGYPLAGDPIYGPRKTLEGKGQF---------LHAQTLGFKHP 275

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  +   APLP     T   L
Sbjct: 276 TTGEFVTFEAPLPQLFEDTLTKL 298


>gi|56419681|ref|YP_146999.1| hypothetical protein GK1146 [Geobacillus kaustophilus HTA426]
 gi|261419335|ref|YP_003253017.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|297530695|ref|YP_003671970.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|319766151|ref|YP_004131652.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
 gi|56379523|dbj|BAD75431.1| hypothetical conserved protein [Geobacillus kaustophilus HTA426]
 gi|261375792|gb|ACX78535.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC61]
 gi|297253947|gb|ADI27393.1| pseudouridine synthase, RluA family [Geobacillus sp. C56-T3]
 gi|317111017|gb|ADU93509.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC52]
          Length = 304

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 88/320 (27%), Positives = 149/320 (46%), Gaps = 36/320 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E++ +  R+D+         +   +Q+ +++G V V+ + VK N + ++G  V + P  
Sbjct: 8   IEDEYDGERIDKVIAALNEEWSRSQVQQWIKNGLVTVNGQTVKANYKCEAGDSVAVSPPE 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
               H+  E   LD               + YED  + V NKP G+ V    G      +
Sbjct: 68  PEPLHVEPEPIPLD---------------IYYEDEDVLVVNKPRGMVVHPAPGHMRGTLV 112

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSG+L+VA+  AA + L E    + + + Y +
Sbjct: 113 NALLAHCRDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDAAHRSLVEQLVNKTVTRRYKA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWL 243
           +V G+  +    I       + IG D     K    E+    A++HF+V++ F + + ++
Sbjct: 173 IVHGVIPHDYGTI------DAPIGRDKRDRKKMAVTEENGKEAVTHFRVLERF-RHYTYV 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E Q  TGRTHQ+RVH  ++G P+ GD +Y     G   +   +   LHA  +   HP  G
Sbjct: 226 ECQLETGRTHQIRVHMKYIGYPLAGDPQY-----GPKKTLAIDGQALHAGVLGFRHPRSG 280

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             L+  APLP    +  D L
Sbjct: 281 EYLEFEAPLPPEFAELLDWL 300


>gi|302871790|ref|YP_003840426.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302574649|gb|ADL42440.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 293

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 84/279 (30%), Positives = 145/279 (51%), Gaps = 29/279 (10%)

Query: 47  RVDKKRVKFNNRIQS-----GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI- 100
           ++ +K++ F++ + S     GQ+  IPP I + N   +E  I++  VNL      +  + 
Sbjct: 18  QILQKKLFFSSTLTSRLKAHGQIRFIPP-IYSTNQYPEENAIIE--VNLISSKSNIVPVE 74

Query: 101 ----LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
               +LYED+     NKP+G+      G  +  I  +++ +++SK     + +RLD+ETS
Sbjct: 75  GSIDILYEDNFFLFVNKPSGLPSHPSKGHYSDTIANYVEYYLNSKNLTSHIINRLDKETS 134

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+       ++  F  R+++K Y ++V G    KK  +    +K+S  G     +
Sbjct: 135 GIVVFAKNSYFHSIVSREFEKRQVEKTYIAIVHG-RLTKKSGLIEKPIKRSQDG-----I 188

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +  ++A ++++VIDCF + F  L+++P TGRTHQLRVH   +G PIVGD+ Y   
Sbjct: 189 KREIHQDGSFASTYYEVIDCF-ENFTLLKLKPITGRTHQLRVHLSSIGHPIVGDYIYGEQ 247

Query: 276 FKGNFTSPIQNKLYLHARYM--DLPHPEGGRLQITAPLP 312
              N        L LHA  +  +    +     IT+PLP
Sbjct: 248 KTQN------TPLLLHAYSIRFNFKLIDNKIYNITSPLP 280


>gi|227904070|ref|ZP_04021875.1| pseudouridine synthase [Lactobacillus acidophilus ATCC 4796]
 gi|227868089|gb|EEJ75510.1| pseudouridine synthase [Lactobacillus acidophilus ATCC 4796]
          Length = 305

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 81/297 (27%), Positives = 146/297 (49%), Gaps = 44/297 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHII 78
           RLD++       ++   ++++++   + V++K  K + +IQ G  + I  P +  L+ I+
Sbjct: 18  RLDKFISEQLSDLSRTRVKELIQDQNILVNEKVEKVSYKIQDGDKIEITVPAVKPLD-IV 76

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E   LD               ++YED  + V NKP G+ V    G         + YH 
Sbjct: 77  AENIPLD---------------IVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHT 121

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               +S    +G +P + HR+D++TSG+L++A+   A + L +    +  ++IYW++V G
Sbjct: 122 QDLAQS---PEGFRPGIVHRIDKDTSGLLMIAKNATARESLEQQLANKTNKRIYWAIVHG 178

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               ++  I +  + ++      + VV+  +K    AI+HFKV+  F + +  +E Q  T
Sbjct: 179 NFSEEQGSI-DAPIGRNPYDRKKMAVVENGKK----AITHFKVLKQF-KGYSLIECQLET 232

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GRTHQ+RVH  ++G  + GD  Y      KGN         +LHA+ +   HP+ G+
Sbjct: 233 GRTHQIRVHLDYIGHAVAGDPLYGPRKTLKGNGQ-------FLHAKILGFKHPKTGK 282


>gi|332520567|ref|ZP_08397029.1| pseudouridine synthase [Lacinutrix algicola 5H-3-7-4]
 gi|332043920|gb|EGI80115.1| pseudouridine synthase [Lacinutrix algicola 5H-3-7-4]
          Length = 236

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 110/227 (48%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK AG  VQG       +   +K ++  K  KP        HRLD+ T+
Sbjct: 17  VIYEDNHIIVVNKRAGDIVQGDKTGDKPLSDVVKEYLAEKYNKPGNVYLGTVHRLDRPTT 76

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ ++T  A   L + F  + I K YW+LV   PK +K+ + +WL K         H+
Sbjct: 77  GLVIFSKTSKALPRLNKLFVSKDISKTYWALVKNKPKKEKDTLIHWLKKNPKNNKSRAHI 136

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+K I      +  LE+   TGR HQ+R     +G PI GD KY  +
Sbjct: 137 --KEVPDSKKAILHYKTIKVL-DNYILLEVNLETGRHHQIRAQLSSIGSPIKGDLKYGFD 193

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
                 S     + LHAR +   HP     L ITAPLP + +  W++
Sbjct: 194 RSNKDAS-----ISLHARNIKFIHPVSKIELDITAPLPNNAI--WNA 233


>gi|297621774|ref|YP_003709911.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
 gi|297377075|gb|ADI38905.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
          Length = 310

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 85/323 (26%), Positives = 151/323 (46%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           + ++   +E   RLD+     YP   +   LQ ++    V ++ K VK   ++ +G  + 
Sbjct: 7   ETLMTTAEEAGKRLDKVLAERYPDAYSRSYLQWLIEENHVLLNHKPVKKRAKVAAGDRID 66

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +  V+     +  E+  LD               +++ED  I V NKPAG+ V  G+G  
Sbjct: 67  VCFVLAPEIELKPEKIFLD---------------IIHEDEAIIVVNKPAGLVVHPGAGNW 111

Query: 125 IAYHIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
               ++G L   K   + +  +P + HRLD+ET+G+LV A+T  A   L E F  RR+ K
Sbjct: 112 TGTFVNGLLYHCKKLPEGETLRPGIVHRLDKETTGLLVAAKTAEAQHKLVELFSSRRVYK 171

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++  G   N  +   +  + +  +    + +V    +G   +++H++ +  +     
Sbjct: 172 EYIAVCVG---NPGKGTVDAPIARHPVHRQKMAIV----EGGRRSVTHYETLK-YDVSLS 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
            +++   TGRTHQ+RVH   +G P++GD  Y ++         Q  +  LHA  +  PHP
Sbjct: 224 LVKLVLETGRTHQIRVHMKQIGFPVLGDPVYGSS---AMNQKFQLGRQMLHAAKLIFPHP 280

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G+ + + AP+P  M K    L
Sbjct: 281 VTGKEMVLEAPVPDEMAKVMARL 303


>gi|206976765|ref|ZP_03237669.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
 gi|206745075|gb|EDZ56478.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
          Length = 302

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 88/320 (27%), Positives = 150/320 (46%), Gaps = 41/320 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDNVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            + +          I E + LD     +NL          + YED+ + V NKP G+ V 
Sbjct: 61  EITV---------TIPEPEELDIQPEDMNLE---------IYYEDADVLVVNKPRGMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V+
Sbjct: 163 VAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA 
Sbjct: 217 ERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAG 270

Query: 294 YMDLPHPEGGR-LQITAPLP 312
            +   HP  G+ +Q  AP+P
Sbjct: 271 ILGFDHPRTGKYIQFEAPIP 290


>gi|294101951|ref|YP_003553809.1| pseudouridine synthase, RluA family [Aminobacterium colombiense DSM
           12261]
 gi|293616931|gb|ADE57085.1| pseudouridine synthase, RluA family [Aminobacterium colombiense DSM
           12261]
          Length = 326

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 90/311 (28%), Positives = 141/311 (45%), Gaps = 32/311 (10%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           + DEE  R+D +       +    +QK++R G V +   R      ++    + I     
Sbjct: 26  QGDEEGKRIDAFLAEEL-GLTRSYVQKLIRLGNVEISGIRRALKPALKVTAEMAI----- 79

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---I 129
              HI+     +  +  L    + +K  ++YED  I V NKPAG+ V    G  +H   +
Sbjct: 80  ---HIV-----VPPAETLEIEPEPVKFGIIYEDPYIIVVNKPAGLVVHPAPG-NWHGTLV 130

Query: 130 DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            G L  + D     +  +P + HRLD  TSG+LVVART    Q+L   FR R ++K Y +
Sbjct: 131 HGLLYKYRDMRKFDEEVRPGIVHRLDSGTSGLLVVARTPKILQNLQNQFRSRSVEKKYLA 190

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L  G  +     I   + +          ++         A++ ++++    QK+ ++E 
Sbjct: 191 LSCGKLRKAAGFIEEPIGRSQR-----NRLMMTVTDTGRPALTEYRIL-WTHQKYSFIEC 244

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
             HTGRTHQ+RVH  H GCPIVGD  Y        T     +++LHA  +   HP  G R
Sbjct: 245 TLHTGRTHQIRVHLKHRGCPIVGDGLYGTKQSLQRTP---GRMFLHAWKLAFDHPINGSR 301

Query: 305 LQITAPLPAHM 315
           +   A LP  +
Sbjct: 302 MSFRACLPQEL 312


>gi|288803980|ref|ZP_06409402.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           melaninogenica D18]
 gi|288333550|gb|EFC72003.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           melaninogenica D18]
          Length = 365

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 91/340 (26%), Positives = 152/340 (44%), Gaps = 64/340 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V+V+  +E +R+D++      H +   +QK   +G + V+   VK N +++   V+ +  
Sbjct: 36  VIVDKGQEPVRIDKFLFERMQHSSRNRIQKAADAGYIHVNNAPVKSNYKVRPEDVITL-- 93

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I    + L          ++YED  + V NKPAG+ V  G+G     
Sbjct: 94  ---MLDRPKHDNTIEAEDIPLD---------VVYEDDILMVVNKPAGLVVHPGAGNFHGT 141

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+        D    +  L HR+D++TSG+LV+A+T  A   L + F  +   
Sbjct: 142 LINAIAWHLKDM--PSFDPNDPEVGLVHRIDKDTSGLLVIAKTPDAKTALGKQFFNKTTH 199

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------VVKQNEKGANYAISHFK 231
           + Y ++VWG          N    +  I G+            V   + +    A++H++
Sbjct: 200 RSYNAIVWG----------NMTEDEGRIEGNIARDPKDRLRMTVFPPDSEVGKPAVTHYR 249

Query: 232 VIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ- 285
           VI+ F       C LE    TGRTHQ+R H  H+G P+ GD +Y      +G  +S  + 
Sbjct: 250 VIERFGYTTLIECILE----TGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSTYKA 305

Query: 286 ---------NKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                    N+  LHAR +   HP  G ++  T+ LPA +
Sbjct: 306 FIRNCLALCNRQALHARTLGFVHPVTGEQMDFTSELPADL 345


>gi|224535322|ref|ZP_03675861.1| hypothetical protein BACCELL_00184 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224523048|gb|EEF92153.1| hypothetical protein BACCELL_00184 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 223

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 110/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKQYLKEKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E F+   ++K YW++V   PK  +  + N+L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFKTSEVRKTYWAIVKNAPKEPEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   +  +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPKSKKAILHYRLIGK-SDNYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             G   S     + LHAR++   HP    + ++ AP+P
Sbjct: 177 --GFARSNPDGSICLHARHISFVHPVSKEMIEVEAPVP 212


>gi|320161265|ref|YP_004174489.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
 gi|319995118|dbj|BAJ63889.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
          Length = 231

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 76/224 (33%), Positives = 121/224 (54%), Gaps = 18/224 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGI-SVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETS 155
           KS++L++D  I V +KPAG+ S++ G       I G L    + K  K  + HRLD++TS
Sbjct: 10  KSMILFQDEWILVISKPAGLLSIRDGYNPNLPTIQGVL----EPKLGKLWMIHRLDKDTS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V+ART  A ++L   F  R+++KIY+++  G+P+  +  I + L     + GD  H 
Sbjct: 66  GIMVLARTSEAHKNLDRQFAERKVRKIYYAICVGVPEWDEILIQSPL----RVNGDRKHR 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--- 272
              + +    A +H +VI  +   + W+E+ PH+G THQ+R H   +G P++GD  Y   
Sbjct: 122 TVVDFEHGKPAETHVRVISRYG-FYTWVEVHPHSGYTHQIRAHLSSIGYPLLGDSLYRIP 180

Query: 273 --CANFKGNFTS-PIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
             CA       + P   ++ LHA  +   HP  G  +  TAPLP
Sbjct: 181 PNCAVIPPKAENLPAFPRVALHAYALTFSHPNSGEEITFTAPLP 224


>gi|300869701|ref|YP_003784572.1| ribosomal large subunit pseudouridine synthase D [Brachyspira
           pilosicoli 95/1000]
 gi|300687400|gb|ADK30071.1| ribosomal large subunit pseudouridine synthase D [Brachyspira
           pilosicoli 95/1000]
          Length = 222

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 65/177 (36%), Positives = 97/177 (54%), Gaps = 12/177 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED    + NK +GI V         ID   K + + K  +  L HRLD+ TSGIL++
Sbjct: 13  IIYEDEYFLIINKESGIEVDDSL-----IDTIKKDYPNIK--ELFLVHRLDKYTSGILIL 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+      +   +F+ R I K+Y ++V G+PKN K  I   + K +      + V    +
Sbjct: 66  AKDNNTKTYFENAFKNREINKVYHAIVEGVPKNIKGTIDIQIAKDTKNPNKRIAV----K 121

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           KG   AI+H+KV+  F +    LE++P TGRTHQ+RVH  ++G PI+GD  Y  N K
Sbjct: 122 KGGEIAITHYKVLKKF-KLHSLLELKPITGRTHQIRVHLSYLGNPIIGDKIYSKNAK 177


>gi|85057870|ref|YP_456786.1| ribosomal large subunit pseudouridine synthase D [Aster yellows
           witches'-broom phytoplasma AYWB]
 gi|84789975|gb|ABC65707.1| ribosomal large subunit pseudouridine synthase D [Aster yellows
           witches'-broom phytoplasma AYWB]
          Length = 306

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 93/316 (29%), Positives = 154/316 (48%), Gaps = 38/316 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++   E   RLD +   H  ++N    QK++ + QV V+ K  K +  ++   ++ +   
Sbjct: 8   LISASEAFQRLDHFLSAHI-NLNKSQCQKLILAQQVLVNTKSSKKSYLLKPQDLITV--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                 II +      S+NL    + L   ++YED  + V NKPA + V           
Sbjct: 64  ------IIPQTH---ESINLQTPQN-LNLDIIYEDPYLAVINKPANLVVHPSLSFQKTTL 113

Query: 129 IDGFLK-----SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++G L      S +D+  Q+P + HRLD+ T+G+L+VA+T   +  L  +F+ R+I KIY
Sbjct: 114 VNGLLHQFNTLSHIDT--QRPGIVHRLDKNTTGLLIVAKTNDVSDKLQIAFQQRKITKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK-QNEKGANYAISHFKVIDCFAQKFCW 242
           W+L+ G  ++K        + K  IG +  + +K Q       A++HFK +  F+  F  
Sbjct: 172 WALIEGFLEDKG-------IIKLPIGRNNHNRLKMQVMPDGKTAVTHFKTLQRFSH-FSL 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-E 301
           +E    TGRTHQLR H   +  PIVGD  Y +    +  +P+    +LH++ +   HP  
Sbjct: 224 MECNLETGRTHQLRAHFSFLKHPIVGDLLYDS---SHHITPLGQ--FLHSKILKFNHPIT 278

Query: 302 GGRLQITAPLPAHMVK 317
              L + APLP +  K
Sbjct: 279 NQNLILEAPLPTNFEK 294


>gi|312866736|ref|ZP_07726950.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
 gi|311097817|gb|EFQ56047.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
          Length = 296

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 87/289 (30%), Positives = 140/289 (48%), Gaps = 37/289 (12%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV----NLTKHSDFLKSILLYEDSK 107
           R   N +I+ G+V+ +   +    + +KE  I+   V     ++  ++ L   ++YED  
Sbjct: 24  RAVANEQIKEGKVL-VNGTVKKAKYTVKEGDIIQYEVPEVEEVSYEAEDLPLDIVYEDQD 82

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFL--------KSWVDSKGQ-KPRLTHRLDQETSGIL 158
           + V NKP G+ V   +G   H  G L        K      G+ +P + HR+D++TSG+L
Sbjct: 83  VVVVNKPQGMVVHPSAG---HTSGTLVNALLYHVKDLSGINGELRPGIVHRIDKDTSGLL 139

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+   A   L E  + ++  + YW++V G   N +  I      ++ IG       KQ
Sbjct: 140 MVAKNDQAHVALAEELKDKKSLRKYWAIVHGNLPNDRGMI------EAPIGRSEKDRKKQ 193

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-- 274
               KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y    
Sbjct: 194 AVTAKG-KPAVTRFQVLERFGN-YTLVELQLETGRTHQIRVHMAYIGHPVAGDPAYGPKK 251

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             KG          +LHAR +   HP  G  L+ TA +PA   KT + L
Sbjct: 252 TLKGQGQ-------FLHARTLGFTHPRTGETLEFTAEVPAIFEKTLEDL 293


>gi|312869892|ref|ZP_07730031.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
 gi|311094477|gb|EFQ52782.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
          Length = 304

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 96/323 (29%), Positives = 149/323 (46%), Gaps = 35/323 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +D    R+D+   + +   +  +LQK +  G VRV+ + VK   ++  G  V I P    
Sbjct: 10  DDTLTGRIDKVLAHQFNQFSRSHLQKWIVDGNVRVNGQPVKPKYKLAVGDQVVIEPEAPQ 69

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDG 131
              +  E+  LD               ++YED  + V NKP G+ V    G   H  ++ 
Sbjct: 70  KVDLTPEKIPLD---------------IVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNA 114

Query: 132 FL--KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            L         G+ +P + HR+D++TSG+L+VA+   A + L    + +  Q+ Y +LV 
Sbjct: 115 LLYHSPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDLAHRSLAAQLKAKTNQREYVALVH 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQP 247
           G+ K     I       + IG       KQ       +A++HFKV+  F + +  +  + 
Sbjct: 175 GVIKQDAGTI------DAPIGRSKKDRKKQAVVSDGRHAVTHFKVLRRF-RHYTLVSCRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH   +G P+ GD  Y        T P + + YLHAR +   HP  G+ L 
Sbjct: 228 ETGRTHQIRVHMKSIGHPLAGDPLYGP----RKTLPGRGQ-YLHARLLGFKHPRTGKDLV 282

Query: 307 ITAPLPAHMVKTWDSLGFKYDRN 329
            TAPLP +  +  D L  K D N
Sbjct: 283 FTAPLPEYFQQMLDKLK-KTDSN 304


>gi|30021981|ref|NP_833612.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|229129170|ref|ZP_04258143.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-Cer4]
 gi|296504387|ref|YP_003666087.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
 gi|29897537|gb|AAP10813.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|228654407|gb|EEL10272.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-Cer4]
 gi|296325439|gb|ADH08367.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
          Length = 302

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 90/317 (28%), Positives = 149/317 (47%), Gaps = 35/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAAEQKNERIDKFVAGINNEWSRTQVQQWIKDNVVTVNGKAVKGNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          I E + LD         + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITV---------TIPEPEELDI------QPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            + + Y ++V G IP +K    A     K       V     +E G N A++HF+V++ F
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV-----DENGKN-AVTHFQVLERF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  + 
Sbjct: 220 -KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGILG 273

Query: 297 LPHPEGGR-LQITAPLP 312
             HP  G  +Q  AP+P
Sbjct: 274 FDHPRTGEYIQFEAPIP 290


>gi|260833883|ref|XP_002611941.1| hypothetical protein BRAFLDRAFT_126415 [Branchiostoma floridae]
 gi|229297314|gb|EEN67950.1| hypothetical protein BRAFLDRAFT_126415 [Branchiostoma floridae]
          Length = 335

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 86/259 (33%), Positives = 128/259 (49%), Gaps = 46/259 (17%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQ 152
           +  LK  LLY++  I    KP G+ V GG G+   I   L     + K  +  L HRLD+
Sbjct: 64  ASILKKSLLYDEGDIVAIEKPYGVPVHGGPGMGVSIADSLPLLQQALKTDRLYLVHRLDK 123

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-- 210
           ET+G++++A+T   A+ L   FR+R++ K YW L  G+P + +E + +  +K+  +    
Sbjct: 124 ETTGVMLLAKTDDMARQLHSLFRLRKVIKKYWVLTMGVPSH-EEGVVDIPIKELEVTAQG 182

Query: 211 ----------DYVH----VVKQNEKG--ANYAISHFKVIDCFAQKFCWL-EMQPHTGRTH 253
                     +Y      +VK+  K   A  AI++F+V+D      C L E QP TG  H
Sbjct: 183 RPHHRMVCVPEYSEETKLIVKKKRKSSDAQIAITNFRVLDSCGS--CALVECQPETGVKH 240

Query: 254 QLRVH-ALHMGCPIVGDHKYCANFKGNFTSP------------IQN------KLYLHARY 294
           Q+R H +  +GCPI+GDHKY  + K    +P            IQ        ++LHAR 
Sbjct: 241 QIRSHLSYGLGCPILGDHKYSHHSK---LAPQRLPTGMLERFGIQQPKARYLPMHLHARQ 297

Query: 295 MDLPHPEGGR-LQITAPLP 312
           + LP    GR L  TA LP
Sbjct: 298 IVLPGFRDGRSLYFTARLP 316


>gi|316931592|ref|YP_004106574.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           DX-1]
 gi|315599306|gb|ADU41841.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           DX-1]
          Length = 334

 Score =  110 bits (274), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 96/350 (27%), Positives = 152/350 (43%), Gaps = 52/350 (14%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQ 60
           S  T V+ V V  DE + RLDR      P ++   L+ ++  G+V +    V+       
Sbjct: 4   SAQTLVE-VTVAGDEGSARLDRVLAARCPELSRSRLKALILDGRVAIAGNPVRDPAYHAS 62

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ + I     A      E   LD               + +ED+ I V NKP G+ V 
Sbjct: 63  PGETITIDVPPPAPAEPAGEAIALD---------------IAHEDADIIVLNKPRGLVVH 107

Query: 121 GGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
             +G  +     + + +   G         ++P + HRLD++T+G++VVA+   A Q L+
Sbjct: 108 PAAG--HETGTLVNALIAHCGASLSGIGGVRRPGIVHRLDKDTTGLMVVAKNDRAHQSLS 165

Query: 172 ESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             F    R   +++ Y++ VWG+P      I   + +  H        V+Q   G   AI
Sbjct: 166 AQFADHGRTGELRRGYFAFVWGVPGRTYGTIDAPIDRHPH--AREKMAVRQ---GGREAI 220

Query: 228 SHFKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--- 279
           +H++V++ FA K        +  Q  TGRTHQ+RVH  H+G P++GD  Y  +FK     
Sbjct: 221 THWEVLESFAGKDGKPVASLIACQLETGRTHQIRVHLAHIGHPLLGDDVYGPHFKTKANQ 280

Query: 280 ------FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                        +  LHA  + L HP  G  L   +PLPA +     +L
Sbjct: 281 LAPAARAALAQLGRQALHAYLLTLEHPSTGEILTWESPLPADLAHLQAAL 330


>gi|312622398|ref|YP_004024011.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202865|gb|ADQ46192.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 299

 Score =  110 bits (274), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 93/315 (29%), Positives = 162/315 (51%), Gaps = 41/315 (13%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           RLDR+         +FV  QKI+  G V V++ +V K   +++SG ++++         +
Sbjct: 9   RLDRYLSEALSKTRSFV--QKIIEEGNVWVNQIQVLKPAYKVKSGDIIKV---------V 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH 128
           I E K       L+  +  +   +LYED  + V NKP G+ V  G+G         + + 
Sbjct: 58  IPEPK------QLSLVAQEIDIEVLYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHK 111

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             G L S   +   +P + HRLD++TSG+LVVA+T  A   L+E+ +  +I++IY+++  
Sbjct: 112 FSGRLSSI--NGVIRPGIVHRLDKDTSGLLVVAKTDEAHIKLSEALKSHQIKRIYYAICE 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+ K     I N  + +  +    + VV   ++    A+++F+V++ F  K+ +++++  
Sbjct: 170 GVLKEDSGVI-NAPIGRHPVNRLKMAVVPNGKE----AVTYFEVLERF-DKYTFIKLRLK 223

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  ++G P++GD  Y    K  F    Q    LHA  ++  HP     L  
Sbjct: 224 TGRTHQIRVHISYIGYPLLGDGIY-GRAKNEFGVEGQ---VLHAGEIEFVHPITSEVLHF 279

Query: 308 TAPLPAHMVKTWDSL 322
           +A LP + +K  + L
Sbjct: 280 SAELPEYFLKILNIL 294


>gi|154331307|ref|XP_001561472.1| pseudouridylate synthase-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
 gi|134058789|emb|CAM36459.1| pseudouridylate synthase-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 413

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 92/355 (25%), Positives = 167/355 (47%), Gaps = 34/355 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV----RVDKKR-VKFNNRIQS 61
           +QY VV  D    R+D +   H+P  ++  ++++++ G +    R  K+R  +  +R++ 
Sbjct: 55  LQYHVVTQDWFGQRVDDFITQHHPEWDYETVKRLVQQGHIYRYRRNGKRRYTRLTDRLEF 114

Query: 62  GQVVRIPPV------------INALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKI 108
            ++V +P              +   +    +Q+      +L+ K  +  + ++L+++  +
Sbjct: 115 DELVVVPTASFWGRQLAPPSGVELQSLSTSQQRERRQKFHLSAKAREMAQEMVLFKNEHV 174

Query: 109 YVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
            V NKP+G+ +      +A +I   L +W  +  Q P + H LD ETSG +++AR+  A 
Sbjct: 175 VVINKPSGVPIMPTHDPLAMNITDLLPAWRYTNTQMPIVCHNLDAETSGCVLLARSANAH 234

Query: 168 QHLTESFRMRRI-QKIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           + L   F  R +   +YW    G P  N      ++ ++K   GGD +         +  
Sbjct: 235 RMLGRMFVKRVVPNSVYWGFAVGKPPVNFGRIRMHFEIQKGQ-GGDVIVARPAPTANSKV 293

Query: 226 AISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK-----G 278
            I+ F V++  A +F  ++   P T R HQ R+ A H +  P++GD KY           
Sbjct: 294 GIAEF-VVNASALEFGSFISFYPLTTRRHQERIMAAHALRAPLLGDAKYGGESAFPHSLS 352

Query: 279 NFTSPIQN--KLYLHARYMDLPHPEGGR--LQITAPLPAHMVKTWDSLGFKYDRN 329
            F  P +    L+LH R + LP+  G    + +TAPLP HM KT+  LG+  D +
Sbjct: 353 LFWDPARKDVPLHLHHRKIQLPYKNGAGAFVCVTAPLPQHMEKTFKRLGWPVDAD 407


>gi|206971264|ref|ZP_03232215.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
 gi|228954169|ref|ZP_04116197.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar kurstaki str. T03a001]
 gi|229071392|ref|ZP_04204614.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           F65185]
 gi|229081145|ref|ZP_04213655.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock4-2]
 gi|229180168|ref|ZP_04307512.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           172560W]
 gi|229192062|ref|ZP_04319031.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           ATCC 10876]
 gi|206734036|gb|EDZ51207.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
 gi|228591388|gb|EEK49238.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           ATCC 10876]
 gi|228603377|gb|EEK60854.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           172560W]
 gi|228702189|gb|EEL54665.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock4-2]
 gi|228711683|gb|EEL63636.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           F65185]
 gi|228805489|gb|EEM52080.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar kurstaki str. T03a001]
          Length = 302

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 90/317 (28%), Positives = 149/317 (47%), Gaps = 35/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAAEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          I E + LD         + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITV---------TIPEPEELDI------QPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            + + Y ++V G IP +K    A     K       V     +E G N A++HF+V++ F
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV-----DENGKN-AVTHFQVLERF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  + 
Sbjct: 220 -KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGILG 273

Query: 297 LPHPEGGR-LQITAPLP 312
             HP  G  +Q  AP+P
Sbjct: 274 FDHPRTGEYIQFEAPIP 290


>gi|309389006|gb|ADO76886.1| ribosomal large subunit pseudouridine synthase D [Halanaerobium
           praevalens DSM 2228]
          Length = 303

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 87/301 (28%), Positives = 157/301 (52%), Gaps = 40/301 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  ++  R+D++   ++  ++   +QK+++  +++V+ + +  + +I +   + +  
Sbjct: 6   LTVKKKDQGQRIDKYLAKYFKDLSRSFIQKLIKEKEIKVNNRVIDKSYKIINNDFIELK- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                   +KEQ   +S V        +K  ++YED  I V NK A   V    G  Y+ 
Sbjct: 65  --------LKEQ---ESKVKAVA----MKLDIVYEDQDIIVINKDADRVVHPAPG-HYND 108

Query: 129 --IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             ++G L + VD+       ++P + HRLD++TSG+L+VA+   + + L + F+ R + K
Sbjct: 109 TIVNGLL-ACVDNLSAINGIKRPGIVHRLDKDTSGLLIVAKNDKSHKSLAKQFKARTVDK 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQK 239
            Y++L+ G    KK  I      ++ IG D  H  K    ++ +  AIS FK+I+ F   
Sbjct: 168 YYFALIEGNLAYKKGKI------EAPIGRDPNHRKKMAVRKRHSKNAISRFKIIEEFNH- 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +E++  TGRTHQ+RVH  ++G PIVGD KY +  K N     Q    LHA+ + + H
Sbjct: 221 YTLVEVKIETGRTHQIRVHFSYLGHPIVGDQKYGS--KNNLNVKRQ---LLHAKKLFIKH 275

Query: 300 P 300
           P
Sbjct: 276 P 276


>gi|170288274|ref|YP_001738512.1| RluA family pseudouridine synthase [Thermotoga sp. RQ2]
 gi|170175777|gb|ACB08829.1| pseudouridine synthase, RluA family [Thermotoga sp. RQ2]
          Length = 311

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 91/309 (29%), Positives = 155/309 (50%), Gaps = 29/309 (9%)

Query: 12  VENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VE  EE  RLD++ K   P  I+   +QK ++ G+V+V+ +  K + +++ G++V +   
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSLIQKAIKEGKVKVNGQIKKPSYKLKEGEIVEV--- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
              L    +E  +    + L          +LYED  I V +KP  + V           
Sbjct: 63  --DLPEKPQEATVQPEEIELK---------VLYEDRDIVVIDKPGDMIVHPVPSKLSGTL 111

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D +G     +P + HRLD+ETSG++VVA+   A Q L++ F+ R+++K Y 
Sbjct: 112 VNALLHHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYI 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  K+  E + +  L +  +    + VV+  ++    AI+ ++V+  F      + 
Sbjct: 172 LLVKGRVKS-DEGVIDLPLARHPVLRIKMAVVETGKE----AITEYRVLKRFDDVATLVL 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P TGRTHQ+RVH   +G PI+GD  Y    K +    I+ ++ LHA  +   HP  G+
Sbjct: 227 AFPKTGRTHQIRVHMKSLGHPIMGDKIY-GKPKEDEIFGIKRQM-LHALKLGFFHPRTGK 284

Query: 305 -LQITAPLP 312
            ++  +PLP
Sbjct: 285 WMEFVSPLP 293


>gi|228922645|ref|ZP_04085945.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar huazhongensis BGSC 4BD1]
 gi|228837074|gb|EEM82415.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar huazhongensis BGSC 4BD1]
          Length = 302

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 90/317 (28%), Positives = 149/317 (47%), Gaps = 35/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAAEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          I E + LD         + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITV---------TIPEPEELDI------QPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGIMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            + + Y ++V G IP +K    A     K       V     +E G N A++HF+V++ F
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV-----DENGKN-AVTHFQVLERF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  + 
Sbjct: 220 -KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGILG 273

Query: 297 LPHPEGGR-LQITAPLP 312
             HP  G  +Q  AP+P
Sbjct: 274 FDHPRTGEYIQFEAPIP 290


>gi|322418237|ref|YP_004197460.1| RluA family pseudouridine synthase [Geobacter sp. M18]
 gi|320124624|gb|ADW12184.1| pseudouridine synthase, RluA family [Geobacter sp. M18]
          Length = 319

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 87/319 (27%), Positives = 146/319 (45%), Gaps = 39/319 (12%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D +  RLD +     P +      +++ +G   V+ ++ K   R++ G+VV +       
Sbjct: 11  DADPERLDSFISRSVPELTRSAALRLIETGFATVNGQKQKPALRLKGGEVVTV------- 63

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGF 132
                   I+          + +   +LYED+ + V NK AG+ V  G+G A    ++  
Sbjct: 64  --------IVPPPTPAEPQPEEIPLEILYEDADVVVVNKGAGMVVHPGAGNAEGTLVNAL 115

Query: 133 LKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L    D  G     +P + HR+D++TSG LV+A++  A   L E F++  I++IY +LV+
Sbjct: 116 LAHCKDLSGIGGELRPGIVHRIDKDTSGTLVIAKSDRAHNGLAEQFKVHSIKRIYLALVY 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQ 246
           G PK ++  I      +S IG   V   K + K      AI+H++V +        + ++
Sbjct: 176 GSPKEERGHI------ESVIGRHPVERKKMSGKARHGKNAITHWRV-EARYPGITLVRLK 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLY-------LHARYMDLP 298
             TGRTHQ+RVH    G P++ D  Y    +      P+  ++        LHA+ +   
Sbjct: 229 LETGRTHQIRVHLSEAGHPLLADEVYGGGSRLAQLKDPVLKQMIKAMGRQALHAKTLGFL 288

Query: 299 HPEGGR-LQITAPLPAHMV 316
           HP  G  L+  A LP  M 
Sbjct: 289 HPVTGEYLEFDAELPPDMA 307


>gi|298292656|ref|YP_003694595.1| pseudouridine synthase [Starkeya novella DSM 506]
 gi|296929167|gb|ADH89976.1| pseudouridine synthase, RluA family [Starkeya novella DSM 506]
          Length = 348

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 85/336 (25%), Positives = 150/336 (44%), Gaps = 51/336 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E +RLDR   NH P ++   LQ ++  G+V R  +     + ++  G+V  +       
Sbjct: 25  DEGLRLDRVLANHLPELSRTRLQALIAEGRVLRAGRPVAGGSAKVAPGEVFTVEVPPPEP 84

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                +   LD               +++ED  + V +KPAG+ V    G         +
Sbjct: 85  AEPEPQDIPLD---------------IVFEDDDLIVIDKPAGLVVHPAPGNPDGTLVNAL 129

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQK 181
            +H    L      +  +P + HRLD++TSG++VVA+   A Q L   F    R   +++
Sbjct: 130 LFHCGASLSGIGGVR--RPGIVHRLDKDTSGLMVVAKNDRAHQKLAAQFADHGRTGPLER 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-- 239
            Y + VWG+P+     + +  L +  +  + +  V+ N +   +AI+H++ ++ +     
Sbjct: 188 AYLAFVWGVPELPSGTV-DAPLARHPVSRERI-AVRANGR---FAITHWQRVEAYEDTQG 242

Query: 240 ---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKLY----- 289
                 +E Q  TGRTHQ+RVH  H+G P++GD  Y      K N  S     +      
Sbjct: 243 RPVASLVECQLETGRTHQIRVHMAHIGHPLLGDAVYGGGQRTKANRLSEEARTMLETLGR 302

Query: 290 --LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             LHA  +   HP  G  +   + LPA +++  ++L
Sbjct: 303 QALHAARLGFEHPSTGEFMSFESELPADLMRLQEAL 338


>gi|184155639|ref|YP_001843979.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
 gi|183226983|dbj|BAG27499.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
          Length = 304

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 85/305 (27%), Positives = 143/305 (46%), Gaps = 32/305 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            D    R+D+   +H+P  +   L++ +  G V V+ + VK   ++Q+G  V I P    
Sbjct: 11  TDGMTGRIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAGDRVVIEP---- 66

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDG 131
                      ++ V +    + +   ++YED  + V NKP G+ V    G   H  ++ 
Sbjct: 67  -----------ETPVEIDLEPENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNA 115

Query: 132 FL--KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +         G+ +P + HR+D++TSG+L+VA+T  A + LT   + +   + Y +LV 
Sbjct: 116 LMYHAPLSSINGELRPGIVHRIDKDTSGLLMVAKTDRAHRSLTAQLKEKSNLREYVALVH 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+ K  +  I   L +          VV     G  +A++HF+V+  + Q +  +  +  
Sbjct: 176 GVIKENEGTIDAPLARSPKDRKKQAVVV-----GGRHAVTHFRVLKRY-QHYTLVACRLE 229

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
           TGRTHQ+RVH  ++  P+ GD  Y        T P   + YLHAR +   HP  G  +  
Sbjct: 230 TGRTHQIRVHMKYINHPLAGDPLYGP----RKTLPGHGQ-YLHARLLGFEHPVTGEEMVF 284

Query: 308 TAPLP 312
           TAP P
Sbjct: 285 TAPWP 289


>gi|148654435|ref|YP_001274640.1| RluA family pseudouridine synthase [Roseiflexus sp. RS-1]
 gi|148566545|gb|ABQ88690.1| ribosomal large subunit pseudouridine synthase D [Roseiflexus sp.
           RS-1]
          Length = 316

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 88/320 (27%), Positives = 155/320 (48%), Gaps = 39/320 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++VVE   E  RLDR+  +H P ++    Q+++ + QV ++ ++ + +  + +G  V 
Sbjct: 5   VLHLVVEAANEGDRLDRYVADHVPDLSRTYAQRLIEAAQVLLNNRQARPSTPVHAGDTVT 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +        H+   Q      V L   ++ L   ++YED  + V +KPA + V    G  
Sbjct: 65  V--------HLPAPQP-----VGLV--AEPLPLQIVYEDRDVVVIDKPASMVVHPAPG-- 107

Query: 127 YHIDGFLKSWVDSK--------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            H  G L + + ++          +P + HRLD++TSG+LV AR   A + L    + R 
Sbjct: 108 -HDRGTLVNALIARYPEMAINGDMRPGIVHRLDRDTSGLLVAARNERALRSLQAQQQART 166

Query: 179 IQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           + KIY ++V G +P  + E + +  + +       + VV     G   A +H++V++   
Sbjct: 167 MLKIYLAVVEGRMP--ELEGVIDAPIARHPTDRVRMAVV----AGGRPARTHWRVLEDLG 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGNFTSPIQNKLYLHARYMD 296
           + +  +E +  TGRTHQ+RVH      PI+GD  Y     +  F      + +LHA  + 
Sbjct: 221 E-YTLIEARLETGRTHQIRVHCASRNRPILGDPLYGPKRPRATFG---LTRQFLHAHRLG 276

Query: 297 LPHPEGGR-LQITAPLPAHM 315
              P GG  ++ T+PLPA +
Sbjct: 277 FKLPSGGEWVEFTSPLPADL 296


>gi|228960110|ref|ZP_04121774.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar pakistani str. T13001]
 gi|229047577|ref|ZP_04193167.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH676]
 gi|229111362|ref|ZP_04240915.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock1-15]
 gi|228672138|gb|EEL27429.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock1-15]
 gi|228723824|gb|EEL75179.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH676]
 gi|228799626|gb|EEM46579.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar pakistani str. T13001]
          Length = 302

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 90/317 (28%), Positives = 149/317 (47%), Gaps = 35/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAAEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          I E + LD         + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITV---------TIPEPEELDI------QPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            + + Y ++V G IP +K    A     K       V     +E G N A++HF+V++ F
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV-----DENGKN-AVTHFQVLERF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  + 
Sbjct: 220 -KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGILG 273

Query: 297 LPHPEGGR-LQITAPLP 312
             HP  G  +Q  AP+P
Sbjct: 274 FDHPRTGEYIQFEAPIP 290


>gi|302345911|ref|YP_003814264.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
 gi|302150113|gb|ADK96375.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
          Length = 365

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 91/340 (26%), Positives = 151/340 (44%), Gaps = 64/340 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V+V+  +E  R+D++      H +   +QK   +G + V+   VK N +++   V+ +  
Sbjct: 36  VIVDKGQEPARIDKFLFERMQHSSRNRIQKAADAGYIHVNNAPVKSNYKVRPEDVITL-- 93

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I    + L          ++YED  + V NKPAG+ V  G+G     
Sbjct: 94  ---MLDRPKHDNTIEAEDIPLD---------VVYEDDVLMVVNKPAGLVVHPGAGNFHGT 141

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+        D    +  L HR+D++TSG+LV+A+T  A   L + F  +   
Sbjct: 142 LINAIAWHLKDM--PSFDPNDPEVGLVHRIDKDTSGLLVIAKTPDAKTALGKQFFNKTTH 199

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------VVKQNEKGANYAISHFK 231
           + Y ++VWG          N    +  I G+            V   + +    A++H++
Sbjct: 200 RSYNAIVWG----------NMTEDEGRIEGNIARDPKDRLRMTVFPPDSEVGKPAVTHYR 249

Query: 232 VIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ- 285
           VI+ F       C LE    TGRTHQ+R H  H+G P+ GD +Y      +G  +S  + 
Sbjct: 250 VIERFGYTTLIECILE----TGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSTYKA 305

Query: 286 ---------NKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                    N+  LHAR +   HP  G ++  T+ LPA +
Sbjct: 306 FIRNCLALCNRQALHARTLGFVHPVTGEQMDFTSELPADL 345


>gi|291519437|emb|CBK74658.1| ribosomal large subunit pseudouridine synthase D [Butyrivibrio
           fibrisolvens 16/4]
          Length = 305

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 89/333 (26%), Positives = 161/333 (48%), Gaps = 47/333 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK--FNNRIQSGQVVRI 67
           ++ E  +E +R+D++     P  +    QK + +G V V+ K++K  +  ++    +V I
Sbjct: 7   IIEEPSDEGIRIDKYLAAALPEKSRSYYQKAIDNGFVLVNGKQIKSKYQTKLGDEIIVSI 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
            PV        KE  IL   + +          +LYEDS + V NKP G+ V    G   
Sbjct: 67  EPV--------KEIDILPEDIPID---------ILYEDSDVIVVNKPKGMVVHPAPGHYS 109

Query: 125 ------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 + YH    L S ++ +  +P + HR+D  T+G L+V +   A   +    ++  
Sbjct: 110 GTLVNALMYHCKDSL-SGINGE-IRPGIVHRIDMNTTGSLLVCKNDKAHNDIAAQIKVHS 167

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + +IY  +V G  K ++  I N  + ++      + VV    +    AI+H+ V++ + +
Sbjct: 168 VNRIYKGIVVGNFKEEEGTI-NANIGRNPKDRKKMAVVSDGRE----AITHYTVLEQY-K 221

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F +++ +  TGRTHQ+RVH  H+G P++GD  Y    KG     ++ +  LHA+ +   
Sbjct: 222 GFSYVQFKLETGRTHQIRVHMAHIGHPLLGDDVYGKPVKG-----LEGQT-LHAQTLGFV 275

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
            P  G  +++ APLPA+    ++ L  KY + +
Sbjct: 276 QPTTGEYVEVNAPLPAY----FEELLTKYRKTI 304


>gi|300725911|ref|ZP_07059373.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella bryantii B14]
 gi|299776762|gb|EFI73310.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella bryantii B14]
          Length = 224

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 114/232 (49%), Gaps = 16/232 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + +K +G  VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHIIIVSKKSGEIVQGDKTGDEPLSEIVKKYIKEKYHKPGNVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L + FR   + K YW++   +PKN +  + NW+ +       YV+ 
Sbjct: 63  GLVVFAKTSKALSRLNQMFRDSNVHKTYWAITKNVPKNPEGTLINWITRNEKQNKSYVY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  A+  +K+I      +  LE+   TGR HQ+R    HMGCPI GD KY   
Sbjct: 122 -DKEVPHSKKAVLSYKLIG-HTDNYSLLEIHLMTGRHHQIRCQLAHMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
             G   S     + L +R+++  HP     ++ TAPLP   +  W S+  K+
Sbjct: 177 --GAPRSNPDGSISLLSRFVEFVHPVSKETIKATAPLPDDNL--WQSIAPKH 224


>gi|298375940|ref|ZP_06985896.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_19]
 gi|298266977|gb|EFI08634.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_19]
          Length = 545

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 80/246 (32%), Positives = 130/246 (52%), Gaps = 26/246 (10%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L+H+++  ++ ++ +    H +  K  +LYED  + V NKP G+    G G A  +   L
Sbjct: 315 LHHMLQGLRVDENPLLADSHRE-TKLDILYEDDYLLVINKPEGMLSVPGKGDADSVYQRL 373

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPK 192
            S +  +   P + HRLD  TSG+L+ A+T+ A Q+L   F+ R IQK Y +L+ G +P+
Sbjct: 374 -SILYPEATGPIIVHRLDMATSGLLLAAKTKEAHQNLQAQFKNRTIQKRYIALLEGEVPQ 432

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           ++ E        +  +  D +   +Q  +E+    A++H++V++  + K   +   P TG
Sbjct: 433 DEGEI-------RLPLCPDPLDRPRQIVSEEFGKPALTHYRVLERTSGK-TLIAFYPQTG 484

Query: 251 RTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
           RTHQLRVHA H   + CPI+GD  Y              +LYLHA Y+   HP    R++
Sbjct: 485 RTHQLRVHAAHPQGLHCPILGDELYGRK---------AERLYLHAEYLAFTHPITSERIE 535

Query: 307 ITAPLP 312
           I A +P
Sbjct: 536 IRAKIP 541


>gi|196228386|ref|ZP_03127253.1| pseudouridine synthase, RluA family [Chthoniobacter flavus
           Ellin428]
 gi|196227789|gb|EDY22292.1| pseudouridine synthase, RluA family [Chthoniobacter flavus
           Ellin428]
          Length = 302

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 92/321 (28%), Positives = 145/321 (45%), Gaps = 47/321 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---P 68
           V+      RLD++  +    ++   +Q +++ G V ++    K + R+++G  V +   P
Sbjct: 8   VDAAAAGPRLDQFLASAAAGLSRARIQDLIKEGHVTLNGGVAKASARLRAGDAVTLHEPP 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
           PV       + E+  LD               +L+ED  + V NKPAG+ V   +G    
Sbjct: 68  PVPT---ETVAEEIALD---------------VLFEDDDLIVINKPAGLVVHPAAGNWSG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L       G    Q+P + HRLD++TSG LVVA+  AA Q L + F  R + KI
Sbjct: 110 TVVNALLHHCQTLSGIGGEQRPGIVHRLDKDTSGCLVVAKNDAAHQSLAKQFAGREVTKI 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVH----VVKQNEKGANYAISHFKVIDCFAQ 238
           Y +L  G    K   I      ++ IG   V      V   +KG      +  +++    
Sbjct: 170 YLALAAGKWARKSGVI------EAPIGRHPVQRKKMTVLPADKGRAAKTGYRVLLELPVG 223

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E   HTGRTHQ+RVH  H+G PI+GD  Y    +G+F      +  LHA  +   
Sbjct: 224 TL--VECTLHTGRTHQIRVHLKHLGHPILGDEVY--GRRGDFA-----RQMLHAWRLGFV 274

Query: 299 HPEGGR-LQITAPLPAHMVKT 318
           HP  G+ L   +P+P   V+ 
Sbjct: 275 HPGTGKHLNFESPIPPDFVEA 295


>gi|327312694|ref|YP_004328131.1| RluA family pseudouridine synthase [Prevotella denticola F0289]
 gi|326946223|gb|AEA22108.1| pseudouridine synthase, RluA family [Prevotella denticola F0289]
          Length = 361

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 94/347 (27%), Positives = 154/347 (44%), Gaps = 67/347 (19%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +E +R+D++      H +   +QK   +G + V+   VK + +++   V+ +  
Sbjct: 33  VNVDKGQEPVRIDKFLYERMQHSSRNRIQKAADAGFIHVNGTAVKSSYKVRPEDVITL-- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I    + L          ++YED  + V NKPAG+ V  G+G     
Sbjct: 91  ---MLDRPKHDNTIEAEDIPLD---------IVYEDDVLMVINKPAGLVVHPGAGNFHGT 138

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H+        D    +  L HR+D++TSG+LVVA+T  A   L   F  +   
Sbjct: 139 LINAVAWHLKDM--PAFDPNDPEVGLVHRIDKDTSGLLVVAKTPDAKTDLGRQFFNKTTH 196

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------VVKQNEKGANYAISHFK 231
           + Y +LVWG          N+  ++  I G+            V     +    A++H++
Sbjct: 197 RSYNALVWG----------NFTEEEGRIEGNIARDPRDRLRMAVFPPGSETGKPAVTHYR 246

Query: 232 VIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS---- 282
           VI+ F       C LE    TGRTHQ+R H  H+G P+ GD +Y      +G  +S    
Sbjct: 247 VIERFGYTTLIECILE----TGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSTYKA 302

Query: 283 ------PIQNKLYLHARYMDLPHPEGGR-LQITAPLP---AHMVKTW 319
                  I N+  LHAR +   HP  GR +  T+ LP   A +++ W
Sbjct: 303 FIRNCLAICNRQALHARTLGFVHPVTGRQMDFTSGLPDDLAALIEKW 349


>gi|113475517|ref|YP_721578.1| ribosomal large subunit pseudouridine synthase D [Trichodesmium
           erythraeum IMS101]
 gi|110166565|gb|ABG51105.1| ribosomal large subunit pseudouridine synthase D [Trichodesmium
           erythraeum IMS101]
          Length = 316

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 88/307 (28%), Positives = 144/307 (46%), Gaps = 33/307 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD W       ++  ++QK++  G V+V+ +       I              ++
Sbjct: 16  EITQRLDIWLSQQMLELSRSHIQKLISQGNVKVNDQLCTSKKAI--------------VH 61

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
              K   ++   + L   ++ +   +LYED  + + NKPAG+ V    G   H +G L +
Sbjct: 62  QGDKIILVIPPPIPLAIEANDIPLDILYEDDALLIINKPAGLVVHPAPG---HSEGTLVN 118

Query: 136 WV----DSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            +    DS       Q+P + HRLD++T+G ++VA+T  A QHL    + +  ++ Y  +
Sbjct: 119 ALLAHCDSLAGIGGVQRPGIVHRLDKDTTGAIMVAKTDHAYQHLQAQLQAKTARREYLGV 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G PK     I N  + +  +    +  V   E+G   A++H++V +     F  +  +
Sbjct: 179 VYGSPKTDSGII-NLPIGRHRVDRKKM-AVTPVERGGKIAVTHWEVKERLG-NFSMILFR 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL- 305
             TGRTHQ+RVH+  +G PIVGD  Y    KG           LHA  ++L HP  G L 
Sbjct: 236 LETGRTHQIRVHSAQVGYPIVGDTIYG---KGRSVGVNLTGQVLHAWRLELQHPVSGELV 292

Query: 306 QITAPLP 312
           +  APLP
Sbjct: 293 EAIAPLP 299


>gi|325860234|ref|ZP_08173359.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
 gi|325482321|gb|EGC85329.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
          Length = 361

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 92/344 (26%), Positives = 153/344 (44%), Gaps = 61/344 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +E +R+D++      H +   +QK   +G + V+   VK + +++   V+ +  
Sbjct: 33  VNVDKGQEPVRIDKFLYERMQHSSRNRIQKAADAGFIHVNGAAVKSSYKVRPEDVITL-- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I    + L          ++YED  + V NKPAG+ V  G+G     
Sbjct: 91  ---MLDRPKHDNTIEAEDIPLD---------IVYEDDVLMVINKPAGLVVHPGAGNFHGT 138

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H+        D    +  L HR+D++TSG+LVVA+T  A   L   F  +   
Sbjct: 139 LINAVAWHLKDM--PAFDPNDPEVGLVHRIDKDTSGLLVVAKTPDAKTDLGRQFFNKTTH 196

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------VVKQNEKGANYAISHFK 231
           + Y +LVWG          N+  ++  I G+            V     +    A++H++
Sbjct: 197 RSYNALVWG----------NFTEEEGRIEGNIARDPRDRLRMAVFPPGSETGKPAVTHYR 246

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS------- 282
           VI+ F      +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S       
Sbjct: 247 VIERFGYT-TLIECVLETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSTYKAFIR 305

Query: 283 ---PIQNKLYLHARYMDLPHPEGGR-LQITAPLP---AHMVKTW 319
               I N+  LHAR +   HP  GR +  T+ LP   A +++ W
Sbjct: 306 NCLAICNRQALHARTLGFVHPVTGRQMDFTSGLPDDLAALIEKW 349


>gi|115372352|ref|ZP_01459661.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|310819495|ref|YP_003951853.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115370565|gb|EAU69491.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|309392567|gb|ADO70026.1| Pseudouridine synthase, RluA family [Stigmatella aurantiaca
           DW4/3-1]
          Length = 324

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 88/284 (30%), Positives = 137/284 (48%), Gaps = 34/284 (11%)

Query: 39  KILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +++ +G V V  +R +    R+++GQVV +         +++E     S +        L
Sbjct: 34  QLVEAGAVYVGGRRCREGGLRLRAGQVVAV---------VLEEGG--RSPLEALAPPPAL 82

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQETSG 156
              +L+ED  +   +KP GI+ Q   G A    G L   V  + GQ   L HRLD+ETSG
Sbjct: 83  G--VLFEDEALIAVDKPVGITAQPTEGRA---GGSLVDLVSERLGQLAGLVHRLDRETSG 137

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKECIANWLLKKSHIGGDYVHV 215
           + V  +T  A   L   FR  R +K Y +    G+P +    +   L +     G +   
Sbjct: 138 VTVFGKTPQATTALAAEFREGRARKRYVAATGPGLPASGT--VDLPLSRDPARPGRW--- 192

Query: 216 VKQNEKGANY--AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY- 272
             +  + AN   A++ F+ +   A  FC +E+ P TGRTHQLR H   +G PI+GD +Y 
Sbjct: 193 --RASRAANGVPALTDFRTLYSGAD-FCLVELLPQTGRTHQLRAHLTALGAPILGDSRYG 249

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            A   G  ++    +  LHA+ ++L HP  G  L+I APLP  +
Sbjct: 250 GAATAGGLSA---GRCLLHAQGLELAHPLTGAALRIEAPLPGDL 290


>gi|121607091|ref|YP_994898.1| RluA family pseudouridine synthase [Verminephrobacter eiseniae
           EF01-2]
 gi|121551731|gb|ABM55880.1| ribosomal large subunit pseudouridine synthase D [Verminephrobacter
           eiseniae EF01-2]
          Length = 344

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 92/322 (28%), Positives = 146/322 (45%), Gaps = 43/322 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           R+DR      P  +   LQ++L  G V ++ + V K  +R+ +G  V     +  +   +
Sbjct: 50  RIDRALVELVPEFSRSYLQQLLAQGGVSLNGRPVRKAASRVNAGDRV-----VLEMRPTV 104

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
           + Q      +++          ++YED+ + V NKPAG+ V    G   A  ++G L   
Sbjct: 105 QSQAFRPQPMDID---------VVYEDAHLLVLNKPAGLVVHPAPGHWSATLLNGLLARD 155

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV---WGIP 191
            ++    PR  + HRLD++TSG++VVAR RA    L      R++Q+ Y +L    W  P
Sbjct: 156 ANAL-LLPRAGIVHRLDKDTSGLMVVARDRATMDALVAQIARRQVQRQYLALAHGAWSGP 214

Query: 192 KNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           +++          ++ IG D      + VV         A +    +D   Q  CWL+ +
Sbjct: 215 RSRS--------VQAPIGRDPRNRLRMAVVDLARHAGKCARTDVLCLDATPQG-CWLQCR 265

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
            HTGRTHQ+RVH   +  P+VGD  Y     G        +  LHA  +   HP  G+ L
Sbjct: 266 LHTGRTHQIRVHMASLQHPLVGDGLYGGAPLGAL-----QRQALHAERLAFVHPATGQAL 320

Query: 306 QITAPLPAHMVKTWDSLGFKYD 327
           Q  A +P  M +   S G  Y+
Sbjct: 321 QFHAEVPQDMQQALSSWGLGYN 342


>gi|291543962|emb|CBL17071.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus sp.
           18P13]
          Length = 304

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 90/327 (27%), Positives = 146/327 (44%), Gaps = 51/327 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRI 67
           V++  D   MRLD+W     P ++   +Q ++  G V  + K    N +++ G   +V+I
Sbjct: 4   VMLTADGSGMRLDKWLTEQLPELSRSGVQHLIEQGAVLCNGKPAAKNLKLREGDGLLVQI 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
           P                D +         L   ++YED  + V NKP G+ V   +G   
Sbjct: 64  P----------------DPAPLEDVQPQNLPLEIVYEDEALLVVNKPKGMVVHPAAGHPD 107

Query: 125 ------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 + YH  G L +   +   +P + HR+D+ TSG+L+VA+T  A QHL E  +   
Sbjct: 108 GTLVNALLYHCQGRLSTI--NGVIRPGIVHRIDKNTSGLLMVAKTDFAHQHLAEQIKGHS 165

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCF 236
             + Y ++  G  +     +       + IG       K    EK A +A++H+ V+  F
Sbjct: 166 FTREYEAIACGRFREPSGTV------DAPIGRSTADRQKMCVTEKNARHAVTHYAVLTQF 219

Query: 237 AQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           A+     C LE    TGRTHQ+RVH  ++G PI GD  Y     G     ++ +  LHA+
Sbjct: 220 AKHAHIRCRLE----TGRTHQIRVHMRYIGHPIYGDDVY-----GTAVPGLEGQC-LHAK 269

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTW 319
            +   HP  G  ++  + LP + V+  
Sbjct: 270 KIGFVHPVSGAYMEFDSALPDYFVQAL 296


>gi|322389731|ref|ZP_08063278.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 903]
 gi|321143570|gb|EFX39001.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 903]
          Length = 296

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/289 (29%), Positives = 140/289 (48%), Gaps = 37/289 (12%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV----NLTKHSDFLKSILLYEDSK 107
           R   N +I+ G+V+ +   +    + +KE  I+   V     ++  ++ L   ++YED  
Sbjct: 24  RAVANEQIKEGKVL-VNGTVKKAKYTVKEGDIIQYEVPEVEEVSYEAEDLPLDIVYEDQD 82

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFL--------KSWVDSKGQ-KPRLTHRLDQETSGIL 158
           + V NKP G+ V   +G   H  G L        K      G+ +P + HR+D++TSG+L
Sbjct: 83  VVVVNKPQGMVVHPSAG---HTSGTLVNALLYHVKDLSGINGELRPGIVHRIDKDTSGLL 139

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+   A   L E  + ++  + YW++V G   N +  I      ++ IG       KQ
Sbjct: 140 MIAKNDQAHVALAEELKDKKSLRKYWAIVHGNLPNDRGMI------EAPIGRSEKDRKKQ 193

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-- 274
               KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y    
Sbjct: 194 AVTAKG-KPAVTRFQVLERFGN-YTLVELQLETGRTHQIRVHMAYIGHPVAGDPAYGPKK 251

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             KG          +LHAR +   HP  G  L+ TA +PA   KT + L
Sbjct: 252 TLKGQGQ-------FLHARTLGFTHPRTGETLEFTAEVPAIFEKTLEDL 293


>gi|332974183|gb|EGK11117.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter sp.
           1501(2011)]
          Length = 456

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 89/329 (27%), Positives = 150/329 (45%), Gaps = 35/329 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L    +Y V  +D+   R+D+     +   +   LQ+ L+SG + V+ +  K   R++ G
Sbjct: 142 LEVEAEYTVT-DDKAGQRIDKLAAELFADHSRSQLQEWLKSGNLTVNGEVEKPKYRVRVG 200

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +   +        E   LD               ++YED  + V NKP G+ V  G
Sbjct: 201 DKLLLQAKLEQHGTDEPEDIALD---------------IMYEDDSVLVINKPVGMVVHPG 245

Query: 123 SG--IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           +G      ++G L  + + +   PR  L HR+D+ TSG+LV+ +T+AA   L +  R + 
Sbjct: 246 AGNWTGTLVNGLLYHYPN-QAHLPRAGLVHRIDKNTSGLLVIGKTKAAQMELQDQLRDKT 304

Query: 179 IQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           + + Y  +V G +   K++   +  + +       + V    +     A++H   I    
Sbjct: 305 VYRHYQCIVAGDVASLKRQRTIDAPIGRHRTQRTKMTVSSVGKP----AVTHIMNITALN 360

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQN--KLY 289
             +  L++Q  TGRTHQ+RVH  H+G PI+GD  Y       A         IQ   +  
Sbjct: 361 DNYSLLDVQLETGRTHQIRVHLSHIGHPIIGDDVYGNRQQLRAGLTPEQREAIQKFPRQA 420

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           LHA  +   HPE G  +++TAPLP  ++K
Sbjct: 421 LHAYQLGFVHPETGEDIEVTAPLPDDIIK 449


>gi|124516586|gb|EAY58094.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Leptospirillum rubarum]
          Length = 339

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 85/343 (24%), Positives = 159/343 (46%), Gaps = 49/343 (14%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           ++++Y +++V    E+  RLD +   +        +Q++L    V ++      +++++ 
Sbjct: 14  NILSYREFLVPRG-EQPKRLDIYLSKNCLGFTRSRVQRLLEEKLVTINDIYPASSHKVRG 72

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  +R+               ++    + T   + ++  +LYED  + V +KP G+ V  
Sbjct: 73  GDRIRV---------------LIPPPRSQTAQPENIRLEILYEDEDLIVISKPPGLVVHP 117

Query: 122 GSGIAYHIDGFLKSWV----DSKGQKPR-----------------LTHRLDQETSGILVV 160
             G   H  G L + +     S+G + +                 L HRLDQ+TSG++VV
Sbjct: 118 APG---HSSGTLVNGLLFHFQSQGDEQKKGEPEEEEEAERPLRAGLVHRLDQDTSGVMVV 174

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T +    L   F+ R + K Y +LV GI   K+  I   + + +H    +   V+Q+ 
Sbjct: 175 GKTESVVLDLMNQFKDRSVSKKYLALVKGILPKKRGEINAPIGRSTHDRKKF--TVRQDG 232

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K    +++ ++V++ + + +  LE+   TGRTHQ+RVH  ++G P++GD  Y +    N 
Sbjct: 233 KP---SVTRYRVLETYHENYSLLEVTLLTGRTHQIRVHFRYLGFPLLGDAVYGSKGTENK 289

Query: 281 TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
             P Q    LHA  +   HP    +++  APLP   V   + L
Sbjct: 290 NFPRQ---MLHAWKLSFQHPSSNSKMEFEAPLPPDFVSALERL 329


>gi|225619888|ref|YP_002721145.1| pseudouridine synthase [Brachyspira hyodysenteriae WA1]
 gi|225214707|gb|ACN83441.1| pseudouridine synthase [Brachyspira hyodysenteriae WA1]
          Length = 241

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 74/220 (33%), Positives = 117/220 (53%), Gaps = 10/220 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGG--SGIAY--HIDGFLKSWVDSKGQK-PRLTHRLDQETSG 156
           +YED+ I V  KP  I  QG     +++  +I  ++K   + KG     L HRLD+  SG
Sbjct: 18  IYEDNHIIVAVKPPNIPTQGDITGDVSFFENIKDYIKIKYNKKGNVFLGLVHRLDRPVSG 77

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I+V A+T  AA  L+E+ R R+ +K Y+++V GI   K+  + N+L+KK++  G+   VV
Sbjct: 78  IIVFAKTSKAASRLSEAIRDRKFEKTYYAVVNGILLEKEAKLENYLIKKTNKLGNIAQVV 137

Query: 217 KQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +N K A  A   + VI +   +    L ++  TGR HQ+RV   ++G  I GD KY + 
Sbjct: 138 FENTKNAKIAKLKYNVIKEDVIKNLSLLRIELETGRFHQIRVQLANIGHVIYGDRKYGSY 197

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAH 314
            K +        L L A+ +  PHP     + + A LP++
Sbjct: 198 IKYDRNDV---PLALFAKSLRFPHPTRDEEIYVEADLPSY 234


>gi|165923990|ref|ZP_02219822.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           RSA 334]
 gi|165916576|gb|EDR35180.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           RSA 334]
          Length = 323

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 89/333 (26%), Positives = 156/333 (46%), Gaps = 39/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   +++  Q + I  
Sbjct: 11  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEA 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 71  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 115

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            I+  L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y +
Sbjct: 116 LINALLH-YDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           +V G+  + +         ++ +G   +H  +    +    AI+HF++I  + +    + 
Sbjct: 175 IVKGVLISGRTI-------EAPVGRHPIHRTRMAVVEFGRPAITHFRIIKRY-RAHTHIR 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKL------YLHARYMD 296
           +Q  TGRTHQ+RVH  H+  P+ GD  Y ++     + + P+Q  L       LHA  + 
Sbjct: 227 VQLETGRTHQIRVHMAHIHHPVAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHAATLQ 286

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             HP   R +   APLPA M    + L   Y +
Sbjct: 287 FSHPVDQRPMACHAPLPADMAHLLECLEDDYSQ 319


>gi|144897894|emb|CAM74758.1| ribosomal large subunit pseudouridine synthase D [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 327

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 87/325 (26%), Positives = 143/325 (44%), Gaps = 53/325 (16%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQ 63
           T +    V  DE   RLD+W     P ++   ++ ++   +V    + +   + R++ GQ
Sbjct: 7   TLLTPDAVTTDEAGSRLDKWLSARLPDLSRTRIKGLIDDSRVSAAGQTITDASARVKPGQ 66

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
             VV IPP         +    L  +++L+         + YED  + V +KP G+ V  
Sbjct: 67  CFVVAIPPE--------RPADPLPQAMDLS---------VAYEDDDLIVIDKPPGLVVHP 109

Query: 122 GSGIAYH--IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             G   H  ++  L    +S       ++P + HR+D++TSG+LVVA+   A   L E F
Sbjct: 110 APGSPDHTLVNALLAHCGESLSGIGGVKRPGIVHRIDKDTSGLLVVAKNDRAHHGLAEQF 169

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK------GANYAIS 228
            +  +++ Y +LVWG+P          +  +  I G+     +  +K      G   A++
Sbjct: 170 SVHSLERAYRALVWGVP----------MPAQGEIHGNIGRSPQDRKKMAIVSHGGKPALT 219

Query: 229 HFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQN 286
            ++V+  FA     L E +  TGRTHQ+RVH   +G P+VGD  Y           P Q 
Sbjct: 220 RYRVLRSFAGGAVSLVECRLATGRTHQIRVHMTSIGHPLVGDQTYGRARSTKVKHLPDQA 279

Query: 287 KL--------YLHARYMDLPHPEGG 303
           +L         LHA  +   HP  G
Sbjct: 280 RLALLEFPRQALHASVLGFIHPNSG 304


>gi|260434078|ref|ZP_05788049.1| ribosomal large subunit pseudouridine synthase D [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260417906|gb|EEX11165.1| ribosomal large subunit pseudouridine synthase D [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 347

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 93/356 (26%), Positives = 154/356 (43%), Gaps = 62/356 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           +++V+ E      RLD+      P    ++   L +++  G V VD K V     ++  G
Sbjct: 6   IEFVIAEAPPP--RLDKALSRDVPADESLSRTRLARLIEEGAVAVDGKLVTDAKAKVAEG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             V I       +HI  E   LD               +++ED+ + V NKPAG+ V   
Sbjct: 64  AAVCITVSEADESHIGPEDIPLD---------------IVHEDADLIVINKPAGLVVHPA 108

Query: 122 -GSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            GS     ++  L    D        ++P + HR+D++TSG+LVVA++ AA Q L   F 
Sbjct: 109 PGSPSGTLVNALLHHCGDDLSGVGGVKRPGIVHRIDKDTSGLLVVAKSDAAHQGLAAQFE 168

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------------G 222
              +++ Y +L +G+P      +   +   S   G+ + +  Q  +             G
Sbjct: 169 AHSVERYYRALCYGVPDANDPRL-RGIKGVSFEPGNVMRITTQLARHKHDRQKQAVLFHG 227

Query: 223 ANYAISHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-- 274
             +A++  +V++ F Q        CWLE    TGRTHQ+RVH  H G  +VGD  Y    
Sbjct: 228 GRHAVTRARVVEVFGQPGAVSLIECWLE----TGRTHQIRVHMAHAGHGLVGDPVYGGKR 283

Query: 275 -----NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                +F  +    +++  +  LHA  +   HP  G  ++  AP+P  M     +L
Sbjct: 284 KLSARSFGADAAEAVRSFPRQALHAAVLGFEHPVTGAGMRFEAPIPQDMQALISAL 339


>gi|73541038|ref|YP_295558.1| ribosomal large subunit pseudouridine synthase D [Ralstonia
           eutropha JMP134]
 gi|72118451|gb|AAZ60714.1| ribosomal large subunit pseudouridine synthase D [Ralstonia
           eutropha JMP134]
          Length = 403

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 90/320 (28%), Positives = 147/320 (45%), Gaps = 32/320 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+    H+   +   LQ+ + SG VRVD +  +  + +Q G  + + P         +
Sbjct: 70  RLDKLLARHFSEFSRSRLQQWIESGAVRVDGEVRRPRDAVQMGNRIEVQP-----QAAPE 124

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL-KSW 136
            Q      V L          ++YED  + V +KPAG+ V   +G      ++G L +  
Sbjct: 125 SQAFAPEDVALD---------VVYEDDALLVIDKPAGLVVHPAAGNWSGTVLNGLLHRDP 175

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +  + HRLD+ETSG++VVART  A   L    + R +++ Y +LVWG  +  +E
Sbjct: 176 TAAALPRAGIVHRLDKETSGLMVVARTLTAQTDLVRQLQARTVKRTYLALVWG--RIYEE 233

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM---QPHTGRTH 253
              +  + +       + +V  N      + +HF+ +        ++ M   Q  TGRTH
Sbjct: 234 GTIDAPIGRDPRERTRMAIVHTNS--GKPSRTHFRTLATVPLGRSFVSMVRCQLETGRTH 291

Query: 254 QLRVHALHMGCPIVGDHKYC-ANFKGNFTS-----PIQ-NKLYLHARYMDLPHPEGGR-L 305
           Q+RVH   +G P+VGD  Y  A  +G   +     P+   +  LHA  + L HP  G+ +
Sbjct: 292 QIRVHFESIGHPLVGDPVYYRATQRGQRPAIRVPLPVPFERQALHAFKLGLVHPVTGKTV 351

Query: 306 QITAPLPAHMVKTWDSLGFK 325
             TAP P  +    D+L F 
Sbjct: 352 SWTAPPPEDLQALIDALDFS 371


>gi|310820148|ref|YP_003952506.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309393220|gb|ADO70679.1| Pseudouridine synthase, RluA family [Stigmatella aurantiaca
           DW4/3-1]
          Length = 304

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 87/323 (26%), Positives = 152/323 (47%), Gaps = 34/323 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           ++V  +    RLD+    H P ++    ++++  G VR+  K+ +   ++  G+ + +  
Sbjct: 1   MIVAREASGERLDKHLSKHVPGLSLERARQLIAQGNVRIRGKKCQPTRKLWGGEEIELSL 60

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            PP +      ++   +                 +L++D  + + +KP G+ V+ G G  
Sbjct: 61  PPPRVPQGTAAVEGPGL----------------PVLHDDPDMVIVDKPVGLVVEPGGGAP 104

Query: 127 YHID--GFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             ++     +   D +G  +P + HRLD+ETSG L+ ART AAA  L ++F+ +R+ K Y
Sbjct: 105 SVVELLAAQRPPFDVEGVARPGVVHRLDRETSGCLMFARTDAAAAALDQAFQQKRVDKRY 164

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--QNEKGANYAISHFKVIDCFAQKFC 241
           W+LV G      E   +  L+  + G D     K     K A  A   F+V +   +   
Sbjct: 165 WTLVLG------ETPEHERLEGPY-GRDPQDPRKFTTRVKSARRAALSFEVRERL-RGAT 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            LE++  TGRTHQ+RV     G P++GD  Y  +  + +  +    +  LHA  + +PHP
Sbjct: 217 LLEVRLETGRTHQIRVQLSEAGFPVLGDSVYGPSEARAHPVAQALGRQALHALRLAVPHP 276

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
             G L ++ APLP    K   +L
Sbjct: 277 STGALVRVEAPLPEDFQKALAAL 299


>gi|217961313|ref|YP_002339881.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|222097338|ref|YP_002531395.1| ribosomal large subunit pseudouridine synthase, rlud subfamily
           [Bacillus cereus Q1]
 gi|229140541|ref|ZP_04269096.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-ST26]
 gi|217063169|gb|ACJ77419.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|221241396|gb|ACM14106.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus Q1]
 gi|228643102|gb|EEK99378.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-ST26]
          Length = 302

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 88/320 (27%), Positives = 149/320 (46%), Gaps = 41/320 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDNVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            + +          I E + LD     +NL          + YED+ + V NKP G+ V 
Sbjct: 61  EITV---------TIPEPEELDIQPEDMNLE---------IYYEDADVLVVNKPRGMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V+
Sbjct: 163 VAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA 
Sbjct: 217 ERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAG 270

Query: 294 YMDLPHPEGGR-LQITAPLP 312
            +   HP  G  +Q  AP+P
Sbjct: 271 ILGFDHPRTGEYIQFEAPIP 290


>gi|114707402|ref|ZP_01440299.1| Prenyl group binding site (CAAX box):RNA-binding S4:Pseudouridine
           synthase:Pseudouridine synthase, Rlu:Pseudouridine
           [Fulvimarina pelagi HTCC2506]
 gi|114537283|gb|EAU40410.1| Prenyl group binding site (CAAX box):RNA-binding S4:Pseudouridine
           synthase:Pseudouridine synthase, Rlu:Pseudouridine
           [Fulvimarina pelagi HTCC2506]
          Length = 339

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 91/349 (26%), Positives = 154/349 (44%), Gaps = 49/349 (14%)

Query: 11  VVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIP 68
            VE +E  MR+D +      P ++   +Q ++R+G V V          R++ G+ V + 
Sbjct: 7   TVEAEEAGMRIDAFLAGRCSPELSRARIQSLIRAGDVTVGGVDTAAAKRRVKEGEAVAL- 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
                        ++   +    +  D   +I+ +ED+ + V +KPAG+ V  G G    
Sbjct: 66  -------------RVPAPAEPEPEPEDIPLTIV-FEDADLVVVDKPAGLVVHPGPGNWSG 111

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--- 177
                  H  G   S ++   ++P + HRLD++TSG+LV+A+T  A + L E F      
Sbjct: 112 TLVNALLHYCGEELSGINGV-KRPGIVHRLDKDTSGLLVIAKTDMAHRSLAEQFAAHGSD 170

Query: 178 -RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV--HVVKQNEKGANYAISHFKVID 234
            R+ + Y ++VWG P      I   L + S    D +   VV   +  A  AI+ ++++ 
Sbjct: 171 GRMVRSYRAIVWGTPVPAVGRIETMLGRSSS---DRLKRDVVAATQPDARQAITDYRILA 227

Query: 235 CFAQKF----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN---FTSPIQNK 287
              +        +E +  TGRTHQ+RVH  H+G P++GD  Y + F         P +  
Sbjct: 228 GAGRAAGAEASLVECRLATGRTHQIRVHMAHIGHPLIGDVVYASGFASKAKALEEPARTT 287

Query: 288 L------YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           +       LHA  +   HP  G   + ++ LP  M +   +LG     N
Sbjct: 288 VEAFRRQALHAAELGFVHPVTGDAKRFSSDLPTDMRELAAALGIALSGN 336


>gi|154705997|ref|YP_001424165.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           Dugway 5J108-111]
 gi|154355283|gb|ABS76745.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           Dugway 5J108-111]
          Length = 323

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 89/333 (26%), Positives = 156/333 (46%), Gaps = 39/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   +++  Q + I  
Sbjct: 11  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEA 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 71  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 115

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            I+  L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y +
Sbjct: 116 LINALLH-YDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKTMKARQIVREYEA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           +V G+  + +         ++ +G   +H  +    +    AI+HF++I  + +    + 
Sbjct: 175 IVKGVLISGRTI-------EAPVGRHPIHRTRMAVVEFGRPAITHFRIIKRY-RAHTHIR 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKL------YLHARYMD 296
           +Q  TGRTHQ+RVH  H+  P+ GD  Y ++     + + P+Q  L       LHA  + 
Sbjct: 227 VQLETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHAATLQ 286

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             HP   R +   APLPA M    + L   Y +
Sbjct: 287 FSHPVDQRPMACHAPLPADMAHLLECLEDDYSQ 319


>gi|325300058|ref|YP_004259975.1| pseudouridine synthase [Bacteroides salanitronis DSM 18170]
 gi|324319611|gb|ADY37502.1| pseudouridine synthase [Bacteroides salanitronis DSM 18170]
          Length = 224

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 72/230 (31%), Positives = 118/230 (51%), Gaps = 15/230 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   LK ++     KP      +THRLD+  S
Sbjct: 3   IVYEDNHIIIVNKTASEIVQGDKTGDTPLSEMLKQYIKEAYAKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L + FR   ++K YW++V   P  ++  + ++L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNDMFRNGEVRKTYWAIVKQCPPAEEGELVHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K +  A+ H+K+ID  ++ +  +E+   TGR HQ+R      GCPI GD KY   
Sbjct: 122 -DREVKDSKKAVLHYKLID-RSENYYLVEVDLKTGRHHQIRCQLAKAGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP-AHMVKTWDSLG 323
             G   S     + LHAR +   HP   +L ++TAPLP  ++ K + ++G
Sbjct: 177 --GFPRSNPDGSICLHARTVSFIHPVSKKLIEVTAPLPEGNLWKAFQTIG 224


>gi|229061498|ref|ZP_04198842.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH603]
 gi|228717732|gb|EEL69382.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH603]
          Length = 302

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 90/321 (28%), Positives = 153/321 (47%), Gaps = 43/321 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVKGNYKVK--- 57

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
                 V + +   I E + LD     +NL          + YED+ + V NKP G+ V 
Sbjct: 58  ------VNDEITVTIPEPEELDIQPEDMNLE---------VYYEDADVLVVNKPRGMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTKGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDVAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKV 232
             + + + Y ++V G+  + K  I       + IG D      +  +E G N A++HF+V
Sbjct: 163 VAKTVTRRYKAIVHGVIPHDKGTI------DAPIGRDKKERQSMTVDENGKN-AVTHFQV 215

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           +D F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA
Sbjct: 216 LDRF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHA 269

Query: 293 RYMDLPHPEGGR-LQITAPLP 312
             +   HP  G  ++  AP+P
Sbjct: 270 GILGFDHPRTGEYIEFEAPIP 290


>gi|188575741|ref|YP_001912670.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae PXO99A]
 gi|188520193|gb|ACD58138.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae PXO99A]
          Length = 333

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 89/343 (25%), Positives = 157/343 (45%), Gaps = 40/343 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +V ++    R D      +P  +   L + ++SG   +D    +  + ++ G+ V+
Sbjct: 15  IRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGGESVQ 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V+    H   +   L                +LYED ++ V +KPAG+ V  G+G  
Sbjct: 75  VQVVLETQTHAAPQDIALS---------------VLYEDEQVLVIDKPAGLVVHPGAG-- 117

Query: 127 YHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            + DG L + +     +    PR  + HRLD++TSG++V+ART  A   L E    R + 
Sbjct: 118 -NPDGTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVLARTVQAQTALVEQLSARDVH 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G   +     AN  + + H        V+ + +    A++H+++ + F +  
Sbjct: 177 RQYLAVVVGALVSG--GTANAPIDR-HPRDRLKMAVRDDGRD---AVTHYRLRERF-RAH 229

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHA 292
             LE +  TGRTHQ+RVH  H+  PIVGD  Y    K     T  + ++L       LHA
Sbjct: 230 TALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQALHA 289

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
             +   HP  G  ++ +AP+PA + +   +L     R   + R
Sbjct: 290 ETLQFLHPVSGEPVRASAPVPADLQRLMTALREDSARAAELAR 332


>gi|86747580|ref|YP_484076.1| pseudouridine synthase RluD [Rhodopseudomonas palustris HaA2]
 gi|86570608|gb|ABD05165.1| ribosomal large subunit pseudouridine synthase D [Rhodopseudomonas
           palustris HaA2]
          Length = 324

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 87/341 (25%), Positives = 149/341 (43%), Gaps = 49/341 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV  DE + RLDR      P ++   L+ ++  G+V +            +G  VR P 
Sbjct: 1   MVVAGDEGSSRLDRVLATRCPALSRSRLKVLILDGRVAI------------AGSAVRDPA 48

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
              +    I        +      +  L+  +++ED  I V NKP G+ V   +G  +  
Sbjct: 49  YHASPGETITIDVPPPVAPEPEGEAIALE--IVHEDDDIIVINKPRGLVVHPAAG--HET 104

Query: 130 DGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESF----RM 176
              + + +   G+         +P + HRLD++T+G++V A+   A Q L+  F    R 
Sbjct: 105 GTLVNALIAHCGESLSGIGGVRRPGIVHRLDKDTTGLMVAAKNDRAHQSLSAQFADHGRT 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             +++ Y++ VWG+P   +  I   + +       Y         G   AI+H++V++ F
Sbjct: 165 GELRRGYYAFVWGVPNRARGTIEAPIDRHP-----YAREKMAVRDGGREAITHWEVLETF 219

Query: 237 AQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT--SPIQ---- 285
             +        +  Q  TGRTHQ+RVH  H+G P++GD  Y  +FK   +  SP      
Sbjct: 220 TGRSGGEIVSLIACQLETGRTHQIRVHLAHLGHPLLGDDVYGPHFKTKASQLSPAARAAL 279

Query: 286 ---NKLYLHARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
               +  LHA  + L HP  G +    + LPA + +   +L
Sbjct: 280 ADLGRQALHAYLLVLEHPSSGEVMAWESGLPADLARLKAAL 320


>gi|229146464|ref|ZP_04274835.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-ST24]
 gi|228637097|gb|EEK93556.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-ST24]
          Length = 302

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 90/317 (28%), Positives = 149/317 (47%), Gaps = 35/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVVAEQKNERIDKFVAGINNEWSRTQVQQWIKDNVVTVNGKAVKGNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          I E + LD         + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITV---------TIPEPEELDI------QPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            + + Y ++V G IP +K    A     K       V     +E G N A++HF+V++ F
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV-----DENGKN-AVTHFQVLERF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  + 
Sbjct: 220 -KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGILG 273

Query: 297 LPHPEGGR-LQITAPLP 312
             HP  G  +Q  AP+P
Sbjct: 274 FDHPRTGEYIQFEAPIP 290


>gi|218262785|ref|ZP_03477143.1| hypothetical protein PRABACTJOHN_02822 [Parabacteroides johnsonii
           DSM 18315]
 gi|218223136|gb|EEC95786.1| hypothetical protein PRABACTJOHN_02822 [Parabacteroides johnsonii
           DSM 18315]
          Length = 223

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 73/228 (32%), Positives = 113/228 (49%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I   NK     VQG       +   LK+W+  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIAVNKTCREIVQGDKTGDTPLSDMLKAWLKEKYCKPGNVFVGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR+  ++K YW++V   P +++  + NWL++       Y + 
Sbjct: 63  GVVLFAKTSKALARLNEMFRVGEVKKTYWAIVKNCPPSEEGELVNWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  AI  +KVI   ++ +  L +   TGR HQ+R     MGCPI GD KY   
Sbjct: 123 TER--PNAKKAILRYKVI-ARSENYYLLAVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             G   S     + LH+R  +  HP   + + I AP+P   +  W +L
Sbjct: 177 --GFPRSNPDGGISLHSRSAEFIHPVSKQPVSIVAPVPVDSL--WKAL 220


>gi|226356664|ref|YP_002786404.1| ribosomal large subunit pseudouridine synthase D [Deinococcus
           deserti VCD115]
 gi|226318654|gb|ACO46650.1| putative ribosomal large subunit pseudouridine synthase D
           [Deinococcus deserti VCD115]
          Length = 321

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 79/303 (26%), Positives = 132/303 (43%), Gaps = 34/303 (11%)

Query: 41  LRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +  G V+V+ + V K + +++ G+ + + P       +  E   LD              
Sbjct: 33  IAGGHVKVEGQPVTKVSLKLRGGERIDVSPPALPDARVEAEDLPLD-------------- 78

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL--------KSWVDSKGQKPRLTHR 149
            ++YED  +   NKP G+      G+     ++  L          +    G +P + HR
Sbjct: 79  -VIYEDDYLIAVNKPPGMVTHPAPGVLSGTLVNALLGRMPLPEQPDYDSEAGYRPGIVHR 137

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG++VVA+T  A   L  +F+ R  +K Y ++  G  +          + +  + 
Sbjct: 138 LDKDTSGVIVVAKTVGAHARLAAAFKDRETRKTYLAIAAGQWRADGPARVEAPIGRHPVQ 197

Query: 210 GDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              + V   N + A    +      D   +    +  QP TGRTHQ+RVH  H+G PI+G
Sbjct: 198 RQRMTVGGANPREAQTLFTPLAAHPDGHGRTLALVRAQPRTGRTHQIRVHLAHLGSPILG 257

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           D  Y        +S    +  LHA ++ +PHP  GR L + AP P  M+  W +LG    
Sbjct: 258 DAVY------GRSSETMLRHALHAHFLSVPHPGTGRLLHLHAPAPDDMLNAWIALGGAMP 311

Query: 328 RNL 330
            +L
Sbjct: 312 SDL 314


>gi|218233909|ref|YP_002368692.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
 gi|229152090|ref|ZP_04280285.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           m1550]
 gi|218161866|gb|ACK61858.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
 gi|228631439|gb|EEK88073.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           m1550]
          Length = 302

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 90/317 (28%), Positives = 149/317 (47%), Gaps = 35/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAAEQKNERIDKFVTGINNEWSRTQVQQWIKDEVVTVNGKAVKGNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          I E + LD         + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITV---------TIPEPEELDI------QPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            + + Y ++V G IP +K    A     K       V     +E G N A++HF+V++ F
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV-----DENGKN-AVTHFQVLERF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  + 
Sbjct: 220 -KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGILG 273

Query: 297 LPHPEGGR-LQITAPLP 312
             HP  G  +Q  AP+P
Sbjct: 274 FDHPRTGEYIQFEAPIP 290


>gi|229019095|ref|ZP_04175930.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH1273]
 gi|229025339|ref|ZP_04181757.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH1272]
 gi|228735924|gb|EEL86501.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH1272]
 gi|228742195|gb|EEL92360.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH1273]
          Length = 302

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 90/320 (28%), Positives = 151/320 (47%), Gaps = 41/320 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKGND 60

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V IP          +E  I    +NL          + YED+ + V NKP G+ V  
Sbjct: 61  EITVTIPDP--------EELDIQPEDMNLE---------IYYEDADVLVVNKPRGMVVHP 103

Query: 122 GSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L     
Sbjct: 104 APGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLV 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVI 233
            + + + Y ++V G+  + K  I       + IG D      +  +E G N A++HF+V+
Sbjct: 164 AKTVTRRYKAIVHGVIPHDKGTI------DAPIGRDKKERQSMTVDENGKN-AVTHFQVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA 
Sbjct: 217 ERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAG 270

Query: 294 YMDLPHPEGGR-LQITAPLP 312
            +   HP  G  +Q  AP+P
Sbjct: 271 ILGFDHPRTGEYIQFEAPIP 290


>gi|52141596|ref|YP_085233.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
 gi|228987037|ref|ZP_04147162.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar tochigiensis BGSC 4Y1]
 gi|229157471|ref|ZP_04285548.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           ATCC 4342]
 gi|51975065|gb|AAU16615.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
 gi|228625921|gb|EEK82671.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           ATCC 4342]
 gi|228772631|gb|EEM21072.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar tochigiensis BGSC 4Y1]
          Length = 302

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 88/320 (27%), Positives = 149/320 (46%), Gaps = 41/320 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVKEND 60

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            + +          I E + LD     +NL          + YED+ + V NKP G+ V 
Sbjct: 61  EITV---------TIPEPEELDIQPEDMNLE---------IYYEDADVLVVNKPRGMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V+
Sbjct: 163 VAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA 
Sbjct: 217 ERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAG 270

Query: 294 YMDLPHPEGGR-LQITAPLP 312
            +   HP  G  +Q  AP+P
Sbjct: 271 ILGFDHPRTGEYIQFEAPIP 290


>gi|42782985|ref|NP_980232.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 10987]
 gi|49186742|ref|YP_029994.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|118479113|ref|YP_896264.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|165872288|ref|ZP_02216925.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|167636442|ref|ZP_02394741.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|167641146|ref|ZP_02399401.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|170688858|ref|ZP_02880061.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|170708814|ref|ZP_02899250.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|177654900|ref|ZP_02936617.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|190565878|ref|ZP_03018797.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|196035788|ref|ZP_03103190.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
 gi|196045901|ref|ZP_03113130.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|218905022|ref|YP_002452856.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|225865874|ref|YP_002751252.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|228916530|ref|ZP_04080096.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar pulsiensis BGSC 4CC1]
 gi|228928941|ref|ZP_04091973.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar pondicheriensis BGSC 4BA1]
 gi|228935208|ref|ZP_04098034.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar andalousiensis BGSC 4AW1]
 gi|228947612|ref|ZP_04109902.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar monterrey BGSC 4AJ1]
 gi|229092938|ref|ZP_04224071.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-42]
 gi|229123406|ref|ZP_04252610.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           95/8201]
 gi|229186133|ref|ZP_04313302.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BGSC 6E1]
 gi|254683398|ref|ZP_05147258.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. CNEVA-9066]
 gi|254735932|ref|ZP_05193638.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Western North America USA6153]
 gi|254739820|ref|ZP_05197513.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Kruger B]
 gi|254751010|ref|ZP_05203049.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Vollum]
 gi|301055383|ref|YP_003793594.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           anthracis CI]
 gi|42738912|gb|AAS42840.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus ATCC 10987]
 gi|49180669|gb|AAT56045.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|118418338|gb|ABK86757.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|164711964|gb|EDR17504.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|167510926|gb|EDR86317.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|167528184|gb|EDR90971.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|170126299|gb|EDS95190.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|170667213|gb|EDT17973.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|172080411|gb|EDT65498.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|190562797|gb|EDV16763.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|195991437|gb|EDX55403.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
 gi|196023341|gb|EDX62019.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|218538740|gb|ACK91138.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|225786554|gb|ACO26771.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|228597309|gb|EEK54960.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BGSC 6E1]
 gi|228660182|gb|EEL15818.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           95/8201]
 gi|228690442|gb|EEL44226.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-42]
 gi|228812132|gb|EEM58463.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar monterrey BGSC 4AJ1]
 gi|228824373|gb|EEM70179.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar andalousiensis BGSC 4AW1]
 gi|228830748|gb|EEM76353.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar pondicheriensis BGSC 4BA1]
 gi|228843109|gb|EEM88191.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar pulsiensis BGSC 4CC1]
 gi|300377552|gb|ADK06456.1| ribosomal large subunit pseudouridylate synthase D [Bacillus cereus
           biovar anthracis str. CI]
 gi|324327791|gb|ADY23051.1| 23S rRNA pseudouridine synthase D [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 302

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 88/320 (27%), Positives = 149/320 (46%), Gaps = 41/320 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            + +          I E + LD     +NL          + YED+ + V NKP G+ V 
Sbjct: 61  EITV---------TIPEPEELDIQPEDMNLE---------IYYEDADVLVVNKPRGMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V+
Sbjct: 163 VAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA 
Sbjct: 217 ERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAG 270

Query: 294 YMDLPHPEGGR-LQITAPLP 312
            +   HP  G  +Q  AP+P
Sbjct: 271 ILGFDHPRTGEYIQFEAPIP 290


>gi|229198004|ref|ZP_04324718.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           m1293]
 gi|228585483|gb|EEK43587.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           m1293]
          Length = 302

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 88/320 (27%), Positives = 149/320 (46%), Gaps = 41/320 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            + +          I E + LD     +NL          + YED+ + V NKP G+ V 
Sbjct: 61  EITV---------TIPEPEELDIQPEDMNLE---------IYYEDADVLVVNKPRGMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V+
Sbjct: 163 VAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA 
Sbjct: 217 ERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAG 270

Query: 294 YMDLPHPEGGR-LQITAPLP 312
            +   HP  G  +Q  AP+P
Sbjct: 271 ILGFDHPRTGEYIQFEAPIP 290


>gi|224025955|ref|ZP_03644321.1| hypothetical protein BACCOPRO_02702 [Bacteroides coprophilus DSM
           18228]
 gi|224019191|gb|EEF77189.1| hypothetical protein BACCOPRO_02702 [Bacteroides coprophilus DSM
           18228]
          Length = 223

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 72/218 (33%), Positives = 110/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIVVNKTASEIVQGDKTGDTPLSETVKQYLKEKYAKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E FR   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFRNGEVKKTYWAIVKNCPKEPEAELTHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K +  A+ H+++I   +  +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVKDSKKAVLHYRLIG-HSVNYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             G+  S     + LHAR +   HP    L  +TAP+P
Sbjct: 177 --GSPRSNPDGSICLHARRVRFVHPVSKELIDLTAPVP 212


>gi|70732611|ref|YP_262374.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens Pf-5]
 gi|68346910|gb|AAY94516.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens Pf-5]
          Length = 353

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 91/336 (27%), Positives = 154/336 (45%), Gaps = 42/336 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G ++ +    
Sbjct: 44  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVHGGSILELTAEQ 103

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    I +   LD               ++YED  I V NKPAG+ V   +G   H DG
Sbjct: 104 EAQGEWIAQDIELD---------------IVYEDDDILVINKPAGLVVHPAAG---HADG 145

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     +      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  
Sbjct: 146 TLLNALLHHIPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVAQLQSRSVSRIYEC 205

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+     +   N  + +       + V++    G   A+SH++V++ F +    + +
Sbjct: 206 IVIGVVTAGGKI--NAPIGRHGQQRQRMAVME----GGKQAVSHYRVLERF-RSHTHVRV 258

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDL 297
           +  TGRTHQ+RVH  H+  P+VGD  Y   F+            ++N  +  LHAR+++L
Sbjct: 259 KLETGRTHQIRVHMAHINFPLVGDPAYGGRFRIPPAASQTMVDSLKNFPRQALHARFLEL 318

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            HP  G R+   +PLP   V  W     K DR  +I
Sbjct: 319 DHPTTGIRMSWESPLPDDFV--WLLSLLKQDREAFI 352


>gi|229162828|ref|ZP_04290785.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           R309803]
 gi|228620710|gb|EEK77579.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           R309803]
          Length = 302

 Score =  109 bits (272), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 89/321 (27%), Positives = 153/321 (47%), Gaps = 43/321 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N ++++  
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKVVKGNYKVKAND 60

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            + +          I E + LD     +NL          + YED+ + V NKP G+ V 
Sbjct: 61  EITV---------TIPEPEELDIQPEDMNLE---------IYYEDADVLVVNKPRGMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKV 232
             + + + Y ++V G+  + K  I       + IG D      +  +E G N A++HF+V
Sbjct: 163 VAKTVTRRYKAIVHGVIPHDKGTI------DAPIGRDKKERQSMTVDENGKN-AVTHFQV 215

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++ F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA
Sbjct: 216 LERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHA 269

Query: 293 RYMDLPHPEGGR-LQITAPLP 312
             +   HP  G  +Q  AP+P
Sbjct: 270 GILGFDHPRTGEYIQFEAPIP 290


>gi|312793558|ref|YP_004026481.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312180698|gb|ADQ40868.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 300

 Score =  109 bits (272), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 90/315 (28%), Positives = 166/315 (52%), Gaps = 41/315 (13%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           RLD++         +FV  QKI+  G V V++ +V K   +++SG ++++         +
Sbjct: 9   RLDKYLSEALSKTRSFV--QKIIEEGNVWVNQTQVLKPAYKVKSGDIIKV---------V 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH 128
           I E K       L+  +  +   ++YED  + V NKP G+ V  G+G         + + 
Sbjct: 58  IPEPK------QLSLVAQDIDIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHK 111

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             G L S   +   +P + HRLD++TSG+L+VA+T  A   L+E+ +  +I++IY+++  
Sbjct: 112 FRGRLSSI--NGVIRPGIVHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICE 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+ K     I N  + +  +    + VV   ++    A+++F+V++ F  K+ +++++  
Sbjct: 170 GVLKEDSGVI-NAPIGRHPVNRLKMAVVPNGKE----AVTYFEVLERF-DKYTFIKLRLK 223

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  ++G P++GD  Y    K  F   +Q ++ LHA  ++  HP   + L  
Sbjct: 224 TGRTHQIRVHMSYIGYPLLGDSSY-GRAKNEFG--VQGQV-LHAGEIEFVHPITSKVLHF 279

Query: 308 TAPLPAHMVKTWDSL 322
           +A LP + V+  + L
Sbjct: 280 SADLPEYFVEILNML 294


>gi|229031524|ref|ZP_04187524.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH1271]
 gi|228729813|gb|EEL80793.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH1271]
          Length = 302

 Score =  109 bits (272), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 89/319 (27%), Positives = 148/319 (46%), Gaps = 39/319 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKEDVVTVNGKSVKVNYKVKEND 60

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V IP          +E  I    +NL          + YED+ + V NKP G+ V  
Sbjct: 61  EITVTIPDP--------EELDIQAEDMNLE---------IYYEDADVLVVNKPRGMVVHP 103

Query: 122 GSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L     
Sbjct: 104 APGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLV 163

Query: 176 MRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            + + + Y ++V G IP +K    A     K       V      ++   +A++HF+VI+
Sbjct: 164 AKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVIE 217

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  
Sbjct: 218 RF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGI 271

Query: 295 MDLPHPEGGR-LQITAPLP 312
           +   HP  G  +Q  AP+P
Sbjct: 272 LGFDHPRTGEYIQFEAPIP 290


>gi|222529363|ref|YP_002573245.1| RluA family pseudouridine synthase [Caldicellulosiruptor bescii DSM
           6725]
 gi|222456210|gb|ACM60472.1| pseudouridine synthase, RluA family [Caldicellulosiruptor bescii
           DSM 6725]
          Length = 300

 Score =  109 bits (272), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 93/320 (29%), Positives = 164/320 (51%), Gaps = 51/320 (15%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           RLDR+         +FV  QKI+  G V V++++V K   +++SG ++++         +
Sbjct: 9   RLDRYLSEALSKTRSFV--QKIIEEGNVWVNQRQVLKPAYKVKSGDIIKV---------V 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I E K       L+  +  +   ++YED  + V NKP G+ V  G+G       F  + V
Sbjct: 58  IPEPK------QLSLVAQDIDIEVVYEDEHLSVINKPRGMVVHPGAG------NFENTLV 105

Query: 138 DS-----KGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++     KG+        +P + HRLD++TSG+LVVA+T  A   L+E+ +  +I++IY+
Sbjct: 106 NALLHKFKGRLSSINGVIRPGIVHRLDKDTSGLLVVAKTDEAHIKLSEALKSHQIKRIYY 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWL 243
           ++  G+ K     +       + IG   V+ +K         A+++F+V++ F  K+ ++
Sbjct: 166 AICEGVLKEDSGVV------DAPIGRHPVNRLKMAIVPNGKEAVTYFEVLERF-DKYTFV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +++  TGRTHQ+RVH  ++G P++GD  Y    K  F    Q    LHA  ++  HP   
Sbjct: 219 KLRLKTGRTHQIRVHMSYIGYPLLGDGIY-GRAKNEFGVEGQ---VLHAGEIEFVHPITS 274

Query: 304 R-LQITAPLPAHMVKTWDSL 322
           + L  +A LP + V+  + L
Sbjct: 275 KVLHFSADLPEYFVEILNML 294


>gi|332297938|ref|YP_004439860.1| pseudouridine synthase, RluA family [Treponema brennaborense DSM
           12168]
 gi|332181041|gb|AEE16729.1| pseudouridine synthase, RluA family [Treponema brennaborense DSM
           12168]
          Length = 318

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 85/331 (25%), Positives = 147/331 (44%), Gaps = 39/331 (11%)

Query: 10  VVVENDEENMRLDRWF------KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           V V       RLD++       +     +N   L+ I  +  + V+ +  K + +I+ G 
Sbjct: 6   VTVPAASAAERLDKYLISCESVQQQCAGLNRSKLKAI--ATGITVNGRDAKLSTKIRPGD 63

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +    N  +HI  E   LD               ++YED  + V NK  G+      
Sbjct: 64  SIVVDWADNIPDHIDPEDIPLD---------------IIYEDGNVAVVNKKQGMVTHPAL 108

Query: 124 G--IAYHIDGFLKSW----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L  W    V    ++P + HRLD++TSG+++  + R + + L   FR R
Sbjct: 109 GNWSGTLVNALLFHWNRESVAQTARRPGIVHRLDKDTSGLIITGKNRESEEWLQAQFRDR 168

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           R++K Y ++V G P +    I   +++       +    +   +   +A + ++ I C+ 
Sbjct: 169 RVKKEYIAIVAGRPPHASGTIKTQIIRDPRNRKRF--KAETGTENGKFAHTQYRCIACYG 226

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-KLYLHARYMD 296
             F  + +Q  TGRTHQ+RVH  ++GCPI+GD  Y     GN T    +  L LH+R + 
Sbjct: 227 S-FSLMRLQLKTGRTHQIRVHMKYLGCPILGDPLY-----GNKTQLFPDATLMLHSRLLS 280

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSLGFKY 326
           +  P +    +  AP+P    K   +L  KY
Sbjct: 281 IRLPGQAAFSEFKAPVPRRFKKVLKTLHGKY 311


>gi|296332341|ref|ZP_06874802.1| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305673620|ref|YP_003865292.1| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296150259|gb|EFG91147.1| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305411864|gb|ADM36983.1| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 302

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 76/233 (32%), Positives = 118/233 (50%), Gaps = 30/233 (12%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +L+ED+ + + NKPAGI+      G +G     IAYH        V+ +  K R  HRLD
Sbjct: 85  ILFEDNHMLIVNKPAGIATHPNEDGQTGTLANLIAYHYQ------VNGEICKVRHVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q+TSG +V A+ R +   L +    + +++ Y ++  G  K KK  I       S IG D
Sbjct: 139 QDTSGAIVFAKHRLSHAILDQQLEKKTLKRTYTAITEGKLKTKKGTI------DSPIGRD 192

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             H  ++        A++HFKV+   A ++   +E++  TGRTHQ+RVH   +G P++GD
Sbjct: 193 RSHPTRRRVSPSGQTAVTHFKVVASNAKERLTLVELELETGRTHQIRVHMASIGHPLIGD 252

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHMVKTWDS 321
             Y         S + N+  LHA+ +   HP  G L +  AP PA +   +D+
Sbjct: 253 ALYGGG------SKLLNRQALHAKKVQAVHPITGELIVAEAPFPADIENLFDT 299


>gi|158425878|ref|YP_001527170.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
 gi|158332767|dbj|BAF90252.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
          Length = 354

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 92/342 (26%), Positives = 152/342 (44%), Gaps = 48/342 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  ++  +R DR+     P ++   LQK++  G+V V             G+VV  P 
Sbjct: 33  LTVGPEDAGLRADRFLAARLPDLSRTRLQKLVADGRVSV------------GGRVVGDPA 80

Query: 70  V-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
             +NA +         + +  + +  D     + YED  + V +KPAG+ V    G    
Sbjct: 81  ERVNAGDEWTVRVPAPEPAAPVPEKMDL---SIAYEDDFLIVVDKPAGLVVHPAPGNWSG 137

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMR 177
             ++G L     S       ++P + HRLD++TSG+LVVA+T AA   L   F    R  
Sbjct: 138 TLVNGLLAHCGASLSGIGGVKRPGIVHRLDKDTSGLLVVAKTDAAHAGLAAQFADHGRTG 197

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y++ VWG+P  +    A      +H        V+Q+ +    AI+H++ ++ FA
Sbjct: 198 PLERAYYAFVWGVPDQRGTVDAPIDRHPTH---RQKMAVRQSGR---EAITHWERLEVFA 251

Query: 238 QK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------- 285
                     +E Q  TGRTHQ+RVH  H+G P++GD  Y   F+   +   +       
Sbjct: 252 GADGAPLASLIECQLETGRTHQIRVHLAHVGHPLLGDEVYGQGFRTKASRLPEGARALLA 311

Query: 286 --NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
              +  LHA  +   HP     L   +PLP  + +  D+L  
Sbjct: 312 ALGRQALHAARLGFAHPVTDEELLFESPLPEDLARLRDALAL 353


>gi|94310295|ref|YP_583505.1| ribosomal large subunit pseudouridine synthase D [Cupriavidus
           metallidurans CH34]
 gi|93354147|gb|ABF08236.1| 23S rRNA pseudouridine synthase [Cupriavidus metallidurans CH34]
          Length = 403

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 93/332 (28%), Positives = 149/332 (44%), Gaps = 34/332 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           Y+ V++     RLD+    H+   +   +Q+ +  G VRVD +  +    +Q GQ + + 
Sbjct: 59  YMEVDSASHGERLDKLLARHFSEFSRSRIQQWIEDGAVRVDGEPSRAKASVQMGQKIEVQ 118

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
           P            +    S+  T     L   ++YED  + V NKPAG+ V   +G    
Sbjct: 119 P------------QAAPESMAFTAEDVPLD--VVYEDDAMLVINKPAGLVVHPAAGNWSG 164

Query: 127 YHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             ++G L     S  + PR  + HRLD+ETSG++VVART  A   L      R +++ Y 
Sbjct: 165 TVLNGLLHR-DPSAARLPRAGIVHRLDKETSGLMVVARTLVAQTDLVRQLAARTVKRTYL 223

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFC 241
           +LVWG  +   +   +  + +       + +V  N      + +HF+ +        K  
Sbjct: 224 ALVWG--ETPDDGTIDAPIGRDPRERTRMAIVHTN--SGKPSRTHFETLGTVPLGRGKVS 279

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTS-----PIQ-NKLYLHARY 294
            +  Q  TGRTHQ+RVH   +G P+VGD  Y  A  +G   +     P+   +  LHA  
Sbjct: 280 MVMCQLETGRTHQIRVHFESIGHPLVGDPVYHKATQRGQRPAIRVPLPVPFTRQALHAYR 339

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           + L HP  GR +   A  P  +    D+L F+
Sbjct: 340 LGLVHPVTGRKMSWEAEPPEDLQALIDALDFE 371


>gi|332141865|ref|YP_004427603.1| ribosomal large subunit pseudouridine synthase D [Alteromonas
           macleodii str. 'Deep ecotype']
 gi|327551887|gb|AEA98605.1| ribosomal large subunit pseudouridine synthase D [Alteromonas
           macleodii str. 'Deep ecotype']
          Length = 327

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 88/313 (28%), Positives = 152/313 (48%), Gaps = 39/313 (12%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+   + +P  +   L+  ++ G V V+            G+V+ +P     ++ +
Sbjct: 20  GLRLDQVLADLFPEYSRSKLKTWIQDGNVSVN------------GEVITVPRHKMQMDEL 67

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW 136
           +  Q  +D  V +T  +  +   ++YED  I V NKPA + V  G+G  +  +   L + 
Sbjct: 68  VTVQAEMD--VQVTSEAQDIALDIVYEDEHILVINKPADLVVHPGAGNPSGTVLNALLNH 125

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           V    + PR  + HRLD++T+G++VVA+T  A  HL +  + R + + Y ++  G     
Sbjct: 126 VPEIDKVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVDQLQRREVSREYEAIALGTMVAG 185

Query: 195 ---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
               E I     K++H+       V++  K    AI+HF+VI+ F + +  L ++  TGR
Sbjct: 186 GIVDEPIGRHATKRTHMA------VREMGKP---AITHFRVIEKF-RAYTHLRLKLETGR 235

Query: 252 THQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDLPHPEGG 303
           THQ+RVH  H+  P++GD  Y    +       +F   ++   +  LHA  + L HPE  
Sbjct: 236 THQIRVHMAHIKHPLLGDQVYGGRPRLPKGASEDFIGVLRGFQRQALHAAQLSLFHPETE 295

Query: 304 R-LQITAPLPAHM 315
             +   APLP  M
Sbjct: 296 EWMTWKAPLPQDM 308


>gi|49478436|ref|YP_037954.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|49329992|gb|AAT60638.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
          Length = 302

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 88/320 (27%), Positives = 149/320 (46%), Gaps = 41/320 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREDD 60

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            + +          I E + LD     +NL          + YED+ + V NKP G+ V 
Sbjct: 61  EITV---------TIPEPEELDIQPEDMNLE---------IYYEDADVLVVNKPRGMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V+
Sbjct: 163 VAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA 
Sbjct: 217 ERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAG 270

Query: 294 YMDLPHPEGGR-LQITAPLP 312
            +   HP  G  +Q  AP+P
Sbjct: 271 ILGFDHPRTGEYIQFEAPIP 290


>gi|33239671|ref|NP_874613.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus subsp. marinus str.
           CCMP1375]
 gi|33237196|gb|AAP99265.1| 23S RNA-specific pseudouridylate synthase [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
          Length = 318

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 87/305 (28%), Positives = 143/305 (46%), Gaps = 36/305 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IPPVINALNH 76
           MRLDRW  +     +   +QK +  G V V+  + K    +++G  ++  +PP    L +
Sbjct: 27  MRLDRWLVSQRSEQSRARIQKFIEDGLVLVNGIQGKSKTPLRTGDEIQLWVPPP-EPLPY 85

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLK 134
           +  ++  LD               +++EDS I V NKPAG++V    G      ++G L 
Sbjct: 86  LKPQKMHLD---------------IIFEDSHIIVINKPAGLTVHPAPGNKDRTLVNGLLH 130

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +V+A+++ A  +L    + R   + Y +LV G+
Sbjct: 131 HCTDLPGINGKLRPGIVHRLDKDTTGCIVIAKSQEALVNLQVQIQKRIASRRYIALVHGV 190

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P   K  I+  + +       Y  V   N+     A +H+++ +     +  L  +  TG
Sbjct: 191 PHGDKGIISAPIGRHPIDRKKYAVV---NDGSGRDACTHWELKERLGD-YSLLSFKLETG 246

Query: 251 RTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
           RTHQ+RVH+ H+G PI+GD  Y  C       T  +     LHA  + L HP     +  
Sbjct: 247 RTHQIRVHSAHIGHPILGDPTYSRCKKLPTKLTGQV-----LHAIQLGLQHPISKTDILF 301

Query: 308 TAPLP 312
            APLP
Sbjct: 302 EAPLP 306


>gi|308177850|ref|YP_003917256.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
 gi|307745313|emb|CBT76285.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
          Length = 314

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 91/312 (29%), Positives = 151/312 (48%), Gaps = 31/312 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           +S  T +  ++V+ D+   RLD +       I       + +  QV+V+ + +  + RI+
Sbjct: 2   ISNGTAIHELLVDPDDAGARLDAYIARVL-QIPRTLASSLCKDSQVQVNGRTISKSLRIK 60

Query: 61  SGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
            G   VV IPP  + L   IK +K+           + LK  ++ +D    V +KP G++
Sbjct: 61  VGDQLVVTIPPQADPLE--IKVEKV-----------EELK--IIADDDDYVVIDKPVGVA 105

Query: 119 VQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTE 172
                G +   + G L +    + + G   R  + HRLD  TSG++VVA+T  A   L  
Sbjct: 106 AHPSPGWVGPTVVGALMAEGYNITTSGAAERQGIVHRLDVGTSGLMVVAKTERAYTELKR 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           +F+ R  +KIY ++V G+P   +  I   + +  H G D+   V     G   +++H+KV
Sbjct: 166 AFKERTPKKIYHAVVQGLPDPLQGTIDAPIGR--HPGHDWKFAVLD---GGRDSVTHYKV 220

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           I+ F  +   +E+   TGRTHQ+RVH    G P VGD  Y A+ K      +  + +LHA
Sbjct: 221 IEAFG-RASLVEVHLETGRTHQIRVHFSAFGHPCVGDQTYGADPKLGAALGL-TRQWLHA 278

Query: 293 RYMDLPHPEGGR 304
           + +   HP  G+
Sbjct: 279 KRLGFSHPVSGQ 290


>gi|229075650|ref|ZP_04208632.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock4-18]
 gi|228707426|gb|EEL59617.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock4-18]
          Length = 302

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 90/329 (27%), Positives = 152/329 (46%), Gaps = 39/329 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKEND 60

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V IP          +E  I    +NL          + YED+ + V NKP G+ V  
Sbjct: 61  EITVTIPDP--------EELDIQAEDMNLE---------IYYEDADVLVVNKPRGMVVHP 103

Query: 122 GSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L     
Sbjct: 104 APGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLV 163

Query: 176 MRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V++
Sbjct: 164 AKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVLE 217

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  
Sbjct: 218 RF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGI 271

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP  G  +Q  AP+P    +T + L
Sbjct: 272 LGFDHPRTGEYIQFEAPIPEVFEETLNVL 300


>gi|313496998|gb|ADR58364.1| RluA family pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 352

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 96/336 (28%), Positives = 149/336 (44%), Gaps = 42/336 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   V+  + +  G ++ +    
Sbjct: 43  VPSELGGQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLVHGGSLLTLEAEQ 102

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    I E   LD               ++YED  I V NKPAG+ V   +G   H  G
Sbjct: 103 EAQGEWIAEDIELD---------------IVYEDDHILVINKPAGLVVHPAAG---HASG 144

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L E  + R++ +IY  
Sbjct: 145 TLLNALLHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTLQAQTKLVEQMQARKVSRIYEC 204

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+     +  A       H G      V     G   A+SH++V+  F +    + +
Sbjct: 205 IVIGVVTAGGKIDAPI---GRHGGMRQRMAVTD---GGKPAVSHYRVLKRF-RSHTHVRV 257

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKLYLHARYMDL 297
           +  TGRTHQ+RVH  H+G P+VGD  Y   F+     SP          +  LHAR++ L
Sbjct: 258 KLETGRTHQIRVHMAHVGFPLVGDQTYGGRFRIPPAASPTMVEAVKTFPRQALHARFLAL 317

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            HP  G  ++  +PLP   V  W       DR  +I
Sbjct: 318 AHPITGEVMKWESPLPDDFV--WLLSLLNQDRESFI 351


>gi|168180134|ref|ZP_02614798.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
 gi|226948812|ref|YP_002803903.1| RluA family pseudouridine synthase [Clostridium botulinum A2 str.
           Kyoto]
 gi|182669142|gb|EDT81118.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
 gi|226841647|gb|ACO84313.1| pseudouridine synthase, RluA family [Clostridium botulinum A2 str.
           Kyoto]
          Length = 305

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 94/327 (28%), Positives = 152/327 (46%), Gaps = 50/327 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE + +N+RLD +    +   +   LQ I+  G V V+ K  K N +++    + +    
Sbjct: 8   VEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVRDNIEVN--- 64

Query: 72  NALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                 I E K+L      +NL          ++YED  + V NKP  + V    G+   
Sbjct: 65  ------IPEPKLLQIEPEDINLD---------IIYEDKDVIVVNKPQEMVVHPAPGVYSG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+   I ++
Sbjct: 110 TLVNALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRV 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFC 241
           Y +LV GI K+++  I      ++ IG   V  +K    K   +A++H+KVI+ F +   
Sbjct: 170 YMALVEGIIKDEQGTI------EAPIGRHPVDRIKMAVVKDGRHAVTHYKVIERF-KNHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLHARYMD 296
            +E +  TGRTHQ+RVH  H+  P+VGD  Y       N KG           LHA+ + 
Sbjct: 223 LVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLKGQM---------LHAKLLG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP   + ++  + LP +  K    L
Sbjct: 274 FIHPTTRQYVEFESELPEYFKKIIKIL 300


>gi|330988806|gb|EGH86909.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           lachrymans str. M301315]
          Length = 320

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 98/338 (28%), Positives = 156/338 (46%), Gaps = 46/338 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+      
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVL------ 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                +I EQ+     V      D     ++YED +I V NKPAG+ V   +G   H DG
Sbjct: 65  ----ELIAEQEAQGEWVAQDIELD-----IIYEDDQILVINKPAGLVVHPAAG---HADG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  
Sbjct: 113 TLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +V G+     +  A        IG  G     +   E G   A+SH++V++ F +    +
Sbjct: 173 IVIGVVTAGGKIDAP-------IGRHGQQRQRMAVME-GGKQAVSHYRVLERF-RSHTHV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK----GNFTSPIQNKLY----LHARYM 295
            ++  TGRTHQ+RVH  H+  P+VGD  Y   F+     + T     K +    LHAR++
Sbjct: 224 RVKLETGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFL 283

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +L HP  G R+   +PLP  +V  W     K DR  +I
Sbjct: 284 ELDHPTTGKRMSWESPLPDDLV--WLLSLLKQDREAFI 319


>gi|228992627|ref|ZP_04152553.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           pseudomycoides DSM 12442]
 gi|229006175|ref|ZP_04163861.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus mycoides
           Rock1-4]
 gi|228755016|gb|EEM04375.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus mycoides
           Rock1-4]
 gi|228766959|gb|EEM15596.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           pseudomycoides DSM 12442]
          Length = 302

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 89/323 (27%), Positives = 152/323 (47%), Gaps = 45/323 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++ G V V+   +K N +++   
Sbjct: 1   MSEVVQVTVTEEQKSERIDKFLAGVNNEWSRSQVQQWIKDGVVTVNGNDIKGNYKVKVND 60

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V IP          +E  IL   +NL          + YED+ + V NKP G+ V  
Sbjct: 61  EIAVAIPDP--------EELDILPEDMNLE---------IYYEDADVLVVNKPRGMVVHP 103

Query: 122 GSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L     
Sbjct: 104 APGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLV 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD----YVHVVKQNEKGANYAISHFK 231
            + + + Y ++V G+  + K  I       + IG D        V +N K   +A++HF+
Sbjct: 164 AKTVTRRYKAIVHGVIPHDKGTI------DAPIGRDKKDRQSMTVDENGK---HAVTHFQ 214

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V++ F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LH
Sbjct: 215 VLERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDI-----NGQALH 268

Query: 292 ARYMDLPHPEGGR-LQITAPLPA 313
           A  +   HP  G  ++  AP+PA
Sbjct: 269 AGILGFDHPRTGEYIEFEAPVPA 291


>gi|215919036|ref|YP_338280.2| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           RSA 493]
 gi|206583921|gb|AAZ22628.2| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           RSA 493]
          Length = 327

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 89/333 (26%), Positives = 156/333 (46%), Gaps = 39/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   +++  Q + I  
Sbjct: 15  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEA 74

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 75  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 119

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            I+  L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y +
Sbjct: 120 LINALLH-YDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           +V G+  + +         ++ +G   +H  +    +    AI+HF++I  + +    + 
Sbjct: 179 IVKGVLISGRTI-------EAPVGRHPIHRTRMAVVEFGRPAITHFRIIKRY-RAHTHIR 230

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKL------YLHARYMD 296
           +Q  TGRTHQ+RVH  H+  P+ GD  Y ++     + + P+Q  L       LHA  + 
Sbjct: 231 VQLETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHAATLQ 290

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             HP   R +   APLPA M    + L   Y +
Sbjct: 291 FSHPVDQRPMACHAPLPADMAHLLECLEDDYSQ 323


>gi|228998673|ref|ZP_04158260.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus mycoides
           Rock3-17]
 gi|228761141|gb|EEM10100.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus mycoides
           Rock3-17]
          Length = 302

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 89/323 (27%), Positives = 152/323 (47%), Gaps = 45/323 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++ G V V+   +K N +++   
Sbjct: 1   MSEVVQVTVTEEQKSERIDKFLAGVNNEWSRSQVQQWIKDGVVTVNGNAIKGNYKVKVND 60

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V IP          +E  IL   +NL          + YED+ + V NKP G+ V  
Sbjct: 61  EIAVAIPDP--------EELDILPEDMNLE---------IYYEDADVLVVNKPRGMVVHP 103

Query: 122 GSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L     
Sbjct: 104 APGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLV 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD----YVHVVKQNEKGANYAISHFK 231
            + + + Y ++V G+  + K  I       + IG D        V +N K   +A++HF+
Sbjct: 164 AKTVTRRYKAIVHGVIPHDKGTI------DAPIGRDKKDRQSMTVDENGK---HAVTHFQ 214

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V++ F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LH
Sbjct: 215 VLERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDI-----NGQALH 268

Query: 292 ARYMDLPHPEGGR-LQITAPLPA 313
           A  +   HP  G  ++  AP+PA
Sbjct: 269 AGILGFDHPRTGEYIEFEAPVPA 291


>gi|229588326|ref|YP_002870445.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens SBW25]
 gi|229360192|emb|CAY47049.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens SBW25]
          Length = 320

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 89/341 (26%), Positives = 153/341 (44%), Gaps = 52/341 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G ++ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVHGGAILELTAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    + +   LD               ++YED  I V NKPAG+ V   +G   H DG
Sbjct: 71  EAQGEWVAQDIELD---------------IVYEDDDILVINKPAGLVVHPAAG---HADG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  
Sbjct: 113 TLLNALLHHVPDIINVPRCGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKF 240
           +V G+           ++    I        +Q ++     G   A+SH++V++ F +  
Sbjct: 173 IVIGV-----------VVAGGKINAPIGRHGQQRQRMAVMEGGKQAVSHYRVLERF-RSH 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHA 292
             + ++  TGRTHQ+RVH  H+  P+VGD  Y   F+            ++   +  LHA
Sbjct: 221 THVRVKLETGRTHQIRVHMAHINFPLVGDPAYGGRFRIPPAASATMVESLKTFPRQALHA 280

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           R+++L HP  G R+   +PLP  +V  W     K DR  ++
Sbjct: 281 RFLELDHPTSGKRMSWESPLPDDLV--WLLSLLKQDREAFV 319


>gi|319937281|ref|ZP_08011688.1| pseudouridine synthase [Coprobacillus sp. 29_1]
 gi|319807647|gb|EFW04240.1| pseudouridine synthase [Coprobacillus sp. 29_1]
          Length = 305

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 93/330 (28%), Positives = 161/330 (48%), Gaps = 41/330 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++  +VE +++  R+D+         +   +Q ++++G V +D+K +K + ++++G+
Sbjct: 1   MEDIKIRIVE-EQKGQRIDKILAKELADFSRTQIQSLIQNGYVVIDEKPIKASYKVETGE 59

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
             +V IP        I+ E   LD               ++YED  + V NKP G+ V  
Sbjct: 60  DVIVYIPK--PESTDILPEDIPLD---------------VVYEDQDVIVINKPTGMIVHP 102

Query: 122 GSGI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             GI     ++  L    D  G     +P + HR+D+ETSG+L+VA+   A Q L++  +
Sbjct: 103 SIGIYSGTLVNALLYHCHDLSGINGVTRPGIVHRIDKETSGLLMVAKNDKAHQSLSKQLQ 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVI 233
              + + Y +LV G+  ++   I      ++ IG D     K    +K A  AI++FKVI
Sbjct: 163 EHTVTRRYLALVHGLIPHEFGRI------EAPIGRDKNDRQKMTCTDKNAKDAITNFKVI 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +    +E +  TGRTHQ+RVH  ++G P+ GD +Y    + + TS  Q   +LHA+
Sbjct: 217 ERF-RDMSLVECRLETGRTHQIRVHMQYIGYPVYGDPQY--GLRRDDTSHGQ---FLHAK 270

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            +   HP  G  +   + LP    K    L
Sbjct: 271 ILGFVHPRTGEEMYFESELPDFFEKKLQEL 300


>gi|15837541|ref|NP_298229.1| ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa 9a5c]
 gi|34395837|sp|Q9PET9|RLUD_XYLFA RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|9105864|gb|AAF83749.1|AE003933_1 ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa 9a5c]
          Length = 331

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 94/347 (27%), Positives = 159/347 (45%), Gaps = 42/347 (12%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L  + +   V +     R D      +P  +   L + ++SG V ++   V+  + +  G
Sbjct: 9   LAGFSRQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVRPRDPVYGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           +VVR+  V +     + +   LD               +LYED  ++V NKPAG+ V  G
Sbjct: 69  EVVRLQVVPDIRTDAVPQDIPLD---------------ILYEDEHVFVLNKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +     +    PR  + HRLD++TSG++VVART  A   L E    
Sbjct: 114 AG---NPDGTLVNALLHRDPALAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSS 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R++ + Y ++V  +         N  +++ H        V    K    A++H+++ + F
Sbjct: 171 RQVHRQYLAVV--VSALVSGGTVNAAIER-HPRDRLRMAVSDTGK---EAVTHYRLRERF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK----GNFTSPIQNKLY--- 289
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y  + K    G     +  + +   
Sbjct: 225 -RAHTALECRLDTGRTHQIRVHMAHLRHPIVGDRLYGGSLKLPKVGTDALVVMLRGFKRQ 283

Query: 290 -LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  ++  HP G   ++I AP+P  + +    L  + D  L+ +R
Sbjct: 284 ALHAEVLEFLHPVGALPVRIVAPVPEDLCQLLAVL--REDSALFFER 328


>gi|148545913|ref|YP_001266015.1| RluA family pseudouridine synthase [Pseudomonas putida F1]
 gi|148509971|gb|ABQ76831.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           putida F1]
          Length = 352

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 96/336 (28%), Positives = 149/336 (44%), Gaps = 42/336 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   V+  + +  G ++ +    
Sbjct: 43  VPSELGGQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLVHGGSLLALEAEQ 102

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    I E   LD               ++YED  I V NKPAG+ V   +G   H  G
Sbjct: 103 EAQGEWIAEDIELD---------------IVYEDDHILVINKPAGLVVHPAAG---HASG 144

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L E  + R++ +IY  
Sbjct: 145 TLLNALLHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTLQAQTKLVEQMQARKVSRIYEC 204

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+     +  A       H G      V     G   A+SH++V+  F +    + +
Sbjct: 205 IVIGVVTAGGKIDAPI---GRHGGMRQRMAVTD---GGKPAVSHYRVLKRF-RSHTHVRV 257

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKLYLHARYMDL 297
           +  TGRTHQ+RVH  H+G P+VGD  Y   F+     SP          +  LHAR++ L
Sbjct: 258 KLETGRTHQIRVHMAHVGFPLVGDQTYGGRFRIPPAASPTMVEAVKTFPRQALHARFLAL 317

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            HP  G  ++  +PLP   V  W       DR  +I
Sbjct: 318 AHPITGEVMKWESPLPDDFV--WLLSLLNQDRESFI 351


>gi|254467318|ref|ZP_05080729.1| ribosomal large subunit pseudouridine synthase D [Rhodobacterales
           bacterium Y4I]
 gi|206688226|gb|EDZ48708.1| ribosomal large subunit pseudouridine synthase D [Rhodobacterales
           bacterium Y4I]
          Length = 341

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 95/357 (26%), Positives = 153/357 (42%), Gaps = 64/357 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           +++V+ EN  +  RLD+      P    ++   L +++  G + VD   V+     + +G
Sbjct: 6   IEFVIAENPPK--RLDKAVSRDVPEEAALSRTRLARLIGEGALTVDGAVVQDPKANVAAG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V+ I       +HI  E   L+               +++ED  + V NKPAG+ V   
Sbjct: 64  AVIAIEVEEAEDSHIGPEDIPLE---------------IVFEDDDLIVINKPAGMVVHPA 108

Query: 123 SG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            G         + +H  G L      K  +P + HR+D+ETSG+LVVA++ AA Q L   
Sbjct: 109 PGSPSGTLVNALLHHFGGNLSGVGGVK--RPGIVHRIDKETSGLLVVAKSDAAHQGLAAQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECI----------ANWLLKKSHIGGDYVHVVKQNE--K 221
           F    +++ Y ++ +G+P      +           N L   +H+        +Q    +
Sbjct: 167 FEKHTVERYYQAICYGVPDGNDPRLRGVKGASFEPGNILKLTTHLARHKTDRQRQAVLFQ 226

Query: 222 GANYAISHFKVID------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           G  +A++  ++ +      C A   CWLE    TGRTHQ+RVH  H G  +VGD  Y   
Sbjct: 227 GGRHAVTRARICESFGNPPCAALIECWLE----TGRTHQIRVHMAHAGHSLVGDPTYGGR 282

Query: 276 FK---GNFTSPIQNKL------YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            K      +   Q  +       LHA  +   HP  G  L+  APLP  M +   +L
Sbjct: 283 RKLPAKALSEEAQEAVRAFPRQALHAAVLGFGHPVSGEPLRFEAPLPQDMAELLAAL 339


>gi|115522842|ref|YP_779753.1| RluA family pseudouridine synthase [Rhodopseudomonas palustris
           BisA53]
 gi|115516789|gb|ABJ04773.1| ribosomal large subunit pseudouridine synthase D [Rhodopseudomonas
           palustris BisA53]
          Length = 327

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 91/349 (26%), Positives = 156/349 (44%), Gaps = 65/349 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI- 67
           + V  DE  +RLDR      P ++   L+ ++ +G+V + +  +      + +G  + I 
Sbjct: 4   ITVAGDEGAVRLDRVLALRAPELSRSRLKALILAGRVAIGETPLCDPAYHVGAGDTITID 63

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            PP I A      E   LD               +++ED  I V +KP G+ V   +G  
Sbjct: 64  VPPAIAA--EPAGEPIALD---------------IVHEDDDIIVIDKPRGLVVHPAAG-- 104

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF--- 174
           +     + + +   G         ++P + HRLD++T+G++V A+   A Q L+  F   
Sbjct: 105 HETGTLVNALIAHCGASLSGIGGVRRPGIVHRLDKDTTGLMVAAKNDRAHQSLSAQFADH 164

Query: 175 -RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAIS 228
            R   +++ Y++ VWG+P      I   + +  H            EK     G   AI+
Sbjct: 165 GRTGALRRGYYAFVWGVPNRPHGTIDAPIDRHPH----------NREKMAVREGGRDAIT 214

Query: 229 HFKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
           H++V++ FA +        +  Q  TGRTHQ+RVH  H+G P++GD  Y  +FK   ++ 
Sbjct: 215 HWEVLETFAGRSGKPVASLIACQLETGRTHQIRVHLAHIGHPLLGDGVYGPHFKTKASAL 274

Query: 284 IQ---------NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
                       +  LHA  + L HP  G + + T+ LPA + K  ++L
Sbjct: 275 PPAARAALEALGRQALHAYLLVLEHPSSGEIREWTSDLPADLAKLQNAL 323


>gi|205373291|ref|ZP_03226095.1| YlyB [Bacillus coahuilensis m4-4]
          Length = 301

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 81/284 (28%), Positives = 138/284 (48%), Gaps = 33/284 (11%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +Q+ ++ G V V+ ++ + N + Q+  V+ I          + E ++LD        ++ 
Sbjct: 33  VQQWIKDGHVLVNMEQKRTNYKSQASDVITIE---------VPEAEVLDVE------AED 77

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRL 150
           L   + YED  + V NKP G+ V    G      ++G +    D  G     +P + HR+
Sbjct: 78  LNLDVYYEDQDVIVVNKPKGMVVHPAPGHYSGTLVNGLMHHCKDLSGINGVMRPGIVHRI 137

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+   A +HL      + + + Y +LV G+ ++    I   + + S    
Sbjct: 138 DKDTSGLLMVAKNDVAHEHLVNQLVEKSVTRKYMALVHGVIQHDYGTIDAPIGRDSK-DR 196

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             + +V Q      +A++HF+V D F Q +  +E Q  TGRTHQ+RVH  ++G P+VGD 
Sbjct: 197 QSMTIVDQ----GKHAVTHFEVKDRFEQ-YTLVECQLETGRTHQIRVHMKYIGFPLVGDP 251

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           KY      +          LHA  +   HP     L+ TAP+P+
Sbjct: 252 KYGPKKTMDIGGQA-----LHAAVLGFIHPRTEEYLEFTAPIPS 290


>gi|330945483|gb|EGH47033.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. pisi str. 1704B]
          Length = 176

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 66/179 (36%), Positives = 103/179 (57%), Gaps = 10/179 (5%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG+L++A+ R+  +HL E+ R   + K Y +LV G      + +   L+K + 
Sbjct: 1   HRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMALVRGNWATALKQVRAPLMKSNL 60

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             G+   +V+ NE+G   A++ FKV+  F      +E +P TGRTHQ+RVH LH G  I 
Sbjct: 61  RSGE--RMVEVNEEGKE-ALTIFKVLRRFGDFATMVEAKPVTGRTHQIRVHTLHAGHAIA 117

Query: 268 GDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           GD KY      NF+  I++    +L+LHA  + +P P+G +L + AP+     KT + L
Sbjct: 118 GDTKYGDE---NFSREIRDLGGKRLFLHAYMLTVPMPDGSKLNVQAPVDDMWAKTVERL 173


>gi|288800657|ref|ZP_06406114.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 299 str. F0039]
 gi|288332118|gb|EFC70599.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 299 str. F0039]
          Length = 358

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 95/334 (28%), Positives = 155/334 (46%), Gaps = 58/334 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V +  ++ +R+D++      H +   +QK   +G V V+ + VK N +I+   VV +  
Sbjct: 28  IVADEGQKPLRVDKFMFEKLQHSSRNRIQKAAEAGFVHVNDQPVKSNYKIRPNDVVTL-- 85

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I   ++ L          ++YED+++ V NKPAG+ V  G G     
Sbjct: 86  ---MLDRPRHDNTIEAENIPLD---------IVYEDAELLVVNKPAGLVVHPGVGNFHGT 133

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H+        D+   +  L HR+D++TSG+LVVA+T  A   L   F  +   
Sbjct: 134 LINAVAWHMKD--DKNFDANSPEVGLVHRIDKDTSGLLVVAKTPNAKTKLGVQFFNKTTT 191

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVID 234
           + Y +LVWG I +++     N       IG D      + V   +      A++H+KVI+
Sbjct: 192 RSYKALVWGHIAEDEGRIEGN-------IGRDPKDRQRMTVFSPDSGIGKPAVTHYKVIE 244

Query: 235 CFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQ 285
            F       C LE    TGRTHQ+R H  H+G P+ GD +Y        N   ++ S +Q
Sbjct: 245 RFGYTTLIECILE----TGRTHQIRAHMKHIGHPLFGDERYGGKEILRGNRSSSYKSFVQ 300

Query: 286 N------KLYLHARYMDLPHPEGGR-LQITAPLP 312
           N      +  LHA+ +   HP   +    T+PLP
Sbjct: 301 NCFNICDRQALHAQTLGFVHPTTQKECHFTSPLP 334


>gi|222054177|ref|YP_002536539.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
 gi|221563466|gb|ACM19438.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
          Length = 298

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 84/323 (26%), Positives = 151/323 (46%), Gaps = 40/323 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           V  +   MRLD   +  +P ++   +++I+  G   +    V+  +R ++ G ++ +   
Sbjct: 7   VSAELAGMRLDDGARQLFPELSKTQIRRIIDWGGCTISDALVRVASRQLREGDLISL--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----SGI 125
                 +++ ++ ++ +        + K  LLYED      NK AG++ Q         +
Sbjct: 64  -----GVMEPERCVEIT--------YGKGDLLYEDGGYLAINKAAGLNSQRTPYQLKGTV 110

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            Y +D +LKS + SK +  R+ HRLD+ TSG++   + + AA H++   +  +++K+YW+
Sbjct: 111 EYAVDCYLKS-LGSK-EPARVIHRLDRGTSGVMFFPKHKKAATHISFLLKEGKVEKVYWA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV  +P+  +  +   + K +     Y   +   E     A + F+VI    +    +E 
Sbjct: 169 LVADVPEQDQWTVDAPIAKLNKF--RYGVALPGRE-----ARTAFRVITA-GKGATLIEA 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            P TGRTHQ+RVH  H G PI+GD  Y     G   +P   ++ LH R M     EG  +
Sbjct: 221 HPFTGRTHQIRVHLAHNGLPIIGDATY-----GGDHAP---RMMLHCRTMAFTSREGKEI 272

Query: 306 QITAPLPAHMVKTWDSLGFKYDR 328
             TAP      +     G + D+
Sbjct: 273 SATAPPDEAFRQVCRDFGIEIDQ 295


>gi|332877311|ref|ZP_08445059.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
 gi|332684694|gb|EGJ57543.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
          Length = 362

 Score =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 93/341 (27%), Positives = 157/341 (46%), Gaps = 64/341 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIP 68
           +  ++ ++ MR+D++   H  + +   LQ+      + V+ + VK + +++   ++V + 
Sbjct: 36  LTADSGQKPMRIDKFLMEHLYNTSRNRLQRAAEQEFILVNGRPVKSSYKVKPLDEIVILL 95

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
                 N II E   LD               ++YED  + V +KPAG+ V  G G    
Sbjct: 96  DRPKYDNEIIAEDIPLD---------------IVYEDEDLMVVDKPAGLVVHPGCGNYTG 140

Query: 125 -----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                IA+H    LK   D     P   L HR+D++TSG+LVVA+   A  HL + F  +
Sbjct: 141 TLVNAIAWH----LKDNPDYDPNDPTVGLVHRIDKDTSGLLVVAKNADAKTHLGKQFFNK 196

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------VVKQNEKGANYAIS 228
             +++Y +LVWG          N+  ++  I G+            V   + +   +A++
Sbjct: 197 TTKRLYNALVWG----------NFQEEEGRIEGNIARHPKDRMQMAVFPPDSEIGKHAVT 246

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTS 282
           H++V++ F      +E +  TGRTHQ+R H  H+G P+  D +Y  N   +G     +  
Sbjct: 247 HYRVLENF-NYVTLVECRLETGRTHQIRAHMKHIGHPLFNDERYGGNEILRGTQFSKYKQ 305

Query: 283 PIQN------KLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
            IQN      +  LHAR +   HP  G+ +  T+ LPA M 
Sbjct: 306 FIQNCFAVCPRQALHARTLGFIHPRSGQEMYFTSELPADMT 346


>gi|294085882|ref|YP_003552642.1| pseudouridine synthase [Candidatus Puniceispirillum marinum
           IMCC1322]
 gi|292665457|gb|ADE40558.1| pseudouridine synthase, RluA family [Candidatus Puniceispirillum
           marinum IMCC1322]
          Length = 341

 Score =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 78/255 (30%), Positives = 121/255 (47%), Gaps = 28/255 (10%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGFLKSWVDSKG 141
           L   V+ T  ++ +   +LYED+ I V NKPAG+ V    GS     ++  +    DS  
Sbjct: 78  LPPPVDATPKAENIPLDVLYEDAHIIVLNKPAGMVVHPAPGSLTGTLVNALIAHCGDSLT 137

Query: 142 -----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                 +P + HRLD++TSG+++ A+T AA   LT  F    + + Y +LVWG   ++  
Sbjct: 138 GIGGVMRPGIVHRLDKDTSGVMMAAKTDAAHHTLTSMFAAHDLDRRYHALVWGTGVDRDG 197

Query: 197 CIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            +   L + +H         KQ  N +G  +AI+H++V+         +E    TGRTHQ
Sbjct: 198 MVDAPLGRSTH------DRKKQAVNPRG-RHAITHWRVMRTLPPFGSLVECTLETGRTHQ 250

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-----------NKLYLHARYMDLPHP-EG 302
           +RVH  H+G P++GD  Y    +       +           N+  LHA ++   HP  G
Sbjct: 251 IRVHMAHIGYPVIGDPLYGRAPRAGQMPDTRARTGLAQMRAFNRQALHAAHLGFEHPITG 310

Query: 303 GRLQITAPLPAHMVK 317
             L  TAP+P  M  
Sbjct: 311 EALAFTAPMPPDMAS 325


>gi|163814069|ref|ZP_02205461.1| hypothetical protein COPEUT_00222 [Coprococcus eutactus ATCC 27759]
 gi|158450518|gb|EDP27513.1| hypothetical protein COPEUT_00222 [Coprococcus eutactus ATCC 27759]
          Length = 304

 Score =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/324 (26%), Positives = 151/324 (46%), Gaps = 39/324 (12%)

Query: 12  VENDEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +E+ EE  + RLD+    ++   +   ++K+   G + V+ K VK + ++++G ++ I  
Sbjct: 6   LESSEEWTDRRLDKVLSEYFDGYSRSFIKKLFDDGLILVNSKAVKPSYKVRAGDMIDISV 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
                  I+ E   LD               ++YED  + + NKP G+ V          
Sbjct: 66  PDPVSIDIVPEDIPLD---------------IIYEDDDVILVNKPKGMVVHPAPGHYSGT 110

Query: 123 --SGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             +G+ YH   F  S     G+ +P + HR+D +T+G+LVV +   A + L+E      I
Sbjct: 111 LVNGLMYH---FGSSLSGINGEFRPGIVHRIDMDTTGVLVVCKNDNAHRALSEQLHEHSI 167

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y+++V+G   + +  +   + +      D   +   N  G   A++H++V++ F  +
Sbjct: 168 TRKYYAIVYGNISSDEGTVDAPIGRSPK---DRKKMAINNRNGRR-AVTHYRVLERFGGR 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           + ++E Q  TGRTHQ+RVH   +G PI+GD  Y    K  F    Q    LHA  +   H
Sbjct: 224 YTYIECQLETGRTHQIRVHMASIGHPILGDEVYGPK-KCPFKLQGQT---LHAGVLGFIH 279

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G  ++  A LP +     + L
Sbjct: 280 PSTGEYVEFKAELPEYFKAVLEKL 303


>gi|189423553|ref|YP_001950730.1| pseudouridine synthase [Geobacter lovleyi SZ]
 gi|189419812|gb|ACD94210.1| pseudouridine synthase, RluA family [Geobacter lovleyi SZ]
          Length = 326

 Score =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 150/320 (46%), Gaps = 39/320 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD +       ++   +Q+++  GQV + + + + + ++  G+ + +  
Sbjct: 8   IEVPAEAAGQRLDAFLATRLTDLSRAAVQRLIDDGQVLLTEGKPRSSMKLAGGEQITVEI 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
              A    + EQ  LD               +LYED  + V NK AG++V  G+G+    
Sbjct: 68  PPPAPAVPLAEQIPLD---------------VLYEDHDLIVINKSAGMTVHPGAGVDSGT 112

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HRLD+ TSG+LVVA+   A + L E F    I+++Y
Sbjct: 113 LVNALLGHCTDLSGIGGEIRPGIVHRLDKGTSGVLVVAKNDIAHRGLAEQFAAHSIKRLY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+L++G P      ++N + +      D + +  + + G   A ++++V++ F      +
Sbjct: 173 WALIYGSPNEDTGKVSNSIGRHPT---DRLRMSGKAKHGKE-ATTNWRVLERFGAA-SLV 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----------YLHAR 293
           +++  TGRTHQ+RVH      P++GD  Y     G F +    +L           LHAR
Sbjct: 228 QLRLETGRTHQIRVHLSEANMPLLGDPLYPDG--GRFNNLKDTRLKGMISHLGRQALHAR 285

Query: 294 YMDLPHPEGGR-LQITAPLP 312
            +   HP  G+ L+ ++  P
Sbjct: 286 VLGFIHPLTGQYLEFSSEPP 305


>gi|332992387|gb|AEF02442.1| ribosomal large subunit pseudouridine synthase D [Alteromonas sp.
           SN2]
          Length = 327

 Score =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 86/313 (27%), Positives = 152/313 (48%), Gaps = 39/313 (12%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+   + +P  +   L+  ++ G V VD            GQV+ +P     ++ +
Sbjct: 20  GLRLDQVLADLFPEYSRSKLKTWIQGGNVSVD------------GQVITVPRHKMQMDEV 67

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW 136
           +     ++  + +T  +  +   ++YED  I V NK A + V  G+G  +  +   L + 
Sbjct: 68  VTVSAEIE--IQVTSQAQDIALDIVYEDEHILVINKSADLVVHPGAGNPSGTVLNALLNH 125

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           V    + PR  + HRLD++T+G++VVA+T  A  HL +  + R + + Y ++  G     
Sbjct: 126 VPDIDKVPRAGIVHRLDKDTTGLMVVAKTLPAQTHLVDQLQTRVMSREYEAVAMGTMVAG 185

Query: 195 ---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
               E I     K++H+       V++N K    A++HF+VI+ F + +  L ++  TGR
Sbjct: 186 GVVDEPIGRHATKRTHMA------VRENGKP---AVTHFRVIEKF-RAYTHLRLKLETGR 235

Query: 252 THQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDLPHPEGG 303
           THQ+RVH  H+  P++GD  Y    +       +F + ++   +  LHA  + L HPE  
Sbjct: 236 THQIRVHMAHIKHPLLGDPTYSGRPRLPKGASDDFVNTLRGFQRQALHAAQLSLYHPETE 295

Query: 304 R-LQITAPLPAHM 315
             +   APLP  M
Sbjct: 296 EWMTWQAPLPQDM 308


>gi|294785400|ref|ZP_06750688.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_27]
 gi|294487114|gb|EFG34476.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_27]
          Length = 290

 Score =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/308 (27%), Positives = 156/308 (50%), Gaps = 27/308 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++Y++ E D E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G +V 
Sbjct: 2   IEYIIDE-DYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDIVF 60

Query: 67  I--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           I  P      N    E+K ++  +N  +    LK ++++E+  ++V NK  G  V  GSG
Sbjct: 61  IFLPESFKENN----EKKFIE--LNQVRKEK-LKQMIVFENENLFVINKSLGDVVHKGSG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +    +S+  +        +R+D+ TSG+++ A+     + + +  +   I K Y+
Sbjct: 114 HDISLLEEFRSYYSNNN--INFVNRIDRLTSGLVIGAKNIKTTREIAKEIQQGNIIKKYF 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  +     + N+L K      + V V    ++G   +I++FK I  +  ++  LE
Sbjct: 172 ILVNGKIEKDNFILENYLKKDE----EKVIVSDIEKEGYKKSITYFKKIKEY-DRYTLLE 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQLR    H+G  IVGD KY  N K       ++ +YL + Y+ +       
Sbjct: 227 AELKTGRTHQLRAQLNHIGNNIVGDTKYGRNEK-------EDIMYLFSYYLKIDLY---N 276

Query: 305 LQITAPLP 312
           L+I   +P
Sbjct: 277 LEIKLEIP 284


>gi|313123676|ref|YP_004033935.1| pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
 gi|312280239|gb|ADQ60958.1| Pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
          Length = 304

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 81/296 (27%), Positives = 151/296 (51%), Gaps = 32/296 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++       ++   +++++++G+V V+ K+ K + ++Q G ++++  +    
Sbjct: 10  EESGQRLDKYLAGEMTDLSRSRIKELVQAGEVLVNGKKSKVSYKVQKGDLIQVTVLPLEP 69

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGF 132
             +  E   LD               ++YED  I V NKP G+ V   +G   H  ++  
Sbjct: 70  LKLEAENIPLD---------------IVYEDEDIIVVNKPQGMVVHPAAGHPSHTLVNAL 114

Query: 133 L---KSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L   +   DS +G +P + HR+D++TSG+L+VA+  AA + L +    +  ++ Y ++V 
Sbjct: 115 LYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVH 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G    ++E   +  + ++      + VV   EKG + A++HFKV++ + Q +  +E Q  
Sbjct: 175 G-NFAEEEGTIDAPIGRNPKDRKQMAVV---EKGKS-AVTHFKVLEQY-QGYSLVECQLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           TGRTHQ+RVH  ++G P+ GD  Y        T P   + +LHA+ +    P  G 
Sbjct: 229 TGRTHQIRVHMAYIGHPLAGDPLYGP----RKTLPGHGQ-FLHAKTLGFEQPSTGE 279


>gi|257413410|ref|ZP_04742958.2| ribosomal large subunit pseudouridine synthase family protein
           [Roseburia intestinalis L1-82]
 gi|257203607|gb|EEV01892.1| ribosomal large subunit pseudouridine synthase family protein
           [Roseburia intestinalis L1-82]
          Length = 221

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 69/210 (32%), Positives = 111/210 (52%), Gaps = 8/210 (3%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++  ++YED  I V  KPAG++ Q        ++  LK++  SKG+ P +   HRLDQ  
Sbjct: 5   MQPAIIYEDEDIIVCKKPAGVATQTRRIGQADMESLLKNYRASKGELPYIGVVHRLDQPV 64

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            GI+V A+ + AA  L+   + +   K Y+++  G+P+ KK  + + LL+      +   
Sbjct: 65  EGIMVFAKNKEAAADLSRQIKTKLADKYYYAMTDGVPEKKKGTLEDELLQNGKT--NTSE 122

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV++    A +A   ++V++    K   L ++  TGR HQ+RV   H G PIVGD KY  
Sbjct: 123 VVERGTPQAKHASLSYEVVEQDG-KHAVLRIKLDTGRHHQIRVQLAHAGMPIVGDKKY-- 179

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           NFK N  +P   +L L +  +   HP+  R
Sbjct: 180 NFKENI-APSGGQLALCSFKIAFRHPKTHR 208


>gi|21232518|ref|NP_638435.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. ATCC 33913]
 gi|66767398|ref|YP_242160.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. 8004]
 gi|34395783|sp|Q8P682|RLUD_XANCP RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|21114309|gb|AAM42359.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. ATCC 33913]
 gi|66572730|gb|AAY48140.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. 8004]
          Length = 331

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 90/347 (25%), Positives = 155/347 (44%), Gaps = 40/347 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L + ++  VV +     R D      +P  +   L + ++SG   +D +  +  + ++ G
Sbjct: 9   LDSSLRQAVVPDSAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGETARPRDTLRGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +   L+               +LYED  + V +KPAG+ V  G
Sbjct: 69  ETVQVQVVLETQTHAAPQDIPLN---------------VLYEDDHVLVIDKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +     +    PR  + HRLD++TSG++VVART  A   L E    
Sbjct: 114 AG---NPDGTLVNALLFRDPNLAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSA 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + + Y ++V G   +     A       H        V+ + +    A++H+++ + F
Sbjct: 171 RDVHRQYLAVVVGALVSGGTADAPI---DRHPRDRLKMAVRDDGRD---AVTHYRLRERF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------ 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y    K     T  +  +L      
Sbjct: 225 -RAHTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDTLVAELRGFKRQ 283

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  ++  HP  G  ++ +AP+P  + +   +L     R   + R
Sbjct: 284 ALHAETLEFLHPVSGEPIRASAPVPEDLQRLMSALREDSARAAELAR 330


>gi|255036339|ref|YP_003086960.1| pseudouridine synthase, RluA family [Dyadobacter fermentans DSM
           18053]
 gi|254949095|gb|ACT93795.1| pseudouridine synthase, RluA family [Dyadobacter fermentans DSM
           18053]
          Length = 343

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/326 (26%), Positives = 149/326 (45%), Gaps = 43/326 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP- 68
           +V +  +  MRLD++   H  + +   +Q  + +  VRV+ +  K + +++   VV +  
Sbjct: 21  IVADKGQSLMRLDKYLNLHVANASRTKIQNGIEAEAVRVNGQPTKASYKVKPFDVVTLSL 80

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------ 122
           P       II E   LD               ++YED  + + NK AG+ V         
Sbjct: 81  PQPPRDTEIIPENLPLD---------------IIYEDDVLLIVNKAAGMVVHPAFGNWTG 125

Query: 123 ---SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              +G+ YH    L +  + +G +P L HR+D++TSG+LV+A+T  A   L   F    I
Sbjct: 126 TLINGLVYHFQQ-LPTGRNGEG-RPGLVHRIDKDTSGLLVIAKTEFAMTFLASQFADHSI 183

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +L+WG PK +K  I   + + +      V  V  +     +A++H++VI    + 
Sbjct: 184 ERTYHALIWGEPKAEKGTITGHVGRSAR--DRRVMDVYVDGSQGKHAVTHYEVIKPL-RY 240

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQNKL----- 288
              ++    TGRTHQ+R H  H+G PI  D  Y  +        G+F + ++N       
Sbjct: 241 VSLIKCNLETGRTHQIRAHMKHIGHPIFNDPMYGGDKILRGGSSGSFKAMVENAFGLISG 300

Query: 289 -YLHARYMDLPHPEGGR-LQITAPLP 312
             LHA+ +   HP   + +Q    LP
Sbjct: 301 QALHAKSLGFIHPTTRKWIQFDTELP 326


>gi|212691724|ref|ZP_03299852.1| hypothetical protein BACDOR_01219 [Bacteroides dorei DSM 17855]
 gi|212665729|gb|EEB26301.1| hypothetical protein BACDOR_01219 [Bacteroides dorei DSM 17855]
          Length = 358

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 94/337 (27%), Positives = 154/337 (45%), Gaps = 49/337 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           VVV+  +  +R+D++      + +   +QK   +G +  + K VK + +++   V+ +  
Sbjct: 33  VVVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKSSYKVKPCDVLTVMM 92

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
             P  +  N II E   LD               ++YED+ + V NKPAG+ V  G G  
Sbjct: 93  DRPRYD--NDIIPEDIPLD---------------IVYEDNDLMVINKPAGLVVHPGCGNY 135

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  IA+H+        D    +  L HR+D++TSG+LVVA+T  A  HL   F  +
Sbjct: 136 HGTLVNAIAWHLKD--NPRYDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNK 193

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCF 236
             ++ Y +LVWGI +N +  I   + +      D + + V  +     +A++H++V++  
Sbjct: 194 TTKRKYNALVWGIVENNEGTIEGNIGRNPK---DRMQMAVLSDPAQGKHAVTHYRVLERL 250

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN-------- 286
                 +E    TGRTHQ+RVH  H+G  +  D +Y  N   KG   S  +         
Sbjct: 251 GY-VTLVECVLETGRTHQIRVHMKHIGHTLFNDERYGGNEILKGTHFSKYKQFVNNCFET 309

Query: 287 --KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
             +  LHA  +   HP  G  +  T+PLP  M    D
Sbjct: 310 CPRQALHAMTLGFVHPRTGEEMFFTSPLPEDMTNLID 346


>gi|239826543|ref|YP_002949167.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239806836|gb|ACS23901.1| pseudouridine synthase, RluA family [Geobacillus sp. WCH70]
          Length = 304

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/310 (28%), Positives = 146/310 (47%), Gaps = 36/310 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ + +N R+D+         +   +Q+ ++ G V V+ + VK N +  +G VV +    
Sbjct: 8   IDAEYDNERIDKVIAALNEEWSRSKVQQWIKDGLVTVNDQHVKANYKSSAGDVVVVRLPE 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
               H++ E   LD               + YED+ + V NKP G+ V    G      +
Sbjct: 68  PEPLHVVPENIPLD---------------IYYEDADVLVVNKPRGMVVHPAPGHMRGTLV 112

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSG+L+VA+   A Q L +    + + + Y +
Sbjct: 113 NALLAHCTDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDMAHQSLVDQLVKKTVTRKYKA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWL 243
           +V G+  +    I       + IG D     K    E+    A++HF+V++ F + + ++
Sbjct: 173 IVHGVIPHDYGTI------DAPIGRDKRDRKKMTVTEENGKEAVTHFRVLERF-RHYTFV 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E Q  TGRTHQ+RVH  ++G P+ GD +Y        T PI  +  LHA  +   HP  G
Sbjct: 226 ECQLETGRTHQIRVHMKYIGYPLAGDPQYGP----KKTLPIDGQA-LHAGVLGFTHPRTG 280

Query: 304 R-LQITAPLP 312
             L+  APLP
Sbjct: 281 EYLEFEAPLP 290


>gi|74316828|ref|YP_314568.1| ribosomal large subunit pseudouridine synthase D [Thiobacillus
           denitrificans ATCC 25259]
 gi|74056323|gb|AAZ96763.1| pseudouridine synthase, RluD [Thiobacillus denitrificans ATCC
           25259]
          Length = 318

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/313 (27%), Positives = 144/313 (46%), Gaps = 32/313 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ +V+ + +  +RLD+      P  +   +Q  +R+ ++ VD        ++  G+ VR
Sbjct: 13  VRELVIPDAQGGLRLDQALSALLPEFSRNRIQNWIRARKIVVDDAWGTTKMKVSGGESVR 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +              ++           + +   ++YEDS + V NKP G+ V  GSG  
Sbjct: 73  V--------------QVEPDPGATPDAPEAIPLDVVYEDSMLLVINKPVGLVVHPGSG-- 116

Query: 127 YHIDGFLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            + DG L +     V    + PR  + HRLD++TSG+LVVA+T  A   L    + R ++
Sbjct: 117 -NRDGTLLNALLHRVPQVAELPRAGIVHRLDKDTSGLLVVAKTLRAHTDLVRQLQARTVK 175

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV+G         A       +     VH + +       A++H+ V++ F    
Sbjct: 176 REYLALVYGEVDRGGTVDAPLARDPHNRTKRTVHSLGKE------AVTHYDVVERFP-GI 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L  +  TGRTHQ+RVH  H+G P+VGD  Y A+ + +   P   +  LHA  + L HP
Sbjct: 229 TLLRCKLETGRTHQIRVHMQHVGHPLVGDTVYSASRRSHLKIPFPRQ-ALHAEKLGLIHP 287

Query: 301 EGGR-LQITAPLP 312
             G  +    PLP
Sbjct: 288 VTGEFVHWECPLP 300


>gi|71898901|ref|ZP_00681068.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|71731313|gb|EAO33377.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
          Length = 328

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 93/344 (27%), Positives = 159/344 (46%), Gaps = 42/344 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           + +   V +     R D      +P  +   L + ++SG V ++   V+  + +  G+VV
Sbjct: 9   FSRQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVRPRDPVYGGEVV 68

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+  V +     + +   LD               +LYED  ++V NKPAG+ V  G+G 
Sbjct: 69  RLQVVPDIRTDAVPQDIPLD---------------ILYEDEHVFVINKPAGLVVHPGAG- 112

Query: 126 AYHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             + DG L + +     +    PR  + HRLD++TSG++VVART  A   L E    R++
Sbjct: 113 --NPDGTLVNALLHRDPALAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSSRQV 170

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V  +         N  +++ H        V    K    A++H+++ + F + 
Sbjct: 171 HRQYLAVV--VSALVSGGTVNAAIER-HPRDRLRMAVSDTGK---EAVTHYRLRERF-RA 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQ-----NKLYLH 291
              LE +  TGRTHQ+RVH  H+  PIVGD  Y  +    KG   + +       +  LH
Sbjct: 224 HTALECRLDTGRTHQIRVHMAHLRHPIVGDRLYGGSLKLPKGGTDALVVMLRGFKRQALH 283

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           A  ++  HP G   ++I AP+P  + +   +L  + D  L+ +R
Sbjct: 284 AEVLEFLHPVGALPVRIVAPVPEDLCQLLAAL--REDSVLFFER 325


>gi|326933214|ref|XP_003212702.1| PREDICTED: tRNA pseudouridine synthase 3-like [Meleagris gallopavo]
          Length = 710

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 77/248 (31%), Positives = 123/248 (49%), Gaps = 40/248 (16%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQ 152
           L+  ++Y++ ++ V NKP G+ V GG G+   I   L    K  ++ K +   L HRLD+
Sbjct: 440 LRQRIVYQNEELVVLNKPYGLPVHGGPGVKNCIADVLPILAKMLMNMKAEPLHLCHRLDK 499

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----------IPKNKKECIANWL 202
           ET+G++V+AR+R  A  +   F+ R+++KIYW++  G          IP  ++E  ++  
Sbjct: 500 ETTGLMVLARSREVADRIRLLFKTRQVEKIYWAISVGSPDPAEGIVEIPMVEREVQSHQP 559

Query: 203 LKKSHIGGDY--------VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             K  +  +Y        V  +++N    N A++ ++V+   +     LE+QP TG  HQ
Sbjct: 560 HYKMTLAPNYRMSPEDGKVLKIRKNRNAEN-AVTRYRVL-ATSSACSLLELQPITGVKHQ 617

Query: 255 LRVH-ALHMGCPIVGDHKYC---------------ANFKGNFTSPIQNKLYLHARYMDLP 298
           LRVH A  +GCPI+GDHKY                   K   +      L+LHA  + LP
Sbjct: 618 LRVHLAYGLGCPILGDHKYSHWSKLAPQKLPEITLKRLKLQQSKSRHLPLHLHAYRLSLP 677

Query: 299 HPEGGRLQ 306
              GG  Q
Sbjct: 678 LGTGGSKQ 685


>gi|118586926|ref|ZP_01544359.1| pseudouridylate synthases, 23S RNA-specific [Oenococcus oeni ATCC
           BAA-1163]
 gi|118432653|gb|EAV39386.1| pseudouridylate synthases, 23S RNA-specific [Oenococcus oeni ATCC
           BAA-1163]
          Length = 308

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 90/307 (29%), Positives = 150/307 (48%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHI 77
           RLD+     +   +   ++K++   +V V+ K V     +Q G   V+++PPV       
Sbjct: 21  RLDKILATDFSAFSRNQIKKLIDQDRVIVNGKPVLAKYLVQDGDHVVIKVPPV------- 73

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKS 135
            K+ ++L   + L          ++YED  + V NKP G+ V   +G + H  ++  L  
Sbjct: 74  -KKTELLPEKIPLD---------IVYEDDDLIVVNKPQGMVVHPSAGHSEHTLVNALLSH 123

Query: 136 WVDS--KGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              S   G+ +P + HR+D++TSG+L+VA+   A +HL+   +  +  + Y ++V G   
Sbjct: 124 APLSTINGEFRPGIVHRIDKDTSGLLMVAKNNFAHEHLSLDLKSHKTGRKYLAIVHGNFS 183

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            K+  I      K+ I  D  +  KQ        AI+HFKV++ F+  +  +E    TGR
Sbjct: 184 EKRGTI------KAPIDRDPKNRQKQAVVANGREAITHFKVLESFSN-YSLIEAVLETGR 236

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P+ GD  Y        T P + + YL A  + L  P  G+ L  +AP
Sbjct: 237 THQIRVHMAYIGHPVAGDPLYGP----RKTLPGRGQ-YLFASSLSLTQPHTGKELSFSAP 291

Query: 311 LPAHMVK 317
           LP +  K
Sbjct: 292 LPDYFQK 298


>gi|265755351|ref|ZP_06090121.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_33FAA]
 gi|263234493|gb|EEZ20083.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_33FAA]
          Length = 358

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 94/337 (27%), Positives = 154/337 (45%), Gaps = 49/337 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           VVV+  +  +R+D++      + +   +QK   +G +  + K VK + +++   V+ +  
Sbjct: 33  VVVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKSSYKVKPCDVLTVMM 92

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
             P  +  N II E   LD               ++YED+ + V NKPAG+ V  G G  
Sbjct: 93  DRPRYD--NDIIPEDIPLD---------------IVYEDNDLMVINKPAGLVVHPGCGNY 135

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  IA+H+        D    +  L HR+D++TSG+LVVA+T  A  HL   F  +
Sbjct: 136 HGTLVNAIAWHLKD--NPRYDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNK 193

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCF 236
             ++ Y +LVWGI +N +  I   + +      D + + V  +     +A++H++V++  
Sbjct: 194 TTKRKYNALVWGIVENNEGTIEGNIGRNPK---DRMQMAVLSDPAQGKHAVTHYRVLERL 250

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN-------- 286
                 +E    TGRTHQ+RVH  H+G  +  D +Y  N   KG   S  +         
Sbjct: 251 GY-VTLVECVLETGRTHQIRVHMKHIGHTLFNDERYGGNEILKGTHFSKYKQFVNNCFET 309

Query: 287 --KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
             +  LHA  +   HP  G  +  T+PLP  M    D
Sbjct: 310 CPRQALHAMTLGFVHPRTGEEMFFTSPLPEDMTNLID 346


>gi|87309950|ref|ZP_01092084.1| ribosomal large subunit pseudouridine synthase [Blastopirellula
           marina DSM 3645]
 gi|87287714|gb|EAQ79614.1| ribosomal large subunit pseudouridine synthase [Blastopirellula
           marina DSM 3645]
          Length = 281

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 76/258 (29%), Positives = 134/258 (51%), Gaps = 33/258 (12%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           D  + +  H D     ++Y+D +I V NKPAG+      G   H  G L   +  KGQ P
Sbjct: 30  DEQIGVNVHLD-----IIYQDDRIAVINKPAGMITHPAKG---HWKGTLTEGL--KGQFP 79

Query: 145 RLT-----------HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +L+           HRLD++TSG++V+A+  AA + L   F+ R  +K Y+++V G P  
Sbjct: 80  QLSTIGGPTRPGIVHRLDRDTSGVIVIAKDDAAHEFLKTQFQDRLTEKEYFAMVIGAPDR 139

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            ++ I   +     I  + + + + +++G + A + ++V++ + Q F  ++  P TGRTH
Sbjct: 140 DRDLINEPVGPHPKI-RERMAIRRGDDEGKD-AQTFYEVLERY-QGFAAIKALPKTGRTH 196

Query: 254 QLRVHALHMGCPIVGDHKYCANF--------KGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           Q+RVH +H G P++ D  Y +            +  + + N+  LHA  + + HP+ G +
Sbjct: 197 QIRVHLMHAGHPVLCDPLYGSRRFLSLGELQHDDDRTVLLNRTALHAHRIAIAHPDDGEI 256

Query: 306 -QITAPLPAHMVKTWDSL 322
            +  APLPA + +T + L
Sbjct: 257 REFIAPLPADLERTQNML 274


>gi|146296933|ref|YP_001180704.1| RluA family pseudouridine synthase [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145410509|gb|ABP67513.1| ribosomal large subunit pseudouridine synthase D
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 300

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 89/315 (28%), Positives = 166/315 (52%), Gaps = 41/315 (13%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           RLD++         +FV  QKI+  G V V++ +V K   +++SG ++++         +
Sbjct: 9   RLDKYLSEALSKTRSFV--QKIIEEGNVWVNQSQVLKPAYKVKSGDIIKV---------V 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH 128
           I E K       L+  +  +   ++YED  + V NKP G+ V  G+G         + + 
Sbjct: 58  IPEPK------QLSLVAQDIDIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHK 111

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             G L S   +   +P + HRLD++TSG+L+VA+T  A   L+E+ +  +I++IY+++  
Sbjct: 112 FSGRLSSI--NGVIRPGIVHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICE 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+ K     I N  + +  +    + VV   ++    A+++F+V++ F  K+ +++++  
Sbjct: 170 GVLKEDSGVI-NAPIGRHPVNRLKMAVVPNGKE----AVTYFEVLERF-DKYTFIKLRLK 223

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  ++G P++GD  Y    K  F   +Q ++ LHA  ++  HP   + L  
Sbjct: 224 TGRTHQIRVHMSYIGYPLLGDSSY-GRAKNEFG--VQGQV-LHAGEIEFVHPITSKVLHF 279

Query: 308 TAPLPAHMVKTWDSL 322
           +A LP + ++  + L
Sbjct: 280 SADLPEYFLEILNIL 294


>gi|282850533|ref|ZP_06259912.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
 gi|282580026|gb|EFB85430.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
          Length = 307

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 93/315 (29%), Positives = 145/315 (46%), Gaps = 42/315 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  ++E MRLD +        +   +Q +++ G V V  K  K N R+    ++R+   
Sbjct: 5   IVSAEQEGMRLDVFLTEQMEG-SRSYIQSLIKGGHVTVGGKVGKANLRLTPDTIIRVEIP 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                 +  E   LD                LYED  I + NKP G+ V    G      
Sbjct: 64  EPESIEVKPEDIPLD---------------YLYEDHDIVIVNKPRGMVVHPAVGNYSGTL 108

Query: 129 IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D  G     +P + HRLD++TSG+++VA+  AA   L E  +    ++ YW
Sbjct: 109 VNALLFHCKDLSGINGEIRPGIVHRLDKDTSGVMMVAKNDAAHIGLAEQVKTHSARRTYW 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +LV G    +K  I      K+ IG        + VV +N K    A++HFKV++ +  +
Sbjct: 169 ALVQGNIVEEKGTI------KAPIGRHPKDRMKMAVVFENSKD---AVTHFKVLERYGHQ 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E    TGRTHQ+RVH  H+G P+V D  Y          PI+ +  LH++ +D+ H
Sbjct: 220 -TLVECNLETGRTHQIRVHFAHIGHPVVNDPFYGYR---RMDFPIEGQA-LHSKSLDVKH 274

Query: 300 P-EGGRLQITAPLPA 313
           P  G  +   AP+PA
Sbjct: 275 PITGEEMHFEAPIPA 289


>gi|327404084|ref|YP_004344922.1| ribosomal large subunit pseudouridine synthase D [Fluviicola
           taffensis DSM 16823]
 gi|327319592|gb|AEA44084.1| ribosomal large subunit pseudouridine synthase D [Fluviicola
           taffensis DSM 16823]
          Length = 342

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 88/330 (26%), Positives = 154/330 (46%), Gaps = 44/330 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E++R+D++  +  P+ +   +Q   +SG V V+   VK N +I+    V I      L 
Sbjct: 27  QESVRIDKYLLDRMPNTSRNKIQSAAKSGSVVVNGSSVKSNYKIKPKDEVTI-----VLP 81

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           + ++E +++   + +          ++YED ++ V NKP  + V  G G         + 
Sbjct: 82  YPVRELELIAQDIPID---------IVYEDDEVIVVNKPPNMVVHPGYGNYTGTLVNALV 132

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH D   +  +D  G +P L HRLD+ T+G++VVA+T  A  +L + F  R  ++ Y +L
Sbjct: 133 YHFDNLPERKLDYFG-RPGLVHRLDKHTTGVMVVAKTEDALTNLAKQFYDRTTERRYQAL 191

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           VWG  +       N  L +S      + V  + + G  +A++H KV+  +      +E +
Sbjct: 192 VWGDVEEDMRIEGN--LGRSLNNRKVMTVFPEGDYG-KHAVTHVKVLKRYGL-VTLIECK 247

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY------------LHARY 294
             TGRTHQ+R H    G P+  D +Y  +     T+  + K +            LHA+ 
Sbjct: 248 LETGRTHQIRTHLKWKGYPLFHDLEYGGDRIVRGTTHDKYKQFISNCFDLIPGQALHAKS 307

Query: 295 MDLPHPEGGRL-QITAPLP---AHMVKTWD 320
           +   HP+ G   Q    LP     +++ WD
Sbjct: 308 LGFQHPKTGEWKQFETDLPLGFQDLLQKWD 337


>gi|312135180|ref|YP_004002518.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           owensensis OL]
 gi|311775231|gb|ADQ04718.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           owensensis OL]
          Length = 300

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/314 (27%), Positives = 166/314 (52%), Gaps = 39/314 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLDR+            +QKI+  G V V++ +V K   ++++G ++++         +I
Sbjct: 9   RLDRYLSEALSKTRSF-IQKIIEEGNVWVNQTQVFKPAYKVRNGDIIKV---------VI 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E K       L+  +  +   ++YED  + V NKP G+ V  G+G         + +  
Sbjct: 59  PEPK------QLSLVAQDIDIDVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKF 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G L S   +   +P + HRLD++TSG+LVVA+T  A   L+E+ +  +I++IY+++  G
Sbjct: 113 SGRLSSI--NGVIRPGIVHRLDKDTSGLLVVAKTDEAHIKLSEALKSHQIKRIYYAICEG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           + K +   + +  + +  +    + VV   ++    A+++F+V++ F  K+ +++++  T
Sbjct: 171 VLK-EDSGVVDAPIGRHPVNRLKMAVVPNGKE----AVTYFEVLERF-DKYTFVKLRLKT 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P++GD+ Y    K  F   +Q ++ LHA  ++  HP   + L  +
Sbjct: 225 GRTHQIRVHMSYIGYPLLGDNTY-GRAKNEFG--VQGQV-LHAGEIEFVHPITSKVLHFS 280

Query: 309 APLPAHMVKTWDSL 322
           A LP + V+  + L
Sbjct: 281 ADLPEYFVEILNML 294


>gi|257126163|ref|YP_003164277.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
 gi|257050102|gb|ACV39286.1| pseudouridine synthase, RluA family [Leptotrichia buccalis
           C-1013-b]
          Length = 326

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/335 (25%), Positives = 158/335 (47%), Gaps = 49/335 (14%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +VV  +E   R+D++       +    +Q++++   + V++K+ K   +I+    +++
Sbjct: 24  ENIVVLKEEAGSRIDKFLSERL-ELTRTRIQQLIKDENILVNEKKTKPAYKIEENDTIKV 82

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
             VI  L  +    +I   ++++          ++YED+ + V NK AGI V   +G   
Sbjct: 83  --VIPELETV----EIKPENIDIE---------IIYEDNDLAVINKKAGIVVHPANGHYS 127

Query: 125 ------IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 I YHI    K      G+ +P + HRLD++TSG+L++A+   A   L++ F  +
Sbjct: 128 GTLVNAILYHI----KDLSGINGEIRPGIVHRLDKDTSGLLIIAKNDKAHLKLSQMFHDK 183

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH----VVKQNEKGANYAISHFKVI 233
            ++KIY +++ G    K   I       + IG D        V  +      AI++++VI
Sbjct: 184 TVKKIYLAILKGKLNQKSGRIV------TQIGRDKNDRKKMTVINDLNSGKTAITNYEVI 237

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
               +KF  +++   TGRTHQ+RVH  H+G PI+GD  Y         +  + +  LHA 
Sbjct: 238 -SQTEKFTLVKVHIETGRTHQIRVHMKHLGYPILGDSVYGR-------TDTEKRQMLHAY 289

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
            ++  HP     L+  A LP    K     G +++
Sbjct: 290 KLEFQHPITEENLEFIAKLPEDFKKALKKCGLEFE 324


>gi|302342169|ref|YP_003806698.1| pseudouridine synthase, RluA family [Desulfarculus baarsii DSM
           2075]
 gi|301638782|gb|ADK84104.1| pseudouridine synthase, RluA family [Desulfarculus baarsii DSM
           2075]
          Length = 317

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 89/301 (29%), Positives = 137/301 (45%), Gaps = 51/301 (16%)

Query: 35  VNLQKILRSGQVRVDKKRVKFNNRIQSGQV--VRIPPVINALNHIIKEQKILDSSVNLTK 92
             +Q++LR G V VD +  K   +++ GQ   VR+P          +  +++  +++L  
Sbjct: 32  AQVQRLLRDGLVLVDGQAAKAAQKLRPGQAIAVRLPDP--------EPSELIPMAMDLA- 82

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL--------KSWVDSKGQ-K 143
                   +L+ED  + + NKP G+ V    G   H +G L            +  G+ +
Sbjct: 83  --------ILHEDEDLIIINKPPGLVVHPSPG---HAEGTLVHGLLHHCGGLAEVGGKLR 131

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD++TSG LV A+   A + L   F   R+QK Y +LV G P  +         
Sbjct: 132 PGIVHRLDKDTSGALVAAKNDRAHRGLVARFAAGRVQKEYLALVHGRPAKRGRV------ 185

Query: 204 KKSHIG---GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             S IG   GD   +  Q  +    A+S ++V   F +    L +  HTGRTHQ+RVH  
Sbjct: 186 -DSGIGRHPGDRKRMSSQGSR-TKPALSQWRVCRSFGEA-SLLRVNIHTGRTHQIRVHLS 242

Query: 261 HMGCPIVGDHKYCANFK-GNFTSPIQNKL------YLHARYMDLPHPEGGR-LQITAPLP 312
             G P++GD  Y A  +      P+   L       LHA  +   HP   + + +TAPLP
Sbjct: 243 EAGHPVLGDQTYGARRRDAALPDPVAAALRQAGRQMLHAVVLSFEHPISAQIIHVTAPLP 302

Query: 313 A 313
           A
Sbjct: 303 A 303


>gi|66043991|ref|YP_233832.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           B728a]
 gi|63254698|gb|AAY35794.1| Pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           B728a]
          Length = 320

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 96/338 (28%), Positives = 154/338 (45%), Gaps = 46/338 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGALRPRDIVHGGAVLELIAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    + +   LD               ++YED +I V NKPAG+ V   +G   H DG
Sbjct: 71  EAQGEWVAQDIELD---------------IIYEDDQILVINKPAGLVVHPAAG---HADG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  
Sbjct: 113 TLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +V G+     +  A        IG  G     +   E G   A+SH++V++ F +    +
Sbjct: 173 IVIGVVTAGGKIDAP-------IGRHGQQRQRMAVME-GGKQAVSHYRVLERF-RSHTHV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK----GNFTSPIQNKLY----LHARYM 295
            ++  TGRTHQ+RVH  H+  P+VGD  Y   F+     + T     K +    LHAR++
Sbjct: 224 RVKLETGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFL 283

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +L HP  G R+   +PLP   V  W     K DR  +I
Sbjct: 284 ELDHPTTGKRMSWESPLPDDFV--WLLSLLKQDREAFI 319


>gi|332880233|ref|ZP_08447912.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
 gi|332681822|gb|EGJ54740.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
          Length = 224

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 68/218 (31%), Positives = 111/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + + NK +   VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHLIIVNKSSSEIVQGDKTGDKPLAEMVKEYIKQKYHKPGNVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ART  A   L E FR + + K YW++V   P  ++  + +WL++       Y + 
Sbjct: 63  GLVVFARTSKALARLNEMFRTKEVHKTYWAIVGNCPPTEEGELVHWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +++E  A  AI  +++I   ++++  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 123 KEKSE--AKKAILDYRLIG-RSERYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             G+  S     + LHAR +   HP     + + AP+P
Sbjct: 177 --GSPRSNPDGSICLHARRVRFVHPVSKQEIDVEAPVP 212


>gi|116491102|ref|YP_810646.1| ribosomal large subunit pseudouridine synthase D [Oenococcus oeni
           PSU-1]
 gi|290890605|ref|ZP_06553676.1| hypothetical protein AWRIB429_1066 [Oenococcus oeni AWRIB429]
 gi|116091827|gb|ABJ56981.1| ribosomal large subunit pseudouridine synthase D [Oenococcus oeni
           PSU-1]
 gi|290479733|gb|EFD88386.1| hypothetical protein AWRIB429_1066 [Oenococcus oeni AWRIB429]
          Length = 304

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 90/307 (29%), Positives = 150/307 (48%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHI 77
           RLD+     +   +   ++K++   +V V+ K V     +Q G   V+++PPV       
Sbjct: 17  RLDKILATDFSAFSRNQIKKLIDQDRVIVNGKPVLAKYLVQDGDHVVIKVPPV------- 69

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKS 135
            K+ ++L   + L          ++YED  + V NKP G+ V   +G + H  ++  L  
Sbjct: 70  -KKTELLPEKIPLD---------IVYEDDDLIVVNKPQGMVVHPSAGHSEHTLVNALLSH 119

Query: 136 WVDS--KGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              S   G+ +P + HR+D++TSG+L+VA+   A +HL+   +  +  + Y ++V G   
Sbjct: 120 APLSTINGEFRPGIVHRIDKDTSGLLMVAKNNFAHEHLSLDLKSHKTGRKYLAIVHGNFS 179

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            K+  I      K+ I  D  +  KQ        AI+HFKV++ F+  +  +E    TGR
Sbjct: 180 EKRGTI------KAPIDRDPKNRQKQAVVANGREAITHFKVLESFSN-YSLIEAVLETGR 232

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P+ GD  Y        T P + + YL A  + L  P  G+ L  +AP
Sbjct: 233 THQIRVHMAYIGHPVAGDPLYGP----RKTLPGRGQ-YLFASSLSLTQPHTGKELSFSAP 287

Query: 311 LPAHMVK 317
           LP +  K
Sbjct: 288 LPDYFQK 294


>gi|229104455|ref|ZP_04235123.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-28]
 gi|229117388|ref|ZP_04246765.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock1-3]
 gi|228666088|gb|EEL21553.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock1-3]
 gi|228678977|gb|EEL33186.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-28]
          Length = 302

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 90/329 (27%), Positives = 152/329 (46%), Gaps = 39/329 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKEND 60

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V IP          +E  I    +NL          + YED+ + V NKP G+ V  
Sbjct: 61  EITVTIPDP--------EELDIQAEDMNLE---------IYYEDADVLVVNKPRGMVVHP 103

Query: 122 GSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L     
Sbjct: 104 APGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLV 163

Query: 176 MRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V++
Sbjct: 164 AKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVLE 217

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  
Sbjct: 218 RF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGI 271

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP  G  +Q  AP+P    +T + L
Sbjct: 272 LGFDHPRTGEYIQFEAPIPEVFEETLNIL 300


>gi|298482488|ref|ZP_07000674.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. D22]
 gi|298271467|gb|EFI13042.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. D22]
          Length = 224

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 71/218 (32%), Positives = 110/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQ        +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQADKTGDTPLSETVKQYLKEKYQKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTSKALTRLNEMFRTSEVKKTYWAVVKNAPKEPEGELVHFLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   ++ +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPNSKKAILHYRLIG-HSENYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             G+  S     + LHAR +   HP    L ++ APLP
Sbjct: 177 --GSPRSNPDGSICLHARRVRFIHPVSKELIELEAPLP 212


>gi|113954535|ref|YP_731894.1| 23S RNA-specific pseudouridylate synthase [Synechococcus sp.
           CC9311]
 gi|113881886|gb|ABI46844.1| 23S RNA-specific pseudouridylate synthase [Synechococcus sp.
           CC9311]
          Length = 295

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 90/308 (29%), Positives = 143/308 (46%), Gaps = 32/308 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +     +   +QK + +G VRV+ K  K    +++G  V++  PP    L +
Sbjct: 1   MRLDRWLVSQRSEQSRSRIQKFIDAGYVRVNGKTGKAKTPLRNGDQVQLWMPPP-EPLPY 59

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E   LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 60  LKPEPMDLD---------------VLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLH 104

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +VVA+++ A   L    + R   + Y ++V G+
Sbjct: 105 HCQDLPGISGKLRPGVVHRLDKDTTGCIVVAKSQEALVRLQAQIQQRIASREYLAVVHGV 164

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P+ +   I   + +       Y  V   ++    YA +H+ + +     +  L  +  TG
Sbjct: 165 PQGESGTIIGAIGRHPVDRKKYAVV---SDDSGRYARTHWTLQERLGD-YSLLRFKLDTG 220

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  H+   +VGD  Y    K     P Q    LHA  + L HP    R+   A
Sbjct: 221 RTHQIRVHCAHINHAVVGDITYSRCRKLPVELPGQA---LHAFQLGLDHPITKERMLFEA 277

Query: 310 PLPAHMVK 317
           P+P+ M K
Sbjct: 278 PVPSVMEK 285


>gi|229174558|ref|ZP_04302089.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           MM3]
 gi|228608927|gb|EEK66218.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           MM3]
          Length = 302

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 86/318 (27%), Positives = 152/318 (47%), Gaps = 37/318 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKEND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          I + + LD        ++ +   + YED+ + V NKP G+ V    
Sbjct: 61  EITV---------TIPDPEELDI------QAEDMGLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDC 235
            + + Y ++V G+  + K  I       + IG D      +  +E G N A++HF+V++ 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTI------DAPIGRDKKERQSMTVDENGKN-AVTHFQVLER 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  +
Sbjct: 219 F-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGIL 272

Query: 296 DLPHPEGGR-LQITAPLP 312
              HP  G  +Q  AP+P
Sbjct: 273 GFDHPRTGEYIQFEAPIP 290


>gi|84623138|ref|YP_450510.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae MAFF 311018]
 gi|84367078|dbj|BAE68236.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae MAFF 311018]
          Length = 331

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 89/343 (25%), Positives = 157/343 (45%), Gaps = 40/343 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +V ++    R D      +P  +   L + ++SG   +D    +  + ++ G+ V+
Sbjct: 13  IRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGGESVQ 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V+    H   +   L                +LYED ++ V +KPAG+ V  G+G  
Sbjct: 73  VQVVLETQTHAAPQDIPLS---------------VLYEDEQVLVIDKPAGLVVHPGAG-- 115

Query: 127 YHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            + DG L + +     +    PR  + HRLD++TSG++V+ART  A   L E    R + 
Sbjct: 116 -NPDGTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVLARTVQAQTALVEQLSARDVH 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G   +     AN  + + H        V+ + +    A++H+++ + F +  
Sbjct: 175 RQYLAVVVGALVSG--GTANAPIDR-HPRDRLKMAVRDDGRD---AVTHYRLRERF-RAH 227

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHA 292
             LE +  TGRTHQ+RVH  H+  PIVGD  Y    K     T  + ++L       LHA
Sbjct: 228 TALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQALHA 287

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
             +   HP  G  ++ +AP+PA + +   +L     R   + R
Sbjct: 288 ETLQFLHPVSGEPVRASAPVPADLQRLMTALREDSARAAELAR 330


>gi|157878817|ref|XP_001687420.1| pseudouridylate synthase-like protein [Leishmania major strain
           Friedlin]
 gi|321438079|emb|CBZ11831.1| pseudouridylate synthase-like protein [Leishmania major strain
           Friedlin]
          Length = 413

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 93/359 (25%), Positives = 159/359 (44%), Gaps = 42/359 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV----RVDKKR-VKFNNRIQS 61
           +QY VV  D    R+D +   H+P  ++  ++++++ G +    +  KKR  +  +R++ 
Sbjct: 55  LQYHVVTQDWFGQRVDDFVTQHHPEWDYETVKRLVQQGHIYRYRKNGKKRYTRLTDRLEF 114

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNL------------------TKHSDFLKSILLY 103
            ++V +P          + Q    S V L                   K  +  + ++L+
Sbjct: 115 DELVVVP-----TASFWERQLAPPSGVELQSSSTSQQQERRQKFHLSAKTREMAQEMVLF 169

Query: 104 EDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           ++  + V NKP+G+ +      +A +I   L +W  +  Q P + H LD ETSG +V+AR
Sbjct: 170 KNEHVIVINKPSGVPIMPTHDPLAMNITDLLPAWRYTNTQTPVICHNLDTETSGCVVLAR 229

Query: 163 TRAAAQHLTESFRMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +    + L   F  R +   +YW    G P      I      +   GGD +        
Sbjct: 230 SANTHRMLGRMFVKRVVPNSVYWGFAVGKPPVNFGRIRMHFEVQKGQGGDVIVARPTPTA 289

Query: 222 GANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK-- 277
            +   I+ F V++  A +F  ++   P T R HQ R+ A H +  P++GD KY       
Sbjct: 290 DSKVGIAEF-VVNASALEFGSFISFYPLTTRRHQERIMAAHALRAPLLGDAKYGGESAFP 348

Query: 278 ---GNFTSPIQN--KLYLHARYMDLPHPEGGR--LQITAPLPAHMVKTWDSLGFKYDRN 329
                F  P +    L+LH R + LP+  G    + +TAPLP HM KT+  LG+  D +
Sbjct: 349 HSLSLFWDPARKDVPLHLHHRKIQLPYKNGAGEFVCVTAPLPPHMEKTFKRLGWPVDAD 407


>gi|150003134|ref|YP_001297878.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           vulgatus ATCC 8482]
 gi|254882415|ref|ZP_05255125.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           4_3_47FAA]
 gi|294778333|ref|ZP_06743757.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|319640483|ref|ZP_07995205.1| pseudouridine synthase [Bacteroides sp. 3_1_40A]
 gi|149931558|gb|ABR38256.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           vulgatus ATCC 8482]
 gi|254835208|gb|EET15517.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           4_3_47FAA]
 gi|294447809|gb|EFG16385.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|317387970|gb|EFV68827.1| pseudouridine synthase [Bacteroides sp. 3_1_40A]
          Length = 358

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 94/337 (27%), Positives = 155/337 (45%), Gaps = 49/337 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           VVV+  +  +R+D++      + +   +QK   +G +  + K VK + +++   V+ +  
Sbjct: 33  VVVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKSSYKVKPCDVLTVMM 92

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
             P  +  N II E   LD               ++YED+ + V NKPAG+ V  G G  
Sbjct: 93  DRPRYD--NDIIPEDIPLD---------------IVYEDNDLMVVNKPAGLVVHPGCGNY 135

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  IA+H+    K   D    +  L HR+D++TSG+LVVA+T  A  HL   F  +
Sbjct: 136 HGTLVNAIAWHLKDNPK--YDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNK 193

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCF 236
             ++ Y +LVWG+ +N +  I   + +      D + + V  +     +A++H++V++  
Sbjct: 194 TTKRKYNALVWGVVENNEGTIEGNIGRNPK---DRMQMAVLSDPAQGKHAVTHYRVLERL 250

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN-------- 286
                 +E    TGRTHQ+RVH  H+G  +  D +Y  N   KG   S  +         
Sbjct: 251 GY-VTLVECVLETGRTHQIRVHMKHIGHTLFNDERYGGNEILKGTHFSKYKQFVNNCFET 309

Query: 287 --KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
             +  LHA  +   HP  G  +  T+PLP  M    D
Sbjct: 310 CPRQALHAMTLGFVHPRTGEEMFFTSPLPEDMTNLID 346


>gi|58581220|ref|YP_200236.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae KACC10331]
 gi|58425814|gb|AAW74851.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae KACC10331]
          Length = 335

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 89/343 (25%), Positives = 157/343 (45%), Gaps = 40/343 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +V ++    R D      +P  +   L + ++SG   +D    +  + ++ G+ V+
Sbjct: 17  IRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGGESVQ 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V+    H   +   L                +LYED ++ V +KPAG+ V  G+G  
Sbjct: 77  VQVVLETQTHAAPQDIPLS---------------VLYEDEQVLVIDKPAGLVVHPGAG-- 119

Query: 127 YHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            + DG L + +     +    PR  + HRLD++TSG++V+ART  A   L E    R + 
Sbjct: 120 -NPDGTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVLARTVQAQTALVEQLSARDVH 178

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G   +     AN  + + H        V+ + +    A++H+++ + F +  
Sbjct: 179 RQYLAVVVGALVSG--GTANAPIDR-HPRDRLKMAVRDDGRD---AVTHYRLRERF-RAH 231

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHA 292
             LE +  TGRTHQ+RVH  H+  PIVGD  Y    K     T  + ++L       LHA
Sbjct: 232 TALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQALHA 291

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
             +   HP  G  ++ +AP+PA + +   +L     R   + R
Sbjct: 292 ETLQFLHPVSGEPVRASAPVPADLQRLMTALREDSARAAELAR 334


>gi|325293793|ref|YP_004279657.1| ribosomal large subunit pseudouridine synthase D [Agrobacterium sp.
           H13-3]
 gi|325061646|gb|ADY65337.1| ribosomal large subunit pseudouridine synthase D [Agrobacterium sp.
           H13-3]
          Length = 340

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 76/244 (31%), Positives = 119/244 (48%), Gaps = 37/244 (15%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           YED  + V  KPAG+ V  G+G         + YH    L      K  +P + HRLD+E
Sbjct: 94  YEDDDLIVLVKPAGLVVHPGAGNWTGTLVNALIYHCGDSLSGIGGVK--RPGIVHRLDKE 151

Query: 154 TSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           TSG++VVA+   A +HL   F    R   +++ Y ++VWG P+  +  I   L +    G
Sbjct: 152 TSGVMVVAKNDNAHRHLAAQFADHGRTGPLERAYKAVVWGRPRTLRGTIDAALGR----G 207

Query: 210 GDYVH--VVKQNEKGANYAISHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVHALH 261
            D     V +++   A  AI+H++V++ F +K         +E +  TGRTHQ+RVH  H
Sbjct: 208 ADRTKRAVKREDTDDAREAITHYEVMERFHEKADASCLASMVECRLETGRTHQIRVHMAH 267

Query: 262 MGCPIVGDHKYCANFKGN---FTSPIQNKL------YLHARYMDLPHPEGGR-LQITAPL 311
           +G P++GD +Y A F+        P ++ +       LHA  +   HP  G  ++    +
Sbjct: 268 IGHPLIGDPEYGAAFRTKANLLEEPARSTVNRFPRQALHAYLLAFEHPRTGEVMEFETDM 327

Query: 312 PAHM 315
           P  M
Sbjct: 328 PDDM 331


>gi|300812431|ref|ZP_07092861.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
 gi|300496598|gb|EFK31690.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
          Length = 304

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 80/296 (27%), Positives = 152/296 (51%), Gaps = 32/296 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++      +++   +++++++G+V V+ K+ K + ++Q G ++++  +    
Sbjct: 10  EESGQRLDKYLAGEMTNLSRSRIKELVQAGEVLVNGKKSKVSYKVQKGDLIQVTVLPLEP 69

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGF 132
             +  E   LD               ++YED  + V NKP G+ V   +G   H  ++  
Sbjct: 70  LKLEAENIPLD---------------IVYEDEDVIVVNKPQGMVVHPAAGHPSHTLVNAL 114

Query: 133 L---KSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L   +   DS +G +P + HR+D++TSG+L+VA+  AA + L +    +  ++ Y ++V 
Sbjct: 115 LYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVH 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G    ++E   +  + ++      + VV   EKG + A++HFKV++ + Q +  +E Q  
Sbjct: 175 G-NFAEEEGTIDAPIGRNPKDRKQMAVV---EKGKS-AVTHFKVLEQY-QGYSLVECQLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           TGRTHQ+RVH  ++G P+ GD  Y        T P   + +LHA+ +    P  G 
Sbjct: 229 TGRTHQIRVHMAYIGHPLAGDPLYGP----RKTLPGHGQ-FLHAKTLGFEQPSTGE 279


>gi|229824765|ref|ZP_04450834.1| hypothetical protein GCWU000182_00113 [Abiotrophia defectiva ATCC
           49176]
 gi|229791094|gb|EEP27208.1| hypothetical protein GCWU000182_00113 [Abiotrophia defectiva ATCC
           49176]
          Length = 326

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 86/331 (25%), Positives = 158/331 (47%), Gaps = 48/331 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRI 67
           VV E+  E  R+D++        +   L+ ++  G+VRV+ K VK + ++  G    + I
Sbjct: 27  VVSEDSGE--RIDKYLSGKLTEYSRSYLKGLIDEGKVRVEGKPVKSSFKVTEGINISISI 84

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
           PPV        KE +I+  ++ L          +LYED  + + NKP G+ V   +G   
Sbjct: 85  PPV--------KEAEIIPENIPLD---------ILYEDEDVILINKPKGMVVHPAAGHYT 127

Query: 125 ------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 + YH    L S ++ +  +P + HR+D +T+G+++  +   + + + E  +   
Sbjct: 128 GTLVNALMYHCRDNL-SGINGE-LRPGIVHRIDMDTTGVIIACKNDVSHRIIAEQLKEHS 185

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-- 236
           I++ Y ++V+G+ K+++  I   +  +S      + V+   +     A++H++VI  +  
Sbjct: 186 IKRKYQAIVYGVFKDEEGRIEGSI-GRSKTDRKKMAVIPDGKP----AVTHYRVIRNYTS 240

Query: 237 --AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHAR 293
                F  +E +  TGRTHQ+RVH   +G P++GD  Y     G   +P + +   LHA 
Sbjct: 241 PNGNNFAHIECELETGRTHQIRVHMTSIGHPLLGDEIY-----GAAKNPFKLDGQALHAE 295

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            +   HP  G  ++  APLP +  K    L 
Sbjct: 296 MLGFVHPRTGEYMEFHAPLPEYFSKLLTKLA 326


>gi|313901079|ref|ZP_07834567.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
 gi|312954037|gb|EFR35717.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
          Length = 304

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 78/325 (24%), Positives = 152/325 (46%), Gaps = 43/325 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++   ++   R+D++       ++   +Q +L  G + V++  VK N ++++   +    
Sbjct: 6   IIAAAEDAGARIDKYISEQ-EDLSRSRVQALLAEGSILVNQNAVKANYKVKADDCI---- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        + +  + +    + ++  + YED  + V NKP  I V   +G     
Sbjct: 61  -----------TAVFNDEMEMEARPEKMELDVRYEDEDVIVINKPKNIVVHPAAGNQSGT 109

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G L    D  G     +P + HR+D++T+G+L++A+   A   L++  + + + ++Y
Sbjct: 110 LVNGLLYHCKDLSGINGTLRPGIVHRIDKDTTGLLIIAKNDLAHASLSKQLQSKTVNRLY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDY-----VHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++LV G+ ++    I       + IG D      + V   N K A    +HF+VI+ F +
Sbjct: 170 YALVHGVIQHDFGTI------DAPIGRDVKDRQKMAVTATNSKDAR---THFQVIERF-E 219

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +E +  TGRTHQ+RVH  ++G P+VGD KY  +++    +   N   LHA  +   
Sbjct: 220 NYTLVECRLETGRTHQIRVHMQYIGHPVVGDEKY--SYRKTMQT---NGQLLHAHQLTFQ 274

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  G  + + A LP       + L
Sbjct: 275 HPRTGEVMTVEAELPKQFADILEEL 299


>gi|297624276|ref|YP_003705710.1| pseudouridine synthase [Truepera radiovictrix DSM 17093]
 gi|297165456|gb|ADI15167.1| pseudouridine synthase, RluA family [Truepera radiovictrix DSM
           17093]
          Length = 312

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 118/237 (49%), Gaps = 28/237 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQ---------KPRLTHR 149
           ++YED  +   +KP G++    + +     ++  L     +K +         +P + HR
Sbjct: 79  IIYEDDDLAAIDKPPGMTAHPTATVREGTVVNALLGRMALAKEKLFDPEDEDYRPGIVHR 138

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ETSG++VVA+  AA + L  +F+ R  +K Y ++  G        + + L     IG
Sbjct: 139 LDKETSGVMVVAKNDAAHRELASAFKKRLTEKEYIAIAVG-------TLEDDLYMDGPIG 191

Query: 210 GDYVHVVKQNEKGAN--YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               H  K    G N   A ++F+V+    ++   +  +PHTGRTHQ+RVH  H+G PI+
Sbjct: 192 RHPHHGRKMTVGGNNPRSASTYFRVL-ARTREAVLVRAKPHTGRTHQIRVHLAHLGAPIL 250

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
           GD  Y         SP+  +  LHA+ + LPHP +   +  +A +P  MV  W SLG
Sbjct: 251 GDSVY------GKPSPLIARHALHAQRLSLPHPRDHHAITFSAQVPLDMVSAWVSLG 301


>gi|291535586|emb|CBL08698.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis M50/1]
          Length = 217

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 69/210 (32%), Positives = 111/210 (52%), Gaps = 8/210 (3%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++  ++YED  I V  KPAG++ Q        ++  LK++  SKG+ P +   HRLDQ  
Sbjct: 1   MQPAIIYEDEDIIVCKKPAGVATQTRRIGQADMESLLKNYRASKGELPYIGVVHRLDQPV 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            GI+V A+ + AA  L+   + +   K Y+++  G+P+ KK  + + LL+      +   
Sbjct: 61  EGIMVFAKNKEAAADLSRQIKTKLADKYYYAMTDGVPEKKKGTLEDELLQNGKT--NTSE 118

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV++    A +A   ++V++    K   L ++  TGR HQ+RV   H G PIVGD KY  
Sbjct: 119 VVERGTPQAKHASLSYEVVEQDG-KHAVLRIKLDTGRHHQIRVQLAHAGMPIVGDKKY-- 175

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           NFK N  +P   +L L +  +   HP+  R
Sbjct: 176 NFKENI-APSGGQLALCSFKIAFRHPKTHR 204


>gi|196038675|ref|ZP_03105983.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
 gi|196030398|gb|EDX68997.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
          Length = 302

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 88/320 (27%), Positives = 149/320 (46%), Gaps = 41/320 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            + +          I E + LD     +NL          + YED+ + V NKP G+ V 
Sbjct: 61  EITV---------TIPEPEELDIQPEDMNLE---------IYYEDADVLVVNKPRGMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V+
Sbjct: 163 VAKTVIRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA 
Sbjct: 217 ERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAG 270

Query: 294 YMDLPHPEGGR-LQITAPLP 312
            +   HP  G  +Q  AP+P
Sbjct: 271 ILGFDHPRTGEYIQFEAPIP 290


>gi|27375585|ref|NP_767114.1| hypothetical protein blr0474 [Bradyrhizobium japonicum USDA 110]
 gi|27348722|dbj|BAC45739.1| blr0474 [Bradyrhizobium japonicum USDA 110]
          Length = 218

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 112/216 (51%), Gaps = 11/216 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  + V +KPAG+ V  G     +++    +      + P L HRLD++TSG L++
Sbjct: 1   MLHRDGLMLVIDKPAGLPVHRGPKGGANLEASFDALRFGLPRPPVLAHRLDKDTSGCLIL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R R A   L   F+  +I K YW++V G P   +  I   L + +   G +     + +
Sbjct: 61  GRHRKATASLGLLFKHGKIGKTYWTVVEGGPAEDEGTIDMPLGRLNAERGWWQKPDPEGQ 120

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K    AI+++KV+      F WL M+P TGRTHQLRVH+   G PI GD+ Y     GN 
Sbjct: 121 K----AITNWKVMG-RGDGFTWLAMEPVTGRTHQLRVHSAATGWPIFGDNIY-----GNG 170

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
               + KL+LH+R + +P       +++ AP P HM
Sbjct: 171 PRFGEPKLHLHSREIVVPISRNKEPVRVVAPAPPHM 206


>gi|163789051|ref|ZP_02183495.1| putative ribosomal large subunit pseudouridine synthase
           [Flavobacteriales bacterium ALC-1]
 gi|159875715|gb|EDP69775.1| putative ribosomal large subunit pseudouridine synthase
           [Flavobacteriales bacterium ALC-1]
          Length = 232

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 75/218 (34%), Positives = 109/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I V NK AG  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 13  VLYEDNHIIVANKRAGDIVQGDKTGDKPLSEVVKEYIKDKYNKPGNVYLGVVHRLDRPTT 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ ++T  A   L + F  ++ +K YW+LV   P    + + +W LKK+         
Sbjct: 73  GIVLFSKTSKALPRLNKLFAEKKAKKTYWALVKNQPPKTNDTLTHW-LKKNPKNNKSTAY 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ E G+  AI H+K+I      F  LE+   TGR HQ+R     +GCPI GD KY  N
Sbjct: 132 HKEVE-GSKKAILHYKIIKTL-DNFYLLEIDLETGRHHQIRTQLASIGCPIKGDLKYGFN 189

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                 S     + LHA+ +   HP +   + ITA LP
Sbjct: 190 RSNKDAS-----ISLHAKTLRFVHPIKKEDIVITASLP 222


>gi|19704361|ref|NP_603923.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|19714613|gb|AAL95222.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 289

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/308 (27%), Positives = 155/308 (50%), Gaps = 27/308 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++Y++ E + E +R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G VV 
Sbjct: 2   IEYIIDE-EYEKVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDVVF 60

Query: 67  I--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           I  P      N    E+K ++ S    +  + LK ++++E+  ++V NK  G  V  GSG
Sbjct: 61  IFLPENFKENN----EEKFIELS---QERKEKLKEMIVFENENLFVINKLLGDVVHKGSG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +    +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+
Sbjct: 114 HDISLLEEFRSYYSNNN--INFVNRIDKLTSGLIIGAKNIKTAREVAKEIQADNIIKRYY 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  +     + N+L K      + V V    ++G   +I++FK I     K+  LE
Sbjct: 172 ILVNGKIEKDNFILENYLKKDE----EKVIVSDIEKEGYKKSITYFKKIKE-HNKYTLLE 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQLR    H+G  IVGD KY  + +       ++ +YL + Y+ +       
Sbjct: 227 AELKTGRTHQLRAQLNHIGNNIVGDTKYGKDER-------EDMMYLFSYYLKIDLY---N 276

Query: 305 LQITAPLP 312
           L+I   +P
Sbjct: 277 LEIKLEIP 284


>gi|167031685|ref|YP_001666916.1| RluA family pseudouridine synthase [Pseudomonas putida GB-1]
 gi|166858173|gb|ABY96580.1| pseudouridine synthase, RluA family [Pseudomonas putida GB-1]
          Length = 352

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 96/336 (28%), Positives = 149/336 (44%), Gaps = 42/336 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   V+  + +  G ++ +    
Sbjct: 43  VPSELGGQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLVYGGSLLALEAEQ 102

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    I E   LD               ++YED  I V NKPAG+ V   +G   H  G
Sbjct: 103 EAQGEWIAEDIELD---------------IVYEDDHIMVINKPAGLVVHPAAG---HASG 144

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L E  + R++ +IY  
Sbjct: 145 TLLNALLHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTLQAQTKLVEQMQARKVSRIYEC 204

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+     +  A       H G      V     G   A+SH++V+  F +    + +
Sbjct: 205 IVIGVVTAGGKIDAPI---GRHGGMRQRMAVTD---GGKPAVSHYRVLKRF-RSHTHVRV 257

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKLYLHARYMDL 297
           +  TGRTHQ+RVH  H+G P+VGD  Y   F+     SP          +  LHAR++ L
Sbjct: 258 KLETGRTHQIRVHMAHVGFPLVGDQTYGGRFRIPPAASPTMVEAVKTFPRQALHARFLAL 317

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            HP  G  ++  +PLP   V  W       DR  +I
Sbjct: 318 AHPITGEIMKWESPLPDDFV--WLLSLLNQDRESFI 351


>gi|302185255|ref|ZP_07261928.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           syringae 642]
          Length = 320

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 96/338 (28%), Positives = 154/338 (45%), Gaps = 46/338 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLELVAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    + +   LD               ++YED +I V NKPAG+ V   +G   H DG
Sbjct: 71  EAQGEWVAQDIELD---------------IIYEDDQILVINKPAGLVVHPAAG---HADG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  
Sbjct: 113 TLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +V G+     +  A        IG  G     +   E G   A+SH++V++ F +    +
Sbjct: 173 IVIGVVTAGGKIDAP-------IGRHGQQRQRMAVME-GGKQAVSHYRVLERF-RSHTHV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK----GNFTSPIQNKLY----LHARYM 295
            ++  TGRTHQ+RVH  H+  P+VGD  Y   F+     + T     K +    LHAR++
Sbjct: 224 RVKLETGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFL 283

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +L HP  G R+   +PLP   V  W     K DR  +I
Sbjct: 284 ELDHPTTGKRMSWESPLPDDFV--WLLSLLKQDREAFI 319


>gi|296327421|ref|ZP_06869968.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
 gi|296155434|gb|EFG96204.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
          Length = 289

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/308 (27%), Positives = 155/308 (50%), Gaps = 27/308 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++Y++ E + E +R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G VV 
Sbjct: 2   IEYIIDE-EYEKVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDVVF 60

Query: 67  I--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           I  P      N    E+K ++ S    +  + LK ++++E+  ++V NK  G  V  GSG
Sbjct: 61  IFLPENFKENN----EEKFIELS---QERKEKLKEMIVFENENLFVINKLLGDVVHKGSG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +    +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+
Sbjct: 114 HDISLLEEFRSYYSNNN--INFVNRIDKLTSGLVIGAKNIKTAREVAKEIQASNIIKRYY 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  +     + N+L K      + V V    ++G   +I++FK I     K+  LE
Sbjct: 172 ILVNGKIEKDNFILENYLKKDE----EKVIVSDIEKEGYKKSITYFKKIKE-HNKYTLLE 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQLR    H+G  IVGD KY  + +       ++ +YL + Y+ +       
Sbjct: 227 AELKTGRTHQLRAQLNHIGNNIVGDTKYGKDER-------EDMMYLFSYYLKIDLY---N 276

Query: 305 LQITAPLP 312
           L+I   +P
Sbjct: 277 LEIKLEIP 284


>gi|319900985|ref|YP_004160713.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           helcogenes P 36-108]
 gi|319416016|gb|ADV43127.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           helcogenes P 36-108]
          Length = 223

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 68/219 (31%), Positives = 112/219 (51%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKQYLKEKYDKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E F+   ++K YW++V   P  ++  + N++++       Y + 
Sbjct: 63  GLVVFAKTGKALSRLNEMFKNSEVKKTYWAVVKNQPPEEEGELVNYMVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   G+  AI H+++I   +Q +  LE+   TGR HQ+R     +GCPI GD KY   
Sbjct: 122 -DKERPGSKRAILHYRLIGK-SQNYYLLEIDLKTGRHHQIRCQLAKIGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
             G   S     + LHAR++   HP     +++ AP+P+
Sbjct: 177 --GFPRSNPDGSICLHARFIRFVHPVSKETIEVEAPIPS 213


>gi|212702767|ref|ZP_03310895.1| hypothetical protein DESPIG_00797 [Desulfovibrio piger ATCC 29098]
 gi|212673824|gb|EEB34307.1| hypothetical protein DESPIG_00797 [Desulfovibrio piger ATCC 29098]
          Length = 531

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 82/307 (26%), Positives = 147/307 (47%), Gaps = 31/307 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHII 78
           RLD+      P ++   +Q+ + +G  R+D   V   + ++++GQ V +  + +  N + 
Sbjct: 21  RLDKALCGLLPELSRAAVQRAITAGACRIDGMPVATASLKLKAGQAVCLD-LPDTANELR 79

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFL 133
            E + +D               +L++D  + + NKPAG++V          +   +    
Sbjct: 80  AEDEAVD---------------ILWQDEHLLLCNKPAGLTVHPCPSCPENTLVQRLLHHF 124

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
               + +G +P + HRLD++TSG+L+VA        ++E+F  R + K Y +LV G+P  
Sbjct: 125 PRLREQEGLRPGVVHRLDKDTSGLLLVALDEPTRLRMSEAFARREVHKEYLALVGGVPPQ 184

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRT 252
              C     L +       + VV +N +G   A S ++V+    +K F  + ++ HTGRT
Sbjct: 185 TGTCREP--LGRHPTAKVKMAVVPEN-RGGKTAHSDWRVLWSSPRKDFSLVAVRIHTGRT 241

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           HQ+RVH  H+G P++GD    A +     +    +  LHA ++   HP  G  L+   P 
Sbjct: 242 HQIRVHMAHVGHPLLGD----ALYAPAPVAARAPRQMLHAWHISFCHPLSGEELEFFCPP 297

Query: 312 PAHMVKT 318
           P  M++T
Sbjct: 298 PGDMIQT 304


>gi|157363528|ref|YP_001470295.1| RluA family pseudouridine synthase [Thermotoga lettingae TMO]
 gi|157314132|gb|ABV33231.1| pseudouridine synthase, RluA family [Thermotoga lettingae TMO]
          Length = 294

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 96/316 (30%), Positives = 148/316 (46%), Gaps = 42/316 (13%)

Query: 15  DEENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVI 71
           +EEN   RLD++ +N    +    + K+LR+G V+V+ K V K    +  G  V     I
Sbjct: 11  NEENSYRRLDKFLRNELKAVPLSEIYKLLRTGCVQVNGKTVRKPYTELYVGDKV----TI 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
            A   + +++K L S          LK  +LYED  + + NK AGI++           I
Sbjct: 67  KADLAVYRQKKDLPSIP--------LKLDILYEDDNLLILNKKAGITIHPSEKTRSTTLI 118

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G L  +   KG KP L HRLD++TSG+LV+A+    A+ L+  FR R ++K Y +LV G
Sbjct: 119 QG-LHFYGAKKGFKPHLVHRLDRDTSGVLVIAKNVKTARTLSHMFRNRLVKKEYITLVSG 177

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                 +   +  + K   G +              A++ +KV++ F +    L +  HT
Sbjct: 178 ------KIFGDGFIDKPLDGSE--------------ALTEYKVLENF-RDTSLLRVILHT 216

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQ 306
           GRTHQ+R H   +G P+VGD  Y             N  + +LH   +   +P E G + 
Sbjct: 217 GRTHQIRKHFALIGNPVVGDILYGDKKVNELFKKKHNLRRQFLHCIRISFTNPSEPGVIS 276

Query: 307 ITAPLPAHMVKTWDSL 322
           I APLP  + +    L
Sbjct: 277 IKAPLPDDLERVIKGL 292


>gi|160887288|ref|ZP_02068291.1| hypothetical protein BACOVA_05306 [Bacteroides ovatus ATCC 8483]
 gi|156107699|gb|EDO09444.1| hypothetical protein BACOVA_05306 [Bacteroides ovatus ATCC 8483]
          Length = 564

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 82/249 (32%), Positives = 124/249 (49%), Gaps = 39/249 (15%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGS---GIAYHI 129
           L+H+++  ++ ++ +  + H D    I+ YED  + V NKPAG +SV G        YH 
Sbjct: 324 LHHMLQGLEVDENPLLNSIHEDEELEIV-YEDEWLVVVNKPAGMLSVPGKEEDRDSVYH- 381

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               K + D+ G  P + HRLD  TSG+L+VA+T+   QHL   F  R I+K Y +++ G
Sbjct: 382 -RLKKKYPDATG--PMIVHRLDMATSGLLLVAKTKEVHQHLQAQFASRSIKKRYVAVLDG 438

Query: 190 IPKNKKECIANWLLKKSHIGG----------DYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +       +    L     G           D    +   E G   AI+ +++I C ++K
Sbjct: 439 V------TVEKTALPPGRTGRIELPLCLNPLDRPRQIVSREHGKE-AITEYRII-CESEK 490

Query: 240 FCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQLRVHA H   +GCPI+GD  Y             ++LYLHA Y++
Sbjct: 491 HTRIAFYPLTGRTHQLRVHAAHPEGLGCPILGDELYGKK---------ADRLYLHAEYIE 541

Query: 297 LPHPEGGRL 305
             HP  G++
Sbjct: 542 FRHPISGKI 550


>gi|119897309|ref|YP_932522.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119669722|emb|CAL93635.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 324

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/317 (27%), Positives = 146/317 (46%), Gaps = 30/317 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ---VVRIPPVINAL 74
             RLD+     +P  +   LQ  L+ G +R+D    +  +++  G+   V  +PP     
Sbjct: 30  GARLDQVLARLFPEHSRSRLQAWLKDGLIRLDGMERQAKHKVHGGEELVVAGLPP----- 84

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGF 132
              + EQ        L    + +   ++YED+ I V +KPAG+ V  GSG      ++  
Sbjct: 85  ---LPEQ--------LAFEPEAIPLDVVYEDASILVIDKPAGLVVHPGSGNWSGTLLNAL 133

Query: 133 LKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L       G  +  + HRLD++T+G++VVA+T  A   L    + R + + Y++LV+G  
Sbjct: 134 LHHAPALAGLPRAGIVHRLDKDTTGLMVVAKTLEAQTDLVRQLQQRTVARHYYALVYGDI 193

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  E  A+  + +  +    + VV     G   A++ + V          +E +  TGR
Sbjct: 194 ASDGEIDAD--IDRHPVQRTRMAVV----PGGRPALTRYAVRQRL-HGLTLVECRLQTGR 246

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAP 310
           THQ+RVH  H+G P+VGD  Y      +      ++  LHA  + L HP  G   + +AP
Sbjct: 247 THQIRVHMAHLGHPLVGDPVYGPRRVTDSRVDGFSRQALHAFRLGLLHPASGEDMVWSAP 306

Query: 311 LPAHMVKTWDSLGFKYD 327
           LPA      + +G + D
Sbjct: 307 LPADFAALLEKVGGRAD 323


>gi|281357295|ref|ZP_06243784.1| pseudouridine synthase, RluA family [Victivallis vadensis ATCC
           BAA-548]
 gi|281316326|gb|EFB00351.1| pseudouridine synthase, RluA family [Victivallis vadensis ATCC
           BAA-548]
          Length = 323

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/331 (26%), Positives = 155/331 (46%), Gaps = 35/331 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP--P 69
           +E  +   RLDR      P  +   LQ+++R G V+ D            G  + +P  P
Sbjct: 10  IEAGDAGTRLDRCLSRLIPGESRSFLQRLIRDGLVKAD------------GVALEVPRYP 57

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
           V   ++  ++         +    ++  +  +LYED  + V +KPAG+ V   +G     
Sbjct: 58  VRAGMSIAVELP----EEESPEPAAEPFEFPILYEDDVMLVIDKPAGVVVHPAAGNPTGT 113

Query: 128 HIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            ++  L  +     Q      +P + HRLD++TSG L VA+T  A   L+ +F  R  +K
Sbjct: 114 VVNALLGRYPQLAEQLACTTSRPGIVHRLDKDTSGCLAVAKTANAQFKLSTAFAGRETRK 173

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA--NYAISHFKVIDCFAQK 239
            Y ++  G+P  +   ++  L+ +  +    + VV++N K A   Y + +  ++D    +
Sbjct: 174 TYLAITRGVPIRRSGELST-LIGRHPVSRQKMAVVERNGKLAITRYRVEYTGMLDGV--E 230

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L ++  TGRTHQ+RVH   +G P++GD  Y         + ++ +L LHA  + +PH
Sbjct: 231 IGVLAVRILTGRTHQIRVHLASLGVPVLGDAVYGGARTA--VAGVERQL-LHAWKLCVPH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           P  G  ++ TAP P  + +  + +G K  R 
Sbjct: 288 PATGTPMEFTAPPPEDIRRILERIGVKTLRE 318


>gi|291540830|emb|CBL13941.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis XB6B4]
          Length = 221

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 68/210 (32%), Positives = 110/210 (52%), Gaps = 8/210 (3%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++  ++YED  I V  KPAG++ Q        ++  LK++  SKG+ P +   HRLDQ  
Sbjct: 5   MQPAIIYEDEDIIVCKKPAGVATQTRRIGQADMESLLKNYRASKGELPYIGVVHRLDQPV 64

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G++V A+ + AA  L+   + +   K Y+++  G+P+ KK  + + LL+          
Sbjct: 65  EGVMVFAKNKEAAADLSRQIKTKLADKYYYAMTDGVPEKKKGTLEDELLQNGKTNAS--E 122

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV++    A +A   ++V++    K   L ++  TGR HQ+RV   H G PIVGD KY  
Sbjct: 123 VVERGTPQAKHASLSYEVVEQDG-KHAVLRIKLDTGRHHQIRVQLAHAGMPIVGDKKY-- 179

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           NFK N  +P   +L L +  +   HP+  R
Sbjct: 180 NFKENI-APSGGQLALCSFKIAFRHPKTHR 208


>gi|313206986|ref|YP_004046163.1| ribosomal large subunit pseudouridine synthase d [Riemerella
           anatipestifer DSM 15868]
 gi|312446302|gb|ADQ82657.1| ribosomal large subunit pseudouridine synthase D [Riemerella
           anatipestifer DSM 15868]
 gi|315024062|gb|EFT37064.1| Ribosomal large subunit pseudouridine synthase D [Riemerella
           anatipestifer RA-YM]
 gi|325335579|gb|ADZ11853.1| Pseudouridylate synthase, 23S RNA-specific [Riemerella
           anatipestifer RA-GD]
          Length = 229

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/232 (33%), Positives = 112/232 (48%), Gaps = 38/232 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ + V NK AG  VQG       +   +K ++ S+  KP      L HR+D+ TS
Sbjct: 6   ILYEDNHLLVINKKAGQLVQGDKTGDVSLLELIKDFIKSRDNKPGNVFLGLVHRIDRPTS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   LT+  + R I+K YW++V       KE I+             VH 
Sbjct: 66  GLVIYAKTSKALTRLTQMIKNREIKKTYWAIV------PKEMISP--------SQKLVHY 111

Query: 216 VKQNEK------------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +K+NEK            GA  AI  + +I      +  LE+   TGR HQ+R     +G
Sbjct: 112 LKKNEKNNKAIIFTKPTEGAKQAILSYNLILSL-DNYLLLEVDLETGRHHQIRAQLSKIG 170

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAH 314
            PI GD KY A+      S     + LHAR +D  HP    ++ I AP+P+H
Sbjct: 171 IPIKGDLKYGAS-----RSNSDGGISLHARRLDFIHPVSKEKITIVAPVPSH 217


>gi|116751075|ref|YP_847762.1| RluA family pseudouridine synthase [Syntrophobacter fumaroxidans
           MPOB]
 gi|116700139|gb|ABK19327.1| ribosomal large subunit pseudouridine synthase D [Syntrophobacter
           fumaroxidans MPOB]
          Length = 344

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 95/325 (29%), Positives = 146/325 (44%), Gaps = 51/325 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ +E+  RLD +     P  +   +QK++R G+V V+   VK +  I+SG  + +    
Sbjct: 14  VDVEEKLRRLDVFLSARSPDCSRSQVQKLIREGRVTVNGLPVKASYEIRSGDCIAV---- 69

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
             L   + E  +    + L          +L+ED  + V NK  G+ V  G+G   H +G
Sbjct: 70  -WLPEAVGEDSLQPRPMPLE---------ILFEDDDVLVLNKAPGVIVHPGAG---HEEG 116

Query: 132 FLK-------SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            L        S + S+G  ++P + HRLD+ TSG L+VA++  A   L   F+   + K 
Sbjct: 117 TLVHGLLAHCSRLASRGAPRRPGIVHRLDRGTSGALMVAKSERAYLELIRQFKHHEVGKE 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-----EKGANYAISHFKVIDCFA 237
           Y +LV+G        I   + +         H V +      EKG   A+S +KV   + 
Sbjct: 177 YLALVYGTMAGASGEIRTGMGR---------HPVDRKRMAVLEKGGREAVSQWKVAVAWG 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQ---NKL 288
           +    L +   TGRTHQ+RVH  HM  P+VGD  Y          K +    +    ++ 
Sbjct: 228 E-VSLLRVVIKTGRTHQIRVHLSHMQHPVVGDETYGGGKRKARAVKSDVLRELLMEVDRQ 286

Query: 289 YLHARYMDLPHP-EGGRLQITAPLP 312
            LHA  +   HP  G  L  TAPLP
Sbjct: 287 MLHAVGLAFRHPVSGADLSFTAPLP 311


>gi|313203182|ref|YP_004041839.1| ribosomal large subunit pseudouridine synthase d [Paludibacter
           propionicigenes WB4]
 gi|312442498|gb|ADQ78854.1| ribosomal large subunit pseudouridine synthase D [Paludibacter
           propionicigenes WB4]
          Length = 227

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 73/219 (33%), Positives = 110/219 (50%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I   NK     VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VLYEDNHIIAVNKTCSEIVQGDKTGDEPLSDTIKKYLKEKYNKPGEVFCGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR + ++K YW++V   PK  +  + ++L++         H 
Sbjct: 63  GVVLFAKTSKALTRLNEMFRTQEVKKTYWAIVKEKPKQPEGRLEHFLVRNEKQNKSVAH- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  A   +K+I   ++ +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -EKMVPNAKAAALSYKLI-AHSETYYLLEVHLETGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
             G   S     + LHAR ++  HP   +L QITAP+PA
Sbjct: 177 --GFARSNPNGGISLHARNVEFIHPVSKQLIQITAPVPA 213


>gi|300854258|ref|YP_003779242.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           ljungdahlii DSM 13528]
 gi|300434373|gb|ADK14140.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           ljungdahlii DSM 13528]
          Length = 302

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 95/322 (29%), Positives = 146/322 (45%), Gaps = 38/322 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V ++EENMRLD +    +   +   +Q ++    V V+ K  K N +I+SG  + I   
Sbjct: 7   LVCSEEENMRLDVFLSKCFQDKSRSYIQNVIEYKLVEVNGKAKKSNYKIKSGDNIEI--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                        +   VNL   S+ +   +LYED  + V NKP G+ V    G+     
Sbjct: 64  ------------TIPDPVNLNIQSEDIPLDILYEDKDVIVVNKPQGMIVHPAPGVYEGTL 111

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D  G     +P + HR+D++TSGILVVA+   +   L +  +   + + Y 
Sbjct: 112 VNALLNHCRDLSGINGVTRPGIVHRIDKDTSGILVVAKNDNSHNKLAKQLKDHSMTREYI 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---C 241
           +LV G+ K  +  +   + +  H        V  N K    AI+H+KVI  F       C
Sbjct: 172 ALVEGVVKLDEGTVDEPIAR--HPKDKIKMAVCVNGK---RAITHYKVIKRFKNNTLIKC 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE    TGRTHQ+RVH  ++G P+VGD  Y    K  F    Q    LHA  +   HP 
Sbjct: 227 ILE----TGRTHQIRVHMAYIGHPLVGDPVYGYK-KQRFKLGGQ---LLHAEKLGFIHPA 278

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G+ ++    +P +  K    L
Sbjct: 279 TGKYIEFETEIPDYFKKVIKVL 300


>gi|313204538|ref|YP_004043195.1| ribosomal large subunit pseudouridine synthase d [Paludibacter
           propionicigenes WB4]
 gi|312443854|gb|ADQ80210.1| ribosomal large subunit pseudouridine synthase D [Paludibacter
           propionicigenes WB4]
          Length = 356

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 88/333 (26%), Positives = 156/333 (46%), Gaps = 41/333 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV+  +  +R+D+   N   + +   +Q+   +G + V+ K VK N RI+   ++ I   
Sbjct: 30  VVDKGQAMVRIDKHLVNCMSNTSRNRIQEAADAGNILVNGKPVKSNYRIKPYDIISI--- 86

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
              L++   + +I+   + +          ++YED  I + NK   + V  G G   + D
Sbjct: 87  --VLSYPPSQFEIIPQDIPIN---------IVYEDDDIILVNKQPNLVVHPGFG---NFD 132

Query: 131 GFLKSWV----------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G L + +          D+   +  L HR+D++TSG++++A+T  A  HL + F  +  Q
Sbjct: 133 GTLLNAIAWHLKDHPEFDANDSRIGLVHRIDKDTSGLILIAKTEEAKAHLGKQFFNKTTQ 192

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG  K  +  I   L +       +    +     A +A++H+KV++ FA   
Sbjct: 193 RRYHALVWGNVKEDEGTIVGALARDPRDRMLFTVFPEGENPLAKHAVTHYKVLERFAY-V 251

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQNKLY----- 289
             +E +  TGRTHQ+RVH  H+G  +  D +Y  +   KG  T+     ++N  Y     
Sbjct: 252 TLVECRLETGRTHQIRVHMKHIGHTLFNDERYGGHIILKGTNTAMYKAFVKNCFYICPRQ 311

Query: 290 -LHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            LHA+ +   HP  G  +   + LP  M +  D
Sbjct: 312 ALHAKTLGFVHPRTGEFMHFESELPDDMQELID 344


>gi|261367025|ref|ZP_05979908.1| ribosomal large subunit pseudouridine synthase D [Subdoligranulum
           variabile DSM 15176]
 gi|282571143|gb|EFB76678.1| ribosomal large subunit pseudouridine synthase D [Subdoligranulum
           variabile DSM 15176]
          Length = 310

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/313 (27%), Positives = 140/313 (44%), Gaps = 33/313 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD W       I+   LQ ++   +V  D + V    ++  G V  +            
Sbjct: 15  RLDAWLAGQCEGISRNALQTLIEQERVTKDGRPVNKKEKVCPGAVYLL------------ 62

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHID 130
             ++ D         D   SI+ YED+ + V NKP G+ V    G         + YH  
Sbjct: 63  --QLPDPKPIEAVPQDIPLSIV-YEDNDLIVVNKPKGMVVHPAPGNPDGTLVNALLYHCA 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G L         +P + HR+D++TSG+LVVA+   A Q L+    +  I ++Y ++V+G 
Sbjct: 120 GQLSGI--GGAIRPGIVHRIDKDTSGLLVVAKNDVAHQALSSQMSVHSIHRVYHAIVYGN 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K  +  +  WL +        + V+ +N  GA YA + ++V++ F   F ++  +  TG
Sbjct: 178 LKEDEGFVEAWLGRDPR-DRKKMAVLSENTTGARYAYTGWRVLERFGN-FTYIACKLKTG 235

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH   +G P+ GD  Y      N    +  +  LHA+ +   HP     +Q  +
Sbjct: 236 RTHQIRVHMASIGHPLAGDVVYGPR---NCIKSLAGQC-LHAKELGFVHPSTENWMQFDS 291

Query: 310 PLPAHMVKTWDSL 322
           PLPA+     + L
Sbjct: 292 PLPAYFTDFLNRL 304


>gi|315924170|ref|ZP_07920396.1| ribosomal large subunit pseudouridine synthase D [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315622572|gb|EFV02527.1| ribosomal large subunit pseudouridine synthase D [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 307

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 91/322 (28%), Positives = 151/322 (46%), Gaps = 39/322 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPP 69
           V  +E+NMRLD       P+++   L++++  G ++VD    K   R+++ +  V++IP 
Sbjct: 8   VHEEEKNMRLDVLCAQICPNLSRQYLKELIVDGDIQVDFANKKPAYRLKADERIVIKIPD 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
            +          +++  S++L          ++YED  + V NKP+G+ V   SG     
Sbjct: 68  PVPC--------QVMPESIDLD---------IVYEDGDVIVVNKPSGMVVHPASGTQSGT 110

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  +    D  G     +P + HR+D++TSGILVVA+   A +HL        + + Y
Sbjct: 111 LVNALMAHTKDLSGINGVNRPGIVHRIDKDTSGILVVAKNDLAHRHLARQLAEHSMVRQY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFC 241
            +LV G        + N       +G   V  V+    E G + A++HF+VI+     F 
Sbjct: 171 VALVKG------NIVENSGTVDMPVGRHPVDRVRMAVVENGKS-AVTHFEVIERLGD-FT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           ++  +  TGRTHQ+RVH   +G PI GD  Y  +    F +  Q    LHAR +   HP 
Sbjct: 223 YVAFRLETGRTHQIRVHMQAIGHPIAGDPVYGGDKHLPFKTDGQ---LLHARELGFIHPR 279

Query: 302 G-GRLQITAPLPAHMVKTWDSL 322
               ++  A LP    K  + L
Sbjct: 280 TKAFMRFEASLPEIFQKVLNQL 301


>gi|300774195|ref|ZP_07084062.1| ribosomal large subunit pseudouridine synthase [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|300758874|gb|EFK55703.1| ribosomal large subunit pseudouridine synthase [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 228

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 115/220 (52%), Gaps = 17/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR----LTHRLDQETSG 156
           ++YED+ +   NK AG  VQ        +D  +K +++ K +KP     + HRLD+  SG
Sbjct: 8   VIYEDNHLIAINKRAGDIVQVDDSGDKSLDMMVKEYLERKYEKPNAFIGVIHRLDRPVSG 67

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVH 214
           ++V A+T      + + F  R ++K Y ++V   P+     + NWL++  K  I   Y  
Sbjct: 68  LIVFAKTSKGLDRMNKLFHDRDVEKSYLAVVRNKPEQMSAKLQNWLVRDRKKMITKAYNR 127

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +K    G++YA   ++VI    + +  L ++P TGRTHQ+R+    MGCPIVGD+KY  
Sbjct: 128 EIK----GSSYAELDYEVIGEL-EGYYLLHVKPKTGRTHQIRIQLSTMGCPIVGDNKY-- 180

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
              G     ++  + LH+R +   HP +   ++I A LP 
Sbjct: 181 ---GYPRGSLRRSICLHSRSLSFVHPVKDEPMKIVAGLPV 217


>gi|258406577|ref|YP_003199319.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
 gi|257798804|gb|ACV69741.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
          Length = 299

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 83/277 (29%), Positives = 131/277 (47%), Gaps = 29/277 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M+  Q++ +  +E N ++    +N     +    L K +R+GQVRVDKKR K  +R+Q G
Sbjct: 1   MSPPQFLEITPEEANSKVLSVLQNRLDGQVPRSALMKWIRTGQVRVDKKRTKPFDRVQPG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q++R+PP           Q  L S+ +       LK   + E   + V  KPAG+ VQ G
Sbjct: 61  QILRLPP-----------QATLKSASS-PGPPPALKLERIAETETLLVLAKPAGLPVQPG 108

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           S     +   L          P+  HRLD++TSGI++VA+     Q + ++++   +QK 
Sbjct: 109 SKHGASLVRELAKAYPETPWPPQPVHRLDKDTSGIILVAKRADVFQIIQQAWQRGEVQKD 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV--VKQNEK-----GANYAISHFKVIDC 235
           Y  L W  P +  +    W     H   D + +    + EK     G   AI H + +  
Sbjct: 169 Y--LAWLAPGD--DVGPGW-----HTWRDRIEICHTDRGEKMCCTEGGKEAILHLRPLRR 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +     + +Q  TGR HQ+RV + + G P+VGD KY
Sbjct: 220 NSLGEILVAIQLETGRKHQIRVQSANRGLPVVGDRKY 256


>gi|138894673|ref|YP_001125126.1| ribosomal large subunit pseudouridine synthase D-like protein
           [Geobacillus thermodenitrificans NG80-2]
 gi|196247711|ref|ZP_03146413.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
 gi|134266186|gb|ABO66381.1| ribosomal large subunit pseudouridine synthase D-like protein
           [Geobacillus thermodenitrificans NG80-2]
 gi|196212495|gb|EDY07252.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
          Length = 304

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/313 (27%), Positives = 146/313 (46%), Gaps = 32/313 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E + +  R+D+         +   +Q+ +++G V V+ + VK N + + G  V I P  
Sbjct: 8   IEEEYDGERIDKVIAALNDEWSRSQVQQWIKNGLVTVNGRTVKANYKSELGDTVAISPPE 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
               H+  E   LD               + YED  + V NKP G+ V    G      +
Sbjct: 68  PEPLHVEPEPIPLD---------------IYYEDEDVLVVNKPRGMVVHPAPGHMRGTLV 112

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSG+L+VA+  AA + L E    + + + Y +
Sbjct: 113 NALLAHCRDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDAAHRSLVEQLVNKTVTRRYKA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+  +    I   + +      D   +   +E G   A++HF+V++ F Q + ++E 
Sbjct: 173 IVHGVIPHDYGTIDAPIGRDKR---DRKKMAVTDENGKE-AVTHFRVLERFRQ-YTYVEC 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD +Y        T  I+ +  LHA  +   HP  G  
Sbjct: 228 QLETGRTHQIRVHMKYIGYPLAGDPQYGP----KKTLSIEGQA-LHAGVLGFRHPRSGDY 282

Query: 305 LQITAPLPAHMVK 317
           L+  APLP    +
Sbjct: 283 LEFEAPLPPEFAE 295


>gi|305664420|ref|YP_003860707.1| ribosomal large subunit pseudouridine synthase D [Maribacter sp.
           HTCC2170]
 gi|88708437|gb|EAR00673.1| ribosomal large subunit pseudouridine synthase D [Maribacter sp.
           HTCC2170]
          Length = 341

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 90/328 (27%), Positives = 157/328 (47%), Gaps = 45/328 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +    +E +R+D++  N   +     +Q+  + G + V++K VK N ++++G  V++   
Sbjct: 21  IASKGQEPLRVDKFLMNFIENATRNKIQQAAKDGHIWVNEKIVKQNYKVKAGDEVKV--- 77

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                H   E  +   ++ L          ++YED  + V NKPAG+ V  G G      
Sbjct: 78  --LFEHPPYELLLTPENIPLD---------IVYEDDVLLVVNKPAGMVVHPGHGNYTGTL 126

Query: 129 IDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           I+  L   K    +   +P L HR+D++TSG+LVVA+T AA  HL + F  +  ++ Y +
Sbjct: 127 INALLYHSKDLPVNSNDRPGLVHRIDKDTSGLLVVAKTEAAMTHLAKQFFDKTSEREYVA 186

Query: 186 LVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF--- 240
           LVWG  +++   I   + +  K+ +    + V  + E+G   A++H+ V++         
Sbjct: 187 LVWGNVEDESGTIEGNIARNPKNRL---QMQVFPEGEQGKE-AVTHYGVLERLGYVTLVS 242

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---------PIQNKL 288
           C LE    TGRTHQ+RVH  ++G  +  D +Y  +   KG  FT           I  + 
Sbjct: 243 CKLE----TGRTHQIRVHMKYIGHTLFNDERYGGDKVLKGTTFTKYKQFVDNAFKILPRQ 298

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHM 315
            LHA+ +   HP  G  ++  + +P  M
Sbjct: 299 ALHAKTLGFVHPVSGEMMRFDSEIPEDM 326


>gi|302806002|ref|XP_002984751.1| hypothetical protein SELMODRAFT_121195 [Selaginella moellendorffii]
 gi|300147337|gb|EFJ14001.1| hypothetical protein SELMODRAFT_121195 [Selaginella moellendorffii]
          Length = 355

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/282 (30%), Positives = 129/282 (45%), Gaps = 59/282 (20%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQETS 155
           LK  +LY+D  + V NKP G+ VQGGS +   +   +   +  +  + PRL HRLD++ S
Sbjct: 36  LKDAVLYKDEDLIVLNKPPGLPVQGGSKVERSLVSMMSLALQFEYKEPPRLVHRLDKDVS 95

Query: 156 GILVVARTRAAAQHL----------------TESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           G++++ RT  +   +                T+    + + + Y +LV G P   K  I+
Sbjct: 96  GVMILGRTYESTVKIQSFLCSKDNLMPSVITTQGSVGKGLDRKYIALVIGSPTADKGFIS 155

Query: 200 NWLLKKSHIGGDYVHV-VKQNEKGANY--AISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             LLK     G    V +  + K  N   AI+ ++V+        WL+++P TGR HQLR
Sbjct: 156 APLLKMVLEDGKSDRVLIAADPKSENAIPAITEYQVLKRSVLGCTWLQLRPLTGRKHQLR 215

Query: 257 VH-ALHMGCPIVGDHKY--------CANFKGNFTSP----IQNK-----------LYLHA 292
           VH A  +G PIVGD KY         A    N   P     +NK           L+LH+
Sbjct: 216 VHCAQGLGLPIVGDMKYGFNTHKKWMAERNMNTVDPQDIKARNKMAGSVVSKNPLLHLHS 275

Query: 293 RYMDLPH-------------PEGGRLQITAPLPAHMVKTWDS 321
           R + +P              PE  R++  APLP HM  +W++
Sbjct: 276 RELTIPRLRKKPGAVDFGLDPE--RMRFVAPLPTHMESSWEA 315


>gi|228471651|ref|ZP_04056425.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           gingivalis ATCC 33624]
 gi|228277070|gb|EEK15756.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           gingivalis ATCC 33624]
          Length = 343

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/325 (26%), Positives = 151/325 (46%), Gaps = 49/325 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  N   + +   +Q+  + G + V+   VK N+R+++   V++        
Sbjct: 24  QEPLRVDKFLMNFVENASRNKVQQAAKDGNIFVNGVAVKANHRVKANDEVKV-----MFA 78

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIA 126
           H   E  ++   + L          ++YED ++ + NKPAG+ V  G         +G+ 
Sbjct: 79  HPPHEYLLVPEPIPLD---------IVYEDEELIIINKPAGLVVHPGHGNYQGTLINGLI 129

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH      +  D    +P L HR+D++TSG+LVVA+T  A  HL + F  +  ++ Y +L
Sbjct: 130 YHFQHLPMNSSD----RPGLVHRIDKDTSGLLVVAKTEEAMNHLAKQFFNKTSEREYVAL 185

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWL 243
           VWG     +  I   + +  H        V  +      AI+H+KV++ F       C L
Sbjct: 186 VWGNLAQDEGTIIGHIGR--HPKNRLQMTVFPDGSEGKEAITHYKVLERFGYVTIVSCRL 243

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKLYLH 291
           E    TGRTHQ+R H  ++G P+  D +Y  +   KG  ++           I  +  LH
Sbjct: 244 E----TGRTHQIRAHFTYIGHPLFNDERYGGDKILKGTTSAKYKQFVENCFKILPRQALH 299

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHM 315
           A+ + +  P  G+ L+  + +P  M
Sbjct: 300 AKTLGVEKPSTGQMLRFDSEIPQDM 324


>gi|330977498|gb|EGH77444.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. aptata str. DSM 50252]
          Length = 320

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 96/338 (28%), Positives = 154/338 (45%), Gaps = 46/338 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLELIAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    + +   LD               ++YED +I V NKPAG+ V   +G   H DG
Sbjct: 71  EAQGEWVAQDIELD---------------IIYEDDQILVINKPAGLVVHPAAG---HADG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  
Sbjct: 113 TLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +V G+     +  A        IG  G     +   E G   A+SH++V++ F +    +
Sbjct: 173 IVIGVVTAGGKIDAP-------IGRHGQQRQRMAVME-GGKQAVSHYRVLERF-RSHTHV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK----GNFTSPIQNKLY----LHARYM 295
            ++  TGRTHQ+RVH  H+  P+VGD  Y   F+     + T     K +    LHAR++
Sbjct: 224 RVKLETGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFL 283

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +L HP  G R+   +PLP   V  W     K DR  +I
Sbjct: 284 ELDHPTTGKRISWESPLPDDFV--WLLSLLKQDREAFI 319


>gi|163747421|ref|ZP_02154773.1| ribosomal large subunit pseudouridine synthase D [Oceanibulbus
           indolifex HEL-45]
 gi|161379274|gb|EDQ03691.1| ribosomal large subunit pseudouridine synthase D [Oceanibulbus
           indolifex HEL-45]
          Length = 348

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 94/359 (26%), Positives = 154/359 (42%), Gaps = 60/359 (16%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M++ +   +  D    RLD+      P   +++   L +++  G V VD   V     ++
Sbjct: 1   MSHRRIDFILGDSPPARLDKALARDVPEAANLSRTRLGRLIEEGAVTVDGAVVHDPRAKV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             GQVV+I     A +HI+ E   L                +++ED  + V +KPAG+ V
Sbjct: 61  AEGQVVQIKVEEAAESHILPEDIPLS---------------VVFEDDDLIVIDKPAGMVV 105

Query: 120 QG--GSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               GS     ++  L    D        ++P + HR+D++T+G+LVVA++ AA   L  
Sbjct: 106 HPAPGSPSGTLVNALLAHCGDDLSGVGGMKRPGIVHRIDKDTTGLLVVAKSDAAHHGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK----------- 221
            F    +++ Y +LV+G+P      +   +   S   G+ + +  Q  +           
Sbjct: 166 QFEKHTVERYYQTLVYGVPDANDPRL-RGVKGASFEAGNILRMTTQLARHKTDRQRQAVL 224

Query: 222 --GANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             G  +A++  + I+ F          CWLE    TGRTHQ+RVH  H G  +VGD  Y 
Sbjct: 225 FQGGRHAVTRARTIERFGTPPVLALLECWLE----TGRTHQIRVHMSHAGHGLVGDATYG 280

Query: 274 ANFKGNFTSPIQN---------KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
              K   T+  +          +  LHA  +   HP  G  L+  APLP+ M    + L
Sbjct: 281 GRRKLAKTALPEATADAIRAFPRQALHAAVLGFEHPVTGENLRFEAPLPSDMAALLNLL 339


>gi|15889714|ref|NP_355395.1| ribosomal large subunit pseudouridine synthase D [Agrobacterium
           tumefaciens str. C58]
 gi|15157624|gb|AAK88180.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Agrobacterium tumefaciens str. C58]
          Length = 340

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/251 (30%), Positives = 121/251 (48%), Gaps = 37/251 (14%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           YED  + V  KPAG+ V  G+G         + YH    L      K  +P + HRLD+E
Sbjct: 94  YEDEDLIVLVKPAGLVVHPGAGNWTGTLVNALIYHCGDSLSGIGGVK--RPGIVHRLDKE 151

Query: 154 TSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           TSG++VVA+   A +HL   F    R   +++ Y ++VWG P+  +  +   L +    G
Sbjct: 152 TSGVMVVAKNDNAHRHLAAQFADHGRTGPLERAYKAVVWGRPRTLRGTVDAALGR----G 207

Query: 210 GDYVHVVKQNEKG--ANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALH 261
            D      +NE    A  AI+H++V++ F +K         +E +  TGRTHQ+RVH  H
Sbjct: 208 TDRTKRAVKNEDSFDAREAITHYEVMERFHEKPDASCLASMVECRLETGRTHQIRVHMAH 267

Query: 262 MGCPIVGDHKYCANFKGN---FTSPIQNKL------YLHARYMDLPHPEGGR-LQITAPL 311
           +G P++GD +Y A F+        P ++ +       LHA  +   HP  G  ++    +
Sbjct: 268 IGHPLIGDPEYGAAFRTKANLLDEPARSTVNRFPRQALHAYLLAFEHPRTGEVMEFETDM 327

Query: 312 PAHMVKTWDSL 322
           P  M +   +L
Sbjct: 328 PEDMEELVTAL 338


>gi|290968210|ref|ZP_06559753.1| pseudouridine synthase, RluA family [Megasphaera genomosp. type_1
           str. 28L]
 gi|290781692|gb|EFD94277.1| pseudouridine synthase, RluA family [Megasphaera genomosp. type_1
           str. 28L]
          Length = 305

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 89/310 (28%), Positives = 143/310 (46%), Gaps = 41/310 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +RLD +       ++    Q +++ G VRV     K N R++ GQ + +        
Sbjct: 12  DEGVRLDVYVARML-SVSRTYAQDLIKKGLVRVQDNMGKANCRLEDGQCITVS------- 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
                      S  L+   + +   +LYED+ I V NK  G+ V    G         + 
Sbjct: 64  --------FSPSAVLSAEPENIPLHILYEDAHIIVVNKARGMVVHPAPGNPSGTLVNALL 115

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH  G L     +   +P + HRLD++TSG++VVA+T  A + L    +     + YW+L
Sbjct: 116 YHCGGELSGI--NGVIRPGIVHRLDKDTSGVMVVAKTDPAHRGLAAQIKAHTAHRTYWAL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLE 244
           V G    ++  I      ++ IG      +K     KG   A +HF V+  + + + WL 
Sbjct: 174 VHGNIAEERGTI------EAPIGRHPKDRIKMAVTFKGGREATTHFHVLQRYGE-YTWLA 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQ+RVH  ++  P+V D  Y    + +F  PIQ ++ LH+R +D  HP  G 
Sbjct: 227 CRLETGRTHQIRVHLAYIRHPVVNDPVY-GYKRDDF--PIQGQV-LHSRCLDFVHPVTGE 282

Query: 305 -LQITAPLPA 313
            + + AP  A
Sbjct: 283 PMHVEAPPAA 292


>gi|89891672|ref|ZP_01203175.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BBFL7]
 gi|89516007|gb|EAS18671.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BBFL7]
          Length = 349

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/317 (27%), Positives = 152/317 (47%), Gaps = 52/317 (16%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--- 67
              + +E +R+D++  N   +     +Q+ ++ G VRV+ + VK N ++++G  +R+   
Sbjct: 25  TASDGQEPLRVDKYLMNFIENATRSKIQQSIKDGAVRVNDEVVKSNYKVKAGDHIRVLFK 84

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
            PP  N L   + E   LD               ++YED  + V NKPAG+ V  G G  
Sbjct: 85  HPPHENLL---VPEDIPLD---------------IVYEDDTLVVVNKPAGMVVHPGHGNY 126

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  + +H D       ++   +P L HR+D++TSG+LVVA+T  A  +L+  F  +
Sbjct: 127 SGTLINALIHHFDNL----PNNSSNRPGLVHRIDKDTSGLLVVAKTEHAMSYLSAQFAAK 182

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             ++ Y ++VWG    +   +   + +  K+ +  +YV   ++  KG   A++H+ VI+ 
Sbjct: 183 TSEREYVAIVWGNFDEQSGTVEGNIGRHPKNRL-QNYVWSGEEAFKGKP-AVTHWSVIEG 240

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---------P 283
                  +  +  TGRTHQ+RVH  H+G  +  D +Y  +   KG +FT           
Sbjct: 241 LGY-VTMISCKLETGRTHQIRVHMKHIGHTLFNDERYGGDKILKGTSFTKYKQFVDNCMK 299

Query: 284 IQNKLYLHARYMDLPHP 300
           I  +  LHA+ +   HP
Sbjct: 300 ILPRQALHAKTLGFEHP 316


>gi|71735208|ref|YP_273032.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|257481618|ref|ZP_05635659.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           tabaci ATCC 11528]
 gi|289626965|ref|ZP_06459919.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           aesculi str. NCPPB3681]
 gi|289651379|ref|ZP_06482722.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           aesculi str. 2250]
 gi|298485413|ref|ZP_07003502.1| Ribosomal large subunit pseudouridine synthase D [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|71555761|gb|AAZ34972.1| Ribosomal large subunit pseudouridine synthase D(Pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|298160063|gb|EFI01095.1| Ribosomal large subunit pseudouridine synthase D [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|320326249|gb|EFW82303.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           glycinea str. B076]
 gi|320330673|gb|EFW86650.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330869191|gb|EGH03900.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           aesculi str. 0893_23]
 gi|330891573|gb|EGH24234.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. mori str. 301020]
 gi|330901397|gb|EGH32816.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. japonica str. M301072PT]
 gi|330954255|gb|EGH54515.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae Cit 7]
 gi|330971944|gb|EGH72010.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. aceris str. M302273PT]
 gi|331008769|gb|EGH88825.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           tabaci ATCC 11528]
          Length = 320

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 96/338 (28%), Positives = 154/338 (45%), Gaps = 46/338 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLELIAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    + +   LD               ++YED +I V NKPAG+ V   +G   H DG
Sbjct: 71  EAQGEWVAQDIELD---------------IIYEDDQILVINKPAGLVVHPAAG---HADG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  
Sbjct: 113 TLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +V G+     +  A        IG  G     +   E G   A+SH++V++ F +    +
Sbjct: 173 IVIGVVTAGGKIDAP-------IGRHGQQRQRMAVME-GGKQAVSHYRVLERF-RSHTHV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK----GNFTSPIQNKLY----LHARYM 295
            ++  TGRTHQ+RVH  H+  P+VGD  Y   F+     + T     K +    LHAR++
Sbjct: 224 RVKLETGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFL 283

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +L HP  G R+   +PLP   V  W     K DR  +I
Sbjct: 284 ELDHPTTGKRMSWESPLPDDFV--WLLSLLKQDREAFI 319


>gi|58698738|ref|ZP_00373623.1| ribosomal large subunit pseudouridine synthase D [Wolbachia
           endosymbiont of Drosophila ananassae]
 gi|58534736|gb|EAL58850.1| ribosomal large subunit pseudouridine synthase D [Wolbachia
           endosymbiont of Drosophila ananassae]
          Length = 282

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 94/284 (33%), Positives = 146/284 (51%), Gaps = 47/284 (16%)

Query: 59  IQSGQVVRIP-PVINALNHIIK--EQKIL-----DSSVNLTKHSDFLKSILLYEDSKIYV 110
           IQ+GQV  +  P+IN  +HI+K  E+ I+     D S ++  + D +K  ++YED  I V
Sbjct: 2   IQNGQVKLLGIPIINN-DHIVKPGEEYIVHLVQPDISTSIEPNYD-IKLDIVYEDEDIIV 59

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTR 164
            +K +G++V  G+G     D  L + +   G+      +P + HRLD++TSG++V+A+  
Sbjct: 60  LSKQSGLTVHPGAGTNN--DTLLNAVIAHLGKIPYSHVRPGIVHRLDKDTSGLMVIAKNE 117

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            A   L+E    R+I++ Y ++VWGI  +++  I   +  K     + + V K   K   
Sbjct: 118 EAHGFLSELLSNRKIKREYLAIVWGILSSQQGTIKTNIAPKRG-NKEMMCVTKITGK--- 173

Query: 225 YAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------ 275
            AI+H+   KVI   +   C LE    TGRTHQ+RVH  H+G  IVGD  Y  N      
Sbjct: 174 LAITHYLVQKVIGQVSLVKCTLE----TGRTHQIRVHMSHIGHSIVGDQVYGKNSSKSTK 229

Query: 276 ------FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
                 F  NF     N+  LHA  + L HP+  G ++  + LP
Sbjct: 230 YAKNSSFIRNF-----NRQALHAYTLGLYHPKSKGYMEFVSDLP 268


>gi|218129090|ref|ZP_03457894.1| hypothetical protein BACEGG_00664 [Bacteroides eggerthii DSM 20697]
 gi|317474871|ref|ZP_07934141.1| RNA pseudouridylate synthase [Bacteroides eggerthii 1_2_48FAA]
 gi|217988725|gb|EEC55044.1| hypothetical protein BACEGG_00664 [Bacteroides eggerthii DSM 20697]
 gi|316909009|gb|EFV30693.1| RNA pseudouridylate synthase [Bacteroides eggerthii 1_2_48FAA]
          Length = 223

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 111/219 (50%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKLYLKEKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L + F+   ++K YW++V   P   +  + N+L++       Y + 
Sbjct: 63  GLVVFAKTSKALTRLNDMFKNGEVKKTYWAVVKNQPHEPEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   +Q +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPNSKKAILHYRLI-AKSQNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
             G+  S     + LHAR++   HP    L ++ AP+P 
Sbjct: 177 --GSPRSNPDGSICLHARFVRFIHPVSKELIEVEAPVPT 213


>gi|227538361|ref|ZP_03968410.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
 gi|227241876|gb|EEI91891.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
          Length = 230

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 115/220 (52%), Gaps = 17/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR----LTHRLDQETSG 156
           ++YED+ +   NK AG  VQ        +D  +K +++ K +KP     + HRLD+  SG
Sbjct: 10  VIYEDNHLIAINKRAGDIVQVDDSGDKSLDMMVKEYLERKYEKPNAFIGVIHRLDRPVSG 69

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVH 214
           ++V A+T      + + F  R ++K Y ++V   P+     + NWL++  K  I   Y  
Sbjct: 70  LIVFAKTSKGLDRMNKLFHDRDVEKSYLAVVRNKPEQMSAKLQNWLVRDRKKMITKAY-- 127

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              +  KG++YA   ++VI    + +  L ++P TGRTHQ+RV    MGCPIVGD+KY  
Sbjct: 128 --NREIKGSSYAELDYEVIGEL-EGYYLLHVKPKTGRTHQIRVQLSTMGCPIVGDNKY-- 182

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
              G     ++  + LH+R +   HP +   +++ A LP 
Sbjct: 183 ---GYPRGSLRRSICLHSRSLSFVHPVKDEPMKLVAGLPV 219


>gi|255012061|ref|ZP_05284187.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis 3_1_12]
 gi|313149904|ref|ZP_07812097.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis 3_1_12]
 gi|313138671|gb|EFR56031.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis 3_1_12]
          Length = 224

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 71/218 (32%), Positives = 110/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQGDKTGDTPLSETVKQYLKDKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E F+   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTSKALSRLNEMFKNSEVRKTYWAVVKNCPKQPEGELIHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI  +K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPNSKKAILSYKLIG-RSDNYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             G+  S     + LHARY+   HP    L ++ AP+P
Sbjct: 177 --GSPRSNPDGSICLHARYVRFVHPVSKELIELDAPVP 212


>gi|237801870|ref|ZP_04590331.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. oryzae str. 1_6]
 gi|330962679|gb|EGH62939.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. maculicola str. ES4326]
 gi|331024728|gb|EGI04784.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. oryzae str. 1_6]
          Length = 320

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 98/338 (28%), Positives = 155/338 (45%), Gaps = 46/338 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLEL---- 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                 I EQ+     V      D     ++YED +I V NKPAG+ V   +G   H DG
Sbjct: 67  ------IAEQEAQGEWVAQDIELD-----IIYEDDQILVINKPAGLVVHPAAG---HADG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  
Sbjct: 113 TLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +V G+     +  A        IG  G     +   E G   A+SH++V++ F +    +
Sbjct: 173 IVIGVVTAGGKIDAP-------IGRHGQQRQRMAVME-GGKQAVSHYRVLERF-RSHTHV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK----GNFTSPIQNKLY----LHARYM 295
            ++  TGRTHQ+RVH  H+  P+VGD  Y   F+     + T     K +    LHAR++
Sbjct: 224 RVKLETGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFL 283

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +L HP  G R+   +PLP   V  W     K DR  +I
Sbjct: 284 ELDHPITGKRMSWESPLPDDFV--WLLSLLKQDREAFI 319


>gi|152976253|ref|YP_001375770.1| RluA family pseudouridine synthase [Bacillus cereus subsp.
           cytotoxis NVH 391-98]
 gi|152025005|gb|ABS22775.1| pseudouridine synthase, RluA family [Bacillus cytotoxicus NVH
           391-98]
          Length = 302

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 84/313 (26%), Positives = 148/313 (47%), Gaps = 33/313 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +N R+D++  +     +   +Q+ ++ G + V+ K VK N +++    + +         
Sbjct: 14  KNERIDKFVASVNHEWSRTQVQQWIKDGVITVNGKTVKGNYKVKENDEITV--------- 64

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
            + E + LD        ++ +   + YED+ + V NKP G+ V    G      ++G + 
Sbjct: 65  TVPEPEELDI------RAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMY 118

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y ++V G+
Sbjct: 119 HCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRRYQAIVHGV 178

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             + K  I   + +           V +N K   +A++HF+V++ F + F  +E +  TG
Sbjct: 179 IPHDKGTIDAPIARDKK--DRQSMAVDENGK---HAVTHFQVLERF-KDFTLVECRLETG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++G P+ GD KY      N      N   LHA  +   HP  G  LQ  A
Sbjct: 233 RTHQIRVHMKYIGYPLAGDPKYGPKKTLNL-----NGQALHAGILGFNHPRTGEYLQFEA 287

Query: 310 PLPAHMVKTWDSL 322
           P PA   +T + L
Sbjct: 288 PAPAIFEETLNIL 300


>gi|162533081|ref|YP_001621404.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213971041|ref|ZP_03399161.1| Ribosomal large subunit pseudouridine synthase D(Pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           tomato T1]
 gi|301384235|ref|ZP_07232653.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. tomato Max13]
 gi|302059468|ref|ZP_07251009.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. tomato K40]
 gi|302134990|ref|ZP_07260980.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. tomato NCPPB 1108]
 gi|118201618|gb|ABK79681.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213924149|gb|EEB57724.1| Ribosomal large subunit pseudouridine synthase D(Pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           tomato T1]
 gi|330878989|gb|EGH13138.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
 gi|330966362|gb|EGH66622.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. actinidiae str. M302091]
 gi|331018389|gb|EGH98445.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. lachrymans str. M302278PT]
          Length = 320

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 98/338 (28%), Positives = 155/338 (45%), Gaps = 46/338 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLEL---- 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                 I EQ+     V      D     ++YED +I V NKPAG+ V   +G   H DG
Sbjct: 67  ------IAEQEAQGEWVAQDIELD-----IIYEDDQILVINKPAGLVVHPAAG---HADG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  
Sbjct: 113 TLLNALLHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +V G+     +  A        IG  G     +   E G   A+SH++V++ F +    +
Sbjct: 173 IVIGVVTAGGKIDAP-------IGRHGQQRQRMAVME-GGKQAVSHYRVLERF-RSHTHV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK----GNFTSPIQNKLY----LHARYM 295
            ++  TGRTHQ+RVH  H+  P+VGD  Y   F+     + T     K +    LHAR++
Sbjct: 224 RVKLETGRTHQIRVHMAHVNYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFL 283

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +L HP  G R+   +PLP   V  W     K DR  +I
Sbjct: 284 ELDHPITGKRMSWESPLPDDFV--WLLSLLKQDREAFI 319


>gi|307564398|ref|ZP_07626939.1| pseudouridine synthase, RluA family [Prevotella amnii CRIS 21A-A]
 gi|307346758|gb|EFN92054.1| pseudouridine synthase, RluA family [Prevotella amnii CRIS 21A-A]
          Length = 361

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 89/342 (26%), Positives = 155/342 (45%), Gaps = 58/342 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  ++  R+D++      H +   +QK  ++G + V+   VK N +++   V+ +  
Sbjct: 31  IEVDKGQKAERIDKYLFERMQHSSRNRIQKAAQAGFIHVNGSPVKSNYKVRPEDVITL-- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I    + L          ++YED  + V  KPAG+ V  G+G     
Sbjct: 89  ---MLDRPKHDNTIEAEDIPLD---------VVYEDDSLMVVMKPAGLVVHPGAGNFHGT 136

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+ G   +  D+   +  L HR+D++TSG+L++A+T  A   L + F  +   
Sbjct: 137 LINAIAWHLRGL--ASFDANDPEVGLVHRIDKDTSGLLLIAKTPEAKSSLGKQFFYKTTH 194

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDY---------VHVVKQNEKGANYAISHFK 231
           + Y +LVWG          N + ++  I G+          + V          A++H+K
Sbjct: 195 RSYIALVWG----------NIVDEQGRIEGNISRDPKDRLRMTVFPPESDIGKPAVTHYK 244

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQ 285
           VI+ F      +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S     +Q
Sbjct: 245 VIERFGYT-TLIECVLETGRTHQIRAHMKHIGHPLFGDERYGGREILRGQRSSSYKAFVQ 303

Query: 286 N------KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
           N      +  LHA+ +   HP  G ++  T+PLP  +    D
Sbjct: 304 NGFKICPRQALHAKTLGFVHPVTGEQMDFTSPLPDDLSALID 345


>gi|308069397|ref|YP_003871002.1| Pseudouridylate synthase, 23S RNA-specific [Paenibacillus polymyxa
           E681]
 gi|305858676|gb|ADM70464.1| Pseudouridylate synthase, 23S RNA-specific [Paenibacillus polymyxa
           E681]
          Length = 248

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 71/217 (32%), Positives = 110/217 (50%), Gaps = 14/217 (6%)

Query: 90  LTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--- 145
           LT+H     +I +LYED+ +    KP  +  Q  +     +   LK  +  +  KP    
Sbjct: 6   LTRHEHAQPNIPVLYEDNHVLAVVKPVNVPTQEDASGDPDLLSLLKEDLKIRHNKPGNVF 65

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+   G ++ A+T  AA  L+ES R R   K+Y +++ G+P   +  + ++LL
Sbjct: 66  LGLVHRLDRPVGGAMIFAKTSKAASRLSESVRSRHFHKLYTAVLNGVPTAPQGRLTHYLL 125

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           K S    + V  V+    GA  AI  ++VI   A     ++++ HTGR+HQ+RV    +G
Sbjct: 126 KDSRT--NTVQAVRPGTAGAKEAILEYRVIGQ-ADGLSLVQIKLHTGRSHQIRVQMQAIG 182

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           CP+ GD KY     GN + P Q +L L +     PHP
Sbjct: 183 CPLYGDQKYG----GNLSRPGQ-QLALWSLLAGAPHP 214


>gi|321314645|ref|YP_004206932.1| putative RNA pseudouridine synthase [Bacillus subtilis BSn5]
 gi|320020919|gb|ADV95905.1| putative RNA pseudouridine synthase [Bacillus subtilis BSn5]
          Length = 302

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 76/227 (33%), Positives = 113/227 (49%), Gaps = 30/227 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED+ + + NKPAGI+      G +G     IAYH        ++ +  K R  HRLD
Sbjct: 85  ILYEDNHMLIVNKPAGIATHPNEDGQTGTLANLIAYHYQ------INGETCKVRHVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q+TSG +V A+ R A   L +    + +++ Y ++  G  + KK  I       S IG D
Sbjct: 139 QDTSGAIVFAKHRLAHAILDQQLEKKTLKRTYTAIAEGKLRTKKGTI------NSPIGRD 192

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             H  ++    G   A++HFKV+   A ++   +E++  TGRTHQ+RVH   +G P+ GD
Sbjct: 193 RSHPTRRRVSPGGQTAVTHFKVMASNAKERLSLVELELETGRTHQIRVHMASIGHPLTGD 252

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHM 315
             Y    K      + N+  LHA  +   HP    L +  AP PA M
Sbjct: 253 SLYGGGSK------LLNRQALHANKVQAVHPITDELIVAEAPFPADM 293


>gi|149371695|ref|ZP_01891111.1| ribosomal large subunit pseudouridine synthase D [unidentified
           eubacterium SCB49]
 gi|149355322|gb|EDM43882.1| ribosomal large subunit pseudouridine synthase D [unidentified
           eubacterium SCB49]
          Length = 348

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/326 (26%), Positives = 148/326 (45%), Gaps = 59/326 (18%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V +  ++ +R+D++  N   +     +QK  + G + V+   VK N ++++  VV +   
Sbjct: 24  VADKGQQPLRVDKYLMNRVENATRSKIQKAAKEGNIFVNNVIVKSNYKVKANDVVTV--- 80

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                H   E  +    +++          ++YED  + V NK  G+ V  G G      
Sbjct: 81  --LFAHPPYELLLTPEDIDID---------IVYEDDDLLVVNKQPGMVVHPGHGNYSGTL 129

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + +HID    +  ++   +P L HR+D++TSG+LVVA+T  A  HL + F  +  ++
Sbjct: 130 INALIHHID----NLPNNSSNRPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTTER 185

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIG-------GDYVHVVKQNEKGANYAISHFKVID 234
            Y +LVWG  ++ +  I      + HIG        + V + +  E+    A++HFKV++
Sbjct: 186 EYVALVWGNIEDDEGTI------EGHIGRHPKNRLQNTVFLDEDAEEKGKAAVTHFKVLE 239

Query: 235 CFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN--- 286
            F       C LE    TGRTHQ+RVH   +G  +  D +Y      KG   S  +    
Sbjct: 240 RFGYVTLVSCKLE----TGRTHQIRVHMKFIGHTLFNDERYGGEKILKGTTFSKYKQFVD 295

Query: 287 -------KLYLHARYMDLPHPEGGRL 305
                  +  LHAR +   HP  G +
Sbjct: 296 NCFKVLPRQALHARTLGFVHPTTGEM 321


>gi|168705355|ref|ZP_02737632.1| pseudouridine synthase [Gemmata obscuriglobus UQM 2246]
          Length = 238

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 75/238 (31%), Positives = 116/238 (48%), Gaps = 30/238 (12%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTH 148
           S  L   +LYED  + V NKPA +  Q   G+  +++  +++++  K  KP      + H
Sbjct: 4   SAALPLAVLYEDHHLVVVNKPAPLLTQAPPGVP-NLEERVRAYIKDKYAKPAGVYLGVPH 62

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+  SG++  AR   AAQ +   F  R ++K+YW+LV G+           +   + +
Sbjct: 63  RLDRPVSGVVCFARNTKAAQRVHSQFEHRSVRKVYWALVEGV-----------VEPDAGV 111

Query: 209 GGDYVHVVK---------QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             DY+  V+         + E GA  A   F+V++ FA     +E+ P TGR HQLRV +
Sbjct: 112 WDDYIRKVENEARAARGHEGEPGAKLATLEFRVLERFA-AHTRIELHPLTGRMHQLRVQS 170

Query: 260 LHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAH 314
              G P++GD  Y +   F      P    + LHAR +   HP     L I AP+PA+
Sbjct: 171 AWRGHPVIGDSLYGSVRPFGPPAELPRDRVIALHARRLTFEHPFTKQELVIEAPVPAY 228


>gi|167957398|ref|ZP_02544472.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [candidate division TM7 single-cell isolate
           TM7c]
          Length = 379

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/309 (27%), Positives = 139/309 (44%), Gaps = 41/309 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++E+  +  RLD          +    QK++ +GQV VD K  K      + Q+V I   
Sbjct: 105 LLESKSDKKRLDILLVEKVGKESRSTYQKMITAGQVLVDGKIAK-----NAKQLVGI--- 156

Query: 71  INALNHIIKEQKILDSSVNL-TKHSDF--LKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                         +S+V + +K   F  +K   +YED+ I V NKPAG+       IA 
Sbjct: 157 --------------ESNVKIESKQQKFTPIKYETIYEDNDIIVINKPAGMLTHAKGAIAE 202

Query: 127 -YHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            +     +K   + K    +P + HRLD+ TSG+L++ +   AA  + + F  R ++K Y
Sbjct: 203 EFTAADIVKPITNYKADTNRPGIIHRLDRNTSGVLLMVKNSDAASKIQKQFSQRTVKKTY 262

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V GIP   K  I   + +       +   V       +Y +          +    +
Sbjct: 263 YAIVCGIPYQHKALIDLPIERNPSRPSTFRVGVNGKSAQTSYEVER----SIIKKNISLI 318

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++QP TGRTHQLRVH  ++  PI+GD  Y          P + +++LHA  +++    G 
Sbjct: 319 KLQPKTGRTHQLRVHMQYLNTPILGDLVYGGK-------PAE-RMFLHAESLEVTLLSGE 370

Query: 304 RLQITAPLP 312
           R    APLP
Sbjct: 371 RKVFKAPLP 379


>gi|253576153|ref|ZP_04853485.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251844496|gb|EES72512.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 315

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 88/315 (27%), Positives = 148/315 (46%), Gaps = 41/315 (13%)

Query: 20  RLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIPPVINALNHI 77
           R+D++ K       +   +Q  + +G + V+   VK N ++  G ++V + P       I
Sbjct: 27  RIDKYAKTQLGEEFSRSQIQLWIEAGNLVVNGAPVKANYKLAEGDRIVLVIPEAEP-TEI 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL---- 133
           + E   L+               + YEDS + V NKP G+ V    G   H  G L    
Sbjct: 86  VPEDIPLE---------------IYYEDSDVIVVNKPRGMVVHPAPG---HTSGTLVNAL 127

Query: 134 ----KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               K      G+ +P + HR+D++TSG+++ A+   A   L    +   + + Y++LV 
Sbjct: 128 MFHCKDLSGINGELRPGIVHRIDKDTSGLIMAAKNDKAHASLAAQLKAHTVTRKYYALVH 187

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G   + +  +   + +  H    Y  V+++N K   +A++HF+V++ F   +  LE++  
Sbjct: 188 GNVSHDQGTVDAPIGRDPHDRKMYT-VIERNSK---HAVTHFQVVERFGD-YTLLELKLE 242

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH   +G P+VGD  Y     G       +   LHA  +   HPE G+ L+ 
Sbjct: 243 TGRTHQIRVHMKFIGHPLVGDPLY-----GRSKGIKMDGQALHAAVLGFDHPEDGQYLEF 297

Query: 308 TAPLPAHMVKTWDSL 322
           +AP+PA M     SL
Sbjct: 298 SAPIPADMENVLQSL 312


>gi|220904744|ref|YP_002480056.1| pseudouridine synthase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|219869043|gb|ACL49378.1| pseudouridine synthase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 360

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 80/300 (26%), Positives = 137/300 (45%), Gaps = 14/300 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           +  +  VV+  E   +L ++ +    ++    L + +R+GQVR++  R K  +R+Q+G  
Sbjct: 17  SVTEIPVVQEPESGQKLLQFLQRRL-NLPQAMLHRWVRTGQVRINGSRCKPFSRVQTGDT 75

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTK----HSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           VR+PP    +           +S   +K            L+ +   ++ F+KPAG+ V 
Sbjct: 76  VRLPPFAMKMAAQCDSASPTPASKGKSKDDAPEDGPPLPPLVGKSGYLWAFDKPAGLPVH 135

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G+G    +   L          P   HRLD+ TSGI++VA + AA      + R   + 
Sbjct: 136 PGTGHEDSLTTRLSCHFAGVSFMPTPVHRLDRGTSGIILVAASYAALDETQRALRANAMH 195

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGG-DYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           K Y + V G   + + C+    L+K  + G + V  VK +   A  A+   + +   A +
Sbjct: 196 KEYVAWVAGRWPHTQTCLVRHFLRKEAVDGFERVRPVKADAPDAKEALCLVRALS-IADR 254

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              ++++  TGRTHQ+RV    +G P++GD KY     G         LYLH+  + LP 
Sbjct: 255 ASLVQVRLLTGRTHQIRVQLSSLGHPVLGDTKYGQTRAG-------VALYLHSLRVILPE 307


>gi|325680269|ref|ZP_08159829.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
 gi|324107978|gb|EGC02234.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
          Length = 304

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/322 (27%), Positives = 148/322 (45%), Gaps = 38/322 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   ++   R+D+        ++   LQK+   G V V  K V  N ++++G V+ +   
Sbjct: 8   IAAPEDAGTRIDKLLSAQLSDMSRSALQKLTEDGSVLVGGKAVSKNYKLKNGDVITV--- 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                 I + Q+       L      +   ++YED  + V NKP G+ V   +G      
Sbjct: 65  -----DIPEPQE-------LKAEPQDIPIDIVYEDDALLVVNKPKGMVVHPAAGNPDGTL 112

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + YH  G L S   +   +P + HR+D+ TSG+L+VA+T  A   L    +     +
Sbjct: 113 VNALLYHCKGRLSSI--NGVIRPGIVHRIDKFTSGLLMVAKTDKAHNSLAAQIKEHSFTR 170

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++  G  K     I N  + +S      + V  QN K    A++H++VI+   Q + 
Sbjct: 171 EYNAVCVGRFKEPTGTI-NEPIGRSKFDRKKMCVTYQNSK---EAVTHYEVIEELGQ-YS 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH+  +G P++GD  Y   +KG     I+ +  LHA+ +   HPE
Sbjct: 226 LVRFRLETGRTHQIRVHSAFIGHPVLGDDVYGRPYKG-----IEGQC-LHAKKLGFVHPE 279

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++  + LP +  +  D L
Sbjct: 280 TGEYMEFDSQLPDYFTRILDKL 301


>gi|108757756|ref|YP_630767.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108461636|gb|ABF86821.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 316

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 93/336 (27%), Positives = 155/336 (46%), Gaps = 38/336 (11%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + +  + V+ D+   R+D  F      ++   L+++  +G V+V+ +  K    + +GQ 
Sbjct: 4   SKLHTLTVDADKAGQRVD-LFIGEALGLSRARLKRLFEAGAVKVNGRPAKKGLTLTAGQ- 61

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV----Q 120
                      HI  E  + + S      +DF  ++L  +DS ++V +KPAG        
Sbjct: 62  -----------HIAVE--VEEESREAVPDADFPLTVLHEDDSLVFV-DKPAGRPSHPLQS 107

Query: 121 GGSG------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G +G      +A + +  L S    +G    L HRLD ETSG++V ARTR A   + E+F
Sbjct: 108 GETGTVANALVARYPECALASLDAREGG---LCHRLDVETSGVVVAARTRDAWNAVREAF 164

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             R + K Y +LV G   ++ +   +  L+      D V       + A  A+S F V+ 
Sbjct: 165 GSRAVDKRYLALVTGPLTDEGDI--DLPLRHHPRHPDRVEPAPYGAEDARDAVSKFTVL- 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
             + +F  +E++  TG  HQ+R H   +G PIVGD  Y     G   +P   + +LHAR 
Sbjct: 222 SRSGEFSVVEVKILTGVLHQVRAHLAGIGAPIVGDSLY-----GGREAPELGRFFLHARS 276

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           + L HP+  R + + +PLP  +    +  G    R 
Sbjct: 277 LGLTHPQTRRNMTVHSPLPPELRAELERRGLPLPRG 312


>gi|118443119|ref|YP_878025.1| ribosomal large subunit pseudouridine synthase D [Clostridium novyi
           NT]
 gi|118133575|gb|ABK60619.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium novyi NT]
          Length = 304

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 95/317 (29%), Positives = 147/317 (46%), Gaps = 48/317 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++  DE N RLD +    +   +    QK++    V V+    K N ++++G  V +   
Sbjct: 7   LINEDEANSRLDVFISKCFEEKSRSYAQKLIEDKNVLVNGSIKKSNYKLKTGDNVEV--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                  IKE    D ++N+      +K  +LYED  + V +KP G+ V  G+G      
Sbjct: 64  ------TIKE----DETINIEPED--IKLNILYEDEDVIVIDKPQGMVVHPGNGNYSGTL 111

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + YH D       D +   P + HR+D++TSG+LVVA+   A   L+E  +   +++
Sbjct: 112 VNGLLYHCDSLSSINGDVR---PGIVHRIDKDTSGVLVVAKNDNAHIILSEQLKEHSMKR 168

Query: 182 IYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            Y +LV GI K+ +  I   L +  K  I    V       +    AI+H++VI  F + 
Sbjct: 169 EYVALVEGIIKDDEGTIDEPLGRNPKDRIKRAVV-------RNGKNAITHYEVIRRFNKN 221

Query: 240 F---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
               C LE    TGRTHQ+RVH  H+  P+VGD  Y    K  F     N   LHAR + 
Sbjct: 222 TLVKCILE----TGRTHQIRVHMAHINHPLVGDPMYGFK-KQRFK---LNGQMLHARKLG 273

Query: 297 LPHPEGGR-LQITAPLP 312
             HP   + ++  + LP
Sbjct: 274 FIHPSSKKYMEFQSELP 290


>gi|153209393|ref|ZP_01947379.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           'MSU Goat Q177']
 gi|120575364|gb|EAX31988.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           'MSU Goat Q177']
          Length = 323

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 88/333 (26%), Positives = 155/333 (46%), Gaps = 39/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   +++  Q + I  
Sbjct: 11  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEA 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 71  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 115

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            I+  L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y +
Sbjct: 116 LINALLH-YDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           +V G+  + +         ++ +G   +H  +    +    AI+HF++I  + +    + 
Sbjct: 175 IVKGVLISGRTI-------EAPVGRHPIHRTRMAVVEFGRPAITHFRIIKRY-RAHTHIR 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKL------YLHARYMD 296
           +Q  TGRTHQ+RVH  H+  P+ GD  Y ++     + + P+Q  L       LH   + 
Sbjct: 227 VQLETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHGATLQ 286

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             HP   R +   APLPA M    + L   Y +
Sbjct: 287 FSHPVDQRPMACHAPLPADMAHLLECLEDDYSQ 319


>gi|154483515|ref|ZP_02025963.1| hypothetical protein EUBVEN_01219 [Eubacterium ventriosum ATCC
           27560]
 gi|149735425|gb|EDM51311.1| hypothetical protein EUBVEN_01219 [Eubacterium ventriosum ATCC
           27560]
          Length = 301

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 84/315 (26%), Positives = 151/315 (47%), Gaps = 42/315 (13%)

Query: 15  DEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPV 70
           DEE  ++R+DR+     P ++   +QK+L+  ++ ++ K VK N ++Q    + I  P  
Sbjct: 8   DEELFDIRIDRYLSELLPDVSRSFIQKLLKDNEILLNDKPVKANYKVQPSDKININIPKP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-------- 122
           + A  +I+ E   LD               ++YED    + NKP  + V           
Sbjct: 68  VEA--NIVAENIPLD---------------IIYEDDDFLIVNKPKDMVVHPAPGHYTGTL 110

Query: 123 -SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            +G+ YH    L +   +   +P + HR+D++T+G L++ +   +   + E  ++  I +
Sbjct: 111 VNGLMYHCKNHLSNI--NGVLRPGIVHRIDKDTTGALIICKNDYSHNFIAEQLKVHSITR 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y  +V G+ K++   I N  + +  +    + +   N K    A++H+KV+  F  K+ 
Sbjct: 169 KYVGIVQGVVKDESGTI-NAPIGRHPVNRKEMAI---NHKNGKEAVTHYKVLKRF-DKYT 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           ++E Q  TGRTHQ+RVH   +  P++GD  Y  N K  F    Q    LHA+ +   HP 
Sbjct: 224 FMEFQLETGRTHQIRVHMASIHHPLLGDTVYNHN-KCPFKLEGQ---CLHAKTIGFIHPT 279

Query: 302 GGR-LQITAPLPAHM 315
               ++  AP+P +M
Sbjct: 280 TKEYVEFEAPIPEYM 294


>gi|259415714|ref|ZP_05739634.1| ribosomal large subunit pseudouridine synthase D [Silicibacter sp.
           TrichCH4B]
 gi|259347153|gb|EEW58930.1| ribosomal large subunit pseudouridine synthase D [Silicibacter sp.
           TrichCH4B]
          Length = 345

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 96/352 (27%), Positives = 153/352 (43%), Gaps = 68/352 (19%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           +++V+ +N  +  RLD+      P   +++   L +++ SG V VD         R+  G
Sbjct: 6   IEFVIADNPPK--RLDKAIARDVPEEANLSRTRLARLIESGGVEVDGAVASDAKARVLEG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--Q 120
             + I       +HI  E   LD               ++YED+ + V NKPAG+ V   
Sbjct: 64  AQIVITVEDAEESHIGPEDIALD---------------VIYEDADLIVINKPAGMVVHPA 108

Query: 121 GGSGIAYHIDGFLK-SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            GS     ++  L     D  G    ++P + HR+D+ETSG+LVVA++ AA Q L   F 
Sbjct: 109 PGSPSGTLVNALLHHCGADLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQFE 168

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------------G 222
              +++ Y ++ +G+P      +   +   S   G+ + +  Q  +             G
Sbjct: 169 RHSVERYYQAVCYGVPDANDPRL-RGVRGASFEPGNILKLTTQLARHKTDRQRQAVLFEG 227

Query: 223 ANYAISHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +A++  ++I+ F          CWLE    TGRTHQ+RVH  H G  ++GD  Y    
Sbjct: 228 GRHAVTRARIIEAFGAPAAASLVECWLE----TGRTHQIRVHMAHAGHGLLGDPTYGGKR 283

Query: 277 KGNFTSP----------IQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           K    SP          I N  +  LHA  +   HP  G  ++  APLP  M
Sbjct: 284 K---ISPKALSAAGLVAINNFHRQALHAAVLGFEHPVSGEMMRFEAPLPEDM 332


>gi|77461057|ref|YP_350564.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens Pf0-1]
 gi|77385060|gb|ABA76573.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens Pf0-1]
          Length = 320

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 89/336 (26%), Positives = 156/336 (46%), Gaps = 42/336 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G ++ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKEGRLTVDGAVIRPRDIVHGGAILELTAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    + +   LD               ++YED  I V NKPAG+ V   +G   H DG
Sbjct: 71  EAQGEWVAQDIELD---------------IVYEDDDILVINKPAGLVVHPAAG---HADG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  
Sbjct: 113 TLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTKLVAQLQSRSVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+     +   N  + +       + V++    G   A+SH++V++ F +    + +
Sbjct: 173 IVIGVVTAGGKI--NAPIGRHGQQRQRMAVME----GGKPAVSHYRVLERF-RSHTHVRV 225

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQN-----KLYLHARYMDL 297
           +  TGRTHQ+RVH  H+  P+VGD  Y   F+       + +++     +  LHAR+++L
Sbjct: 226 KLETGRTHQIRVHMAHINFPLVGDPAYGGRFRIPPAASQTMVESLKHFPRQALHARFLEL 285

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            HP  G R+   +PLP  +V  W     K DR  ++
Sbjct: 286 DHPTTGERMSWESPLPEDLV--WLLTLLKQDREAFV 319


>gi|297182616|gb|ADI18775.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF4000_36I10]
          Length = 319

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 88/313 (28%), Positives = 147/313 (46%), Gaps = 44/313 (14%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T     V+ ++    RLD+     +P  +   LQ  ++SG++ V+  + +  ++I  G+ 
Sbjct: 4   TIALSAVIPDELAGSRLDQAVAQLFPDYSRSRLQSWIKSGELTVNGSQYRPRDKIMGGEE 63

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+              ++ D      +  DF    L YED  + V NKP G+ V   +G
Sbjct: 64  IRV------------GAELQDEGDWQPQQIDF---GLFYEDEHLLVLNKPVGLVVHPAAG 108

Query: 125 IAYHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              H DG L + +        Q PR  + HRLD++TSG++VVA+T  A   L +  + R 
Sbjct: 109 ---HYDGTLVNALIEHCPGLAQLPRAGIVHRLDKDTSGLMVVAKTLEAHTSLVKQLQARN 165

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--- 235
           + + Y +LV+G+     +   +  + +       + VV+    G   AI+H+++I+    
Sbjct: 166 VHREYEALVYGVMTGGGKV--DEPMGRHPQQRKKMAVVR---AGGKEAITHYRIIERFTH 220

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQN-----K 287
           F+   C LE    TGRTHQ+RVH  H+  P++GD  Y       KG     I+      +
Sbjct: 221 FSHVRCLLE----TGRTHQIRVHMAHIKHPLIGDALYAGRLRQPKGASELLIETLRTFRR 276

Query: 288 LYLHARYMDLPHP 300
             LHAR ++L HP
Sbjct: 277 QALHARKLELIHP 289


>gi|47570307|ref|ZP_00240954.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           G9241]
 gi|47553016|gb|EAL11420.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           G9241]
          Length = 302

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 88/319 (27%), Positives = 148/319 (46%), Gaps = 39/319 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINGEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKEND 60

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V IP          +E  I    +NL          + YED+ + V NKP G+ V  
Sbjct: 61  EITVTIPDP--------EELDIQAEDMNLE---------IYYEDADVLVVNKPRGMVVHP 103

Query: 122 GSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L     
Sbjct: 104 APGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLV 163

Query: 176 MRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V++
Sbjct: 164 AKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVLE 217

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  
Sbjct: 218 RF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGI 271

Query: 295 MDLPHPEGGR-LQITAPLP 312
           +   HP  G  +Q  AP+P
Sbjct: 272 LGFDHPRTGEYIQFEAPIP 290


>gi|255014662|ref|ZP_05286788.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_1_7]
          Length = 549

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 79/236 (33%), Positives = 124/236 (52%), Gaps = 31/236 (13%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---YHID 130
           LNH+++  ++ ++ +    H +  K  +LYED  + + NKPAG+    G G A   YH  
Sbjct: 316 LNHMLQGLQVDENPLLADSHRE-TKLDILYEDDYLLIVNKPAGMLSVPGKGDADSVYHRL 374

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG- 189
             L  + D+ G  P + HRLD  TSG+L+ A+T+ A Q+L   F+ R IQK Y +L+ G 
Sbjct: 375 RIL--YPDATG--PIIVHRLDMATSGLLLAAKTKEAHQNLQAQFKNRTIQKRYIALLEGE 430

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +P+++ E        +  +  D +   +Q  +E+    A + ++V++  + K   +   P
Sbjct: 431 VPQDEGEI-------RLPLCPDPLDRPRQIVSEEFGKPAFTRYRVLERTSGK-TLIAFYP 482

Query: 248 HTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            TGRTHQLRVHA H   + CPI+GD  Y              +LYLHA Y+   HP
Sbjct: 483 QTGRTHQLRVHAAHPLGLHCPILGDELYGRK---------AERLYLHAEYLAFTHP 529


>gi|312114651|ref|YP_004012247.1| pseudouridine synthase [Rhodomicrobium vannielii ATCC 17100]
 gi|311219780|gb|ADP71148.1| pseudouridine synthase, RluA family [Rhodomicrobium vannielii ATCC
           17100]
          Length = 358

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 101/363 (27%), Positives = 163/363 (44%), Gaps = 68/363 (18%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQV-------V 65
            D+  +RLDR+  +     + V LQ+++R+G  VR+   R    +   S +V       V
Sbjct: 15  EDDAGVRLDRFLASRIETQSRVRLQELIRAGHVVRLAAGRDAETSTDPSAKVRLGDTFEV 74

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
             PP   A N+ ++ + I    +N           ++YED+ + V +KPAG+ V  G+G 
Sbjct: 75  TTPP---AENYAVEGEAI---ELN-----------VVYEDASLIVIDKPAGLVVHPGAGN 117

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF---- 174
                ++  +    DS        +P + HRLD+ TSG++VVA+T  A + L+  F    
Sbjct: 118 PNGTLVNALIAHCGDSLSGIGGVTRPGIVHRLDKNTSGLMVVAKTDKAHRSLSAQFADHG 177

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAISH-F 230
           R   +++ Y +LVWG P+     I   + +  H G      V +N   E    YA    F
Sbjct: 178 RTGALRREYLALVWGEPQPTSGRIEARIAR--HAGSRIKMAVVRNGGREAATIYATERVF 235

Query: 231 KVIDCFAQKFC---W--------LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG- 278
           ++ +  +Q      W        L  +  TGRTHQ+RVH  H+G P+VGD  Y A F+  
Sbjct: 236 RLGNVESQSAAMGKWNKTATLSVLRCKLETGRTHQVRVHLAHIGVPLVGDSVYGAGFRTK 295

Query: 279 ----------NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
                     NF      +  LHA  +   HP   + L   +PLP  + +  ++L  ++D
Sbjct: 296 ALALPDEAARNFA--CAERQALHAAGLRFEHPSSRKVLSFESPLPEDIAQLCNAL-ERFD 352

Query: 328 RNL 330
             L
Sbjct: 353 AKL 355


>gi|326203544|ref|ZP_08193408.1| pseudouridine synthase, RluA family [Clostridium papyrosolvens DSM
           2782]
 gi|325986364|gb|EGD47196.1| pseudouridine synthase, RluA family [Clostridium papyrosolvens DSM
           2782]
          Length = 304

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/303 (28%), Positives = 145/303 (47%), Gaps = 35/303 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++E D + +R+D W   +    +   +QK+   G + V++ + K N +++ G  +++   
Sbjct: 5   ILECDTDGVRIDSWLAGNLEDYSRSYIQKLCLDGNIWVNEVQAKSNYKVKPGDNIKVS-- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                  + + +ILD         + +   ++YED  I V NKP G+ V    G      
Sbjct: 63  -------VPDAEILDVE------PEDIPLDIVYEDKHIIVINKPKGMVVHPAVGNYSGTL 109

Query: 129 IDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  +K   DS        +P + HR+D++TSG+LVVA++  A + L+E  +   I++ Y
Sbjct: 110 VNALMKHCGDSLSDINGVIRPGIVHRIDKDTSGLLVVAKSNIAHERLSEKLKTHDIKREY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC 241
            +LV GI       I       + IG   V   K   N +    AI+HFKV++ F     
Sbjct: 170 IALVDGIIYENSGKI------DAPIGRHPVERKKMSVNTQNGRNAITHFKVLERFPSA-T 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +++++  TGRTHQ+RVH  ++  PI+GD  Y    K  F +  Q    LHA  +   HP 
Sbjct: 223 YVQLKLETGRTHQIRVHMSYINHPIIGDMVY-GRRKQKFKTKGQ---VLHAWRLSFQHPV 278

Query: 302 GGR 304
            G 
Sbjct: 279 TGE 281


>gi|119513315|ref|ZP_01632353.1| Pseudouridine synthase, RluD [Nodularia spumigena CCY9414]
 gi|119462022|gb|EAW43021.1| Pseudouridine synthase, RluD [Nodularia spumigena CCY9414]
          Length = 309

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 92/316 (29%), Positives = 149/316 (47%), Gaps = 49/316 (15%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-------RVKFNNRIQSGQVVRI 67
           +E   RLDR+   + P+++   +Q+++  G V ++++        VK  +RI     + I
Sbjct: 9   EETGERLDRYLSENLPNLSRSRIQQLIEQGNVHLNEQICTTKKITVKAGDRI----TLEI 64

Query: 68  PPVINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           P V   L   ++ Q I LD               +LYED  + + NKPAG+ V    G  
Sbjct: 65  PEV-QPLQ--VQAQDIPLD---------------ILYEDDHLLILNKPAGLVVHPAPG-- 104

Query: 127 YHIDGFLKSWV-----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            H DG L + +     +  G    Q+P + HRLD++T+G + +A+T  A   L    + +
Sbjct: 105 -HPDGTLVNALLAHCPNLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYHSLQAQLQAK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++ Y  +V+G PK +   I   + +  H        V   EKG   A++H+++++   
Sbjct: 164 TARREYLGVVYGAPKTENGKIDEPIGR--HPQDRKKMAVVPIEKGGRNAVTHWQILERLG 221

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            +   L  Q  TGRTHQ+RVH+  +G PIVGD  Y +           N   LHA  + L
Sbjct: 222 NQTLVL-FQLETGRTHQIRVHSAKIGHPIVGDPIYSSAHSVGVKL---NGQALHAWRLKL 277

Query: 298 PHPEGGRL-QITAPLP 312
            HP    L ++TAP P
Sbjct: 278 QHPISENLIEVTAPPP 293


>gi|265768298|ref|ZP_06095557.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_16]
 gi|263252233|gb|EEZ23781.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_16]
          Length = 221

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 111/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VIYEDNHIIVVNKTASEIVQGDKTGDTPLSETVKQYLKDKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E F+   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTSKALSRLNEMFKNSEVKKTYWAIVKNCPKQSEGELVHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI ++K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPNSKKAILNYKLIG-HSDHYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             G+  S     + LHAR++   HP    L ++ AP+P
Sbjct: 177 --GSARSNPDGSICLHARHVRFVHPVSKELIELDAPVP 212


>gi|163941632|ref|YP_001646516.1| RluA family pseudouridine synthase [Bacillus weihenstephanensis
           KBAB4]
 gi|229013077|ref|ZP_04170242.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus mycoides
           DSM 2048]
 gi|163863829|gb|ABY44888.1| pseudouridine synthase, RluA family [Bacillus weihenstephanensis
           KBAB4]
 gi|228748331|gb|EEL98191.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus mycoides
           DSM 2048]
          Length = 302

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 152/321 (47%), Gaps = 43/321 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVKGNYKVKGND 60

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            + +          I E + LD     +NL          + YED+ + V NKP G+ V 
Sbjct: 61  EITV---------TIPEPEELDIQPEDMNLE---------VYYEDADVLVVNKPRGMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTKGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKV 232
             + + + Y ++V G+  + K  I       + IG D      +  +E G N A++HF+V
Sbjct: 163 VAKTVTRRYKAIVHGVIPHDKGII------DAPIGRDKKERQSMTVDENGKN-AVTHFQV 215

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++ F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA
Sbjct: 216 LERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHA 269

Query: 293 RYMDLPHPEGGR-LQITAPLP 312
             +   HP  G  ++  AP+P
Sbjct: 270 GILGFDHPRTGEYIEFEAPIP 290


>gi|123965457|ref|YP_001010538.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9515]
 gi|123199823|gb|ABM71431.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9515]
          Length = 320

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 88/313 (28%), Positives = 148/313 (47%), Gaps = 42/313 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +  P  +   +Q ++ +G V ++ K  K    +++G  ++I  PP    L +
Sbjct: 27  MRLDRWLVSKRPEQSRARIQNLINAGLVLINYKTAKAKTPLKTGDNIQIWMPPP-EPLVY 85

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E+  L+               +LYED  I V NK +G+ V    G      ++G L 
Sbjct: 86  LKPEKMHLN---------------ILYEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLF 130

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++TSG +VVA+++ +  +L    R +   + Y +++ G+
Sbjct: 131 HCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQESLVNLQIQIRDKIASRNYIAVIHGV 190

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           P   +  I        HIG D ++ +K    +E    YA +++K+++ F   +  +  + 
Sbjct: 191 PNTSEGKIV------GHIGRDKINRLKYAVVDENSGRYACTYWKLLERFGN-YSLMSFKL 243

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
            TGRTHQ+RVH  ++  PI+GD  Y  C            +   LHA  + L HP  G  
Sbjct: 244 DTGRTHQIRVHCAYINHPILGDPLYGRCKKLPCKL-----DGQALHAIELGLFHPINGEE 298

Query: 305 LQITAPLPAHMVK 317
           ++  A LP   VK
Sbjct: 299 MKFEADLPQEFVK 311


>gi|225375845|ref|ZP_03753066.1| hypothetical protein ROSEINA2194_01477 [Roseburia inulinivorans DSM
           16841]
 gi|225212280|gb|EEG94634.1| hypothetical protein ROSEINA2194_01477 [Roseburia inulinivorans DSM
           16841]
          Length = 216

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 66/203 (32%), Positives = 108/203 (53%), Gaps = 8/203 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +LYED ++ V  KPAG++ Q        ++  LK++   KG++P +   HRLDQ   G++
Sbjct: 5   ILYEDEEVIVCEKPAGVAAQTRRLGQADMESLLKNYRAGKGEQPYIGVVHRLDQPVRGVM 64

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+T+ AA  L+   + +   K Y+++  G+P+ KK  + ++LL+      +   VV +
Sbjct: 65  VFAKTKEAAADLSRQVQTKMADKFYYAVTDGVPEQKKGTLEDYLLRDGKT--NTSKVVSK 122

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +GA  A   ++V     +    L ++  TGR HQ+RV   + G PIVGD KY  NFK 
Sbjct: 123 STEGAKSARLDYEVT-AQNKTNAVLRIRLDTGRHHQIRVQLANAGIPIVGDTKY--NFKE 179

Query: 279 NFTSPIQNKLYLHARYMDLPHPE 301
             T    N L L +  +   HP+
Sbjct: 180 TMTRS-GNGLLLCSYKIGFKHPK 201


>gi|291543834|emb|CBL16943.1| pseudouridine synthase, RluA family [Ruminococcus sp. 18P13]
          Length = 326

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 69/282 (24%), Positives = 139/282 (49%), Gaps = 32/282 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + ++ ++   RLD++     P +    + K +R+  ++ + KR   ++R++ G V  
Sbjct: 1   MRQITIQQNDAGQRLDKFLAKSMPALPKGLMCKFIRTKHIKRNGKRCAISDRLEPGDV-- 58

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI----LLYEDSKIYVFNKPAGISVQGG 122
                  L   I +    + +   T   DFLK+     ++YED+++ + NKP G+ V   
Sbjct: 59  -------LTFFISDDFFPEHAPQQT--PDFLKAPAKLDVVYEDTQVLILNKPVGLVVHAD 109

Query: 123 SG---------IAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHL 170
           +G         + +H+  +     D  G++   P L +RLD+ T G+++ A+T AA + +
Sbjct: 110 NGGTEDTLIHRVLHHL--YQAGTYDPAGEQSFTPALCNRLDRNTGGLVIAAKTAAALRDV 167

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            E  R R++ K Y  +   +P  +++ +  +  K+    G+ V +     +G     + +
Sbjct: 168 NELIRSRQLCKQYLCVTAALPPRQQDRVQAYHRKQP--AGNLVEIRDAPAEGFAPIDTEY 225

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +V+    Q    + +  HTGRTHQ+R H  H+G P++GD+KY
Sbjct: 226 RVL-AQEQGLSLVLVTLHTGRTHQIRAHLAHLGAPLLGDNKY 266


>gi|325265702|ref|ZP_08132391.1| ribosomal large subunit pseudouridine synthase D [Kingella
           denitrificans ATCC 33394]
 gi|324982833|gb|EGC18456.1| ribosomal large subunit pseudouridine synthase D [Kingella
           denitrificans ATCC 33394]
          Length = 367

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 87/320 (27%), Positives = 151/320 (47%), Gaps = 39/320 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V N+    RLD       P  +   +   ++ G V+ + +     +++  G+++R+  
Sbjct: 25  LTVPNELAGTRLDAALAKLLPDYSRSRITSWIKDGLVQCNGQTASPKHKLIGGELLRV-- 82

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                       +I  S  N     + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 83  ------------QIQPSDENQAFEPEAMDLDIVYEDDSVIVLNKPAGLVVHPAAGNWTGT 130

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++G L +     GQ PR  + HRLD++TSG++VVA+T  A  HL +  + R +++IY +
Sbjct: 131 LLNGLL-AHCPELGQVPRAGIVHRLDKDTSGLMVVAKTLPAQNHLVQQLQNRSVKRIYRA 189

Query: 186 LVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCW 242
           +  GI P + K         ++ IG D  + +K    + G   A++H  V++ + Q   +
Sbjct: 190 VADGIVPFDGK--------IETLIGRDPHNRLKMAVVKFGGKEAVTHVSVLERY-QAHSY 240

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL------YLHARYMD 296
           +E +  TGRTHQ+RVH      P+ GD  Y  N +   +  ++  +       LHA  + 
Sbjct: 241 IECRLETGRTHQIRVHMREARHPLAGDPVY-GNPRHACSPAVKETVKQLARQALHAHRLS 299

Query: 297 LPHPEGGR-LQITAPLPAHM 315
             HP+ G  L   AP+PA M
Sbjct: 300 FIHPKSGEWLSFEAPIPADM 319


>gi|229134702|ref|ZP_04263511.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-ST196]
 gi|228648748|gb|EEL04774.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-ST196]
          Length = 302

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 152/321 (47%), Gaps = 43/321 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVKGNYKVKGND 60

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            + +          I E + LD     +NL          + YED+ + V NKP G+ V 
Sbjct: 61  EITV---------TIPEPEELDIQPEDMNLE---------VYYEDADVLVVNKPRGMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTKGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKV 232
             + + + Y ++V G+  + K  I       + IG D      +  +E G N A++HF+V
Sbjct: 163 VAKTVTRRYKAIVHGVIPHDKGII------DAPIGRDKKERQSMTVDENGKN-AVTHFQV 215

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++ F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA
Sbjct: 216 LERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHA 269

Query: 293 RYMDLPHPEGGR-LQITAPLP 312
             +   HP  G  ++  AP+P
Sbjct: 270 GILGFDHPRTGEYIEFEAPIP 290


>gi|212212777|ref|YP_002303713.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           CbuG_Q212]
 gi|212011187|gb|ACJ18568.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           CbuG_Q212]
          Length = 327

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 89/333 (26%), Positives = 155/333 (46%), Gaps = 39/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   ++   Q + I  
Sbjct: 15  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVWENQFIEIEA 74

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 75  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 119

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            I+  L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y +
Sbjct: 120 LINALLH-YDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           +V G+  + +         ++ +G   +H  +    +    AI+HF++I  + +    + 
Sbjct: 179 IVKGVLISGRTI-------EAPVGRHPIHRTRMAVVEFGRPAITHFRIIKRY-RAHTHIR 230

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKL------YLHARYMD 296
           +Q  TGRTHQ+RVH  H+  P+ GD  Y ++     + + P+Q  L       LHA  + 
Sbjct: 231 VQLETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHAATLQ 290

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             HP   R +   APLPA M    + L   Y +
Sbjct: 291 FSHPVDQRPMACHAPLPADMAHLLECLEDDYSQ 323


>gi|150024746|ref|YP_001295572.1| 23S rRNA pseudouridine synthase [Flavobacterium psychrophilum
           JIP02/86]
 gi|149771287|emb|CAL42756.1| Probable 23S rRNA pseudouridine synthase [Flavobacterium
           psychrophilum JIP02/86]
          Length = 347

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 84/319 (26%), Positives = 149/319 (46%), Gaps = 43/319 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D++  +   +     +Q+   SG + V+   VK N +++   VV I      L+H  
Sbjct: 30  LRIDKYLMHLLENATRNKIQQAATSGNIFVNNIPVKSNYKVKPFDVVTI-----MLSHPP 84

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E ++    + L          ++YED  + + NKPAG+ V  G G         +A+H 
Sbjct: 85  FENRVDPEDIPLD---------IVYEDDALLLINKPAGLVVHPGHGNYTGTLVNALAFH- 134

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               ++   +  ++P L HR+D++T+G+LV+A+T  A  HL + F  +  ++ Y ++VWG
Sbjct: 135 ---FQNLPLNSSERPGLVHRIDKDTTGLLVIAKTEQAMTHLAKQFENKTSEREYIAIVWG 191

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +  +  I   L +  H+       V  + +    AI+H+KV++ F      +  +  T
Sbjct: 192 NVQKDEGTIEGNLAR--HLKDRMQMAVFADPEIGKPAITHYKVLERFGY-ITVISCKLET 248

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---------PIQNKLYLHARYMDL 297
           GRTHQ+R H  H+G P+  D +Y  +   KG  FT           I  +  LHA+ +  
Sbjct: 249 GRTHQIRAHLKHIGHPLFNDERYGGHLILKGTTFTKYKQFIDNCFKILPRQALHAKTLGF 308

Query: 298 PHPEGGR-LQITAPLPAHM 315
            HP     ++    LP+ M
Sbjct: 309 EHPTTKEMMRFDTNLPSDM 327


>gi|27262446|gb|AAN87504.1| Ribosomal large subunit pseudouridine synthase D [Heliobacillus
           mobilis]
          Length = 327

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 93/325 (28%), Positives = 147/325 (45%), Gaps = 50/325 (15%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E + RLD W  N     +  + Q  ++ G ++V+   VK N R++ G  + + P     
Sbjct: 32  EEVDSRLDVWLVNRELVPSRTHGQNWIKEGLIKVEGMTVKANYRLRPGDRIEVVPAEPVS 91

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
             II E   +D               ++Y+D+ + V NK AG+ V    G         +
Sbjct: 92  TEIIPENIPID---------------IVYQDAHVAVINKSAGLVVHPAEGHTSGTLVNAL 136

Query: 126 AYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            YHI    K      G+ +P + HR+D++TSG+LVVA+   A  HL E  +   +++ Y 
Sbjct: 137 LYHI----KDLSGINGELRPGIVHRIDKDTSGLLVVAKHDEAHIHLAEQVKDHLVRREYL 192

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVIDCFAQK 239
           ++V GI   +   I       + IG D     K  +K A       +++H +V++ F + 
Sbjct: 193 AIVHGIIGAETGRI------DAPIGRDP----KDRQKMAVVSSGKASVTHLRVLERFPES 242

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F  +     TGRTHQ+RVH  ++G P+ GD KY    K  F    Q    LHA  +D  
Sbjct: 243 GFSLVRCNLETGRTHQIRVHMAYIGHPVAGDPKYGPK-KAAFGLEGQ---ALHAHRLDFT 298

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  GR +   A  P    K  ++L
Sbjct: 299 HPHDGREMTFQAEPPETFQKVLETL 323


>gi|212218242|ref|YP_002305029.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           CbuK_Q154]
 gi|212012504|gb|ACJ19884.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           CbuK_Q154]
          Length = 327

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 88/333 (26%), Positives = 155/333 (46%), Gaps = 39/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   +++  Q + I  
Sbjct: 15  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEA 74

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 75  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 119

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            I+  L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y +
Sbjct: 120 LINALLH-YDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           +V G+  + +         ++ +G   +H  +    +    AI+HF++I  + +    + 
Sbjct: 179 IVKGVLISGRTI-------EAPVGRHPIHRTRMAVVEFGRPAITHFRIIKRY-RAHTHIR 230

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKL------YLHARYMD 296
           +Q  TGRTHQ+RVH  H+  P+ GD  Y ++     + + P+Q  L       LH   + 
Sbjct: 231 VQLETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHGATLQ 290

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             HP   R +   APLPA M    + L   Y +
Sbjct: 291 FSHPVDQRPMACHAPLPADMAHLLECLEDDYSQ 323


>gi|53715401|ref|YP_101393.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis YCH46]
 gi|60683368|ref|YP_213512.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis NCTC 9343]
 gi|253567423|ref|ZP_04844871.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_2_5]
 gi|52218266|dbj|BAD50859.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis YCH46]
 gi|60494802|emb|CAH09608.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis NCTC 9343]
 gi|251943805|gb|EES84344.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_2_5]
 gi|301164854|emb|CBW24414.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis 638R]
          Length = 221

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 111/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VIYEDNHIIVVNKTASEIVQGDKTGDTPLSETVKQYLKDKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E F+   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTSKALSRLNEMFKNSEVKKTYWAIVKNCPKQPEGELVHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI ++K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPNSKKAILNYKLIG-HSDHYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             G+  S     + LHAR++   HP    L ++ AP+P
Sbjct: 177 --GSARSNPDGSICLHARHVRFVHPVSKELIELDAPVP 212


>gi|283853730|ref|ZP_06370958.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
 gi|283570880|gb|EFC18912.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
          Length = 333

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 96/316 (30%), Positives = 142/316 (44%), Gaps = 34/316 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           + T VQ   V   E   +L ++        +    LQK +R+GQVR+D KR K  +RI  
Sbjct: 1   MKTPVQTFTVSPAEAGQKLLQYLARRLGSGVPQAALQKFIRTGQVRLDGKRCKPFDRISE 60

Query: 62  GQVVRIPP----VINALNHIIKEQKILDSSVNLTKHS------------DFLKSILLYED 105
           GQ+VR+PP       A      E      +++L +              D +  IL +ED
Sbjct: 61  GQLVRVPPYETDAPGAPPPPKAETGTRGQALHLLRRGGEPARPGDGGRRDIVLDIL-HED 119

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
            ++ V  KPAG+ V  GSG  + +   L          P   HRLD++T+G+L+VA+T  
Sbjct: 120 DELLVVVKPAGLPVHPGSGHPFALTTLLHERHADAPFAPTPAHRLDRDTTGLLLVAKTYR 179

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI---GGDYVHVVKQNEKG 222
             + L E+      +K Y++ V G     +E    WL  +  +   GG     V+ +E G
Sbjct: 180 KLRALHEAMVTGAARKDYFAWVRGRWLLGEE--GEWLTLRDRLAKEGGPGRQRVEASEAG 237

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A+S  +++    Q    LE++  TGRT Q+R      G PIVGD KY     G    
Sbjct: 238 KE-AVSKVRLLAATPQA-SLLEVRLETGRTQQIRAQLASRGYPIVGDAKY-----GGGVP 290

Query: 283 PIQNKLYLHARYMDLP 298
           P    L LHA  + LP
Sbjct: 291 P----LLLHAWRVTLP 302


>gi|313903976|ref|ZP_07837356.1| pseudouridine synthase, RluA family [Eubacterium cellulosolvens 6]
 gi|313471125|gb|EFR66447.1| pseudouridine synthase, RluA family [Eubacterium cellulosolvens 6]
          Length = 311

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 86/323 (26%), Positives = 148/323 (45%), Gaps = 34/323 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            VE ++E+ R+D +  +    ++   +QKIL+ G V V+ K VK N ++     + I   
Sbjct: 7   TVETEDEDTRVDAYLASQIDRMSRSYIQKILKQGGVLVNGKAVKPNYKVCEDDRIEIEIP 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-- 128
            N    I  E   LD               +LYED  + + NKP  + V   +G   H  
Sbjct: 67  ENEELDIEAEDIPLD---------------ILYEDDDVLIVNKPKDMVVHPAAGHYEHTL 111

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L    D         +P + HR+D++T+G LV+ +  AA Q L     +  I + Y
Sbjct: 112 VNALLFHCRDRLSGINGVMRPGIVHRIDKDTTGALVICKNDAAHQSLAAQLAVHSITRRY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G  K++   +   + + ++   D   +   +     +A++H KV+    + + ++
Sbjct: 172 RAIVAGNFKDETFTVEGNIGRSAN---DRKKMAVVSPDKGKHAVTHVKVLQNL-KGYAYV 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPE 301
           E +  TGRTHQ+RVH  H+G P++GD  Y     G    P++      LHA  +   HP 
Sbjct: 228 ECELETGRTHQIRVHMAHIGHPLLGDEIY-----GPKKCPVKGLQGQTLHAMVLGFQHPS 282

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
               ++ TAPLP +  +    LG
Sbjct: 283 TNEYVEFTAPLPEYFEELLRKLG 305


>gi|163786072|ref|ZP_02180520.1| ribosomal large subunit pseudouridine synthase D [Flavobacteriales
           bacterium ALC-1]
 gi|159877932|gb|EDP71988.1| ribosomal large subunit pseudouridine synthase D [Flavobacteriales
           bacterium ALC-1]
          Length = 343

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 95/341 (27%), Positives = 153/341 (44%), Gaps = 60/341 (17%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---- 67
           V+  ++ +R+D++  N   +     +Q   + G + ++   VK N +++    V +    
Sbjct: 22  VDKGQQPLRIDKYLMNFVENATRNKIQSAAKDGCIFINNSPVKSNYKVKPNDFVTVKFKH 81

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
           PP  N L   I E   +D               ++YED  + V NKPAG+ V  G G   
Sbjct: 82  PPHENLL---IAEDIPID---------------VVYEDDDLLVVNKPAGMVVHPGHGNYS 123

Query: 125 ------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 + +H +    +  D    +P L HR+D++TSG+LVVA+T  A  HL+  F  + 
Sbjct: 124 GTLINALIFHFENLPNNSSD----RPGLVHRIDKDTSGLLVVAKTEQAMAHLSNQFAKKT 179

Query: 179 IQKIYWSLVWGIPKNKKECI-ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++ Y +LVWG     +  I  N      +   + V++  + +KG   AI+H+KVI+   
Sbjct: 180 SEREYVALVWGNMTEDEGIIEGNIGRHPKNRLQNTVYLDDEADKGKP-AITHYKVIERLG 238

Query: 238 QKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS---------- 282
                 C LE    TGRTHQ+RVH  H+G  +  D +Y      KG   S          
Sbjct: 239 YVTLVSCKLE----TGRTHQIRVHMKHIGHTLFNDARYGGERILKGTTFSKYKQFVENCF 294

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLP---AHMVKTW 319
            I  +  LHAR +   HP  G  L+  + +P   A  ++ W
Sbjct: 295 KILPRQALHARTLGFEHPTTGEFLRFESEIPEDIAQCIEKW 335


>gi|126738738|ref|ZP_01754434.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           SK209-2-6]
 gi|126719919|gb|EBA16626.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           SK209-2-6]
          Length = 344

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 96/357 (26%), Positives = 153/357 (42%), Gaps = 64/357 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           +++V+ EN  +  RLD+      P    ++   L +++ +G + VD   V     RI  G
Sbjct: 6   IEFVITENPPK--RLDKAVSRDVPEEAALSRTRLARLIEAGSLLVDGVVVLDPKARIAEG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I       +HI  E   L+               ++YED  + V NKPAG+ V   
Sbjct: 64  AQISITVEEAEDSHIGPEDIPLE---------------VIYEDDDLIVINKPAGMVVHPA 108

Query: 123 SGIA--------YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            G           H  G   S V    ++P + HR+D+ETSG+LVVA+T AA Q L   F
Sbjct: 109 PGTPSGTLVNALLHHCGEKLSGVGGV-KRPGIVHRIDKETSGLLVVAKTDAAHQGLAAQF 167

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK------------- 221
               +++ Y ++ +G+P      +   +   S   G+ + +  Q  +             
Sbjct: 168 EKHTVERYYRAVCYGVPDGNDPRL-RGVKGASFESGNILKLTTQLARHKHDRQRQAVLFQ 226

Query: 222 GANYAISHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           G  +A++  ++++ F          CWLE    TGRTHQ+RVH  H G  ++GD  Y   
Sbjct: 227 GGRHAVTRARIVEPFGNPGTAALIECWLE----TGRTHQIRVHMTHAGHSLIGDPTYGGK 282

Query: 276 FKGNF-------TSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            K           S +Q+  +  LHA  +   HP  G  ++  APLP  M +  D L
Sbjct: 283 RKLAAKALSLAGISAVQSFPRQALHAAVLGFTHPVSGEAMRFEAPLPDDMEELIDKL 339


>gi|225010881|ref|ZP_03701348.1| pseudouridine synthase, RluA family [Flavobacteria bacterium
           MS024-3C]
 gi|225004928|gb|EEG42883.1| pseudouridine synthase, RluA family [Flavobacteria bacterium
           MS024-3C]
          Length = 379

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 89/336 (26%), Positives = 153/336 (45%), Gaps = 59/336 (17%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +    +E +R+D++  N   +     +Q+  + G + V+   VK N ++++G  +++   
Sbjct: 58  IASKGQEPLRIDKYLMNFIENATRNKIQQAAKEGHIWVNDLVVKQNYKVKAGDQIKV--- 114

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                H   E  +    + L          ++YEDS + V NKP G+ V  G G      
Sbjct: 115 --MFTHPPYEFLLTPEDIPLD---------VVYEDSDLMVVNKPPGMVVHPGHGNYSGTL 163

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + +H+    K    +  ++P L HR+D++TSG+LVVA+T  A  HL + F  +  ++
Sbjct: 164 INALLFHV----KDLPLNADERPGLVHRIDKDTSGLLVVAKTAKAMTHLAKQFFDKTSER 219

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCF 236
            Y ++VWG  + ++  +      + HIG        + V    ++G   A++H+KV++  
Sbjct: 220 EYVAIVWGNVEEEQGTV------RGHIGRHPKNRLQMAVFPDGDQGKE-AVTHYKVMERL 272

Query: 237 AQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTSPIQ----- 285
                  C LE    TGRTHQ+R H  H+G  +  D +Y      KG  FT   Q     
Sbjct: 273 GYVTLVSCVLE----TGRTHQIRAHMKHIGHTLFNDERYGGEKILKGTTFTKYKQFVDNA 328

Query: 286 ----NKLYLHARYMDLPHPEGGRL-QITAPLPAHMV 316
                +  LHA+ +   HP  G L +   P+P  MV
Sbjct: 329 FKALPRQALHAKTLGFVHPSSGELMRFNTPIPEDMV 364


>gi|282859628|ref|ZP_06268730.1| RNA pseudouridine synthase [Prevotella bivia JCVIHMP010]
 gi|282587546|gb|EFB92749.1| RNA pseudouridine synthase [Prevotella bivia JCVIHMP010]
          Length = 233

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 112/231 (48%), Gaps = 16/231 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + +  K AG  VQG       +   +K W+  K QKP      + HRLD+  +
Sbjct: 3   VVYEDNHLIIVYKEAGEIVQGDKSGDEPLSEMVKRWIKEKYQKPGNVFLGVVHRLDRPVA 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ ART  A   L E FR   I K YW++V   P   +  + +WL++ +     Y + 
Sbjct: 63  GLVIFARTSKALTRLNEMFRNGDIHKTYWAIVQQPPIESENTLTDWLVRNTQQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  A  +I H+K I    +++  LE+   TGR HQ+R    ++GCPI GD KY   
Sbjct: 122 -NMPAPMAKKSILHYKTISS-TERYTLLEVNLMTGRHHQIRCQLANIGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
             G   S     + L +  ++  HP    ++++ +PLP  M   W ++  K
Sbjct: 177 --GAARSNPDGSICLLSHKVEFVHPVSKKKIKVVSPLP--MDNLWQAINPK 223


>gi|255528132|ref|ZP_05394960.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
 gi|296186658|ref|ZP_06855060.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
 gi|255508173|gb|EET84585.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
 gi|296048695|gb|EFG88127.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
          Length = 305

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 91/331 (27%), Positives = 153/331 (46%), Gaps = 43/331 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK--KRVKFNNRIQS 61
           M   ++++ EN   N RLD +        +   +Q ++   QV+V+   K+  +  +I+ 
Sbjct: 1   METREFIIDEN-SVNTRLDLFLSERMEDKSRSYIQGLIEKSQVKVNGILKKSNYKLKIKD 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
             ++ IP                   V L    + +   ++YEDS + V NKP G+ V  
Sbjct: 60  KILITIP-----------------DPVGLDIEPEDIPLDIVYEDSDVIVVNKPQGMVVHP 102

Query: 122 GSGI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            SG+     ++  L    D  G     +P + HR+D++TSGILVVA+   +   L E  +
Sbjct: 103 ASGVYTGTLVNALLNHCSDLSGINGVTRPGIVHRIDKDTSGILVVAKNDKSHNKLAEQLK 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              + + Y +LV GI K + E   +  L +  +    + V+K  ++    A++H++V++ 
Sbjct: 163 DHSMTRAYTALVEGILK-EDEGTIDKPLGRHPVERIKISVIKDGKR----AVTHYRVLER 217

Query: 236 FAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           F       C LE    TGRTHQ+RVH  ++G P+VGD  Y    K  F     N   LHA
Sbjct: 218 FKSNTLVECVLE----TGRTHQIRVHMAYIGHPLVGDPVYGYK-KQKFN---LNGQMLHA 269

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + +   HP     ++ T+ LP +  K  + L
Sbjct: 270 KKLGFIHPSTNEYIEFTSDLPDYFKKVLNVL 300


>gi|188585950|ref|YP_001917495.1| pseudouridine synthase, RluA family [Natranaerobius thermophilus
           JW/NM-WN-LF]
 gi|179350637|gb|ACB84907.1| pseudouridine synthase, RluA family [Natranaerobius thermophilus
           JW/NM-WN-LF]
          Length = 328

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 90/322 (27%), Positives = 145/322 (45%), Gaps = 51/322 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +RLD +       ++    + ++ +  V V+   VK +  I SG VV++        
Sbjct: 22  DEGLRLDLYLSEQIEDLSRSKAKMLINNNSVMVNDNWVKASYSITSGDVVKV-------- 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
               + +++ S + L   S  L   ++YED  + V NKP  + V  G+G         + 
Sbjct: 74  ----DTQLIQSEITLIPQSIPLD--IVYEDEYLLVVNKPRNMVVHPGAGNYRDTMVNALL 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH          +  ++P + HRLD++TSG+LVVA+       L+E  + RR+ + Y +L
Sbjct: 128 YHCQNLSDG---TSYERPGIVHRLDKDTSGLLVVAKQNETHDILSEEIKNRRVARTYLAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK------GANYAISHFKVIDCF--AQ 238
           V G    KK  I         IG D      +N K      G   AI+  +++  F   +
Sbjct: 185 VIGDFSKKKATI------DLPIGRD-----PRNRKKMAVVHGGKRAITKVEMLRSFQNPE 233

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY---LHARYM 295
           K  +L+    TGRTHQ+RVH  H+G P++GD  Y      N    I   L    LH+  +
Sbjct: 234 KISYLKCSLETGRTHQIRVHLSHLGYPLLGDPVYRGKTGKNVD--IDKNLTGQALHSFSL 291

Query: 296 DLPHPEGGRLQI-TAPLPAHMV 316
              HP   +  +  APLP+ M+
Sbjct: 292 AFTHPVFKKTMVFRAPLPSDMM 313


>gi|320354569|ref|YP_004195908.1| RluA family pseudouridine synthase [Desulfobulbus propionicus DSM
           2032]
 gi|320123071|gb|ADW18617.1| pseudouridine synthase, RluA family [Desulfobulbus propionicus DSM
           2032]
          Length = 302

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 83/313 (26%), Positives = 153/313 (48%), Gaps = 30/313 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +V + ++  RLD +     P  +   + K++ +  V V+ ++VK   R+   +++ +  P
Sbjct: 1   MVTSGDQGQRLDHYLIRQLPEQSRSAIGKLIGAAHVLVNGQQVKAGYRLHQDEIITVSFP 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAY 127
              +L+  +  +KI           DF    +L+ED  + V  KP G+ V    G G   
Sbjct: 61  PTPSLD--LAPEKI-----------DF---SILFEDEHLLVIGKPPGLVVHPACGHGGGT 104

Query: 128 HIDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            + G L    D       +P + HRLD++TSG+++VA++  + + L   F+ R+I K Y 
Sbjct: 105 LVHGLLYHCQDLPALDAGRPGIVHRLDKDTSGVMLVAKSERSLRSLMADFKNRKIHKTYH 164

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L+   P+ ++  +   + +      D   +  + ++G  YA +H++V++ F   +C +E
Sbjct: 165 ALLLRSPREREGRLVAPIGRHP---VDRKKMAIRPDQG-KYAATHWRVLESFINGWCLVE 220

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP-EG 302
           +   TGRTHQ+RVH   +  P+ GD  Y    +    +PI+  +  LHA  +   HP   
Sbjct: 221 IGIETGRTHQIRVHMASLRAPVAGDALYGGRVERG--APIKPPRQMLHASTLRFHHPLTN 278

Query: 303 GRLQITAPLPAHM 315
             + +TAPL A M
Sbjct: 279 EEMCLTAPLWADM 291


>gi|160885619|ref|ZP_02066622.1| hypothetical protein BACOVA_03622 [Bacteroides ovatus ATCC 8483]
 gi|237715236|ref|ZP_04545717.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D1]
 gi|237719607|ref|ZP_04550088.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_2_4]
 gi|260172064|ref|ZP_05758476.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D2]
 gi|262405080|ref|ZP_06081630.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_22]
 gi|293371645|ref|ZP_06618056.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|294643576|ref|ZP_06721380.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|294808675|ref|ZP_06767409.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|299147480|ref|ZP_07040545.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 3_1_23]
 gi|315920374|ref|ZP_07916614.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D2]
 gi|156109241|gb|EDO10986.1| hypothetical protein BACOVA_03622 [Bacteroides ovatus ATCC 8483]
 gi|229444545|gb|EEO50336.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D1]
 gi|229450876|gb|EEO56667.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_2_4]
 gi|262355955|gb|EEZ05045.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_22]
 gi|292633342|gb|EFF51912.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|292641071|gb|EFF59285.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|294444114|gb|EFG12847.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|295088159|emb|CBK69682.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           xylanisolvens XB1A]
 gi|298514758|gb|EFI38642.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 3_1_23]
 gi|313694249|gb|EFS31084.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D2]
          Length = 223

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 110/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQ        +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQADKTGDTPLSETVKQYLKEKYQKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR   ++K YW++V   P+  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTSKALTRLNEMFRTSEVKKTYWAVVKNAPQEPEGELVHFLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   ++ +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPNSKKAILHYRLIG-HSENYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             G+  S     + LHAR +   HP    L ++ APLP
Sbjct: 177 --GSPRSNPDGSICLHARRVRFIHPVSKELIELEAPLP 212


>gi|225572138|ref|ZP_03781002.1| hypothetical protein RUMHYD_00432 [Blautia hydrogenotrophica DSM
           10507]
 gi|225040404|gb|EEG50650.1| hypothetical protein RUMHYD_00432 [Blautia hydrogenotrophica DSM
           10507]
          Length = 307

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 94/325 (28%), Positives = 147/325 (45%), Gaps = 44/325 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
            E  +EN R+D++     P I+    QK+L+ G V +D K  K ++R+Q G  +      
Sbjct: 11  AEEQDENQRIDKYLARVMPEISRSYFQKLLKDGGVFIDGKVAKASDRLQCGDEIYFQMPK 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
           +    I  E   LD               +LYED  + V NKP G+ V    G   H  G
Sbjct: 71  SREPDIEPEDLSLD---------------ILYEDPYLLVINKPKGMVVHPCPG---HYSG 112

Query: 132 FLKSWV--DSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            L + V    KGQ        +P + HR+D++T+G LVV +     ++L        I +
Sbjct: 113 TLVNGVLFHCKGQLSGINGVLRPGIVHRIDKDTTGALVVCKDDQTHRNLAVQLAEHTITR 172

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQK 239
            Y ++V G         A+    +  IG   V   K   N K    A++H++V++ F  K
Sbjct: 173 RYRAIVTG------NLSADEGTVEGPIGRHPVDRKKMSINFKNGKDAVTHYRVLERFG-K 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
             ++E +  TGRTHQ+RVH   +G P++GD  Y     G+  +P +     LHA  +   
Sbjct: 226 ATYIECRLETGRTHQIRVHLSSIGHPLLGDTVY-----GSSKNPYELQGQTLHAMVLGFT 280

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP   + ++  APLP +  K  + L
Sbjct: 281 HPYYEKYVEFEAPLPEYFQKMLEKL 305


>gi|289674871|ref|ZP_06495761.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           FF5]
          Length = 256

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 83/249 (33%), Positives = 124/249 (49%), Gaps = 31/249 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW----VDSKGQKPR--LTHRLDQET 154
           ++YED +I V NKPAG+ V   +G   H DG L +     V      PR  + HRLD++T
Sbjct: 21  IIYEDDQILVINKPAGLVVHPAAG---HADGTLLNALLHHVPDIINVPRAGIVHRLDKDT 77

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG--GDY 212
           +G++VVA+T  A   L    + R + +IY  +V G+     +  A        IG  G  
Sbjct: 78  TGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAP-------IGRHGQQ 130

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +   E G   A+SH++V++ F +    + ++  TGRTHQ+RVH  H+  P+VGD  Y
Sbjct: 131 RQRMAVME-GGKQAVSHYRVLERF-RSHTHVRVKLETGRTHQIRVHMAHINYPLVGDPAY 188

Query: 273 CANFK----GNFTSPIQNKLY----LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
              F+     + T     K +    LHAR+++L HP  G R+   +PLP   V  W    
Sbjct: 189 GGRFRIPPAASLTMVDSLKTFPRQALHARFLELDHPTTGKRMSWESPLPDDFV--WLLSL 246

Query: 324 FKYDRNLYI 332
            K DR  +I
Sbjct: 247 LKQDREAFI 255


>gi|326799702|ref|YP_004317521.1| pseudouridine synthase [Sphingobacterium sp. 21]
 gi|326550466|gb|ADZ78851.1| pseudouridine synthase [Sphingobacterium sp. 21]
          Length = 235

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 71/220 (32%), Positives = 110/220 (50%), Gaps = 14/220 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQE 153
           S +LYED+ +   NK AG  VQ        +D  +K ++  K  KP      + HRLD+ 
Sbjct: 11  SDILYEDNHLIAVNKRAGDIVQVDDTGDEPLDEKVKQYLAKKYNKPNGAFLGVVHRLDRP 70

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
            SG+++ A+T  A   + + F+ R + K YW++V   P      + +WL+K S  G +  
Sbjct: 71  VSGVILFAKTSKALDRINKMFKSREMHKTYWAVVRNRPAQTAGTLVHWLVKNS--GKNVT 128

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                  KG+  A  H+K+I      +  +E+ P TGR HQ+RV    + CPIVGD+KY 
Sbjct: 129 KAYDHEVKGSLRAELHYKLIGEL-NGYYLVEVNPVTGRPHQIRVQLASLNCPIVGDNKY- 186

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
               G     ++  + LHAR +   HP +   ++I A LP
Sbjct: 187 ----GYPRGSLKKSICLHARKLVFEHPVKKEEVKIFASLP 222


>gi|301311874|ref|ZP_07217796.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           20_3]
 gi|300829976|gb|EFK60624.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           20_3]
          Length = 546

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/249 (32%), Positives = 131/249 (52%), Gaps = 32/249 (12%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---YHID 130
           L+H+++  ++ ++ +    H +  K  +LYED  + + NKPAG+    G G A   YH  
Sbjct: 316 LHHMLQGLRVDENPLLADSHQE-TKLDILYEDDYLLIVNKPAGMLSVPGKGDADSVYHRL 374

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG- 189
             L  + D+ G  P + HRLD  TSG+L+ A+T+ A Q+L   F+ R IQK Y +L+ G 
Sbjct: 375 HIL--YPDATG--PIIVHRLDMATSGLLLAAKTKEAHQNLQAQFKNRTIQKRYIALLEGE 430

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +P+++ E        +  +  D +   +Q  +E+    A + ++V++  + K   +   P
Sbjct: 431 VPQDEGEI-------RLPLCPDPLDRPRQIVSEEFGKPAFTRYRVLERTSGK-TLIAFYP 482

Query: 248 HTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
            TGRTHQLRVHA H   + CPI+GD  Y              +LYLHA Y+   HP    
Sbjct: 483 QTGRTHQLRVHAAHPLGLHCPILGDELYGRK---------AERLYLHAEYLAFTHPITFE 533

Query: 304 RLQITAPLP 312
           R++I A +P
Sbjct: 534 RIEIRAKIP 542


>gi|332295618|ref|YP_004437541.1| pseudouridine synthase, RluA family [Thermodesulfobium narugense
           DSM 14796]
 gi|332178721|gb|AEE14410.1| pseudouridine synthase, RluA family [Thermodesulfobium narugense
           DSM 14796]
          Length = 319

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 124/247 (50%), Gaps = 23/247 (9%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-------KGQKPRLT 147
           D L   +LYED  I V NK   + V  G G     +  L + ++S         ++P + 
Sbjct: 85  DKLNITVLYEDDYIIVINKERNMVVHPGPG--NFRNTILNALINSINKDEFTDQERPGIV 142

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ET+G+L++A++    + L+E F+ R+++K Y +LV+G   N KE   +  +K+S 
Sbjct: 143 HRLDKETTGVLIIAKSEKIMRKLSEQFKNRQVKKTYLALVYG-DVNYKEGFISMPIKRSK 201

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFC-WLEMQPHTGRTHQLRVHALHMGC 264
           I    + V   N  G   A + + VI+   F ++    L++   TGRTHQ+RVH  ++G 
Sbjct: 202 IHRQKMEV---NLSGK-VAFTEYSVINKGIFEKQIVSLLKVNIFTGRTHQIRVHMSYIGH 257

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
           PIVGD KY      N       ++ LHA  ++  HP   ++    APLP  +        
Sbjct: 258 PIVGDKKYSTKSCKNCP-----EIALHALKIEFLHPITNKIVSFKAPLPQDLQDFLKRCN 312

Query: 324 FKYDRNL 330
             YD +L
Sbjct: 313 INYDLDL 319


>gi|257898611|ref|ZP_05678264.1| pseudouridylate synthase [Enterococcus faecium Com15]
 gi|257836523|gb|EEV61597.1| pseudouridylate synthase [Enterococcus faecium Com15]
          Length = 303

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 90/322 (27%), Positives = 154/322 (47%), Gaps = 51/322 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E+ R+D+   N +   +   +Q  L+   V V+ + VK N +++ G  + +         
Sbjct: 11  ESGRIDKVLTNLFSDYSRSQIQLWLKERAVSVNGQPVKANYKVKQGDEITV--------- 61

Query: 77  IIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
           +I E + LD    ++ LT         ++YED  + V NKP G+ V   +G         
Sbjct: 62  LIPEPETLDVVPENIPLT---------IVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNA 112

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + YHI     S ++    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y 
Sbjct: 113 LMYHIKDL--STINGV-IRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKDKTSLRKYV 169

Query: 185 SLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G IP  K    A     K +     +  ++++ K A   ++HF V++ F + F  +
Sbjct: 170 ALVHGEIPHEKGTINAPIGRSKEN---RKMQAIREDGKPA---VTHFTVLERF-EGFTLV 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E++  TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP 
Sbjct: 223 ELKLETGRTHQIRVHMKYIGYPLAGDPVYGPKKTLKGNGQ-------FLHAQMLGFTHPT 275

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
              ++   APLP    KT + L
Sbjct: 276 TNEKMVFEAPLPEVFEKTLEKL 297


>gi|163742953|ref|ZP_02150336.1| ribosomal large subunit pseudouridine synthase D [Phaeobacter
           gallaeciensis 2.10]
 gi|161383636|gb|EDQ08022.1| ribosomal large subunit pseudouridine synthase D [Phaeobacter
           gallaeciensis 2.10]
          Length = 344

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 91/357 (25%), Positives = 155/357 (43%), Gaps = 62/357 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           +++V+ EN  +  RLD+      P    ++   L +++ +GQ++V+   V     ++  G
Sbjct: 6   IEFVIAENPPK--RLDKAVSRDVPEEATLSRTRLARLIEAGQLQVNGTVVSDAKAKVDEG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++ I       +HI  E   L+               ++YED  + V NKP G+ V   
Sbjct: 64  ALIEITIEEAEDSHIGPEDIPLE---------------VIYEDDDLIVINKPTGMVVHPA 108

Query: 123 SGIAYH--IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G      ++  L    D+       ++P + HR+D+ETSG+LVVA++  A Q L   F 
Sbjct: 109 PGTPSGTLVNALLHHCGDNLSGVGGVKRPGIVHRIDKETSGLLVVAKSDVAHQGLAAQFE 168

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------------G 222
              +++ Y ++ +G+P +  +     +   S   G+ + +  Q  +             G
Sbjct: 169 KHTVERYYRAICYGVP-DANDPRLRGVKGTSFEPGNILKLTTQLARHKTDRQRQAVLFQG 227

Query: 223 ANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---- 272
             +AI+  +++D F          CWLE    TGRTHQ+RVH  H G  +VGD  Y    
Sbjct: 228 GRHAITRARIVDSFGTPPVVALIECWLE----TGRTHQIRVHMAHAGHGLVGDPVYGGKR 283

Query: 273 ---CANFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
                +   +  + IQ   +  LHA  +   HP  G  ++  APLP  M      LG
Sbjct: 284 KLAAKSLPEDTAAAIQAFPRQALHAAVLGFIHPVTGDAMRFEAPLPEDMAHLLQKLG 340


>gi|150008790|ref|YP_001303533.1| ribosomal large subunit pseudouridine synthase A [Parabacteroides
           distasonis ATCC 8503]
 gi|149937214|gb|ABR43911.1| ribosomal large subunit pseudouridine synthase A [Parabacteroides
           distasonis ATCC 8503]
          Length = 549

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 76/233 (32%), Positives = 123/233 (52%), Gaps = 25/233 (10%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L+H+++  ++ ++ +    H +  K  +LYED  + V NKP G+    G G A  +   L
Sbjct: 316 LHHMLQGLRVDENPLLADSHRE-TKLDILYEDDYLLVINKPEGMLSVPGKGDADSVYQRL 374

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPK 192
            S +  +   P + HRLD  TSG+L+ A+T+ A Q+L   F+ R IQK Y +L+ G +P+
Sbjct: 375 -SILYPEATGPIIVHRLDMATSGLLLAAKTKEAHQNLQAQFKNRTIQKRYIALLEGEVPQ 433

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           ++ E        +  +  D +   +Q  +E+    A++H++V++  + K   +   P TG
Sbjct: 434 DEGEI-------RLPLCPDPLDRPRQIVSEEFGKPALTHYRVLERTSGK-TLIAFYPQTG 485

Query: 251 RTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           RTHQLRVHA H   + CPI+GD  Y              +LYLHA Y+   HP
Sbjct: 486 RTHQLRVHAAHPLGLHCPILGDELYGRK---------AERLYLHAEYLAFTHP 529


>gi|88810811|ref|ZP_01126068.1| ribosomal large subunit pseudouridine synthase C [Nitrococcus
           mobilis Nb-231]
 gi|88792441|gb|EAR23551.1| ribosomal large subunit pseudouridine synthase C [Nitrococcus
           mobilis Nb-231]
          Length = 314

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 87/322 (27%), Positives = 159/322 (49%), Gaps = 25/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ V ++ E  RLD +       +    + ++LR GQVRV+  RV+   R++ G  +R
Sbjct: 1   MRHIQVASEYEGQRLDNFLLRELKGLPRTRVYRLLRQGQVRVNGGRVRPEYRLRRGDRLR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGS 123
           +PP+           ++ +  +     +  L+ I   +LYE+ ++ + +KP+G++V GGS
Sbjct: 61  LPPM-----------RLQERELGGAPSARILQRIEQAILYENEQLLILDKPSGLAVHGGS 109

Query: 124 GIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G+AY +   +++     G  P  L HRLD++TSG L++A+ R   + +    R  R++K 
Sbjct: 110 GLAYGVIEAIRAR--RPGTLPLDLAHRLDRDTSGCLIIAKRRETLRQIHALMRSNRVEKR 167

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L+ G   +     A     +   G   +  V Q   G   A++ F  I+   + +  
Sbjct: 168 YLALLRGKLASAMRVEAPL---ERRPGQGLLQPV-QVSIGGRQALTVFHPIERH-RGWTL 222

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYMDLPHP 300
           +++  HTGR HQ+RVHA + G P+ GD +Y  + + N T       +L+LHA  +    P
Sbjct: 223 VDVMLHTGRMHQIRVHAAYSGYPVAGDARY-GDPQANRTLRRFGLRRLFLHASRVAFALP 281

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
              +L + A L   +      L
Sbjct: 282 GQDKLVVQAALSEELAAVLQYL 303


>gi|260171398|ref|ZP_05757810.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D2]
 gi|315919711|ref|ZP_07915951.1| conserved hypothetical protein [Bacteroides sp. D2]
 gi|313693586|gb|EFS30421.1| conserved hypothetical protein [Bacteroides sp. D2]
          Length = 561

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/245 (33%), Positives = 123/245 (50%), Gaps = 29/245 (11%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGS---GIAYHI 129
           L H+++  K+ ++ +  + H D    I+ YED  + V NKPAG +SV G        YH 
Sbjct: 324 LQHMLQGLKVDENPLLNSIHEDEELEIV-YEDEWLVVVNKPAGMLSVPGKEEDRDSVYH- 381

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               K + D+ G  P + HRLD  TSG+L+VA+T+   QHL   F  R I+K Y +++ G
Sbjct: 382 -RLKKKYPDATG--PMIVHRLDMATSGLLLVAKTKEVHQHLQAQFASRSIKKRYVAVLDG 438

Query: 190 IPKNKKECI------ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
                ++ +          L       D    +   E G   AI+ +++I C ++K   +
Sbjct: 439 ATATVEKTVPLPGKAGRIELPLCLNPLDRPRQIVSREHGKE-AITEYRII-CESEKHTRI 496

Query: 244 EMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
              P TGRTHQLRVHA H   +GCPI+GD  Y             ++LYLHA Y++  HP
Sbjct: 497 AFYPLTGRTHQLRVHAAHPEGLGCPILGDELYGKK---------ADRLYLHAEYIEFRHP 547

Query: 301 EGGRL 305
             G++
Sbjct: 548 ISGKI 552


>gi|325287572|ref|YP_004263362.1| pseudouridine synthase [Cellulophaga lytica DSM 7489]
 gi|324323026|gb|ADY30491.1| pseudouridine synthase [Cellulophaga lytica DSM 7489]
          Length = 232

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 72/227 (31%), Positives = 112/227 (49%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I   NK  G  VQG       +   +K+++  K  KP      + HRLD+ T+
Sbjct: 14  VLYEDNHIIAINKRVGDIVQGDKTGDAPLSDIVKAYIKEKYNKPGNVYLGVAHRLDRPTT 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  A   L + F  +  +K YW++V   PK   E + ++L + +     Y ++
Sbjct: 74  GIVVFAKTSKALPRLNKLFAEKDAKKTYWAVVKQQPKKNNETLVHYLKRNTKQNKSYANI 133

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI  + ++      +  LE+   TGR HQ+R     +GCPI GD KY  N
Sbjct: 134 --KEVPDSKKAILDYTILKKL-DNYYLLEINLQTGRHHQIRSQLSGIGCPIKGDLKYGFN 190

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
                 S     ++LHAR +   HP +   L+ITAPLP   +  WD+
Sbjct: 191 -----RSNTDGGIHLHARKLSFIHPVKKEPLEITAPLPKDPI--WDA 230


>gi|255015082|ref|ZP_05287208.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_7]
 gi|256840691|ref|ZP_05546199.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           sp. D13]
 gi|256737963|gb|EEU51289.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           sp. D13]
          Length = 224

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 107/218 (49%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I   +K     VQG       +   LK+W+  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIAVDKTCREIVQGDKTGDKPLSEMLKAWLKEKYCKPGNVFVGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR+  ++K YW++V   P   +  + +WL++       Y + 
Sbjct: 63  GVVIFAKTSKALSRLNEMFRVGEVRKTYWAIVKNRPPQDEGELVDWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  AI  +K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 123 TER--PNAKKAILRYKLI-AHSDNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             G   S     + LHAR  +  HP     ++I AP+P
Sbjct: 177 --GFDRSNKDGGISLHARSAEFIHPVSKENVRIVAPVP 212


>gi|237708677|ref|ZP_04539158.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           9_1_42FAA]
 gi|229457377|gb|EEO63098.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           9_1_42FAA]
          Length = 357

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 94/338 (27%), Positives = 153/338 (45%), Gaps = 51/338 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           VVV+  +  +R+D++      + +   +QK   +G +  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKSSYKVKPCDVLTVMM 91

Query: 68  --PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
             P   NA   II E   LD               ++YED+ + V NKPAG+ V  G G 
Sbjct: 92  DRPRYDNA---IIPEDIPLD---------------IVYEDNDLMVINKPAGLVVHPGCGN 133

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                   IA+H+        D    +  L HR+D++TSG+LVVA+T  A  HL   F  
Sbjct: 134 YHGTLVNAIAWHLKD--NPRYDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYN 191

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDC 235
           +  ++ Y +LVWGI +N +  I   + +      D + + V  +     +A++H++V++ 
Sbjct: 192 KTTKRKYNALVWGIVENNEGTIEGNIGRNPK---DRMQMAVLSDPAQGKHAVTHYRVLER 248

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN------- 286
                  +E    TGRTHQ+RVH  H+G  +  D +Y  N   KG   S  +        
Sbjct: 249 LGY-VTLVECVLETGRTHQIRVHMKHIGHTLFNDERYGGNEILKGTHFSKYKQFVNNCFE 307

Query: 287 ---KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
              +  LHA  +   HP     +  T+PLP  M    D
Sbjct: 308 TCPRQALHAMTLGFVHPRTSEEMFFTSPLPEDMTNLID 345


>gi|221308760|ref|ZP_03590607.1| hypothetical protein Bsubs1_05088 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221313082|ref|ZP_03594887.1| hypothetical protein BsubsN3_05029 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221318008|ref|ZP_03599302.1| hypothetical protein BsubsJ_04973 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221322282|ref|ZP_03603576.1| hypothetical protein BsubsS_05074 [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|255767213|ref|NP_388802.2| RNA pseudouridine synthase [Bacillus subtilis subsp. subtilis str.
           168]
 gi|239938792|sp|P54604|YHCT_BACSU RecName: Full=Uncharacterized RNA pseudouridine synthase yhcT;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|225184840|emb|CAB12749.2| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|291483387|dbj|BAI84462.1| hypothetical protein BSNT_01587 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 302

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 86/283 (30%), Positives = 133/283 (46%), Gaps = 45/283 (15%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           Q++V+ + V  N  ++ G  V I    +  + +I E   LD               +L+E
Sbjct: 44  QIKVNHESVLNNMIVKKGDRVFIDLQESEASSVIPEYGELD---------------ILFE 88

Query: 105 DSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           D+ + + NKPAGI+      G +G     IAYH        ++ +  K R  HRLDQ+TS
Sbjct: 89  DNHMLIINKPAGIATHPNEDGQTGTLANLIAYHYQ------INGETCKVRHVHRLDQDTS 142

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G +V A+ R A   L +    + +++ Y ++  G  + KK  I       S IG D  H 
Sbjct: 143 GAIVFAKHRLAHAILDQQLEKKTLKRTYTAIAEGKLRTKKGTI------NSPIGRDRSHP 196

Query: 216 VKQN-EKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            ++    G   A++HFKV+   A ++   +E++  TGRTHQ+RVH   +G P+ GD  Y 
Sbjct: 197 TRRRVSPGGQTAVTHFKVMASNAKERLSLVELELETGRTHQIRVHLASLGHPLTGDSLYG 256

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHM 315
                   S + N+  LHA  +   HP    L +  AP PA M
Sbjct: 257 GG------SKLLNRQALHANKVQAVHPITDELIVAEAPFPADM 293


>gi|325285479|ref|YP_004261269.1| pseudouridine synthase, RluA family [Cellulophaga lytica DSM 7489]
 gi|324320933|gb|ADY28398.1| pseudouridine synthase, RluA family [Cellulophaga lytica DSM 7489]
          Length = 344

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 94/331 (28%), Positives = 154/331 (46%), Gaps = 46/331 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV    +E +R+D++  N   +     +QK  + G + V+   VK N ++++G  +R+  
Sbjct: 20  VVAAKGQEPLRIDKFLMNFIENATRSQIQKAAKDGHIWVNNVLVKQNYKVKAGDDIRV-- 77

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                +H   E  +    + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 78  ---MFSHPPYEFLLQPEDIPLD---------IVYEDDVLLVVNKPAGMVVHPGHGNYSGT 125

Query: 128 HIDGFLK----SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            I+  L        ++   +P L HR+D++TSG+LVVA+T AA   L++ F  +  ++ Y
Sbjct: 126 LINALLHHCKVDLPNNSSDRPGLVHRIDKDTSGLLVVAKTEAAMTFLSKQFFDKTSEREY 185

Query: 184 WSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF- 240
            ++VWG  +  +  I   L +  K+ +    +HV  + ++G   AI+H+KV++       
Sbjct: 186 VAIVWGNVEADEGTIEGHLGRHPKNRL---QMHVFPEGDQGKE-AITHYKVLERLGYVTV 241

Query: 241 --CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---------PIQN 286
             C LE    TGRTHQ+RVH  H+G  +  D +Y      KG  FT           I  
Sbjct: 242 ISCKLE----TGRTHQIRVHMKHIGHTLFNDERYGGERILKGTTFTKYKQFVENAFKILP 297

Query: 287 KLYLHARYMDLPHPEGGRL-QITAPLPAHMV 316
           +  LHA+ +   HP    L Q    +P  M 
Sbjct: 298 RQALHAKTLGFVHPVTKELMQFNTEIPEDMA 328


>gi|160933118|ref|ZP_02080507.1| hypothetical protein CLOLEP_01961 [Clostridium leptum DSM 753]
 gi|156868192|gb|EDO61564.1| hypothetical protein CLOLEP_01961 [Clostridium leptum DSM 753]
          Length = 306

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 87/333 (26%), Positives = 152/333 (45%), Gaps = 44/333 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+    +V+   EE +RLD+      P +    +Q++L   QV ++ K    N + ++G 
Sbjct: 1   MSEPVELVLSEREEGIRLDKVLAERLPDLTRTAIQRLLEEEQVLINGKPAAKNRKGRAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +              +I D    L   ++ +   ++YED  + V NKP G+ V    
Sbjct: 61  SVAL--------------RIPDPE-PLCLQAENVPLDIVYEDDDLLVVNKPQGMVVHPAP 105

Query: 124 G--IAYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  L    +S        +P + HR+D++TSG+L+VA+   A Q L    + 
Sbjct: 106 GNYQGTLVNALLAHCGNSLSGINGVIRPGIVHRIDKDTSGLLMVAKNDFAHQGLARQIKE 165

Query: 177 RRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              ++ Y ++V G  + K+E  + N  + +  I    + V ++N K    A+++F+VI  
Sbjct: 166 HSFRREYEAVVAG--RMKQESGVVNAPIGRHPIDRKKMAVTEKNSK---EAVTYFRVIAE 220

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYL 290
           +   +  + ++  TGRTHQ+RVH  ++G P+ GD  Y         KG           L
Sbjct: 221 YP-GYTHIRLRLETGRTHQIRVHMAYLGHPVAGDPAYGPRKPDLGLKGQC---------L 270

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           HAR +   HP  GR L+  +PLP +  +    L
Sbjct: 271 HARLIGFVHPRDGRYLEFESPLPDYFTRLLTKL 303


>gi|302808237|ref|XP_002985813.1| hypothetical protein SELMODRAFT_123269 [Selaginella moellendorffii]
 gi|300146320|gb|EFJ12990.1| hypothetical protein SELMODRAFT_123269 [Selaginella moellendorffii]
          Length = 355

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 86/283 (30%), Positives = 130/283 (45%), Gaps = 61/283 (21%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQETS 155
           LK  +LY+D  + V NKP G+ VQGGS +   +   +   +  +  + PRL HRLD++ S
Sbjct: 36  LKDAVLYKDEDLIVLNKPPGLPVQGGSKVERSLVSMMSLALQFEYKEPPRLVHRLDKDVS 95

Query: 156 GILVVARTRAAAQHLTESFRMRR-----------------IQKIYWSLVWGIPKNKKECI 198
           G++++ RT  +   + +SF   +                 + + Y +LV G P   K  I
Sbjct: 96  GVMILGRTYESTVKI-QSFLCSKDNLMPSVITIQGSVGKGLDRKYIALVIGSPTADKGFI 154

Query: 199 ANWLLKKSHIGGDYVHV-VKQNEKGANY--AISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           +  LLK     G    V +  + K  N   AI+ ++V+        WL+++P TGR HQL
Sbjct: 155 SAPLLKMVLEDGKSDRVLIAADPKSENAIPAITEYQVLKRSVLGCTWLQLRPLTGRKHQL 214

Query: 256 RVH-ALHMGCPIVGDHKY--------CANFKGNFTSP----IQNK-----------LYLH 291
           RVH A  +G PIVGD KY         A    N   P     +NK           L+LH
Sbjct: 215 RVHCAQGLGLPIVGDMKYGFNTHKKWMAERNMNTVDPQDIKARNKMAGSVVSKNPLLHLH 274

Query: 292 ARYMDLPH-------------PEGGRLQITAPLPAHMVKTWDS 321
           +R + +P              PE  R++  APLP HM  +W++
Sbjct: 275 SRELTIPRLRKKPGAVDFGLDPE--RMRFVAPLPTHMESSWEA 315


>gi|227551404|ref|ZP_03981453.1| pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|257887487|ref|ZP_05667140.1| pseudouridylate synthase [Enterococcus faecium 1,141,733]
 gi|257895982|ref|ZP_05675635.1| pseudouridylate synthase [Enterococcus faecium Com12]
 gi|293570492|ref|ZP_06681547.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E980]
 gi|227179523|gb|EEI60495.1| pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|257823541|gb|EEV50473.1| pseudouridylate synthase [Enterococcus faecium 1,141,733]
 gi|257832547|gb|EEV58968.1| pseudouridylate synthase [Enterococcus faecium Com12]
 gi|291609438|gb|EFF38705.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E980]
          Length = 303

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 90/322 (27%), Positives = 154/322 (47%), Gaps = 51/322 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E+ R+D+   N + + +   +Q  L+   V V+ + VK N +++ G  + +         
Sbjct: 11  ESGRIDKVLTNLFSNYSRSQIQLWLKERAVSVNGEPVKANYKVKQGDEITV--------- 61

Query: 77  IIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
           +I E + LD    ++ LT         ++YED  + V NKP G+ V   +G         
Sbjct: 62  LIPEPETLDVVPENIPLT---------IVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNA 112

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + YH+     S ++    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y 
Sbjct: 113 LMYHVKDL--STINGV-IRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKDKTSLRKYV 169

Query: 185 SLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G IP  K    A     K +     +  ++++ K A   ++HF V++ F + F  +
Sbjct: 170 ALVHGEIPHEKGTINAPIGRSKEN---RKMQAIREDGKPA---VTHFTVLERF-EGFTLV 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E++  TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP 
Sbjct: 223 ELKLETGRTHQIRVHMKYIGYPLAGDPVYGPKKTLKGNGQ-------FLHAQMLGFTHPT 275

Query: 302 GGRLQI-TAPLPAHMVKTWDSL 322
                I  APLP    KT + L
Sbjct: 276 TNEKMIFEAPLPEVFEKTLEKL 297


>gi|99081958|ref|YP_614112.1| ribosomal large subunit pseudouridine synthase D [Ruegeria sp.
           TM1040]
 gi|99038238|gb|ABF64850.1| ribosomal large subunit pseudouridine synthase D [Ruegeria sp.
           TM1040]
          Length = 337

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 93/344 (27%), Positives = 147/344 (42%), Gaps = 66/344 (19%)

Query: 15  DEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           D    RLD+      P   +++   L +++ SG V VD  R     +R+  G ++ I   
Sbjct: 4   DNPPKRLDKAIARDVPEEANLSRTRLARLIESGGVFVDGARANDAKSRVAEGALIVITVE 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYH 128
               +HI  E   LD               +++ED+ + V NKPAG+ V    GS     
Sbjct: 64  EAEDSHIGPEDIPLD---------------VIHEDADLIVINKPAGMVVHPAPGSPSGTL 108

Query: 129 IDGFLK-SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L     D  G    ++P + HR+D+ETSG+LVVA++ AA Q L   F    +++ Y
Sbjct: 109 VNALLHHCGADLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQFERHTVERYY 168

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------------GANYAISHF 230
            ++ +G+P      +   +   S   G+ + +  Q  +             G  +A++  
Sbjct: 169 QAVCYGVPDGNDPRL-RGVRGTSFEPGNILKITTQLARHKTDRQRQAVLFEGGRHAVTRA 227

Query: 231 KVIDCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           ++I+ F          CWLE    TGRTHQ+RVH  H G  ++GD  Y    K    SP 
Sbjct: 228 RIIEAFGAPAAASLVECWLE----TGRTHQIRVHMAHAGHGLLGDPTYGGKRK---ISPK 280

Query: 285 Q------------NKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
                         +  LHA  +   HP  G  ++  APLP  M
Sbjct: 281 ALSAAGLAAINSFQRQALHAAVLGFEHPVSGEMMRFEAPLPEDM 324


>gi|329849859|ref|ZP_08264705.1| ribosomal large subunit pseudouridine synthase D [Asticcacaulis
           biprosthecum C19]
 gi|328841770|gb|EGF91340.1| ribosomal large subunit pseudouridine synthase D [Asticcacaulis
           biprosthecum C19]
          Length = 335

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 97/342 (28%), Positives = 155/342 (45%), Gaps = 55/342 (16%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQ-V 64
           V    V  DE   RLDR    H+P ++   LQ ++  G++  +   +    ++ + G   
Sbjct: 20  VLTATVTADEAGDRLDRALTVHFPDLSRARLQALIAEGRLSHNGAVITDGKHKARPGDYS 79

Query: 65  VRIPPVINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           + IP +I+A     + Q I LD               +L+ED  + V NK  G++     
Sbjct: 80  LSIPALISANP---EPQDIPLD---------------ILFEDEHLIVINKAPGMAAHPAP 121

Query: 124 GIAYHIDGFL---------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           G     DG L         +S     G  +P + HRLD++TSG++V A++  A + L+E 
Sbjct: 122 GTR---DGTLVNALLFHCGESLSGIGGVLRPGIVHRLDKDTSGVMVAAKSDVAHRSLSEL 178

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F    I + Y ++V G P+     + N  + +SH     + V++    G   AI+H+++ 
Sbjct: 179 FGRHDIDREYKAVVRGAPRYVSGTV-NTRIGRSHHDRKKMAVLR---GGGREAITHYRLE 234

Query: 234 DCF-------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           + F       A   C LE    TGRTHQ+RVH  H+GCP +GD  Y +         I  
Sbjct: 235 EVFGTVKPLAALLSCRLE----TGRTHQIRVHMAHLGCPCLGDPVYGSGAPAREVQEIVR 290

Query: 287 KL-----YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            L      LHA  +   HP  G +L+  A +P  MV+  ++L
Sbjct: 291 DLEFGRQALHAGLLGFVHPITGEKLKFKAKMPDDMVQLVEAL 332


>gi|206603460|gb|EDZ39940.1| pseudouridylate synthase, 23S RNA-specific [Leptospirillum sp.
           Group II '5-way CG']
          Length = 340

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 89/333 (26%), Positives = 151/333 (45%), Gaps = 46/333 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IP 68
           +V   E+  RLD +   +        +Q++L    V ++      +++I+ G  +R  IP
Sbjct: 22  LVPRGEQPKRLDIYLSRNCLGFTRSRVQRLLEEKLVTINDIYPASSHKIRGGDRIRVLIP 81

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P         + Q      ++L          +LYED  + V +KP G+ V    G A  
Sbjct: 82  PP--------RSQAAQPEDIHLE---------ILYEDDDLIVISKPPGLVVHPAPGHASG 124

Query: 129 --IDGFL---KSWVDSKGQ-------------KPRLTHRLDQETSGILVVARTRAAAQHL 170
             ++G L   +S  D + +             +  L HRLDQ+TSG++VV ++      L
Sbjct: 125 TLVNGLLFHFQSQGDEQKKGEPEEEEEAERPLRAGLVHRLDQDTSGVMVVGKSETVVLDL 184

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              F+ R + K Y +LV GI   K+  I   + + +H    +   V+Q+ K +   ++ +
Sbjct: 185 MNQFKDRSVSKKYLALVKGILPKKRGEINAPIGRSTHDRKKFA--VRQDGKPS---LTRY 239

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           +V++ + + +  LE+   TGRTHQ+RVH  H+G P++GD  Y +    N   P Q    L
Sbjct: 240 RVLETYHENYSLLEVTLLTGRTHQIRVHFRHLGFPLLGDAVYGSKGMENRNFPRQ---ML 296

Query: 291 HARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           HA  +   HP    +++  APLP   V     L
Sbjct: 297 HAWKLAFQHPRSAAKMEFEAPLPPDFVSAMKRL 329


>gi|197103876|ref|YP_002129253.1| ribosomal large subunit pseudouridine synthase d [Phenylobacterium
           zucineum HLK1]
 gi|196477296|gb|ACG76824.1| ribosomal large subunit pseudouridine synthase d [Phenylobacterium
           zucineum HLK1]
          Length = 326

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 89/325 (27%), Positives = 142/325 (43%), Gaps = 45/325 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+      P ++   LQ +L  G+V      V    + Q+G                +
Sbjct: 24  RIDKALAGLLPTLSRARLQALLAEGRVTRGGAPVDAKAKAQAG-------AYAIAVPPPE 76

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWV 137
             +    ++ LT         +L+ED+ + V +KPAG+++    GS     ++  L    
Sbjct: 77  PAEPQPEAIPLT---------VLFEDAHLIVVDKPAGMAMHPAPGSERGTLVNALLAHCG 127

Query: 138 DSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           DS        +P + HR+D+ETSG++V A+T AA Q L+  F    I+++Y +L  G P+
Sbjct: 128 DSLSGIGGVARPGVVHRIDKETSGVVVAAKTDAAHQGLSALFAAHDIERVYIALTRGAPR 187

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF--------AQKFCWLE 244
            ++  I   + + +H       V    + G  +A++H+ V   F        A+  C LE
Sbjct: 188 PERGVIEGAIARSAHDRKKMALV----KSGGRHAVTHYAVERVFGPQERPLAARVACRLE 243

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKL---YLHARYMDLPH 299
               TGRTHQ+RVH    G P +GD  Y +            Q  L    LHA  +   H
Sbjct: 244 ----TGRTHQIRVHLASKGTPCLGDPTYGSGPPAEAVREAIRQAGLARQALHAAVLGFRH 299

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  G+ L+  +PLPA M      LG
Sbjct: 300 PVSGQALRFESPLPADMAALEVLLG 324


>gi|294666973|ref|ZP_06732202.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 10535]
 gi|292603262|gb|EFF46684.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 10535]
          Length = 331

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 89/343 (25%), Positives = 157/343 (45%), Gaps = 40/343 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +V ++    R D      +P  +   L + ++SG   +D +  +  + ++ G+ V+
Sbjct: 13  IRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGEMARPRDTLRGGESVQ 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V+    H   +   L                +LYED ++ V +KPAG+ V  G+G  
Sbjct: 73  VQVVLETQTHAAPQDIPLS---------------VLYEDEQVLVIDKPAGLVVHPGAG-- 115

Query: 127 YHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            + D  L + +     +    PR  + HRLD++TSG++VVART  A   L E    R + 
Sbjct: 116 -NPDRTLVNALLFRDPALASVPRSGVVHRLDKDTSGVMVVARTVQAQTALVEQLSAREVH 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G   +     AN  + + H        V+ + +    A++H+++ + F +  
Sbjct: 175 RQYLAVVVGALVSG--GTANAPIDR-HPRDRLKMAVRDDGRD---AVTHYRLRERF-RAH 227

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHA 292
             LE +  TGRTHQ+RVH  H+  PIVGD  Y    K     T  + ++L       LHA
Sbjct: 228 TALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQALHA 287

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
             ++  HP  G  ++ +AP+PA + +    L     R   + R
Sbjct: 288 ETLEFLHPVSGEPVRASAPVPADLQRLMTVLREDSARAAELAR 330


>gi|256847299|ref|ZP_05552745.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           coleohominis 101-4-CHN]
 gi|256715963|gb|EEU30938.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           coleohominis 101-4-CHN]
          Length = 308

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 92/316 (29%), Positives = 152/316 (48%), Gaps = 39/316 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E  R+D+        ++   ++K +  G V V+K+ VK    +Q+G +V++        
Sbjct: 13  QETGRIDKQLATLLSDVSRSQIKKWIEDGNVTVNKQSVKPKYHLQAGDIVQV-------- 64

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL 133
             I EQ      ++L   +  L+  ++YED  + V NKP G+ V   +G   H  ++  L
Sbjct: 65  --IPEQP---QKIDLEPENIPLE--IVYEDDDVLVVNKPQGMVVHPSAGHPNHTLVNALL 117

Query: 134 KSWVDS--KGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                S   G+ +P + HR+D++TSG+L+VA+   A + L    + +  Q+ Y +LV G+
Sbjct: 118 YHCPLSHINGEYRPGIVHRIDKDTSGLLMVAKNDRAHRSLAAQLKAKTNQREYVALVHGV 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K  +  I +  L +S        VV         A++HF+V+  +   +  +  +  TG
Sbjct: 178 IKEDQGTI-DAPLGRSPKDRKKQAVVADGRP----AVTHFRVLKRYLH-YTLVACKLETG 231

Query: 251 RTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI- 307
           RTHQ+RVH  ++G P+ GD  Y      KGN         YLHAR +   HP  G+  + 
Sbjct: 232 RTHQIRVHMKYIGHPLAGDPLYGPRKTLKGNGQ-------YLHARLLGFKHPVTGKEMVF 284

Query: 308 TAPLP---AHMVKTWD 320
            APLP   A M+K  D
Sbjct: 285 EAPLPTWFAQMLKHLD 300


>gi|2995386|emb|CAA63803.1| hypothetical protein [Zymomonas mobilis subsp. mobilis ATCC 29191]
          Length = 219

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 123/230 (53%), Gaps = 14/230 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L   +L+ D++  + +KPAG+ V      +  ++ +L S      + P + HRLD++TS
Sbjct: 3   ILAERVLFIDAEAMIIDKPAGLPVTSVRDGSLSLENYLASLCFGFKRWPSIVHRLDRDTS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L++AR     + L+E+F   +++K YW+++ G+P+  +  I   LLK S     +  V
Sbjct: 63  GCLLLARNPKMHRRLSEAFSQGQVKKCYWAILEGVPEKNEGTIDLPLLKISSPKSGWRIV 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCA 274
              ++KG   A++H++++    +    +  +P TGRTHQLRVHA   +G PIVGD  Y +
Sbjct: 123 A--DDKG-KRAVTHWEIL-AKNKGRSLVAFRPETGRTHQLRVHAATGLGLPIVGDPFYSS 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           +   N +     ++ LHA  +++   E   +   APLP    K +  LGF
Sbjct: 179 HKDENIS-----RMMLHAHSLEIARLEKKPIAAEAPLP----KAFTDLGF 219


>gi|197301721|ref|ZP_03166791.1| hypothetical protein RUMLAC_00447 [Ruminococcus lactaris ATCC
           29176]
 gi|197299161|gb|EDY33691.1| hypothetical protein RUMLAC_00447 [Ruminococcus lactaris ATCC
           29176]
          Length = 304

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 88/317 (27%), Positives = 145/317 (45%), Gaps = 44/317 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHII 78
           R+D++   +   ++   +QK+L+ G + V+ K+VK N ++  G  + +  P    L+ I 
Sbjct: 14  RIDKFLGENLDDLSRSYIQKLLKDGLILVNGKKVKANYKLNEGDQIDVEVPDPEPLD-IA 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E   LD               +LYED  I + NKP G+ V    G         I YH 
Sbjct: 73  AENIPLD---------------ILYEDEDILIVNKPKGMVVHPSPGHPDHTLVNAILYHC 117

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L     +   +P + HR+D  T+G L++ +   A Q L E  +   I + Y ++V G
Sbjct: 118 GEHLSGI--NGVIRPGIVHRIDMNTTGSLLICKNDHAHQILAEQLKEHSITRRYHAIVHG 175

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN--YAISHFKVIDCFAQKFCWLEMQP 247
             K      A+     + IG       K + K  N  +A++H++V++     + ++E + 
Sbjct: 176 SLK------ADTGTVNASIGRHPTDRKKMSTKALNGRHAVTHYRVLERLGN-YTYIECEL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR-L 305
            TGRTHQ+RVH   +G PI+GD  Y     G    P       LHA+ + + HP  G  +
Sbjct: 229 ETGRTHQIRVHMASIGHPILGDDVY-----GPAKCPFHLEGQTLHAKILGITHPATGEYM 283

Query: 306 QITAPLPAHMVKTWDSL 322
           +  APLP + +K   +L
Sbjct: 284 EFDAPLPEYFMKLLSTL 300


>gi|21243943|ref|NP_643525.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           axonopodis pv. citri str. 306]
 gi|294625813|ref|ZP_06704430.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 11122]
 gi|34395784|sp|Q8PHN2|RLUD_XANAC RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|21109553|gb|AAM38061.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           axonopodis pv. citri str. 306]
 gi|292599888|gb|EFF44008.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 11122]
          Length = 331

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 89/343 (25%), Positives = 157/343 (45%), Gaps = 40/343 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +V ++    R D      +P  +   L + ++SG   +D +  +  + ++ G+ V+
Sbjct: 13  IRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGEMARPRDTLRGGESVQ 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V+    H   +   L                +LYED ++ V +KPAG+ V  G+G  
Sbjct: 73  VQVVLETQTHAAPQDIPLS---------------VLYEDEQVLVIDKPAGLVVHPGAG-- 115

Query: 127 YHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            + D  L + +     +    PR  + HRLD++TSG++VVART  A   L E    R + 
Sbjct: 116 -NPDRTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSAREVH 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G   +     AN  + + H        V+ + +    A++H+++ + F +  
Sbjct: 175 RQYLAVVVGALVSG--GTANAPIDR-HPRDRLKMAVRDDGRD---AVTHYRLRERF-RAH 227

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHA 292
             LE +  TGRTHQ+RVH  H+  PIVGD  Y    K     T  + ++L       LHA
Sbjct: 228 TALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQALHA 287

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
             ++  HP  G  ++ +AP+PA + +    L     R   + R
Sbjct: 288 ETLEFLHPVSGEPVRASAPVPADLQRLMTVLREDSARAAELAR 330


>gi|163755046|ref|ZP_02162167.1| guanosine 5'-monophosphate oxidoreductase [Kordia algicida OT-1]
 gi|161325113|gb|EDP96441.1| guanosine 5'-monophosphate oxidoreductase [Kordia algicida OT-1]
          Length = 231

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 113/227 (49%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I + NK AG  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 13  VLYEDNHIIIVNKRAGDIVQGDKTGDKPLSDVVKEYIAEKYNKPGNVFLGVVHRLDRPTT 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V ART  A   L + F  ++ +K YW++V  +P  +++ + +WL K      +    
Sbjct: 73  GIIVFARTSKALPRLNKLFAEKKAKKTYWAIVNNMPPKQQDTLIHWLRKNPK--NNKSTA 130

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   G+  AI  + V      ++  LE+  HTGR HQ+R     +GC I GD KY  +
Sbjct: 131 FNKEIPGSKKAILDYTVQKKL-DRYVLLEIALHTGRHHQIRTQLSAIGCKIKGDLKYGFD 189

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
                 S     ++LHAR +   HP +   L+I APLP   V  W++
Sbjct: 190 RSNKDAS-----IHLHARKLVFTHPVKKELLEIIAPLPNDPV--WNA 229


>gi|330996580|ref|ZP_08320462.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
 gi|329573136|gb|EGG54755.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
          Length = 224

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 68/218 (31%), Positives = 110/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + + +K +   VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHLIIVDKSSSEIVQGDKTGDKPLAEMVKEYIKQKYHKPGNVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ART  A   L E FR + + K YW++V   P  ++  + +WL++       Y + 
Sbjct: 63  GLVVFARTGKALARLNEMFRTKEVHKTYWAIVGNCPPAEEGELVHWLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             + + GA  AI  +K+I   ++++  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEKPGAKKAILDYKLIG-RSERYFLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             G   S     + LHAR +   HP   + + + AP+P
Sbjct: 177 --GAPRSNPDGSICLHARRVRFVHPVSKQEIDVEAPVP 212


>gi|260887804|ref|ZP_05899067.1| ribosomal large subunit pseudouridine synthase D [Selenomonas
           sputigena ATCC 35185]
 gi|330838700|ref|YP_004413280.1| pseudouridine synthase, RluA family [Selenomonas sputigena ATCC
           35185]
 gi|260862480|gb|EEX76980.1| ribosomal large subunit pseudouridine synthase D [Selenomonas
           sputigena ATCC 35185]
 gi|329746464|gb|AEB99820.1| pseudouridine synthase, RluA family [Selenomonas sputigena ATCC
           35185]
          Length = 301

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 90/319 (28%), Positives = 148/319 (46%), Gaps = 42/319 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR- 66
           + ++V+      RLDR+       ++  ++QK++ SG V V+ +  K N +++ G  V  
Sbjct: 3   ERLIVDEGAAGERLDRFLAGRELEVSRSHIQKLIESGCVLVNGRTAKANAKLREGDAVET 62

Query: 67  -IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +P          +E +IL   + L          +LYEDS + V NK  G+ V   +G 
Sbjct: 63  ELPEA--------RELEILPEDIPLD---------ILYEDSDVIVINKARGMVVHPAAGA 105

Query: 126 A--YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           A    ++  L    D  G     +P + HRLD++TSG++V A+   A   L E  R +  
Sbjct: 106 ADGTLVNALLHHCEDLSGINGVIRPGIVHRLDKDTSGVMVAAKNDRAHVDLAEQIREKTA 165

Query: 180 QKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFA 237
           Q+IY ++V G I +++ E        ++ IG       K     G   A + F+V++ F 
Sbjct: 166 QRIYRAIVCGTIAEDRGEI-------RAPIGRHPTERKKMAVVPGGKEATTLFRVVERFP 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +E +  TGRTHQ+RVH  ++  P++GD KY     G  T  I  +  LH+  +  
Sbjct: 219 A-HTLVECRLKTGRTHQIRVHMAYIDHPLLGDPKY-----GRKTPDIAGQ-ALHSCELSF 271

Query: 298 PHPEGG-RLQITAPLPAHM 315
            HP    R+   A +P  M
Sbjct: 272 AHPRTKERMTFAAEMPEDM 290


>gi|326405195|ref|YP_004285277.1| ribosomal large subunit pseudouridine synthase D [Acidiphilium
           multivorum AIU301]
 gi|325052057|dbj|BAJ82395.1| ribosomal large subunit pseudouridine synthase D [Acidiphilium
           multivorum AIU301]
          Length = 332

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 89/326 (27%), Positives = 138/326 (42%), Gaps = 45/326 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+  +    ++   L+ ++ +G V  D            G V+R+P        I  
Sbjct: 24  RLDRFLASRLSEMSRSRLKALIEAGTVTCD------------GAVIRLPSAAVRPGAIYT 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL------ 133
                  ++        L   +LYEDS + V +KPAG+ V    G   + DG L      
Sbjct: 72  VALP--PAIPAAPQGQALDLTVLYEDSDLIVIDKPAGLVVHPAPG---NPDGTLVNALIA 126

Query: 134 ---KSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               S     G++ P + HRLD++TSG++V A+T  A   L+ +F  R + + Y +L WG
Sbjct: 127 HCGDSLAGIGGERRPGIVHRLDKDTSGVMVAAKTELALNALSAAFAARDLDREYLALCWG 186

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQP 247
            P+  +  I      +  IG D     +     +G   A++H++ +  F      L  + 
Sbjct: 187 APQPAEGEI------EGPIGRDPRDRKRMAVVARGGKPALTHYRTLRRFGLGATLLACRL 240

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLY------LHARYMDLP 298
            TGRTHQ+RVH    G P+VGD  Y             P ++ L       LHA  +   
Sbjct: 241 ATGRTHQIRVHLASRGHPLVGDPVYLRRRPAAASQMQQPQRDFLLDFPRQALHAATLGFA 300

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLG 323
           HP  G +L+  A  PA +      LG
Sbjct: 301 HPRSGAKLRFEAAPPADLATLLSHLG 326


>gi|152986388|ref|YP_001350515.1| pseudouridine synthase [Pseudomonas aeruginosa PA7]
 gi|150961546|gb|ABR83571.1| pseudouridine synthase [Pseudomonas aeruginosa PA7]
          Length = 320

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 92/334 (27%), Positives = 152/334 (45%), Gaps = 50/334 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RLD+     +P  +   L   ++ G++ VD    +  + + SG  + +     A    
Sbjct: 17  GQRLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAAARPRDIVHSGAQLVLEAEQEAQGEW 76

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW- 136
           + +   LD               +++ED  I V +KPAG+ V   +G   H DG L +  
Sbjct: 77  VAQDIELD---------------IVHEDEHILVIDKPAGLVVHPAAG---HQDGTLLNAL 118

Query: 137 ---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
              V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY ++V G+ 
Sbjct: 119 LYHVPGIANVPRAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGV- 177

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQPHTG 250
                 I +     + IG   V   K     A   A+SH++V++ F +      ++  TG
Sbjct: 178 ------ITSGGTIDAPIGRHGVQRQKMAVVDAGKVAVSHYRVLERF-RAHTHTRVKLETG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY-----------LHARYMDLPH 299
           RTHQ+RVH  H+G P+VGD  Y   FK     P+ ++             LHAR+++L H
Sbjct: 231 RTHQIRVHMSHIGYPLVGDPVYGGRFK---IPPVASQTLVQTLREFPRQALHARFLELDH 287

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           P  G R++  +PLP   +  W     + DR  ++
Sbjct: 288 PATGVRMKWESPLPEDFL--WLLSLLRQDREAFV 319


>gi|65321221|ref|ZP_00394180.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Bacillus
           anthracis str. A2012]
 gi|229600532|ref|YP_002868128.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|270000606|ref|YP_003329045.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. Ames]
 gi|291612221|ref|YP_003541035.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. 'Ames Ancestor']
 gi|224552855|gb|ACN55066.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. 'Ames Ancestor']
 gi|229264940|gb|ACQ46577.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|269850243|gb|ACZ49983.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. Ames]
          Length = 302

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 87/320 (27%), Positives = 148/320 (46%), Gaps = 41/320 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            + +          I E + LD     +NL          + YED+ + V NKP  + V 
Sbjct: 61  EITV---------TIPEPEELDIQPEDMNLE---------IYYEDADVLVVNKPRSMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V+
Sbjct: 163 VAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA 
Sbjct: 217 ERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAG 270

Query: 294 YMDLPHPEGGR-LQITAPLP 312
            +   HP  G  +Q  AP+P
Sbjct: 271 ILGFDHPRTGEYIQFEAPIP 290


>gi|330824017|ref|YP_004387320.1| RluA family pseudouridine synthase [Alicycliphilus denitrificans
           K601]
 gi|329309389|gb|AEB83804.1| pseudouridine synthase, RluA family [Alicycliphilus denitrificans
           K601]
          Length = 336

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 87/328 (26%), Positives = 151/328 (46%), Gaps = 29/328 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVV 65
           ++ V+V   +   RLD+      P  +   LQ++L  G VR++ +   K  +++++G  V
Sbjct: 31  LREVMVPAAQHQARLDKALAELVPEFSRSYLQQLLAQGDVRLNGQPAAKPAHKVRAGDQV 90

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +      +    + Q     S+ L          +++ED  + V +KPAG+ V    G 
Sbjct: 91  AV-----RMRPTQQSQAFKPESLPLD---------VVHEDEHLLVIDKPAGLVVHPAPGN 136

Query: 125 -IAYHIDGFLKSWVDSKG-QKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                ++  L    D++  Q PR  + HRLD++TSG++VVAR RAA   L      R + 
Sbjct: 137 WSGTLLNALLGR--DAQAMQVPRAGIVHRLDKDTSGLMVVARNRAAMDALVRMIAAREVS 194

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +L WG     ++      + +       + VV   +     A + F ++    ++ 
Sbjct: 195 RQYLALAWGAWSGSEQRRIRAPIGRDPRNRLRMAVVDLGQHAGKEACTDFDLL-ASGEEV 253

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           C +    HTGRTHQ+RVH   +  P+V D    A + G    P++ +  LHA  +   HP
Sbjct: 254 CLVRCTLHTGRTHQIRVHMASIRHPLVAD----ALYGGAVGGPMRRQ-ALHAFRLAFTHP 308

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             G+ ++  APLP  M +  D  G +Y+
Sbjct: 309 VTGKPMEFHAPLPEDMRQALDFWGLRYN 336


>gi|325273287|ref|ZP_08139564.1| RluA family pseudouridine synthase [Pseudomonas sp. TJI-51]
 gi|324101572|gb|EGB99141.1| RluA family pseudouridine synthase [Pseudomonas sp. TJI-51]
          Length = 320

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 95/336 (28%), Positives = 148/336 (44%), Gaps = 42/336 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   V+  + +  G  + +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLVHGGSQLALQAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    + E   LD               ++YED  I V NKPAG+ V   +G   H  G
Sbjct: 71  EAQGEWVAEDIELD---------------IVYEDDHIMVINKPAGLVVHPAAG---HASG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     V      PR  + HRLD++T+G++VVA+T  A   L E  + R++ +IY  
Sbjct: 113 TLLNALLHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTLQAQTKLVEQMQARKVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+     +  A       H G      V     G   A+SH++V+  F +    + +
Sbjct: 173 IVIGVVTAGGKIDAPI---GRHGGMRQRMAVTD---GGKPAVSHYRVLKRF-RSHTHVRV 225

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKLYLHARYMDL 297
           +  TGRTHQ+RVH  H+G P+VGD  Y   F+     SP          +  LHAR++ L
Sbjct: 226 KLETGRTHQIRVHMAHVGFPLVGDQTYGGRFRIPPAASPTMVEAVKSFPRQALHARFLAL 285

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            HP  G  ++  +PLP   V  W       DR  +I
Sbjct: 286 AHPITGEVMKWESPLPDDFV--WLLSLLNQDRESFI 319


>gi|146296964|ref|YP_001180735.1| RluA family pseudouridine synthase [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145410540|gb|ABP67544.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 292

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 84/274 (30%), Positives = 135/274 (49%), Gaps = 28/274 (10%)

Query: 60  QSGQVVRIPPVINALNH----IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
            +GQ+  IPP+ +   H     I E ++ D   N+      +   +L+ED      NKP+
Sbjct: 36  SNGQIRFIPPIFSINQHPTVESIIELELKDVYSNIVPIKGSID--ILFEDQFFLFVNKPS 93

Query: 116 GISVQGGSGIAYHIDGFLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           GI      G  ++ D    +   +++S+G    + +RLD++TSGI+V A+       ++ 
Sbjct: 94  GIPSHPSKG--HYFDTLANNVEWYLNSQGVTSHIINRLDKDTSGIVVFAKNSYFHSIVSS 151

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F  R I+K Y ++V GI   KK       + +S+ G     + ++  +  +YAI++++V
Sbjct: 152 EFEKRTIEKTYIAVVDGI-LTKKSGFIEKPISRSNDG-----IKREINEDGDYAITYYEV 205

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           +D +   +  L+++P TGRTHQLRVH   +G PIVGD  Y      NF       L LHA
Sbjct: 206 VD-YKNNYSILKLKPITGRTHQLRVHLASIGYPIVGDVLYGTGKNKNF------PLLLHA 258

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
             M        R   ITAPLP +     + LGF+
Sbjct: 259 YSMKFDFKLIERQYNITAPLPPYF---SEFLGFE 289


>gi|15895383|ref|NP_348732.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|15025103|gb|AAK80072.1|AE007712_8 Predicted pseudouridylate synthase, YLYB B.subtilis ortholog
           [Clostridium acetobutylicum ATCC 824]
 gi|325509529|gb|ADZ21165.1| pseudouridylate synthase [Clostridium acetobutylicum EA 2018]
          Length = 305

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 91/315 (28%), Positives = 155/315 (49%), Gaps = 34/315 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++E + EN R+D +    + +I+  ++Q ++   +V V+ K VK N +++S   V     
Sbjct: 7   IIEEEYENQRIDVYLAQEFENISRSHIQDLIGKKKVFVNGKAVKSNYKLKSRDNVEFEIP 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-- 128
            N      +E KI   ++ L          ++YED  I V NK  G+ V    G  Y+  
Sbjct: 67  DN------EELKIEAENIPLD---------IVYEDRDIVVVNKAQGMVVHPAPG-NYNGT 110

Query: 129 -IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HR+D++TSGILVVA+  AA ++L    +   + ++Y
Sbjct: 111 LVNALLYHCKDLSGINGVLRPGIVHRIDKDTSGILVVAKNDAAHKNLANQLKEHSMNRVY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V GI K + E   +  L +  +    + VV    KG   A++H+KV++ + +    +
Sbjct: 171 RAVVEGIIK-EDEGTVDKPLARHPVERVKIAVV----KGGRNAVTHYKVLERY-RNSTLI 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E +  TGRTHQ+RVH  ++G  +VGD  Y    K  F    Q    LHA+ +   HP  G
Sbjct: 225 ECKLETGRTHQIRVHMAYIGHALVGDPLYGYK-KQRFNLEGQ---MLHAQKLGFIHPTKG 280

Query: 304 R-LQITAPLPAHMVK 317
           + ++     P+H  K
Sbjct: 281 KYMEFEREAPSHFQK 295


>gi|312130058|ref|YP_003997398.1| ribosomal large subunit pseudouridine synthase d [Leadbetterella
           byssophila DSM 17132]
 gi|311906604|gb|ADQ17045.1| ribosomal large subunit pseudouridine synthase D [Leadbetterella
           byssophila DSM 17132]
          Length = 347

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 91/338 (26%), Positives = 157/338 (46%), Gaps = 50/338 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV++ +  MRLD++  +H  +I+   +Q  + +  V+V+   VK + +++    + I  
Sbjct: 24  IVVDSGQSMMRLDKYLSHHLKNISRNRIQNAIDTDSVKVNGSSVKSSYKVKPFDDISISI 83

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
           V ++   I KE  ++  ++ L          ++YED  + + NK   + V  G G     
Sbjct: 84  VRSS--RIPKE--VIPQNIPLD---------IVYEDDDVLLVNKAQEMVVHPGHGNPDGT 130

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH  G L S  D +  +P L HR+D+ TSG+LV+A+   A Q L + F     +
Sbjct: 131 LVNALVYHF-GNLPSARDGE-IRPGLVHRIDKGTSGLLVIAKNEYALQFLAKQFADHTTE 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-----VHVVKQNEKGANYAISHFKVIDC 235
           + Y++L+WG PK  K  I       +HIG  +       V  + E G   AI+H++V+  
Sbjct: 189 RTYYALIWGEPKEPKGTI------NAHIGRGFKDRRISDVFPEGEYGKE-AITHYEVLKS 241

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------P 283
             +    ++    TGRTHQ+R H  ++G P+  D  Y  +   +G   S           
Sbjct: 242 L-RYVSLIKCNLETGRTHQIRAHMKYLGHPLFNDAAYGGDRVLRGEIFSKYKQFVENCFE 300

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           I  +  LHA+ +   HP   + +Q  + LPA      D
Sbjct: 301 IIPRQALHAKSLGFIHPTTKKWMQFDSELPADFQAVLD 338


>gi|325686216|gb|EGD28262.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 304

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 81/296 (27%), Positives = 150/296 (50%), Gaps = 32/296 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++       ++   +++++++G+V V+ K+ K + ++Q G ++++  +    
Sbjct: 10  EESGQRLDKYLAGEMIDLSRSRIKELVQAGEVLVNGKKSKVSYKVQKGDLIQVTVLPLEP 69

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGF 132
             +  E   LD               ++YED  I V NKP G+ V    G   H  ++  
Sbjct: 70  LKLEAENIPLD---------------IVYEDEDIIVVNKPQGMVVHPAVGHPSHTLVNAL 114

Query: 133 L---KSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L   +   DS +G +P + HR+D++TSG+L+VA+  AA + L +    +  ++ Y ++V 
Sbjct: 115 LYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVH 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G    ++E   +  + ++      + VV   EKG + A++HFKV++ + Q +  +E Q  
Sbjct: 175 G-NFAEEEGTIDAPIGRNPKDRKQMAVV---EKGKS-AVTHFKVLEQY-QGYSLVECQLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           TGRTHQ+RVH  ++G P+ GD  Y        T P   + +LHA+ +    P  G 
Sbjct: 229 TGRTHQIRVHMAYIGHPLAGDPLYGP----RKTLPGHGQ-FLHAKTLGFEQPSTGE 279


>gi|323141904|ref|ZP_08076765.1| pseudouridine synthase, RluA family [Phascolarctobacterium sp. YIT
           12067]
 gi|322413651|gb|EFY04509.1| pseudouridine synthase, RluA family [Phascolarctobacterium sp. YIT
           12067]
          Length = 314

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 91/331 (27%), Positives = 154/331 (46%), Gaps = 50/331 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   E   R D         +   N+QK+L  G+     K +K N +++ G     
Sbjct: 12  QRLIITEQEAGQRADVGLAAML-ELTRSNMQKLLEEGRAVRGSKVLKSNYKLRLG----- 65

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
               + ++  + E + LD         + +   ++YED  + V NK  G+ V   +G   
Sbjct: 66  ----DEIDVTLPEPQPLDV------QPENIPLDIIYEDEDVVVVNKARGMVVHPAAGNLN 115

Query: 125 ------IAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
                 + YH      I+G ++         P + HRLD++TSGI++ A+  AA   L++
Sbjct: 116 GTLVNALLYHCKNLSGINGVIR---------PGIVHRLDKDTSGIMICAKNDAAHLSLSQ 166

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
             + +  Q+ Y ++V G  K     I   L+ +       + VVK+   G   A++ ++V
Sbjct: 167 QIQAKTAQRTYLAVVRGNIKTDSGVI-ETLIARDKNDRKKMAVVKE---GGRDAVTEYEV 222

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++ F  K+  +  +  TGRTHQ+RVH  ++G P+VGD KY    K  F+  IQ +  LH+
Sbjct: 223 LERFG-KYTIVRCRLRTGRTHQIRVHMEYLGYPLVGDPKYSP-MKTPFS--IQGQ-ALHS 277

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           + ++  HP  G RL   APLP  M K    L
Sbjct: 278 QTLEFTHPRTGERLSFEAPLPEDMHKIVTRL 308


>gi|161830503|ref|YP_001596932.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           RSA 331]
 gi|161762370|gb|ABX78012.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           RSA 331]
          Length = 323

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 88/333 (26%), Positives = 155/333 (46%), Gaps = 39/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   +++  Q + I  
Sbjct: 11  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEA 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 71  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 115

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            I+  L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y +
Sbjct: 116 LINALLH-YDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           +V G+       + +    ++ +G   +H  +    +    AI+HF++I  + +    + 
Sbjct: 175 IVKGV-------LISGRTIEAPVGRHPIHRTRMAVVEFGRPAITHFRIIKRY-RAHTHIR 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKL------YLHARYMD 296
           +Q  TGRTHQ+RVH  H+  P+ GD  Y ++     + + P+Q  L       LHA  + 
Sbjct: 227 VQLETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHAATLQ 286

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             HP   R +   AP PA M    + L   Y +
Sbjct: 287 FSHPVDQRPMACHAPPPADMAHLLECLEDDYSQ 319


>gi|293401501|ref|ZP_06645644.1| ribosomal large subunit pseudouridine synthase D
           [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305139|gb|EFE46385.1| ribosomal large subunit pseudouridine synthase D
           [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 305

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 87/326 (26%), Positives = 152/326 (46%), Gaps = 44/326 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V+V  +E   R+D++       ++   +Q++L+ G V V+    K N +I+         
Sbjct: 6   VIVTEEEAFQRIDKYISEKEDDLSRSRVQQLLQEGIVCVNGNACKANYKIKPK------- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                +HI     +    + +    + +   + YED  + V NKP G+ V    G     
Sbjct: 59  -----DHITA---VFCDEIEMEAKPEQMDLDIRYEDHDVIVINKPKGMVVHPAVGNQTGT 110

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G L    D  G     +P + HR+D++T+G+L+VA+   A   L++  + + + ++Y
Sbjct: 111 LVNGLLYHCKDLSGINGVLRPGIVHRIDKDTTGLLIVAKNDKAHTALSKQLQNKTVNRLY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK------GANYAISHFKVIDCFA 237
           ++LV G+ ++      ++    + IG D    VK  +K       A  A +HFKVI+ FA
Sbjct: 171 YALVHGVIEH------DFGTIDAPIGRD----VKDRQKMAVTATNAKDARTHFKVIERFA 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +E +  TGRTHQ+RVH  ++  P+VGD KY        T   Q +L LHA  +  
Sbjct: 221 H-YTLVECRLETGRTHQIRVHMQYIKHPVVGDEKYSY----RKTMQTQGQL-LHAHQLTF 274

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL 322
            HP    ++ + A LP       + L
Sbjct: 275 VHPTTNEKITVEAELPKQFADILEEL 300


>gi|312958894|ref|ZP_07773413.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens WH6]
 gi|311286664|gb|EFQ65226.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens WH6]
          Length = 320

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 88/341 (25%), Positives = 154/341 (45%), Gaps = 52/341 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G ++ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVHGGAILELTAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    + +   LD               ++YED  I V NKPAG+ V   +G   H DG
Sbjct: 71  EAQGEWVAQDIELD---------------IVYEDDDILVINKPAGLVVHPAAG---HADG 112

Query: 132 FLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L +     +      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  
Sbjct: 113 TLLNALLHHIPDIINVPRCGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYEC 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKF 240
           +V G+           ++    I        +Q ++     G   A+SH++V++ F +  
Sbjct: 173 IVIGV-----------VVAGGKINAPIGRHGQQRQRMAVMEGGKQAVSHYRVLERF-RSH 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQN-----KLYLHA 292
             + ++  TGRTHQ+RVH  H+  P+VGD  Y   F+       + +++     +  LHA
Sbjct: 221 THVRVKLETGRTHQIRVHMAHINFPLVGDPAYGGRFRIPPAASQTMVESLKTFPRQALHA 280

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           R+++L HP  G R+   +PLP   V  W     K DR  ++
Sbjct: 281 RFLELDHPTSGQRMSWESPLPDDFV--WLLSLLKQDREAFV 319


>gi|23098941|ref|NP_692407.1| hypothetical protein OB1486 [Oceanobacillus iheyensis HTE831]
 gi|22777169|dbj|BAC13442.1| hypothetical conserved protein [Oceanobacillus iheyensis HTE831]
          Length = 303

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 93/315 (29%), Positives = 149/315 (47%), Gaps = 49/315 (15%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  Q++V E  +   R+D+         +   +Q  +  G V V+   VK N +   G 
Sbjct: 1   MTKSQHIVTEQ-QGKTRVDKLLTQLLADQSRSQIQGWIDEGLVEVNGVSVKANYKCVEG- 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                   +AL   I E K       L    + +   ++YEDS + V NKP G+ V   +
Sbjct: 59  --------DALTWEIPETK------PLILEPENIPLDVVYEDSDVIVINKPKGMVVHPSA 104

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + YH D    S ++   ++P + HR+D++TSG+LVVA+   A Q L++  
Sbjct: 105 GHQTGTLVHALLYHCDDL--SGINGI-ERPGIVHRIDKDTSGLLVVAKNDVAHQKLSDQL 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISH 229
           + +++++ Y ++V G      E   +  L  + IG D     K  +K A       AI+H
Sbjct: 162 QQKQLKRKYVAIVHG------EIGHDTGLIDAPIGRD----PKDRQKMAVVDNGKSAITH 211

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           F+VI+ F   + ++E Q  TGRTHQ+RVH  ++G P+VGD KY      N      +   
Sbjct: 212 FRVIERFPD-YTFVECQLETGRTHQIRVHMQYIGFPLVGDPKYSQRKTMNV-----DGQA 265

Query: 290 LHARYMDLPHPEGGR 304
           LHA+ +   HP+ G 
Sbjct: 266 LHAKEIGFYHPKTGE 280


>gi|330501971|ref|YP_004378840.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           mendocina NK-01]
 gi|328916257|gb|AEB57088.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           mendocina NK-01]
          Length = 327

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 92/337 (27%), Positives = 159/337 (47%), Gaps = 42/337 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  ++   RLD+     +   +   L   ++ G++ VD    +  + + +G  +    V
Sbjct: 17  IVPFEQGGQRLDQVAAQLFGEYSRSRLSTWIKEGRLTVDGAVARPRDTVHAGSTL----V 72

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           ++A      E    D  +N+           +YED  + V +KPAG+ V   +G   H D
Sbjct: 73  LDAEQEAQGEWIAQDIELNI-----------VYEDEHMLVIDKPAGLVVHPAAG---HAD 118

Query: 131 GFLKSW----VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L +     V      PR  + HRLD++T+G++VVA+T  A  +L E  + R + +IY 
Sbjct: 119 GTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTLQAQTNLVEQLQKRTVSRIYE 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +  G+        A   + +S      + V      G   AISH++V++ + +    + 
Sbjct: 179 CICIGVITAGGTIDAP--IGRSSSQRQRMAVTD----GGKPAISHYRVLERY-RSHTHVR 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSP--IQN-----KLYLHARYMD 296
           ++  TGRTHQ+RVH  H+G P+VGD  Y   F+     SP  +Q+     +  LHAR+++
Sbjct: 232 VKLETGRTHQIRVHMTHVGYPLVGDPVYAGRFRIPPAASPTLVQSLKEFPRQALHARFLE 291

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           L HP  G R++  + LP  +V  W     + DR  ++
Sbjct: 292 LDHPATGQRMKWESELPDDLV--WLLTLLRQDREAFV 326


>gi|296284607|ref|ZP_06862605.1| pseudouridine synthase D large subunit [Citromicrobium
           bathyomarinum JL354]
          Length = 314

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 89/319 (27%), Positives = 147/319 (46%), Gaps = 38/319 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHII 78
           RLD+   +    ++   ++ ++  GQV V  KR    + ++ +G    I           
Sbjct: 16  RLDKALADAT-DLSRERIKGLIADGQVSVGGKRATSPSAKVAAGTPFTI----------- 63

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
                L +   L      +  ++ YED+ + V +KPAG+ V   +G         + YH 
Sbjct: 64  ----ALPAPTPLEAEPQDIPLVVAYEDAHLIVVDKPAGMVVHPAAGNRDGTLVNALLYHC 119

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G L S ++   ++P + HR+D++TSG+LVVA+T AA + L   F    I + Y ++  G
Sbjct: 120 RGQL-SGINGV-ERPGIVHRIDKDTSGLLVVAKTDAAHEGLARQFADHSISRRYVAVCAG 177

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            P+  +  I +  L +S      + V+        +A++H++    F      LE +  T
Sbjct: 178 QPRPAEGTI-DARLGRSDRDRKKMAVLDPQSTRGKHAVTHYRTTKTFGVA-SILECRLET 235

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-----YLHARYMDLPHPEGG- 303
           GRTHQ+RVH   +G P++GD +Y  + K     PI  KL      LHA  +   HP  G 
Sbjct: 236 GRTHQVRVHCASIGHPLLGDPQYGRDPKA--LRPIIEKLAFRRQALHAASLGFIHPATGE 293

Query: 304 RLQITAPLPAHMVKTWDSL 322
           RL+  A LP  M +  D +
Sbjct: 294 RLEFRADLPRDMGELIDEI 312


>gi|209963797|ref|YP_002296712.1| RNA pseudouridine synthase, putative [Rhodospirillum centenum SW]
 gi|209957263|gb|ACI97899.1| RNA pseudouridine synthase, putative [Rhodospirillum centenum SW]
          Length = 242

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 68/197 (34%), Positives = 102/197 (51%), Gaps = 11/197 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ +L+ D+ + + +KP G+ V  G+    H++ +L      + + PRL HRLD++TSG
Sbjct: 8   IRARVLHRDADVLILDKPHGLPVHYGTKTVEHLEQYLPWIAFEREEPPRLAHRLDKDTSG 67

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+AR    A  L   F    + K YW++V G P+     I   LL K HI G    VV
Sbjct: 68  CLVLARDAEVAARLGRLFLHGHVGKTYWAVVLGRPRGDAGRIDLPLL-KVHIPGCSKVVV 126

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             + K    A++ ++++     +  WLE+ P TGR HQLR H    G PI+GD  Y A  
Sbjct: 127 DPDGK---PALTDWRLL-ATDGRLSWLELTPRTGRMHQLRAHCACSGFPILGDPIYGAE- 181

Query: 277 KGNFTSPIQNKLYLHAR 293
                 P    L+LHAR
Sbjct: 182 -----QPPPVPLHLHAR 193


>gi|15618629|ref|NP_224915.1| pseudouridine synthase [Chlamydophila pneumoniae CWL029]
 gi|15836251|ref|NP_300775.1| pseudouridine synthase [Chlamydophila pneumoniae J138]
 gi|16752321|ref|NP_444579.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           pneumoniae AR39]
 gi|33242078|ref|NP_877019.1| ribosomal large subunit pseudouridine synthase A [Chlamydophila
           pneumoniae TW-183]
 gi|4377023|gb|AAD18858.1| predicted Pseudouridine Synthase [Chlamydophila pneumoniae CWL029]
 gi|7188966|gb|AAF37922.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           pneumoniae AR39]
 gi|8979091|dbj|BAA98926.1| pseudouridine synthase [Chlamydophila pneumoniae J138]
 gi|33236588|gb|AAP98676.1| ribosomal large subunit pseudouridine synthase A [Chlamydophila
           pneumoniae TW-183]
 gi|269302507|gb|ACZ32607.1| pseudouridine synthase, RluA family [Chlamydophila pneumoniae
           LPCoLN]
          Length = 325

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 89/315 (28%), Positives = 148/315 (46%), Gaps = 43/315 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINAL 74
           E + RLD++    +P  +    Q+ + SG V+++ +   +   R+  G +V I      +
Sbjct: 12  ENSGRLDKYLTEVHPKYSRAFYQEHILSGLVQINGQINTRVATRLNCGDIVTI-----DI 66

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
               +  ++L  ++ L K         +YED  I V NKP  + V    G         +
Sbjct: 67  QEKEELLELLPEAIPLDK---------VYEDGMILVINKPRDMVVHPAPGHFHGTLVHAL 117

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + I   LK     +  +P + HRLD++TSG+++ A+TR A +  +E F  +R++K Y +
Sbjct: 118 LHEIGERLKEEFPEEPWRPGIVHRLDKDTSGLIITAKTRQAKKVFSELFSTKRLKKSYLA 177

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQKFC 241
           +  G P++            +HI     H  K+ E   +     A++H +V+  F  K  
Sbjct: 178 VCIGKPRSTT--------IHTHISR---HQNKRKEMTVSSQGKEAVTHCQVL-AFNGKLS 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           ++ + P TGRTHQLRVH  H+G PI+GD  Y        +S   +K  LHA  +D  HPE
Sbjct: 226 FVALSPETGRTHQLRVHMKHLGTPILGDPVY--GIPSMNSSYGLDKQQLHAYSVDFTHPE 283

Query: 302 GGRL-QITAPLPAHM 315
             +   + A LP  M
Sbjct: 284 TRQFCSLKAGLPEDM 298


>gi|282859073|ref|ZP_06268205.1| pseudouridine synthase, RluA family [Prevotella bivia JCVIHMP010]
 gi|282588153|gb|EFB93326.1| pseudouridine synthase, RluA family [Prevotella bivia JCVIHMP010]
          Length = 364

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 89/340 (26%), Positives = 156/340 (45%), Gaps = 64/340 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +E  R+D++      H +   +QK   SG + V+ + VK N +++   V+ +  
Sbjct: 34  IEVDKGQEKERIDKFLFERMQHSSRNRIQKAADSGFIHVNGQPVKSNYKVRPLDVITL-- 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I    + L          ++YED  + V  KPAG+ V  G+G     
Sbjct: 92  ---MLDRPKHDNTIEPEDIPLD---------VIYEDDDLMVIMKPAGLVVHPGAGNFHGT 139

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+     +  D+   +  L HR+D++TSG+L++A+T  A   L + F  +   
Sbjct: 140 LINAIAWHLKDL--ASFDANDPEVGLVHRIDKDTSGLLLIAKTPEAKTKLGKQFFNKTTH 197

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------VVKQNEKGANYAISHFK 231
           + Y +LVWG          N++  +  I G+            V   + +   +A++H+K
Sbjct: 198 RSYIALVWG----------NFVEDEGRIEGNIARDPKDRLRMTVFPPDSEIGKHAVTHYK 247

Query: 232 VIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP--- 283
           VI+ F       C LE    TGRTHQ+R H  ++G P+ GD +Y      +G  +S    
Sbjct: 248 VIERFGYTTLIECILE----TGRTHQIRAHMKYIGHPLFGDERYGGKEVLRGTRSSTYNA 303

Query: 284 -IQN------KLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            ++N      +  LHA+ +   HP  G+ +  T+ LPA +
Sbjct: 304 FVKNGFKLCPRQALHAKTLGFVHPTTGKQMDFTSKLPADL 343


>gi|260589549|ref|ZP_05855462.1| ribosomal large subunit pseudouridine synthase D [Blautia hansenii
           DSM 20583]
 gi|331082975|ref|ZP_08332095.1| hypothetical protein HMPREF0992_01019 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540117|gb|EEX20686.1| ribosomal large subunit pseudouridine synthase D [Blautia hansenii
           DSM 20583]
 gi|330399970|gb|EGG79628.1| hypothetical protein HMPREF0992_01019 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 294

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 125/231 (54%), Gaps = 31/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---------GSGIA--YHIDGFLKSWVDSKGQKPRLTHR 149
           ++YED  I + NKPA + V            +GIA  Y + G  +++V       R  +R
Sbjct: 83  IVYEDEDILLVNKPADMPVHPSINNYDNTLANGIAHYYQVQG--ETFVF------RCINR 134

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++T+G+L++A+   +A  L+   + R I + Y ++V+GIPK + + I   + +K +  
Sbjct: 135 LDRDTTGLLIIAKNALSASILSNQMKAREIHRTYLAVVFGIPKKEADTITAPIARKENSA 194

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +        E+    A+++++V+    + +  L++   TGRTHQ+RVHA +MG P++GD
Sbjct: 195 IERCVDFINGER----AVTNYQVVAS-KEDYSLLKLSLETGRTHQIRVHAKYMGNPLLGD 249

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           + Y  +F     S IQ ++ LH+  +   HP  G+ ++ +APLP  M   +
Sbjct: 250 YLYNPDF-----SRIQ-RVALHSYSLSFIHPLTGQPMKFSAPLPEDMASLF 294


>gi|226943324|ref|YP_002798397.1| Pseudouridine synthase [Azotobacter vinelandii DJ]
 gi|226718251|gb|ACO77422.1| Pseudouridine synthase [Azotobacter vinelandii DJ]
          Length = 336

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 93/311 (29%), Positives = 149/311 (47%), Gaps = 46/311 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +   +   L   ++ G++ VD   ++  + +  G ++ +     A    I 
Sbjct: 36  RLDQVAAQLFAEHSRSRLAAWIKDGRLTVDGAALRPRDIVHGGALLELDAEQQAQGEWIA 95

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW--- 136
           +   LD               +++ED +I V NKPAG+ V   +G   H DG L +    
Sbjct: 96  QAIELD---------------IVHEDEQILVLNKPAGLVVHPAAG---HADGTLLNALLH 137

Query: 137 -VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            V      PR  + HRLD++T+G++VVA+T  A   L E  + R + +IY ++V G+   
Sbjct: 138 HVPGLVNVPRAGIVHRLDKDTTGLMVVAKTLQAQTRLVEQLQKRSVSRIYEAIVVGV--- 194

Query: 194 KKECIANWLLKKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTG 250
               I       + IG  G     +   E G   A+SH++V++ F A     ++++  TG
Sbjct: 195 ----ITAGATIDAPIGRHGQQRQRMAVVE-GGKPAVSHYRVLERFRAHTHARIKLE--TG 247

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSP--IQN-----KLYLHARYMDLPHPEG 302
           RTHQ+RVH  H+G  +VGD  Y   F+     SP  +Q      +  LHAR+++L HP  
Sbjct: 248 RTHQIRVHMAHVGYSLVGDPVYGGRFRIPPAASPTLVQALREFPRQALHARFLELDHPAS 307

Query: 303 G-RLQITAPLP 312
           G RL+  APLP
Sbjct: 308 GERLKWEAPLP 318


>gi|229168633|ref|ZP_04296355.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH621]
 gi|228614789|gb|EEK71892.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH621]
          Length = 302

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 152/321 (47%), Gaps = 43/321 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVKGNYKVKGND 60

Query: 64  VVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            + +          I E + LD     +NL          + YED+ + V NKP G+ V 
Sbjct: 61  EITV---------TIPEPEELDIQPEDMNLE---------VYYEDADVLVVNKPRGMVVH 102

Query: 121 GGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    
Sbjct: 103 PAPGHTKGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 162

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKV 232
             + + + Y ++V G+  + K  I       + IG D      +  +E G N A++HF+V
Sbjct: 163 VEKTVTRRYKAIVHGVIPHDKGII------DAPIGRDKKERQSMTVDENGKN-AVTHFQV 215

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++ F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA
Sbjct: 216 LERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHA 269

Query: 293 RYMDLPHPEGGR-LQITAPLP 312
             +   HP  G  ++  AP+P
Sbjct: 270 GILGFNHPRTGEYIEFEAPIP 290


>gi|209542655|ref|YP_002274884.1| RluA family pseudouridine synthase [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209530332|gb|ACI50269.1| pseudouridine synthase, RluA family [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 322

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 86/325 (26%), Positives = 143/325 (44%), Gaps = 54/325 (16%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP--PV 70
           E +    R DR+  +    ++   ++ ++  G V            ++ G V+R P  PV
Sbjct: 13  ETEHAGQRTDRFLADMVGTLSRSRVKALMEGGHV------------LRDGHVLREPADPV 60

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
              L + I+    +  ++  T  +  +   +LYEDS + V +KPAG+ V    G      
Sbjct: 61  RAGLCYEIR----MPPAIPATPRAQAIPFAILYEDSDLIVLDKPAGLVVHPAPGNEDGTL 116

Query: 129 IDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L    DS       ++P + HRLD++TSG++VVA+T  A   L+++F  R I + Y
Sbjct: 117 VNALLAHCGDSLTGIGGERRPGIVHRLDKDTSGVMVVAKTEQAHTALSDAFAARDIDRTY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------GANYAISHFKVIDCF 236
            +L WGI              +  IG D     +++ K       G  +A++H++ +  F
Sbjct: 177 LALAWGILSPASGTF------EGAIGRD-----RRDRKRMAVVTHGGKHAMTHYRTLHSF 225

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---------K 287
                 +E +  TGRTHQ+RVH    G P+VGD  Y         +  ++         +
Sbjct: 226 HGGISSVECRLATGRTHQIRVHFSTSGHPLVGDPVYLRRIPAAARALPEDARRAALDFPR 285

Query: 288 LYLHARYMDLPHPEGGR--LQITAP 310
             LHA  +   HP  G   L  TAP
Sbjct: 286 QALHAARLGFTHPRTGESLLFETAP 310


>gi|269798295|ref|YP_003312195.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269094924|gb|ACZ24915.1| pseudouridine synthase, RluA family [Veillonella parvula DSM 2008]
          Length = 305

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 93/315 (29%), Positives = 145/315 (46%), Gaps = 42/315 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  ++E MRLD +        +   +Q +++ G V V  K  K N R+    V+R+   
Sbjct: 5   IVSAEQEGMRLDVFLTEQMEG-SRSYIQSLIKGGHVTVGGKVGKANLRLTPDTVIRVEIP 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                 +  E   LD                LYED  I + NKP G+ V    G      
Sbjct: 64  EPESIEVKPEDIPLD---------------YLYEDHDIVIVNKPRGMVVHPAVGNYSGTL 108

Query: 129 IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D  G     +P + HRLD++TSG+++VA+  AA   L E  +    ++ YW
Sbjct: 109 VNALLFHCKDLSGINGEIRPGIVHRLDKDTSGVMMVAKNDAAHIGLAEQVKAHSARRTYW 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +LV G    +K  I      K+ IG        + VV +N K    A++HFKV+  +  +
Sbjct: 169 ALVQGNIVEEKGTI------KAPIGRHPKDRMKMAVVFENSKD---AVTHFKVLARYGHQ 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E    TGRTHQ+RVH +++G P+V D  Y          PI+ +  LH++ +D+ H
Sbjct: 220 -TLVECNLETGRTHQIRVHFVYIGHPVVNDPFYGYR---RMDFPIEGQA-LHSKSLDVKH 274

Query: 300 P-EGGRLQITAPLPA 313
           P  G  +   AP+PA
Sbjct: 275 PITGEEMHFEAPVPA 289


>gi|13357670|ref|NP_077944.1| pseudouridine synthase (uracil hydrolase) [Ureaplasma parvum
           serovar 3 str. ATCC 700970]
 gi|170762339|ref|YP_001752196.1| pseudouridine synthase [Ureaplasma parvum serovar 3 str. ATCC
           27815]
 gi|171920337|ref|ZP_02691044.2| pseudouridine synthase [Ureaplasma parvum serovar 1 str. ATCC
           27813]
 gi|183508769|ref|ZP_02689887.2| pseudouridine synthase [Ureaplasma parvum serovar 14 str. ATCC
           33697]
 gi|186701771|ref|ZP_02553233.2| pseudouridine synthase [Ureaplasma parvum serovar 6 str. ATCC
           27818]
 gi|11357016|pir||C82933 pseudouridine synthase (uracil hydrolase) UU113 [imported] -
           Ureaplasma urealyticum
 gi|6899069|gb|AAF30519.1|AE002111_8 pseudouridine synthase (uracil hydrolase) [Ureaplasma parvum
           serovar 3 str. ATCC 700970]
 gi|168827916|gb|ACA33178.1| pseudouridine synthase [Ureaplasma parvum serovar 3 str. ATCC
           27815]
 gi|171902761|gb|EDT49050.1| pseudouridine synthase [Ureaplasma parvum serovar 1 str. ATCC
           27813]
 gi|182675707|gb|EDT87612.1| pseudouridine synthase [Ureaplasma parvum serovar 14 str. ATCC
           33697]
 gi|186701046|gb|EDU19328.1| pseudouridine synthase [Ureaplasma parvum serovar 6 str. ATCC
           27818]
          Length = 315

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 83/274 (30%), Positives = 137/274 (50%), Gaps = 32/274 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++ N RLDR+   ++P+++ + + KI+R+  V+V+ K+V  N  ++   VV I    N L
Sbjct: 11  NDANQRLDRFLLKNFPNLSRIAVYKIIRTKDVKVNHKKVDHNYLLKENDVVSIYAKENFL 70

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-- 132
                E+K+  S  N     D     ++YED  I V +KP G+ V   +   Y  D    
Sbjct: 71  -----EKKVDLSFANAKDELD-----IIYEDKNILVVHKPIGLIVHEDNR--YKNDTLQN 118

Query: 133 -LKSWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +K ++         D     P L HRLD  TSG++V A+T  A + +TE F+   + +I
Sbjct: 119 RIKKYLVKKDEYHPFDESAFVPSLCHRLDLNTSGLIVAAKTANALRVITEMFKNNDVIRI 178

Query: 183 YWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKF 240
           Y  L +  +PKN  + I N++ K      D   +V+  +   N  AI+ +  ID + + F
Sbjct: 179 YKCLTYNQLPKN-NDVIYNFMYK----ADDNTMIVQNFKTKFNKTAITKYTYIDKYKKYF 233

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + +++  TGRTHQ+R     +  PIVG+ KY  
Sbjct: 234 IY-DIELLTGRTHQIRAVLNFLHAPIVGEQKYIT 266


>gi|330814173|ref|YP_004358412.1| crcB-like protein [Candidatus Pelagibacter sp. IMCC9063]
 gi|327487268|gb|AEA81673.1| crcB-like protein [Candidatus Pelagibacter sp. IMCC9063]
          Length = 297

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 147/273 (53%), Gaps = 27/273 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFK---NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M + +   ++ +  N R+D+W K     +P  +FV  +K+LRSG+++V+ K+VK + ++Q
Sbjct: 1   MKFNEKFTIDENYANTRIDKWLKLNTQKFPQ-SFV--EKLLRSGKIKVNNKKVKSSYKLQ 57

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
               +     +       KE +    S N+ ++ + +++ +++E+    + NKP+GISVQ
Sbjct: 58  LEDEI----FLQFSYEEKKENEKFSYSANIKEYKE-IRNNIIFENHDYLILNKPSGISVQ 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G+    ++   L  +  S+ +K  L HR+D+ETSGI+V A  R  AQ L+E FR + ++
Sbjct: 113 SGTKSPKNLIDILNKF--SEDKKFYLVHRIDKETSGIIVFACNRLFAQTLSEQFRNKEVK 170

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           K Y ++++G IP+N           +  +  D V  VK N+     A + F V+    + 
Sbjct: 171 KSYLAILYGSIPRN-----------EGTLDHDLVFKVK-NQMKTFKAETDFSVLSK-NKD 217

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           F ++E  P TGR HQ+R     +  PIVGD KY
Sbjct: 218 FSYVEATPITGRKHQIRQQFFKVNHPIVGDGKY 250


>gi|258405122|ref|YP_003197864.1| pseudouridine synthase, RluA family [Desulfohalobium retbaense DSM
           5692]
 gi|257797349|gb|ACV68286.1| pseudouridine synthase, RluA family [Desulfohalobium retbaense DSM
           5692]
          Length = 547

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 89/309 (28%), Positives = 144/309 (46%), Gaps = 34/309 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VVE  E   RLD++  +    +  V+  +I  S  +R ++ RV       +G +      
Sbjct: 16  VVEAGEAGKRLDKFLSDRLADLG-VSRSRI--SQWIRQERVRV-------AGALC----- 60

Query: 71  INALNHIIKEQKI--LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
           +     ++  QK+  L  S+      +     ++Y D  + V NK AG++V  G+G    
Sbjct: 61  LQGKTKVLNGQKVVLLAPSLQSGIKPEVGPVEVVYSDPDVVVVNKAAGVTVHPGTGCESG 120

Query: 125 -IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + +H+           G++P + HRLD++TSG+L VA   +A   LT SF  R + K Y
Sbjct: 121 TLVHHLAALYPELARFDGERPGVVHRLDKDTSGLLTVALNESARLALTRSFARREVDKEY 180

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK-VIDCFAQKFCW 242
            +LV G P  + E   +  L +       + VV    +G   A++ FK V      +   
Sbjct: 181 LTLVHGRP--EAEGTVDHPLGRDPQSKIRMAVVP---RGGKEALTRFKRVWTSPDGRVSL 235

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKL----YLHARYMD 296
           L ++  TGRTHQ+RVH  ++G P+VGD  Y    +  F  + P+  +L     LHA  + 
Sbjct: 236 LRVRILTGRTHQIRVHMAYLGFPLVGDALYGPQAQAAFQRSRPLLARLAKHHMLHAWRLA 295

Query: 297 LPHPEGGRL 305
            PHP  GR+
Sbjct: 296 FPHPRSGRM 304


>gi|255692700|ref|ZP_05416375.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides finegoldii DSM 17565]
 gi|260621534|gb|EEX44405.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides finegoldii DSM 17565]
          Length = 229

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 110/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQ        +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQADKTGDTPLSETVKQYLKEKYQKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR   ++K YW++V   P+  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTGKALTRLNEMFRTSEVKKTYWAVVKNAPQEPEGELVHFLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   ++ +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPNSKKAILHYRLIG-HSENYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             G+  S     + LHAR +   HP    L ++ APLP
Sbjct: 177 --GSPRSNPDGSICLHARRVRFIHPVSKELIELEAPLP 212


>gi|163738662|ref|ZP_02146076.1| riboflavin synthase subunit alpha [Phaeobacter gallaeciensis BS107]
 gi|161387990|gb|EDQ12345.1| riboflavin synthase subunit alpha [Phaeobacter gallaeciensis BS107]
          Length = 344

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 91/357 (25%), Positives = 155/357 (43%), Gaps = 62/357 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           +++V+ EN  +  RLD+      P    ++   L +++ +GQ++V+   V     ++  G
Sbjct: 6   IEFVIAENPPK--RLDKAVSRDVPEEATLSRTRLARLIEAGQLQVNGTVVSDAKAKVDEG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++ I       +HI  E   L+               ++YED  + V NKP G+ V   
Sbjct: 64  ALIEITIEEAEDSHIGPEDIPLE---------------VIYEDDDLIVINKPTGMVVHPA 108

Query: 123 SGIAYH--IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G      ++  L    D+       ++P + HR+D+ETSG+LVVA++  A Q L   F 
Sbjct: 109 PGTPSGTLVNALLHHCGDNLSGVGGVKRPGIVHRIDKETSGLLVVAKSDVAHQGLAAQFE 168

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------------G 222
              +++ Y ++ +G+P +  +     +   S   G+ + +  Q  +             G
Sbjct: 169 KHTVERYYRAICYGVP-DANDPRLRGVKGTSFEPGNILKLTTQLARHKTDRQRQAVLFQG 227

Query: 223 ANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---- 272
             +AI+  +++D F          CWLE    TGRTHQ+RVH  H G  +VGD  Y    
Sbjct: 228 GRHAITRARIVDSFGTPPVVALIECWLE----TGRTHQIRVHMAHGGHGLVGDPVYGGKR 283

Query: 273 ---CANFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
                +   +  + IQ   +  LHA  +   HP  G  ++  APLP  M      LG
Sbjct: 284 KLAAKSLPEDTAAAIQAFPRQALHAAVLGFIHPVTGDAMRFEAPLPEDMAHLLQKLG 340


>gi|238013094|gb|ACR37582.1| unknown [Zea mays]
          Length = 272

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 78/267 (29%), Positives = 113/267 (42%), Gaps = 61/267 (22%)

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           + VQGG GI   ID     + +   + PRL HRLD++ SG+LV+ RT+ +A  +   FR 
Sbjct: 1   MPVQGGVGIKNSIDILAPMFENGSSEVPRLVHRLDRDCSGVLVLGRTQFSASLMHAIFRE 60

Query: 177 RR-----------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV---VKQNEKG 222
           +            +Q+ Y +LV G P++ K  ++  L K     G    +      N   
Sbjct: 61  KTADALGDGTQQVLQRKYVALVIGRPRHPKGLLSAPLAKVVLQDGRSERLTVCAGSNTAS 120

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKY--------- 272
              A++ ++VI+ F Q + WLE+ P TGR HQLRVH    +G PIVGD+KY         
Sbjct: 121 VQDALTEYRVIESFPQGYTWLELFPRTGRKHQLRVHCAEVLGTPIVGDYKYGRQAHQNWM 180

Query: 273 --------------------CANFKGNFTSPIQNKLYLHARYMDLPHPEGG--------- 303
                                    G   +  Q +L+LH + M LP              
Sbjct: 181 PLPMPQTIDKEMLKKRKLPFGLTLGGGSVAEQQPQLHLHCKQMILPDISAAMQQLRSSDA 240

Query: 304 --------RLQITAPLPAHMVKTWDSL 322
                   +L   APLP HM  +W  L
Sbjct: 241 DHDFSDLEKLSFVAPLPLHMQLSWKIL 267


>gi|27382447|ref|NP_773976.1| pseudouridine synthase-like protein [Bradyrhizobium japonicum USDA
           110]
 gi|27355618|dbj|BAC52601.1| blr7336 [Bradyrhizobium japonicum USDA 110]
          Length = 335

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 90/337 (26%), Positives = 147/337 (43%), Gaps = 53/337 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIP 68
           VVV  DE + RLDR      P ++   L+ ++ +G V +    V+     +  G  + I 
Sbjct: 12  VVVAGDEGSARLDRVLAARLPDLSRSRLKALILAGAVSLKASAVRDPAYHVSHGDTIIID 71

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
               A      E+  LD               +++ED  I V NKP G+ V   +G   H
Sbjct: 72  VPEAAPAEPKGEEIALD---------------IVFEDDDIIVINKPRGLVVHPAAG---H 113

Query: 129 IDGFL--------KSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESF---- 174
             G L         S +   G  ++P + HRLD++T+G++VVA+   A   L+  F    
Sbjct: 114 ETGTLVNALIAHCGSTLSGIGGVRRPGIVHRLDKDTTGLMVVAKNDLAHASLSAQFADHG 173

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R   +++ Y +  WG+P   +  +   + +       Y        +G   A++H+++++
Sbjct: 174 RTGAMRRGYMAFAWGVPGRHRGTVDAPIDRHP-----YAREKMAVRQGGREAVTHWEILE 228

Query: 235 CFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSP---- 283
            F  +        L  +  TGRTHQ+RVH  H+G P++GD  Y  +F  K N  +P    
Sbjct: 229 SFPGRDGKPIAALLACELETGRTHQIRVHLAHIGHPLMGDAVYGPHFKTKANQLAPESQA 288

Query: 284 ---IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
                 +  LHA  + L HP  G  L   APLP  ++
Sbjct: 289 ALATLGRQALHAYLLVLEHPRTGELLHWEAPLPEDLL 325


>gi|260654228|ref|ZP_05859718.1| ribosomal large subunit pseudouridine synthase C [Jonquetella
           anthropi E3_33 E1]
 gi|260630861|gb|EEX49055.1| ribosomal large subunit pseudouridine synthase C [Jonquetella
           anthropi E3_33 E1]
          Length = 276

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 88/302 (29%), Positives = 136/302 (45%), Gaps = 42/302 (13%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSD 95
           + K  R G VR+D  R  F  ++ +GQ+V +P    +A   +    + LD          
Sbjct: 1   MMKFFRKGSVRLDGARADFRTKVAAGQMVFVPWEAPDAQPEVQVRHRPLD---------- 50

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
                +LY    + V NKPAG+  Q  +     +      +        +L HRLD+ TS
Sbjct: 51  -----VLYRSDSVLVINKPAGLLSQPDTKGEDSVATRALGYASDPAFGAQLVHRLDRNTS 105

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVH 214
           G++++A    A + L   F+ R   K Y +LV G +P + +  I   LLK        V 
Sbjct: 106 GVMILALDGQALRSLMVCFKERTANKTYLALVSGQLPPSGQ--IDAPLLKDPD--KKLVR 161

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V    E+    A++ F+ +    Q F   E++  TGRTHQ+RVH  H+G PI+GD KY  
Sbjct: 162 VASNGER----AVTRFRRLATDGQ-FSLAEVEILTGRTHQIRVHMNHIGHPILGDAKY-- 214

Query: 275 NFKGNFTSPIQ------NKLYLHARYMDLPHPEGGRLQIT-----APLPAHMVKTWDSLG 323
              G+F++  Q       +  LHA  + +  P+    +I+     APL A M      LG
Sbjct: 215 ---GDFSAKPQVRRLGIRRPMLHATCLVVNSPDDCLKEISGRRFDAPLAADMASVCQKLG 271

Query: 324 FK 325
           F+
Sbjct: 272 FE 273


>gi|156402477|ref|XP_001639617.1| predicted protein [Nematostella vectensis]
 gi|156226746|gb|EDO47554.1| predicted protein [Nematostella vectensis]
          Length = 330

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 79/294 (26%), Positives = 136/294 (46%), Gaps = 62/294 (21%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLD 151
           + +L   +++ ++ +   NKP G+ V GG G+   +   L+ +   K    KP L HRLD
Sbjct: 18  AQYLADNVIFSNNDLIAINKPYGLPVHGGPGVVLSVAELLEEFAAIKNYQNKPELAHRLD 77

Query: 152 Q----------ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA-- 199
           +          + SG+L++ R + AAQ + E F+ R ++K Y ++  G+P+ ++  I+  
Sbjct: 78  KYGTDYTIMLIDCSGVLLLTRNKTAAQKIAEMFQSRMVKKRYLAVSVGVPRYEEGTISIP 137

Query: 200 -------NW---LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   W   ++++  +G  +  +    E G   AI+ FK++D        LE++P T
Sbjct: 138 VGYGRVGPWERIIIRQDLVGKTHKEI---TEAGFKQAITKFKILDENQSTCSLLEIEPIT 194

Query: 250 GRTHQLRVH-ALHMGCPIVGDHKYCANFKGNFTSPI------------------------ 284
           G   Q+RVH A  + CPI+GDHK+ ++       P+                        
Sbjct: 195 GHKQQIRVHLADALRCPILGDHKFSSDKPQPQVIPLRLLQLLQISGVKGVDGKKGRIRPW 254

Query: 285 ---QNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
              Q  L+LH+  + LP +  G  L I+APLP + + T   L      NL+ KR
Sbjct: 255 QRGQIPLHLHSHQLVLPKYHTGSDLVISAPLPKYYLDTLSRL------NLHPKR 302


>gi|32423742|gb|AAP81266.1| pseudouridine synthase [Pseudomonas aeruginosa PA14]
          Length = 320

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 93/332 (28%), Positives = 153/332 (46%), Gaps = 50/332 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   L   ++ G++ VD   ++  + + SG  +    V+ A      
Sbjct: 19  RLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVHSGAQL----VLEAEQEAQG 74

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW--- 136
           E    D  + +           +YED  I V +KPAG+ V   +G   H DG L +    
Sbjct: 75  EWLAQDIELEI-----------VYEDEHILVIDKPAGLVVHPAAG---HQDGTLLNALLY 120

Query: 137 -VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY ++V G+   
Sbjct: 121 HVPDIANVPRAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGV--- 177

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQPHTGRT 252
               I +     + IG   V   K     A   A+SH++V++ F +      ++  TGRT
Sbjct: 178 ----ITSGGTIDAPIGRHGVQRQKMAVVDAGKVAVSHYRVLERF-RAHTHTRVKLETGRT 232

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY-----------LHARYMDLPHPE 301
           HQ+RVH  H+G P+VGD  Y   F+     P+ ++             LHAR+++L HP 
Sbjct: 233 HQIRVHMSHIGYPLVGDPVYGGRFR---IPPVASQTLVQTLREFPRQALHARFLELDHPA 289

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            G R++  +PLP   +  W     + DR  ++
Sbjct: 290 TGVRMKWESPLPEEFL--WLLSLLRQDREAFV 319


>gi|297180551|gb|ADI16763.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0010_11B23]
          Length = 307

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 84/266 (31%), Positives = 135/266 (50%), Gaps = 29/266 (10%)

Query: 15  DEENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           DEEN   R+D +  N+   I+   +Q+++  G+V ++ K  K N  ++   +V I   + 
Sbjct: 9   DEENSNNRVDIFLANNLDAISRGIVQQLISEGKVTINGKETKRNYLLKPSDIVEITFELE 68

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--ID 130
           +      E +  D  V++T           +E+   +V NK +G++V  G+G   +  I+
Sbjct: 69  SNG----EDEAQDIPVDIT-----------FENDDFFVINKHSGLTVHPGAGQKDNTLIN 113

Query: 131 GFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           G L    + +   PR  L HRLD++TSG++V+A+   A   LTE  + + IQ+ Y++LV 
Sbjct: 114 GILHIRKEQR-DIPRYGLVHRLDKDTSGLMVLAKNLKAHTVLTELIQAKSIQRKYYALVH 172

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G P + K      L    H     +  VK    G   AI+HFK+   F + F  L ++  
Sbjct: 173 GTPISGKTI---DLPIGRHPKNRLLFCVKD---GGREAITHFKIEKRF-KNFSLLNVELE 225

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA 274
           TGRTHQ+RVH  H+G PI GD  Y +
Sbjct: 226 TGRTHQIRVHLKHIGHPIAGDASYNS 251


>gi|298376445|ref|ZP_06986400.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 3_1_19]
 gi|298266323|gb|EFI07981.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 3_1_19]
          Length = 224

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 107/218 (49%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I   +K     VQG       +   LK+W+  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIAVDKTCREIVQGDKTGDKPLSEMLKAWLKKKYCKPGNVFVGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR+  ++K YW++V   P   +  + +WL++       Y + 
Sbjct: 63  GVVIFAKTSKALSRLNEMFRVGEVRKTYWAIVKNRPPQDEGELVDWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  AI  +K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 123 TER--PNAKKAILRYKLI-AHSDHYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             G   S     + LHAR  +  HP     ++I AP+P
Sbjct: 177 --GFDRSNKDGGISLHARSAEFIHPVSKENVRIVAPVP 212


>gi|296135788|ref|YP_003643030.1| pseudouridine synthase, RluA family [Thiomonas intermedia K12]
 gi|295795910|gb|ADG30700.1| pseudouridine synthase, RluA family [Thiomonas intermedia K12]
          Length = 342

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 84/331 (25%), Positives = 148/331 (44%), Gaps = 33/331 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T ++ VV E D    RLD+     +   +   LQ+   +G VR+  +     ++ ++G+ 
Sbjct: 30  TVLEAVVPEADA-GQRLDKVLAAQFSQYSRSRLQQWCEAGLVRMGAQVAGVRDKARAGET 88

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RI     A+  + ++       + L          +++ED+ + V NKPAG+ V   +G
Sbjct: 89  LRI-----AVPALPEDTAFAPEDLPLN---------VVFEDADLAVLNKPAGLVVHPAAG 134

Query: 125 --IAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                 ++G L  + ++ G  +  + HRLD++TSG++V ART  A   L    + R I +
Sbjct: 135 NWSGTLLNGLLARYPETAGLPRAGIVHRLDKDTSGLMVTARTLEAQTELVRRLQARTIHR 194

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIG---GDYVHV-VKQNEKGANYAISHFKVIDCFA 237
            Y +L WG        ++     ++ IG    D + + V    K A    +    +D   
Sbjct: 195 QYLALAWG-------SVSRAFNVEAPIGRHPRDRLRMAVVHGGKPARTDFTPLAELDTRW 247

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                L  + H+GRTHQ+RVH       +V D  Y    + +   P+Q +  LHA  +  
Sbjct: 248 GPLTALRCKLHSGRTHQIRVHLQFAKLEMVADSVYGGRLRPDL--PLQRQ-ALHAARLAF 304

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            HP   + +   AP+P  +   WD+ G + D
Sbjct: 305 AHPLNDKPMDFIAPIPDDIASFWDACGGEMD 335


>gi|319763720|ref|YP_004127657.1| pseudouridine synthase, rlua family [Alicycliphilus denitrificans
           BC]
 gi|317118281|gb|ADV00770.1| pseudouridine synthase, RluA family [Alicycliphilus denitrificans
           BC]
          Length = 332

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 87/328 (26%), Positives = 151/328 (46%), Gaps = 29/328 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVV 65
           ++ V+V   +   RLD+      P  +   LQ++L  G VR++ +   K  +++++G  V
Sbjct: 27  LREVMVPAAQHQARLDKALAELVPEFSRSYLQQLLAQGDVRLNGQPAAKPAHKVRAGDQV 86

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +      +    + Q     S+ L          +++ED  + V +KPAG+ V    G 
Sbjct: 87  AV-----RMRPTQQSQAFKPESLPLD---------VVHEDEHLLVIDKPAGLVVHPAPGN 132

Query: 125 -IAYHIDGFLKSWVDSKG-QKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                ++  L    D++  Q PR  + HRLD++TSG++VVAR RAA   L      R + 
Sbjct: 133 WSGTLLNALLGR--DAQAMQVPRAGIVHRLDKDTSGLMVVARNRAAMDALVRMIAAREVS 190

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +L WG     ++      + +       + VV   +     A + F ++    ++ 
Sbjct: 191 RQYLALAWGAWSGSEQRRIRAPIGRDPRNRLRMAVVDLGQHAGKEACTDFDLL-ASGEEV 249

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           C +    HTGRTHQ+RVH   +  P+V D    A + G    P++ +  LHA  +   HP
Sbjct: 250 CLVRCTLHTGRTHQIRVHMASIRHPLVAD----ALYGGAVGGPMRRQ-ALHAFRLAFTHP 304

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             G+ ++  APLP  M +  D  G +Y+
Sbjct: 305 VTGKPMEFHAPLPEDMRQALDFWGLRYN 332


>gi|220915339|ref|YP_002490643.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219953193|gb|ACL63577.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 301

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 89/298 (29%), Positives = 140/298 (46%), Gaps = 32/298 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIP 68
           ++V + +   R+DR+       I+    ++ + +G V VD +R K   R +  GQ V   
Sbjct: 6   LLVPDADRYERIDRFIAARG-GISRGLARRAIEAGGVFVDGRRCKVAGRTLTPGQQV--- 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            V+N L    +    L +           +  LLY D+ +   +KPAG+  Q        
Sbjct: 62  -VVN-LEEGGRAAPALAA---------LGRERLLYADADLCAVDKPAGVPAQ----PTLT 106

Query: 129 ID-GFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            D G L   V +  G    L HRLD+ETSG+ V ARTR AA  L E+FR    +K Y +L
Sbjct: 107 TDRGALPELVSALLGAPVTLVHRLDRETSGVTVFARTRDAAAALAEAFRTGTPEKTYLAL 166

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
               P   +  +A  L K     G     +++ +   + A + ++ +   A     +E +
Sbjct: 167 CARAPSPAEGRVALALGKDPARPG-----LRRVDPAGDPAATRYRTLR-EAPGGALVEAR 220

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGG 303
           P TGRTHQ+RVH   +G P++GD +Y    + G   +P   ++ LHA  ++LPHP  G
Sbjct: 221 PETGRTHQIRVHLAALGAPLLGDARYGGPRRVGEVAAP---RVMLHATRLELPHPATG 275


>gi|42563328|ref|NP_178012.2| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|75110951|sp|Q5XET6|PUS3_ARATH RecName: Full=RNA pseudourine synthase 3, mitochondrial; AltName:
           Full=RNA pseudouridylate synthase 3; AltName:
           Full=RNA-uridine isomerase 3; Flags: Precursor
 gi|53850479|gb|AAU95416.1| At1g78910 [Arabidopsis thaliana]
 gi|56790228|gb|AAW30031.1| At1g78910 [Arabidopsis thaliana]
 gi|332198052|gb|AEE36173.1| RNA pseudourine synthase 3 [Arabidopsis thaliana]
          Length = 478

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 122/248 (49%), Gaps = 25/248 (10%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD---FLKSILLYE 104
           +  +++K N  +Q G  + +P  I  +  I K    + S   L  ++D   +L+ ++ ++
Sbjct: 127 IPMRKIKHNEVMQIGDKIWLPVSIAEMR-ISKRYDTIPSG-TLYPNADEIAYLQRLVRFK 184

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVART 163
           DS I V NKP  + V+G   I   +D    + +     + PRL HRLD+ETSG+LV+ RT
Sbjct: 185 DSAIIVLNKPPKLPVKGNVPIHNSMDALAAAALSFGNDEGPRLVHRLDRETSGLLVMGRT 244

Query: 164 RAAAQHLTESFR---------------MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           + +  +L   F                   + + YW+LV G PK K+  I+  L K    
Sbjct: 245 KESIDYLHSVFSDYKGRNSSCKAWNKACEAMYQQYWALVIGSPKEKEGLISAPLSKVLLD 304

Query: 209 GGDYVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC 264
            G    VV     G   +  AI+ +KV+        W+E++P T R HQLRVH A  +G 
Sbjct: 305 DGKTDRVVLAQGSGFEASQDAITEYKVLGPKINGCSWVELRPITSRKHQLRVHCAEALGT 364

Query: 265 PIVGDHKY 272
           PIVGD+KY
Sbjct: 365 PIVGDYKY 372


>gi|115374968|ref|ZP_01462239.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|115367995|gb|EAU66959.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
          Length = 272

 Score =  106 bits (264), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 89/284 (31%), Positives = 133/284 (46%), Gaps = 37/284 (13%)

Query: 61  SGQVVRIPPVINALNHIIKE------QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
           +G+ V+   +++A  HI+ E      + + D+   L         ++L+ED+ + V +KP
Sbjct: 4   NGRAVKKGLLVSAGQHILVEWEEETREAVPDTGFPL---------VVLHEDAALVVVDKP 54

Query: 115 AGISVQ----GGSG------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           AG        G +G      IA + +    S    +G    L HRLD ETSG+L+ ARTR
Sbjct: 55  AGRPSHPLKPGETGTVANALIARYPECAQASEDAREGG---LCHRLDIETSGVLLAARTR 111

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            A Q L  +F  R + K Y +LV G   ++ E          H   D V      E+GA 
Sbjct: 112 EAWQRLRTAFSGREVDKHYVALVTGPLADEGEIEIPLRHHPRHP--DRVEPALPGEEGAR 169

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
            A S F+V    +  F  +E++  TG  HQ+R H   +G P+VGD  Y     G    P 
Sbjct: 170 EAHSLFQV-QARSGDFSLVEVRILTGVLHQVRAHLAGIGAPLVGDSLY-----GGREEPG 223

Query: 285 QNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            ++ +LHAR +   HPE G RLQ+ +PLP  + +     G   D
Sbjct: 224 LSRFFLHARALGFTHPETGQRLQVESPLPQELAEVLRHHGLSAD 267


>gi|297172314|gb|ADI23291.1| pseudouridylate synthases, 23S RNA-specific [uncultured
           actinobacterium HF0770_13M05]
          Length = 244

 Score =  106 bits (264), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 85/266 (31%), Positives = 136/266 (51%), Gaps = 29/266 (10%)

Query: 59  IQSGQVVRIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           +Q G  +RIPPV I++ N       I ++++N       ++  ++YED ++ V NKP G+
Sbjct: 1   MQRGDRLRIPPVRIDSRN----ASHIGEATINQ------IRRAIIYEDEELLVLNKPVGV 50

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +V GGSGI + I   L+        +  L HRLD++TSG +++A+TR     L  +FR  
Sbjct: 51  AVHGGSGIRHGIIEILRQTRSDVAFE--LVHRLDRDTSGCMLIAKTRRMLLELHAAFREA 108

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCF 236
           R++K Y ++V G        + + L + +   G+  V +    +K    A + F+V    
Sbjct: 109 RVKKRYDAVVAGDWPQGLRTVRHSLRRHTLQSGERRVRIDLHGDK----ARTDFEVQQRG 164

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           A +   L + PHTGRTHQ+RVHA   G  +VGD+KY  N       P   ++ LH+  + 
Sbjct: 165 A-RVTRLWVYPHTGRTHQIRVHAAAEGHAVVGDNKYQLN------GPDVPRMMLHSSSLK 217

Query: 297 LPHPEGGRLQITAPLPAHMVKTWDSL 322
           L  P+G R    A      ++TW  L
Sbjct: 218 L--PDGRRFD--ADPDETFLETWSHL 239


>gi|294339951|emb|CAZ88314.1| Ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Thiomonas sp. 3As]
          Length = 342

 Score =  106 bits (264), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 84/331 (25%), Positives = 148/331 (44%), Gaps = 33/331 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T ++ VV E D    RLD+     +   +   LQ+   +G VR+  +     ++ ++G+ 
Sbjct: 30  TVLEAVVPEADA-GQRLDKVLAAQFSQYSRSRLQQWCEAGLVRMGAQVAGVRDKARAGET 88

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RI     A+  + ++       + L          +++ED+ + V NKPAG+ V   +G
Sbjct: 89  LRI-----AVPALPEDTAFAPEDLPLN---------VVFEDADLAVLNKPAGLVVHPAAG 134

Query: 125 --IAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                 ++G L  + ++ G  +  + HRLD++TSG++V ART  A   L    + R I +
Sbjct: 135 NWSGTLLNGLLARYPETAGLPRAGIVHRLDKDTSGLMVTARTLEAQTELVRRLQARTIHR 194

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIG---GDYVHV-VKQNEKGANYAISHFKVIDCFA 237
            Y +L WG        ++     ++ IG    D + + V    K A    +    +D   
Sbjct: 195 QYLALAWG-------SVSRAFNVEAPIGRHPRDRLRMAVVHGGKPARTDFTPLAELDTRW 247

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                L  + H+GRTHQ+RVH       +V D  Y    + +   P+Q +  LHA  +  
Sbjct: 248 GPLTALRCKLHSGRTHQIRVHLQFAKLEMVADSVYGGRLRPDL--PLQRQ-ALHAARLAF 304

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            HP   + +   AP+P  +   WD+ G + D
Sbjct: 305 AHPLNDKPMDFIAPIPDDIASFWDACGGEMD 335


>gi|149916264|ref|ZP_01904785.1| NAD(P) transhydrogenase subunit alpha [Roseobacter sp. AzwK-3b]
 gi|149809924|gb|EDM69775.1| NAD(P) transhydrogenase subunit alpha [Roseobacter sp. AzwK-3b]
          Length = 348

 Score =  106 bits (264), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 98/363 (26%), Positives = 152/363 (41%), Gaps = 68/363 (18%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNR 58
           L T V + +  +     RLD+      P    ++   L +++  G V V+   V    +R
Sbjct: 2   LSTLVTFRIAADPPP--RLDKALSRDVPEDAALSRTRLARLIAEGAVSVNGTPVTDPKSR 59

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           I  G  + I        HI  E   LD               +++ED  + V +KPAG+ 
Sbjct: 60  ISEGDSIAITVPQAQDTHIAAESIPLD---------------IVFEDDDLIVIDKPAGMV 104

Query: 119 V--QGGSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           V    GS     ++  L    D+       ++P + HR+D++TSG+LVVA++  A   L 
Sbjct: 105 VHPAPGSPGGTLVNALLHHCGDTLSGVGGMKRPGIVHRIDKDTSGLLVVAKSDRAHHGLA 164

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV---------KQNE-- 220
             F    +++ Y ++V+G+P      +   L   S   G+ + +          +Q +  
Sbjct: 165 AQFEDHSVERYYRAVVYGVPDAADPRL-RGLRGVSFETGNIIKITSGLARHRTDRQKQAV 223

Query: 221 --KGANYAISHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +G  +A++  +V+D F Q        CWLE    TGRTHQ+RVH  H G  +VGD  Y
Sbjct: 224 TFEGGRHAVTRARVVDTFGQPPVAALMECWLE----TGRTHQIRVHMAHAGHGLVGDPVY 279

Query: 273 C------------ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
                        A  K     P Q    LHA  +   HP  G  L+  APLP  M    
Sbjct: 280 GGRRKLPLRALSEAGLKAARDFPRQ---ALHAAVLGFVHPVSGEALEFEAPLPDDMTALI 336

Query: 320 DSL 322
           D+L
Sbjct: 337 DAL 339


>gi|150008130|ref|YP_001302873.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           distasonis ATCC 8503]
 gi|149936554|gb|ABR43251.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           distasonis ATCC 8503]
          Length = 224

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 106/218 (48%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I   +K     VQG       +   LK W+  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIAVDKTCREIVQGDKTGDKPLSEMLKVWLKEKYCKPGNVFVGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR+  ++K YW++V   P   +  + +WL++       Y + 
Sbjct: 63  GVVIFAKTSKALSRLNEMFRVGEVRKTYWAIVKNRPPQDEGELVDWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  AI  +K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 123 TER--PNAKKAILRYKLI-AHSDNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             G   S     + LHAR  +  HP     ++I AP+P
Sbjct: 177 --GFDRSNKDGGISLHARSAEFIHPVSKENVRIVAPVP 212


>gi|237724045|ref|ZP_04554526.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D4]
 gi|229437505|gb|EEO47582.1| ribosomal large subunit pseudouridine synthase D [Bacteroides dorei
           5_1_36/D4]
          Length = 357

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 93/337 (27%), Positives = 153/337 (45%), Gaps = 49/337 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           VVV+  +  +R+D++      + +   +QK   +G +  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKSSYKVKPCDVLTVMM 91

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
             P  +  N II E   LD               ++YED+ + V NKPAG+ V  G G  
Sbjct: 92  DRPRYD--NDIIPEDIPLD---------------IVYEDNDLMVINKPAGLVVHPGCGNY 134

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  IA+H+        D    +  L HR+D++TSG+LVVA+T  A  HL   F  +
Sbjct: 135 HGTLVNAIAWHLKD--NPRYDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNK 192

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCF 236
             ++ Y +LVWGI +N +  I   + +      D + + V  +     +A++H++V++  
Sbjct: 193 TTKRKYNALVWGIVENNEGTIEGNIGRNPK---DRMQMAVLSDPAQGKHAVTHYRVLERL 249

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN-------- 286
                 +E    TGRTHQ+RVH  H+G  +  D +Y  N   KG   S  +         
Sbjct: 250 GY-VTLVECVLETGRTHQIRVHMKHIGHTLFNDERYGGNEILKGTHFSKYKQFVNNCFET 308

Query: 287 --KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
             +  LHA  +   HP     +  T+PLP  M    D
Sbjct: 309 CPRQALHAMTLGFVHPRTSEEMFFTSPLPEDMTNLID 345


>gi|212702057|ref|ZP_03310185.1| hypothetical protein DESPIG_00059 [Desulfovibrio piger ATCC 29098]
 gi|212674572|gb|EEB35055.1| hypothetical protein DESPIG_00059 [Desulfovibrio piger ATCC 29098]
          Length = 335

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 86/299 (28%), Positives = 143/299 (47%), Gaps = 17/299 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V+V+  E   +L ++ +     +    L + +R+GQVR++  R K    + +G  VR+PP
Sbjct: 11  VIVDPREGGQKLLQFLQRRL-DLPPSLLHRWIRTGQVRINGGRAKPFGLVAAGDSVRLPP 69

Query: 70  VINALNHIIKE---QKILDSSVNLTKHSDFLKSIL--LYEDSKIYVFNKPAGISVQGGSG 124
               ++   K    Q   +        +  L      L +D  ++VF KPAG+    G+G
Sbjct: 70  FALGMSRRSKATGGQASPEQGHEPRPRAQALPPAPRPLQKDGDLWVFCKPAGLPTHPGTG 129

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +   L +       KP   HRLD++TSGIL+VA + A  + +T + R RR++K Y 
Sbjct: 130 HEDSLSSRLAAGAGDAPFKPTPVHRLDKDTSGILLVAASFAVLREMTTALRERRMKKEYL 189

Query: 185 SLVWGI-PKNKKECIANWLLKKSHIGG--DYVHVVKQN--EKGANYAISHFKVIDCFAQK 239
           + V G+ P +      +WL K++  G   + +HV +    +KG   A+   + +     +
Sbjct: 190 AWVEGLWPHSGVRLFRHWLRKEAGTGNGREQMHVRQTGAPDKGETEALLLVRPVRV-EDR 248

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              L ++  TGRTHQ+R     +G PI GD KY A  + + T      +YLHA  + LP
Sbjct: 249 RSLLLVRLLTGRTHQIRAQLSSLGHPIEGDVKYGARGRASGTP-----MYLHAMRVILP 302


>gi|310642458|ref|YP_003947216.1| ribosomal large subunit pseudouridine synthase d [Paenibacillus
           polymyxa SC2]
 gi|309247408|gb|ADO56975.1| Ribosomal large subunit pseudouridine synthase D [Paenibacillus
           polymyxa SC2]
          Length = 248

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 68/205 (33%), Positives = 104/205 (50%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +    KP  +  Q  +     +   LK  +  +  KP      L HRLD+   
Sbjct: 18  VLYEDNHVLAVVKPVNVPTQEDASGDPDLLSLLKEDLKIRHNKPGNVFLGLVHRLDRPVG 77

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++ A+T  AA  L+ES R R   K+Y +++ G+P   +  + ++LLK S    + V  
Sbjct: 78  GAMIFAKTSKAASRLSESVRSRHFHKLYTAVLNGVPAALQGRLTHYLLKDSRT--NTVKT 135

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V+    GA  AI  ++VI   A     +E++ HTGR+HQ+RV    +GCP+ GD KY   
Sbjct: 136 VRPGTAGAKEAILEYRVIGQ-AAGLSLVEIKLHTGRSHQIRVQMQAIGCPLYGDQKYG-- 192

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             GN + P Q +L L +     PHP
Sbjct: 193 --GNLSRPGQ-QLALWSLLAGAPHP 214


>gi|222529402|ref|YP_002573284.1| RluA family pseudouridine synthase [Caldicellulosiruptor bescii DSM
           6725]
 gi|222456249|gb|ACM60511.1| pseudouridine synthase, RluA family [Caldicellulosiruptor bescii
           DSM 6725]
          Length = 293

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 84/278 (30%), Positives = 146/278 (52%), Gaps = 27/278 (9%)

Query: 47  RVDKKRVKFNNRIQS-----GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK--- 98
           ++ +KR+ F++ + S     GQ+  IPP I +++   +E  +++  +  +K S+ +    
Sbjct: 18  QILQKRLFFSSTLMSRLKALGQIRFIPP-IYSVHQYPQENAVIEVDLIFSK-SNIVPVEG 75

Query: 99  SI-LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           SI +LYED+     NKP+G+      G  +  I  +++ +++SK     + +RLD++TSG
Sbjct: 76  SIDILYEDNFFLFVNKPSGLPSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRLDKDTSG 135

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I+V A+       ++  F  RR+ K Y ++V GI   KK  +    +K+S  G     + 
Sbjct: 136 IVVFAKNSYFHSIVSYEFEKRRVDKTYIAIVHGI-LTKKSGLIEKPIKRSDDG-----IK 189

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           ++  +  ++A ++++VID F + F  L+++P TGRTHQLRVH   +G PIVGD+ Y    
Sbjct: 190 REIHQDGSFASTYYEVIDSF-ENFSVLKLKPITGRTHQLRVHLSSIGHPIVGDYIYGEEK 248

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLP 312
             N        L LHA  +             IT+PLP
Sbjct: 249 TQN------TPLLLHAYSISFNFKLINNKVYDITSPLP 280


>gi|255280911|ref|ZP_05345466.1| ribosomal large subunit pseudouridine synthase D [Bryantella
           formatexigens DSM 14469]
 gi|255268359|gb|EET61564.1| ribosomal large subunit pseudouridine synthase D [Bryantella
           formatexigens DSM 14469]
          Length = 325

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 87/321 (27%), Positives = 146/321 (45%), Gaps = 33/321 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++VE D    R+D++            LQK+L+  +V      VK + RI +G V+R+  
Sbjct: 27  LIVEPDAVPERIDKYLSERLSGSRSF-LQKLLKENRVSAGGVPVKASYRICAGDVIRVDI 85

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
              +   I+ E   LD               +LYED  + V NKP G+ V  G+G   H 
Sbjct: 86  PAQSEPDILAEDIPLD---------------ILYEDDDLLVVNKPKGMVVHPGAGHYSHT 130

Query: 129 -IDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++  +    D+        +P + HR+DQ T+G L+V +   +   +    +   I + 
Sbjct: 131 LVNALMYHCRDNLSGINGVLRPGIVHRIDQNTTGSLLVCKNDFSHNFIAGQLKEHSITRR 190

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G  K   +   N  + +  +    + V   NEK    A++H++V++ F +KF +
Sbjct: 191 YRAIVHG--KISSDGTVNAPIGRHPVERKKMAV---NEKNGKPAVTHYRVLEQF-EKFTY 244

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E    TGRTHQ+RVH   +  PI+GD  Y          P      LHA+ +   HP  
Sbjct: 245 IECVLETGRTHQIRVHMSSIHHPILGDDVYGP---ARCPFPGLQGQTLHAQVLGFIHPRT 301

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
           G  ++ +APLP +  +  + L
Sbjct: 302 GEYMEFSAPLPQYFEELLEKL 322


>gi|326403197|ref|YP_004283278.1| putative pseudouridine synthase [Acidiphilium multivorum AIU301]
 gi|325050058|dbj|BAJ80396.1| putative pseudouridine synthase [Acidiphilium multivorum AIU301]
          Length = 224

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 62/183 (33%), Positives = 93/183 (50%), Gaps = 6/183 (3%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +  ++LY  + + V +KPAG+    G G    ++ +   W       P L HRLD +T+
Sbjct: 1   MIDPVILYHSTHLVVIDKPAGLPSHRGRGGGPSVEDWFPRW-RRGADGPWLVHRLDADTA 59

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L +AR +     L  +F  RR+ K YW++V G+P      I   L +++  GG     
Sbjct: 60  GCLAIARRKTTLVALQRAFAQRRVGKTYWAIVEGVPAAAHGTIELALARRTVPGG---WR 116

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  + +G + AI+ ++ +    Q    LE++P TGRTHQLRVH    G PIVGD  Y A 
Sbjct: 117 VAPDPRG-DPAITDWRCL-VAGQGRALLELRPRTGRTHQLRVHCAESGFPIVGDPLYGAE 174

Query: 276 FKG 278
             G
Sbjct: 175 AGG 177


>gi|225443375|ref|XP_002267010.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 479

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 81/267 (30%), Positives = 134/267 (50%), Gaps = 28/267 (10%)

Query: 31  HINFVNL--QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           H+   NL    + + GQ++  +K +K N  +++G  + +P V  A   I K    + S  
Sbjct: 109 HMERSNLDDSSLEKEGQIKPLRK-IKPNEVMEAGTRIYVP-VSVAEARISKRFDTIPSG- 165

Query: 89  NLTKHSD---FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-P 144
            L  ++D   +L+ ++ Y+D  I V NKP  + ++G   +   +D    + +    ++ P
Sbjct: 166 TLHPNADEIEYLQRLVTYKDPAILVLNKPPKVPLKGNLPVHNSMDALAAAALTFDYEEGP 225

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKI-----------YWSLVWG 189
           +L HRLD+E+SG+L++ RT+ +  HL   F    + + + K            YW+LV G
Sbjct: 226 KLVHRLDRESSGLLLMGRTKESVAHLHWLFSDINKAKSLSKAWDDACEATCQRYWALVIG 285

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQ 246
            PK K+  I   L K     G    V+  N+ G   +  AI+ ++V+        W+E+ 
Sbjct: 286 SPKQKEGVIHAPLSKVLLDDGKTERVILANQSGLEASQEAITEYRVLGPMINGCSWIELC 345

Query: 247 PHTGRTHQLRVH-ALHMGCPIVGDHKY 272
           P T R HQLRVH A  +G PIVGD+KY
Sbjct: 346 PRTSRKHQLRVHCAEALGTPIVGDYKY 372


>gi|226325122|ref|ZP_03800640.1| hypothetical protein COPCOM_02914 [Coprococcus comes ATCC 27758]
 gi|225206470|gb|EEG88824.1| hypothetical protein COPCOM_02914 [Coprococcus comes ATCC 27758]
          Length = 341

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 87/354 (24%), Positives = 161/354 (45%), Gaps = 52/354 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V  +E   RLD+    +  +     + K+LR   ++++ K+ + N ++  G  V 
Sbjct: 1   MQKITVSANEAGQRLDKLLGKYLSNAPMSFVYKMLRKKNIKLNGKKAQGNEKLTKGDQVE 60

Query: 67  I-------------PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
           +             P     L   +   + ++SS+ L+         ++YED  I + NK
Sbjct: 61  VFLSDDTWQKFAGAPGAEKQLPADL--ARAMESSIRLS---------VIYEDPDILILNK 109

Query: 114 PAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTR 164
           P+G+  Q  +     ++ ++ +++  KG          +P + +RLD+ TSG++   ++ 
Sbjct: 110 PSGMLSQKAAPSDLSLNEYMIAYLLKKGDLKLAELATFRPSVCNRLDRNTSGLVTAGKSL 169

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           A  Q L+E  R R ++K Y ++V G+ K++++ I  +LLK      + V ++K+ +  A 
Sbjct: 170 AGLQQLSEILRDRTVKKYYLTIVDGVIKDRQK-IEGYLLKNEMT--NQVKILKEAKGEAK 226

Query: 225 -YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKG 278
             A  +  + D   Q    L++   TGRTHQ+R H    G PI+GD KY      + F+ 
Sbjct: 227 PIATEYIPLADNGQQTI--LKVHLITGRTHQIRAHLSSTGHPIIGDSKYGNPKVNSIFRK 284

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-----RLQITAPLPAHMVKTWDSLGFKYD 327
            +    Q    LHA  M  P  E         ++TAPLP          G +++
Sbjct: 285 KYALKYQ---LLHAWKMQFPKREDALAKVSEKEVTAPLPEGFTTIIKGEGLEWE 335


>gi|107099793|ref|ZP_01363711.1| hypothetical protein PaerPA_01000811 [Pseudomonas aeruginosa PACS2]
          Length = 317

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 93/334 (27%), Positives = 153/334 (45%), Gaps = 50/334 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RLD+     +P  +   L   ++ G++ VD   ++  + + SG  +    V+ A    
Sbjct: 14  GQRLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVHSGAQL----VLEAEQEA 69

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW- 136
             E    D  + +           +YED  I V +KPAG+ V   +G   H DG L +  
Sbjct: 70  QGEWLAQDIELEI-----------VYEDEHILVIDKPAGLVVHPAAG---HQDGTLLNAL 115

Query: 137 ---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
              V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY ++V G+ 
Sbjct: 116 LYHVPDIANVPRAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGV- 174

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQPHTG 250
                 I +     + IG   V   K     A   A+SH++V++ F +      ++  TG
Sbjct: 175 ------ITSGGTIDAPIGRHGVQRQKMAVVDAGKVAVSHYRVLERF-RAHTHTRVKLETG 227

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY-----------LHARYMDLPH 299
           RTHQ+RVH  H+G P+VGD  Y   F+     P+ ++             LHAR+++L H
Sbjct: 228 RTHQIRVHMSHIGYPLVGDPVYGGRFR---IPPVASQTLVQTLREFPRQALHARFLELDH 284

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           P  G R++  +PLP   +  W     + DR  ++
Sbjct: 285 PATGVRMKWESPLPEDFL--WLLSLLRQDREAFV 316


>gi|262381293|ref|ZP_06074431.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_33B]
 gi|301309765|ref|ZP_07215704.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 20_3]
 gi|262296470|gb|EEY84400.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_33B]
 gi|300831339|gb|EFK61970.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 20_3]
          Length = 224

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 106/218 (48%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I   +K     VQG       +   LK W+  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIAVDKTCREIVQGDKTGDKPLSEMLKVWLKEKYCKPGNVFVGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR+  ++K YW++V   P   +  + +WL++       Y + 
Sbjct: 63  GVVIFAKTSKALSRLNEMFRVGEVRKTYWAIVKSRPPQDEGELVDWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  AI  +K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 123 TER--PNAKKAILRYKLI-AHSDNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             G   S     + LHAR  +  HP     ++I AP+P
Sbjct: 177 --GFDRSNKDGGISLHARSAEFIHPVSKENVRIVAPVP 212


>gi|237741960|ref|ZP_04572441.1| tRNA pseudouridine synthase A [Fusobacterium sp. 4_1_13]
 gi|229429608|gb|EEO39820.1| tRNA pseudouridine synthase A [Fusobacterium sp. 4_1_13]
          Length = 290

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 85/310 (27%), Positives = 156/310 (50%), Gaps = 31/310 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++Y++ E D E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G +V 
Sbjct: 2   IEYIIDE-DYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDIVF 60

Query: 67  I--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           I  P      N    E+K ++  +N  +    LK ++++E+  ++V NK  G  V  GSG
Sbjct: 61  IFLPESFKENN----EKKFIE--LNQVRKEK-LKQMIVFENENLFVINKSLGDVVHKGSG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +    +S+  +        +R+D+ TSG+++ A+     + + +  +   I K Y+
Sbjct: 114 HDISLLEEFRSYYSNNN--INFVNRIDRLTSGLVIGAKNIKTTREIAKEIQQGNIIKKYF 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQKFCW 242
            LV G  +     + N+L K      D   V+  + +   Y  +I++FK I  +  ++  
Sbjct: 172 ILVNGKIEKDNFILENYLKK------DEEKVIVSDIEKERYKKSITYFKKIKEY-DRYTL 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           LE +  TGRTHQLR    H+G  IVGD KY  N K       ++ +YL + Y+ +     
Sbjct: 225 LEAELKTGRTHQLRAQLNHIGNNIVGDTKYGRNEK-------EDIMYLFSYYLKIDLY-- 275

Query: 303 GRLQITAPLP 312
             L+I   +P
Sbjct: 276 -NLEIKLEIP 284


>gi|332665601|ref|YP_004448389.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
 gi|332334415|gb|AEE51516.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
          Length = 224

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 71/222 (31%), Positives = 114/222 (51%), Gaps = 12/222 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILV 159
           L E       NKP G SV+   G    I+  + +++  +   P   + HRLD+ TSGIL+
Sbjct: 10  LAETGAWIAVNKPFGFSVEKTLGADDTIEDQVLAYLSRQTTMPFVGIVHRLDRVTSGILL 69

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ ++A + L E F  R ++K+YW++V GIP+  +  ++ WL K          V  + 
Sbjct: 70  LAKKKSALRKLNEQFSQRSVKKMYWAMVEGIPQVPEATLSQWLYKDQK--EKKAVVFDEP 127

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +  +    H++V+    Q    LE++  TG+ HQ+RV    +G PI+GD KY A    +
Sbjct: 128 AENRDACQLHYRVVQ-HNQTKALLEIELFTGKFHQIRVQMAALGSPIIGDEKYGA----S 182

Query: 280 FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWD 320
             S     + LHAR ++   P+ G  + + A LPAH V  WD
Sbjct: 183 HFSYADKGIALHARSLEFVDPQSGAPVVLVANLPAHPV--WD 222


>gi|15599740|ref|NP_253234.1| pseudouridine synthase [Pseudomonas aeruginosa PAO1]
 gi|116052689|ref|YP_793005.1| pseudouridine synthase [Pseudomonas aeruginosa UCBPP-PA14]
 gi|218893639|ref|YP_002442508.1| pseudouridine synthase [Pseudomonas aeruginosa LESB58]
 gi|254238708|ref|ZP_04932031.1| pseudouridine synthase [Pseudomonas aeruginosa C3719]
 gi|254244558|ref|ZP_04937880.1| pseudouridine synthase [Pseudomonas aeruginosa 2192]
 gi|296391365|ref|ZP_06880840.1| pseudouridine synthase [Pseudomonas aeruginosa PAb1]
 gi|313107189|ref|ZP_07793388.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           aeruginosa 39016]
 gi|12231021|sp|P33640|RLUD_PSEAE RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|9950788|gb|AAG07932.1|AE004868_3 pseudouridine synthase [Pseudomonas aeruginosa PAO1]
 gi|115587910|gb|ABJ13925.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|126170639|gb|EAZ56150.1| pseudouridine synthase [Pseudomonas aeruginosa C3719]
 gi|126197936|gb|EAZ61999.1| pseudouridine synthase [Pseudomonas aeruginosa 2192]
 gi|218773867|emb|CAW29681.1| pseudouridine synthase [Pseudomonas aeruginosa LESB58]
 gi|310879890|gb|EFQ38484.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           aeruginosa 39016]
          Length = 320

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 93/332 (28%), Positives = 153/332 (46%), Gaps = 50/332 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   L   ++ G++ VD   ++  + + SG  +    V+ A      
Sbjct: 19  RLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVHSGAQL----VLEAEQEAQG 74

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW--- 136
           E    D  + +           +YED  I V +KPAG+ V   +G   H DG L +    
Sbjct: 75  EWLAQDIELEI-----------VYEDEHILVIDKPAGLVVHPAAG---HQDGTLLNALLY 120

Query: 137 -VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY ++V G+   
Sbjct: 121 HVPDIANVPRAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGV--- 177

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQPHTGRT 252
               I +     + IG   V   K     A   A+SH++V++ F +      ++  TGRT
Sbjct: 178 ----ITSGGTIDAPIGRHGVQRQKMAVVDAGKVAVSHYRVLERF-RAHTHTRVKLETGRT 232

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY-----------LHARYMDLPHPE 301
           HQ+RVH  H+G P+VGD  Y   F+     P+ ++             LHAR+++L HP 
Sbjct: 233 HQIRVHMSHIGYPLVGDPVYGGRFR---IPPVASQTLVQTLREFPRQALHARFLELDHPA 289

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            G R++  +PLP   +  W     + DR  ++
Sbjct: 290 TGVRMKWESPLPEDFL--WLLSLLRQDREAFV 319


>gi|260889966|ref|ZP_05901229.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           hofstadii F0254]
 gi|260860572|gb|EEX75072.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           hofstadii F0254]
          Length = 326

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 82/331 (24%), Positives = 157/331 (47%), Gaps = 41/331 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +VV  +E   R+D++       +    +Q++++   + V++K+ K   +I+    +++
Sbjct: 24  ENIVVLKEEAESRIDKFLSERL-ELTRTRIQQLIKDENILVNEKKTKPAYKIEENDTIKV 82

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
             VI  L  +    +I   ++++          ++YED+ + V NK AGI V   +G   
Sbjct: 83  --VIPELETV----EIKPENIDIE---------IIYEDNDLAVINKKAGIVVHPANGHYS 127

Query: 125 --IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             +   I  ++K      G+ +P + HRLD++TSG+L++A+   A   L++ F  + ++K
Sbjct: 128 GTLVNAILYYIKDLSGINGEIRPGIVHRLDKDTSGLLIIAKNDKAHLKLSQMFHDKTVKK 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH----VVKQNEKGANYAISHFKVIDCFA 237
            Y +++ G    K   I       + IG D        V  +      AI++++VI    
Sbjct: 188 TYLAILKGKLSQKSGRIV------TQIGRDKNDRKKMTVTNDLNSGKTAITNYEVI-SQT 240

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +KF  +++   TGRTHQ+RVH  H+G PI+GD  Y         +  + +  LHA  ++ 
Sbjct: 241 EKFTLVKVHIETGRTHQIRVHMKHLGYPILGDSVYGR-------TDTEKRQMLHAYKLEF 293

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
            HP     ++  A LP    K     G +++
Sbjct: 294 EHPIIEKEIEFIAELPEDFEKALKKCGLEFE 324


>gi|288940534|ref|YP_003442774.1| RluA family pseudouridine synthase [Allochromatium vinosum DSM 180]
 gi|288895906|gb|ADC61742.1| pseudouridine synthase, RluA family [Allochromatium vinosum DSM
           180]
          Length = 326

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 89/307 (28%), Positives = 142/307 (46%), Gaps = 41/307 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE D    RLDR      P  +   LQ+ + +GQV VD +  +  +++  G+ +RI   +
Sbjct: 15  VEPDLAGGRLDRVLAQLLPEFSRGRLQQWIEAGQVLVDDRPCRVRDKVWGGESIRIEAEL 74

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
             ++    +   LD               L+YED  + V +KPAG+ V   +G   + DG
Sbjct: 75  AVVDEHRPQAIALD---------------LVYEDEHLLVIDKPAGLVVHPAAG---NPDG 116

Query: 132 FLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L + +          PR  + HRLD++T+G++VVART  A   L E  + R + + Y +
Sbjct: 117 TLLNALLHHAPELATLPRAGIVHRLDKDTTGLMVVARTLQAHCALVEQLQRRIVHREYRA 176

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFCWLE 244
           LV G        +A   ++   IG      VK    G    AI+H++V++ +      L 
Sbjct: 177 LVLGT------LVAGGRVEAP-IGRHPTQRVKMAVVGNGREAITHYRVLESYP-GHTLLA 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQN--KLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y          +    + +Q+  +  LHA  + 
Sbjct: 229 VELETGRTHQIRVHMTHIHHPLVGDTTYGGRPRPPRGCRPELAAALQSFPRQALHAIRLG 288

Query: 297 LPHPEGG 303
           L HP  G
Sbjct: 289 LIHPATG 295


>gi|198276202|ref|ZP_03208733.1| hypothetical protein BACPLE_02391 [Bacteroides plebeius DSM 17135]
 gi|198271014|gb|EDY95284.1| hypothetical protein BACPLE_02391 [Bacteroides plebeius DSM 17135]
          Length = 223

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 115/231 (49%), Gaps = 16/231 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQGDKTGDIPLSETVKQYLKEKYAKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E FR   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFRNGEVKKTYWAIVKQQPKETEGELVHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K +  A+ ++++I   ++ +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVKNSKKAVLNYRLIG-RSENYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
             G   S     + LHAR +   HP     + + APLPA  +  W+  G +
Sbjct: 177 --GFPRSNPDGSICLHARRVRFIHPVSKEPIDLVAPLPAGNL--WNGFGME 223


>gi|222086840|ref|YP_002545374.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221724288|gb|ACM27444.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 343

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 88/341 (25%), Positives = 150/341 (43%), Gaps = 57/341 (16%)

Query: 10  VVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRI 67
           V+  ++    RLD W        ++   +Q ++++  V ++   V    R ++ G +  I
Sbjct: 16  VLTADETAEGRLDAWLTAQMDEELSRSRVQALIKANAVLLNGTPVTDAKRKVRPGDIYEI 75

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           +    + T   + +   +L+ED  + V +KPAG+ V  G+G   
Sbjct: 76  S---------------MPEPEDPTPQGEDIPLDVLFEDDDVIVISKPAGLVVHPGAGNWT 120

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RM 176
              ++  +    DS       ++P + HRLD++T+G++VVA+   A +HL+  F    R 
Sbjct: 121 GTLVNALIHHCGDSLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHGRT 180

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVID 234
             +++ Y ++VWG P+     +   L + +   GD     V +     A+ AI+H++VI+
Sbjct: 181 TPLERAYQAIVWGRPRQLVGTVNAPLGRAT---GDRTRRSVKRPGSPDADEAITHYEVIE 237

Query: 235 CFAQKF----------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTS 282
            F +            C LE    TGRTHQ+RVH  H+G P++GD  Y   F  K N   
Sbjct: 238 RFHEAPDATALASLIDCHLE----TGRTHQIRVHMAHIGHPLLGDAAYGGGFKTKANLLP 293

Query: 283 PIQNKLY-------LHARYMDLPHPEGGR-LQITAPLPAHM 315
               +         LHA  +   HP  G  +   APLP  M
Sbjct: 294 DAAREAVNRFPRQALHAYLLQFEHPRTGEVMHFEAPLPDDM 334


>gi|49083826|gb|AAT51150.1| PA4544 [synthetic construct]
          Length = 321

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 93/334 (27%), Positives = 153/334 (45%), Gaps = 50/334 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RLD+     +P  +   L   ++ G++ VD   ++  + + SG  +    V+ A    
Sbjct: 17  GQRLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVHSGAQL----VLEAEQEA 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW- 136
             E    D  + +           +YED  I V +KPAG+ V   +G   H DG L +  
Sbjct: 73  QGEWLAQDIELEI-----------VYEDEHILVIDKPAGLVVHPAAG---HQDGTLLNAL 118

Query: 137 ---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
              V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY ++V G+ 
Sbjct: 119 LYHVPDIANVPRAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGV- 177

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQPHTG 250
                 I +     + IG   V   K     A   A+SH++V++ F +      ++  TG
Sbjct: 178 ------ITSGGTIDAPIGRHGVQRQKMAVVDAGKVAVSHYRVLERF-RAHTHTRVKLETG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY-----------LHARYMDLPH 299
           RTHQ+RVH  H+G P+VGD  Y   F+     P+ ++             LHAR+++L H
Sbjct: 231 RTHQIRVHMSHIGYPLVGDPVYGGRFR---IPPVASQTLVQTLREFPRQALHARFLELDH 287

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           P  G R++  +PLP   +  W     + DR  ++
Sbjct: 288 PATGVRMKWESPLPEDFL--WLLSLLRQDREAFV 319


>gi|303236145|ref|ZP_07322746.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
 gi|302483651|gb|EFL46645.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
          Length = 360

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 90/344 (26%), Positives = 155/344 (45%), Gaps = 62/344 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V+  +E +R+D++      H +   +QK   +G + V+ K VK N +++   ++ +  
Sbjct: 35  LIVDKGQEPVRVDKYIFEKMQHSSRNRIQKAADAGCIYVNDKPVKSNYKVRPDDIITL-- 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I    + L          ++YED +I V NKPAG+ V  G+G     
Sbjct: 93  ---MLDRPKHDNTIEAEEIPLD---------IVYEDDEIMVINKPAGLVVHPGAGNFHGT 140

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    LK   D     P   L HR+D++TSG+L++A+T  A   L + F  + 
Sbjct: 141 LINAIAWH----LKDLKDFDPNDPAVGLVHRIDKDTSGLLLIAKTPDAKTFLGKQFFNKT 196

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY---------AISH 229
             + Y +LVWG          N +  +  I G+     K   + A +         A++H
Sbjct: 197 THRSYNALVWG----------NLVEDEGRIEGNIGRDPKDRLRMAVFPPESGIGKNAVTH 246

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ-- 285
           ++V++ F      +E +  TGRTHQ+R H  H+G P+  D +Y      +G  T+  +  
Sbjct: 247 YRVLERFGYT-TLVECRLETGRTHQIRAHMKHIGHPLFADERYGGMEILRGERTAAYKAY 305

Query: 286 --------NKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWD 320
                   N+  LHAR +   HP    ++  T+ LP  +    D
Sbjct: 306 IKNCLKLCNRQALHARTLGFIHPRTHEQMDFTSELPEDLGAVID 349


>gi|254995115|ref|ZP_05277305.1| sfhb-like protein [Anaplasma marginale str. Mississippi]
          Length = 328

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 89/317 (28%), Positives = 147/317 (46%), Gaps = 37/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSG 62
           M  V  V V  +++  R+D+        I+    Q ++  GQV +  + +  N+ + ++G
Sbjct: 1   MKCVHEVCVTKEDDQQRIDKLISCAL-EISRNRAQGLIAGGQVTISGRVINNNSYLTKTG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF-LKSILLYEDSKIYVFNKPAGISVQG 121
            V  I   +   +              L+ + D  LK  ++YED  + V +K   I+V  
Sbjct: 60  DVYTIVTAVQKPS-------------TLSPNYDIDLK--VVYEDHDVIVIDKDPYIAVHP 104

Query: 122 GSGIAYHI--DGFLKSW---VDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G+GI +H   +  L  +   + S G   +P + HRLD++TSG++V A+T  A   L+E  
Sbjct: 105 GNGIEHHTITNALLARFGAGLQSVGSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEEL 164

Query: 175 RMRRIQKIYWSLVWGIPKNKKECI-ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             +  +K Y ++ WGIP  K+  I  N  +K+S I      +++    G   A + ++V 
Sbjct: 165 ANQGFKKEYLAVAWGIPCPKRGVIHTNIRVKRSDI-----TMMEAANSGGKPAKTEYEVE 219

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NK 287
               +    +    HTGRTHQ+RVH  H+G  IVGD KY  N K    S +        +
Sbjct: 220 QELGEVASLIRCTLHTGRTHQIRVHMSHIGHSIVGDQKYGKNCKKCMRSGVPPDVKNFRR 279

Query: 288 LYLHARYMDLPHPEGGR 304
             LHA  +   HP  G+
Sbjct: 280 QALHASLLGFRHPSTGK 296


>gi|86134338|ref|ZP_01052920.1| RNA pseudouridylate synthase [Polaribacter sp. MED152]
 gi|85821201|gb|EAQ42348.1| RNA pseudouridylate synthase [Polaribacter sp. MED152]
          Length = 228

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 116/235 (49%), Gaps = 16/235 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LT 147
           HS+     +L+ED+ I + NK +G   QG       +   +K ++  K  K       + 
Sbjct: 2   HSNKQNLQVLFEDNHIIIVNKRSGDITQGDKTGDKPLSDVVKEYIKEKYNKAGNVFLGVV 61

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+++ ART  A + L +  R + I K YW++V   PK +K  + N+L K   
Sbjct: 62  HRLDRPTSGVIIFARTSKALERLNKMLRDKEIHKTYWAVVKNHPKKEKATLINYLRKNPK 121

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              +   V ++  +G+  AI H+  +      +  LE+   TGR HQ+R    ++G PI 
Sbjct: 122 --NNKSSVFQKEIEGSKKAILHYSTLKKL-DNYSLLEIDLETGRHHQIRAQLSNIGFPIK 178

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           GD KY  N      S     ++LHAR ++  HP    ++ + AP P  ++  W++
Sbjct: 179 GDLKYGFN-----RSNKDGSIHLHARKIEFIHPVAKEKITVIAPTPNEVI--WNA 226


>gi|56551401|ref|YP_162240.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis ZM4]
 gi|59802982|sp|O66114|Y505_ZYMMO RecName: Full=Uncharacterized RNA pseudouridine synthase ZMO0505;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|56542975|gb|AAV89129.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis ZM4]
          Length = 219

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 70/225 (31%), Positives = 122/225 (54%), Gaps = 14/225 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D++  + +KPAG+ V      +  ++ +L S      + P + HRLD++TSG L++
Sbjct: 8   VLFIDAEAMIIDKPAGLPVTSVRDGSLSLENYLASLCFGFKRWPSIVHRLDRDTSGCLLL 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR     + L+E+F   +++K YW+++ G+P+  +  I   LLK S     +  V   ++
Sbjct: 68  ARNPKMHRRLSEAFSQGQVKKCYWAILEGVPEKNEGIIDLPLLKISSPKSGWRIVA--DD 125

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCANFKGN 279
           KG   A++H++++    +    +  +P TGRTHQLRVH A  +G PIVGD  Y ++   N
Sbjct: 126 KG-KRAVTHWEIL-AKNKGRSLVAFRPETGRTHQLRVHAATGLGLPIVGDPFYGSHKDEN 183

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
            +     ++ LHA  +++   E   +   APLP    K +  LGF
Sbjct: 184 IS-----RMMLHAHSLEIARLEKKPITAEAPLP----KAFTDLGF 219


>gi|46579437|ref|YP_010245.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Desulfovibrio vulgaris str. Hildenborough]
 gi|46448851|gb|AAS95504.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Desulfovibrio vulgaris str. Hildenborough]
 gi|311233254|gb|ADP86108.1| pseudouridine synthase, RluA family [Desulfovibrio vulgaris RCH1]
          Length = 541

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 86/311 (27%), Positives = 139/311 (44%), Gaps = 43/311 (13%)

Query: 18  NMRLDRWFKNHYPHINFV--NLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINAL 74
           N RLDR+      H +     +++ +R GQ  VD       + R++SGQ V +  +  A 
Sbjct: 25  NERLDRFLGEALSHTDLSREKIKRAIRDGQCTVDGTVCTTPSTRLRSGQRVELA-IAPAA 83

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
             +  E+  L                +++ D  + V +KPAG++V              +
Sbjct: 84  TAVEPEEGDL---------------TIIHRDEHLLVIDKPAGLTVHPCPSCPEGTLVHRL 128

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H D         +G +P + HR+D++TSG+L+VA +      L+E+F  R ++K Y +
Sbjct: 129 VHHFDALRAQ----EGFRPGIVHRIDKDTSGLLLVALSEGVRLKLSEAFAERTVEKEYLA 184

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQK-FCWL 243
           LV G+P    E  A        IG    H V+    KG   A S ++V+    +  +  +
Sbjct: 185 LVHGVPPATGEVDAP-------IGRHPTHKVRMAVVKGGKPARSEWRVLHAAPEGHYALV 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-TSPIQNKLYLHARYMDLPHP-E 301
            ++ H+GRTHQ+RVH  H G P+ GD  Y               +  LHA ++   HP  
Sbjct: 238 AVRIHSGRTHQIRVHMAHAGFPLWGDQLYGPGTPARLREQGYGARQMLHAWHLAFTHPVT 297

Query: 302 GGRLQITAPLP 312
           G RL+ T P P
Sbjct: 298 GERLRFTCPPP 308


>gi|78355167|ref|YP_386616.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
 gi|78217572|gb|ABB36921.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 332

 Score =  105 bits (263), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 81/274 (29%), Positives = 125/274 (45%), Gaps = 21/274 (7%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           L +I+R G+VRV+K R K  +R+  G VVRIPPV  A       +   D++  +   S  
Sbjct: 40  LMRIIRKGEVRVNKGRAKPYDRVSEGDVVRIPPVRPA------AEPSCDAACAVPAVSAS 93

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
               ++     + V NKPAG+ VQ G+G    +   L +        P   HRLD+ TSG
Sbjct: 94  PLPQIIASGDGLLVINKPAGLPVQPGTGHTDCVTARLAAHFAGADFMPAPAHRLDKNTSG 153

Query: 157 ILVVARTRAAAQHLTESFR-MRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVH 214
           +L+   T  A + L + FR    + K Y + V GI P+ +   + + L+K+   G + +H
Sbjct: 154 LLLAGTTYTALRTLQDLFRNGHSLIKDYCAWVCGIWPEQEALTLTDVLVKEGTPGKEKIH 213

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLE------MQPHTGRTHQLRVHALHMGCPIVG 268
            +       + A    +   C       L+      ++  TGRTHQ+RV       P++G
Sbjct: 214 ALPAGSAQPHTAPPKGREALCQVVPLLRLDNATLLGIRLATGRTHQIRVQLASRNHPVIG 273

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           D KY A          +  + LHA  + LP P G
Sbjct: 274 DVKYGAPA-------CRAGMLLHAFRLVLPAPFG 300


>gi|153002938|ref|YP_001377263.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152026511|gb|ABS24279.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 339

 Score =  105 bits (263), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 88/323 (27%), Positives = 153/323 (47%), Gaps = 32/323 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            +  D    RLD+  +     +   ++ K+ R+ ++RV+  R K    + +G VV    V
Sbjct: 5   TISEDAAGQRLDKLVRKALRDVPLSHVYKMFRTRKIRVNGGRGKAEQLVAAGDVV----V 60

Query: 71  INALNHIIKEQKILD-SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           I        E+++L          +  +   +L+ED+ +   +KPAG++   G+GI+   
Sbjct: 61  IRG-----DEERLLARQEPEPGARAGAVTFGVLHEDADVLAVDKPAGLAAHPGTGISGAT 115

Query: 130 -----DGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQK 181
                   L +  D      KP   HRLD++TSG+++VA+ R     LTE F     ++K
Sbjct: 116 LVEMARAHLGTPADLPPTEFKPSPAHRLDRDTSGVVLVAKNRKTMVRLTELFTDGADVKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQK 239
            Y +LV G  K  +E     L    H          +  +G N   A++ +KV+    ++
Sbjct: 176 TYLALVKG--KMPREAGTIDLPLAEH----EQTARSKAARGVNLQEALTRWKVVSAM-KE 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMD 296
              L +   TGRTHQ+R H   +G P++GD +Y  +F  N  +  +    +++LHA  ++
Sbjct: 229 ASLLAVTIETGRTHQIRRHLEAVGHPVLGDRRY-GDFPTNRAARQRWGLRRMFLHAWRLE 287

Query: 297 LPHP-EGGRLQITAPLPAHMVKT 318
           LPHP  G  L++ APLP  +++ 
Sbjct: 288 LPHPTTGAPLRLEAPLPGELLEA 310


>gi|56416931|ref|YP_154005.1| sfhb-like protein [Anaplasma marginale str. St. Maries]
 gi|255003281|ref|ZP_05278245.1| sfhb-like protein [Anaplasma marginale str. Puerto Rico]
 gi|56388163|gb|AAV86750.1| sfhb-like protein [Anaplasma marginale str. St. Maries]
          Length = 327

 Score =  105 bits (263), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 89/317 (28%), Positives = 147/317 (46%), Gaps = 37/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSG 62
           M  V  V V  +++  R+D+        I+    Q ++  GQV +  + +  N+ + ++G
Sbjct: 1   MKCVHEVCVTKEDDQQRIDKLISCAL-EISRNRAQGLIAGGQVTISGRVINNNSYLTKTG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF-LKSILLYEDSKIYVFNKPAGISVQG 121
            V  I   +   +              L+ + D  LK  ++YED  + V +K   I+V  
Sbjct: 60  DVYTIVTAVQKPS-------------TLSPNYDIDLK--VVYEDHDVIVIDKDPYIAVHP 104

Query: 122 GSGIAYHI--DGFLKSW---VDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G+GI +H   +  L  +   + S G   +P + HRLD++TSG++V A+T  A   L+E  
Sbjct: 105 GNGIEHHTITNALLARFGAGLQSVGSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEEL 164

Query: 175 RMRRIQKIYWSLVWGIPKNKKECI-ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             +  +K Y ++ WGIP  K+  I  N  +K+S I      +++    G   A + ++V 
Sbjct: 165 ANQGFKKEYLAVAWGIPCPKRGVIHTNIRVKRSDI-----TMMEAANSGGKPAKTEYEVE 219

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NK 287
               +    +    HTGRTHQ+RVH  H+G  IVGD KY  N K    S +        +
Sbjct: 220 QELGEVASLIRCTLHTGRTHQIRVHMSHIGHSIVGDQKYGKNCKKCMRSGVPPDVKNFRR 279

Query: 288 LYLHARYMDLPHPEGGR 304
             LHA  +   HP  G+
Sbjct: 280 QALHASLLGFRHPSTGK 296


>gi|86137869|ref|ZP_01056445.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           MED193]
 gi|85825461|gb|EAQ45660.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           MED193]
          Length = 346

 Score =  105 bits (263), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 89/358 (24%), Positives = 156/358 (43%), Gaps = 66/358 (18%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           +++++ E+  +  RLD+      P    ++   L +++ +G + VD   V+    R+  G
Sbjct: 6   IEFIIAEDPPK--RLDKAVSRDVPAEATLSRTRLARLIEAGSLTVDGVVVQDAKARVAEG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V+ I       +HI  E   LD               +++ED  + V NKP+G+ V   
Sbjct: 64  AVITITVEEAEDSHIGPEDIALD---------------VIFEDDDLIVINKPSGMVVHPA 108

Query: 123 SG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            G         + +H    L      K  +P + HR+D+ETSG+LVVA++ AA Q L   
Sbjct: 109 PGTPSGTLVNALLHHCGENLSGVGGVK--RPGIVHRIDKETSGLLVVAKSDAAHQGLAAQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK------------ 221
           F    +++ Y ++ +G+P +  +     +   S   G+ + +  Q  +            
Sbjct: 167 FEKHTVERYYRAICYGVP-DANDPRLRGVKGTSFEPGNILKLTTQLARHKHDRQRQAVLF 225

Query: 222 -GANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-- 272
            G  +A++  ++++ F          CWLE    TGRTHQ+RVH  H G  +VGD  Y  
Sbjct: 226 QGGRHAVTRARIVEPFGAPPVVALIECWLE----TGRTHQIRVHMTHAGHGLVGDPTYGG 281

Query: 273 -----CANFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                  +      + +Q+  +  LHA  +   HP  G  ++  APLP  M    ++L
Sbjct: 282 KRKLAAKSLATTAIAAVQSFPRQALHAAVLGFVHPVSGAEMRFEAPLPQDMSDLIETL 339


>gi|312143925|ref|YP_003995371.1| pseudouridine synthase, RluA family [Halanaerobium sp.
           'sapolanicus']
 gi|311904576|gb|ADQ15017.1| pseudouridine synthase, RluA family [Halanaerobium sp.
           'sapolanicus']
          Length = 304

 Score =  105 bits (263), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 82/313 (26%), Positives = 151/313 (48%), Gaps = 40/313 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  E   R+D++  + +   +   +QK++   +++V+      +N +Q+  +++    I
Sbjct: 8   VDKSEAGKRVDKFLASQFDDFSRNYIQKLIEDSKIKVN------SNPVQNSYLIKEADEI 61

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------- 124
             +    K+  I    + L          ++YED  I + NK A + V    G       
Sbjct: 62  KVIIDKAKKSSIKAVDIELD---------IIYEDQDIIIINKDADMVVHPAPGHYDDTIV 112

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              +AY  D    + V    ++P + HRLD++TSG+L+VA+   + + L+  F+ R + K
Sbjct: 113 NALLAYTNDLSAINGV----KRPGIVHRLDKDTSGLLLVAKNDKSHKELSRQFKKREVDK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L+ GI   K   I   + +  H        V++  + +  A+S FK+++ F +   
Sbjct: 169 YYLALLKGILPYKTGKIDAPIGR--HPNQRKKMAVRK--RKSKKAVSRFKILESF-KNHT 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E++  TGRTHQ+RVH  ++G P+VGD KY     G+  S    +  LHA+ +   HP 
Sbjct: 224 LVEVKIETGRTHQIRVHFAYLGYPVVGDQKY-----GSKDSLGAKRQLLHAKRLLFKHPS 278

Query: 302 GG-RLQITAPLPA 313
            G +++  A L A
Sbjct: 279 TGKKVEFEAELKA 291


>gi|296111936|ref|YP_003622318.1| pseudouridine synthase [Leuconostoc kimchii IMSNU 11154]
 gi|295833468|gb|ADG41349.1| pseudouridine synthase [Leuconostoc kimchii IMSNU 11154]
          Length = 308

 Score =  105 bits (263), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 89/313 (28%), Positives = 146/313 (46%), Gaps = 37/313 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D          +   L + L++G + V+  +VK + ++  G  + I P   A   II 
Sbjct: 15  RIDAILAKEDLQYSRTTLAEWLQNGHILVNNNKVKRSYKVSVGDTISIFPPEVASTEIIA 74

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   LD               ++YED+ I V NKP G+ V   +G   H  G L + +  
Sbjct: 75  EDIPLD---------------IVYEDNDILVVNKPQGMVVHPAAG---HSSGTLVNALLH 116

Query: 140 KGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      +P + HR+D++TSG+L+VA+   A + L+   +  +  +IY++LV G  
Sbjct: 117 HAPLSTINGTFRPGIVHRIDRDTSGLLMVAKNDVAHKALSAQLKAHKNDRIYYALVRGEF 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                 I       + IG   V   +Q  + G   AI+HF+V+  +   F  L+++  TG
Sbjct: 177 SEDSGTI------NAPIGRHPVDRKRQAVQVGGREAITHFEVVHRYV-GFTLLKVRLETG 229

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           RTHQ+RVH  ++G PIVGD  Y  N +      +  +L LHA+ + L  P  G  L+  +
Sbjct: 230 RTHQIRVHLTYIGHPIVGDPVY-GNAQKLADVSLMGQL-LHAKTLSLTQPTTGEELRFDS 287

Query: 310 PLPAHMVKTWDSL 322
            LP +  +   +L
Sbjct: 288 SLPTYFQEALATL 300


>gi|126663902|ref|ZP_01734897.1| putative ribosomal large subunit pseudouridine synthase
           [Flavobacteria bacterium BAL38]
 gi|126624166|gb|EAZ94859.1| putative ribosomal large subunit pseudouridine synthase
           [Flavobacteria bacterium BAL38]
          Length = 231

 Score =  105 bits (262), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 74/229 (32%), Positives = 113/229 (49%), Gaps = 18/229 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +++ED+ I V NK  G  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 14  IIHEDNHIIVVNKRVGDIVQGDITGDKPLSDVVKEYIKIKYNKPGDVFLGVVHRLDRPTT 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  A   L ESF+ R  QK YW++V   P  +K+ + ++L + S       H+
Sbjct: 74  GIVVFAKTSKALTRLNESFKNRETQKTYWAVVKNTPPKEKDTLTHFLKRNSKNNTSKAHL 133

Query: 216 VK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +  + K A+ +    K +D     +  LE+  HTGR HQ+R     +GCPI GD KY  
Sbjct: 134 KEIPDSKKASLSYQIIKKLD----NYFALEIDLHTGRHHQIRAQLQAIGCPIKGDLKY-- 187

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              G   S     ++LHA+ + L HP     +   A  P   +  W+SL
Sbjct: 188 ---GFDRSNPDGGIHLHAKKLVLKHPVSKEIITFNATTPNDSI--WNSL 231


>gi|104774018|ref|YP_618998.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103423099|emb|CAI97824.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
          Length = 303

 Score =  105 bits (262), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 78/296 (26%), Positives = 153/296 (51%), Gaps = 33/296 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++       ++   +++++++G++ V+ K+ K + ++Q   ++++  ++  L
Sbjct: 10  EESGQRLDKYLAGEMTDLSRSRIKELVQAGEILVNGKKSKVSYKVQKDDLIQV--IVLPL 67

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGF 132
             +    K+   ++ L          ++YED  + V NKP G+ V   +G   H  ++  
Sbjct: 68  EPL----KLEAENIPLD---------IVYEDKDVIVVNKPQGMVVHPAAGHPSHTLVNAL 114

Query: 133 L---KSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L   +   DS +G +P + HR+D++TSG+L+VA+  AA + L +    +  ++ Y ++V 
Sbjct: 115 LYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVH 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G     +E   +  + ++      + VV   EKG + A++HFKV++ + Q +  +E Q  
Sbjct: 175 G--NFAEEGTIDAPIGRNPKDRKQMAVV---EKGKS-AVTHFKVLEQY-QGYSLVECQLE 227

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           TGRTHQ+RVH  ++G P+ GD  Y        T P   + +LHA+ +    P  G 
Sbjct: 228 TGRTHQIRVHMAYIGHPLAGDPLYGP----RKTLPGHGQ-FLHAKTLGFEQPSTGE 278


>gi|222475297|ref|YP_002563714.1| Ribosomal large subunit pseudouridine synthase D (rluD) [Anaplasma
           marginale str. Florida]
 gi|222419435|gb|ACM49458.1| Ribosomal large subunit pseudouridine synthase D (rluD) [Anaplasma
           marginale str. Florida]
          Length = 321

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 85/287 (29%), Positives = 132/287 (45%), Gaps = 32/287 (11%)

Query: 45  QVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           Q R+DK         R +    I  GQV     VIN  +++ K   +      + K S  
Sbjct: 9   QQRIDKLISCALEISRNRAQGLIAGGQVTISGRVINNNSYLTKTGDVYTIVTAVQKPSTL 68

Query: 97  -----LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW---VDSKGQ--KP 144
                +   ++YED  + V +K   I+V  G+GI +H   +  L  +   + S G   +P
Sbjct: 69  SPNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGIEHHTITNALLARFGAGLQSVGSSSRP 128

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-ANWLL 203
            + HRLD++TSG++V A+T  A   L+E    +  +K Y ++ WGIP  K+  I  N  +
Sbjct: 129 GIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGIPCPKRGVIHTNIRV 188

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           K+S I      +++    G   A + ++V     +    +    HTGRTHQ+RVH  H+G
Sbjct: 189 KRSDI-----TMMEAANSGGKPAKTEYEVEQELGEVASLIRCTLHTGRTHQIRVHMSHIG 243

Query: 264 CPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPEGGR 304
             IVGD KY  N K    S +        +  LHA  +   HP  G+
Sbjct: 244 HSIVGDQKYGKNCKKCMRSGVPPDVKNFRRQALHASLLGFRHPSTGK 290


>gi|58039270|ref|YP_191234.1| ribosomal large subunit pseudouridine synthase A [Gluconobacter
           oxydans 621H]
 gi|58001684|gb|AAW60578.1| Ribosomal large subunit pseudouridine synthase A [Gluconobacter
           oxydans 621H]
          Length = 265

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 120/228 (52%), Gaps = 14/228 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L E  +  +  KPAG++V  G      ++  L   +      P L HRLD +TSG L+V
Sbjct: 48  VLLETPRFLILYKPAGLAVHPGPSTQDSVETRL---LPHPRGGPWLAHRLDADTSGCLLV 104

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           AR + A     ++F+ R+  K+YW++V G +P++  E  A  LL++S   G +  VV  +
Sbjct: 105 ARRKTALIEAQKAFQERQAHKLYWAVVVGDLPQDSGEIDAP-LLRQSDASG-WRMVV--D 160

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            KG + A + ++V+   ++  CW+E++  TGRTHQ R+H   +G PI+GD  Y       
Sbjct: 161 AKG-DEARTRWRVLG-RSKGLCWVELELLTGRTHQARIHCAELGTPILGDPVYGMPAPDG 218

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
              P    L+L AR ++L  P    L   AP P  M  +  ++GF+ D
Sbjct: 219 SALP---GLHLLARSLELSLPS-DTLSAQAPPPEFMAASLRAMGFESD 262


>gi|241761046|ref|ZP_04759135.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis ATCC
           10988]
 gi|260752988|ref|YP_003225881.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis NCIMB
           11163]
 gi|241374665|gb|EER64126.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis ATCC
           10988]
 gi|258552351|gb|ACV75297.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis NCIMB
           11163]
          Length = 219

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 70/225 (31%), Positives = 122/225 (54%), Gaps = 14/225 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D++  + +KPAG+ V      +  ++ +L S      + P + HRLD++TSG L++
Sbjct: 8   VLFIDAEAMIIDKPAGLPVTSVRDGSLSLENYLASLCFGFKRWPSIVHRLDRDTSGCLLL 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR     + L+E+F   +++K YW+++ G+P+  +  I   LLK S     +  V   ++
Sbjct: 68  ARNPKMHRRLSEAFSQGQVKKCYWAILEGVPEKNEGIIDLPLLKISSPKSGWRIVA--DD 125

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCANFKGN 279
           KG   A++H++++    +    +  +P TGRTHQLRVH A  +G PIVGD  Y ++   N
Sbjct: 126 KG-KRAVTHWEIL-AKNKGRSLVAFRPETGRTHQLRVHAATGLGLPIVGDPFYGSHKDEN 183

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
            +     ++ LHA  +++   E   +   APLP    K +  LGF
Sbjct: 184 IS-----RMMLHAHSLEIARLEKKPIAAEAPLP----KAFTDLGF 219


>gi|240139473|ref|YP_002963948.1| pseudouridine synthase [Methylobacterium extorquens AM1]
 gi|240009445|gb|ACS40671.1| pseudouridine synthase [Methylobacterium extorquens AM1]
          Length = 213

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 73/222 (32%), Positives = 110/222 (49%), Gaps = 19/222 (8%)

Query: 108 IYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           + V +KPAG+ V    +GG  +  H+D           ++P   HRLD++TSG LV+ R 
Sbjct: 1   MLVIDKPAGLPVHPGPKGGPTLTDHLDALRFGLP----RRPEAAHRLDRDTSGCLVLGRH 56

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
             A   L   F   ++ K YW+LV G P+  +  I   L K+S    D      + +   
Sbjct: 57  AKALARLNRLFADGKVDKTYWALVEGGPEAMEGRIDLPLAKRSD---DPRSWWMKTDPAG 113

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
             +++ ++V+   ++   WLE++P TGRTHQLRVH   MG PI GD  Y    +      
Sbjct: 114 APSLTLYRVLG-RSECLSWLELKPVTGRTHQLRVHCAAMGWPIRGDAIYGGAGRDG---- 168

Query: 284 IQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
               L LHAR + LP +P+   + + AP PAHM    ++ G 
Sbjct: 169 --PGLQLHARGLSLPLYPKREAIAVEAPAPAHMRAGLEACGM 208


>gi|332668251|ref|YP_004451039.1| RluA family pseudouridine synthase [Haliscomenobacter hydrossis DSM
           1100]
 gi|332337065|gb|AEE54166.1| pseudouridine synthase, RluA family [Haliscomenobacter hydrossis
           DSM 1100]
          Length = 366

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/331 (25%), Positives = 159/331 (48%), Gaps = 49/331 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+ ++  +R+D++  +    ++   +Q  +++G V V+ + +K N +I+ GQ + +  
Sbjct: 29  IEVDGNQSPLRIDKFLMDRIGEVSRNRVQNAIKTGSVLVNDQEIKPNFKIKPGQKITLIL 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
             +  + +    +I+  ++ L          ++YED  + V NKP G+ V  G G     
Sbjct: 89  PKSTTDKL----RIVPQNIPLN---------VVYEDEDLLVVNKPPGLVVHPGVGHFKGT 135

Query: 125 ----IAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               +AYH+   L     S G   ++  L HR+D+ TSG+LVVA+   A  HL + F   
Sbjct: 136 LVNALAYHLR--LDPNQISTGNFQERVGLVHRIDKNTSGLLVVAKNEFALSHLAKQFFYH 193

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF- 236
            I++ Y +LVWG P+  +  I   + +      D+  V  + ++G  +A++H++V++   
Sbjct: 194 TIERTYNALVWGEPEEDRGTINAHVGRHPRFRKDFT-VFPEGDQG-KWAVTHYQVLERLY 251

Query: 237 --AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS---------- 282
             +   C LE    TGRTHQ+RVH  ++G  +  D KY  +   KG   S          
Sbjct: 252 YVSLIKCTLE----TGRTHQIRVHLKYLGHTLFNDEKYGGDEILKGTIFSKYKIFVDHMF 307

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            +  +  LHA+ +   HP   + +   + LP
Sbjct: 308 DVLPRHALHAKSLGFIHPRTNKFMHFDSDLP 338


>gi|168182405|ref|ZP_02617069.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
 gi|237794814|ref|YP_002862366.1| RluA family pseudouridine synthase [Clostridium botulinum Ba4 str.
           657]
 gi|182674415|gb|EDT86376.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
 gi|229261378|gb|ACQ52411.1| pseudouridine synthase, RluA family [Clostridium botulinum Ba4 str.
           657]
          Length = 305

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 90/301 (29%), Positives = 146/301 (48%), Gaps = 43/301 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE + +N+RLD +    +   +   LQ I+  G V V+ K+ K N +++ G  + +    
Sbjct: 8   VEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKKKKRNYKLKVGDNIEVN--- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                 I E K+L+         + +K  ++YED  + V NKP  + V    G+     +
Sbjct: 65  ------IPEPKLLEIE------PEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLV 112

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+   I ++Y +
Sbjct: 113 NALLNHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           LV GI K+++  I      ++ IG   V  +K    K   +A++H+KVI+ F +    +E
Sbjct: 173 LVEGIIKDEQGTI------EAPIGRHPVDRIKMAVVKDGRHAVTHYKVIERF-KNHTLVE 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLHARYMDLPH 299
            +  TGRTHQ+RVH  H+  P+VGD  Y       N KG           LHA+ +   H
Sbjct: 226 CRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLKGQM---------LHAKLLGFIH 276

Query: 300 P 300
           P
Sbjct: 277 P 277


>gi|260587704|ref|ZP_05853617.1| ribosomal large subunit pseudouridine synthase D [Blautia hansenii
           DSM 20583]
 gi|331084005|ref|ZP_08333112.1| hypothetical protein HMPREF0992_02036 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260541969|gb|EEX22538.1| ribosomal large subunit pseudouridine synthase D [Blautia hansenii
           DSM 20583]
 gi|330402367|gb|EGG81937.1| hypothetical protein HMPREF0992_02036 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 305

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 92/321 (28%), Positives = 144/321 (44%), Gaps = 61/321 (19%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D++        +   LQK L+ G V V++K  K + ++     VRI    N    I+ 
Sbjct: 16  RIDKYLAEVMNDYSRSFLQKQLKDGNVSVNEKTAKASLKVAEDDEVRIFIPENKEPDIVP 75

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH-- 128
           E   LD               +LYED ++ V NKP G+ V   +G         + +H  
Sbjct: 76  EDIPLD---------------ILYEDQQLLVVNKPKGMVVHPSAGHYSQTLVNALMFHCK 120

Query: 129 -----IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                I+G L+         P + HR+D +T+G LVV +T  A Q L E  ++  I ++Y
Sbjct: 121 DQLSGINGVLR---------PGIVHRIDMDTTGALVVCKTDLAHQSLAEQLKVHSITRLY 171

Query: 184 WSLVWGIPKNKKECIANWL------LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++V G  K     I   +       KK  I          N +    A +H+KV++ F 
Sbjct: 172 RAIVHGRLKEDFGTIEGTIGRHPTDRKKMAI----------NVRNGKPATTHYKVLERF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            +F ++E +  TGRTHQ+RVH   +G P++GD  Y    K +    +Q +  LHA  +  
Sbjct: 221 DRFTYVECELETGRTHQIRVHMSSIGHPLLGDIVYGP--KKSALPNLQGQT-LHAMVLGF 277

Query: 298 PHPEGGR-LQITAPLPAHMVK 317
            HP     ++ TAPLP +  K
Sbjct: 278 LHPVSNEYMEFTAPLPEYFEK 298


>gi|269958655|ref|YP_003328442.1| putative pseudouridylate synthase [Anaplasma centrale str. Israel]
 gi|269848484|gb|ACZ49128.1| putative pseudouridylate synthase [Anaplasma centrale str. Israel]
          Length = 327

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 85/287 (29%), Positives = 132/287 (45%), Gaps = 32/287 (11%)

Query: 45  QVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           Q R+DK         R +    I  GQV     VIN  +++ K   +      + K S  
Sbjct: 15  QQRIDKLISCALEISRNRAQGLIAGGQVTISGRVINDNSYLTKTGDVYTIVTAVQKPSTL 74

Query: 97  -----LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW---VDSKGQ--KP 144
                +   ++YED  + V +K   I+V  G+GI +H   +  L  +   + S G   +P
Sbjct: 75  SPNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGIEHHTITNALLARFGAGLQSVGSSSRP 134

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-ANWLL 203
            + HRLD++TSG++V A+T  A   L+E    +  +K Y ++ WGIP  K+  I  N  +
Sbjct: 135 GIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGIPCPKRGVIHTNIRV 194

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           K+S I      +++    G   A + ++V     +    +    HTGRTHQ+RVH  H+G
Sbjct: 195 KRSDI-----TMMEAANSGGKPAKTEYEVEQELGEVASLIRCTLHTGRTHQIRVHMSHIG 249

Query: 264 CPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPEGGR 304
             IVGD KY  N K    S +        +  LHA  +   HP  G+
Sbjct: 250 HSIVGDQKYGKNCKKCMRSGVPPDVKNFRRQALHASLLGFRHPSTGK 296


>gi|114570956|ref|YP_757636.1| ribosomal large subunit pseudouridine synthase D [Maricaulis maris
           MCS10]
 gi|114341418|gb|ABI66698.1| ribosomal large subunit pseudouridine synthase D [Maricaulis maris
           MCS10]
          Length = 335

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 90/345 (26%), Positives = 147/345 (42%), Gaps = 50/345 (14%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRI 59
           M+ +   + +    ++   RLDRW       ++   L+ ++ +GQV VD   V   + ++
Sbjct: 1   MTDIAETRTLEATEEDAGQRLDRWLAASVESLSRSRLKALIEAGQVAVDGVAVTDPSAKV 60

Query: 60  QSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
            +G    V IP      +    E   LD               +L+ED  + V NKPAG+
Sbjct: 61  LAGSEYTVGIPE--PRADTPTPEPMDLD---------------VLHEDDHLIVINKPAGL 103

Query: 118 SVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           SV   +G         + +H  G L        ++P + HRLD+ETSG++VVA++  A +
Sbjct: 104 SVHPAAGNWTGTLVHGLLHHCAGSLSGI--GGVERPGIVHRLDKETSGVMVVAKSDVAHK 161

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            L+  F    +++ Y +     P  K   IA  L + S     +      N +   +AI+
Sbjct: 162 GLSIQFARHTVERAYIAFTRNAPSPKAGRIATQLARSSRDRKKFEVPHDPNSEAGKHAIT 221

Query: 229 HFKVIDCFAQK---------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           ++  +  F Q             +E +  TGRTHQ+RVH  H+ CP++GD  Y    +G 
Sbjct: 222 NYTTLKRFGQAEGAAIGTGMAAKVECRLETGRTHQIRVHMAHINCPLLGDPVY-GQKRGR 280

Query: 280 F--------TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                    T     +  LHA  +   HP  G  L+  + LP  M
Sbjct: 281 LLEYDDDSGTLRAFRRQALHAAILGFEHPVTGEALRFESELPDDM 325


>gi|118444250|ref|YP_878581.1| ribosomal large subunit pseudouridine synthase D [Clostridium novyi
           NT]
 gi|118134706|gb|ABK61750.1| ribosomal large subunit pseudouridine synthases, RluD subfamily
           [Clostridium novyi NT]
          Length = 301

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 87/313 (27%), Positives = 152/313 (48%), Gaps = 37/313 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+ DEE +RL+ + KNH  + +   ++K  R G+++V+ + V+ +  +++  V+ +  
Sbjct: 10  IKVQIDEEEIRLNHYLKNH-ANCSSRFIRKAAREGRIKVNNENVRLSYMLKNDDVIELQI 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  I+ E+  LD               ++YED  I V NKP GI V        H 
Sbjct: 69  NREENQDIVPEKMHLD---------------VIYEDKDIVVINKPKGIVVHP---TKRHQ 110

Query: 130 DGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +G L + V       ++    RL +RLD +TSG++++A+   +   L+   +     K Y
Sbjct: 111 NGTLSNGVLYYFKEKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFVKSY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G  K K   I   + +     G    V+  +E+G   +++ FKV++ + +    +
Sbjct: 171 LAIVHGNLKEKSGVINKPIYRVGE--GTLRRVI--DERGQR-SVTRFKVVESY-EDADLV 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E+   TGRTHQ+RVH   +G PI GD  Y     G       ++  LHA  + +PHP+ G
Sbjct: 225 ELTLETGRTHQIRVHLSSIGHPIYGDSLY-----GKEEHEYIDRQALHAYKLQIPHPKDG 279

Query: 304 R-LQITAPLPAHM 315
           R L++ + LP  M
Sbjct: 280 RILKLESDLPDDM 292


>gi|72127019|ref|XP_792641.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4 [Strongylocentrotus purpuratus]
 gi|115753235|ref|XP_001180714.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4 [Strongylocentrotus purpuratus]
          Length = 414

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 68/205 (33%), Positives = 112/205 (54%), Gaps = 28/205 (13%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK--SW-VDSKG----QKPRL 146
           +  L+  ++++   I   +KP G+ V GG G+ + ID  L   +W +++KG    ++  L
Sbjct: 142 AKILRDRVIFDKGDIIALDKPYGLPVHGGPGMKHSIDSLLPQLAWTLNNKGGGNTEELHL 201

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ET+G++++AR    A+ L E FR R+I K Y  +  GIP + KE I +  + + 
Sbjct: 202 IHRLDKETTGVMLLARNERTARVLHEMFRKRQIIKRYLVITVGIP-SPKEGILDMPMIEK 260

Query: 207 HIGGDYVHVVKQN----------------EKGANYAISHFKVIDCFAQKFCWL-EMQPHT 249
            I G +  V+K +                 + +  AI+ +KV+    +  C L +++P T
Sbjct: 261 EIDGKHRMVIKPDMADLYPDTIGMRSGRKSRDSKEAITRYKVLS--ERGNCALVQLEPET 318

Query: 250 GRTHQLRVH-ALHMGCPIVGDHKYC 273
           G  HQ+RVH A  +GCPI+GDHKY 
Sbjct: 319 GVKHQIRVHLAQGLGCPILGDHKYS 343


>gi|332702347|ref|ZP_08422435.1| pseudouridine synthase, RluA family [Desulfovibrio africanus str.
           Walvis Bay]
 gi|332552496|gb|EGJ49540.1| pseudouridine synthase, RluA family [Desulfovibrio africanus str.
           Walvis Bay]
          Length = 297

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 81/305 (26%), Positives = 138/305 (45%), Gaps = 33/305 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M  V ++ V   E   +L ++ +      +    + K LR+GQ+RVD +R K  +R+++G
Sbjct: 1   MPSVSHIEVTPAEAGHKLLQFLERRLGKGVPRALVMKWLRTGQLRVDGRRAKPFDRLEAG 60

Query: 63  QVVRIPP---VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q VR+PP   V+      ++ + +                 +++ED ++ V  KPAG++ 
Sbjct: 61  QTVRVPPYEAVVEPEGQPLRARPL----------------TIIHEDDELLVIAKPAGLAS 104

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           Q GSG+   +   LK+        P   HRLD +TSG+LV  +T  + + L + F    +
Sbjct: 105 QPGSGLTDSVQTRLKALYAGADFMPSCAHRLDMDTSGLLVAGKTYQSVRRLGDLFASGGV 164

Query: 180 QKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            K Y + V G  P+  +  + + ++K    G  +V +   N             +   A+
Sbjct: 165 DKTYLAWVQGQWPEQGQILLRDHIIKD---GRAHVRIGADNAPDGEQGKLALARVRPMAR 221

Query: 239 K--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           +     L ++  TGRTHQ+R+     G P++GD KY          P    L LHA  + 
Sbjct: 222 RPDATLLAVELLTGRTHQIRIQLASRGHPVLGDRKYGRR-------PHATHLLLHAWKLR 274

Query: 297 LPHPE 301
           LP  E
Sbjct: 275 LPDRE 279


>gi|289209195|ref|YP_003461261.1| pseudouridine synthase [Thioalkalivibrio sp. K90mix]
 gi|288944826|gb|ADC72525.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. K90mix]
          Length = 319

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 92/331 (27%), Positives = 149/331 (45%), Gaps = 54/331 (16%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +   +  +E   RLD      +P  +   L + L+ G + V+  + K    +Q G+
Sbjct: 1   MNEPRSAELPEEEAGQRLDAALARLFPEYSRSQLTQWLKEGALTVNGGQPKPRTPVQGGE 60

Query: 64  -VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VV  PP          E  +L++        + +   +++ED  + V NKPAG+ V   
Sbjct: 61  HVVLEPP----------EAPVLEAE------PEPIALDIVHEDPAVLVINKPAGLVVHPA 104

Query: 123 SGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   H  G L + +     +  Q PR  + HRLD++T+G++VVART  A   L    + 
Sbjct: 105 AG---HRAGTLVNALLHHDPNLSQLPRAGVVHRLDKDTTGLMVVARTPQAQTALVRQLQQ 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDC 235
           R + + Y +LV G        I+   +++  IG   V   +Q    G   A++H++V + 
Sbjct: 162 RTVHREYRALVQG------RVISGATIEEP-IGRHPVDRKRQAVTGGGKPAVTHYRVAER 214

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--------- 286
           F      L ++  TGRTHQ+RVH  H+  PIVGD  Y     G    P++          
Sbjct: 215 FP-AHTLLNVRLETGRTHQIRVHMAHIRHPIVGDPAY-----GGRPRPVRGMGEAAKAAL 268

Query: 287 ----KLYLHARYMDLPHPEGGR-LQITAPLP 312
               +  LHA  ++  HP+ G  L   AP+P
Sbjct: 269 AAFRRQALHAARLEFEHPDSGEVLAFEAPVP 299


>gi|255004408|ref|ZP_05279209.1| sfhb-like protein [Anaplasma marginale str. Virginia]
          Length = 340

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 85/287 (29%), Positives = 132/287 (45%), Gaps = 32/287 (11%)

Query: 45  QVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           Q R+DK         R +    I  GQV     VIN  +++ K   +      + K S  
Sbjct: 15  QQRIDKLISCALEISRNRAQGLIAGGQVTISGRVINNNSYLTKTGDVYTIVTAVQKPSTL 74

Query: 97  -----LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW---VDSKGQ--KP 144
                +   ++YED  + V +K   I+V  G+GI +H   +  L  +   + S G   +P
Sbjct: 75  SPNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGIEHHTITNALLARFGAGLQSVGSSSRP 134

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-ANWLL 203
            + HRLD++TSG++V A+T  A   L+E    +  +K Y ++ WGIP  K+  I  N  +
Sbjct: 135 GIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGIPCPKRGVIHTNIRV 194

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           K+S I      +++    G   A + ++V     +    +    HTGRTHQ+RVH  H+G
Sbjct: 195 KRSDIT-----MMEAANSGGKPAKTEYEVEQELGEVASLIRCTLHTGRTHQIRVHMSHIG 249

Query: 264 CPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPEGGR 304
             IVGD KY  N K    S +        +  LHA  +   HP  G+
Sbjct: 250 HSIVGDQKYGKNCKKCMRSGVPPDVKNFRRQALHASLLGFRHPSTGK 296


>gi|189464334|ref|ZP_03013119.1| hypothetical protein BACINT_00675 [Bacteroides intestinalis DSM
           17393]
 gi|189438124|gb|EDV07109.1| hypothetical protein BACINT_00675 [Bacteroides intestinalis DSM
           17393]
          Length = 357

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 90/346 (26%), Positives = 160/346 (46%), Gaps = 47/346 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ I  
Sbjct: 33  VVVDRGQEMMRVDKYLFDRLTNASRNRIQKSAEAGFVMANNKPVKSSYKVKPMDVITI-- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +++   + L          ++YED  + + NKPAG+ V  G G     
Sbjct: 91  ---MMDRPRYENEVIPEDIPLN---------IVYEDKYLMIVNKPAGLVVHPGHGNYHGT 138

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 139 LVNAIAWH----MKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKT 194

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LVWGI +  +  I   + +      D + +    +    +A++H++V++    
Sbjct: 195 TKRRYRALVWGIVEQDEGTIIGNIGRNPK---DRMQMTVLPDDQGKHAVTHYRVLERLGY 251

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN---------- 286
               +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           
Sbjct: 252 -VTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCP 310

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS-LGFKYDRNL 330
           +  LHA  +   HP  G  +  T+ +P  M +  D   G+  +R+L
Sbjct: 311 RQALHAMTLGFVHPATGEEMYFTSEMPDDMTQLIDKWRGYISNRDL 356


>gi|311748604|ref|ZP_07722389.1| ribosomal large subunit pseudouridine synthase family protein
           [Algoriphagus sp. PR1]
 gi|126577128|gb|EAZ81376.1| ribosomal large subunit pseudouridine synthase family protein
           [Algoriphagus sp. PR1]
          Length = 245

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 71/219 (32%), Positives = 109/219 (49%), Gaps = 16/219 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQETS 155
           ++YED+ + + NK AG+ VQG       +  + K ++  K  KP        HRLD+  S
Sbjct: 9   VVYEDNHLLIVNKTAGVLVQGDKTGDKTLTDYCKDYIAKKYDKPGAVFLHPVHRLDRPVS 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++  ART    + + E FR R I K+YW++V   PK K   + +WL+K      + V  
Sbjct: 69  GLVAFARTSKGLERMMELFRKRDIHKVYWAVVKRKPKEKSGKLTHWLVKDEQ--RNVVTA 126

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                 G+  A  ++K +  F      LE++P +GR HQ+RV    MGCPI GD KY   
Sbjct: 127 HDHEVPGSQKAELNYKTL-GFMNDHWLLEVRPISGRPHQIRVQLSSMGCPIRGDLKY--- 182

Query: 276 FKGNFTSPIQN-KLYLHARYMDLPHP-EGGRLQITAPLP 312
               F  P  +  + LHA ++   HP +  ++ + A LP
Sbjct: 183 ---GFAKPNPDASINLHAFHLVFVHPVKKEKMYLRAALP 218


>gi|291563387|emb|CBL42203.1| pseudouridine synthase, RluA family [butyrate-producing bacterium
           SS3/4]
          Length = 332

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 93/340 (27%), Positives = 151/340 (44%), Gaps = 37/340 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+E +E   RLD++   +    +     K++R   + ++ K+ + N ++  G VV++  
Sbjct: 4   IVIEKNEAGQRLDKFLAKYMNEASKSFFYKMMRKKNITLNGKKCEGNEKLAEGDVVKLFL 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----SG 124
             + +      +K     V   K  D     +LYED +I + NKPAG+  Q       S 
Sbjct: 64  AEDTI------EKFSSVQVQEVKKVDL---DILYEDDEIILVNKPAGMLSQKAKETDESL 114

Query: 125 IAYHIDGFLKS--WVDS--KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           + Y ID  L S    +S  +  +P + +RLD+ TSGI+   ++ A  Q L+  F+ R I 
Sbjct: 115 VEYLIDYLLGSGKLTESGLRAFRPSVCNRLDRNTSGIVAAGKSLAGLQMLSGVFKDRSIH 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK---GANYAISHFKVIDCFA 237
           K Y  LV G  ++ K  +  WLLK      + V ++ + E    G        K I    
Sbjct: 175 KYYQCLVSGEIRDVK-TVDGWLLKDEK--KNQVRILTEAEAKRFGGRGGDEEPKRIRTKY 231

Query: 238 Q------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           +      +F  L++   TGR+HQ+R H   +G PIVGD KY    K N +        LH
Sbjct: 232 EPIATDGRFTLLKVTLLTGRSHQIRAHLASLGHPIVGDFKYGGVSKVNPSGRTVKYQLLH 291

Query: 292 ARYMDLPHPE------GGRLQITAPLPAHMVKTWDSLGFK 325
           +  ++ P          GR+   APLP +        G +
Sbjct: 292 SYRLEFPKLAEPFVYLSGRV-FEAPLPGYFGSVLKETGIR 330


>gi|120553810|ref|YP_958161.1| RluA family pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120323659|gb|ABM17974.1| ribosomal large subunit pseudouridine synthase D [Marinobacter
           aquaeolei VT8]
          Length = 325

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 96/331 (29%), Positives = 154/331 (46%), Gaps = 47/331 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           + RLD+      P  +   LQ  ++SG + V+ K  K  +++  G  +       AL+  
Sbjct: 19  DKRLDQAAAELMPEHSRSRLQSWIKSGALTVNGKSRKPRDKVMMGDSL-------ALD-- 69

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-- 135
                  +  V +T  ++ +   ++YED  + V NKPAG+ V   +G   H DG L +  
Sbjct: 70  ------AEPEVQVTWEAEPISLDIVYEDEHLLVINKPAGLVVHPAAG---HTDGTLVNAL 120

Query: 136 --WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             +       PR  + HRLD++TSGI+VVAR+  A   L +  + R + + Y ++V G  
Sbjct: 121 LNYAPEVENLPRAGIVHRLDKDTSGIMVVARSLIAHTSLVDQLQTRTMGREYEAVVVGAL 180

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPH 248
                  A   + +       + VV   +     A++H+++++ FA      C LE    
Sbjct: 181 TGGATVDAP--IGRHPQDRKRMAVVSSGKP----AVTHYRLLERFAAHTLVRCKLE---- 230

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHARYMDLPHP 300
           +GRTHQ+RVH  H+  P+VGD  Y    +     T  +++ L       LHAR + L HP
Sbjct: 231 SGRTHQIRVHMAHVRHPLVGDPAYGGRLRLPKGTTEELRDVLAAFTRQALHARQLTLEHP 290

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           E G  L    PLP  MV   ++L  K+ R L
Sbjct: 291 ETGEILSWEVPLPEDMVHLIEAL-RKHAREL 320


>gi|78048898|ref|YP_365073.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325929044|ref|ZP_08190199.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           perforans 91-118]
 gi|78037328|emb|CAJ25073.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325540577|gb|EGD12164.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           perforans 91-118]
          Length = 331

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 88/343 (25%), Positives = 154/343 (44%), Gaps = 40/343 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +V ++    R D      +P  +   L + ++SG   +D +  +  + ++ G+ V+
Sbjct: 13  IRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGEMARPRDTLRGGESVQ 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V+    H   +   L                +LYED ++ V +KPAG+ V  G+G  
Sbjct: 73  LQVVLETQTHAAPQDIPLS---------------VLYEDEQVLVIDKPAGLVVHPGAG-- 115

Query: 127 YHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            + D  L + +     +    PR  + HRLD++TSG++VVART  A   L E    R + 
Sbjct: 116 -NPDQTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSAREVH 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G   +     A       H        V+ + +    A++H+++ + F +  
Sbjct: 175 RQYLAVVVGALVSGGTVNAPI---DRHPRDRLKMAVRDDGRD---AVTHYRLRERF-RAH 227

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHA 292
             LE +  TGRTHQ+RVH  H+  PIVGD  Y    K     T  + ++L       LHA
Sbjct: 228 TALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRSFKRQALHA 287

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
             ++  HP  G  ++ +AP+PA + +    L     R   + R
Sbjct: 288 ETLEFLHPVSGEPVRASAPVPADLQRLMTVLREDSARAAELAR 330


>gi|225018395|ref|ZP_03707587.1| hypothetical protein CLOSTMETH_02342 [Clostridium methylpentosum
           DSM 5476]
 gi|224948813|gb|EEG30022.1| hypothetical protein CLOSTMETH_02342 [Clostridium methylpentosum
           DSM 5476]
          Length = 308

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 85/324 (26%), Positives = 153/324 (47%), Gaps = 38/324 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP- 68
           V+VE ++   RLD++     P      LQK++   QVR + + +   +++++G+ + +  
Sbjct: 7   VLVEPEQAGERLDKFLPTVLPGYTRSALQKLIEGEQVRCEGEPLNKKHKLRAGETISVTI 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
           P    L+ ++ E+  LD               +LYEDS + V NKP  + V   +G    
Sbjct: 67  PDPEPLD-VLPEEIPLD---------------ILYEDSDLLVVNKPKHMVVHPAAGNYTG 110

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + +H  G L     +   +P + HR+D++TSG+L+VA+   A   L    +    
Sbjct: 111 TLVNALLHHCRGSLSGI--NGVIRPGIVHRIDKDTSGLLIVAKNDQAHVGLAAQIKEHSF 168

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V+G        + +  + +S      + V  +N K A   ++H++V+  + Q 
Sbjct: 169 DRTYEAVVYGKFVESTGTV-DKPIGRSEKDRKKMCVTTKNSKPA---VTHYEVLGEYGQ- 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           F  L ++  TGRTHQ+RVH   +G P+ GD  Y         + ++ +  LHAR +   H
Sbjct: 224 FTHLRLRLETGRTHQIRVHMASIGHPVAGDPVYGPK---KCITELEGQC-LHARSIGFVH 279

Query: 300 P-EGGRLQITAPLPAHMVKTWDSL 322
           P  G RL   + LP++ V   D +
Sbjct: 280 PGTGERLSFESELPSYFVSFLDKI 303


>gi|71907236|ref|YP_284823.1| ribosomal large subunit pseudouridine synthase D [Dechloromonas
           aromatica RCB]
 gi|71846857|gb|AAZ46353.1| ribosomal large subunit pseudouridine synthase D [Dechloromonas
           aromatica RCB]
          Length = 318

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 90/316 (28%), Positives = 146/316 (46%), Gaps = 38/316 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD+      P  +   LQ  +R   V+VD K   +   ++  G+ + +     +    +
Sbjct: 29  RLDQVLAELLPQHSRNRLQGWVREACVQVDGKPETEPKRKMMGGEKLLV-----SEPEDV 83

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
           + Q  L   + L          +++ED  + V NKPAG+ V  GSG         + +H+
Sbjct: 84  RNQPELPEDIPLD---------VVFEDETLLVINKPAGLVVHPGSGNWSGTLMNALLHHV 134

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G     V   G    + HRLD++TSG+LVVA+T  A   L    + R +++IY +L  G
Sbjct: 135 PGI--EVVPRAG----IVHRLDKDTSGLLVVAKTLEAQTDLVRQLQARTVRRIYLALAAG 188

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               K E   N  + +       + +V +N +G   AI++ ++++ F     ++E    T
Sbjct: 189 --AMKHEGTVNEPIGRHPSQRIKMAIVPEN-RGGKPAITNIRILEAFTYT-TFVECSLET 244

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
           GRTHQ+RVH   +  P+VGD  Y    K N   P   +  LHA  + L HP  G ++Q  
Sbjct: 245 GRTHQIRVHMAAIHHPLVGDQVYG---KHNPKLPEFPRQALHATRLGLVHPLTGLKMQWE 301

Query: 309 APLPAHMVKTWDSLGF 324
            P+P  M    D+L +
Sbjct: 302 VPMPEDMRNLLDNLRY 317


>gi|296122965|ref|YP_003630743.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
 gi|296015305|gb|ADG68544.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
          Length = 246

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 69/222 (31%), Positives = 108/222 (48%), Gaps = 17/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+   V  KPAG+   G      ++       +  + QKP      L HRLD+  S
Sbjct: 6   ILFEDNHCLVVEKPAGVLTMGDETGDENMVQLAMDDLKIRHQKPGNVYVGLVHRLDRPVS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A+T  AA  L+  FR R  +K+Y ++V G        I +WL+K      ++  V
Sbjct: 66  GVLLLAKTSKAASRLSAQFREREPEKVYLAIVEGQLNPAAGEIVDWLIKDQE--RNHTRV 123

Query: 216 VKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                 GA  A   ++ ++           +E+QP TGR+HQ+RV   H G  I+GD +Y
Sbjct: 124 TSPQTPGAKQAKLRYRQLETLVTPEGIRTLVEVQPMTGRSHQIRVQLAHAGASILGDLRY 183

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
            +       +P+   + LHAR +   HP +   L I APLP+
Sbjct: 184 GSK------TPLGKMIALHARSLTFEHPVQKQPLTIYAPLPS 219


>gi|11279841|pir||A81748 ribosomal large chain pseudouridine synthase D TC0029 [imported] -
           Chlamydia muridarum (strain Nigg)
          Length = 345

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 83/287 (28%), Positives = 138/287 (48%), Gaps = 32/287 (11%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           Q ++D  RV+ N R+Q+    R   +++  + +  E    ++  +LT  +  L  +  YE
Sbjct: 51  QQQIDLGRVRVNGRVQT----RASYLLSQGDLVDLELVEEETPSSLTPENIPLDKV--YE 104

Query: 105 DSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           D+ I V NKP  + V    G         + + I   LK     +  +P + HRLD++TS
Sbjct: 105 DNMILVINKPRNMVVHPAPGHVQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTS 164

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSHIGGDYV 213
           G+L+  +TR A    +E F  ++++K+Y ++    P  K     IA   +K+  +     
Sbjct: 165 GLLITVKTRRAKAVYSELFSSKQMKKMYIAICINSPAQKHIHTRIARHPVKRKEMT---- 220

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY- 272
            V+ ++ +G   AI+H  V+     +   + + P TGRTHQLRVH  H+G PI+GD  Y 
Sbjct: 221 -VLSKDTEGGKEAITHCHVLASNG-RLSVVALYPETGRTHQLRVHMKHLGTPILGDPVYG 278

Query: 273 --CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
               NF+        +K  LHA  +   HPE   R+++   LP  M 
Sbjct: 279 VPSINFRYGL-----DKQQLHAYSLVFTHPESAERVELVTKLPDDMT 320


>gi|327385684|gb|AEA57158.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Lactobacillus casei BD-II]
          Length = 306

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 94/326 (28%), Positives = 155/326 (47%), Gaps = 42/326 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  R+D+    H        +QK L+ G V V+ +  K N ++ SG V+ I         
Sbjct: 10  EQGRIDKVITAHETTHTRSQVQKWLQDGLVTVNGQPTKANYKVASGDVIAIS-------- 61

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            I E K L++        + +   ++YED ++ V +KP G+ V    G   H DG L + 
Sbjct: 62  -IPEAKPLEAI------PEPIPLDIVYEDDQVIVVDKPQGMVVHPAPG---HPDGTLVNG 111

Query: 137 V----DSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +    D  G     +P + HR+D++TSG+L+VA+T  A   L+   + +   + Y +LV 
Sbjct: 112 LLYHTDLPGINGVIRPGIVHRIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVH 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQP 247
           G  K  +  I       + +G D     +Q    A  +A++HF+V++ F + + +++   
Sbjct: 172 GTFKEDEGTI------DAPLGRDPRDRKRQAVVAAGRHAVTHFQVLERF-EHYTFIKCIL 224

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH  ++  P+ GD  Y        T P + + +LHA  +   HP  G+L +
Sbjct: 225 ETGRTHQIRVHMAYIHHPVAGDPLYGP----KRTLPGKGQ-FLHAAKLGFVHPTTGQLLV 279

Query: 308 -TAPLPAHMVKTWDSL--GFKYDRNL 330
             AP+P    KT   L  G    RN+
Sbjct: 280 FEAPVPPIFEKTLADLRAGIDKTRNV 305


>gi|191638454|ref|YP_001987620.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|190712756|emb|CAQ66762.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|327382486|gb|AEA53962.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Lactobacillus casei LC2W]
          Length = 307

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 94/326 (28%), Positives = 155/326 (47%), Gaps = 42/326 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  R+D+    H        +QK L+ G V V+ +  K N ++ SG V+ I         
Sbjct: 11  EQGRIDKVITAHETTHTRSQVQKWLQDGLVTVNGQPTKANYKVASGDVIAIS-------- 62

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            I E K L++        + +   ++YED ++ V +KP G+ V    G   H DG L + 
Sbjct: 63  -IPEAKPLEAI------PEPIPLDIVYEDDQVIVVDKPQGMVVHPAPG---HPDGTLVNG 112

Query: 137 V----DSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +    D  G     +P + HR+D++TSG+L+VA+T  A   L+   + +   + Y +LV 
Sbjct: 113 LLYHTDLPGINGVIRPGIVHRIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVH 172

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQP 247
           G  K  +  I       + +G D     +Q    A  +A++HF+V++ F + + +++   
Sbjct: 173 GTFKEDEGTI------DAPLGRDPRDRKRQAVVAAGRHAVTHFQVLERF-EHYTFIKCIL 225

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH  ++  P+ GD  Y        T P + + +LHA  +   HP  G+L +
Sbjct: 226 ETGRTHQIRVHMAYIHHPVAGDPLYGP----KRTLPGKGQ-FLHAAKLGFVHPTTGQLLV 280

Query: 308 -TAPLPAHMVKTWDSL--GFKYDRNL 330
             AP+P    KT   L  G    RN+
Sbjct: 281 FEAPVPPIFEKTLADLRAGIDKTRNV 306


>gi|325268629|ref|ZP_08135259.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           multiformis DSM 16608]
 gi|324989157|gb|EGC21110.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           multiformis DSM 16608]
          Length = 364

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 91/340 (26%), Positives = 152/340 (44%), Gaps = 64/340 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++      H +   +QK   +G + V+   VK N +++   V+ +  
Sbjct: 36  VAVDKGQVPVRIDKFLFERMQHSSRNRIQKAADAGFIHVNGSPVKSNYKVRPEDVITL-- 93

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I    + L          ++YED+ + V NKPAG+ V  G+G     
Sbjct: 94  ---MLDRPKHDNTIEAEDIPLD---------IVYEDTVLMVINKPAGLVVHPGAGNFHGT 141

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H+        D    +  L HR+D++TSG+LVVA+T  A   L + F  +   
Sbjct: 142 LINAVAWHLRDM--PAFDPNDPEVGLVHRIDKDTSGLLVVAKTPDAKTALGKQFFNKTTH 199

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------VVKQNEKGANYAISHFK 231
           + Y +LVWG          N+   +  I G+            V     +   +A++H++
Sbjct: 200 RSYNALVWG----------NFTEDEGRIEGNIARDPRDRLRMTVFPPGSETGKHAVTHYR 249

Query: 232 VIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP--- 283
           V++ F       C LE    TGRTHQ+R H  H+G P+ GD +Y      +G  +S    
Sbjct: 250 VLERFGYTTLIECILE----TGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSSYKA 305

Query: 284 -IQNKL------YLHARYMDLPHP-EGGRLQITAPLPAHM 315
            I+N L       LHAR +   HP  G ++  T+ LP  +
Sbjct: 306 FIRNCLACCSRQALHARTLGFVHPVTGEQMNFTSDLPEDL 345


>gi|326522893|dbj|BAJ88492.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 357

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 122/245 (49%), Gaps = 25/245 (10%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD---FLKSILLYEDSK 107
           KR+K +  ++ G  + +P  ++     IK++     +  L  + D   +LK +++Y+DS 
Sbjct: 10  KRIKHSEVMEPGMRIHLP--VSVAEAEIKKRYETIPTATLHPNRDEIEYLKRLVIYKDSA 67

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAA 166
           I V NKP  + ++G   +   +D    + +    ++ P+L HRLD+++SG+L++ RTR  
Sbjct: 68  ILVLNKPPKVPMKGNLPVHNSMDVLAAAALSFGNEEGPKLVHRLDRDSSGLLLMGRTREG 127

Query: 167 AQHLTESFRMRRIQKI---------------YWSLVWGIPKNKKECIANWLLKKSHIGGD 211
              L   F   ++ K                YW+LV G P   +  I+  L K     G 
Sbjct: 128 FTRLHWLFTSIKLAKTASQTWNTACESYLQRYWALVIGTPTESEGVISAPLTKVLLDDGK 187

Query: 212 YVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIV 267
              V+  +  G   A  A++ ++V+        W+E++P TGR HQLRVH A  +G PIV
Sbjct: 188 AERVILAHPSGIDGAQEAVTEYRVMGPTINGCSWIELRPLTGRKHQLRVHCAEALGTPIV 247

Query: 268 GDHKY 272
           GD+KY
Sbjct: 248 GDYKY 252


>gi|160892655|ref|ZP_02073445.1| hypothetical protein CLOL250_00185 [Clostridium sp. L2-50]
 gi|156865696|gb|EDO59127.1| hypothetical protein CLOL250_00185 [Clostridium sp. L2-50]
          Length = 305

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 87/321 (27%), Positives = 150/321 (46%), Gaps = 33/321 (10%)

Query: 12  VENDEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +E DE   + R+D+   +++ + +   L+K+L  G + V+ K+ K + +I SG  + I  
Sbjct: 6   IEADENWTDKRVDKGLADYFDNYSRSFLKKLLDDGNILVNDKKAKPSLKIASGDRIDITI 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
              A   I  E   LD               ++YED  I + NKP G+ V    G     
Sbjct: 66  PSIASVEIEPENIPLD---------------IVYEDEDIIIVNKPKGMVVHPAPGHYSGT 110

Query: 128 HIDGFLKSWVDS----KGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++G +  + DS     G+ +P + HR+D +T+G+LVV +  AA   L+E   +  I + 
Sbjct: 111 LVNGLMYHFKDSLSGINGELRPGIVHRIDMDTTGLLVVCKNDAAHNFLSEQLAVHSITRK 170

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y+++ +     + E I +  + +       + V   N K    A++H+KV+      FC 
Sbjct: 171 YYAICFNY-FTEDEGIVDLPIGRHPTDRKKMAV---NYKNGRNAVTHYKVLKKLKNNFCL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E Q  TGRTHQ+RVH  ++  P++GD  Y      N    +Q +  LHA  +   HP  
Sbjct: 227 IECQLETGRTHQIRVHMSYIKHPLLGDAIYGPK---NQPYHLQGQT-LHAGVLGFIHPST 282

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
              ++ ++ LP +  K    L
Sbjct: 283 KEYVEFSSELPEYFQKLLKQL 303


>gi|116511823|ref|YP_809039.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. cremoris SK11]
 gi|116107477|gb|ABJ72617.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. cremoris SK11]
          Length = 301

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/316 (27%), Positives = 155/316 (49%), Gaps = 47/316 (14%)

Query: 11  VVENDEEN--MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           +++  EEN  +RLD+   N   +   + L +++++ +V V+ +  K   ++++G  +   
Sbjct: 3   IIKITEENKDLRLDKALANQTEYSRSL-LTELIKNDKVFVNNEAKKAKYKVKTGDRIEFE 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
                    I + ++LD +      ++ L   ++YEDS + V NKP G+ V   +G    
Sbjct: 62  ---------IPQAEVLDVA------AEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASG 106

Query: 125 -----IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                I YHI    K      G  +P + HR+D++TSG+L++A+   A + L    + + 
Sbjct: 107 TLVNAIMYHI----KDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKT 162

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFA 237
            ++ Y ++V G   N K  I      ++ IG +     KQ    G   A++HF+V++ F 
Sbjct: 163 SKRRYLAIVHGELANDKGTI------EAPIGRNLKDRKKQAVVSGGKPAVTHFEVLERFV 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  + ++  TGRTHQ+RVH  ++G P+ GD  Y  N      +P + + +LHA  +  
Sbjct: 217 -GYTLIALRLETGRTHQIRVHMHYIGHPVAGDPLYGPN---KTLTPNKGQ-FLHAETLGF 271

Query: 298 PHPEGGRL---QITAP 310
            HP  G L   Q+ AP
Sbjct: 272 EHPTSGELMEFQVDAP 287


>gi|325106618|ref|YP_004267686.1| pseudouridine synthase [Planctomyces brasiliensis DSM 5305]
 gi|324966886|gb|ADY57664.1| pseudouridine synthase [Planctomyces brasiliensis DSM 5305]
          Length = 296

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 114/238 (47%), Gaps = 16/238 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++ ED  +   NKPAG+  QG     + +  ++K+++  K +KP      + HRLD+  +
Sbjct: 61  VICEDGPVVAVNKPAGMLSQGSPQGVFCLPDYVKAYLKHKYEKPGNVYLGVVHRLDRPVT 120

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V +R    A  L E FR R +QK+Y +L+  +P   +  + +++ K        +  
Sbjct: 121 GVVVFSRNSKGAARLAEQFREREVQKVYLALLENVPDQPEGTLKDFIRKVPEQARAVIEP 180

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +  E  A  A   ++V+     K+  +E+ P TGR HQ+R+     GCPIVGD  Y A 
Sbjct: 181 GETQE--AKAAELSYRVLASDG-KYALVEVLPKTGRMHQIRIQFASRGCPIVGDQLYGAK 237

Query: 276 FKGN---FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
              +    T     ++ LHA  + + HP     L I AP PA     W  +  +  RN
Sbjct: 238 KTIDLKPLTDDYTQRIALHAWKLTIKHPVRYDDLTIQAPPPAD----WPEVAHRLFRN 291


>gi|282880676|ref|ZP_06289379.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
 gi|281305459|gb|EFA97516.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
          Length = 315

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 90/319 (28%), Positives = 144/319 (45%), Gaps = 40/319 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQV 64
           Y  YVV E D     L  W  NH  H++   L+  L    + V+ K++ +F+  +  G  
Sbjct: 10  YQCYVVEETDT----LLNWLLNHVTHLSKSKLKATLAGRGIIVNGKQITQFDYPVTPGTK 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I                  S  N    S ++K  ++YED  + V  K AGI       
Sbjct: 66  IAIS----------------KSKKNTLFKSKYVK--IVYEDRYLVVIEKQAGILSMAAGH 107

Query: 125 IAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            + ++   L S+     QK    + HRLD++TSG+++ A+    AQ L   +      + 
Sbjct: 108 ASLNVKKVLDSYFKQSKQKCTAHVVHRLDRDTSGLMIYAKDIQTAQLLEHDWHHNVYDRR 167

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G  +  +  IANWL         Y+      + G  +A++HF  ++    +   
Sbjct: 168 YVAVVSGEMEQDEGTIANWLKDNR----AYITYSSPEDNGGKFAVTHFHTLN-RTTEHSL 222

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGR +Q+RVH+  MG P+ GDHKY     GN  +PI  +L LHA  +   HP  
Sbjct: 223 VEYRLETGRKNQIRVHSADMGHPVCGDHKY-----GNGDNPI-GRLCLHAYVLCFYHPVT 276

Query: 303 GR-LQITAPLP---AHMVK 317
            R ++   P+P   AH+ K
Sbjct: 277 HRPMEFETPIPPAFAHLFK 295


>gi|270284819|ref|ZP_06194213.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           muridarum Nigg]
 gi|270288848|ref|ZP_06195150.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           muridarum Weiss]
 gi|301336199|ref|ZP_07224401.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           muridarum MopnTet14]
          Length = 338

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 83/287 (28%), Positives = 138/287 (48%), Gaps = 32/287 (11%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           Q ++D  RV+ N R+Q+    R   +++  + +  E    ++  +LT  +  L  +  YE
Sbjct: 44  QQQIDLGRVRVNGRVQT----RASYLLSQGDLVDLELVEEETPSSLTPENIPLDKV--YE 97

Query: 105 DSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           D+ I V NKP  + V    G         + + I   LK     +  +P + HRLD++TS
Sbjct: 98  DNMILVINKPRNMVVHPAPGHVQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTS 157

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSHIGGDYV 213
           G+L+  +TR A    +E F  ++++K+Y ++    P  K     IA   +K+  +     
Sbjct: 158 GLLITVKTRRAKAVYSELFSSKQMKKMYIAICINSPAQKHIHTRIARHPVKRKEMT---- 213

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY- 272
            V+ ++ +G   AI+H  V+     +   + + P TGRTHQLRVH  H+G PI+GD  Y 
Sbjct: 214 -VLSKDTEGGKEAITHCHVLASNG-RLSVVALYPETGRTHQLRVHMKHLGTPILGDPVYG 271

Query: 273 --CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
               NF+        +K  LHA  +   HPE   R+++   LP  M 
Sbjct: 272 VPSINFRYGL-----DKQQLHAYSLVFTHPESAERVELVTKLPDDMT 313


>gi|253681471|ref|ZP_04862268.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum D str. 1873]
 gi|253561183|gb|EES90635.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum D str. 1873]
          Length = 304

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 97/324 (29%), Positives = 150/324 (46%), Gaps = 45/324 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++++ EN   N RLD +  N     +   +QK+++ G V+V+ K  K N +++   
Sbjct: 1   MCTKEFIIHEN-LVNCRLDVFISNSLEGKSRSYIQKLIQEGHVKVNGKDKKSNYKLKLHD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +  + N    I  E   LD               +LYED  I V NKP G+ V   +
Sbjct: 60  SVIVNNIENEFQKINPENIDLD---------------ILYEDKDIIVINKPQGMVVHPAT 104

Query: 124 ---------GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                    G+ YH D       D++   P + HR+D++TSG+LVVA+   A + L E  
Sbjct: 105 SNYSGTLVNGLLYHCDTLSTLNDDTR---PGIVHRIDKDTSGVLVVAKNNKAHEVLAEQL 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +   +++ Y +LV GI K     I   L +      D + +    E G N AI+H++V+ 
Sbjct: 162 KEHSMKREYIALVEGILKKDNGFIDKPLGRNPK---DRIKMAVVQE-GKN-AITHYEVLK 216

Query: 235 CFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
            F +     C LE    TGRTHQ+RVH  ++G P+VGD  Y    K  F    Q    LH
Sbjct: 217 RFKKNTLVKCILE----TGRTHQIRVHMSYIGHPLVGDPMYGFK-KQRFKLKGQ---MLH 268

Query: 292 ARYMDLPHPEGGR-LQITAPLPAH 314
           A+ +   HP     ++  + LP +
Sbjct: 269 AKKLGFIHPTTQEYIEFQSDLPKY 292


>gi|114327513|ref|YP_744670.1| ribosomal large subunit pseudouridine synthase D [Granulibacter
           bethesdensis CGDNIH1]
 gi|114315687|gb|ABI61747.1| ribosomal large subunit pseudouridine synthase D [Granulibacter
           bethesdensis CGDNIH1]
          Length = 330

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 88/334 (26%), Positives = 148/334 (44%), Gaps = 43/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIP 68
           V    D    R+DR+   H P ++   L+ ++ SG V  D + V+     ++ G + R+ 
Sbjct: 15  VSAAPDAVPERIDRFLAIHLPDMSRSRLKSLIESGAVHRDGQSVRGPAEMVRPGSLYRL- 73

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                             ++ + +H  F    +L+ED  + V +KPAG+ V    G    
Sbjct: 74  -----------RLPTPAPAIPIAQHIAF---PILFEDDDLIVLDKPAGMVVHPAPGSP-- 117

Query: 129 IDGFL---------KSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            DG L         ++     G+K P + HRLD++TSG++VVA+T  A   L+  F  R 
Sbjct: 118 -DGTLVNALLAYCGENLPGIGGEKRPGIVHRLDKDTSGVMVVAKTEFALAALSALFAARD 176

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++++Y +L WG+    +E      + +       + +V+    G   A++H++ +  +  
Sbjct: 177 LERLYTALAWGV-LTPREGDIEGAIGRDPRDRKRMAIVRH---GGKPALTHYRAMATWYD 232

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG---NFTSPIQNKLY------ 289
               +E +  TGRTHQ+RVH    G PI+GD  Y         +    ++N L       
Sbjct: 233 AVTRMECKLATGRTHQIRVHLSANGHPIIGDPVYLRRIPAVAKSLDQDVKNALLDFPRQA 292

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           LHA  +   HP  G  L+   PLP  M+   D L
Sbjct: 293 LHAGVLGFRHPRTGENLRFETPLPEDMMSLIDLL 326


>gi|228909719|ref|ZP_04073542.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis IBL 200]
 gi|228850008|gb|EEM94839.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis IBL 200]
          Length = 302

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/308 (27%), Positives = 145/308 (47%), Gaps = 43/308 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +N R+D++        +   +Q+ ++   V V+ K VK N +++    + +         
Sbjct: 14  KNERIDKFVAGINNEWSRSQVQQWIKDDVVTVNGKTVKVNYKVKEEDEITV--------- 64

Query: 77  IIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
            I E + LD     +NL          + YED+ + V NKP G+ V    G      ++G
Sbjct: 65  TIPEPEALDIQPEDMNLE---------IYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNG 115

Query: 132 FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y ++V
Sbjct: 116 LMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            G+  + K  I       + IG D      +  +E G N A++HF+V++ F + F  +E 
Sbjct: 176 HGVIPHDKGTI------DAPIGRDKKERQSMTVDENGKN-AVTHFQVLERF-KDFTLVEC 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  +   HP  G  
Sbjct: 228 RLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGILGFDHPRTGEY 282

Query: 305 LQITAPLP 312
           +Q  AP+P
Sbjct: 283 IQFEAPIP 290


>gi|218509234|ref|ZP_03507112.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli Brasil 5]
          Length = 274

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 64/198 (32%), Positives = 107/198 (54%), Gaps = 26/198 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  + V +KPAG+ V  GSG         + +H    L      +  +P + HRLD
Sbjct: 73  ILYEDDDLIVISKPAGLVVHPGSGNWTGTLVNALIHHCGATLSGIGGVR--RPGIVHRLD 130

Query: 152 QETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           ++T+G++VVA+   A +HL+  F    R   +++ Y ++VWG P++    +   L + + 
Sbjct: 131 KDTTGVMVVAKNDVAHRHLSLQFADHGRTMPLERAYQAIVWGRPRSLTGTVDAPLGRAT- 189

Query: 208 IGGDYVH--VVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHA 259
             GD     V + + + A+ AI+H++VI+ F +          +E +  TGRTHQ+RVH 
Sbjct: 190 --GDRTRRAVKRPDSQDADQAITHYEVIERFHETPDATALASLVECRLETGRTHQIRVHM 247

Query: 260 LHMGCPIVGDHKYCANFK 277
            H+G P++GD  Y A F+
Sbjct: 248 AHIGHPLLGDTVYGAGFR 265


>gi|254785221|ref|YP_003072649.1| ribosomal large subunit pseudouridine synthase D [Teredinibacter
           turnerae T7901]
 gi|237685566|gb|ACR12830.1| ribosomal large subunit pseudouridine synthase D [Teredinibacter
           turnerae T7901]
          Length = 333

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 83/310 (26%), Positives = 141/310 (45%), Gaps = 42/310 (13%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           + RLD+     +P  +   LQ+ ++ G++ V+ +  K   ++  G+ +R+  +       
Sbjct: 34  DSRLDQVAAELFPEFSRARLQQWIKQGRLTVNGEPAKPKLKLAGGECLRLSVLEEPQGEW 93

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL-- 133
           + E   LD               ++YED  I V NKPAG+ V   +G      ++G +  
Sbjct: 94  LPEPIPLD---------------VVYEDEAILVLNKPAGLVVHPAAGNYTGTLLNGLIHH 138

Query: 134 ---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +S +   G    + HRLD++TSG++VVA+T AA  +L    + R +++ Y +L  G 
Sbjct: 139 RQAQSLLPRAG----IVHRLDKDTSGLMVVAKTTAAQNNLVAQLQARTVKREYEALAIG- 193

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            + +     +  + +       + VV   +     A++H+  +  F   F  L +Q  TG
Sbjct: 194 -EVRSSGFVDAPIGRHPTNRTRMAVVSSGKP----AVTHYTALARF-DGFTHLRLQLETG 247

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------PIQN--KLYLHARYMDLPHPEG 302
           RTHQ+RVH  H+G P+VGD  Y                P+ +  +  LHA  + L HP  
Sbjct: 248 RTHQIRVHMAHLGYPLVGDPVYGRRLPAKLLRENPDLVPLSSLPRQALHAVQLGLQHPAS 307

Query: 303 GR-LQITAPL 311
           G  LQ   PL
Sbjct: 308 GEYLQWQVPL 317


>gi|312622364|ref|YP_004023977.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202831|gb|ADQ46158.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 293

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/278 (30%), Positives = 146/278 (52%), Gaps = 27/278 (9%)

Query: 47  RVDKKRVKFNNRIQS-----GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK--- 98
           ++ +KR+ F++ + S     GQ+  IPP I +++   +E  +++  +  +K S+ +    
Sbjct: 18  QILQKRLFFSSTLMSRLKAHGQIRFIPP-IYSVHQYPQENAVIEVDLIFSK-SNIVPVEG 75

Query: 99  SI-LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           SI +LYED+     NKP+G+      G  +  I  +++ +++SK     + +RLD++TSG
Sbjct: 76  SIDILYEDNFFLFVNKPSGLPSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRLDKDTSG 135

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I+V A+       ++  F  RR+ K Y ++V GI   KK  +    +K+S  G     + 
Sbjct: 136 IVVFAKNSYFHSIVSYEFEKRRVDKTYIAIVHGI-LTKKSGLIEKPIKRSDDG-----IK 189

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           ++  +  ++A ++++VID F + F  L+++P TGRTHQLRVH   +G PIVGD  Y    
Sbjct: 190 REIHQDGSFAFTYYEVIDTF-ENFSVLKLKPITGRTHQLRVHLSSIGHPIVGDCIYGKEK 248

Query: 277 KGNFTSPIQNKLYLHARYM--DLPHPEGGRLQITAPLP 312
             N        L LHA  +  +          IT+PLP
Sbjct: 249 TQN------TPLLLHAYSIRFNFKLISNKAYDITSPLP 280


>gi|239948112|ref|ZP_04699865.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Rickettsia endosymbiont of Ixodes scapularis]
 gi|239922388|gb|EER22412.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Rickettsia endosymbiont of Ixodes scapularis]
          Length = 310

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 88/329 (26%), Positives = 154/329 (46%), Gaps = 52/329 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V N+  N+RLD+       +++   +QK ++S  V+V+              ++  P V+
Sbjct: 6   VPNELNNIRLDKALSQLLENVSRNQIQKSIKSSCVQVND------------VIISDPDVL 53

Query: 72  NALNHII-------KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
              N +I       +E KI  +++ L          ++YED  + V NK AG++V  G+G
Sbjct: 54  VKENDVILFSFKEPEELKIAAANIALD---------IIYEDDDLIVINKAAGMTVHPGAG 104

Query: 125 IAYHIDGFL-------KSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             +H D  +       K+  D    ++P + HRLD+ T+G++VVA+   A   L      
Sbjct: 105 --HHDDTLVNALLYHTKNLSDIGSSERPGIVHRLDKNTTGLMVVAKNNKAHMLLANQIEQ 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R++ + Y +LVWG+  N  E +    + +S      + ++K    G   A++H+K ++ F
Sbjct: 163 RQVIRKYKALVWGVI-NPLEGVIKNNIGRSRSDRQKMTILKY---GGKEAVTHYKTLELF 218

Query: 237 -AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLY---- 289
            +     +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP  ++ KL     
Sbjct: 219 YSGTISMVECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAHSPPELKAKLIDFKR 278

Query: 290 --LHARYMDLPHPEGGR-LQITAPLPAHM 315
             LH+ Y+   HP     ++ +  LP  M
Sbjct: 279 QALHSWYLSFTHPTSNEIMEFSCELPRDM 307


>gi|224368793|ref|YP_002602954.1| RluD1 [Desulfobacterium autotrophicum HRM2]
 gi|223691509|gb|ACN14792.1| RluD1 [Desulfobacterium autotrophicum HRM2]
          Length = 313

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 88/296 (29%), Positives = 139/296 (46%), Gaps = 36/296 (12%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           + +  G + V   R K   R++ G+VV       +L          +S +     ++ + 
Sbjct: 34  RAIEKGLILVSGNRKKPAYRVKPGEVV-----CGSLGS--------ESEIESKPRAESIS 80

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHR 149
              L+ED  I V NKPAG+ V  G+G         + +H      +  D    +  + HR
Sbjct: 81  LDFLHEDQWIVVVNKPAGMVVHPGAGNSSGTLLNALLHHFPSLTDTHCDPP-LRGGIVHR 139

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG +VVA+++ A + L + FR RR++K Y +L  GI    +  I         IG
Sbjct: 140 LDKDTSGTIVVAKSKKAYEFLQKEFRFRRVEKRYIALATGIITETQGRIT------LPIG 193

Query: 210 GDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              +H  +   N + A  A + ++V+   A     L++   TGRTHQ+RVH   +G P+ 
Sbjct: 194 RHPIHRKRMAVNTERARPAETLWRVLGQMA-GHTLLDVGLKTGRTHQIRVHFRALGHPLA 252

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GD  Y    K +  +P Q    LHA  +   HP  G R++ TAPLP  MV+  + L
Sbjct: 253 GDRVYGFRGKQSARAPRQ---MLHAGTLGFRHPWSGKRVEFTAPLPEDMVEVLERL 305


>gi|261400385|ref|ZP_05986510.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           lactamica ATCC 23970]
 gi|269209820|gb|EEZ76275.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           lactamica ATCC 23970]
          Length = 374

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/307 (28%), Positives = 140/307 (45%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   +R G V V+ K  +  +++  G+ +R+            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKPSQPKDKMIGGEQIRV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWSGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAGDPVYGNLRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|331004934|ref|ZP_08328347.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC1989]
 gi|330421258|gb|EGG95511.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC1989]
          Length = 333

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 80/329 (24%), Positives = 160/329 (48%), Gaps = 40/329 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V + +   R+D+   + +   +   +Q+ ++ G + VD ++ +  +++ SG+++ +   
Sbjct: 10  IVPDTDAGKRVDQVAASLFQQYSRSRIQEWIKQGTILVDGQKCRSKDKLLSGEMITLA-- 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                 +I++ + L   + + +         +Y D  I + NKPAG+ V  G+G+     
Sbjct: 68  ----VELIEDDRWLPQDIAIDE---------VYSDEHIIIINKPAGLVVHPGAGMPDGTL 114

Query: 129 IDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++G L  + + S   +  + HRLD++T+G++VVAR+  A   L +  + R + + Y ++V
Sbjct: 115 LNGLLFHYPELSTLPRAGIVHRLDKDTTGLMVVARSLLAHTSLVQQLQDRSLGREYEAVV 174

Query: 188 WG-----------IPKNKKECIANWLLKKSHIGGDYV-HVVKQNEKGANYAISHFKVIDC 235
            G           I ++  + I   ++ +SH  G Y     + + +    AI+H++++  
Sbjct: 175 MGELTGGGVIDKPIGRHPTQRIKMAVIDRSHRRGGYSDESSRPDSQAGKEAITHYRLLKR 234

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NK 287
           F+  +  +  Q  TGRTHQ+RVH  H   P+VGD  Y    K    + ++         +
Sbjct: 235 FS-GYTHIACQLETGRTHQIRVHLAHSNHPLVGDPVYLTRQKWVAGTVVELKSILTAFTR 293

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHM 315
             LHAR + L HP+ G  L+  + LP  M
Sbjct: 294 QALHARKLTLVHPQSGDTLEWESELPKDM 322


>gi|317131689|ref|YP_004091003.1| pseudouridine synthase, RluA family [Ethanoligenens harbinense
           YUAN-3]
 gi|315469668|gb|ADU26272.1| pseudouridine synthase, RluA family [Ethanoligenens harbinense
           YUAN-3]
          Length = 302

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/323 (26%), Positives = 151/323 (46%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q  V   ++   RLDR      P      LQK+L  G V ++ K    ++R+++G  +  
Sbjct: 4   QTFVAGMEQAGERLDRALARLCPDQTRSGLQKLLECGLVTLNGKPAGKHDRMRAGDEI-- 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
             V+   + +  E K  D  + +           +YED  + V NKP G+ V  G+G   
Sbjct: 62  --VVEFPDPVPLEAKAQDIPIEV-----------VYEDDDLLVVNKPQGMVVHPGAGNPD 108

Query: 126 AYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++  L    DS        +P + HR+D++TSG+L+VA+   A Q L    +     
Sbjct: 109 GTLVNALLFHCGDSLSGIGGVLRPGIVHRIDKDTSGLLMVAKNDRAHQSLAAQIKAHSFL 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G+ K     + +  + +       + V ++N +   +A++H+ V+  +   +
Sbjct: 169 REYEAVVCGVIKEDSGTV-DAPVGRHPTNRKRMAVTQKNSR---HAVTHYTVLRRYTH-Y 223

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L ++  TGRTHQ+R+H  ++G P+ GD  Y     G     ++ +  LHAR +   HP
Sbjct: 224 THLRLRLETGRTHQIRLHMAYIGHPVAGDPVYGKPLCG-----LRGQC-LHARTLGFVHP 277

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             GR ++ T+ LPA+  +   +L
Sbjct: 278 STGRYMEFTSELPAYFRQFLTTL 300


>gi|1239996|emb|CAA65704.1| hypothetical protein [Bacillus subtilis subsp. subtilis str. 168]
          Length = 302

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 85/283 (30%), Positives = 132/283 (46%), Gaps = 45/283 (15%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           Q++V+ + V  N  ++ G  V I    +  + +I E   LD               +L+E
Sbjct: 44  QIKVNHESVLNNMIVKKGDRVFIDLQESEASSVIPEYGELD---------------ILFE 88

Query: 105 DSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           D+ + + NKPAGI+      G +G     IAYH        ++ +  K R  HRLDQ+TS
Sbjct: 89  DNHMLIINKPAGIATHPNEDGQTGTLANLIAYHYQ------INGETCKVRHVHRLDQDTS 142

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G +V A+ R A   L +    + +++ Y ++  G  + KK  I         IG D  H 
Sbjct: 143 GAIVFAKHRLAHAILDQQLEKKTLKRTYTAIAEGKLRTKKGTI------NPPIGRDRSHP 196

Query: 216 VKQN-EKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            ++    G   A++HFKV+   A ++   +E++  TGRTHQ+RVH   +G P+ GD  Y 
Sbjct: 197 TRRRVSPGGQTAVTHFKVMASNAKERLSLVELELETGRTHQIRVHLASLGHPLTGDSLYG 256

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHM 315
              K      + N+  LHA  +   HP    L +  AP PA M
Sbjct: 257 GGSK------LLNRQALHANKVQAVHPITDELIVAEAPFPADM 293


>gi|120603012|ref|YP_967412.1| RluA family pseudouridine synthase [Desulfovibrio vulgaris DP4]
 gi|120563241|gb|ABM28985.1| dephospho-CoA kinase / ribosomal large subunit pseudouridine
           synthase D [Desulfovibrio vulgaris DP4]
          Length = 541

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/311 (27%), Positives = 138/311 (44%), Gaps = 43/311 (13%)

Query: 18  NMRLDRWFKNHYPHINFV--NLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINAL 74
           N RLDR+      H +     +++ +R GQ  VD       + R++SGQ V +  +  A 
Sbjct: 25  NERLDRFLGEALSHTDLSREKIKRAIRDGQCTVDGTVCTTPSTRLRSGQRVELA-IAPAA 83

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
             +  E+  L                +++ D  + V +KPAG++V              +
Sbjct: 84  TAVEPEEGDL---------------TIIHRDEHLLVIDKPAGLTVHPCPSCPEGTLVHRL 128

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +H D         +G +P + HR+D++TSG+L+VA +      L+E+F  R ++K Y +
Sbjct: 129 VHHFDALRAQ----EGFRPGIVHRIDKDTSGLLLVALSEGVRLKLSEAFAERTVEKEYLA 184

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQK-FCWL 243
           LV G+P    E  A        IG    H V+    KG   A S ++V+    +  +  +
Sbjct: 185 LVHGVPPATGEVDAP-------IGRHPTHKVRMAVVKGGKPARSEWRVLHAAPEGHYALV 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-TSPIQNKLYLHARYMDLPHP-E 301
            ++ H+GRTHQ+RVH  H G P+ GD  Y               +  LHA  +   HP  
Sbjct: 238 AVRIHSGRTHQIRVHMAHAGFPLWGDQLYGPGTPARLREQGYGARQMLHAWRLAFTHPVT 297

Query: 302 GGRLQITAPLP 312
           G RL+ T P P
Sbjct: 298 GERLRFTCPPP 308


>gi|85707640|ref|ZP_01038706.1| pseudouridine synthase D large subunit [Erythrobacter sp. NAP1]
 gi|85689174|gb|EAQ29177.1| pseudouridine synthase D large subunit [Erythrobacter sp. NAP1]
          Length = 317

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 91/323 (28%), Positives = 151/323 (46%), Gaps = 44/323 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRI--PPVINALNH 76
           RLD+   +    ++   +Q ++  G V +  K V   + ++      RI  P V+ A   
Sbjct: 16  RLDKALADAT-ELSRARVQALIAEGAVEIAGKAVTSASVKVTENTPFRITVPAVVEA--- 71

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
              E +  D ++++            +ED  + V NKPAG+ V   +G   + DG L + 
Sbjct: 72  ---EAQAQDIALDVA-----------FEDEDLIVVNKPAGMVVHPAAG---NPDGTLVNA 114

Query: 137 V--DSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +    +GQ        +P + HR+D++TSG+LVVA++ AA + L   F    + + Y ++
Sbjct: 115 LLHHCRGQLSGIGGVARPGIVHRIDKDTSGLLVVAKSDAAHEGLAAQFAEHSVHRRYLAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G P   +  I N  L +S      + V+ +N     +AI+H+KV+         +E +
Sbjct: 175 CGGHPSPAEGTI-NERLGRSDANRKKMAVLPKNSSRGKHAITHYKVLKPIGAA-ALIECR 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-----YLHARYMDLPHP- 300
             TGRTHQ+RVH   +G  ++GD  Y    K     P+ ++L      LHA  +   HP 
Sbjct: 233 LETGRTHQVRVHCASIGHALLGDPIYGRTPK--VLKPLLSQLKFARQALHAAELGFIHPI 290

Query: 301 EGGRLQITAPLPAHMVKTWDSLG 323
            G  L+ +A LPA M +  D LG
Sbjct: 291 LGSELRFSADLPADMQELIDELG 313


>gi|302871828|ref|YP_003840464.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302574687|gb|ADL42478.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 303

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 91/316 (28%), Positives = 162/316 (51%), Gaps = 43/316 (13%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           RLDR+         +FV  QKI+  G V V++ +V K   +++SG ++RI         +
Sbjct: 9   RLDRYLSEVLSKTRSFV--QKIIEEGNVWVNQTQVLKPAYKVRSGDIIRI---------V 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH 128
           I E K       L+  +  +   ++YED  + V NKP G+ V  G+G         + + 
Sbjct: 58  IPEPK------QLSLVAQDIDIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHK 111

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             G L S   +   +P + HRLD++TSG+L+VA+T  A   L+E+ +  +I++IY+++  
Sbjct: 112 FSGKLSSI--NGVIRPGIVHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICE 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQP 247
           G+ K     +       + IG   V+ +K         A+++F+V++ +  K+ +++++ 
Sbjct: 170 GVLKEDSGVV------DAPIGRHPVNRLKMAVIPNGKQAVTYFEVLERY-DKYTFVKLRL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGRTHQ+RVH  ++G P++GD  Y  + K  F   IQ ++ LHA  +   HP     L 
Sbjct: 223 KTGRTHQIRVHMSYIGYPLLGDSTYGRS-KNEFG--IQGQV-LHAGEIKFVHPITSDVLH 278

Query: 307 ITAPLPAHMVKTWDSL 322
            +  LP + ++  + L
Sbjct: 279 FSTELPEYFLEILNIL 294


>gi|188994625|ref|YP_001928877.1| ribosomal large subunit pseudouridine synthase [Porphyromonas
           gingivalis ATCC 33277]
 gi|188594305|dbj|BAG33280.1| ribosomal large subunit pseudouridine synthase [Porphyromonas
           gingivalis ATCC 33277]
          Length = 365

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 91/336 (27%), Positives = 153/336 (45%), Gaps = 54/336 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V +  +  +R+D++  +   +     +Q+   +G + V+ + VK N RI+ G VV +  
Sbjct: 35  TVADPGQTLIRIDKFLVDRMNNATRSRIQQAAEAGAIFVNGRPVKSNYRIKPGDVVTL-- 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L    +E +I+   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 93  ---ELLRPRRELEIIPEDIPLD---------IVYEDDVLLVINKPAGLVVHPGHGNYTGT 140

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +AY    +L+   +     P L   HR+D++TSG+LVVA+   A   L + F  + 
Sbjct: 141 LVNALAY----YLREDPEYDPMDPSLGLVHRIDKDTSGLLVVAKRAEAKSDLCKQFYYKT 196

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-----VHVVKQNEKGANYAISHFKVI 233
             + Y +LVWG        I        +IG D      + V   +      A++H++V+
Sbjct: 197 THRSYRALVWGRFDYPIGTIT------GNIGRDLKDRLQMAVFPPDGDIGKPAVTHYQVL 250

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQNK 287
           +  A    W+E +  TGRTHQ+R H  H+G  +  D +Y  +   +GN T+     +QN 
Sbjct: 251 EELAY-VSWIECRLETGRTHQIRAHMKHIGHTLFADERYGGDQILRGNNTANYRRFVQNC 309

Query: 288 L------YLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           L       LHA+ +   HP  G  +Q  + +PA + 
Sbjct: 310 LAICPRQALHAKTLGFRHPVTGVEMQFDSDIPADLT 345


>gi|154504404|ref|ZP_02041142.1| hypothetical protein RUMGNA_01908 [Ruminococcus gnavus ATCC 29149]
 gi|153795333|gb|EDN77753.1| hypothetical protein RUMGNA_01908 [Ruminococcus gnavus ATCC 29149]
          Length = 309

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 90/331 (27%), Positives = 147/331 (44%), Gaps = 40/331 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++   E    N R+D++     P  +   +QK+++ G V V+ K+VK N ++ S  
Sbjct: 1   MREERFFTAEETVTNERIDKFLSAQMPDRSRSYIQKLIKDGLVEVNGKQVKTNYKLGSED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++      +  I+ E+  LD               +LYED+ + V NKP G+ V    
Sbjct: 61  EVKLQIPELEVPDILPEEIPLD---------------ILYEDTDLLVVNKPKGMVVHPAP 105

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + YH    L     +   +P + HR+D +T+G L+V +   A Q L E  
Sbjct: 106 GHYTGTLVNALMYHCRENLSGI--NGVMRPGIVHRIDMDTTGSLLVCKNDRAHQILAEQL 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           +   I + Y ++V G  K     +   + +  +      VH     E     A++H++V+
Sbjct: 164 KDHSITRRYEAIVHGNLKEDSGTVNAPIGRHPTDRKKMSVHAPHGRE-----AVTHYRVL 218

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHA 292
           + F   +  +E +  TGRTHQ+RVH   +G PI+GD  Y     G    P +     LHA
Sbjct: 219 ERFGN-YTHIECELETGRTHQIRVHMASIGHPILGDLVY-----GPTKCPFRLQGQTLHA 272

Query: 293 RYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
           R +   HP  G  +Q  APLP +  +    L
Sbjct: 273 RILGFVHPSTGAYVQFDAPLPEYFEELLKKL 303


>gi|157826322|ref|YP_001494042.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Rickettsia akari str. Hartford]
 gi|157800280|gb|ABV75534.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Rickettsia akari str. Hartford]
          Length = 329

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 88/329 (26%), Positives = 153/329 (46%), Gaps = 52/329 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V N+  N+RLD+        I+   +QK +++ QV V+              ++  P V+
Sbjct: 6   VPNELNNIRLDKALSQLLEKISRNQIQKAIKNSQVLVND------------VIISDPDVL 53

Query: 72  NALNHII-------KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
              N +I       +E KI   ++ L          ++YED  + V NK AG++V  G+G
Sbjct: 54  VKENDVILFAFKEPEELKIAAVNIALD---------IIYEDDDLIVINKAAGMTVHPGAG 104

Query: 125 IAYHIDGFLKSWV--------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             +H D  + + +             +P + HRLD++T+G++VVA+   A   L      
Sbjct: 105 --HHDDTLVNALLYHTKNLSDIGSAARPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQ 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R++ + Y +LVWG+       I N  + +S +    + ++K    G   A++H+K ++ F
Sbjct: 163 RQVIRKYKALVWGVINPLAGVIKNN-IGRSRVERQKMSILKY---GGKEAVTHYKTLELF 218

Query: 237 -AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSP-IQNKLY---- 289
                  +E + +TGRTHQ+RV   H+   +VGD  Y  N  K   +SP ++ KL     
Sbjct: 219 YGGTISMVECRLNTGRTHQIRVQLSHVKHSVVGDQTYGNNDRKIAHSSPALKAKLIDFKR 278

Query: 290 --LHARYMDLPHPEGGR-LQITAPLPAHM 315
             LH+ Y+   HP   + ++ +  LP  M
Sbjct: 279 QALHSWYLSFTHPTSNKIMEFSCELPRDM 307


>gi|300726252|ref|ZP_07059705.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bryantii B14]
 gi|299776449|gb|EFI73006.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bryantii B14]
          Length = 352

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 90/340 (26%), Positives = 162/340 (47%), Gaps = 53/340 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++     P+ +   +Q    +G ++V+   VK N +++   V+ +  
Sbjct: 22  VQVDEGQTPVRIDKYLAEKNPYQSRNRIQNAADAGFIQVNGTPVKSNYKVRPNDVITL-- 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L++   +  I+  ++ +          ++YED  + V NK AG+ V  G+G     
Sbjct: 80  ---MLDYPKHDTSIVAENIPID---------VVYEDDDLMVINKAAGMVVHPGAGNFTGT 127

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IAY++   L+S+ D+   +  L HR+D++TSG+LVVA+T  A   L + F  +   
Sbjct: 128 LINAIAYYLRD-LESF-DANNPEVGLVHRIDKDTSGLLVVAKTPEAKSALGKQFFNKTTH 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDC 235
           + Y +LVWG        + +    + +IG D      + V + +      A++H++V++ 
Sbjct: 186 RSYNALVWG------NIVEDEGRIEGNIGRDPKNRLRMKVFEPDSGIGKSAVTHYRVLER 239

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQN--- 286
           F      +E    TGRTHQ+R H  H+G P+  D  Y  N   +G  +S     IQN   
Sbjct: 240 FGYT-TLIECILETGRTHQIRAHMKHIGHPLFADETYGGNEVLRGQRSSSYKAYIQNCFK 298

Query: 287 ---KLYLHARYMDLPHPEGG-RLQITAPLPAH---MVKTW 319
              +  LHA+ +   HP  G +L  T+  PA    +++ W
Sbjct: 299 ICPRQALHAKTLGFIHPRTGQQLDFTSEWPADFSALIEKW 338


>gi|299144084|ref|ZP_07037164.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus sp.
           oral taxon 386 str. F0131]
 gi|298518569|gb|EFI42308.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus sp.
           oral taxon 386 str. F0131]
          Length = 304

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 94/321 (29%), Positives = 158/321 (49%), Gaps = 39/321 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V YV    + +N+R+DR+      +IN   ++K +  G + ++      N+ +++G 
Sbjct: 9   MVKVNYVC---ESDNIRIDRYLVEKL-NINRSQIKKYIDFGNILIN------NSVVKAGY 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           + +I  +I+    +  E +IL     L +  DF    ++YED  I V +KP  + V  GS
Sbjct: 59  MTKIGDIID----VSYEDEILL----LPEEIDFK---IIYEDEHIAVISKPQNLVVHPGS 107

Query: 124 GIAYH--IDGFLKSW--VDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H  ++G L  +  + + G K  P + HRLD++TSG++++A+T  A   L + F+  
Sbjct: 108 GNYNHTLVNGLLFKFKNLSNCGDKLRPGIVHRLDKDTSGLMIIAKTNLAYLKLVKDFKES 167

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +I+K Y ++V G  K  +  I N  + +       + V+ +N K    AI+ +K I  F 
Sbjct: 168 KIRKTYIAVVEG--KTDEFGIINEPIGRDPKNRKKMAVIYENSKN---AITEYKKIREF- 221

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  + +   TGRTHQ+RVH  ++  P++GD  Y     GN      +K  LHA  +  
Sbjct: 222 NNFSLISINILTGRTHQIRVHLSYIKHPVLGDLTY-----GNKNKYKIDKQMLHAYRLKF 276

Query: 298 PHP-EGGRLQITAPLPAHMVK 317
            HP  G  L     +P   VK
Sbjct: 277 NHPITGEELSFEDDIPNRFVK 297


>gi|229552260|ref|ZP_04440985.1| pseudouridylate synthase [Lactobacillus rhamnosus LMS2-1]
 gi|258539670|ref|YP_003174169.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
 gi|229314396|gb|EEN80369.1| pseudouridylate synthase [Lactobacillus rhamnosus LMS2-1]
 gi|257151346|emb|CAR90318.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
          Length = 306

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 94/326 (28%), Positives = 152/326 (46%), Gaps = 42/326 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E+ R+D+    H        +QK L+ G V V+   VK N ++ +G VV +         
Sbjct: 10  ESGRIDKIITAHETTHTRSQVQKWLQDGLVTVNGNPVKANFKVTAGDVVTV--------- 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            I E K L +       ++ +   ++YED ++ V NKP G+ V    G   H DG L + 
Sbjct: 61  TIPEVKPLKAV------AEPIPLEIVYEDDQVIVVNKPQGMVVHPAPG---HPDGTLVNG 111

Query: 137 VDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +    +        +P + HR+D++TSG+L+VA+T AA   L+   + +   + Y +LV 
Sbjct: 112 LLYHTKLPGINGVIRPGIVHRIDKDTSGLLMVAKTEAAQLSLSAQLKAKTSIREYLALVH 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQP 247
           G  K  +  I       + +G D     +Q       +A++HF+V++ F   +  ++   
Sbjct: 172 GTFKEDEGTI------DAPLGRDPRDRKRQAVVADGRHAVTHFQVLERFTN-YTLVKCIL 224

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++  P+ GD  Y        T P   + +LHA  +   HP  G+ L 
Sbjct: 225 DTGRTHQIRVHMAYIHHPVAGDPLYGP----KRTLPGHGQ-FLHAAKLGFVHPVTGKLLT 279

Query: 307 ITAPLPAHMVKTWDSL--GFKYDRNL 330
            TAP+P    KT   L  G    RN+
Sbjct: 280 FTAPVPPIFEKTLTDLRAGIDKTRNV 305


>gi|116514036|ref|YP_812942.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|116093351|gb|ABJ58504.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|325125726|gb|ADY85056.1| Pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           2038]
          Length = 304

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 78/296 (26%), Positives = 154/296 (52%), Gaps = 32/296 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++       ++   +++++++G++ V+ K+ K + ++Q   ++++  ++  L
Sbjct: 10  EESGQRLDKYLAGEMTDLSRSRIKELVQAGEILVNGKKSKVSYKVQKDDLIQV--IVLPL 67

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGF 132
             +    K+   ++ L          ++YED  + V NKP G+ V   +G   H  ++  
Sbjct: 68  EPL----KLEAENIPLD---------IVYEDKDVIVVNKPQGMVVHPAAGHPSHTLVNAL 114

Query: 133 L---KSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L   +   DS +G +P + HR+D++TSG+L+VA+  AA + L +    +  ++ Y ++V 
Sbjct: 115 LYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVH 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G    ++E   +  + ++      + VV   EKG + A++HFKV++ + Q +  +E Q  
Sbjct: 175 G-NFAEEEGTIDAPIGRNPKDRKQMAVV---EKGKS-AVTHFKVLEQY-QGYSLVECQLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           TGRTHQ+RVH  ++G P+ GD  Y        T P   + +LHA+ +    P  G 
Sbjct: 229 TGRTHQIRVHMAYIGHPLAGDPLYGP----RKTLPGHGQ-FLHAKTLGFEQPSTGE 279


>gi|294507190|ref|YP_003571248.1| Ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber M8]
 gi|294343518|emb|CBH24296.1| Ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber M8]
          Length = 379

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 78/318 (24%), Positives = 139/318 (43%), Gaps = 61/318 (19%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-----QVVRIPPVINAL 74
           R+D++    YP  +   +Q+ ++ G ++V+   VK +  ++ G     +++R PP     
Sbjct: 40  RIDKYLTRFYPEASRTKIQRAIKKGHLKVNGADVKKSYGVEPGDEIVFRLIRKPP----- 94

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
                          +    + +   +++ED  + V NKPAG+ V    G         +
Sbjct: 95  ---------------MQAEPEAIPLDVVHEDDDLLVVNKPAGMVVHPAPGHRSGTLVHAL 139

Query: 126 AYHIDGFLKSWVDSKGQ-----------------------KPRLTHRLDQETSGILVVAR 162
            +H+DG   +  D + +                       +P + HRLD+ TSG+LVVA+
Sbjct: 140 LHHVDGGEVAADDERDEVSEDEVGLSLVNALPQSPDHPVVRPGIVHRLDKGTSGLLVVAK 199

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
              A Q L E F+   + + Y ++VWG        I   + +  H     + VV  +E  
Sbjct: 200 RGRAHQPLAEQFKAHTVDRRYRAIVWGHFAPSDGTIEGAIGRDPH-HRQRMAVVPGDE-- 256

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             +A +H++ ++ +A     +E +  TGRTHQ+RVHA   G P++GD KY        T 
Sbjct: 257 GKWARTHYETVETYAHTSV-VEFELETGRTHQIRVHARAQGHPLLGDPKYGGQRVRYGTQ 315

Query: 283 PIQNKLYLHARYMDLPHP 300
             + + +    +  LPHP
Sbjct: 316 SGKRRAFYDQLFGTLPHP 333


>gi|189467632|ref|ZP_03016417.1| hypothetical protein BACINT_04022 [Bacteroides intestinalis DSM
           17393]
 gi|189435896|gb|EDV04881.1| hypothetical protein BACINT_04022 [Bacteroides intestinalis DSM
           17393]
          Length = 510

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 118/236 (50%), Gaps = 20/236 (8%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++  ++ ++ +       + K  ++YED  + V NKP+G+    G G    +    
Sbjct: 282 LQHMLQGLEVEENPMLQLPEQGYGKLKIVYEDKWLLVVNKPSGMLSVPGKGEKESVYSLA 341

Query: 134 KS-WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +  + ++ G  P + HRLD  TSG+L+VA+ +   QHL   F+   I+K+Y +L+ GI  
Sbjct: 342 RQLYPEADG--PMIVHRLDMATSGLLIVAKNKKVHQHLQAQFKNHTIRKMYIALLDGIIP 399

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +  I   +        D    V   E G   AI+H++V++    K   +   PHTGRT
Sbjct: 400 QDEGTIELPICPDPL---DRPRQVVDMEYGKP-AITHYQVLE-RRDKCTRIAFHPHTGRT 454

Query: 253 HQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           HQLRVHA H   + CPI+GD  Y    K         +LYLHA  ++  HP  GR+
Sbjct: 455 HQLRVHAAHPSGLHCPIIGDELYGRKDK---------RLYLHAESIEFTHPADGRI 501


>gi|296445496|ref|ZP_06887453.1| pseudouridine synthase, RluA family [Methylosinus trichosporium
           OB3b]
 gi|296257062|gb|EFH04132.1| pseudouridine synthase, RluA family [Methylosinus trichosporium
           OB3b]
          Length = 338

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 90/316 (28%), Positives = 146/316 (46%), Gaps = 48/316 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           V  +    RLDR+     P I   +L              R +    I+ G++   P P 
Sbjct: 18  VPPEAAGTRLDRFLAER-PEIVAASLS-------------RTRLKALIEDGRLTIGPAPT 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILL---YEDSKIYVFNKPAGISVQGGSG--I 125
            +A   +    ++  +           ++I L   +ED+ + V +KPAG+ V    G   
Sbjct: 64  RDAARKLAAGDRVSLAVPPPQPPEPQPENIPLDIRFEDAHLIVVDKPAGLVVHPAHGHES 123

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RM 176
              ++  L    DS       +KP + HR+D++TSG+LVVA+T AA + L+  F    R 
Sbjct: 124 GTLVNALLGHCGDSLSGIGGVKKPGIVHRIDKDTSGLLVVAKTDAAHKGLSRLFEDHGRS 183

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + + Y + VWG+P+  +  +   + + S I  + + VV + E+G   AI+H+++I+ F
Sbjct: 184 LGLMREYLAFVWGVPERARGTVEAPIGRHS-IQRERMAVVSE-ERG-REAITHWELIESF 240

Query: 237 ---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLY-- 289
              +   C LE    TGRTHQ+RVH  H+G P++GD  Y A FK      +P    +   
Sbjct: 241 GVVSLVACRLE----TGRTHQIRVHMAHIGHPLIGDATYGAGFKTKTALLAPAARAVVEA 296

Query: 290 -----LHARYMDLPHP 300
                LHA  +  PHP
Sbjct: 297 LGRQALHAATLGFPHP 312


>gi|194289464|ref|YP_002005371.1| 23S rRNA pseudouridine synthase [Cupriavidus taiwanensis LMG 19424]
 gi|193223299|emb|CAQ69304.1| 23S rRNA pseudouridine synthase [Cupriavidus taiwanensis LMG 19424]
          Length = 418

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 94/330 (28%), Positives = 150/330 (45%), Gaps = 36/330 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP-V 70
           V++     RLD+    H+   +   LQ+ + SG VRVD +  +  + +Q G  + + P  
Sbjct: 68  VDSASHGERLDKLLARHFSEFSRSRLQQWIESGAVRVDGQVRRPRDAVQMGNRIEVQPQA 127

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
               +    E   LD               ++YED  + V NKPAG+ V   +G      
Sbjct: 128 APEASAFAPEDVPLD---------------VVYEDDTLLVINKPAGLVVHPAAGNWSGTV 172

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           ++G L          PR  + HRLD+ETSG++VVART  A   L    + R +++ Y +L
Sbjct: 173 LNGLLHR-DPGAASLPRAGIVHRLDKETSGLMVVARTLTAQTDLVRQLQARTVKRTYIAL 231

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--FAQKFCWLE 244
           VWG  +   E   +  + +       + +V Q   G   + +HF+ +      + F  + 
Sbjct: 232 VWG--RTYDEGTIDAPIGRDPRERTRMAIV-QTASG-KPSRTHFRTLATVPLGRGFVSMV 287

Query: 245 M-QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTS-----PIQ-NKLYLHARYMD 296
           M +  TGRTHQ+RVH   +G P+VGD  Y  A  +G   +     P+   +  LHA  + 
Sbjct: 288 MCKLETGRTHQIRVHFESIGHPLVGDPVYFRATQRGQRPAIRVPLPVPYERQALHAYKLG 347

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           L HP  G+ +  TA  P  +    D+L F+
Sbjct: 348 LVHPATGKHMSWTAQPPEDLQALIDALDFE 377


>gi|312127537|ref|YP_003992411.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311777556|gb|ADQ07042.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           hydrothermalis 108]
          Length = 293

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 82/279 (29%), Positives = 144/279 (51%), Gaps = 29/279 (10%)

Query: 47  RVDKKRVKFNNRIQS-----GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI- 100
           ++ +KR+ F++ + S     GQ+  IPP I +++   +E  +++  V+L  +   +  + 
Sbjct: 18  QILQKRLFFSSTLMSRLKAHGQIRFIPP-IYSIHQYPQENAVIE--VDLISYKSNIVPVE 74

Query: 101 ----LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETS 155
               +LYED+     NKP+G+      G  +  I  +++ +++SK     + +RLD+ETS
Sbjct: 75  GSIDILYEDNFFLFVNKPSGLPSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRLDKETS 134

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+       ++  F  RR+ K Y ++V G    KK  +    +K+S  G     +
Sbjct: 135 GIVVFAKNSYFHSIVSYEFEKRRVDKTYIAIVHG-RLTKKSGLIEKPIKRSDDG-----I 188

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +  ++A ++++VID F + F  L+++P TGRTHQLRVH   +G PIVGD+ Y   
Sbjct: 189 KREIHQDGSFASTYYEVIDTF-ENFSVLKLKPITGRTHQLRVHLSSIGHPIVGDYIYGEE 247

Query: 276 FKGNFTSPIQNKLYLHARYM--DLPHPEGGRLQITAPLP 312
              N        L LHA  +  +          IT+PLP
Sbjct: 248 KTQN------TPLLLHAYSIRFNFKLINNKVYDITSPLP 280


>gi|285017490|ref|YP_003375201.1| pseudouridine synthase [Xanthomonas albilineans GPE PC73]
 gi|283472708|emb|CBA15213.1| probable pseudouridine synthase protein [Xanthomonas albilineans]
          Length = 335

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 87/329 (26%), Positives = 149/329 (45%), Gaps = 46/329 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +     R D      +P  +   L + ++SG   +D    +  + ++ G++  +  V+
Sbjct: 22  VPDHAAGRRFDAVLAELFPEYSRSRLAEWIKSGDALLDGAPARPRDPLRGGEIASLHAVL 81

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------- 124
           +   H + E   L+               +LYED ++ V NKPAG+ V  G+G       
Sbjct: 82  DTQTHALPEDIALE---------------VLYEDDQVIVLNKPAGLVVHPGAGNPGGTLV 126

Query: 125 --IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + Y   G   S +   G    + HRLD++TSG +VVART  A   L      R++ + 
Sbjct: 127 NALLYRDPGL--SALPRAG----IVHRLDKDTSGAMVVARTLQAHTALVAQLAARQVHRQ 180

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G   +     AN  + + H        V+++ + A   ++H+++ + F +    
Sbjct: 181 YLALVVGALVSG--GTANAPIDR-HPRDRLRMAVREDGRDA---LTHYRLRERF-RAHTA 233

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHARY 294
           LE +  TGRTHQ+RVH  H+  PI+GD  Y    K       P+  +L       LHA  
Sbjct: 234 LECRLETGRTHQIRVHMAHLKHPIIGDPLYGGPLKLPKGAADPLIAELRGFKRQALHAEI 293

Query: 295 MDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           ++  HP  G  +++TA +PA + +   +L
Sbjct: 294 LEFKHPLHGEPVRVTAAVPADLQRLLAAL 322


>gi|281425096|ref|ZP_06256009.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           F0302]
 gi|281400940|gb|EFB31771.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           F0302]
          Length = 377

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 92/324 (28%), Positives = 155/324 (47%), Gaps = 55/324 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++     P+ +   +Q+   SG + V+ K VK N +++ G V+ +  
Sbjct: 47  VEVDMGQTPVRIDKFLAEKNPYQSRNRIQQAADSGFIYVNDKPVKSNYKVRPGDVITL-- 104

Query: 70  VINALNH---IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +++   H   I+ E   LD               ++YED  + V NK AG+ V  G+G  
Sbjct: 105 MLDRPKHDTSIVAEDIPLD---------------IVYEDDALMVINKQAGMVVHPGAGNF 149

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  +A+H+   L+S+ D+   +  L HR+D++TSG+LVVA+T  A   L + F  +
Sbjct: 150 TGTLINAVAWHLKD-LESF-DANDPEVGLVHRIDKDTSGLLVVAKTADAKSALGKQFFNK 207

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              + Y +LVWG   + +  I   + +  K+ +    + V   +      A++H++VI+ 
Sbjct: 208 STHRSYNALVWGNLIDDEGTIEGNIARDPKNRL---RMKVFSPDSGIGKNAVTHYRVIER 264

Query: 236 FAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQN 286
           F       C LE    TGRTHQ+R H  H+G P+  D  Y      +G  +S     IQN
Sbjct: 265 FGYTTLVECILE----TGRTHQIRAHMKHIGHPLFADATYGGEQVLRGQRSSTYKAFIQN 320

Query: 287 ------KLYLHARYMDLPHPEGGR 304
                 +  LHA+ +   HP  GR
Sbjct: 321 CFKLCPRQALHAKTLGFVHPSTGR 344


>gi|332686651|ref|YP_004456425.1| ribosomal large subunit pseudouridine synthase D [Melissococcus
           plutonius ATCC 35311]
 gi|332370660|dbj|BAK21616.1| ribosomal large subunit pseudouridine synthase D [Melissococcus
           plutonius ATCC 35311]
          Length = 302

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 86/305 (28%), Positives = 144/305 (47%), Gaps = 43/305 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+         +   +Q+ L+   VRV+ K VK N ++Q        P    +  + K
Sbjct: 15  RIDKVLSEELIAYSRSQIQQWLKDSLVRVNNKVVKANYKVQ--------PADEVIIQLPK 66

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHID 130
            + ++ S  N+          ++YED  + V NKP G+ V   +G         + YHI 
Sbjct: 67  PKMMVVSPENIPLD-------IVYEDQDVVVINKPQGMVVHPSAGHFKGTMVHALLYHIK 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L S  D    +P + HR+D++TSG+L+VA+   A + L +  + + I + Y +LV G 
Sbjct: 120 D-LSSINDVI--RPGIVHRIDKDTSGLLIVAKNNQAHEALAKQLKDKTILRKYIALVHGE 176

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             +++  I +  + +S        ++K        A++HFKV++ F   +  +E+Q  TG
Sbjct: 177 VPHEQGTI-DAPIGRSKTNRKMQAIIKDGRS----AVTHFKVLEKFT-GYTLIELQLETG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           RTHQ+RVH  ++G P+ GD  Y      KG          +LHA+ +   HP    R+  
Sbjct: 231 RTHQIRVHMKYIGHPVAGDPVYGPKKTLKGEGQ-------FLHAKVLGFTHPTTHERMVF 283

Query: 308 TAPLP 312
            APLP
Sbjct: 284 EAPLP 288


>gi|189219158|ref|YP_001939799.1| pseudouridylate synthase, 23S RNA-specific [Methylacidiphilum
           infernorum V4]
 gi|189186016|gb|ACD83201.1| Pseudouridylate synthase, 23S RNA-specific [Methylacidiphilum
           infernorum V4]
          Length = 325

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 91/305 (29%), Positives = 141/305 (46%), Gaps = 29/305 (9%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           L  +L   + ++ KK +  + R+++G V+     I  +  I     + +   +L K  + 
Sbjct: 30  LSSLLNVSRNKIKKKILSGDLRLKNGAVLEPSHRIRGIEEIEIRGGLTEEIPSLPKAEEI 89

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL---------KSWVDSKGQKPRLT 147
              IL YED +I + NK  G+ V    G   H  G L         +S   S   +P + 
Sbjct: 90  ALEIL-YEDEEILIVNKQRGMVVHPSCG---HWSGTLVNSLLFHYGESLPGSSLLRPGIV 145

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKS 206
           HRLD++TSG++V+A+T  + + L   F  R +QK+Y  L     P  +    AN     S
Sbjct: 146 HRLDKDTSGVMVIAKTERSLKSLLLQFSQRTVQKVYLCLCKNRFPYLRYSFEANIHRHAS 205

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                 VH +K        A + F ++   +Q   +L+ +P +GRTHQ+RVH  H+G PI
Sbjct: 206 DRKKMAVHRLK-----GKTAETRFTLLFASSQA-SFLKCEPVSGRTHQIRVHLSHLGFPI 259

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           +GD  Y    KG    P    L LHA  + + HP  G +++  APLP    +  D   F 
Sbjct: 260 IGDPLYG---KGVRKYPF--PLLLHAYALKIEHPRSGKKIEFMAPLPQDFKEALD---FF 311

Query: 326 YDRNL 330
           Y RN 
Sbjct: 312 YGRNF 316


>gi|120598338|ref|YP_962912.1| pseudouridylate synthase [Shewanella sp. W3-18-1]
 gi|120558431|gb|ABM24358.1| Pseudouridylate synthase [Shewanella sp. W3-18-1]
          Length = 223

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 68/202 (33%), Positives = 105/202 (51%), Gaps = 8/202 (3%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP+G+      GIA H      + +     +  L HRLD  TSGI+V AR
Sbjct: 18  YKDRDLIIINKPSGL--LSNPGIAAHTYDCALTRLQRLYPETILVHRLDCATSGIMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            + A  HL   F+ R+ +K+Y + V G+  N ++ I N  +  +     Y   ++  E G
Sbjct: 76  NKKAESHLKTQFQDRQSKKVYIAEVMGLITN-EQGIINLSIAPNCEHPPYQKALQAGEAG 134

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++HF+V++   +    +E+ P TGRTHQLRVH L +G PI+GD  Y      N   
Sbjct: 135 GKSALTHFRVLE-RRKNSTLVELTPETGRTHQLRVHMLALGHPILGDEFYGDPAVIN--- 190

Query: 283 PIQNKLYLHARYMDLPHPEGGR 304
             + +L LHA+ +   HP  G+
Sbjct: 191 -AKPRLCLHAQSLRFSHPYSGK 211


>gi|323489511|ref|ZP_08094738.1| putative RNA pseudouridine synthase ylyB [Planococcus donghaensis
           MPA1U2]
 gi|323396642|gb|EGA89461.1| putative RNA pseudouridine synthase ylyB [Planococcus donghaensis
           MPA1U2]
          Length = 303

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 83/295 (28%), Positives = 141/295 (47%), Gaps = 45/295 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++ G V+V+ + VK N +++   ++ + PP +  L+       ++   +NL         
Sbjct: 37  VKEGAVKVNGETVKPNYKVRLQDIIIVTPPELEELD-------VVPEDLNLE-------- 81

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKG----QKPRLTHRLDQE 153
            ++YED  + V NKP G+ V    G A    ++G +    D  G     +P + HR+D++
Sbjct: 82  -IVYEDEDVLVVNKPKGMVVHPAPGHAKGTLVNGLMHHCTDLSGINGVVRPGIVHRIDKD 140

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDY 212
           TSG+L+VA+  AA   L +    + + + Y +LV G IP +K    A             
Sbjct: 141 TSGLLMVAKNDAAHTSLVDQLVKKTVTRKYVALVHGHIPHDKGTIQAPIARDPKE----- 195

Query: 213 VHVVKQN----EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +QN    +KG  +A++HF+V++ F   F  +E +  TGRTHQ+RVH  ++G P+VG
Sbjct: 196 ----RQNMAIVDKG-KHAVTHFRVLERFGN-FTLVECRLETGRTHQIRVHMKYIGFPLVG 249

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           D KY      +          LHA  +   HP     ++ +A  PA   +  +SL
Sbjct: 250 DPKYGPKKTMDIGG-----QALHAEVIGFNHPRTNEYMEFSAEPPAEFAELLESL 299


>gi|284037752|ref|YP_003387682.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283817045|gb|ADB38883.1| pseudouridine synthase, RluA family [Spirosoma linguale DSM 74]
          Length = 308

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 81/301 (26%), Positives = 140/301 (46%), Gaps = 34/301 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALN 75
           E   L  +     PH N  N++ +L + Q+ VD K   +FN+ ++ GQ V +        
Sbjct: 24  EPAELMAFLIAQLPHKNRNNIKSLLSNKQILVDGKVFTQFNHPLKPGQSVTV-------- 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     ++    + S +    +LYED  + V NK AG+ S+           G L 
Sbjct: 76  ----------AANRAPQTSQYRGLTILYEDQFLIVINKQAGLLSMATNKERDRTAYGILS 125

Query: 135 SWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +   +  K ++   HRLD+ETSG+++ A++    + + ES+     ++ Y +LV GIP+
Sbjct: 126 EYTKKENPKNKIFIIHRLDRETSGVMMFAKSEKVQRLMQESWNATTKERTYVALVEGIPE 185

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +  I ++L +   +    +    QN      +I+++ V       +  LE++  TGR 
Sbjct: 186 PPQGTITSYLRESKAL----IVYSSQNPDTGQLSITNYTVTKT-GNGYALLELELETGRK 240

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           +Q+RVH   +G P+ GD KY A      + PI  +L LHA  +   HP  G  ++  AP+
Sbjct: 241 NQIRVHMQDIGHPVAGDEKYGAE-----SDPI-GRLGLHAEVLAFEHPITGVPMRFDAPI 294

Query: 312 P 312
           P
Sbjct: 295 P 295


>gi|254423656|ref|ZP_05037374.1| pseudouridine synthase, RluA family [Synechococcus sp. PCC 7335]
 gi|196191145|gb|EDX86109.1| pseudouridine synthase, RluA family [Synechococcus sp. PCC 7335]
          Length = 309

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 88/309 (28%), Positives = 138/309 (44%), Gaps = 44/309 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDRW  ++    +   +Q+++  G V V+ +       + +     I  V  A  + + 
Sbjct: 14  RLDRWLADNVEAFSRNRVQQLIEQGAVSVNGEVCDRKKELVTAGDYIILSVPEAQPYELT 73

Query: 80  EQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----- 133
            + I LD               +LYED ++ + NKPAG+ V    G   H  G L     
Sbjct: 74  PEDIPLD---------------ILYEDDQLLIVNKPAGMVVHPAPG---HATGTLVHALL 115

Query: 134 ----KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               +      G Q+P + HRLD+ T+G +VVA+T  A  +L +  + +  ++ Y  +V 
Sbjct: 116 FYCGEQLTGVGGVQRPGIVHRLDKNTTGAMVVAKTETALCNLQQQIQAKTAKREYLGIVN 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQN----EKGANYAISHFKVIDCFAQKFCWLE 244
           G PK ++  I         IG    H  K +    E G   AI+H+K ++     +  + 
Sbjct: 176 GAPKAEQGTI------DQPIGRHPKHRKKMSILPVESGGRTAITHWKTVERLG-NYTLIH 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
            Q  TGRTHQ+RVH+ ++G PI+GD  Y +        P Q    LHA  + L HP    
Sbjct: 229 FQLETGRTHQIRVHSAYLGLPIIGDPDYGSTRFPGVKLPGQ---ALHAFRLTLSHPITQA 285

Query: 304 RLQITAPLP 312
            +   APLP
Sbjct: 286 VVSAEAPLP 294


>gi|58697309|ref|ZP_00372669.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Drosophila simulans]
 gi|225630832|ref|YP_002727623.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia sp. wRi]
 gi|58536323|gb|EAL59813.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Drosophila simulans]
 gi|225592813|gb|ACN95832.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia sp. wRi]
          Length = 276

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 89/273 (32%), Positives = 139/273 (50%), Gaps = 46/273 (16%)

Query: 69  PVINALNHIIK--EQKIL-----DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           P+IN  +HI+K  E+ I+     D S ++  + D +K  ++YED  I V +K +G++V  
Sbjct: 7   PIINN-DHIVKPGEEYIVHLVQPDISTSIEPNYD-IKLDIVYEDEDIIVLSKQSGLTVHP 64

Query: 122 GSGIAYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G+G     D  L + +   G+      +P + HRLD++TSG++V+A+   A   L+E   
Sbjct: 65  GAGTNN--DTLLNAVIAHLGKIPYSHVRPGIVHRLDKDTSGLMVIAKNEEAHGFLSELLS 122

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF---KV 232
            R+I++ Y ++VWGI  +++  I   +  K     + + V K   K    AI+H+   KV
Sbjct: 123 NRKIKREYLAIVWGILSSQQGTIKTNIAPKRG-NKEMMCVTKITGK---LAITHYLVQKV 178

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------------FKGNF 280
           I   +   C LE    TGRTHQ+RVH  H+G  IVGD  Y  N            F  NF
Sbjct: 179 IGQVSLVKCTLE----TGRTHQIRVHMSHIGHSIVGDQVYGKNSSKSTKYAKNSSFIRNF 234

Query: 281 TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
                N+  LHA  + L HP+  G ++  + LP
Sbjct: 235 -----NRQALHAYTLGLYHPKSKGYMEFVSDLP 262


>gi|224536385|ref|ZP_03676924.1| hypothetical protein BACCELL_01259 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224521998|gb|EEF91103.1| hypothetical protein BACCELL_01259 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 357

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 90/346 (26%), Positives = 158/346 (45%), Gaps = 47/346 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ I  
Sbjct: 33  VVVDRGQEMMRVDKYLFDRLTNASRNRIQKSAEAGFVMANNKPVKSSYKVKPMDVITI-- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 91  ---MMDRPRYENEVIPEDIPLN---------IIYEDKYLMVVNKPAGLVVHPGHGNYQGT 138

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 139 LVNAIAWH----MKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGMQFFNKT 194

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LVWG  +  +  I   + +      D + +    +    +A++H++V++    
Sbjct: 195 TKRRYRALVWGTVEQDEGTITGNIGRNPR---DRMQMTVLPDDQGKHAVTHYRVLERLGY 251

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN---------- 286
               +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           
Sbjct: 252 -VTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCP 310

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS-LGFKYDRNL 330
           +  LHA  +   HP  G  +  T+ +P  M    D   G+  +R+L
Sbjct: 311 RQALHAMTLGFVHPATGEEMYFTSEMPEDMTLLIDKWRGYISNRDL 356


>gi|113867448|ref|YP_725937.1| pseudouridylate synthase, 23S RNA-specific [Ralstonia eutropha H16]
 gi|113526224|emb|CAJ92569.1| pseudouridylate synthase, 23S RNA-specific [Ralstonia eutropha H16]
          Length = 396

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 93/330 (28%), Positives = 149/330 (45%), Gaps = 36/330 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V++     RLD+    H+   +   LQ+ + SG VRVD    +  + +Q G  + I P  
Sbjct: 49  VDSASHGERLDKLLARHFSEFSRSRLQQWIESGAVRVDGHVRRPRDAVQMGNRIEIQPQA 108

Query: 72  NALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
              +     + + LD               ++YED  + V NKPAG+ V   +G      
Sbjct: 109 APESSAFSPEDVPLD---------------VVYEDDTLLVINKPAGLVVHPAAGNWSGTV 153

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           ++G L          PR  + HRLD+ETSG++VVAR+  A   L    + R +++ Y +L
Sbjct: 154 LNGLLHR-DPGAALLPRAGIVHRLDKETSGLMVVARSLTAQTDLVRQLQARTVKRTYIAL 212

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--FAQKFCWLE 244
           VWG  +   E   +  + +       + VV  +      + +HF+ +      + F  + 
Sbjct: 213 VWG--RTYDEGTIDAPIGRDPRERTRMAVV--HTASGKPSRTHFRTLATVPLGRGFVSMV 268

Query: 245 M-QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGN---FTSPIQ---NKLYLHARYMD 296
           M +  TGRTHQ+RVH   +G P+VGD  Y  A  +G      +P+     +  LHA  + 
Sbjct: 269 MCKLETGRTHQIRVHFESIGHPLVGDPAYFRATQRGQRPAVRAPLPVPYERQALHAYQLG 328

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           L HP  G R+  TA  P  +    D+L F+
Sbjct: 329 LVHPATGKRMSWTAQPPQDLQALIDALDFE 358


>gi|149923941|ref|ZP_01912327.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
 gi|149815173|gb|EDM74722.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
          Length = 324

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 90/330 (27%), Positives = 148/330 (44%), Gaps = 50/330 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPH------INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +V+  D    RLD+   + +        ++   L +   +G+VR+  ++VK + R+++  
Sbjct: 5   LVLGEDAIGQRLDKALVDAFARSEAHESLSRSQLARAFAAGEVRIAGRKVKASFRLEAAG 64

Query: 64  V---VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           V   +R+P     L H   E      ++ LT         +++ED+ + V +KPAG+ V 
Sbjct: 65  VCVELRVP-APAPLAHARPE------AIPLT---------VVHEDASLLVLDKPAGMVVH 108

Query: 121 GGSG-------------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
            G G             +  H D  L     +  ++P + HRLD++TSG++V AR   A 
Sbjct: 109 AGPGHDSGTLVNAVLHHLQVHADA-LPVLPGNGPERPGVVHRLDKDTSGLIVFARGLRAQ 167

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK-QNEKGANYA 226
             L E FR   I + Y  +V G P  ++       L+ +H G D     +   ++G   A
Sbjct: 168 TVLAEQFRDHSIDRAYLGVVLGRPSFERRR-----LETTH-GRDPADRRRFAPDQGTRRA 221

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++  +V+               TGRTHQ+R+HA  +G PI  D  Y    K      + +
Sbjct: 222 VTTMEVLRPLGAHAALARFTLETGRTHQIRMHARMVGHPIFADPLYGRRPKHPALRRLAD 281

Query: 287 KL---YLHARYMDLPHPEG-GRLQITAPLP 312
            L    LHA  +   HP+G GRL + APLP
Sbjct: 282 GLGRHALHAALLGFAHPDGSGRLVLEAPLP 311


>gi|126733181|ref|ZP_01748928.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           CCS2]
 gi|126716047|gb|EBA12911.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           CCS2]
          Length = 341

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 92/344 (26%), Positives = 145/344 (42%), Gaps = 60/344 (17%)

Query: 20  RLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L K++  G V VD   V    +RI  G VV +   +   +
Sbjct: 17  RLDKALGRDVPDDASLSRSRLAKLIAEGAVSVDGAVVTDPRHRIAEGSVVEVTVAMAEES 76

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--------Y 127
           HI+ E   LD               +++ED  + V NKPAG+ V    G           
Sbjct: 77  HIVGEDIPLD---------------VVFEDDDLIVVNKPAGMVVHPAPGTPNGTLVNALI 121

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           H  G   S V    ++P + HR+D+ET+G+LV A++  A  HL + F    +++ Y ++ 
Sbjct: 122 HHCGETLSGVGGM-KRPGIVHRIDKETTGLLVAAKSDRAHHHLADQFAAHTVERRYLAVC 180

Query: 188 WGIPKNKKECI----------ANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVID- 234
           +G+P      +           N L  ++ +G       +Q  +     +A++  ++++ 
Sbjct: 181 YGLPDQNDPRLRGIKGTSFEPGNILKIQTFLGRHRTDRQRQAVSFTAGRHAVTRSRIVEG 240

Query: 235 -----CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNF 280
                C A   CWLE    TGRTHQ+RVH  H G  ++GD  Y    K         G  
Sbjct: 241 LGNPACAALIECWLE----TGRTHQIRVHMAHCGHALIGDPVYGGRRKLSQKAIGEVGVE 296

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                ++  LHA  +   HP  G  LQ  A +P  M     +LG
Sbjct: 297 AVAAFSRQALHAATLGFEHPVSGEFLQFEAEIPQDMRDLLRALG 340


>gi|255037524|ref|YP_003088145.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
 gi|254950280|gb|ACT94980.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
          Length = 243

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 74/206 (35%), Positives = 102/206 (49%), Gaps = 15/206 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
           ++YED+ + + NK  GI VQ   +G A  +D  +K ++     KP        HRLD+  
Sbjct: 8   VVYEDNHLIIVNKEPGILVQADVTGDACLLD-LVKDYIKEAYNKPGAVFLGTVHRLDRPV 66

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V ART  A + + E FR R +QK YW++V   P  KK  + +WL K         H
Sbjct: 67  SGLVVFARTSKALERMNEIFRKRDVQKTYWAVVKNKPAEKKGKLVHWLTKNEARNVTTAH 126

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              +   G+  A   ++ +     KF  LE+ P TGR HQ+RV    M CPI GD KY  
Sbjct: 127 --DEEVPGSQRAELSYRWVGEI-NKFHLLEVMPVTGRPHQIRVQLASMNCPIRGDVKY-G 182

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
             KGN    I     LHAR +   HP
Sbjct: 183 YPKGNPDGSIN----LHARRLYFEHP 204


>gi|325106295|ref|YP_004275949.1| ribosomal large subunit pseudouridine synthase D [Pedobacter
           saltans DSM 12145]
 gi|324975143|gb|ADY54127.1| ribosomal large subunit pseudouridine synthase D [Pedobacter
           saltans DSM 12145]
          Length = 235

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 72/220 (32%), Positives = 114/220 (51%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +    K AG  VQ        +D  +KS++  K +KP      + HRLD+  S
Sbjct: 13  ILYEDNHLIAIYKKAGWIVQVDDTGDLSLDEMVKSYIAEKYKKPNGAFLGVVHRLDRPVS 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYV 213
           G+++ A+T  A   + + F+ R + K YW++V   P      + +WL+K  + +I   Y 
Sbjct: 73  GVILFAKTSKALDRVNKMFKEREMHKTYWAVVKNKPSKMSGNLVHWLVKNPRKNITTAYN 132

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V   ++    A  +FKVI      +  +E+ P TGR HQ+RV    +G PIVGD+KY 
Sbjct: 133 QEVPNGQR----AELNFKVIGHIDGYYV-IEVDPITGRPHQIRVQMASLGSPIVGDNKYG 187

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              +G+ T  I     LHA+ ++  HP +  ++ I APLP
Sbjct: 188 YP-RGSRTKSIS----LHAKRLEFIHPVKKEKIVIEAPLP 222


>gi|291239041|ref|XP_002739435.1| PREDICTED: hypothetical protein [Saccoglossus kowalevskii]
          Length = 467

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 72/254 (28%), Positives = 122/254 (48%), Gaps = 34/254 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG---FLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++Y+   +   +KP G+   GG  I  +++     L   +D    K  L HRLD+ET+G+
Sbjct: 211 IIYDHDDVIAIDKPYGLPSHGGPTITNNVNDTLTILAKLIDKSLPKLYLVHRLDKETTGV 270

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-----------ANWLLKKS 206
           +++A++   A+ L   FR + + K YW L  G+P+  +  +            N +L + 
Sbjct: 271 MLLAKSEIIAKQLNALFRKKMVIKRYWVLTVGVPEPSEGVVDIPMEEGEVAGKNRMLLRP 330

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVH-ALHMGC 264
             G  Y +++K +      A+++FKV+   ++  C L E+QP TG  HQ+R H A  +GC
Sbjct: 331 DYGLVYKNLIKSSSGKGATALTNFKVL--ASEGNCALVELQPETGIKHQIRCHLASGLGC 388

Query: 265 PIVGDHKYC-------ANFKGNFTSPIQNK--------LYLHARYMDLPHPEGGR-LQIT 308
           PI+GDHKY            G+    +  +        ++LHA+ + +P    GR L I+
Sbjct: 389 PILGDHKYSHHDKLAPQKLPGDMLQRLNIRQAKVRTVPMHLHAKQLIIPQFRDGRNLFIS 448

Query: 309 APLPAHMVKTWDSL 322
             LP    K    L
Sbjct: 449 TKLPEFFKKNMTRL 462


>gi|125624328|ref|YP_001032811.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. cremoris MG1363]
 gi|124493136|emb|CAL98100.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. cremoris MG1363]
 gi|300071111|gb|ADJ60511.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. cremoris NZ9000]
          Length = 301

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 86/316 (27%), Positives = 155/316 (49%), Gaps = 47/316 (14%)

Query: 11  VVENDEEN--MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           +++  EEN  +RLD+   N   +   + L +++++ +V V+ +  K   ++++G  ++  
Sbjct: 3   IIKITEENKDLRLDKALANQTEYSRSL-LTELIKNDKVFVNNEAKKAKYKVKTGDRIQFE 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
                    I + ++LD        ++ L   ++YEDS + V NKP G+ V   +G    
Sbjct: 62  ---------IPQAEVLDVV------AEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASG 106

Query: 125 -----IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                I YHI    K      G  +P + HR+D++TSG+L++A+   A + L    + + 
Sbjct: 107 TLVNAIMYHI----KDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKT 162

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFA 237
            ++ Y ++V G   N K  I      ++ IG +     KQ    G   A++HF+V++ F 
Sbjct: 163 SKRRYLAIVHGELANDKGTI------EAPIGRNLKDRKKQAVVSGGKPAVTHFEVLEGFV 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  + ++  TGRTHQ+RVH  ++G P+ GD  Y  N      +P + + +LHA  +  
Sbjct: 217 -GYTLIALRLETGRTHQIRVHMHYIGHPVAGDPLYGPN---KTLTPNKGQ-FLHAETLGF 271

Query: 298 PHPEGGRL---QITAP 310
            HP  G L   Q+ AP
Sbjct: 272 EHPTSGELMEFQVDAP 287


>gi|330814384|ref|YP_004358623.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Pelagibacter sp. IMCC9063]
 gi|327487479|gb|AEA81884.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Pelagibacter sp. IMCC9063]
          Length = 327

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 95/347 (27%), Positives = 160/347 (46%), Gaps = 65/347 (18%)

Query: 4   MTYVQYVVVENDEENM-RLDRWFKNHYPHINFVNLQKILRSGQVRVD-------KKRVKF 55
           MT  +Y    ++E+N+ R+D++     P  +   + K+++ G + ++        K+V F
Sbjct: 1   MTDKKYKFTVSEEQNLKRVDQFIVEELPTFSRTKISKLIKEGALLINNEPIEERSKKVSF 60

Query: 56  NNRIQSGQVVRIP-PVINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
            + ++    + +P PV   L    K Q I LD               ++YED  + V NK
Sbjct: 61  GDEVE----LSVPEPVPTDL----KPQNIPLD---------------VVYEDDDLLVINK 97

Query: 114 PAGISVQGGSGIAYHIDGFL---------KSWVDSKGQ-KPRLTHRLDQETSGILVVART 163
           P G+ V  G+G   + DG L         ++     G+ +P + HR+D++TSG+LVVA+ 
Sbjct: 98  PIGMVVHPGAG---NPDGTLVNALLHHCKENLSGINGELRPGIVHRIDKDTSGLLVVAKN 154

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
             A   L + F    IQ+ Y + VWG+PK     I   + +       Y       E G+
Sbjct: 155 DIAHNVLAKQFEDHSIQRTYLAFVWGMPKPIHGRIETLIGRSK-----YNRQKMSAEVGS 209

Query: 224 NY-AISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY------ 272
              AI+++K ++ F  K       +E +  TGRTHQ+RVH  H G PI+GD  Y      
Sbjct: 210 GKDAITNYKTLEVFKGKTIPDISLIECRLETGRTHQIRVHLAHQGNPILGDQMYGKKVRK 269

Query: 273 CANFKGNFTSPIQNKLY--LHARYMDLPHPEGGR-LQITAPLPAHMV 316
             +     +  ++N  +  LHA+ +   HP+  + L  T  LP  ++
Sbjct: 270 IRDLDEQLSILLENINFQALHAQSLGFLHPKSDKELFFTTELPKDLL 316


>gi|304389307|ref|ZP_07371272.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii subsp. curtisii ATCC 35241]
 gi|304327425|gb|EFL94658.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii subsp. curtisii ATCC 35241]
          Length = 304

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 87/290 (30%), Positives = 140/290 (48%), Gaps = 28/290 (9%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +L SG V  D + +K ++++ +G ++ I   I      + E   +D   NL         
Sbjct: 34  LLESGAVIQDGETLKKSDQLAAGNLLEID--IPEPTGYVPEATRVD---NLG-------- 80

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQE 153
            +LY D  + V +KPAG++   G G     + G L++    V + G   R  + HRLD  
Sbjct: 81  -ILYADDDLVVVDKPAGVAAHTGPGWEGPTVVGALRAAGIRVSTSGPVEREGIVHRLDAG 139

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG +VVA++  A   L   FR  R++KIY +L  G  K     I   + +    G ++ 
Sbjct: 140 TSGAMVVAKSELAYGKLKNEFRYHRVEKIYTALATGKVKPPVGTIDAPIGRAP--GREFK 197

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V     G   A++H+ +I+        L++Q  TGRTHQ+RVH   +G P+VGD +Y 
Sbjct: 198 MAVVS---GGKPAVTHYDIIEEL-PGATLLKVQLETGRTHQIRVHLAAIGHPLVGDTEYG 253

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A+ K      ++ + +LHA  +   HP  G  + + APLPA +    + L
Sbjct: 254 ADRKTAARLGLERQ-WLHASRLAFKHPRTGLEVAVQAPLPADLATAVELL 302


>gi|313901894|ref|ZP_07835313.1| ribosomal large subunit pseudouridine synthase D [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467835|gb|EFR63330.1| ribosomal large subunit pseudouridine synthase D [Thermaerobacter
           subterraneus DSM 13965]
          Length = 321

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 90/327 (27%), Positives = 145/327 (44%), Gaps = 48/327 (14%)

Query: 11  VVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV       RLD +        +    +Q+++RS +V V+ +  + + R++ G+ V I  
Sbjct: 18  VVPGSAAGERLDVFLAEQDGLDLTRSAIQRLIRSHRVWVNGRTARPSRRLEPGEEVVIEL 77

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
              A + ++ E   LD               ++YED  + V NKP G  V    G   H 
Sbjct: 78  PEPAPSGVVPEALPLD---------------VVYEDPDVVVLNKPRGWVVHPAPG---HP 119

Query: 130 DG-----FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G      L  + + +G     +P + HRLD++T+G+LVVAR+  A + L    + RR+ 
Sbjct: 120 QGTLANALLARYPEMEGVGGPGRPGIVHRLDRDTTGLLVVARSPLAYRELVRQIKERRVH 179

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQ 238
           + Y +LV G P+ ++  +      ++ IG       +      G   A +HF V++   +
Sbjct: 180 REYLALVRGWPEVREGTV------EAPIGRHPADRTRMTVLTTGGRPARTHFAVVEQVGR 233

Query: 239 KF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARY 294
                CWL+    TGRTHQ+RVH   +G P+ GD  Y     +G      Q    LHA  
Sbjct: 234 YTLLRCWLD----TGRTHQIRVHLAFIGLPVAGDPVYGGRRAQGELGLEGQA---LHATR 286

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWD 320
           +   HP  GR +  T P PA  +   +
Sbjct: 287 LAFAHPRDGRPMDFTVPPPADFLAALE 313


>gi|298507387|gb|ADI86110.1| RNA pseudouridine synthase, RluA family [Geobacter sulfurreducens
           KN400]
          Length = 296

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 78/324 (24%), Positives = 144/324 (44%), Gaps = 46/324 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPV 70
           V  D+  +RLD      +P ++   ++ I+  G   V    V+  + R+Q+G  + +   
Sbjct: 7   VGADQAGVRLDEGAARLFPQLSKTRIRTIIDWGGCAVGGTMVRVASRRLQAGDEIVL--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 +++ ++  +  + L          +L+ED+     NK +G++ Q      Y + 
Sbjct: 64  -----GVMEPERYRE--ITLAPED------ILFEDAGYLAVNKASGLNCQR---TPYQLK 107

Query: 131 GFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G ++  V          +  R+ HRLD+ TSG+++   +R AA H++   +  R++K+YW
Sbjct: 108 GTVEYAVTLHFRACGSAEPARVIHRLDRGTSGVMIFPASRRAAAHISRELKEGRVEKVYW 167

Query: 185 SLVWGIPKNKKECIANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           +LV G+P        +W +    + +G     V    +     A++ F+V+         
Sbjct: 168 ALVAGMPLAD-----SWQVDAPVAKVGTSRYGVAPVGKA----ALTEFRVV-ARGNGATL 217

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +P TGRTHQ+RVH  H G  I+GD  Y     G   +P   ++ LH R M     +G
Sbjct: 218 VEARPRTGRTHQIRVHLAHGGLSIIGDTTY-----GGIAAP---RMMLHCRTMTFRAEDG 269

Query: 303 GRLQITAPLPAHMVKTWDSLGFKY 326
             +  TAP         +  G ++
Sbjct: 270 RPVSATAPPDREFTAACEQHGIQF 293


>gi|229829077|ref|ZP_04455146.1| hypothetical protein GCWU000342_01162 [Shuttleworthia satelles DSM
           14600]
 gi|229792240|gb|EEP28354.1| hypothetical protein GCWU000342_01162 [Shuttleworthia satelles DSM
           14600]
          Length = 306

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 85/324 (26%), Positives = 144/324 (44%), Gaps = 43/324 (13%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +E  +R+DR+  +H    +  ++QK++  G V V+    + + ++Q    + +      
Sbjct: 10  GEESGLRIDRYLADHLDGQSRNSIQKLIEEGLVLVNGNACRASYKLQEKDQIFVSVPDAV 69

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
           L  +  E+  LD               +LYED ++ + NKP  + V    G         
Sbjct: 70  LTELRPERIPLD---------------ILYEDDQLLIVNKPKEMVVHPAPGHNTGTLVNA 114

Query: 125 IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           I YH     K      G+ +P + HR+D  T+G L+V +T AA + +    +   + ++Y
Sbjct: 115 IMYHCG---KELSGINGEIRPGIVHRIDMNTTGSLIVCKTDAAHRFIASQIKEHSVHRVY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFC 241
            ++V+G     +  I      ++ IG D     K +   K    AI+H++ +      F 
Sbjct: 172 RAIVYGHLNPTEGTI------RTSIGRDPRDRKKMSVGVKNGRQAITHYRELARLRNNFS 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
           ++E +  TGRTHQ+RVH   +G PI+GD  Y     G   SP   +   LHA  +   HP
Sbjct: 226 YVEFELETGRTHQIRVHMASIGHPILGDQVY-----GPKKSPYHLDGQTLHAMTIGFVHP 280

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
              R ++ TAPLP +       LG
Sbjct: 281 TSKRYVEFTAPLPEYFQHLLAILG 304


>gi|261856619|ref|YP_003263902.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261837088|gb|ACX96855.1| pseudouridine synthase, RluA family [Halothiobacillus neapolitanus
           c2]
          Length = 340

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 91/328 (27%), Positives = 155/328 (47%), Gaps = 43/328 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   +Q  ++SG++ +D +  +    +  G+ V +   I      + 
Sbjct: 17  RLDQALAKCWPDYSRSRIQDWIKSGEILLDGEVARPRATVLGGESVELLAEIEEAVAAVP 76

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-- 137
           +   LD               ++YED  I V NK   I V   +G   + DG L + +  
Sbjct: 77  QDIPLD---------------IIYEDDAIIVLNKSPDIVVHPAAG---NPDGTLVNALLF 118

Query: 138 --DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              S    PR  + HRLD++TSG++VVA+T AA + L E+   R+I++ Y ++V G    
Sbjct: 119 HDPSLVSVPRAGVVHRLDKQTSGVMVVAKTLAAHKILVENLAARKIRREYDTVVMG---- 174

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQPHTGRT 252
               +A   +    IG       +Q        A++H++V+  + ++  WL +Q  TGRT
Sbjct: 175 --HVVAGGTVDAP-IGRHPRDRQRQAVTATGKRAVTHYRVLQHYGEQ-TWLRVQLETGRT 230

Query: 253 HQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKL------YLHARYMDLPHP-EGG 303
           HQ+RVH  H+  P++GD  Y          ++ + + L       LHARY+ L HP  G 
Sbjct: 231 HQIRVHMAHIRHPVIGDPVYGGRPRIPPRASTALIDVLRHFERQALHARYLTLAHPVTGT 290

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNLY 331
           +++  AP+P  M +   +L  +Y  NL+
Sbjct: 291 QMRFEAPMPDDM-RELIALLTEYRDNLH 317


>gi|125604035|gb|EAZ43360.1| hypothetical protein OsJ_27960 [Oryza sativa Japonica Group]
          Length = 509

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 89/343 (25%), Positives = 152/343 (44%), Gaps = 75/343 (21%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD---FLKSILLYEDSK 107
           K++K N+ ++ G  + +P  ++     IK++     +  L  + D   +L+ +++++DS 
Sbjct: 162 KKIKHNDVMEPGMRIHLP--VSVAEGEIKKRYETIPTATLHPNKDEIEYLRRLVIHKDSA 219

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAA 166
           I V NKP  + ++G   +   +D    + +    ++ P+L HRLD+E+SG+L+  RT+ +
Sbjct: 220 ILVLNKPPKVPMKGNLPVHNSMDVLAAAALSYGNEEGPKLVHRLDRESSGLLLFGRTKES 279

Query: 167 AQHLTESFRMRRIQKI---------------YWSLVWGIPKNKKECIANWLLKKSHIGGD 211
              L   F    + K                YW+LV G PK ++  I+  L K     G 
Sbjct: 280 FTRLHWLFTSVNLAKTNSQVWNAACEAYMQRYWALVIGTPKEREGIISAPLSKVLLDDGK 339

Query: 212 YVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIV 267
              V+  +  G   A  A++ ++V+        W+E++P TGR HQLRVH A  +G PIV
Sbjct: 340 AERVILAHPSGIDGAQEAVTAYRVMGPTIHGCSWIELRPLTGRKHQLRVHCAEALGTPIV 399

Query: 268 GDHKYC------------ANFKGNFTSPIQNK------------------LYLHARYMDL 297
           GD+KY              +F+     P + +                  L+LH R M +
Sbjct: 400 GDYKYGWFVHQRWKQNPQPDFEPFTGEPYKLRRPEGLEIQKGSVLSKVPLLHLHCREMVI 459

Query: 298 P------------HPEGGR--------LQITAPLPAHMVKTWD 320
           P            H  G          L+  AP+PAHM  +W+
Sbjct: 460 PNIAKFLSSNGEWHENGAPWSKEKPNLLRFIAPMPAHMKISWN 502


>gi|148261702|ref|YP_001235829.1| RluA family pseudouridine synthase [Acidiphilium cryptum JF-5]
 gi|146403383|gb|ABQ31910.1| ribosomal large subunit pseudouridine synthase D [Acidiphilium
           cryptum JF-5]
          Length = 332

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 88/326 (26%), Positives = 138/326 (42%), Gaps = 45/326 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+  +    ++   L+ ++ +G V  D            G V+R+P        I  
Sbjct: 24  RLDRFLASRLSEMSRSRLKALIEAGTVTCD------------GAVIRLPSAAVRPGAIYT 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL------ 133
                  ++        L   +LYEDS + V +KPAG+ V    G   + DG L      
Sbjct: 72  VALP--PAIPAAPQGQALDLTVLYEDSDLIVIDKPAGLVVHPAPG---NPDGTLVNALIA 126

Query: 134 ---KSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               S     G++ P + HRLD++TSG++V A+T  A   L+ +F  R + + Y +L WG
Sbjct: 127 HCGDSLAGIGGERRPGIVHRLDKDTSGVMVAAKTELALNALSAAFAARDLDREYLALCWG 186

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQP 247
            P+  +  I      +  IG D     +     +G   A+++++ +  F      L  + 
Sbjct: 187 APQPAEGEI------EGPIGRDPRDRKRMAVVARGGKPALTYYRTLRRFGLGATLLACRL 240

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLY------LHARYMDLP 298
            TGRTHQ+RVH    G P+VGD  Y             P ++ L       LHA  +   
Sbjct: 241 ATGRTHQIRVHLASRGHPLVGDPVYLRRRPAAASQMQQPQRDFLLDFPRQALHAATLGFA 300

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLG 323
           HP  G +L+  A  PA +      LG
Sbjct: 301 HPRSGAKLRFEAAPPADLATLLSHLG 326


>gi|326791366|ref|YP_004309187.1| pseudouridine synthase [Clostridium lentocellum DSM 5427]
 gi|326542130|gb|ADZ83989.1| pseudouridine synthase, RluA family [Clostridium lentocellum DSM
           5427]
          Length = 304

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 85/317 (26%), Positives = 150/317 (47%), Gaps = 33/317 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           N E   R+D++    +P      +QK +  G + V++K +  N++ Q          + A
Sbjct: 10  NSEAKGRVDKYLAEVFPEYTRSFIQKQIEKGGILVNQKVI--NSKYQ----------VKA 57

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
            +HII     +   + +    + +   ++YED  + + NKP  + V    G      ++G
Sbjct: 58  DDHIIM---TIPDPIEVDIIPEPIDIEIVYEDDDLMIVNKPQDMVVHPAPGNYSGTLVNG 114

Query: 132 FLKSWVDS----KGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            L    D      G+ +P + HR+D++TSG+L++A+   A   L+E  +   I + Y ++
Sbjct: 115 LLYHCKDKLSGINGEIRPGIVHRIDKDTSGLLMIAKNDKAHLGLSELLKDHHITRKYHAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G  K  +  I   + + +        V     +   YA + +KV++ F Q F ++E+ 
Sbjct: 175 VYGGFKEDEGTIEEPIGRSTQDRKKMAIV-----RDGRYAKTDYKVLERFKQ-FTYIELT 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
            HTGRTHQ+RVH  H+G P++GD  Y    K +F     NK  LHA+ +   HP     +
Sbjct: 229 LHTGRTHQIRVHMKHIGHPLLGDPVYGPT-KMSFGI---NKQMLHAKVIGFTHPITHKEM 284

Query: 306 QITAPLPAHMVKTWDSL 322
              + LP + V+  D L
Sbjct: 285 YFESELPDYFVRVIDKL 301


>gi|218899046|ref|YP_002447457.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
 gi|228902397|ref|ZP_04066552.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis IBL 4222]
 gi|228966845|ref|ZP_04127889.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar sotto str. T04001]
 gi|218543499|gb|ACK95893.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
 gi|228792944|gb|EEM40502.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar sotto str. T04001]
 gi|228857254|gb|EEN01759.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis IBL 4222]
          Length = 302

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 86/306 (28%), Positives = 145/306 (47%), Gaps = 39/306 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALN 75
           +N R+D++        +   +Q+ ++   V V+ K VK N +++    + +  P   AL+
Sbjct: 14  KNERIDKFVAGINNEWSRSQVQQWIKDDVVTVNGKAVKVNYKVKEEDEITVTIPDPEALD 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                  I    +NL          + YED+ + V NKP G+ V    G      ++G +
Sbjct: 74  -------IQPEDMNLE---------IYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLM 117

Query: 134 KSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y ++V G
Sbjct: 118 HHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHG 177

Query: 190 IPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +  + K  I       + IG D      +  +E G N A++HF+V++ F + F  +E + 
Sbjct: 178 VIPHDKGTI------DAPIGRDKKERQSMTVDENGKN-AVTHFQVLERF-KDFTLVECRL 229

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  +   HP  G  +Q
Sbjct: 230 ETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDMNGQALHAGILGFDHPRTGEYIQ 284

Query: 307 ITAPLP 312
             AP+P
Sbjct: 285 FEAPIP 290


>gi|148259875|ref|YP_001234002.1| pseudouridine synthase [Acidiphilium cryptum JF-5]
 gi|146401556|gb|ABQ30083.1| pseudouridine synthase [Acidiphilium cryptum JF-5]
          Length = 224

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 61/183 (33%), Positives = 92/183 (50%), Gaps = 6/183 (3%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +  ++LY  + + V +KPAG+    G G    ++ +   W       P L HRLD +T+
Sbjct: 1   MIDPVILYHSTHLVVIDKPAGLPSHRGRGGGPSVEDWFPRW-RRGADGPWLVHRLDADTA 59

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L +AR +     L  +F  RR+ K YW++V G+P      I   L +++  GG     
Sbjct: 60  GCLAIARRKTTLVALQRAFAQRRVGKTYWAIVEGVPAAAHGTIELALARRTVPGG---WR 116

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  + +G + AI+ ++ +    Q    LE++P TGRTHQLRVH    G PIVGD  Y   
Sbjct: 117 VAPDPRG-DPAITDWRCL-AAGQGRALLELRPRTGRTHQLRVHCAESGFPIVGDPLYGTE 174

Query: 276 FKG 278
             G
Sbjct: 175 AGG 177


>gi|116515147|ref|YP_802776.1| RluC [Buchnera aphidicola str. Cc (Cinara cedri)]
 gi|116257001|gb|ABJ90683.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. Cc (Cinara cedri)]
          Length = 317

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 82/229 (35%), Positives = 126/229 (55%), Gaps = 12/229 (5%)

Query: 88  VNLTKH--SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKP 144
           +NL+K     F+K+IL +ED+ + +FNKP G +V GGSGI+Y  I+ F K   D K  + 
Sbjct: 80  INLSKSIIQLFIKNIL-FEDNDLIIFNKPYGFAVHGGSGISYGVIEIFRKIRSDLKFLE- 137

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HR+D+ETSGIL++++ R+  + +  + R ++I K Y +++ G    K + +   LLK
Sbjct: 138 -LVHRIDKETSGILILSKKRSILKKMHINLREKKIYKEYLAILHGYWSKKNKIVKLPLLK 196

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           K +I       V +  K A    ++F++      K   +++ P TGRTHQ+RVH    G 
Sbjct: 197 KKNIKQKKKVCVHKEGKLAQ---TNFEIKKYLNNK-TLVKIIPITGRTHQIRVHTAQFGH 252

Query: 265 PIVGDHKYCANFKGNFTSPIQN-KLYLHARYMDLPHPEGGR-LQITAPL 311
           PIV D++Y    K       +N +L LHA  +   HP       ITAPL
Sbjct: 253 PIVFDNRYGKIEKKKKKIIKKNSRLLLHAFKVSFLHPRNNENFSITAPL 301


>gi|325921580|ref|ZP_08183425.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           gardneri ATCC 19865]
 gi|325547934|gb|EGD18943.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           gardneri ATCC 19865]
          Length = 331

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 86/331 (25%), Positives = 157/331 (47%), Gaps = 40/331 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +V ++    R D      +P  +   L + ++SG   ++ +  +  + ++ G+ V+
Sbjct: 13  IRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLNGEMARPRDTLRGGESVQ 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V+    H              ++  D   S+L YED ++ V +KPAG+ V  G+G  
Sbjct: 73  VQVVLEIQTH--------------SEPQDIPLSVL-YEDDQVLVIDKPAGLVVHPGAG-- 115

Query: 127 YHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            + DG L + +     +    PR  + HRLD++TSG++VVART  A   L E    R + 
Sbjct: 116 -NPDGTLVNALLFRDPALAAVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSARDVH 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G   +     AN  + + H        V+ + +    A++H+++ + F +  
Sbjct: 175 RQYLAVVVGALVSG--GTANAPIDR-HPRDRLKMAVRDDGRD---AVTHYRLRERF-RAH 227

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHA 292
             LE +  TGRTHQ+RVH  H+  PIVGD  Y    K     +  + ++L       LHA
Sbjct: 228 TALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGASDELVHELRTFKRQALHA 287

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             ++  HP  G  ++ +AP+P  + +   +L
Sbjct: 288 ETLEFLHPVSGEPVRASAPVPVDLQRLMTAL 318


>gi|115477338|ref|NP_001062265.1| Os08g0520100 [Oryza sativa Japonica Group]
 gi|122234516|sp|Q0J4D4|PUS3_ORYSJ RecName: Full=RNA pseudourine synthase 3, mitochondrial; AltName:
           Full=RNA pseudouridylate synthase 3; AltName:
           Full=RNA-uridine isomerase 3; Flags: Precursor
 gi|113624234|dbj|BAF24179.1| Os08g0520100 [Oryza sativa Japonica Group]
 gi|125562210|gb|EAZ07658.1| hypothetical protein OsI_29911 [Oryza sativa Indica Group]
          Length = 475

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 89/343 (25%), Positives = 152/343 (44%), Gaps = 75/343 (21%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD---FLKSILLYEDSK 107
           K++K N+ ++ G  + +P  ++     IK++     +  L  + D   +L+ +++++DS 
Sbjct: 128 KKIKHNDVMEPGMRIHLP--VSVAEGEIKKRYETIPTATLHPNKDEIEYLRRLVIHKDSA 185

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAA 166
           I V NKP  + ++G   +   +D    + +    ++ P+L HRLD+E+SG+L+  RT+ +
Sbjct: 186 ILVLNKPPKVPMKGNLPVHNSMDVLAAAALSYGNEEGPKLVHRLDRESSGLLLFGRTKES 245

Query: 167 AQHLTESFRMRRIQKI---------------YWSLVWGIPKNKKECIANWLLKKSHIGGD 211
              L   F    + K                YW+LV G PK ++  I+  L K     G 
Sbjct: 246 FTRLHWLFTSVNLAKTNSQVWNAACEAYMQRYWALVIGTPKEREGIISAPLSKVLLDDGK 305

Query: 212 YVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIV 267
              V+  +  G   A  A++ ++V+        W+E++P TGR HQLRVH A  +G PIV
Sbjct: 306 AERVILAHPSGIDGAQEAVTAYRVMGPTIHGCSWIELRPLTGRKHQLRVHCAEALGTPIV 365

Query: 268 GDHKYC------------ANFKGNFTSPIQNK------------------LYLHARYMDL 297
           GD+KY              +F+     P + +                  L+LH R M +
Sbjct: 366 GDYKYGWFVHQRWKQNPQPDFEPFTGEPYKLRRPEGLEIQKGSVLSKVPLLHLHCREMVI 425

Query: 298 P------------HPEGGR--------LQITAPLPAHMVKTWD 320
           P            H  G          L+  AP+PAHM  +W+
Sbjct: 426 PNIAKFLSSNGEWHENGAPWSKEKPNLLRFIAPMPAHMKISWN 468


>gi|319942386|ref|ZP_08016700.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
 gi|319804074|gb|EFW00982.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
          Length = 363

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 92/336 (27%), Positives = 146/336 (43%), Gaps = 46/336 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD+    H P ++   L K++ +G V+++     K   +   G  + +           
Sbjct: 47  RLDKVLAAHLPDVSRARLAKLIENGSVKLNGAVTTKIRAKATEGDEIEL----------- 95

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
            E   LD ++     S F++  ++YED  I V NKPAG+ V  G+G      ++G L  +
Sbjct: 96  LEPPKLDEALAFEPQS-FVEFEVIYEDPSIIVVNKPAGLVVHPGAGNPDGTLLNGLLYHF 154

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----- 189
            + K   PR  + HRLD++T+G++VVART AA  +L    + R +++ YW+L  G     
Sbjct: 155 PELK-DVPRAGIVHRLDRDTTGLMVVARTLAAQTNLVRQLQERTVKREYWALTMGTAAED 213

Query: 190 ------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
                 I ++ K  I      K   G   V       +      S    I        W+
Sbjct: 214 FVVDVPIGRDPKSRIRF----KGFPGSTGVRAKPARTRARAVGWSSVDGIPA-----SWV 264

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-----YLHARYMDLP 298
             +  TGRTHQ+RVH      P++GD  Y     G     ++N L      LHA  + L 
Sbjct: 265 ACRLDTGRTHQIRVHLTGEDLPLIGDQLYRGRAPG-IAVKVENFLEFHRQALHASRLGLI 323

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGF-KYDRNLYI 332
           HP  G  ++     P  M+   + LGF  +DR + +
Sbjct: 324 HPATGEEMEWFVEPPEDMIDLMEQLGFGPWDRPVTV 359


>gi|171920745|ref|ZP_02695367.2| pseudouridine synthase [Ureaplasma urealyticum serovar 13 str. ATCC
           33698]
 gi|188524118|ref|ZP_02557392.2| pseudouridine synthase [Ureaplasma urealyticum serovar 12 str. ATCC
           33696]
 gi|195867425|ref|ZP_03079429.1| pseudouridine synthase [Ureaplasma urealyticum serovar 9 str. ATCC
           33175]
 gi|198273522|ref|ZP_03206058.1| pseudouridine synthase [Ureaplasma urealyticum serovar 4 str. ATCC
           27816]
 gi|225550899|ref|ZP_03771848.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           2 str. ATCC 27814]
 gi|171903495|gb|EDT49784.1| pseudouridine synthase [Ureaplasma urealyticum serovar 13 str. ATCC
           33698]
 gi|195659776|gb|EDX53156.1| pseudouridine synthase [Ureaplasma urealyticum serovar 12 str. ATCC
           33696]
 gi|195660901|gb|EDX54154.1| pseudouridine synthase [Ureaplasma urealyticum serovar 9 str. ATCC
           33175]
 gi|198250042|gb|EDY74822.1| pseudouridine synthase [Ureaplasma urealyticum serovar 4 str. ATCC
           27816]
 gi|225380053|gb|EEH02415.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           2 str. ATCC 27814]
          Length = 315

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/275 (28%), Positives = 139/275 (50%), Gaps = 34/275 (12%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++ N RLDR+   ++P+++ + + K++R+  ++V+ K+ + N  ++   VV I    N L
Sbjct: 11  NDANQRLDRFLLKNFPNLSRIAIYKLIRTKDIKVNHKKAEHNYLLKENDVVSIYAKENFL 70

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                E+KI    ++  K  D L+  ++YEDS I V +KP G+ V        H +  L+
Sbjct: 71  -----EKKI---DLDFAKAKDELE--IIYEDSNILVVHKPIGLIVHEDDN---HKNDTLQ 117

Query: 135 SWV-------------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + +             D     P L HRLD  TSG++V A+T  A + + E F+   + +
Sbjct: 118 NRIKKYLVKKNEYHPFDESAFVPSLCHRLDLNTSGLIVAAKTANALRIIAEMFKNNDVNR 177

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQK 239
           +Y  L +  +PKN  + + N++ K      D   +V+  +   N  AI+ ++ I  + + 
Sbjct: 178 VYKCLTYNRLPKN-NDIVYNYMYK----ANDNTMIVQNFKTKVNKTAITKYQYIGNYKKY 232

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           F + +++  TGRTHQ+R     +  PIVG+ KY  
Sbjct: 233 FVY-DIELLTGRTHQIRAVLNFLHAPIVGEQKYIT 266


>gi|153809024|ref|ZP_01961692.1| hypothetical protein BACCAC_03328 [Bacteroides caccae ATCC 43185]
 gi|149128357|gb|EDM19576.1| hypothetical protein BACCAC_03328 [Bacteroides caccae ATCC 43185]
          Length = 223

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 69/218 (31%), Positives = 109/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQ        +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQADKTGDTPLSETVKQYLKEKYQKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTSKALTRLNEMFRAGEVKKTYWAVVKNAPKESEGELVHFLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  A+  +++I   ++ +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPNSKKAVLDYRLIG-RSENYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             G+  S     + LHAR +   HP    L ++ APLP
Sbjct: 177 --GSPRSNPDGSICLHARRVRFVHPVSKELIELKAPLP 212


>gi|227890010|ref|ZP_04007815.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
 gi|227849454|gb|EEJ59540.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
          Length = 304

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 90/317 (28%), Positives = 155/317 (48%), Gaps = 37/317 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV--VRIPPVIN 72
           D E  RLD+        ++   +++++    + V+ K  K + ++QSG V  V IPPV  
Sbjct: 10  DGEKGRLDKVIAEKITDLSRTKIKELVNDKNILVNNKAEKVSYKVQSGDVIDVTIPPV-- 67

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--ID 130
                            L+  ++ L   ++YEDS + V NKP GI V   +G   H  ++
Sbjct: 68  ---------------KPLSLEAENLHLDIVYEDSDVIVVNKPQGIVVHPSAGHPDHTLVN 112

Query: 131 GFL---KSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           G L   +   DS +G +P + HR+D++TSG+L++A+   A + L +    +  ++ Y ++
Sbjct: 113 GLLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMIAKNDRARESLEKQLAEKINKREYLAI 172

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + K   I N  + ++      + V   N KG   A++HF V++ F + +  ++  
Sbjct: 173 VHGNFEVKNGVI-NAPIGRNPNNRKQMAV---NPKG-KAAVTHFTVLEQF-KNYSLVKCV 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  ++G P+ GD  Y    K   +   Q   +LHA+ +    P     L
Sbjct: 227 LETGRTHQIRVHMKYIGHPLAGDPLYGP--KKTLSGHGQ---FLHAKTLGFYQPSTNEWL 281

Query: 306 QITAPLPAHMVKTWDSL 322
           + +APLP    K  ++L
Sbjct: 282 EFSAPLPTIFEKQLENL 298


>gi|307565639|ref|ZP_07628117.1| RNA pseudouridine synthase [Prevotella amnii CRIS 21A-A]
 gi|307345671|gb|EFN91030.1| RNA pseudouridine synthase [Prevotella amnii CRIS 21A-A]
          Length = 235

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 109/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + +  K AG  VQG       +   +K W+  K  KP      + HRLD+  +
Sbjct: 3   VIYEDNHLIIVYKEAGEIVQGDKTGDQPLSETVKLWIKDKYNKPGNVFLGIVHRLDRPVA 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ ART  A   L + FR   I K YW++V   P   ++ + +WL++ +     Y + 
Sbjct: 63  GLVIFARTSKALSRLNDMFRNGNIHKTYWAIVQQQPLKPEDTLTDWLIRNTQQNKSYAYN 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +      A  ++ H+K I+  ++ +  LE+   TGR HQ+R    +MGCPI GD KY   
Sbjct: 123 IPL--PTAKKSVLHYKTINT-SKHYTLLEINLMTGRHHQIRCQLANMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             G   S     + L +  ++  HP   + ++I +P+P
Sbjct: 177 --GAARSNPDGSISLFSHKIEFIHPVSKKTIRIVSPIP 212


>gi|288802466|ref|ZP_06407905.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella melaninogenica D18]
 gi|302346484|ref|YP_003814782.1| RNA pseudouridine synthase [Prevotella melaninogenica ATCC 25845]
 gi|288334994|gb|EFC73430.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella melaninogenica D18]
 gi|302151026|gb|ADK97287.1| RNA pseudouridine synthase [Prevotella melaninogenica ATCC 25845]
          Length = 223

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 72/231 (31%), Positives = 115/231 (49%), Gaps = 20/231 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I +  K AG  VQG       +   +K W+  K QKP      + HRLD+  +
Sbjct: 3   VLYEDNHIIIVYKEAGEIVQGDKTGDEPLSEIVKQWIKEKYQKPGNVFLGVVHRLDRPVA 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV-- 213
           G++V A+T  A   L + FR   + K YW++V   P   +  + +WL++       Y   
Sbjct: 63  GLVVFAKTSKALTRLNDMFRNGEVHKTYWAIVTRPPFETEATLTDWLVRNERQNKSYAYN 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H V  ++K    +I H+KVI+  ++++  LE+   TGR HQ+R    +M CPI GD KY 
Sbjct: 123 HQVPTSKK----SILHYKVIN-QSERYTLLEINLMTGRHHQIRCQLSNMDCPIKGDLKY- 176

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
               G   S     + L +  ++  HP    ++ I +PLP   +  W ++G
Sbjct: 177 ----GAPRSNPDGSICLLSHRVEFIHPVSKEKICIESPLPKDNL--WQAIG 221


>gi|99034795|ref|ZP_01314715.1| hypothetical protein Wendoof_01000461 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 276

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 116/228 (50%), Gaps = 31/228 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I V +K +G++V  G+G   + D  L + +     +P + HRLD++TSG++V+
Sbjct: 50  IVYEDEDIIVLSKQSGLTVHPGAGT--NNDTLLNAVIAHLNVRPGIVHRLDKDTSGLMVI 107

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+  AA   L+E    R+I++ Y ++VWG   +++  I   +  K     + + V K   
Sbjct: 108 AKNEAAHSFLSELLSNRKIKREYLAVVWGTLSSQQGTIKTSIAPKRG-NKEMMCVTKITG 166

Query: 221 KGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-- 275
           K    AI+H+   KVI   +   C LE    TGRTHQ+RVH  H+G  IVGD  Y  N  
Sbjct: 167 K---LAITHYLVQKVIGQVSLVKCTLE----TGRTHQIRVHMSHIGHSIVGDQVYGKNSS 219

Query: 276 ----------FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                     F  NF     N+  LHA  + L HP+    ++  + LP
Sbjct: 220 KSTKYAKNSSFIRNF-----NRQALHAYTLGLYHPKSKEYMEFVSDLP 262


>gi|327282066|ref|XP_003225765.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like [Anolis carolinensis]
          Length = 361

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 66/200 (33%), Positives = 105/200 (52%), Gaps = 27/200 (13%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS----KGQKPRLTHRLDQ 152
           LK  +L+++S+I V NKP G+ V GG  +   I   L +        K +   L HRLD+
Sbjct: 88  LKKGVLFQNSEIVVINKPYGLPVHGGPKVKTCITDVLPTLAKMLYGMKAEPLHLCHRLDK 147

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK------- 205
           ET+G++V+AR +  A  + E F+ R+++K YW++  G PK  +  +   +++K       
Sbjct: 148 ETTGVMVLARDQDIAHKVQELFKTRQVEKKYWAVCVGHPKPTEGLVDIPIVEKEVESHQS 207

Query: 206 ------------SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                       SH  G    V  +  + A+ A++ ++V+        +LE+ P TG  H
Sbjct: 208 HFKMALAPNYYMSHEDGKTFKV--RQHRDAHSAVTRYRVLS-SCSSCSFLELHPITGVKH 264

Query: 254 QLRVH-ALHMGCPIVGDHKY 272
           QLRVH A  +GCPI+GDHKY
Sbjct: 265 QLRVHMAFGLGCPILGDHKY 284


>gi|315656560|ref|ZP_07909447.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii subsp. holmesii ATCC 35242]
 gi|315492515|gb|EFU82119.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii subsp. holmesii ATCC 35242]
          Length = 304

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 88/290 (30%), Positives = 140/290 (48%), Gaps = 28/290 (9%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +L SG V  D + +K ++++ +G ++ I   I      + E   +D   NL         
Sbjct: 34  LLESGAVIQDGETLKKSDQLAAGNLLEID--IPEPTGYVPEVTRVD---NLG-------- 80

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQE 153
            +LY D  + V +KPAG++   G G     + G L++    V + G   R  + HRLD  
Sbjct: 81  -ILYADDDLVVVDKPAGVAAHTGPGWEGPTVVGALRAAGIRVSTSGPVEREGIVHRLDAG 139

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG +VVA++  A   L   FR  R++KIY +L  G  K     I   + +    G ++ 
Sbjct: 140 TSGAMVVAKSELAYGKLKNEFRYHRVEKIYTALATGGVKPPVGTIDAPIGRAP--GREFK 197

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V     G   A++H+ VI+        L++Q  TGRTHQ+RVH   +G P+VGD +Y 
Sbjct: 198 MAVVS---GGKPAVTHYDVIEEL-PGATLLKVQLETGRTHQIRVHLAAIGHPLVGDTEYG 253

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A+ K      ++ + +LHA  +   HP  G  + + APLPA +    + L
Sbjct: 254 ADRKTAARLGLERQ-WLHASRLAFKHPRTGLEVAVQAPLPADLATAVELL 302


>gi|185178732|ref|ZP_02554745.2| pseudouridine synthase [Ureaplasma urealyticum serovar 5 str. ATCC
           27817]
 gi|188024269|ref|ZP_02569983.2| pseudouridine synthase [Ureaplasma urealyticum serovar 7 str. ATCC
           27819]
 gi|188518686|ref|ZP_02557148.2| pseudouridine synthase [Ureaplasma urealyticum serovar 11 str. ATCC
           33695]
 gi|209554557|ref|YP_002284535.1| pseudouridine synthase [Ureaplasma urealyticum serovar 10 str. ATCC
           33699]
 gi|225551323|ref|ZP_03772269.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           8 str. ATCC 27618]
 gi|184209334|gb|EDU06377.1| pseudouridine synthase [Ureaplasma urealyticum serovar 5 str. ATCC
           27817]
 gi|188018935|gb|EDU56975.1| pseudouridine synthase [Ureaplasma urealyticum serovar 7 str. ATCC
           27819]
 gi|188997684|gb|EDU66781.1| pseudouridine synthase [Ureaplasma urealyticum serovar 11 str. ATCC
           33695]
 gi|209542058|gb|ACI60287.1| pseudouridine synthase [Ureaplasma urealyticum serovar 10 str. ATCC
           33699]
 gi|225379138|gb|EEH01503.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           8 str. ATCC 27618]
          Length = 315

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/275 (28%), Positives = 139/275 (50%), Gaps = 34/275 (12%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++ N RLDR+   ++P+++ + + K++R+  ++V+ K+ + N  ++   VV I    N L
Sbjct: 11  NDANQRLDRFLLKNFPNLSRIAIYKLIRTKDIKVNHKKAEHNYLLKENDVVSIYAKENFL 70

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                E+KI    ++  K  D L+  ++YEDS I V +KP G+ V        H +  L+
Sbjct: 71  -----EKKI---DLDFAKAKDELE--IIYEDSNILVVHKPIGLIVHEDDN---HKNDTLQ 117

Query: 135 SWV-------------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + +             D     P L HRLD  TSG++V A+T  A + + E F+   + +
Sbjct: 118 NRIKKYLVKKNEYHPFDESAFVPSLCHRLDLNTSGLIVAAKTANALRIIAEMFKNNDVNR 177

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQK 239
           +Y  L +  +PKN  + + N++ K      D   +V+  +   N  AI+ ++ I  + + 
Sbjct: 178 VYKCLTYNRLPKN-NDIVYNYMYK----ANDNTMIVQNFKTKVNKTAITKYQYIGNYKKY 232

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           F + +++  TGRTHQ+R     +  PIVG+ KY  
Sbjct: 233 FVY-DIELLTGRTHQIRAVLNFLHAPIVGEQKYIT 266


>gi|332522697|ref|ZP_08398949.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
 gi|332313961|gb|EGJ26946.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 299

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 93/322 (28%), Positives = 152/322 (47%), Gaps = 50/322 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RLD+   N    ++     + ++ G V V+ + VK    ++SG         + + 
Sbjct: 7   ETGLRLDKALAN-VTDLSRSQANEQIKKGLVLVNGQVVKAKYSVKSG---------DEIT 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           + + E++ILD        ++ L   ++YEDS + + NK  G+ V   +G         + 
Sbjct: 57  YQLPEEEILDYK------AENLPIDIIYEDSDLAIVNKAQGMVVHPSAGHSSGTLVNALM 110

Query: 127 YHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           YHI    K      G  +P + HR+D++TSG+L+VA+   A Q L E  + ++  + Y +
Sbjct: 111 YHI----KDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDKAHQVLAEELKAKKSLRKYLA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWL 243
           +V G   N +  I      ++ IG       KQ+   KG + A++ F V++ F   +  L
Sbjct: 167 IVHGNLPNDRGMI------EAPIGRSEKDRKKQSVTVKGKD-AVTRFTVLERFGD-YTLL 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E+   TGRTHQ+RVH  ++G P+ GD  Y      KG          +LHA+ + L HP 
Sbjct: 219 ELSLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGAGQ-------FLHAQTLGLTHPT 271

Query: 302 GGRLQ-ITAPLPAHMVKTWDSL 322
            G L   TA  PA  +KT   L
Sbjct: 272 SGELMTFTAEPPAIFLKTLAHL 293


>gi|329964664|ref|ZP_08301718.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
 gi|328525064|gb|EGF52116.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
          Length = 356

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 88/338 (26%), Positives = 154/338 (45%), Gaps = 52/338 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDRGQEMMRVDKYLFDRLTNASRNRIQKAADAGFVMANGKPVKSSYKVKPQDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYENEVIPEDIPLN---------IVYEDRCLMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    +K   D     P   L HR+D++TSG+LV+A+T  A  HL   F  + 
Sbjct: 138 LVNAIAWH----MKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTHLGNQFFNKT 193

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LVWG  +  +  +   + +      D + +   ++    +A++H++V++    
Sbjct: 194 TKRRYRALVWGNVEQDEGTVVGNIGRNPK---DRMQMAVLSDDQGKHAVTHYRVLERLGY 250

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNF-------------TSP 283
               +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG               T P
Sbjct: 251 -VTLVECILETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFETCP 309

Query: 284 IQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
            Q    LHA  +   HP  G  +  T+ +P  M +  D
Sbjct: 310 RQ---ALHAMTLGFVHPVTGEEMYFTSEMPDDMTRLID 344


>gi|262038336|ref|ZP_06011717.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           goodfellowii F0264]
 gi|261747640|gb|EEY35098.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           goodfellowii F0264]
          Length = 346

 Score =  104 bits (259), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 84/301 (27%), Positives = 149/301 (49%), Gaps = 40/301 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V  ++ N R+D +  +    +    +Q++++ G V V+ K VK + +++     RI  
Sbjct: 42  VTVSTEKTNKRVDSFL-SEKTDLTRSRIQQLIKDGNVSVNNKSVKSSYKVEEND--RIEI 98

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
           +I     +    +I+  ++++          ++YED  I V NK AG+ V    G     
Sbjct: 99  IIPEAEKV----EIIAENIDIN---------IIYEDKDIAVINKKAGMVVHPAHGNYSRT 145

Query: 125 ----IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               I YHI    K      G+ +P + HRLD++TSG++VVA+   A   L E F+ + +
Sbjct: 146 LVNAILYHI----KDLSGINGEIRPGIVHRLDKDTSGLIVVAKNDKAHIKLAEMFQKKEV 201

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +++ G   N++       + +       + V+K+N+KG   AI+++ VI    + 
Sbjct: 202 KKTYLAILKG-KLNRESGRLETQIGRDADDRKKMSVLKENDKGKK-AITNYNVI-LSNEL 258

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           F  +++   TGRTHQ+RVH  ++G PI+GD  Y     G   S  + +  LHA  ++  H
Sbjct: 259 FTLVKVYIETGRTHQIRVHMKYLGYPILGDQVY-----GRKDS--EKRQMLHAYKLEFLH 311

Query: 300 P 300
           P
Sbjct: 312 P 312


>gi|90421737|ref|YP_530107.1| pseudouridine synthase [Rhodopseudomonas palustris BisB18]
 gi|90103751|gb|ABD85788.1| pseudouridine synthase [Rhodopseudomonas palustris BisB18]
          Length = 240

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 75/219 (34%), Positives = 109/219 (49%), Gaps = 17/219 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  + V +KPAG+ V  G     +++   +       + P L HRLD++TSG LV+
Sbjct: 23  VLYRDGLMLVIDKPAGLPVHRGPKGGANLESSFEFLRYGLPRPPVLAHRLDRDTSGCLVL 82

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R R A   L   F+  RI K YW++V G P   +  I    L    +  +     K + 
Sbjct: 83  GRHRKATASLGLLFKHGRISKTYWAVVEGGPIEDEGTIE---LPIGRLNAERGWWQKIDP 139

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +G   A + ++V+        WL +QP TGRTHQLRVH+  MG PIVGD+ Y     GN 
Sbjct: 140 EG-QPATTKWRVLG-RGDGLTWLALQPVTGRTHQLRVHSAAMGWPIVGDNIY-----GNG 192

Query: 281 TSPIQNKLYLHARYMDLP----HPEGGRLQITAPLPAHM 315
               +  L+LHA  + +P     P    + +TAP P H+
Sbjct: 193 PRFGEPTLHLHASEIVIPISRNKPP---IVVTAPAPVHL 228


>gi|312796112|ref|YP_004029034.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           rhizoxinica HKI 454]
 gi|312167887|emb|CBW74890.1| Ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70)
           [Burkholderia rhizoxinica HKI 454]
          Length = 373

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 75/266 (28%), Positives = 119/266 (44%), Gaps = 38/266 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ  + +G+V +D    +    +  G  VR+ P          
Sbjct: 41  RLDKVLARLFPTFSRSRLQTWIDAGRVTLDGAPARLRQSVPLGATVRLVP---------- 90

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +L  ++        L   ++YED  + V +KPAG+ V   +G      ++G L  + 
Sbjct: 91  --DLLPQALAFAPEPVPLP--IVYEDETLVVIDKPAGLVVHPAAGNWSGTLLNGLLHRYP 146

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD++TSG++VVART AA   L    + R +++ Y +  WG+      
Sbjct: 147 DAAGLPRAGIVHRLDKDTSGLMVVARTLAAQTDLVRQLQARTVKRRYIAFAWGV-TPPSG 205

Query: 197 CIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVIDC-------FAQKFCWLEMQ 246
           CI       + IG D      +          A +HFK +          ++  C LE  
Sbjct: 206 CI------DAPIGRDPRERTRMAVLAGAAGKAARTHFKTVATGVWSGQPVSRLLCDLE-- 257

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
             TGRTHQ+RVH  H G P++GD  Y
Sbjct: 258 --TGRTHQIRVHLAHTGHPLLGDPLY 281


>gi|329961725|ref|ZP_08299756.1| RNA pseudouridine synthase [Bacteroides fluxus YIT 12057]
 gi|328531466|gb|EGF58306.1| RNA pseudouridine synthase [Bacteroides fluxus YIT 12057]
          Length = 223

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 67/219 (30%), Positives = 111/219 (50%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + +K A   VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIIVSKTASEIVQGDKTGDTPLSETVKQYLKEKYNKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E F+   ++K YW++V   P  ++  + +++++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFKDGEVKKTYWAVVKNRPPEEEGELVHYMVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   G+  AI H+++I   +Q +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKERPGSKKAILHYRLIGK-SQNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
             G   S     + LHAR++   HP    +  + AP+P+
Sbjct: 177 --GFPRSNPDGSICLHARFIRFVHPVSKEMVAVEAPVPS 213


>gi|254455970|ref|ZP_05069399.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter sp. HTCC7211]
 gi|207082972|gb|EDZ60398.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter sp. HTCC7211]
          Length = 292

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 87/278 (31%), Positives = 145/278 (52%), Gaps = 27/278 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+DRW +     I    ++K  RSG+++++KK++K + ++++  V      I+  N   
Sbjct: 1   MRIDRWTRLKIGKIPQGLIEKYFRSGKIKINKKKIKSSTKVKTNDV------ISFFNLDF 54

Query: 79  KEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLK 134
           KEQ I+   +      + +KS    ++  +    V NK +GISVQGG+    + +D F K
Sbjct: 55  KEQ-IIQKKIKFEPSKEIIKSNEDQIIDNNENFIVLNKSSGISVQGGTKSKKNLVDIFAK 113

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           S +  +G KP   HRLD++TSG+ ++A+TR +AQ LT  FR+R++ K Y ++  G     
Sbjct: 114 SEI-FQGTKPYSVHRLDKDTSGVFIMAKTRQSAQLLTSLFRLRKVHKTYLAICHG----- 167

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                  L K S    D +      +K    A + ++V+D  ++    +E++P TGR HQ
Sbjct: 168 ------ELNKDSGEWNDDLIRYDGEKKIIEKAKTIYRVLDKNSEA-SLVELKPITGRKHQ 220

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           LR     +G PI GD KY  +   N +  +   L LH+
Sbjct: 221 LRKQLYALGQPIFGDIKYKLS---NSSRGLNKNLMLHS 255


>gi|199598373|ref|ZP_03211792.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|258508458|ref|YP_003171209.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus GG]
 gi|199590692|gb|EDY98779.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|257148385|emb|CAR87358.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus GG]
 gi|259649771|dbj|BAI41933.1| pseudouridylate synthase [Lactobacillus rhamnosus GG]
          Length = 306

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 94/326 (28%), Positives = 151/326 (46%), Gaps = 42/326 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E+ R+D+    H        +QK L+ G V V+   VK N ++ +G VV +         
Sbjct: 10  ESGRIDKIITAHETTHTRSQVQKWLQDGLVTVNGNPVKANFKVTAGDVVTV--------- 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            I E K L +       ++ +   ++YED ++ V NKP G+ V    G   H DG L + 
Sbjct: 61  TIPEVKPLKAV------AEPIPLEIVYEDDQVIVVNKPQGMVVHPAPG---HPDGTLVNG 111

Query: 137 VDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +    +        +P + HR+D++TSG+L+VA+T AA   L+   + +   + Y +LV 
Sbjct: 112 LLYHTKLPGINGVIRPGIVHRIDKDTSGLLMVAKTEAAQLSLSAQLKAKTSIREYLALVH 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQP 247
           G  K  +  I       + +G D     +Q       +A++HF+V++ F   +  ++   
Sbjct: 172 GTFKEDEGTI------DAPLGRDPRDRKRQAVVADGRHAVTHFQVLERFTN-YTLVKCIL 224

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  +   P+ GD  Y        T P   + +LHA  +   HP  G+ L 
Sbjct: 225 DTGRTHQIRVHMAYTHHPVAGDPLYGP----KRTLPGHGQ-FLHAAKLGFVHPVTGKLLT 279

Query: 307 ITAPLPAHMVKTWDSL--GFKYDRNL 330
            TAP+P    KT   L  G    RN+
Sbjct: 280 FTAPVPPIFEKTLTDLRAGIDKTRNV 305


>gi|197120627|ref|YP_002132578.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196170476|gb|ACG71449.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 302

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 89/298 (29%), Positives = 139/298 (46%), Gaps = 32/298 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIP 68
           ++V + +   R+DR+       I+    ++ + +G V VD +R K   R +  GQ V   
Sbjct: 6   LLVPDADRYERIDRFIAARG-GISRGLARRAIEAGGVFVDGRRCKVAGRTLTPGQQV--- 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            V+N L    +    L +           +  LLY D+ +   +KPAG+  Q        
Sbjct: 62  -VVN-LEEGGRAAPALAA---------LGRERLLYADADLCAVDKPAGVPAQ----PTLT 106

Query: 129 ID-GFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            D G L   V +  G    L HRLD+ETSG+ V ARTR AA  L E+FR    +K Y +L
Sbjct: 107 TDRGALPELVSALLGAPVTLVHRLDRETSGVTVFARTRDAAAALAEAFRTGTPEKTYLAL 166

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
               P   +  +A  L K     G     +++ +   + A + ++ +   A     +E +
Sbjct: 167 CARAPSPAEGRVALALGKDPARPG-----LRRVDPAGDPAATRYRTLR-EAPGGARVEAR 220

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGG 303
           P TGRTHQ+RVH   +G P++GD +Y    + G    P   ++ LHA  ++LPHP  G
Sbjct: 221 PETGRTHQIRVHLAALGAPLLGDARYGGPRRVGEVAVP---RVMLHATRLELPHPATG 275


>gi|303238761|ref|ZP_07325293.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
 gi|302593640|gb|EFL63356.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
          Length = 233

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 69/209 (33%), Positives = 109/209 (52%), Gaps = 13/209 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           +K  +LYED+ + V  KP  I VQ  S     +   LK  +  +  KP      L HRLD
Sbjct: 7   MKIKILYEDNHLLVVEKPVNIPVQQDSTNDVDMLTLLKEDIKVRYNKPGNVYLGLVHRLD 66

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +   G +V A+T  AA  L++  R R + K Y+++V G  ++K+  + N+LLK      +
Sbjct: 67  RPVGGAMVFAKTSKAASRLSDQVRTRGLNKTYYAVVHGKFEDKQGRLENYLLKDEKT--N 124

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V VV     GA  AI  +KVID F + +  +++  HTGR+HQ+RV   ++G P+ GD +
Sbjct: 125 MVSVVSPEVAGAKQAILDYKVIDVF-KDYTLIKVDLHTGRSHQIRVQFSNIGHPLYGDQR 183

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y     G   + +  ++ L +  + L HP
Sbjct: 184 Y-----GKSVNKVGQQIALWSCGIALKHP 207


>gi|78778581|ref|YP_396693.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9312]
 gi|78712080|gb|ABB49257.1| ribosomal large subunit pseudouridine synthase D [Prochlorococcus
           marinus str. MIT 9312]
          Length = 319

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 90/303 (29%), Positives = 144/303 (47%), Gaps = 43/303 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +  P  +   +Q  + SG V V+ K  K    +++G  V+I  PP    L +
Sbjct: 27  MRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNVQIWMPPP-EPLIY 85

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E+  L+               +L+ED  I V NK +G+ V    G      ++G L 
Sbjct: 86  LKPEKMDLN---------------ILFEDKHIIVINKQSGLIVHPAPGHKSGTLVNGLLF 130

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++TSG +VVA+++ A  +L +  + +   + Y +++ G 
Sbjct: 131 HCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGA 190

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           P +++  I        HIG D ++ +K     E    YA +++K+ + F   +  +  + 
Sbjct: 191 PNSEEGQIV------GHIGRDKLNRLKYKVVEETTGRYACTYWKLEERFGN-YSLMSFKL 243

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR 304
            TGRTHQ+RVH  H+  PIVGD  Y  C         P Q +   LHA  + L HP  G+
Sbjct: 244 DTGRTHQIRVHCAHINHPIVGDPLYGRCKKL------PCQLDGQALHAIKLGLIHPINGK 297

Query: 305 LQI 307
             I
Sbjct: 298 EMI 300


>gi|269121328|ref|YP_003309505.1| pseudouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268615206|gb|ACZ09574.1| pseudouridine synthase, RluA family [Sebaldella termitidis ATCC
           33386]
          Length = 285

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 80/267 (29%), Positives = 135/267 (50%), Gaps = 16/267 (5%)

Query: 10  VVVENDE--ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++++ DE  E +RLDR+ +          + + +R G+V+++ K+ K N R+  G V+ I
Sbjct: 1   MIIKCDENMEGVRLDRFLRKKLKDTALNTIFEYIRKGKVKINGKKKKENYRLVLGDVIEI 60

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +  + N     +K   SS+ + K  D    ++ +ED    + NKP G++V  G+G  Y
Sbjct: 61  KSLEESENT----EKKHYSSLRIDK--DRYMKMVFFEDDDCLIINKPGGVAVHKGTGNQY 114

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +    KS    K +     +R+D+ET G+L+ A+     ++LTE  R   ++K Y ++V
Sbjct: 115 GLAEVYKSIY--KNENLNFANRIDKETKGLLLGAKNLKFLRYLTEKIRNNELEKRYIAVV 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI    +  I N+L  K +       VV  +++    A + FK I     K+  LE++ 
Sbjct: 173 SGIITEDEFTIDNFLETKEN------KVVVSDKENGKAAKAVFKKIKTIKNKYTVLEVEL 226

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCA 274
            TGR HQ+RV    MG PI GD KY +
Sbjct: 227 ITGRKHQIRVQLADMGFPIAGDKKYGS 253


>gi|126730410|ref|ZP_01746221.1| ribosomal large subunit pseudouridine synthase A [Sagittula
           stellata E-37]
 gi|126709143|gb|EBA08198.1| ribosomal large subunit pseudouridine synthase A [Sagittula
           stellata E-37]
          Length = 214

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 71/210 (33%), Positives = 105/210 (50%), Gaps = 22/210 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++L+EDS + V +KPAG+    G G A  +   L S +++     RL HRLD++TSG++V
Sbjct: 12  VVLHEDSDLLVVDKPAGLLSVPGKGAA--LADCLLSRLEAAFPTVRLVHRLDRDTSGVMV 69

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKK---ECIANWLLKKSHIGGDYVH 214
              T  A +HL   F  R+ +K Y + V G   PK+ +     I +W  +   +      
Sbjct: 70  FGLTAHAQRHLGAQFEARKTKKTYVARVAGRLAPKSGEVDLPLIVDWPNRPRQM------ 123

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V   N K A       K  D  ++    + + PHTGR+HQLRVH L +G PI+GD  Y  
Sbjct: 124 VCHDNGKPALTGWKVMKASDAESR----VRLFPHTGRSHQLRVHMLALGHPILGDELYAP 179

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                +      ++ LHA  + L HPE GR
Sbjct: 180 ETAAQYP-----RMMLHAEELRLSHPESGR 204


>gi|42519111|ref|NP_965041.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           johnsonii NCC 533]
 gi|41583398|gb|AAS09007.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           johnsonii NCC 533]
          Length = 304

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 89/317 (28%), Positives = 155/317 (48%), Gaps = 37/317 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV--VRIPPVIN 72
           D+E  RLD+        ++   +++++    + V+ K  K + ++QSG V  V IPPV  
Sbjct: 10  DDEKGRLDKVIAEKITDLSRTKIKELVNDKNILVNNKAEKVSYKVQSGDVIDVTIPPV-- 67

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--ID 130
                            L+  ++ L   ++YEDS + V NKP G+ V   +G   H  ++
Sbjct: 68  ---------------KPLSLEAENLHLDIVYEDSDVIVVNKPQGMVVHPSAGHPDHTLVN 112

Query: 131 GFL---KSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           G L   +   DS +G +P + HR+D++TSG+L++A+   A + L +    +  ++ Y ++
Sbjct: 113 GLLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMIAKNDKARESLEKQLAEKINKREYLAI 172

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + K   I N  + ++      + V   N KG   A++HF V++ F + +  ++  
Sbjct: 173 VHGNFEVKNGVI-NAPIGRNPNNRKQMAV---NPKG-KAAVTHFTVLEQF-KNYSLVKCV 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  ++G P+ GD  Y    K   +   Q   +LHA+ +    P     L
Sbjct: 227 LETGRTHQIRVHMKYIGHPLAGDPLYGP--KKTLSGHGQ---FLHAKTLGFYQPSTNEWL 281

Query: 306 QITAPLPAHMVKTWDSL 322
           + +APLP    K   +L
Sbjct: 282 EFSAPLPTIFEKQLKNL 298


>gi|168187890|ref|ZP_02622525.1| hypothetical RNA pseudouridine synthase YhcT [Clostridium botulinum
           C str. Eklund]
 gi|169294254|gb|EDS76387.1| hypothetical RNA pseudouridine synthase YhcT [Clostridium botulinum
           C str. Eklund]
          Length = 301

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 89/316 (28%), Positives = 151/316 (47%), Gaps = 38/316 (12%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           NDEE +RL+ + KN Y   +   ++K  R G+++V+ + V+ +  +++  ++ I      
Sbjct: 15  NDEE-IRLNHYLKN-YAKCSSRFIRKAAREGRIKVNNENVRLSYMLKNNDLIEIQINRKE 72

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              I+ E+  LD               ++YED  I V NKP  I V        H++G L
Sbjct: 73  EQDIVPEKMKLD---------------IIYEDEDIIVINKPKAIVVHPTK---RHLNGTL 114

Query: 134 KSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            + V       ++    RL +RLD +TSG++++A+   +   L+   +     K Y ++V
Sbjct: 115 SNGVLYYFKEKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFIKRYLAIV 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  + K   I   + +     G    V+  +E+G   +I+ FKVI+ + +    +E+  
Sbjct: 175 HGNLEEKSGVIDKPIYRVGE--GTLKRVI--DERGQK-SITRFKVIESY-ENADLIELTL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH   +G PI GD  Y     G       ++  LHA  + +PHP+ GR L+
Sbjct: 229 ETGRTHQIRVHLSSIGHPIYGDALY-----GKEEHEYIDRQALHAYKLQIPHPKDGRILK 283

Query: 307 ITAPLPAHMVKTWDSL 322
           + + LP  M    D L
Sbjct: 284 LQSDLPDDMKNLIDKL 299


>gi|300113280|ref|YP_003759855.1| RluA family pseudouridine synthase [Nitrosococcus watsonii C-113]
 gi|299539217|gb|ADJ27534.1| pseudouridine synthase, RluA family [Nitrosococcus watsonii C-113]
          Length = 319

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 91/341 (26%), Positives = 157/341 (46%), Gaps = 48/341 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + + ++    RLD+     +P  +   LQ+ ++ GQV+V+    +  + +Q G+ + +  
Sbjct: 9   ITLPSELAGKRLDQALAQVFPAYSRSRLQQWIKHGQVKVNDALARPRDTVQGGEWIVV-- 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                        I ++       S  L   ++YED  I V NKPAG+ V   +G   + 
Sbjct: 67  -------------IAEAEAETGWKSQPLPLEIIYEDEAIIVVNKPAGLVVHPAAG---NR 110

Query: 130 DGFLKSWVDSKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG L + +     +    PR  + HRLD++TSG+LVVAR   A   L +  + RRI + Y
Sbjct: 111 DGTLVNALLHHAPELERIPRAGIVHRLDKDTSGLLVVARNLVAHHGLIQQLQARRITREY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
            ++  G+  +     A   +++  +    + V+   +     A++H++V+  F       
Sbjct: 171 QAITVGVMTSGGRIEAP--IQRHPVNRKRMAVISTGKP----ALTHYRVVSRFRIHTHIL 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF------KGNFTSPIQN--KLYLHA 292
           C LE    TGRTHQ+RVH  H+G P++GD  Y              ++ +++  +  LHA
Sbjct: 225 CRLE----TGRTHQIRVHLAHIGYPLLGDPTYGKRLHIPRESSEELSTALRHFKRQALHA 280

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
             + L HPE  + +   APLP  M      L  + DR  +I
Sbjct: 281 ARLGLVHPEKKQAMNWEAPLPEDMATMLALL--EQDRQHHI 319


>gi|190575601|ref|YP_001973446.1| putative ribosomal large subunit pseudouridine synthase D
           [Stenotrophomonas maltophilia K279a]
 gi|190013523|emb|CAQ47158.1| putative ribosomal large subunit pseudouridine synthase D
           [Stenotrophomonas maltophilia K279a]
          Length = 329

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 87/321 (27%), Positives = 145/321 (45%), Gaps = 38/321 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +V +     R D      +P  +   L + +++G+V +D  +V+  + ++ G+VV +  
Sbjct: 12  AIVPDTAAGRRFDAVVAELFPEYSRSRLTEWIKAGEVLLDGAQVRPRDPLRGGEVVTLNV 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V+        E   LD               +L+ED  + V NKP G+ V  G+G   H 
Sbjct: 72  VLETQTDAQPEDIPLD---------------VLFEDEHLLVINKPVGLVVHPGAG--NHS 114

Query: 130 DGFLKSWV---DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              + + +    S    PR  + HRLD++TSG++VVA+T  A   L E    R + + Y 
Sbjct: 115 GTLVNALLFRDPSVAVLPRAGIVHRLDKDTSGVMVVAKTLEAQTALVEQLAARDVHRQYL 174

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G         A       H        V+++ K    AI+H+++ + F +    LE
Sbjct: 175 AIVMGALVAGGTADAPI---DRHPRDRLKMAVREDGK---EAITHYRLRERF-RAHTALE 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMD 296
            +  TGRTHQ+RVH  H+  PI+GD  Y    K          + ++   +  LHA  ++
Sbjct: 228 CRLETGRTHQIRVHMAHVRHPIIGDPLYGGALKLPKGASDELVAALRGFKRQALHAETLE 287

Query: 297 LPHPEGGRL-QITAPLPAHMV 316
             HP  G L + TAP+P  M+
Sbjct: 288 FTHPITGELVRNTAPVPEDML 308


>gi|170756442|ref|YP_001781114.1| RluA family pseudouridine synthase [Clostridium botulinum B1 str.
           Okra]
 gi|169121654|gb|ACA45490.1| pseudouridine synthase, RluA family [Clostridium botulinum B1 str.
           Okra]
          Length = 305

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 94/324 (29%), Positives = 154/324 (47%), Gaps = 44/324 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE + +N+RLD +    +   +   LQ I+  G V V+ K+ K N +++ G  + +    
Sbjct: 8   VEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDQGSVLVNNKKKKRNYKLKVGDNIEVN--- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                 I E K+L          + +K  ++YED  + V NKP  + V    G+     +
Sbjct: 65  ------IPEPKLLQIE------PEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLV 112

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+   I ++Y +
Sbjct: 113 NALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           LV GI K+++  I      ++ IG   V  +K    K   +A++H+KVI+ F +    +E
Sbjct: 173 LVEGIIKDEQGTI------EAPIGRHPVDRIKMAVVKDGRHAVTHYKVIERF-KNHTLVE 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPH 299
            +  TGRTHQ+RVH  H+  P+VGD  Y       N KG           LHA+ +   H
Sbjct: 226 CRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQRFNLKGQM---------LHAKLLGFIH 276

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P   + ++  + LP +  K    L
Sbjct: 277 PTTEQYVEFESELPEYFKKIIKIL 300


>gi|329667353|gb|AEB93301.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           johnsonii DPC 6026]
          Length = 304

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 89/317 (28%), Positives = 155/317 (48%), Gaps = 37/317 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV--VRIPPVIN 72
           D+E  RLD+        ++   +++++    + V+ K  K + ++QSG V  V IPPV  
Sbjct: 10  DDEKGRLDKVIAEKITDLSRTKIKELVNDKNILVNNKAEKVSYKVQSGDVIDVTIPPV-- 67

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--ID 130
                            L+  ++ L   ++YEDS + V NKP G+ V   +G   H  ++
Sbjct: 68  ---------------KPLSLEAENLHLDIVYEDSDVIVVNKPQGMVVHPSAGHPDHTLVN 112

Query: 131 GFL---KSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           G L   +   DS +G +P + HR+D++TSG+L++A+   A + L +    +  ++ Y ++
Sbjct: 113 GLLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMIAKNDKARESLEKQLAEKINKREYLAI 172

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + K   I N  + ++      + V   N KG   A++HF V++ F + +  ++  
Sbjct: 173 VHGNFEVKNGVI-NAPIGRNPNNRKQMAV---NPKG-KAAVTHFTVLEQF-KNYSLVKCV 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  ++G P+ GD  Y    K   +   Q   +LHA+ +    P     L
Sbjct: 227 LETGRTHQIRVHMKYIGHPLAGDPLYGP--KKTLSGHGQ---FLHAKTLGFYQPSTNEWL 281

Query: 306 QITAPLPAHMVKTWDSL 322
           + +APLP    K   +L
Sbjct: 282 EFSAPLPTIFEKQLKNL 298


>gi|270290265|ref|ZP_06196490.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
 gi|304384921|ref|ZP_07367267.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici DSM 20284]
 gi|270281046|gb|EFA26879.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
 gi|304329115|gb|EFL96335.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici DSM 20284]
          Length = 302

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 84/292 (28%), Positives = 140/292 (47%), Gaps = 35/292 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+    +   +    +Q +++ GQ+ V+   V   NR Q     ++         IIK
Sbjct: 15  RLDKVIAENVADLTRSQVQSLIKKGQILVND--VPTTNRYQVKPNDQV---------IIK 63

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLK--S 135
               L   V +    + +   ++YED  + V NKP G+ V    G  +   ++G L    
Sbjct: 64  ----LPDPVAIDVQPEKMDLDIVYEDDDVIVVNKPQGMVVHPAPGHDHGTLVNGLLAHTP 119

Query: 136 WVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                G+ +P + HR+D++TSG+L+VA+   A   L++  + +  Q+ YW++V G  K  
Sbjct: 120 LATINGELRPGIVHRIDKDTSGLLMVAKNDQALVSLSKQLKDKTNQRKYWAIVHGNIKED 179

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I N  + +S      + +   NE+G   A++HFKV++ F + +  +E Q  TGRTHQ
Sbjct: 180 TGTI-NAPIGRSKKDRKKMAI---NEEG-RPAVTHFKVLERFGE-YTLIECQLETGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP  G 
Sbjct: 234 IRVHLKYIGHPVAGDPLYGPRKTLKGNGQ-------FLHAKLLGFKHPRTGE 278


>gi|67920300|ref|ZP_00513820.1| Pseudouridine synthase, RluD [Crocosphaera watsonii WH 8501]
 gi|67857784|gb|EAM53023.1| Pseudouridine synthase, RluD [Crocosphaera watsonii WH 8501]
          Length = 313

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 88/335 (26%), Positives = 153/335 (45%), Gaps = 52/335 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-------KKRVKFNNRIQSG 62
           + VEN  +  RLD W  N    I+   +QK++  G + ++       K ++K  +R+Q  
Sbjct: 5   LTVENQGD--RLDIWLSNQLTDISRSRIQKLIEQGNITLNNEVCPNKKIKLKIGDRLQ-- 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V IP                     L    + +   +LYED ++ + NK A + V   
Sbjct: 61  --VNIP-----------------EPQPLELQPEPIPLDILYEDEQLIIINKSANLVVHPA 101

Query: 123 SG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      +   L    +  G    Q+P + HRLD++T+G +VVA+T  A Q+L    + 
Sbjct: 102 PGHETGTLVHALLYHCSNLAGIGGVQRPGIVHRLDKDTTGAIVVAKTDFAHQNLQFQIKN 161

Query: 177 RRIQKIYWSLVWGI------PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
           R  ++ Y  +++G+        N+ + + N  + +  +    + VV + EK    A++++
Sbjct: 162 RTAKREYLGIIYGVLNNEEDENNRDKGMINLPIGRHPVDRKRMAVVPR-EKPGREAVTYW 220

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKL 288
           ++I+     +  ++    TGRTHQ+RVH+ + G PIVGD  Y  N   K N +       
Sbjct: 221 EIIERLG-NYSLVKFILETGRTHQIRVHSSYFGNPIVGDPLYSNNRSLKMNLSGQ----- 274

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            LHA  + L HP    +++  APLP   +K  + L
Sbjct: 275 ALHAHKLTLTHPITSEKIEAIAPLPDEFIKLLNYL 309


>gi|299142141|ref|ZP_07035274.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           C735]
 gi|298576230|gb|EFI48103.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           C735]
          Length = 360

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 90/321 (28%), Positives = 153/321 (47%), Gaps = 49/321 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++     P+ +   +Q+   SG + V+ K VK N +++ G V+ +  
Sbjct: 30  VEVDMGQTPVRIDKFLAEKNPYQSRNRIQQAADSGFIHVNDKPVKSNYKVRPGDVITL-- 87

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I+   + L          ++YED  + V NK AG+ V  G+G     
Sbjct: 88  ---MLDRPKHDTSIVAEDIPLD---------IVYEDDALMVINKQAGMVVHPGAGNFTGT 135

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H+   L+S+ D+   +  L HR+D++TSG+LVVA+T  A   L + F  +   
Sbjct: 136 LINAVAWHLKD-LESF-DANDPEVGLVHRIDKDTSGLLVVAKTADAKSALGKQFFNKTTH 193

Query: 181 KIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + Y +LVWG   + +  I   + +  K+ +    + V   +      A++H++VI+ F  
Sbjct: 194 RSYNALVWGNLIDDEGTIEGNIARDPKNRL---RMKVFSPDSGIGKNAVTHYRVIERFGY 250

Query: 239 KF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQN--- 286
                C LE    TGRTHQ+R H  H+G P+  D  Y      +G  +S     IQN   
Sbjct: 251 TTLVECILE----TGRTHQIRAHMKHIGHPLFADATYGGEQVLRGQRSSTYKAFIQNCFK 306

Query: 287 ---KLYLHARYMDLPHPEGGR 304
              +  LHA+ +   HP  GR
Sbjct: 307 LCPRQALHAKTLGFVHPLTGR 327


>gi|120437019|ref|YP_862705.1| ribosomal large subunit pseudouridine synthase D [Gramella forsetii
           KT0803]
 gi|117579169|emb|CAL67638.1| ribosomal large subunit pseudouridine synthase D [Gramella forsetii
           KT0803]
          Length = 354

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 86/331 (25%), Positives = 149/331 (45%), Gaps = 47/331 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V E  +  +R+D++  N   +     +QK  +SG + V+   VK N +++ G  V++   
Sbjct: 27  VAEVGQNPLRVDKYLMNFIENATRNKIQKAAKSGNIYVNGDTVKQNYKVKGGDTVQV--- 83

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                H   E  ++   + L          ++YED  + V NK AG+ V  G G      
Sbjct: 84  --MFEHPPYEYLLVPEDIPLD---------IVYEDDTLLVVNKQAGMVVHPGHGNYSGTL 132

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + +H D    +  D    +P L HR+D++TSG+LVVA+T  A  HL++ F  +  ++
Sbjct: 133 INALVHHFDNLPNNSSD----RPGLVHRIDKDTSGLLVVAKTEEAMAHLSKQFFDKSSER 188

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF- 240
            Y ++VWG    ++  I   + +        +     + +    A++H+KV++       
Sbjct: 189 EYVAIVWGNLAEEEGTIEGNIGRNPRNRLQNIVFEGDDVENGKAAVTHYKVLERLGYVTL 248

Query: 241 --CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---------PIQN 286
             C LE    TGRTHQ+RVH  ++G  +  D +Y  +   KG  FT           I  
Sbjct: 249 VACKLE----TGRTHQIRVHMKYIGHTLFNDERYGGDRILKGTTFTKYKQFVDNCFKILP 304

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           +  LHA+ +   HP+    +   + +P  MV
Sbjct: 305 RQALHAKTLGFVHPKTEEWMSFNSDIPQDMV 335


>gi|42520963|ref|NP_966878.1| ribosomal large subunit pseudouridine synthase D [Wolbachia
           endosymbiont of Drosophila melanogaster]
 gi|42410704|gb|AAS14812.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Drosophila melanogaster]
          Length = 276

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 116/228 (50%), Gaps = 31/228 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I V +K +G++V  G+G   + D  L + +     +P + HRLD++TSG++V+
Sbjct: 50  IVYEDEDIIVLSKQSGLTVHPGAGT--NNDTLLNAVIAHLNVRPGIVHRLDKDTSGLMVI 107

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+  AA   L+E    R+I++ Y ++VWG   +++  I   +  K     + + V K   
Sbjct: 108 AKNEAAHSFLSELLSNRKIKREYLAVVWGTLSSQQGTIKTNIAPKRG-NKEMMCVTKITG 166

Query: 221 KGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-- 275
           K    AI+H+   KVI   +   C LE    TGRTHQ+RVH  H+G  IVGD  Y  N  
Sbjct: 167 K---LAITHYLVQKVIGQVSLVKCTLE----TGRTHQIRVHMSHIGHSIVGDQVYGKNSS 219

Query: 276 ----------FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                     F  NF     N+  LHA  + L HP+    ++  + LP
Sbjct: 220 KSTKYAKNSSFIRNF-----NRQALHAYTLGLYHPKSKEYMEFVSDLP 262


>gi|325184958|emb|CCA19450.1| ribosomal large subunit pseudouridine synthase C pu [Albugo
           laibachii Nc14]
          Length = 344

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 88/314 (28%), Positives = 152/314 (48%), Gaps = 29/314 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK--------KRVKFNNRIQSG 62
           ++  ++ N+RLDRW    +   +   +QK +R G +R+          +R   N ++QSG
Sbjct: 16  LLSPNDHNIRLDRWLSQEFGDKSNSFIQKHIRKGNIRLSVSQTKHERVRRAPANQKLQSG 75

Query: 63  QVVRIPP-VINALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            +V I     +  +    E   L+  ++  K + + L   + Y D+  ++ +KP+G++VQ
Sbjct: 76  NLVAIRKNTFHEFSQKTNEFLPLEPFISSEKRYFEALYERIRYRDANYFILDKPSGLAVQ 135

Query: 121 GGSGIAYHIDGFLKSWVDSKGQK-------------PRLTHRLDQETSGILVVARTRAAA 167
           GG      +  +   + +   +              PRL HR+D+ TSG++V+AR R AA
Sbjct: 136 GGERSTKSLADYFHMFHERLSKTDDPEMDYEILPELPRLVHRIDKGTSGLVVIARHRRAA 195

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
              +E  R RRI+K Y + V  IP    E      L+    G + + + K  +   +  I
Sbjct: 196 AAFSELLRERRIEKEYQAFV--IPSRTFEVPETGRLESVIEGKEAITMYKVIDP-VSREI 252

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           +  K+   F Q  C L++ P TGR HQ+R+H A  +  PI+GD +Y    + N    + N
Sbjct: 253 TLAKLSFEFPQGKC-LKVWPITGRKHQIRIHCATILHAPILGDGRYGCR-ESNALDLLPN 310

Query: 287 KLYLHARYMDLPHP 300
           ++YLHA  +  P+P
Sbjct: 311 RMYLHAAKISFPNP 324


>gi|291166433|gb|EFE28479.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Filifactor alocis ATCC 35896]
          Length = 293

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 91/307 (29%), Positives = 146/307 (47%), Gaps = 37/307 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  ++ P I+   +QK++   +V V+ K  K +  ++S   + I        +I 
Sbjct: 1   MRLDQFISSNLPSISRSYIQKLIDEKRVLVNGKYEKKSFLLKSFDNIEI--------YIP 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
           + + I  S  N+  +       +L+ED  I + NK  G+ V    G         I YH 
Sbjct: 53  EPKSIEISPENIPLN-------ILFEDKDILIVNKEKGMVVHPAPGNYSHTLVNAILYHC 105

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G L     +   +P + HR+D++TSGILV+A+   A Q L+E F+   IQ+ Y  + +G
Sbjct: 106 KGNLSEI--NGYIRPGIVHRIDKDTSGILVIAKNNDAHQFLSEQFKEHSIQREYQLITFG 163

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             K     I   + +           V  N K    AI+H  VI+ F  K  +L+ +  T
Sbjct: 164 NIKTTHLSIEQPIGRNP--KNRLQMAVVPNGKP---AITHLTVIENFKDK-TYLKARLET 217

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P++GD  Y  N K  +    Q    LHA Y+   HP   + ++  
Sbjct: 218 GRTHQIRVHCTYIGHPLLGDSLY-TNRKCEYQLQGQT---LHAGYLGFVHPTSKKFIEFY 273

Query: 309 APLPAHM 315
           +PLP + 
Sbjct: 274 SPLPEYF 280


>gi|254478536|ref|ZP_05091911.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
 gi|214035544|gb|EEB76243.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
          Length = 309

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 96/346 (27%), Positives = 162/346 (46%), Gaps = 57/346 (16%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  +V+  E ++E  R+D +  +   + +   ++K++  G V V+ K VK + +++ 
Sbjct: 1   MNIVDRIVLQGEKEDEGKRIDVFLASELDY-SRSYIKKLIEEGLVLVNGKNVKPSYKVKE 59

Query: 62  GQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
               VV IP        ++ E   LD               +LYED  I V NKP G+ V
Sbjct: 60  DDEVVVNIPEAEKI--EVVPENIPLD---------------ILYEDEDIIVINKPQGMVV 102

Query: 120 QGGSG---------IAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
               G         + YH      I+G L+         P + HRLD++TSG++VVA+  
Sbjct: 103 HPAPGNYSGTLVNALLYHCKNLSGINGILR---------PGIVHRLDKDTSGVMVVAKND 153

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            A   L+   + R + K Y ++V G+ K ++E      + +  +    + VV+       
Sbjct: 154 KAHMSLSNQIKERSVLKKYVAIVEGVIK-EEEGKIEAPIGRHPVDRKRMAVVQD----GR 208

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           YA++ +KV++ F     ++E    TGRTHQ+RVH  ++G P+VGD  Y    K  F    
Sbjct: 209 YALTLYKVLERFKNN-TFVEATIKTGRTHQIRVHFSYIGHPVVGDPVYGYK-KQKFKLEG 266

Query: 285 QNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           Q    LH++ +   HP +G  ++  APLP +  +  + L  + DR+
Sbjct: 267 QA---LHSKVLGFIHPTKGVYMEFEAPLPDYFTRLLEILRAEKDRD 309


>gi|297839759|ref|XP_002887761.1| hypothetical protein ARALYDRAFT_477057 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297333602|gb|EFH64020.1| hypothetical protein ARALYDRAFT_477057 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 477

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 77/248 (31%), Positives = 122/248 (49%), Gaps = 25/248 (10%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD---FLKSILLYE 104
           +  +++K N  ++ G  + +P  I  +  I K    + S   L  ++D   +L+ ++ ++
Sbjct: 126 IPMRKIKHNEVMEIGDKIWLPVSIAEM-RISKRYDTIPSG-TLYPNADEIAYLQRLVRFK 183

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVART 163
           DS I V NKP  + V+G   I   +D    + +   K + PRL HRLD+ETSG+LV+ R+
Sbjct: 184 DSAIIVLNKPPKLPVKGNVPIHNSMDALAAAALSFGKDEGPRLVHRLDRETSGLLVMGRS 243

Query: 164 RAAAQHLTESFR---------------MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           + +  +L   F                   + + YW+LV G PK K+  I+  L K    
Sbjct: 244 KESIHYLHSVFSDYKGRNSSCKAWNKACEAMYQQYWALVIGSPKEKEGLISAPLSKVLLD 303

Query: 209 GGDYVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC 264
            G    VV     G   +  AI+ ++V+        WLE++P T R HQLRVH A  +G 
Sbjct: 304 DGKTDRVVLAQGSGFEASQEAITEYRVLGPMINGCSWLELRPITSRKHQLRVHCAEALGT 363

Query: 265 PIVGDHKY 272
            IVGD+KY
Sbjct: 364 SIVGDYKY 371


>gi|289547904|ref|YP_003472892.1| pseudouridine synthase [Thermocrinis albus DSM 14484]
 gi|289181521|gb|ADC88765.1| pseudouridine synthase, RluA family [Thermocrinis albus DSM 14484]
          Length = 324

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 76/269 (28%), Positives = 136/269 (50%), Gaps = 28/269 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           VE  +   RLD++    YP  +   +++++  G V VD + V K + +++ G+VV +   
Sbjct: 14  VEEHQAGKRLDQFLAEAYPDFSRSYIKELVEGGYVLVDGQVVYKPSRKVKGGEVVVL--- 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-- 128
                        +     L+  ++ +   +LYED  + V  KP G+ V    G      
Sbjct: 71  ------------CVPKVEPLSLPAEDIPLEILYEDDDLAVVVKPCGLVVHPSPGYTSGTL 118

Query: 129 IDGFLKSWVD--SKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L  W D  + G+  +P + HRLD+ T G++VVA+   A + L E F  R++ K+Y 
Sbjct: 119 VNALLFRWRDLPTVGEWYRPGIVHRLDRNTMGVMVVAKRELAHRRLAEQFEKRKVLKVYR 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWL 243
           +LV G+ +  +  ++  L +       +      +EKG + AI+H+KV+  + +     L
Sbjct: 179 ALVKGLVERDEGTLSMPLARDPRHRKRFT----VSEKGRD-AITHYKVLKRYRSLSVSLL 233

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           E++ +TGRTHQ+RVH   +G P++GD  Y
Sbjct: 234 EIRIYTGRTHQIRVHMAGIGHPVLGDRIY 262


>gi|103487227|ref|YP_616788.1| pseudouridine synthase, RluD [Sphingopyxis alaskensis RB2256]
 gi|98977304|gb|ABF53455.1| ribosomal large subunit pseudouridine synthase D [Sphingopyxis
           alaskensis RB2256]
          Length = 376

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 84/339 (24%), Positives = 154/339 (45%), Gaps = 52/339 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV-- 64
           +  V + +    +RLDR      P+++   L+ +++ G+V      + ++   ++     
Sbjct: 65  ILTVTLGDTAAGLRLDRALAEALPNLSRERLKSLIKGGRVVDAHGAILWDPAAKAAPPAT 124

Query: 65  --VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +R+P  + A N                  +  L  ++ YED+ + V +KPAG+ V   
Sbjct: 125 IEIRVPAALPAHNA-----------------AQDLDLVIAYEDAHLIVIDKPAGMVVHPA 167

Query: 123 SGIAYHIDGFLKSWV--DSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           +G   ++DG + + +     GQ        +P + HR+D++TSG++V A+   A + L +
Sbjct: 168 AG---NLDGTMVNALLHHCAGQLSGIGGVARPGIVHRIDKDTSGLIVAAKHDKAHEGLAK 224

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F    I + Y ++  G P      + +  L +S      + VV        +A++H++ 
Sbjct: 225 QFAAHSIDRRYLAIATGRPMPANGTV-DAALGRSATNRKKMAVVAAGR--GKHALTHYRT 281

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---- 288
           ++   Q    +E +  TGRTHQ+RVH  H+G P+VGD  Y     G    P+ + L    
Sbjct: 282 VEPL-QGATLIECRLETGRTHQVRVHMAHIGHPLVGDPVY-----GRARKPLSDVLKARN 335

Query: 289 ----YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                LHA ++   HP  G R+ + + LPA M +  D L
Sbjct: 336 FARQALHAAHLGFIHPVTGNRIALDSELPADMRELIDEL 374


>gi|298346986|ref|YP_003719673.1| putative pseudouridylate synthase [Mobiluncus curtisii ATCC 43063]
 gi|298237047|gb|ADI68179.1| possible pseudouridylate synthase [Mobiluncus curtisii ATCC 43063]
          Length = 304

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 87/290 (30%), Positives = 140/290 (48%), Gaps = 28/290 (9%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +L SG V  D + +K ++++ +G ++ I   I      + E   +D   NL         
Sbjct: 34  LLESGAVIQDGETLKKSDQLAAGNLLEID--IPEPTGYVPEVTRVD---NLG-------- 80

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQE 153
            +LY D  + V +KPAG++   G G     + G L++    V + G   R  + HRLD  
Sbjct: 81  -ILYADDDLVVVDKPAGVAAHTGPGWEGPTVVGALRAAGIRVSTSGPVEREGIVHRLDAG 139

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG +VVA++  A   L   FR  R++KIY +L  G  K     I   + +    G ++ 
Sbjct: 140 TSGAMVVAKSELAYGKLKNEFRYHRVEKIYTALATGKVKPPVGTIDAPIGRAP--GREFK 197

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V     G   A++H+ +I+        L++Q  TGRTHQ+RVH   +G P+VGD +Y 
Sbjct: 198 MAVVS---GGKPAVTHYDIIEEL-PGATLLKVQLETGRTHQIRVHLAAIGHPLVGDTEYG 253

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A+ K      ++ + +LHA  +   HP  G  + + APLPA +    + L
Sbjct: 254 ADRKTAARLGLERQ-WLHASRLAFKHPRTGLEVAVQAPLPADLATAVELL 302


>gi|254478004|ref|ZP_05091388.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
 gi|214036008|gb|EEB76698.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
          Length = 309

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 94/344 (27%), Positives = 167/344 (48%), Gaps = 53/344 (15%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  +V+  E ++E  R+D +  +   + +   ++K++  G V V+ K VK + +++ 
Sbjct: 1   MNIVDRIVLQGEKEDEGKRIDVFLASELDY-SRSYIKKLIEEGLVLVNGKNVKPSYKVKE 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              +    V+N     IKE + ++         + +   +LYED  I V NKP G+ V  
Sbjct: 60  DDEI----VVN-----IKEAEKIEVV------PENIPLDILYEDEDIIVINKPQGMVVHP 104

Query: 122 GSG---------IAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
            +G         + YH      I+G L+         P + HRLD++TSG++VVA+   A
Sbjct: 105 AAGNYSGTLVNALLYHCKNLSGINGILR---------PGIVHRLDKDTSGVMVVAKNDKA 155

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
              L+   + R + K Y ++V G+ K ++E      + +  +    + VV++      YA
Sbjct: 156 HMSLSNQIKERSVLKKYIAIVEGVIK-EEEGKVEAPIGRHPVDRKRMAVVQE----GRYA 210

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++ +KV++ F     ++E    TGRTHQ+RVH  ++G P+VGD  Y    K  F    Q 
Sbjct: 211 LTLYKVLERFKNN-TFVEATIKTGRTHQIRVHFSYIGHPVVGDPVYGYK-KQRFKLEGQA 268

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
              LH++ +   HP +G  ++  APLP +  +  + L  + DR+
Sbjct: 269 ---LHSKVLGFIHPTKGVYMEFEAPLPDYFTRLLEILRAEKDRD 309


>gi|126032015|gb|ABN71573.1| putative pseudouridylate synthase [uncultured bacterium]
          Length = 353

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 81/295 (27%), Positives = 135/295 (45%), Gaps = 36/295 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+      P ++   LQ+ + +G V V+   V+  + +  G VV++ P          
Sbjct: 45  RLDKALAFLIPDVSRSRLQQWVVAGAVTVNGGAVRARHTLTFGDVVKVTP---------- 94

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            Q   D++       + +   +++ED  I V NKP  + V   +G      ++G L ++ 
Sbjct: 95  -QPAPDAAA---YKPEPMPLEVIFEDDAILVLNKPPKLVVHPAAGHWSGTLLNGLL-AYA 149

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    PR  + HRLD +TSG++VVA+T AA   L    + R + + YW+LV G+P  + 
Sbjct: 150 PTLIDVPRAGIVHRLDADTSGLMVVAKTLAAQTDLVRQLQSRTVTREYWALVLGVPSQRG 209

Query: 196 ECIANWLLKKSHIGGDYVHVVK---QNEKGANYAISHFKVIDC---FAQKFCWLEMQPHT 249
                  +  + IG D  + ++      + A  A +H+  +D          WL  +  T
Sbjct: 210 -------VIDAAIGRDPRNPLRFKVSTTEAAKPARTHYATLDSTKNAGADISWLACRLET 262

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY----LHARYMDLPHP 300
           GRTHQ+RVH  H+G P++GD  Y            + K +    LHA  + L HP
Sbjct: 263 GRTHQIRVHLEHVGHPLIGDPVYRRRLPPRGEPAARWKEFDRQALHACRLALDHP 317


>gi|39998442|ref|NP_954393.1| RNA pseudouridine synthase family protein [Geobacter sulfurreducens
           PCA]
 gi|39985389|gb|AAR36743.1| RNA pseudouridine synthase family protein [Geobacter sulfurreducens
           PCA]
          Length = 296

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 78/324 (24%), Positives = 143/324 (44%), Gaps = 46/324 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPV 70
           V  D+  +RLD      +P ++   ++ I+  G   V    V+  + R+Q+G  + +   
Sbjct: 7   VGADQAGVRLDEGAARLFPQLSKTRIRTIIDWGGCAVGGTMVRVASRRLQAGDEIVL--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 +++ ++  +  + L          +L+ED      NK +G++ Q      Y + 
Sbjct: 64  -----GVMEPERYRE--ITLAPED------ILFEDGGYLAVNKASGLNCQR---TPYQLK 107

Query: 131 GFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G ++  V          +  R+ HRLD+ TSG+++   +R AA H++   +  R++K+YW
Sbjct: 108 GTVEYAVTLHFRACGSAEPARVIHRLDRGTSGVMIFPASRRAAAHISRELKEGRVEKVYW 167

Query: 185 SLVWGIPKNKKECIANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           +LV G+P        +W +    + +G     V    +     A++ F+V+         
Sbjct: 168 ALVAGMPLAD-----SWQVDAPVAKVGTSRYGVAPVGKA----ALTEFRVV-ARGNGATL 217

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +P TGRTHQ+RVH  H G  I+GD  Y     G   +P   ++ LH R M     +G
Sbjct: 218 VEARPRTGRTHQIRVHLAHGGLSIIGDTTY-----GGIAAP---RMMLHCRTMTFRAEDG 269

Query: 303 GRLQITAPLPAHMVKTWDSLGFKY 326
             +  TAP         +  G ++
Sbjct: 270 RPVSATAPPDREFTAACEQHGIQF 293


>gi|85704967|ref|ZP_01036067.1| ribosomal large subunit pseudouridine synthase D [Roseovarius sp.
           217]
 gi|85670289|gb|EAQ25150.1| ribosomal large subunit pseudouridine synthase D [Roseovarius sp.
           217]
          Length = 342

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 93/351 (26%), Positives = 151/351 (43%), Gaps = 64/351 (18%)

Query: 14  NDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
            D+   RLD+      P    ++   L ++L  G V+V+   ++    R+ +G ++ I  
Sbjct: 11  GDDPPQRLDKALSRDVPEEATLSRTRLARLLEEGAVQVNGAVMRDAKARVTAGDLIEI-- 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L    +E  I   ++ LT         ++YED  + V NKPAG+ V    G     
Sbjct: 69  ----LVPEARESHISAEAIALT---------VVYEDDDLIVINKPAGMVVHPAPGSPEGT 115

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + +H    L     SK  +P + HR+D++TSG+LVVA++ AA Q L   F    ++
Sbjct: 116 LVNALLHHCGDSLSGVGGSK--RPGIVHRIDKDTSGLLVVAKSDAAHQGLAAQFEAHSVE 173

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV---------KQNE----KGANYAI 227
           + Y ++V G+P      +   L   S   G+ + +          +Q +    +G  +A+
Sbjct: 174 RSYRAVVNGVPDAGDPRL-RGLPGISFEAGNILRIATRLARHKTDRQKQAVLFEGGRHAV 232

Query: 228 SHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           +  +VI+ F          CWLE    TGRTHQ+RVH  H G  ++GD  Y    K +  
Sbjct: 233 TRARVIESFGTPGVVSLMECWLE----TGRTHQIRVHMAHAGHGLIGDPVYGGRRKLSEK 288

Query: 282 SPIQN---------KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           +             +  LHA  +   HP  G  L+  A LP  M     +L
Sbjct: 289 ALSATAVAAARDFPRQALHAAVLGFVHPVSGMALRFEAALPEDMTTLIAAL 339


>gi|297621954|ref|YP_003710091.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
 gi|297377255|gb|ADI39085.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
          Length = 214

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 71/208 (34%), Positives = 106/208 (50%), Gaps = 16/208 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRL----THRLDQETS 155
           +LYED+ + V  KP G+  Q        ++   K W+  S G++  +     HRLDQ   
Sbjct: 5   ILYEDNHLLVLEKPGGVLTQPSGTNQISLEEMGKQWIKKSYGKQGNVFLEAVHRLDQAAC 64

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+TR A   L  + R +R++K Y + V   P+  +  + ++L+ K H       V
Sbjct: 65  GIVVFAKTRKALSRLMLAIREKRVKKWYRTQVECAPQQNEGRLIHYLMHKKH----RAEV 120

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  +E GA YA   +KVI     K+  LE+Q  TGR HQ+R     +GCPI+GD KY ++
Sbjct: 121 VSGDELGAKYASLTYKVIK--PGKYPILEIQLETGRYHQIRCQLSAIGCPIIGDKKYGSS 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
               +  P       H R M++PHP  G
Sbjct: 179 IP--YHGP--GIALCHVR-MEIPHPVTG 201


>gi|268319474|ref|YP_003293130.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
 gi|262397849|emb|CAX66863.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
          Length = 304

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 91/323 (28%), Positives = 155/323 (47%), Gaps = 49/323 (15%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV--VRIPPVIN 72
           D E  RLD+        ++   +++++    + V+ K  K + ++QSG V  V IPPV  
Sbjct: 10  DGEKGRLDKVITEKITDLSRTKIKELVNDKNILVNNKAEKVSYKVQSGDVIDVTIPPV-- 67

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--ID 130
                            L+  ++ L   ++YEDS + V NKP G+ V   +G   H  ++
Sbjct: 68  ---------------KPLSLEAENLHLDIVYEDSDVIVVNKPQGMVVHPSAGHPDHTLVN 112

Query: 131 GFL---KSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           G L   +   DS +G +P + HR+D++TSG+L++A+   A + L +    +  ++ Y ++
Sbjct: 113 GLLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMIAKNDRARESLEKQLAKKINKREYLAI 172

Query: 187 VWGIPKNKKECIANWLLKKSHIG---GDYVHVVKQ---NEKGANYAISHFKVIDCFAQKF 240
           V G          N+ +K   I    G   +  KQ   N KG   A++HF V++ F + +
Sbjct: 173 VHG----------NFEVKNGVINAPIGRNPNSRKQMAVNPKG-KAAVTHFTVLEQF-KNY 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             ++    TGRTHQ+RVH  ++G P+ GD  Y    K   +   Q   +LHA+ +    P
Sbjct: 221 SLVKCVLETGRTHQIRVHMKYIGHPLAGDPLYGP--KKTLSGHGQ---FLHAKTLGFYQP 275

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                L+ +APLP    K  ++L
Sbjct: 276 STNEWLEFSAPLPTIFEKQLENL 298


>gi|296123212|ref|YP_003630990.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
 gi|296015552|gb|ADG68791.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
          Length = 623

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 71/217 (32%), Positives = 107/217 (49%), Gaps = 13/217 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  I V NKPA + V        +   +L + +    Q PR  HRLD  T+G+LV++
Sbjct: 406 LYEDESIVVINKPAPLPVHASGRFHRNTLQYLLAQIYDP-QSPRAAHRLDAMTTGVLVLS 464

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-ECIANWLLKKSHIGGDYVHVVKQNE 220
           RTR  A  L   F  R ++K+Y + V G P  +  EC A        +G   +     +E
Sbjct: 465 RTRHMAGRLQPQFSRREVEKVYLARVQGEPAEESFECHAPMTDVAGVMGSRDI-----DE 519

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            G   A + F+++         LE++P TGRT+Q+RVH  H+G PI+GD  Y  +  G  
Sbjct: 520 SGGVEASTLFRLVQRLEDGTSLLEVRPITGRTNQIRVHLWHLGLPILGDPLYLPS--GEL 577

Query: 281 TSPIQNK---LYLHARYMDLPHP-EGGRLQITAPLPA 313
            +  ++    + LHA  +   HP +   ++  AP PA
Sbjct: 578 ATEPKDSEQVMCLHAWRICFQHPVDRTTMEFMAPPPA 614


>gi|150020811|ref|YP_001306165.1| RluA family pseudouridine synthase [Thermosipho melanesiensis
           BI429]
 gi|149793332|gb|ABR30780.1| pseudouridine synthase, RluA family [Thermosipho melanesiensis
           BI429]
          Length = 293

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 92/311 (29%), Positives = 141/311 (45%), Gaps = 40/311 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHII 78
           RLD++ +    ++    + KI+R G+V V+ KRVK  + R++ G  + I       N   
Sbjct: 11  RLDKFLRKQLQNMPLSAIYKIIRKGKVLVNGKRVKEPSFRLEIGDEIEIKEETTKYNRE- 69

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
           K  +I+   ++           +LYED  + + NKPAGI +  G G  IA  I+G +  +
Sbjct: 70  KNNQIIPIKMDFE---------ILYEDENLLIINKPAGIPIHPGKGTHIATLIEGLM-YY 119

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                  P L HRLD+ TSG+ VVA+    A+ L E    R ++K+Y +L  G  K K E
Sbjct: 120 GKEHNFTPYLVHRLDKHTSGVFVVAKNVNTARELNEIISSRAVEKVYTTLCVGEMK-KSE 178

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   L  K+ +        KQ + G  Y              F  L +Q  TGR HQ+R
Sbjct: 179 VIKIPLDGKNAV--TIYEKQKQFKSGLGY--------------FSLLRVQIKTGRKHQIR 222

Query: 257 VHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
            H   +G P++GD  Y        FK  +      + +LH   M L + +   ++I APL
Sbjct: 223 KHLSLIGHPVIGDDLYGDKKLNRKFKQKYA---LKRYFLHCSMMLLYYND-KEIRINAPL 278

Query: 312 PAHMVKTWDSL 322
           P  +     +L
Sbjct: 279 PNDLKDVLKNL 289


>gi|308048517|ref|YP_003912083.1| ribosomal large subunit pseudouridine synthase D [Ferrimonas
           balearica DSM 9799]
 gi|307630707|gb|ADN75009.1| ribosomal large subunit pseudouridine synthase D [Ferrimonas
           balearica DSM 9799]
          Length = 323

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 95/341 (27%), Positives = 158/341 (46%), Gaps = 52/341 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           V+ + +   RLD+     +P  +   +++ + + +V ++ K V K   ++  G+ V I  
Sbjct: 10  VISDSQLGQRLDQALAECFPDYSRSRIKEWILAERVSLNGKTVAKPREKVMGGEAVLI-- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                      Q   +  V   K  D    I+ YED  I V NKPA + V  G+G   H 
Sbjct: 68  -----------QAEFEEEVA-AKPQDIALDIV-YEDDDILVINKPADLVVHPGAG--NHD 112

Query: 130 DGFLKSWV---DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              L + +    S    PR  + HRLD++T+G++VVA+T  A  HL    + R I + Y 
Sbjct: 113 GTVLNALLHHCPSIANVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVAQLQAREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G+     +  E I     +++H+           E G   A++H+++ + F +   
Sbjct: 173 AIALGVMTAGGHVDEPIGRHPQRRTHMA--------VTELG-KPAVTHYRIREKF-RAHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG--NFTSPIQ------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+G P+VGD  Y    +    ++  ++      N+  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHLGHPLVGDPLYSGRPRPVKGWSEELREFLRRFNRQALHAA 282

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSL-------GFKY 326
            + L HP  G  +Q TAP+P  MV+  + L       GF Y
Sbjct: 283 MLRLEHPITGEMMQWTAPIPDDMVRLTELLRRDTEEHGFDY 323


>gi|317970429|ref|ZP_07971819.1| putative pseudouridylate synthase [Synechococcus sp. CB0205]
          Length = 207

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 70/213 (32%), Positives = 114/213 (53%), Gaps = 17/213 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+YED  + V  KP+G+  Q   G+   +   L + V S+  + RL HRLD++TSG++VV
Sbjct: 7   LVYEDPALLVLEKPSGLLSQ--PGLGPELSDSLITAVQSEWPEARLVHRLDRDTSGLIVV 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR+    + L+E+F  RR++K Y + V G+P  ++  I + + K+ H    Y       +
Sbjct: 65  ARSALVHRTLSEAFAERRVEKRYVADVSGVPDGEEGWIDHPIAKRQHRPPLY-----GVD 119

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                  +H++ +         L +QP TGR+HQLRVH   +G PI+GD  Y     G  
Sbjct: 120 PAGKPCRTHWR-LSAQHSSCSRLALQPLTGRSHQLRVHLQALGHPILGDPLY-----GER 173

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           ++    +L+LHA  ++  HP  GR +   +P+P
Sbjct: 174 SA---ARLHLHACCLEFSHPSDGRWMHFDSPVP 203


>gi|317056645|ref|YP_004105112.1| RluA family pseudouridine synthase [Ruminococcus albus 7]
 gi|315448914|gb|ADU22478.1| pseudouridine synthase, RluA family [Ruminococcus albus 7]
          Length = 304

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 83/319 (26%), Positives = 150/319 (47%), Gaps = 40/319 (12%)

Query: 16  EENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           EEN+  R+D+      P ++  +LQK++  G V V+   V  N +I++   + +      
Sbjct: 11  EENIGDRIDKVLSKQLPEMSRSSLQKLVNDGCVLVNGNIVSKNYKIKNSDTISVE----- 65

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
                     +  +  L      +   ++YED  + V NKP G+ V   +G         
Sbjct: 66  ----------IPEAEELKAEPQDIPIDIVYEDDSLLVVNKPQGMVVHPAAGNPDGTLVNA 115

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +H  G L S   +   +P + HR+D+ TSG+L+VA+T  A   L +  +     + Y 
Sbjct: 116 LLFHCKGRLSSI--NGVIRPGIVHRIDKFTSGLLMVAKTDKAHNFLAQQIKDHNFTREYN 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G  K     + N  + +S      + V  QN K    A++H++V++   Q +  ++
Sbjct: 174 AICIGRFKEPTGTV-NEPIGRSKFDRKKMCVTYQNCK---EAVTHYEVLEDLGQ-YSLVK 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQ+RVH+  +G P++GD  Y   +KG     ++ +  LHA+ +   HPE   
Sbjct: 229 FRLETGRTHQIRVHSAFIGHPVLGDDVYGKAYKG-----LEGQC-LHAKKLGFIHPETKE 282

Query: 305 -LQITAPLPAHMVKTWDSL 322
            ++  + LP + VK  + L
Sbjct: 283 YMEFDSELPVYFVKVLEKL 301


>gi|126695551|ref|YP_001090437.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9301]
 gi|126542594|gb|ABO16836.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9301]
          Length = 319

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 92/321 (28%), Positives = 148/321 (46%), Gaps = 42/321 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +  P  +   +Q  + SG V V+ K  K    +++G  ++I  PP    L +
Sbjct: 27  MRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNIQIWMPPP-EPLIY 85

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E+  L+               +L+ED  I V NK +G+ V    G      ++G L 
Sbjct: 86  LKPEKMDLN---------------ILFEDEHIIVINKQSGLIVHPAPGNKSGTLVNGLLF 130

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++TSG +VVA+++ A  +L +  + +   + Y +++ G 
Sbjct: 131 HCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGA 190

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           P +++  I        HIG D ++ +K     E    YA +++K+ + F   +  +  + 
Sbjct: 191 PNSEEGQIV------GHIGRDKLNRLKYKVVEETSGRYARTYWKLEERFGN-YSLMSFKL 243

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            TGRTHQ+RVH  H+  PIVGD  Y  C            +   LHA  + L HP  G+ 
Sbjct: 244 DTGRTHQIRVHCAHINHPIVGDPLYGRCKKLPCKL-----DGQALHAIKLGLIHPINGKE 298

Query: 306 QI-TAPLPAHMVKTWDSLGFK 325
            I  + LP    K    L  K
Sbjct: 299 MIFESELPLDFQKLLSVLKVK 319


>gi|319786173|ref|YP_004145648.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317464685|gb|ADV26417.1| pseudouridine synthase, RluA family [Pseudoxanthomonas suwonensis
           11-1]
          Length = 326

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 85/327 (25%), Positives = 148/327 (45%), Gaps = 48/327 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             V ++    R D      +P  +   L   ++SG   +D +  +  + ++ G+ V +  
Sbjct: 11  ATVPDEAAGRRFDAVLAELFPEYSRSRLAAWIKSGDALLDGQPARPRDAVKGGETVSLAE 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
           V       + E   LD               +LY+D  ++V +KPAG+ V  G+G     
Sbjct: 71  VSEIQTEAVAEDIPLD---------------VLYQDEHLFVLDKPAGLVVHPGAGNPAGT 115

Query: 125 ---IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                 H D  L +        PR  + HRLD++TSG++VVART  A   L      R +
Sbjct: 116 LVNALLHRDPGLAAL-------PRAGIVHRLDKDTSGVMVVARTLQAHTGLVAQLAAREV 168

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y ++V G   +     AN  + + H        V+++ + A   ++H+++ + F + 
Sbjct: 169 RRQYVAVVVGALVSG--GTANAPIDR-HPRDRLRMAVREDGRDA---VTHYRLRERF-RA 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLH 291
              LE +  TGRTHQ+RVH  H+  PIVGD  Y    K       +  + ++   +  LH
Sbjct: 222 HTALECRLETGRTHQIRVHMQHLRHPIVGDPLYGGPLKLPRGATEDLVASLRGFGRQALH 281

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVK 317
           A  ++  HP  G ++++ APLP  M++
Sbjct: 282 AEVLEFQHPVTGAQVRVEAPLPKDMLE 308


>gi|229587213|ref|YP_002845714.1| Ribosomal large subunit pseudouridine synthases RluD subfamily
           protein [Rickettsia africae ESF-5]
 gi|228022263|gb|ACP53971.1| Ribosomal large subunit pseudouridine synthases RluD subfamily
           protein [Rickettsia africae ESF-5]
          Length = 313

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 86/322 (26%), Positives = 149/322 (46%), Gaps = 52/322 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD+   +   +++   +QK ++  QV V+              ++  P V+   N II
Sbjct: 13  IRLDKALSSLLENVSRNQIQKAIKDSQVLVND------------VIISDPDVLVKENDII 60

Query: 79  -------KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +E KI  ++V L          ++YED  + V NK AG++V  G+G  +H D 
Sbjct: 61  LFSFKEPEELKIATANVALD---------IIYEDDDLIVINKAAGMTVHPGAG--HHDDT 109

Query: 132 FLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + + +            ++P + HRLD++T+G++VVA+   A   L      R++ + Y
Sbjct: 110 LVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCW 242
             LVWG+  N  E +    + +S      + ++K    G   A++H+K ++ F +     
Sbjct: 170 KVLVWGVI-NPLEGVIKNNIGRSRSDRQKMTILKY---GGKEAVTHYKTLELFYKGSISM 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLY------LHARY 294
           +E +  TGRTHQ+RV   H+   IVGD  Y  N +    SP  ++ KL       LH+ Y
Sbjct: 226 VECKLSTGRTHQIRVQLSHLKHSIVGDQTYGNNDRKIAHSPPELKAKLIDFKRQALHSWY 285

Query: 295 MDLPHPEGGR-LQITAPLPAHM 315
           +   HP     ++ +  LP  M
Sbjct: 286 LSFTHPTSNEIMEFSCELPRDM 307


>gi|226226809|ref|YP_002760915.1| ribosomal large subunit pseudouridine synthase D [Gemmatimonas
           aurantiaca T-27]
 gi|226090000|dbj|BAH38445.1| ribosomal large subunit pseudouridine synthase D [Gemmatimonas
           aurantiaca T-27]
          Length = 329

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 85/314 (27%), Positives = 142/314 (45%), Gaps = 35/314 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IPPVINALNHI 77
           RLD    +H   ++      ++ +G V V+  R K + + ++G VVR  IPP       I
Sbjct: 20  RLDLLVADHA-SVSRTQAATLIANGNVLVNGAREKASYKGETGDVVRVTIPPPPG--RDI 76

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGF 132
           + EQ  LD               ++YED  + V +K AG+ V    G     +   + G 
Sbjct: 77  VAEQIPLD---------------VVYEDEHLLVVDKAAGMVVHPAPGNWTGTLVNALLGR 121

Query: 133 LKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +   +  G+ +  L HRLD++TSG+LVVA++ AA + L+ +   R++ + Y ++ WG  
Sbjct: 122 GEPLAEGGGEDRAGLVHRLDKDTSGLLVVAKSDAAHRTLSSALAARQVTRRYAAVCWGHL 181

Query: 192 KNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             ++  +   + +      D   + + Q+ K +    +     D        L    HTG
Sbjct: 182 AEERITVEKPIARDPR---DRTRMAIVQSGKASRTDFTRLARFDS----VDLLRAHLHTG 234

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITA 309
           RTHQ+RVH    G P+VGD  Y              + +LHA ++   HP  G L  + +
Sbjct: 235 RTHQIRVHLASTGHPVVGDDTYGGGGGRRLALLPPRRHFLHAAWLRFRHPISGDLIDLRS 294

Query: 310 PLPAHMVKTWDSLG 323
           PLPA +  +  +LG
Sbjct: 295 PLPADLRTSLAALG 308


>gi|91216414|ref|ZP_01253381.1| ribosomal large subunit pseudouridine synthase [Psychroflexus
           torquis ATCC 700755]
 gi|91185552|gb|EAS71928.1| ribosomal large subunit pseudouridine synthase [Psychroflexus
           torquis ATCC 700755]
          Length = 345

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 84/328 (25%), Positives = 147/328 (44%), Gaps = 49/328 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI----PPVI 71
           +E +R+D++  N   +     +Q+  + G + V+   VK N ++++G  V++    PP  
Sbjct: 25  QEPLRVDKFLMNFIENATRNKVQQAAKDGNIYVNGIPVKQNYKVKAGDEVKVLLAYPPYE 84

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------- 124
           N L     E   LD               ++YED  + V NK AG+ V  G G       
Sbjct: 85  NLL---TPEDIPLD---------------IVYEDDALLVVNKAAGMVVHPGHGNYSGTLI 126

Query: 125 --IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + YH +    +  D    +P L HR+D++TSG+LVVA+T AA  +L+  F  +  ++ 
Sbjct: 127 NALVYHFENLPNNSSD----RPGLVHRIDKDTSGLLVVAKTEAAMAYLSRQFFHKTSKRE 182

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++ WG    ++  I   + +        +  +  +      A++H+KVI+        
Sbjct: 183 YVAIAWGNLNEEEGTIEGNIGRNPKNRLQNIVYLGDDADQGKPAVTHYKVIERLGY-VTL 241

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---------PIQNKLYL 290
           +  Q  TGRTHQ+RVH  H+G  +  D +Y  +   KG  FT           +  +  L
Sbjct: 242 ISCQLETGRTHQIRVHLKHIGHTLFNDERYGGDKILKGTTFTKYKQFVDNCFKVLPRQAL 301

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVK 317
           HA+ +   HP     ++  + +P  M +
Sbjct: 302 HAKKLAFEHPTTKEWMEFNSEIPEDMTQ 329


>gi|163758760|ref|ZP_02165847.1| putative ribosomal large subunit pseudouridine synthase protein
           [Hoeflea phototrophica DFL-43]
 gi|162284050|gb|EDQ34334.1| putative ribosomal large subunit pseudouridine synthase protein
           [Hoeflea phototrophica DFL-43]
          Length = 339

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 81/337 (24%), Positives = 153/337 (45%), Gaps = 50/337 (14%)

Query: 10  VVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
            +V  ++   RLD W      P ++   ++ ++ +G V V+    +   ++I+ G  + +
Sbjct: 12  TLVVGEDAAGRLDAWLAEALAPGLSRSRVKALIEAGAVSVNGTPARQAKHKIKPGDEISL 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                          ++    +     + +   +LYED+ + V NK AG+ V  G+G   
Sbjct: 72  ---------------VVPDPEDPEPEGEDIPLSILYEDADLIVINKQAGLVVHPGAGNWT 116

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----M 176
              ++  +    DS       ++P + HRLD++T+G++VVA+   A +HL + F      
Sbjct: 117 GTLVNALIHHCGDSLSGIGGVRRPGIVHRLDRDTTGVMVVAKHDQAHRHLADQFADHGLT 176

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN--YAISHFKVID 234
             +++ Y ++VWG P   K  I   L +      D +    + +   +  +A++H+ V +
Sbjct: 177 GPLERAYQAVVWGKPAGLKGTIDAGLGRAR----DRIRRAVRTDDAPDVRHAVTHYLVRE 232

Query: 235 CFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQ 285
            + +K         +E +  TGRTHQ+RVH  H+G P++GD  Y A ++        P++
Sbjct: 233 RYGEKPDGTCAATLVECRLETGRTHQIRVHMAHIGHPLIGDEDYGAGYRTKANRLPEPLR 292

Query: 286 N------KLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
                  +  LHA  +   HP  G  ++  APLP  M
Sbjct: 293 GIVGDFKRQALHAFLLVFEHPATGETMRFEAPLPDDM 329


>gi|15615105|ref|NP_243408.1| hypothetical protein BH2542 [Bacillus halodurans C-125]
 gi|10175162|dbj|BAB06261.1| BH2542 [Bacillus halodurans C-125]
          Length = 305

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 79/320 (24%), Positives = 151/320 (47%), Gaps = 44/320 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            +   ++  R+D++        +   +Q+ ++ G V ++ + +K N ++++G        
Sbjct: 8   TISEQQQGERIDKFLTAQGEEWSRTQVQQWIKDGHVLINGRTIKSNYKVETG-------- 59

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
            + L   + E ++L+         + +   ++YED  + V NKP G+ V    G      
Sbjct: 60  -DTLELFVPEPEVLEVV------PENIPIEIIYEDEDVAVVNKPRGMVVHPAPGHTTGTL 112

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + YH +    S ++    +P + HR+D++TSG+L++A+   A + L    + +  ++
Sbjct: 113 VNALMYHCNDL--SSINGV-VRPGIVHRIDKDTSGLLMIAKNDRAHESLVNQLKAKTTER 169

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV--HVVKQNEKGANYAISHFKVIDCFAQ 238
           +Y ++V G IP +     A        IG D V    +   E+ +  A++HF V++ F  
Sbjct: 170 VYQAIVHGNIPHDHGTIDAP-------IGRDKVDRQSMTVTEENSRDAVTHFTVLERFGD 222

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F ++E Q  TGRTHQ+RVH  ++G P+ GD KY     G   +   +   LHA+ +   
Sbjct: 223 -FTFVECQLETGRTHQIRVHFKYIGFPLAGDPKY-----GPKKTLSIDGQALHAQKLGFE 276

Query: 299 HPEGGR-LQITAPLPAHMVK 317
           HP  G  ++    +P  M K
Sbjct: 277 HPRTGEFMRFKVEMPEEMKK 296


>gi|293376242|ref|ZP_06622485.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|325845167|ref|ZP_08168476.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
 gi|292645134|gb|EFF63201.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|325488832|gb|EGC91232.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
          Length = 302

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 84/329 (25%), Positives = 157/329 (47%), Gaps = 50/329 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           ++V  +   +RLD+     +   +   LQ++++ G+V ++ +  K N + +    + I  
Sbjct: 6   MIVTEELVGVRLDKVLNESFEDYSRSYLQQLIKEGRVLINGQVAKANYKCRLNDQIEINI 65

Query: 68  --PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GS 123
             P V++    +I E+  LD               ++Y+D  + V NKP  + V    GS
Sbjct: 66  PEPEVLD----VIPEEMDLD---------------IVYQDDYVIVVNKPENMVVHPAPGS 106

Query: 124 GIAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + +
Sbjct: 107 MSGTLVNGLMAQVTDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVEKTV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVID 234
            + Y +LV G+  +    I       + IG D     K  +K A      +A++HFKV+ 
Sbjct: 167 TRRYVALVHGVIPHDNGTI------DAPIGRD----PKDRKKMAVVESGKHAVTHFKVLQ 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F ++F  +E +  TGRTHQ+RVH  ++G P+ GD +Y        T   ++  +LHA+ 
Sbjct: 217 RF-KEFTLIECRLETGRTHQIRVHMRYIGYPLAGDPQYGP----RKTIGAEHGQFLHAKV 271

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP+    ++ +AP+P +  +   +L
Sbjct: 272 LGFVHPKTEEYMEFSAPIPTYFEEALANL 300


>gi|288799919|ref|ZP_06405378.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella sp. oral taxon 299 str. F0039]
 gi|288333167|gb|EFC71646.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella sp. oral taxon 299 str. F0039]
          Length = 222

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 68/218 (31%), Positives = 110/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I + +K +G  VQG       +   +K+++  K  KP      + HRLD+  S
Sbjct: 3   VLYEDNHIIIVHKNSGEIVQGDKTGDTPLSDIVKAYIKEKYAKPGNVFVGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  A   L   F    + K YW++    PK ++  + NWL++       Y + 
Sbjct: 63  GIVVFAKTSKALSRLNTMFSKGEVHKTYWAITANTPKEEQGTLVNWLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             + +  +  AI ++++I   ++++  LE+   TGR HQ+R    HMGC I GD KY A 
Sbjct: 122 -DEEKPNSKKAILNYQLI-SKSERYALLEVALLTGRHHQIRCQLAHMGCVIKGDLKYGAP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            + N  + I     L AR ++  HP     + + APLP
Sbjct: 180 -RSNPDASIS----LLARRIEFIHPVSKEAIVVEAPLP 212


>gi|293377440|ref|ZP_06623642.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
 gi|292643958|gb|EFF62066.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
          Length = 305

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 87/312 (27%), Positives = 150/312 (48%), Gaps = 51/312 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E+ R+D+   N + + +   +Q  L+   V V+ + VK N +++ G  + +         
Sbjct: 11  ESGRIDKVLTNLFSNYSRSQIQLWLKERAVSVNGEPVKANYKVKQGDEITV--------- 61

Query: 77  IIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
           +I E + LD    ++ LT         ++YED  + V NKP G+ V   +G         
Sbjct: 62  LIPEPETLDVVPENIPLT---------IVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNA 112

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + YH+     S ++    +P + HR+D++TSG+L+VA+   A + L +  + +   + Y 
Sbjct: 113 LMYHVKDL--STINGV-IRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKDKTSLRKYV 169

Query: 185 SLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G IP  K    A     K +     +  ++++ K A   ++HF V++ F + F  +
Sbjct: 170 ALVHGEIPHEKGTINAPIGRSKEN---RKMQAIREDGKPA---VTHFTVLERF-EGFTLV 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E++  TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP 
Sbjct: 223 ELKLETGRTHQIRVHMKYIGYPLAGDPVYGPKKTLKGNGQ-------FLHAQMLGFTHPT 275

Query: 302 GGRLQI-TAPLP 312
                I  APLP
Sbjct: 276 TNEKMIFEAPLP 287


>gi|224538849|ref|ZP_03679388.1| hypothetical protein BACCELL_03745 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224519524|gb|EEF88629.1| hypothetical protein BACCELL_03745 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 510

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 71/208 (34%), Positives = 109/208 (52%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  + + NKPAG +SV G        D   +++ +++G  P + HRLD  TSG+L+
Sbjct: 309 IVYEDQWLLIINKPAGMLSVPGKERQTSIYDLAREAYPEAEG--PMIVHRLDMATSGLLI 366

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ +   QHL   F+ R I+K Y +L+ GI    +  I   L        D    +   
Sbjct: 367 IAKDKKTHQHLQAQFKNRSIRKKYIALLDGIVPEDEGTIELSLCPNPL---DRPRQMVDT 423

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANF 276
           + G   AI++++V++    K+  +   PHTGRTHQLRVHA H   + CPI+GD  Y    
Sbjct: 424 QYGKP-AITYYQVLE-RTDKYTRIAFYPHTGRTHQLRVHAAHPSGLHCPIIGDELYGKKD 481

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           K         +LYLHA  ++  HP  G+
Sbjct: 482 K---------RLYLHAESIEFTHPVNGQ 500


>gi|218886014|ref|YP_002435335.1| pseudouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|218756968|gb|ACL07867.1| pseudouridine synthase, RluA family [Desulfovibrio vulgaris str.
           'Miyazaki F']
          Length = 558

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 91/369 (24%), Positives = 154/369 (41%), Gaps = 55/369 (14%)

Query: 5   TYVQYVVVENDEENMRLDRWFKN----------HYPHINFVNLQKILRSGQVRVDKKRVK 54
           T      V  +    RLDR+  +          H   ++   +++ +R G   V  +   
Sbjct: 11  TRTHSFTVAPEHAGQRLDRFLGDAMAEQRERDGHGDAVSREKVKRAIRDGAATVQGRACT 70

Query: 55  F-NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
             N R++ GQ V        L   +   K+     +L          +LY D+ I V +K
Sbjct: 71  VPNTRVEPGQTV-------TLTLAVPAAKVTPEDGDLA---------VLYRDAAIAVLDK 114

Query: 114 PAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           PAG++V          + + +          +G +P + HR+D++TSG+L+VA T A   
Sbjct: 115 PAGLTVHPCPSCPEGTLVHRLVRHFPELAAQEGFRPGIVHRIDKDTSGLLLVALTEAVRL 174

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK----QNEKGAN 224
            L+ +F  R++ K Y +LV G+PK + E        ++ IG   +H VK       +G  
Sbjct: 175 ELSRAFAERQVHKEYLALVHGVPKAQGEL-------EAPIGRHPLHKVKMAVVPENRGGK 227

Query: 225 YAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCP-----IVGDHKYCANFKG 278
            A S ++V+      +F  + ++  TGRTHQ+RVH  H+G P     + G  +  A   G
Sbjct: 228 PARSAWRVLLADPDGRFALVAVRIFTGRTHQIRVHMAHLGHPLWQDAVYGPSEAVAPAAG 287

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
                   +  LHA  +   HPE  R +  T P P      + +L  +  R +    +  
Sbjct: 288 ELPD-FPPRQMLHAWRLSFRHPETDRDMHFTCPPP----PDFAALALRLSRRMQRVVVTG 342

Query: 338 QDECKQNIL 346
              C ++ L
Sbjct: 343 SPGCGKSAL 351


>gi|34581099|ref|ZP_00142579.1| sfhB protein homolog [Rickettsia sibirica 246]
 gi|28262484|gb|EAA25988.1| sfhB protein homolog [Rickettsia sibirica 246]
          Length = 313

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 89/322 (27%), Positives = 150/322 (46%), Gaps = 45/322 (13%)

Query: 24  WFKNHYPH-INFVNLQKILRSGQVRVDK----KRVKFNNRIQSGQVVRIPPVINALNHII 78
             K   PH +N + L K+L S    V +    K +K +  + +  ++  P V+   N II
Sbjct: 1   MLKYSVPHELNGIRLDKVLSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDII 60

Query: 79  -------KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +E KI  ++V L          ++YED  + V NK AG++V  G+G  +H D 
Sbjct: 61  LFSFKEPEELKIAAANVALD---------IIYEDDDLIVINKAAGMTVHPGAG--HHDDT 109

Query: 132 FLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + + +            ++P + HRLD++T+G++VVA+   A   L      R++ + Y
Sbjct: 110 LVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCW 242
             LVWG+  N  E I    + +S      + ++K    G   A++H+K ++ F +     
Sbjct: 170 KVLVWGVI-NPLEGIIKNNIGRSRSDRQKMTILKY---GGKEAVTHYKTLELFYKGSISM 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLY------LHARY 294
           +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP  ++ KL       LH+ Y
Sbjct: 226 VECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAHSPPELKAKLIDFKRQALHSWY 285

Query: 295 MDLPHPEGGR-LQITAPLPAHM 315
           +   HP     ++ +  LP  M
Sbjct: 286 LSFTHPTSNEIMEFSCELPRDM 307


>gi|327441137|dbj|BAK17502.1| pseudouridylate synthase, 23S RNA-specific [Solibacillus silvestris
           StLB046]
          Length = 300

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 86/289 (29%), Positives = 143/289 (49%), Gaps = 43/289 (14%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           N+++ ++IL +G     K +VK  + I+    V +P V        ++ +I+   +NL  
Sbjct: 34  NWLDEERILVNGAAVKAKYKVKQGDVIE----VTVPEV--------EDLEIIPEDLNLE- 80

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKG----QKPRL 146
                   ++YED+ + V NKP G+ V    G A    ++G +    D  G     +P +
Sbjct: 81  --------IVYEDADVLVVNKPRGMVVHPAPGHATGTLVNGLMHHCKDLSGINGVARPGI 132

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HR+D++TSG+L+VA+   A + L      + + + Y +LV G   ++K  I       +
Sbjct: 133 VHRIDKDTSGLLMVAKNDVAHESLVNQLVEKSVTRKYTALVHGHIAHEKGTI------DA 186

Query: 207 HIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            IG D     KQ   +KG  +A++HF+VI+ F + F  +E +  TGRTHQ+RVH  ++G 
Sbjct: 187 PIGRDQKDRQKQAVVDKG-KHAVTHFQVIERFGE-FTLVECRLETGRTHQIRVHMNYIGF 244

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           P+ GD KY      +F   +     LHA  +   HP     L+  +PLP
Sbjct: 245 PLAGDPKYGPRKTIDFGGQV-----LHAGVLGFIHPVTKEYLEFESPLP 288


>gi|257468836|ref|ZP_05632930.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
          Length = 342

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 88/334 (26%), Positives = 155/334 (46%), Gaps = 48/334 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           V  + +++  R+D +            +QKI+  G V +  K+V K  N+++  + + + 
Sbjct: 39  VYADENDKGKRIDSFLNEVIDDATRSYIQKIIDGGYVEITGKKVTKSGNKLKGTETITVN 98

Query: 69  PVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
                    I E +ILD    ++ L          ++YED  I V NK   + V    G 
Sbjct: 99  ---------IPEDEILDVIPENIPLN---------IIYEDKDIVVINKAPDMVVHPAHGN 140

Query: 125 --------IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                   + YHI    K      G  +P + HRLD++TSG++VVA+   A   L++ F+
Sbjct: 141 YNGTLVNALLYHI----KDLSTINGVIRPGIVHRLDKDTSGVIVVAKNDEAHSTLSDMFK 196

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            + ++K Y  +  GI K+K   I   + + S    D   +   +  G N AIS+++++D 
Sbjct: 197 EKTLEKTYICIAKGIFKDKSGRIETLIGRDSR---DRKKMAVVDINGKN-AISNYEILDE 252

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             + F  ++++  TGRTHQ+RVH  ++  PI+GD  Y ++ +G        +  LHA  +
Sbjct: 253 -EKNFSLVKVRIETGRTHQIRVHMKYLNHPILGDSVYGSSGEG------AKRQMLHAYRL 305

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
              HP   + +++TA +P    K     G   D+
Sbjct: 306 KFTHPVTKKEMEVTADIPEDFKKAAKFAGVNIDK 339


>gi|254486310|ref|ZP_05099515.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           GAI101]
 gi|214043179|gb|EEB83817.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           GAI101]
          Length = 344

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 94/357 (26%), Positives = 153/357 (42%), Gaps = 60/357 (16%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M++ +   +  D    RLD+      P   +++   L +++  G V+VD   V     RI
Sbjct: 1   MSHRRISFIIADTPPPRLDKALARDVPEDANLSRTRLGRLIADGSVQVDGIVVTDPRARI 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             GQ + +       +HI+ E   L+               +++EDS + V NKPAG+ V
Sbjct: 61  FEGQEITVDVEEAEDSHILAESIPLE---------------VVFEDSDLIVINKPAGMVV 105

Query: 120 QG--GSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               GS     ++  L    D        ++P + HR+D++TSG+LVVA++ AA   L +
Sbjct: 106 HPAPGSPSGTLVNALLAHCGDDLSGVGGMKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAK 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK----------- 221
            F    +++ Y +LV+G+P +  +     +   S   G+ + +  Q  +           
Sbjct: 166 QFEKHTVERYYQALVYGVP-DANDPRLRGIKGTSFEPGNILKMTTQLARHRTDRQRQAVL 224

Query: 222 --GANYAISHFKVID------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             G  +A++  + I         A   CWLE    TGRTHQ+RVH  H G  +VGD  Y 
Sbjct: 225 FQGGRHAVTRARTISRYGTPPVLALMECWLE----TGRTHQIRVHMAHAGHSLVGDPTYG 280

Query: 274 ANFKGNFTSPIQ---------NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWD 320
              K   T+  +          +  LHA  +   HP  G + +  APLP  M    D
Sbjct: 281 GKRKLPKTALPEIASDAVRAFPRQALHAAVLGFEHPVTGEMVRFEAPLPRDMTDLLD 337


>gi|262383706|ref|ZP_06076842.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_1_33B]
 gi|262294604|gb|EEY82536.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_1_33B]
          Length = 549

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 75/233 (32%), Positives = 121/233 (51%), Gaps = 25/233 (10%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L+H+++  ++ ++ +    H +  K  +LYED  + V NKP G+    G G A  +   L
Sbjct: 316 LHHMLQGLRVDENPLLADSHRE-TKLDILYEDDYLLVINKPEGMLSVPGKGDADSVYQRL 374

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPK 192
            S +  +   P + HRLD  TSG+L+ A+T+ A Q+L   F+ R IQK Y +L+ G +P+
Sbjct: 375 -SILYPEATGPIIVHRLDMATSGLLLAAKTKEAHQNLQAQFKNRTIQKRYIALLEGEVPQ 433

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           ++ E        +  +  D +   +Q  +E+    A + ++V++  + K   +   P TG
Sbjct: 434 DEGEI-------RLPLCPDPLDRPRQIVSEEFGKPAFTRYRVLERTSGK-TLIAFYPQTG 485

Query: 251 RTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           RTHQLRVHA H   + CPI+GD  Y              +LYLHA Y+   HP
Sbjct: 486 RTHQLRVHAAHPLGLHCPILGDELYGRK---------AERLYLHAEYLAFTHP 529


>gi|260593408|ref|ZP_05858866.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           veroralis F0319]
 gi|260534684|gb|EEX17301.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           veroralis F0319]
          Length = 366

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 90/344 (26%), Positives = 154/344 (44%), Gaps = 61/344 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++      H +   +QK   +G + V+   VK N +++    + +  
Sbjct: 37  VEVDKGQVPVRIDKFLFERMQHSSRNRIQKAADAGFIHVNGAPVKSNYKVRPEDTITL-- 94

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I    + L          ++YED+ + V NKPAG+ V  G+G     
Sbjct: 95  ---MLDRPKHDNTIEAEDIPLD---------IVYEDNALMVVNKPAGLVVHPGAGNFHGT 142

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+   L S+ D    +  L HR+D++TSG+LV+A+T  A   L + F  +   
Sbjct: 143 LINAIAWHLKD-LPSF-DPNDPEVGLVHRIDKDTSGLLVIAKTPDAKTILGKQFFNKTTH 200

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------VVKQNEKGANYAISHFK 231
           + Y +LVWG          N    +  I G+            V   + +    A++H++
Sbjct: 201 RSYNALVWG----------NLTADEGRIEGNIARDPKDRLRMTVFPPDSEIGKPAVTHYR 250

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ---- 285
           V++ F      +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S  +    
Sbjct: 251 VLERFGYT-TLIECVLETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSSYKAFIR 309

Query: 286 ------NKLYLHARYMDLPHP-EGGRLQITAPLP---AHMVKTW 319
                 N+  LHAR +   HP  G ++  T+ LP   A ++  W
Sbjct: 310 NCLTLCNRQALHARTLGFVHPVTGQQMDFTSDLPQDLASLITKW 353


>gi|148244467|ref|YP_001219161.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Vesicomyosocius okutanii HA]
 gi|146326294|dbj|BAF61437.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 314

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 89/333 (26%), Positives = 149/333 (44%), Gaps = 50/333 (15%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSL++    +++ N   N R+D       P+ +   +   ++SG   + +K  K   ++ 
Sbjct: 1   MSLLS----IIIPNRFINQRVDVAMAQMLPNYSRTKITYWIKSGNALIHRKTFKPKEKVL 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G++V +       N  + E   +D               ++YEDS+I + NKP G+   
Sbjct: 57  GGEMVNLLIKTKKANSWLAEDAAID---------------VVYEDSEIIIVNKPVGLVTH 101

Query: 121 GGSG--------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
            G+            H D  L + +D  G    + HRLD+ TSG++VVAR+  A ++LT+
Sbjct: 102 PGASNWTGTLANALLHYDSSLAN-LDRAG----IVHRLDKNTSGLMVVARSEYAQKYLTK 156

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFK 231
             +   I + Y ++V+G   +     A        IG D    +KQ   K   YA++H++
Sbjct: 157 QLQTHSISREYSAIVYGYMISGGSVDAP-------IGRDPKDRIKQAVVKDGKYALTHYR 209

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF------KGNFTSPIQ 285
           +I+ F      ++    TGRTHQ+RVH   +G P++ D  Y              T  ++
Sbjct: 210 IIERFTH-HTHVKAILETGRTHQIRVHLSFIGHPLIADPIYGGKVYFPKKADKQLTKALK 268

Query: 286 --NKLYLHARYMDLPHPEGGRLQI-TAPLPAHM 315
             N+  LHA+ + L HP  G L     PLP  M
Sbjct: 269 NFNRQTLHAKKLTLTHPISGELMSWKMPLPQDM 301


>gi|255534470|ref|YP_003094841.1| Ribosomal large subunit pseudouridine synthase D [Flavobacteriaceae
           bacterium 3519-10]
 gi|255340666|gb|ACU06779.1| Ribosomal large subunit pseudouridine synthase D [Flavobacteriaceae
           bacterium 3519-10]
          Length = 352

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 86/329 (26%), Positives = 157/329 (47%), Gaps = 42/329 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  ++ +R+D++      +     + +  R+G V V+   VK N R++ G  + +  
Sbjct: 32  ITVDRGQQPLRIDKFLHIFRQNSTRNKISQSCRAGNVVVNGTAVKQNYRVKPGDRISV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+   +E  I+   + L          ++YED  + V +K  G+ V  G G     
Sbjct: 90  ---LLSRPPRENVIIPQDIPLN---------IVYEDDDLVVVDKDPGMVVHPGHGNWDGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H   F K+ V S   +  L HR+D++TSG+LV+A+   A  +L + F  R+ +
Sbjct: 138 LINALAFH---FEKNGVKSDLDRVGLVHRIDKDTSGLLVIAKNEYALSYLAKQFFDRKTK 194

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           ++YW+ VWG    +   I   + +  H+       V ++     +A++H+KV++ F +  
Sbjct: 195 RLYWAFVWGNLDQENGTITGNIGR--HLKNRMQMAVFEDGSLGKHAVTHYKVVERF-KYM 251

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG----NFTSPIQN------KL 288
            W+E +  TGRTHQ+R H  H+G  +  D +Y  N   KG     +   I+N      + 
Sbjct: 252 TWVECKLETGRTHQIRAHFKHIGHTLFNDERYEGNQILKGVNMPKYKQFIKNVFEILPRH 311

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMV 316
            LHA  +   HP +   +   +P+PA M+
Sbjct: 312 ALHAHTLGFIHPTKKEEMYFESPMPADML 340


>gi|239996651|ref|ZP_04717175.1| ribosomal large subunit pseudouridine synthase D [Alteromonas
           macleodii ATCC 27126]
          Length = 327

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 84/313 (26%), Positives = 149/313 (47%), Gaps = 39/313 (12%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+   + +P  +   L+  ++ G V V+            G+V+ +P     ++ +
Sbjct: 20  GLRLDQVLADLFPEYSRSKLKTWIQDGNVAVN------------GEVITVPRHKMQMDEL 67

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
           +  Q  +D  V +T  +  +   ++YED  I V NKPA + V  G+G      ++  L  
Sbjct: 68  VTVQAEMD--VQVTSEAQDIALNIVYEDEHILVINKPADLVVHPGAGNPSGTVLNALLNH 125

Query: 136 WVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             +  K  +  + HRLD++T+G++VVA+T  A  HL +  + R + + Y ++  G     
Sbjct: 126 CPEIDKVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVDQLQRREMSREYEAVALGTMVAG 185

Query: 195 ---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I     K++H+       V++  K    A++HF+VI+ F + +  L ++  TGR
Sbjct: 186 GIVDAPIGRHATKRTHMA------VREMGKP---AVTHFRVIEKF-RAYTHLRLKLETGR 235

Query: 252 THQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDLPHPEGG 303
           THQ+RVH  H+  P++GD  Y    +        F + ++   +  LHA  + L HPE  
Sbjct: 236 THQIRVHMAHIKHPLLGDQVYGGRPRLPKGASEEFIAALRGFQRQALHAAQLSLFHPETE 295

Query: 304 R-LQITAPLPAHM 315
             +   APLP  M
Sbjct: 296 EWMTWKAPLPQDM 308


>gi|325280294|ref|YP_004252836.1| pseudouridine synthase, RluA family [Odoribacter splanchnicus DSM
           20712]
 gi|324312103|gb|ADY32656.1| pseudouridine synthase, RluA family [Odoribacter splanchnicus DSM
           20712]
          Length = 353

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 85/335 (25%), Positives = 155/335 (46%), Gaps = 54/335 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +  +N +  +R+D++  +  P+ +   +Q+   +G + V+ K VK + +++   +V +  
Sbjct: 28  IEADNGQNLLRVDKFLMSRLPNASRTKIQEAADAGNILVNGKAVKSSYKVKPKDIVSV-- 85

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               + +  +E +I+  ++ L          ++YED  + V NKPAG+ V    G     
Sbjct: 86  ---VMAYPRREIEIIPENIPLN---------IVYEDDDLMVVNKPAGMVVHPSYGHYTGT 133

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H+ G    + D+   +P L HR+D++TSG+LV+A+T  A  HL   F  +   
Sbjct: 134 LVNALAWHLKGN-PLFKDNNDPRPGLVHRIDKDTSGLLVIAKTEKAKTHLGLQFFNKTSD 192

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDY----VHVVKQNEKGANYAISHFKVIDCF 236
           + Y ++ WG  +++   I        HIG +     V     +     +A++H++V++  
Sbjct: 193 RKYVAVCWGNLEDETGTIT------GHIGRNLTNRKVMACFPDGSHGKHAVTHYRVLERL 246

Query: 237 AQ---KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG----------NFT 281
                  C LE    TGRTHQ+R H  ++  P+  D +Y  N   KG          N  
Sbjct: 247 GYVNVVECILE----TGRTHQIRAHFKYIKHPLFNDKEYGGNEILKGTTFARYKQFVNNC 302

Query: 282 SPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
             I  +  LHA+ +   HP  G RL   + +P  M
Sbjct: 303 FEICPRQALHAKTLGFEHPTTGERLSFDSEIPDDM 337


>gi|282881599|ref|ZP_06290268.1| RNA pseudouridine synthase [Prevotella timonensis CRIS 5C-B1]
 gi|281304585|gb|EFA96676.1| RNA pseudouridine synthase [Prevotella timonensis CRIS 5C-B1]
          Length = 226

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 72/228 (31%), Positives = 108/228 (47%), Gaps = 15/228 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSG 156
           LYED+ I + +K +G  VQG       +   +K ++  K QKP      + HRLD+   G
Sbjct: 4   LYEDNHIIIVSKRSGEIVQGDKTGDLPLSETVKQYIKEKYQKPGNVFLGVVHRLDRPVWG 63

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V A+T  A   L + FR   + K YW++    P   +  + +WL++       Y H  
Sbjct: 64  LVVFAKTSKALTRLNKMFREGEVHKTYWAITKEAPPAAEGVLTDWLVRNERQNKSYAH-- 121

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            Q    A  A+  +KVI   +  +  LE+Q  TGR HQ+R    +MGCPI GD KY    
Sbjct: 122 SQETPNAKKAVLKYKVI-AHSDHYHLLEVQLMTGRHHQIRCQLANMGCPIKGDLKY---- 176

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            G   S     + L AR +   HP     + + APLP    + W++L 
Sbjct: 177 -GAKRSNPDGSICLLARSIAFVHPVSKENIVVEAPLPPQD-RLWEALA 222


>gi|33860753|ref|NP_892314.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus subsp. pastoris str.
           CCMP1986]
 gi|33633695|emb|CAE18652.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus subsp. pastoris str.
           CCMP1986]
          Length = 322

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 87/314 (27%), Positives = 146/314 (46%), Gaps = 44/314 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---PPVINALN 75
           MRLDRW  +  P  +   +Q  + +G V V+ K  K    +++G  ++I   PP    L 
Sbjct: 27  MRLDRWLVSKRPEQSRARIQYFINAGLVLVNYKTAKAKTPLKTGDNIQIWMPPP--EPLI 84

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
           ++  E+  L+               +L+ED  I V NK +G+ V    G      ++G L
Sbjct: 85  YLKPEKMNLN---------------ILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLL 129

Query: 134 KSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D  G     +P + HRLD++TSG +VVA+++ +  +L    + +   + Y +++ G
Sbjct: 130 FHCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQESLVNLQIQIKEKIASRNYIAVIHG 189

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           +P   +  I        HIG D ++ +K    +EK   YA +++K+++     +  +  +
Sbjct: 190 VPNTSEGKIV------GHIGRDKLNRLKYAVVDEKSGRYACTYWKLLERLGN-YSLMSFK 242

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
             TGRTHQ+RVH  H+  PI+GD  Y  C            +   LHA  + L HP  G 
Sbjct: 243 LDTGRTHQIRVHCAHINHPILGDPLYGRCKKLPCKL-----DGQALHAVELGLFHPINGE 297

Query: 304 RLQITAPLPAHMVK 317
            ++  A LP    K
Sbjct: 298 EMKFEAELPQEFQK 311


>gi|313904059|ref|ZP_07837439.1| pseudouridine synthase, RluA family [Eubacterium cellulosolvens 6]
 gi|313471208|gb|EFR66530.1| pseudouridine synthase, RluA family [Eubacterium cellulosolvens 6]
          Length = 370

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 125/242 (51%), Gaps = 20/242 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRL 150
           +++YED  I + NKPAGI  Q        ++  L+S++  KG+          P + +R+
Sbjct: 132 MIVYEDEDIILINKPAGILSQKAKPEDVSLNEMLQSYLFEKGELTEGKLKFYSPSVVNRI 191

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSG+++ A+  AAA+ ++E  R R +QK Y++LV G  K +KE +  WL+K      
Sbjct: 192 DRNTSGLVLGAKNLAAAREMSEMLRNRTLQKYYYALVNGQVK-EKEHVRAWLVKDK--AK 248

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           + V +      GA+   + ++ +    +++  L ++  TG+THQ+R H   +G  +VGD 
Sbjct: 249 NQVKIYDHPVDGADLIETVYEPM-AKVERYTLLRVELLTGKTHQIRAHLSFIGHSLVGDV 307

Query: 271 KYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGRLQIT-----APLPAHMVKTWDSLG 323
           KY      + T      ++ +LHA  +  P  +G    ++     APLPA + KT +  G
Sbjct: 308 KYGQKSMNSATREHTGLSRQFLHAEKVIFPDTDGALKSLSGRCFRAPLPADLQKTLEIFG 367

Query: 324 FK 325
            +
Sbjct: 368 IR 369


>gi|313672276|ref|YP_004050387.1| pseudouridine synthase, rlua family [Calditerrivibrio nitroreducens
           DSM 19672]
 gi|312939032|gb|ADR18224.1| pseudouridine synthase, RluA family [Calditerrivibrio nitroreducens
           DSM 19672]
          Length = 320

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 80/239 (33%), Positives = 128/239 (53%), Gaps = 24/239 (10%)

Query: 47  RVDKKRVKFNNRIQ------SGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKS 99
           ++++ R  F N I       +G++ +    + A +HII    I D S++LT K  DF   
Sbjct: 37  KLNRSRSYFKNLIDEGLVTLNGKICKPSSKVVAGDHII--VLIPDDSIDLTPKEIDFE-- 92

Query: 100 ILLYEDSKIY-VFNKPAGISVQGGSGIAYH--IDGFL---KSWVDSKGQKPRLTHRLDQE 153
            ++Y DSK Y V NKPAG+ V    G      ++G L   K+  D+   +P + HRLD++
Sbjct: 93  -VIY-DSKWYAVINKPAGLVVHPAPGNTTDTLVNGLLAKFKNIDDNDNVRPGIIHRLDKD 150

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+L++A+ R   Q ++E F+ R ++K+Y ++  G PKN    I N++ +   +     
Sbjct: 151 TSGLLIIAKNRDVRQQMSELFQKREVKKVYLAVCMGEPKNDYYMIDNFIGRS--LTDRKK 208

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V QN  G   A+S  K++   +  F    +  HTGRTHQ+RVH  ++  PI+GD  Y
Sbjct: 209 MAVLQN--GGKRAVSEVKILKRSSGIFLA-SVAIHTGRTHQIRVHMSYLNYPILGDFLY 264


>gi|326389927|ref|ZP_08211490.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           JW 200]
 gi|325993987|gb|EGD52416.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           JW 200]
          Length = 305

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 92/328 (28%), Positives = 156/328 (47%), Gaps = 55/328 (16%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPV 70
           E ++E  R+D +      +     ++K++  G V V+ K VK + +++     VV IP  
Sbjct: 12  EKEDEGKRIDVFLAAELDYTRSY-IKKLIVDGLVFVNGKTVKPSYKVKENDEVVVNIPEA 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                   ++  +L  ++ L          +LYED  I V NKP G+ V    G      
Sbjct: 71  --------EKIDVLPENIPLD---------ILYEDDDIIVINKPQGMVVHPAPGNYSGTL 113

Query: 125 ---IAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
              + YH      I+G L+         P + HRLD++TSG++VVA+   A   L+   +
Sbjct: 114 VNALLYHCKNLSGINGILR---------PGIVHRLDKDTSGVMVVAKNDKAHISLSNQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y ++V G+ K+++  I   L+ +  +    + V++       YA++ +KV++ 
Sbjct: 165 ERSVFKKYVAIVEGVIKHEEGKI-EALIGRHPVDRKKMAVIED----GRYALTLYKVLER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F +    +E    TGRTHQ+RVH  ++G P+VGD  Y    K  F    Q    LH+R +
Sbjct: 220 FKEN-TLIEAVIKTGRTHQIRVHMAYIGHPVVGDPVYGFK-KQKFKLEGQA---LHSRVL 274

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSL 322
              HP +G  ++  APLP + V+  + L
Sbjct: 275 GFMHPTKGVYMEFEAPLPEYFVRLIEIL 302


>gi|317063086|ref|ZP_07927571.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
 gi|313688762|gb|EFS25597.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
          Length = 313

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 88/334 (26%), Positives = 155/334 (46%), Gaps = 48/334 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           V  + +++  R+D +            +QKI+  G V +  K+V K  N+++  + + + 
Sbjct: 10  VYADENDKGKRIDSFLNEVIDDATRSYIQKIIDGGYVEITGKKVTKSGNKLKGTETITVN 69

Query: 69  PVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
                    I E +ILD    ++ L          ++YED  I V NK   + V    G 
Sbjct: 70  ---------IPEDEILDVIPENIPLN---------IIYEDKDIVVINKAPDMVVHPAHGN 111

Query: 125 --------IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                   + YHI    K      G  +P + HRLD++TSG++VVA+   A   L++ F+
Sbjct: 112 YNGTLVNALLYHI----KDLSTINGVIRPGIVHRLDKDTSGVIVVAKNDEAHSTLSDMFK 167

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            + ++K Y  +  GI K+K   I   + + S    D   +   +  G N AIS+++++D 
Sbjct: 168 EKTLEKTYICIAKGIFKDKSGRIETLIGRDSR---DRKKMAVVDINGKN-AISNYEILDE 223

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             + F  ++++  TGRTHQ+RVH  ++  PI+GD  Y ++ +G        +  LHA  +
Sbjct: 224 -EKNFSLVKVRIETGRTHQIRVHMKYLNHPILGDSVYGSSGEG------AKRQMLHAYRL 276

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
              HP   + +++TA +P    K     G   D+
Sbjct: 277 KFTHPVTKKEMEVTADIPEDFKKAAKFAGVNIDK 310


>gi|312135211|ref|YP_004002549.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           owensensis OL]
 gi|311775262|gb|ADQ04749.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           owensensis OL]
          Length = 293

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 79/278 (28%), Positives = 142/278 (51%), Gaps = 27/278 (9%)

Query: 47  RVDKKRVKFNNRIQS-----GQVVRIPPVIN----ALNHIIKEQKILDSSVNLTKHSDFL 97
           ++ +K++ F++ + S     GQ+  IPP+ +       + + E  ++ S  N+      +
Sbjct: 18  QILQKKLFFSSTLMSRLKAHGQIRFIPPIYSIHQYPQENAVIEVDLISSKSNIVPVEGSI 77

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSG 156
              +LYED+     NKP+G+      G  +  I  +++ +++SK     + +RLD+ETSG
Sbjct: 78  D--ILYEDNFFLFVNKPSGLPSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRLDKETSG 135

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I+V A+       ++  F  R+++K Y ++V G    KK  +    +K+S  G     + 
Sbjct: 136 IVVFAKNSYFHSIVSREFEKRQVEKTYIAIVHG-KLTKKSGLIEKPIKRSQDG-----IK 189

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           ++  +  ++A ++++VID F + F  L+++P TGRTHQLRVH   +G PIVGD+ Y    
Sbjct: 190 REIHQDGSFASTYYEVIDSF-ENFSVLKLKPITGRTHQLRVHLSSIGHPIVGDYIYGQQK 248

Query: 277 KGNFTSPIQNKLYLHARYM--DLPHPEGGRLQITAPLP 312
             N        L LHA  +  +    +     IT+PLP
Sbjct: 249 TQN------TPLLLHAYSIRFNFKLIDNKIYNITSPLP 280


>gi|110679108|ref|YP_682115.1| ribosomal large subunit pseudouridine synthase D [Roseobacter
           denitrificans OCh 114]
 gi|109455224|gb|ABG31429.1| ribosomal large subunit pseudouridine synthase D [Roseobacter
           denitrificans OCh 114]
          Length = 342

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 95/355 (26%), Positives = 153/355 (43%), Gaps = 60/355 (16%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKK-RVKFNNRIQSG 62
           +Q+V+  ++    RLD+      P    ++   L +++  G V VD   +     R+ +G
Sbjct: 6   IQFVI--DEAPPPRLDKALARDVPVEAALSRTRLARLIDEGGVLVDGVVQSNAKARVAAG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I       +HI+ E   LD               +++EDS + V NKPAG+ V   
Sbjct: 64  AQITIQVQQAQDSHILPEDIALD---------------VIHEDSDLIVVNKPAGMVVHPA 108

Query: 123 SGIAYH--IDGFLK-SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G      ++  L     D  G    ++P + HR+D++TSG+LVVA++ AA   L   F+
Sbjct: 109 PGTPSGTLVNALLSHCGADLSGVGGLKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAAQFQ 168

Query: 176 MRRIQKIYWSLVWGIP----------KNKKECIANWLLKKSHIGGDYVHVVKQNE--KGA 223
              +++ Y  LV+G P          K  +    N L   + +        +Q    +G 
Sbjct: 169 AHTVERYYNCLVYGAPDANDPRLRGVKGARFEAGNILKLTTQLARHKTDRQRQAVLFQGG 228

Query: 224 NYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +A++  + ++ F          CWLE    TGRTHQ+RVH  H G  +VGD  Y    K
Sbjct: 229 RHAVTRARSLERFGTPPVLTLMECWLE----TGRTHQIRVHMAHAGHALVGDPTYGGKRK 284

Query: 278 GNFTSPIQ---------NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
               S  +         N+  LHA  +   HP  G  L+  APLP  M +  ++L
Sbjct: 285 LPAKSLPETALEAVKCFNRQALHAAVLGFEHPVTGEHLRFEAPLPQDMAQLLNTL 339


>gi|57233860|ref|YP_182086.1| ribosomal large subunit pseudouridine synthase D [Dehalococcoides
           ethenogenes 195]
 gi|57224308|gb|AAW39365.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Dehalococcoides ethenogenes 195]
          Length = 300

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 85/322 (26%), Positives = 157/322 (48%), Gaps = 40/322 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RI 67
           +V E+D E  RLD++       ++   +Q+++ +G ++V+ K  K + ++++G  +   I
Sbjct: 6   LVAESDGE--RLDKYITQKETDLSRSFIQELVEAGHIQVNGKNAKPSLKLKNGDTITIEI 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP          E K  D  + +           +++D  + + NKP G++V    G   
Sbjct: 64  PP------ETPPELKAEDIPLEI-----------IFQDKDLLLINKPPGLTVHPAPGHPD 106

Query: 128 H--IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H  I+G L    + +      +P + HRLD++TSG+L+VA+ R A  +L+  F+ R ++K
Sbjct: 107 HTLINGVLALEPEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNREALANLSAQFKERTVRK 166

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   +  E      L +       + VV         A + +KV+  + Q + 
Sbjct: 167 YYLTLVQG-ELHPAEGFIEAPLGRDPQNRQKIAVVSNGRP----ARTGYKVL-RYIQGYS 220

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE++  TGRTHQ+RVH   +G P+ GD  Y     G   + ++ + +LHA  +    P 
Sbjct: 221 LLEVKLETGRTHQIRVHFAAIGHPVAGDAVY-----GQKETWLKRQ-FLHAHRLSFSLPS 274

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G+ ++ ++PLP  + +   +L
Sbjct: 275 NGQNVEFSSPLPPDLEEALKTL 296


>gi|229086457|ref|ZP_04218629.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-44]
 gi|228696774|gb|EEL49587.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-44]
          Length = 302

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 84/318 (26%), Positives = 152/318 (47%), Gaps = 37/318 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V+ ++++ R+D++        +   +Q+ ++ G V V+   +K N +++   
Sbjct: 1   MSEVVQVTVKEEQKSERIDKFLAGINNEWSRSQVQQWIKDGVVTVNGNDIKGNYKVKEND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          I E + LD        ++ +   + YED+ + V NKP G+ V    
Sbjct: 61  EIAVA---------IPEPEELDI------RAEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMYHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDC 235
            + + Y ++V G+  + K  I       + IG D      +  +E G N A++HF+V++ 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTI------DAPIGRDKKERQSMAVDENGKN-AVTHFQVLER 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G   +   N   LHA  +
Sbjct: 219 F-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----GPKKTLDINGQALHAGIL 272

Query: 296 DLPHPEGGR-LQITAPLP 312
              HP     ++  AP+P
Sbjct: 273 GFDHPRTDEYIEFEAPIP 290


>gi|209883418|ref|YP_002287275.1| pseudouridine synthase, RluD [Oligotropha carboxidovorans OM5]
 gi|209871614|gb|ACI91410.1| pseudouridine synthase, RluD [Oligotropha carboxidovorans OM5]
          Length = 244

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 74/232 (31%), Positives = 119/232 (51%), Gaps = 17/232 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ +L+ D  + V +KPAGI+V  G     +++    +      + P L HRLD++TSG
Sbjct: 11  MQARVLHRDGLMLVIDKPAGIAVHRGPKGGPNLEASFDALRYGLPRPPVLAHRLDRDTSG 70

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R R A   L   F+  +I K YW++V G P   +  I   L + +   G +    
Sbjct: 71  CLVLGRHRKATASLGLLFKHGKIGKTYWAVVEGGPAEDEGEIDIPLGRLNAERGWW---- 126

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           ++ +     + S + V+        WL ++P TGRTHQLRVH   MG PIVGD+ Y    
Sbjct: 127 QKPDPNGLPSKSRWSVLG-RNNGLSWLALEPLTGRTHQLRVHCAAMGFPIVGDNIY---- 181

Query: 277 KGNFTSPIQNKLYLHARYMDLP----HPEGGRLQITAPLPAHMVKTWDSLGF 324
            GN     +  L+LHAR + +P     P    +++ AP+PAH+ +   + G+
Sbjct: 182 -GNGPRFGEPSLHLHAREIVVPLSRNKPP---VRVIAPVPAHLQERLQACGW 229


>gi|150390556|ref|YP_001320605.1| RluA family pseudouridine synthase [Alkaliphilus metalliredigens
           QYMF]
 gi|149950418|gb|ABR48946.1| pseudouridine synthase, RluA family [Alkaliphilus metalliredigens
           QYMF]
          Length = 310

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 88/323 (27%), Positives = 151/323 (46%), Gaps = 41/323 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV-- 64
           +Q+  V  ++E +RLD +    Y  ++   +QK+++   V VD +  K    ++ GQV  
Sbjct: 3   IQHFCVLEEDEGVRLDIYIAEQYDDLSRSYIQKVIKDNGVTVDGRPEKNRYIVKVGQVIV 62

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V +P          KE ++   ++ L          ++YED  + V NKP  + V    G
Sbjct: 63  VSLPEA--------KELEVTAQNIPLD---------IVYEDDDLLVVNKPQDMVVHPAPG 105

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                    + YH  G L S   +   +P + HR+D++TSG+L+VA+   A Q L+E  +
Sbjct: 106 NYENTMVNALLYHCKGKLSSI--NGIIRPGIVHRIDKDTSGLLMVAKNNHAHQFLSEQLK 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
                + Y  +  G  K ++  I N  + +       + V+     G   A++H +V++ 
Sbjct: 164 DHSTTRKYHGISVGTIKEERATI-NAPIARHQTDRLKMAVLA----GGRNAVTHIQVLNR 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F     ++E Q  TGRTHQ+RVH  ++G P++GD  Y  + K  F    Q    LHA+ +
Sbjct: 219 FGD-HTYMEAQLETGRTHQIRVHLGYIGHPLLGDFVY-GHKKSKFNLKGQ---VLHAKTL 273

Query: 296 DLPHP-EGGRLQITAPLPAHMVK 317
              HP +   ++  A LP +  K
Sbjct: 274 GFIHPTKKTYMEFNAALPTYFEK 296


>gi|87311869|ref|ZP_01093981.1| putative 23S rRNA pseudouridine synthase [Blastopirellula marina
           DSM 3645]
 gi|87285400|gb|EAQ77322.1| putative 23S rRNA pseudouridine synthase [Blastopirellula marina
           DSM 3645]
          Length = 250

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 73/234 (31%), Positives = 115/234 (49%), Gaps = 22/234 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF---LKSWV---DSKGQKPRL--THRLDQ 152
           +LYE    +   KPAG+  Q       HID      K+++   D K  K  L   HRLD+
Sbjct: 11  ILYEQGPCFCIAKPAGLLTQAPP----HIDSLESRFKAFIRQRDFKTGKVYLGVPHRLDR 66

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
             SG+L  AR   AA+ +++ F  R ++K+YW+ V G P + +    + + K   +    
Sbjct: 67  PVSGVLTFARNVRAARRISQQFETRLVRKLYWAFVAGQPPDDQGVWEDPIRKIPDVA--M 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +V  ++ GA +A   ++V+    Q   WLE++  TGR HQ+RV     G PI+GD  Y
Sbjct: 125 AEIVSPSDPGARWAKLKYEVLQRTEQG-AWLEIELDTGRYHQIRVQCASRGFPILGDVSY 183

Query: 273 CANFKGNFTSPIQNK--LYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
                    S  +    + LHARY+ L HP    +  +TAPLP    ++W+++ 
Sbjct: 184 GGEIPFGPQSEDERARHIALHARYLRLKHPMVDEIVAVTAPLP----ESWNAIA 233


>gi|51970580|dbj|BAD43982.1| unnamed protein product [Arabidopsis thaliana]
          Length = 326

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 68/197 (34%), Positives = 100/197 (50%), Gaps = 20/197 (10%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQET 154
           +L+ ++ ++DS I V NKP  + V+G   I   +D    + +     + PRL HRLD+ET
Sbjct: 24  YLQRLVRFKDSAIIVLNKPPKLPVKGNVPIHNSMDALAAAALSFGNDEGPRLVHRLDRET 83

Query: 155 SGILVVARTRAAAQHLTESFR---------------MRRIQKIYWSLVWGIPKNKKECIA 199
           SG+LV+ RT+ +  +L   F                   + + YW+LV G PK K+  I+
Sbjct: 84  SGLLVMGRTKESIDYLHSVFSDYKGRNSSCKAWNKACEAMYQQYWALVIGSPKEKEGLIS 143

Query: 200 NWLLKKSHIGGDYVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             L K     G    VV     G   +  AI+ +KV+        W+E++P T R HQLR
Sbjct: 144 APLSKVLLDDGKTDRVVLAQGSGFEASQDAITEYKVLGPKINGCSWVELRPITSRKHQLR 203

Query: 257 VH-ALHMGCPIVGDHKY 272
           VH A  +G PIVGD+KY
Sbjct: 204 VHCAEALGTPIVGDYKY 220


>gi|319638102|ref|ZP_07992866.1| ribosomal large subunit pseudouridine synthase D [Neisseria mucosa
           C102]
 gi|317400747|gb|EFV81404.1| ribosomal large subunit pseudouridine synthase D [Neisseria mucosa
           C102]
          Length = 374

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 85/310 (27%), Positives = 141/310 (45%), Gaps = 38/310 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+++ +            
Sbjct: 40  RLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQPKDKMIGGELIAV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   SG      ++G L +  
Sbjct: 88  --TVRPSEENLAFTPEPMDLDIIYEDDTVIVINKPAGLVVHPASGNWSGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAIANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   AI+H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAITHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C++        +  +  LHA  +   HP+ G  +
Sbjct: 256 HQIRVHMREANHPLAADPVYGNLRHPCSDAVKEAVKALGARQALHAYRLSFVHPKTGETV 315

Query: 306 QITAPLPAHM 315
              AP+P  M
Sbjct: 316 SFEAPMPDDM 325


>gi|319649641|ref|ZP_08003797.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317398803|gb|EFV79485.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 300

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 83/321 (25%), Positives = 147/321 (45%), Gaps = 35/321 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           ++ +++   R+D+         +   +Q+ ++ G V V+ ++ K N +  +   + I  P
Sbjct: 4   IIPDEQAGERIDKVLSTLNADWSRTQVQQWIKDGNVLVNGQKPKTNYKCTANDKIEISIP 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ--GGSGIAY 127
               L+ ++ E+  LD               + YED  + V NKP G+ V    G G   
Sbjct: 64  EPEELD-VVPEKMDLD---------------IYYEDKDVLVVNKPKGMVVHPAAGHGTGT 107

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y
Sbjct: 108 LVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLMNKTVTRKY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G+  +    I   + +           V  N K   +A++HF+V++ F + F  +
Sbjct: 168 RAVVHGVIPHDYGTIDAPIARDPK--DRQSMTVVDNGK---HAVTHFQVLERF-RDFTLV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E Q  TGRTHQ+RVH  ++G P+ GD KY     G   +       LHA  +   HP  G
Sbjct: 222 ECQLETGRTHQIRVHMKYIGYPLAGDPKY-----GPRKTLDIGGQALHAGVLGFEHPRTG 276

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L+  A +PA+  +  D L 
Sbjct: 277 EYLEFEASIPAYFEELLDKLA 297


>gi|255994448|ref|ZP_05427583.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Eubacterium saphenum ATCC 49989]
 gi|255993161|gb|EEU03250.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Eubacterium saphenum ATCC 49989]
          Length = 318

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 68/216 (31%), Positives = 118/216 (54%), Gaps = 18/216 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQ--KPRLTHRLDQETSGIL 158
           +YED  + V +KPAGI V    G   + I   L  ++D+ G+  K R  +RLD +T+G+L
Sbjct: 99  VYEDEHLLVIDKPAGIVVHPTHGYEENTIAHALIHYMDTVGEEFKIRFINRLDMDTTGLL 158

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+ +     +    +   ++K Y ++V G+P N+ E I +  +K   + G+     +Q
Sbjct: 159 MIAKNQFIQNAVVSEMKRGNVEKRYLAVVHGLPCNR-EGIIDAPIKA--VEGE---PRRQ 212

Query: 219 NEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             +G   +I+ +KV+    +    +L+++ HTGRTHQ+RVH  H+GCPI+GD  Y     
Sbjct: 213 VMEGGKPSITEYKVVGVSDELNVSFLDVRLHTGRTHQIRVHLKHIGCPILGDEFYGGKES 272

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
                   ++  LH+RY+   HP   ++ ++TA LP
Sbjct: 273 A-------DRQLLHSRYLRFTHPVSKKIVELTANLP 301


>gi|29349180|ref|NP_812683.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|253571343|ref|ZP_04848750.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           1_1_6]
 gi|29341088|gb|AAO78877.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|251839296|gb|EES67380.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           1_1_6]
          Length = 223

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 74/230 (32%), Positives = 109/230 (47%), Gaps = 38/230 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQ        +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQADKTGDTPLSETVKQYLKEKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR   ++K YW++V   PK  +              G+ VH 
Sbjct: 63  GLVIFAKTSKALTRLNEMFRTSEVKKTYWAVVKNAPKEPE--------------GELVHY 108

Query: 216 VKQNEK------------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           + +NEK             +  AI ++++I   ++ +  LE+   TGR HQ+R     MG
Sbjct: 109 LARNEKQNKSFAYDKEVPNSKKAILNYRLIG-HSENYYLLEVDLKTGRHHQIRCQLAKMG 167

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
           CPI GD KY     G   S     + LHAR +   HP    L ++ APLP
Sbjct: 168 CPIKGDLKY-----GAPRSNPDGSICLHARKVRFIHPVSKELIELEAPLP 212


>gi|296314698|ref|ZP_06864639.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           polysaccharea ATCC 43768]
 gi|296838532|gb|EFH22470.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           polysaccharea ATCC 43768]
          Length = 374

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 85/307 (27%), Positives = 138/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   +R G V V+ K  +  +++  G+ +R+            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKPSQPKDKMIGGEQIRV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFMPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAADPVYGNLRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|325261335|ref|ZP_08128073.1| ribosomal large subunit pseudouridine synthase family protein
           [Clostridium sp. D5]
 gi|324032789|gb|EGB94066.1| ribosomal large subunit pseudouridine synthase family protein
           [Clostridium sp. D5]
          Length = 226

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 72/211 (34%), Positives = 100/211 (47%), Gaps = 11/211 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLT--HRLDQETS 155
           +LYED  I V  KPAG+  Q        +   LK+ +     K Q+P L   HRLDQ   
Sbjct: 5   ILYEDQDIIVCAKPAGVPTQSSRVGTPDMVSILKNHIYKNSEKKQQPYLAVIHRLDQPVE 64

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LV A+T AAA+ L          K Y +L+ GIP   +  + ++L+K      +   V
Sbjct: 65  GLLVFAKTPAAARELNRQLTQYGFGKHYRALLAGIPVCMEGDLEDYLVKDGR--NNTAQV 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              +  GA  A  H+K+I+  +   C L ++   TGR HQ+RV   HMG PI GD KY  
Sbjct: 123 CTPDTPGAKKARLHYKIIETCSTPDCSLADITLETGRHHQIRVQMAHMGTPIAGDKKYGK 182

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
                  S    KL L A  +   HP  G++
Sbjct: 183 ESPALAAS---RKLQLFACRLKFKHPRTGKI 210


>gi|311748343|ref|ZP_07722128.1| ribosomal large subunit pseudouridine synthase C [Algoriphagus sp.
           PR1]
 gi|126576852|gb|EAZ81100.1| ribosomal large subunit pseudouridine synthase C [Algoriphagus sp.
           PR1]
          Length = 237

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 73/234 (31%), Positives = 112/234 (47%), Gaps = 26/234 (11%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K  DF K ++L+E++   V NKP  +S       A +I    K++        +L HRLD
Sbjct: 2   KKIDFQK-LILFENADYLVINKPPYLSSLDDRHEAQNILDLAKAYTPD----AQLCHRLD 56

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG LV+A+   A +HL   F  R++ KIY ++V GI   + E +   L+  +     
Sbjct: 57  KETSGCLVIAKNPEAYRHLAIQFENRKVDKIYHAVVEGIQDYQNELVDRNLIATN----- 111

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V +  KG   A ++F+ +  +A     +E +P TGR HQ+RVH  ++  PI GD  
Sbjct: 112 --KGVAKVSKGGKSAQTYFQTLKTYA-AHTLVECKPVTGRLHQIRVHLAYLKSPICGDTL 168

Query: 272 YCANF-------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           Y  N              K     PI  ++ LHA  +     +G +LQ+ AP P
Sbjct: 169 YGGNILYLSSLKRRFNLKKDTEELPIMQRVSLHAFSIGFEGLDGTKLQLNAPYP 222


>gi|332667785|ref|YP_004450573.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
 gi|332336599|gb|AEE53700.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
          Length = 233

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 109/219 (49%), Gaps = 13/219 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ +   NKPAGI VQG +     +  ++K ++  + +KP      + HRLD+  S
Sbjct: 5   VIYEDNHLIAVNKPAGILVQGDATEDTPLVDYVKDYIKFRYKKPGDVFLGVVHRLDRPVS 64

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDYVH 214
           G ++ ART  A   + E F+ R+++K YW++    P  +   + +++LK         + 
Sbjct: 65  GAVIFARTSKALTRMNELFKERKVEKNYWAVTERRPSPEAGHLTHYILKDHEKNISKALD 124

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +    K A  +   +++I     K   L ++P TGR HQ+RV    +GCPIVGD KY  
Sbjct: 125 QMSNRSKDAKKSDLDYELIGALEGKHLLL-VKPITGRPHQIRVQLSKIGCPIVGDLKYGH 183

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
               N  S     +YLH R M   HP    L +I A  P
Sbjct: 184 TQPNNDGS-----IYLHCRSMIFLHPVTKELVKIVADAP 217


>gi|154504965|ref|ZP_02041703.1| hypothetical protein RUMGNA_02475 [Ruminococcus gnavus ATCC 29149]
 gi|153794848|gb|EDN77268.1| hypothetical protein RUMGNA_02475 [Ruminococcus gnavus ATCC 29149]
          Length = 321

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 86/323 (26%), Positives = 144/323 (44%), Gaps = 32/323 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + +   E   R D+    +        L K+LR   + ++ K+   N ++  G  V+
Sbjct: 1   MQEIKITEQEAGQRFDKLLGKYLNKAPKSFLYKMLRKKNITLNGKKASGNEKLAKGDCVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +          + ++ I   S   + +++    IL YED  I + NKP G+  Q  +   
Sbjct: 61  L---------FLSDETIQKFSETFSGYTNVSLDIL-YEDEDIILINKPVGMLSQKAARSD 110

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  I+Y I     +  D +  +P + +RLD+ TSGI+   ++ A  Q L++ F  R
Sbjct: 111 ESLVEHLISYLIQSHALTEEDLRTFRPSICNRLDRNTSGIVAAGKSMAGLQSLSQMFHDR 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I K Y  L  GI + K   +  WL K      + V ++ Q   G+   I+ ++ I    
Sbjct: 171 TIGKYYLCLTAGIIE-KPSRVEGWLFKDERT--NKVEILFQERPGSARIITEYRPIKSH- 226

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARY 294
                LE+   TG+THQ+R H   +G P++GDHKY A   N +      +Q++L LHA  
Sbjct: 227 DGVTLLEVHLITGKTHQIRAHLASVGHPLIGDHKYGASQINREYEQKYHLQSQL-LHAAR 285

Query: 295 MDLPHPEG-----GRLQITAPLP 312
           +  P          + + TAPLP
Sbjct: 286 LQFPVCTQTLCNVSKKEFTAPLP 308


>gi|258647905|ref|ZP_05735374.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella tannerae ATCC 51259]
 gi|260851740|gb|EEX71609.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella tannerae ATCC 51259]
          Length = 245

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 71/219 (32%), Positives = 106/219 (48%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I + NK AG  +QG       +   +K+++  K  KP      + HRLD+  S
Sbjct: 9   ILYEDNHIIIVNKQAGEIIQGDKTGDRTVADEIKAYLKEKYNKPGAVFLGIPHRLDRPVS 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+ + ART  A   L E FR   I+K Y ++V   P+     + +WL +       Y H 
Sbjct: 69  GVSIFARTSKALARLNEMFRKGEIEKTYQAIVIHEPQIASGTLVHWLTRNEKQNKAYAH- 127

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K  +K A  AI  +KV +  + ++  + +Q  TGR HQ+R     +GCPI GD KY   
Sbjct: 128 -KAPQKNAKKAILDYKV-EAKSDRYWLINVQLQTGRHHQIRCQLAAIGCPIKGDLKY--- 182

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPA 313
             G   S     + LHAR +   HP   ++    AP P+
Sbjct: 183 --GAPRSNADGSICLHARSIRFEHPVSHKIIFAEAPYPS 219


>gi|257869391|ref|ZP_05649044.1| pseudouridylate synthase [Enterococcus gallinarum EG2]
 gi|257803555|gb|EEV32377.1| pseudouridylate synthase [Enterococcus gallinarum EG2]
          Length = 301

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 154/321 (47%), Gaps = 48/321 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINA 73
           EE  R+D+   +     +   +Q+ L+ G V      ++ N ++++G   V+++P     
Sbjct: 11  EEKGRVDKVLADRL-EASRSQIQQWLKEGAVTCQGDPIRANYKVKAGDQLVIQVP----- 64

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
                 E + LD         + +   ++Y+D  + V NKP G+ V   +G         
Sbjct: 65  ------EPESLDLE------PEDIPLTIVYQDQDVAVINKPQGMVVHPSAGHPNGTLVNA 112

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + YH+   L S  D    +P + HR+D++TSG+L++A+   A + L +  + +   + Y 
Sbjct: 113 LLYHMTD-LSSINDVV--RPGIVHRIDKDTSGLLMIAKNDHAHEALAKQLKDKTSLRKYV 169

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   ++K  I N  + +S +    +  V+++ K A   ++HF V++ F Q F  +E
Sbjct: 170 ALVHGNISHEKGTI-NAPIGRSKVN-RKMQAVQEDGKPA---VTHFTVLERFDQ-FTLVE 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +Q  TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP  
Sbjct: 224 LQLETGRTHQIRVHMQYIGFPLAGDPVYGPKKTLKGNGQ-------FLHAKLLGFTHPTT 276

Query: 303 GRLQI-TAPLPAHMVKTWDSL 322
           G   +  APLP    +T   L
Sbjct: 277 GESMVFEAPLPELFEETLKKL 297


>gi|116494944|ref|YP_806678.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
 gi|227535056|ref|ZP_03965105.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|301066507|ref|YP_003788530.1| 23S RNA-specific pseudouridylate synthase [Lactobacillus casei str.
           Zhang]
 gi|116105094|gb|ABJ70236.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           casei ATCC 334]
 gi|227187271|gb|EEI67338.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|300438914|gb|ADK18680.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           str. Zhang]
          Length = 306

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 93/326 (28%), Positives = 154/326 (47%), Gaps = 42/326 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  R+D+    H        +QK L+ G V V+ +  K N ++ SG V+ I         
Sbjct: 10  EQGRIDKVITAHETTHTRSQVQKWLQDGLVTVNGQPTKANYKVASGDVIAIS-------- 61

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            I E K L++        + +   ++YED ++ V +KP G+ V    G   H DG L + 
Sbjct: 62  -IPEAKPLEAI------PEPIPLDIVYEDDQVIVVDKPQGMVVHPAPG---HPDGTLVNG 111

Query: 137 V----DSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +    D  G     +P + HR+D++TSG+L+VA+T  A   L+   + +   + Y +LV 
Sbjct: 112 LLYHTDLPGINGVIRPGIVHRIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVH 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQP 247
           G  K  +  I       + +G D     +Q       +A++HF+V++ F + + +++   
Sbjct: 172 GTFKEDEGTI------DAPLGRDPRDRKRQAVVADGRHAVTHFQVLERF-EHYTFIKCIL 224

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH  ++  P+ GD  Y        T P + + +LHA  +   HP  G+L +
Sbjct: 225 ETGRTHQIRVHMAYIHHPVAGDPLYGP----KRTLPGKGQ-FLHAAKLGFVHPTTGQLLV 279

Query: 308 -TAPLPAHMVKTWDSL--GFKYDRNL 330
             AP+P    KT   L  G    RN+
Sbjct: 280 FEAPVPPIFEKTLADLRAGIDKTRNV 305


>gi|227824343|ref|ZP_03989175.1| pseudouridine synthase [Acidaminococcus sp. D21]
 gi|226904842|gb|EEH90760.1| pseudouridine synthase [Acidaminococcus sp. D21]
          Length = 311

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 88/325 (27%), Positives = 150/325 (46%), Gaps = 47/325 (14%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V     E D+  +R D +  +    ++  +LQ  +  G V  + K VK + +++ G V
Sbjct: 7   TKVTEPAAEKDQ-GLRADCYLADVL-DLSRSSLQHDMEKGLVTKEGKPVKASYKVKLGDV 64

Query: 65  --VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V IPP                 +V+L    + +   +LYED  + V NKP G+ V   
Sbjct: 65  FTVVIPP-----------------AVSLEAEPEPIPLAILYEDEDVIVVNKPRGMVVHPA 107

Query: 123 SG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G      ++  L    D  G     +P + HRLD++TSG++V A+   A   L++  + 
Sbjct: 108 AGNYTGTLVNALLYHCKDLSGINGVVRPGIVHRLDKDTSGVMVCAKNDRAHLSLSQQIKD 167

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           +  ++ Y ++V G  K+ +  I   L+ +       + VV     G   A++ ++V++ +
Sbjct: 168 KEAKRTYIAVVRGNIKDDRGHI-ETLIDRDPKDRMRMAVVPS---GGRLAVTDYEVLERY 223

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-----CANFKGNFTSPIQNKLYLH 291
             +F  +  +  TGRTHQ+RVH  ++G P+VGD KY     C +  G           LH
Sbjct: 224 G-RFTVVRCRLQTGRTHQIRVHMTYLGHPLVGDPKYQPQKTCFSIDGQ---------ALH 273

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHM 315
           +  +   HP  G+ +  TAPLP  M
Sbjct: 274 SETLTFRHPRTGKIMSFTAPLPGDM 298


>gi|237746821|ref|ZP_04577301.1| ribosomal large subunit pseudouridine synthase D [Oxalobacter
           formigenes HOxBLS]
 gi|229378172|gb|EEO28263.1| ribosomal large subunit pseudouridine synthase D [Oxalobacter
           formigenes HOxBLS]
          Length = 342

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 85/315 (26%), Positives = 142/315 (45%), Gaps = 35/315 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V+   E   RLD+    H P  +   +Q+ +  G V VD K  +    +   + + + P 
Sbjct: 32  VLSLKEGGERLDKIVARHLPDYSRSRIQRWIEQGYVTVDGKAAQGKQTVVGDEEIVVLPQ 91

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           +              +  +L    + +   +L+ED  I V NKPAG+ V   +G      
Sbjct: 92  L--------------AEEDLAFVPEPVGFPVLFEDRDILVVNKPAGLVVHPAAGNWSGTL 137

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++G L     S    +  + HRLD++TSG++VVA+T  A  HL    + R +++ Y +LV
Sbjct: 138 LNGLLHHLPKSAAIPRAGIVHRLDKDTSGLMVVAKTLEAQTHLVRQLQARTVRREYLALV 197

Query: 188 WGIPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVID---CFAQKFC 241
           WG     +  +A  +     IG    D + +          A++H+++++   C   K  
Sbjct: 198 WG-----ETPVAGTV--DQPIGRHPKDRIKMAVLQTASGKPAVTHYRLLETGVCNGSKVS 250

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++ +  TGRTHQ+RVH    G P+VGD  Y      +  S +  +  LHA  + L HP 
Sbjct: 251 LVKCRLETGRTHQIRVHMQFSGFPLVGDPLYGK----SRLSAVFPRQALHAFRLGLLHPA 306

Query: 302 GGRL-QITAPLPAHM 315
                +  APLP+ M
Sbjct: 307 KNEWNEWMAPLPSDM 321


>gi|146293584|ref|YP_001184008.1| pseudouridylate synthase [Shewanella putrefaciens CN-32]
 gi|145565274|gb|ABP76209.1| Pseudouridylate synthase [Shewanella putrefaciens CN-32]
 gi|319426883|gb|ADV54957.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 223

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 67/202 (33%), Positives = 105/202 (51%), Gaps = 8/202 (3%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP+G+      GIA H      + +     +  L HRLD  TSGI+V AR
Sbjct: 18  YKDRDLIIINKPSGL--LSNPGIAAHTYDCALTRLQRLYPETILVHRLDCATSGIMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            + A  HL   F+ R+ +K+Y + V G+  N++  I N  +  +     Y   ++  E G
Sbjct: 76  NKKAESHLKTQFQDRQSKKVYIAEVMGLIANEQGII-NLSIAPNCEHPPYQKALQAGEAG 134

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++H++V++   +    +E+ P TGRTHQLRVH L +G PI+GD  Y      N   
Sbjct: 135 GKSALTHYRVLE-RRKNSTLVELTPETGRTHQLRVHMLALGHPILGDEFYGDAAVIN--- 190

Query: 283 PIQNKLYLHARYMDLPHPEGGR 304
             + +L LHA+ +   HP  G+
Sbjct: 191 -AKPRLCLHAQSLRFSHPYSGK 211


>gi|30248520|ref|NP_840590.1| rluD; ribosomal large subunit pseudouridine synthase D
           [Nitrosomonas europaea ATCC 19718]
 gi|34395760|sp|Q82WZ5|RLUD_NITEU RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|30138406|emb|CAD84416.1| rluD; ribosomal large subunit pseudouridine synthase D
           [Nitrosomonas europaea ATCC 19718]
          Length = 344

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 92/318 (28%), Positives = 151/318 (47%), Gaps = 36/318 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V ++   +RLD+      P  +   LQ  +    V VD        ++  G+ +R+  
Sbjct: 34  LTVPDNLAGLRLDQALAQLLPQWSRSRLQGWIEQKCVSVDSAAATCKQKVWGGESIRV-- 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                   I  Q   D S      ++ +   +L+ED  + + +KPAG+ V  G+G  +H 
Sbjct: 92  --------IAGQTENDQS----HQAEAIPLKILFEDDHLIIIDKPAGLVVHPGNG-NWHG 138

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   L +      Q PR  + HRLD++T+G+LVVA+T  A   L    + R +++ Y +
Sbjct: 139 TLLNALLNHAPQLSQVPRAGIVHRLDKDTTGLLVVAKTIEAQFDLARQLQQRTVKRHYLA 198

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CW 242
           LV G  K +K+ + +  + +  I    + VV QN K A    +H++V++ F       C 
Sbjct: 199 LVLG--KLEKDGVVDAPIGRHPIHRTRMAVV-QNGKPAR---THYRVLEKFTASTLLHCS 252

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---YLHARYMDLPH 299
           LE    TGRTHQ+RVH L +G P+ GD  Y        T+    +L    LHA  ++L H
Sbjct: 253 LE----TGRTHQIRVHLLSIGHPLAGDPVYGRTSPDPSTADAVVRLPRQALHAWQLELTH 308

Query: 300 PEGGRLQI-TAPLPAHMV 316
           P  G++ +  +PLP  M 
Sbjct: 309 PHSGQILLWESPLPDDMA 326


>gi|312880111|ref|ZP_07739911.1| ribosomal large subunit pseudouridine synthase D [Aminomonas
           paucivorans DSM 12260]
 gi|310783402|gb|EFQ23800.1| ribosomal large subunit pseudouridine synthase D [Aminomonas
           paucivorans DSM 12260]
          Length = 344

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 139/293 (47%), Gaps = 34/293 (11%)

Query: 39  KILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           K++R GQV V    RVK + ++  G  V       A+    +E  ++   V         
Sbjct: 66  KLIRDGQVSVSWCPRVKPSMKVLPGGSV------TAVVPPPEELDLVPEDVPFR------ 113

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLD 151
              ++YED+ + V +KPAG+ V    G      + G L  + D +     ++P + HRLD
Sbjct: 114 ---VVYEDADLIVVDKPAGLVVHPAPGHWRGTLVHGLLFRYPDMEALNGVRRPGIVHRLD 170

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG+LVVAR   A + L   F+ R ++K Y +L  G P+  +  I      +  IG D
Sbjct: 171 ATTSGLLVVARNGLAMEELVRCFKQRTLRKEYLALAHGRPQLPEGEI------RLPIGRD 224

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +  +    +G   +++ ++ +     +   L  Q  TGRTHQ+RVH   +GCP+VGD 
Sbjct: 225 PKNRKRMTILEGGRDSLTRYRTL-WTRGRISLLLCQLCTGRTHQIRVHLKALGCPLVGDR 283

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            Y    +  F     ++++LHA  +   HP  G  L   +PLP  +++  ++L
Sbjct: 284 VYAPGRETPFHP---DRVFLHAWKLGFSHPRTGEPLLFRSPLPPDLLEALEAL 333


>gi|262068065|ref|ZP_06027677.1| tRNA pseudouridine synthase A [Fusobacterium periodonticum ATCC
           33693]
 gi|291378151|gb|EFE85669.1| tRNA pseudouridine synthase A [Fusobacterium periodonticum ATCC
           33693]
          Length = 295

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 85/317 (26%), Positives = 160/317 (50%), Gaps = 32/317 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--P 68
           +++ + E +R+DR+ + H  +I    + K+LR  +V+V+ K+V  + R+  G +V +  P
Sbjct: 5   IIDEEYETVRIDRFLRKHLKNIALSEVYKMLRKAKVKVNNKKVSQDYRLVLGDIVFVFLP 64

Query: 69  PVINALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                      E+K  + S+ L +   + LK +++YED  +++ NK  G  +  GSG   
Sbjct: 65  ESF--------EEKNEEKSIELNEVRKEKLKFMIVYEDENLFIINKNLGDVIHKGSGHDV 116

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +    +S+  +   K    +R+D+ TSG+++ A+    A+ + +  ++  I K Y+ LV
Sbjct: 117 SLLEEFRSYYSN--NKINFVNRIDKLTSGLVIGAKNIKTAREIAKEIQLGNISKKYYILV 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQKFCWLEM 245
           +G  + +K  + N+L K      D   V+  + +  +Y  +I+++K I+     +  LE 
Sbjct: 175 YGKIEKEKFVLENYLKK------DEEKVIVSDIEKEDYKKSITYYKRING-NDDYTLLEA 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +  TGRTHQLR    H+G  IVGD KY  N K       ++ +YL + Y+ +       L
Sbjct: 228 ELKTGRTHQLRAQLNHLGHTIVGDTKYGKNIK-------EDIMYLFSYYLKIDLY---NL 277

Query: 306 QITAPLPAHMVKTWDSL 322
           ++   +P   +K  D L
Sbjct: 278 ELELGIPNFFLKKCDML 294


>gi|331001807|ref|ZP_08325329.1| hypothetical protein HMPREF0491_00191 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412781|gb|EGG92164.1| hypothetical protein HMPREF0491_00191 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 304

 Score =  103 bits (256), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 80/315 (25%), Positives = 146/315 (46%), Gaps = 37/315 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++ E  + N R+D +   +    +   +Q +++ G+  +  K +K N R++ G +V +  
Sbjct: 6   IIAEESDINKRIDVFLSKNLESFSRSYIQDLIKKGKATIGGKTIKANYRLREGDIVALAI 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                  I+ E   LD               ++YED+ + + NKP G+ V   +G     
Sbjct: 66  PKPEPLEILPENIPLD---------------IVYEDNDVILVNKPKGMVVHPAAGHYSGT 110

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH    L     +   +P + HR+D +T+GI++V +   A QH+ +      I 
Sbjct: 111 LVNALLYHCKDNLSGI--NGVLRPGIVHRIDMDTTGIIIVCKNDNAHQHIAKQLAEHSIT 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G  K + E + +  + +S      + V    +K    A++HFKV++     +
Sbjct: 169 RKYVAIVSGNIK-EDEGVVDAAIARSKNDRKKMTV----DKDGKRAVTHFKVLERL-NNY 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++E    TGRTHQ+RVH  ++  P++GD  Y +N K N     Q    LHA+ +   HP
Sbjct: 223 TYIECVLETGRTHQIRVHMSYLHHPLLGDEVY-SNKKENTKLKGQ---CLHAKVLGFIHP 278

Query: 301 EGGR-LQITAPLPAH 314
                ++  APLP +
Sbjct: 279 STNEYMEFEAPLPEY 293


>gi|168186171|ref|ZP_02620806.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum C str. Eklund]
 gi|169295643|gb|EDS77776.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum C str. Eklund]
          Length = 304

 Score =  103 bits (256), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 93/321 (28%), Positives = 146/321 (45%), Gaps = 48/321 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++   E N RLD +    +   +    QK++    V V+    K N +++ G  V 
Sbjct: 3   IKDFLINESEVNSRLDVFISKCFEEKSRSYAQKLIEEKNVFVNNSSKKSNYKLKIGDYVE 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           I          IKE    D  +N+      +K  ++YED  + V +KP G+ V  G+G  
Sbjct: 63  IK---------IKE----DEKINIKPED--IKLNIIYEDEDVIVIDKPQGMVVHPGAGNY 107

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  + YH D       D +   P + HR+D++TSG+LVVA+  +A   L+E  +  
Sbjct: 108 SGTLVNGLLYHCDSLSSINGDVR---PGIVHRIDKDTSGVLVVAKNDSAHIILSEQLKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +++ Y +LV GI KN +  I   L +  K  I    V       +    A++H+ V+  
Sbjct: 165 SMKREYIALVEGIIKNDEGIIDAPLGRNPKDRIKRAVV-------RNGKSAVTHYNVLRR 217

Query: 236 FAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           F +     C LE    TGRTHQ+RVH  H+  P+VGD  Y    K  F     N   LHA
Sbjct: 218 FNKNTLVKCILE----TGRTHQIRVHMAHINHPLVGDPMYGFR-KQRFK---LNGQMLHA 269

Query: 293 RYMDLPHPEGGR-LQITAPLP 312
           R +   HP   + ++  + LP
Sbjct: 270 RKLGFIHPSSKKYMEFQSELP 290


>gi|332970080|gb|EGK09077.1| ribosomal large subunit pseudouridine synthase D [Kingella kingae
           ATCC 23330]
          Length = 371

 Score =  103 bits (256), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 86/320 (26%), Positives = 149/320 (46%), Gaps = 39/320 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V ND   MRLD       P  +   +   ++ G V+ + K      ++  G+ + +  
Sbjct: 30  LIVPNDLAGMRLDAALAKLLPDYSRSRITTWIKDGFVQCNGKTASPKEKLIGGEELSV-- 87

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                       +I  S  N     + +   +++ED  + V NKPAG+ V   +G     
Sbjct: 88  ------------QIQQSDENQAYEPEHMDLNIVFEDDTVIVLNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++G L +      Q PR  + HRLD++TSG++VVA+T  A   L +  + R +++IY +
Sbjct: 136 LLNGLL-AHCPELSQVPRAGIVHRLDKDTSGLMVVAKTLPAQNSLVQQLQNRTVKRIYRA 194

Query: 186 LVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCW 242
           +  GI P + K         ++ IG D  + +K    + G   A++H KV++ +     +
Sbjct: 195 VADGIVPFDGK--------IETLIGRDPHNRLKMAVVKFGGKEAVTHVKVLERY-HAHSY 245

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------KLYLHARYMD 296
           +E    TGRTHQ+RVH      P+ GD  Y  N +   + P+++      +  LHA ++ 
Sbjct: 246 IECSLETGRTHQIRVHMKEARHPLAGDPVY-GNPRHVCSQPVKDVVKSLARQALHAYHLS 304

Query: 297 LPHPEGGRL-QITAPLPAHM 315
             HP+ G L    AP+P  M
Sbjct: 305 FVHPKSGELVSFEAPMPDDM 324


>gi|317498467|ref|ZP_07956761.1| RluA family pseudouridine synthase [Lachnospiraceae bacterium
           5_1_63FAA]
 gi|316894160|gb|EFV16348.1| RluA family pseudouridine synthase [Lachnospiraceae bacterium
           5_1_63FAA]
          Length = 305

 Score =  103 bits (256), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 82/323 (25%), Positives = 146/323 (45%), Gaps = 36/323 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RI 67
           + V N+    RLD         +    + K+ +  +  ++ K  K N + + G V+  ++
Sbjct: 7   IKVTNEMAGKRLDVVLSEQCSDLTRSYINKLCKEERAALNGKTSKGNKKCKEGDVITLQV 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
           P           E +IL   +NL          ++YED  + + NKP G+ V   +G   
Sbjct: 67  PEPT--------ELEILPEEMNLD---------IVYEDQDVILINKPKGMVVHPAAGHYS 109

Query: 126 AYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++G +    D         +P + HR+D++T+GIL+V +   A Q + +      I 
Sbjct: 110 GTLVNGLMAHCKDDLSGINGVLRPGIVHRIDKDTTGILIVCKNDMAHQSIAKQLYDHSIT 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V+G  K ++E   N  + +S      + +V        +A++H+KV+    + F
Sbjct: 170 RKYHAIVYGNIK-EEEGTVNAPIGRSLKDRKKMGIVMD----GKHAVTHYKVLKRLKKGF 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++E Q  TGRTHQ+RVH   +  P++GD  Y    K  +T   Q    LHA+ +   HP
Sbjct: 225 TYIECQLETGRTHQIRVHMASIKHPLLGDDVYGPK-KSKYTLEGQ---CLHAKVLGFVHP 280

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  ++   PLP +  K  + L
Sbjct: 281 RTGEYMEFEVPLPEYFEKLLNKL 303


>gi|320168809|gb|EFW45708.1| pseudouridine synthase [Capsaspora owczarzaki ATCC 30864]
          Length = 748

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 84/262 (32%), Positives = 127/262 (48%), Gaps = 34/262 (12%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           D ++  +L++D  I V NKPAG+SV      A  +   L +        P + HRLD+ T
Sbjct: 359 DRIRQCVLHKDQHIIVINKPAGLSVMADGFEALDLSRLLPALQFEAPCLPHIVHRLDKNT 418

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-------ECIANWLLKKSH 207
           +G L++AR    A+ L+ +F+ +RI K Y ++V G P           E I+    +K  
Sbjct: 419 TGALLLARNPRVARILSRAFQKQRIGKTYTAIVAGAPPFDSGIINCPLEVISATTARKVG 478

Query: 208 IGGDYV----HVVKQNE-------KGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQL 255
           +    V     +V  NE       + A  AI+HF V+   ++    L E  P +GR HQL
Sbjct: 479 VTPGTVLCRHDLVYANETSYLRTRRDALSAITHFSVVGRSSRGPAALIEFVPMSGRKHQL 538

Query: 256 RVHAL-HMGCPIVGDHKYCANFKGNFTSPI-------QN---KLYLHARYMDLPHPEGGR 304
           RVH+  ++G PI+GD++Y          P+       +N   KL LHAR + +P  +  R
Sbjct: 539 RVHSSKYLGHPILGDNRYGNGCPVELHEPLGIAGWDAKNDVVKLQLHARSIVVPSLDQQR 598

Query: 305 ----LQITAPLPAHMVKTWDSL 322
               L + APLPAHM +  D L
Sbjct: 599 NNKPLVVLAPLPAHMKEVMDKL 620


>gi|239906997|ref|YP_002953738.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Desulfovibrio magneticus RS-1]
 gi|239796863|dbj|BAH75852.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Desulfovibrio magneticus RS-1]
          Length = 554

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 81/243 (33%), Positives = 113/243 (46%), Gaps = 21/243 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSK---GQKPRLTHRLDQETS 155
           LLY D  + V NKPAG+++   S       ++  L  + D +   G +P + HRLD++TS
Sbjct: 95  LLYLDGDVLVLNKPAGLTIHPASSQPDGTLVNRLLHHFPDMRAMAGDRPGIVHRLDKDTS 154

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+VA+T +A   L   F  RR+ K Y +LV G P+     I      +  +G D  H 
Sbjct: 155 GLLLVAQTESARLALAADFAERRVAKTYLALVHGRPERSDGVI------ELPVGRDPKHP 208

Query: 216 VKQN--EKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            K     KG   A S +K+           LE+   TGRTHQ+RVH   MG PIVGD  Y
Sbjct: 209 TKMAVVAKGGREAKSSWKLAWTAPDGTASLLEVAIATGRTHQIRVHMAAMGHPIVGDAVY 268

Query: 273 CA------NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            A        +G   + +  +  LHA  +   HP  G  L    P PA   +    LG +
Sbjct: 269 GARQHSDWTRRGGAMARLAKRQMLHAWKLAFSHPGTGEELSFCQPPPADFWRLLLMLGRR 328

Query: 326 YDR 328
             R
Sbjct: 329 CQR 331


>gi|328957863|ref|YP_004375249.1| uncharacterized RNA pseudouridine synthase YlyB [Carnobacterium sp.
           17-4]
 gi|328674187|gb|AEB30233.1| uncharacterized RNA pseudouridine synthase YlyB [Carnobacterium sp.
           17-4]
          Length = 302

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 89/295 (30%), Positives = 139/295 (47%), Gaps = 36/295 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           E M L  +  +   H +  +++ IL  GQV VD K +K  N+ +   QVV I        
Sbjct: 22  EPMELLPFLLSIMSHTSRNSVKSILTRGQVTVDGKVIKKHNHPLLPNQVVAI-------- 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG---ISVQGGSGIAYHIDGF 132
                     S+    K +  +   +LYED  I V +K AG   I+ +    +  H    
Sbjct: 74  ---------QSNKAAIKETALVGMTILYEDDAIIVIDKEAGLLSIAAKFAQELTAHRQ-- 122

Query: 133 LKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           L ++V  +    R+   HRLD++TSG++V A+T    Q + E+++    ++IY  LV GI
Sbjct: 123 LINYVKQENHNNRIYVVHRLDRDTSGVMVFAKTEQVKQEMQENWKDIVKERIYSVLVEGI 182

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
               +  I  WL +   +    VH     + G   AI+H+K I     +F  LE +  TG
Sbjct: 183 VSEDEGSIKTWLTESKAMK---VHSATY-DNGGKLAITHYKKIRN-NDEFTLLEARLETG 237

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           R +Q+RVH   +G P+ GD KY     G  ++P++ +L LHA  + L HP    L
Sbjct: 238 RKNQIRVHMETLGHPVAGDKKY-----GATSNPLK-RLGLHATTLALIHPTSKEL 286


>gi|302875571|ref|YP_003844204.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
 gi|307690100|ref|ZP_07632546.1| pseudouridine synthase, RluA family protein [Clostridium
           cellulovorans 743B]
 gi|302578428|gb|ADL52440.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
          Length = 298

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 81/260 (31%), Positives = 126/260 (48%), Gaps = 25/260 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDF----LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           LN+++K   +++  +N  +  D     +   + YEDS I V NKP  I V       Y  
Sbjct: 51  LNYVLKAGDVIEVKLNKEESQDIEPENIPLKVAYEDSDIIVLNKPPFIVVHPTKNYPYGT 110

Query: 130 --DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             +G L  +   KG+    RL  RLD  TSG+++VA+ + +   L         +K Y +
Sbjct: 111 LANGLL-YYFKEKGENCIVRLVSRLDMNTSGLIIVAKNQFSHMSLQRDMNKEEFKKQYLA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWL 243
           +V G    K E  A++      I  +    +K+  +++G   +I+H+KVI+ ++     L
Sbjct: 170 IVHG----KME--ADFGTIDLPIYKEEDEPIKRIIDDRGQR-SITHYKVIETYSNA-QLL 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++   TGRTHQ+RVH  H+GCPI GD  Y     G        +  LHA  +  PHP  G
Sbjct: 222 KLTLETGRTHQIRVHLSHLGCPIFGDSLY-----GELEDQYIKRQALHAFSLSFPHPRDG 276

Query: 304 R-LQITAPLPAHMVKTWDSL 322
           R + I A LPA M +  + L
Sbjct: 277 RIINIEAELPADMSELLEKL 296


>gi|295706351|ref|YP_003599426.1| pseudouridine synthase [Bacillus megaterium DSM 319]
 gi|294804010|gb|ADF41076.1| pseudouridine synthase [Bacillus megaterium DSM 319]
          Length = 304

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 85/316 (26%), Positives = 145/316 (45%), Gaps = 44/316 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP- 68
            V+  ++   R+D+         +   +Q+ ++ G  +V+ K VK N + ++G  + I  
Sbjct: 6   TVINEEQAGERIDKVLSTVNAEWSRSQVQQWIKEGHAKVNDKTVKGNYKCKTGDAIIIEV 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
           P +  L+ ++ E+  LD               + YED  + V NKP G+ V    G    
Sbjct: 66  PELEELD-VVAEEMDLD---------------IYYEDQDVLVVNKPRGMVVHPAPGHHSG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + 
Sbjct: 110 TLVNGLMAHCKDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDLAHESLVSQLVAKTVTRR 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFA 237
           Y ++V GI  +    I       + IG D      + V  +N + A   ++HF V+  F 
Sbjct: 170 YKAIVHGIIAHDHGTI------DAPIGRDKQDRQSMTVTDENSRDA---VTHFTVLQRF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY        T PI  +  LHA  +  
Sbjct: 220 KDFSLVECKLETGRTHQIRVHMKYIGFPLAGDPKYGP----KKTLPIDGQ-ALHAGVLGF 274

Query: 298 PHPEGGR-LQITAPLP 312
            HP     ++  AP P
Sbjct: 275 IHPRTNEYMEFEAPAP 290


>gi|259046729|ref|ZP_05737130.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           adiacens ATCC 49175]
 gi|259036625|gb|EEW37880.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           adiacens ATCC 49175]
          Length = 308

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 91/309 (29%), Positives = 143/309 (46%), Gaps = 43/309 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E+  RLD+        ++   +Q  L++G + V+ + VK N + QSG  V I        
Sbjct: 13  EKTQRLDKVLTGELG-LSRTTIQSWLKAGLISVNGEVVKSNYKAQSGDEVTI-------- 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-- 133
            + KE+ ++      T   + +   +++ED  + V NKP+G+ V    G   H  G L  
Sbjct: 64  -LQKEEDVI------TIQPENIPLDIVFEDDSLIVVNKPSGMVVHPSKG---HYSGTLVN 113

Query: 134 ------KSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                  S  DS  +   +P L HR+D++TSG+LV+A+     Q L E     ++ + Y 
Sbjct: 114 ALLYHSNSLSDSTSEEIYRPGLVHRIDKDTSGLLVIAKNNDVHQKLAEQIAENKMNREYI 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G   ++   +   L +  H       VV   EKG   AI+HF+V+D F+  +  + 
Sbjct: 174 AIVDGHFAHETGVVDAPLSR--HQTNRLKRVV---EKGGKNAITHFEVLDSFSD-YSLVS 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQ+R H   +  PIV D  Y    K N T   Q   +LHAR +   HP  G 
Sbjct: 228 CRLETGRTHQIRAHMEFIKHPIVNDPLYHPKGK-NATEFGQ---FLHARTLSFTHPLTGE 283

Query: 305 ---LQITAP 310
               Q+  P
Sbjct: 284 TLNFQVEPP 292


>gi|150020881|ref|YP_001306235.1| RluA family pseudouridine synthase [Thermosipho melanesiensis
           BI429]
 gi|149793402|gb|ABR30850.1| pseudouridine synthase, RluA family [Thermosipho melanesiensis
           BI429]
          Length = 306

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 92/308 (29%), Positives = 145/308 (47%), Gaps = 36/308 (11%)

Query: 16  EENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           E+  RLD++ +   P  I+   +Q+ ++SG V V+ +  K + ++++G VV        L
Sbjct: 10  EKGWRLDKFIQEKAPDWISRTYIQRAIKSGMVTVNNEEKKPSYKLKNGDVVSF-----EL 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI------SVQGGS---GI 125
               K+ +IL  ++ L          ++YED  I V NK  G+      +   G+    +
Sbjct: 65  PEEPKKVEILPENLPLK---------IIYEDKDIIVVNKDPGVVTHPTPTFLSGTLVNAL 115

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            YH + F     +    +P + HRLD++TSG++VVA+   A Q L+  F+ R+ +K Y +
Sbjct: 116 MYHCNDFQGIGGE---LRPGIVHRLDKDTSGVIVVAKNDKAHQSLSMQFKERKTEKTYIA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G  K     I   L +   +      V    + G N AI++FKVI  F      L  
Sbjct: 173 IVSGEVKKNYGTIDVPLGRNPVVRTKIAPV----DWGKN-AITYFKVIKRFKNATLLLAF 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            P TGRTHQ+RVH  ++G P++GD  Y    K         +  LHA  +   HP     
Sbjct: 228 -PKTGRTHQIRVHMKYIGHPLLGDELYGRGKKDEIFG--VKRQMLHALKLSFYHPSTNEK 284

Query: 306 QI-TAPLP 312
            I  APLP
Sbjct: 285 MIFVAPLP 292


>gi|167644317|ref|YP_001681980.1| RluA family pseudouridine synthase [Caulobacter sp. K31]
 gi|167346747|gb|ABZ69482.1| pseudouridine synthase, RluA family [Caulobacter sp. K31]
          Length = 351

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 94/337 (27%), Positives = 141/337 (41%), Gaps = 69/337 (20%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV----DKKRVKFNNRIQSG----QVVR 66
           D    RLD+      P ++   LQ ++ +GQV +       R   + + ++     +VV 
Sbjct: 38  DLAGQRLDKALATAAPELSRARLQALIAAGQVSLVVEGAAPRAMPDGKAKAPAGLYEVVV 97

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
            PP            + L  ++ L+         +LYED+ + V +KPAG++     G  
Sbjct: 98  PPPT---------AAEPLPENIPLS---------VLYEDAHLIVIDKPAGMAAHPAPGCE 139

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  + +H    L         +P + HRLD+ETSG++V A+T AA Q L+  F   
Sbjct: 140 TGTLVNALLFHCGASLSGI--GGVARPGIVHRLDKETSGVMVAAKTDAAHQGLSALFAKH 197

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY--VHVVKQNEKGANYAISHFKVIDC 235
            I ++Y +L  G P      I   L +     GD   + V+K    G   AI+H++V   
Sbjct: 198 DIDRMYLALTRGAPHPVVGTIITQLGRSP---GDRKKMAVLKS---GGREAITHYRVEKS 251

Query: 236 FAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           F            C LE    TGRTHQ+RVH    G P +GD  Y A   G   +P++  
Sbjct: 252 FGPPDKPLASRVACRLE----TGRTHQIRVHMASKGSPCLGDPVYGA---GAPAAPVKAA 304

Query: 288 L--------YLHARYMDLPHPEGGR-LQITAPLPAHM 315
           L         LHA  +   HP     L+   PLP  M
Sbjct: 305 LTEIGFSRQALHAAVLGFVHPITRELLRFETPLPPDM 341


>gi|238651091|ref|YP_002916949.1| ribosomal large subunit pseudouridine synthase D [Rickettsia
           peacockii str. Rustic]
 gi|238625189|gb|ACR47895.1| ribosomal large subunit pseudouridine synthase D [Rickettsia
           peacockii str. Rustic]
          Length = 313

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 85/322 (26%), Positives = 149/322 (46%), Gaps = 52/322 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD+   +   +++   +QK ++  QV V+              ++  P V+   N II
Sbjct: 13  IRLDKALSSLLENVSRNQIQKAIKDSQVLVND------------VIISDPDVLVKENDII 60

Query: 79  -------KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +E KI  ++V L          ++YED  + V NK AG++V  G+G  +H D 
Sbjct: 61  LFSFKEPEELKIAAANVALD---------IIYEDDDLIVINKAAGMTVHPGAG--HHDDT 109

Query: 132 FLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + + +            ++P + HRLD++T+G++VVA+   A   L      R++ + Y
Sbjct: 110 LVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCW 242
             LVWG+  N  E +    + +S      + ++K    G   A++H+K ++ F +     
Sbjct: 170 KVLVWGVI-NPLEGVIKNNIGRSRSDRQKMTILKY---GGKEAVTHYKTLELFYKGSISM 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLY------LHARY 294
           +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP  ++ KL       LH+ Y
Sbjct: 226 VECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAHSPPELKAKLIDFKRQALHSWY 285

Query: 295 MDLPHPEGGR-LQITAPLPAHM 315
           +   HP     ++ +  LP  M
Sbjct: 286 LSFTHPTSNEIMEFSCELPRDM 307


>gi|268316750|ref|YP_003290469.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
 gi|262334284|gb|ACY48081.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
          Length = 242

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 77/239 (32%), Positives = 119/239 (49%), Gaps = 26/239 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LY D+ + V NKP+G+  QG    A  +    K+ +  +  KP      L HRLD   S
Sbjct: 9   VLYLDNHLLVINKPSGLRSQGDRSGAPTVLSLGKALIKERFNKPGNVYLGLVHRLDAPVS 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG--DYV 213
           G++V+ART  AA  L + FR R ++K+Y +LV G    + E    W   +  I    D++
Sbjct: 69  GVMVLARTSKAAARLMQQFRERTVEKVYLALVEG----ELEGSGTW---EDFIAPARDHM 121

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +V ++      A+ H++ +         + + P TGR HQ+RV     G PI+GD +Y 
Sbjct: 122 RLVPEDHPFGKRAVLHWQAL-MTRNGLTLMRLVPETGRKHQIRVQLAFRGYPILGDRRYR 180

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD-SLGFKYDRNL 330
           A     + +P Q  + LHA  + L HP    R+Q TAP+P+     WD +   + DR L
Sbjct: 181 AR---RWLAPGQ--MALHAWKLALTHPTRRERMQWTAPVPSF----WDEAFRVRVDRLL 230


>gi|238018931|ref|ZP_04599357.1| hypothetical protein VEIDISOL_00791 [Veillonella dispar ATCC 17748]
 gi|237864415|gb|EEP65705.1| hypothetical protein VEIDISOL_00791 [Veillonella dispar ATCC 17748]
          Length = 307

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 92/314 (29%), Positives = 143/314 (45%), Gaps = 42/314 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  +++ MRLD +   H    +   +Q +++ G + V  K  K N R+    VVR+   
Sbjct: 5   IVNAEQDGMRLDVFLTEHMEG-SRSYIQSLIKGGHITVGAKVGKANLRLTPNAVVRV--- 60

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                      +I +      K  D    +L YED  I + NK  G+ V    G      
Sbjct: 61  -----------EIPEPESVEVKPEDIPLDVL-YEDHDIIIVNKQRGMVVHPAVGNYSGTL 108

Query: 129 IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D  G     +P + HRLD++TSG+++ A+  AA   L E  +    ++ Y 
Sbjct: 109 VNALLYHCKDLSGINGEIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKEHSAKRTYL 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +LV G    +K  I      K+ IG        + VV +N K    A++HF V++ F  +
Sbjct: 169 ALVQGNIVEEKGTI------KAPIGRHPKDRMKMAVVFENSKD---AVTHFNVVERFGHQ 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E    TGRTHQ+RVH  H+G P+V D  Y          PI+ +  LH+R +D+ H
Sbjct: 220 -TLVECNLETGRTHQIRVHFAHIGHPVVNDPFYGYR---RMDFPIEGQA-LHSRSLDVKH 274

Query: 300 P-EGGRLQITAPLP 312
           P  G  +   APLP
Sbjct: 275 PITGESMHFEAPLP 288


>gi|150024977|ref|YP_001295803.1| 23S rRNA pseudouridine synthase [Flavobacterium psychrophilum
           JIP02/86]
 gi|149771518|emb|CAL42987.1| Probable 23S rRNA pseudouridine synthase [Flavobacterium
           psychrophilum JIP02/86]
          Length = 231

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 72/222 (32%), Positives = 107/222 (48%), Gaps = 14/222 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L++D+ I V NK  G  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 14  ILHQDNHIIVVNKRVGDIVQGDKTGDKPLSEVVKEYIKDKYDKPGEVFLGVVHRLDRPTT 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V ART  A   L E F  R  QK YW++V   P+  +  + ++L +         H+
Sbjct: 74  GIVVFARTSKALTRLNEMFSNRETQKTYWAVVKNKPEKNEAKLVHYLKRNEKNNTSKAHI 133

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +  E  +  A   +K+I      F  LE+  HTGR HQ+R     +G PI GD KY   
Sbjct: 134 KEVPE--SKLASLDYKIIKELNNYFA-LEINLHTGRHHQIRAQLSAIGTPIKGDLKY--- 187

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
             G   S     ++LHAR +   HP     +QI AP+P  ++
Sbjct: 188 --GFDRSNPNGGIHLHARKLVFIHPVTKENIQIIAPVPDDVI 227


>gi|91200050|emb|CAJ73092.1| similar to ribosomal large subunit pseudouridine synthase D
           [Candidatus Kuenenia stuttgartiensis]
          Length = 335

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 84/305 (27%), Positives = 147/305 (48%), Gaps = 45/305 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E+ R+DR+  + +P ++   +QK+++ G + V+   VK +  I+ G V      I+A   
Sbjct: 24  ESKRIDRFISSRFPDLSRTYIQKLVKEGAIVVNGNVVKSSYFIKKGDV------ISATVP 77

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           + +E KI    + L          ++YED  + + NKP  + V    G   H  G L + 
Sbjct: 78  VPEETKITPEDIPLN---------IIYEDDYLMLINKPYDMVVHPAGG---HPSGTLVNA 125

Query: 137 VDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           V    Q         K  + HRLD++TSG+++V ++ A   H+   F  R ++K Y+++V
Sbjct: 126 VTFYCQNLSQINGPLKAGIVHRLDRDTSGVMLVIKSDAVHSHIAMQFEKRLVKKEYFAVV 185

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            G +  +  E   N  + +  +  D   +  + + G N A S ++VI+ F + +  +++ 
Sbjct: 186 EGEVAFDSNEI--NMPIGRHRV--DRQKMAVRRDTGKN-ATSVYEVIERF-RGYTLVKIM 239

Query: 247 PHTGRTHQLRVHALHMGCPIVGDH---KYCANFKGNF--------TSPIQNKLYLHARYM 295
           P TGRTHQ+RVH   +G P+V D    KY A F+ +            I  +  LHA  +
Sbjct: 240 PKTGRTHQIRVHMQAIGHPVVADEMYSKYNACFRSDLLGKERAPDEGSIIERQALHAHRI 299

Query: 296 DLPHP 300
           +  HP
Sbjct: 300 EFFHP 304


>gi|260912047|ref|ZP_05918609.1| RluA family ribosomal large subunit pseudouridine synthase
           [Prevotella sp. oral taxon 472 str. F0295]
 gi|260633852|gb|EEX51980.1| RluA family ribosomal large subunit pseudouridine synthase
           [Prevotella sp. oral taxon 472 str. F0295]
          Length = 298

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 90/311 (28%), Positives = 148/311 (47%), Gaps = 37/311 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQV 64
           Y +YVV E   E+M LD W  ++    +   L+ ILR   V VD K V +F+ R+Q G  
Sbjct: 14  YDRYVVAE---ESMLLD-WLLHNVKGKSRNKLKDILRGHGVFVDGKCVTQFDYRLQPGMK 69

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V +     A                    S ++K  ++YED  + V +K AG+       
Sbjct: 70  VTVSRAKKAAPF----------------KSRYIK--IVYEDRYLIVVDKSAGVLSMAAGH 111

Query: 125 IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            + ++   L ++ +  GQK R  + HRLD+ETSG++V A+     Q L  ++      + 
Sbjct: 112 SSLNVKAILDTYFEKSGQKCRAHVVHRLDRETSGLMVYAKDMDTEQILEHNWHDIVYDRR 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G   ++   I++WL   +     Y+      + G  YA++HF V++        
Sbjct: 172 YVAVVSGEIVDEGGTISSWLKDNN----SYITYSSPVDNGGKYAVTHFHVLN-RTTTHSL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-E 301
           +E +  TGR +Q+RVH   +G P+ GD KY     GN  +P+ ++L LHA  +   HP  
Sbjct: 227 VEYKLETGRKNQIRVHTADIGHPVCGDLKY-----GNGDNPL-DRLCLHAYMLCFYHPIT 280

Query: 302 GGRLQITAPLP 312
             R++   P+P
Sbjct: 281 RERMEFFTPIP 291


>gi|313890534|ref|ZP_07824162.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
 gi|313121051|gb|EFR44162.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
          Length = 299

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 90/322 (27%), Positives = 152/322 (47%), Gaps = 50/322 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RLD+        ++     + ++ G V V+ + VK    ++SG         + + 
Sbjct: 7   EAGLRLDKALA-ETTDLSRSQANEQIKKGLVLVNGQAVKAKYNVKSG---------DNIT 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           + + E+++LD        ++ L   ++YEDS + + NK  G+ V   +G         + 
Sbjct: 57  YQLPEEEVLDY------QAENLPIDIIYEDSDLAIINKAQGMVVHPSAGHSSGTLVNALM 110

Query: 127 YHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           YHI    K      G  +P + HR+D++TSG+L+VA+   A Q L E  + ++  + Y +
Sbjct: 111 YHI----KDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDKAHQVLAEELKAKKSLRNYLA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWL 243
           +V G   N +  I      ++ IG       KQ+   KG + A++ F V++ F   +  L
Sbjct: 167 IVHGNLPNDRGMI------EAPIGRSEKDRKKQSVTVKGKD-AVTRFTVLERFGD-YTLL 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E+   TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ + L HP 
Sbjct: 219 ELSLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGNGQ-------FLHAQTLGLTHPS 271

Query: 302 GGRL-QITAPLPAHMVKTWDSL 322
            G L   +A  PA  +K  + L
Sbjct: 272 SGELMTFSAEPPAIFLKRLEQL 293


>gi|270308540|ref|YP_003330598.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Dehalococcoides sp. VS]
 gi|270154432|gb|ACZ62270.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Dehalococcoides sp. VS]
          Length = 302

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 87/322 (27%), Positives = 157/322 (48%), Gaps = 40/322 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++ E+D E  RLD++       ++   +Q ++ SG V+V+ K  K + ++++G  + I  
Sbjct: 8   LIAESDGE--RLDKYIAQKETDLSRSFIQALIDSGHVQVNGKTAKPSLKLKNGDTITI-- 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                       +I   +    K  D    I+ ++D  + + NKP G++V    G   H 
Sbjct: 64  ------------EISPETPPELKAEDIPLEII-FQDKDLLLINKPPGLTVHPAPGHPDHT 110

Query: 129 -IDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            I+G L   ++ K +      +P + HRLD++TSG+L+VA+ R    +L+  F+ R ++K
Sbjct: 111 LINGVL--ALEPKMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRETLANLSAQFKERTVRK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   +  E      L +       + VV        +A + +KV+  + Q + 
Sbjct: 169 YYLTLVKG-ELHPAEGFIEAPLGRDPQNRQKIAVVSN----GRHARTGYKVL-RYIQGYS 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE++  TGRTHQ+RVH   +G P+ GD  Y     G   + ++ + +LHA  +    P 
Sbjct: 223 LLEVKLETGRTHQIRVHFAAIGHPVAGDAIY-----GQKETWLKRQ-FLHAHRLSFTLPS 276

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G+ ++ T+PLP  + +T   L
Sbjct: 277 NGQTVEFTSPLPPDLEETLKIL 298


>gi|261380320|ref|ZP_05984893.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           subflava NJ9703]
 gi|284796836|gb|EFC52183.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           subflava NJ9703]
          Length = 374

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 142/310 (45%), Gaps = 38/310 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+++ +            
Sbjct: 40  RLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQPKDKMIGGELIAV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFTPEPMDLDIIYEDDTVIVINKPAGLVVHPAAGNWSGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAIANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   AI+H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAITHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C++        +  +  LHA ++   HP+ G  +
Sbjct: 256 HQIRVHMREANHPLAADPVYGNLRHPCSDAVKEAIKALGARQALHAYHLSFVHPKTGETV 315

Query: 306 QITAPLPAHM 315
              AP+P  M
Sbjct: 316 SFEAPMPDDM 325


>gi|315655527|ref|ZP_07908426.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii ATCC 51333]
 gi|315490182|gb|EFU79808.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii ATCC 51333]
          Length = 304

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 115/229 (50%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY D  + V +KPAG++   G G     + G L++    V + G   R  + HRLD  T
Sbjct: 81  ILYADDDLVVVDKPAGVAAHTGPGWEGPTVVGALRAAGIRVSTSGPVEREGIVHRLDAGT 140

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG +VVA++  A   L   FR  R++KIY +L  G  K     I   + +    G ++  
Sbjct: 141 SGAMVVAKSELAYGKLKNEFRYHRVEKIYTALATGGVKPPVGTIDAPIGRAP--GREFKM 198

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V     G   A++H+ VI+        L++Q  TGRTHQ+RVH   +G P+VGD +Y A
Sbjct: 199 AVVS---GGKPAVTHYDVIEEL-PGATLLKVQLETGRTHQIRVHLAAIGHPLVGDTEYGA 254

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           + K      ++ + +LHA  +   HP  G  + + APLPA +    + L
Sbjct: 255 DRKTAARLGLERQ-WLHASRLAFKHPRTGLEVAVQAPLPADLATAVELL 302


>gi|83859151|ref|ZP_00952672.1| ribosomal large subunit pseudouridine synthase d [Oceanicaulis
           alexandrii HTCC2633]
 gi|83852598|gb|EAP90451.1| ribosomal large subunit pseudouridine synthase d [Oceanicaulis
           alexandrii HTCC2633]
          Length = 310

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 69/256 (26%), Positives = 115/256 (44%), Gaps = 28/256 (10%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSW 136
           + V  T   + +   +L+ED  + V NKPAG++V   +G         + +H  G L   
Sbjct: 47  APVEATPKPEDIPLEVLFEDDHLIVINKPAGMAVHPAAGNWTGTLVHALLFHCAGSLSGI 106

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++P + HRLD++TSG++V A+T  A Q L+  F    +++ Y +     P+ +  
Sbjct: 107 --GGVERPGIVHRLDKDTSGVMVAAKTDKAHQGLSAQFAAHTVERAYLAFTRSAPQPRTG 164

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------FCWL-EMQP 247
            I   L + SH       +     +   +AI++++ +  F Q+         C L   + 
Sbjct: 165 RIETRLARSSHDRKKMAVIDAPGSQAGKHAITNYETLATFGQEPGKSVGHPMCALVRCRL 224

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY-------LHARYMDLPHP 300
            TGRTHQ+RVH  H+GCP++GD  Y              K +       LHA  +   HP
Sbjct: 225 ETGRTHQIRVHMAHIGCPLLGDPVYGRGRSTPLAKLDSGKDFKDFRRQALHAAVLGFDHP 284

Query: 301 -EGGRLQITAPLPAHM 315
             G +++    LP  M
Sbjct: 285 VTGEQVRFETELPKDM 300


>gi|90022196|ref|YP_528023.1| ribosomal large subunit pseudouridine synthase D [Saccharophagus
           degradans 2-40]
 gi|89951796|gb|ABD81811.1| ribosomal large subunit pseudouridine synthase D [Saccharophagus
           degradans 2-40]
          Length = 321

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 92/321 (28%), Positives = 146/321 (45%), Gaps = 40/321 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+   + +P  +   +Q+ ++SG++ VD K  K   ++  G+ + + P +       +
Sbjct: 19  RLDQVCADLFPDYSRSRIQQWIKSGKLLVDDKTGKAKQKVFGGENLVLEPELQ------E 72

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           E + L   +NL          ++YED  I V NK AG+ V   +G      ++G L   V
Sbjct: 73  EGEWLPEPINLN---------IVYEDEHILVINKQAGLVVHPAAGNWSGTLLNGLLHH-V 122

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKN 193
            S    PR  + HRLD++T+G++VVA++     HL    + R + + Y ++V G    K+
Sbjct: 123 PSLVNVPRAGIVHRLDKDTTGLMVVAKSLPTQTHLVAQLQARTVSRHYQAVVHGTFAAKD 182

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K   +         IG      VK    E     A++H++V+    Q F  + +Q  TGR
Sbjct: 183 KLGTV------DIAIGRHPTQRVKMAALENSGKPAVTHYRVVKDL-QGFAHVHLQLETGR 235

Query: 252 THQLRVHALHMGCPIVGDHKYCANF--------KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           THQ+RVH  H+G P+VGD  Y             G   +    +  LHA  + L HP   
Sbjct: 236 THQIRVHMAHIGYPLVGDQVYGKKVPTKVRNHNPGAVHAEAFPRQALHAWRLSLVHPVTE 295

Query: 304 RLQI-TAPLPAHMVKTWDSLG 323
                 A LP  MV+  D L 
Sbjct: 296 ETVFWEADLPEDMVQLIDQLA 316


>gi|312111747|ref|YP_003990063.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
 gi|311216848|gb|ADP75452.1| pseudouridine synthase, RluA family [Geobacillus sp. Y4.1MC1]
          Length = 304

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 88/315 (27%), Positives = 148/315 (46%), Gaps = 46/315 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPP 69
           ++ + +N R+D+         +   +Q+ +++  V V+ + VK N +  +G   VVR+P 
Sbjct: 8   IDEEYDNERIDKVIAALNEDWSRSKVQQWIKNQLVTVNDQHVKANYKCSAGDIVVVRLP- 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                               L    + +   + YED+ + V NKP G+ V    G   H+
Sbjct: 67  ----------------EPEPLYVEPENIPLDIYYEDADVLVVNKPRGMVVHPAPG---HM 107

Query: 130 DGFLKSWV-----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G L + +     D  G     +P + HR+D++TSG+L+VA+   A Q L +    + + 
Sbjct: 108 RGTLVNALLAHCHDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDMAHQALVDQLVKKTVT 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQ 238
           + Y ++V G+  +    I       + IG D     K    E+    A++HF+V++ F Q
Sbjct: 168 RKYKAIVHGVIPHDYGTI------DAPIGRDKRDRKKMAVTEENGKEAVTHFRVLERFRQ 221

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            + ++E Q  TGRTHQ+RVH  ++G P+ GD +Y        T PI  +  LHA  +   
Sbjct: 222 -YTFIECQLETGRTHQIRVHMKYIGYPLAGDPQYGP----KKTLPIDGQA-LHAGVLGFS 275

Query: 299 HPEGGR-LQITAPLP 312
           HP  G  L+  APLP
Sbjct: 276 HPRTGEYLEFEAPLP 290


>gi|167823889|ref|ZP_02455360.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei 9]
          Length = 318

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 73/259 (28%), Positives = 118/259 (45%), Gaps = 24/259 (9%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRV     K    +  G  + + P +        
Sbjct: 63  RLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIELLPELLPEQLAFT 122

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            + +  S              ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 123 PEPVPLS--------------IVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 168

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 169 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWG--RMPDE 226

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 227 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTH 284

Query: 254 QLRVHALHMGCPIVGDHKY 272
           Q+RVH  H+G P++GD  Y
Sbjct: 285 QIRVHCAHVGHPLLGDPVY 303


>gi|116515184|ref|YP_802813.1| RluD [Buchnera aphidicola str. Cc (Cinara cedri)]
 gi|116257038|gb|ABJ90720.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Cc (Cinara cedri)]
          Length = 321

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 96/331 (29%), Positives = 157/331 (47%), Gaps = 62/331 (18%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-------KKRV 53
           MS +  + ++V +  E+++RLD+    H    +  +++K + SG ++V+       KK++
Sbjct: 1   MSNLKKINFIVPKLKEKSIRLDKILVKHLNSFSRSSIKKWILSGFIKVNNITANKPKKKI 60

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
            F +RI          +IN  ++ IK          + K + FL   +++EDS+I + NK
Sbjct: 61  LFKDRISL--------IINKKSNFIK----------IKKENIFLN--IIFEDSEILIINK 100

Query: 114 PAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQH 169
           P    V  G G      ++  +  + D+    PR  + HRLD+ T+GILVVA+T +    
Sbjct: 101 PTNFVVHLGYGNTSGTLLNALIFHYPDN-LLIPRAGIVHRLDRNTTGILVVAKTISTYYF 159

Query: 170 LTESFRMRRIQKIYWSLVWG-------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           L   F+ R+I K Y  +V G       I K  K  I N       IGG      KQ    
Sbjct: 160 LINLFKKRKIIKEYDVIVIGRIEVDGKIEKPIKRDIYNRTKMTVGIGG------KQ---- 209

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              AI+++ VI  F +   +L +Q  TGR HQ+RVH   +  P++GD  Y    K NF++
Sbjct: 210 ---AITYYSVITIF-KNHTYLRIQLKTGRMHQIRVHLSSIFHPVLGDKIYSKGIKSNFSN 265

Query: 283 PIQ---------NKLYLHARYMDLPHPEGGR 304
             +         N+  LHAR ++  HP+  +
Sbjct: 266 CSKKMKNFLSKFNRPALHARMLNFIHPKTNK 296


>gi|42525117|ref|NP_970497.1| pseudouridylate synthase [Bdellovibrio bacteriovorus HD100]
 gi|39577328|emb|CAE81151.1| Pseudouridylate synthase [Bdellovibrio bacteriovorus HD100]
          Length = 319

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 62/200 (31%), Positives = 103/200 (51%), Gaps = 23/200 (11%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLT 147
           LK  +L+ED  + V NKPAG+ V   +G         + +H D     + +   ++P + 
Sbjct: 67  LKLDVLFEDEDLIVINKPAGLVVHPAAGHAHDTLVNALIHHTDDLSMKFGE---ERPGIV 123

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--- 204
           HRLD+ETSGI+V+A+   A + LT  F+ R   +IY+++  G  +     + ++L +   
Sbjct: 124 HRLDKETSGIIVIAKNDKAHESLTSQFKERSTHRIYYAVCLGTARTLSGSVRSFLARHPV 183

Query: 205 -----KSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                 S +G D   +   N+      +A++HF+V+        +L+++  TGRTHQ+RV
Sbjct: 184 DRKRYASVLGDDRKPLTDPNDDPGLGKWAVTHFEVLQR-KSGMSYLKLKLETGRTHQIRV 242

Query: 258 HALHMGCPIVGDHKYCANFK 277
           H    G PI GD  Y A+ K
Sbjct: 243 HMSESGLPIAGDTLYGADRK 262


>gi|322387558|ref|ZP_08061167.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           infantis ATCC 700779]
 gi|321141425|gb|EFX36921.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           infantis ATCC 700779]
          Length = 297

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 84/308 (27%), Positives = 149/308 (48%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   +   +
Sbjct: 5   IETGGIRLDKALSDLTELSRSLANEQIKSGQVL-VNGHVKKAKYTVQEGDVITYQIPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   +    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDIPLEIIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDEAHMALAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F+V++ F   +  LE+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFQVLERFGD-YTLLELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG+         +LHA+ +   HP  G  L+ TA +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGETLEFTADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKQTLEKL 293


>gi|83815887|ref|YP_445314.1| ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber DSM 13855]
 gi|83757281|gb|ABC45394.1| ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber DSM 13855]
          Length = 349

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 78/325 (24%), Positives = 139/325 (42%), Gaps = 61/325 (18%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-----QVVRI 67
           E +    R+D++    YP  +   +Q+ ++ G ++V+   VK +  ++ G     +++R 
Sbjct: 3   ETETGGPRIDKYLTRFYPEASRTKIQRAIKKGHLKVNGTDVKKSYGVEPGDEIVFRLIRK 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
           PP                    +    + +   +++E   + V NKPAG+ V    G   
Sbjct: 63  PP--------------------MQAEPEAIPLDVVHEGDDLLVVNKPAGMVVHPAPGHRS 102

Query: 125 ------IAYHIDGFLKSWVDSKGQ-----------------------KPRLTHRLDQETS 155
                 + +H+DG   +  D + +                       +P + HRLD+ TS
Sbjct: 103 GTLVHALLHHVDGGEVAADDERDEVSEDEVGLSLVNALPQSPDHPVVRPGIVHRLDKGTS 162

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LVVA+   A Q L E F+   + + Y ++VWG        I   + +  H     + V
Sbjct: 163 GLLVVAKRGRAHQPLAEQFKAHTVDRRYRAIVWGRFAPSDGTIEGAIGRDPHH-RQRMAV 221

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V ++E    +A +H++ ++  A     +E +  TGRTHQ+RVHA   G P++GD KY   
Sbjct: 222 VPEDE--GKWARTHYETVETHAHTSV-VEFELETGRTHQIRVHARAQGHPLLGDPKYGGQ 278

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                T     + +    +  LPHP
Sbjct: 279 RVRYGTQSGTRRTFYDQLFETLPHP 303


>gi|115477922|ref|NP_001062556.1| Os09g0103500 [Oryza sativa Japonica Group]
 gi|75117672|sp|Q69K07|PUS4_ORYSJ RecName: Full=RNA pseudourine synthase 4, mitochondrial; AltName:
           Full=RNA pseudouridylate synthase 4; AltName:
           Full=RNA-uridine isomerase 4; Flags: Precursor
 gi|50725212|dbj|BAD34146.1| ribosomal large subunit pseudouridine synthase C-like [Oryza sativa
           Japonica Group]
 gi|51091882|dbj|BAD36694.1| ribosomal large subunit pseudouridine synthase C-like [Oryza sativa
           Japonica Group]
 gi|113630789|dbj|BAF24470.1| Os09g0103500 [Oryza sativa Japonica Group]
          Length = 448

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 65/220 (29%), Positives = 109/220 (49%), Gaps = 23/220 (10%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKI 108
           +RV   +++  G ++ +P  +N     +KE  + + +      ++  FL+ + +Y+D  I
Sbjct: 133 RRVSAKDQLMPGDILFLP--VN-----LKESSVAEKTKKFDNRNEINFLRGLEIYKDEAI 185

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V NKP G+ VQGG GI   ID     + ++  + PRL HRLD++ SGILV+ R + +  
Sbjct: 186 IVVNKPPGMPVQGGVGIKNSIDVLASMFEENSSEAPRLVHRLDRDCSGILVLGRNQLSTS 245

Query: 169 HLTESFRMRR-----------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV- 216
            L   FR +            +Q+ Y +LV G P++ K  ++  L K     G    +  
Sbjct: 246 MLHAIFREKTADALADGTQHVLQRKYVALVIGTPRHPKGLLSAPLAKILLQDGKSERLTI 305

Query: 217 --KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
               N      A++ ++VI+   Q + WLE+ P TGR HQ
Sbjct: 306 RASSNAASVQDALTEYRVIESCPQGYTWLELFPRTGRKHQ 345


>gi|255531126|ref|YP_003091498.1| pseudouridine synthase, RluA family [Pedobacter heparinus DSM 2366]
 gi|255344110|gb|ACU03436.1| pseudouridine synthase, RluA family [Pedobacter heparinus DSM 2366]
          Length = 342

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 80/326 (24%), Positives = 154/326 (47%), Gaps = 42/326 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+D++  +   + +   +Q  + +G V V++K VK + +++    + I  
Sbjct: 21  IVVDKGQSLLRIDKFLMHRMENASRNRIQNAIEAGNVLVNQKTVKASYKVKPADEISI-- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
                 H  ++ ++    + L          ++YED+ + V NKPAG+ V  G       
Sbjct: 79  ---VFPHPPRDTEVYPEDIPLD---------IVYEDNDLLVVNKPAGMVVHPGYNNYTGT 126

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             + +A+H +  L     ++G +P L HR+D++TSG+L++++       L + F    I 
Sbjct: 127 LVNALAFHFEQ-LPQLPGNEG-RPGLVHRIDKDTSGLLLISKNEITMTRLAKQFFDHTIT 184

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +L WG    +K+      + +S      + V    EKG  ++++H+ V++      
Sbjct: 185 RKYVALAWG--DIEKDGTVTGYIGRSAKNRIVMDVYDDEEKG-KWSVTHYAVLERLGY-V 240

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN------KL 288
             +  Q  TGRTHQ+R H  H+G P+  D  Y  +   KG     +   +QN      + 
Sbjct: 241 TLISCQLETGRTHQIRAHMQHIGHPLFNDANYGGDKILKGTTFNKYKQFVQNCFELLPRQ 300

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPA 313
            LHA+ +   HP   + ++  APLP+
Sbjct: 301 ALHAQTLGFIHPGTKKYMEFEAPLPS 326


>gi|171913853|ref|ZP_02929323.1| pseudouridine synthase, RluA family protein [Verrucomicrobium
           spinosum DSM 4136]
          Length = 303

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 91/317 (28%), Positives = 139/317 (43%), Gaps = 36/317 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           + + V E+     RLD + +   P ++   LQ +++ G + ++ K  K N  ++ G  + 
Sbjct: 1   MDFTVNESAPAKQRLDHYLQGELPDMSRTRLQGLIKDGHILLNGKAAKPNTPLKQGDRI- 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
               +   + +  E    D  +N+           L+ED  I V NKP G+ V   +G  
Sbjct: 60  ---TMEVPDPVPTEVVPQDIPLNV-----------LFEDEHIIVINKPDGLVVHPAAG-- 103

Query: 127 YHIDGFL--------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            + DG L        K+     G+ +P + HRLD+ETSG +V A+   A   LTE+F  R
Sbjct: 104 -NPDGTLVNALLFHCKNLSGIGGELRPGIVHRLDKETSGCMVAAKHDLAHTRLTEAFSQR 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + KIY + V G P +    I N + +          V  +  K A        V    A
Sbjct: 163 DLTKIYLAAVNGTPSSSSGRIENRIGRHPVDRKRMALVTGEAGKEALTEWDRVAVHQGCA 222

Query: 238 QKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              C L     TGRTHQ+RVH    +GCPI+GD  Y    +     P   +L LHA  ++
Sbjct: 223 LIRCRL----LTGRTHQIRVHMKEALGCPILGDTIYAQIQRQLIKMP---RLMLHAWKLE 275

Query: 297 LPHP-EGGRLQITAPLP 312
             HP     L+  AP+P
Sbjct: 276 FQHPITKLGLKFEAPVP 292


>gi|157829144|ref|YP_001495386.1| hypothetical protein A1G_07185 [Rickettsia rickettsii str. 'Sheila
           Smith']
 gi|157801625|gb|ABV76878.1| hypothetical protein A1G_07185 [Rickettsia rickettsii str. 'Sheila
           Smith']
          Length = 313

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 85/322 (26%), Positives = 149/322 (46%), Gaps = 52/322 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD+   +   +++   +QK ++  QV V+              ++  P V+   N II
Sbjct: 13  IRLDKALSSLLENVSRNQIQKAIKDSQVLVND------------VIISDPDVLVKENDII 60

Query: 79  -------KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +E KI  ++V L          ++YED  + V NK AG++V  G+G  +H D 
Sbjct: 61  LFSFKEPEELKIAAANVALD---------IIYEDDDLIVINKAAGMTVHPGAG--HHDDT 109

Query: 132 FLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + + +            ++P + HRLD++T+G++VVA+   A   L      +++ + Y
Sbjct: 110 LVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQKQVIRKY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCW 242
             LVWG+  N  E +    + +S      + ++K    G   A++H+K I+ F +     
Sbjct: 170 KVLVWGVI-NPLEGVIKNNIGRSRSDRQKMTILKY---GGKEAVTHYKTIELFYKGSISM 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLY------LHARY 294
           +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP  ++ KL       LH+ Y
Sbjct: 226 VECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAYSPPELKAKLIDFKRQALHSWY 285

Query: 295 MDLPHPEGGR-LQITAPLPAHM 315
           +   HP     ++ +  LP  M
Sbjct: 286 LSFTHPTSNEIMEFSCELPRDM 307


>gi|304396538|ref|ZP_07378419.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304356047|gb|EFM20413.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 217

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 70/209 (33%), Positives = 111/209 (53%), Gaps = 22/209 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D+ I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++V
Sbjct: 14  ILYQDAHIMVVNKPSGLLSVPGR--LDEHKDSVM-TRIQRDFPQAESVHRLDMATSGVMV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVH 214
           VA T+AA + L   FR R   K Y + +WG P+ ++       I +W  +   +      
Sbjct: 71  VALTKAAERELKRQFREREPSKTYVACIWGHPEKEEGLVDLPLICDWPNRPKQM------ 124

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V  +N K A    + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD+ Y A
Sbjct: 125 VCFENGKAAQ---TEYQVLEYRADNSTRISLKPITGRSHQLRVHMLALGHPILGDNFY-A 180

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + +    +P   +L LHA  + + HP  G
Sbjct: 181 HPEAKAMAP---RLLLHAESLTITHPAFG 206


>gi|270293651|ref|ZP_06199853.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|270275118|gb|EFA20978.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 511

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 70/208 (33%), Positives = 106/208 (50%), Gaps = 21/208 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  + V NKPAG+    G   A  +   ++  + ++ G  P   HRLD  TSG+++
Sbjct: 309 IVYEDPWLSVINKPAGMLSVPGKEDAVSVYSLMREQYPEADG--PLTVHRLDMATSGLML 366

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +A+T+   Q+L   F+ R ++K Y +L+ GI PK+K        L         VH    
Sbjct: 367 IAKTKRVHQNLQAQFKNRLVRKRYVALLEGIVPKDKGTVDLPLCLNPLDRPRQMVHT--- 423

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
            E G   AI+ ++V++    K   +   P TGRTHQLR+HA H   + CPI+GD  Y   
Sbjct: 424 -EHG-KPAITDYQVLERLDGKRTRIAFYPRTGRTHQLRIHAAHPLGLHCPIIGDELYGEK 481

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                     ++LYLHA Y++  HP  G
Sbjct: 482 ---------ADRLYLHAEYLEFTHPITG 500


>gi|212550472|ref|YP_002308789.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
 gi|212548710|dbj|BAG83378.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
          Length = 342

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 88/332 (26%), Positives = 156/332 (46%), Gaps = 44/332 (13%)

Query: 12  VENDEEN-MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V N E+  +R+D++  +     +   +Q+    G +  +   +K N +++ G ++ I   
Sbjct: 12  VANKEQGFLRVDKFLVDKIIGTSRNRIQQAANVGSICANNHPIKSNYKVKPGDIITI--- 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----SGI 125
              +N   +E +I   ++ L          ++YED  + V +KPA + V  G       +
Sbjct: 69  --VMNQPHREVEIAPENIPLN---------IVYEDDDVIVVDKPAELVVHPGHDNYTGTL 117

Query: 126 AYHIDGFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
              I G+  S           ++  +  L HR+D+ TSG+LV A+   A  +L   F  +
Sbjct: 118 VNAIAGYYSSTTSSIIQSTFYNEDFRSGLVHRIDKGTSGLLVFAKNLNAKTNLDMQFFRK 177

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I++ YW++VWG  K ++E I   + +  H     +  V  N      AI+H+KV++ F 
Sbjct: 178 TIRRNYWAVVWGNVKKEEETIKCNIGRNLH--NRMLMDVFPNNNHGKPAITHYKVLERF- 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN----- 286
           +    +E    TGRTHQ+RVH  ++G  +  D +Y  N   KGN    +   +QN     
Sbjct: 235 EYVTLIECSLETGRTHQIRVHMKYIGHVLFNDRRYGGNEILKGNHHTKYKQFVQNCFAIC 294

Query: 287 -KLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
            +  LHAR +   HP+ G+ + + +PLP  M+
Sbjct: 295 QRQALHARVLGFTHPKTGKEILLESPLPKDMI 326


>gi|160938833|ref|ZP_02086184.1| hypothetical protein CLOBOL_03727 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437796|gb|EDP15556.1| hypothetical protein CLOBOL_03727 [Clostridium bolteae ATCC
           BAA-613]
          Length = 294

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 83/328 (25%), Positives = 151/328 (46%), Gaps = 57/328 (17%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF------NNRIQSGQVVRIPP 69
           E+++R+D++     P ++   +QK+L+SGQV V+ + +K       ++RI+      + P
Sbjct: 2   EDHVRIDKYLAEACPDLSRSYIQKLLKSGQVLVNGQGIKASYIVVEDDRIELEVPEAVEP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            I+A      E   LD               +LYED  + + NKP G+ V   +G   H 
Sbjct: 62  EIDA------EPMDLD---------------ILYEDQDLILINKPKGMVVHPAAGHYSHT 100

Query: 129 -IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++G +    D         +P + HR+D +T+G+++  +   A   +    +   I + 
Sbjct: 101 LVNGLMYHCKDQLSGINGVMRPGIVHRIDMDTTGVIIACKNDMAHSSIAAQLKEHSITRR 160

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-----AISHFKVIDCFA 237
           Y ++V G+    +  +   + +         H V++ +   NY     A++H++V++ F 
Sbjct: 161 YQAIVHGVIAEDEGTVDAPIGR---------HPVERKKMSINYQNGKNAVTHYRVLNRFR 211

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL--YLHARYM 295
           Q +  +E +  TGRTHQ+RVH   +  P++GD  Y     G    PI       LHA  +
Sbjct: 212 Q-YTHVECRLETGRTHQIRVHMASIRHPLLGDAVY-----GPARCPISGLCGQTLHAGIL 265

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP  G  ++ +APLP +  K   +L
Sbjct: 266 GFIHPRTGEYMEFSAPLPDYFEKLLRTL 293


>gi|160888881|ref|ZP_02069884.1| hypothetical protein BACUNI_01301 [Bacteroides uniformis ATCC 8492]
 gi|156861780|gb|EDO55211.1| hypothetical protein BACUNI_01301 [Bacteroides uniformis ATCC 8492]
          Length = 511

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 70/208 (33%), Positives = 106/208 (50%), Gaps = 21/208 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  + V NKPAG+    G   A  +   ++  + ++ G  P   HRLD  TSG+++
Sbjct: 309 IVYEDPWLSVINKPAGMLSVPGKEDAVSVYSLMREQYPEADG--PLTVHRLDMATSGLML 366

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +A+T+   Q+L   F+ R ++K Y +L+ GI PK+K        L         VH    
Sbjct: 367 IAKTKRVHQNLQAQFKNRLVRKRYVALLEGIVPKDKGTVDLPLCLNPLDRPRQMVHT--- 423

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
            E G   AI+ ++V++    K   +   P TGRTHQLR+HA H   + CPI+GD  Y   
Sbjct: 424 -EHG-KPAITDYQVLERLDGKRTRIAFYPRTGRTHQLRIHAAHPLGLHCPIIGDELYGEK 481

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                     ++LYLHA Y++  HP  G
Sbjct: 482 ---------ADRLYLHAEYLEFTHPITG 500


>gi|73749059|ref|YP_308298.1| ribosomal large subunit pseudouridine synthase D [Dehalococcoides
           sp. CBDB1]
 gi|73660775|emb|CAI83382.1| ribosomal large subunit pseudouridine synthase,RluD subfamily
           [Dehalococcoides sp. CBDB1]
          Length = 300

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 82/303 (27%), Positives = 147/303 (48%), Gaps = 34/303 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++       ++   +Q+++ SG + V+ +  K + R+++G  + I            
Sbjct: 14  RLDKYITQKESGLSRSFIQELVSSGHILVNNQSAKPSLRLKTGDTITI------------ 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWV 137
             +I   + +  K  D    I+ ++D  + + NKP G++V    G   H  ++G L    
Sbjct: 62  --EIPPETPSELKAEDIPLEII-FQDKDLLLINKPPGLTVHPAPGHPDHTLVNGVLALEP 118

Query: 138 DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           + +      +P + HRLD++TSG+L+VA+ R A  +L+  F+ R I+K Y +LV G    
Sbjct: 119 EMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRQALANLSAQFKERTIRKYYLALVKG-ELR 177

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E      L +       + VV        +A + +KV+  + Q +  LE++  TGRTH
Sbjct: 178 PAEGFIEAPLGRDPQNRQKIAVVSD----GRHARTGYKVL-RYIQGYSLLEVKLETGRTH 232

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Q+RVH   +G P+ GD  Y     G   S ++ + +LHA  +    P  G+ ++ T+PLP
Sbjct: 233 QIRVHFAAIGHPVAGDAVY-----GQKESWVKRQ-FLHAHRLSFALPSNGQVVEFTSPLP 286

Query: 313 AHM 315
             +
Sbjct: 287 PDL 289


>gi|255065280|ref|ZP_05317135.1| ribosomal large subunit pseudouridine synthase D [Neisseria sicca
           ATCC 29256]
 gi|255050701|gb|EET46165.1| ribosomal large subunit pseudouridine synthase D [Neisseria sicca
           ATCC 29256]
          Length = 374

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 84/308 (27%), Positives = 142/308 (46%), Gaps = 40/308 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLMPDYSRSRLTSWIKEGAVIVNDKPAQPKDKMIGGESISV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +L S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVLPSEENLAFKPEAMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P + 
Sbjct: 145 PELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YLHARYMDLPHPEGGR- 304
           HQ+RVH      P+  D  Y  N +   + P++  +        LHA  +   HP+ G  
Sbjct: 256 HQIRVHMREANHPLAADPVY-GNLRHPCSEPVKEAVKSLGARQALHAYRLSFVHPKTGET 314

Query: 305 LQITAPLP 312
           +   AP+P
Sbjct: 315 VSFEAPIP 322


>gi|51892381|ref|YP_075072.1| 23S rRNA pseudouridine synthase [Symbiobacterium thermophilum IAM
           14863]
 gi|51856070|dbj|BAD40228.1| 23S rRNA pseudouridine synthase [Symbiobacterium thermophilum IAM
           14863]
          Length = 304

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 91/326 (27%), Positives = 145/326 (44%), Gaps = 46/326 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVN--LQKILRSGQVRVDKKRVKFNNRIQSGQV--VRI 67
           +  +E + R+D +     P I      +Q ++  GQV ++    K    +  G V  VR+
Sbjct: 6   ITAEEGHPRIDVFLAGR-PEIGLSRSRIQALIDEGQVTLNGAMPKARQAVNPGDVIVVRV 64

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
           P        ++ E   LD               ++YED  I V NK  G+ V   +G   
Sbjct: 65  PD--PEPMELVPEDIPLD---------------IVYEDEDILVVNKQRGLVVHPAAGHWT 107

Query: 126 AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              +   L    D +G     +P + HRLD++T+G+LVVA++  A   L E  R   +Q+
Sbjct: 108 GTLVHALLDKVDDLEGIGGELRPGIVHRLDKDTTGLLVVAKSERAMASLQEQIRDHMVQR 167

Query: 182 IYWSLVWG--IPKNKK--ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +YW+LV G  +P   +    I      +  +          N K    A+++F+V++ + 
Sbjct: 168 VYWALVHGNSMPDTGRIEAPIGRHPRDRKRMA--------VNPKTGRDAVTYFRVLERY- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  LE +  TGRTHQ+RVH   +G P+VGD  Y    K +   P Q    LHAR +  
Sbjct: 219 RGYALLECRLETGRTHQIRVHLSFIGHPVVGDPLYGPR-KPHLGMPPQA---LHARQLSF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  ++ T   PA M+     L
Sbjct: 275 RHPASGEWMEFTVDPPADMMAVVQRL 300


>gi|325954258|ref|YP_004237918.1| pseudouridine synthase [Weeksella virosa DSM 16922]
 gi|323436876|gb|ADX67340.1| pseudouridine synthase [Weeksella virosa DSM 16922]
          Length = 227

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 115/232 (49%), Gaps = 17/232 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ + + NK  G   QG +     +   LK+++  +  KP      L HRLD+ TS
Sbjct: 6   ILFEDNHLLIINKKPGELAQGDNTGDIPLVDSLKAYIKERDHKPGNVFLGLVHRLDRPTS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ A+T  A   + ++F+ R + K+Y +L+ G P  + + + ++L K      +   V
Sbjct: 66  GIIMFAKTSKALARMNDAFQKREVTKVYRALIQGKPPKEHDRLTHYLRKNQK--NNKTTV 123

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             Q    A  AI  +  +      +  L++Q  TGR+HQ+R     +GCPI GD KY A 
Sbjct: 124 FSQPTNNAKEAILEYYWVGSL-DSYEVLDVQLFTGRSHQIRAQLSFIGCPIKGDLKYGAK 182

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD-SLGFK 325
                 S     + LHAR +   HP     + I AP P  ++  W+ SLGF+
Sbjct: 183 -----RSNPDGSISLHARKLIFTHPVSKEEITIIAPPPKDVL--WEASLGFE 227


>gi|310828937|ref|YP_003961294.1| pseudouridine synthase [Eubacterium limosum KIST612]
 gi|308740671|gb|ADO38331.1| pseudouridine synthase [Eubacterium limosum KIST612]
          Length = 321

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 95/320 (29%), Positives = 154/320 (48%), Gaps = 33/320 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           QY + EN   N RLDR+     P  +   LQK+LR  +++++  R +  + I SG  V++
Sbjct: 3   QYTIDEN-SGNQRLDRYLSKLMPLADRNFLQKMLRKKRIKLNGVRAEPKDMIHSGDTVQV 61

Query: 68  PPVINALNHIIKEQKILD-SSVNLTKHSDF---LKSIL---LYEDSKIYVFNKPAGISVQ 120
                       E+ I       + +H D    +K I    +YED  + V NKPAG+  Q
Sbjct: 62  ---------YFSEETIAGFQEKKVQRHFDLKPEIKKIFEPPVYEDDHLLVVNKPAGLLSQ 112

Query: 121 G-GSGIAYHIDG----FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
              SG    ID       K+  D+K  +  +++RLD+ TSGI+++ +     Q +  + R
Sbjct: 113 ADSSGNISLIDAARTYLKKNATDTKAFEVVISNRLDRNTSGIILMPKDYPTLQTVNAAIR 172

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA-ISHFKVID 234
            R+  K Y ++V G+ K K   +  +L K +      +    Q+EKGA    + +  +++
Sbjct: 173 ERQALKEYHTIVLGVLK-KPGTLTGFLTKDTIENKSAIQ--SQSEKGAKEVRLDYCPLMN 229

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLY-LHA 292
               KF  LE+  HTGR+HQ+R      G PI+GD+KY  A+   +F+     K + LH+
Sbjct: 230 N--GKFTLLEITLHTGRSHQIRSQLADYGFPIIGDYKYGDASINRHFSQKYGLKHHLLHS 287

Query: 293 RYMDLPHPEGGRLQITAPLP 312
           R+  +   E      TAP P
Sbjct: 288 RHYAIKDLE---YDFTAPYP 304


>gi|291550385|emb|CBL26647.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           torques L2-14]
          Length = 304

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 87/317 (27%), Positives = 146/317 (46%), Gaps = 44/317 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D++       ++   +QK+++  ++ V++  VK N ++ +G  + +          I 
Sbjct: 14  RIDKFLDGRIESLSRSYIQKLIKEKKILVNQLPVKANYKLTTGDTIILQ---------IP 64

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHID 130
           + + LD         + +   +LYED  I V NKP G+ V    G         + YH  
Sbjct: 65  DPEPLDIQ------PENIPLDILYEDDDILVVNKPKGMVVHPAPGHYSHTLVNAVLYHCG 118

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L     +   +P + HR+D  T+G L++ +   A Q L E  +   I + Y S+V G 
Sbjct: 119 ENLSGI--NGVIRPGIVHRIDMNTTGSLLICKNDKAHQILAEQLKEHSITRKYHSIVHG- 175

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN--YAISHFKVIDCFAQKFCWLEMQPH 248
             N KE         + IG       K + K  N  +A++H++V++ F   F ++E Q  
Sbjct: 176 --NLKEDTGTV---NAPIGRHPTDRKKMSTKAPNGRHAVTHYRVLERFGN-FTYIECQLE 229

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR-L 305
           TGRTHQ+RVH   +G PI+GD  Y     G    P  +Q +  LHA+ + + HP  G  +
Sbjct: 230 TGRTHQIRVHMSSIGHPILGDEIY-----GPAKCPYKLQGQT-LHAKILGITHPSTGEYI 283

Query: 306 QITAPLPAHMVKTWDSL 322
           +  APLP +     + L
Sbjct: 284 EFDAPLPEYFKDLLNKL 300


>gi|218961736|ref|YP_001741511.1| Pseudouridylate synthase, 23S RNA-specific [Candidatus Cloacamonas
           acidaminovorans]
 gi|167730393|emb|CAO81305.1| Pseudouridylate synthase, 23S RNA-specific [Candidatus Cloacamonas
           acidaminovorans]
          Length = 351

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 78/269 (28%), Positives = 127/269 (47%), Gaps = 33/269 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NK AG+ V  G G         I Y     L S    +  +P + HRLD
Sbjct: 91  VVYEDEYLAIINKKAGMIVHPGFGNPEGTLVNAILYRFGENLSS--GKEFNRPGIVHRLD 148

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG++++A+       L++ F  R I+K Y+++  GIP+ +K  I  + L +S+    
Sbjct: 149 RGTSGLIIIAKNDLTHAKLSDMFARREIKKTYFAITTGIPEPEKGEIETY-LARSNKNPR 207

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + V  +      YA++H+K I  +   F  +E+ P TGR HQ+RVH  H+  PI+GD  
Sbjct: 208 TICVTNE----GRYALTHYKTIKTW-HYFALVEINPATGRMHQIRVHFAHIRYPILGDLL 262

Query: 272 YCA----------NFKGNFTSPIQNKL---YLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           Y +          N K   T  + N L    LH+  ++  HP  G  + ++AP+P  +  
Sbjct: 263 YNSRRYVQSLVPQNMKKKVTELLVNHLRRQALHSWKLEFFHPITGYPISVSAPIPDDIQY 322

Query: 318 T--WDSLGFKYDRNLYIKRLYSQDECKQN 344
           T  W    F  D +     L   +E   +
Sbjct: 323 TLNWLDNNFSIDTDTSDANLILNEEINND 351


>gi|160900458|ref|YP_001566040.1| RluA family pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160366042|gb|ABX37655.1| pseudouridine synthase, RluA family [Delftia acidovorans SPH-1]
          Length = 356

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 94/338 (27%), Positives = 146/338 (43%), Gaps = 49/338 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V   +  +R D+         +   LQ++L  G V         N R+    +V+
Sbjct: 46  LREITVPPAQHGLRADKVLAECVAEFSRSYLQQLLAQGAV-------TLNGRV----LVK 94

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
               + A + ++ E +    S+        L   ++YED  + V NKPAG+ V    G  
Sbjct: 95  PATKVAAGDRMVLEMRPTQQSMAFQPEDMALD--VVYEDEHLLVVNKPAGLVVHPAPGNW 152

Query: 125 IAYHIDGFLKSWVDSKGQK-PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
               ++G L    D K ++ PR  + HRLD++TSG++VVAR+RAA   L      R + +
Sbjct: 153 TGTLLNGLLGR--DPKAREVPRAGIVHRLDKDTSGLMVVARSRAAMDALVAMIAARDVSR 210

Query: 182 IYWSL---VWGIPKNKKECIANWLLKKSHIGGD--------YVHVVKQNEKGANYAISHF 230
            Y +L    WG P+  +E  A        IG D         V + +   K A   I   
Sbjct: 211 QYLALAHKAWG-PRKHREVDAP-------IGRDPRNRLRMAVVDLAQHAGKTARTDIDLL 262

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
              +  +   C L    HTGRTHQ+RVH   +G P+V D  Y     G        +  L
Sbjct: 263 AGNEEVSLVRCTL----HTGRTHQIRVHMASLGHPLVADAVYGGKEAGGMA-----RQAL 313

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           HA  +   HP  G+ L + APLP  M +  ++ G  Y+
Sbjct: 314 HAFRLAFTHPMTGQALVLRAPLPPDMAQALENWGLSYN 351


>gi|117926248|ref|YP_866865.1| ribosomal large subunit pseudouridine synthase A [Magnetococcus sp.
           MC-1]
 gi|117610004|gb|ABK45459.1| ribosomal large subunit pseudouridine synthase A [Magnetococcus sp.
           MC-1]
          Length = 224

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 71/224 (31%), Positives = 106/224 (47%), Gaps = 17/224 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D+ + +FNKP  + +  G G    +   L      +G+ P   HRLD  TSG LV+
Sbjct: 13  ILHMDADLLIFNKPNRMPIYRGPGGGETLADHLPQLCFERGKPPAAVHRLDSATSGCLVL 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R +   + L+  F    ++K+YW++V G P   +  I   L      G   V V     
Sbjct: 73  GRHKGMRRSLSNLFAQGGVEKLYWAVVQGRPLMDQGLIELPLQDVGWPGRPRVKV----R 128

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            G  +  + F+V+  + Q    L + P TGRTHQLRVH   MGCPIVGD  Y        
Sbjct: 129 MGGKWGRTLFQVMG-YGQNETLLALMPQTGRTHQLRVHCAAMGCPIVGDPLY------GG 181

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQ--ITAPLPAHMVKTWDSL 322
            +     ++LHAR + L     G +Q   TAP P H+ +  + +
Sbjct: 182 AACDGPPMHLHARRILL----HGAIQQSFTAPAPPHLQRFLEQM 221


>gi|315186195|gb|EFU19957.1| pseudouridine synthase, RluA family [Spirochaeta thermophila DSM
           6578]
          Length = 319

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 144/321 (44%), Gaps = 50/321 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + +RLD+        +     Q   R   + +D +  K + R+ +G              
Sbjct: 16  DGLRLDQALAEL---LGITRSQVKQRIADLALDGRPAKPSQRVHAGAR------------ 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL- 133
            I    + ++  +LT     +   +LYED    V +KP G+ V  G+G      + G L 
Sbjct: 61  -IAGTLLPEAPPDLTPEP--VPFTVLYEDPHCLVIDKPQGLVVHPGAGNPTGTLVHGLLH 117

Query: 134 -------KSWVDSKGQKPRL----THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  ++  D    + RL     HRLD++TSG+LVVA+  A    L   F+ +  +K+
Sbjct: 118 YSHELATRASSDDLDDEERLRIGIVHRLDKDTSGVLVVAKDPATHHFLATQFKEKETKKL 177

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-----VVKQNEKGANYAISHFKVIDCFA 237
           Y +++ G P  ++  I      + H+  D VH     ++ + ++G  Y+ + ++++  F 
Sbjct: 178 YLAVLKGTPPAREGEI------EGHLARDPVHRKKFTLLSRPDRG-KYSHTRYRLLAAFG 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
               ++ + P TGRTHQLRVH   +GCPI+GD  Y A     F       L LHA  + +
Sbjct: 231 TH-SFVALYPTTGRTHQLRVHTAALGCPILGDPLY-ARPDPRFP---DATLMLHAYLLTI 285

Query: 298 PHPEGGRLQITAPLPAHMVKT 318
             P  G L   APLP H  KT
Sbjct: 286 RIPGRGLLTFRAPLP-HRFKT 305


>gi|123967748|ref|YP_001008606.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. AS9601]
 gi|123197858|gb|ABM69499.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. AS9601]
          Length = 319

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 91/321 (28%), Positives = 148/321 (46%), Gaps = 42/321 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +  P  +   +Q  + SG V V+ K  K    +++G  ++I  PP    L +
Sbjct: 27  MRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNIQIWMPPP-EPLIY 85

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E+  L+               +L+ED  I V NK +G+ V    G      ++G L 
Sbjct: 86  LKPEKMDLN---------------ILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLF 130

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++TSG +VVA+++ A  +L +  + +   + Y +++ G 
Sbjct: 131 HCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGA 190

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           P +++  I        +IG D ++ +K     E    YA +++K+ + F   +  +  + 
Sbjct: 191 PNSEEGQIV------GNIGRDKLNRLKYKVVEETSGRYACTYWKLEERFGN-YSLMSFKL 243

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            TGRTHQ+RVH  H+  PIVGD  Y  C            +   LHA  + L HP  G+ 
Sbjct: 244 DTGRTHQIRVHCAHINHPIVGDPLYGRCKKLPCKL-----DGQALHAIKLGLIHPINGKE 298

Query: 306 QI-TAPLPAHMVKTWDSLGFK 325
            I  + LP    K    L  K
Sbjct: 299 MIFESELPLDFQKLLSVLKIK 319


>gi|146338456|ref|YP_001203504.1| pseudouridine synthase [Bradyrhizobium sp. ORS278]
 gi|146191262|emb|CAL75267.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Bradyrhizobium sp. ORS278]
          Length = 384

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 81/300 (27%), Positives = 136/300 (45%), Gaps = 52/300 (17%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           LMT    ++V  DE + RLDR      P ++   L+ ++ +GQV +       ++   SG
Sbjct: 53  LMT----IIVAGDEGSPRLDRVLAARLPELSRSRLKALILAGQVSL------TSDSFGSG 102

Query: 63  QVVRIPPVINALNHIIKEQKI---LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             VR P       H+     I   +  +V     ++ +   ++YED  I V +KP+G+ V
Sbjct: 103 -AVRDPAY-----HVTTGDTITIDVPEAVAPEPQAEAIPLQIIYEDDDIIVIDKPSGLVV 156

Query: 120 QGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHL 170
              +G  +     + + +   G         ++P + HRLD++T+G++VVA+   A   L
Sbjct: 157 HPAAG--HETGTLVNALIAHCGASLSGIGGVKRPGIVHRLDKDTTGLMVVAKNDMAHASL 214

Query: 171 TESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           +  F    R   +++ Y +  WG+P      I   + +  H         K  E     A
Sbjct: 215 SAQFADHGRTGAMERGYLAFAWGVPHRPHGTINAAIDRHPHARDKMAVRAKGRE-----A 269

Query: 227 ISHFKVIDCFAQK---------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           I+H++V + F  +          C LE    TGRTHQ+RVH  H+G P++GD  Y  +FK
Sbjct: 270 ITHYEVQESFTGRDGKPVASLIACHLE----TGRTHQIRVHLAHLGHPLLGDAVYGPHFK 325


>gi|291614496|ref|YP_003524653.1| pseudouridine synthase, RluA family [Sideroxydans lithotrophicus
           ES-1]
 gi|291584608|gb|ADE12266.1| pseudouridine synthase, RluA family [Sideroxydans lithotrophicus
           ES-1]
          Length = 331

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 90/324 (27%), Positives = 146/324 (45%), Gaps = 40/324 (12%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+     +P  +   LQ  +  G V V+ K      ++  G+ + + P I+     
Sbjct: 31  GLRLDQALVKLFPEYSRSRLQDWVEQGLVTVNGKAGSVKQKVWGGEHISVSPQIHP---- 86

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
             EQ           H++ +   ++YED  + + NKP G+ V  GSG      ++  L  
Sbjct: 87  -SEQPY---------HAEDIPLDIVYEDDAMLIINKPVGLVVHPGSGNWQGTLLNALLHH 136

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                   PR  + HRLD++TSG++VVA++  A   L    + R +++ Y +LVWG    
Sbjct: 137 -APQLADVPRAGIVHRLDKDTSGLMVVAKSLVAQTALVRQMQARSVKREYLALVWG---- 191

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGR 251
             E   ++ +    IG      VK    +    AI+H  + + F   +C L   +  TGR
Sbjct: 192 --ELDRDYTINVP-IGRHPSQRVKMATTESGKEAITHVGIEERFP--YCTLVRCRLETGR 246

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY-------LHARYMDLPHP-EGG 303
           THQ+RVH  H+G P++GD  Y    +    SP   +L        LHA  + L HP  G 
Sbjct: 247 THQIRVHMTHIGHPLIGDAVYQRGTQK--CSPQLRELLNGFPRQALHATQLALNHPVTGE 304

Query: 304 RLQITAPLPAHMVKTWDSLGFKYD 327
           R++  +PLP  M +  + +    D
Sbjct: 305 RMEFHSPLPEDMEELLEQIDEASD 328


>gi|323136929|ref|ZP_08072009.1| pseudouridine synthase, RluA family [Methylocystis sp. ATCC 49242]
 gi|322397690|gb|EFY00212.1| pseudouridine synthase, RluA family [Methylocystis sp. ATCC 49242]
          Length = 339

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 96/344 (27%), Positives = 150/344 (43%), Gaps = 57/344 (16%)

Query: 11  VVENDEENMRLDRWFKNHY----PHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVV 65
           +V  +    RLDR+          H++   ++ ++ SG+V +    ++    ++ +G  V
Sbjct: 19  LVAPEAAGARLDRFLAERPEIVDAHLSRSRIKALIESGRVSLRGAAIRDPAKKLAAGDAV 78

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +            E+  LD               ++YED+ + V +KPAG+ V   SG 
Sbjct: 79  SLDVPPPEPAEPQAEEIALD---------------IVYEDAHLIVIDKPAGLVVHPASG- 122

Query: 126 AYHIDGFL---------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESF- 174
             H  G L         +S     G +KP + HR+D++T+G+LVVA+T AA   L+  F 
Sbjct: 123 --HESGTLVNALIAHCGESLSGVGGVKKPGIVHRIDKDTTGLLVVAKTDAAHHGLSRLFA 180

Query: 175 ---RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF- 230
              R   + + Y + VWG+P      I   L + S I  + + VV   E     AI+H+ 
Sbjct: 181 DHGRTLSLTREYLAFVWGVPDRAHGTIETSLGRHS-IQREKMAVVP--EARGREAITHWE 237

Query: 231 KVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
           KV D        C LE    TGRTHQ+RVH  H+G P++GD  Y A FK       +   
Sbjct: 238 KVADYGVASLVRCQLE----TGRTHQIRVHMAHIGHPLIGDSTYGAGFKTKVAKLPEAAR 293

Query: 286 ------NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                  +  LHA  +   HP  G  +  T+ LP  +     +L
Sbjct: 294 AAVEKLGRQALHAATLGFEHPITGEEMMFTSELPDDLAALMAAL 337


>gi|295687954|ref|YP_003591647.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
 gi|295429857|gb|ADG09029.1| pseudouridine synthase, RluA family [Caulobacter segnis ATCC 21756]
          Length = 340

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 90/337 (26%), Positives = 144/337 (42%), Gaps = 50/337 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIP 68
            V+  +    RLD+     +P ++   LQ ++  G++  + + V   +R  ++G  V   
Sbjct: 27  AVLPAELAGQRLDKALAPLFPDLSRARLQALIAEGRLSAEGQPVTDASRKAKAGTYVL-- 84

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIA 126
                L            ++ LT         +LYED+ + V +KPAG++     GS   
Sbjct: 85  -----LVPPPIPADPEPEAIPLT---------VLYEDAHLIVVDKPAGMAAHPAPGSLTG 130

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             ++  L    DS        +P + HRLD++TSG++V A++ AA + L+  F    I +
Sbjct: 131 TLVNALLHHCGDSLSGVGGVARPGIVHRLDKDTSGVMVAAKSDAAHKGLSALFATHDIDR 190

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDY--VHVVKQNEKGANYAISHFKVIDCF--- 236
           +Y +L  G P      I   L +     GD   + V++    G   A++H++V   F   
Sbjct: 191 LYIALTRGAPSPPAGTITTQLGRSP---GDRKKMAVLRS---GGREAVTHYRVEAAFGPQ 244

Query: 237 -----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-----CANFKGNFTSPIQN 286
                A+  C LE    TGRTHQ+RVH    G P +GD  Y      A  +    +    
Sbjct: 245 EKPLAARVACRLE----TGRTHQIRVHMASKGSPCLGDPVYGTGQPAAAVREAIQAAGLK 300

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +  LHA  +   HP  G  L+   PLP  M     SL
Sbjct: 301 RQALHAAVLGFVHPITGEALRFETPLPEDMAALQKSL 337


>gi|323343983|ref|ZP_08084209.1| ribosomal large subunit pseudouridine synthase [Prevotella oralis
           ATCC 33269]
 gi|323094712|gb|EFZ37287.1| ribosomal large subunit pseudouridine synthase [Prevotella oralis
           ATCC 33269]
          Length = 233

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 68/220 (30%), Positives = 111/220 (50%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I + +K +G  VQG       +   +K ++  K  KP      + HRLD+  +
Sbjct: 3   VLYEDNHIIIVSKRSGEIVQGDKTGDVPLSETVKQYIKDKYAKPGNVFIGVVHRLDRPVA 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYV 213
           GI+V A+T  A   L   FR   + K YW++    P+  +  + +WL++  K +    Y 
Sbjct: 63  GIVVFAKTSKALSRLNSMFRDGEVHKTYWAITKNCPQQTEGTLTDWLVRNEKQNKSYAYD 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H V  ++K    A+  + +I   ++++  +E+Q  TGR HQ+R     +GCPI GD KY 
Sbjct: 123 HEVPNSKK----AVLKYDIIG-KSERYTLIEVQLMTGRHHQIRCQLARIGCPIKGDLKY- 176

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
               G   S     + L AR ++  HP   + + +TAPLP
Sbjct: 177 ----GAPRSNTDGSISLLARGVEFVHPVSKKTISVTAPLP 212


>gi|282856468|ref|ZP_06265745.1| ribosomal large subunit pseudouridine synthase D [Pyramidobacter
           piscolens W5455]
 gi|282585708|gb|EFB90999.1| ribosomal large subunit pseudouridine synthase D [Pyramidobacter
           piscolens W5455]
          Length = 345

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 85/319 (26%), Positives = 149/319 (46%), Gaps = 36/319 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIP 68
           + V  ++   RLD +       ++    + ++  G V   + K+++   +IQ GQ+ R+ 
Sbjct: 42  LAVPEEDSGARLDLFLAGEL-SLSRSRARSLIDGGAVSSGQVKKIRPAFKIQPGQIYRVE 100

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
               A   I  +    D               ++YED  + V NKPAG+ V  G+G    
Sbjct: 101 IPEAAPAEIAAQDMPFD---------------VVYEDDDVIVVNKPAGVVVHPGAGRPDG 145

Query: 127 YHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +  + +        +P + HRLD  TSG++VVAR+ AA + LTE+F+   + K 
Sbjct: 146 TLVNGLMFRYPEIGRIGDSVRPGIVHRLDVGTSGLMVVARSDAAFRGLTEAFQAHEVLKE 205

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFC 241
           Y  L  G  K  +  +       + IG D  + +K         A++ +KV+  + +  C
Sbjct: 206 YLGLGVGALKAPEGTV------DAPIGRDPRNRLKMCVSWDGRDAVTDYKVL--WTRARC 257

Query: 242 -WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++ HTGRTHQ+RVH   +GC + GD  Y           ++++++LH+  +   HP
Sbjct: 258 NLIRVRLHTGRTHQIRVHMRALGCSLDGDTLYGPKDPAQHI--LKDRVFLHSWRLGFRHP 315

Query: 301 -EGGRLQITAPLPAHMVKT 318
             G RL+  APLP  ++  
Sbjct: 316 VSGERLEFRAPLPPELIAA 334


>gi|294501002|ref|YP_003564702.1| pseudouridine synthase [Bacillus megaterium QM B1551]
 gi|294350939|gb|ADE71268.1| pseudouridine synthase [Bacillus megaterium QM B1551]
          Length = 304

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 84/316 (26%), Positives = 145/316 (45%), Gaps = 44/316 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP- 68
            V+  ++   R+D+         +   +Q+ ++ G  +V+ K VK N + ++G  + I  
Sbjct: 6   TVINEEQAGERIDKVLSTVNAEWSRSQVQQWIKEGHAKVNDKTVKGNYKCKTGDAIIIEV 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
           P +  L+ ++ E+  LD               + YED  + V NKP G+ V    G    
Sbjct: 66  PELEELD-VVAEEMDLD---------------IYYEDQDVLVVNKPRGMVVHPAPGHHSG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + 
Sbjct: 110 TLVNGLMAHCKDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDLAHESLVSQLVAKTVTRR 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFA 237
           Y ++V G+  +    I       + IG D      + V  +N + A   ++HF V+  F 
Sbjct: 170 YKAIVHGVIAHDHGTI------DAPIGRDKQDRQSMTVTDENSRDA---VTHFTVLQRF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY        T PI  +  LHA  +  
Sbjct: 220 KDFSLVECKLETGRTHQIRVHMKYIGFPLAGDPKYGP----KKTLPIDGQ-ALHAGVLGF 274

Query: 298 PHPEGGR-LQITAPLP 312
            HP     ++  AP P
Sbjct: 275 IHPRTNEYMEFEAPAP 290


>gi|254523997|ref|ZP_05136052.1| ribosomal large subunit pseudouridine synthase D [Stenotrophomonas
           sp. SKA14]
 gi|219721588|gb|EED40113.1| ribosomal large subunit pseudouridine synthase D [Stenotrophomonas
           sp. SKA14]
          Length = 329

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 86/321 (26%), Positives = 144/321 (44%), Gaps = 38/321 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +V +     R D      +P  +   L + +++G V +D  +V+  + ++ G+VV +  
Sbjct: 12  AIVPDTAAGRRFDAVVAELFPEYSRSRLTEWIKAGDVLLDGAQVRPRDPLRGGEVVTLTV 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V+        E   LD               +L+ED  + V NKP G+ V  G+G   H 
Sbjct: 72  VLETQTDAQPEDIPLD---------------VLFEDEHLLVINKPVGLVVHPGAG--NHS 114

Query: 130 DGFLKSWV---DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              + + +    S    PR  + HRLD++TSG++VVA+T  A   L E    R + + Y 
Sbjct: 115 GTLVNALLFRDPSVAVLPRAGIVHRLDKDTSGVMVVAKTLEAQTALVEQLAARDVHRQYL 174

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G         A       H        V+++ K    AI+H+++ + F +    LE
Sbjct: 175 AIVMGALVAGGTADAPI---DRHPRDRLKMAVREDGK---EAITHYRLRERF-RAHTALE 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMD 296
            +  TGRTHQ+RVH  H+  PI+GD  Y    K          + ++   +  LHA  ++
Sbjct: 228 CRLETGRTHQIRVHMAHVRHPIIGDPLYGGALKLPKGASDELVAALRGFKRQALHAETLE 287

Query: 297 LPHP-EGGRLQITAPLPAHMV 316
             HP  G  ++ TAP+P  M+
Sbjct: 288 FTHPITGEPVRNTAPVPEDML 308


>gi|218131974|ref|ZP_03460778.1| hypothetical protein BACEGG_03597 [Bacteroides eggerthii DSM 20697]
 gi|217985850|gb|EEC52190.1| hypothetical protein BACEGG_03597 [Bacteroides eggerthii DSM 20697]
          Length = 357

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 92/349 (26%), Positives = 158/349 (45%), Gaps = 53/349 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 33  VVVDKGQEMMRVDKYLFDRLTNASRNRIQKAADAGFVMANDKPVKSSYKVKPLDVITV-- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 91  ---MMDRPRYENEVIPEDIPLN---------IVYEDKFLMVVNKPAGLVVHPGHGNYHGT 138

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 139 LVNAIAWH----MKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKT 194

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LVWG  +  +  I   + +      D + +    +    +A++H++V++    
Sbjct: 195 TKRRYRALVWGNVEQDEGTIVGNVGRNPK---DRMQMTVLPDDQGKHAVTHYRVLERLGY 251

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNF-------------TSP 283
               +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG               T P
Sbjct: 252 -VTLVECVLETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFAKYKQFVNNCFDTCP 310

Query: 284 IQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS-LGFKYDRNL 330
            Q    LHA  +   HP  G  +  T+ LP  M +  D   G+  +R L
Sbjct: 311 RQ---ALHAMTLGFVHPVTGEEMYFTSELPDDMTRLIDKWRGYISNREL 356


>gi|295399734|ref|ZP_06809715.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294978137|gb|EFG53734.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 304

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 88/315 (27%), Positives = 147/315 (46%), Gaps = 46/315 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPP 69
           ++ + +N R+D+         +   +Q+ ++   V V+ + VK N +  +G   VVR+P 
Sbjct: 8   IDEEYDNERIDKVIAALNEDWSRSKVQQWIKKQLVTVNDQHVKANYKCSAGDIVVVRLP- 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                               L    + +   + YED+ + V NKP G+ V    G   H+
Sbjct: 67  ----------------EPEPLYVEPENIPLDIYYEDADVLVVNKPRGMVVHPAPG---HM 107

Query: 130 DGFLKSWV-----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G L + +     D  G     +P + HR+D++TSG+L+VA+   A Q L +    + + 
Sbjct: 108 RGTLVNALLAHCHDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDMAHQALVDQLVKKTVT 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQ 238
           + Y ++V G+  +    I       + IG D     K    E+    A++HF+V++ F Q
Sbjct: 168 RKYKAIVHGVIPHDYGTI------DAPIGRDKRDRKKMAVTEENGKEAVTHFRVLERFRQ 221

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            + ++E Q  TGRTHQ+RVH  ++G P+ GD +Y        T PI  +  LHA  +   
Sbjct: 222 -YTFIECQLETGRTHQIRVHMKYIGYPLAGDPQYGP----KKTLPIDGQA-LHAGVLGFS 275

Query: 299 HPEGGR-LQITAPLP 312
           HP  G  L+  APLP
Sbjct: 276 HPRTGEYLEFEAPLP 290


>gi|167719292|ref|ZP_02402528.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei DM98]
          Length = 318

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 73/259 (28%), Positives = 118/259 (45%), Gaps = 24/259 (9%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ + S +VRV     K    +  G  + + P +        
Sbjct: 63  RLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIELLPELLPEQLAFT 122

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
            + +  S              ++YED  I V +KPAG+ V   +G      ++G L  + 
Sbjct: 123 PEPVPLS--------------IVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYA 168

Query: 138 DSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++L WG  +   E
Sbjct: 169 DAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWG--RMPDE 226

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTH 253
              +  + +       + VV         A +HF+ +D      Q    +     TGRTH
Sbjct: 227 GTIDAPIGRDPRERTRMAVV--TGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTH 284

Query: 254 QLRVHALHMGCPIVGDHKY 272
           Q+RVH  H+G P++GD  Y
Sbjct: 285 QIRVHCAHVGHPLLGDPVY 303


>gi|313893115|ref|ZP_07826692.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313442468|gb|EFR60883.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 307

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 91/315 (28%), Positives = 145/315 (46%), Gaps = 42/315 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  ++E MRLD +        +   +Q +++ G V V  K  K N R+    V+++   
Sbjct: 5   IVSAEQEGMRLDVFLTEQMEG-SRSYIQSLIKGGHVIVGGKVGKANLRLTPNMVIQV--- 60

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                      +I +      K  D    +L YED  I + NK  G+ V    G      
Sbjct: 61  -----------EIPEPESVEVKPEDIPLDVL-YEDHDIIIVNKARGMVVHPAVGNYSGTL 108

Query: 129 IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D  G     +P + HRLD++TSG+++ A+  AA   L E  +    ++ YW
Sbjct: 109 VNALLFHCKDLSGINGEIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKEHSAKRTYW 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +LV G    +K  I      K+ IG        + VV +N K    A++HF+V++ +  +
Sbjct: 169 ALVQGNIVEEKGTI------KAPIGRHPKDRMKMAVVFENSKD---AVTHFRVLERYGHQ 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E    TGRTHQ+RVH  H+G P+V D  Y          PI+ +  LH+R +D+ H
Sbjct: 220 -TLVECNLETGRTHQIRVHFAHIGHPVVNDPFYGYR---RMDFPIEGQA-LHSRSLDVKH 274

Query: 300 P-EGGRLQITAPLPA 313
           P  G  +   AP+PA
Sbjct: 275 PITGEDMHFEAPVPA 289


>gi|157964996|ref|YP_001499820.1| ribosomal large subunit pseudouridine synthases RluD subfamily
           protein [Rickettsia massiliae MTU5]
 gi|157844772|gb|ABV85273.1| Ribosomal large subunit pseudouridine synthases RluD subfamily
           protein [Rickettsia massiliae MTU5]
          Length = 313

 Score =  102 bits (254), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/323 (26%), Positives = 149/323 (46%), Gaps = 52/323 (16%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           ++RLD+   +   +++   +QK ++  QV V+              ++  P V+   N I
Sbjct: 12  DIRLDKALSSLLENVSRNQIQKAIKDSQVLVN------------DVIISDPDVLVKENDI 59

Query: 78  I-------KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           I       +E KI  ++V L          ++YED  + V NK AG++V  G+G  +H D
Sbjct: 60  ILFSFKEPEELKIAAANVALD---------IIYEDDDLIVINKAAGMTVHPGAG--HHDD 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD++T+G++VVA+   A   L      R++ + 
Sbjct: 109 TLVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFC 241
           Y  LVWG+  N  E +    + +S      + ++K    G   A++H+K ++ F +    
Sbjct: 169 YKVLVWGVI-NPLEGVIKNNIGRSRSDRQKMTILKY---GGKEAVTHYKTLELFYKGSIS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLY------LHAR 293
            +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP  ++ KL       LH+ 
Sbjct: 225 MVECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAHSPPELKAKLIDFKRQALHSW 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHM 315
           Y+   HP     +  +  LP  M
Sbjct: 285 YLSFTHPTSNEIMAFSCKLPRDM 307


>gi|126729199|ref|ZP_01745013.1| putative Pseudouridine synthase, Rlu [Sagittula stellata E-37]
 gi|126710189|gb|EBA09241.1| putative Pseudouridine synthase, Rlu [Sagittula stellata E-37]
          Length = 342

 Score =  102 bits (254), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 81/303 (26%), Positives = 129/303 (42%), Gaps = 40/303 (13%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL----LYEDS 106
            R +    I  G V R   ++      + E  +L+ +V   +  D +   +    ++ED+
Sbjct: 31  SRTRLGRLIAEGAVTRDGALLTDPKAKVAEGDVLEIAVPEAEDYDVVAQDIPLEIVFEDA 90

Query: 107 KIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
            + V NKPAG+ V    G         + +H  G L      K  +P + HR+D++TSG+
Sbjct: 91  DLLVVNKPAGMVVHPAPGTPDGTLVNALLHHFGGELSGVGGEK--RPGIVHRIDKDTSGL 148

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV---- 213
           LVVA++  A   L   F     ++ Y ++V G+P      +       +  GG       
Sbjct: 149 LVVAKSDRAHHGLARQFEKHTARRAYLAVVHGVPDVADPRLMGTRGVSAGAGGGITITSG 208

Query: 214 ---HVVKQNEKG------ANYAISHFKVIDCFAQKFC--WLEMQPHTGRTHQLRVHALHM 262
              H   +  +         +AI+H +V++ F    C   +E +  TGRTHQ+RVH  H 
Sbjct: 209 LARHKTDRQRQAVFFVGQGRHAITHARVLETFGAPECLALVECRLETGRTHQIRVHMAHA 268

Query: 263 GCPIVGDHKYCA--NFKGNFTSPIQ-------NKLYLHARYMDLPHP-EGGRLQITAPLP 312
           G  +VGD  Y      KG+  SP         ++  LHA  +   HP     +   APLP
Sbjct: 269 GHALVGDSTYGGRRKLKGSALSPEAFAVASAFDRQALHAAELGFVHPVTEEEMLFEAPLP 328

Query: 313 AHM 315
           A M
Sbjct: 329 ADM 331


>gi|325295189|ref|YP_004281703.1| pseudouridine synthase, RluA family [Desulfurobacterium
           thermolithotrophum DSM 11699]
 gi|325065637|gb|ADY73644.1| pseudouridine synthase, RluA family [Desulfurobacterium
           thermolithotrophum DSM 11699]
          Length = 313

 Score =  102 bits (254), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 86/330 (26%), Positives = 156/330 (47%), Gaps = 39/330 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIP 68
           +VV+++++  RLD++  +    I+    + ++  G+V ++ + VK  + +++ G+ V   
Sbjct: 4   IVVDSEKKGKRLDQFIAS-IADISRSQAKNLIEDGEVSINGRIVKKPSYKVKEGETVSFE 62

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                          +   + L    + +   ++YED  + V NKPAG+ V    G    
Sbjct: 63  ---------------IPEPIPLDLQPENIPLDIVYEDKDVIVINKPAGLVVHPAPGHYSG 107

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D +G     +P + HRLD++T+G+LVVA+   A Q L E F+ R + + 
Sbjct: 108 TLVNALLYYCKDFQGINGTLRPGIVHRLDKDTAGLLVVAKNDLAQQSLIEQFKRRTVGRF 167

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--QNEKGANYAISHFKVIDCF-AQK 239
           Y +LV GI + + + I         IG D     K   N      AI+++ V++ F    
Sbjct: 168 YRALVLGIFEKQHDRIV------VPIGRDKFDRKKFSPNTTSPKEAITNYWVLESFPTHN 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHAR--- 293
              ++ +  TGRTHQ+RVH  H+G P++GD  Y    +  K      + +++ +HA    
Sbjct: 222 VSDIKCKLETGRTHQIRVHMSHIGHPLLGDKTYGYKPSRIKDETLRRLIDEMRMHALCAY 281

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           Y+   HP   + ++    LP +M K  D L
Sbjct: 282 YLGFKHPRTEKWIEFEIDLPENMKKVLDFL 311


>gi|223937244|ref|ZP_03629150.1| pseudouridine synthase, RluA family [bacterium Ellin514]
 gi|223894029|gb|EEF60484.1| pseudouridine synthase, RluA family [bacterium Ellin514]
          Length = 599

 Score =  102 bits (254), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 82/243 (33%), Positives = 113/243 (46%), Gaps = 12/243 (4%)

Query: 76  HIIKE-QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           HI+   ++IL    NLT+        +L+ED  + V NKPA + +  G     +   ++ 
Sbjct: 355 HIVSAGKRILQKMPNLTEPEVNGDIQILHEDEALIVLNKPAPLPMHAGGRFNRNTLEYIL 414

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             V    QKPR  HRLD  TSG+++V RTR  A HL   F    + K Y   V G PK  
Sbjct: 415 HQV-YHPQKPRAAHRLDANTSGVVLVTRTRHFASHLQPQFAHGEVGKFYLVKVQGTPKED 473

Query: 195 K-ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
              C A    + S  G   V      E+G   + + F+V+   A     LE +P TGRT+
Sbjct: 474 SFSCNAPISAEPSEAGAREVDF----EEGLP-SRTEFRVLQRNADGTTLLEARPLTGRTN 528

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGRLQITA 309
           Q+RVH   MG P+ GD  Y    K   T  ++     L LHA  +   HP    R++ TA
Sbjct: 529 QIRVHLWQMGLPVCGDPVYLPGNKLGETQTLRVEDAPLCLHAWRVTFLHPLHRQRMEFTA 588

Query: 310 PLP 312
           P P
Sbjct: 589 PKP 591


>gi|15893233|ref|NP_360947.1| pseudouridylate synthase [Rickettsia conorii str. Malish 7]
 gi|15620450|gb|AAL03848.1| sfhB protein homolog [Rickettsia conorii str. Malish 7]
          Length = 313

 Score =  102 bits (254), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/322 (26%), Positives = 149/322 (46%), Gaps = 52/322 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD+   +   + +   +QK ++  QV V+              ++  P V+   N II
Sbjct: 13  IRLDKALSSLLENASRNQIQKAIKDSQVLVND------------VIISDPDVLVKENDII 60

Query: 79  -------KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +E KI  ++V L          ++YED  + V NK AG++V  G+G  +H D 
Sbjct: 61  LFSFKEPEELKIAAANVALD---------IIYEDDDLIVINKAAGMTVHPGAG--HHDDT 109

Query: 132 FLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + + +            ++P + HRLD++T+G++VVA+   A   L      R++ + Y
Sbjct: 110 LVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCW 242
             LVWG+  N  E +    + +S      + ++K    G   A++H+K+++ F +     
Sbjct: 170 KVLVWGVI-NPLEGVIKNNIGRSRSDRQKMTILKY---GGKEAVTHYKILELFYKGSISM 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLY------LHARY 294
           +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP  ++ KL       LH+ Y
Sbjct: 226 VECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAHSPPELKAKLIDFKRQALHSWY 285

Query: 295 MDLPHPEGGR-LQITAPLPAHM 315
           +   HP     ++ +  LP  M
Sbjct: 286 LSFTHPTSNEIMEFSCELPRDM 307


>gi|78221275|ref|YP_383022.1| pseudouridine synthase, RluD [Geobacter metallireducens GS-15]
 gi|78192530|gb|ABB30297.1| Pseudouridine synthase, RluD [Geobacter metallireducens GS-15]
          Length = 295

 Score =  102 bits (254), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 84/308 (27%), Positives = 145/308 (47%), Gaps = 52/308 (16%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINAL 74
           E  MRLD      +P ++   ++KI+  G   V    V+  +R +++G+ + +       
Sbjct: 11  EAGMRLDDGAVRLFPQLSKTRVRKIIDWGGCAVAGAMVRVASRTLRAGEEIVL------- 63

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +++ ++  + +        + +  LL+E+      NK AG++ Q      Y + G ++
Sbjct: 64  -GVMEPERYQELA--------YTRDDLLFENDDYLAVNKAAGLNCQR---TPYQLKGTVE 111

Query: 135 SWVDS-----KGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             V         Q+P R+ HRLD+ TSG+++  +T+ AA H++   +  R++K+YW+LV 
Sbjct: 112 HAVTLYLRTLGSQEPARVIHRLDRGTSGVMIFPKTKRAAAHISAQLKEGRVEKVYWALVT 171

Query: 189 GIPKNKKECIANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC--WLE 244
             P + +     W +    + +G     V     +    A++ F VI   A+  C   +E
Sbjct: 172 AEPASDQ-----WEVNAPIAKVGSARYGVATPGRE----ALTRFAVI---ARGTCGVLVE 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +P TGRTHQ+RVH  H G PIVGD  Y     G   +P   ++ LH R M     +  R
Sbjct: 220 ARPLTGRTHQIRVHLAHCGLPIVGDPTY-----GGEKAP---RMMLHCRAMSFTAAD--R 269

Query: 305 LQITAPLP 312
             ITA  P
Sbjct: 270 RPITAEAP 277


>gi|241764488|ref|ZP_04762509.1| pseudouridine synthase, RluA family [Acidovorax delafieldii 2AN]
 gi|241366072|gb|EER60669.1| pseudouridine synthase, RluA family [Acidovorax delafieldii 2AN]
          Length = 353

 Score =  102 bits (254), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 92/339 (27%), Positives = 149/339 (43%), Gaps = 47/339 (13%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQ 63
           + ++ V V   +   RLDR   +  P  +   LQ++L  G V ++ ++  K   R+++G 
Sbjct: 44  SELRRVEVNAAQHGSRLDRALVDLVPEFSRSYLQQLLSQGLVALNGQQATKAAARVKAGD 103

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +      +   ++ Q             + L   ++YED+ + V NKPAG+ V    
Sbjct: 104 TLTV-----EMRPTLQSQAF---------RPEALPIDVVYEDAHLLVVNKPAGLVVHPAP 149

Query: 124 G--IAYHIDGFLKSWVDSKGQ-KPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G      ++G L    D+K Q  PR  + HRLD++TSG++VVAR R     L      R 
Sbjct: 150 GNWGGTLLNGLLAR--DAKAQLVPRAGIVHRLDKDTSGLMVVARDRTTMDALVRMIAART 207

Query: 179 IQKIYWSLV---W-GIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISH 229
           + + Y ++    W G+P    +         + IG D      + VV  +      A + 
Sbjct: 208 VHRQYLAIAHRPWTGVPNRAVQ---------APIGRDPRNRLRMAVVNLDTHAGKPARTD 258

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
            + +       CW+E   HTGRTHQ+RVH   +G P+V D  Y     G   +    +  
Sbjct: 259 IRWL-AGNDLGCWVECTLHTGRTHQIRVHMASLGHPLVADALY-----GGAPAAGLQRQA 312

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           LHA  +   HP  G+ L+  APLP  M +     G  Y+
Sbjct: 313 LHAYRLSFTHPVSGQALEFRAPLPDDMRRALAEWGLGYN 351


>gi|224065743|ref|XP_002301949.1| predicted protein [Populus trichocarpa]
 gi|222843675|gb|EEE81222.1| predicted protein [Populus trichocarpa]
          Length = 444

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 81/293 (27%), Positives = 135/293 (46%), Gaps = 47/293 (16%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V++     RLD W  +    I+   +Q  ++SG V V+ K + K ++ +++G        
Sbjct: 87  VDSKSGKSRLDSWISSRISGISRARVQSSIKSGLVSVNGKVIDKVSHNVKAG-------- 138

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-------- 122
            + +N +I E + L +        + +   ++YED  + V NKPA + V           
Sbjct: 139 -DKVNCVISELQPLRA------EPENIPLDIVYEDENVLVVNKPAHMVVHPAPGNATGTL 191

Query: 123 -SGIAYHI---------------------DGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
            +GI +H                      D  L S   +   +P + HRLD+ TSG+LVV
Sbjct: 192 VNGILHHCSLPTVSSQEVLSGAEDVSDDDDEGLCSSSYAASVRPGIVHRLDKGTSGLLVV 251

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+   +  HL+E F++  I+++Y SL  G+P      I   + +          +V+ N 
Sbjct: 252 AKDEHSHAHLSEQFKLHTIKRVYVSLTCGVPAPMAGRIDVPIGRDVSNRIRMAAIVEPNR 311

Query: 221 KGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             A +A S +KVI+  A     L E +  TGRTHQ+R HA ++G P++GD  Y
Sbjct: 312 GQARHAASRYKVIEILAGGGSALVEWRLETGRTHQIRAHAKYIGIPLLGDEVY 364


>gi|303245339|ref|ZP_07331623.1| pseudouridine synthase, RluA family [Desulfovibrio fructosovorans
           JJ]
 gi|302493188|gb|EFL53050.1| pseudouridine synthase, RluA family [Desulfovibrio fructosovorans
           JJ]
          Length = 551

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 74/220 (33%), Positives = 111/220 (50%), Gaps = 26/220 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--------DSKGQKPRLTHRLDQ 152
           LL+ D+ + V +KPAG++V    G+    +G L + +        D  G++P + HRLD+
Sbjct: 91  LLHADTDVIVLDKPAGLTVHPAPGLP---EGTLVNRLLYRFPQLRDMAGERPGIVHRLDK 147

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+L+VA T +A Q L   F  RR++K Y +LV G P+     I      +  IG D 
Sbjct: 148 DTSGLLLVALTESARQALAADFAARRVRKTYLALVHGRPERDGGDI------RLPIGRDP 201

Query: 213 VHVVKQN--EKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            H  K     KG   A S ++++          LE+   TGRTHQ+RVH   +G PIVGD
Sbjct: 202 KHRAKMAVVAKGGREARSRWRLVWSAPDAAASLLEVDIFTGRTHQIRVHLAAIGHPIVGD 261

Query: 270 HKYCANFKGNFT------SPIQNKLYLHARYMDLPHPEGG 303
             Y A+ + ++       S +  +  LHA  +   HP  G
Sbjct: 262 AVYGASRQNDWKRRPGVLSGLATRQMLHAWKLSFTHPGTG 301


>gi|28199626|ref|NP_779940.1| ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa Temecula1]
 gi|34395764|sp|Q87AR7|RLUD_XYLFT RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|28057741|gb|AAO29589.1| ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa Temecula1]
          Length = 331

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 89/347 (25%), Positives = 159/347 (45%), Gaps = 42/347 (12%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L  + +   V +     R D      +P  +   L + ++SG V ++   V+  + +  G
Sbjct: 9   LAGFSRQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVRPRDPVYGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           +VV +  + +     + +   LD               +LYED  ++V NKPAG+ V  G
Sbjct: 69  EVVWLQVMPDIRTDAVPQDIPLD---------------ILYEDEHVFVINKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +     +    PR  + HRLD++TSG++VVART  A   L E    
Sbjct: 114 AG---NPDGTLVNALLHRDPALAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSS 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R++ + Y ++V  +         N  +++       + V    ++    A++H+++ + F
Sbjct: 171 RQVHRQYLAVV--VSALVSGGTVNAAIERHPRDRLRMEVSDTGKE----AVTHYRLRERF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQ-----NKL 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y  +    KG   + +       + 
Sbjct: 225 -RAHTALECRLDTGRTHQIRVHMAHLRHPIVGDRLYGGSLKLPKGGTDALVAMLRGFKRQ 283

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  ++  HP     ++I AP+P  + +   +L  + D  L+ +R
Sbjct: 284 ALHAEVLEFLHPVRALPVRIVAPVPEDLCQLLAAL--REDSALFFER 328


>gi|300715284|ref|YP_003740087.1| ribosomal large subunit pseudouridine synthase A [Erwinia
           billingiae Eb661]
 gi|299061120|emb|CAX58227.1| Ribosomal large subunit pseudouridine synthase A [Erwinia
           billingiae Eb661]
          Length = 217

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 73/205 (35%), Positives = 111/205 (54%), Gaps = 18/205 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G   +  H D  + + V          HRLD  TSG++V
Sbjct: 14  ILYQDEHIMVINKPSGLLSVPGR--LEDHKDSVM-TRVQRDFPAAESVHRLDMATSGVIV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  QK Y + +WG P+  K  +   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPQKQYVARIWGHPEKAKGLVDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + A + ++V+D        ++++P TGR+HQLRVH L +G PI+GD+ Y A+ 
Sbjct: 125 VCFETGKS-AQTEYEVLDYADDNSARIQLKPITGRSHQLRVHMLALGHPILGDNFY-AHD 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPE 301
           +    +P   +L LHA  + + HP+
Sbjct: 183 EAKAMAP---RLQLHAEMLTITHPQ 204


>gi|255311484|ref|ZP_05354054.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 6276]
          Length = 335

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 87/326 (26%), Positives = 151/326 (46%), Gaps = 47/326 (14%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRI 67
           +  V +++   RLD+   ++    +    Q+ +  G+VRV+ +   + ++ +  G VV +
Sbjct: 12  FSFVIDEQLTGRLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGDVVEV 71

Query: 68  PPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
                    +I+E++   ++   + L K         +YED  I V NKP  + V    G
Sbjct: 72  --------ELIEEKEPSSLIPEDIPLDK---------VYEDDMILVINKPRDMVVHPAPG 114

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                    + + I   LK     +  +P + HRLD++TSG+L+  +TR A    +E F 
Sbjct: 115 HTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKALYSELFA 174

Query: 176 MRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            ++++K+Y ++    P  +     IA   LK+  +      V+  + +G   AI+H  V+
Sbjct: 175 TKQVKKLYVAICINAPSQELIHTRIARHPLKRKEMT-----VLSTHAEGGKEAITHCHVL 229

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYL 290
                +   + + P TGRTHQLRVH  H+G PI+GD  Y     NF+        +K  L
Sbjct: 230 ATNG-RLSVVALYPETGRTHQLRVHMKHLGTPILGDPVYGIPSINFRYGL-----DKQQL 283

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHM 315
           HA  +   HPE   R+++   LP  M
Sbjct: 284 HAYSLVFAHPESAERVKLVTKLPDDM 309


>gi|317474426|ref|ZP_07933700.1| RluA family pseudouridine synthase [Bacteroides eggerthii
           1_2_48FAA]
 gi|316909107|gb|EFV30787.1| RluA family pseudouridine synthase [Bacteroides eggerthii
           1_2_48FAA]
          Length = 356

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 92/349 (26%), Positives = 158/349 (45%), Gaps = 53/349 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQEMMRVDKYLFDRLTNASRNRIQKAADAGFVMANDKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYENEVIPEDIPLN---------IVYEDKFLMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 138 LVNAIAWH----MKDIPDYNANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKT 193

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LVWG  +  +  I   + +      D + +    +    +A++H++V++    
Sbjct: 194 TKRRYRALVWGNVEQDEGTIVGNVGRNPK---DRMQMTVLPDDQGKHAVTHYRVLERLGY 250

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNF-------------TSP 283
               +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG               T P
Sbjct: 251 -VTLVECVLETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFAKYKQFVNNCFDTCP 309

Query: 284 IQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS-LGFKYDRNL 330
            Q    LHA  +   HP  G  +  T+ LP  M +  D   G+  +R L
Sbjct: 310 RQ---ALHAMTLGFVHPVTGEEMYFTSELPDDMTRLIDKWRGYISNREL 355


>gi|258648417|ref|ZP_05735886.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Prevotella tannerae ATCC 51259]
 gi|260851164|gb|EEX71033.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Prevotella tannerae ATCC 51259]
          Length = 294

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/283 (30%), Positives = 133/283 (46%), Gaps = 39/283 (13%)

Query: 37  LQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           ++ IL  G ++VD+  VK F++ ++ G  V I                     + +K   
Sbjct: 35  IKAILGGGGIKVDRAIVKQFDHPLRPGMQVEI---------------------SQSKPKS 73

Query: 96  FLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRL 150
            LKS    L+YED  I V +K AGI    GS   + +   L  +     ++ R  + HRL
Sbjct: 74  ELKSSHLRLVYEDEFIVVIDKSAGILSMAGSPHIFSVKTILDDYFAKTHKRCRAHVVHRL 133

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ETSG+LV A+T  A Q L  +++     + Y +++ G+ +     + NWL        
Sbjct: 134 DRETSGLLVYAKTIEAEQILEHNWQRIVRDRRYVAVLSGVLETPSGTVRNWLKDNK---- 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            YV      + G  +A++HF+ +   ++     E +  TGR +Q+RVHA  +G P+ GD 
Sbjct: 190 AYVTYSSPTDNGGKFAVTHFRRLK-HSETHTLAEFKLETGRKNQIRVHAQDLGHPVCGDT 248

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           KY     GN  +PI  +L LHA  +D  HP  G  L    P P
Sbjct: 249 KY-----GNGDNPI-GRLCLHAYRLDFYHPITGELLHFETPYP 285


>gi|326575838|gb|EGE25761.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis CO72]
          Length = 355

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 82/323 (25%), Positives = 150/323 (46%), Gaps = 32/323 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD+   + +   +  NL+K +  GQ+ V+ K VK    ++ G ++ +  V 
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVKPKYAVKVGDILTLEAVH 107

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            + +  + E   +D               ++YED  + + NKPAG+ V  G+G      +
Sbjct: 108 ESHSEDLPENIDID---------------IIYEDEAVIIINKPAGMVVHPGAGNRTGTLV 152

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +  L  +   +   PR  L HR+D++T+G+LV+ART++A   L +  + + + + Y  + 
Sbjct: 153 NALLYHF-PKQAHLPRAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIA 211

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQ 246
            G      E + +  +    IG    H  K   K     A++H        +++  L++ 
Sbjct: 212 LGA---VHEVLRHAQIDAP-IGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIH 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHP 300
             TGRTHQ+RVH  ++G P+VGD  Y  + +   +   +       +  LHA  +   HP
Sbjct: 268 LKTGRTHQIRVHLSYVGHPLVGDPVYGTSPRAGLSDRQRCAILDFGRQALHAYMLGFIHP 327

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  ++  APLP  M +  + L
Sbjct: 328 VTGEAMKFHAPLPKDMQQLIEVL 350


>gi|297544813|ref|YP_003677115.1| RluA family pseudouridine synthase [Thermoanaerobacter mathranii
           subsp. mathranii str. A3]
 gi|296842588|gb|ADH61104.1| pseudouridine synthase, RluA family [Thermoanaerobacter mathranii
           subsp. mathranii str. A3]
          Length = 305

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 101/341 (29%), Positives = 159/341 (46%), Gaps = 61/341 (17%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  VV+  E ++E  R+D +      +     ++K++  G   V+ K VK + +++ 
Sbjct: 1   MNIVDKVVLQGEKEDEGKRIDVFLAAELDYTRSY-IKKLIVDGLAFVNGKTVKPSYKVKE 59

Query: 62  GQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
               VV IP          ++  +L  ++ L          +LYED  I V NKP G+ V
Sbjct: 60  NDKVVVNIPEA--------EKIDVLPENIPLD---------ILYEDDDIIVINKPQGMVV 102

Query: 120 QGGSG---------IAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
               G         + YH      I+G L+         P + HRLD++TSG++VVA+  
Sbjct: 103 HPAPGNYSGTLVNALLYHCKNLSGINGILR---------PGIVHRLDKDTSGVMVVAKND 153

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKG 222
            A   L+   + R + K Y ++V G+ KN++E I      ++ IG   V   K    E G
Sbjct: 154 KAHISLSNQIKERSVFKKYVAIVEGVIKNEEEKI------EAPIGRHPVDRKKMAVIEDG 207

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             YA++ +KV++ F +    +E    TGRTHQ+RVH   +G P+VGD  Y    K  F  
Sbjct: 208 -RYALTLYKVLERFKEN-TLIEAVIKTGRTHQIRVHMAFIGHPVVGDPVYGFK-KQKFKL 264

Query: 283 PIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             Q    LH+R +   HP +G  ++  APLP +  K  + L
Sbjct: 265 EGQA---LHSRVLGFMHPTKGVYMEFEAPLPEYFKKLIEIL 302


>gi|20807974|ref|NP_623145.1| pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter
           tengcongensis MB4]
 gi|20516547|gb|AAM24749.1| Pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter
           tengcongensis MB4]
          Length = 309

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 94/344 (27%), Positives = 165/344 (47%), Gaps = 53/344 (15%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  +V+  E ++E  R+D +  +   + +   ++K++  G V V+ K VK + +++ 
Sbjct: 1   MNIVDRIVLQGEKEDEGKRIDVFLASELDY-SRSYIKKLIEEGLVLVNGKNVKPSYKVKE 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V    ++N     IKE + ++         + +   +LYED  I V NKP G+ V  
Sbjct: 60  DDEV----IVN-----IKEAEKIEVV------PENIPLDILYEDEDIIVINKPQGMVVHP 104

Query: 122 GSG---------IAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
             G         + YH      I+G L+         P + HRLD++TSG++VVA+   A
Sbjct: 105 APGNYSGTLVNALLYHCKNLSGINGILR---------PGIVHRLDKDTSGVMVVAKNDKA 155

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
              L+   + R + K Y ++V G+ K ++E      + +  +    + VV+       YA
Sbjct: 156 HMSLSNQIKERSVLKKYVAIVEGVIK-EEEGKIEAPIGRHPVDRKRMAVVQD----GRYA 210

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++ +KV++ F     ++E    TGRTHQ+RVH  ++G P+VGD  Y    K  F    Q 
Sbjct: 211 LTLYKVLERFKNN-TFVEATIKTGRTHQIRVHLSYIGHPVVGDPVYGYK-KQKFKLEGQA 268

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
              LH++ +   HP +G  ++  APLP +  +  + L  + DR+
Sbjct: 269 ---LHSKVLGFIHPTKGVYMEFEAPLPDYFTRLLEILRAEKDRD 309


>gi|319410076|emb|CBY90410.1| K06180 ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis WUE 2594]
          Length = 392

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/307 (27%), Positives = 139/307 (45%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ +R+            
Sbjct: 58  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKPSQPKDKMIGGEQIRV------------ 105

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 106 --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 162

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 163 PELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 222

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 223 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 273

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 274 HQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 333

Query: 306 QITAPLP 312
              AP+P
Sbjct: 334 SFEAPIP 340


>gi|71083312|ref|YP_266031.1| pseudouridylate synthase [Candidatus Pelagibacter ubique HTCC1062]
 gi|71062425|gb|AAZ21428.1| pseudouridylate synthase [Candidatus Pelagibacter ubique HTCC1062]
          Length = 326

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 88/326 (26%), Positives = 160/326 (49%), Gaps = 38/326 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V  DE N+RLD +       I+   ++ ++        K+++K N++I +    ++  
Sbjct: 7   LIVGEDENNLRLDVFINKRENLISRTRIKNLIL-------KEKLKINDQIINSPSKKVLS 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
             + +N  I E K  ++S+   K  +F K  ++YED  + + NKPAGI +  G+G     
Sbjct: 60  G-DEINLQIPEPK--EASL---KPYNF-KLQIVYEDDDLLIINKPAGIIMHPGAGNYDET 112

Query: 125 IAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           I   +  + K  + + G   +P + HR+D++TSG++V+A+     ++L+  F    I ++
Sbjct: 113 IVNALMHYNKDSLSTIGDELRPGIVHRIDKDTSGLIVIAKNNETHENLSHQFSEHTITRV 172

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ---- 238
           Y  L+WG  +     I  ++ + S    +   +   N KG   AI+++K I+ F      
Sbjct: 173 YQLLIWGKLRPSSGKIDTFITRSSK---NRQMMEVSNSKGK-RAITNYKTIEIFENDKTP 228

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLY------L 290
               +E +  TGRTHQ+RVH  HMG  I+GD  +K       N  + ++N +Y      L
Sbjct: 229 TLSLVECRLETGRTHQIRVHMTHMGNSIMGDGKYKKKYKKLKNIDTNLENLIYKLDRQFL 288

Query: 291 HARYMDLPHPEGGRLQI-TAPLPAHM 315
           HA+ +   HP      + T+ LP  +
Sbjct: 289 HAQTLGFIHPRTNEEMVFTSILPQEL 314


>gi|317504079|ref|ZP_07962082.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           salivae DSM 15606]
 gi|315664821|gb|EFV04485.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           salivae DSM 15606]
          Length = 355

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 94/330 (28%), Positives = 153/330 (46%), Gaps = 69/330 (20%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +  +R+D++     P+ +   +Q+   SG +RV+ + VK N +++ G V+ +  
Sbjct: 25  IEVDKGQTPVRIDKFLAEKNPYQSRNRIQQAADSGCIRVNNQPVKSNYKVRPGDVITL-- 82

Query: 70  VINALNH---IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +++   H   II E   LD               ++YED  + V NKPAG+ V  G+G  
Sbjct: 83  MLDRPKHDTSIIAEDIPLD---------------IVYEDDVLMVVNKPAGMVVHPGAGNF 127

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  +A+H+   LK + D+   +  L HR+D++TSG+LVVA+T  A   L + F  +
Sbjct: 128 TGTLINAVAWHLKD-LKGF-DANDPEVGLVHRIDKDTSGLLVVAKTPEAKTVLGKQFFNK 185

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--------EKG-ANYAIS 228
              + Y +LVWG          N +  +  I G+     K          E G    A++
Sbjct: 186 TTHRSYNALVWG----------NLVEDEGTIEGNVARDPKNRLRMKVFSPESGIGKNAVT 235

Query: 229 HFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP 283
           H++VI+ +       C LE    TGRTHQ+RVH  H+G P+  D  Y      +G  +S 
Sbjct: 236 HYRVIERYGYTTLVECILE----TGRTHQIRVHMKHIGHPLFADATYGGEEVLRGQRSST 291

Query: 284 ----IQN------KLYLHARYMDLPHPEGG 303
               I N      +  LHA+ +   HP  G
Sbjct: 292 YKAFINNCFKCCPRQALHAKTLGFIHPITG 321


>gi|189461733|ref|ZP_03010518.1| hypothetical protein BACCOP_02399 [Bacteroides coprocola DSM 17136]
 gi|189431493|gb|EDV00478.1| hypothetical protein BACCOP_02399 [Bacteroides coprocola DSM 17136]
          Length = 224

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 68/219 (31%), Positives = 110/219 (50%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDIPLSETVKQYLKEKYSKPGNVFLGVAHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L + FR   ++K YW++V   P  ++  + ++L++       Y + 
Sbjct: 63  GLVVFAKTSKALARLNDMFRNSEVKKTYWAIVKQCPPAEEGELVHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K +  A+ ++++I   +Q +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVKNSKKAVLNYRLIG-HSQNYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
             G   S     + LHAR +   HP     + ITAP+P+
Sbjct: 177 --GFPRSNPDGSICLHARRVRFIHPVSKEPIDITAPVPS 213


>gi|118594976|ref|ZP_01552323.1| pseudouridine synthase D [Methylophilales bacterium HTCC2181]
 gi|118440754|gb|EAV47381.1| pseudouridine synthase D [Methylophilales bacterium HTCC2181]
          Length = 349

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 74/270 (27%), Positives = 133/270 (49%), Gaps = 31/270 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP- 68
           +++  +   +R+D      +P  +   +Q  +R G ++VD + +    +I  G+ + I  
Sbjct: 8   ILMPQELSGLRIDAAIHKIFPEYSRGRIQAWIRDGHIKVDGQSLAPKKKIIGGENISIDF 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
              + L     E  I+++               +YED  I V NKPAG+ V  G+G    
Sbjct: 68  QPDDELKQFEAEDMIIEA---------------VYEDDHILVINKPAGLVVHPGAGNWSG 112

Query: 127 YHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             ++G L  + ++K   +  + HRLD++TSG++VV++T  A QHL +  + + +++ Y  
Sbjct: 113 TLLNGLLHHFPENKVLARAGIVHRLDKDTSGLMVVSKTEVAQQHLIKQLQNKTVKREYRC 172

Query: 186 LVWG-IPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           +VWG + KN   KE I      +  +  + +H           +++H++V++ F     +
Sbjct: 173 IVWGQVWKNGVVKEPIGRHPTVRVKMAVNKIH--------GKESVTHYEVLERFGH-HSY 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           L     TGRTHQ+RVH  H+  PIVGD  Y
Sbjct: 224 LRCNLETGRTHQIRVHMSHVQAPIVGDPVY 253


>gi|157412550|ref|YP_001483416.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9215]
 gi|157387125|gb|ABV49830.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9215]
          Length = 319

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 91/321 (28%), Positives = 148/321 (46%), Gaps = 42/321 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +  P  +   +Q  + SG V V+ K  K    +++G  ++I  PP    L +
Sbjct: 27  MRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNIQIWMPPP-EPLIY 85

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E+  L+               +L+ED  I V NK +G+ V    G      ++G L 
Sbjct: 86  LKPEKMDLN---------------ILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLF 130

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++TSG +VVA+++ A  +L +  + +   + Y +++ G 
Sbjct: 131 HCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGA 190

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           P +++  I        +IG D ++ +K     E    YA +++K+ + F   +  +  + 
Sbjct: 191 PNSEEGQIV------GNIGRDKLNRLKYKVVEETSGRYACTYWKLEERFGN-YSLMSFKL 243

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            TGRTHQ+RVH  H+  PIVGD  Y  C            +   LHA  + L HP  G+ 
Sbjct: 244 DTGRTHQIRVHCAHINHPIVGDPLYGRCKKLPCKL-----DGQALHAIKLGLIHPINGKE 298

Query: 306 QI-TAPLPAHMVKTWDSLGFK 325
            I  + LP    K    L  K
Sbjct: 299 MIFESELPLDFQKLLSVLKVK 319


>gi|325677946|ref|ZP_08157588.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
 gi|324110500|gb|EGC04674.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
          Length = 321

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 74/289 (25%), Positives = 140/289 (48%), Gaps = 42/289 (14%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++ + +ND  + R+D++     P +    L K +R  +++++ KR + + R++ G +V++
Sbjct: 3   EFTISKNDA-DQRMDKFLTKAVPALPKNLLYKYIRLKRIKLNGKRCEISTRLKDGDIVQL 61

Query: 68  -------PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV- 119
                  P   +A +  +   K ++               ++YED  + + NKP G+ V 
Sbjct: 62  YINDEFFPEKRDAAHRFLNAPKDIE---------------VVYEDDDVILCNKPCGLVVH 106

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHL 170
           +  SG +  +   +  ++  KG+          P L +R+D+ T+GI++ A+   + + L
Sbjct: 107 EDESGESDTLIDRILHYLYDKGEYDPDSELSFTPALCNRIDRNTAGIVICAKNAESLRIL 166

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK---GANYAI 227
            +  + R ++K Y  +  G+PK K     +  LK  H   +    VK  +K   G    I
Sbjct: 167 NQKVKDRELEKKYLCVTVGVPKAK-----SAELKAYHRRNEQTKTVKVADKPFDGCKTMI 221

Query: 228 SHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           + +KV++   Q     LE+   TGRTHQ+R H  H+GCP++GD KY  N
Sbjct: 222 TRYKVLEENKQSGLALLEVDLVTGRTHQIRAHLAHIGCPLLGDGKYGIN 270


>gi|254526037|ref|ZP_05138089.1| pseudouridylate synthase, 23S rRNA-specific [Prochlorococcus
           marinus str. MIT 9202]
 gi|221537461|gb|EEE39914.1| pseudouridylate synthase, 23S rRNA-specific [Prochlorococcus
           marinus str. MIT 9202]
          Length = 319

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 91/321 (28%), Positives = 148/321 (46%), Gaps = 42/321 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNH 76
           MRLDRW  +  P  +   +Q  + SG V V+ K  K    +++G  ++I  PP    L +
Sbjct: 27  MRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNIQIWMPPP-EPLIY 85

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +  E+  L+               +L+ED  I V NK +G+ V    G      ++G L 
Sbjct: 86  LKPEKMDLN---------------ILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLF 130

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++TSG +VVA+++ A  +L +  + +   + Y +++ G 
Sbjct: 131 HCKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGA 190

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           P +++  I        +IG D ++ +K     E    YA +++K+ + F   +  +  + 
Sbjct: 191 PNSEEGQIV------GNIGRDKLNRLKYKVVEETSGRYACTYWKLEERFGN-YSLMSFKL 243

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            TGRTHQ+RVH  H+  PIVGD  Y  C            +   LHA  + L HP  G+ 
Sbjct: 244 DTGRTHQIRVHCAHINHPIVGDPLYGRCKKLPCKL-----DGQALHAIKLGLIHPINGKE 298

Query: 306 QI-TAPLPAHMVKTWDSLGFK 325
            I  + LP    K    L  K
Sbjct: 299 MIFKSELPLDFQKLLSVLKVK 319


>gi|91762258|ref|ZP_01264223.1| pseudouridylate synthase [Candidatus Pelagibacter ubique HTCC1002]
 gi|91718060|gb|EAS84710.1| pseudouridylate synthase [Candidatus Pelagibacter ubique HTCC1002]
          Length = 326

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 88/326 (26%), Positives = 161/326 (49%), Gaps = 38/326 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V  DE N+RLD +       I+   ++ ++        K+++K N++I +    ++  
Sbjct: 7   LIVGEDENNLRLDVFINKRENLISRSRIKNLIL-------KEKLKINDQIINSPSKKVLS 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
             + +N  I E K  ++S+   K  +F K  ++YED  + + NKPAGI +  G+G     
Sbjct: 60  G-DEINLQIPEPK--EASL---KPYNF-KLQIVYEDDDLLIINKPAGIIMHPGAGNYDET 112

Query: 125 IAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           I   +  + K  + + G   +P + HR+D++TSG++V+A+     ++L+  F    I ++
Sbjct: 113 IVNALMHYNKDSLSTIGDELRPGIVHRIDKDTSGLIVIAKNNETHENLSHQFSEHTITRV 172

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ---- 238
           Y  L+WG  +     I  ++ + S    +   +   N KG   AI+++K I+ F      
Sbjct: 173 YQLLIWGKLRPSSGKIDTFITRSSK---NRQMMEVSNSKGK-RAITNYKTIEIFENDKTP 228

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLY------L 290
               +E +  TGRTHQ+RVH  HMG  I+GD  +K       N  + ++N +Y      L
Sbjct: 229 TLSLVECRLETGRTHQIRVHMTHMGNSIMGDGKYKKKYKKLKNIDTNLENLIYKLDRQFL 288

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHM 315
           HA+ +   HP    ++  T+ LP  +
Sbjct: 289 HAQTLGFIHPRTNEKMVFTSILPQEL 314


>gi|331696640|ref|YP_004332879.1| RluA family pseudouridine synthase [Pseudonocardia dioxanivorans
           CB1190]
 gi|326951329|gb|AEA25026.1| pseudouridine synthase, RluA family [Pseudonocardia dioxanivorans
           CB1190]
          Length = 312

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/319 (26%), Positives = 149/319 (46%), Gaps = 27/319 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +  + MR+D         ++   +  +   G+V VD +    ++R+ +G  + I    
Sbjct: 11  VPDGLDGMRVDAGLSRLL-GLSRTVVATLAEEGRVAVDGRAAGKSDRLAAGGWLEI---- 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
             L    +E   +   V +          +L+ED  I V +KP G++     G     + 
Sbjct: 66  -ELPDPERESDGITGPVEVVA-----GLTILHEDDDIVVVDKPVGVAAHPSPGWTGPTVV 119

Query: 131 GFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           G L +    V + G   R  + HRLD  T+G++VVA++ +A   L  +F+ R + K Y +
Sbjct: 120 GGLAALGVRVATSGAAERQGIVHRLDAGTTGVMVVAKSESAYSELKRAFKERTVDKRYHA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G P   +  I   + +  H   D+   V +   G   +++H+  I+ F +    L++
Sbjct: 180 VVQGHPDPSRGTIDAPIDR--HPRHDWRFAVVE---GGRPSVTHYDTIEAF-RAASLLDI 233

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP-EGG 303
           +  TGRTHQ+RVH   M  P VGD  Y A+        +  ++ +LHAR +   HP +G 
Sbjct: 234 RLETGRTHQIRVHFSAMRHPCVGDLTYGADP--TLAKRLHLDRQWLHARELGFAHPADGR 291

Query: 304 RLQITAPLPAHMVKTWDSL 322
           R++ T+P PA + +  D L
Sbjct: 292 RVEFTSPYPADLARALDLL 310


>gi|194015109|ref|ZP_03053726.1| YhcT [Bacillus pumilus ATCC 7061]
 gi|194014135|gb|EDW23700.1| YhcT [Bacillus pumilus ATCC 7061]
          Length = 302

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 71/222 (31%), Positives = 113/222 (50%), Gaps = 20/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +L+ED  + +  KPAG       QG +G   ++  F     + + ++ R  HRLDQ+TSG
Sbjct: 85  VLFEDEHLLIVQKPAGRPTHPNEQGQTGTLANLVAF-HFQANGEEKRVRHIHRLDQDTSG 143

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            ++ A+ R A   L +    + I++ Y ++  G+ K KK  I       + IG D  H V
Sbjct: 144 TVIFAKHRLAHAALDQMLSKKTIKRTYIAIAEGLFKKKKGTI------DAAIGRDKHHAV 197

Query: 217 KQN-EKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           ++        A++HF+V+D   + +   +++Q  TGRTHQ+RVH   +G P+ GD  Y  
Sbjct: 198 RRRISPNGQKAVTHFQVMDMNKRLQLTAVKLQLETGRTHQIRVHLSSLGHPLAGDTLY-- 255

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
               +      N+  LHA+ +D+ HP  G  L I APLP  M
Sbjct: 256 ----DGVRDYINRCALHAKQVDMKHPFTGEHLIIEAPLPPDM 293


>gi|167745608|ref|ZP_02417735.1| hypothetical protein ANACAC_00300 [Anaerostipes caccae DSM 14662]
 gi|167654920|gb|EDR99049.1| hypothetical protein ANACAC_00300 [Anaerostipes caccae DSM 14662]
          Length = 305

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 83/321 (25%), Positives = 141/321 (43%), Gaps = 31/321 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V   E   RLD      +P      LQK+ +   V VD    K N +++ G+ V     
Sbjct: 8   TVSQKETGSRLDVCLAGRFPEFTRSYLQKLCKDSAVLVDDAEKKSNYKVREGERV----- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                 I+K  K  + S+   K    +   ++YED  I + NKP  + V    G      
Sbjct: 63  ------ILKVPKPTELSIKPEK----MDLDIVYEDRDIILINKPKNMVVHPAPGHYEGTL 112

Query: 129 IDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++G ++   D         +P + HR+D++T+GIL+V +   A Q L E  +   I + Y
Sbjct: 113 VNGLMEHCRDELSGINGVLRPGIVHRIDKDTTGILIVCKNDMAHQCLAEQLKDHTITRRY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V    K +   +   + +      D   +    E G   A++H++V++   + F ++
Sbjct: 173 HAIVCHNIKEESGTVDAPIARSRK---DRKKMAIDREAGRR-AVTHYRVLERLKEGFTYI 228

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E +  TGRTHQ+RVH   +G P++GD  Y    K  ++   Q    LHA+ +   HP   
Sbjct: 229 ECRLETGRTHQIRVHMASIGHPLLGDTVYGPK-KSKYSLEGQ---CLHAKVLGFTHPRTK 284

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             ++    LPA+  +    LG
Sbjct: 285 EYMEFEVGLPAYFEELLKRLG 305


>gi|326560261|gb|EGE10649.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis 7169]
 gi|326570229|gb|EGE20274.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis BC8]
 gi|326570966|gb|EGE20990.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis BC7]
          Length = 355

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 81/316 (25%), Positives = 147/316 (46%), Gaps = 32/316 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD+   + +   +  NL+K +  GQ+ V+ K VK    ++ G ++ +  V 
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVKPKYAVKVGDILTLEAVH 107

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            + +  + E   +D               ++YED  + + NKPAG+ V  G+G      +
Sbjct: 108 ESHSEDLPENIDID---------------IIYEDEAVIIINKPAGMVVHPGAGNRTGTLV 152

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +  L  +   +   PR  L HR+D++T+G+LV+ART++A   L +  + + + + Y  + 
Sbjct: 153 NALLYHF-PKQAHLPRAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIA 211

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQ 246
            G      E + +  +    IG    H  K   K     A++H        +++  L++ 
Sbjct: 212 LGA---VHEVLRHAQIDAP-IGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIH 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHP 300
             TGRTHQ+RVH  ++G P+VGD  Y  + +   +   +       +  LHA  +   HP
Sbjct: 268 LKTGRTHQIRVHLSYVGHPLVGDPVYGTSPRSGLSDRQRCAILDFGRQALHAYMLGFIHP 327

Query: 301 -EGGRLQITAPLPAHM 315
             G  ++  APLP  M
Sbjct: 328 VTGEAMKFHAPLPKDM 343


>gi|317479385|ref|ZP_07938519.1| RNA pseudouridylate synthase [Bacteroides sp. 4_1_36]
 gi|316904459|gb|EFV26279.1| RNA pseudouridylate synthase [Bacteroides sp. 4_1_36]
          Length = 511

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 103/207 (49%), Gaps = 19/207 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + V NKPAG+    G   A  +   ++     +   P   HRLD  TSG++++
Sbjct: 309 IVYEDPWLSVINKPAGMLSVPGKEDAVSVYSLMREQY-PEADSPLTVHRLDMATSGLMLI 367

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+T+   Q+L   F+ R ++K Y +L+ GI PK+K        L         VH     
Sbjct: 368 AKTKRVHQNLQAQFKNRLVRKRYVALLEGIVPKDKGTVDLPLCLNPLDRPRQMVHT---- 423

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANF 276
           E G   AI+ ++V++    K   +   P TGRTHQLR+HA H   + CPI+GD  Y    
Sbjct: 424 EHG-KPAITDYQVLERLDGKRTRIVFYPRTGRTHQLRIHAAHPLGLHCPIIGDELYGEK- 481

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
                    ++LYLHA Y++  HP  G
Sbjct: 482 --------ADRLYLHAEYLEFTHPITG 500


>gi|157691654|ref|YP_001486116.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
 gi|157680412|gb|ABV61556.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
          Length = 302

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 71/222 (31%), Positives = 113/222 (50%), Gaps = 20/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +L+ED  + +  KPAG       QG +G   ++  F     + + ++ R  HRLDQ+TSG
Sbjct: 85  VLFEDEHLLIVQKPAGRPTHPNEQGQTGTLANLVAF-HFQANGEEKRVRHIHRLDQDTSG 143

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            ++ A+ R A   L +    + I++ Y ++  G+ K KK  I       + IG D  H V
Sbjct: 144 TVIFAKHRLAHAALDQMLSKKTIKRTYIAIAEGLFKKKKGTI------DAAIGRDKHHAV 197

Query: 217 KQN-EKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           ++        A++HF+V+D   + +   +++Q  TGRTHQ+RVH   +G P+ GD  Y  
Sbjct: 198 RRRISPTGQKAVTHFQVMDVNKRLQLTAVKLQLETGRTHQIRVHLSSLGHPLAGDTLY-- 255

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
               +      N+  LHA+ +D+ HP  G  L I APLP  M
Sbjct: 256 ----DGVREYINRCALHAKQVDMKHPFTGEHLIIEAPLPPDM 293


>gi|325856422|ref|ZP_08172138.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
 gi|325483606|gb|EGC86578.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
          Length = 255

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 113/231 (48%), Gaps = 20/231 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I +  K AG  VQG       +   ++ W+  K QKP      + HRLD+  S
Sbjct: 33  VLYEDNHIIIVYKEAGEIVQGDKSGDEPLSETVRRWIKEKYQKPGNVFLGIVHRLDRPVS 92

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV-- 213
           G+++ A+T  A   L   FR   + K YW++V   P   +  + +WL++       Y   
Sbjct: 93  GLVIFAKTSKALARLNNMFRNGEVHKTYWAIVTRPPFEPEATLTDWLVRNERQNKSYAYN 152

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H V  ++K    +I H+K+I+  + ++  LE+   TGR HQ+R    +M CPI GD KY 
Sbjct: 153 HQVPTSKK----SILHYKIIN-RSDRYTLLEINLMTGRHHQIRCQLSNMDCPIKGDLKY- 206

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
               G   S     + L +  ++  HP     ++I +PLP   +  W ++G
Sbjct: 207 ----GAPRSNPDGSISLLSHRVEFVHPVSKENIRIESPLPDDTL--WHAIG 251


>gi|170768656|ref|ZP_02903109.1| pseudouridine synthase, RluA family [Escherichia albertii TW07627]
 gi|170122760|gb|EDS91691.1| pseudouridine synthase, RluA family [Escherichia albertii TW07627]
          Length = 219

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 74/216 (34%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VVLYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA Q L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAEQELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|261879207|ref|ZP_06005634.1| ribosomal large subunit pseudouridine synthase [Prevotella
           bergensis DSM 17361]
 gi|270334154|gb|EFA44940.1| ribosomal large subunit pseudouridine synthase [Prevotella
           bergensis DSM 17361]
          Length = 230

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 107/218 (49%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + +  K +G  VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHLIIVYKESGEIVQGDKTGDLPLSEIVKGYIKEKYHKPGAVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ ART  A   L + FR   + K YW++    P N    + NWL++ +     Y + 
Sbjct: 63  GLVIFARTSKALARLNDMFRRGDVHKTYWAITKNAPPNPMGTLTNWLVRNTKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI ++++I   ++ +  LE+   TGR HQ+R    HMGCP+ GD KY A 
Sbjct: 122 -DKEMPDSKKAILNYRLI-AHSENYNLLEIHLLTGRHHQIRCQLSHMGCPVKGDLKYGAK 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                 S     + L +R ++  HP   + + + +PLP
Sbjct: 180 -----RSNPDGSISLLSRRVEFTHPVSKKQIALNSPLP 212


>gi|237653787|ref|YP_002890101.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|237625034|gb|ACR01724.1| pseudouridine synthase, RluA family [Thauera sp. MZ1T]
          Length = 327

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 88/314 (28%), Positives = 135/314 (42%), Gaps = 35/314 (11%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI----PPVINA 73
            +RLD+      P  +   LQ  L+ G +RVD        ++  G+ V I    PP + A
Sbjct: 35  GLRLDQALARLLPQHSRSRLQGWLKEGWIRVDGASPDARRKVCGGECVEIDAPPPPEVTA 94

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
                     L   + L          ++YED  + V +KP G+ V  GSG      ++ 
Sbjct: 95  ---------ALPEDIPLA---------VVYEDEDLLVIDKPVGLVVHPGSGNWSGTLLNA 136

Query: 132 FLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            L       G  +  + HRLD++TSG++VVA+T AA   L    + R + + Y +LV G 
Sbjct: 137 LLHRNPALAGVPRAGIVHRLDKDTSGLMVVAKTLAAQTELVRQLQARTVGRHYRALVQG- 195

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHT 249
                  +       + IG       +    G    A++H++V + F  +   +E +  T
Sbjct: 196 ------ALTAGGTVDAPIGRHPTQRTRMAVVGNGRPAVTHYRVTERF-PRATLVECRLET 248

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  H+G  +VGD  Y A   G+       +  LHA  + L HP  G  ++  
Sbjct: 249 GRTHQIRVHMAHIGHALVGDPLYGARRCGDVRLDAFPRQALHAFRLGLTHPRSGEAMRWE 308

Query: 309 APLPAHMVKTWDSL 322
            PL A      D L
Sbjct: 309 VPLAADFAALLDEL 322


>gi|217968192|ref|YP_002353698.1| pseudouridine synthase, RluA family [Dictyoglomus turgidum DSM
           6724]
 gi|217337291|gb|ACK43084.1| pseudouridine synthase, RluA family [Dictyoglomus turgidum DSM
           6724]
          Length = 303

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 86/317 (27%), Positives = 152/317 (47%), Gaps = 41/317 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IPPVINAL 74
           E+ R+D++     P ++   +Q ++    ++V++K +K + +++ G  +   IPP +   
Sbjct: 13  ESERIDKYLSKKVP-LSRSQIQDLIEKELIKVNEKPIKNSYKVKLGDRIEVIIPPPVET- 70

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDG 131
                E K  D  + +           +YED  + + NKP G+ V    G  Y+   ++ 
Sbjct: 71  -----EVKPQDIPIEI-----------VYEDEDMVIINKPKGMVVHPAHG-HYNDTLVNA 113

Query: 132 FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    D  G     +P + HRLD++T+G+L++A+   + Q L+E  + R +++ YW+L 
Sbjct: 114 LLYRVKDLSGIGGELRPGIIHRLDKDTTGLLIIAKNDLSHQKLSEQLKNRTLRRTYWALC 173

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            G IP  +K   A   + +  I    + +V         AI++FKV++ F + +  +   
Sbjct: 174 EGEIPWEEKRIEAP--IGRHPINRKKMAIVPY----GKIAITNFKVLERF-KGYTLISAD 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
             TGRTHQ+RVH  H+G PIVGD  Y       F   ++ +L LHA+ +   HP  G  +
Sbjct: 227 LETGRTHQIRVHISHLGFPIVGDEVY-GRIDKKFG--VKGQL-LHAKKVSFIHPTKGIPM 282

Query: 306 QITAPLPAHMVKTWDSL 322
           +    LP    K    L
Sbjct: 283 EFEIDLPEEFKKVLTLL 299


>gi|182417977|ref|ZP_02949285.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum 5521]
 gi|237667420|ref|ZP_04527404.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum E4 str. BoNT E BL5262]
 gi|182378148|gb|EDT75683.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum 5521]
 gi|237655768|gb|EEP53324.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum E4 str. BoNT E BL5262]
          Length = 304

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/332 (25%), Positives = 158/332 (47%), Gaps = 56/332 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +E +R+D++  N +   +   +Q ++    V+V+ K +K N +++    + I  
Sbjct: 6   IKVDEQDEGLRIDKYLSNIFKDKSRSFIQGLIEKENVKVNSKTLKSNYKLKKADEIEI-- 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                  +I E +IL      +  ++ +   ++YED  + V NK  G+ V    G     
Sbjct: 64  -------MIPEPEIL------SVEAENIPIDIVYEDEDVIVVNKAQGMVVHPAPGNYNGT 110

Query: 125 ----IAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
               + YH      I+G ++         P + HR+D++TSGILV+A+   A   L+E  
Sbjct: 111 LVNALLYHCKDLSSINGVIR---------PGIVHRIDKDTSGILVIAKNDDAHNKLSEQL 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWL--LKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           +   +++ Y++L+ G  KN    I   L   KK  +    + +++  ++    A++H++V
Sbjct: 162 KDHSMKREYYALIEGRLKNNDGTIDKPLGRCKKDRLK---IGIIEDGKR----AVTHYEV 214

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLH 291
           ++ +   +  ++    TGRTHQ+RVH   +G P+VGD  Y   FK   F    Q    LH
Sbjct: 215 VERY-NGYTLVKCVLETGRTHQIRVHMASIGFPLVGDPLY--GFKRQKFKLEGQ---VLH 268

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           AR +   HP  G  ++ T+ LP +     + L
Sbjct: 269 ARTLGFIHPRTGEYMEFTSELPQYFCDLINKL 300


>gi|306821486|ref|ZP_07455089.1| RluA family pseudouridine synthase [Eubacterium yurii subsp.
           margaretiae ATCC 43715]
 gi|304550501|gb|EFM38489.1| RluA family pseudouridine synthase [Eubacterium yurii subsp.
           margaretiae ATCC 43715]
          Length = 300

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 75/267 (28%), Positives = 127/267 (47%), Gaps = 42/267 (15%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKS----ILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           NHII E+ ++   ++  K SD++       +L+ED  I +F+KPAGI          H++
Sbjct: 57  NHIISEKDVIKVVMHDEK-SDYISQEKNLDILFEDEDIIIFDKPAGIVSHPTKS---HLE 112

Query: 131 GFL---KSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +     W+  K     K R   RLD +TSGI+ +A+   +   L++ F   +IQK Y 
Sbjct: 113 NTMLNYAQWIFEKKNIESKVRFISRLDMDTSGIITIAKNAFSHYALSQGFLSDKIQKRYT 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--------ANYAISHFKVIDCF 236
           ++V G            +L  S   G     ++++E G           AI+H+K++   
Sbjct: 173 AIVSG---------DTSILSDS---GTIAEKIEKSEDGIKRIITDEGQEAITHYKIVK-R 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +K+  LE+   TGRTHQ+RVH  H+G PI+GD  Y  +        + ++  LH   ++
Sbjct: 220 GEKYSVLELLLETGRTHQIRVHLSHLGLPIIGDELYGGDM------SVMSRQALHCHSLE 273

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWDSL 322
           +  P    ++ +T+P P  M    D +
Sbjct: 274 IISPRSMEKISVTSPYPKDMQDIMDEI 300


>gi|182682370|ref|YP_001830530.1| RluA family pseudouridine synthase [Xylella fastidiosa M23]
 gi|182632480|gb|ACB93256.1| pseudouridine synthase, RluA family [Xylella fastidiosa M23]
 gi|307578653|gb|ADN62622.1| ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa subsp. fastidiosa GB514]
          Length = 327

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 89/347 (25%), Positives = 159/347 (45%), Gaps = 42/347 (12%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L  + +   V +     R D      +P  +   L + ++SG V ++   V+  + +  G
Sbjct: 5   LAGFSRQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVRPRDPVYGG 64

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           +VV +  + +     + +   LD               +LYED  ++V NKPAG+ V  G
Sbjct: 65  EVVWLQVMPDIRTDAVPQDIPLD---------------ILYEDEHVFVINKPAGLVVHPG 109

Query: 123 SGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +     +    PR  + HRLD++TSG++VVART  A   L E    
Sbjct: 110 AG---NPDGTLVNALLHRDPALAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSS 166

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R++ + Y ++V  +         N  +++       + V    ++    A++H+++ + F
Sbjct: 167 RQVHRQYLAVV--VSALVSGGTVNAAIERHPRDRLRMEVSDTGKE----AVTHYRLRERF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQ-----NKL 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y  +    KG   + +       + 
Sbjct: 221 -RAHTALECRLDTGRTHQIRVHMAHLRHPIVGDRLYGGSLKLPKGGTDALVAMLRGFKRQ 279

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  ++  HP     ++I AP+P  + +   +L  + D  L+ +R
Sbjct: 280 ALHAEVLEFLHPVRALPVRIVAPVPEDLCQLLAAL--REDSALFFER 324


>gi|289525702|emb|CBJ15183.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis Sweden2]
 gi|296435271|gb|ADH17449.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis E/150]
 gi|296438990|gb|ADH21143.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis E/11023]
 gi|297748789|gb|ADI51335.1| Ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis D-EC]
 gi|297749669|gb|ADI52347.1| Ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis D-LC]
          Length = 335

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 112/230 (48%), Gaps = 26/230 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +YED  + V NKP  + V    G         + + I   LK     +  +P + HRLD+
Sbjct: 92  VYEDDMMLVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDK 151

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSHIGG 210
           +TSG+L+  +TR A    +E F  ++++K+Y ++    P  ++    IA   LK+  +  
Sbjct: 152 DTSGLLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQERIHTRIARHPLKRKEMT- 210

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               V+  + +G   AI+H +V+     +   + + P TGRTHQLRVH  H+G PI+GD 
Sbjct: 211 ----VLSTHAEGGKEAITHCQVLATNG-RLSVVALYPETGRTHQLRVHMKHLGTPILGDP 265

Query: 271 KY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
            Y     NF+        +K  LHA  +   HPE   R+++   LP  M 
Sbjct: 266 VYGIPSINFRYGL-----DKQQLHAYSLVFAHPESAERVKLVTKLPDDMT 310


>gi|332360785|gb|EGJ38592.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK355]
          Length = 298

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 82/293 (27%), Positives = 141/293 (48%), Gaps = 37/293 (12%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL----LY 103
            D  R   N +I+ GQ++ +        + +KE  ++   ++  +  +++   +    +Y
Sbjct: 22  TDLSRSLANEQIKDGQIL-VNGQAKKAKYAVKEGDVVSYELSEPEVVEYVAEDIPLEIVY 80

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLDQET 154
           +D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D++T
Sbjct: 81  QDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRIDKDT 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG     
Sbjct: 138 SGLLMIAKNDQAHAALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRSEKD 191

Query: 215 VVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             KQ    KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y
Sbjct: 192 RKKQAVTAKG-KPALTRFQVLERFGD-YTLVELQLETGRTHQIRVHMAYIGHPVAGDEVY 249

Query: 273 CA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 KG+         +LHAR +   HP  G  L+ TA  PA   +T D L
Sbjct: 250 GPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEAPAIFQETLDKL 295


>gi|284048842|ref|YP_003399181.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
 gi|283953063|gb|ADB47866.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
          Length = 305

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 81/281 (28%), Positives = 130/281 (46%), Gaps = 21/281 (7%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILD----SSVNLTKHSDFLKSIL 101
            R+D  R    + IQ G+V R      A N  +KE  +        V+L    + +   +
Sbjct: 22  ARLDCTRSAVQHDIQEGRVTRNGKPAKA-NTKVKEGDVFQVQVLPPVDLEARPENIPLDI 80

Query: 102 LYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETS 155
           LYED  + V NKP G+ V   +G      ++  L    D  G     +P + HRLD++TS
Sbjct: 81  LYEDQDVIVVNKPRGMVVHPAAGNPDGTLVNALLYHCRDLSGINGVIRPGIVHRLDKDTS 140

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+   A   L E  + +  ++ Y ++V G  K+ +  I   L +          V
Sbjct: 141 GVMICAKNDRAHLSLAEQIQKKEAKRTYLAIVRGNIKDDRGHIETQLDRDPRDRKKMAVV 200

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                 G  +A + ++V++ +  KF  +  +  TGRTHQ+RVH  ++G P+VGD KYC  
Sbjct: 201 ----PSGGRWAATDYEVLERYG-KFTVVRCRLLTGRTHQIRVHMTYIGHPLVGDPKYCPQ 255

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            K  F+    N   LH+  +   HP  G  +   AP+P  M
Sbjct: 256 -KTCFSI---NGQALHSEQLTFRHPRTGEWMTFRAPVPEDM 292


>gi|317503596|ref|ZP_07961617.1| ribosomal large subunit pseudouridine synthase [Prevotella salivae
           DSM 15606]
 gi|315665288|gb|EFV04934.1| ribosomal large subunit pseudouridine synthase [Prevotella salivae
           DSM 15606]
          Length = 221

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 71/220 (32%), Positives = 109/220 (49%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  K +G  VQG       +   +K ++  K QKP      + HRLD+  S
Sbjct: 3   VVYEDNHLIVVYKASGEIVQGDKTGDEPLSDTVKRYLKEKYQKPGNVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV-- 213
           G++V A+T  A   L + FR   + K YW+L    P   +  + NWL++       YV  
Sbjct: 63  GLVVFAKTSKALTRLNKMFREGEVHKTYWALTKNNPSQPEATLTNWLVRNEKQNKSYVYD 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H V +++K    AI  ++VI   ++ +  LE+   TGR HQ+R     MGCPI GD KY 
Sbjct: 123 HEVPRSKK----AILSYRVI-GRSEHYSLLEVNLMTGRHHQIRSQLAAMGCPIKGDLKYG 177

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
           A       S     + L +R+++  HP    L  + +PLP
Sbjct: 178 AQ-----RSNPDGSISLLSRHVEFVHPVSKTLISLDSPLP 212


>gi|165933873|ref|YP_001650662.1| ribosomal large subunit pseudouridine synthase D [Rickettsia
           rickettsii str. Iowa]
 gi|165908960|gb|ABY73256.1| ribosomal large subunit pseudouridine synthase D [Rickettsia
           rickettsii str. Iowa]
          Length = 313

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 84/322 (26%), Positives = 149/322 (46%), Gaps = 52/322 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD+   +   +++   +QK ++  QV V+              ++  P V+   N II
Sbjct: 13  IRLDKALSSLLENVSRNQIQKAIKDSQVLVND------------VIISDPDVLVKENDII 60

Query: 79  -------KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +E KI  ++V L          ++YED  + V NK AG++V  G+G  +H D 
Sbjct: 61  LFSFKEPEELKIAAANVALD---------IIYEDDDLIVINKAAGMTVHPGAG--HHDDT 109

Query: 132 FLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + + +            ++P + HRLD++T+G++VVA+   A   L      +++ + Y
Sbjct: 110 LVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQKQVIRKY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCW 242
             LVWG+  N  E +    + +S      + ++K    G   A++H+K ++ F +     
Sbjct: 170 KVLVWGVI-NPLEGVIKNNIGRSRSDRQKMTILKY---GGKEAVTHYKTLELFYKGSISM 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLY------LHARY 294
           +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP  ++ KL       LH+ Y
Sbjct: 226 VECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAYSPPELKAKLIDFKRQALHSWY 285

Query: 295 MDLPHPEGGR-LQITAPLPAHM 315
           +   HP     ++ +  LP  M
Sbjct: 286 LSFTHPTSNEIMEFSCELPRDM 307


>gi|311748762|ref|ZP_07722547.1| ribosomal large subunit pseudouridine synthase D [Algoriphagus sp.
           PR1]
 gi|126577297|gb|EAZ81545.1| ribosomal large subunit pseudouridine synthase D [Algoriphagus sp.
           PR1]
          Length = 344

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 73/277 (26%), Positives = 134/277 (48%), Gaps = 32/277 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++  ++N+R+D++      +     +Q+ + +G V V+ K  K N +I+    +++  
Sbjct: 22  ISIDKGQKNIRIDKFLSEKLANATRNKVQQAIDAGSVLVNGKPTKANYKIKPMDDIKV-- 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                   + E+   D+ V    + + ++  ++YED  + + NKPAG+ V    G     
Sbjct: 80  --------MMEKPPRDTEV----YPEKIELDIIYEDKYLLIVNKPAGMVVHPAHGNWSGT 127

Query: 125 ----IAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               + YH     +   + KG   +P L HR+D++TSG+LV+A+   A  HL   F    
Sbjct: 128 LANALVYH----FQDLPEMKGNEGRPGLVHRIDKDTSGLLVIAKQEEAMTHLASQFFHHT 183

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y +LVWG PK  +  I    + +S      + V    E+G  +AI+H+KV+    +
Sbjct: 184 IDRTYIALVWGEPKEDEGTIEGN-VGRSAKNRKVMDVFPDGEQG-KHAITHWKVLKRL-R 240

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               ++    TGRTHQ+R H  ++G P+  D  Y  +
Sbjct: 241 YVSLIQCNLETGRTHQIRAHMKYIGHPLFNDAMYGGD 277


>gi|315651236|ref|ZP_07904266.1| RluA family pseudouridine synthase [Eubacterium saburreum DSM 3986]
 gi|315486532|gb|EFU76884.1| RluA family pseudouridine synthase [Eubacterium saburreum DSM 3986]
          Length = 338

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 77/274 (28%), Positives = 129/274 (47%), Gaps = 13/274 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ +V EN E   RLDR  +  + + +   + K+LR   + +D KR     R+++G  ++
Sbjct: 2   VEIIVGEN-ESGQRLDRVLEKIFVNADTGFIFKMLRKKNITLDDKRADGKERLKTGSSIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKH---SDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +     +   + K+  +  S     K    SD  KS ++YED    + NKPAG+  Q   
Sbjct: 61  MWFSDESFEKLTKKTCLAPSGKIKNKDNKVSDVFKSYIIYEDENTIIINKPAGLLSQKSQ 120

Query: 124 GIAYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  L  ++          KP + +RLD+ TSG+LV  ++    +   E  + R 
Sbjct: 121 INDISVNDMLLEYLKFDENALHTFKPSICNRLDRNTSGLLVCGKSLEGLRVNNELIKTRA 180

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y ++V G   N+K  I+ WL K      + V +       A+Y  + +K I  F  
Sbjct: 181 VKKYYLAIVKG-RVNEKCAISGWLYKDEKT--NKVSIKNNKFDKADYIETEYKPIGYF-D 236

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               L ++  TG+THQ+R H   M  PI+GD KY
Sbjct: 237 DITLLSVKLITGKTHQIRAHLASMAHPIIGDFKY 270


>gi|225076527|ref|ZP_03719726.1| hypothetical protein NEIFLAOT_01575 [Neisseria flavescens
           NRL30031/H210]
 gi|224952206|gb|EEG33415.1| hypothetical protein NEIFLAOT_01575 [Neisseria flavescens
           NRL30031/H210]
          Length = 374

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 141/310 (45%), Gaps = 38/310 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+++ +            
Sbjct: 40  RLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQPKDKMIGGELIAV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFTPEPMDLDIIYEDDTVIVINKPAGLVVHPAAGNWSGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P + 
Sbjct: 145 SELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   AI+H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAITHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C++        +  +  LHA  +   HP+ G  +
Sbjct: 256 HQIRVHMREANHPLAADPVYGNLRHPCSDAVKEAIKALGARQALHAYRLSFVHPKTGETV 315

Query: 306 QITAPLPAHM 315
              AP+P  M
Sbjct: 316 SFEAPMPDDM 325


>gi|84688066|ref|ZP_01015925.1| ribosomal large subunit pseudouridine synthase D [Maritimibacter
           alkaliphilus HTCC2654]
 gi|84663916|gb|EAQ10421.1| ribosomal large subunit pseudouridine synthase D [Rhodobacterales
           bacterium HTCC2654]
          Length = 344

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 98/357 (27%), Positives = 150/357 (42%), Gaps = 78/357 (21%)

Query: 20  RLDRWFKNHYPHI---------NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           RLD+      P             +    ++R+G+V  D K      ++  G+V+ I   
Sbjct: 17  RLDKALARDVPEAANLSRSRLAKLIAEGAVMRAGEVLTDAK-----AKVTEGEVIEITVP 71

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-- 128
           +   +H+  E   LD               +++ED  + V NKPAG+ V    G      
Sbjct: 72  VAEESHMRPEAIALD---------------VVWEDHDLIVVNKPAGMVVHPAPGTPSGTL 116

Query: 129 IDGFLKSWVDS----KGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L    D      G+K P + HR+D++TSG+LVVA+T AA   L   F    +++ Y
Sbjct: 117 VNALLHHCGDDLSGVGGEKRPGIVHRIDKDTSGLLVVAKTDAAHHGLAAQFEKHTVERHY 176

Query: 184 WSLVWGIPKNKKECIANWLLKK----SHIGGDYVHVVKQNEK-------------GANYA 226
            +LV+G+P      +A+  LK     S   G  V +  Q  +             G  +A
Sbjct: 177 RALVYGMPD-----LADPRLKGVRGVSFEQGGIVKITTQLARHKTDRQKQAVTWSGGRHA 231

Query: 227 ISHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN- 279
           I+  +V++ F +        CWLE    TGRTHQ+RVH  H G  +VGD  Y    K + 
Sbjct: 232 ITRARVVETFGRPPSVSLLDCWLE----TGRTHQIRVHMAHAGHGLVGDPVYGGRRKPSE 287

Query: 280 --FTSPIQNKLY------LHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
               +     L+      LHA  +   HP    +L+  A LP  M    + LG K D
Sbjct: 288 SALGAEAAKALWGFERQALHAATLGFEHPVTKEQLRFEARLPDDMAGLIEVLGAKPD 344


>gi|15605391|ref|NP_220177.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis D/UW-3/CX]
 gi|255349046|ref|ZP_05381053.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 70]
 gi|255503584|ref|ZP_05381974.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 70s]
 gi|255507264|ref|ZP_05382903.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis D(s)2923]
 gi|3329108|gb|AAC68253.1| Pseudouridine Synthase [Chlamydia trachomatis D/UW-3/CX]
          Length = 334

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 112/230 (48%), Gaps = 26/230 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +YED  + V NKP  + V    G         + + I   LK     +  +P + HRLD+
Sbjct: 91  VYEDDMMLVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDK 150

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSHIGG 210
           +TSG+L+  +TR A    +E F  ++++K+Y ++    P  ++    IA   LK+  +  
Sbjct: 151 DTSGLLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQERIHTRIARHPLKRKEMT- 209

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               V+  + +G   AI+H +V+     +   + + P TGRTHQLRVH  H+G PI+GD 
Sbjct: 210 ----VLSTHAEGGKEAITHCQVLATNG-RLSVVALYPETGRTHQLRVHMKHLGTPILGDP 264

Query: 271 KY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
            Y     NF+        +K  LHA  +   HPE   R+++   LP  M 
Sbjct: 265 VYGIPSINFRYGL-----DKQQLHAYSLVFAHPESAERVKLVTKLPDDMT 309


>gi|296533864|ref|ZP_06896396.1| ribosomal large subunit pseudouridine synthase C [Roseomonas
           cervicalis ATCC 49957]
 gi|296265811|gb|EFH11904.1| ribosomal large subunit pseudouridine synthase C [Roseomonas
           cervicalis ATCC 49957]
          Length = 236

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 71/225 (31%), Positives = 105/225 (46%), Gaps = 16/225 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L +   + V +KPAG+ V  G      ++  L +    K   P+  HRLD +T+G LV+
Sbjct: 23  ILLQTEAVLVIDKPAGLPVHRGPRGGASLEDHLPALAQGKRHWPQPAHRLDTDTAGCLVL 82

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            RT+ A   L   F   R +K YW++V G P  +   I   L K S     +      + 
Sbjct: 83  GRTKPALAALGRLFAEGRARKTYWAVVRGGPAAQSGRIDLPLRKTSSAATGWRMEAHPD- 141

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A++ ++V         WLE++P TGRTHQLRVH    G PI+GD  Y     G  
Sbjct: 142 --GQPALTRWRVRG-RGPGLAWLELRPETGRTHQLRVHCASQGWPILGDPFYGTKAPGG- 197

Query: 281 TSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
                  L+L AR ++LP  P    L  TAP+P  +   + + G+
Sbjct: 198 -------LHLLARAIELPLDPP---LSATAPVPPALRDAFAACGW 232


>gi|85373063|ref|YP_457125.1| pseudouridine synthase D large subunit [Erythrobacter litoralis
           HTCC2594]
 gi|84786146|gb|ABC62328.1| pseudouridine synthase D large subunit [Erythrobacter litoralis
           HTCC2594]
          Length = 322

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 82/257 (31%), Positives = 127/257 (49%), Gaps = 31/257 (12%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--DSKG 141
           L  +V+       +K  +++ED  + V NKPAG+ V   +G   + DG L + +    +G
Sbjct: 73  LPPTVDPEAQPQDIKLDVVFEDEHLLVVNKPAGMVVHPAAG---NPDGTLVNALLHHCRG 129

Query: 142 Q--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           Q        +P + HR+D++TSG+LVVA+T  A + L   F    I + Y +L  G P N
Sbjct: 130 QLSGINGVARPGIVHRIDKDTSGLLVVAKTDNAHEGLAAQFAEHTINRRYLALCAGHP-N 188

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----DCFAQKFCWLEMQPHT 249
             E      + +S      +  + ++     +A++H+K +    DC A   C LE    T
Sbjct: 189 PAEGTIEGRIGRSERDRKKMAPLPEDSSRGKHAVTHYKTLRRLRDC-ALIECRLE----T 243

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-----YLHARYMDLPHPEGGR 304
           GRTHQ+RVH   +G P++GD  Y  + KG    PI  +L      LHA  +   HP  G+
Sbjct: 244 GRTHQVRVHCQSIGHPLLGDPTYGRDPKG--LRPILKELGFARQALHAAMLGFEHPVTGQ 301

Query: 305 -LQITAPLPAHMVKTWD 320
            ++ TA LPA M +  D
Sbjct: 302 WVEFTADLPADMQELID 318


>gi|293977792|ref|YP_003543222.1| pseudouridine synthase, RluA family [Candidatus Sulcia muelleri
           DMIN]
 gi|292667723|gb|ADE35358.1| pseudouridine synthase, RluA family [Candidatus Sulcia muelleri
           DMIN]
          Length = 314

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 94/307 (30%), Positives = 152/307 (49%), Gaps = 37/307 (12%)

Query: 9   YVVVENDEENM-RLDRWFKN--HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Y   +  +EN+ R+D + K   H  + NF+  QKI+  G V V+      N  I+   +V
Sbjct: 3   YFFYDKKKENLIRIDTYIKFILHKKNRNFI--QKIIEKGFVYVN------NILIKKNYIV 54

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           +I  VI        E  + +   N+   +  LK  + YED  + + NK +G+ V  G G 
Sbjct: 55  KINDVI--------EIFLPEGKKNIIPEN--LKINIFYEDEYVIIINKQSGLVVHPGKGN 104

Query: 125 -IAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                I+G    ++  K    + P L HR+D+ TSG+++VA+ +   + +++ F +  I+
Sbjct: 105 ESMTLINGLHFYFLKKKNIYNKIPILVHRIDKGTSGLILVAKDKNILEKISKQFYINHIK 164

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           + Y +LVWG I  NK   I N  + +S     Y++V      G  ++I+H+KV++ F + 
Sbjct: 165 RKYITLVWGYIKNNKGTIICN--IGRSLKNRIYMNVFPNGIYGK-FSITHYKVLERF-KY 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF----KGNFTSPIQNKLY--LHAR 293
              L+    TGRTHQ+RVH  ++G PI+ D  Y  N     K N      N  Y  LHA 
Sbjct: 221 VTLLKCTLETGRTHQIRVHLKYIGHPILNDKDYGGNHTFKEKKNIKKLFINMKYQALHAY 280

Query: 294 YMDLPHP 300
           Y++  HP
Sbjct: 281 YIEYIHP 287


>gi|253576492|ref|ZP_04853821.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251844129|gb|EES72148.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 256

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 68/223 (30%), Positives = 105/223 (47%), Gaps = 15/223 (6%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +DS    T     +   +LYED+ +    KP  I  Q  +     +   LK+ +  +  K
Sbjct: 1   MDSEAKRTSGQPAMA--ILYEDNHLLGIEKPVNIPTQEDASGDPDLLNLLKADIKERYGK 58

Query: 144 PR-----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           P      L HRLD+   G ++ A+T  AA  L E  R RR  K Y ++V G P  ++  +
Sbjct: 59  PGNVYLGLVHRLDRPVGGAMIFAKTSKAASRLAEMVRSRRFSKTYVAVVHGTPPQRQGHL 118

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRV 257
            + LLK      + V VV     G   A   ++V+   A ++   ++++ HTGR HQ+RV
Sbjct: 119 TDTLLKDERT--NTVSVVPAGTSGGKEARLDYRVLGTSASERLSLVQVELHTGRPHQIRV 176

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
               +GCP+ GD KY A        P Q ++ L + Y+  PHP
Sbjct: 177 QMSQIGCPLYGDQKYGA----GRNKPGQ-QIALWSLYVGFPHP 214


>gi|315612946|ref|ZP_07887857.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis ATCC 49296]
 gi|315315056|gb|EFU63097.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis ATCC 49296]
          Length = 299

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 87/308 (28%), Positives = 149/308 (48%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G  R+DK         R   N +I++GQV+ +   +    +I++E  I+   V   +
Sbjct: 5   IETGGQRLDKALSDLTELSRSLANEQIKAGQVL-VNGQVKKAKYIVQEGDIVAYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   L    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAENLPLEIIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F+V++ F   +  LE+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFQVLERFGD-YSLLELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG+         +LHA+ +   HP  G  L+ TA +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGETLEFTADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKETLERL 293


>gi|166033157|ref|ZP_02235986.1| hypothetical protein DORFOR_02879 [Dorea formicigenerans ATCC
           27755]
 gi|166027514|gb|EDR46271.1| hypothetical protein DORFOR_02879 [Dorea formicigenerans ATCC
           27755]
          Length = 249

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 69/198 (34%), Positives = 100/198 (50%), Gaps = 17/198 (8%)

Query: 90  LTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK---SWVDSKGQKPR 145
           +TK  D + +I +LYED++I V  KPAG++ Q     +  +   LK   S    K  +P 
Sbjct: 14  ITKEYDMINNINILYEDTQILVCVKPAGVATQSKRIGSPDMVSLLKNHISMTSGKSGEPY 73

Query: 146 LT--HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           L   HRLDQ  SGILV A+T AAA+ L          K Y++LV G P+     + N+L+
Sbjct: 74  LAVIHRLDQPVSGILVFAKTPAAAKDLNRQLTTSGFGKHYYALVAGTPEPTSADLENFLV 133

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--FAQ-------KFCWLEMQPHTGRTHQ 254
           K +        + ++    A  A  H+ ++D   FA            L+++  TGR HQ
Sbjct: 134 KDARTNTS--RICQKGTADAKLAKLHYDLVDTTFFADIASSIPVATSQLKIKLDTGRHHQ 191

Query: 255 LRVHALHMGCPIVGDHKY 272
           +RV    MGCPI+GD KY
Sbjct: 192 IRVQLSGMGCPIIGDTKY 209


>gi|313886881|ref|ZP_07820585.1| putative ribosomal large subunit pseudouridine synthase D
           [Porphyromonas asaccharolytica PR426713P-I]
 gi|312923678|gb|EFR34483.1| putative ribosomal large subunit pseudouridine synthase D
           [Porphyromonas asaccharolytica PR426713P-I]
          Length = 374

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 88/336 (26%), Positives = 146/336 (43%), Gaps = 46/336 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+DR+  +  PH +   +Q   ++G + VD + VK N +++  + + +  
Sbjct: 47  VQVDPGQTPLRIDRFLVDRMPHTSRHRIQLAAKAGLIWVDGEPVKSNYKVKPLETITM-- 104

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L H  ++  I    + L          ++YED ++ V NKPAG+ V  G G     
Sbjct: 105 ---MLAHPKQDWSITPEDIPLD---------IVYEDDQLLVVNKPAGMVVHPGHGNYSGT 152

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +AY++        D       L HR+D++TSG+L+VA+   A   L   F ++   
Sbjct: 153 LVHALAYYLRN--DPLYDPNDASVGLVHRIDKDTSGLLLVAKRTEAKIRLARQFFLKTTG 210

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--- 237
           + Y +LVWG     +  I   + +              +E G   A++H+  ++      
Sbjct: 211 RRYQALVWGKLDQPQGTIEGNIARDPRDRTRMTVYPPTSEIGKP-AVTHYTQLERLGFVT 269

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN--------- 286
              C LE    TGRTHQ+R H   +  P+ GD +Y  +    G  TS  Q          
Sbjct: 270 LIACELE----TGRTHQIRAHMKSIDHPLFGDERYGGDQILWGQRTSSYQQFVNNCLKIC 325

Query: 287 -KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            +  LHA  +   HP  G R+  +APLP  M +  D
Sbjct: 326 PRQALHAETLAFDHPTTGERMHFSAPLPDDMRQLID 361


>gi|118602363|ref|YP_903578.1| ribosomal large subunit pseudouridine synthase D [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
 gi|118567302|gb|ABL02107.1| ribosomal large subunit pseudouridine synthase D [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
          Length = 314

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 94/348 (27%), Positives = 155/348 (44%), Gaps = 53/348 (15%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSL++    V++ N     R+D       P+ + V +   ++SG   +  K  K   ++ 
Sbjct: 1   MSLLS----VIIPNRFIGQRIDAAMAQMLPNYSRVKITYWIKSGDALIHHKTFKPKEKVL 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+V+ +   I   N  + +  ++D               ++YED  I + NKP  +   
Sbjct: 57  GGEVITLSIKIEKTNAWLAQDIVID---------------VVYEDEAIIIVNKPVNLVTH 101

Query: 121 GG--------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
            G        +    H D  L + +D  G    + HRLD+ TSG++VVAR+  A ++LT 
Sbjct: 102 PGVSNWTGTLANALLHYDSSLAN-LDRAG----IVHRLDKNTSGLMVVARSEYAQKYLTR 156

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHF 230
             +   I + Y ++V+G        I+   + K  IG D    ++Q   E G + A++H+
Sbjct: 157 QLQTHSISREYSAIVYG------HMISGGTVDKP-IGRDPKDRIRQTVTESGKD-ALTHY 208

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKL 288
           +VI+ FA     +++   TGRTHQ+RVH   +G P++ D  Y     F       ++N L
Sbjct: 209 RVIERFAH-HTHVKVMLETGRTHQIRVHLSFIGHPLIADPMYGGKIRFPKKADKQLKNSL 267

Query: 289 ------YLHARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSLGFKYDRN 329
                  LHA+ + L HP    L     PLP  M      L  K+D N
Sbjct: 268 KNFNRQTLHAKKLTLIHPTSTELMSWKVPLPQDMQDLLQVLA-KFDAN 314


>gi|332299970|ref|YP_004441891.1| pseudouridine synthase, RluA family [Porphyromonas asaccharolytica
           DSM 20707]
 gi|332177033|gb|AEE12723.1| pseudouridine synthase, RluA family [Porphyromonas asaccharolytica
           DSM 20707]
          Length = 376

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 88/336 (26%), Positives = 146/336 (43%), Gaps = 46/336 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+DR+  +  PH +   +Q   ++G + VD + VK N +++  + + +  
Sbjct: 49  VQVDPGQTPLRIDRFLVDRMPHTSRHRIQLAAKAGLIWVDGEPVKSNYKVKPLETITM-- 106

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L H  ++  I    + L          ++YED ++ V NKPAG+ V  G G     
Sbjct: 107 ---MLAHPKQDWSITPEDIPLD---------IVYEDDQLLVVNKPAGMVVHPGHGNYSGT 154

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +AY++        D       L HR+D++TSG+L+VA+   A   L   F ++   
Sbjct: 155 LVHALAYYLRN--DPLYDPNDASVGLVHRIDKDTSGLLLVAKRTEAKIRLARQFFLKTTG 212

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--- 237
           + Y +LVWG     +  I   + +              +E G   A++H+  ++      
Sbjct: 213 RRYQALVWGKLDQPQGTIEGNIARDPRDRTRMTVYPPTSEIGKP-AVTHYTQLERLGFVT 271

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN--------- 286
              C LE    TGRTHQ+R H   +  P+ GD +Y  +    G  TS  Q          
Sbjct: 272 LIACELE----TGRTHQIRAHMKSIDHPLFGDERYGGDQILWGQRTSSYQQFVNNCLKIC 327

Query: 287 -KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            +  LHA  +   HP  G R+  +APLP  M +  D
Sbjct: 328 PRQALHAETLAFDHPTTGERMHFSAPLPDDMRQLID 363


>gi|326576921|gb|EGE26827.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis O35E]
          Length = 355

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 81/316 (25%), Positives = 147/316 (46%), Gaps = 32/316 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD+   + +   +  NL+K +  GQ+ V+ K VK    ++ G ++ +  V 
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVKPKYAVKVGDILTLEAVH 107

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            + +  + E   +D               ++YED  + + NKPAG+ V  G+G      +
Sbjct: 108 ESHSEDLPENIDID---------------IIYEDEAVIIINKPAGMVVHPGAGNRTGTLV 152

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +  L  +   +   PR  L HR+D++T+G+LV+ART++A   L +  + + + + Y  + 
Sbjct: 153 NALLYHF-PKQAHLPRAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCVA 211

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQ 246
            G      E + +  +    IG    H  K   K     A++H        +++  L++ 
Sbjct: 212 LGA---VHEVLRHAQIDAP-IGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIH 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHP 300
             TGRTHQ+RVH  ++G P+VGD  Y  + +   +   +       +  LHA  +   HP
Sbjct: 268 LKTGRTHQIRVHLSYVGHPLVGDPVYGTSPRSGLSDRQRCAILDFGRQALHAYMLGFIHP 327

Query: 301 -EGGRLQITAPLPAHM 315
             G  ++  APLP  M
Sbjct: 328 VTGEAMKFHAPLPKDM 343


>gi|237734795|ref|ZP_04565276.1| ribosomal large subunit pseudouridine synthase D [Mollicutes
           bacterium D7]
 gi|229382123|gb|EEO32214.1| ribosomal large subunit pseudouridine synthase D [Coprobacillus sp.
           D7]
          Length = 316

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/321 (26%), Positives = 157/321 (48%), Gaps = 35/321 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++E D  N+RLD+        ++   +Q ++  G V V++K+ K + + +    + I  
Sbjct: 16  LIIEEDN-NLRLDKVIAMQLQELSRTQIQDMINQGLVLVNQKKEKASYKTKLNDEIEI-- 72

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                        ILD+ V+L    + +   ++YED  + V +KP G+ V   +GI +  
Sbjct: 73  ------------TILDN-VDLDIEPEDISLKIVYEDEDVIVVDKPTGMIVHPSAGIMHGT 119

Query: 129 -IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HR+D+ETSG+L+VA+   A + L++  +   + + Y
Sbjct: 120 LVNALLFHCKDLSGINGVNRPGIVHRIDKETSGLLMVAKNDNAHRLLSKQLKDHTVVRRY 179

Query: 184 WSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            +LV G IP    +  A   + ++      + V + N K A   +++F V+  +      
Sbjct: 180 VALVHGLIPHEHGKVDAP--IGRNPKDRQSMAVTRTNSKEA---VTNFTVLKRY-NAMSL 233

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+RVH  ++G P+ GD KY    K +F+    +  +LHA+ +   HP  
Sbjct: 234 IECRLETGRTHQIRVHMSYIGYPVYGDPKYGYR-KDDFS----HGQFLHAKKLGFIHPTT 288

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
            + ++  +PLP +     D L
Sbjct: 289 QKYMEFESPLPDYFQAKLDEL 309


>gi|114775487|ref|ZP_01451055.1| possible pseudouridine synthase [Mariprofundus ferrooxydans PV-1]
 gi|114553598|gb|EAU55979.1| possible pseudouridine synthase [Mariprofundus ferrooxydans PV-1]
          Length = 325

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 88/336 (26%), Positives = 143/336 (42%), Gaps = 43/336 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV--KFNNRIQSGQ--VV 65
           + V  +    RLD         ++   +Q +LR G VR     V  + + R+  G+  ++
Sbjct: 13  ITVSTEASGKRLDAVLAAAC-ELSRSRIQTLLREGHVRTAGGSVISQASARVWEGERYLL 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +PPV   +  +  E   LD               +L+ED  + V NKPAGI V    G 
Sbjct: 72  TLPPVKPLI--LEPEDLPLD---------------ILFEDEHLIVLNKPAGIVVHPSHGH 114

Query: 125 ----IAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + + +    K+     G ++P + HRLD++TSG LV+A++    Q L+E F    +
Sbjct: 115 DHGTLVHALLHHCKTLPGINGVERPGIVHRLDKDTSGSLVIAKSEVVHQRLSEMFAEHNL 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y +   G+P  + +CI   + +  H            E   + A+ H      F   
Sbjct: 175 NRQYIAWCRGVPSWRVKCIELPIGRHPHQRQKMAVTDSGRESITDAAVEHI-----FG-P 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNKLYLH 291
           F  + +  HTGRTHQ+RVH  H   P++GD  Y  ++      P          ++  LH
Sbjct: 229 FSQMRLTLHTGRTHQIRVHMAHENLPVLGDPVYARSYHPGREIPEPARHAIATLSRQALH 288

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           A  ++  HP  G  +   APLP  +    D+L   Y
Sbjct: 289 AELLEFDHPISGEPMSFRAPLPEDLTILHDALTKSY 324


>gi|261364920|ref|ZP_05977803.1| ribosomal large subunit pseudouridine synthase D [Neisseria mucosa
           ATCC 25996]
 gi|288566705|gb|EFC88265.1| ribosomal large subunit pseudouridine synthase D [Neisseria mucosa
           ATCC 25996]
          Length = 374

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 84/311 (27%), Positives = 142/311 (45%), Gaps = 40/311 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLMPDYSRSRLTSWIKEGAVIVNDKPAQPKDKMIGGESISV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFKPEAMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P + 
Sbjct: 145 PELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YLHARYMDLPHPEGGR- 304
           HQ+RVH      P+  D  Y  N +   + P++  +        LHA  +   HP+ G  
Sbjct: 256 HQIRVHMREANHPLAADPVY-GNLRHPCSEPVKEAVKSLGARQALHAYRLSFVHPKTGET 314

Query: 305 LQITAPLPAHM 315
           +   AP+P  M
Sbjct: 315 VSFEAPIPEDM 325


>gi|145294446|ref|YP_001137267.1| hypothetical protein cgR_0401 [Corynebacterium glutamicum R]
 gi|140844366|dbj|BAF53365.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 294

 Score =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 91/324 (28%), Positives = 155/324 (47%), Gaps = 62/324 (19%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI- 67
           ++ V     + R+D++ +     ++   + + +R G +RV+ ++V  N R+Q G  +R+ 
Sbjct: 5   FIEVSAGHADRRIDKFLRAQLKGVSASLIFRQMRKGDIRVNGRKVDPNYRLQEGDRIRMW 64

Query: 68  ---------PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
                    PPV++   HI K   + DS              +L+ED+++ V NKPAGI 
Sbjct: 65  QMDLPADLPPPVVD--KHIFK--AVADS--------------VLFEDAELLVINKPAGIP 106

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           V GG+G    +   L+     + +   L HRLD++TSG+L+V++T +  + L E  R R 
Sbjct: 107 VHGGTGHGGGVIEALRQKFPQE-RDLELVHRLDRDTSGLLLVSKTTSVLRELQEILRDR- 164

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLK-KSHIGGDYVHV---VKQNE------KGANYAIS 228
                          ++E    +LLK +    GD   +   +K+ E           A +
Sbjct: 165 ---------------EEEIFRGYLLKVEGAWPGDLRQIDVPLKRTETTVVPHSDGLRART 209

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
           +F+V+         ++ Q  TGR HQ+RVHA + G PIVGD +Y +  +G   +     +
Sbjct: 210 YFEVVKRLPGA-TLVKAQLATGRKHQIRVHAQYAGHPIVGDPRYGS--RGGRAA----TM 262

Query: 289 YLHARYMDLPHPEGGRLQITAPLP 312
           +LHA  + +P   G R + TAPLP
Sbjct: 263 HLHAAELVVPRGAGKRQKFTAPLP 286


>gi|313675550|ref|YP_004053546.1| ribosomal large subunit pseudouridine synthase d [Marivirga
           tractuosa DSM 4126]
 gi|312942248|gb|ADR21438.1| ribosomal large subunit pseudouridine synthase D [Marivirga
           tractuosa DSM 4126]
          Length = 343

 Score =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 82/325 (25%), Positives = 158/325 (48%), Gaps = 41/325 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  ++ +R+D++  +  P++    +QK ++ G V+V+   +K N ++     +RI  
Sbjct: 21  IKVDPKQDLLRIDKFLMDRLPNVTRNKVQKAIKDGFVQVNGVTIKPNYKVHPDDNIRI-- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
              AL    ++ ++   ++ L          ++YEDS + + NK AG+ V          
Sbjct: 79  ---ALPEPPRDTEVKPENIPLD---------IVYEDSDLLIVNKEAGMVVHPAHQNWEGT 126

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             + +AYH    L     ++G +P L HR+D++TSG+LV+A+T  +   L + F    I+
Sbjct: 127 LVNALAYHFQQ-LPEMQGNEG-RPGLVHRIDKDTSGLLVIAKTEKSMTALAKQFFDHSIE 184

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y++LVWG  ++++  I +  L +S           + + G   AI+H+KV++   +  
Sbjct: 185 RTYYALVWGELEDEEGTI-DVNLGRSFKDRRITDAFPEGDFGRT-AITHYKVLERL-RYV 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN------KL 288
             ++    TGRTHQ+R H  ++G P+  D  Y  +   KG     + S + N      + 
Sbjct: 242 TLIQCNLETGRTHQIRAHMKYIGHPLFNDATYGGDRILKGTQFSKYKSFVDNCFKIIPRQ 301

Query: 289 YLHARYMDLPHPEGGR-LQITAPLP 312
            LHA+ +   HP   + +   + LP
Sbjct: 302 ALHAKSLGFIHPSSNKSVHFESELP 326


>gi|110677435|ref|YP_680442.1| ribosomal large subunit pseudouridine synthase A [Roseobacter
           denitrificans OCh 114]
 gi|109453551|gb|ABG29756.1| ribosomal large subunit pseudouridine synthase A [Roseobacter
           denitrificans OCh 114]
          Length = 215

 Score =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 111/219 (50%), Gaps = 25/219 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED+++ + +KPAG+    G G   H+   L + V +      L HRLD++TSG+++ 
Sbjct: 14  VLHEDAEVLLVDKPAGLLSVPGKGP--HLADCLLARVQAMFADALLVHRLDRDTSGVMIF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A T  A +HL   F  R  +K Y + VWG+P +K        I +W  +   +      V
Sbjct: 72  ALTPHAQRHLGLQFEKRMTRKTYVARVWGVPCDKTGTVDLPLIVDWPNRPRQM------V 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K A    + ++V+    Q    + + PHTGR+HQLRVH   +G PI+GD  Y   
Sbjct: 126 CHETGKPAQ---TEWRVLKDDGQT-ARMRLHPHTGRSHQLRVHMRALGHPILGDPFYATG 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAPL 311
              ++      +L LH+  +   HP+GGR   ++ TAP 
Sbjct: 182 PARDYP-----RLMLHSEELRFKHPQGGRSMKVRATAPF 215


>gi|89098727|ref|ZP_01171609.1| ribosomal large subunit pseudouridine synthase D [Bacillus sp. NRRL
           B-14911]
 gi|89086689|gb|EAR65808.1| ribosomal large subunit pseudouridine synthase D [Bacillus sp. NRRL
           B-14911]
          Length = 301

 Score =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 91/329 (27%), Positives = 152/329 (46%), Gaps = 38/329 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++Y++ E +    RLD+        ++    Q++++ G + V+ +  K N +     
Sbjct: 1   MEKMEYIINE-EVAGERLDKAVSLLNEELSRSQAQQMIKDGHILVNGQGTKTNYKCSIDD 59

Query: 64  VVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            + I  P    L+ ++ E+  LD               + YED  + V NKP G+ V   
Sbjct: 60  KIEISFPEPEELD-VLPEEMDLD---------------IYYEDGDVLVVNKPKGMVVHPA 103

Query: 123 SGIAYH--IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G A    ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      
Sbjct: 104 PGHASGTLVNGLMAHCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVE 163

Query: 177 RRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           + + + Y ++V G IP +     A   L +       + VV     G  +A++HF VI  
Sbjct: 164 KTVTRKYQAIVHGTIPHDYGTVDAP--LGRDPKDRQSMTVVD----GGKHAVTHFHVIHR 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           + + F  +E Q  TGRTHQ+RVH  ++G P+ GD KY        T  I  +  LHA  +
Sbjct: 218 Y-KDFTHVECQLETGRTHQIRVHMKYIGYPLAGDPKYGP----RKTLEIGGQA-LHAGVL 271

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              HP  G  ++  APLPA+  +  + LG
Sbjct: 272 GFVHPRTGEYMEFEAPLPAYFSELLEKLG 300


>gi|313891514|ref|ZP_07825127.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
 gi|313120091|gb|EFR43270.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
          Length = 307

 Score =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 95/327 (29%), Positives = 154/327 (47%), Gaps = 52/327 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  ++ MRLD++ K                SG  R + ++      I+ G  + +P  +
Sbjct: 8   VDEKQDGMRLDQFLKE--------------VSGLTRSEVQKW-----IKEGYAISLPNRM 48

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFL----KSILLYEDSKIYVFNKPAGISVQGGSG--- 124
              N+ I +++ +  S    K  + +    K  +LYED  I V NK  G+ V  G+G   
Sbjct: 49  VRSNYHISDKEKIQFSWEEKKEIELIPQKIKLDILYEDEHIIVINKSRGMVVHPGAGNID 108

Query: 125 ------IAYHI-DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 + YH  +  LK     +  +P + HRLD++TSG++V  ++  A + +       
Sbjct: 109 NTLVNALLYHCGESLLKV---GEKTRPGIVHRLDKDTSGVMVAVKSDIAYEKVKNEIATH 165

Query: 178 RIQKIYWSLVWGI---PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             ++ Y +LV G    P  K +      LK      D +    Q + G N AI+HF V++
Sbjct: 166 EAKRTYLTLVHGQMEGPDGKIDLPLGRSLK------DRMKWDVQPKTGKN-AITHFHVLE 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F  K+  LE +  TGRTHQ+RVH  ++G P++ D  Y    K NF  PIQ +  LH+  
Sbjct: 219 -FMTKYSLLECKLETGRTHQIRVHMSYIGHPVINDPLY-GRKKDNF--PIQGQA-LHSFT 273

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWD 320
           ++L HP  G+ ++  APLP  M K  +
Sbjct: 274 LELKHPLTGKIMKFEAPLPEDMKKCLE 300


>gi|160934208|ref|ZP_02081595.1| hypothetical protein CLOLEP_03079 [Clostridium leptum DSM 753]
 gi|156866881|gb|EDO60253.1| hypothetical protein CLOLEP_03079 [Clostridium leptum DSM 753]
          Length = 319

 Score =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 75/282 (26%), Positives = 133/282 (47%), Gaps = 34/282 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  ++   RLD++    Y  +    L K +R+  ++++ KR + ++RIQ G ++ +  
Sbjct: 4   ITVGKNDAGQRLDKFLTKTYTKLPQSMLYKGIRTKNIKLNGKRCQISSRIQEGDIISL-- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI----LLYEDSKIYVFNKPAGISVQGGSGI 125
                   +KE+    +        DFLK+      +YED  I + NK  G+ V      
Sbjct: 62  -------YLKEEFFEQTPTEY----DFLKAPKVVDCVYEDENILLLNKKPGLLVHPDEN- 109

Query: 126 AYHIDGFL---KSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            YH D  +   + ++  KG+          P L +R+D+ TSGI++ A+   A + L + 
Sbjct: 110 -YHFDSLIARVQHYLYEKGEYQPQNENSFAPALVNRIDRNTSGIVIAAKNAEALRILNDK 168

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R R + K Y  +V G  + K + +  +L K      + V++  +   GA    + ++ +
Sbjct: 169 MRKRELHKYYLCVVHGKMEKKSDLLVGYLEKNE--SKNRVYISARPFPGAKTIQTKYRTL 226

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               +K+  LE+   TGRTHQ+R H   +G P+VGD KY  N
Sbjct: 227 QQ-KEKYSLLEVDLLTGRTHQIRAHMASIGHPLVGDGKYGKN 267


>gi|167755826|ref|ZP_02427953.1| hypothetical protein CLORAM_01342 [Clostridium ramosum DSM 1402]
 gi|167704765|gb|EDS19344.1| hypothetical protein CLORAM_01342 [Clostridium ramosum DSM 1402]
          Length = 306

 Score =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 85/321 (26%), Positives = 157/321 (48%), Gaps = 35/321 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++E D  N+RLD+        ++   +Q ++  G V V++K+ K + + +    + I  
Sbjct: 6   LIIEEDN-NLRLDKVIAMQLQELSRTQIQDMINQGLVLVNQKKEKASYKTKLNDEIEI-- 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                        ILD+ V+L    + +   ++YED  + V +KP G+ V   +GI +  
Sbjct: 63  ------------TILDN-VDLDIEPEDISLKIVYEDEDVIVVDKPTGMIVHPSAGIMHGT 109

Query: 129 -IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HR+D+ETSG+L+VA+   A + L++  +   + + Y
Sbjct: 110 LVNALLFHCKDLSGINGVNRPGIVHRIDKETSGLLMVAKNDNAHRLLSKQLKDHTVVRRY 169

Query: 184 WSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            +LV G IP    +  A   + ++      + V + N K    A+++F V+  +      
Sbjct: 170 VALVHGLIPHEHGKVDAP--IGRNPKDRQSMAVTRTNSK---EAVTNFTVLKRY-NAMSL 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+RVH  ++G P+ GD KY    K +F+    +  +LHA+ +   HP  
Sbjct: 224 IECRLETGRTHQIRVHMSYIGYPVYGDPKYGYR-KDDFS----HGQFLHAKKLGFIHPTT 278

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
            + ++  +PLP +     D L
Sbjct: 279 QKYMEFESPLPDYFQAKLDEL 299


>gi|241760159|ref|ZP_04758257.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           flavescens SK114]
 gi|241319613|gb|EER56043.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           flavescens SK114]
          Length = 374

 Score =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 141/310 (45%), Gaps = 38/310 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+++ +            
Sbjct: 40  RLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQPKDKMIGGELIAV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFTPEPMDLDIIYEDDAVIVINKPAGLVVHPAAGNWSGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   AI+H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAITHVKVLERYLS-HSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C++        +  +  LHA  +   HP+ G  +
Sbjct: 256 HQIRVHMREANHPLAADPVYGNLRHPCSDAVKEAIKALGARQALHAYRLSFVHPKTGETV 315

Query: 306 QITAPLPAHM 315
              AP+P  M
Sbjct: 316 AFEAPMPDDM 325


>gi|332976359|gb|EGK13213.1| ribosomal large subunit pseudouridine synthase D [Desmospora sp.
           8437]
          Length = 270

 Score =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 84/277 (30%), Positives = 136/277 (49%), Gaps = 46/277 (16%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           +R  +VRVD + VK N+R+Q G+ V +  PP         +E ++   ++ L        
Sbjct: 1   IREHRVRVDGRIVKSNHRLQGGEQVEVAVPPP--------EEAEVKPEALPLE------- 45

Query: 99  SILLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGFLKSWVDSKG----QKPRLTHRLDQ 152
             +++ED  + + NKP G+ V    GS     ++  L    D  G     +P + HR+D+
Sbjct: 46  --VVFEDGDVIMVNKPRGMVVHPAPGSPSGTLVNALLAHCDDLSGIGGVLRPGIVHRIDK 103

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGD 211
           +TSG+++VA+   A + L    +   + + Y +LV G IP ++    A        IG D
Sbjct: 104 DTSGLIMVAKNDFAHRSLAAQLKNHTVDREYTALVQGNIPHDRGTVDAP-------IGRD 156

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPI 266
             H  +     +    A++HF+VI+ F++     C LE    TGRTHQ+RVH   +G P+
Sbjct: 157 PHHRKRMAVEHRHGKPAVTHFEVIERFSRATLIRCRLE----TGRTHQIRVHMKSIGHPL 212

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           VGD  Y   ++ +F  PI  +  LHAR +   HP  G
Sbjct: 213 VGDPVYSTRYR-DF--PIDGQ-ALHARLLGFDHPRTG 245


>gi|326803607|ref|YP_004321425.1| putative ribosomal large subunit pseudouridine synthase D
           [Aerococcus urinae ACS-120-V-Col10a]
 gi|326650706|gb|AEA00889.1| putative ribosomal large subunit pseudouridine synthase D
           [Aerococcus urinae ACS-120-V-Col10a]
          Length = 315

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 84/311 (27%), Positives = 142/311 (45%), Gaps = 42/311 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           ++++RLDR+        +   + + +++GQV+V+K+ VK + R+     + +        
Sbjct: 11  DQSLRLDRYLSQRLDSYSRSEIAQWIKTGQVKVNKQVVKPSYRLNPMDKISLA------- 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
            I +EQK       L    + L   ++YED  + V NK  G+ V    G   H+ G L +
Sbjct: 64  -IEEEQK-------LPIEGESLDLDIVYEDKDLLVINKAKGMVVHPSKG---HLSGTLVN 112

Query: 136 WVDSKGQK-------------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            + +  QK             P + HRLD++TSG++VVA++  A Q L E     ++ + 
Sbjct: 113 ALLAYAQKNHFTLSDLGDYYRPGIVHRLDKDTSGLMVVAKSDPAYQALLEDLANHQLDRK 172

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L++G   +K+  I   L +       YV      +     A++HFK I    + +  
Sbjct: 173 YLALIYGHLPDKQGTIDIPLRRHPKDRMRYV-----GDPLGKEAVTHFKQI-AQVENYAL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-- 300
           L +   TGRTHQ+R H  ++  P+V D  Y   ++  F S  Q    LHA  +   HP  
Sbjct: 227 LRLSLETGRTHQIRAHLAYLDHPVVDDPLYAKAYQQRFFS--QQGQCLHAYGLSFNHPIT 284

Query: 301 -EGGRLQITAP 310
            E    Q+  P
Sbjct: 285 KEKLSFQVKPP 295


>gi|253996250|ref|YP_003048314.1| RluA family pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253982929|gb|ACT47787.1| pseudouridine synthase, RluA family [Methylotenera mobilis JLW8]
          Length = 368

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 90/316 (28%), Positives = 149/316 (47%), Gaps = 47/316 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +T + ++ + +D   +RLD   +   P  +   LQ  ++SG V VD K      ++  G+
Sbjct: 9   LTNLIHLTISSDLGGLRLDVALQRLLPEHSRSRLQSWIKSGLVTVDGKASTAKTKVWGGE 68

Query: 64  VVRIPPVINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V +   +   +     Q I LD               ++YED  I V NKPAG+ V   
Sbjct: 69  KVSVDVQVKPESRAFIAQDIPLD---------------IVYEDDHILVVNKPAGMVVHPA 113

Query: 123 SGIAYHIDGFLKSWVDSKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +     +    PR  + HRLD+ETSG+LVVA+T  A  HL    + 
Sbjct: 114 AG---NWDGTLLNALLFHAPQLHDVPRAGIVHRLDKETSGLLVVAKTLNAQTHLVRQLQA 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDC 235
           R +++ Y ++VWG      +   N ++ +  +G D     K    +    AI+ +++++ 
Sbjct: 171 RTVKREYRAIVWG------QLWRNGVVDQP-LGRDPRSRTKMAINRMGKPAITRYEILER 223

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-----NFTSPIQNKL-- 288
           F+ +  +L     TGRTHQ+RVH  H+  P+VGD  Y   F+G       T  +++ +  
Sbjct: 224 FSVQ-TYLRCNLETGRTHQIRVHMQHLKAPLVGDPVY--GFRGIVPIRAMTQTLRDAVSQ 280

Query: 289 ----YLHARYMDLPHP 300
                LHA  + L HP
Sbjct: 281 FHRQALHAIKLGLVHP 296


>gi|56696292|ref|YP_166649.1| ribosomal large subunit pseudouridine synthase D [Ruegeria pomeroyi
           DSS-3]
 gi|56678029|gb|AAV94695.1| ribosomal large subunit pseudouridine synthase D [Ruegeria pomeroyi
           DSS-3]
          Length = 342

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 92/363 (25%), Positives = 150/363 (41%), Gaps = 72/363 (19%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQ 60
           T +++V+        RLD+      P    ++   L +++  G V VD + V     R+ 
Sbjct: 4   TRLEFVIAAAPPP--RLDKALSRDVPETAALSRTRLARLITEGAVSVDGQVVTDPKARVV 61

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  V I       +HI  E   L               +++YED  + V +KPAG+ V 
Sbjct: 62  EGAQVAIALTEAEESHIAPEAIPL---------------VVVYEDDDLIVIDKPAGMVVH 106

Query: 121 GGSGIAYH--IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              G      ++  L    D+       ++P + HR+D++TSG+LVVA++ AA   L   
Sbjct: 107 PAPGTPSGTLVNALLAHCGDNLSGVGGVKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAAQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK------------ 221
           F     ++ Y +L +G+P      +   +   S   G+ + +  Q  +            
Sbjct: 167 FAAHSAERHYTALCYGVPDGSDPRL-RGVKGASFEPGNILRLTTQLTRHPTDRQRQAVVF 225

Query: 222 -GANYAISHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            G  +A++  +V++ F Q        CWLE    TGRTHQ+RVH  H G  ++GD  Y  
Sbjct: 226 HGGRHAVTRARVVESFGQPAAVSLIDCWLE----TGRTHQIRVHMAHAGHGLLGDPVYGG 281

Query: 275 NFK--------------GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
             K              G F      +  LHA  +   HP  G +L  +APLP  + +  
Sbjct: 282 RRKLSPRALSPEAVDAIGAFP-----RQALHAAVLGFEHPLSGEKLSFSAPLPDDLERLL 336

Query: 320 DSL 322
           + L
Sbjct: 337 EVL 339


>gi|332292825|ref|YP_004431434.1| pseudouridine synthase [Krokinobacter diaphorus 4H-3-7-5]
 gi|332170911|gb|AEE20166.1| pseudouridine synthase [Krokinobacter diaphorus 4H-3-7-5]
          Length = 232

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/218 (33%), Positives = 105/218 (48%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK +G  VQG       +   +K ++  K  KP      + HRLD+ TS
Sbjct: 13  VIYEDNHIIVINKRSGDIVQGDKTGDAPLSEVVKKYIAIKYDKPGAVYLGVVHRLDRPTS 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V ART  A   L ++F  R  QK YW+LV   P  +   + ++L +       Y H 
Sbjct: 73  GIVVFARTSKALPRLNKAFAERETQKTYWALVKNPPPAESGTLIHYLKRNPKQNKSYAH- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K     +  AI  ++VI    + F  LE+  HTGR HQ+R     +G PI GD KY   
Sbjct: 132 -KHEVPDSKKAILDYRVIKKL-KTFFLLEIDLHTGRHHQIRAQLTAIGSPIKGDLKY--- 186

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             G   S     + L +R + L HP +   +  TA +P
Sbjct: 187 --GFDRSNPDGSISLLSRKLTLTHPVKKEEMTFTAEVP 222


>gi|256841173|ref|ZP_05546680.1| ribosomal large subunit pseudouridine synthase A [Parabacteroides
           sp. D13]
 gi|256737016|gb|EEU50343.1| ribosomal large subunit pseudouridine synthase A [Parabacteroides
           sp. D13]
          Length = 548

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 74/235 (31%), Positives = 121/235 (51%), Gaps = 29/235 (12%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L+H+++  ++ ++ +    H +  K  +LYED  + V NKP G+    G G    +D   
Sbjct: 315 LHHMLQGLRVDENPLLADSHRE-TKLDILYEDDYLLVINKPEGMLSVPGKG---DVDSVY 370

Query: 134 K--SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-I 190
           +  S +  +   P + HRLD  TSG+L+ A+T+ A Q+L   F+ R IQK Y +L+ G +
Sbjct: 371 QRLSILYPEATGPIIVHRLDMATSGLLLAAKTKEAHQNLQAQFKNRTIQKRYIALLEGEV 430

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           P+++ E        +  +  D +   +Q  +E+    A + ++V++  + K   +   P 
Sbjct: 431 PQDEGEI-------RLPLCPDPLDRPQQIVSEEFGKPAFTRYRVLERTSGK-TLIAFYPQ 482

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           TGRTHQLRVHA H   + CPI+GD  Y              +LYLHA Y+   HP
Sbjct: 483 TGRTHQLRVHAAHPLGLHCPILGDELYGRK---------AERLYLHAEYLAFTHP 528


>gi|212634509|ref|YP_002311034.1| pseudouridylate synthase [Shewanella piezotolerans WP3]
 gi|212555993|gb|ACJ28447.1| Pseudouridylate synthase [Shewanella piezotolerans WP3]
          Length = 217

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 71/205 (34%), Positives = 104/205 (50%), Gaps = 14/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L Y D  I + NKP+G+      GIA +      S +  + +   L HRLD  TSG++V 
Sbjct: 16  LRYVDRDIIIINKPSGL--LSNPGIADYTHDCALSRIQQRFKDAILVHRLDCSTSGVMVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           AR + A  +L   F+ R+ QK Y + V G  +N +  I      +  I  D  +  KQ  
Sbjct: 74  ARNKKAESNLKTQFQDRKTQKTYITEVSGHLQNAQGVI------ELPITADKANPPKQQV 127

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 AI+HF+ ++  A     LE++P TGRTHQLRVH L +G PI+GD  Y      +
Sbjct: 128 SATGKVAITHFETLEVRANS-TLLELKPVTGRTHQLRVHLLAIGNPILGDDFYAEQHIVD 186

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR 304
            ++P   +L LHA+ +   HP  G+
Sbjct: 187 -SAP---RLKLHAQSLSFTHPYSGK 207


>gi|312886031|ref|ZP_07745658.1| ribosomal large subunit pseudouridine synthase D [Mucilaginibacter
           paludis DSM 18603]
 gi|311301488|gb|EFQ78530.1| ribosomal large subunit pseudouridine synthase D [Mucilaginibacter
           paludis DSM 18603]
          Length = 347

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/333 (24%), Positives = 152/333 (45%), Gaps = 42/333 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+D++  +   + +   +Q  +  G V V+ K +K + +++   V+ +  
Sbjct: 21  IVVDKGQSLLRIDKFLMHRVENASRNRIQNAIELGNVLVNDKAIKSSYKVKPLDVISV-- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
               L H  ++ ++   ++ L          ++YED  + V NKPAG+ V  G       
Sbjct: 79  ---VLPHPPRDTEVYPENIPLD---------IVYEDDDVLVVNKPAGLVVHPGYNNYTGT 126

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             +G+ YH    L +   + G +P L HR+D++TSG+L++++   +   L   F    I 
Sbjct: 127 LVNGLVYHFQQ-LPTLPGNDG-RPGLVHRIDKDTSGLLLISKNERSMTWLARQFYEHTIA 184

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG    + +      + +S      + +    EKG  ++++H++V+       
Sbjct: 185 RKYLALVWG--DLEIDGTVTGYIGRSIKDRRVMSIYDDPEKG-KWSVTHYRVLQRMTY-V 240

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKL 288
             +E +  TGRTHQ+R H  H+G P+  D  Y  +   KG   +           +  + 
Sbjct: 241 TLIECELETGRTHQIRAHMKHIGHPLFSDATYGGDHILKGTLFNKYKQFVENCFALMPRQ 300

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWD 320
            LHA+ +   HP    R+   APLP   V   +
Sbjct: 301 ALHAQTLGFVHPTARKRVHFEAPLPQDFVAVLE 333


>gi|283798031|ref|ZP_06347184.1| pseudouridine synthase, RluA family [Clostridium sp. M62/1]
 gi|291074333|gb|EFE11697.1| pseudouridine synthase, RluA family [Clostridium sp. M62/1]
          Length = 345

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 87/337 (25%), Positives = 148/337 (43%), Gaps = 38/337 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVN---LQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           ++ V V  +E   RLD+     + ++N      + K+LR   + ++ K+   + R+  G 
Sbjct: 1   MRLVTVTKNEAGQRLDKLL---FKYMNLAGKSFVYKMLRKKNITLNGKKCDGSERLLEGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+          + E+ I   S    +    +K  ++YED  +   NKPAG+  Q   
Sbjct: 58  EIRL---------FLSEETIEKFSEVRVQKVSRVKLEIVYEDEDVIFINKPAGMLSQKAR 108

Query: 124 GIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                +  +L +++   GQ         +P + +RLD+ TSG++   ++    Q L+   
Sbjct: 109 DGDESLVEYLITYLMESGQLTKEELKSFRPSVCNRLDRNTSGLVAAGKSLPGLQELSRII 168

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R I K Y  LV G  K     I  WLLK      + V V K+ E+G +  I       
Sbjct: 169 KDRSIGKYYLCLVKGQVKQPSR-IEGWLLKDERT--NRVEVTKE-ERGGSLPICTEYTPL 224

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLH 291
             +     L+++  TGR+HQ+R H   +GCP+VGD KY     N K      +  +L LH
Sbjct: 225 LRSGAHTLLKVKLITGRSHQIRAHLASIGCPVVGDRKYGDPAENRKAREQFGVTGQL-LH 283

Query: 292 ARYMDLPHPEGGRL------QITAPLPAHMVKTWDSL 322
           A  + +P    G L      +  APLP   +   +++
Sbjct: 284 AAELVMPGELSGPLCRLRGRKFAAPLPEAFLTMAEAV 320


>gi|163734280|ref|ZP_02141720.1| ribosomal large subunit pseudouridine synthase A [Roseobacter
           litoralis Och 149]
 gi|161392288|gb|EDQ16617.1| ribosomal large subunit pseudouridine synthase A [Roseobacter
           litoralis Och 149]
          Length = 215

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 68/219 (31%), Positives = 111/219 (50%), Gaps = 25/219 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED+++ + +KPAG+    G G   H+   L + V +      L HRLD++TSG+++ 
Sbjct: 14  VLHEDAEVLLVDKPAGLLSVPGKGP--HLADCLLARVQAMFADALLVHRLDRDTSGVMIF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A T  A +HL   F  R  +K Y + +WG+P  K        I +W  +   +      V
Sbjct: 72  ALTPHAQRHLGLQFEKRMTRKTYVARIWGVPLEKTGTVDLPLIVDWPNRPRQM------V 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K A    + ++V+    Q    + + P+TGR+HQLRVH L +G PI+GD  Y   
Sbjct: 126 CHETGKSAQ---TEWRVLKDDGQT-ARVRLHPYTGRSHQLRVHMLALGHPILGDPFYATG 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAPL 311
              ++      +L LH+  +   HP+GGR   ++ TAP 
Sbjct: 182 PARDYP-----RLMLHSEELRFKHPQGGRSMKVRATAPF 215


>gi|328948465|ref|YP_004365802.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
 gi|328448789|gb|AEB14505.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
          Length = 223

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 77/233 (33%), Positives = 114/233 (48%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E+ +I + NK  G+SVQGG+GIA+ +D  L   +   G K  L HRLD+ETSGILVV
Sbjct: 6   IIFENEEILLVNKEGGVSVQGGAGIAHPLDAELSIQL---GYKIFLVHRLDKETSGILVV 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+   AA   T      +++K Y ++ +GIP  + K+C +  L      G    H   Q 
Sbjct: 63  AKNAQAAAKWTNLISGGKVKKEYVAVCFGIPVVDGKKCYSGVLE-----GTVEAHGRTQA 117

Query: 220 EKGANYAISHFKVIDCFAQK---------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            K      + FKV   +  K           +L++   TGR HQ+R+      CPI GD 
Sbjct: 118 AK------TFFKVESVWNVKIPESEKELELSFLKLTLGTGRMHQIRIQLAKASCPIAGDD 171

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSL 322
           K+  +FK N  +       L    + L  P  G+ Q    PLP H+  T D++
Sbjct: 172 KH-GDFKKNKLARKIGIKKLQLASVKLSLPVDGKTQTFEIPLPEHIKTTLDNM 223


>gi|261879908|ref|ZP_06006335.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bergensis DSM 17361]
 gi|270333420|gb|EFA44206.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bergensis DSM 17361]
          Length = 367

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 89/334 (26%), Positives = 155/334 (46%), Gaps = 56/334 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++      H +   +Q    +G + V+ + VK N +++   V+ +  
Sbjct: 37  VQVDAGQAPLRIDKFLAERMQHSSRNRIQTAADAGCIFVNDRPVKSNYKVRPLDVITL-- 94

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
           ++    H        DS++    H++ +   ++YED  + V NK AG+ V  G+G     
Sbjct: 95  MLGRPKH--------DSTI----HAEDIPLDIVYEDRDLMVVNKKAGMVVHPGAGNFNGT 142

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H+        D       L HR+D++TSG+LVVA+T  A   L + F  +   
Sbjct: 143 LINAVAWHLRDL--DTFDPNDPNVGLVHRIDKDTSGLLVVAKTADAKTALGKQFYNKTTH 200

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDC 235
           + Y +LVWG P      +A+    + +IG D      + V   +      A++H++V++ 
Sbjct: 201 RSYHALVWGNP------VADEGRIEGNIGRDPKDRLRMKVFPPDSGIGKAAVTHYRVLER 254

Query: 236 FAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKG----NFTSPIQN 286
           F       C LE    TGRTHQ+R H  HMG P+  D +Y  C   +G     + + +QN
Sbjct: 255 FGYVTLVQCVLE----TGRTHQIRAHMKHMGHPLFCDERYGGCEILRGQRSTTYKAFVQN 310

Query: 287 ------KLYLHARYMDLPHPEGG-RLQITAPLPA 313
                 +  LHA+ +   HP  G ++   +  PA
Sbjct: 311 CFKLCPRQALHAKTLGFVHPRTGEQMDFDSEWPA 344


>gi|227510357|ref|ZP_03940406.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
 gi|227190009|gb|EEI70076.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
          Length = 303

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 90/321 (28%), Positives = 145/321 (45%), Gaps = 48/321 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E  RLD+      P I+    +K++  G + V+  + K     ++   + I  V     
Sbjct: 9   DELGRLDKIVSMLDPEISRSRAKKMIEDGDIIVNDSKKKPKYETKASDTLLIKDVKPETV 68

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL 133
            I  E   LD               ++YED  + V NKP G+ V   +G   H  ++  L
Sbjct: 69  SIKPENMPLD---------------IVYEDEDVIVVNKPQGMVVHPSAGHPNHTLVNALL 113

Query: 134 --KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                    G+ +P + HR+D++TSG+L+VA+   A + L++  + ++  + Y +LV G 
Sbjct: 114 FHSPLSSINGEYRPGIVHRIDKDTSGLLMVAKNDMAHKALSKQLKAKKNLRKYVALVHGR 173

Query: 191 PKNKKECIANWLL------KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            K     I   +       KK  I  D              AI+HF+V++ F Q +  +E
Sbjct: 174 IKEDSGVIKAPIARSPKDRKKQAIVAD-----------GRPAITHFEVMERF-QDYTLIE 221

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            +  TGRTHQ+RVH  ++G PIVGD  Y      KG+         +LHA+ +   HP  
Sbjct: 222 CRLETGRTHQIRVHMQYIGHPIVGDPLYGPKKTIKGHGQ-------FLHAQELGFEHPRT 274

Query: 303 GRLQI-TAPLPAHMVKTWDSL 322
            +L I +AP+P    KT  +L
Sbjct: 275 HQLMIFSAPIPEIFEKTLRTL 295


>gi|94676946|ref|YP_588650.1| ribosomal large subunit pseudouridine synthase D [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
 gi|94220096|gb|ABF14255.1| ribosomal large subunit pseudouridine synthase D [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
          Length = 319

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 85/296 (28%), Positives = 150/296 (50%), Gaps = 43/296 (14%)

Query: 43  SGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
            G+V+V D+  +  N +I  G++++I  +I       +E +    + N+  +       +
Sbjct: 43  EGKVKVNDQVTILPNKKILGGEIIKISVMIE------REHEQYWKAQNIALN-------I 89

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS----WVDSKGQKPR--LTHRLDQETS 155
           +YED  I V NKP  + V  G+G   ++DG + +    +  +    PR  + HRLD+ T+
Sbjct: 90  VYEDDDIIVINKPRDMVVHSGAG---NLDGTILNALLYYYPAIANVPRAGIVHRLDKNTT 146

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDY 212
           G+++V +T +A   L E  R R I + Y ++  GI  N    ++ IA    K++H+  + 
Sbjct: 147 GLMIVGKTLSAQTKLVELLRTRSIIREYEAITIGIINNDGTVEQPIARHATKRTHMTVNP 206

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +            AI+H+ +I+ F +    L ++  TGRTHQ+RVH  +M   +VGD  Y
Sbjct: 207 L---------GKPAITHYSIIERF-RAHTRLRLRLETGRTHQIRVHMAYMNHHLVGDQLY 256

Query: 273 CANFKGNFTSPIQ-----NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            ++ + N  S I+     N+  LHA  + L HP   R +++ A LP  MV+  ++L
Sbjct: 257 RSS-QQNHHSNIEVLRRFNRQALHATTLRLHHPITAREMELHAALPQDMVELVNAL 311


>gi|331269364|ref|YP_004395856.1| RluA family pseudouridine synthase [Clostridium botulinum
           BKT015925]
 gi|329125914|gb|AEB75859.1| pseudouridine synthase, RluA family [Clostridium botulinum
           BKT015925]
          Length = 304

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 89/312 (28%), Positives = 148/312 (47%), Gaps = 48/312 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N RLD +  N     +   +QK+++ G V+V+ K  K N +++    V        +N+I
Sbjct: 14  NCRLDLFISNSLEGKSRSYIQKLIQEGHVKVNGKDKKSNYKLKLHDSV-------VVNNI 66

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS---------GIAYH 128
            KE K ++         + ++  +LYED+ I V NK  G+ V   +          + YH
Sbjct: 67  EKEDKKINP--------ENIEMDILYEDNDIIVINKSQGMVVHPATSNYSGTLVNALLYH 118

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            D       D++   P + HR+D++TSG+LVVA+   A + L E  +   +++ Y ++V 
Sbjct: 119 CDTLSTLNDDTR---PGIVHRIDKDTSGVLVVAKNNKAHEILAEQLKEHSMKREYIAVVE 175

Query: 189 GIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWL 243
           GI K +   +   L +  K  I    V       +G   A++H++V+  F +     C L
Sbjct: 176 GIVKEENGLVDEPLGRNPKDRIKMAVV-------EGGKNAVTHYEVLKRFKKNTLVKCIL 228

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E    TGRTHQ+RVH  ++G P+VGD  Y   FK        N   LHA+ +   HP   
Sbjct: 229 E----TGRTHQIRVHMSYIGHPLVGDPMY--GFKKQRFK--LNGQMLHAKKLGFIHPTTE 280

Query: 304 R-LQITAPLPAH 314
           + ++  + LP +
Sbjct: 281 KYIEFESDLPQY 292


>gi|317472795|ref|ZP_07932106.1| RluA family pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
 gi|316899714|gb|EFV21717.1| RluA family pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 305

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 82/321 (25%), Positives = 141/321 (43%), Gaps = 31/321 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V   E   RLD      +P      LQK+ +   V VD    K N +++ G+ V     
Sbjct: 8   TVSQKETGSRLDVCLAGRFPEFTRSYLQKLCKDSAVLVDDAEKKSNYKVREGERV----- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                 I+K  K  + S+   K    +   ++YED  I + NKP  + V    G      
Sbjct: 63  ------ILKVPKPTELSIKPEK----MDLDIVYEDRDIILINKPKNMVVHPAPGHYEGTL 112

Query: 129 IDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++G ++   D         +P + HR+D++T+GIL+V +   A Q L E  +   I + Y
Sbjct: 113 VNGLMEHCRDELSGINGVLRPGIVHRIDKDTTGILIVCKNDMAHQCLAEQLKDHTITRRY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V+   K +   +   + +      +   +    E G   A++H++V++   + F ++
Sbjct: 173 HAIVYHNIKEESGTVDAPIARSRK---ERKKMAIDREAGRR-AVTHYRVLERLKEGFTYI 228

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E    TGRTHQ+RVH   +G P++GD  Y    K  ++   Q    LHA+ +   HP   
Sbjct: 229 ECSLETGRTHQIRVHMASIGHPLLGDTVYGPK-KSKYSLEGQ---CLHAKVLGFTHPRTK 284

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             ++    LPA+  +    LG
Sbjct: 285 EYMEFEVGLPAYFEELLKRLG 305


>gi|183597510|ref|ZP_02959003.1| hypothetical protein PROSTU_00783 [Providencia stuartii ATCC 25827]
 gi|188023155|gb|EDU61195.1| hypothetical protein PROSTU_00783 [Providencia stuartii ATCC 25827]
          Length = 325

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 90/326 (27%), Positives = 158/326 (48%), Gaps = 47/326 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + +  +I   N   
Sbjct: 19  RLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKPKEKVLGGEQILVDALIEEDNRWE 78

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +   LD               ++YED  I V NKP G+ V  G+G   + DG + + + 
Sbjct: 79  PQDIPLD---------------VVYEDEDILVINKPRGLVVHPGAG---NPDGTILNALL 120

Query: 139 SKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--- 189
            +  +    PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y ++  G   
Sbjct: 121 HRYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAVGRMT 180

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +E I+    K++H+    VH +         AI+H++V++ F +    L ++  T
Sbjct: 181 AGGMVEEPISRHPTKRTHMA---VHPM------GKPAITHYRVMEHF-RAHTRLRLRLET 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLHARYMDLPHPE 301
           GRTHQ+RVH  H+  P++GD  Y       KG      +     ++  LHA  + L HP 
Sbjct: 231 GRTHQIRVHMAHINHPLIGDPLYGGRPRPLKGASEEFFEVMRKFDRQALHATMLRLYHPI 290

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFKY 326
            G +++  APLP  MV+  ++L   Y
Sbjct: 291 SGIQMEWHAPLPDDMVELIEALKADY 316


>gi|197294534|ref|YP_001799075.1| Pseudouridine synthase [Candidatus Phytoplasma australiense]
 gi|171853861|emb|CAM11823.1| Pseudouridine synthase [Candidatus Phytoplasma australiense]
          Length = 302

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 78/292 (26%), Positives = 143/292 (48%), Gaps = 33/292 (11%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           QK++ + +V V++K  K N  +++  ++ IP  +              + +N+ K  + L
Sbjct: 34  QKLIAAKKVLVNQKPTKKNYLLKNQDLITIPTTV------------FKTPLNIQKPYN-L 80

Query: 98  KSILLYEDSKIYVFNKPA------GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
              ++YEDS + V NKP+       +S +G + +   +  F  S  +    +P + HRLD
Sbjct: 81  NLEVVYEDSDLAVINKPSNLIVHPSLSFEGITLVNALLHQF-SSLSNIDTPRPGIVHRLD 139

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + T+G++++A+    +Q L  +F  R I+K+YW L+ G  +N  E   N  + ++     
Sbjct: 140 KNTTGLMLIAKNDNTSQKLQTAFSQRTIKKVYWGLIEGFLEN--EGTINLPIARNPNDRL 197

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + V+   ++    A++HFK +      F  ++    TGRTHQ+R H  ++  P++GD  
Sbjct: 198 KMTVLPNGKE----AVTHFKTLKRL-NNFSLMQFVLETGRTHQIRAHLSYLKKPLLGDKL 252

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y +  K   T   Q   +LHA+ +   HP     + + APLP +  K  D L
Sbjct: 253 YGS--KHYNTDEGQ---FLHAKELIFKHPISFQEINLQAPLPLNFQKLLDKL 299


>gi|315646052|ref|ZP_07899173.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
 gi|315278813|gb|EFU42127.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
          Length = 323

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 83/316 (26%), Positives = 144/316 (45%), Gaps = 39/316 (12%)

Query: 11  VVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V+ D    RLD++        ++   +Q  +  G V+V+++ VK N ++  G  + +  
Sbjct: 26  TVDADSSKTRLDKYITESLGEEVSRSQVQLWITDGHVKVNEEPVKSNYKVSQGDHIVLSV 85

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
              ++  II E   L+               + +ED  + V NKP G+ V    G   H 
Sbjct: 86  PQPSVVEIIPEDIPLE---------------IAFEDRDVIVVNKPRGMVVHPAPG---HS 127

Query: 130 DGFL--------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G L        K      G+ +P + HR+D++T+G+++ A+   A   L    +   + 
Sbjct: 128 SGTLVNALMFHCKDLSGINGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKDHSVN 187

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV G   + +  I   + + +     Y  V  +N K   +A++HF V++ F   +
Sbjct: 188 RRYLALVHGNISHDQGTIDAPIGRDAQDRKLYT-VTDRNSK---HAVTHFTVVERFGD-Y 242

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE++  TGRTHQ+RVH  ++G P+VGD  Y     G       N   LHA  +   HP
Sbjct: 243 SLLELKLETGRTHQIRVHMKYIGHPLVGDPVY-----GKSKGIKLNGQALHAAVLGFVHP 297

Query: 301 EGGR-LQITAPLPAHM 315
             G+ ++ +AP+P  M
Sbjct: 298 SSGQYMEFSAPMPKDM 313


>gi|325973159|ref|YP_004250223.1| tRNA pseudouridine synthase [Mycoplasma suis str. Illinois]
 gi|325989602|ref|YP_004249301.1| putative pseudouridine synthase [Mycoplasma suis KI3806]
 gi|323574687|emb|CBZ40343.1| probable pseudouridine synthase [Mycoplasma suis]
 gi|323651761|gb|ADX97843.1| tRNA pseudouridine synthase [Mycoplasma suis str. Illinois]
          Length = 337

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/264 (27%), Positives = 134/264 (50%), Gaps = 16/264 (6%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---PPVINA 73
           E   L ++ K H+P+   + + K LR   + ++ +   F  +++ G  ++I   P +   
Sbjct: 15  EGYTLWKYIKLHFPYYTKLLIIKELRLKHILLNDESTYFQYKLKFGDTIKIFLLPDLSEI 74

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGF 132
               +   K+LD        ++ +K  +++E++ + + NK A   VQ  S  + Y ++  
Sbjct: 75  GKKRVNRAKLLDRE---EFKAETIKFQIVFENNDVIIINKKATQIVQPDSSSSNYSLEEL 131

Query: 133 LKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L+S++  K      KP+  HRLD+   G+++ A+   A   L+++ + R+IQK Y ++V 
Sbjct: 132 LQSYLKKKDPDSTYKPKFIHRLDKPVEGLIIGAKNAQAHSVLSQAIKDRKIQKFYKAIVL 191

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G    +++ + NW+L K       V V+ Q   G  Y+IS  + I  F   +  +E++  
Sbjct: 192 GCFPYREKQLENWILDKQ----SKVKVLDQENHGTKYSISIVRGIKKFPN-YSIVEIKLV 246

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGR +Q+R    H+G PIVGD KY
Sbjct: 247 TGRKNQIRAQLSHLGYPIVGDRKY 270


>gi|161504785|ref|YP_001571897.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160866132|gb|ABX22755.1| hypothetical protein SARI_02909 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 219

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 74/216 (34%), Positives = 109/216 (50%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LEAHKDSIM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  I   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYIARVWGHPTPAEGLIDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + + V+D  A     + +QP TGR+HQLRVH   +G PI+GD  Y + 
Sbjct: 126 KVCYETG-KPAQTEYNVVDFAADNTARVALQPITGRSHQLRVHMQALGHPILGDRFYASP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
              +       +L+LHA  + + HP  G  +   AP
Sbjct: 185 EALSLAP----RLHLHAEMLTITHPTYGTSMTFKAP 216


>gi|323342856|ref|ZP_08083088.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322463968|gb|EFY09162.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 308

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 95/319 (29%), Positives = 151/319 (47%), Gaps = 44/319 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++VE   + MR+D++        +   LQ  +++G + V+   VK N R++   VV    
Sbjct: 10  LIVEEMFDGMRIDQYMALAVTDYSRSVLQTWIKNGNITVNGNVVKPNLRLKEDDVVE--- 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                 + I E++I  S V +    D     ++YED  I V NKP G+ V          
Sbjct: 67  ------YEITEEQI--SIVPVPMDLD-----IVYEDDAILVVNKPKGLIVHPSPSTLNQP 113

Query: 129 --IDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + G L       D  G+ +P + HR+D++T+G+LVVA+T  A + L E  + R I + 
Sbjct: 114 TLVHGLLAHTTQLSDLNGELRPGIVHRIDKDTTGLLVVAKTNEAHEILVEDLKQRLISRE 173

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFA 237
           Y ++V    K++   +       + IG D      + V  QN K    A++HF + + F 
Sbjct: 174 YVAIVHHQFKHQSATV------DAPIGRDPKNRQRMAVTDQNSK---QAVTHFYLAERF- 223

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  L  +  TGRTHQ+RVHA ++  PIVGD  Y  ++K  + +   N   LHA+ + L
Sbjct: 224 NDFSVLRCKLDTGRTHQIRVHAQYIKHPIVGDQTY--SYKNTWET---NGQCLHAQKLTL 278

Query: 298 PHPEGGR-LQITAPLPAHM 315
            HP     +   A LP  M
Sbjct: 279 THPVSKEVMTFEAELPQTM 297


>gi|168700598|ref|ZP_02732875.1| ribosomal large subunit pseudouridine synthase [Gemmata
           obscuriglobus UQM 2246]
          Length = 354

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 123/243 (50%), Gaps = 27/243 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LY+D  + + NKPA + V    G         + +H    L +   +   +  + HRLD
Sbjct: 111 ILYQDEWLALVNKPADMVVHPAKGNWSGTLVNALQWHFREHLST--GAGHLRAGIVHRLD 168

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++VA+     + L   F  R++ K Y ++  G  +   + I   L    +   D
Sbjct: 169 KDTSGVILVAKDDLTHRDLAMQFESRKVFKEYVAIAAGELERDSDYIEGALKMHPY---D 225

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + ++   +  A +A+S+++V++ F + F  +++QP TGRTHQ+RVH LH+GC ++ D  
Sbjct: 226 RLKMIVSTDPDAKHALSYYEVLERF-RGFTLVKVQPRTGRTHQIRVHLLHVGCAVLADKI 284

Query: 272 YCANFKGNF------TSPIQNKLY-----LHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           Y    +         T P ++++      LHA  +   HP  G+ ++  APLP  M +T 
Sbjct: 285 YGGRAQVKLSEIAPGTPPAEDEVLLGRQALHAFRLRFQHPRTGQWIEAEAPLPPDMRRTL 344

Query: 320 DSL 322
           D+L
Sbjct: 345 DAL 347


>gi|218667498|ref|YP_002424927.1| ribosomal large subunit pseudouridine synthase D [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|218519711|gb|ACK80297.1| ribosomal large subunit pseudouridine synthase D [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 319

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 90/324 (27%), Positives = 146/324 (45%), Gaps = 42/324 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP- 68
           +++  ++   RLD       P  +   +Q +LR G++ VD    K + R++ G+ V +  
Sbjct: 10  MILPEEQAGERLDTVLSQLLPETSRSRIQALLRDGRILVDGTPEKPSARVRGGEQVMVDW 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P I   N +                ++ L   +L+ED+ I V +KPAG     G+G   H
Sbjct: 70  PQIEPSNWL----------------AEGLPLHILHEDADILVLHKPAGQLTHPGAG---H 110

Query: 129 IDGFLK----SWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG L     + V      PR  + HRLD++T+G+LVVA+T  A Q L +      + + 
Sbjct: 111 ADGTLVNGVLAHVPENAYLPRGGIVHRLDKDTTGLLVVAKTEMARQSLIDQLGDHTMHRE 170

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G         A       H        V+ + + A    + +++++ F  +  +
Sbjct: 171 YLALVTGAMTGGGRVDAPI---GRHAQDRLRMTVRDDGRPAQ---TDYRLVERFP-RHSY 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQ-----NKLYLHARY 294
           L ++  TGRTHQ+RVH  H+G P+VGD  Y       KG   + +       +  LHA  
Sbjct: 224 LRLRLATGRTHQIRVHMTHIGHPLVGDPVYGGRMTVPKGLDEAGLARWRQFRRQALHAWR 283

Query: 295 MDLPHPEGGRLQI-TAPLPAHMVK 317
           + L HP  G L    +PLP  M +
Sbjct: 284 LRLYHPASGELMTWESPLPDDMTE 307


>gi|162148037|ref|YP_001602498.1| ribosomal large subunit pseudouridine synthase D [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|161786614|emb|CAP56196.1| putative ribosomal large subunit pseudouridine synthase D
           [Gluconacetobacter diazotrophicus PAl 5]
          Length = 295

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/279 (28%), Positives = 128/279 (45%), Gaps = 42/279 (15%)

Query: 59  IQSGQVVRIP--PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           ++ G V+R P  PV   L + I+    +  ++  T  +  +   +LYEDS + V +KPAG
Sbjct: 20  LRDGHVLREPADPVRAGLCYEIR----MPPAIPATPRAQAIPFAILYEDSDLIVLDKPAG 75

Query: 117 ISVQGGSG--IAYHIDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           + V    G      ++  L    DS       ++P + HRLD++TSG++VVA+T  A   
Sbjct: 76  LVVHPAPGNEDGTLVNALLAHCGDSLTGIGGERRPGIVHRLDKDTSGVMVVAKTEQAHTA 135

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------G 222
           L+++F  R I + Y +L WGI              +  IG D     +++ K       G
Sbjct: 136 LSDAFAARDIDRTYLALAWGILSPASGTF------EGAIGRD-----RRDRKRMAVVTHG 184

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             +A++H++ +  F      +E +  TGRTHQ+RVH    G P+VGD  Y         +
Sbjct: 185 GKHAMTHYRTLHSFHGGISSVECRLATGRTHQIRVHFSTSGHPLVGDPVYLRRIPAAARA 244

Query: 283 PIQN---------KLYLHARYMDLPHPEGGR--LQITAP 310
             ++         +  LHA  +   HP  G   L  TAP
Sbjct: 245 LPEDARRAALDFPRQALHAARLGFTHPRTGESLLFETAP 283


>gi|198282733|ref|YP_002219054.1| RluA family pseudouridine synthase [Acidithiobacillus ferrooxidans
           ATCC 53993]
 gi|198247254|gb|ACH82847.1| pseudouridine synthase, RluA family [Acidithiobacillus ferrooxidans
           ATCC 53993]
          Length = 310

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 90/324 (27%), Positives = 146/324 (45%), Gaps = 42/324 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP- 68
           +++  ++   RLD       P  +   +Q +LR G++ VD    K + R++ G+ V +  
Sbjct: 1   MILPEEQAGERLDTVLSQLLPETSRSRIQALLRDGRILVDGTPEKPSARVRGGEQVMVDW 60

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P I   N +                ++ L   +L+ED+ I V +KPAG     G+G   H
Sbjct: 61  PQIEPSNWL----------------AEGLPLHILHEDADILVLHKPAGQLTHPGAG---H 101

Query: 129 IDGFLK----SWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG L     + V      PR  + HRLD++T+G+LVVA+T  A Q L +      + + 
Sbjct: 102 ADGTLVNGVLAHVPENAYLPRGGIVHRLDKDTTGLLVVAKTEMARQSLIDQLGDHTMHRE 161

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G         A       H        V+ + + A    + +++++ F  +  +
Sbjct: 162 YLALVTGAMTGGGRVDAPI---GRHAQDRLRMTVRDDGRPAQ---TDYRLVERFP-RHSY 214

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQ-----NKLYLHARY 294
           L ++  TGRTHQ+RVH  H+G P+VGD  Y       KG   + +       +  LHA  
Sbjct: 215 LRLRLATGRTHQIRVHMTHIGHPLVGDPVYGGRMTVPKGLDEAGLARWRQFRRQALHAWR 274

Query: 295 MDLPHPEGGRLQI-TAPLPAHMVK 317
           + L HP  G L    +PLP  M +
Sbjct: 275 LRLYHPASGELMTWESPLPDDMTE 298


>gi|329956079|ref|ZP_08296850.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
 gi|328524838|gb|EGF51892.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
          Length = 356

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 93/350 (26%), Positives = 159/350 (45%), Gaps = 55/350 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQEMMRVDKYLFDRLTNASRNRIQKAADAGFVMANDKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYENEVIPEDIPLD---------IVYEDKYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 138 LVNAIAWH----MKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKT 193

Query: 179 IQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++ Y +LVWG + +++   I N          D + +    +    +A++H++V++   
Sbjct: 194 TKRRYRALVWGNVEQDEGTIIGNVGRNPK----DRMQMTVLPDDQGKHAVTHYRVLERLG 249

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNF-------------TS 282
                +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG               T 
Sbjct: 250 Y-VTLVECILETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFDTC 308

Query: 283 PIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS-LGFKYDRNL 330
           P Q    LHA  +   HP  G  +  T+ LP  M +  D   G+  +R L
Sbjct: 309 PRQA---LHAMTLGFVHPVTGEEMYFTSELPDDMSRLIDKWRGYISNREL 355


>gi|147669825|ref|YP_001214643.1| ribosomal large subunit pseudouridine synthase D [Dehalococcoides
           sp. BAV1]
 gi|289433036|ref|YP_003462909.1| pseudouridine synthase [Dehalococcoides sp. GT]
 gi|146270773|gb|ABQ17765.1| ribosomal large subunit pseudouridine synthase D [Dehalococcoides
           sp. BAV1]
 gi|288946756|gb|ADC74453.1| pseudouridine synthase, RluA family [Dehalococcoides sp. GT]
          Length = 300

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 81/305 (26%), Positives = 151/305 (49%), Gaps = 38/305 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVINALNHI 77
           RLD++       ++   +Q+++ SG + V+ +  K + R+++G  +   IPP        
Sbjct: 14  RLDKYITQKESGLSRSFIQELVSSGHILVNNQSAKPSLRLKTGDTITIEIPP-------- 65

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKS 135
                  ++   L   +  L+  ++++D  + + NKP G++V    G   H  ++G L  
Sbjct: 66  -------ETPSELKAENIPLE--IIFQDKDLLLINKPPGLTVHPAPGHPDHTLVNGVLAL 116

Query: 136 WVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             + +      +P + HRLD++TSG+L+VA+ R A  +L+  F+ R ++K Y +LV G  
Sbjct: 117 EPEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRQALANLSAQFKERTVRKYYLALVKGEL 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           +  +  I   L +        + VV        +A + +KV+  + Q +  LE++  TGR
Sbjct: 177 RPAEGFIEAPLGRDPQ-NRQKIAVVSD----GRHARTGYKVLR-YIQGYSLLEVKLETGR 230

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH   +G P+ GD  Y     G   S ++ + +LHA  +    P  G+ ++ T+P
Sbjct: 231 THQIRVHFAAIGHPVAGDAVY-----GQKESWVKRQ-FLHAHRLSFALPSNGQVVEFTSP 284

Query: 311 LPAHM 315
           LP  +
Sbjct: 285 LPPDL 289


>gi|329122166|ref|ZP_08250773.1| ribosomal large subunit pseudouridine synthase D [Dialister
           micraerophilus DSM 19965]
 gi|327466804|gb|EGF12327.1| ribosomal large subunit pseudouridine synthase D [Dialister
           micraerophilus DSM 19965]
          Length = 307

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 95/327 (29%), Positives = 154/327 (47%), Gaps = 52/327 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  ++ MRLD++ K                SG  R + ++      I+ G  + +P  +
Sbjct: 8   VDEKQDGMRLDQFLKE--------------VSGLTRSEVQKW-----IKEGYAISLPNRM 48

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFL----KSILLYEDSKIYVFNKPAGISVQGGSG--- 124
              N+ I +++ +  S    K  + +    K  +LYED  I V NK  G+ V  G+G   
Sbjct: 49  VRSNYHISDKEKIQFSWEEKKEIELIPQKIKLDILYEDEHIIVINKSRGMVVHPGAGNID 108

Query: 125 ------IAYHI-DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 + YH  +  LK     +  +P + HRLD++TSG++V  ++  A + +       
Sbjct: 109 NTLVNALLYHCGESLLKV---GEKTRPGIVHRLDKDTSGVMVAVKSDIAYEKVKNEIATH 165

Query: 178 RIQKIYWSLVWGI---PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             ++ Y +LV G    P  K +      LK      D +    Q + G N AI+HF V++
Sbjct: 166 EAKRTYLTLVHGQMEGPDGKIDLPLGRSLK------DRMKWDVQPKTGKN-AITHFHVLE 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F  K+  LE +  TGRTHQ+RVH  ++G P++ D  Y    K NF  PIQ +  LH+  
Sbjct: 219 -FMPKYSLLECKLETGRTHQIRVHMSYIGHPVINDPLY-GRKKDNF--PIQGQA-LHSFT 273

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWD 320
           ++L HP  G+ ++  APLP  M K  +
Sbjct: 274 LELKHPLTGKIMKFEAPLPEDMKKCLE 300


>gi|317049249|ref|YP_004116897.1| RluA family pseudouridine synthase [Pantoea sp. At-9b]
 gi|316950866|gb|ADU70341.1| pseudouridine synthase, RluA family [Pantoea sp. At-9b]
          Length = 326

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/256 (31%), Positives = 128/256 (50%), Gaps = 39/256 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP  + V  G+G         + YH    +   V   G    + HRLD
Sbjct: 86  IVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLYHYPPIVD--VPRAG----IVHRLD 139

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHI 208
           ++T+G++VVA+T  A  HL E+ ++R I + Y ++  G         E +A    K++H+
Sbjct: 140 KDTTGLMVVAKTVPAQTHLVETLQLREITREYEAVAIGTMTAGGTVNEPMARHSTKRTHM 199

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A +H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VG
Sbjct: 200 A---VHPMGKP------ATTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMAHINHPLVG 249

Query: 269 DHKYCAN---FKGNFTSPIQ-----NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           D  Y       KG   + I+     ++  LHA  + L HP  G  ++  APLP  MV   
Sbjct: 250 DPLYGGRPRPPKGASDAFIETLRGFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVDLI 309

Query: 320 DSLGFKYDRNLYIKRL 335
           D+L  K D N++  +L
Sbjct: 310 DAL--KADTNMFRDQL 323


>gi|237803088|ref|YP_002888282.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis B/Jali20/OT]
 gi|231274322|emb|CAX11117.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis B/Jali20/OT]
          Length = 335

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 110/230 (47%), Gaps = 26/230 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +YED  I V NKP  + V    G         + + I   LK     +  +P + HRLD+
Sbjct: 92  VYEDDMILVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDK 151

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGG 210
           +TSG+L+  +TR A    +E F  ++++K+Y ++    P  +     IA   LK+  +  
Sbjct: 152 DTSGLLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQELIHTRIARHPLKRKEMT- 210

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               V+  + +G   AI+H  V+     +   + + P TGRTHQLRVH  H+G PI+GD 
Sbjct: 211 ----VLSTHAEGGKEAITHCHVLATNG-RLSVVALYPETGRTHQLRVHMKHLGTPILGDS 265

Query: 271 KY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
            Y     NF+        +K  LHA  +   HPE   R+++   LP  M 
Sbjct: 266 VYGIPSINFRYGL-----DKQQLHAYSLVFAHPESAERVKLVTKLPDDMT 310


>gi|332530535|ref|ZP_08406474.1| pseudouridine synthase, RluA family protein [Hylemonella gracilis
           ATCC 19624]
 gi|332040010|gb|EGI76397.1| pseudouridine synthase, RluA family protein [Hylemonella gracilis
           ATCC 19624]
          Length = 361

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 92/341 (26%), Positives = 146/341 (42%), Gaps = 56/341 (16%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RLDR      P  +   LQ+++ +G V +  +  +               V+    H 
Sbjct: 29  GQRLDRALSELVPEFSRSYLQQLIEAGAVTLGPQPSQL--------------VVRKSAHK 74

Query: 78  IKEQKILDSSVNLTKHSDFLKSILL-----YEDSKIYVFNKPAGISVQGGSG--IAYHID 130
           ++  ++    +  T  S   K  ++     +ED+ + V +KPAG+ V    G      ++
Sbjct: 75  VRAGEVGTIELRPTPQSQAFKPEVMDLDIVHEDAHLLVIHKPAGLVVHPAPGNWSGTLLN 134

Query: 131 GFL---KSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           G L   +   +   Q PR  + HRLD++TSG++VVARTR A + L      R + + Y +
Sbjct: 135 GLLGRDQGRGEVAAQLPRAGIVHRLDKDTSGLMVVARTRVAMEALVRMIAAREVSRQYLA 194

Query: 186 LV---WGIPKNKKECIANWLLKKSHIGGDYVH-----VVKQNEKGANYAISHFKVI---- 233
           L    W  P  +    A     +  IG D  +     VV         A++ F+++    
Sbjct: 195 LAHRAWNGPVLRDVGGA----AQEGIGRDPANRLRMAVVDLARHPGKPALTTFELLGNAA 250

Query: 234 ----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--K 287
               +  AQ  C L    HTGRTHQ+RVHA  +G P++GD  Y         +P+    +
Sbjct: 251 PRPDEGLAQGACLLRCTLHTGRTHQIRVHAASIGHPLLGDGVYGG-------APVVGLRR 303

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             LHA  + L HP  G  L   AP P  + K   +LG  Y+
Sbjct: 304 QALHAWRLALRHPVSGEALVFHAPPPDDLAKACAALGLDYN 344


>gi|327312478|ref|YP_004327915.1| RNA pseudouridine synthase [Prevotella denticola F0289]
 gi|326944338|gb|AEA20223.1| RNA pseudouridine synthase [Prevotella denticola F0289]
          Length = 225

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 112/231 (48%), Gaps = 20/231 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I +  K AG  VQG       +   ++ W+  K QKP      + HRLD+  S
Sbjct: 3   VLYEDNHIIIVYKEAGEIVQGDKSGDEPLSETVRRWIKEKYQKPGNVFLGIVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV-- 213
           G+++ A+T  A   L   FR   + K YW++V   P   +  + +WL++       Y   
Sbjct: 63  GLVIFAKTSKALARLNNMFRNGEVHKTYWAIVTRPPFEPEATLTDWLVRNERQNKSYAYN 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H V  ++K    +I H+K+I+  + ++  LE+   TGR HQ+R    +M CPI GD KY 
Sbjct: 123 HQVPTSKK----SILHYKIIN-RSDRYTLLEINLMTGRHHQIRCQLSNMDCPIKGDLKY- 176

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
               G   S     + L +  ++  HP     + I +PLP   +  W ++G
Sbjct: 177 ----GAPRSNPDGSISLLSHRVEFVHPVSKENICIESPLPDDTL--WHAIG 221


>gi|159899422|ref|YP_001545669.1| RluA family pseudouridine synthase [Herpetosiphon aurantiacus ATCC
           23779]
 gi|159892461|gb|ABX05541.1| pseudouridine synthase, RluA family [Herpetosiphon aurantiacus ATCC
           23779]
          Length = 323

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 89/329 (27%), Positives = 148/329 (44%), Gaps = 35/329 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V   E   RLDR    + P ++   +Q+++    +RV+ +  K +  +Q G  + I   +
Sbjct: 12  VGEAEAGQRLDRLVSANMPDLSRTYVQQLITDLHIRVNGRGAKASLPVQIGDQIEIFLPL 71

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                I+ E   LD               ++YED+ + + NK AG+ V    G   H  G
Sbjct: 72  AKPTDIVAEDLPLD---------------VIYEDADVLLVNKAAGMVVHPAPG---HTTG 113

Query: 132 FLKS--------WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            L +           S   +P + HRLD+ETSG+LV+A+   A   LTE    RR+ K Y
Sbjct: 114 TLVNALLYRYPHLTTSGDLRPGIVHRLDKETSGLLVIAKHDQARMMLTEQQMARRMHKKY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G  +     I   + +  +   + + ++   E    YA++H++V++     +  +
Sbjct: 174 LALVEGHWREPTGTIDAPIGRNPN---NRLRMMVMPE--GRYAVTHYQVLEVLG-PYSLV 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                TGRTHQ+RVH  +   PI+ D  Y  + K   T  I+   +LHA ++    P  G
Sbjct: 228 RATLETGRTHQIRVHFSYRNRPILNDALY-GHRKPKETFGIERH-FLHAYHLGFRLPSTG 285

Query: 304 R-LQITAPLPAHMVKTWDSLGFKYDRNLY 331
                  PLPA + K   +L  +Y+  +Y
Sbjct: 286 EWCSWEVPLPAELEKILTTLRTRYETIVY 314


>gi|292489389|ref|YP_003532276.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           CFBP1430]
 gi|292898392|ref|YP_003537761.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           ATCC 49946]
 gi|291198240|emb|CBJ45346.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           ATCC 49946]
 gi|291554823|emb|CBA22677.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           CFBP1430]
 gi|312173554|emb|CBX81808.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           ATCC BAA-2158]
          Length = 217

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/204 (35%), Positives = 111/204 (54%), Gaps = 18/204 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G   +A + D  + + V          HRLD  TSG++V
Sbjct: 14  VLYQDEHIIVVNKPSGLLSVPGR--LAEYKDSVM-TRVQRDYPAAESVHRLDMATSGVMV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  QK Y + VWG P+ +   +   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPQKTYVARVWGHPQPESGSVDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + A + ++V+D  +     + ++P TGR+HQLRVH L +G PI+GD+ Y A+ 
Sbjct: 125 VCFETGKS-AQTEYQVLDYASDHSARVRLKPVTGRSHQLRVHMLALGHPILGDNFY-AHD 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
           +    +P   +L LHA  + + HP
Sbjct: 183 EARAMAP---RLQLHAESLSITHP 203


>gi|153004820|ref|YP_001379145.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152028393|gb|ABS26161.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 293

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 81/298 (27%), Positives = 135/298 (45%), Gaps = 47/298 (15%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---PPVINALNHIIKEQKILDSSVNLTKH 93
           +Q+++  G+VRVD +  K + R++ G+ V +   PP  + L  + +E             
Sbjct: 1   MQRLVEEGRVRVDGRAAKASARLRGGETVDVEIPPPEPSGL--VAQE------------- 45

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL-----KSWVDSKGQKPRL 146
              L   +LYED+ + V +K AG+ V    G  +   ++  L      +   ++G +  L
Sbjct: 46  ---LPLAVLYEDADLLVLDKAAGMVVHPARGAPHSTVVNALLHRLGVGAAAPAEGLRLGL 102

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLK 204
            HRLD++TSG LVVA+T  A   L   F+ R ++K Y +L  G+  P+ + +       +
Sbjct: 103 VHRLDKDTSGCLVVAKTEPALAALQAQFKGRTVEKRYLALCHGLLAPEGRLDTPYGRHPR 162

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                 D +    +  K A  A++ ++ ++ F       E+   TGRTHQ+RVH    G 
Sbjct: 163 ------DRIRFTTRV-KSARRAVTEWRALESFPAGATLAEVTLLTGRTHQIRVHLAEAGH 215

Query: 265 PIVGDHKYCANFKGNFTSPIQ---------NKLYLHARYMDLPHPEGG-RLQITAPLP 312
           P++ D  Y    +     P            +  LHA  +   HP  G RL + APLP
Sbjct: 216 PLLADAVYGGTRREARLPPEHPVRLAAGAIGRQALHAARLAFDHPRTGRRLALEAPLP 273


>gi|86132103|ref|ZP_01050699.1| ribosomal large subunit pseudouridine synthase D [Dokdonia
           donghaensis MED134]
 gi|85817437|gb|EAQ38617.1| ribosomal large subunit pseudouridine synthase D [Dokdonia
           donghaensis MED134]
          Length = 229

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 69/205 (33%), Positives = 100/205 (48%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK +G  VQG       +   +K ++  K  KP      + HRLD+ TS
Sbjct: 10  VIYEDNHIIVVNKRSGDIVQGDKTGDLPLSEVVKKYIAVKYNKPGAVYLGVVHRLDRPTS 69

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ ART  A   L + F  R+ +K YW+LV   P  +   + ++L +       Y H 
Sbjct: 70  GIVIFARTSKALPRLNKMFSERQTKKTYWALVKNPPPAESGTLTHFLKRNPKQNKSYAH- 128

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K     +  AI  ++VI    + F  LE+  HTGR HQ+R     +GCPI GD KY   
Sbjct: 129 -KHEVPDSKKAILDYRVIKKL-KTFYLLEIDLHTGRHHQIRAQLTAIGCPIKGDLKY--- 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G   S     + L +R + L HP
Sbjct: 184 --GFDRSNPDGSISLLSRKLTLTHP 206


>gi|194366931|ref|YP_002029541.1| RluA family pseudouridine synthase [Stenotrophomonas maltophilia
           R551-3]
 gi|194349735|gb|ACF52858.1| pseudouridine synthase, RluA family [Stenotrophomonas maltophilia
           R551-3]
          Length = 329

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 86/321 (26%), Positives = 144/321 (44%), Gaps = 38/321 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +V +     R D      +P  +   L + +++G V +D  + +  + ++ G+VV +  
Sbjct: 12  AIVPDTSAGRRFDAVVAELFPEYSRSRLTEWIKNGDVLLDGAQARPRDPLRGGEVVTLTV 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V+        E   LD               +L+ED  + V NKP G+ V  G+G   H 
Sbjct: 72  VLETQTDAQPEDIPLD---------------VLFEDEYLLVINKPVGLVVHPGAG--NHS 114

Query: 130 DGFLKSWV---DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              + + +    S    PR  + HRLD++TSG++VVA+T  A   L E    R + + Y 
Sbjct: 115 GTLVNALLFRDPSVAVLPRAGIVHRLDKDTSGVMVVAKTLEAQTALVEQLAARDVHRQYL 174

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G         A       H        V+++ K    A++H+++ + F +    LE
Sbjct: 175 AIVMGALVAGGTADAPI---DRHPRDRLKMGVREDGK---EAVTHYRLRERF-RAHTALE 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMD 296
            +  TGRTHQ+RVH  H+  PIVGD  Y    K          + ++   +  LHA  ++
Sbjct: 228 CRLETGRTHQIRVHMAHIRHPIVGDPLYGGALKLPKGASDELVAALRGFKRQALHAETLE 287

Query: 297 LPHP-EGGRLQITAPLPAHMV 316
             HP  G  ++ TAP+PA M+
Sbjct: 288 FVHPITGETVRNTAPVPADML 308


>gi|297735761|emb|CBI18448.3| unnamed protein product [Vitis vinifera]
          Length = 481

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 77/256 (30%), Positives = 128/256 (50%), Gaps = 28/256 (10%)

Query: 42  RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI- 100
           + GQ++  +K +K N  +++G  + +P V  A   I K    + S   L  ++D ++ + 
Sbjct: 122 KEGQIKPLRK-IKPNEVMEAGTRIYVP-VSVAEARISKRFDTIPSG-TLHPNADEIEYLQ 178

Query: 101 ----LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETS 155
               L ++D  I V NKP  + ++G   +   +D    + +    ++ P+L HRLD+E+S
Sbjct: 179 RLWLLKFQDPAILVLNKPPKVPLKGNLPVHNSMDALAAAALTFDYEEGPKLVHRLDRESS 238

Query: 156 GILVVARTRAAAQHLTESF----RMRRIQKI-----------YWSLVWGIPKNKKECIAN 200
           G+L++ RT+ +  HL   F    + + + K            YW+LV G PK K+  I  
Sbjct: 239 GLLLMGRTKESVAHLHWLFSDINKAKSLSKAWDDACEATCQRYWALVIGSPKQKEGVIHA 298

Query: 201 WLLKKSHIGGDYVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            L K     G    V+  N+ G   +  AI+ ++V+        W+E+ P T R HQLRV
Sbjct: 299 PLSKVLLDDGKTERVILANQSGLEASQEAITEYRVLGPMINGCSWIELCPRTSRKHQLRV 358

Query: 258 H-ALHMGCPIVGDHKY 272
           H A  +G PIVGD+KY
Sbjct: 359 HCAEALGTPIVGDYKY 374


>gi|298251897|ref|ZP_06975700.1| pseudouridine synthase, RluA family [Ktedonobacter racemifer DSM
           44963]
 gi|297546489|gb|EFH80357.1| pseudouridine synthase, RluA family [Ktedonobacter racemifer DSM
           44963]
          Length = 317

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 91/323 (28%), Positives = 150/323 (46%), Gaps = 39/323 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE+++   RLDR+  +    ++   +Q+++    V V+ K  K       G V+R+   +
Sbjct: 17  VESEQVGQRLDRFLVSVLDGVSRSGVQQLIADALVLVNGKVSK------PGYVLRLKDRV 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------I 125
            AL      Q    +  NL          +++ED  + + NK AG+ V    G      +
Sbjct: 71  TALRATPASQMKQVTPQNLPLE-------VVFEDDDLLIVNKAAGMVVHPAPGNYEGTLV 123

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +  + +   D    +P + HRLD++TSG+L+VA+   +   L E  +  +I K Y +
Sbjct: 124 NALVAHYPELQQDEGDMRPGIIHRLDKDTSGLLMVAKNAQSQAALIEQMKQHKIIKRYLA 183

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           LV G  +  +  I       + IG D  H  ++         A++HF+V+  F +K   +
Sbjct: 184 LVEGNVELDQGSI------DAPIGRDTRHRQMMAVTLTEGRDAVTHFRVLQRF-RKHTLV 236

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-KL---YLHARYMDLPH 299
            +Q  TGRTHQ+RVH   +  P+ GD  Y +  +      I N KL   +LHA  ++L H
Sbjct: 237 LVQIVTGRTHQIRVHFQAIKHPVAGDQTYGSGHR------IPNVKLEHQFLHAYQLELTH 290

Query: 300 PEGGR-LQITAPLPAHMVKTWDS 321
           P  G  L I APLP  + K  D+
Sbjct: 291 PRTGESLHIEAPLPPDLQKVLDN 313


>gi|296113272|ref|YP_003627210.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis RH4]
 gi|295920966|gb|ADG61317.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis RH4]
 gi|326566421|gb|EGE16571.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis BC1]
          Length = 355

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 81/316 (25%), Positives = 146/316 (46%), Gaps = 32/316 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD+   + +   +  NL+K +  GQ+ V+ K VK    ++ G ++ +  V 
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVKPKYAVKVGDILTLEAVH 107

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            + +  + E   +D               ++YED  + + NKPAG+ V  G+G      +
Sbjct: 108 ESHSEDLPENIDID---------------IIYEDEAVIIINKPAGMVVHPGAGNRTGTLV 152

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +  L  +   +   PR  L HR+D++T+G+LV+ART++A   L    + + + + Y  + 
Sbjct: 153 NALLYHF-PKQAHLPRAGLVHRIDKDTTGLLVIARTKSAQLSLINQLKDKSVYRHYQCIA 211

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQ 246
            G      E + +  +    IG    H  K   K     A++H        +++  L++ 
Sbjct: 212 LGA---VHEVLRHAQIDAP-IGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIH 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHP 300
             TGRTHQ+RVH  ++G P+VGD  Y  + +   +   +       +  LHA  +   HP
Sbjct: 268 LKTGRTHQIRVHLSYVGHPLVGDPVYGTSPRSGLSDRQRCAILDFGRQALHAYMLGFIHP 327

Query: 301 -EGGRLQITAPLPAHM 315
             G  ++  APLP  M
Sbjct: 328 VTGEAMKFHAPLPKDM 343


>gi|212639635|ref|YP_002316155.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
 gi|212561115|gb|ACJ34170.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
          Length = 303

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 90/330 (27%), Positives = 151/330 (45%), Gaps = 53/330 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRI 67
           + +E   +  R+D+         +   +Q+ L+ G V V+ K VK N +  +    V+ I
Sbjct: 6   LTIEEQHDGERIDKVIAELNEQWSRSQVQQWLKEGHVLVNGKAVKPNYKCHVDDEVVISI 65

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P                 S   L    + +   + YED+ + V NKP G+ V    G   
Sbjct: 66  P-----------------SPEPLDVAPEPIPLDIYYEDADVLVVNKPRGMVVHPAPG--- 105

Query: 128 HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           H+ G L + + +  Q         +P + HR+D++TSG+L+VA+   A + L      + 
Sbjct: 106 HMHGTLVNALLAHCQDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDLAHESLVNQLVNKT 165

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVI 233
           + + Y ++V G+  +    I       + IG D      + VV+  ++    A++HF+V+
Sbjct: 166 VTRKYVAIVHGVIPHDYGTI------DAPIGRDPRDRQSMAVVENGKE----AVTHFRVL 215

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F + + ++E Q  TGRTHQ+RVH  ++G P+ GD KY        T PI  +  LHA 
Sbjct: 216 ERF-EHYTFVECQLETGRTHQIRVHMKYIGYPLAGDPKYGP----RKTLPIDGQA-LHAG 269

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +   HP  G  LQ  AP+P    +  D L
Sbjct: 270 VLGFQHPRTGEYLQFEAPIPHEFERLLDML 299


>gi|304382476|ref|ZP_07364973.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
 gi|304336388|gb|EFM02627.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
          Length = 302

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 109/233 (46%), Gaps = 17/233 (7%)

Query: 87  SVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ- 142
           SV+ +K S+  KS    ++YED  + V  K  GI        A H+   L  +     Q 
Sbjct: 70  SVSRSKQSEPFKSKYVKIVYEDRYLVVIEKNVGILSMAAGRRALHVKAVLDDYFKMSRQR 129

Query: 143 -KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            K  + HRLD+ETSG+++ A+     Q L   +      + Y ++V G  +  +  +ANW
Sbjct: 130 CKAHVVHRLDRETSGLMIYAKDMQTEQLLEHDWHRNVYDRRYMAVVSGEMEEDEGTVANW 189

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L         Y+      + G  YA++HF+ +         +E +  TGR +Q+RVH   
Sbjct: 190 LKDNK----AYITYASPVDNGGKYAVTHFRTL-ARTTTHSLVEFRLETGRKNQIRVHTAD 244

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           MG P+ GD KY     GN  +P  N+L LHA  +   HP    R++   P+PA
Sbjct: 245 MGHPVCGDTKY-----GNGDNPC-NRLCLHAYVLCFYHPVTHERMEFQTPIPA 291


>gi|257056703|ref|YP_003134535.1| ribosomal large subunit pseudouridine synthase D [Saccharomonospora
           viridis DSM 43017]
 gi|256586575|gb|ACU97708.1| ribosomal large subunit pseudouridine synthase D [Saccharomonospora
           viridis DSM 43017]
          Length = 308

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 88/324 (27%), Positives = 148/324 (45%), Gaps = 40/324 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +  + MR+D         ++   + ++  SG V +D K    ++R+ +G ++ +    
Sbjct: 8   VPDGLDGMRVDVGLAKLL-GLSRTVVAELAASGDVLIDGKVASKSDRLTAGDLLEV---- 62

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
             L       ++    V   +        +L+ED  I V +KP G++V    G     + 
Sbjct: 63  -TLPEPDTPAEVSAEPVEGLR--------ILHEDDDIVVVDKPVGVAVHPSPGWTGPTVV 113

Query: 131 GFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           G L +    + + G   R  + HRLD  T+G++VVA++  A   L  +F+ R + K Y +
Sbjct: 114 GGLAAAGLRISTSGAAERQGVVHRLDAGTTGVMVVAKSEHAYSVLKRAFKERTVSKGYHA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G P   +  I   + +  H   DY   V     G   +I+H++VI+ F +    +++
Sbjct: 174 LVQGHPDPTRGTIDAPIDR--HPRYDYKFAVVT---GGKPSITHYEVIEAF-RAASLVDV 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI------QNKLYLHARYMDLPH 299
           Q  TGRTHQ+RVH   M  P VGD  Y A+       P+        + +LHAR +   H
Sbjct: 228 QLETGRTHQIRVHFSAMRHPCVGDLTYGAD-------PVLARRLGLTRQWLHARTLGFAH 280

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  GR ++ T+  PA +    D L
Sbjct: 281 PADGRWVEFTSEYPADLAAALDIL 304


>gi|317478569|ref|ZP_07937726.1| RluA family pseudouridine synthase [Bacteroides sp. 4_1_36]
 gi|316905210|gb|EFV27007.1| RluA family pseudouridine synthase [Bacteroides sp. 4_1_36]
          Length = 356

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 91/349 (26%), Positives = 157/349 (44%), Gaps = 53/349 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQEMMRVDKYLFDRLTNSSRNRIQKAADAGFVMANGKAVKSSYKVKPMDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYENEVIPEDIPLD---------IVYEDKYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 138 LVNAIAWH----MKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKT 193

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LVWG  +  +  +   + +      D + +    +    +A++H++V+     
Sbjct: 194 TKRRYRALVWGNVEQDEGTVVGNIGRNPR---DRMQMTVLPDDQGKHAVTHYRVLKRLGY 250

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNF-------------TSP 283
               +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG               T P
Sbjct: 251 -VTLVECILETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFDTCP 309

Query: 284 IQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS-LGFKYDRNL 330
            Q    LHA  +   HP  G  +  T+ LP  M +  D   G+  +R L
Sbjct: 310 RQA---LHAMTLGFVHPVTGEEMYFTSELPDDMTRLIDKWRGYISNREL 355


>gi|183222495|ref|YP_001840491.1| pseudouridine synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Paris)']
 gi|189912533|ref|YP_001964088.1| 23S RNA-specific pseudouridylate synthase [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Ames)']
 gi|167777209|gb|ABZ95510.1| Pseudouridylate synthase, 23S RNA-specific [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Ames)']
 gi|167780917|gb|ABZ99215.1| Pseudouridine synthase (Uracil hydrolyase) [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 312

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 91/309 (29%), Positives = 148/309 (47%), Gaps = 44/309 (14%)

Query: 9   YVVVENDEENMRLDRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +V V  D +  RLD + K N    ++   +QK + SG V          N+ +  QVV  
Sbjct: 4   FVTVSEDYDQSRLDVFLKDNAGDDLSRSTVQKWIDSGFV---------TNKTKD-QVVHK 53

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-----LLYEDSKIYVFNKPAGISVQGG 122
               N     + E+ ++D    + +    L+ I     +LY++ +  V +K AGI+   G
Sbjct: 54  ----NGYKVALGEEFVVDV---IARPPSRLEPIAMDIPVLYDEDEFMVIHKKAGIACHSG 106

Query: 123 SG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++G L  + +  G    ++P + HRLD+ T G+L++A+T  A   L++ F+ 
Sbjct: 107 PGDDSPSLVNGLLYQFKNLSGTGGERRPGIVHRLDKPTEGVLIIAKTDRAHAALSKLFQD 166

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFK---- 231
           R ++K Y++ V   P   +  I         IG   V  VK    +    AI+H+K    
Sbjct: 167 RLVEKTYYAWVLQAPVEAEGTI------NMPIGRHPVERVKMCVREDGRMAITHYKTEKI 220

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V     +KF  +++   TGRTHQ+RVH   +GCP+VGD  Y  + K ++T   Q  L L 
Sbjct: 221 VQTQTGRKFSLMKLGLETGRTHQIRVHMAKVGCPVVGDSLYSRSAK-DYT---QYGLLLF 276

Query: 292 ARYMDLPHP 300
           A+ +D PHP
Sbjct: 277 AKKLDFPHP 285


>gi|221133960|ref|ZP_03560265.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity [Glaciecola sp.
           HTCC2999]
          Length = 227

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/205 (35%), Positives = 111/205 (54%), Gaps = 21/205 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D  I V  KP G+ SV+G +  A H D   K   D      R+ HRLD  TSGI+V
Sbjct: 16  ILHQDEDIIVLAKPPGLLSVRGRA--ANHQDSLQKRVTDVYPNA-RIVHRLDMATSGIIV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +A  ++A QHL+  F  R+ QK Y++ V G +  ++ E  A  ++       D+ +  KQ
Sbjct: 73  MAMHKSANQHLSAQFAERKTQKRYFARVLGQMSVSEGEITAPLIV-------DWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   +++HFKV++   +K   +E+ P TGR+HQLRVH L +G PI+GD  Y   
Sbjct: 126 KVCYETGKK-SLTHFKVVEV-GEKTTLVELHPVTGRSHQLRVHLLSIGHPILGDRLYTEA 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
           +     +    +L+LHA  +   HP
Sbjct: 184 YTREGVT----RLWLHAAELGFYHP 204


>gi|319935496|ref|ZP_08009931.1| pseudouridine synthase [Coprobacillus sp. 29_1]
 gi|319809527|gb|EFW05944.1| pseudouridine synthase [Coprobacillus sp. 29_1]
          Length = 324

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 94/325 (28%), Positives = 147/325 (45%), Gaps = 50/325 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++++ +  N R+D++ K          + K+LR   V+V+  +VK N  +Q+  VV +  
Sbjct: 4   LIIDENHANQRIDKYLKKLLCQAPSQLIYKMLRKKDVKVNGVKVKENYILQNHDVVELFL 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSG 124
             +      + Q I D  +            ++YED KI V  KPAG+ V     +  + 
Sbjct: 64  YEDKFQEYTRAQTIFDLKIEFQ---------VIYEDDKILVVGKPAGLLVHEDINEDMNT 114

Query: 125 IAYHIDGFL--KSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR- 178
           ++  +  +L  K   D   S G  P   HRLD+ TSGI++  +T  A Q L E  + R  
Sbjct: 115 LSNQVITYLYQKGEYDPQISLGFTPGPVHRLDRNTSGIVIFGKTMRALQDLNEMMKKRHC 174

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDCF 236
           I+K Y ++  G   +    +  ++ K     GD   V VV QN  GA    +  + I+ +
Sbjct: 175 IEKTYLTICKGHMSSAD--LVGYMKK----DGDQSLVKVVTQNTPGALMMHTLVENIE-Y 227

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN----------------- 279
            Q F  L++Q  TGRTHQ+RVH   +G PI+GD KY  +F+ N                 
Sbjct: 228 HQGFSLLKVQLVTGRTHQIRVHLASVGHPIIGDSKY-GDFELNREMKKKYHLQHQFLHAY 286

Query: 280 ---FTSPIQNKLYLHARYMDLPHPE 301
              F  PI    YL  + M  P P+
Sbjct: 287 TIKFVKPIGCLKYLQNQVMICPLPQ 311


>gi|93005955|ref|YP_580392.1| pseudouridine synthase, RluD [Psychrobacter cryohalolentis K5]
 gi|92393633|gb|ABE74908.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter
           cryohalolentis K5]
          Length = 396

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 92/340 (27%), Positives = 149/340 (43%), Gaps = 43/340 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++ V+E DE  +R+D+     +   + V LQ  +  G +        +N  IQ  ++  
Sbjct: 81  VKHTVIE-DEAGLRIDKLASKIFTDFSRVQLQGWVSDGSLL-------YNGSIQKPKIR- 131

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSI---LLYEDSKIYVFNKPAGISVQGG 122
                      +K   IL  S  L +HS D  + I   ++YED  + V NKP G+ V  G
Sbjct: 132 -----------VKAGDILHLSTTLEQHSEDQPEDIAIDVVYEDDDVLVINKPVGMVVHPG 180

Query: 123 SG--IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           +G      ++  L  +   +   PR  L HR+D++TSG+L++ +T+ A   L E  + + 
Sbjct: 181 AGNQTGTLVNALLYHY-PQQHHLPRAGLVHRIDKDTSGLLLIGKTKPAQLALMEQLKDKS 239

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFA 237
           + + Y  +V G        ++      + IG       K     A   A++H   +    
Sbjct: 240 VYRHYQCVVAG----DAASLSRHRRIDAPIGRHRNQRTKMTVMTAGREAVTHLLNVTALN 295

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTS----PIQN--KLY 289
             +C L++   TGRTHQ+RVH  H+  PIVGD  Y      +   T      I N  +  
Sbjct: 296 GNYCLLDIGLETGRTHQIRVHLSHITYPIVGDRVYGGRRQLRAGLTEAQRQAINNFPRQA 355

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           LHA  +   HP  G  +++T P+P  M +    L   YD 
Sbjct: 356 LHAYTLGFVHPTTGEDVEVTTPMPEDMQQLMAVLSDGYDE 395


>gi|315648999|ref|ZP_07902093.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
 gi|315275680|gb|EFU39034.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
          Length = 358

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 88/307 (28%), Positives = 136/307 (44%), Gaps = 59/307 (19%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           + ++  RV  + ++Q+G ++ I            EQ+  D  +      D     +LYED
Sbjct: 46  IMLNGTRVYISAKVQTGDIIEIR----------MEQERSDDMLPQPMELD-----ILYED 90

Query: 106 SKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVAR 162
             + V NKPAGI V    G       +G +  W++     + R  HRLDQETSG+LVVA+
Sbjct: 91  GHLLVLNKPAGIIVHPTKGHYTDTLANGVVHYWLEQGWNYRFRAVHRLDQETSGVLVVAK 150

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                QH++E      + K Y +LV G P ++   I      +  I  D +   ++    
Sbjct: 151 NPYVHQHVSEQMIAGTVDKRYIALVHGTPASRSGDI------EGPIDRDPLEPHRRIVTP 204

Query: 223 ANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--------- 272
             Y +++ +KV + F +    +E++  TGRTHQ+RVH L +GCP++GD  Y         
Sbjct: 205 GGYPSLTRYKVCETF-KSASMVELKLETGRTHQIRVHMLSIGCPLIGDRMYRHPVYDTRV 263

Query: 273 -----------CANFKGNF------TSPIQ------NKLYLHARYMDLPHPEGGRLQI-T 308
                       A   G         + IQ       +  LHA  + L HP  GR  + +
Sbjct: 264 QRNDQVQTIAPEAALNGVVPRTELEAASIQELDSSIGRQALHAASLTLVHPIEGRTMVFS 323

Query: 309 APLPAHM 315
           APLP  M
Sbjct: 324 APLPEDM 330


>gi|331661428|ref|ZP_08362352.1| pseudouridine synthase A [Escherichia coli TA143]
 gi|331061343|gb|EGI33306.1| pseudouridine synthase A [Escherichia coli TA143]
          Length = 219

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 115/216 (53%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R+ +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFRERKPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|257458325|ref|ZP_05623473.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
 gi|257444260|gb|EEV19355.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
          Length = 326

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 87/349 (24%), Positives = 157/349 (44%), Gaps = 52/349 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT +    V +    +RLD +  +  P++    L+  ++S  V ++ ++ K ++ +Q+G 
Sbjct: 1   MTEIFEFKVPDGTGKLRLDAFCSSVLPNMTRSRLKTGMQS--VELNGRQAKLSSSVQAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +++     + + +I E   L                +LYED+ +   NK  G+     +
Sbjct: 59  RIKLMWNNPSPDFLIPEHIPLQ---------------ILYEDNDVIAVNKRVGMVTHPAA 103

Query: 124 G---------IAYHI-------DGFLKSWVDSKGQ-------KPRLTHRLDQETSGILVV 160
           G         +AY+        D F       +G+       +  + HRLD++TSG+L+ 
Sbjct: 104 GNWTGTLVQALAYYRLHTSPIHDKFAGLLEAEQGRGNFEDLLRAGIVHRLDKDTSGVLIT 163

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR+ AA   L + F+MRR +K Y +++ G+P+ +   I   + +  H           + 
Sbjct: 164 ARSAAAEAFLKDEFKMRRTEKYYAAILNGVPEKRTGVIETSVFRDEH--SRIRFTASADL 221

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               YA S +KV+  +  ++  +  +  TGRTHQ+R+HA  +GCPIVGD  Y    K   
Sbjct: 222 AKGKYARSRYKVLRVYG-RYALVLFKIDTGRTHQIRLHARFIGCPIVGDPLYGK--KEAE 278

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLP------AHMVKTWDSLG 323
             P    L+ +   + LP     +   TAPLP       H+++T  + G
Sbjct: 279 WKPYGMMLHAYRLCVALPSTR-EKTVFTAPLPRRFQTVLHLLRTQQANG 326


>gi|167765516|ref|ZP_02437580.1| hypothetical protein CLOSS21_00010 [Clostridium sp. SS2/1]
 gi|167712701|gb|EDS23280.1| hypothetical protein CLOSS21_00010 [Clostridium sp. SS2/1]
 gi|291558984|emb|CBL37784.1| ribosomal large subunit pseudouridine synthase D
           [butyrate-producing bacterium SSC/2]
          Length = 305

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/313 (25%), Positives = 142/313 (45%), Gaps = 36/313 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVINALNHI 77
           RLD         +    + K+ +  +  ++ K  K N + + G V+  ++P         
Sbjct: 17  RLDVVLSEQCSDLTRSYINKLCKEERAALNGKTSKGNKKCKEGDVITLQVPEPT------ 70

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
             E +IL   +NL          ++YED  + + NKP G+ V   +G      ++G +  
Sbjct: 71  --ELEILPEEMNLD---------IVYEDQDVILINKPKGMVVHPAAGHYSGTLVNGLMAH 119

Query: 136 WVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             D         +P + HR+D++T+GIL+V +   A Q + +      I + Y ++V+G 
Sbjct: 120 CKDDLSGINGVLRPGIVHRIDKDTTGILIVCKNDMAHQSIAKQLYDHSITRKYHAIVYGN 179

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K ++E   N  + +S      + +V        +A++H+KV+    + F ++E Q  TG
Sbjct: 180 IK-EEEGTVNAPIGRSLKDRKKMGIVMD----GKHAVTHYKVLKRLKKGFTYIECQLETG 234

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH   +  P++GD  Y    K  +T   Q    LHA+ +   HP  G  ++   
Sbjct: 235 RTHQIRVHMASIKHPLLGDDVYGPK-KSKYTLEGQ---CLHAKVLGFVHPRTGEYMEFEV 290

Query: 310 PLPAHMVKTWDSL 322
           PLP +  K  + L
Sbjct: 291 PLPEYFEKLLNKL 303


>gi|91215096|ref|ZP_01252068.1| hypothetical protein P700755_12402 [Psychroflexus torquis ATCC
           700755]
 gi|91186701|gb|EAS73072.1| hypothetical protein P700755_12402 [Psychroflexus torquis ATCC
           700755]
          Length = 292

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 78/291 (26%), Positives = 136/291 (46%), Gaps = 55/291 (18%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           L+K ++ G + +D +  + ++ I+ GQV+ +         ++ ++K+             
Sbjct: 41  LKKAIKKGLLFLDGRVAETSDWIEEGQVLEL-----FAEELLYKKKVFP----------- 84

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGG------SGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           L+  +++ED  + V NKP G    G       + + Y++     S    K   P+  HRL
Sbjct: 85  LQLKVIFEDDSMAVVNKPEGYPTNGNYFKTIENALTYNLK---TSSEKDKLPYPQPVHRL 141

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+L++A+T ++  +L+  F   ++ KIY ++V G                 H  G
Sbjct: 142 DNPTSGLLIIAKTLSSKSYLSVLFEHNKVHKIYLAIVEG-----------------HFEG 184

Query: 211 --DYVHV-VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             D + + +   +   NY +   K+      +F  L ++P +GRTHQLR+H   +G PIV
Sbjct: 185 LSDIISLDIDGKQSSTNYGVE--KMFKINQDEFSLLSLKPSSGRTHQLRIHLSKIGHPIV 242

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           GD  Y     G+ T  + NKL LHA  ++L HP+  + L     +P   VK
Sbjct: 243 GDKTY-----GSLT--LSNKLMLHASSLELRHPKTDKSLSFETEVPHKFVK 286


>gi|295091829|emb|CBK77936.1| pseudouridine synthase, RluA family [Clostridium cf.
           saccharolyticum K10]
          Length = 345

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 87/337 (25%), Positives = 148/337 (43%), Gaps = 38/337 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVN---LQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           ++ V V  +E   RLD+     + ++N      + K+LR   + ++ K+   + R+  G 
Sbjct: 1   MRLVTVTKNEAGQRLDKLL---FKYMNLAGKSFVYKMLRKKNITLNGKKCDGSERLLEGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+          + E+ I   S    +    +K  ++YED  +   NKPAG+  Q   
Sbjct: 58  EIRL---------FLSEETIEKFSEVKVQKVSRVKLEIVYEDEDVIFINKPAGMLSQKAR 108

Query: 124 GIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                +  +L +++   GQ         +P + +RLD+ TSG++   ++    Q L+   
Sbjct: 109 DGDESLVEYLIAYLMESGQLTKEELKSFRPSVCNRLDRNTSGLVAAGKSLPGLQELSRII 168

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R I K Y  LV G  K     I  WLLK      + V V K+ E+G +  I       
Sbjct: 169 KDRSIGKYYLCLVKGQVKQPSR-IEGWLLKDERT--NRVEVTKE-ERGGSLPICTEYTPL 224

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLH 291
             +     L+++  TGR+HQ+R H   +GCP+VGD KY     N K      +  +L LH
Sbjct: 225 LRSGAHTLLKVKLITGRSHQIRAHLASIGCPVVGDRKYGDPAENRKAREQFGVTGQL-LH 283

Query: 292 ARYMDLPHPEGGRL------QITAPLPAHMVKTWDSL 322
           A  + +P    G L      +  APLP   +   +++
Sbjct: 284 AAELVMPGELSGPLCRLRGRKFAAPLPEAFLTMAEAV 320


>gi|225572187|ref|ZP_03781051.1| hypothetical protein RUMHYD_00481 [Blautia hydrogenotrophica DSM
           10507]
 gi|225040359|gb|EEG50605.1| hypothetical protein RUMHYD_00481 [Blautia hydrogenotrophica DSM
           10507]
          Length = 343

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 94/329 (28%), Positives = 158/329 (48%), Gaps = 33/329 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + ++ ++   RLD++            L K+LR   + ++KK+   N +++ G  V+
Sbjct: 1   MQQMDIKENDAGQRLDKYLSKLLFKAPKSFLYKMLRKKNITLNKKKASGNEKLKPGDQVQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---- 122
           +            ++     S +    +D L+  +LYEDS++ + NKPAGI  Q      
Sbjct: 61  L---------FFSQETFEKFSRDDFYPTDDLQLEILYEDSQVMILNKPAGILSQKSRPED 111

Query: 123 -SGIAYHIDGFLKS----WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            S + Y +   L+S      D +  +P + +RLD+ T+GI+   +T A+ Q L++ F  R
Sbjct: 112 VSLVEYMLSYLLESGQFTQTDFRTFRPGICNRLDRNTTGIVAAGKTLASLQSLSQMFHDR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  LV G    KK  I  +L K +      V  V    KGA    + ++ +   A
Sbjct: 172 TLEKYYLCLVKG-KIIKKNFIKGYLHKDTKCNKVIVSSVPI--KGAQPIETSYEPLTSNA 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTS--PIQNKLYLHARY 294
            K   L +   TGRTHQ+R H   +G PI+GD KY  A++  ++     +Q+++ LHA  
Sbjct: 229 -KLTLLRVHLITGRTHQIRSHLASIGHPILGDPKYGDASWNQDYFRRYKLQHQV-LHAVQ 286

Query: 295 MDLPHPEG------GRLQITAPLPAHMVK 317
           ++ P  EG      GR    APLPA   +
Sbjct: 287 LNFPVMEGTLEHLSGR-HFFAPLPAQFTE 314


>gi|311693418|gb|ADP96291.1| pseudouridine synthase, RluA family [marine bacterium HP15]
          Length = 325

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 94/348 (27%), Positives = 159/348 (45%), Gaps = 61/348 (17%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV  +  + RLD+      P  +   LQ  ++SG + V+ +  K  +++           
Sbjct: 12  VVPPELSDRRLDQAAAELMPEHSRSRLQSWIKSGALTVNGEVRKPRDKV----------- 60

Query: 71  INALNHIIKEQKILDSS--VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                 ++ ++  LD+     ++  ++ +   ++YED  + V NKPAG+ V   +G   H
Sbjct: 61  ------MLDDRLALDAEPEAQVSWQAEEISLDIVYEDEHLLVINKPAGLVVHPAAG---H 111

Query: 129 IDGFLKS----WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG L +    +       PR  + HRLD++TSGI+VVAR+  A   L +  + R + + 
Sbjct: 112 ADGTLVNALLNYAPEVENLPRAGIVHRLDKDTSGIMVVARSLIAHTSLVDQLQTRTMGRE 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVIDCFA 237
           Y ++V G            L   + +        ++ +K A       A++H+++++ FA
Sbjct: 172 YEAVVVGT-----------LTGGATVDAPIGRHPRERKKMAVVASGKPAVTHYRLVERFA 220

Query: 238 QKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQ------N 286
                 C LE    +GRTHQ+RVH  H+  P+VGD  Y    +     T  ++      N
Sbjct: 221 AHTHVRCKLE----SGRTHQIRVHMAHVKHPLVGDPLYGGRLRLPKGTTDELREALSTFN 276

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
           +  LHAR + L HPE G  L    PLP  MV   ++L  K+ R L  +
Sbjct: 277 RQALHARQLTLEHPETGEILTWEVPLPEDMVALIEAL-RKHARELETR 323


>gi|309800529|ref|ZP_07694680.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           infantis SK1302]
 gi|308115840|gb|EFO53365.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           infantis SK1302]
          Length = 297

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 83/308 (26%), Positives = 147/308 (47%), Gaps = 42/308 (13%)

Query: 39  KILRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           KI R G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   V  
Sbjct: 4   KIERGG-IRLDKALSDLTELSRSLANEQIKSGQVL-VNGQVKKAKYTVQEGDVVTYQVPE 61

Query: 91  TKHSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG 141
            +  +++   +    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G
Sbjct: 62  PEVLEYVAEDIPLEIIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSG 118

Query: 142 ----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  
Sbjct: 119 INGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGV 178

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +           VK        A++ F+V++ F   +  LE+Q  TGRTHQ+RV
Sbjct: 179 IEAPIGRSEKDRKKQAVTVK-----GKPAVTRFQVLERFGD-YTLLELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG+         +LHA+ +   HP+ G  ++ TA +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPKTGETMEFTADIPDI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKQTLEKL 293


>gi|157150916|ref|YP_001450379.1| RluA family pseudouridine synthase [Streptococcus gordonii str.
           Challis substr. CH1]
 gi|157075710|gb|ABV10393.1| pseudouridine synthase, RluA family [Streptococcus gordonii str.
           Challis substr. CH1]
          Length = 296

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/293 (27%), Positives = 143/293 (48%), Gaps = 37/293 (12%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS----ILLY 103
            D  R   N +I++G+++ +  ++    + +KE  ++   +   +  +++       ++Y
Sbjct: 20  TDLSRSLANEQIKTGKIL-VNGLVKKAKYTVKEGDVISYELPEIEEIEYVTENIPLEIVY 78

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLDQET 154
           +D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D++T
Sbjct: 79  QDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRIDKDT 135

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG     
Sbjct: 136 SGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRSEKD 189

Query: 215 VVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             KQ    KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y
Sbjct: 190 RKKQAVTAKG-KPALTRFQVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGDEVY 247

Query: 273 CA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 KG+         +LHAR +   HP  G  L+ TA +PA   +T   L
Sbjct: 248 GPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAGVPAIFQETLKKL 293


>gi|298386878|ref|ZP_06996433.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 1_1_14]
 gi|298260552|gb|EFI03421.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 1_1_14]
          Length = 223

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/230 (31%), Positives = 108/230 (46%), Gaps = 38/230 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQ        +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQADKTGDTPLSETVKQYLKEKYHKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR   ++K YW++V   PK  +              G+ VH 
Sbjct: 63  GLVIFAKTSKALTRLNEMFRTSEVKKTYWAVVKNAPKEPE--------------GELVHY 108

Query: 216 VKQNEK------------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           + +NEK             +  AI ++++I   ++ +  LE+   TGR HQ+R     MG
Sbjct: 109 LARNEKQNKSFAYDKEVPNSKKAILNYRLIG-HSENYYLLEVDLKTGRHHQIRCQLAKMG 167

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
           CPI GD KY     G   S     + LHAR +   HP    L ++ APLP
Sbjct: 168 CPIKGDLKY-----GAPRSNPDGSICLHARKVRFIHPVSKELIELEAPLP 212


>gi|325263985|ref|ZP_08130718.1| ribosomal large subunit pseudouridine synthase C [Clostridium sp.
           D5]
 gi|324031023|gb|EGB92305.1| ribosomal large subunit pseudouridine synthase C [Clostridium sp.
           D5]
          Length = 331

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 87/335 (25%), Positives = 150/335 (44%), Gaps = 24/335 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V ++E   RLD+    +        L K+LR   + ++ K+   N ++  G  ++
Sbjct: 1   MQQITVGDNEAGQRLDKLLAKYLREAPKSFLYKMLRKKNITLNGKKASGNEKLLRGDEIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +     + K    +  L + S      ++YEDS I + NKPAG+  Q  +   
Sbjct: 61  LFLADETIAKFAGDAKPHAENGMLNRLSYGESLNIIYEDSHIILINKPAGMLSQKAADTD 120

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   L +++   G          +P + +RLD+ TSG++   ++    Q L+  F+ R
Sbjct: 121 VSLVEHLTAYLLRSGALTEDEMRTFRPSVCNRLDRNTSGMVAAGKSLQGLQELSRLFKDR 180

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  LV G   N+   I  +L K +    + VH+    E+G+    + F+ +    
Sbjct: 181 TLGKYYHCLVKG-EVNETSHIHGFLKKDAE--NNQVHITAGQEEGSTAIETEFRPLKS-G 236

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARY 294
                LE+   TG+THQ+R H   +G PI+GD+KY     N +      ++++L LHA  
Sbjct: 237 NDVTLLEVHLITGKTHQIRAHLASVGHPILGDYKYGDRRLNDRCRSAYGLKHQL-LHAYR 295

Query: 295 MDLPHPEG------GRLQITAPLPAHMVKTWDSLG 323
           +  P  EG      GR +  APLPA   K     G
Sbjct: 296 ITFPALEGPLAGLSGR-EFLAPLPAEFQKIAKEKG 329


>gi|325197923|gb|ADY93379.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis G2136]
          Length = 374

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 85/307 (27%), Positives = 140/307 (45%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ +R+            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKPSQPKDKMIGGEQIRV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWRGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-PHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C++        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAGDPVYGNPRHPCSDPVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|163745453|ref|ZP_02152813.1| ribosomal large subunit pseudouridine synthase A [Oceanibulbus
           indolifex HEL-45]
 gi|161382271|gb|EDQ06680.1| ribosomal large subunit pseudouridine synthase A [Oceanibulbus
           indolifex HEL-45]
          Length = 215

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 68/220 (30%), Positives = 113/220 (51%), Gaps = 25/220 (11%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++L+ED+++ + +KPAG+    G G   H+   L + V +   +  L HRLD++TSG+++
Sbjct: 13  VILHEDAEVLLVDKPAGLLSVPGKG--EHLADCLIARVQAVFPEALLVHRLDRDTSGVMI 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVH 214
            A T  A +HL   F  R  +K Y + VWG+P+ K        I +W  +   +      
Sbjct: 71  FAMTAHAQRHLGLQFEKRMTRKTYVARVWGVPEEKSGSIDLPLIVDWPNRPLQM------ 124

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V  +  K A    + +KVI    +    + + P TGR+HQLRVH L +G PI+GD  Y  
Sbjct: 125 VCHETGKPAQ---TDWKVIKTDGET-SRVRLFPKTGRSHQLRVHMLALGHPILGDPFYAT 180

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAPL 311
               ++      +L LH+  +   HP+GG   ++++ AP 
Sbjct: 181 GPARDYP-----RLMLHSEELRFNHPQGGASTKVRVKAPF 215


>gi|86158324|ref|YP_465109.1| ribosomal large subunit pseudouridine synthase D [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|85774835|gb|ABC81672.1| ribosomal large subunit pseudouridine synthase D [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 353

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 87/338 (25%), Positives = 146/338 (43%), Gaps = 55/338 (16%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPP 69
           V  +    RLD       P ++   +Q+++ +G+V+VD +  K + R++ G+ +   IPP
Sbjct: 28  VPPELAGARLDAALVRLAPELSRARVQRLVEAGRVQVDGRAAKASARLRGGEAIALEIPP 87

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                    +   ++   + L          +L+ED+ + V +K  G+ V    G  +  
Sbjct: 88  P--------EPSGLVAQDLPLA---------VLHEDADLIVLDKAPGMVVHPARGTPHST 130

Query: 129 -IDGFL-----KSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            ++  L      +     G  PRL   HRLD++TSG LVVA+T AA   L   ++ R ++
Sbjct: 131 VVNALLHRLGLPAAAGPDGALPRLGLVHRLDKDTSGCLVVAKTEAALAALQAQWKGRSVE 190

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK------GANYAISHFKVID 234
           K+Y +L  G            L     +   Y    +   +       +  AI+ ++V +
Sbjct: 191 KVYLALCHGA-----------LAAAGRLDTPYGRHPRDRLRFTGRLASSRRAITEWRVRE 239

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP---------IQ 285
            F       E+  HTGRTHQ+RVH    G P++GD  Y    +    +P           
Sbjct: 240 AFGPAASLAEVTLHTGRTHQIRVHLSEAGHPLLGDAVYGGTRREARLAPDDPARRAAEAV 299

Query: 286 NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            +  LHA  + L HP  G RL + AP+PA +    + L
Sbjct: 300 GRQALHALRLGLDHPRTGRRLVVEAPVPADLRAALEIL 337


>gi|119952824|ref|YP_945033.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           turicatae 91E135]
 gi|119861595|gb|AAX17363.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           turicatae 91E135]
          Length = 326

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 109/226 (48%), Gaps = 21/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  + V +KP GI    G           + YHI G   S+ + K  +P + HRLD
Sbjct: 86  ILYEDINVIVVDKPQGILSHPGISNLENTIVNFLLYHISGLRDSFQEDK-LRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG+++ A+       L+  F+ R ++K+Y ++V G  K     I  ++ +  H    
Sbjct: 145 KETSGVMICAKNLKTLNFLSRQFKERFVKKVYIAVVKGNFKIDSGIIETFIDRDRHDRKR 204

Query: 212 Y-VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           + VH     E     A++ ++V+      +  + ++P TGRTHQLRVH  H+  PI+GD 
Sbjct: 205 FSVH-----ENRGKRALTEYRVLASIGN-YSLVALKPKTGRTHQLRVHMKHLNHPILGDS 258

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
            Y A     F    +  L LHA  +++   EG   +  +  P   +
Sbjct: 259 IY-ARLDKEFK---EMSLMLHAFKLEINIKEGSLKKFISVFPQRFI 300


>gi|121634501|ref|YP_974746.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis FAM18]
 gi|120866207|emb|CAM09947.1| putative ribosomal large subunit pseudouridine synthase D
           [Neisseria meningitidis FAM18]
 gi|325131843|gb|EGC54543.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M6190]
 gi|325137893|gb|EGC60468.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis ES14902]
          Length = 374

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 85/307 (27%), Positives = 140/307 (45%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ +R+            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKPSQPKDKMIGGEQIRV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWRGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-THSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C++        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAGDPVYGNPRHPCSDPVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|298207134|ref|YP_003715313.1| hypothetical protein CA2559_02735 [Croceibacter atlanticus
           HTCC2559]
 gi|83849768|gb|EAP87636.1| hypothetical protein CA2559_02735 [Croceibacter atlanticus
           HTCC2559]
          Length = 283

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 109/223 (48%), Gaps = 31/223 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSKGQK---PRLTHRLDQETS 155
           +L+ED  + V NKPAG    G     IA  +   LK  + +K      P+  HRLD  TS
Sbjct: 81  VLFEDDYVAVINKPAGYPTSGNFFKTIAKALPYNLK--ISTKNDALLIPQPIHRLDNPTS 138

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LVVA+T+++  +L +   ++ IQK Y ++V   P +        +L   +I G     
Sbjct: 139 GVLVVAKTKSSQINLNKQLELKGIQKTYIAVVHNTPDSN-------MLFNDNIDG----- 186

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K++E      I  FKV D     +  +E+ P TGRTHQLR+H    G PIVGD  Y  +
Sbjct: 187 -KESESKLEI-IKTFKVKDDI---YSLVELFPKTGRTHQLRIHTSKAGYPIVGDQLYGIS 241

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            + N       KL LHA+ +   HP  G  +  T+ LP    K
Sbjct: 242 SEKN------KKLLLHAKSIQFKHPVTGNEVFTTSELPKRFEK 278


>gi|189502073|ref|YP_001957790.1| hypothetical protein Aasi_0665 [Candidatus Amoebophilus asiaticus
           5a2]
 gi|189497514|gb|ACE06061.1| hypothetical protein Aasi_0665 [Candidatus Amoebophilus asiaticus
           5a2]
          Length = 341

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 94/333 (28%), Positives = 156/333 (46%), Gaps = 55/333 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           + V+  ++  R+D++  +  P+ +   +Q  + +  + V+    K N +I+    ++I  
Sbjct: 19  ITVDPGQKPYRIDKFLIDRLPNTSRNKIQLAIDNQFILVNGIPTKANYKIRPYDKIQIVL 78

Query: 68  --PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--- 122
             PP  N L   I E   LD               ++YED  + V +KPAG+ V  G   
Sbjct: 79  PNPPRNNEL---IPENIPLD---------------IVYEDEALMVVHKPAGMVVHPGYNN 120

Query: 123 ------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                 + + Y+ D  L +  ++ G +P L HR+D++TSG+LVVA+T A+   L + F  
Sbjct: 121 WTGTLVNALIYYFDN-LPTAPNNIG-RPGLVHRIDKDTSGLLVVAKTEASLIALAKQFYD 178

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y++L+WG P+ +   I +  L +S      V      EKG   A++H++V++  
Sbjct: 179 HSIARTYYALIWGEPETETGTI-DINLDRSLQDRRIVAPYTNPEKGKR-AVTHYQVVERL 236

Query: 237 ---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN- 286
              +   C LE    TGRTHQ+R H  HMG PI  D  Y  +   KG     + S ++N 
Sbjct: 237 RYVSLVKCTLE----TGRTHQIRAHMKHMGHPIFADAAYGGHEIVKGEQFSKYKSFVENC 292

Query: 287 -----KLYLHARYMDLPHPEGGR-LQITAPLPA 313
                +  LHA  +   HP     +   +PLP 
Sbjct: 293 FQIMPRQALHAYSLGFIHPTTQENMYFESPLPT 325


>gi|295105659|emb|CBL03203.1| ribosomal large subunit pseudouridine synthase D [Faecalibacterium
           prausnitzii SL3/3]
          Length = 310

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 84/313 (26%), Positives = 145/313 (46%), Gaps = 35/313 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +VE +    R+DR+       ++   LQ ++  G V+ + K V  + ++++G  V +   
Sbjct: 7   IVEQETAGQRIDRFLSGEDTGLSRSALQALVAEGHVQCNGKTVAKSLKLKAGDTVLL--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                      +I D+        D    I+ YEDS + V NKP G+ V    G      
Sbjct: 64  -----------EIPDAKPIEAVPQDIPLEIV-YEDSHLLVVNKPKGMVVHPAPGNQDGTL 111

Query: 125 ---IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + +H  G L       G+ +P + HR+D++TSG+LVVA+  A    L++   +  ++
Sbjct: 112 VNALLWHCKGSLSGI---GGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVE 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V+G    + E      L +S      + V   NE    YA + +KV++   + F
Sbjct: 169 RAYQTVVYG-GFAQDEGFVEANLGRSKTDRKKMAVYPANEPHTKYAYTGYKVLERLGE-F 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE +  TGRTHQ+RVH   +  P+ GD  Y  +   N  + +  +  LHA+ +   HP
Sbjct: 227 TLLECRLKTGRTHQIRVHMASIHHPVAGDPVYGPH---NCITSLHGQC-LHAKTLGFVHP 282

Query: 301 -EGGRLQITAPLP 312
             G +L+  + LP
Sbjct: 283 ITGEQLRFDSELP 295


>gi|260221244|emb|CBA29613.1| Ribosomal large subunit pseudouridine synthase D [Curvibacter
           putative symbiont of Hydra magnipapillata]
          Length = 335

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 90/320 (28%), Positives = 145/320 (45%), Gaps = 37/320 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ--VVRIPPVINALNH 76
           RLDR         +   LQ+++ SG V+V+ K V K + +++ G+   V + P   +   
Sbjct: 35  RLDRALAFSVQEFSRSYLQQLIESGFVQVNGKVVTKTSGKVKVGEELTVELKPTPQS-QA 93

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
              E   LD               +++ED  + V NKPAG+ V    G      ++G L 
Sbjct: 94  FKPEPMALD---------------VVHEDEHVLVINKPAGLVVHPAPGNWSGTLLNGLL- 137

Query: 135 SWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV---WG 189
           ++       PR  + HRLD++TSG++VVAR+R A   L  +   R + + Y+++    W 
Sbjct: 138 AYSPHAALVPRAGIVHRLDKDTSGLMVVARSRTAMDALVNAIAAREVSRQYFAIAHKTWP 197

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             + K+         ++ +    V +V Q+ K A    + F +I   +Q  CW+    HT
Sbjct: 198 WTRLKEVDAPIGRDPRNRLRMAVVDLVHQSGKEAR---TDFSLISN-SQVACWVRCILHT 253

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  H+G P+V D  Y     G  T     +  LHA  +   HP  G  L+  
Sbjct: 254 GRTHQIRVHMAHIGHPLVADAVYGGAVLGEMT-----RQALHACRLAFKHPVSGESLEFE 308

Query: 309 APLPAHMVKTWDSLGFKYDR 328
              P+  +     LG  Y++
Sbjct: 309 CGPPSDFMALCAELGLGYNQ 328


>gi|251798409|ref|YP_003013140.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247546035|gb|ACT03054.1| pseudouridine synthase, RluA family [Paenibacillus sp. JDR-2]
          Length = 332

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 76/230 (33%), Positives = 114/230 (49%), Gaps = 18/230 (7%)

Query: 101 LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGI 157
           +LYED    V NKPAG+ V +  SG    +D     W+  +G     R  HRLD +TSG 
Sbjct: 114 VLYEDDFSLVLNKPAGMPVHESHSGQTGTLDEAAARWLLEQGDPLPVRHIHRLDDDTSGP 173

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ ++   A   L E+ R +RI + Y ++V G  K     +       + IG D  H  +
Sbjct: 174 VLYSKNDLAQWVLDEAMREKRIDRRYLAVVQGKVKKSSGTV------NAPIGKDRHHSSR 227

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +    G + AI+H++ I  F+     + +Q  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 228 RRVTPGGDLAITHYETIRAFSDATL-VRLQLETGRTHQIRVHMSHLGHPLLGDKLY---- 282

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
            G  T  +Q++  LH   +  PHP  G L +  A  P  +V   D LG +
Sbjct: 283 -GGDTRLLQHQ-ALHGERLLFPHPWTGELVEAAAAKPEWLVNLLDKLGGR 330


>gi|134095125|ref|YP_001100200.1| pseudouridine synthase [Herminiimonas arsenicoxydans]
 gi|133739028|emb|CAL62076.1| Ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Herminiimonas arsenicoxydans]
          Length = 318

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 85/303 (28%), Positives = 142/303 (46%), Gaps = 31/303 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+      P  +   LQ+ + +G V VD +  +    +   + V I P     +  
Sbjct: 24  GVRLDKVLSTLVPQYSRSRLQQWIDAGHVSVDGEIARAKMTVYGDEKVVIYPQPAPEDEA 83

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
            K + +    +N+            YED+ I V +KPAG+ V   +G      ++G L  
Sbjct: 84  FKPEAM---DLNIA-----------YEDAAILVIDKPAGLVVHPAAGNWSGTLLNGLLH- 128

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           ++ +    PR  + HRLD++TSG++VVA+T  A   L    + R +++ Y +LVWG P N
Sbjct: 129 YLPAIAGVPRAGIVHRLDKDTSGLMVVAKTLVAHTDLVRQLQARTVKREYLALVWGTP-N 187

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTG 250
               +   + + S    D V +       A  A++HF+ +       +    +  Q  TG
Sbjct: 188 VSGKVDTSIGRHSR---DRVKMAVSENLTAKPALTHFQRLATGMLDGRPVSLMMCQLETG 244

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH   +G  +VGD  Y    K + T+ +  +  LHAR + L HP  G  ++ ++
Sbjct: 245 RTHQIRVHMQSIGFALVGDALYG---KQHLTT-VFPRQALHARRLGLVHPVSGAAVEWSS 300

Query: 310 PLP 312
            LP
Sbjct: 301 ELP 303


>gi|148257971|ref|YP_001242556.1| ribosomal large subunit pseudouridine synthase D [Bradyrhizobium
           sp. BTAi1]
 gi|146410144|gb|ABQ38650.1| ribosomal large subunit pseudouridine synthase D [Bradyrhizobium
           sp. BTAi1]
          Length = 326

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 86/328 (26%), Positives = 145/328 (44%), Gaps = 58/328 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIP 68
           V+V  DE + RLDR      P ++   L+ ++ +GQV +    V+     + SG  +   
Sbjct: 3   VIVAGDEGSPRLDRVLAARLPELSRSRLKALILAGQVSLSTGAVRDPAYHVASGDTI--- 59

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I+       E K           ++ +   ++YED  I V +KPAG+ V   +G  + 
Sbjct: 60  -TIDVPEAAPPEPK-----------AEAIPLHVVYEDDDIVVLDKPAGLVVHPAAG--HE 105

Query: 129 IDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----R 175
               + + +   G         ++P + HRLD++T+G++VVA+   A   L+  F    R
Sbjct: 106 TGTLVNALIAHCGASLSGIGGVKRPGIVHRLDKDTTGLMVVAKNDHAHASLSAQFADHGR 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              +++ Y +  WG+P      I   L +  H   D + V  +  +    AI+H++V + 
Sbjct: 166 TGAMERGYLAFSWGLPHRPHGTINAPLDRHPH-ARDKMAVRPRGRE----AITHYEVQES 220

Query: 236 FAQK---------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSP- 283
           F  +          C LE    TGRTHQ+RVH  H+G  ++GD  Y  +F  K N  +P 
Sbjct: 221 FVGRDGKPVASLIACHLE----TGRTHQIRVHLAHLGHTLLGDAVYGPHFKTKANQLAPG 276

Query: 284 ------IQNKLYLHARYMDLPHPEGGRL 305
                    +  LHA  + + HP  G +
Sbjct: 277 ARAALEALGRQALHAYLLVIEHPRTGEI 304


>gi|91974839|ref|YP_567498.1| pseudouridine synthase RluD [Rhodopseudomonas palustris BisB5]
 gi|91681295|gb|ABE37597.1| ribosomal large subunit pseudouridine synthase D [Rhodopseudomonas
           palustris BisB5]
          Length = 426

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 83/326 (25%), Positives = 137/326 (42%), Gaps = 54/326 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV  DE + RLDR      P ++   L+ ++  G+V                  +R  P
Sbjct: 103 VVVAGDEGSPRLDRVLATRCPALSRSRLKALILDGRV-----------------AIRGAP 145

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILL---YEDSKIYVFNKPAGISVQGGSGIA 126
           V +   H    + I              ++I L   +ED  I V +KP G+ V   +G  
Sbjct: 146 VRDPAYHAASGETITIDVPPPVAPEPAGEAIALEIVHEDDDIIVIDKPRGLVVHPAAG-- 203

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESF--- 174
           +     + + +   G+         +P + HRLD++T+G++V A+   A Q L+  F   
Sbjct: 204 HETGTLVNALIAHCGESLSGIGGVRRPGIVHRLDKDTTGLMVAAKNDRAHQSLSAQFADH 263

Query: 175 -RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R   +++ Y++ VWG P   +  I   + +  H              G   AI+H++V+
Sbjct: 264 GRTGELRRGYYAFVWGAPNRIRGTIDAPIDRHPH-----AREKMAVRDGGREAITHWEVL 318

Query: 234 DCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--PIQ- 285
           + F  +        +  Q  TGRTHQ+RVH  H+G P++GD  Y  +FK   +   P   
Sbjct: 319 ETFTGRSGGEIVSLIACQLETGRTHQIRVHLAHIGHPLLGDDVYGPHFKTKASQLRPDAR 378

Query: 286 ------NKLYLHARYMDLPHPEGGRL 305
                  +  LHA  + L HP  G +
Sbjct: 379 AALTDLGRQALHAYLLVLEHPSTGEV 404


>gi|293365185|ref|ZP_06611902.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           oralis ATCC 35037]
 gi|307703723|ref|ZP_07640664.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
 gi|291316635|gb|EFE57071.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           oralis ATCC 35037]
 gi|307622558|gb|EFO01554.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
          Length = 299

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 83/296 (28%), Positives = 143/296 (48%), Gaps = 47/296 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +++GQV V+ +  K    +Q G +V          + + E ++L+        ++ L   
Sbjct: 31  IKAGQVLVNGQAKKAKYTVQDGDIV---------TYHVPEPEVLEYV------AENLPLE 75

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 76  IIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 132

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 133 KDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 186

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  LE+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 187 EKDRKKQAVTAKG-KPAVTRFQVLERFGD-YSLLELQLETGRTHQIRVHMAYIGHPVAGD 244

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHA+ +   HP  G  L+ TA +P    +T + L
Sbjct: 245 EVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGETLEFTADIPEIFKETLERL 293


>gi|167037761|ref|YP_001665339.1| RluA family pseudouridine synthase [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|320116174|ref|YP_004186333.1| RluA family pseudouridine synthase [Thermoanaerobacter brockii
           subsp. finnii Ako-1]
 gi|166856595|gb|ABY95003.1| pseudouridine synthase, RluA family [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|319929265|gb|ADV79950.1| pseudouridine synthase, RluA family [Thermoanaerobacter brockii
           subsp. finnii Ako-1]
          Length = 305

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 97/342 (28%), Positives = 163/342 (47%), Gaps = 63/342 (18%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-Q 60
           M  V  +V+  E ++E  R+D +      +     ++K++  G V V+ K VK + ++ +
Sbjct: 1   MNIVDKIVLQGEKEDEGKRIDVFLAAELDYTRSY-IKKLIVDGLVFVNGKTVKPSYKVKE 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           + +VV   P    ++ ++ E   LD               +LYED  I V NKP G+ V 
Sbjct: 60  NDEVVLNVPEAEKID-VLPEDIPLD---------------ILYEDDDIIVINKPQGMVVH 103

Query: 121 GGSG---------IAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
              G         + YH      I+G L+         P + HRLD++TSG++VVA+   
Sbjct: 104 PAPGNYSGTLVNALLYHCKNLSGINGILR---------PGIVHRLDKDTSGVMVVAKNDK 154

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE----K 221
           A   L+   + R + K Y ++V G+ K+++  I      ++ IG    H V + +    +
Sbjct: 155 AHISLSNQIKERSVFKKYVAIVEGVIKDEEGKI------EAPIGR---HPVDRKKMAVIE 205

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
              YA++ +KV++ F +    +E    TGRTHQ+RVH  ++G PIVGDH Y    +  F 
Sbjct: 206 DGRYALTLYKVLERFKEN-TLVEAVIKTGRTHQIRVHMAYIGHPIVGDHVYGFK-RQKFK 263

Query: 282 SPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
              Q    LH+  +   HP +G  ++  APLP + V+  + L
Sbjct: 264 LEGQA---LHSSVLGFMHPTKGVYMEFEAPLPEYFVRLIEIL 302


>gi|76789398|ref|YP_328484.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis A/HAR-13]
 gi|237805009|ref|YP_002889163.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis B/TZ1A828/OT]
 gi|255317785|ref|ZP_05359031.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 6276s]
 gi|76167928|gb|AAX50936.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis A/HAR-13]
 gi|231273309|emb|CAX10224.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis B/TZ1A828/OT]
 gi|296436198|gb|ADH18372.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis G/9768]
 gi|296437127|gb|ADH19297.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis G/11222]
 gi|296438058|gb|ADH20219.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis G/11074]
 gi|297140560|gb|ADH97318.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis G/9301]
          Length = 335

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 110/230 (47%), Gaps = 26/230 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +YED  I V NKP  + V    G         + + I   LK     +  +P + HRLD+
Sbjct: 92  VYEDDMILVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDK 151

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGG 210
           +TSG+L+  +TR A    +E F  ++++K+Y ++    P  +     IA   LK+  +  
Sbjct: 152 DTSGLLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQELIHTRIARHPLKRKEMT- 210

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               V+  + +G   AI+H  V+     +   + + P TGRTHQLRVH  H+G PI+GD 
Sbjct: 211 ----VLSTHAEGGKEAITHCHVLATNG-RLSVVALYPETGRTHQLRVHMKHLGTPILGDP 265

Query: 271 KY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
            Y     NF+        +K  LHA  +   HPE   R+++   LP  M 
Sbjct: 266 VYGIPSINFRYGL-----DKQQLHAYSLVFAHPESAERVKLVTKLPDDMT 310


>gi|291547301|emb|CBL20409.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus sp.
           SR1/5]
          Length = 245

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/212 (33%), Positives = 105/212 (49%), Gaps = 15/212 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK--GQKPRL--THRLDQETSG 156
           +LYED +I V  K AG+ VQ        ++  LK+++  K  G+ P L   HRLDQ   G
Sbjct: 10  ILYEDKEILVCRKTAGMPVQAAKIGTMDMESALKNYLAQKTPGKIPYLGVVHRLDQPVEG 69

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ILV A+T  AA +L++        K Y ++  G  K+ +  + ++L K      +   VV
Sbjct: 70  ILVFAKTSEAAGNLSKQMMAGGAGKYYLAVTEGKAKSSEGTLTDYLKKNGK--ANMSQVV 127

Query: 217 KQNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             N  GA  AI H+KV+D      +    L+++  TGR HQ+RV   H G PI+GD KY 
Sbjct: 128 SANTPGAKKAILHYKVLDQQEINGKSRTLLKIRLETGRHHQIRVQLSHEGLPILGDRKY- 186

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
                N +      L L +  ++  HP  G++
Sbjct: 187 -----NPSGEKGTSLGLCSSCLEFKHPRTGKM 213


>gi|260853270|ref|YP_003227161.1| pseudouridine synthase [Escherichia coli O26:H11 str. 11368]
 gi|260866210|ref|YP_003232612.1| pseudouridine synthase [Escherichia coli O111:H- str. 11128]
 gi|257751919|dbj|BAI23421.1| pseudouridine synthase [Escherichia coli O26:H11 str. 11368]
 gi|257762566|dbj|BAI34061.1| pseudouridine synthase [Escherichia coli O111:H- str. 11128]
 gi|323157880|gb|EFZ43983.1| RNA pseudouridylate synthase family protein [Escherichia coli
           EPECa14]
 gi|323176365|gb|EFZ61957.1| RNA pseudouridylate synthase family protein [Escherichia coli 1180]
 gi|324118408|gb|EGC12302.1| RNA pseudouridylate synthase [Escherichia coli E1167]
          Length = 219

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETGKP-AQTEYEVVEYVADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|331645166|ref|ZP_08346277.1| pseudouridine synthase A [Escherichia coli M605]
 gi|331045923|gb|EGI18042.1| pseudouridine synthase A [Escherichia coli M605]
          Length = 219

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETGKP-AQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGYPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|227513366|ref|ZP_03943415.1| pseudouridylate synthase [Lactobacillus buchneri ATCC 11577]
 gi|227524509|ref|ZP_03954558.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
 gi|227083239|gb|EEI18551.1| pseudouridylate synthase [Lactobacillus buchneri ATCC 11577]
 gi|227088319|gb|EEI23631.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
          Length = 303

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 90/316 (28%), Positives = 145/316 (45%), Gaps = 38/316 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E  RLD+      P I+    +K++  G V V+  + K     +    + I  V     
Sbjct: 9   DELGRLDKIVSKLDPEISRSRAKKMIEDGDVIVNDSKKKPKYETKVSDTILIKDVKPETV 68

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL 133
            I  E   LD               ++YED  + V NKP G+ V   +G   H  ++  L
Sbjct: 69  SIKPENMPLD---------------IVYEDEDVIVVNKPQGMVVHPSAGHPNHTLVNALL 113

Query: 134 --KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                    G+ +P + HR+D++TSG+L+VA+   A + L++  + ++  + Y +LV G 
Sbjct: 114 FHSPLSSINGEYRPGIVHRIDKDTSGLLMVAKNDMAHKALSKQLKAKKNLRKYVALVHGR 173

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            K     I      K+ IG       KQ        AI+HF+V++ F + +  ++ +  T
Sbjct: 174 IKEDSGVI------KAPIGRSPKDRKKQAIVADGRPAITHFEVMERF-EDYTLIDCRLET 226

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           GRTHQ+RVH  ++G PIVGD  Y      KG+         +LHA+ +   HP   +L I
Sbjct: 227 GRTHQIRVHMQYIGHPIVGDPLYGPKKTIKGHGQ-------FLHAQELGFEHPRNHKLMI 279

Query: 308 -TAPLPAHMVKTWDSL 322
            +AP+P    KT  +L
Sbjct: 280 FSAPIPEIFEKTLRTL 295


>gi|222151016|ref|YP_002560170.1| hypothetical protein MCCL_0767 [Macrococcus caseolyticus JCSC5402]
 gi|222120139|dbj|BAH17474.1| conserved hypothetical protein [Macrococcus caseolyticus JCSC5402]
          Length = 301

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 77/311 (24%), Positives = 148/311 (47%), Gaps = 33/311 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  +E  +R+D++  +  P  +   +Q  +++  V V+ K +K N ++      R+   I
Sbjct: 8   INEEETGIRIDKFLADANPDWSRSQIQDWIKNEFVLVNGKVIKSNYKL------RLNDEI 61

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
           +     ++E  ++   + L          + YED  + +  KP G+ V    G      +
Sbjct: 62  SVTEKPVEEVDLVAQDLGLE---------IYYEDKDVAIVYKPKGMVVHPAPGHPDGTLV 112

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +G + +  D  G     +P + HR+D++TSG+L++A+   A + L +    + + + Y +
Sbjct: 113 NGLMHAITDLSGINGEIRPGIVHRIDKDTSGLLMIAKNDIAHRGLVDQLVDKSVTRKYTA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G+  ++   I +  + ++      + +V        +A++HF V++ F  K+  +E 
Sbjct: 173 LVHGVIPHEFGTI-DAPIGRNQKDRQEMAIVDN----GKHAVTHFNVLETF-DKYTLVEC 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
              TGRTHQ+RVH  H+G P+VGD KY      +          LHA  +   HP  G  
Sbjct: 227 VLETGRTHQIRVHMKHIGFPLVGDPKYGPKKTMDIGGQ-----ALHAGVLGFEHPVTGEY 281

Query: 305 LQITAPLPAHM 315
           ++ +APLPA+ 
Sbjct: 282 IERSAPLPAYF 292


>gi|114566812|ref|YP_753966.1| pseudouridylate synthase [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
 gi|114337747|gb|ABI68595.1| ribosomal large subunit pseudouridine synthase D [Syntrophomonas
           wolfei subsp. wolfei str. Goettingen]
          Length = 305

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 85/318 (26%), Positives = 149/318 (46%), Gaps = 55/318 (17%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + ++V+ + E  RLD +       ++   ++ ++ +G++RVD K+ K + R+++G+
Sbjct: 1   MPRTEILLVDEEMEGERLDAFVTEQLDELSRSLVKTLIENGEIRVDSKQQKPSYRLKAGE 60

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
             +V IP V        +E K+    + L+          +Y+D  I V +KP G+    
Sbjct: 61  EIIVEIPAV--------RELKLKAQDIPLS---------FIYQDKDIAVIDKPKGMVAHP 103

Query: 122 GSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLT 171
             G         + +H    LK      G+ +P + HRLD++TSG++V+A+   A + L 
Sbjct: 104 AHGNWENTLVNALLFH----LKDLSGINGELRPGIVHRLDKDTSGVMVIAKNDMAHRQLA 159

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK------GANY 225
              +   I + Y +LV GI K     I      ++ IG       KQ+ K      G   
Sbjct: 160 AQIKDHSINREYITLVHGIIKENLGSI------EAPIGRS-----KQDRKKMAVIAGGRP 208

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           A+S+++V++     +  L+++  TGRTHQ+RVH  ++  P+VGD  Y +  K       Q
Sbjct: 209 AVSNYQVLERLGN-YTLLKVKLLTGRTHQIRVHFAYIKHPVVGDPLYGSG-KKQLGLDTQ 266

Query: 286 NKLYLHARYMDLPHPEGG 303
               LHA  +   HP  G
Sbjct: 267 ---ALHAHLLGFKHPSSG 281


>gi|116629656|ref|YP_814828.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           ATCC 33323]
 gi|238854259|ref|ZP_04644603.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri 202-4]
 gi|311110701|ref|ZP_07712098.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri MV-22]
 gi|116095238|gb|ABJ60390.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri ATCC 33323]
 gi|238833070|gb|EEQ25363.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri 202-4]
 gi|311065855|gb|EFQ46195.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri MV-22]
          Length = 304

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 91/331 (27%), Positives = 161/331 (48%), Gaps = 45/331 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT   ++V+E  EE  RLD+        ++   +++++    + V+ K  K + ++Q+G 
Sbjct: 1   MTENYHLVIE--EEKGRLDKVIAEKLKDLSRTKIKELVNDKNILVNHKAEKVSYKVQAGD 58

Query: 64  VVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            + I  PP         K   +   ++NL          ++YED+ + V NKP G+ V  
Sbjct: 59  SIDITVPPA--------KPLSLEAQNLNLD---------IVYEDADVIVVNKPQGMVVHP 101

Query: 122 GSGIAYH--IDGFL---KSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +G   H  ++G L       DS +G +P + HR+D++TSG+L+VA+   A + L +   
Sbjct: 102 SAGHPDHTLVNGLLYHTHELADSPEGFRPGIVHRIDKDTSGLLMVAKNDKARESLEKQLA 161

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKV 232
            +  ++ Y ++V G  + K   I   +       G   +  KQ   N KG   A++HF V
Sbjct: 162 EKINKREYLAIVHGNFETKNGVIDAPI-------GRNPNNRKQMAVNPKG-KAAVTHFTV 213

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++ F + +  ++    TGRTHQ+RVH  ++G P+ GD  Y     G   +   +  +LHA
Sbjct: 214 LEQF-KDYSLVKCILETGRTHQIRVHMKYIGHPLAGDPLY-----GPKKTLAGHGQFLHA 267

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + +    P   + L+ +APLPA   K  ++L
Sbjct: 268 KTLGFYQPSTHKWLEFSAPLPAIFEKQLENL 298


>gi|322391774|ref|ZP_08065239.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           peroris ATCC 700780]
 gi|321145254|gb|EFX40650.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           peroris ATCC 700780]
          Length = 297

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 84/308 (27%), Positives = 149/308 (48%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G VR+DK         R   N +I+SGQV+ +   +    + ++E  ++   V   +
Sbjct: 5   IETGGVRLDKALSDLTELSRSLANEQIKSGQVL-VNGQLKKAKYSVQEGDVITYQVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   +    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNIPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F+V++ F   +  LE+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFRVLERFGD-YTLLELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG+         +LHA+ +   HP  G  ++ T+ +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGETMEFTSDIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKQTLEKL 293


>gi|158319738|ref|YP_001512245.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158139937|gb|ABW18249.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 230

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 110/217 (50%), Gaps = 13/217 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ + V  KP+ I  Q        +   LK  +  +  KP      L HRLD+   
Sbjct: 7   ILFEDNHLLVVEKPSNILSQEDHTGDLDMLTLLKEDIKERYNKPGNVYLGLVHRLDRPVG 66

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  +A  L++  R R  +K Y ++V G P  +KE + ++LLK +    + V V
Sbjct: 67  GVMVFAKTSKSAARLSDQIRKREFKKTYMAVVHGRPMKEKETLVHYLLKDNK--SNIVSV 124

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           VK++ +GA  AI  +++++   + +  +++  HTGR HQ+RV    +G P+ GD +Y   
Sbjct: 125 VKKDREGAKEAILDYEIVET-VESYSLVKINLHTGRPHQIRVQFATIGNPLHGDQRY--- 180

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
             G   + +  ++ L +  +   HP      +   LP
Sbjct: 181 --GKGVNQVGQQIALWSHEIACQHPTSKEDMVFTSLP 215


>gi|255534329|ref|YP_003094700.1| Ribosomal large subunit pseudouridine synthase D [Flavobacteriaceae
           bacterium 3519-10]
 gi|255340525|gb|ACU06638.1| Ribosomal large subunit pseudouridine synthase D [Flavobacteriaceae
           bacterium 3519-10]
          Length = 233

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 76/227 (33%), Positives = 117/227 (51%), Gaps = 20/227 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
           ++S +++ED+ + V NK AG  VQG  +G A  +D  +K ++  +  K       L HR+
Sbjct: 9   IESQIVFEDNHLLVINKKAGQLVQGDKTGDASLLD-LIKDFIKKRDNKAGNVFLGLVHRI 67

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL--LKKSHI 208
           D+ TSG+++ A+T  A   LT+  + R I+K YW++V   PK      A  L  L+K+  
Sbjct: 68  DRPTSGLVIYAKTSKALTRLTQMVKNREIKKTYWAVV---PKEVIPHSARLLHYLQKNEK 124

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                  +K  E  A  ++ ++ VI      F  LE+   TGR HQ+R     +G PI G
Sbjct: 125 TNKSTVFIKPTE-NAKESVLNYTVIKTL-DNFQLLEIDLETGRHHQIRAQLSKIGVPIKG 182

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           D KY A+      S     ++LHAR ++  HP   +  +I APLPAH
Sbjct: 183 DLKYGAS-----RSNPDGGIHLHARKLEFIHPVSLKNTEIVAPLPAH 224


>gi|191167762|ref|ZP_03029569.1| pseudouridine synthase, RluA family [Escherichia coli B7A]
 gi|190902188|gb|EDV61930.1| pseudouridine synthase, RluA family [Escherichia coli B7A]
          Length = 219

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETGKP-AQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLSLGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|332095345|gb|EGJ00368.1| RNA pseudouridylate synthase family protein [Shigella boydii
           5216-82]
          Length = 219

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETGKP-AQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPSYGNSMTFKAP 216


>gi|253563535|ref|ZP_04840992.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_2_5]
 gi|265762620|ref|ZP_06091188.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_1_16]
 gi|251947311|gb|EES87593.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_2_5]
 gi|263255228|gb|EEZ26574.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_1_16]
          Length = 539

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 72/210 (34%), Positives = 106/210 (50%), Gaps = 24/210 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + V +KP G+    G      I   L++ + ++ G  P + HRLD  TSG+L+
Sbjct: 338 ILFEDQWLLVLHKPEGVLSVPGKSEEQSIYSLLRARYPEATG--PLVVHRLDMATSGLLL 395

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A+T+   +HL   F  R I+K Y +L+ GI   ++  I         I  DY+   +Q 
Sbjct: 396 AAKTQEVHRHLQAQFENRSIKKRYIALLDGILPEEEGVI------DLPICPDYLDRPRQM 449

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCA 274
            NE+    AI+ ++V+D        +   P TGRTHQLRVHA H   + CPIVGD  Y  
Sbjct: 450 VNEELGKTAITRYRVMD-RKNGQTRIAFFPLTGRTHQLRVHAAHPLGLNCPIVGDELYGR 508

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                       +LYLHA Y++  HP  G+
Sbjct: 509 K---------AERLYLHAEYLEFIHPVSGQ 529


>gi|157147524|ref|YP_001454843.1| 23S rRNA/tRNA pseudouridine synthase A [Citrobacter koseri ATCC
           BAA-895]
 gi|157084729|gb|ABV14407.1| hypothetical protein CKO_03324 [Citrobacter koseri ATCC BAA-895]
          Length = 219

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 75/217 (34%), Positives = 115/217 (52%), Gaps = 19/217 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           I+LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  IILYQDEHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPAPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V+D  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETG-KPAQTGYEVVDFAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
            +    +P   +L LHA  + + HP  G  +   AP+
Sbjct: 184 PEALAMAP---RLLLHAETLTITHPAYGNSMTFKAPV 217


>gi|320182959|gb|EFW57827.1| Ribosomal large subunit pseudouridine synthase A [Shigella flexneri
           CDC 796-83]
          Length = 206

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 2   VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 58

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 59  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 112

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 113 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 170

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 171 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 203


>gi|312864274|ref|ZP_07724508.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
 gi|322517241|ref|ZP_08070120.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           vestibularis ATCC 49124]
 gi|311100275|gb|EFQ58484.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
 gi|322124147|gb|EFX95681.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           vestibularis ATCC 49124]
          Length = 296

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 89/321 (27%), Positives = 148/321 (46%), Gaps = 48/321 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++     + +++G V V+ K  K    ++ G V+          
Sbjct: 7   EAGNRLDKALAD-LTELSRSQANEAIKAGTVLVNGKSAKAKYAVKEGDVI---------T 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-- 133
           +++ E+++L+      K  D    I+ YED+ + V NKP G+ V   +G   H  G L  
Sbjct: 57  YVLPEEEVLEY-----KAEDIPLDII-YEDADVAVVNKPQGMVVHPSAG---HTSGTLVN 107

Query: 134 ------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 K      G  +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++
Sbjct: 108 ALMYHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAI 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLE 244
           V G   N +  I      ++ IG       KQ    KG   A++ F V++ F   +  +E
Sbjct: 168 VHGNLPNDRGVI------EAPIGRSDKDRKKQAVTAKG-KPAVTRFTVLERFGN-YTLVE 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +Q  TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   HP  
Sbjct: 220 LQLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGHGQ-------FLHAKTLGFTHPTT 272

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
           G L + TA  PA   KT + L
Sbjct: 273 GELVEFTAEEPAIFKKTLEKL 293


>gi|258646966|ref|ZP_05734435.1| ribosomal large subunit pseudouridine synthase C [Dialister invisus
           DSM 15470]
 gi|260404405|gb|EEW97952.1| ribosomal large subunit pseudouridine synthase C [Dialister invisus
           DSM 15470]
          Length = 305

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 72/267 (26%), Positives = 133/267 (49%), Gaps = 31/267 (11%)

Query: 12  VENDEENMRLDRWFKN--HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +E      RLDR+ +   H+PH   V   K +R+ +++V+ K+     R+  G  V    
Sbjct: 6   IEGRHAGKRLDRFMEEIEHWPHGMVV---KAVRTKKLKVNGKKEDGTYRLCEGDRV---- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYH 128
               +++++ ++K  D ++             +YED  I + +K AG+     +G     
Sbjct: 59  ----VSYVLPKEKRRDFTI-------------VYEDEHILIADKKAGLLCMDSTGKTTRT 101

Query: 129 IDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           + G +  ++  KG+    + HR+D  TSG++V+A+   +   L    + R ++K+Y  +V
Sbjct: 102 LIGEVNEYLADKGEPSAYMVHRIDFNTSGLMVIAKDEESKGILDRMIKERELEKVYLCIV 161

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+PK K+  + ++L K S  G  ++  V Q  KGA  A++ + ++    Q    LE   
Sbjct: 162 SGVPKKKEGHLIHYLFKDSKQGKVFLSDVPQ--KGAKSAVTDYHIVKT-GQNLSLLECTL 218

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCA 274
            TGRTHQ+R    ++G P++GD KY +
Sbjct: 219 LTGRTHQIRSQMAYIGHPLIGDDKYGS 245


>gi|294673069|ref|YP_003573685.1| RNA pseudouridine synthase family protein [Prevotella ruminicola
           23]
 gi|294472960|gb|ADE82349.1| RNA pseudouridine synthase family protein [Prevotella ruminicola
           23]
          Length = 223

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 68/218 (31%), Positives = 104/218 (47%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK +G  VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHIIIVNKQSGEIVQGDKTGDRPLSELVKDYIKEKYAKPGAVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ART  A   L + F   ++ K YW++V   PK  +  + NWL++       Y + 
Sbjct: 63  GLVVFARTSKALTRLNKMFAEGQVHKTYWAIVKNRPKALEGTLENWLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    A  A+  ++VI      +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKERPNAKKALLKYRVIGQ-TDNYTVLEVNLMTGRHHQIRCQLAAMGCPIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             G   S     + L +R ++  HP     + + APLP
Sbjct: 177 --GAPRSNPDGSISLMSRRVEFVHPVSKETIIVEAPLP 212


>gi|288818020|ref|YP_003432367.1| pseudouridine synthase [Hydrogenobacter thermophilus TK-6]
 gi|288787419|dbj|BAI69166.1| pseudouridine synthase [Hydrogenobacter thermophilus TK-6]
          Length = 318

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 80/287 (27%), Positives = 139/287 (48%), Gaps = 35/287 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRI-P 68
           VV+ + +  RLD +    Y   +   +QK++  G V VD K +K  + R+++GQ +    
Sbjct: 7   VVDQEAQGKRLDLFLTEAYGEFSRSYVQKLIEDGFVLVDDKEIKKPSRRLKAGQKITFYI 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P +  L  ++ E    D               ++YED  I V  KP G+ V    G +  
Sbjct: 67  PQVEPLE-VLPEDIPFD---------------VVYEDEDILVLIKPCGLVVHPSPGYSSG 110

Query: 129 --IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    +  G    ++P + HRLD+ T+G++VVA++  A + L E F  RR+ K 
Sbjct: 111 TLVNALLFRIKELSGIGGKERPGIVHRLDKNTAGLMVVAKSDKAHRSLVEEFMQRRVLKR 170

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFC 241
           Y +LV G+ +     +    + +  +      VV+  +     A + ++VI  F + +  
Sbjct: 171 YHALVSGLLREDSGTVEKS-IGRHPVDRKKFSVVEDGKP----AKTEYEVIKRFEKHRIT 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
           +L+++ HTGRTHQ+RVH   +G P++GD  Y     G  TS +  K+
Sbjct: 226 FLDVRIHTGRTHQIRVHLSFIGHPVLGDKTY-----GFKTSSVDRKI 267


>gi|332360722|gb|EGJ38531.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK49]
          Length = 298

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 118/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKNKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   F  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTRFQVLERFGD-FSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA +PA   +T   L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEVPAIFQETLKKL 295


>gi|300928645|ref|ZP_07144164.1| pseudouridine synthase A [Escherichia coli MS 187-1]
 gi|300463314|gb|EFK26807.1| pseudouridine synthase A [Escherichia coli MS 187-1]
          Length = 219

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFFAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|121999014|ref|YP_001003801.1| RluA family pseudouridine synthase [Halorhodospira halophila SL1]
 gi|121590419|gb|ABM62999.1| ribosomal large subunit pseudouridine synthase D [Halorhodospira
           halophila SL1]
          Length = 313

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 88/312 (28%), Positives = 138/312 (44%), Gaps = 44/312 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RLDR     +P  +   LQ+ +R+G + VD    +  + + +G+       I+     
Sbjct: 16  GQRLDRVLAALFPDYSRSRLQQWIRAGWITVDGAVRRPRDPVHAGEQ------ISVDAEP 69

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------IAYHI 129
             E  +    + L          LLYED  + V +KPAG+ V  G+G           H 
Sbjct: 70  EPETPLAPEPIPLR---------LLYEDDHLLVVDKPAGLVVHPGAGNPGGTLVNALLHY 120

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           D  L++   +      + HRLD+ETSG+LVVART AA   L    + R + + Y ++V G
Sbjct: 121 DPGLEALPRAG-----IVHRLDKETSGVLVVARTYAAHHALVAQLQARTVGRGYQAVVVG 175

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            P       A   + +       + VV+        A++H++V + F      L+++  T
Sbjct: 176 RPTAGGRVDAP--IARHPRDRKRMAVVETGRP----AVTHYRVAERFT-AHTLLDVELET 228

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKL------YLHARYMDLPHPE 301
           GRTHQ+RVH  H   P+VGD  Y     +    +  ++  L       LHAR++ L HP 
Sbjct: 229 GRTHQIRVHMAHCRLPLVGDPVYGRRPVYPKGASETLRAVLDGFRRQALHARHLRLEHPR 288

Query: 302 GGR-LQITAPLP 312
            G  +   AP P
Sbjct: 289 TGEAMHWEAPPP 300


>gi|90418990|ref|ZP_01226901.1| ribosomal large subunit pseudouridine synthase [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90337070|gb|EAS50775.1| ribosomal large subunit pseudouridine synthase [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 344

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 82/253 (32%), Positives = 124/253 (49%), Gaps = 33/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQE 153
           +++ED  + V +KPAG+ V  G G      ++  +    DS       ++P + HRLD++
Sbjct: 95  IVFEDEHLVVIDKPAGLVVHPGPGNWTGTLVNALIHHCGDSLSGVGGVKRPGIVHRLDKD 154

Query: 154 TSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           TSG+LVVA++ AA Q L + F    R  R+ + Y +LVWG+P      I +  L +S   
Sbjct: 155 TSGLLVVAKSDAAHQGLADQFAAHGRDGRLSRAYLALVWGVPLRPSGTI-DAALGRSTTD 213

Query: 210 GDYVHVVKQNEKGANYAISHFKVI------DCFAQKF-CWLEMQPHTGRTHQLRVHALHM 262
                VV  +   A +A++ F ++      D  A    C LE    TGRTHQ+RVH  H+
Sbjct: 214 RVKRAVVAADRADARHAVTRFNLVKASMLDDGIASLVECVLE----TGRTHQIRVHMAHI 269

Query: 263 GCPIVGDHKYCANFKG-------NFTSPIQ--NKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G P+VGD  Y A F+        +    ++  ++  LHA  +   HP  G  L   A LP
Sbjct: 270 GHPLVGDDVYGAGFRSKSRRLEDDARHVVERFDRQALHAFRLGFVHPVTGEDLAFQADLP 329

Query: 313 AHMVKTWDSLGFK 325
           A MV+   + G  
Sbjct: 330 ADMVELCAAFGIS 342


>gi|308751621|gb|ADO45104.1| pseudouridine synthase, RluA family [Hydrogenobacter thermophilus
           TK-6]
          Length = 326

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 81/287 (28%), Positives = 140/287 (48%), Gaps = 35/287 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRI-P 68
           VV+ + +  RLD +    Y   +   +QK++  G V VD K +K  + R+++GQ +    
Sbjct: 15  VVDQEAQGKRLDLFLTEAYGEFSRSYVQKLIEDGFVLVDDKEIKKPSRRLKAGQKITFYI 74

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P +  L  ++ E    D               ++YED  I V  KP G+ V    G +  
Sbjct: 75  PQVEPLE-VLPEDIPFD---------------VVYEDEDILVLIKPCGLVVHPSPGYSSG 118

Query: 129 --IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    +  G    ++P + HRLD+ T+G++VVA++  A + L E F  RR+ K 
Sbjct: 119 TLVNALLFRIKELSGIGGKERPGIVHRLDKNTAGLMVVAKSDKAHRSLVEEFMQRRVLKR 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFC 241
           Y +LV G+ +     +    + +  +      VV+  +     A + ++VI  F + +  
Sbjct: 179 YHALVSGLLREDSGTVEKS-IGRHPVDRKKFSVVEDGKP----AKTEYEVIKRFEKHRIT 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
           +L+++ HTGRTHQ+RVH   +G P++GD  Y   FK   TS +  K+
Sbjct: 234 FLDVRIHTGRTHQIRVHLSFIGHPVLGDKTY--GFK---TSSVDRKI 275


>gi|260591041|ref|ZP_05856499.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella veroralis F0319]
 gi|260536906|gb|EEX19523.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella veroralis F0319]
          Length = 223

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 72/231 (31%), Positives = 113/231 (48%), Gaps = 20/231 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ + +  K AG  VQG       +   +K W+  K QKP      + HRLD+  S
Sbjct: 3   VLYEDNHVIIVYKEAGEIVQGDKSGDIPLSEIVKQWLKEKYQKPGNVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYV 213
           G+++ A+T  A   L   FR   + K YW++V   P   +  + +WL++  K +    Y 
Sbjct: 63  GLVIFAKTSKALTRLNNMFRNGEVHKTYWAIVTRPPFEPEATLTDWLVRNEKQNKSYAYN 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H V  ++K    +I H+KVI+     +  LE+   TGR HQ+R    +M CPI GD KY 
Sbjct: 123 HQVPTSKK----SILHYKVINQ-TDHYTLLEVNLMTGRHHQIRCQLSNMDCPIKGDLKY- 176

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
               G   S     + L +  ++  HP    L ++ +PLP   +  W ++G
Sbjct: 177 ----GAPRSNPDGGICLLSHRVEFIHPVSKELIKVESPLPNDNL--WQAIG 221


>gi|238756473|ref|ZP_04617780.1| Ribosomal large subunit pseudouridine synthase D [Yersinia ruckeri
           ATCC 29473]
 gi|238705322|gb|EEP97732.1| Ribosomal large subunit pseudouridine synthase D [Yersinia ruckeri
           ATCC 29473]
          Length = 325

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 94/344 (27%), Positives = 160/344 (46%), Gaps = 60/344 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V VD K + K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILDDKVSVDGKTINKPKEKVLGGEIVAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        ++  LD               ++YEDS I V NKP G+ V  G+G   +
Sbjct: 69  AQIEEAARWEPQEIPLD---------------IVYEDSDILVINKPRGLVVHPGAG---N 110

Query: 129 IDG--------FLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            DG        +    VD     PR  + HRLD++T+G++VVA+T  A   L E+ + R 
Sbjct: 111 PDGTVLNALLYYYPEIVDV----PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQARE 166

Query: 179 IQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           I + Y ++  G         E I+    K++H+    VH + +       A++H+++++ 
Sbjct: 167 ITREYEAVAIGKMTAGGLVDEPISRHSTKRTHMA---VHPMGKP------AVTHYRIMEH 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NK 287
           F +    L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       NF + ++  ++
Sbjct: 218 F-RAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDNFITVLRGFDR 276

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLPAHMVK-----TWDSLGFK 325
             LHA  + L HP  G +++  A LP  M++       D+L FK
Sbjct: 277 QALHATMLRLYHPISGVQMEWHAALPEDMIELITALKADTLEFK 320


>gi|215485220|ref|YP_002327651.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O127:H6
           str. E2348/69]
 gi|312966179|ref|ZP_07780405.1| RNA pseudouridylate synthase family protein [Escherichia coli
           2362-75]
 gi|215263292|emb|CAS07607.1| pseudouridine synthase for 23S rRNA (position 746) and tRNAphe
           (position 32) [Escherichia coli O127:H6 str. E2348/69]
 gi|312289422|gb|EFR17316.1| RNA pseudouridylate synthase family protein [Escherichia coli
           2362-75]
          Length = 219

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 74/216 (34%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           I+LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  IVLYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|294788953|ref|ZP_06754193.1| ribosomal large subunit pseudouridine synthase D [Simonsiella
           muelleri ATCC 29453]
 gi|294483055|gb|EFG30742.1| ribosomal large subunit pseudouridine synthase D [Simonsiella
           muelleri ATCC 29453]
          Length = 391

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 84/318 (26%), Positives = 147/318 (46%), Gaps = 39/318 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V N+   MRLD       P  +   +   ++ G V  + +     +++  G+ + I    
Sbjct: 51  VPNELAGMRLDAALAKMLPDYSRSRITTWIKDGLVLCNNQEASPKDKLIGGEELHI---- 106

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
                     +I  S  N     + +   +++ED  + V NKPAG+ V   +G      +
Sbjct: 107 ----------QIQQSDENQAFEPELMDLDIVFEDDAVIVLNKPAGLVVHPAAGNWTGTLL 156

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +G L +      Q PR  + HRLD++TSG++VVA+T     HL +  + R +++IY ++ 
Sbjct: 157 NGLL-AHCPELSQVPRAGIVHRLDKDTSGLMVVAKTLPVQNHLVQQLQNRSVKRIYRAVA 215

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLE 244
            G +P + K         ++ IG D  + +K    + G   AI+H KV++ + Q   ++E
Sbjct: 216 DGVVPFDGK--------IETLIGRDPHNRLKMAVVKFGGKEAITHVKVLERY-QSHSYIE 266

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL------YLHARYMDLP 298
               TGRTHQ+RVH      P+ GD  Y  N +   + P+++ +       LHA  +   
Sbjct: 267 CSLETGRTHQIRVHMREARHPLAGDLVY-GNPRHVCSQPVKDAVKKLARQALHAYRLSFV 325

Query: 299 HPEGGR-LQITAPLPAHM 315
           HP+  + +   AP+P  M
Sbjct: 326 HPKSDQSVSFEAPIPDDM 343


>gi|227813199|ref|YP_002813208.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|227006370|gb|ACP16113.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
          Length = 239

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 110/220 (50%), Gaps = 20/220 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQET 154
           + YED+ + V NKP G+ V    G      ++G +    D  G     +P + HR+D++T
Sbjct: 20  IYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDT 79

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV 213
           SG+L+VA+   A + L      + + + Y ++V G IP +K    A     K        
Sbjct: 80  SGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKE---RQS 136

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V +N K   +A++HF+V++ F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY 
Sbjct: 137 MTVDENGK---HAVTHFQVLERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY- 191

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
               G   +   N   LHA  +   HP  G  +Q  AP+P
Sbjct: 192 ----GPKKTLDMNGQALHAGILGFDHPRTGEYIQFEAPIP 227


>gi|304385442|ref|ZP_07367787.1| RluA family pseudouridine synthase [Pediococcus acidilactici DSM
           20284]
 gi|304328649|gb|EFL95870.1| RluA family pseudouridine synthase [Pediococcus acidilactici DSM
           20284]
          Length = 292

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 76/220 (34%), Positives = 114/220 (51%), Gaps = 17/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSG 156
           ++YED    V NKPAG++ V G S     +   +K    + G     P L  RLD+ TSG
Sbjct: 80  VIYEDDNWLVVNKPAGLTAVPGPSNRTDTLVNRIKGHWQANGAVNLVPHLITRLDRFTSG 139

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I +VAR + A   L+E  R R+I+K Y +LV G+   +K      L     +  D +H  
Sbjct: 140 ITLVARHQVANSLLSEQVRHRKIKKTYLALVDGVVSAEKGTFNQPL----GLAADGIH-- 193

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           ++ ++G   A + FKV+  FA +   +++   TGRTHQ+RVH  + G P+VGD  Y    
Sbjct: 194 REVQEGGQSATTSFKVVQRFANQ-TLVQVHLKTGRTHQIRVHFANAGHPLVGDQLYG--- 249

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     I+ +  LHA+ +    P    +L+ TAPLPA +
Sbjct: 250 -GPMDRGIERQ-ALHAQSIRFFDPFTNQKLEFTAPLPADL 287


>gi|209965021|ref|YP_002297936.1| ribosomal large subunit pseudouridine synthase D, putative
           [Rhodospirillum centenum SW]
 gi|209958487|gb|ACI99123.1| ribosomal large subunit pseudouridine synthase D, putative
           [Rhodospirillum centenum SW]
          Length = 364

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 86/313 (27%), Positives = 143/313 (45%), Gaps = 34/313 (10%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           L K+L          R +  + I  G V      I+  +  +K  +I++  V   + +  
Sbjct: 59  LDKVLSDALGGAGLSRSRLRSLIDQGCVSSGGETIDDASRRVKPGQIVEVLVPAAEPAVP 118

Query: 97  LKSIL----LYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVD-----SKGQKPR 145
           L   +    ++ED  + V +K A + V   +G      ++  L    D        ++P 
Sbjct: 119 LPQAIPLAIVHEDEDLLVIDKAAEMVVHPAAGNPDGTLVNALLAHCGDRLSGIGGVRRPG 178

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+ TSG+LV A+T  A Q LT  F  R + + Y ++VWG+P  ++  I      +
Sbjct: 179 IVHRLDKGTSGLLVAAKTDRAHQGLTAQFADRSLSRTYLAVVWGVPAAREGVI------E 232

Query: 206 SHIG---GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            +IG   GD   +   + +G   A++ ++V+  F      +E +  TGRTHQ+RVH  H+
Sbjct: 233 GNIGRHPGDRKRMAVLS-RGGKPAVTRYRVVRSFGLLASLVECKLLTGRTHQIRVHMAHV 291

Query: 263 GCPIVGDHKYC---ANFKGNFTSPIQNKL------YLHARYMDLPHPEGG-RLQITAPLP 312
           G P+VGD  Y       KG    P+   L       LHA  ++  HP    +L  TA LP
Sbjct: 292 GHPLVGDPLYGRLRPPRKGTAPEPVLRALAGFPRQALHAAALEFRHPASDLKLGFTAALP 351

Query: 313 ---AHMVKTWDSL 322
              A +++  ++L
Sbjct: 352 EDLAGLIQGLETL 364


>gi|301162138|emb|CBW21683.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis 638R]
          Length = 539

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 72/210 (34%), Positives = 106/210 (50%), Gaps = 24/210 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + V +KP G+    G      I   L++ + ++ G  P + HRLD  TSG+L+
Sbjct: 338 ILFEDQWLLVLHKPEGVLSVPGKSEEQSIYSLLRARYPEATG--PLVVHRLDMATSGLLL 395

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A+T+   +HL   F  R I+K Y +L+ GI   ++  I         I  DY+   +Q 
Sbjct: 396 AAKTQEVHRHLQAQFENRSIKKRYIALLDGILPEEEGVI------DLPICPDYLDRPRQM 449

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCA 274
            NE+    AI+ ++V+D        +   P TGRTHQLRVHA H   + CPIVGD  Y  
Sbjct: 450 VNEELGKTAITRYRVMD-RKNGQTRIAFFPLTGRTHQLRVHAAHPLGLNCPIVGDELYGR 508

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                       +LYLHA Y++  HP  G+
Sbjct: 509 K---------AERLYLHAEYLEFIHPVSGQ 529


>gi|218767826|ref|YP_002342338.1| putative ribosomal large subunit pseudouridine synthase D
           [Neisseria meningitidis Z2491]
 gi|34395831|sp|Q9JVB6|RLUD_NEIMA RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|121051834|emb|CAM08140.1| putative ribosomal large subunit pseudouridine synthase D
           [Neisseria meningitidis Z2491]
          Length = 374

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 85/307 (27%), Positives = 139/307 (45%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ +R+            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKPSQPKDKMIGGEQIRV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVWQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|332762292|gb|EGJ92559.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           2747-71]
 gi|332768845|gb|EGJ99024.1| 23S rRNA/tRNA pseudouridine synthase [Shigella flexneri 2930-71]
          Length = 219

 Score =  100 bits (249), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCFETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|319953859|ref|YP_004165126.1| ribosomal large subunit pseudouridine synthase d [Cellulophaga
           algicola DSM 14237]
 gi|319422519|gb|ADV49628.1| ribosomal large subunit pseudouridine synthase D [Cellulophaga
           algicola DSM 14237]
          Length = 363

 Score =  100 bits (249), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 88/334 (26%), Positives = 153/334 (45%), Gaps = 45/334 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV    +E +R+D++  N   +     +Q+  R+G + V+  +VK N R+++G  VR+  
Sbjct: 37  VVASKGQEPLRVDKFLMNFIENAVRNKIQQAARAGHIWVNDIQVKQNYRVKAGDEVRV-- 94

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                 H   E  ++   + +          ++YED  + V NK  G+ V  G G     
Sbjct: 95  ---LFEHPPHEFLLVPEDIPIN---------IVYEDDVLMVVNKEPGMVVHPGHGNYSGT 142

Query: 128 HIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            I+  L   K    +  ++P L HR+D++TSG+LV+A+T  A   L++ F  +  ++ Y 
Sbjct: 143 LINALLHHTKDLAVNSNERPGLVHRIDKDTSGLLVIAKTDEAMTFLSKQFFDKTSEREYV 202

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +LVWG  +  +  I      + H+G        + V    E+G + A++HFKV++     
Sbjct: 203 ALVWGNMEEDEGTI------EGHVGRHPSNRLQMTVFPDGEQGKD-AVTHFKVLERLGY- 254

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG-NFTS---------PIQNK 287
              +  +  TGRTHQ+RVH  ++G  +  D +Y      KG  FT           I  +
Sbjct: 255 LTLISCKLETGRTHQIRVHLKYIGHTLFNDERYGGERILKGTTFTKYKQFVDNAFKILPR 314

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             LHA+ +   HP     ++  + +P  M    D
Sbjct: 315 QALHAKTLGFVHPVTKEFMRFDSEIPEDMANCID 348


>gi|257455986|ref|ZP_05621197.1| ribosomal large subunit pseudouridine synthase A [Enhydrobacter
           aerosaccus SK60]
 gi|257446614|gb|EEV21646.1| ribosomal large subunit pseudouridine synthase A [Enhydrobacter
           aerosaccus SK60]
          Length = 243

 Score =  100 bits (249), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 110/236 (46%), Gaps = 7/236 (2%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I ++ + +S    +   DF KS+ LY D  I+V +KP G+    G  +       L+S +
Sbjct: 13  IAQRNLEESQQPQSFFDDFAKSVTLYRDDDIWVIDKPHGLLSVDGKELKVS----LQSRL 68

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                  +L HRLD +TSGI++ AR   A  H+++ F  R   K Y +LVWG P  + E 
Sbjct: 69  LKADPNVKLIHRLDMDTSGIIIFARHSEAQTHISKQFIDRIPSKEYQALVWGTPPQQGEI 128

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                          V +         Y   H ++ +  A     + + P TGR+HQLRV
Sbjct: 129 DVPVRYDPPQKPKHIVDMSWDKRAYTKYETLHHELREGKA--VSRVALYPVTGRSHQLRV 186

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           H LH+G  ++GD  Y  +        +  +L LHAR + L HP  G  ++  +P+P
Sbjct: 187 HMLHIGHVMLGDPIYAQDVLNGQAFDLSPRLCLHARKLRLKHPNTGVWMEWESPVP 242


>gi|261342024|ref|ZP_05969882.1| ribosomal large subunit pseudouridine synthase D [Enterobacter
           cancerogenus ATCC 35316]
 gi|288315680|gb|EFC54618.1| ribosomal large subunit pseudouridine synthase D [Enterobacter
           cancerogenus ATCC 35316]
          Length = 326

 Score =  100 bits (249), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 76/247 (30%), Positives = 130/247 (52%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP G+ V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRGLVVHPGAG---NPDGTVLNALLHYYPPIIDVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL ES ++R I + Y ++  G   +     E I+    K++H+   
Sbjct: 143 TGLMVVAKTIPAQTHLVESLQLREITREYEAVAIGHMTSGGTVDEPISRHPTKRTHMS-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RIHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G +++  AP+P  MV+  D++
Sbjct: 253 YGGRPRPPKGASEEFISVLRKFDRQALHATMLRLYHPVTGIQMEWHAPIPQDMVELIDAM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|56750191|ref|YP_170892.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 6301]
 gi|81300183|ref|YP_400391.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 7942]
 gi|56685150|dbj|BAD78372.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 6301]
 gi|81169064|gb|ABB57404.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 7942]
          Length = 543

 Score =  100 bits (249), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 79/223 (35%), Positives = 114/223 (51%), Gaps = 29/223 (13%)

Query: 88  VNLTKHSD-FLKSILLYEDSKIYVFNKPAGI-SVQGGSGI--AYHIDGFLKSWVDSKGQK 143
             L   SD  L+  +LYED+ +    KPAG+ SV G  G+  A  I    + + D     
Sbjct: 326 AGLPPSSDEPLELPILYEDADLLAIIKPAGLLSVPGTRGLQQASAIQLLRQQFPDLPTYC 385

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL- 202
             + HRLDQ TSGIL+VAR R     L E FR R++ K+Y +L+ G P    +C A  + 
Sbjct: 386 --VVHRLDQATSGILLVARNRPTQVALFEQFRRRQVHKVYEALLEGQP----DCTAGTID 439

Query: 203 --LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             L+       Y  V +   +    A+++++ ID    + C +E++P TGRTHQLRVH  
Sbjct: 440 LPLRPDWTRRPYQLVDRDRGRP---ALTYYRCIDQTGDR-CRMELEPITGRTHQLRVHMA 495

Query: 261 H---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           H   +G PI+GD  Y  +          ++LYLHAR +   HP
Sbjct: 496 HPEGLGQPILGDDLYGQS---------SDRLYLHARSIRFRHP 529


>gi|320535819|ref|ZP_08035900.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
 gi|320147367|gb|EFW38902.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
          Length = 248

 Score =  100 bits (249), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 72/221 (32%), Positives = 106/221 (47%), Gaps = 22/221 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           L+Y+D  I   NK AGISV     +     +D  L+     K +K    HR+D++TSG++
Sbjct: 11  LVYQDEDIIAVNKSAGISVTADRWNPDEQRLDILLQQSPALKDKKFFTVHRIDKDTSGLI 70

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A    + + L ESF  R +QK Y  L+  IP      + +  LK     GD  H    
Sbjct: 71  LYALNEESHKKLNESFMRRNVQKTYHCLIADIPYENSFSV-DLKLKSD---GDEKHRTII 126

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           ++K    A++HF+V+     +F  LE +P +GRTHQ+R H    G PI+ D  Y  N K 
Sbjct: 127 DKKNGKEALTHFEVLKPLG-RFTLLEAKPVSGRTHQIRAHLAAAGLPILCDSLY-GNAKP 184

Query: 279 NFTS--------------PIQNKLYLHARYMDLPHPEGGRL 305
            F S              P+ ++L LHA  ++  HP  G L
Sbjct: 185 LFLSELKKNWRGEKAQEQPLISRLALHAYKLEFEHPRTGTL 225


>gi|326800939|ref|YP_004318758.1| pseudouridine synthase [Sphingobacterium sp. 21]
 gi|326551703|gb|ADZ80088.1| pseudouridine synthase, RluA family [Sphingobacterium sp. 21]
          Length = 348

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 77/317 (24%), Positives = 149/317 (47%), Gaps = 41/317 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+D++  +   + +   +Q  + +  V V+ + VK + +++ G ++ +  
Sbjct: 24  IVVDKGQTLLRIDKFLMHRVENASRNRVQNAIEAENVLVNNRPVKSSYKVKPGDLITV-- 81

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
               L H  ++ +I   ++ L          + YED  + + NKPAG+ V  G       
Sbjct: 82  ---VLPHPPRDTEIYPENIPLD---------IRYEDDDLLIVNKPAGMVVHPGYNNYTGT 129

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             + + YH +   +  +     +P L HR+D++TSG+LV+A+      +L + F    IQ
Sbjct: 130 LVNALVYHFNQLPQ--LPGNDGRPGLVHRIDKDTSGLLVIAKNEWTITNLAKQFFDHTIQ 187

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG    +   ++ ++ +   +    V  V +NE    ++++H++V++      
Sbjct: 188 RKYLALVWG-DLQENGTVSGYIGRS--LKDRRVMSVYENEDKGKWSVTHYRVLERLGY-V 243

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN-FTS---------PIQNKL 288
             +E Q  TGRTHQ+R H   +G P+  D  Y  +   KG  FT           I  + 
Sbjct: 244 TLIECQLETGRTHQIRAHMQSIGHPLFNDTLYGGDKILKGTVFTKYKQFVDNCFSILPRQ 303

Query: 289 YLHARYMDLPHPEGGRL 305
            LHA+ +   HP+   L
Sbjct: 304 ALHAKSLGFTHPKSKEL 320


>gi|160888049|ref|ZP_02069052.1| hypothetical protein BACUNI_00457 [Bacteroides uniformis ATCC 8492]
 gi|270295585|ref|ZP_06201786.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|156862548|gb|EDO55979.1| hypothetical protein BACUNI_00457 [Bacteroides uniformis ATCC 8492]
 gi|270274832|gb|EFA20693.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 356

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 90/349 (25%), Positives = 158/349 (45%), Gaps = 53/349 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E +R+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQEMVRVDKYLFDRLTNSSRNRIQKAADAGFVMANGKAVKSSYKVKPMDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYENEVIPEDIPLD---------IVYEDKYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 138 LVNAIAWH----MKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKT 193

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LVWG  +  +  +   + +      D + +    +    +A++H++V++    
Sbjct: 194 TKRRYRALVWGNVEQDEGTVVGNIGRNPR---DRMQMTVLPDDQGKHAVTHYRVLERLGY 250

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNF-------------TSP 283
               +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG               T P
Sbjct: 251 -VTLVECILETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFDTCP 309

Query: 284 IQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS-LGFKYDRNL 330
            Q    LHA  +   HP  G  +  T+ LP  M +  D   G+  +R L
Sbjct: 310 RQA---LHAMTLGFVHPVTGEEMYFTSELPDDMTRLIDKWRGYISNREL 355


>gi|255690880|ref|ZP_05414555.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           finegoldii DSM 17565]
 gi|260623516|gb|EEX46387.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           finegoldii DSM 17565]
          Length = 561

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 80/249 (32%), Positives = 120/249 (48%), Gaps = 37/249 (14%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGS---GIAYHI 129
           L H+++  ++ ++ +  + H D    I+ YED  + V NKPAG +SV G        YH 
Sbjct: 324 LQHMLQGLEVDENPLLNSIHEDEELEIV-YEDEWLVVVNKPAGMLSVPGKEEDRDSVYH- 381

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               K + D+ G  P + HRLD  TSG+L+VA+T+   QHL   F  R I+K Y +++ G
Sbjct: 382 -RLKKKYPDATG--PMIVHRLDMATSGLLLVAKTKEVHQHLQAQFASRSIKKRYVAVLDG 438

Query: 190 IPKNKKECIANWLLKKSHIGG----------DYVHVVKQNEKGANYAISHFKVIDCFAQK 239
                   +    L     G           D    +   E G   AI+ +++I   ++K
Sbjct: 439 ATAT----VEKTALPPGRTGRIELPLCLNPLDRPRQIVSREHGKE-AITEYRII-SESEK 492

Query: 240 FCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQLRVHA H   + CPI+GD  Y             ++LYLHA Y++
Sbjct: 493 HIRIAFYPLTGRTHQLRVHAAHPEGLSCPILGDELYGKK---------ADRLYLHAEYIE 543

Query: 297 LPHPEGGRL 305
             HP  G++
Sbjct: 544 FRHPISGKI 552


>gi|32477768|ref|NP_870762.1| ribosomal large subunit pseudouridine synthase [Rhodopirellula
           baltica SH 1]
 gi|32448322|emb|CAD77839.1| ribosomal large subunit pseudouridine synthase [Rhodopirellula
           baltica SH 1]
          Length = 334

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 82/336 (24%), Positives = 155/336 (46%), Gaps = 51/336 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IP 68
           VV       R+D +        +   ++  +++    VD + ++ + ++++GQ VR  +P
Sbjct: 6   VVPESANGFRIDLFLTQSCDGYSRSQIRDAVQNDGAEVDGRIIRPSYKVKAGQKVRFRVP 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
           P   A +  + E   LD               +LYED  + V NKPAG+ V    G    
Sbjct: 66  P--PASDDTVPENIPLD---------------ILYEDDGLVVINKPAGMVVHPARGNWTG 108

Query: 125 -IAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +   +    +S  D  G  +P + HRLD++TSG++VVA+  A   +L   +  R +QK 
Sbjct: 109 TLTSALAFRFQSLSDVGGPTRPGIVHRLDRDTSGVIVVAKNNAVHLNLAAQWHDRLVQKE 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++ +G     ++ I   + +  H        +++    +  A + ++V++    +   
Sbjct: 169 YTAITFGRLDRDRDWIHASIGR--HPYQRDKQAIREGHATSKTASTFYEVVERHG-RVTR 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-----------------GNFTSP-- 283
           ++++P TGRTHQ+RVH  H+GCPI+ D  Y  + +                 G   +P  
Sbjct: 226 VDVRPKTGRTHQIRVHLAHIGCPILCDRLYGGHSELSRSQIRRLAGTEVATPGVKPTPEG 285

Query: 284 ---IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
              + ++  LHA+ +   +P+ G+ + +TAPLP  +
Sbjct: 286 EEILLSRQALHAKALTFTNPQTGKEMTLTAPLPPDL 321


>gi|146302439|ref|YP_001197030.1| pseudouridine synthase [Flavobacterium johnsoniae UW101]
 gi|146156857|gb|ABQ07711.1| ribosomal large subunit pseudouridine synthase D [Flavobacterium
           johnsoniae UW101]
          Length = 229

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 108/228 (47%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ I V NK  G  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 12  ILHEDNHIIVVNKRVGDIVQGDKTGDKPLSDIVKEYIKDKYNKPGDVFLGVIHRLDRPTT 71

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V ART  A   + E F  R  +K YW++V   P      + ++L +         H+
Sbjct: 72  GIVVFARTSKALSRMNELFSNRETKKTYWAVVKNKPVEAAAKLVHYLKRNEKNNTSKAHL 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  A   +K+I    Q +  LE+  HTGR HQ+R     +G PI GD KY A+
Sbjct: 132 --KEVPDSKLASLDYKIIKEL-QNYTALEINLHTGRHHQIRAQLSAIGSPIKGDLKYGAD 188

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                 S     ++LHAR +   HP     + I AP+P   +  W+++
Sbjct: 189 -----RSNPDGGIHLHARKLVFVHPVSKENITIIAPVPDETI--WNAV 229


>gi|309787283|ref|ZP_07681895.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
 gi|308924861|gb|EFP70356.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
 gi|323181753|gb|EFZ67166.1| RNA pseudouridylate synthase family protein [Escherichia coli 1357]
          Length = 217

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 13  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 70  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 123

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 124 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 182 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 214


>gi|260450733|gb|ACX41155.1| pseudouridine synthase [Escherichia coli DH1]
 gi|315134754|dbj|BAJ41913.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           DH1]
          Length = 219

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KICYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|328768352|gb|EGF78399.1| hypothetical protein BATDEDRAFT_90882 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 490

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 82/266 (30%), Positives = 124/266 (46%), Gaps = 51/266 (19%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           LK  +LY+D  IYV +K  G++ QGGS I  H+D  +      K +  RL HRLD+ TSG
Sbjct: 196 LKMRILYKDQHIYVIDKEHGLASQGGSKIDMHLDKLISHLETDKSKTLRLVHRLDKNTSG 255

Query: 157 ILVVARTRAAAQHLTESFRMR-RIQKIYWSL-------------------VWGIPKNKKE 196
            +++ART+ +A  ++  FR   RI + Y +L                   V GI  N +E
Sbjct: 256 AMIIARTKESAARVSAMFRQEGRISRKYLALLTPTLLDHSNFKDGGQHKIVSGIVSNGRE 315

Query: 197 C------IANW---LLKKSHIGGDYVHVVKQNEKGANYAISHFKVI--DCFAQKFCWLEM 245
                  +  W   + K+    GD V            A++   ++  +      C   +
Sbjct: 316 APHERMDLVEWHDGIPKQMSTNGDPV----------KKAVTKVTLLQSNPLTSLVC---L 362

Query: 246 QPHTGRTHQLRVH-ALHMGCPIVGDHKY----CANFKGNFTSPIQNKLYLHARYMDLPH- 299
           +P TGR HQLR+H A  +G  IVGD+KY      NFK + +   +  L+LH   + +   
Sbjct: 363 EPTTGRKHQLRLHCADALGSFIVGDYKYGQGCLKNFKAHVSDWKKVPLHLHLYQLSIKDW 422

Query: 300 -PEGGRLQITAPLPAHMVKTWDSLGF 324
             +G  L ++APLP +  KT  S G 
Sbjct: 423 FRDGLDLTVSAPLPIYFQKTLTSTGL 448


>gi|325133782|gb|EGC56438.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M13399]
          Length = 356

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 139/307 (45%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 22  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 69

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 70  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 126

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T +A   L    + R +++IY ++  GI P + 
Sbjct: 127 PELSQIPRAGIVHRLDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDG 186

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 187 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-THSYIECSLETGRT 237

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 238 HQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 297

Query: 306 QITAPLP 312
              AP+P
Sbjct: 298 SFEAPIP 304


>gi|160880488|ref|YP_001559456.1| RluA family pseudouridine synthase [Clostridium phytofermentans
           ISDg]
 gi|160429154|gb|ABX42717.1| pseudouridine synthase, RluA family [Clostridium phytofermentans
           ISDg]
          Length = 313

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 85/344 (24%), Positives = 153/344 (44%), Gaps = 59/344 (17%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++   ++++ E+ R+D +       I+   +QK+++   V+++   +K N R++ G 
Sbjct: 1   MENIKTCCIDSEYEDERIDSFLAEFEEGISRSYIQKLIKDSLVKINGNVIKANYRLKEGD 60

Query: 64  VV--RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           ++   +P  ++    I  E   LD               +LYED  I V NKP G+ V  
Sbjct: 61  ILTYEVPQPVSL--EIAAENIPLD---------------ILYEDEDIIVINKPKGLVVHP 103

Query: 122 GSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
            +G         + YH    L     +   +P + HR+D  T+G+LVV +   + Q + E
Sbjct: 104 AAGHYSGTLVNALLYHCKDRLSGI--NGVMRPGIVHRIDMNTTGVLVVCKNDKSHQSIAE 161

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHF 230
             ++  I + Y +LV+   K  +  +       + IG   V   K   N K    A++++
Sbjct: 162 QLKVHSITRKYEALVYNSFKQTEGTV------DAPIGRHPVDRKKMAINHKNGKNAVTNY 215

Query: 231 KVIDCF------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           +V++ F       Q +  +E    TGRTHQ+RVH   +  P++GD  Y          P 
Sbjct: 216 RVLENFNLGYVHNQGYAHIECTLKTGRTHQIRVHMASLHHPLLGDDVY---------GPE 266

Query: 285 QNKLY-----LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           ++K +     LHAR +   HP     ++  APLP +  +  + L
Sbjct: 267 KDKFHLEGQALHARVLGFLHPTTQEYMEFEAPLPEYFQQLIEKL 310


>gi|16128052|ref|NP_414600.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           MG1655]
 gi|30061623|ref|NP_835794.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella flexneri 2a str.
           2457T]
 gi|74310675|ref|YP_309094.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella sonnei Ss046]
 gi|82542662|ref|YP_406609.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella boydii Sb227]
 gi|82775462|ref|YP_401809.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella dysenteriae Sd197]
 gi|89106942|ref|AP_000722.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           W3110]
 gi|110640270|ref|YP_667998.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli 536]
 gi|110804122|ref|YP_687642.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella flexneri 5 str.
           8401]
 gi|157159461|ref|YP_001461228.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli E24377A]
 gi|157159527|ref|YP_001456845.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli HS]
 gi|170021586|ref|YP_001726540.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli ATCC 8739]
 gi|170079719|ref|YP_001729039.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170679993|ref|YP_001742177.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli SMS-3-5]
 gi|188492494|ref|ZP_02999764.1| pseudouridine synthase, RluA family [Escherichia coli 53638]
 gi|191174210|ref|ZP_03035721.1| pseudouridine synthase, RluA family [Escherichia coli F11]
 gi|193065885|ref|ZP_03046946.1| pseudouridine synthase, RluA family [Escherichia coli E22]
 gi|193070842|ref|ZP_03051775.1| pseudouridine synthase, RluA family [Escherichia coli E110019]
 gi|194429362|ref|ZP_03061887.1| pseudouridine synthase, RluA family [Escherichia coli B171]
 gi|209917249|ref|YP_002291333.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli SE11]
 gi|218547506|ref|YP_002381297.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia fergusonii ATCC
           35469]
 gi|218552641|ref|YP_002385554.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli IAI1]
 gi|218687934|ref|YP_002396146.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli ED1a]
 gi|218693528|ref|YP_002401195.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli 55989]
 gi|218698480|ref|YP_002406109.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli IAI39]
 gi|218703318|ref|YP_002410837.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli UMN026]
 gi|238899461|ref|YP_002925257.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli BW2952]
 gi|253774912|ref|YP_003037743.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254037473|ref|ZP_04871550.1| pseudouridine synthase for 23S rRNA and tRNA [Escherichia sp.
           1_1_43]
 gi|254160181|ref|YP_003043289.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B str.
           REL606]
 gi|256020104|ref|ZP_05433969.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella sp. D9]
 gi|256025373|ref|ZP_05439238.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia sp. 4_1_40B]
 gi|260842293|ref|YP_003220071.1| pseudouridine synthase [Escherichia coli O103:H2 str. 12009]
 gi|293403132|ref|ZP_06647229.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           FVEC1412]
 gi|293408151|ref|ZP_06651991.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B354]
 gi|293476720|ref|ZP_06665128.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           B088]
 gi|297517418|ref|ZP_06935804.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli OP50]
 gi|298378660|ref|ZP_06988544.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           FVEC1302]
 gi|300816093|ref|ZP_07096316.1| pseudouridine synthase A [Escherichia coli MS 107-1]
 gi|300821939|ref|ZP_07102083.1| pseudouridine synthase A [Escherichia coli MS 119-7]
 gi|300900916|ref|ZP_07119052.1| pseudouridine synthase A [Escherichia coli MS 198-1]
 gi|300905460|ref|ZP_07123226.1| pseudouridine synthase A [Escherichia coli MS 84-1]
 gi|300919609|ref|ZP_07136101.1| pseudouridine synthase A [Escherichia coli MS 115-1]
 gi|300923165|ref|ZP_07139223.1| pseudouridine synthase A [Escherichia coli MS 182-1]
 gi|300939473|ref|ZP_07154135.1| pseudouridine synthase A [Escherichia coli MS 21-1]
 gi|300948662|ref|ZP_07162745.1| pseudouridine synthase A [Escherichia coli MS 116-1]
 gi|300956988|ref|ZP_07169239.1| pseudouridine synthase A [Escherichia coli MS 175-1]
 gi|300984199|ref|ZP_07176927.1| pseudouridine synthase A [Escherichia coli MS 200-1]
 gi|301024876|ref|ZP_07188512.1| pseudouridine synthase A [Escherichia coli MS 196-1]
 gi|301026173|ref|ZP_07189644.1| pseudouridine synthase A [Escherichia coli MS 69-1]
 gi|301305052|ref|ZP_07211153.1| pseudouridine synthase A [Escherichia coli MS 124-1]
 gi|301330173|ref|ZP_07222835.1| pseudouridine synthase A [Escherichia coli MS 78-1]
 gi|301648375|ref|ZP_07248112.1| pseudouridine synthase A [Escherichia coli MS 146-1]
 gi|306815344|ref|ZP_07449493.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli NC101]
 gi|307136660|ref|ZP_07496016.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli H736]
 gi|307311490|ref|ZP_07591132.1| pseudouridine synthase [Escherichia coli W]
 gi|309796045|ref|ZP_07690457.1| pseudouridine synthase A [Escherichia coli MS 145-7]
 gi|312970151|ref|ZP_07784333.1| RNA pseudouridylate synthase family protein [Escherichia coli
           1827-70]
 gi|331640509|ref|ZP_08341657.1| pseudouridine synthase A [Escherichia coli H736]
 gi|331650951|ref|ZP_08351979.1| pseudouridine synthase A [Escherichia coli M718]
 gi|331666293|ref|ZP_08367174.1| pseudouridine synthase A [Escherichia coli TA271]
 gi|331680629|ref|ZP_08381288.1| pseudouridine synthase A [Escherichia coli H591]
 gi|332281257|ref|ZP_08393670.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella sp. D9]
 gi|76363883|sp|P0AA37|RLUA_ECOLI RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|92090791|sp|P0AA38|RLUA_SHIFL RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|1786244|gb|AAC73169.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           MG1655]
 gi|30039865|gb|AAP15599.1| hypothetical protein S0055 [Shigella flexneri 2a str. 2457T]
 gi|73854152|gb|AAZ86859.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|81239610|gb|ABB60320.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
 gi|81244073|gb|ABB64781.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|85674306|dbj|BAE76039.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K12 substr.
           W3110]
 gi|110341862|gb|ABG68099.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           536]
 gi|110613670|gb|ABF02337.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|157065207|gb|ABV04462.1| pseudouridine synthase, RluA family [Escherichia coli HS]
 gi|157081491|gb|ABV21199.1| pseudouridine synthase, RluA family [Escherichia coli E24377A]
 gi|169756514|gb|ACA79213.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|169887554|gb|ACB01261.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170517711|gb|ACB15889.1| pseudouridine synthase, RluA family [Escherichia coli SMS-3-5]
 gi|188487693|gb|EDU62796.1| pseudouridine synthase, RluA family [Escherichia coli 53638]
 gi|190905495|gb|EDV65123.1| pseudouridine synthase, RluA family [Escherichia coli F11]
 gi|192926472|gb|EDV81105.1| pseudouridine synthase, RluA family [Escherichia coli E22]
 gi|192955872|gb|EDV86342.1| pseudouridine synthase, RluA family [Escherichia coli E110019]
 gi|194412582|gb|EDX28879.1| pseudouridine synthase, RluA family [Escherichia coli B171]
 gi|209910508|dbj|BAG75582.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           SE11]
 gi|218350260|emb|CAU95943.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli 55989]
 gi|218355047|emb|CAQ87653.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia fergusonii ATCC 35469]
 gi|218359409|emb|CAQ96948.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli IAI1]
 gi|218368466|emb|CAR16202.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli IAI39]
 gi|218425498|emb|CAR06280.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli ED1a]
 gi|218430415|emb|CAR11282.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli UMN026]
 gi|226840579|gb|EEH72581.1| pseudouridine synthase for 23S rRNA and tRNA [Escherichia sp.
           1_1_43]
 gi|238863331|gb|ACR65329.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli BW2952]
 gi|242375895|emb|CAQ30576.1| 23S rRNA and tRNA pseudouridine synthase [Escherichia coli
           BL21(DE3)]
 gi|253325956|gb|ACT30558.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253972082|gb|ACT37753.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli B str. REL606]
 gi|253976291|gb|ACT41961.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli BL21(DE3)]
 gi|257757440|dbj|BAI28937.1| pseudouridine synthase [Escherichia coli O103:H2 str. 12009]
 gi|281177273|dbj|BAI53603.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           SE15]
 gi|284919840|emb|CBG32895.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           042]
 gi|291321173|gb|EFE60615.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           B088]
 gi|291430047|gb|EFF03061.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           FVEC1412]
 gi|291472402|gb|EFF14884.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B354]
 gi|298280994|gb|EFI22495.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           FVEC1302]
 gi|299880242|gb|EFI88453.1| pseudouridine synthase A [Escherichia coli MS 196-1]
 gi|300306729|gb|EFJ61249.1| pseudouridine synthase A [Escherichia coli MS 200-1]
 gi|300316231|gb|EFJ66015.1| pseudouridine synthase A [Escherichia coli MS 175-1]
 gi|300355628|gb|EFJ71498.1| pseudouridine synthase A [Escherichia coli MS 198-1]
 gi|300395642|gb|EFJ79180.1| pseudouridine synthase A [Escherichia coli MS 69-1]
 gi|300402676|gb|EFJ86214.1| pseudouridine synthase A [Escherichia coli MS 84-1]
 gi|300413355|gb|EFJ96665.1| pseudouridine synthase A [Escherichia coli MS 115-1]
 gi|300420558|gb|EFK03869.1| pseudouridine synthase A [Escherichia coli MS 182-1]
 gi|300451839|gb|EFK15459.1| pseudouridine synthase A [Escherichia coli MS 116-1]
 gi|300455694|gb|EFK19187.1| pseudouridine synthase A [Escherichia coli MS 21-1]
 gi|300525539|gb|EFK46608.1| pseudouridine synthase A [Escherichia coli MS 119-7]
 gi|300531300|gb|EFK52362.1| pseudouridine synthase A [Escherichia coli MS 107-1]
 gi|300839659|gb|EFK67419.1| pseudouridine synthase A [Escherichia coli MS 124-1]
 gi|300843813|gb|EFK71573.1| pseudouridine synthase A [Escherichia coli MS 78-1]
 gi|301073563|gb|EFK88369.1| pseudouridine synthase A [Escherichia coli MS 146-1]
 gi|305851006|gb|EFM51461.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli NC101]
 gi|306908469|gb|EFN38967.1| pseudouridine synthase [Escherichia coli W]
 gi|308120287|gb|EFO57549.1| pseudouridine synthase A [Escherichia coli MS 145-7]
 gi|309700270|emb|CBI99558.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           ETEC H10407]
 gi|310337649|gb|EFQ02760.1| RNA pseudouridylate synthase family protein [Escherichia coli
           1827-70]
 gi|313646565|gb|EFS11026.1| RNA pseudouridylate synthase family protein [Shigella flexneri 2a
           str. 2457T]
 gi|315059282|gb|ADT73609.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli W]
 gi|315255668|gb|EFU35636.1| pseudouridine synthase A [Escherichia coli MS 85-1]
 gi|315616165|gb|EFU96784.1| RNA pseudouridylate synthase family protein [Escherichia coli 3431]
 gi|320179617|gb|EFW54566.1| Ribosomal large subunit pseudouridine synthase A [Shigella boydii
           ATCC 9905]
 gi|320200424|gb|EFW75010.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           EC4100B]
 gi|323160072|gb|EFZ46034.1| RNA pseudouridylate synthase family protein [Escherichia coli
           E128010]
 gi|323166108|gb|EFZ51887.1| RNA pseudouridylate synthase family protein [Shigella sonnei 53G]
 gi|323380161|gb|ADX52429.1| pseudouridine synthase [Escherichia coli KO11]
 gi|323935111|gb|EGB31478.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323939843|gb|EGB36044.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323945687|gb|EGB41735.1| RNA pseudouridylate synthase [Escherichia coli H120]
 gi|323960005|gb|EGB55651.1| RNA pseudouridylate synthase [Escherichia coli H489]
 gi|323964843|gb|EGB60310.1| RNA pseudouridylate synthase [Escherichia coli M863]
 gi|323975775|gb|EGB70871.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
 gi|324008404|gb|EGB77623.1| pseudouridine synthase A [Escherichia coli MS 57-2]
 gi|324012314|gb|EGB81533.1| pseudouridine synthase A [Escherichia coli MS 60-1]
 gi|324017675|gb|EGB86894.1| pseudouridine synthase A [Escherichia coli MS 117-3]
 gi|324112541|gb|EGC06518.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
 gi|325495982|gb|EGC93841.1| pseudouridine synthase [Escherichia fergusonii ECD227]
 gi|327255037|gb|EGE66640.1| RNA pseudouridylate synthase family protein [Escherichia coli
           STEC_7v]
 gi|330909906|gb|EGH38416.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           AA86]
 gi|331040255|gb|EGI12462.1| pseudouridine synthase A [Escherichia coli H736]
 gi|331051405|gb|EGI23454.1| pseudouridine synthase A [Escherichia coli M718]
 gi|331066504|gb|EGI38381.1| pseudouridine synthase A [Escherichia coli TA271]
 gi|331072092|gb|EGI43428.1| pseudouridine synthase A [Escherichia coli H591]
 gi|332098910|gb|EGJ03861.1| RNA pseudouridylate synthase family protein [Shigella boydii
           3594-74]
 gi|332103609|gb|EGJ06955.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella sp. D9]
 gi|332341388|gb|AEE54722.1| pseudouridine synthase RluA [Escherichia coli UMNK88]
 gi|332762617|gb|EGJ92882.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           4343-70]
 gi|332764899|gb|EGJ95127.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-671]
 gi|333009190|gb|EGK28646.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-218]
 gi|333011440|gb|EGK30854.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-272]
 gi|333021679|gb|EGK40928.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-227]
 gi|333022430|gb|EGK41668.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-304]
          Length = 219

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|270291159|ref|ZP_06197382.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
 gi|270280555|gb|EFA26390.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
          Length = 292

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 76/220 (34%), Positives = 114/220 (51%), Gaps = 17/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSG 156
           ++YED    V NKPAG++ V G S     +   +K    + G     P L  RLD+ TSG
Sbjct: 80  VIYEDDNWLVVNKPAGLTAVPGPSNRTDTLVNRVKGHWQANGAVNLVPHLITRLDRFTSG 139

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I +VAR + A   L+E  R R+I+K Y +LV G+   +K      L     +  D +H  
Sbjct: 140 ITLVARHQVANSLLSEQVRHRKIKKTYLALVDGVVSAEKGTFNQPL----GLAADGIH-- 193

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           ++ ++G   A + FKV+  FA +   +++   TGRTHQ+RVH  + G P+VGD  Y    
Sbjct: 194 REVQEGGQSATTSFKVVQRFANQ-TLVQVHLKTGRTHQIRVHFANAGHPLVGDQLYG--- 249

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     I+ +  LHA+ +    P    +L+ TAPLPA +
Sbjct: 250 -GPMDRGIERQ-ALHAQSIRFFDPFTNQKLEFTAPLPADL 287


>gi|91209118|ref|YP_539104.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli UTI89]
 gi|117622346|ref|YP_851259.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli APEC O1]
 gi|218556997|ref|YP_002389910.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli S88]
 gi|237704202|ref|ZP_04534683.1| ribosomal large subunit pseudouridine synthase A [Escherichia sp.
           3_2_53FAA]
 gi|91070692|gb|ABE05573.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           UTI89]
 gi|115511470|gb|ABI99544.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           APEC O1]
 gi|218363766|emb|CAR01427.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli S88]
 gi|222031890|emb|CAP74628.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           LF82]
 gi|226902114|gb|EEH88373.1| ribosomal large subunit pseudouridine synthase A [Escherichia sp.
           3_2_53FAA]
 gi|294491670|gb|ADE90426.1| pseudouridine synthase, RluA family [Escherichia coli IHE3034]
 gi|307629632|gb|ADN73936.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli UM146]
 gi|312944664|gb|ADR25491.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O83:H1
           str. NRG 857C]
 gi|315285114|gb|EFU44559.1| pseudouridine synthase A [Escherichia coli MS 110-3]
 gi|323950944|gb|EGB46821.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323955254|gb|EGB51027.1| RNA pseudouridylate synthase [Escherichia coli H263]
          Length = 219

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VVLYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|53712433|ref|YP_098425.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           fragilis YCH46]
 gi|52215298|dbj|BAD47891.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           fragilis YCH46]
          Length = 539

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 72/210 (34%), Positives = 106/210 (50%), Gaps = 24/210 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + V +KP G+    G      I   L++ + ++ G  P + HRLD  TSG+L+
Sbjct: 338 ILFEDQWLLVLHKPEGVLSVPGKSEEQSIYSLLRARYPEATG--PLVVHRLDMATSGLLL 395

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A+T+   +HL   F  R I+K Y +L+ GI   ++  I         I  DY+   +Q 
Sbjct: 396 AAKTQEVHRHLQAQFENRSIKKRYIALLDGILPEEEGVI------DLPICPDYLDRPRQM 449

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCA 274
            NE+    AI+ ++V+D        +   P TGRTHQLRVHA H   + CPIVGD  Y  
Sbjct: 450 VNEELGKTAITRYQVMD-RKNGQTRIAFFPLTGRTHQLRVHAAHPLGLNCPIVGDELYGR 508

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                       +LYLHA Y++  HP  G+
Sbjct: 509 K---------AERLYLHAEYLEFIHPVSGQ 529


>gi|329922661|ref|ZP_08278213.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
 gi|328942003|gb|EGG38286.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
          Length = 322

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 85/318 (26%), Positives = 145/318 (45%), Gaps = 43/318 (13%)

Query: 11  VVENDEENMRLDRWF-KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRI 67
            VE D    R+D++  +N    ++   +Q  +  G V V+   +K N ++  G   V+++
Sbjct: 25  TVEADAAKTRIDKYITENLGEDVSRSQVQLWIADGHVSVNDGPIKSNYKVSQGDRIVLKV 84

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P    +   II E   L+               + +ED  + V NKP G+ V    G   
Sbjct: 85  PE--PSAVEIIPEDIPLE---------------IAFEDGDVIVVNKPRGMVVHPAPG--- 124

Query: 128 HIDGFL--------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           H  G L        K      G+ +P + HR+D++T+G+++ A+   A   L    +   
Sbjct: 125 HSSGTLVNALMFHCKDLSGINGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKEHS 184

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + + Y +LV G   + +  I   + + +     Y  V  +N K   +A++HF V++ F  
Sbjct: 185 VNRRYLALVHGNISHDQGTIDAPIGRDAQDRKLYT-VTDRNSK---HAVTHFTVVERFGD 240

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  LE++  TGRTHQ+RVH  ++G P+VGD  Y     G       N   LHA  +   
Sbjct: 241 -YSLLELKLETGRTHQIRVHMKYIGHPLVGDPVY-----GKSKGIKLNGQALHAAVLGFV 294

Query: 299 HPEGGR-LQITAPLPAHM 315
           HP  G  ++ +AP+P+ M
Sbjct: 295 HPSTGEYMEFSAPMPSDM 312


>gi|327539710|gb|EGF26317.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica WH47]
          Length = 333

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 82/336 (24%), Positives = 155/336 (46%), Gaps = 51/336 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IP 68
           VV       R+D +        +   ++  +++    VD + ++ + ++++GQ VR  +P
Sbjct: 5   VVPESANGFRIDLFLTQSCDGYSRSQIRDAVQNDGAEVDGRIIRPSYKVKAGQKVRFRVP 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
           P   A +  + E   LD               +LYED  + V NKPAG+ V    G    
Sbjct: 65  P--PASDDTVPENIPLD---------------ILYEDDGLVVINKPAGMVVHPARGNWTG 107

Query: 125 -IAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +   +    +S  D  G  +P + HRLD++TSG++VVA+  A   +L   +  R +QK 
Sbjct: 108 TLTSALAFRFQSLSDVGGPTRPGIVHRLDRDTSGVIVVAKNNAVHLNLAAQWHDRLVQKE 167

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++ +G     ++ I   + +  H        +++    +  A + ++V++    +   
Sbjct: 168 YTAITFGRLDRDRDWIHASIGR--HPYQRDKQAIREGHATSKTASTFYEVVERHG-RVTR 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-----------------GNFTSP-- 283
           ++++P TGRTHQ+RVH  H+GCPI+ D  Y  + +                 G   +P  
Sbjct: 225 VDVRPKTGRTHQIRVHLAHIGCPILCDRLYGGHSELSRSQIRRLAGTEVATPGVKPTPEG 284

Query: 284 ---IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
              + ++  LHA+ +   +P+ G+ + +TAPLP  +
Sbjct: 285 EEILLSRQALHAKALTFTNPQTGKEMTLTAPLPPDL 320


>gi|303238360|ref|ZP_07324895.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
 gi|302594064|gb|EFL63777.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
          Length = 322

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 80/283 (28%), Positives = 140/283 (49%), Gaps = 27/283 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q +++  D  N R+D+  K  YP++    + K  R   V+V+  RVK +     G  V 
Sbjct: 1   MQTLIIAEDSSNKRIDKVLKEKYPNMPQNFMYKAFRKKDVKVNGIRVKEDYIANLGDKVE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISV-----Q 120
           +        +II E  IL+   ++++ +D+ K+  ++YED  + + NK  GI V     Q
Sbjct: 61  V--------YIIDE--ILEGK-SISEPTDYFKAFTVIYEDKNLLIVNKKQGIPVHPDKDQ 109

Query: 121 GGSGIAYHIDGFLKS-WVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             + +   +  +++   V SK  G  P L HRLD+ T G++++A+   A + + E  + +
Sbjct: 110 AENTLIDLVTAYIREKEVTSKTSGFSPALCHRLDRNTGGLIIIAKNNEALKVMLEKIKNK 169

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---VID 234
            ++K Y  LV G  +  +  +  +L K       Y++  K   + +   I+ +K   +ID
Sbjct: 170 EVKKYYQCLVRGKMEKPQGILKAYLEKDERKSRVYINDYKT--RNSLEIITKYKTLSIID 227

Query: 235 CFA--QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     LE++  TGRTHQ+R H  ++G PIVGD KY  N
Sbjct: 228 NITADDSASLLEVELVTGRTHQIRAHMSYIGHPIVGDGKYGDN 270


>gi|109897660|ref|YP_660915.1| RluA family pseudouridine synthase [Pseudoalteromonas atlantica
           T6c]
 gi|109699941|gb|ABG39861.1| ribosomal large subunit pseudouridine synthase D [Pseudoalteromonas
           atlantica T6c]
          Length = 327

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 94/321 (29%), Positives = 151/321 (47%), Gaps = 45/321 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   ++  + + QV VD            GQ+V  P        ++ 
Sbjct: 22  RLDQALAEMFPDYSRSRIKDWILADQVAVD------------GQIVNKP-----REKLLG 64

Query: 80  EQKI-LDSSVNL-TKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKS 135
           E+ I +D+S+ +  +HS   ++  ++YED  I V NKP  + V  G+G A   I   L S
Sbjct: 65  EELIEIDASIEIQERHSAQEIELNIVYEDEHILVINKPTNLVVHPGAGNASGTILNALLS 124

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---I 190
            V      PR  + HRLD++T+G++VVA+T  A  HL E  + R I + Y ++V+G    
Sbjct: 125 HVPEIASVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVEKLQAREISREYEAVVYGNLIA 184

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             +  E I     K++ +      VV+  +     A++H++V   + +    L ++  +G
Sbjct: 185 GGSVDEPIGRHPTKRTSMA-----VVQSGKP----ALTHYRVKHKY-RAHTHLRLKLESG 234

Query: 251 RTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQN-----KLYLHARYMDLPHPEG 302
           RTHQ+RVH  H+  P+VGD  Y       K      I+      +  LHA  ++L HP  
Sbjct: 235 RTHQIRVHMAHLRHPLVGDQAYGGRPRLPKAASELMIETIRGFKRQALHAIQLELEHPIT 294

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
           G  +   APLP   V   D L
Sbjct: 295 GEWMSFQAPLPDDFVNLLDVL 315


>gi|325202501|gb|ADY97955.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M01-240149]
 gi|325207748|gb|ADZ03200.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis NZ-05/33]
          Length = 374

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 139/307 (45%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T +A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQIPRAGIVHRLDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|167464208|ref|ZP_02329297.1| pseudouridine synthase, RluA family protein [Paenibacillus larvae
           subsp. larvae BRL-230010]
 gi|322383741|ref|ZP_08057492.1| pseudouridylate synthase-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
 gi|321151953|gb|EFX44896.1| pseudouridylate synthase-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
          Length = 310

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 75/234 (32%), Positives = 119/234 (50%), Gaps = 26/234 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKG--QKPRLTHRLDQETS 155
           +L+ED ++ V NK AG+ V    G  ++++    + V     KG   + R  HRLDQETS
Sbjct: 85  ILHEDEQLLVLNKEAGMIVHPTHG--HYVNTVANAVVFHWQQKGICHRFRPVHRLDQETS 142

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L +A+     Q ++E   M  + K Y +LV+G+ K  +  + + + +      D  H+
Sbjct: 143 GVLAIAKNPYVHQQISEQMMMHALDKQYLALVYGVVKEDRGTLDDPIDRNK----DNPHI 198

Query: 216 VKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                 G   A++H++V+           WLE    TGRTHQ+RVH  H+G P++GD  Y
Sbjct: 199 RTVTPSGYP-AVTHYEVLKRMNGATLVRLWLE----TGRTHQIRVHMQHLGHPLLGDKLY 253

Query: 273 -CANFK--GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP---AHMVKTW 319
               F+  G  T  + ++  LHA  +   HP  G ++  TA LP   AH++K W
Sbjct: 254 RLEQFEQLGEKTKKLISRHALHAESLGFVHPGTGQKVTFTASLPKDMAHVIKEW 307


>gi|297172749|gb|ADI23715.1| pseudouridylate synthases, 23S RNA-specific [uncultured
           Oceanospirillales bacterium HF4000_21D01]
          Length = 321

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 146/310 (47%), Gaps = 43/310 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  D    RLD+     +P  +   LQ  ++ G + V+ +R++  +R+ +G  + +   +
Sbjct: 11  VPQDLSGYRLDQIAAKLFPDYSRARLQIWIKDGSLLVNARRLRPRDRLHAGDKLEVNAEL 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
               + + E   LD               +++ED  + + NKPA + V   SG   H DG
Sbjct: 71  PVQENWLAEPMALD---------------IVFEDDCLIIVNKPANMVVHPASG---HGDG 112

Query: 132 FLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L + +    ++  Q PR  + HRLD++T+G++VVA+T A+   L    + R I + Y +
Sbjct: 113 TLLNGLLHHHNALQQLPRAGIVHRLDKDTTGLMVVAKTLASHAALVNQMQARGIAREYEA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+        A   L +  +      V++  ++    A++H++VI  + +    LE+
Sbjct: 173 VVQGVLTGGGTVDAA--LGRHPVNRKKRAVLEIGQR----AVTHYRVIKRY-RSHTHLEV 225

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY----------LHARYM 295
           +  TGRTHQ+RVH  H+  PIVGD  Y    +    +    +L           LHAR +
Sbjct: 226 KLDTGRTHQIRVHMAHLNHPIVGDPMYGG--RQRIPAACSEELIHCLKAFKRQALHARRL 283

Query: 296 DLPHPEGGRL 305
            L HP  G+L
Sbjct: 284 ALHHPGNGKL 293


>gi|254427100|ref|ZP_05040807.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881]
 gi|196193269|gb|EDX88228.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881]
          Length = 324

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 119/237 (50%), Gaps = 24/237 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----PR--LTHRLDQET 154
           ++Y+D  + V NKP G+ V   +G   H DG L + +    ++    PR  + HRLD++T
Sbjct: 89  VVYQDDDLIVINKPTGLVVHPAAG---HADGTLLNGLLHLDERLNSLPRAGIVHRLDRDT 145

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++VVAR+  A Q L    + + + + Y ++  G+     +  A   + +  +      
Sbjct: 146 TGLMVVARSLEAHQSLVAQLQDKSLFRQYEAIAVGVMTGGGKVDAP--MGRHPVDRKKQA 203

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VVK    G   A++H++V+D + +    +++Q  TGRTHQ+RVH  H   P+VGD  Y  
Sbjct: 204 VVK---TGGKNAVTHYRVLDRY-RAHTRIQVQLETGRTHQIRVHMAHRNYPLVGDPLYGG 259

Query: 275 NFK--GNFTSPIQNKLY------LHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
             K     T  ++  L+      LHAR + L HP  G   +  APLPA M     +L
Sbjct: 260 RLKQPAGATEALRQALHKFPRQALHARKLGLIHPATGEYREFEAPLPADMTGLIAAL 316


>gi|119505582|ref|ZP_01627653.1| pseudouridine synthase [marine gamma proteobacterium HTCC2080]
 gi|119458525|gb|EAW39629.1| pseudouridine synthase [marine gamma proteobacterium HTCC2080]
          Length = 324

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 80/318 (25%), Positives = 136/318 (42%), Gaps = 40/318 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R D+     +P  +   LQ  + +G + +D    +  +++  GQ++ +   +        
Sbjct: 23  RFDQAAATLFPEFSRSRLQSYIGAGTLTLDGHAARAKDKVAQGQLLVLAAAVEPAVSWSG 82

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK----S 135
           + + LD               +++ED  + V NKPAG+ V   +G   H DG L      
Sbjct: 83  DSRPLD---------------IIFEDEHVLVVNKPAGVVVHPAAG---HADGTLVNSLIG 124

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +     Q PR  + HRLD++T+GI+ VAR+  A Q L +    R ++++Y ++  G    
Sbjct: 125 YAPELEQLPRGGIVHRLDKDTTGIMFVARSYLAHQSLVKQLAARSVKRVYAAVCRGALSG 184

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                A      S      V        G   AI+H+++ + F +    L +   TGRTH
Sbjct: 185 GGSVDAPIGRHSS------VRTRMAVTVGGKPAITHYRIAERF-KHHTALSVSLETGRTH 237

Query: 254 QLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHARYMDLPHPEGG-R 304
           Q+RVH      P++GD  Y    +     ++ +Q  L       LHA+ +   HP  G R
Sbjct: 238 QIRVHLASRNNPLIGDPVYGGRPRPPAAASTELQTMLRTFSRQALHAQTLAFDHPATGQR 297

Query: 305 LQITAPLPAHMVKTWDSL 322
            Q   PLP  +++    L
Sbjct: 298 CQFETPLPEDLLQLLSVL 315


>gi|26245982|ref|NP_752021.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli CFT073]
 gi|227885043|ref|ZP_04002848.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli 83972]
 gi|300981032|ref|ZP_07175309.1| pseudouridine synthase A [Escherichia coli MS 45-1]
 gi|301048442|ref|ZP_07195469.1| pseudouridine synthase A [Escherichia coli MS 185-1]
 gi|331661098|ref|ZP_08362030.1| pseudouridine synthase A [Escherichia coli TA206]
 gi|331681442|ref|ZP_08382079.1| pseudouridine synthase A [Escherichia coli H299]
 gi|34395780|sp|Q8FL93|RLUA_ECOL6 RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|26106379|gb|AAN78565.1|AE016755_65 Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           CFT073]
 gi|227837872|gb|EEJ48338.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli 83972]
 gi|300299735|gb|EFJ56120.1| pseudouridine synthase A [Escherichia coli MS 185-1]
 gi|300409068|gb|EFJ92606.1| pseudouridine synthase A [Escherichia coli MS 45-1]
 gi|307551903|gb|ADN44678.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           ABU 83972]
 gi|315293367|gb|EFU52719.1| pseudouridine synthase A [Escherichia coli MS 153-1]
 gi|315298424|gb|EFU57679.1| pseudouridine synthase A [Escherichia coli MS 16-3]
 gi|331052140|gb|EGI24179.1| pseudouridine synthase A [Escherichia coli TA206]
 gi|331081663|gb|EGI52824.1| pseudouridine synthase A [Escherichia coli H299]
          Length = 219

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VVLYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|319892189|ref|YP_004149064.1| Ribosomal large subunit pseudouridine synthase D [Staphylococcus
           pseudintermedius HKU10-03]
 gi|317161885|gb|ADV05428.1| Ribosomal large subunit pseudouridine synthase D [Staphylococcus
           pseudintermedius HKU10-03]
          Length = 305

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 85/315 (26%), Positives = 150/315 (47%), Gaps = 61/315 (19%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+         +   LQ+ ++ G + V+ K VK N +++ G  + I            
Sbjct: 17  RIDKILPEFNSEWSRSQLQEWIKEGLIEVNGKAVKSNYKLKLGDRIEI-----------T 65

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL---K 134
           E++++++ +     ++ L   + YED  + +  KP G+ V    G      ++G +   K
Sbjct: 66  EKEVVEADI----QAENLNLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIK 121

Query: 135 SWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP- 191
           +     G+ +P + HR+D++TSG+L+VA+   A + L E    + +++ Y +LV G IP 
Sbjct: 122 NLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVEQLMAKTVKRKYIALVHGHIPH 181

Query: 192 ------------KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
                       KN ++ +A               VV   ++    A++HF VI+ F + 
Sbjct: 182 EFGTIDAPIGRNKNDRQSMA---------------VVDDGKE----AVTHFNVIETF-KN 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +E +  TGRTHQ+RVH  ++G P+VGD KY        T  I  +  LHA  +   H
Sbjct: 222 YTLVECELETGRTHQIRVHMKYIGYPLVGDPKYGP----KKTLEIGGQA-LHAGLIGFEH 276

Query: 300 PEGGR-LQITAPLPA 313
           P+ G  ++  APLPA
Sbjct: 277 PKTGEYIERFAPLPA 291


>gi|153853839|ref|ZP_01995195.1| hypothetical protein DORLON_01186 [Dorea longicatena DSM 13814]
 gi|149753589|gb|EDM63520.1| hypothetical protein DORLON_01186 [Dorea longicatena DSM 13814]
          Length = 296

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 81/315 (25%), Positives = 149/315 (47%), Gaps = 33/315 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           ++Y++ E  E+ +R++++ +   Y   N   ++++ +S  + V+         + +G ++
Sbjct: 5   IEYLITEK-EDGLRIEQFLRRKGYSGQNLAEIKRMPKS--ILVNGVHYYMRQTLTAGDIL 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           ++         II E K  +    +    D     ++YED  I V NKPAG+ +      
Sbjct: 62  KV---------IICETKCSEKIPPVEIPLD-----IIYEDEDIIVINKPAGMPIHPSMNN 107

Query: 126 AYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            Y+      +W   K  KP   R  +RLD++TSG+ VV++   +   L+   + R + + 
Sbjct: 108 YYNSLANALAWYYQKQDKPFIFRCCNRLDRDTSGLTVVSKHLVSGSILSTMTKNREVHRE 167

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G        I   L +K    G  +  +   E G   AI+H+K+I   A     
Sbjct: 168 YLAVVKGRVTPSSGTICAPLARKE---GTIIERMVDFEHGEE-AITHYKLIR-EANGHSL 222

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++  TGRTHQ+R+H  ++G P++GD+ Y  + +         +  LH+ +M+  HP  
Sbjct: 223 VSLKLETGRTHQIRIHMKYLGFPLIGDYLYNPDMEH------MTRQALHSHHMEFAHPIT 276

Query: 303 GR-LQITAPLPAHMV 316
           G  +  TAPLPA M 
Sbjct: 277 GEWMSFTAPLPADMA 291


>gi|81428560|ref|YP_395560.1| pseudouridylate synthase, 23S rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610202|emb|CAI55251.1| Pseudouridylate synthase, 23S rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 301

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 85/318 (26%), Positives = 149/318 (46%), Gaps = 44/318 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINAL 74
           E  R+D+      P  +   +Q+ L+   V ++ +  K N+++ + +   V IP  ++  
Sbjct: 12  ETGRIDKVLSQLLPDYSRSQIQQWLKKDLVEINGQTSKGNHKVVADEKISVTIPDPVSL- 70

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             ++ E   LD               ++YED ++ V NKP G+ V    G   H +G L 
Sbjct: 71  -DLVPEDIPLD---------------IVYEDDQVLVVNKPQGMVVHPSPG---HPNGTLV 111

Query: 135 SWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + + +           +P + HR+D++TSG+L+VA+T  A + L+E  + +   + Y +L
Sbjct: 112 NALLAHTPLSEINGVFRPGIVHRIDKDTSGLLMVAKTNEAHESLSEQLKAKSNLREYLAL 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEM 245
           V G  +  +  I       + IG   +  +KQ        A++HF+V++ F   +  +  
Sbjct: 172 VHGNIEEDEGTI------DAPIGRSKLDRMKQAIVPDGRPAVTHFEVVERFTD-YTLIRC 224

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +  TGRTHQ+RVH  ++  P+ GD  Y        T P + + +LHA  +   HP  G  
Sbjct: 225 RLETGRTHQIRVHLAYINRPVAGDPTYGP----RKTLPGKGQ-FLHAAVLGFKHPTTGEN 279

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++  APLPA   KT   L
Sbjct: 280 MRFEAPLPAIFEKTLQEL 297


>gi|168702909|ref|ZP_02735186.1| ribosomal large subunit pseudouridine synthase D [Gemmata
           obscuriglobus UQM 2246]
          Length = 204

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 65/184 (35%), Positives = 88/184 (47%), Gaps = 23/184 (12%)

Query: 129 IDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +D  +K+++  K  KP      + HRLD+  SG LV ART  AA  L+E FR   ++K+Y
Sbjct: 4   VDRLVKAYLKEKYDKPGNVFLGVVHRLDKPVSGSLVFARTSKAAARLSEQFREGGVEKVY 63

Query: 184 WSLV-------WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           W+++       W    N    + +WL K        V  V     GA +A   F+V    
Sbjct: 64  WAVIEAQAPGPWVTADNG--SLEDWLQKDDD--NARVETVAPETPGAQFARLLFQVRGRH 119

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                WLE++PHTGR HQLRV     G  I GDHKY +        P  N + LHAR + 
Sbjct: 120 -NGLIWLELRPHTGRKHQLRVQLASRGASIYGDHKYGSKL------PFGNGIALHARSLT 172

Query: 297 LPHP 300
             HP
Sbjct: 173 FLHP 176


>gi|306825452|ref|ZP_07458792.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|304432390|gb|EFM35366.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
          Length = 299

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 88/310 (28%), Positives = 150/310 (48%), Gaps = 46/310 (14%)

Query: 39  KILRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           KI R G +R+DK         R   N +I++GQV+ +   +    + ++E  I+   V  
Sbjct: 4   KIERGG-LRLDKALSDLTELSRSLANEQIKAGQVL-VNGQVKKAKYTVQEGDIVTYHVPE 61

Query: 91  TKHSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG 141
            +  +++   +    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G
Sbjct: 62  PEVLEYVAEDIPLDIIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSG 118

Query: 142 ----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  
Sbjct: 119 INGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGV 178

Query: 198 IANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           I      ++ IG       KQ    KG   A++ F+V++ F   +  LE+Q  TGRTHQ+
Sbjct: 179 I------EAPIGRSEKDRKKQAVTAKG-KPAVTRFQVLERFGD-YSLLELQLETGRTHQI 230

Query: 256 RVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           RVH  ++G P+ GD  Y      KG+         +LHA+ +   HP  G  L+ TA +P
Sbjct: 231 RVHMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGEILEFTADIP 283

Query: 313 AHMVKTWDSL 322
               +T + L
Sbjct: 284 EIFKETLERL 293


>gi|326562905|gb|EGE13192.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis 46P47B1]
 gi|326563654|gb|EGE13906.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis 103P14B1]
 gi|326573262|gb|EGE23230.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis 101P30B1]
          Length = 355

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 80/316 (25%), Positives = 146/316 (46%), Gaps = 32/316 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD+   + +   +  NL+  +  GQ+ V+ K VK    ++ G ++ +  V 
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKNFIDEGQLTVNGKVVKPKYAVKVGDILTLEAVH 107

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            + +  + E   +D               ++YED  + + NKPAG+ V  G+G      +
Sbjct: 108 ESHSEDLPENIDID---------------IIYEDEAVIIINKPAGMVVHPGAGNRTGTLV 152

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +  L  +   +   PR  L HR+D++T+G+LV+ART++A   L +  + + + + Y  + 
Sbjct: 153 NALLYHF-PKQAHLPRAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIA 211

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQ 246
            G      E + +  +    IG    H  K   K     A++H        +++  L++ 
Sbjct: 212 LGA---VHEVLRHAQIDAP-IGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIH 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHP 300
             TGRTHQ+RVH  ++G P+VGD  Y  + +   +   +       +  LHA  +   HP
Sbjct: 268 LKTGRTHQIRVHLSYVGHPLVGDPVYGTSPRSGLSDRQRCAILDFGRQALHAYMLGFIHP 327

Query: 301 EGGR-LQITAPLPAHM 315
             G  ++  APLP  M
Sbjct: 328 VTGEAMKFHAPLPKDM 343


>gi|33151686|ref|NP_873039.1| 23S rRNA pseudouridine synthase D [Haemophilus ducreyi 35000HP]
 gi|34395836|sp|Q9L7A7|RLUD_HAEDU RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|33147907|gb|AAP95428.1| pseudouridine synthase [Haemophilus ducreyi 35000HP]
          Length = 325

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 79/254 (31%), Positives = 131/254 (51%), Gaps = 33/254 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           +++ED  I + NKP  + V  G+G   + DG     L  +     + PR  + HRLD++T
Sbjct: 86  IVHEDDDIIIINKPKNLVVHPGAG---NPDGTVLNALLYYYPPIAEVPRAGIIHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+   A  HL  + + RRI + Y ++  GI        E +A    K++ +   
Sbjct: 143 TGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMTQGGKVDEPMARHPTKRTAMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       AI+H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 201 -VHPMGKP------AITHYRIMERF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQL 252

Query: 272 YCAN---FKGN---FTSPIQ--NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           Y       KG+   F + ++   +  LHA  + L HP  G L +  APLPA  V+  ++L
Sbjct: 253 YGGRPRPPKGSSEAFLTVLRAFQRQALHATMLRLEHPINGELIECHAPLPADFVELIEAL 312

Query: 323 GFKYDRNLYIKRLY 336
              Y R  Y + LY
Sbjct: 313 KTDYQR--YKEDLY 324


>gi|319947181|ref|ZP_08021415.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
 gi|319747229|gb|EFV99488.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
          Length = 296

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 77/285 (27%), Positives = 141/285 (49%), Gaps = 37/285 (12%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSV----NLTKHSDFLKSILLYEDSKIYVF 111
           N +I+ G+++ +   +    + +KE  ++   V     +T  ++ +   ++Y+D+ + V 
Sbjct: 28  NEQIKEGKIL-VNGQVKKAKYTVKEGDVISYEVPQMEEVTYEAEDIPLEIVYQDADVVVV 86

Query: 112 NKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           NKP G+ V   +G         + YHI     S ++ +  +P + HR+D++TSG+L+VA+
Sbjct: 87  NKPQGMVVHPSAGHTSGTLVNALMYHIKDL--SGINGE-LRPGIVHRIDKDTSGLLMVAK 143

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NE 220
             AA   L +  + ++  + YW++V G   N +  I      ++ IG       KQ    
Sbjct: 144 NDAAHVALADELKAKKSLRKYWAIVHGNLPNDRGVI------EAPIGRSDKDRKKQAVTA 197

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKG 278
           KG   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y      KG
Sbjct: 198 KG-KPALTRFHVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPRRTLKG 255

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +         +LHA+ +   HP  G  ++ +  +P    KT + L
Sbjct: 256 HGQ-------FLHAKTLGFTHPRTGEVMEFSVEVPEVFQKTLEQL 293


>gi|301301197|ref|ZP_07207353.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300851196|gb|EFK78924.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 298

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 89/311 (28%), Positives = 146/311 (46%), Gaps = 36/311 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHII 78
           RLD+   N +       L+K++  G ++V+    K N ++  G  +    P +  L+ + 
Sbjct: 13  RLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGDVKKANYKVNLGDEITFDKPEVKKLS-LE 71

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLK-- 134
            E   LD               ++YED  + V NKP G+ V    G   H  ++  L   
Sbjct: 72  PENIPLD---------------IVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNALLYHS 116

Query: 135 --SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             S ++    +P + HR+D++TSG+L+VA+   A Q L +  + +   + Y +LV G  K
Sbjct: 117 PLSTINGT-YRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYIALVHGNIK 175

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I +  L +S +      VVK    G N A++HF+V+  +   +  ++    TGRT
Sbjct: 176 EDSGTI-DAPLGRSKVDRKKQAVVKD---GRN-AVTHFEVLKRYGD-YTLVKCVLETGRT 229

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           HQ+RVH  ++G P+VGD  Y     G   +   +  +LHA  +   HP     L+ TAPL
Sbjct: 230 HQIRVHMKYIGHPLVGDQLY-----GPRKTLGNSGQFLHAEKLGFVHPRTNEYLEFTAPL 284

Query: 312 PAHMVKTWDSL 322
           P +  K  +SL
Sbjct: 285 PENFKKLLESL 295


>gi|329116866|ref|ZP_08245583.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
 gi|326907271|gb|EGE54185.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
          Length = 295

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 78/314 (24%), Positives = 147/314 (46%), Gaps = 34/314 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++       +++G V V+ +  K    +++G ++          
Sbjct: 7   EAGSRLDKAIAD-LTELSRGQANDAIKAGIVLVNGQAAKAKYSVKAGDII---------T 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
           + I+E+++LD        ++ +   ++YED  + + NKP G+ V   +G      ++  L
Sbjct: 57  YEIQEEEVLDY------QAEDIPLDVVYEDEDLAIINKPQGMVVHPSAGHSSGTMVNALL 110

Query: 134 KSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D  G     +P + HR+D++TSG+L+VA+  AA + L +  + ++  + Y ++V G
Sbjct: 111 YQIKDLSGINGVVRPGIVHRIDKDTSGLLMVAKNDAAHRALADELKAKKSLRKYLAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +          + +  E     A++ F+VI+ F   +  +E+   T
Sbjct: 171 NLPNDRGIIEAPIGRSEKDRKKQAVIARGKE-----AVTRFQVIERFGD-YTLVELTLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ + L HP  G  +  T
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLY-----GPRKTLPGNGQFLHAQTLGLTHPRTGEVMTFT 279

Query: 309 APLPAHMVKTWDSL 322
           A  P    +T + L
Sbjct: 280 AEPPLIFQQTIEKL 293


>gi|161833681|ref|YP_001597877.1| ribosomal large subunit pseudouridine synthase D [Candidatus Sulcia
           muelleri GWSS]
 gi|152206171|gb|ABS30481.1| ribosomal large subunit pseudouridine synthase D [Candidatus Sulcia
           muelleri GWSS]
          Length = 337

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 92/299 (30%), Positives = 147/299 (49%), Gaps = 36/299 (12%)

Query: 16  EENMRLDRWFKN--HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           E  +R+D + K   H  + NF+  QKI+  G V V+      N  I+   +V+I  VI  
Sbjct: 34  ENLIRIDTYLKFILHKKNRNFI--QKIIEKGFVYVN------NILIKKNYIVKINDVI-- 83

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
                 E  + +   N+   +  LK  + YED  + + NK +G+ V  G G      I+G
Sbjct: 84  ------EIFLPEGKKNIIPEN--LKINIFYEDEYVIIINKQSGLVVHPGKGNESMTLING 135

Query: 132 FLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               ++  K    + P L HR+D+ TSG+++VA+ +   + + + F +  I++ Y +LVW
Sbjct: 136 LHFYFLKKKNIYNKIPILVHRIDKGTSGLILVAKDKNILEKIYKQFYINHIKRKYITLVW 195

Query: 189 G-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           G I  NK   I N  + +S     Y++V      G  ++I+H+KV++ F +    L+   
Sbjct: 196 GYIKNNKGTIICN--IGRSLKNRIYMNVFPNGIYGK-FSITHYKVLERF-KYVTLLKCTL 251

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANF----KGNFTSPIQNKLY--LHARYMDLPHP 300
            TGRTHQ+RVH  ++G PI+ D  Y  N     K N      N  Y  LHA Y++  HP
Sbjct: 252 ETGRTHQIRVHLKYIGHPILNDKDYGGNHTFKEKKNIKKLFINMKYQALHAYYIEYIHP 310


>gi|125717901|ref|YP_001035034.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK36]
 gi|125497818|gb|ABN44484.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Streptococcus sanguinis SK36]
 gi|327474176|gb|EGF19586.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK408]
          Length = 298

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 119/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVINKPQGMVVHPSAG---HTSGTLVNALMYHIQDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTRFQVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA +PA   +T + L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEVPAIFQETLEKL 295


>gi|94502329|ref|ZP_01308802.1| ribosomal large subunit pseudouridine synthase D [Candidatus Sulcia
           muelleri str. Hc (Homalodisca coagulata)]
 gi|94451116|gb|EAT14068.1| ribosomal large subunit pseudouridine synthase D [Candidatus Sulcia
           muelleri str. Hc (Homalodisca coagulata)]
          Length = 338

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 92/299 (30%), Positives = 147/299 (49%), Gaps = 36/299 (12%)

Query: 16  EENMRLDRWFKN--HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           E  +R+D + K   H  + NF+  QKI+  G V V+      N  I+   +V+I  VI  
Sbjct: 35  ENLIRIDTYLKFILHKKNRNFI--QKIIEKGFVYVN------NILIKKNYIVKINDVI-- 84

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
                 E  + +   N+   +  LK  + YED  + + NK +G+ V  G G      I+G
Sbjct: 85  ------EIFLPEGKKNIIPEN--LKINIFYEDEYVIIINKQSGLVVHPGKGNESMTLING 136

Query: 132 FLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               ++  K    + P L HR+D+ TSG+++VA+ +   + + + F +  I++ Y +LVW
Sbjct: 137 LHFYFLKKKNIYNKIPILVHRIDKGTSGLILVAKDKNILEKIYKQFYINHIKRKYITLVW 196

Query: 189 G-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           G I  NK   I N  + +S     Y++V      G  ++I+H+KV++ F +    L+   
Sbjct: 197 GYIKNNKGTIICN--IGRSLKNRIYMNVFPNGIYGK-FSITHYKVLERF-KYVTLLKCTL 252

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANF----KGNFTSPIQNKLY--LHARYMDLPHP 300
            TGRTHQ+RVH  ++G PI+ D  Y  N     K N      N  Y  LHA Y++  HP
Sbjct: 253 ETGRTHQIRVHLKYIGHPILNDKDYGGNHTFKEKKNIKKLFINMKYQALHAYYIEYIHP 311


>gi|329902613|ref|ZP_08273174.1| Ribosomal large subunit pseudouridine synthase D [Oxalobacteraceae
           bacterium IMCC9480]
 gi|327548721|gb|EGF33364.1| Ribosomal large subunit pseudouridine synthase D [Oxalobacteraceae
           bacterium IMCC9480]
          Length = 355

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 88/295 (29%), Positives = 128/295 (43%), Gaps = 38/295 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+      P  +   +Q+ +  G V VD            G+V R    +    HI+ 
Sbjct: 50  RLDKVVARLVPQFSRSRMQQWIDDGFVTVD------------GKVGRTRMTVYGDEHIVV 97

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
             +              L   ++YED  I V NKPAG+ V  GSG      ++G L  W 
Sbjct: 98  LPQAAPEDTAFAPEEMALN--IVYEDEAIIVVNKPAGLVVHPGSGNWSGTLLNGLLHYWP 155

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              G  PR  + HRLD++TSG++VVA+T      L      R +++ Y++LVWG P N  
Sbjct: 156 ALIG-VPRAGIVHRLDKDTSGLMVVAKTLEVHTDLVRQLAARTVKREYFALVWGTP-NLS 213

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-------FAQKFCWLEMQPH 248
             I   + +      D + +       A  AI+HF+ I+         +   C LE    
Sbjct: 214 GTIDASMGRHPR---DRIRMAVLESMSAKPAITHFERIESGLLDRRPVSLMRCRLE---- 266

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           TGRTHQ+RVH   +G  +VGD  Y         +P  ++  L AR + L HP  G
Sbjct: 267 TGRTHQIRVHMQSIGFALVGDTLYGK----QHLAPAFHRQALQARRLGLVHPVTG 317


>gi|324991250|gb|EGC23184.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK353]
          Length = 298

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 120/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIQDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG + A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKGKS-ALTRFQVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA +PA   +T + L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEVPAIFQETLEKL 295


>gi|281426229|ref|ZP_06257142.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella oris F0302]
 gi|281399643|gb|EFB30474.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella oris F0302]
          Length = 221

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 69/220 (31%), Positives = 111/220 (50%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + +  K +G  VQG       +   +K ++  K QKP      + HRLD+  S
Sbjct: 3   IVYEDNHLIIVYKHSGEIVQGDKTGDVPLSEDVKCYLKEKYQKPGNVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYV 213
           G++V A+T  A   L + FR   + K YW++   +P   +  + +WL++  K +    Y 
Sbjct: 63  GLVVFAKTSKALTRLNKMFRDGEVHKTYWAITKNLPPQSEGTLTDWLVRNEKQNKSYAYD 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H V  ++K    AI  +++I   +  +C LE+   TGR HQ+R    HMGCPI GD KY 
Sbjct: 123 HEVPHSKK----AILKYRLIG-QSDHYCLLEVNLMTGRHHQIRCQLAHMGCPIKGDLKYG 177

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
           A       S     + L A +++  HP   +L  + +PLP
Sbjct: 178 AQ-----RSNPDGSICLLAHHVEFVHPVSKQLISLDSPLP 212


>gi|19551566|ref|NP_599568.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glutamicum ATCC 13032]
 gi|62389214|ref|YP_224616.1| ribosomal large subunit pseudouridine synthase C [Corynebacterium
           glutamicum ATCC 13032]
 gi|21323080|dbj|BAB97709.1| Pseudouridylate synthases, 23S RNA-specific [Corynebacterium
           glutamicum ATCC 13032]
 gi|41324547|emb|CAF18887.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE C [Corynebacterium
           glutamicum ATCC 13032]
          Length = 294

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 91/324 (28%), Positives = 151/324 (46%), Gaps = 62/324 (19%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI- 67
           ++ V     + R+D++ +     +    + + +R G +RV+ ++V  N R+Q G  +R+ 
Sbjct: 5   FIEVSAGHADRRIDKFLRAQLKGVPASLIFRQMRKGDIRVNGRKVDPNYRLQEGDRIRMW 64

Query: 68  ---------PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
                    PPV++   HI K   + DS              +L+ED+++ V NKPAGI 
Sbjct: 65  QMDLLADLPPPVVD--KHIFK--AVADS--------------VLFEDAELLVINKPAGIP 106

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           V GG+G    +   L+     + +   L HRLD++TSG+L+V++T +  + L E  R R 
Sbjct: 107 VHGGTGHGGGVIEALRQKFPQE-RDLELVHRLDRDTSGLLLVSKTTSVLRELQEILRDR- 164

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLK-KSHIGGDYVHV---VKQNE------KGANYAIS 228
                          ++E    +LLK +    GD   +   +K+ E           A +
Sbjct: 165 ---------------EEEIFRGYLLKVEGAWPGDLRQIDVPLKRTETTVVPHSDGLRART 209

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
           +F+V+         ++ Q  TGR HQ+RVHA + G PIVGD +Y +      T      +
Sbjct: 210 YFEVVKRLPGA-TLVKAQLATGRKHQIRVHAQYAGHPIVGDPRYGSRGGRAAT------M 262

Query: 289 YLHARYMDLPHPEGGRLQITAPLP 312
           +LHA  +  P   G R + TAPLP
Sbjct: 263 HLHAAELVAPRGAGKRQKFTAPLP 286


>gi|194439387|ref|ZP_03071464.1| pseudouridine synthase, RluA family [Escherichia coli 101-1]
 gi|194421646|gb|EDX37656.1| pseudouridine synthase, RluA family [Escherichia coli 101-1]
 gi|323970730|gb|EGB65984.1| RNA pseudouridylate synthase [Escherichia coli TA007]
          Length = 230

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|332361351|gb|EGJ39155.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1056]
          Length = 298

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 119/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTRFQVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA +PA   +T + L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEVPAVFQETLEKL 295


>gi|268593137|ref|ZP_06127358.1| ribosomal large subunit pseudouridine synthase D [Providencia
           rettgeri DSM 1131]
 gi|291311410|gb|EFE51863.1| ribosomal large subunit pseudouridine synthase D [Providencia
           rettgeri DSM 1131]
          Length = 325

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 79/249 (31%), Positives = 129/249 (51%), Gaps = 33/249 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I + NKP  + V  G+G   + DG + + +          PR  + HRLD++T
Sbjct: 86  VIYEDEDILIINKPRDLVVHPGAG---NPDGTILNALLYRYPEIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL E+ + R I + Y ++  G        +E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVEALQRREITREYEAVAVGRMTAGGMVEEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH +         A++H++V++ F +    L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 201 -VHPM------GKPAVTHYRVMEHF-RAHTRLRLRLETGRTHQIRVHMAHINHPLIGDPL 252

Query: 272 YCAN---FKG---NFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y       KG    F   ++N  +  LHA  + L HP  G +++  APLP  MVK  ++L
Sbjct: 253 YGGRPRPLKGATEEFLEVMRNFDRQALHATMLRLYHPISGIQMEWHAPLPDDMVKLIEAL 312

Query: 323 GFKYDRNLY 331
             K D  L+
Sbjct: 313 --KADTELH 319


>gi|332307416|ref|YP_004435267.1| pseudouridine synthase, RluA family [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332174745|gb|AEE23999.1| pseudouridine synthase, RluA family [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 327

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 92/321 (28%), Positives = 151/321 (47%), Gaps = 45/321 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   ++  + + QV +D            GQ+V  P        ++ 
Sbjct: 22  RLDQALAEMFPDYSRSRIKDWILADQVSID------------GQIVNKP-----REKLLG 64

Query: 80  EQKI-LDSSVNL-TKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKS 135
           E+ I +D+S+ +  +HS   +   ++YED  I V NKP  + V  G+G A   I   L S
Sbjct: 65  EELIEIDASIEIQERHSAQEIDLNIVYEDEHILVINKPTNLVVHPGAGNANGTILNALLS 124

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---I 190
            V      PR  + HRLD++T+G++VVA+T  A  HL E  + R I + Y ++V+G    
Sbjct: 125 HVPDIASVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVEKLQAREISREYEAVVYGNLIA 184

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             +  E I     K++++      VV+  +     A++H++V   + +    L ++  +G
Sbjct: 185 GGSVDEPIGRHPTKRTNMA-----VVQSGKP----ALTHYRVKHKY-RAHTHLRLKLESG 234

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKLYLHARYMDLPHPEG 302
           RTHQ+RVH  H+  P+VGD  Y    +     S +         +  LHA  ++L HP  
Sbjct: 235 RTHQIRVHMAHLRHPLVGDQAYGGRPRLPKAASEVMIETIRGFKRQALHAIQLELEHPIT 294

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
           G  +   APLP   V   D L
Sbjct: 295 GEWMSFQAPLPDDFVNLLDVL 315


>gi|299134311|ref|ZP_07027504.1| pseudouridine synthase, RluA family [Afipia sp. 1NLS2]
 gi|298591058|gb|EFI51260.1| pseudouridine synthase, RluA family [Afipia sp. 1NLS2]
          Length = 347

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 78/319 (24%), Positives = 141/319 (44%), Gaps = 54/319 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK---FNNRIQSGQVVRIPPVINA 73
           ++ RLDR        ++   L+ ++ +G V +    V+   +  +     +V +PP +  
Sbjct: 31  QSQRLDRVLAEQVEDLSRTRLKALIVAGHVSIGGAPVQDPAYQVKADETIIVEVPPAV-- 88

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                 E +  +  +N+           +YED  + V NKP G+ V   +G  +     +
Sbjct: 89  ----APEPEGENIPLNI-----------VYEDDDLLVLNKPKGLVVHPAAG--HETGTLV 131

Query: 134 KSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQ 180
            + +   G         ++P + HRLD++T+G++VVA+   A Q LT  F    R   ++
Sbjct: 132 NALIAHCGTSLSGIGGVKRPGIVHRLDKDTTGLMVVAKNDRAHQSLTAQFADHGRTGALR 191

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK- 239
           + Y + VWG P      I   + +  H        V+Q   G  +A++H+++++ F  + 
Sbjct: 192 RGYMAFVWGAPSRSHGTIDQPIDR--HPFAREKMAVRQ---GGRHAVTHWEMLESFEGRD 246

Query: 240 ----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKL---- 288
                  L  Q  TGRTHQ+RVH  H G P++GD  Y + F+       +P +  +    
Sbjct: 247 GKPLAALLACQLETGRTHQIRVHLGHAGHPLIGDDVYGSGFRTKANQLGTPAKTAVAALG 306

Query: 289 --YLHARYMDLPHPEGGRL 305
              LHA  + + HP  G +
Sbjct: 307 RQALHAYLLQIEHPATGEI 325


>gi|90961803|ref|YP_535719.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|90820997|gb|ABD99636.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|300214544|gb|ADJ78960.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 298

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 89/311 (28%), Positives = 146/311 (46%), Gaps = 36/311 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHII 78
           RLD+   N +       L+K++  G ++V+    K N ++  G  +    P +  L+ + 
Sbjct: 13  RLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGDVKKANYKVNLGDEITFDKPEVKKLS-LE 71

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLK-- 134
            E   LD               ++YED  + V NKP G+ V    G   H  ++  L   
Sbjct: 72  PENIPLD---------------IVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNALLYHS 116

Query: 135 --SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             S ++    +P + HR+D++TSG+L+VA+   A Q L +  + +   + Y +LV G  K
Sbjct: 117 PLSTINGT-YRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYVALVHGNIK 175

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I +  L +S +      VVK    G N A++HF+V+  +   +  ++    TGRT
Sbjct: 176 EDSGTI-DAPLGRSKVDRKKQAVVKD---GRN-AVTHFEVLKRYGD-YTLVKCVLETGRT 229

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           HQ+RVH  ++G P+VGD  Y     G   +   +  +LHA  +   HP     L+ TAPL
Sbjct: 230 HQIRVHMKYIGHPLVGDQLY-----GPRKTLGNSGQFLHAEKLGFVHPRTNEYLEFTAPL 284

Query: 312 PAHMVKTWDSL 322
           P +  K  +SL
Sbjct: 285 PENFKKLLESL 295


>gi|149280326|ref|ZP_01886447.1| pseudouridylate synthase, 23S RNA-specific [Pedobacter sp. BAL39]
 gi|149228875|gb|EDM34273.1| pseudouridylate synthase, 23S RNA-specific [Pedobacter sp. BAL39]
          Length = 343

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 82/327 (25%), Positives = 152/327 (46%), Gaps = 44/327 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+D++      + +   +Q  + +G V V+ K VK + +++    + I  
Sbjct: 21  IVVDKGQSLLRVDKFLMGRMENASRNRIQNAIDAGNVLVNGKTVKSSYKVKPADEISI-- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
                 H  ++ ++    + L          ++YED+ + V NKPAG+ V  G       
Sbjct: 79  ---VFPHPPRDTEVYPEDIPLD---------IVYEDNDLLVVNKPAGMVVHPGYNNYTGT 126

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             + +A+H +  L     ++G +P L HR+D++TSG+L++++       L + F    I 
Sbjct: 127 LVNALAFHFEQ-LPQLPGNEG-RPGLVHRIDKDTSGLLLISKNEITMTKLAKQFFDHSIT 184

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           + Y +L WG I +N         + +S      + V    EKG  ++++H+ V++     
Sbjct: 185 RKYIALAWGDIAEN---GTVTGFIGRSLKNRIVMDVYDDEEKGK-WSVTHYTVLERLGY- 239

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN------K 287
              +  Q  TGRTHQ+R H  H+G P+  D  Y  +   KG     +   +QN      +
Sbjct: 240 VTLISCQLETGRTHQIRAHMQHIGHPLFNDANYGGDKIVKGTTFNKYKQFVQNCFEIMPR 299

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPA 313
             LHA+ +   HP   + ++  APLPA
Sbjct: 300 QSLHAQTLGFIHPTTKKYMEFEAPLPA 326


>gi|146306264|ref|YP_001186729.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           mendocina ymp]
 gi|145574465|gb|ABP83997.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           mendocina ymp]
          Length = 211

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 71/214 (33%), Positives = 112/214 (52%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D+ + V NKP  + SV G +    + D  +    ++   + R+ HRLD ETSGI+V
Sbjct: 8   ILHQDAALLVINKPTLLLSVPGRAD--DNKDCLVTRLQENGYPEARIVHRLDWETSGIIV 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG P+     I   L  +        HVV  +
Sbjct: 66  LARDADSHRELSRQFHDRETEKAYTALCWGQPEADSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++H++VI+     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HELGKHALTHWRVIE-RCGDWCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY----AHE 176

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                  +L LHA  + L HP+ G RL+   P P
Sbjct: 177 QALAAHERLCLHASMLALTHPQSGERLRFECPAP 210


>gi|281599417|gb|ADA72401.1| Ribosomal large subunit pseudouridine synthase A [Shigella flexneri
           2002017]
          Length = 238

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 79/247 (31%), Positives = 123/247 (49%), Gaps = 22/247 (8%)

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAY 127
           P  +  N  + E K+   + N  +       ++LY+D  I V NKP+G+ SV G   +  
Sbjct: 6   PAFDRCNASVTEPKMGMENYNPPQEPWL---VILYQDDHIMVVNKPSGLLSVPGR--LEE 60

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           H D  + + +     +    HRLD  TSG++VVA T+AA + L   FR R  +K Y + V
Sbjct: 61  HKDSVM-TRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARV 119

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKFCWLE 244
           WG P   +  +   L+       D+ +  KQ    E G   A + ++V++  A     + 
Sbjct: 120 WGHPSPAEGLVDLPLI------CDWPNRPKQKVCYETG-KPAQTEYEVVEYAADNTARVV 172

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++P TGR+HQLRVH L +G PI+GD  Y A+ +    +P   +L LHA  + + HP  G 
Sbjct: 173 LKPITGRSHQLRVHMLALGHPILGDRFY-ASPEARAMAP---RLLLHAEMLTITHPAYGN 228

Query: 304 RLQITAP 310
            +   AP
Sbjct: 229 SMTFKAP 235


>gi|257469932|ref|ZP_05634024.1| pseudouridine synthase, RluA family protein [Fusobacterium ulcerans
           ATCC 49185]
 gi|317064162|ref|ZP_07928647.1| RNA pseudouridylate synthase [Fusobacterium ulcerans ATCC 49185]
 gi|313689838|gb|EFS26673.1| RNA pseudouridylate synthase [Fusobacterium ulcerans ATCC 49185]
          Length = 294

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 70/224 (31%), Positives = 117/224 (52%), Gaps = 15/224 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           ++YED  + V  K +GI S+   +         LK ++ +K  K ++   HRLD++TSGI
Sbjct: 82  IIYEDDDVLVVEKESGILSIATDNEREKTAYNMLKEYLKNKDPKNKIFVVHRLDRDTSGI 141

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+T  A   L  ++     ++ Y +LV G+   +K+ I ++L +       ++    
Sbjct: 142 MIFAKTEKAQDILQTTWNDSVKERTYVALVEGVVYKEKDTIISYLQENKA----FITYSS 197

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           QN K    AISH+KV+    + +  LE+   TGR +Q+RVH   +G  +VGD KY     
Sbjct: 198 QNPKEGKKAISHYKVLKK-NKNYSLLEVNIETGRKNQIRVHMQDLGHSVVGDKKY----- 251

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           G+  SPI N+L LHA  +   HP   + L  ++ +PA   K ++
Sbjct: 252 GSGKSPI-NRLGLHANTIVFVHPITKKVLHFSSKIPAVFTKIFN 294


>gi|325127790|gb|EGC50698.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis N1568]
          Length = 374

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 138/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-THSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|331266599|ref|YP_004326229.1| 23S rluA family pseudouridine synthase [Streptococcus oralis Uo5]
 gi|326683271|emb|CBZ00889.1| 23S rluA family pseudouridine synthase [Streptococcus oralis Uo5]
          Length = 299

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 82/296 (27%), Positives = 143/296 (48%), Gaps = 47/296 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +++GQV V+ +  K    +Q G +V          + + E ++L+        ++ +   
Sbjct: 31  IKAGQVLVNGQAKKAKYTVQEGDIV---------TYHVPEPEVLEYV------AEDIPLE 75

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 76  IIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 132

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 133 KDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 186

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  LE+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 187 EKDRKKQAVTAKG-KPAVTRFQVLERFGD-YSLLELQLETGRTHQIRVHMAYIGHPVAGD 244

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHA+ +   HP  G  L+ TA +P    +T + L
Sbjct: 245 EVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGETLEFTADIPEIFKETLERL 293


>gi|322385620|ref|ZP_08059264.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           cristatus ATCC 51100]
 gi|321270358|gb|EFX53274.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           cristatus ATCC 51100]
          Length = 300

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 140/285 (49%), Gaps = 37/285 (12%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL----LYEDSKIYVF 111
           N +I++GQ++ +        + +KE  ++   V   +  +++   L    +Y+D  + V 
Sbjct: 30  NEQIKNGQIL-VNGEAKKAKYAVKEGDVISYEVPDPEVVEYVAEDLPLEIVYQDEDVAVV 88

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLDQETSGILVVAR 162
           NKP G+ V   +G   H  G L + +     D  G     +P + HR+D++TSG+L++A+
Sbjct: 89  NKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAK 145

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NE 220
              A   L +  + ++  + YW++V G   N +  I      ++ IG       KQ    
Sbjct: 146 NDQAHLALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRSEKDRKKQAVTA 199

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKG 278
           KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y      KG
Sbjct: 200 KG-KPALTRFQVLERFGD-YTLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPRKTLKG 257

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +         +LHAR +   HP  G  L+ TA  P+  ++T + L
Sbjct: 258 HGQ-------FLHARTLGFTHPRTGEVLEFTAEAPSIFLETLEKL 295


>gi|288924796|ref|ZP_06418733.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella buccae D17]
 gi|315607815|ref|ZP_07882808.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
 gi|288338583|gb|EFC76932.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella buccae D17]
 gi|315250284|gb|EFU30280.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
          Length = 223

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 69/221 (31%), Positives = 109/221 (49%), Gaps = 18/221 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           L+YED+ + +  K +G  VQG       +   +K ++  K QKP      + HRLD+  S
Sbjct: 3   LVYEDNHLIIVFKESGEIVQGDKTGDEPLSEAVKRYIKEKYQKPGNVFIGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV-- 213
           G++V A+T  A   L   FR   + K YW++V   P +++  + NW+++       Y   
Sbjct: 63  GLVVFAKTSKALSRLNMMFRNGDVHKTYWAIVKDAPMHEEGTLENWIVRNEQQNKSYAYD 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H V  ++K    A+  + VI   ++ +C LE+   TGR HQ+R    H+GCPI GD KY 
Sbjct: 123 HEVPNSKK----AVLKYHVI-SRSEHYCLLEVNLLTGRHHQIRCQLAHIGCPIKGDLKY- 176

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
               G   S     + L +R ++  HP     +   +PLPA
Sbjct: 177 ----GFPRSNPDGGISLLSRRVEFVHPVSKETISAVSPLPA 213


>gi|75674513|ref|YP_316934.1| pseudouridine synthase [Nitrobacter winogradskyi Nb-255]
 gi|74419383|gb|ABA03582.1| pseudouridine synthase [Nitrobacter winogradskyi Nb-255]
          Length = 264

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 114/237 (48%), Gaps = 22/237 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ +L+ D  + V +KPAGI+V  G     +++    +      + P L HRLD++TSG
Sbjct: 20  IQARVLHRDGLMLVIDKPAGIAVHRGPKGGANLEASFDALRFGLPRPPVLAHRLDRDTSG 79

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R R A   L   F+  +I K YW++V G P   +  I   L + +   G +    
Sbjct: 80  CLVLGRHRKATASLGLLFKHGKISKTYWAVVEGGPSEDEGAIDIPLGRLNEERGWW---- 135

Query: 217 KQNEKGANYAISHFKV----------IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           ++ +     + + +KV          +     +  WL ++P TGRTHQLRVH   MG PI
Sbjct: 136 QKPDPNGLPSTTKWKVLGRSSPDTSTVSGAGVQLTWLSLEPLTGRTHQLRVHCAAMGWPI 195

Query: 267 VGDHKYCANFKGNFTSPIQ-------NKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           VGD+ Y        +   Q         L+LHAR + +P       + +TAP PAH+
Sbjct: 196 VGDNIYGTQASLRRSRNEQYVPRLDEPGLHLHARQIAIPLSRNKPPVVVTAPAPAHL 252


>gi|323464710|gb|ADX76863.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus pseudintermedius ED99]
          Length = 305

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 84/305 (27%), Positives = 150/305 (49%), Gaps = 41/305 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+         +   LQ+ ++ G + V+ K VK N +++ G  + I            
Sbjct: 17  RIDKILPEFNSEWSRSQLQEWIKEGLIEVNGKAVKSNYKLKLGDRIEI-----------T 65

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYHID 130
           E++++++ +     ++ L   + YED  + +  KP G+ V            +G+ Y I 
Sbjct: 66  EKEVVEADI----QAENLNLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIK 121

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG- 189
               S ++S+  +P + HR+D++TSG+L+VA+   A + L E    + +++ Y +LV G 
Sbjct: 122 NL--SGINSE-IRPGIVHRIDKDTSGLLMVAKNDVAHRSLVEQLMAKTVKRKYIALVHGH 178

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           IP       A   + ++      + VV   ++    A++HF VI+ F + +  +E +  T
Sbjct: 179 IPHEFGTIDAP--IGRNKNDRQSMAVVDDGKE----AVTHFNVIETF-KNYTLVECELET 231

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+VGD KY        T  I  +  LHA  +   HP+ G  ++  
Sbjct: 232 GRTHQIRVHMKYIGYPLVGDPKYGP----KKTLEIGGQA-LHAGLIGFEHPKTGEYIERF 286

Query: 309 APLPA 313
           APLPA
Sbjct: 287 APLPA 291


>gi|332366655|gb|EGJ44398.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1059]
          Length = 298

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 118/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVINKPQGMVVHPSAG---HTSGTLVNALMYHIQDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKAKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTRFQVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA  PA   +T + L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEAPAIFQETLEKL 295


>gi|19745906|ref|NP_607042.1| hypothetical protein spyM18_0889 [Streptococcus pyogenes MGAS8232]
 gi|19748060|gb|AAL97541.1| conserved hypothetical protein [Streptococcus pyogenes MGAS8232]
          Length = 296

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 113/218 (51%), Gaps = 27/218 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP G+ V   +G         + YHI     S ++    +P + HR+D
Sbjct: 76  IIYEDDALAIINKPQGMVVHPSAGHPSETMVNALMYHIKDL--SSINGV-VRPGIVHRID 132

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+VA+T AA Q LTE  + ++  + Y ++V G   N +  I      ++ IG  
Sbjct: 133 KDTSGLLMVAKTDAAHQALTEELKAKKSLRKYLAIVHGNLPNDRGMI------EAPIGRS 186

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 187 EKDRKKQAVTAKGKE-AVTRFTVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 244

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
             Y     G   +   +  +LHA+ + L HP  G+  I
Sbjct: 245 PLY-----GPRKTLSGHGQFLHAKTLGLTHPMTGKEMI 277


>gi|326565266|gb|EGE15451.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis 12P80B1]
          Length = 355

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 80/316 (25%), Positives = 146/316 (46%), Gaps = 32/316 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD+   + +   +  NL+  +  GQ+ V+ K VK    ++ G ++ +  V 
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKNFIDEGQLMVNGKVVKPKYAVKVGDILTLEAVH 107

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            + +  + E   +D               ++YED  + + NKPAG+ V  G+G      +
Sbjct: 108 ESHSEDLPENIDID---------------IIYEDEAVIIINKPAGMVVHPGAGNRTGTLV 152

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +  L  +   +   PR  L HR+D++T+G+LV+ART++A   L +  + + + + Y  + 
Sbjct: 153 NALLYHF-PKQAHLPRAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIA 211

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQ 246
            G      E + +  +    IG    H  K   K     A++H        +++  L++ 
Sbjct: 212 LGA---VHEVLRHAQIDAP-IGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIH 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHP 300
             TGRTHQ+RVH  ++G P+VGD  Y  + +   +   +       +  LHA  +   HP
Sbjct: 268 LKTGRTHQIRVHLSYVGHPLVGDPVYGTSPRSGLSDRQRCAILDFGRQALHAYMLGFIHP 327

Query: 301 EGGR-LQITAPLPAHM 315
             G  ++  APLP  M
Sbjct: 328 VTGEAMKFHAPLPKDM 343


>gi|306829292|ref|ZP_07462482.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           mitis ATCC 6249]
 gi|304428378|gb|EFM31468.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           mitis ATCC 6249]
          Length = 299

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 83/296 (28%), Positives = 142/296 (47%), Gaps = 47/296 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           ++ GQV V+ +  K    +Q G +V          + + E ++L+        ++ L   
Sbjct: 31  IKVGQVLVNGQAKKAKYTVQEGDIV---------TYHVPEPEVLEYV------AEDLPLE 75

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 76  IIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 132

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 133 KDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 186

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  LE+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 187 EKDRKKQAVTAKG-KPAVTRFQVLERFGD-YSLLELQLETGRTHQIRVHMAYIGHPVAGD 244

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHA+ +   HP  G  L+ TA +P    +T + L
Sbjct: 245 EVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGETLEFTADIPEIFKETLERL 293


>gi|313668816|ref|YP_004049100.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           lactamica ST-640]
 gi|313006278|emb|CBN87741.1| putative ribosomal large subunit pseudouridine synthase D
           [Neisseria lactamica 020-06]
          Length = 374

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 87/308 (28%), Positives = 140/308 (45%), Gaps = 40/308 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA-LNHII 78
           RLD       P  +   L   +R G V V+ K  +  +++  G+ +R+    +A  +   
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKPSQPKDKMIGGEQIRVTVRPSAEYSAFA 99

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
            E   LD               ++YED  + V NKPAG+ V   +G      ++G L + 
Sbjct: 100 PEPMDLD---------------IVYEDDTVIVVNKPAGLVVHPAAGNWSGTLLNGLL-AH 143

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKN 193
                Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P +
Sbjct: 144 CPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFD 203

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGR
Sbjct: 204 GK--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGR 254

Query: 252 THQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           THQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HPE G  
Sbjct: 255 THQIRVHMREANHPLAGDPVYGNLRHPCGDTVKEAVKSLGARQALHAYRLSFVHPETGET 314

Query: 305 LQITAPLP 312
           +   AP+P
Sbjct: 315 VSFEAPIP 322


>gi|255692432|ref|ZP_05416107.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           finegoldii DSM 17565]
 gi|260621900|gb|EEX44771.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           finegoldii DSM 17565]
          Length = 357

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 87/333 (26%), Positives = 152/333 (45%), Gaps = 47/333 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEGGFVMANGKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +I+   + LT         ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYENEIIPEDIPLT---------IVYEDPYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +A+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 138 LVNALAWH----MKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKT 193

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFA 237
            ++ Y +LVWGI +  +  I   + +      D + + V  +     +A++H++V++   
Sbjct: 194 TKRKYRALVWGIVEQDEGTIIGNIARNPK---DRMQMAVMSDPTVGKHAVTHYRVLERLG 250

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN--------- 286
                +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +          
Sbjct: 251 Y-VTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTC 309

Query: 287 -KLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            +  LHA  +   HP  G  +  T+ LP  M +
Sbjct: 310 PRQALHAMTLGFVHPVTGEEMHFTSELPDDMTR 342


>gi|158320206|ref|YP_001512713.1| RluA family pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158140405|gb|ABW18717.1| pseudouridine synthase, RluA family [Alkaliphilus oremlandii
           OhILAs]
          Length = 305

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 87/317 (27%), Positives = 155/317 (48%), Gaps = 36/317 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVN--LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            END+    L +  KN    ++F +  L ++ R   + V+ + +K++  I +G  ++I  
Sbjct: 16  AENDDAGKELKKILKNK---LDFSSRLLARVKRGKTIFVNGEYLKYHETINAGDEIKIV- 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYH 128
           + +  NH   +    ++               +YED  + + NK  GI      S   + 
Sbjct: 72  MEDEPNHFTLQDVPFEA---------------VYEDVDLILVNKEPGIVTHPTKSHPDWT 116

Query: 129 IDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           I      ++ SKG   K R  +RLD +TSG+L++A+   A   L+E  +  RI+K Y + 
Sbjct: 117 IANGAALYLKSKGIDCKVRFVNRLDMDTSGLLIIAKNAYAHHVLSEQMQEDRIEKKYIAF 176

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           VWG+ K  +  I   + + +    D +  V  +E+G   +I+ FKV++ + +    +E++
Sbjct: 177 VWGVIKEDEGRIEAPIYRTTM---DSIKRV-VDERGQE-SITEFKVLERY-KNATMVEVK 230

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  H+G P++GD  Y     G   + + ++  LHA Y+    P   R +
Sbjct: 231 LLTGRTHQIRVHMEHLGHPLIGDTLY-----GKEDAELIDRQALHAEYLRFWQPRFKRAI 285

Query: 306 QITAPLPAHMVKTWDSL 322
           ++ A LPA ++   D L
Sbjct: 286 EVKADLPADLLSLRDKL 302


>gi|322376434|ref|ZP_08050927.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           M334]
 gi|321282241|gb|EFX59248.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           M334]
          Length = 296

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 82/295 (27%), Positives = 140/295 (47%), Gaps = 45/295 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           ++SGQV V+ +  K    +Q G VV          + + E ++L+        ++ L   
Sbjct: 31  IKSGQVLVNGQVKKAKYTVQEGDVV---------TYHVPEPEVLEYV------AENLPLE 75

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 76  IVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 132

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 133 KDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 186

Query: 212 YVHVVKQNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                KQ        A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD 
Sbjct: 187 EKDRKKQGVTAKGKPAVTRFHVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGDE 245

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            Y      KG+         +LHA+ +   HP  G  L+ TA +P    +T + L
Sbjct: 246 VYGPRKTLKGHGQ-------FLHAKTLGFTHPSTGETLEFTADIPELFKETLERL 293


>gi|306833765|ref|ZP_07466891.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           bovis ATCC 700338]
 gi|304424102|gb|EFM27242.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           bovis ATCC 700338]
          Length = 298

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 87/322 (27%), Positives = 149/322 (46%), Gaps = 50/322 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RLD+   +    ++       ++ G V V+ K VK    ++ G VV          
Sbjct: 7   EAGIRLDKALAD-LTELSRSQANDEIKKGTVLVNGKAVKAKYAVKVGDVV---------T 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           + + ++++L+ +      ++ +   ++YED+ + V NKP G+ V    G         + 
Sbjct: 57  YEVPKEEVLEYT------AENIPLDIIYEDADVAVVNKPQGMVVHPSVGHTSGTLVNALM 110

Query: 127 YHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           YHI    K      G  +P + HR+D++TSG+L++A+   A   L    + ++  + Y +
Sbjct: 111 YHI----KDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDTAHNALAAELKDKKSLRKYVA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWL 243
           +V G   N +  I      ++ IG       KQ    KG   A++HFKV++ F   +  +
Sbjct: 167 IVHGTIPNDRGVI------EAPIGRSEKDRKKQAVTAKG-KPALTHFKVLERFGN-YTLV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E+   TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP 
Sbjct: 219 ELTLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGNGQ-------FLHAQTLGFTHPT 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  L   A  PA   +T ++L
Sbjct: 272 TGETLTFMAEAPAIFKETLENL 293


>gi|300718035|ref|YP_003742838.1| ribosomal large subunit pseudouridine synthase D [Erwinia
           billingiae Eb661]
 gi|299063871|emb|CAX60991.1| Ribosomal large subunit pseudouridine synthase D [Erwinia
           billingiae Eb661]
          Length = 325

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 77/234 (32%), Positives = 119/234 (50%), Gaps = 31/234 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP G+ V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDEDILVINKPRGLVVHPGAG---NPDGTVLNALLHHFPAIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL ES ++R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVESLQLREITREYEAVAIGRMTAGGTVDEPISRHSTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH           A +H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VH------PTGKPATTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHINHPLVGDQL 252

Query: 272 YCAN---FKGNFTSPIQ-----NKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
           Y       KG   S I      ++  LHA  + L HP  G  ++  APLP  MV
Sbjct: 253 YGGRPRPPKGASESFIAMLRKFDRQALHATMLRLYHPISGIEMEWHAPLPQDMV 306


>gi|291086115|ref|ZP_06354861.2| pseudouridine synthase A [Citrobacter youngae ATCC 29220]
 gi|291069419|gb|EFE07528.1| pseudouridine synthase A [Citrobacter youngae ATCC 29220]
          Length = 219

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 72/208 (34%), Positives = 111/208 (53%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LDEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPAPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A 
Sbjct: 126 KVCYETG-KPAQTEYEVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAP 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    +P   +L LHA  + + HPE G
Sbjct: 184 PEALAMAP---RLLLHAEMLTITHPEYG 208


>gi|206900390|ref|YP_002251511.1| pseudouridylate synthase, 23S RNA-specific [Dictyoglomus
           thermophilum H-6-12]
 gi|206739493|gb|ACI18551.1| pseudouridylate synthase, 23S RNA-specific [Dictyoglomus
           thermophilum H-6-12]
          Length = 303

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 83/302 (27%), Positives = 151/302 (50%), Gaps = 44/302 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG---QVVR 66
           ++VE+  E  R+D++       ++   +Q ++  G ++V++K VK + +++ G   +V+ 
Sbjct: 8   ILVEDGGE--RIDKYLSQKI-SLSRSQIQDLIDKGLIKVNEKEVKSSYKVKVGDKIEVIV 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            PP         +E +I    + +          ++YED  I + NKP G+ V    G  
Sbjct: 65  PPP---------EETEIKPQDIPIE---------IVYEDDDIVIINKPKGMVVHPAHG-H 105

Query: 127 YH---IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           Y+   ++  L    D  G     +P + HRLD++T+G+L++A+   + Q L+E  + R +
Sbjct: 106 YNDTLVNALLYRIKDLSGIGGEIRPGIVHRLDKDTTGLLIIAKNDVSHQRLSEQLKNRIL 165

Query: 180 QKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++ YW++  G IP  +K   A   L +  I    + +V         AI++FKV++ F +
Sbjct: 166 KRTYWAICEGEIPWEEKRVEAP--LGRHPIDRKRMAIVPY----GKLAITNFKVLERF-K 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +     TGRTHQ+RVH  H+G PI+GD  Y       F   ++ +L LHA+ +   
Sbjct: 219 GYTLISADLETGRTHQIRVHISHLGFPILGDEVY-GRIDKRFG--VRGQL-LHAKKISFI 274

Query: 299 HP 300
           HP
Sbjct: 275 HP 276


>gi|281421451|ref|ZP_06252450.1| ribosomal large subunit pseudouridine synthase A [Prevotella copri
           DSM 18205]
 gi|281404523|gb|EFB35203.1| ribosomal large subunit pseudouridine synthase A [Prevotella copri
           DSM 18205]
          Length = 556

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 73/230 (31%), Positives = 117/230 (50%), Gaps = 30/230 (13%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK-SWVDSKGQKPRLTH 148
           T+ + + K   LYED ++ V  KP G+ SV G       +   ++  + ++ G  P + H
Sbjct: 331 TETTIYNKVETLYEDRELAVIYKPEGLLSVPGKDAAQPSVYALMRRKYQEATG--PLIVH 388

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++++A+T  A   L + F   R+QK Y ++V G  K+K+ C  N +LK++  
Sbjct: 389 RLDMATSGLMIIAKTEFAYHRLQKEFLNHRVQKKYVAIVCG--KDKESC--NRILKEAEG 444

Query: 209 G---------GDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           G          D++   +Q  N +    AI+ ++V++        L + P TGRTHQLRV
Sbjct: 445 GRGYISLPLIADFLDRPRQMVNREQGKEAITEYEVLERIDDTHLRLALYPKTGRTHQLRV 504

Query: 258 HALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           H  H   +  PI+GD  Y     GN  +    +L+LHA  +   HP  G+
Sbjct: 505 HCAHQEGLNAPIIGDPLY-----GNEPA---TRLHLHAEEITFEHPMTGK 546


>gi|254442724|ref|ZP_05056200.1| pseudouridine synthase, RluA family [Verrucomicrobiae bacterium
           DG1235]
 gi|198257032|gb|EDY81340.1| pseudouridine synthase, RluA family [Verrucomicrobiae bacterium
           DG1235]
          Length = 307

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 81/305 (26%), Positives = 142/305 (46%), Gaps = 31/305 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+     +P  +  + Q+   S  V +D   +    ++  G++V       A+  +  
Sbjct: 17  RIDKLLSEAFPDHSRSDFQRAFDSDLVTLDGAPIAKKQKVSEGEIVTF-----AMPTV-- 69

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHID 130
            QK+  S +++          +++ED  + V NKPAG+ V  G+G         + +H  
Sbjct: 70  -QKLDMSPIDMDLE-------VIFEDEHMVVVNKPAGLVVHPGAGPDEPTLAHGLLHHCQ 121

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G L        ++P + HRLD+ETSG+++ A+T  A + L+E F+ R + K Y +L  GI
Sbjct: 122 GQLSGI--GGVERPGIVHRLDRETSGLIMAAKTDVAHRALSELFQSRSLVKEYSALCCGI 179

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P+     +    +++       + V  +    A  A + + ++  +   +C L  + HTG
Sbjct: 180 PELMSGTVERP-IERHPTQRHKMRVGFEGRGRAREAKTDWTLVKAYDAGYCHLRCRIHTG 238

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGRLQIT 308
           RTHQ+RVH   +   I+GD  Y      N   P Q  ++ LH+ Y+   HP  G  L + 
Sbjct: 239 RTHQIRVHLKSIRHIILGDAVYGYRPLPNL--PKQPERVMLHSCYLKFDHPLTGSELVLE 296

Query: 309 APLPA 313
           A  PA
Sbjct: 297 AKPPA 301


>gi|330718578|ref|ZP_08313178.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc fallax KCTC
           3537]
          Length = 258

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 74/237 (31%), Positives = 122/237 (51%), Gaps = 22/237 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-------DSKGQ-KPRLTHRLDQ 152
           ++YED  + V NKP G+ V   +G   H  G L + +          G+ +P + HR+D+
Sbjct: 34  IVYEDDDLLVVNKPQGMVVHPSAG---HSSGTLVNALLHHAPLSTINGEFRPGIVHRIDR 90

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+L+VA+   A Q L+   +  + Q+IY++LV G  K     + N  + +  I    
Sbjct: 91  DTSGLLMVAKNDTAHQALSAQLKAHKNQRIYYALVRGEFKENSGTV-NAPIARHKIDRKK 149

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +V   +     A++HF+V+  +   +  L+++  TGRTHQ+RVH  ++G PIVGD  Y
Sbjct: 150 QAIVSDGKP----AVTHFEVVQRYV-GYTLLKVRLETGRTHQIRVHMTYIGHPIVGDPVY 204

Query: 273 CANFK-GNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
               K  N T  +  +L LHA+ + L  P     L   +PLP +  +  D+L   Y+
Sbjct: 205 GNAPKMPNVT--LHGQL-LHAKTLSLMQPTTQAELTFDSPLPVYFQQALDTLTPLYE 258


>gi|328946167|gb|EGG40312.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1087]
          Length = 298

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 119/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVINKPQGMVVHPSAG---HTSGTLVNALMYHIQDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTSFQVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA +PA   +T + L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEVPAIFQETLEKL 295


>gi|70608135|ref|NP_001020455.1| RNA pseudouridylate synthase domain-containing protein 4 [Rattus
           norvegicus]
 gi|81918145|sp|Q4QQT0|RUSD4_RAT RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 4
 gi|67678357|gb|AAH98023.1| RNA pseudouridylate synthase domain containing 4 [Rattus
           norvegicus]
 gi|149027812|gb|EDL83272.1| RNA pseudouridylate synthase domain containing 4 [Rattus
           norvegicus]
          Length = 377

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 61/192 (31%), Positives = 97/192 (50%), Gaps = 21/192 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           +L++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 99  ILHQDKDLVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R+++K YW++   +P      +   +++K   G    H  
Sbjct: 159 VMVLAWEKDMAHQVQELFRTRQVEKKYWAITVRVPLPSAGVVDIPIMEKEVAGQQQHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  +  + A+ A++ ++V+         +E+QP TG  HQLRVH A 
Sbjct: 219 TLRPSYRMDNGKMVKVRASRDAHVAVTQYQVLSSTPSS-ALVELQPVTGIKHQLRVHLAF 277

Query: 261 HMGCPIVGDHKY 272
            + CPI+GDHKY
Sbjct: 278 GLDCPILGDHKY 289


>gi|317486057|ref|ZP_07944910.1| RluA family pseudouridine synthase [Bilophila wadsworthia 3_1_6]
 gi|316922684|gb|EFV43917.1| RluA family pseudouridine synthase [Bilophila wadsworthia 3_1_6]
          Length = 532

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 88/318 (27%), Positives = 145/318 (45%), Gaps = 42/318 (13%)

Query: 19  MRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALN 75
           MRLDR+         ++   +++ +R G   VD       + ++ +GQ +          
Sbjct: 1   MRLDRFLGEALREQDVSREKVKRAIRDGGCLVDGAVCTDVSAKVGAGQSI---------- 50

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHID 130
               E ++     ++      L+  +LY+D+ + V NKPAG++V          + + + 
Sbjct: 51  ----ELRMEAEPTSVQPEEGELE--ILYQDAWLAVLNKPAGMTVHPAPSCPDGTLVHRLV 104

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
               S    +G +P + HRLD++TSG++ VA T  A   L+E+F  R I+K Y +LV G+
Sbjct: 105 ARFPSLRAQEGFRPGIVHRLDKDTSGLICVALTEEARMRLSEAFAAREIRKEYLALVQGV 164

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P       A   L +       V V K  ++    A S ++V+    Q +  LE++  TG
Sbjct: 165 PAPAGTVDAP--LGRHPTVKVKVAVAKNGKE----ARSEWRVLH-KGQGYSLLEVRIFTG 217

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---------YLHARYMDLPHP- 300
           RTHQ+RVH  H+G P+ GD  Y    +   T P+   L          LHA ++   HP 
Sbjct: 218 RTHQIRVHMAHIGHPLWGDKLYGRGGQ-VLTPPVPGVLLKHDPAPRQMLHAWHLSFIHPF 276

Query: 301 EGGRLQITAPLPAHMVKT 318
            G ++  T P P   V+T
Sbjct: 277 TGEKMAFTCPPPEDFVQT 294


>gi|42408521|dbj|BAD09700.1| putative ribosomal large subunit pseudouridine synthase C protein
           [Oryza sativa Japonica Group]
 gi|42409169|dbj|BAD10435.1| putative ribosomal large subunit pseudouridine synthase C protein
           [Oryza sativa Japonica Group]
          Length = 340

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 80/296 (27%), Positives = 131/296 (44%), Gaps = 70/296 (23%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQE 153
           ++L+ +++++DS I V NKP  + ++G   +   +D    + +    ++ P+L HRLD+E
Sbjct: 38  EYLRRLVIHKDSAILVLNKPPKVPMKGNLPVHNSMDVLAAAALSYGNEEGPKLVHRLDRE 97

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKI---------------YWSLVWGIPKNKKECI 198
           +SG+L+  RT+ +   L   F    + K                YW+LV G PK ++  I
Sbjct: 98  SSGLLLFGRTKESFTRLHWLFTSVNLAKTNSQVWNAACEAYMQRYWALVIGTPKEREGII 157

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           +  L K     G    V+  +  G   A  A++ ++V+        W+E++P TGR HQL
Sbjct: 158 SAPLSKVLLDDGKAERVILAHPSGIDGAQEAVTAYRVMGPTIHGCSWIELRPLTGRKHQL 217

Query: 256 RVH-ALHMGCPIVGDHKYC------------ANFKGNFTSPIQNK--------------- 287
           RVH A  +G PIVGD+KY              +F+     P + +               
Sbjct: 218 RVHCAEALGTPIVGDYKYGWFVHQRWKQNPQPDFEPFTGEPYKLRRPEGLEIQKGSVLSK 277

Query: 288 ---LYLHARYMDLP------------HPEGGR--------LQITAPLPAHMVKTWD 320
              L+LH R M +P            H  G          L+  AP+PAHM  +W+
Sbjct: 278 VPLLHLHCREMVIPNIAKFLSSNGEWHENGAPWSKEKPNLLRFIAPMPAHMKISWN 333


>gi|300722272|ref|YP_003711556.1| pseudouridine synthase [Xenorhabdus nematophila ATCC 19061]
 gi|297628773|emb|CBJ89351.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Xenorhabdus nematophila ATCC 19061]
          Length = 325

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 91/327 (27%), Positives = 158/327 (48%), Gaps = 47/327 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
            +V   +   RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + I 
Sbjct: 9   AIVAGSQLGQRLDQALAELFPDYSRSRIKEWILDNKVQVNGKLINKPKEKMLGGEDISID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            +I       ++ +     + L          ++YED  I V NKP  + V  G+G   +
Sbjct: 69  AIIE------EDARWEPQDIELN---------VVYEDDDILVINKPRDLVVHPGAG---N 110

Query: 129 IDGFLKSWVDSKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG + + +  +  K    PR  + HRLD++T+G++VVA+T  A   L ES ++R I + 
Sbjct: 111 PDGTVLNALLYRYPKIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITRE 170

Query: 183 YWSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G        +E I+    K++H+    VH +         AI+H++V++ F + 
Sbjct: 171 YEAIALGCMTAGGMVEEPISRHPTKRTHMA---VHPM------GKPAITHYRVLEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKG---NFTSPIQN--KLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y       KG    F   ++N  +  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMAHIKHPLVGDQLYGGRPRPLKGASDEFREVMRNFDRQALH 280

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVK 317
           A  + L HP  G  ++  APLP  MV+
Sbjct: 281 ATMLRLYHPITGIEMEWHAPLPDDMVR 307


>gi|254510505|ref|ZP_05122572.1| ribosomal large subunit pseudouridine synthase A [Rhodobacteraceae
           bacterium KLH11]
 gi|221534216|gb|EEE37204.1| ribosomal large subunit pseudouridine synthase A [Rhodobacteraceae
           bacterium KLH11]
          Length = 215

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 69/206 (33%), Positives = 111/206 (53%), Gaps = 18/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED+++ V NKPAG+    G G   H+   L + V +   +  L HRLD++TSG++V 
Sbjct: 14  VLFEDTQLIVVNKPAGLLSVPGRG--EHLADCLLTRVQAAFPQALLVHRLDRDTSGVMVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A+T  A +HL   F  R+ +K Y + VWG  + K   +   L+       D+ +  +Q  
Sbjct: 72  AQTPHAQRHLGLQFENRQTRKTYIARVWGRVEAKTGTVDLPLIV------DWPNRPRQMV 125

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +E G + AI+ ++V+  +  +   + + P TGR+HQLRVH   +G PI+GD  Y     
Sbjct: 126 CHETGKS-AITDWRVVK-YEGETTRIRLFPKTGRSHQLRVHMQALGSPILGDPFYAEGPA 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
             F      +L LH+  + L +PEGG
Sbjct: 184 RAFP-----RLMLHSEELRLKNPEGG 204


>gi|312875913|ref|ZP_07735903.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311797394|gb|EFR13733.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 293

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 76/259 (29%), Positives = 132/259 (50%), Gaps = 24/259 (9%)

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-----LLYEDSKIYVFNKPAG 116
           GQ+  IPP I +++   +E  +++  V+L      +  +     +LYED+     NKP+G
Sbjct: 38  GQIRFIPP-IYSVHQYPQENAVIE--VDLISSKSNIAPVEGNIDILYEDNFFLFVNKPSG 94

Query: 117 ISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +      G  +  I  +++ +++SK     + +RLD++TSGI+V A+       ++  F 
Sbjct: 95  LPSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRLDKDTSGIVVFAKNSYFHSIVSHEFE 154

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R+++K Y ++V G    KK  +    +K+S  G     + ++  +  ++A ++++VID 
Sbjct: 155 KRQVEKTYIAIVHG-RLTKKSGLIEKPIKRSDDG-----IKREIHQDGSFASTYYEVIDS 208

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F + F  L+++P TGRTHQLRVH   +G PIVGD  Y      N        L LHA  +
Sbjct: 209 F-ENFSLLKLKPITGRTHQLRVHLSSIGYPIVGDCIYGKERTQN------TPLLLHAYSI 261

Query: 296 DLPHP--EGGRLQITAPLP 312
                  +     IT+PLP
Sbjct: 262 RFTFKLIDNKVYYITSPLP 280


>gi|311067404|ref|YP_003972327.1| putative RNA pseudouridine synthase [Bacillus atrophaeus 1942]
 gi|310867921|gb|ADP31396.1| putative RNA pseudouridine synthase [Bacillus atrophaeus 1942]
          Length = 303

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 113/229 (49%), Gaps = 30/229 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +L+EDS + + NKPAG+      +G +G     IAYH+        + +  K R  HRLD
Sbjct: 85  ILFEDSHMLIVNKPAGMPTHPNEEGQTGTLANLIAYHLQ------ANGEQTKVRHVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG +V A+ R A   L +    + +++ Y +L  G  K KK  I       S IG D
Sbjct: 139 LDTSGAVVFAKHRLAHAILDQQLEKKELKRTYIALAEGKLKPKKGTI------DSPIGRD 192

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGD 269
             H  ++    G   A++HF+V     +    L E++  TGRTHQ+RVH   +G P+ GD
Sbjct: 193 RSHPTRRRVSPGGQAAVTHFRVKGYHPKAGLSLAELELETGRTHQIRVHMASIGHPLTGD 252

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHMVK 317
             Y        ++ I ++  LHA+ +   HP  G   I  APLPA + +
Sbjct: 253 ELYGG------STFILDRQALHAKKVQAVHPITGEFIIAEAPLPADLAE 295


>gi|262282338|ref|ZP_06060106.1| pseudouridine synthase [Streptococcus sp. 2_1_36FAA]
 gi|262261629|gb|EEY80327.1| pseudouridine synthase [Streptococcus sp. 2_1_36FAA]
          Length = 296

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 119/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 76  IVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 132

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 133 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 186

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG + A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 187 EKDRKKQAVTAKGKS-ALTRFQVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 244

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA +PA   +T   L
Sbjct: 245 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEVPAIFQETLKKL 293


>gi|110803816|ref|YP_699133.1| pseudouridine synthase [Clostridium perfringens SM101]
 gi|110684317|gb|ABG87687.1| pseudouridine synthase, RluA family [Clostridium perfringens SM101]
          Length = 306

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 119/236 (50%), Gaps = 28/236 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + V NKP G+ V    G         + YH D    S ++    +P + HR+D
Sbjct: 84  IIYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLYHCDDL--SGINGV-IRPGIVHRID 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSGILVVA+   A Q L E F+   I++ Y+++V G  K +   I +  L + H    
Sbjct: 141 KDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTI-DAPLGRHHRDRL 199

Query: 212 YVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              VVK  ++    A++H++V+  F   +   C LE    TGRTHQ+RVH   +G P++G
Sbjct: 200 KYAVVKDGKR----AVTHYEVLKVFNSCSLVKCTLE----TGRTHQIRVHMAFIGHPLLG 251

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           D  Y    +   +   Q    LHA+ +   HP  G+ ++  + LP +  K  + LG
Sbjct: 252 DTVYGLKKQKKLS---QEGQVLHAKTLGFIHPTTGKYVEFDSELPEYFEKIVEKLG 304


>gi|299470964|emb|CBN79948.1| Pseudouridine synthase, RluD [Ectocarpus siliculosus]
          Length = 489

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 97/371 (26%), Positives = 146/371 (39%), Gaps = 75/371 (20%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + + VE  E   RLD +     P  +      + + G V V  K  K + +++ GQ V 
Sbjct: 103 TEMLTVEEGEGGKRLDSFLGARMPEQSRSYFGGLCQLGMVLVGGKTAKKSVKVEEGQEVE 162

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +  +I+    +  E   LD               +LYED +I   +KPAG+ V    G  
Sbjct: 163 VRFIISPELSLQGEDIPLD---------------ILYEDDEIIAVSKPAGMVVHPAPGSW 207

Query: 125 -------IAYHIDGFLKSWVDSKGQ-------------------KPRLTHRLDQETSGIL 158
                  + +H++   KS  D  G                    +P + HRLD+ T+G+L
Sbjct: 208 NGTFVNALVFHLE---KSGADGNGLGVAEAAFQSVPDGEHNPSLRPGIVHRLDKGTTGVL 264

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK- 217
           + A+       L E F  RRI K Y ++  G P  K   I   + +        V V   
Sbjct: 265 LAAKNPTMQAKLAELFAQRRISKSYLAVCVGNP-GKAATIDVPIGRHPRDRQRMVAVPTI 323

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF- 276
           Q    +  A+S    +  F  K    E+   TGRTHQ+RVH  H   P++GD  Y  N  
Sbjct: 324 QPNIRSRRALSVVTTV-AFDGKLSVAEVSIETGRTHQIRVHLQHRRTPVLGDEVYGNNDW 382

Query: 277 ------KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
                     T P+     LHAR ++  HP  G  + + APLP+             D  
Sbjct: 383 NRRLRQSTGLTRPL-----LHARSLEFKHPNTGEVVSLAAPLPS-------------DVE 424

Query: 330 LYIKRLYSQDE 340
             ++R+Y Q E
Sbjct: 425 AVVRRIYPQVE 435


>gi|239631456|ref|ZP_04674487.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           paracasei subsp. paracasei 8700:2]
 gi|239525921|gb|EEQ64922.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           paracasei subsp. paracasei 8700:2]
          Length = 306

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 91/326 (27%), Positives = 152/326 (46%), Gaps = 42/326 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  R+D+    H        +QK L+ G V V+ +  K N ++ SG V+ I         
Sbjct: 10  EQGRIDKVITAHETTHTRSQVQKWLQDGLVTVNGQPTKANYKVASGDVIAIS-------- 61

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            I E K L++        + +   ++YED ++ V +KP G+ V    G   H DG L + 
Sbjct: 62  -IPEAKPLEAI------PEPIPLDIVYEDDQVIVVDKPQGMVVHPAPG---HPDGTLVNG 111

Query: 137 V----DSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +    D  G     +P + HR+D++TSG+L+VA+T  A   L+   + +   + Y +LV 
Sbjct: 112 LLYHTDLPGINGVIRPGIVHRIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVH 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQP 247
           G  K  +  I       + +G D     +Q       +A++HF+V++ F + + +++   
Sbjct: 172 GTFKEDEGTI------DAPLGRDPRDRKRQAVVADGRHAVTHFQVLERF-EHYTFIKCIL 224

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH  ++  P+ GD  Y        T P + + +LHA  +   HP   +L +
Sbjct: 225 ETGRTHQIRVHMAYIHHPVAGDPLYGP----KRTLPGEGQ-FLHAAKLGFVHPTTSQLLV 279

Query: 308 -TAPLPAHMVKTWDSL--GFKYDRNL 330
              P+P    KT   L  G    RN+
Sbjct: 280 FETPVPPIFEKTLADLRAGIDKTRNV 305


>gi|197303943|ref|ZP_03168975.1| hypothetical protein RUMLAC_02680 [Ruminococcus lactaris ATCC
           29176]
 gi|197296911|gb|EDY31479.1| hypothetical protein RUMLAC_02680 [Ruminococcus lactaris ATCC
           29176]
          Length = 230

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 106/219 (48%), Gaps = 15/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +L+ED +I V +KP+G+  Q        +   LK+ +  + + P   L HRLDQ   G++
Sbjct: 9   ILFEDQEILVCHKPSGVPAQTNRIGTPDLVSILKNHLRKESRSPYLALIHRLDQPVEGLM 68

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+T  +A+ L+         K Y ++  G+P   +  + ++L+K +    +  H+  +
Sbjct: 69  VFAKTPRSAKELSRQLTTSGFGKYYLAVAEGVPSEAEADLTDYLVKDAR--SNTSHICSK 126

Query: 219 NEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +   A  A  H+KV+             L++   TGR HQ+RV   HMG P++GD KY  
Sbjct: 127 DTPQAKIAKLHYKVLAAGTTADGSSCSLLKIHLDTGRHHQIRVQMAHMGHPLIGDRKY-- 184

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
               N T     KL L A  +   HP  G +++ T P+P
Sbjct: 185 ----NLTGTSSPKLLLCAFRLSFRHPVTGKKMEFTLPVP 219


>gi|288573309|ref|ZP_06391666.1| pseudouridine synthase, RluA family [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288569050|gb|EFC90607.1| pseudouridine synthase, RluA family [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 305

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 82/328 (25%), Positives = 144/328 (43%), Gaps = 41/328 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV   ++  RLD+  +  +P +    + K  R  QVR+D  R  F+ R+  GQ + +P  
Sbjct: 5   VVSRHDDGRRLDKVIRKKWPSLPLGAMMKAFRKKQVRIDGARASFDQRLVEGQEILVP-- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ----GGSGIA 126
                      +   + V   +    L  + +Y D  ++V +KPAG+  Q    GG  + 
Sbjct: 63  ----------WESAPTDVGAKRTGGHL--VTVYRDESLWVVSKPAGLLSQPDKKGGDSVV 110

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                  ++++     +P+  +RLD+ TSGI+V+A T  + + L+  +R   ++K+Y +L
Sbjct: 111 T------RAFLPGSSFQPQAVNRLDRNTSGIMVLALTGESLRDLSSRWRDGEMEKVYLAL 164

Query: 187 VWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G +P  ++  I   L K       +V     + KG +    + ++        C + +
Sbjct: 165 VVGDLP--EEGSIDAPLSKDGSSNKVFV-----DSKGQSSLTLYRRLASGGGLSLCLVTL 217

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              TGR+HQ+RVH  H+G P++GD KY              +  LHA  +  P   G   
Sbjct: 218 I--TGRSHQIRVHMSHIGHPVLGDVKYGDRALNGVKG--AKRPMLHAFSVSFPDMSGDLS 273

Query: 306 QITA-----PLPAHMVKTWDSLGFKYDR 328
            +++     P+P  M       G   DR
Sbjct: 274 SLSSKTFRTPMPEDMADMCSKNGIVPDR 301


>gi|257462593|ref|ZP_05627003.1| tRNA pseudouridine synthase A [Fusobacterium sp. D12]
 gi|317060244|ref|ZP_07924729.1| ribosomal large subunit pseudouridine synthase C [Fusobacterium sp.
           D12]
 gi|313685920|gb|EFS22755.1| ribosomal large subunit pseudouridine synthase C [Fusobacterium sp.
           D12]
          Length = 290

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 79/281 (28%), Positives = 137/281 (48%), Gaps = 22/281 (7%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE     +R+DR+ +  +P ++  ++ K LR+G+++V+ KRVK N R  S   ++     
Sbjct: 6   VEEKYIGVRVDRYLRKEFPDLSLGDIFKALRTGKIKVNGKRVKENYRFVSEDWIQ----- 60

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
             L   I+EQK  +     ++    L+  + Y+D  I V+ K AG  +  GS   Y +  
Sbjct: 61  --LYLEIEEQKKREFLTLSSEERAELEEGIFYQDQDILVYYKKAGELMHKGSSHDYGLAE 118

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             +++  +  +     +RLD+ETSG+++  +     + L E+ + R I K Y+ +V G P
Sbjct: 119 QFQAYFQN--EDFHFVNRLDKETSGLVLGGKCLKIVRELAEAIKKRTIVKKYYIIVEGNP 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 + ++L K    G   V   +  ++      + F+V+    +++  LE    TGR
Sbjct: 177 PKNHFSLRSYLKK----GESRVLESQCAKEDYRECSASFQVLKR-KKEYSLLEANLETGR 231

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           THQLRV    MG PI+GD KY     G        ++YLH+
Sbjct: 232 THQLRVQLAGMGFPILGDGKYGKKKAG--------RMYLHS 264


>gi|160945091|ref|ZP_02092317.1| hypothetical protein FAEPRAM212_02610 [Faecalibacterium prausnitzii
           M21/2]
 gi|158442822|gb|EDP19827.1| hypothetical protein FAEPRAM212_02610 [Faecalibacterium prausnitzii
           M21/2]
          Length = 310

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 83/313 (26%), Positives = 145/313 (46%), Gaps = 35/313 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +VE +    R+DR+       ++   LQ ++  G V+ + K V  + ++++G  V +   
Sbjct: 7   IVEQETAGQRIDRFLSGEDTGLSRSALQALVAEGHVQCNGKAVAKSLKLKAGDTVLL--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                      +I D+        D    I+ YED+ + V NKP G+ V    G      
Sbjct: 64  -----------EIPDAKPIEAVPQDIPLEIV-YEDAHLLVVNKPKGMVVHPAPGNPDGTL 111

Query: 125 ---IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + +H  G L       G+ +P + HR+D++TSG+LVVA+  A    L++   +  ++
Sbjct: 112 VNALLWHCKGSLSGI---GGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVE 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V+G    + E      L +S I    + V    E    YA + +KV++   + F
Sbjct: 169 RAYQTVVYG-GFAQDEGFVEANLGRSKIDRKKMAVYPATEPHTKYAYTGYKVLERLGE-F 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE +  TGRTHQ+RVH   +  P+ GD  Y  +   N  + +  +  LHA+ +   HP
Sbjct: 227 TLLECRLKTGRTHQIRVHMASIHHPVAGDPVYGPH---NCITSLHGQC-LHAKTLGFVHP 282

Query: 301 -EGGRLQITAPLP 312
             G +L+  + LP
Sbjct: 283 ITGEQLRFDSELP 295


>gi|282890613|ref|ZP_06299136.1| hypothetical protein pah_c022o218 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281499610|gb|EFB41906.1| hypothetical protein pah_c022o218 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 295

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 69/223 (30%), Positives = 110/223 (49%), Gaps = 15/223 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED+ + V++KPAGI+    SGI           +  K    +L HRLD++T+GIL+ 
Sbjct: 84  IIYEDADLLVYDKPAGINCDT-SGIV--------RLIHQKDPSLKLVHRLDRDTTGILLF 134

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T A    +   F+  +++K Y+ +V G    +K  I N L       G  V       
Sbjct: 135 AKTDAVLHKMIRLFKTFKVKKTYYVIVDGAISKEKGVIDNNLAPLHKYQGQTVWGQATGS 194

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG +      K  +   Q    ++  P TG THQ+RVH   MG PI+GD++Y   F  ++
Sbjct: 195 KGVHARTGWRK--EKKGQDCTLIQCYPVTGITHQIRVHMSEMGHPILGDYQYGRRFICSY 252

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                ++  LHA  +  PHP   + +++ APLP+   +  D L
Sbjct: 253 QP---SRYLLHAYEITFPHPSSEKEIRLKAPLPSDFKQALDHL 292


>gi|71065814|ref|YP_264541.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter
           arcticus 273-4]
 gi|71038799|gb|AAZ19107.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter
           arcticus 273-4]
          Length = 400

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 86/335 (25%), Positives = 143/335 (42%), Gaps = 42/335 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V  +E  +R+D+     +   + V LQ  +  G +  +    K   R+++G V+ +  +
Sbjct: 88  TVTEEEAGLRIDKLASKIFIDFSRVQLQGWVSDGSLLYNGSVQKPKIRVKAGDVLHLSTI 147

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           +        EQ   D   ++          ++YED ++ V NKP G+ V  G+G      
Sbjct: 148 L--------EQHSADQPEDIAID-------VVYEDDEVLVINKPVGMVVHPGAGNQAGTL 192

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           ++  L  +       PR  L HR+D++TSG+L++ +T+ A   L E  + + + + Y  +
Sbjct: 193 VNALLYHYPQHH-HLPRAGLVHRIDKDTSGLLLIGKTKPAQLALMEQLKDKSVYRHYQCV 251

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFC 241
           V G         A  LL+   I         Q  K         A++H   +      +C
Sbjct: 252 VAGD--------AASLLRHRRIDAPIGRHRNQRTKMTVMTAGREAVTHLLNVTALNGNYC 303

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTS----PIQN--KLYLHAR 293
            L++   TGRTHQ+RVH  H+  PIVGD  Y      +   T      I N  +  LHA 
Sbjct: 304 LLDVGLETGRTHQIRVHLSHITYPIVGDRVYGGRRQLRAGLTEAQRQAINNFPRQALHAY 363

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +   HP  G  +++T P+P  M +    L   YD
Sbjct: 364 ILGFVHPTTGEDIEVTTPMPEDMQQLMAVLSDGYD 398


>gi|312793590|ref|YP_004026513.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312180730|gb|ADQ40900.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 293

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 75/258 (29%), Positives = 129/258 (50%), Gaps = 22/258 (8%)

Query: 62  GQVVRIPPVINALNH----IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           GQ+  IPP+ +   +     + E  ++ S  N+      +   +LYED+     NKP+G+
Sbjct: 38  GQIRFIPPIYSVHQYPQENAVIEVDLISSKSNIAPVEGNID--ILYEDNFFLFVNKPSGL 95

Query: 118 SVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                 G  +  I  +++ +++SK     + +RLD++TSGI+V A+       ++  F  
Sbjct: 96  PSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRLDKDTSGIVVFAKNSYFHSIVSHEFEK 155

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R+++K Y ++V G    KK  +    +K+S  G     + ++  +  ++A ++++VID F
Sbjct: 156 RQVEKTYIAIVHG-RLAKKSGLIEKPIKRSDDG-----IKREIHQDGSFASTYYEVIDSF 209

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F  L+++P TGRTHQLRVH   +G PIVGD  Y      N        L LHA  + 
Sbjct: 210 -ENFSLLKLKPITGRTHQLRVHLSSIGYPIVGDCIYGKERTQN------TPLLLHAYSIR 262

Query: 297 LPHP--EGGRLQITAPLP 312
                 +     IT+PLP
Sbjct: 263 FTFKLIDNKVYDITSPLP 280


>gi|304387998|ref|ZP_07370170.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis ATCC 13091]
 gi|304337997|gb|EFM04135.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis ATCC 13091]
          Length = 374

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 138/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-THSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|260583810|ref|ZP_05851558.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           elegans ATCC 700633]
 gi|260158436|gb|EEW93504.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           elegans ATCC 700633]
          Length = 301

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 90/307 (29%), Positives = 143/307 (46%), Gaps = 39/307 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E++ RLD+       H   V +Q+ L+SG V V+ + VK N + + G  V I        
Sbjct: 13  EKSERLDKILTKELSHTRSV-IQQWLKSGFVSVNGEVVKANYKAKDGDHVTIQ------- 64

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
             I+E++       LT  ++ +   +++ED  + V NKP+G+ V    G         + 
Sbjct: 65  --IEEEE------ELTVLAENIPLEIVFEDEHLLVINKPSGMVVHPSKGHSTGTLVNALL 116

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH+D   K    S+  +P + HR+D++TSG+LVVA+T  A   L+       + + Y ++
Sbjct: 117 YHVDQLSKG---SESYRPGIVHRIDKDTSGLLVVAKTPQAHVGLSNQLMDHSMTRSYVAI 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++    +   L +  H       + +  +K    AI+HF VI    +    L + 
Sbjct: 174 VEGSFEHITGTVDAPLARDPH-----NRLKRCVQKEGKQAITHFTVIQALKET-SVLRLN 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
             TGRTHQ+R H   +  PI+ D  Y  N K N T   Q   YLHA  +   HP    +L
Sbjct: 228 LETGRTHQIRAHMDFIHHPILNDPMYHPNGK-NATEFGQ---YLHAETLGFVHPITQEKL 283

Query: 306 QITAPLP 312
              +PLP
Sbjct: 284 YFESPLP 290


>gi|324993007|gb|EGC24927.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK405]
 gi|327462303|gb|EGF08630.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1]
          Length = 298

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 119/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G         + YHI+    S ++    +P + HR+D
Sbjct: 78  IVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHINDL--SGINGV-LRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTRFQVLERFGD-YTLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA  PA   +T + L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEAPAIFQETLEKL 295


>gi|241896496|ref|ZP_04783792.1| pseudouridylate synthase [Weissella paramesenteroides ATCC 33313]
 gi|241870218|gb|EER73969.1| pseudouridylate synthase [Weissella paramesenteroides ATCC 33313]
          Length = 304

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 85/319 (26%), Positives = 145/319 (45%), Gaps = 41/319 (12%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            D+E  RLD+     +       + K +  G + V+ +  K   ++ +G V+        
Sbjct: 9   TDQEG-RLDKVVAEAFTDYTRTQMSKWIDDGILTVNGETKKAKYKVHAGDVISF------ 61

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              ++ E  +LD         + L   ++YED  + V NKP G+ V   +G   H +G L
Sbjct: 62  ---VVPEPVVLDIK------PENLPLDIVYEDDDLLVVNKPQGMVVHPAAG---HPNGTL 109

Query: 134 KSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + +    +        +P + HR+D++TSG+L+VA+   A + L+   + ++  + Y++
Sbjct: 110 VNALMYHTELSSINGVIRPGIVHRIDKDTSGLLMVAKNDQAHEALSADLKDKKNLRQYYA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLE 244
           LV G     K  I      K+ +G       KQ    G   A++HF+V+  +   +  L 
Sbjct: 170 LVHGEFSENKGTI------KAPLGRSKTDRKKQAVIAGGRDAVTHFEVVKRYV-GYTLLR 222

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA  + L  P   +
Sbjct: 223 VTLETGRTHQIRVHMAYIGHPVAGDPLY-----GPKKTLAGNGQFLHAATLGLTQPTTKK 277

Query: 305 -LQITAPLPAHMVKTWDSL 322
            L   APLP + V+T   L
Sbjct: 278 ELTFEAPLPQYFVETLAQL 296


>gi|152979640|ref|YP_001345269.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150841363|gb|ABR75334.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 219

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 66/205 (32%), Positives = 106/205 (51%), Gaps = 14/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D+ I V NKP+G+    G+   Y+      S V  K       HRLD  TSGI++ 
Sbjct: 16  IIHHDNHILVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPAHRLDMATSGIILF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A ++ A   L   FR R+ +K Y ++VWG PK     +   L+       D+ +  +Q  
Sbjct: 74  AMSKLADSELKRQFRERQTEKFYQAVVWGHPKQDSGTVNLPLI------CDWENRPRQRI 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      A++ F+V++        L++ P TGR+HQLR+H L +G PI+GD K+ A+ + 
Sbjct: 128 DFNAGKSAVTKFEVLERLPNNSTRLKLTPITGRSHQLRLHMLALGHPILGD-KFYAHPQA 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
              +P   +LYLHA  + + HP  G
Sbjct: 187 KAMAP---RLYLHAESLTITHPVTG 208


>gi|146312715|ref|YP_001177789.1| 23S rRNA pseudouridine synthase D [Enterobacter sp. 638]
 gi|145319591|gb|ABP61738.1| ribosomal large subunit pseudouridine synthase D [Enterobacter sp.
           638]
          Length = 326

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 92/338 (27%), Positives = 164/338 (48%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPP 69
            V  ++   RLD+     +P  +   +++ +   +V V+ K       ++  G+VV    
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVMVNGKVWDTPKEKVLGGEVV---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            INA   I +E +     + LT         ++YED  I V NKP G+ V  G+G   + 
Sbjct: 66  AINA--EIDEEVRFEAQDIPLT---------IVYEDDDILVINKPRGLVVHPGAG---NP 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y
Sbjct: 112 DGTVLNALLHYYPPITDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREY 171

Query: 184 WSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G   +    +E I+    K++H+    VH + +       A++H+++++ F +  
Sbjct: 172 EAVAIGHMTSGGTVEEPISRHPTKRTHMS---VHPMGKP------AVTHYRIMEHF-RIH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHA 292
             L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA
Sbjct: 222 TRLRLRLETGRTHQIRVHMSHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHA 281

Query: 293 RYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
             + L HP  G  ++  AP+P  MV+  +++   ++ +
Sbjct: 282 TMLRLYHPITGIEMEWHAPIPQDMVELIEAMRADFEEH 319


>gi|333010548|gb|EGK29981.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           VA-6]
          Length = 219

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 113/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A       ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETG-KPAQTEYEVVEYAADNTARAVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|300361720|ref|ZP_07057897.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri JV-V03]
 gi|300354339|gb|EFJ70210.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri JV-V03]
          Length = 304

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 92/331 (27%), Positives = 160/331 (48%), Gaps = 45/331 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    +V+E  +E  RLD+        ++   +++++    + V+ K  K + ++Q+G 
Sbjct: 1   MTENYQLVIE--KEKGRLDKVIAEKIKDLSRTKIKELVNDKNILVNNKAEKVSYKVQAGD 58

Query: 64  VVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           ++ I  PP         K   +   ++NL          ++YED+ + V NKP G+ V  
Sbjct: 59  LIDITVPPA--------KPLSLEAQNLNLD---------IVYEDADVIVVNKPQGMVVHP 101

Query: 122 GSGIAYH--IDGFL---KSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +G   H  ++G L       DS +G +P + HR+D++TSG+L+VA+   A + L +   
Sbjct: 102 SAGHPDHTLVNGLLYHTHKLADSPEGFRPGIVHRIDKDTSGLLMVAKNDKARESLEKQLA 161

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKV 232
            +  ++ Y ++V G  + K   I   +       G   +  KQ   N KG   A++HF V
Sbjct: 162 EKINKREYLAIVHGNFETKNGVIDAPI-------GRNPNNRKQMAVNPKG-KAAVTHFTV 213

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++ F + +  ++    TGRTHQ+RVH  ++G P+ GD  Y    K   T   Q   +LHA
Sbjct: 214 LEQF-KDYSLVKCVLETGRTHQIRVHMKYIGHPLAGDPLYGP--KKTLTGHGQ---FLHA 267

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +    P   + L+ +APLPA   K  ++L
Sbjct: 268 ETLGFYQPSTHKWLEFSAPLPAIFEKQLENL 298


>gi|219871128|ref|YP_002475503.1| 23S rRNA pseudouridine synthase D [Haemophilus parasuis SH0165]
 gi|219691332|gb|ACL32555.1| 23S rRNA pseudouridine synthase D [Haemophilus parasuis SH0165]
          Length = 325

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 74/244 (30%), Positives = 125/244 (51%), Gaps = 31/244 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +        + PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPKDLVVHPGAG---NPDGTVLNALLHHYPQIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL  + + R I + Y ++  GI        E +A    K++ +   
Sbjct: 143 TGLMVVAKTVPAQTHLVTALQRREITREYEAVASGIMTQGGKVDEPMARHPTKRTAMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 201 -VHPMGKP------AVTHYRIMERF-RNYSRLRLRLETGRTHQIRVHMAHIAHPLLGDQL 252

Query: 272 YCANFK------GNFTSPIQN--KLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           Y    +      G F   ++N  +  LHA  + L HP  G L +  APLP   V+  ++L
Sbjct: 253 YGGRPRPPKGASGEFLEVLRNFKRQALHATMLRLHHPITGELMEWHAPLPDDFVELIEAL 312

Query: 323 GFKY 326
              Y
Sbjct: 313 KADY 316


>gi|307824793|ref|ZP_07655016.1| pseudouridine synthase, RluA family [Methylobacter tundripaludum
           SV96]
 gi|307734151|gb|EFO05005.1| pseudouridine synthase, RluA family [Methylobacter tundripaludum
           SV96]
          Length = 314

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 85/324 (26%), Positives = 159/324 (49%), Gaps = 46/324 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLD+     +   +   LQ  ++SG+V+V+   +K  +++  G+ +       AL+  
Sbjct: 14  GMRLDQVLAELFADYSRSKLQSWVKSGRVQVNGLTLKPRDKLVGGETI-------ALD-- 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                  ++ + +T   + +   +++ED  + + NKPAG+ V    G   + +G L + +
Sbjct: 65  ------AEAEIVITAEPEPIPLEIIFEDESLLIVNKPAGLVVHPAIG---NWNGTLLNAL 115

Query: 138 ---DSKGQK-PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
              DS  +  PR  + HR+D+ETSG+L+VA+T  A   LT+  + R I + Y ++  G  
Sbjct: 116 LNHDSSLETLPRAGIVHRIDKETSGLLMVAKTLQAHNSLTQQLQDRDITREYLAITRG-- 173

Query: 192 KNKKECIANWLLKKS---HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
                  A   + +    H      + V++N K   +A++H++V   F  +   ++++  
Sbjct: 174 ----RMTAGGTVDEPIGRHPTDRKRYAVRENGK---HAVTHYRVGQRFT-RHTLVQVKLE 225

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P++GD  Y   F+   + +  ++ +L       LHA  + L HP
Sbjct: 226 TGRTHQIRVHMAHIRFPLLGDQVYGGRFQMPPDCSEQLEKELRSFKRQALHAAKLGLQHP 285

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
                L+   PLP  M++  ++L 
Sbjct: 286 VTDEYLEWEQPLPEDMIRLLEALA 309


>gi|166154000|ref|YP_001654118.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 434/Bu]
 gi|166154875|ref|YP_001653130.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis L2b/UCH-1/proctitis]
 gi|301335199|ref|ZP_07223443.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis L2tet1]
 gi|165929988|emb|CAP03471.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 434/Bu]
 gi|165930863|emb|CAP06425.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis L2b/UCH-1/proctitis]
          Length = 335

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 110/228 (48%), Gaps = 22/228 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +YED  I V NKP  + V    G         + + I   LK     +  +P + HRLD+
Sbjct: 92  VYEDDMILVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDK 151

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+L+  +TR A    +E F  ++++K+Y ++    P  +   + +  + +  +    
Sbjct: 152 DTSGLLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQE---LIHTRITRHPLKRKE 208

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + V+  + +G   AI+H  V+     +   + + P TGRTHQLRVH  H+G PI+GD  Y
Sbjct: 209 MTVLSTHAEGGKEAITHCHVLATNG-RLSVVALYPETGRTHQLRVHMKHLGTPILGDPVY 267

Query: 273 ---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
                NF+        +K  LHA  +   HPE   R+++   LP  M 
Sbjct: 268 GIPSINFRYGL-----DKQQLHAYSLVFAHPESAERVKLVTKLPDDMT 310


>gi|119492077|ref|ZP_01623530.1| Pseudouridine synthase, RluD [Lyngbya sp. PCC 8106]
 gi|119453287|gb|EAW34452.1| Pseudouridine synthase, RluD [Lyngbya sp. PCC 8106]
          Length = 319

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 87/318 (27%), Positives = 149/318 (46%), Gaps = 47/318 (14%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-------RVKFNNRIQSGQVVRI 67
           + +N RLDRW       ++   +Q ++  G V V++K        +K  + I+    V+I
Sbjct: 20  EPQNYRLDRWLSESLETLSRSRIQTLISQGHVTVNQKVCVSKKLTLKRGDHIE----VKI 75

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP     N  + E + +D  +++           LYED  + + NK AG+ V   +G   
Sbjct: 76  PP-----NEPL-ELEAVDIPLDI-----------LYEDEHLIIINKQAGLVVHPSAG--- 115

Query: 128 HIDGFLKSWV----DSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           H++  L + +    D+       ++P + HRLD++T+G +VVA+T  + Q L +  + + 
Sbjct: 116 HVNDTLVNALLAHCDTLAGIGGVERPGIVHRLDKDTTGAIVVAKTDFSLQSLQQQIKNKT 175

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            Q+ Y  +V+G  K     I   + +  H+       V   E+G   AI+H+++ +    
Sbjct: 176 AQRQYLGVVYGSHKADFGTIEQPIGR--HLADRKKMAVVTIERGGRNAITHWQIQERLG- 232

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +     TGRTHQ+RVH+  +G PIVGD  Y +   G       +   LHA  + L 
Sbjct: 233 NYSLILFTLETGRTHQIRVHSNFIGHPIVGDLDYSS---GRSVGVNLSGQALHAWKLKLQ 289

Query: 299 HPEGGR-LQITAPLPAHM 315
           HP     ++  APLP  M
Sbjct: 290 HPVTEEWIEAIAPLPEEM 307


>gi|307708571|ref|ZP_07645035.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           mitis NCTC 12261]
 gi|307615320|gb|EFN94529.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           mitis NCTC 12261]
          Length = 295

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 85/308 (27%), Positives = 148/308 (48%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  I+   V   +
Sbjct: 5   IETGGLRLDKALSDLTELSRSLANEQIKSGQVL-VNGQVKKAKYTVQEGDIVTYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   L    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAENLPLDIIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG+         +LHA+ +   HP  G  ++ TA +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGETMEFTADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKETLERL 293


>gi|121604767|ref|YP_982096.1| RluA family pseudouridine synthase [Polaromonas naphthalenivorans
           CJ2]
 gi|120593736|gb|ABM37175.1| ribosomal large subunit pseudouridine synthase D [Polaromonas
           naphthalenivorans CJ2]
          Length = 344

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 85/334 (25%), Positives = 144/334 (43%), Gaps = 35/334 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVV 65
           +++V V  +    RLD+      P  +   LQ+++  G V V   K +K + ++++G  +
Sbjct: 36  LRHVSVPVESHGCRLDKALAGLVPEFSRSYLQQLIEDGGVLVKGLKAIKTSAKVKAGDEL 95

Query: 66  RIPPVINALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
            I       +   K E+  LD               ++YED  + V NKPAG+ V    G
Sbjct: 96  TIELRPTPQSQAFKPEEMALD---------------IVYEDRHLIVVNKPAGLVVHPAPG 140

Query: 125 --IAYHIDGFLK-----SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++G L      S++   G    + HRLD++TSG++VVAR R     L      R
Sbjct: 141 NWSGTLLNGLLAHDPQASFMPRAG----IVHRLDKDTSGLMVVARQRQTMDQLVSMIAAR 196

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L  G  +  K       + +       + VV   +     A +   ++D  A
Sbjct: 197 TVSREYIALAHGTWEGAKTRQVEAPIGRDPRNRLRMAVVDLEKNSGKAASTVISLLDN-A 255

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +K C ++ + HTGRTHQ+RVH   +G P+V D  Y     G+       +  LHA  +  
Sbjct: 256 EKHCLVKCKLHTGRTHQIRVHMAFLGHPLVSDEVYGGAVAGSL-----QRQALHACRLAF 310

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
            HP  G  ++  +  P  +       G +Y++ L
Sbjct: 311 AHPVTGAAMEFKSLPPPDLEMAIAGFGLRYNQAL 344


>gi|310821071|ref|YP_003953429.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309394143|gb|ADO71602.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 269

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 84/283 (29%), Positives = 136/283 (48%), Gaps = 42/283 (14%)

Query: 46  VRVDKKRVKFNNRIQSGQVVR--IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           +R D + VK ++R++ G+++   +PP + AL                   ++ L   +L+
Sbjct: 1   MRADGRPVKASSRLRGGELLSLHVPPPVAAL-----------------PEAEELPLEVLH 43

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFL--------KSWVDSKGQ-KPRLTHRLDQET 154
           ED  + V NK AG+ V  G+G   H  G L        K      G+ +P + HRLD++T
Sbjct: 44  EDRDLVVVNKAAGMVVHPGAG---HASGTLVNALLHRVKDLAGVGGELRPGIVHRLDKDT 100

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G LVVA+   A   L ++F+ R ++K Y +LV G PK +      +     H    +  
Sbjct: 101 TGCLVVAKNEQALVALQKAFKTRAVEKTYLALVHGHPKAEGRIETLYGRHPVHR-QRFTG 159

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            VK+ +     A++ F+  + F +    +E+   TGRTHQ+RVH    G P++ D  Y A
Sbjct: 160 KVKEGKS----AVTVFRTREFF-EGAALVEVDLLTGRTHQIRVHLSESGHPLLCDALYGA 214

Query: 275 NFKGNF-TSPIQNKL---YLHARYMDLPHPEGGR-LQITAPLP 312
             K     +  Q +L    LHA  +   HP  G+ L++ APLP
Sbjct: 215 GRKAKGQVAQAQERLGRQALHAWRLGFAHPRTGKALKLEAPLP 257


>gi|289167775|ref|YP_003446044.1| 23S_rRNA pseudouridine synthase [Streptococcus mitis B6]
 gi|288907342|emb|CBJ22179.1| 23S rRNA pseudouridine synthase [Streptococcus mitis B6]
          Length = 295

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 84/308 (27%), Positives = 148/308 (48%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   V   +
Sbjct: 5   IETGSLRLDKALSDLTELSRSLANEQIKSGQVL-VNGQVKKAKYTVQEGDVVTYHVPEPE 63

Query: 93  HSDFLKS----ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++       ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAENIPLEIIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQDLKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG+         +LHA+ +   HP  G  L+ TA +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGETLEFTADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKETLERL 293


>gi|218439930|ref|YP_002378259.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
 gi|218172658|gb|ACK71391.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
          Length = 548

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 89/273 (32%), Positives = 130/273 (47%), Gaps = 41/273 (15%)

Query: 56  NNRIQS----GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           N+RIQ       V R  P++  L   + E+K         +H+      ++YED  + + 
Sbjct: 300 NDRIQGKFYPACVARCQPIMGFLLSGLPEKK------TTFRHTIKEPLPIVYEDDYLIII 353

Query: 112 NKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           NKP G+ SV G S   Y       + +   G   R  HRLD +TSG+L++AR      HL
Sbjct: 354 NKPEGLLSVPGRSSDRYDSVISRLNHLLPDGHLLRSVHRLDLDTSGLLLLARNDQIYNHL 413

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD-------YVHVVKQNEKGA 223
            + FR R+I+KIY +LV G     +  I      K  + GD        V  ++  E   
Sbjct: 414 AQQFRDRKIEKIYQALVQGRVSQPQGTI------KLPLWGDPRFRPLQTVDFIRGKE--- 464

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA---LHMGCPIVGDHKYCANFKGNF 280
             +I+ F+VI  F   F  +E  P TGRTHQ+RVH    L +G PI+GD  Y    KG+ 
Sbjct: 465 --SITQFRVI-AFEDNFTRVEFMPITGRTHQIRVHCADQLGLGTPIIGDRLYG---KGDD 518

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            +    +L+LHA+ +   HP   + L + AP P
Sbjct: 519 LT----RLHLHAQKLRFLHPITKQFLSVNAPPP 547


>gi|194212968|ref|XP_001502415.2| PREDICTED: similar to RNA pseudouridylate synthase
           domain-containing protein 4 [Equus caballus]
          Length = 377

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 79/266 (29%), Positives = 125/266 (46%), Gaps = 46/266 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           ++++D  + V NKP G+ V GG G+   I   L    K     K     L HRLD+ET+G
Sbjct: 99  IIHQDKDLLVINKPYGLPVHGGPGVQLCISDVLPILAKILHGHKADPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P      +   +++K   G  + H  
Sbjct: 159 VMVLAWEKEVAHQVQELFRTRQVAKKYWAITVRVPVPSAGVVDIPIIEKEVQGRQHHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  +  + A+ A++ ++V+         LE+QP TG  HQLRVH + 
Sbjct: 219 TLSPSYRMDSGKMVRVRMRRNAHVAVTQYQVLSNTLSS-ALLELQPATGIKHQLRVHLSF 277

Query: 261 HMGCPIVGDHKYCANFKGNFTSP-------------IQNK-----LYLHARYMDLPHPEG 302
            + CPI+GDHKY      N  +P              Q+K     L+LHAR + LP   G
Sbjct: 278 GLDCPILGDHKYS---DWNRLAPQKLSVGTLKKLGLQQSKARHIPLHLHARQLILPA-LG 333

Query: 303 GR---LQITAPLPAHMVKTWDSLGFK 325
            R   L +   LP + V++ + LG +
Sbjct: 334 SRKEELNLVCRLPRYFVRSLNRLGLE 359


>gi|327460457|gb|EGF06794.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1057]
          Length = 298

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 119/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ FA  +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTRFQVLERFAD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA +P    +T + L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEVPVIFQETLEKL 295


>gi|223940477|ref|ZP_03632327.1| pseudouridine synthase [bacterium Ellin514]
 gi|223890839|gb|EEF57350.1| pseudouridine synthase [bacterium Ellin514]
          Length = 536

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 69/206 (33%), Positives = 108/206 (52%), Gaps = 24/206 (11%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
           ++L+ED  + V NKPAG++    S   Y  +G  + W+  K ++PR     + HRLD+ET
Sbjct: 11  LILFEDEHLLVVNKPAGMNTHAPS--PYAGEGIYE-WL--KHREPRWASLAIVHRLDKET 65

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V  +T  A + LTE F    I+K Y  L   +  ++   + + L++   +G  Y+ 
Sbjct: 66  SGVMVFGKTTVANRSLTEQFTNHSIRKKYLLLTDKVVSSQTSTMVSCLVR---VGEKYLS 122

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             +    G   A +HF+VI   A+    +E +P TGRTHQ+RVHA   G PI+GD  Y  
Sbjct: 123 --RPVHAGGEKAETHFEVI-TKAEGGTLVEAEPITGRTHQIRVHAAEQGFPILGDALYGG 179

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
                      +++ LHA  + L HP
Sbjct: 180 T--------KASRVCLHAAELKLKHP 197


>gi|307706435|ref|ZP_07643244.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK321]
 gi|307618145|gb|EFN97303.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK321]
          Length = 295

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 84/296 (28%), Positives = 142/296 (47%), Gaps = 47/296 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           ++SGQV V+ +  K    +Q G VV          + + E ++L+        ++ L   
Sbjct: 31  IKSGQVLVNGQVKKAKYTVQEGDVV---------TYHLPEPEVLEYV------AENLPLE 75

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 76  IIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 132

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 133 KDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 186

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 187 EKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 244

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHA+ +   HP  G  L+ TA +P    +T + L
Sbjct: 245 EVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGEILEFTADIPEIFKETLERL 293


>gi|289422301|ref|ZP_06424151.1| ribosomal large subunit pseudouridine synthase D
           [Peptostreptococcus anaerobius 653-L]
 gi|289157246|gb|EFD05861.1| ribosomal large subunit pseudouridine synthase D
           [Peptostreptococcus anaerobius 653-L]
          Length = 320

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 87/337 (25%), Positives = 159/337 (47%), Gaps = 57/337 (16%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V   +V +D+ + RLD +  + Y  I+   +QK+++  ++RV+ K  K + ++++G  + 
Sbjct: 19  VDVYIVSDDDADSRLDFYIASQYRDISRSYIQKLIKEDRIRVNSKIEKASYKVKTGDKIE 78

Query: 67  IP-PVINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +  P   AL   I+ Q I +D               ++YED  + V NK  G+ V    G
Sbjct: 79  VNMPEPQALE--IEPQDIGID---------------IVYEDDYLMVVNKQQGMVVHPAPG 121

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                    + +H    L S   +   +P + HR+D+ TSG+LV+A+     Q L++ F+
Sbjct: 122 NPDRTLVNAVLFHCGDRLSSI--NGVIRPGIVHRIDKNTSGLLVIAKDNQTHQGLSDQFK 179

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY---------VHVVKQNEKGANYA 226
           +  I + Y  +          CI N   ++  I G           + +VK N K    A
Sbjct: 180 VHSITREYEMI----------CIGNVEWQEKTIDGPIGRNPKDRMKMAIVKTNGK---RA 226

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++HF++++ +   +  L  +  TGRTHQ+RVH   +  PI+GD+ Y   +K    + ++ 
Sbjct: 227 VTHFRLVENY-DGYSHLSARLETGRTHQIRVHISSINRPILGDNLY--GYKVKTFAKLEG 283

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +  LHAR +   HP  G+ ++  + LP +     + L
Sbjct: 284 QC-LHARKLGFIHPISGKYMEFDSDLPEYFEDVLNKL 319


>gi|323190261|gb|EFZ75537.1| RNA pseudouridylate synthase family protein [Escherichia coli
           RN587/1]
          Length = 219

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 113/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYHDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|223042001|ref|ZP_03612184.1| 23S rRNA pseudouridine synthase D [Actinobacillus minor 202]
 gi|223017199|gb|EEF15628.1| 23S rRNA pseudouridine synthase D [Actinobacillus minor 202]
          Length = 325

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 94/343 (27%), Positives = 162/343 (47%), Gaps = 49/343 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V  D    RLD+     +P  +   L+  + + QV V+ K V K   ++  G+++ I   
Sbjct: 11  VSADLLGARLDQALAQLFPDYSRSRLKVWIENDQVWVNGKIVNKAREKVFGGELIEI--- 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                     Q  ++  V     +  L   ++YED  I V NKP  + V  G+G   + D
Sbjct: 68  ----------QAEVEEEVRFEPQNIPLN--IVYEDDDIIVINKPKDLVVHPGAG---NPD 112

Query: 131 GFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + + +        + PR  + HRLD++T+G++VVA+   A  HL  + + RRI + Y 
Sbjct: 113 GTVLNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKNIPAQTHLVTALQKRRITREYE 172

Query: 185 SLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  GI        E +A    K++ +    VH + +       A++H+++++ F + + 
Sbjct: 173 AIASGIMTQGGKVDEPMARHPTKRTAMA---VHPMGKP------AVTHYRIMERF-RNYT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQN--KLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P++GD  Y    +        F + ++   +  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHIAHPLLGDQLYGGXPRPPKGASEEFLTVLRGFQRQALHAT 282

Query: 294 YMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            + L HP  G L +  APLP   V+  ++L  K D  LY  +L
Sbjct: 283 MLRLEHPITGELMEWHAPLPDDFVELVEAL--KADYELYKDQL 323


>gi|307709119|ref|ZP_07645578.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
 gi|307620065|gb|EFN99182.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
          Length = 295

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 84/308 (27%), Positives = 148/308 (48%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   V   +
Sbjct: 5   IETGGLRLDKALSDLTELSRSLANEQIKSGQVL-VNDQVKKAKYTVQEGDVVTYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   +    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDIPLEIIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG+         +LHA+ +   HP  G  L+ TA +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGETLEFTADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKETLEKL 293


>gi|188995238|ref|YP_001929490.1| putative ribosomal large subunit pseudouridine synthase D
           [Porphyromonas gingivalis ATCC 33277]
 gi|188594918|dbj|BAG33893.1| putative ribosomal large subunit pseudouridine synthase D
           [Porphyromonas gingivalis ATCC 33277]
          Length = 227

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 72/232 (31%), Positives = 110/232 (47%), Gaps = 17/232 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + + NK  G  VQG       +   +K W+  K  KP      + HRLD+  +
Sbjct: 3   VVYEDNHLIIVNKAVGEIVQGDKTGDSPLSETVKQWIKEKYAKPGKVFLGVAHRLDRPVA 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L   FR  ++QK+Y ++V   P    + + +++ +   +   +  V
Sbjct: 63  GLVVFAKTSKALARLNNMFRDGKVQKVYRAIVKQRPPKDGDTLVHYISRNERLNKSFASV 122

Query: 216 VK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            K  N K A+ +       D     +  LE++ HTGR HQ+R     MGCPI GD KY  
Sbjct: 123 CKVPNSKKASLSYRLLASSD----NYHLLEIELHTGRHHQIRCQLAAMGCPIKGDLKY-- 176

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
              G   S     + L A  +   HP  G L  +TAPLP++  K W  L  K
Sbjct: 177 ---GFGRSNPDGGISLLAHRIRFTHPVSGVLIDLTAPLPSND-KLWSLLTSK 224


>gi|150009274|ref|YP_001304017.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           distasonis ATCC 8503]
 gi|255015880|ref|ZP_05288006.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_7]
 gi|256841839|ref|ZP_05547345.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           sp. D13]
 gi|262384161|ref|ZP_06077297.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_33B]
 gi|301311073|ref|ZP_07217002.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           20_3]
 gi|149937698|gb|ABR44395.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           distasonis ATCC 8503]
 gi|256736733|gb|EEU50061.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           sp. D13]
 gi|262295059|gb|EEY82991.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_33B]
 gi|300831136|gb|EFK61777.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           20_3]
          Length = 359

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 87/337 (25%), Positives = 157/337 (46%), Gaps = 51/337 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V +  +  +R+D++  +         +Q    +G + V+ K VK N R++   VV I   
Sbjct: 36  VADKGQSLLRVDKFLVDRMMGATRNRIQLAAEAGCILVNDKPVKSNYRVKPLDVVSI--- 92

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
              ++   +E +I+   + L          ++YED  + V NKPAG+ V  G G      
Sbjct: 93  --VMDRPRRELEIIPEDIPLN---------IVYEDDDLLVVNKPAGLVVHPGHGNYTGTL 141

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              +AY++      + D    +  L HR+D++TSG+LVVA+   A  +L+  F  +  ++
Sbjct: 142 VNALAYYLKD--DPYYDPSDPRLGLVHRIDKDTSGLLVVAKRPEAKSNLSLQFFNKTTKR 199

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCF 236
            Y +LVWGI +  +  I      + +IG D      + V  + ++G   A++H+ V++  
Sbjct: 200 KYRALVWGIVQEDEGRI------EGNIGRDPRDRMQMTVFPEGDQGKT-AVTHYTVLERL 252

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN---- 286
                 +E +  TGRTHQ+RVH  ++G  +  D +Y  +   KG     +   +QN    
Sbjct: 253 GY-VSLVECRLETGRTHQIRVHMKYIGHTLFNDERYGGHDILKGTTFTKYKQFVQNCFAI 311

Query: 287 --KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
             +  LHA+ +   HP  G  +   + +P+ M +  D
Sbjct: 312 CPRQALHAKTLGFVHPTTGEEMFFDSEIPSDMQQLID 348


>gi|311746883|ref|ZP_07720668.1| RNA pseudouridine synthase family protein [Algoriphagus sp. PR1]
 gi|126578569|gb|EAZ82733.1| RNA pseudouridine synthase family protein [Algoriphagus sp. PR1]
          Length = 237

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 78/241 (32%), Positives = 109/241 (45%), Gaps = 31/241 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  I   NKPAG+ V   S  A      L+   D  G      HRLD+ TSGIL+ 
Sbjct: 5   ILFEDDSIIAINKPAGLLVHRTSIAAQETVFALQILRDQIGMHVHPVHRLDRPTSGILLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG------DYVH 214
           A+      HL   F  R+I+K Y ++V GIP+ KK  I + L  KS   G       +  
Sbjct: 65  AKKEEILPHLKNLFSERQIKKNYLTIVRGIPEQKKALIDHPL--KSERSGRLQEAQTWYK 122

Query: 215 VVKQNE----KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           V+ + E        Y  S          ++  L + P TGRTHQ+R H  H+   I+GD 
Sbjct: 123 VISETEIPFDTTGRYPTS----------RYSLLSVNPETGRTHQIRRHLAHIRHYIIGDK 172

Query: 271 KYCANFKGNFTSPIQNK-----LYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
           K+  N +  F    QN+     L LHA  +   HP     ++I+ P+P H      SL  
Sbjct: 173 KHGDNKQNIF---FQNQFGLENLLLHAIRLSFNHPITEETIEISCPVPEHFQSILKSLNL 229

Query: 325 K 325
           +
Sbjct: 230 Q 230


>gi|15799742|ref|NP_285754.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H7
           EDL933]
 gi|15829316|ref|NP_308089.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H7
           str. Sakai]
 gi|168751433|ref|ZP_02776455.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4113]
 gi|168755664|ref|ZP_02780671.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4401]
 gi|168764065|ref|ZP_02789072.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4501]
 gi|168771280|ref|ZP_02796287.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4486]
 gi|168781941|ref|ZP_02806948.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4076]
 gi|168789583|ref|ZP_02814590.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC869]
 gi|168801483|ref|ZP_02826490.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC508]
 gi|195939274|ref|ZP_03084656.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H7
           str. EC4024]
 gi|208813925|ref|ZP_03255254.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4045]
 gi|208819721|ref|ZP_03260041.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4042]
 gi|209396031|ref|YP_002268666.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4115]
 gi|254791196|ref|YP_003076033.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H7
           str. TW14359]
 gi|261226817|ref|ZP_05941098.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. FRIK2000]
 gi|261255220|ref|ZP_05947753.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. FRIK966]
 gi|291280883|ref|YP_003497701.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O55:H7 str. CB9615]
 gi|34395800|sp|Q8XA10|RLUA_ECO57 RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|12512752|gb|AAG54362.1|AE005182_11 orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]
 gi|13359518|dbj|BAB33485.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|188014525|gb|EDU52647.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4113]
 gi|189000435|gb|EDU69421.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4076]
 gi|189357052|gb|EDU75471.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4401]
 gi|189359892|gb|EDU78311.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4486]
 gi|189365889|gb|EDU84305.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4501]
 gi|189370824|gb|EDU89240.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC869]
 gi|189376359|gb|EDU94775.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC508]
 gi|208735202|gb|EDZ83889.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4045]
 gi|208739844|gb|EDZ87526.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4042]
 gi|209157431|gb|ACI34864.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4115]
 gi|209746854|gb|ACI71734.1| hypothetical protein ECs0062 [Escherichia coli]
 gi|209746856|gb|ACI71735.1| hypothetical protein ECs0062 [Escherichia coli]
 gi|209746858|gb|ACI71736.1| hypothetical protein ECs0062 [Escherichia coli]
 gi|209746860|gb|ACI71737.1| hypothetical protein ECs0062 [Escherichia coli]
 gi|209746862|gb|ACI71738.1| hypothetical protein ECs0062 [Escherichia coli]
 gi|254590596|gb|ACT69957.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. TW14359]
 gi|290760756|gb|ADD54717.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O55:H7 str. CB9615]
 gi|320190420|gb|EFW65070.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC1212]
 gi|320642099|gb|EFX11450.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H7
           str. G5101]
 gi|320647462|gb|EFX16257.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H-
           str. 493-89]
 gi|320652796|gb|EFX21034.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H-
           str. H 2687]
 gi|320658185|gb|EFX25914.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O55:H7
           str. 3256-97 TW 07815]
 gi|320663494|gb|EFX30778.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O55:H7
           str. USDA 5905]
 gi|320668806|gb|EFX35601.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H7
           str. LSU-61]
 gi|326345223|gb|EGD68966.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. 1125]
 gi|326346924|gb|EGD70658.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. 1044]
          Length = 219

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFRERVPKKQYVTRVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETGKP-AQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|167855786|ref|ZP_02478539.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           parasuis 29755]
 gi|167853065|gb|EDS24326.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           parasuis 29755]
          Length = 325

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 74/244 (30%), Positives = 125/244 (51%), Gaps = 31/244 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +        + PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPKDLVVHPGAG---NPDGTVLNALLHHYPQIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL  + + R I + Y ++  GI        E +A    K++ +   
Sbjct: 143 TGLMVVAKTVPAQTHLVTALQKREITREYEAVASGIMTQGGKVDEPMARHPTKRTAMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 201 -VHPMGKP------AVTHYRIMERF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQL 252

Query: 272 YCANFK------GNFTSPIQN--KLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           Y    +      G F   ++N  +  LHA  + L HP  G L +  APLP   V+  ++L
Sbjct: 253 YGGRPRPPKGASGEFLEVLRNFKRQALHATMLRLHHPITGELMEWHAPLPDDFVELIEAL 312

Query: 323 GFKY 326
              Y
Sbjct: 313 KADY 316


>gi|219666529|ref|YP_002456964.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
 gi|219536789|gb|ACL18528.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
          Length = 233

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 66/205 (32%), Positives = 103/205 (50%), Gaps = 8/205 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V +KP  I  Q  S     I   LK  +  +  KP      L HRLD+   
Sbjct: 6   IVYEDNHLLVVDKPPNILSQKDSTGDMDILTLLKQDIKIRYNKPGNVYLGLVHRLDRPVG 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  +A  L+E  R R   K Y +L+ G P  +K  + ++L+K      + V  
Sbjct: 66  GVMVFAKTSKSAARLSEQIRNREFTKTYLALIQGQPAKQKNTLIHYLVKDEK--SNKVSA 123

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           VK+  KGA  AI  ++V+   +     +++   TGR HQ+RV   H+G P+ GD+KY   
Sbjct: 124 VKKGAKGAKEAILDYEVVHSQSD-LSLVKVNLRTGRPHQIRVQFAHLGHPLYGDYKYGKI 182

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
            K + TS  +  L L +  +   HP
Sbjct: 183 VKTSKTSLTKPHLGLWSYEISCLHP 207


>gi|323343472|ref|ZP_08083699.1| ribosomal large subunit pseudouridine synthase A [Prevotella oralis
           ATCC 33269]
 gi|323095291|gb|EFZ37865.1| ribosomal large subunit pseudouridine synthase A [Prevotella oralis
           ATCC 33269]
          Length = 573

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 72/224 (32%), Positives = 109/224 (48%), Gaps = 21/224 (9%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK-SWVDSKGQKP 144
           S  N T   D     ++YED  I V NKPAG+    G   A  +   ++  + DS    P
Sbjct: 356 SPTNATSVPDI---PIVYEDEAIVVINKPAGMLSVPGKACALSVYDLMRMRYPDSNS--P 410

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL-L 203
            + HRLD  TSG+L++A+T+ A + L   F    I+K Y +++ G+P + +   A  + L
Sbjct: 411 LIVHRLDMATSGLLIIAKTKNAHRILQRQFAEHTIRKQYIAVLDGVPDSCRWPSAGIISL 470

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
                  D    +   E G   A++ +K++    ++   + + PHTGRTHQLR+H  H  
Sbjct: 471 PLRPDLADRPRQLVDFEHGKE-AVTEYKILRTAGEE-TRIALFPHTGRTHQLRIHCAHPY 528

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            + CPI GD+ Y              +LYLHA  M+  HP  GR
Sbjct: 529 GLNCPIKGDNLYGTR---------SQRLYLHAESMEFIHPVSGR 563


>gi|120436437|ref|YP_862123.1| pseudouridylate synthase [Gramella forsetii KT0803]
 gi|117578587|emb|CAL67056.1| pseudouridylate synthase [Gramella forsetii KT0803]
          Length = 232

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 121/248 (48%), Gaps = 25/248 (10%)

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +KIL +  NL          +L+ED+ I + NK  G  VQG       +   +KS++  K
Sbjct: 4   EKILSNRDNLQ---------VLHEDNHIIIVNKRPGDIVQGDKTGDKPLSEVVKSYLKEK 54

Query: 141 GQKPR-----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +KP      + HRLD+ TSGI++ ++T  A   L + F+ ++ +K YW++V   P+ K 
Sbjct: 55  YKKPGNVYLGVVHRLDRPTSGIVLFSKTSKALPRLNKLFQDKKAKKTYWAIVKNAPQEKS 114

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             + +++ + S     Y H  K     +  A+  ++++      +  LE+  HTGR HQ+
Sbjct: 115 GELVHFMKRNSKQNKSYAH--KNEVPDSKKAMLDYRLLKKL-DNYYLLEIDLHTGRHHQI 171

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           R     +G PI GD KY  N      S     ++LH+R +   HP     + I AP P+ 
Sbjct: 172 RSQLSAIGSPIKGDLKYGFNRSNKDAS-----IHLHSRELKFTHPVKKEFIHIIAPPPSD 226

Query: 315 MVKTWDSL 322
            +  WD++
Sbjct: 227 PI--WDAV 232


>gi|114799098|ref|YP_762171.1| RluA family pseudouridine synthase [Hyphomonas neptunium ATCC
           15444]
 gi|114739272|gb|ABI77397.1| pseudouridine synthase, RluA family [Hyphomonas neptunium ATCC
           15444]
          Length = 341

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 87/351 (24%), Positives = 147/351 (41%), Gaps = 59/351 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQV--V 65
           +  E  +   RLD +       I+    + ++  G V V    V+ N R  ++ G V  V
Sbjct: 6   ITSEAADAGQRLDAFLGARAEGISRSRAKTLIEEGAVTVGGA-VETNPRAPVKKGLVYAV 64

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +PP + A+                   ++ +   +L+ED+ + + NK AG++V    G 
Sbjct: 65  NMPPPVPAM-----------------PEAEAIPLEILFEDAHLVILNKAAGMAVHPAPGS 107

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                   + +H  G L        ++P + HRLD+ TSG++V A+T +A   L   F  
Sbjct: 108 QTGTLVNALLHHCQGQLSGI--GGVERPGIVHRLDKLTSGVMVAAKTESAHTGLAALFER 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             I ++Y ++  G P+     I   + + +S      VH    +   A +A++H+K ++ 
Sbjct: 166 HDIDRVYRAVTRGAPRPLSGTIEAAIARSESDRKKMSVH-RNPDSPAARHAVTHYKAVET 224

Query: 236 FAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY----------CANFK 277
           F  K           LE +  TGRTHQ+RVH  H G P++GD  Y              +
Sbjct: 225 FGYKDRATRLPAAALLECRLETGRTHQIRVHMAHSGAPLIGDPVYGRQAGIMAWKAPGSE 284

Query: 278 GNFTSPIQ-----NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             +   +      ++  LHA  +   HP  G  L+  APLP  M     +L
Sbjct: 285 ARYDKALAAARAFSRQALHAAVLGFVHPITGETLRYEAPLPEDMTGLIAAL 335


>gi|261392924|emb|CAX50509.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D; rRNA pseudouridylate synthase D) [Neisseria
           meningitidis 8013]
          Length = 374

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 138/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIIYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|89893256|ref|YP_516743.1| hypothetical protein DSY0510 [Desulfitobacterium hafniense Y51]
 gi|89332704|dbj|BAE82299.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 241

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 66/205 (32%), Positives = 103/205 (50%), Gaps = 8/205 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V +KP  I  Q  S     I   LK  +  +  KP      L HRLD+   
Sbjct: 14  IVYEDNHLLVVDKPPNILSQKDSTGDMDILTLLKQDIKIRYNKPGNVYLGLVHRLDRPVG 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  +A  L+E  R R   K Y +L+ G P  +K  + ++L+K      + V  
Sbjct: 74  GVMVFAKTSKSAARLSEQIRNREFTKTYLALIQGQPAKQKNTLIHYLVKDEK--SNKVSA 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           VK+  KGA  AI  ++V+   +     +++   TGR HQ+RV   H+G P+ GD+KY   
Sbjct: 132 VKKGAKGAKEAILDYEVVHSQSD-LSLVKVNLRTGRPHQIRVQFAHLGHPLYGDYKYGKI 190

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
            K + TS  +  L L +  +   HP
Sbjct: 191 VKTSKTSLTKPHLGLWSYEISCLHP 215


>gi|77919474|ref|YP_357289.1| pseudouridylate synthase, 23S RNA-specific [Pelobacter carbinolicus
           DSM 2380]
 gi|77545557|gb|ABA89119.1| pseudouridylate synthase, 23S RNA-specific [Pelobacter carbinolicus
           DSM 2380]
          Length = 301

 Score = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 90/312 (28%), Positives = 151/312 (48%), Gaps = 37/312 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +  P  +    +KI+  G V ++ +R++ ++          P   +A   + 
Sbjct: 1   MRLDQYLASAIPDFSRSFARKIIDLGGVHLNGRRMRRSS---------FPVPGHAAVEVY 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLK 134
            + + LD      +H       +L  D  + V NKP GI+ Q       G  Y  +  L+
Sbjct: 52  LDHRDLDIFALDDEH-------ILLRDRYLVVVNKPPGINSQPTPARYKGTLY--EALLR 102

Query: 135 SWVD--SKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  +KG+KP L    RLD++TSG+++ +    A + L++ F  RR+QK Y +LV G 
Sbjct: 103 LLDDPYNKGRKPSLGMVQRLDRDTSGVMIFSIHARAHKSLSDIFAARRVQKHYLALVAGC 162

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +  +    + LL + H      +++K   +G   A++ ++VI+ F      LE++  TG
Sbjct: 163 MQAPQGEFRS-LLARQH----RTNLMKSVARGGKEAVTRYRVIEKFGDA-ELLEVEIPTG 216

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           R+HQ+RVH    G P++GD +Y    +      P Q    LHAR ++L HP     L I 
Sbjct: 217 RSHQIRVHFAEAGHPLLGDIRYGGPDRWRGVDVPRQ---MLHARRLELLHPISKEPLNIE 273

Query: 309 APLPAHMVKTWD 320
           APLP   +K  +
Sbjct: 274 APLPQDFLKLLE 285


>gi|163782801|ref|ZP_02177797.1| hypothetical protein HG1285_15736 [Hydrogenivirga sp. 128-5-R1-1]
 gi|159881922|gb|EDP75430.1| hypothetical protein HG1285_15736 [Hydrogenivirga sp. 128-5-R1-1]
          Length = 322

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 92/323 (28%), Positives = 147/323 (45%), Gaps = 48/323 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V  ++   RLD +    YP ++   +++++  G   V+ K  K + R++ G  V +   
Sbjct: 11  TVSEEQAGERLDTFLAKAYPELSRSYIKRLIEEGFALVEGKVRKPSYRVKEGDRVTLS-- 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                  + E + L+      K  D    ++ YED  + V  KP G+ V    G      
Sbjct: 69  -------VPEPEPLE-----VKPEDIPIEVV-YEDRDVVVIVKPCGLVVHPSPGYTSGTL 115

Query: 125 ---IAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + YHI    K      G ++P + HRLD+ET+G++VVA+   + ++L E F  RR +
Sbjct: 116 VNALLYHI----KDLSSIGGVERPGIVHRLDKETAGLMVVAKNDTSHRNLVEQFASRRTE 171

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--QNEKGANYAISHFKVIDCF-A 237
           K+Y +LV G  K +   +      +  IG    H  K   +   +  A S F V++ F  
Sbjct: 172 KLYRALVKGTVKEEHGIL------ELPIGRHPFHRKKFSTSSPRSKPAKSEFWVLERFPG 225

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY-----LHA 292
            +   L+++ +TGRTHQ+RVH   +G PIVGD  Y   FK +      N+L      L A
Sbjct: 226 LELTLLKVKIYTGRTHQIRVHLSSIGHPIVGDTTY--GFKRSSVPEAINRLLGECNMLVA 283

Query: 293 RYMDLPHPEGGR---LQITAPLP 312
             +   HP  GR    +I  P P
Sbjct: 284 YKLGFYHPSSGRWLEFEIDDPEP 306


>gi|67459733|ref|YP_247357.1| ribosomal large subunit pseudouridine synthase D [Rickettsia felis
           URRWXCal2]
 gi|67005266|gb|AAY62192.1| Ribosomal large subunit pseudouridine synthases, RluD subfamily
           [Rickettsia felis URRWXCal2]
          Length = 385

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 117/233 (50%), Gaps = 24/233 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-------KSWVD-SKGQKPRLTHRLDQ 152
           ++YED  + V NK AG++V  G+G  +H D  +       K+  D    ++P + HRLD+
Sbjct: 123 IIYEDDDLIVINKAAGMTVHPGAG--HHDDTLVNALLYHTKNLSDIGSAERPGIVHRLDK 180

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +T+G++VVA+   A   L      R++ + Y +LVWG+  N  E +    + +S +    
Sbjct: 181 DTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKALVWGVI-NPLEGVIKNNIGRSRVDRQK 239

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           + ++K    G   A++H+K ++ F +     +E +  TGRTHQ+RV   H+   +VGD  
Sbjct: 240 MTILKY---GGKEAVTHYKTLELFHKGTISMVECKLSTGRTHQIRVQLSHLKHSVVGDQT 296

Query: 272 YCANFK--GNFTSPIQNKLY------LHARYMDLPHPEGGR-LQITAPLPAHM 315
           Y  N +   +    ++ KL       LH+ Y+   HP     ++ +  LP  M
Sbjct: 297 YGNNDRKIAHSLPELKAKLIDFKRQALHSWYLSFTHPTSNEIMKFSCELPRDM 349


>gi|46447425|ref|YP_008790.1| putative 23S rRNA pseudouridine synthase [Candidatus Protochlamydia
           amoebophila UWE25]
 gi|46401066|emb|CAF24515.1| putative 23S rRNA pseudouridine synthase [Candidatus Protochlamydia
           amoebophila UWE25]
          Length = 219

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 64/206 (31%), Positives = 107/206 (51%), Gaps = 17/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQETS 155
           ++YED+ ++V NKPAG+  Q        ++   K+++    QKP        HRLD+  S
Sbjct: 7   IVYEDNHLFVLNKPAGLLTQPSGTAHDSLESQAKAYLKIVYQKPGNVFLEAVHRLDKPVS 66

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VH 214
           GI+V  +T  A   L  S R ++ +KIY++ V  +P ++++ + N+L     I  D+   
Sbjct: 67  GIVVFGKTSKALTRLNASVRAKQTKKIYYAWVDSVPVDEQKTLENFL-----IHNDFQAQ 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV      A  A   ++VI+  +     LE++  TGR HQ+R    H+GCPI GD +Y +
Sbjct: 122 VVSSKHPQAKLAKLTYRVIERKSVG-ALLEIKLETGRYHQIRAQLAHLGCPIRGDIRYGS 180

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
            +   FT    + + LH   +++ HP
Sbjct: 181 QYP--FTP---HAIALHHESLEISHP 201


>gi|297617022|ref|YP_003702181.1| pseudouridine synthase [Syntrophothermus lipocalidus DSM 12680]
 gi|297144859|gb|ADI01616.1| pseudouridine synthase, RluA family [Syntrophothermus lipocalidus
           DSM 12680]
          Length = 305

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 85/318 (26%), Positives = 150/318 (47%), Gaps = 42/318 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV--VRI 67
           VV+E   E  RLDR+       ++   ++ ++  G V V  +  K   RI+ G +  VRI
Sbjct: 6   VVIEGSHEGERLDRFLAETLCDVSRSQVKNLIDEGLVLVGGRPQKPGYRIRKGDIIQVRI 65

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P          +E  ++   + L          ++YED  + V +KP G+ V    G   
Sbjct: 66  PAA--------RETGLVAQEMPLN---------IVYEDRDLVVIDKPQGLVVHPAHG--- 105

Query: 128 HIDGFL--------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           H +G L        K      G+ +P + HRLD++TSG++VVA+   A + L +  + R+
Sbjct: 106 HWEGTLVNALLYRVKDLSGINGELRPGIVHRLDKDTSGLMVVAKNDQAHRDLADQIKARK 165

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I++ Y ++V G+ +     I +  + +S      + VV++       A++H+ V+  + +
Sbjct: 166 IRREYVAVVHGVIRENSGTI-DAPIGRSPSDRKKMAVVREGRP----AVTHYTVLRRY-R 219

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +  +  TGRTHQ+RVH  ++  P+VGD  Y  + +  F    Q    LHA Y+   
Sbjct: 220 DYTLVRARLETGRTHQIRVHFAYIRHPVVGDQVYGPS-RSRFELKGQA---LHACYLAFY 275

Query: 299 HPEGGR-LQITAPLPAHM 315
           HP     L+  +P P ++
Sbjct: 276 HPTTKELLEFDSPFPPYV 293


>gi|261346208|ref|ZP_05973852.1| ribosomal large subunit pseudouridine synthase D [Providencia
           rustigianii DSM 4541]
 gi|282565514|gb|EFB71049.1| ribosomal large subunit pseudouridine synthase D [Providencia
           rustigianii DSM 4541]
          Length = 325

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 89/331 (26%), Positives = 158/331 (47%), Gaps = 49/331 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + I  +I       
Sbjct: 19  RLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKAKEKVLGGEQISIDALIEEDTRWE 78

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV- 137
            +   LD               ++YED  I V NKP G+ V  G+G   + DG + + + 
Sbjct: 79  PQDIPLD---------------VVYEDEDILVINKPRGLVVHPGAG---NPDGTILNALL 120

Query: 138 ---DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--- 189
                    PR  + HRLD++T+G++VVA+T  A  HL ++ + R I + Y ++  G   
Sbjct: 121 YRYPEIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAVAVGRMT 180

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +E I+    K++H+    VH +         A++H+++++ F +    L ++  T
Sbjct: 181 AGGMVEEPISRHPTKRTHMA---VHPM------GKPAVTHYRIMEHF-RAHTRLRLRLET 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLHARYMDLPHPE 301
           GRTHQ+RVH  H+  P++GD  Y       KG      +     ++  LHA  + L HP 
Sbjct: 231 GRTHQIRVHMAHINHPLIGDQLYGGRPRPLKGATEEFFEVMRKFDRQALHATMLRLYHPI 290

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFKYDRNLY 331
            G +++  APLP  MV+  ++L  K D  L+
Sbjct: 291 SGIQMEWHAPLPDDMVELINAL--KADAELH 319


>gi|330502180|ref|YP_004379049.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           mendocina NK-01]
 gi|328916466|gb|AEB57297.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           mendocina NK-01]
          Length = 211

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 71/215 (33%), Positives = 114/215 (53%), Gaps = 15/215 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D+ + V NKP  + SV G +    + D  +    ++   + R+ HRLD ETSGI+V
Sbjct: 8   ILHQDTALLVINKPTLLLSVPGRAD--DNKDCLVTRLQENGYPEARIVHRLDWETSGIIV 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG P+     I   L  +        HVV  +
Sbjct: 66  LARDADSHRELSRQFHDRETEKAYTALCWGQPQADSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKG 278
            +   +A++H++VI+     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HELGKHALTHWRVIE-RCGDWCRVELTPITGRSHQLRVHMLSIGHPLLGDRLYAHEQALA 180

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            F     ++L LHA  + L HP+ G R++   P P
Sbjct: 181 AF-----DRLCLHASMLALTHPQTGERMRFECPAP 210


>gi|289524245|ref|ZP_06441099.1| ribosomal large subunit pseudouridine synthase [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289502901|gb|EFD24065.1| ribosomal large subunit pseudouridine synthase [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 307

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 141/318 (44%), Gaps = 25/318 (7%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ D + +RLDR+ +  Y  +    + + +R G+V V+ ++   + R+  G  V +P   
Sbjct: 7   IDEDYDCVRLDRFLRKKYSEVPLGAIMRAIRKGRVTVNGEKTDPSYRLYRGDEVSVP--- 63

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  ++   L  S+N+      L+ I +  D  + + NKPAG+  Q  S     +  
Sbjct: 64  ------FEDPAKLKPSLNVADKP--LEVIFM--DENVLIINKPAGLLSQPASNEDDSVVN 113

Query: 132 FLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              + ++    G  P   HRLD+  SG++ +A    + + LT  FR RR+ K Y ++V G
Sbjct: 114 RALNLINKTKGGFIPTPAHRLDRNISGVMALALNFRSLRALTAMFRNRRVAKKYLAVVRG 173

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +   E +    L++      ++  V     G   A  +  +          + ++P T
Sbjct: 174 --RLTGEGVIEAPLERDE---RFLKTVVNKGAGKRSATRYMSL--SAGNHASLVALEPIT 226

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           GR+HQLRVH  H+G PIVGD KY  + K     P+ +   L     DL +  G +    A
Sbjct: 227 GRSHQLRVHLSHIGHPIVGDVKYGDSGK-EARRPMLHAYSLEIFGNDLSYLAGKKF--CA 283

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLPA +    +      D
Sbjct: 284 PLPADLAAVINLFDLSLD 301


>gi|293392744|ref|ZP_06637062.1| ribosomal large subunit pseudouridine synthase D [Serratia
           odorifera DSM 4582]
 gi|291424603|gb|EFE97814.1| ribosomal large subunit pseudouridine synthase D [Serratia
           odorifera DSM 4582]
          Length = 325

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 91/332 (27%), Positives = 155/332 (46%), Gaps = 47/332 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V+V+ K   K   ++  G+ V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVQVNGKTTNKPKEKVLGGETVAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        +   LD               ++YEDS I V NKP  + V  G+G   +
Sbjct: 69  AQIEEEARWEPQDIPLD---------------IVYEDSDILVINKPRDLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ ++R I + 
Sbjct: 111 PDGTVLNALLHYYPEIIDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITRE 170

Query: 183 YWSLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G        +E IA    K++H+    VH + +       A++H+++++ F + 
Sbjct: 171 YEAVAIGTMTAGGTVEEPIARHSTKRTHMA---VHPMGKP------AVTHYRIMEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F + ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMSHISHPLVGDPLYGGRPRPPKGASEAFITTLRGFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A  + L HP  G +++  APLP  MV   D+L
Sbjct: 281 ATMLRLYHPISGIQMEWHAPLPQDMVDLIDAL 312


>gi|308172908|ref|YP_003919613.1| RNA pseudouridine synthase [Bacillus amyloliquefaciens DSM 7]
 gi|307605772|emb|CBI42143.1| putative RNA pseudouridine synthase [Bacillus amyloliquefaciens DSM
           7]
 gi|328552548|gb|AEB23040.1| RNA pseudouridine synthase [Bacillus amyloliquefaciens TA208]
 gi|328910948|gb|AEB62544.1| putative RNA pseudouridine synthase [Bacillus amyloliquefaciens
           LL3]
          Length = 302

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 75/253 (29%), Positives = 123/253 (48%), Gaps = 33/253 (13%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLK 134
           L    + T   ++ ++ +L+EDS + + NKPAG+      +G +G     IAYH      
Sbjct: 68  LQEKTDSTVVPEYGEAEILFEDSHMLIANKPAGMPTHPNEEGQTGTLSNLIAYHFQ---- 123

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             ++ +  K R  HRLD++TSG +V A+ R A   L      + +++ Y +   G  K K
Sbjct: 124 --INGEQAKVRHVHRLDRDTSGAVVFAKHRLAHAILDRQLETKTLKRTYIAAAEGKVKPK 181

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRT 252
           K  +       S IG D  H V++    G   A++H+KV       +   +E++  TGRT
Sbjct: 182 KGTV------DSPIGRDRSHSVRRRVSPGGQAAVTHYKVKGYHPGAQLSLVELELETGRT 235

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           HQ+RVH   +G P+ GD  Y        +  + ++  LHA+ + + HP  G  +   AP+
Sbjct: 236 HQIRVHMASIGHPLAGDELYGG------SRALFHRQALHAKKVSVVHPISGEEIVAEAPM 289

Query: 312 P---AHMVKTWDS 321
           P   AH  +T+ S
Sbjct: 290 PADLAHFAETYFS 302


>gi|307566026|ref|ZP_07628484.1| pseudouridine synthase, RluA family [Prevotella amnii CRIS 21A-A]
 gi|307345214|gb|EFN90593.1| pseudouridine synthase, RluA family [Prevotella amnii CRIS 21A-A]
          Length = 297

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 72/232 (31%), Positives = 110/232 (47%), Gaps = 17/232 (7%)

Query: 87  SVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           S++ +K +D  KS    L+YED  + V  K  GI        + ++   L  +     Q 
Sbjct: 69  SISKSKKNDQFKSRYVKLVYEDKYLVVIEKNVGILSMAAGHSSLNVKSVLDDYFQKSKQH 128

Query: 144 PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            R  + HRLD++TSG++V A+     Q L   +      + Y +++ G    ++  +ANW
Sbjct: 129 CRAHVVHRLDRDTSGLMVYAKDMQTEQLLEHDWHNIVYDRRYVAVLSGELMQQQGTVANW 188

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L         YV      + G  YA++HF  ID  A  +  +E +  TGR +Q+RVHA  
Sbjct: 189 LKDNK----SYVTYSSAVDNGGKYAVTHFFTIDTTAS-YSLVEFKLETGRKNQIRVHAAD 243

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           MG P+ GD KY     GN   PI  +L LHA  +   HP    R++   P+P
Sbjct: 244 MGYPVCGDTKY-----GNGDDPI-GRLCLHAFMLCFYHPVTHERMEFETPIP 289


>gi|188532876|ref|YP_001906673.1| 23S rRNA/tRNA pseudouridine synthase A [Erwinia tasmaniensis
           Et1/99]
 gi|188027918|emb|CAO95775.1| Ribosomal large subunit pseudouridine synthase A [Erwinia
           tasmaniensis Et1/99]
          Length = 217

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 73/206 (35%), Positives = 109/206 (52%), Gaps = 16/206 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G   +A + D  + + V          HRLD  TSG++V
Sbjct: 14  VLYQDEHIIVVNKPSGLLSVPGR--LAEYKDSVM-TRVQRDYPAAESVHRLDMATSGVMV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  QK Y + VWG PK     +   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPQKTYVARVWGHPKPAIGLVDLPLI------CDWPNRPKQK 124

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A + ++V+D  +     + ++P TGR+HQLRVH L +G PI+GD+ Y A+ +
Sbjct: 125 VCFDSGKSAQTEYQVLDYASDNSARVLLKPITGRSHQLRVHMLALGHPILGDNFY-AHDE 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
               +P   +L LHA  + + HP+ G
Sbjct: 184 ARAMAP---RLQLHAESLCISHPQYG 206


>gi|189462984|ref|ZP_03011769.1| hypothetical protein BACCOP_03686 [Bacteroides coprocola DSM 17136]
 gi|189430266|gb|EDU99250.1| hypothetical protein BACCOP_03686 [Bacteroides coprocola DSM 17136]
          Length = 355

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 90/337 (26%), Positives = 156/337 (46%), Gaps = 49/337 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +Q    +G V  + K VK + +++   V+ +  
Sbjct: 31  VVVDKGQTPVRIDKYLFERIVNASRNRIQTAADAGFVMANGKPVKSSYKVKPLDVLTV-- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E  I+   + L          ++YED+ + V NKPAG+ V  G G     
Sbjct: 89  ---MMDRPRYENDIIPEDIPLD---------IVYEDNDLMVINKPAGLVVHPGCGNYHGT 136

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+   + S+ D    +  L HR+D++TSG+LVVA+T  A   L   F  +  +
Sbjct: 137 LVNAIAWHLRD-VPSY-DPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTSLGMQFYNKTTK 194

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFAQK 239
           + Y +LVWGI +  +  I   + +      D + + V  +     +A++H++V++     
Sbjct: 195 REYNALVWGIVEEDEGTITGNIGRNPK---DRMQMAVMSDPTQGKHAVTHYQVLERLGYV 251

Query: 240 F---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PI 284
               C LE    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S           I
Sbjct: 252 TLVKCVLE----TGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDI 307

Query: 285 QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             +  LHA+ +   HP  G+ +  T+ LP  M +  D
Sbjct: 308 CPRQALHAKTLGFVHPRTGKEMFFTSELPEDMTRLLD 344


>gi|139473995|ref|YP_001128711.1| RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo]
 gi|134272242|emb|CAM30494.1| putative RNA pseudouridylate synthase [Streptococcus pyogenes str.
           Manfredo]
          Length = 296

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 71/219 (32%), Positives = 112/219 (51%), Gaps = 29/219 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++YED  + + NKP G+ V   +G         + YHI    K      G  +P + HR+
Sbjct: 76  IIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHI----KDLSSINGVVRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+T AA Q LTE  + ++  + Y ++V G   N +  I      ++ IG 
Sbjct: 132 DKDTSGLLMVAKTDAAHQVLTEELKAKKSLRKYLAIVHGNLPNDRGMI------EAPIGR 185

Query: 211 DYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ G
Sbjct: 186 SEKDRKKQAVTAKGKE-AVTRFTVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAG 243

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           D  Y     G   +   +  +LHA+ + L HP  G+  I
Sbjct: 244 DPLY-----GPRKTLSGHGQFLHAKTLGLTHPMTGKEMI 277


>gi|254670508|emb|CBA06264.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis alpha153]
          Length = 373

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 138/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 58  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 105

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 106 --TVRPSEENLAFVPEPMALDIIYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 162

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P + 
Sbjct: 163 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDG 222

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 223 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 273

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 274 HQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 333

Query: 306 QITAPLP 312
              AP+P
Sbjct: 334 SFEAPIP 340


>gi|302874641|ref|YP_003843274.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
 gi|307690747|ref|ZP_07633193.1| pseudouridine synthase, RluA family protein [Clostridium
           cellulovorans 743B]
 gi|302577498|gb|ADL51510.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
          Length = 313

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 90/327 (27%), Positives = 152/327 (46%), Gaps = 42/327 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI--QSGQVV 65
           + +++ N+  + R+D++        +   +Q I+    V V+ K  K N ++  Q    V
Sbjct: 3   EIIIIFNELSSKRIDKFLAEQLDGYSRSFIQNIIDGNNVLVNGKPCKSNLKLKMQDEITV 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            IP          +E  ++  +++L          +LYED  + V NKP G+ V   SG+
Sbjct: 63  IIPEP--------QEMNVVPENISLN---------ILYEDEDLIVINKPQGMVVHPASGV 105

Query: 126 AYH--IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             +  ++  L    D  G     +P + HR+D++TSG++VVA+   +   L    +   +
Sbjct: 106 YNNTLVNALLYHCKDLSGINGKLRPGIVHRIDKDTSGVIVVAKNDKSHNFLAAQLKEHSM 165

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +LV GI K ++E   N  L +       + VV    KG   AI+H+KVI+ F + 
Sbjct: 166 KREYIALVEGIIK-EEEGTINQPLARDPKERIKIAVV----KGGREAITHYKVIERFKEN 220

Query: 240 F---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
               C LE    TGRTHQ+RVH  +   P+VGD  Y    K  F+    N   LHA+ + 
Sbjct: 221 TLVRCILE----TGRTHQIRVHMNYKKHPLVGDPVYGYK-KQRFSL---NGQLLHAQKLG 272

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP   + ++ +  +P   +K    L
Sbjct: 273 FIHPTTMKYMEFSTNIPQEFLKVLKVL 299


>gi|220933994|ref|YP_002512893.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. HL-EbGR7]
 gi|219995304|gb|ACL71906.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. HL-EbGR7]
          Length = 315

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 91/316 (28%), Positives = 136/316 (43%), Gaps = 36/316 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD      +P  +   +Q+ + +G VRVD +  +  +    G  V    VI A      
Sbjct: 22  RLDAALARMFPSYSRSRIQQWMEAGWVRVDGETPRRRDTALGGARV----VIEARVEAAS 77

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           E +  D  + +           +YED  + V NKP G+     +G      ++  L    
Sbjct: 78  EDRAEDIPLEV-----------IYEDDSLLVINKPPGLVTHPAAGNREGTLVNALLHHAP 126

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D     PR  + HRLD+ETSG+LVVART  A   L    + R + + Y +LV G+     
Sbjct: 127 DLAAL-PRAGIVHRLDKETSGLLVVARTLEAHTDLVRQLQARTVGREYLALVQGVIVAGG 185

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
              A   + +  +    + VV     G   AI+H++V +        L ++  TGRTHQ+
Sbjct: 186 TVDAP--IGRHPVDRKRMAVV----AGGKEAITHYRV-EARLPHHTLLRVRLETGRTHQI 238

Query: 256 RVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHARYMDLPHP-EGGRLQ 306
           RVH  H+  PIVGD  Y    K     +   Q  L       LHA  ++L HP  G  + 
Sbjct: 239 RVHMAHVHHPIVGDPVYGGRLKVPAGLSEADQAVLRGFRRQALHAARLELVHPVTGEEMG 298

Query: 307 ITAPLPAHMVKTWDSL 322
             AP+PA      ++L
Sbjct: 299 WEAPMPADFAALLEAL 314


>gi|119390059|pdb|2I82|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
           Sequence Readout Through Protein-Induced Rna Structure
 gi|119390060|pdb|2I82|B Chain B, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
           Sequence Readout Through Protein-Induced Rna Structure
 gi|119390061|pdb|2I82|C Chain C, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
           Sequence Readout Through Protein-Induced Rna Structure
 gi|119390062|pdb|2I82|D Chain D, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
           Sequence Readout Through Protein-Induced Rna Structure
          Length = 217

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/208 (34%), Positives = 111/208 (53%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 13  VILYQDDHIXVVNKPSGLLSVPGR--LEEHKDS-VXTRIQRDYPQAESVHRLDXATSGVI 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 70  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 123

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 124 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHXLALGHPILGD-RFYAS 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    +P   +L LHA  + + HP  G
Sbjct: 182 PEARAXAP---RLLLHAEXLTITHPAYG 206


>gi|262038157|ref|ZP_06011554.1| ribosomal large subunit pseudouridine synthase C [Leptotrichia
           goodfellowii F0264]
 gi|261747805|gb|EEY35247.1| ribosomal large subunit pseudouridine synthase C [Leptotrichia
           goodfellowii F0264]
          Length = 297

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/295 (25%), Positives = 143/295 (48%), Gaps = 41/295 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V+++ E MRLDR+ K  + + +   + + LR G V+++ K+ K N R+  G  + +  +
Sbjct: 7   IVDSESEGMRLDRYLKKTFKNESLSKIFQALRKGDVKINGKKSKENYRLCLGDKITVKYL 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDF----LKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            +      KE+K         K  DF     K+++++E++  ++ NKP  + +  G+G  
Sbjct: 67  YSE-----KEEKT-------KKTFDFDEKKYKNMIIFENNDFFIINKPGNVPMHKGTGHK 114

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +    K   ++        +RLD ETSG+++  +     ++++E  R   +QK Y + 
Sbjct: 115 HGLSEIFKKIYEN--DNINFANRLDYETSGLVIGCKNLKFLRYISEKIRNNEVQKKYVAA 172

Query: 187 VWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DC 235
           V G  +  K  I N+L + ++ +   YV     ++K A  +I+ +K I          + 
Sbjct: 173 VDGEIEKDKFIIENYLKITENGVIQSYV-----SDKDAKRSITKYKKINNRFFDKILNNI 227

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
             +K   L++   TGR HQ+RV    +G P++GD KY            +NKLYL
Sbjct: 228 KKEKVTLLDIDLVTGRKHQIRVQLSSIGNPVIGDRKYGK-------KKEENKLYL 275


>gi|226941139|ref|YP_002796213.1| RluD [Laribacter hongkongensis HLHK9]
 gi|226716066|gb|ACO75204.1| RluD [Laribacter hongkongensis HLHK9]
          Length = 349

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 89/300 (29%), Positives = 134/300 (44%), Gaps = 47/300 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L + ++ G VRVD            G  V +P     L   ++
Sbjct: 30  RLDAALAALMPDQSRSRLTQWIKDGHVRVD------------GSTVTVPRSKTVLGQQVE 77

Query: 80  --EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
             EQ  LD    +    + ++  ++YED +I V NKPAG+    G+G      ++G L  
Sbjct: 78  VDEQLSLD---EMAFAPEDIEIPVIYEDRQILVVNKPAGLVTHPGNGNWSGTLLNGLLYR 134

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            V      PR  + HRLD++TSG++VVA+T AA   L    + R +++ Y ++  G    
Sbjct: 135 -VPELAHVPRAGIVHRLDKDTSGLMVVAKTVAAQLDLIRQLQARTVKRHYRAIACG---- 189

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
               +A  +     IG D    VK      G   AI+H + ++ F +    +E +  TGR
Sbjct: 190 ---NVAGDITIDKAIGRDPKTRVKMAVVAFGGKPAITHVRPLEMF-EHHTLVECRLETGR 245

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----------YLHARYMDLPHPE 301
           THQ+RVH   +GCP+ GD  Y     GN   P   ++           LHA  + L HPE
Sbjct: 246 THQIRVHMASIGCPLAGDPLY-----GNPRLPASPEVREAINDFGRQALHAAKLALIHPE 300


>gi|288928581|ref|ZP_06422428.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella sp. oral taxon 317 str. F0108]
 gi|288331415|gb|EFC69999.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella sp. oral taxon 317 str. F0108]
          Length = 221

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 104/219 (47%), Gaps = 14/219 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
           I +YED+ I + +K +G  VQ        +   +KS++  K  KP      + HRLD+  
Sbjct: 2   IPVYEDNHIIIVSKHSGEIVQSDKTGDVPLVDIVKSYLKEKYAKPGNVFLGVVHRLDRPV 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G++  A+T  A   +   FR   ++K YW++V   P+N+   + +WL +       Y H
Sbjct: 62  WGLVAFAKTSKALSRMNALFRTGDVEKTYWAIVQSPPENETGELVHWLTRNEKQNKSYAH 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                  GA  AI  +KVI   ++ +  LE+Q  TGR HQ+R     MGCPI GD KY  
Sbjct: 122 --NHEVAGAKKAILSYKVIG-RSENYTLLEVQLMTGRHHQIRCQLAAMGCPIKGDLKY-- 176

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G   S     + L +R +   HP     + + APLP
Sbjct: 177 ---GARRSNADGSISLLSRKISFVHPVSKETICVEAPLP 212


>gi|237715324|ref|ZP_04545805.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D1]
 gi|262405165|ref|ZP_06081715.1| conserved hypothetical protein [Bacteroides sp. 2_1_22]
 gi|294643535|ref|ZP_06721341.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|294807042|ref|ZP_06765861.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|298482426|ref|ZP_07000612.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D22]
 gi|229444633|gb|EEO50424.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D1]
 gi|262356040|gb|EEZ05130.1| conserved hypothetical protein [Bacteroides sp. 2_1_22]
 gi|292641110|gb|EFF59322.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|294445741|gb|EFG14389.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|295088097|emb|CBK69620.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           xylanisolvens XB1A]
 gi|298271405|gb|EFI12980.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D22]
          Length = 357

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 86/333 (25%), Positives = 152/333 (45%), Gaps = 47/333 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEGGFVMANGKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +I+   + LT         ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYENEIIPEDIPLT---------IVYEDPYVMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +A+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 138 LVNALAWH----MKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKT 193

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFA 237
            ++ Y +LVWG+ +  +  I   + +      D + + V  +     +A++H++V++   
Sbjct: 194 TKRRYRALVWGVVEQDEGTIVGNIARNPK---DRMQMAVMSDPTVGKHAVTHYRVLERLG 250

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN--------- 286
                +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +          
Sbjct: 251 Y-VTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTC 309

Query: 287 -KLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            +  LHA  +   HP  G  +  T+ LP  M +
Sbjct: 310 PRQALHAMTLGFVHPVTGEEMYFTSELPDDMTR 342


>gi|62184670|ref|YP_219455.1| putative pseudouridine synthase [Chlamydophila abortus S26/3]
 gi|62147737|emb|CAH63481.1| putative pseudouridine synthase [Chlamydophila abortus S26/3]
          Length = 325

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 85/316 (26%), Positives = 147/316 (46%), Gaps = 41/316 (12%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           N+    RLD++  +  P  +    Q+        +  +RV  N +IQ+    ++ P  + 
Sbjct: 12  NETNRDRLDKFLVSQNPKYSRAFYQQ-------HIVDQRVTINEQIQTKVSTQLVPG-DT 63

Query: 74  LNHIIKEQK----ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
           ++  I+E++    +L  ++ L K         +YED  I V NKP  + V    G     
Sbjct: 64  VSITIEEKEEPSELLPEAIPLEK---------IYEDEMILVINKPRDMVVHPAPGHTRGT 114

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + + I   LK     +  +P + HRLD++TSG+L+ A+TR A    +E F  ++++
Sbjct: 115 VVHALLHEIGERLKQEFPEEPWRPGIIHRLDKDTSGLLITAKTRQAKMIYSELFATKQLK 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++  G P      + +  L + H     + V    ++    AI+  +V+  +  KF
Sbjct: 175 KSYLAICVGKP---SASVIHTKLARHHTKRKEMAVSSTGKE----AITRCEVL-AYNGKF 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + + P TGRTHQLRVH  H+  PI+GD  Y +    +      +K  LHA  ++  HP
Sbjct: 227 SLVLLHPETGRTHQLRVHMKHLSTPILGDPVYGSASANSCYG--LDKQQLHAYSVNFIHP 284

Query: 301 EGGR-LQITAPLPAHM 315
           +  + L +T  LP  M
Sbjct: 285 QTHKHLNLTTELPRDM 300


>gi|319789350|ref|YP_004150983.1| pseudouridine synthase, RluA family [Thermovibrio ammonificans
           HB-1]
 gi|317113852|gb|ADU96342.1| pseudouridine synthase, RluA family [Thermovibrio ammonificans
           HB-1]
          Length = 314

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/232 (31%), Positives = 116/232 (50%), Gaps = 30/232 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQET 154
           ++YED  + V NKPAG+ V    G      ++  L    D  G     +P + HRLD++T
Sbjct: 76  VIYEDQDVIVINKPAGMVVHPAPGHYSGTLVNALLHHCKDLGGIGGALRPGIVHRLDKDT 135

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++VVA+   A Q L E F+ R + + Y +L++GIPK + + I         IG D   
Sbjct: 136 AGLIVVAKNDLAQQSLIEQFKNRSVGRFYRALIYGIPKREHDRIV------LPIGRDKFD 189

Query: 215 VVK--QNEKGANYAISHFKVIDCF-----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             K   N      AI+++ VI+ F     A+  C LE    TGRTHQ+RVH  ++G P++
Sbjct: 190 RKKFSPNTTSPKEAITNYWVIEKFPEHNVAEIKCKLE----TGRTHQIRVHMSNLGHPLL 245

Query: 268 GDHKYC---ANFKGNFTSPIQNKLYLH---ARYMDLPHPEGG-RLQITAPLP 312
           GD  Y    +  +      + +++ +H   A Y+   HP  G R++    LP
Sbjct: 246 GDRTYGYKPSRIEDEKLRRLIDEMGMHALCAYYLAFDHPRTGKRMEFEVELP 297


>gi|237719675|ref|ZP_04550156.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_2_4]
 gi|229450944|gb|EEO56735.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_2_4]
          Length = 357

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 86/333 (25%), Positives = 153/333 (45%), Gaps = 47/333 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +I+  ++ LT         ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYENEIIPENIPLT---------IVYEDPYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +A+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 138 LVNALAWH----MKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKT 193

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFA 237
            ++ Y +LVWG+ +  +  I   + +      D + + V  +     +A++H++V++   
Sbjct: 194 TKRRYRALVWGVVEQDEGTIVGNIARNPK---DRMQMAVMSDPTVGKHAVTHYRVLERLG 250

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN--------- 286
                +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +          
Sbjct: 251 Y-VTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTC 309

Query: 287 -KLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            +  LHA  +   HP  G  +  T+ LP  M +
Sbjct: 310 PRQALHAMTLGFVHPVTGEEMYFTSELPDDMTR 342


>gi|254491724|ref|ZP_05104903.1| pseudouridine synthase, RluA family [Methylophaga thiooxidans
           DMS010]
 gi|224463202|gb|EEF79472.1| pseudouridine synthase, RluA family [Methylophaga thiooxydans
           DMS010]
          Length = 320

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 87/325 (26%), Positives = 145/325 (44%), Gaps = 49/325 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ ++   MRLD+     +P  +   L K +++G V VD+  ++  + +  G+ V     
Sbjct: 10  IIPDELGGMRLDQALAKLFPDFSRGQLTKWIKAGDVTVDEAILRPRDSVIGGENV----- 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILL---YEDSKIYVFNKPAGISVQGGSGIAY 127
                       I+D+ +     S   + I L   +ED  + + NKPAG+ V  G+G   
Sbjct: 65  ------------IIDTELQSQDESWSAEPIALDIVHEDDDVIIINKPAGMVVHPGAG--N 110

Query: 128 HIDGFLKSWVDSKGQK---PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           H    + + +    Q    PR  + HRLD+ T+G+L+VA+T  A   L    + R +Q+ 
Sbjct: 111 HQGTLVNALLAHAPQLANIPRAGIVHRLDKATTGLLMVAKTLQAHNSLVSQLQARTVQRE 170

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-- 240
           Y ++  G+         +  + + HI    + + +  +     AI+H++V   F      
Sbjct: 171 YQAIAIGV--MTAGGTVDEPIGRHHIDRKRMAISQTGKP----AITHYRVEQRFRAHTHI 224

Query: 241 -CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLH 291
            C LE    TGRTHQ+RVH  H+  P++GD  Y   FK       N    +Q   +  LH
Sbjct: 225 RCKLE----TGRTHQIRVHMAHIRHPLLGDQVYAGRFKMAKGMSENCREAVQGFRRQALH 280

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHM 315
           A  +   HP  G  +   APLP  M
Sbjct: 281 AGLLGFKHPASGEDVSWQAPLPEDM 305


>gi|167764292|ref|ZP_02436419.1| hypothetical protein BACSTE_02677 [Bacteroides stercoris ATCC
           43183]
 gi|167698408|gb|EDS14987.1| hypothetical protein BACSTE_02677 [Bacteroides stercoris ATCC
           43183]
          Length = 356

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 90/346 (26%), Positives = 157/346 (45%), Gaps = 47/346 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E +R+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQEMVRVDKYLFDRLTNASRNRIQKAADAGFVMANGKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYENEVIPEDIPLD---------IVYEDKYLMVVNKPAGLVVHPGHGNYRGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 138 LVNAIAWH----MKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKT 193

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LVWG     +  I   + +      D + +    +    +A++H++V++    
Sbjct: 194 TKRRYRALVWGNVGQDEGTIVGNVGRNPK---DRMQMTVLPDDQGKHAVTHYRVLERLGY 250

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKG----------NFTSPIQN 286
               +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG          N    I  
Sbjct: 251 -VTLVECVLETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFDICP 309

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS-LGFKYDRNL 330
           +  LHA  +   HP  G  +  T+ LP  M +  D   G+  +R L
Sbjct: 310 RQALHAMTLGFVHPVTGEEMYFTSELPDDMNRLLDKWRGYISNREL 355


>gi|187731746|ref|YP_001878869.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella boydii CDC
           3083-94]
 gi|187428738|gb|ACD08012.1| pseudouridine synthase, RluA family [Shigella boydii CDC 3083-94]
          Length = 219

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPFPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETGKP-AQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|281421312|ref|ZP_06252311.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella copri DSM 18205]
 gi|281404847|gb|EFB35527.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella copri DSM 18205]
          Length = 222

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 108/220 (49%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + +K +G  VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHIIIVSKRSGEIVQGDKTGDEPLSETVKQYIKEKYHKPGNVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYV 213
           G++V A+T  A   L   FR   + K YW++V  +PK  +  + +W+++  K +    Y 
Sbjct: 63  GLVVFAKTSKALSRLNNMFRDGEVHKTYWAIVKNMPKEPEATLTHWIVRNEKQNKSYAYD 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H VK ++K    AI  +KVI      +  LE+   TGR HQ+R     MGCPI GD KY 
Sbjct: 123 HEVKNSKK----AILKYKVIG-HTDHYTLLEVNLMTGRHHQIRCQLAKMGCPIKGDLKY- 176

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLP 312
               G+  S     + L +  ++  HP      +  APLP
Sbjct: 177 ----GSPRSNADGSISLLSHRVEFVHPVSKETIVAEAPLP 212


>gi|149377766|ref|ZP_01895499.1| Pseudouridylate synthase, 23S RNA-specific [Marinobacter algicola
           DG893]
 gi|149357938|gb|EDM46427.1| Pseudouridylate synthase, 23S RNA-specific [Marinobacter algicola
           DG893]
          Length = 325

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 93/351 (26%), Positives = 155/351 (44%), Gaps = 62/351 (17%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  +  + RLD+      P  +   LQ  ++SG + V+ K  K  +++  G  + +    
Sbjct: 13  VPPEHSDRRLDQAAAELMPEHSRSRLQGWIKSGALTVNGKSCKPRDKVMLGDRLELD--- 69

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                        +    ++  ++ +   ++YED  + V NKPAG+ V   +G   H DG
Sbjct: 70  ------------AEPEAQVSWEAESIDLDIVYEDEHLLVINKPAGLVVHPAAG---HADG 114

Query: 132 FLKSWVDSKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L + + +   +    PR  + HRLD++TSGI+VVAR+  A   L +  + R + + Y +
Sbjct: 115 TLVNALLNHAPEVENLPRAGIVHRLDKDTSGIMVVARSLIAHTSLVDQLQTRTMGREYEA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVIDCFAQKF 240
           +V G            L   S +        ++ +K A       A++H+++++ FA   
Sbjct: 175 IVVGT-----------LTGGSTVDAPIGRHPRERKKMAVVPTGKPAVTHYRLVERFAAHT 223

Query: 241 ---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------Y 289
              C LE    +GRTHQ+RVH  H+  P+VGD +Y    +     T  ++  L       
Sbjct: 224 HVRCKLE----SGRTHQIRVHMAHVKHPLVGDPQYGGRLRLPKGTTDELREVLASFQRQA 279

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQD 339
           LHAR + L HP+ G  L    PLP       D  G       ++K L S D
Sbjct: 280 LHARQLTLEHPQTGEILTWEVPLPD------DIEGLLAALRKHVKELESHD 324


>gi|261378502|ref|ZP_05983075.1| tRNA pseudouridine synthase C [Neisseria cinerea ATCC 14685]
 gi|269145046|gb|EEZ71464.1| tRNA pseudouridine synthase C [Neisseria cinerea ATCC 14685]
          Length = 234

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/215 (32%), Positives = 106/215 (49%), Gaps = 15/215 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y D +    NKPAGI V      +      +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IIYRDGRTVAVNKPAGILVHRSWLDSRETVFAMQTLRDQIGQHVYPVHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLK--KSHIGGDYVHVVK 217
           A    AA+ LT+ F  + I+K YW++V G +P +    I ++ LK     I   +   V 
Sbjct: 64  ALDTEAARLLTQQFEQKNIRKTYWAIVRGHLPSDG---IIDYPLKYCPDKIAEAHTESVI 120

Query: 218 QNEKGANYAISHFKV-----IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           Q+ + A   I+  ++     +     ++ W E+ PHTGR HQLR H  H+  PIVGD  Y
Sbjct: 121 QDAQTACRCIARTELPFQSALRYPTSRYSWAELTPHTGRKHQLRRHMKHIFHPIVGDTNY 180

Query: 273 CANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGR 304
             + + N          +L LHAR +    P+GG+
Sbjct: 181 -GDLRQNHAVAAHLGTQRLMLHARSLTFRSPDGGQ 214


>gi|160885528|ref|ZP_02066531.1| hypothetical protein BACOVA_03528 [Bacteroides ovatus ATCC 8483]
 gi|260172152|ref|ZP_05758564.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D2]
 gi|293371714|ref|ZP_06618125.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|299147380|ref|ZP_07040445.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_23]
 gi|315920461|ref|ZP_07916701.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D2]
 gi|156109150|gb|EDO10895.1| hypothetical protein BACOVA_03528 [Bacteroides ovatus ATCC 8483]
 gi|292633411|gb|EFF51981.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|298514658|gb|EFI38542.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_23]
 gi|313694336|gb|EFS31171.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D2]
          Length = 357

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 86/333 (25%), Positives = 153/333 (45%), Gaps = 47/333 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +I+  ++ LT         ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYENEIIPENIPLT---------IVYEDPYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +A+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 138 LVNALAWH----MKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKT 193

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFA 237
            ++ Y +LVWG+ +  +  I   + +      D + + V  +     +A++H++V++   
Sbjct: 194 TKRKYRALVWGVMEQDEGTIVGNIARNPR---DRMQMAVMSDPTVGKHAVTHYRVLERLG 250

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN--------- 286
                +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +          
Sbjct: 251 Y-VTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTC 309

Query: 287 -KLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            +  LHA  +   HP  G  +  T+ LP  M +
Sbjct: 310 PRQALHAMTLGFVHPVTGEEMYFTSELPDDMTR 342


>gi|228470977|ref|ZP_04055822.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas uenonis 60-3]
 gi|228307374|gb|EEK16388.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas uenonis 60-3]
          Length = 228

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/221 (31%), Positives = 108/221 (48%), Gaps = 20/221 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ + + NKPAG+ VQG S     +   ++ ++  K  KP      +THR+D+ TS
Sbjct: 6   ILYEDNHLLIVNKPAGMLVQGDSTGDTPLSELVERYLIDKYDKPGRAFVGVTHRIDRPTS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++ A+T  A   L   F+ R I K+Y ++V G    K     N L +       YV V
Sbjct: 66  GAVLFAKTSKALARLNAMFQRREIHKVYHAVVCGAFPQKAGEAKNLLYRNRKQNKSYV-V 124

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            + + +     +++ ++      ++  L +  HTGR HQ+R    HMG PI GD KY A 
Sbjct: 125 TEPHAEAKRAWLTYERL--SVGDRYSLLAVTLHTGRHHQIRTQLSHMGYPIKGDLKYGA- 181

Query: 276 FKGNFTSPIQNK---LYLHARYMDLPHP-EGGRLQITAPLP 312
                  P  NK   + LHAR +   HP     +++ AP P
Sbjct: 182 -------PRSNKDGGISLHARILSFEHPVTHEHVEVVAPYP 215


>gi|270292781|ref|ZP_06198992.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M143]
 gi|270278760|gb|EFA24606.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M143]
          Length = 298

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/218 (31%), Positives = 113/218 (51%), Gaps = 18/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           +LYED    V NKP GI+       +  I  F+K +   +G   Q+  +  RLD++TSG+
Sbjct: 78  ILYEDDHFLVLNKPYGIASIPSVNHSNTIANFIKGYYVKRGYENQQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV   G+ + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQRKSIEKRYFALVKGAGVLEPEGEIIAPIARDVDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  KG  YA + +KV+  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVAKGGKYAHTSYKVVASYGN-IHLVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             G+    IQ +  LH   +   HP  GR L++ +PLP
Sbjct: 249 --GSLEDGIQRQA-LHCHSLSFYHPFLGRQLELESPLP 283


>gi|262277120|ref|ZP_06054913.1| ribosomal large subunit pseudouridine synthase C [alpha
           proteobacterium HIMB114]
 gi|262224223|gb|EEY74682.1| ribosomal large subunit pseudouridine synthase C [alpha
           proteobacterium HIMB114]
          Length = 288

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 78/263 (29%), Positives = 132/263 (50%), Gaps = 27/263 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V+  D E  R+DR+ K  +P+I     +K LR   + V+ K+VK   +++   +V I   
Sbjct: 9   VINKDFEGSRVDRFLKKQFPNIPQSLFEKNLRKKNITVNNKKVKNLFKLEINDIVNIFTE 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +   N I K+++I     N+  +++ LK   ++E     V NKP G + Q GS +   + 
Sbjct: 69  LKIENKINKKKQIF----NINDYNE-LKKNFVFECEDYCVLNKPYGYASQDGSKVKLSVI 123

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG- 189
             L    +S  +   + HRLD++TSG++++A+ R  A+  +E F+ R ++K Y  ++ G 
Sbjct: 124 DIL----NSTKKNYYIVHRLDKDTSGLMLLAKNRFYAKKFSEMFKSREVKKKYLVIINGK 179

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I KNK E  +     K  + G  +            +  +F+VI      F +LE+   T
Sbjct: 180 IKKNKGEIHS-----KEKVNGKEIE-----------SKLYFEVISK-KNNFSYLEIDLIT 222

Query: 250 GRTHQLRVHALHMGCPIVGDHKY 272
           GR HQ+R     +G P+VGD KY
Sbjct: 223 GRKHQIRKQFSDIGHPVVGDLKY 245


>gi|308069860|ref|YP_003871465.1| RNA pseudouridine synthase (RNA-uridine isomerase) [Paenibacillus
           polymyxa E681]
 gi|305859139|gb|ADM70927.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Paenibacillus polymyxa E681]
          Length = 334

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 84/318 (26%), Positives = 145/318 (45%), Gaps = 40/318 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIPPVINAL 74
           +  +R+D++       ++   +Q  + +G+V V+   +K N ++  G ++V   P   ++
Sbjct: 43  DAKIRIDKYIAEEMKEVSRSQIQMWIGNGRVLVNGTAIKANYKLAEGDRIVLSVPEPESV 102

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           + I+ E   LD               ++YEDS + V NK  G+ V    G   H  G L 
Sbjct: 103 D-IVPENIPLD---------------VVYEDSDVIVINKQRGLVVHPAPG---HSSGTLV 143

Query: 135 SWV-----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + +     D  G     +P + HR+D++TSG+L+ A+   A   L    +   + + Y +
Sbjct: 144 NALMYHCHDLSGINGELRPGIVHRIDKDTSGLLMAAKNDQAHASLAAQLKDHSVTRKYIA 203

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   + +  +   + + S   GD   +    E+ + +A++HF VI+     +  LE+
Sbjct: 204 LVHGHLSHDQGTVDAPIGRDS---GDR-KLFTVTERNSKHAVTHFLVIERLGD-YTLLEL 258

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH   +G P+VGD  Y     G           LHA  +   HP  G  
Sbjct: 259 QLETGRTHQIRVHMKFIGHPLVGDPMY-----GRSKGVRMEGQALHAAVLGFKHPSTGEY 313

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++ + P+P  M     SL
Sbjct: 314 MEFSRPIPPDMEDVLASL 331


>gi|261377888|ref|ZP_05982461.1| ribosomal large subunit pseudouridine synthase D [Neisseria cinerea
           ATCC 14685]
 gi|269145743|gb|EEZ72161.1| ribosomal large subunit pseudouridine synthase D [Neisseria cinerea
           ATCC 14685]
          Length = 374

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 140/310 (45%), Gaps = 38/310 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   +R G V V+ K  +  +++  G+ +R+            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKPSQPKDKMIGGEQIRV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWSGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLQAQNSLVQQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C+         +  +  LHA  +   +P+ G  +
Sbjct: 256 HQIRVHMREANHPLAADPVYGNLRHPCSESAKEAVKSLGARQALHAYRLSFVYPKTGETV 315

Query: 306 QITAPLPAHM 315
              AP+P  M
Sbjct: 316 SFEAPIPDDM 325


>gi|253702050|ref|YP_003023239.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251776900|gb|ACT19481.1| pseudouridine synthase, RluA family [Geobacter sp. M21]
          Length = 319

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 113/233 (48%), Gaps = 24/233 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQET 154
           +LYED ++ V NK AG+ V  G+G      ++  L    D  G     +P + HR+D++T
Sbjct: 82  VLYEDGELVVVNKGAGMVVHPGAGNPEGTLVNALLAHCKDLSGIGGELRPGIVHRIDKDT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG LVVA++  A   L E F+   I+++Y +LV+G PK  K  I      +S IG     
Sbjct: 142 SGTLVVAKSDRAHNALAEQFKEHTIKRVYLALVYGSPKEDKGRI------ESSIGRHPTD 195

Query: 215 VVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             K + K      A++H++V+  +      + ++  TGRTHQ+RVH    G P++ D  Y
Sbjct: 196 RKKMSAKARHGKQAVTHWRVVARYP-GITLIRLRLETGRTHQIRVHMSEAGHPLLADEVY 254

Query: 273 CANFK-GNFTSPIQNKL-------YLHARYMDLPHPEGGR-LQITAPLPAHMV 316
               +      P+  ++        LHA+ +   HP  G+ L+    LP  M 
Sbjct: 255 GGTGRLSGVQDPVLKQMIKSMGRQALHAKTLGFLHPVSGKYLEFDTELPPDMA 307


>gi|325298577|ref|YP_004258494.1| pseudouridine synthase, RluA family [Bacteroides salanitronis DSM
           18170]
 gi|324318130|gb|ADY36021.1| pseudouridine synthase, RluA family [Bacteroides salanitronis DSM
           18170]
          Length = 360

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 89/339 (26%), Positives = 153/339 (45%), Gaps = 52/339 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++      + +   +Q    +G V  + K VK + +++   V+ +  
Sbjct: 35  VTVDKGQAPVRIDKYLFERIVNASRNRIQTAADNGYVMANGKPVKSSYKVKPLDVLTV-- 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E  I+   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 93  ---MMDRPRYENDIIPEDIPLD---------IVYEDDDLMVVNKPAGLVVHPGCGNYHGT 140

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+        D    +  L HR+D++TSG+LV+A+T  A  HL   F  +  +
Sbjct: 141 LVNAIAWHLRNV--PTYDPNDPQVGLVHRIDKDTSGLLVIAKTPDAKTHLGMQFYNKTTK 198

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFAQK 239
           + Y +LVWGI    +  I   + +      D + + V  +     +A++H++V++     
Sbjct: 199 REYNALVWGIIDEDEGTIEGNIGRNPK---DRMQMAVMSDPTQGKHAVTHYQVLERLGYV 255

Query: 240 F---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PI 284
               C LE    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S           I
Sbjct: 256 TLVKCVLE----TGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFAI 311

Query: 285 QNKLYLHARYMDLPHPEGGR-LQITAPLP---AHMVKTW 319
             +  LHA+ +   HP  G+ L  T+ LP    H+++ W
Sbjct: 312 CPRQALHAKTLGFVHPRTGKELFFTSELPEDMTHLLEKW 350


>gi|253581824|ref|ZP_04859048.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           varium ATCC 27725]
 gi|251836173|gb|EES64710.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           varium ATCC 27725]
          Length = 313

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 94/328 (28%), Positives = 156/328 (47%), Gaps = 43/328 (13%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVI 71
           END+   R+D +            +QKI+  G V +  K+V K  N+++  +++    V+
Sbjct: 14  ENDK-GKRIDSFLNEIIDDATRSYIQKIIDGGYVEITGKKVTKSGNKLKGTEII----VV 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------- 124
           N     I E +IL    N+   +  L   ++YED  I + NK A + V    G       
Sbjct: 69  N-----IPEDEIL----NVVPENIPLN--IIYEDKDIVIINKTANMVVHPAHGNYNGTLV 117

Query: 125 --IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + Y I    K      G  +P + HRLD++TSG++VVA+   A   L++ F+ + ++K
Sbjct: 118 NALLYQI----KDLSTINGVIRPGIVHRLDKDTSGVIVVAKNDEAHSTLSDMFKEKTLEK 173

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y  +  GI K+K   I   L+ +       + VV  N K    AIS+++V+D   + F 
Sbjct: 174 TYICITKGIFKDKSGKIE-TLIGRDPKDRKKMTVVDINGKN---AISNYEVLDE-GKNFS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++  TGRTHQ+RVH  ++  PI+GD  Y     GN    I  ++ LHA  +   HP 
Sbjct: 229 LVKVRIETGRTHQIRVHMKYLNHPILGDSVY-----GNSNEGITRQM-LHAYRLKFTHPV 282

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             + + +TA +P    K     G   ++
Sbjct: 283 TKKEMIVTADIPEDFKKAAKFAGVDINK 310


>gi|59800728|ref|YP_207440.1| RluD [Neisseria gonorrhoeae FA 1090]
 gi|240016030|ref|ZP_04722570.1| RluD [Neisseria gonorrhoeae FA6140]
 gi|240080171|ref|ZP_04724714.1| RluD [Neisseria gonorrhoeae FA19]
 gi|240115125|ref|ZP_04729187.1| RluD [Neisseria gonorrhoeae PID18]
 gi|240122965|ref|ZP_04735921.1| RluD [Neisseria gonorrhoeae PID332]
 gi|240125216|ref|ZP_04738102.1| RluD [Neisseria gonorrhoeae SK-92-679]
 gi|240127670|ref|ZP_04740331.1| RluD [Neisseria gonorrhoeae SK-93-1035]
 gi|260441058|ref|ZP_05794874.1| RluD [Neisseria gonorrhoeae DGI2]
 gi|268596320|ref|ZP_06130487.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae FA19]
 gi|268600798|ref|ZP_06134965.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae PID18]
 gi|268681584|ref|ZP_06148446.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae PID332]
 gi|268683812|ref|ZP_06150674.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae SK-92-679]
 gi|268686054|ref|ZP_06152916.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae SK-93-1035]
 gi|293399573|ref|ZP_06643726.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae F62]
 gi|59717623|gb|AAW89028.1| putative ribosomal large subunit pseudouridine synthase D
           [Neisseria gonorrhoeae FA 1090]
 gi|268550108|gb|EEZ45127.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae FA19]
 gi|268584929|gb|EEZ49605.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae PID18]
 gi|268621868|gb|EEZ54268.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae PID332]
 gi|268624096|gb|EEZ56496.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae SK-92-679]
 gi|268626338|gb|EEZ58738.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae SK-93-1035]
 gi|291610142|gb|EFF39264.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae F62]
          Length = 374

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 137/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K      G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAAVKFGGKPAVTHVKVLERYL-AHSYIECSLGTGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|227872363|ref|ZP_03990714.1| pseudouridylate synthase [Oribacterium sinus F0268]
 gi|227841792|gb|EEJ52071.1| pseudouridylate synthase [Oribacterium sinus F0268]
          Length = 303

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 86/319 (26%), Positives = 150/319 (47%), Gaps = 49/319 (15%)

Query: 12  VENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V  +EE  RLD++      H  +   L K ++ G V V+ ++ K + ++++G        
Sbjct: 5   VAKEEEGQRLDKYLSEQKDHDFSRSYLGKCIQEGCVSVNGEKAKASLKVKAG-------- 56

Query: 71  INALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            + ++  I EQK   +L  ++ L          ++YED  + V NK  G+ V   +G   
Sbjct: 57  -DRIDFDIPEQKDPEVLPEAIPLD---------IVYEDDDLLVVNKERGMVVHPAAG--- 103

Query: 128 HIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           H  G L + V +             +P + HR+D++T+G+L++ +   + Q L +     
Sbjct: 104 HYSGTLVNAVLAHAGSSLSSINGVNRPGIVHRIDKDTTGLLLICKNDLSHQSLAKQLEEH 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDC 235
            I + Y +LV+G  K +   I+      + IG D     KQ  + K    A++H+KV++ 
Sbjct: 164 SITRRYHALVFGKIKEEDGIIS------APIGRDEKDRKKQAISYKHGKEALTHYKVLER 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F+     +E +  TGRTHQ+RVH   +G P++GD  Y    + +  S       LHA  +
Sbjct: 218 FSDS-TLVECRLETGRTHQIRVHMKSIGHPLLGDPVYGLKNRKDGIS----GQALHAMIL 272

Query: 296 DLPHPEGGR-LQITAPLPA 313
              HP  G  ++ +AP PA
Sbjct: 273 GFQHPRTGEYMEFSAPYPA 291


>gi|298376939|ref|ZP_06986893.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_19]
 gi|298265923|gb|EFI07582.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_19]
          Length = 359

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 86/337 (25%), Positives = 157/337 (46%), Gaps = 51/337 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V +  +  +R+D++  +         +Q    +G + V+ K VK N R++   VV +   
Sbjct: 36  VADKGQSLLRVDKFLVDRMMGATRNRIQLAAEAGCILVNDKPVKSNYRVKPLDVVSV--- 92

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
              ++   +E +I+   + L          ++YED  + V NKPAG+ V  G G      
Sbjct: 93  --VMDRPRRELEIIPEDIPLN---------IVYEDDDLLVVNKPAGLVVHPGHGNYTGTL 141

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              +AY++      + D    +  L HR+D++TSG+LVVA+   A  +L+  F  +  ++
Sbjct: 142 VNALAYYLKD--DPYYDPSDPRLGLVHRIDKDTSGLLVVAKRPEAKSNLSLQFFNKTTKR 199

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCF 236
            Y +LVWGI +  +  I      + +IG D      + V  + ++G   A++H+ V++  
Sbjct: 200 KYRALVWGIVQEDEGRI------EGNIGRDPRDRMQMTVFPEGDQGKT-AVTHYTVLERL 252

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN---- 286
                 +E +  TGRTHQ+RVH  ++G  +  D +Y  +   KG     +   +QN    
Sbjct: 253 GY-VSLVECRLETGRTHQIRVHMKYIGHTLFNDERYGGHDILKGTTFTKYKQFVQNCFAI 311

Query: 287 --KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
             +  LHA+ +   HP  G  +   + +P+ M +  D
Sbjct: 312 CPRQALHAKTLGFVHPTTGEEMFFDSEIPSDMQQLID 348


>gi|283780592|ref|YP_003371347.1| pseudouridine synthase [Pirellula staleyi DSM 6068]
 gi|283439045|gb|ADB17487.1| pseudouridine synthase [Pirellula staleyi DSM 6068]
          Length = 245

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/231 (32%), Positives = 113/231 (48%), Gaps = 13/231 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI---AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +L EDS + V NKPAGI  Q   GI    + I  +L+S   S+     + HRLD+  SG 
Sbjct: 8   ILLEDSAVLVVNKPAGILTQAPLGIDSLEWQIKRYLQSTEKSEVPYLGVPHRLDRPVSGC 67

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +  A+ + AA+ +++ F  R +QK YW+LV GI    +    + L K    G     VV 
Sbjct: 68  ICFAKNQKAARKISQQFEARLVQKTYWALVSGIVHPTRSTWVDHLKKLD--GEPRTIVVD 125

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANF 276
           + +     AI H+++++    +   L +   TGRTHQ+RV     G P++GD  Y  A  
Sbjct: 126 ERDPEGKNAILHYELLETREGR-SLLAITLETGRTHQIRVQCGSRGFPLLGDRLYGSAEP 184

Query: 277 KGNFTSPIQNKLY-LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            G   +  +++L  LHAR +   HP     L  TA +PA     W   G +
Sbjct: 185 FGPLAADERDQLIALHARTLAFRHPVTKEDLIFTAQVPA----IWSPFGLE 231


>gi|56698216|ref|YP_168588.1| ribosomal large subunit pseudouridine synthase A [Ruegeria pomeroyi
           DSS-3]
 gi|56679953|gb|AAV96619.1| ribosomal large subunit pseudouridine synthase A [Ruegeria pomeroyi
           DSS-3]
          Length = 215

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/216 (32%), Positives = 112/216 (51%), Gaps = 19/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED+++ V NKPAG+    G G   H+   L S V +      L HRLD++TSG++V 
Sbjct: 14  VLHEDAELIVLNKPAGLLSVPGRGA--HLADCLLSRVQAAFPGALLVHRLDRDTSGVMVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A+T  A ++L   F  R+ +K Y + +WG  + K   +   L+       D+ +  +Q  
Sbjct: 72  AQTPHAQRNLGRQFEERKTRKTYVARLWGRLEPKTGTVDLPLIV------DWPNRPRQMV 125

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +E G   A++ ++V+  +      + + P TGR+HQLRVH   +G PI+GD  Y     
Sbjct: 126 CHETG-KPAVTDWRVLR-YEGDTTRVRLLPRTGRSHQLRVHCQALGHPILGDPFYATGAA 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             F      +L LH+  + L HPE GR +   AP P
Sbjct: 184 QAFP-----RLMLHSEELRLKHPESGRSMTFRAPAP 214


>gi|299133083|ref|ZP_07026278.1| pseudouridine synthase [Afipia sp. 1NLS2]
 gi|298593220|gb|EFI53420.1| pseudouridine synthase [Afipia sp. 1NLS2]
          Length = 244

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 66/205 (32%), Positives = 105/205 (51%), Gaps = 10/205 (4%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           ++ +++ +L+ D  + V +KPAGI+V  G     +++    +      + P L HRLD++
Sbjct: 8   AEEMQARVLHRDGLMLVIDKPAGIAVHKGPKGGPNLEASFDALRYGLPRPPVLAHRLDRD 67

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG LV+ R R A   L   F+  +I K YW++V G P   +  I   L +     G + 
Sbjct: 68  TSGCLVLGRHRKATASLGLLFKHGKIGKTYWAVVEGGPAENQGEIDIPLGRLDETRGWW- 126

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              ++ +     + S + V+        WL ++P TGRTHQLRVH   MG PIVGD+ Y 
Sbjct: 127 ---QKPDPNGLPSQSRWSVMG-RGDGLTWLALEPITGRTHQLRVHCAAMGFPIVGDNIY- 181

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLP 298
               GN     +  L+LH+R + +P
Sbjct: 182 ----GNGPRFGEPSLHLHSREIVVP 202


>gi|85375216|ref|YP_459278.1| pseudouridylate synthase [Erythrobacter litoralis HTCC2594]
 gi|84788299|gb|ABC64481.1| pseudouridylate synthase [Erythrobacter litoralis HTCC2594]
          Length = 229

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 111/221 (50%), Gaps = 20/221 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +L+ED +  V +KPAG+ ++    GG  +  H+D     +     + P   HR+D +TSG
Sbjct: 5   ILFEDGEALVIDKPAGLPIERPRRGGPSLEDHLDALKLGFQ----RAPVPVHRIDTDTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            L++AR   A +   ++F  RR+ K Y  +V G+P+ ++  IA  L K S     +  + 
Sbjct: 61  CLLLARNPKALKRFAKAFEERRVGKRYLGIVDGVPQPEEGEIALALAKISSAEKGWRMIP 120

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCAN 275
            +  K    +++ ++++    ++   LE +P TGRTHQ+RVH A  +G P++GD  Y   
Sbjct: 121 AKKGK---ASLTRWRLLQKL-ERGALLEFEPETGRTHQIRVHVASGLGLPLLGDPVYGDA 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
             G  T        LHA  + +       +  TAPLPA  +
Sbjct: 177 STGPRT-------MLHAAGLTVERDGKPSISATAPLPADFL 210


>gi|325689795|gb|EGD31799.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK115]
          Length = 298

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/227 (31%), Positives = 116/227 (51%), Gaps = 32/227 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG + A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKGKS-ALTRFQVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
             Y      KG+         +LHAR +   HP  G  L+ TA +PA
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEVPA 286


>gi|154496189|ref|ZP_02034885.1| hypothetical protein BACCAP_00473 [Bacteroides capillosus ATCC
           29799]
 gi|150274744|gb|EDN01808.1| hypothetical protein BACCAP_00473 [Bacteroides capillosus ATCC
           29799]
          Length = 304

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 84/331 (25%), Positives = 144/331 (43%), Gaps = 52/331 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRI 67
           + +  D    R+D++     P ++    QK+L  G V +    VK N +   G   V+ +
Sbjct: 4   LTLRADRVGERVDQFLSRQLPQLSRSAAQKLLEEGAVTLKGLPVKKNYKTAEGDELVLSL 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P  +     ++ +   LD               ++YED  + V NKP G+ V   +G   
Sbjct: 64  PDPVEV--DVVPQDIPLD---------------VVYEDGDVIVINKPVGMVVHPAAG--- 103

Query: 128 HIDGFL---------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           H DG L         KS     G+ +P + HR+D++TSG+++ A++  A   L E  +  
Sbjct: 104 HPDGTLVNALLYHCGKSLSGINGELRPGIVHRIDRDTSGLIIAAKSDFAHLALAEQLQDH 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-----AISHFKV 232
            + + Y ++  G  K  +  +   + +         H   + +   N+     A++H+ V
Sbjct: 164 SLYREYEAVAVGGFKEDEGTVRAPIAR---------HPTDRKKMAVNFLQGREAVTHYTV 214

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++ F+     L+ +  TGRTHQ+RVH  H+G P++GD  Y +        P      LHA
Sbjct: 215 LERFS-GCTHLQCRLETGRTHQIRVHMAHIGHPLLGDTVYGSKKP----YPGLAGQCLHA 269

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           R +   HP  G R+ +  PLP       D L
Sbjct: 270 RRLSFVHPRTGERMTVECPLPDWFEAVLDKL 300


>gi|212712902|ref|ZP_03321030.1| hypothetical protein PROVALCAL_03999 [Providencia alcalifaciens DSM
           30120]
 gi|212684447|gb|EEB43975.1| hypothetical protein PROVALCAL_03999 [Providencia alcalifaciens DSM
           30120]
          Length = 325

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 89/331 (26%), Positives = 158/331 (47%), Gaps = 49/331 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + I  +I       
Sbjct: 19  RLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKAKEKVLGGEQISIDALIEEDTRWE 78

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV- 137
            +   LD               ++YED  I + NKP  + V  G+G   + DG + + + 
Sbjct: 79  PQDIPLD---------------VVYEDEDILIINKPRDLVVHPGAG---NPDGTILNALL 120

Query: 138 ---DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                    PR  + HRLD++T+G++VVA+T  A  HL E+ + R I + Y ++  G   
Sbjct: 121 YRYPEIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAVAVGRMT 180

Query: 193 NK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +E I+    K++H+    VH +         A++H++V++ F +    L ++  T
Sbjct: 181 AGGMVEEPISRHPTKRTHMA---VHPM------GKPAVTHYRVMEHF-RAHTRLRLRLET 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLHARYMDLPHP- 300
           GRTHQ+RVH  H+  P++GD  Y       KG     ++     ++  LHA  + L HP 
Sbjct: 231 GRTHQIRVHMAHINHPLIGDQLYGGRPRPLKGATEEFLEVMRKFDRQALHATMLRLYHPI 290

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRNLY 331
            G +++  APLP  MV+  ++L  K D  L+
Sbjct: 291 TGIQMEWHAPLPDDMVELIEAL--KADTELH 319


>gi|259907390|ref|YP_002647746.1| 23S rRNA/tRNA pseudouridine synthase A [Erwinia pyrifoliae Ep1/96]
 gi|224963012|emb|CAX54495.1| Ribosomal large subunit pseudouridine synthase A [Erwinia
           pyrifoliae Ep1/96]
 gi|283477223|emb|CAY73130.1| ribosomal large subunit pseudouridine synthase A [Erwinia
           pyrifoliae DSM 12163]
          Length = 217

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/203 (34%), Positives = 108/203 (53%), Gaps = 16/203 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G   +A + D  + + V          HRLD  TSG++V
Sbjct: 14  VLYQDEHIIVVNKPSGLLSVPGR--LAEYKDSVM-TRVQRDYPAAESVHRLDMATSGVMV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  QK Y + VWG P+     +   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPQKTYVARVWGHPQPATGLVDLPLI------CDWPNRPKQK 124

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A + ++V+D  +     ++++P TGR+HQLRVH L +G P++GD+ Y A+ +
Sbjct: 125 VCFDSGKSAQTEYQVLDYASDNSARVQLKPITGRSHQLRVHMLALGHPMLGDNFY-AHDE 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               +P   +L LHA  + + HP
Sbjct: 184 ARAMAP---RLQLHAESLSITHP 203


>gi|153953520|ref|YP_001394285.1| RluD1 [Clostridium kluyveri DSM 555]
 gi|219854142|ref|YP_002471264.1| hypothetical protein CKR_0799 [Clostridium kluyveri NBRC 12016]
 gi|146346401|gb|EDK32937.1| RluD1 [Clostridium kluyveri DSM 555]
 gi|219567866|dbj|BAH05850.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 299

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 85/288 (29%), Positives = 142/288 (49%), Gaps = 44/288 (15%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           SG++ +D KRVK N+ ++SG V+          ++IKE+     S N+   ++ +   ++
Sbjct: 40  SGRIEIDNKRVKLNHVLKSGDVICF--------NLIKEE-----SQNIG--AEKMDIEVV 84

Query: 103 YEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           YED  I V NK  GI V            +G+ Y+   F KS  +      RL  RLD +
Sbjct: 85  YEDRDIIVVNKKPGIVVHPTRSYPSGTLANGLIYY---FQKSGENCI---VRLVSRLDMD 138

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++VA+ + A   L+   +    +K Y +++ G  K  +  I   + +    G D  
Sbjct: 139 TSGLIIVAKNQFAHMCLSRDMKSEDFEKSYIAVIHGKMKEGQGIIDLPIYRPE--GDDIR 196

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +V   +K    +I+H+KVI+ F      L++   TGRTHQ+RVH  ++G P+ GD  Y 
Sbjct: 197 RIV---DKRGQRSITHYKVIEEFKHD-QLLKLILKTGRTHQIRVHLSYLGHPLYGDTLYG 252

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP---AHMVK 317
                 +     N+  LHA  +  PHP G + L++   +P   +H++K
Sbjct: 253 IEGDNRYI----NRQALHAYRLKFPHPRGNKILELETDIPEDISHLIK 296


>gi|329297086|ref|ZP_08254422.1| RluA family pseudouridine synthase [Plautia stali symbiont]
          Length = 326

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/245 (31%), Positives = 125/245 (51%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDDHILVINKPRDLVVHPGAG---NPDGTVLNVLLYHYPAIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL E+ ++R I + Y ++  G         E +A    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVETLQLREITREYEAVAIGTMTAGGTVNEPMARHSTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A +H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------ATTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMAHIKHPLVGDPL 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  APLP  MV   D+L
Sbjct: 253 YGGRPRPPKGASEAFISTLRGFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVDLIDAL 312

Query: 323 GFKYD 327
               D
Sbjct: 313 KADTD 317


>gi|194098000|ref|YP_002001048.1| RluD [Neisseria gonorrhoeae NCCP11945]
 gi|239998466|ref|ZP_04718390.1| RluD [Neisseria gonorrhoeae 35/02]
 gi|240112385|ref|ZP_04726875.1| RluD [Neisseria gonorrhoeae MS11]
 gi|254493184|ref|ZP_05106355.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae 1291]
 gi|268594325|ref|ZP_06128492.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae 35/02]
 gi|268598444|ref|ZP_06132611.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae MS11]
 gi|193933290|gb|ACF29114.1| RluD [Neisseria gonorrhoeae NCCP11945]
 gi|226512224|gb|EEH61569.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae 1291]
 gi|268547714|gb|EEZ43132.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae 35/02]
 gi|268582575|gb|EEZ47251.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae MS11]
          Length = 374

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 137/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K      G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAAVKFGGKPAVTHVKVLERYL-AHSYIECSLGTGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|325696405|gb|EGD38295.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK160]
          Length = 298

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/227 (31%), Positives = 116/227 (51%), Gaps = 32/227 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG + A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKGKS-ALTRFQVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
             Y      KG+         +LHAR +   HP  G  L+ TA +PA
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEVPA 286


>gi|313886583|ref|ZP_07820296.1| pseudouridine synthase, RluA family [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|332300873|ref|YP_004442794.1| pseudouridine synthase [Porphyromonas asaccharolytica DSM 20707]
 gi|312923939|gb|EFR34735.1| pseudouridine synthase, RluA family [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|332177936|gb|AEE13626.1| pseudouridine synthase [Porphyromonas asaccharolytica DSM 20707]
          Length = 228

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/221 (31%), Positives = 109/221 (49%), Gaps = 20/221 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ + + NKPAG+ VQG S     +   ++ ++  K  KP      +THR+D+ TS
Sbjct: 6   ILYEDNHLLIVNKPAGMLVQGDSTGDTPLSELVERYLIDKYDKPGRAFVGVTHRIDRPTS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++ A+T  A   L   F+ R I K+Y ++V G    K     + L +       YV V
Sbjct: 66  GAVLFAKTSKALARLNAMFQRREIHKVYHAVVCGAFPQKAGEAKDLLYRNRKQNKSYV-V 124

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            + + +     +++ ++      ++  L +  HTGR HQ+R    HMG PI GD KY A 
Sbjct: 125 TEAHAEAKRAWLTYERL--AVGDRYSLLAVTLHTGRHHQIRTQLSHMGFPIKGDLKYGA- 181

Query: 276 FKGNFTSPIQNK---LYLHARYMDLPHP-EGGRLQITAPLP 312
                  P  NK   + LHAR +   HP    ++++ AP P
Sbjct: 182 -------PRSNKDGGISLHARILSFEHPVTHEQIEVVAPYP 215


>gi|322514978|ref|ZP_08067990.1| ribosomal large subunit pseudouridine synthase D [Actinobacillus
           ureae ATCC 25976]
 gi|322119031|gb|EFX91195.1| ribosomal large subunit pseudouridine synthase D [Actinobacillus
           ureae ATCC 25976]
          Length = 325

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 90/339 (26%), Positives = 158/339 (46%), Gaps = 49/339 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V  D    RLD+     +P+ +   L+  + S  V+V+   V K   ++  G+++ +   
Sbjct: 11  VSADLLGARLDQALAQLFPYYSRSRLKVWIESDLVKVNGNIVNKAREKVFGGELIEV--- 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                     Q  ++  V        L   ++YED  I V NKP  + V  G+G   + D
Sbjct: 68  ----------QAEIEEEVRFEPQDIPLN--IVYEDDDILVINKPKDLVVHPGAG---NPD 112

Query: 131 GF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G     L  +     + PR  + HRLD++T+G++VVA+   A  HL  + + RRI + Y 
Sbjct: 113 GTVLNALLHYYPPIAEVPRAGIVHRLDKDTTGLMVVAKNIPAQTHLVTALQKRRITREYE 172

Query: 185 SLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G+        E +A    K++ +    VH + +       A++H+++++ F + + 
Sbjct: 173 AVTSGVMTQGGKVDEPMARHPTKRTAMA---VHPMGKP------AVTHYRIMERF-RNYT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQN--KLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P++GD  Y    +        F + ++   +  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMTHIAHPLLGDQLYGGRPRPPKGASEEFLAVLRGFQRQALHAT 282

Query: 294 YMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYDRNLY 331
            + L HP  G L +  APLP   ++  ++L  K D  LY
Sbjct: 283 MLRLEHPITGELMEWHAPLPDDFIELIEAL--KADYQLY 319


>gi|291044392|ref|ZP_06570101.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae DGI2]
 gi|291011286|gb|EFE03282.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae DGI2]
          Length = 392

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 137/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 58  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 105

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 106 --TVRPSEENLAFVPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 162

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 163 PELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 222

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K      G   A++H KV++ +     ++E    TGRT
Sbjct: 223 K--------IETQIGRDPHNRLKMAAVKFGGKPAVTHVKVLERYL-AHSYIECSLGTGRT 273

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 274 HQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 333

Query: 306 QITAPLP 312
              AP+P
Sbjct: 334 SFEAPIP 340


>gi|258653360|ref|YP_003202516.1| pseudouridine synthase [Nakamurella multipartita DSM 44233]
 gi|258556585|gb|ACV79527.1| pseudouridine synthase, RluA family [Nakamurella multipartita DSM
           44233]
          Length = 308

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 90/333 (27%), Positives = 151/333 (45%), Gaps = 42/333 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V +    MRLD         ++   + +++ +G V VD   V  ++R+    
Sbjct: 1   MPDVRRLPVPDGLAGMRLDAGVARLL-GLSRTTVAEMIDAGDVLVDGVPVARSSRMALDT 59

Query: 64  VVRI-------PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
            + I       PP + A        +++D    L+         +LY D+ I V +KP G
Sbjct: 60  WLEITLPEPDRPPAVQA--------QVVD---GLS---------VLYRDADIVVVDKPVG 99

Query: 117 ISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHL 170
           ++     G     + G L      V + G   R  + HRLD  T+G++VVA +  A   L
Sbjct: 100 VAAHPSPGWTGPTVLGALAGLGIAVSTSGSAERQGIVHRLDVGTTGVMVVALSERAYTTL 159

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
             +F+ R + KIY +LV G P      I   + +  H   D+   V     G   +++H+
Sbjct: 160 KAAFKERTVDKIYHALVQGHPDPSAGTIDAPIGR--HPSSDWKFAVV---AGGKDSVTHY 214

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           + ++ F +    L++   TGRTHQ+RVH   +  P VGD  Y A+        +Q + +L
Sbjct: 215 ETLEAF-RAASLLQVHLETGRTHQIRVHFAAVRHPCVGDRTYGADPTLADRLGLQRQ-WL 272

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           HAR +   HP+ GR ++ T+P PA +    + L
Sbjct: 273 HARTLGFAHPDDGRWVEFTSPYPADLAHALEVL 305


>gi|225858727|ref|YP_002740237.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae 70585]
 gi|225722071|gb|ACO17925.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae 70585]
          Length = 295

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 89/320 (27%), Positives = 152/320 (47%), Gaps = 50/320 (15%)

Query: 18  NMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
            +RLD+   +      +F N Q  ++SGQV V+ +  K    +Q G VV          +
Sbjct: 9   GLRLDKALSDLSELSRSFANEQ--IKSGQVLVNGQVKKAKYTVQEGDVV---------TY 57

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G   H  G L + 
Sbjct: 58  HVPEPEVLEYV------AEDLPLEIVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNA 108

Query: 137 V-----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +     D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V
Sbjct: 109 LMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEM 245
            G   N +  I      ++ IG       KQ    KG   A++ F V++ F   +  +E+
Sbjct: 169 HGNLPNDRGVI------EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           Q  TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   HP  G
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTG 273

Query: 304 R-LQITAPLPAHMVKTWDSL 322
           + L+  A +P    +T + L
Sbjct: 274 KTLEFKADIPEIFKETLERL 293


>gi|310765109|gb|ADP10059.1| 23S rRNA/tRNA pseudouridine synthase A [Erwinia sp. Ejp617]
          Length = 217

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/203 (34%), Positives = 108/203 (53%), Gaps = 16/203 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G   +A + D  + + V          HRLD  TSG++V
Sbjct: 14  VLYQDEHIIVVNKPSGLLSVPGR--LAEYKDSVM-TRVQRDYPAAESVHRLDMATSGVMV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  QK Y + VWG P+     +   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPQKTYVARVWGHPQPATGLVDLPLI------CDWPNRPKQK 124

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A + ++V+D  +     ++++P TGR+HQLRVH L +G P++GD+ Y A+ +
Sbjct: 125 VCFDSGKSAQTEYQVLDNASDNSARVQLKPITGRSHQLRVHMLAIGHPMLGDNFY-AHDE 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               +P   +L LHA  + + HP
Sbjct: 184 ARAMAP---RLQLHAESLSITHP 203


>gi|152981261|ref|YP_001353083.1| ribosomal large subunit pseudouridine synthase D [Janthinobacterium
           sp. Marseille]
 gi|151281338|gb|ABR89748.1| ribosomal large subunit pseudouridine synthase D [Janthinobacterium
           sp. Marseille]
          Length = 342

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 86/320 (26%), Positives = 143/320 (44%), Gaps = 39/320 (12%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+      P  +   LQ+ +  G V VD +  +    +   + V I P     +  
Sbjct: 48  GVRLDKVLSTLVPQYSRSRLQQWIDGGHVSVDGEVARAKMTVYGDEKVVIYPQPAPEDEA 107

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
            K +               +   +++ED+++ V NKPAG+ V   +G      ++G L  
Sbjct: 108 FKPEA--------------MDLAIVHEDAEMLVINKPAGLVVHPAAGNWSGTLLNGLLH- 152

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           ++ S    PR  + HRLD++TSG++VVA+T  A   L    + R +++ Y +LVWG P  
Sbjct: 153 YLPSISGVPRAGIVHRLDKDTSGLMVVAKTLIAHTDLVRQLQARTVKREYLALVWGTPNI 212

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-------FAQKFCWLEMQ 246
             +  A+          D + +       A  A++HF+ +          +   C LE  
Sbjct: 213 TGKIDASI----GRHARDRIKMAVSENLTAKPAVTHFQRLATGMLDGRPVSLMLCRLE-- 266

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH   +G  +VGD  Y    K + T+ +  +  LHAR + L HP  G  +
Sbjct: 267 --TGRTHQIRVHMQSIGFALVGDGLYG---KQHLTT-VFPRQALHARRLGLIHPVSGEAV 320

Query: 306 QITAPLPAHMVKTWDSLGFK 325
           + ++ LP    +     G K
Sbjct: 321 EWSSELPQDFAELIARAGIK 340


>gi|16759090|ref|NP_454707.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|29140640|ref|NP_803982.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|213027943|ref|ZP_03342390.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
 gi|213161694|ref|ZP_03347404.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213427538|ref|ZP_03360288.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
 gi|213580242|ref|ZP_03362068.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213646894|ref|ZP_03376947.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213853061|ref|ZP_03382593.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|289826179|ref|ZP_06545291.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|34395804|sp|Q8Z9J5|RLUA_SALTI RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|25514250|pir||AC0514 pseudouridylate synthase (EC 4.2.1.70) - Salmonella enterica subsp.
           enterica serovar Typhi (strain CT18)
 gi|16501380|emb|CAD01251.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Typhi]
 gi|29136264|gb|AAO67831.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Typhi str. Ty2]
          Length = 219

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/208 (33%), Positives = 106/208 (50%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LEAHKDSIM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y + 
Sbjct: 126 KVCYETG-KPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDQFYASP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +       +L LHA  + + HP  G
Sbjct: 185 EALSLAP----RLQLHAEMLTITHPAYG 208


>gi|327470139|gb|EGF15603.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK330]
          Length = 298

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 117/236 (49%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   F  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTRFQVLERFGD-FSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA  P    +T + L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEAPVIFQETLEKL 295


>gi|213609301|ref|ZP_03369127.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 139

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 59/143 (41%), Positives = 92/143 (64%), Gaps = 8/143 (5%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           +ILR G+VRV+KKR+K   +++SG  VRIPPV  A      E++    S +L K +  L 
Sbjct: 4   RILRKGEVRVNKKRIKPEYKLESGDEVRIPPVRVA------EREEEAVSPHLQKVA-ALA 56

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            ++LYED  I V NKP+G +V GGSG+++ +   L++ +  + +   L HRLD++TSG+L
Sbjct: 57  DVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVL 115

Query: 159 VVARTRAAAQHLTESFRMRRIQK 181
           +VA+ R+A + L E  R + +QK
Sbjct: 116 LVAKKRSALRSLHEQLREKGMQK 138


>gi|308274565|emb|CBX31164.1| Uncharacterized RNA pseudouridine synthase ylyB [uncultured
           Desulfobacterium sp.]
          Length = 335

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 94/327 (28%), Positives = 145/327 (44%), Gaps = 48/327 (14%)

Query: 17  ENMRLDRWFKNHYP------HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
             +RLD    ++ P        + +N  KI    Q++    +VKF ++I +G +    PV
Sbjct: 32  SGIRLDIVVSSYIPLCSRSIAASLINKGKITVCNQIKKQGYKVKFGDKI-TGTIPDPEPV 90

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                        L   + L          +LYEDS I V NKP GI      G      
Sbjct: 91  -----------SFLPEPIELN---------ILYEDSDIIVINKPPGIVAHPAPGHYSGTL 130

Query: 129 IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D  G     +P + HRLD++TSG LVVA+   +  +L   F+ RRI+K Y 
Sbjct: 131 VNALLFHCPDLTGIGGEIRPGIVHRLDKDTSGALVVAKNDISHTNLCLQFKERRIRKKYL 190

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG P++    I    + +       + V+ +  K A    + +KVI+ +     W E
Sbjct: 191 ALVWGNPEHDSGSI-TLPIGRHPSNRKKMSVLTRKPKTAE---TLWKVIERYKSVSLW-E 245

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--------GNFTSPIQNKLYLHARYMD 296
           +   TGRTHQ+RVH   +  P++GD  Y    K         +F   I+ ++ LHA  + 
Sbjct: 246 IDLKTGRTHQIRVHCAAIKHPVIGDQVYGNRPKLSVDLKNTQDFYKQIKRQM-LHAWKIG 304

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP   + ++  APLP  M +   SL
Sbjct: 305 FMHPVTNKTMEFEAPLPDDMKELISSL 331


>gi|16761516|ref|NP_457133.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|16765978|ref|NP_461593.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|29142987|ref|NP_806329.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|62181235|ref|YP_217652.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|167553892|ref|ZP_02347635.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|167992440|ref|ZP_02573538.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|168234182|ref|ZP_02659240.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|168239430|ref|ZP_02664488.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           SL480]
 gi|168244683|ref|ZP_02669615.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|168262167|ref|ZP_02684140.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|168464166|ref|ZP_02698083.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|168822474|ref|ZP_02834474.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|194446496|ref|YP_002041926.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194447791|ref|YP_002046668.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194471474|ref|ZP_03077458.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194737121|ref|YP_002115673.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197247406|ref|YP_002147565.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197262464|ref|ZP_03162538.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197363556|ref|YP_002143193.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|198242257|ref|YP_002216673.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200389193|ref|ZP_03215805.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|204929503|ref|ZP_03220577.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|207858012|ref|YP_002244663.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|213051815|ref|ZP_03344693.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213424875|ref|ZP_03357625.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
 gi|213585773|ref|ZP_03367599.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213619387|ref|ZP_03373213.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
 gi|213646598|ref|ZP_03376651.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213850144|ref|ZP_03381042.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|224584515|ref|YP_002638313.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|238909508|ref|ZP_04653345.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|289824162|ref|ZP_06543757.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|54039251|sp|P65837|RLUD_SALTI RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|54041742|sp|P65836|RLUD_SALTY RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|25322403|pir||AC0832 pseudouridylate synthase (EC 4.2.1.70) - Salmonella enterica subsp.
           enterica serovar Typhi (strain CT18)
 gi|16421209|gb|AAL21552.1| pseudouridine synthase [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
 gi|16503817|emb|CAD05842.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29138619|gb|AAO70189.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|62128868|gb|AAX66571.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Salmonella enterica subsp. enterica serovar
           Choleraesuis str. SC-B67]
 gi|194405159|gb|ACF65381.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194406095|gb|ACF66314.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|194457838|gb|EDX46677.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194712623|gb|ACF91844.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|195633435|gb|EDX51849.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197095033|emb|CAR60579.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|197211109|gb|ACH48506.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
 gi|197240719|gb|EDY23339.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197287851|gb|EDY27239.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           SL480]
 gi|197936773|gb|ACH74106.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|199606291|gb|EDZ04836.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|204321222|gb|EDZ06422.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205321769|gb|EDZ09608.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|205329256|gb|EDZ16020.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|205331842|gb|EDZ18606.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|205336483|gb|EDZ23247.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|205341144|gb|EDZ27908.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|205349079|gb|EDZ35710.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|206709815|emb|CAR34167.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|224469042|gb|ACN46872.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|261247856|emb|CBG25685.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267994803|gb|ACY89688.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301159209|emb|CBW18724.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312913652|dbj|BAJ37626.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320087095|emb|CBY96863.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
 gi|322614488|gb|EFY11419.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322621447|gb|EFY18300.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322624308|gb|EFY21141.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322629393|gb|EFY26171.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322633633|gb|EFY30375.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322638324|gb|EFY35022.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322639762|gb|EFY36445.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322647376|gb|EFY43872.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322650454|gb|EFY46864.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322656053|gb|EFY52353.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322661447|gb|EFY57672.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322662647|gb|EFY58855.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322667020|gb|EFY63195.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322671389|gb|EFY67512.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322677604|gb|EFY73667.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322681570|gb|EFY77600.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322683970|gb|EFY79980.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|322715721|gb|EFZ07292.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323130996|gb|ADX18426.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323195539|gb|EFZ80717.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323197912|gb|EFZ83035.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323203090|gb|EFZ88122.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323205331|gb|EFZ90306.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323210519|gb|EFZ95403.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323218200|gb|EGA02912.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323221534|gb|EGA05947.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323223754|gb|EGA08059.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323230963|gb|EGA15081.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323234685|gb|EGA18771.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323238724|gb|EGA22774.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323241423|gb|EGA25454.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323246879|gb|EGA30846.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323253278|gb|EGA37108.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323257074|gb|EGA40783.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323260453|gb|EGA44064.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323264490|gb|EGA47996.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323269625|gb|EGA53078.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326624429|gb|EGE30774.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332989587|gb|AEF08570.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 326

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 124/245 (50%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPISRHPTKRTHMS-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV   D++
Sbjct: 253 YGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPVSGIEMEWHAPIPQDMVDLIDAM 312

Query: 323 GFKYD 327
              ++
Sbjct: 313 RADFE 317


>gi|60680595|ref|YP_210739.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis NCTC 9343]
 gi|60492029|emb|CAH06791.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis NCTC 9343]
          Length = 539

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/210 (33%), Positives = 105/210 (50%), Gaps = 24/210 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + V +KP G+    G      I   L++ + ++ G  P + HRLD  TSG+L+
Sbjct: 338 ILFEDQWLLVLHKPEGVLSVPGKSEEQSIYSLLRARYPEATG--PLVVHRLDMATSGLLL 395

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A+ +   +HL   F  R I+K Y +L+ GI   ++  I         I  DY+   +Q 
Sbjct: 396 AAKAQEVHRHLQAQFENRSIKKRYIALLDGILPEEEGVI------DLPICPDYLDRPRQM 449

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCA 274
            NE+    AI+ ++V+D        +   P TGRTHQLRVHA H   + CPIVGD  Y  
Sbjct: 450 VNEELGKTAITRYRVMD-RKNGQTRIAFFPLTGRTHQLRVHAAHPLGLNCPIVGDELYGR 508

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                       +LYLHA Y++  HP  G+
Sbjct: 509 K---------AERLYLHAEYLEFIHPVSGQ 529


>gi|322374526|ref|ZP_08049040.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           C300]
 gi|321280026|gb|EFX57065.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           C300]
          Length = 299

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 81/296 (27%), Positives = 142/296 (47%), Gaps = 47/296 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +++GQV V+ +  K    +Q G +V          + + E ++L+        ++ L   
Sbjct: 31  IKAGQVLVNGQAKKAKYTVQEGDIV---------TYHVPEPEVLEYV------AENLPLE 75

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G         + YHI     S ++    +P + HR+D
Sbjct: 76  IIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNSLMYHIKDL--SGINGV-LRPGIVHRID 132

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 133 KDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 186

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 187 EKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 244

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHA+ +   HP  G  L+ TA +P    +T + L
Sbjct: 245 EVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGETLEFTADIPEIFKETLERL 293


>gi|296114958|ref|ZP_06833603.1| pseudouridine synthase, RluA family protein [Gluconacetobacter
           hansenii ATCC 23769]
 gi|295978476|gb|EFG85209.1| pseudouridine synthase, RluA family protein [Gluconacetobacter
           hansenii ATCC 23769]
          Length = 323

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/324 (23%), Positives = 140/324 (43%), Gaps = 38/324 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V+    +   R DR+  +    ++   ++ ++ +G +            ++ G V+R 
Sbjct: 8   EPVIATVGDAGQRTDRFMADTIGTLSRSRIKALMEAGHL------------LRDGVVLRD 55

Query: 68  P--PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           P  PV   + + ++    + ++   T     +   +L+ED  + V +KPAG+ V    G 
Sbjct: 56  PADPVRAGMRYELR----VPAAAPATPQGQDIALDVLFEDRDLIVLDKPAGLVVHPAPGN 111

Query: 125 -IAYHIDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  L    DS       ++P + HRLD++TSG++V A+T  A   L+ +F  R 
Sbjct: 112 EDGTLVNALLGHCGDSLTGIGGERRPGIVHRLDKDTSGVMVAAKTELAHHALSAAFASRD 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I++ Y ++ WG+           + +      +   +   +  G  +A++H++ +D F  
Sbjct: 172 IERAYQAVCWGVLAPTTGSFDGAIGRDRR---ERKRMAVISNGGGKHALTHYRTLDTFHG 228

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC----ANFKGNFTSPIQNKL-----Y 289
               +E +  TGRTHQ+RVH  H G  +VGD  Y     A  +G         L      
Sbjct: 229 SLSHVECKLATGRTHQIRVHFAHAGHALVGDPTYLRRIPAAARGLPADARATALDFPRQA 288

Query: 290 LHARYMDLPHPE-GGRLQITAPLP 312
           LHA  +   HP  G  L    P P
Sbjct: 289 LHAARLGFVHPRTGAHLLFETPPP 312


>gi|190571305|ref|YP_001975663.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Culex quinquefasciatus Pel]
 gi|213018702|ref|ZP_03334510.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Culex quinquefasciatus JHB]
 gi|190357577|emb|CAQ55016.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Culex quinquefasciatus Pel]
 gi|212995653|gb|EEB56293.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Culex quinquefasciatus JHB]
          Length = 315

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 87/294 (29%), Positives = 141/294 (47%), Gaps = 47/294 (15%)

Query: 52  RVKFNNRIQSGQVVRIP-PVINALNHIIK--EQKIL-----DSSVNLTKHSDFLKSILLY 103
           R K    IQ+ QV  +  P+IN  +HI+K  E+ ++     D S ++  + D +K  ++Y
Sbjct: 28  RSKAQRLIQNEQVKLLGIPIINN-DHIVKPGEEYVVHLIQPDISTSIEPNYD-IKLDIVY 85

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGI 157
           ED  I V +K + ++V  G+G     D  L + +   G+      +P + HRLD++TSG+
Sbjct: 86  EDDDIIVLSKQSRLTVHPGAGTNN--DTLLNAVIAHLGKIPYTNTRPGIVHRLDKDTSGL 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+A+   +   L+E    R+I++ Y +++WG   N +  +   +  K     + + V K
Sbjct: 144 MVIAKNEQSHSFLSELLSNRKIKREYLAVIWGALPNLQGTVKTHIAPKRS-NKEMMCVTK 202

Query: 218 QNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                   AI+H+ V     Q     C LE    TGRTHQ+RVH  H+G  +VGD  Y  
Sbjct: 203 T---AGKLAITHYSVKKIIGQASLVKCTLE----TGRTHQIRVHMSHIGHSVVGDQVYGK 255

Query: 275 N------------FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           N            F  NF     N+  LHA  + L HP+    ++  + LP  M
Sbjct: 256 NSSKSEKHAKNSDFIRNF-----NRQALHAHTLGLYHPKSKEYIEFVSDLPQDM 304


>gi|299142856|ref|ZP_07035984.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella oris C735]
 gi|298575724|gb|EFI47602.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella oris C735]
          Length = 221

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/231 (30%), Positives = 115/231 (49%), Gaps = 20/231 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + +  K +G  VQG       +   +K ++  K QKP      + HRLD+  +
Sbjct: 3   IVYEDNHLIIVYKHSGEIVQGDKTGDVPLSEDVKCYLKEKYQKPGNVFLGVVHRLDRPVT 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYV 213
           G++V A+T  A   L + FR   + K YW++   +P   +  +++WL++  K +    Y 
Sbjct: 63  GLVVFAKTSKALTRLNKMFRDGEVHKTYWAITKNLPPQPEGTLSHWLVRNEKQNKSYAYD 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H V  ++K    AI  +++I   +  +C LE+   TGR HQ+R    HMGCPI GD KY 
Sbjct: 123 HEVPHSKK----AILKYRLIG-QSDHYCLLEVNLMTGRHHQIRCQLAHMGCPIKGDLKYG 177

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
           A       S     + L A +++  HP   +L  + +PLP    K W   G
Sbjct: 178 AQ-----RSNPDGSICLLAHHVEFVHPVSKQLISLDSPLPED--KLWQVWG 221


>gi|291280358|ref|YP_003497193.1| ribosomal large subunit pseudouridine synthase D [Deferribacter
           desulfuricans SSM1]
 gi|290755060|dbj|BAI81437.1| ribosomal large subunit pseudouridine synthase D [Deferribacter
           desulfuricans SSM1]
          Length = 288

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 78/275 (28%), Positives = 130/275 (47%), Gaps = 44/275 (16%)

Query: 38  QKILRSGQVRVDKKRVK--FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
            KI++ G V V+ K VK  +N  +    +V+IP          +E+K+     N+  +  
Sbjct: 19  SKIIKKGLVLVNNKTVKPSYNVNLGDEILVKIP----------QEEKLDLKPANIPLN-- 66

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-------DSKGQKPRLTH 148
                ++YE+    + NKPAG+ V    G   + D  L + +       D    +P + H
Sbjct: 67  -----IIYENQYYLIINKPAGLCVHPAPG---NFDNTLVNALLYHFQINDDNDVRPGIVH 118

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW--LLKKS 206
           RLD++TSG+++VA+ R   + ++E F+ R + K Y ++ +G PK        W  +L ++
Sbjct: 119 RLDKDTSGLILVAKNRDVREKMSEMFKEREVDKKYLAICYGNPK--------WDEILVEN 170

Query: 207 HIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            IG   V   K    +   YA +   V+  +   F   +++ +TGRTHQ+RVH  ++GCP
Sbjct: 171 SIGRHPVDRKKMAVVENGRYAKTKITVLKRYDNIF-LADVKIYTGRTHQIRVHCSYLGCP 229

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           I+GD  Y            Q    LHA Y+    P
Sbjct: 230 IIGDKVYGNKLSNKIRFERQ---ALHAYYLAFDCP 261


>gi|24379309|ref|NP_721264.1| putative pseudouridylate synthase [Streptococcus mutans UA159]
 gi|24377230|gb|AAN58570.1|AE014926_13 putative pseudouridylate synthase [Streptococcus mutans UA159]
          Length = 296

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 86/324 (26%), Positives = 148/324 (45%), Gaps = 46/324 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E  E  +RLD+   +    ++     + +++G V V+ K  K    ++ G ++      
Sbjct: 3   IEIKEAGVRLDKALAD-LTDLSRSQASEQIKAGLVLVNGKTQKAKYAVKEGDII------ 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              ++   ++++LD        +  +   ++YED  + V NKP G+ V    G   H  G
Sbjct: 56  ---HYERPQEEVLDCV------AQNIPLEIVYEDEDVAVINKPQGMVVHPSVG---HPSG 103

Query: 132 FL--------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            L        K      G  +P + HR+D++TSG+L++A+   A Q L +  + ++  + 
Sbjct: 104 TLVNALLFHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDQAHQALAKELKEKKSLRQ 163

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFC 241
           Y +LV G   N +  I      ++ IG       KQ        A++HFKV++ F Q + 
Sbjct: 164 YIALVHGNLPNDRGVI------EAPIGRSEKDRKKQTVTAKGKPAVTHFKVLERFGQ-YS 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPH 299
            +E+   TGRTHQ+RVH  ++G P+ GD  Y      KG          +LHA+ +   H
Sbjct: 217 LVELTLETGRTHQIRVHMAYIGHPVAGDPLYAPKKTLKGQGQ-------FLHAKTLGFTH 269

Query: 300 PEGGRL-QITAPLPAHMVKTWDSL 322
           P+ G L Q T  +P    +  D L
Sbjct: 270 PKTGELMQFTTEVPVIFQEVLDHL 293


>gi|83949443|ref|ZP_00958176.1| ribosomal large subunit pseudouridine synthase D [Roseovarius
           nubinhibens ISM]
 gi|83837342|gb|EAP76638.1| ribosomal large subunit pseudouridine synthase D [Roseovarius
           nubinhibens ISM]
          Length = 341

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 86/359 (23%), Positives = 148/359 (41%), Gaps = 60/359 (16%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M   Q V         RLD+      P   H++   L +++  G V V+    +   +R+
Sbjct: 1   MASTQVVFTIAANPPPRLDKALSRDVPEEAHLSRTRLARLVEEGAVSVNGAEARDVKSRV 60

Query: 60  QSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
             G   V+ +P        + +E  IL  ++ L          ++YED+ + V NKPAG+
Sbjct: 61  AEGDEVVITVP--------VAEESDILPENIPLD---------IVYEDADLLVVNKPAGM 103

Query: 118 SVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V    G         + +H  G L      +  +P + HR+D++TSG+LVVA++  A  
Sbjct: 104 VVHPAPGTPRGTLVNALLHHCGGDLSGVGGVR--RPGIVHRIDKDTSGLLVVAKSDQAHH 161

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK------- 221
            L   F     +++Y ++V+G+P      +   L       G+ + +  Q  +       
Sbjct: 162 GLAAQFEAHSAERVYQAIVYGVPDAADPRL-GGLRGVGFEPGNVLRITTQLARHRTDRQK 220

Query: 222 ------GANYAISHFKVIDCFAQ--KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                 G  +A++  +V +          +E +  TGRTHQ+RVH  + G  ++GD  Y 
Sbjct: 221 QAVLFDGGKHAVTRAQVTERLGDPASVALIECRLETGRTHQIRVHLAYAGHGLLGDPVYG 280

Query: 274 A-------NFKGNFTSPIQ--NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                    F       +   N+  LHA ++ + HP  G  L+  A LP  M     +L
Sbjct: 281 GRRGLPKRGFSAEAAETLATFNRQALHAGHLGVIHPASGEPLRFDARLPEDMAGLLAAL 339


>gi|254510211|ref|ZP_05122278.1| ribosomal large subunit pseudouridine synthase D [Rhodobacteraceae
           bacterium KLH11]
 gi|221533922|gb|EEE36910.1| ribosomal large subunit pseudouridine synthase D [Rhodobacteraceae
           bacterium KLH11]
          Length = 344

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 89/343 (25%), Positives = 140/343 (40%), Gaps = 60/343 (17%)

Query: 20  RLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L +++  G V VD   V     ++     + I       +
Sbjct: 17  RLDKALARDVPAEESLSRTRLARLIGEGAVTVDGAVVDDPKAKVAEDAQIAITVAEAEDS 76

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGFL 133
           HI  E   LD               ++YED  + V NKPAG+ V    GS     ++  L
Sbjct: 77  HIGPEDIPLD---------------VVYEDDDLIVINKPAGMVVHPAPGSPNGTLVNALL 121

Query: 134 KSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               D        ++P + HR+D+ETSG+LVVA++ AA   L   F    +++ Y ++ +
Sbjct: 122 HHCGDDLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHHGLAAQFEAHSVERYYRAVCY 181

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------------GANYAISHFKVIDC 235
           G+P      +   +   S   G+ + +  Q  +             G  +A++  ++++ 
Sbjct: 182 GVPDANDPRL-RGIKGVSFEPGNIMRLTTQLARHKTDRQKQAVLFHGGRHAVTRSRIVEV 240

Query: 236 FAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------FKGNFTS 282
           F          CWLE    TGRTHQ+RVH  H G  +VGD  Y          F      
Sbjct: 241 FGNPGAISLVECWLE----TGRTHQIRVHMAHAGHGLVGDPVYGGKRKLAARAFAPTAVE 296

Query: 283 PIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            +Q   +  LHA  +   HP  G  L+  APLP  M +    L
Sbjct: 297 AVQAFPRQALHAAVLGFEHPVSGADLRFEAPLPEDMERLLSEL 339


>gi|323351668|ref|ZP_08087322.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis VMC66]
 gi|322122154|gb|EFX93880.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis VMC66]
          Length = 298

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 118/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVINKPQGMVVHPSAG---HTSGTLVNALMYHIQDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTRFQVLERFGN-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA +PA   +T   L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEELEFTAEVPAIFQETLAKL 295


>gi|306831623|ref|ZP_07464781.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325978527|ref|YP_004288243.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|304426408|gb|EFM29522.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325178455|emb|CBZ48499.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 298

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 87/322 (27%), Positives = 149/322 (46%), Gaps = 50/322 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RLD+   +    ++       ++ G V V+ K VK    ++ G VV          
Sbjct: 7   EAGVRLDKALAD-LTELSRSQANDEIKKGTVLVNGKAVKAKYAVKVGDVV---------T 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           + + ++++L+ +      ++ +   ++YED  + V NKP G+ V    G         + 
Sbjct: 57  YEVPKEEVLEYT------AENIPLDIIYEDDDVAVVNKPQGMVVHPSVGHTSGTLVNALM 110

Query: 127 YHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           YHI    K      G  +P + HR+D++TSG+L++A+   A   L    + ++  + Y +
Sbjct: 111 YHI----KDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWL 243
           +V G   N +  I      ++ IG       KQ    KG   A++HFKV++ F   +  +
Sbjct: 167 IVHGNIPNDRGVI------EAPIGRSEKDRKKQAVTAKG-KPAVTHFKVLERFGN-YTLV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E+   TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   HP 
Sbjct: 219 ELTLETGRTHQIRVHMAYIGYPVAGDPLYGPRKTLKGDGQ-------FLHAQTLGFTHPT 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  L  TA  PA   +T ++L
Sbjct: 272 TGETLTFTAEAPAIFKETLENL 293


>gi|283783845|ref|YP_003363710.1| ribosomal large subunit pseudouridine synthase A [Citrobacter
           rodentium ICC168]
 gi|282947299|emb|CBG86844.1| ribosomal large subunit pseudouridine synthase A [Citrobacter
           rodentium ICC168]
          Length = 219

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VVLYQDEHIMVVNKPSGLLSVPGR--LEEHKDSIM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPVPAEGVVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETG-KAAQTGYEVVEYAADNTARVVLKPTTGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEALAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|293417934|ref|ZP_06660556.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B185]
 gi|291430652|gb|EFF03650.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B185]
          Length = 219

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 72/216 (33%), Positives = 113/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VVLYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++        + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETGKP-AQTEYEVVEYATDNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|213421914|ref|ZP_03354980.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 216

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/208 (33%), Positives = 106/208 (50%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LEAHKDSIM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y + 
Sbjct: 126 KVCYETG-KPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDQFYASP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +       +L LHA  + + HP  G
Sbjct: 185 EALSLAP----RLQLHAEMLTITHPAYG 208


>gi|253584151|ref|ZP_04861349.1| pseudouridine synthase [Fusobacterium varium ATCC 27725]
 gi|251834723|gb|EES63286.1| pseudouridine synthase [Fusobacterium varium ATCC 27725]
          Length = 294

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 120/227 (52%), Gaps = 21/227 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGS---GIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++YED  I V  K  GI S+   +     AY+I   LK ++ +K  K ++   HRLD++T
Sbjct: 82  VIYEDDDILVVEKENGILSIATNNEREKTAYNI---LKDYLKNKDPKNKIFVVHRLDRDT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI++ A+T  A   L  ++     ++ Y +LV G  + +K+ I ++L +       ++ 
Sbjct: 139 SGIMIFAKTEKAQDILQTTWNDSVKERTYIALVEGTVQKEKDTIISYLQENRA----FIT 194

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              QN K    AISH+KV+    + +  LE+   TGR +Q+RVH   +G  +VGD KY  
Sbjct: 195 YSSQNPKDGKKAISHYKVLKK-NKNYSLLEVNIETGRKNQIRVHMQDIGHSVVGDKKY-- 251

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
              G+  SPI N+L LHA  +   HP   + L  ++ +P+   K ++
Sbjct: 252 ---GSGKSPI-NRLGLHANTIVFVHPITKKVLHFSSKIPSVFTKIFN 294


>gi|332638853|ref|ZP_08417716.1| pseudouridine synthase [Weissella cibaria KACC 11862]
          Length = 304

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 110/229 (48%), Gaps = 19/229 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETS 155
           ++YED  + V NKP G+ V       SG   +   F        G  +P + HR+D++TS
Sbjct: 80  IVYEDDDLLVVNKPQGMVVHPALGHESGTLVNALMFHTPLSTINGVVRPGIVHRIDKDTS 139

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+VA+   A + L+   + ++  + Y++LV G      E + N    K+ +G      
Sbjct: 140 GLLMVAKNDKAHESLSAQLKDKKNLRQYYALVHG------EFVENEGTIKAPLGRSSADR 193

Query: 216 VKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            KQ    G   A++HFKV+  F   +  L++   TGRTHQ+RVH  ++G P+ GD  Y  
Sbjct: 194 KKQAVVAGGRDAVTHFKVVKRFV-GYTLLQVTLETGRTHQIRVHMAYIGHPVAGDPLY-- 250

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              G   +   N  YLHA  + L  P  G  +   APLP +     D L
Sbjct: 251 ---GPKKTLPGNGQYLHAATLGLTQPTTGEDMTFEAPLPDYFTAMLDQL 296


>gi|269978156|ref|ZP_06185106.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           mulieris 28-1]
 gi|306818529|ref|ZP_07452252.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           mulieris ATCC 35239]
 gi|307700922|ref|ZP_07637947.1| pseudouridine synthase, RluA family [Mobiluncus mulieris FB024-16]
 gi|269933665|gb|EEZ90249.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           mulieris 28-1]
 gi|304648702|gb|EFM46004.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           mulieris ATCC 35239]
 gi|307613917|gb|EFN93161.1| pseudouridine synthase, RluA family [Mobiluncus mulieris FB024-16]
          Length = 306

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 80/284 (28%), Positives = 139/284 (48%), Gaps = 27/284 (9%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           +IL  G V + +  +K ++ +QSG+ + +   I+   ++ +   +             LK
Sbjct: 33  EILAQGGVAMGETVLKKSDALQSGETLEVTAPIHPKVYVPEVTPV-----------PGLK 81

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQ 152
             LLYED+ + V +KPAG++   G G     + G L++    + + G   R  + HRLD 
Sbjct: 82  --LLYEDADLVVVDKPAGVAAHTGPGWDGPTVVGALRAAGVRISTSGPVEREGIVHRLDA 139

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG +VVA++  A   L  +FR  R++KIY ++  GI K     I   + +    G ++
Sbjct: 140 GTSGAMVVAKSELAYGKLKNAFRYHRVEKIYLAVARGILKPSLGTIDAPIGRAP--GREF 197

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              V     G   A++H+   +          +Q  TGRTHQ+RVH   +G P++GD +Y
Sbjct: 198 KMAVVV---GGKPAVTHYDTAESLPGA-TLARVQLETGRTHQIRVHFAAIGHPLLGDTEY 253

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
            A+ K      ++ + +LHA  +   HP  G  + + +PLP+ +
Sbjct: 254 GADAKQAVRLGLERQ-WLHASRLVFKHPRTGIEIAMDSPLPSDL 296


>gi|168215478|ref|ZP_02641103.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
 gi|182382386|gb|EDT79865.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
          Length = 306

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 118/236 (50%), Gaps = 28/236 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + V NKP G+ V    G         + YH D    S ++    +P + HR+D
Sbjct: 84  IVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLYHCDDL--SGINGV-IRPGIVHRID 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSGILVVA+   A Q L E F+   I++ Y+++V G  K +   I +  L + H    
Sbjct: 141 KDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTI-DAPLGRHHRDRL 199

Query: 212 YVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              VVK  ++    A++H++V+  F   +   C LE    TGRTHQ+RVH   +G P++G
Sbjct: 200 KYAVVKDGKR----AVTHYEVLKVFNSCSLVKCTLE----TGRTHQIRVHMAFIGHPLLG 251

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           D  Y    +   +   Q    LHA+ +   HP  G  ++  + LP +  K  + LG
Sbjct: 252 DTVYGLKKQKKLS---QEGQVLHAKTLGFIHPTTGEYVEFDSELPEYFEKIVEKLG 304


>gi|89093551|ref|ZP_01166499.1| pseudouridine synthase [Oceanospirillum sp. MED92]
 gi|89082241|gb|EAR61465.1| pseudouridine synthase [Oceanospirillum sp. MED92]
          Length = 322

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 83/308 (26%), Positives = 146/308 (47%), Gaps = 39/308 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +D    RLD+     +P  +   LQ  ++ G + V+ +  K   ++  G+ +     I
Sbjct: 11  VTDDLVGKRLDQAVAQLFPDYSRSRLQGWIKDGSLTVNGEVKKPREKLLGGEAI----AI 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
           +A   +I++ K  +  +++           +YED  I V NKPAG+ V    G   H DG
Sbjct: 67  DANLEVIEDHKPQNIPLDI-----------VYEDEHILVINKPAGLVVHPAVG---HRDG 112

Query: 132 FLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L + +        Q PR  + HRLD +T+G++VVA+T AA   L E  + R + + Y +
Sbjct: 113 TLLNALLYHCPDIAQVPRAGIVHRLDMDTTGLMVVAKTIAAQTELVEQLQERSMGREYEA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+       + +  + +       + VV   ++    A++H++V+    +    + +
Sbjct: 173 VVNGVMTGG--GVVDEPMGRHSKNRQKMAVVGVGKE----AVTHYRVLKKL-RSHTHIRL 225

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHARYMDL 297
           +  TGRTHQ+RVH  H+  P+VGD  Y   F+     +  + + L       LHA+ ++L
Sbjct: 226 KLETGRTHQIRVHMSHINYPLVGDQMYGGRFRLPKGCSDEMMDALRDFKRQALHAKKLEL 285

Query: 298 PHPEGGRL 305
            HP  G L
Sbjct: 286 WHPHSGEL 293


>gi|225620833|ref|YP_002722091.1| Pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
 gi|225215653|gb|ACN84387.1| Pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
          Length = 329

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 67/212 (31%), Positives = 106/212 (50%), Gaps = 30/212 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPR--LTHR 149
           +LYED  + V NKPAG+SV            + + Y I  F     D  G K R  + HR
Sbjct: 111 ILYEDKYLLVINKPAGMSVHCSPSEMSGTLVNALLYKIKDF-----DFVGNKERAGIIHR 165

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG++++ +       + E F+ R I+KIY ++V G+ K+      N++     IG
Sbjct: 166 LDKDTSGLMIIGKNANIVSSIQEQFKNRTIKKIYHAIVVGVLKD------NYIEINLPIG 219

Query: 210 GDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +V+  K    +    A++H KV+  F      +E+   TGRTHQ+RVH+ + G P+ G
Sbjct: 220 RHHVYRKKMTVREDGKEALTHIKVLKRF-NSHTLIEINLKTGRTHQIRVHSSYKGFPVAG 278

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           D  Y  +F         + L L A+ ++  HP
Sbjct: 279 DKIYSKSFSK------YSGLMLVAKKIEFMHP 304


>gi|322376764|ref|ZP_08051257.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M334]
 gi|321282571|gb|EFX59578.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M334]
          Length = 298

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 115/219 (52%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     D + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-DYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    +++ E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGYLESEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|169343529|ref|ZP_02864528.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
 gi|169298089|gb|EDS80179.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
          Length = 306

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 115/231 (49%), Gaps = 18/231 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQET 154
           ++YED  + V NKP G+ V    G      ++  L    D  G     +P + HR+D++T
Sbjct: 84  IVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCDDLSGINGVIRPGIVHRIDKDT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGILVVA+   A Q L E F+   I++ Y+++V G  K +   I +  L + H       
Sbjct: 144 SGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTI-DAPLGRHHRDRLKYA 202

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           VVK  ++    A++H++V+  F    C L +    TGRTHQ+RVH   +G P++GD  Y 
Sbjct: 203 VVKDGKR----AVTHYEVLKVFNS--CSLVKCNLETGRTHQIRVHMAFIGHPLLGDTVYG 256

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              +   +   Q    LHA+ +   HP  G  ++  + LP +  K  + LG
Sbjct: 257 LKKQKKLS---QEGQVLHAKTLGFIHPTTGEYVEFDSELPEYFEKIVEKLG 304


>gi|227875267|ref|ZP_03993409.1| possible pseudouridylate synthase [Mobiluncus mulieris ATCC 35243]
 gi|227844172|gb|EEJ54339.1| possible pseudouridylate synthase [Mobiluncus mulieris ATCC 35243]
          Length = 306

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 79/284 (27%), Positives = 137/284 (48%), Gaps = 27/284 (9%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           +IL  G V + +  +K ++ +QSG+ + +   I+               V + + +    
Sbjct: 33  EILAQGGVAMGETVLKKSDALQSGETLEVTAPIH-------------PKVYVPEVTPVPG 79

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQ 152
             LLYED+ + V +KPAG++   G G     + G L++    + + G   R  + HRLD 
Sbjct: 80  MKLLYEDADLVVVDKPAGVAAHTGPGWDGPTVVGALRAAGVRISTSGPVEREGIVHRLDA 139

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG +VVA++  A   L  +FR  R++KIY ++  GI K     I   + +    G ++
Sbjct: 140 GTSGAMVVAKSELAYGKLKNAFRYHRVEKIYLAVARGILKPSLGTIDAPIGRAP--GREF 197

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              V     G   A++H+   +          +Q  TGRTHQ+RVH   +G P++GD +Y
Sbjct: 198 KMAVVV---GGKPAVTHYDTAESL-PGATLARVQLETGRTHQIRVHFAAIGHPLLGDTEY 253

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
            A+ K      ++ + +LHA  +   HP  G  + + +PLP+ +
Sbjct: 254 GADAKQAVRLGLERQ-WLHASRLVFKHPRTGIEIAMDSPLPSDL 296


>gi|254361974|ref|ZP_04978105.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261493691|ref|ZP_05990210.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261494358|ref|ZP_05990852.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|153093521|gb|EDN74501.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261310007|gb|EEY11216.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261310691|gb|EEY11875.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 222

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/202 (34%), Positives = 106/202 (52%), Gaps = 13/202 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+     +  V  K       HRLD  TSGIL+ A
Sbjct: 17  VYRDNHILVINKPSGLLSVPGNRPEYYDSAMTR--VQQKYGFTEPAHRLDMATSGILLFA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            ++AA + L   FR R  +K Y +L+WG      E + +       +  D+ +  +Q   
Sbjct: 75  LSKAAEKELKRQFREREPKKHYIALLWG---KLGEKVGDKGEMNFPLICDWENRPRQKIC 131

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   AI+H++V+  +      +++ P TGR+HQLRVH+L +G PI+GD K+ AN   
Sbjct: 132 YERGKK-AITHYEVLAHYPNNIARVKLTPITGRSHQLRVHSLALGHPIIGD-KFYANPLA 189

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
              SP   +L LHA  + + HP
Sbjct: 190 KSLSP---RLCLHAESLTITHP 208


>gi|42572121|ref|NP_974151.1| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|122215273|sp|Q3ECD0|PUS2_ARATH RecName: Full=RNA pseudourine synthase 2, chloroplastic; AltName:
           Full=RNA pseudouridylate synthase 2; AltName:
           Full=RNA-uridine isomerase 2; Flags: Precursor
 gi|332197669|gb|AEE35790.1| RNA pseudourine synthase 2 [Arabidopsis thaliana]
          Length = 430

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 91/363 (25%), Positives = 158/363 (43%), Gaps = 72/363 (19%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           +V+  +  +RLD W  +    ++   +Q  +R G V V+ + V K ++ ++SG       
Sbjct: 74  IVDAAKGKIRLDSWISSRINGVSRARVQSSIRLGLVTVNGRVVDKVSHNVKSG------- 126

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
             + +N  I E + L +       ++ +   ++YED  + V NKPA + V    G     
Sbjct: 127 --DEVNCTISELQPLKA------EAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGT 178

Query: 128 HIDGFL---------------------KSWVD-----------SKGQKPRLTHRLDQETS 155
            ++G L                     +++ D           +   +P + HRLD+ T+
Sbjct: 179 LVNGILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRPGIVHRLDKGTT 238

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LVVA+   +  HL E F++  I+++Y SL  G+P   +  I   + + S        +
Sbjct: 239 GLLVVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPSPPQGRIEIPIGRDSSNRIRMAAI 298

Query: 216 VKQNEKG-ANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                 G A +A S +KVI+ FA     L E +  TGRTHQ+R HA +MG P++GD  Y 
Sbjct: 299 PGGVRGGRARHAASRYKVIETFAGGGSALVEWRLETGRTHQIRAHAKYMGVPLLGDEVY- 357

Query: 274 ANFKGNFTSPIQNKLY------------------LHARYMDLPHPEGGRL-QITAPLPAH 314
              K    S +Q ++                   LHA  +   HP  G + + + P P+ 
Sbjct: 358 GGTKSMALSLLQKRVSRSDQEEIIELISRMDRPCLHAIVLGFTHPCTGEIVKFSCPPPSD 417

Query: 315 MVK 317
           + +
Sbjct: 418 LAE 420


>gi|18310832|ref|NP_562766.1| hypothetical protein CPE1850 [Clostridium perfringens str. 13]
 gi|110801362|ref|YP_696533.1| RluA family pseudouridine synthase [Clostridium perfringens ATCC
           13124]
 gi|168206096|ref|ZP_02632101.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
 gi|168210787|ref|ZP_02636412.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
 gi|18145514|dbj|BAB81556.1| conserved hypothetical protein [Clostridium perfringens str. 13]
 gi|110676009|gb|ABG84996.1| pseudouridine synthase, RluA family [Clostridium perfringens ATCC
           13124]
 gi|170662443|gb|EDT15126.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
 gi|170711120|gb|EDT23302.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
          Length = 306

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/233 (31%), Positives = 116/233 (49%), Gaps = 22/233 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQET 154
           ++YED  + V NKP G+ V    G      ++  L    D  G     +P + HR+D++T
Sbjct: 84  IVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCDDLSGINGVIRPGIVHRIDKDT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGILVVA+   A Q L E F+   I++ Y+++V G  K +   I +  L + H       
Sbjct: 144 SGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTI-DAPLGRHHRDRLKYA 202

Query: 215 VVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           VVK  ++    A++H++V+  F   +   C LE    TGRTHQ+RVH   +G P++GD  
Sbjct: 203 VVKDGKR----AVTHYEVLKVFNSCSLVKCTLE----TGRTHQIRVHMAFIGHPLLGDTV 254

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           Y    +   +   Q    LHA+ +   HP  G  ++  + LP +  K  + LG
Sbjct: 255 YGLKKQKKLS---QEGQVLHAKTLGFIHPTTGEYVEFDSELPEYFEKIVEKLG 304


>gi|149178869|ref|ZP_01857448.1| ribosomal large subunit pseudouridine synthase D [Planctomyces
           maris DSM 8797]
 gi|148842281|gb|EDL56665.1| ribosomal large subunit pseudouridine synthase D [Planctomyces
           maris DSM 8797]
          Length = 317

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 83/312 (26%), Positives = 146/312 (46%), Gaps = 26/312 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++VE+  +  R+DR+   H+ + +   LQ+I+++G  +V+        R+  GQ + I  
Sbjct: 9   LIVEDYLDGARIDRFLSRHFRNYSTHRLQRIVQAGFAKVNGIPADPLQRVFRGQQINI-- 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYH 128
                         L    + T   + L   +LYED+ + + NKP G I+   G+ ++  
Sbjct: 67  -------------RLPEPPDKTYDPEPLPLEVLYEDAWLIIVNKPPGMIAHPAGNILSGT 113

Query: 129 IDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +   L+ ++D +       +P + HRLDQ TSGIL+VA+     + L+  F+  R+ K Y
Sbjct: 114 VANALQYYLDQQTGVRSLLRPGIVHRLDQFTSGILIVAKEHLGHRSLSIQFQQNRVSKSY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCW 242
            ++V   P  K++   N      H     V +    E   A  A + F+V++        
Sbjct: 174 LAIVRDQP--KQDLFENNDAIGEHPTQAGVCMTTHPEALRAKAAFTRFEVVERLP-GHSL 230

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +   P TGR HQ+RVH   +G PI+ D  Y  + +      + ++  LHA  ++  HP  
Sbjct: 231 IRAFPKTGRLHQIRVHLADLGFPIIADDFYGNDARLLDDRELISRQALHAEQIEFSHPVT 290

Query: 303 G-RLQITAPLPA 313
             R+ I+A +PA
Sbjct: 291 SLRMNISAGVPA 302


>gi|302879313|ref|YP_003847877.1| pseudouridine synthase, RluA family [Gallionella capsiferriformans
           ES-2]
 gi|302582102|gb|ADL56113.1| pseudouridine synthase, RluA family [Gallionella capsiferriformans
           ES-2]
          Length = 326

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 95/327 (29%), Positives = 146/327 (44%), Gaps = 48/327 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V + V+ N    +RLD+      P  +   LQ+ +   QV +D K      ++  G+ + 
Sbjct: 13  VIHFVIPNSSAGLRLDQVLATLLPEYSRSRLQEWVTLNQVLLDGKPAISKQKVWGGEKLA 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           + P +        EQ      + L          ++YED  + V NKP G+ V  GSG  
Sbjct: 73  VLPQVTQ-----SEQPYQAEDIPLD---------IVYEDDDLLVINKPVGLVVHPGSGNW 118

Query: 125 IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               ++  L  W +     PR  + HRLD++TSG+LVVA+T  +  +L    + R +++ 
Sbjct: 119 QGTLLNALLHHWPE-LALVPRAGIVHRLDKDTSGLLVVAKTLISQTNLVRQLQERSVKRE 177

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKF 240
           Y +LV G        +++       IG    + VK    E G + A++H+KV   F    
Sbjct: 178 YLALVHG-------ELSHGGYVDQPIGRHPSNRVKMAVVETGKD-AVTHYKVERTFPSCT 229

Query: 241 ---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLY 289
              C LE    TGRTHQ+RVH  ++  P+VGD  Y    KG     +Q         +  
Sbjct: 230 LLRCTLE----TGRTHQIRVHMTYLKHPLVGDSVY---LKGPQKCVLQLRDVLTRFPRQA 282

Query: 290 LHARYMDLPHP-EGGRLQITAPLPAHM 315
           LHA  + L HP  G R++   PLP  M
Sbjct: 283 LHATRLALEHPISGERMEWHVPLPDDM 309


>gi|300853931|ref|YP_003778915.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           ljungdahlii DSM 13528]
 gi|300434046|gb|ADK13813.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           ljungdahlii DSM 13528]
          Length = 299

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 82/316 (25%), Positives = 154/316 (48%), Gaps = 30/316 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V+  +E ++L R++      ++   ++    SG++ ++ KRVK N+ ++SG+ + +   
Sbjct: 9   TVDEKDEGLKL-RYYLQRVQRLSGRLIKGAALSGRIEINNKRVKLNHIVKSGESISL--- 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHI 129
                +++KE+     S N+      ++  + YED  + V NK  GI V    S  +  +
Sbjct: 65  -----NLVKEE-----SQNVEPEKMDIE--VAYEDDDLIVVNKRPGIVVHPTRSYPSGTL 112

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L  +   KG+    RL  RLD +TSG+++V + + A   L    +    +K Y +++
Sbjct: 113 ANGLMYYFKEKGEDCIVRLVSRLDMDTSGLIIVGKNQFAHMALARDMKSEEFEKSYIAVI 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  K  +  I   + ++   G D   ++  +E+G   +I+H+KVI  F      L++  
Sbjct: 173 HGKMKENEGTIDLPIYRQE--GEDIRRII--DERGQK-SITHYKVIKDFKND-QLLKLTL 226

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++G P+ GD  Y       +     N+  LHA  +  PHP G + L+
Sbjct: 227 ETGRTHQIRVHLSYLGHPLYGDTLYGKEDDSMYI----NRQALHAYRLKFPHPRGNKILE 282

Query: 307 ITAPLPAHMVKTWDSL 322
           +   +P  ++K  + +
Sbjct: 283 LETAIPEDILKLIEKI 298


>gi|78485714|ref|YP_391639.1| pseudouridine synthase, RluD [Thiomicrospira crunogena XCL-2]
 gi|78364000|gb|ABB41965.1| ribosomal large subunit pseudouridine synthase D [Thiomicrospira
           crunogena XCL-2]
          Length = 352

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/242 (30%), Positives = 124/242 (51%), Gaps = 34/242 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKPAG+ V  G+G   + DG L + +    ++  + PR  + HRLD+ET
Sbjct: 85  VVYEDEDILVLNKPAGLVVHPGAG---NPDGTLLNALLFHYETIREVPRAGIVHRLDKET 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA+   A  HL E  +   ++++Y ++V G      + I+   + K  IG    H
Sbjct: 142 SGLMVVAKNVPAQTHLVEQLQQHDVERVYDAIVVG------KMISGGTISKP-IGR---H 191

Query: 215 VVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
              +        G   A SH++V++ F ++   + ++  TGRTHQ+RVH  ++G P+VGD
Sbjct: 192 PTDRKRMAVLTVGGKPATSHYRVLERF-REHTHVRVKLETGRTHQIRVHMAYLGFPLVGD 250

Query: 270 HKYCANFK------GNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             Y    +        F   ++   +  LHA  + L HP  G+ ++    +P  M++  D
Sbjct: 251 PVYAGRLRIPQQMMPEFADYLRGFKRQALHAGQLSLTHPRTGKTMKWKVSMPDDMLELID 310

Query: 321 SL 322
            L
Sbjct: 311 IL 312


>gi|127511717|ref|YP_001092914.1| pseudouridylate synthase [Shewanella loihica PV-4]
 gi|126637012|gb|ABO22655.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           loihica PV-4]
          Length = 225

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/215 (32%), Positives = 111/215 (51%), Gaps = 16/215 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  I V NKP+G+    G   AY+   + +   D    +  + HRLD  TSGI+VV
Sbjct: 16  ILHEDKDILVVNKPSGLLSVPGRDPAYYDSVYTRVLRDHPNAQ--IVHRLDMATSGIIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A  R+A + L   FR R   KIY++ V G  K ++  +   L+       D+ +  KQ  
Sbjct: 74  ALRRSAERELKRQFRDRETHKIYYARVAGHLKAEQGSVDYPLI------CDWPNRPKQKV 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    + + F+VI   A++   +++ P TGR+HQLRVH + +G PI+GD+ Y      
Sbjct: 128 DHQIGKASKTLFEVI-SRAKRSTLVKLTPITGRSHQLRVHMMAIGHPILGDNFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                   +L LHA+ + L HP   + +  + P+P
Sbjct: 187 RLAP----RLLLHAQSLSLTHPYSKQPMTFSTPIP 217


>gi|89898789|ref|YP_515899.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           felis Fe/C-56]
 gi|89332161|dbj|BAE81754.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           felis Fe/C-56]
          Length = 330

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/230 (31%), Positives = 110/230 (47%), Gaps = 32/230 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +YED  I V NKP  + V    G         + + I   LK     +  +P + HRLD+
Sbjct: 87  VYEDEMILVINKPRDMVVHPAPGHIRGTVVHALLHEIGERLKQEFPEEPWRPGIIHRLDK 146

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+L+ A+TR A    +E F  ++++K Y ++  G P      + +  L + H     
Sbjct: 147 DTSGLLITAKTRQAKTIYSELFATKQLKKSYLAICVGKP---TATLIHTKLARHHSKRKE 203

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + V    ++    AI+H +V+  +  K   + ++P TGRTHQLRVH  H+  PI+GD  Y
Sbjct: 204 MAVSLTGKE----AITHCEVL-AYNGKLSLVLLRPETGRTHQLRVHMKHLNTPILGDPVY 258

Query: 273 CANFKGNFTSPIQNKLY------LHARYMDLPHPEG-GRLQITAPLPAHM 315
                    SP  N  Y      LHA  +D  HP+   RL +T  LP  M
Sbjct: 259 G--------SPSINAGYGLDKQQLHAYSLDFIHPQTHRRLNLTTELPCDM 300


>gi|296104263|ref|YP_003614409.1| 23S rRNA pseudouridine synthase D [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295058722|gb|ADF63460.1| 23S rRNA pseudouridine synthase D [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 282

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/247 (29%), Positives = 127/247 (51%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 42  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 98

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G         E I+    K++H+   
Sbjct: 99  TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMS-- 156

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 157 -VHPMGKP------AVTHYRIMEHF-RIHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 208

Query: 272 YCANFK------GNFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G +++  AP+P  MV+  D++
Sbjct: 209 YGGRPRPPKGASDEFISVLRKFDRQALHATMLRLYHPVSGIQMEWHAPIPQDMVELIDAM 268

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 269 RADFEEH 275


>gi|315651411|ref|ZP_07904436.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saburreum DSM 3986]
 gi|315486370|gb|EFU76727.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saburreum DSM 3986]
          Length = 303

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/315 (23%), Positives = 146/315 (46%), Gaps = 38/315 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++ E  + + R+D +   +    +   +Q +++ G+V ++ K +K N R++ G+ V +  
Sbjct: 6   IIAEESDVDKRIDLFLAKNLESFSRSYIQDLIKKGKVTINNKIIKANYRLKEGECVVLDI 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                  I+ E   +D               +LYED  + + NKP G+ V   +G     
Sbjct: 66  PKPEPLEIVPENIPID---------------ILYEDEDVILVNKPKGMVVHPAAGHYKGT 110

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH    L     +   +P + HR+D +T+G++++ +   A QH+ +      I 
Sbjct: 111 LVNALLYHCKSNLSGI--NGVLRPGIVHRIDMDTTGVIIICKNDIAHQHIAKQLANHSIT 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G  K + E + +  + +S      + V    +K    A++H+KV++     +
Sbjct: 169 RKYVAIVTGNIK-EDEGVIDAAIARSKSDRKKMAV----DKDGKRAVTHYKVLERL-NGY 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++E    TGRTHQ+RVH  ++  P++GD  Y     G     +Q +  LHA  +   HP
Sbjct: 223 TYIECVLETGRTHQIRVHMAYIHHPLLGDEVYA----GKSGMKLQGQC-LHAMVLGFIHP 277

Query: 301 EGGR-LQITAPLPAH 314
           +    ++  AP+P +
Sbjct: 278 KTKEYMEFEAPIPEY 292


>gi|313884116|ref|ZP_07817882.1| pseudouridine synthase, RluA family [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620563|gb|EFR31986.1| pseudouridine synthase, RluA family [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 314

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 149/318 (46%), Gaps = 36/318 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++++ RLD+        ++   +Q +++ G V V+ +  K N ++   +++ +       
Sbjct: 17  EDQSGRLDKVLVEE-SELSRTQIQSLIKQGLVTVNGQVEKANYKLSGQELIEMQ------ 69

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
              + E+++L+        +  +   ++YED  + V NK AG+ V    G         +
Sbjct: 70  ---VPEEEVLEIE------AQAIPLDIIYEDDDLLVINKEAGMVVHPSKGHPRDTLVNAL 120

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            YH    L +  DS   +P L HR+D++TSG+LVVA+   + ++L++      + +IY+ 
Sbjct: 121 VYHFGNHLAAGSDSY--RPGLVHRIDKDTSGLLVVAKNNESHRYLSQQLMDHTLGRIYYC 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  + K+  I   L +       Y H   Q +     A + F+V++ +      ++ 
Sbjct: 179 LVEGQMEVKQGSIEIPLARDPKNRLKY-HADAQGKP----AWTDFEVLESYPSA-SLIQA 232

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +  TGRTHQ+R H  H+G PI+GD  Y  N       P     +LHA ++   HP    L
Sbjct: 233 ELKTGRTHQIRAHFEHIGHPIIGDPVY--NRDSLNLWPTDQGQFLHAGHIHFIHPRSHEL 290

Query: 306 -QITAPLPAHMVKTWDSL 322
            +  APLPA  +   + L
Sbjct: 291 IEFHAPLPASFINLQNHL 308


>gi|182625703|ref|ZP_02953472.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
 gi|177909105|gb|EDT71580.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
          Length = 306

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/233 (31%), Positives = 116/233 (49%), Gaps = 22/233 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQET 154
           ++YED  + V NKP G+ V    G      ++  L    D  G     +P + HR+D++T
Sbjct: 84  IVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCDDLSGINGVIRPGIVHRIDKDT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGILVVA+   A Q L E F+   I++ Y+++V G  K +   I +  L + H       
Sbjct: 144 SGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKKEGGTI-DAPLGRHHRDRLKYA 202

Query: 215 VVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           VVK  ++    A++H++V+  F   +   C LE    TGRTHQ+RVH   +G P++GD  
Sbjct: 203 VVKDGKR----AVTHYEVLKVFNSCSLVKCTLE----TGRTHQIRVHMAFIGHPLLGDTV 254

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           Y    +   +   Q    LHA+ +   HP  G  ++  + LP +  K  + LG
Sbjct: 255 YGLKKQKKLS---QEGQVLHAKTLGFIHPTTGEYVEFDSELPEYFKKIVEKLG 304


>gi|198244685|ref|YP_002214048.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|205351435|ref|YP_002225236.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|207855608|ref|YP_002242259.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|197939201|gb|ACH76534.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|205271216|emb|CAR36004.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Gallinarum str. 287/91]
 gi|206707411|emb|CAR31684.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Enteritidis str.
           P125109]
 gi|326621792|gb|EGE28137.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|326626458|gb|EGE32801.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 219

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/208 (33%), Positives = 106/208 (50%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LEAHKDSIM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y + 
Sbjct: 126 KVCYETG-KPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +       +L LHA  + + HP  G
Sbjct: 185 EALSLAP----RLQLHAEMLTITHPAYG 208


>gi|146328697|ref|YP_001210177.1| ribosomal large subunit pseudouridine synthase, RluD [Dichelobacter
           nodosus VCS1703A]
 gi|146232167|gb|ABQ13145.1| ribosomal large subunit pseudouridine synthase, RluD [Dichelobacter
           nodosus VCS1703A]
          Length = 322

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 93/327 (28%), Positives = 152/327 (46%), Gaps = 40/327 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIPP 69
           +V+++   +RLD+    +YP  +    Q  + +G V ++    K  + + +G Q+  +  
Sbjct: 13  IVDHNNHALRLDQVLARNYPEFSRNRWQDAINAGTVLLNGAAAKSKSLVCAGDQITGV-- 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  + +E +  DS+ NL  +       +LY D  I V NKPAG+ V    G   H 
Sbjct: 71  -------LTQEIQTEDSAQNLPLN-------ILYADDDIIVINKPAGLVVHPAVG--NHD 114

Query: 130 DGFLKSWVDSKGQK---PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +  L + +    Q    PR  + HRLD++TSG +V+A +  A   L    + R + +IY 
Sbjct: 115 NTLLNALLYHFPQTKHLPRSGIVHRLDKDTSGAMVIAHSARAHTDLVRQLQNRSMGRIYL 174

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV+G      + I   L    H        V+ + K    AI+H+++ + + Q    L 
Sbjct: 175 ALVYGY-ITAGDTID--LPIGRHAKDRLKMAVRPDGKP---AITHYRIEERW-QTLTLLR 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLY-------LHARYMD 296
           +Q  TGRTHQ+RVH  H   P+VGD  Y A  F  +  + +Q +         LHA  + 
Sbjct: 228 VQLETGRTHQIRVHLSHHRHPLVGDKLYGARPFLASSLTELQRQALAEFPRQALHAVELH 287

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
           L HP     ++ TAPLP  M + +  L
Sbjct: 288 LHHPATNEIMRFTAPLPDDMTQLFTIL 314


>gi|308185634|ref|YP_003929765.1| ribosomal large subunit pseudouridine synthase A [Pantoea vagans
           C9-1]
 gi|308056144|gb|ADO08316.1| ribosomal large subunit pseudouridine synthase A [Pantoea vagans
           C9-1]
          Length = 217

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 106/209 (50%), Gaps = 22/209 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D+ I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++V
Sbjct: 14  ILYQDAHIMVVNKPSGLLSVPGR--LDEHKDSVM-TRIQRDFPQAESVHRLDMATSGVMV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVH 214
           VA T+AA + L   FR R   K Y + +WG P+ ++       I +W  +   +      
Sbjct: 71  VALTKAAERELKRQFREREPSKTYVACIWGHPEKEEGLVDLPLICDWPNRPKQM------ 124

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V  +  K A    + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD+ Y  
Sbjct: 125 VCFETGKAAQ---TEYQVLEYRADNSARVSLKPITGRSHQLRVHMLALGHPILGDNFYAH 181

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                  +    +L LHA  + + HP  G
Sbjct: 182 PEAKAMAA----RLLLHAESLTITHPAFG 206


>gi|291519368|emb|CBK74589.1| pseudouridine synthase, RluA family [Butyrivibrio fibrisolvens
           16/4]
          Length = 311

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/272 (26%), Positives = 133/272 (48%), Gaps = 18/272 (6%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PP 69
           ++  + N R D++ K   P+ +   + K+LR   + +++K+   + ++  G V++I    
Sbjct: 6   IDTGDSNQRFDKFLKRVLPNASTSFIYKMLRKKNITLNEKKADGSEKLNVGDVIKIWFSD 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
              A    + E+  L  S+   K +      +++ED  + + NKPAG+  Q  S     I
Sbjct: 66  ETFAKMAGVSERDELYYSIKEIKPN----INIVFEDDDMIIINKPAGVKSQKDSPSDISI 121

Query: 130 DGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           +    S++ +  Q          P + +RLD+ TSGI++ A+   AAQ L ++ + R  +
Sbjct: 122 NEMAISYMIASNQLSEESFKHFHPSVCNRLDRNTSGIVLFAKNLHAAQSLGQALKERSCK 181

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y ++V G   +K++ I  +L K      + V + K     +    + +  I     KF
Sbjct: 182 KLYRAVVLGKVDSKQQ-IEGFLWKDE--ATNKVTISKNEIPDSKPIKTAYNPIKNIGDKF 238

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             LE+   TGRTHQ+R H   +G PI+GD+KY
Sbjct: 239 TLLEIHLITGRTHQIRAHLASIGHPILGDNKY 270


>gi|217077277|ref|YP_002334995.1| ribosomal large subunit pseudouridine synthase C [Thermosipho
           africanus TCF52B]
 gi|217037132|gb|ACJ75654.1| ribosomal large subunit pseudouridine synthase C [Thermosipho
           africanus TCF52B]
          Length = 293

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 80/262 (30%), Positives = 130/262 (49%), Gaps = 33/262 (12%)

Query: 16  EENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVIN 72
           EEN   RLD++ +    ++    + K++R+G+++V+ K+VK  + +I+ G  + I   I+
Sbjct: 5   EENYYSRLDKFLRKKLLNLPLSAIYKLIRTGKIKVNGKKVKNPSYKIEIGDEITIEEDIS 64

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
             N  I   K++   ++L          ++YED+ I + NKPAGI +  G G  IA  I+
Sbjct: 65  KYNREI-NNKVVPIKMDLD---------IVYEDNDILIINKPAGIPIHPGKGTHIATLIE 114

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G +  +   K   P L HRLD+ TSGIL++A+   +A+ L +    R I+K Y +L  G 
Sbjct: 115 GLI-YYGQEKNFTPHLVHRLDKHTSGILIIAKNTQSARELGDIIAGRSIKKEYIALCKG- 172

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K  KE   +  L              +N++     I+  KV      +F  L +   TG
Sbjct: 173 -KLSKEGKIDIPL--------------ENKQALTTFITQ-KVYKTHLGEFSLLNVNIKTG 216

Query: 251 RTHQLRVHALHMGCPIVGDHKY 272
           R HQ+R H   +  PI+GD  Y
Sbjct: 217 RKHQIRKHLSLINHPIIGDDVY 238


>gi|161615592|ref|YP_001589557.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|161364956|gb|ABX68724.1| hypothetical protein SPAB_03373 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
          Length = 300

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 124/245 (50%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 60  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 116

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G         E I+    K++H+   
Sbjct: 117 TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPISRHPTKRTHMS-- 174

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 175 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 226

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV   D++
Sbjct: 227 YGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPVSGIEMEWHAPIPQDMVDLIDAM 286

Query: 323 GFKYD 327
              ++
Sbjct: 287 RADFE 291


>gi|154498381|ref|ZP_02036759.1| hypothetical protein BACCAP_02370 [Bacteroides capillosus ATCC
           29799]
 gi|150272449|gb|EDM99634.1| hypothetical protein BACCAP_02370 [Bacteroides capillosus ATCC
           29799]
          Length = 299

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 116/225 (51%), Gaps = 19/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----IAYHIDGFLKSWVD-SKGQKPRLTHRLDQETS 155
           +LY+D  +   +KPAG+   G  G     AY +     +  D S+ +K  + HRLD++TS
Sbjct: 81  ILYQDRDLIAIDKPAGLLTVGHEGERQRTAYRL--LADTLRDGSREKKLFVVHRLDRDTS 138

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++ AR     + L E +     ++IY ++  G P+ ++  + +WL + S      V  
Sbjct: 139 GAVLFARNEEMKRALQEDWDSLVKERIYLAVTVGAPEREEGVVRSWLRETST----RVVY 194

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                 GA  A++ +KV+   + ++  + +   TGR +Q+RVH   +GCP+ GD KY   
Sbjct: 195 SGGPGSGAKEAVTRYKVL-ARSGEYALVRVALDTGRKNQIRVHMADLGCPVAGDKKY--- 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTW 319
             G+ + P+ ++L LHA  + +  P  G  L +TAP+P   ++ +
Sbjct: 251 --GDGSGPM-DRLALHAVRLTITDPRTGAPLTVTAPVPKSFLRLF 292


>gi|309378792|emb|CBX22618.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 374

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 87/312 (27%), Positives = 144/312 (46%), Gaps = 42/312 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA-LNHII 78
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ +R+    +A  +   
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKPSQPKDKMIGGEHIRVSIRPSAEYSAFA 99

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
            E   LD               ++YED  + V NKPAG+ V   +G      ++G L + 
Sbjct: 100 PEPMALD---------------IVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AH 143

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKN 193
                Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P +
Sbjct: 144 CPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFD 203

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGR
Sbjct: 204 GK--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGR 254

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YLHARYMDLPHPEGGR 304
           THQ+RVH      P+ GD  Y  N +   + P++  +        LHA  +   HP+ G 
Sbjct: 255 THQIRVHMREANHPLAGDPVY-GNLRHPCSEPVKEAVKSLGARQALHAYRLSFVHPKTGE 313

Query: 305 -LQITAPLPAHM 315
            +   AP+P  M
Sbjct: 314 TVSFEAPIPDDM 325


>gi|16763485|ref|NP_459100.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|161612432|ref|YP_001586397.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167550721|ref|ZP_02344478.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|168234851|ref|ZP_02659909.1| pseudouridine synthase, RluA family protein [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. SL480]
 gi|168243497|ref|ZP_02668429.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|168262227|ref|ZP_02684200.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|168464361|ref|ZP_02698264.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|168820922|ref|ZP_02832922.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|194448284|ref|YP_002044064.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194737390|ref|YP_002113113.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197250796|ref|YP_002145080.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197265379|ref|ZP_03165453.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|204927079|ref|ZP_03218281.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|238911153|ref|ZP_04654990.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|34395809|sp|Q8ZRV9|RLUA_SALTY RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|16418593|gb|AAL19059.1| 23S rRNA pseudouridylate 746 synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|161361796|gb|ABX65564.1| hypothetical protein SPAB_00121 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194406588|gb|ACF66807.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194712892|gb|ACF92113.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|195632683|gb|EDX51137.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|197214499|gb|ACH51896.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197243634|gb|EDY26254.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197291993|gb|EDY31343.1| pseudouridine synthase, RluA family protein [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. SL480]
 gi|204323744|gb|EDZ08939.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|205324422|gb|EDZ12261.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|205337540|gb|EDZ24304.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|205342421|gb|EDZ29185.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|205348767|gb|EDZ35398.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|261245328|emb|CBG23116.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           D23580]
 gi|267991767|gb|ACY86652.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301156724|emb|CBW16198.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           SL1344]
 gi|312911065|dbj|BAJ35039.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320084333|emb|CBY94126.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           2007-60-3289-1]
 gi|321222334|gb|EFX47406.1| Ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|323128413|gb|ADX15843.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|332987047|gb|AEF06030.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 219

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/208 (33%), Positives = 106/208 (50%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LEAHKDSIM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y + 
Sbjct: 126 KVCYETG-KPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +       +L LHA  + + HP  G
Sbjct: 185 EALSLAP----RLQLHAEMLTITHPAYG 208


>gi|218288262|ref|ZP_03492561.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|218241621|gb|EED08794.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
          Length = 303

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 81/324 (25%), Positives = 157/324 (48%), Gaps = 37/324 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + + + ++   + +W +   P +    + K +R+G+V+V+ KR K + R+  G +V +  
Sbjct: 4   ITIGSSDDGKPVHKWLRLLLPGLPLSGVYKSIRTGRVKVNGKRAKQDTRLHEGDIVHL-- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG---- 124
                 +   E      +  + K+    ++I +LYED +I   NKPAG+      G    
Sbjct: 62  ------YFSDEDYASLHAHPVAKYQGVSRAIDILYEDDEIVAVNKPAGVLTHPADGEYKT 115

Query: 125 -IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +A  ++ ++      +G  +    HRLD+ TSG+++ A+T  AA+   ++F+   ++K 
Sbjct: 116 SLAAQVEAYVYDRGAREGAFRAAPVHRLDRNTSGVVIFAKTARAAKAWADAFQRGEVEKE 175

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G    +     +   +     G+   VV+ + K +  A   ++V+   ++    
Sbjct: 176 YLAIVEGAWSGRGRVAVDVQRE-----GNVTRVVEDSGKPSETA---YEVV-ASSRGTSL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHPE 301
           + ++  TGRTHQ+RVH  ++G P++ D KY A        PI+ +  YLHA  +      
Sbjct: 227 VRLRLLTGRTHQIRVHMANLGHPLLADRKYGAR-------PIRGESFYLHAHRVRW---- 275

Query: 302 GGRLQITAPLPAHMVKTWDSLGFK 325
              + +TAPLP  M +   +LG+K
Sbjct: 276 -NEVDVTAPLPDRMTEKLRTLGYK 298


>gi|168230365|ref|ZP_02655423.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|194471112|ref|ZP_03077096.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194457476|gb|EDX46315.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|205334924|gb|EDZ21688.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
          Length = 219

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/208 (33%), Positives = 106/208 (50%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LEAHKDSIM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y + 
Sbjct: 126 KVCYETGKP-AQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +       +L LHA  + + HP  G
Sbjct: 185 EALSLAP----RLQLHAEMLTITHPTYG 208


>gi|62178660|ref|YP_215077.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|194443178|ref|YP_002039326.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|224581938|ref|YP_002635736.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|62126293|gb|AAX63996.1| 23S rRNA pseudouridylate 746 synthase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|194401841|gb|ACF62063.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|224466465|gb|ACN44295.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Paratyphi C strain
           RKS4594]
 gi|322615916|gb|EFY12833.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322620701|gb|EFY17561.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322623948|gb|EFY20785.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322627396|gb|EFY24187.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322630703|gb|EFY27467.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322638077|gb|EFY34778.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322640563|gb|EFY37214.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322647703|gb|EFY44188.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322648053|gb|EFY44520.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322656915|gb|EFY53201.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322657374|gb|EFY53646.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322663694|gb|EFY59894.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322666527|gb|EFY62705.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322672314|gb|EFY68426.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322676374|gb|EFY72445.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322679533|gb|EFY75578.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322686138|gb|EFY82122.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|322713113|gb|EFZ04684.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323194982|gb|EFZ80168.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323200109|gb|EFZ85196.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323201070|gb|EFZ86139.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323209467|gb|EFZ94400.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323212281|gb|EFZ97105.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323216586|gb|EGA01312.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323222475|gb|EGA06845.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323225786|gb|EGA10006.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323228673|gb|EGA12802.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323236713|gb|EGA20789.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323239786|gb|EGA23833.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323242166|gb|EGA26195.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323249409|gb|EGA33325.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323252256|gb|EGA36107.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323256653|gb|EGA40383.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323261313|gb|EGA44900.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323265507|gb|EGA49003.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323271705|gb|EGA55123.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
          Length = 219

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/208 (33%), Positives = 106/208 (50%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LEAHKDSIM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y + 
Sbjct: 126 KVCYETG-KPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +       +L LHA  + + HP  G
Sbjct: 185 EALSLAP----RLQLHAEMLTITHPAYG 208


>gi|330836420|ref|YP_004411061.1| pseudouridine synthase, RluA family [Spirochaeta coccoides DSM
           17374]
 gi|329748323|gb|AEC01679.1| pseudouridine synthase, RluA family [Spirochaeta coccoides DSM
           17374]
          Length = 329

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 79/256 (30%), Positives = 120/256 (46%), Gaps = 40/256 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----------IAYHIDGFLKSW------------- 136
           +LYED  I   +KP GI V  G+G             Y  D F++++             
Sbjct: 81  ILYEDDDILFIDKPQGIVVHPGAGNPDGTVVNALVFRYGPD-FIRAYGGQDEHEDAGDET 139

Query: 137 ---VD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              VD +   +P + HRLD++TSG++V+ARTR A  ++   F      K Y +LV G  K
Sbjct: 140 DEAVDRTDFLRPGIVHRLDKDTSGVMVIARTRLAHGYMARQFSEHTAVKHYIALVEGSMK 199

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGR 251
           + +  I   L +  +   D         K    A + ++V+  +    C  L ++  TGR
Sbjct: 200 DDEGVIITNLARDRN---DRKKFRVSTGKEGKRAETRWRVVARYG--VCTLLRIRIMTGR 254

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  H+G P+VGD  Y    K +F       L LHAR +D+  P  GR L+I+AP
Sbjct: 255 THQIRVHMAHLGHPVVGDGVYGGRRK-SFPG---VTLMLHARLLDVSRPSDGRHLKISAP 310

Query: 311 LPAHMVKTWDSLGFKY 326
           +P   ++     G  +
Sbjct: 311 VPQRFIELVHEAGGSF 326


>gi|310640966|ref|YP_003945724.1| pseudouridine synthase, rlua family protein [Paenibacillus polymyxa
           SC2]
 gi|309245916|gb|ADO55483.1| pseudouridine synthase, RluA family protein [Paenibacillus polymyxa
           SC2]
          Length = 319

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/244 (30%), Positives = 122/244 (50%), Gaps = 31/244 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQ--KPRLTHRLDQET 154
           +L+ED  + V NK AG+ V    G   H  G L + V     +KG+  + R  HRLDQET
Sbjct: 86  ILFEDEHLLVVNKAAGMVVHPTHG---HYTGTLANGVVHYWQAKGELFRFRPVHRLDQET 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+LVVA+     QH++E      + K Y +LV G P+ ++  +   + +      D  H
Sbjct: 143 TGVLVVAKNPYVHQHISEQMIAGTVDKRYTALVHGRPQQQEGRVDGPIDRNP----DNPH 198

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +      G   A++ +K+ + ++     + ++  +GRTHQ+RVH  ++GCP++GD  Y  
Sbjct: 199 LRMVTPDGYP-ALTLYKLEEVWSGG-SRIGLKLESGRTHQIRVHMTYIGCPLIGDKMY-- 254

Query: 275 NFKGNFTSPIQNKLY-----------LHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             +      +Q +LY           LHA  + L HP  G R+   APLP  M++  + L
Sbjct: 255 --RITPNDAVQRELYDQLDARMPRQALHASELSLVHPVTGERMTFYAPLPDDMIRMQELL 312

Query: 323 GFKY 326
             +Y
Sbjct: 313 RAQY 316


>gi|307267026|ref|ZP_07548541.1| pseudouridine synthase, RluA family [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|306917951|gb|EFN48210.1| pseudouridine synthase, RluA family [Thermoanaerobacter wiegelii
           Rt8.B1]
          Length = 305

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 119/238 (50%), Gaps = 35/238 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYH------IDGFLKSWVDSKGQKPR 145
           +LYED  I V NKP G+ V    G         + YH      I+G L+         P 
Sbjct: 84  ILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGILR---------PG 134

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD++TSG++VVA+   A   L+   + R + K Y ++V G+ K+++  I   L+ +
Sbjct: 135 IVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKHEEGKI-EALIGR 193

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
             +    + V++       YA++ +KV++ F +    +E    TGRTHQ+RVH  ++G P
Sbjct: 194 HPVDRKKMAVIED----GRYALTLYKVLERFKEN-TLVEAVIKTGRTHQIRVHMAYIGHP 248

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +VGD  Y    K  F    Q    LH+  +   HP +G  ++  APLP + V+  + L
Sbjct: 249 VVGDPVYGFK-KQKFKLEGQA---LHSHVLGFMHPTKGVYMEFEAPLPEYFVRLIEIL 302


>gi|167040454|ref|YP_001663439.1| RluA family pseudouridine synthase [Thermoanaerobacter sp. X514]
 gi|300914505|ref|ZP_07131821.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X561]
 gi|307724259|ref|YP_003904010.1| RluA family pseudouridine synthase [Thermoanaerobacter sp. X513]
 gi|166854694|gb|ABY93103.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X514]
 gi|300889440|gb|EFK84586.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X561]
 gi|307581320|gb|ADN54719.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X513]
          Length = 305

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 79/240 (32%), Positives = 119/240 (49%), Gaps = 39/240 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYH------IDGFLKSWVDSKGQKPR 145
           +LYED  I V NKP G+ V    G         + YH      I+G L+         P 
Sbjct: 84  ILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGILR---------PG 134

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD++TSG++VVA+   A   L+   + R + K Y ++V G+ K+++  I      +
Sbjct: 135 IVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDEEGKI------E 188

Query: 206 SHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           + IG   V   K    E G  YA++ +KV++ F +    +E    TGRTHQ+RVH  ++G
Sbjct: 189 APIGRHPVDRKKMAVIEDG-RYALTLYKVLERFKEN-TLVEAVIKTGRTHQIRVHMAYIG 246

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            PIVGDH Y    +  F    Q    LH+  +   HP +G  ++  APLP +  K  + L
Sbjct: 247 HPIVGDHVYGFK-RQKFKLEGQA---LHSSVLGFMHPTKGVYMEFEAPLPEYFKKLIEIL 302


>gi|213023738|ref|ZP_03338185.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 282

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 124/245 (50%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 42  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 98

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G         E I+    K++H+   
Sbjct: 99  TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPISRHPTKRTHMS-- 156

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 157 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 208

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV   D++
Sbjct: 209 YGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPVSGIEMEWHAPIPQDMVDLIDAM 268

Query: 323 GFKYD 327
              ++
Sbjct: 269 RADFE 273


>gi|152997613|ref|YP_001342448.1| RluA family pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150838537|gb|ABR72513.1| pseudouridine synthase, RluA family [Marinomonas sp. MWYL1]
          Length = 327

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 90/320 (28%), Positives = 150/320 (46%), Gaps = 43/320 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R D+     +   +   +Q  ++ G ++VD K  K   ++  G+VV +  VI A      
Sbjct: 19  RFDQIATELFSDYSRSRIQSWIKEGVLKVDGKITKPKEKLFGGEVVTLDIVIEAQEE--H 76

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-- 137
           E + +D  V             +YED  I + NKPAG+ V    G   + DG L + +  
Sbjct: 77  EAQAMDLDV-------------VYEDDDIMIINKPAGLVVHPAVG---NRDGTLMNAILH 120

Query: 138 --DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                   PR  + HRLD+ET+G++VVA+T AA   L    + R + + Y ++  G+   
Sbjct: 121 HAPETAHIPRAGIVHRLDKETTGLMVVAKTLAAQTDLVMQLQERSMGREYEAVSIGV--- 177

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQKFCWLEMQPHTGR 251
               +    +    IG    +  KQ  +  N   A++H+++++ F +    + ++  TGR
Sbjct: 178 ----MTGGGVVDEPIGRHPHNRQKQAVEPVNGKDAVTHYRLVERF-KNHTHIRLKLETGR 232

Query: 252 THQLRVHALHMGCPIVGDHKYCANFK-GNFTSP-IQNKL------YLHARYMDLPHPEGG 303
           THQ+RVH   +  P+VGD +Y    K     SP +Q++L       LHA+ ++L HP  G
Sbjct: 233 THQIRVHMAFIQYPLVGDPQYGGRLKMPKACSPELQDELRHFRRQALHAKKLELSHPITG 292

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             ++    LP  M K  D+L
Sbjct: 293 EWMEWEIDLPDDMKKLLDAL 312


>gi|182414827|ref|YP_001819893.1| RluA family pseudouridine synthase [Opitutus terrae PB90-1]
 gi|177842041|gb|ACB76293.1| pseudouridine synthase, RluA family [Opitutus terrae PB90-1]
          Length = 311

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 116/233 (49%), Gaps = 20/233 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---------SKGQKPRLTHRLD 151
           +L+ED  +   NK AG+ V    G+A   D  + + +             ++P + HRLD
Sbjct: 82  VLFEDKHMLAVNKAAGMVVH--PGVATSEDTLVHALLAHCAGSLSGIGGVERPGIVHRLD 139

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ET+G++VVA+T AA + L + F  R ++K Y +LV G+P+     I   + +       
Sbjct: 140 KETTGVIVVAKTDAAHRALADQFATRTLKKEYVALVAGVPRLLSGSIDRAIARHP----V 195

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           + H +   E G   A + +++++ F      +  +  TGRTHQ+RVH   +G PI+GD  
Sbjct: 196 HRHRMTVGE-GGRPARTDWELVEAFGDIGALVRCRIFTGRTHQIRVHLKSLGHPILGDAL 254

Query: 272 YCANFKGNF-TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           Y    +    T P   ++ LHA ++ L HP  G+ L + APLP   V     L
Sbjct: 255 YGWKPEPRLATQP--ARVMLHAEHLVLTHPISGKELDLRAPLPKDFVAMIKEL 305


>gi|46446340|ref|YP_007705.1| hypothetical protein pc0706 [Candidatus Protochlamydia amoebophila
           UWE25]
 gi|46399981|emb|CAF23430.1| conserved hypothetical protein [Candidatus Protochlamydia
           amoebophila UWE25]
          Length = 298

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 84/315 (26%), Positives = 148/315 (46%), Gaps = 33/315 (10%)

Query: 11  VVENDEENMRLDRWF-KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIP 68
           VV N+E   +L  +  K   PH +   L++++     +V+ +  +F +  + +G  V   
Sbjct: 8   VVSNEESGSKLVSFLSKQLSPHYSSRQLKRMIEQNDCQVNGRIERFASTFLGTGDRV--- 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
               +LN    +Q         T +    +S +LYED  +++++KPA ++      IA  
Sbjct: 65  ----SLNLKNPQQ---------TFNRQLEQSRILYEDEDLFIYDKPAEMNCDEQGIIALL 111

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              F            +L HRLD++T+G+L +A+ +   + L   F+  ++ K Y ++V 
Sbjct: 112 RPSF---------PSIQLIHRLDRQTTGVLALAKNKTTFEALVNQFKQLKVSKSYRAIVD 162

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           GI  + K  I N+L KK    G  +     + +G  YA +++  ++   +K   +   P 
Sbjct: 163 GILTSSKGHIENYLGKKHVYQGQSIWGEVPSFQGL-YASTYWSCLE-IGKKASLVRCFPK 220

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           TGRTHQ+RVH   +G PI+GD++Y   F   +  P   +  LHA  M   HP    +L +
Sbjct: 221 TGRTHQIRVHLAGLGHPILGDYQYGKKFTCLYNPP---RYLLHAEEMGFIHPRTRQKLIV 277

Query: 308 TAPLPAHMVKTWDSL 322
            A LP   +  +  L
Sbjct: 278 QAILPEDFLGAYKKL 292


>gi|256752464|ref|ZP_05493322.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           CCSD1]
 gi|256748666|gb|EEU61712.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           CCSD1]
          Length = 305

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 79/240 (32%), Positives = 119/240 (49%), Gaps = 39/240 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYH------IDGFLKSWVDSKGQKPR 145
           +LYED  I V NKP G+ V    G         + YH      I+G L+         P 
Sbjct: 84  ILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGILR---------PG 134

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD++TSG++VVA+   A   L+   + R + K Y ++V G+ K+++  I      +
Sbjct: 135 IVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDEEGKI------E 188

Query: 206 SHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           + IG   V   K    E G  YA++ +KV++ F +    +E    TGRTHQ+RVH  ++G
Sbjct: 189 APIGRHPVDRKKMAVIEDG-RYALTLYKVLERFKEN-TLVEAVIKTGRTHQIRVHMAYIG 246

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            PIVGDH Y    +  F    Q    LH+  +   HP +G  ++  APLP +  K  + L
Sbjct: 247 HPIVGDHVYGFK-RQKFKLEGQA---LHSSVLGFMHPTKGVYMEFEAPLPEYFKKLIEIL 302


>gi|89095078|ref|ZP_01168005.1| Pseudouridine synthase [Oceanospirillum sp. MED92]
 gi|89080639|gb|EAR59884.1| Pseudouridine synthase [Oceanospirillum sp. MED92]
          Length = 210

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/218 (32%), Positives = 109/218 (50%), Gaps = 22/218 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y D  I V NKP  +    G G        L   V +     R+ HRLD  TSGI+++
Sbjct: 8   IIYADEHIVVANKPWDMLSVPGKGEDKQ--DCLWRRVQTSYPTARIVHRLDYATSGIIIL 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-----ANWLLKKSHIGGDYVHV 215
           A T  A + L+ SF+ R  QK Y +++ G PK     +      +W  +   I       
Sbjct: 66  ALTLDAQRALSRSFQERETQKRYQAIIAGRPKEDSGSVDLPLRCDWENRPLQI------- 118

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              +E+G + A++H+ +ID   +    + + P TGR+HQLRVH   MG PI+GD  Y + 
Sbjct: 119 -VDHEQGKS-ALTHW-LIDEVTELGSRVLLTPVTGRSHQLRVHMQAMGHPIIGDRFYASE 175

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            +   +     +L LHA ++ LPHPE G+ ++  AP P
Sbjct: 176 EQVAAS----ERLLLHAEFLKLPHPESGKMMEFNAPCP 209


>gi|115522347|ref|YP_779258.1| pseudouridine synthase [Rhodopseudomonas palustris BisA53]
 gi|115516294|gb|ABJ04278.1| pseudouridine synthase [Rhodopseudomonas palustris BisA53]
          Length = 278

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 83/276 (30%), Positives = 123/276 (44%), Gaps = 48/276 (17%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + E  +  ++  LT   D + + +L+ D  + V +KPAG+ V  G     +++    +  
Sbjct: 1   MNESDLEPTAKELTP--DEILARVLHRDGLMLVIDKPAGLPVHRGPKGGANLESSFDALC 58

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               + P L HRLD++TSG LV+ R R A   L   F+  +I K YW++V G P+  +  
Sbjct: 59  YGLPRPPVLAHRLDRDTSGCLVLGRHRKATATLGLLFKHGKISKTYWAVVEGGPEQDQGT 118

Query: 198 I-------------------------ANW-LLKKSHIG---GDYVHVVKQNEK---GANY 225
           I                          NW +L +S      G+   V   N     G  +
Sbjct: 119 IDLPIGRLNAERGWWQKIDPEGLPSVTNWTVLGRSFSPPPCGEGSGVGVPNGSLALGPPH 178

Query: 226 AISHFKV--IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
                K     C + +  WL ++P TGRTHQLRVH   MG PI GD+ Y     GN    
Sbjct: 179 PSPPHKGEGAGCASGQLTWLALEPLTGRTHQLRVHCAAMGWPIFGDNIY-----GNGPRF 233

Query: 284 IQNKLYLHARYMDLP----HPEGGRLQITAPLPAHM 315
            + KL+LHAR + +P     P    +  TAP PAH+
Sbjct: 234 GEPKLHLHAREIVIPISRNKPP---VVATAPAPAHL 266


>gi|313888344|ref|ZP_07822015.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus
           harei ACS-146-V-Sch2b]
 gi|312845747|gb|EFR33137.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus
           harei ACS-146-V-Sch2b]
          Length = 297

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 85/317 (26%), Positives = 145/317 (45%), Gaps = 52/317 (16%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ +   +RLD++ +     IN   ++K +  G + ++      NN++++G  ++     
Sbjct: 8   VDKESVGLRLDKFLE-EILEINRSQIKKNIVDGNILLN------NNKVKAGYNLK----- 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKS------ILLYEDSKIYVFNKPAGISVQGGSG- 124
                       LD  + +    DF  S       +LYED  + V +KP  + V  G+G 
Sbjct: 56  ------------LDDEITVEYEDDFSLSPEKIDFDVLYEDDYLAVISKPQELVVHPGAGN 103

Query: 125 -IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++G L  + +        +P + HRLD++TSG++++A+   A   L E F+ R+I
Sbjct: 104 KSGTLVNGLLYKFKELSNPIDNDRPGIVHRLDKDTSGLMLIAKKDEAYYKLVEMFKNRQI 163

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFA 237
            K Y ++  G        I      K+ IG D  + +K    ++ +  A + FKV+  F 
Sbjct: 164 DKHYLAICHG-------NIYEDFDVKAPIGRDPNNRIKMRVIDENSKEAYTSFKVLKNF- 215

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            K+  L++  HTGRTHQ+RVH  ++  P+VGD  Y    K   +     K  LHA  +  
Sbjct: 216 DKYTLLDVHLHTGRTHQIRVHLAYVNHPVVGDEVYGIKNKFKIS-----KQLLHAYKLKF 270

Query: 298 PHP-EGGRLQITAPLPA 313
            HP  G  L+I    P 
Sbjct: 271 NHPISGEELEIIDKFPV 287


>gi|157376631|ref|YP_001475231.1| lysozyme [Shewanella sediminis HAW-EB3]
 gi|157319005|gb|ABV38103.1| Lysozyme [Shewanella sediminis HAW-EB3]
          Length = 323

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 89/316 (28%), Positives = 154/316 (48%), Gaps = 47/316 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD+   + +P  +   +++ +++G V +D    +K   ++  GQV+++   +      +
Sbjct: 19  RLDQTLADLFPDYSRTRIKEWIQAGWVYIDGTVSIKPREKVLEGQVIQVEATL------V 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV- 137
           +E K    +++L          ++YED  I V NK AG+ V  G+G   + DG L + + 
Sbjct: 73  EETKAKAQAIDLD---------IVYEDDHILVINKQAGLVVHPGAG---NSDGTLMNALL 120

Query: 138 ---DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--- 189
               +    PR  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V G   
Sbjct: 121 HHCPNIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVQGSLI 180

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                 E I     K++H+       V  N K    A++H++V + F +    L ++  +
Sbjct: 181 SGGTVDEPIDRHPTKRTHMA------VVHNGKP---AMTHYRVAEKF-RAHTRLRLRLES 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLY-------LHARYMDLPHPE 301
           GRTHQ+RVH  H+G  +VGD  Y    +     SP   ++Y       LHA  ++L HP 
Sbjct: 231 GRTHQIRVHMSHIGHTLVGDPVYGGRPRPPKGVSPEFFEIYMGFKRQALHAIRLELAHPY 290

Query: 302 GGRLQI-TAPLPAHMV 316
              +    AP+P  MV
Sbjct: 291 TCEIMSWQAPVPEDMV 306


>gi|205353701|ref|YP_002227502.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205273482|emb|CAR38459.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|326628807|gb|EGE35150.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 326

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 123/245 (50%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G         E I     K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPIGRHPTKRTHMS-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV   D++
Sbjct: 253 YGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPVSGIEMEWHAPIPQDMVDLIDAM 312

Query: 323 GFKYD 327
              ++
Sbjct: 313 RADFE 317


>gi|307151795|ref|YP_003887179.1| pseudouridine synthase [Cyanothece sp. PCC 7822]
 gi|306982023|gb|ADN13904.1| pseudouridine synthase [Cyanothece sp. PCC 7822]
          Length = 562

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/207 (35%), Positives = 107/207 (51%), Gaps = 22/207 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK--SWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED  +   NKP G+    G G ++  D  +   + + + G +  + HRLDQ+TSGIL
Sbjct: 357 IIYEDEYLIAINKPEGLLSVPGRG-SHQYDSVISRITHLLADGDQCMVVHRLDQDTSGIL 415

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR R    HL + FR R+I K+Y +LV G    +K  I   L       GD     +Q
Sbjct: 416 LLARHRQIYNHLAQQFRQRKIHKVYHALVKGGVSAQKGTINLPLW------GDPNTRPRQ 469

Query: 219 NEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
                    +I+HF+VI   A+ F  LE  P TGRTHQ+RVH      +G PI+GD  Y 
Sbjct: 470 KVDFCYGKESITHFQVI-AVAENFTRLEFIPVTGRTHQIRVHCADQNGLGTPIIGDRLY- 527

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
               G+ ++    +L+LHA  +   HP
Sbjct: 528 ----GHESAT--TRLHLHAYSLSFVHP 548


>gi|310642966|ref|YP_003947724.1| RNA pseudouridine synthase ylyb [Paenibacillus polymyxa SC2]
 gi|309247916|gb|ADO57483.1| Uncharacterized RNA pseudouridine synthase ylyB [Paenibacillus
           polymyxa SC2]
          Length = 323

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 86/314 (27%), Positives = 142/314 (45%), Gaps = 40/314 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ-VVRIPPVINALNHII 78
           R+D++       ++   +Q  + +G+V V+   VK N ++  G  +V   P   +++ I+
Sbjct: 36  RIDKYIAEEMKEVSRSQIQLWIGNGRVLVNGTAVKANYKLAEGDHIVLSVPEPESVD-IM 94

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV- 137
            E   LD               ++YEDS + V NK  G+ V    G   H  G L + + 
Sbjct: 95  PENIPLD---------------VVYEDSDVIVINKQRGLVVHPAPG---HSSGTLVNALM 136

Query: 138 ----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D  G     +P + HR+D++TSG+L+ A+   A   L    +   + + Y +LV G
Sbjct: 137 YHCHDLSGINGELRPGIVHRIDKDTSGLLMAAKNDQAHASLAAQLKDHSVTRKYIALVHG 196

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              + +  +   + + S   GD   +    E+ + +A++HF VI+     +  LE+Q  T
Sbjct: 197 HLSHDQGTVDAPIGRDS---GDR-KMFTVTERNSKHAVTHFLVIERLGD-YTLLELQLET 251

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH   +G P+VGD  Y     G           LHA  +   HP  G  L+ +
Sbjct: 252 GRTHQIRVHMKFIGHPLVGDPMY-----GRSKGVRMEGQALHAAVLGFKHPTTGEYLEFS 306

Query: 309 APLPAHMVKTWDSL 322
            P+P  M     SL
Sbjct: 307 RPIPPDMEDVLTSL 320


>gi|295136359|ref|YP_003587035.1| RNA pseudouridylate synthase [Zunongwangia profunda SM-A87]
 gi|294984374|gb|ADF54839.1| RNA pseudouridylate synthase [Zunongwangia profunda SM-A87]
          Length = 288

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 84/303 (27%), Positives = 135/303 (44%), Gaps = 49/303 (16%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVN-LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V    E +RL  +  + +  I   + ++K ++  Q+ VD +  +  + I  GQ +    
Sbjct: 8   IVPQLSEKIRLQEYAASIFTSITTRSAVKKAIKKQQILVDGEIGQTGDWILEGQQIE--- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------S 123
               L    K+QK+ +           L+  ++YED  I V NKPAG    G       +
Sbjct: 65  ----LLQPQKQQKVFE-----------LRLEVIYEDDHIAVINKPAGYPTSGNYHKTIKN 109

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + +++     S    K + P+  HRLD  TSGIL+ A+T  A   L   F+ + IQK Y
Sbjct: 110 ALPFNLQA---SKEIDKLEIPQPAHRLDNPTSGILLCAKTNKALIELNRQFQDKEIQKTY 166

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G       C      ++  I  D +      EK A  A+     I   + K   L
Sbjct: 167 IAIVEG-------CFP----EEQQIFNDEIE-----EKQATTAVKLLGTIMFKSAKLSLL 210

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E +P TGRTHQ+R+H    G PI+G++ Y     G+   P +  L+L +  ++  HP G 
Sbjct: 211 EAKPLTGRTHQIRIHLAKNGFPILGENLY-----GSPAIPFKKGLFLTSIAVNFKHPTGS 265

Query: 304 RLQ 306
             Q
Sbjct: 266 AQQ 268


>gi|296126237|ref|YP_003633489.1| pseudouridine synthase, RluA family [Brachyspira murdochii DSM
           12563]
 gi|296018053|gb|ADG71290.1| pseudouridine synthase, RluA family [Brachyspira murdochii DSM
           12563]
          Length = 307

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 67/212 (31%), Positives = 106/212 (50%), Gaps = 30/212 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS---------GIAYHIDGFLKSWVDSKGQKPR--LTHR 149
           ++YED  + V NKPAG+SV   +          + Y+I  F     D  G K R  + HR
Sbjct: 89  IIYEDKYLLVINKPAGMSVHCSASEITGTLVNALLYNIKDF-----DFIGNKSRAGIIHR 143

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSGI+++ +       + E F+ R+I+KIY ++V G+ K+      N+L     IG
Sbjct: 144 LDKDTSGIMIIGKNADIVSSIQEQFKNRKIKKIYHAIVIGVLKD------NYLEINLPIG 197

Query: 210 GDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              V+  K    +    A++H KV+  F +    +E+   TGRTHQ+RVH+ +   P+ G
Sbjct: 198 RHQVYRKKMTVREDGKKALTHIKVLKRF-KNHTLIEIDLKTGRTHQIRVHSSYKNFPVAG 256

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           D  Y        +S     L L A+ ++  HP
Sbjct: 257 DKIYSK------SSNKYKSLMLVAKKIEFTHP 282


>gi|302141717|emb|CBI18920.3| unnamed protein product [Vitis vinifera]
          Length = 433

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 84/311 (27%), Positives = 138/311 (44%), Gaps = 74/311 (23%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V +D   +RLD W  +    I+   +Q  +RSG V V       N+RI          
Sbjct: 68  VDVNSDSGKLRLDSWISSRIIGISRARVQSSIRSGLVSV-------NDRI---------- 110

Query: 70  VINALNHIIKEQKILDSSVN----LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            ++ ++H+I+    ++ +++    L    + +   ++YED  + V NKPA + V    G 
Sbjct: 111 -VDKVSHVIRAGDKVNCTISELQPLRAEPEDIPLDIVYEDEHVLVVNKPAHMVVHPAPGN 169

Query: 126 AYH--IDGFL-------------------------KSWVDSKGQ---------KPRLTHR 149
           A    ++G L                          S+  + GQ         +P + HR
Sbjct: 170 ASGTLVNGILHHCSLPTVALPNRDSEEDDISDDEFNSF--AAGQNCGTCETNIRPGIVHR 227

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-------ANWL 202
           LD+ TSG+LVVA+   +  HL+E F++  I ++Y SL  G+P      +        N  
Sbjct: 228 LDKGTSGLLVVAKDEHSHAHLSEQFKLHSIHRVYISLTSGVPTPLSGRVEIPVGRDPNNR 287

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALH 261
           ++ + + G        N   A +A S +KVI+  A     L E +  TGRTHQ+R HA +
Sbjct: 288 IRMTAVPG------PSNSGQARHAASRYKVIEILAAGGSALVEWRLETGRTHQIRAHAKY 341

Query: 262 MGCPIVGDHKY 272
           +G P++GD  Y
Sbjct: 342 LGIPLLGDEVY 352


>gi|197119760|ref|YP_002140187.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           bemidjiensis Bem]
 gi|197089120|gb|ACH40391.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           bemidjiensis Bem]
          Length = 319

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 113/233 (48%), Gaps = 24/233 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQET 154
           +LYED+++ V NK AG+ V  G+G      ++  L    D  G     +P + HR+D++T
Sbjct: 82  VLYEDAELVVVNKGAGMVVHPGAGNPEGTLVNALLAHCKDLSGIGGELRPGIVHRIDKDT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG LVVA+   A   L E F+   I+++Y +LV+G PK  K  I      +S IG     
Sbjct: 142 SGTLVVAKCDRAHNALAEQFKEHSIKRVYLALVYGSPKEDKGRI------ESTIGRHPTD 195

Query: 215 VVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             K + K      A++H++V+  +      + ++  TGRTHQ+RVH    G P++ D  Y
Sbjct: 196 RKKMSAKARHGKQAVTHWRVVARYP-GITLIRLRLETGRTHQIRVHMSEAGHPLLADEVY 254

Query: 273 CANFK-GNFTSPIQNKL-------YLHARYMDLPHPEGGR-LQITAPLPAHMV 316
               +      P+  ++        LHA+ +   HP  G+ L+    LP  M 
Sbjct: 255 GGTGRLSGVQDPVLKQMIKSMGRQALHAKTLGFLHPVSGKYLEFDTELPPDMA 307


>gi|312865253|ref|ZP_07725481.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
 gi|311099364|gb|EFQ57580.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
          Length = 298

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 150/321 (46%), Gaps = 48/321 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           EE +RLD+   +   +++     + ++ G V V+ +  K    +++G V+          
Sbjct: 7   EEGLRLDKALAD-LSNLSRSQANQAIKDGSVLVNGRPKKAKYSVKAGDVISFEE------ 59

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-- 133
               E+++LD        ++ L   ++YED  + V NKP G+ V    G   H  G L  
Sbjct: 60  ---PEEEVLDY------QAENLPLEIVYEDQDLAVVNKPQGMVVHPSVG---HSSGTLVN 107

Query: 134 ------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 K      G  +P + HR+D++TSG+L+VA+   A Q L +  + ++  + Y ++
Sbjct: 108 ALLYRIKDLSTINGVVRPGIVHRIDKDTSGLLMVAKNDQAHQALADELKAKKSLRKYLAI 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLE 244
           V G   N +  I      ++ IG       KQ    KG   A++HF V++ F   +  LE
Sbjct: 168 VHGNLPNDRGKI------EAPIGRSEKDRKKQAVTAKG-RPAVTHFHVLERFGN-YSLLE 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           ++  TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   HP  
Sbjct: 220 LRLETGRTHQIRVHMAYIGHPLAGDPLYGPRKTLKGHGQ-------FLHAQTLGFTHPRT 272

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
           G+ L+ +   PA   +T + L
Sbjct: 273 GQVLEFSVQPPAIFQETLEKL 293


>gi|293390711|ref|ZP_06635045.1| ribosomal large subunit pseudouridine synthase D [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951245|gb|EFE01364.1| ribosomal large subunit pseudouridine synthase D [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 324

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 121/242 (50%), Gaps = 27/242 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           ++YED  I V NKP  + V  G+G      ++  L  +     + PR  + HRLD++T+G
Sbjct: 85  IVYEDDDILVINKPKDLVVHPGAGNPSGTVLNALLYHY-PPIAEVPRAGIVHRLDKDTTG 143

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYV 213
           ++VVA+T  A   L    + R+I + Y ++  GI        E +A    K++H+    V
Sbjct: 144 LMVVAKTIPAQTQLVRDLQKRKITREYEAVACGIMTKGGMVDEPMARHPTKRTHMA---V 200

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  Y 
Sbjct: 201 HPMGKP------AVTHYRIMERF-RDYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYG 253

Query: 274 A------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
                  N      S ++N  +  LHA  + L HP  G  ++  APLP   V+   +L  
Sbjct: 254 GRPRPPKNASEELMSVLRNFKRQALHAVMLRLQHPISGEMMEWYAPLPEDFVELITALKA 313

Query: 325 KY 326
            Y
Sbjct: 314 DY 315


>gi|200387471|ref|ZP_03214083.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|199604569|gb|EDZ03114.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
          Length = 219

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/208 (33%), Positives = 106/208 (50%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LEAHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y + 
Sbjct: 126 KVCYETG-KPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +       +L LHA  + + HP  G
Sbjct: 185 EALSLAP----RLQLHAEMLTITHPAYG 208


>gi|327489656|gb|EGF21448.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1058]
          Length = 298

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 118/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTRFQVLERFGD-YTLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA +P    +T + L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEVPVIFQETLEKL 295


>gi|94990203|ref|YP_598303.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94543711|gb|ABF33759.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
          Length = 296

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 111/219 (50%), Gaps = 29/219 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++YED  + + NKP G+ V   +G         + YHI    K      G  +P + HR+
Sbjct: 76  IIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHI----KDLSSINGVVRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+T AA Q L E  + ++  + Y ++V G   N +  I      ++ IG 
Sbjct: 132 DKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMI------EAPIGR 185

Query: 211 DYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ G
Sbjct: 186 SEKDRKKQAVTAKGKE-AVTRFTVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAG 243

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           D  Y     G   +   +  +LHA+ + L HP  G+  I
Sbjct: 244 DPLY-----GPRKTLSGHGQFLHAKTLGLTHPMTGKEMI 277


>gi|325288659|ref|YP_004264840.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324964060|gb|ADY54839.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 295

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 80/322 (24%), Positives = 151/322 (46%), Gaps = 37/322 (11%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           +Y++Y + E + + + ++ + K     I+   +QK+ R   + ++ K+V    ++++G +
Sbjct: 3   SYLKYTIAE-EHQGLTVEEYLKKAL-QISGRKIQKLTRLTGILLNGKKVFLQKKLRAGDL 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GGS 123
           + +  + +    +  E   +D               +LYED  + V NKPAG+ V   G 
Sbjct: 61  LSVLSLQDRSYGVNPEAGAID---------------ILYEDESLIVLNKPAGLLVHPAGM 105

Query: 124 GIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             +  +  +L  +    G     R  HRLD++TSG LV A+       + +     +I++
Sbjct: 106 TTSGTLANYLADYFRQLGVICTIRPLHRLDRDTSGCLVFAKGPVVQSKMEDLLAAGKIKR 165

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQK 239
            Y +L  G+    +  I+      + I  D     ++  +EKG+  AI+H++ +  F Q 
Sbjct: 166 TYLALAEGLIIPAEGTIS------APIASDPAKPNRRMVSEKGSQ-AITHYRKLKTFGQN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E+   TGRTHQ+RVH  ++G PI+GD  Y         SP+ ++  LHA  +   H
Sbjct: 219 -SLVELNLETGRTHQIRVHLAYLGHPILGDRMY------GRKSPLISRQALHAVKISFQH 271

Query: 300 P-EGGRLQITAPLPAHMVKTWD 320
           P +   + + A LP   +K  +
Sbjct: 272 PVKETEICLEAKLPGDFLKCLE 293


>gi|16124708|ref|NP_419272.1| ribosomal large subunit pseudouridine synthase d [Caulobacter
           crescentus CB15]
 gi|221233422|ref|YP_002515858.1| ribosomal large subunit pseudouridine synthase D [Caulobacter
           crescentus NA1000]
 gi|13421626|gb|AAK22440.1| ribosomal large subunit pseudouridine synthase d [Caulobacter
           crescentus CB15]
 gi|220962594|gb|ACL93950.1| ribosomal large subunit pseudouridine synthase D [Caulobacter
           crescentus NA1000]
          Length = 342

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 87/325 (26%), Positives = 137/325 (42%), Gaps = 51/325 (15%)

Query: 17  ENM---RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           EN+   RLD+     +P ++   LQ ++  G++  D + V   +R     V  +      
Sbjct: 33  ENLAGQRLDKVLAPLFPDLSRARLQALIAEGRLTFDGETVADASRKARAGVYSL------ 86

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
                    ++          + L   +LYED+ + V +K AG++V    G         
Sbjct: 87  ---------VVPPPAPADPEPEALPLSILYEDAHLIVVDKAAGMAVHPAPGTYNGTLVNA 137

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +H    L S V     +P + HRLD++TSG++V A++ AA + L+  F    I ++Y 
Sbjct: 138 LLHHCGASL-SGVGGV-ARPGIVHRLDKDTSGVMVAAKSDAAHRGLSTLFATHDIDRLYV 195

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-------- 236
           +L  G P      I   + +     GD   +      G   AI+H++V   F        
Sbjct: 196 ALTRGAPNPPTGTIQTQIGRSP---GDRKKMAVLR-AGGREAITHYRVEAAFGPADRPLA 251

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-----CANFKGNFTSPIQNKLYLH 291
           A+  C LE    TGRTHQ+RVH    G P +GD  Y      A  +    +    +  LH
Sbjct: 252 ARVACRLE----TGRTHQIRVHMASKGSPCLGDPVYGAAQPAAAVRERIEAAGLRRQALH 307

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHM 315
           A  +   HP  G  L+   PLPA M
Sbjct: 308 AAVLGFVHPITGETLRFETPLPADM 332


>gi|270264067|ref|ZP_06192335.1| ribosomal large subunit pseudouridine synthase D [Serratia
           odorifera 4Rx13]
 gi|270042260|gb|EFA15356.1| ribosomal large subunit pseudouridine synthase D [Serratia
           odorifera 4Rx13]
          Length = 325

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 90/335 (26%), Positives = 161/335 (48%), Gaps = 53/335 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V+V+ K   K   ++  G+ V   
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKTTNKPKEKVLGGETV--- 65

Query: 69  PVINALNHIIKEQ---KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
               A++  I+E+   +  D ++N+           +YEDS I V NKP  + V  G+G 
Sbjct: 66  ----AIDAQIEEEARWEPQDIALNI-----------VYEDSDILVINKPRDLVVHPGAG- 109

Query: 126 AYHIDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             + DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I
Sbjct: 110 --NPDGTVLNALLHYYPEIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREI 167

Query: 180 QKIYWSLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            + Y ++  G        +E I+    K++H+    VH + +       A++H+++++ F
Sbjct: 168 TREYEAVAIGTMTAGGTVEEPISRHSTKRTHMA---VHPMGKP------AVTHYRIMEHF 218

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKL 288
            +    L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F + ++  ++ 
Sbjct: 219 -RAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASEAFIATLRGFDRQ 277

Query: 289 YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            LHA  + L HP  G +++  APLP  MV   ++L
Sbjct: 278 ALHATMLRLYHPISGIQMEWHAPLPQDMVDLINAL 312


>gi|152977723|ref|YP_001343352.1| 23S rRNA pseudouridine synthase D [Actinobacillus succinogenes
           130Z]
 gi|150839446|gb|ABR73417.1| pseudouridine synthase, RluA family [Actinobacillus succinogenes
           130Z]
          Length = 324

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 87/332 (26%), Positives = 153/332 (46%), Gaps = 43/332 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPV 70
           V++ +   RLD+     +P  +   L+  +    VRV+         ++  G+ + I   
Sbjct: 10  VQSHQMGQRLDQTLAELFPDYSRSRLKTWIEGNLVRVNGNIQNIPRTKVLGGEQIEIRAE 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           +    H   E   LD               ++YED  I V NKP    V  G+G      
Sbjct: 70  VEEETHYEPENLPLD---------------IVYEDDHILVLNKPKNFVVHPGAGNPRGTV 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           ++  L  +     + PR  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++
Sbjct: 115 LNALLYHY-PQIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAV 173

Query: 187 VWGI-PKNKK--ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +G+  K  K  E +A    K++ +    VH + +       A++H+++++ F + +  L
Sbjct: 174 AFGVMTKGGKVDEPMARHPTKRTAMA---VHPMGKP------AVTHYRIMEHF-RNYTRL 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQN--KLYLHARYM 295
            ++  TGRTHQ+RVH  H+  P++GD  Y        N   +F+  ++N  +  LHA  +
Sbjct: 224 RLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPRNASEHFSEVLRNFQRQALHAIML 283

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSLGFKY 326
            L HP  GG ++  APLP    +   +L   Y
Sbjct: 284 RLEHPISGGLMEWFAPLPDDFAELIAALKEDY 315


>gi|270292963|ref|ZP_06199174.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           M143]
 gi|270278942|gb|EFA24788.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           M143]
          Length = 299

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 85/314 (27%), Positives = 149/314 (47%), Gaps = 45/314 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G  R+DK         R   N +I++GQV+ +   +    + ++E  I+   V   +
Sbjct: 5   IETGGQRLDKALSDLTELSRSLANEQIKAGQVL-VNGQVKKAKYTVQEGDIVTYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   +    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDIPLDIIYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG+         +LHA+ +   HP  G  ++ TA +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGETMEFTADIPEI 285

Query: 315 MVKTWDSLGFKYDR 328
             +T + L    DR
Sbjct: 286 FKETLERLRKNEDR 299


>gi|239815171|ref|YP_002944081.1| pseudouridine synthase, RluA family [Variovorax paradoxus S110]
 gi|239801748|gb|ACS18815.1| pseudouridine synthase, RluA family [Variovorax paradoxus S110]
          Length = 327

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 90/330 (27%), Positives = 147/330 (44%), Gaps = 39/330 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   E   RLDR      P  +   LQ+++ +G V +  + + K +  +++GQ   I  
Sbjct: 24  TVGPTEHGQRLDRALAALVPEFSRNYLQQLIEAGAVELQGRTLLKASATVRAGQTGHI-- 81

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
               L    + Q      +++         + ++ED  + + +KPAG+ V    G     
Sbjct: 82  ---ELRPTPQSQAFRPEPMDI---------VTVHEDEHLRIIDKPAGLVVHPAPGHWSGT 129

Query: 128 HIDGFLKSWVDSKGQK-PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            ++G L   +D K    PR  + HRLD++TSG++VVARTRAA   +      R +++ Y 
Sbjct: 130 LLNGLLA--LDPKAALLPRAGIVHRLDRDTSGLMVVARTRAAMDAMVALIAAREVKRQYL 187

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +L      +K    A      + IG D      + VV         A +  + +D  AQ 
Sbjct: 188 AL-----GHKPWAGAAARQVDAPIGRDPRNRLRMAVVDLERHAGKTARTLIERLDSNAQA 242

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
            C +     TGRTHQ+RVH   +G P+VGD  Y     G   +    +  LHA  +   H
Sbjct: 243 -CAVRCTLETGRTHQIRVHMASIGHPLVGDALY-----GGAPAAGLGRQALHAFRLAFVH 296

Query: 300 P-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           P     L++ +  PA +V+ + +LG  Y+R
Sbjct: 297 PVTQAALELRSLPPADLVQAFQALGLDYNR 326


>gi|209886260|ref|YP_002290117.1| ribosomal large subunit pseudouridine synthase D [Oligotropha
           carboxidovorans OM5]
 gi|209874456|gb|ACI94252.1| ribosomal large subunit pseudouridine synthase D [Oligotropha
           carboxidovorans OM5]
          Length = 366

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 80/320 (25%), Positives = 141/320 (44%), Gaps = 56/320 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRI--PPVINA 73
           ++ RLDR        ++   L+ ++ +G V +    V+    ++++G+ + I  PP ++ 
Sbjct: 50  KSQRLDRLLAEQIDDLSRTRLKALILAGHVSLGDTVVRDPAYQVKAGEAITIEVPPAVDP 109

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
               + E   LD               ++YED  I V +K  G+ V   +G   H +G L
Sbjct: 110 --EPVGENIPLD---------------IVYEDDDIIVLDKQRGLVVHPAAG---HENGTL 149

Query: 134 ---------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRI 179
                     S     G ++P + HRLD++T+G++V+A+   A Q LT  F    R   +
Sbjct: 150 VNALIAHCGASLSGIGGVKRPGIVHRLDKDTTGLMVIAKNDHAHQSLTAQFADHGRTGEL 209

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y + VWG+P   +  I   + +       +             AI+H+++++ FA +
Sbjct: 210 RRGYLAFVWGVPARPRGTIDQPIDRHP-----FAREKMAVRASGRQAITHWEMLESFAGR 264

Query: 240 -----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQ------ 285
                   L  Q  TGRTHQ+RVH  H G P++GD  Y + F+        P +      
Sbjct: 265 DGKPLAALLACQLETGRTHQIRVHLSHAGHPLIGDDVYGSGFRTKVNQLAEPAKIAVTTL 324

Query: 286 NKLYLHARYMDLPHPEGGRL 305
            +  LHA  + + HP  G +
Sbjct: 325 GRQALHAYLLQIEHPTTGEV 344


>gi|91792374|ref|YP_562025.1| pseudouridine synthase [Shewanella denitrificans OS217]
 gi|91714376|gb|ABE54302.1| pseudouridine synthase [Shewanella denitrificans OS217]
          Length = 229

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/218 (31%), Positives = 108/218 (49%), Gaps = 19/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG----FLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED  I   +KP+G+    G     ++D      ++ + D+     RL HRLD  TSG
Sbjct: 24  ILYEDEAILAIDKPSGLLSLSGKN-PLNLDSVHYRLVQDFADA-----RLLHRLDFGTSG 77

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I++VAR +     LT+ F+ R + K Y +L+ G        I   + K + +       +
Sbjct: 78  IILVARNKHINGLLTQQFQNRSVTKTYQALLMGKLSTDSGVIDAPIAKDAAL----FPRL 133

Query: 217 KQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           K  E     A++ +KV+  C       ++  P TGRTHQLR+H+ H+G PI+G   Y   
Sbjct: 134 KICELEGKSAMTEYKVLSYCEQTDLSRVQFTPITGRTHQLRLHSQHLGHPILGCDLYGGI 193

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             G    P+ +++ LHA+ +   HP  GG +QI  P P
Sbjct: 194 VDGR--EPV-SRMMLHAQSLAFTHPLTGGDMQINCPCP 228


>gi|21910093|ref|NP_664361.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28896209|ref|NP_802559.1| hypothetical protein SPs1297 [Streptococcus pyogenes SSI-1]
 gi|71903284|ref|YP_280087.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94994123|ref|YP_602221.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|21904284|gb|AAM79164.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28811460|dbj|BAC64392.1| conserved hypothetical protein [Streptococcus pyogenes SSI-1]
 gi|71802379|gb|AAX71732.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94547631|gb|ABF37677.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
          Length = 296

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 111/219 (50%), Gaps = 29/219 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++YED  + + NKP G+ V   +G         + YHI    K      G  +P + HR+
Sbjct: 76  IIYEDDTLAIINKPQGMVVHPSAGHPSGTMVNALMYHI----KDLSSINGVVRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+T AA Q L E  + ++  + Y ++V G   N +  I      ++ IG 
Sbjct: 132 DKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMI------EAPIGR 185

Query: 211 DYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ G
Sbjct: 186 SEKDRKKQAVTAKGKE-AVTRFTVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAG 243

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           D  Y     G   +   +  +LHA+ + L HP  G+  I
Sbjct: 244 DPLY-----GPRKTLSGHGQFLHAKTLGLTHPMTGKEMI 277


>gi|309812701|ref|ZP_07706445.1| pseudouridine synthase, RluA family [Dermacoccus sp. Ellin185]
 gi|308433396|gb|EFP57284.1| pseudouridine synthase, RluA family [Dermacoccus sp. Ellin185]
          Length = 309

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 88/333 (26%), Positives = 152/333 (45%), Gaps = 40/333 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V+ + V    E  R+D          +     ++   G V VD KRV  + R+ +G 
Sbjct: 1   MSEVKSLFVPEGLEGERVDAAIARLL-GFSRTRAAELAAEGAVSVDGKRVAKSERVSAGA 59

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V +P          + + +    +N+           +++D++I V +KPAG++   
Sbjct: 60  WLEVAMPERTGPREATPRVEPV--PGMNI-----------VHDDTEIVVVDKPAGVAAHP 106

Query: 122 GSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G     + G L +    + + G   R  +  RLD  TSG++VVA++  A   L ++FR
Sbjct: 107 SVGWDGPDVVGGLAAAGYRISTSGAPERQGIVQRLDVGTSGLMVVAKSERAYTLLKQAFR 166

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y +LV G+P   +  I   + +  H   DY   V  + +    +++H+++++ 
Sbjct: 167 DRTVDKTYHALVQGLPDPIEGTIDAPIGR--HPNHDYKFAVMDSGRA---SVTHYELLEA 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-----YL 290
           F +    LE+   TGRTHQ+RVH   M  P VGD  Y ++        +  KL     +L
Sbjct: 222 F-RSASLLEIHLETGRTHQIRVHVSAMHHPCVGDPLYGSDPT------LAKKLGLERQWL 274

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           HA  +   HP  G R+  T+P PA + +  D +
Sbjct: 275 HAVELGFDHPGSGERVTFTSPYPADLQRALDRI 307


>gi|261405686|ref|YP_003241927.1| RluA family pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261282149|gb|ACX64120.1| pseudouridine synthase, RluA family [Paenibacillus sp. Y412MC10]
          Length = 324

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 84/318 (26%), Positives = 144/318 (45%), Gaps = 43/318 (13%)

Query: 11  VVENDEENMRLDRWF-KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRI 67
            V+ D    R+D++  +N    ++   +Q  +  G V V+   +K N ++  G   V+++
Sbjct: 27  TVDADAAKTRIDKYLTENLGEDVSRSQVQLWIADGHVSVNDGPIKSNYKVSQGDRIVLKV 86

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P    +   II E   L+               + +ED  + V NKP G+ V    G   
Sbjct: 87  PE--PSAVEIIPEDIPLE---------------IAFEDGDVIVVNKPRGMVVHPAPG--- 126

Query: 128 HIDGFL--------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           H  G L        K      G+ +P + HR+D++T+G+++ A+   A   L    +   
Sbjct: 127 HSSGTLVNALMFHCKDLSGINGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKEHS 186

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + + Y +LV G   + +  I   + + +     Y  V  +N K   +A++HF V++ F  
Sbjct: 187 VNRRYLALVHGNISHDQGTIDAPIGRDAQDRKLYT-VTDRNSK---HAVTHFTVVERFGD 242

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  LE++  TGRTHQ+RVH  ++G P+VGD  Y     G       N   LHA  +   
Sbjct: 243 -YSLLELKLETGRTHQIRVHMKYIGHPLVGDPVY-----GKSKGIKLNGQALHAAVLGFV 296

Query: 299 HPEGGRL-QITAPLPAHM 315
           HP  G   + +AP+P+ M
Sbjct: 297 HPSTGEYKEFSAPMPSDM 314


>gi|239618296|ref|YP_002941618.1| pseudouridine synthase, RluA family [Kosmotoga olearia TBF 19.5.1]
 gi|239507127|gb|ACR80614.1| pseudouridine synthase, RluA family [Kosmotoga olearia TBF 19.5.1]
          Length = 311

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 85/322 (26%), Positives = 147/322 (45%), Gaps = 34/322 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V N E+  RLD++     P  ++   +Q+ ++ G V V+ ++ K + R++SG +V    
Sbjct: 6   IVTNREDGWRLDKFLSEKAPQWVSRTAIQRHIKDGGVLVNGEKKKASYRVKSGDIVTY-- 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG----GSGI 125
                   ++   +   ++ L          ++YED  I V NKP  + V       SG 
Sbjct: 64  ---TFPEKVEPGTVEPENIPLN---------IIYEDHDIIVVNKPPDMIVHPVHNKTSGT 111

Query: 126 AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D +G     +P + HRLD+ETSG++VVA+   A   L + F+ R  +K
Sbjct: 112 L--VNALLNYCNDLQGIGGIMRPGIVHRLDKETSGVIVVAKNDRAHNSLVQQFKARTTEK 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++  G  K   +   N+ L +  +    + V    ++        FK I  F     
Sbjct: 170 YYLAIARG--KTPLQGEINFSLARHPVNRLKMTVSATGKESHTL----FKTITYFGNIAS 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +P TGRTHQ+RVH   +G P++GD  Y    K +     +  + LHA  + + HP 
Sbjct: 224 LVLAKPKTGRTHQIRVHFKEIGHPLLGDKLY-GRHKDDIILGAERHM-LHALQISIHHPR 281

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
            G ++   A +P  M+K   +L
Sbjct: 282 TGEKMTFVARVPEDMLKVIRNL 303


>gi|307719385|ref|YP_003874917.1| ribosomal large subunit pseudouridine synthase D [Spirochaeta
           thermophila DSM 6192]
 gi|306533110|gb|ADN02644.1| ribosomal large subunit pseudouridine synthase D [Spirochaeta
           thermophila DSM 6192]
          Length = 319

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 84/330 (25%), Positives = 142/330 (43%), Gaps = 49/330 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + +RLD+        +     Q   R   + +D +  K + R+ +G              
Sbjct: 16  DGLRLDQALAEL---LGITRSQVKQRIADLALDGRPAKPSQRVHAGAR------------ 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL- 133
            I    + ++  +LT     +   +LYED    V +KP G+ V  G+G      + G L 
Sbjct: 61  -IAGTLLPEAPPDLTPEP--VPFTILYEDPHCLVIDKPQGLVVHPGAGNPTGTLVHGLLH 117

Query: 134 -----------KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                      +   D +  +  + HRLD++TSG+LVVA+  A    L   F+ +  +K+
Sbjct: 118 YSHELAARATSEELDDEERMRIGIVHRLDKDTSGVLVVAKDPATHHFLAAQFKEKETKKL 177

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-----VVKQNEKGANYAISHFKVIDCFA 237
           Y +++ G P  ++  I      + H+    VH     ++   ++G  Y+ + ++++  F 
Sbjct: 178 YLAVLKGTPPAREGDI------EGHLARHPVHRKKFTLLSTPDRG-KYSHTRYRLLAAFG 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
               ++ + P TGRTHQLRVH   +GCPI+GD  Y A     F       L LHA  + +
Sbjct: 231 TH-SFVALYPTTGRTHQLRVHTAALGCPILGDPLY-ARPDTRFP---DATLMLHAYLLTI 285

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
             P  G L   APLP    +   +L    D
Sbjct: 286 RIPGRGLLTFRAPLPRRFKQILRALARASD 315


>gi|15674865|ref|NP_269039.1| hypothetical protein SPy_0827 [Streptococcus pyogenes M1 GAS]
 gi|50914002|ref|YP_059974.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|71910451|ref|YP_282001.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
 gi|94988324|ref|YP_596425.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|306827571|ref|ZP_07460852.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes ATCC 10782]
 gi|13622001|gb|AAK33760.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS]
 gi|50903076|gb|AAT86791.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|71853233|gb|AAZ51256.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
 gi|94541832|gb|ABF31881.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|304430223|gb|EFM33251.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes ATCC 10782]
          Length = 296

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 111/219 (50%), Gaps = 29/219 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++YED  + + NKP G+ V   +G         + YHI    K      G  +P + HR+
Sbjct: 76  IIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHI----KDLSSINGVVRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+T AA Q L E  + ++  + Y ++V G   N +  I      ++ IG 
Sbjct: 132 DKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMI------EAPIGR 185

Query: 211 DYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ G
Sbjct: 186 SEKDRKKQAVTAKGKE-AVTRFTVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAG 243

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           D  Y     G   +   +  +LHA+ + L HP  G+  I
Sbjct: 244 DPLY-----GPRKTLSGHGQFLHAKTLGLTHPMTGKEMI 277


>gi|296536195|ref|ZP_06898317.1| ribosomal large subunit pseudouridine synthase D [Roseomonas
           cervicalis ATCC 49957]
 gi|296263477|gb|EFH09980.1| ribosomal large subunit pseudouridine synthase D [Roseomonas
           cervicalis ATCC 49957]
          Length = 343

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 111/235 (47%), Gaps = 27/235 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL---------KSWVDSKGQK-PRLTHRL 150
           +L+ED  + V +KPAG+ V    G   + DG L         +      G+K P + HRL
Sbjct: 104 ILFEDRHLIVLDKPAGLVVHPAPG---NQDGTLVNALLAHAGEELTGIGGEKRPGIVHRL 160

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++VVA++  A   L+ +F  R +++ Y +L WG+P      + +  + +     
Sbjct: 161 DKDTSGVMVVAKSEVAHTALSAAFASRDLERAYLALAWGVPAPASGEV-DAPVGRHPTDR 219

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             + VV +N K   +A++ +     +      L  +  TGRTHQ+RVH  H+G P+VGD 
Sbjct: 220 KRMAVVARNGK---HALTRYATERAWGTSCALLRCRLATGRTHQIRVHMAHIGHPLVGDP 276

Query: 271 KYCANFKGNFTS-PIQN--------KLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            Y           P+          +  LHA  +   HP  G  L+ + PLP  M
Sbjct: 277 VYLRRLPATARGLPVAARDALLAFPRQALHAESLGFHHPVTGEMLRFSTPLPPDM 331


>gi|290476241|ref|YP_003469141.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Xenorhabdus bovienii SS-2004]
 gi|289175574|emb|CBJ82377.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Xenorhabdus bovienii SS-2004]
          Length = 325

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/240 (31%), Positives = 125/240 (52%), Gaps = 31/240 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLYRYPAIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++V+A+T  A   L ES ++R I + Y ++  G        +E I+    K++H+   
Sbjct: 143 TGLMVIAKTVPAQTRLVESLQLREITREYEAIALGCMTAGGMVEEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + ++      A++H++V++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKS------AVTHYRVMEHF-RAHTRLRLRLETGRTHQIRVHMAHIKHPLVGDPL 252

Query: 272 YCAN---FKG---NFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y       KG    F   ++N  +  LHA  + L HP  G  ++  A LP  MVK  D +
Sbjct: 253 YGGRPRPLKGASDEFREVMRNFDRQALHATMLRLYHPISGIEMEWHAELPDDMVKLIDVM 312


>gi|288905537|ref|YP_003430759.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
 gi|288732263|emb|CBI13830.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus gallolyticus UCN34]
          Length = 298

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 87/321 (27%), Positives = 149/321 (46%), Gaps = 48/321 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RLD+   +    ++       ++ G V V+ K VK    ++ G VV          
Sbjct: 7   EAGVRLDKALAD-LTELSRSQANDEIKKGTVLVNGKAVKAKYAVKVGDVV---------T 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-- 133
           + + ++++L+ +      ++ +   ++YED  + V NKP G+ V    G   H+ G L  
Sbjct: 57  YEVPKEEVLEYT------AENIPLDIIYEDDDVAVVNKPQGMVVHPSVG---HMSGTLVN 107

Query: 134 ------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 K      G  +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++
Sbjct: 108 ALMYHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAI 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLE 244
           V G   N +  I      ++ IG       KQ    KG   A++HFKV++ F   +  +E
Sbjct: 168 VHGNIPNDRGVI------EAPIGRSEKDRKKQAVTAKG-KPAVTHFKVLERFGN-YTLVE 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +   TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   HP  
Sbjct: 220 LTLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGHGQ-------FLHAQTLGFTHPTT 272

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
           G  L  TA  PA   +T ++L
Sbjct: 273 GETLTFTAEAPAIFKETLENL 293


>gi|283786206|ref|YP_003366071.1| ribosomal large subunit pseudouridine synthase D [Citrobacter
           rodentium ICC168]
 gi|282949660|emb|CBG89279.1| ribosomal large subunit pseudouridine synthase D [Citrobacter
           rodentium ICC168]
          Length = 326

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 90/337 (26%), Positives = 158/337 (46%), Gaps = 47/337 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPV 70
           V  ++   RLD+     +P  +   +++ +   +V V DK   K   ++  G+VV I   
Sbjct: 11  VSENQLGQRLDQALAEMFPDYSRSRIKEWILDRRVLVNDKICDKPKEKVLGGEVVAIDAE 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           I+       +   LD               ++YED  I V NKP  + V  G+G   + D
Sbjct: 71  IDEEIRFEPQDIPLD---------------IVYEDDDIIVINKPRDLVVHPGAG---NPD 112

Query: 131 GF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITREYE 172

Query: 185 SLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    VH + +       A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMS---VHPMGKP------AVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
            + L HP  G  ++  AP+P  MV+  D++   ++ +
Sbjct: 283 MLRLYHPVSGIEMEWHAPIPQDMVELIDAMRADFEEH 319


>gi|206889653|ref|YP_002248865.1| pseudouridylate synthase, 23S RNA-specific [Thermodesulfovibrio
           yellowstonii DSM 11347]
 gi|206741591|gb|ACI20648.1| pseudouridylate synthase, 23S RNA-specific [Thermodesulfovibrio
           yellowstonii DSM 11347]
          Length = 315

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 97/335 (28%), Positives = 163/335 (48%), Gaps = 47/335 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
            E  +E  RLD +  +       +N+ +     Q  ++KK VK NN +++ +  +I    
Sbjct: 7   TEKADEGKRLDIFISDK------LNISR--AKAQEAIEKKFVKVNNYVKT-KSYKIK--F 55

Query: 72  NALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           N L  +  E  + L++S  L   +  ++  ++Y+D  + V +KPAG+ V   +G   H D
Sbjct: 56  NDLIEVSDEFSLKLENSEKLIPQNIPIQ--VIYKDDYLIVLSKPAGMVVYPCAG---HPD 110

Query: 131 GFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G L + +    +K         P + HRLD++TSG++VVA        L E+F+ R I+K
Sbjct: 111 GTLMNALAYHVKKLANVGAPFRPGIVHRLDKDTSGVMVVALDDETYYKLVEAFKKREIKK 170

Query: 182 IYWSLVWGIPKNKKECI-----ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            Y +LV+G  +   +       A +  KK  I            K A  AI+ ++VI  F
Sbjct: 171 EYLALVYGQLRGSGKITTPVGRAIYDRKKMSI----------KSKKAKEAITEWEVIKNF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKLYLHAR 293
            + + +L+++  TGRTHQ+RVH   +G P++GD  Y        GN   P+  ++ LHA 
Sbjct: 221 -KNYTFLKVKILTGRTHQIRVHFSSIGHPVIGDKTYGRKTYIEIGNKKIPVSRQM-LHAH 278

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            ++L HP   + LQ  A LP  +    + L  +Y+
Sbjct: 279 KIELIHPITEKLLQFEASLPDDIQYILNILEDRYE 313


>gi|329955390|ref|ZP_08296298.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
 gi|328525793|gb|EGF52817.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
          Length = 600

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/235 (31%), Positives = 114/235 (48%), Gaps = 20/235 (8%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGF 132
           L H+++  ++ ++ +     S+  +  ++YED  + V NKPAG +SV G    A      
Sbjct: 372 LRHMLQGLEVDENPMLKELQSNKKELEIIYEDEWLAVVNKPAGMLSVPGKEDAASVYSVV 431

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            + + D+ G  P + HRLD  TSG+LVVA+T+   Q+L   F+ R IQK Y +L+ G+  
Sbjct: 432 RERYPDADG--PLIVHRLDMATSGLLVVAKTKQVHQNLQAQFKNRSIQKRYIALLQGMVS 489

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                +   L        D    +   E G   A++ F+V+         +   P TGRT
Sbjct: 490 QDTGTVELPLCPNPL---DRPRQMVHAEYGKP-AVTDFEVLK-RGDNRTRIAFYPRTGRT 544

Query: 253 HQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           HQLRVHA H   + CPI+GD  Y              +LYLHA  ++  HP  G+
Sbjct: 545 HQLRVHAAHPLGLHCPIIGDELYGKK---------AERLYLHAETLEFTHPITGK 590


>gi|89891472|ref|ZP_01202977.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BBFL7]
 gi|89516246|gb|EAS18908.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BBFL7]
          Length = 227

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 67/218 (30%), Positives = 107/218 (49%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ +   NK +G  VQG       +   +K ++  K  KP      +THRLD+ TS
Sbjct: 7   ILFEDNHLIAVNKKSGDLVQGDKTGDVILPEMIKEYIAVKYDKPGAVFLGVTHRLDRPTS 66

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ART  A   + + F     +K YW++V G    K++ + + L++ +     Y H 
Sbjct: 67  GVVVFARTSKALPRMNKLFANHETRKTYWAVVEGTTPKKQDRLIHHLVRNTKQNKSYAH- 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +  AI  + VI     ++  LE+   TGR HQ+R     +GC I GD KY A 
Sbjct: 126 -DHGVPNSKEAILSYTVIQKL-DRYTLLEIALETGRHHQIRAQLSKIGCVIKGDLKYGAR 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                 S     ++LHAR ++  HP +   ++I AP+P
Sbjct: 184 -----RSNKDGSIHLHARQLEFIHPVKKEPVKIIAPVP 216


>gi|325687371|gb|EGD29392.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK72]
          Length = 298

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 117/236 (49%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVINKPQGMVVHPSAG---HTSGTLVNALMYHIQDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+VA+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMVAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTRFQVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG          +LHAR +   HP  G  L+ TA +P    +T + L
Sbjct: 247 EVYGPRKTLKGYGQ-------FLHARTLGFTHPRTGEVLEFTAEVPVIFQETLEKL 295


>gi|325203791|gb|ADY99244.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M01-240355]
          Length = 374

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 139/307 (45%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T +A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQIPRAGIVHRLDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HP+ G  +
Sbjct: 256 HQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPKTGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|257060968|ref|YP_003138856.1| pseudouridine synthase [Cyanothece sp. PCC 8802]
 gi|256591134|gb|ACV02021.1| pseudouridine synthase [Cyanothece sp. PCC 8802]
          Length = 551

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/235 (31%), Positives = 113/235 (48%), Gaps = 52/235 (22%)

Query: 90  LTKHSDFLKSIL--LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDS--KGQKP 144
           L  +  F KS +  +YED  I   +KP+G+ SV G     +  D  L    +S    Q+ 
Sbjct: 333 LGNNQSFFKSEIKVIYEDQWIIAIDKPSGLLSVPGRYFETF--DSVLTRLQNSLPDAQEL 390

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL---------------VWG 189
           R  HRLDQ+TSGIL++AR R   +HL++ F  R+++KIY ++               +WG
Sbjct: 391 RTVHRLDQDTSGILLLARDRYTHRHLSQQFAQRKVEKIYEAILAGSVMMNEGVIQLPLWG 450

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            P N+     +W L K                    +I+ FKVI    +    ++  P T
Sbjct: 451 DPNNRPYQKVDWELGKP-------------------SITQFKVITT-QENLTRIQFIPLT 490

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           GRTHQ+RVHA+    +G  I+GD+ Y  N          ++L+LHAR +   HP+
Sbjct: 491 GRTHQIRVHAVDTQGLGSVILGDYLYGCNAG-------VSRLHLHARELKFEHPQ 538


>gi|251793936|ref|YP_003008668.1| 23S rRNA pseudouridine synthase D [Aggregatibacter aphrophilus
           NJ8700]
 gi|247535335|gb|ACS98581.1| ribosomal large subunit pseudouridine synthase D [Aggregatibacter
           aphrophilus NJ8700]
          Length = 324

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 121/242 (50%), Gaps = 27/242 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           ++YED  I V NKP  + V  G+G      ++  L  +     + PR  + HRLD++T+G
Sbjct: 85  IVYEDDDILVINKPKDLVVHPGAGNPKGTVLNALLYHY-PQIAEVPRAGIVHRLDKDTTG 143

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYV 213
           ++VVA+T  A   L    + R+I + Y ++  GI        E +A    K++H+    V
Sbjct: 144 LMVVAKTIPAQTQLVRDLQKRKITREYEAVACGIMTKGGTVDEPMARHPTKRTHMA---V 200

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  Y 
Sbjct: 201 HPMGKP------AVTHYRIMERF-RDYTRLRLRLETGRTHQIRVHMAHLAHPLLGDQTYG 253

Query: 274 ANFKG--NFTSPIQNKL------YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
              +   N +  + N L       LHA  + L HP  G  ++  APLP   V+   +L  
Sbjct: 254 GRPRPPKNASEELMNVLRNFKRQALHAIMLRLQHPISGEMMEWYAPLPEDFVELITALKA 313

Query: 325 KY 326
            Y
Sbjct: 314 DY 315


>gi|305667192|ref|YP_003863479.1| putative ribosomal large subunit pseudouridine synthase [Maribacter
           sp. HTCC2170]
 gi|88708126|gb|EAR00364.1| putative ribosomal large subunit pseudouridine synthase [Maribacter
           sp. HTCC2170]
          Length = 230

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/227 (30%), Positives = 109/227 (48%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +   NK  G  VQG       +   +K ++  K  KP      + HRLD+ TS
Sbjct: 13  ILYEDNHLIAINKRPGDIVQGDKTGDNPLSDIVKQYIKEKYNKPGNVYLGVPHRLDRPTS 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A++  A   L + F  +  +K YW++V   P ++ + + +WL + +     Y + 
Sbjct: 73  GIVVFAKSSKALPRLNKLFAEKEAKKTYWAIVKNQPPSQADQLVHWLKRNTRQNKSYAN- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+    +  AI  +K+       F  LE+   TGR HQ+R     +G PI GD KY  +
Sbjct: 132 -KKEVPDSKKAILEYKIRKKLNSYFL-LEIDLKTGRHHQIRAQLTAIGSPIKGDLKYGFD 189

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
                 S     ++LHAR +   HP +   L+I AP P   V  W++
Sbjct: 190 RSNKGGS-----IHLHARKLSFIHPVKKEPLEIVAPTPNDPV--WNA 229


>gi|193215325|ref|YP_001996524.1| pseudouridine synthase, RluA family [Chloroherpeton thalassium ATCC
           35110]
 gi|193088802|gb|ACF14077.1| pseudouridine synthase, RluA family [Chloroherpeton thalassium ATCC
           35110]
          Length = 346

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/239 (31%), Positives = 111/239 (46%), Gaps = 30/239 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED  + V NKPAG+ V              + YH    L S    +  +P + HRLD
Sbjct: 102 IVFEDEFLLVINKPAGMVVHPAYANWTGTLAGAVLYHTQNRL-SETGKEALRPGIVHRLD 160

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN--WLLKKSH-I 208
           ++TSG++VVA+  A    L + F  R  +KIY +LVWG PK     I    W  K+   I
Sbjct: 161 KDTSGLIVVAKDDATHYALAKQFAERTTEKIYTALVWGCPKPPSGTIQTNIWRSKRDRKI 220

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +Y     ++E G   AI+ ++V + F   F  L++Q HTGRTHQ+R H  H+G  I  
Sbjct: 221 MANYPF---ESETG-KPAITDYEVKEDF-HWFSLLDLQLHTGRTHQIRAHLQHLGHAIFS 275

Query: 269 DHKYCANFKGNFTSP-----IQN------KLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           D  Y          P     ++N      +  LHA+ +   HP     +   A LP  M
Sbjct: 276 DEVYGGKSVRKLGFPQSEAFVRNLFQVIPRQALHAKKLGFKHPATENFVTFEASLPEDM 334


>gi|307704906|ref|ZP_07641797.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
 gi|307621520|gb|EFO00566.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
          Length = 295

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 84/308 (27%), Positives = 147/308 (47%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   V   +
Sbjct: 5   IETGGLRLDKALSDLTELSRSLANEQIKSGQVL-VNGQVKKAKYTVQEGDVITYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   +    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG          +LHA+ +   HP  G  L+ TA +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGLGQ-------FLHAKTLGFTHPRTGEILEFTADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKETLERL 293


>gi|329890476|ref|ZP_08268819.1| pseudouridine synthase, RluA family protein [Brevundimonas diminuta
           ATCC 11568]
 gi|328845777|gb|EGF95341.1| pseudouridine synthase, RluA family protein [Brevundimonas diminuta
           ATCC 11568]
          Length = 341

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 78/281 (27%), Positives = 122/281 (43%), Gaps = 50/281 (17%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQ-VVRIPPVIN 72
           D   +RLD+     +P ++   LQ +L  G V  D   V   + + Q G  VV +PPV  
Sbjct: 29  DAPGVRLDKALAEAFPTLSRARLQALLADGAVTRDGLTVSNGSAKAQPGLYVVALPPVAP 88

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
           A                 T   + +   +L+ED+ + V +K  G++     G      ++
Sbjct: 89  A-----------------TPQPEAIPLTVLFEDADLIVIDKAPGMAAHPAPGCETGTLVN 131

Query: 131 GFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             L    DS        +P + HRLD++TSG++V A++  A   L+  F    I++ Y +
Sbjct: 132 ALLAHCGDSLSGIGGVARPGIVHRLDKDTSGVMVAAKSDRAHAGLSALFAAHDIERTYVA 191

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDY--VHVVKQNEKGANYAISHFKVIDCF------- 236
           L  G P  +K  I   + + S   GD   + V++    G   AI+ + V   F       
Sbjct: 192 LTRGAPSPEKGRIQTQIGRSS---GDRKKMAVLR---SGGREAITDYVVQQTFGRPAKAS 245

Query: 237 -----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                A+  C L    HTGRTHQ+RVH    G P++GD  Y
Sbjct: 246 NARLAARVACTL----HTGRTHQIRVHMASKGAPLLGDPVY 282


>gi|238752927|ref|ZP_04614389.1| Ribosomal large subunit pseudouridine synthase D [Yersinia rohdei
           ATCC 43380]
 gi|238708835|gb|EEQ01091.1| Ribosomal large subunit pseudouridine synthase D [Yersinia rohdei
           ATCC 43380]
          Length = 325

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 90/332 (27%), Positives = 156/332 (46%), Gaps = 47/332 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   ++  +   +V VD K++ K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKDWILDDKVTVDGKKINKPKEKVLGGELVAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        ++  LD               ++YED+ I V NKP G+ V  G+G   +
Sbjct: 69  AQIEEDARWAPQEIPLD---------------IVYEDNDILVINKPRGLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + 
Sbjct: 111 PDGTVLNALLYYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH + +       A +H+++++ F + 
Sbjct: 171 YEAVAIGNMTAGGRVDEPISRHSTKRTHMA---VHPMGKP------ATTHYRIMEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       +F S ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFISILRGFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A  + L HP  G +++  A LP  MV+  ++L
Sbjct: 281 ATMLRLYHPISGIQMEWHAALPEDMVELINAL 312


>gi|238785831|ref|ZP_04629800.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           bercovieri ATCC 43970]
 gi|238713244|gb|EEQ05287.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           bercovieri ATCC 43970]
          Length = 325

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 91/336 (27%), Positives = 157/336 (46%), Gaps = 55/336 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V VD K + K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVTID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        ++  LD               ++YEDS I V NKP G+ V  G+G   +
Sbjct: 69  AQIEEDARWAPQEIPLD---------------IVYEDSDILVINKPRGLVVHPGAG---N 110

Query: 129 IDG--------FLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            DG        +    VD     PR  + HRLD++T+G++VVA+T  A   L E+ + R 
Sbjct: 111 PDGTVLNALLYYYPEIVDV----PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQARE 166

Query: 179 IQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           I + Y ++  G         E I+    K++H+    VH + +       A +H+++++ 
Sbjct: 167 ITREYEAVAIGNMTAGGRVDEPISRHSTKRTHMA---VHPMGKP------ATTHYRIMEH 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NK 287
           F +    L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       +F + ++  ++
Sbjct: 218 F-RAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFITILRGFDR 276

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
             LHA  + L HP  G +++  A LP  MV+  ++L
Sbjct: 277 QALHATMLRLYHPISGIQMEWHAALPEDMVELINAL 312


>gi|308388890|gb|ADO31210.1| putative ribosomal large subunit pseudouridine synthase D
           [Neisseria meningitidis alpha710]
 gi|325136074|gb|EGC58684.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M0579]
 gi|325139918|gb|EGC62448.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis CU385]
          Length = 374

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 137/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-THSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|289578538|ref|YP_003477165.1| pseudouridine synthase [Thermoanaerobacter italicus Ab9]
 gi|289528251|gb|ADD02603.1| pseudouridine synthase, RluA family [Thermoanaerobacter italicus
           Ab9]
          Length = 305

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 98/341 (28%), Positives = 159/341 (46%), Gaps = 61/341 (17%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  +V+  E ++E  R+D +      +     ++K++  G V V+ K VK + +++ 
Sbjct: 1   MNIVDKIVLQGEKEDEGKRIDVFLAAELDYTRSY-IKKLIVDGLVFVNGKTVKPSYKVKE 59

Query: 62  GQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
               VV IP          ++  +L  ++ L          +LYED  I V NKP G+ V
Sbjct: 60  NDEVVVNIPEA--------EKIDVLPENIPLD---------ILYEDDDIIVINKPQGMVV 102

Query: 120 QGGSG---------IAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
               G         + YH      I+G L+         P + HRLD++TSG++VVA+  
Sbjct: 103 HPAPGNYSGTLVNALLYHCKNLSGINGILR---------PGIVHRLDKDTSGVMVVAKND 153

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKG 222
            A   L+   + R + K Y ++V G+ K+++  I      ++ IG   V   K    E G
Sbjct: 154 KAHISLSNQIKERSVFKKYVAIVEGVIKDEEGKI------EAPIGRHPVDRKKMAVIEDG 207

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             YA++ +KV++ F +    +E    TGRTHQ+RVH   +G P+VGD  Y    K  F  
Sbjct: 208 -RYALTLYKVLERFKEN-TLVEAVIKTGRTHQIRVHMAFIGHPVVGDPVYGFK-KQKFKL 264

Query: 283 PIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             Q    LH+  +   HP +G  ++  APLP + V+  + L
Sbjct: 265 EGQA---LHSSILGFIHPTKGVYMEFEAPLPEYFVRLIEIL 302


>gi|51474013|ref|YP_067770.1| pseudouridine synthase [Rickettsia typhi str. Wilmington]
 gi|51460325|gb|AAU04288.1| Pseudouridine synthase [Rickettsia typhi str. Wilmington]
          Length = 313

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 86/317 (27%), Positives = 150/317 (47%), Gaps = 40/317 (12%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N RLD+   +    ++   +QK +++  V++       N+ I S   V +      L   
Sbjct: 12  NTRLDKALSSLLEKVSRNQVQKAIKNSCVQI-------NDVIISDSDVLVKENDTILFSF 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL---- 133
            + +++  +S N+T         ++YED  + V NK AGI+V  G   A H D  L    
Sbjct: 65  KEPEELKITSANITLD-------IIYEDDDLIVINKAAGITVHPG---AKHHDNTLVNAL 114

Query: 134 ----KSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               K+  D    ++P + HRLD+ET+G++VVA+   A   L +    R++ + Y +LVW
Sbjct: 115 LHHTKNLSDIGSAERPGIVHRLDKETTGLMVVAKNNKAHMLLAKQIEQRQVIRKYKALVW 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQP 247
           G+  N  E I N  + ++      + ++K    G   A++H+K ++ F       +E + 
Sbjct: 175 GVI-NPLEGIINNNIGRNRNNRKKMTILKY---GGKKAVTHYKTLELFYGGTLSMVECKL 230

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLY------LHARYMDLPH 299
            TGRTHQ+RV   ++   +VGD  Y  N +    SP  ++ KL       LH+ Y+   H
Sbjct: 231 STGRTHQIRVQLSNLKHSVVGDQTYGNNNRKIINSPPKLKAKLIDFKRQALHSWYLSFTH 290

Query: 300 PEGGR-LQITAPLPAHM 315
           P   + ++ +  +P  M
Sbjct: 291 PTSNKIMEFSCAIPRDM 307


>gi|15676602|ref|NP_273746.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis MC58]
 gi|34395832|sp|Q9K0B0|RLUD_NEIMB RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|7225933|gb|AAF41121.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis MC58]
 gi|316983681|gb|EFV62662.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis H44/76]
 gi|325200611|gb|ADY96066.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis H44/76]
          Length = 374

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 137/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-THSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|217324150|ref|ZP_03440234.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           TW14588]
 gi|217320371|gb|EEC28795.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           TW14588]
          Length = 279

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 114/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFRERVPKKQYVTRVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 126 KVCYETGKP-AQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|148996979|ref|ZP_01824633.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP11-BS70]
 gi|168491017|ref|ZP_02715160.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae CDC0288-04]
 gi|168575592|ref|ZP_02721528.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae MLV-016]
 gi|237651118|ref|ZP_04525370.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CCRI 1974]
 gi|237821884|ref|ZP_04597729.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CCRI 1974M2]
 gi|307067586|ref|YP_003876552.1| 23S RNA-specific pseudouridylate synthase [Streptococcus pneumoniae
           AP200]
 gi|147756679|gb|EDK63719.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP11-BS70]
 gi|183574680|gb|EDT95208.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae CDC0288-04]
 gi|183578513|gb|EDT99041.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae MLV-016]
 gi|306409123|gb|ADM84550.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           pneumoniae AP200]
          Length = 295

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 84/308 (27%), Positives = 148/308 (48%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   V   +
Sbjct: 5   IETGGLRLDKALSDLTELSRSLANEQIKSGQVL-VNGQVKKAKYTVQEGDVVTYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   L    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG+         +LHA+ +   HP  G+ L+  A +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGKTLEFKADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKETLERL 293


>gi|56414629|ref|YP_151704.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|56128886|gb|AAV78392.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
          Length = 326

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 124/245 (50%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHLGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPISRHPTKRTHMS-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV   D++
Sbjct: 253 YGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPVSGIEMEWHAPIPQDMVDLIDAM 312

Query: 323 GFKYD 327
              ++
Sbjct: 313 RADFE 317


>gi|255009930|ref|ZP_05282056.1| ribosomal large subunit pseudouridine synthase [Bacteroides
           fragilis 3_1_12]
 gi|313147717|ref|ZP_07809910.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis 3_1_12]
 gi|313136484|gb|EFR53844.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis 3_1_12]
          Length = 357

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 89/347 (25%), Positives = 157/347 (45%), Gaps = 48/347 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    + +I+   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYDNEIIPEDIPLN---------IVYEDKYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    LK   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 138 LVNAIAWH----LKDNSDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKT 193

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFA 237
            ++ Y +LVWGI    +  +   + +      D + + V  +     +A++H++V++   
Sbjct: 194 TKRRYRALVWGIVDQNEGTVVGSIARNPK---DRMQMAVMPDPAQGKHAVTHYRVLERLG 250

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN--------- 286
                +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +          
Sbjct: 251 Y-VTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTC 309

Query: 287 -KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS-LGFKYDRNL 330
            +  LHA  +   HP  G  +  T+ LP  M +  +   G+  +R+L
Sbjct: 310 PRQALHAMTLGFVHPVTGEEMHFTSELPDDMTRLIEKWRGYISNRDL 356


>gi|320172856|gb|EFW48088.1| Ribosomal large subunit pseudouridine synthase A [Shigella
           dysenteriae CDC 74-1112]
          Length = 219

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/216 (33%), Positives = 112/216 (51%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++        + ++P TGR+HQLRVH L  G PI+GD ++ A+
Sbjct: 126 KVCYETGKP-AQTEYEVVEYAPDNTARVVLKPITGRSHQLRVHMLAQGHPILGD-RFYAS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|161510965|ref|YP_089013.2| 23S rRNA pseudouridine synthase D [Mannheimia succiniciproducens
           MBEL55E]
          Length = 324

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 74/247 (29%), Positives = 122/247 (49%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP    V  G+G         + YH      + V   G    + HRLD
Sbjct: 85  IVYEDDDILVINKPKDFVVHPGAGNPNGTVLNALLYHYPQI--TEVPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L  + + R+I + Y ++ +GI        E ++    K++ +
Sbjct: 139 KDTTGLMVVAKTIPAQTQLVRALQKRKITREYEAIAFGIMTKGGTVDEPMSRHPTKRTLM 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A++H++V++ F + +  L ++  TGRTHQ+RVH  H+  P++G
Sbjct: 199 A---VHPMGKP------AVTHYRVMEHF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLG 248

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
           D  Y        N    F S ++N  +  LHA  + L HP  G L +  APLP   V+  
Sbjct: 249 DQTYGGRPRPPKNASEEFMSVLRNFQRQALHAIMLRLEHPITGELMEWHAPLPEDFVELV 308

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 309 NALKADY 315


>gi|53711780|ref|YP_097772.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis YCH46]
 gi|60680012|ref|YP_210156.1| ribosomal large subunit pseudouridine synthase [Bacteroides
           fragilis NCTC 9343]
 gi|265765162|ref|ZP_06093437.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_16]
 gi|52214645|dbj|BAD47238.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis YCH46]
 gi|60491446|emb|CAH06196.1| ribosomal large subunit pseudouridine synthase [Bacteroides
           fragilis NCTC 9343]
 gi|263254546|gb|EEZ25980.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_16]
          Length = 357

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 90/347 (25%), Positives = 157/347 (45%), Gaps = 48/347 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    + +I+   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYDNEIIPEDIPLH---------IVYEDKYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    LK   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 138 LVNAIAWH----LKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGVQFFNKT 193

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFA 237
            ++ Y +LVWGI    +  I   + +      D + + V  +     +A++H++V++   
Sbjct: 194 TKRRYRALVWGIVDQDEGTIVGSIARNPK---DRMQMAVMADPTQGKHAVTHYRVLERLG 250

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN--------- 286
                +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +          
Sbjct: 251 Y-VTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTC 309

Query: 287 -KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS-LGFKYDRNL 330
            +  LHA  +   HP  G  +  T+ LP  M +  +   G+  +R+L
Sbjct: 310 PRQALHAMTLGFVHPVTGEEMHFTSELPDDMTRLIEKWRGYISNRDL 356


>gi|229918562|ref|YP_002887208.1| pseudouridine synthase, RluA family [Exiguobacterium sp. AT1b]
 gi|229469991|gb|ACQ71763.1| pseudouridine synthase, RluA family [Exiguobacterium sp. AT1b]
          Length = 303

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 79/311 (25%), Positives = 147/311 (47%), Gaps = 47/311 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINA 73
           +E  R+D+W  +     +   +Q+ +++G + V+   VK N ++Q G  V +  P  +  
Sbjct: 9   DEKARIDKWVSDR-GEWSRSQVQEWIKTGALLVNGSAVKANYKLQVGDEVEVNVPEAV-- 65

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
                 E ++L   + L          +++ED  + V NK  G+ V   +G         
Sbjct: 66  ------ELEVLPEDIPLE---------IVFEDEDVIVVNKARGMVVHPAAGHTSGTLVNA 110

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + YH D    S ++   ++P + HR+D++T+G+L+VA+   A + L    + + I++ Y 
Sbjct: 111 LLYHCDDL--SGINGV-KRPGIVHRIDKDTTGLLMVAKNDLAHESLASQLKDKTIKREYI 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           +LV G      E +      ++ IG D      +   ++ A  A++HF++++ + + F  
Sbjct: 168 ALVHG------ELVHELGTIEAPIGRDTNDRQRMTVTDRNAKEAVTHFRLLERY-KDFTL 220

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+RVH  ++G P+ GD KY      +          LHA  +   HP  
Sbjct: 221 VECKLETGRTHQIRVHMRYIGHPLAGDPKYGPRRTIDLGGQA-----LHAATLGFHHPRT 275

Query: 303 GR-LQITAPLP 312
              ++  APLP
Sbjct: 276 KEWMEFEAPLP 286


>gi|85711025|ref|ZP_01042085.1| Pseudouridylate synthase [Idiomarina baltica OS145]
 gi|85694938|gb|EAQ32876.1| Pseudouridylate synthase [Idiomarina baltica OS145]
          Length = 322

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 86/320 (26%), Positives = 149/320 (46%), Gaps = 43/320 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD+     +P  +   ++K +  G+V VD + + K   +++ G +V I   +       
Sbjct: 19  RLDQILAELFPDYSRSRMKKWITEGKVSVDAQVIEKPREKLEFGALVAIDAELE------ 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSW 136
           +E++     + L          ++YED  I + NKPAG+ V  G+G      ++G L   
Sbjct: 73  REERYQAQPIELD---------IVYEDEDILIINKPAGLVVHPGAGAPDGTLLNGLLHYD 123

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            D     PR  + HRLD++T+G++VVAR   A   L +  + R I + Y ++  G+    
Sbjct: 124 PDID-HVPRAGIIHRLDKDTTGLMVVARNIPAQTQLVDMMQKREITREYEAVCNGVMTAG 182

Query: 195 ---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
               E I     K++H+      VV   +     A++H++V++ F +    L ++  +GR
Sbjct: 183 GMVDEPIGRHPTKRTHMA-----VVSSGKP----AVTHYRVVERF-RAHTLLRLRLESGR 232

Query: 252 THQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLHARYMDLPHPEGG 303
           THQ+RVH  H+  P+VGD  Y    +        F + ++  ++  LHA  + L HP  G
Sbjct: 233 THQIRVHMAHIRHPLVGDLTYGGRPRPPKQASDEFLASLRGFSRQALHAAKLSLHHPITG 292

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             +   AP P   V    S+
Sbjct: 293 DWMSFEAPRPDDFVALIQSM 312


>gi|238798952|ref|ZP_04642415.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           mollaretii ATCC 43969]
 gi|238717181|gb|EEQ09034.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           mollaretii ATCC 43969]
          Length = 325

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 91/336 (27%), Positives = 157/336 (46%), Gaps = 55/336 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V VD K + K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        ++  LD               ++YEDS I V NKP G+ V  G+G   +
Sbjct: 69  AQIEEDARWAPQEIPLD---------------IVYEDSDILVINKPRGLVVHPGAG---N 110

Query: 129 IDG--------FLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            DG        +    VD     PR  + HRLD++T+G++VVA+T  A   L E+ + R 
Sbjct: 111 PDGTVLNALLYYYPEIVDV----PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQARE 166

Query: 179 IQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           I + Y ++  G         E I+    K++H+    VH + +       A +H+++++ 
Sbjct: 167 ITREYEAVAIGNMTAGGRVDEPISRHSTKRTHMA---VHPMGKP------ATTHYRIMEH 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NK 287
           F +    L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       +F + ++  ++
Sbjct: 218 F-RAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFIAILRGFDR 276

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
             LHA  + L HP  G +++  A LP  MV+  ++L
Sbjct: 277 QALHATMLRLYHPISGIQMEWHAALPEDMVELINAL 312


>gi|15900809|ref|NP_345413.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae TIGR4]
 gi|111658131|ref|ZP_01408829.1| hypothetical protein SpneT_02000697 [Streptococcus pneumoniae
           TIGR4]
 gi|148992939|ref|ZP_01822558.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP9-BS68]
 gi|149010429|ref|ZP_01831800.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP19-BS75]
 gi|168485879|ref|ZP_02710387.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CDC1087-00]
 gi|168490255|ref|ZP_02714454.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP195]
 gi|169834331|ref|YP_001694382.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae Hungary19A-6]
 gi|182683874|ref|YP_001835621.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CGSP14]
 gi|194398681|ref|YP_002037566.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae G54]
 gi|303259840|ref|ZP_07345815.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP-BS293]
 gi|303262254|ref|ZP_07348198.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP14-BS292]
 gi|303264676|ref|ZP_07350594.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS397]
 gi|303267177|ref|ZP_07353044.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS457]
 gi|303269425|ref|ZP_07355194.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS458]
 gi|14972404|gb|AAK75053.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae TIGR4]
 gi|147764910|gb|EDK71839.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP19-BS75]
 gi|147928391|gb|EDK79407.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP9-BS68]
 gi|168996833|gb|ACA37445.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae Hungary19A-6]
 gi|182629208|gb|ACB90156.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CGSP14]
 gi|183571050|gb|EDT91578.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CDC1087-00]
 gi|183571388|gb|EDT91916.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP195]
 gi|194358348|gb|ACF56796.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae G54]
 gi|301801775|emb|CBW34486.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           INV200]
 gi|302636577|gb|EFL67068.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP14-BS292]
 gi|302639045|gb|EFL69505.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP-BS293]
 gi|302641044|gb|EFL71422.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS458]
 gi|302643292|gb|EFL73572.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS457]
 gi|302645763|gb|EFL75992.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS397]
 gi|332073261|gb|EGI83740.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA17570]
 gi|332076208|gb|EGI86674.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA41301]
 gi|332204930|gb|EGJ18995.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA47901]
          Length = 295

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 84/308 (27%), Positives = 148/308 (48%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   V   +
Sbjct: 5   IETGGLRLDKALSDLSELSRSLANEQIKSGQVL-VNGQVKKAKYTVQEGDVVTYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   L    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG+         +LHA+ +   HP  G+ L+  A +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGKTLEFKADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKETLERL 293


>gi|254517173|ref|ZP_05129231.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium NOR5-3]
 gi|219674678|gb|EED31046.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium NOR5-3]
          Length = 282

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/221 (32%), Positives = 111/221 (50%), Gaps = 27/221 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPR--LTHRLDQETSGI 157
           +LYED ++ V +KPAG+ V  G+G  +  +   L S   +    PR  + HRLD+ETSG+
Sbjct: 40  ILYEDEELLVIDKPAGLVVHPGAGNHHGTLVNALLSHRPALESVPRGGIVHRLDKETSGL 99

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYVH 214
           LVVA T  A + L    + + +Q+ Y+++V G+P      +  I     +++ +      
Sbjct: 100 LVVAGTLNAHRSLVAQLQKKDVQREYFAIVRGVPSGGGRIETAIGRHPRQRTRMA----- 154

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV  + K    A++H+++   FAQ +  L +Q  TGRTHQ+RVH  H G P++GD  Y  
Sbjct: 155 VVPNSGK---PAVTHYRIAQRFAQ-YTALSVQLETGRTHQIRVHMAHRGYPLLGDPVYGG 210

Query: 275 NFKGNFTSPIQNKL----------YLHARYMDLPHPEGGRL 305
             +         +L           LHAR +   HP  G L
Sbjct: 211 RLQ--LPRACSERLAETLRGFRRQALHARRLSFIHPGSGDL 249


>gi|322372447|ref|ZP_08046983.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           C150]
 gi|321277489|gb|EFX54558.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           C150]
          Length = 297

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 89/321 (27%), Positives = 147/321 (45%), Gaps = 48/321 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++     + +++G V V+ K  K    ++ G V+          
Sbjct: 7   EAGNRLDKALAD-LTELSRSQANEAIKAGTVLVNGKSAKAKYAVKEGDVI---------T 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-- 133
           + + E+++L+      K  D    I+ YED+ + V NKP G+ V   +G   H  G L  
Sbjct: 57  YELPEEEVLEY-----KAEDIPLDII-YEDADVAVVNKPQGMVVHPSAG---HTSGTLVN 107

Query: 134 ------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 K      G  +P + HR+D++TSG+L+VA+   A   L    + ++  + Y ++
Sbjct: 108 ALMYHVKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDKAHNALAAELKDKKSLRKYVAI 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLE 244
           V G   N +  I      ++ IG       KQ    KG   A++ F V++ F   +  +E
Sbjct: 168 VHGNLPNDRGVI------EAPIGRSDKDRKKQAVTAKG-KPAVTRFTVLERFGN-YTLVE 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +Q  TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   HP  
Sbjct: 220 LQLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGHGQ-------FLHAKTLGFTHPTT 272

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
           G L + TA  PA   +T + L
Sbjct: 273 GELVEFTAEEPAIFKETLEKL 293


>gi|254482837|ref|ZP_05096074.1| pseudouridine synthase, RluA family [marine gamma proteobacterium
           HTCC2148]
 gi|214036918|gb|EEB77588.1| pseudouridine synthase, RluA family [marine gamma proteobacterium
           HTCC2148]
          Length = 312

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 93/324 (28%), Positives = 143/324 (44%), Gaps = 45/324 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +N RLD+     +P  +   LQ  ++ G + VD K+++  +++  G  + I         
Sbjct: 2   DNERLDQIAAKLFPDYSRSRLQTWIKKGDLLVDGKQLRTRDKVFYGAQLSI--------D 53

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
              EQ +     N+          ++YED+ I V NKPAG+ V   +G   H DG L + 
Sbjct: 54  TEPEQAVGWQPQNIDLD-------IIYEDAHILVVNKPAGLVVHPAAG---HPDGTLVNA 103

Query: 137 V----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           +        Q PR  + HRLD ETSGI+V A++  A Q L    + R +++ Y ++  G+
Sbjct: 104 LLAHSPEMAQLPRGGIVHRLDMETSGIMVAAKSLLAHQDLVSQLQERTVRREYVAVCIGV 163

Query: 191 PKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                   E +     ++  +    V VV     G   AI+H++V   +      + +  
Sbjct: 164 MTGGGTVDEPMGRHPKQRKKMA---VLVV-----GGKPAITHYRVTKRYGH-HTRIAVNL 214

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQN-----KLYLHARYMDLPH 299
            TGRTHQ+RVH  H   P+VGD  Y       KG     I       +  LHAR + L H
Sbjct: 215 ETGRTHQIRVHMAHKHYPLVGDPTYGGRPRIPKGASEELIAALRGFPRQALHARALGLFH 274

Query: 300 PEGG-RLQITAPLPAHMVKTWDSL 322
           PE G  +    PLP  +    D L
Sbjct: 275 PETGEEMNFECPLPTDLQGLLDVL 298


>gi|15672980|ref|NP_267154.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis Il1403]
 gi|281491492|ref|YP_003353472.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
 gi|12723945|gb|AAK05096.1|AE006334_2 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
 gi|281375210|gb|ADA64723.1| Ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
 gi|326406542|gb|ADZ63613.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis CV56]
          Length = 301

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 85/316 (26%), Positives = 153/316 (48%), Gaps = 47/316 (14%)

Query: 11  VVENDEEN--MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           +++ +EEN  +RLD+   N   +   + L +++++ +V V+ +  K   +++ G  +   
Sbjct: 3   IIKINEENKGLRLDKALANQTEYSRSL-LTELIKNDKVFVNSEAKKAKYKVKVGDRIEFE 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
                    + E ++LD        ++ L   ++YEDS + V NKP G+ V   +G    
Sbjct: 62  ---------VPEAEVLDIV------AEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASG 106

Query: 125 -----IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                I YHI    K      G  +P + HR+D++TSG+L++A+   A + L    + + 
Sbjct: 107 TLVNAIMYHI----KDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKT 162

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFA 237
            ++ Y ++V G   N K  I      ++ IG +     KQ    G   A++HF+V++ F 
Sbjct: 163 SKRRYLAIVHGEIANDKGTI------EAPIGRNLKDRKKQAVVSGGKPAVTHFEVLERF- 215

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  + ++  TGRTHQ+RVH  ++G P+ GD  Y  N      +P + + +LHA  +  
Sbjct: 216 YGYTLIALRLETGRTHQIRVHMNYIGHPVAGDPLYGPN---KTLTPNKGQ-FLHAETLGF 271

Query: 298 PHPEGG---RLQITAP 310
            HP  G     Q+ AP
Sbjct: 272 DHPTTGEFMEFQVDAP 287


>gi|323171216|gb|EFZ56864.1| RNA pseudouridylate synthase family protein [Escherichia coli
           LT-68]
          Length = 219

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/216 (33%), Positives = 109/216 (50%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y + 
Sbjct: 126 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
                      +L LHA  + + HP  G  +   AP
Sbjct: 185 EARAMAL----RLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|332879235|ref|ZP_08446932.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
 gi|332682655|gb|EGJ55555.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
          Length = 320

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 77/286 (26%), Positives = 134/286 (46%), Gaps = 33/286 (11%)

Query: 38  QKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           + IL    + VD+K V ++N  ++ G VVR+    +  N+ +K + +             
Sbjct: 49  KDILTGHGITVDRKSVSQYNYELRPGMVVRVSK--HKRNNELKNKYVK------------ 94

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQET 154
               ++YED  + V  K AGI         + I   L  +   +  K    + HRLD++T
Sbjct: 95  ----IVYEDKDLIVIEKSAGILSMPAVTQQFSIKTVLDEYFTRRHFKCTAHVVHRLDRDT 150

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+     + L E ++     + Y ++V G  + +   I++WL         YV 
Sbjct: 151 SGLMMYAKNIEVQRILEEHWQEIVTDRRYVAVVSGKMEKEGGTISSWLKDNK----AYVT 206

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                + G  YA++HF  +D   +++  +E++  TGR +Q+RVH   +G P+VGD KY  
Sbjct: 207 YSSPTDNGGKYAVTHFHTLDA-RERYSLVELKLETGRKNQIRVHMQDIGHPVVGDSKY-- 263

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
              GN + PI  +L LHA  ++  HP  G  ++   P P    K +
Sbjct: 264 ---GNGSDPI-GRLGLHAYRLNFYHPITGEPMEFETPFPTLFTKLF 305


>gi|291550323|emb|CBL26585.1| pseudouridine synthase, RluA family [Ruminococcus torques L2-14]
          Length = 342

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 86/335 (25%), Positives = 153/335 (45%), Gaps = 39/335 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++ +E   R+D++   +          K++R   + ++ K+   N +++ G V+++  
Sbjct: 4   ISIQKNEAGQRMDKFLAKYLNKAPKSFFYKMMRKKNITLNGKKAVGNEQLKQGDVIKLFL 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSG-- 124
               + + I   +      +  +     K +   +LYED      NKP G+  Q  S   
Sbjct: 64  AEETIENFIDHSQFSKKKASSARKQTAGKKVQLDILYEDEAAVFINKPVGMLSQKASPTD 123

Query: 125 ---IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
              + Y ID  L++   ++ +     P + +RLD+ TSGI+   +T  A Q L+E FR R
Sbjct: 124 TSLVEYFIDYLLENGKITEEELHTFHPSVCNRLDRNTSGIVAAGKTLQALQGLSEMFRDR 183

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNE-----KGANYAISHFK 231
            ++K Y  LV G + +N++  I  +L+K        V   K  E     K A+   + +K
Sbjct: 184 TLKKYYLCLVKGQVKENQR--IHGYLVKNEKTNKVTVSQKKPAEQTKDGKEASAIDTEYK 241

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKL- 288
           V+    ++   LE+   TG+THQ+R H   +G PI GD+KY     GN  F   ++ +  
Sbjct: 242 VL-ARNRETTLLEVHLITGKTHQIRAHLASIGHPIAGDYKY-----GNRSFNDALKKEYG 295

Query: 289 ----YLHARYMDLPHPEGGRLQ------ITAPLPA 313
                LHA  ++ P    G ++      I AP+PA
Sbjct: 296 LRSQLLHAYRLEFPENCEGDIKQLSGKIIKAPVPA 330


>gi|83647350|ref|YP_435785.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83635393|gb|ABC31360.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 224

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 75/220 (34%), Positives = 112/220 (50%), Gaps = 18/220 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  I V NKP+GI    G G   H+   + S V  K     + HRLD  TSG+LV+A
Sbjct: 18  LYEDKDIIVVNKPSGILTSPGRGA--HLYDSVWSRVKEKHPLSHVVHRLDLATSGVLVLA 75

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
             R A + L   F  R ++K Y + VWG+ K  +  +   L+       D+ +  KQ   
Sbjct: 76  LRRKAEKELKRQFMQREVRKTYVAKVWGVIKEDQGEVDLPLI------CDWPNRPKQKVC 129

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E G   A++ ++V+    +    +E+ P TGR+HQLRVH L +G PI+GD ++ A+ + 
Sbjct: 130 FEHGKP-AVTGYRVL-AREENATLVELYPITGRSHQLRVHMLSLGHPILGD-RFYASPEA 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
              S    +L LHA+ +   HP  G   +T   PA   ++
Sbjct: 187 LAAS---ERLLLHAQSLSFKHPYSGE-DMTFHTPADFAQS 222


>gi|302340475|ref|YP_003805681.1| pseudouridine synthase [Spirochaeta smaragdinae DSM 11293]
 gi|301637660|gb|ADK83087.1| pseudouridine synthase [Spirochaeta smaragdinae DSM 11293]
          Length = 229

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 68/220 (30%), Positives = 111/220 (50%), Gaps = 15/220 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ + V NK  G  VQG       +   +K ++  K  KP      + HRLD+ TS
Sbjct: 4   VLYEDNHLIVVNKRCGDIVQGDKSGDPTLADEVKEYLREKYNKPGNVFLGIPHRLDRPTS 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ ART  A + L+ SFR + ++KIYW++V  +P  +   + ++L +       +   
Sbjct: 64  GVVLYARTEKALRRLSLSFREQHVEKIYWAVVDKMPPAESGTLVHYLRRDRKKNKSFASD 123

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               +  +  A   ++++     ++  LE++  TGR HQ+R     +GC I GD KY   
Sbjct: 124 TPTAD--SQEAKMRYRLVGA-TNRYYLLEIELLTGRHHQIRAQLAAVGCRIRGDLKY--- 177

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEG--GRLQITAPLPA 313
             G   S     ++LHAR + L HP G   R+ ITA  P+
Sbjct: 178 --GYPRSNRDGGIHLHARKVSLDHPVGERNRITITADPPS 215


>gi|158522832|ref|YP_001530702.1| RluA family pseudouridine synthase [Desulfococcus oleovorans Hxd3]
 gi|158511658|gb|ABW68625.1| pseudouridine synthase, RluA family [Desulfococcus oleovorans Hxd3]
          Length = 329

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/230 (33%), Positives = 116/230 (50%), Gaps = 26/230 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           LL+ED+ + V NKP G+ V      +GG+ +   +  F       +  +P + HRLD+ T
Sbjct: 84  LLFEDAFLLVVNKPPGLVVHPAPGHEGGTLVNRLLHHFPAIGTVGEPDRPGIVHRLDRNT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG LVVA+T AA Q L++ F+ R+++K Y +LV+G  K+    +         IG   + 
Sbjct: 144 SGALVVAKTAAAHQALSDMFKSRQVRKTYLALVYGQMKSTGGVVT------LPIGRHSLE 197

Query: 215 VVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             K   +   A  A + +KV   F      LE++ HTGRTHQ+RVH   +  P+VGD  Y
Sbjct: 198 RKKMSVSSPQARPAETRWKVRKAFVDA-SLLELEIHTGRTHQIRVHCTALQRPVVGDPTY 256

Query: 273 CANF---KGNFTSPIQNKL-------YLHARYMDLPHP-EGGRLQITAPL 311
              +   + +F+S    +L        LHA  ++  HP  G  +  TAPL
Sbjct: 257 PCKWTRKRQHFSSRASFELLNAAGRQMLHAWRLEFDHPVTGAPMCFTAPL 306


>gi|87201058|ref|YP_498315.1| ribosomal large subunit pseudouridine synthase D [Novosphingobium
           aromaticivorans DSM 12444]
 gi|87136739|gb|ABD27481.1| ribosomal large subunit pseudouridine synthase D [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 332

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 68/232 (29%), Positives = 113/232 (48%), Gaps = 25/232 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--DSKGQ--------KPRLTHR 149
           ++++ED  + V +KPAG+ V   +G   + DG L + +    +GQ        +P + HR
Sbjct: 90  VVVHEDDALIVVDKPAGLVVHPAAG---NPDGTLVNALLHHCRGQLSGIGGVARPGIVHR 146

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D++TSG+LVVA+T AA + L   F    I + Y  +  G+P      +   + + SH  
Sbjct: 147 IDKDTSGLLVVAKTDAAHEGLARQFADHSITRAYKCVTAGVPMPPSGTVRGAIARSSH-- 204

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            D   +   ++    +A++HF+ +    Q    +E +  TGRTHQ+RVH   +G P++GD
Sbjct: 205 -DRKKMALVDDGRGKHAVTHFRTLAAL-QGAALVECRLETGRTHQVRVHLASIGHPLLGD 262

Query: 270 HKYCANFKGNFTSPIQNKL-----YLHARYMDLPHP-EGGRLQITAPLPAHM 315
             Y      +   P+  +L      LHA  +   HP  G  L   +P P  M
Sbjct: 263 PVY--GRTPSRLRPLLQRLGFHRQALHAAELGFIHPVTGAPLHFASPTPVDM 312


>gi|254468337|ref|ZP_05081743.1| ribosomal large subunit pseudouridine synthase D [beta
           proteobacterium KB13]
 gi|207087147|gb|EDZ64430.1| ribosomal large subunit pseudouridine synthase D [beta
           proteobacterium KB13]
          Length = 346

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 88/313 (28%), Positives = 145/313 (46%), Gaps = 42/313 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD    N  P  +   +Q ++++  + ++   V  N ++  G+ + I  VI     +I 
Sbjct: 20  RLDAVLSNLVPEFSRSKIQSMIKNDLIFLNGSHVSQNYKVVGGEEIVINGVIEDEIDVIA 79

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWV 137
           E   LD               ++YED  I V NKP  + V  GSG A    ++G L    
Sbjct: 80  ENISLD---------------IVYEDDDILVLNKPYNLVVHPGSGNANGTLLNGLLYYNK 124

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
           D + + PR  + HRLD++T+G++VVA+   +  +L    + + + + Y ++VWG I +NK
Sbjct: 125 DLE-KLPRGGIVHRLDKDTTGLMVVAKNEESQNNLISQLQSKSVYREYRAIVWGQIWQNK 183

Query: 195 --KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             ++ I     +++ +      V K N K A   +   +  +      C L+    TGRT
Sbjct: 184 VIQKPIGRHPRQRTKMA-----VTKVNGKDAETKLEILERFNYHTYVRCLLK----TGRT 234

Query: 253 HQLRVHALHMGCPIVGDHKY-------CANFKGNFTSPIQN--KLYLHARYMDLPHPEGG 303
           HQ+RVH L    PIVGD  Y         N + +    I+N  +  LHA  + L HP+  
Sbjct: 235 HQIRVHMLDNNSPIVGDKDYGLKKIIPTKNMEMDLLKSIKNFDRQALHAIALGLIHPKTN 294

Query: 304 R-LQITAPLPAHM 315
           + ++ T  LP  M
Sbjct: 295 KEMKWTIDLPEDM 307


>gi|237708087|ref|ZP_04538568.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           9_1_42FAA]
 gi|229457915|gb|EEO63636.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           9_1_42FAA]
          Length = 540

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/232 (32%), Positives = 122/232 (52%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++  ++ ++ + L KH   +   ++YED+ + V NKPAG+    G G    +   +
Sbjct: 313 LKHMLQGLEVEENPL-LKKHYHEIPLEIVYEDNYLVVVNKPAGMLSVPGKGEIDSVYQHI 371

Query: 134 KS-WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP 191
           K+ + D+ G  P + HRLD  TSG+L++A+ +   QHL   F+ R I+K Y +L+ G IP
Sbjct: 372 KTLYPDATG--PLIVHRLDMATSGVLLIAKNKKVHQHLQAQFKNRMIKKRYIALLDGKIP 429

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
              KE      L+ + +  D    +  +E G   AI+ ++V++   +    +   P TGR
Sbjct: 430 --SKEGTITLPLRMNPL--DRPRQIVDHEHGKT-AITLYRVLNE-QEGRTLIAFYPLTGR 483

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVHA H   + CPI GD  Y             ++LYLHA  ++  HP
Sbjct: 484 THQLRVHAAHPEGLHCPIRGDELYGRK---------ADRLYLHAESLEFVHP 526


>gi|156932863|ref|YP_001436779.1| 23S rRNA pseudouridine synthase D [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156531117|gb|ABU75943.1| hypothetical protein ESA_00660 [Cronobacter sakazakii ATCC BAA-894]
          Length = 326

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 77/245 (31%), Positives = 124/245 (50%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L E+ ++R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVEALQLREITREYEAVAIGHMTAGGTVSEPISRHPTKRTHMS-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RIHTRLRLRLETGRTHQIRVHMAHITHPLVGDQL 252

Query: 272 YCAN---FKGNFTSPIQ-----NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           Y       KG   + IQ     ++  LHA  + L HP  G L +  AP+P  MV   D+L
Sbjct: 253 YGGRPRPPKGASEAFIQALRKFDRQALHATMLRLYHPISGILMEWHAPIPQDMVDLIDAL 312

Query: 323 GFKYD 327
              ++
Sbjct: 313 RADFE 317


>gi|94987255|ref|YP_595188.1| pseudouridylate synthases, 23S RNA-specific [Lawsonia
           intracellularis PHE/MN1-00]
 gi|94731504|emb|CAJ54867.1| Pseudouridylate synthases, 23S RNA-specific [Lawsonia
           intracellularis PHE/MN1-00]
          Length = 541

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 84/313 (26%), Positives = 147/313 (46%), Gaps = 40/313 (12%)

Query: 19  MRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRVKFN--NRIQSGQ--VVRIPPVIN 72
           +RLD++  N+     ++   L+K++ SG  ++D K V F+   R++ G    +++P V++
Sbjct: 16  VRLDQFLYNNLCTHGVSRERLKKVIVSGGCKIDDK-VCFSPSTRLKVGMHIFIQLPEVVS 74

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----SGIAY 127
           AL   + E+  L+               +L+ D  + + NKP G++V        S + +
Sbjct: 75  AL---LPEEGFLE---------------ILFSDEHLAIINKPPGLTVHPAPSCQESTLVH 116

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  +    ++  G +P + HR+D++TSG+L +A T      L++ F  R+I K Y +LV
Sbjct: 117 RLLKYFPKLIEQGGLRPGIVHRIDKDTSGLLCIALTEDTRLKLSKIFLDRKINKEYLALV 176

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+P + +  IA  L +            K       + + H    D ++     L +  
Sbjct: 177 HGVP-SMEGYIAVPLGRDPKTKVKVAVNPKGKPAHTEWRVLHRGKNDVYS----ILALTI 231

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGRL 305
            TGRTHQ+RVH  H+G P+VGD  Y     G+     Q N+  LHA  +   HP  G ++
Sbjct: 232 QTGRTHQIRVHMKHIGHPLVGDKLYAG---GHVNKTFQCNRQMLHAWKLSFEHPITGKKM 288

Query: 306 QITAPLPAHMVKT 318
               P P   + T
Sbjct: 289 NFLCPPPKDFLDT 301


>gi|300871333|ref|YP_003786206.1| pseudouridylate synthase, 23S RNA-specific [Brachyspira pilosicoli
           95/1000]
 gi|300689034|gb|ADK31705.1| pseudouridylate synthase, 23S RNA-specific [Brachyspira pilosicoli
           95/1000]
          Length = 298

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 119/237 (50%), Gaps = 35/237 (14%)

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYHI 129
           +E+ IL  +++L          +LYED  + V NKP  +SV            + + YHI
Sbjct: 67  EEEDILAENIDLD---------ILYEDEYLLVVNKPCNMSVHCSPSERHGTLVNALLYHI 117

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             F  ++V  K  +  + HRLD++TSGI++V +       + E F+ R I+KIY ++V G
Sbjct: 118 KDF--NFVGDKS-RAGIIHRLDKDTSGIMIVGKNADIVSAIQEQFKNRTIKKIYHAIVIG 174

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           + +       N+      IG   V+  K    +    A+S+ KV++ F +K   +E+   
Sbjct: 175 VLR------ENFYEINLPIGRHSVYRKKMTVREDGKKALSYIKVLNRF-KKHTLIEVNIK 227

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           TGRTHQ+RVH  + G P+ GD  Y  ++  N+++     L L A+ ++  HP  G +
Sbjct: 228 TGRTHQIRVHCSYKGFPVAGDKIYSKSY-SNYSN-----LMLIAKQIEFTHPISGEI 278


>gi|125974463|ref|YP_001038373.1| RluA family pseudouridine synthase [Clostridium thermocellum ATCC
           27405]
 gi|256005181|ref|ZP_05430149.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281418990|ref|ZP_06250008.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|125714688|gb|ABN53180.1| pseudouridine synthase, RluA family [Clostridium thermocellum ATCC
           27405]
 gi|255990835|gb|EEU00949.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281407447|gb|EFB37707.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|316941600|gb|ADU75634.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           1313]
          Length = 320

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 74/280 (26%), Positives = 130/280 (46%), Gaps = 21/280 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +  D+ N R+D+  +  +P +    L K  R   ++V+  RVK ++ ++    V 
Sbjct: 1   MRTITITEDKANKRIDKVLRETFPRLPNGALFKAFRKKDIKVNGVRVKEDHIVKLNDRVD 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QG 121
           I        +II E  ILD      + +      + YEDS + + NK  GI V     Q 
Sbjct: 61  I--------YIIDE--ILDGVPKAGELNYETAFSVAYEDSNLLIVNKKQGIPVHPDRTQT 110

Query: 122 GSGIAYHIDGFLK---SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            + +   +  +LK    + ++ G  P L HRLD+ T G++++A+  +    + +  +   
Sbjct: 111 ENTLIDFVKEYLKLKGEFEENSGFTPSLCHRLDRNTGGLVMIAKNSSTLHMVLKKMKSGE 170

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAISHFKVIDC 235
           I K Y  LV G  + K++ +  +L K       ++   K     E    Y +  +K +  
Sbjct: 171 ISKYYQCLVKGKMEKKEDILKAYLEKDEKKSRVFIKDTKSKNAVEIITGYKVLSYKELPD 230

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    LE+  +TGRTHQ+R H  H+G P+VGD KY  N
Sbjct: 231 IGEGISNLEVTLYTGRTHQIRAHLAHIGHPVVGDGKYGIN 270


>gi|255261883|ref|ZP_05341225.1| ribosomal large subunit pseudouridine synthase D [Thalassiobium sp.
           R2A62]
 gi|255104218|gb|EET46892.1| ribosomal large subunit pseudouridine synthase D [Thalassiobium sp.
           R2A62]
          Length = 341

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/260 (29%), Positives = 119/260 (45%), Gaps = 45/260 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGFLKSWVDS----KGQK-PRLTHRLDQE 153
           L++ED  + V NKP+G+ V    GS     ++  +    DS     G+K P + HR+D+E
Sbjct: 87  LVFEDDDLIVINKPSGMVVHPAPGSPSGTLVNALMHHCGDSLSGVGGEKRPGIVHRIDKE 146

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN---KKECIANWLLKKSHIGG 210
           TSG+LVVA++  A   L   F    +++ Y ++V+G+P +   +   I     ++S+I  
Sbjct: 147 TSGLLVVAKSDKAHHGLAAQFEAHTVERYYRAVVYGVPDSNDPRLRGIRGVNFERSNIMK 206

Query: 211 DYVHVVKQNEK---------GANYAISHFKVIDCFAQKF------CWLEMQPHTGRTHQL 255
               + +                +A++  +V++ F Q        CWLE    TGRTHQ+
Sbjct: 207 ITTQLARHKTDRQRQAVLFGNGRHAVTRARVVERFGQPVVASLVECWLE----TGRTHQI 262

Query: 256 RVHALHMGCPIVGDHKY------------CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH  H G  +VGD  Y             A F+   + P Q    LHA  +   HP  G
Sbjct: 263 RVHMTHAGHNLVGDPTYGGRRKLSPKAINAAGFEAVASFPRQ---ALHAAVLGFKHPVTG 319

Query: 304 RL-QITAPLPAHMVKTWDSL 322
            + +  APLP  M     +L
Sbjct: 320 EMVRFEAPLPDDMADLLCAL 339


>gi|212691882|ref|ZP_03300010.1| hypothetical protein BACDOR_01377 [Bacteroides dorei DSM 17855]
 gi|237724767|ref|ZP_04555248.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D4]
 gi|265756237|ref|ZP_06090566.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_33FAA]
 gi|212665554|gb|EEB26126.1| hypothetical protein BACDOR_01377 [Bacteroides dorei DSM 17855]
 gi|229436962|gb|EEO47039.1| ribosomal large subunit pseudouridine synthase A [Bacteroides dorei
           5_1_36/D4]
 gi|263233828|gb|EEZ19437.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_33FAA]
          Length = 540

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/232 (32%), Positives = 122/232 (52%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++  ++ ++ + L KH   +   ++YED+ + V NKPAG+    G G    +   +
Sbjct: 313 LKHMLQGLEVEENPL-LKKHYHEIPLEIVYEDNYLVVVNKPAGMLSVPGKGEIDSVYQHI 371

Query: 134 KS-WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP 191
           K+ + D+ G  P + HRLD  TSG+L++A+ +   QHL   F+ R I+K Y +L+ G IP
Sbjct: 372 KTLYPDATG--PLIVHRLDMATSGVLLIAKNKKVHQHLQAQFKNRMIKKRYIALLDGKIP 429

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
              KE      L+ + +  D    +  +E G   AI+ ++V++   +    +   P TGR
Sbjct: 430 --SKEGTITLPLRMNPL--DRPRQIVDHEHGKT-AITLYRVLNE-QEGRTLIAFYPLTGR 483

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVHA H   + CPI GD  Y             ++LYLHA  ++  HP
Sbjct: 484 THQLRVHAAHPEGLHCPIRGDELYGRK---------ADRLYLHAESLEFVHP 526


>gi|52307928|gb|AAU38428.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 327

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 74/247 (29%), Positives = 122/247 (49%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP    V  G+G         + YH      + V   G    + HRLD
Sbjct: 88  IVYEDDDILVINKPKDFVVHPGAGNPNGTVLNALLYHYPQI--TEVPRAG----IVHRLD 141

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L  + + R+I + Y ++ +GI        E ++    K++ +
Sbjct: 142 KDTTGLMVVAKTIPAQTQLVRALQKRKITREYEAIAFGIMTKGGTVDEPMSRHPTKRTLM 201

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A++H++V++ F + +  L ++  TGRTHQ+RVH  H+  P++G
Sbjct: 202 A---VHPMGKP------AVTHYRVMEHF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLG 251

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
           D  Y        N    F S ++N  +  LHA  + L HP  G L +  APLP   V+  
Sbjct: 252 DQTYGGRPRPPKNASEEFMSVLRNFQRQALHAIMLRLEHPITGELMEWHAPLPEDFVELV 311

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 312 NALKADY 318


>gi|319954878|ref|YP_004166145.1| ribosomal large subunit pseudouridine synthase d [Cellulophaga
           algicola DSM 14237]
 gi|319423538|gb|ADV50647.1| ribosomal large subunit pseudouridine synthase D [Cellulophaga
           algicola DSM 14237]
          Length = 232

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 107/226 (47%), Gaps = 22/226 (9%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + KIL ++ NL         +++YED+ +   NK  G  VQG       +   +K ++  
Sbjct: 2   DNKILSTANNL---------LVIYEDNHLIAINKRPGDIVQGDKTGDAPLSDVVKEYIKI 52

Query: 140 KGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           K  KP      + HRLD+ TSGI+V A+T  A   L + F  +  +K YW++V   P  +
Sbjct: 53  KYNKPGNVYLGVAHRLDRPTSGIVVFAKTSKALPRLNKLFAEKEAKKTYWAVVKNQPPKQ 112

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + + +WL + +     Y +  +  E  +  AI  + +       F  LE+  HTGR HQ
Sbjct: 113 NDLLTHWLKRNTKQNKSYANTKEVPE--SKKAILSYTIAKKLDNYFL-LEIDLHTGRHHQ 169

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +R     +GC I GD KY A+      S     ++LHAR +   HP
Sbjct: 170 IRAQLTAIGCVIKGDLKYGADRSNKDGS-----IHLHARKLSFIHP 210


>gi|301782173|ref|XP_002926501.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 1 [Ailuropoda melanoleuca]
 gi|281338700|gb|EFB14284.1| hypothetical protein PANDA_016152 [Ailuropoda melanoleuca]
          Length = 377

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 74/250 (29%), Positives = 119/250 (47%), Gaps = 22/250 (8%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S Q   +K R +   +    Q V   PV   +  +++  + L   V+    +  L   ++
Sbjct: 42  SAQRLAEKLRAQKQEQKTKNQPVPTSPVQRRVQELVRFTQQLQR-VHPNVLAKALSRGIV 100

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGIL 158
           ++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G++
Sbjct: 101 HQDMDLVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTGVM 160

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSL----------VWGIPKNKKECIAN-----WLL 203
           V+A  +  A  + E FR R++ K YW++          V  IP  +KE           L
Sbjct: 161 VLAWEKEVAHQVQELFRTRQVAKKYWAVTVRVPVPPAGVVDIPVIEKEVQGQQQHYKMTL 220

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHM 262
             S+   D   V  + ++ A+ A++ ++V+         +E+QP TG  HQLRVH +  +
Sbjct: 221 SPSYRMEDGKMVRTRRDRNAHTAVTQYQVLSSTLSS-ALVELQPITGVKHQLRVHLSFGL 279

Query: 263 GCPIVGDHKY 272
            CPI+GDHKY
Sbjct: 280 DCPILGDHKY 289


>gi|217978454|ref|YP_002362601.1| pseudouridine synthase, RluA family [Methylocella silvestris BL2]
 gi|217503830|gb|ACK51239.1| pseudouridine synthase, RluA family [Methylocella silvestris BL2]
          Length = 342

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 114/241 (47%), Gaps = 24/241 (9%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETS 155
           +ED  + V +KPAG+ V  G+G      ++  +    DS       ++P + HRLD++TS
Sbjct: 101 FEDEHLLVLDKPAGLVVHPGAGHESGTLVNALIAHCGDSLSGIGGVKRPGIVHRLDKDTS 160

Query: 156 GILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           G++VVA+T  A Q L   F    R   + + Y + VWG P ++   + +  L +  +  +
Sbjct: 161 GLMVVAKTDRAHQGLARLFADHGRTLPLLREYLAFVWGAP-DRASGLVDAPLGRHPVDRE 219

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +V         A++H+++++    +   L  +  TGRTHQ+RVH   +G P++GD  
Sbjct: 220 KIAIVAAAR--GRRAVTHWRLLEQLGPEVAALACRLETGRTHQIRVHMASLGWPLLGDPV 277

Query: 272 YCANFK---GNFTSPIQNKL------YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
           Y   FK   G      Q  L       LHAR +   HP  G  L   +  P  M +   +
Sbjct: 278 YGRGFKTKAGRLPPEAQAALIALGRQALHARALGFEHPVTGAALAFESDPPPDMAELQAA 337

Query: 322 L 322
           L
Sbjct: 338 L 338


>gi|91206061|ref|YP_538416.1| ribosomal large subunit pseudouridine synthase RluD subfamily
           protein [Rickettsia bellii RML369-C]
 gi|157826559|ref|YP_001495623.1| ribosomal large subunit pseudouridine synthase RluD subfamily
           protein [Rickettsia bellii OSU 85-389]
 gi|91069605|gb|ABE05327.1| Ribosomal large subunit pseudouridine synthase RluD subfamily
           protein [Rickettsia bellii RML369-C]
 gi|157801863|gb|ABV78586.1| Ribosomal large subunit pseudouridine synthase RluD subfamily
           protein [Rickettsia bellii OSU 85-389]
          Length = 312

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 85/319 (26%), Positives = 149/319 (46%), Gaps = 46/319 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD+       +++   +QK ++S  V++       NN I           I   + ++
Sbjct: 13  LRLDKALSQLLENVSRNQIQKAIKSSCVQI-------NNVI-----------ILDSDILV 54

Query: 79  KEQKILDSSV----NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           KE  I+  S      LT  +  +K  ++YED  + V NK AG++V  G+G  +H D  + 
Sbjct: 55  KENDIILFSFKEPEELTIEAADIKLDIVYEDEDLIVINKAAGMTVHPGAG--HHDDTLVN 112

Query: 135 SWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +            ++P + HRLD++T+G++VVA+   A   L      R++ + Y +L
Sbjct: 113 ALLHHTRNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVVRKYKAL 172

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEM 245
           VWG+    +  I N  + +S      + ++K    G   A++++K ++ F       +E 
Sbjct: 173 VWGVINPLEGTIKNN-IGRSRSDRQKMTILKY---GGKEAVTYYKTLELFYGGSISMVEC 228

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSP-IQNKLY------LHARYMDL 297
           +  TGRTHQ+RV   H+   +VGD  Y  N  K N   P ++ KL       LH+ Y+  
Sbjct: 229 KLATGRTHQIRVQLSHLKHSVVGDQIYGNNDRKINHAPPELKAKLLDFKRQALHSWYLSF 288

Query: 298 PHPEGGR-LQITAPLPAHM 315
            HP     ++ +  LP  M
Sbjct: 289 THPTSNEVMEFSCELPKDM 307


>gi|111114840|ref|YP_709458.1| hypothetical protein BAPKO_0017 [Borrelia afzelii PKo]
 gi|216263838|ref|ZP_03435832.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia afzelii ACA-1]
 gi|110890114|gb|ABH01282.1| conserved hypothetical protein [Borrelia afzelii PKo]
 gi|215979882|gb|EEC20704.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia afzelii ACA-1]
          Length = 326

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 19/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS I V NKP GI    G         + + YHI G LK   + +  +P + HRLD
Sbjct: 86  IIYEDSNIIVLNKPQGILSHPGISHWDNTVVNFLLYHIKG-LKINFNEEKIRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ RR  K+Y ++V G   +    I +++ +  +    
Sbjct: 145 KDTSGVLICAKNISTVRFLAQQFKDRRTNKVYIAIVKGNFNSFFGSIESFIDRDKYNRKK 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ +K++  F   +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 205 FSVSKDRGKK----ALTEYKLLLNFGG-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 259

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           Y     G+F       L LH+  +++   +    +  +  P   V
Sbjct: 260 Y-GRVDGSFKKIT---LMLHSYKLEIDVGKNSFKKFISEFPKRFV 300


>gi|82703097|ref|YP_412663.1| pseudouridine synthase, RluD [Nitrosospira multiformis ATCC 25196]
 gi|82411162|gb|ABB75271.1| ribosomal large subunit pseudouridine synthase D [Nitrosospira
           multiformis ATCC 25196]
          Length = 318

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 74/224 (33%), Positives = 111/224 (49%), Gaps = 17/224 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           +++ED  I + +KPAG+ V  GSG      ++  L       G  PR  + HRLD+ETSG
Sbjct: 80  IVHEDHAIIIIDKPAGLVVHPGSGNWQGTLLNALLHHSPQLSG-IPRSGIVHRLDKETSG 138

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LVVA+T  A   L    + R +++ Y +LVWG   +     A   + +  +    + VV
Sbjct: 139 LLVVAKTLEAQTSLVRQLQKRTVKREYLALVWGSVSSHGRVDAP--VGRHPVQRTRMAVV 196

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              ++         +  DC   + C LE    TGRTHQ+RVH   +G P+VGD  Y    
Sbjct: 197 ASGKEARTRYEVLEQFTDCTLLR-CGLE----TGRTHQIRVHMQSLGHPLVGDPLYGGKA 251

Query: 277 KGNFTSPIQNKLY----LHARYMDLPHPEGG-RLQITAPLPAHM 315
           K   ++ +Q   +    LHA  ++L HP+ G R+   APLP  M
Sbjct: 252 KKGSSATMQLAAFPRQALHAHKLELTHPQNGQRMGWEAPLPEDM 295


>gi|330997883|ref|ZP_08321717.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
 gi|329569487|gb|EGG51257.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
          Length = 313

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 77/286 (26%), Positives = 134/286 (46%), Gaps = 33/286 (11%)

Query: 38  QKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           + IL    + V+KK V ++N  ++ G VVR+    +  N+ +K + +             
Sbjct: 42  KDILTGHGITVNKKSVSQYNYELRPGMVVRVSK--HKRNNELKNKYVK------------ 87

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQET 154
               ++YED  + V  K AGI         + I   L  +   +  K    + HRLD++T
Sbjct: 88  ----IVYEDKDLIVIEKSAGILSMPAVAQQFSIKTVLDEYFTRRHFKCTAHVVHRLDRDT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+     + L E ++     + Y ++V G  + +   I++WL         YV 
Sbjct: 144 SGLMMYAKNIEVQRILEEHWQEIVTDRRYVAIVSGKMEKEGGTISSWLKDNK----AYVT 199

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                + G  YA++HF  +D   +++  +E++  TGR +Q+RVH   +G P+VGD KY  
Sbjct: 200 YSSPTDNGGKYAVTHFHTLDA-RERYSLVELKLETGRKNQIRVHMQDIGHPVVGDSKY-- 256

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
              GN + PI  +L LHA  ++  HP  G  ++   P P    K +
Sbjct: 257 ---GNGSDPI-GRLGLHAYRLNFYHPITGEPMEFETPFPTLFTKLF 298


>gi|327404859|ref|YP_004345697.1| ribosomal large subunit pseudouridine synthase D [Fluviicola
           taffensis DSM 16823]
 gi|327320367|gb|AEA44859.1| ribosomal large subunit pseudouridine synthase D [Fluviicola
           taffensis DSM 16823]
          Length = 235

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 109/231 (47%), Gaps = 14/231 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ + V NK AG +VQG     + +   ++ ++  K  KP      L HRLD+  S
Sbjct: 9   VLYEDNHLLVVNKHAGENVQGDISGDFPLVEKVREFIRHKFDKPGNVFCGLIHRLDRPVS 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G +  ART  A   + + F  +  +KIYW++V   PK K   + + L +       Y   
Sbjct: 69  GAIAFARTSKALTRMNKLFAEKHPRKIYWAVVEKAPKEKSGSLTHHLERNEKQNKTY--A 126

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  K    A   ++ +   +  +  LE++  TGR HQ+R     +GC I GD KY A 
Sbjct: 127 FQEERKNTKEARLKYRQL-LSSDNYTLLEVELETGRHHQIRAQLSAIGCIIKGDLKYGAK 185

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
                 S     +YLH+R ++  HP     ++I AP+P   +  W  +  K
Sbjct: 186 -----RSNPDGSIYLHSRELEFEHPTSKEVVKIIAPVPQDKLWQWFEIELK 231


>gi|88607282|ref|YP_504969.1| ribosomal large subunit pseudouridine synthase A [Anaplasma
           phagocytophilum HZ]
 gi|88598345|gb|ABD43815.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Anaplasma phagocytophilum HZ]
          Length = 324

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 90/318 (28%), Positives = 146/318 (45%), Gaps = 39/318 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSG 62
           MT+V  ++VE+     RLD        +I+    Q I+  G V +    V  N+ +  +G
Sbjct: 1   MTHVHTILVEHYNAKKRLDVLISASL-NISRSKAQCIISDGGVTLLDTPVLNNSHLTNTG 59

Query: 63  QV--VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            V  V +P           +   +D + ++  H       ++YED  I V +K   I+V 
Sbjct: 60  DVYTVTVPDT--------PQSTSIDPNHDIPLH-------IIYEDEHIIVIDKAPNIAVH 104

Query: 121 GGSG-----IAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            G G     +A+ +     + + + G   +P + HRLD++TSG++V+A+T  A   L+++
Sbjct: 105 PGHGTKNDTLAHALLAHCGNALCAVGNSHRPGIIHRLDKDTSGLMVIAKTEKAYLVLSQA 164

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECI-ANWLLKKSHIGGDYVHVVKQNEKGANYAISH-FK 231
              ++ +K Y +L+WG+P  K   I  N  +K+S      V + +       Y I   F 
Sbjct: 165 LEEKKFRKEYLALIWGVPTTKHCFIQTNLDVKRSDKTMMEVTLSRGKHANTEYIIEKTFG 224

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----- 286
            +   A+  C L    HTGRTHQ+RVH  H+G  +VGD KY  N K +    I       
Sbjct: 225 NVASLAR--CIL----HTGRTHQIRVHMSHIGHSVVGDQKYGKNNKKSLRCGIPEVRNFK 278

Query: 287 KLYLHARYMDLPHPEGGR 304
           +  LHA  +   HP  G 
Sbjct: 279 RQALHACLLGFHHPCTGE 296


>gi|238021276|ref|ZP_04601702.1| hypothetical protein GCWU000324_01175 [Kingella oralis ATCC 51147]
 gi|237868256|gb|EEP69262.1| hypothetical protein GCWU000324_01175 [Kingella oralis ATCC 51147]
          Length = 371

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 75/233 (32%), Positives = 115/233 (49%), Gaps = 33/233 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           ++YED  + V NKPAG+ V   +G      ++G L +      Q PR  + HRLD++TSG
Sbjct: 105 IVYEDDSVLVLNKPAGLVVHPAAGNWTGTLLNGLL-AHASELSQVPRAGIVHRLDKDTSG 163

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHV 215
           ++VVA+T  A  HL +  + R +++IY ++  GI P + K         ++ IG D  + 
Sbjct: 164 LMVVAKTLPAQNHLVQQLQSRSVKRIYRAIADGIVPFDGK--------IETQIGRDPHNR 215

Query: 216 VKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           +K    + G   AI+H KV++ + Q   ++E    TGRTHQ+RVH      P+ GD  Y 
Sbjct: 216 LKMAVVKFGGKEAITHVKVLERY-QAHSYIECSLETGRTHQIRVHLREARHPLAGDPVY- 273

Query: 274 ANFKGNFTSPIQNKL----------YLHARYMDLPHPEGGR-LQITAPLPAHM 315
               GN   P   ++           LHA  +   HP+    L   AP+P  M
Sbjct: 274 ----GNPRHPCSPEVKAEVKALARQALHAYRLSFVHPKTNETLSFEAPMPDDM 322


>gi|331266315|ref|YP_004325945.1| 23S rRNA pseudouridine synthase [Streptococcus oralis Uo5]
 gi|326682987|emb|CBZ00604.1| 23S rRNA pseudouridine synthase [Streptococcus oralis Uo5]
          Length = 298

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 116/219 (52%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-EYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV   G+ + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQRKSIEKRYFALVKGAGVLEPEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +KV+  + +    ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKVVVSY-RNIHLVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|312879313|ref|ZP_07739113.1| pseudouridine synthase, RluA family [Aminomonas paucivorans DSM
           12260]
 gi|310782604|gb|EFQ23002.1| pseudouridine synthase, RluA family [Aminomonas paucivorans DSM
           12260]
          Length = 308

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 143/321 (44%), Gaps = 32/321 (9%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D+   R+DR  K  +P +      K LR G VR++ ++V  + R ++GQV+R+P      
Sbjct: 9   DQAGRRIDRILKEGWPDVPLGARMKALRIGLVRLEGRKVSCDERAEAGQVLRVP------ 62

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ----GGSGIAYHID 130
               +  +     V            +L+    + V +KPAG   Q    GG  +   + 
Sbjct: 63  --WAEAPRWGVPLVTPAPEGRDDPPWVLFRGRNLLVADKPAGWLTQPDRPGGDSLVTRV- 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            +    V     +P   HRLD+ TSG++++  T    + L +  R RR++K YW+LV G+
Sbjct: 120 -WELEGVGEGSFRPAAAHRLDRNTSGVVLLPLTAPLLRLLADLLRRRRLRKTYWALVAGV 178

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P    E   +  L+K     +  + V ++ +G + A++ ++++    +    LE+   TG
Sbjct: 179 PPATGEITRS--LRKL----EEENRVVEDPRG-DQALTRYRLLGTDGEASL-LELDLVTG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-----GGRL 305
           R HQ R H    G PI+GD KY      +       +  LHAR + LP         GR 
Sbjct: 231 RPHQARAHLAFSGFPILGDRKYAPPVPASAAP----RPLLHAREVVLPEDPALEDLAGR- 285

Query: 306 QITAPLPAHMVKTWDSLGFKY 326
             TAPLP  M       G +Y
Sbjct: 286 GFTAPLPEDMAGVLRRRGIRY 306


>gi|261493667|ref|ZP_05990186.1| 23S rRNA pseudouridine synthase D [Mannheimia haemolytica serotype
           A2 str. BOVINE]
 gi|261494334|ref|ZP_05990828.1| 23S rRNA pseudouridine synthase D [Mannheimia haemolytica serotype
           A2 str. OVINE]
 gi|261309983|gb|EEY11192.1| 23S rRNA pseudouridine synthase D [Mannheimia haemolytica serotype
           A2 str. OVINE]
 gi|261310667|gb|EEY11851.1| 23S rRNA pseudouridine synthase D [Mannheimia haemolytica serotype
           A2 str. BOVINE]
          Length = 325

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/253 (30%), Positives = 128/253 (50%), Gaps = 33/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +     + PR  + HRLD++T
Sbjct: 86  IVYEDDDIIVINKPKDLVVHPGAG---NPDGTVLNALLHYYPPIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+   A  HL  + + RRI + Y ++  GI        E +A    K++ +   
Sbjct: 143 TGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMTQGGKVDEPMARHPTKRTAMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 201 -VHPMGKP------AVTHYRIMERF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQL 252

Query: 272 YCANFK------GNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y    +       +F S ++   +  LHA  + L HP  G  ++  APLP   ++   +L
Sbjct: 253 YGGRPRPPKGASDSFLSVLRGFQRQALHATMLRLEHPITGEMMEWHAPLPDDFIELIQAL 312

Query: 323 GFKYDRNLYIKRL 335
             K D  LY  +L
Sbjct: 313 --KADYELYKDQL 323


>gi|256822306|ref|YP_003146269.1| RluA family pseudouridine synthase [Kangiella koreensis DSM 16069]
 gi|256795845|gb|ACV26501.1| pseudouridine synthase, RluA family [Kangiella koreensis DSM 16069]
          Length = 324

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 88/326 (26%), Positives = 147/326 (45%), Gaps = 45/326 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIPPVINALNHII 78
           RLD      +   +   +Q+ +++G V+V+ + +  N    +G + + I   I       
Sbjct: 20  RLDAALSQQFSEYSRSRIQEWIQNGFVKVNDEVITSNKYKMAGFEDIEINAEIEVAGEWK 79

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
            E   LD               ++YED  + V NKPAG+ V  G+G      ++  L   
Sbjct: 80  PEAIDLD---------------IVYEDDALLVINKPAGLVVHPGAGNQDGTMVNALLHHC 124

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            D     PR  + HR+D+ET+G+LVVA+T AA   L E  + R   + Y ++V       
Sbjct: 125 PDL-ANLPRAGIIHRIDKETTGLLVVAKTIAAHTSLVEQLQNRAFTREYDAVV------N 177

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKG----ANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           +  ++   + K  IG    H  K+           AI+H++V++ F      L+++  TG
Sbjct: 178 RVMVSGGTIDKP-IGR---HPTKRTSMAVVADGKRAITHYRVVEKFLD-HTHLKLRLETG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHARYMDLPHPEG 302
           RTHQ+RVH  ++  P++GD  Y   ++     T  ++N +       LHA  + L HPE 
Sbjct: 233 RTHQIRVHMAYLKFPLIGDPLYSGRYRVPTRITPELRNTVDNFKRQALHASLLGLQHPET 292

Query: 303 GR-LQITAPLPAHMVKTWDSLGFKYD 327
              ++  AP+P  M +  D L    D
Sbjct: 293 DEYIEWRAPMPQDMARLLDDLRVNRD 318


>gi|127513878|ref|YP_001095075.1| RluA family pseudouridine synthase [Shewanella loihica PV-4]
 gi|126639173|gb|ABO24816.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           loihica PV-4]
          Length = 323

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 90/322 (27%), Positives = 148/322 (45%), Gaps = 47/322 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD+     +P  +   +++ +++G V VD   + K   ++  GQ + I   +     I 
Sbjct: 19  RLDQTLAELFPDYSRTRIKEWIQAGAVYVDGMVQTKPREKVLEGQEIEIEATLK--EEIK 76

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E + +D  +             +YED  I V NK AG+ V  G+G   + DG L + + 
Sbjct: 77  AEAQAIDLDI-------------VYEDDHIIVINKQAGLVVHPGAG---NSDGTLMNALL 120

Query: 139 SKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
               +    PR  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V G   
Sbjct: 121 HHCPEIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVSGTMT 180

Query: 193 NK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                 E IA    K++H+    VH           +++H++V + F +    L ++  T
Sbjct: 181 AGGVVDEPIARHPTKRTHMA---VH------HSGRPSVTHYRVAEKF-RAHTRLRLRLET 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKG--NFTSPIQNKL------YLHARYMDLPHPE 301
           GRTHQ+RVH  H+G  +VGD  Y    +     T  +   L       LHA  ++L HP 
Sbjct: 231 GRTHQIRVHMAHIGHILVGDPVYGGRPRPPKKATPELMEALNGFKRQALHAVRLELAHPF 290

Query: 302 GGRLQI-TAPLPAHMVKTWDSL 322
              +    AP+P  MV    +L
Sbjct: 291 TCEIMSWQAPIPEDMVALTRAL 312


>gi|261867120|ref|YP_003255042.1| 23S rRNA pseudouridine synthase D [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412452|gb|ACX81823.1| ribosomal large subunit pseudouridine synthase D [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 324

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 121/242 (50%), Gaps = 27/242 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           ++YED  I V NKP  + V  G+G      ++  L  +     + PR  + HRLD++T+G
Sbjct: 85  IVYEDDDILVINKPKDLVVHPGAGNPSGTVLNALLYHY-PPIAEVPRAGIVHRLDKDTTG 143

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYV 213
           ++VVA+T  A   L    + R+I + Y ++  GI        E +A    K++H+    V
Sbjct: 144 LMVVAKTIPAQTQLVRDLQKRKIIREYEAVACGIMTKGGTVDEPMARHPTKRTHMA---V 200

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  Y 
Sbjct: 201 HPMGKP------AVTHYRIMERF-RDYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYG 253

Query: 274 A------NFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
                  N      S ++N  +  LHA  + L HP  G  ++  APLP   V+   +L  
Sbjct: 254 GRPRPPKNASEELMSVLRNFKRQALHAVMLRLQHPISGEMMEWYAPLPEDFVELITALKA 313

Query: 325 KY 326
            Y
Sbjct: 314 DY 315


>gi|304309991|ref|YP_003809589.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium HdN1]
 gi|301795724|emb|CBL43923.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium HdN1]
          Length = 318

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 83/331 (25%), Positives = 151/331 (45%), Gaps = 43/331 (12%)

Query: 4   MTYVQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           MT +Q+   + +D    RLD+     +P  +   LQ+ ++ G + ++++      ++  G
Sbjct: 1   MTQIQHQATIPDDLSGKRLDQAAAQLFPDYSRARLQEWIKMGALTINQQVGVAKEKVIGG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + + +   + A   +  +   LD               +++ED  + + NKPAG+ V  G
Sbjct: 61  EQLFLSVELQADERVKPQNISLD---------------IVHEDDSLLIINKPAGLVVHPG 105

Query: 123 SGIAYHIDGFLKSWVDSKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           SG   H +G L + + +   K    PR  L HR+D++T+G+LVVA+T  A   L    + 
Sbjct: 106 SG---HSEGTLVNALVNHAPKLAELPRAGLVHRIDKDTTGLLVVAKTLEAHTDLVAQLQA 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDC 235
           + +++ Y ++  G+     +  A        IG       KQ        A++H++V+  
Sbjct: 163 KLVKREYEAIAQGVMTGGGKVDAP-------IGRHPTQRTKQAVVSSGREAVTHYRVVAR 215

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--K 287
           + +    + +   TGRTHQ+RVH  H+  P++GD  Y    +        F   +Q   +
Sbjct: 216 Y-RAHTHIRLALETGRTHQIRVHMAHIHYPLLGDPDYGGRLRLPKAASPEFIEALQGFRR 274

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
             LHA+ + L HPE G  +    PLP   V+
Sbjct: 275 QALHAQRLALHHPESGDWVAWEVPLPEDFVQ 305


>gi|56461324|ref|YP_156605.1| pseudouridylate synthase Rlu family protein [Idiomarina loihiensis
           L2TR]
 gi|56180334|gb|AAV83056.1| Predicted pseudouridylate synthase, Rlu family [Idiomarina
           loihiensis L2TR]
          Length = 218

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/222 (32%), Positives = 120/222 (54%), Gaps = 20/222 (9%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           + FL+ I  YEDS++ V +K +G+ SV G      H D  + + V     + R+ HRLD 
Sbjct: 11  TPFLQVI--YEDSQLLVVDKQSGLLSVPGKR--PEHKDS-VYTRVQRVHPEIRVVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+L++A+T+AA  HL   F+ R  +K Y + VWG P   +  I      +  +  D+
Sbjct: 66  ATSGVLLLAKTKAAQSHLNRQFQNRTTRKRYIAQVWGKPPALQGEI------ELPLSCDW 119

Query: 213 VHVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  +Q+        + + ++V   F +    +E+ PHTGR+HQLRVH   +GCPI+GD 
Sbjct: 120 PNRPRQHMDFFTGKPSTTLYRVT-AFDKGCSRVELTPHTGRSHQLRVHMQAIGCPILGDK 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPL 311
            Y  +    F +    +L LHA Y+ + HP+  +L + ++P+
Sbjct: 179 FYAHS--DAFAA--AERLLLHAEYLGVTHPQTEQLIEFSSPV 216


>gi|291542920|emb|CBL16030.1| pseudouridine synthase, RluA family [Ruminococcus bromii L2-63]
          Length = 317

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/277 (25%), Positives = 132/277 (47%), Gaps = 33/277 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ ++ N RLD++ +  +  +    + K +R   ++V+ K+      ++ G V       
Sbjct: 6   IKKNDANQRLDKFLQKRFKTLPKSLMYKYIRKKCIKVNGKKCDIQTMLKEGDV------- 58

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKS----ILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             L   IK++    S     K  +F+K+     ++YED  + + +K  GI V       Y
Sbjct: 59  --LTFYIKDEFFEASE---QKSYEFMKAPKTFDIVYEDENLILIDKKPGIIVHPDKN--Y 111

Query: 128 HIDGFL---KSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           H D  +   + ++  KG+          P L +R+D+ T GI++ A+   + + L    +
Sbjct: 112 HFDSLVARVQHYLYDKGEYNPDEEKAFAPALVNRIDRNTGGIVIAAKNADSLRILNAKMK 171

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R ++K Y  L++G PK   + +  ++ K      + V V K   +G+    + ++++D 
Sbjct: 172 TRELEKYYLCLLYGKPKKDSDTLHGYMTKNE--SKNKVTVFKNEVEGSKEIKTKYEILD- 228

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           F  KF   E++  TGRTHQ+R H   +G P+VGD KY
Sbjct: 229 FNGKFSLAEIELLTGRTHQIRAHMASIGHPLVGDTKY 265


>gi|290580687|ref|YP_003485079.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
 gi|254997586|dbj|BAH88187.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
          Length = 296

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/235 (31%), Positives = 112/235 (47%), Gaps = 30/235 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL--------KSWVDSKGQ-KPRLTHRLD 151
           ++YED  + V NKP G+ V    G   H  G L        K      G  +P + HR+D
Sbjct: 76  IVYEDEDVAVINKPQGMVVHPSVG---HPSGTLVNALLFHIKDLSSINGVIRPGIVHRID 132

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A Q L +  + ++  + Y +LV G   N +  I      ++ IG  
Sbjct: 133 KDTSGLLMIAKNDQAHQALAKELKEKKSLRQYIALVHGNLPNDRGVI------EAPIGRS 186

Query: 212 YVHVVKQNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                KQ        A++HFKV++ F Q +  +E+   TGRTHQ+RVH  ++G P+ GD 
Sbjct: 187 EKDRKKQTVTAKGKPAVTHFKVLERFDQ-YSLVELTLETGRTHQIRVHMAYIGHPVAGDP 245

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
            Y      KG          +LHA+ +   HP+ G L Q T  +P    +  D L
Sbjct: 246 LYAPKKTLKGQGQ-------FLHAKTLGFTHPKTGELMQFTTEVPVIFQEVLDHL 293


>gi|253579159|ref|ZP_04856429.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251849257|gb|EES77217.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 233

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 69/218 (31%), Positives = 102/218 (46%), Gaps = 24/218 (11%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK--GQKPRL--THRLDQ 152
           ++  +LYED  I V +KPAG++VQ     +  ++  LK+++  K  G+ P L   HRLDQ
Sbjct: 6   IRDYILYEDKDILVCHKPAGLAVQNARVGSMDMESLLKNYIAQKVPGKMPYLGIIHRLDQ 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              G+LV A    AA  L+      +I+K Y ++  G  K K   + +WL K        
Sbjct: 66  PVEGVLVFALNPKAAADLSRQMTAGKIKKTYLAVTEGTVKVKSAKLVDWLKKDGRTNSSA 125

Query: 213 VHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             VV+    GA  AI  ++V+          DC  +    +++   TGR HQ+RV   H 
Sbjct: 126 --VVEGGTSGAKKAILSYEVLETWKNKEDAQDCGERNLIRIDLD--TGRHHQIRVQMAHA 181

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           G P+VGD KY      N     Q  L L +  +   HP
Sbjct: 182 GMPLVGDRKY------NPGQNSQEPLALCSAKLGFQHP 213


>gi|94992202|ref|YP_600301.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
 gi|94545710|gb|ABF35757.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
          Length = 223

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 111/219 (50%), Gaps = 29/219 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++YED  + + NKP G+ V   +G         + YHI    K      G  +P + HR+
Sbjct: 3   IIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHI----KDLSSINGVVRPGIVHRI 58

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+T AA Q L E  + ++  + Y ++V G   N +  I      ++ IG 
Sbjct: 59  DKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMI------EAPIGR 112

Query: 211 DYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ G
Sbjct: 113 SEKDRKKQAVTAKGKE-AVTRFTVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAG 170

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           D  Y     G   +   +  +LHA+ + L HP  G+  I
Sbjct: 171 DPLY-----GPRKTLSGHGQFLHAKTLGLTHPMTGKEMI 204


>gi|289640971|ref|ZP_06473141.1| pseudouridine synthase, RluA family [Frankia symbiont of Datisca
           glomerata]
 gi|289509286|gb|EFD30215.1| pseudouridine synthase, RluA family [Frankia symbiont of Datisca
           glomerata]
          Length = 340

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 83/318 (26%), Positives = 140/318 (44%), Gaps = 36/318 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPP 69
           V +  + +RLD      +  ++     +++  GQ  VD      ++R+ +G+   VR+PP
Sbjct: 40  VPDGLDGLRLDAVIARMF-GLSRTAAAQLVDDGQASVDGTVRGRSDRVGAGEWLDVRLPP 98

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
             N +    +    L               +++++D  I V +KP G++     G     
Sbjct: 99  PPNPVRVAAEPVPGL---------------LVIHDDDDIVVVSKPIGVAAHPAPGFTGPT 143

Query: 129 -IDGFLKSW--VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            I G   +   V + G   R  + HRLD  T+GI+VVA++  A   L  +FR R ++KIY
Sbjct: 144 VIGGLAAAGYRVATSGAAERQGVVHRLDVGTTGIMVVAKSERAYTALKRAFRDREVEKIY 203

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G P      +   + +     G +  V      G   +++H+   + F +    L
Sbjct: 204 RALVQGHPDPSSGTVDAPIDRHPRKPGLFAVVA-----GGKPSVTHYDTEEAF-RAASLL 257

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++  TGRTHQ+RVH   +  P VGD  Y A+    G      Q   +LHA  +   HP 
Sbjct: 258 SVRLETGRTHQIRVHMSALRHPCVGDLAYGADPVLAGRLGLARQ---WLHAAQLSFAHPA 314

Query: 302 GGR-LQITAPLPAHMVKT 318
            GR +  T+P P  + + 
Sbjct: 315 DGRKVTFTSPDPPDLAEA 332


>gi|227890823|ref|ZP_04008628.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
 gi|227867232|gb|EEJ74653.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
          Length = 301

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 88/311 (28%), Positives = 145/311 (46%), Gaps = 36/311 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHII 78
           RLD+   N +       L+K++  G ++V+    K N ++  G  +    P +  L+ + 
Sbjct: 16  RLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGDVKKANYKVNLGDEITFDKPEVKKLS-LE 74

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLK-- 134
            E   LD               ++YED  + V NKP G+ V    G   H  ++  L   
Sbjct: 75  PENIPLD---------------IVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNALLYHS 119

Query: 135 --SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             S ++    +P + HR+D++TSG+L+VA+   A Q L +  + +   + Y +LV G  K
Sbjct: 120 PLSTINGT-YRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYVALVHGNIK 178

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I +  L +S +      VVK    G N A++HF+V+  +   +  ++    TGRT
Sbjct: 179 EDSGTI-DAPLGRSKVDRKKQAVVKD---GRN-AVTHFEVLKRYGD-YTLVKCVLETGRT 232

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           HQ+RVH  ++G P+VGD  Y     G   +   +  +LHA  +   HP     L+ TAPL
Sbjct: 233 HQIRVHMKYIGHPLVGDQLY-----GPRKTLGNSGQFLHAEKLGFIHPRTNEYLEFTAPL 287

Query: 312 PAHMVKTWDSL 322
           P +  K  + L
Sbjct: 288 PENFKKLLELL 298


>gi|240013591|ref|ZP_04720504.1| RluD [Neisseria gonorrhoeae DGI18]
 gi|240117408|ref|ZP_04731470.1| RluD [Neisseria gonorrhoeae PID1]
 gi|240120661|ref|ZP_04733623.1| RluD [Neisseria gonorrhoeae PID24-1]
 gi|268603103|ref|ZP_06137270.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae PID1]
 gi|268587234|gb|EEZ51910.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae PID1]
 gi|317163748|gb|ADV07289.1| RluD [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 374

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 136/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K      G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAAVKFGGKPAVTHVKVLERYL-AHSYIECSLGTGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+ GD  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
               P+P
Sbjct: 316 SFETPIP 322


>gi|260912603|ref|ZP_05919132.1| ribosomal large subunit pseudouridine synthase [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260633281|gb|EEX51442.1| ribosomal large subunit pseudouridine synthase [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 229

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 68/219 (31%), Positives = 104/219 (47%), Gaps = 14/219 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
           I +YED+ I + +K +G  VQ        +   +K+++  K  KP      + HRLD+  
Sbjct: 10  IPVYEDNHIIIVSKHSGEIVQSDKTGDVPLVDIVKNYLKEKYAKPGNVFLGVVHRLDRPV 69

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G++  A+T  A   +   FR   ++K YW++V   P+N+   + +WL +       Y H
Sbjct: 70  WGLVAFAKTSKALSRMNALFRTGDVEKTYWAIVQSPPENESGELVHWLTRNEKQNKSYAH 129

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                  GA  AI  +KVI   ++ +  LE+Q  TGR HQ+R     MGCPI GD KY A
Sbjct: 130 --NHEVAGAKKAILSYKVIGQ-SENYTLLEVQLMTGRHHQIRCQLAAMGCPIKGDLKYGA 186

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                  S     + L +R +   HP     + + APLP
Sbjct: 187 K-----RSNPDGSISLLSRKISFVHPVSKETICVEAPLP 220


>gi|149907608|ref|ZP_01896355.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Moritella sp. PE36]
 gi|149809278|gb|EDM69207.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Moritella sp. PE36]
          Length = 326

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 89/313 (28%), Positives = 144/313 (46%), Gaps = 42/313 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           VV   +   RLD+     +P  +   L++ + +G V ++   V K   ++Q G  +    
Sbjct: 10  VVAEHQVGQRLDQVLAEMFPDYSRTRLKEWILAGFVNLNGNVVVKAREKMQYGDKI---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
           ++NA          +D  V        L  +++YED  I V NKPAG  V  G+G     
Sbjct: 66  ILNAE---------VDEEVRYEPQD--LPLVIVYEDDDILVINKPAGFVVHPGAGNPDGT 114

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L  + D     PR  + HRLD++T+G++V+A+T  A  HL  + + RRI + Y +
Sbjct: 115 VLNALLFHYPDII-DVPRAGIVHRLDKDTTGLMVIAKTIPAQTHLVTALQARRITREYEA 173

Query: 186 LVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           +V G         E I     K++ +       V+   K A    +H++V + + +    
Sbjct: 174 VVSGTMTAGGFVDEPIGRHATKRTQMA------VRPLGKPAK---THYRVAEKY-RAHSL 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHARY 294
           L ++  +GRTHQ+RVH  H+  PIVGD  Y    K   N T  +   L       LHAR 
Sbjct: 224 LRLRLESGRTHQIRVHMTHIMHPIVGDTVYAGRPKPPSNATDTLILALRGFGRQALHARM 283

Query: 295 MDLPHPEGGRLQI 307
           + L HP  G + +
Sbjct: 284 LKLEHPVTGEMMM 296


>gi|118588379|ref|ZP_01545788.1| pseudouridine synthase [Stappia aggregata IAM 12614]
 gi|118439085|gb|EAV45717.1| pseudouridine synthase [Stappia aggregata IAM 12614]
          Length = 223

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 116/216 (53%), Gaps = 18/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP+G+ SV G +  A H D  ++S    +    R+ HRLD +TSGI+V
Sbjct: 21  VLHADDDLLVVDKPSGLLSVPGKA--AEHAD-CIESRAQERYADARIVHRLDMDTSGIMV 77

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +AR  AA +HL   F  R+  K Y + +WG P   +  +   L+       D+ +  KQ 
Sbjct: 78  LARNPAAHRHLGLQFERRKTLKTYIADIWGSPSEDEGEVDLPLI------CDWPNRPKQM 131

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +    A++ ++V++        + + PHTGR+HQLRVH L +G PI GD ++ A   
Sbjct: 132 VSFEFGKPALTRWQVLE-RKDTTSRVRLFPHTGRSHQLRVHMLALGHPIAGD-RFYAQGA 189

Query: 278 GNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
               SP   +L LHA  ++L HP  GGR+   + +P
Sbjct: 190 ALTASP---RLALHAETLELHHPAHGGRICFRSEVP 222


>gi|260593255|ref|ZP_05858713.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           veroralis F0319]
 gi|260534812|gb|EEX17429.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           veroralis F0319]
          Length = 296

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 111/232 (47%), Gaps = 17/232 (7%)

Query: 87  SVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           SV+ +K +D  +S    ++YED  + V  K  GI        A ++   L  +     QK
Sbjct: 68  SVSKSKKNDLFRSRYVKIVYEDRFLVVIEKNIGILSMAAGHSALNVKAVLDDYFHKSRQK 127

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               + HRLD++TSG+++ A+     Q L   +      + Y ++V G  +N +  IANW
Sbjct: 128 CTAHVVHRLDRDTSGLMIYAKDMQTEQLLERDWHNIVYDRRYVAVVSGEMENDEGTIANW 187

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L         YV      + G  YA++HF V+D    +   +E +  TGR +Q+RVH+  
Sbjct: 188 LKDNK----AYVTYSSPVDNGGKYAVTHFHVLD-RTVRHSLVEYRLETGRKNQIRVHSAD 242

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           MG P+ GD KY     GN   P+  +L LHA  +   HP    R++   P+P
Sbjct: 243 MGHPVCGDVKY-----GNGDDPLH-RLCLHAYVLCFYHPVTHQRMEFETPIP 288


>gi|255530619|ref|YP_003090991.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
 gi|255343603|gb|ACU02929.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
          Length = 228

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 66/219 (30%), Positives = 106/219 (48%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +    K AG  VQ        +D  +K ++  K  KP      + HRLD+  S
Sbjct: 8   VLYEDNHLIAVCKKAGDIVQIDETGDEPLDEQVKKYLAIKYNKPNSAFLGVVHRLDRPVS 67

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A + +   F+ R ++K YW++V   P      + +WL+K      + V  
Sbjct: 68  GVILFAKTSKALERMNAIFKNREVKKTYWAIVRKKPVKTSGTLIHWLIKNPQ--KNVVTA 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   G+      +++I      +  +E+ P TGR+HQ+RV    MGCPIVGD+KY   
Sbjct: 126 YAEEVPGSQRCELSYRLIGTL-NDYYLIEVDPLTGRSHQIRVQLSTMGCPIVGDNKY--- 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
             G      +  + LHAR +   HP +   + I A LP 
Sbjct: 182 --GYPRGSRKGSICLHARRLQFIHPVKKEPVNIFAELPV 218


>gi|59857911|gb|AAX08790.1| hypothetical protein FLJ14494 [Bos taurus]
 gi|157279001|gb|AAI34591.1| RNA pseudouridylate synthase domain containing 4 [Bos taurus]
 gi|296471773|gb|DAA13888.1| RNA pseudouridylate synthase domain-containing protein 4 [Bos
           taurus]
          Length = 377

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 78/277 (28%), Positives = 127/277 (45%), Gaps = 43/277 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSG 156
           ++++D ++ V NKP G+ V GG G+   I   L          K +   L HRLD+ET+G
Sbjct: 99  IVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P  +   +   +++K   G  + H  
Sbjct: 159 VMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIVEKEAQGQQHHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  ++ + A  A++ ++V+   +     LE+QP TG  HQLRVH + 
Sbjct: 219 TLSPSYRMDDGKMVRVRSSRNAQLAVTQYRVLS-SSLSAALLELQPITGIKHQLRVHMSF 277

Query: 261 HMGCPIVGDHKYC---ANFKGNFTSPIQNK------------LYLHARYMDLP--HPEGG 303
            + CPI+GDHKY           ++ I  K            L+LHA  + LP   P+  
Sbjct: 278 GLDCPILGDHKYSDWNRLAPQKLSAGILKKLGLQQSKARHLPLHLHACQLTLPALQPQKE 337

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
            L +    P + V +   LG K        R +S DE
Sbjct: 338 ELTLLCRPPRYFVNSLRRLGLKMP-----SRDHSADE 369


>gi|323339837|ref|ZP_08080106.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           ruminis ATCC 25644]
 gi|323092710|gb|EFZ35313.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           ruminis ATCC 25644]
          Length = 301

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 88/305 (28%), Positives = 145/305 (47%), Gaps = 38/305 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +N RLD+     +   +   ++++L  G + V+ K  K   +++SG V+R+         
Sbjct: 9   QNGRLDKVCSEIFSDYSRSQIKQLLDGGNITVNGKTEKAKYKVKSGDVIRLEEPETKTLE 68

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLK 134
           +  E   LD               ++YED  + V NKP G+ V    G   H  ++  L 
Sbjct: 69  LRPENIPLD---------------IVYEDDDVIVINKPQGMVVHPAPGHDEHTLVNALLY 113

Query: 135 SWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-I 190
               S      +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G I
Sbjct: 114 HCPLSTINGTFRPGIVHRIDKDTSGLLMVAKNDKAHRSLAKQLKDKTNIREYVALVHGRI 173

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            ++  E   N  + +S        VVK    G N A++HF+V+  + + + +++    TG
Sbjct: 174 AED--EGTINAPIGRSLKDRKKQAVVKD---GRN-AVTHFEVLKKY-RDYTFVKCILETG 226

Query: 251 RTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI- 307
           RTHQ+RVH  ++G P+VGD  Y      KGN         +LHA  +   HP  G+L I 
Sbjct: 227 RTHQIRVHMKYIGHPLVGDPLYGPKKTIKGNGQ-------FLHAGKLGFVHPTTGKLLIF 279

Query: 308 TAPLP 312
            APLP
Sbjct: 280 EAPLP 284


>gi|156935424|ref|YP_001439340.1| 23S rRNA/tRNA pseudouridine synthase A [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156533678|gb|ABU78504.1| hypothetical protein ESA_03282 [Cronobacter sakazakii ATCC BAA-894]
          Length = 218

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/208 (34%), Positives = 109/208 (52%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     K    HRLD  TSG++
Sbjct: 14  LILYQDEHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDFPKAESVHRLDMATSGVI 70

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            VA T+AA + L   FR R  +K Y + VWG P+N +  +   L+       D+ +  KQ
Sbjct: 71  AVALTKAAERELKRQFREREPKKHYVARVWGHPENAQGVVDLPLI------CDWPNRPKQ 124

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++        + ++P TGR+HQLRVH + +G PI+GD K+ A 
Sbjct: 125 KVCYETG-KAAQTEYEVLEYADDNTARVLLRPITGRSHQLRVHMMALGHPILGD-KFYAT 182

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 +P   +L LHA  + + HP  G
Sbjct: 183 PDAFARAP---RLLLHAEQLTITHPAYG 207


>gi|238790742|ref|ZP_04634503.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           frederiksenii ATCC 33641]
 gi|238721183|gb|EEQ12862.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           frederiksenii ATCC 33641]
          Length = 325

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 90/332 (27%), Positives = 156/332 (46%), Gaps = 47/332 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V VD K++ K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVTVDGKKINKPKEKVLGGELVAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        +   LD               ++YED+ I V NKP G+ V  G+G   +
Sbjct: 69  AQIEEDARWAPQDIPLD---------------IVYEDNDILVINKPRGLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + 
Sbjct: 111 PDGTVLNALLHYYPKIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH + +       A +H+++++ F + 
Sbjct: 171 YEAVAIGNMTAGGRVDEPISRHSTKRTHMA---VHPMGKP------ATTHYRIMEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       +F S ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFISILRGFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A  + L HP  G +++  A LP  MV+  ++L
Sbjct: 281 ATMLRLYHPISGIQMEWHAALPEDMVELINAL 312


>gi|297464864|ref|XP_002703537.1| PREDICTED: RNA pseudouridylate synthase domain containing 4-like
           [Bos taurus]
 gi|110331955|gb|ABG67083.1| RNA pseudouridylate synthase domain containing 4 [Bos taurus]
          Length = 377

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 78/277 (28%), Positives = 127/277 (45%), Gaps = 43/277 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSG 156
           ++++D ++ V NKP G+ V GG G+   I   L          K +   L HRLD+ET+G
Sbjct: 99  IVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P  +   +   +++K   G  + H  
Sbjct: 159 VMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIVEKEAQGQQHHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  ++ + A  A++ ++V+   +     LE+QP TG  HQLRVH + 
Sbjct: 219 TLSPSYRMDDGKMVRVRSSRNAQLAVTQYRVLS-SSLSAALLELQPITGIKHQLRVHMSF 277

Query: 261 HMGCPIVGDHKYC---ANFKGNFTSPIQNK------------LYLHARYMDLP--HPEGG 303
            + CPI+GDHKY           ++ I  K            L+LHA  + LP   P+  
Sbjct: 278 GLDCPILGDHKYSDWNRLAPQKLSAGILKKLGLQQSKARHLPLHLHACQLTLPALQPQKE 337

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
            L +    P + V +   LG K        R +S DE
Sbjct: 338 ELTLLCRPPRYFVNSLRRLGLKMP-----SRDHSADE 369


>gi|258511340|ref|YP_003184774.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478066|gb|ACV58385.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 303

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 82/324 (25%), Positives = 154/324 (47%), Gaps = 37/324 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++   ++   + +W +   P +    + K +R+G+V+V+ KR K + R+  G +V +  
Sbjct: 4   IIIGPSDDGKPVHKWLRLLLPGLPLSGVYKSIRTGRVKVNGKRAKQDTRLHEGDIVHL-- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG---- 124
                 +   E      +  + K+    ++I +LYED +I   NKP G+      G    
Sbjct: 62  ------YFSDEDYASLHAHPVAKYQGVSRAIDILYEDDEIVAVNKPVGVLTHPADGEYKT 115

Query: 125 -IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +A  ++ ++      +G  +    HRLD+ TSG++V A+T  AA+   ++F    ++K 
Sbjct: 116 SLAAQVEAYVYDRGAREGAFRAAPVHRLDRNTSGVVVFAKTARAAKAWADAFHRGEVEKE 175

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G    +     +   +     G+   VV  + K +  A   ++V+   ++    
Sbjct: 176 YLAIVEGEWSGRGRVAVDVRRE-----GNVTRVVDDSGKPSETA---YEVV-ASSRGTSL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHPE 301
           + +   TGRTHQ+RVH  H+G P++ D KY A        PI+ +  YLHA  +      
Sbjct: 227 VRLHLLTGRTHQIRVHMAHLGHPLLADRKYGAR-------PIRGESFYLHAHRVRW---- 275

Query: 302 GGRLQITAPLPAHMVKTWDSLGFK 325
             ++ +TAPLP  M +   +LG+K
Sbjct: 276 -NQVHVTAPLPDRMTEKLRTLGYK 298


>gi|126435691|ref|YP_001071382.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           JLS]
 gi|126235491|gb|ABN98891.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           JLS]
          Length = 304

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 79/294 (26%), Positives = 139/294 (47%), Gaps = 35/294 (11%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           I   G+V +D      ++R+ +G    VR+P     + +   E + +             
Sbjct: 30  IAEDGRVDIDGAPAGKSDRLTAGAWLEVRLPEAPPPVENTPVEIEGM------------- 76

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYH----IDGFLKSW--VDSKG--QKPRLTHR 149
              +LY D  I   +KP G++    + + +H    + G   +   + + G  ++  + HR
Sbjct: 77  --AVLYSDDDIVAVDKPPGVAAH--ATVGWHGPTVLGGLAAAGFRISTSGIHERQGIVHR 132

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++VVA +  A   L  +F+ R ++K Y +LV G P      I   + +  H G
Sbjct: 133 LDVGTSGVMVVALSERAYTVLKRAFKQRTVEKRYHALVQGHPDPSSGTIDAPIGR--HRG 190

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            D+   V +   G  ++++H+  ++ F Q    L+++  TGRTHQ+RVH   +  P  GD
Sbjct: 191 HDWKFAVTE---GGRHSVTHYDTLEAF-QAASLLDIELETGRTHQIRVHFAALHHPCCGD 246

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             Y A+        ++ + +LHAR +   HP +G R++IT+P PA +    D L
Sbjct: 247 LTYGADPTLARRLGLERQ-WLHARSLAFAHPADGRRIEITSPYPADLQHALDVL 299


>gi|157148106|ref|YP_001455425.1| 23S rRNA pseudouridine synthase D [Citrobacter koseri ATCC BAA-895]
 gi|157085311|gb|ABV14989.1| hypothetical protein CKO_03916 [Citrobacter koseri ATCC BAA-895]
          Length = 326

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 74/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMS-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH +         A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPM------GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  D +
Sbjct: 253 YGGRPRPPKGASEAFISTLRQFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIDVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|27467790|ref|NP_764427.1| hypothetical protein SE0872 [Staphylococcus epidermidis ATCC 12228]
 gi|251810627|ref|ZP_04825100.1| pseudouridylate synthase RluD [Staphylococcus epidermidis
           BCM-HMP0060]
 gi|282876372|ref|ZP_06285239.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|293366838|ref|ZP_06613514.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|27315334|gb|AAO04469.1|AE016746_259 conserved hypothetical protein [Staphylococcus epidermidis ATCC
           12228]
 gi|251805787|gb|EES58444.1| pseudouridylate synthase RluD [Staphylococcus epidermidis
           BCM-HMP0060]
 gi|281295397|gb|EFA87924.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|291319139|gb|EFE59509.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|329729961|gb|EGG66352.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU144]
 gi|329736346|gb|EGG72618.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU028]
 gi|329736639|gb|EGG72905.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU045]
          Length = 305

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 82/327 (25%), Positives = 152/327 (46%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    + ++E  +   R+D+   +     +   LQ  ++ G V+V+ K +K N +++   
Sbjct: 1   MENYNFNIIEQSQVGQRIDKLVSDLNKDWSRSQLQDWIKEGLVKVNGKVIKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           ++ E++++++ +      + L   + YED  + V  KP G+ V    
Sbjct: 61  KI-----------VVTEKEVVEADIK----PENLNLDIYYEDEDVAVVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A +HL E    +
Sbjct: 106 GHYSGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRHLVEQLMSK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 TVKRKYTALVHGNIPHDYGTIDAP--IGRNKNDRQSMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KDYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPKKTLDIDGQA-----LHAGIIG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP     ++  A LP    K  D +
Sbjct: 274 FEHPVTHEYIEKHATLPNDFEKLLDDI 300


>gi|315303759|ref|ZP_07874262.1| ribosomal large subunit pseudouridine synthase D [Listeria ivanovii
           FSL F6-596]
 gi|313627868|gb|EFR96498.1| ribosomal large subunit pseudouridine synthase D [Listeria ivanovii
           FSL F6-596]
          Length = 302

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 84/299 (28%), Positives = 142/299 (47%), Gaps = 45/299 (15%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQV----VRIPPVINALNHIIKEQKILDSSVNLTK 92
           +Q +L++G + V  +  K N ++Q G      VR P          +E ++L   + L  
Sbjct: 32  IQIMLKNGDITVSGEIAKPNYKVQVGDEIHLEVREP----------EELEVLAEDIPLD- 80

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQ----KPRL 146
                   + +ED  + V NKP G+ V   +G A    ++  L    D  G     +P +
Sbjct: 81  --------IYFEDKDMLVVNKPEGMVVHPSAGHASSTLVNALLFHCKDLSGINGKIRPGI 132

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    + ++
Sbjct: 133 VHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPIGRA 191

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                 + VV+  ++    A +HF+VI+   + +  +  +  TGRTHQ+RVH  ++G P+
Sbjct: 192 KEDRQKMAVVRDGKE----ARTHFEVIERL-EGYTLINCKLDTGRTHQIRVHLKYIGHPL 246

Query: 267 VGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            GD KY      KGN         +LHA  +   HP  G R+   APLP+  VK   +L
Sbjct: 247 AGDPKYGPKNTLKGNGQ-------FLHAAKLGFDHPATGERMTFEAPLPSSFVKALKTL 298


>gi|255571790|ref|XP_002526838.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223533842|gb|EEF35573.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 468

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 81/279 (29%), Positives = 133/279 (47%), Gaps = 30/279 (10%)

Query: 21  LDRWFKNHY----PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           LD   ++H+     HI   N    +  G  ++  +++K N+ +++G  V +  V  A   
Sbjct: 88  LDSAIQSHFNKGLAHIECPNGSGSIEYGG-QMSLRKIKHNDIMEAGARVHVA-VSVAETR 145

Query: 77  IIKEQKILDSSVNLTKHSD---FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           I K    + S   L  ++D   +L+ ++ Y+DS I V NKP  + V+G   +   +D   
Sbjct: 146 ISKRFDTIPSGT-LYPNADEIQYLQRLVKYKDSAIIVLNKPPRLPVKGNLPLHNSMDALA 204

Query: 134 KSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR---------------MR 177
            + +     + P+L  RLD+E+SG+L++ RT+ +  HL   F                 +
Sbjct: 205 AAALSYDYDEGPKLVQRLDRESSGLLLMGRTKESIDHLQWLFSDVNKSNSRCKAWNDACK 264

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG---ANYAISHFKVID 234
              + YW+LV G PK K+  I   L K     G    VV     G   +  A++ ++V+ 
Sbjct: 265 ATYQRYWALVIGSPKEKEGLIRAPLSKVLLNDGKTERVVLAQHSGLEASQEALTEYRVLG 324

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
                  W+E++P T R HQLRVH A  +G PIVGD+KY
Sbjct: 325 PRINGCSWIELRPLTSRKHQLRVHCAEALGTPIVGDYKY 363


>gi|167771608|ref|ZP_02443661.1| hypothetical protein ANACOL_02980 [Anaerotruncus colihominis DSM
           17241]
 gi|167666248|gb|EDS10378.1| hypothetical protein ANACOL_02980 [Anaerotruncus colihominis DSM
           17241]
          Length = 338

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 136/286 (47%), Gaps = 26/286 (9%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           SL   ++   +  ++   R+D++     P +    L K +R+ +++++ KR + + R+ +
Sbjct: 13  SLEDVMREFQINGNDAGQRVDKFLTKAVPLLPQSMLYKAIRTKRIKLNGKRCEISTRLCT 72

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-- 119
           G  + +      LN    + +  D + +  +    +   ++YED  I + NKPAG+ V  
Sbjct: 73  GDQLTL-----YLNDSFFDSR--DGAFSFLRSPAAID--IIYEDENILLVNKPAGLVVHE 123

Query: 120 ---QGGSGIAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
              Q    +   I   L +       +     P L +R+D+ T+GI++ A+  AA + L 
Sbjct: 124 DEHQSSDTLINRIQHHLYNCGVYNPAEENSFAPALCNRIDRNTAGIVIAAKNAAALRILN 183

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           E  + R +QK+Y  +V G    + + +  +L K +    + V V           ++H++
Sbjct: 184 EKIKARELQKLYLCIVHGTMPKESDTLKAFLRKDART--NTVAVYDHPIPDGRTILTHYR 241

Query: 232 VIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V+   AQK     LE+   TGRTHQ+R H  H+G P++GD KY  N
Sbjct: 242 VV---AQKDRLSLLEIDLLTGRTHQIRAHLAHIGHPLLGDAKYGRN 284


>gi|228478264|ref|ZP_04062872.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           salivarius SK126]
 gi|228249943|gb|EEK09213.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           salivarius SK126]
          Length = 296

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 147/321 (45%), Gaps = 48/321 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++     + +++G V V+ K  K    ++ G V+          
Sbjct: 7   EAGNRLDKALAD-LTELSRSQANEAIKAGTVLVNGKSAKAKYAVKEGDVI---------T 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-- 133
           + + E+++L+      K  D    I+ YED+ + V NKP G+ V   +G   H  G L  
Sbjct: 57  YELPEEEVLEY-----KAEDIPLDII-YEDADVAVVNKPQGMVVHPSAG---HTSGTLVN 107

Query: 134 ------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 K      G  +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++
Sbjct: 108 ALMYHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAI 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLE 244
           V G   N +  I      ++ IG       KQ    KG   A++ F V++ F   +  +E
Sbjct: 168 VHGNLPNDRGVI------EAPIGRSDKDRKKQAVTAKG-KPAVTRFTVLERFGN-YTLVE 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +Q  TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   HP  
Sbjct: 220 LQLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGHGQ-------FLHAKTLGFTHPTT 272

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
           G L + TA  PA   +T + L
Sbjct: 273 GELVEFTAEEPAIFKETLEKL 293


>gi|57866712|ref|YP_188346.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           epidermidis RP62A]
 gi|242242479|ref|ZP_04796924.1| pseudouridylate synthase RluD [Staphylococcus epidermidis W23144]
 gi|57637370|gb|AAW54158.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus epidermidis RP62A]
 gi|242234053|gb|EES36365.1| pseudouridylate synthase RluD [Staphylococcus epidermidis W23144]
 gi|319401509|gb|EFV89719.1| pseudouridine synthase, RluA family protein [Staphylococcus
           epidermidis FRI909]
          Length = 305

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 81/327 (24%), Positives = 153/327 (46%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    + ++E  +   R+D+   +     +   LQ  ++ G V+V+ K +K N +++   
Sbjct: 1   MGNYNFNIIEQSQVGQRIDKLVSDLNKDWSRSQLQDWIKEGLVKVNGKVIKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           ++ E++++++ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  KI-----------VVTEKEVVEADIK----PENLNLDIYYEDEDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A +HL E    +
Sbjct: 106 GHYSGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRHLVEQLMSK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 TVKRKYTALVHGNIPHDYGTIDAP--IGRNKNDRQAMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KDYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPKKTLDIGGQA-----LHAGIIG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP   + ++  A LP    K  D +
Sbjct: 274 FEHPVTHKYIEKHATLPNDFEKLLDDI 300


>gi|254455655|ref|ZP_05069084.1| pseudouridylate synthase [Candidatus Pelagibacter sp. HTCC7211]
 gi|207082657|gb|EDZ60083.1| pseudouridylate synthase [Candidatus Pelagibacter sp. HTCC7211]
          Length = 325

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 117/236 (49%), Gaps = 26/236 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQ--KPRLTHRLDQE 153
           ++YED  + V NKPAGI +  G+G     I   +  + K  + + G   +P + HR+D+ 
Sbjct: 84  IIYEDEDLLVINKPAGIIMHPGAGNYDKTIVNALMNYDKDSLSNIGDELRPGIVHRIDKN 143

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA+     + L++ F    I ++Y  L+WG  +     I  ++ + S       
Sbjct: 144 TSGLVVVAKNNETHESLSKQFSDHSITRVYQLLIWGKLRPSSGKIDTFITRSSK----NR 199

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +++ +      AI+++K I  F          +E +  TGRTHQ+RVH  +MG  IVGD
Sbjct: 200 QLMEVSRSKGKRAITNYKTIKIFESNKTPTLSLIECKLETGRTHQIRVHMTYMGNSIVGD 259

Query: 270 HKYCANFKG---------NFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAPLPAHM 315
            KY   +K          N  S ++ + +LHA+ +   HP+  +  I ++ LP  +
Sbjct: 260 DKYKKKYKKLKNVDVGLENLISKLKRQ-FLHAKTLGFVHPKTDKEMIFSSNLPKEL 314


>gi|325971290|ref|YP_004247481.1| pseudouridine synthase [Spirochaeta sp. Buddy]
 gi|324026528|gb|ADY13287.1| pseudouridine synthase, RluA family [Spirochaeta sp. Buddy]
          Length = 333

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 86/334 (25%), Positives = 147/334 (44%), Gaps = 53/334 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VVEND E MRLD +       ++   L +      + ++ K VK +  +++G  +++  
Sbjct: 10  MVVENDSEAMRLDIYIATKQQSVSRSQLSE--EKTHLFLNGKEVKKSKLVKAGDCIKVIY 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
             +    II +   LD               +LYED  + + NK  G+ V   +G   + 
Sbjct: 68  YEDFFEGIIAQDIPLD---------------VLYEDQDLLIINKKQGMVVHPAAG--NYE 110

Query: 130 DGFLKSWVDSKGQ---------------------KPRLTHRLDQETSGILVVARTRAAAQ 168
           D  + + +   GQ                     +P + HRLD++TSG+LV+AR R + +
Sbjct: 111 DTLVNALLFRYGQDFSPSLEDDEETEVESPDMALRPGIVHRLDKDTSGVLVIARNRQSHR 170

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           +L++ F+ R   K+Y +L  G  K  +  I   L + S+   D       ++     A +
Sbjct: 171 NLSQQFKDRTTHKVYIALAKGNFKGTEGSIRANLKRDSN---DRKKFTTCSDTEGRDART 227

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
            + V+  + + F  + +   TGRTHQ+RVH   +G P+VGD  Y          P    L
Sbjct: 228 DYTVLRQY-RDFALVRITLFTGRTHQIRVHFKSIGHPLVGDPVYG--------KPEGLTL 278

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            LHA  + +  P  G+ ++  AP+P    K   S
Sbjct: 279 MLHALVLVVFSPSSGKQIRCVAPMPERFRKVLCS 312


>gi|88811115|ref|ZP_01126371.1| ribosomal large subunit pseudouridine synthase D [Nitrococcus
           mobilis Nb-231]
 gi|88791654|gb|EAR22765.1| ribosomal large subunit pseudouridine synthase D [Nitrococcus
           mobilis Nb-231]
          Length = 315

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 83/308 (26%), Positives = 137/308 (44%), Gaps = 45/308 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            ++   +   R DR     +P  +   LQ  L+SG + VD   ++  + +  G+ VR+  
Sbjct: 9   AIIPIAQAGQRFDRALATIFPQYSRSRLQAWLKSGAITVDTTVLRAKDLVCGGEQVRLSV 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           ++     +  E   L                ++YED  + V +KP  + V  G+G   H 
Sbjct: 69  LLEEEGAVAAEPIALR---------------IVYEDDSLLVIDKPPSLIVHPGAG---HA 110

Query: 130 DGFLKSWV---DSK-GQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G L++ +   D +    PR  + HRLD+ TSG++VVAR   A + L E  + R +++ Y
Sbjct: 111 GGTLQNALLHYDPRLAGLPRAGIVHRLDKGTSGLMVVARNLTAHKLLVEQLQARSVKRDY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF--- 240
            +LV  +  +     A       H        V+Q+ +    A++HF+V++ FA      
Sbjct: 171 LALVSAVVTSGGRATAAI---GRHRRDRTRMAVRQDGRA---AVTHFRVVERFAAHTLLR 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHA 292
           C LE    TGRTHQ+RVH   +  P+VGD  Y    +     +  ++  L       LHA
Sbjct: 225 CSLE----TGRTHQIRVHMAWLRQPVVGDPVYGGRTRLPKGASEELKTALSGFRRQALHA 280

Query: 293 RYMDLPHP 300
             + L HP
Sbjct: 281 LELRLVHP 288


>gi|322411546|gb|EFY02454.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. dysgalactiae ATCC 27957]
          Length = 297

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 86/316 (27%), Positives = 146/316 (46%), Gaps = 46/316 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V++           + 
Sbjct: 11  RLDKALADLSP-LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVIQFE---------LP 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHID 130
           E+++L+        +  +   ++YED  + + NKP G+ V   +G         + YHI 
Sbjct: 61  EEEVLEY------QAQVIPLDIIYEDEALAIINKPQGMVVHPSAGHPSGTMVNALMYHI- 113

Query: 131 GFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              K      G  +P + HR+D++TSG+L+VA+T  A Q L    + ++  + Y ++V G
Sbjct: 114 ---KDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDEAHQALAAELKAKKSLRKYLAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
              N +  I      ++ IG       KQ    KG   A++ F V++ F   +  +E+Q 
Sbjct: 171 NLPNDRGMI------EAPIGRSEKDRKKQAVTAKGKE-AVTRFTVLERFGD-YSLVELQL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGRTHQ+RVH  ++G P+ GD  Y     G   +   +  +LHA  + L HP  G  + 
Sbjct: 223 ETGRTHQIRVHMAYIGHPVAGDPLY-----GPRKTLSGHGQFLHAETLGLTHPLTGEDML 277

Query: 307 ITAPLPAHMVKTWDSL 322
            T   PA   KT   L
Sbjct: 278 FTVAPPAIFQKTLQQL 293


>gi|288928148|ref|ZP_06421995.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 317 str. F0108]
 gi|288330982|gb|EFC69566.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 317 str. F0108]
          Length = 300

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 65/215 (30%), Positives = 108/215 (50%), Gaps = 14/215 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           ++YED  + V +K  G+        + ++   L ++ ++ GQK R  + HRLD+ETSG+L
Sbjct: 89  IVYEDRYLIVVDKSVGVLSMAAGHSSLNVKAILDTYFENSGQKCRAHVVHRLDRETSGLL 148

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+     Q L  ++      + Y ++V G   ++   I++WL   S     Y+     
Sbjct: 149 VYAKDMETEQILEHNWHDMVYDRRYVAVVSGEIVDEGGTISSWLKDNS----SYITYSSP 204

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            + G  YA++HF V+         +E +  TGR +Q+RVH+  +G P+ GD KY     G
Sbjct: 205 VDNGGKYAVTHFHVLK-RTTTHSLVEYKLETGRKNQIRVHSADIGHPVCGDLKY-----G 258

Query: 279 NFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           N  +PI  +L LHA  +   HP    R++   P+P
Sbjct: 259 NGDNPI-GRLCLHAYMLCFYHPATRERMEFNTPIP 292


>gi|6721111|gb|AAF26765.1|AC007396_14 T4O12.25 [Arabidopsis thaliana]
          Length = 980

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 94/380 (24%), Positives = 167/380 (43%), Gaps = 80/380 (21%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV------KFNN--RIQSG 62
           +V+  +  +RLD W  +    ++   +Q  +R G V V+ + V      KF++  + Q  
Sbjct: 598 IVDAAKGKIRLDSWISSRINGVSRARVQSSIRLGLVTVNGRVVDKVLTSKFDSSKKFQFC 657

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVN----LTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
             V I   +  ++H +K    ++ +++    L   ++ +   ++YED  + V NKPA + 
Sbjct: 658 NQVSISLTLFQVSHNVKSGDEVNCTISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMV 717

Query: 119 VQGGSG--IAYHIDGFL---------------------KSWVDSK-----------GQKP 144
           V    G      ++G L                     +++ D +             +P
Sbjct: 718 VHPAPGNPTGTLVNGILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRP 777

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HRLD+ T+G+LVVA+   +  HL E F++  I+++Y SL  G+P   +  I      
Sbjct: 778 GIVHRLDKGTTGLLVVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPSPPQGRI------ 831

Query: 205 KSHIGGDYVHVVKQNE-----KG--ANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLR 256
           +  IG D  + ++        +G  A +A S +KVI+ FA     L E +  TGRTHQ+R
Sbjct: 832 EIPIGRDSSNRIRMAAIPGGVRGGRARHAASRYKVIETFAGGGSALVEWRLETGRTHQIR 891

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY------------------LHARYMDLP 298
            HA +MG P++GD  Y    K    S +Q ++                   LHA  +   
Sbjct: 892 AHAKYMGVPLLGDEVYGGT-KSMALSLLQKRVSRSDQEEIIELISRMDRPCLHAIVLGFT 950

Query: 299 HPEGGRL-QITAPLPAHMVK 317
           HP  G + + + P P+ + +
Sbjct: 951 HPCTGEIVKFSCPPPSDLAE 970


>gi|313202664|ref|YP_004041321.1| pseudouridine synthase, rlua family [Paludibacter propionicigenes
           WB4]
 gi|312441980|gb|ADQ78336.1| pseudouridine synthase, RluA family [Paludibacter propionicigenes
           WB4]
          Length = 299

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 65/203 (32%), Positives = 106/203 (52%), Gaps = 13/203 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +++ED  + V  K  G+ +V  G+         LK+ V       R+   HRLD+ETSG+
Sbjct: 86  IIFEDEYLIVVEKKEGLLTVSTGNPDETTAFSILKNHVKKSSPDNRIYVVHRLDRETSGV 145

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+ +     L E++     ++IY +LV G  + +++ I +WLL+        +H   
Sbjct: 146 IMFAKNKEVQTILQENWHRIITRRIYVALVEGKVEKEQDTIVSWLLENEK--SLKIH-SS 202

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             + G   A++H++ +      +  LE++  TGR +Q+RVH   +G PIVGD KY AN  
Sbjct: 203 ATDNGGQQAVTHYRCVRS-NDNYSLLEIELETGRKNQIRVHMQDIGHPIVGDKKYGANI- 260

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               SPI N+L LHAR +   HP
Sbjct: 261 ----SPI-NRLGLHARLLAFYHP 278


>gi|296269399|ref|YP_003652031.1| pseudouridine synthase, RluA family [Thermobispora bispora DSM
           43833]
 gi|296092186|gb|ADG88138.1| pseudouridine synthase, RluA family [Thermobispora bispora DSM
           43833]
          Length = 310

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 86/310 (27%), Positives = 140/310 (45%), Gaps = 30/310 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RLD      +   +      ++ +G V VD      ++R+++GQ + +         
Sbjct: 14  EGERLDAALSRLF-GFSRTRAADLIAAGDVLVDGAVPSKSDRLRAGQWLDVTIPPPPAPP 72

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ---GGSGIAYHIDGFL 133
             + + I   S+             LYED  I V NKPAG++     G +G    + G L
Sbjct: 73  APRLEPIPGMSI-------------LYEDEDIIVINKPAGVAAHPTVGWTGPTV-LGGLL 118

Query: 134 KSW--VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            +   V + G   R  + HRLD  T+G +VVA++  A   L  +F+ R+++K Y ++V G
Sbjct: 119 GAGHRVSTSGAAERQGIVHRLDANTTGAMVVAKSELAYARLKRAFKERKVEKRYHAMVQG 178

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I   + +  H  GD    V     G   AI+H+  I+ F +    L+++  T
Sbjct: 179 HMDPLRGTIDAPIDR--HPSGDGRFAVV---AGGKEAITHYDTIEAF-RAASLLDVKIET 232

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH   +G P VGD  Y A+        + N+ +LHA  +   HP  G  +  T
Sbjct: 233 GRTHQIRVHLSALGHPCVGDFMYGADPTLAAKLGV-NRQWLHAITLAFEHPVTGEWMSFT 291

Query: 309 APLPAHMVKT 318
           A  P  + ++
Sbjct: 292 AEYPDDLARS 301


>gi|256830871|ref|YP_003159599.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256580047|gb|ACU91183.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 306

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 86/299 (28%), Positives = 134/299 (44%), Gaps = 41/299 (13%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T VQ V V  +E   +L  + +     +      +++R+GQVR+D +R K  +R+ +GQ 
Sbjct: 6   TSVQLVEVGREENGRKLVSFLEARLGTLPTGLFMRLVRTGQVRIDGRRCKPFDRVLTGQT 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PPV      + +++K L     L           ++E+ ++ V +K AG+ V GG+G
Sbjct: 66  VRVPPVT-----VQRKEKSLRDLPGLRG---------VFENDEMLVIDKLAGLPVHGGTG 111

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +   LK+    +   P   HRLD++TSG+L+ A+T    + +  S+    + K Y 
Sbjct: 112 WTDSVHDRLKACFAGQAFVPIPVHRLDRDTSGLLLCAKTHDFLRAMHASWPT--LTKGYL 169

Query: 185 SLVWGIPKNKKECIANWL-----LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
             V G         A W      L K+  G     V  Q ++    A+SH   +   A K
Sbjct: 170 CWVEG-----AWAAAGWRTVVSELAKAQTGSGEQVVSGQGKR----AVSHVHPVLVTAGK 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              L +   TGRTHQ+RVH    G  IVGD +Y               L LHA  +  P
Sbjct: 221 SLLLVVL-GTGRTHQIRVHLADCGHAIVGDPRYGQG----------GGLLLHAAALSWP 268


>gi|226312125|ref|YP_002772019.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226095073|dbj|BAH43515.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
          Length = 302

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/223 (32%), Positives = 115/223 (51%), Gaps = 30/223 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-------IDG-FLKSWVDSKGQKPRLTHRLDQ 152
           +LYED  + + NKP G+ +       YH       + G F ++ +++K    R  HRLDQ
Sbjct: 88  ILYEDDHLLIVNKPVGLLLHPTE--RYHHVTLDHLVSGHFFRTGLEAK---VRHVHRLDQ 142

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGD 211
           +TSG+++ A+   A+  L E  R R I++ Y + V G +PK + +           IG D
Sbjct: 143 DTSGVVLYAKHPWASALLDEMLRERTIKRTYVAYVSGQMPKERGKI-------NEPIGKD 195

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             H  ++      + AI+H++V + F Q    +E Q  TGRTHQ+RVH  H+G P++GD 
Sbjct: 196 RNHGTRRRVTPNGDPAITHYQVKERF-QTATKVECQLETGRTHQIRVHFSHIGHPLLGDE 254

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            Y    +      +  +  LHA  +   HP GG  +++TAPLP
Sbjct: 255 LYGGKRE------LIKRQALHAAVLKFEHPFGGEVIEVTAPLP 291


>gi|146310269|ref|YP_001175343.1| 23S rRNA/tRNA pseudouridine synthase A [Enterobacter sp. 638]
 gi|145317145|gb|ABP59292.1| ribosomal large subunit pseudouridine synthase A [Enterobacter sp.
           638]
          Length = 217

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/208 (33%), Positives = 110/208 (52%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + V     +    HRLD  TSG++
Sbjct: 13  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRVQRDYPQAESVHRLDMATSGVI 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + +WG P+  +  +   L+       D+ +  KQ
Sbjct: 70  VVALTKAAERELKRQFRDREPKKQYIARIWGHPEKAEGLVDLPLI------CDWPNRPKQ 123

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++        + ++P TGR+HQLRVH L +G PI+GD ++ A 
Sbjct: 124 KVCFETG-KAAQTEYEVLEYAPDNTARILLKPITGRSHQLRVHMLALGHPILGD-RFYAT 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    +P   +L LHA  + + HP  G
Sbjct: 182 PEALAMAP---RLQLHAEMLTITHPAFG 206


>gi|84515394|ref|ZP_01002756.1| ribosomal large subunit pseudouridine synthase D [Loktanella
           vestfoldensis SKA53]
 gi|84510677|gb|EAQ07132.1| ribosomal large subunit pseudouridine synthase D [Loktanella
           vestfoldensis SKA53]
          Length = 349

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 94/364 (25%), Positives = 157/364 (43%), Gaps = 72/364 (19%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVKFNN-RIQ 60
           T + + + +N     RLD+      P+   ++   L +++  G V VD + V     RI 
Sbjct: 10  TLITFTIAQNPPP--RLDKALGRDVPNDAALSRSRLARLIADGAVAVDGQVVTDPRFRIA 67

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  V +   +   +HI  +   LD               +++ED  + V NKPAG+ V 
Sbjct: 68  EGAQVAVTVAVAVESHIEAQDITLD---------------VVFEDDDLIVINKPAGMVVH 112

Query: 121 GGSGIAYHIDGFLKSWV-----DSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHL 170
              G A   DG L + +     DS       ++P + HR+D++TSG+LVVA++  A  HL
Sbjct: 113 PAPGTA---DGTLVNALIHHCGDSLSGVGGLKRPGIVHRIDKDTSGLLVVAKSDRAHHHL 169

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECI----------ANWLLKKSHIGGDYVHVVKQ-- 218
            + F    +++ Y ++ +G+P+     +           N L  ++ +G       +Q  
Sbjct: 170 ADQFADHTVERRYIAVCYGVPEANDPRLRGIKGTSFEPGNILKIQTQLGRHRTDRQRQAV 229

Query: 219 NEKGANYAISHFKVIDCF------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +     +A++  +++         A   CWLE    TGRTHQ+RVH  H G  ++GD  Y
Sbjct: 230 SFTAGRHAVTRVRILAALGAMPVAALVECWLE----TGRTHQIRVHLAHCGHALIGDPTY 285

Query: 273 CANFKGNFTSPIQ------------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
            +  K    SP               +  LHA  +   HP     L+ +APLPA M    
Sbjct: 286 GSRRK---MSPKALGEAGVAAVAAFPRQALHAATLGFVHPVTEEFLEFSAPLPADMQALL 342

Query: 320 DSLG 323
            ++G
Sbjct: 343 AAMG 346


>gi|298208702|ref|YP_003716881.1| ribosomal large subunit pseudouridine synthase D [Croceibacter
           atlanticus HTCC2559]
 gi|83848627|gb|EAP86496.1| ribosomal large subunit pseudouridine synthase D [Croceibacter
           atlanticus HTCC2559]
          Length = 232

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 65/222 (29%), Positives = 107/222 (48%), Gaps = 14/222 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V NK AG  VQG       +   +KS++  K  KP      + HRLD+ T+
Sbjct: 12  VIYEDNHLIVVNKRAGDIVQGDKTGDKPLSDVVKSYIKEKYNKPGDVYLGVVHRLDRPTT 71

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ ++T  A   L + F      K YW++V   P  +K+ + ++L +       Y H 
Sbjct: 72  GVVLFSKTSKALSRLNKMFANHETSKTYWAVVKNNPPKEKDRLVHYLKRNPKQNKSYAH- 130

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K     +  AI  + ++      +  LE+   TGR HQ+R     + CPI GD KY A+
Sbjct: 131 -KHEVPDSKKAILDY-ILKFRLNNYNLLEVNLLTGRHHQIRSQLSSIECPIKGDLKYGAD 188

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
                 S     ++LHAR++ + HP +   +   APLP   +
Sbjct: 189 -----RSNPDGSIHLHARFLTIQHPVKKEPITFKAPLPEDAI 225


>gi|319641478|ref|ZP_07996168.1| pseudouridine synthase [Bacteroides sp. 3_1_40A]
 gi|317386879|gb|EFV67768.1| pseudouridine synthase [Bacteroides sp. 3_1_40A]
          Length = 540

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 119/234 (50%), Gaps = 27/234 (11%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++  ++ ++ + L KH   +   ++YED+ + V NKPAG+    G G    ID   
Sbjct: 313 LGHMLQGLEVEENPL-LKKHYHEMPLEIVYEDNYLVVINKPAGMLSVPGKG---EIDSVY 368

Query: 134 KS----WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +     + D+ G  P + HRLD  TSG+L++A+ +   QHL   F+ R I+K Y +L+ G
Sbjct: 369 QHIKILYPDTTG--PLIVHRLDMATSGVLLIAKNKEVHQHLQAQFKNRMIKKRYIALLDG 426

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              +K+  I   +L       D    V  +E G   AI+ ++V++   +    +   P T
Sbjct: 427 KISSKEGTI---ILPLRMDPLDRPRQVVDHEHGKT-AITQYQVLNE-QEGNTLIAFYPLT 481

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           GRTHQLRVHA H   + CPI GD  Y             ++LYLHA  ++  HP
Sbjct: 482 GRTHQLRVHAAHPEGLHCPIRGDELYGQK---------ADRLYLHAESLEFVHP 526


>gi|299469961|emb|CBN79138.1| Ribosomal large subunit pseudouridine synthase D [Ectocarpus
           siliculosus]
          Length = 543

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 93/336 (27%), Positives = 139/336 (41%), Gaps = 59/336 (17%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHI--NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +Y V E    N  L       YP +   F++ Q       V   +K V+    + +G  V
Sbjct: 150 EYAVPEEAPTN--LPEGEDEGYPMLIYQFMHAQYRDDFPSVSSARKAVRRKELLLNGTEV 207

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R    +N  + +  +++         K S  L   +L+ED  I V  KPAG++V GG+G 
Sbjct: 208 RNDSKVNPGDTVTMQKRTQPGLFPQGKPSCTLP--ILWEDDFIAVIIKPAGVAVHGGTGE 265

Query: 126 AYHIDGFLKS-------------WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
                G  +S               D    +P   HRLD+ T G+L+ A+TR A   + +
Sbjct: 266 DDPGPGGRRSVRQALPYMLTPTKSEDRPLHRPLHCHRLDKATGGLLICAKTRPALSAVGD 325

Query: 173 SFRMRRIQKIYWSLVWG---------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
           +F  R + K Y +LV G          P + K C+ N+ ++     G  V  +K      
Sbjct: 326 AFEQRLVSKRYVALVAGELEGSGAIVTPLDGKACLTNYRVR-----GPPVRSLK------ 374

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
               S    +D +          P TGR HQLR H L +GCPI+GD +Y  +       P
Sbjct: 375 ---TSVITTVDLW----------PVTGRLHQLRRHLLSIGCPILGDRRYTPD-----EVP 416

Query: 284 IQ-NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            Q   +YL A  +  PHP  G  +  + P PA   K
Sbjct: 417 FQEGGMYLQAVGLTFPHPITGEEMNFSIPEPAKFEK 452


>gi|157369129|ref|YP_001477118.1| 23S rRNA pseudouridine synthase D [Serratia proteamaculans 568]
 gi|157320893|gb|ABV39990.1| pseudouridine synthase, RluA family [Serratia proteamaculans 568]
          Length = 325

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 90/335 (26%), Positives = 160/335 (47%), Gaps = 53/335 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   ++  +   +V+V+ K + K   ++  G+ V   
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKDWILDNRVQVNGKTINKPKEKVLGGETV--- 65

Query: 69  PVINALNHIIKEQ---KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
               A++  I+E    +  D ++N+           +YEDS I V NKP  + V  G+G 
Sbjct: 66  ----AIDAQIEEDARWEPQDIALNI-----------VYEDSDILVINKPRDLVVHPGAG- 109

Query: 126 AYHIDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             + DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I
Sbjct: 110 --NPDGTVLNALLHYYPEIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQARDI 167

Query: 180 QKIYWSLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            + Y ++  G        +E I+    K++H+    VH + +       A++H+++++ F
Sbjct: 168 TREYEAVAIGTMTAGGTVEEPISRHSTKRTHMA---VHPMGKP------AVTHYRIMEHF 218

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKL 288
            +    L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F + ++  ++ 
Sbjct: 219 -RAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDAFIATLRGFDRQ 277

Query: 289 YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            LHA  + L HP  G +++  APLP  MV   ++L
Sbjct: 278 ALHATMLRLYHPISGIQMEWHAPLPQDMVDLINAL 312


>gi|315221340|ref|ZP_07863261.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
 gi|315189459|gb|EFU23153.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
          Length = 298

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 85/312 (27%), Positives = 148/312 (47%), Gaps = 45/312 (14%)

Query: 37  LQKILRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           +Q  +  G VR+DK         R   N +I++GQ++ +   +    + +K   ++   +
Sbjct: 1   MQVKVEIGGVRLDKAVADLTSLSRSHANEQIKNGQIL-VNGQVKKAKYAVKAGDVITYEL 59

Query: 89  NLTKHSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DS 139
              +  +++   L    +Y+D  + V NK  G+ V   +G   H  G L + +     D 
Sbjct: 60  PEPEALEYVAENLPLDIVYQDEDVAVVNKAQGMVVHPSAG---HTSGTLVNALMYHIKDL 116

Query: 140 KG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            G     +P + HR+D++TSG+L++A+   A   L E  + ++  + YW++V G   N +
Sbjct: 117 SGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHIKLAEELKDKKSLRKYWAIVHGNLPNDR 176

Query: 196 ECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             I      ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTH
Sbjct: 177 GVI------EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGN-YTLVELQLETGRTH 228

Query: 254 QLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           Q+RVH  ++G P+ GD  Y      KG+         +LHAR +   HP+ G  ++ TA 
Sbjct: 229 QIRVHMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHARTLGFTHPKTGEVMEFTAE 281

Query: 311 LPAHMVKTWDSL 322
            PA   +T + L
Sbjct: 282 APAIFQETLEKL 293


>gi|90408473|ref|ZP_01216632.1| Ribosomal large subunit pseudouridine synthase D [Psychromonas sp.
           CNPT3]
 gi|90310405|gb|EAS38531.1| Ribosomal large subunit pseudouridine synthase D [Psychromonas sp.
           CNPT3]
          Length = 322

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 82/316 (25%), Positives = 150/316 (47%), Gaps = 44/316 (13%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNH 76
             RLD+     +P  +   +++ +    V++D   V +   ++ +GQ V +       N 
Sbjct: 17  GFRLDKALAALFPDYSRTRIKEWILDDLVKIDDVTVNRPREKVYTGQQVEV-------NA 69

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            ++++ +         H   +   +++ED  I V NKPAG+ V  G+G   + DG + + 
Sbjct: 70  TLEDEVVF--------HPQNIPLDIIFEDEHILVINKPAGLVVHPGAG---NPDGTVLNA 118

Query: 137 V----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           +        + PR  + HRLD++T+G++V+A+T  A  HL  S + R I + Y ++  G 
Sbjct: 119 LLHHYPEIVEVPRAGIVHRLDKDTTGLMVIAKTVPAQTHLVTSLQAREITREYDAIAMG- 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPH 248
                 C       ++ IG D  + VK      G  +A++H++V + + +    L ++  
Sbjct: 178 ------CFTAGGRVEAPIGRDKANRVKMAVATVGGKHAVTHYRVAEKY-RAHTRLRLRLE 230

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+G  + GD  Y    +       + T+ ++   +  LHA  + L HP
Sbjct: 231 TGRTHQIRVHMSHIGHVLAGDPVYGGRPRPPKGASESLTTTLRAFKRQALHAIMLRLEHP 290

Query: 301 EGGR-LQITAPLPAHM 315
             G  ++  AP+P  M
Sbjct: 291 ITGEIMEWHAPVPDDM 306


>gi|148552990|ref|YP_001260572.1| ribosomal large subunit pseudouridine synthase D [Sphingomonas
           wittichii RW1]
 gi|148498180|gb|ABQ66434.1| ribosomal large subunit pseudouridine synthase D [Sphingomonas
           wittichii RW1]
          Length = 321

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/273 (26%), Positives = 121/273 (44%), Gaps = 28/273 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           + VV  D E  RLDR      P ++   L+ ++ SGQV               G + R P
Sbjct: 9   HAVVPQDAEGWRLDRALAAALPTLSRERLKALISSGQVS-----------HADGALARDP 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
            +  A     +   I+         +  +  ++ YED  + V +KPAG+ V   +G    
Sbjct: 58  AMKVAPG--ARFAVIVPDPAPAHNAAQDIPLVVAYEDEHLIVIDKPAGLVVHPAAGNPDG 115

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + +H  G L        ++P + HR+D++TSG++V A+T  A   L   F    I
Sbjct: 116 TLVNALLHHCRGSLSGI--GGVERPGIVHRIDKDTSGLMVAAKTDPAHVGLAAQFARHSI 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G P+     +   L + +    D   +    +     A++H+ VI+   ++
Sbjct: 174 DRRYRAIVAGTPRLAAGTVDAPLARST---ADRKKIAIVADGRGKRAVTHYSVIEPL-RR 229

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +E +  TGRTHQ+RVH   +G P++GD  Y
Sbjct: 230 AALVECRLETGRTHQVRVHMASLGHPLLGDPVY 262


>gi|116627406|ref|YP_820025.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMD-9]
 gi|116100683|gb|ABJ65829.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMD-9]
          Length = 296

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 147/321 (45%), Gaps = 48/321 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++     + +++G V V+ K  K    ++ G V+          
Sbjct: 7   EAGNRLDKSLAD-LTELSRSQANEAIKAGTVLVNGKLAKAKYVVKEGDVI---------T 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-- 133
           +++ E+++L+      K  D    I+ YED+ + V NKP GI V   +G   H  G L  
Sbjct: 57  YVLPEEEVLEY-----KAEDIPLDII-YEDADVAVVNKPQGIVVHPSAG---HTSGTLVN 107

Query: 134 ------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 K      G  +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++
Sbjct: 108 ALMYHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAI 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLE 244
           V G   N +  I      ++ IG       KQ    KG   A++ F V++ F   +  +E
Sbjct: 168 VHGNLPNDRGVI------EAPIGRSDKDRKKQAVTAKG-KPAVTRFTVLERFGN-YTLVE 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +Q  TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   HP  
Sbjct: 220 LQLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGHGQ-------FLHAKTLGFTHPTT 272

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
           G L + TA  P    +T + L
Sbjct: 273 GELVEFTAEEPIIFKETLEKL 293


>gi|15902874|ref|NP_358424.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae R6]
 gi|116515398|ref|YP_816303.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae D39]
 gi|148988365|ref|ZP_01819812.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP6-BS73]
 gi|168482999|ref|ZP_02707951.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae CDC1873-00]
 gi|15458431|gb|AAK99634.1| 23S rRNA pseudouridine synthase (supresses ftsH(ts) mutants)
           [Streptococcus pneumoniae R6]
 gi|116075974|gb|ABJ53694.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae D39]
 gi|147926046|gb|EDK77120.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP6-BS73]
 gi|172043419|gb|EDT51465.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae CDC1873-00]
 gi|301794072|emb|CBW36476.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           INV104]
 gi|332201394|gb|EGJ15464.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA47368]
          Length = 295

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 84/308 (27%), Positives = 148/308 (48%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   V   +
Sbjct: 5   IETGGLRLDKALSDLSELSRSLANEQIKSGQVL-VNGQVKKAKYTVQEGDVVTYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   L    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDDAHLVLAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG+         +LHA+ +   HP  G+ L+  A +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGKTLEFKADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKETLERL 293


>gi|218678880|ref|ZP_03526777.1| pseudouridine synthase, RluA family protein [Rhizobium etli CIAT
           894]
          Length = 231

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 104/203 (51%), Gaps = 25/203 (12%)

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKEC 197
           ++P + HRLD++T+G++VVA+   A +HL+  F    R   +++ Y ++VWG P+     
Sbjct: 30  RRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHGRTMPLERAYQAVVWGRPRALTGT 89

Query: 198 IANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHT 249
           I   L + +   GD     V + +   A+ AI+H++VI+ F +K         +E    T
Sbjct: 90  IDAPLGRAT---GDRTRRAVKRPDSHDADEAITHYEVIERFQEKPDATALASLVECHLET 146

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---------KLYLHARYMDLPHP 300
           GRTHQ+RVH  H+G P++GD  Y A FK       ++         +  LHA  +   HP
Sbjct: 147 GRTHQIRVHMAHIGHPLLGDTVYGAGFKTKANRLPEDIRKVVNGFGRQALHAFMLQFEHP 206

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  +    PLP  MV+  ++L
Sbjct: 207 RTGEIMHFEVPLPDDMVELVEAL 229


>gi|292493653|ref|YP_003529092.1| pseudouridine synthase [Nitrosococcus halophilus Nc4]
 gi|291582248|gb|ADE16705.1| pseudouridine synthase, RluA family [Nitrosococcus halophilus Nc4]
          Length = 321

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 87/314 (27%), Positives = 144/314 (45%), Gaps = 46/314 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ ++ GQV+V+    +  + ++ G+ V +            
Sbjct: 19  RLDQALACVFPAYSRSRLQQWIKQGQVKVNDAPARPRDTVRGGEWVVL------------ 66

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-- 137
              + +    +   +  L   ++YED  I V NKPAG+ V   +G   + DG L + +  
Sbjct: 67  ---MAEMETAVVWQAQPLPLEIVYEDEAIIVVNKPAGLVVHPAAG---NRDGTLVNALLN 120

Query: 138 --DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 + PR  + HRLD++TSG+LVVART  A   L +    RR+ + Y ++  G+   
Sbjct: 121 HAPELAEIPRAGIVHRLDKDTSGLLVVARTLTAHHGLVQQLHARRVTRQYRAIAVGVMTG 180

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTG 250
               I    + +  +    + VV   +     AI+H++V   F       C LE    TG
Sbjct: 181 G--GIIEAPIHRHPVDRKRMAVVSTGKP----AITHYRVRARFRAHTDVSCRLE----TG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANF------KGNFTSPIQN--KLYLHARYMDLPHPEG 302
           RTHQ+RVH  H+G P++GD  Y              ++ +++  +  LHA  + L HPE 
Sbjct: 231 RTHQIRVHLAHIGYPLLGDPTYGKRLHIPRESGEELSTALRHFKRQALHAARLGLLHPER 290

Query: 303 GR-LQITAPLPAHM 315
            + +   APLP  M
Sbjct: 291 KQAMSWEAPLPEDM 304


>gi|255656576|ref|ZP_05401985.1| putative pseudouridylate synthase [Clostridium difficile QCD-23m63]
 gi|296449972|ref|ZP_06891736.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           difficile NAP08]
 gi|296878353|ref|ZP_06902361.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           difficile NAP07]
 gi|296261242|gb|EFH08073.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           difficile NAP08]
 gi|296430651|gb|EFH16490.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           difficile NAP07]
          Length = 315

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 85/310 (27%), Positives = 146/310 (47%), Gaps = 45/310 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK--RVKFNNRIQSGQVVRIPPVINALNHI 77
           RLD +       ++   +QKI++ G+V+V+ K  + K+  + +   V+ IP         
Sbjct: 29  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKIEKAKYLVKEEDNIVIEIP--------- 79

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYH 128
             E K+L+           +   ++YED  + + NKP  + V            +GI YH
Sbjct: 80  --EPKVLEVV------PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYH 131

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               L S   +   +P + HR+D++TSG+L++A+   A   L E  +   I + Y  + +
Sbjct: 132 CKDKLSSI--NGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICY 189

Query: 189 GIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           G+ K  K  +   + +  K  +    + VVK    G N AI+HF+V++ F  KF  +  +
Sbjct: 190 GVVKENKITVDKPIGRNPKDRLK---MAVVKD---GKN-AITHFEVVERF-DKFTHMRAK 241

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVHAL +  P++GD+ Y    +  F    Q    LHA+ +   HP     +
Sbjct: 242 LETGRTHQIRVHALSINHPLLGDYVYGPK-ETKFKLKGQT---LHAKKLGFIHPTTKEYI 297

Query: 306 QITAPLPAHM 315
           +  + LP + 
Sbjct: 298 EFNSELPEYF 307


>gi|126666670|ref|ZP_01737647.1| Pseudouridylate synthases, 23S RNA-specific [Marinobacter sp.
           ELB17]
 gi|126628715|gb|EAZ99335.1| Pseudouridylate synthases, 23S RNA-specific [Marinobacter sp.
           ELB17]
          Length = 325

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 86/313 (27%), Positives = 143/313 (45%), Gaps = 46/313 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           + RLD+      P  +   LQ  ++SG + V+  + K  +++  G               
Sbjct: 19  DKRLDQAAAELMPEHSRSRLQSWVKSGALTVNGGQCKPRDKVMLGD-------------- 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            K +   +    +T  ++ +   ++YED  I + NKPAG+ V   +G   H DG L + +
Sbjct: 65  -KLELDAEPEAQVTWQAEAITLDIVYEDEHILIINKPAGLVVHPAAG---HADGTLVNAI 120

Query: 138 DSKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +   +    PR  + HRLD++TSG++VVAR+  A   L    + R + + Y ++V G  
Sbjct: 121 LNIAPEVENLPRAGIVHRLDKDTSGVMVVARSLIAHTSLVNQLQTRTMGREYEAVVVGTL 180

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPH 248
                  A   + +       + VVK  +     A++H++VI+ F+      C LE    
Sbjct: 181 TGGATVDAP--IGRHPTERKRMAVVKSGKP----AVTHYRVIERFSAHTHVRCKLE---- 230

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHARYMDLPHP 300
           +GRTHQ+RVH  H+  P+VGD  Y    +     T  ++  L       LHAR + L HP
Sbjct: 231 SGRTHQIRVHLTHVKHPLVGDPVYGGRLRLPKGTTEELREVLSGFHRQALHARQLTLEHP 290

Query: 301 EGGR-LQITAPLP 312
           + G  +    PLP
Sbjct: 291 QTGETMSWDVPLP 303


>gi|254673628|emb|CBA09173.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis alpha275]
          Length = 374

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 137/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-IHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C +        +  +  LHA  +   HPE G  +
Sbjct: 256 HQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPESGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|319900222|ref|YP_004159950.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           helcogenes P 36-108]
 gi|319415253|gb|ADV42364.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           helcogenes P 36-108]
          Length = 355

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 86/338 (25%), Positives = 151/338 (44%), Gaps = 52/338 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 31  VVVDKGQVMMRVDKYLFDRLTNASRNRIQKAADAGFVMANGKPVKSSYKVKPQDVITV-- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 89  ---MMDRPRYENEVIPEDIPLN---------IVYEDKHLMVVNKPAGLVVHPGHGNYHGT 136

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 137 LVNAIAWH----MKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKT 192

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LVWG  +  +  +   + +      D + +    +    +A++H++V++    
Sbjct: 193 TKRRYRALVWGNVEQDEGTVVGNIGRNPK---DRMQMTVLPDDQGKHAVTHYRVLERLGY 249

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNF-------------TSP 283
               +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG               T P
Sbjct: 250 -VTLVECILETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFDTCP 308

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            Q    LHA  +   HP     +  T+ LP  M +  D
Sbjct: 309 RQ---ALHAMTLGFVHPVTKEAMDFTSELPDDMARLID 343


>gi|296122834|ref|YP_003630612.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
 gi|296015174|gb|ADG68413.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
          Length = 325

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 81/332 (24%), Positives = 141/332 (42%), Gaps = 58/332 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V VE     +R+D +   H+       + +++ +G V +D +      R+  GQ V    
Sbjct: 8   VTVEKYLAGVRVDSFLVKHFRSYTSWRILRMVAAGLVTIDGQVAATTQRVHPGQQV---- 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI------LLYEDSKIYVFNKPAGISVQGGS 123
                            ++ LT+  D           +L+ED  + V NKPAG+      
Sbjct: 64  -----------------TIQLTEPPDLFVPPEPTPLEILFEDDSLLVINKPAGLIAHPTG 106

Query: 124 GIAYHIDGFL----KSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            I    DG L    + ++D +      ++P + HRLD++TSG + + +   + + L+  F
Sbjct: 107 EIP---DGTLINAVQHYLDKQSTHPGLERPGIVHRLDRDTSGAMAICKEHLSHRLLSIQF 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           ++ RI K Y +LV G+     + + +  + ++      +   + +   A  + +  +V++
Sbjct: 164 QLGRISKSYLALVEGV-LTDDQLVIDLPIGRAPGCSSALMSCRADALEAQASKTSLRVVE 222

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------- 285
            F Q    +E +P TGR HQ+R+H   +G PIVGD  Y    KG    P+          
Sbjct: 223 RFPQH-TLVEAKPRTGRMHQIRIHLATIGFPIVGDEFY---LKGGEIRPLVWPESERVQV 278

Query: 286 ----NKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
               N+  LHA  +   HP     Q   APLP
Sbjct: 279 SLLINRQALHAACLSFAHPLTNEWQDFQAPLP 310


>gi|225023856|ref|ZP_03713048.1| hypothetical protein EIKCOROL_00722 [Eikenella corrodens ATCC
           23834]
 gi|224943330|gb|EEG24539.1| hypothetical protein EIKCOROL_00722 [Eikenella corrodens ATCC
           23834]
          Length = 372

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 143/321 (44%), Gaps = 47/321 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD       P  +   L   ++ G V ++ +  +   R+  G+ + +  
Sbjct: 32  LTVPTDLAGQRLDAALAKLLPDYSRSRLSTWIKDGNVLLNGQVARPKERLIGGETLEV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                 HI    +    +   T     L   +++ED  + V NKPAG+ V   +G     
Sbjct: 90  ------HIQHSHE----TAAFTPEPMPLD--IVFEDDSVIVLNKPAGLVVHPAAGNWSGT 137

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++G L +   +  + PR  + HRLD++TSG++VVA+T AA   L +  + R +++IY +
Sbjct: 138 LLNGLL-AHCPALAEIPRAGIVHRLDKDTSGLMVVAKTPAAQNSLVQQLQERSVKRIYRA 196

Query: 186 LVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFCW 242
           +  GI P + K          + IG D  + +K      G   A++H KV++ + Q   +
Sbjct: 197 VADGIVPFDGK--------IDTLIGRDPHNRLKMAVVGFGGKKAVTHIKVLERY-QSHSY 247

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----------YLHA 292
           +E    TGRTHQ+RVH      P+  D  Y     GN   P  + +           LHA
Sbjct: 248 IECTLETGRTHQIRVHMREAKHPLAADPVY-----GNPRHPCSDAVKEAVLQLARQALHA 302

Query: 293 RYMDLPHPEGGR-LQITAPLP 312
             +   HPE G  +Q  APLP
Sbjct: 303 YRLSFVHPESGETVQFEAPLP 323


>gi|62751988|ref|NP_001015616.1| RNA pseudouridylate synthase domain-containing protein 4 [Bos
           taurus]
 gi|75057865|sp|Q5E9Z1|RUSD4_BOVIN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 4
 gi|59857799|gb|AAX08734.1| hypothetical protein FLJ14494 [Bos taurus]
 gi|59857921|gb|AAX08795.1| hypothetical protein FLJ14494 [Bos taurus]
          Length = 377

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 78/277 (28%), Positives = 127/277 (45%), Gaps = 43/277 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSG 156
           ++++D ++ V NKP G+ V GG G+   I   L          K +   L HRLD+ET+G
Sbjct: 99  IVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P  +   +   +++K   G  + H  
Sbjct: 159 VMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIVEKEAQGQQHHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  ++ + A  A++ ++V+   +     LE+QP TG  HQLRVH + 
Sbjct: 219 TLSPSYRMDDGKMVRVRSSRNAQLAVTQYQVLS-SSLSAALLELQPITGIKHQLRVHMSF 277

Query: 261 HMGCPIVGDHKYC---ANFKGNFTSPIQNK------------LYLHARYMDLP--HPEGG 303
            + CPI+GDHKY           ++ I  K            L+LHA  + LP   P+  
Sbjct: 278 GLDCPILGDHKYSDWNRLAPQKLSAGILKKLGLQQSKARHLPLHLHACQLTLPALQPQKE 337

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
            L +    P + V +   LG K        R +S DE
Sbjct: 338 ELTLLCRPPRYFVNSLRRLGLKMP-----SRDHSADE 369


>gi|150006268|ref|YP_001301012.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           vulgatus ATCC 8482]
 gi|294776519|ref|ZP_06741993.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|149934692|gb|ABR41390.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           vulgatus ATCC 8482]
 gi|294449648|gb|EFG18174.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
          Length = 540

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 119/234 (50%), Gaps = 27/234 (11%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++  ++ ++ + L KH   +   ++YED+ + V NKPAG+    G G    ID   
Sbjct: 313 LGHMLQGLEVEENPL-LKKHYHEMPLEIVYEDNYLVVINKPAGMLSVPGKG---EIDSVY 368

Query: 134 KS----WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +     + D+ G  P + HRLD  TSG+L++A+ +   QHL   F+ R I+K Y +L+ G
Sbjct: 369 QHIKILYPDATG--PLIVHRLDMATSGVLLIAKNKEVHQHLQAQFKNRMIKKRYIALLDG 426

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              +K+  I   +L       D    V  +E G   AI+ ++V++   +    +   P T
Sbjct: 427 KISSKEGTI---ILPLRMDPLDRPRQVVDHEHGKT-AITQYQVLNE-QEGNTLIAFYPLT 481

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           GRTHQLRVHA H   + CPI GD  Y             ++LYLHA  ++  HP
Sbjct: 482 GRTHQLRVHAAHPEGLHCPIRGDELYGQK---------ADRLYLHAESLEFVHP 526


>gi|323704148|ref|ZP_08115727.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323536214|gb|EGB25986.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 306

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 86/317 (27%), Positives = 150/317 (47%), Gaps = 27/317 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++ E D+ + R+D +  +   +     L+K++    V+V+ K VK N +++ G V+    
Sbjct: 9   IIAEKDDVDKRIDSFLASEVDYTRSY-LKKLILDELVKVNGKSVKPNYKVREGDVI---- 63

Query: 70  VINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                N  I E + +D    ++ L    +    I++ +   + V   P  +S    + + 
Sbjct: 64  -----NLNIPEAEEIDLKPENIPLDIIYEDDDIIVVNKPQGMVVHPAPGNLSGTLVNALL 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           YH      S ++ +  +P + HRLD++TSG++VVA+   A   L+   + R I K Y ++
Sbjct: 119 YHCTNL--SGINGE-LRPGIVHRLDKDTSGVMVVAKNDKAHLELSNQIKNRTILKKYLAI 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+ KN  E      + + HI    + VVK       YA++ ++V++ +      +E  
Sbjct: 176 VEGVIKN-DEGAVEAPIGRDHIERKKMAVVKD----GRYALTLYRVLERYKNN-SLVEAI 229

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
             TGRTHQ+RVH  ++G PIVGD  Y    K  F    Q    LH++ + L HP     +
Sbjct: 230 IKTGRTHQIRVHMAYIGHPIVGDEVYGYK-KQRFNLSGQ---VLHSKLLGLVHPSKKVYM 285

Query: 306 QITAPLPAHMVKTWDSL 322
           +  AP P +  K    L
Sbjct: 286 EFEAPTPEYFEKLMKVL 302


>gi|114326764|ref|YP_743921.1| ribosomal large subunit pseudouridine synthase A [Granulibacter
           bethesdensis CGDNIH1]
 gi|114314938|gb|ABI60998.1| ribosomal large subunit pseudouridine synthase A [Granulibacter
           bethesdensis CGDNIH1]
          Length = 224

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 66/216 (30%), Positives = 100/216 (46%), Gaps = 13/216 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D    V NKPAG+    G      ++ +    +  + + P L HRLD +TSG L++
Sbjct: 13  ILYQDQHFVVLNKPAGLPAHAGPAGGPSVEDWFP-LLSRRKEGPWLAHRLDTDTSGCLII 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDYVHVVKQN 219
           A  +         F   +  K YW++V G P   +  I   L ++S  G     H     
Sbjct: 72  ALRKTPLLEAQAMFAKGQAGKRYWAVVRGAPPAAEGRIDRKLSRRSESGEAGRGHWRMVE 131

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +     A + +++++       WLE+ P TGRTHQLRVH   +GCPI+GD  Y       
Sbjct: 132 DAQGQSASTSWRIME-HQDGLSWLELSPLTGRTHQLRVHCALLGCPILGDPVYGDGRDA- 189

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
                   L L A  + LP      +++ AP+PAHM
Sbjct: 190 -------PLCLLACEIRLPLDP--VIKVRAPVPAHM 216


>gi|311741553|ref|ZP_07715377.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           pseudogenitalium ATCC 33035]
 gi|311303723|gb|EFQ79802.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           pseudogenitalium ATCC 33035]
          Length = 308

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 85/306 (27%), Positives = 142/306 (46%), Gaps = 28/306 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E MR D         ++     ++   G V +D + +  + R+ SG VV +         
Sbjct: 15  EGMRADAALAKLL-GLSRSATAQLCAEGSVTIDSQELGKSERLTSGNVVSV--------L 65

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKS 135
           + + +K L     L +  D     +LY D+ I   +KP G++     G     + G L++
Sbjct: 66  LPEPEKPLLPREELVEGMD-----VLYNDADIICVHKPVGVAAHPSVGWDGPTVIGGLRA 120

Query: 136 W---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
               V S G   R  + HRLD  TSG++VVA +  A   L  +F+ R ++K Y ++V G+
Sbjct: 121 AGYTVASSGPTERKGIVHRLDVGTSGVMVVASSERAYSALKHAFKYRSVKKTYHAVVQGL 180

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P   +  +   + +    G  +   V  + K    AI+H+ +I+ F ++   +E+   TG
Sbjct: 181 PDPIEGTVDAPIGRHPKSGWKF--AVLDDGKA---AITHYSLIEAF-REASLIEVHLETG 234

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH    G P VGD  Y ++        +Q + +LHA  +   HP  G+  +I A
Sbjct: 235 RTHQIRVHMSATGHPCVGDPMYGSDPNLAKRLGLQRQ-WLHAVKLGFTHPGTGKWFEIEA 293

Query: 310 PLPAHM 315
           P PA +
Sbjct: 294 PYPADL 299


>gi|15603584|ref|NP_246658.1| 23S rRNA pseudouridine synthase D [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|20139708|sp|Q9CKA6|RLUD_PASMU RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|12722131|gb|AAK03803.1| SfB [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 324

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 122/242 (50%), Gaps = 27/242 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           ++YED  I V NKP    V  G+G A    ++  L  +  +  + PR  + HRLD++T+G
Sbjct: 85  IVYEDDDILVINKPKDFVVHPGAGNASGTVLNALLYHY-PAIAEVPRAGIVHRLDKDTTG 143

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYV 213
           ++V+A+T  A   L    + R+I + Y ++  GI        + +A    K++H+    V
Sbjct: 144 LMVIAKTIPAQTKLVRDLQKRKITREYEAIACGIMTKGGMVDQPMARHPTKRTHMA---V 200

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  Y 
Sbjct: 201 HPMGKP------AVTHYRIMERF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYG 253

Query: 274 ANFKG--NFTSPIQNKL------YLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
              +   N +  +   L       LHA  + L HP  G L +  APLP   V+  ++L  
Sbjct: 254 GRPRPPKNASEELMQTLRDFKRQALHAIMLRLAHPITGELMEWHAPLPTDFVELVEALKA 313

Query: 325 KY 326
            Y
Sbjct: 314 DY 315


>gi|297538120|ref|YP_003673889.1| RluA family pseudouridine synthase [Methylotenera sp. 301]
 gi|297257467|gb|ADI29312.1| pseudouridine synthase, RluA family [Methylotenera sp. 301]
          Length = 363

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 89/310 (28%), Positives = 143/310 (46%), Gaps = 47/310 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + + ND   +RLD   +   P  +   LQ  ++ G V VDK       ++  G+ V +  
Sbjct: 15  LTISNDLGGLRLDVALQRMLPEHSRSRLQTWIKEGLVTVDKLPSTSKTKVWGGEQVVVQV 74

Query: 70  VINALNHI-IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                N+  + E   LD               +++ED  I + NKPAG+ V   +G    
Sbjct: 75  QAKPENYAYVAEDIPLD---------------IVFEDDHIIIINKPAGMVVHPAAGNWSG 119

Query: 127 YHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             ++  L    + K   PR  + HRLD++TSGILVVA+T AA  +L    + R +++ Y 
Sbjct: 120 TLLNALLFHAPELK-DVPRAGIVHRLDKDTSGILVVAKTLAAQTNLVRQLQARTVKREYR 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWL 243
           ++VWG      +   N ++ ++ IG D     K    +    AI+ +++++ F+ +  +L
Sbjct: 179 AIVWG------QLWRNGVVDQA-IGRDPRSRTKMALNRMGKPAITRYEILERFSVQ-TYL 230

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------------NKLYL 290
                TGRTHQ+RVH   +  PIVGD  Y   F+G    PI+             N+  L
Sbjct: 231 RCNLETGRTHQIRVHMQSLKAPIVGDPVY--GFRGII--PIRVMTQTLRDEVSQFNRQAL 286

Query: 291 HARYMDLPHP 300
           HA  + L HP
Sbjct: 287 HAIKLGLMHP 296


>gi|210615565|ref|ZP_03290663.1| hypothetical protein CLONEX_02881 [Clostridium nexile DSM 1787]
 gi|210150232|gb|EEA81241.1| hypothetical protein CLONEX_02881 [Clostridium nexile DSM 1787]
          Length = 323

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 81/334 (24%), Positives = 150/334 (44%), Gaps = 54/334 (16%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q ++V  +E   RLD+    +        L K+LR   + ++ K+   N ++  G  V+
Sbjct: 1   MQEIIVAANEAGQRLDKMLAKYLNEAPKSFLYKMLRKKNIVLNGKKATGNEKLAVGDSVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +          + ++ I   S     H++    I+ YED  + + NKP G+  Q  +   
Sbjct: 61  L---------FLADETIAKFSNIHAVHTNVTLDII-YEDENVLLINKPVGMLSQKAAADD 110

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  I+Y ++    +  + +  +P + +RLD+ TSG++   ++ A  Q +   F+ R
Sbjct: 111 ESLVEHIISYMLETRQLTEEELRKFRPSVCNRLDRNTSGLVAAGKSLAGLQEMGTLFKNR 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  LV G  K+  + ++ +L+K              +EK     +S  +  DC  
Sbjct: 171 SLRKYYRCLVAGEVKHS-QSVSGYLVK--------------DEKTNKVTVSKAEKGDCLP 215

Query: 238 -----------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSP 283
                       K+ +LE+   TGRTHQ+R H   +G PI+GD+KY +   N +      
Sbjct: 216 IETEYEPLWSNGKYTYLEVHLITGRTHQIRAHLASIGYPIIGDYKYGSKKVNDRLKEQYG 275

Query: 284 IQNKLYLHARYMDLPHPEG-----GRLQITAPLP 312
           ++++L LHA  +++P   G        +  APLP
Sbjct: 276 LKSQL-LHAYRLEMPACTGELSNLSERKFVAPLP 308


>gi|95767470|gb|ABF57296.1| RNA pseudouridylate synthase domain containing 4 [Bos taurus]
          Length = 373

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 78/277 (28%), Positives = 127/277 (45%), Gaps = 43/277 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSG 156
           ++++D ++ V NKP G+ V GG G+   I   L          K +   L HRLD+ET+G
Sbjct: 95  IVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKPLHLCHRLDKETTG 154

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P  +   +   +++K   G  + H  
Sbjct: 155 VMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIVEKEAQGQQHHHKM 214

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  ++ + A  A++ ++V+   +     LE+QP TG  HQLRVH + 
Sbjct: 215 TLSPSYRMDDGKMVRVRSSRNAQLAVTQYQVLS-SSLSAALLELQPITGIKHQLRVHMSF 273

Query: 261 HMGCPIVGDHKYC---ANFKGNFTSPIQNK------------LYLHARYMDLP--HPEGG 303
            + CPI+GDHKY           ++ I  K            L+LHA  + LP   P+  
Sbjct: 274 GLDCPILGDHKYSDWNRLAPQKLSAGILKKLGLQQSKARHLPLHLHACQLTLPALQPQKE 333

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
            L +    P + V +   LG K        R +S DE
Sbjct: 334 ELTLLCRPPRYFVNSLRRLGLKMP-----SRDHSADE 365


>gi|206579088|ref|YP_002240476.1| pseudouridine synthase, RluA family [Klebsiella pneumoniae 342]
 gi|290512597|ref|ZP_06551963.1| ribosomal large subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
 gi|206568146|gb|ACI09922.1| pseudouridine synthase, RluA family [Klebsiella pneumoniae 342]
 gi|289774938|gb|EFD82940.1| ribosomal large subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
          Length = 219

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 71/217 (32%), Positives = 113/217 (52%), Gaps = 19/217 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDFPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  +AA + L   FR R  +K Y + VWG P+  +  +   L+       D+ +  KQ
Sbjct: 72  VVALNKAAERELKRQFREREPKKQYVARVWGHPQPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++        + ++P TGR+HQLRVH L +G PI+GD ++ A 
Sbjct: 126 KVCYETG-KAAQTEYEVLEYAEDNTARVRLKPITGRSHQLRVHMLALGHPILGD-RFYAT 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
            +    +P   +L LHA  + + HP  G  +   AP+
Sbjct: 184 PEALAMAP---RLLLHAETLTITHPAYGNAMTFRAPV 217


>gi|124006880|ref|ZP_01691710.1| ribosomal large subunit pseudouridine synthase D [Microscilla
           marina ATCC 23134]
 gi|123987561|gb|EAY27270.1| ribosomal large subunit pseudouridine synthase D [Microscilla
           marina ATCC 23134]
          Length = 297

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 77/272 (28%), Positives = 118/272 (43%), Gaps = 48/272 (17%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
            ++K ++ G VR++    +    +Q G ++                 ++D      K  +
Sbjct: 34  GVKKAIKKGAVRLNGMPAETGRWVQPGDII----------------TLVDLEETPPKQYE 77

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQK-PRLTHRLDQ 152
           F   ++ YED    V NKPAG+ V G     I   + G LK+       K  +  HRLD 
Sbjct: 78  FTLEVV-YEDDHFAVINKPAGVKVSGNQYRTIVNMLPGNLKASPLPDALKWAKPVHRLDV 136

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+L+VA+T  A  HL +    + I+K Y ++V G P  +          ++ I G  
Sbjct: 137 PTSGLLMVAKTTQAHIHLGQQLEQKTIKKAYHAIVKGTPAARGHI-------RTPINGQS 189

Query: 213 VHVVKQNEKGANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            H             S F+V+        +    + + PHTGRTHQLRVH   +G PI G
Sbjct: 190 AH-------------SEFEVLQTVPSLRNETLSLVRLSPHTGRTHQLRVHLASLGHPITG 236

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           D  Y  +  GN  + +   L+L A  + L HP
Sbjct: 237 DTTY--DEAGN--TMLHKGLFLAATSLQLQHP 264


>gi|271501679|ref|YP_003334705.1| pseudouridine synthase, RluA family [Dickeya dadantii Ech586]
 gi|270345234|gb|ACZ77999.1| pseudouridine synthase, RluA family [Dickeya dadantii Ech586]
          Length = 325

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/240 (31%), Positives = 121/240 (50%), Gaps = 31/240 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +          PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHHYPEIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E IA    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQAREITREYEAVAIGTMTAGGTVDEPIARHSTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMAHINHPLVGDPL 252

Query: 272 YCANFK------GNFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F   ++N  +  LHA  + L HP  G +++  APLP  MV    +L
Sbjct: 253 YGGRPRLPKGASDEFIETLRNFDRQALHATMLRLYHPISGIQMEWHAPLPQDMVDLIAAL 312


>gi|95769474|gb|ABF57439.1| RNA pseudouridylate synthase domain containing 4 [Bos taurus]
          Length = 375

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 78/277 (28%), Positives = 127/277 (45%), Gaps = 43/277 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSG 156
           ++++D ++ V NKP G+ V GG G+   I   L          K +   L HRLD+ET+G
Sbjct: 97  IVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKPLHLCHRLDKETTG 156

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P  +   +   +++K   G  + H  
Sbjct: 157 VMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIVEKEAQGQQHHHKM 216

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  ++ + A  A++ ++V+   +     LE+QP TG  HQLRVH + 
Sbjct: 217 TLSPSYRMDDGKMVRVRSSRNAQLAVTQYQVLS-SSLSAALLELQPITGIKHQLRVHMSF 275

Query: 261 HMGCPIVGDHKYC---ANFKGNFTSPIQNK------------LYLHARYMDLP--HPEGG 303
            + CPI+GDHKY           ++ I  K            L+LHA  + LP   P+  
Sbjct: 276 GLDCPILGDHKYSDWNRLAPQKLSAGILKKLGLQQSKARHLPLHLHACQLTLPALQPQKE 335

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
            L +    P + V +   LG K        R +S DE
Sbjct: 336 ELTLLCRPPRYFVNSLRRLGLKMP-----SRDHSADE 367


>gi|307132187|ref|YP_003884203.1| 23S rRNA pseudouridine synthase [Dickeya dadantii 3937]
 gi|306529716|gb|ADM99646.1| 23S rRNA pseudouridine synthase [Dickeya dadantii 3937]
          Length = 325

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 94/342 (27%), Positives = 161/342 (47%), Gaps = 57/342 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   ++  +   +V+++ K V K   ++  G+ V   
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGKMVDKPKEKVLGGESV--- 65

Query: 69  PVINALNHIIKEQKILDS-SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
               A++ +I+E    ++  ++L          ++YED  I V NKP  + V  G+G   
Sbjct: 66  ----AIDALIEEDARWEAQPISLD---------IVYEDEDILVINKPRDLVVHPGAG--- 109

Query: 128 HIDGFL--------KSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           + DG +           VD     PR  + HRLD++T+G++VVA+T  A   L ES + R
Sbjct: 110 NPDGTVLNALLHHYPEIVDV----PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAR 165

Query: 178 RIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            I + Y ++  G        +E IA    K++H+    VH + +       A++H+++++
Sbjct: 166 EITREYEAVAIGTMTAGGTVEEPIARHSTKRTHMA---VHPMGKP------AVTHYRIME 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----N 286
            F +    L ++  TGRTHQ+RVH  H+  P+VGD  Y       KG   + I+     +
Sbjct: 217 HF-RAHTRLRLRLETGRTHQIRVHMAHINHPLVGDPLYGGRPRLPKGASEAFIETLRNFD 275

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
           +  LHA  + L HP  G  ++  APLP  MV+   +L    D
Sbjct: 276 RQALHATMLRLYHPISGIEMEWHAPLPQDMVELIAALKADTD 317


>gi|330446994|ref|ZP_08310645.1| 23S rRNA pseudouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328491185|dbj|GAA05142.1| 23S rRNA pseudouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 324

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 93/326 (28%), Positives = 152/326 (46%), Gaps = 51/326 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNH 76
            MRLD+     YP  +   ++  + +G V V+ K VK    ++  G+ + I   I     
Sbjct: 17  GMRLDQVVAELYPDYSRSRIKDWILNGMVSVNGKVVKKPREKMMGGEELFIQAEIEDEVR 76

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            + +   LD               ++YED  I V NKP    V  G+G     DG + + 
Sbjct: 77  WVAQDIPLD---------------IVYEDDDILVINKPRDFVVHPGAGTP---DGTVLNA 118

Query: 137 V----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           +     S  + PR  + HRLD++T+G++VVA+T  A   L  + + R+I + Y +L  G 
Sbjct: 119 LLHHCPSLAEVPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEALAIG- 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQN-----EKGANYAISHFKVIDCFAQKFCWLEM 245
                +      ++K  IG    H  K+      E G + AI+H++V + F ++   + +
Sbjct: 178 -----QMTGGGTVEKP-IGR---HSTKRTCMAVHEMGKD-AITHYRVAERF-REHTRIVL 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQ--NKLYLHARYMDL 297
           +  TGRTHQ+RVH  ++  P++GD  Y        N    F   ++  ++  LHAR + L
Sbjct: 227 RLETGRTHQIRVHMSYLSHPLIGDVTYGGRPRPPRNASPEFIQALRAFDRQALHARMLRL 286

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSL 322
            HP  G +++  APLP  MV   D L
Sbjct: 287 DHPITGEKMEWHAPLPNDMVAMIDIL 312


>gi|210622438|ref|ZP_03293170.1| hypothetical protein CLOHIR_01118 [Clostridium hiranonis DSM 13275]
 gi|210154254|gb|EEA85260.1| hypothetical protein CLOHIR_01118 [Clostridium hiranonis DSM 13275]
          Length = 309

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 90/338 (26%), Positives = 154/338 (45%), Gaps = 61/338 (18%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK--RVKFNNRIQSGQV 64
           ++  +VE DE+  RLD +  + +  ++   +QKI++  +V V+ K  + K+  + +   V
Sbjct: 9   IREFLVEEDEDGDRLDVYLADQFVDMSRSYIQKIIKDKKVTVNGKVEKAKYLVKEEDKIV 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + IP           + K+L+           +   ++YED  I + NKP G+ V    G
Sbjct: 69  IEIP-----------KPKVLEVV------PQDIPIEIVYEDDDIIIVNKPQGMVVHPAPG 111

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                    I YH  G L S   +   +P + HR+D++TSGIL++A+   A   L E  +
Sbjct: 112 NYEGTLVNAILYHCKGNLSSI--NGVIRPGIVHRIDKDTSGILMIAKNNNAHNCLAEQLK 169

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK---------GANYA 226
              I + Y            E I + + K+ ++  D    + +N K             A
Sbjct: 170 DHSITREY------------EFICHSVFKEDNVTVD--RPIGRNPKDRLKMAIVPNGKRA 215

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ- 285
           ++HF+VI+ F   +  +  +  TGRTHQ+RVHA+ +  P+VGD  Y     G   S I+ 
Sbjct: 216 VTHFEVIERF-NGYTHVRARLETGRTHQIRVHAMSINHPLVGDPVY-----GPKNSKIKL 269

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           N   LHA+ +   HP     ++  + LP +  K  + L
Sbjct: 270 NGQALHAKKLGFIHPTTKEYVEFDSELPDYFQKLLEKL 307


>gi|238760705|ref|ZP_04621826.1| Ribosomal large subunit pseudouridine synthase D [Yersinia aldovae
           ATCC 35236]
 gi|238701078|gb|EEP93674.1| Ribosomal large subunit pseudouridine synthase D [Yersinia aldovae
           ATCC 35236]
          Length = 325

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 90/332 (27%), Positives = 156/332 (46%), Gaps = 47/332 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V V+ K + K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILEDKVTVNGKTINKPKEKVLGGELVAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        ++  LD               ++YEDS I V NKP G+ V  G+G   +
Sbjct: 69  AQIEEDARWAPQEIPLD---------------IVYEDSDILVINKPRGLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + 
Sbjct: 111 PDGTVLNALLYYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH + +       A +H+++++ F + 
Sbjct: 171 YEAVAIGNMTAGGRVDEPISRHSTKRTHMA---VHPMGKP------ATTHYRIMEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       +F S ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDSFISILRGFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A  + L HP  G +++  A LP  MV+  ++L
Sbjct: 281 ATMLRLYHPISGIQMEWHAALPKDMVELINAL 312


>gi|227503303|ref|ZP_03933352.1| pseudouridylate synthase [Corynebacterium accolens ATCC 49725]
 gi|306836462|ref|ZP_07469436.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           accolens ATCC 49726]
 gi|227075806|gb|EEI13769.1| pseudouridylate synthase [Corynebacterium accolens ATCC 49725]
 gi|304567655|gb|EFM43246.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           accolens ATCC 49726]
          Length = 308

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 86/313 (27%), Positives = 147/313 (46%), Gaps = 28/313 (8%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E MR D         ++     ++   G V VD + +  + R+ SGQVV +         
Sbjct: 15  EGMRADAALAKLL-GLSRSATAQLCAEGGVTVDSQELGKSERLASGQVVSV--------L 65

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKS 135
           + + +K L     L +  D     +LY D+ I   +KP G++     G     + G L++
Sbjct: 66  LPEPEKPLLPREELVEGMD-----VLYSDADIICVHKPVGVAAHPSVGWDGPTVIGGLRA 120

Query: 136 W---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
               V S G   R  + HRLD  TSG++VVA +  A   L  +F+ R ++K Y ++V G+
Sbjct: 121 AGYNVASLGPTERQGIVHRLDVGTSGVMVVASSGRAYSALKHAFKHRTVKKTYHAVVQGL 180

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P   +  I   + +    G  +   V  + K    A++H+++I+ F ++   +E+   TG
Sbjct: 181 PDPIEGTIDAPIGRHPKSGWKF--AVLDDGKA---AVTHYRLIEAF-REASLIEVHLETG 234

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH    G P VGD  Y +N + +    ++ + +LHA  +   HP  G+  +  A
Sbjct: 235 RTHQIRVHMSATGHPCVGDPMYGSNPQLSARLGLERQ-WLHAVQLGFTHPGTGKWFEARA 293

Query: 310 PLPAHMVKTWDSL 322
           P P  + +  + L
Sbjct: 294 PYPDDLQQALERL 306


>gi|149182321|ref|ZP_01860799.1| ribosomal large subunit pseudouridine synthase D [Bacillus sp.
           SG-1]
 gi|148849940|gb|EDL64112.1| ribosomal large subunit pseudouridine synthase D [Bacillus sp.
           SG-1]
          Length = 303

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 80/311 (25%), Positives = 143/311 (45%), Gaps = 37/311 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIP 68
           +V  +E+++RLD+         +   +Q+ ++ G V+V+  +VK N +  I+   ++ IP
Sbjct: 7   IVREEEKSVRLDKVLTQLEEKWSRSQVQQWIKDGNVKVNGSQVKTNYKCAIEDKIIISIP 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                     +E  ++  +++L          + +ED+ + V NKP G+ V    G    
Sbjct: 67  EP--------EELDVVPENMDLD---------IYFEDADVIVVNKPRGMVVHPAPGHPSG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L E    + + + 
Sbjct: 110 TLVNGLMAHCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDLAHEKLVEQLVNKTVTRK 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V GI  +    I   L +      +   V          A++HF V++ F   F +
Sbjct: 170 YKAIVHGIIPHDHGTIDAPLGRDPKDRQNMAVV-----DSGRDAVTHFNVLERFTD-FTY 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+RVH  ++G P+ GD KY      +          LHA  +   HP  
Sbjct: 224 VECKLETGRTHQIRVHMKYIGYPLAGDPKYGPRKTLDLGG-----QALHAAVLGFIHPRT 278

Query: 303 GR-LQITAPLP 312
           G  L+  A  P
Sbjct: 279 GEYLEFEAEPP 289


>gi|126726068|ref|ZP_01741910.1| pseudouridine synthase [Rhodobacterales bacterium HTCC2150]
 gi|126705272|gb|EBA04363.1| pseudouridine synthase [Rhodobacterales bacterium HTCC2150]
          Length = 218

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 120/236 (50%), Gaps = 25/236 (10%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           ++D +      +D L  +++++D ++ + +KPAG+    G G   H+   L + V +   
Sbjct: 1   MIDPTAAYNPPNDPL--VIIHDDHEVLLVDKPAGLLSVPGKG--EHLADCLLTRVQAAFP 56

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----EC 197
              L HRLD++TSG++V A TR A +HL   F  R+ +K Y + V+G+P  K        
Sbjct: 57  MALLVHRLDRDTSGVMVFALTRNAQRHLGLQFEKRQTKKTYVADVYGVPSEKSGTVDLPL 116

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I +W  +          + K   +    A + +KV+         + + P TGR+HQLRV
Sbjct: 117 IVDWPNRP---------LQKVCHETGKAAQTDWKVMRTKGN-VTRVRLMPLTGRSHQLRV 166

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           H L +G PI+GD  Y    +    +P   ++ LH++ +   HP+GG+ ++ TA LP
Sbjct: 167 HMLAIGHPIMGDPFYAT--EPEMAAP---RMMLHSQTLAFRHPDGGKGVRYTAKLP 217


>gi|238791395|ref|ZP_04635034.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           intermedia ATCC 29909]
 gi|238729528|gb|EEQ21043.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           intermedia ATCC 29909]
          Length = 325

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 89/332 (26%), Positives = 156/332 (46%), Gaps = 47/332 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V VD K + K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        +   LD               ++YED+ I V NKP G+ V  G+G   +
Sbjct: 69  AQIEEDARWAPQDIPLD---------------IVYEDNDILVINKPRGLVVHPGAG---N 110

Query: 129 IDGFLKS----WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG + +    +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + 
Sbjct: 111 PDGTILNALLYYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH + +       A +H+++++ F + 
Sbjct: 171 YEAVAIGNMTAGGRVDEPISRHSTKRTHMA---VHPMGKP------ATTHYRIMEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       +F S ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFISILRGFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A  + L HP  G +++  A LP  MV+  ++L
Sbjct: 281 ATMLRLYHPISGIQMEWHAALPEDMVELINAL 312


>gi|311278476|ref|YP_003940707.1| pseudouridine synthase, RluA family [Enterobacter cloacae SCF1]
 gi|308747671|gb|ADO47423.1| pseudouridine synthase, RluA family [Enterobacter cloacae SCF1]
          Length = 326

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 125/245 (51%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G        ++ I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEQPISRHPTKRTHMS-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQL 252

Query: 272 YCANFK------GNFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F + ++  ++  LHA  + L HP  G  ++  AP+P  MV   D++
Sbjct: 253 YGGRPRPPKGASDEFITALRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVDLIDAM 312

Query: 323 GFKYD 327
              ++
Sbjct: 313 RADFE 317


>gi|125972800|ref|YP_001036710.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           thermocellum ATCC 27405]
 gi|256004990|ref|ZP_05429962.1| pseudouridine synthase [Clostridium thermocellum DSM 2360]
 gi|281416999|ref|ZP_06248019.1| pseudouridine synthase [Clostridium thermocellum JW20]
 gi|125713025|gb|ABN51517.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           thermocellum ATCC 27405]
 gi|255991059|gb|EEU01169.1| pseudouridine synthase [Clostridium thermocellum DSM 2360]
 gi|281408401|gb|EFB38659.1| pseudouridine synthase [Clostridium thermocellum JW20]
 gi|316940963|gb|ADU74997.1| pseudouridine synthase [Clostridium thermocellum DSM 1313]
          Length = 231

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 57/177 (32%), Positives = 93/177 (52%), Gaps = 8/177 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +++ED+ + V  KP  I  Q        +   LK  +  +  KP      L HRLD+   
Sbjct: 11  IIFEDNHLLVVKKPVNIPTQKDKSNDSDMLTLLKEDIKKRYNKPGNVYLGLVHRLDRPVG 70

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  L++  R R+ +K+Y ++V GI    +  + N+LLK +    + V V
Sbjct: 71  GVMVFAKTSKAASRLSDQVRTRQFKKVYLAVVHGILDKLEGRLENYLLKDTR--NNTVSV 128

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           VK++  G   A+  +KV +     F  +++  HTGR HQ+RV   ++G P+ GD KY
Sbjct: 129 VKEDTPGGKLAVLDYKV-EGIYNGFSLVKVSLHTGRPHQIRVQLANIGHPLYGDQKY 184


>gi|310829101|ref|YP_003961458.1| RluA family pseudouridine synthase [Eubacterium limosum KIST612]
 gi|308740835|gb|ADO38495.1| RluA family pseudouridine synthase [Eubacterium limosum KIST612]
          Length = 304

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 122/227 (53%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK--SWV-DSKGQ--KPRLTHRLDQETS 155
           ++YED ++ V NK A          ++ +D      +W  + +G   K R  +RLD++T+
Sbjct: 86  IVYEDDEVLVVNKDADCVTHPTK--SHQLDTLANHVAWYWEERGTPGKIRFVNRLDRDTT 143

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V+A+ +    ++    +   ++K Y + V  +P+ K+ CI   + + S        +
Sbjct: 144 GLVVIAKNKYVHHYIQSRMKTDAVKKTYIAFVNNVPEEKEGCIRVPIGRPSE--DSLERI 201

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V ++ K    +++HF+V++ + +    +E+   TGRTHQ+RVH  ++GCPI+GD  Y  N
Sbjct: 202 VMEDGK---ESVTHFRVLESY-RNAAMVELVLETGRTHQIRVHLKYIGCPIIGDSLY--N 255

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
             GN +  +  +  LHA  ++L  P+ G L+++A L   +V   ++L
Sbjct: 256 HDGNPSYGMARQA-LHAAKLNLTLPKSGELELSAGLTEDLVTLQETL 301


>gi|146296753|ref|YP_001180524.1| pseudouridine synthase [Caldicellulosiruptor saccharolyticus DSM
           8903]
 gi|145410329|gb|ABP67333.1| pseudouridine synthase [Caldicellulosiruptor saccharolyticus DSM
           8903]
          Length = 311

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 70/266 (26%), Positives = 130/266 (48%), Gaps = 28/266 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++E +   M+L++  K  YP I    + K+LR G++RV+ +        Q GQ+++   
Sbjct: 5   MLIEKNFAGMKLEKAIKKKYPTIPMSVIFKLLRKGRIRVNFEVA------QKGQILQFGD 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +I+     I+E+ +    V ++K         +YED  I V +KP GI     +   Y +
Sbjct: 59  LIS---FDIEEKYLDQKKVEISK---------VYEDDNIIVIDKPYGIPSHPDTNNEYSV 106

Query: 130 DGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                +W++   S  Q P L HRLD+ TSG++++A+ R     + +    R I+K Y  +
Sbjct: 107 ----VNWIEDNYSGNQLPALCHRLDRNTSGLMIIAKNRQVLNEMLKYMSRRAIKKKYLCI 162

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
              +   K   + ++L K S      V++     +G +  ++ +K+I         ++++
Sbjct: 163 TKKVDLPKSGVLVHYLKKDSK--KSKVYISDLPAEGYSEIVTRYKIIRG-KDDLLLVDVE 219

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
             TG+THQ+R    H+G  I+GD KY
Sbjct: 220 IETGKTHQIRSQLAHVGLCILGDSKY 245


>gi|115376841|ref|ZP_01464064.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|115366144|gb|EAU65156.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
          Length = 240

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 118/228 (51%), Gaps = 13/228 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID--GFLKSWVDSKG-QKPRLTHRLDQETSGI 157
           +L++D  + + +KP G+ V+ G G    ++     +   D +G  +P + HRLD+ETSG 
Sbjct: 15  VLHDDPDMVIVDKPVGLVVEPGGGAPSVVELLAAQRPPFDVEGVARPGVVHRLDRETSGC 74

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVV 216
           L+ ART AAA  L ++F+ +R+ K YW+LV G  P++++  +     +       +   V
Sbjct: 75  LMFARTDAAAAALDQAFQQKRVDKRYWTLVLGETPEHER--LEGPYGRDPQDPRKFTTRV 132

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-AN 275
           K     A  A   F+V +   +    LE++  TGRTHQ+RV     G P++GD  Y  + 
Sbjct: 133 KS----ARRAALSFEVRERL-RGATLLEVRLETGRTHQIRVQLSEAGFPVLGDSVYGPSE 187

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
            + +  +    +  LHA  + +PHP  G L ++ APLP    K   +L
Sbjct: 188 ARAHPVAQALGRQALHALRLAVPHPSTGALVRVEAPLPEDFQKALAAL 235


>gi|108757849|ref|YP_631549.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108461729|gb|ABF86914.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 346

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 85/313 (27%), Positives = 148/313 (47%), Gaps = 44/313 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D++    +P +    +  ++ +G V  D +  K   R++ G+++ +        HI  
Sbjct: 19  RVDQYLARAFPDLTRSRIHGLIEAGHVLADGQPAKPARRLRGGELLVL--------HI-- 68

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL------ 133
                 + V     ++ L   LL+ED  + V +K AG+ V  G+G   H  G L      
Sbjct: 69  -----PAPVPAVPLAEELPLALLHEDRDLVVVDKAAGMVVHPGAG---HASGTLVNALLH 120

Query: 134 --KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             K      G+ +P + HRLD++T+G LVVA+   A   L ++F+ R ++K Y +LV G+
Sbjct: 121 RVKDLAGVGGELRPGIVHRLDKDTTGCLVVAKNEQALVALQKAFKTRAVEKTYLALVHGV 180

Query: 191 PKNKKECIANWLLKKSHIGGDYVH---VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           P  +          ++  G   +H      + ++G N AI+ ++V++ F      +E+  
Sbjct: 181 PPAEGRI-------ETLYGRHPIHRQRFTGKVKEGKN-AITEYRVLETF-DGAALVEVDL 231

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKL---YLHARYMDLPHPEGG 303
            TGRTHQ+RVH    G P++ D  Y          +  Q +L    LHA  +   HP  G
Sbjct: 232 LTGRTHQIRVHLSEAGHPLLCDALYGAGRKAKGAAAEAQERLGRQALHAWRLSFAHPRTG 291

Query: 304 R-LQITAPLPAHM 315
           + L++ AP+PA +
Sbjct: 292 KVLKLEAPIPADL 304


>gi|301089114|ref|XP_002894895.1| ribosomal large subunit pseudouridine synthase A, putative
           [Phytophthora infestans T30-4]
 gi|262105251|gb|EEY63303.1| ribosomal large subunit pseudouridine synthase A, putative
           [Phytophthora infestans T30-4]
          Length = 363

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 76/227 (33%), Positives = 110/227 (48%), Gaps = 22/227 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V NKPA I SV G    A      +   V       R+ HRLDQETSG+LV
Sbjct: 119 ILFRDDAVIVVNKPANILSVDGTDPDALM---SVHRCVARVYPNARMVHRLDQETSGLLV 175

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN-----WLLKKSHIGGDYV- 213
           VA T++AAQ L   FR R + K Y + V G   N  E  +       +  + H+    + 
Sbjct: 176 VALTKSAAQSLNAQFRDRSVDKTYVARVDGWMMNDLEEKSESPRRVQIPMEKHLTKSLIQ 235

Query: 214 HVVKQNE---KGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           HVV   E     + ++ + + V+        +K   +E++P TG+THQLR+H  H+G PI
Sbjct: 236 HVVSDREVDPSSSLWSTTEYSVLSRDESGDDRKSTLVELKPVTGKTHQLRLHMQHLGHPI 295

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +GD  Y  +   +  S    +L LHA  +   HP    RL   +P P
Sbjct: 296 LGDSLYSPDVVYHRAS----RLCLHAAKLSFTHPVTNERLTFESPCP 338


>gi|269926450|ref|YP_003323073.1| pseudouridine synthase, RluA family [Thermobaculum terrenum ATCC
           BAA-798]
 gi|269790110|gb|ACZ42251.1| pseudouridine synthase, RluA family [Thermobaculum terrenum ATCC
           BAA-798]
          Length = 313

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 88/330 (26%), Positives = 147/330 (44%), Gaps = 52/330 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ---VVR 66
           +++  ++   RLD    +    ++   +Q+ +  G + V+    K + +++ G    ++ 
Sbjct: 14  LIISPEDVGERLDTLLAHKLESVSRSQVQRAIEQGTILVNDHPSKPSYKLREGDRILILT 73

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           IP V         E  ++ S V+L          ++YED KI V +KPAG+ V    G  
Sbjct: 74  IPRVPQG------EVALIPSYVDLR---------VVYEDDKIIVIDKPAGMVVHPSPGHY 118

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                   IA + D  LK   D    +P + HRLD++TSG+++VAR      +L    + 
Sbjct: 119 DNTLVNALIARYPD-LLKQPTD----RPGIVHRLDKDTSGLIIVARDLDTLNYLQGQMKA 173

Query: 177 RRIQKIYWSLVWGI---PKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKV 232
           R+I K Y  L  G    P+ + E         + IG D     K +   G   A++ +  
Sbjct: 174 RKIFKEYTLLCCGALDPPEGRIE---------APIGRDLRDRTKMSVIAGGKEAVTEYST 224

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           I     K+     +P TGRTHQ+RVH   +G PI GD  Y     GN      N+ +LHA
Sbjct: 225 IQSLG-KYTLAIARPITGRTHQIRVHFAAIGHPIAGDPIY-----GNCRLEGLNRQFLHA 278

Query: 293 RYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
             + +  P G   +  +PLP  + ++ + +
Sbjct: 279 SRLGVVMPNGEYKEWHSPLPEDLRQSLEKV 308


>gi|223042061|ref|ZP_03612237.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           minor 202]
 gi|223017136|gb|EEF15572.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           minor 202]
          Length = 222

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 107/207 (51%), Gaps = 13/207 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+     +  V  K       HRLD  TSGIL+ A
Sbjct: 17  VYRDNHILVINKPSGLLSVPGNRPEYYDSAMTR--VQQKYGFTEPAHRLDMATSGILLFA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            ++ A + L   FR R  +K Y +L+WG      E + +  +    +  D+ +  +Q   
Sbjct: 75  LSKVAEKELKRQFREREPKKHYIALLWG---KLGEQVGDKGVMDFPLICDWENRPRQKIC 131

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD K+ AN   
Sbjct: 132 YERGKK-AITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGD-KFYANPLA 189

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRL 305
              +P   +L LHA  + + HP  G L
Sbjct: 190 KSLAP---RLCLHAESLTITHPITGEL 213


>gi|330861063|emb|CBX71332.1| ribosomal large subunit pseudouridine synthase C [Yersinia
           enterocolitica W22703]
          Length = 200

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 63/176 (35%), Positives = 98/176 (55%), Gaps = 6/176 (3%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +LV G  ++  + +   LLK 
Sbjct: 17  LVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLALVRGQWQSHCKAVQAPLLKN 76

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
               G+   +VK + +G   + + FK+ + F +    ++  P TGRTHQ+RVHALH G P
Sbjct: 77  IMQSGE--RMVKVSSEG-KPSETRFKIEERF-EHATLVKASPITGRTHQIRVHALHAGHP 132

Query: 266 IVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           I  D +Y    F         ++L+LHA  +   HP  G  ++I APL   +   W
Sbjct: 133 IAFDDRYGDREFDSQLQGTGLHRLFLHAAALRFEHPNTGETMRIEAPLDNQLRIAW 188


>gi|325124374|gb|ADY83897.1| 23S rRNA pseudouridylate synthase [Acinetobacter calcoaceticus
           PHEA-2]
          Length = 233

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 57/184 (30%), Positives = 105/184 (57%), Gaps = 11/184 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   +++ G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLEVGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAAPVSDSVAQSLLSRVVYEDEGLLVINKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           Y   G +++   + G+K   L HR+D++TSG++++++ R+  + L +  R  +I+K Y +
Sbjct: 123 Y---GLIEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAA 179

Query: 186 LVWG 189
           +V G
Sbjct: 180 IVKG 183


>gi|108800058|ref|YP_640255.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           MCS]
 gi|119869184|ref|YP_939136.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           KMS]
 gi|108770477|gb|ABG09199.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           MCS]
 gi|119695273|gb|ABL92346.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           KMS]
          Length = 304

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 79/294 (26%), Positives = 138/294 (46%), Gaps = 35/294 (11%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           I   G V +D      ++R+ +G    VR+P     + +   E + +             
Sbjct: 30  IAEDGGVDIDGAPAGKSDRLTAGAWLEVRLPEAPPPVENTPVEIEGM------------- 76

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYH----IDGFLKSW--VDSKG--QKPRLTHR 149
              +LY D  I   +KP G++    + + +H    + G   +   + + G  ++  + HR
Sbjct: 77  --AVLYSDDDIVAVDKPPGVAAH--ATVGWHGPTVLGGLAAAGFRISTSGIHERQGIVHR 132

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++VVA +  A   L  +F+ R ++K Y +LV G P      I   + +  H G
Sbjct: 133 LDVGTSGVMVVALSERAYTVLKRAFKQRTVEKRYHALVQGHPDPSSGTIDAPIGR--HRG 190

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            D+   V +   G  ++++H+  ++ F Q    L+++  TGRTHQ+RVH   +  P  GD
Sbjct: 191 HDWKFAVTE---GGRHSVTHYDTLEAF-QAASLLDIELETGRTHQIRVHFAALHHPCCGD 246

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             Y A+        ++ + +LHAR +   HP +G R++IT+P PA +    D L
Sbjct: 247 LTYGADPTLARRLGLERQ-WLHARSLAFAHPADGRRIEITSPYPADLQHALDVL 299


>gi|331092518|ref|ZP_08341340.1| hypothetical protein HMPREF9477_01983 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330400739|gb|EGG80342.1| hypothetical protein HMPREF9477_01983 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 217

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 66/210 (31%), Positives = 107/210 (50%), Gaps = 10/210 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLT--HRLD 151
           +K  ++YED  + V +K   I+ Q        +   LK+++    SK Q+P L   HRLD
Sbjct: 3   IKDYIVYEDEHLLVCHKLPKIATQTSRIGEKDMVSLLKNYLHQQSSKKQEPYLAVIHRLD 62

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q   G+LV A+T  AA+ L+   + +   K Y ++V   P+ ++  + N+++K      +
Sbjct: 63  QMVEGLLVFAKTPFAAKELSRQLQQKGFGKEYRAVVCKTPQQQEGTLVNYMVKDKR--SN 120

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              V  +NE GA  A+ H+KV +        L +   TGR HQ+RV   ++GC I+GD K
Sbjct: 121 TSRVCGENEMGAKKAVLHYKVTEEQGDGTAVLHICLETGRHHQIRVQLSNIGCGIMGDAK 180

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           Y A   GN+     +K+ L A  +   HP+
Sbjct: 181 YNA---GNYEQEKWDKIALCAYRLRFVHPK 207


>gi|293365515|ref|ZP_06612224.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           oralis ATCC 35037]
 gi|307703473|ref|ZP_07640415.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
 gi|291315883|gb|EFE56327.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           oralis ATCC 35037]
 gi|307622880|gb|EFO01875.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
          Length = 298

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 114/219 (52%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-EYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV   G+ + + E IA        I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQRKSIEKRYFALVKGAGVLEPEGEIIAPIARDVDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +KV+  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKVVASYGN-IHLVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|156740304|ref|YP_001430433.1| RluA family pseudouridine synthase [Roseiflexus castenholzii DSM
           13941]
 gi|156231632|gb|ABU56415.1| pseudouridine synthase, RluA family [Roseiflexus castenholzii DSM
           13941]
          Length = 315

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 81/320 (25%), Positives = 142/320 (44%), Gaps = 31/320 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++VE  +E  RLDR+     P ++    + ++   +V ++ ++V+  + ++ G VV +  
Sbjct: 9   LIVEAADEGHRLDRYIAGKVPDLSRTYARHLIEDARVLLNNRQVRPASPVRVGDVVTV-- 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                      Q      V L   +  L+  ++YED  + V +KPAGI V    G     
Sbjct: 67  -----------QLPEPQPVGLVAEALPLQ--IVYEDDDVVVIDKPAGIVVHPAPGHNRGT 113

Query: 128 HIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            ++  +  + +   S   +P + HRLD++TSG+LV AR   A   L    + RR+ KIY 
Sbjct: 114 LVNALIARYPEMAISGDLRPGIVHRLDRDTSGLLVAARNDRALHSLQAQQQARRMLKIYL 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +V G        I   + +      D V +      G   A +H++V++   + +  +E
Sbjct: 174 VVVEGRMNESGGVIDAPIARHP---TDRVRMAVM--AGGRPARTHWRVLEELGE-YALIE 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +  TGRTHQ+RVH      P++ D  Y     +  F      + +LHA  +    P  G
Sbjct: 228 ARLETGRTHQIRVHFASRNRPVLADPLYGPKRPRATFG---LTRQFLHAHRLGFALPSSG 284

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             ++ T+PLP  +      L
Sbjct: 285 AWVEFTSPLPDDLAAALARL 304


>gi|332098238|gb|EGJ03211.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           155-74]
          Length = 217

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 72/216 (33%), Positives = 113/216 (52%), Gaps = 19/216 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NK +G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 13  VILYQDDHIMVVNKRSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 70  VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 123

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD ++ A+
Sbjct: 124 KVCYETG-KPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGD-RFYAS 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            +    +P   +L LHA  + + HP  G  +   AP
Sbjct: 182 PEARAMAP---RLLLHAEMLTITHPAYGNSMTFKAP 214


>gi|313677455|ref|YP_004055451.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
 gi|312944153|gb|ADR23343.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
          Length = 237

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/226 (31%), Positives = 112/226 (49%), Gaps = 25/226 (11%)

Query: 101 LLYEDSKIYVF-NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           L+ E+S+ Y+F NKP  +S          I   +K + D      ++ HRLD+ETSG+L+
Sbjct: 9   LIIEESEDYIFINKPPFVSTLADRNDTVTILSLVKKYNDDY----QICHRLDKETSGVLL 64

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+   A ++ +  F  R+++KIY ++V G+ + K E + N  L  +  G  YV +  + 
Sbjct: 65  VAKNPEAYRNASMQFEHRQVEKIYTAIVDGLHQFKDEEV-NLPLHTTASG--YVKISHRQ 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK------YC 273
            K A    + F  I+ F +K   +  +P TGR HQ+RVH   +   I GD        Y 
Sbjct: 122 GKNAK---TIFNTIETF-KKHTLVACRPETGRMHQIRVHLASLNASITGDETYGGQPLYL 177

Query: 274 ANFKGNFTS-------PIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           ++FK NF         PI  +  LHA  + L   +G  + + AP P
Sbjct: 178 SSFKRNFVRGKEKEEHPIIKRFALHAVSISLTDLKGKVVSVEAPYP 223


>gi|237729509|ref|ZP_04559990.1| 23S rRNA pseudouridine synthase D [Citrobacter sp. 30_2]
 gi|226908115|gb|EEH94033.1| 23S rRNA pseudouridine synthase D [Citrobacter sp. 30_2]
          Length = 326

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 126/247 (51%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G        +E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 252

Query: 272 YCANFK------GNFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 253 YGGRPRPPKGASDEFISVLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVQLIEVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|15606824|ref|NP_214204.1| hypothetical protein aq_1758 [Aquifex aeolicus VF5]
 gi|3915479|sp|O67638|Y1758_AQUAE RecName: Full=Uncharacterized RNA pseudouridine synthase aq_1758;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2984062|gb|AAC07603.1| hypothetical protein aq_1758 [Aquifex aeolicus VF5]
          Length = 316

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 86/331 (25%), Positives = 153/331 (46%), Gaps = 54/331 (16%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           VE +EE  RLD++    YP  +   ++K+++ G V V+ + V+  +R ++ G+ V     
Sbjct: 11  VEGEEE--RLDKFLARAYPDFSRSYIKKLVKEGLVYVNGEEVRKPSRKLREGERV----- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
              + H+ + + +     N+  +       ++YED  I V  KP G+ V    G      
Sbjct: 64  ---ILHVPEPEPLDVKPENIPIN-------IIYEDEDIAVVEKPCGLVVHPSPGYTSGTL 113

Query: 125 ---IAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              + YHI       + S G  ++P + HRLD+ET+G++V+A+   A ++L   F+ R+ 
Sbjct: 114 VNALLYHIKD-----LSSIGGVERPGIVHRLDKETAGVMVIAKNNTAHRNLVRQFQERKT 168

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN----EKGANYAISHFKVIDC 235
           +K Y  LV G+ K     I   + +         H V +      K    A++ + V+  
Sbjct: 169 EKFYKVLVKGLVKKDYGAIDTPIAR---------HPVDRKRFWVRKEGKEALTEYWVLKR 219

Query: 236 FAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLH 291
           + + +   L+++ HTGRTHQ+RVH   +G P++GD  Y    ++      S +     L 
Sbjct: 220 YEKYEITLLKVKIHTGRTHQIRVHFASIGHPVLGDRTYGFKSSSVPKELLSLMGECNMLI 279

Query: 292 ARYMDLPHPEGGR---LQITAPLPAHMVKTW 319
           A ++   HP  G     +I  P     V +W
Sbjct: 280 AYHLGFYHPTKGEWMVFEIEEPETFKSVYSW 310


>gi|323138304|ref|ZP_08073375.1| pseudouridine synthase [Methylocystis sp. ATCC 49242]
 gi|322396387|gb|EFX98917.1| pseudouridine synthase [Methylocystis sp. ATCC 49242]
          Length = 238

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 74/232 (31%), Positives = 110/232 (47%), Gaps = 9/232 (3%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L S LL+ D  + + +KPAG+ V  G      ++           + P L HRLD++TSG
Sbjct: 3   LLSRLLHRDGLMLIIDKPAGVPVHRGPKGGPSLEDAFDELRFGLPRAPALAHRLDKDTSG 62

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R R A   L + F+  RI K YW++V G P+ ++  I   L +     G +   +
Sbjct: 63  CLVLGRHRKALDRLGKLFKSGRISKTYWAVVEGAPEAEEGEIDLALGRLDAARGWW---M 119

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           + +  G     S   +         ++E  PHTGRTHQ+RVHA  MG PI+GD  Y    
Sbjct: 120 RPDPLGLPSRTSWRVLGRSPDASLAFVEFTPHTGRTHQIRVHAQAMGWPILGDPIY---- 175

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            G+        L+LHAR + +P  +    ++  AP P HM +     G   D
Sbjct: 176 -GHGRREGAPPLHLHARAITIPMQDSKEPVRAEAPPPDHMSEALALCGLAPD 226


>gi|283835694|ref|ZP_06355435.1| ribosomal large subunit pseudouridine synthase D [Citrobacter
           youngae ATCC 29220]
 gi|291068911|gb|EFE07020.1| ribosomal large subunit pseudouridine synthase D [Citrobacter
           youngae ATCC 29220]
          Length = 326

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 126/247 (51%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G        +E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 252

Query: 272 YCANFK------GNFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 253 YGGRPRPPKGASDEFISVLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|260598975|ref|YP_003211546.1| 23S rRNA pseudouridine synthase D [Cronobacter turicensis z3032]
 gi|260218152|emb|CBA32977.1| Ribosomal large subunit pseudouridine synthase D [Cronobacter
           turicensis z3032]
          Length = 328

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 77/245 (31%), Positives = 124/245 (50%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 88  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIVDVPRAGIVHRLDKDT 144

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L E+ ++R I + Y ++  G         E I+    K++H+   
Sbjct: 145 TGLMVVAKTVPAQTRLVEALQLREITREYEAVAIGHMTAGGTVSEPISRHPTKRTHMS-- 202

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 203 -VHPMGKP------AVTHYRIMEHF-RIHTRLRLRLETGRTHQIRVHMAHITHPLVGDQL 254

Query: 272 YCAN---FKGNFTSPIQ-----NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           Y       KG   + IQ     ++  LHA  + L HP  G L +  AP+P  MV   D+L
Sbjct: 255 YGGRPRPPKGASEAFIQALRKFDRQALHATMLRLYHPVSGILMEWHAPIPQDMVDLIDAL 314

Query: 323 GFKYD 327
              ++
Sbjct: 315 RADFE 319


>gi|328948648|ref|YP_004365985.1| pseudouridine synthase, RluA family [Treponema succinifaciens DSM
           2489]
 gi|328448972|gb|AEB14688.1| pseudouridine synthase, RluA family [Treponema succinifaciens DSM
           2489]
          Length = 317

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 79/314 (25%), Positives = 151/314 (48%), Gaps = 33/314 (10%)

Query: 17  ENMRLDRWFKNHYPH-----INFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPV 70
           E   L+ + +   P      I+   +++++ SG V ++ ++ +  + +I SG  +++  +
Sbjct: 10  EKKTLNEFLRQKIPELLEGEISNSKIRRLIVSGAVYINSRQCRIPSFKINSGTAIKV--L 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHI 129
           I+      ++Q   D+   LT++       +L+ED  +   NKP  +   Q  +G   + 
Sbjct: 68  IDKEKFFFEKQP-EDADFELTEND------VLFEDEYLIAINKPPFLPTEQTITGQRKNA 120

Query: 130 DGFLKSWVDSKGQKPR------LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                 ++  K    R      + HRLD+ETSGIL+  ++R+  + ++E F+ R I+KIY
Sbjct: 121 HDCTVKYLWQKNSSLRNPPYVGIMHRLDRETSGILLFTKSRSVNKDISEMFKTRGIKKIY 180

Query: 184 WSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            ++  G +P+ K+  + N++ + S         +    +G  +  + FK+I      F  
Sbjct: 181 RAVCTGKLPEQKEFTVENFIARISPKSSACKMGIVPESRGGLFTKTDFKIISE-KNGFIQ 239

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-E 301
           ++ Q HTGRTHQ+RV    M  PI GD  Y     G   S   +++ LHAR ++  HP  
Sbjct: 240 IDCQLHTGRTHQIRVQLSSMNLPIAGDELY-----GGIKS---DRIKLHARKIEFVHPVS 291

Query: 302 GGRLQITAPLPAHM 315
             ++ I + +P + 
Sbjct: 292 KEKITIESEIPKNF 305


>gi|283769500|ref|ZP_06342396.1| pseudouridine synthase, RluA family [Bulleidia extructa W1219]
 gi|283103768|gb|EFC05154.1| pseudouridine synthase, RluA family [Bulleidia extructa W1219]
          Length = 303

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 91/324 (28%), Positives = 150/324 (46%), Gaps = 50/324 (15%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++  +RLD++  +H   ++   LQ +++  QV V+ K VK      S   V +  +I   
Sbjct: 9   EKSGLRLDKYVSDHC-ELSRSFLQDLIKEQQVLVNGKAVK------SSYKVNLEDIIEFA 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
              ++E +++   + L          +LYED  + V NK  G+ V    G   H DG L 
Sbjct: 62  VPDLEEIEVIPQDIPLN---------VLYEDEDVIVVNKEKGMVVHPSLG---HQDGTLV 109

Query: 135 SWV-----DSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + +     D  G     +P + HR+D++TSG LV+A+   A   L++    +   + Y  
Sbjct: 110 NALLFHCQDLSGINGKIRPGIVHRIDKDTSGCLVIAKNDVAHIALSKQIETKEAYREYRL 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           +V G  +++   I       + IG D      + VV +N + A    +HF V+  F Q +
Sbjct: 170 IVHGNIQHEDGLI------DAPIGRDPKDRQRMAVVAENSRPAK---THFHVLKRFGQ-Y 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPH 299
            +L     TGRTHQ+RVH  ++  P++GD KY     G+  S  + K   LHA  +   H
Sbjct: 220 TYLSCLLETGRTHQIRVHMKYIQHPVLGDEKY-----GSACSFYETKGQVLHAHTLKFKH 274

Query: 300 P-EGGRLQITAPLPAHMVKTWDSL 322
           P  G  ++  APLP +     D L
Sbjct: 275 PITGKEMEFIAPLPTYFTDVLDYL 298


>gi|171778236|ref|ZP_02919442.1| hypothetical protein STRINF_00281 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171282936|gb|EDT48360.1| hypothetical protein STRINF_00281 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 298

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 86/322 (26%), Positives = 147/322 (45%), Gaps = 50/322 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++       ++ G V V+ K VK    ++ G VV          
Sbjct: 7   EAGARLDKALAD-LTDLSRSQANDEIKKGTVLVNGKAVKAKYAVKVGDVV---------T 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           + + E+++L+        ++ +   ++YED  + V  KP G+ V   +G         + 
Sbjct: 57  YEVPEEEVLEYK------AENIPLDIVYEDEDVAVVYKPQGMVVHPSAGHTSGTLVNALM 110

Query: 127 YHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           YHI    K      G  +P + HR+D++TSG+L++A+   A   L    + ++  + Y +
Sbjct: 111 YHI----KDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDTAHNALAAELKDKKSLRKYVA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWL 243
           +V G   N +  I      ++ IG       KQ    KG   A++HFKV++ F   +  +
Sbjct: 167 IVHGNIPNDRGVI------EAPIGRSEKDRKKQAVTAKG-KPAVTHFKVLERFGN-YTLV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E+   TGRTHQ+RVH  ++G P+ GD  Y      KGN         +LHA+ +   HP+
Sbjct: 219 ELTLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGNGQ-------FLHAQTLGFTHPK 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  +  TA +P    +T + L
Sbjct: 272 TGETMTFTAEVPVIFKETLEKL 293


>gi|145589104|ref|YP_001155701.1| RluA family pseudouridine synthase [Polynucleobacter necessarius
           subsp. asymbioticus QLW-P1DMWA-1]
 gi|145047510|gb|ABP34137.1| ribosomal large subunit pseudouridine synthase D [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 318

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 88/302 (29%), Positives = 135/302 (44%), Gaps = 31/302 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+      P  +   L+  + +G V VD K  K    ++ G+ V++ P        + 
Sbjct: 5   RLDKVLAGSLPDYSRNRLKAWVEAGAVMVDGKVTKARYLLRGGESVKVFP------QEMP 58

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ    S  N+          ++YED  I V NKP G+ V   +G      ++G L  + 
Sbjct: 59  EQFAF-SPENIPLE-------VVYEDDSIIVINKPPGLVVHPAAGNWSGTLLNGLLHRFP 110

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + K   PR  + HRLD++TSG++VVART  A   L    + R + + Y + VWG   ++ 
Sbjct: 111 ELK-SLPRAGIVHRLDKDTSGLMVVARTAHAQTALVRQLQERTVGRRYLAWVWGDAPSQG 169

Query: 196 ECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVI---DCFAQKFCWLEMQPHTG 250
           + +A+       +G D    +K          A + F+ I   +        LE +  TG
Sbjct: 170 KVLAS-------VGRDQRDRLKMAAGSPQGKPAATLFRRIAKGNVENAPVALLECRLETG 222

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQ+RVH   +G P+VGD  Y     G   +   ++  LHA  + L HP    LQ    
Sbjct: 223 RTHQIRVHLESLGFPLVGDPVYRKKAPGVAKALSFDRQALHAFALSLQHPVTQELQTWFR 282

Query: 311 LP 312
           LP
Sbjct: 283 LP 284


>gi|206896098|ref|YP_002247034.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Coprothermobacter proteolyticus DSM 5265]
 gi|206738715|gb|ACI17793.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Coprothermobacter proteolyticus DSM 5265]
          Length = 315

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 135/285 (47%), Gaps = 27/285 (9%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILD----SSVNLTKHSDFLKSILLYEDSK 107
           R    N I++G V     V+   +  +K+  +L+    S ++  + +D   S++ Y D  
Sbjct: 34  RTWIQNNIKAGLVRCNGDVVTKPSLRVKKGDLLEIRLRSRISELQPADVEYSVVYY-DEH 92

Query: 108 IYVFNKPAGISVQGGSGIA--YHIDGFLKSWVDSK----GQKPRLTHRLDQETSGILVVA 161
           + V +KP  + V     +       G LK +   K     ++P + HRLD++TSG+++VA
Sbjct: 93  LAVIDKPPNLVVHPAPSVKGLTLCHGLLKDFPQVKNVGSAERPGIVHRLDKDTSGLMLVA 152

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            +      LT+    + + + Y   V+G+     E  A        IG D  +  +    
Sbjct: 153 LSEKGYAGLTKMISEKSVSRKYLVAVYGVANRPFEVDAP-------IGRDPRNPTRMAVV 205

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
             G N A + F+ + C  +K   LE +  TGRTHQ+RVH  H G  ++GD  Y  N +  
Sbjct: 206 PHGKN-AYTRFRPVQCL-EKVSLLEAELFTGRTHQIRVHLSHAGFYVLGDPVY-GNVESR 262

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
             +P   +++LH+ Y++L HP  G RL   +PLP  + + W  LG
Sbjct: 263 LLAP---RVFLHSYYLELEHPITGERLFFVSPLPEDLDECWHILG 304


>gi|320536301|ref|ZP_08036344.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
 gi|320146861|gb|EFW38434.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
          Length = 320

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 54/167 (32%), Positives = 90/167 (53%), Gaps = 7/167 (4%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD++TSG+L+  R   A +     F+  +  KIY ++V G P+  K  I   + + 
Sbjct: 145 IVHRLDKDTSGVLITERNTRAEEFFKAQFKQHKTTKIYLAVVQGCPRTLKGKIETSIYRD 204

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                 +      +     YA + ++V+  F  K+  ++ +  TGRTHQ+R+HA  +GCP
Sbjct: 205 PKHRTKF--AASSDLSVGRYADTLYRVLKTFG-KYSIVQFKLGTGRTHQIRMHAAFIGCP 261

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           I+GD  Y       F+S   + L LHA+++ +  P+G  ++ITAPLP
Sbjct: 262 ILGDPLYGKK-DSRFSS---SSLMLHAQHLKINLPDGNPIKITAPLP 304


>gi|90580793|ref|ZP_01236596.1| putative ribosomal large subunit pseudouridine synthase A [Vibrio
           angustum S14]
 gi|90438061|gb|EAS63249.1| putative ribosomal large subunit pseudouridine synthase A [Vibrio
           angustum S14]
          Length = 233

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 69/201 (34%), Positives = 102/201 (50%), Gaps = 15/201 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ DS I   NKPAGI    G    +H   F +  V  K    ++ HRLD  TSG++V+A
Sbjct: 20  LFLDSDIIAVNKPAGILSNPGRAPEHHDSIFAR--VLEKYPNSQIVHRLDMGTSGLIVLA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE- 220
             + A  HL   FR R  QK+Y++ VWG  +     +   L+       D+ +  +Q   
Sbjct: 78  LNKKAECHLKAQFRERETQKVYYARVWGHIEQDTGTVDLPLI------CDWPNRPRQKVC 131

Query: 221 -KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 +I+H++V+    +K   + + P TGR+HQLRVH   +G PI+GD K+ AN +  
Sbjct: 132 FDDGKPSITHYEVLS-RDEKTTLVRLLPVTGRSHQLRVHMQALGHPILGD-KFYANEEAM 189

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
             SP   +L LHA  +   HP
Sbjct: 190 AASP---RLLLHAAELTFTHP 207


>gi|268315647|ref|YP_003289366.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
 gi|262333181|gb|ACY46978.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
          Length = 235

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 114/227 (50%), Gaps = 22/227 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  +   +KP G++       +       +    ++G++  + HRLD+E SG+L+ 
Sbjct: 5   ILYEDDDLLAVHKPEGLAAIPERDPSR--PSARRLLEAARGERLWVVHRLDKEASGVLLF 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           AR   A +++   F  R+++K+Y +LV G   P   +      +     +G D       
Sbjct: 63  ARNAEAHRYMNTLFEQRQVRKVYRALVHGRLEPGQGQIRAPIRMYGSGRMGVD------- 115

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   + + ++V++   + +  +E  P TGR HQ+RVH  H+G PIVGD +Y     G
Sbjct: 116 PERGKP-SETRYRVLEYLDEAYSLIEALPLTGRRHQIRVHCYHIGHPIVGDPRY-----G 169

Query: 279 NFTSPIQN---KLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           + +  +Q    +L LHA  +   HP G  L+I AP+P    +  D+L
Sbjct: 170 DRS--VQQRYPRLMLHALSIRFRHPNGQELEIVAPVPESFQQVLDAL 214


>gi|315613225|ref|ZP_07888135.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus sanguinis
           ATCC 49296]
 gi|315314787|gb|EFU62829.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus sanguinis
           ATCC 49296]
          Length = 298

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 114/219 (52%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  VLYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-EYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV   G+ + + E IA        I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQRKSIEKRYFALVKGAGVLEPEGEIIAPIARDVDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +KV+  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKVVASYGN-IHLVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|296216599|ref|XP_002754668.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 4
           [Callithrix jacchus]
          Length = 397

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 119/250 (47%), Gaps = 22/250 (8%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           + Q   +K R +   ++   + V   PV   +  +++  + L   V+    +  L   +L
Sbjct: 42  NAQRLAEKLRAQKQEQVTKKEPVSTNPVQRRVQELVRYTRQLQR-VHPNVLAKALTRGIL 100

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGIL 158
           ++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G++
Sbjct: 101 HQDKNLVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGRKAEPLHLCHRLDKETTGVM 160

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSL----------VWGIPKNKKECIAN-----WLL 203
           V+A  +  A  + E FR+R++ K YW++          V  IP  +KE           L
Sbjct: 161 VLAWDKDMAHQVQELFRIRQVVKKYWAITVRVPIPSAGVVDIPIVEKEAQGQQQHHKMTL 220

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHM 262
             S+   D   V  ++ + A  A++ ++V+         +E+ P TG  HQLRVH +  +
Sbjct: 221 SPSYRMEDGKMVKMRSSRNAQVAVTQYRVLSSTLSS-ALMELHPITGVKHQLRVHLSFGL 279

Query: 263 GCPIVGDHKY 272
            CP++GDHKY
Sbjct: 280 DCPVLGDHKY 289


>gi|53728774|ref|ZP_00135229.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
 gi|126208592|ref|YP_001053817.1| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae
           L20]
 gi|165976548|ref|YP_001652141.1| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|190150449|ref|YP_001968974.1| ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|303253303|ref|ZP_07339452.1| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307246037|ref|ZP_07528119.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307248145|ref|ZP_07530173.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|307250378|ref|ZP_07532326.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|307255019|ref|ZP_07536837.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|307257175|ref|ZP_07538947.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|307259455|ref|ZP_07541180.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|307261604|ref|ZP_07543272.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|126097384|gb|ABN74212.1| ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
 gi|165876649|gb|ABY69697.1| pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 3
           str. JL03]
 gi|189915580|gb|ACE61832.1| ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|302647985|gb|EFL78192.1| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306852972|gb|EFM85195.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|306855322|gb|EFM87497.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|306857588|gb|EFM89696.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|306861892|gb|EFM93868.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|306864337|gb|EFM96248.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|306866391|gb|EFM98254.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|306868727|gb|EFN00536.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
          Length = 325

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 126/249 (50%), Gaps = 33/249 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +     + PR  + HRLD++T
Sbjct: 86  IVYEDDDIIVINKPKDLVVHPGAG---NPDGTVLNALLHYYPPIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+   A  HL  + + RRI + Y ++  G+        E +A    K++ +   
Sbjct: 143 TGLMVVAKNIPAQTHLVTALQKRRITREYEAVASGVMTQGGKVDEPMARHPTKRTAMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 201 -VHPMGKP------AVTHYRIMERF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQL 252

Query: 272 YCANFKG------NFTSPIQN--KLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           Y    +        F + ++   +  LHA  + L HP  G L +  APLP   V+  ++L
Sbjct: 253 YGGRPRPPKGASEEFLAVLRGFQRQALHATMLRLEHPITGELMEWHAPLPDDFVELIEAL 312

Query: 323 GFKYDRNLY 331
             K D  LY
Sbjct: 313 --KADYQLY 319


>gi|8575702|gb|AAF78056.1|AF263561_1 23S rRNA pseudouridine synthase [secondary endosymbiont of
           Glycaspis brimblecombei]
          Length = 314

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 75/234 (32%), Positives = 124/234 (52%), Gaps = 31/234 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----PR--LTHRLDQET 154
           ++YED +I V NKP  + V  G+G   + DG + + +  +  +    PR  + HRLD++T
Sbjct: 75  IVYEDDEIIVINKPRDLVVHPGAG---NPDGTVLNALLYRYPEIINVPRAGIVHRLDKDT 131

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++V+A+T  A  HL E+ ++R I + Y ++V G         E IA    K++H+   
Sbjct: 132 TGLMVIAKTIPAQTHLVEALQLREITREYEAVVNGRMTAGGTVDEPIARHPTKRTHMA-- 189

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +H + +       AI+H++V++ F +    L ++  +GRTHQ+RVH  H+  P+VGD  
Sbjct: 190 -IHPLGKP------AITHYRVMEHF-RAHTRLRLRLESGRTHQIRVHMAHINHPLVGDPV 241

Query: 272 YCAN---FKG---NFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
           Y       KG    F   + N  +  LHA  + L HP  G  ++  A +PA MV
Sbjct: 242 YGGRPRPLKGVSEEFRQVMNNFDRQALHATMLRLYHPRTGIEMEWHADIPADMV 295


>gi|320354847|ref|YP_004196186.1| pseudouridine synthase [Desulfobulbus propionicus DSM 2032]
 gi|320123349|gb|ADW18895.1| pseudouridine synthase [Desulfobulbus propionicus DSM 2032]
          Length = 219

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/207 (34%), Positives = 107/207 (51%), Gaps = 22/207 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +LY D ++ V +KP G+    G G      +   L+  V    ++P + HRLD +T+G++
Sbjct: 8   VLYLDKELAVVDKPGGLLAVPGRGPDKQDCVVSRLRQMVPWCIEQPAV-HRLDMDTAGVM 66

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHVV 216
           V+  T AA +HL+  F  RR++K Y +L+ G+   +K   C+A  L   +       H V
Sbjct: 67  VLGLTGAAHRHLSRQFAERRVEKQYLALLEGVVSGEKGEICLAFRLDPDNR-----PHQV 121

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
               +G    +SH++ I+   Q+   +E  P TGRTHQLR+HA H   +GCPIVGD  Y 
Sbjct: 122 YDAVRG-KMGVSHWRRIEIRGQR-TLVEFIPQTGRTHQLRLHASHPLGLGCPIVGDRLYG 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
           A   G       + L LHA  +   HP
Sbjct: 180 AGRDG-------DSLKLHATRLHFLHP 199


>gi|303250129|ref|ZP_07336331.1| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307252760|ref|ZP_07534651.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|302651192|gb|EFL81346.1| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306859792|gb|EFM91814.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
          Length = 325

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 126/249 (50%), Gaps = 33/249 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +     + PR  + HRLD++T
Sbjct: 86  IVYEDDDIIVINKPKDLVVHPGAG---NPDGTVLNALLHYYPPIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+   A  HL  + + RRI + Y ++  G+        E +A    K++ +   
Sbjct: 143 TGLMVVAKNIPAQTHLVTALQKRRITREYEAVASGVMTQGGKVDEPMARHPTKRTAMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 201 -VHPMGKP------AVTHYRIMERF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQL 252

Query: 272 YCANFKG------NFTSPIQN--KLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           Y    +        F + ++   +  LHA  + L HP  G L +  APLP   V+  ++L
Sbjct: 253 YGGRPRPPKGASEEFLAVLRGFQRQALHATMLRLEHPITGELMEWHAPLPDDFVELIEAL 312

Query: 323 GFKYDRNLY 331
             K D  LY
Sbjct: 313 --KADYQLY 319


>gi|166030562|ref|ZP_02233391.1| hypothetical protein DORFOR_00225 [Dorea formicigenerans ATCC
           27755]
 gi|166029564|gb|EDR48321.1| hypothetical protein DORFOR_00225 [Dorea formicigenerans ATCC
           27755]
          Length = 296

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 64/222 (28%), Positives = 113/222 (50%), Gaps = 17/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSG 156
           ++YED  + V NKPAG+ +    +     I   L  +  S+G KP   R  +RLD++TSG
Sbjct: 83  IIYEDEDLLVLNKPAGMPIHPSLNNYTNSIANALAYYFQSQG-KPFIFRCCNRLDRDTSG 141

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           + +V++   +   L++  + R + + Y ++  G     +  I   L +K   GG  +   
Sbjct: 142 LTIVSKHLVSGSILSDMTKYREVHREYLAIARGSVTPSEGTIQAPLGRK---GGTIIERT 198

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + A++H+KV+   A     + ++  TGRTHQ+R+H  ++G P++GD+ Y  + 
Sbjct: 199 VDWEHGED-AVTHYKVVK-EANGHSLVSLRLETGRTHQIRIHMKYLGYPLIGDYLYNPDM 256

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           +         +  LH+ +M+  HP  G  +  TAPLP  M +
Sbjct: 257 E------YMTRQALHSHHMEFTHPITGEHMSFTAPLPEDMAR 292


>gi|89895611|ref|YP_519098.1| hypothetical protein DSY2865 [Desulfitobacterium hafniense Y51]
 gi|89335059|dbj|BAE84654.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 300

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 83/304 (27%), Positives = 142/304 (46%), Gaps = 53/304 (17%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +Q ++  G + V+    K N ++++     V IPP         +E K+   ++ L    
Sbjct: 26  IQGLIEEGHILVNGAARKANYKVRAMDQITVVIPPP--------RELKVEAENIPLE--- 74

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH------IDGFLKSWVDS 139
                 +LYED  + V NKP G+ V    G         + YH      I+G L+     
Sbjct: 75  ------VLYEDEDVLVVNKPQGMVVHPAPGAWTKTMVNALLYHCRNLSGINGVLR----- 123

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
               P + HR+D++TSG+LVVA+   A Q L E  +   + + Y ++V G+       + 
Sbjct: 124 ----PGIVHRIDKDTSGLLVVAKNDLAHQGLAEQIKAHSMARRYLAIVHGVVFEPSGTV- 178

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +  + +       + VV QN   A  A++H++V++ F + F  LE +  TGRTHQ+RVH 
Sbjct: 179 DAPVGRDPADRKKMAVVFQN---AKEAVTHYEVLERF-RDFTLLEARLETGRTHQIRVHM 234

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
            ++  P++GD  Y    K  F   +Q ++ LHA+ +   HP  G  ++ +AP      K 
Sbjct: 235 AYLKHPVLGDPLYGPR-KNPFG--LQGQM-LHAQLLGFQHPRSGEYMEFSAPASGMFQKV 290

Query: 319 WDSL 322
            + +
Sbjct: 291 LEEI 294


>gi|310817246|ref|YP_003965210.1| ribosomal large subunit pseudouridine synthase A
           [Ketogulonicigenium vulgare Y25]
 gi|308755981|gb|ADO43910.1| ribosomal large subunit pseudouridine synthase A
           [Ketogulonicigenium vulgare Y25]
          Length = 215

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 72/219 (32%), Positives = 112/219 (51%), Gaps = 23/219 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++L++D +I V +KP+G+    G G   H+   L + V        L HRLD++TSG++V
Sbjct: 13  VILHQDHEIVVVDKPSGLLSVPGKG--EHLADCLIARVQRVFPTALLVHRLDRDTSGVMV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKE--CIANWLLKKSHIGGDYVH 214
            A T  A +HL   F  R+ +KIY + VWG    P+   +   I +W  +   +      
Sbjct: 71  FALTPHAQRHLGLQFENRQTKKIYIARVWGEVAAPEGHIDLPLIVDWPNRPLQM------ 124

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V  +N + A    + +K +     +   + + P TGR+HQLRVH L +G PI+GD  Y  
Sbjct: 125 VDHENGRPAQ---TDWKRVRTGGGE-SRMRLMPKTGRSHQLRVHMLEIGHPILGDPFYAT 180

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
               +F      +L LH+  + L HP+GGR L+ TA  P
Sbjct: 181 GPARDFP-----RLMLHSETLQLRHPDGGRTLRFTAKAP 214


>gi|294634724|ref|ZP_06713255.1| ribosomal large subunit pseudouridine synthase D [Edwardsiella
           tarda ATCC 23685]
 gi|291091854|gb|EFE24415.1| ribosomal large subunit pseudouridine synthase D [Edwardsiella
           tarda ATCC 23685]
          Length = 326

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 118/233 (50%), Gaps = 31/233 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDEDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPQIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G        +E IA    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGTMTAGGTVREPIARHPTKRTHMS-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMAHINHPLVGDQL 252

Query: 272 YCA------NFKGNFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           Y        +    F   ++  ++  LHA  + L HP  G  ++  AP+P  M
Sbjct: 253 YGGRPRPPRDASPEFIQTLRAFDRQALHATMLRLYHPISGIEMEWHAPIPEDM 305


>gi|224825454|ref|ZP_03698559.1| pseudouridine synthase, RluA family [Lutiella nitroferrum 2002]
 gi|224602375|gb|EEG08553.1| pseudouridine synthase, RluA family [Lutiella nitroferrum 2002]
          Length = 362

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 90/316 (28%), Positives = 141/316 (44%), Gaps = 35/316 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L + ++ G V +D K      ++  G+            HI  
Sbjct: 35  RLDAALAKLLPDYSRSRLTQWVKDGHVLLDGKPAAPKTKLLGGE------------HI-- 80

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           E  +  +   L  H + ++  ++YED  I + NKPAG+ V   +G      ++G L    
Sbjct: 81  EVAVQQTEEQLAYHPEAIELPIVYEDDHIIIINKPAGLVVHPAAGNWTGTLLNGLLHH-C 139

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
            +    PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++  G +P + 
Sbjct: 140 PALTHVPRAGIVHRLDKETSGLMVVAKTIPAQTELVRQMQARSVKRIYRAIADGVVPFDG 199

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K  I   + +  H     + VVK    G   AI+H +V+  F     ++E +  TGRTHQ
Sbjct: 200 K--IETLIGRDPH-NRMRMAVVK---FGGKQAITHVRVLATFP-SHSYIECRLETGRTHQ 252

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL------YLHARYMDLPHPEGGR-LQI 307
           +RVH      P+ GD  Y  N +      I+  +       LHA  + L HP  G+ +  
Sbjct: 253 IRVHMREARHPLAGDPLY-GNPRHTMPDEIEEAVKALGRQALHAYSLTLTHPATGKEMTW 311

Query: 308 TAPLPAHMVKTWDSLG 323
            A LP  M      LG
Sbjct: 312 KAKLPDDMKHLLAVLG 327


>gi|150015406|ref|YP_001307660.1| RluA family pseudouridine synthase [Clostridium beijerinckii NCIMB
           8052]
 gi|149901871|gb|ABR32704.1| pseudouridine synthase, RluA family [Clostridium beijerinckii NCIMB
           8052]
          Length = 299

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 85/290 (29%), Positives = 140/290 (48%), Gaps = 41/290 (14%)

Query: 39  KILRSG----QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++RS     ++ V+ + VK N  +  G++++I    +    I  E+  +D         
Sbjct: 30  RLIRSASLGKRIFVNDEVVKMNRVLNEGEIIKIDLAKDESQDIAPEKMDID--------- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQK--PRL 146
                 ++YED  I V NK   + V      Q G+     I+ F++S     GQ    RL
Sbjct: 81  ------IVYEDEDILVVNKKPFMVVHPTKSYQSGTLANGVINYFMES-----GQNCIVRL 129

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD  TSG++++A+ + +   L++     +++K Y +LV GI K K+  I   + K  
Sbjct: 130 VSRLDMNTSGLIIIAKNQFSHGMLSKEMSENKVEKKYLALVHGIMKEKQGTIDLPIYKPE 189

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            I      VV  +E+G   +I+H+KV++ + +    +E +  TGRTHQ+RVH  H+G PI
Sbjct: 190 GIENGIRRVV--DERGQR-SITHYKVVEEYNES-SLVECKLETGRTHQIRVHLSHLGHPI 245

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            GD  Y     G+    I+ +  LHA  +D   P  G  L + A LP  M
Sbjct: 246 YGDTLYG---DGDEEDLIKRQ-ALHAFGLDFKSPRSGEILSLRAELPDDM 291


>gi|288937176|ref|YP_003441235.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|288891885|gb|ADC60203.1| pseudouridine synthase [Klebsiella variicola At-22]
          Length = 219

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/217 (32%), Positives = 113/217 (52%), Gaps = 19/217 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDKHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDLPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  +AA + L   FR R  +K Y + VWG P+  +  +   L+       D+ +  KQ
Sbjct: 72  VVALNKAAERELKRQFREREPKKQYVARVWGHPQPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++        + ++P TGR+HQLRVH L +G PI+GD ++ A 
Sbjct: 126 KVCYETG-KAAQTEYEVLEYAEDNTARVRLKPITGRSHQLRVHMLALGHPILGD-RFYAT 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
            +    +P   +L LHA  + + HP  G  +   AP+
Sbjct: 184 PEALAIAP---RLLLHAETLTITHPAYGNAMTFRAPV 217


>gi|289168022|ref|YP_003446291.1| 23S_rRNA pseudouridine synthase [Streptococcus mitis B6]
 gi|288907589|emb|CBJ22426.1| 23S rRNA pseudouridine synthase [Streptococcus mitis B6]
          Length = 298

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 115/219 (52%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    +++ E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLESEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYG-SIHLVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|268317176|ref|YP_003290895.1| pseudouridine synthase, RluA family [Rhodothermus marinus DSM 4252]
 gi|262334710|gb|ACY48507.1| pseudouridine synthase, RluA family [Rhodothermus marinus DSM 4252]
          Length = 355

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 90/362 (24%), Positives = 148/362 (40%), Gaps = 65/362 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +Q  V     E  RLD +        +   +Q+ +R G+V V+   V K    +Q G V+
Sbjct: 8   IQLEVPPGYREGGRLDAYLARFLAQASRTKIQRGIREGRVTVNGVVVQKPAYTVQPGDVI 67

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +  +      I+ E   LD               ++YED  + V NK AG+ V    G 
Sbjct: 68  TLRILRPPPVEIVPEPIPLD---------------IVYEDPYLIVVNKQAGLVVHPARGN 112

Query: 125 --------IAYHI-DGFLK---------------SWVDS-------KGQKPRLTHRLDQE 153
                   + Y+I  G ++               S V +       +  +P + HRLD++
Sbjct: 113 RSGTLVNALLYYIGSGPVRFDEEDDLPEDDEIGLSMVSTGPTEAKLEAPRPGIVHRLDKD 172

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G++VVA+       L   F  R I + Y ++VWG+P   +  I   + +      D  
Sbjct: 173 TTGLIVVAKDDVTHTGLARQFEHRTIARTYLAIVWGVPDPPRGRIEAAIGRDPR---DRQ 229

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +    +     A++H++V++        +  +  TGRTHQ+RVHA H+G P++GD  Y 
Sbjct: 230 RMAVVPDDRGKRAVTHYEVVEALPAA-ALVRFKLETGRTHQIRVHARHIGHPVLGDPTYG 288

Query: 274 A-NFKGNFTSPIQNKLY-----------LHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
               +    +P +   Y           LHA  +   HP  G  L+  APLP  M    +
Sbjct: 289 GRTIRYGPHTPRRRAFYDQLFARLTRQALHAHTLGFRHPRTGEWLEFEAPLPEDMACALE 348

Query: 321 SL 322
            L
Sbjct: 349 QL 350


>gi|152971444|ref|YP_001336553.1| 23S rRNA pseudouridine synthase D [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238896040|ref|YP_002920776.1| 23S rRNA pseudouridine synthase D [Klebsiella pneumoniae
           NTUH-K2044]
 gi|262043838|ref|ZP_06016928.1| ribosomal large subunit pseudouridine synthase D [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|330012968|ref|ZP_08307538.1| ribosomal large subunit pseudouridine synthase D [Klebsiella sp. MS
           92-3]
 gi|150956293|gb|ABR78323.1| 23S rRNA pseudouridine synthase [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238548358|dbj|BAH64709.1| 23S rRNA pseudouridine synthase [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|259038808|gb|EEW39989.1| ribosomal large subunit pseudouridine synthase D [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|328533634|gb|EGF60346.1| ribosomal large subunit pseudouridine synthase D [Klebsiella sp. MS
           92-3]
          Length = 326

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 126/245 (51%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G        +E I+    K++H+   
Sbjct: 143 TGLMVVAKTIPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RIHTRLRLRLETGRTHQIRVHMSHITHPLVGDQV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F + ++  ++  LHA  + L HP  G  ++  AP+P  MV+  +++
Sbjct: 253 YGGRPRPPKGASEEFITALRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEAM 312

Query: 323 GFKYD 327
              ++
Sbjct: 313 RADFE 317


>gi|284008559|emb|CBA75113.1| ribosomal large subunit pseudouridine synthase A [Arsenophonus
           nasoniae]
          Length = 215

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/205 (34%), Positives = 103/205 (50%), Gaps = 15/205 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G  +  H D  + + V +        HRLD  TSGI+VV
Sbjct: 13  VLYQDQHIIVVNKPSGLLSVPGKAVE-HKDSIM-TRVQADFPTAESVHRLDMATSGIMVV 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + A + L   FR R  +KIY + VWG   NKK  I   L+       D+ +  KQ  
Sbjct: 71  ALNKTAEKELKRQFREREPEKIYQARVWGHITNKKGLIDLPLI------CDWPNRPKQKV 124

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A + +KV+  + ++   +++ P TGR+HQLRVH L +G PI+GD  Y      
Sbjct: 125 CFTTGKPAQTKYKVL-AYEEQTTLVKLIPITGRSHQLRVHLLSLGHPIIGDQFYAHQAAL 183

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
             +S    +L LHA  + + HP  G
Sbjct: 184 ILSS----RLQLHAEELYITHPIYG 204


>gi|255325321|ref|ZP_05366427.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           tuberculostearicum SK141]
 gi|255297886|gb|EET77197.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           tuberculostearicum SK141]
          Length = 308

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 84/306 (27%), Positives = 142/306 (46%), Gaps = 28/306 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E MR D         ++     ++   G V +D + +  + R+ SG VV +         
Sbjct: 15  EGMRADAALAKLL-GLSRSATAQLCAEGSVTIDSQELGKSERLTSGNVVSV--------L 65

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKS 135
           + + +K L     L +  D     +LY D+ I   +KP G++     G     + G L++
Sbjct: 66  LPEPEKPLLPREELVEGMD-----VLYNDADIICVHKPVGVAAHPSVGWDGPTVIGGLRA 120

Query: 136 W---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
               V S G   R  + HRLD  TSG++VVA +  A   L  +F+ R ++K Y ++V G+
Sbjct: 121 AGYTVASSGPTERKGIVHRLDVGTSGVMVVASSERAYSALKHAFKYRSVKKTYHAVVQGL 180

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P   +  +   + +    G  +   V  + K    A++H+ +I+ F ++   +E+   TG
Sbjct: 181 PDPIEGTVDAPIGRHPKSGWKF--AVLDDGKA---AVTHYSLIEAF-REASLIEVHLETG 234

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH    G P VGD  Y ++        +Q + +LHA  +   HP  G+  +I A
Sbjct: 235 RTHQIRVHMSATGHPCVGDPMYGSDPNLAKRLGLQRQ-WLHAVKLGFTHPGTGKWFEIEA 293

Query: 310 PLPAHM 315
           P PA +
Sbjct: 294 PYPADL 299


>gi|219872253|ref|YP_002476628.1| pseudouridylate synthase, 23S RNA-specific [Haemophilus parasuis
           SH0165]
 gi|219692457|gb|ACL33680.1| pseudouridylate synthase, 23S RNA-specific [Haemophilus parasuis
           SH0165]
          Length = 236

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 68/202 (33%), Positives = 104/202 (51%), Gaps = 13/202 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y     ++  V  K       HRLD  TSGIL+ A
Sbjct: 31  VYRDNHILVINKPSGLLSIPGNRPEYQDSAMVR--VQQKYGFTEPAHRLDMATSGILLFA 88

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            ++ A + L   FR R  +K Y +LVWG      E + +       +  D+ +  +Q   
Sbjct: 89  LSKQAEKELKRQFREREPKKHYQALVWG---KLGEKVGDTGTMNFPLICDWENRPRQKIC 145

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   A++ ++V+  +      +++ P+TGR+HQLRVH L +G PIVGD K+ AN   
Sbjct: 146 YERGKQ-AVTFYEVLAHYPNNTTRVKLTPYTGRSHQLRVHCLALGHPIVGD-KFYANPLA 203

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
              SP   +L LHA  + + HP
Sbjct: 204 KSLSP---RLCLHAEALTITHP 222


>gi|303254977|ref|ZP_07341056.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS455]
 gi|302598057|gb|EFL65124.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS455]
          Length = 295

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 84/308 (27%), Positives = 147/308 (47%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   V   +
Sbjct: 5   IETGGLRLDKALSDLSELSRSLANEQIKSGQVL-VNGQVKKAKYTVQEGDVVTYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   L    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G P+ GD  Y      KG+         +LHA+ +   HP  G+ L   A +P  
Sbjct: 233 HMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGKTLGFKADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKETLERL 293


>gi|330444047|ref|YP_004377033.1| RluA family pseudouridine synthase [Chlamydophila pecorum E58]
 gi|328807157|gb|AEB41330.1| pseudouridine synthase, RluA family [Chlamydophila pecorum E58]
          Length = 328

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 89/308 (28%), Positives = 141/308 (45%), Gaps = 35/308 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++    YP  +    QK + +  V ++ + + K ++R+  G VV I      +   
Sbjct: 23  MRLDKYLAMMYPEYSRAFYQKHIVNHNVFINGEVQTKVSSRLSEGDVVTI-----HIQEK 77

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH 128
            +  ++L   + L K         +YEDS I V NKP  + V    G         + + 
Sbjct: 78  EELSELLPEEIPLHK---------VYEDSMIIVVNKPRDMVVHPSPGHHAGTIVHALLHE 128

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           I   LK     +  +P + HRLD++TSG+L+ A+T  A +   E F  + +QK Y ++  
Sbjct: 129 IGERLKQEFPEEPWRPGIVHRLDKDTSGLLITAKTLKAKKIYGELFAKKLLQKRYLAVCV 188

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G P   +  I   L +      ++       E     A +H +V+  +  K   + + P 
Sbjct: 189 GKPLQTQ--IHTRLARHPQKRKEFTVSSVGKE-----ATTHCQVL-AYNGKLSLVLLSPE 240

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQLRVH  H   PI+GD  Y ++          +K  LHA  +D  HPE  + L++
Sbjct: 241 TGRTHQLRVHMKHSHSPILGDPIYGSSSANRVYG--LDKQQLHAYSLDFIHPETHQPLKL 298

Query: 308 TAPLPAHM 315
           TA LP  M
Sbjct: 299 TAALPEDM 306


>gi|255079396|ref|XP_002503278.1| predicted protein [Micromonas sp. RCC299]
 gi|226518544|gb|ACO64536.1| predicted protein [Micromonas sp. RCC299]
          Length = 279

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 71/220 (32%), Positives = 114/220 (51%), Gaps = 20/220 (9%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGIS----VQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTH 148
           D  +  + +ED+   V  KP G++     +GG      +  FL   +  +G   +PR  H
Sbjct: 26  DLPRLEVAHEDAHFAVVVKPEGVNTVGDARGGWTAERMLPYFLAPTIGVEGALVRPRPVH 85

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG+LVVA+TR AA  L+E+F  RR+ K Y +++ G P   +  + +    ++  
Sbjct: 86  RLDALTSGLLVVAKTRLAATSLSEAFASRRVTKRYRAVLCGTPAEPEVLVDDDDDDENDR 145

Query: 209 GGDY---VHVVKQNEKGANYAISHFKVI----DCFAQ--KFCWLEMQPHTGRTHQLRVHA 259
            G     + V+    +G    +SH++V+    D   +  +   ++M P TGRTHQLR HA
Sbjct: 146 AGAAALKLGVIDAPMEG-KQCVSHWRVVRDAPDASMRHGRLTLVDMWPKTGRTHQLRRHA 204

Query: 260 L-HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              +GCPI+GD +Y  N K +    + + L+L A  + LP
Sbjct: 205 AGALGCPILGDARY--NPKHSPEDDV-DGLFLRAVEVTLP 241


>gi|301154795|emb|CBW14258.1| 23S rRNA pseudouridine synthase [Haemophilus parainfluenzae T3T1]
          Length = 324

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 123/244 (50%), Gaps = 31/244 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +        + PR  + HRLD++T
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAG---NPDGTVLNALLYHYPPIAEVPRAGIVHRLDKDT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++ +   
Sbjct: 142 TGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLMA-- 199

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 200 -VHPMGKP------AVTHYRIMENF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQT 251

Query: 272 YCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y        N    FT  ++N  +  LHA  + L HP  G  ++  APLP   V+   +L
Sbjct: 252 YGGRPRPPKNASEAFTEVLRNFKRQALHAVMLRLAHPITGETMEWYAPLPDDFVELLHAL 311

Query: 323 GFKY 326
              Y
Sbjct: 312 KADY 315


>gi|238765380|ref|ZP_04626304.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           kristensenii ATCC 33638]
 gi|238696422|gb|EEP89215.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           kristensenii ATCC 33638]
          Length = 325

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 89/332 (26%), Positives = 156/332 (46%), Gaps = 47/332 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V VD K + K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        ++  LD               ++YED+ I V NKP G+ V  G+G   +
Sbjct: 69  AQIEEDARWAPQEIPLD---------------IVYEDNDILVINKPRGLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + 
Sbjct: 111 PDGTVLNALLYYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH + +       A +H+++++ F + 
Sbjct: 171 YEAVAIGNMTAGGRVDEPISRHSTKRTHMA---VHPMGKP------ATTHYRIMEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       +F + ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFIAILRGFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A  + L HP  G +++  A LP  MV+  ++L
Sbjct: 281 ATMLRLYHPISGIQMEWHAALPEDMVELINAL 312


>gi|110833337|ref|YP_692196.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
 gi|110646448|emb|CAL15924.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
          Length = 323

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 71/231 (30%), Positives = 116/231 (50%), Gaps = 24/231 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----PR--LTHRLDQET 154
           ++Y+D  + V NKP G+ V   +G   H DG L + +    ++    PR  + HRLD++T
Sbjct: 89  VVYQDDDLIVINKPTGLVVHPAAG---HADGTLLNGLLHLDERLNSLPRAGIVHRLDRDT 145

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++VVAR+  A Q L    + + + + Y ++  G+     +  A   + +  +      
Sbjct: 146 TGLMVVARSLEAHQSLVAQLQDKSLFRQYEAIAVGVMTGGGKVDAP--MGRHPVDRKKQA 203

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VVK    G   A++H++V+D + +    +++Q  TGRTHQ+RVH  H   P+VGD  Y  
Sbjct: 204 VVK---TGGKNAVTHYRVLDRY-RAHTRIQVQLETGRTHQIRVHMAHRNYPLVGDPLYGG 259

Query: 275 NFK--GNFTSPIQNKLY------LHARYMDLPHPEGGR-LQITAPLPAHMV 316
             K     T  ++  L+      LHAR + L HP  G   +  A LPA M 
Sbjct: 260 RLKQPAGATEALRQALHKFPRQALHARKLGLIHPARGEYCEFQAELPADMT 310


>gi|154685381|ref|YP_001420542.1| YhcT [Bacillus amyloliquefaciens FZB42]
 gi|154351232|gb|ABS73311.1| YhcT [Bacillus amyloliquefaciens FZB42]
          Length = 302

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 115/236 (48%), Gaps = 33/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +L+ED+ + + NKPAG+      +G +G     IAYH        ++ +  K R  HRLD
Sbjct: 85  ILFEDNHMLIANKPAGMPTHPNEEGQTGTLSNLIAYHF------HINGEQAKVRHVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V A+ R A   L      + +++ Y +   G    KK  +       S IG D
Sbjct: 139 RDTSGAVVFAKHRLAHAILDRQLETKTLKRTYIAAAEGKVTPKKGTV------DSPIGRD 192

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             H V++    G   A++H+KV D     +    E++  TGRTHQ+RVH   +G P+ GD
Sbjct: 193 RSHSVRRRVSPGGQAAVTHYKVKDYHPGAQLTLAELELETGRTHQIRVHMASIGHPLAGD 252

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP---AHMVKTWDS 321
             Y        +  + ++  LHA+ + + HP  G  +   AP+P   AH  +T+ S
Sbjct: 253 DLYGG------SRTLFHRQALHAKKVSVVHPISGEEIVAEAPMPADLAHFTETYFS 302


>gi|307706671|ref|ZP_07643477.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK321]
 gi|307617915|gb|EFN97076.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK321]
          Length = 298

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 114/219 (52%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     D + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-DYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + IQK Y++LV G    +++ E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIQKRYFALVKGDGYLESEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH   +   HP   + LQ+ +PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHSLTFYHPFLEQDLQLESPLP 283


>gi|163733966|ref|ZP_02141407.1| ribosomal large subunit pseudouridine synthase D [Roseobacter
           litoralis Och 149]
 gi|161392502|gb|EDQ16830.1| ribosomal large subunit pseudouridine synthase D [Roseobacter
           litoralis Och 149]
          Length = 342

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 94/351 (26%), Positives = 150/351 (42%), Gaps = 62/351 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVKFN--NRIQS 61
           +Q+V+  ++   +RLD+      P    ++   L +++  G V VD   V+ N   RI++
Sbjct: 6   IQFVI--DEAPPLRLDKALARDVPVEAALSRTRLARLIDEGGVWVDGV-VQHNPKARIEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  V I       +HI+ E   LD               +++ED+ + V NKPAG+ V  
Sbjct: 63  GAQVTIHVQEAQDSHILPEDIPLD---------------IIHEDADLIVVNKPAGMVVHP 107

Query: 122 GSGIAYH--IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             G      ++  L    D        ++P + HR+D++TSG+LVVA++ AA   L   F
Sbjct: 108 APGTPSGTLVNALLAHCGDDLSGVGGLKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAAQF 167

Query: 175 RMRRIQKIYWSLVWGIP----------KNKKECIANWLLKKSHIGGDYVHVVKQNE--KG 222
           +   +++ Y  LV+G P          K  +    N L   + +        +Q    +G
Sbjct: 168 QAHTVERYYNCLVYGAPDANDPRLRGVKGARFEAGNILKMTTQLARHKTDRQRQAVLFQG 227

Query: 223 ANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +A++  + ++ +          CWLE    TGRTHQ+RVH  H G  +VGD  Y    
Sbjct: 228 GRHAVTRARSVERYGTPPVLTLMECWLE----TGRTHQIRVHMAHAGHALVGDPTYGGKR 283

Query: 277 KGNFTSPIQNKL---------YLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           K    S     L          LHA  +   HP  G  L+  A LP  M +
Sbjct: 284 KLPAKSLPDATLEAVKCFKRQALHAAVLGFEHPVSGEHLRFEAALPDDMAQ 334


>gi|153808958|ref|ZP_01961626.1| hypothetical protein BACCAC_03259 [Bacteroides caccae ATCC 43185]
 gi|149128291|gb|EDM19510.1| hypothetical protein BACCAC_03259 [Bacteroides caccae ATCC 43185]
          Length = 357

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 86/338 (25%), Positives = 153/338 (45%), Gaps = 50/338 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +I+   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---VMDRPRYENEIIPEDIPLN---------IVYEDKYVMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +A+H    +K   D     P   L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 138 LVNALAWH----MKDVPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKT 193

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFA 237
            ++ Y +LVWG  +  +  I   + +      D + + V  +     +A++H++V++   
Sbjct: 194 TKRKYRALVWGTVEQDEGTIVGNIARNPK---DRMQMAVMSDPAVGKHAVTHYRVLERLG 250

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN--------- 286
                +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +          
Sbjct: 251 Y-VTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTC 309

Query: 287 -KLYLHARYMDLPHP-EGGRLQITAPLP---AHMVKTW 319
            +  LHA  +   HP  G  +  T+ LP   A +++ W
Sbjct: 310 PRQALHAMTLGFVHPVTGEEMYFTSELPDDMARLIEKW 347


>gi|304320252|ref|YP_003853895.1| putative ribosomal large subunit pseudouridine synthase protein
           [Parvularcula bermudensis HTCC2503]
 gi|303299154|gb|ADM08753.1| putative ribosomal large subunit pseudouridine synthase protein
           [Parvularcula bermudensis HTCC2503]
          Length = 338

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 77/291 (26%), Positives = 126/291 (43%), Gaps = 38/291 (13%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN--- 57
           MS    + + V E D    RLD+W  +     +   ++ ++  G +   K    F +   
Sbjct: 1   MSDTEPLSFTVAEADV-GARLDKWIADQTDAYSRARIKALIEGGALT--KDAAPFTDPKW 57

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           +++ G+V  + P          E       + LT         +L+ED  + V NKPAG+
Sbjct: 58  KLRQGEVFTLVPPPPEDPTPKPED------IPLT---------VLFEDGDLIVINKPAGL 102

Query: 118 SVQGGSG--IAYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHL 170
            V   +G      ++  L    D+        +P + HRLD++TSG++V+A+   A Q L
Sbjct: 103 VVHPAAGNWTGTLVNALLHHCGDTLSGIGGVIRPGIVHRLDKDTSGVMVIAKNDHAHQGL 162

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
           +  F    I + Y +L  G P+     I  W L +S      + VV  +      AI+HF
Sbjct: 163 SALFAAHDIDRAYLALCEGSPRPTSGTI-TWPLARSSGDRKKMTVVGVDRPEGKEAITHF 221

Query: 231 KVIDCFA---------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +D +               +E +  TGRTHQ+RVH  H+G P++GD  Y
Sbjct: 222 ARLDAYGIGRAKLPGDALASLVECRLETGRTHQIRVHMSHIGHPLLGDPVY 272


>gi|89070986|ref|ZP_01158209.1| ribosomal large subunit pseudouridine synthase A [Oceanicola
           granulosus HTCC2516]
 gi|89043449|gb|EAR49664.1| ribosomal large subunit pseudouridine synthase A [Oceanicola
           granulosus HTCC2516]
          Length = 215

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 112/215 (52%), Gaps = 17/215 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED ++ + +KPAG+    G G   H+   L + V +      L HRLD++TSG+++ 
Sbjct: 14  VLHEDHEVVLVDKPAGLLSVPGKG--EHLADCLLARVQAAFPTALLVHRLDRDTSGVMIF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A T  A +HL   F  R+ +K Y + V G   +K   +   L+       D+ +  KQ  
Sbjct: 72  ALTPHAQRHLGLQFEKRQTRKTYVARVAGRIADKTGTVDLPLIV------DWPNRPKQMV 125

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    A++ ++V+   +     + + P TGR+HQLRVH L +G PI+GD  Y      
Sbjct: 126 DHENGKPAVTDWRVVRA-SDAETRVRLFPKTGRSHQLRVHMLALGHPILGDPFYAEG--- 181

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              +    ++ LH+  +   HP+GGR ++ITAP P
Sbjct: 182 --PARAHPRMMLHSETLQFRHPDGGRGMRITAPAP 214


>gi|45440505|ref|NP_992044.1| 23S rRNA pseudouridine synthase D [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51595196|ref|YP_069387.1| 23S rRNA pseudouridine synthase D [Yersinia pseudotuberculosis IP
           32953]
 gi|145600172|ref|YP_001164248.1| 23S rRNA pseudouridine synthase D [Yersinia pestis Pestoides F]
 gi|162420770|ref|YP_001607807.1| 23S rRNA pseudouridine synthase D [Yersinia pestis Angola]
 gi|170025566|ref|YP_001722071.1| 23S rRNA pseudouridine synthase D [Yersinia pseudotuberculosis
           YPIII]
 gi|186894214|ref|YP_001871326.1| 23S rRNA pseudouridine synthase D [Yersinia pseudotuberculosis
           PB1/+]
 gi|229896561|ref|ZP_04511728.1| 23S rRNA pseudouridine synthase [Yersinia pestis Pestoides A]
 gi|45435362|gb|AAS60921.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Microtus str. 91001]
 gi|51588478|emb|CAH20086.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Yersinia pseudotuberculosis IP 32953]
 gi|145211868|gb|ABP41275.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           Pestoides F]
 gi|162353585|gb|ABX87533.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           Angola]
 gi|169752100|gb|ACA69618.1| pseudouridine synthase, RluA family [Yersinia pseudotuberculosis
           YPIII]
 gi|186697240|gb|ACC87869.1| pseudouridine synthase, RluA family [Yersinia pseudotuberculosis
           PB1/+]
 gi|229700339|gb|EEO88371.1| 23S rRNA pseudouridine synthase [Yersinia pestis Pestoides A]
          Length = 325

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 91/332 (27%), Positives = 155/332 (46%), Gaps = 47/332 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V V+ K++ K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKVLGGELVAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        ++  LD               ++YED+ I V NKP G+ V  G+G   +
Sbjct: 69  AQIEEDARWAPQEIPLD---------------IVYEDNDILVINKPRGLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + 
Sbjct: 111 PDGTVLNALLHYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH + +       A +H+++++ F + 
Sbjct: 171 YEAVAIGNMTAGGRVDEPISRHSTKRTHMA---VHPMGKP------ATTHYRIMEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y       KG   S I      ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDSFIAILRGFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A  + L HP  G +++  A LP  MV+  ++L
Sbjct: 281 ATMLRLYHPISGIQMEWHAALPEDMVELINAL 312


>gi|241574172|ref|XP_002403064.1| ribosomal pseudouridine synthase, putative [Ixodes scapularis]
 gi|215502139|gb|EEC11633.1| ribosomal pseudouridine synthase, putative [Ixodes scapularis]
          Length = 443

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 80/275 (29%), Positives = 130/275 (47%), Gaps = 41/275 (14%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPR---- 145
           T+  D L+ ++LY D+ I V NKP G+   G +          K   D S    PR    
Sbjct: 174 TEAVDLLRKLVLYNDNDILVLNKPYGMLCHGPAPGVSDACVLTKLLPDLSSALYPRQDAK 233

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD++ +G+L++ART+  A  L   F+  ++ K Y ++  G+P +  E + +  L
Sbjct: 234 LYTVHRLDRDVTGVLLLARTQRMADMLNSLFQKHQVSKTYLAITAGVP-DHLEGVIDMPL 292

Query: 204 KKSHIGG------------DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  + G            ++  +V +  K +  A++ ++V+     +  +LE++P TG 
Sbjct: 293 AEGEVEGAKRMVLNPKLDPEFQRLVPKFRK-SFAAVTTYRVL-ASCGRAGYLELRPTTGV 350

Query: 252 THQLRVH-ALHMGCPIVGDHKYC-------ANFKGNFTSPI---QNK-----LYLHARYM 295
            HQLR H  L + CPI+GDHKY            G+    +   Q+K     L+LHAR +
Sbjct: 351 KHQLRAHLGLGLRCPILGDHKYSHLRRLAPQKLPGDMLDRLGIRQSKVRDAPLHLHARAV 410

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
            +P    GR L + A +P H  K    L  K +RN
Sbjct: 411 VVPEILDGRNLTVAAEVPYHFAKNLRRL--KLNRN 443


>gi|145637336|ref|ZP_01792996.1| SfhB [Haemophilus influenzae PittHH]
 gi|145269428|gb|EDK09371.1| SfhB [Haemophilus influenzae PittHH]
          Length = 324

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 122/247 (49%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP  + V  G+G         + YH      S V   G    + HRLD
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI--SEVPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++ +
Sbjct: 139 KDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLM 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P++G
Sbjct: 199 A---VHPMGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLG 248

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           D  Y        N + +F   ++N  +  LHA  + L HP  G  ++  APLP   V+  
Sbjct: 249 DQTYGGRPRPPKNAREDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 309 NALKADY 315


>gi|329120908|ref|ZP_08249540.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
 gi|327471367|gb|EGF16818.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
          Length = 328

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 83/312 (26%), Positives = 146/312 (46%), Gaps = 16/312 (5%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E  +L ++     P  +   + K LR   +  + K+   N  I+SG V+ I      L 
Sbjct: 10  DEGQKLIKFLFKLLPGASKSLIYKSLRKKNILYNNKKANGNEIIKSGDVIEIWFSDETLE 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           +  K++       N+ K S   K I+LYE+  I V NKP G+  Q        ++ +L  
Sbjct: 70  NFSKKESKEILKGNIEKFS--FKDIILYENEDIIVVNKPKGMLSQRDISRQKSLNDYLLE 127

Query: 136 WVDSK---GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           ++ +    G KP + +RLD+ TSG L+ A+T   A+ + E  +   I K Y  LV+G  K
Sbjct: 128 YIKNSNYSGFKPSICNRLDKNTSGTLICAKTFKIAREINELIKNHVINKKYLCLVFGDIK 187

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHT 249
           +    + ++L K  ++  +   V  + ++G     +   VI  F        +LE+   T
Sbjct: 188 DDL-YLKDYLFK--NVENNKAIVSNEKKEGFLEIKTKVHVIKSFKLHEYPVTFLEVTLLT 244

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH----PEGGR 304
           G+ HQ+R H  ++G PI+GD KY  N     +  ++  +  LH+  ++ P      E   
Sbjct: 245 GKFHQIRAHLSYIGHPILGDRKYGNNESLEISKILEIGRQLLHSYSIEFPENHCLKELSG 304

Query: 305 LQITAPLPAHMV 316
           ++I AP+P  ++
Sbjct: 305 MKIKAPIPKDIM 316


>gi|295098569|emb|CBK87659.1| ribosomal large subunit pseudouridine synthase A [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 210

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 72/217 (33%), Positives = 113/217 (52%), Gaps = 19/217 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 6   VILYQDEHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 62

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  +AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 63  VVALNKAAERELKRQFREREPKKQYVARVWGHPAQAEGLVDLPLI------CDWPNRPKQ 116

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++        + ++P TGR+HQLRVH L MG PI+GD ++ A 
Sbjct: 117 KVCYETG-KAAQTEYEVLEYAPDNTARVLLKPITGRSHQLRVHMLAMGHPILGD-RFYAP 174

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
            +    +P   +L LHA+ + + HP  G  +   AP+
Sbjct: 175 PEALALAP---RLQLHAQTLTITHPAFGNAMTFKAPV 208


>gi|261253959|ref|ZP_05946532.1| ribosomal large subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
 gi|260937350|gb|EEX93339.1| ribosomal large subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
          Length = 245

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 76/240 (31%), Positives = 111/240 (46%), Gaps = 40/240 (16%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ED  I V NKP+G+ SV G   +A H D      V+S     ++ HRLD +TSG+++
Sbjct: 16  IVFEDQHILVANKPSGLLSVPGR--LAEHYDSMWSRLVESYPDI-QVVHRLDMDTSGLML 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW--------LLKKS 206
            A+ + A + L + F+ R   K+Y++ VWG P+ +        IA+W          +  
Sbjct: 73  FAKHKEAERSLKKQFQYRLTHKVYYARVWGHPEQQSGQVDLPLIADWPNRPKQKVCYQDG 132

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                   VVKQ EK A                   + + P TGR+HQLRVH   +G PI
Sbjct: 133 KPSQTLYQVVKQEEKTA------------------IVRLLPITGRSHQLRVHMQALGHPI 174

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
           VGD  Y       F+     +L LHA  +   HP+   LQ T  +P       DS+ F Y
Sbjct: 175 VGDEFYSEGEAFEFSV----RLELHAAELSFYHPDSELLQ-TIFVPCDFYLEADSVIFNY 229


>gi|229824816|ref|ZP_04450885.1| hypothetical protein GCWU000182_00165 [Abiotrophia defectiva ATCC
           49176]
 gi|229790819|gb|EEP26933.1| hypothetical protein GCWU000182_00165 [Abiotrophia defectiva ATCC
           49176]
          Length = 353

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 122/254 (48%), Gaps = 29/254 (11%)

Query: 95  DFLKSI--------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---- 142
           DFLKS+        ++YED  I + NKP  +  Q        ++ +L S++ + G     
Sbjct: 103 DFLKSLKWEFDEPKVIYEDRDIIIVNKPVNVLSQIAKTGDVSMNEWLISYLINSGSLTAE 162

Query: 143 -----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
                KP + +RLD+ TSGI++  +T    + L++  + R++ K Y ++V G IP N   
Sbjct: 163 DMLTVKPAVVNRLDRNTSGIILAGKTLTGLRFLSDIIKTRKLTKYYLTIVKGEIPNN--F 220

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
               +LLK  +   + V + K   +GA Y  + ++V+         L+++  TG++HQ+R
Sbjct: 221 TAEAYLLKNDN--HNTVKIYKDKVEGAEYIKTAYEVLQV-KDGHSLLKVELITGKSHQIR 277

Query: 257 VHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEG-----GRLQITAP 310
            H   +G P++GD KY    +  N+     N  +LH+  +  P  EG          +A 
Sbjct: 278 AHLSFLGYPVIGDGKYGLKSENTNYRRMGLNTQFLHSYEIKFPKFEGEFAYLSERSFSAK 337

Query: 311 LPAHMVKTWDSLGF 324
           LP  + K  + LGF
Sbjct: 338 LPERLEKVANKLGF 351


>gi|119775737|ref|YP_928477.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119768237|gb|ABM00808.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           amazonensis SB2B]
          Length = 324

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 91/330 (27%), Positives = 147/330 (44%), Gaps = 47/330 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +  +RLD+     +P  +   L++ +  G V VD   V K   ++   QV+ I   
Sbjct: 11  ISATQTGLRLDQAIAELFPDYSRTRLKEWILGGNVYVDGVVVTKPREKVLESQVIEIEAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +        ++  LD               ++YED  I V NK AG+ V  G+G A   D
Sbjct: 71  LEEEVAAEAQEIDLD---------------IVYEDDHILVINKQAGLVVHPGAGNA---D 112

Query: 131 GFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + +          PR  + HRLD++T+G++VVA+T  A  HL  + + R I + Y 
Sbjct: 113 GTLMNALLHHCPEIEHVPRAGIIHRLDKDTTGLMVVAKTVEAQTHLVAALQARDITREYE 172

Query: 185 SLVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++V G           I     K++H+    VH           +++H++V + F +   
Sbjct: 173 AIVLGTMTAGGTVDAPIGRHPTKRTHMA---VH------HSGRPSVTHYRVAEKF-RAHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQN--KLYLHAR 293
            L ++  TGRTHQ+RVH  H+G  +VGD  Y        N    F   ++N  +  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHIGHVLVGDPVYGGRPKPPKNASPEFFEVLKNFTRQALHAV 282

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            ++L HP     +   AP+P  MV    +L
Sbjct: 283 RLELAHPVTMEIMSFNAPIPEDMVLLTKAL 312


>gi|94499372|ref|ZP_01305910.1| hypothetical protein RED65_11299 [Oceanobacter sp. RED65]
 gi|94429004|gb|EAT13976.1| hypothetical protein RED65_11299 [Oceanobacter sp. RED65]
          Length = 236

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 75/243 (30%), Positives = 117/243 (48%), Gaps = 32/243 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   NKP+G+ V   S +A     F    V D  G+     HRLD+ TSG+L+
Sbjct: 9   ILYQDDDLIAINKPSGLLVHK-SWVAKDAKEFALQIVRDMSGKHVFPVHRLDRPTSGVLL 67

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
              +   AQ +   +   +  K YW++V G    K++ + +  LK     G  V +V++ 
Sbjct: 68  FGFSGEIAQQVQAQWE--QANKTYWAVVRGW--LKEQTLVDHALKGMADYGQDVEIVQE- 122

Query: 220 EKGANYAISHFKVIDCFA----------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A +HFK ID              +F W+E +P  GRTHQ+R H  H+  PI+GD
Sbjct: 123 ------AQTHFKPIDYVEIDAEIDRYPKSRFSWVEAKPKQGRTHQIRRHLKHLSHPIIGD 176

Query: 270 HKYCANFKGNFTSPIQN-----KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
            +Y    KG +   I       +L LH + +++ HP  G +L ITAPL   M   + +  
Sbjct: 177 ARYG---KGKYNRYITEHYDCPRLLLHHQQLEMTHPVSGSKLMITAPLEGAMQSLFSTFD 233

Query: 324 FKY 326
           +K+
Sbjct: 234 WKH 236


>gi|319939285|ref|ZP_08013648.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319811681|gb|EFW07957.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 298

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 85/320 (26%), Positives = 151/320 (47%), Gaps = 50/320 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNH 76
            +RLD+   +  P ++  +  + +++GQ+ V+ +  K    +++G V+    P   AL +
Sbjct: 9   GVRLDKAVADLTP-LSRSHANEQIKNGQILVNGQVKKAKYAVKAGDVITYELPEPEALEY 67

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +                ++ L   ++Y+D  + V NK  G+ V   +G   H  G L + 
Sbjct: 68  V----------------AENLPLDIVYQDEDVAVVNKAQGMVVHPSAG---HTSGTLVNA 108

Query: 137 V-----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +     D  G     +P + HR+D++TSG+L++A+   A   L E  + ++  + YW++V
Sbjct: 109 LMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHIKLAEELKDKKSLRKYWAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEM 245
            G   N +  I      ++ IG       KQ    KG   A++ F V++ F   +  +E+
Sbjct: 169 HGNLPNDRGVI------EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGN-YTLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           Q  TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHAR +   HP+  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPRKTLKGHGQ-------FLHARTLGFTHPKTA 273

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             ++ TA  PA   +T + L
Sbjct: 274 EVMEFTAEAPAIFQETLEKL 293


>gi|83855236|ref|ZP_00948766.1| ribosomal large subunit pseudouridine synthase A [Sulfitobacter sp.
           NAS-14.1]
 gi|83941758|ref|ZP_00954220.1| ribosomal large subunit pseudouridine synthase A [Sulfitobacter sp.
           EE-36]
 gi|83843079|gb|EAP82246.1| ribosomal large subunit pseudouridine synthase A [Sulfitobacter sp.
           NAS-14.1]
 gi|83847578|gb|EAP85453.1| ribosomal large subunit pseudouridine synthase A [Sulfitobacter sp.
           EE-36]
          Length = 215

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 66/207 (31%), Positives = 106/207 (51%), Gaps = 18/207 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++L+ED+++ + +KPAG+    G G   H+   L + V        L HRLD++TSG+++
Sbjct: 13  VVLHEDAEVLLVDKPAGLLSVPGKG--PHLADCLIARVQDAFPDALLVHRLDRDTSGVMI 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A T  A +HL   F  R  +K Y + VWG+P+ K   I   L+       D+ +  +Q 
Sbjct: 71  FALTPHAQRHLGLQFEKRMTRKTYVARVWGVPQEKTGTIDLPLIV------DWPNRPRQM 124

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +E G   A + ++V+         + + P TGR+HQLRVH L +G PI+GD  Y    
Sbjct: 125 VCHETG-KPAQTDWRVLKDEGDT-ARVRLSPKTGRSHQLRVHMLSLGHPILGDPFYATGP 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +      +L LH+  +   HP+GG
Sbjct: 183 ALAYP-----RLMLHSEELRFNHPQGG 204


>gi|320103316|ref|YP_004178907.1| pseudouridine synthase [Isosphaera pallida ATCC 43644]
 gi|319750598|gb|ADV62358.1| pseudouridine synthase [Isosphaera pallida ATCC 43644]
          Length = 285

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 118/237 (49%), Gaps = 15/237 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
            ++ + LYED+ + V +KPAG+  QG       +  + +  +  +  KP      LTHRL
Sbjct: 1   MIEPLRLYEDNHLLVVSKPAGLLSQGDRTGDPDLTTWARDDLKRRYNKPGGVFVGLTHRL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-----NKKECIANWLLKK 205
           D+  SG++++ART  AA  L + FR   I+K Y +++   P       +   + ++LLK 
Sbjct: 61  DRPVSGLVILARTGKAAARLAQQFRAGTIRKRYVAVLESSPNASFRFEESGILEDYLLKL 120

Query: 206 SHIGGDYV--HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           S      V        E G   AIS + V++ + Q++  + ++P TGR HQLR      G
Sbjct: 121 SDSNRSSVLGESRGHAESGTRQAISSYMVLERW-QRYLLILLEPVTGRFHQLRAQTASRG 179

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
            PI GD KY A+ +    +    ++ LH+  ++  HP    R++++AP P+     W
Sbjct: 180 WPIAGDVKYGAS-RALRAADGYGRIALHSWQVEFEHPTRRERMRLSAPKPSDWPAGW 235


>gi|315634974|ref|ZP_07890255.1| ribosomal large subunit pseudouridine synthase D [Aggregatibacter
           segnis ATCC 33393]
 gi|315476236|gb|EFU66987.1| ribosomal large subunit pseudouridine synthase D [Aggregatibacter
           segnis ATCC 33393]
          Length = 324

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 120/242 (49%), Gaps = 27/242 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           ++YED  I V NKP  + V  G+G      ++  L  +     + PR  + HRLD++T+G
Sbjct: 85  IVYEDEDILVINKPKDLVVHPGAGNPKGTVLNALLYHY-PQIAEVPRAGIVHRLDKDTTG 143

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYV 213
           ++VVA+T  A   L    + R+I + Y ++  GI        E +A    K++H+    V
Sbjct: 144 LMVVAKTIPAQTQLVRDLQKRKITREYEAVACGIMTKGGTVDEPMARHPTKRTHMA---V 200

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  Y 
Sbjct: 201 HPMGKP------AVTHYRIMERF-RDYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYG 253

Query: 274 A------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
                  N        ++N  +  LHA  + L HP  G  ++  APLP   V+   +L  
Sbjct: 254 GRPRPPKNASEELMEVLRNFKRQALHAVMLRLQHPISGEMMEWYAPLPDDFVELVTALKA 313

Query: 325 KY 326
            Y
Sbjct: 314 DY 315


>gi|325577679|ref|ZP_08147954.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325160424|gb|EGC72550.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 324

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 123/244 (50%), Gaps = 31/244 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +        + PR  + HRLD++T
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAG---NPDGTVLNALLYHYPPIAEVPRAGIVHRLDKDT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++ +   
Sbjct: 142 TGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLMA-- 199

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 200 -VHPMGKP------AVTHYRIMENF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQT 251

Query: 272 YCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y        N    FT  ++N  +  LHA  + L HP  G  ++  APLP   V+   +L
Sbjct: 252 YGGRPRPPKNASKAFTEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELLHAL 311

Query: 323 GFKY 326
              Y
Sbjct: 312 KADY 315


>gi|294142197|ref|YP_003558175.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           violacea DSS12]
 gi|293328666|dbj|BAJ03397.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           violacea DSS12]
          Length = 324

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 87/319 (27%), Positives = 145/319 (45%), Gaps = 53/319 (16%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD+   + +P  +   +++ +  G V +D     K   ++  GQ+V    V+ A   ++
Sbjct: 19  RLDQTLADLFPDYSRTRIKEWILDGSVTIDGDVSNKPREKVLEGQIV----VVGAT--LV 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
           +E      +++L          ++YED  I V NK AG+ V  G+G         + +H 
Sbjct: 73  EETTAKAQAIDLN---------IVYEDDHILVINKQAGLVVHPGAGNSDGTLLNALLHHC 123

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G     V   G    + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V G
Sbjct: 124 PGI--ELVPRAG----IVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAIVLG 177

Query: 190 ---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                    E I     K++H+   Y             A++HF+V + F +    L ++
Sbjct: 178 SLISGGTVDEPIDRHPTKRTHMAVVY---------SGKPAMTHFRVAEKF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLY-------LHARYMDLP 298
             +GRTHQ+RVH  H+G  +VGD  Y    +     +P    +Y       LHA  ++L 
Sbjct: 228 LESGRTHQIRVHMAHLGHTLVGDPVYGGRPRPPKAVTPEFFDVYMNFKRQALHAIRLELA 287

Query: 299 HPEGGRLQI-TAPLPAHMV 316
           HP    +    AP+P  MV
Sbjct: 288 HPYTCEIMSWQAPVPEDMV 306


>gi|88800777|ref|ZP_01116334.1| pseudouridine synthase [Reinekea sp. MED297]
 gi|88776483|gb|EAR07701.1| pseudouridine synthase [Reinekea sp. MED297]
          Length = 328

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 87/333 (26%), Positives = 153/333 (45%), Gaps = 40/333 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V N+    R D+     +   +   +Q+ ++ G++ V+ K +K  +++  G+ + +   
Sbjct: 13  IVPNELGQKRFDQIAAQLFADYSRSRIQQWIKEGRLTVNGKTLKPRDKLIGGETLTLDVT 72

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-- 128
           + +      +++     V L          ++YED +I V +KPAG+ V  G+G      
Sbjct: 73  LES------DERWEAEPVELN---------VVYEDEQIIVIDKPAGLVVHPGAGTPSGTV 117

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           ++G L  + +     PR  + HRLD++T+G++VVART  A  HL    + R + + Y++L
Sbjct: 118 LNGLLYRYPELAA-VPRAGIVHRLDKDTTGLMVVARTLTAQTHLAGQLQDRSMGREYYAL 176

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWL 243
             G+       + N  + + H        V     G + AI+H++V   F       C L
Sbjct: 177 CMGVMTGG--GVVNEPIDR-HPKHRTKMAVAPTGMGKD-AITHYRVEQRFRNHTLVRCKL 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKL------YLHARYM 295
           E    TGRTHQ+RVH  H+G P+VGD  Y   +      +  +   L       LHA Y+
Sbjct: 233 E----TGRTHQIRVHLSHIGYPLVGDPLYAGRSRLPKGISPEVMTVLKAFKRQALHAGYL 288

Query: 296 DLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYD 327
           +L HP    +    + LP   +   D+L  + D
Sbjct: 289 ELIHPATDEMVSWESDLPEDFLGLLDALQEEVD 321


>gi|291166075|gb|EFE28121.1| pseudouridine synthase, RluA family [Filifactor alocis ATCC 35896]
          Length = 298

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 115/219 (52%), Gaps = 16/219 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGI 157
           ++YED  I   NK   I V   G+ +   +  +++SW    G  +K R   RLD++TSGI
Sbjct: 85  VIYEDEDIVAVNKSPFIVVHPTGTHLTGTLLNYMESWFRQNGILEKVRFISRLDRDTSGI 144

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+ R A   ++++ +   +QK Y +L+ G  K ++  I   + ++ + G     + +
Sbjct: 145 LLIAKNRYAHHRMSQAHQDMMMQKTYVALIEGKMKRQEGEINAPIGRRENDG-----IKR 199

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +  +    AI+ +KV+    +KF  +E+ P TGRTHQLR H  ++G P++GD  Y  N +
Sbjct: 200 EVMEDGQTAITKYKVLKE-GEKFSLVELTPVTGRTHQLRCHMAYIGYPLIGDSLYGGNME 258

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                   N+  LH+  ++   P +  ++ + A LP  M
Sbjct: 259 ------YMNRQALHSVTLEFFSPRKEEKIYLKAELPQDM 291


>gi|229591788|ref|YP_002873907.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens SBW25]
 gi|229363654|emb|CAY50999.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens SBW25]
          Length = 211

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 71/214 (33%), Positives = 113/214 (52%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D+ + V NKP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   ILYQDAAVLVVNKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P+     I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALAWGQPELDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEFGKHALTFWKVLE-RCGDWCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHEQAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
              P   +L LHA  +   HP+ G RL+   P P
Sbjct: 180 AAWP---RLCLHASMLSFTHPQSGERLRFECPAP 210


>gi|22124820|ref|NP_668243.1| 23S rRNA pseudouridine synthase D [Yersinia pestis KIM 10]
 gi|108808759|ref|YP_652675.1| 23S rRNA pseudouridine synthase D [Yersinia pestis Antiqua]
 gi|108810984|ref|YP_646751.1| 23S rRNA pseudouridine synthase D [Yersinia pestis Nepal516]
 gi|153997673|ref|ZP_02022773.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           CA88-4125]
 gi|165926534|ref|ZP_02222366.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165936735|ref|ZP_02225302.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166010204|ref|ZP_02231102.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166213045|ref|ZP_02239080.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167398582|ref|ZP_02304106.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167421637|ref|ZP_02313390.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167423313|ref|ZP_02315066.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|167470273|ref|ZP_02334977.1| 23S rRNA pseudouridine synthase D [Yersinia pestis FV-1]
 gi|218930302|ref|YP_002348177.1| 23S rRNA pseudouridine synthase D [Yersinia pestis CO92]
 gi|229838893|ref|ZP_04459052.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229899460|ref|ZP_04514603.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229901200|ref|ZP_04516323.1| 23S rRNA pseudouridine synthase [Yersinia pestis Nepal516]
 gi|270489385|ref|ZP_06206459.1| pseudouridine synthase, RluA family [Yersinia pestis KIM D27]
 gi|294504991|ref|YP_003569053.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           Z176003]
 gi|34395805|sp|Q8ZBV7|RLUD_YERPE RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|21957646|gb|AAM84494.1|AE013693_10 suppressor of ftsH mutation [Yersinia pestis KIM 10]
 gi|108774632|gb|ABG17151.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           Nepal516]
 gi|108780672|gb|ABG14730.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           Antiqua]
 gi|115348913|emb|CAL21870.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           CO92]
 gi|149289310|gb|EDM39390.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           CA88-4125]
 gi|165915384|gb|EDR33994.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|165921462|gb|EDR38659.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165991111|gb|EDR43412.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166205832|gb|EDR50312.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166960556|gb|EDR56577.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167051086|gb|EDR62494.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167057483|gb|EDR67229.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|229681925|gb|EEO78018.1| 23S rRNA pseudouridine synthase [Yersinia pestis Nepal516]
 gi|229687862|gb|EEO79935.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229695259|gb|EEO85306.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|262363056|gb|ACY59777.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           D106004]
 gi|262366980|gb|ACY63537.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           D182038]
 gi|270337889|gb|EFA48666.1| pseudouridine synthase, RluA family [Yersinia pestis KIM D27]
 gi|294355450|gb|ADE65791.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           Z176003]
 gi|320016469|gb|ADW00041.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 325

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 91/332 (27%), Positives = 155/332 (46%), Gaps = 47/332 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V V+ K++ K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKVLGGELVAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        ++  LD               ++YED+ I V NKP G+ V  G+G   +
Sbjct: 69  AQIEEDARWAPQEIPLD---------------IVYEDNDILVINKPRGLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + 
Sbjct: 111 PDGTVLNALLHYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH + +       A +H+++++ F + 
Sbjct: 171 YEAVAIGNMTAGGRVDEPISRHSTKRTHMA---VHPMGKP------ATTHYRIMEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y       KG   S I      ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDSFIAILRGFDRQALH 280

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           A  + L HP  G +++  A LP  MV+  ++L
Sbjct: 281 ATMLRLYHPIRGIQMEWHAALPEDMVELINAL 312


>gi|289627475|ref|ZP_06460429.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aesculi str. NCPPB3681]
 gi|289646428|ref|ZP_06477771.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aesculi str. 2250]
 gi|330868108|gb|EGH02817.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aesculi str. 0893_23]
          Length = 211

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 70/214 (32%), Positives = 111/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIYQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HQGGKHALTFWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              P   +L LHA  +   HP  G RL    P P
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|330891514|gb|EGH24175.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. mori str. 301020]
          Length = 211

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 70/214 (32%), Positives = 111/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIYQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDPPL--RYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEGGKHALTFWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              P   +L LHA  +   HP  G RL    P P
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|89075039|ref|ZP_01161480.1| putative ribosomal large subunit pseudouridine synthase D
           [Photobacterium sp. SKA34]
 gi|89049126|gb|EAR54691.1| putative ribosomal large subunit pseudouridine synthase D
           [Photobacterium sp. SKA34]
          Length = 324

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 94/333 (28%), Positives = 154/333 (46%), Gaps = 51/333 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
            V  ++  MRLD+     YP  +   ++  + +G V V+   VK    ++  G+ + I  
Sbjct: 10  TVGENQLGMRLDQVIAQLYPDYSRSRIKDWILNGMVSVNGDVVKKPREKMMGGEELFIQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I      + +   LD               ++YED  I V NKP    V  G+G     
Sbjct: 70  EIEDEVRWVAQDIPLD---------------IVYEDDDILVINKPRDFVVHPGAGTP--- 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +  S  + PR  + HRLD++T+G++VVA+T  A   L  + + R+I + Y
Sbjct: 112 DGTILNALLHYCPSLAEVPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-----NEKGANYAISHFKVIDCFAQ 238
            +L  G      +      ++K  IG    H  K+     +E G + AI+H++V + F +
Sbjct: 172 EALAIG------QMTGGGTIEKP-IGR---HSTKRICMAVHEMGKD-AITHYRVAERF-R 219

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQ--NKLYL 290
           +   + ++  TGRTHQ+RVH  +M  P++GD  Y        +    F   ++  ++  L
Sbjct: 220 EHTRIVLRLETGRTHQIRVHMSYMSHPLIGDVIYGGRPRPPRDASPEFIQALRAFDRQAL 279

Query: 291 HARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           HAR + L HP  G +++  APLP  MV   D L
Sbjct: 280 HARMLRLDHPITGEKMEWHAPLPIDMVAMIDIL 312


>gi|224532575|ref|ZP_03673198.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi WI91-23]
 gi|224512518|gb|EEF82896.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi WI91-23]
          Length = 326

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 56/181 (30%), Positives = 99/181 (54%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 86  IIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +RI K+Y ++V G   +    I +++ +  H    
Sbjct: 145 KDTSGVLICAKNISTLRFLAQQFKDKRINKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 205 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 259

Query: 272 Y 272
           Y
Sbjct: 260 Y 260


>gi|325143909|gb|EGC66219.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M01-240013]
          Length = 356

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 82/307 (26%), Positives = 138/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 22  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 69

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 70  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 126

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T +A   L    + R +++IY ++  GI P + 
Sbjct: 127 PELSQIPRAGIVHRLDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDG 186

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 187 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 237

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C +        +  +  LHA  +   HP+ G  +
Sbjct: 238 HQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPKTGETV 297

Query: 306 QITAPLP 312
              AP+P
Sbjct: 298 SFEAPIP 304


>gi|320327741|gb|EFW83749.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330877702|gb|EGH11851.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|331012591|gb|EGH92647.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 211

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 70/214 (32%), Positives = 111/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIYQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEGGKHALTFWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              P   +L LHA  +   HP  G RL    P P
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|149915492|ref|ZP_01904019.1| DNA mismatch repair protein [Roseobacter sp. AzwK-3b]
 gi|149810781|gb|EDM70622.1| DNA mismatch repair protein [Roseobacter sp. AzwK-3b]
          Length = 215

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 105/208 (50%), Gaps = 22/208 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED +I V NKPAG+    G G   H+   L + V        L HRLD++TSG++V 
Sbjct: 14  VLHEDHEILVVNKPAGLLSVPGKG--PHLADCLIARVQEAFPNALLVHRLDRDTSGVMVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A +  A +HL   F  R+++K Y + VWG+ + K        I +W  +          +
Sbjct: 72  ALSPHAQRHLGLQFEKRQMKKTYVARVWGMLEPKTGTVDLPLIVDWPNRP---------L 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K   +    A++ ++V+    +    + + P TGR+HQLRVH L +G PI+GD  Y + 
Sbjct: 123 QKVCHETGKPALTDWRVLR-HVKGETRVRLAPKTGRSHQLRVHMLALGHPILGDPLYASG 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +       +L LH+  + L HP+GG
Sbjct: 182 AAAD-----HPRLMLHSEELRLRHPDGG 204


>gi|307704763|ref|ZP_07641659.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
 gi|307621672|gb|EFO00713.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
          Length = 298

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 114/219 (52%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLETEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|304414306|ref|ZP_07395674.1| 23S rRNA pseudouridine synthase [Candidatus Regiella insecticola
           LSR1]
 gi|304283520|gb|EFL91916.1| 23S rRNA pseudouridine synthase [Candidatus Regiella insecticola
           LSR1]
          Length = 325

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 76/240 (31%), Positives = 125/240 (52%), Gaps = 31/240 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V NKP G+ V  G+G A   DG     L  +  +    PR  + HRLD++T
Sbjct: 86  IVYEDNDILVINKPRGLVVHPGAGNA---DGTILNALLHYYPAISNVPRAGIIHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL E+ + R+I + Y ++  G        +E IA    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVEALQARKITREYEAIAIGNMIAGGAVEEPIARHASKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH   +  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RAHTHLRLRLETGRTHQIRVHMSFIRHPLVGDPL 252

Query: 272 YCANF---KGNFTSPIQ-----NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y +     KG   + I+     ++  LHA  + L HP  G  ++  A LP  +V    +L
Sbjct: 253 YGSRACHPKGASDAFIKILRGFDRQALHASMLRLKHPISGIEMEWRAALPQDIVDLISAL 312


>gi|329120441|ref|ZP_08249106.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327461899|gb|EGF08229.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 373

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 81/304 (26%), Positives = 140/304 (46%), Gaps = 47/304 (15%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
           P  +   L   ++ G V VD K  +  +++  G+ + +              ++ + +  
Sbjct: 50  PDYSRSRLAGWIKEGAVAVDGKAARPKDKLIGGETLAV--------------RVRERNET 95

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR-- 145
           L    + +   ++YED  + V +KPAG+ V   +G      ++G L ++  +    PR  
Sbjct: 96  LAFTPEPMDLDIVYEDDSVMVLDKPAGLVVHPAAGNWSGTLLNGLL-AYCPALQNVPRAG 154

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLK 204
           + HRLD++TSG++VVA+T AA   L    + R +++IY ++  GI P + K         
Sbjct: 155 IVHRLDKDTSGLMVVAKTLAAQTDLVRQMQARSVKRIYRAVADGIVPFDGK--------I 206

Query: 205 KSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           ++ IG D  +  K      G   A++H KV++ +     ++E    TGRTHQ+RVH    
Sbjct: 207 ETLIGRDPHNRTKMAVVGFGGKEAVTHVKVLERYL-AHSYIECALETGRTHQIRVHMREA 265

Query: 263 GCPIVGDHKYCANFKGNFTSPIQN----------KLYLHARYMDLPHPEGGR-LQITAPL 311
             P+ GD  Y     GN   P  +          +  LHA  +   HP+ G  ++  APL
Sbjct: 266 RHPLAGDPVY-----GNLRHPASDIVKTAVRGLGRQALHAYRLSFAHPQSGETMRFEAPL 320

Query: 312 PAHM 315
           PA +
Sbjct: 321 PADI 324


>gi|240948986|ref|ZP_04753340.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           minor NM305]
 gi|240296573|gb|EER47191.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           minor NM305]
          Length = 222

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 67/207 (32%), Positives = 107/207 (51%), Gaps = 13/207 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+     +  V  K       HRLD  TSGIL+ A
Sbjct: 17  VYRDNHILVINKPSGLLSVPGNRPEYYDSAMTR--VQQKYGFTEPAHRLDMATSGILLFA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            ++ A + L   FR R  +K Y +L+WG      E + +  +    +  D+ +  +Q   
Sbjct: 75  LSKVAEKELKRQFREREPKKHYIALLWG---KLGERVGDKGVMNFPLICDWENRPRQKIC 131

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   A++H++V+         +++ P TGR+HQLRVH+L +G PI+GD K+ AN   
Sbjct: 132 YERGKK-AVTHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGD-KFYAN--- 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRL 305
                + ++L LHA  + + HP  G L
Sbjct: 187 PLAKSLASRLCLHAESLTITHPITGEL 213


>gi|330985554|gb|EGH83657.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. lachrymans str. M301315]
          Length = 211

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/214 (32%), Positives = 111/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIYQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSPDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEGGKHALTLWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              P   +L LHA  +   HP  G RL    P P
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|322831462|ref|YP_004211489.1| pseudouridine synthase, RluA family [Rahnella sp. Y9602]
 gi|321166663|gb|ADW72362.1| pseudouridine synthase, RluA family [Rahnella sp. Y9602]
          Length = 325

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 88/332 (26%), Positives = 152/332 (45%), Gaps = 47/332 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   ++  +   +V V+ K+V K   ++  G+ + I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKDWILEDRVTVNGKKVTKPKEKVLGGEAIAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I       +E + L   + L          ++YED+ I V NKP  + V  G+G   +
Sbjct: 69  AQIE------EEARWLPQDIALD---------IVYEDTDILVINKPRDLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +  +    PR  + HRLD++T+G++VVA++  A  HL  + + R I + 
Sbjct: 111 PDGTVLNALLHYYPAIIDVPRCGIVHRLDKDTTGLMVVAKSVPAQTHLVTALQAREITRE 170

Query: 183 YWSLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E IA    K++H+    VH   +       A +H+++++ F + 
Sbjct: 171 YEAVAIGTMTAGGTVNEPIARHSTKRTHMA---VHPTGKP------ATTHYRIMEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKL------YLH 291
              L ++  +GRTHQ+RVH  H+  P++GD  Y          + P  N L       LH
Sbjct: 221 HTRLRLRLESGRTHQIRVHMAHINHPLLGDQLYGGRPRLPKGASEPFINMLRGFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A  + L HP  G +++  AP+P  MV   ++L
Sbjct: 281 ATMLRLYHPVTGIQMEWHAPIPQDMVDLINAL 312


>gi|145641509|ref|ZP_01797087.1| SfhB [Haemophilus influenzae R3021]
 gi|145273800|gb|EDK13668.1| SfhB [Haemophilus influenzae 22.4-21]
          Length = 324

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 121/247 (48%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP  + V  G+G         + YH      S V   G    + HRLD
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI--SEVPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++ +
Sbjct: 139 KDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLM 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P++G
Sbjct: 199 A---VHPIGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLG 248

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           D  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+  
Sbjct: 249 DQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 309 NALKADY 315


>gi|216264271|ref|ZP_03436263.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 156a]
 gi|215980744|gb|EEC21551.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 156a]
          Length = 326

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 56/181 (30%), Positives = 99/181 (54%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 86  IIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +RI K+Y ++V G   +    I +++ +  H    
Sbjct: 145 KDTSGVLICAKNISTLRFLAQQFKDKRINKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 205 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 259

Query: 272 Y 272
           Y
Sbjct: 260 Y 260


>gi|331701446|ref|YP_004398405.1| RluA family pseudouridine synthase [Lactobacillus buchneri NRRL
           B-30929]
 gi|329128789|gb|AEB73342.1| pseudouridine synthase, RluA family [Lactobacillus buchneri NRRL
           B-30929]
          Length = 302

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 82/301 (27%), Positives = 142/301 (47%), Gaps = 36/301 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+        I+    + ++    ++++ + VK   +++SG  +++  V      +  
Sbjct: 12  RLDKVISELDSSISRSRAKNLIDDQHLKINGEPVKPKYQVKSGDKIQVDSVQPTPISLEP 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL--KS 135
           E   LD               ++YED  + V NKP G+ V    G   H  ++  L    
Sbjct: 72  ENMPLD---------------IVYEDDDVIVVNKPQGMVVHPSPGHPDHTLVNALLYHSP 116

Query: 136 WVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                G+ +P + HR+D++TSG+L+VA+   A Q L++  + ++  + Y +LV G  K +
Sbjct: 117 LSTINGEFRPGIVHRIDKDTSGLLMVAKNDKAHQFLSQQLQAQKNLRKYVALVHGRIK-E 175

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              + N  + +S        VV         A++HF+V++ FA  +  +  +  TGRTHQ
Sbjct: 176 DSGVVNAPIGRSPKDRKKQAVVSDGRS----AVTHFEVLERFAD-YTLVACRLETGRTHQ 230

Query: 255 LRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAPL 311
           +RVH  ++G PIVGD  Y      +GN         +LHA+ +   HP   +L I +APL
Sbjct: 231 IRVHMKYIGHPIVGDPLYGPRKTIRGNGQ-------FLHAQELGFEHPRTHQLMIFSAPL 283

Query: 312 P 312
           P
Sbjct: 284 P 284


>gi|325206453|gb|ADZ01906.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M04-240196]
          Length = 374

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 82/307 (26%), Positives = 138/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T +A   L    + R +++IY ++  GI P + 
Sbjct: 145 PELSQIPRAGIVHRLDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C +        +  +  LHA  +   HP+ G  +
Sbjct: 256 HQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPKTGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|152968638|ref|YP_001333747.1| 23S rRNA/tRNA pseudouridine synthase A [Klebsiella pneumoniae
           subsp. pneumoniae MGH 78578]
 gi|238893033|ref|YP_002917767.1| 23S rRNA/tRNA pseudouridine synthase A [Klebsiella pneumoniae
           NTUH-K2044]
 gi|262044907|ref|ZP_06017949.1| pseudouridine synthase A [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|330009270|ref|ZP_08306486.1| pseudouridine synthase A [Klebsiella sp. MS 92-3]
 gi|150953487|gb|ABR75517.1| 23S rRNA pseudouridylate 746 synthase [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238545349|dbj|BAH61700.1| 23S rRNA pseudouridylate 746 synthase [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|259037634|gb|EEW38863.1| pseudouridine synthase A [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|328534847|gb|EGF61389.1| pseudouridine synthase A [Klebsiella sp. MS 92-3]
          Length = 219

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/214 (32%), Positives = 109/214 (50%), Gaps = 13/214 (6%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDFPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  +AA + L   FR R  +K Y + VWG P+   E + +  L           V  +
Sbjct: 72  VVALNKAAERELKRQFREREPKKQYVARVWGHPQ-PAEGLVDLPLICDWPNRPMQKVCYE 130

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K A    + ++V++        + ++P TGR+HQLRVH L +G PI+GD ++ A  + 
Sbjct: 131 TGKAAQ---TEYEVLEYAEDNTARVRLKPITGRSHQLRVHMLALGHPILGD-RFYATPEA 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
              +P   +L LHA  + + HP  G  +   AP+
Sbjct: 187 LAMAP---RLLLHAETLTITHPAYGNAMTFRAPI 217


>gi|307708761|ref|ZP_07645223.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus mitis NCTC 12261]
 gi|307615127|gb|EFN94338.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus mitis NCTC 12261]
          Length = 298

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 114/219 (52%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLEQEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|312149435|gb|ADQ29506.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi N40]
          Length = 326

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 56/181 (30%), Positives = 99/181 (54%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 86  IIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +RI K+Y ++V G   +    I +++ +  H    
Sbjct: 145 KDTSGVLICAKNISTLRFLAQQFKDKRINKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 205 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 259

Query: 272 Y 272
           Y
Sbjct: 260 Y 260


>gi|226328713|ref|ZP_03804231.1| hypothetical protein PROPEN_02608 [Proteus penneri ATCC 35198]
 gi|225201899|gb|EEG84253.1| hypothetical protein PROPEN_02608 [Proteus penneri ATCC 35198]
          Length = 325

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 76/240 (31%), Positives = 120/240 (50%), Gaps = 31/240 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +          PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLYRYPEIANVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL E+ + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVEALQRREITREYEAVATGRMTAGGLVNEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH +         A++H++V++ F +    L ++  TGRTHQ+RVH  H+   ++GD  
Sbjct: 201 -VHPM------GKPAVTHYRVMEHF-RAHTRLRLRLETGRTHQIRVHMAHIHHALIGDQL 252

Query: 272 YCAN---FKG-----NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y       KG       T  + ++  LHA  + L HP  G  ++  APLP  MVK  D L
Sbjct: 253 YAGRPRPLKGASDELRETLRLFDRQALHATMLRLYHPITGIEMEWHAPLPDDMVKLIDVL 312


>gi|149184985|ref|ZP_01863302.1| pseudouridylate synthase [Erythrobacter sp. SD-21]
 gi|148831096|gb|EDL49530.1| pseudouridylate synthase [Erythrobacter sp. SD-21]
          Length = 218

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 116/233 (49%), Gaps = 32/233 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHID----GFLKSWVDSKGQKPRLTHRLDQ 152
           +++ED +  V +KPAG+SV    +GG  +  H +    GF +         P   HRLD 
Sbjct: 6   IIFEDGEALVIDKPAGLSVDRPKRGGPCLEDHFEQLKLGFQRP--------PAAVHRLDT 57

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG L++AR   A +   ++F  R ++K Y  ++ GIP  ++  IA  L K S  G  +
Sbjct: 58  DTSGCLLLARNPKALKRFAKAFEDRLVEKRYLGVLAGIPDGEEGTIALSLSKISSAGKGW 117

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA-LHMGCPIVGDHK 271
             +  +  K    +++H++ +     K   LE +P TGRTHQ+R+H    +G P++GD  
Sbjct: 118 RMIAAKKGK---PSVTHWRKLMEHDGK-ALLEFRPETGRTHQIRIHCEAGLGLPLLGDPV 173

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           Y    KG        +  LHA  + +P      ++  APLP    + + +LGF
Sbjct: 174 Y-GTGKG------APRTMLHAAGLMVPRESKPAIEAAAPLP----RDFAALGF 215


>gi|281420977|ref|ZP_06251976.1| ribosomal large subunit pseudouridine synthase D [Prevotella copri
           DSM 18205]
 gi|281404895|gb|EFB35575.1| ribosomal large subunit pseudouridine synthase D [Prevotella copri
           DSM 18205]
          Length = 387

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 84/320 (26%), Positives = 148/320 (46%), Gaps = 55/320 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+ +++ +R+D++  +   + +   +Q+   +G + V+ K VK N +++   +V +  
Sbjct: 56  VQVDANQDPVRIDKYLADKMAYQSRNRIQQAADAGFIHVNGKPVKSNYKVRPNDLVTL-- 113

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    E  I    + +          ++YED ++ V NK AG+ V  G+G     
Sbjct: 114 ---MLDRPRHETSIKPEEIAIN---------VVYEDDQLMVVNKEAGMVVHPGAGNFHGT 161

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H+    +   D+   +  L HR+D++TSG+LVVA+T  A   L + F  +   
Sbjct: 162 LIQAVAWHLRDMPE--FDANDPEVGLVHRIDKDTSGLLVVAKTPTAKNALGKQFFNKTTH 219

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDC 235
           + Y +LVWG        + +    + +IG D      + V   +      A++H+KV++ 
Sbjct: 220 RSYNALVWG------NIVEDEGRIEGNIGRDPKNRLRMKVFDPDSGIGKTAVTHYKVLER 273

Query: 236 FAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----IQN 286
           F       C LE    TGRTHQ+R H  H+G P+  D  Y      +G  +S     IQN
Sbjct: 274 FGYTTLVQCVLE----TGRTHQIRAHMKHIGHPLFMDETYGGTEILRGQRSSSYKAFIQN 329

Query: 287 ------KLYLHARYMDLPHP 300
                 +  LHA+ +   HP
Sbjct: 330 CFKLCPRQALHAKTLGFVHP 349


>gi|145297342|ref|YP_001140183.1| ribosomal large subunit pseudouridine synthase D [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142850114|gb|ABO88435.1| ribosomal large subunit pseudouridine synthase D [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 326

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 116/232 (50%), Gaps = 27/232 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           ++YED  I V +KPAG+ V  G+G      ++  L  + D   + PR  + HRLD++T+G
Sbjct: 86  IVYEDEHILVIDKPAGLVVHPGAGTPDGTILNALLHRYPDI-AEVPRAGIVHRLDKDTTG 144

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYV 213
           ++VVA+T  A  HL E+ + R+I + Y ++  G           I     +++H+     
Sbjct: 145 LMVVAKTVPAQTHLVEALQARQITREYEAIAIGHMTAGGTVDAPIGRHPTQRTHMA---- 200

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            VV         +++H++V + F +    L ++  TGRTHQ+RVH  H+  P+VGD  Y 
Sbjct: 201 -VVPNGRP----SVTHYRVHEKF-RGHTRLRLRLETGRTHQIRVHMSHIKHPLVGDPAYG 254

Query: 274 ANFKG--NFTSPIQ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
              +   N T  +       N+  LHA  + L HP  G  +Q  +P P  M+
Sbjct: 255 GRLRPLRNATPELTLALRNFNRQALHATMLQLAHPITGEVMQWHSPTPQDML 306


>gi|326572905|gb|EGE22890.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis CO72]
          Length = 242

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 119/229 (51%), Gaps = 23/229 (10%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +F KSI +YED  I+V +KPAG+    G  +       L+S +       RL HRLD +T
Sbjct: 25  EFAKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPNIRLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDY 212
           SG+++ A++  A  H+++ F  R  QK Y ++V+G  +  +KK  +   +  +      +
Sbjct: 81  SGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVPVRYEPTTKPRH 140

Query: 213 VHVVKQNEKGANYAISHFKVI--------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +  +  N++    A++H++V+        +  A     + ++P TGR+HQLRVH LH+G 
Sbjct: 141 IVDMDWNKR----ALTHYEVMHHELRCDDNSRAYPVTRVALKPITGRSHQLRVHMLHLGH 196

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            ++GD  Y  +     +    N+L LHA  + L HP  G  +   +P+P
Sbjct: 197 VMIGDPIYAEDVALKLS----NRLNLHAHKLRLKHPMHGIWMDWVSPVP 241


>gi|322514814|ref|ZP_08067833.1| pseudouridine synthase A [Actinobacillus ureae ATCC 25976]
 gi|322119196|gb|EFX91337.1| pseudouridine synthase A [Actinobacillus ureae ATCC 25976]
          Length = 226

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 68/207 (32%), Positives = 106/207 (51%), Gaps = 13/207 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+     +        +P   HRLD  TSGIL+ A
Sbjct: 21  VYRDNHILVINKPSGLLSVPGNRPEYYDSAMTRVQQKYGFTEP--AHRLDMATSGILLFA 78

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            ++AA + L   FR R  +K Y +L+WG      E + +       +  D+ +  +Q   
Sbjct: 79  LSKAAEKELKRQFREREPKKHYIALLWG---KLGEKVGDTGEMNFPLICDWENRPRQKIC 135

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   AI+H++V+         +++ P TGR+HQLRVH L +G PI+GD K+ AN   
Sbjct: 136 YERGKK-AITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHLLALGHPILGD-KFYANPLA 193

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRL 305
              +P   +L LHA  + + HP  G +
Sbjct: 194 KSLAP---RLCLHAESLTITHPISGEV 217


>gi|218249610|ref|YP_002374552.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi ZS7]
 gi|226321152|ref|ZP_03796693.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 29805]
 gi|218164798|gb|ACK74859.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi ZS7]
 gi|226233444|gb|EEH32184.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 29805]
          Length = 326

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 56/181 (30%), Positives = 99/181 (54%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 86  IIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +RI K+Y ++V G   +    I +++ +  H    
Sbjct: 145 KDTSGVLICAKNISTLRFLAQQFKDKRINKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 205 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 259

Query: 272 Y 272
           Y
Sbjct: 260 Y 260


>gi|332298758|ref|YP_004440680.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332181861|gb|AEE17549.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 254

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 107/226 (47%), Gaps = 24/226 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG-FLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  I V NK +G+ V       Y  D   L +    +  K    HR+D++TSGI++
Sbjct: 9   VLYGDDSIVVLNKRSGLLVAADR---YDPDAPRLDTAASDEFGKLYAVHRIDKDTSGIVI 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            ART  A + L+  F+ R ++K+Y +LV G P  +   +   L+      GD  H    N
Sbjct: 66  YARTAEAHRVLSLQFQNREVEKVYHALVNGRPAWQSLHVDLKLIPD----GDARHRTVVN 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           ++    A++ F ++      + W+E +P TGRTHQ+R H    G  IV D  Y  N K  
Sbjct: 122 KREGKSAVTDFTLL-GVCPPYSWIEARPETGRTHQIRAHLAANGLGIVCDPLYSGNQKPV 180

Query: 280 FTS--------------PIQNKLYLHARYMDLPHPEGG-RLQITAP 310
             S              P+  +L LHA  + + HPE G R+  TAP
Sbjct: 181 RLSEIKRSWNGDPDDERPLLARLALHAYRLTVTHPETGERMTFTAP 226


>gi|300724846|ref|YP_003714171.1| 23S rRNA pseudouridylate 746 synthase [Xenorhabdus nematophila ATCC
           19061]
 gi|297631388|emb|CBJ92085.1| 23S rRNA pseudouridylate 746 synthase [Xenorhabdus nematophila ATCC
           19061]
          Length = 217

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/209 (33%), Positives = 113/209 (54%), Gaps = 23/209 (11%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  + + + ++       HRLD  TSGI+V
Sbjct: 15  VLYQDEHIMVVNKPSGLLSVPGKA--EEHKDSIM-TRIQAEFPTAESVHRLDMATSGIMV 71

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKK---ECIANWLLKKSHIGGDYVH 214
           VA T+AA + L   FR R  +K+Y + VWG  +P+  +     I +W  +          
Sbjct: 72  VALTKAAERELKRQFREREPKKVYIARVWGKLVPEKGRVDLPLICDWPNRPKQ------K 125

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V  +  K A    + ++V++ + ++   + + P TGR+HQLRVH L +G PI+GD ++ A
Sbjct: 126 VCFETGKSAQ---TEYQVLE-YEEQATRVRLAPITGRSHQLRVHMLALGNPIMGD-RFYA 180

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + +    +P   +L LHA+ + + HP  G
Sbjct: 181 HSQARELAP---RLQLHAQELFITHPAYG 206


>gi|254804587|ref|YP_003082808.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis alpha14]
 gi|254668128|emb|CBA04722.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis alpha14]
          Length = 374

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 82/307 (26%), Positives = 138/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 88  --TVRPSEENLAFVPEPMALDIIYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 144

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P + 
Sbjct: 145 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQHLQERTVKRIYRAVANGIVPFDG 204

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 205 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 255

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH      P+  D  Y      C +        +  +  LHA  +   HP+ G  +
Sbjct: 256 HQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPKTGETV 315

Query: 306 QITAPLP 312
              AP+P
Sbjct: 316 SFEAPIP 322


>gi|254461389|ref|ZP_05074805.1| ribosomal large subunit pseudouridine synthase D [Rhodobacterales
           bacterium HTCC2083]
 gi|206677978|gb|EDZ42465.1| ribosomal large subunit pseudouridine synthase D [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 341

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 89/347 (25%), Positives = 143/347 (41%), Gaps = 58/347 (16%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKK-RVKFNNRI 59
           ++ + + V E+     RLD+      P    ++   + K+L +G + ++   +     +I
Sbjct: 3   VSIISFAVQED--PPARLDKALSRDVPESASLSRTRIAKLLDAGAITINGAVQTDPKAKI 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            +G  V I       +HI  E   LD               ++YED  + V NKPAG+ V
Sbjct: 61  TAGAQVDITVEEAVDSHIEPEDIPLD---------------VMYEDDDLIVVNKPAGMVV 105

Query: 120 QGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
               G         + +H  G L     SK  +P + HR+D+ET+G+LVVA++ AA   L
Sbjct: 106 HPAPGTPSGTLVNALLHHFAGKLSGVGGSK--RPGVVHRIDKETTGLLVVAKSDAAHHGL 163

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK--------- 221
              F     ++ Y ++  G P+     I          GG  + V  Q  +         
Sbjct: 164 AAQFAAHTAERAYLAVTQGAPEASDPRIRGVRGVSFETGG-VLKVTTQLARHKHDRQRQA 222

Query: 222 ----GANYAISHFKVIDCFAQKFC--WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +A++  + I+ F    C   +E +  TGRTHQ+RVH  H+G  ++GD  Y   
Sbjct: 223 VLFENGRHAVTRARTIERFGNPHCLALVECRLETGRTHQIRVHMAHVGHGLLGDPTYGGR 282

Query: 276 FK---------GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            K         G   +   N+  LHA  +   HP  G  L+  A LP
Sbjct: 283 RKLPAKALSEVGLEAAKTFNRQALHAAVLGFEHPISGELLRFEADLP 329


>gi|167625160|ref|YP_001675454.1| RluA family pseudouridine synthase [Shewanella halifaxensis
           HAW-EB4]
 gi|167355182|gb|ABZ77795.1| pseudouridine synthase, RluA family [Shewanella halifaxensis
           HAW-EB4]
          Length = 324

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 89/325 (27%), Positives = 150/325 (46%), Gaps = 53/325 (16%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD+   + +P  +   +++ + +G V +D +   K   ++  GQVV +   +       
Sbjct: 19  RLDQTLADLFPDYSRTRIKEWILAGSVFIDGEVSDKPRFKVLEGQVVTVGATLE------ 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
           +E K    +++L          ++YED  I + NK AG+ V  G+G         + +H 
Sbjct: 73  EETKAQAEAIDLD---------IIYEDDHILIINKQAGLVVHPGAGNQDGTLMNALLHHC 123

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G     V   G    + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V G
Sbjct: 124 PGI--ELVPRAG----IVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVTG 177

Query: 190 I---PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                    E I     K++H+       V  N K    A++H++V + F +    L ++
Sbjct: 178 TIISGGTIDEPIDRHPTKRTHMA------VVHNGKP---AMTHYRVAEKF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLY-------LHARYMDLP 298
             +GRTHQ+RVH  H+G  +VGD  Y    +     +P   + Y       LHA  ++L 
Sbjct: 228 LESGRTHQIRVHMAHIGHVLVGDPVYAGRPRPPKGAAPDFFETYMGFRRQALHAVRLELA 287

Query: 299 HPEGGRLQI-TAPLPAHMVKTWDSL 322
           HP    +    AP+P  MVK   +L
Sbjct: 288 HPFTCEIMSWQAPIPDDMVKLTRAL 312


>gi|51011075|ref|NP_001003495.1| RNA pseudouridylate synthase domain-containing protein 4 [Danio
           rerio]
 gi|82182079|sp|Q6DBR0|RUSD4_DANRE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 4
 gi|50418114|gb|AAH78405.1| Zgc:92006 [Danio rerio]
          Length = 358

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 83/296 (28%), Positives = 143/296 (48%), Gaps = 47/296 (15%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSIL---LYEDSKIYVFNKPAGISVQGGSGIAY 127
           ++ L   + E K     +     S F K++    LYED  I   NKP  + +   +GI  
Sbjct: 58  VSPLQSRVNELKQFSQQLQSVHPSVFAKALYRSSLYEDQNIIAINKPYDVPLHNINGIRN 117

Query: 128 HID---GFLKSWVDS--KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            I      L    D+   G +  L H+L++ET+G+L++A+T  AA+H+    +  +++  
Sbjct: 118 SIAECLPLLAKITDNMRPGSQLHLCHKLEKETTGVLILAKTEEAAEHVQTLIQSHKVEMK 177

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG------------------GDYVHVVKQNEKGAN 224
           Y ++  G+P   +  I   +++++ +G                  GD V  V+ + + A+
Sbjct: 178 YLAITVGVPVPSEGVIDIPVIERAVVGPQPHFKMALSPLFKVNEDGDGVTRVRAHRQ-AH 236

Query: 225 YAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCANFK----- 277
            A++ ++V+D  +   C L E+QP TG  +QLRVH AL + CPI+GDHKY    K     
Sbjct: 237 AAVTRYQVLDNTSG--CSLVELQPLTGVKNQLRVHMALALTCPILGDHKYSHWSKLAPQK 294

Query: 278 ---GNF--TSPIQNK-----LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              G       +Q+K     L+LH+R + LP  +G R + ++ PLP + +     L
Sbjct: 295 LPEGTLRRLGLVQSKTRYLPLHLHSRRIVLPGFKGHRDITVSCPLPKYFINALKRL 350


>gi|330837755|ref|YP_004412396.1| ribosomal large subunit pseudouridine synthase D [Spirochaeta
           coccoides DSM 17374]
 gi|329749658|gb|AEC03014.1| ribosomal large subunit pseudouridine synthase D [Spirochaeta
           coccoides DSM 17374]
          Length = 233

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 61/209 (29%), Positives = 104/209 (49%), Gaps = 13/209 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           + S +LYED+ +   NK  G  VQG       +   ++ ++  K  KP      + HRLD
Sbjct: 9   VASRVLYEDNHLIAVNKLPGELVQGDKTGDVTLADAVRDYLKVKYGKPGNVYLGIPHRLD 68

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG+++  RT  A   + E FR   + K+YW++V  +P+N +  + +++ + +     
Sbjct: 69  RPTSGVVLYCRTEKALGRMNEMFRGSDVSKVYWAVVDALPQNTEGTLVHYIFRDTRTNKS 128

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V+    G+ +A   +++I   ++ +  LE+  HTGR HQ+R     +G  I GD K
Sbjct: 129 VARPVET--VGSKFAKLDYRIIGA-SRNYHLLEIVLHTGRHHQIRAQLAAIGLHIKGDLK 185

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y     G   S     ++LHAR +  PHP
Sbjct: 186 Y-----GAARSNPDGGIHLHARSISFPHP 209


>gi|332208640|ref|XP_003253415.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 4
           [Nomascus leucogenys]
          Length = 377

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 119/247 (48%), Gaps = 30/247 (12%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK-HSDFLKSIL----LYED 105
           +R++   R Q  +  ++P   NA+   ++E  I+  +  L + H + L   L    L++D
Sbjct: 48  ERLRAQKREQDTK--KVPVSTNAVQRRVQE--IVRFTRQLQQVHPNVLAKALTRGILHQD 103

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGILVVA 161
             + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G++V+A
Sbjct: 104 KNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLA 163

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH------- 214
             +  A  + E FR R++ K YW++   +P      +   +++K   G    H       
Sbjct: 164 WDKDMAHQVQELFRTRQVVKKYWAITVRVPMPSAGVVDIPIVEKEVQGQQQHHKMTLSPS 223

Query: 215 --------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCP 265
                   V  +  + A  A++ ++V+         +E+QP TG  HQLRVH +  + CP
Sbjct: 224 YRVDDGKMVKVRRSRNAQVAVTQYQVLSSTLSS-ALVELQPITGIKHQLRVHLSFGLDCP 282

Query: 266 IVGDHKY 272
           I+GDHKY
Sbjct: 283 ILGDHKY 289


>gi|253564151|ref|ZP_04841608.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_2_5]
 gi|251947927|gb|EES88209.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_2_5]
 gi|301161553|emb|CBW21093.1| ribosomal large subunit pseudouridine synthase [Bacteroides
           fragilis 638R]
          Length = 357

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 87/345 (25%), Positives = 156/345 (45%), Gaps = 44/345 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    + +I+   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYDNEIIPEDIPLH---------IVYEDKYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  +
Sbjct: 138 LVNAIAWHLKD--DPVYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGVQFFNKTTK 195

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFAQK 239
           + Y +LVWGI    +  I   + +      D + + V  +     +A++H++V++     
Sbjct: 196 RRYRALVWGIVDQDEGTIVGSIARNPK---DRMQMAVMADPTQGKHAVTHYRVLERLGY- 251

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------K 287
              +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +
Sbjct: 252 VTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPR 311

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS-LGFKYDRNL 330
             LHA  +   HP  G  +  T+ LP  M +  +   G+  +R+L
Sbjct: 312 QALHAMTLGFVHPVTGEEMHFTSELPDDMTRLIEKWRGYISNRDL 356


>gi|71737110|ref|YP_273849.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|71557663|gb|AAZ36874.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. phaseolicola 1448A]
          Length = 237

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/214 (32%), Positives = 111/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 34  IIYQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGFPEARIVHRLDWETSGIIL 91

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 92  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 147

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 148 HEGGKHALTFWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 205

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              P   +L LHA  +   HP  G RL    P P
Sbjct: 206 AAYP---RLCLHASMLSFTHPGTGERLTFECPAP 236


>gi|188534767|ref|YP_001908564.1| 23S rRNA pseudouridine synthase D [Erwinia tasmaniensis Et1/99]
 gi|188029809|emb|CAO97690.1| Ribosomal large subunit pseudouridine synthase D [Erwinia
           tasmaniensis Et1/99]
          Length = 325

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 75/253 (29%), Positives = 130/253 (51%), Gaps = 33/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLYHFPAIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL ++ + R I + Y ++  G         + I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVDALQRREITREYEAVAIGRMTAGGTVDQPISRHSTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A +H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------ATTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMSHISHPLVGDPL 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F + ++  ++  LHA  + L HP  G  ++  APLP  MV   D+L
Sbjct: 253 YGGRPRPPKGASEAFITTLRAFDRQALHATMLRLYHPISGIEMEWHAPLPQDMVDLIDAL 312

Query: 323 GFKYDRNLYIKRL 335
             K D  ++ ++L
Sbjct: 313 --KADTEMFKEQL 323


>gi|161869644|ref|YP_001598812.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis 053442]
 gi|161595197|gb|ABX72857.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis 053442]
          Length = 392

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 82/307 (26%), Positives = 138/307 (44%), Gaps = 38/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +            
Sbjct: 58  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICV------------ 105

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G      ++G L +  
Sbjct: 106 --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLL-AHC 162

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK 194
               Q PR  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++  GI P + 
Sbjct: 163 PELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDG 222

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           K         ++ IG D  + +K    + G   A++H KV++ +     ++E    TGRT
Sbjct: 223 K--------IETQIGRDPHNRLKMAVVKFGGKPAVTHVKVLERYL-AHSYIECSLETGRT 273

Query: 253 HQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           HQ+RVH      P+  D  Y      C +        +  +  LHA  +   HP+ G  +
Sbjct: 274 HQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHPKTGETR 333

Query: 307 -ITAPLP 312
              AP+P
Sbjct: 334 SFEAPIP 340


>gi|302386355|ref|YP_003822177.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
 gi|302196983|gb|ADL04554.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
          Length = 320

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 90/340 (26%), Positives = 161/340 (47%), Gaps = 48/340 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q ++V  +E   RLD+    +        L K++R   + ++ K+   + ++  G  V+
Sbjct: 1   MQSLIVSQNEAGQRLDKLLSKYLNLAEKSFLYKMMRKKNITLNGKKCDGSEKLVQGDEVK 60

Query: 67  I---PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +      I   + I K  ++   S+N+           LYED  I + NKPAG+  Q   
Sbjct: 61  LFLSDETIGKFSQI-KLPEVRKVSLNI-----------LYEDEHILLINKPAGMLSQKAR 108

Query: 124 GIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                +  ++ +++ S G+         +P + +RLD+ TSG++V  ++ A  Q ++ +F
Sbjct: 109 ESDESLVEYMINYLVSNGRLSTEQLRSFRPSVCNRLDRNTSGLVVGGKSLAGLQLMSAAF 168

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R I K Y  +V G   ++ + I  +L K      + V V KQ   G+   ++ ++ + 
Sbjct: 169 KDRSIHKYYQCVVKGHISDR-QVITGYLTKSE--ASNQVTVHKQPVTGSVPIVTEYEPVQ 225

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY-LHAR 293
            +  ++  L +   TGRTHQ+R H   +G PIVGD+KY  N + N  +    KLY +H++
Sbjct: 226 -YHGEYTLLRITLITGRTHQIRAHLSSIGYPIVGDYKY-GNSRVNEEA---KKLYHIHSQ 280

Query: 294 YM--------DLPHPEG---GRLQITAPLP---AHMVKTW 319
            +        +LP P     GR  I APLP   + + K W
Sbjct: 281 LLHSYQVIFPELPEPLAYLSGRTFI-APLPKTFSKICKDW 319


>gi|298486181|ref|ZP_07004244.1| Ribosomal large subunit pseudouridine synthase A [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|298159188|gb|EFI00246.1| Ribosomal large subunit pseudouridine synthase A [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
          Length = 211

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/214 (32%), Positives = 111/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIYQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDPDTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HQGGKHALTFWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              P   +L LHA  +   HP  G RL    P P
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|258645705|ref|ZP_05733174.1| ribosomal large subunit pseudouridine synthase D [Dialister invisus
           DSM 15470]
 gi|260403074|gb|EEW96621.1| ribosomal large subunit pseudouridine synthase D [Dialister invisus
           DSM 15470]
          Length = 308

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 89/319 (27%), Positives = 153/319 (47%), Gaps = 42/319 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPP 69
           +V   +E  RLD++ K     +    +QK +++G V +  KK +  N  +  G       
Sbjct: 7   LVSVADEGKRLDQFLKERTG-LTRSEVQKWIKAGNVSLLPKKMIHSNYHVSEGDR----- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
            I+      K+Q+++  ++ L          +LYED+ + V NK  G+ V  G+G     
Sbjct: 61  -ISFFWEEKKKQELIGQNIPLD---------ILYEDNDMIVINKRRGVVVHPGAGNTEGT 110

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + +H    L+S  D   ++P + HRLD++TSG++V A++  A   L +     + Q
Sbjct: 111 LVNALLFHCGEQLRSVGDP--ERPGIVHRLDKDTSGVMVAAKSERAYGILQKEIASHKAQ 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + Y +LV G  +     I   L +  K  +  D +H      +    A++HF VI+ +  
Sbjct: 169 RCYIALVHGQMEGDTGVIRLPLGRSTKDRMKWDVLH------ETGRPAVTHFHVIE-YLP 221

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            + W+E +  TGRTHQ+RVH  H+   +V D  Y    K +F  PI+ +  LH+  ++L 
Sbjct: 222 HYSWIECKLETGRTHQIRVHMAHIRHAVVNDPLYGWK-KDHF--PIKGQA-LHSHTLELC 277

Query: 299 HPEGGR-LQITAPLPAHMV 316
           HP  G  +   AP+P  M+
Sbjct: 278 HPITGEVMHFEAPVPEDMI 296


>gi|90411938|ref|ZP_01219946.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium profundum 3TCK]
 gi|90327196|gb|EAS43568.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium profundum 3TCK]
          Length = 239

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/203 (32%), Positives = 106/203 (52%), Gaps = 17/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  I + NKP+G+    G    ++   + +   D    +  + HRLD  TSG++++
Sbjct: 19  ILHHDEDIIMLNKPSGLLSNPGRNPEHYDSVYSRVLRDYP--EAHIVHRLDMSTSGLIML 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A  + A +HL   FR R  QK+Y++ +WG P      +   L+       D+ +  KQ  
Sbjct: 77  AVNKDAERHLHAQFRERATQKVYYARIWGHPDQDTGTVDLPLI------CDWPNRPKQKV 130

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E G   +++H++V+   AQ    + + P TGR+HQLRVH   +G PI+GD  Y AN +
Sbjct: 131 CYEDGKP-SVTHYEVVAREAQT-TLVRLHPITGRSHQLRVHMQALGHPIIGDEFY-ANDE 187

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
            N    I ++L+LHA  +   HP
Sbjct: 188 ANA---IADRLHLHAAEIAFTHP 207


>gi|114641168|ref|XP_508851.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein 4
           [Pan troglodytes]
          Length = 377

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/262 (29%), Positives = 119/262 (45%), Gaps = 44/262 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           +L++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 99  ILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P      +   +++K   G    H  
Sbjct: 159 VMVLAWDKDMAHQVQELFRTRQVVKKYWAITVHVPMPSAGVVDIPIVEKEAQGQQQHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  +  + A  A++ ++V+         +E+QP TG  HQLRVH + 
Sbjct: 219 TLSPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSSTLSS-ALVELQPITGIKHQLRVHLSF 277

Query: 261 HMGCPIVGDHKYCANFKGNFTSPI-------------QNK-----LYLHARYMDLPHPEG 302
            + CPI+GDHKY      N  +P              Q+K     L+LHAR + LP    
Sbjct: 278 GLDCPILGDHKYS---DWNRLAPQKLSVGTLKKLGLEQSKARYIPLHLHARQLILPALGS 334

Query: 303 GR--LQITAPLPAHMVKTWDSL 322
           G+  L +   LP   V +   L
Sbjct: 335 GKEELNLVCKLPRFFVHSLHRL 356


>gi|77166008|ref|YP_344533.1| pseudouridine synthase, RluD [Nitrosococcus oceani ATCC 19707]
 gi|254436382|ref|ZP_05049888.1| pseudouridine synthase, RluA family [Nitrosococcus oceani AFC27]
 gi|76884322|gb|ABA59003.1| ribosomal large subunit pseudouridine synthase D [Nitrosococcus
           oceani ATCC 19707]
 gi|207088072|gb|EDZ65345.1| pseudouridine synthase, RluA family [Nitrosococcus oceani AFC27]
          Length = 319

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 84/325 (25%), Positives = 150/325 (46%), Gaps = 46/325 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + + ++    RLD+     +P  +   LQ+ ++ GQV+V+    +  + +Q G+ + +  
Sbjct: 9   ITLPSELAGKRLDQALAQVFPAYSRSRLQQWIKHGQVKVNDAPARPRDTVQGGEWIVV-- 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                        + ++   +   S  L   + YED  I V NKPAG+ V   +G   + 
Sbjct: 67  -------------MAEAEAEVIWKSQPLPLEIRYEDEAIIVVNKPAGLVVHPAAG---NR 110

Query: 130 DGFLKSWVDSKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG L + +     +    PR  + HRLD++TSG+LVVAR   A   L    + R+I + Y
Sbjct: 111 DGTLVNALLHHAPELERIPRAGIVHRLDKDTSGLLVVARNLVAHHGLVRQLQARQITREY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
            ++  G+        A   +++  +    + V+   +     A++H++V++ F       
Sbjct: 171 QAITVGVMTGGGRIEAP--IQRHPVHRKRMAVISTGKP----ALTHYRVLNRFRVHTHVS 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF------KGNFTSPIQN--KLYLHA 292
           C LE    TGRTHQ+RVH  H+G  ++GD  Y              ++ +++  +  LHA
Sbjct: 225 CRLE----TGRTHQIRVHLAHIGYSLLGDPTYGKRLHIPRESSEKLSTALRHFKRQALHA 280

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMV 316
             + L HPE  R ++  +PLP  M 
Sbjct: 281 ARLGLVHPEKKREMRWESPLPEDMA 305


>gi|89056515|ref|YP_511966.1| ribosomal large subunit pseudouridine synthase A [Jannaschia sp.
           CCS1]
 gi|88866064|gb|ABD56941.1| ribosomal large subunit pseudouridine synthase A [Jannaschia sp.
           CCS1]
          Length = 217

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/208 (33%), Positives = 99/208 (47%), Gaps = 22/208 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  + + NKPAG+    G G   H+   L + +     +  L HRLD +TSG++V 
Sbjct: 16  IIHEDHDLLLVNKPAGLLSVPGKG--EHLSDCLIARLKIAFPEVLLVHRLDMDTSGVMVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           ART  A +HL   F  R  +K Y + VWG   +K        I +W  +         HV
Sbjct: 74  ARTPHAQRHLGLQFEKRHTKKAYVARVWGEVTDKDGHIDLPLIVDWPNRPLQ------HV 127

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K A       +V D   +    + + P TGR+HQLRVH L +G PI+GD  Y   
Sbjct: 128 NHETGKPAQTDWRRIRVEDGTTR----MRLFPKTGRSHQLRVHMLAIGHPILGDPFYATG 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
               F      +L LHA  + L HP+GG
Sbjct: 184 PALAFP-----RLMLHAESLKLRHPDGG 206


>gi|206577750|ref|YP_002237068.1| ribosomal large subunit pseudouridine synthase D [Klebsiella
           pneumoniae 342]
 gi|290510910|ref|ZP_06550279.1| ribosomal large subunit pseudouridine synthase D [Klebsiella sp.
           1_1_55]
 gi|206566808|gb|ACI08584.1| ribosomal large subunit pseudouridine synthase D [Klebsiella
           pneumoniae 342]
 gi|289775903|gb|EFD83902.1| ribosomal large subunit pseudouridine synthase D [Klebsiella sp.
           1_1_55]
          Length = 326

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 127/245 (51%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G   +    +E I+    K++H+   
Sbjct: 143 TGLMVVAKTIPAQTRLVESLQLREITREYEAVAIGHMTSGGTVEEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RIHTRLRLRLETGRTHQIRVHMSHITHPLVGDQV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y    +        F + ++  ++  LHA  + L HP  G  ++  AP+P  MV+  +++
Sbjct: 253 YGGRPRPPKGASEEFITALRKFDRQALHATMLRLYHPITGIEMEWHAPIPQDMVELIEAM 312

Query: 323 GFKYD 327
              ++
Sbjct: 313 RADFE 317


>gi|317493978|ref|ZP_07952395.1| RluA family pseudouridine synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918305|gb|EFV39647.1| RluA family pseudouridine synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 326

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 88/322 (27%), Positives = 159/322 (49%), Gaps = 47/322 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ +     I+AL  I 
Sbjct: 19  RLDQALAELFPDYSRSRIKEWILDDRVKVNGKIINKPKEKVLGGEEI----AIDAL--IE 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS--- 135
           +E +    ++ L          ++YEDS I V NKP  + V  G+G   + DG + +   
Sbjct: 73  EEARWEPQNIPLD---------IVYEDSDILVINKPRDLVVHPGAG---NPDGTILNALL 120

Query: 136 -WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++  G   
Sbjct: 121 YYYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGTMT 180

Query: 193 ---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +E I+    K++H+    VH + +       A++H+++++ F +    L ++  T
Sbjct: 181 AGGTVEEPISRHPTKRTHMA---VHPMGKP------AVTHYRIMEHF-RAHTRLRLRLET 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHARYMDLPHPE 301
           GRTHQ+RVH  H+  P+VGD  Y    +        F + ++  ++  LHA  + L HP 
Sbjct: 231 GRTHQIRVHMAHISHPLVGDPLYGGRPRPPKGASEEFITILRGFDRQALHATMLRLYHPI 290

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
            G +++  APLP  MV    +L
Sbjct: 291 SGIQMEWHAPLPQDMVDLITAL 312


>gi|298384162|ref|ZP_06993723.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           1_1_14]
 gi|298263766|gb|EFI06629.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           1_1_14]
          Length = 549

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 68/215 (31%), Positives = 111/215 (51%), Gaps = 37/215 (17%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGIL 158
           +++ED  + V NKP+G +SV G       +   +K+ + ++ G  P + HRLD  TSG+L
Sbjct: 343 IVFEDEWLVVVNKPSGMLSVPGKEEETDSVYHRVKAKYPEATG--PMIVHRLDMATSGLL 400

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKE--------CIANWLLKKSHI 208
           +VA+T+   QHL E F  R I+K Y +L+   G+ +  +E        C+      +  +
Sbjct: 401 LVAKTKEVHQHLQEQFINRSIKKRYVALLDRNGLNQQLEETGTINLPLCLNPLDRPRQMV 460

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCP 265
             +Y             A++ ++V++ ++ K+  +   P TGRTHQLRVHA H   + CP
Sbjct: 461 SEEY----------GKPAVTEYRVLN-YSDKYIRIAFYPLTGRTHQLRVHAAHHQGLNCP 509

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           I+GD  Y             ++LYLHA Y++  HP
Sbjct: 510 ILGDELYGKK---------ADRLYLHAEYIEFRHP 535


>gi|166031887|ref|ZP_02234716.1| hypothetical protein DORFOR_01588 [Dorea formicigenerans ATCC
           27755]
 gi|166028340|gb|EDR47097.1| hypothetical protein DORFOR_01588 [Dorea formicigenerans ATCC
           27755]
          Length = 335

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/275 (25%), Positives = 132/275 (48%), Gaps = 25/275 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +++ +E   RLD++ K + P      + K+LR   + ++ K+     ++ +G  ++   
Sbjct: 4   TIIKENESGQRLDKYLKKYLPQAPGSFIYKMLRKKNITLNGKKAAGQEKLNTGDSIKF-- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDF-LKSIL--LYEDSKIYVFNKPAGISVQGG---- 122
                   + E+ I   + N      + +K  L  +YED  I + NKPAG+  Q      
Sbjct: 62  -------FLAEETIDKFTGNAAASESYPVKKDLEIIYEDDNILLINKPAGMLSQKAKKED 114

Query: 123 -SGIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            S + Y I   L +   +K +     P + +RLD+ TSG++V  ++ A  Q + E+F+ R
Sbjct: 115 VSLVEYVIGYLLSNGSVTKEELLTFHPGICNRLDRNTSGMVVAGKSLAGLQIMGEAFKER 174

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  LV G  K     I  +L K      + V + ++  +GA    + ++ +  + 
Sbjct: 175 TLAKYYLCLVKGCIKETSH-IRGYLKKDEKT--NKVMISRKMSEGAAAIETEYEPV-AYQ 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++   L++   TGRTHQ+R H   +G P++GD+KY
Sbjct: 231 KELTLLKVHLITGRTHQIRAHLASIGHPLMGDYKY 265


>gi|72161527|ref|YP_289184.1| ribosomal large subunit pseudouridine synthase D [Thermobifida
           fusca YX]
 gi|71915259|gb|AAZ55161.1| ribosomal large subunit pseudouridine synthase D [Thermobifida
           fusca YX]
          Length = 309

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 116/230 (50%), Gaps = 16/230 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQ---GGSGIAYHIDGFLKSWV----DSKGQKPRLTHRLDQE 153
           ++YED+ I V +KPAG+      G SG    +DG L + V        ++  + HRLD  
Sbjct: 84  IVYEDADIVVVDKPAGVVAHPTIGWSGPTV-VDGLLAAGVAVATSGAAERQGIVHRLDAN 142

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G++VVA++  A   L  +F+ R ++K+Y +LV G P   +  I   + +  H  GD  
Sbjct: 143 TTGLMVVAKSEIAYSSLKRAFKERTVEKVYHALVQGHPDPLRGTIDAPIDR--HPSGDGR 200

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V     G   +++H+  ++ F +    LE+   TGRTHQ+RVH   +  P VGD  Y 
Sbjct: 201 FAVV---AGGRPSVTHYTTLEAF-RAASLLEIDLETGRTHQIRVHMSAIRHPCVGDTLYG 256

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           A+        +  + +LHA  +   HP +  R++ T+  P  + K+ + L
Sbjct: 257 ADPTLAERLGVHRQ-WLHAIRLAFTHPTQYRRVEFTSSYPEDLAKSLEIL 305


>gi|288934030|ref|YP_003438089.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|288888759|gb|ADC57077.1| pseudouridine synthase, RluA family [Klebsiella variicola At-22]
          Length = 326

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 127/245 (51%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G   +    +E I+    K++H+   
Sbjct: 143 TGLMVVAKTIPAQTRLVESLQLREITREYEAVAIGHMTSGGTVEEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RIHTRLRLRLETGRTHQIRVHMSHITHPLVGDQV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y    +        F + ++  ++  LHA  + L HP  G  ++  AP+P  MV+  +++
Sbjct: 253 YGGRPRPPKGASEEFITALRKFDRQALHATMLRLYHPITGIEMEWHAPIPQDMVELIEAM 312

Query: 323 GFKYD 327
              ++
Sbjct: 313 RADFE 317


>gi|323700732|ref|ZP_08112644.1| pseudouridine synthase, RluA family [Desulfovibrio sp. ND132]
 gi|323460664|gb|EGB16529.1| pseudouridine synthase, RluA family [Desulfovibrio desulfuricans
           ND132]
          Length = 562

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 85/309 (27%), Positives = 141/309 (45%), Gaps = 36/309 (11%)

Query: 16  EENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVIN 72
           +   RLD+++        ++   ++  + SG   VD +   K N ++  GQV     VI 
Sbjct: 18  DAGTRLDKFWGRELAGEGVSRGRVKGWIESGLALVDGEVTTKGNLKLARGQVA----VIR 73

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--ID 130
           A      E   L  +      S  ++++  YED  + V  KPAG++V           ++
Sbjct: 74  A---AAPEADPLGPASPPEPVSGDIEAV--YEDEHMLVIVKPAGLTVHPAPSEPGPTLVN 128

Query: 131 GFLKSWVDSKG-------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             +  W D          Q+P + HRLD++TSG++ VART +A   L+ SF      K+Y
Sbjct: 129 LLIHQWPDIAAENSGMDPQRPGIVHRLDKDTSGLMAVARTESARLALSASFAGHETFKVY 188

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVIDCFAQKFC 241
            +LV G P+  +  I       + +G    H  ++    KG   A S ++V+    +   
Sbjct: 189 LALVHGRPELAEGVI------DAPMGRHPTHKTLMAVLPKGGREARSDYRVLWTGPRGLA 242

Query: 242 WL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT------SPIQNKLYLHARY 294
            L  ++ HTGRTHQ+RVH  H+G P++GD  Y       ++      + +  +  LHA Y
Sbjct: 243 SLAAVRIHTGRTHQIRVHMAHIGHPLIGDAAYGPRENAEWSRRPDRLAGLAPRQMLHAFY 302

Query: 295 MDLPHPEGG 303
           + +PHP  G
Sbjct: 303 LSVPHPVTG 311


>gi|300775344|ref|ZP_07085206.1| ribosomal large subunit pseudouridine synthase D [Chryseobacterium
           gleum ATCC 35910]
 gi|300506084|gb|EFK37220.1| ribosomal large subunit pseudouridine synthase D [Chryseobacterium
           gleum ATCC 35910]
          Length = 225

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 111/236 (47%), Gaps = 42/236 (17%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           +K  ++YED+ + V NK  G  VQG       +   +K+++  +  KP      L HR+D
Sbjct: 1   MKEQIIYEDNHLLVVNKKVGQLVQGDKTGDESLLESIKNFIKIRDAKPGNVFLGLVHRID 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIG 209
           + TSG+++ A+T  A   LT+  + R ++K YW++V    IP++++              
Sbjct: 61  RPTSGLVIYAKTSKALSRLTQMVKNREVKKTYWAVVGKEMIPQSQR-------------- 106

Query: 210 GDYVHVVKQNEK------------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
              VH +K+NEK            GA  AI  + VI      +  LE+   TGR HQ+R 
Sbjct: 107 --LVHYLKKNEKNNKAIVFPKATEGAKEAILTYHVIKTL-DNYLLLEIDLETGRHHQIRA 163

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                G PI GD KY     G   S     + LHAR ++  HP     ++I AP+P
Sbjct: 164 QLSKTGVPIKGDLKY-----GAPRSNPDGGINLHARKLEFIHPVTKENIEIIAPVP 214


>gi|307256344|ref|ZP_07538127.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 10
           str. D13039]
 gi|306865170|gb|EFM97070.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 10
           str. D13039]
          Length = 226

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 66/205 (32%), Positives = 104/205 (50%), Gaps = 13/205 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+     +  V  K       HRLD  TSGIL+ A
Sbjct: 21  VYRDNHILVINKPSGLLSVPGNRPEYYDSAMTR--VQQKYGFTEPAHRLDMATSGILLFA 78

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            ++AA + L   FR R  +K Y +L+WG      E + +       +  D+ +  +Q   
Sbjct: 79  LSKAAEKELKRQFRDREPKKHYIALLWG---KLGEKVGDTGEMNFPLICDWENRPRQKIC 135

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y +    
Sbjct: 136 YERGKK-AITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGDKFYASPLAK 194

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
           + +     +L LHA  + + HP  G
Sbjct: 195 SLSP----RLCLHAESLSITHPITG 215


>gi|126207799|ref|YP_001053024.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae L20]
 gi|126096591|gb|ABN73419.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
          Length = 237

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 121/243 (49%), Gaps = 19/243 (7%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +N++  ++++  +++    L     FL  +  Y D+ I V NKP+G+    G+   Y+  
Sbjct: 6   VNSVFFMVRKMALIEYHPPL---EPFLTEV--YRDNHILVINKPSGLLSVPGNRPEYYDS 60

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +  V  K       HRLD  TSGIL+ A ++AA + L   FR R  +K Y +L+WG 
Sbjct: 61  AMTR--VQQKYGFTEPAHRLDMATSGILLFALSKAAEKELKRQFRDREPKKHYIALLWG- 117

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKFCWLEMQP 247
                E + +       +  D+ +  +Q    E+G   AI+H++V+         +++ P
Sbjct: 118 --KLGEKVGDTGEMNFPLICDWENRPRQKICYERGKK-AITHYEVLAHLPNNTTRVKLTP 174

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGR+HQLRVH+L +G PI+GD  Y +    + +     +L LHA  + + HP  G  + 
Sbjct: 175 ITGRSHQLRVHSLALGHPILGDKFYASPLAKSLSP----RLCLHAESLSITHPITGEAMT 230

Query: 307 ITA 309
            TA
Sbjct: 231 FTA 233


>gi|157962983|ref|YP_001503017.1| RluA family pseudouridine synthase [Shewanella pealeana ATCC
           700345]
 gi|157847983|gb|ABV88482.1| pseudouridine synthase, RluA family [Shewanella pealeana ATCC
           700345]
          Length = 323

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 93/340 (27%), Positives = 150/340 (44%), Gaps = 53/340 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +   RLD+   + +P  +   +++ + SG V +D +   K   ++  GQVV I   
Sbjct: 11  ITATQTGQRLDQTLADLFPDYSRTRIKEWILSGSVFIDGETSDKPRFKVLEGQVVTIGAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
           +        E   LD               ++YED  I V NK AG+ V  G+G      
Sbjct: 71  LEEETKAEAEAIDLD---------------IIYEDDHILVINKQAGLVVHPGAGNQSGTL 115

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + +H  G     V   G    + HRLD++T+G++VVA+T  A  HL  + + R I +
Sbjct: 116 MNALLHHCPGI--ELVPRAG----IVHRLDKDTTGLMVVAKTVEAQTHLVTALQAREITR 169

Query: 182 IYWSLVWGI---PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            Y ++V G         E I     K++H+       V  N K    A++H++V + F +
Sbjct: 170 EYEAIVTGTIIAGGTVDEPIDRHPTKRTHMA------VVHNGKP---AMTHYRVAEKF-R 219

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLY-------L 290
               L ++  +GRTHQ+RVH  H+G  +VGD  Y    +     +P   + Y       L
Sbjct: 220 AHTRLRLRLESGRTHQIRVHMAHIGHVLVGDPVYAGRPRPPKGAAPDFFETYMGFRRQAL 279

Query: 291 HARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSLGFKYDRN 329
           HA  ++L HP    +    AP+P  MVK   +L    + N
Sbjct: 280 HAVRLELAHPFTCEIMSWQAPIPEDMVKLTRALRKDTEEN 319


>gi|148380931|ref|YP_001255472.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 3502]
 gi|153932924|ref|YP_001385300.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           ATCC 19397]
 gi|153936215|ref|YP_001388708.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           Hall]
 gi|148290415|emb|CAL84542.1| putative ribosomal large subunit pseudouridine synthase
           [Clostridium botulinum A str. ATCC 3502]
 gi|152928968|gb|ABS34468.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 19397]
 gi|152932129|gb|ABS37628.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           Hall]
          Length = 300

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 82/283 (28%), Positives = 138/283 (48%), Gaps = 35/283 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K +R G+V V+K++V   +++    ++ I   +    H    Q I    +N+      
Sbjct: 33  IRKAVRDGRVFVNKEKVIKKHKLSQDDLIEI--YMQEDEH----QNIEPEDMNIE----- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKP--RLTHRL 150
               ++YED+ I V NK  GI V    G   H  G L + +       G+K   RL  RL
Sbjct: 82  ----IVYEDNDIIVINKRPGIVVHPTKG---HPTGTLSNGILYHFKKNGEKSIVRLVSRL 134

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ + +   L       R +KIY ++V G  K +KE   N  + K     
Sbjct: 135 DRDTSGLIIIAKNQFSHMRLASDMSKDRFRKIYIAVVHGSMK-EKEGRINLPIYKEEESE 193

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +V  +E+G   +I+ ++V++  + K   + ++  TGRTHQ+RVH  H+G P+ GD 
Sbjct: 194 SIKRIV--DERGQE-SITTYEVLEELS-KGSVVRLELETGRTHQIRVHMSHLGHPLYGDS 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
            Y    KG        +  LHA  ++ PHP  G   +LQ + P
Sbjct: 250 LYG---KGEEEKEYIERQALHAYKLEFPHPRTGDVLKLQCSLP 289


>gi|218247695|ref|YP_002373066.1| pseudouridine synthase [Cyanothece sp. PCC 8801]
 gi|218168173|gb|ACK66910.1| pseudouridine synthase [Cyanothece sp. PCC 8801]
          Length = 551

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 74/235 (31%), Positives = 112/235 (47%), Gaps = 52/235 (22%)

Query: 90  LTKHSDFLKSIL--LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDS--KGQKP 144
           L  +  F KS +  +YED  I   +KP+ + SV G     +  D  L    +S    Q+ 
Sbjct: 333 LGNNQSFFKSEIKVIYEDQWIIAIDKPSSLLSVPGRYFETF--DSVLTRLQNSLPDAQEL 390

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL---------------VWG 189
           R  HRLDQ+TSGIL++AR R   +HL++ F  R+++KIY ++               +WG
Sbjct: 391 RTVHRLDQDTSGILLLARDRYTHRHLSQQFAQRKVEKIYEAILAGSVMMNEGVIQLPLWG 450

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            P N+     +W L K                    +I+ FKVI    +    ++  P T
Sbjct: 451 DPNNRPYQKVDWELGKP-------------------SITQFKVITT-QENLTRIQFIPLT 490

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           GRTHQ+RVHA+    +G  I+GD+ Y  N          ++L+LHAR +   HP+
Sbjct: 491 GRTHQIRVHAVDTQGLGSVILGDYLYGCNAG-------VSRLHLHARELKFEHPQ 538


>gi|156230593|gb|AAI52263.1| Zgc:92006 protein [Danio rerio]
          Length = 358

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 82/296 (27%), Positives = 141/296 (47%), Gaps = 47/296 (15%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSIL---LYEDSKIYVFNKPAGISVQGGSGIAY 127
           ++ L   + E K     +     S F K++    LYED  I   NKP  + +   +GI  
Sbjct: 58  VSPLQSRVNELKQFSQQLQSVHPSVFAKALYRSSLYEDQNIIAINKPYDVPLHNINGIRN 117

Query: 128 HIDGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            I   L            G +  L H+L++ET+G+L++A+T  AA+H+    +  +++  
Sbjct: 118 SIAECLPLLAKISDNMRPGSQLHLCHKLEKETTGVLILAKTEEAAEHVQTLIQSHKVEMK 177

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG------------------GDYVHVVKQNEKGAN 224
           Y ++  G+P   +  I   +++++ +G                  GD V  V+ + + A+
Sbjct: 178 YLAITVGVPVPSEGVIDIPVIERAVVGPQPHFKMALSPLFKVNEDGDGVTRVRAHRQ-AH 236

Query: 225 YAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCANFK----- 277
            A++ ++V+D  +   C L E+QP TG  +QLRVH AL + CPI+GDHKY    K     
Sbjct: 237 AAVTRYRVLDNTSG--CSLVELQPLTGVKNQLRVHMALALTCPILGDHKYSHWSKLAPQK 294

Query: 278 ---GNF--TSPIQNK-----LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              G       +Q+K     L+LH+R + LP  +G R + ++ PLP + +     L
Sbjct: 295 LPEGTLRRLGLVQSKTRYLPLHLHSRRIVLPGFKGHRDITVSCPLPKYFINALKRL 350


>gi|315185514|gb|EFU19284.1| pseudouridine synthase [Spirochaeta thermophila DSM 6578]
          Length = 256

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 76/249 (30%), Positives = 122/249 (48%), Gaps = 27/249 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL--THRLDQETS 155
           ++YED+ I   NK     VQ    +   +  FL   +   D  G  PRL   +RLD+ TS
Sbjct: 3   IIYEDAHIIAVNKSGEELVQQNDVMKGTLQEFLLEHLRRRDGAGAPPRLHLVNRLDRPTS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ AR R AA   ++ FR R + K+YW+++   P    + + +++++   +   +   
Sbjct: 63  GIVLFARHRKAAGKFSDLFRRRGVYKLYWAVLDAPPPLPSDTVEHFIVESRRVNKSFAFP 122

Query: 216 VKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            K+    + YA   ++VI   DC    + ++ ++ HTGR HQ+R     +GC I GD KY
Sbjct: 123 EKRER--SEYARLSYQVIGSGDC----YFFVVVRLHTGRHHQIRAQFSALGCHIKGDIKY 176

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR-NL 330
            A             ++LHAR +   HP  G R+ ITA  PA      DSL  ++ R + 
Sbjct: 177 GAKRTNR-----GGGIHLHARLLAFVHPFTGERVVITADPPA------DSLWEEFARQDA 225

Query: 331 YIKRLYSQD 339
           + +R Y  D
Sbjct: 226 HFRRTYRYD 234


>gi|311280961|ref|YP_003943192.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308750156|gb|ADO49908.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 219

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/217 (33%), Positives = 109/217 (50%), Gaps = 19/217 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + V     +    HRLD  TSG++
Sbjct: 15  VVLYQDKHIMVVNKPSGLLSVPGR--LEEHKDSIM-TRVQRDFPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P  ++  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYLARVWGHPHPEEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++        + ++P TGR+HQLRVH   +G PI+GD  Y   
Sbjct: 126 KVCFETG-KAAQTEYQVLEYSDDNTARVLLKPITGRSHQLRVHMQALGHPILGDRFYATP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
                 S    +L LHA  + + HP  G  +   AP+
Sbjct: 185 EALAMAS----RLLLHAETLTITHPAYGNSMTFKAPV 217


>gi|254294738|ref|YP_003060761.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254043269|gb|ACT60064.1| pseudouridine synthase, RluA family [Hirschia baltica ATCC 49814]
          Length = 369

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 85/352 (24%), Positives = 147/352 (41%), Gaps = 71/352 (20%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQ-VVR 66
           +V   +    RLD+W     P ++    + I+  G V +D   +       I  G+ V+ 
Sbjct: 23  IVAPAEFAGERLDKWLPIAAPELSRSRAKAIIEKGDVLLDDTAITSPKHKVIADGRYVIL 82

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +PP ++A    + E   LD               +L+ED  + + NKPAG+ V    G  
Sbjct: 83  MPPPLDA--EPLPEDIPLD---------------VLFEDEHLIILNKPAGLVVHPAPGST 125

Query: 125 -------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  + +H  G L         +P + HRLD++TSG++V A+T  A   L+  F+  
Sbjct: 126 SGTLVNALLHHCAGQLPGI--GGVARPGIVHRLDKDTSGVMVAAKTEFAHTGLSSLFQAH 183

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN----------------EK 221
            +++ Y ++  G P+     I   +  +S      + VV+++                E+
Sbjct: 184 FMERAYLAVTRGAPRPLLGKIETRI-ARSTTDRKKMAVVRESRLSASAEWHGESEEDYEQ 242

Query: 222 GANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              +AI+++KV++ F +             E +  TGRTHQ+RVH  H+G P++GD  Y 
Sbjct: 243 KGKHAITNYKVLEQFGRIDATSGLPAATLTECRLETGRTHQIRVHMAHIGAPLLGDQTYG 302

Query: 274 --ANFKGNFTSPIQN----------KLYLHARYMDLPHPEGG---RLQITAP 310
                K + + P             +  LHA  +   HP  G   R ++  P
Sbjct: 303 RYRGLKAHGSGPAFETATHACKEFKRQALHAAILGFEHPVTGENLRFEVEPP 354


>gi|221316667|ref|NP_001138299.1| RNA pseudouridylate synthase domain-containing protein 4 isoform b
           [Homo sapiens]
          Length = 346

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 58/177 (32%), Positives = 90/177 (50%), Gaps = 22/177 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           +L++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 99  ILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V+A  +  A  + E FR R++ K YW++   +P      +   ++             
Sbjct: 159 VMVLAWDKDMAHQVQELFRTRQVVKKYWAITVHVPMPSAGVVDIPIV------------- 205

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
              EK A  A++ ++V+         +E+QP TG  HQLRVH +  + CPI+GDHKY
Sbjct: 206 ---EKEAQVAVTQYQVLSSTLSS-ALVELQPITGIKHQLRVHLSFGLDCPILGDHKY 258


>gi|315121810|ref|YP_004062299.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Candidatus Liberibacter solanacearum CLso-ZC1]
 gi|313495212|gb|ADR51811.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Candidatus Liberibacter solanacearum CLso-ZC1]
          Length = 340

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 91/337 (27%), Positives = 148/337 (43%), Gaps = 53/337 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP- 69
           ++ N+E   R+DRW          +NL++      V    K +  N  I    VV I P 
Sbjct: 15  LLANNEAEGRIDRWLA--------INLKEKFSRSYV----KTLILNGAISINGVVSINPS 62

Query: 70  --VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
             V+   +  I   ++    +N+   +  L   +LYED  I V NK AG+ V    G   
Sbjct: 63  RKVVPGESFFIDVPQL--QQLNIAAENIPLD--ILYEDDDIIVINKQAGLVVHPAPGNWT 118

Query: 125 ------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR--- 175
                 + +H +  L      K  +P + HRLD++T+G +VVA+   A Q L+E F    
Sbjct: 119 GTLVNALLHHCNNNLSGINGIK--RPGIVHRLDKDTTGTMVVAKNDIAHQRLSEQFADHG 176

Query: 176 -MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y+++VWG+P      I N  L +         V +  +K  + A++ ++ ++
Sbjct: 177 LHMGLKRSYYAMVWGVPSPDSGTI-NAPLGRCKSNRLRRAVKRIEDKTGDRAVTRYQTVE 235

Query: 235 C------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-------NFT 281
                  FA      +++  TGRTHQ+RVH  H G PI+GD  Y   FK        +  
Sbjct: 236 IYNKNSNFAASLLRCDLE--TGRTHQIRVHMAHKGYPIIGDPLYGKGFKTKENIVNHSTK 293

Query: 282 SPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           S I +  +  LHA  +   HP +   +    P+P  M
Sbjct: 294 SAILSLARQALHAYSLSFTHPCKNKDMNFKTPIPEDM 330


>gi|296101220|ref|YP_003611366.1| pseudouridine synthase, RluA family [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295055679|gb|ADF60417.1| pseudouridine synthase, RluA family [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 219

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/217 (32%), Positives = 114/217 (52%), Gaps = 19/217 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LDEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  +AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALNKAAERELKRQFREREPKKQYVARVWGHPAQTEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++        + ++P TGR+HQLRVH L +G PI+GD ++ A 
Sbjct: 126 KVCYETG-KAAQTEYEVLEYAPDNTARVLLKPITGRSHQLRVHMLALGHPILGD-RFYAP 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
            +   ++P   +L LHA+ + + HP  G  +   AP+
Sbjct: 184 PEALASAP---RLQLHAQTLTITHPAFGNAMTFKAPV 217


>gi|254496550|ref|ZP_05109419.1| hypothetical protein LDG_0200 [Legionella drancourtii LLAP12]
 gi|254354229|gb|EET12895.1| hypothetical protein LDG_0200 [Legionella drancourtii LLAP12]
          Length = 321

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 94/336 (27%), Positives = 152/336 (45%), Gaps = 42/336 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +  N R+D    +  P  +   +   ++SG V +++K  K  ++   G  + I  
Sbjct: 9   LTVPREYHNQRIDSVLAHLLPDYSRSQISNWIKSGAVILNQKPCKPKDKALDGDQITISV 68

Query: 70  VINA----LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +N      +H   E   L+               +++ED ++ V NKPA + V  G+G 
Sbjct: 69  DLNLTDNNFDHCAPEAIPLN---------------VVFEDDELLVLNKPANMVVHPGAGN 113

Query: 126 AYH-IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             H +   L     S    PR  + HRLD++T+G+LVVA+T  A   L    + R IQ+ 
Sbjct: 114 REHTLVNALLHHAPSLHHLPRAGIIHRLDKDTTGLLVVAKTLTAHTSLIRQMQAREIQRH 173

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKF 240
           Y +LV G        I+   ++    G    + +K    E+G   AI+H+ V   + Q +
Sbjct: 174 YVTLVQG------HVISGGTIETG-FGRHPRNRLKMAVLEQGRE-AITHYTVKKQY-QDY 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQN--KLYLHA 292
             L+++  TGRTHQ+RVH  H+  P+VGD  Y       AN      + IQ   +  LHA
Sbjct: 225 TLLDVKLMTGRTHQIRVHLTHINHPVVGDQLYGGRMKVPANASQELRTLIQEFKRQALHA 284

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             +   HP+  + L  TAPLP       ++L   Y+
Sbjct: 285 CSLAFFHPKTEQELTFTAPLPDDFQLLLNTLDEHYE 320


>gi|221316663|ref|NP_116184.2| RNA pseudouridylate synthase domain-containing protein 4 isoform a
           [Homo sapiens]
 gi|74731354|sp|Q96CM3|RUSD4_HUMAN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 4
 gi|15559540|gb|AAH14131.1| RNA pseudouridylate synthase domain containing 4 [Homo sapiens]
          Length = 377

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 95/192 (49%), Gaps = 21/192 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           +L++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 99  ILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P      +   +++K   G    H  
Sbjct: 159 VMVLAWDKDMAHQVQELFRTRQVVKKYWAITVHVPMPSAGVVDIPIVEKEAQGQQQHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  +  + A  A++ ++V+         +E+QP TG  HQLRVH + 
Sbjct: 219 TLSPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSSTLSS-ALVELQPITGIKHQLRVHLSF 277

Query: 261 HMGCPIVGDHKY 272
            + CPI+GDHKY
Sbjct: 278 GLDCPILGDHKY 289


>gi|14042050|dbj|BAB55086.1| unnamed protein product [Homo sapiens]
          Length = 377

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 95/192 (49%), Gaps = 21/192 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           +L++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 99  ILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P      +   +++K   G    H  
Sbjct: 159 VMVLAWDKDMAHQVQELFRTRQVVKKYWAITVHVPMPSAGVVDIPIVEKEAQGQQQHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  +  + A  A++ ++V+         +E+QP TG  HQLRVH + 
Sbjct: 219 TLSPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSSTLSS-ALVELQPITGIKHQLRVHLSF 277

Query: 261 HMGCPIVGDHKY 272
            + CPI+GDHKY
Sbjct: 278 GLDCPILGDHKY 289


>gi|307245129|ref|ZP_07527222.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|307247308|ref|ZP_07529356.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|307251849|ref|ZP_07533750.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|307254085|ref|ZP_07535932.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
 gi|307258540|ref|ZP_07540277.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 11
           str. 56153]
 gi|307260783|ref|ZP_07542470.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 12
           str. 1096]
 gi|306854018|gb|EFM86230.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|306856152|gb|EFM88307.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|306860541|gb|EFM92553.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|306863010|gb|EFM94957.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
 gi|306867444|gb|EFM99295.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 11
           str. 56153]
 gi|306869509|gb|EFN01299.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 12
           str. 1096]
          Length = 248

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/205 (31%), Positives = 104/205 (50%), Gaps = 13/205 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+     +        +P   HRLD  TSGIL+ A
Sbjct: 43  VYRDNHILVINKPSGLLSVPGNRPEYYDSAMTRVQQKYGFTEP--AHRLDMATSGILLFA 100

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            ++AA + L   FR R  +K Y +L+WG      E + +       +  D+ +  +Q   
Sbjct: 101 LSKAAEKELKRQFRDREPKKHYIALLWG---KLGEKVGDTGEMNFPLICDWENRPRQKIC 157

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y +    
Sbjct: 158 YERGKK-AITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGDKFYASPLAK 216

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
           + +     +L LHA  + + HP  G
Sbjct: 217 SLSP----RLCLHAESLSITHPITG 237


>gi|291533845|emb|CBL06958.1| ribosomal large subunit pseudouridine synthase D [Megamonas
           hypermegale ART12/1]
          Length = 304

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 83/312 (26%), Positives = 145/312 (46%), Gaps = 36/312 (11%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +DE   RLD +      + +  ++QK++  G + V+ +  + N ++++   + +      
Sbjct: 8   SDEIGTRLDVFLAGQEDNPSRASIQKMITDGAITVNNQVKRANYKLKANDQITM------ 61

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-------- 125
                    + +    +    + +   +LYED+ I V NK  G+ V   +G+        
Sbjct: 62  ---------VFEPPTEIEVKPENIPLDILYEDNDIIVINKARGMVVHPAAGVYSGTLVNA 112

Query: 126 -AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             YH    L S ++ K  +P + HRLD++TSG++VVA+   A   L      +   K Y 
Sbjct: 113 LLYHCHDEL-SGINGK-IRPGIVHRLDKDTSGVMVVAKNDFAHNDLALQIGSKTAIKEYV 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G    +K  I N  + +  I    + VV     G   A + F V++ + +   +++
Sbjct: 171 ALVHGNITEEKGII-NGNIGRHPIDRKKMAVVTN---GGKPATTVFHVLERY-KNCTFVQ 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
            +  TGRTHQ+RVH  ++G P++GD KYC N K  F    Q    LH+  + + HP    
Sbjct: 226 CRLLTGRTHQIRVHMAYIGHPLIGDPKYC-NSKNKFNIEGQ---ALHSLNLKIIHPRTKE 281

Query: 304 RLQITAPLPAHM 315
            +  TAP+P  M
Sbjct: 282 EMTFTAPIPEDM 293


>gi|224534885|ref|ZP_03675454.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           spielmanii A14S]
 gi|224513825|gb|EEF84150.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           spielmanii A14S]
          Length = 328

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 84/272 (30%), Positives = 134/272 (49%), Gaps = 38/272 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP---PVIN 72
           E  +RLD +  N        NL+   RS   R + +  K NN    G+  +I    PV  
Sbjct: 12  ENALRLDLYLSN--------NLEGFTRSQIKRRNVEAFKKNN----GKFFKIKLSKPVFK 59

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------S 123
             + ++ E     S ++  + S+   +I+ YED  I V NKP GI    G         +
Sbjct: 60  D-DEMLIEFDEESSQIDCLRPSNIPIAII-YEDPNIIVLNKPQGILSHPGISHWDDTVVN 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + YHI G LK   + +  +P + HRLD++TSG+L+ A+  +  + L + F+ +RI K+Y
Sbjct: 118 FLLYHIKG-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFKDKRINKVY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK---QNEKGANYAISHFKVIDCFAQKF 240
            ++V G   N    I +    +S I  D  +  K     +KG   A++ +K++  F   +
Sbjct: 177 IAIVKG---NFNSFIGSI---ESFIDRDKYNRKKFSVSKDKGKK-ALTEYKLLLNFGG-Y 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             L ++P TGRTHQLRVH  ++  PI+GD  Y
Sbjct: 229 SLLALKPKTGRTHQLRVHMKYLNFPILGDDVY 260


>gi|119588079|gb|EAW67675.1| RNA pseudouridylate synthase domain containing 4, isoform CRA_a
           [Homo sapiens]
 gi|119588080|gb|EAW67676.1| RNA pseudouridylate synthase domain containing 4, isoform CRA_a
           [Homo sapiens]
          Length = 377

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 95/192 (49%), Gaps = 21/192 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           +L++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 99  ILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P      +   +++K   G    H  
Sbjct: 159 VMVLAWDKDMAHQVQELFRTRQVVKKYWAITVHVPMPSAGVVDIPIVEKEAQGQQQHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  +  + A  A++ ++V+         +E+QP TG  HQLRVH + 
Sbjct: 219 TLSPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSSTLSS-ALVELQPITGIKHQLRVHLSF 277

Query: 261 HMGCPIVGDHKY 272
            + CPI+GDHKY
Sbjct: 278 GLDCPILGDHKY 289


>gi|312889804|ref|ZP_07749350.1| ribosomal large subunit pseudouridine synthase D [Mucilaginibacter
           paludis DSM 18603]
 gi|311297730|gb|EFQ74853.1| ribosomal large subunit pseudouridine synthase D [Mucilaginibacter
           paludis DSM 18603]
          Length = 253

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/214 (30%), Positives = 106/214 (49%), Gaps = 17/214 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTH 148
            D     +LYED+ +   NK AG  VQ        +D  +K ++  K  KP      + H
Sbjct: 23  GDITDKDVLYEDNHLIAINKRAGDIVQVDDTGDESLDEKVKKYIAKKYNKPNGAFLGVVH 82

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KS 206
           RLD+  SG+++ A+T  A + +   F+ R I K Y ++V   P  +   + +WL+K  + 
Sbjct: 83  RLDRPVSGVIMFAKTSKALERMNALFKGREIHKTYLAVVRNRPVPESGNLVHWLIKNPQK 142

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           ++   Y H V     G+  +  ++++I      +  +E+ P TGR HQ+RV    +GCPI
Sbjct: 143 NVTKPYDHEVP----GSLRSELNYRLIGEL-NGYYLIEVDPITGRPHQIRVQLSTLGCPI 197

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           VGD+KY     G     ++  + LHAR +   HP
Sbjct: 198 VGDNKY-----GYPRGSLKKSICLHARRIQFIHP 226


>gi|310779318|ref|YP_003967651.1| pseudouridine synthase, RluA family [Ilyobacter polytropus DSM
           2926]
 gi|309748641|gb|ADO83303.1| pseudouridine synthase, RluA family [Ilyobacter polytropus DSM
           2926]
          Length = 313

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 85/332 (25%), Positives = 154/332 (46%), Gaps = 44/332 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQ--VVR 66
           +  EN ++  RLD +    + ++    +QK++    + ++ K++ K  N+++  +  +VR
Sbjct: 10  IYAENSDKGKRLDAFVNESFDYLTRSYIQKLIEQRDIIIEGKEKNKSGNKLKGNEKILVR 69

Query: 67  IPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           IP           E ++LD     + + K         +YED  + V NK   + V    
Sbjct: 70  IP-----------EDEMLDIEPQDIPIEK---------VYEDKDLVVINKAPDMVVHPAP 109

Query: 124 G-----IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     +   +   +K   +  G  +P + HRLD+ TSG++V+A+   +   L++ F+ +
Sbjct: 110 GNYSGTLVNALMHNIKDLSNINGVIRPGIVHRLDKNTSGLIVIAKNDFSHLKLSDMFKNK 169

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I K Y  +  GI   K   I N L+ ++      + VV++N K    AIS++K++D  A
Sbjct: 170 DISKTYICICKGIFSEKTGRIEN-LIGRNPKNRKTMTVVQKNGKN---AISNYKILD-EA 224

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  +E++  TGRTHQ+RVH   +  PI+GD  Y         S I  +  LHA  ++ 
Sbjct: 225 GDFSLVEVKIETGRTHQIRVHMKSINHPILGDEVYGK------PSKICKRQMLHAYRLEF 278

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
            HP  G ++ +   +P          G   ++
Sbjct: 279 HHPLSGEKMTVFGEIPEDFKNAAKKTGLDINK 310


>gi|145639768|ref|ZP_01795370.1| SfhB [Haemophilus influenzae PittII]
 gi|145271136|gb|EDK11051.1| SfhB [Haemophilus influenzae PittII]
 gi|309750408|gb|ADO80392.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae R2866]
          Length = 324

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 122/247 (49%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP  + V  G+G         + YH    ++  V   G    + HRLD
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVE--VPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++ +
Sbjct: 139 KDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLM 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P++G
Sbjct: 199 A---VHPIGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLG 248

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           D  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+  
Sbjct: 249 DQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 309 NALKADY 315


>gi|320546984|ref|ZP_08041285.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equinus ATCC 9812]
 gi|320448386|gb|EFW89128.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equinus ATCC 9812]
          Length = 298

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 86/322 (26%), Positives = 148/322 (45%), Gaps = 50/322 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++       ++   V V+ K VK    ++ G VV          
Sbjct: 7   EAGARLDKALAD-LTELSRSQANDEIKKETVLVNGKAVKAKYAVKVGDVV---------T 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
           + + E+++L+ +      ++ +   ++YED  + V NKP G+ V    G         + 
Sbjct: 57  YEVPEEEVLEYT------AENIPLDIIYEDEDVAVVNKPQGMVVHPSVGHTSGTLVNALM 110

Query: 127 YHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           YHI    K      G  +P + HR+D++TSG+L++A+  AA   L    + ++  + Y +
Sbjct: 111 YHI----KDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDAAHNALAAELKDKKSLRKYVA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWL 243
           +V G   N +  I      ++ IG       KQ    KG   A++HFKV++ F   +  +
Sbjct: 167 IVHGNIPNDRGVI------EAPIGRSDKDRKKQAVTAKG-KPAVTHFKVLERFGS-YTLV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E+   TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   HP+
Sbjct: 219 ELTLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGHGQ-------FLHAQTLGFTHPK 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  +  TA +P    +T + L
Sbjct: 272 TGETITFTAEVPEIFKETLEKL 293


>gi|297184316|gb|ADI20433.1| pseudouridylate synthases, 23S RNA-specific [uncultured alpha
           proteobacterium EB080_L43F08]
          Length = 217

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 68/222 (30%), Positives = 112/222 (50%), Gaps = 30/222 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  + V NKP+G+    G  + +H    L+  ++       L HRLD +TSG+++ 
Sbjct: 15  ILYIDEDVLVVNKPSGLLTVPGKELKHHDSLELRVKIEYPNS--FLVHRLDMDTSGVIIF 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--------CIANWLLKKSHIGGDY 212
           A +++  + L   F  R ++K+Y + V+G   N KE         I +W  +        
Sbjct: 73  ALSKSTQRSLNLQFEKRIVKKLYEARVFG---NIKEDNGFIDLPLIVDWPNRP------- 122

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             + K + K    A++H++V+D        + + P TGRTHQLRVH + +G  I+GD   
Sbjct: 123 --LQKIDAKEGKSALTHWQVLDREGD-VTRVALMPETGRTHQLRVHMMSLGHTILGDR-- 177

Query: 273 CANFKGNFTS-PIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
              F GN     + N+L LHA+ + + HP+ G ++   APLP
Sbjct: 178 ---FYGNVAEINLANELQLHAKDLMIIHPKNGKKITFKAPLP 216


>gi|282877384|ref|ZP_06286207.1| RNA pseudouridine synthase [Prevotella buccalis ATCC 35310]
 gi|281300436|gb|EFA92782.1| RNA pseudouridine synthase [Prevotella buccalis ATCC 35310]
          Length = 227

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 110/228 (48%), Gaps = 15/228 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSG 156
           LYED+ I + +K +G  VQG       +   +K ++  K  KP      + HRLD+   G
Sbjct: 4   LYEDNHIIIVSKRSGEIVQGDKTGDEPLSETVKQYIKEKYHKPGNVFLGVVHRLDRPVWG 63

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V A+T  A   L + F+  ++ K YW++    P  ++  + +WL++       Y H  
Sbjct: 64  LVVFAKTSKALTRLNKMFKEGQVHKTYWAITKNAPPAEEGVLTDWLVRNERQNKSYAH-- 121

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            Q    A  A+  ++VI   + ++  +E+   TGR HQ+R    +MGC I GD KY A+ 
Sbjct: 122 PQEVPNAKKAVLKYRVI-AHSDRYHLIEVNLLTGRHHQIRCQLANMGCAIKGDLKYGAS- 179

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                S     + L AR +   HP     + + APLP +  K W++L 
Sbjct: 180 ----RSNPDGSISLLARRIMFVHPVSKENIVVEAPLPPND-KLWEALA 222


>gi|255101761|ref|ZP_05330738.1| putative pseudouridylate synthase [Clostridium difficile QCD-63q42]
 gi|255307629|ref|ZP_05351800.1| putative pseudouridylate synthase [Clostridium difficile ATCC
           43255]
          Length = 315

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 146/310 (47%), Gaps = 45/310 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK--RVKFNNRIQSGQVVRIPPVINALNHI 77
           RLD +       ++   +QKI++ G+V+V+ K  + ++  + +   V+ IP         
Sbjct: 29  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKARYLVKEEDNIVIEIP--------- 79

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYH 128
             E K+L+           +   ++YED  + + NKP  + V            +GI YH
Sbjct: 80  --EPKVLEVL------PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYH 131

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               L S   +   +P + HR+D++TSG+L++A+   A   L E  +   I + Y  + +
Sbjct: 132 CKDKLSSI--NGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICY 189

Query: 189 GIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           G+ K  K  +   + +  K  +    + VVK    G N AI+HF+V++ F  KF  +  +
Sbjct: 190 GVVKEDKITVDKPIGRNPKDRLK---MAVVKD---GKN-AITHFEVVERF-DKFTHMRAR 241

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVHAL +  P++GD+ Y    +  F    Q    LHA+ +   HP     +
Sbjct: 242 LETGRTHQIRVHALSINHPLLGDYVYGPK-ETKFKLKGQT---LHAKKLGFIHPTTKEYI 297

Query: 306 QITAPLPAHM 315
           +  + LP + 
Sbjct: 298 EFNSELPEYF 307


>gi|163748427|ref|ZP_02155681.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           benthica KT99]
 gi|161332005|gb|EDQ02682.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           benthica KT99]
          Length = 225

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/222 (32%), Positives = 118/222 (53%), Gaps = 24/222 (10%)

Query: 94  SDFLKSI-------LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           SDF+ S        ++Y+D  I V NK +G+ SV G +    H D  + S V ++    +
Sbjct: 2   SDFIYSPPTDPWLEIIYQDKDILVVNKHSGLLSVPGRA--PEHQDS-VYSRVLAEYPNAQ 58

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD  TSG+++VA  R A + L   FR R  +K Y++ V G  K +K  +   L+  
Sbjct: 59  VVHRLDMATSGVILVALRRNAEKELKRQFRERETKKTYYARVAGHIKQQKGSVDLPLI-- 116

Query: 206 SHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                D+ +  KQ  + +    +++HF+VI  +A++   +++ P TGR+HQLRVH + +G
Sbjct: 117 ----CDWPNRPKQKVDHEIGKPSLTHFEVI-SYAKRSTLVKLTPITGRSHQLRVHMMAIG 171

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            PI+GD+ Y         S    +L LHA+ + +  P  GR+
Sbjct: 172 HPILGDNFYADPLAKRLAS----RLLLHAQELTIKQPYSGRV 209


>gi|168181665|ref|ZP_02616329.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
 gi|182675008|gb|EDT86969.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
          Length = 300

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 82/283 (28%), Positives = 138/283 (48%), Gaps = 35/283 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K +R G+V V+K++V   +++    ++ I   +    H    Q I    +N+      
Sbjct: 33  IRKAVRDGRVFVNKEKVIKKHKLSQDDLIEI--YMQEDEH----QNIEPEDMNIE----- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKP--RLTHRL 150
               ++YED+ I V NK  GI V    G   H  G L + +       G+K   RL  RL
Sbjct: 82  ----IVYEDNDIIVINKRPGIVVHPTKG---HPTGTLSNGILYHFKKNGEKSIVRLVSRL 134

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ + +   L         +KIY ++V G  K K++ I N  + K     
Sbjct: 135 DRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEKRI-NLPIYKEEESE 193

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +V  +E+G   +I+ +KV++  + K   + ++  TGRTHQ+RVH  H+G P+ GD 
Sbjct: 194 SIKRIV--DERGQE-SITTYKVLEELS-KGSVVRLELETGRTHQIRVHMSHLGHPLYGDS 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
            Y    KG        +  LHA  ++ PHP  G   +LQ + P
Sbjct: 250 LYG---KGEEEKEYVERQALHAYKLEFPHPRTGDILKLQCSLP 289


>gi|332140106|ref|YP_004425844.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity [Alteromonas
           macleodii str. 'Deep ecotype']
 gi|332143096|ref|YP_004428834.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity [Alteromonas
           macleodii str. 'Deep ecotype']
 gi|327550128|gb|AEA96846.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity [Alteromonas
           macleodii str. 'Deep ecotype']
 gi|327553118|gb|AEA99836.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity [Alteromonas
           macleodii str. 'Deep ecotype']
          Length = 238

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/222 (32%), Positives = 116/222 (52%), Gaps = 25/222 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V +KP+G+    G  +  H D  + S V++      + HRLD  TSGILV+
Sbjct: 18  ILYQDEDMVVAHKPSGLLSVPGKALE-HRDSLI-SRVNTVYPTATVVHRLDMATSGILVL 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC----IANWLLKKSHIGGDYVHV 215
           A  + + +H+++ F +R  QK Y++ V G I ++  E     I +W  +   +  D+   
Sbjct: 76  ALNKDSHRHISKQFELRLTQKRYFARVHGHIEEDSGEVDLPLICDWPNRPKQMV-DF--- 131

Query: 216 VKQNEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               E+G   AI+ F+VI    D  A+++  + + P TGR+HQLRVH L +G PI+GD  
Sbjct: 132 ----ERGKK-AITRFEVIERATDDAARRYTLVALYPITGRSHQLRVHMLALGHPILGDRL 186

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y  +   +       +L LHA  + L HP   + L    P+P
Sbjct: 187 YAHDEALSMAP----RLQLHAESLSLTHPTLEKWLHFKTPIP 224


>gi|114561852|ref|YP_749365.1| pseudouridine synthase, RluA family protein [Shewanella
           frigidimarina NCIMB 400]
 gi|114333145|gb|ABI70527.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           frigidimarina NCIMB 400]
          Length = 324

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 86/333 (25%), Positives = 155/333 (46%), Gaps = 47/333 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINAL 74
           +  +RLD+     +P  +   +++ + SG + +D   V K   ++   Q+V +   +   
Sbjct: 15  QTGLRLDQALAGLFPDYSRTRIKEWILSGAITIDGITVDKPREKVFESQLVEVTATL--- 71

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                E+++   + N+  +       ++YED  I V NK AG+ V  G+G A   DG L 
Sbjct: 72  -----EEEVSAKAQNIDLN-------IVYEDDHILVINKQAGLVVHPGAGNA---DGTLM 116

Query: 135 SWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           + +          PR  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V 
Sbjct: 117 NALLYHCPDIEHVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQARDIVREYEAIVL 176

Query: 189 GIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           G         E I     +++ +    +H       G   +++H++V + F +    L +
Sbjct: 177 GTMTAGGTVDEPIERHATRRTQMA--VIH-------GGRPSVTHYRVSEKF-RAHTRLRL 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQN--KLYLHARYMDL 297
           +  +GRTHQ+RVH  H+G  +VGD  Y        +    F   ++N  +  LHA  ++L
Sbjct: 227 RLESGRTHQIRVHMAHIGHELVGDPVYGGRPRPPKSASPEFFELLKNFKRQALHAVRLEL 286

Query: 298 PHPEGGRLQI-TAPLPAHMVKTWDSLGFKYDRN 329
            HP    +    AP+P  MV+   +L    + N
Sbjct: 287 AHPFTCEIMTWHAPIPDDMVELTKALRVDTELN 319


>gi|315924134|ref|ZP_07920360.1| ribosomal large subunit pseudouridine synthase D [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315622536|gb|EFV02491.1| ribosomal large subunit pseudouridine synthase D [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 287

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 111/222 (50%), Gaps = 17/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQ--KPRLTHRLDQETS 155
           ++YED +I   NK AG+        ++ +D     +  + +S GQ  K R   RLD +TS
Sbjct: 66  IIYEDDEILAVNKDAGLVTHPTK--SHQLDTLGNLVAGYFESTGQYAKVRFVTRLDSDTS 123

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V+A+ +    +L     + + +K Y + V G P+     I   + +      D +H 
Sbjct: 124 GVIVIAKNKYIHHYLQSHQLIPKPEKRYLAFVNGCPEEMVGTIDLPIGRAE----DGIHR 179

Query: 216 VKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               E     +I+H++V++ F  QK   + ++  TGRTHQ+RVH   +GCPI+GD  Y  
Sbjct: 180 CVMPE--GKPSITHYRVVETFPEQKASAIALRLETGRTHQIRVHLATIGCPIIGDSLYNT 237

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
              G +      +  LHAR + L  P+ G+  + APL + +V
Sbjct: 238 TADGAYGI---RRTALHARSIALSLPKTGQHILYAPLKSDLV 276


>gi|170759270|ref|YP_001788292.1| RluA family pseudouridine synthase [Clostridium botulinum A3 str.
           Loch Maree]
 gi|169406259|gb|ACA54670.1| pseudouridine synthase, RluA family [Clostridium botulinum A3 str.
           Loch Maree]
          Length = 300

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 82/283 (28%), Positives = 137/283 (48%), Gaps = 35/283 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K +R G+V V+K++V   N++    ++ I   +    H    Q I    +N+      
Sbjct: 33  IRKAVRDGRVFVNKEKVIKKNKLSQDDLIEI--YMQEDEH----QNIEPEDMNIE----- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKP--RLTHRL 150
               ++YED+ I V NK  GI V    G   H  G L + +       G+K   RL  RL
Sbjct: 82  ----IVYEDNDIIVINKRPGIVVHPTKG---HPTGTLSNGILYHFKKNGEKSIVRLVSRL 134

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ + +   L         +KIY ++V G  K +KE   N  + K     
Sbjct: 135 DRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMK-EKEGRINLPIYKEEESE 193

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +V  +E+G   +I+ ++V++  + K   + ++  TGRTHQ+RVH  H+G P+ GD 
Sbjct: 194 SIKRIV--DERGQE-SITTYEVLEELS-KGSVVRLELETGRTHQIRVHMSHLGHPLYGDS 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
            Y    KG        +  LHA  ++ PHP  G   +LQ + P
Sbjct: 250 LYG---KGEEEKEYIERQALHAYKLEFPHPRTGDILKLQCSLP 289


>gi|315633348|ref|ZP_07888639.1| pseudouridine synthase A [Aggregatibacter segnis ATCC 33393]
 gi|315477848|gb|EFU68589.1| pseudouridine synthase A [Aggregatibacter segnis ATCC 33393]
          Length = 219

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/215 (33%), Positives = 110/215 (51%), Gaps = 17/215 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+Y D  I V NKP+G+    G+   Y+      S V  K       HRLD  TSGIL+ 
Sbjct: 16  LVYRDDYIAVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPAHRLDMATSGILLF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A ++AA + L   FR R  +K Y +LVWG  +     +   L+       D+ +  +Q  
Sbjct: 74  ALSKAADRELKRQFREREPKKYYQALVWGHVEQDHGVVELPLI------CDWENRPRQKI 127

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+G   A++ + V+  +      +++ P TGR+HQLR+H L +G PI+GD K+ A+ +
Sbjct: 128 CFERGKR-AVTFYDVLQRYPNNTTRIKLTPITGRSHQLRLHMLALGHPILGD-KFYAHPQ 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
               SP   +L LHA  + + HP  G  +  TAP+
Sbjct: 186 AKALSP---RLCLHAESLQIQHPITGETMGFTAPV 217


>gi|116873278|ref|YP_850059.1| ribosomal large subunit pseudouridine synthase [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|116742156|emb|CAK21280.1| Ribosomal large subunit pseudouridine synthase [Listeria welshimeri
           serovar 6b str. SLCC5334]
          Length = 302

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 84/302 (27%), Positives = 142/302 (47%), Gaps = 51/302 (16%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVV----RIPPVINALNHIIKEQKILDSSVNLTK 92
           +Q +L++G + V+ +  K N ++Q G  +    R P          +E ++L   + L  
Sbjct: 32  IQLMLKNGDITVNGELAKPNYKVQVGDEIHYEIREP----------EELEVLAEDIPLD- 80

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQK 143
                   + +ED  + V NKP G+ V   +G A         +H D    S ++ K  +
Sbjct: 81  --------IYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL--SGINGK-IR 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    +
Sbjct: 130 PGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPI 188

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++      + VV+  ++    A +HF+V++     +  +  +  TGRTHQ+RVH  ++G
Sbjct: 189 GRAKEDRQKMAVVRDGKE----ARTHFEVLERLP-GYTLINCKLDTGRTHQIRVHLKYIG 243

Query: 264 CPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            P+ GD KY      KGN         YLHA  +   HP    R+   APLPA   K   
Sbjct: 244 HPLAGDPKYGPKNTIKGNGQ-------YLHAAKLGFDHPTTNERMTFEAPLPASFEKALK 296

Query: 321 SL 322
           SL
Sbjct: 297 SL 298


>gi|332185831|ref|ZP_08387578.1| pseudouridine synthase, RluA family protein [Sphingomonas sp. S17]
 gi|332014189|gb|EGI56247.1| pseudouridine synthase, RluA family protein [Sphingomonas sp. S17]
          Length = 315

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 142/318 (44%), Gaps = 39/318 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR   +  P ++   L+ ++ SG V             + G + R P    A   +  
Sbjct: 20  RLDRALADAVPTLSRERLKVLIASGAV------------TREGVMARDPAKRAAAGDLF- 66

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL------ 133
            Q  + +       +  +  ++ YED  + V +KPAG+ V   +G   ++DG L      
Sbjct: 67  -QVAVPAPTPAHNEAQDIPLVIAYEDEHLIVIDKPAGLVVHPAAG---NLDGTLVNALLH 122

Query: 134 ---KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               S     G  +P + HR+D++TSG++V A+T    + L + F    I + Y ++  G
Sbjct: 123 YCGGSLSGIGGVARPGIVHRIDKDTSGLMVAAKTDRTHEGLAKQFAAHSIDRRYRAITGG 182

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           IP+     + +  L +S      V +V    +G   A++H++ I+        +E +  T
Sbjct: 183 IPRPADGTV-DAPLARSPQNRKKVAIV----QGGKRAVTHYRTIEKL-NNAALVECRLET 236

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHP-EGGR 304
           GRTHQ+RVH   +G  ++GD  Y    KG   + +      +  LHA ++   HP  G  
Sbjct: 237 GRTHQVRVHMQSLGHALLGDPVY-GRTKGAQKALLDELDFRRQALHAAHLGFIHPISGNA 295

Query: 305 LQITAPLPAHMVKTWDSL 322
           L   +P+PA M + +  L
Sbjct: 296 LAFESPMPADMQELFSRL 313


>gi|190149589|ref|YP_001968114.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|189914720|gb|ACE60972.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
          Length = 226

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 66/205 (32%), Positives = 104/205 (50%), Gaps = 13/205 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+     +  V  K       HRLD  TSGIL+ A
Sbjct: 21  VYRDNHILVINKPSGLLSVPGNRPEYYDSAMTR--VQQKYGFTEPAHRLDMATSGILLFA 78

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            ++AA + L   FR R  +K Y +L+WG      E + +       +  D+ +  +Q   
Sbjct: 79  LSKAAEKELKRQFRDREPKKHYIALLWG---KLGEKVGDTGEMNFPLICDWENRPRQKIC 135

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y +    
Sbjct: 136 YERGKK-AITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGDKFYASPLAK 194

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
           + +     +L LHA  + + HP  G
Sbjct: 195 SLSP----RLCLHAESLSITHPITG 215


>gi|307262909|ref|ZP_07544533.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 13
           str. N273]
 gi|306871814|gb|EFN03534.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 13
           str. N273]
          Length = 237

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 66/205 (32%), Positives = 104/205 (50%), Gaps = 13/205 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+     +  V  K       HRLD  TSGIL+ A
Sbjct: 32  VYRDNHILVINKPSGLLSVPGNRPEYYDSAMTR--VQQKYGFTEPAHRLDMATSGILLFA 89

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            ++AA + L   FR R  +K Y +L+WG      E + +       +  D+ +  +Q   
Sbjct: 90  LSKAAEKELKRQFRDREPKKHYIALLWG---KLGEKVGDTGEMNFPLICDWENRPRQKIC 146

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y +    
Sbjct: 147 YERGKK-AITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGDKFYASPLAK 205

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
           + +     +L LHA  + + HP  G
Sbjct: 206 SLSP----RLCLHAESLSITHPITG 226


>gi|251795307|ref|YP_003010038.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247542933|gb|ACS99951.1| pseudouridine synthase, RluA family [Paenibacillus sp. JDR-2]
          Length = 322

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 83/279 (29%), Positives = 141/279 (50%), Gaps = 43/279 (15%)

Query: 36  NLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS--SVNLTK 92
           +++ +L  GQV V D+   K+N  +Q G+ V           +I++++  +    + LT 
Sbjct: 49  SVKSLLAHGQVYVNDRVETKYNYPLQPGETV-----------VIRKEREKEKFPLIGLT- 96

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRL-- 146
                   +L+ED  + V +K AG+    S +     AY     L ++V     K R+  
Sbjct: 97  --------ILHEDEHVIVASKEAGLLTIASDKETDMTAYRQ---LMAYVRESDPKNRIFI 145

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG+L+ A++ A  Q L E ++    ++ Y +LV G  K ++  I++W LK++
Sbjct: 146 VHRLDRDTSGVLMFAKSEAVQQKLQEEWQTIVKERSYVALVEGEVKRQEGTISSW-LKET 204

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                Y      +     +A++H+K++    + F  +E+   TGR +Q+RVH   +G PI
Sbjct: 205 KTLRMY---SSPHPNDGQHAVTHYKLLQA-GKVFSLVEVHLETGRKNQIRVHMQDIGHPI 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            GD KY     G+ T PI  +L LHAR +   HP  G+L
Sbjct: 261 AGDKKY-----GSTTKPI-GRLGLHARVLAFEHPVTGKL 293


>gi|294142362|ref|YP_003558340.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293328831|dbj|BAJ03562.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 225

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 74/230 (32%), Positives = 119/230 (51%), Gaps = 25/230 (10%)

Query: 94  SDFLKSI-------LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           SDF+ S        ++Y+D  I V NKP+G+ SV G +    H D  + S V ++    +
Sbjct: 2   SDFIYSPPTDPWLEIIYQDKDILVINKPSGLLSVPGRA--PEHRDS-VYSRVLAEHPNAQ 58

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD  TSG++VVA  R A + L   FR R  +K Y++ V G  K     +   L+  
Sbjct: 59  IVHRLDMATSGVIVVALRRNAEKELKRQFRDRETKKTYYARVAGYIKEHTGSVDLPLI-- 116

Query: 206 SHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                D+ +  KQ  + +    +++HF+VI   A++   +++ P TGR+HQLRVH + +G
Sbjct: 117 ----CDWPNRPKQKVDHEVGKSSLTHFEVI-SKAKRSTLVKLTPITGRSHQLRVHMMAIG 171

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            PI+GD+ Y         S    +L LHA  + +  P  G+ L  ++ +P
Sbjct: 172 HPILGDNFYADPLAKRLAS----RLLLHAHKLTIKQPYSGKELTFSSEVP 217


>gi|225568048|ref|ZP_03777073.1| hypothetical protein CLOHYLEM_04121 [Clostridium hylemonae DSM
           15053]
 gi|225163144|gb|EEG75763.1| hypothetical protein CLOHYLEM_04121 [Clostridium hylemonae DSM
           15053]
          Length = 341

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/326 (23%), Positives = 144/326 (44%), Gaps = 30/326 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++++ +E   RLD++ K +        L K+LR   + ++ +R   N ++ +G  VR
Sbjct: 1   MKIIIIKPNESEQRLDKFLKKYMNRAPGSFLYKMLRKKNITLNGRRAGGNEKLHTGDEVR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +     + + +  +       D     ++YEDS +   NKPAG+  Q      
Sbjct: 61  LFLSDETIEKFTGDDEPVAGAKGRNTTLD-----IIYEDSHVLFVNKPAGMLSQKAEKTD 115

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   + S++   GQ         +P + +RLD+ TSG++   +T A  Q     FR R
Sbjct: 116 ISLVEHIISYLLDSGQLTREELRTFRPSVCNRLDRNTSGLVAAGKTLAGLQMFGSLFRDR 175

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  +V G   +K   I  +L+K        +    + EK A     +  +   ++
Sbjct: 176 NLRKYYLCIVKG-KVDKPSHIKGYLIKNEQTNEVRIVTSGEAEKAAPIETEYIPL--AYS 232

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHA 292
           ++   L +   TGRTHQ+R H  ++  P+ GD+KY        ++  +    Q    LH+
Sbjct: 233 REHSLLRVHLITGRTHQIRAHLAYVSHPLCGDYKYGDRDVNERYRKKYGVTSQ---MLHS 289

Query: 293 RYMDLPHPEGGRLQIT-----APLPA 313
             + LP  EG    ++     AP+PA
Sbjct: 290 YELVLPVLEGEFAALSERTFRAPVPA 315


>gi|157804237|ref|YP_001492786.1| type II citrate synthase [Rickettsia canadensis str. McKiel]
 gi|157785500|gb|ABV74001.1| type II citrate synthase [Rickettsia canadensis str. McKiel]
          Length = 325

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 80/315 (25%), Positives = 150/315 (47%), Gaps = 31/315 (9%)

Query: 24  WFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
             K+  PH +N + L K L      V + +++    ++  QV+    +I+  + ++KE  
Sbjct: 1   MLKHSVPHELNGIRLDKALSLLLKNVSRNQIQ--KAVKDSQVLVNDIIISDPDVLVKEND 58

Query: 83  ILDSSV----NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           I+  S      L   +  +   ++YE+  + V NK AG++V  G G  +H D  + + + 
Sbjct: 59  IILFSFKEPEELKIEAANIALDIIYENDDLIVINKAAGMTVHPGLG--HHNDTLVNALLH 116

Query: 139 --------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                      ++P + HRLD++T+G++VVA+   A   L      R++ + Y +L+WG+
Sbjct: 117 YTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKALIWGV 176

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHT 249
             N  E +    + +S      + ++K    G   A++H+K ++ F       +E + +T
Sbjct: 177 I-NPLEGVIQNNIGRSRSDRQKMTILKY---GGKEAVTHYKTLELFYGGTISMVECKLNT 232

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLY------LHARYMDLPHPE 301
           GRTHQ+RV   H+   +VGD  Y  N +    SP  ++ KL       LH+ Y+   +P 
Sbjct: 233 GRTHQIRVQLSHLKHSVVGDQTYGNNDRKVAHSPPELKAKLIDFKRQALHSWYLSFTNPT 292

Query: 302 GGR-LQITAPLPAHM 315
             + ++ +  LP  M
Sbjct: 293 SNKIMEFSCKLPRDM 307


>gi|291616241|ref|YP_003518983.1| RluA [Pantoea ananatis LMG 20103]
 gi|291151271|gb|ADD75855.1| RluA [Pantoea ananatis LMG 20103]
          Length = 217

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 107/207 (51%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D+ I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++V
Sbjct: 14  ILYQDAHIMVVNKPSGLLSVPGR--LDEHKDSVM-TRIQRDYPEAESVHRLDMATSGVIV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R   K Y + VWG P  +K  +   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPAKTYVARVWGHPAQEKGMVDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              + G + A + ++V++        + ++P TGR+HQLRVH L +G PI+GD  Y    
Sbjct: 125 VCFDTGKS-AQTDYQVVEYGEDNSARVALKPITGRSHQLRVHMLALGHPILGDGFYA--- 180

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
                  + ++L LHA  + + HP  G
Sbjct: 181 -HPEAKAMADRLLLHAESLTITHPAFG 206


>gi|149190306|ref|ZP_01868580.1| ribosomal large subunit pseudouridine synthase A [Vibrio shilonii
           AK1]
 gi|148835913|gb|EDL52876.1| ribosomal large subunit pseudouridine synthase A [Vibrio shilonii
           AK1]
          Length = 245

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 106/229 (46%), Gaps = 38/229 (16%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ED  I   NKP+G+    G  +  H D      V+   +  ++ HRLD  TSG++++A
Sbjct: 17  VFEDEHILAVNKPSGLLSVPGKALE-HYDSMWSRLVEVYPEI-QVVHRLDMSTSGLMLLA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW--------LLKKSHI 208
           + + A + L + F+ R   K+Y++ VWG P   +       I +W          +    
Sbjct: 75  KNKEAERSLKKQFQYRLTHKVYYARVWGTPDESEGLIDLPLICDWPNRPRQKVCYEHGKP 134

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              Y  VVKQ ++ +        ++  F          P TGR+HQLRVH L +G PIVG
Sbjct: 135 SQTYYQVVKQEQQTS--------IVRLF----------PITGRSHQLRVHLLELGHPIVG 176

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMV 316
           D  Y      +F+    ++L LHA  +   HPE  +LQ I  P   H V
Sbjct: 177 DEFYAHEEAMSFS----DRLELHAAELCFYHPETEKLQSIFVPCDFHQV 221


>gi|317046871|ref|YP_004114519.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316948488|gb|ADU67963.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 217

 Score = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/214 (33%), Positives = 110/214 (51%), Gaps = 17/214 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++V
Sbjct: 14  ILYQDDHIMVVNKPSGLLSVPGR--LDEHKDSVM-TRIQRDYPQAESVHRLDMATSGVIV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R   K Y + VWG P  ++  I   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPAKQYVARVWGHPAEEQGLIDLPLI------CDWPNRPKQK 124

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A + ++V+   A     + ++P TGR+HQLRVH L +G PI+GD ++ A+ +
Sbjct: 125 VCFDSGKPAQTEYQVLAYDADNSARVLLKPITGRSHQLRVHLLALGHPILGD-RFYASPE 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
               +P   +L LHA  + + HP  G R+    P
Sbjct: 184 ALAMAP---RLLLHAESLTITHPAFGNRMTFRQP 214


>gi|170756838|ref|YP_001782613.1| RluA family pseudouridine synthase [Clostridium botulinum B1 str.
           Okra]
 gi|169122050|gb|ACA45886.1| pseudouridine synthase, RluA family [Clostridium botulinum B1 str.
           Okra]
          Length = 300

 Score = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 82/283 (28%), Positives = 137/283 (48%), Gaps = 35/283 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K +R G+V V+K++V   N++    ++ I   +    H    Q I    +N+      
Sbjct: 33  IRKAVRDGRVFVNKEKVIKKNKLSQDDLIEI--YMQEDEH----QNIEPEDMNIE----- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKP--RLTHRL 150
               ++YED+ I V NK  GI V    G   H  G L + +       G+K   RL  RL
Sbjct: 82  ----IVYEDNDIIVINKRPGIVVHPTKG---HPTGTLSNGILYHFKKNGEKSIVRLVSRL 134

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ + +   L         +KIY ++V G  K +KE   N  + K     
Sbjct: 135 DRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMK-EKEGRINLPIYKEEESE 193

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +V  +E+G   +I+ ++V++  + K   + ++  TGRTHQ+RVH  H+G P+ GD 
Sbjct: 194 SIKRIV--DERGQE-SITTYEVLEELS-KGSVVRLELETGRTHQIRVHMSHLGHPLYGDS 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
            Y    KG        +  LHA  ++ PHP  G   +LQ + P
Sbjct: 250 LYG---KGEEEKEYIERQALHAYKLEFPHPRTGDILKLQCSLP 289


>gi|82545047|ref|YP_408994.1| 23S rRNA pseudouridine synthase D [Shigella boydii Sb227]
 gi|187732689|ref|YP_001881382.1| 23S rRNA pseudouridine synthase D [Shigella boydii CDC 3083-94]
 gi|81246458|gb|ABB67166.1| suppressor of ftsH mutation [Shigella boydii Sb227]
 gi|187429681|gb|ACD08955.1| ribosomal large subunit pseudouridine synthase D [Shigella boydii
           CDC 3083-94]
 gi|320177087|gb|EFW52104.1| Ribosomal large subunit pseudouridine synthase D [Shigella
           dysenteriae CDC 74-1112]
          Length = 326

 Score = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 125/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   ++DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDLVVHPGAG---NLDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 253 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPEDMVELIEVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|296164416|ref|ZP_06846990.1| RluA family RNA pseudouridine synthase [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295900198|gb|EFG79630.1| RluA family RNA pseudouridine synthase [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 308

 Score = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 85/298 (28%), Positives = 134/298 (44%), Gaps = 43/298 (14%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRI------PPVINALNHIIKEQKILDSSVNLTKH 93
           I   G V +D  +   ++R+  G  +++      PPV N                     
Sbjct: 35  IAEDGGVELDGVQAGKSDRLTGGAWLQVRLPEAPPPVEN-------------------TP 75

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LT 147
            D     +LY D  I   +KPA ++     G     + G L +    + + G   R  + 
Sbjct: 76  VDIEGMTILYSDEDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRITTSGVPERQGIV 135

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA +  A   L  +F+ R + K Y +LV G P      I   + +  H
Sbjct: 136 HRLDVGTSGVMVVALSERAYTVLKRAFKQRTVDKRYHALVQGHPDPSSGTIDAPIGR--H 193

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH--ALHMGCP 265
            GG++   V  N +   ++++H+  I+ F      L++   TGRTHQ+RVH  ALH  C 
Sbjct: 194 RGGEWKFAVTTNGR---HSLTHYDTIEAFTAA-SLLDVHLETGRTHQIRVHFSALHHPC- 248

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             GD  Y A+ K      ++ + +LHAR +   HP +G R++I +P PA +    D L
Sbjct: 249 -CGDLVYGADPKLAKRLGLERQ-WLHARSLSFAHPADGRRMEIVSPYPADLQHALDVL 304


>gi|237796432|ref|YP_002863984.1| pseudouridine synthase, RluA family [Clostridium botulinum Ba4 str.
           657]
 gi|229261661|gb|ACQ52694.1| pseudouridine synthase, RluA family [Clostridium botulinum Ba4 str.
           657]
          Length = 300

 Score = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 82/283 (28%), Positives = 138/283 (48%), Gaps = 35/283 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K +R G+V V+K++V   +++    ++ I   +    H    Q I    +N+      
Sbjct: 33  IRKAVRDGRVFVNKEKVIKKHKLSQDDLIEI--YMQEDEH----QNIEPEDMNIE----- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKP--RLTHRL 150
               ++YED+ I V NK  GI V    G   H  G L + +       G+K   RL  RL
Sbjct: 82  ----IVYEDNDIIVINKRPGIVVHPTKG---HPTGTLSNGILYHFKKNGEKSIVRLVSRL 134

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ + +   L         +KIY ++V G  K K++ I N  + K     
Sbjct: 135 DRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEKRI-NLPIYKEEESE 193

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +V  +E+G   +I+ +KV++  + K   + ++  TGRTHQ+RVH  H+G P+ GD 
Sbjct: 194 SIKRIV--DERGQE-SITTYKVLEELS-KGSVVRLELETGRTHQIRVHMSHLGHPLYGDS 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
            Y    KG        +  LHA  ++ PHP  G   +LQ + P
Sbjct: 250 LYG---KGEEEKEYIERQALHAYKLEFPHPRTGDILKLQCSLP 289


>gi|171463620|ref|YP_001797733.1| pseudouridine synthase, RluA family [Polynucleobacter necessarius
           subsp. necessarius STIR1]
 gi|171193158|gb|ACB44119.1| pseudouridine synthase, RluA family [Polynucleobacter necessarius
           subsp. necessarius STIR1]
          Length = 344

 Score = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/287 (27%), Positives = 131/287 (45%), Gaps = 25/287 (8%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+      P  +   L+  + +G V VD K  K    ++ G+ +++ P        + 
Sbjct: 33  RLDKVLVGTLPDYSRNRLKTWVEAGAVMVDGKVTKARYLLRGGESIKVFP------QEMP 86

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           EQ           + + +   ++YED  I V NKP G+ V   +G      ++G L  + 
Sbjct: 87  EQ--------FAFNPEDIPLDVVYEDGDIIVINKPPGLVVHPAAGNWSGTLLNGLLFRYP 138

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + K   PR  + HRLD++TSG++VVART  A   L    + R + + Y + VWG   ++ 
Sbjct: 139 ELK-MFPRAGIVHRLDKDTSGLMVVARTSQAQTSLVRQLQDRTVGRRYLAWVWGDAPSQG 197

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTH 253
           + +A+    +     D + +   + +G   A    ++     Q+     LE +  TGRTH
Sbjct: 198 KVLASVGRDQR----DRLKMAAGSPQGKPAATLFRRLSKGLVQETPVTLLECRLETGRTH 253

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Q+RVH   +G P+VGD  Y     G   +    +  LHA  + L HP
Sbjct: 254 QIRVHFESLGFPLVGDPVYRKKTPGAANNLEFKRQALHAFALSLQHP 300


>gi|86156624|ref|YP_463409.1| pseudouridine synthase RluD [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85773135|gb|ABC79972.1| Pseudouridine synthase, RluD [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 299

 Score = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 86/288 (29%), Positives = 134/288 (46%), Gaps = 32/288 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHII 78
           R+DR+       I+    ++ + +G V VD +R K   R +  GQ V    V+N      
Sbjct: 16  RIDRFIAARG-GISRGLARRAIEAGGVFVDGRRCKVAGRTLTPGQQV----VVN------ 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWV 137
               + +     +  +   +  LLY D+ +   +KPAG+  Q         D G L   V
Sbjct: 65  ----LEEGGRAASAPAALGRERLLYADADLCAVDKPAGVPAQ----PTLTTDRGALPELV 116

Query: 138 DSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            +  G    L HRLD+ETSG+ V ARTR AA  L E+FR    +K Y +L    P   + 
Sbjct: 117 SALLGAPVTLVHRLDRETSGVTVFARTREAAAALAEAFRTGAPEKTYLALCARAPSPAEG 176

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +A  L K     G     +++ +   + A + ++ +   A     +E +P TGRTHQ+R
Sbjct: 177 RVALALGKDPARPG-----LRRVDPAGDPAATRYRTLR-EAPGGAQVEARPETGRTHQIR 230

Query: 257 VHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGG 303
           VH   +G P++GD +Y    + G    P   ++ LHA  ++LPHP  G
Sbjct: 231 VHLAALGAPLLGDARYGGPRRVGEVAVP---RVMLHAARLELPHPVTG 275


>gi|299530513|ref|ZP_07043933.1| pseudouridine synthase, RluA family protein [Comamonas testosteroni
           S44]
 gi|298721489|gb|EFI62426.1| pseudouridine synthase, RluA family protein [Comamonas testosteroni
           S44]
          Length = 352

 Score = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 93/336 (27%), Positives = 147/336 (43%), Gaps = 51/336 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIP 68
           ++V  +    R+D+         +   LQ++L  G V ++ K  +K + ++  G  +R+ 
Sbjct: 45  LMVGTEHHGQRVDKVLALGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLRV- 103

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                      E +    S+     +  L+  ++YED  + V NKPAG+ V    G    
Sbjct: 104 -----------EMRPTQQSMAFQPETMDLQ--VVYEDEDLLVINKPAGLVVHPAPGNWTG 150

Query: 127 YHIDGFLKSWVDSKG-QKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             ++G L    D K  Q PR  + HRLD++TSG++VVAR R+    L +    R + + Y
Sbjct: 151 TLLNGLLAR--DEKARQVPRAGIVHRLDKDTSGLMVVARNRSTMDALIKMIAAREVSRQY 208

Query: 184 WSLV---WGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDC 235
            +L    WG  + ++E  A        IG D      + VV  N      A + F ++D 
Sbjct: 209 LALAHKQWG-SRKRREVDAP-------IGRDPRNRLRMAVVDLNLHPGKQARTDFDLLDG 260

Query: 236 FAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            A      C L    HTGRTHQ+RVH   +G P++ D  Y    +G        +  LHA
Sbjct: 261 DAAHSLVRCTL----HTGRTHQIRVHMASLGHPLIADTLYGGKPEGGL-----ERQALHA 311

Query: 293 RYMDLPHPEGGRLQI-TAPLPAHMVKTWDSLGFKYD 327
             +   HP   +  +  APLP  M    D  G +Y+
Sbjct: 312 FRLAFEHPVTKKPLVHYAPLPQDMAGALDLWGLRYN 347


>gi|307249532|ref|ZP_07531519.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
 gi|306858387|gb|EFM90456.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
          Length = 237

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 66/205 (32%), Positives = 104/205 (50%), Gaps = 13/205 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+     +  V  K       HRLD  TSGIL+ A
Sbjct: 32  VYRDNHILVINKPSGLLSVPGNRPEYYDSAMTR--VQQKYGFTEPAHRLDMATSGILLFA 89

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            ++AA + L   FR R  +K Y +L+WG      E + +       +  D+ +  +Q   
Sbjct: 90  LSKAAEKELKRQFRDREPKKHYIALLWG---KLGEKVGDTGEMNFPLICDWENRPRQKIC 146

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y +    
Sbjct: 147 YERGKK-AITHYEVLAHLPNNATRVKLTPITGRSHQLRVHSLALGHPILGDKFYASPLAK 205

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
           + +     +L LHA  + + HP  G
Sbjct: 206 SLSP----RLCLHAESLSITHPITG 226


>gi|254976188|ref|ZP_05272660.1| putative pseudouridylate synthase [Clostridium difficile QCD-66c26]
 gi|255093577|ref|ZP_05323055.1| putative pseudouridylate synthase [Clostridium difficile CIP
           107932]
 gi|255315322|ref|ZP_05356905.1| putative pseudouridylate synthase [Clostridium difficile QCD-76w55]
 gi|255517989|ref|ZP_05385665.1| putative pseudouridylate synthase [Clostridium difficile QCD-97b34]
 gi|255651105|ref|ZP_05398007.1| putative pseudouridylate synthase [Clostridium difficile QCD-37x79]
          Length = 315

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 85/310 (27%), Positives = 145/310 (46%), Gaps = 45/310 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK--RVKFNNRIQSGQVVRIPPVINALNHI 77
           RLD +       ++   +QKI++ G+V+V+ K  + K+  + +   V+ IP         
Sbjct: 29  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKAKYLVKEEDNIVIEIP--------- 79

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYH 128
             E K+L+           +   ++YED  + + NKP  + V            +GI YH
Sbjct: 80  --EPKVLEVL------PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYH 131

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               L S   +   +P + HR+D++TSG+L++A+   A   L E  +   I + Y  + +
Sbjct: 132 CKDKLSSI--NGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICY 189

Query: 189 GIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           G+ K  K  +   + +  K  +    + VVK    G N AI+HF+V++ F  KF  +  +
Sbjct: 190 GVVKEDKITVDKPIGRNPKDRLK---MAVVKD---GKN-AITHFEVVERF-DKFTHMRAR 241

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVHAL +  P++GD  Y    +  F    Q    LHA+ +   HP     +
Sbjct: 242 LETGRTHQIRVHALSINHPLLGDFVYGPK-ETKFKLKGQT---LHAKKLGFIHPTTKEYI 297

Query: 306 QITAPLPAHM 315
           +  + LP + 
Sbjct: 298 EFNSELPEYF 307


>gi|218281133|ref|ZP_03487668.1| hypothetical protein EUBIFOR_00229 [Eubacterium biforme DSM 3989]
 gi|218217647|gb|EEC91185.1| hypothetical protein EUBIFOR_00229 [Eubacterium biforme DSM 3989]
          Length = 304

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 87/316 (27%), Positives = 146/316 (46%), Gaps = 34/316 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVN--LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +E+ +LDR  K     ++F    ++ +L  G V V++K +K + ++     + +      
Sbjct: 9   DEDTKLDRLDKVLAEKLDFSRKRIKDLLDEGNVLVNQKVMKASYKVCVNDEIEVS----- 63

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
               I E   LDS+  L +  D     ++YED  I V NKP G+ V    G      ++ 
Sbjct: 64  ----IPE---LDSTQVLPEPIDL---DIVYEDHDIIVINKPKGMVVHPAPGHYSGTLVNA 113

Query: 132 FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    D  G     +P + HR+D++TSG+LVVA+   A + L++  + +   + Y ++V
Sbjct: 114 LLYHCKDLSGINGVMRPGIVHRIDKDTSGLLVVAKNDKAHEALSQQLQDKTCHREYVAIV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
              P   +    +  + +       + V   N K A   I+HF V++ F+ KF +++ Q 
Sbjct: 174 HK-PFTHEYGTIHAPIGRDEKDRQKMAVTANNSKDA---ITHFSVLENFS-KFAYIKCQL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  ++  PI GD KY     G   +   N   LHA  ++  HP    ++ 
Sbjct: 229 ETGRTHQIRVHMQYIEHPIAGDPKY-----GPRKTIQANGQLLHACALEFVHPTTHEKMH 283

Query: 307 ITAPLPAHMVKTWDSL 322
              PL     K  + L
Sbjct: 284 FEVPLEPTFEKVLNEL 299


>gi|46143820|ref|ZP_00133946.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
 gi|165975772|ref|YP_001651365.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|303249525|ref|ZP_07335732.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|303252557|ref|ZP_07338720.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|165875873|gb|ABY68921.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|302648525|gb|EFL78718.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|302651599|gb|EFL81748.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
          Length = 222

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 66/205 (32%), Positives = 104/205 (50%), Gaps = 13/205 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+     +  V  K       HRLD  TSGIL+ A
Sbjct: 17  VYRDNHILVINKPSGLLSVPGNRPEYYDSAMTR--VQQKYGFTEPAHRLDMATSGILLFA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            ++AA + L   FR R  +K Y +L+WG      E + +       +  D+ +  +Q   
Sbjct: 75  LSKAAEKELKRQFRDREPKKHYIALLWG---KLGEKVGDTGEMNFPLICDWENRPRQKIC 131

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y +    
Sbjct: 132 YERGKK-AITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGDKFYASPLAK 190

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
           + +     +L LHA  + + HP  G
Sbjct: 191 SLSP----RLCLHAESLSITHPITG 211


>gi|319760323|ref|YP_004124261.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Blochmannia vafer str. BVAF]
 gi|318039037|gb|ADV33587.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Blochmannia vafer str. BVAF]
          Length = 333

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/318 (24%), Positives = 150/318 (47%), Gaps = 52/318 (16%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           ++ RW  N          +K++ + Q+ V  K+     ++ SG+++ I  + N       
Sbjct: 40  QIKRWIIN----------KKVVINNQISVLPKK-----KVISGEIIEINDINNDSTSDCN 84

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW--- 136
              ++  +++L          ++YED+ I V NKP+ + V    G+  + D  L +    
Sbjct: 85  NNILIPQNISLN---------IVYEDNDILVINKPSNMVVH--PGVKNNKDTVLNALLYR 133

Query: 137 ---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              +    ++  +  RLD++T+G++++A+T  A  +L +SF+M+++ K Y ++V G    
Sbjct: 134 YPSIMQISKQAGIVQRLDKDTTGLMIIAKTYLAYTNLLQSFKMKQVIKEYDAVVCGTFSY 193

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               I+  +  + H        V  + K A   ++ + V++ F + +  + +   TGRTH
Sbjct: 194 NAGIISQPI--RRHSINRTCMTVHPHGKPA---VTRYSVVESFGRTYSRIRVYLETGRTH 248

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLHARYMDLPHPE 301
           Q+RVH  ++  P+VGD KY   FK + T  +             N+  LHA  + L HP 
Sbjct: 249 QIRVHMAYINHPVVGDVKYGIKFKNSTTGKLSISDDVSICLSSFNRQALHACKLQLVHPI 308

Query: 302 GGRLQI--TAPLPAHMVK 317
             RL++    PLP  M+K
Sbjct: 309 -TRLKMHWIVPLPEDMLK 325


>gi|239636325|ref|ZP_04677327.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus warneri L37603]
 gi|239597680|gb|EEQ80175.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus warneri L37603]
          Length = 305

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/317 (25%), Positives = 149/317 (47%), Gaps = 35/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +Y + +++    RLD+         +   +Q  ++   V+V+ K VK N +++   
Sbjct: 1   METYEYTITDSNHVGQRLDKVLPELNSDWSRSQIQDWIKEDLVKVNDKVVKPNYKVKQND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                      N ++ EQ+++D+ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  -----------NIVVTEQEVVDADIT----PENLNLDIYYEDDDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +   K+     G+ +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMAK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 SVKRKYVALVHGNIPHDYGTVDAP--IGRNKKDRQAMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KDYTLIECELETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQA-----LHAGVIG 273

Query: 297 LPHPEGGR-LQITAPLP 312
             HP     ++ TA LP
Sbjct: 274 FEHPVTHEYIERTAELP 290


>gi|290474823|ref|YP_003467703.1| 23S rRNA pseudouridylate 746 synthase [Xenorhabdus bovienii
           SS-2004]
 gi|289174136|emb|CBJ80923.1| 23S rRNA pseudouridylate 746 synthase [Xenorhabdus bovienii
           SS-2004]
          Length = 217

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/207 (34%), Positives = 114/207 (55%), Gaps = 19/207 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+ + SV G +    H D  + + + ++       HRLD  TSG++V
Sbjct: 15  VLYQDEHIMVVNKPSELLSVPGKA--EDHKDSIM-TRIQAEFPTAESVHRLDMATSGVMV 71

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K+Y + VWG  + +K  +   L+       D+ +  KQ 
Sbjct: 72  VALTKAAERELKRQFREREPKKVYIARVWGKLEREKGLVDLPLI------CDWPNRPKQK 125

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + A + ++V++  AQ    + + P TGR+HQLRVH L +G PI+GD ++ A+ 
Sbjct: 126 VCFETGKS-AQTEYQVLEYEAQA-TRVRLAPITGRSHQLRVHMLALGNPILGD-RFYAHQ 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    +P   +L LHA+ + + HP  G
Sbjct: 183 QARELAP---RLQLHAQELSITHPAYG 206


>gi|126700216|ref|YP_001089113.1| putative pseudouridylate synthase [Clostridium difficile 630]
 gi|115251653|emb|CAJ69486.1| putative pseudouridylate synthase, RluC/RluD family [Clostridium
           difficile]
          Length = 303

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 146/310 (47%), Gaps = 45/310 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK--RVKFNNRIQSGQVVRIPPVINALNHI 77
           RLD +       ++   +QKI++ G+V+V+ K  + ++  + +   V+ IP         
Sbjct: 17  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKARYLVKEEDNIVIEIP--------- 67

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYH 128
             E K+L+           +   ++YED  + + NKP  + V            +GI YH
Sbjct: 68  --EPKVLEVL------PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYH 119

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               L S   +   +P + HR+D++TSG+L++A+   A   L E  +   I + Y  + +
Sbjct: 120 CKDKLSSI--NGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICY 177

Query: 189 GIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           G+ K  K  +   + +  K  +    + VVK    G N AI+HF+V++ F  KF  +  +
Sbjct: 178 GVVKEDKITVDKPIGRNPKDRLK---MAVVKD---GKN-AITHFEVVERF-DKFTHMRAR 229

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVHAL +  P++GD+ Y    +  F    Q    LHA+ +   HP     +
Sbjct: 230 LETGRTHQIRVHALSINHPLLGDYVYGPK-ETKFKLKGQT---LHAKKLGFIHPTTKEYI 285

Query: 306 QITAPLPAHM 315
           +  + LP + 
Sbjct: 286 EFNSELPEYF 295


>gi|221135103|ref|ZP_03561406.1| RluA family pseudouridine synthase [Glaciecola sp. HTCC2999]
          Length = 330

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 88/336 (26%), Positives = 159/336 (47%), Gaps = 47/336 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPP 69
           +V+  + + RLD+   + +P  +   L++ + +G V+VD + V     ++Q  + + I  
Sbjct: 16  IVDQTQFDKRLDQVLADLFPEYSRSKLKEWILAGFVKVDDEVVTVARQKMQGDEQIDIHA 75

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           VI          ++L++  N+       +  +++ED  + V NKPAG+ V  G+G A   
Sbjct: 76  VIAV--------QVLNTPQNI-------ELDIVFEDEHVLVINKPAGLVVHPGAGNA--- 117

Query: 130 DGFLKSWVDSKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG + + + +   +    PR  + HRLD++T+G++VVA+T  A  +L E  + R + + Y
Sbjct: 118 DGTVLNALLAHHPEIENIPRAGIVHRLDKDTTGLMVVAKTLIAQTYLVEQLQTRVMSREY 177

Query: 184 WSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            +LV G         E I     K++ +       V+   K A    +H+++ + F +  
Sbjct: 178 EALVMGTMVAGGFVDEPIGRHPTKRTSMA------VRATGKEAT---THYRIKEKF-RAH 227

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHA 292
             L ++  +GRTHQ+RVH  H+  P+VGD  Y    +        F   ++N  +  LHA
Sbjct: 228 THLRLKLESGRTHQIRVHMAHIRHPLVGDQLYGGRPRMPKAASEAFMQALRNFKRQALHA 287

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             +   HP     L   APLP   V+  + +    D
Sbjct: 288 AQLSFAHPITEDWLTFNAPLPDDFVQLLEDVRADTD 323


>gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudouridine synthase D [Herbaspirillum
           seropedicae SmR1]
 gi|300075092|gb|ADJ64491.1| ribosomal large subunit pseudouridine synthase D protein
           [Herbaspirillum seropedicae SmR1]
          Length = 370

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 90/324 (27%), Positives = 142/324 (43%), Gaps = 41/324 (12%)

Query: 15  DEE--NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           D+E    RLD+      P  +   +Q+ +  G V V+    K    +   ++V + P   
Sbjct: 47  DDEVIGQRLDKVLSGLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAP--- 103

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
               +  +Q      + L          +L+ED  + V NKPAG+ V   +G      ++
Sbjct: 104 --QSVPSDQPYGPEPMALD---------ILHEDKALIVLNKPAGLVVHPAAGNWSGTLLN 152

Query: 131 GFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           G L     +  + PR  + HRLD++TSGI+VVA+T AA   L    + R +++ Y +LVW
Sbjct: 153 GLLHH-CPALAKVPRAGIVHRLDKDTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVW 211

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-------FAQKFC 241
           G+P+      A           D + +       A  A++H++ +          +   C
Sbjct: 212 GLPQLSGTINAPMARHPR----DRIKMAVSQSMRAKPAVTHYRRLATGEIDRKPVSLIHC 267

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE    TGRTHQ+RVH   +G P+VGD  Y    K +  S +  +  L A  + L HP 
Sbjct: 268 RLE----TGRTHQIRVHLQSLGFPLVGDALYG---KHHLVS-VFPRQALLAGRLGLLHPS 319

Query: 302 GGRL-QITAPLPAHMVKTWDSLGF 324
            G+  Q  APLP  +V      G 
Sbjct: 320 TGKFRQWAAPLPEDIVALLQRAGI 343


>gi|260582391|ref|ZP_05850183.1| pseudouridylate synthase [Haemophilus influenzae NT127]
 gi|260094542|gb|EEW78438.1| pseudouridylate synthase [Haemophilus influenzae NT127]
          Length = 324

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 121/247 (48%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP  + V  G+G         + YH      S V   G    + HRLD
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI--SEVPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++ +
Sbjct: 139 KDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLM 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P++G
Sbjct: 199 A---VHPMGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLG 248

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           D  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+  
Sbjct: 249 DQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 309 NALKADY 315


>gi|261406141|ref|YP_003242382.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261282604|gb|ACX64575.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
          Length = 239

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 63/205 (30%), Positives = 98/205 (47%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ +    KP  I  Q  +     +   LK  +  +  KP      L HRLD+   
Sbjct: 14  ILFEDNHVLGVTKPVNIPSQEDATGDPDMLTILKQDIKERYNKPGNVFLGLVHRLDRPVG 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G +V A+T  AA  L+E+ R R  +K Y ++V G+P      + N L K +    + VHV
Sbjct: 74  GAMVFAKTSKAASRLSEAVRSRSFRKQYVAVVHGVPAKTSGRLVNMLYKDAKT--NTVHV 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   GA  AI  + V+   A+    + ++ HTGR HQ+RV   H G P+ GD KY   
Sbjct: 132 TSKGTDGAKEAILDYTVLQA-AEGVSLVLIELHTGRPHQIRVQLSHAGHPLFGDQKY--- 187

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G+  +    ++ L +  +  PHP
Sbjct: 188 --GSKVNKAGQQIALWSVLVGFPHP 210


>gi|1665844|emb|CAA70352.1| yfiI [Borrelia burgdorferi]
          Length = 309

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 56/181 (30%), Positives = 99/181 (54%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 86  IIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +RI K+Y ++V G   +    I +++ +  H    
Sbjct: 145 KDTSGVLICAKNISTLRFLAQQFKDKRINKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 205 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 259

Query: 272 Y 272
           Y
Sbjct: 260 Y 260


>gi|56412366|ref|YP_149441.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197361303|ref|YP_002140938.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|56126623|gb|AAV76129.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Paratyphi A str. ATCC
           9150]
 gi|197092778|emb|CAR58203.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Paratyphi A str.
           AKU_12601]
          Length = 219

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/208 (33%), Positives = 105/208 (50%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LEAHKDSIM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VW  P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWRHPSPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y + 
Sbjct: 126 KVCYETG-KPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +       +L LHA  + + HP  G
Sbjct: 185 EALSLAP----RLQLHAEMLTITHPAYG 208


>gi|55822493|ref|YP_140934.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus CNRZ1066]
 gi|55738478|gb|AAV62119.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus CNRZ1066]
          Length = 292

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 85/318 (26%), Positives = 146/318 (45%), Gaps = 48/318 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++     + +++G V V+ K  K    ++ G V+          
Sbjct: 7   EAGNRLDKSLAD-LTELSRSQANEAIKAGTVLVNGKSAKAKYVVKEGDVI---------T 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-- 133
           +++ E+++L+      K  D    I+ YED+ + V NKP G+ V   +G   H  G L  
Sbjct: 57  YVLPEEEVLEY-----KAEDIPLDII-YEDADVAVVNKPQGMVVHPSAG---HTSGTLVN 107

Query: 134 ------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 K      G  +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++
Sbjct: 108 ALMYHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAI 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLE 244
           V G   N +  I      ++ IG       KQ    KG   A++ F V++ F   +  +E
Sbjct: 168 VHGNLPNDRGVI------EAPIGRSDKDRKKQAVTAKG-KPAVTRFTVLERFGN-YTLVE 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +Q  TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   HP  
Sbjct: 220 LQLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGHGQ-------FLHAKTLGFTHPTT 272

Query: 303 GRL-QITAPLPAHMVKTW 319
           G+L ++T   P    + W
Sbjct: 273 GKLVELTQKNPLFSRRPW 290


>gi|113971328|ref|YP_735121.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           MR-4]
 gi|114048565|ref|YP_739115.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           MR-7]
 gi|113886012|gb|ABI40064.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           MR-4]
 gi|113890007|gb|ABI44058.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           MR-7]
          Length = 323

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 90/324 (27%), Positives = 147/324 (45%), Gaps = 47/324 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +  +RLD+     +P  +   +++ + S  V VD   V K   ++   Q + I   
Sbjct: 11  ISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVYVDGVMVNKPREKVFELQRIEINAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +    H   +   LD               ++YED  I V NK AG+ V  G+G A   D
Sbjct: 71  LEEEVHAAAQAIELD---------------IVYEDDDILVINKQAGLVVHPGAGNA---D 112

Query: 131 GFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + +     +    PR  + HRLD++T+G++VVA+T  A  HL  + + R I + Y 
Sbjct: 113 GTLMNALLHHCPNIEHVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++V G         E I     K++H+    VH           A++H++V + F +   
Sbjct: 173 AIVLGTMTAGGTVDEPIGRHPTKRTHMA---VH------HSGKPAVTHYRVAEKF-RNHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHAR 293
            L ++  +GRTHQ+RVH  ++G  +VGD  Y    K        F   ++N  +  LHA 
Sbjct: 223 RLRLRLESGRTHQIRVHMAYIGHVLVGDPVYGGRPKPPKAASPEFFEILKNFKRQALHAV 282

Query: 294 YMDLPHPEGGRLQI-TAPLPAHMV 316
            ++L HP    +   TAP+P  MV
Sbjct: 283 RLELAHPVTCEIMSWTAPIPEDMV 306


>gi|303236245|ref|ZP_07322841.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
 gi|302483559|gb|EFL46558.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
          Length = 532

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/225 (31%), Positives = 111/225 (49%), Gaps = 28/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++YED+ + V  KP G+    G      ++  L++ W  +    P + HRLD  TSG+LV
Sbjct: 320 IIYEDNDLAVIVKPCGMLTVAGRSQRQSVEAILRTRW--NLSNMPIIVHRLDMATSGLLV 377

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVV 216
           VAR + A + L   F  R ++K Y +L+      K    E   +  L+   +  D    +
Sbjct: 378 VARNKEAHKDLQAQFNNRSVKKRYTALLSTALLTKDLPTEGTISLPLRADLL--DRPRQI 435

Query: 217 KQNEKGANYAISHFKVI------DCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIV 267
             +E+G   A +++K+I      D   ++   +E+QP TGRTHQLRVH  H   +  PI+
Sbjct: 436 VDHEQGKP-ATTYYKIIGKTPFKDSKIKEAVRVELQPLTGRTHQLRVHCAHLEGLNTPIL 494

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           GD  Y  +          ++LYLHA Y+   HP  G+ LQ   P+
Sbjct: 495 GDTLYGTH---------ADRLYLHAEYLSFVHPRTGKELQFQYPM 530


>gi|295100789|emb|CBK98334.1| ribosomal large subunit pseudouridine synthase D [Faecalibacterium
           prausnitzii L2-6]
          Length = 310

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 83/323 (25%), Positives = 145/323 (44%), Gaps = 35/323 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +VE +    R+DR+       ++   LQ ++  G V  + K +  + ++++G  + +   
Sbjct: 7   IVEAEAAGQRIDRFLSGEDTGLSRSALQGLVAEGHVLCNGKSIAKSLKLKAGDTILL--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                      +I D+        D    I+ YED  + V NKP G+ V    G      
Sbjct: 64  -----------EIPDAKPIEAVPQDIPLDIV-YEDDHLLVVNKPKGMVVHPAPGNPDGTL 111

Query: 125 ---IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + +H  G L       G+ +P + HR+D++TSG+LVVA+  A    L++   +  ++
Sbjct: 112 VNALLWHCKGSLSGI---GGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVE 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V+G    + E      L +S      + V   +E    YA + +KV++ F   F
Sbjct: 169 RAYQTVVYG-GFAQDEGFVEANLGRSKTDRKKMAVYPASEPHTKYAYTGYKVLERFG-GF 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE +  TGRTHQ+RVH   +  P+ GD  Y  +   N  + +  +  LHA+ +   HP
Sbjct: 227 TLLECRLKTGRTHQIRVHMASIQHPVAGDPVYGPH---NCITRLHGQC-LHAKTLGFIHP 282

Query: 301 -EGGRLQITAPLPAHMVKTWDSL 322
             G  L+  + LP +      SL
Sbjct: 283 ITGEHLRFDSGLPEYFTHFIASL 305


>gi|254487090|ref|ZP_05100295.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           GAI101]
 gi|214043959|gb|EEB84597.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           GAI101]
          Length = 215

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 64/209 (30%), Positives = 101/209 (48%), Gaps = 22/209 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++L+ED+++ + +KPAG+    G G   H+   L + V +      L HRLD++TSG+++
Sbjct: 13  VILHEDAEVLLVDKPAGLLSVPGKGP--HLADCLIARVQAVFPDALLVHRLDRDTSGVMI 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVH 214
            A T  A +HL   F  R  +K Y + VWG+P           I +W  +   +      
Sbjct: 71  FALTPYAQRHLGLQFEKRMTRKTYVARVWGVPTENSGTIDLPLIVDWPNRPLQM------ 124

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V  +  K A       K     A+    + + P TGR+HQLRVH L +G PI+GD  Y  
Sbjct: 125 VCHETGKSAQTDWRLLKNEGDTAR----VRLSPKTGRSHQLRVHMLSLGHPILGDPFYAT 180

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
               N+      ++ LH+  +   HP+GG
Sbjct: 181 GPALNYP-----RMMLHSEELRFNHPQGG 204


>gi|85711787|ref|ZP_01042843.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
 gi|85694402|gb|EAQ32344.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
          Length = 218

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/222 (33%), Positives = 111/222 (50%), Gaps = 30/222 (13%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDG----FLKSWVDSKGQKPRLTHRLDQETS 155
           +++ D+ + V +KPAG+ SV G   +  H D       + + D K     L HRLD  TS
Sbjct: 16  IIHRDNALVVVDKPAGLLSVPGK--LLEHRDSVYTRLARIFPDIK-----LVHRLDMATS 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A  +AA  HL+  F+ R  +K Y + VWG       CI         +  D+ + 
Sbjct: 69  GVMVFALGKAAQSHLSRQFQQRTPKKTYLAKVWGALPADNGCI------DLPLSCDWPNR 122

Query: 216 VKQNEKGANYAISH--FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            KQ     N   S   ++V+   AQ  C +++ P+TGR+HQLRVH L + CPI+GD  Y 
Sbjct: 123 PKQQVDFFNGKPSQTFYRVLKRQAQG-CTVKLSPYTGRSHQLRVHMLALNCPILGDKFYA 181

Query: 274 --ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             A F+         +L LHA  + + HP+  + L  T+P P
Sbjct: 182 HSAAFEA------AERLLLHAFELRITHPQTEQTLTFTSPCP 217


>gi|192360779|ref|YP_001983659.1| pseudouridine synthase Rlu family protein [Cellvibrio japonicus
           Ueda107]
 gi|190686944|gb|ACE84622.1| pseudouridine synthase, RluA family subfamily [Cellvibrio japonicus
           Ueda107]
          Length = 320

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 86/322 (26%), Positives = 142/322 (44%), Gaps = 35/322 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MR D+     +P  +   LQ  ++ G + VD +  K  +++  G+ + +   + A    
Sbjct: 17  GMRFDQAASELFPDFSRSRLQGWIKDGLLTVDGRVAKPKDKLIGGETLALHAELEAQGDW 76

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
             E   LD               +++ED  + + NK AG+ V   +G      ++  L +
Sbjct: 77  EPEAIELD---------------IIHEDDDLLIINKQAGLVVHPAAGNYTGTLVNALL-N 120

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              S    PR  + HRLD++T+G++VVA+T  A   L      R + + Y ++  G    
Sbjct: 121 HAPSLVNIPRAGIVHRLDKDTTGLMVVAKTLEAHTDLVAQLADRSVSREYEAVAVGAMTG 180

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                A   + +  +    + V+ Q   G   A++H++V   +      + ++  TGRTH
Sbjct: 181 GGTVDAP--IGRHPLQRKLMAVLSQ---GGKRAVTHYRVAKRYPH-HTHIRVKLETGRTH 234

Query: 254 QLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQN-----KLYLHARYMDLPHPEGGR- 304
           Q+RVH  H+G P+VGD  Y   F   KG     I+      +  LHA  + L HP  G  
Sbjct: 235 QIRVHMAHVGHPLVGDQTYGNRFKIPKGANQQLIEALKHFPRQALHAFKLGLEHPGTGEY 294

Query: 305 LQITAPLPAHMVKTWDSLGFKY 326
            + TAPLPA   K  D+L   Y
Sbjct: 295 TEWTAPLPADFRKLLDALDQGY 316


>gi|225861064|ref|YP_002742573.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298230857|ref|ZP_06964538.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae str. Canada MDR_19F]
 gi|298255783|ref|ZP_06979369.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae str. Canada MDR_19A]
 gi|298502886|ref|YP_003724826.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus pneumoniae
           TCH8431/19A]
 gi|225728340|gb|ACO24191.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298238481|gb|ADI69612.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus pneumoniae
           TCH8431/19A]
 gi|327389344|gb|EGE87689.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA04375]
          Length = 298

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 114/219 (52%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|331674037|ref|ZP_08374799.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA280]
 gi|331068776|gb|EGI40169.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA280]
          Length = 326

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  D +
Sbjct: 253 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIDVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|209559192|ref|YP_002285664.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
 gi|209540393|gb|ACI60969.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
          Length = 296

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 109/219 (49%), Gaps = 29/219 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++YED  + +  KP G+ V    G         + YHI    K      G  +P + HR+
Sbjct: 76  IIYEDDTLAIITKPQGMVVHPSGGHPSGTMVNALMYHI----KDLSSINGVVRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+T AA Q L E  + ++  + Y ++V G   N +  I      ++ IG 
Sbjct: 132 DKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMI------EAPIGR 185

Query: 211 DYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ G
Sbjct: 186 SEKDRKKQAVTAKGKE-AVTRFTVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAG 243

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           D  Y     G   +   +  +LHA+ + L HP  G+  I
Sbjct: 244 DPLY-----GPRKTLSGHGQFLHAKTLGLTHPMTGKEMI 277


>gi|126173261|ref|YP_001049410.1| RluA family pseudouridine synthase [Shewanella baltica OS155]
 gi|152999620|ref|YP_001365301.1| RluA family pseudouridine synthase [Shewanella baltica OS185]
 gi|160874239|ref|YP_001553555.1| RluA family pseudouridine synthase [Shewanella baltica OS195]
 gi|217974428|ref|YP_002359179.1| RluA family pseudouridine synthase [Shewanella baltica OS223]
 gi|304410382|ref|ZP_07392000.1| pseudouridine synthase, RluA family [Shewanella baltica OS183]
 gi|307304474|ref|ZP_07584224.1| pseudouridine synthase, RluA family [Shewanella baltica BA175]
 gi|125996466|gb|ABN60541.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           baltica OS155]
 gi|151364238|gb|ABS07238.1| pseudouridine synthase, RluA family [Shewanella baltica OS185]
 gi|160859761|gb|ABX48295.1| pseudouridine synthase, RluA family [Shewanella baltica OS195]
 gi|217499563|gb|ACK47756.1| pseudouridine synthase, RluA family [Shewanella baltica OS223]
 gi|304350866|gb|EFM15266.1| pseudouridine synthase, RluA family [Shewanella baltica OS183]
 gi|306911876|gb|EFN42300.1| pseudouridine synthase, RluA family [Shewanella baltica BA175]
 gi|315266473|gb|ADT93326.1| pseudouridine synthase, RluA family [Shewanella baltica OS678]
          Length = 324

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 90/324 (27%), Positives = 147/324 (45%), Gaps = 47/324 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +  +RLD+     +P  +   +++ + S  V VD   V K   ++   Q + I   
Sbjct: 11  ISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVHVDGVVVNKPREKVYELQQILIDAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +    H   +   LD               ++YED  I V NK AG+ V  G+G A   D
Sbjct: 71  LEEEVHAAAQAIDLD---------------IVYEDDDIIVINKQAGLVVHPGAGNA---D 112

Query: 131 GFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + +          PR  + HRLD++T+G++VVA+T  A  HL  + + R I + Y 
Sbjct: 113 GTLMNALLHHCPDIEHVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYE 172

Query: 185 SLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++V G         E I   L K++H+    +H  K        A++H++V + F +   
Sbjct: 173 AIVMGTMTGGGTVDEPIGRHLTKRTHMA--VLHSGKP-------AVTHYRVAEKF-RNHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHAR 293
            L ++  +GRTHQ+RVH  ++G  +VGD  Y    K        F   ++N  +  LHA 
Sbjct: 223 RLRLRLESGRTHQIRVHMEYIGHVLVGDPVYGGRPKPPKAASPEFFDILKNFKRQALHAV 282

Query: 294 YMDLPHPEGGRLQI-TAPLPAHMV 316
            ++L HP    +    AP+P  MV
Sbjct: 283 RLELAHPVSCEIMSWQAPIPEDMV 306


>gi|116618468|ref|YP_818839.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
 gi|116097315|gb|ABJ62466.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
          Length = 312

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/282 (28%), Positives = 134/282 (47%), Gaps = 37/282 (13%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L  G + V+  +VK + ++ SG  + I P         +E KI   ++ L    +     
Sbjct: 36  LVDGTILVNNHKVKRSYKVVSGDTISITPPET------QETKIEAENIPLDIIYEDDDI- 88

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-------DSKGQ-KPRLTHRLDQ 152
                    V NKP G+ V   +G   H  G L + +          G+ +P + HR+D+
Sbjct: 89  --------IVVNKPQGMVVHPAAG---HSSGTLVNALLHHSPLSTINGEFRPGIVHRIDR 137

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+L+VA+   A + L+E  +  + Q++Y++LV G      E   +    ++ IG   
Sbjct: 138 DTSGLLMVAKNDKAHRSLSEQLKSHKNQRVYYALVRG------EFTEDSGTIEAPIGRHK 191

Query: 213 VHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +   KQ   +G   A++HF+V+  +   +  L++   TGRTHQ+RVH  ++G P+VGD  
Sbjct: 192 IDRKKQAVIEGGREAVTHFRVLKRYV-GYTLLKVSLETGRTHQIRVHMSYIGHPVVGDPV 250

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y    K + T    N   LHA+ + L  P  G  L   +PLP
Sbjct: 251 YGTAQKLDGTQ--LNGQLLHAKTLTLEQPTTGDELSFDSPLP 290


>gi|324995685|gb|EGC27597.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK678]
          Length = 298

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 117/236 (49%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G         + YHI     S ++    +P + HR+D
Sbjct: 78  IVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIQDL--SGINGV-LRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHLALADELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTRFQVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHA+ +   HP  G  L+ TA +P    +T   L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHAQTLGFTHPRTGEVLEFTAEVPVIFQETLKKL 295


>gi|309972703|gb|ADO95904.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae R2846]
          Length = 324

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 121/247 (48%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP  + V  G+G         + YH      S V   G    + HRLD
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI--SEVPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++ +
Sbjct: 139 KDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLM 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P++G
Sbjct: 199 A---VHPMGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLG 248

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           D  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+  
Sbjct: 249 DQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 309 NALKADY 315


>gi|92112630|ref|YP_572558.1| ribosomal large subunit pseudouridine synthase D [Chromohalobacter
           salexigens DSM 3043]
 gi|91795720|gb|ABE57859.1| ribosomal large subunit pseudouridine synthase D [Chromohalobacter
           salexigens DSM 3043]
          Length = 325

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 85/332 (25%), Positives = 144/332 (43%), Gaps = 64/332 (19%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+     +   +   L+  ++SG +  D    +  +++  G+ + +          
Sbjct: 23  GLRLDQAAAELFADFSRERLKAWIKSGALTRDGAPARPKDKLFGGERLTL---------- 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
              +  L+        +  L   +++ED  + V +KPAG+ V   +G   + DG L + +
Sbjct: 73  ---EATLEEDTRFAPQAMALS--IVHEDDDVLVIDKPAGLVVHPAAG---NPDGTLLNAL 124

Query: 138 ----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                 + Q PR  + HRLD++T+G++VVA+T AA   L E  + R + + Y ++V G  
Sbjct: 125 LHHAPGQMQLPRAGIVHRLDKDTTGLMVVAKTLAAHASLVEQLQARTVSREYDAVVTG-- 182

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEK---------GANYAISHFKVIDCFAQKF-- 240
                        +   GG     + ++ K             A++H++V++ F      
Sbjct: 183 -------------RMTAGGSVDAPIGRHPKDRKRQAVTPSGKPAVTHYRVVERFPAHTHV 229

Query: 241 -CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLH 291
            C LE    TGRTHQ+RVH  H   P++GD  Y    K     T  +++ L       LH
Sbjct: 230 RCRLE----TGRTHQIRVHMAHRRFPLIGDPVYAGRLKMPAGATDALKDVLRHFPRQALH 285

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           AR +   HP  G  L   APLP  M+   D L
Sbjct: 286 ARKLAFVHPGTGETLTFRAPLPDDMLMLLDFL 317


>gi|114764218|ref|ZP_01443456.1| ribosomal large subunit pseudouridine synthase A [Pelagibaca
           bermudensis HTCC2601]
 gi|114543370|gb|EAU46386.1| ribosomal large subunit pseudouridine synthase A [Roseovarius sp.
           HTCC2601]
          Length = 215

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/212 (32%), Positives = 101/212 (47%), Gaps = 30/212 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+EDS + V +KPAG+    G G    +   L + ++      RL HRLD++TSG++V 
Sbjct: 14  ILHEDSDLLVVDKPAGLLSVPGKG--PELADCLIARLERAFPTVRLVHRLDRDTSGVMVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKK---ECIANW----LLKKSHIGGD 211
           A T  A +HL + F  R+ +K Y + V G   PK        I +W    L K  H  G 
Sbjct: 72  ALTAHAQRHLGQQFETRKTRKTYIARVAGRLEPKTGSVDLPLIVDWPNRPLQKVCHETG- 130

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                         A++ +KV    +     + + P TGR+HQLRVH L +G PI+GD  
Sbjct: 131 ------------KPALTEYKVTKA-SDAESRVRLHPLTGRSHQLRVHMLALGHPIIGDPL 177

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           Y       +      ++ LHA  + L HPE G
Sbjct: 178 YAPETAAEYP-----RMMLHAEELRLHHPESG 204


>gi|114331227|ref|YP_747449.1| pseudouridine synthase, RluA family protein [Nitrosomonas eutropha
           C91]
 gi|114308241|gb|ABI59484.1| ribosomal large subunit pseudouridine synthase D [Nitrosomonas
           eutropha C91]
          Length = 342

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/306 (25%), Positives = 145/306 (47%), Gaps = 35/306 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++  ++   +RLD+      P  +   LQ+ +   +V VD        +I  G+++ +  
Sbjct: 33  LIAPDNLAGLRLDQVLAQLLPQWSRSRLQRWIGEDRVSVDGSAGSTRQKIWGGEIIHV-- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                        +++S  + +  ++ +   ++YED  + V +KPAG+ V  G+G  +H 
Sbjct: 91  ----------TAGLVES--DQSHQAEAIPLSIIYEDDHLIVIDKPAGLVVHPGNG-NWHG 137

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   L +      Q PR  + HRLD++T+G+LVVA+T  A   L    + R +++ Y++
Sbjct: 138 TLLNALLNHAPQLSQVPRAGIVHRLDKDTTGLLVVAKTIEAQLDLVRQLQQRTVKRHYFA 197

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L  G    +K+ + +  + +  +    + VVK  +    Y     K + C   + C LE 
Sbjct: 198 LALG--GIEKDGLVDAPIGRHPVHRTRMAVVKNGKPARTYYRILEKFVACTLLQ-CSLE- 253

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY------LHARYMDLPH 299
              TGRTHQ+RVH + +G P+ GD  Y    K +   P  + +       LHAR ++L H
Sbjct: 254 ---TGRTHQIRVHLMSIGHPLAGDPVYG---KISSDPPTADAIVHLPRQALHARQLELTH 307

Query: 300 PEGGRL 305
           P  G++
Sbjct: 308 PNSGQI 313


>gi|224532212|ref|ZP_03672844.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia valaisiana VS116]
 gi|224511677|gb|EEF82083.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia valaisiana VS116]
          Length = 326

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 57/183 (31%), Positives = 97/183 (53%), Gaps = 19/183 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQK--PRLTHR 149
           ++YEDS I V NKP GI    G         + + YHI       +D  G+K  P + HR
Sbjct: 86  IIYEDSNIIVLNKPQGILSHPGISHWDDTVVNFLLYHIKSL---KIDFNGEKIRPGIVHR 142

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG+L+ A+  +  + L + FR +R  K+Y ++V G   +    I +++ +  H  
Sbjct: 143 LDKDTSGVLICAKNISTLRFLAQQFRDKRTNKVYIAIVKGNFNSFSGSIESFIDRDKHNR 202

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             +     + +K    +++ ++++  F   +  L ++P TGRTHQLRVH  ++  PI+GD
Sbjct: 203 KKFAVSKDRGKK----SLTEYRLLLNFGG-YSLLALKPKTGRTHQLRVHMKYLNFPILGD 257

Query: 270 HKY 272
             Y
Sbjct: 258 EVY 260


>gi|162447675|ref|YP_001620807.1| ribosomal large subunit pseudouridine synthase, RluA-like protein
           [Acholeplasma laidlawii PG-8A]
 gi|161985782|gb|ABX81431.1| ribosomal large subunit pseudouridine synthase, RluA-like protein
           [Acholeplasma laidlawii PG-8A]
          Length = 297

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 111/233 (47%), Gaps = 23/233 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP G+ V            SG+ +H D    S  +    +P + HR+D
Sbjct: 78  IVYEDDDIMVINKPKGLVVHPSETFSETTLVSGLLHHTDTL--STHNDDPLRPGILHRID 135

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++VA+T  A + L +  +   I++ Y +LV G+  + K  I   + +   I   
Sbjct: 136 KDTSGLILVAKTNEAHKILAQDLKSHDIKREYIALVEGVLDHNKGVIDAPIARHPKIRTK 195

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              V          AI+HF+V+  F +    L  +  TGRTHQ+RVH  ++  P+ GD  
Sbjct: 196 MAVVAT-----GKPAITHFEVMRTF-RDHTLLHCKLETGRTHQIRVHLAYIKHPVTGDPL 249

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           Y     G     +++   LHA  ++  HP   + + + APLP        +LG
Sbjct: 250 Y-----GTKAKILKDGQLLHAFRLEFVHPITKKVMMLEAPLPPEFESYLVTLG 297


>gi|157961293|ref|YP_001501327.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157846293|gb|ABV86792.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 217

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/204 (35%), Positives = 103/204 (50%), Gaps = 16/204 (7%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y D  I V NKP+G+      GIA +      + +  + +   L HRLD  TSGI+V AR
Sbjct: 18  YLDRDIIVINKPSGL--LSNPGIAEYTHDCALTRLQQRFKDCILVHRLDCATSGIMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NE 220
            + A  +L   F+ R+ QK Y + V GI K +   I      +  I  D ++  KQ  +E
Sbjct: 76  NKKAESNLKTQFQDRQTQKTYIAEVDGIFKLQSGVI------ELSIAADKLNPPKQMVSE 129

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            G   AI+H+KV+         +E++P TGRTHQLRVH L +G PI+GD  Y +      
Sbjct: 130 LG-KAAITHYKVLQQKPHS-TLVELKPVTGRTHQLRVHMLAIGHPILGDDFYGS----EQ 183

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR 304
                 +L LHA+ +   HP  G+
Sbjct: 184 VMSAAKRLQLHAQSLSFTHPYSGK 207


>gi|329924939|ref|ZP_08279886.1| RNA pseudouridine synthase [Paenibacillus sp. HGF5]
 gi|328940323|gb|EGG36652.1| RNA pseudouridine synthase [Paenibacillus sp. HGF5]
          Length = 239

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 63/205 (30%), Positives = 97/205 (47%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ +    KP  I  Q  +     +   LK  +  +  KP      L HRLD+   
Sbjct: 14  ILFEDNHVLGVTKPVNIPSQEDATGDPDMLTILKQDIKERYNKPGNVFLGLVHRLDRPVG 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G +V A+T  AA  L+E+ R R   K Y ++V G+P      + N L K +    + VHV
Sbjct: 74  GAMVFAKTSKAASRLSEAVRSRSFLKQYVAVVHGVPAKTSGRLVNMLYKDAKT--NTVHV 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   GA  AI  + V+   A+    + ++ HTGR HQ+RV   H G P+ GD KY   
Sbjct: 132 TSKGTDGAKEAILDYTVLQA-AEGVSLVRIELHTGRPHQIRVQLSHAGHPLFGDQKY--- 187

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G+  +    ++ L +  +  PHP
Sbjct: 188 --GSKVNKAGQQIALWSVLVGFPHP 210


>gi|222099185|ref|YP_002533753.1| Pseudouridine synthase [Thermotoga neapolitana DSM 4359]
 gi|221571575|gb|ACM22387.1| Pseudouridine synthase [Thermotoga neapolitana DSM 4359]
          Length = 271

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/222 (30%), Positives = 110/222 (49%), Gaps = 20/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           +LYED  I V +KP  + V     +   + G L + +     D +G     +P + HRLD
Sbjct: 42  ILYEDRDIIVIDKPGDMIVHP---VPSKLSGTLVNAILYHCSDLQGVGGKLRPGIVHRLD 98

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG++VVA+   A Q L+  F+ R+++K Y  L  G  K  +  +   L +       
Sbjct: 99  KETSGVIVVAKNDLAHQSLSRQFKDRKVKKTYILLARGRIKEDEGTVELPLARHP----- 153

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + V     +    AI+H++V+  F      +   P TGRTHQ+RVH   +G PI+GD  
Sbjct: 154 VLRVKMTVSENGKEAITHYRVLKRFDDVATLVLAFPQTGRTHQIRVHMKSLGHPIMGDKI 213

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y   +K +    I+ ++ LHA  +   HP  G  ++  +P+P
Sbjct: 214 Y-GKYKEDEMFGIKRQM-LHALKLGFFHPRTGEWMEFVSPIP 253


>gi|73954899|ref|XP_546413.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4 [Canis familiaris]
          Length = 404

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 61/194 (31%), Positives = 97/194 (50%), Gaps = 25/194 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           +L++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 100 VLHQDKDLVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTG 159

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG------- 209
           ++V+A  +  A  + E FR R++ K YW++   +P      +   + +K+  G       
Sbjct: 160 VMVLAWEKEVAHQVQEFFRTRQVAKKYWAITVRVPVPSAGVVDIPITEKAVQGQQQHYKM 219

Query: 210 ----------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH- 258
                     G  V V  ++ + A+ A++ + V+         +E+QP TG  HQLRVH 
Sbjct: 220 TLSPDYRMDNGKMVRV--RSNRNAHIAVTQYHVLSSTLSS-ALVELQPITGIKHQLRVHL 276

Query: 259 ALHMGCPIVGDHKY 272
           +  + CPI+GDHKY
Sbjct: 277 SFGLNCPILGDHKY 290


>gi|307127518|ref|YP_003879549.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae 670-6B]
 gi|306484580|gb|ADM91449.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae 670-6B]
          Length = 295

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 83/308 (26%), Positives = 147/308 (47%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   V   +
Sbjct: 5   IETGGLRLDKALSDLSELSRSLANEQIKSGQVL-VNGQVKKAKYTVQEGDVVTYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   L    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 180 -----EASIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G  + GD  Y      KG+         +LHA+ +   HP  G+ L+  A +P  
Sbjct: 233 HMAYIGHSVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGKTLEFKADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKETLERL 293


>gi|260684170|ref|YP_003215455.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260687829|ref|YP_003218963.1| putative pseudouridylate synthase [Clostridium difficile R20291]
 gi|260210333|emb|CBA64669.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260213846|emb|CBE05842.1| putative pseudouridylate synthase [Clostridium difficile R20291]
          Length = 303

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 85/310 (27%), Positives = 145/310 (46%), Gaps = 45/310 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK--RVKFNNRIQSGQVVRIPPVINALNHI 77
           RLD +       ++   +QKI++ G+V+V+ K  + K+  + +   V+ IP         
Sbjct: 17  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKAKYLVKEEDNIVIEIP--------- 67

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYH 128
             E K+L+           +   ++YED  + + NKP  + V            +GI YH
Sbjct: 68  --EPKVLEVL------PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYH 119

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               L S   +   +P + HR+D++TSG+L++A+   A   L E  +   I + Y  + +
Sbjct: 120 CKDKLSSI--NGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICY 177

Query: 189 GIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           G+ K  K  +   + +  K  +    + VVK    G N AI+HF+V++ F  KF  +  +
Sbjct: 178 GVVKEDKITVDKPIGRNPKDRLK---MAVVKD---GKN-AITHFEVVERF-DKFTHMRAR 229

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVHAL +  P++GD  Y    +  F    Q    LHA+ +   HP     +
Sbjct: 230 LETGRTHQIRVHALSINHPLLGDFVYGPK-ETKFKLKGQT---LHAKKLGFIHPTTKEYI 285

Query: 306 QITAPLPAHM 315
           +  + LP + 
Sbjct: 286 EFNSELPEYF 295


>gi|304404905|ref|ZP_07386565.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
 gi|304345784|gb|EFM11618.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
          Length = 317

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/284 (26%), Positives = 132/284 (46%), Gaps = 31/284 (10%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           V+ KRV  ++R+ +G ++++       + I+ E   ++               +++ED  
Sbjct: 50  VNGKRVYTSDRVSTGDLLQVRMEKERSDDILPEPIPIE---------------VVFEDDD 94

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQ--KPRLTHRLDQETSGILVVA 161
           + + NKPAGI V    G   H  G L + V      +G+  + R  HRLD+ TSG++V+A
Sbjct: 95  LLIVNKPAGIIVHPTHG---HYTGTLANGVVHYWQERGEIVRFRPIHRLDEHTSGLVVIA 151

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +T    Q L+E  +   I+K Y + V+G P+  +  +   + +      +  H+     +
Sbjct: 152 KTPYVHQQLSEQLQAGTIEKRYLAFVYGKPEPSEGTVNEPIDRDP----ERPHIRIVTPE 207

Query: 222 GANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           G   +++H++ I  + +     + +   TGRTHQ+RVH   +GCP++GD  Y        
Sbjct: 208 GYP-SVTHYETIAQYNEGTASCVRLNLETGRTHQIRVHMKFLGCPLIGDDMYGREEGHGP 266

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
                 +  LHA  +   HP    R+   APLP  + +    LG
Sbjct: 267 ADEKARRQALHAESIAFTHPMTAERMTWKAPLPEDLQQLAHFLG 310


>gi|219682312|ref|YP_002468696.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Tuc7 (Acyrthosiphon pisum)]
 gi|219622045|gb|ACL30201.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Tuc7 (Acyrthosiphon pisum)]
 gi|311086711|gb|ADP66792.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. TLW03 (Acyrthosiphon pisum)]
 gi|311087807|gb|ADP67886.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. JF98 (Acyrthosiphon pisum)]
          Length = 312

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 91/308 (29%), Positives = 147/308 (47%), Gaps = 39/308 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD      +   +   L+K++   QV V++  V + + +I  G+++ I P    L   I
Sbjct: 19  RLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKILGGEILTIHPFSKDLLVDI 78

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
            E   LD               ++YEDS I + NKPAG+ V  GSG      ++  L  +
Sbjct: 79  PENIFLD---------------IVYEDSDILIINKPAGLVVHPGSGNKSGTILNALLYHY 123

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +SK   PR  + HRLD++TSG++V+A+   +  HL    + ++I + Y  +V G     
Sbjct: 124 KNSK-DLPRAGIVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGIVHG----- 177

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTH 253
            + IA   + K  +                 +++H+KV+  F  KF   + ++  TGRTH
Sbjct: 178 -KMIAGGTINKPIMRHYNRRTCMMVHHLGKPSVTHYKVLSRF--KFHTHIAIRLETGRTH 234

Query: 254 QLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQ-NKLY------LHARYMDLPHP-EGGR 304
           Q+RVH LH+  P+VGD  Y     + N+    + NK+Y      LHA ++ L HP +   
Sbjct: 235 QIRVHMLHIKYPLVGDPCYSGFKIQSNYRKDKKTNKIYKFPRQALHANHLSLHHPIKKNV 294

Query: 305 LQITAPLP 312
           +  T PLP
Sbjct: 295 MSWTVPLP 302


>gi|325694604|gb|EGD36513.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK150]
          Length = 298

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 117/236 (49%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 78  IVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 135 KDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLSNDRGVI------EAPIGRS 188

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  +E+Q  TGRTHQ+RVH  ++  P+ GD
Sbjct: 189 EKDRKKQAVTAKG-KPALTRFQVLERFGD-YSLVELQLETGRTHQIRVHMAYIEHPVAGD 246

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHAR +   HP  G  L+ TA +P    +T + L
Sbjct: 247 EVYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVLEFTAEVPDIFQETLEKL 295


>gi|320185010|gb|EFW59792.1| Ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           CDC 796-83]
 gi|332091934|gb|EGI97012.1| ribosomal large subunit pseudouridine synthase D [Shigella boydii
           3594-74]
          Length = 300

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 125/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   ++DG     L  +       PR  + HRLD++T
Sbjct: 60  IVYEDEDIIVINKPRDLVVHPGAG---NLDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 116

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 117 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 174

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 175 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 226

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 227 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPEDMVELIEVM 286

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 287 RADFEEH 293


>gi|292487319|ref|YP_003530191.1| ribosomal large subunit pseudouridine synthase D [Erwinia amylovora
           CFBP1430]
 gi|292900315|ref|YP_003539684.1| ribosomal large subunit pseudouridine synthase D [Erwinia amylovora
           ATCC 49946]
 gi|291200163|emb|CBJ47289.1| ribosomal large subunit pseudouridine synthase D [Erwinia amylovora
           ATCC 49946]
 gi|291552738|emb|CBA19783.1| ribosomal large subunit pseudouridine synthase D [Erwinia amylovora
           CFBP1430]
          Length = 325

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/253 (29%), Positives = 130/253 (51%), Gaps = 33/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHHFPAIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  +  HL ++ + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPSQTHLVDALQRREITREYEAVAIGRMTAGGTVNEPISRHSTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A +H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------ATTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMSHISHPLVGDPL 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F + ++  ++  LHA  + L HP  G  ++  APLP  MV+  D+L
Sbjct: 253 YGGRPRPPKGASEAFIATLRAFDRQALHATMLRLYHPISGIEMEWHAPLPQDMVELIDAL 312

Query: 323 GFKYDRNLYIKRL 335
             K D   + ++L
Sbjct: 313 --KADTEAFKEQL 323


>gi|31544701|ref|NP_853279.1| RNA pseudouridine synthase [Mycoplasma gallisepticum str. R(low)]
 gi|31541547|gb|AAP56847.1| RNA pseudouridine synthase [Mycoplasma gallisepticum str. R(low)]
 gi|284930765|gb|ADC30704.1| RNA pseudouridine synthase [Mycoplasma gallisepticum str. R(high)]
 gi|284931330|gb|ADC31268.1| RNA pseudouridine synthase [Mycoplasma gallisepticum str. F]
          Length = 330

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/291 (24%), Positives = 136/291 (46%), Gaps = 36/291 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+++ ++ +R+D++   +  +    N+ K++R   + V+ +R+ F+       ++++  
Sbjct: 5   IVIKSVDDCIRIDKFLFKYLKNYTRTNIYKMIRKKDITVNNQRIDFD------YILKVND 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKS----ILLYEDSKIYVFNKPAGISVQGGSG- 124
            I   + +  + K         K  +F K+     L+YED  + +F KP GI  Q     
Sbjct: 59  KITYYDFLRTDHK--------KKVPEFFKAKPELDLIYEDENLVIFEKPLGIPAQQTDEP 110

Query: 125 ----------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                     + Y +      +++++   P + +RLD  T+GI++ A+   A Q L +  
Sbjct: 111 SQYDHMQNRLVHYLVKSNQYDYLNNQAYLPSIVNRLDTYTTGIMLGAKNLKAQQALNQII 170

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R ++K Y  LV G    KK  +  +L K        V + K+        I+ ++ + 
Sbjct: 171 KNRDLKKFYHCLVHGEINPKKATLTAYLTKDP--NRSLVSIQKEKTNDNKIIITRYQTLY 228

Query: 235 CFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA----NFKGNF 280
            F  Q +  L+++  TGRTHQ+R H   +  P+VGD+KY      N +GNF
Sbjct: 229 YFKKQNYTLLDVELITGRTHQIRAHLASINHPVVGDYKYAKKQYQNNQGNF 279


>gi|304410623|ref|ZP_07392241.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|304351107|gb|EFM15507.1| pseudouridine synthase [Shewanella baltica OS183]
          Length = 225

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/218 (32%), Positives = 110/218 (50%), Gaps = 22/218 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           +LY+D  I V NKP+G+ SV G S   Y        +   K + P  ++ HRLD  TSG+
Sbjct: 16  ILYQDKDIIVINKPSGLLSVPGRSPAHYD-----SVYARVKAEHPHSQIVHRLDMATSGV 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +VVA  R+A + L   F  R   K Y++ V G  KN    +   L+       D+ +  K
Sbjct: 71  IVVALIRSAERELKRQFHDRETSKTYFARVAGHVKNDTGSVDYPLI------CDWPNRPK 124

Query: 218 Q--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           Q  +      +++H+KVI   A++   +++ P TGR+HQLRVH + +G PI+GD  Y   
Sbjct: 125 QKVDHLVGKQSLTHYKVI-SRAKRSTLVKLTPITGRSHQLRVHMMALGHPILGDGFYADP 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              +       +L LHA  + + HP  G  +  +A +P
Sbjct: 184 LAKSLAP----RLLLHAAELTIKHPYTGVSMTFSAEVP 217


>gi|288802331|ref|ZP_06407771.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           melaninogenica D18]
 gi|288335298|gb|EFC73733.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           melaninogenica D18]
          Length = 296

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 112/233 (48%), Gaps = 17/233 (7%)

Query: 87  SVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           SV+ +K +D  +S    ++YED  + V  K  GI        + ++   L  +     QK
Sbjct: 68  SVSKSKKNDLFRSRYVKIVYEDRFLVVIEKNIGILSMAAGHSSLNVKTVLDDYFRKTKQK 127

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               + HRLD++TSG+++ A+     Q L   +      + Y ++V G  ++ +  IANW
Sbjct: 128 CTAHVVHRLDRDTSGLMIYAKDIQTEQLLEHDWHNIVYDRRYVAVVSGEMEHDEGTIANW 187

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L         YV      + G  YA++HF V+D        +E Q  TGR +Q+RVH+  
Sbjct: 188 LKDNK----SYVTYSSPVDNGGKYAVTHFHVLD-RTVAHSLVEYQLETGRKNQIRVHSAD 242

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           MG P+ GD KY     GN   P+ ++L LHA  +   HP    R++   P+PA
Sbjct: 243 MGHPVCGDIKY-----GNGDDPL-HRLCLHAYVLCFHHPVTHQRMEFETPIPA 289


>gi|114769616|ref|ZP_01447226.1| ribosomal large subunit pseudouridine synthase A [alpha
           proteobacterium HTCC2255]
 gi|114549321|gb|EAU52203.1| ribosomal large subunit pseudouridine synthase A [alpha
           proteobacterium HTCC2255]
          Length = 217

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/222 (30%), Positives = 112/222 (50%), Gaps = 30/222 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  + V NKP+G+    G  + +H    L+  ++       L HRLD +TSG+++ 
Sbjct: 15  ILYIDEDVLVVNKPSGLLTVPGKELKHHDSLELRVKIEYPNS--FLVHRLDMDTSGVIIF 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--------CIANWLLKKSHIGGDY 212
           A +++  + L   F  R ++K+Y + V+G   N KE         I +W  +        
Sbjct: 73  AFSKSTQRSLNLQFEKRIVKKLYEARVFG---NIKEDNGFIDLPLIVDWPNRP------- 122

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             + K + K    A++H++V+D        + + P TGRTHQLRVH + +G  I+GD   
Sbjct: 123 --LQKIDAKEGKSALTHWQVLDREGD-VTRVALMPETGRTHQLRVHMMSLGHTILGDR-- 177

Query: 273 CANFKGNFTS-PIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
              F GN     + N+L LHA+ + + HP+ G ++   APLP
Sbjct: 178 ---FYGNVAEINLANELQLHAKDLMIIHPKNGKKITFKAPLP 216


>gi|264679430|ref|YP_003279337.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
 gi|262209943|gb|ACY34041.1| pseudouridine synthase, RluA family [Comamonas testosteroni CNB-2]
          Length = 352

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 92/336 (27%), Positives = 147/336 (43%), Gaps = 51/336 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIP 68
           ++V  +    R+D+         +   LQ++L  G V ++ K  +K + ++  G  +R+ 
Sbjct: 45  LMVGTEHHGQRVDKVLALGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLRV- 103

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                      E +    S+     +  L+  ++YED  + V NKPAG+ V    G    
Sbjct: 104 -----------EMRPTQQSMAFQPETMDLQ--VVYEDEDLLVINKPAGLVVHPAPGNWTG 150

Query: 127 YHIDGFLKSWVDSKG-QKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             ++G L    D K  Q PR  + HRLD++TSG++VVAR R+    L +    R + + Y
Sbjct: 151 TLLNGLLAR--DEKARQVPRAGIVHRLDKDTSGLMVVARNRSTMDALIKMIAAREVSRQY 208

Query: 184 WSLV---WGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDC 235
            +L    WG  K+++          + IG D      + VV  N      A + F ++D 
Sbjct: 209 LALAHKQWGSRKHRE--------VDAPIGRDPRNRLRMAVVDLNLHPGKQARTDFDLLDG 260

Query: 236 FAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            A      C L    HTGRTHQ+RVH   +G P++ D  Y    +G        +  LHA
Sbjct: 261 DAAHSLVRCTL----HTGRTHQIRVHMASLGHPLIADTLYGGQPEGGL-----ERQALHA 311

Query: 293 RYMDLPHPEGGRLQI-TAPLPAHMVKTWDSLGFKYD 327
             +   HP   +  +  APLP  M    D  G +Y+
Sbjct: 312 FRLAFEHPVTKKPLVHYAPLPQDMAGALDLWGLRYN 347


>gi|225552312|ref|ZP_03773252.1| ribosomal large subunit pseudouridine synthase D [Borrelia sp. SV1]
 gi|225371310|gb|EEH00740.1| ribosomal large subunit pseudouridine synthase D [Borrelia sp. SV1]
          Length = 326

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 55/182 (30%), Positives = 99/182 (54%), Gaps = 15/182 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRL
Sbjct: 85  VIIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRL 143

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+ A+  +  + L + F+ +R  K+Y ++V G   +    I +++ +  H   
Sbjct: 144 DKDTSGVLICAKNISTLRFLAQQFKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRK 203

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD 
Sbjct: 204 KFSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDE 258

Query: 271 KY 272
            Y
Sbjct: 259 VY 260


>gi|149279581|ref|ZP_01885710.1| ribosomal large subunit pseudouridine synthase D [Pedobacter sp.
           BAL39]
 gi|149229617|gb|EDM35007.1| ribosomal large subunit pseudouridine synthase D [Pedobacter sp.
           BAL39]
          Length = 228

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 61/205 (29%), Positives = 100/205 (48%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +    K AG  VQ        +D  +K ++     KP      + HRLD+  S
Sbjct: 8   ILYEDNHLIAICKRAGDIVQVDETGDEPLDEQVKKYLAKTYNKPNSAFLGVVHRLDRPVS 67

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A + +   F+ R ++K YW++V   P      + +WL+K      + V  
Sbjct: 68  GVILFAKTSKALERMNAVFKNREVKKTYWAIVRNKPAKPSGTLVHWLVKNPQ--KNVVTP 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +    G+  A   +++I      +  +E+ P TGR+HQ+RV    +GCPIVGD+KY   
Sbjct: 126 HQSEVPGSQRAELSYRLIGEL-NGYYLIEVDPLTGRSHQIRVQLSTLGCPIVGDNKY--- 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G      +  + LHAR +   HP
Sbjct: 182 --GYPRGSRKGSICLHARRLQFVHP 204


>gi|91775965|ref|YP_545721.1| ribosomal large subunit pseudouridine synthase D [Methylobacillus
           flagellatus KT]
 gi|91709952|gb|ABE49880.1| ribosomal large subunit pseudouridine synthase D [Methylobacillus
           flagellatus KT]
          Length = 356

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 86/305 (28%), Positives = 140/305 (45%), Gaps = 47/305 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLD+  +   P  +   +Q  ++ G V +D +      ++  G+ V+I P        
Sbjct: 18  GMRLDQALQRLMPEHSRSRIQGWIKDGLVTIDDETPTAKFKVWGGEQVQIKPQA------ 71

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
                   +   L    + +   +++ED  I V NKPAG+ V   +G      ++  L  
Sbjct: 72  --------TPEALAFEPENIPLEVVFEDEHILVINKPAGMVVHPAAGNWSGTLLNALLYH 123

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPK 192
               K   PR  + HRLD++TSG+LVVA+T AA  +L    + R +++ Y ++VWG + +
Sbjct: 124 APQLK-DVPRAGIVHRLDKDTSGLLVVAKTLAAQTNLVRQLQARTVKREYRTIVWGQVWR 182

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHT 249
           N K  +   + +  H             +    A++H++V+D F+      C LE    T
Sbjct: 183 NGK--VDQPIGRHPH-----ARTKMAVNRMGKPAVTHYEVLDRFSVHTYMRCLLE----T 231

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKG-----NFTSPIQNKLY------LHARYMDLP 298
           GRTHQ+RVH  H+  PIVGD  Y    +G     + +  ++N L       LHA  + L 
Sbjct: 232 GRTHQIRVHMQHLKAPIVGDPVY--GIRGILPLRHISDNLRNVLLEFKRQALHAIRLGLK 289

Query: 299 HPEGG 303
           HP  G
Sbjct: 290 HPVSG 294


>gi|224476300|ref|YP_002633906.1| putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus carnosus subsp. carnosus TM300]
 gi|222420907|emb|CAL27721.1| putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus carnosus subsp. carnosus TM300]
          Length = 305

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 143/313 (45%), Gaps = 44/313 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT   Y + E ++   R+D+         +   +Q  ++   V V+ K+VK N++++   
Sbjct: 1   MTEFNYEITEAEQAGQRIDKLLPEFNSDWSRSQIQDWIKEDLVTVNGKKVKANHKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +            E++ +++ +      + L   + YEDS + +  KP G+ V    
Sbjct: 61  KIEV-----------TEKETVEADIK----PENLNLDIYYEDSDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A ++L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRNLVEQLMAK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFK 231
            + + Y +LV G IP +       +    + IG D      + VV   +     A++HF 
Sbjct: 166 TVTRKYTALVHGNIPHD-------YGTIDAPIGRDKKDRQSMAVVDDGKD----AVTHFN 214

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V++ F + +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +          LH
Sbjct: 215 VLEHF-KDYTLVECELETGRTHQIRVHMKYIGHPLVGDPKYGPKKTMDIGGQA-----LH 268

Query: 292 ARYMDLPHPEGGR 304
           A  +   HP  G 
Sbjct: 269 AGVIGFEHPVTGE 281


>gi|39998250|ref|NP_954201.1| RNA pseudouridine synthase family protein [Geobacter sulfurreducens
           PCA]
 gi|39985196|gb|AAR36551.1| RNA pseudouridine synthase family protein [Geobacter sulfurreducens
           PCA]
 gi|307635144|gb|ADI85911.2| tRNA pseudouridine-65 synthase [Geobacter sulfurreducens KN400]
          Length = 250

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 111/240 (46%), Gaps = 26/240 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  +   +KPAG+ V   S I  H   F L+   D  G++    HRLD+ TSG+LV
Sbjct: 3   ILFRDQYLVAVHKPAGLLVHR-SPIDRHETRFALQEVRDLLGRRVYPVHRLDKPTSGVLV 61

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A   A A+ L ++F   R+ K Y ++  GI     E I +  L +     D +   K +
Sbjct: 62  FALDPATARSLGDAFAGGRVNKTYLAVTRGI--VPPEGIIDHSLSEEP---DRLDGAKSS 116

Query: 220 EKGANYAISHFK---------VIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++ F+         V   +A  ++   E+ PHTGR HQLR H  H+  PI+GD
Sbjct: 117 PAAPQPAVTVFRRLAEAELPVVTGRYASSRYSLAELTPHTGRRHQLRRHMKHIFHPIIGD 176

Query: 270 HKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             Y        F+  F      +L LHA  + LPHP  G  L I AP    + +  D LG
Sbjct: 177 TTYGEGRHNRFFREEFGC---GRLLLHAAELSLPHPASGETLTIAAPPDRELARLLDRLG 233


>gi|55820603|ref|YP_139045.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMG 18311]
 gi|55736588|gb|AAV60230.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMG 18311]
 gi|312277926|gb|ADQ62583.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 296

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 86/321 (26%), Positives = 147/321 (45%), Gaps = 48/321 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++     + +++G V V+ K  K    ++ G V+          
Sbjct: 7   EAGNRLDKSLAD-LTELSRSQANEAIKAGTVLVNGKSAKAKYVVKEGDVI---------T 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-- 133
           +++ E+++L+      K  D    I+ YED+ + V NKP G+ V   +G   H  G L  
Sbjct: 57  YVLPEEEVLEY-----KAEDIPLDII-YEDADVAVVNKPQGMVVHPSAG---HTSGTLVN 107

Query: 134 ------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 K      G  +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++
Sbjct: 108 ALMYHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAI 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLE 244
           V G   N +  I      ++ IG       KQ    KG   A++ F V++ F   +  +E
Sbjct: 168 VHGNLPNDRGVI------EAPIGRSDKDRKKQAVTAKG-KPAVTRFTVLERFGN-YTLVE 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +Q  TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +   HP  
Sbjct: 220 LQLETGRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGHGQ-------FLHAKTLGFTHPTT 272

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
           G+L +  A  P    +T + L
Sbjct: 273 GKLVEFNAEEPIIFKETLEKL 293


>gi|254556664|ref|YP_003063081.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254045591|gb|ACT62384.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 307

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/237 (32%), Positives = 112/237 (47%), Gaps = 22/237 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL--KSWVDSKGQ-KPRLTHRLDQETS 155
           ++YED  + V NKP G+ V    G   H  ++  L         G+ +P + HR+D++TS
Sbjct: 84  IVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTS 143

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+VA+   A Q L    + +   + Y +LV G+ K     I N  L +S        +
Sbjct: 144 GLLMVAKNDRAHQSLAAQLKAKTNLREYVALVHGVIKEDTGTI-NAPLGRSPKDRKKQAI 202

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
           VK        AI+HFKV+  + Q +  +  +  TGRTHQ+RVH   +G P+VGD  Y   
Sbjct: 203 VKTGRP----AITHFKVLKRY-QHYTLISCRLETGRTHQIRVHLQSIGHPLVGDPLYGPK 257

Query: 275 -NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
              KG+         +LHA+ +   HP  G  L   APLP     T   L  K D N
Sbjct: 258 KTIKGHGQ-------FLHAKLLGFKHPVTGDLLTFEAPLPPIFTTTLAKLD-KTDGN 306


>gi|312962216|ref|ZP_07776708.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens WH6]
 gi|311283553|gb|EFQ62142.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens WH6]
          Length = 211

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/214 (33%), Positives = 111/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  + V NKP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   ILYQDDAVLVVNKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALAWGQPALDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEFGKHALTFWKVLE-RCGDWCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHEQAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
              P   +L LHA  +   HP+ G RL+   P P
Sbjct: 180 AAWP---RLCLHASMLSFTHPQSGERLRFECPAP 210


>gi|310766696|gb|ADP11646.1| 23S rRNA pseudouridine synthase D [Erwinia sp. Ejp617]
          Length = 325

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/253 (30%), Positives = 129/253 (50%), Gaps = 33/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHHFPAIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL +S + R I + Y ++  G         + I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVDSLQRREITREYEAVAIGRMTAGGTVDQPISRHSTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A +H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------ATTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMSHISHPLVGDPL 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F + ++  ++  LHA  + L HP  G  ++  APLP  MV   D+L
Sbjct: 253 YGGRPRPPKGASEAFIATLRAFDRQALHATMLRLYHPISGIEMEWHAPLPQDMVDLIDAL 312

Query: 323 GFKYDRNLYIKRL 335
             K D   + ++L
Sbjct: 313 --KADTEAFKEQL 323


>gi|293415867|ref|ZP_06658507.1| rluD [Escherichia coli B185]
 gi|291432056|gb|EFF05038.1| rluD [Escherichia coli B185]
          Length = 326

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 90/339 (26%), Positives = 159/339 (46%), Gaps = 47/339 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V   
Sbjct: 9   ATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQV--- 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             INA   I +E +     + L          ++YED  I V NKP  + V  G+G   +
Sbjct: 66  -AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + 
Sbjct: 111 PDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH + +       A++H+++++ F + 
Sbjct: 171 YEAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPMGKP------AVTHYRIMEHF-RV 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
           A  + L HP  G  ++  AP+P  MV+  +++   ++ +
Sbjct: 281 ATMLRLYHPISGIEMEWHAPIPQDMVELIEAMRADFEEH 319


>gi|169350183|ref|ZP_02867121.1| hypothetical protein CLOSPI_00927 [Clostridium spiroforme DSM 1552]
 gi|169292966|gb|EDS75099.1| hypothetical protein CLOSPI_00927 [Clostridium spiroforme DSM 1552]
          Length = 306

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/320 (25%), Positives = 151/320 (47%), Gaps = 33/320 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++VEN+  N RLD+    +   ++   +Q+++  G V V+ K  K + + +    + I  
Sbjct: 6   LLVENNN-NYRLDKIIALNMEELSRTQIQEMIGRGLVLVNGKVEKASYKTKLNDQIEI-- 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                         ++ + +L   ++ +   ++YED  + V +KP G+ V    GI    
Sbjct: 63  -------------TIEDNSDLEIEAEDIPLNVVYEDKDVIVIDKPTGMIVHPSPGITSGT 109

Query: 129 -IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HR+D+ETSG+L+VA+   A + L+E  +   + + Y
Sbjct: 110 LVNALLFHCKDLSGINGVNRPGIVHRIDKETSGLLMVAKNDIAHRFLSEQLKDHSVTRRY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G+  + +  I +  + ++      + V K N K    AI++F V+  + +    +
Sbjct: 170 VALVHGLIPHVQGKI-DAPIGRNPNDRQSMCVTKNNSKN---AITNFTVLKRY-KNMSLI 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E +  TGRTHQ+RVH  ++G P+ GD KY     G       +  +LHA+ +   HP   
Sbjct: 225 ECRLETGRTHQIRVHMSYIGYPVYGDPKY-----GYRKDDCSHGQFLHAKKLGFIHPTTK 279

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             ++  + LP +     D L
Sbjct: 280 EYMEFESELPDYFKAKLDEL 299


>gi|160947739|ref|ZP_02094906.1| hypothetical protein PEPMIC_01674 [Parvimonas micra ATCC 33270]
 gi|158446873|gb|EDP23868.1| hypothetical protein PEPMIC_01674 [Parvimonas micra ATCC 33270]
          Length = 310

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 90/342 (26%), Positives = 153/342 (44%), Gaps = 47/342 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++Y+     ++ +R D +      +++  ++QK+++   V V+ K +K N  ++ G 
Sbjct: 1   MAELKYI----SDKKIRCDVFLSEKISNLSRTSIQKLIKGKLVFVNGKNIKPNVILEIGD 56

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V IP          KE  ++   ++L          ++YED  I + NKP  + V  
Sbjct: 57  EITVSIPDK--------KEITLVAEDIDLD---------IVYEDDYIIIINKPRNMVVHP 99

Query: 122 GSGIAYH--IDGFLK----SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G   H  ++  L     S ++S  ++P + HRLD++T+G+++ A+       L E F 
Sbjct: 100 AVGNEKHTLVNALLNHCKLSMINS--ERPGIVHRLDKDTTGLIICAKDDETHLKLVEMFA 157

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVI 233
            R I K Y ++  G     KE   N L+ K  IG D     K +   K    AI+ + V+
Sbjct: 158 NREINKKYLAICNG--SFSKE---NGLIDKP-IGRDEKDRKKMSVKSKSGKAAITEYNVL 211

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHA 292
                K+  +++  HTGRTHQ+RVH   +  PI+GD  Y     G     I+ N   LH+
Sbjct: 212 -ISNLKYSLVDVTLHTGRTHQIRVHFSSLNHPIIGDETY-----GKKNEKIKANGQMLHS 265

Query: 293 RYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
            Y++  HP     L  T     +     +  G K++  L  K
Sbjct: 266 YYLEFSHPITDENLSFTVLPDEYFFSILNKTGLKFNEELLCK 307


>gi|327392692|dbj|BAK10114.1| ribosomal large subunit pseudouridine synthase A RluA [Pantoea
           ananatis AJ13355]
          Length = 217

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 107/207 (51%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D+ I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++V
Sbjct: 14  ILYQDAHIMVVNKPSGLLSVPGR--LDEHKDSVM-TRIQRDYPEAESVHRLDMATSGVIV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R   K Y + VWG P  +K  +   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPAKTYVARVWGHPAQEKGMVDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              + G + A + ++V++        + ++P TGR+HQLRVH L +G PI+GD  Y    
Sbjct: 125 VCFDTGKS-AQTDYQVVEYGDDNSARVALKPITGRSHQLRVHMLALGHPILGDGFYA--- 180

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
                  + ++L LHA  + + HP  G
Sbjct: 181 -HPEAKAMADRLLLHAESLTITHPAFG 206


>gi|312171425|emb|CBX79684.1| ribosomal large subunit pseudouridine synthase D [Erwinia amylovora
           ATCC BAA-2158]
          Length = 325

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/253 (29%), Positives = 130/253 (51%), Gaps = 33/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHHFPAIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  +  HL ++ + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPSQTHLVDALQRREITREYEAVAIGRMTAGGTVNEPISRHSTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A +H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------ATTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMSHISHPLVGDPL 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F + ++  ++  LHA  + L HP  G  ++  APLP  MV+  D+L
Sbjct: 253 YGGRPRPPKGASEAFIATLRAFDRQALHATMLRLYHPISGIEMEWHAPLPQDMVELIDAL 312

Query: 323 GFKYDRNLYIKRL 335
             K D   + ++L
Sbjct: 313 --KADTEAFKEQL 323


>gi|88797409|ref|ZP_01112999.1| putative 23S rRNA pseudouridylate 746 synthase [Reinekea sp.
           MED297]
 gi|88780278|gb|EAR11463.1| putative 23S rRNA pseudouridylate 746 synthase [Reinekea sp.
           MED297]
          Length = 223

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 65/215 (30%), Positives = 107/215 (49%), Gaps = 15/215 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  + V NKP+G+    G     + D      V  +    R+ HRLD  TSG++V+
Sbjct: 20  IVHEDDALLVINKPSGLLALSGKD-PRNRDSVHARLV-KRCPSIRMIHRLDFGTSGLMVL 77

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A+++  A  L   F+ R + K+Y +++WG   N    I       +HI  D  +  K   
Sbjct: 78  AKSKTMATTLNRQFQQREVTKVYQAILWGQLANASGRI------NAHIARDDENFPKMRI 131

Query: 220 EKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +G   A + ++V +         +E  P TGRTHQLR+H+ H+G PI+G    C  +  
Sbjct: 132 GEGGKPAQTDYQVLVTDMRANTSTVEFYPRTGRTHQLRIHSAHIGHPILG----CDIYGT 187

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             ++   ++L LHA  + L HPE  + L+  +P P
Sbjct: 188 QASTQAASRLLLHATELTLKHPETDQLLRFQSPRP 222


>gi|150016471|ref|YP_001308725.1| RluA family pseudouridine synthase [Clostridium beijerinckii NCIMB
           8052]
 gi|149902936|gb|ABR33769.1| pseudouridine synthase, RluA family [Clostridium beijerinckii NCIMB
           8052]
          Length = 305

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/330 (24%), Positives = 150/330 (45%), Gaps = 54/330 (16%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V+  +   R+D++    +   +   +Q ++    ++V+ K  K N ++++         
Sbjct: 7   IVDEKDRGERIDKYLAEIFVDKSRSFIQGLIEKDDIKVNNKTPKSNYKLRA--------- 57

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
           ++ +     E ++L         ++ +   +LYED  + V NKP G+ V    G      
Sbjct: 58  LDEIEVTFSEPEVLRVE------AEEIPINILYEDKDVVVVNKPQGMVVHPAPGNYNGTL 111

Query: 125 ---IAYH------IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
              + YH      I+G ++         P + HR+D++TSG+LVVA+   A   L++  +
Sbjct: 112 VNALLYHCKDLSSINGIIR---------PGIVHRIDKDTSGVLVVAKNDEAHNKLSDQLK 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLL--KKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
              +++ Y++LV G  KN K  I   L   K+  +    V       +G   A++H++V+
Sbjct: 163 DHSMKREYYALVEGRLKNDKGIIDKPLARNKRDRLKIGIV-------EGGKRAVTHYEVL 215

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F   +  ++    TGRTHQ+RVH   +G P+VGD  Y    K  F    Q    LHA+
Sbjct: 216 ERF-NGYTLIKCILETGRTHQIRVHMASIGFPLVGDPLYGFK-KQRFKLKGQ---VLHAK 270

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +   HP     ++ T  LP +  +  + L
Sbjct: 271 TLGFVHPSKNEYMEFTTELPEYFQEIIEKL 300


>gi|326564292|gb|EGE14522.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis 103P14B1]
 gi|326573848|gb|EGE23801.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis O35E]
 gi|326574731|gb|EGE24667.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis 101P30B1]
          Length = 242

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 119/229 (51%), Gaps = 23/229 (10%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +F KSI +YED  I+V +KPAG+    G  +       L+S +       RL HRLD +T
Sbjct: 25  EFTKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPNIRLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDY 212
           SG+++ A++  A  H+++ F  R  QK Y ++V+G  +  +KK  +   +  +      +
Sbjct: 81  SGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVPVRYEPTTKPRH 140

Query: 213 VHVVKQNEKGANYAISHFKVI--------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +  +  N++    A++H++V+        +  A     + ++P TGR+HQLRVH +H+G 
Sbjct: 141 IVDMDWNKR----ALTHYEVMHHELRCDDNGRAYPVTRVSLKPITGRSHQLRVHMVHLGH 196

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            ++GD  Y  +     +    N+L LHA  + L HP  G  +   +P+P
Sbjct: 197 VMIGDPIYAEDVALKLS----NRLNLHAHKLRLKHPTHGIWMDWVSPVP 241


>gi|291618565|ref|YP_003521307.1| RluD [Pantoea ananatis LMG 20103]
 gi|291153595|gb|ADD78179.1| RluD [Pantoea ananatis LMG 20103]
 gi|327394946|dbj|BAK12368.1| ribosomal large subunit pseudouridine synthase D RluD [Pantoea
           ananatis AJ13355]
          Length = 326

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/253 (28%), Positives = 128/253 (50%), Gaps = 33/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP    V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDFVVHPGAG---NPDGTVLNALLHHYPAIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL ++ + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVDALQRREITREYEAVAIGTMTAGGTVDEPISRHSTKRTHMS-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH +         A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPM------GKPAVTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMSHINHPLVGDPL 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +       +F + ++  ++  LHA  + L HP  G  ++  A +P  M+   D+L
Sbjct: 253 YGGRPRPPKGASEDFITTLRGFDRQALHATMLRLYHPISGIEMEFHAAIPQDMIDLIDAL 312

Query: 323 GFKYDRNLYIKRL 335
             K D  ++  +L
Sbjct: 313 --KADTEMFKDQL 323


>gi|82778018|ref|YP_404367.1| 23S rRNA pseudouridine synthase D [Shigella dysenteriae Sd197]
 gi|309789452|ref|ZP_07684038.1| ribosomal large subunit pseudouridine synthase D [Shigella
           dysenteriae 1617]
 gi|81242166|gb|ABB62876.1| suppressor of ftsH mutation [Shigella dysenteriae Sd197]
 gi|308922695|gb|EFP68216.1| ribosomal large subunit pseudouridine synthase D [Shigella
           dysenteriae 1617]
          Length = 326

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 88/336 (26%), Positives = 157/336 (46%), Gaps = 41/336 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V   
Sbjct: 9   ATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNSKLCDKPKEKVLGGEQV--- 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAY 127
             INA   I +E +     + L          ++YED  I V NKP  + V  G+G    
Sbjct: 66  -AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAGNPDS 113

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   L  +       PR  + HRLD++T+G++VVA+T  A + L ES + R I + Y +
Sbjct: 114 TVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQRRLVESLQRREITREYEA 173

Query: 186 LVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           +  G         E I+    K++H+    VH +         A++H+++++ F +    
Sbjct: 174 VAIGHMTAGGTVDEPISRHPTKRTHMA---VHPM------GKPAVTHYRIMEHF-RVHTR 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHARY 294
           L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA  
Sbjct: 224 LRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATM 283

Query: 295 MDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
           + L HP  G  ++  AP+P  MV+  +++   ++ +
Sbjct: 284 LRLYHPISGIEMEWHAPIPQDMVELIEAMRADFEEH 319


>gi|61554746|gb|AAX46608.1| hypothetical protein FLJ14494 [Bos taurus]
          Length = 304

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 59/192 (30%), Positives = 99/192 (51%), Gaps = 21/192 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSG 156
           ++++D ++ V NKP G+ V GG G+   I   L          K +   L HRLD+ET+G
Sbjct: 99  IVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P  +   +   +++K   G  + H  
Sbjct: 159 VMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIVEKEAQGQQHHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  ++ + A  A++ ++V+   +     LE+QP TG  HQLRVH + 
Sbjct: 219 TLSPSYRMDDGKMVRVRSSRNAQLAVTQYRVLS-SSLSAALLELQPITGIKHQLRVHMSF 277

Query: 261 HMGCPIVGDHKY 272
            + CPI+GDHKY
Sbjct: 278 GLDCPILGDHKY 289


>gi|68248781|ref|YP_247893.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae 86-028NP]
 gi|145635280|ref|ZP_01790983.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           influenzae PittAA]
 gi|68056980|gb|AAX87233.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           influenzae 86-028NP]
 gi|145267424|gb|EDK07425.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           influenzae PittAA]
          Length = 324

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 121/247 (48%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP  + V  G+G         + YH      S V   G    + HRLD
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI--SEVPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++ +
Sbjct: 139 KDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLM 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P++G
Sbjct: 199 A---VHPMGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLG 248

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           D  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+  
Sbjct: 249 DQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAHPITGEIMEWYAPLPDDFVELL 308

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 309 NALKADY 315


>gi|256825466|ref|YP_003149426.1| ribosomal large subunit pseudouridine synthase D [Kytococcus
           sedentarius DSM 20547]
 gi|256688859|gb|ACV06661.1| ribosomal large subunit pseudouridine synthase D [Kytococcus
           sedentarius DSM 20547]
          Length = 309

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 86/313 (27%), Positives = 144/313 (46%), Gaps = 39/313 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + VVV +  E  R+D         ++   +  I   G V +  K +   +R+ +G+
Sbjct: 1   MSDTRTVVVPDGLEGERVDAGLSRLL-GLSRNKVADIAAEGGVLMGSKALGKGDRLLAGE 59

Query: 64  VVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           +V +  PP   A   +   + I    V             ++ED++I V +KPAG++   
Sbjct: 60  LVTVTLPPENQAPPVLPSTESIPGLRV-------------VHEDTEIIVVDKPAGVAAHP 106

Query: 122 GSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G     + G L +    + + G   R  +  RLD  TSG++VVA++  A   L ++FR
Sbjct: 107 SVGWKGPDVVGGLAAEGYRISTSGAAERQGIVQRLDVGTSGLMVVAKSERAYSVLKQAFR 166

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R ++K Y +LV G+P   +  I   + +  H G DY   V  N +    +I+H+++++ 
Sbjct: 167 DRVVEKTYHTLVQGLPDPLQGTIDAPIGR--HPGHDYRFAVMSNGR---PSITHYELLEA 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-----YL 290
             +    LE+   TGRTHQ+RVH   MG P  GD  Y A+        +  +L     +L
Sbjct: 222 H-RAASLLEVHLETGRTHQIRVHFSAMGHPCAGDLTYGAD------PTLAKRLGLVRQWL 274

Query: 291 HARYMDLPHPEGG 303
           HA  +   HP  G
Sbjct: 275 HAVELGFTHPGSG 287


>gi|87198472|ref|YP_495729.1| pseudouridylate synthase [Novosphingobium aromaticivorans DSM
           12444]
 gi|87134153|gb|ABD24895.1| Pseudouridylate synthase [Novosphingobium aromaticivorans DSM
           12444]
          Length = 222

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/232 (31%), Positives = 117/232 (50%), Gaps = 28/232 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +L+ED +  V +KPAG+ +     GG  +  H+D     +     ++P   HRLD++TSG
Sbjct: 6   ILFEDGEALVIDKPAGLPLDRPRAGGDSLENHLDALRFGFQ----REPFPVHRLDRDTSG 61

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            L++AR   A +  + +F  R ++K+Y  +V G    +K  I   L K S     +  + 
Sbjct: 62  CLLLARNPKALKRFSAAFEAREVEKVYLGIVAGEVTGEKGTIDLALSKVSSAEKGWRMIP 121

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCAN 275
            +  K    A++H++V+         +E +P TGRTHQ+R+HAL  +G  +VGD  Y  +
Sbjct: 122 ARKGK---PALTHWRVV-ARKPGLTLVEFRPETGRTHQIRIHALAGLGHALVGDPVY-GD 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT--APLPAHMVKTWDSLGFK 325
            KG +      +  LHA   DL  P  G+  I   APLP      +D+ GF+
Sbjct: 177 GKGAW------RTMLHAS--DLVVPRAGKAPIVAHAPLPL----DFDAFGFE 216


>gi|237800319|ref|ZP_04588780.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. oryzae str. 1_6]
 gi|331023176|gb|EGI03233.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. oryzae str. 1_6]
          Length = 211

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/214 (32%), Positives = 112/214 (52%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIYQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDPDTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++++KV++  A   C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEAGKHALTYWKVLERHASH-CRVELTPVTGRSHQLRVHMLSIGHPLLGDGLY-AHSEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              P   +L LHA  +   HP  G R+    P+P
Sbjct: 180 AAYP---RLCLHASMLSFTHPGSGERMTFECPVP 210


>gi|146318440|ref|YP_001198152.1| YlyB [Streptococcus suis 05ZYH33]
 gi|145689246|gb|ABP89752.1| YlyB [Streptococcus suis 05ZYH33]
          Length = 309

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/293 (27%), Positives = 138/293 (47%), Gaps = 47/293 (16%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +++GQV V+ +  K    +Q G V         L + I E + +D        ++ +   
Sbjct: 31  IKAGQVLVNGQPKKAKYSVQVGDV---------LTYQIPEVEEIDYV------AEDIPLE 75

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++++D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 76  IVFQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALLYHVKDLSGINGVLRPGIVHRID 132

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L    + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 133 KDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 186

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F+V++ F   +  +E+   TGRTHQ+RVH  ++G P+ GD
Sbjct: 187 EKDRKKQAVTAKGKE-AVTRFQVLERFGD-YTLVELTLETGRTHQIRVHMAYIGHPVAGD 244

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
             Y      KG+         +LHAR +   HP  G  ++ TA  PA   + W
Sbjct: 245 EAYGPRKTLKGHGQ-------FLHARTLGFTHPRTGEVVEFTAEAPAIFQEHW 290


>gi|255263975|ref|ZP_05343317.1| ribosomal large subunit pseudouridine synthase A [Thalassiobium sp.
           R2A62]
 gi|255106310|gb|EET48984.1| ribosomal large subunit pseudouridine synthase A [Thalassiobium sp.
           R2A62]
          Length = 215

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 112/216 (51%), Gaps = 17/216 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++L+ED ++ + +KP G+    G G   H+   L + + +      L HRLD++TSG+++
Sbjct: 13  VILHEDHEVILVDKPEGLLSVPGKG--EHLADCLLTRLQAAFPTALLVHRLDRDTSGVMI 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A TR A +HL   F  R  +K Y + VWG  + K+  +   ++       D+ +  +Q 
Sbjct: 71  FAATRHAQRHLGLQFEKRHTKKTYVARVWGDLQPKEGTVDQPIIV------DWENRPRQK 124

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              +    A + ++V+     +   + + P TGR+HQLR+H LH+G PI+GD  Y     
Sbjct: 125 ICAETGRAAQTDWRVVRGDGAE-TRVRLMPKTGRSHQLRLHMLHLGHPILGDPFYATGAA 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            +       ++ LH+  +   HP+GG+ ++ITA  P
Sbjct: 184 LD-----HPRMMLHSETLQFRHPDGGQGMRITAKAP 214


>gi|217964005|ref|YP_002349683.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HCC23]
 gi|290893028|ref|ZP_06556017.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J2-071]
 gi|217333275|gb|ACK39069.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HCC23]
 gi|290557388|gb|EFD90913.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J2-071]
 gi|307571425|emb|CAR84604.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes L99]
 gi|313608111|gb|EFR84172.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL F2-208]
          Length = 302

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 84/302 (27%), Positives = 142/302 (47%), Gaps = 51/302 (16%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQV----VRIPPVINALNHIIKEQKILDSSVNLTK 92
           +Q +L+SG + V+ +  K N ++Q G      VR P          +E ++L   + L  
Sbjct: 32  IQLMLKSGDITVNGELAKPNYKVQVGDEIHYEVREP----------EELEVLAEDIPLD- 80

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQK 143
                   + +ED  + V NKP G+ V   +G A         +H D    S ++ K  +
Sbjct: 81  --------IYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL--SGINGK-IR 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    +
Sbjct: 130 PGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPI 188

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++      + VV+  ++    A +HF+V++     +  +  +  TGRTHQ+RVH  ++G
Sbjct: 189 GRAKEDRQKMAVVRDGKE----ARTHFEVLERLP-GYTLINCKLDTGRTHQIRVHLKYIG 243

Query: 264 CPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            P+ GD KY      KGN         +LHA  +   HP    R+   APLP+   K   
Sbjct: 244 HPLAGDPKYGPKNTIKGNGQ-------FLHAAKLGFDHPTTNERMTFEAPLPSSFEKALK 296

Query: 321 SL 322
           SL
Sbjct: 297 SL 298


>gi|197284293|ref|YP_002150165.1| 23S rRNA pseudouridine synthase D [Proteus mirabilis HI4320]
 gi|227357802|ref|ZP_03842150.1| ribosomal large subunit pseudouridine synthase D [Proteus mirabilis
           ATCC 29906]
 gi|194681780|emb|CAR40996.1| ribosomal large subunit pseudouridine synthase D [Proteus mirabilis
           HI4320]
 gi|227161912|gb|EEI46930.1| ribosomal large subunit pseudouridine synthase D [Proteus mirabilis
           ATCC 29906]
          Length = 325

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/235 (31%), Positives = 122/235 (51%), Gaps = 31/235 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----PR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +  +  +    PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLYRYPEIVNVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL E+ + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVEALQRREITREYEAVATGRMTAGGLVNEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH +         A++H++V++ F +    L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 201 -VHPM------GKPAVTHYRVMEHF-RAHTRLRLRLETGRTHQIRVHMAHIHHPLIGDQL 252

Query: 272 YCAN---FKG---NFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           Y       KG    F   ++  ++  LHA  + L HP  G  ++  APLP  MV+
Sbjct: 253 YGGRPRPLKGASEEFRETLRRFDRQALHATMLRLYHPITGIEMEWHAPLPDDMVE 307


>gi|26553465|ref|NP_757399.1| pseudouridine synthase [Mycoplasma penetrans HF-2]
 gi|26453471|dbj|BAC43803.1| pseudouridine synthase [Mycoplasma penetrans HF-2]
          Length = 301

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 129/281 (45%), Gaps = 31/281 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ----VV 65
           + ++ +EEN  L  +    +  ++   + K +++G ++V+ K+  +N ++Q        +
Sbjct: 4   IFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQIFL 63

Query: 66  RIPPVINALN-HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           R+ P+   L  + ++ + IL+               ++YED  I V NKP G+  Q    
Sbjct: 64  RLKPIKKELKLNFLEAKPILN---------------VIYEDKNIIVVNKPRGLICQPDKN 108

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                +   I  +L    D    +  L HRLD+ T+G+ V A+ +     L   +    +
Sbjct: 109 EKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAV 168

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y  L +G  K K + + +++          +  + +  K     I+ ++VI+   + 
Sbjct: 169 SKYYLCLCYGKFKKKSDTLKDFIFLNEE---KQIMEIDRENKFNKEIITKYRVIEQ-KKD 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              LE+Q  TG+ HQ+RVH   +G P++GD KY  N KGNF
Sbjct: 225 MALLEIQLLTGKKHQIRVHMASIGHPVLGDTKY--NKKGNF 263


>gi|260912661|ref|ZP_05919147.1| ribosomal large subunit pseudouridine synthase D [Pasteurella
           dagmatis ATCC 43325]
 gi|260633039|gb|EEX51204.1| ribosomal large subunit pseudouridine synthase D [Pasteurella
           dagmatis ATCC 43325]
          Length = 324

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/263 (27%), Positives = 130/263 (49%), Gaps = 31/263 (11%)

Query: 84  LDSSVNLTKHSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           ++ +V + + S F+   L    +YED  I V NKP    V  G+G      ++  L  + 
Sbjct: 64  IEITVEIEEDSRFMPENLPLNIVYEDDDILVINKPKDFVVHPGAGNPTGTVLNALLYHY- 122

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK- 194
               + PR  + HRLD++T+G++V+A+T  A   L    + R+I + Y ++  GI     
Sbjct: 123 PQIAEVPRAGIVHRLDKDTTGLMVIAKTIPAQTKLVRDLQKRKITREYEAIASGIMTKGG 182

Query: 195 --KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + +A    K++ +    VH + +       AI+H+++++ F + +  L ++  TGRT
Sbjct: 183 MVDQPMARHPTKRTQMA---VHPMGKP------AITHYRIMERF-RNYTRLRLRLETGRT 232

Query: 253 HQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGG 303
           HQ+RVH  H+  P++GD  Y        N    F + +++  +  LHA  + L HP  G 
Sbjct: 233 HQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEEFMAVLRDFKRQALHAIMLRLKHPITGE 292

Query: 304 RLQITAPLPAHMVKTWDSLGFKY 326
            ++  APLP   ++  ++L   Y
Sbjct: 293 MMEWYAPLPEDFIQLVEALKADY 315


>gi|240949469|ref|ZP_04753809.1| 23S rRNA pseudouridine synthase D [Actinobacillus minor NM305]
 gi|240296042|gb|EER46703.1| 23S rRNA pseudouridine synthase D [Actinobacillus minor NM305]
          Length = 325

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/253 (30%), Positives = 128/253 (50%), Gaps = 33/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +        + PR  + HRLD++T
Sbjct: 86  IVYEDDDIIVINKPKDLVVHPGAG---NPDGTVLNALLYHYPPIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+   A  HL  + + R I + Y ++  GI        E +A    K++ +   
Sbjct: 143 TGLMVVAKNIPAQTHLVTALQKRHITREYEAIASGIMTQGGKVDEPMARHPTKRTAMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 201 -VHPMGKP------AVTHYRIMERF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQL 252

Query: 272 YCANFKG------NFTSPIQN--KLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           Y    +        F S ++   +  LHA  + L HP  G L +  APLP   V+  ++L
Sbjct: 253 YGGRPRPPKGASEEFLSVLRGFQRQALHATMLRLEHPITGELMEWHAPLPDDFVELVEAL 312

Query: 323 GFKYDRNLYIKRL 335
             K D  LY  +L
Sbjct: 313 --KADYELYKDQL 323


>gi|319947093|ref|ZP_08021327.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
 gi|319747141|gb|EFV99400.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
          Length = 296

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/218 (31%), Positives = 110/218 (50%), Gaps = 18/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGI 157
           +LYED    V NKPAG++    S  +  I  F+K +      + +L H   RLD++TSGI
Sbjct: 78  ILYEDDHFLVLNKPAGVASIPSSLHSNTIANFVKGYYVRNQYENQLVHIVTRLDKDTSGI 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + IQK Y++LV G  +  +K + IA     +  I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQAKTIQKHYFALVKGKGELASKGDIIAPIARDEDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  KG  YA + ++V+  F      +++Q HTGRTHQ+RVH  H+G P++GD  Y  +
Sbjct: 192 TRKVAKGGKYAHTSYQVVQSFGD-IHLVDIQLHTGRTHQIRVHFSHIGFPLLGDDLYGGS 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
            +         +  LH   +   HP     L+I + LP
Sbjct: 251 LEDGIL-----RQALHCHSLAFYHPFWEEELRIESSLP 283


>gi|223934286|ref|ZP_03626210.1| pseudouridine synthase, RluA family [Streptococcus suis 89/1591]
 gi|253751575|ref|YP_003024716.1| RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|253753476|ref|YP_003026617.1| RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|253755698|ref|YP_003028838.1| RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|330832720|ref|YP_004401545.1| RluA family pseudouridine synthase [Streptococcus suis ST3]
 gi|31364860|gb|AAP49462.1| YlyB [Streptococcus suis]
 gi|223897042|gb|EEF63479.1| pseudouridine synthase, RluA family [Streptococcus suis 89/1591]
 gi|251815864|emb|CAZ51475.1| putative RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|251818162|emb|CAZ55959.1| putative RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|251819722|emb|CAR45564.1| putative RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|292558226|gb|ADE31227.1| YlyB [Streptococcus suis GZ1]
 gi|319758010|gb|ADV69952.1| pseudouridine synthase, RluA family [Streptococcus suis JS14]
 gi|329306943|gb|AEB81359.1| pseudouridine synthase, RluA family [Streptococcus suis ST3]
          Length = 297

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 85/310 (27%), Positives = 145/310 (46%), Gaps = 48/310 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+   +       V  ++I ++GQV V+ +  K    +Q G V         L + 
Sbjct: 9   GIRLDKALSDLTDLSRSVANEQI-KAGQVLVNGQPKKAKYSVQVGDV---------LTYQ 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I E + +D        ++ +   ++++D  + V NKP G+ V   +G   H  G L + +
Sbjct: 59  IPEVEEIDYV------AEDIPLEIVFQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNAL 109

Query: 138 -----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                D  G     +P + HR+D++TSG+L++A+   A   L    + ++  + YW++V 
Sbjct: 110 LYHVKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIVH 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           G   N +  I      ++ IG       KQ    KG   A++ F+V++ F   +  +E+ 
Sbjct: 170 GNLPNDRGVI------EAPIGRSEKDRKKQAVTAKGKE-AVTRFQVLERFGD-YTLVELT 221

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHAR +   HP  G 
Sbjct: 222 LETGRTHQIRVHMAYIGHPVAGDEAYGPRKTLKGHGQ-------FLHARTLGFTHPRTGE 274

Query: 305 -LQITAPLPA 313
            ++ TA  PA
Sbjct: 275 VVEFTAEAPA 284


>gi|319898141|ref|YP_004136338.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae F3031]
 gi|317433647|emb|CBY82032.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae F3031]
          Length = 324

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 122/247 (49%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP  + V  G+G         + YH    ++  V   G    + HRLD
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVE--VPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++ +
Sbjct: 139 KDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLM 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P++G
Sbjct: 199 A---VHPMGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLG 248

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           D  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+  
Sbjct: 249 DQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 309 NALKADY 315


>gi|148549194|ref|YP_001269296.1| pseudouridine synthase [Pseudomonas putida F1]
 gi|148513252|gb|ABQ80112.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           putida F1]
          Length = 211

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/214 (33%), Positives = 111/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED+ I V NKP  + SV G +    + D  +    ++      + HRLD ETSGI++
Sbjct: 8   ILFEDAAILVINKPTLLLSVPGRA--EDNKDCLITRLQENGYPDALIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADSHRELSRQFHDRETEKAYTALCWGQPALDSGSID--LPLRYDPPTKPRHVV-DH 122

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E+G  +A++ +++++     +C +E+ P TGR+HQLRVH L +G P++GD  Y AN +  
Sbjct: 123 EQG-KHALTFWRIVE-RCGDYCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY-ANPQAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL+   P P
Sbjct: 180 AA---HERLCLHASMLSFTHPVSGQRLKFECPAP 210


>gi|311086138|gb|ADP66220.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. LL01 (Acyrthosiphon pisum)]
          Length = 312

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 91/308 (29%), Positives = 147/308 (47%), Gaps = 39/308 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD      +   +   L+K++   QV V++  V + + +I  G+++ I P    L   I
Sbjct: 19  RLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKILGGEILTIHPFSKDLLVDI 78

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
            E   LD               ++YEDS I + NKPAG+ V  GSG      ++  L  +
Sbjct: 79  PENIFLD---------------IVYEDSDILIINKPAGLVVHPGSGNKSGTILNALLYHY 123

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +SK   PR  + HRLD++TSG++V+A+   +  HL    + ++I + Y  +V G     
Sbjct: 124 KNSK-DLPRAGIVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGVVHG----- 177

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTH 253
            + IA   + K  +                 +++H+KV+  F  KF   + ++  TGRTH
Sbjct: 178 -KMIAGGTINKPIMRHYNRRTCMMVHHLGKPSVTHYKVLSRF--KFHTHIAIRLETGRTH 234

Query: 254 QLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQ-NKLY------LHARYMDLPHP-EGGR 304
           Q+RVH LH+  P+VGD  Y     + N+    + NK+Y      LHA ++ L HP +   
Sbjct: 235 QIRVHMLHIKYPLVGDPCYSGFKIQSNYRKDKKTNKIYKFPRQALHANHLSLHHPIKKNV 294

Query: 305 LQITAPLP 312
           +  T PLP
Sbjct: 295 MSWTVPLP 302


>gi|331654054|ref|ZP_08355054.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli M718]
 gi|331047436|gb|EGI19513.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli M718]
          Length = 326

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 90/339 (26%), Positives = 159/339 (46%), Gaps = 47/339 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V   
Sbjct: 9   ATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV--- 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             INA   I +E +     + L          ++YED  I V NKP  + V  G+G   +
Sbjct: 66  -AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + 
Sbjct: 111 PDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH + +       A++H+++++ F + 
Sbjct: 171 YEAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPMGKP------AVTHYRIMEHF-RV 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
           A  + L HP  G  ++  AP+P  MV+  +++   ++ +
Sbjct: 281 ATMLRLYHPISGIEMEWHAPIPQDMVELIEAMRADFEEH 319


>gi|167623481|ref|YP_001673775.1| lysozyme [Shewanella halifaxensis HAW-EB4]
 gi|167353503|gb|ABZ76116.1| Lysozyme [Shewanella halifaxensis HAW-EB4]
          Length = 222

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/205 (35%), Positives = 104/205 (50%), Gaps = 19/205 (9%)

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           NKP+G+      GIA +      + +  + +   L HRLD  TSGI+V AR + A   L 
Sbjct: 27  NKPSGL--LSNPGIAEYTHDCALTRLQQRFKDAILVHRLDCATSGIMVFARNKKAESSLK 84

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHF 230
             F+ R+ QK Y + V GI K +   I      +  I  D ++  KQ        AI+H+
Sbjct: 85  TQFQNRQTQKTYIAEVDGILKQQSGVI------ELAIAADKLNPPKQIVSASGKTAITHY 138

Query: 231 KVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
           KV+   AQK   C +E++P TGRTHQLRVH L +G  I+GD  Y  +   N       +L
Sbjct: 139 KVL---AQKPASCLVELKPVTGRTHQLRVHMLALGHTILGDDFYGEDQVINAA----KRL 191

Query: 289 YLHARYMDLPHPEGGR-LQITAPLP 312
            LHA+ +   HP  G+ +Q ++  P
Sbjct: 192 QLHAQTLSFTHPYSGKAMQFSSAHP 216


>gi|16272141|ref|NP_438344.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae Rd KW20]
 gi|260580943|ref|ZP_05848767.1| sfhB protein [Haemophilus influenzae RdAW]
 gi|1175998|sp|P44445|RLUD_HAEIN RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|1573131|gb|AAC21845.1| sfhB protein (sfhB) [Haemophilus influenzae Rd KW20]
 gi|260092432|gb|EEW76371.1| sfhB protein [Haemophilus influenzae RdAW]
          Length = 324

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 122/247 (49%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP  + V  G+G         + YH    ++  V   G    + HRLD
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVE--VPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++ +
Sbjct: 139 KDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLM 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P++G
Sbjct: 199 A---VHPMGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLG 248

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           D  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+  
Sbjct: 249 DQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 309 NALKADY 315


>gi|323128176|gb|ADX25473.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus dysgalactiae subsp. equisimilis ATCC
           12394]
          Length = 303

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 64/199 (32%), Positives = 94/199 (47%), Gaps = 13/199 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  + + NKP G+   G       +   + ++    G+   + HRLD ETSG++V A
Sbjct: 92  LYEDDHLIIVNKPEGMKTHGNEPTELALLNHVSAYT---GRTCYVVHRLDMETSGVIVFA 148

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +T      L      R I + YW+LV G   +K+      + +  H     V  VKQ +K
Sbjct: 149 KTPFILPILNRLLEKREISRDYWTLVHGTLSSKEVSYREPIGRHRHDRRKRVVDVKQGQK 208

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               A++  K++  F Q    +  +  TGRTHQ+RVH  H G  ++GD  Y    KG   
Sbjct: 209 ----AVTDVKLLKSFKQNVSLINCRLQTGRTHQIRVHLSHHGHALLGDPLYS---KGKAE 261

Query: 282 SPIQNKLYLHARYMDLPHP 300
            P   +L LHA  + L HP
Sbjct: 262 CP---RLMLHAHQLRLRHP 277


>gi|297171550|gb|ADI22548.1| pseudouridylate synthases, 23S RNA-specific [uncultured
           Oceanospirillales bacterium HF0500_09M11]
          Length = 519

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 78/316 (24%), Positives = 144/316 (45%), Gaps = 39/316 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+     +RLD+     +   +   LQ  ++ G + VD +  +  +++  G+ + +    
Sbjct: 211 VDAQYAGIRLDQAAAELFDGFSRSRLQNWIKEGVLTVDGRAARPKDKLLGGEALTLA--- 267

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                       ++ +  +    + ++  ++Y+D  + V NKPAG+ V   +G   H DG
Sbjct: 268 ------------VELAPEIDDQPEAIELPVIYQDQDLIVINKPAGLVVHPAAG---HADG 312

Query: 132 FLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L + +    D     PR  + HRLD++T+G++VVAR+  A   L    + + + + Y +
Sbjct: 313 TLLNGLLHLDDRLSSLPRAGIVHRLDRDTTGLMVVARSVEAHTGLVAQLQDKSLYREYQA 372

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G+        A   + +  +      VV     G   A++H++V+D + +    +++
Sbjct: 373 IAMGVMTGGGTVDAP--MGRHPVDRKRQAVVTH---GGKPAVTHYRVLDRY-RAHTRVQV 426

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHARYMDL 297
           +  TGRTHQ+RVH  H   P+VGD  Y    K     T  ++  L       LHA  + L
Sbjct: 427 RLETGRTHQIRVHLAHRRYPLVGDPLYGGRLKQPAGATEALREALRGFRRQALHAFKLGL 486

Query: 298 PHPEGGR-LQITAPLP 312
            HP  G  ++  APLP
Sbjct: 487 VHPASGEYMEFEAPLP 502


>gi|298372061|ref|ZP_06982051.1| ribosomal large subunit pseudouridine synthase D [Bacteroidetes
           oral taxon 274 str. F0058]
 gi|298274965|gb|EFI16516.1| ribosomal large subunit pseudouridine synthase D [Bacteroidetes
           oral taxon 274 str. F0058]
          Length = 357

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/318 (24%), Positives = 138/318 (43%), Gaps = 42/318 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+D++  N    ++    Q     G + V+   VK + R++      +  
Sbjct: 30  IVVDKGQGLIRIDKYLTNLLGGVSRTRFQNAADFGFITVNGDTVKSSYRVKP-----LDE 84

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           ++ +L     +  I+   + L+         +++ED  I V NK   + V  G G   ++
Sbjct: 85  IVISLETPPSDYTIVPQDIPLS---------VVFEDDDIMVVNKTPDMVVHPGVG---NL 132

Query: 130 DGFLKSWV----------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           DG L + +          D    +  L HR+D++TSG+L++A+   A   L + F+ +  
Sbjct: 133 DGTLLNAIAWYLRDNPKFDVNNPRVGLVHRIDKDTSGLLLIAKNEQAKSFLGKQFQDKTT 192

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +LVWGI K     +   L +       +          A +A++H++V+  F   
Sbjct: 193 KRTYNALVWGIVKEDNGTVDGALARNPKDRMQFCVFDPDENPLAKHAVTHYRVLRRFKYT 252

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------------FKGNFTSPIQN 286
              LE    TGRTHQ+RVH  H+G  +  D +Y  N             F GN    +  
Sbjct: 253 -TLLECNLETGRTHQIRVHMKHIGHTLFNDERYGGNEILFGERTAKYKQFVGNCFE-VCP 310

Query: 287 KLYLHARYMDLPHPEGGR 304
           +  LHA+ +   HP  G 
Sbjct: 311 RQALHAKTLGFVHPTTGE 328


>gi|222152892|ref|YP_002562069.1| RNA pseudouridylate synthase [Streptococcus uberis 0140J]
 gi|222113705|emb|CAR41656.1| putative RNA pseudouridylate synthase [Streptococcus uberis 0140J]
          Length = 296

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 85/315 (26%), Positives = 150/315 (47%), Gaps = 51/315 (16%)

Query: 37  LQKILRSGQVRVDK--------KRVKFNNRIQSGQV-VRIPPVI--------NALNHIIK 79
           ++ I+++G  R+DK         R + N+ I+ G V V   PV         + +++ + 
Sbjct: 1   MELIIKTGGARLDKALADLTDLSRSQANDEIKKGTVLVNGEPVKAKYTVKEGDIISYQLP 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHID 130
           E++ILD        ++ +   ++YED  + + NK  G+ V   +G         + YHI 
Sbjct: 61  EEEILDYE------AEDIPIEIVYEDEYLAIINKAQGMVVHPSAGHSSGTLVNALLYHIK 114

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
               S ++    +P + HR+D++TSG+L++A+   A   L +  + ++  + Y ++V G 
Sbjct: 115 DL--STINGV-VRPGIVHRIDKDTSGLLMIAKNDKAHHILADELKAKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
             N +  I      ++ IG       KQ    KG + AI+ F+V++ F   F  +E+   
Sbjct: 172 LPNDRGMI------EAPIGRSEKDRKKQAVTAKGKD-AITRFQVVERFGD-FTLVELSLE 223

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QI 307
           TGRTHQ+RVH  ++G P+ GD  Y     G   +   N  +LHA+ +   HP  G +   
Sbjct: 224 TGRTHQIRVHMAYIGHPVAGDPLY-----GPRKTLAGNGQFLHAQTLGFTHPSTGEMVTF 278

Query: 308 TAPLPAHMVKTWDSL 322
           TA  P    +T + L
Sbjct: 279 TAEPPIIFRQTLEKL 293


>gi|326562457|gb|EGE12775.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis 46P47B1]
          Length = 242

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 119/229 (51%), Gaps = 23/229 (10%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +F KSI +YED  I+V +KPAG+    G  +       L+S +       RL HRLD +T
Sbjct: 25  EFTKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPNIRLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDY 212
           SG+++ A++  A  H+++ F  R  QK Y ++V+G  +  +KK  +   +  +      +
Sbjct: 81  SGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVPVRYEPTTKPRH 140

Query: 213 VHVVKQNEKGANYAISHFKVI--------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +  +  N++    A++H++V+        +  A     + ++P TGR+HQLRVH +H+G 
Sbjct: 141 IVDMDWNKR----ALTHYEVMHHELRCDDNGRAYPVTRVALKPITGRSHQLRVHMVHLGH 196

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            ++GD  Y  +     +    N+L LHA  + L HP  G  +   +P+P
Sbjct: 197 VMIGDPIYAEDVALKLS----NRLNLHAHKLRLKHPTHGIWMDWVSPVP 241


>gi|283780483|ref|YP_003371238.1| pseudouridine synthase [Pirellula staleyi DSM 6068]
 gi|283438936|gb|ADB17378.1| pseudouridine synthase [Pirellula staleyi DSM 6068]
          Length = 230

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/232 (29%), Positives = 115/232 (49%), Gaps = 20/232 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ + V NK   ++ QG +     +   ++ ++  K +KP      +  RLD  TS
Sbjct: 9   ILHEDNHLLVINKRPLLATQGVAEGTPSLVTEVQQYLKVKYKKPGNVYVGVVSRLDAHTS 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V+ART  AA  L E FR + ++K YW+ V   P+     + +W++K        + +
Sbjct: 69  GVVVLARTSKAASRLAEQFREQGVEKTYWAAVEAAPEPASGELVSWVVKDDK--NRRMTI 126

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCA 274
             +   G   A+  ++ ++   +    + ++  TGR HQ+R+  A  +  P++GD KY +
Sbjct: 127 ADRKLAGCQKAVLTYETLEQ-NKSAALVSVKLETGRKHQIRLQLADELSLPVIGDRKYGS 185

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
             +          + LHAR +   HP GG RL   APLPA    TW  L FK
Sbjct: 186 RIE------FPEGIALHARELAFDHPVGGKRLSFVAPLPA----TWKGLKFK 227


>gi|323341916|ref|ZP_08082149.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322464341|gb|EFY09534.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 298

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/227 (30%), Positives = 112/227 (49%), Gaps = 35/227 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + V NKP G+ V  G+G+          Y+++     ++     +P L HR+D
Sbjct: 79  VVYEDEYLLVVNKPRGLVVHPGNGVKSDTLLHGLLYYLNSNCDHYI-----RPGLVHRID 133

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG+LV+A+     Q L E    + + + Y++LV G+           +L  + IG D
Sbjct: 134 RNTSGLLVIAKDDKTHQFLAEQLLDKTMNRTYYALVHGVLPQAH------VLIDAPIGPD 187

Query: 212 Y--VHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPI 266
                ++  N+  +  A +HF+ I+ +       C LE    TGRTHQ+RVHALH   P+
Sbjct: 188 KSNTKIMTVNQARSKPARTHFEKIETYINSSLICCKLE----TGRTHQIRVHALHANIPL 243

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
            GD +Y     G+ +   +   YL A  ++  HP+  +L Q   PLP
Sbjct: 244 HGDPQY-----GHPSDTDKTGQYLCAARLEFVHPKYLKLMQFEIPLP 285


>gi|54307622|ref|YP_128642.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium profundum SS9]
 gi|46912045|emb|CAG18840.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium profundum SS9]
          Length = 239

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 65/203 (32%), Positives = 105/203 (51%), Gaps = 17/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L  D  I + NKP+G+    G    ++   + +   D    +  + HRLD  TSG++++
Sbjct: 19  ILQHDEDIIMLNKPSGLLSNPGRNPEHYDSVYSRVLRDYP--EAHIVHRLDMSTSGLIML 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A  + A +HL   FR R  QK+Y++ +WG P      +   L+       D+ +  KQ  
Sbjct: 77  AVNKDAERHLHAQFRERATQKVYYARIWGHPDQDTGTVDLPLI------CDWPNRPKQKV 130

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E G   +++H++V+   AQ    + + P TGR+HQLRVH   +G PI+GD  Y AN +
Sbjct: 131 CYEDGKP-SVTHYEVVAREAQT-TLVRLHPITGRSHQLRVHMQALGHPIIGDEFY-ANDE 187

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
            N    I ++L+LHA  +   HP
Sbjct: 188 ANA---IADRLHLHAAEIAFTHP 207


>gi|300727932|ref|ZP_07061310.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bryantii B14]
 gi|299774774|gb|EFI71388.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bryantii B14]
          Length = 298

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 104/218 (47%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGIL 158
           ++YED  + V  K AGI        + +    L  + +   Q  +  + HRLD++TSG++
Sbjct: 87  IVYEDQYLVVIEKNAGILSMAAGHSSLNCKTVLDQYFNETRQHCQAHVVHRLDRDTSGLM 146

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A+ +     L E +      + Y ++V G  +  +  +ANWL         Y+     
Sbjct: 147 IYAKDKKTELSLEEDWHNTVYDRRYVAVVSGEMREDEGTVANWLKDNR----AYITFSSP 202

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            + G  YA++HF+V+D        +E +  TGR +Q+RVH   MG P+ GD KY     G
Sbjct: 203 VDNGGKYAVTHFRVLD-RTPNHSLVEFKLETGRKNQIRVHTADMGHPVCGDIKY-----G 256

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           N  +P+  +L LHA  +   HP    RL+   P+P + 
Sbjct: 257 NGDNPL-GRLCLHAYVLCFVHPVTHKRLEFETPIPGNF 293


>gi|293391529|ref|ZP_06635863.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952063|gb|EFE02182.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 219

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/215 (32%), Positives = 112/215 (52%), Gaps = 17/215 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+Y D  I V NKP+G+    G+   Y+      S V  K       HRLD  TSGIL+ 
Sbjct: 16  LVYRDDYIAVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPAHRLDMATSGILLF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A +++A + L   FR R  +K Y +LVWG  + ++  +   L+       D+ +  +Q  
Sbjct: 74  ALSKSADRELKRQFREREPKKYYQALVWGHLEQEQGVVELPLI------CDWENRPRQKI 127

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+G   A++ ++V+         +++ P TGR+HQLR+H L +G PI+GD K+ A+ +
Sbjct: 128 CFERGKR-AVTFYEVLQRHPNNTTRIKLTPITGRSHQLRLHMLALGHPILGD-KFYAHPQ 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
               SP   +L LHA  + + HP  G  ++ T P+
Sbjct: 186 AKALSP---RLCLHAESLQIRHPITGETMEFTTPV 217


>gi|89075565|ref|ZP_01161970.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium sp. SKA34]
 gi|89048705|gb|EAR54277.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium sp. SKA34]
          Length = 233

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/201 (34%), Positives = 101/201 (50%), Gaps = 15/201 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ DS I   NKPAGI    G    +H   F +  V  K  K ++ HRLD  TSG++V+A
Sbjct: 20  LFLDSDIIAVNKPAGILSNPGRAPEHHDSIFAR--VLEKYPKSQIVHRLDMGTSGLIVLA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE- 220
             + A  HL   FR R  QK+Y++ VWG  K     +   L+       D+ +  +Q   
Sbjct: 78  LNKKAECHLKAQFRERETQKVYYARVWGHIKQNTGTVDLPLI------CDWPNRPRQKVC 131

Query: 221 -KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 +++H++V+    +K   + + P TGR+HQLRVH   +G  I+GD K+ AN    
Sbjct: 132 FDDGKPSVTHYEVLS-RDEKSTLVRLLPVTGRSHQLRVHMQALGHSILGD-KFYANEDAM 189

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
             SP   +L LHA  +   HP
Sbjct: 190 AASP---RLQLHAAELTFTHP 207


>gi|160899764|ref|YP_001565346.1| pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160365348|gb|ABX36961.1| pseudouridine synthase [Delftia acidovorans SPH-1]
          Length = 245

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/212 (32%), Positives = 109/212 (51%), Gaps = 20/212 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYH--IDG-FLKSWVDSKGQKPRLTHRLDQETSGIL 158
           LYED+++ V +KP+G+    G G      + G  L+ W D+      + HRLDQ TSG++
Sbjct: 35  LYEDAELLVLDKPSGLLCVPGRGPDKQDCLSGRALQRWPDAL-----VVHRLDQATSGLV 89

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY----VH 214
           V+AR+ A+ + L+E+F  RR+ K+Y ++V G P  ++     W      I  D+    + 
Sbjct: 90  VMARSLASQRLLSEAFAQRRVHKLYVAVVAGRPAAQQA--DAWQSIDLPIAADWERRPLR 147

Query: 215 VVK--QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++   Q +       +     +        +++QP TGRTHQLRVH   +G  I+GD  Y
Sbjct: 148 IIDALQGKPSQTLWRAMPAATEGHDTPTTRVQLQPVTGRTHQLRVHMAALGHAILGDALY 207

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            A+      SP   +L LHA  ++L HP  G+
Sbjct: 208 -ADAAVQALSP---RLLLHAHQLELAHPLSGQ 235


>gi|312898193|ref|ZP_07757584.1| pseudouridine synthase, RluA family [Megasphaera micronuciformis
           F0359]
 gi|310620690|gb|EFQ04259.1| pseudouridine synthase, RluA family [Megasphaera micronuciformis
           F0359]
          Length = 306

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 83/299 (27%), Positives = 145/299 (48%), Gaps = 36/299 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV + +  +R+D +       I+      ++++G+V +  + +K N R+  G        
Sbjct: 7   VVTDKDTGIRVDIYVARAL-DISRSYAGNLIKNGKVSMRNRILKANYRVAEG-------- 57

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
               + I+ E+   D + +LT  ++ +   ++YED  I + NK  G+ V   +G      
Sbjct: 58  ----DEIVIEK---DEAEDLTVEAENIPLDIVYEDKDIIIVNKARGMVVHPAAGNPNGTL 110

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + +H  G L     +   +P + HRLD++TSG++V A+T AA + L E  +    ++
Sbjct: 111 VNALLWHCGGELSGI--NGVIRPGIVHRLDKDTSGLMVAAKTDAAHKSLAEQIKSHTARR 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G     K  I   L +      D V +   N K    AI+HF V++ F   + 
Sbjct: 169 TYVALVHGNIVEAKGRIDAPLGRHPK---DRVKMA-VNMKDGKDAITHFTVLERFGN-YT 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++ +  TGRTHQ+RVH  ++G P+V D  Y   +K +   PI+ +  LH+  +DL HP
Sbjct: 224 LVQCRLETGRTHQIRVHMAYIGHPVVNDPLY--GYKRD-AFPIEGQA-LHSCALDLVHP 278


>gi|225856592|ref|YP_002738103.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae P1031]
 gi|225724891|gb|ACO20743.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae P1031]
          Length = 295

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 78/306 (25%), Positives = 143/306 (46%), Gaps = 41/306 (13%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   V   +
Sbjct: 5   IETGGLRLDKALSDLTELSRSLANEQIKSGQVL-VNGQVKKAKYTVQEGDVVTYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   L    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIE 180

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + +          + K        A++ F V++ F   +  +E+Q  TGRTHQ+RVH 
Sbjct: 181 APIGRSEKDRKKQAVIAK-----GKPAVTRFHVLERFGD-YSLVELQLETGRTHQIRVHM 234

Query: 260 LHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
            ++  P+ GD  Y      KG+         +LHA+ +   HP  G+ L+  A +P    
Sbjct: 235 AYIDHPVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGKTLEFKADIPEIFK 287

Query: 317 KTWDSL 322
           +T + L
Sbjct: 288 ETLERL 293


>gi|269140174|ref|YP_003296875.1| 23S rRNA pseudouridine synthase D [Edwardsiella tarda EIB202]
 gi|267985835|gb|ACY85664.1| 23S rRNA pseudouridine synthase D [Edwardsiella tarda EIB202]
 gi|304560007|gb|ADM42671.1| Ribosomal large subunit pseudouridine synthase D [Edwardsiella
           tarda FL6-60]
          Length = 280

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 117/233 (50%), Gaps = 31/233 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 40  IVYEDEDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPQIADVPRAGIVHRLDKDT 96

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G        +E IA    K++H+   
Sbjct: 97  TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGTMTAGGTVREPIARHPTKRTHMS-- 154

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 155 -VHPMGKP------AVTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMAHINHPLVGDPL 206

Query: 272 YCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           Y    +    +  +        ++  LHA  + L HP  G  ++  AP+P  M
Sbjct: 207 YGGRPRPPRDASPEFIRVLREFDRQALHATMLRLYHPISGIEMEWHAPIPEDM 259


>gi|117921609|ref|YP_870801.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           ANA-3]
 gi|117613941|gb|ABK49395.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           ANA-3]
          Length = 323

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 90/324 (27%), Positives = 147/324 (45%), Gaps = 47/324 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +  +RLD+     +P  +   +++ + S  V VD   V K   ++   Q + I   
Sbjct: 11  ISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVYVDGVIVNKPREKVFELQRIEINAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +    H   +   LD               ++YED  I V NK AG+ V  G+G A   D
Sbjct: 71  LEEEVHAAAQAIELD---------------IVYEDDDILVINKQAGLVVHPGAGNA---D 112

Query: 131 GFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + +     +    PR  + HRLD++T+G++VVA+T  A  HL  + + R I + Y 
Sbjct: 113 GTLMNALLHHCPNIEHVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++V G         E I     K++H+    VH           A++H++V + F +   
Sbjct: 173 AIVLGTMTAGGTVDEPIGRHPTKRTHMA---VH------HSGKPAVTHYRVAEKF-RNHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHAR 293
            L ++  +GRTHQ+RVH  ++G  +VGD  Y    K        F   ++N  +  LHA 
Sbjct: 223 RLRLRLESGRTHQIRVHMAYIGHVLVGDPVYGGRPKPPKAASPEFFEILKNFKRQALHAV 282

Query: 294 YMDLPHPEGGRLQI-TAPLPAHMV 316
            ++L HP    +   TAP+P  MV
Sbjct: 283 RLELAHPVTCEIMSWTAPIPEDMV 306


>gi|256370634|ref|YP_003108459.1| putative RNA pseudouridine synthase fragment [Candidatus Sulcia
           muelleri SMDSEM]
 gi|256009426|gb|ACU52786.1| putative RNA pseudouridine synthase fragment [Candidatus Sulcia
           muelleri SMDSEM]
          Length = 246

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 69/222 (31%), Positives = 112/222 (50%), Gaps = 30/222 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           LLYED  I + NK +G+ V  G+G     ++  +  + K+        P L HR+D+ TS
Sbjct: 5   LLYEDEYILIINKKSGLVVHPGNGNKSMTLSNGLHFYFKNKKIMNDNYPFLGHRIDKGTS 64

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGD 211
           G+++V+++      +++ F   +I++ Y +LVWGI   K+      I   L  K+H+   
Sbjct: 65  GLILVSKSEKILNKISKQFWFNKIKRKYITLVWGIFFKKEGTIICNIGRCLKNKTHMN-- 122

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V  N      AI+H+KV++ F + F  L+    TGRTHQ+RVH  ++G PI  D  
Sbjct: 123 ----VFPNGCLGKQAITHYKVLETF-KYFSLLKCSLETGRTHQIRVHLKYIGHPIFNDKN 177

Query: 272 YCANFK-GNFTSPIQNKLY------------LHARYMDLPHP 300
           Y  + K  NF S  + +++            LHA Y++  HP
Sbjct: 178 YGEDKKYKNFLS-FKERIFLEKCFKTLKSQALHAYYLEFKHP 218


>gi|251782204|ref|YP_002996506.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|242390833|dbj|BAH81292.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
          Length = 297

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 87/316 (27%), Positives = 143/316 (45%), Gaps = 46/316 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V++           + 
Sbjct: 11  RLDKALADLSP-LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVIQF----ELPKEEVL 65

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHID 130
           E +  D  +N+           +YED  + + NKP G+ V   +G         + YHI 
Sbjct: 66  EYQAQDIPLNI-----------IYEDEALAIINKPQGMVVHPSAGHPSGTMVNALMYHI- 113

Query: 131 GFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              K      G  +P + HR+D++TSG+L+VA+T  A Q L    + ++  + Y ++V G
Sbjct: 114 ---KDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDEAHQALAAELKAKKSLRKYLAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
              N +  I      ++ IG       KQ    KG   A++ F V++ F   +  +E+Q 
Sbjct: 171 NLPNDRGMI------EAPIGRSEKDRKKQAVTAKGKE-AVTRFTVLERFGD-YSLVELQL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGRTHQ+RVH  ++G P+ GD  Y     G   +   +  +LHA  + L HP  G  + 
Sbjct: 223 ETGRTHQIRVHMAYIGHPVAGDPLY-----GPRKTLSGHGQFLHAETLGLTHPLTGEDML 277

Query: 307 ITAPLPAHMVKTWDSL 322
            T   PA   KT   L
Sbjct: 278 FTVAPPAIFQKTLQQL 293


>gi|317055012|ref|YP_004103479.1| RluA family pseudouridine synthase [Ruminococcus albus 7]
 gi|315447281|gb|ADU20845.1| pseudouridine synthase, RluA family [Ruminococcus albus 7]
          Length = 321

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 76/282 (26%), Positives = 140/282 (49%), Gaps = 28/282 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++ + +ND    R+D++     P +    + K +R  +++++ KR + + ++  G  V++
Sbjct: 3   EFSINKNDA-GQRMDKFLTKAVPALPKNLMYKYIRLKRIKLNGKRCEISTKLSEGDSVQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIA 126
                 +N     +K  ++   L    D     ++YED  I + +KP G+ V +  SG A
Sbjct: 62  -----YINDEFFPEKRDEAHRFLNSPKDIE---IVYEDENIILCDKPCGLVVHEDESGEA 113

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   +  ++  KG+          P L +R+D+ TSGI++ A+   + + L +  + R
Sbjct: 114 DTLIDRVLHYLYDKGEYDPDTENSFTPALCNRIDRNTSGIVICAKNAESLRVLNQKVKDR 173

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK---GANYAISHFKVID 234
            ++K+Y  +  GIP NKK    +  LK  H   +   VV+  +K   G+   I+ +KV+ 
Sbjct: 174 ELEKLYLCVTVGIP-NKK----SAELKAFHRRDEKTKVVRVEDKSFPGSKTMITRYKVLA 228

Query: 235 CFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              Q     LE+   TGRTHQ+R H  H+G P++GD KY +N
Sbjct: 229 ENKQSGLALLEVDLVTGRTHQIRAHLAHIGYPLLGDGKYGSN 270


>gi|29349120|ref|NP_812623.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|253571283|ref|ZP_04848690.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           1_1_6]
 gi|298386817|ref|ZP_06996372.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           1_1_14]
 gi|29341027|gb|AAO78817.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|251839236|gb|EES67320.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           1_1_6]
 gi|298260491|gb|EFI03360.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           1_1_14]
          Length = 357

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 83/331 (25%), Positives = 151/331 (45%), Gaps = 43/331 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E +I+  ++ L          ++YED  + V NKPAG+ V  G G     
Sbjct: 90  ---MMDRPRYENEIIPENIPLN---------IVYEDPYVMVVNKPAGLVVHPGHGNYHGT 137

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A+H+    +   D+      L HR+D++TSG+LV+A+T  A  +L   F  +  +
Sbjct: 138 LVNALAWHMKDIPE--YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTK 195

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFAQK 239
           + Y +LVWG  +  +  I   + +      D + + V  +     +A++H++V++     
Sbjct: 196 RRYRALVWGNVEQDEGTIVGSIARNPK---DRMQMAVMSDPSMGKHAVTHYRVLERLGY- 251

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------K 287
              +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +
Sbjct: 252 VTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPR 311

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
             LHA  +   HP  G  +  T+ LP  M +
Sbjct: 312 QALHAMTLGFVHPVTGEEMYFTSELPDDMTR 342


>gi|260063065|ref|YP_003196145.1| ribosomal large subunit pseudouridine synthase D [Robiginitalea
           biformata HTCC2501]
 gi|88784634|gb|EAR15804.1| ribosomal large subunit pseudouridine synthase D [Robiginitalea
           biformata HTCC2501]
          Length = 236

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 69/230 (30%), Positives = 109/230 (47%), Gaps = 16/230 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
           ++LYED+ +   +K AG  VQG       +   +K ++  K QKP      + HRLD+ T
Sbjct: 12  MVLYEDNHLIAVSKRAGDIVQGDKTGDTPLPETVKDYIAHKYQKPGKVFLGVVHRLDRPT 71

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++V ART  A   +   F     +K YW+LV   P      + +WL +       Y  
Sbjct: 72  TGVIVFARTSKALSRMNRLFAEGGTRKTYWALVGTPPPETAGRLVHWLERNQKQNKSYAR 131

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              +   G+  AI +++++     ++  LE+   TGR HQ+R     +G PI GD KY  
Sbjct: 132 A--KEVPGSKQAILNYRLLGSL-DRYHLLEIDLETGRHHQIRAQLAAIGSPIKGDLKY-- 186

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
              G   S     ++LHAR ++  HP     + I APLP   +  W++ G
Sbjct: 187 ---GFPRSNPDGGIHLHARRLEFIHPVRQDPVSILAPLPDDPL--WEACG 231


>gi|324999316|ref|ZP_08120428.1| ribosomal large subunit pseudouridine synthase [Pseudonocardia sp.
           P1]
          Length = 310

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 81/327 (24%), Positives = 149/327 (45%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++ + V +  + MR+D         ++   +  +   G+++VD +    ++R+  G 
Sbjct: 1   MGELRSMPVPDGLDGMRIDAGLSRLL-GLSRTVVAGLAEEGRIQVDGRDAGKSDRLPGGS 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +     A   +I+    + + +++           L++D  I V +KP G++     
Sbjct: 60  WLEVELPDAAAPAVIEGPAEVVAGLSV-----------LHDDEDIVVVDKPVGVAAHPSP 108

Query: 124 G-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +    + + G   R  + HRLD  T+G++VVA +  A   L  +F+ R
Sbjct: 109 GWTGPTVTGGLAALGYRLSTSGAAERQGIVHRLDVGTTGVMVVATSEHAYTALKRAFKER 168

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y ++V G P      I   + +  H   DY   V Q   G   +I+H+  I+ F 
Sbjct: 169 TVEKRYHAVVQGHPDPSSGTIDAPIDR--HPRHDYRFAVLQ---GGKPSITHYDTIEAF- 222

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMD 296
           +    L++   TGRTHQ+RVH   +  P VGD  Y A+        +  ++ +LHAR + 
Sbjct: 223 RSASLLDVHLETGRTHQIRVHFSALRHPCVGDLTYGADP--TLAKRVGLSRQWLHARTLG 280

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  GR ++ T+P P  +     +L
Sbjct: 281 FEHPADGRYVEFTSPYPDDLASALAAL 307


>gi|325279229|ref|YP_004251771.1| pseudouridine synthase [Odoribacter splanchnicus DSM 20712]
 gi|324311038|gb|ADY31591.1| pseudouridine synthase [Odoribacter splanchnicus DSM 20712]
          Length = 230

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 107/220 (48%), Gaps = 16/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I   NK     VQ        +   +K+++  K  KP      + HR+D+  S
Sbjct: 4   VLYEDNHIIAVNKKISDIVQADKTGDTPLSEEVKAYIKKKYNKPGEVYLGVPHRVDRPVS 63

Query: 156 GILVVARTRAAAQHLTESFRM--RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           G+++ ART  A   L + F+   + I KIYW++V  +P      + ++L++      +  
Sbjct: 64  GVVIFARTSKALTRLNKMFQEHEKEISKIYWAIVGNLPAEDHAVLTHYLMRDPE--KNKS 121

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H   Q + GA  A   +K++   +Q++  LE++ +TGR HQ+R     +GCPI GD KY 
Sbjct: 122 HAYNQPKAGAKEATLEYKLLGS-SQRYYLLEVKLYTGRHHQIRCQLAKIGCPIKGDLKY- 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
               G   S     + LHAR +   HP    +  ITA  P
Sbjct: 180 ----GFPRSNEGGGISLHARSITFKHPVSREMITITAKPP 215


>gi|217077318|ref|YP_002335036.1| ribosomal large subunit pseudouridine synthase D [Thermosipho
           africanus TCF52B]
 gi|217037173|gb|ACJ75695.1| ribosomal large subunit pseudouridine synthase D [Thermosipho
           africanus TCF52B]
          Length = 245

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 119/249 (47%), Gaps = 40/249 (16%)

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI------SVQGGS---GIAYHI 129
           KE +IL  ++ L          +LYED  I V NK AG+      S   G+    + YH 
Sbjct: 8   KEVEILPENIPLD---------ILYEDKDIVVVNKSAGMITHPTPSFTSGTLVNALMYHC 58

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             F      S   +P + HRLD++TSG++VVA+   A Q L++ F+ R  +K+Y ++V G
Sbjct: 59  KDFQGI---SGELRPGIVHRLDKDTSGVIVVAKNDKAHQSLSKQFKDRVTEKVYAAIVKG 115

Query: 190 IPKNKKECIA-----NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           I K     I      N +++      D+         G N A+++FKV+  F +    + 
Sbjct: 116 IVKKDYGTIEVPVGRNPVVRTKMAAVDW---------GKN-ALTYFKVLRRF-KDATLVF 164

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
             P TGRTHQ+R+H  ++G P++GD  Y +  K         +  LHA  +   HP    
Sbjct: 165 AYPKTGRTHQIRIHMKYIGHPLLGDELYGSGKKDEIYG--ATRQMLHALRLSFYHPTTEE 222

Query: 304 RLQITAPLP 312
           ++   APLP
Sbjct: 223 KMTFVAPLP 231


>gi|238854437|ref|ZP_04644777.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 269-3]
 gi|260664477|ref|ZP_05865329.1| pseudouridylate synthase [Lactobacillus jensenii SJ-7A-US]
 gi|282932582|ref|ZP_06338003.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 208-1]
 gi|313472076|ref|ZP_07812568.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 1153]
 gi|238832930|gb|EEQ25227.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 269-3]
 gi|239530107|gb|EEQ69108.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 1153]
 gi|260561542|gb|EEX27514.1| pseudouridylate synthase [Lactobacillus jensenii SJ-7A-US]
 gi|281303278|gb|EFA95459.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 208-1]
          Length = 301

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 78/307 (25%), Positives = 143/307 (46%), Gaps = 50/307 (16%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++   H   ++   +Q++L SG + V+ K+ K + ++  G  + +        H+ K
Sbjct: 14  RLDKYISEHS-DLSRSRVQELLTSGDILVNSKQEKPSYKVAIGDKISV--------HVPK 64

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL---- 133
                   V L    + +   ++YED+ + V NKP G+ V   +G   H  ++  +    
Sbjct: 65  -------LVPLNVEPEDIPLDIVYEDNDVIVVNKPQGMVVHPSAGHPNHTLVNALMNHTK 117

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +     +G +P + HR+D++TSG+L++A+   A + L      +  +++Y ++V G   N
Sbjct: 118 ELAASPEGFRPGIVHRIDKDTSGLLMIAKNTQARESLESQLAHKTNKRVYLAIVHG---N 174

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVIDCFAQKFCWLEMQPH 248
            KE           I        K+ +K A       A++HFKV++ +   +  +  Q  
Sbjct: 175 FKEASGT-------IDAPIARNPKERKKMAVVESGKAAVTHFKVLEQYPN-YALVSCQLE 226

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-- 304
           TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +    P+ G+  
Sbjct: 227 TGRTHQIRVHMKYIGHPLAGDPLYGPKKTLKGHGQ-------FLHAKILGFKQPKTGQWL 279

Query: 305 -LQITAP 310
             Q+  P
Sbjct: 280 EFQVEPP 286


>gi|254441292|ref|ZP_05054785.1| pseudouridine synthase, RluA family [Octadecabacter antarcticus
           307]
 gi|198251370|gb|EDY75685.1| pseudouridine synthase, RluA family [Octadecabacter antarcticus
           307]
          Length = 344

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 90/359 (25%), Positives = 149/359 (41%), Gaps = 62/359 (17%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRIQ 60
           T V + + EN     R+D+    + P    ++   L ++L  G V+V+   V     +  
Sbjct: 4   TTVLFTLAENPPA--RMDKALALNVPLDASLSRSRLMRLLADGAVQVNGAVVTDPRAKPV 61

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  V I   I    H++ E   LD               +++ED  + V NKP G+ V 
Sbjct: 62  EGDAVEILVEIADDYHVLPEDIPLD---------------VVFEDDDLIVINKPTGMVVH 106

Query: 121 GGSGI--AYHIDGFLKSWVDS----KGQK-PRLTHRLDQETSGILVVARTRAAAQHLTES 173
              G      ++  L    D+     G+K P + HR+D+ETSG+LVVA+T  A   L   
Sbjct: 107 PAPGTPGGTLVNALLHHCGDALSGVGGEKRPGIVHRIDKETSGLLVVAKTDRAHHGLAAQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK------------ 221
           F    +++ Y ++ +G+P +    +   +   S   G+ + +  Q  +            
Sbjct: 167 FEAHTVERHYRAICYGVPDSNDPRV-RGIKGASFDPGNILKLQTQLARHKHDRQKQAVVW 225

Query: 222 -GANYAISHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               +A++  +++             CWLE    TGRTHQ+RVH  H G  ++GD  Y  
Sbjct: 226 HNGRHAVTRARIVQPLGNPAVAAVMDCWLE----TGRTHQIRVHMTHAGHGLIGDPTYGG 281

Query: 275 NFK---------GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             K         G   +    +  LHA  +   HP     L+  AP+PA M++   +LG
Sbjct: 282 RRKLSEKAVGEAGRIAAYTFPRQALHAATLGFQHPVSKEMLRFEAPMPADMIRLIAALG 340


>gi|167761861|ref|ZP_02433988.1| hypothetical protein BACSTE_00204 [Bacteroides stercoris ATCC
           43183]
 gi|167700231|gb|EDS16810.1| hypothetical protein BACSTE_00204 [Bacteroides stercoris ATCC
           43183]
          Length = 517

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/218 (33%), Positives = 106/218 (48%), Gaps = 31/218 (14%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  + V NKPAG +SV G   +        + + D+ G  P + HRLD  TSG+LV
Sbjct: 316 IIYEDEWLAVVNKPAGMLSVPGKEDVVSVYSMMRERYPDADG--PLIVHRLDMATSGLLV 373

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-----ANWLLKKSHIGGDYVH 214
           VA+T+   Q+L   F+ R I K Y +L+ G        +      N L +   +    VH
Sbjct: 374 VAKTKQVHQNLQAQFKNRSIGKRYIALLQGSVSQDAGTVELPLCPNPLDRPRQM----VH 429

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHK 271
                      A++ F+V++    +   +   P TGRTHQLRVHA H   + CPI+GD  
Sbjct: 430 T-----GYGKPAVTDFEVLERKDNR-TRIAFYPRTGRTHQLRVHAAHPLGLHCPIIGDEL 483

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
           Y    +         +LYLHA  ++  HP  G R+ IT
Sbjct: 484 YGRKAE---------RLYLHAEMLEFTHPVTGKRISIT 512


>gi|149921425|ref|ZP_01909878.1| pseudouridine synthase, RluA family protein [Plesiocystis pacifica
           SIR-1]
 gi|149817745|gb|EDM77210.1| pseudouridine synthase, RluA family protein [Plesiocystis pacifica
           SIR-1]
          Length = 311

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 137/285 (48%), Gaps = 36/285 (12%)

Query: 51  KRVKFNNR-----IQSGQV------VRIPPVINALNH-IIKEQKILDSSVNLTKHSDFLK 98
           +RVK + +     IQ+G V      VR+P V+ A    I    + LD+     K  D  +
Sbjct: 30  RRVKLDRKQAAAVIQAGGVYVNRLRVRLPQVLVAHGERITVYLEALDA-----KPLDPER 84

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKG-QKP--RLTHRLD 151
              ++      V +KPAG+ V   S +     G L   +    +S+G ++P   + HRLD
Sbjct: 85  VRFVHRGEDFVVLDKPAGVPV---SAVRETCVGSLSEALIHQLESEGLERPYVGVVHRLD 141

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q  SG+++      A + L + FR   I++ Y   V G P  +  C A  +  +S  GG 
Sbjct: 142 QGASGLVLFTIRDVANKSLHKQFRDHEIRRGYRVRVTGEPPAQLRCDAPLIKLRS--GG- 198

Query: 212 YVHVVKQNEKGANYAISHFK---VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            V V    +  +  A +HF+    +D  A     L+++  TGRTHQ+R HA H+G PIVG
Sbjct: 199 -VKVGSPGDGRSKPATTHFRHVARVDGEAGPEHLLDVEIETGRTHQIRAHAAHLGFPIVG 257

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
           D +Y A+ +G   S   ++L LHAR ++  HP  G  Q  T  LP
Sbjct: 258 DRRYGADGEGEAGSD-HSRLCLHARSLEFEHPLTGAPQSFTCELP 301


>gi|315646518|ref|ZP_07899636.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315278161|gb|EFU41481.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 244

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 62/205 (30%), Positives = 99/205 (48%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ +    KP  +  Q  +     +   LK  +  +  KP      L HRLD+   
Sbjct: 14  ILFEDNHVLGVAKPVNVPSQEDATGDPDMLTILKQDIKERFNKPGNVFLGLVHRLDRPVG 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G +V A+T  AA  L+E+ R R  +K Y ++V GIP      + + L K +    + VHV
Sbjct: 74  GAMVFAKTSKAASRLSEAVRSRSFRKQYVAVVHGIPSKPSGRLVDMLYKDAKT--NTVHV 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   GA  AI  + V+   ++ F  + ++ HTGR HQ+RV   H G P+ GD KY   
Sbjct: 132 TSEGTDGAKEAILDYTVLQT-SEGFSLVLIELHTGRPHQIRVQLNHAGHPLFGDQKY--- 187

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G+  +    ++ L +  +  PHP
Sbjct: 188 --GSKVNKAGQQIALWSVLVGFPHP 210


>gi|325289223|ref|YP_004265404.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324964624|gb|ADY55403.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 303

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 79/290 (27%), Positives = 135/290 (46%), Gaps = 45/290 (15%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           +++V+ + V  N R+Q+G  V I   ++  N+II E   LD               ++YE
Sbjct: 42  KIQVNGQLVHTNYRLQAGDFVTINIDLSEENNIIPESIPLD---------------IVYE 86

Query: 105 DSKIYVFNKPAGISVQ----GGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           D      NKPAG+S+     GG+G     + YH  G  ++ +       R  +RLD++TS
Sbjct: 87  DEDFVAVNKPAGMSIHPSRLGGTGTLANAVTYHWQGLGRNILF------RPINRLDKDTS 140

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKECIANWLLKKSHIGGDYVH 214
           G++++ +++ A Q +    +  +I + Y +LV   + ++            ++     VH
Sbjct: 141 GLVLIGKSQFAHQGIFNQLKQHKIDRRYIALVERALTRDHGHIDQPIARPDANKRRRIVH 200

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              Q       A +H++V+D +      L ++  TGRTHQ+RVH  ++G P+ GD  Y  
Sbjct: 201 PAGQ------AATTHYQVLDRYPDH-TLLSLKLETGRTHQIRVHLSYIGHPVSGDLLY-- 251

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                F SP+  +  LHA  +   HP  G+ + +  PL   M    D LG
Sbjct: 252 ----GFASPLIKRQALHADRIRFTHPRSGKEVILDIPLAQDMQTAVDYLG 297


>gi|90580377|ref|ZP_01236184.1| putative ribosomal large subunit pseudouridine synthase D [Vibrio
           angustum S14]
 gi|90438679|gb|EAS63863.1| putative ribosomal large subunit pseudouridine synthase D [Vibrio
           angustum S14]
          Length = 324

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 93/333 (27%), Positives = 155/333 (46%), Gaps = 51/333 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
            V  ++  MRLD+     YP  +   ++  + +G V V+   VK    ++  G+ + I  
Sbjct: 10  TVGENQLGMRLDQVIAQLYPDYSRSRIKDWILNGMVSVNGDVVKKPREKMMGGEELFIQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I      + +   LD               ++YED  I V NKP    V  G+G     
Sbjct: 70  EIEDEVRWVAQDIPLD---------------IVYEDDDILVINKPRDFVVHPGAGTP--- 111

Query: 130 DGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG + + +     S  + PR  + HRLD++T+G++VVA+T  A   L  + + R+I + Y
Sbjct: 112 DGTVLNALLHHCPSLAEVPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-----NEKGANYAISHFKVIDCFAQ 238
            +L  G      +      ++K  IG    H  K+     +E G + AI+H++V + F +
Sbjct: 172 EALAIG------QMTGGGTIEKP-IGR---HSTKRICMAVHEMGKD-AITHYRVAERF-R 219

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQ--NKLYL 290
           +   + ++  TGRTHQ+RVH  +M  P++GD  Y        +    F   ++  ++  L
Sbjct: 220 EHTRIVLRLETGRTHQIRVHMSYMSHPLIGDVIYGGRPRPPRDASPEFIQALRAFDRQAL 279

Query: 291 HARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           HAR + L HP  G +++  APLP  MV   D L
Sbjct: 280 HARMLRLDHPITGEKMEWHAPLPIDMVAMIDIL 312


>gi|329296582|ref|ZP_08253918.1| 23S rRNA/tRNA pseudouridine synthase A [Plautia stali symbiont]
          Length = 219

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 69/206 (33%), Positives = 109/206 (52%), Gaps = 16/206 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++V
Sbjct: 16  ILYQDEHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDFPQAESVHRLDMATSGVIV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           VA T+AA + L   FR R   K Y + VWG P  ++  I   L+       D+ +  KQ 
Sbjct: 73  VALTKAAERELKRQFREREPAKQYVARVWGHPAAEQGMIDLPLI------CDWPNRPKQM 126

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +    A + ++V+   A     ++++P TGR+HQLRVH L +G PI+GD ++ A+ +
Sbjct: 127 VSVELGKPAQTEYQVLAYDADNSARVQLKPITGRSHQLRVHLLALGHPILGD-RFYAHPE 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
               +P   +L LH   + + HP  G
Sbjct: 186 ALAMAP---RLQLHTESLTITHPAFG 208


>gi|296452795|ref|ZP_06894482.1| ribosomal large subunit pseudouridine synthase [Clostridium
           difficile NAP08]
 gi|296879953|ref|ZP_06903925.1| ribosomal large subunit pseudouridine synthase [Clostridium
           difficile NAP07]
 gi|296258343|gb|EFH05251.1| ribosomal large subunit pseudouridine synthase [Clostridium
           difficile NAP08]
 gi|296429067|gb|EFH14942.1| ribosomal large subunit pseudouridine synthase [Clostridium
           difficile NAP07]
          Length = 226

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 61/205 (29%), Positives = 104/205 (50%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  KP  I  QG +     +   LK ++  K  KP      L HRLD+   
Sbjct: 9   VIYEDNHLLVVEKPVNILSQGDNTNDKDMVNLLKDYIKKKYNKPGNVYIGLIHRLDRPVG 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  L+E  R +  +K Y ++V G  K+  + + ++L K      + V V
Sbjct: 69  GVMVFAKTSKAASRLSEQVRSKTFKKTYLAVVHGKIKSNSDILKDFLYKNKKT--NMVTV 126

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           VK+N K A  A  ++ V++ F +    +++   TGR+HQ+RV       P+ GD +Y   
Sbjct: 127 VKKNHKDAKEAELNYNVLN-FKENLSLVQVNLKTGRSHQIRVQFASRKHPLYGDQRY--- 182

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G   + I  ++ L +  +++ HP
Sbjct: 183 --GKEINKIGQQISLWSNKIEIYHP 205


>gi|221066026|ref|ZP_03542131.1| pseudouridine synthase, RluA family [Comamonas testosteroni KF-1]
 gi|220711049|gb|EED66417.1| pseudouridine synthase, RluA family [Comamonas testosteroni KF-1]
          Length = 358

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 93/336 (27%), Positives = 146/336 (43%), Gaps = 51/336 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIP 68
           + V  +    R+D+         +   LQ++L  G V ++ K  +K + ++  G  +R+ 
Sbjct: 45  LTVAAEHHGQRVDKVLALGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLRV- 103

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                      E +    S+     +  L+  ++YED  + V NKPAG+ V    G    
Sbjct: 104 -----------EMRPTQQSMAFQPEAMDLQ--VVYEDEDLLVINKPAGLVVHPAPGNWTG 150

Query: 127 YHIDGFLKSWVDSKG-QKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             ++G L    D K  Q PR  + HRLD++TSG++VVAR R+    L +    R + + Y
Sbjct: 151 TLLNGLLAR--DEKARQVPRAGIVHRLDKDTSGLMVVARNRSTMDALIKMIAAREVSRQY 208

Query: 184 WSLV---WGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDC 235
            +L    WG  + ++E  A        IG D      + VV  N      A + F ++D 
Sbjct: 209 LALAHKQWG-SRKRREVDAP-------IGRDPRNRLRMAVVDLNLHPGKQARTDFDLLDG 260

Query: 236 FAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            A      C L    HTGRTHQ+RVH   +G P++ D  Y    +G        +  LHA
Sbjct: 261 DAAHSLVRCTL----HTGRTHQIRVHMASLGHPLIADTLYGGQPEGGL-----ERQALHA 311

Query: 293 RYMDLPHPEGGRLQI-TAPLPAHMVKTWDSLGFKYD 327
             +   HP   +  +  APLP  M    D  G +Y+
Sbjct: 312 FRLAFEHPVTKKPLVHHAPLPQDMAGALDLWGLRYN 347


>gi|297269584|ref|XP_002799894.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 2 [Macaca mulatta]
          Length = 346

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 58/177 (32%), Positives = 92/177 (51%), Gaps = 22/177 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           +L++++ + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 99  ILHQNNNLVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V+A  +  A  + E FR R++ K YW++   +P      +              + +V
Sbjct: 159 VMVLAWDKDMAHQVQELFRTRQVVKKYWAITVRVPMPSAGVVD-------------IPIV 205

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
              EK A  A++ ++V+         +E+QP TG  HQLRVH +  + CPI+GDHKY
Sbjct: 206 ---EKEAQVAVTRYQVLSSTLSS-ALVELQPITGIKHQLRVHLSFGLDCPILGDHKY 258


>gi|256420955|ref|YP_003121608.1| pseudouridine synthase, RluA family [Chitinophaga pinensis DSM
           2588]
 gi|256035863|gb|ACU59407.1| pseudouridine synthase, RluA family [Chitinophaga pinensis DSM
           2588]
          Length = 356

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 85/332 (25%), Positives = 149/332 (44%), Gaps = 52/332 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++ +  +E +R+D++  N         +Q+   +G V V+ K VK N ++++   + +  
Sbjct: 27  IIADKGQEPLRVDKFLMNRVEGATRNKIQQACDNGMVIVNDKPVKSNYKVKAHDRIVVYS 86

Query: 70  VINALN-HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
             N  N  +I E+  L+               ++YED  + + NK  G+ V  G G    
Sbjct: 87  NKNPENTQVIPEELPLN---------------IIYEDEDLMIINKLPGMVVHPGCGNYTG 131

Query: 127 YHIDG---FLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             ++G   +L     +   +P      L HR+D+ TSG+LVVA++  A   L + F    
Sbjct: 132 TLVNGLAWYLGDHTTTPAPEPSIPRFGLVHRIDKNTSGLLVVAKSEKAMNDLAKQFFDHT 191

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIG-----GDYVHVVKQNEKGANYAISHFKVI 233
           +Q+ Y +LVWG  +  +  I      ++H+G        +    + E G   AI+H+KV+
Sbjct: 192 VQRRYLALVWGDFEEDEGTI------EAHVGRHQRFRKIMDAYPEGEYGKE-AITHYKVL 244

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS--------- 282
           + F      +E +  TGRTHQ+RVH  H+G  +  D  Y  +   KG   +         
Sbjct: 245 ERF-NYVTLIECRLETGRTHQIRVHMQHIGHSLFNDDTYNGDRILKGTVFAKYKQFVENC 303

Query: 283 -PIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             I  +  LHA+ +   HP   + +   +PLP
Sbjct: 304 FEIMPRHALHAQTLGFIHPRTRKPIHFESPLP 335


>gi|228473894|ref|ZP_04058636.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga gingivalis ATCC 33624]
 gi|228274735|gb|EEK13569.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga gingivalis ATCC 33624]
          Length = 235

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 108/224 (48%), Gaps = 15/224 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +   NK AG  VQG       +   +KS++  K  KP      + HRLD+ T+
Sbjct: 10  VLYEDNHLIAINKRAGDIVQGDKTGDIPLSEIVKSYLVEKYHKPGEAYLGVVHRLDRPTT 69

Query: 156 GILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           G++V A+T  A   L  +F  +  + K YW+LV       +  + ++L++ +     Y +
Sbjct: 70  GVVVFAKTSKALPRLNAAFATKEEVSKQYWALVEKKAIPHQGTLTHFLVRNTSQNKSYAY 129

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              + +  +  A+  +KV+      +  +E+   TGR HQ+R     +GCP+ GD KY A
Sbjct: 130 --PEEKPQSQKAVLTYKVLATLTH-YLLVEITLLTGRHHQIRAQFAALGCPLKGDLKYGA 186

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
                  S     + LHAR ++L HP     L I APLP    K
Sbjct: 187 K-----RSNPDGSISLHARALELLHPVRKEPLHIVAPLPESFCK 225


>gi|34497647|ref|NP_901862.1| pseudouridine synthase D [Chromobacterium violaceum ATCC 12472]
 gi|34103503|gb|AAQ59865.1| pseudouridine synthase D [Chromobacterium violaceum ATCC 12472]
          Length = 363

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 86/306 (28%), Positives = 137/306 (44%), Gaps = 37/306 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L + ++ G V+VD + V    ++  G+ + +      L    +
Sbjct: 35  RLDAALAKLLPDYSRSRLTQWVKDGLVKVDGQVVAPKTKMLGGEKLEV-----TLQLTNE 89

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           E       ++L          +++ED  I V NKPAG+ V   +G      ++G L    
Sbjct: 90  EMAFQPEPMDLP---------IVFEDEHILVINKPAGLVVHPAAGNWSGTLLNGLLHH-C 139

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    PR  + HRLD++TSG++VVA+T  A   L    + R ++++Y ++  G+     
Sbjct: 140 PALASVPRAGIVHRLDKDTSGLMVVAKTLPAQTELVRQLQARTVKRVYRAIADGVVPFDG 199

Query: 196 ECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
              AN       IG D  + +K    + G   AI+H +V++ FA     +E +  TGRTH
Sbjct: 200 TIDAN-------IGRDANNRLKMAVLKFGGKPAITHIRVLERFAS-HSHVECKLETGRTH 251

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPEGGRLQI 307
           Q+RVH    G P+ GD  Y  N +      I        +  LHA  + L HP  G  + 
Sbjct: 252 QIRVHMREAGHPLAGDPVY-GNPRHKMDEEIAAGVKALGRQALHAFALALVHPATGEERS 310

Query: 308 -TAPLP 312
             APLP
Sbjct: 311 WKAPLP 316


>gi|255657533|ref|ZP_05402942.1| putative pseudouridylate synthase [Clostridium difficile QCD-23m63]
          Length = 221

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 61/205 (29%), Positives = 104/205 (50%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  KP  I  QG +     +   LK ++  K  KP      L HRLD+   
Sbjct: 4   VIYEDNHLLVVEKPVNILSQGDNTNDKDMVNLLKDYIKKKYNKPGNVYIGLIHRLDRPVG 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  L+E  R +  +K Y ++V G  K+  + + ++L K      + V V
Sbjct: 64  GVMVFAKTSKAASRLSEQVRSKTFKKTYLAVVHGKIKSNSDILKDFLYKNKKT--NMVTV 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           VK+N K A  A  ++ V++ F +    +++   TGR+HQ+RV       P+ GD +Y   
Sbjct: 122 VKKNHKDAKEAELNYNVLN-FKENLSLVQVNLKTGRSHQIRVQFASRKHPLYGDQRY--- 177

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G   + I  ++ L +  +++ HP
Sbjct: 178 --GKEINKIGQQISLWSNKIEIYHP 200


>gi|303237284|ref|ZP_07323854.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
 gi|302482671|gb|EFL45696.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
          Length = 299

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 117/241 (48%), Gaps = 17/241 (7%)

Query: 87  SVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           SV+ +K +D  +S    LLYED  I V  K  GI        + ++   L  +     QK
Sbjct: 69  SVSTSKKNDQFQSRYVKLLYEDRYIVVIEKAQGILSMEAGHASLNVKKVLDDYFKKSKQK 128

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               + HRLD++TSG+++ A+   A Q L   +      + Y +++ GI ++    I+NW
Sbjct: 129 CTAHVVHRLDRDTSGLMIYAKDMQAEQILEHEWHNIVYDRRYVAVLSGIMEDDSGTISNW 188

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L         YV      + G  YA++HF V+   +     +E +  TGR +Q+RVHA  
Sbjct: 189 LKDNKA----YVTYSSPFDNGGKYAVTHFSVLK-RSNSHSLVEFKLDTGRKNQIRVHAAD 243

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           M  P+ GD+KY     GN   P++ +L LHA  +   HP   + ++ +  +PA   + ++
Sbjct: 244 MNHPVCGDNKY-----GNGDDPLR-RLCLHAYMLCFYHPITRQPMEFSTYIPAGFKRLFE 297

Query: 321 S 321
           S
Sbjct: 298 S 298


>gi|167032335|ref|YP_001667566.1| pseudouridine synthase [Pseudomonas putida GB-1]
 gi|166858823|gb|ABY97230.1| pseudouridine synthase [Pseudomonas putida GB-1]
          Length = 211

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/214 (33%), Positives = 111/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED+ I V NKP  + SV G +    + D  +    ++      + HRLD ETSGI++
Sbjct: 8   ILFEDAAILVINKPTLLLSVPGRA--EDNKDCLITRLQENGYPDALIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADSHRELSRQFHDRETEKSYTALCWGQPALDSGSID--LPLRYDPPTKPRHVV-DH 122

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E+G  +A++ +++++     +C +E+ P TGR+HQLRVH L +G P++GD  Y AN +  
Sbjct: 123 EQG-KHALTFWRIVE-RCGDYCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY-ANPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL+   P P
Sbjct: 180 AA---HERLCLHASMLSFTHPVSGERLKFECPAP 210


>gi|148984670|ref|ZP_01817938.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP3-BS71]
 gi|149006397|ref|ZP_01830109.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP18-BS74]
 gi|225861177|ref|YP_002742686.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298231008|ref|ZP_06964689.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae str. Canada MDR_19F]
 gi|298254573|ref|ZP_06978159.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae str. Canada MDR_19A]
 gi|298503058|ref|YP_003724998.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|147762174|gb|EDK69136.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP18-BS74]
 gi|147923061|gb|EDK74176.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP3-BS71]
 gi|225727922|gb|ACO23773.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298238653|gb|ADI69784.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|301799912|emb|CBW32491.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           OXC141]
 gi|327389210|gb|EGE87555.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA04375]
 gi|332075542|gb|EGI86010.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA17545]
 gi|332202784|gb|EGJ16853.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA41317]
          Length = 295

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 83/308 (26%), Positives = 147/308 (47%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   V   +
Sbjct: 5   IETGGLRLDKALSDLSELSRSLANEQIKSGQVL-VNGQVKKAKYTVQEGDVVTYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   L    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G  + GD  Y      KG+         +LHA+ +   HP  G+ L+  A +P  
Sbjct: 233 HMAYIGHSVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGKTLEFKADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKETLERL 293


>gi|109109212|ref|XP_001112402.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 1 [Macaca mulatta]
          Length = 377

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 59/192 (30%), Positives = 97/192 (50%), Gaps = 21/192 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           +L++++ + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 99  ILHQNNNLVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P      +   +++K   G    H  
Sbjct: 159 VMVLAWDKDMAHQVQELFRTRQVVKKYWAITVRVPMPSAGVVDIPIVEKEAQGQQQHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  ++ + A  A++ ++V+         +E+QP TG  HQLRVH + 
Sbjct: 219 TLSPSYRMDNGKMVKVRHSRNAQVAVTRYQVLSSTLSS-ALVELQPITGIKHQLRVHLSF 277

Query: 261 HMGCPIVGDHKY 272
            + CPI+GDHKY
Sbjct: 278 GLDCPILGDHKY 289


>gi|219670033|ref|YP_002460468.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
 gi|219540293|gb|ACL22032.1| pseudouridine synthase, RluA family [Desulfitobacterium hafniense
           DCB-2]
          Length = 334

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 86/309 (27%), Positives = 143/309 (46%), Gaps = 63/309 (20%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +Q ++  G V V+    K N ++++     V IPP         +E K+   ++ L    
Sbjct: 60  IQGLIEEGHVLVNGAARKANYKVRAMDQIAVVIPPP--------RELKVEAENIPLE--- 108

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH------IDGFLKSWVDS 139
                 +LYED  + V NK  G+ V    G         + YH      I+G L+     
Sbjct: 109 ------ILYEDEDVLVVNKSQGMVVHPAPGAWTKTLVNALLYHCRNLSGINGVLR----- 157

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
               P + HR+D++TSG+LVVA+   A Q L E  +   + + Y ++V G+       + 
Sbjct: 158 ----PGIVHRIDKDTSGLLVVAKNDLAHQGLAEQIKAHSMARRYLAIVHGVVFEPSGTV- 212

Query: 200 NWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                ++ IG D      + VV QN   A  A++H++V++ F + F  LE +  TGRTHQ
Sbjct: 213 -----EAPIGRDPADRKKMAVVFQN---AKEAVTHYEVLERF-RDFTLLEARLETGRTHQ 263

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH  ++  P++GD  Y    K  F   +Q ++ LHA+ +   HP  G  ++ +AP   
Sbjct: 264 IRVHMAYLKHPVLGDPLYGPR-KNPFG--LQGQM-LHAQLLGFQHPRSGEYMEFSAPASG 319

Query: 314 HMVKTWDSL 322
              K  + +
Sbjct: 320 MFQKVLEEI 328


>gi|326570051|gb|EGE20097.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis BC7]
          Length = 242

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 119/229 (51%), Gaps = 23/229 (10%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +F KSI +YED  I+V +KPAG+    G  +       L+S +       RL HRLD +T
Sbjct: 25  EFAKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPNIRLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDY 212
           SG+++ A++  A  H+++ F  R  QK Y ++V+G  +  +KK  +   +  +      +
Sbjct: 81  SGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVPVRYEPTTKPRH 140

Query: 213 VHVVKQNEKGANYAISHFKVI--------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +  +  N++    A++H++V+        +  A     + ++P TGR+HQLRVH +H+G 
Sbjct: 141 IVDMDWNKR----ALTHYEVMHHELRCDDNGRAYPVTRVALKPITGRSHQLRVHMVHLGH 196

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            ++GD  Y  +     +    N+L LHA  + L HP  G  +   +P+P
Sbjct: 197 VMIGDPIYAEDVALKLS----NRLNLHAHKLRLKHPTHGIWMDWVSPVP 241


>gi|257439832|ref|ZP_05615587.1| ribosomal large subunit pseudouridine synthase D [Faecalibacterium
           prausnitzii A2-165]
 gi|257197741|gb|EEU96025.1| ribosomal large subunit pseudouridine synthase D [Faecalibacterium
           prausnitzii A2-165]
          Length = 314

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 79/322 (24%), Positives = 148/322 (45%), Gaps = 33/322 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +VE +    R+DR+       ++   LQ ++  G V  + K    + ++++G ++ +   
Sbjct: 7   IVEAEGAGQRIDRFLSGEDTGLSRSALQGLVAEGHVLCNGKAPAKSLKLKAGDIILLEIP 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                  + ++  LD               ++YED+ + V NKP G+ V    G      
Sbjct: 67  DAKPIEAVPQEIPLD---------------IIYEDAHLLVVNKPKGMVVHPAPGNPDGTL 111

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + +H  G L S +  +  +P + HR+D++TSG+LVVA+  A    L++   +  +++
Sbjct: 112 VNALLWHCKGSL-SGIGGE-IRPGIVHRVDKDTSGLLVVAKDDATHIGLSQQMAVHSVER 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V+G    + E      L +S      + V   +E    YA + +KV++   + F 
Sbjct: 170 AYNTIVYG-GFAQDEGFVESNLGRSKTDRKKMAVYPASEPHTKYAYTGYKVLERLGE-FT 227

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            LE +  TGRTHQ+RVH   +  P+ GD  Y  +   N  + +  +  LHA+ +   HP 
Sbjct: 228 MLECRLKTGRTHQIRVHMASIHHPVAGDPVYGPH---NCITSLHGQC-LHAKTLGFIHPI 283

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
            G  L+  + LP +  +   +L
Sbjct: 284 TGEHLRFDSELPDYFTRFLTTL 305


>gi|237748962|ref|ZP_04579442.1| ribosomal large subunit pseudouridine synthase D [Oxalobacter
           formigenes OXCC13]
 gi|229380324|gb|EEO30415.1| ribosomal large subunit pseudouridine synthase D [Oxalobacter
           formigenes OXCC13]
          Length = 342

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 85/307 (27%), Positives = 144/307 (46%), Gaps = 37/307 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+         +   LQ+ +  G + V+ ++ +    +   + + + P          
Sbjct: 41  RLDKLVAGRLSQYSRSRLQRWIEDGHITVNGEKAQAKQTVIGDEEICVIP---------- 90

Query: 80  EQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
             ++ +  +  T  + DF    +++ED+ I V NKPA + V   +G      ++G L  +
Sbjct: 91  --QLAEEDLAFTPEAVDF---PVVFEDNAILVVNKPASLVVHPAAGNWSGTLLNGLL--Y 143

Query: 137 VDSKGQK-PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPK 192
            D K    PR  + HRLD+ETSG++VVA+T  A   L    + R +++ Y +LVWG  P+
Sbjct: 144 RDPKSATVPRAGIVHRLDKETSGVMVVAKTIEAQTDLVRQLQARTVKREYLALVWGDTPQ 203

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHT 249
           +    I   + +      D V +   + +    A++HF+ I    C       ++ +  T
Sbjct: 204 SG--TIDEPIGRHPR---DRVKMAVIHTQSGKPAVTHFRKIAEGVCNNMNVSLVKCRLET 258

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QIT 308
           GRTHQ+RVH   +G P+VGD  Y    K +  S +  +  LHA  + L HP    + + T
Sbjct: 259 GRTHQIRVHLQSIGFPLVGDPVYG---KSHLAS-VFPRQALHAFRLGLIHPCTKEVCEWT 314

Query: 309 APLPAHM 315
           APLP  M
Sbjct: 315 APLPQDM 321


>gi|120610104|ref|YP_969782.1| ribosomal large subunit pseudouridine synthase D [Acidovorax
           citrulli AAC00-1]
 gi|120588568|gb|ABM32008.1| ribosomal large subunit pseudouridine synthase D [Acidovorax
           citrulli AAC00-1]
          Length = 339

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 87/324 (26%), Positives = 138/324 (42%), Gaps = 39/324 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPVINAL 74
           +   RLD+      P  +   LQ++L  G V V+ +   K + R+Q+G V+ +      L
Sbjct: 41  QHGARLDKALAELVPEFSRSYLQQLLGEGGVLVNGRAAAKPSARVQAGDVLSV-----EL 95

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGF 132
               + Q     ++ L           +YED  + + NKPAG+ V    G      ++G 
Sbjct: 96  RPTPQSQAFRPEAMALDT---------VYEDEHLRIVNKPAGLVVHPAPGNWSGTLLNGL 146

Query: 133 LKSWVDSK-GQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           L   +D + G  PR  + HRLD++TSG++VVAR R+    L      R + + Y +L   
Sbjct: 147 LA--LDPRAGNVPRAGIVHRLDKDTSGLMVVARERSVMDALVRMIAAREVSRQYLAL--- 201

Query: 190 IPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
              ++    A   + +  IG D      +  V         A +   V+D   +  C + 
Sbjct: 202 --GHRAWQGAQTRVVEEAIGRDPRNRLRMAAVDLAVHAGKPARTDIAVLDTC-ENGCLVH 258

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              HTGRTHQ+RVH   +  P+V D  Y        +     +  LHA  +   HP  G+
Sbjct: 259 CTLHTGRTHQIRVHMAWLRHPLVADALYGGEPAAGLS-----RQALHAYRLAFAHPVTGQ 313

Query: 305 -LQITAPLPAHMVKTWDSLGFKYD 327
            L   APLP  M     + G +Y+
Sbjct: 314 PLLFHAPLPGDMAGALQAWGLRYN 337


>gi|126701209|ref|YP_001090106.1| putative pseudouridylate synthase [Clostridium difficile 630]
 gi|254977209|ref|ZP_05273681.1| putative pseudouridylate synthase [Clostridium difficile QCD-66c26]
 gi|255094537|ref|ZP_05324015.1| putative pseudouridylate synthase [Clostridium difficile CIP
           107932]
 gi|255102795|ref|ZP_05331772.1| putative pseudouridylate synthase [Clostridium difficile QCD-63q42]
 gi|255308616|ref|ZP_05352787.1| putative pseudouridylate synthase [Clostridium difficile ATCC
           43255]
 gi|255316290|ref|ZP_05357873.1| putative pseudouridylate synthase [Clostridium difficile QCD-76w55]
 gi|255518951|ref|ZP_05386627.1| putative pseudouridylate synthase [Clostridium difficile QCD-97b34]
 gi|255652130|ref|ZP_05399032.1| putative pseudouridylate synthase [Clostridium difficile QCD-37x79]
 gi|260685103|ref|YP_003216388.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260688761|ref|YP_003219895.1| putative pseudouridylate synthase [Clostridium difficile R20291]
 gi|306521862|ref|ZP_07408209.1| putative pseudouridylate synthase [Clostridium difficile QCD-32g58]
 gi|115252646|emb|CAJ70489.1| putative pseudouridine synthase RsuA-like [Clostridium difficile]
 gi|260211266|emb|CBA66814.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260214778|emb|CBE07493.1| putative pseudouridylate synthase [Clostridium difficile R20291]
          Length = 221

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 61/205 (29%), Positives = 104/205 (50%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  KP  I  QG +     +   LK ++  K  KP      L HRLD+   
Sbjct: 4   VIYEDNHLLVVEKPVNILSQGDNTNDKDMVNLLKDYIKKKYNKPGNVYIGLIHRLDRPVG 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  L+E  R +  +K Y ++V G  K+  + + ++L K      + V V
Sbjct: 64  GVMVFAKTSKAASRLSEQVRSKTFKKTYLAVVHGKIKSNSDILKDFLYKNKKT--NMVTV 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           VK++ K A  A  ++ V+D F +    +++   TGR+HQ+RV       P+ GD +Y   
Sbjct: 122 VKKSHKDAKEAELNYNVLD-FKENLSLVQVNLKTGRSHQIRVQFASRKHPLYGDQRY--- 177

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G   + I  ++ L +  +++ HP
Sbjct: 178 --GKEINKIGQQISLWSNKIEICHP 200


>gi|28378455|ref|NP_785347.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|308180606|ref|YP_003924734.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28271291|emb|CAD64195.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|308046097|gb|ADN98640.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 307

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 112/237 (47%), Gaps = 22/237 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL--KSWVDSKGQ-KPRLTHRLDQETS 155
           ++YED  + V NKP G+ V    G   H  ++  L         G+ +P + HR+D++TS
Sbjct: 84  IVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTS 143

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+VA+   A Q L    + +   + Y +LV G+ K     I N  L +S        +
Sbjct: 144 GLLMVAKNDRAHQSLAAQLKAKTNLREYVALVHGVIKEDTGTI-NAPLGRSPKDRKKQAI 202

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
           VK        A++HFKV+  + Q +  +  +  TGRTHQ+RVH   +G P+VGD  Y   
Sbjct: 203 VKTGRP----AVTHFKVLKRY-QHYTLISCRLETGRTHQIRVHLQSIGHPLVGDPLYGPK 257

Query: 275 -NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
              KG+         +LHA+ +   HP  G  L   APLP     T   L  K D N
Sbjct: 258 KTIKGHGQ-------FLHAKLLGFKHPVTGDLLTFEAPLPPIFTTTLAKLD-KTDGN 306


>gi|326203344|ref|ZP_08193209.1| pseudouridine synthase, RluA family [Clostridium papyrosolvens DSM
           2782]
 gi|325986602|gb|EGD47433.1| pseudouridine synthase, RluA family [Clostridium papyrosolvens DSM
           2782]
          Length = 303

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 76/287 (26%), Positives = 134/287 (46%), Gaps = 35/287 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +  E + E  ++DR  ++ +P++    L K LR   ++V+  R+K +  +  G  + I  
Sbjct: 4   ITAEKNHEGKKIDRVVRDFFPNLASGMLYKALRKKDIKVNGIRIKEDYIVSCGDKIDIYI 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAY 127
           + + L               L ++ +     ++Y+D  + + NK AGI V        A 
Sbjct: 64  IDDYL---------------LGRNDEGFS--VVYDDDNLLIVNKEAGIPVHPDKNQKEAT 106

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            ID     +    G    L HRLD+ TSG+++VA+     + + +  + R IQK Y  +V
Sbjct: 107 LIDKLQSIY----GPNLALCHRLDRNTSGLVIVAKNNPTLEVMLDKIKDREIQKYYSCIV 162

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  + KK  + ++L K   +    V +  +  + +   I+ ++V +        LE++ 
Sbjct: 163 SGKMEKKKAELVDYLDKNEKLS--RVFITSEKTRNSVQIITRYRVTESL-NSLSMLEVEL 219

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            TGRTHQ+R H  + G PI+GD KY  N        I+NK Y +A+Y
Sbjct: 220 VTGRTHQIRAHLAYYGHPIIGDGKYGKN--------IENKQY-NAKY 257


>gi|145628474|ref|ZP_01784274.1| SfhB [Haemophilus influenzae 22.1-21]
 gi|144978944|gb|EDJ88630.1| SfhB [Haemophilus influenzae 22.1-21]
          Length = 324

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 121/249 (48%), Gaps = 41/249 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPR--LTHR 149
           ++YED  I V NKP  + V  G+G         + YH             + PR  + HR
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI--------AEVPRAGIVHR 136

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKS 206
           LD++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++
Sbjct: 137 LDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRT 196

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +    VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P+
Sbjct: 197 LMA---VHPMGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPL 246

Query: 267 VGDHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           +GD  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+
Sbjct: 247 LGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLSHPITGEMMEWYAPLPDDFVE 306

Query: 318 TWDSLGFKY 326
             ++L   Y
Sbjct: 307 LLNALKADY 315


>gi|86133978|ref|ZP_01052560.1| RNA pseudouridylate synthase [Polaribacter sp. MED152]
 gi|85820841|gb|EAQ41988.1| RNA pseudouridylate synthase [Polaribacter sp. MED152]
          Length = 288

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/222 (32%), Positives = 105/222 (47%), Gaps = 37/222 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +L ED  + V  KPAGI V G     IA  +   LK        KP+  HRLD  TSG+L
Sbjct: 83  VLLEDDFLAVIYKPAGILVSGNKFVTIANALSQNLKKSNQVDAVKPQPVHRLDYATSGLL 142

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +V +T +A Q L+E F+ + I+K Y+++  G  K K   I +  +               
Sbjct: 143 LVGKTSSAIQKLSELFQKKEIKKTYYAVTIG--KMKPLGIIDKPIDDKE----------- 189

Query: 219 NEKGANYAISHFKVI-DCFAQKFCWL---EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                  A + +KVI +  +++F +L   E+ P TGR HQLR H L +  PI+GD +Y  
Sbjct: 190 -------AYTQYKVISNEISKRFNFLNLVELSPKTGRKHQLRKHLLSLKNPILGDKEYFI 242

Query: 275 N---FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                KG         LYLHA  ++  HP    ++ I   LP
Sbjct: 243 EGKILKG-------KGLYLHAAKLEFTHPFTAEKITIRKELP 277


>gi|317475813|ref|ZP_07935070.1| RNA pseudouridylate synthase [Bacteroides eggerthii 1_2_48FAA]
 gi|316907973|gb|EFV29670.1| RNA pseudouridylate synthase [Bacteroides eggerthii 1_2_48FAA]
          Length = 518

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 100/207 (48%), Gaps = 20/207 (9%)

Query: 102 LYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +YED  + V NKPAG +SV G            + + ++ G  P + HRLD  TSG+LV+
Sbjct: 318 VYEDEWLLVVNKPAGMLSVPGKEEAVSVYSVMRRRYPEADG--PLIVHRLDMATSGLLVI 375

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T+   Q+L   FR R + K Y +L+ GI       +   L        D    +   E
Sbjct: 376 AKTKQVHQNLQAQFRDRSVSKRYIALLQGIVSPDTGTVELPLCLNPL---DRPRQMVHTE 432

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFK 277
            G + A++ F+V++        +   P TGRTHQLRVHA H   + CPI+GD  Y     
Sbjct: 433 HGKS-AVTDFEVLE-RKDNHTRIAFYPRTGRTHQLRVHAAHPLGLHCPIIGDELYGKK-- 488

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR 304
                    +LYLHA  ++  HP  G+
Sbjct: 489 -------AERLYLHAEALEFTHPITGK 508


>gi|313892058|ref|ZP_07825656.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
 gi|313119510|gb|EFR42704.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
          Length = 328

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 82/312 (26%), Positives = 145/312 (46%), Gaps = 16/312 (5%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E  +L ++     P  +   + K LR   +  + K+   N  I+SG V+ I      L 
Sbjct: 10  DEGQKLIKFLFKLLPGASKSLIYKSLRKKNILYNNKKANGNEIIKSGDVIEIWFSDETLE 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           +  K++       N+   S   K I+LYE+  I V NKP G+  Q        ++ +L  
Sbjct: 70  NFSKKESKEILKGNIENFS--FKDIILYENEDIIVVNKPKGMLSQRDISRQKSLNDYLLE 127

Query: 136 WVDSK---GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           ++ +    G KP + +RLD+ TSG L+ A+T   A+ + E  +   I K Y  LV+G  K
Sbjct: 128 YIKNSNYSGFKPSICNRLDKNTSGTLICAKTFKIAREINELIKNHVINKKYLCLVFGDIK 187

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHT 249
           +    + ++L K  ++  +   V  + ++G     +   VI  F        +LE+   T
Sbjct: 188 DDL-YLKDYLFK--NVENNKAIVSNEKKEGFLEIKTKVHVIKSFKLHEYPVTFLEVTLLT 244

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH----PEGGR 304
           G+ HQ+R H  ++G PI+GD KY  N     +  ++  +  LH+  ++ P      E   
Sbjct: 245 GKFHQIRAHLSYIGHPILGDRKYGNNESLEISKILEIGRQLLHSYSIEFPENHCLKELSG 304

Query: 305 LQITAPLPAHMV 316
           ++I AP+P  ++
Sbjct: 305 MKIKAPIPKDIM 316


>gi|289435186|ref|YP_003465058.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
 gi|289171430|emb|CBH27974.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
 gi|313632720|gb|EFR99690.1| ribosomal large subunit pseudouridine synthase D [Listeria
           seeligeri FSL N1-067]
 gi|313637301|gb|EFS02795.1| ribosomal large subunit pseudouridine synthase D [Listeria
           seeligeri FSL S4-171]
          Length = 303

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 85/302 (28%), Positives = 141/302 (46%), Gaps = 51/302 (16%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQV----VRIPPVINALNHIIKEQKILDSSVNLTK 92
           +Q +L+SG + V+ +  K N ++Q G      VR P          +E ++L   + L  
Sbjct: 32  IQIMLKSGDITVNGEIAKPNYKVQVGDEIYLEVREP----------EELEVLAEDIPLD- 80

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQK 143
                   + +ED  + V NKP G+ V   +G A         +H D    S ++ K  +
Sbjct: 81  --------IYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL--SGINGK-IR 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    +
Sbjct: 130 PGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPI 188

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++      + VV+  ++    A +HF+VI+     +  +  +  TGRTHQ+RVH  ++G
Sbjct: 189 GRAKEDRQKMAVVRDGKE----ARTHFEVIERLP-GYTLINCKLDTGRTHQIRVHLKYIG 243

Query: 264 CPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            P+ GD KY      KGN         YLHA  +   HP    R+   APLP+   K   
Sbjct: 244 HPLAGDPKYGPKNTIKGNGQ-------YLHAAKLGFDHPTTNERMTFEAPLPSSFEKALK 296

Query: 321 SL 322
            L
Sbjct: 297 ML 298


>gi|123441245|ref|YP_001005232.1| 23S rRNA pseudouridine synthase D [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332160281|ref|YP_004296858.1| 23S rRNA pseudouridine synthase D [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122088206|emb|CAL10994.1| ribosomal large subunit pseudouridine synthase D [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|318604491|emb|CBY25989.1| ribosomal large subunit pseudouridine synthase D [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325664511|gb|ADZ41155.1| 23S rRNA pseudouridine synthase D [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330863600|emb|CBX73710.1| ribosomal large subunit pseudouridine synthase D [Yersinia
           enterocolitica W22703]
          Length = 325

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 88/332 (26%), Positives = 156/332 (46%), Gaps = 47/332 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V V+ K + K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILEDKVTVNGKTINKPKEKVLGGELVAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        ++  LD               ++YED+ I V NKP G+ V  G+G   +
Sbjct: 69  AQIEEDARWAPQEIPLD---------------IVYEDNDILVINKPRGLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + 
Sbjct: 111 PDGTVLNALLYYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH + +       A +H+++++ F + 
Sbjct: 171 YEAVAIGNMTAGGRVDEPISRHSTKRTHMA---VHPMGKP------ATTHYRIMEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       +F + ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFIAILRGFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           A  + L HP  G +++  A LP  MV+  ++L
Sbjct: 281 ATMLRLYHPISGIQMEWHAALPEDMVELINAL 312


>gi|153948512|ref|YP_001402171.1| 23S rRNA pseudouridine synthase D [Yersinia pseudotuberculosis IP
           31758]
 gi|152960007|gb|ABS47468.1| ribosomal large subunit pseudouridine synthase D [Yersinia
           pseudotuberculosis IP 31758]
          Length = 327

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 92/333 (27%), Positives = 155/333 (46%), Gaps = 47/333 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V V+ K++ K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKVLGGELVAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        ++  LD               ++YED+ I V NKP G+ V  G+G   +
Sbjct: 69  AQIEEDARWAPQEIPLD---------------IVYEDNDILVINKPRGLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + 
Sbjct: 111 PDGTVLNALLHYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQ 238
           Y ++  G         E I+    K++H+    VH + +       A +H+++++ F A 
Sbjct: 171 YEAVAIGNMTAGGRVDEPISRHSTKRTHMA---VHPMGKP------ATTHYRIMEHFRAH 221

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYL 290
               L ++  TGRTHQ+RVH  H+  P+VGD  Y       KG   S I      ++  L
Sbjct: 222 TRLRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDSFIAILRGFDRQAL 281

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           HA  + L HP  G +++  A LP  MV+  ++L
Sbjct: 282 HATMLRLYHPISGIQMEWHAALPEDMVELINAL 314


>gi|260856684|ref|YP_003230575.1| 23S rRNA pseudouridine synthase [Escherichia coli O26:H11 str.
           11368]
 gi|257755333|dbj|BAI26835.1| 23S rRNA pseudouridine synthase [Escherichia coli O26:H11 str.
           11368]
          Length = 326

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 90/338 (26%), Positives = 159/338 (47%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G++V    
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGELV---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            INA   I +E +     + L          ++YED  I V NKP  + V  G+G   + 
Sbjct: 66  AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---NP 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y
Sbjct: 112 DGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREY 171

Query: 184 WSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G         E I+    K++H+    VH + +       A++H+++++ F +  
Sbjct: 172 EAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPMGKP------AVTHYRIMEHF-RVH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHA 292
             L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA
Sbjct: 222 TRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISMLRKFDRQALHA 281

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
             + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 282 TMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 319


>gi|326567226|gb|EGE17346.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis 12P80B1]
          Length = 242

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 119/229 (51%), Gaps = 23/229 (10%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +F KSI +YED  I+V +KPAG+    G  +       L+S +       RL HRLD +T
Sbjct: 25  EFAKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLCINPNIRLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDY 212
           SG+++ A++  A  H+++ F  R  QK Y ++V+G  +  +KK  +   +  +      +
Sbjct: 81  SGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVPVRYEPTTKPRH 140

Query: 213 VHVVKQNEKGANYAISHFKVI--------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +  +  N++    A++H++V+        +  A     + ++P TGR+HQLRVH +H+G 
Sbjct: 141 IVDMDWNKR----ALTHYEVMHHELRCDDNGRAYPVTRVALKPITGRSHQLRVHMVHLGH 196

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            ++GD  Y  +     +    N+L LHA  + L HP  G  +   +P+P
Sbjct: 197 VMIGDPIYAEDVALKLS----NRLNLHAHKLRLKHPTHGIWMDWVSPVP 241


>gi|318043192|ref|NP_001187897.1| RNA pseudouridylate synthase domain-containing protein 4 [Ictalurus
           punctatus]
 gi|308324268|gb|ADO29269.1| RNA pseudouridylate synthase domain-containing protein 4 [Ictalurus
           punctatus]
          Length = 386

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 67/211 (31%), Positives = 104/211 (49%), Gaps = 28/211 (13%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSK--G 141
           SV+    +  L   +LY+D  +   NKP G+ V    GI   I      L   +D    G
Sbjct: 105 SVHPNVFAKALSKSILYQDQNLIAINKPYGVPVYSTGGIGNSIAESLPVLAKIIDCTKGG 164

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            K  + + L+++T+G+L +ART   A+ +    R  + +K Y  +  G+P   +  I   
Sbjct: 165 SKLHVCYNLEKDTTGVLFLARTEETAERIHNLIRSHQAEKRYMVITVGVPVPSEGVIDIP 224

Query: 202 LLKKSHIG------------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++K  +G                  GD +  V+ N + A  A++H+KV+D  +   C L
Sbjct: 225 IIEKEVMGDQHHFKMGLSPLYRPTEEGDGLVRVRANRQ-AQSAVTHYKVLD--SSSGCSL 281

Query: 244 -EMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
            E+QP TG  HQLRVH AL + CPI+GDHKY
Sbjct: 282 VELQPVTGVKHQLRVHMALALACPILGDHKY 312


>gi|53804663|ref|YP_113451.1| ribosomal large subunit pseudouridine synthase D [Methylococcus
           capsulatus str. Bath]
 gi|53758424|gb|AAU92715.1| ribosomal large subunit pseudouridine synthase D [Methylococcus
           capsulatus str. Bath]
          Length = 334

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 86/327 (26%), Positives = 149/327 (45%), Gaps = 49/327 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+     +P  +   LQ  ++ G   +D  +V    ++  G+ V +          
Sbjct: 36  GLRLDQALAVLFPDFSRARLQTWIKDGHALLDGIQVAPRQKLLGGERVEL---------- 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
              +   D++V     ++ +   +++ D  I+V +KPAG+ V   +G   H  G L++ +
Sbjct: 86  ---RAEADAAVEC--EAEAIPLTVVHADESIFVIDKPAGLVVHPAAG---HPAGTLQNAL 137

Query: 138 ----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI- 190
                +    PR  + HRLD++TSG+LVVART  A + L +  + R + + Y +LV G+ 
Sbjct: 138 LHLDPALAAIPRCGIVHRLDKDTSGLLVVARTLEAHKSLVDQLKDRSVNREYLALVQGMV 197

Query: 191 --PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
                  E I        H        V+ + +    +++H++V + F      L ++  
Sbjct: 198 TAGATVDEPIGR------HPADRKRFAVRPDGR---ESVTHYRVEERFLHH-TLLRVRLE 247

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P+VGD  Y    +      P+         +  LHA  + L HP
Sbjct: 248 TGRTHQIRVHMAHLHHPLVGDPVYGGRARIPAAADPVLIDVLRGFRRQALHAARLGLIHP 307

Query: 301 E-GGRLQITAPLPAH---MVKTWDSLG 323
           E GG +   +PLP     +++   SLG
Sbjct: 308 EKGGEMAWESPLPPDFDALLRLLRSLG 334


>gi|115379077|ref|ZP_01466202.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|115363904|gb|EAU63014.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
          Length = 262

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 82/278 (29%), Positives = 132/278 (47%), Gaps = 46/278 (16%)

Query: 53  VKFNNRIQSGQVVR--IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYV 110
           +K ++R++ G+++   +PP + AL                   ++ L   +L+ED  + V
Sbjct: 1   MKASSRLRGGELLSLHVPPPVAAL-----------------PEAEELPLEVLHEDRDLVV 43

Query: 111 FNKPAGISVQGGSGIAYHIDGFL--------KSWVDSKGQ-KPRLTHRLDQETSGILVVA 161
            NK AG+ V  G+G   H  G L        K      G+ +P + HRLD++T+G LVVA
Sbjct: 44  VNKAAGMVVHPGAG---HASGTLVNALLHRVKDLAGVGGELRPGIVHRLDKDTTGCLVVA 100

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--QN 219
           +   A   L ++F+ R ++K Y +LV G PK +          ++  G   VH  +    
Sbjct: 101 KNEQALVALQKAFKTRAVEKTYLALVHGHPKAEGRI-------ETLYGRHPVHRQRFTGK 153

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K    A++ F+  + F +    +E+   TGRTHQ+RVH    G P++ D  Y A  K  
Sbjct: 154 VKEGKSAVTVFRTREFF-EGAALVEVDLLTGRTHQIRVHLSESGHPLLCDALYGAGRKAK 212

Query: 280 F-TSPIQNKL---YLHARYMDLPHPEGGR-LQITAPLP 312
              +  Q +L    LHA  +   HP  G+ L++ APLP
Sbjct: 213 GQVAQAQERLGRQALHAWRLGFAHPRTGKALKLEAPLP 250


>gi|91794214|ref|YP_563865.1| pseudouridine synthase, RluD [Shewanella denitrificans OS217]
 gi|91716216|gb|ABE56142.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           denitrificans OS217]
          Length = 324

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 88/331 (26%), Positives = 151/331 (45%), Gaps = 47/331 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNH 76
            +RLD+     +P  +   +++ + SG V VD  +V K   ++   Q + I         
Sbjct: 17  GLRLDQALAELFPDYSRTRIKEWILSGAVYVDGVKVDKPREKVLESQQIEIEATFE---- 72

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
             +E K    +++L          ++YED  I + NK AG+ V  G+G A   DG L + 
Sbjct: 73  --EEVKAKAQAIDLN---------IVYEDDHIIIVNKQAGLVVHPGAGNA---DGTLMNA 118

Query: 137 V----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           +     +    PR  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V G 
Sbjct: 119 LLHHCPAIEMVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREIVREYEAIVLGT 178

Query: 191 PK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                   E I     K++ +   +         G   +++H++V + F +    L ++ 
Sbjct: 179 MTAGGTVDEPIERHPTKRTQMSVQH---------GGRPSVTHYRVSEKF-RAHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPH 299
            +GRTHQ+RVH  ++G  +VGD  Y        N    F   ++N  +  LHA  ++L H
Sbjct: 229 ESGRTHQIRVHMDYIGHVLVGDPVYGGRPKPPKNASPEFFDILKNFGRQALHAVRLELAH 288

Query: 300 PEGGRLQI-TAPLPAHMVKTWDSLGFKYDRN 329
           P    +    AP+P  MV    +L    + N
Sbjct: 289 PYTHEIMSWQAPIPEDMVMLTKALRKDTEEN 319


>gi|261414686|ref|YP_003248369.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261371142|gb|ACX73887.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 386

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 115/226 (50%), Gaps = 19/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSG 156
           L+ +     + NKP+G++ Q GSG      +  +L  W  ++G   KP + HRLDQETSG
Sbjct: 145 LVVQTEDYVIVNKPSGLASQPGSGTRPGESLVEYLWEWGRNEGLDFKPTIAHRLDQETSG 204

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++ A      +  T   R   + K Y++LV G  K  +  I+  LL+     G  + +V
Sbjct: 205 LIIAALHGDTLRDFTRMIREHVVDKFYFALVKGNLKKDRGTISESLLRTDSAKGSKM-LV 263

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            Q+++ A  AI+H++V   + + +  ++++  TGR HQ+R H   +G P++GD +Y    
Sbjct: 264 GQDDENAQKAITHYRVKQHY-EGYDLVKIKLETGRMHQIRAHFASIGHPLLGDTRY---- 318

Query: 277 KGNFTSPIQ-------NKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
            G+F    +       N+L+LH+  ++    +G       PLP  +
Sbjct: 319 -GDFALNREVKKLFGLNRLFLHSCRLEFDW-QGEHKVFDCPLPKEL 362


>gi|326335663|ref|ZP_08201850.1| ribosomal large subunit pseudouridine synthase [Capnocytophaga sp.
           oral taxon 338 str. F0234]
 gi|325692429|gb|EGD34381.1| ribosomal large subunit pseudouridine synthase [Capnocytophaga sp.
           oral taxon 338 str. F0234]
          Length = 235

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 109/220 (49%), Gaps = 17/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +   NK AG  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 10  VLYEDNHLIAINKRAGDIVQGDKTGDIPLSEIVKEYLVKKYNKPGDAYLGVVHRLDRPTT 69

Query: 156 GILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           GI++ A+T  A   L  +F  +  + K YW+LV       +  + ++L++ +     Y +
Sbjct: 70  GIVLFAKTSKALPRLNAAFATKEEVCKRYWALVEKKTIPAEGTLTHFLVRNTSQNKSYAY 129

Query: 215 VVKQNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              Q EK  +  A+  +KV+      +  +E+   TGR HQ+R     +GCP+ GD KY 
Sbjct: 130 ---QTEKPQSQKAVLTYKVLATLTH-YLLVEINLLTGRHHQIRAQFAALGCPLKGDLKY- 184

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
               G   S     + LHAR ++L HP +   L ITAPLP
Sbjct: 185 ----GAKRSNPDGSICLHARTLELLHPIKKEPLSITAPLP 220


>gi|145633599|ref|ZP_01789327.1| SfhB [Haemophilus influenzae 3655]
 gi|229847288|ref|ZP_04467391.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae 7P49H1]
 gi|144985805|gb|EDJ92419.1| SfhB [Haemophilus influenzae 3655]
 gi|229809831|gb|EEP45554.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae 7P49H1]
          Length = 324

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 121/249 (48%), Gaps = 41/249 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPR--LTHR 149
           ++YED  I V NKP  + V  G+G         + YH             + PR  + HR
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI--------AEVPRAGIVHR 136

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKS 206
           LD++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++
Sbjct: 137 LDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRT 196

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +    VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P+
Sbjct: 197 LMA---VHPMGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPL 246

Query: 267 VGDHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           +GD  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+
Sbjct: 247 LGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVE 306

Query: 318 TWDSLGFKY 326
             ++L   Y
Sbjct: 307 LLNALKADY 315


>gi|326790893|ref|YP_004308714.1| pseudouridine synthase [Clostridium lentocellum DSM 5427]
 gi|326541657|gb|ADZ83516.1| pseudouridine synthase [Clostridium lentocellum DSM 5427]
          Length = 322

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 78/292 (26%), Positives = 135/292 (46%), Gaps = 39/292 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E N RLD++   +        + K +R+ +++ + K+ + N  +Q G  ++I        
Sbjct: 10  EANQRLDKFLMKYLNECPKSFIYKGMRTKKIKYNGKKPQGNEILQEGDEIKI-------- 61

Query: 76  HIIKEQ-KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
              +EQ K   S   + K     +++  YED  I + NKP G+  Q  +   + +   + 
Sbjct: 62  FFTEEQFKTFSSEKEVKKVPISFQTV--YEDEHILIVNKPMGLLTQKDTATGHSLADEVL 119

Query: 135 SWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           S++          SKG  P   +RLD+ T+GI++V +   A Q L E  + ++I K Y S
Sbjct: 120 SYLKDNGSYDPKTSKGFTPAPCNRLDRNTAGIVLVGKHIPAVQVLGEMLQTKQISKYYMS 179

Query: 186 LVWGIPKNKKECIANWLLKKSHI---GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           +V G         A  +LK  HI   G + V +  +  +GA    +    +     ++  
Sbjct: 180 IVLG------RVTAPMILKGYHIKQEGKNEVKITTEYVEGAKPVETRILPLKTNG-RYTL 232

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
           +E+Q  TG+THQ+R H   +G PI+GD KY          PI+N+ Y  ++Y
Sbjct: 233 VEVQLVTGKTHQIRAHLSKIGHPIIGDPKY--------GDPIENQ-YFASQY 275


>gi|251783426|ref|YP_002997731.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|242392058|dbj|BAH82517.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
          Length = 341

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 64/199 (32%), Positives = 94/199 (47%), Gaps = 13/199 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  + + NKP G+   G       +   + ++    G+   + HRLD ETSG++V A
Sbjct: 130 LYEDDHLIIVNKPEGMKTHGNEPTELALLNHVSAYT---GRTCYVVHRLDMETSGVIVFA 186

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +T      L      R I + YW+LV G   +K+      + +  H     V  VKQ +K
Sbjct: 187 KTPFILPILNRLLEKREISRDYWALVHGTLSSKEVSYREPIGRHRHDRRKRVVDVKQGQK 246

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               A++  K++  F Q    +  +  TGRTHQ+RVH  H G  ++GD  Y    KG   
Sbjct: 247 ----AVTDVKLLKSFKQNVSLINCRLQTGRTHQIRVHLSHHGHALLGDPLYS---KGKAE 299

Query: 282 SPIQNKLYLHARYMDLPHP 300
            P   +L LHA  + L HP
Sbjct: 300 CP---RLMLHAHQLRLRHP 315


>gi|326316273|ref|YP_004233945.1| pseudouridine synthase, RluA family [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323373109|gb|ADX45378.1| pseudouridine synthase, RluA family [Acidovorax avenae subsp.
           avenae ATCC 19860]
          Length = 339

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 83/318 (26%), Positives = 135/318 (42%), Gaps = 27/318 (8%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPVINAL 74
           +   RLD+      P  +   LQ++L  G V V+ +   K + R+Q+G V+ +      L
Sbjct: 41  QHGARLDKALAELVPEFSRSYLQQLLGEGGVLVNGRAAAKPSARVQAGDVLSV-----EL 95

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGF 132
               + Q     ++ L           +YED  + + NKPAG+ V    G      ++G 
Sbjct: 96  RPTPQSQAFRPEAMALDT---------VYEDEHLRIVNKPAGLVVHPAPGNWSGTLLNGL 146

Query: 133 LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           L S     G  PR  + HRLD++TSG++VVAR R+    L      R + + Y +L    
Sbjct: 147 L-SLDPRAGNVPRAGIVHRLDKDTSGLMVVARERSVMDALVRMIAAREVSRQYLALGHRA 205

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +  +  +    + +       +  V         A +   V+D   +  C +    HTG
Sbjct: 206 WQGSQTRVVEEAIGRDPRNRLRMAAVDLAVHAGKPARTDLAVLDT-CEDGCLVHCTLHTG 264

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH   +  P++ D  Y     G   +   ++  LHA  +   HP  G+ L   A
Sbjct: 265 RTHQIRVHMAWLRHPLLADTLY-----GGEPAAGMSRQALHAYRLAFAHPVTGQPLLFHA 319

Query: 310 PLPAHMVKTWDSLGFKYD 327
           PLP  M     + G +Y+
Sbjct: 320 PLPGDMAGALQAWGLRYN 337


>gi|322418067|ref|YP_004197290.1| RluA family pseudouridine synthase [Geobacter sp. M18]
 gi|320124454|gb|ADW12014.1| pseudouridine synthase, RluA family [Geobacter sp. M18]
          Length = 300

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 76/309 (24%), Positives = 141/309 (45%), Gaps = 40/309 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           ++ ++  +RLD   K  +  ++   +++++  G   +++  V+  +R ++ G  V +   
Sbjct: 7   IDAEQSGLRLDDAAKALFSQLSKGEIRRVIDWGGCNINQVLVRVASRQVKEGDEVAL--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----SGI 125
                 +++ ++ +D          + K+ LLYED       K AG++ Q         +
Sbjct: 64  -----GVMEAERCIDLV--------YQKNELLYEDKDFLAVYKAAGVNSQRTPYQLKGTV 110

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            Y ++ ++KS         R+ HRLD+ TSG++   + + AA  ++   +  ++QK YW+
Sbjct: 111 EYAVECYMKSI--GLRDPSRVVHRLDRGTSGVMFFPKHKQAATLISNLLKEGKVQKTYWA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G P  +   +   L +     G + + V    K A    S    +    +    +E 
Sbjct: 169 LVSGSPDQQGWKVDAPLDRV----GKFRYGVSLRGKPARTVFS----VLGEGKGVTVIEA 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +P TGRTHQ+RVH  H G PI+GD  Y     G   +   +++ LH R M    P G  +
Sbjct: 221 KPLTGRTHQIRVHLAHSGFPIIGDESY-----GGIPA---SRMMLHCRAMRFTGPRGKII 272

Query: 306 QITAPLPAH 314
           +  APL A 
Sbjct: 273 EAVAPLDAE 281


>gi|300767399|ref|ZP_07077311.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|300495218|gb|EFK30374.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 320

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 75/237 (31%), Positives = 112/237 (47%), Gaps = 22/237 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL--KSWVDSKGQ-KPRLTHRLDQETS 155
           ++YED  + V NKP G+ V    G   H  ++  L         G+ +P + HR+D++TS
Sbjct: 97  IVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTS 156

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+VA+   A Q L    + +   + Y +LV G+ K     I N  L +S        +
Sbjct: 157 GLLMVAKNDRAHQSLAAQLKAKTNLREYVALVHGVIKEDTGTI-NAPLGRSPKDRKKQAI 215

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
           +K        A++HFKV+  + Q +  +  +  TGRTHQ+RVH   +G P+VGD  Y   
Sbjct: 216 IKTGRP----AVTHFKVLKRY-QHYTLISCRLETGRTHQIRVHLQSIGHPLVGDPLYGPK 270

Query: 275 -NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
              KG+         +LHA+ +   HP  G  L   APLP     T   L  K D N
Sbjct: 271 KTIKGHGQ-------FLHAKLLGFKHPVTGDLLTFEAPLPPIFTTTLAKLD-KTDGN 319


>gi|284007738|emb|CBA73551.1| 23S rRNA pseudouridine synthase D [Arsenophonus nasoniae]
          Length = 325

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 76/239 (31%), Positives = 123/239 (51%), Gaps = 41/239 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----PR--LTHRLDQET 154
           ++YED +I V NKP  + V  G+G   + DG + + +  +  +    PR  + HRLD++T
Sbjct: 86  IVYEDDEILVINKPRDLVVHPGAG---NPDGTVLNALLYRYPEIINVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++V+A+T  A  HL E+ + R I + Y ++V G         E IA    K++H+   
Sbjct: 143 TGLMVIAKTIPAQTHLVEALQRREITREYEAVVNGRMTAGGTVDEPIARHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +H + +       AI+H++V++ F +    L ++  +GRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -IHPMGKP------AITHYRVMEHF-RAHTRLRLRLESGRTHQIRVHMAHINHPLVGDPV 252

Query: 272 YCAN---FKG----------NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
           Y       KG          NF     N+  LHA  + L HP  G  ++  A +PA MV
Sbjct: 253 YGGRPRPLKGVSEEFRQIMSNF-----NRQALHATMLRLYHPLTGIEMEWHADIPADMV 306


>gi|94501303|ref|ZP_01307824.1| Pseudouridylate synthases, 23S RNA-specific [Oceanobacter sp.
           RED65]
 gi|94426574|gb|EAT11561.1| Pseudouridylate synthases, 23S RNA-specific [Oceanobacter sp.
           RED65]
          Length = 322

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 86/320 (26%), Positives = 144/320 (45%), Gaps = 42/320 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV N+  N RLD+     +P  +   LQ  ++ G++++D    K  +++  G+ + +
Sbjct: 7   ETVVVPNELGNRRLDQIAAQLFPDYSRARLQSWIKDGELKIDGAVRKPKDKLIGGETLTL 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              + A    I E              DF    ++YED  I V +KPA + V   +G   
Sbjct: 67  DVTLQAEGEWIAED------------IDF---PIVYEDEHIIVIDKPADLVVHPAAGNLT 111

Query: 128 HIDGFLKSW-VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                       S    PR  + HRLD++T+G++VVA+T  A  HL E  + R++ + Y 
Sbjct: 112 GTLLNGLLHHCPSLETIPRAGIVHRLDKDTTGLMVVAKTLQAQNHLVEQLQSRQMGREYE 171

Query: 185 SLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +++ G         E IA     ++ +    VH   +       AI+H++V+  +     
Sbjct: 172 AVIQGKMTGGGKISEPIARHSKDRTKMA---VHPTGKE------AITHYRVVKQYP-AHT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKL------YLHAR 293
            + ++  TGRTHQ+RVH  HM  P+VGD  Y     F    +  ++  L       LHA 
Sbjct: 222 HIRVKLETGRTHQIRVHMAHMQHPLVGDATYGGKVRFPKGLSQELREVLREFPRQALHAV 281

Query: 294 YMDLPHPEGGRL---QITAP 310
            ++L HP    L   Q++ P
Sbjct: 282 KLELHHPATNELMSWQVSLP 301


>gi|195941758|ref|ZP_03087140.1| hypothetical protein Bbur8_02614 [Borrelia burgdorferi 80a]
          Length = 336

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 114/226 (50%), Gaps = 21/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 96  IIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 154

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +R  K+Y ++V G   +    I +++ +  H    
Sbjct: 155 KDTSGVLICAKNISTLRFLAQQFKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 214

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 215 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 269

Query: 272 YCANFKGNFTSPIQN-KLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           Y     G   S ++   L LH+  +++   +    +  +  P   +
Sbjct: 270 Y-----GRVDSSLKKITLMLHSYKLEIDVGKNSFKKFISEFPKRFI 310


>gi|116333479|ref|YP_795006.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
 gi|116098826|gb|ABJ63975.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           brevis ATCC 367]
          Length = 307

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 88/338 (26%), Positives = 146/338 (43%), Gaps = 70/338 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+   +    ++    +  + +GQ+ VD   VK  ++ + G  +R+          + 
Sbjct: 13  RLDKLVADAVATVSRSQAKLAIEAGQITVDGATVKPKDKPKVGATIRV---------SLP 63

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH-- 128
           + + LD    LT     L+  ++YED+ + V NKP G+ V    G         + YH  
Sbjct: 64  DPEPLD----LTPEDIPLE--IVYEDADVLVVNKPQGMVVHPAPGHPNHTLVNALLYHSP 117

Query: 129 ---IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              I+G L+         P + HR+D++TSG+L+VA+   A Q L+   + +   + Y +
Sbjct: 118 LSQINGTLR---------PGIVHRIDKDTSGLLMVAKNDHAHQSLSAQLQAKTNLREYVA 168

Query: 186 LVWGIPKNKKECIANWL------LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +V G  K +   I   L       KK  I  D              A++HF+V++ +   
Sbjct: 169 IVHGNIKEEDGVIRAPLGRSPKDRKKQAIVAD-----------GRPAVTHFRVLERYG-T 216

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDL 297
           +  +  +  TGRTHQ+RVH  ++  P+ GD  Y      KG          +LHAR +  
Sbjct: 217 YTLIACRLETGRTHQIRVHMAYINHPVAGDPLYGPKKTLKGAGQ-------FLHARELGF 269

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL----GFKYDRNL 330
             P  G  L  TAP+P +  K    L    G   D+ +
Sbjct: 270 KQPTTGEELVFTAPVPENFAKAVRHLRQQAGLPVDKAI 307


>gi|330831468|ref|YP_004394420.1| ribosomal large subunit pseudouridine synthase D [Aeromonas veronii
           B565]
 gi|328806604|gb|AEB51803.1| Ribosomal large subunit pseudouridine synthase D [Aeromonas veronii
           B565]
          Length = 326

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 119/240 (49%), Gaps = 31/240 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK----GQKPR--LTHRLDQET 154
           ++YED  I V +KPAG+ V  G+G     DG + + +  +     + PR  + HRLD++T
Sbjct: 86  IVYEDEHILVIDKPAGLVVHPGAGTP---DGTILNALLHRYPGIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL E+ + R+I + Y ++  G           I     +++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVEALQARQITREYEAIAIGHMTAGGTVDAPIGRHPTQRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              VV         +++H++V + F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 ---VVPNGRP----SVTHYRVHEKF-RGHTRLRLRLETGRTHQIRVHMAHIKHPLVGDPA 252

Query: 272 YCANFKG--NFTSPIQ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           Y    +   N T  +       N+  LHA  + L HP  G  +Q  +  P  MV+  + L
Sbjct: 253 YGGRLRPLRNATPELTQALRNFNRQALHATMLQLAHPITGEVMQWHSATPQDMVELMEVL 312


>gi|215487933|ref|YP_002330364.1| 23S rRNA pseudouridine synthase D [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218690713|ref|YP_002398925.1| 23S rRNA pseudouridine synthase D [Escherichia coli ED1a]
 gi|312965509|ref|ZP_07779741.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           2362-75]
 gi|215266005|emb|CAS10416.1| 23S rRNA pseudouridine synthase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218428277|emb|CAR09055.1| 23S rRNA pseudouridine synthase [Escherichia coli ED1a]
 gi|281179642|dbj|BAI55972.1| putative pseudouridine synthase [Escherichia coli SE15]
 gi|312289929|gb|EFR17817.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           2362-75]
          Length = 326

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 90/339 (26%), Positives = 157/339 (46%), Gaps = 47/339 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V   
Sbjct: 9   ATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV--- 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             INA   I +E +     + L          ++YED  I V NKP  + V  G+G   +
Sbjct: 66  -AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + 
Sbjct: 111 PDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH +         A++H+++++ F + 
Sbjct: 171 YEAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPM------GKPAVTHYRIMEHF-RV 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
           A  + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 281 ATMLRLYHPISGIEMEWHAPIPQDMVELIEEMRADFEEH 319


>gi|261866897|ref|YP_003254819.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412229|gb|ACX81600.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 219

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 68/206 (33%), Positives = 107/206 (51%), Gaps = 16/206 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+Y D  I V NKP+G+    G+   Y+      S V  K       HRLD  TSGIL+ 
Sbjct: 16  LVYRDDYIAVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPAHRLDMATSGILLF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A +++A + L   FR R  +K Y +LVWG  + ++  +   L+       D+ +  +Q  
Sbjct: 74  ALSKSADRELKRQFREREPKKYYQALVWGYLEQEQGMVELPLI------CDWENRPRQKI 127

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+G   A++ + V+  +      +++ P TGR+HQLR+H L +G PI+GD K+ A+ +
Sbjct: 128 CFERGKR-AVTFYDVLQRYPNNTTRIKLTPITGRSHQLRLHMLALGHPILGD-KFYAHPQ 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
               SP   +L LHA  + + HP  G
Sbjct: 186 AKALSP---RLCLHAESLQIRHPITG 208


>gi|168179470|ref|ZP_02614134.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
 gi|182669738|gb|EDT81714.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
          Length = 300

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 81/283 (28%), Positives = 138/283 (48%), Gaps = 35/283 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K +R G+V V++++V   +++    ++ I   +    H    Q I    +N+      
Sbjct: 33  IRKAVRDGRVFVNEEKVIKKHKLSQDDLIEI--YMQEDEH----QNIEPEDMNIE----- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKP--RLTHRL 150
               ++YED+ I V NK  GI V    G   H  G L + +       G+K   RL  RL
Sbjct: 82  ----IVYEDNDIIVINKRPGIVVHPTKG---HPTGTLSNGILYHFKKNGEKSIVRLVSRL 134

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ + +   L         +KIY ++V G  K K++ I N  + K     
Sbjct: 135 DRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEKRI-NLPIYKEEESE 193

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +V  +E+G   +I+ +KV++  + K   + ++  TGRTHQ+RVH  H+G P+ GD 
Sbjct: 194 SIKRIV--DERGQE-SITTYKVLEELS-KGSVVRLELETGRTHQIRVHMSHLGHPLYGDS 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
            Y    KG        +  LHA  ++ PHP  G   +LQ + P
Sbjct: 250 LYG---KGEEEKEYIERQALHAYKLEFPHPRTGDILKLQCSLP 289


>gi|153006285|ref|YP_001380610.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152029858|gb|ABS27626.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 295

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 81/324 (25%), Positives = 128/324 (39%), Gaps = 52/324 (16%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  +    RLDRW       I     + ++ +G+ R+  K      R+  G+ V +    
Sbjct: 7   VPREAAGERLDRWLAGAL-AIPLDRARALVEAGRARIRGKTCAIQRRLFGGERVEV---- 61

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-------G 124
                        +      + +      +LY+D    V +KPAG++V+  S       G
Sbjct: 62  -------------ERPAPRAERASGPALTVLYDDPDCLVVSKPAGLAVEPSSPGAPSAVG 108

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            A  I  F    VD +   P L HRLD++T+G L++AR   A   L  +F  R ++K Y 
Sbjct: 109 AASRIGTF---DVDGR-AAPGLPHRLDRDTTGALLLARHDRALAALRAAFEGRAVEKEYL 164

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-----QK 239
            L  G P +           +  +   Y        +    A S  +    FA       
Sbjct: 165 VLAAGAPPD-----------RGALDTPYGRSAADPRRFTTRAPSPRRARLTFAVERRLTG 213

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L +   TGRTHQ+RV     G P++GD  Y         S    +  LHA  +  P 
Sbjct: 214 AALLRVVLDTGRTHQIRVQLAEAGFPVLGDAVY------GVASEAIARQALHAERLAFPR 267

Query: 300 P-EGGRLQITAPLPAHMVKTWDSL 322
           P +G R+++ APLP  + +  ++L
Sbjct: 268 PSDGARVEVRAPLPEDLARAIEAL 291


>gi|148977837|ref|ZP_01814392.1| ribosomal large subunit pseudouridine synthase A [Vibrionales
           bacterium SWAT-3]
 gi|145962906|gb|EDK28177.1| ribosomal large subunit pseudouridine synthase A [Vibrionales
           bacterium SWAT-3]
          Length = 244

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 109/209 (52%), Gaps = 19/209 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I V NKPAG+ SV G   +  H D      V+      ++ HRLD  TSG+++
Sbjct: 16  IVYQDDDILVVNKPAGLLSVPGR--LPEHHDSMWSRLVEEFADI-QVVHRLDMSTSGLML 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A +HL + F+ R   K+Y++ VWG  ++K+  I   L+       D+ +  KQ 
Sbjct: 73  LAKHKQAERHLKKQFQYRLTHKLYYARVWGAVEHKEGLIDLPLI------CDWPNRPKQK 126

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G +    +  V++    +   L++ P TGR+HQLRVH + +G PIVGD  Y    
Sbjct: 127 VCFEDGKSSQTRY--VVEQQEPQTTLLKLLPITGRSHQLRVHCMEIGAPIVGDEFYATPE 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              ++    ++L LHA  +   HP   +L
Sbjct: 185 AFEYS----DRLALHACELSFYHPANNQL 209


>gi|116073082|ref|ZP_01470344.1| putative pseudouridylate synthase [Synechococcus sp. RS9916]
 gi|116068387|gb|EAU74139.1| putative pseudouridylate synthase [Synechococcus sp. RS9916]
          Length = 210

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 68/213 (31%), Positives = 102/213 (47%), Gaps = 13/213 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL++D  + V +KPAG+  Q G G         +      G    L HRLD++TSG+L++
Sbjct: 9   LLHQDPWLLVVDKPAGLLSQPGLGPELRDSLITRLQRQEPGLA--LVHRLDRDTSGVLLL 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           ART  + + L+  F  RR+ K+Y + V   P     CI   L +       Y        
Sbjct: 67  ARTPESLRALSALFAARRVHKLYGADVCAPPPGLGGCIDVPLARLQRHPPRYGADPDGRA 126

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               + +S        + +  WL  QP TGR+HQLR H   +GCPI+GD  Y A+   + 
Sbjct: 127 CRTRWRLSGRDA----SSRRIWL--QPLTGRSHQLRAHLASLGCPILGDPIYAADQGRSA 180

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           T     +++LHA  + L HP  G RL+  + +P
Sbjct: 181 T----GRMHLHATALSLRHPFTGERLRCRSAMP 209


>gi|306520956|ref|ZP_07407303.1| putative pseudouridylate synthase [Clostridium difficile QCD-32g58]
          Length = 453

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 87/310 (28%), Positives = 145/310 (46%), Gaps = 45/310 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK--RVKFNNRIQSGQVVRIPPVINALNHI 77
           RLD +       ++   +QKI++ G+V+V+ K  + K+  + +   V+ IP         
Sbjct: 167 RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKAKYLVKEEDNIVIEIP--------- 217

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYH 128
             E K+L+         D    I+ YED  + + NKP  + V            +GI YH
Sbjct: 218 --EPKVLE-----VLPQDIPIDIV-YEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYH 269

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               L S   +   +P + HR+D++TSG+L++A+   A   L E  +   I + Y  + +
Sbjct: 270 CKDKLSSI--NGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICY 327

Query: 189 GIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           G+ K  K  +   + +  K  +    + VVK    G N AI+HF+V++ F  KF  +  +
Sbjct: 328 GVVKEDKITVDKPIGRNPKDRLK---MAVVKD---GKN-AITHFEVVERF-DKFTHMRAR 379

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVHAL +  P++GD  Y    +  F    Q    LHA+ +   HP     +
Sbjct: 380 LETGRTHQIRVHALSINHPLLGDFVYGPK-ETKFKLKGQT---LHAKKLGFIHPTTKEYI 435

Query: 306 QITAPLPAHM 315
           +  + LP + 
Sbjct: 436 EFNSELPEYF 445


>gi|251795436|ref|YP_003010167.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247543062|gb|ACT00081.1| pseudouridine synthase, RluA family [Paenibacillus sp. JDR-2]
          Length = 316

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 109/224 (48%), Gaps = 13/224 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPRL--THRLDQETSG 156
           +++ED  + V NKPAGI V    G       +G +  W   +G++ R    HRLD++TSG
Sbjct: 91  IVFEDDYLLVVNKPAGIIVHPTKGHYTNTLANGIVHHW-QVRGERVRFRPVHRLDEDTSG 149

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V+A+     Q L+E  +   I KIY + V+G P      +   + +       +V +V
Sbjct: 150 LVVIAKNPYIHQQLSEQLQAGTIMKIYCAYVYGTPSPADGTVGAPIDRNPE--DPHVRIV 207

Query: 217 KQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CA 274
                    +++H+K    F   +   + ++  TGRTHQ+RVH  H+GCP++GD  Y   
Sbjct: 208 TPE---GYPSVTHYKTAAVFGGGQASKVRLKLETGRTHQIRVHMKHIGCPLIGDGMYGLQ 264

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
             K +       +  LHA  + L HP      + TA LP  +V+
Sbjct: 265 TGKVDEWETAAGRQALHAETLGLTHPMTKEWSEWTAALPPDLVQ 308


>gi|16801023|ref|NP_471291.1| hypothetical protein lin1957 [Listeria innocua Clip11262]
 gi|16414458|emb|CAC97187.1| lin1957 [Listeria innocua Clip11262]
 gi|313618258|gb|EFR90322.1| ribosomal large subunit pseudouridine synthase D [Listeria innocua
           FSL S4-378]
          Length = 302

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 82/298 (27%), Positives = 138/298 (46%), Gaps = 43/298 (14%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +Q +L++G + V+ +  K N ++Q G  +R          I+ E   LD           
Sbjct: 32  IQLMLKNGDITVNGELAKPNYKVQVGDEIRYEAREPEELEILAEDIPLD----------- 80

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQKPRLT 147
               + +ED  + V NKP G+ V   +G A         +H D    S ++ K  +P + 
Sbjct: 81  ----IYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL--SGINGK-IRPGIV 133

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    + ++ 
Sbjct: 134 HRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPIGRAK 192

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                + VV+  ++    A +HF+VI+     +  +  +  TGRTHQ+RVH  ++G P+ 
Sbjct: 193 EDRQKMAVVRDGKE----ARTHFEVIERLP-GYTLINCKLDTGRTHQIRVHLKYIGHPLA 247

Query: 268 GDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           GD KY      KGN         +LHA  +   HP    R+   APLP    +   SL
Sbjct: 248 GDPKYGPKNTIKGNGQ-------FLHAAKLGFDHPTTNERMTFEAPLPDSFEQALKSL 298


>gi|298373557|ref|ZP_06983546.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroidetes oral taxon 274 str. F0058]
 gi|298274609|gb|EFI16161.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroidetes oral taxon 274 str. F0058]
          Length = 223

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 110/228 (48%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I   NK +   VQG       +   ++ ++  +  K       + HRLD+  S
Sbjct: 3   ILYEDNHIIAINKSSSDIVQGDKTGDKPLVDTVREYLKERYSKSGNVFCGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E  R   I+K YW++V   P+ ++  + ++L++       Y + 
Sbjct: 63  GVVLFAKTSKALARLNEMLRGHEIKKKYWAIVVKPPQEQEATLKHYLVRNEKQNKSYAYT 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  K +  A+ H+  I   ++++  LE+  HTGR HQ+R     +G  I GD KY   
Sbjct: 123 TEK--KDSKLAVLHYVTIGK-SERYTLLEVDLHTGRHHQIRCQLAAVGAVIKGDLKY--- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
             G   S     + LHAR ++  HP    L  ITAPLP    K W + 
Sbjct: 177 --GAPRSNPDGGISLHARSVEFVHPVRKELVVITAPLPTD--KLWTAF 220


>gi|91214528|ref|ZP_01251501.1| ribosomal large subunit pseudouridine synthase D [Psychroflexus
           torquis ATCC 700755]
 gi|91186955|gb|EAS73325.1| ribosomal large subunit pseudouridine synthase D [Psychroflexus
           torquis ATCC 700755]
          Length = 229

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 110/227 (48%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +++ED+ + V NK  G  VQG       +   +K ++  K  KP      + HRLD+ TS
Sbjct: 10  VIFEDNHLIVINKRPGDIVQGDKTGDLPLSEVVKLYLKEKYNKPGEAYLGVVHRLDRPTS 69

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ++T  A   L ++F  R   K+YW++V   PK +   + ++L + +     Y H 
Sbjct: 70  GVVVFSKTSKALSRLNKAFADRDTHKVYWAVVKNKPKPESARLVHYLKRNTKQNKSYAH- 128

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +K  E      +S+ K+       +  LE+   TGR HQ+R     +GCPI GD KY  +
Sbjct: 129 IKPVEDSKEAVLSYQKIQSL--DNYHVLEITLETGRHHQIRSQLSAIGCPIKGDLKYGFD 186

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
                 S     ++LH++ + + HP     +   A LP  ++  W+S
Sbjct: 187 RSNKNAS-----IHLHSKKLTITHPVRKEDISFEAKLPDDVI--WNS 226


>gi|332704325|ref|ZP_08424413.1| Dephospho-CoA kinase [Desulfovibrio africanus str. Walvis Bay]
 gi|332554474|gb|EGJ51518.1| Dephospho-CoA kinase [Desulfovibrio africanus str. Walvis Bay]
          Length = 556

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 68/216 (31%), Positives = 105/216 (48%), Gaps = 17/216 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LY D  + V NKPAG++           + + +            ++P + HRLD++TS
Sbjct: 90  VLYRDDWLLVLNKPAGLTTHPAPSCPEGTLVHRLLHHFPELAALDSERPGIVHRLDKDTS 149

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LVVA T  A   L E F  RR+ K+Y +LV G P+++ +         +H     + V
Sbjct: 150 GLLVVALTERARLALAEDFAERRVDKVYLALVHGRPQDRGDIDLPMGRHPTHK--TRMAV 207

Query: 216 VKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +K   KG   A S ++++      +F  L ++  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 208 LK---KGGRPARSAYEMLWSSRDGRFSLLRVRIFTGRTHQIRVHLAAIGHPIIGDSVYGP 264

Query: 275 N-FKG-----NFTSPIQNKLYLHARYMDLPHPEGGR 304
             F G      +   +  +  LHA  + L HP  GR
Sbjct: 265 GPFAGWDKDLPWARLLAKRQMLHAHRLRLAHPADGR 300


>gi|331084165|ref|ZP_08333271.1| hypothetical protein HMPREF0992_02195 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330402020|gb|EGG81593.1| hypothetical protein HMPREF0992_02195 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 224

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 59/180 (32%), Positives = 92/180 (51%), Gaps = 5/180 (2%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQET 154
           ++  +LYED  I V  KPAG  VQ        ++  L++++  KGQ+P +   HRLDQ  
Sbjct: 6   IEDTVLYEDKYILVCQKPAGFPVQSKRLGTLDMECALRNYLAKKGQEPYVAVIHRLDQPV 65

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G+LV A+ + +A  L++  +  + +K Y +   G    K+E + + L K    G +   
Sbjct: 66  QGVLVFAKDKESAAKLSKQMQQGKFEKTYLAYTQGHTDKKQETLIDELEKDG--GTNTSK 123

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV +    +  A   +KV+    ++   LE+   TGR HQ+RV   H G PI GD KY A
Sbjct: 124 VVAKKTANSKRAELSYKVLK-ETEEGSLLEVSLKTGRHHQIRVQLAHAGLPIFGDAKYNA 182


>gi|295133553|ref|YP_003584229.1| pseudouridylate synthase [Zunongwangia profunda SM-A87]
 gi|294981568|gb|ADF52033.1| pseudouridylate synthase [Zunongwangia profunda SM-A87]
          Length = 235

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 101/205 (49%), Gaps = 13/205 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ I + NK  G  VQG       +   +K+++  K  KP      + HRLD+ TS
Sbjct: 14  VLHEDNHIIIVNKRVGDIVQGDKTGDKPLSEVVKAYLKEKHNKPGNVYLGVVHRLDRPTS 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ ++T  A   L + F+ +  +K YW++V   P   ++ + ++L +       + H 
Sbjct: 74  GIVLFSKTSKALPRLNKLFQQKDAKKTYWAVVKNRPPKDQDILVHYLKRNPKQNKSFAH- 132

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K     +  AI  ++++      F  LE+   TGR HQ+R     +GCPI GD KY  +
Sbjct: 133 -KNEVPDSKKAILEYRILKELDNYFL-LEVDLKTGRHHQIRSQLSAIGCPIKGDLKYGFD 190

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
              N        ++LHAR ++  HP
Sbjct: 191 RSNNDAG-----IHLHARKLEFIHP 210


>gi|225868421|ref|YP_002744369.1| RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
 gi|225701697|emb|CAW99033.1| putative RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
          Length = 296

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 120/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++Y+D  + + NKP G+ V   +G         + YH+    K      G  +P + HR+
Sbjct: 76  IVYQDDVLAIINKPQGMVVHPSAGHSTGTLVNALLYHV----KDLSSINGVIRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIG 209
           D++TSG+L+VA+T  A Q L +  + ++  + Y ++V G +PK++        + ++ IG
Sbjct: 132 DKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHGNLPKDRG-------VIEAPIG 184

Query: 210 GDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  KQ    KG   A++ FKV++ F  ++  +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 185 RSDKDRKKQTVTAKGKE-ALTRFKVLERFG-RYSLVELQLETGRTHQIRVHMAYIGHPLA 242

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GD  Y     G   +   N  +LHA+ + L HP  G  L  T   P    +T + L
Sbjct: 243 GDPLY-----GPRKTLAGNGQFLHAQTLGLTHPVTGEELVFTVEPPEIFQRTLEQL 293


>gi|87119407|ref|ZP_01075304.1| ribosomal large subunit pseudouridine synthase D [Marinomonas sp.
           MED121]
 gi|86164883|gb|EAQ66151.1| ribosomal large subunit pseudouridine synthase D [Marinomonas sp.
           MED121]
          Length = 322

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 76/297 (25%), Positives = 131/297 (44%), Gaps = 66/297 (22%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +Q  ++ G + VD K+ K   ++  G+V+ +  ++  ++    E   LD           
Sbjct: 36  IQAWIKEGVLLVDGKKSKAKEKLFVGEVISLETLVEDIDDHQPEDIPLD----------- 84

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRL 150
               ++YED  I V NKP+G+ V    G   H  G L + +          PR  + HRL
Sbjct: 85  ----IVYEDEDILVVNKPSGLVVHPAVG---HRSGTLMNAILFHCPESAHVPRAGIVHRL 137

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--------------PKNKKE 196
           D+ET+G++VVA+T AA   L    + R + + Y ++  GI              P+N+++
Sbjct: 138 DKETTGLMVVAKTLAAQTELVSQLQDRSMGREYEAVAIGIMTGGGTVNEPIGRHPQNRQK 197

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                L  K                    A++H++++  F +    + ++  TGRTHQ+R
Sbjct: 198 MAVEPLNGKD-------------------AVTHYRLLQRF-KNHTHIRLKLETGRTHQIR 237

Query: 257 VHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDLPHPEGGRL 305
           VH  H+  P++GD +Y    K            +QN  +  LHA+ ++L HP  G  
Sbjct: 238 VHMSHIQFPLLGDPQYAGRMKMPKACIPELRDELQNFRRQALHAKRLELSHPITGEF 294


>gi|311087296|gb|ADP67376.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. JF99 (Acyrthosiphon pisum)]
          Length = 312

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 90/308 (29%), Positives = 147/308 (47%), Gaps = 39/308 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD      +   +   L+K++   QV V++  V + + +I  G+++ I P    L   I
Sbjct: 19  RLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKILGGEILTIHPFSKDLLVDI 78

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
            E   LD               ++YEDS I + NKPAG+ V  GSG      ++  L  +
Sbjct: 79  PENIFLD---------------IVYEDSDILIINKPAGLVVHPGSGNKSGTILNALLYHY 123

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +S+   PR  + HRLD++TSG++V+A+   +  HL    + ++I + Y  +V G     
Sbjct: 124 KNSR-DLPRAGIVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGIVHG----- 177

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTH 253
            + IA   + K  +                 +++H+KV+  F  KF   + ++  TGRTH
Sbjct: 178 -KMIAGGTINKPIMRHYNRRTCMMVHHLGKPSVTHYKVLSRF--KFHTHIAIRLETGRTH 234

Query: 254 QLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQ-NKLY------LHARYMDLPHP-EGGR 304
           Q+RVH LH+  P+VGD  Y     + N+    + NK+Y      LHA ++ L HP +   
Sbjct: 235 QIRVHMLHIKYPLVGDPCYSGFKIQSNYRKDKKTNKIYKFPRQALHANHLSLHHPIKKNV 294

Query: 305 LQITAPLP 312
           +  T PLP
Sbjct: 295 MSWTVPLP 302


>gi|148827314|ref|YP_001292067.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae PittGG]
 gi|148718556|gb|ABQ99683.1| SfhB [Haemophilus influenzae PittGG]
          Length = 324

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 121/249 (48%), Gaps = 41/249 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPR--LTHR 149
           ++YED  I V NKP  + V  G+G         + YH             + PR  + HR
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI--------AEVPRAGIVHR 136

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKS 206
           LD++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++
Sbjct: 137 LDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRT 196

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +    VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P+
Sbjct: 197 LMA---VHPMGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPL 246

Query: 267 VGDHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           +GD  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+
Sbjct: 247 LGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLSHPITGEMMEWYAPLPDDFVE 306

Query: 318 TWDSLGFKY 326
             ++L   Y
Sbjct: 307 LLNALKADY 315


>gi|78356492|ref|YP_387941.1| pseudouridine synthase, RluD [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
 gi|78218897|gb|ABB38246.1| dephospho-CoA kinase / ribosomal large subunit pseudouridine
           synthase D [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
          Length = 578

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 74/247 (29%), Positives = 115/247 (46%), Gaps = 26/247 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LY D+ + V NKPAG++V          + + +          +G +P + HR+D++TS
Sbjct: 121 VLYRDAHMLVINKPAGLTVHPAPSCPEGTLVHRLLHHFPELEAQEGFRPGIVHRIDKDTS 180

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A T  A   L+++F  RRI K Y +LV GIP+     I       + +G    H 
Sbjct: 181 GLLLIALTEKARLALSDAFAGRRIHKEYLALVKGIPEGDSGEI------DAPVGRHPTHK 234

Query: 216 VKQN-EKGANYAISHFKVI-----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +    +G   A+S ++V+           +  + ++ HTGRTHQ+RVH  H G P+ GD
Sbjct: 235 TRMAVVRGGREALSTWRVLLADPHGGGGTGWTLVAVRIHTGRTHQIRVHMQHTGHPLWGD 294

Query: 270 HKYCANFKGNF---TSP----IQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
             Y     G     T+P       +  LHA  +   HP  G  +Q T P PA        
Sbjct: 295 ALY-GGMPGREELQTTPALAQTATRQMLHAWKISFDHPVTGAPMQFTLPPPADFGTLIRD 353

Query: 322 LGFKYDR 328
           LG +  R
Sbjct: 354 LGSRCQR 360


>gi|223889096|ref|ZP_03623685.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 64b]
 gi|223885345|gb|EEF56446.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 64b]
          Length = 322

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 55/181 (30%), Positives = 98/181 (54%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 86  IIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +R  K+Y ++V G   +    I +++ +  H    
Sbjct: 145 KDTSGVLICAKNISTLRFLAQQFKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 205 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 259

Query: 272 Y 272
           Y
Sbjct: 260 Y 260


>gi|167464425|ref|ZP_02329514.1| YlyB [Paenibacillus larvae subsp. larvae BRL-230010]
 gi|322384100|ref|ZP_08057818.1| pseudouridylate synthase-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
 gi|321151180|gb|EFX44489.1| pseudouridylate synthase-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
          Length = 311

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 85/316 (26%), Positives = 144/316 (45%), Gaps = 44/316 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D++       ++   +Q+ ++ G + V++K+VK N ++  G  ++       LN    
Sbjct: 24  RIDKFVSECLDGVSRTQIQQWIKEGHISVNEKQVKPNYKLAEGDRIK-------LNIPDP 76

Query: 80  EQ-KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV- 137
           EQ  I    + L          + YED  + V NKP G+ V    G   H  G L + + 
Sbjct: 77  EQVDIRPEPIPLD---------IYYEDKDVIVVNKPRGMVVHPAPG---HSSGTLVNALM 124

Query: 138 ----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D  G     +P + HR+D++TSG+++ A+   A   L +  +   + + Y +LV G
Sbjct: 125 YHCKDLSGINGEMRPGIVHRIDKDTSGLIMAAKHDKAHASLADQLKEHSVTRKYLALVQG 184

Query: 190 IPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
              +++  +      ++ IG D     +    EK +  A++HF V++ F   +   E++ 
Sbjct: 185 NLAHEQGTV------EAPIGRDPKDRKLYTVTEKNSKEAVTHFVVMERFGD-YTLTELKL 237

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH   +G P+VGD  Y  + K            LHA  +   HP     L+
Sbjct: 238 ETGRTHQIRVHMKFIGHPLVGDPAYGKSKKEWIRGQA-----LHAAVLGFKHPMTREYLE 292

Query: 307 ITAPLPAHMVKTWDSL 322
             APLP  M +   SL
Sbjct: 293 FEAPLPEDMKQLIHSL 308


>gi|302874505|ref|YP_003843138.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
 gi|307690886|ref|ZP_07633332.1| pseudouridine synthase, RluA family protein [Clostridium
           cellulovorans 743B]
 gi|302577362|gb|ADL51374.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
          Length = 321

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 82/279 (29%), Positives = 129/279 (46%), Gaps = 37/279 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E+  R D++ +     +    L K  R G +RV+ K+VK N  +Q G VV    
Sbjct: 3   ITIGTNEQGQRTDKFVRKWLQDLPLSALYKAFRKGDIRVNGKKVKENYFLQEGDVVETSK 62

Query: 70  VINAL-NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIA 126
            + A     +  QKI +  + +T           +ED  I +  K  G+ V     +G  
Sbjct: 63  YVQASPKKELNFQKIENVHLKIT-----------FEDENILLVEKWPGVLVHADKKNGDP 111

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
              D ++ S++  KG           P   +RLD+ TSGI++  +T    + L E  R R
Sbjct: 112 TLTD-YVLSYLHDKGDYLPENEVTFTPASCNRLDRNTSGIVIFGKTFEGLKALNEMVRDR 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYA-IS-HFKVI 233
           RIQK Y +LV G  K+ +          ++I  D    + +  NE GA+   IS   K +
Sbjct: 171 RIQKYYMALVQGKLKDGRY--------DAYISKDESQNLSKIYNEGGADRKKISMEVKTL 222

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +     +  L+++  TGR+HQLR H  H+G PIVGD KY
Sbjct: 223 ETVGS-YSLLDIELITGRSHQLRAHLSHLGNPIVGDSKY 260


>gi|157373960|ref|YP_001472560.1| pseudouridylate synthase [Shewanella sediminis HAW-EB3]
 gi|157316334|gb|ABV35432.1| pseudouridylate synthase [Shewanella sediminis HAW-EB3]
          Length = 225

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 64/205 (31%), Positives = 106/205 (51%), Gaps = 15/205 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NKP+G+    G   A+    F +  V ++    ++ HRLD  TSG++VV
Sbjct: 16  IIYQDKDILVVNKPSGLLSVPGRDPAHSDSIFTR--VLAEHPNAQIVHRLDMATSGVIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A  ++A + L   FR R  +K Y++ V G  K     +   L+       D+ +  KQ  
Sbjct: 74  ALRKSAERELKRQFRDRETKKTYYARVAGHVKADNGSVDLPLI------CDWPNRPKQKV 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      +++HF+VI   A++   +++ P TGR+HQLRVH + +G PI+GD+ Y      
Sbjct: 128 DHDIGKASLTHFEVI-SRAKRSTLVKLTPITGRSHQLRVHMMAVGHPILGDNFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
              S    +L LHA+ + +  P  G
Sbjct: 187 RLAS----RLLLHAQELTIKQPYSG 207


>gi|15617005|ref|NP_240218.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. APS (Acyrthosiphon pisum)]
 gi|219681757|ref|YP_002468143.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. 5A (Acyrthosiphon pisum)]
 gi|257471459|ref|ZP_05635458.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. LSR1 (Acyrthosiphon pisum)]
 gi|11387080|sp|P57481|RLUD_BUCAI RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|25322332|pir||H84976 pseudouridylate synthase (EC 4.2.1.70) [imported] - Buchnera sp.
           (strain APS)
 gi|10039070|dbj|BAB13104.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. APS (Acyrthosiphon pisum)]
 gi|219624600|gb|ACL30755.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. 5A (Acyrthosiphon pisum)]
          Length = 312

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 91/308 (29%), Positives = 146/308 (47%), Gaps = 39/308 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD      +   +   L+K++   QV V++  V + + +I  G+ + I P    L   I
Sbjct: 19  RLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKILGGETLTIHPFSKDLLVDI 78

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
            E   LD               ++YEDS I + NKPAG+ V  GSG      ++  L  +
Sbjct: 79  PENIFLD---------------IVYEDSDILIINKPAGLVVHPGSGNKSGTILNALLYHY 123

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +SK   PR  + HRLD++TSG++V+A+   +  HL    + ++I + Y  +V G     
Sbjct: 124 KNSK-DLPRAGIVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGIVHG----- 177

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTH 253
            + IA   + K  +                 +++H+KV+  F  KF   + ++  TGRTH
Sbjct: 178 -KMIAGGTINKPIMRHYNRRTCMMVHHLGKPSVTHYKVLSRF--KFHTHIAIRLETGRTH 234

Query: 254 QLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQ-NKLY------LHARYMDLPHP-EGGR 304
           Q+RVH LH+  P+VGD  Y     + N+    + NK+Y      LHA ++ L HP +   
Sbjct: 235 QIRVHMLHIKYPLVGDPCYSGFKIQSNYRKDKKTNKIYKFPRQALHANHLSLHHPIKKNV 294

Query: 305 LQITAPLP 312
           +  T PLP
Sbjct: 295 MSWTVPLP 302


>gi|104780626|ref|YP_607124.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           entomophila L48]
 gi|95109613|emb|CAK14314.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           entomophila L48]
          Length = 211

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 71/214 (33%), Positives = 111/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED+ I V NKP  + SV G +    + D  +    ++      + HRLD ETSGI++
Sbjct: 8   ILHEDAAILVINKPTLLLSVPGRA--EDNKDCLITRLQENGYPDALIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADSHRELSRQFHDRETEKAYTALCWGQPALDSGSID--LPLRYDPPTKPRHVV-DH 122

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E+G  +A++ +++++     +C +E+ P TGR+HQLRVH L +G P++GD  Y AN +  
Sbjct: 123 EQG-KHALTFWRIVE-RCGDYCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY-ANPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL+   P P
Sbjct: 180 AA---HERLCLHASMLSFTHPVSGERLKFECPAP 210


>gi|15594364|ref|NP_212152.1| hypothetical protein BB0018 [Borrelia burgdorferi B31]
 gi|2687903|gb|AAC66413.1| conserved hypothetical protein [Borrelia burgdorferi B31]
          Length = 336

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 55/181 (30%), Positives = 98/181 (54%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 96  IIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 154

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +R  K+Y ++V G   +    I +++ +  H    
Sbjct: 155 KDTSGVLICAKNISTLRFLAQQFKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 214

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 215 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 269

Query: 272 Y 272
           Y
Sbjct: 270 Y 270


>gi|310658221|ref|YP_003935942.1| pseudouridylate synthase [Clostridium sticklandii DSM 519]
 gi|308824999|emb|CBH21037.1| putative pseudouridylate synthase [Clostridium sticklandii]
          Length = 223

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 111/226 (49%), Gaps = 17/226 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V  KP G+  Q        +  ++K++V  K  KP      L HRLD+ + 
Sbjct: 5   VIYEDNHIIVVVKPFGMPSQEDDSKDLDMLSWVKAYVKEKYNKPGEVFIGLVHRLDRVSG 64

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ART  AA  L++  R ++I+K Y  +  G  + K   + ++LLK      + V  
Sbjct: 65  GLMVFARTSKAASRLSDQIRKKQIEKKYTLVAEGSLEKKSGFMEDFLLKDK--SNNKVKA 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K   K +  A   ++V+D   Q    + +   TGR+HQ+RV      CP+ GD KY + 
Sbjct: 123 FKNEVKDSKDAKLSYEVMDE-RQGLSLVSVDLITGRSHQIRVQFSSRRCPLYGDLKYGS- 180

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
                ++P +  + L + Y+   HP +  +L+    LP H  K WD
Sbjct: 181 -----SNPQKKSIALWSYYLSFEHPTKKEKLEFKIELPDH--KPWD 219


>gi|253569722|ref|ZP_04847131.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           1_1_6]
 gi|251840103|gb|EES68185.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           1_1_6]
          Length = 549

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 68/218 (31%), Positives = 112/218 (51%), Gaps = 37/218 (16%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGIL 158
           +++ED  + V NKP+G +SV G       +   +K+ + ++ G  P + HRLD  TSG+L
Sbjct: 343 IVFEDEWLVVVNKPSGMLSVPGKEEETDSVYHRVKAKYPEATG--PMIVHRLDMATSGLL 400

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKE--------CIANWLLKKSHI 208
           +VA+T+   QHL E F  R I+K Y +L+   G+ +  +E        C+      +  +
Sbjct: 401 LVAKTKEVHQHLQEQFINRSIKKRYVALLDRNGLNQQLEETGTINLPLCLNPLDRPRQMV 460

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCP 265
             +Y             A++ +++++  + K+  + + P TGRTHQLRVHA H   + CP
Sbjct: 461 SEEY----------GKPAVTEYRILNN-SDKYIRIALYPLTGRTHQLRVHAAHHQGLNCP 509

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           I+GD  Y             ++LYLHA Y++  HP  G
Sbjct: 510 ILGDELYGKK---------ADRLYLHAEYIEFRHPVYG 538


>gi|255556673|ref|XP_002519370.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223541437|gb|EEF42987.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 399

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 85/302 (28%), Positives = 134/302 (44%), Gaps = 61/302 (20%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           VV      +RLD W  +    I+   +Q  ++SG V V+ + V K ++ ++ G   ++  
Sbjct: 64  VVHAKSVKLRLDSWISSRISGISRARVQSSIKSGLVSVNGRVVDKVSHNVKFGD--KVTC 121

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
            I+ L  +  E + +   +             +YED  + V NKP  + V          
Sbjct: 122 TISELQPLRAEPEDMPLDI-------------VYEDEHLLVVNKPPHMVVHPAPGNPTGT 168

Query: 123 --SGIAYHI--------------DGFLKSWVDSKGQ--------KPRLTHRLDQETSGIL 158
             +GI +H               D   +S  D +          +P + HRLD+ TSG+L
Sbjct: 169 LVNGILHHCNLPTVAISSQEVLSDAEDRSDDDERSYSSSCESSIRPGIVHRLDKGTSGLL 228

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-------ANWLLKKSHIGGD 211
           VVA+   A  HL+E F+   IQ++Y SL  G+P      I        N  ++ + I G 
Sbjct: 229 VVAKDEHAHAHLSEQFKQHTIQRVYISLTSGVPSALTGRIDIPIGRDVNNRIRMTAIPGP 288

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +KQ    A +A S FKV++  A     L E +  TGRTHQ+R HA ++G P++GD 
Sbjct: 289 ----IKQGR--ARHAASRFKVVETLAGGGSALVEWRLETGRTHQIRAHAKYIGIPLLGDE 342

Query: 271 KY 272
            Y
Sbjct: 343 VY 344


>gi|329919667|ref|ZP_08276645.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
 gi|328937319|gb|EGG33743.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
          Length = 292

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 75/280 (26%), Positives = 131/280 (46%), Gaps = 37/280 (13%)

Query: 6   YVQYVVVENDEENMRLDRWFKN-----HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           Y+ Y+ +  +E N  +D+  +N      + H  F+ ++K      + V+ K +  N ++ 
Sbjct: 13  YIYYLTISQNENNQNVDQIMRNLLIPRKWRH--FLRIEK-----NILVNDKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V NKPAG   Q
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENDDVLVINKPAG---Q 109

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L    +  G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 110 KTHPNLYETDTALNDCANYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQ 238
           + Y++ +            N       IG D + + K+   E G   AI+H++V+   A 
Sbjct: 170 RSYFAWIEATNDISDNGTINL-----PIGDDPLDMRKRMVREDGLK-AITHYQVVKKTAN 223

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           K   +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++ 
Sbjct: 224 KIL-VKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQA 262


>gi|323143516|ref|ZP_08078196.1| pseudouridine synthase A [Succinatimonas hippei YIT 12066]
 gi|322416710|gb|EFY07364.1| pseudouridine synthase A [Succinatimonas hippei YIT 12066]
          Length = 242

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 75/214 (35%), Positives = 108/214 (50%), Gaps = 15/214 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  I V NKP+G+ SV G   +  H D  L S + S        HRLD  TSG+LV
Sbjct: 17  VLYEDDDIMVVNKPSGLLSVPGR--LKEHHDSIL-SRIKSSYPDAFAVHRLDMGTSGVLV 73

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           V   + A  +L + F  R ++KIY ++V GI +         +L  ++         K +
Sbjct: 74  VGLNKNAVSNLGKQFMGREVKKIYIAIVDGIIEKSGSVSLPLILDINN-----RPYQKVD 128

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +    A++ ++ + C   K   + + P TGR+HQLRVH   +G PI+GDH Y A  +  
Sbjct: 129 FEVGKPALTFYEPL-CHDGKTTLVRLFPLTGRSHQLRVHLKEIGHPILGDHLY-APPEIR 186

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             SP    LYLHA  +   HP  G R++  AP P
Sbjct: 187 DASP---HLYLHAGCLSFCHPVSGNRMEFCAPPP 217


>gi|262275057|ref|ZP_06052868.1| ribosomal large subunit pseudouridine synthase A [Grimontia
           hollisae CIP 101886]
 gi|262221620|gb|EEY72934.1| ribosomal large subunit pseudouridine synthase A [Grimontia
           hollisae CIP 101886]
          Length = 240

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 113/238 (47%), Gaps = 29/238 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           ++Y+D  I   NKP+G+    G   A+    +  +W   K + P   L HRLD  TSG++
Sbjct: 16  VIYQDDDIIAINKPSGLLTNPGRDPAH----YDSAWSRIKAEYPDAELVHRLDMSTSGLI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYV 213
           V A+ + A +HL   FR R   K+Y++ VWG  + +K       I +W  +         
Sbjct: 72  VFAKHKEAERHLKAQFRERVTHKLYYARVWGHVEQEKGRVDLPLICDWPNRPKQ------ 125

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            V  +N K    +++ ++VI    +K   + + P TGR+HQLRVH L +  PIVGD  Y 
Sbjct: 126 KVCFENGKP---SVTDYEVIK-REKKTTLVRLLPITGRSHQLRVHMLALDHPIVGDEFYA 181

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL---GFKYD 327
                 ++     +L LHA  +   HP  G  + + AP   +     D+L   G K D
Sbjct: 182 PPQAQKYSP----RLQLHAGELCFLHPGSGDPMHLAAPCDFYRQAPGDTLVQRGIKAD 235


>gi|301632247|ref|XP_002945202.1| PREDICTED: ribosomal large subunit pseudouridine synthase D-like
           [Xenopus (Silurana) tropicalis]
          Length = 341

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 136/321 (42%), Gaps = 39/321 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V   +  +RLD+      P ++   LQ++L  G V +D            G   R
Sbjct: 26  VRSLFVGPGQHGLRLDKALAELVPELSRSYLQQLLAQGLVCLD------------GAASR 73

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL-----YEDSKIYVFNKPAGISVQG 121
            P       H +K    L   +  T+ S   K   +     +ED+ + V NKPAG+ V  
Sbjct: 74  KP------AHKVKAGDALVVEIRPTQQSQAFKPEPVPVPVVFEDAHLLVVNKPAGLVVHP 127

Query: 122 GSGIAYHIDGFLKSWVDSKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G   H  G L + +  +  K    PR  + HRLD++TSG++VVAR R     L     
Sbjct: 128 APG---HWSGTLLNGLMGRDPKAMLLPRAGIVHRLDKDTSGLMVVARERTTMDALVRLIA 184

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R++++ Y +L   + +       +  L +       + VV   +     A + F+ +  
Sbjct: 185 QRQVRRQYLALGHCVWRGGGLRTVDAALGRDPRNRLRMAVVDLAQHAGKPARTDFEYL-A 243

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                C +    HTGRTHQ+RVH L MG P+V D  Y  +           +  LHA  +
Sbjct: 244 GNDLGCLVRCTLHTGRTHQIRVHMLSMGHPLVADVLYGGSAAAGLA-----RQALHADRL 298

Query: 296 DLPHPEGGR-LQITAPLPAHM 315
              HP  G+ L+  APLP  M
Sbjct: 299 AFVHPVTGQALEFHAPLPEDM 319


>gi|227548930|ref|ZP_03978979.1| pseudouridine synthase [Corynebacterium lipophiloflavum DSM 44291]
 gi|227078955|gb|EEI16918.1| pseudouridine synthase [Corynebacterium lipophiloflavum DSM 44291]
          Length = 308

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 75/314 (23%), Positives = 148/314 (47%), Gaps = 30/314 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E MR+D+     +  ++     +++  G V +D  RV  ++R++SG ++ +         
Sbjct: 15  EGMRVDQAVSKLF-GLSRSVAAELVAEGSVLIDASRVAKSDRVRSGALLEV--------- 64

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-----GSGIAYHIDG 131
            + E +   +     +  D L   ++Y D  +   +KP G++        G  +   +  
Sbjct: 65  TLPEPR--QAPAPKAELVDGLS--IIYSDDDVIAVDKPVGVAAHPTLGWEGPTVVGGLTA 120

Query: 132 FLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +  D+   ++  +  RLD  TSG++VVA +      L  +F+ R + K+Y ++V G+
Sbjct: 121 MGFTLPDAGPPERKGIVQRLDVGTSGVMVVANSVQGYSVLKRAFKERTVSKLYHAVVQGL 180

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +  H    +   V  + +   +A++H+++++ F ++   LE++  TG
Sbjct: 181 PDPIAGTIDAPIGR--HPSSGWKFAVTSDGR---HAVTHYELVEAF-REASLLEIRLETG 234

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR-LQIT 308
           RTHQ+RVH   +G P VGD  Y +N   N T  +   + +LHA  +   HP  G  +++ 
Sbjct: 235 RTHQIRVHMSAVGHPCVGDPMYGSNP--NLTMRVGLVRQWLHATKLGFTHPRTGDYMEVE 292

Query: 309 APLPAHMVKTWDSL 322
           +P PA +    + L
Sbjct: 293 SPYPADLAHALEVL 306


>gi|239917851|ref|YP_002957409.1| ribosomal large subunit pseudouridine synthase D [Micrococcus
           luteus NCTC 2665]
 gi|239839058|gb|ACS30855.1| ribosomal large subunit pseudouridine synthase D [Micrococcus
           luteus NCTC 2665]
          Length = 320

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 114/229 (49%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LYED  +   +KP G++     G +   + G L +    + + G   R  + HRLD  T
Sbjct: 94  ILYEDDDLVAVDKPTGVAAHPSPGWVGPTVVGALAALGYDITTSGAPERQGIVHRLDVGT 153

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++VVA+T  A   + + FR R  +K+Y ++V GIP      +   + +  H G  +  
Sbjct: 154 TGVMVVAKTERAYTAMKDQFRERVPEKVYHAVVQGIPDPLSGTVDAPIGR--HPGHHWKF 211

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  + +    +++H++ ++ F  +   LE+   TGRTHQ+RVH   +  P VGD  Y A
Sbjct: 212 AVLDDGR---PSVTHYETLEVFG-RGTLLEVHLETGRTHQIRVHTSALRHPCVGDLTYGA 267

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + +      +  + +LHA  +  PHP  G  + IT+P P  +     +L
Sbjct: 268 DPRLAAELGLTRQ-WLHAHRLAFPHPVTGEPVTITSPYPDDLAHALAAL 315


>gi|313890421|ref|ZP_07824052.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
 gi|313121264|gb|EFR44372.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
          Length = 296

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 62/203 (30%), Positives = 94/203 (46%), Gaps = 22/203 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           LY+DS + V NKP G+   G       +  H+  F+       GQ   + HRLD ETSG 
Sbjct: 92  LYQDSHLIVVNKPEGMKTHGNEPNELALLNHVSAFV-------GQTCYIIHRLDMETSGA 144

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       +      R I + YW+L+ G+ +NK   I   + +  H     V  +K
Sbjct: 145 IIFAKNPFILPIMNRLLEDREIGRNYWALIDGVIENKDTAIQFPIGRHRHDRRKRVVDLK 204

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             +K    AI+  K +  + Q+   ++    TGRTHQ+RVH  ++G PI+GD  YC    
Sbjct: 205 HGQK----AITQVKCLKRYRQQLSLVDCSLKTGRTHQIRVHLSYIGHPIIGDPLYCQR-- 258

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
                    +L LHA  +   HP
Sbjct: 259 -----TTTQRLMLHAHQLYFKHP 276


>gi|71278616|ref|YP_271168.1| ribosomal large subunit pseudouridine synthase A [Colwellia
           psychrerythraea 34H]
 gi|71144356|gb|AAZ24829.1| ribosomal large subunit pseudouridine synthase A [Colwellia
           psychrerythraea 34H]
          Length = 227

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 111/220 (50%), Gaps = 21/220 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I V NK +GI SV G   +  H D  L++ V        + HRLD  TSGI++
Sbjct: 19  IIYQDDDIVVLNKASGILSVPGR--LPEHQD-CLQNRVQRVLPTATIVHRLDMATSGIMI 75

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +A  + A   ++  F  R+ QK Y + VWG+ +  +  +   L+       D+ +  KQ 
Sbjct: 76  MALNKPAHVAISRQFEQRKTQKSYLARVWGLVELNEGSVDLPLI------SDWPNRPKQK 129

Query: 219 -NEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + +    +++H++V+        Q    LE+ P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 130 VDHENGKKSLTHYRVLSHNDSIDEQANTLLELTPITGRSHQLRVHMLALGHPILGDRLYA 189

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                     ++N+L LHA  + L HP   + +   AP P
Sbjct: 190 PEEALT----MRNRLQLHALKLSLFHPRTEQAITFDAPCP 225


>gi|238782665|ref|ZP_04626695.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           bercovieri ATCC 43970]
 gi|238716325|gb|EEQ08307.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           bercovieri ATCC 43970]
          Length = 217

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/205 (35%), Positives = 109/205 (53%), Gaps = 18/205 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  + + + +        HRLD  TSG+++
Sbjct: 14  ILYQDQHIMVVNKPSGLLSVPGRA--PEHKDSVM-TRIQADYPTAESVHRLDMATSGVII 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPKKTYIARVWGHLAQDEGLIDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + A + ++V+   A     +++ P TGR+HQLRVH L MG PI+GD  Y A+ 
Sbjct: 125 VCYETGKS-AQTEYQVLSRDADGSTRVKLSPITGRSHQLRVHMLAMGHPILGDGFY-AHP 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPE 301
           +    +P   +L LHA+ + + HPE
Sbjct: 183 EAKAMAP---RLQLHAQELCITHPE 204


>gi|326568269|gb|EGE18351.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis BC8]
          Length = 242

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 119/229 (51%), Gaps = 23/229 (10%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +F KSI +YED  I+V +KPAG+    G  +       L+S +       RL HRLD +T
Sbjct: 25  EFAKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPNIRLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDY 212
           SG+++ A++  A  H+++ F  R  QK Y ++V+G  +  +KK  +   +  +      +
Sbjct: 81  SGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVPVRYEPTTKPRH 140

Query: 213 VHVVKQNEKGANYAISHFKVI--------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +  +  N++    A++H++V+        +  A     + ++P TGR+HQLRVH +H+G 
Sbjct: 141 IVDMDWNKQ----ALTHYEVMHHELRCDDNGRAYPVTRVALKPITGRSHQLRVHMVHLGH 196

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            ++GD  Y  +     +    N+L LHA  + L HP  G  +   +P+P
Sbjct: 197 VMIGDPIYAEDVALKLS----NRLNLHAHKLRLKHPTHGIWMDWVSPVP 241


>gi|326559332|gb|EGE09759.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis 7169]
 gi|326569969|gb|EGE20016.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis BC1]
          Length = 242

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 66/219 (30%), Positives = 114/219 (52%), Gaps = 22/219 (10%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +F KSI +YED  I+V +KPAG+    G  +       L+S +       RL HRLD +T
Sbjct: 25  EFAKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPNIRLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDY 212
           SG+++ A++  A  H+++ F  R  QK Y ++V+G  +  +KK  +   +  +      +
Sbjct: 81  SGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVPVRYEPTTKPRH 140

Query: 213 VHVVKQNEKGANYAISHFKVI--------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +  +  N++    A++H++V+        +  A     + ++P TGR+HQLRVH +H+G 
Sbjct: 141 IVDMDWNKR----ALTHYEVMHHELRCDDNGRAYPVTRVALKPITGRSHQLRVHMVHLGH 196

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++GD  Y  +     +    N+L LHA  + L HP  G
Sbjct: 197 VMIGDPIYAEDVALKLS----NRLNLHAHKLRLKHPTHG 231


>gi|170725279|ref|YP_001759305.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169810626|gb|ACA85210.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 225

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 70/232 (30%), Positives = 112/232 (48%), Gaps = 29/232 (12%)

Query: 94  SDFLKSI-------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           SDF+ S        ++Y+D  I V NKP+G+    G   A+    + +   +    +  +
Sbjct: 2   SDFIYSPPTTPWLEIIYQDKDILVVNKPSGLLSVPGRDPAHRDSIYARVLAEYPNAQ--V 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-----IPKNKKECIANW 201
            HRLD  TSGI+V+A  R A + L   FR R  +K Y++ V G       K +   I +W
Sbjct: 60  VHRLDMATSGIIVLALRRNAEKELKRQFRERETKKTYYARVAGHIRSDSGKVELPLICDW 119

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
             +            K + K    +++H++VI   A++   +++ P TGR+HQLRVH L 
Sbjct: 120 PNRPKQ---------KVDHKVGKPSLTHYEVI-SRAKRSTLVKLTPITGRSHQLRVHMLA 169

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +G PI+GD+ Y      +  S    +L LHA+ + +  P  G  L  T  +P
Sbjct: 170 IGHPILGDNFYADPLAKSLAS----RLLLHAQELTIKQPYSGETLTFTCEVP 217


>gi|251788633|ref|YP_003003354.1| pseudouridine synthase, RluA family [Dickeya zeae Ech1591]
 gi|247537254|gb|ACT05875.1| pseudouridine synthase, RluA family [Dickeya zeae Ech1591]
          Length = 325

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 121/245 (49%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHHYPAIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E IA    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQAREITREYEAVAIGTMTAGGTVDEPIARHSTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMAHINHPLIGDPL 252

Query: 272 YCANFK------GNFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F   ++N  +  LHA  + L HP  G  ++  A LP  MV    +L
Sbjct: 253 YGGRPRLPKGASDTFIETLRNFDRQALHATMLRLYHPISGIEMEWHAALPQDMVDLIAAL 312

Query: 323 GFKYD 327
               D
Sbjct: 313 KADTD 317


>gi|226322067|ref|ZP_03797592.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi Bol26]
 gi|3915840|sp|P70870|RLUD_BORBU RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|226232657|gb|EEH31411.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi Bol26]
          Length = 326

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 55/181 (30%), Positives = 98/181 (54%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 86  IIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +R  K+Y ++V G   +    I +++ +  H    
Sbjct: 145 KDTSGVLICAKNISTLRFLAQQFKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 205 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 259

Query: 272 Y 272
           Y
Sbjct: 260 Y 260


>gi|225549251|ref|ZP_03770224.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 94a]
 gi|225370109|gb|EEG99549.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 94a]
          Length = 326

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 55/181 (30%), Positives = 98/181 (54%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 86  IIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +R  K+Y ++V G   +    I +++ +  H    
Sbjct: 145 KDTSGVLICAKNISTLRFLAQQFKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 205 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 259

Query: 272 Y 272
           Y
Sbjct: 260 Y 260


>gi|331004271|ref|ZP_08327749.1| hypothetical protein HMPREF0491_02611 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330411436|gb|EGG90848.1| hypothetical protein HMPREF0491_02611 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 338

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 69/272 (25%), Positives = 130/272 (47%), Gaps = 14/272 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           ++V  +E+  RL+R  +  + + N   + K+LR   + ++ K+     R+ +G  +++  
Sbjct: 4   IIVGKNEDGQRLERVLEKIFVNANAGFIFKMLRKKNITLNDKKADGKERLVAGSSIKLWF 63

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                  L+    E   + ++    K+ +   S ++YED    + NKP GI  Q  +   
Sbjct: 64  SDESFEKLSGKKVENTKVKNNCTDKKNVEKFNSYIVYEDDNTIILNKPEGILSQKSNIKD 123

Query: 127 YHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             I+  L  ++D         KP + +RLD+ T+G+LV  ++    +   E  + + + K
Sbjct: 124 ASINDMLLEYLDFDDSVLNTFKPSICNRLDRNTTGLLVCGKSLEGLRVNNELIKTKAVDK 183

Query: 182 IYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y +LV G  K K  C I+ WL K      + V +  +  + A++  + ++V+D F    
Sbjct: 184 FYLALVKGYIKEK--CLISGWLYKDE--SSNKVIIKNKAFEAADFIQTEYEVLDYFENNT 239

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             L ++  TG+THQ+R H   +  PI+GD KY
Sbjct: 240 LLL-VKLITGKTHQIRAHLSSISHPIIGDFKY 270


>gi|323188383|gb|EFZ73674.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           RN587/1]
          Length = 300

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 60  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 116

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 117 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 174

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 175 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 226

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 227 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEEM 286

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 287 RADFEEH 293


>gi|221217384|ref|ZP_03588855.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 72a]
 gi|225549717|ref|ZP_03770682.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 118a]
 gi|221192662|gb|EEE18878.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 72a]
 gi|225369677|gb|EEG99125.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 118a]
          Length = 326

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 55/181 (30%), Positives = 98/181 (54%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 86  IIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +R  K+Y ++V G   +    I +++ +  H    
Sbjct: 145 KDTSGVLICAKNISTLRFLAQQFKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 205 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 259

Query: 272 Y 272
           Y
Sbjct: 260 Y 260


>gi|254449436|ref|ZP_05062873.1| ribosomal large subunit pseudouridine synthase A [Octadecabacter
           antarcticus 238]
 gi|198263842|gb|EDY88112.1| ribosomal large subunit pseudouridine synthase A [Octadecabacter
           antarcticus 238]
          Length = 215

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 105/203 (51%), Gaps = 12/203 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D +I + NKP+G+    G G   H+   L + V     +  L HRLD++TSG++V 
Sbjct: 14  VIHADHEILIVNKPSGLLSVPGKG--PHLADCLIARVQVAFPQALLIHRLDRDTSGVMVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A TR A +H+   F  R  +K Y + VWG+   KK  +   L+    +  +   + K   
Sbjct: 72  ALTRHAQRHIGLQFEKRMTKKTYVARVWGMLDPKKGTVDLPLI----VDWENRPLQKVCH 127

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    A + ++V+   A++   + + P TGR+HQLRVH L +G PI+GD  Y       +
Sbjct: 128 ETGKSAQTDWRVLRNDARE-SRVRLMPKTGRSHQLRVHMLSLGHPILGDPFYAQGEAREY 186

Query: 281 TSPIQNKLYLHARYMDLPHPEGG 303
                 +L LH+  + L HP+GG
Sbjct: 187 -----ERLMLHSEELRLRHPDGG 204


>gi|195978250|ref|YP_002123494.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
 gi|195974955|gb|ACG62481.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
          Length = 296

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 120/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++Y+D  + + NKP G+ V   +G         + YH+    K      G  +P + HR+
Sbjct: 76  IVYQDDVLVIINKPQGMVVHPSAGHSTGTLVNALLYHV----KDLSSINGVIRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIG 209
           D++TSG+L+VA+T  A Q L +  + ++  + Y ++V G +PK++        + ++ IG
Sbjct: 132 DKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHGNLPKDRG-------VIEAPIG 184

Query: 210 GDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  KQ    KG   A++ FKV++ F  ++  +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 185 RSDKDRKKQTVTAKGKE-ALTRFKVLERFG-RYSLVELQLETGRTHQIRVHMAYIGHPLA 242

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GD  Y     G   +   N  +LHA+ + L HP  G  L  T   P    +T + L
Sbjct: 243 GDPLY-----GPRKTLDGNGQFLHAQTLGLTHPVTGEELVFTVEPPEIFQRTLEQL 293


>gi|324005834|gb|EGB75053.1| pseudouridine synthase, RluA family [Escherichia coli MS 57-2]
          Length = 326

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYSPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 253 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|323127056|gb|ADX24353.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis ATCC 12394]
          Length = 297

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 87/316 (27%), Positives = 143/316 (45%), Gaps = 46/316 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V++           + 
Sbjct: 11  RLDKALADLSP-LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVIQF----ELPKEEVL 65

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHID 130
           E +  D  +N+           +YED  + + NKP G+ V   +G         + YHI 
Sbjct: 66  EYQAQDIPLNI-----------IYEDEALAIINKPQGMVVHPSAGHPSGTMVNALMYHI- 113

Query: 131 GFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              K      G  +P + HR+D++TSG+L+VA+T  A Q L    + ++  + Y ++V G
Sbjct: 114 ---KDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDEAHQALAAELKAKKSLRKYLAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
              N +  I      ++ IG       KQ    KG   A++ F V++ F   +  +E+Q 
Sbjct: 171 NLPNDRGMI------EAPIGRSEKDRKKQAVTAKGKE-AVTRFTVLERFGD-YSLVELQL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGRTHQ+RVH  ++G P+ GD  Y     G   +   +  +LHA  + L HP  G  + 
Sbjct: 223 ETGRTHQIRVHMAYIGHPVAGDPLY-----GPRKTLSGHGQFLHAETLGLTHPLTGEDML 277

Query: 307 ITAPLPAHMVKTWDSL 322
            T   PA   KT   L
Sbjct: 278 FTVAPPAIFHKTLQQL 293


>gi|281413656|ref|ZP_06245398.1| ribosomal large subunit pseudouridine synthase D [Micrococcus
           luteus NCTC 2665]
          Length = 320

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 114/229 (49%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LYED  +   +KP G++     G +   + G L +    + + G   R  + HRLD  T
Sbjct: 94  ILYEDDDLVAVDKPTGVAAHPSPGWVGPTVVGALAALGYDITTSGAPERQGIVHRLDVGT 153

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++VVA+T  A   + + FR R  +K+Y ++V GIP      +   + +  H G  +  
Sbjct: 154 TGVMVVAKTERAYTAMKDQFRERVPEKVYHAVVQGIPDPLSGTVDAPIGR--HPGHHWKF 211

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  + +    +++H++ ++ F  +   LE+   TGRTHQ+RVH   +  P VGD  Y A
Sbjct: 212 AVLDDGR---PSVTHYETLEVFG-RGTLLEVHLETGRTHQIRVHTSALRHPCVGDLTYGA 267

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + +      +  + +LHA  +  PHP  G  + IT+P P  +     +L
Sbjct: 268 DPRLAAELGLTRQ-WLHAHRLAFPHPVTGEPVTITSPYPDDLAHALAAL 315


>gi|117618510|ref|YP_858498.1| ribosomal large subunit pseudouridine synthase D [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117559917|gb|ABK36865.1| ribosomal large subunit pseudouridine synthase D [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 326

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 119/240 (49%), Gaps = 31/240 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V +KPAG+ V  G+G     DG + + +     +  + PR  + HRLD++T
Sbjct: 86  IVYEDEHILVIDKPAGLVVHPGAGTP---DGTILNALLHRYPAIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL E+ + R+I + Y ++  G           I     +++H+   
Sbjct: 143 TGLMVVAKTIPAQTHLVEALQARQITREYEAIAIGHMTAGGTVDAPIGRHPTQRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              VV    +    +++H++V + F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 ---VVPNGRE----SVTHYRVHEKF-RGHTRLRLRLETGRTHQIRVHMAHIKHPLVGDPA 252

Query: 272 YCANFK--GNFTSPIQNKL------YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           Y    +   N T  +   L       LHA  + L HP  G  ++  +P P  M+   + L
Sbjct: 253 YGGRLRLLRNATPELTEALRGFHRQALHATMLKLAHPITGEVMEWHSPTPQDMLDLMEVL 312


>gi|315127724|ref|YP_004069727.1| pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
 gi|315016238|gb|ADT69576.1| pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
          Length = 209

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 66/202 (32%), Positives = 107/202 (52%), Gaps = 15/202 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  + + NKP+ +    G     H D  + + V+      ++ HRLD  TSGIL +
Sbjct: 7   ILFQDDDLLIVNKPSELLTVPGKD-PKHADSLI-NRVNRVFPSAKIVHRLDMATSGILCL 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A  +AA +HL+  F+ R   K Y + V+G  + +   +   L+       D+ +  KQ  
Sbjct: 65  AMNKAAHRHLSMQFQERETAKRYIARVYGQLETETGSVDLPLI------CDWPNRPKQMV 118

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      +++HFKV++  AQ    +E+ P TGR+HQLRVH L +G PI+GD  Y A+   
Sbjct: 119 DHDNGKPSLTHFKVLEREAQA-TRVELTPITGRSHQLRVHMLSLGHPILGDRLY-AHKDA 176

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
              +P   +L LHA+ + L HP
Sbjct: 177 LAAAP---RLQLHAQMLQLKHP 195


>gi|307709450|ref|ZP_07645907.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
 gi|307619764|gb|EFN98883.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
          Length = 298

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 68/219 (31%), Positives = 114/219 (52%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  ++   HP   + LQ+ +PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHFLSFYHPFLKQDLQLESPLP 283


>gi|313623251|gb|EFR93499.1| ribosomal large subunit pseudouridine synthase D [Listeria innocua
           FSL J1-023]
          Length = 297

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 82/298 (27%), Positives = 138/298 (46%), Gaps = 43/298 (14%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +Q +L++G + V+ +  K N ++Q G  +R          I+ E   LD           
Sbjct: 27  IQLMLKNGDITVNGELAKPNYKVQVGDEIRYEAREPEELEILAEDIPLD----------- 75

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQKPRLT 147
               + +ED  + V NKP G+ V   +G A         +H D    S ++ K  +P + 
Sbjct: 76  ----IYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL--SGINGK-IRPGIV 128

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    + ++ 
Sbjct: 129 HRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPIGRAK 187

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                + VV+  ++    A +HF+VI+     +  +  +  TGRTHQ+RVH  ++G P+ 
Sbjct: 188 EDRQKMAVVRDGKE----ARTHFEVIERLP-GYTLINCKLDTGRTHQIRVHLKYIGHPLA 242

Query: 268 GDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           GD KY      KGN         +LHA  +   HP    R+   APLP    +   SL
Sbjct: 243 GDPKYGPKNTIKGNGQ-------FLHAAKLGFDHPTTNERMTFEAPLPDSFEQALKSL 293


>gi|297571262|ref|YP_003697036.1| pseudouridine synthase [Arcanobacterium haemolyticum DSM 20595]
 gi|296931609|gb|ADH92417.1| pseudouridine synthase, RluA family [Arcanobacterium haemolyticum
           DSM 20595]
          Length = 306

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 114/230 (49%), Gaps = 16/230 (6%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LYED  I V +KP G++       +G + +   +   ++       ++  + HRLD  T
Sbjct: 80  VLYEDDDIIVVDKPVGVAAHASQNFEGPNVLGALLAAGVRLTTSGPQERMGIVHRLDVGT 139

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G +VVA++  A   L  +FR R + KIY +LV G P      +      ++ IG D+ H
Sbjct: 140 TGAMVVAKSELAYTMLKRAFRDRTVTKIYHALVQGHPDPMNGTV------EAPIGRDHRH 193

Query: 215 VVKQNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             K   +    ++++H+  I+  A     LE+   TGRTHQ+RVH   +  P VGD  Y 
Sbjct: 194 QWKMGVRADGKHSVTHYDTIEAMAGA-SLLEVHLETGRTHQIRVHMSALRHPCVGDDMYG 252

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           A+ + +    ++ + +LHA  +   HP  G  +++ +  PA +    D++
Sbjct: 253 ADPRLSAKLGLERQ-WLHAVRLGFDHPRTGHYIEVESAYPADLQHALDTM 301


>gi|255019802|ref|ZP_05291878.1| Ribosomal large subunit pseudouridine synthase D [Acidithiobacillus
           caldus ATCC 51756]
 gi|254970731|gb|EET28217.1| Ribosomal large subunit pseudouridine synthase D [Acidithiobacillus
           caldus ATCC 51756]
          Length = 320

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 87/298 (29%), Positives = 137/298 (45%), Gaps = 39/298 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD   K   P ++   LQ +L+ G V VD    + + RI+ G+ V +        H   
Sbjct: 20  RLDAVLKELLPELSRSRLQTLLQQGSVLVDGSAHRPSYRIRGGEGVVLHLPQTPAEHWQA 79

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-- 137
           E      +++LT         +++EDS++ V +KPAG++   G+G      G L + V  
Sbjct: 80  E------AMDLT---------IVHEDSQLLVIDKPAGLATHPGAGRPR---GTLANAVLA 121

Query: 138 --DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              +  + PR  + HRLD +TSG+LVVA+T  A Q L      R + + Y +LV G    
Sbjct: 122 HCPANERLPRAGIVHRLDMDTSGLLVVAKTELARQSLIAQLADRSMHREYLALVQGALTG 181

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                A       H        V+++ + A    + +++++ F  +   L ++  TGRTH
Sbjct: 182 GGHVEAPI---GRHPQDRLRMTVRRDGRPAR---TDYRLVERFP-RHSLLRLRLATGRTH 234

Query: 254 QLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQ--NKLYLHARYMDLPHPEGG 303
           Q+RVH  H+G P+VGD  Y       A       +  Q   +  LHA  + L HPE G
Sbjct: 235 QIRVHMRHLGHPLVGDPLYGGRPILPAGLGAAGLARWQAFRRQALHAWRLILEHPESG 292


>gi|242280705|ref|YP_002992834.1| pseudouridine synthase [Desulfovibrio salexigens DSM 2638]
 gi|242123599|gb|ACS81295.1| pseudouridine synthase [Desulfovibrio salexigens DSM 2638]
          Length = 292

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 80/295 (27%), Positives = 127/295 (43%), Gaps = 33/295 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++V V   E   +L R+ +      +    + + +R G VRVDK R K  + ++ GQ V
Sbjct: 3   AEFVQVTKAEAGQKLVRFLERRVDGAVPRSAIMRWIRKGNVRVDKGRCKPFDLVKEGQTV 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP                 +    +H    +  ++YED       KPAG+  QGG+G 
Sbjct: 63  RIPPY---------------KAEETAQHKKLPELPIIYEDDNYLAVCKPAGLPTQGGTGH 107

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF-RMRRIQKIYW 184
              +   L S       KP   HRLD++TSG+++  ++    + L++ F       K Y 
Sbjct: 108 DDSVADRLLSMFADAHYKPAPAHRLDRDTSGVILAGKSHQGQKDLSDFFAEHGEGGKFYL 167

Query: 185 SLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           + V G  P+     + + + K    G +   VV  + K A+ ++    +     +K   L
Sbjct: 168 AEVEGRWPEEDWVELHDKMEKSGSKGRE--KVVVGSGKDASSSVCPVTI----GEKSSLL 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            ++ HTGRTHQ+RV     G PI GD KY              K+ LH   +D P
Sbjct: 222 IVKLHTGRTHQIRVQLSSRGFPIAGDVKYGGQ---------NGKMKLHCLRIDTP 267


>gi|56460291|ref|YP_155572.1| 23S rRNA pseudouridine synthase D [Idiomarina loihiensis L2TR]
 gi|56179301|gb|AAV82023.1| Pseudouridylate synthase [Idiomarina loihiensis L2TR]
          Length = 322

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 89/330 (26%), Positives = 147/330 (44%), Gaps = 51/330 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD+     +P  +   L+  +  G+V +D K + K   ++ +G +V +   I       
Sbjct: 19  RLDQALAELFPDYSRSRLKSWITDGKVTIDTKVIEKPREKVVAGALVAVDAEIEG----- 73

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSW 136
            E++     V L          ++YED  I V NKPAG+ V  G+G      ++G L  +
Sbjct: 74  -EERHAAQPVELD---------IVYEDDDILVINKPAGLVVHPGAGAPDRTLLNGLLH-Y 122

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  PR  + HRLD++T+G++VVAR   A   L    + R I + Y ++  G+    
Sbjct: 123 DPQLDLVPRAGIIHRLDKDTTGLMVVARNVPAQTQLVSMMQDRDITREYEAVCNGVMTAG 182

Query: 195 ---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
               + I     K++H+      VV+  +     A++H++V+D + +    L ++  +GR
Sbjct: 183 GMVDQPIGRHPTKRTHMA-----VVQSGKP----AVTHYRVLDRY-RAHTLLRLRLESGR 232

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLHARYMDLPH 299
           THQ+RVH  H+  P+VGD  Y     G    P Q            N+  LHA  + L H
Sbjct: 233 THQIRVHMAHIRHPLVGDLTYG----GRPRPPKQAEDRLLQTLRGFNRQALHAASLGLHH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           P  G  L+   P P       + L   ++R
Sbjct: 289 PITGDWLEFNVPRPTDFQYLIEELRVDHER 318


>gi|15639330|ref|NP_218779.1| hypothetical protein TP0339 [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189025572|ref|YP_001933344.1| hypothetical protein TPASS_0339 [Treponema pallidum subsp. pallidum
           SS14]
 gi|3322614|gb|AAC65324.1| conserved hypothetical protein [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189018147|gb|ACD70765.1| hypothetical protein TPASS_0339 [Treponema pallidum subsp. pallidum
           SS14]
          Length = 331

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/252 (28%), Positives = 116/252 (46%), Gaps = 39/252 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG-----------------------FLKSWV 137
           +L+E+  I   NK  G+ V  G+G   H  G                       F K + 
Sbjct: 92  ILFENEDIIAVNKAQGMIVHPGAG---HWTGTLVQALSFYRVYRARFEDEFSRQFQKGFP 148

Query: 138 DS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D     +  + HRLD++TSG+L+ +R   A + L  SF+ R+++K+Y +L+ G+P     
Sbjct: 149 DFFSTLRQGIVHRLDKDTSGVLLTSRNMHAHEALVRSFKKRQVRKVYLALLQGVPARGVG 208

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQL 255
            I   +++       +  V  ++     YA + +KV+  C A  F    +   TGRTHQ+
Sbjct: 209 VIETTIVRDRRRRTRF--VASEDFSKGKYARTRYKVMKICGACAFVQFLLD--TGRTHQI 264

Query: 256 RVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
           RVHA ++GCP+VGD  Y + N  G     I   L LHA  +    P    R+ + AP+P 
Sbjct: 265 RVHARYLGCPVVGDPLYGSRNICG-----IPTTLMLHAYAVRFVLPRTKKRITLVAPIPL 319

Query: 314 HMVKTWDSLGFK 325
             V+    L  +
Sbjct: 320 RFVRLIHRLSVR 331


>gi|58037279|ref|NP_082316.1| RNA pseudouridylate synthase domain-containing protein 4 [Mus
           musculus]
 gi|81904256|sp|Q9CWX4|RUSD4_MOUSE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 4
 gi|12845681|dbj|BAB26852.1| unnamed protein product [Mus musculus]
 gi|38511726|gb|AAH61256.1| RNA pseudouridylate synthase domain containing 4 [Mus musculus]
 gi|74140035|dbj|BAE33761.1| unnamed protein product [Mus musculus]
 gi|148693444|gb|EDL25391.1| RNA pseudouridylate synthase domain containing 4 [Mus musculus]
          Length = 377

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 87/315 (27%), Positives = 147/315 (46%), Gaps = 45/315 (14%)

Query: 51  KRVKFNNRIQSGQVVRIP--PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKI 108
           ++++   + Q  + VR+P  PV   +  +++  + L   V+    +  L   +L++D+ +
Sbjct: 48  EKLRAQKQEQKAKEVRVPTNPVQRRVQELVRFTQQLQR-VHPNVLAKELSRRILHQDNDL 106

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
            V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G++V+A  +
Sbjct: 107 VVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEK 166

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------- 214
             A  + E FR R+++K YW++   +P      + +  +K+  + G   H          
Sbjct: 167 DMAHQVQELFRTRQVEKKYWAITVRVPL-PSAGVVDIPIKEKEVQGPQQHHKMTLSPSYR 225

Query: 215 ------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIV 267
                 V  +  + A+ A++ ++V+   A     +E+QP TG  HQLRVH +  + CPI+
Sbjct: 226 LDNGKMVKVRASRDAHVAVTQYQVLS-SASSSALVELQPVTGIKHQLRVHLSFGLDCPIL 284

Query: 268 GDHKYC-------ANFKGNFTSPI---QNK-----LYLHARYMDLPHPEGGR---LQITA 309
           GDHKY                  +   Q+K     L+LHAR + LP   G R   L +T 
Sbjct: 285 GDHKYSDWTRLAPQKLSAGTLKKLGLQQSKARYIPLHLHARQLILPA-LGSRTEELLLTC 343

Query: 310 PLPAHMVKTWDSLGF 324
            LP    ++   LG 
Sbjct: 344 KLPHFFARSLLRLGL 358


>gi|145631295|ref|ZP_01787067.1| SfhB [Haemophilus influenzae R3021]
 gi|144983080|gb|EDJ90580.1| SfhB [Haemophilus influenzae R3021]
          Length = 324

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 119/244 (48%), Gaps = 31/244 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP  + V  G+G         + YH    ++  V   G    + HRLD
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVE--VPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G++VVA+T  A   L    + R+I + Y ++  GI   K   +   + +  H    
Sbjct: 139 KDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGI-MTKGGTVDQPMAR--HATKR 195

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  V    K A   ++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 196 ILMAVHPMGKPA---VTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQT 251

Query: 272 YCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+  ++L
Sbjct: 252 YGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELLNAL 311

Query: 323 GFKY 326
              Y
Sbjct: 312 KADY 315


>gi|325189052|emb|CCA23580.1| ribosomal large subunit pseudouridine synthase A put [Albugo
           laibachii Nc14]
          Length = 350

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 65/204 (31%), Positives = 101/204 (49%), Gaps = 21/204 (10%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-----WVDSKGQKPRLTHRLDQETSGI 157
           Y D  I V +KP+G+    G G    +   LK      WV          HRLD +TSG+
Sbjct: 148 YCDDAIAVVSKPSGMLTVDGKGSQLSLQRQLKKLHGNVWV---------VHRLDMDTSGL 198

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LVVA ++ AA  L   FR R I+K+Y + V G P + +  I+ ++   +     +   + 
Sbjct: 199 LVVAWSKLAADRLGSQFRDRTIRKVYHARVHGHPNDDEGVISGYM--NAQPDERFRQRMV 256

Query: 218 QNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           + +    ++ + ++V+   +  K   LE+ P TGRTHQLRVH  H+G PI+GD  Y    
Sbjct: 257 ETQTDGKWSQTGWRVLSRSSNPKSSLLELTPVTGRTHQLRVHLSHIGHPILGDEWYAP-- 314

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                  + ++L LHA  ++  HP
Sbjct: 315 --QHVYKLADRLLLHATALEFVHP 336


>gi|306825158|ref|ZP_07458500.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus sp. oral
           taxon 071 str. 73H25AP]
 gi|304432594|gb|EFM35568.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus sp. oral
           taxon 071 str. 73H25AP]
          Length = 298

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 112/219 (51%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-EYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQRKSIEKRYFALVKGNGDLEPEGEIIAPIARDVDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +KV+  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKVVASYGD-IHLIDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+  PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHYLSFYHPFLEQDLQLENPLP 283


>gi|291059729|gb|ADD72464.1| ribosomal large subunit pseudouridine synthase D [Treponema
           pallidum subsp. pallidum str. Chicago]
          Length = 336

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/252 (28%), Positives = 116/252 (46%), Gaps = 39/252 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG-----------------------FLKSWV 137
           +L+E+  I   NK  G+ V  G+G   H  G                       F K + 
Sbjct: 97  ILFENEDIIAVNKAQGMIVHPGAG---HWTGTLVQALSFYRVYRARFEDEFSRQFQKGFP 153

Query: 138 DS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D     +  + HRLD++TSG+L+ +R   A + L  SF+ R+++K+Y +L+ G+P     
Sbjct: 154 DFFSTLRQGIVHRLDKDTSGVLLTSRNMHAHEALVRSFKKRQVRKVYLALLQGVPARGVG 213

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQL 255
            I   +++       +  V  ++     YA + +KV+  C A  F    +   TGRTHQ+
Sbjct: 214 VIETTIVRDRRRRTRF--VASEDFSKGKYARTRYKVMKICGACAFVQFLLD--TGRTHQI 269

Query: 256 RVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
           RVHA ++GCP+VGD  Y + N  G     I   L LHA  +    P    R+ + AP+P 
Sbjct: 270 RVHARYLGCPVVGDPLYGSRNICG-----IPTTLMLHAYAVRFVLPRTKKRITLVAPIPL 324

Query: 314 HMVKTWDSLGFK 325
             V+    L  +
Sbjct: 325 RFVRLIHRLSVR 336


>gi|219115441|ref|XP_002178516.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217410251|gb|EEC50181.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 240

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 63/186 (33%), Positives = 95/186 (51%), Gaps = 10/186 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQG---GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LY D  I V NKP+GI SV G      IA  +   L   +D       + HR+D +TSG
Sbjct: 3   ILYCDEHICVVNKPSGILSVPGPRRNPSIANLVYEILNPPIDIDQM---VVHRIDMDTSG 59

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV A T  A + L + FR RR++K Y +L+ G  +   +   +  L++      ++   
Sbjct: 60  VLVFALTELALRQLHDDFRSRRVKKTYEALLAGHFRKATQVEIDVALERDPYHPPFMRRY 119

Query: 217 KQNEKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + ++ A Y+    ++    AQ       + M PHTGRTHQLRVHA  +G PI+GD  Y 
Sbjct: 120 WEPQRSATYSRQFSQIYQPSAQAHLPVSRVHMSPHTGRTHQLRVHAAALGYPIIGDDIYG 179

Query: 274 ANFKGN 279
              +G+
Sbjct: 180 FEGEGD 185


>gi|159045150|ref|YP_001533944.1| ribosomal large subunit pseudouridine synthase D [Dinoroseobacter
           shibae DFL 12]
 gi|157912910|gb|ABV94343.1| ribosomal large subunit pseudouridine synthase D [Dinoroseobacter
           shibae DFL 12]
          Length = 347

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 97/344 (28%), Positives = 148/344 (43%), Gaps = 59/344 (17%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALN 75
           RLDR      P    ++   L K++ +G VR   + +     R+ +G V+ +     A  
Sbjct: 22  RLDRALARDVPEGLGLSRSRLVKLIEAGDVRRGAEVLASPKARVAAGDVLTLRLGAPAEV 81

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFL 133
            ++ E   LD               +++ED+ + V NKPAG+ V    GS     ++  +
Sbjct: 82  PLVAEAIPLD---------------VIFEDADLIVVNKPAGMVVHPAPGSPAGTLVNALM 126

Query: 134 KSWVDS----KGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               DS     G+K P + HR+D++TSG+LVVA++  A Q L   F    +++IY +LV 
Sbjct: 127 HHCGDSLSGIGGEKRPGIVHRIDKDTSGLLVVAKSDHAHQGLAAQFAAHSVERIYDALVH 186

Query: 189 GIPKNKKECIANWLLKKSHIGG-------------DYVHVVKQNEKGANYAISHFKVIDC 235
           G+P+     +    + +   GG             D        E    +A++  +V   
Sbjct: 187 GVPEASDPRLRGLPMVRFEPGGVLCLRASLARHRTDRQRQAVVAEGQGRHAVTRARVEAR 246

Query: 236 F------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQ-- 285
           F      A   CWLE    TGRTHQ+RVH  H+G  ++GD  Y           SP    
Sbjct: 247 FGDPAGVAHLACWLE----TGRTHQIRVHLAHIGHGLLGDPVYGGRKRLSAKAFSPQALA 302

Query: 286 -----NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
                 +  LHAR +   HP  G  L   AP+PA M   W +LG
Sbjct: 303 AAEAFPRQALHARTLGFVHPVTGAALSFAAPMPADMAALWAALG 346


>gi|46445989|ref|YP_007354.1| 23S RNA-specific pseudouridine synthase D [Candidatus
           Protochlamydia amoebophila UWE25]
 gi|46399630|emb|CAF23079.1| probable 23S RNA-specific pseudouridine synthase D [Candidatus
           Protochlamydia amoebophila UWE25]
          Length = 318

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 91/324 (28%), Positives = 140/324 (43%), Gaps = 43/324 (13%)

Query: 7   VQYVVVENDEENMRLD----RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           V  +++  DE   RLD    R F   Y    F   Q ++    + V+   VK    +Q G
Sbjct: 9   VDLLIISEDEVGERLDKVLARRFNAKYSRTYF---QFLIDKHLILVNGIAVKKRTLLQEG 65

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V +             Q +     NL   +  L   +LYED  + V NKPAG+ V   
Sbjct: 66  DEVEV-------------QFLASPESNLMPENIPLS--ILYEDEHLLVINKPAGMVVHPA 110

Query: 123 SG--IAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++  L    K  +     +P + HRLD+ TSG+LV A+T    Q L E F  
Sbjct: 111 PGNWSGTFVNALLYYCQKLPLLPDTIRPGIVHRLDKGTSGLLVAAKTLETQQKLIELFAS 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDC 235
           R++ K Y ++  G P + +         ++ IG   +H  +         AIS  K +  
Sbjct: 171 RKVYKAYLAICIGRPADGE--------IQAPIGRHPIHRKQMAVIPTGKPAISFCKTLG- 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARY 294
           ++ K  +++++  TGRTHQ+RVH  + G PI+GD  Y   +    ++ P Q    LHA  
Sbjct: 222 WSDKLSFVQIEIATGRTHQIRVHMKYRGSPILGDPLYGQISLNQYYSVPHQ---LLHAAV 278

Query: 295 MDLPHPEG-GRLQITAPLPAHMVK 317
           +   HP     L+   P P  MV+
Sbjct: 279 LRFQHPISLENLEFCTPPPPEMVR 302


>gi|86147828|ref|ZP_01066134.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp.
           MED222]
 gi|85834355|gb|EAQ52507.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp.
           MED222]
          Length = 244

 Score = 93.6 bits (231), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/207 (31%), Positives = 109/207 (52%), Gaps = 15/207 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I V NKPAG+ SV G   +  H D      V  +  + ++ HRLD  TSG+++
Sbjct: 16  IIYQDDDILVVNKPAGLLSVPGR--LPEHYDSMWSRLV-VEFPEIQVVHRLDMSTSGLML 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A +HL + F+ R   K+Y++ VWG  ++K   I   L+       D+ +  +Q 
Sbjct: 73  LAKHKQAERHLKKQFQYRLTHKLYYARVWGSMEDKAGLIDLPLI------CDWTNRPRQK 126

Query: 220 EKGANYAISHFK-VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
               +   S  + V++    +   L++ P TGR+HQLRVH + +G PIVGD  Y      
Sbjct: 127 VCFDDGKPSQTRYVVEQQEPQTTLLKLLPITGRSHQLRVHCMELGNPIVGDEFYATPDAF 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRL 305
           N++    ++L LHA  +   HP   +L
Sbjct: 187 NYS----DRLALHACELSFYHPANNQL 209


>gi|15832711|ref|NP_311484.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str.
           Sakai]
 gi|168752065|ref|ZP_02777087.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4113]
 gi|168758664|ref|ZP_02783671.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4401]
 gi|168762387|ref|ZP_02787394.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4501]
 gi|168771700|ref|ZP_02796707.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4486]
 gi|168773478|ref|ZP_02798485.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4196]
 gi|168778572|ref|ZP_02803579.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4076]
 gi|168789497|ref|ZP_02814504.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC869]
 gi|168801712|ref|ZP_02826719.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC508]
 gi|195940189|ref|ZP_03085571.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str.
           EC4024]
 gi|208808732|ref|ZP_03251069.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4206]
 gi|208812778|ref|ZP_03254107.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4045]
 gi|208821085|ref|ZP_03261405.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4042]
 gi|209396635|ref|YP_002272067.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4115]
 gi|217326855|ref|ZP_03442938.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. TW14588]
 gi|254794542|ref|YP_003079379.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str.
           TW14359]
 gi|261227479|ref|ZP_05941760.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261255673|ref|ZP_05948206.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291283867|ref|YP_003500685.1| Ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O55:H7 str. CB9615]
 gi|34395799|sp|Q8X9F0|RLUD_ECO57 RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|13362928|dbj|BAB36880.1| suppressor of ftsH mutation [Escherichia coli O157:H7 str. Sakai]
 gi|187770638|gb|EDU34482.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4196]
 gi|188014009|gb|EDU52131.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4113]
 gi|189003176|gb|EDU72162.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4076]
 gi|189354550|gb|EDU72969.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4401]
 gi|189359603|gb|EDU78022.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4486]
 gi|189367297|gb|EDU85713.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4501]
 gi|189370886|gb|EDU89302.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC869]
 gi|189376176|gb|EDU94592.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC508]
 gi|208728533|gb|EDZ78134.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4206]
 gi|208734055|gb|EDZ82742.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4045]
 gi|208741208|gb|EDZ88890.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4042]
 gi|209158035|gb|ACI35468.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4115]
 gi|209762678|gb|ACI79651.1| suppressor of ftsH mutation [Escherichia coli]
 gi|209762680|gb|ACI79652.1| suppressor of ftsH mutation [Escherichia coli]
 gi|209762682|gb|ACI79653.1| suppressor of ftsH mutation [Escherichia coli]
 gi|209762684|gb|ACI79654.1| suppressor of ftsH mutation [Escherichia coli]
 gi|209762686|gb|ACI79655.1| suppressor of ftsH mutation [Escherichia coli]
 gi|217319222|gb|EEC27647.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. TW14588]
 gi|254593942|gb|ACT73303.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           TW14359]
 gi|290763740|gb|ADD57701.1| Ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O55:H7 str. CB9615]
 gi|320640778|gb|EFX10276.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str.
           G5101]
 gi|320646123|gb|EFX15068.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H- str.
           493-89]
 gi|320651420|gb|EFX19821.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H- str. H
           2687]
 gi|320657025|gb|EFX24848.1| 23S rRNA pseudouridine synthase D [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320662689|gb|EFX30033.1| 23S rRNA pseudouridine synthase D [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|320667506|gb|EFX34430.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 326

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 90/338 (26%), Positives = 158/338 (46%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V    
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQV---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            INA   I +E +     + L          ++YED  I V NKP  + V  G+G   + 
Sbjct: 66  AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---NP 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y
Sbjct: 112 DGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREY 171

Query: 184 WSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G         E I+    K++H+    VH + +       A++H+++++ F +  
Sbjct: 172 EAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPMGKP------AVTHYRIMEHF-RVH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHA 292
             L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA
Sbjct: 222 TRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHA 281

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
             + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 282 TMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 319


>gi|302325509|gb|ADL24710.1| putative ribosomal large subunit pseudouridine synthase C
           [Fibrobacter succinogenes subsp. succinogenes S85]
          Length = 411

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 115/226 (50%), Gaps = 19/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSG 156
           L+ +     + NKP+G++ Q GSG      +  +L  W  ++G   KP + HRLDQETSG
Sbjct: 170 LVVQTEDYVIVNKPSGLASQPGSGTRPGESLVEYLWEWGRNEGLDFKPTIAHRLDQETSG 229

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++ A      +  T   R   + K Y++LV G  K  +  I+  LL+     G  + +V
Sbjct: 230 LIIAALHGDTLRDFTRMIREHVVDKFYFALVKGNLKKDRGTISESLLRTDSAKGSKM-LV 288

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            Q+++ A  AI+H++V   + + +  ++++  TGR HQ+R H   +G P++GD +Y    
Sbjct: 289 GQDDENAQKAITHYRVKQHY-EGYDLVKIKLETGRMHQIRAHFASIGHPLLGDTRY---- 343

Query: 277 KGNFTSPIQ-------NKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
            G+F    +       N+L+LH+  ++    +G       PLP  +
Sbjct: 344 -GDFALNREVKKLFGLNRLFLHSCRLEFDW-QGEHKVFDCPLPKEL 387


>gi|259417867|ref|ZP_05741786.1| ribosomal large subunit pseudouridine synthase A [Silicibacter sp.
           TrichCH4B]
 gi|259346773|gb|EEW58587.1| ribosomal large subunit pseudouridine synthase A [Silicibacter sp.
           TrichCH4B]
          Length = 217

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 65/206 (31%), Positives = 105/206 (50%), Gaps = 12/206 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D++I V NKPAG+    G G   H+   L S + +   +  L HRLD++TSG++V 
Sbjct: 16  ILHHDAQILVVNKPAGLLSVPGKG--EHLSDCLISRIQAAFPEALLVHRLDRDTSGVMVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A T  A +HL   F  R  +K Y + + G  + +   +   L+    +      + K  +
Sbjct: 74  AMTAHAQRHLGLQFEKRMTKKTYVARLTGKLEPRSGAVDLPLI----VDWPNRPLQKVCK 129

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    A + +KVI    +    + +QP TGR+HQLRVH   +G PI+GD  Y +    ++
Sbjct: 130 ETGKPAYTDWKVI-SHGEDETRVRLQPKTGRSHQLRVHMQSLGHPILGDPLYASGAARDY 188

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQ 306
                 ++ LH+  + L HPEGG  Q
Sbjct: 189 P-----RMMLHSEELRLKHPEGGASQ 209


>gi|162147092|ref|YP_001601553.1| RNA pseudouridine synthase [Gluconacetobacter diazotrophicus PAl 5]
 gi|209544152|ref|YP_002276381.1| pseudouridine synthase [Gluconacetobacter diazotrophicus PAl 5]
 gi|161785669|emb|CAP55240.1| putative RNA pseudouridine synthase [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209531829|gb|ACI51766.1| pseudouridine synthase [Gluconacetobacter diazotrophicus PAl 5]
          Length = 227

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 71/227 (31%), Positives = 115/227 (50%), Gaps = 20/227 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D++  V +KP G+ V  G SG     D F    +  +   P L HRLD++TSG L+
Sbjct: 14  VLFRDNRFIVIDKPPGLPVHPGPSGGPSVEDSF--PLLSRRADGPWLAHRLDRDTSGCLL 71

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  + A      +F   +++K YW++V G P      +A  + + S   G +  V   +
Sbjct: 72  IALRKQALLAAQAAFAAGQVRKTYWAVVQGRPAADSGTVAMTMARHSDRQG-WRMVAAPD 130

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            + +    + ++V+    ++  WLE+   TGRTHQ R+H   +GCPI+GD  Y     G 
Sbjct: 131 GQASR---TDWRVLASDGRE-SWLELHLLTGRTHQARLHCASLGCPILGDPVY-----GG 181

Query: 280 FTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGFK 325
              P    L+L +R++ LP  P    +  TAP PAH+  T D  G++
Sbjct: 182 AEGPT---LHLMSRHLALPLSPP---VSATAPPPAHIRATLDRHGWQ 222


>gi|83319260|ref|YP_424375.1| ribosomal large subunit pseudouridine synthase A [Mycoplasma
           capricolum subsp. capricolum ATCC 27343]
 gi|83283146|gb|ABC01078.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma capricolum subsp. capricolum ATCC 27343]
          Length = 322

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 82/287 (28%), Positives = 147/287 (51%), Gaps = 24/287 (8%)

Query: 37  LQKILRSGQVRVDKKRVKFNN---RIQSGQVVRI-PPVINALNHIIKEQKILDSSVNLTK 92
           +QK+++   + V+ + +  NN   +  S  ++ I  PV++  N    +  +LD   N+TK
Sbjct: 33  IQKLIKEECISVNNQIITSNNFLVKPNSQIIITIKDPVLDP-NITKNKDPVLDP--NITK 89

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKG----QKPRL 146
           + D   +I+ Y+D  + V NK   I+V        +  ++  L S V+        +P +
Sbjct: 90  NKDIDLNII-YQDDDLLVINKQNNITVHPSLNNTNNTIVNALLASDVELSSINGELRPGI 148

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HR+D++T+G+L+VA+     + L+E F+  +I K Y ++V G+ K  K  I +  + +S
Sbjct: 149 VHRIDKQTTGLLIVAKNDKTHKLLSEMFKNHQIYKEYLAIVTGVIKPNKGLI-DAPIGRS 207

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                 + V  +N K   +AI+ F+V++ F  K   ++ Q  TGRTHQ+RVH  ++  P+
Sbjct: 208 QTDRKKMSVTAKNSK---HAITTFEVVERFL-KNTLIKCQIQTGRTHQIRVHFNYINHPV 263

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           + D  Y    +  FT   Q   YLHA  +   HP     +++ +PLP
Sbjct: 264 LNDPIYGKKHQ-EFTDFGQ---YLHAYKLKFTHPITKKEIELISPLP 306


>gi|330685506|gb|EGG97159.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU121]
          Length = 305

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 80/317 (25%), Positives = 149/317 (47%), Gaps = 35/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +Y + +++    RLD+         +   +Q  ++   V+V+ K VK N +++   
Sbjct: 1   METYEYTITDSNHVGQRLDKVLPELNSGWSRSQIQDWIKEDLVKVNDKVVKPNYKVKQND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                      N ++ EQ+++++ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  -----------NIVVTEQEVVEADIT----PENLNLDIFYEDDDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +   K+     G+ +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMAK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 SVKRKYIALVHGNIPHDYGTVDAP--IGRNKKDRQAMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KDYTLIECELETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQA-----LHAGVIG 273

Query: 297 LPHPEGGR-LQITAPLP 312
             HP     ++ TA LP
Sbjct: 274 FEHPVTHEYIERTAELP 290


>gi|218547883|ref|YP_002381674.1| 23S rRNA pseudouridine synthase D [Escherichia fergusonii ATCC
           35469]
 gi|218355424|emb|CAQ88032.1| 23S rRNA pseudouridine synthase [Escherichia fergusonii ATCC 35469]
 gi|324111235|gb|EGC05217.1| RluA family protein pseudouridine synthase [Escherichia fergusonii
           B253]
          Length = 326

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 90/338 (26%), Positives = 159/338 (47%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           +V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V    
Sbjct: 10  MVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            INA   I +E +     + L          ++YED  I V NKP  + V  G+G   + 
Sbjct: 66  AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---NP 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y
Sbjct: 112 DGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREY 171

Query: 184 WSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G         E I+    K++H+    VH + +       A++H+++++ F +  
Sbjct: 172 EAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPMGKP------AVTHYRIMEHF-RVH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHA 292
             L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA
Sbjct: 222 TRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHA 281

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
             + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 282 TMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 319


>gi|226360214|ref|YP_002777992.1| pseudouridine synthase RluD [Rhodococcus opacus B4]
 gi|226238699|dbj|BAH49047.1| pseudouridine synthase RluD [Rhodococcus opacus B4]
          Length = 308

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 86/329 (26%), Positives = 149/329 (45%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  E MR+D         ++   + ++   G V VD   V  ++R+ +G 
Sbjct: 1   MRETRSMPVPDGLEAMRVDAGLARLL-GLSRTAVAQLTEEGSVLVDGAPVGKSDRLSAGT 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGG 122
            +              E ++ +    LT  ++ ++ + +LY D  +   +KP G++    
Sbjct: 60  WL--------------EVELPEPPRPLTIEAEPVEGMEILYADDDVVAVDKPVGVAAHAS 105

Query: 123 SG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G     + G L +    + + G   R  + HRLD  TSG++VVA +  A   L  +F+ 
Sbjct: 106 VGWTGPTVIGGLAAAGFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTLLKRAFKQ 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I K Y +LV G P      I   + +  H   D+   V  + K    +I+H+  ++ F
Sbjct: 166 RTIDKRYHALVQGHPDPSSGTIDAPIGR--HRSNDWKFAVTADGK---PSITHYDTVEAF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q    L++   TGRTHQ+RVH   +  P  GD  Y A+ +      ++ + +LHAR + 
Sbjct: 221 -QAASLLDIHLETGRTHQIRVHFAALRHPCCGDLTYGADPRLAERLGLERQ-WLHARSLG 278

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
             HP  GR ++IT+  P  +    D+LG 
Sbjct: 279 FAHPADGRWVEITSKYPKDLE---DALGV 304


>gi|282881245|ref|ZP_06289932.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
 gi|281305049|gb|EFA97122.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
          Length = 566

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 68/208 (32%), Positives = 105/208 (50%), Gaps = 18/208 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + V +KPAGI    G      +   L+S + S  +   + HRLD  TSG+L++
Sbjct: 353 VVYEDDALIVVDKPAGILSVPGRSQRPSVYSILRSQMPSSVELFSV-HRLDMATSGLLIL 411

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+     +HL   FR   IQK Y +++ G   +++E +    L+      D    V   E
Sbjct: 412 AKNSVVYRHLQRQFRTHHIQKEYIAILEGA-LSQREGVVTLPLRPDPF--DRPRQVVDWE 468

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFK 277
            G   A++ ++V++    K  W+ + P TGRTHQLR+H  H   + CPI+GD  Y  +  
Sbjct: 469 HGKK-AVTSYRVLNVRHGK-TWVALFPETGRTHQLRMHCAHAEGLNCPILGDPLYGHH-- 524

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRL 305
                   N+LYLHA  +   HP  G+L
Sbjct: 525 -------ANRLYLHATSITFEHPISGQL 545


>gi|168494358|ref|ZP_02718501.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae CDC3059-06]
 gi|221231700|ref|YP_002510852.1| RNA pseudouridylate synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225854435|ref|YP_002735947.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae JJA]
 gi|183575636|gb|EDT96164.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae CDC3059-06]
 gi|220674160|emb|CAR68683.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           ATCC 700669]
 gi|225722558|gb|ACO18411.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae JJA]
          Length = 295

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 83/308 (26%), Positives = 147/308 (47%), Gaps = 45/308 (14%)

Query: 41  LRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + +G +R+DK         R   N +I+SGQV+ +   +    + ++E  ++   V   +
Sbjct: 5   IETGGLRLDKALSDLSELSRSLANEQIKSGQVL-VNGQVKKAKYTVQEGDVVTYHVPEPE 63

Query: 93  HSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG-- 141
             +++   L    +Y+D  + V NKP G+ V   +G   H  G L + +     D  G  
Sbjct: 64  VLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGIN 120

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I 
Sbjct: 121 GVLRPGIVHRIDKDTSGLLMIAKNDDAHLVLAQELKDKKSLRKYWAIVHGNLPNDRGVI- 179

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++ IG       KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 180 -----EAPIGRSEKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           H  ++G  + GD  Y      KG+         +LHA+ +   HP  G+ L+  A +P  
Sbjct: 233 HMAYIGHSVAGDEVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGKTLEFKADIPEI 285

Query: 315 MVKTWDSL 322
             +T + L
Sbjct: 286 FKETLERL 293


>gi|167854620|ref|ZP_02477401.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           parasuis 29755]
 gi|167854375|gb|EDS25608.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           parasuis 29755]
          Length = 222

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 67/202 (33%), Positives = 103/202 (50%), Gaps = 13/202 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y     ++  V  K       HRLD  TSGIL+ A
Sbjct: 17  VYCDNHILVINKPSGLLSVPGNRPEYQDSAMVR--VQQKYGFTEPAHRLDMATSGILLFA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
            ++ A + L   FR R  +K Y +LVWG      E + +       +  D+ +  +Q   
Sbjct: 75  LSKQAEKELKRQFREREPKKHYQALVWG---KLGEKVGDTGTMNFPLICDWENRPRQKIC 131

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   A++ ++++  +      + + P+TGR+HQLRVH L +G PIVGD K+ AN   
Sbjct: 132 YERGKQ-AVTFYEILAHYPNNTTRVTLTPYTGRSHQLRVHCLALGHPIVGD-KFYANPLA 189

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
              SP   +L LHA  + + HP
Sbjct: 190 KSLSP---RLCLHAEALTITHP 208


>gi|15803118|ref|NP_289149.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 EDL933]
 gi|12517018|gb|AAG57707.1|AE005490_2 suppressor of ftsH mutation [Escherichia coli O157:H7 str. EDL933]
          Length = 326

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 90/339 (26%), Positives = 158/339 (46%), Gaps = 47/339 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V   
Sbjct: 9   ATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQV--- 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             INA   I +E +     + L          ++YED  I V NKP  + V  G+G   +
Sbjct: 66  -AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + 
Sbjct: 111 PDGTXLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH + +       A++H+++++ F + 
Sbjct: 171 YEAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPMGKP------AVTHYRIMEHF-RV 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
           A  + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 281 ATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 319


>gi|147771519|emb|CAN66750.1| hypothetical protein VITISV_034413 [Vitis vinifera]
          Length = 611

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 83/309 (26%), Positives = 140/309 (45%), Gaps = 53/309 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK----FNNRIQSGQVV 65
           V V +D   +RLD W  +    I+   +Q  +RSG V V+ + V      + + + G+  
Sbjct: 197 VDVNSDSGKLRLDSWISSRIIGISRARVQSSIRSGLVSVNDRIVDKAMLVSRKFEVGEGK 256

Query: 66  RIP---PVI--NALNHIIKEQKILDSSVN----LTKHSDFLKSILLYEDSKIYVFNKPAG 116
           +I    P+     ++H+I+    ++ +++    L    + +   ++YED  + V   P  
Sbjct: 257 KIEEKDPITYSEQVSHVIRAGDKVNCTISELQPLRAEPEDIPLDIVYEDEHV-VHPAPGN 315

Query: 117 ISVQGGSGIAYHI--------------DGFLKSWVDS--KGQ---------KPRLTHRLD 151
            S    +GI +H               D  L    +S   GQ         +P + HRLD
Sbjct: 316 ASGTLVNGILHHCSLPTVALPNRDSEEDDILDDEFNSFAAGQNCGTCETNIRPGIVHRLD 375

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-------ANWLLK 204
           + TSG+LVVA+   +  HL+E F++  I ++Y SL  G+P      +        N  ++
Sbjct: 376 KGTSGLLVVAKDEHSHAHLSEQFKLHSIHRVYISLTSGVPTPLSGRVEIPVGRDPNNRIR 435

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMG 263
            + + G        N   A +A S +KVI+  A     L E +  TGRTHQ+R HA ++G
Sbjct: 436 MTAVPG------PSNSGQARHAASRYKVIEILAAGGSALVEWRLETGRTHQIRAHAKYLG 489

Query: 264 CPIVGDHKY 272
            P++GD  Y
Sbjct: 490 IPLLGDEVY 498


>gi|157960566|ref|YP_001500600.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157845566|gb|ABV86065.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 225

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 64/202 (31%), Positives = 102/202 (50%), Gaps = 15/202 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  I V NKP+G+    G   A+    + +   +    K  + HRLD  TSG++VV
Sbjct: 16  VLHQDKDIMVVNKPSGLLSVPGRDPAHADSTYTRVLAEFPHAK--IVHRLDMATSGVIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A  R+A   L   FR R  QK Y++ V G  K     I   L+       D+ +  KQ  
Sbjct: 74  ALLRSAESELKRQFRDRETQKTYYARVAGHVKQSHGTINLPLI------CDWPNRPKQKV 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + K    + +H++VI  + ++   +++ P TGR+HQLRVH + +G PI+GD+ Y      
Sbjct: 128 DHKIGKPSQTHYEVI-SYGKRSTLVKLTPITGRSHQLRVHMMALGHPILGDNFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                   +L LHA+ + + HP
Sbjct: 187 RLAP----RLLLHAQSLTITHP 204


>gi|253988118|ref|YP_003039474.1| tRNA pseudouridine synthase C [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253779568|emb|CAQ82729.1| tRNA pseudouridine synthase C [Photorhabdus asymbiotica]
          Length = 256

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 71/223 (31%), Positives = 112/223 (50%), Gaps = 19/223 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I   NKPAG  V   S +A H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 4   VLYQDDHIVAVNKPAGWLVHR-SWLARHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A +   A+ L++ F   ++QK Y ++V G            + +   I   +      +
Sbjct: 63  MALSSDIARQLSQQFEHHQLQKTYHAVVRGYVLESDVIDYALVEELDKIADKFA----DS 118

Query: 220 EKGANYAISHFKV---IDCFAQ-------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +KGA  +I++++    ++C  +       +F  LE+ P TGR HQLR H  H+  PI+GD
Sbjct: 119 DKGAQPSITYYRPLAKVECPVEIGRYPTSRFSLLELTPKTGRKHQLRRHMAHIRHPIIGD 178

Query: 270 --HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
             H      +G       N+L LHA ++ L HP  G +L +TA
Sbjct: 179 TTHGDLRQNRGISAHYQTNRLMLHASHLKLDHPVTGEQLSLTA 221


>gi|288926989|ref|ZP_06420884.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           D17]
 gi|315608748|ref|ZP_07883726.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
 gi|288336235|gb|EFC74621.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           D17]
 gi|315249598|gb|EFU29609.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
          Length = 294

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 110/233 (47%), Gaps = 17/233 (7%)

Query: 87  SVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           SV+  K +D  +S    L+YED  I V  K  GI        + ++   L  +     QK
Sbjct: 66  SVSRNKRNDTFRSRYVRLVYEDRHIVVLEKAVGILSMAAGHSSLNVKKVLDDYFKKTRQK 125

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               + HRLD++TSG+++ A+++   Q L   +      + Y ++V G   + +  IANW
Sbjct: 126 CTAHVVHRLDRDTSGLMIYAKSKEIEQMLEHDWHHVVYDRRYVAVVSGEVYDDEGTIANW 185

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L         YV      + G  YA++HF V+         +E +  TGR +Q+RVH+  
Sbjct: 186 LKDNK----AYVTYSSPVDNGGKYAVTHFHVLR-RTTDHSLVEYRLETGRKNQIRVHSAD 240

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           MG P+ GD KY     GN   P+  +L LHA  +   HP    R++   P+P+
Sbjct: 241 MGHPVCGDIKY-----GNGDDPLH-RLCLHAYVLCFYHPVTHERMEFDTPVPS 287


>gi|260575494|ref|ZP_05843493.1| pseudouridine synthase, RluA family [Rhodobacter sp. SW2]
 gi|259022414|gb|EEW25711.1| pseudouridine synthase, RluA family [Rhodobacter sp. SW2]
          Length = 356

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 91/363 (25%), Positives = 147/363 (40%), Gaps = 81/363 (22%)

Query: 10  VVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQ-- 63
           VV+  D  + RLD+      P    ++   L K++  G V ++   V     R+  GQ  
Sbjct: 22  VVIGEDPPD-RLDKALARQVPEDAALSRSRLMKMIADGDVTLEGVAVTNPKARVAEGQEY 80

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++R+ P                 +V++    + +   +++ED+ + V +KP G+ V    
Sbjct: 81  LLRLAP-----------------AVDIDAQPEDIPLTVVWEDADLIVVDKPVGMVVHPAP 123

Query: 124 G--IAYHIDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  L    D+       ++P + HR+D++TSG+LVVA+T  A   L   F  
Sbjct: 124 GSYTGTLVNALLHHCGDTLSGVGGAKRPGIVHRIDKDTSGLLVVAKTDRAHHGLAAQFEA 183

Query: 177 RRIQKIYWSLVWGIPKNKKE----------------CIANWLLKKSHIGGDYVHVVKQNE 220
             + + Y +LV G P                     CIA  L +         H   +  
Sbjct: 184 HSVTRHYIALVHGAPNAADPRLRGIRGVSFEPGGIVCIATNLAR---------HKTDRQR 234

Query: 221 KG-----ANYAISHFKVIDCF------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +        +A++  +V++ +      A   CWLE    TGRTHQ+RVH  H G  ++GD
Sbjct: 235 QAVLFDSGRHAVTRVRVLESYGTPPVAALVECWLE----TGRTHQIRVHMSHAGHALLGD 290

Query: 270 HKYCANFK------GNFTSPIQNKL---YLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
             Y    K      G   +   N      LHA  +   HP  G  L  T+PLPA M    
Sbjct: 291 QTYGGRRKVAPKAVGEAVAQAANDFPRQALHAASLGFVHPVSGEELLFTSPLPADMAALT 350

Query: 320 DSL 322
            +L
Sbjct: 351 AAL 353


>gi|229845163|ref|ZP_04465297.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae 6P18H1]
 gi|229811874|gb|EEP47569.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae 6P18H1]
          Length = 324

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 121/249 (48%), Gaps = 41/249 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPR--LTHR 149
           ++YED  I V NKP  + V  G+G         + YH             + PR  + HR
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI--------AEVPRAGIVHR 136

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKS 206
           LD++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++
Sbjct: 137 LDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRT 196

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +    VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P+
Sbjct: 197 LMA---VHPMGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPL 246

Query: 267 VGDHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           +GD  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+
Sbjct: 247 LGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLVHPITGEMMEWYAPLPDDFVE 306

Query: 318 TWDSLGFKY 326
             ++L   Y
Sbjct: 307 LLNALKADY 315


>gi|261408890|ref|YP_003245131.1| RluA family pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261285353|gb|ACX67324.1| pseudouridine synthase, RluA family [Paenibacillus sp. Y412MC10]
          Length = 354

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 75/250 (30%), Positives = 113/250 (45%), Gaps = 43/250 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSG 156
           +LYED  + V NKPAG+ V    G       +G +  W   KG   + R  HRLDQETSG
Sbjct: 86  ILYEDEHLLVLNKPAGVIVHPTHGHYTDTLANGVVHYW-QEKGWNYRFRAVHRLDQETSG 144

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV+A+     QH++E      + K Y + V G P ++   I         I  D +   
Sbjct: 145 VLVIAKNAYIHQHVSEQMIAGTVDKRYVAFVHGRPSSQTGDI------DGPIDRDPLEPH 198

Query: 217 KQNEKGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--- 272
           ++      Y +++ ++V + +      +E++  TGRTHQ+RVH L +GCP++GD  Y   
Sbjct: 199 RRIVTPEGYPSLTRYRVCETYPSA-SLVELKLETGRTHQIRVHMLSIGCPLIGDQMYRHP 257

Query: 273 ----------------CANFKGNFTSPI----------QNKLYLHARYMDLPHP-EGGRL 305
                            +N       P+           ++  LHA  + L HP EG  +
Sbjct: 258 VYSEQGLLPDAPERDEDSNGAVGSLDPLAATIMRLDGYMDRQALHAASLTLMHPIEGKTM 317

Query: 306 QITAPLPAHM 315
             TAPLP  M
Sbjct: 318 VFTAPLPEDM 327


>gi|154492071|ref|ZP_02031697.1| hypothetical protein PARMER_01702 [Parabacteroides merdae ATCC
           43184]
 gi|154087857|gb|EDN86902.1| hypothetical protein PARMER_01702 [Parabacteroides merdae ATCC
           43184]
          Length = 359

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 88/338 (26%), Positives = 151/338 (44%), Gaps = 53/338 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V +  +  +R+D++  +         +Q    +G +  + K VK N R++   VV I   
Sbjct: 36  VADRGQSLLRVDKFLVDRMFGATRNRIQSAADAGCIMANGKPVKSNYRVKPEDVVTI--- 92

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----I 125
              +    +  +IL  ++ +          ++YED  + V +KPAG+ V  G G     +
Sbjct: 93  --MMTRPPRTFEILPENIPIK---------IVYEDDDLLVVDKPAGLVVHPGHGNYTGTL 141

Query: 126 AYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              +  +LK         P L   HR+D++TSG+LVVA+   A  HL+  F  +  ++ Y
Sbjct: 142 VNALAWYLKDDPTYDPNDPALGLVHRIDKDTSGLLVVAKKPEAKAHLSMQFFHKTTKREY 201

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQ 238
            +LVWGI +  +  I      + +IG +      + V  + ++G   A++H+ V++    
Sbjct: 202 RALVWGIVREDEGRI------EGNIGRNPRDRMQMTVFPEGDQGKT-AVTHYSVLERLGY 254

Query: 239 KF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------P 283
                C LE    TGRTHQ+RVH  ++G  +  D +Y  N   KG  +S           
Sbjct: 255 VTLVKCRLE----TGRTHQIRVHMKYIGHTLFNDERYGGNEILKGTTSSKYKQFVDNCFA 310

Query: 284 IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
           I  +  LHA+ +   HP  G  +   + +PA M    D
Sbjct: 311 ICPRQALHAKTLGFVHPTTGEEMFFDSEIPADMTALID 348


>gi|325496332|gb|EGC94191.1| 23S rRNA pseudouridine synthase D [Escherichia fergusonii ECD227]
          Length = 326

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 90/338 (26%), Positives = 159/338 (47%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           +V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V    
Sbjct: 10  MVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            INA   I +E +     + L          ++YED  I V NKP  + V  G+G   + 
Sbjct: 66  AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---NP 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y
Sbjct: 112 DGTVLNALLYYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREY 171

Query: 184 WSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G         E I+    K++H+    VH + +       A++H+++++ F +  
Sbjct: 172 EAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPMGKP------AVTHYRIMEHF-RVH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHA 292
             L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA
Sbjct: 222 TRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHA 281

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
             + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 282 TMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 319


>gi|198277498|ref|ZP_03210029.1| hypothetical protein BACPLE_03720 [Bacteroides plebeius DSM 17135]
 gi|198269996|gb|EDY94266.1| hypothetical protein BACPLE_03720 [Bacteroides plebeius DSM 17135]
          Length = 356

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 88/335 (26%), Positives = 150/335 (44%), Gaps = 53/335 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV+  +  +R+D++      + +   +Q    +G V  + K VK + +++   V+ +  
Sbjct: 33  TVVDKGQAPVRIDKYLFERIVNASRNRIQMAADNGFVMANGKPVKSSYKVKPLDVLTV-- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E  I+   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 91  ---MMDRPRYENDIIPEDIPLN---------IVYEDDDLMVINKPAGLVVHPGCGNYHGT 138

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    L+         P+  L HR+D++TSG+LVVA+T  A   L   F  + 
Sbjct: 139 LVNAIAWH----LRDVPTYNPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTSLGLQFYNKT 194

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFA 237
            ++ Y +LVWGI +  +  I   + +      D + + V  + +   +A++H++V++   
Sbjct: 195 TKREYNALVWGIVEQDEGTITGNIGRNPR---DRMQMAVMSDPEQGKHAVTHYQVLERLG 251

Query: 238 QKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS---------- 282
                 C LE    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S          
Sbjct: 252 YVTLVKCVLE----TGRTHQIRVHMKHIGHTLFNDERYGGHEILKGTHFSKYKQFVNNCF 307

Query: 283 PIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
            I  +  LHA+ +   HP  G  +  T+ LP  M 
Sbjct: 308 EICPRQALHAKTLGFVHPRTGEEMFFTSELPEDMT 342


>gi|331684250|ref|ZP_08384842.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli H299]
 gi|222034298|emb|CAP77039.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           LF82]
 gi|312947168|gb|ADR27995.1| 23S rRNA pseudouridine synthase D [Escherichia coli O83:H1 str. NRG
           857C]
 gi|331077865|gb|EGI49071.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli H299]
          Length = 326

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 253 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPEDMVELIEVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|259909396|ref|YP_002649752.1| 23S rRNA pseudouridine synthase D [Erwinia pyrifoliae Ep1/96]
 gi|224965018|emb|CAX56548.1| Ribosomal large subunit pseudouridine synthase D [Erwinia
           pyrifoliae Ep1/96]
 gi|283479469|emb|CAY75385.1| ribosomal large subunit pseudouridine synthase D [Erwinia
           pyrifoliae DSM 12163]
          Length = 325

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 75/253 (29%), Positives = 129/253 (50%), Gaps = 33/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDEDILVVNKPRDLVVHPGAG---NPDGTVLNALLHHFPAIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL ++ + R I + Y ++  G         + I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVDALQRREITREYEAVAIGRMTAGGTVDQPISRHSTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A +H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------ATTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMSHISHPLVGDPL 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F + ++  ++  LHA  + L HP  G  ++  APLP  MV   D+L
Sbjct: 253 YGGRPRPPKGASEAFIATLRAFDRQALHATMLRLYHPISGIEMEWHAPLPQDMVDLIDAL 312

Query: 323 GFKYDRNLYIKRL 335
             K D   + ++L
Sbjct: 313 --KADTEAFKEQL 323


>gi|109897951|ref|YP_661206.1| pseudouridylate synthase [Pseudoalteromonas atlantica T6c]
 gi|109700232|gb|ABG40152.1| Pseudouridylate synthase [Pseudoalteromonas atlantica T6c]
          Length = 223

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/223 (29%), Positives = 114/223 (51%), Gaps = 30/223 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LY+D  +   NKP+G+    G        + Y I     + +        + HRLD  T
Sbjct: 19  VLYQDEYLLAVNKPSGLLSLSGKNPLNKDSVHYRIVQEFPTAL--------MAHRLDFGT 70

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A  + +   LT+ F+ R ++K Y +++ G  +  +  ++  + K      D  +
Sbjct: 71  SGVLLLALDKNSNAQLTKQFQARTVKKRYTAVLLGKIEQTEGRVSVPIAK------DPPN 124

Query: 215 VVKQN---EKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +Q    + G   AISH++VI+      C  +E  P TGRTHQLR+H+L MG PI+G  
Sbjct: 125 FPRQKICYDTGKE-AISHYRVIEYVDNPLCTRVEFTPETGRTHQLRLHSLAMGHPILG-- 181

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             C  +  + +  + ++L LHA ++   HP  G+ ++I AP+P
Sbjct: 182 --CDLYGNSHSVQMASRLLLHASHIKFTHPYSGKSMEIEAPIP 222


>gi|332184383|gb|AEE26637.1| Ribosomal large subunit pseudouridine synthase D [Francisella cf.
           novicida 3523]
          Length = 331

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 84/320 (26%), Positives = 144/320 (45%), Gaps = 38/320 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K    +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDIAINEQFEQFSRAQIQKWLKEGSIIVNGQATKPKYIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E                +K  ++YED  I V +KP  + V  G+G   
Sbjct: 72  NVELLPTNEWIAED---------------IKLNIIYEDDDIIVIDKPVNMVVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +  L  + D + + PR  + HRLD++TSG++V A++  A  +L +    R++ + Y
Sbjct: 117 GTVSNALLHRYKD-QDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC 241
            ++V G      E      + +  IG D  +  K   N +G   AI+H+  I+ +   F 
Sbjct: 176 LAIVEG------EIYQQGTINQP-IGRDSTNRTKMAINHRGKE-AITHYTPIEVY-DGFT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF----KGNFTSPIQNKLYLHARYMDL 297
            LE Q  TGRTHQ+RVH   +  P+VGD  Y  +     K   T+P +    LHA  +  
Sbjct: 227 LLECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITTPTRQA--LHAYKLSF 284

Query: 298 PHPEGGRL-QITAPLPAHMV 316
            HP+  ++ +  + LP  M+
Sbjct: 285 IHPKTAKIVKFKSKLPEDML 304


>gi|325285555|ref|YP_004261345.1| pseudouridine synthase [Cellulophaga lytica DSM 7489]
 gi|324321009|gb|ADY28474.1| pseudouridine synthase [Cellulophaga lytica DSM 7489]
          Length = 287

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 71/220 (32%), Positives = 106/220 (48%), Gaps = 34/220 (15%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK----GQKP 144
           N TK    LK  ++++D+ + + NKP GI V G +     ID  L+  +         KP
Sbjct: 71  NNTKKRLNLKLEVVFQDNYLAIINKPPGILVSGNT--FKTIDNALEQNITKSSLPDATKP 128

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  HRLD  T+G+L++ +T A+   L + F  ++IQK Y ++  G            ++K
Sbjct: 129 RPVHRLDFPTTGLLIIGKTSASILALNKLFENKKIQKTYLAVTIG-----------EMIK 177

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL---EMQPHTGRTHQLRVHALH 261
           K  I  +    V   E    Y +    +    + KF +L   +++P TGR HQLRVH   
Sbjct: 178 KGTINTN----VDNKEAFTTYNV----LKTVTSNKFNYLNLVKLEPKTGRKHQLRVHLSS 229

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHP 300
           +  PI+GD KY    K      I+ K LYLHA  +D  HP
Sbjct: 230 INNPILGDAKYGIPGK-----IIKGKGLYLHAYSLDFTHP 264


>gi|257900349|ref|ZP_05680002.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|257838261|gb|EEV63335.1| pseudouridine synthase [Enterococcus faecium Com15]
          Length = 285

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 69/205 (33%), Positives = 105/205 (51%), Gaps = 23/205 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+            +   L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKKQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            A+       L      + I + Y ++VWG I K++   I N + +  H   D    V  
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGEIAKDR--TITNKIGRDRH---DRRKRVVD 197

Query: 219 NEKGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           ++ G N A++H    KV+    Q +C LE    TGRTHQ+RVH  H+G PIVGD  Y   
Sbjct: 198 DKNGQN-ALTHVTVDKVLSGKTQVYCVLE----TGRTHQIRVHLAHIGHPIVGDPLYQ-- 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                  P + +L LHA  + + HP
Sbjct: 251 -----NRPAE-RLMLHALELHMIHP 269


>gi|255073601|ref|XP_002500475.1| predicted protein [Micromonas sp. RCC299]
 gi|226515738|gb|ACO61733.1| predicted protein [Micromonas sp. RCC299]
          Length = 327

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 78/297 (26%), Positives = 123/297 (41%), Gaps = 73/297 (24%)

Query: 86  SSVNLTKHSDFLKSIL---LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           S +++  H+    S +   L+ D+ + V +KPAG+ ++   G+   +D FL         
Sbjct: 9   SRIDVCAHAPRAASAVSWVLHRDADVLVVDKPAGVPMRSVHGV-KGVDAFLADLRFDLAH 67

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR---------------------IQK 181
            P   HRLD++T+G L++ARTR A + L   F+ R                      +++
Sbjct: 68  PPMTVHRLDRDTTGCLILARTREAQRTLAGYFQDRARVARRGSGRSTKTTSPESLGDVRR 127

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +YW+LV            +  L  +H G     V  +   GA  A + ++VI   +   C
Sbjct: 128 VYWALVSATSTLASRGTIDAALVTTHAG-----VTLKPGAGAKPAATDYEVISRASPDSC 182

Query: 242 W----------LEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYC----------------- 273
                      L + P TGR HQLRVH A  +   IVGD+KY                  
Sbjct: 183 APTAAGRVPAVLALVPRTGRKHQLRVHCAGALDAAIVGDYKYGYRDVSRTGGVADDWRRV 242

Query: 274 -----------ANFKGNFTSPIQNK---LYLHARYMDLPHPEGG-RLQITAPLPAHM 315
                       N  G     ++     L+LHAR ++  HP  G R+++ AP P+HM
Sbjct: 243 LRDIDERSTRRLNDAGTADGEVRGAGVPLHLHARCVEFTHPSSGERVRVVAPAPSHM 299


>gi|210624201|ref|ZP_03294256.1| hypothetical protein CLOHIR_02212 [Clostridium hiranonis DSM 13275]
 gi|210153188|gb|EEA84194.1| hypothetical protein CLOHIR_02212 [Clostridium hiranonis DSM 13275]
          Length = 226

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 56/182 (30%), Positives = 91/182 (50%), Gaps = 8/182 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ + V  KP  I  QG +     +   LK+++  K  KP      L HRLD+   
Sbjct: 8   VLYEDNHLLVVEKPVNILSQGDNTNDKDMVNLLKAYLKEKYNKPGNVYLGLVHRLDRPVG 67

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G +V A+T  AA  L+E  R +  +K Y +++ G  + + + + ++L K      + V V
Sbjct: 68  GAMVFAKTSKAASRLSEQVRNKTFKKTYRAVINGKMRKQSDTLKDYLYKNKKT--NMVSV 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V ++ K + YA   +  +  F  K   +++   TGR HQ+RV       P+VGD +Y  N
Sbjct: 126 VSESHKDSKYAELSYATL-AFKDKMSLVQIDLKTGRPHQIRVQFASRNNPLVGDQRYGKN 184

Query: 276 FK 277
            K
Sbjct: 185 SK 186


>gi|120403758|ref|YP_953587.1| RluA family pseudouridine synthase [Mycobacterium vanbaalenii
           PYR-1]
 gi|119956576|gb|ABM13581.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           vanbaalenii PYR-1]
          Length = 309

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 79/296 (26%), Positives = 142/296 (47%), Gaps = 36/296 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
           G V +D  R   ++++ +G    VR+P              + ++ V++          +
Sbjct: 39  GGVELDGARAAKSDKLTAGAWLEVRLPEA---------PAPVENTPVDIEGMG------I 83

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYH----IDGFLKSW--VDSKG--QKPRLTHRLDQE 153
           LY D  I   +KP G++    + + +H    + G   +   + + G  ++  + HRLD  
Sbjct: 84  LYSDEDIVAVDKPPGVAAH--ATVGWHGPTVLGGLAAAGFRISTSGIHERQGIVHRLDVG 141

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA +  A   L  +F+ R ++K Y +LV G P      I   + +  H G D+ 
Sbjct: 142 TSGVMVVALSERAYTALKRAFKQRTVEKRYHALVQGHPDPSSGTIDAPIGR--HRGHDWK 199

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V +   G  ++++H+  ++   Q    L+++  TGRTHQ+RVH   +  P  GD  Y 
Sbjct: 200 FAVVE---GGRHSVTHYDTLEAH-QAASLLDIELETGRTHQIRVHFAALHHPCCGDLTYG 255

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A+        ++ + +LHAR +   HP +G R++IT+P PA +    D L  ++DR
Sbjct: 256 ADPTLAKKLGLERQ-WLHARSLAFVHPADGRRIEITSPYPADLQHALDVL-RQHDR 309


>gi|226945565|ref|YP_002800638.1| Pseudouridylate synthase RluA [Azotobacter vinelandii DJ]
 gi|226720492|gb|ACO79663.1| Pseudouridylate synthase RluA [Azotobacter vinelandii DJ]
          Length = 211

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 69/214 (32%), Positives = 112/214 (52%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ D  + V NKP  + SV G +    + D  +    ++   + R+ HRLD ETSG++V
Sbjct: 8   IVHRDDALLVVNKPTLLLSVPGRA--EDNRDCLVTRLQENGYPEARIVHRLDWETSGLIV 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG P+     I   L  +        HVV Q 
Sbjct: 66  LARDADSHRELSRQFHDRETEKAYTALCWGEPEADSGRIE--LPLRYDPPTKPRHVVDQQ 123

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +    +A++ ++V++    +F  +E+ P TGR+HQLRVH L +G P++GD  Y     G 
Sbjct: 124 Q--GRHALTFWRVLE-RCGRFSRIELTPITGRSHQLRVHMLAIGHPLLGDRLYA---HGE 177

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
             +  + +L LHA  + L HP  G RL+  +P P
Sbjct: 178 ALAAAE-RLCLHASLLVLGHPRSGERLRFESPAP 210


>gi|227550294|ref|ZP_03980343.1| pseudouridylate synthase RluD [Enterococcus faecium TX1330]
 gi|227180554|gb|EEI61526.1| pseudouridylate synthase RluD [Enterococcus faecium TX1330]
          Length = 299

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 69/205 (33%), Positives = 105/205 (51%), Gaps = 23/205 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+            +   L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 97  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKKQRPYVVHRLDKETSGAVL 156

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            A+       L      + I + Y ++VWG I K++   I N + +  H   D    V  
Sbjct: 157 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGKIAKDR--TITNKIGRDRH---DRRKRVVD 211

Query: 219 NEKGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           ++ G N A++H    KV+    Q +C LE    TGRTHQ+RVH  H+G PIVGD  Y   
Sbjct: 212 DKNGQN-ALTHVTVDKVLSGKTQVYCVLE----TGRTHQIRVHLAHIGHPIVGDPLYQ-- 264

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                  P + +L LHA  + + HP
Sbjct: 265 -----NRPAE-RLMLHALELHMIHP 283


>gi|257889020|ref|ZP_05668673.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257897615|ref|ZP_05677268.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|293571088|ref|ZP_06682128.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E980]
 gi|257825083|gb|EEV52006.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257834180|gb|EEV60601.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|291608818|gb|EFF38100.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E980]
          Length = 285

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 69/205 (33%), Positives = 105/205 (51%), Gaps = 23/205 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+            +   L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKKQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            A+       L      + I + Y ++VWG I K++   I N + +  H   D    V  
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGKIAKDR--TITNKIGRDRH---DRRKRVVD 197

Query: 219 NEKGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           ++ G N A++H    KV+    Q +C LE    TGRTHQ+RVH  H+G PIVGD  Y   
Sbjct: 198 DKNGQN-ALTHVTVDKVLSGKTQVYCVLE----TGRTHQIRVHLAHIGHPIVGDPLYQ-- 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                  P + +L LHA  + + HP
Sbjct: 251 -----NRPAE-RLMLHALELHMIHP 269


>gi|218283674|ref|ZP_03489635.1| hypothetical protein EUBIFOR_02229 [Eubacterium biforme DSM 3989]
 gi|218215663|gb|EEC89201.1| hypothetical protein EUBIFOR_02229 [Eubacterium biforme DSM 3989]
          Length = 295

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 76/304 (25%), Positives = 144/304 (47%), Gaps = 38/304 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           + +  ++ N RLD++    +P +    + K +R+ +++V++KR  F+ +IQ    + +  
Sbjct: 4   IKINQNDANQRLDKFLMKTFPKLGKSMMYKAIRNKKIKVNRKRCTFDQKIQENDSILLFL 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL--LYEDSKIYVFNKPAGISVQGGSG- 124
           PP       +++E+K+          ++++ S L  +YED  I + NKP G+  Q     
Sbjct: 64  PP------DVLEEKKV---------ETNYISSKLDVIYEDENILIVNKPYGLLSQSDQSQ 108

Query: 125 ----IAYHIDGFL--KSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
               +   +  +L  K+  D   +    P + HRLD+ T+G+++ A+   A + + E+  
Sbjct: 109 NQDCLVNRVQAYLMEKNEYDPNKEHSFAPSICHRLDRNTTGLVIAAKNANALRKVNEAIA 168

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-D 234
            R IQK+Y + V G  + K   +  ++ K++ I      V  +  +G   A+    V  D
Sbjct: 169 NRTIQKMYRAHVVGTFEQKDFTMCYYIRKENTIAK----VSDKKLEGYQKALMDVHVERD 224

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                 C + +  HTGR HQ+R    H+  P++GD KY  + K      +  +L  H   
Sbjct: 225 DGENSICTITL--HTGRFHQIRALMGHIQHPLLGDVKYGYHGKKRPIELMAYRLEFHE-- 280

Query: 295 MDLP 298
           +DLP
Sbjct: 281 VDLP 284


>gi|332753864|gb|EGJ84241.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           4343-70]
 gi|332997822|gb|EGK17432.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           K-218]
          Length = 326

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 90/338 (26%), Positives = 157/338 (46%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V    
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            INA   I +E +     + L          ++YED  I V NKP  + V  G+G   + 
Sbjct: 66  AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---NP 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y
Sbjct: 112 DGTVLNALLHYYPPIADVPRSGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREY 171

Query: 184 WSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G         E I+    K++H+    VH +         A++H+++++ F +  
Sbjct: 172 EAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPM------GKPAVTHYRIMEHF-RVH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHA 292
             L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA
Sbjct: 222 TRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHA 281

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
             + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 282 TMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 319


>gi|217974669|ref|YP_002359420.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499804|gb|ACK47997.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 225

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 68/208 (32%), Positives = 105/208 (50%), Gaps = 21/208 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           +LY+D  I V NKP+G+ SV G S   Y        +   K + P  ++ HRLD  TSG+
Sbjct: 16  ILYQDKDIIVINKPSGLLSVPGRSPAHYD-----SVYARVKAEHPHSQIVHRLDMATSGV 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +VVA  R+A + L   F  R   K Y++ V G  KN    +   L+       D+ +  K
Sbjct: 71  IVVALIRSAERELKRQFHDRETSKTYFARVAGHVKNDTGSVDYPLI------CDWPNRPK 124

Query: 218 Q--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           Q  +      +++H++VI   A++   +++ P TGR+HQLRVH + +G PI+GD  Y   
Sbjct: 125 QKVDHLVGKPSLTHYQVI-SRAKRSTLVKLTPITGRSHQLRVHMMALGHPILGDGFYADP 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +       +L LHA  + + HP  G
Sbjct: 184 LAKSLAP----RLLLHAAELTIKHPYTG 207


>gi|117624818|ref|YP_853731.1| 23S rRNA pseudouridine synthase D [Escherichia coli APEC O1]
 gi|218559515|ref|YP_002392428.1| 23S rRNA pseudouridine synthase D [Escherichia coli S88]
 gi|237706817|ref|ZP_04537298.1| 23S rRNA pseudouridine synthase D [Escherichia sp. 3_2_53FAA]
 gi|115513942|gb|ABJ02017.1| 23S rRNA pseudouridine synthase [Escherichia coli APEC O1]
 gi|218366284|emb|CAR04036.1| 23S rRNA pseudouridine synthase [Escherichia coli S88]
 gi|226899857|gb|EEH86116.1| 23S rRNA pseudouridine synthase D [Escherichia sp. 3_2_53FAA]
 gi|315284807|gb|EFU44252.1| pseudouridine synthase, RluA family [Escherichia coli MS 110-3]
 gi|323951205|gb|EGB47081.1| RluA family protein pseudouridine synthase [Escherichia coli H252]
 gi|323957037|gb|EGB52763.1| RluA family protein pseudouridine synthase [Escherichia coli H263]
          Length = 326

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 123/247 (49%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH +         A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPM------GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 253 YGGRPRPPKGASEAFISTLRKFDRQSLHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|225571170|ref|ZP_03780168.1| hypothetical protein CLOHYLEM_07258 [Clostridium hylemonae DSM
           15053]
 gi|225160001|gb|EEG72620.1| hypothetical protein CLOHYLEM_07258 [Clostridium hylemonae DSM
           15053]
          Length = 242

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 107/238 (44%), Gaps = 44/238 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-------LTHRLDQE 153
           +LYED  I V  KP G +VQ  +  A  +   LK+ + S  Q+P+       + HRLDQ 
Sbjct: 8   ILYEDKDIIVCVKPHGTAVQTKNTSAPDMVSMLKTHIFS--QEPQNGEPYLAVIHRLDQP 65

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
             GILV A++  AA+ L    + +   K Y +LV GIP  +++ + N++LK      +  
Sbjct: 66  VEGILVFAKSPFAAKELNRQLQNKGFGKYYRALVDGIPPREEDTLENYMLKDGRT--NTS 123

Query: 214 HVVKQNEKGANYAISHFKVID------------------------CFAQKFCWLEMQPHT 249
            +   +  GA  A  H+K+I                           A     L++Q  T
Sbjct: 124 RICTPDTPGAKQARLHYKIIQEGHGYFKKGHGETKRGRGKSQFPPSPAGPQTELDIQLDT 183

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR 304
           GR HQ+RV   H+GCPI GD KY      N  +P      ++ L A  +   HP  GR
Sbjct: 184 GRHHQIRVQMAHLGCPIAGDTKY------NPGAPNDGEWQQIQLCAYKLSFRHPRTGR 235


>gi|24113932|ref|NP_708442.1| 23S rRNA pseudouridine synthase D [Shigella flexneri 2a str. 301]
 gi|26248957|ref|NP_754997.1| 23S rRNA pseudouridine synthase D [Escherichia coli CFT073]
 gi|30063991|ref|NP_838162.1| 23S rRNA pseudouridine synthase D [Shigella flexneri 2a str. 2457T]
 gi|74313153|ref|YP_311572.1| 23S rRNA pseudouridine synthase D [Shigella sonnei Ss046]
 gi|110642757|ref|YP_670487.1| 23S rRNA pseudouridine synthase D [Escherichia coli 536]
 gi|110806535|ref|YP_690055.1| 23S rRNA pseudouridine synthase D [Shigella flexneri 5 str. 8401]
 gi|191174579|ref|ZP_03036074.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           F11]
 gi|218555174|ref|YP_002388087.1| 23S rRNA pseudouridine synthase D [Escherichia coli IAI1]
 gi|218696219|ref|YP_002403886.1| 23S rRNA pseudouridine synthase D [Escherichia coli 55989]
 gi|293411985|ref|ZP_06654708.1| rluD [Escherichia coli B354]
 gi|300940369|ref|ZP_07154957.1| pseudouridine synthase, RluA family [Escherichia coli MS 21-1]
 gi|300976568|ref|ZP_07173520.1| pseudouridine synthase, RluA family [Escherichia coli MS 200-1]
 gi|300986849|ref|ZP_07177832.1| pseudouridine synthase, RluA family [Escherichia coli MS 45-1]
 gi|301026354|ref|ZP_07189802.1| pseudouridine synthase, RluA family [Escherichia coli MS 69-1]
 gi|301050463|ref|ZP_07197345.1| pseudouridine synthase, RluA family [Escherichia coli MS 185-1]
 gi|306812486|ref|ZP_07446684.1| 23S rRNA pseudouridine synthase D [Escherichia coli NC101]
 gi|331648338|ref|ZP_08349426.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli M605]
 gi|331658744|ref|ZP_08359686.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA206]
 gi|331664161|ref|ZP_08365070.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA143]
 gi|54039250|sp|P65835|RLUD_SHIFL RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|54041741|sp|P65834|RLUD_ECOL6 RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|26109363|gb|AAN81565.1|AE016764_247 Ribosomal large subunit pseudouridine synthase D [Escherichia coli
           CFT073]
 gi|24053038|gb|AAN44149.1| ftsH mutation suppressor [Shigella flexneri 2a str. 301]
 gi|30042247|gb|AAP17972.1| ftsH mutation suppressor [Shigella flexneri 2a str. 2457T]
 gi|73856630|gb|AAZ89337.1| suppressor of ftsH mutation [Shigella sonnei Ss046]
 gi|110344349|gb|ABG70586.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           536]
 gi|110616083|gb|ABF04750.1| suppressor of ftsH mutation [Shigella flexneri 5 str. 8401]
 gi|190905152|gb|EDV64796.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           F11]
 gi|218352951|emb|CAU98750.1| 23S rRNA pseudouridine synthase [Escherichia coli 55989]
 gi|218361942|emb|CAQ99544.1| 23S rRNA pseudouridine synthase [Escherichia coli IAI1]
 gi|281602002|gb|ADA74986.1| Ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           2002017]
 gi|284922542|emb|CBG35629.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           042]
 gi|291468756|gb|EFF11247.1| rluD [Escherichia coli B354]
 gi|300297834|gb|EFJ54219.1| pseudouridine synthase, RluA family [Escherichia coli MS 185-1]
 gi|300308510|gb|EFJ63030.1| pseudouridine synthase, RluA family [Escherichia coli MS 200-1]
 gi|300395569|gb|EFJ79107.1| pseudouridine synthase, RluA family [Escherichia coli MS 69-1]
 gi|300407859|gb|EFJ91397.1| pseudouridine synthase, RluA family [Escherichia coli MS 45-1]
 gi|300454823|gb|EFK18316.1| pseudouridine synthase, RluA family [Escherichia coli MS 21-1]
 gi|305854524|gb|EFM54962.1| 23S rRNA pseudouridine synthase D [Escherichia coli NC101]
 gi|313648270|gb|EFS12714.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           2a str. 2457T]
 gi|315290937|gb|EFU50302.1| pseudouridine synthase, RluA family [Escherichia coli MS 153-1]
 gi|315298638|gb|EFU57893.1| pseudouridine synthase, RluA family [Escherichia coli MS 16-3]
 gi|323184529|gb|EFZ69903.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           1357]
 gi|323963904|gb|EGB59397.1| RluA family protein pseudouridine synthase [Escherichia coli M863]
 gi|323978453|gb|EGB73537.1| RluA family protein pseudouridine synthase [Escherichia coli
           TW10509]
 gi|324012460|gb|EGB81679.1| pseudouridine synthase, RluA family [Escherichia coli MS 60-1]
 gi|327252300|gb|EGE63972.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           STEC_7v]
 gi|330912359|gb|EGH40869.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           AA86]
 gi|331042085|gb|EGI14227.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli M605]
 gi|331053326|gb|EGI25355.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA206]
 gi|331058618|gb|EGI30596.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA143]
 gi|332754015|gb|EGJ84387.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           K-671]
 gi|332755617|gb|EGJ85980.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           2747-71]
 gi|332765571|gb|EGJ95784.1| 23S rRNA pseudouridine synthase [Shigella flexneri 2930-71]
 gi|333015902|gb|EGK35238.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           K-304]
          Length = 326

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 90/338 (26%), Positives = 158/338 (46%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V    
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            INA   I +E +     + L          ++YED  I V NKP  + V  G+G   + 
Sbjct: 66  AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---NP 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y
Sbjct: 112 DGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREY 171

Query: 184 WSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G         E I+    K++H+    VH + +       A++H+++++ F +  
Sbjct: 172 EAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPMGKP------AVTHYRIMEHF-RVH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHA 292
             L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA
Sbjct: 222 TRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHA 281

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
             + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 282 TMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 319


>gi|195644818|gb|ACG41877.1| RNA binding protein [Zea mays]
          Length = 439

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 82/338 (24%), Positives = 137/338 (40%), Gaps = 66/338 (19%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN----LTKHSDFLKSILLYEDS 106
            R +    I++G V      ++ ++H +K   ++  +V+    L   ++ +   ++YED 
Sbjct: 86  SRARVQASIRAGLVAVNGRPVSKVSHTVKGGDLVSCTVSELQPLRAEAEDIPLDIVYEDD 145

Query: 107 KIYVFNKPAGISVQGGSGIA---------------------------------------Y 127
            + V NKPA + V    G A                                       +
Sbjct: 146 HVLVVNKPAHMVVHPAPGNAKGTLVNAILHHCKISTFTCLARSSAGDECPDSSDEDTDVF 205

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           H+D F    V S+ +    +P + HRLD+ TSG+LVVA+   +   L E F++  I+++Y
Sbjct: 206 HVDQFAAEDVSSEVRNALVRPGIVHRLDKGTSGLLVVAKDEHSHARLAEQFKLHTIRRVY 265

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            SL  G P      I   + +  +       +     + A  A S +KV + FA     L
Sbjct: 266 ISLTCGAPNPNSGRIEASIARDPNNRIRMTAIAGSGHRYARNAASRYKVREVFAGGGSAL 325

Query: 244 -EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------FKGNFTSPIQNKLY-- 289
            E +  TGRTHQ+R HA ++G P++GD  Y                  + S + N L   
Sbjct: 326 VEWRLETGRTHQIRAHAKYIGIPLLGDETYGGTQSMALSLLRPRSPSKYHSGLSNLLSKV 385

Query: 290 ----LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
               LHA  +   HP  G+ L+ + P P   ++    L
Sbjct: 386 DRPCLHAASLGFKHPRSGKVLEFSCPPPDDFLEVLGEL 423


>gi|332999362|gb|EGK18947.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           VA-6]
          Length = 326

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 123/247 (49%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH +         A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPM------GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 253 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|224533917|ref|ZP_03674502.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi CA-11.2a]
 gi|224512920|gb|EEF83286.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi CA-11.2a]
          Length = 251

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 55/181 (30%), Positives = 98/181 (54%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 11  IIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 69

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +R  K+Y ++V G   +    I +++ +  H    
Sbjct: 70  KDTSGVLICAKNISTLRFLAQQFKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 129

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 130 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 184

Query: 272 Y 272
           Y
Sbjct: 185 Y 185


>gi|304383656|ref|ZP_07366115.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           marshii DSM 16973]
 gi|304335180|gb|EFM01451.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           marshii DSM 16973]
          Length = 534

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 65/206 (31%), Positives = 107/206 (51%), Gaps = 17/206 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ED  + V  KPAG+    G      + G ++S          + HRLD +TSG+LV+A
Sbjct: 333 VFEDEHLTVVCKPAGMLSVPGRSPKESVVGIVQSQCGGNADVLPV-HRLDMQTSGLLVIA 391

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +++AA +HL E FR + ++K Y +++ G     KE      L+   +  D    +  +++
Sbjct: 392 KSKAAHKHLQEQFRKQEVKKRYVAVLDGEWNGTKEGRIELPLRPDPL--DRPRQLVDSKR 449

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM---GCPIVGDHKYCANFKG 278
           G   A++ +KV++   +    + + P TGRTHQLR+H  HM   G PIVGD  Y  +   
Sbjct: 450 GKR-ALTLYKVLET-GRGHTRIALYPKTGRTHQLRIHCAHMAGLGIPIVGDELYGRH--- 504

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR 304
                  ++LYLHA  ++  HP  G+
Sbjct: 505 ------SDRLYLHAECIEFQHPATGK 524


>gi|332654559|ref|ZP_08420302.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Ruminococcaceae bacterium D16]
 gi|332516523|gb|EGJ46129.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Ruminococcaceae bacterium D16]
          Length = 301

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 82/283 (28%), Positives = 124/283 (43%), Gaps = 29/283 (10%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           + VD  RV      Q GQV+ +      L+   +   IL S   L          ++YED
Sbjct: 44  ILVDGARVNTRFCPQEGQVLSV-----RLSDPERRSGILPSPGPLD---------IVYED 89

Query: 106 SKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVAR 162
             + V NK  G+ V  G G  +  I  +L  + D +G +      HRLD+ TSG+LVVAR
Sbjct: 90  GDVVVLNKAPGVPVHPGPGHYSDTIGNYLLYYYDQEGTEGDFHPVHRLDRGTSGLLVVAR 149

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
              A + L E        + Y ++  GI +     I   L  K   G     +V+ + K 
Sbjct: 150 HPHAQEVLKEQLHTDGFHREYLAVCEGILEPPVGTIEEPLGPKP--GSLVEQMVRPDGK- 206

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             +A +H++V+    ++   + +   TGRTHQ+RVH  H+G P+VGD  Y          
Sbjct: 207 --FARTHYEVVKA-GERCTLVRLVLDTGRTHQIRVHLAHLGHPLVGDFLYGKEEPERIPR 263

Query: 283 PIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
           P      LH+  +   HP  G  +  TAP+P  M +  +  G 
Sbjct: 264 PA-----LHSHRLTFRHPITGQEMTFTAPVPQDMKRLLEQEGL 301


>gi|113461656|ref|YP_719725.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           somnus 129PT]
 gi|112823699|gb|ABI25788.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           somnus 129PT]
          Length = 221

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 68/216 (31%), Positives = 108/216 (50%), Gaps = 21/216 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y D  I V NKP+G+    G+   Y+      S V  K       HRLD  TSGIL+ 
Sbjct: 16  IVYRDDHILVVNKPSGLLSVSGNQPQYYDSAM--SRVKEKYGFCEPAHRLDMATSGILLF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC----IANWLLKKSHIGGDYVHV 215
           A ++ A + L   FR R  +K Y +L+WG + ++        I +W   +      +VH 
Sbjct: 74  AMSKMADRELKRQFREREPKKHYQALIWGHLAQDTGSVNLPLICDWE-NRPRQKVCFVH- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A+++FKV+  F      + + P TGR+HQLR+H L +G PI+GD K+ A+
Sbjct: 132 -------GKRAVTNFKVLHRFENNITQVRLTPITGRSHQLRLHMLALGHPILGD-KFYAH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            +    +P   +L LHA ++ + HP   + +Q + P
Sbjct: 184 PQAKSLAP---RLCLHAEFLQITHPLTKKVIQFSTP 216


>gi|91211928|ref|YP_541914.1| 23S rRNA pseudouridine synthase D [Escherichia coli UTI89]
 gi|91073502|gb|ABE08383.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           UTI89]
 gi|294490521|gb|ADE89277.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           IHE3034]
 gi|307625854|gb|ADN70158.1| 23S rRNA pseudouridine synthase D [Escherichia coli UM146]
          Length = 326

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 90/338 (26%), Positives = 157/338 (46%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V    
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            INA   I +E +     + L          ++YED  I V NKP  + V  G+G   + 
Sbjct: 66  AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---NP 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y
Sbjct: 112 DGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREY 171

Query: 184 WSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G         E I+    K++H+    VH +         A++H+++++ F +  
Sbjct: 172 EAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPM------GKPAVTHYRIMEHF-RVH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHA 292
             L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA
Sbjct: 222 TRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQSLHA 281

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
             + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 282 TMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 319


>gi|326382577|ref|ZP_08204268.1| pseudouridine synthase, RluA family protein [Gordonia neofelifaecis
           NRRL B-59395]
 gi|326198696|gb|EGD55879.1| pseudouridine synthase, RluA family protein [Gordonia neofelifaecis
           NRRL B-59395]
          Length = 308

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 75/230 (32%), Positives = 113/230 (49%), Gaps = 16/230 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQ---GGSGI----AYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           ++Y DS I V +KPAG++     G SG     A    GF  S      ++  + HRLD  
Sbjct: 84  VIYHDSDIIVVDKPAGVAAHPSLGWSGPTVIGALAAAGFRIS-TSGAHERQGIVHRLDAG 142

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA +  A   L  +F+ R + K Y +LV G        I   + +  H G D+ 
Sbjct: 143 TSGVMVVAASERAYTLLKRAFKQRTVDKRYHALVQGHLDPPSGTIDAPIGR--HPGSDWR 200

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V  N +    +++H+  ++ FA     L++   TGRTHQ+RVH   M  P  GD  Y 
Sbjct: 201 FAVTANGR---ESVTHYDTLEMFAAA-SLLDVHLETGRTHQIRVHFSAMHHPCCGDPTYG 256

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           A+ K      + ++ +LHAR +   HP +G R++ TA  PA +    D L
Sbjct: 257 ADPKLAARLGL-DRQWLHARTLGFAHPADGRRVEFTAEYPADLQHALDVL 305


>gi|293379048|ref|ZP_06625201.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
 gi|292642327|gb|EFF60484.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
          Length = 285

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 69/205 (33%), Positives = 105/205 (51%), Gaps = 23/205 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+            +   L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKKQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            A+       L      + I + Y ++VWG I K++   I N + +  H   D    V  
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGKIAKDR--TITNKIGRDRH---DRRKRVVD 197

Query: 219 NEKGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           ++ G N A++H    KV+    Q +C LE    TGRTHQ+RVH  H+G PIVGD  Y   
Sbjct: 198 DKNGQN-ALTHVTVDKVLSGKTQVYCVLE----TGRTHQIRVHLAHIGHPIVGDPLYQ-- 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                  P + +L LHA  + + HP
Sbjct: 251 -----NRPAE-RLMLHALELHMIHP 269


>gi|167757067|ref|ZP_02429194.1| hypothetical protein CLORAM_02616 [Clostridium ramosum DSM 1402]
 gi|167703242|gb|EDS17821.1| hypothetical protein CLORAM_02616 [Clostridium ramosum DSM 1402]
          Length = 279

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 86/280 (30%), Positives = 144/280 (51%), Gaps = 31/280 (11%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIK--EQKILDSSVNLTKHSDFLKSILLYEDS 106
           +KK VK  N ++  QV     VI+  ++ +K  ++ ++D + N     D     ++YED 
Sbjct: 21  NKKNVK--NLLKFKQVSVNGQVISQFDYSLKRDDEIVVDRNPNNNSSLD-----IIYEDR 73

Query: 107 KIYVFNKPAGI-SVQGGS---GIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVV 160
           ++ V NKPAG+ S+ GG+     AYH+ G    ++ SK +  R  + HRLD+ETSG+L+ 
Sbjct: 74  ELIVINKPAGLLSMAGGNEKEKTAYHLVG---EYLKSKNKNARVFIVHRLDKETSGVLLF 130

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L  ++     ++ Y +++ G  K K   I N  L +S     Y   +  N 
Sbjct: 131 AKNEIIKNKLQNNWNDIVYKRGYLAIIEGKLKKKHGTIKNH-LDESKTQMVY---IANNG 186

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG   AI+++KV+   ++    +E+   TGR +Q+RVH   +G  IVGD KY A      
Sbjct: 187 KGK-LAITNYKVLKE-SRYNSLIEVFLETGRKNQIRVHMQSLGHSIVGDKKYGAT----- 239

Query: 281 TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
           T+PI+ ++ LH+      HP+   R++  A +P    K +
Sbjct: 240 TNPIK-RMGLHSHVFAFVHPDTKARMEFKAVVPEEFKKMF 278


>gi|227833472|ref|YP_002835179.1| pseudouridylate synthase [Corynebacterium aurimucosum ATCC 700975]
 gi|227454488|gb|ACP33241.1| pseudouridylate synthase [Corynebacterium aurimucosum ATCC 700975]
          Length = 307

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 83/304 (27%), Positives = 137/304 (45%), Gaps = 30/304 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + MR+D         I+   + ++  +G V +D   V  + R+ +G  + +         
Sbjct: 14  DGMRVDAALAKLL-GISRARVSQLCAAGDVEIDGAAVGKSERLNAGGWIDV--------M 64

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKS 135
           +   ++ L     L +  D     +LY D  I    KP G++     G     + G L++
Sbjct: 65  MPAPEEPLIPKEELVEGMD-----VLYADEDIICVCKPVGVAAHPTLGWDGPTVIGGLRA 119

Query: 136 W---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
               +   G   R  + HRLD  TSG++VVA +  A   L  +FR R +QK Y ++V G+
Sbjct: 120 AGYALADAGPTERKGIVHRLDVGTSGVMVVAASERAYSQLKNAFRERTVQKTYHAVVQGL 179

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +    G  +  VV   +     A++H+K+++ F ++   LE+   TG
Sbjct: 180 PDPIVGTIDAPIGRHPSAGWKF-GVVDDGKP----AVTHYKLLEAF-REASLLEVHLETG 233

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR-LQIT 308
           RTHQ+RVH    G P VGD  Y  +   N    +  N+ +LHA  +   HP  G+  + T
Sbjct: 234 RTHQIRVHMSATGHPCVGDPMYGCDP--NLAKRVGLNRQWLHAVELGFTHPGTGKWFECT 291

Query: 309 APLP 312
           AP P
Sbjct: 292 APYP 295


>gi|84683903|ref|ZP_01011805.1| ribosomal large subunit pseudouridine synthase A [Maritimibacter
           alkaliphilus HTCC2654]
 gi|84667656|gb|EAQ14124.1| ribosomal large subunit pseudouridine synthase A [Rhodobacterales
           bacterium HTCC2654]
          Length = 215

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 67/207 (32%), Positives = 107/207 (51%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D +I V NKP+G+    G G   H+   L + + +   +  L HRLD++TSG++V 
Sbjct: 14  IIHMDHEILVVNKPSGLLSVPGKG--EHLADCLIARLQTAFPEVLLVHRLDRDTSGVMVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A T  A +HL   F  R+++K Y + VWG  +     +   L+       D+ +  +Q+ 
Sbjct: 72  ALTPHAQRHLGLQFEKRQVKKTYVARVWGDVQEDTGTVDLPLIV------DWPNRPRQHV 125

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             EKG   A++ +KV+         + + P TGR+HQLRVH L +G PI GD  Y     
Sbjct: 126 DFEKG-KPAVTDWKVLKREGAT-TRMRLFPQTGRSHQLRVHMLELGHPICGDPFYAEGPA 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +F      +L LHA  +   HP+GG+
Sbjct: 184 RDFP-----RLMLHAESLRFRHPDGGK 205


>gi|319638811|ref|ZP_07993569.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317399715|gb|EFV80378.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 238

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 67/223 (30%), Positives = 107/223 (47%), Gaps = 16/223 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ DS+    NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IIHRDSRTIAVNKPAGMLVHRSWLDKHETRFAVQTLRDQIGQHVYPVHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLK--KSHIGGDYVHVVK 217
           A    AA+ LT+ F  + I+K YW++V G +P +    + ++ LK     I         
Sbjct: 64  ALDTEAARLLTQQFENKTIEKTYWAIVRGHLPSD---GLIDYALKYMPDKIAEAQTEATL 120

Query: 218 QNEKGANYAISHFKV-----IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           Q  + A   ++  ++     +     ++ W E+ PHTGR HQLR H  H+  PIVGD  Y
Sbjct: 121 QEAQTAYRCLAQTELPFQSALRYPTSRYSWAELTPHTGRKHQLRRHMKHIFHPIVGDTNY 180

Query: 273 CANFKGNFTSPIQ---NKLYLHARYMDLPHPE-GGRLQITAPL 311
             + + N          +L LHAR +     E G R+ + AP+
Sbjct: 181 -GDLRQNHAVAEHVGTQRLMLHARSLSFQSIEDGSRMTVQAPI 222


>gi|269219521|ref|ZP_06163375.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 848 str. F0332]
 gi|269211100|gb|EEZ77440.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 848 str. F0332]
          Length = 309

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 74/290 (25%), Positives = 131/290 (45%), Gaps = 31/290 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           ++ G+  +D      ++R+ SG V+ I               ++    +L         +
Sbjct: 37  VQKGEAWIDGAVASKSDRVPSGAVLEI---------------LVPDPPSLEPRPSAEGIV 81

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
            LYED  + V +KPAG++       +G   +   +   +K       ++  + HRLD  T
Sbjct: 82  RLYEDEDVVVVDKPAGMAAHPSLNFEGPDVLGTLMAEGVKLTTHGPQERKGIVHRLDVGT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G +VVA++ AA   L  +FR R ++K+Y +LV G P      I      ++ IG D   
Sbjct: 142 TGCMVVAKSEAAYSALKRAFRDRAVEKVYHALVQGHPDPMSGTI------EAPIGRDNRR 195

Query: 215 VVKQNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             K   +     +++H++ ++  A     LE++  TGRTHQ+RVH   M  P VGD  Y 
Sbjct: 196 QWKMAVRADGRPSVTHYEALEAMAGA-SLLEVRLETGRTHQIRVHMSAMSHPCVGDDMYG 254

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           A+   +    +  + +LHA  +   HP  G  +   AP P  +  + +++
Sbjct: 255 ADPTLSARLGL-TRQWLHAVRLGFEHPTSGEWVAFAAPYPEDLQNSLEAM 303


>gi|227888161|ref|ZP_04005966.1| 23S rRNA pseudouridine synthase [Escherichia coli 83972]
 gi|227834801|gb|EEJ45267.1| 23S rRNA pseudouridine synthase [Escherichia coli 83972]
 gi|307554609|gb|ADN47384.1| 23S rRNA pseudouridine synthase [Escherichia coli ABU 83972]
          Length = 326

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 253 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|148989142|ref|ZP_01820532.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP6-BS73]
 gi|147925365|gb|EDK76443.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP6-BS73]
          Length = 298

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 112/219 (51%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      + +  HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVYIHLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLEDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|126736207|ref|ZP_01751950.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           CCS2]
 gi|126714373|gb|EBA11241.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           CCS2]
          Length = 214

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 111/216 (51%), Gaps = 17/216 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++L++D ++ + +KP+G+    G G   H+   L + V +      L HRLD++TSG+++
Sbjct: 12  VILHDDHQVLLVDKPSGLLSVPGKG--EHLADCLLARVQAAFPMALLVHRLDRDTSGVMI 69

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A T  A +HL   F  R+ +K Y + VWG    K   +   L+       D+ +  +Q 
Sbjct: 70  FALTPHAQRHLGLQFEKRQTKKTYVARVWGEMTEKTGTVDLPLIV------DWPNRPRQM 123

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +    A++ ++V+         + + P TGR+HQLRVH L +G PI+GD  Y     
Sbjct: 124 VDHENGKQAVTDWRVVRA-KDGETRVRLMPRTGRSHQLRVHMLALGHPILGDPFYAEGKA 182

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            +       +L LH+  +   HP+GG+ ++ITA  P
Sbjct: 183 RD-----HPRLMLHSETLQFRHPDGGQGIRITAKCP 213


>gi|16803883|ref|NP_465368.1| hypothetical protein lmo1843 [Listeria monocytogenes EGD-e]
 gi|47097693|ref|ZP_00235203.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|224500073|ref|ZP_03668422.1| hypothetical protein LmonF1_10499 [Listeria monocytogenes Finland
           1988]
 gi|224501356|ref|ZP_03669663.1| hypothetical protein LmonFR_02345 [Listeria monocytogenes FSL
           R2-561]
 gi|254829161|ref|ZP_05233848.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL N3-165]
 gi|254831556|ref|ZP_05236211.1| hypothetical protein Lmon1_09383 [Listeria monocytogenes 10403S]
 gi|254899460|ref|ZP_05259384.1| hypothetical protein LmonJ_06589 [Listeria monocytogenes J0161]
 gi|254912401|ref|ZP_05262413.1| conserved hypothetical protein [Listeria monocytogenes J2818]
 gi|254936728|ref|ZP_05268425.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|255027649|ref|ZP_05299635.1| hypothetical protein LmonocytFSL_17157 [Listeria monocytogenes FSL
           J2-003]
 gi|284802289|ref|YP_003414154.1| hypothetical protein LM5578_2045 [Listeria monocytogenes 08-5578]
 gi|284995431|ref|YP_003417199.1| hypothetical protein LM5923_1996 [Listeria monocytogenes 08-5923]
 gi|16411297|emb|CAC99921.1| lmo1843 [Listeria monocytogenes EGD-e]
 gi|47013931|gb|EAL04954.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|258601571|gb|EEW14896.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL N3-165]
 gi|258609325|gb|EEW21933.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|284057851|gb|ADB68792.1| hypothetical protein LM5578_2045 [Listeria monocytogenes 08-5578]
 gi|284060898|gb|ADB71837.1| hypothetical protein LM5923_1996 [Listeria monocytogenes 08-5923]
 gi|293590383|gb|EFF98717.1| conserved hypothetical protein [Listeria monocytogenes J2818]
          Length = 303

 Score = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 83/302 (27%), Positives = 142/302 (47%), Gaps = 51/302 (16%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQV----VRIPPVINALNHIIKEQKILDSSVNLTK 92
           +Q +L++G + V+ +  K N ++Q G      VR P          +E ++L   + L  
Sbjct: 32  IQLMLKNGDITVNGELAKPNYKVQVGDEIHYEVREP----------EELEVLAEDIPLD- 80

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQK 143
                   + +ED  + V NKP G+ V   +G A         +H D    S ++ K  +
Sbjct: 81  --------IYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL--SGINGK-IR 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    +
Sbjct: 130 PGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPI 188

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++      + VV+  ++    A +HF+V++     +  +  +  TGRTHQ+RVH  ++G
Sbjct: 189 GRAKEDRQKMAVVRDGKE----ARTHFEVLERLP-GYTLINCKLDTGRTHQIRVHLKYIG 243

Query: 264 CPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            P+ GD KY      KGN         +LHA  +   HP    R+   APLP+   K   
Sbjct: 244 HPLAGDPKYGPKNTIKGNGQ-------FLHAAKLGFDHPTTNERMTFEAPLPSSFEKALK 296

Query: 321 SL 322
           SL
Sbjct: 297 SL 298


>gi|237735862|ref|ZP_04566343.1| RNA pseudouridylate synthase [Mollicutes bacterium D7]
 gi|229381607|gb|EEO31698.1| RNA pseudouridylate synthase [Coprobacillus sp. D7]
          Length = 294

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 86/280 (30%), Positives = 144/280 (51%), Gaps = 31/280 (11%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIK--EQKILDSSVNLTKHSDFLKSILLYEDS 106
           +KK VK  N ++  QV     VI+  ++ +K  ++ ++D + N     D     ++YED 
Sbjct: 36  NKKNVK--NLLKFKQVSVNGQVISQFDYSLKRDDEIVVDRNPNNNSSLD-----IIYEDR 88

Query: 107 KIYVFNKPAGI-SVQGGS---GIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVV 160
           ++ V NKPAG+ S+ GG+     AYH+ G    ++ SK +  R  + HRLD+ETSG+L+ 
Sbjct: 89  ELIVINKPAGLLSMAGGNEKEKTAYHLVG---EYLKSKNKNARVFIVHRLDKETSGVLLF 145

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L  ++     ++ Y +++ G  K K   I N  L +S     Y   +  N 
Sbjct: 146 AKNEIIKNKLQNNWNDIVYKRGYLAIIEGKLKKKHGTIKNH-LDESKTQMVY---IANNG 201

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG   AI+++KV+   ++    +E+   TGR +Q+RVH   +G  IVGD KY A      
Sbjct: 202 KGK-LAITNYKVLKE-SRYNSLIEVFLETGRKNQIRVHMQSLGHSIVGDKKYGAT----- 254

Query: 281 TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
           T+PI+ ++ LH+      HP+   R++  A +P    K +
Sbjct: 255 TNPIK-RMGLHSHVFAFVHPDTKARMEFKAVVPEEFKKMF 293


>gi|170683711|ref|YP_001744779.1| 23S rRNA pseudouridine synthase D [Escherichia coli SMS-3-5]
 gi|218701106|ref|YP_002408735.1| 23S rRNA pseudouridine synthase D [Escherichia coli IAI39]
 gi|170521429|gb|ACB19607.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           SMS-3-5]
 gi|218371092|emb|CAR18921.1| 23S rRNA pseudouridine synthase [Escherichia coli IAI39]
          Length = 326

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 253 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|325911610|ref|ZP_08174018.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
 gi|325476596|gb|EGC79754.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
          Length = 292

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 72/279 (25%), Positives = 130/279 (46%), Gaps = 35/279 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKN-----HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           Y+ Y+ +  +E N  +D+  +N      + H  F+ ++K      + V+ K +  N ++ 
Sbjct: 13  YIYYLTISQNENNQNVDQIMRNLLIPRKWRH--FLRIEK-----NILVNDKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE++ + V NKPAG   Q
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENADVLVINKPAG---Q 109

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L    +  G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 110 KTHPNLYETDTALNDCANYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQK 239
           + Y++ +            N       IG D + + K+  +     AI+H++V+     K
Sbjct: 170 RSYFAWIEATNDISDNGTINL-----PIGDDPLDMRKRMVRADGLKAITHYQVVKKIGSK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++ 
Sbjct: 225 IL-VKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQA 262


>gi|300727412|ref|ZP_07060821.1| ribosomal large chain pseudouridine synthase A [Prevotella bryantii
           B14]
 gi|299775292|gb|EFI71891.1| ribosomal large chain pseudouridine synthase A [Prevotella bryantii
           B14]
          Length = 531

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 75/227 (33%), Positives = 107/227 (47%), Gaps = 29/227 (12%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D+ +NL K  +  +   +Y D  + V  KPAG+    G  I   +   LK     K  
Sbjct: 319 IEDNLLNLQKKQELEE---IYSDHDLIVVYKPAGMLSVPGKNIRESVLSILKERY-PKAT 374

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P + HRLD  TSG+LVV +   A  +L + F    I+K Y +L+  IP      +   L
Sbjct: 375 GPMIVHRLDMATSGLLVVTKNLEAYINLQKQFAEHTIKKRYVALLEHIPDQSIGIVDLPL 434

Query: 203 LKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           L       D +   +Q  ++K    AI+ ++VI   AQ   WL   P TGRTHQLR+H  
Sbjct: 435 LP------DIMDRPRQKVDKKNGKKAITKYQVI---AQNRVWL--YPLTGRTHQLRMHCA 483

Query: 261 H---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           H   +  PI+GD         N      ++LYLHA Y++  HP  G+
Sbjct: 484 HEEGLNNPILGD---------NLYGKPADRLYLHAEYLEFTHPSTGK 521


>gi|169795158|ref|YP_001712951.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii AYE]
 gi|184158990|ref|YP_001847329.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|213158176|ref|YP_002320227.1| pseudouridine synthase A [Acinetobacter baumannii AB0057]
 gi|215482708|ref|YP_002324906.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB307-0294]
 gi|301348011|ref|ZP_07228752.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB056]
 gi|301512677|ref|ZP_07237914.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB058]
 gi|301597067|ref|ZP_07242075.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB059]
 gi|169148085|emb|CAM85948.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii AYE]
 gi|183210584|gb|ACC57982.1| Pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|213057336|gb|ACJ42238.1| pseudouridine synthase A [Acinetobacter baumannii AB0057]
 gi|213988340|gb|ACJ58639.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB307-0294]
 gi|322508972|gb|ADX04426.1| rluA [Acinetobacter baumannii 1656-2]
 gi|323518957|gb|ADX93338.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           TCDC-AB0715]
          Length = 212

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 73/225 (32%), Positives = 109/225 (48%), Gaps = 21/225 (9%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLD 151
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V     +PR  L HRLD
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLV---AIEPRTLLIHRLD 56

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSGILV   ++     +   F+ R+  KIY +LV G  + +       +   S     
Sbjct: 57  RDTSGILVFGLSKRGQSAIARQFQDRQTSKIYEALVAGHLEGEGTVDIPVVYDPSR---P 113

Query: 212 YVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +H+V  +      A++H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVG
Sbjct: 114 PLHIVDASHNKP--ALTHWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVG 171

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           D  Y A  +      +  +L LHA+ +   HP  G  L    P+P
Sbjct: 172 DTLYAAPEQL-----LVPRLCLHAKQLSFNHPVTGESLTFNCPVP 211


>gi|154245928|ref|YP_001416886.1| RluA family pseudouridine synthase [Xanthobacter autotrophicus Py2]
 gi|154160013|gb|ABS67229.1| pseudouridine synthase, RluA family [Xanthobacter autotrophicus
           Py2]
          Length = 377

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 90/371 (24%), Positives = 160/371 (43%), Gaps = 80/371 (21%)

Query: 6   YVQYVVVENDEENMRLDRWFKN----HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           +   V +  ++   RLDR          P ++   +Q+++  G+V V  + V     R+ 
Sbjct: 29  FTLTVQIAAEDAGERLDRVLARRLALEAPELSRTRIQRLVTEGRVSVSGRVVGDAAGRVN 88

Query: 61  SGQV--VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +  V  + +PP   A        + +  ++ LT         +++ED+ + V +KPAG+ 
Sbjct: 89  AADVYTLFLPPPEAA--------EPVAENLPLT---------IVFEDAHLVVIDKPAGLV 131

Query: 119 VQGGSGIAYH--IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           V    G A    ++  L    DS       ++P + HR+D++TSG+LVVA++  A + L 
Sbjct: 132 VHPAPGHASGTLVNALLYHCGDSLSGIGGVRRPGIVHRIDKDTSGLLVVAKSDLAHKGLA 191

Query: 172 ESF----RMRRIQKIYWSLVWGIPK-----------------------NKKECIANWLLK 204
             F    R   +++ Y + VWG+P+                       + +  I +W ++
Sbjct: 192 AQFADHGRTGPLERAYLAFVWGVPEAHGSVDAPIDRHPSHRQKMAVRLSGRNAITHWEVQ 251

Query: 205 KSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHM 262
           ++ +G    H+  + + KG        K+ +  A    C LE    TGRTHQ+RVH  H+
Sbjct: 252 EAFVGHGRTHLRNKGQVKG------EVKMEEGVASLIECRLE----TGRTHQIRVHMAHV 301

Query: 263 GCPIVGDHKYCANFKGNFTSPIQN---------KLYLHARYMDLPHP-EGGRLQITAPLP 312
           G P++GD  Y   F+   T   ++         +  LHA  +   HP  G  L   + LP
Sbjct: 302 GHPLLGDEVYGQGFRTKETLLPEDAREHLARLGRQALHAARLGFAHPVTGETLSFESQLP 361

Query: 313 AHMVKTWDSLG 323
             +    + LG
Sbjct: 362 EDLAALAEVLG 372


>gi|329961970|ref|ZP_08299981.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
 gi|328530618|gb|EGF57476.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
          Length = 541

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 65/212 (30%), Positives = 107/212 (50%), Gaps = 30/212 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           +++ED  + V NKPAG+    G   A  +   ++  + D++G  P + HRLD  TSG+L+
Sbjct: 340 IIFEDRWLAVINKPAGMLSVPGKEEAISVYSLMRQRYPDAEG--PMIVHRLDMATSGLLI 397

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKN----KKECIANWLLKKSHIGGDYVH 214
           +A+T+   ++L   F+ R ++K Y +L+ GI P+N    +     N L +   +      
Sbjct: 398 IAKTKQVHRNLQAQFKERTVRKRYIALLDGIVPQNTGTIELPLCPNLLDRPRQMV----- 452

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHK 271
               N +    AI+ F+V++        + + PHTGRTHQLR+H  H   + CPI+GD  
Sbjct: 453 ----NTEHGKVAITDFEVLERKG-NITRISLYPHTGRTHQLRIHTAHPLGLHCPIIGDEL 507

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           Y             ++L LHA  ++  HP  G
Sbjct: 508 YGKK---------ADRLCLHAETIEFIHPISG 530


>gi|118617189|ref|YP_905521.1| RluA family pseudouridine synthase [Mycobacterium ulcerans Agy99]
 gi|118569299|gb|ABL04050.1| pseudouridine synthase, RluA-family [Mycobacterium ulcerans Agy99]
          Length = 345

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 119/250 (47%), Gaps = 25/250 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY D  I   +KPA ++     G     + G L +    + + G   R  + HRLD  T
Sbjct: 84  ILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRISTSGVHERQGIVHRLDVGT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA +  A   L  +F+ R + K Y +LV G P      I   + +  H GG++  
Sbjct: 144 SGVMVVALSERAYTVLKRAFKQRTVDKRYHALVQGHPDPSSGTIDAPIGR--HPGGEWKF 201

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V +N +   ++++H+  ++ F      L++   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 202 AVTKNGR---HSLTHYDTVEAFVAA-SLLDVHLETGRTHQIRVHFAALHHPCCGDLVYGA 257

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD-----------SL 322
           + K      +Q + +LHAR +   HP +G R++I +P P  +    D           S+
Sbjct: 258 DPKLAKRLGLQRQ-WLHARSLAFAHPADGRRVEIVSPYPPDLQHALDVLPRRGVSDAHSV 316

Query: 323 GFKYDRNLYI 332
           GF+   N  +
Sbjct: 317 GFRASTNTRV 326


>gi|77462967|ref|YP_352471.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides 2.4.1]
 gi|77387385|gb|ABA78570.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides 2.4.1]
          Length = 349

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 85/336 (25%), Positives = 142/336 (42%), Gaps = 58/336 (17%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L K++  G VR++   V     ++  GQV  I        
Sbjct: 22  RLDKALVREAPEEAALSRSRLMKLIGEGAVRLEGAPVTDPKAKVAEGQVYEI-------- 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                   LD+   +    + +   +++ED  + V +KP G+ V    G      ++  L
Sbjct: 74  -------ALDAPAEVEARPEAIPLSVVWEDEDLIVIDKPVGMVVHPAPGQWTGTLVNALL 126

Query: 134 ----KSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               +S     G+K P + HR+D++TSG+LVVA+T  A Q L   F    +++ Y +LV 
Sbjct: 127 HHCGESLSGIGGEKRPGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRYLALVH 186

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVV---------KQNE----KGANYAISHFKVIDC 235
           G+P+     +   +   S   G  + +          +Q +    +G  +A++  ++++ 
Sbjct: 187 GVPEVSDPRL-RGVRGTSFEPGGVLRIATGLARHRTDRQRQAVTFEGGRHAVTRARLLER 245

Query: 236 FAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------- 285
           F        +E +  TGRTHQ+RVH  H G  ++GD  Y    K    SP          
Sbjct: 246 FGMPSVLALVECRLETGRTHQIRVHMAHAGHGLIGDQTYGGRRK---LSPKALGAEAAAA 302

Query: 286 ----NKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
                +  LHA  +   HP  G  L   +PLPA M 
Sbjct: 303 AEAFPRQALHAASLGFRHPVSGEELSFESPLPADMA 338


>gi|126461841|ref|YP_001042955.1| RluA family pseudouridine synthase [Rhodobacter sphaeroides ATCC
           17029]
 gi|126103505|gb|ABN76183.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides ATCC 17029]
          Length = 349

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 84/333 (25%), Positives = 141/333 (42%), Gaps = 52/333 (15%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L K++  G VR++   V     ++  GQV  I        
Sbjct: 22  RLDKALVREAPEEAALSRSRLMKLIGEGAVRLEGAPVTDPKAKVAEGQVYEI-------- 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                   LD+   +    + +   +++ED  + V +KP G+ V    G      ++  L
Sbjct: 74  -------ALDAPAEVEARPEAIPLSVVWEDEDLIVIDKPVGMVVHPAPGQWTGTLVNALL 126

Query: 134 ----KSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               +S     G+K P + HR+D++TSG+LVVA+T  A Q L   F    +++ Y +LV 
Sbjct: 127 HHCGESLSGIGGEKRPGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRYLALVH 186

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVV---------KQNE----KGANYAISHFKVIDC 235
           G+P+     +   +   S   G  + +          +Q +    +G  +A++  ++++ 
Sbjct: 187 GVPEVSDPRL-RGVRGTSFEPGGVLRIATGLARHRTDRQRQAVTFEGGRHAVTRARLLER 245

Query: 236 FAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQN----- 286
           F        +E +  TGRTHQ+RVH  H G  ++GD  Y    K       P        
Sbjct: 246 FGTPPVLALVECRLETGRTHQIRVHMAHAGHGLIGDQTYGGRRKLSPKALGPEAAAAAEA 305

Query: 287 --KLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
             +  LHA  +   HP  G  L   +PLPA M 
Sbjct: 306 FPRQALHAASLGFRHPVSGEELSFESPLPADMA 338


>gi|113971474|ref|YP_735267.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           MR-4]
 gi|113886158|gb|ABI40210.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           MR-4]
          Length = 225

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 69/217 (31%), Positives = 110/217 (50%), Gaps = 20/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +LY+D  I V NKP+G+    G   A H D     +   K + P  ++ HRLD  TSG++
Sbjct: 16  VLYQDKDIIVVNKPSGLLSVPGRDPA-HYDSV---YARVKAEHPHCQIVHRLDMATSGVM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  R+A + L   F  R   K Y + V G  KN    +   L+       D+ +  KQ
Sbjct: 72  VVALIRSAERELKRQFHDRETSKTYLARVAGHIKNDTGSVDYPLI------CDWPNRPKQ 125

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             + +    +++HF+V+   A++   ++++P TGR+HQLRVH + +G PI+GD  Y    
Sbjct: 126 KVDHEIGKPSLTHFEVL-SRAKRSTLVKLKPITGRSHQLRVHMMALGHPILGDGFYADPL 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             +       +L LHA  + + HP  G  +  +A +P
Sbjct: 185 AKSLAP----RLLLHAAELTIKHPYTGESMTFSADVP 217


>gi|124009089|ref|ZP_01693772.1| ribosomal large subunit pseudouridine synthase C [Microscilla
           marina ATCC 23134]
 gi|123985303|gb|EAY25223.1| ribosomal large subunit pseudouridine synthase C [Microscilla
           marina ATCC 23134]
          Length = 238

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 113/234 (48%), Gaps = 27/234 (11%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
            K ++++ED    + NKP  +S      S    +I G  K +++S     ++ HRLD+ET
Sbjct: 6   FKDLIVFEDEDYLIINKPPHMSTLDDRASEGKDNIIGMAKDYLESA----QVCHRLDKET 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGIL +A+   A +HL   F  R++ K+Y +++ GI + K   +   +L       +   
Sbjct: 62  SGILAIAKNPEAYRHLAIQFEKRQVNKVYHAVIGGIQEYKDTLVDRAILP------NRTG 115

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-- 272
            VK + KG   A ++FK +  + +    +E +P TGR HQ+R+H   +G PIV D +Y  
Sbjct: 116 TVKIDLKGKP-AQTYFKTLKIY-KAHTLIEARPVTGRMHQIRIHLAVLGSPIVQDEQYGG 173

Query: 273 ----CANFKGNFT-------SPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
                +  K +F         P+ +++ LHA  +      G    + AP P  M
Sbjct: 174 KPVFLSQIKRHFNLKKYEEERPLISRVALHAHALHFKLLNGETQIVEAPYPKDM 227


>gi|301060346|ref|ZP_07201209.1| pseudouridine synthase, RluA family [delta proteobacterium NaphS2]
 gi|300445542|gb|EFK09444.1| pseudouridine synthase, RluA family [delta proteobacterium NaphS2]
          Length = 265

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 75/244 (30%), Positives = 114/244 (46%), Gaps = 32/244 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQET 154
           + +ED+ I V  KP GI V  G G      + G LK   D  G     +P + HRLD++T
Sbjct: 21  VFFEDTWIIVLYKPPGIVVHPGPGHSSGTLVHGLLKHCTDLSGIGGTLRPGIVHRLDKDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA+   A Q L   F+   + K Y +LV G+  ++   I   + +         H
Sbjct: 81  SGLMLVAKNDMAHQALARQFKDGTVHKEYVALVHGLLPSESGTIDLPICR---------H 131

Query: 215 VVKQNE-----KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            V++ E      G   A++ +K I    + F  L +   TGRTHQ+RVH  H+G P+VGD
Sbjct: 132 PVRRKEMSIAKSGGRNALTLWKKIAECEEGFSLLSITIKTGRTHQIRVHFAHLGHPLVGD 191

Query: 270 HKYCAN--------FKGN--FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             Y            K N    + ++ ++ LHA  +   HPE    +   APLP  M + 
Sbjct: 192 TVYGHGPDTLKKRFLKSNPGLVTAVKRQM-LHAARIGFLHPEEKTYMTFEAPLPEDMRQV 250

Query: 319 WDSL 322
             +L
Sbjct: 251 LRAL 254


>gi|168486485|ref|ZP_02710993.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1087-00]
 gi|183570531|gb|EDT91059.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1087-00]
          Length = 298

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 112/219 (51%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHTRLDKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      + +  HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVYIHLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLEDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|329942341|ref|ZP_08291151.1| pseudouridine synthase, RluA family protein [Chlamydophila psittaci
           Cal10]
 gi|332286982|ref|YP_004421883.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           psittaci 6BC]
 gi|313847579|emb|CBY16567.1| putative pseudouridine synthase [Chlamydophila psittaci RD1]
 gi|325506899|gb|ADZ18537.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           psittaci 6BC]
 gi|328815251|gb|EGF85239.1| pseudouridine synthase, RluA family protein [Chlamydophila psittaci
           Cal10]
 gi|328914213|gb|AEB55046.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           psittaci 6BC]
          Length = 325

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 87/324 (26%), Positives = 148/324 (45%), Gaps = 41/324 (12%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T + ++V E + +  RLD++  +  P  +    Q+        +  KRV  N +IQ+   
Sbjct: 5   TPLLFIVNETNRD--RLDKFLVSQNPKYSRAFYQQ-------HILDKRVTINEQIQTKVS 55

Query: 65  VRIPP---VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            ++ P   V   +    +  ++L  ++ L K         +YED  I V NKP  + V  
Sbjct: 56  TQLAPGDIVSITIEEKEELSELLPEAIPLEK---------IYEDEMILVINKPRDMVVHP 106

Query: 122 GSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
             G         + + I   LK     +  +P + HRLD++TSG+L+ A+TR A    +E
Sbjct: 107 APGHTRGTVVHALLHEIGERLKQEFPEEPWRPGIIHRLDKDTSGLLITAKTRQAKMIYSE 166

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F  ++++K Y ++  G P      I +  L + H     + V    ++    AI+  +V
Sbjct: 167 LFATKQLKKSYLAICVGKP---SASIIHTKLARHHTKRKEMAVSSIGKE----AITRCEV 219

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           +  +  K   + + P TGRTHQLRVH  H+  PI+GD  Y +    +      +K  LHA
Sbjct: 220 L-AYNGKLSLVLLYPETGRTHQLRVHMKHLSTPILGDPVYGSASANSCYG--LDKQQLHA 276

Query: 293 RYMDLPHPEGGR-LQITAPLPAHM 315
             ++  HP+  + L +T  LP  M
Sbjct: 277 YSVNFIHPQTHKHLNLTTELPRDM 300


>gi|148985070|ref|ZP_01818313.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP3-BS71]
 gi|148998365|ref|ZP_01825807.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP11-BS70]
 gi|149024900|ref|ZP_01836301.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP23-BS72]
 gi|225856742|ref|YP_002738253.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae P1031]
 gi|225858911|ref|YP_002740421.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 70585]
 gi|307067719|ref|YP_003876685.1| 23S RNA-specific pseudouridylate synthase [Streptococcus pneumoniae
           AP200]
 gi|147755762|gb|EDK62807.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP11-BS70]
 gi|147922768|gb|EDK73885.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP3-BS71]
 gi|147929523|gb|EDK80517.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP23-BS72]
 gi|225721947|gb|ACO17801.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 70585]
 gi|225724376|gb|ACO20228.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae P1031]
 gi|301800069|emb|CBW32664.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           OXC141]
 gi|306409256|gb|ADM84683.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           pneumoniae AP200]
 gi|332200523|gb|EGJ14595.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA41317]
          Length = 298

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 112/219 (51%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      + +  HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVYIHLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLEDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|118471435|ref|YP_887490.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           smegmatis str. MC2 155]
 gi|118172722|gb|ABK73618.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           smegmatis str. MC2 155]
          Length = 309

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 120/233 (51%), Gaps = 22/233 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH----IDGFLKSW--VDSKG--QKPRLTHRLDQ 152
           +LY D+ I   +KP G++    + + +H    + G   +   + + G  ++  + HRLD 
Sbjct: 83  ILYSDADIVAVDKPPGVAAH--ATVGWHGPTVLGGLAAAGFRISTSGIHERQGIVHRLDV 140

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA +  A   L  +F+ R ++K Y +LV G P      I   + +  H G D+
Sbjct: 141 GTSGVMVVALSERAYTVLKRAFKQRTVEKRYHALVQGHPDPSSGTIDAPIGR--HRGHDW 198

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH--ALHMGCPIVGDH 270
              V +   G  ++++H+  ++ F Q    L+++  TGRTHQ+RVH  ALH  C   GD 
Sbjct: 199 KFAVVE---GGRHSVTHYDTLEMF-QAASLLDIELETGRTHQIRVHFSALHHPC--CGDL 252

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y A+        ++ + +LHAR +   HP +G R++IT+P P  +    D L
Sbjct: 253 TYGADPTLAKRLGLERQ-WLHARSLAFAHPADGRRVEITSPYPDDLQNALDLL 304


>gi|328955606|ref|YP_004372939.1| pseudouridine synthase, RluA family [Coriobacterium glomerans PW2]
 gi|328455930|gb|AEB07124.1| pseudouridine synthase, RluA family [Coriobacterium glomerans PW2]
          Length = 350

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 83/331 (25%), Positives = 144/331 (43%), Gaps = 40/331 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPP 69
           VV+  E   RLD +              +++  G V VD   +   +  + SGQ V +  
Sbjct: 20  VVDATEAGQRLDAYLGGRRACPTRSACARLIERGAVSVDGAMQCSKSFIVLSGQRVDL-- 77

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
              A +  ++   +    + L          + +ED  + V +K  G+    G G   H 
Sbjct: 78  ---AYSEQVEAAVVAGEPIPLD---------IRFEDEYLIVLSKQRGLVCHPGHG---HD 122

Query: 130 DGFLKS------WVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            G L +       +D  G      +P + HRLD++TSG+++ A+  A  + L +  R+R 
Sbjct: 123 SGTLANALVHHCGIDHLGTLQGEDRPGIVHRLDRDTSGLMLAAKDDATQRALQDLIRLRT 182

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-- 236
           + + Y +LV G+       I   L + S    D + +   ++  A  AI+ F+V++ F  
Sbjct: 183 LDRRYIALVHGVIARDAGTIDTGLARSSR---DRLKMAVSDDPAARQAITTFRVLERFDA 239

Query: 237 ---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
               + +  +E   +TGRTHQ+RVH  ++  PIVGD  Y    K         + +LH+ 
Sbjct: 240 ARGDEGYTLIECHLYTGRTHQIRVHMRYISHPIVGDPLY--GRKSKRAELGLTRQFLHSW 297

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
            +   HP  G R+++T  LP  +  + D L 
Sbjct: 298 RLRFTHPVSGERVEVTDTLPWDLAASLDDLA 328


>gi|77457919|ref|YP_347424.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens Pf0-1]
 gi|77381922|gb|ABA73435.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens Pf0-1]
          Length = 211

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 68/214 (31%), Positives = 113/214 (52%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+ + V NKP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIHQDAAVLVVNKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P+     I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPELDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ ++V++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HELGKHALTFWRVLE-RCDDWCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHEQAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
              P   +L LHA  +   HP+ G RL+   P P
Sbjct: 180 AAWP---RLCLHASMLSFTHPQSGERLRFECPAP 210


>gi|296876557|ref|ZP_06900608.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus parasanguinis
           ATCC 15912]
 gi|296432550|gb|EFH18346.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus parasanguinis
           ATCC 15912]
          Length = 297

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 66/218 (30%), Positives = 109/218 (50%), Gaps = 18/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           +L+ED    V NKP GI+    +  +  +  F+K +   +G   Q+  +  RLD++TSG+
Sbjct: 78  ILFEDDHFLVLNKPFGIASIPSAIHSNTLANFVKGYYVKQGYENQQVHIVTRLDKDTSGV 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + IQK Y++LV G  K     E IA     +  I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQSKSIQKRYYALVKGSGKLDPVGEIIAPIARDEESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  KG  YA + ++V+  F   +  +++Q HTGRTHQ+RVH  H+G P++GD  Y  +
Sbjct: 192 TRKVAKGGKYAHTSYQVVQSFGDIYL-VDIQLHTGRTHQIRVHFSHIGFPLLGDDLYGGS 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            +         +  LH   +   HP     L I +PLP
Sbjct: 251 LEDGI-----ERQALHCHRLSYYHPFLEEELVIESPLP 283


>gi|167627646|ref|YP_001678146.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017]
 gi|167597647|gb|ABZ87645.1| Lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017]
          Length = 328

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 84/317 (26%), Positives = 146/317 (46%), Gaps = 32/317 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++  D    R+D      +   +   +QK ++ G + V+ K  K  + +   + V I
Sbjct: 12  QKIMMHPDHAGKRIDSTINELFEQFSRSQIQKWIKDGLITVNGKTTKSKHILLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
              +   N  + E    D  +N+           ++ED+ I V +KP  + V  G+G + 
Sbjct: 72  NIELLPTNEWLAE----DIDLNI-----------VFEDNDIIVIDKPIDMVVHPGAGNMT 116

Query: 127 YHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             I   L     ++ + PR  + HRLD++TSG++V A++  A  +L +    R++ + Y 
Sbjct: 117 GTISNALLHKYPNQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLSERKVSRKYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCW 242
           ++V G      E      + +  IG D  +  K   N KG   AI+H+K I+ +   F  
Sbjct: 177 AIVEG------EIYEEGTINQP-IGRDLNNRTKMTINHKGKE-AITHYKPIEVY-DGFTL 227

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHP 300
           +E Q  TGRTHQ+RVH   +  P+VGD  Y  +        I+  N+  LHA  +   HP
Sbjct: 228 IECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLDKVGIENINRQALHAYKLSFMHP 287

Query: 301 EGGRL-QITAPLPAHMV 316
              ++ +  + LP  M+
Sbjct: 288 TSQKIVRFKSKLPEDML 304


>gi|153004836|ref|YP_001379161.1| pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152028409|gb|ABS26177.1| pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
          Length = 238

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 114/236 (48%), Gaps = 26/236 (11%)

Query: 101 LLYEDSKIYVFNKPAG---ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +L  D+ + V +KPAG   I  +GG  ++      L+  +++   +  + HRLD+ T+G+
Sbjct: 12  VLLADAALLVVDKPAGRLVIPGRGGDELS------LREELEAAHGRLWVVHRLDRGTTGV 65

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV ART  A + L  +F     +K Y ++V G P    E   +  +  +  G   +   +
Sbjct: 66  LVFARTAEAHRALNLAFDRGEPRKRYAAIVRGDPP--AEACLDAPIAPARRG--RMRPAR 121

Query: 218 QNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             +  A  A++  + ++ F  +         +E  P TGRTHQ+RVH +H G P+  D  
Sbjct: 122 PGDPRAKAAVTRIRTLETFPPRAWAGGALALVEAAPETGRTHQIRVHLMHAGYPLAVDPD 181

Query: 272 YCANFKGNFTSP----IQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
           Y    +G    P    + ++  LHA  ++L HP  G  L + APLPA M +   +L
Sbjct: 182 Y--GDEGPLHGPDARVLLSRTPLHASRLELRHPSTGATLVLEAPLPADMAEALQAL 235


>gi|333029726|ref|ZP_08457787.1| pseudouridine synthase, RluA family [Bacteroides coprosuis DSM
           18011]
 gi|332740323|gb|EGJ70805.1| pseudouridine synthase, RluA family [Bacteroides coprosuis DSM
           18011]
          Length = 355

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 89/349 (25%), Positives = 154/349 (44%), Gaps = 79/349 (22%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           ++V+  +  +R+D++  +   + +   +QK   +G V+V+   VK N +++  + + I  
Sbjct: 31  IIVDKGQSLVRIDKFLCDRIENASRNQVQKAAEAGFVKVNGNPVKSNYKVKPLEEITIYM 90

Query: 68  --PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
             PP          E +I+   + L          ++YED  + V NKPAG+ V  G G 
Sbjct: 91  DTPP---------HEIEIIPEDIPLN---------IVYEDDYLMVVNKPAGLVVHPGHGN 132

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                   IA+H+     S  D+   +  L HR+D++TSG+LV+A+T  A   L   F  
Sbjct: 133 YRGTLVNAIAWHMKN--NSCYDANDPRVGLVHRIDKDTSGLLVIAKTPEAKSKLGIQFFN 190

Query: 177 RRIQKIYWSLVWG------------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           +  ++ Y +LVWG            I +N K+ +   +     IG               
Sbjct: 191 KTTKREYRALVWGNIEEEEGRIEGNIARNPKDRLQMAVFADPEIG--------------K 236

Query: 225 YAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN 279
           +A++H+KV++         C LE    TGRTHQ+RVH  H+G  +  D +Y  +   +G 
Sbjct: 237 HAVTHYKVLERLGYVTLVACRLE----TGRTHQIRVHMKHIGHVLFNDARYGGSDILRGT 292

Query: 280 ----FTSPIQN------KLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
               +   ++N      +  LHA  +   HP     +  T+ LP  M +
Sbjct: 293 HFAKYKQFVENCFNICPRQALHALSLGFIHPVTNEEMFFTSELPDDMTE 341


>gi|323167770|gb|EFZ53465.1| ribosomal large subunit pseudouridine synthase D [Shigella sonnei
           53G]
 gi|323173090|gb|EFZ58721.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           LT-68]
 gi|333001156|gb|EGK20726.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           K-272]
 gi|333015794|gb|EGK35131.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           K-227]
          Length = 300

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 60  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 116

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 117 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 174

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 175 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 226

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 227 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 286

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 287 RADFEEH 293


>gi|257453790|ref|ZP_05619068.1| ribosomal large subunit pseudouridine synthase D [Enhydrobacter
           aerosaccus SK60]
 gi|257448717|gb|EEV23682.1| ribosomal large subunit pseudouridine synthase D [Enhydrobacter
           aerosaccus SK60]
          Length = 380

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 82/337 (24%), Positives = 146/337 (43%), Gaps = 45/337 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q   V +++   R+D+     +   +   ++  L SG++ V+    K   R++   ++ 
Sbjct: 66  IQNYTVNSEQIGERIDKIAALVFSDYSREQIKNWLESGELTVNGAAQKPKYRLKPNDMLV 125

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ--GGSG 124
           +   + A    + E   LD               +LYED  + V NKP G+ V    G+G
Sbjct: 126 LKASLTAQQQDLPENIPLD---------------ILYEDEAVLVINKPVGLVVHPGAGNG 170

Query: 125 IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               ++  L  + DS+   PR  L HR+D+ETSG++V+A+   +  HL    + + + ++
Sbjct: 171 SGTLVNALLFHYPDSR-TLPRAGLVHRIDKETSGLMVIAKDSQSQLHLINQLKDKSVYRL 229

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVIDCFA 237
           Y ++V           A  L +   I         Q  K A       A++H + I   +
Sbjct: 230 YQAIVL--------ASAAELARHRTIDAPIGRHPTQRTKMAVVSSGKPAVTHLEKITAIS 281

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----------- 286
                + ++  TGRTHQ+RVH  ++G P++GD  Y A  K        +           
Sbjct: 282 DAVSLVSVRLETGRTHQIRVHLSNLGFPLLGDPLYGAARKNAILLKTLDDDQKHIVQQFQ 341

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +  LHA  +   HP+ G  +++ A LP  M +  D+L
Sbjct: 342 RQALHAYELGFIHPKTGEPIKVQARLPEDMQQLLDTL 378


>gi|218706096|ref|YP_002413615.1| 23S rRNA pseudouridine synthase D [Escherichia coli UMN026]
 gi|293406104|ref|ZP_06650030.1| rluD [Escherichia coli FVEC1412]
 gi|298381836|ref|ZP_06991433.1| rluD [Escherichia coli FVEC1302]
 gi|300900220|ref|ZP_07118406.1| pseudouridine synthase, RluA family [Escherichia coli MS 198-1]
 gi|218433193|emb|CAR14092.1| 23S rRNA pseudouridine synthase [Escherichia coli UMN026]
 gi|291426110|gb|EFE99142.1| rluD [Escherichia coli FVEC1412]
 gi|298276976|gb|EFI18492.1| rluD [Escherichia coli FVEC1302]
 gi|300356255|gb|EFJ72125.1| pseudouridine synthase, RluA family [Escherichia coli MS 198-1]
          Length = 326

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 90/338 (26%), Positives = 158/338 (46%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V    
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            INA   I +E +     + L          ++YED  I V NKP  + V  G+G   + 
Sbjct: 66  AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---NP 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y
Sbjct: 112 DGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREY 171

Query: 184 WSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G         E I+    K++H+    VH + +       A++H+++++ F +  
Sbjct: 172 EAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPMGKP------AVTHYRIMEHF-RVH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHA 292
             L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA
Sbjct: 222 TRLRLRLETGRTHQIRVHMAHITHPLVGDPIYGGRPRPPKGASEAFISTLRKFDRQALHA 281

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
             + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 282 TMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 319


>gi|15900967|ref|NP_345571.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae TIGR4]
 gi|15903050|ref|NP_358600.1| 23S rRNA pseudouridine synthase [Streptococcus pneumoniae R6]
 gi|111657593|ref|ZP_01408329.1| hypothetical protein SpneT_02001203 [Streptococcus pneumoniae
           TIGR4]
 gi|116516162|ref|YP_816460.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae D39]
 gi|149006229|ref|ZP_01829941.1| phosphotransacetylase [Streptococcus pneumoniae SP18-BS74]
 gi|149012907|ref|ZP_01833820.1| phosphotransacetylase [Streptococcus pneumoniae SP19-BS75]
 gi|168483173|ref|ZP_02708125.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1873-00]
 gi|168491992|ref|ZP_02716135.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC0288-04]
 gi|168494532|ref|ZP_02718675.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC3059-06]
 gi|169832712|ref|YP_001694523.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae Hungary19A-6]
 gi|182684150|ref|YP_001835897.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CGSP14]
 gi|221231840|ref|YP_002510992.1| RNA pseudouridylate synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225854594|ref|YP_002736106.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae JJA]
 gi|303254191|ref|ZP_07340303.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           BS455]
 gi|303259761|ref|ZP_07345736.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP-BS293]
 gi|303262936|ref|ZP_07348871.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS292]
 gi|303264899|ref|ZP_07350815.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS397]
 gi|303266879|ref|ZP_07352757.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS457]
 gi|303268916|ref|ZP_07354701.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS458]
 gi|307127370|ref|YP_003879401.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 670-6B]
 gi|14972575|gb|AAK75211.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae TIGR4]
 gi|15458622|gb|AAK99810.1| 23S rRNA pseudouridine synthase [Streptococcus pneumoniae R6]
 gi|116076738|gb|ABJ54458.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae D39]
 gi|147762006|gb|EDK68968.1| phosphotransacetylase [Streptococcus pneumoniae SP18-BS74]
 gi|147763196|gb|EDK70136.1| phosphotransacetylase [Streptococcus pneumoniae SP19-BS75]
 gi|168995214|gb|ACA35826.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Hungary19A-6]
 gi|172043330|gb|EDT51376.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1873-00]
 gi|182629484|gb|ACB90432.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CGSP14]
 gi|183573763|gb|EDT94291.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC0288-04]
 gi|183575559|gb|EDT96087.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC3059-06]
 gi|220674300|emb|CAR68842.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           ATCC 700669]
 gi|225722385|gb|ACO18238.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae JJA]
 gi|301802010|emb|CBW34739.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           INV200]
 gi|302598862|gb|EFL65896.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           BS455]
 gi|302635913|gb|EFL66413.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS292]
 gi|302638966|gb|EFL69426.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP-BS293]
 gi|302641534|gb|EFL71896.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS458]
 gi|302643577|gb|EFL73846.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS457]
 gi|302645587|gb|EFL75818.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS397]
 gi|306484432|gb|ADM91301.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 670-6B]
 gi|332075053|gb|EGI85524.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA17545]
 gi|332201583|gb|EGJ15653.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA47368]
          Length = 298

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 112/219 (51%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      + +  HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVYIHLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLEDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|149003786|ref|ZP_01828618.1| phosphotransacetylase [Streptococcus pneumoniae SP14-BS69]
 gi|237650771|ref|ZP_04525023.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae CCRI 1974]
 gi|237822358|ref|ZP_04598203.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae CCRI 1974M2]
 gi|147758232|gb|EDK65234.1| phosphotransacetylase [Streptococcus pneumoniae SP14-BS69]
 gi|301794215|emb|CBW36634.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           INV104]
 gi|332075432|gb|EGI85901.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA41301]
 gi|332202956|gb|EGJ17024.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA47901]
          Length = 298

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 112/219 (51%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      + +  HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVYIHLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLEDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|331091184|ref|ZP_08340025.1| hypothetical protein HMPREF9477_00668 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330404631|gb|EGG84170.1| hypothetical protein HMPREF9477_00668 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 320

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 42/336 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + +  +E   RLD+    +        L K+LR   + ++ K+   N ++ +G  V+
Sbjct: 1   MQEIQIAANEAGQRLDKLLAKYLSEAPKSFLYKMLRKKNIVLNGKKASGNEKLVAGDSVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +    KE  +  S+  L          +LYED  I + NKPAG+  Q      
Sbjct: 61  LFLSDETIQKFSKEITVCKSNTKLD---------ILYEDDDILLVNKPAGMLSQKAEAKD 111

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   L S++   GQ         KP + +RLD+ TSG++V  ++    Q + + F+ R
Sbjct: 112 ISLVEHLISYLLESGQLTRENLKSFKPSICNRLDRNTSGLVVCGKSLKGLQTMGQLFKER 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLL---KKSHIGGDYVHVVKQNEKGANY-AISHFKVI 233
           +++K Y  +V G    +K+ +  +L+   KK+ +     +  +  E    Y  I   K  
Sbjct: 172 KLKKYYRCIVAG-NVTEKQYVKGYLIKDEKKNQVTVSDTYFPESQEIETEYRPIQQLK-- 228

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKL 288
                +   LE+   TG+THQ+R H    G  ++GD+KY +      +K  +    Q   
Sbjct: 229 -----QGTLLEVHLITGKTHQIRAHLASQGHAVIGDYKYGSREINDRYKKEYQLSHQ--- 280

Query: 289 YLHARYMDLPH----PEGGRLQITAPLPAHMVKTWD 320
            LHA  +++P     P+       APLP    K  +
Sbjct: 281 LLHAYRLEVPKTKELPQLSEKMFVAPLPKQFQKIIE 316


>gi|322807303|emb|CBZ04877.1| similar to ribosomal large subunit pseudouridine synthase D,
           CAC1266-type [Clostridium botulinum H04402 065]
          Length = 300

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 81/283 (28%), Positives = 137/283 (48%), Gaps = 35/283 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K +R G+V V+K++V   +++    ++ I   +    H    Q I    +N+      
Sbjct: 33  IRKAVRDGRVFVNKEKVIKKHKLSQDDLIEI--YMQEDEH----QNIEPEDMNIE----- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKP--RLTHRL 150
               ++YED+ I V NK  GI V    G   H  G L + +       G+K   RL  RL
Sbjct: 82  ----IVYEDNDIIVINKRPGIVVHPTKG---HPTGTLSNGILYHFKKNGEKSIVRLVSRL 134

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ + +   L         +KIY ++V G  K +KE   N  + K     
Sbjct: 135 DRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMK-EKEGRINLPIYKEEESE 193

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +V  +E+G   +I+ ++V++  + K   + ++  TGRTHQ+RVH  H+G P+ GD 
Sbjct: 194 SIKRIV--DERGQE-SITTYEVLEELS-KGSVVRLELETGRTHQIRVHMSHLGHPLYGDS 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
            Y    KG        +  LHA  ++ PHP  G   +LQ + P
Sbjct: 250 LYG---KGEEEKEYIERQALHAYKLEFPHPRTGDILKLQYSLP 289


>gi|22127552|ref|NP_670975.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           KIM 10]
 gi|45443414|ref|NP_994953.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Microtus str. 91001]
 gi|51594989|ref|YP_069180.1| 23S rRNA pseudouridylate 746 synthase [Yersinia pseudotuberculosis
           IP 32953]
 gi|108810081|ref|YP_653997.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Antiqua]
 gi|108810536|ref|YP_646303.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|145600392|ref|YP_001164468.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Pestoides F]
 gi|150260466|ref|ZP_01917194.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           CA88-4125]
 gi|153948334|ref|YP_001402394.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           pseudotuberculosis IP 31758]
 gi|162419457|ref|YP_001605342.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Angola]
 gi|165928068|ref|ZP_02223900.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165937798|ref|ZP_02226359.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166008924|ref|ZP_02229822.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166211832|ref|ZP_02237867.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167401530|ref|ZP_02307024.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167421997|ref|ZP_02313750.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167426100|ref|ZP_02317853.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|167467289|ref|ZP_02331993.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           FV-1]
 gi|170025783|ref|YP_001722288.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186893990|ref|YP_001871102.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
 gi|218927695|ref|YP_002345570.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           CO92]
 gi|229836920|ref|ZP_04457085.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Pestoides A]
 gi|229840385|ref|ZP_04460544.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229842465|ref|ZP_04462620.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229900724|ref|ZP_04515848.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|270487905|ref|ZP_06204979.1| pseudouridine synthase A [Yersinia pestis KIM D27]
 gi|294502592|ref|YP_003566654.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Z176003]
 gi|34395807|sp|Q8ZIK1|RLUA_YERPE RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|21960656|gb|AAM87226.1|AE013971_2 hypothetical protein y3678 [Yersinia pestis KIM 10]
 gi|45438283|gb|AAS63830.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Microtus str. 91001]
 gi|51588271|emb|CAH19878.1| 23S rRNA pseudouridylate 746 synthase [Yersinia pseudotuberculosis
           IP 32953]
 gi|108774184|gb|ABG16703.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|108781994|gb|ABG16052.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Antiqua]
 gi|115346306|emb|CAL19177.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           CO92]
 gi|145212088|gb|ABP41495.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Pestoides F]
 gi|149289874|gb|EDM39951.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           CA88-4125]
 gi|152959829|gb|ABS47290.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           pseudotuberculosis IP 31758]
 gi|162352272|gb|ABX86220.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Angola]
 gi|165914210|gb|EDR32826.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|165919929|gb|EDR37230.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165992263|gb|EDR44564.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166206578|gb|EDR51058.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166960134|gb|EDR56155.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167048912|gb|EDR60320.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167055023|gb|EDR64823.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|169752317|gb|ACA69835.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186697016|gb|ACC87645.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
 gi|229682063|gb|EEO78155.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|229690775|gb|EEO82829.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229696751|gb|EEO86798.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229705863|gb|EEO91872.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Pestoides A]
 gi|262360622|gb|ACY57343.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           D106004]
 gi|262364568|gb|ACY61125.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           D182038]
 gi|270336409|gb|EFA47186.1| pseudouridine synthase A [Yersinia pestis KIM D27]
 gi|294353051|gb|ADE63392.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Z176003]
 gi|320016868|gb|ADW00440.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Medievalis str. Harbin 35]
          Length = 206

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 74/208 (35%), Positives = 104/208 (50%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           I+LY+D  I V NKP+G+ SV    G A      + + V +        HRLD  TSG++
Sbjct: 2   IVLYQDKHIMVVNKPSGLLSV---PGRAPENKDSVMTRVQNDFPTAESVHRLDMATSGVI 58

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ
Sbjct: 59  VVALTKAAERELKRQFREREPKKTYIARVWGHLAQDEGLIDLPLI------CDWPNRPKQ 112

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G + A + ++VI         +++ P TGR+HQLRVH L MG PI+GD  Y   
Sbjct: 113 KVCYETGKS-AQTEYQVISRDDDGSTRVKLSPITGRSHQLRVHMLAMGHPILGDGFYAHP 171

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 S    +L LHA+ + + HPE G
Sbjct: 172 EAKAMAS----RLQLHAQQLCITHPEFG 195


>gi|304438735|ref|ZP_07398663.1| RluA family pseudouridine synthase [Peptoniphilus duerdenii ATCC
           BAA-1640]
 gi|304372737|gb|EFM26315.1| RluA family pseudouridine synthase [Peptoniphilus duerdenii ATCC
           BAA-1640]
          Length = 292

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 86/291 (29%), Positives = 134/291 (46%), Gaps = 40/291 (13%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +++ +R   + +++K  K N  +Q G VV I              KI D   N     D+
Sbjct: 33  IRRSIREEMIYINEKLNKRNVDLQPGDVVSI--------------KIPDEEPNAIP-EDY 77

Query: 97  LKSILLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            K  +LYED  I   NK   + V      Q G+   Y    FLK  +    +K RL +RL
Sbjct: 78  -KVEILYEDGDILAVNKEPFMIVHAVDFKQTGTISNYVQCYFLKHDIH---RKVRLINRL 133

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+   A   +    + R I K Y+++V G+ +     I    + +   G 
Sbjct: 134 DRDTSGVILIAKNSNAHSTVARELQDRNILKKYYAIVEGVVEGS--GIIEEPIDRGPDG- 190

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               ++++      YA + ++ I         L +  HTGRTHQ+RVH  ++G PIVGD 
Sbjct: 191 ----ILREVNPNGKYAKTSYEAI-LSKNNMTLLRVVLHTGRTHQIRVHLKYIGHPIVGDT 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            Y     GN T  I N+  LH+ Y  +  P  G  ++I APLP  M    D
Sbjct: 246 LY-----GNETELI-NRQALHSYYTKIKSPRTGEEIEIEAPLPQDMKNLLD 290


>gi|291459221|ref|ZP_06598611.1| ribosomal large subunit pseudouridine synthase D [Oribacterium sp.
           oral taxon 078 str. F0262]
 gi|291418475|gb|EFE92194.1| ribosomal large subunit pseudouridine synthase D [Oribacterium sp.
           oral taxon 078 str. F0262]
          Length = 308

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 84/336 (25%), Positives = 155/336 (46%), Gaps = 49/336 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVN--LQKILRSGQVRVDKKRVKFNNRIQS 61
           MT  + + VE +    RLDR+     P ++      ++++  G+V +D +  K + R++ 
Sbjct: 1   MTGTESIRVEAECAGERLDRYLSKR-PELSLSRSYAERLIGEGRVLLDGQAEKPSKRLRG 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G+ + I         I  E+  LD               ++YEDS++ + NKP G+ V  
Sbjct: 60  GEQISICFPEEKPTEIRAEEIPLD---------------IVYEDSELLLVNKPKGMVVHP 104

Query: 122 GSGIAYHIDGFL-KSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLT 171
             G   H  G L  + +   G          +P + HR+D++T+G+L+V +   A + L 
Sbjct: 105 APG---HSGGTLVNALLGRPGPELSSINGVLRPGIVHRIDRDTTGLLLVCKKDRAHRALA 161

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAIS 228
           E  +   I + Y +++ G  +  +  +       + IG       KQ    E+G   A++
Sbjct: 162 EQLKEHTITRRYHAILCGRMREDEGKV------DAPIGRSRRDRKKQAIDWERGRE-AVT 214

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NK 287
           H++V++ F++ +  +E +  TGRTHQ+RVH   +G P++GD  Y     G    P +   
Sbjct: 215 HYRVLERFSE-YTLVECRLETGRTHQIRVHMASIGHPVLGDEVY-----GPRHCPFRLEG 268

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             LHA+ +   HP  G+ ++  +  PA+  +    L
Sbjct: 269 QCLHAKLLGFVHPVSGKYMEFDSEYPAYFEELLQKL 304


>gi|194435119|ref|ZP_03067355.1| ribosomal large subunit pseudouridine synthase D [Shigella
           dysenteriae 1012]
 gi|194416650|gb|EDX32783.1| ribosomal large subunit pseudouridine synthase D [Shigella
           dysenteriae 1012]
 gi|332089232|gb|EGI94339.1| ribosomal large subunit pseudouridine synthase D [Shigella
           dysenteriae 155-74]
          Length = 326

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHMRLRLRLETGRTHQIRVHMAHITHPLVGDPV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 253 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|183982375|ref|YP_001850666.1| RluA family pseudouridine synthase [Mycobacterium marinum M]
 gi|183175701|gb|ACC40811.1| pseudouridine synthase, RluA-family [Mycobacterium marinum M]
          Length = 303

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 113/229 (49%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY D  I   +KPA ++     G     + G L +    + + G   R  + HRLD  T
Sbjct: 78  ILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRISTSGVHERQGIVHRLDVGT 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA +  A   L  +F+ R + K Y +LV G P      I   + +  H GG++  
Sbjct: 138 SGVMVVALSERAYTVLKRAFKQRTVDKRYHALVQGHPDPSSGTIDAPIGR--HPGGEWKF 195

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V +N +   ++++H+  ++ F      L++   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 196 AVTKNGR---HSLTHYDTVEAFVAA-SLLDVHLETGRTHQIRVHFAALHHPCCGDLVYGA 251

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           + K      +Q + +LHAR +   HP +G R++I +P P  +    D L
Sbjct: 252 DPKLAKRLGLQRQ-WLHARSLAFAHPADGRRVEIVSPYPPDLQHALDVL 299


>gi|28493478|ref|NP_787639.1| pseudouridylate synthase-like protein [Tropheryma whipplei str.
           Twist]
 gi|28476520|gb|AAO44608.1| pseudouridylate synthase-like protein [Tropheryma whipplei str.
           Twist]
          Length = 303

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 107/214 (50%), Gaps = 16/214 (7%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPR--LTHRLD 151
           D L+  ++Y D  ++V +KPAG++     G     + G L   + + G + R  + HRLD
Sbjct: 74  DLLR--VIYSDDDLFVIDKPAGVAAHASPGWCGPTVTGCLSGLLAACGPQDRQGIVHRLD 131

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG++V+A++  A  +L  +FR R I K Y +LV G P      I       + IG D
Sbjct: 132 ANTSGLMVLAKSDLAYHNLKAAFRDRAIHKRYKALVQGYPDPSSGVI------NAPIGRD 185

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             H  +   +     A++ +   + +   F  L + P TGRTHQ+RVH   +  P+VGD 
Sbjct: 186 LKHRDRFCIDYSGRDAVTQYSTEEVY-PGFTLLSVAPKTGRTHQIRVHFSALRHPLVGDV 244

Query: 271 KYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGG 303
           KY A+    F+  +   + +LHA ++   HP  G
Sbjct: 245 KYGAD--PVFSQKVNLKRQWLHAYHLSFTHPVSG 276


>gi|315282847|ref|ZP_07871166.1| ribosomal large subunit pseudouridine synthase D [Listeria marthii
           FSL S4-120]
 gi|313613517|gb|EFR87342.1| ribosomal large subunit pseudouridine synthase D [Listeria marthii
           FSL S4-120]
          Length = 302

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 82/302 (27%), Positives = 142/302 (47%), Gaps = 51/302 (16%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVV----RIPPVINALNHIIKEQKILDSSVNLTK 92
           +Q +L++G + V+ +  K N ++Q G  +    R P          +E ++L   + L  
Sbjct: 32  IQLMLKNGDITVNGELAKPNYKVQVGDEIHYEAREP----------EELEVLAEDIPLD- 80

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQK 143
                   + +ED  + V NKP G+ V   +G A         +H D    S ++ K  +
Sbjct: 81  --------IYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL--SGINGK-IR 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    +
Sbjct: 130 PGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPI 188

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++      + VV+  ++    A +HF+V++     F  +  +  TGRTHQ+RVH  ++G
Sbjct: 189 GRAKEDRQKMAVVRDGKE----ARTHFEVLERLP-GFTLINCKLDTGRTHQIRVHLKYIG 243

Query: 264 CPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            P+ GD KY      KGN         +LHA  +   HP    R+   APLP+   K   
Sbjct: 244 HPLAGDPKYGPKNTIKGNGQ-------FLHAAKLGFDHPTTNERMTFEAPLPSSFEKALK 296

Query: 321 SL 322
           +L
Sbjct: 297 TL 298


>gi|225570461|ref|ZP_03779486.1| hypothetical protein CLOHYLEM_06562 [Clostridium hylemonae DSM
           15053]
 gi|225160658|gb|EEG73277.1| hypothetical protein CLOHYLEM_06562 [Clostridium hylemonae DSM
           15053]
          Length = 291

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 108/221 (48%), Gaps = 20/221 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD--SKGQKP---RLTHRLDQETS 155
           ++YED  + V +KPAG+  Q   G   H +    + V   S+   P   R  +RLD+ TS
Sbjct: 83  IIYEDEDLLVIDKPAGMPTQPSQG--NHDNTLANALVCYYSRRGIPFTYRCINRLDKNTS 140

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+VA+   +A  L    + RRI + Y +L  G+  ++    A    +        V  
Sbjct: 141 GLLIVAKHMLSASILYAMIKERRIHREYLALAEGLTPSEGTITAPIARRSRSTIERCV-- 198

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              +E    YA +H++ +D + + +  L +   TGRTHQ+RVH  H+G P+ GD  Y  +
Sbjct: 199 ---DETNGEYACTHYRRLD-YRKGYSLLSVTLDTGRTHQIRVHLKHIGHPLPGDFLYHPD 254

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           +       I ++  LH+  +  PHP  GRL    +PLP  M
Sbjct: 255 YT------IISRQALHSCRLTFPHPVTGRLMDFESPLPDDM 289


>gi|3834304|gb|AAC83020.1| Contains similarity to gi|1786244 hypothetical 24.9 kD protein in
           surA-hepA intergenic region yab0 from Escherichia coli
           genome gb|AE000116, and to hypothetical YABO family
           PF|00849 [Arabidopsis thaliana]
          Length = 491

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 79/261 (30%), Positives = 122/261 (46%), Gaps = 38/261 (14%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD---FLKSILLYE 104
           +  +++K N  +Q G  + +P  I  +  I K    + S   L  ++D   +L+ ++ ++
Sbjct: 127 IPMRKIKHNEVMQIGDKIWLPVSIAEMR-ISKRYDTIPSG-TLYPNADEIAYLQRLVRFK 184

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLT-------HRLDQETSG 156
           DS I V NKP  + V+G   I   +D    + +     + PRL        HRLD+ETSG
Sbjct: 185 DSAIIVLNKPPKLPVKGNVPIHNSMDALAAAALSFGNDEGPRLVKLTFLGVHRLDRETSG 244

Query: 157 ILVVARTRAAAQHLTESFR---------------MRRIQKIYWSLVWGIPKNKKECIANW 201
           +LV+ RT+ +  +L   F                   + + YW+LV G PK K+  I+  
Sbjct: 245 LLVMGRTKESIDYLHSVFSDYKGRNSSCKAWNKACEAMYQQYWALVIGSPKEKEGLISAP 304

Query: 202 LLKKSHIGGDYVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTH----- 253
           L K     G    VV     G   +  AI+ +KV+        W+E++P T R H     
Sbjct: 305 LSKVLLDDGKTDRVVLAQGSGFEASQDAITEYKVLGPKINGCSWVELRPITSRKHQPPSK 364

Query: 254 -QLRVH-ALHMGCPIVGDHKY 272
            QLRVH A  +G PIVGD+KY
Sbjct: 365 KQLRVHCAEALGTPIVGDYKY 385


>gi|295087068|emb|CBK68591.1| Pseudouridylate synthases, 23S RNA-specific [Bacteroides
           xylanisolvens XB1A]
          Length = 564

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 72/220 (32%), Positives = 109/220 (49%), Gaps = 36/220 (16%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ED  + + NKPAG +SV G +      YH     K + ++ G  P + HRLD  TSG
Sbjct: 347 IVFEDEWLLIVNKPAGMLSVPGKAEDRDSVYH--RLKKKYPEATG--PMIVHRLDMATSG 402

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+VA+T+   Q L   F  R I+K Y +++ GI  +++       L  + +  D    +
Sbjct: 403 LLLVAKTKKVHQDLQAQFANRSIKKRYVAVLDGIVLSERTGRIELPLCLNPL--DRPRQI 460

Query: 217 KQNEKGANYAISHFKVIDCFAQ-------------KFCWLEMQPHTGRTHQLRVHALH-- 261
              E G   AI+ +K+I    +             K+  +   P TGRTHQLRVHA H  
Sbjct: 461 VSKEYGKE-AITEYKIISESEKIIDESERSINEPRKYTRIVFYPLTGRTHQLRVHAAHPE 519

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            +GCPI+GD  Y             ++LYLHA Y++  HP
Sbjct: 520 GLGCPILGDELYGKK---------ADRLYLHAEYIEFRHP 550


>gi|294897749|ref|XP_002776058.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Perkinsus marinus ATCC 50983]
 gi|239882591|gb|EER07874.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Perkinsus marinus ATCC 50983]
          Length = 604

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 73/253 (28%), Positives = 118/253 (46%), Gaps = 31/253 (12%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETS 155
           L+  +L+ D+     NKP G+SV  G  + Y +   L+++   S  + P L HRLD  T+
Sbjct: 268 LEDAVLHRDADFIAINKPWGLSVTDGPKVKYSLQRHLRAFTSPSSSEVPILIHRLDTATA 327

Query: 156 GILVVARTRAAAQHLTESFRMRRI-QKIYWSLVWGI----PKNKKECIANWLLKKSHIGG 210
           G+ ++AR ++AA    +    R    +IYW LVWG     P+     I   L+ + H   
Sbjct: 328 GVQLLARHKSAATMARDRIGARSFWNRIYWVLVWGRVQLGPRQFSGTINIPLIHRGH--- 384

Query: 211 DYVHVVKQNEKGANY-AISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPI 266
              HV   +   A   AI+ ++++    FA     L+++P+TGR  QL+ H A  +  PI
Sbjct: 385 ---HVKPASFHTAELSAITRWEILKFSPFAGGITLLKLEPYTGRRDQLQAHCAFGLRTPI 441

Query: 267 VGDHKYCANF---------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           VGD  Y                   K  F   +  K  + +R + +    G ++ I AP+
Sbjct: 442 VGDDVYSKEAIRWNDAYPEKHMLQRKEMFGEELICKRMVCSRQISMHSFGGDQIDIIAPV 501

Query: 312 PAHMVKTWDSLGF 324
           P HM + +D LG+
Sbjct: 502 PPHMQQMFDKLGW 514


>gi|154495180|ref|ZP_02034185.1| hypothetical protein PARMER_04229 [Parabacteroides merdae ATCC
           43184]
 gi|154085730|gb|EDN84775.1| hypothetical protein PARMER_04229 [Parabacteroides merdae ATCC
           43184]
          Length = 544

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 73/235 (31%), Positives = 110/235 (46%), Gaps = 23/235 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGF 132
           L H+++   + ++ +    H D    I+ YED  + V NKPAG +SV G S I       
Sbjct: 313 LKHMLQGLHVEENPLETDMHRDTELEIM-YEDEWLSVVNKPAGMLSVPGKSDIDSVYGRV 371

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            + + ++ G  P + HRLD  TSG++++A+T+   Q+L   F+ R + K Y + + GI +
Sbjct: 372 RRMYPEATG--PMIVHRLDMATSGLILIAKTKEVHQNLQAQFKNRTVCKRYVAWLDGIVE 429

Query: 193 NKKECIANWLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            K+  I   L           V  V       +Y + H+     F      +   P TGR
Sbjct: 430 KKEGHIELPLRPDPEDRPRQVVDAVHGKPAVTDYTVLHYDSGRTF------ISFIPKTGR 483

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           THQLRVH+ H   +  PIVGD  Y             ++LYLHA Y+   HP  G
Sbjct: 484 THQLRVHSAHPLGLNAPIVGDELYGRK---------ADRLYLHAEYLGFIHPVSG 529


>gi|332088103|gb|EGI93228.1| ribosomal large subunit pseudouridine synthase D [Shigella boydii
           5216-82]
          Length = 300

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 60  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 116

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 117 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 174

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 175 -VHPMGKP------AVTHYRIMEHF-RVHMRLRLRLETGRTHQIRVHMAHITHPLVGDPV 226

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 227 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 286

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 287 RADFEEH 293


>gi|260596481|ref|YP_003209052.1| 23S rRNA/tRNA pseudouridine synthase A [Cronobacter turicensis
           z3032]
 gi|260215658|emb|CBA27961.1| Ribosomal large subunit pseudouridine synthase A [Cronobacter
           turicensis z3032]
          Length = 217

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 69/208 (33%), Positives = 107/208 (51%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +          HRLD  TSG++
Sbjct: 13  LILYQDEHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDFPNAESAHRLDMATSGVI 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            VA T+AA + L   FR R  +K Y + VWG P+  +  +   L+       D+ +  KQ
Sbjct: 70  AVALTKAAERELKRQFREREPKKHYVARVWGHPEKAQGVVDLPLI------CDWPNRPKQ 123

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + + V++        + ++P TGR+HQLRVH + +G PI+GD K+ A 
Sbjct: 124 KVCYETG-KAAQTEYDVLEYADDNTARVLLRPITGRSHQLRVHMMALGHPILGD-KFYAT 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    +P   +L LHA  + + HP  G
Sbjct: 182 PEALARAP---RLLLHAEQLTITHPAYG 206


>gi|218129851|ref|ZP_03458655.1| hypothetical protein BACEGG_01432 [Bacteroides eggerthii DSM 20697]
 gi|217987961|gb|EEC54286.1| hypothetical protein BACEGG_01432 [Bacteroides eggerthii DSM 20697]
          Length = 518

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 68/207 (32%), Positives = 100/207 (48%), Gaps = 20/207 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILVV 160
           +YED  + V NKPAG+    G   A  +   ++  + ++ G  P + HRLD  TSG+LV+
Sbjct: 318 VYEDEWLLVVNKPAGMLSVPGKEEAVSVYSVMRGRYPEADG--PLIVHRLDMATSGLLVI 375

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T+   Q+L   FR R + K Y +L+ GI       +   L        D    +   E
Sbjct: 376 AKTKQVHQNLQAQFRDRSVSKRYIALLQGIVSPDTGTVELPLCLNPL---DRPRQMVHTE 432

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFK 277
            G   A++ F+V++        +   P TGRTHQLRVHA H   + CPI+GD  Y     
Sbjct: 433 HG-KPAVTDFEVLE-RKDNHTRIAFYPRTGRTHQLRVHAAHPLGLHCPIIGDELYGKK-- 488

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR 304
                    +LYLHA  ++  HP  G+
Sbjct: 489 -------AERLYLHAEALEFTHPITGK 508


>gi|331002782|ref|ZP_08326296.1| hypothetical protein HMPREF0491_01158 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330413271|gb|EGG92639.1| hypothetical protein HMPREF0491_01158 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 216

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 57/175 (32%), Positives = 91/175 (52%), Gaps = 7/175 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  I V  KP GIS Q  SG    +   LK  +  K     + HRLD+   GI++ 
Sbjct: 5   ILYEDEDIIVAVKPRGISSQSSSGFEDDMVSLLKKHL-GKDAYIGVIHRLDKPVYGIILY 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T+ A + L+   R + I+K Y +LV G+P+NK+  + ++L K  +   +   VV +N 
Sbjct: 64  GKTKVATEILSNELRKKNIEKTYEALVEGLPENKEGELRDYLKKYDN---NISKVVDKNT 120

Query: 221 KGANYAISHFKVIDCFAQKFCW---LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            GA  ++  + V + + +   +   L +   TGR HQ+R+     G P+ GD KY
Sbjct: 121 PGAKESVLKYSVEESYQRDDTFITRLRINLLTGRNHQIRLQCAAHGFPLFGDFKY 175


>gi|312881916|ref|ZP_07741679.1| 23S rRNA pseudouridine synthase D [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309370434|gb|EFP97923.1| 23S rRNA pseudouridine synthase D [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 325

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 89/330 (26%), Positives = 153/330 (46%), Gaps = 45/330 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L+  L  G+V+VD + V K   ++  G+V+    
Sbjct: 10  TVKDAQLGQRLDQAIAELFSDFSRSRLKDWLLDGKVQVDGEVVTKPRTKVMGGEVI---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
           V++A   +  E++     + L          ++YED  I V NKP G  V  G+G     
Sbjct: 66  VLHA--ELEDEERWEAQDIPLD---------IVYEDDDIIVINKPRGFVVHPGAGTPDGT 114

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L  + D   + PR  + HRLD++T+G++VVA+T  A   L  + + R I + Y +
Sbjct: 115 VLNALLHHFPDI-AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG----ANYAISHFKVIDCFAQKFC 241
           +  G         A   +++  IG    H  K+           A++H++V + F ++  
Sbjct: 174 IAIG------RMTAGGRVEQP-IGR---HSTKRTLMAVAPLGKPAVTHYRVAEHF-REHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKL------YLHAR 293
            + ++  TGRTHQ+RVH  ++  P++GD  Y   A      T  +  K+       LHA 
Sbjct: 223 RIRLRLETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPRGATPELAEKIRQFDRQALHAV 282

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            +   HP  G  L+  AP+P  MV   D+L
Sbjct: 283 MLKFEHPITGEELEFHAPVPDDMVAMSDAL 312


>gi|242097088|ref|XP_002439034.1| hypothetical protein SORBIDRAFT_10g030300 [Sorghum bicolor]
 gi|241917257|gb|EER90401.1| hypothetical protein SORBIDRAFT_10g030300 [Sorghum bicolor]
          Length = 441

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 78/338 (23%), Positives = 140/338 (41%), Gaps = 66/338 (19%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN----LTKHSDFLKSILLYEDS 106
            R +    I++G V      ++ ++H +K   ++  +V+    L   ++ +   ++YED 
Sbjct: 89  SRARVQASIRAGLVAVNGRPVSKVSHTVKGGDLVSCTVSELQPLRAEAEDIPLDIVYEDD 148

Query: 107 KIYVFNKPAGISVQGGSGIA---------------------------------------Y 127
            + V NKPA + V    G A                                       +
Sbjct: 149 HVLVVNKPAHMVVHPAPGNANGTLVNAILHHCKISTFTCLARSSTGDECLDSSDDDIDVF 208

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++D F      S+ +    +P + HRLD+ TSG+LVVA+   +   L E F++  I+++Y
Sbjct: 209 NVDQFATEDASSEVRNALVRPGIVHRLDKGTSGLLVVAKDEHSHAQLAEQFKLHTIRRVY 268

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            SL  G+P      I   + +  +     + +     + A +A S +KV + F      L
Sbjct: 269 ISLTCGVPNPNSGRIEASIARDPNNRIRMIAIAGSGHRYARHAASRYKVREVFVGGGSAL 328

Query: 244 -EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---------------FKGNFTSPIQ-- 285
            E +  TGRTHQ+R HA ++G P++GD  Y                  +  + ++ I   
Sbjct: 329 VEWRLETGRTHQIRAHAKYIGIPLLGDETYGGTKSMALSLLRPRTPSKYHSDLSNLISKV 388

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           ++  LHA  +   HP  G+ L+ + P P    +  D L
Sbjct: 389 DRPCLHAALLGFKHPHSGKILEFSCPPPDDFSEVLDEL 426


>gi|148994152|ref|ZP_01823467.1| phosphotransacetylase [Streptococcus pneumoniae SP9-BS68]
 gi|168488941|ref|ZP_02713140.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae SP195]
 gi|147927395|gb|EDK78425.1| phosphotransacetylase [Streptococcus pneumoniae SP9-BS68]
 gi|183572419|gb|EDT92947.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae SP195]
 gi|332073458|gb|EGI83937.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA17570]
          Length = 298

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 112/219 (51%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      + +  HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVYIHLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLEDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|114046948|ref|YP_737498.1| pseudouridylate synthase [Shewanella sp. MR-7]
 gi|113888390|gb|ABI42441.1| Pseudouridylate synthase [Shewanella sp. MR-7]
          Length = 223

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 102/208 (49%), Gaps = 16/208 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           L Y+D  + + NKP+G+    G   A+  D  L    + + D+      L HRLD  TSG
Sbjct: 16  LRYQDRDLIIINKPSGLLSNPGRA-AHTFDCALTRLQRLYPDTI-----LVHRLDCATSG 69

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I+V AR + A   L   F+ R+ +K+Y + V G+   K   I +  +        Y    
Sbjct: 70  IMVFARNKKAESQLKTQFQDRQNEKVYVAEVMGL-IAKDAGIIDLAIAPDPEHPPYQKTQ 128

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                GA  A++H++V++   +    +E+ P TGRTHQLRVH L +G PI+GD  Y    
Sbjct: 129 TAGTAGAKSALTHYRVLE-RRENSTLVELTPQTGRTHQLRVHMLALGHPILGDEFY---- 183

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             +     + +L LHA+ +   HP  G+
Sbjct: 184 GDDEVIKARPRLCLHAQSLRFTHPYSGK 211


>gi|261879059|ref|ZP_06005486.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           bergensis DSM 17361]
 gi|270334340|gb|EFA45126.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           bergensis DSM 17361]
          Length = 421

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 70/224 (31%), Positives = 107/224 (47%), Gaps = 24/224 (10%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +D   N  +  +  +  ++YED  + V +KPAG +SV G       +D   +   D+ G 
Sbjct: 207 MDVDPNPLEQEETHELKIVYEDDTLCVVDKPAGMLSVPGKGCRESVLDVMRRRCPDATGA 266

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              + HRLD  TSG++VVA+T  A + L   F  R ++K Y +++   P+  K  IA  L
Sbjct: 267 L--VVHRLDMATSGLMVVAKTAEAYRELQRQFATRSVRKRYVAILSRQPREPKGEIA--L 322

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH- 261
             +  +      VV  +      A++H+++ID      C + + P TGRTHQLRVH  H 
Sbjct: 323 PLRPDLDDRPRQVV--DSVYGKPALTHYEIIDG-----CRVALYPRTGRTHQLRVHCAHR 375

Query: 262 --MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +  PI GD  Y              +LYLHA ++   HP  G
Sbjct: 376 DGLDSPIKGDELYGRR---------AERLYLHAEWLAFRHPATG 410


>gi|126172980|ref|YP_001049129.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|153002090|ref|YP_001367771.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|307304720|ref|ZP_07584470.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|125996185|gb|ABN60260.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           baltica OS155]
 gi|151366708|gb|ABS09708.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|306912122|gb|EFN42546.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 225

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 64/205 (31%), Positives = 105/205 (51%), Gaps = 15/205 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G   A++   + +  V ++    ++ HRLD  TSG++VV
Sbjct: 16  ILYQDKDIIVINKPSGLLSVPGRDPAHYDSVYAR--VKAEHPHSQIVHRLDMATSGVIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A  R+A + L   F  R   K Y++ V G  KN    +   L+       D+ +  KQ  
Sbjct: 74  ALIRSAERELKRQFHDRETSKTYFARVAGHVKNDTGSVDYPLI------CDWPNRPKQKV 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      +++H++VI   A++   +++ P TGR+HQLRVH + +G PI+GD  Y      
Sbjct: 128 DHLVGKPSLTHYQVI-SRAKRSTLVKLTPITGRSHQLRVHMMALGHPILGDGFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
           +       +L LHA  + + HP  G
Sbjct: 187 SLAP----RLLLHAAELTIKHPYTG 207


>gi|326203527|ref|ZP_08193391.1| pseudouridine synthase, RluA family [Clostridium papyrosolvens DSM
           2782]
 gi|325986347|gb|EGD47179.1| pseudouridine synthase, RluA family [Clostridium papyrosolvens DSM
           2782]
          Length = 299

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 79/263 (30%), Positives = 129/263 (49%), Gaps = 26/263 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSI-----LLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           +N+++KE+  L   ++L +  + ++       ++YED  + V NK  GI V   S   YH
Sbjct: 49  VNYVVKEEDKLKVILDLEEECENIEPQDIPLNIIYEDECMLVLNKQPGIVVHPTS---YH 105

Query: 129 IDGFLKS----WVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            D  + +    ++  KG  +K R   RLD+ETSGI++ A+ +   + L +       +K 
Sbjct: 106 PDNTIANGIVYYLKQKGVIKKVRPVSRLDRETSGIIIFAKNQFTQETLIQQMHANLFKKE 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFC 241
           Y  +V GIP+ K E   N  + +        H+   +E+GA  +I+H+KV++ F      
Sbjct: 166 YLGVVQGIPE-KSEGTINLPIARKPGSIMLRHI---SEEGAP-SITHYKVLNSFPLHNSA 220

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L     TGRTHQ+RVH   MG PI GD  Y  N     T+   ++  LH+   ++ HP 
Sbjct: 221 LLGFNLETGRTHQIRVHCHAMGFPIYGDTLYSDN-----TNLFISRQALHSYRTEILHPV 275

Query: 302 GGRLQI-TAPLPAHMVKTWDSLG 323
             +  I TA LP+ +    + L 
Sbjct: 276 TRKEVIFTAELPSDIAGLLEILS 298


>gi|226950404|ref|YP_002805495.1| pseudouridine synthase, RluA family [Clostridium botulinum A2 str.
           Kyoto]
 gi|226842595|gb|ACO85261.1| pseudouridine synthase, RluA family [Clostridium botulinum A2 str.
           Kyoto]
          Length = 300

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 81/283 (28%), Positives = 137/283 (48%), Gaps = 35/283 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K +R G+V V+K++V   +++    ++ I   +    H    Q I    +N+      
Sbjct: 33  IRKAVRDGRVFVNKEKVIKKHKLSQDDLIEI--YMQEDEH----QNIEPEDMNIE----- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKP--RLTHRL 150
               ++YED+ I V NK  GI V    G   H  G L + +       G+K   RL  RL
Sbjct: 82  ----IVYEDNDIIVINKRPGIVVHPTKG---HPTGTLSNGILYHFKKNGEKSIVRLVSRL 134

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ + +   L         +KIY ++V G  K +KE   N  + K     
Sbjct: 135 DRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMK-EKEGRINLPIYKEEESE 193

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +V  +E+G   +I+ ++V++  + K   + ++  TGRTHQ+RVH  H+G P+ GD 
Sbjct: 194 SIKRIV--DERGQE-SITTYEVLEELS-KGSVVRLELETGRTHQIRVHMSHLGHPLYGDS 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
            Y    KG        +  LHA  ++ PHP  G   +LQ + P
Sbjct: 250 LYG---KGEEEKEYIERQALHAYKLEFPHPRTGDILKLQCSLP 289


>gi|160935585|ref|ZP_02082960.1| hypothetical protein CLOBOL_00475 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441329|gb|EDP19039.1| hypothetical protein CLOBOL_00475 [Clostridium bolteae ATCC
           BAA-613]
          Length = 287

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 69/223 (30%), Positives = 112/223 (50%), Gaps = 22/223 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD----SKGQK--PRLTHRLDQET 154
           ++YED  I V NK AG+ +    G   H D  L + V      KG+    R+ +RLD++T
Sbjct: 71  IVYEDEDILVINKDAGVPIHPSQG---HYDNTLANAVSWYFHEKGEAFTYRVINRLDRDT 127

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+LV+AR   +A  L+E    RRI++ Y ++V G     +E   +  + ++   G  + 
Sbjct: 128 TGLLVLARHMLSACILSEQMTGRRIRREYRAIVLG--HTPEEGTVDSPIARAE--GSTIE 183

Query: 215 VVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               +E G   A++HF+ +    +K    + +   TGRTHQ+RVH   +G P+ GD  YC
Sbjct: 184 RRVDHETGER-AVTHFRTLLYNEEKDLSLVSLSLETGRTHQIRVHMRSIGHPLPGDFLYC 242

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            +++     P      LH+  +   HP  G  ++ TA LP  M
Sbjct: 243 PDYRYIDRQP------LHSYLLRFEHPITGKEMEFTAGLPEDM 279


>gi|37524666|ref|NP_928010.1| tRNA pseudouridine synthase C [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36784091|emb|CAE12960.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 256

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 69/223 (30%), Positives = 111/223 (49%), Gaps = 19/223 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I   NKPAG  V   S +A H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 4   VLYQDDHIVAVNKPAGWLVHR-SWLARHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A +   A+ L++ F   ++QK Y ++V G            + +   I   +     + 
Sbjct: 63  MALSSDVARQLSQQFEHHQLQKTYHAVVRGYVLESAIIDYALVEELDKIADKFA----EG 118

Query: 220 EKGANYAISHFK---VIDCFAQ-------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +K A   +++++    ++C  +       +F  LE+ P TGR HQLR H  H+  PI+GD
Sbjct: 119 DKEAQSCVTYYRPLATVECPVEIGRYPTSRFSLLELTPKTGRKHQLRRHMAHIRHPIIGD 178

Query: 270 --HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
             H      +G       ++L LHA Y++L HP  G +L +TA
Sbjct: 179 TTHGDLRQNRGVAVHYQTSRLMLHASYLELDHPVTGEKLSLTA 221


>gi|296113951|ref|YP_003627889.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis RH4]
 gi|295921645|gb|ADG61996.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis RH4]
          Length = 242

 Score = 92.8 bits (229), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 112/238 (47%), Gaps = 41/238 (17%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +F KSI +YED  I+V +KPAG+    G  +       L+S +       RL HRLD +T
Sbjct: 25  EFAKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPNIRLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-----------------PKNKKEC 197
           SG+++ A++  A  H+++ F  R  QK Y ++V+G                  P  K   
Sbjct: 81  SGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVPVRYEPTTKPRH 140

Query: 198 IANWLLKKSHIGGDYV--HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           I +    K  +    V  H ++ ++ G  Y ++              + ++P TGR+HQL
Sbjct: 141 IVDMDWNKQALTHYEVMHHELRCDDNGRTYPVTR-------------VALKPITGRSHQL 187

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           RVH +H+G  ++GD  Y  +     +    N+L LHA  + L HP  G  +   +P+P
Sbjct: 188 RVHMVHLGHVMIGDPIYAEDVALKLS----NRLNLHAHKLRLKHPTHGIWMDWVSPVP 241


>gi|254463248|ref|ZP_05076664.1| ribosomal large subunit pseudouridine synthase A [Rhodobacterales
           bacterium HTCC2083]
 gi|206679837|gb|EDZ44324.1| ribosomal large subunit pseudouridine synthase A [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 216

 Score = 92.8 bits (229), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 70/212 (33%), Positives = 104/212 (49%), Gaps = 29/212 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D +I + NKPAG+    G G    +   L + +     +  L HRLD++TSG++V 
Sbjct: 14  ILHDDHEILIVNKPAGLLSVPGKG--EELADCLIARIQKVFPQALLVHRLDRDTSGVMVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKK---ECIANW----LLKKSHIGGD 211
           A TR A +HL   F  R  QK Y + V G+  PK        I +W    L K  H  G 
Sbjct: 72  ALTRHAQRHLGLQFEKRMTQKTYVARVAGVLEPKTGSVELPLIVDWPNRPLQKVCHETGK 131

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             H             + ++V+  + +    + + P TGR+HQLRVH L +G PI+GD  
Sbjct: 132 AAH-------------TDYRVMR-YGEGETRVRLTPRTGRSHQLRVHMLALGHPILGDPF 177

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           Y +   G   S    +L LH+  + L HP+GG
Sbjct: 178 YAS---GTDLSD-HPRLMLHSEELRLKHPDGG 205


>gi|227431875|ref|ZP_03913898.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
 gi|227352342|gb|EEJ42545.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
          Length = 312

 Score = 92.8 bits (229), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 82/283 (28%), Positives = 133/283 (46%), Gaps = 39/283 (13%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L  G + V+  +VK + ++ SG  + I P         +E KI   ++ L    +     
Sbjct: 36  LVDGTILVNNHKVKRSYKVVSGDTISITPPET------QETKIEAENIPLDIIYEDDDI- 88

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-------DSKGQ-KPRLTHRLDQ 152
                    V NKP G+ V   +G   H  G L + +          G+ +P + HR+D+
Sbjct: 89  --------IVVNKPQGMVVHPAAG---HSSGTLVNALLHHSPLSTINGEFRPGIVHRIDR 137

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+L+VA+   A   L+E  +  + Q++Y++LV G      E   +    ++ IG   
Sbjct: 138 DTSGLLMVAKNDKAHHSLSEQLKSHKNQRVYYALVRG------EFTEDSGTIEAPIGRHK 191

Query: 213 VHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +   KQ   +G   A++HF+V+  +   +  L++   TGRTHQ+RVH  ++G P+VGD  
Sbjct: 192 IDRKKQAVIEGGREAVTHFRVLKRYV-GYTLLKVNLETGRTHQIRVHMSYIGHPVVGDPV 250

Query: 272 YCANFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y    K      IQ N   LHA+ + L  P  G  L   +PLP
Sbjct: 251 YGTAQK---LDGIQLNGQLLHAKTLTLEQPTTGDELSFDSPLP 290


>gi|330962664|gb|EGH62924.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. maculicola str. ES4326]
          Length = 211

 Score = 92.8 bits (229), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 69/214 (32%), Positives = 111/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETS I++
Sbjct: 8   IIHQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGFPEARIVHRLDWETSAIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KVI+     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEGGKHALTFWKVIE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              P   +L LHA  ++  HP  G RL    P P
Sbjct: 180 AAYP---RLCLHASMLNFTHPGTGERLTFECPAP 210


>gi|56478105|ref|YP_159694.1| ribosomal large subunit pseudouridine synthase D [Aromatoleum
           aromaticum EbN1]
 gi|56314148|emb|CAI08793.1| ribosomal large subunit pseudouridine synthase D [Aromatoleum
           aromaticum EbN1]
          Length = 306

 Score = 92.8 bits (229), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 78/309 (25%), Positives = 137/309 (44%), Gaps = 29/309 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  D   +R+D+     +P  +   LQ  L+SG+V +D  +     ++  G+ + +  
Sbjct: 5   LTIPADCAGLRVDQALARLFPSHSRSRLQGWLKSGRVSLDGDQPDAKFKVWGGESLEVDA 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                      + I                ++++ED +I V +KP G+ V  GSG     
Sbjct: 65  APPPEAAAEAPEDI--------------PLVVVHEDEEILVIDKPVGLVVHPGSGNWSGT 110

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L          PR  + HRLD++TSG+LVVA+T  +   L    + R +++ Y +
Sbjct: 111 LLNALLHH-APQLAAVPRAGIVHRLDKDTSGLLVVAKTLESQTALVRQLQARTVRRHYLA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLE 244
           LV          +A   + ++ IG       +    +    A++ ++  + FA +   +E
Sbjct: 170 LV-------HRAVAGAGMVEAPIGRHPTQRTRMAVVQSGRAAVTRYRPRERFA-RVTLVE 221

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
            Q  TGRTHQ+RVH  ++G P+VGD  Y     G+       +  LHA  + L HP  G 
Sbjct: 222 CQLETGRTHQIRVHMAYIGHPLVGDATYGLRRSGSPVLDAFARQALHAFRLGLLHPASGA 281

Query: 304 RLQITAPLP 312
            +   +PLP
Sbjct: 282 EMTWESPLP 290


>gi|322375304|ref|ZP_08049817.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C300]
 gi|321279567|gb|EFX56607.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C300]
          Length = 298

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 68/219 (31%), Positives = 114/219 (52%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +L+ED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILFEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-EYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA      + I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQRKSIEKRYFALVKGNGDLEPEGEIIAPIARDVNSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +KV+  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKVVASYGD-IHLIDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  ++   HP   R L++ +PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHFLSFYHPFLERQLELESPLP 283


>gi|307719808|ref|YP_003875340.1| pseudouridine synthase [Spirochaeta thermophila DSM 6192]
 gi|306533533|gb|ADN03067.1| pseudouridine synthase [Spirochaeta thermophila DSM 6192]
          Length = 256

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 120/243 (49%), Gaps = 21/243 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL--THRLDQETS 155
           ++YED+ I   NK     VQ  S +   +   L   +   D     PRL   +RLD+ TS
Sbjct: 3   IIYEDAHIIAVNKTGEELVQQNSVMEGTLQESLLEHLRMRDGAEAPPRLHLVNRLDRPTS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ AR R AA   +  FR R + K+YW+++   P    + + +++++   I   +   
Sbjct: 63  GIVLFARHRKAAGKFSHLFRRRGVYKLYWAVLDAPPPLPSDTVEHYIVENRRINKSFAFA 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+  +G+ YA   ++VI     ++ ++ ++ HTGR HQ+R     +GC I GD KY A 
Sbjct: 123 EKK--EGSEYARLSYQVIGS-GDRYFFVVVRLHTGRHHQIRAQFSALGCHIKGDIKYGAK 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR-NLYIK 333
                       ++LHAR +   HP  G R+ ITA  PA      DSL  ++ R + + +
Sbjct: 180 RTNR-----GGGIHLHARLLAFIHPFTGERVVITADPPA------DSLWEEFARQDAHFR 228

Query: 334 RLY 336
           R Y
Sbjct: 229 REY 231


>gi|302346727|ref|YP_003815025.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
 gi|302151131|gb|ADK97392.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
          Length = 296

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 70/232 (30%), Positives = 111/232 (47%), Gaps = 17/232 (7%)

Query: 87  SVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           SV+ +K +D  +S    ++YED  + V  K  GI        + ++   L  +     QK
Sbjct: 68  SVSKSKKNDLFRSRYVKIVYEDRFLVVIEKNIGILSMAAGHSSLNVKTVLDDYFRKTKQK 127

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               + HRLD++TSG+++ A+     Q L   +      + Y ++V G  ++ +  IANW
Sbjct: 128 CTAHVVHRLDRDTSGLMIYAKDIQTEQLLEHDWHNIVYDRRYVAVVSGEMEHDEGTIANW 187

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L         YV      + G  YA++HF V+D        +E Q  TGR +Q+RVH+  
Sbjct: 188 LKDNK----SYVTYSSPVDNGGKYAVTHFHVLD-RTVAHSLVEYQLETGRKNQIRVHSAD 242

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           MG P+ GD KY     GN   P+ ++L LHA  +   HP    R++   P+P
Sbjct: 243 MGHPVCGDIKY-----GNGDDPL-HRLCLHAYVLCFHHPVTHQRMEFETPVP 288


>gi|261338949|ref|ZP_05966807.1| hypothetical protein ENTCAN_05150 [Enterobacter cancerogenus ATCC
           35316]
 gi|288318776|gb|EFC57714.1| pseudouridine synthase A [Enterobacter cancerogenus ATCC 35316]
          Length = 219

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 70/217 (32%), Positives = 108/217 (49%), Gaps = 19/217 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDEHIMVVNKPSGLLSVPGR--LDEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  + A + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALNKDAERELKRQFREREPKKQYVARVWGHPAQAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y   
Sbjct: 126 KVCYETG-KAAQTEYEVLEYAADNTARVLLKPITGRSHQLRVHMLAIGHPILGDRFYAPP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
                      +L LHA+ + + HP  G  +   AP+
Sbjct: 185 DALALAP----RLQLHAQTLTITHPAFGNSMTFKAPV 217


>gi|300921138|ref|ZP_07137519.1| pseudouridine synthase, RluA family [Escherichia coli MS 115-1]
 gi|300411911|gb|EFJ95221.1| pseudouridine synthase, RluA family [Escherichia coli MS 115-1]
          Length = 326

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 90/338 (26%), Positives = 158/338 (46%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V    
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            INA   I +E +     + L          ++YED  I V NKP  + V  G+G   + 
Sbjct: 66  AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIVINKPRDLVVHPGAG---NP 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y
Sbjct: 112 DGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREY 171

Query: 184 WSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G         E I+    K++H+    VH + +       A++H+++++ F +  
Sbjct: 172 EAVAIGHMTAGGTVDEPISRHPSKRTHMA---VHPMGKP------AVTHYRIMEHF-RVH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHA 292
             L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA
Sbjct: 222 TRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHA 281

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
             + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 282 TMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 319


>gi|291549821|emb|CBL26083.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           torques L2-14]
          Length = 222

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 101/215 (46%), Gaps = 20/215 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV------DSKGQKPRLT--HRLDQ 152
           ++YED  I V +KPAG+  Q        +   LK+ +       +  ++P L   HRLDQ
Sbjct: 9   IIYEDKDIIVCHKPAGVPTQSSRIGTKDMVSILKNHLIKNTAKKTASREPYLAVIHRLDQ 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              G+LV A+T AAA+ L+         K Y +   GI ++ +  + ++L+K      + 
Sbjct: 69  PVEGLLVFAKTPAAAKELSRQLTTSGFGKYYRAQALGIFEHNEGTLEDYLVKDGRT--NT 126

Query: 213 VHVVKQNEKGANYAISHFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             V K+N   A YA  H+KVI        + F  LE+   TGR HQ+RV   H G P++G
Sbjct: 127 SRVCKENVPDAKYARLHYKVIHTGTLPSGEPFSQLEIHLDTGRHHQIRVQFAHAGHPLIG 186

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           D KY         +    +L L A  ++  HP  G
Sbjct: 187 DRKY------GTAACTSRQLMLCACRLEFTHPTTG 215


>gi|258423760|ref|ZP_05686646.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus A9635]
 gi|257845992|gb|EEV70020.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus A9635]
          Length = 305

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 85/327 (25%), Positives = 148/327 (45%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +     
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYK----- 55

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++   I      + E  IL  ++NL          + YED  + V  KP G+ V    
Sbjct: 56  -VKLNDHIVVTEKEVVEADILPENLNLD---------IYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKDLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAP--IGRNKNDRQSMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQA-----LHAGLIG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G  ++  A LP       D++
Sbjct: 274 FEHPVTGEYIERHAELPQDFEDLLDTI 300


>gi|291285956|ref|YP_003502772.1| pseudouridine synthase, RluA family [Denitrovibrio acetiphilus DSM
           12809]
 gi|290883116|gb|ADD66816.1| pseudouridine synthase, RluA family [Denitrovibrio acetiphilus DSM
           12809]
          Length = 302

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 110/220 (50%), Gaps = 14/220 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSW--VDSKGQKPRLTHRLDQETSG 156
           ++Y+  +  V NKPAGI+V    G A    ++  L  +   D    +P + HRLD++TSG
Sbjct: 83  IIYDCDEFAVINKPAGITVHPAPGHADDTIVNAMLAEFDITDDNDLRPGIVHRLDKDTSG 142

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++VA+ R + + L++ F  R I K Y ++ WG PK  +  I   + +  H        V
Sbjct: 143 LMIVAKNRKSREVLSKVFADRDIDKRYLAVCWGKPKELEFTIEQPIGR--HYKDRKRMCV 200

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +++     Y+ S  +V+      F   E++  TGRTHQ+RVH  H G P+ GD  Y    
Sbjct: 201 RED---GRYSKSGVRVLKQNNNAFLA-EIRIFTGRTHQIRVHMSHAGFPLAGDVVY--GH 254

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           + +   PI+ +  LH+  +    P  G  +   +PLP  M
Sbjct: 255 RQSLKLPIKRQ-ALHSFRLAFVSPFTGEDMVFESPLPLDM 293


>gi|171912659|ref|ZP_02928129.1| hypothetical protein VspiD_15805 [Verrucomicrobium spinosum DSM
           4136]
          Length = 596

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 71/217 (32%), Positives = 105/217 (48%), Gaps = 11/217 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  I V +KPA + +        +   ++ S V +  Q+PRL HRLD  T+G++V 
Sbjct: 381 VLHEDEAIVVLDKPAPLPMHPAGRFNRNTAQYILSQVYAP-QRPRLVHRLDANTTGLVVC 439

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-ANWLLKKSHIGGDYVHVVKQN 219
           ARTR  A  L + F+   I+K Y   V G P+  +  + A    +  H+G   V     +
Sbjct: 440 ARTRHFANLLQKQFKDFSIEKGYVVRVLGHPEADQFMVDAPISAEPGHLGSYAV-----D 494

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E+    A + F V+         LE +P TGRT+Q+R+H  H+G  IVGD  Y       
Sbjct: 495 EEMGQSARTDFVVLSRDGDGTSLLEARPLTGRTNQIRLHLAHLGHNIVGDPTYLQGGGLG 554

Query: 280 FTSPIQ---NKLYLHARYMDLPHP-EGGRLQITAPLP 312
            T  ++     + LHA  +   HP  G RL    PLP
Sbjct: 555 DTQTLELGSPPMCLHAWKLGFKHPLTGERLAFETPLP 591


>gi|197122384|ref|YP_002134335.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196172233|gb|ACG73206.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 353

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 83/328 (25%), Positives = 141/328 (42%), Gaps = 49/328 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---P 68
           V  +    RLD       P ++   +Q+++ +G V+VD +  K + R++ G+ + +   P
Sbjct: 28  VPPELAGTRLDAALVRLAPELSRARVQRLVEAGLVQVDGRGAKASARLRGGEAIALELPP 87

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P  + L                   +  L   +L+ED+ + V +K  G+ V    G  + 
Sbjct: 88  PEPSGLV------------------AQDLPLAVLHEDADLIVLDKAPGMVVHPARGTPHS 129

Query: 129 --IDGFL-----KSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             ++  L            G  PRL   HRLD++TSG LVVA+T AA   L   ++ R +
Sbjct: 130 TVVNALLHRLGLPGAAGPDGALPRLGLVHRLDKDTSGCLVVAKTEAALAALQAQWKGRSV 189

Query: 180 QKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +K+Y +L  G   P+ + +       +      D +    +    +  A++ ++V + F 
Sbjct: 190 EKVYLALCHGALAPEGRLDTPYGRHPR------DRLRFTGRVTS-SRRAVTEWRVREAFG 242

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFTSPIQNKL 288
                 E+  HTGRTHQ+RVH    G P++ D  Y    +             +    + 
Sbjct: 243 AAASLAEVTLHTGRTHQIRVHLSEAGHPLLADAVYGGTRREARLAPADPARRAAEAVGRQ 302

Query: 289 YLHARYMDLPHPEGG-RLQITAPLPAHM 315
            LHA  +   HP  G RL + APLPA +
Sbjct: 303 ALHALRLGFDHPRTGRRLVVEAPLPADL 330


>gi|257891490|ref|ZP_05671143.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|257827850|gb|EEV54476.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
          Length = 285

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 67/201 (33%), Positives = 101/201 (50%), Gaps = 15/201 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+            +   L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+       L      + I + Y ++VWG   +K   I N + +  H     V V  +N
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWG-EIDKDMTITNKIGRDRHDRRKRV-VDDKN 200

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            + A   ++  KV+    Q +C LE    TGRTHQ+RVH  H G PIVGD  Y      N
Sbjct: 201 GQSALTHVTVNKVLSEQTQVYCVLE----TGRTHQIRVHLAHKGHPIVGDPLY-----QN 251

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
            T+    +L LHA  + + HP
Sbjct: 252 RTA---ERLMLHALELHMIHP 269


>gi|172040870|ref|YP_001800584.1| pseudouridylate synthase D [Corynebacterium urealyticum DSM 7109]
 gi|171852174|emb|CAQ05150.1| pseudouridylate synthase D [Corynebacterium urealyticum DSM 7109]
          Length = 314

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 76/293 (25%), Positives = 129/293 (44%), Gaps = 39/293 (13%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +G +  + K +  ++R+ +GQ   V +P           E+ +      L +  D     
Sbjct: 41  AGDITAEGKSLGKSDRLVAGQWLDVTLP---------APERDLAAEPPQLVEGMD----- 86

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LY D  +   NKP G++       +G +  A       +       ++  +  RLD  T
Sbjct: 87  ILYSDDDVIAVNKPVGVAAHPTLGWEGPTVTAGLAAAGFRISTSGPPERKGIVQRLDVGT 146

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA +  A  HL  +FR R +QKIY +LV G P      I   + +  H    +  
Sbjct: 147 SGVMIVAASERAYTHLKRAFRNREVQKIYHALVQGHPDPTSGTIDAPIGR--HPSAGWRF 204

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V+ + K   +A++H+  ++   Q    L +   TGRTHQ+RVH   +  P+ GD  Y +
Sbjct: 205 AVRDDGK---HAVTHYDTLEAHRQA-SLLRVNLETGRTHQIRVHFSSLHHPLCGDPMYGS 260

Query: 275 NFKGNFTSPIQNKL-----YLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           +        +  KL     +LHA  +   HP G  +QI +P P  + +  D L
Sbjct: 261 D------PALSEKLGLIRQWLHAVSLRFEHPTGRMMQIDSPYPEDLQQALDRL 307


>gi|86140463|ref|ZP_01059022.1| pseudouridylate synthase [Leeuwenhoekiella blandensis MED217]
 gi|85832405|gb|EAQ50854.1| pseudouridylate synthase [Leeuwenhoekiella blandensis MED217]
          Length = 297

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 108/229 (47%), Gaps = 37/229 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +LYED  + V +KPAGI V G S   +A  +   L +        P+  HRLD  T+G +
Sbjct: 66  VLYEDEFLAVVHKPAGILVSGNSFKTVARALPQNLNASSAPDACTPQPAHRLDYATTGAV 125

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +V +TR + + L + F  + I K Y+++  G+        A+  +     G         
Sbjct: 126 LVGKTRESIRQLNQLFEDKAITKTYYAVTLGV------MPASGTINTPVDG--------- 170

Query: 219 NEKGANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                  A+S + ++   A    ++   + +QP TGR HQLR H   +G PI+GD  YC 
Sbjct: 171 -----KAAVSVYTLVASVASPRFEQLNLVRLQPQTGRRHQLRKHLAGIGHPILGDRDYCP 225

Query: 275 NFKGNFTSPIQNK-LYLHARYMDLPHPEGGRLQ---ITAPLPAHMVKTW 319
                    +Q K +YLHA  +   HP+  +LQ   ITAPLP   +K +
Sbjct: 226 K-----ELLLQGKGMYLHAFSLRFNHPQ--KLQPVAITAPLPQKFLKLF 267


>gi|253682097|ref|ZP_04862894.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum D str. 1873]
 gi|253561809|gb|EES91261.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum D str. 1873]
          Length = 302

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 83/311 (26%), Positives = 145/311 (46%), Gaps = 37/311 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE + E +RL+ + K      +   ++K  R G+++V+    + +  + +  +V +    
Sbjct: 12  VEIETEEIRLNHYLK-EVAQCSSRFIRKAAREGRIKVNGNNARLSYMLTNNDIVELQINR 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                II E+  LD               ++YED+ I V NKP GI V        H++G
Sbjct: 71  KEEQDIIPEKMDLD---------------IIYEDNDIIVVNKPKGIVVHP---TKRHLNG 112

Query: 132 FLKSWV----DSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L + V    + K +    RL +RLD +TSG++++A+   +   L+   +     K Y +
Sbjct: 113 TLSNGVLYYFNDKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFVKKYLA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G        I   + +     G    ++  +E+G   +I+ FKVI+ + +    +E+
Sbjct: 173 IVHGNFNEDSGVIDKPIYRVGE--GTLKRII--DERGQR-SITLFKVIEQY-KNASLVEL 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
              TGRTHQ+RVH   +G PI GD  Y     G       ++  LHA  + +PHP+ G+ 
Sbjct: 227 TLETGRTHQIRVHLSSIGHPIYGDSLY-----GEEEPQYIDRQALHAYKLQIPHPKDGKI 281

Query: 305 LQITAPLPAHM 315
           L++ + LP  M
Sbjct: 282 LKLESSLPEDM 292


>gi|16130515|ref|NP_417085.1| 23S rRNA pseudouridine synthase; specific to U1911, U1915, and
           U1917 [Escherichia coli str. K-12 substr. MG1655]
 gi|89109396|ref|AP_003176.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           W3110]
 gi|157162070|ref|YP_001459388.1| 23S rRNA pseudouridine synthase D [Escherichia coli HS]
 gi|170019127|ref|YP_001724081.1| 23S rRNA pseudouridine synthase D [Escherichia coli ATCC 8739]
 gi|170082199|ref|YP_001731519.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|188493998|ref|ZP_03001268.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           53638]
 gi|194439337|ref|ZP_03071415.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           101-1]
 gi|238901755|ref|YP_002927551.1| 23S rRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|253772510|ref|YP_003035341.1| 23S rRNA pseudouridine synthase D [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254037671|ref|ZP_04871729.1| 23S rRNA pseudouridine synthase D [Escherichia sp. 1_1_43]
 gi|254162565|ref|YP_003045673.1| 23S rRNA pseudouridine synthase D [Escherichia coli B str. REL606]
 gi|256024877|ref|ZP_05438742.1| 23S rRNA pseudouridine synthase D [Escherichia sp. 4_1_40B]
 gi|297516262|ref|ZP_06934648.1| 23S rRNA pseudouridine synthase D [Escherichia coli OP50]
 gi|300905086|ref|ZP_07122893.1| pseudouridine synthase, RluA family [Escherichia coli MS 84-1]
 gi|300930681|ref|ZP_07146065.1| pseudouridine synthase, RluA family [Escherichia coli MS 187-1]
 gi|301305760|ref|ZP_07211847.1| pseudouridine synthase, RluA family [Escherichia coli MS 124-1]
 gi|301644036|ref|ZP_07244054.1| pseudouridine synthase, RluA family [Escherichia coli MS 146-1]
 gi|307139315|ref|ZP_07498671.1| 23S rRNA pseudouridine synthase D [Escherichia coli H736]
 gi|331643311|ref|ZP_08344442.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli H736]
 gi|2507541|sp|P33643|RLUD_ECOLI RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|1236631|gb|AAA92957.1| SfhB [Escherichia coli]
 gi|1788946|gb|AAC75643.1| 23S rRNA pseudouridine synthase; specific to U1911, U1915, and
           U1917 [Escherichia coli str. K-12 substr. MG1655]
 gi|85675474|dbj|BAA16479.2| 23S rRNA pseudouridine synthase [Escherichia coli str. K12 substr.
           W3110]
 gi|157067750|gb|ABV07005.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           HS]
 gi|169754055|gb|ACA76754.1| pseudouridine synthase, RluA family [Escherichia coli ATCC 8739]
 gi|169890034|gb|ACB03741.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|188489197|gb|EDU64300.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           53638]
 gi|194421699|gb|EDX37708.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           101-1]
 gi|226839295|gb|EEH71316.1| 23S rRNA pseudouridine synthase D [Escherichia sp. 1_1_43]
 gi|238859758|gb|ACR61756.1| 23S rRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|242378190|emb|CAQ32965.1| 23S rRNA pseudouridine synthase [Escherichia coli BL21(DE3)]
 gi|253323554|gb|ACT28156.1| pseudouridine synthase, RluA family [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253974466|gb|ACT40137.1| 23S rRNA pseudouridine synthase [Escherichia coli B str. REL606]
 gi|253978633|gb|ACT44303.1| 23S rRNA pseudouridine synthase [Escherichia coli BL21(DE3)]
 gi|260448330|gb|ACX38752.1| pseudouridine synthase, RluA family [Escherichia coli DH1]
 gi|300403013|gb|EFJ86551.1| pseudouridine synthase, RluA family [Escherichia coli MS 84-1]
 gi|300461455|gb|EFK24948.1| pseudouridine synthase, RluA family [Escherichia coli MS 187-1]
 gi|300839014|gb|EFK66774.1| pseudouridine synthase, RluA family [Escherichia coli MS 124-1]
 gi|301077610|gb|EFK92416.1| pseudouridine synthase, RluA family [Escherichia coli MS 146-1]
 gi|309702976|emb|CBJ02307.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           ETEC H10407]
 gi|315137214|dbj|BAJ44373.1| 23S rRNA pseudouridine synthase D [Escherichia coli DH1]
 gi|315253122|gb|EFU33090.1| pseudouridine synthase, RluA family [Escherichia coli MS 85-1]
 gi|323935610|gb|EGB31930.1| RluA family protein pseudouridine synthase [Escherichia coli E1520]
 gi|323941386|gb|EGB37570.1| RluA family protein pseudouridine synthase [Escherichia coli E482]
 gi|323960546|gb|EGB56175.1| RluA family protein pseudouridine synthase [Escherichia coli H489]
 gi|323971461|gb|EGB66697.1| RluA family protein pseudouridine synthase [Escherichia coli TA007]
 gi|331036782|gb|EGI09006.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli H736]
 gi|332344465|gb|AEE57799.1| ribosomal large subunit pseudouridine synthase [Escherichia coli
           UMNK88]
          Length = 326

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 89/338 (26%), Positives = 158/338 (46%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V    
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            INA   I +E +     + L          ++YED  I + NKP  + V  G+G   + 
Sbjct: 66  AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIIINKPRDLVVHPGAG---NP 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y
Sbjct: 112 DGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREY 171

Query: 184 WSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G         E I+    K++H+    VH + +       A++H+++++ F +  
Sbjct: 172 EAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPMGKP------AVTHYRIMEHF-RVH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLHA 292
             L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LHA
Sbjct: 222 TRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHA 281

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
             + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 282 TMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 319


>gi|213861507|ref|ZP_03385977.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
          Length = 208

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 69/210 (32%), Positives = 111/210 (52%), Gaps = 11/210 (5%)

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +V GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R +
Sbjct: 1   AVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREK 59

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +QK Y +LV G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A
Sbjct: 60  GMQKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA 116

Query: 238 QKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHAR 293
             F  L    P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA 
Sbjct: 117 --FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAA 174

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            +   HP  G  ++I AP+   + +  + L
Sbjct: 175 ALKFTHPGTGDVMRIEAPMDKQLKRCLEVL 204


>gi|160876810|ref|YP_001556126.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160862332|gb|ABX50866.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315269012|gb|ADT95865.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 225

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 64/205 (31%), Positives = 105/205 (51%), Gaps = 15/205 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G   A++   + +  V ++    ++ HRLD  TSG++VV
Sbjct: 16  ILYQDKDIIVINKPSGLLSVPGRDPAHYDSVYAR--VKAEHPHSQIVHRLDMATSGVIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A  R+A + L   F  R   K Y++ V G  KN    +   L+       D+ +  KQ  
Sbjct: 74  ALIRSAERELKRQFHDRETSKTYFARVAGHVKNDTGSVDYPLI------CDWPNRPKQKV 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      +++H++VI   A++   +++ P TGR+HQLRVH + +G PI+GD  Y      
Sbjct: 128 DHLVGKPSLTHYQVI-SRAKRSTLVKLTPITGRSHQLRVHMMALGHPILGDGFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
           +       +L LHA  + + HP  G
Sbjct: 187 SLAP----RLLLHAAELTIKHPYTG 207


>gi|288800367|ref|ZP_06405825.1| ribosomal large subunit pseudouridine synthase A [Prevotella sp.
           oral taxon 299 str. F0039]
 gi|288332580|gb|EFC71060.1| ribosomal large subunit pseudouridine synthase A [Prevotella sp.
           oral taxon 299 str. F0039]
          Length = 540

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 63/215 (29%), Positives = 109/215 (50%), Gaps = 16/215 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ED  I V  KP G+    G      ++  +++   +    P + HRLD +TSGI+++A
Sbjct: 338 LFEDESIRVVVKPCGMPSVEGHHSLVSVEQLMRNEYPT-ADSPLIVHRLDMDTSGIMIIA 396

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +T+ A + L E F + +++K Y +++ G+ K++  C    L    ++    + +V  ++ 
Sbjct: 397 KTKQAHKCLQEQFALHQVKKRYIAVLEGVFKHQPTCGCIELPLLPNVNERPLQMV--DDV 454

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKG 278
               A ++++VI    Q+   + + P TGRTHQLRVH  H   +  PIVGD  Y      
Sbjct: 455 YGKEATTYYRVIGVENQR-TRVALYPQTGRTHQLRVHCSHGEGLALPIVGDCLY------ 507

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
                  ++L+LHA  + L HP  G+  +    PA
Sbjct: 508 ---GKPDSRLHLHAAAIALKHPVNGKRMVFKSSPA 539


>gi|241668214|ref|ZP_04755792.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25015]
 gi|254876749|ref|ZP_05249459.1| ribosomal large subunit pseudouridine synthase D [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|254842770|gb|EET21184.1| ribosomal large subunit pseudouridine synthase D [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
          Length = 328

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 84/317 (26%), Positives = 146/317 (46%), Gaps = 32/317 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++  D    R+D      +   +   +QK ++ G + V+ K  K  + +   + V I
Sbjct: 12  QKIMMHPDHAGKRIDSTINELFEQFSRSQIQKWIKDGLITVNGKTTKSKHILLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
              +   N  + E    D  +N+           ++ED+ I V +KP  + V  G+G + 
Sbjct: 72  NIELLPTNEWLAE----DIDLNI-----------VFEDNDIIVIDKPIDMVVHPGAGNMT 116

Query: 127 YHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             I   L     ++ + PR  + HRLD++TSG++V A++  A  +L +    R++ + Y 
Sbjct: 117 GTISNALLHKYPNQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLSERKVSRKYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCW 242
           ++V G      E      + +  IG D  +  K   N KG   AI+H+K I+ +   F  
Sbjct: 177 AIVEG------EIYEEGTINQP-IGRDINNRTKMTINHKGKE-AITHYKPIEVY-DGFTL 227

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHP 300
           +E Q  TGRTHQ+RVH   +  P+VGD  Y  +        I+  N+  LHA  +   HP
Sbjct: 228 IECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLDKVGIENINRQALHAYKLSFIHP 287

Query: 301 EGGRL-QITAPLPAHMV 316
              ++ +  + LP  M+
Sbjct: 288 TSQKIVRFKSKLPEDML 304


>gi|306829567|ref|ZP_07462757.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus mitis ATCC
           6249]
 gi|304428653|gb|EFM31743.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus mitis ATCC
           6249]
          Length = 298

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 68/219 (31%), Positives = 113/219 (51%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +L+ED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILFEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-EYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQRKSIEKRYFALVKGNGDLEPEGEIIAPIARDVDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +KV+  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKVVASYGD-IHLIDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  ++   HP   R L++ +PLP
Sbjct: 249 ---GSLDDGIQRQA-LHCHFLSFYHPFLERQLELESPLP 283


>gi|167463935|ref|ZP_02329024.1| pseudouridine synthase [Paenibacillus larvae subsp. larvae
           BRL-230010]
 gi|322384790|ref|ZP_08058452.1| RNA pseudouridine synthase [Paenibacillus larvae subsp. larvae
           B-3650]
 gi|321150361|gb|EFX43862.1| RNA pseudouridine synthase [Paenibacillus larvae subsp. larvae
           B-3650]
          Length = 243

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 55/180 (30%), Positives = 94/180 (52%), Gaps = 8/180 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ + V  KP  +  Q  S     +   LK+ +  +  KP      L HRLD+   
Sbjct: 16  VLFEDNHLLVVEKPVNMPTQEDSSRDPDLLSVLKADLKHRYGKPGNVYLGLIHRLDRPVG 75

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  ++++ R R   K Y ++V G P + +  + + L K +    +   V
Sbjct: 76  GVMVFAKTSKAASRISDAVRTRAFDKTYLAVVHGKPADPQGTLRHHLRKDTRT--NTALV 133

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V+   +GA  AI  ++V+   A+    ++++ HTGR HQ+RV    +GCP+ GD +Y A 
Sbjct: 134 VRPGAEGAKEAILDYRVL-GHAEGLSLVQVKLHTGRPHQIRVQLAAIGCPLYGDQRYGAG 192


>gi|170718603|ref|YP_001783805.1| pseudouridine synthase [Haemophilus somnus 2336]
 gi|168826732|gb|ACA32103.1| pseudouridine synthase [Haemophilus somnus 2336]
          Length = 221

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 65/205 (31%), Positives = 103/205 (50%), Gaps = 20/205 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y D  I V NKP+G+    G+   Y+      S V  K       HRLD  TSG+L+ 
Sbjct: 16  IVYRDDHILVVNKPSGLLSVSGNQPQYYDSAM--SRVKEKYGFCEPAHRLDMATSGVLLF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC----IANWLLKKSHIGGDYVHV 215
           A ++ A + L   FR R  +K Y +L+WG + ++        I +W   +      +VH 
Sbjct: 74  AMSKMADRELKRQFREREPKKHYQALIWGHLAQDTGSVNLPLICDWE-NRPRQKVCFVH- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A+++FKV+  F      + + P TGR+HQLR+H L +G PI+GD K+ A+
Sbjct: 132 -------GKRAVTNFKVLHRFENNITQVRLTPITGRSHQLRLHMLALGHPILGD-KFYAH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
            +    +P   +L LHA ++ + HP
Sbjct: 184 PQAKSLAP---RLCLHAEFLQITHP 205


>gi|301024188|ref|ZP_07187895.1| pseudouridine synthase, RluA family [Escherichia coli MS 196-1]
 gi|312973162|ref|ZP_07787335.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           1827-70]
 gi|299880530|gb|EFI88741.1| pseudouridine synthase, RluA family [Escherichia coli MS 196-1]
 gi|310333104|gb|EFQ00318.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           1827-70]
 gi|315615335|gb|EFU95969.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           3431]
          Length = 300

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I + NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 60  IVYEDEDIIIINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 116

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 117 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 174

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 175 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 226

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 227 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 286

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 287 RADFEEH 293


>gi|28572410|ref|NP_789190.1| pseudouridine synthase [Tropheryma whipplei TW08/27]
 gi|28410541|emb|CAD66927.1| putative pseudouridine synthase [Tropheryma whipplei TW08/27]
          Length = 303

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 107/214 (50%), Gaps = 16/214 (7%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPR--LTHRLD 151
           D L+  ++Y D  ++V +KPAG++     G     + G L   + + G + R  + HRLD
Sbjct: 74  DLLR--VIYSDDDLFVIDKPAGVAAHASPGWCGPTVTGCLSGLLAACGPQDRQGVVHRLD 131

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG++V+A++  A  +L  +FR R I K Y +LV G P      I       + IG D
Sbjct: 132 ANTSGLMVLAKSDLAYHNLKAAFRDRAIHKRYKALVQGYPDPSSGVI------NAPIGRD 185

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             H  +   +     A++ +   + +   F  L + P TGRTHQ+RVH   +  P+VGD 
Sbjct: 186 LKHRDRFCIDYSGRDAVTQYSTEEVY-PGFTLLSVAPKTGRTHQIRVHFSALRHPLVGDV 244

Query: 271 KYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGG 303
           KY A+    F+  +   + +LHA ++   HP  G
Sbjct: 245 KYGAD--PVFSQKVNLKRQWLHAYHLSFTHPVSG 276


>gi|46908075|ref|YP_014464.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|47094208|ref|ZP_00231922.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|226224446|ref|YP_002758553.1| hypothetical protein Lm4b_01859 [Listeria monocytogenes Clip81459]
 gi|254826115|ref|ZP_05231116.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
 gi|254852749|ref|ZP_05242097.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|254931987|ref|ZP_05265346.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|300763844|ref|ZP_07073841.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
 gi|46881345|gb|AAT04641.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Listeria monocytogenes serotype 4b str. F2365]
 gi|47017415|gb|EAL08234.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|225876908|emb|CAS05617.1| unnamed protein product [Listeria monocytogenes serotype 4b str.
           CLIP 80459]
 gi|258606073|gb|EEW18681.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|293583538|gb|EFF95570.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|293595355|gb|EFG03116.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
 gi|300515580|gb|EFK42630.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
 gi|328466193|gb|EGF37350.1| hypothetical protein LM1816_11407 [Listeria monocytogenes 1816]
 gi|328473565|gb|EGF44402.1| hypothetical protein LM220_09240 [Listeria monocytogenes 220]
 gi|332312284|gb|EGJ25379.1| Pseudouridylate synthase [Listeria monocytogenes str. Scott A]
          Length = 303

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 83/302 (27%), Positives = 142/302 (47%), Gaps = 51/302 (16%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQV----VRIPPVINALNHIIKEQKILDSSVNLTK 92
           +Q +L++G + V+ +  K N ++Q G      VR P          +E ++L   + L  
Sbjct: 32  IQLMLKNGDITVNGELAKPNYKVQVGDEIHYEVREP----------EELEVLAEDIPLD- 80

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQK 143
                   + +ED  + V NKP G+ V   +G A         +H D    S ++ K  +
Sbjct: 81  --------IYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL--SGINGK-IR 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    +
Sbjct: 130 PGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPI 188

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++      + VV+  ++    A +HF+V++     +  +  +  TGRTHQ+RVH  ++G
Sbjct: 189 GRAKEDRQKMAVVRDGKE----ARTHFEVLERLP-GYTLINCKLDTGRTHQIRVHLKYIG 243

Query: 264 CPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            P+ GD KY      KGN         +LHA  +   HP    R+   APLP+   K   
Sbjct: 244 HPLAGDPKYGPKNTIKGNGQ-------FLHAAKLGFDHPTTKERMMFEAPLPSSFEKALK 296

Query: 321 SL 322
           SL
Sbjct: 297 SL 298


>gi|262282807|ref|ZP_06060574.1| 23S rRNA pseudouridine synthase [Streptococcus sp. 2_1_36FAA]
 gi|262261059|gb|EEY79758.1| 23S rRNA pseudouridine synthase [Streptococcus sp. 2_1_36FAA]
          Length = 295

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 121/231 (52%), Gaps = 27/231 (11%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDS--KGQKPRLTHRLDQET 154
           +++ED    + +KPAG+    SV   + +A ++  +   ++DS  +  +  +  RLD++T
Sbjct: 78  VVFEDDHFLILDKPAGVASIPSVNHSNTMANYVKAY---YIDSGYENHQVHIVTRLDKDT 134

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDY 212
           SG+++ A+   A   L +  + R I+K Y +LV G  + + + E IA     +  I    
Sbjct: 135 SGLMLFAKHGYAHARLDKQLQKRAIEKRYLALVKGDGLLEKEGEIIAPIARDEDSI---- 190

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             + ++  KG  YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y
Sbjct: 191 --ITRRVAKGGKYAHTSYKVIEQFGNIYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLY 247

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA---HMVKTW 319
                G+ T  I  +  LH   +   +P  G  +   +PLP    H+V+T+
Sbjct: 248 G----GSLTEGISRQA-LHCHTLKFYNPFSGEEIGRASPLPTDFEHVVQTF 293


>gi|114046333|ref|YP_736883.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           MR-7]
 gi|113887775|gb|ABI41826.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           MR-7]
          Length = 225

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 67/207 (32%), Positives = 105/207 (50%), Gaps = 19/207 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +LY+D  I V NKP+G+    G   A H D     +   K + P  ++ HRLD  TSG++
Sbjct: 16  VLYQDKDIIVVNKPSGLLSVPGRDPA-HYDSV---YARVKAEHPHCQIVHRLDMATSGVM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  R+A + L   F  R   K Y + V G  KN    +   L+       D+ +  KQ
Sbjct: 72  VVALIRSAERELKRQFHDRETSKTYLARVAGHIKNDTGSVDYPLI------CDWPNRPKQ 125

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             + +    +++HF+V+   A++   ++++P TGR+HQLRVH + +G PI+GD  Y    
Sbjct: 126 KVDHEIGKPSLTHFEVL-SRAKRSTLVKLKPITGRSHQLRVHMMALGHPILGDGFYADPL 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +       +L LHA  + + HP  G
Sbjct: 185 AKSLAP----RLLLHAAELTIKHPYTG 207


>gi|323484810|ref|ZP_08090167.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323401916|gb|EGA94257.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 333

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 88/338 (26%), Positives = 153/338 (45%), Gaps = 45/338 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q V +  +E   RLD+    +        + K+LR   + ++ K+   + ++  G  V+
Sbjct: 1   MQVVKITKNEAGQRLDKLLAKYLNLAGKSFIYKMLRKKNITLNGKKCDGSEKLSEGDEVK 60

Query: 67  I---PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +      I   + + K QK+    +++           +YED  I + NKP+G+  Q   
Sbjct: 61  LFLSDETIEKFSEV-KIQKVRKRKLDV-----------VYEDDDIILINKPSGMLSQKAK 108

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                     I Y +DG   +  D +  KP + +RLD+ TSGI++  ++    Q ++E+ 
Sbjct: 109 ETDESLVEYLIQYLLDGGKLTKEDMRQFKPSVCNRLDRNTSGIVIAGKSLPGLQLMSEAI 168

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-----KGANYAISH 229
           + R I K Y  +V G     KE I  +L K      + V V+K NE     K A    + 
Sbjct: 169 KERTIGKYYLCIVKGSVAGPKE-IDGYLKKNEKT--NQVTVLKANELCREDKDALPIRTQ 225

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQN 286
           ++ + C   +   LE++  TGR+HQ+R H   +G PI GD+KY     N +      +Q+
Sbjct: 226 YRPL-CSDGRHTLLEVKLITGRSHQIRAHLASIGHPIAGDYKYGDPAVNREARDKYAVQS 284

Query: 287 KLYLHARYMDLPHP-------EGGRLQITAPLPAHMVK 317
           ++ LHA  + +P          GGR + TA  P   ++
Sbjct: 285 QM-LHAWRLVMPKELREPLAGLGGR-EFTAKPPEEFMR 320


>gi|308068172|ref|YP_003869777.1| RNA pseudouridine synthase (RNA-uridine isomerase) [Paenibacillus
           polymyxa E681]
 gi|305857451|gb|ADM69239.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Paenibacillus polymyxa E681]
          Length = 319

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 117/240 (48%), Gaps = 23/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQ--KPRLTHRLDQET 154
           +L+ED  + V NK AG+ V    G   H  G L + V     +KG+  + R  HRLDQET
Sbjct: 86  ILFEDEHLLVVNKAAGMIVHPTHG---HYTGTLANGVVHYWQAKGELFRFRPVHRLDQET 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+LVVA+     QH++E      + K Y +LV G P+ ++  +   + +      D  H
Sbjct: 143 TGVLVVAKNPYVHQHISEQMIAGTVDKRYTALVHGRPELQEGKVDGPIDRNP----DNPH 198

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +      G   A++ +K+ + +      + ++  +GRTHQ+RVH  ++GCP++GD  Y  
Sbjct: 199 LRMVTPDGYP-ALTLYKLEEVW-NGGSRIGLKLESGRTHQIRVHMTYIGCPLIGDKMYRI 256

Query: 275 NFKGNFTSPIQNKL-------YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKY 326
                      ++L        LHA  + L HP  G RL   APLP  M +  + L  +Y
Sbjct: 257 TPDDAAQRERYDQLDARMPRQALHASELSLEHPVTGERLTFYAPLPDDMAEMQELLRAQY 316


>gi|293401025|ref|ZP_06645170.1| pseudouridine synthase (uracil hydrolase) [Erysipelotrichaceae
           bacterium 5_2_54FAA]
 gi|291306051|gb|EFE47295.1| pseudouridine synthase (uracil hydrolase) [Erysipelotrichaceae
           bacterium 5_2_54FAA]
          Length = 314

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 68/274 (24%), Positives = 132/274 (48%), Gaps = 23/274 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ D+ N R+D++ +   P +    + K +R+ +++V++KR +   R+  G  V     
Sbjct: 5   IIQEDDANQRVDKFLQKTLPALPKSLMYKYIRNKKIKVNRKRCEIAQRLLPGDHV----- 59

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHI 129
              L  I +E        +  K S  L   +LYED+ + +  KP+G+     S  I  ++
Sbjct: 60  ---LCFIAEEFFETGEDCSFLKVSSELD--VLYEDANVILMKKPSGLLTHKDSNEIQDNL 114

Query: 130 DGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 ++  KGQ          P L HRLD+ T GI++ A+T  A + +    R  +++
Sbjct: 115 ADRFLHYLYKKGQYDPQTRQSFTPALCHRLDRNTEGIVIGAKTAEALRRMNAYIREHKVE 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y  +V G+ + K   +  W   K     + VH+    +K +    + ++ +    +++
Sbjct: 175 KHYVCIVEGVMEQKTGHVVLW--HKKDAKSNKVHLYAHEQKNSQRIETSYRTLHQ-GKRY 231

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            ++E+Q HTG++HQ+R    ++  P+ GD KY A
Sbjct: 232 AYVEVQLHTGKSHQIRAVMAYLHHPLFGDVKYGA 265


>gi|312196232|ref|YP_004016293.1| pseudouridine synthase, RluA family [Frankia sp. EuI1c]
 gi|311227568|gb|ADP80423.1| pseudouridine synthase, RluA family [Frankia sp. EuI1c]
          Length = 325

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 82/325 (25%), Positives = 143/325 (44%), Gaps = 41/325 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPP 69
           V +  + +RLD      +  ++      ++  GQV VD      ++R++ G    V +PP
Sbjct: 24  VPDGLDGLRLDAAIARMF-GLSRTVAAALVDDGQVSVDGAAPGRSDRVRGGAWLEVELPP 82

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYH 128
               +  +I     +D    LT         +++ED  + V +KP G++     G     
Sbjct: 83  SPRPVTEVIATP--VD---GLT---------IVHEDDDLVVVDKPVGVAAHPAPGYTGPT 128

Query: 129 IDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           + G L +    + + G   R  + HRLD  T+G++VVA++      L  +FR R + K Y
Sbjct: 129 VIGALAAAGYRISTSGAAERQGVVHRLDVGTTGVMVVAKSELGYAALKRAFREREVDKRY 188

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G P   +  +   + +     G +  V          +++H+ + + F +    L
Sbjct: 189 RAVVQGHPDPLRGTVDAPIDRHPRKPGLFAVVAD-----GKPSVTHYDLEEAF-RAASLL 242

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-----YLHARYMDLP 298
           E++  TGRTHQ+RVH   +  P VGD  Y A+        +  KL     +LHA  +   
Sbjct: 243 EVRLETGRTHQIRVHMSALRHPCVGDLAYGADPT------LAEKLGLRRQWLHAFQLSFE 296

Query: 299 HPEGGRL-QITAPLPAHMVKTWDSL 322
           HP  GRL   T+P P  + +  + L
Sbjct: 297 HPADGRLVTFTSPDPPDLAEALERL 321


>gi|117919251|ref|YP_868443.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           ANA-3]
 gi|117611583|gb|ABK47037.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           ANA-3]
          Length = 225

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 67/207 (32%), Positives = 105/207 (50%), Gaps = 19/207 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +LY+D  I V NKP+G+    G   A H D     +   K + P  ++ HRLD  TSG++
Sbjct: 16  VLYQDKDIIVVNKPSGLLSVPGRDPA-HYDSV---YARVKAEHPHCQIVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  R+A + L   F  R   K Y + V G  KN    +   L+       D+ +  KQ
Sbjct: 72  VVALIRSAERELKRQFHDRETSKTYLARVAGHVKNTTGSVDYPLI------CDWPNRPKQ 125

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             + +    +++HF+V+   A++   ++++P TGR+HQLRVH + +G PI+GD  Y    
Sbjct: 126 KVDHEIGKPSLTHFEVL-SRAKRSTLVKLKPITGRSHQLRVHMMALGHPILGDGFYADPL 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +       +L LHA  + + HP  G
Sbjct: 185 AKSLAP----RLLLHAAELTIKHPYTG 207


>gi|157156608|ref|YP_001463915.1| 23S rRNA pseudouridine synthase D [Escherichia coli E24377A]
 gi|191169060|ref|ZP_03030823.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           B7A]
 gi|193064062|ref|ZP_03045147.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           E22]
 gi|193071695|ref|ZP_03052596.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           E110019]
 gi|194430158|ref|ZP_03062659.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           B171]
 gi|209920071|ref|YP_002294155.1| 23S rRNA pseudouridine synthase D [Escherichia coli SE11]
 gi|256019585|ref|ZP_05433450.1| 23S rRNA pseudouridine synthase D [Shigella sp. D9]
 gi|260845276|ref|YP_003223054.1| 23S rRNA pseudouridine synthase [Escherichia coli O103:H2 str.
           12009]
 gi|260869276|ref|YP_003235678.1| 23S rRNA pseudouridine synthase [Escherichia coli O111:H- str.
           11128]
 gi|293448946|ref|ZP_06663367.1| rluD [Escherichia coli B088]
 gi|300819932|ref|ZP_07100115.1| pseudouridine synthase, RluA family [Escherichia coli MS 107-1]
 gi|300825129|ref|ZP_07105222.1| pseudouridine synthase, RluA family [Escherichia coli MS 119-7]
 gi|300922522|ref|ZP_07138631.1| pseudouridine synthase, RluA family [Escherichia coli MS 182-1]
 gi|301326710|ref|ZP_07220028.1| pseudouridine synthase, RluA family [Escherichia coli MS 78-1]
 gi|307315092|ref|ZP_07594676.1| pseudouridine synthase, RluA family [Escherichia coli W]
 gi|309794107|ref|ZP_07688531.1| pseudouridine synthase, RluA family [Escherichia coli MS 145-7]
 gi|331669346|ref|ZP_08370192.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA271]
 gi|331678588|ref|ZP_08379262.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli H591]
 gi|332280710|ref|ZP_08393123.1| ribosomal large subunit pseudouridine synthase D [Shigella sp. D9]
 gi|157078638|gb|ABV18346.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           E24377A]
 gi|190900901|gb|EDV60687.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           B7A]
 gi|192929297|gb|EDV82906.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           E22]
 gi|192954990|gb|EDV85492.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           E110019]
 gi|194411783|gb|EDX28104.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           B171]
 gi|209913330|dbj|BAG78404.1| putative pseudouridine synthase [Escherichia coli SE11]
 gi|257760423|dbj|BAI31920.1| 23S rRNA pseudouridine synthase [Escherichia coli O103:H2 str.
           12009]
 gi|257765632|dbj|BAI37127.1| 23S rRNA pseudouridine synthase [Escherichia coli O111:H- str.
           11128]
 gi|291322036|gb|EFE61465.1| rluD [Escherichia coli B088]
 gi|300421134|gb|EFK04445.1| pseudouridine synthase, RluA family [Escherichia coli MS 182-1]
 gi|300522401|gb|EFK43470.1| pseudouridine synthase, RluA family [Escherichia coli MS 119-7]
 gi|300527520|gb|EFK48582.1| pseudouridine synthase, RluA family [Escherichia coli MS 107-1]
 gi|300846633|gb|EFK74393.1| pseudouridine synthase, RluA family [Escherichia coli MS 78-1]
 gi|306905521|gb|EFN36055.1| pseudouridine synthase, RluA family [Escherichia coli W]
 gi|308122012|gb|EFO59274.1| pseudouridine synthase, RluA family [Escherichia coli MS 145-7]
 gi|315061909|gb|ADT76236.1| 23S rRNA pseudouridine synthase [Escherichia coli W]
 gi|323377510|gb|ADX49778.1| pseudouridine synthase, RluA family [Escherichia coli KO11]
 gi|323946277|gb|EGB42310.1| RluA family protein pseudouridine synthase [Escherichia coli H120]
 gi|324016579|gb|EGB85798.1| pseudouridine synthase, RluA family [Escherichia coli MS 117-3]
 gi|324120053|gb|EGC13929.1| RluA family protein pseudouridine synthase [Escherichia coli E1167]
 gi|331063014|gb|EGI34927.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA271]
 gi|331073418|gb|EGI44739.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli H591]
 gi|332103062|gb|EGJ06408.1| ribosomal large subunit pseudouridine synthase D [Shigella sp. D9]
          Length = 326

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 253 YGGRPRPPKGASEAFISMLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|312867737|ref|ZP_07727943.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
 gi|311096800|gb|EFQ55038.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
          Length = 297

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 65/218 (29%), Positives = 109/218 (50%), Gaps = 18/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           +L+ED    + NKP GI+    +  +  +  F+K +   +G   Q+  +  RLD++TSG+
Sbjct: 78  ILFEDDHFLILNKPFGIASIPSAIHSNTLANFVKGYYVKQGYENQQVHIVTRLDKDTSGV 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + IQK Y++LV G  K     E IA     +  I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQSKTIQKRYYALVKGSGKLDPVGEIIAPIARDEDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  KG  YA + ++V+  F   +  +++Q HTGRTHQ+RVH  H+G P++GD  Y  +
Sbjct: 192 TRKVAKGGKYAHTSYQVVQSFGDIYL-VDIQLHTGRTHQIRVHFSHIGFPLLGDDLYGGS 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            +         +  LH   +   HP     L I +PLP
Sbjct: 251 LEDGI-----ERQALHCHRLSYYHPFLEEELVIESPLP 283


>gi|240167932|ref|ZP_04746591.1| RluA family pseudouridine synthase [Mycobacterium kansasii ATCC
           12478]
          Length = 308

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 80/295 (27%), Positives = 134/295 (45%), Gaps = 31/295 (10%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +  I   G V++D      ++R+ SG    VR+P     L +                  
Sbjct: 32  VAAIAEGGGVQLDGVPAGKSDRLTSGAWLQVRLPEAPPPLEN---------------TPV 76

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKG--QKPRLTH 148
           D     +LY D  I   +KPA ++     G     + G L +    + + G  ++  + H
Sbjct: 77  DIEGMTILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRITTSGVHERQGIVH 136

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++VVA +  A   L  +F+ R ++K Y +LV G P      I   + +  H 
Sbjct: 137 RLDVGTSGVMVVALSERAYTVLKRAFKHRTVEKRYHALVQGHPDPSSGTIDAPIGR--HP 194

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           G ++   V  N +   ++++H+  I+ F      L+++  TGRTHQ+RVH   +  P  G
Sbjct: 195 GPEWKFAVTTNGR---HSVTHYDTIEAFVAA-SLLDIELETGRTHQIRVHFAALRHPCCG 250

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           D  Y A+ K      ++ + +LHAR +   HP +G R++I +P P  +    D L
Sbjct: 251 DLVYGADPKLAKKLGLERQ-WLHARSLAFAHPADGRRIEIVSPYPPDLQHALDVL 304


>gi|256379746|ref|YP_003103406.1| pseudouridine synthase, RluA family [Actinosynnema mirum DSM 43827]
 gi|255924049|gb|ACU39560.1| pseudouridine synthase, RluA family [Actinosynnema mirum DSM 43827]
          Length = 310

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 71/226 (31%), Positives = 114/226 (50%), Gaps = 26/226 (11%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQE 153
           I+L+ED  + V +KP G++V    G     + G L +    V + G   R  + HRLD  
Sbjct: 84  IVLHEDDDVIVVDKPVGVAVHPSPGWTGPTVVGGLAAAGVRVSTSGAAERQGVVHRLDVG 143

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G++VVA++  A   L ++F+ R + K+Y +LV G P   K  I   + +  H   DY 
Sbjct: 144 TTGVMVVAKSEHAYSVLKQAFKDRTVDKLYHALVQGHPDPIKGTIDAPIDR--HPKHDYK 201

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V     G   +I+H++V++ F +    L++   TGRTHQ+RVH   +  P VGD  Y 
Sbjct: 202 FAVM---AGGKPSITHYEVVEAF-RAASLLDVHLETGRTHQIRVHFSALKHPCVGDLTYT 257

Query: 274 ANFKGNFTSPI------QNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           A+       P+       ++ +LHAR +   HP  G  ++ T+  P
Sbjct: 258 AD-------PVLAKRLGMSRQWLHARRLGFHHPADGEWVEFTSEYP 296


>gi|313158249|gb|EFR57651.1| pseudouridine synthase, RluA family [Alistipes sp. HGB5]
          Length = 228

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 106/224 (47%), Gaps = 14/224 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
           F    +LYED+ + + NK  G  VQ        ++  +K++V  +  KP      + HR+
Sbjct: 2   FTPEDILYEDNHLLIVNKRCGDLVQPDPSGESALEDQIKAFVKRRDAKPGDVFLGVVHRI 61

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+  SG ++ A+T  A   L E  R  RI+K+YW+L    P  +   + +++L+ +    
Sbjct: 62  DRPVSGAVLFAKTSKALTRLNEMIREGRIRKVYWALTERTPDPESGELRHYILRDART-- 119

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +        + GA  A   ++ +      +  +E++  TGR HQ+R     +GCPI GD 
Sbjct: 120 NRSRACDGPKPGAKEARLRYETLGA-GTNYTLVEVELLTGRHHQIRAQLSKIGCPIRGDL 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           KY     G   S     + LH+R ++  HP     + +TAP PA
Sbjct: 179 KY-----GARRSLPGGGISLHSRRVEFEHPVRREPVSVTAPAPA 217


>gi|262277480|ref|ZP_06055273.1| ribosomal large subunit pseudouridine synthase D [alpha
           proteobacterium HIMB114]
 gi|262224583|gb|EEY75042.1| ribosomal large subunit pseudouridine synthase D [alpha
           proteobacterium HIMB114]
          Length = 325

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 78/295 (26%), Positives = 137/295 (46%), Gaps = 50/295 (16%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    +VV EN ++  R+D+     YP I+   + KI+++  ++++            GQ
Sbjct: 1   MNNYNFVVDENFDQK-RIDQVVAKQYPKISRSKVSKIIKTELLKLN------------GQ 47

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +++ P         I+ + +++ ++NL      L   +++ED  I + +KP G+ V  G+
Sbjct: 48  ILKDPSHKVKSGDQIEFENLIEETINLIPKKMDLN--IIFEDQDIIIIDKPIGMVVHPGA 105

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + YH    L     +   +P + HR+D++TSG+LVVA+   A   + + F
Sbjct: 106 GNYEDTMVNGLLYHCKNNLSGM--NGEDRPGIVHRIDKDTSGLLVVAKNDQAHAFIAKQF 163

Query: 175 RMRRIQKIYWSLVWGI--PKNKK--ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
               I++ Y   V+GI  P + K    I      +  +  D +       +G + AI+++
Sbjct: 164 EEHSIKRSYLVFVYGILRPLHGKIETLIGRNKTNRQKMSADVI-------RGKD-AITNY 215

Query: 231 KVIDCF-AQKF-------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           + ++ F   K        C LE    TGRTHQ+RVH  H G PI+GD  Y    K
Sbjct: 216 ETLEVFKGNKIPDISLVKCILE----TGRTHQIRVHMSHKGNPILGDQTYGKKIK 266


>gi|295694723|ref|YP_003587961.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
 gi|295410325|gb|ADG04817.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
          Length = 322

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 88/342 (25%), Positives = 153/342 (44%), Gaps = 51/342 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+Y +    E   +L R+ + + P +    + K +R G+V+V++K+ K +  +  G  V+
Sbjct: 2   VEYPITRA-ENGKKLHRFLRQNLPGLPLSGVYKWIRVGRVKVNRKKGKPDLVLHEGDTVQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG- 124
           +          + +++         K     ++  +LYED  + V NKPAG+        
Sbjct: 61  L---------FVSDEEYAALRRRGPKFQGVPRTFEILYEDGDLLVVNKPAGLLTHPDRQE 111

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                    +AY  D   K   D +   P   +RLD+ TSGI+++ +   A + L ++ R
Sbjct: 112 HRDTLINRVLAYLYD---KGEWDGRAFAPAAANRLDRNTSGIVLIGKHAQALRELADALR 168

Query: 176 MRRIQKIYWSLVWG---IPKN-KKECIANWLLKKSHIGGDYVHVVKQNEKGAN----YAI 227
            RR+ K Y +LV G    P   K+  I +    ++ + G+     K+   G       A 
Sbjct: 169 GRRVDKRYLALVHGRIETPGTLKQALIRDHENNRTRLAGE-----KRGRHGVAPETLEAE 223

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN- 286
           + ++ +   A++   L++   +GRTHQ+R H    G P+VGD KY          P++  
Sbjct: 224 TRYRPL-AVAERLTLLDITLVSGRTHQIRAHLAAAGHPLVGDIKYGGK-------PLRGL 275

Query: 287 -KLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
              +LHA  + L     GR +  APLPA + K  +S G   D
Sbjct: 276 RHQFLHAYALTLAD---GR-RFVAPLPAELRKLLESYGLSTD 313


>gi|49259508|pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine
           Synthase Rlud From Escherichia Coli
 gi|118138510|pdb|2IST|A Chain A, Crystal Structure Of Rlud From E. Coli
          Length = 325

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I + NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 85  IVYEDEDIIIINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 142 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 199

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 200 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 251

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 252 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 311

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 312 RADFEEH 318


>gi|323159115|gb|EFZ45108.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           E128010]
 gi|323177278|gb|EFZ62866.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           1180]
          Length = 300

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 60  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 116

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 117 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 174

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 175 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 226

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 227 YGGRPRPPKGASEAFISMLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 286

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 287 RADFEEH 293


>gi|262163884|ref|ZP_06031623.1| ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           VM223]
 gi|262027412|gb|EEY46078.1| ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           VM223]
          Length = 324

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 91/340 (26%), Positives = 157/340 (46%), Gaps = 51/340 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +   RLD+     +   +   L++ L  G++ V+ + V K   ++  G+V+    
Sbjct: 10  TVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVVTKPRTKVMGGEVI---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V+ A   +  EQ+     + L          ++YED  I V NKP    V  G+G A   
Sbjct: 66  VVQA--ELEDEQRWEAQDLPLN---------IVYEDDDIIVINKPRDFVVHPGAGQA--- 111

Query: 130 DGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG + + +        + PR  + HRLD++T+G++VVA+T  A   L  + + R + + Y
Sbjct: 112 DGTVLNALLFHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN----EKGANYAISHFKVIDCFAQK 239
            ++V G         A  ++ K  IG    H  K+          +A++H++V + F ++
Sbjct: 172 EAIVIGT------MTAGGMIDKP-IGR---HSTKRTLMSVSPMGKHAVTHYRVAEHF-RE 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLH 291
              L ++  TGRTHQ+RVH  ++  P++GD  Y    +         T+ I+N  +  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGASEELTAMIRNFDRQALH 280

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
           A  +   HP  G  L+  AP+P  MV    +L  + D  L
Sbjct: 281 AVMLKFEHPITGEELEFHAPVPDDMVTM--TLALREDSKL 318


>gi|323691883|ref|ZP_08106137.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
 gi|323504090|gb|EGB19898.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
          Length = 333

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 88/338 (26%), Positives = 153/338 (45%), Gaps = 45/338 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q V +  +E   RLD+    +        + K+LR   + ++ K+   + ++  G  V+
Sbjct: 1   MQVVKITKNEAGQRLDKLLAKYLNLAGKSFIYKMLRKKNITLNGKKCDGSEKLSEGDEVK 60

Query: 67  I---PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +      I   + + K QK+    +++           +YED  I + NKP+G+  Q   
Sbjct: 61  LFLSDETIEKFSEV-KIQKVRKRKLDV-----------VYEDDDIILINKPSGMLSQKAK 108

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                     I Y +DG   +  D +  KP + +RLD+ TSGI++  ++    Q ++E+ 
Sbjct: 109 ETDESLVEYLIQYLLDGGKLTKEDMRQFKPSVCNRLDRNTSGIVIAGKSLPGLQLMSEAI 168

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-----KGANYAISH 229
           + R I K Y  +V G     KE I  +L K      + V V+K NE     K A    + 
Sbjct: 169 KERTIGKYYLCIVKGSVAGPKE-IDGYLKKNEKT--NQVTVLKANELCREDKDALPIRTQ 225

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQN 286
           ++ + C   +   LE++  TGR+HQ+R H   +G PI GD+KY     N +      +Q+
Sbjct: 226 YRPL-CSDGRHTLLEVKLITGRSHQIRAHLASIGHPIAGDYKYGDPAVNREARDKYAVQS 284

Query: 287 KLYLHARYMDLPHP-------EGGRLQITAPLPAHMVK 317
           ++ LHA  + +P          GGR + TA  P   ++
Sbjct: 285 QM-LHAWRLVMPKELREPLAGLGGR-EFTAKPPEEFMR 320


>gi|295695962|ref|YP_003589200.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
 gi|295411564|gb|ADG06056.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
          Length = 308

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 85/314 (27%), Positives = 143/314 (45%), Gaps = 33/314 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           + VV+ +E   RLDR+        +   +Q  +  G+VRV ++ VK ++R++ G+     
Sbjct: 12  WFVVDPEEAGERLDRFLAERLADTSRSQIQGWIDEGRVRVGERPVKASHRVRPGE----- 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                                L    + +   +++ED  + V +KP G+ V    G +  
Sbjct: 67  ----------DVLVEPPEPEPLELVPEPIPLKIVFEDEDVVVVDKPRGLVVHPAPGHSRG 116

Query: 129 --IDGFLK--SWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + G L     +   G   +P + HR+D++TSG+LV A+T  A   L + F    + + 
Sbjct: 117 TLVHGLLAHCGRLSRLGGSLRPGIVHRIDRDTSGLLVAAKTDLAYMGLAKQFHDHTVDRE 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G+  +    +   + +  H+      V     +G   A++HF VI+ FA +   
Sbjct: 177 YLALVHGVVPHDHGTVDAPVGRHPHLRQQMAVV-----RGGRPAVTHFIVIERFA-RATL 230

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L ++  TGRTHQ+RVH   +G P++GD KY     G   S       LHA  +   HP  
Sbjct: 231 LRLRLETGRTHQIRVHMEFIGFPVIGDPKY-----GPRRSLGMKGQALHAAVLGFDHPRT 285

Query: 303 G-RLQITAPLPAHM 315
           G R++  +PLP  M
Sbjct: 286 GERVRFESPLPEDM 299


>gi|291326503|ref|ZP_06124794.2| pseudouridine synthase A [Providencia rettgeri DSM 1131]
 gi|291313961|gb|EFE54414.1| pseudouridine synthase A [Providencia rettgeri DSM 1131]
          Length = 217

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 69/214 (32%), Positives = 109/214 (50%), Gaps = 18/214 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G    +H D  + S V          HRLD  TSG++VV
Sbjct: 15  ILYQDDHIIVVNKPSGLLSVPGKAPEHH-DSIM-SRVQRDFPAAESVHRLDMATSGVMVV 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A  + A + L   FR R  +K Y + VWG  + ++  +   L+       D+ +  KQ  
Sbjct: 73  ALHKKAERELKRQFREREPKKFYIARVWGHLEKEEGLVDLPLI------CDWPNRPKQKV 126

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E G + A + ++V+  + ++   +++ P TGR+HQLRVH L +G PI+GD  Y  +  
Sbjct: 127 CFETGKS-AQTEYQVLQ-YEEQATRVKLSPITGRSHQLRVHMLALGHPILGDRFYAQDEA 184

Query: 278 GNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
               +    +L LHA+ + + HPE G  +  T P
Sbjct: 185 KALAT----RLQLHAQELYITHPEYGTSMHFTCP 214


>gi|225077010|ref|ZP_03720209.1| hypothetical protein NEIFLAOT_02062 [Neisseria flavescens
           NRL30031/H210]
 gi|224951567|gb|EEG32776.1| hypothetical protein NEIFLAOT_02062 [Neisseria flavescens
           NRL30031/H210]
          Length = 238

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 67/222 (30%), Positives = 106/222 (47%), Gaps = 16/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ DS+    NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IIHRDSRTIAVNKPAGMLVHRSWLDKHETRFAVQTLRDQIGQHVYPVHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLK--KSHIGGDYVHVVK 217
           A    AA+ LT+ F  + I+K YW++V G +P +    + ++ LK     I         
Sbjct: 64  ALDTEAARLLTQQFENKTIEKTYWAIVRGHLPSD---GLIDYALKYMPDKIAEAQTEATL 120

Query: 218 QNEKGANYAISHFKV-----IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           Q  + A   ++  ++     +     ++ W E+ PHTGR HQLR H  H+  PIVGD  Y
Sbjct: 121 QEAQTAYRCLAQTELPFQSALRYPTSRYSWAELTPHTGRKHQLRRHMKHIFHPIVGDTNY 180

Query: 273 CANFKGNFTSPIQ---NKLYLHARYMDLPHPE-GGRLQITAP 310
             + + N          +L LHAR +     E G R+ + AP
Sbjct: 181 -GDLRQNHAVAEHIGTQRLMLHARSLSFQSIEDGSRMTVQAP 221


>gi|111018085|ref|YP_701057.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
 gi|110817615|gb|ABG92899.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
          Length = 302

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 85/321 (26%), Positives = 146/321 (45%), Gaps = 33/321 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +  E MR+D         ++   + ++   G V VD   V  ++R+ +G  +      
Sbjct: 3   VPDGLEAMRVDAGLARLL-GLSRTAVAQLTEEGSVLVDGAPVGKSDRLSAGAWL------ 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG-IAYHI 129
                   E ++ +    LT  ++ ++ + +LY D  +   +KP G++     G     +
Sbjct: 56  --------EVELPEPPRPLTIEAEPVEGMEILYADDDVVAVDKPVGVAAHASVGWTGPTV 107

Query: 130 DGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            G L +    + + G   R  + HRLD  TSG++VVA +  A   L  +F+ R I K Y 
Sbjct: 108 IGGLAAAGFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTLLKRAFKQRTIDKRYH 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G P      I   + +  H   D+   V  + K    +I+H+  ++ F Q    L+
Sbjct: 168 ALVQGHPDPSSGTIDAPIGR--HRSNDWKFAVTADGK---PSITHYDTVEAF-QAASLLD 221

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TGRTHQ+RVH   +  P  GD  Y A+ +      ++ + +LHAR +   HP  GR
Sbjct: 222 IHLETGRTHQIRVHFAALRHPCCGDLTYGADPRLAERLGLERQ-WLHARSLGFAHPADGR 280

Query: 305 -LQITAPLPAHMVKTWDSLGF 324
            ++IT+  P  +    D+LG 
Sbjct: 281 WVEITSKYPKDLE---DALGV 298


>gi|84515048|ref|ZP_01002411.1| ribosomal large subunit pseudouridine synthase A [Loktanella
           vestfoldensis SKA53]
 gi|84511207|gb|EAQ07661.1| ribosomal large subunit pseudouridine synthase A [Loktanella
           vestfoldensis SKA53]
          Length = 214

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 65/221 (29%), Positives = 111/221 (50%), Gaps = 27/221 (12%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++L+ D ++ + +KP+G+    G G    +   L + V        L HRLD++TSG+++
Sbjct: 12  VILHHDHQVLLVDKPSGLLSVPGKG--EDLTDCLIARVQRIFPDALLVHRLDRDTSGVMI 69

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVH 214
            A T  A +HL   F  R+ +K Y + VWG   +K        I +W  +   +      
Sbjct: 70  FAMTPHAQRHLGLQFENRQTKKTYVARVWGEMADKTGTVDLPLIVDWPNRPLQM------ 123

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               + +    A++ ++V+     +   + + P TGR+HQLRVH L +G PI+GD  Y  
Sbjct: 124 ---VDHENGRAAVTDWRVVRVGGGE-TRVRLMPKTGRSHQLRVHMLALGHPILGDPFYA- 178

Query: 275 NFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLP 312
                 T P ++  +L LH+  +   HP+GG+ ++ITAP P
Sbjct: 179 ------TGPARDHPRLMLHSETLQFRHPDGGQGIRITAPCP 213


>gi|240949536|ref|ZP_04753876.1| RNA pseudouridine synthase [Actinobacillus minor NM305]
 gi|240296109|gb|EER46770.1| RNA pseudouridine synthase [Actinobacillus minor NM305]
          Length = 212

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 66/201 (32%), Positives = 92/201 (45%), Gaps = 30/201 (14%)

Query: 103 YEDSKIYVFNKPAGISVQG---GSGIAYHID---GFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++     V NKP G+SV      SG+   I    G  + W         L HRLD+ TSG
Sbjct: 9   FQHPDFIVINKPEGVSVHKDNEASGLTERIAQQLGVPQIW---------LVHRLDKATSG 59

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A T+ AA      F+  +IQK YW+L    PK K+  I   + K  +      H  
Sbjct: 60  LLILALTKEAAVEFYHLFKQHKIQKTYWALSTTKPKKKQGKIIGDMKKSRNSAWKLCHTK 119

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +      N AI+ F      A +  W  + PHTGRTHQLRV    +G PI+GD  Y    
Sbjct: 120 E------NPAITQF-TSQSVAPQLRWFTLNPHTGRTHQLRVAMRSLGSPILGDSLYGGE- 171

Query: 277 KGNFTSPIQNKLYLHARYMDL 297
                    ++LYLHA  ++ 
Sbjct: 172 -------KADRLYLHAYQLEF 185


>gi|294054947|ref|YP_003548605.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
 gi|293614280|gb|ADE54435.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
          Length = 227

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 64/223 (28%), Positives = 107/223 (47%), Gaps = 25/223 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+Y+D+ + + +KP+G+ V      A + +  ++   D  GQ+    HRLD+ TSG+LV 
Sbjct: 5   LIYQDTDLVIIDKPSGLLVHRSKLDAQNTEFAVQQLRDQIGQEVFPCHRLDRPTSGLLVF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  RA  + + + F   R+ K Y ++V G P    + I ++ L++     +  H +++  
Sbjct: 65  ALNRATLRTVAQQFAEGRVWKSYLAIVRGWP--NADGIIDYPLRQE----EPPHKIQE-- 116

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A +H+  + C             +   LE+QP +GRTHQLR H  H+  PI+GD 
Sbjct: 117 -----AQTHYTTLKCSELPVPVGRYATARVALLELQPQSGRTHQLRRHLAHIRHPILGDT 171

Query: 271 KYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGRLQITAPL 311
           ++    +  F       N+L L A  +    P G    I APL
Sbjct: 172 RHGDGAQNRFMRETAKCNRLLLRATQLRFTLPNGVEQHIEAPL 214


>gi|282916446|ref|ZP_06324208.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus D139]
 gi|283770258|ref|ZP_06343150.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
 gi|282319886|gb|EFB50234.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus D139]
 gi|283460405|gb|EFC07495.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
 gi|298694490|gb|ADI97712.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           ED133]
          Length = 305

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 85/327 (25%), Positives = 148/327 (45%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +     
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYK----- 55

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++   I      + E  IL  ++NL          + YED  + V  KP G+ V    
Sbjct: 56  -VKLNDHIVVTEKEVVEADILPENLNLD---------IYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKDLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAP--IGRNKNDRQSMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQA-----LHAGLIG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G  ++  A LP       D++
Sbjct: 274 FEHPVTGEYIERHAELPQDFEDLLDTI 300


>gi|224024462|ref|ZP_03642828.1| hypothetical protein BACCOPRO_01187 [Bacteroides coprophilus DSM
           18228]
 gi|224017684|gb|EEF75696.1| hypothetical protein BACCOPRO_01187 [Bacteroides coprophilus DSM
           18228]
          Length = 547

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 81/247 (32%), Positives = 122/247 (49%), Gaps = 28/247 (11%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGF 132
           L H++   ++  + +   +H D    I+ YED  I V NKPAG +SV G +G+   +   
Sbjct: 320 LKHMLIGLEVDPNPLVENRHHDTPLEII-YEDPWIVVVNKPAGMLSVPGKNGLDSVLQRL 378

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            + + +S    P L HRLD +TSG+L+ A+ +   Q L   F  R+I+K Y +L+ G P+
Sbjct: 379 QELYPESDS--PLLVHRLDMDTSGLLLAAKDKNIHQCLQALFETRQIRKRYTALLQGNPR 436

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             +  I   L        D+    +Q  N +    A++ F+V +  +     +   P TG
Sbjct: 437 QDEGTIDLPLCP------DFSDRPRQQVNWELGKKAVTRFRVEE-RSGGTTRVSFWPLTG 489

Query: 251 RTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---R 304
           RTHQLRVHA H   +  PI+GD  Y     GN      ++LYLHA  ++  HP  G   R
Sbjct: 490 RTHQLRVHAAHPEGLDSPILGDPLY-----GNQA----DRLYLHAAELEFTHPVTGETIR 540

Query: 305 LQITAPL 311
           L   AP 
Sbjct: 541 LCKEAPF 547


>gi|212637049|ref|YP_002313574.1| pseudouridylate synthase [Shewanella piezotolerans WP3]
 gi|212558533|gb|ACJ30987.1| Pseudouridylate synthase [Shewanella piezotolerans WP3]
          Length = 225

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 63/202 (31%), Positives = 105/202 (51%), Gaps = 15/202 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  I V NKP+G+    G   A++   +  S V ++  + ++ HRLD  TSG++VV
Sbjct: 16  ILHQDQDIMVLNKPSGLLSVPGRDPAHNDSTY--SRVLAQYPEAKIVHRLDMATSGVIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A  R+A   L   FR R   K Y++ V G  K     +   L+       D+ +  KQ  
Sbjct: 74  ALLRSAESELKRQFRDRETAKTYYARVAGHVKADSGTVNLPLI------CDWPNRPKQKV 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    + +H+ V+   A++   +++ P TGR+HQLRVH + +G PI+GD+ Y      
Sbjct: 128 DHQIGKASQTHYDVV-SRAKRSTLVKLTPITGRSHQLRVHMMALGHPILGDNFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
              S    +L LHA+ + + HP
Sbjct: 187 RLAS----RLLLHAQSLTITHP 204


>gi|322834449|ref|YP_004214476.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321169650|gb|ADW75349.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 239

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/204 (33%), Positives = 110/204 (53%), Gaps = 18/204 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D  I V NKP+G+ SV G   +A H D  + + +  +  +    HRLD  TSG++V
Sbjct: 36  VIFQDEHIMVVNKPSGLLSVPGK--LAEHQDSLM-TRIQQEFPEAESVHRLDMSTSGVIV 92

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           VA T+ A + L   FR R  +K+Y + VWG  +     I   L+       DY +  KQ 
Sbjct: 93  VALTKDAERELKRQFRERETKKVYIARVWGRVEEDYGIIDLPLI------CDYPNRPKQK 146

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +E G   A++ ++V+         ++++P TGR+HQLRVH L +G PI+GD K+ A+ 
Sbjct: 147 VCHETGKK-ALTQYEVMSWDDDGTTRVKLRPITGRSHQLRVHLLALGHPILGD-KFYAHP 204

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
           +    +    +L LHA+ +   HP
Sbjct: 205 QALAAA---GRLQLHAQELSFYHP 225


>gi|317052412|ref|YP_004113528.1| pseudouridine synthase, RluA family [Desulfurispirillum indicum S5]
 gi|316947496|gb|ADU66972.1| pseudouridine synthase, RluA family [Desulfurispirillum indicum S5]
          Length = 313

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 116/235 (49%), Gaps = 25/235 (10%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETS 155
           YED  + V NKPAG+ V   +G     +   +  +L   + + G   +P + HRLD++TS
Sbjct: 84  YEDESLLVVNKPAGMVVHPAAGNYDATLVNALVHYLGDGLPAIGGVLRPGIVHRLDKDTS 143

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH- 214
           G+++VA+T  A Q L   F  + I + Y +L  G        + +  + + +IG D    
Sbjct: 144 GLMLVAKTEVAHQRLVSMFAAKEIDRCYLALCHG-------SLDDSGVIEGNIGRDPKDR 196

Query: 215 ---VVKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               + + +KG   A +H+++++   C  Q    +E +  TGRTHQ+RVH   +  P++G
Sbjct: 197 KRMAIVEADKGKT-ARTHYRLLEKFFCHQQWVSLIECRLDTGRTHQIRVHLRSVQRPLLG 255

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           D  Y    +  + S    +  LH+  + L HP  G  +++  PLP  M    +SL
Sbjct: 256 DQVYGVKKEPGYVS--MRRQALHSASLCLQHPISGEVVELQCPLPEDMRDQVESL 308


>gi|262184460|ref|ZP_06043881.1| pseudouridylate synthase [Corynebacterium aurimucosum ATCC 700975]
          Length = 292

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 83/302 (27%), Positives = 136/302 (45%), Gaps = 30/302 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D         I+   + ++  +G V +D   V  + R+ +G  + +         + 
Sbjct: 1   MRVDAALAKLL-GISRARVSQLCAAGDVEIDGAAVGKSERLNAGGWIDV--------MMP 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW- 136
             ++ L     L +  D     +LY D  I    KP G++     G     + G L++  
Sbjct: 52  APEEPLIPKEELVEGMD-----VLYADEDIICVCKPVGVAAHPTLGWDGPTVIGGLRAAG 106

Query: 137 --VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             +   G   R  + HRLD  TSG++VVA +  A   L  +FR R +QK Y ++V G+P 
Sbjct: 107 YALADAGPTERKGIVHRLDVGTSGVMVVAASERAYSQLKNAFRERTVQKTYHAVVQGLPD 166

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I   + +    G  +  VV   +     A++H+K+++ F ++   LE+   TGRT
Sbjct: 167 PIVGTIDAPIGRHPSAGWKF-GVVDDGKP----AVTHYKLLEAF-REASLLEVHLETGRT 220

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR-LQITAP 310
           HQ+RVH    G P VGD  Y  +   N    +  N+ +LHA  +   HP  G+  + TAP
Sbjct: 221 HQIRVHMSATGHPCVGDPMYGCDP--NLAKRVGLNRQWLHAVELGFTHPGTGKWFECTAP 278

Query: 311 LP 312
            P
Sbjct: 279 YP 280


>gi|256394870|ref|YP_003116434.1| pseudouridine synthase [Catenulispora acidiphila DSM 44928]
 gi|256361096|gb|ACU74593.1| pseudouridine synthase, RluA family [Catenulispora acidiphila DSM
           44928]
          Length = 312

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 77/309 (24%), Positives = 141/309 (45%), Gaps = 27/309 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  M+ ++ + + +  E  RLD      +  ++     ++   G+VRVD      ++R++
Sbjct: 1   MVAMSDLRSLPIPDGLEGERLDAALARMF-GLSRTRAAELAAEGRVRVDGSEAGKSDRVR 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + I     A    +K + +    +             +++D  I V +KP G++  
Sbjct: 60  GGAWLEIELPAAADPVAVKAEAVEGMRI-------------VHDDEDIVVIDKPVGVAAH 106

Query: 121 GGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESF 174
              G +   + G L +    + + G   R  + HRLD  TSG++VVA++  A   L ++F
Sbjct: 107 PSPGWLGTTVVGGLAAAGYRISTSGASERQGVVHRLDVGTSGLMVVAKSERAYTLLKQAF 166

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R + K Y +LV G P   +  +   + +  H   DY   V    +G   +++H++ I+
Sbjct: 167 RDRTVDKRYHTLVQGHPDPMRGTVDAPIGRHPHH--DYKFAVV---RGGKDSVTHYETIE 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            + +    L ++  TGRTHQ+RVH   +  P VGD +Y A+        +  + +LHA  
Sbjct: 222 AY-RAATLLAIKLETGRTHQIRVHMAALRHPCVGDLQYGADPTLGERLGL-GRQWLHAVS 279

Query: 295 MDLPHPEGG 303
           +   HP  G
Sbjct: 280 LGFEHPGTG 288


>gi|41407349|ref|NP_960185.1| hypothetical protein MAP1251 [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41395701|gb|AAS03568.1| hypothetical protein MAP_1251 [Mycobacterium avium subsp.
           paratuberculosis K-10]
          Length = 308

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 116/237 (48%), Gaps = 18/237 (7%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTH 148
           D     +LY D  I   +KPA ++     G     + G L +    + + G   R  + H
Sbjct: 77  DIEGMTILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRITTSGVPERQGIVH 136

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++VVA +  A   L  +F+ R + K Y +LV G P      I   + +  H 
Sbjct: 137 RLDVGTSGVMVVALSERAYTLLKRAFKQRTVDKRYHALVQGHPDPSSGTIDAPIGR--HR 194

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH--ALHMGCPI 266
           GG++   V ++ +   ++++H+  ++ F      L++   TGRTHQ+RVH  ALH  C  
Sbjct: 195 GGEWKFAVTKDGR---HSLTHYDTVEAFVAA-SLLDVHLETGRTHQIRVHFSALHHPC-- 248

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            GD  Y A+ K      +Q + +LHAR +   HP +G R++I +P P  +    D L
Sbjct: 249 CGDLVYGADPKLAKKLGLQRQ-WLHARSLSFAHPADGRRMEIVSPYPPDLQHALDVL 304


>gi|258624747|ref|ZP_05719681.1| Ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           VM603]
 gi|258583034|gb|EEW07849.1| Ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           VM603]
          Length = 324

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 91/340 (26%), Positives = 157/340 (46%), Gaps = 51/340 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +   RLD+     +   +   L++ L  G++ V+ + V K   ++  G+V+    
Sbjct: 10  TVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVVTKPRTKVMGGEVI---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V+ A   +  EQ+     + L          ++YED  I V NKP    V  G+G A   
Sbjct: 66  VVQA--ELEDEQRWEAQDLPLN---------IVYEDDDIIVINKPRDFVVHPGAGQA--- 111

Query: 130 DGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG + + +        + PR  + HRLD++T+G++VVA+T  A   L  + + R + + Y
Sbjct: 112 DGTVLNALLFHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN----EKGANYAISHFKVIDCFAQK 239
            ++V G         A  ++ K  IG    H  K+          +A++H++V + F ++
Sbjct: 172 EAIVIGT------MTAGGMIDKP-IGR---HSTKRTLMSVSPMGKHAVTHYRVAEHF-RE 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLH 291
              L ++  TGRTHQ+RVH  ++  P++GD  Y    +         T+ I+N  +  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGASEELTAMIRNFDRQALH 280

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
           A  +   HP  G  L+  AP+P  MV    +L  + D  L
Sbjct: 281 AVMLKFKHPITGEELEFHAPVPDDMVTM--TLALREDSKL 318


>gi|332523959|ref|ZP_08400211.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
 gi|332315223|gb|EGJ28208.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 275

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 63/203 (31%), Positives = 93/203 (45%), Gaps = 22/203 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           LY+DS + V NK  G+   G       +  H+  F+       GQ   + HRLD ETSG 
Sbjct: 71  LYQDSHLIVVNKSEGMKTHGNEPNELALLNHVSAFV-------GQTCYIIHRLDMETSGA 123

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       +      R I + YW+L+ GI +NK   +   + +  H     V  +K
Sbjct: 124 IIFAKNPFILPIMNRLLENREIGRNYWALIDGIIENKDTTLRFPIGRHRHDRRKRVVDLK 183

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             +K    AI+H K +  +  KF  ++    TGRTHQ+RVH  H+G PI+GD  Y     
Sbjct: 184 NGQK----AITHVKRLKAYRPKFSLVDCSLKTGRTHQIRVHLSHIGHPIIGDPLY----- 234

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
                    +L LHA  +   HP
Sbjct: 235 --HQQTTSQRLMLHAHQLYFKHP 255


>gi|304411822|ref|ZP_07393433.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307303410|ref|ZP_07583165.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304349682|gb|EFM14089.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306913770|gb|EFN44192.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 223

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 63/199 (31%), Positives = 107/199 (53%), Gaps = 10/199 (5%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP+G+    G   A+  D  L + + +   +  L HRLD  TSGI+V AR
Sbjct: 18  YKDRDLIIINKPSGLLSNPGRA-AHTFDCAL-TRLQTLYPETILVHRLDCATSGIMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
            + A  HL   F+ R+ +K+Y + V G +P  +++ + +  +        Y   ++  E 
Sbjct: 76  NKKAESHLKTQFQDRQSKKVYIAEVMGHVP--QEQGMIDLAIAPDTEHSPYQKTLQAGET 133

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           G   A+++++V++   +    +E+ P TGRTHQLRVH L +G  I+GD  Y  + +    
Sbjct: 134 GGKSALTYYRVLE-RRENSTLVELSPETGRTHQLRVHMLALGHAILGDEFY-GDAEVIKA 191

Query: 282 SPIQNKLYLHARYMDLPHP 300
           +P   +L LHA+ + L HP
Sbjct: 192 AP---RLCLHAQSLSLTHP 207


>gi|323156250|gb|EFZ42409.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           EPECa14]
          Length = 300

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 60  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 116

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 117 TGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 174

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 175 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 226

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  + +
Sbjct: 227 YGGRPRPPKGASEAFISMLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVM 286

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 287 RADFEEH 293


>gi|319775954|ref|YP_004138442.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae F3047]
 gi|329123818|ref|ZP_08252376.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           aegyptius ATCC 11116]
 gi|317450545|emb|CBY86762.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae F3047]
 gi|327469305|gb|EGF14776.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           aegyptius ATCC 11116]
          Length = 324

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 121/247 (48%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP  + V  G+G         + YH    ++  V   G    + HRLD
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVE--VPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++ +
Sbjct: 139 KDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLM 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A++H+++++ + + +  L ++  TGR HQ+RVH  H+  P++G
Sbjct: 199 A---VHPMGKP------AVTHYRIMENY-RNYTRLRLRLETGRMHQIRVHMAHIAHPLLG 248

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           D  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+  
Sbjct: 249 DQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 309 NALKADY 315


>gi|118463205|ref|YP_882412.1| ribosomal large subunit pseudouridine synthase d [Mycobacterium
           avium 104]
 gi|118164492|gb|ABK65389.1| ribosomal large subunit pseudouridine synthase d [Mycobacterium
           avium 104]
          Length = 294

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 116/237 (48%), Gaps = 18/237 (7%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTH 148
           D     +LY D  I   +KPA ++     G     + G L +    + + G   R  + H
Sbjct: 63  DIEGMTILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRITTSGVPERQGIVH 122

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++VVA +  A   L  +F+ R + K Y +LV G P      I   + +  H 
Sbjct: 123 RLDVGTSGVMVVALSERAYTLLKRAFKQRTVDKRYHALVQGHPDPSSGTIDAPIGR--HR 180

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH--ALHMGCPI 266
           GG++   V ++ +   ++++H+  ++ F      L++   TGRTHQ+RVH  ALH  C  
Sbjct: 181 GGEWKFAVTKDGR---HSLTHYDTVEAFVAA-SLLDVHLETGRTHQIRVHFSALHHPC-- 234

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            GD  Y A+ K      +Q + +LHAR +   HP +G R++I +P P  +    D L
Sbjct: 235 CGDLVYGADPKLAKKLGLQRQ-WLHARSLSFAHPADGRRMEIVSPYPPDLQHALDVL 290


>gi|256832316|ref|YP_003161043.1| pseudouridine synthase, RluA family [Jonesia denitrificans DSM
           20603]
 gi|256685847|gb|ACV08740.1| pseudouridine synthase, RluA family [Jonesia denitrificans DSM
           20603]
          Length = 313

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/291 (25%), Positives = 138/291 (47%), Gaps = 25/291 (8%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           +G V VD +     +RI  G V+ +         ++ + + +D++ +  +    ++  ++
Sbjct: 40  AGDVYVDGRPAAKGDRIVQGAVIDV---------VLPDPREVDATEDEPQPVPGMR--IV 88

Query: 103 YEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSG 156
           ++D  I V +KP G++     G     + G L +    + + G   R  + HRLD  TSG
Sbjct: 89  HDDEHIVVVDKPVGVAAHSAVGWSGPTVVGALAAAGYRISTSGAAERQGIVHRLDVGTSG 148

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++VVA++  A   L  +FR R + K+Y ++V G P+  K  I   + +  H   ++   V
Sbjct: 149 LMVVAKSELAYTRLKRAFRERTVDKVYHTVVQGHPEPTKGTIDAPIGR--HPKAEFKFAV 206

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             + K    +I+H++V++        + +   TGRTHQ+RVH   M  P VGD  Y A+ 
Sbjct: 207 MADGK---RSITHYEVMEMLPSA-SLVTVHLETGRTHQIRVHFSAMRHPCVGDSMYGADP 262

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
                + + ++ +LHA  +   HP  G R  + +  P  + +  D L   Y
Sbjct: 263 TLARRTGL-DRQWLHAVELSFEHPASGERFTVASEYPQDLQQALDVLRGDY 312


>gi|325067131|ref|ZP_08125804.1| pseudouridine synthase, RluA family protein [Actinomyces oris K20]
          Length = 306

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 77/293 (26%), Positives = 139/293 (47%), Gaps = 28/293 (9%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++ +  +G+VR   + +  ++R+++G+++ +          + + + ++      +  + 
Sbjct: 32  VEDLCEAGEVRRGGETLAKSSRLRAGELLEVD---------LPDPRPVEPVATPVEGME- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRL 150
               LLYED  I V +KPAG++     G     + G LK+    V + G   R  +  RL
Sbjct: 82  ----LLYEDEDIVVVDKPAGVAAHPSMGWDGPDVLGALKAMHVRVATSGAAERQGIVSRL 137

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+++VA+   A   L  +FR   + K+Y +LV G        I   + +  H   
Sbjct: 138 DVGTSGVMIVAKGERAYSVLKRAFREHTVDKVYHALVQGHLDPSSGTIDAPIGR--HPSR 195

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           ++   + +   G   +I+H+ VI+      C  E+   TGRTHQ+RVH   +G P VGD 
Sbjct: 196 EWKMAIIE---GGRESITHYDVIEAMPGA-CLAEIHLETGRTHQIRVHMAAVGHPCVGDA 251

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y A+   +  + +  + +LHAR + + HP  G  +  T+  P  +V   D L
Sbjct: 252 TYGADPAISARTGLIRQ-WLHARELGIAHPITGEHMVFTSDYPDDLVHALDVL 303


>gi|257466757|ref|ZP_05631068.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315917906|ref|ZP_07914146.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
 gi|313691781|gb|EFS28616.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 291

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 74/262 (28%), Positives = 135/262 (51%), Gaps = 16/262 (6%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE     +R+DR+ +  +P+++  ++ K LR+G+++V+ K+VK N R      ++     
Sbjct: 6   VEEKYIGVRIDRYLRKEFPNLSLGDIFKTLRTGKIKVNGKKVKENYRFLEEDRIQ----- 60

Query: 72  NALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
              N++  E+K   + ++L++     L+  + Y+D+ I VF K AG  +  GS   Y + 
Sbjct: 61  ---NYLQVEEKEKMTFIHLSQEEKKRLEDGIFYQDTDILVFYKKAGELMHKGSSHDYGLA 117

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +++  +  +     +RLD+ETSG+++  +     + L E+ + R I K Y+ ++ GI
Sbjct: 118 EQFQAYFQN--EDFHFVNRLDKETSGLVLGGKCLKIVRELAEAIKKRTIIKKYYIIIEGI 175

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P+     +  +L K    G + V   K  ++      + F VI    +++  LE    TG
Sbjct: 176 PEKNHFSLKTYLKK----GENKVLESKTAKEEYKECSASFSVIRK-NKEYSLLEAVLETG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKY 272
           RTHQLRV    +G PI+GD KY
Sbjct: 231 RTHQLRVQLAGIGFPILGDIKY 252


>gi|297170255|gb|ADI21292.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0010_09F21]
          Length = 305

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 89/331 (26%), Positives = 157/331 (47%), Gaps = 57/331 (17%)

Query: 15  DEENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK------FNNRIQSGQVVR 66
           DE N+  RLD +  +    I+   +Q+++  G V V+   VK       N++IQ   +++
Sbjct: 9   DEANINKRLDSFLSDILDDISRGLVQQLIEQGNVLVNDLEVKKNYKLRLNDQIQV--ILQ 66

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            P VI             D   N+          +++E+   Y+ NK AG++V  G+G  
Sbjct: 67  FPEVIE------------DEPQNIPLD-------IVFENEDFYIINKQAGLTVHPGAGQK 107

Query: 127 YH--IDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            +  ++G L   ++ K     +  + HRLD+ETSG++VVA+  ++   LT   + R I++
Sbjct: 108 DNTLLNGLL--HLNKKACELSRCGIVHRLDKETSGLMVVAKNHSSQTILTNLIKDRAIER 165

Query: 182 IYWSLVWGIPKNKKECIANWLLKKS---HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            Y++LV G        I+   + +    H     + +V Q  K +    +H+ V + + +
Sbjct: 166 KYYALVHG------NVISGGTIDEPIERHPKNRLIFIVDQEGKESK---THYLVKERY-E 215

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQ--NKL---YLH 291
            F  L+++  TGRTHQ+RVH  H+G PI GD +Y   +N+KG+    +   N L   +LH
Sbjct: 216 NFSLLDVKLETGRTHQIRVHLKHIGFPIAGDKQYTKISNWKGSSEKELNVINSLKGQFLH 275

Query: 292 ARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           A  +     +      +A LP ++      L
Sbjct: 276 AYSLAFLF-KNESFSFSAELPDYLTTVLKDL 305


>gi|294674059|ref|YP_003574675.1| RNA pseudouridine synthase family protein [Prevotella ruminicola
           23]
 gi|294471803|gb|ADE81192.1| RNA pseudouridine synthase family protein [Prevotella ruminicola
           23]
          Length = 277

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 65/216 (30%), Positives = 102/216 (47%), Gaps = 14/216 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           ++YED  + V  K  GI        + ++   L  +     QK    + HRLD++TSG++
Sbjct: 66  IVYEDKWLIVIEKAEGILSMAAGHSSLNVKTVLDDYFKKSRQKCTAHVVHRLDRDTSGLM 125

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+     Q L  ++      + Y ++  G  +N +  IANWL         YV     
Sbjct: 126 VYAKDMETEQILEHNWHDIVYDRRYVAVCSGEMENDEGTIANWLKDNKA----YVTYSSP 181

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            + G  YA++H+ V+D        +E +  TGR +Q+RVH+  MG P+ GD KY     G
Sbjct: 182 TDNGGKYAVTHYHVLD-RTTDHSLVEFKLETGRKNQIRVHSADMGHPVCGDPKY-----G 235

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           N   PI ++L LHA  +   HP  G  ++   P+P 
Sbjct: 236 NGDDPI-HRLCLHAWLLCFHHPVTGEPMEFETPVPT 270


>gi|309806639|ref|ZP_07700635.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
 gi|309810106|ref|ZP_07703952.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
 gi|312870915|ref|ZP_07731020.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
 gi|315653177|ref|ZP_07906102.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
 gi|308166944|gb|EFO69127.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
 gi|308169605|gb|EFO71652.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
 gi|311093605|gb|EFQ51944.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
 gi|315489542|gb|EFU79179.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
          Length = 292

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/279 (26%), Positives = 129/279 (46%), Gaps = 35/279 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKN-----HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           Y+ Y+ +  +E N  +D+  +N      + H  F+ ++K      + V+ K +  N ++ 
Sbjct: 13  YIYYLTISQNENNQNIDQIMRNLLIPRKWRH--FLRIEK-----NILVNNKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V NKPAG   Q
Sbjct: 66  TNDLITI-----KLNHVESLQQKYPASGNMPN--------IIYENDDVLVINKPAG---Q 109

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 110 KTHPNLYETDTALNDCASYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQK 239
           + Y++ +            N       IG D + + K+  +     AI+H++V+   A K
Sbjct: 170 RSYFAWIDATNDISDNGTINL-----PIGDDPLDMRKRMVRTDGLKAITHYQVVKKTANK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++ 
Sbjct: 225 IL-VKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQA 262


>gi|148825561|ref|YP_001290314.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae PittEE]
 gi|148715721|gb|ABQ97931.1| SfhB [Haemophilus influenzae PittEE]
          Length = 324

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 35/246 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPR--LTHR 149
           ++YED  I V NKP  + V  G+G         + YH             + PR  + HR
Sbjct: 85  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPI--------AEVPRAGIVHR 136

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++T+G++VVA+T  A   L    + R+I + Y ++  GI   K   +   +    H  
Sbjct: 137 LDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGI-MTKGGTVDQPM--DRHAT 193

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
              +  V    K A   ++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P++GD
Sbjct: 194 KRTLMAVHPMGKPA---VTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGD 249

Query: 270 HKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
             Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+  +
Sbjct: 250 QTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELLN 309

Query: 321 SLGFKY 326
           +L   Y
Sbjct: 310 ALKADY 315


>gi|255022986|ref|ZP_05294972.1| hypothetical protein LmonocyFSL_05005 [Listeria monocytogenes FSL
           J1-208]
          Length = 302

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 83/302 (27%), Positives = 142/302 (47%), Gaps = 51/302 (16%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQV----VRIPPVINALNHIIKEQKILDSSVNLTK 92
           +Q +L++G + V+ +  K N ++Q G      VR P          +E ++L   + L  
Sbjct: 32  IQLMLKNGDITVNGELAKPNYKVQVGDEIHYEVREP----------EELEVLAEDIPLD- 80

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQK 143
                   + +ED  + V NKP G+ V   +G A         +H D    S ++ K  +
Sbjct: 81  --------IYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL--SGINGK-IR 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    +
Sbjct: 130 PGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPI 188

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++      + VV+  ++    A +HF+V++     +  ++ +  TGRTHQ+RVH  ++G
Sbjct: 189 GRAKEDRQKMAVVRDGKE----ARTHFEVLERLP-GYTLIKCKLDTGRTHQIRVHLKYIG 243

Query: 264 CPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            P+ GD KY      KGN         +LHA  +   HP    R+   APLP    K   
Sbjct: 244 HPLAGDPKYGPKNTIKGNGQ-------FLHAAKLGFDHPTTNERMTFEAPLPNSFEKALK 296

Query: 321 SL 322
           SL
Sbjct: 297 SL 298


>gi|254775679|ref|ZP_05217195.1| hypothetical protein MaviaA2_13575 [Mycobacterium avium subsp.
           avium ATCC 25291]
          Length = 303

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 116/237 (48%), Gaps = 18/237 (7%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTH 148
           D     +LY D  I   +KPA ++     G     + G L +    + + G   R  + H
Sbjct: 72  DIEGMTILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRITTSGVPERQGIVH 131

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++VVA +  A   L  +F+ R + K Y +LV G P      I   + +  H 
Sbjct: 132 RLDVGTSGVMVVALSERAYTLLKRAFKQRTVDKRYHALVQGHPDPSSGTIDAPIGR--HR 189

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH--ALHMGCPI 266
           GG++   V ++ +   ++++H+  ++ F      L++   TGRTHQ+RVH  ALH  C  
Sbjct: 190 GGEWKFAVTKDGR---HSLTHYDTVEAFVAA-SLLDVHLETGRTHQIRVHFSALHHPC-- 243

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            GD  Y A+ K      +Q + +LHAR +   HP +G R++I +P P  +    D L
Sbjct: 244 CGDLVYGADPKLAKKLGLQRQ-WLHARSLSFAHPADGRRMEIVSPYPPDLQHALDVL 299


>gi|220917183|ref|YP_002492487.1| pseudouridine synthase [Anaeromyxobacter dehalogenans 2CP-1]
 gi|219955037|gb|ACL65421.1| pseudouridine synthase [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 241

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 111/230 (48%), Gaps = 20/230 (8%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED+ +   +KPAG + + G  G     +  L+  ++++  +  + HRLD+ TSG+LV
Sbjct: 11  VLHEDAHLLAVDKPAGRLVIPGRDGG----EPSLREELEARFGRLWVVHRLDRNTSGVLV 66

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQ 218
           +ART AA + L  +F     +K Y +LV G+P  ++   +A    +K  +          
Sbjct: 67  LARTAAAHRTLNLAFDRGEPRKRYLALVRGVPPAEQRIEVAIAPGRKGRM-----RAAAP 121

Query: 219 NEKGANYAISHFKVIDCFAQ------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++     + +  + +D F +          +E  P TGRTHQ+RVH    G P+  D  Y
Sbjct: 122 DDPRGKASATVVRRLDAFPRHPLGGGPLALVEALPETGRTHQIRVHLAAAGTPLAVDPAY 181

Query: 273 --CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
              A   G     +  +  LHA  + L HP  GR L + APLPA +  T 
Sbjct: 182 GDAAPLLGPGGEAVLARTPLHAARLALRHPADGRELVLEAPLPADLAGTL 231


>gi|258620374|ref|ZP_05715412.1| Ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           VM573]
 gi|262172216|ref|ZP_06039894.1| ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           MB-451]
 gi|258587253|gb|EEW11964.1| Ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           VM573]
 gi|261893292|gb|EEY39278.1| ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           MB-451]
          Length = 324

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 87/336 (25%), Positives = 153/336 (45%), Gaps = 43/336 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +   RLD+     +   +   L++ L  G++ V+ + V K   ++  G+V+    
Sbjct: 10  TVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVVTKPRTKVMGGEVI---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V+ A   +  EQ+     + L          ++YED  I V NKP    V  G+G A   
Sbjct: 66  VVQA--ELEDEQRWEAQDLPLN---------IVYEDDDIIVINKPRDFVVHPGAGQA--- 111

Query: 130 DGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG + + +        + PR  + HRLD++T+G++VVA+T  A   L  + + R + + Y
Sbjct: 112 DGTVLNALLFHFPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G         A  ++ K          +        +A++H++V + F ++   L
Sbjct: 172 EAIVIGT------MTAGGMIDKPIGRHSTKRTLMSVSPMGKHAVTHYRVAEHF-REHTRL 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYM 295
            ++  TGRTHQ+RVH  ++  P++GD  Y    +         T+ I+N  +  LHA  +
Sbjct: 225 RLRLETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGASEELTAMIRNFDRQALHAVML 284

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
              HP  G  L+  AP+P  MV    +L  + D  L
Sbjct: 285 KFEHPITGEELEFHAPVPDDMVTM--TLALREDSKL 318


>gi|282859371|ref|ZP_06268479.1| pseudouridine synthase, RluA family [Prevotella bivia JCVIHMP010]
 gi|282587856|gb|EFB93053.1| pseudouridine synthase, RluA family [Prevotella bivia JCVIHMP010]
          Length = 297

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 108/232 (46%), Gaps = 17/232 (7%)

Query: 87  SVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +++ +K +D  KS    L+YED  + V  K  GI   G    + ++   L  +     Q 
Sbjct: 69  AISKSKKNDQFKSRYVKLVYEDKYLVVVEKNVGILSMGAGHASLNVKKVLDDYFHKTKQN 128

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               + HRLD++TSG+++ A+     Q L   +      + Y +++ G   + +  IANW
Sbjct: 129 CTAHVVHRLDRDTSGLMIYAKDMQTEQLLEHDWHNIVYDRRYIAVLSGEMADDEGTIANW 188

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L         Y+      + G  YA++HF  ID        +E +  TGR +Q+RVHA  
Sbjct: 189 LKDNK----SYITYSSPVDNGGKYAVTHFFTIDRTVN-HSLVEFKLETGRKNQIRVHAAD 243

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           MG P+ GD KY     GN   PI  +L LHA  +   HP    R++   P+P
Sbjct: 244 MGHPVCGDIKY-----GNGDDPI-GRLCLHAFLLCFYHPVTHERMEFETPVP 289


>gi|254883850|ref|ZP_05256560.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           4_3_47FAA]
 gi|254836643|gb|EET16952.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           4_3_47FAA]
          Length = 538

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 74/230 (32%), Positives = 117/230 (50%), Gaps = 27/230 (11%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++  ++ ++ + L KH   +   ++YED+ + V NKPAG+    G G    ID   
Sbjct: 329 LGHMLQGLEVEENPL-LKKHYHEMPLEIVYEDNYLVVINKPAGMLSVPGKG---EIDSVY 384

Query: 134 KS----WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +     + D+ G  P + HRLD  TSG+L++A+ +   QHL   F+ R I+K Y +L+ G
Sbjct: 385 QHIKILYPDTTG--PLIVHRLDMATSGVLLIAKNKEVHQHLQAQFKNRMIKKRYIALLDG 442

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              +K+  I   +L       D    V  +E G   AI+ ++V++   +    +   P T
Sbjct: 443 KISSKEGTI---ILPLRMDPLDRPRQVVDHEHGKT-AITQYQVLN-EQEGNTLIAFYPLT 497

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           GRTHQLRVHA H   + CPI GD  Y             ++LYLHA  ++
Sbjct: 498 GRTHQLRVHAAHPEGLHCPIRGDELYGQK---------ADRLYLHAESLE 538


>gi|323345230|ref|ZP_08085453.1| ribosomal large subunit pseudouridine synthase D [Prevotella oralis
           ATCC 33269]
 gi|323093344|gb|EFZ35922.1| ribosomal large subunit pseudouridine synthase D [Prevotella oralis
           ATCC 33269]
          Length = 299

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 115/233 (49%), Gaps = 19/233 (8%)

Query: 87  SVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           SV+ +K ++ L+S    ++YED  + V  K  GI    G     ++   L  +  SKG++
Sbjct: 71  SVSKSKRNNNLQSKYVRIVYEDRFLVVVEKNIGILSMAGGHSTLNVKNILDDYF-SKGRQ 129

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                + HRLD++TSG++V  +    AQ L   +      + Y ++V G  ++ +  IAN
Sbjct: 130 HCTAHVVHRLDRDTSGLMVYTKDTQTAQLLESDWHDIVYDRRYVAVVSGEMEDDEGTIAN 189

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           WL         Y+      + G  YA++HF  +   A  +  +E +  TGR +Q+RVH+ 
Sbjct: 190 WLKDNK----SYISYSSPVDNGGKYAVTHFHTLQRTAD-YSLVEYKLETGRKNQIRVHSA 244

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            MG P+ GD KY     GN   P+ ++L LHA  +   HP    R++   P+P
Sbjct: 245 DMGHPVCGDIKY-----GNGDDPL-HRLCLHAYLLCFYHPVTHERMEFYTPIP 291


>gi|70731732|ref|YP_261474.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens Pf-5]
 gi|68346031|gb|AAY93637.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens Pf-5]
          Length = 211

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/214 (32%), Positives = 113/214 (52%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D+ + V NKP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   ILHQDAAVLVVNKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P+     I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPELDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ ++V++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEFGKHALTFWRVLE-RCGDWCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPQAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
              P   +L LHA  +   HP+ G RL+   P P
Sbjct: 180 AAWP---RLCLHASMLSFTHPQTGERLRFECPAP 210


>gi|312872184|ref|ZP_07732257.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
 gi|311092268|gb|EFQ50639.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
          Length = 292

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/279 (26%), Positives = 129/279 (46%), Gaps = 35/279 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKN-----HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           Y+ Y+ +  +E N  +D+  +N      + H  F+ ++K      + V+ K +  N ++ 
Sbjct: 13  YIYYLTISQNENNQNVDQIMRNLLIPRKWRH--FLRIEK-----NILVNNKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V NKPAG   Q
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENDDVLVINKPAG---Q 109

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 110 KTHPNLYETDTALNDCASYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLY 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQK 239
           + Y++ +            N       IG D + + K+  +     AI+H++V+   A K
Sbjct: 170 RSYFAWIEATNDISDNGTINL-----PIGDDPLDMRKRMVRADGLKAITHYQVVKKTANK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++ 
Sbjct: 225 IL-VKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQA 262


>gi|91788477|ref|YP_549429.1| ribosomal large subunit pseudouridine synthase D [Polaromonas sp.
           JS666]
 gi|91697702|gb|ABE44531.1| ribosomal large subunit pseudouridine synthase D [Polaromonas sp.
           JS666]
          Length = 344

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 81/340 (23%), Positives = 148/340 (43%), Gaps = 39/340 (11%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           S+   ++ V+V       RLDR      P  +   LQ+++ +  V+++ + V K + +++
Sbjct: 31  SVELELRRVMVPAGSHGARLDRALAGIVPEFSRSYLQQLIEAAVVQLNGRAVTKPSAKVK 90

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G            + +I E +    S      +  L   +++ED  + V +KPAG+ V 
Sbjct: 91  AG------------DELIIELRPTPQSQAFKPEAMALD--IVFEDPYLLVIDKPAGLVVH 136

Query: 121 GGSG--IAYHIDGFLK-----SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              G      ++G L      S++   G    + HRLD++TSG++VVAR R A   L   
Sbjct: 137 PAPGNWSGTLLNGLLARDPQASFLPRAG----IVHRLDKDTSGLMVVARQRQAMDQLVSM 192

Query: 174 FRMRRIQKIYWSLV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              R + + Y +L    W   + ++   A     ++ +    V + K   K A   IS  
Sbjct: 193 IAARSVSREYIALAHGAWQGARTREVSAAIGRDPRNRLRMAAVDLEKNAGKPALTVISLL 252

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           +      ++ C ++ + HTGRTHQ+RVH   +G P++ D  Y              +  L
Sbjct: 253 Q----NGERHCLVKCKLHTGRTHQIRVHMALLGHPLISDGLYGGAVAAGL-----ERQAL 303

Query: 291 HARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           HA  +   HP  G  ++  +P P  +      +G  Y+++
Sbjct: 304 HACRLAFEHPVTGAPMEFRSPPPPDLRAAIADVGLIYNQS 343


>gi|289422957|ref|ZP_06424779.1| ribosomal large subunit pseudouridine synthase D
           [Peptostreptococcus anaerobius 653-L]
 gi|289156637|gb|EFD05280.1| ribosomal large subunit pseudouridine synthase D
           [Peptostreptococcus anaerobius 653-L]
          Length = 307

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/239 (28%), Positives = 113/239 (47%), Gaps = 22/239 (9%)

Query: 94  SDF----LKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQ--KPRL 146
           SDF    L   +LYED  + V +KP  + V    S     +   L   +D +GQ  + R 
Sbjct: 74  SDFEGQDLNVRVLYEDFDLVVVDKPPFMVVHPTKSHYQNTLANHLSYHLDQEGQDVRVRF 133

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            +RLD  TSG+++VA+   A   L+     + ++K Y+++V G+P +K+  I   + +++
Sbjct: 134 VNRLDMNTSGLVIVAKNAYAHHKLSSDMSDKLVEKEYYAIVNGVPDHKEATIDQPIYRET 193

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                   + +  +     +I+H+ +I    DC       L +   TGRTHQ+RVH  ++
Sbjct: 194 EDS-----IKRIVDPRGQRSITHYSLIGSYKDCEGHLISLLRISLETGRTHQIRVHMDYI 248

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWD 320
           G PIV D  Y     G     +  +  LHAR +    P     +++ A LP  MV+  D
Sbjct: 249 GHPIVSDELY-----GQLQDNLIGRQALHARKLVFNQPRMKNEIELVADLPDDMVRLLD 302


>gi|159897698|ref|YP_001543945.1| pseudouridine synthase [Herpetosiphon aurantiacus ATCC 23779]
 gi|159890737|gb|ABX03817.1| pseudouridine synthase [Herpetosiphon aurantiacus ATCC 23779]
          Length = 312

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/225 (32%), Positives = 107/225 (47%), Gaps = 16/225 (7%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSG 156
           +L+ED  I V NKPA   SV        H++G L+ +    D +     L HRLD  TSG
Sbjct: 67  ILFEDEWILVLNKPAAWYSVATPWDTFGHLEGALQRFFLERDGEAVPFHLVHRLDHGTSG 126

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI-----ANWLLKKSHIGG 210
            L+V++  +        F   R+QK Y +L  G+P   K E +       + L   +   
Sbjct: 127 ALIVSKNPSLNSRFQRMFNEGRVQKTYLALCSGLPDWTKLEVVTGHSRGEFGLWSVYPAA 186

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +    ++    A + F V          L  + HTGRTHQ+R+HA H+G P+VGD 
Sbjct: 187 MIDQLYGPKDRRVRRAHTSFTV-QAVGNAAALLAARLHTGRTHQIRLHAKHIGHPLVGDQ 245

Query: 271 KYCANFK-GNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPA 313
           +Y    + GN + P Q    LHA ++  PHP  G  L++ AP+P+
Sbjct: 246 RYGGVTQFGNLSIPDQ---LLHAAWLQFPHPRYGSMLELIAPVPS 287


>gi|320531632|ref|ZP_08032574.1| pseudouridine synthase, RluA family [Actinomyces sp. oral taxon 171
           str. F0337]
 gi|320136161|gb|EFW28167.1| pseudouridine synthase, RluA family [Actinomyces sp. oral taxon 171
           str. F0337]
          Length = 306

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 110/229 (48%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           LLYED  I V +KPAG++     G     + G LK+    V + G   R  +  RLD  T
Sbjct: 82  LLYEDEDIVVVDKPAGVAAHPSMGWDGPDVLGALKAMRVRVATSGAAERQGIVSRLDVGT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA+   A   L  +FR   + K+Y +LV G        I   + +  H   ++  
Sbjct: 142 SGVMIVAKGERAYSVLKRAFREHTVDKVYHALVQGHLDPSSGTIEAPIGR--HPSREWKM 199

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + +   G   +I+H+ VI+      C  E+   TGRTHQ+RVH   +G P VGD  Y A
Sbjct: 200 AIIE---GGRESITHYDVIEAM-PGACLAEIHLETGRTHQIRVHMAAVGHPCVGDATYGA 255

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +      + +  + +LHAR + + HP  G  +  T+  PA +    D L
Sbjct: 256 DPAMTARTGLIRQ-WLHARELGIAHPITGEHMVFTSGYPADLTHALDVL 303


>gi|237729353|ref|ZP_04559834.1| ribosomal large subunit pseudouridine synthase A [Citrobacter sp.
           30_2]
 gi|226909082|gb|EEH95000.1| ribosomal large subunit pseudouridine synthase A [Citrobacter sp.
           30_2]
          Length = 219

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 63/178 (35%), Positives = 96/178 (53%), Gaps = 14/178 (7%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LDEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPAPAEGLVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               E G + A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 126 KVCYETGKS-AQTEYEVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYA 182


>gi|238921072|ref|YP_002934587.1| ribosomal large subunit pseudouridine synthase D [Edwardsiella
           ictaluri 93-146]
 gi|238870641|gb|ACR70352.1| ribosomal large subunit pseudouridine synthase D [Edwardsiella
           ictaluri 93-146]
          Length = 300

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 118/233 (50%), Gaps = 31/233 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +          PR  + HRLD++T
Sbjct: 60  IVYEDEDILVINKPRDLVVHPGAG---NPDGTVLNALLHHYPQIADVPRAGIVHRLDKDT 116

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G        +E IA    K++H+   
Sbjct: 117 TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGTMTAGGTVREPIARHPTKRTHMS-- 174

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 175 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHINHPLVGDPL 226

Query: 272 YCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           Y    +    +  +        ++  LHA  + L HP  G  ++  AP+P  M
Sbjct: 227 YGGRPRPPRDASPEFIRVLREFDRQALHATMLRLYHPISGIEMEWHAPIPDDM 279


>gi|325962959|ref|YP_004240865.1| ribosomal large subunit pseudouridine synthase D [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323469046|gb|ADX72731.1| ribosomal large subunit pseudouridine synthase D [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 308

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/219 (30%), Positives = 113/219 (51%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +L +D    V +KP G++     G +   + G L      + + G   R  + HRLD  T
Sbjct: 82  ILLDDEDFAVVDKPVGVAAHPSPGWVGPTVVGGLAGAGYRISTSGSPERAGIVHRLDVGT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA++  A   L  +F+ R + K+Y ++V G+P      I   + +  H G D+  
Sbjct: 142 SGVMVVAKSERAYTALKRAFKERSVDKVYHAVVQGLPDPVVGTIDAPIGR--HPGHDWRF 199

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V ++ +    +I+H++V++ F  K   +E+   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 200 AVIEDGR---PSITHYEVLEAFG-KASLVEVHLETGRTHQIRVHFSALRHPCAGDLTYGA 255

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           + +   T  +  + +LHAR +   HP  G R+++T+  P
Sbjct: 256 DPRLAATLGLTRQ-WLHARELGFDHPVTGERVRVTSDYP 293


>gi|311032387|ref|ZP_07710477.1| pseudouridine synthase, RluA family protein [Bacillus sp. m3-13]
          Length = 307

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/282 (26%), Positives = 128/282 (45%), Gaps = 35/282 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           L ++  S +V V+ +   + + ++ G  V +P +   +  I  E  I             
Sbjct: 33  LHELRMSKKVMVNGENPNWTHLLKEGDRVSVPILPEDITPIATEMDIK------------ 80

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKG--QKPRLTHRLDQE 153
               ++YE   + V NK AG+     S   +  +   +  + ++ G   K R  HRLDQ+
Sbjct: 81  ----IIYETEHLLVINKEAGMDTHPSSDQDFRSLSNGVAHYFNNNGISSKVRHIHRLDQD 136

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG ++ A+   +   L      R++++ Y +LV GI K  +  I         IG D  
Sbjct: 137 TSGAILFAKHAISGAILDRMLEERKVKRTYLALVEGIVKTPEGTIDKP------IGKDRH 190

Query: 214 HVVKQN-EKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           H  ++        AI+H+KV+  +  ++   +E+   TGRTHQ+RVH   +G PI GD  
Sbjct: 191 HASRRRVSPNGQKAITHYKVVKTYPKEQLTLVELTLDTGRTHQIRVHMSSIGHPIYGDKL 250

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
           Y +  K        ++  LHA  + +PHP  G +  + AP+P
Sbjct: 251 YGSKNK-------HHRHSLHAWKLTVPHPFNGEIVTVHAPVP 285


>gi|119470572|ref|ZP_01613275.1| pseudouridylate synthase [Alteromonadales bacterium TW-7]
 gi|119446273|gb|EAW27550.1| pseudouridylate synthase [Alteromonadales bacterium TW-7]
          Length = 209

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 65/202 (32%), Positives = 107/202 (52%), Gaps = 15/202 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  + + NKP+ +    G     H D  + + V+      R+ HRLD  TSGIL +
Sbjct: 7   ILFQDDDLLIVNKPSELLTVPGKD-PKHADSLI-NRVNRVFPTARIVHRLDMATSGILCL 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A  +AA +HL+  F+ R   K Y + V+G  +     +   L+       D+ +  KQ  
Sbjct: 65  AMNKAAHRHLSMQFQDRETAKRYIARVFGKLEQNNGSVDLPLI------CDWPNRPKQMV 118

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    +++HFKV++   +    +E+ P TGR+HQLRVH L +G PI+GD  Y A+ + 
Sbjct: 119 DHENGKPSLTHFKVLE-RDESATRVELTPITGRSHQLRVHMLSLGHPILGDRLY-AHKEA 176

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
              +P   +L LHA+ + L HP
Sbjct: 177 LAAAP---RLQLHAQMLQLKHP 195


>gi|119385528|ref|YP_916584.1| pseudouridylate synthase [Paracoccus denitrificans PD1222]
 gi|119375295|gb|ABL70888.1| ribosomal large subunit pseudouridine synthase A [Paracoccus
           denitrificans PD1222]
          Length = 215

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/220 (31%), Positives = 103/220 (46%), Gaps = 27/220 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           +++ D +I V  KPAG+    G G     D  ++     +G  P   L HRLD +TSG++
Sbjct: 14  VIHADHEILVVEKPAGLLSVPGRG-EDRADCLIERL---RGAFPTVLLVHRLDMDTSGVM 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYV 213
           V   T  A +HL+  F  RR +K Y + +WG  + K        I +W  +         
Sbjct: 70  VFGLTPHAQRHLSRQFEDRRTKKTYVARLWGRLEPKTGMVDLPLIVDWPNRPRQ------ 123

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              K +      A + ++V+     +   + + P TGR+HQLRVH   +G PI+GD  Y 
Sbjct: 124 ---KVDHAEGRPAQTEWRVVKATDAE-TRVRLMPITGRSHQLRVHMAQLGHPILGDPLYA 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
           A    +F      +L LHA  +   HPE G +Q  TAP P
Sbjct: 180 AGAAADFP-----RLMLHAESLRFKHPETGVMQSFTAPAP 214


>gi|254283218|ref|ZP_04958186.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium NOR51-B]
 gi|219679421|gb|EED35770.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium NOR51-B]
          Length = 319

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 86/321 (26%), Positives = 144/321 (44%), Gaps = 46/321 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             V  D    RLD+     +P  +   L+  ++ G++ VD   ++  +++          
Sbjct: 9   AAVPADLHGARLDQASAELFPDYSRSRLKTWIQEGKLTVDGVVLRPKDKV---------- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
              AL++ +  + I ++   +    + L   + YED  + V NKPAG+ V   +G   H 
Sbjct: 59  ---ALDNQL--ELIAEAEAEVAWSGESLPLDICYEDDDVIVVNKPAGLVVHPAAG---HP 110

Query: 130 DGFLKSWVDSKG----QKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G L + + +      Q+PR  + HRLD++TSG++ VA++  A + L      R + + Y
Sbjct: 111 TGTLVNALLAHAPELQQQPRGGIVHRLDKDTSGVMFVAKSHRAHRSLVTQLSARSVTREY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCW 242
            +L  G      + +A   + +  IG       K         AI+HF+V + F + F  
Sbjct: 171 AALCSG------QLVAGGTIDQP-IGRHPTARTKMAVVSDGKPAITHFRVANRF-EHFTQ 222

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----------YLHA 292
           L++   TGRTHQ+RVH      P+VGD  Y    +    + I ++L           LHA
Sbjct: 223 LQVNLETGRTHQIRVHMAWCRHPLVGDPVYGGRLR--IPAGISDRLKSALADFQRQALHA 280

Query: 293 RYMDLPHPEGG-RLQITAPLP 312
           R +   HP  G R+Q  A LP
Sbjct: 281 RSLGFDHPATGERMQFDANLP 301


>gi|313114073|ref|ZP_07799625.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310623482|gb|EFQ06885.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 310

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 82/325 (25%), Positives = 146/325 (44%), Gaps = 39/325 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIP 68
           VVE +    R+DR+       ++   LQ ++  G V  + + V  + ++++G   V+ IP
Sbjct: 7   VVEQETAGQRIDRFLSGEDTGLSRSALQALVADGHVLCNGRLVAKSLKLKAGDTIVLEIP 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
                     K  + +   + L          ++YED  + V NKP G+ V    G    
Sbjct: 67  DA--------KPIEAVPQDIPLE---------IVYEDEHLLVVNKPKGMVVHPAPGNPDG 109

Query: 125 -----IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                + +H  G L       G+ +P + HR+D++TSG+LVVA+  A    L++   +  
Sbjct: 110 TLVNALLWHCKGSLSGI---GGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHS 166

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           +++ Y ++V+G    + E      L +S      + V   +E    YA + ++V++    
Sbjct: 167 VERAYRTIVYG-GFAQDEGFVESNLGRSKTDRKKMAVYPASEPHTKYAYTGYQVLERL-N 224

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F  LE +  TGRTHQ+RVH   +  P+ GD  Y  +   N  + +  +  LHA+ +   
Sbjct: 225 NFTMLECRLKTGRTHQIRVHMASIQHPVAGDPVYGPH---NCITSLHGQC-LHAKTLGFV 280

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSL 322
           HP  G  L+  + LP +      +L
Sbjct: 281 HPITGEHLRFDSELPEYFTHFLATL 305


>gi|225013036|ref|ZP_03703452.1| pseudouridine synthase [Flavobacteria bacterium MS024-2A]
 gi|225002852|gb|EEG40832.1| pseudouridine synthase [Flavobacteria bacterium MS024-2A]
          Length = 227

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 64/210 (30%), Positives = 101/210 (48%), Gaps = 15/210 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           +K  +L+ED+ + + NK A   VQG       +   LK+++  K +KP      + HR+D
Sbjct: 3   IKERILFEDNHLIIVNKEAKELVQGDKTGDPTLADHLKAYIKVKYKKPGEVYLGIVHRID 62

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG++V  +T  A   L   F  R  +K YW++V      +K  + +W+ +       
Sbjct: 63  RPTSGVVVFTKTSKALARLNAQFEKRSPRKTYWAVVDKSFPTQKGNLTHWMTRNQKQNKS 122

Query: 212 YVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             H+   NE   +  A   +K I  F + +C LE+   TGR HQ+R     +G PI GD 
Sbjct: 123 KAHI---NEVPNSKIAKLSYKRIQEF-EHYCLLEVTLETGRHHQIRAQLSSLGFPIQGDL 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           KY A+      S     + LHAR + + HP
Sbjct: 179 KYGAD-----RSNKDGSISLHARKLQIEHP 203


>gi|237809510|ref|YP_002893950.1| pseudouridine synthase, RluA family [Tolumonas auensis DSM 9187]
 gi|237501771|gb|ACQ94364.1| pseudouridine synthase, RluA family [Tolumonas auensis DSM 9187]
          Length = 326

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 93/337 (27%), Positives = 153/337 (45%), Gaps = 59/337 (17%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPP 69
            +E   E  RLD+   + +   +   L++ +  G+V++D K       ++  GQ V I  
Sbjct: 10  TIEPHHEGKRLDQVLADLFTDYSRTRLKEWILGGKVQLDGKVCLLPKEKVMGGQQVEI-- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
               L    + Q   D  +N+           +YED  + V +KPAG+ V  G+G     
Sbjct: 68  -ATELEDDTRWQA-QDLPLNI-----------VYEDEHLLVIDKPAGLVVHPGAGTPDGT 114

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L  + D   + PR  + HRLD+ET+G++VVA+T  A   L  + + RRI + Y +
Sbjct: 115 VLNALLHRYPDI-AEVPRAGIVHRLDKETTGLMVVAKTIPAQIRLVYALQKRRITREYEA 173

Query: 186 LVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQK 239
           +V G         E I+    +++        ++  N  G   AI+H++V + F    + 
Sbjct: 174 IVVGHMTAGGTVDEPISRHSTQRT--------MMAVNPMG-KPAITHYRVAERFRAHTRL 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------------- 286
            C LE    TGRTHQ+RVH  H+   +VGD  Y    +     PI+N             
Sbjct: 225 RCRLE----TGRTHQIRVHMAHINHALVGDPVYGGRLR-----PIRNASVELSDFLRTFR 275

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +  LHA  + L HP  G  ++  +P+P  MV+  + L
Sbjct: 276 RQALHATMLRLTHPITGEEMEWHSPIPDDMVQLIEVL 312


>gi|69244119|ref|ZP_00602655.1| Pseudouridine synthase, RluD [Enterococcus faecium DO]
 gi|257880479|ref|ZP_05660132.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257883291|ref|ZP_05662944.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257894567|ref|ZP_05674220.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|258614127|ref|ZP_05711897.1| RNA pseudouridylate synthase [Enterococcus faecium DO]
 gi|260562478|ref|ZP_05832988.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|293559878|ref|ZP_06676390.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1162]
 gi|293568196|ref|ZP_06679530.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1071]
 gi|294617460|ref|ZP_06697092.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1679]
 gi|294620663|ref|ZP_06699873.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium U0317]
 gi|68196576|gb|EAN11002.1| Pseudouridine synthase, RluD [Enterococcus faecium DO]
 gi|257814707|gb|EEV43465.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257818949|gb|EEV46277.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257830946|gb|EEV57553.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|260073163|gb|EEW61508.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|291589096|gb|EFF20910.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1071]
 gi|291596267|gb|EFF27528.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1679]
 gi|291599760|gb|EFF30767.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium U0317]
 gi|291606150|gb|EFF35572.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1162]
          Length = 285

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/206 (33%), Positives = 102/206 (49%), Gaps = 25/206 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+            +   L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A+       L      + I + Y ++VWG        IA  +   + IG D     K+ 
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWG-------EIAKDMTITNKIGRDRHDRRKRV 195

Query: 219 -NEKGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            ++K    A++H    KV+    Q +C LE    TGRTHQ+RVH  H G PIVGD  Y  
Sbjct: 196 VDDKNGQSALTHVTVNKVLSEQTQVYCVLE----TGRTHQIRVHLAHKGHPIVGDPLY-- 249

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
               N T+    +L LHA  + + HP
Sbjct: 250 ---QNRTA---ERLMLHALELHMIHP 269


>gi|86158289|ref|YP_465074.1| ribosomal large subunit pseudouridine synthase A [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|85774800|gb|ABC81637.1| ribosomal large subunit pseudouridine synthase A [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 241

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 108/226 (47%), Gaps = 18/226 (7%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED+ +   +KPAG + + G  G     +  L+  ++++  +  + HRLD+ TSG+LV
Sbjct: 11  VLHEDAALLAVDKPAGRLVIPGREGG----EPSLREELEARFGRLWVVHRLDRNTSGVLV 66

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQ 218
           +ART AA + L  +F     +K Y +LV G+P  ++   +A    +K    G        
Sbjct: 67  LARTAAAHRALNLAFDRGEPRKRYLALVRGVPPAEQRIEVAIAPARK----GRMRPAAPD 122

Query: 219 NEKGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY- 272
           + +G   A     +  +            +E  P TGRTHQ+RVH    G P+  D  Y 
Sbjct: 123 DPRGKPSATVVRRLEAYPSHPLGGGPLALVEALPETGRTHQIRVHLAAAGTPLALDPAYG 182

Query: 273 -CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
             A   G    P+  +  LHA  + L HP  GR L + APLPA + 
Sbjct: 183 DAAPLLGPGGEPVLARTPLHAARLALRHPADGRELVLEAPLPADLA 228


>gi|227357295|ref|ZP_03841652.1| ribosomal large subunit pseudouridine synthase A [Proteus mirabilis
           ATCC 29906]
 gi|227162558|gb|EEI47547.1| ribosomal large subunit pseudouridine synthase A [Proteus mirabilis
           ATCC 29906]
          Length = 217

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/203 (32%), Positives = 110/203 (54%), Gaps = 17/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G  + +H D  + S + +        HRLD  TSG++VV
Sbjct: 15  VLYQDEHIIVVNKPSGLLSVPGKALEHH-DSIM-SRIKADFPDAESVHRLDMATSGVMVV 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A  +AA + L   FR R  +K Y + VWG  +  +  +   L+       D+ +  KQ  
Sbjct: 73  ALNKAAERELKRQFREREPKKTYIARVWGKLEKPQGLVDLPLI------CDWPNRPKQKV 126

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E G + A + ++V++ + +    +++ P TGR+HQLRVH L +G PI+GD ++ A+ +
Sbjct: 127 CYETGKS-AQTFYEVLE-YEENATRVKLSPITGRSHQLRVHMLALGHPILGD-RFYAHPQ 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               +P   +L LHA+ + + HP
Sbjct: 184 ARALAP---RLQLHAQELFITHP 203


>gi|291383615|ref|XP_002708351.1| PREDICTED: RNA pseudouridylate synthase domain containing 4
           [Oryctolagus cuniculus]
          Length = 367

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 145/321 (45%), Gaps = 51/321 (15%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           ++R  K+  K   R+ +       PV   +  +++  + L   V+    +  L   +L++
Sbjct: 49  KLRAQKREEKLKERVPTN------PVQRRVRELVRFTQQLQR-VHPNVLAKALSRGILHQ 101

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGILVV 160
           D  + V +KP G+ V GG G+   I   L    K     K +   L HRLD+ET+G++V+
Sbjct: 102 DKDLVVISKPYGLPVHGGPGVRLCISDVLPILAKMLRGHKAEPLHLCHRLDKETTGVMVL 161

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG----------- 209
              +  A  + E FR R++ K YW++   +P      +   +++K   G           
Sbjct: 162 TWEKEVAHQVQELFRTRQVVKKYWAITVHVPVPSAGVVDIPIIEKEVQGQRQHHKMTLSP 221

Query: 210 ------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHM 262
                 G  V V  ++ + A+ A++ ++V+         LE+QP TG  HQLRVH +  +
Sbjct: 222 SYRMDNGKMVKV--RSSRSAHLAVTQYQVLS-STLSSALLELQPITGIKHQLRVHLSFGL 278

Query: 263 GCPIVGDHKYC-------ANFKGNFTSPI---QNK-----LYLHARYMDLPHPEGGR--- 304
            CPI+GDHKY            G     +   Q+K     L+LHAR + LP   G R   
Sbjct: 279 ECPILGDHKYSDWNRLAPQKLPGGTLKKLGLEQSKARHIPLHLHARQLILP-ALGSRKEE 337

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L +T  LP   V++   LG +
Sbjct: 338 LNLTCKLPHFFVRSLSRLGLE 358


>gi|114763109|ref|ZP_01442535.1| ribosomal large subunit pseudouridine synthase D [Pelagibaca
           bermudensis HTCC2601]
 gi|114544162|gb|EAU47171.1| ribosomal large subunit pseudouridine synthase D [Roseovarius sp.
           HTCC2601]
          Length = 343

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 95/363 (26%), Positives = 150/363 (41%), Gaps = 81/363 (22%)

Query: 11  VVENDEENMRLDRWFKNHYPH---INFVNLQKIL------RSGQVRVDKK-RVKFNNRIQ 60
           ++  +    RLD+      P    ++   L K++      R G+V  D K +V   + I 
Sbjct: 7   IIIGEAPPARLDKALARDVPEAAALSRTRLAKLIAEGAVTRGGEVLSDPKVKVAEGDEI- 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
              V+ +P      +HI  E   LD               +++ED  + V NKPAG+ V 
Sbjct: 66  ---VIAVPQAEE--SHIGPEDIPLD---------------IVWEDDDLVVVNKPAGMVVH 105

Query: 121 GGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
              G         + +H  G L S V     +P + HR+D++TSG+LVVA++  A   L 
Sbjct: 106 PAPGTPTGTLVNALLHHFGGKL-SGVGGV-ARPGIVHRIDKDTSGLLVVAKSDRAHHGLA 163

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKE----------------CIANWLLKKSHIGGDYVHV 215
             F      + Y ++ +G+P                     CI + L +  H        
Sbjct: 164 AQFEAHSADRAYRAICYGVPNQGDPRLLGTRGVSVEPGGVLCIQSGLAR--HKTDRQRQA 221

Query: 216 VKQNEKGANYAISHFKVIDCFAQ--KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           V  + +G  +A++  +V++ F        LE +  TGRTHQ+RVH  H G  +VGD  Y 
Sbjct: 222 VFFDGQG-RHAVTRARVLESFGAPPAMALLECRLETGRTHQIRVHMAHAGHGLVGDPVY- 279

Query: 274 ANFKGNFTSPIQ-------------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
               G    P++             ++  LHA  +   HP  G RL+  APLPA M    
Sbjct: 280 ---GGRRKPPVKAIGEAVATEVAGFDRQALHAAELGFDHPATGERLRFEAPLPADMQSLL 336

Query: 320 DSL 322
           ++L
Sbjct: 337 EAL 339


>gi|85058407|ref|YP_454109.1| ribosomal large subunit pseudouridine synthase A [Sodalis
           glossinidius str. 'morsitans']
 gi|84778927|dbj|BAE73704.1| ribosomal large subunit pseudouridine synthase A [Sodalis
           glossinidius str. 'morsitans']
          Length = 217

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/206 (33%), Positives = 107/206 (51%), Gaps = 16/206 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D+ I   NKP+G+ SV G +    H D  + + + +   +    HRLD  TSG+LV
Sbjct: 14  ILYQDTHIMAVNKPSGLLSVPGRA--PEHRDSVM-TRIQANFPQAESVHRLDMATSGVLV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + V+G P   +  I   L+       D+ +  +Q 
Sbjct: 71  VALTKAAERELKRQFREREPRKTYIASVYGHPACDEGDIDLPLI------CDWPNRPRQK 124

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A++H++V+         + + P TGR+HQLRVH   +G PI+GD  Y A  +
Sbjct: 125 VCFGTGKAALTHYEVLSRDPDGSARVRLTPMTGRSHQLRVHIQSLGHPILGDGFY-ATPE 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
               +P   +L LHA+ + + HP+ G
Sbjct: 184 AKAMAP---RLLLHAQTLAITHPQYG 206


>gi|58038975|ref|YP_190939.1| ribosomal large subunit pseudouridine synthase D [Gluconobacter
           oxydans 621H]
 gi|58001389|gb|AAW60283.1| Ribosomal large subunit pseudouridine synthase D [Gluconobacter
           oxydans 621H]
          Length = 322

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 74/280 (26%), Positives = 124/280 (44%), Gaps = 46/280 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ--VVR 66
           +VV+      R DR   +    ++   ++ ++ SG + V+ K V +    ++ G   V+ 
Sbjct: 10  LVVDASTAGQRADRALADAIGTVSRSRVKALIESGNLSVNGKTVCEPAETLRDGMEMVLT 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
            P    A    + EQ  L+               +LYED  + V +K AG+      G  
Sbjct: 70  FPAPTPA--RPVAEQIPLN---------------ILYEDDDLIVLDKQAGLVTHPAPGNE 112

Query: 125 IAYHIDGFL-----KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  L             ++P + HRLD++TSG++VVA+T      L+E+F  R I
Sbjct: 113 TGTLVNALLGHCGEGFEGIGGEKRPGIVHRLDKDTSGLMVVAKTAMVHNALSEAFAARDI 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------GANYAISHFKV 232
            + Y +L WG+   + E           IG D     K++ K       G   A++ FK+
Sbjct: 173 DRAYLALAWGLLPAEGEF-------DGSIGRD-----KRDRKRMAVVGSGGKVALTRFKL 220

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           I+ +      +E +  TGRTHQ+RVH  + G P++GD  Y
Sbjct: 221 IEPYQAAVSLIECRLATGRTHQIRVHLSNAGHPLLGDPVY 260


>gi|56807621|ref|ZP_00365521.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Streptococcus
           pyogenes M49 591]
          Length = 218

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/215 (31%), Positives = 108/215 (50%), Gaps = 27/215 (12%)

Query: 104 EDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ED  + + NKP G+ V    G         + YHI     S ++    +P + HR+D++T
Sbjct: 1   EDDTLAIINKPQGMVVHPSVGHPSGTMVNALMYHIKDL--SSINGV-VRPGIVHRIDKDT 57

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+VA+T AA Q L E  + ++  + Y ++V G   N +  I      ++ IG     
Sbjct: 58  SGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMI------EAPIGRSEKD 111

Query: 215 VVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y
Sbjct: 112 RKKQAVTAKGKE-AVTRFTVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGDPLY 169

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
                G   +   +  +LHA+ + L HP  G+  I
Sbjct: 170 -----GPRKTLSGHGQFLHAKTLGLTHPMTGKEMI 199


>gi|197286175|ref|YP_002152047.1| ribosomal large subunit pseudouridine synthase A [Proteus mirabilis
           HI4320]
 gi|194683662|emb|CAR44607.1| ribosomal large subunit pseudouridine synthase A [Proteus mirabilis
           HI4320]
          Length = 216

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/203 (32%), Positives = 110/203 (54%), Gaps = 17/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G  + +H D  + S + +        HRLD  TSG++VV
Sbjct: 14  VLYQDEHIIVVNKPSGLLSVPGKALEHH-DSIM-SRIKADFPDAESVHRLDMATSGVMVV 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A  +AA + L   FR R  +K Y + VWG  +  +  +   L+       D+ +  KQ  
Sbjct: 72  ALNKAAERELKRQFREREPKKTYIARVWGKLEKPQGLVDLPLI------CDWPNRPKQKV 125

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E G + A + ++V++ + +    +++ P TGR+HQLRVH L +G PI+GD ++ A+ +
Sbjct: 126 CYETGKS-AQTFYEVLE-YEENATRVKLSPITGRSHQLRVHMLALGHPILGD-RFYAHPQ 182

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               +P   +L LHA+ + + HP
Sbjct: 183 ARALAP---RLQLHAQELFITHP 202


>gi|307293297|ref|ZP_07573143.1| pseudouridine synthase [Sphingobium chlorophenolicum L-1]
 gi|306881363|gb|EFN12579.1| pseudouridine synthase [Sphingobium chlorophenolicum L-1]
          Length = 225

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/227 (29%), Positives = 110/227 (48%), Gaps = 22/227 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D +  + +KPAG+ V      +  ++  L S      + P   HRLD++TSG L++
Sbjct: 8   VLFIDGEAIILDKPAGLPVDAPRDGSLALENHLSSLTFGFQRWPLPVHRLDRDTSGCLLL 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR   A +  + +F    + K Y ++V G+P  +   I   L K S     +  +  +  
Sbjct: 68  ARNPKAHKRFSAAFEAGTVAKRYVAVVDGVPAEESSVIELALKKISTQAQGWRMIPARAG 127

Query: 221 KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK 277
           K    AI+ ++ I   A+K     +   P TGRTHQ+R HALH +G  IVGD  Y +   
Sbjct: 128 KA---AITEWRKI---AEKDGRALVVFTPRTGRTHQIRTHALHGLGFGIVGDPVYGSG-- 179

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
                     + LH+R++ +P  E    + TAPLP    +T+ + GF
Sbjct: 180 -------DGPMLLHSRFLSIPRGEKAPAEATAPLP----ETFAAAGF 215


>gi|307944492|ref|ZP_07659832.1| pseudouridine synthase A [Roseibium sp. TrichSKD4]
 gi|307772241|gb|EFO31462.1| pseudouridine synthase A [Roseibium sp. TrichSKD4]
          Length = 223

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/223 (33%), Positives = 116/223 (52%), Gaps = 32/223 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQK----PRLTHRLDQETS 155
           +L+ D  I V NKP+G+ SV G +  A H D      V+ + Q+     R+ HRLD +TS
Sbjct: 21  VLHVDQDILVVNKPSGLLSVPGKA--AEHAD-----CVEQRAQEQFPDARIVHRLDLDTS 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA-----NWLLKKSHIGG 210
           G+ V+A  R A +HL   F  R+  K Y + V G+P  +K  +      +W  +   +  
Sbjct: 74  GVFVLAMNREAHRHLGLQFERRKTSKTYVARVSGVPVTEKGRVTLPLRCDWPNRPKQM-- 131

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               V  ++ K A+   + ++V++    K   L + P TGR+HQLRVH L +G PI+GD 
Sbjct: 132 ----VCFEHGKAAH---TDWQVME-HDLKTAKLRLIPITGRSHQLRVHLLAIGHPILGDR 183

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y    +G+  +   ++L LHA+ + L HP  G R+  T P P
Sbjct: 184 FYA---QGDALT-ASDRLLLHAQTLTLHHPSNGERVTFTVPCP 222


>gi|82750802|ref|YP_416543.1| hypothetical protein SAB1061 [Staphylococcus aureus RF122]
 gi|82656333|emb|CAI80750.1| conserved hypothetical protein [Staphylococcus aureus RF122]
          Length = 305

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 85/327 (25%), Positives = 150/327 (45%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +     
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYK----- 55

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++   I      + E  IL  ++NL          + YED  + V  KP G+ V    
Sbjct: 56  -VKLNDHIVVTEKEVVEADILPENLNLD---------IYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +   K+     G+ +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRELVEQLMDK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAP--IGRNKNDRQSMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQA-----LHAGLIG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G  ++  A LP       D++
Sbjct: 274 FEHPVTGEYIERHAELPQDFEDLLDTI 300


>gi|332557842|ref|ZP_08412164.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides WS8N]
 gi|332275554|gb|EGJ20869.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides WS8N]
          Length = 349

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 84/333 (25%), Positives = 140/333 (42%), Gaps = 52/333 (15%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L K++  G VR++   V     ++  GQV  I        
Sbjct: 22  RLDKALVREAPEEAALSRSRLMKLIGEGAVRLEGAPVTDPKAKVAEGQVYEI-------- 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                   LD+   +    + +   +++ED  + V +KP G+ V    G      ++  L
Sbjct: 74  -------ALDAPAEVEARPEAIPLSVVWEDEDLIVIDKPVGMVVHPAPGQWTGTLVNALL 126

Query: 134 ----KSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               +S     G+K P + HR+D++TSG+LVVA+T  A Q L   F    +++ Y +LV 
Sbjct: 127 HHCGESLSGIGGEKRPGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRYLALVH 186

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVV---------KQNE----KGANYAISHFKVIDC 235
           G+P+     +   +   S   G  + +          +Q +    +G  +A++  ++++ 
Sbjct: 187 GVPEVSDPRL-RGVRGTSFEPGGVLRIATGLARHRTDRQRQAVTFEGGRHAVTRARLLER 245

Query: 236 FAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQN----- 286
           F        +E +  TGRTHQ+RVH  H G  ++GD  Y    K       P        
Sbjct: 246 FGMPSVLALVECRLETGRTHQIRVHMAHAGHGLIGDQTYGGRRKLSPKALGPEAAAAAEA 305

Query: 287 --KLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
             +  LHA  +   HP  G  L    PLPA M 
Sbjct: 306 FPRQALHAASLGFRHPVSGEELSFERPLPADMA 338


>gi|15828769|ref|NP_326129.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Mycoplasma pulmonis UAB
           CTIP]
 gi|14089712|emb|CAC13471.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE D (PSEUDOURIDYLATE
           SYNTHASE) (URACIL HYDROLYASE) [Mycoplasma pulmonis]
          Length = 296

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/266 (28%), Positives = 125/266 (46%), Gaps = 31/266 (11%)

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+V++ P  I   +  I+  K++D +++L      L   ++YED  + V NKP+G+ V 
Sbjct: 39  NGKVIQKPNFILKPDAEIEVIKVIDKTIDLKPEKMDLD--IVYEDEHLIVINKPSGLVVH 96

Query: 121 GG---------SGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHL 170
                      +G+ YH     K+  +  G  +P + HR+D++TSG+L++A+T    Q L
Sbjct: 97  PAPGHYSQTLVNGLIYH----FKNLSNENGLLRPGIVHRIDKDTSGLLIIAKTNQVHQLL 152

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            +  +   I++ Y ++V G  +NK   + N  + +S      + +   N K    AI+H 
Sbjct: 153 AKMLKNHEIKRSYIAIVEGFFENKIVHL-NLPIGRSQKDRKKMEITNNNSKN---AITHV 208

Query: 231 KVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            +I  F    Q    +E Q  TGRTHQ+RVH  +   P+  D  Y  +F           
Sbjct: 209 YLIKQFYYEKQPLSLVECQLETGRTHQIRVHLNYFKHPVWNDPLYGKSFSDYGQ------ 262

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLP 312
            YLHA  +   HP     L    P+P
Sbjct: 263 -YLHAYKLFFVHPITNQELTFEIPMP 287


>gi|257886368|ref|ZP_05666021.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257822224|gb|EEV49354.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
          Length = 285

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/206 (33%), Positives = 102/206 (49%), Gaps = 25/206 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+            +   L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A+       L      + I + Y ++VWG        IA  +   + IG D     K+ 
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWG-------EIAKDMTITNKIGRDRHDRRKRV 195

Query: 219 -NEKGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            ++K    A++H    KV+    Q +C LE    TGRTHQ+RVH  H G PIVGD  Y  
Sbjct: 196 VDDKNGQSALTHVTVNKVLSEQTQVYCVLE----TGRTHQIRVHLAHKGHPIVGDPLY-- 249

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
               N T+    +L LHA  + + HP
Sbjct: 250 ---QNRTA---ERLMLHALELHMIHP 269


>gi|163841219|ref|YP_001625624.1| ribosomal large subunit pseudouridine synthase D [Renibacterium
           salmoninarum ATCC 33209]
 gi|162954695|gb|ABY24210.1| ribosomal large subunit pseudouridine synthase D [Renibacterium
           salmoninarum ATCC 33209]
          Length = 308

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 63/213 (29%), Positives = 113/213 (53%), Gaps = 14/213 (6%)

Query: 110 VFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVART 163
           V +KP G++     G +   + G L +    + + G   R  + HRLD  TSG++VVA+T
Sbjct: 94  VIDKPVGVAAHPSPGWVGPTVVGALAAAGYRISTSGAAERAGIVHRLDVGTSGVMVVAKT 153

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
             A   L  +F+ R + K+Y+++V G+P   +  +   + +  H G D+   V ++ +  
Sbjct: 154 EQAYTVLKRAFKERTVNKVYYAVVQGLPDPLRGTVDAPIGR--HPGHDWRFAVIEDGR-- 209

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
             +++H++V++ F  K   LE+   TGRTHQ+RVH   +  P VGD  Y A+ K      
Sbjct: 210 -PSVTHYEVLEAFG-KASLLEVHLETGRTHQIRVHFSALNHPCVGDLTYGADPKLAAELG 267

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           +  + +LHA+ +   HP  G  +++++  PA +
Sbjct: 268 LTRQ-WLHAKSLGFDHPVTGEWVEVSSEYPADL 299


>gi|85710030|ref|ZP_01041095.1| pseudouridylate synthase [Erythrobacter sp. NAP1]
 gi|85688740|gb|EAQ28744.1| pseudouridylate synthase [Erythrobacter sp. NAP1]
          Length = 234

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/225 (31%), Positives = 107/225 (47%), Gaps = 26/225 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHID----GFLKSWVDSKGQKPRLTHRLDQ 152
           ++YED +  V +KPAG+ V    +GG  +  HI+    GF +  V          HRLD 
Sbjct: 5   IIYEDGEALVIDKPAGLPVDRPKRGGPALFDHIEQLKLGFQRPPVP--------VHRLDT 56

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG L++AR   A +   ++F  R + K Y +++   P      I   L K S     +
Sbjct: 57  DTSGCLLLARNPKALKRFNKAFEDRLVGKTYLAVIDFEPSESSGTIELSLSKISSAEKGW 116

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALH-MGCPIVG 268
             +  +  K    AISH+++I+   +   K   +  +P TGRTHQLRVHAL  +G P++G
Sbjct: 117 RMIAARKGK---PAISHWELIETIGEGDKKRSLIRFRPETGRTHQLRVHALQGLGAPLLG 173

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           D  Y      N  +P   +  LHA  + +       +   AP PA
Sbjct: 174 DPVYGPVRGQNKGAP---RTMLHAETISVKREGKNTIFAHAPFPA 215


>gi|323448015|gb|EGB03919.1| hypothetical protein AURANDRAFT_33292 [Aureococcus anophagefferens]
          Length = 259

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 67/247 (27%), Positives = 119/247 (48%), Gaps = 20/247 (8%)

Query: 90  LTKHSDFLKSI-------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +T+H  FL +              +++ED ++ V +K +G+    G G  +  D  +   
Sbjct: 14  VTRHRTFLAATADDGSTRPWATFRVVFEDDEVIVCDKGSGLLAVPGRG-DHKQDSLITRL 72

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             ++G    L HRLD++TSG++V A+T+ A + L+ +F  R ++K Y   V G P+    
Sbjct: 73  RATRGASTTLAHRLDRDTSGLVVAAKTKRALRSLSMAFEAREVEKSYVGAVLGWPEATFG 132

Query: 197 CIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
            +   + K K+  G + V VV + + G   + +++ +++        L +QP TGR+ QL
Sbjct: 133 TVDEPIGKVKTDAGHNRVAVVAEAD-GGRRSRTNWALLEKRDDGSSLLSLQPVTGRSQQL 191

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           RVH   +G P++GD  +    +    +P   +L LHA  + L  P  G +   A  P   
Sbjct: 192 RVHCALIGLPLLGDALH-GTEEAAGRAP---RLCLHAARLSLDLPTAGPMTFEAEAPFAA 247

Query: 316 VKTWDSL 322
              + SL
Sbjct: 248 SADYASL 254


>gi|322389492|ref|ZP_08063043.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 903]
 gi|321143767|gb|EFX39194.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 903]
          Length = 297

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/218 (30%), Positives = 108/218 (49%), Gaps = 18/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           +L+ED    V NKP GI+    +  +  +  F+K +   +G   Q+  +  RLD++TSG+
Sbjct: 78  ILFEDDHFLVLNKPFGIASIPSAIHSNTLANFVKGYYVKQGYENQQVHIVTRLDKDTSGV 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + IQK Y++LV G  K     E IA     +  I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQSKTIQKRYYALVKGSGKLDPVGEIIAPIARDEDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  KG  YA + ++V+  F      +++Q HTGRTHQ+RVH  H+G P++GD  Y  +
Sbjct: 192 TRKVAKGGKYAHTSYQVVQSFGD-IHLVDIQLHTGRTHQIRVHFSHIGFPLLGDDLYGGS 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            +         +  LH   +   HP     L I +PLP
Sbjct: 251 LEDGI-----ERQALHCHRLSYYHPFLEEELVIESPLP 283


>gi|218442079|ref|YP_002380408.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
 gi|218174807|gb|ACK73540.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7424]
          Length = 308

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 83/271 (30%), Positives = 122/271 (45%), Gaps = 19/271 (7%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
            RI SGQV+      N    +I  QK+        + S  L   LLY DS + V  KPAG
Sbjct: 43  ERITSGQVLLDGHSCNPHTRLITGQKLAYHRPPWEEPSAPLNFDLLYSDSDVLVVAKPAG 102

Query: 117 ISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           + +  G G   H + G LK         P   HRL + TSG++++AR+  A   L+E  R
Sbjct: 103 LPILPGGGFVEHTLLGQLKQHYPE--DTPFPIHRLGRGTSGLVLLARSSFARGFLSEQMR 160

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R+I KIY +L+          I   + K  H    Y+     N K    A+S  +V+  
Sbjct: 161 SRQISKIYRALIPKSDLTDHFTINQPIGKIPHPVLGYIFGATPNGKD---ALSECRVLKR 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-------- 287
            ++    +E++  TGR HQ+R+H   +G P++GD  Y         +PI  +        
Sbjct: 218 TSET-TLVEVKILTGRPHQIRIHLAAIGYPLIGDPLYTMGGIPKIQTPITPEKLPVPGDC 276

Query: 288 -LYLHARYM--DLPHPEGGRLQITAPLPAHM 315
             YLHA  +  +LPH E   L +T P P  +
Sbjct: 277 GYYLHAYQLTFNLPHRE-SPLTVTCPPPREL 306


>gi|325270275|ref|ZP_08136882.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           multiformis DSM 16608]
 gi|324987576|gb|EGC19552.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           multiformis DSM 16608]
          Length = 296

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 112/233 (48%), Gaps = 17/233 (7%)

Query: 87  SVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           SV+ +K +D  +S    ++YED  + V  K  GI        + ++   L  +     QK
Sbjct: 68  SVSKSKKNDQFRSRYVKIIYEDRFLVVVEKNTGILSMAAGHASLNVKTVLDDYFRMTRQK 127

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               + HRLD++TSG+++ A+     Q L   +      + Y ++V G  + ++  +ANW
Sbjct: 128 CTAHVVHRLDRDTSGLMIYAKDMQTEQLLERDWHNIVYDRRYIAVVSGEMEQEEGTVANW 187

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L         YV      + G  YA++HF+V+D        +E +  TGR +Q+RVH+  
Sbjct: 188 LKDNK----AYVTYSSPVDNGGKYAVTHFRVLD-RTVAHSLVEYRLETGRKNQIRVHSAD 242

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           MG P+ GD KY     GN   P+ ++L LHA  +   HP    R++   P+P 
Sbjct: 243 MGHPVCGDVKY-----GNGDDPL-HRLCLHAYVLCFYHPVNHQRMEFETPVPT 289


>gi|218265033|ref|ZP_03478645.1| hypothetical protein PRABACTJOHN_04355 [Parabacteroides johnsonii
           DSM 18315]
 gi|218221638|gb|EEC94288.1| hypothetical protein PRABACTJOHN_04355 [Parabacteroides johnsonii
           DSM 18315]
          Length = 359

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 87/338 (25%), Positives = 152/338 (44%), Gaps = 53/338 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V +  +  +R+D++  +         +Q    +G +  + K VK N R++   VV I   
Sbjct: 36  VADRGQSLLRVDKFLVDRMFGATRNRIQSAADAGCIMANGKPVKSNYRVKPEDVVTI--- 92

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----I 125
              +    +  +IL  ++ +          ++YED  + V +KPAG+ V  G G     +
Sbjct: 93  --MMTRPPRTFEILPENIPIK---------IVYEDDDLLVVDKPAGLVVHPGHGNYTGTL 141

Query: 126 AYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              +  +LK         P L   HR+D++TSG+LVVA+   A  +L+  F  +  ++ Y
Sbjct: 142 VNALAWYLKDDPTYDPNDPALGLVHRIDKDTSGLLVVAKKPEAKANLSMQFFHKTTKREY 201

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQ 238
            +LVWGI ++ +  I      + +IG +      + V  + ++G   A++H+ V++    
Sbjct: 202 RALVWGIVRDDEGRI------EGNIGRNPRDRMQMTVFPEGDQGKT-AVTHYSVLERLGY 254

Query: 239 KF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------P 283
                C LE    TGRTHQ+RVH  ++G  +  D +Y  N   KG  +S           
Sbjct: 255 VTLVKCRLE----TGRTHQIRVHMKYIGHTLFNDERYGGNEILKGTTSSKYKQFVDNCFA 310

Query: 284 IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
           I  +  LHA+ +   HP  G  +   + +PA M    D
Sbjct: 311 ICPRQALHAKTLGFVHPSTGEEMFFDSEIPADMTALID 348


>gi|323492963|ref|ZP_08098101.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           brasiliensis LMG 20546]
 gi|323312794|gb|EGA65920.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           brasiliensis LMG 20546]
          Length = 245

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 116/232 (50%), Gaps = 24/232 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D +I   NKP+G+ SV G   +  H D      V++     ++ HRLD +TSG++V
Sbjct: 16  IIYQDEQILAVNKPSGLLSVPGR--LEEHYDSMWSRLVETYPDI-QVVHRLDMDTSGLMV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVH 214
           +A+++ A + L + F+ R   K+Y++ VWG P+  +       I +W  +          
Sbjct: 73  LAKSKQAERSLKKQFQYRLTHKVYYARVWGHPQQDEGEVDLPLICDWPNRPRQ------K 126

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V  ++ K +    + ++V+    +K   + + P TGR+HQLRVH   +G PIVGD  Y  
Sbjct: 127 VCFEHGKPSQ---TRYQVVKR-EEKTSIVRLLPITGRSHQLRVHMQALGHPIVGDEFYSE 182

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                F+     +L LHA  +   HP+   LQ T  +P       +S+ F Y
Sbjct: 183 GEAFEFS----ERLELHAAELSFYHPDSELLQ-TIFVPCDFYLEAESVIFNY 229


>gi|27363948|ref|NP_759476.1| 23S rRNA pseudouridine synthase D [Vibrio vulnificus CMCP6]
 gi|320157325|ref|YP_004189704.1| ribosomal large subunit pseudouridine synthase D [Vibrio vulnificus
           MO6-24/O]
 gi|34395776|sp|Q8DEV0|RLUD_VIBVU RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|27360065|gb|AAO09003.1| Ribosomal large subunit pseudouridine synthase D [Vibrio vulnificus
           CMCP6]
 gi|319932637|gb|ADV87501.1| ribosomal large subunit pseudouridine synthase D [Vibrio vulnificus
           MO6-24/O]
          Length = 325

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 89/332 (26%), Positives = 151/332 (45%), Gaps = 49/332 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V VD   V K   ++  G+V     
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVTVDGNVVTKPRTKVMGGEV----- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I  L  +  E +     + L          ++YED  I V NKP    V  G+G     
Sbjct: 65  -ITVLAELEDEVRWEAQDIPLD---------IVYEDDDILVINKPRDFVVHPGAGTP--- 111

Query: 130 DGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG + + +        + PR  + HRLD++T+G++VVA+T  A   L  + + R I + Y
Sbjct: 112 DGTVLNALLFHCPEVAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQK 239
            ++  G         A   + K  IG    H  K+     +     A++HF+V + F ++
Sbjct: 172 EAIAIG------RMTAGGKVDKP-IGR---HATKRTLMAVSPMGKPAVTHFRVAEHF-RE 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQN--KLYLH 291
              + ++  TGRTHQ+RVH  ++  P++GD  Y       A    + T+ I+N  +  LH
Sbjct: 221 HTRIRLRLETGRTHQIRVHMSYLQHPLLGDAAYGGRARIPAGASEDVTAMIRNFDRQALH 280

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           A  +   HP  G  ++  AP+P  MV+  ++L
Sbjct: 281 AVMLRFEHPITGEEMEFHAPVPDDMVELTETL 312


>gi|330448797|ref|ZP_08312444.1| 23S rRNA and tRNA pseudouridine synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
 gi|328492988|dbj|GAA06941.1| 23S rRNA and tRNA pseudouridine synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
          Length = 232

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/204 (32%), Positives = 104/204 (50%), Gaps = 21/204 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ DS I   NKP+GI    G    +H   F +  V ++  + ++ HRLD  TSG++V+A
Sbjct: 17  LFLDSDIIAVNKPSGILSNPGRAPEHHDSIFAR--VLAEHPESQIVHRLDMGTSGLIVLA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC----IANWLLKKSHIGGDYVHVV 216
             + + +HL   FR R  QK+Y++ VWG I ++        I +W  +          V 
Sbjct: 75  LNKNSERHLKAQFRERETQKVYYARVWGHIAQDTGTVDLPLICDWPNRPRQ------KVC 128

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             N K    +++H++V+    +K   + + P TGR+HQLRVH   +G PI+GD  Y  + 
Sbjct: 129 FDNGKP---SVTHYEVV-SRDEKTTLVRLLPVTGRSHQLRVHMQALGHPILGDQFYATD- 183

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
           +    SP   +L LHA  +   HP
Sbjct: 184 EALEASP---RLLLHAAELTFTHP 204


>gi|269101904|ref|ZP_06154601.1| ribosomal large subunit pseudouridine synthase D [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268161802|gb|EEZ40298.1| ribosomal large subunit pseudouridine synthase D [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 324

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 92/331 (27%), Positives = 153/331 (46%), Gaps = 47/331 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V + +   RLD+     YP  +   ++  + +G+V VD + + K   ++  G+ +    
Sbjct: 10  TVNDSQLGKRLDQVIAELYPDYSRTRIKDWILAGKVAVDGEIIDKPRIKMMGGEQL---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           VINA   I  E +     + L          ++YED  I V NKP    V  G+G     
Sbjct: 66  VINA--EIEDEVRWEAQDIPLD---------IVYEDDDIIVINKPRDFVVHPGAGTP--- 111

Query: 130 DGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG + + +     S  + PR  + HRLD++T+G++VVA+T  A   L  + + R I + Y
Sbjct: 112 DGTVLNALLWHCPSLAEVPRAGIVHRLDKDTTGLMVVAKTVQAQTRLVRALQKRNITREY 171

Query: 184 WSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G        ++ I     K++ +    VH +         AI+H++V + F ++ 
Sbjct: 172 EAIAMGKMTGGGTVEKAIGRHSTKRTCMA---VHEL------GKPAITHYRVAEHF-REH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQ--NKLYLHA 292
             + ++  TGRTHQ+RVH  ++  P+VGD  Y        N        ++  ++  LHA
Sbjct: 222 TRIVLRLETGRTHQIRVHMSYLTHPLVGDATYGGRPRPPRNASDELIQALRAFDRQALHA 281

Query: 293 RYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           R + L HP  G L +  APLP  MV   D L
Sbjct: 282 RMLRLTHPITGELMEWHAPLPNDMVAMIDIL 312


>gi|291542663|emb|CBL15773.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           bromii L2-63]
          Length = 306

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 80/315 (25%), Positives = 147/315 (46%), Gaps = 38/315 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +    ++      ++ +G V V+   V    ++  G +V    V+N  +   
Sbjct: 13  VRLDKFISDANIDLSRSAAVNLIENGAVLVNDSVVSKKYKLSQGDIV----VVNVPDPTP 68

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
            E K  +  +++           +YED  + V NKP G+ V   +G         + YH 
Sbjct: 69  YEAKAENIPLDI-----------VYEDECLLVVNKPKGMVVHPAAGNYDGTLVNALLYHC 117

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L     +   +P + HR+D++TSG+L+VA+   + + L E  +     + Y S+V+G
Sbjct: 118 GDSLSGI--NGVLRPGIVHRIDKDTSGLLIVAKNDFSHRSLAEQIKEHSFTREYESIVFG 175

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             KN  E   +  + ++      + V+++N K    A++H+ VI  + + +  ++ +  T
Sbjct: 176 NLKN-DEGTVDAPIGRNPKDRKKMCVIEKNSKN---AVTHYSVITRY-KGYTHIKCKLET 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           GRTHQ+RVH  ++G P+ GD  Y   N K +F         LHAR +   HP+    ++ 
Sbjct: 231 GRTHQIRVHMAYIGHPVSGDKVYGVKNEKVDFEGQC-----LHARKIGFIHPKTNEYIEF 285

Query: 308 TAPLPAHMVKTWDSL 322
           T+ LP +  K    L
Sbjct: 286 TSELPDYFKKYLKKL 300


>gi|37678897|ref|NP_933506.1| 23S rRNA pseudouridine synthase D [Vibrio vulnificus YJ016]
 gi|37197638|dbj|BAC93477.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
          Length = 325

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 89/332 (26%), Positives = 151/332 (45%), Gaps = 49/332 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V VD   V K   ++  G+V     
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVTVDGNVVTKPRTKVMGGEV----- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I  L  +  E +     + L          ++YED  I V NKP    V  G+G     
Sbjct: 65  -ITVLAELEDEVRWEAQDIPLD---------IVYEDDDILVINKPRDFVVHPGAGTP--- 111

Query: 130 DGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG + + +        + PR  + HRLD++T+G++VVA+T  A   L  + + R I + Y
Sbjct: 112 DGTVLNALLFHCPEVAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRHITREY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQK 239
            ++  G         A   + K  IG    H  K+     +     A++HF+V + F ++
Sbjct: 172 EAIAIG------RMTAGGKVDKP-IGR---HATKRTLMAVSPMGKPAVTHFRVAEHF-RE 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQN--KLYLH 291
              + ++  TGRTHQ+RVH  ++  P++GD  Y       A    + T+ I+N  +  LH
Sbjct: 221 HTRIRLRLETGRTHQIRVHMSYLQHPLLGDAAYGGRARIPAGASEDVTAMIRNFDRQALH 280

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           A  +   HP  G  ++  AP+P  MV+  ++L
Sbjct: 281 AVMLRFEHPITGEEMEFHAPVPDDMVELTETL 312


>gi|62260278|gb|AAX77894.1| unknown protein [synthetic construct]
          Length = 367

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 142/318 (44%), Gaps = 34/318 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 38  QNIIMHPKDAGKRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 97

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E       +NL          +++ED  I V +KP  + V  G+G   
Sbjct: 98  NIELLPTNEWIAE------DINLK---------IIFEDDDIIVIDKPVNMIVHPGAGNPT 142

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +  L  + D + + PR  + HRLD++TSG++V A++  A  +L +    R++ + Y
Sbjct: 143 GTVSNALLHRYKD-QDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKY 201

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC 241
            ++V G      E      + +  IG D  +  K   N +G   AI+H+  I+ +   F 
Sbjct: 202 LAIVEG------EIYKQGTINQP-IGRDPTNRTKMAINYRGKE-AITHYTSIEVY-DGFT 252

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPH 299
            +E Q  TGRTHQ+RVH   +  P+VGD  Y   +         I  +  LHA  +   H
Sbjct: 253 LIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITIPTRQALHAYKLSFIH 312

Query: 300 PEGGRL-QITAPLPAHMV 316
           P   ++ +  + LP  M+
Sbjct: 313 PTTAKMVKFKSKLPEDML 330


>gi|224024580|ref|ZP_03642946.1| hypothetical protein BACCOPRO_01306 [Bacteroides coprophilus DSM
           18228]
 gi|224017802|gb|EEF75814.1| hypothetical protein BACCOPRO_01306 [Bacteroides coprophilus DSM
           18228]
          Length = 354

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 87/336 (25%), Positives = 151/336 (44%), Gaps = 53/336 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +Q    +G V  + K VK + +++   V+ +  
Sbjct: 31  VVVDKGQSPVRIDKYLFERIVNASRNRIQTAADAGFVMANGKPVKSSYKVKPQDVLTV-- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               ++    E  I+   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 89  ---MMDRPRYENDIIPEDIPLD---------VVYEDEDLMVINKPAGLVVHPGCGNYHGT 136

Query: 125 ----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               IA+H    L+         P+  L HR+D++TSG+LV+A+T  A  +L   F  + 
Sbjct: 137 LVNAIAWH----LRDVPTYNPNDPQVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFYNKT 192

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFA 237
            ++ Y +LVWGI +  +  I   + +      D + + V  +     +A++H++V++   
Sbjct: 193 TKREYNALVWGIVEEDEGTITGNIGRNPR---DRMQMAVISDPTQGKHAVTHYQVLERLG 249

Query: 238 QKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS---------- 282
                 C LE    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S          
Sbjct: 250 YVTLVKCVLE----TGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCF 305

Query: 283 PIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
            I  +  LHA+ +   HP     +  T+ LP  M +
Sbjct: 306 DICPRQALHAKTLGFVHPRTKEEMFFTSELPEDMTR 341


>gi|119961612|ref|YP_947480.1| RNA RluA family pseudouridine synthase [Arthrobacter aurescens TC1]
 gi|119948471|gb|ABM07382.1| putative RNA pseudouridine synthase, RluA family [Arthrobacter
           aurescens TC1]
          Length = 308

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 116/231 (50%), Gaps = 18/231 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +L +D    V +KP G++     G +   + G L      + + G   R  + HRLD  T
Sbjct: 82  ILLDDEDFVVIDKPVGVAAHPSPGWVGPTVVGGLAGAGYRISTSGAPERAGIVHRLDVGT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA+T  A   L  +F+ R ++K+Y ++V G+P   +  I   + +  H G D+  
Sbjct: 142 SGVMVVAKTEHAYTVLKRAFKERTVEKVYHAVVQGLPDPLEGTIDAPIGR--HPGHDWRF 199

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V ++ +    +++H++V++ F  K   +E+   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 200 AVIEDGR---PSVTHYEVLEAFG-KATLVEVHLETGRTHQIRVHFSALRHPCAGDLTYGA 255

Query: 275 N--FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +     N       + +LHAR +   HP  G  +++++  PA +    D L
Sbjct: 256 DPRLAANLG---LTRQWLHARQLGFTHPRTGDWVEVSSEYPADLQYALDLL 303


>gi|288553393|ref|YP_003425328.1| hypothetical protein BpOF4_01845 [Bacillus pseudofirmus OF4]
 gi|288544553|gb|ADC48436.1| hypothetical protein BpOF4_01845 [Bacillus pseudofirmus OF4]
          Length = 322

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 82/294 (27%), Positives = 136/294 (46%), Gaps = 46/294 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
            + G++ V++K V     I SG  V +  PP         K + +    + L  H     
Sbjct: 61  FKGGKILVNQKEVTVRTTIFSGDRVEVYVPPEP-------KNESLRPECIPLDIH----- 108

Query: 99  SILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RL 150
               YED  + V NKP G+            +A  + G+ +S        P   H   RL
Sbjct: 109 ----YEDDHLLVINKPQGMPTIPSREHPSRTLANAVMGYYESH-----HIPFTFHAVNRL 159

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-ANWLLKKSHIG 209
           D++TSG+LVVA+   A   L++  R  ++++ Y +L  G  + ++  I A    + S I 
Sbjct: 160 DRDTSGLLVVAKHGLAHDQLSKGQRAGKLKRYYLALAEGFVQPREGTIHAPIKRRPSSI- 218

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                + +        AI+H+KVI+   Q +  +E+   TGRTHQ+RVH  H+G P++GD
Sbjct: 219 -----IERMVAADGQEAITHYKVIND-NQAYSEVEINLETGRTHQIRVHFAHLGHPLLGD 272

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y  + +      +  +  LH + ++L HP  G+ L  +APLP  +++  D L
Sbjct: 273 DLYGGSIE------LLARQALHCQRVELIHPFTGKHLHFSAPLPKDLIEVKDKL 320


>gi|149907518|ref|ZP_01896265.1| pseudouridylate synthase for 23S rRNA (position 746)
           andtRNAphe(position 32), dual specificity [Moritella sp.
           PE36]
 gi|149809188|gb|EDM69117.1| pseudouridylate synthase for 23S rRNA (position 746)
           andtRNAphe(position 32), dual specificity [Moritella sp.
           PE36]
          Length = 229

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/213 (31%), Positives = 110/213 (51%), Gaps = 29/213 (13%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I V NKP+G+ SV G   +  H D  + S V  +     + HRLD  TSG+++
Sbjct: 16  IIYQDDAIIVLNKPSGLLSVPGR--LPEHTDS-IASRVQERFPTATIVHRLDMCTSGVIL 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-----ANWLLKKSHIGGDYVH 214
           +A ++AA  H++  F+ R   K Y++ + GIP  K   I      +W  +   +  D++ 
Sbjct: 73  MALSKAAQSHISRQFQQRSTAKYYYARLEGIPTAKSGSIDLPLRCDWPNRPRQM-IDFI- 130

Query: 215 VVKQNEKGANYAISHFKVI-------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                      A++H++VI       +   Q    + ++P TGR+HQLRVH L +G PI+
Sbjct: 131 -------DGKPALTHWQVIAEQPANNNNNQQASATVLLKPVTGRSHQLRVHMLALGTPIL 183

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           GD  Y A+ +G   +     L LHA  +++ HP
Sbjct: 184 GDELY-ASAQGVAAA---EHLQLHAAMLEIDHP 212


>gi|304440211|ref|ZP_07400101.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus
           duerdenii ATCC BAA-1640]
 gi|304371260|gb|EFM24876.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus
           duerdenii ATCC BAA-1640]
          Length = 307

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 87/320 (27%), Positives = 146/320 (45%), Gaps = 35/320 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV++  E MRLD + K    + +   + K +++  V V+   VK      SG +++   
Sbjct: 13  LVVQSQYEGMRLDIFLKEVLDY-SRSKINKEIKNKSVLVNGVSVK------SGYIIKKND 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
           +I          +IL+  VNL       K  +L+ED  I V +KP  + V  G+G+    
Sbjct: 66  IITL--------EILEDQVNLEPQKIDFK--ILFEDEYIMVISKPENLVVHPGAGVFSET 115

Query: 129 -IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G L   ++ K      +P + HRLD++TSG++++A+   A + L   F+   I K Y
Sbjct: 116 LVNGLLDYNINIKDIGEEDRPGIVHRLDKDTSGLMIIAKDALAYKKLVNMFKYGEIHKEY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +++ G  +N  E   +  + ++        V+  N K    AIS F  I  +   F   
Sbjct: 176 IAILTGHLEN--EIRVDEPIGRNPKDRKSFTVIYSNSKN---AISTFVPIK-YMNGFTLC 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
            +   TGRTHQ+RVHA ++  P++GD  Y   +K +     Q    LHA  +   HP  G
Sbjct: 230 RVIIETGRTHQIRVHARYLNHPVLGDSIY--GYKNSLGIKTQ---LLHAYKLTFNHPITG 284

Query: 303 GRLQITAPLPAHMVKTWDSL 322
             L      P    K  + +
Sbjct: 285 EELSFEDDFPDRFTKALEKI 304


>gi|314938511|ref|ZP_07845796.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|314942472|ref|ZP_07849312.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|314949504|ref|ZP_07852839.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
 gi|314952915|ref|ZP_07855882.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|314992184|ref|ZP_07857627.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|314995258|ref|ZP_07860370.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313590514|gb|EFR69359.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313593242|gb|EFR72087.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|313594987|gb|EFR73832.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|313598780|gb|EFR77625.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|313642139|gb|EFS06719.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|313644118|gb|EFS08698.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
          Length = 299

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/206 (33%), Positives = 102/206 (49%), Gaps = 25/206 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+            +   L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 97  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVL 156

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A+       L      + I + Y ++VWG        IA  +   + IG D     K+ 
Sbjct: 157 FAKNPFVLPILGRMLEQKMIYRRYQAIVWG-------EIAKDMTITNKIGRDRHDRRKRV 209

Query: 219 -NEKGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            ++K    A++H    KV+    Q +C LE    TGRTHQ+RVH  H G PIVGD  Y  
Sbjct: 210 VDDKNGQSALTHVTVNKVLSEQTQVYCVLE----TGRTHQIRVHLAHKGHPIVGDPLY-- 263

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
               N T+    +L LHA  + + HP
Sbjct: 264 ---QNRTA---ERLMLHALELHMIHP 283


>gi|52424286|ref|YP_087423.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52306338|gb|AAU36838.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 219

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/207 (32%), Positives = 107/207 (51%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y D+ I V NKP+G+    G+   Y+      S V  K       HRLD  TSGIL+ 
Sbjct: 16  IVYHDNHILVVNKPSGLLSVPGNQPRYYDSAM--SRVKDKYGFCEPAHRLDMATSGILLF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A ++AA   L   FR R  +K Y +LVWG + ++  E     +        D+ +  +Q 
Sbjct: 74  AMSKAADSELKRQFRERETKKYYEALVWGHLEQDSGEVNLPLVC-------DWENRPRQT 126

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E+G + A++ ++V+         +++ P TGR+HQLR+H L +G PI+GD K+ A+ 
Sbjct: 127 ICFERGKS-AVTKYEVLQRLPNNTTRVKLTPITGRSHQLRLHMLALGHPILGD-KFYAHP 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    +P   +L LHA  + + HP  G
Sbjct: 185 QAKTMAP---RLCLHAESLTIKHPISG 208


>gi|326796213|ref|YP_004314033.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326546977|gb|ADZ92197.1| pseudouridine synthase, RluA family [Marinomonas mediterranea
           MMB-1]
          Length = 327

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 84/342 (24%), Positives = 152/342 (44%), Gaps = 49/342 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V  +    R D+     +   +   +Q  ++ G + VD K  K   ++  G+VV 
Sbjct: 6   VKEAQVPFESSGQRFDQITTELFQDFSRSRIQAWIKEGALLVDGKACKAKEKLLGGEVV- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                 +L+  ++EQ+           +  +   ++YED  I V NKPAG+ V    G  
Sbjct: 65  ------SLDVALEEQE--------AHEAQDIPIDIVYEDEHILVINKPAGLVVHPAVG-- 108

Query: 127 YHIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            H +G L + +          PR  + HRLD+ET+G++VVA+T  A   L    + R + 
Sbjct: 109 -HREGTLLNAILHHAPETAHVPRAGIVHRLDKETTGLMVVAKTLQAQTDLVAQLQERSMG 167

Query: 181 KIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           + Y ++  G+        E I      +  +  + +H           A++H++++  F 
Sbjct: 168 REYEAITIGVMTGGGMVDEPIGRHPTNRQRMAVEPIH--------GKDALTHYRLLKRF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLY 289
           +    + ++  TGRTHQ+RVH  H+  P++GD +Y    K            ++N  +  
Sbjct: 219 KNHTHIRLKLETGRTHQIRVHMSHIQYPLLGDPQYSGRLKMPKACGEELQITLRNFRRQA 278

Query: 290 LHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
           LHA+ ++L HP  G  ++    LP  M +  + L    DR++
Sbjct: 279 LHAKRLELNHPFTGDWMEWEVDLPDDMAELLEVL----DRDM 316


>gi|257063802|ref|YP_003143474.1| pseudouridine synthase, RluA family [Slackia heliotrinireducens DSM
           20476]
 gi|256791455|gb|ACV22125.1| pseudouridine synthase, RluA family [Slackia heliotrinireducens DSM
           20476]
          Length = 320

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 83/334 (24%), Positives = 147/334 (44%), Gaps = 40/334 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            +Y+ V+   + MRLD +      +       K + +G+V ++    + +  +++G VV 
Sbjct: 5   TEYLYVDETGDGMRLDAFLAKEGAYTTRSAAAKRVAAGEVSINGVAARKSATVKAGDVVE 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                         Q  +D  V   + +D    +  YED ++ V +K AG+      G  
Sbjct: 65  Y-------------QVFIDPRVFDLESADIPLDVR-YEDDQVLVISKQAGLVTHPADGHP 110

Query: 127 YHIDGFLKSWV---------DSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFR 175
              D  + + +         + +G++ RL   HRLD++TSG+++ A+T  A Q L E   
Sbjct: 111 QQ-DTLVNALIHHCGRENLCNVQGEQDRLGIVHRLDRDTSGLMLAAKTNEAGQKLMEDIA 169

Query: 176 MRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            R + + Y +LV G IP      + +  + +S    D + +   +   A  A++ F V+ 
Sbjct: 170 DRDVDRHYLALVHGWIPLETG--LVDAPIGRSD--RDRLRMCVSDRDNARDAMTSFSVVK 225

Query: 235 CFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
            F        +  ++ +  TGRTHQ+RVH  ++  P VGD  Y      N      ++ +
Sbjct: 226 RFEAGRNDDGYTLIDCKLFTGRTHQIRVHMEYIKHPCVGDPVYGWAKHDNLG---LDRQF 282

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           LH+  +   HP  G RLQ    LPA + +  D L
Sbjct: 283 LHSYKLAFTHPTTGERLQFEDTLPADLQRVIDEL 316


>gi|260587511|ref|ZP_05853424.1| pseudouridine synthase, RluA family [Blautia hansenii DSM 20583]
 gi|260541776|gb|EEX22345.1| pseudouridine synthase, RluA family [Blautia hansenii DSM 20583]
          Length = 244

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 107/232 (46%), Gaps = 18/232 (7%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           IK   I + ++N     D     +LYED  I V  KPAG  VQ        ++  L++++
Sbjct: 11  IKNTGIYEGAMNTINIED----TVLYEDKYILVCQKPAGFPVQSKRLGTLDMECALRNYL 66

Query: 138 DSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             KGQ+P   + HRLDQ   G+LV A+ + +A  L++  +  + +K Y +   G    K+
Sbjct: 67  AKKGQEPYVAVIHRLDQPVQGVLVFAKDKESAAKLSKQMQQGKFEKTYLAYTQGHTDKKQ 126

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E + + L K      +   VV +    +  A   +KV+    ++   LE+   TGR HQ+
Sbjct: 127 ETLIDELEKDGRT--NTSKVVAKKTANSKRAELSYKVLK-ETEEGSLLEVSLKTGRHHQI 183

Query: 256 RVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           RV   H G PI GD KY   C     N      + + L A  +   HP  G+
Sbjct: 184 RVQLAHAGLPIFGDAKYNVKCTKEDAN------HGVSLCAYKLSFLHPAKGK 229


>gi|160875996|ref|YP_001555312.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160861518|gb|ABX50052.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315268192|gb|ADT95045.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 223

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 63/199 (31%), Positives = 107/199 (53%), Gaps = 10/199 (5%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP+G+    G   A+  D  L + + +   +  L HRLD  TSGI+V AR
Sbjct: 18  YKDRDLIIINKPSGLLSNPGRA-AHTFDCAL-TRLQTLYPETILVHRLDCATSGIMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
            + A  HL   F+ R+ +K+Y + V G +P  +++ + +  +        Y   ++  E 
Sbjct: 76  NKKAESHLKTQFQDRQSKKVYIAEVMGHVP--QEQGMIDLAIAPDTEHPPYQKTLQAGET 133

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           G   A+++++V++   +    +E+ P TGRTHQLRVH L +G  I+GD  Y  + +    
Sbjct: 134 GGKSALTYYRVLE-RRENSTLVELSPETGRTHQLRVHMLALGHAILGDEFY-GDAEVIKA 191

Query: 282 SPIQNKLYLHARYMDLPHP 300
           +P   +L LHA+ + L HP
Sbjct: 192 AP---RLCLHAQSLSLTHP 207


>gi|71280552|ref|YP_270573.1| 23S rRNA pseudouridine synthase D [Colwellia psychrerythraea 34H]
 gi|71146292|gb|AAZ26765.1| ribosomal large subunit pseudouridine synthase D [Colwellia
           psychrerythraea 34H]
          Length = 324

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 120/243 (49%), Gaps = 37/243 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKPAG+ V  G+G   + DG L + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDDYILVINKPAGLVVHPGAG---NPDGTLLNALLHHYPALNVVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV- 213
           +G++VVA+T AA  +L ++ ++R I + Y            E +AN ++    +  + + 
Sbjct: 143 TGLMVVAKTIAAQTNLVDALQLREITREY------------EAVANGVMTAGGLVDEPIG 190

Query: 214 -HVVKQNEKGANY----AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            H  K+ +   +Y    +++H++V++ +            TGRTHQ+RVH  H+  P+VG
Sbjct: 191 RHSTKRTQMAVSYIGRPSVTHYRVMEKYRLHTRLRLRL-ETGRTHQIRVHMSHITHPLVG 249

Query: 269 DHKYCANFKG--NFTSPIQNKL------YLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           D  Y    +   N T  +  KL       LHA  + L HP  G  +   A LP   V+  
Sbjct: 250 DPVYGGRPRPPKNSTEALLMKLRSFKRQALHAAMLSLFHPITGEEMTWHAELPEDFVELI 309

Query: 320 DSL 322
           + L
Sbjct: 310 ELL 312


>gi|154496245|ref|ZP_02034941.1| hypothetical protein BACCAP_00530 [Bacteroides capillosus ATCC
           29799]
 gi|150274328|gb|EDN01405.1| hypothetical protein BACCAP_00530 [Bacteroides capillosus ATCC
           29799]
          Length = 300

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/274 (25%), Positives = 123/274 (44%), Gaps = 29/274 (10%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           + +D  RV   +R+++GQ++ +         ++ + ++  + V      D     ++Y+D
Sbjct: 45  ILLDGVRVTVGDRVRAGQILSV---------VVGDTEVSGAIVPAPGPLD-----IVYQD 90

Query: 106 SKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVAR 162
             + V NK  G++V  G G  +  I  FL  +   +G        HRLD+ TSG+L+VA 
Sbjct: 91  QDVLVLNKAPGVAVHPGPGHYSDTIGNFLMDYYRKQGILADFHPVHRLDRGTSGLLLVAL 150

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
              A + L E       +++Y ++  G P      I   + +    G      V+ +   
Sbjct: 151 HGHAQEVLKEQLHSPSFRRVYLAVCEGAPNPPSGVIDAPIGRLE--GSVLARTVRPD--- 205

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++H++ +     +   + ++  TGRTHQ+RVH  H+G P+ GD  Y    +     
Sbjct: 206 GQRAVTHYRTLRTVNDR-ALVRLELETGRTHQIRVHMAHLGHPLTGDFLYGTEDQSLIPR 264

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           P      LHA  +   HP  G+ +  TAPLP  M
Sbjct: 265 P-----ALHAAELSFTHPITGKTMAFTAPLPQDM 293


>gi|257458419|ref|ZP_05623561.1| ribosomal large subunit pseudouridine synthase C [Treponema
           vincentii ATCC 35580]
 gi|257444223|gb|EEV19324.1| ribosomal large subunit pseudouridine synthase C [Treponema
           vincentii ATCC 35580]
          Length = 240

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 91  TKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           T+ +   KSI ++YED  + + NKP GI VQGG+ I+  +   L   +   G +    HR
Sbjct: 4   TQQAIVKKSIPIVYEDEALCIVNKPYGIPVQGGAHISVCLTEILSKQL---GSEIFPVHR 60

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSH 207
           LD+ETSG+LV A++  AA+     F  + ++K Y +L +G   P   K+ +   LL +  
Sbjct: 61  LDKETSGLLVTAKSADAARSCRALFESQAVEKEYLALCFGGFEPSAHKKPVKK-LLPEGI 119

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           I  D   V   + K A+ A       D ++       ++ HTGR HQ+R+H   +G PI+
Sbjct: 120 I--DTPVVENGSPKPASSAYKLLASTDAYS----LFSVRLHTGRMHQIRIHLAGIGYPII 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLP-------HPEGG-RLQITAPLPAHMVKTW 319
           GD K+     GNF   +  +L+  AR   L         P GG +   T P P H+    
Sbjct: 174 GDDKH-----GNFA--LNKQLWKTARIKKLQLCAYRLMFPIGGKKCLFTVPAPEHIQAAI 226

Query: 320 DSL 322
           D L
Sbjct: 227 DVL 229


>gi|153807696|ref|ZP_01960364.1| hypothetical protein BACCAC_01978 [Bacteroides caccae ATCC 43185]
 gi|149129305|gb|EDM20519.1| hypothetical protein BACCAC_01978 [Bacteroides caccae ATCC 43185]
          Length = 590

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 76/256 (29%), Positives = 120/256 (46%), Gaps = 42/256 (16%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGF 132
           L H+++  ++ ++ +    H D    I+ +ED  + V NKP+G +SV G       +   
Sbjct: 334 LQHMLQGLEVDENPLLSNTHKDTELEIV-FEDEWLVVVNKPSGMLSVPGKEEDMDSVYHR 392

Query: 133 LKS-WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-- 189
           LK  + D+ G  P + HRLD  TSG+L+VA+T+   QHL   F  R I+K Y +L+ G  
Sbjct: 393 LKEKYPDATG--PMIVHRLDMATSGLLLVAKTKEVHQHLQAQFENRSIKKRYIALLDGCI 450

Query: 190 -------------IPKNKKECIANWLLKKSHIGGDYVHVVKQ---------NEKGANYAI 227
                          K +K      +     +G   + +            +E+    AI
Sbjct: 451 TETEETTNQTTGNTRKTEKVRATEVISTTGKVGRIELPLCPNPLDRPCQSVDEEHGKEAI 510

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPI 284
           + +++I   ++K   +   P TGRTHQLRVHA H   + CPI+GD  Y            
Sbjct: 511 TEYQII-TNSEKHTRIAFCPLTGRTHQLRVHAAHPKGLNCPILGDELYGKK--------- 560

Query: 285 QNKLYLHARYMDLPHP 300
            ++LYLHA Y++  HP
Sbjct: 561 ADRLYLHAEYIEFRHP 576


>gi|149183528|ref|ZP_01861954.1| ribosomal large subunit pseudouridylate synthase D [Bacillus sp.
           SG-1]
 gi|148848774|gb|EDL62998.1| ribosomal large subunit pseudouridylate synthase D [Bacillus sp.
           SG-1]
          Length = 334

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 108/226 (47%), Gaps = 36/226 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQG----------GSGIAYHIDGFLKSWVDSKGQKPRL--TH 148
           +LYED+ + + NKPAG++              + +A+H+          KG+K  +   H
Sbjct: 114 ILYEDAHMMIVNKPAGMNTHPNNPSLEKDTLANAVAWHLQ--------QKGEKVDVQHIH 165

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD++T+G +V A+       L      R+I++ YW++V G+  NKK  I         I
Sbjct: 166 RLDKDTTGAVVFAKHALVKGILDRLLAERKIKRTYWAIVHGLITNKKGTITKA------I 219

Query: 209 GGDYVHVVKQN-EKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPI 266
           G D  H  ++        A +HF++++    K    +++   TGRTHQ+RVH   +G P+
Sbjct: 220 GRDRHHNTRRRVSPSGQPATTHFQLLEQNKPKNLSLVQLVLDTGRTHQIRVHMSSIGHPL 279

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
            GD  Y          PI ++  LHA+Y++  HP    RL   AP 
Sbjct: 280 AGDTLYGGK-------PIVSRQALHAKYIEFDHPLTEERLAFEAPF 318


>gi|300741275|ref|ZP_07071296.1| RNA pseudouridine synthase, RluA family [Rothia dentocariosa M567]
 gi|300380460|gb|EFJ77022.1| RNA pseudouridine synthase, RluA family [Rothia dentocariosa M567]
          Length = 302

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/232 (29%), Positives = 118/232 (50%), Gaps = 20/232 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW------VDSKGQKPR--LTHRLDQ 152
           ++Y D  I V +KPAG++     G  +H    L +       V + G   R  + HRLD 
Sbjct: 73  IVYCDDDIVVVDKPAGVAAHPSHG--WHGPTVLSALLGEGVTVATSGAAERQGIVHRLDV 130

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVAR+  A   L  +F+ R ++K+Y +LV G+P      I   + +  H G ++
Sbjct: 131 GTSGLMVVARSERAYTELKRAFKDRTVEKVYHTLVQGLPDPLMGTIDAPIGR--HPGHEW 188

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              V ++ +    +I+H++ ++ F      +E+   TGRTHQ+RVH   +  P  GD  Y
Sbjct: 189 KFAVIEDGRS---SITHYETLESFGSA-SLVEVHLETGRTHQIRVHFSSLRHPCCGDLTY 244

Query: 273 CANFKGNFTSPIQ-NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            A+ +  F++ +   + +LHA  +   HP  G R++  +P P  +    ++L
Sbjct: 245 GADPR--FSAELGLTRQWLHAHRLGFTHPTTGERVEFESPYPQDLDYALEAL 294


>gi|269792594|ref|YP_003317498.1| pseudouridine synthase, RluA family [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100229|gb|ACZ19216.1| pseudouridine synthase, RluA family [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 320

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 86/322 (26%), Positives = 141/322 (43%), Gaps = 50/322 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVV--RIP 68
           V  D E  RLD         ++     K+++ G V+V    RVK + +++ G  V  ++P
Sbjct: 24  VGEDGEGHRLDFVLSREI-GVSRSYASKLIKEGMVQVSWSPRVKPSLKVRVGGTVTAQLP 82

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
           P                 S  L      +   ++Y+D  + V +KPAG+ V    G    
Sbjct: 83  P-----------------SEELELEPQDVPFRVVYQDQDLVVVDKPAGLVVHPAPGHWRG 125

Query: 127 YHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + G L  + D    +  ++P + HRLD  TSG++VVAR   A + L  +F+ RR+ K+
Sbjct: 126 TLVHGLLYRYPDLMELNGVKRPGIVHRLDATTSGLMVVARNGLAMEGLVRAFKDRRVGKV 185

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG------ANYAISHFKVIDCF 236
           Y ++  G  + +             IG D       N K          A++ ++VI   
Sbjct: 186 YLAMAAGTLRGEGSV-------SLPIGRD-----PDNRKRMACVPWGREALTRYRVIWSR 233

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  +  Q  TGRTHQ+RVH   +G P+VGD  Y       F  P+  +++LH+  ++
Sbjct: 234 G-GYSLVACQIKTGRTHQIRVHMRSLGHPLVGDRIYGGPCPEGF--PL-GRVFLHSWRLE 289

Query: 297 LPHPE-GGRLQITAPLPAHMVK 317
             HP  G  +    PLP  +V+
Sbjct: 290 FDHPRTGAPMSFICPLPPDLVR 311


>gi|164686622|ref|ZP_02210650.1| hypothetical protein CLOBAR_00215 [Clostridium bartlettii DSM
           16795]
 gi|164604351|gb|EDQ97816.1| hypothetical protein CLOBAR_00215 [Clostridium bartlettii DSM
           16795]
          Length = 221

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 58/180 (32%), Positives = 90/180 (50%), Gaps = 8/180 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  KP  I  QG +     +   LK ++  K  KP      L HRLD+   
Sbjct: 4   VIYEDNHLLVVEKPVNILSQGDNTNDDDMVNLLKKYLKEKYNKPGNVFVGLVHRLDRPVG 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  AA  L+E  R +  +K Y +++ G  K K++ ++++L K      + V V
Sbjct: 64  GIMVFAKTSKAASRLSEQVRNKTFKKTYKAVLHGEMKKKQDNLSDYLYKDKKT--NMVSV 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V +N K A  A   +K +      F  +E+   TGR HQ+RV       P+ GD +Y  N
Sbjct: 122 VNKNHKDAKDAKLSYKTL-ASNNGFSLVEIDLQTGRPHQIRVQFSSRNHPLYGDQRYGKN 180


>gi|301782175|ref|XP_002926502.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 2 [Ailuropoda melanoleuca]
          Length = 345

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 110/235 (46%), Gaps = 24/235 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S Q   +K R +   +    Q V   PV   +  +++  + L   V+    +  L   ++
Sbjct: 42  SAQRLAEKLRAQKQEQKTKNQPVPTSPVQRRVQELVRFTQQLQR-VHPNVLAKALSRGIV 100

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGIL 158
           ++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G++
Sbjct: 101 HQDMDLVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTGVM 160

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A  +  A  + E FR R++ K YW++   +P      +   +++K             
Sbjct: 161 VLAWEKEVAHQVQELFRTRQVAKKYWAVTVRVPVPPAGVVDIPVIEKE------------ 208

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
                  A++ ++V+         +E+QP TG  HQLRVH +  + CPI+GDHKY
Sbjct: 209 -----VQAVTQYQVLSSTLSS-ALVELQPITGVKHQLRVHLSFGLDCPILGDHKY 257


>gi|330952657|gb|EGH52917.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae Cit 7]
          Length = 211

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/215 (31%), Positives = 111/215 (51%), Gaps = 15/215 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIHQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEGGKHALTFWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR---LQITAPL 311
              P   +L LHA  +   HP  G     + TAP 
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTGERLTFECTAPF 211


>gi|169632854|ref|YP_001706590.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii SDF]
 gi|239501123|ref|ZP_04660433.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii AB900]
 gi|260556640|ref|ZP_05828858.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 19606]
 gi|169151646|emb|CAP00433.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii]
 gi|193077967|gb|ABO12881.2| putative ribosomal large subunit pseudouridine synthase
           A(RluA-like) [Acinetobacter baumannii ATCC 17978]
 gi|260409899|gb|EEX03199.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 19606]
          Length = 212

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/225 (32%), Positives = 108/225 (48%), Gaps = 21/225 (9%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLD 151
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V     +PR  L HRLD
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLV---AIEPRTLLIHRLD 56

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSGILV   ++     +   F+ R+  KIY +LV G  + +       +   S     
Sbjct: 57  RDTSGILVFGLSKRGQSAIARQFQDRQTSKIYEALVAGHLEGEGTVDIPVVYDPSR---P 113

Query: 212 YVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +H+V  +      A++H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVG
Sbjct: 114 PLHIVDASHNKP--ALTHWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVG 171

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           D  Y    +      +  +L LHA+ +   HP  G  L    P+P
Sbjct: 172 DTLYATPEQL-----LVPRLCLHAKQLSFNHPVTGESLTFNCPVP 211


>gi|89067930|ref|ZP_01155374.1| ribosomal large subunit pseudouridine synthase D [Oceanicola
           granulosus HTCC2516]
 gi|89046528|gb|EAR52584.1| ribosomal large subunit pseudouridine synthase D [Oceanicola
           granulosus HTCC2516]
          Length = 341

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 89/341 (26%), Positives = 141/341 (41%), Gaps = 66/341 (19%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L +++  G VR++   V     R+  G  V I        
Sbjct: 17  RLDKALARDVPEDAALSRSRLARLVPDGAVRINGVVVTDVKARLGEGDAVEI-------- 68

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-- 133
                   LD  V+     + +   ++YED ++ V NKPAG+ V    G     DG L  
Sbjct: 69  -------ALDIPVDSDMGGEPIPLDVVYEDDELIVINKPAGMVVHPAPGSP---DGTLVN 118

Query: 134 -------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                  +S     G ++P + HR+D++TSG+LV A+T  A   L   F    +++ Y +
Sbjct: 119 ALIHHCGESLSGVGGLRRPGIVHRIDKDTSGLLVAAKTDRAHHGLAAQFEAHDVERHYQA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------------GANYAISHFKV 232
           L +G+P      +   +   S   G+ + +  Q  +                +A++  + 
Sbjct: 179 LCFGLPDAADPRL-RGIRGTSFEPGNILKIQTQLARHKTDRQRQAVVWSNGRHAVTRARR 237

Query: 233 IDCF------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSP 283
           ++ F      A+  CWLE    TGRTHQ+RVH  H G  +VGD  Y       KG  +  
Sbjct: 238 VETFGGPPVVARIECWLE----TGRTHQIRVHMAHAGHGLVGDPVYGGKRKIAKGAVSEA 293

Query: 284 IQNKL------YLHARYMDLPHPEGGRLQ-ITAPLPAHMVK 317
               L       LHA  +   HP  G L+   A +PA M +
Sbjct: 294 AMRALATFPRQALHAATLGFKHPVTGELKRFAADMPADMTE 334


>gi|103486532|ref|YP_616093.1| pseudouridine synthase [Sphingopyxis alaskensis RB2256]
 gi|98976609|gb|ABF52760.1| pseudouridine synthase [Sphingopyxis alaskensis RB2256]
          Length = 227

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 64/186 (34%), Positives = 92/186 (49%), Gaps = 21/186 (11%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQ----GGSGIAYHID----GFLKSWVDSKGQKPRLT 147
            L   +L+ D +  V +KPAG+ V     G   I  H+D    GF K W       P   
Sbjct: 2   LLSDRVLFLDGEALVIDKPAGLPVDAPRDGSLSIENHLDLLRFGF-KRW-------PLPV 53

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG L++AR   A    T +F  R ++K Y +++ G+P +    I   L K S 
Sbjct: 54  HRLDRDTSGCLLLARNPKAHGRFTRAFENREVEKQYLAIIDGVPADDGGTIDLPLAKTST 113

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPI 266
               +  VV   +     +ISH++ +   A     L  +P TGRTHQLRVHA+  +G P+
Sbjct: 114 AEAGWRMVV---DPAGKPSISHWEKL-AVADGRALLRFRPETGRTHQLRVHAIEGLGFPL 169

Query: 267 VGDHKY 272
            GD  Y
Sbjct: 170 AGDPVY 175


>gi|269123695|ref|YP_003306272.1| pseudouridine synthase [Streptobacillus moniliformis DSM 12112]
 gi|268315021|gb|ACZ01395.1| pseudouridine synthase [Streptobacillus moniliformis DSM 12112]
          Length = 280

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 76/293 (25%), Positives = 141/293 (48%), Gaps = 28/293 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V+ D  N+RLD++ + +    +   +  ++R G V+V+ K+ K N R+     +  P  
Sbjct: 6   LVDKDHVNIRLDKFMRKYSKEESLSIIFSLIRKGFVKVNGKKSKENYRLLLNDEIFFPDA 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 I+ ++KI    +++    D  K+++++ED  +++ NKP  + +  G    + + 
Sbjct: 66  A----KIVMDKKIEKEIIDI----DLFKNMIVFEDEDVFIINKPNNMPMHKGDKHKFGLS 117

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              K++ ++        +RLD ET G+++  +     + + E  R ++I K Y + V   
Sbjct: 118 ETAKAYYNNPN--VNFANRLDLETEGLVIGCKNLQILRKVNEEIRNKKIIKRYIAKV--- 172

Query: 191 PKNKKECIANWLL--KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
            + KK  +       KK  I  D V V K   +   Y    FKVI+    K   L+++  
Sbjct: 173 -EQKKLQLDEEFFSDKKIKIFEDRVRVSKDGLEAKTY----FKVIEVKDFK-VLLDIELI 226

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           TGR HQ+RVH   +G PI+GD KY     GN+    ++++YL   Y+   + E
Sbjct: 227 TGRKHQIRVHLSDIGHPIIGDSKY-----GNYQK--KDRMYLKCYYIKFLNYE 272


>gi|50084392|ref|YP_045902.1| putative ribosomal large subunit pseudouridine synthase
           A(RluA-like) [Acinetobacter sp. ADP1]
 gi|49530368|emb|CAG68080.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. ADP1]
          Length = 214

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/216 (32%), Positives = 100/216 (46%), Gaps = 16/216 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           S+FL   L++ D+   V +KPAGI    G G A   D  L   V+ +  K  L HRLD++
Sbjct: 2   SNFLTDYLIHRDNDFMVIHKPAGILSVPGKGDAL-FDSLLVRLVEIE-PKTLLIHRLDRD 59

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK----ECIANWLLKKSHIG 209
           TSGILV    + A   ++  F+ R+  KIY +LV G    +       + +      HI 
Sbjct: 60  TSGILVFGLNKMAQSAISRQFQERQTDKIYQALVVGEVYGEGLIDVPVVYDAARPPLHIA 119

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
               H   Q E  A       +  +   +    + + P TGR+HQLRVH  ++G PIVGD
Sbjct: 120 DPAHHKPAQTEWQA------LEQFELNGKMVTRMRLTPITGRSHQLRVHMQYIGHPIVGD 173

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
             Y +       S    +L LHA  +   HP+ G L
Sbjct: 174 TLYASLADQQLVS----RLCLHAEQLSFYHPKTGEL 205


>gi|332969275|gb|EGK08302.1| RluA family pseudouridine synthase [Desmospora sp. 8437]
          Length = 308

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/272 (29%), Positives = 136/272 (50%), Gaps = 23/272 (8%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI----LLYEDSKIYVFN 112
           NR+   + +R+   +  L  ++KE   L  +V   + +D         + YED    V N
Sbjct: 36  NRLTRSRGIRLNRQMPFLKRVVKEGDRLQVAVRPRERADLEPEPFPLEVPYEDEDWMVVN 95

Query: 113 KPAGISVQ----GGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAA 167
           KPAGI+V     G +G   H  G +  W +   + K R  HRLD+ TSG+LVVA++  A 
Sbjct: 96  KPAGINVHPVRPGETGTLAH--GIVHWWKEQGWEGKVRPVHRLDRHTSGLLVVAKSAYAH 153

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYA 226
           Q +    R RR++++Y++ + G   +  +  A      + I  D  H +++      + A
Sbjct: 154 QLMDRELRERRLKRVYYAFLEG---SLTQAPAAEGTIDAAIDRDPDHPLRRRVSPAGDPA 210

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++H++V+         ++++  TGRTHQ+RVH  H+G P+ GD  Y +      TSP+  
Sbjct: 211 VTHYRVL-ARNNDATLVQVELETGRTHQIRVHFSHLGFPLFGDGLYGS------TSPLIR 263

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           +  LHA  +   HP +G  + + +PLP  + +
Sbjct: 264 RQALHACEVGFHHPLQGEPVTVHSPLPKDLTR 295


>gi|170728051|ref|YP_001762077.1| RluA family pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169813398|gb|ACA87982.1| pseudouridine synthase, RluA family [Shewanella woodyi ATCC 51908]
          Length = 323

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 90/333 (27%), Positives = 151/333 (45%), Gaps = 55/333 (16%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD+     YP  +   +++ +++G V +D     K   ++  GQ +       A+   +
Sbjct: 19  RLDQTLAELYPDYSRTRIKEWIQAGWVYIDGVVSTKPREKVLEGQEI-------AIEATL 71

Query: 79  KEQKILDS-SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH 128
           KE+    + +++L          ++YED  I V NK AG+ V  G+G         + +H
Sbjct: 72  KEETAAKAQAIDLD---------IVYEDDHIIVINKQAGLVVHPGAGNQDGTLMNALLHH 122

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             G     V   G    + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V 
Sbjct: 123 CPGI--ELVPRAG----IVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAVVL 176

Query: 189 GI---PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           G         E I     K++H+       V  N K    A++H++V + F +    L +
Sbjct: 177 GTLISGGTVDEPIDRHPTKRTHMA------VVHNGKP---AMTHYRVAEKF-RAHTRLRL 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLY-------LHARYMDL 297
           +  +GRTHQ+RVH  H+G  +VGD  Y    +     +P   + Y       LHA  ++L
Sbjct: 227 RLESGRTHQIRVHMSHIGHTLVGDPVYGGRPRPPKGVTPEFFETYMGFKRQALHAIRLEL 286

Query: 298 PHPEGGRLQI-TAPLPAHMVKTWDSLGFKYDRN 329
            HP    +    AP+P  MV    +L    + N
Sbjct: 287 AHPYTFEIMSWQAPVPEDMVTLTRALRKDTEEN 319


>gi|302382390|ref|YP_003818213.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
 gi|302193018|gb|ADL00590.1| pseudouridine synthase, RluA family [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 336

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 95/345 (27%), Positives = 149/345 (43%), Gaps = 58/345 (16%)

Query: 4   MTYVQYVVVENDEENM--RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQ 60
           +T  Q +VV  D   +  RLD+      P ++   LQ +L  G V  D   V   ++R  
Sbjct: 11  ITDDQVIVVHLDAGMVGDRLDKALARALPTLSRGRLQALLAQGAVSHDGAVVTDGSSRAI 70

Query: 61  SGQV-VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G   + +PPV+ A      E +    ++ LT         +LYED+ + V +KPAG++ 
Sbjct: 71  PGDYDITVPPVMAA------EPRA--QAIPLT---------VLYEDADLIVIDKPAGMAA 113

Query: 120 QGGSGIAYHIDGFL--------KSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQH 169
               G     DG L         + +   G   +P + HRLD++TSG++V A++  A   
Sbjct: 114 HPAPGTP---DGTLVNALLHHCGATLSGIGGVARPGIVHRLDKDTSGVMVAAKSDRAHAG 170

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG------- 222
           L+  F    I++ Y +L  G P      I   L+ +S      + V+K   +        
Sbjct: 171 LSALFATHDIERTYIALTRGAPSPTLGRI-ETLIGRSSSDRKKMAVLKSGGRNAITDYVV 229

Query: 223 -ANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-N 279
            A YA+         A +  C L+    TGRTHQ+RVH    G PI+GD  Y +     +
Sbjct: 230 QARYAVPAKPGAAPLAARVACTLQ----TGRTHQIRVHMASKGSPILGDATYGSGSPALS 285

Query: 280 FTSPIQ----NKLYLHARYMDLPHP---EGGRLQITAPLPAHMVK 317
             + I+     +  LHA  +   HP   E  R + +  LPA M +
Sbjct: 286 VRAAIEQSGLTRQALHAAVLGFVHPVTDEALRFETS--LPADMAR 328


>gi|331703570|ref|YP_004400257.1| ribosomal large subunit pseudouridylatesynthase D [Mycoplasma
           mycoides subsp. capri LC str. 95010]
 gi|328802125|emb|CBW54279.1| Ribosomal large subunit pseudouridylatesynthase D [Mycoplasma
           mycoides subsp. capri LC str. 95010]
          Length = 310

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/267 (29%), Positives = 132/267 (49%), Gaps = 21/267 (7%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
           +  NN+I +     + P  N+   I  +  ILD   NL K+ D    I+ Y+D  + V N
Sbjct: 42  ISVNNQIITNNNFLVKP--NSQITITIKDPILDP--NLVKNEDIDLDIV-YQDDDLLVIN 96

Query: 113 KPAGISVQGGSGIAYH--IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAA 166
           K   I+V        +  ++  L S V+        +P + HR+D++T+G+L+VA+    
Sbjct: 97  KQNNITVHPSLNNTNNTIVNALLASDVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKT 156

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
            + L+E F+  +I K Y ++V G+ K  K  I +  + +S      + V  +N K    A
Sbjct: 157 HKLLSEMFKNHQIYKEYLAIVTGVIKPNKGLI-DAPIGRSQTDRKKMSVTAKNSKQ---A 212

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           I+ F+V++ F  K   ++ Q  TGRTHQ+RVH  ++  P++ D  Y    +  FT   Q 
Sbjct: 213 ITTFEVVERFL-KNTLVKCQIQTGRTHQIRVHFNYINHPVLNDPVYGKKHQ-EFTDFGQ- 269

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLP 312
             YLHA  +   HP     +++ +PLP
Sbjct: 270 --YLHAYKLKFTHPITKKEIELISPLP 294


>gi|325969898|ref|YP_004246089.1| pseudouridine synthase [Spirochaeta sp. Buddy]
 gi|324025136|gb|ADY11895.1| pseudouridine synthase [Spirochaeta sp. Buddy]
          Length = 229

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/222 (30%), Positives = 112/222 (50%), Gaps = 14/222 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKGQK-PRLTHRLD 151
           +K  +LYED+ + + NK  G  VQG       +A  +  +L+   + +G     + HRLD
Sbjct: 3   IKDRILYEDNHLIIINKLCGELVQGDVTGDETLADLVKEYLRVNYNKQGNVFLGIPHRLD 62

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSGI+V A+T  A   L E F+   ++K YW++V  +P   +  + +++++ +     
Sbjct: 63  RPTSGIVVYAKTEKALIRLNELFKGSAMKKTYWAIVDHMPNQTEGTLVHYIVRDTKTNKS 122

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V++  KG   A   +K+I   ++ +  LE+  HTGR HQ+R     +G  I GD K
Sbjct: 123 VALSVEK--KGGKLAKLDYKLISA-SKNYFLLEVNLHTGRHHQIRAQFAAIGLHIKGDLK 179

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y     G   S     + LHAR +   HP +  ++ +TAP P
Sbjct: 180 Y-----GAARSNPDGGICLHARSISFTHPVKKEQITLTAPPP 216


>gi|299143272|ref|ZP_07036352.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           386 str. F0131]
 gi|298517757|gb|EFI41496.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           386 str. F0131]
          Length = 329

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 78/286 (27%), Positives = 127/286 (44%), Gaps = 44/286 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  V ENDE   R+DR+ K ++       + K LR   ++++ K+ +  + +  G  ++
Sbjct: 2   IEIFVNENDE-GQRIDRFLKKYFEKATLSFIYKNLRKKNIKLNDKKAEPEDLLSKGDCIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +    +E       +N  K++ F K  +++ED  I + NKPAGI     S   
Sbjct: 61  LYLSDETIEKFKRE------PINF-KNNKFPK--IIFEDENIILMNKPAGILSHNDSK-- 109

Query: 127 YHIDGFLKSWVD----------------SKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
                F K+ VD                    +P + +RLD+ TSGIL+ A+     + L
Sbjct: 110 ----DFKKNMVDMMIDYLIARQEYNPRNENSFRPAICNRLDRNTSGILIGAKKSGVLRSL 165

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD----YVHVVKQNEKGANYA 226
               +   I K Y +LV G  K +          +S++  D     V V+K+N  GA  +
Sbjct: 166 NYEIKKNNIDKFYLALVSGEAKEQ-------FSDRSYLSKDGDRNKVTVLKKNSIGAKES 218

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           I+ FK I      +  L++   TGRTHQ+R        PIVGD KY
Sbjct: 219 ITEFKRI-AMQNDYSLLKVNLITGRTHQIRTVLSSKKLPIVGDVKY 263


>gi|325577153|ref|ZP_08147637.1| pseudouridine synthase A [Haemophilus parainfluenzae ATCC 33392]
 gi|325160735|gb|EGC72856.1| pseudouridine synthase A [Haemophilus parainfluenzae ATCC 33392]
          Length = 219

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 107/208 (51%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ I V NKP+G+    G+   Y+      S V  K       HRLD  TSGI++ 
Sbjct: 16  IIYQDNHICVVNKPSGLLSVPGNQPEYYDSAM--SRVKEKFGFCEPAHRLDMATSGIILF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC----IANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y +LVWG + ++  E     I +W   +     D+V  
Sbjct: 74  ALSKAADKELKRQFREREPKKYYQALVWGHLEQDSGEINLPMICDW-ENRPRQRIDFVF- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ ++V++        +++ P TGR+HQLR+H L +G PI+GD K+ ++
Sbjct: 132 -------GKRAVTFYEVLERLPTNCTRVKLTPITGRSHQLRLHTLALGHPILGD-KFYSH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    SP   +L LHA  + + HP  G
Sbjct: 184 PQAKAMSP---RLCLHAEELTITHPITG 208


>gi|260654932|ref|ZP_05860420.1| ribosomal large subunit pseudouridine synthase D [Jonquetella
           anthropi E3_33 E1]
 gi|260630247|gb|EEX48441.1| ribosomal large subunit pseudouridine synthase D [Jonquetella
           anthropi E3_33 E1]
          Length = 301

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 113/225 (50%), Gaps = 23/225 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW--VDSKGQKPRLTHRLDQETSGI 157
           +Y D  + V  K AGI+V  G+G      ++G +K++  +   G +P + HRLD  TSG+
Sbjct: 81  VYADDWLAVVEKLAGIAVHPGAGRKDGTLVNGLVKTFGPLPGAGLRPGIVHRLDIGTSGL 140

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVV 216
           +VVART  A   L   F  RR++K Y +LV G IP ++     +  + +S     Y  + 
Sbjct: 141 MVVARTPQAYLFLQREFSQRRVEKTYLALVHGWIPASQGTL--DGPIGRSR----YDRLK 194

Query: 217 KQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                    A++ ++ +      +   C +E    TGRTHQ+RVH   +GC + GD  Y 
Sbjct: 195 MAVRADGRRAVTRYRTLWTRGSLSLTACRIE----TGRTHQIRVHMASIGCYLDGDRLYG 250

Query: 274 A-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
             +   +F   ++ +++LHA  +   HP  GR +   +PLP  ++
Sbjct: 251 PKDVSRHF---LEGRVFLHAWRLSFHHPSDGRTMNFRSPLPDELI 292


>gi|94987157|ref|YP_595090.1| pseudouridylate synthases, 23S RNA-specific [Lawsonia
           intracellularis PHE/MN1-00]
 gi|94731406|emb|CAJ54769.1| Pseudouridylate synthases, 23S RNA-specific [Lawsonia
           intracellularis PHE/MN1-00]
          Length = 321

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 81/306 (26%), Positives = 134/306 (43%), Gaps = 16/306 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M +   +Q ++V ++E   +L ++          + L + +R+GQ R++ KRV     + 
Sbjct: 1   MYIELIMQPIIVSSNEAGQKLFQFLTRRLTVPKSI-LHRWIRTGQTRINGKRVTPFTIVN 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL---LYEDSKIYVFNKPAGI 117
               +RIPP             ++ +  +++  S    S L   +    +  +F KPAG+
Sbjct: 60  FKDKIRIPPFAYEYKKKDLTTSLIHNQYDISPISSHTTSPLPPVIAHSPEFIIFYKPAGL 119

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +V GG+G    +   L          P   HRLD++TSG+L+VA+T  + ++ +E F   
Sbjct: 120 AVHGGTGQTDSLAHRLSQHYAHSTFMPTPVHRLDKDTSGLLLVAKTYNSLRYFSELFASH 179

Query: 178 RIQ--KIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             Q  K Y + V GI P  +  C+ + L KK            QN+     A      + 
Sbjct: 180 STQLTKEYLAWVVGICPWTQPICLEDILTKKQKQDNYSRLNSYQNKLQQTSAQKASLTVR 239

Query: 235 CFAQ--KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           C  Q      L ++ HTGRTHQ+R+     G PI+GD KY    +        + L LHA
Sbjct: 240 CIKQYKDKSLLLIKLHTGRTHQIRIQLSIHGFPIIGDKKYGNTIRS-------HNLKLHA 292

Query: 293 RYMDLP 298
             +  P
Sbjct: 293 FRLSFP 298


>gi|329113807|ref|ZP_08242578.1| Putative RNA pseudouridine synthase [Acetobacter pomorum DM001]
 gi|326696817|gb|EGE48487.1| Putative RNA pseudouridine synthase [Acetobacter pomorum DM001]
          Length = 206

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 63/188 (33%), Positives = 92/188 (48%), Gaps = 14/188 (7%)

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
            NKPAG+ V  G      ++ +    +  +   P L HRLD +TSG L +A  +     L
Sbjct: 1   MNKPAGLPVHAGPAGGPSVEDWFPL-LSRRKDGPWLAHRLDTDTSGCLAIALRKQPLLAL 59

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            ++F  +  QKIYW++V   P+     I   L K+S   G +  V   +     +A + +
Sbjct: 60  QQAFATKTAQKIYWAVVQTGPQANTGRIDLPLEKQSSKKG-WQMVASPS---GTHAATKW 115

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           KV+   ++  CWLE+   TGRTHQ RVH   MG PI+GD  Y         +P    L+L
Sbjct: 116 KVLG-RSKGVCWLELTLETGRTHQARVHCAAMGWPIIGDPLY--------GTPHSEGLHL 166

Query: 291 HARYMDLP 298
            AR + LP
Sbjct: 167 LARSLTLP 174


>gi|251793535|ref|YP_003008264.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           aphrophilus NJ8700]
 gi|247534931|gb|ACS98177.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           aphrophilus NJ8700]
          Length = 219

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/207 (32%), Positives = 104/207 (50%), Gaps = 14/207 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+Y D  I V NKP+G+    G+   Y+      S V  K       HRLD  TSGIL+ 
Sbjct: 16  LVYRDDYIAVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPAHRLDMATSGILLF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A ++AA + L   FR R  +K Y +LVWG  +     +   L+       D+ +  +Q  
Sbjct: 74  ALSKAADRELKRQFREREPKKYYQALVWGHVEQDHGVVELPLI------CDWENRPRQKI 127

Query: 221 KGAN--YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             A    A++ + V+  +      +++ P TGR+HQLR+H L +G PI+GD K+ A+ + 
Sbjct: 128 CFAQGKRAVTFYDVLQRYPNNTTRVKLTPITGRSHQLRLHMLALGHPILGD-KFYAHPQA 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRL 305
              SP   +L LHA  + + HP  G +
Sbjct: 187 KAMSP---RLCLHAESLQIQHPISGEI 210


>gi|27804835|gb|AAO22876.1| AgmF [Myxococcus xanthus]
          Length = 264

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/269 (27%), Positives = 124/269 (46%), Gaps = 37/269 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHI 77
           R+D++    +P +    +  ++ +G V  D +  K   R++ G+  V+ IP  + A+   
Sbjct: 19  RVDQYLARAFPDLTRSRIHGLIEAGHVLADGQPAKPARRLRGGELLVLHIPAPVPAVPLA 78

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL---- 133
            +                     LL+ED  + V +K AG+ V  G+G   H  G L    
Sbjct: 79  EELP-----------------LALLHEDRDLVVVDKAAGMVVHPGAG---HASGTLVNAL 118

Query: 134 ----KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               K      G+ +P + HRLD++T+G LVVA+   A   L ++F+ R ++K Y +LV 
Sbjct: 119 LHRVKDLAGVGGELRPGIVHRLDKDTTGCLVVAKNEQALVALQKAFKTRAVEKTYLALVH 178

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+P  +      +     H          + ++G N AI+ ++V++ F      +E+   
Sbjct: 179 GVPPAEGRIETLYGRHPIH----RQRFTGKVKEGKN-AITEYRVLETF-DGAALVEVDLL 232

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           TGRTHQ+RVH    G P++ D  Y A  K
Sbjct: 233 TGRTHQIRVHLSEAGHPLLCDALYGAGRK 261


>gi|56708307|ref|YP_170203.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis SCHU S4]
 gi|110670778|ref|YP_667335.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis FSC198]
 gi|224457427|ref|ZP_03665900.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|254370790|ref|ZP_04986795.1| hypothetical protein [Francisella tularensis subsp. tularensis
           FSC033]
 gi|254875128|ref|ZP_05247838.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|54113047|gb|AAV29157.1| NT02FT0135 [synthetic construct]
 gi|56604799|emb|CAG45878.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis SCHU S4]
 gi|110321111|emb|CAL09261.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis FSC198]
 gi|151569033|gb|EDN34687.1| hypothetical protein FTBG_00600 [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254841127|gb|EET19563.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|282159538|gb|ADA78929.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis NE061598]
          Length = 332

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 142/318 (44%), Gaps = 34/318 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E       +NL          +++ED  I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWIAE------DINLK---------IIFEDDDIIVIDKPVNMIVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +  L  + D + + PR  + HRLD++TSG++V A++  A  +L +    R++ + Y
Sbjct: 117 GTVSNALLHRYKD-QDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC 241
            ++V G      E      + +  IG D  +  K   N +G   AI+H+  I+ +   F 
Sbjct: 176 LAIVEG------EIYKQGTINQP-IGRDPTNRTKMAINYRGKE-AITHYTSIEVY-DGFT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPH 299
            +E Q  TGRTHQ+RVH   +  P+VGD  Y   +         I  +  LHA  +   H
Sbjct: 227 LIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITIPTRQALHAYKLSFIH 286

Query: 300 PEGGRL-QITAPLPAHMV 316
           P   ++ +  + LP  M+
Sbjct: 287 PTTAKMVKFKSKLPEDML 304


>gi|145637747|ref|ZP_01793398.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae PittHH]
 gi|145269045|gb|EDK08997.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae PittHH]
          Length = 219

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/212 (32%), Positives = 107/212 (50%), Gaps = 20/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+ D  + S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVSGNQPQYY-DSVM-SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG  +N         I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD K+ ++
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGD-KFYSH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            +    SP   +L LHA  + + HP  G   I
Sbjct: 184 PQAKVMSP---RLCLHAEELTITHPITGETMI 212


>gi|118497849|ref|YP_898899.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. novicida U112]
 gi|254374659|ref|ZP_04990140.1| hypothetical protein FTDG_00834 [Francisella novicida GA99-3548]
 gi|118423755|gb|ABK90145.1| ribosomal large subunit pseudouridine synthase D [Francisella
           novicida U112]
 gi|151572378|gb|EDN38032.1| hypothetical protein FTDG_00834 [Francisella novicida GA99-3548]
          Length = 332

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 83/320 (25%), Positives = 145/320 (45%), Gaps = 38/320 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E       +NL          +++ED  I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWIAE------DINLK---------IIFEDDDIIVIDKPVNMIVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +  L  + D + + PR  + HRLD++TSG++V A++  A  +L +    R++ + Y
Sbjct: 117 GTVSNALLHRYKD-QDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC 241
            ++V G      E      + +  IG D  +  K   N +G   AI+H+  I+ +   F 
Sbjct: 176 LAIVEG------EIYQQGTINQP-IGRDPTNRTKMAINYRGKE-AITHYTPIEVY-DGFT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF----KGNFTSPIQNKLYLHARYMDL 297
            +E Q  TGRTHQ+RVH   +  P+VGD  Y  +     K   T+P +    LHA  +  
Sbjct: 227 LIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITTPTRQA--LHAYKLSF 284

Query: 298 PHPEGGRL-QITAPLPAHMV 316
            HP   ++ +  + LP  M+
Sbjct: 285 IHPTTAKMVKFKSKLPEDML 304


>gi|313665289|ref|YP_004047160.1| pseudouridine synthase, RluA family [Mycoplasma leachii PG50]
 gi|312949430|gb|ADR24026.1| pseudouridine synthase, RluA family [Mycoplasma leachii PG50]
          Length = 310

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 121/237 (51%), Gaps = 19/237 (8%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSK 140
           ILD+  NL K+ D    I+ Y+D  + V NK   I+V        +  ++  L S V+  
Sbjct: 70  ILDT--NLVKNKDIDLDII-YQDDDLLVINKQNNITVHPSLNNTNNTIVNALLASDVELS 126

Query: 141 G----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                 +P + HR+D++T+G+L++A+     + L+E F+  RI K Y ++V G+ K  K 
Sbjct: 127 SINGELRPGIVHRIDKQTTGLLIIAKNDKTHKLLSEMFKSHRIYKEYLAIVTGVIKPNKG 186

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I +  + +S      + V  +N K    AI+ F++++ F  K   ++ Q  TGRTHQ+R
Sbjct: 187 LI-DAPIGRSQTDRKKMSVTAKNSKQ---AITTFELVERFL-KNTLVKCQIQTGRTHQIR 241

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           VH  ++  P++ D  Y    +  FT   Q   YLHA  +   HP     +++ +PLP
Sbjct: 242 VHFNYINHPVLNDPVYGKKHQ-EFTDFGQ---YLHAYKLKFTHPITKKEIELISPLP 294


>gi|294678837|ref|YP_003579452.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           capsulatus SB 1003]
 gi|294477657|gb|ADE87045.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           capsulatus SB 1003]
          Length = 217

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/220 (33%), Positives = 109/220 (49%), Gaps = 26/220 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           +L+ D +I V +K +G+    G G  +  D  ++     KG  P+  L HRLD +TSG++
Sbjct: 15  ILHADHEILVVDKQSGLLSVPGKG-DHKADCLIERL---KGAFPQVLLVHRLDGDTSGVM 70

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKK---ECIANWLLKKSHIGGDYV 213
           V A T  A +HL   F  R+ +K Y + +WG   PK  +       +W  +         
Sbjct: 71  VFALTAHAQRHLGLQFETRQTKKHYLARLWGHLEPKAGRVDLPLCVDWPNRPKQ------ 124

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           HV  +N K A    + +KV+         + + P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 125 HVDPENGKPAQ---TDWKVLRHDPDGTTRVRLTPLTGRSHQLRVHMLELGHPILGDPFYA 181

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                +F      +L LHA  + L HP+GG+ +  TAP P
Sbjct: 182 EGPARDFP-----RLMLHAESLRLRHPDGGQYMTFTAPCP 216


>gi|330878293|gb|EGH12442.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
 gi|330967569|gb|EGH67829.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 211

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/214 (31%), Positives = 110/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIHQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEAGKHALTFWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              P   +L LHA  +   HP  G RL    P P
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|325122993|gb|ADY82516.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter calcoaceticus PHEA-2]
          Length = 212

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/223 (31%), Positives = 107/223 (47%), Gaps = 17/223 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V +   K  L HRLD++
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLV-AIEPKTLLIHRLDRD 58

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     +   F+ R+  KIY +LV G  + +       +   S      +
Sbjct: 59  TSGILVFGLSKRGQSAIARQFQDRQTSKIYEALVAGHLEGEGTVDIPVIYDPSR---PPL 115

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+V  +      A++H++VI+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD 
Sbjct: 116 HIVDASHNKP--ALTHWQVIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDT 173

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            Y    +      +  +L LHA+ +   HP     L    P+P
Sbjct: 174 LYATPEQQ-----LVPRLCLHAKQLSFNHPVTAETLTFDCPVP 211


>gi|85058561|ref|YP_454263.1| 23S rRNA pseudouridine synthase D [Sodalis glossinidius str.
           'morsitans']
 gi|84779081|dbj|BAE73858.1| ribosomal large subunit pseudouridine synthase D [Sodalis
           glossinidius str. 'morsitans']
          Length = 326

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 90/340 (26%), Positives = 154/340 (45%), Gaps = 49/340 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   ++  +  G VRV+++       ++  G+ V I  
Sbjct: 10  TVSESQLGQRLDQALAELFPDYSRSRIKAWILDGLVRVNRRVTAVPKEKMLGGESVEI-- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                      Q  ++ +      +  L   ++YED  I V NKP  + V  G+G A   
Sbjct: 68  -----------QAFIEEAPRWEAQAIPLN--IVYEDDDILVINKPRDLVVHPGAGNA--- 111

Query: 130 DGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG     L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y
Sbjct: 112 DGTVLNALLHYFPPIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREY 171

Query: 184 WSLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            ++  G        ++ IA    K++H+    VH + +       A++++++++ F +  
Sbjct: 172 EAVAIGTMTAGGTLEQPIARHATKRTHMA---VHPMGKP------AVTNYRIMEHF-RAH 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLHA 292
             L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F   ++  ++  LHA
Sbjct: 222 TRLRLRLETGRTHQIRVHMAHINHPLVGDPLYGGRSRPPKGASDAFNEVLRSFDRQALHA 281

Query: 293 RYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLY 331
             + L HP     ++  APLP  MV    +L  K D  L+
Sbjct: 282 TLLRLYHPITSIEMEWHAPLPQDMVALIAAL--KADTELF 319


>gi|108804319|ref|YP_644256.1| ribosomal large subunit pseudouridine synthase D [Rubrobacter
           xylanophilus DSM 9941]
 gi|108765562|gb|ABG04444.1| ribosomal large subunit pseudouridine synthase D [Rubrobacter
           xylanophilus DSM 9941]
          Length = 305

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 142/307 (46%), Gaps = 43/307 (14%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+    Q++L  G  RV  +    + R++ G+VV              E ++ +  +   
Sbjct: 27  ISRSRAQRLLAEGLARVGGEAAAPSLRVRGGEVV--------------EARLPEEGLE-- 70

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-------QKP 144
             ++ +   +L+ED  I V +KPAG+ V  G+G   +  G L + +  +G       ++P
Sbjct: 71  --AEEIPVPILFEDEHIAVVDKPAGMVVHPGAG---NRSGTLVNALLGRGIAGGEDPERP 125

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HRLD++TSG++VVA+   A   L E    RR++++Y +LV G      E +      
Sbjct: 126 GIVHRLDRDTSGLMVVAKGEPAYSRLVEMLAARRVRRVYRALVVG------EGLPPSGTV 179

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            S +G D  +           A++HF+V+   A     L ++  TGRTHQ+RVH   +G 
Sbjct: 180 DSPVGRDPENPALMAAGVGRPAVTHFEVL-GEAAGHTMLRVRLETGRTHQIRVHLSAIGY 238

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           P+  D  Y     G        +L+LHA  +   HP  GR L   +P+P  + +    L 
Sbjct: 239 PVYADPLYGRAVPG-------RRLWLHAERLSFEHPAEGRPLDFFSPVPEELRRAAAELD 291

Query: 324 FKYDRNL 330
            +++  L
Sbjct: 292 ARFEELL 298


>gi|217972743|ref|YP_002357494.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217497878|gb|ACK46071.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 223

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 63/200 (31%), Positives = 106/200 (53%), Gaps = 12/200 (6%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP+G+    G   A+  D  L + + +   +  L HRLD  TSGI+V AR
Sbjct: 18  YKDRDLIIINKPSGLLSNPGRA-AHTFDCAL-TRLQTLYPETILVHRLDCATSGIMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
            + A  HL   F+ R+ +K+Y + V G +P  +++ + +  +        Y   ++  E 
Sbjct: 76  NKKAESHLKTQFQDRQSKKVYIAEVMGHVP--QEQGMIDLAIAPDTEHPPYQKTLQAGET 133

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           G   A+++++V++   +    +E+ P TGRTHQLRVH L +G  I+GD      F G+  
Sbjct: 134 GGKSALTYYRVLE-RRENSTLVELSPETGRTHQLRVHMLALGHAILGD-----EFYGDAE 187

Query: 282 S-PIQNKLYLHARYMDLPHP 300
               + +L LHA+ + L HP
Sbjct: 188 VIKAKPRLCLHAQSLSLTHP 207


>gi|296388259|ref|ZP_06877734.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           aeruginosa PAb1]
          Length = 211

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 116/214 (54%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D  + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSG++V
Sbjct: 8   IVHQDDALLVVDKPTLLLSVPGRAD--DNKDCLVTRLQENGYPEARIVHRLDWETSGLMV 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG+P+     I   L  +        HVV  +
Sbjct: 66  LARDADSHRELSRQFHDRETEKAYTALCWGLPELDSGRIE--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ ++V++   +++  +E+ P TGR+HQLRVH L +G P++GD  Y AN +  
Sbjct: 122 FEHGRHALTFWRVVE-RHERWSRVELTPITGRSHQLRVHMLSIGHPLLGDRLY-ANPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                  +L LHA  + L HP+ G RL+  +P P
Sbjct: 180 VA---HERLCLHASLLCLTHPQSGERLRFESPAP 210


>gi|225870653|ref|YP_002746600.1| RNA pseudouridylate synthase [Streptococcus equi subsp. equi 4047]
 gi|225700057|emb|CAW94108.1| putative RNA pseudouridylate synthase [Streptococcus equi subsp.
           equi 4047]
          Length = 296

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 119/236 (50%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++Y+D  + + NKP G+ V   +G         + YHI    K      G  +P + HR+
Sbjct: 76  IVYQDDVLAIINKPQGMVVHPSAGHSTGTLVNALLYHI----KDLSSINGVIRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIG 209
           D++TSG+L+VA+T  A Q L +  + ++  + Y ++V G +PK++        + ++ IG
Sbjct: 132 DKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHGNLPKDRG-------VIEAPIG 184

Query: 210 GDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  KQ    KG   A++ FKV++ F   + ++E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 185 RSEKDRKKQTVTAKGKE-ALTLFKVLERFGH-YTFVELQLETGRTHQIRVHMAYIGHPLA 242

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GD  Y     G   +      +LHA+ + L HP  G  L  T   P    +T + L
Sbjct: 243 GDPLY-----GPRKTLAGKGQFLHAQTLGLTHPVTGEELVFTVEPPEIFQRTLEQL 293


>gi|118361718|ref|XP_001014087.1| RNA pseudouridylate synthase family protein [Tetrahymena
           thermophila]
 gi|89295854|gb|EAR93842.1| RNA pseudouridylate synthase family protein [Tetrahymena
           thermophila SB210]
          Length = 881

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 82/286 (28%), Positives = 137/286 (47%), Gaps = 36/286 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRV----DKKRVKFNNRI-QSGQVVRIP-PVIN 72
           MRLD++ K HY  I + +LQ  LR  ++ V    D  + K  + I + G ++RIP   + 
Sbjct: 1   MRLDKYLKEHYG-IPWTSLQICLRKKEIFVKDVQDLSKHKNPDYILKEGDIIRIPFSFVE 59

Query: 73  ALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
               I   QK   + + L +   D  K +++YE+  I + NK  G+S QGG  ++ ++  
Sbjct: 60  KKEQIQNSQKQEQNEIKLDQSQIDKFKQMIIYENKNIIILNKANGVSCQGGQDVSLNLVT 119

Query: 132 FLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWG 189
             + + ++   QK  + HRLD+ TSG+L+V + +  A+     F  +  I K Y +LV  
Sbjct: 120 MGQQYLINQTNQKYLVAHRLDKVTSGVLMVPKNQQIAKIYGNLFNDKSNINKYYIALVRN 179

Query: 190 IPKNKKECI-ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------- 239
            PKN K  I A     +S       +++ +N K A+   +H++V+  F  +         
Sbjct: 180 SPKNFKAMINAPIEYSQSKQRAIVSNIIDENSKSAH---THYQVLAQFKMEDKNLAAKII 236

Query: 240 ------------FCWLEMQPHTGRTHQLRVHALHMG-CPIVGDHKY 272
                       F  L+++   GR HQ+RVH   +   PIVGD +Y
Sbjct: 237 NSEHDYIKDWGDFSLLKIRIQEGRKHQIRVHLSEISKTPIVGDARY 282


>gi|325913377|ref|ZP_08175744.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
 gi|325477303|gb|EGC80448.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
          Length = 292

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/279 (25%), Positives = 129/279 (46%), Gaps = 35/279 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKN-----HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           Y+ Y+ +  +E N  +D+  +N      + H  F+ ++K      + V+ K +  N ++ 
Sbjct: 13  YIYYLTISQNENNQNVDQIMRNLLIPRKWRH--FLRIEK-----NILVNDKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V NKPAG   Q
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENDDVLVINKPAG---Q 109

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L    +  G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 110 KTHPNLYETDTALNDCANYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQK 239
           + Y++ +            N       IG D + + K+  +     AI+H++V+     K
Sbjct: 170 RSYFAWIDATNDISDNGTINL-----PIGDDPLDMRKRMVRTDGLKAITHYQVVKKIGSK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++ 
Sbjct: 225 IL-VKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQA 262


>gi|303229468|ref|ZP_07316258.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302516004|gb|EFL57956.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 305

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 88/291 (30%), Positives = 137/291 (47%), Gaps = 47/291 (16%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +Q +++SG V V+ K  K N R+ +   + +          I E +    SV +      
Sbjct: 30  IQSLIKSGHVLVNGKVGKANLRLNADSTISVD---------IPEPE----SVEILPED-- 74

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRL 150
           +    LYED  I + NKP G+ V    G      ++  L    D  G     +P + HRL
Sbjct: 75  IPVEYLYEDHDIIIVNKPRGMVVHPAIGNYSGTLVNALLYHCKDLSGINGEIRPGIVHRL 134

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+++ A+  AA   L E  +    ++ Y +LV G    +K  I      K+ IG 
Sbjct: 135 DKDTSGVMMAAKNDAAHIGLAEQVKAHSAKRTYLALVQGNIVEEKGII------KAPIGR 188

Query: 211 D-----YVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHM 262
                  + VV +N K    A++HFKV++ +       C LE    TGRTHQ+RVH  H+
Sbjct: 189 HPKDRMKMAVVFENSK---EAVTHFKVLERYGYHTLVECVLE----TGRTHQIRVHFAHI 241

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           G P+V D  Y    + +F  PI+ +  LH+  +D+ HP  G  +   AP+P
Sbjct: 242 GHPVVNDPFYGYR-RMDF--PIEGQA-LHSHTLDVVHPITGEPMHFEAPVP 288


>gi|15598442|ref|NP_251936.1| pseudouridine synthase RluA [Pseudomonas aeruginosa PAO1]
 gi|107102775|ref|ZP_01366693.1| hypothetical protein PaerPA_01003843 [Pseudomonas aeruginosa PACS2]
 gi|218890561|ref|YP_002439425.1| pseudouridine synthase RluA [Pseudomonas aeruginosa LESB58]
 gi|254236207|ref|ZP_04929530.1| pseudouridine synthase RluA [Pseudomonas aeruginosa C3719]
 gi|254241933|ref|ZP_04935255.1| pseudouridine synthase RluA [Pseudomonas aeruginosa 2192]
 gi|9949369|gb|AAG06634.1|AE004747_7 pseudouridine synthase RluA [Pseudomonas aeruginosa PAO1]
 gi|126168138|gb|EAZ53649.1| pseudouridine synthase RluA [Pseudomonas aeruginosa C3719]
 gi|126195311|gb|EAZ59374.1| pseudouridine synthase RluA [Pseudomonas aeruginosa 2192]
 gi|218770784|emb|CAW26549.1| pseudouridine synthase RluA [Pseudomonas aeruginosa LESB58]
          Length = 211

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/214 (31%), Positives = 116/214 (54%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D  + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSG++V
Sbjct: 8   IVHQDDALLVVDKPTLLLSVPGRAD--DNKDCLVTRLQENGYPEARIVHRLDWETSGLMV 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG+P+     I   L  +        HVV  +
Sbjct: 66  LARDADSHRELSRQFHDRETEKAYTALCWGLPELDSGRIE--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ ++VI+   +++  +E+ P TGR+HQLRVH L +G P++GD  Y AN +  
Sbjct: 122 FEHGRHALTFWRVIERH-ERWSRVELTPITGRSHQLRVHMLSIGHPLLGDRLY-ANPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                  +L LHA  + L HP+ G RL+  +P P
Sbjct: 180 AA---HERLCLHASLLCLTHPQSGERLRFESPAP 210


>gi|283780201|ref|YP_003370956.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
 gi|283438654|gb|ADB17096.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
          Length = 313

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/224 (29%), Positives = 111/224 (49%), Gaps = 20/224 (8%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED  + V  KPA +    + +   G +   +  ++K  + S+G+     HRLD+  S
Sbjct: 89  IVYEDRHLIVVEKPAALLTVPTPKNDRGTLLERVANYVK--IVSRGKGAFQVHRLDRGVS 146

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+  +T   AQ L + F M + ++ Y ++V G     +  I ++L        D    
Sbjct: 147 GLLIFGKTTELAQMLRDQFAMHKPEREYVAIVRGKLDKPEGMIESFLATDR----DLNRY 202

Query: 216 VKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +E    +A++H++VI+  A       WLE    TGR +Q+RVH    G P++GD +Y
Sbjct: 203 STDDESIGQHAVTHYRVIEELAGASVVQVWLE----TGRRNQIRVHFAEAGHPLIGDQRY 258

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            A+   + T     ++ LHAR + L HP  G  L+  +PLP  M
Sbjct: 259 RADEAAD-TRWTHARIALHARLLGLSHPMTGEPLRFESPLPHEM 301


>gi|121534542|ref|ZP_01666364.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
 gi|121306794|gb|EAX47714.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
          Length = 300

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 80/284 (28%), Positives = 128/284 (45%), Gaps = 35/284 (12%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
            +QK+ R   + ++ K V    ++++   +R+    ++   +  EQ  ++          
Sbjct: 34  QIQKLTRHKGILLNGKTVYLQKKVKADDTLRVLISGDSAYGVQPEQGPVE---------- 83

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQ 152
                +LYED  + V NKPA   V   GS  +  +  +L   ++ +G     R  HRLD+
Sbjct: 84  -----ILYEDDYLLVINKPAYQLVHPTGSTTSGTLANYLAYHLEQRGIICTIRAVHRLDR 138

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           ETSG ++ A+   +   L +    R +++ YW+LV G        I   +       G +
Sbjct: 139 ETSGCIIFAKDAHSQFLLEQQLAARTLKRTYWALVKGSVSPPAGTIDAPI-------GPH 191

Query: 213 VHVVKQNEKGA--NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            H   +    A  + AI+H++ I  F      LE+   TGRTHQ+RVH  H+G PIVGD 
Sbjct: 192 PHFANRRAVTAHGDPAITHYQTIRSFPDA-TLLELILDTGRTHQIRVHLAHLGYPIVGDG 250

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
            Y         SP   +  LHA  +   H +  R L + APLPA
Sbjct: 251 MY------GVRSPWIGRQALHAVSVSFQHLQDQRELTVHAPLPA 288


>gi|50122269|ref|YP_051436.1| 23S rRNA pseudouridine synthase D [Pectobacterium atrosepticum
           SCRI1043]
 gi|49612795|emb|CAG76245.1| ribosomal large subunit pseudouridine synthase D [Pectobacterium
           atrosepticum SCRI1043]
          Length = 325

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 87/332 (26%), Positives = 157/332 (47%), Gaps = 47/332 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V+++   + K   ++  G+ V   
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILDNRVQINGNVINKPKEKVLGGESV--- 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
               A++ +I+E+   ++          +K  ++YED  I V NKP  + V  G+G   +
Sbjct: 66  ----AIDALIEEEARWEAQ--------DIKLDIVYEDQDILVINKPRDLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + 
Sbjct: 111 PDGTVLNALLHYYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITRE 170

Query: 183 YWSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G        ++ IA    K++H+    VH + +       A++H+++++ F + 
Sbjct: 171 YEAVAIGSMTAGGMVEQPIARHATKRTHMA---VHPMGKP------AVTHYRIMEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y       KG     I+     ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMSHIDHPLVGDQLYGGRPRPPKGASDDFIEMLRGFDRQALH 280

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           A  +   HP  G +++  A LP  MV   D+L
Sbjct: 281 ATMLRFYHPITGIQMEWHAALPQDMVDLIDAL 312


>gi|148654105|ref|YP_001281198.1| pseudouridine synthase [Psychrobacter sp. PRwf-1]
 gi|148573189|gb|ABQ95248.1| ribosomal large subunit pseudouridine synthase A [Psychrobacter sp.
           PRwf-1]
          Length = 237

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 65/216 (30%), Positives = 109/216 (50%), Gaps = 27/216 (12%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           DF+  + +YED  + + +KPAG+    G  +       L S ++    + +L HRLD +T
Sbjct: 25  DFMTQVTVYEDEDLLLVDKPAGLLSIDGKDLKVS----LLSRLERANPEVKLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIA----NWLLKKSH 207
           SG+++ A+ + A  H+++ F  R  QK Y ++V G   IP  K E          +K  H
Sbjct: 81  SGLMIFAKNKQAQTHISKQFIERIPQKEYQAIVQGTLAIPGKKGEINIPVRYEPSIKPKH 140

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGC 264
           +          + +   +A++H++V+    +K      + + P TGR+HQLRVH +H+G 
Sbjct: 141 VA---------DPEWKKHALTHYEVLHHELRKGRPVTRVALHPVTGRSHQLRVHMVHLGH 191

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            I+GD  Y    +G   S +  +L LHA  + L HP
Sbjct: 192 VIIGDPIYA---EGEALS-LAPRLNLHAHKLRLKHP 223


>gi|114561701|ref|YP_749214.1| pseudouridylate synthase [Shewanella frigidimarina NCIMB 400]
 gi|114332994|gb|ABI70376.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           frigidimarina NCIMB 400]
          Length = 225

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 62/205 (30%), Positives = 99/205 (48%), Gaps = 21/205 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NKP+G+    G    YH    + S V ++    ++ HRLD  TSG++VV
Sbjct: 16  IVYQDKDILVANKPSGLLSVPGREAIYH--DSIYSRVLAEHPNAQIVHRLDMATSGVIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-----IPKNKKECIANWLLKKSHIGGDYVHV 215
           A  R+A + L   FR R   K Y++ V G     I K     I +W  +           
Sbjct: 74  ALRRSAERELKRQFRDRETAKTYFARVAGHMKSNISKVDLPLICDWPNRPKQ-------- 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K +      +++  +V+  +  K   +++ P TGR+HQLRVH + +G PI+GD  Y   
Sbjct: 126 -KVDHTVGKPSVTLVEVV-SYGAKSTLVKLTPITGRSHQLRVHMMALGHPILGDGFYADP 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
              + +     +L LHA  + + HP
Sbjct: 184 LAKSLSP----RLLLHAAALSITHP 204


>gi|328946974|ref|YP_004364311.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
 gi|328447298|gb|AEB13014.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
          Length = 248

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 74/246 (30%), Positives = 114/246 (46%), Gaps = 28/246 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++Y D +I V NK +G+ V        A  +D   +    S        HR+D++TSGI+
Sbjct: 9   VIYSDDEIVVLNKKSGLLVAADRYDAEAPRLDLLAEKEFGSLFA----VHRIDKDTSGIV 64

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A+T  A ++++  F  R ++K Y  LV G P      +   LL      GD  H    
Sbjct: 65  IYAKTPEAHRNISIQFTERTVKKTYHCLVNGHPAWDNFTVDLPLLPD----GDDRHRTVI 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           N+K    ++++ +V+      + W++  P TGRTHQ+R H    G PIV D  Y  N K 
Sbjct: 121 NKKFGKPSVTYLEVVG-HCGPYSWIKAFPKTGRTHQIRAHLQSTGFPIVCDPLYSGNQKP 179

Query: 279 NFTS--------------PIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
              S              P+ N+L LHA  +++ HP+ G ++  TAP P  M    + L 
Sbjct: 180 VRLSDIKRKWNGDVYEERPLLNRLALHAYSIEIAHPKTGEQIIFTAPYPKDMDAVRNQLA 239

Query: 324 --FKYD 327
             FK D
Sbjct: 240 KIFKID 245


>gi|317493312|ref|ZP_07951734.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918705|gb|EFV40042.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 248

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/207 (34%), Positives = 111/207 (53%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  + + V          HRLD  TSG++ 
Sbjct: 45  VLYQDDHIIVVNKPSGLLSVPGKA--EEHKDSVM-TRVQVDFPIAESVHRLDMATSGVIA 101

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG  ++ +  I   L+       D+ +  KQ 
Sbjct: 102 VALTKAAERELKRQFREREPKKSYIARVWGHMEHDEGLIDLPLI------CDWPNRPKQK 155

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + A + ++V+   A     +++ P TGR+HQLRVH L +G PI+GD K+ A+ 
Sbjct: 156 VCFEHGKS-AQTQYQVLSRDADGSTRVKLTPITGRSHQLRVHMLALGHPILGD-KFYAHP 213

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    +   ++L LHA+ + + HPE G
Sbjct: 214 EAKAMA---SRLQLHAQELQITHPEFG 237


>gi|84394045|ref|ZP_00992782.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           12B01]
 gi|84375331|gb|EAP92241.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           12B01]
          Length = 244

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 65/207 (31%), Positives = 107/207 (51%), Gaps = 15/207 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I V NKPAG+ SV G   +  H D      V    +  ++ HRLD  TSG+++
Sbjct: 16  IVYQDDDILVVNKPAGLLSVPGR--LPEHYDSMWSRLVVEFAEI-QVVHRLDMSTSGLML 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A +HL + F+ R   K+Y++ VWG  +  +  I   L+       D+ +  +Q 
Sbjct: 73  LAKHKQAERHLKKQFQYRLTHKLYYARVWGSVEEAEGLIDLPLI------CDWPNRPRQK 126

Query: 220 EKGANYAISHFK-VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
               +   S  + V++    +   L++ P TGR+HQLRVH + +G PIVGD  Y      
Sbjct: 127 VCFEDGKPSQTRYVVERQEAQTALLKLLPITGRSHQLRVHCMELGNPIVGDEFYATPDAF 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRL 305
           N++    ++L LHA  +   HP   +L
Sbjct: 187 NYS----DRLALHACELSFYHPANNQL 209


>gi|330973896|gb|EGH73962.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aceris str. M302273PT]
          Length = 211

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/204 (32%), Positives = 108/204 (52%), Gaps = 12/204 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+ + V +KPA + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIHQDAAVLVIDKPALLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEGGKHALTFWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG 303
              P   +L LHA  +   HP  G
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTG 200


>gi|87308280|ref|ZP_01090421.1| pseudouridine synthase RluA [Blastopirellula marina DSM 3645]
 gi|87288837|gb|EAQ80730.1| pseudouridine synthase RluA [Blastopirellula marina DSM 3645]
          Length = 210

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/215 (31%), Positives = 107/215 (49%), Gaps = 16/215 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  + V +KP+G+    G G   +    ++   D  G   R  HRLD++TSG++V+
Sbjct: 8   VLHQDEHLIVLDKPSGLLSVPGRGADKYDSLAVQVADDFPGA--RNVHRLDRDTSGVIVM 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A   AA + L+  F  R   K Y ++  G+   +   I   L K      D+ H  +   
Sbjct: 66  ACDAAAHRELSRQFEQRETDKRYIAIAAGVVIEEAGKIELPLRK------DFDHPPRHMV 119

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    A+SH++V   +A     L + P TGR+HQLRVH   +G PI+GD  Y      
Sbjct: 120 DVQLGKLALSHWQVEARYADS-TRLSLIPQTGRSHQLRVHLQAIGHPILGDPLYAP---- 174

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
             T    N+L LHA  +++ HP  G R++  AP P
Sbjct: 175 AETQAAANRLMLHAIELEITHPASGERIRFVAPAP 209


>gi|320325275|gb|EFW81342.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. glycinea str. B076]
          Length = 211

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/214 (32%), Positives = 110/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIYQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L  G P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCCGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEGGKHALTFWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              P   +L LHA  +   HP  G RL    P P
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|330991266|ref|ZP_08315217.1| Putative RNA pseudouridine synthase [Gluconacetobacter sp. SXCC-1]
 gi|329761285|gb|EGG77778.1| Putative RNA pseudouridine synthase [Gluconacetobacter sp. SXCC-1]
          Length = 242

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 56/177 (31%), Positives = 83/177 (46%), Gaps = 8/177 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L   +LY DS+  V +KP G+ V         ++ +    +      P L HRLDQ+T+G
Sbjct: 7   LPCAVLYHDSRFIVLDKPPGLPVHPARAGGPSVEDWFPL-ISRHRNGPWLAHRLDQDTAG 65

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LVVA  + A     E F   R +K YW++V G+P      + +  L +   G  +   V
Sbjct: 66  CLVVALRKQALVAAQECFAAGRARKTYWAIVQGMPAGPSGTV-DAPLARVEQGRQWRMQV 124

Query: 217 KQNEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
               +G   A + ++ +    D       WLE+   TGRTHQ R H   +GCPI+GD
Sbjct: 125 --TARGGQPARTRWRTLATGQDGAGNPISWLELVLETGRTHQARAHCAALGCPILGD 179


>gi|329728841|gb|EGG65262.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 305

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 85/327 (25%), Positives = 150/327 (45%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +     
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYK----- 55

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++   I      + E  IL  ++NL          + YED  + V  KP G+ V    
Sbjct: 56  -VKLNDHIVVTEKEVVEADILPENLNLD---------IYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +   K+     G+ +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAP--IGRNKNDRQSMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KNYTLVECQLETGRTHQIRVHMRYIGFPLVGDPKYGPKKTLDIGGQA-----LHAGLIG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G  ++  A LP       D++
Sbjct: 274 FEHPVTGEYIERHAELPQDFEDLLDTI 300


>gi|304316700|ref|YP_003851845.1| pseudouridine synthase [Thermoanaerobacterium thermosaccharolyticum
           DSM 571]
 gi|302778202|gb|ADL68761.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 306

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 93/328 (28%), Positives = 158/328 (48%), Gaps = 43/328 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++ E D+ + R+D +  +   +     L+K++  G V+V+   +K N +++ G  V +  
Sbjct: 9   IIAEKDDVDKRIDSFLASELDYTRSY-LKKLILDGLVKVNGLLIKPNYKLKEGDSVDVN- 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                   I E + +D S       + +   ++YED  I V NKP G+ V    G     
Sbjct: 67  --------IPEAEEIDLS------PENIPLDIIYEDDDIIVINKPQGMVVHPAPGNYSGT 112

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH      S ++ +  +P + HRLD++TSG++VVA+   A   L+   + R I 
Sbjct: 113 LVNALLYHCKNL--SGINGE-LRPGIVHRLDKDTSGVMVVAKNDKAHLDLSNQIKERTIL 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQ 238
           K Y ++V G+ K+ +  I      ++ IG D+V   K    E G  YA++ +KV++ +  
Sbjct: 170 KKYIAIVEGVIKDDEGSI------EAPIGRDHVERKKMAVTEDG-RYALTLYKVLERYKN 222

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E    TGRTHQ+RVH  ++G PIVGD  Y    K  F    Q    LH++ + L 
Sbjct: 223 N-SLIEATIKTGRTHQIRVHMSYIGHPIVGDEVYGYK-KQRFNLLGQ---ALHSKLLGLV 277

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           HP     ++  AP+P +  +  + L  K
Sbjct: 278 HPSKKIYMEFEAPIPEYFERLINILKSK 305


>gi|300948988|ref|ZP_07163044.1| pseudouridine synthase, RluA family [Escherichia coli MS 116-1]
 gi|300957377|ref|ZP_07169594.1| pseudouridine synthase, RluA family [Escherichia coli MS 175-1]
 gi|300315880|gb|EFJ65664.1| pseudouridine synthase, RluA family [Escherichia coli MS 175-1]
 gi|300451545|gb|EFK15165.1| pseudouridine synthase, RluA family [Escherichia coli MS 116-1]
          Length = 326

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 88/339 (25%), Positives = 157/339 (46%), Gaps = 47/339 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V   
Sbjct: 9   ATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV--- 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             INA   I +E +     + L          ++YED  I + NKP  + V  G+G   +
Sbjct: 66  -AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIIINKPRDLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++ VA+T  A   L ES + R I + 
Sbjct: 111 PDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMAVAKTVPAQTRLVESLQRREITRE 170

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    VH + +       A++H+++++ F + 
Sbjct: 171 YEAVAIGHMTAGGTVDEPISRHPTKRTHMA---VHPMGKP------AVTHYRIMEHF-RV 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
           A  + L HP  G  ++  AP+P  MV+  + +   ++ +
Sbjct: 281 ATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH 319


>gi|149199657|ref|ZP_01876690.1| ribosomal large subunit pseudouridine synthase D [Lentisphaera
           araneosa HTCC2155]
 gi|149137310|gb|EDM25730.1| ribosomal large subunit pseudouridine synthase D [Lentisphaera
           araneosa HTCC2155]
          Length = 221

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/224 (31%), Positives = 105/224 (46%), Gaps = 14/224 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETS 155
           +L+ED+ I + NK AG  VQ    G + +   +  FLK     +G     +THRLD+  S
Sbjct: 6   VLHEDNHIIIVNKRAGQVVQIDESGDTPLCEIVQAFLKKKHKKEGNVFLGVTHRLDRPVS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L + F+ + IQK YW+     P    + + ++L+K         H 
Sbjct: 66  GVIIFAKTSKALTRLNKMFQEKEIQKTYWAFCLANPAKASDLLTHYLVKDRRKNKTKAHN 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K  E    ++   +K I    ++   LE+ P TGR HQ+RV    +GC I GD KY A 
Sbjct: 126 KKVTE--GKFSQLEYKEIKRSGRQ-SLLEVNPLTGRPHQIRVQLASIGCIIKGDLKYGAP 182

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
            K N    I     LH+R +   HP   + +I    P H    W
Sbjct: 183 -KANEDKSI----CLHSRRVRFIHPV-SKEEIDLEAPLHRPGLW 220


>gi|312147848|gb|ADQ30507.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi JD1]
          Length = 326

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 97/181 (53%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 86  IIYEDFNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+  +  + L + F+ +R  K+Y ++V G   +    I +++ +  H    
Sbjct: 145 KDTSGVLICAKNISTLRFLAQQFKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKK 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 205 FSVSKDRGKK----ALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 259

Query: 272 Y 272
           Y
Sbjct: 260 Y 260


>gi|227494657|ref|ZP_03924973.1| possible pseudouridylate synthase [Actinomyces coleocanis DSM
           15436]
 gi|226831839|gb|EEH64222.1| possible pseudouridylate synthase [Actinomyces coleocanis DSM
           15436]
          Length = 304

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 86/329 (26%), Positives = 146/329 (44%), Gaps = 38/329 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSG 62
           M+ ++Y+ V +   N R+D              +  + RS   + +D ++V+ N      
Sbjct: 1   MSDIRYLPVPDGLANERIDSALSR---------MLGLSRSAAGKLIDDEKVRVNG----- 46

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVN--LTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
                  V+ A +H +   +I+++ +     K +  +   ++YED  + V NKP G++  
Sbjct: 47  -------VVVAKSHRLSINEIIEADLEPPALKPAPIVGMDIVYEDEDLVVVNKPVGVAAH 99

Query: 121 GGSG--IAYHIDGFLKSW--VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESF 174
           GG G      ID    +   + + G   R  + HRLD  TSG + VA++  A   L  +F
Sbjct: 100 GGPGWDGPTVIDNLEAAGFRISTSGPPERKGIVHRLDVGTSGAMAVAKSELAYTKLKHAF 159

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + RR+ K Y +LV G P   K  I   + +  H   ++   V     G   AI+H++  +
Sbjct: 160 KERRVHKTYHALVSGHPDPAKGTIDAPIAR--HPSKEWRMAVV---AGGRPAITHYQTQE 214

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                   L++   TGRTHQ+RVH   +G P VGD  Y A+ K      +  + +LH+  
Sbjct: 215 LLPGA-ALLDITLETGRTHQIRVHFSAIGHPCVGDTFYGADQKQADQLGLTRQ-WLHSVE 272

Query: 295 MDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           +   HP    L  + AP    + K  + L
Sbjct: 273 LQFVHPRTNALTTVKAPYTEDLSKALEQL 301


>gi|242280738|ref|YP_002992867.1| pseudouridine synthase [Desulfovibrio salexigens DSM 2638]
 gi|242123632|gb|ACS81328.1| pseudouridine synthase [Desulfovibrio salexigens DSM 2638]
          Length = 214

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/211 (33%), Positives = 102/211 (48%), Gaps = 28/211 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++Y D KI V NKP+G+    G G       +    K + + +  K    HRLD +TSG+
Sbjct: 9   IVYADRKIVVVNKPSGLLSVPGRGPENQDCVVTRVQKMFPECR--KFPAVHRLDMDTSGL 66

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL----LKKSHIGGDYV 213
           LV+  T  A + L E F+ R+++K Y +L+ GI K     I          + +   D +
Sbjct: 67  LVLGLTARAVRELMEQFQKRQVKKRYEALLEGIVKEDSGVIEMAFRLDPYNRPYQVYDPI 126

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDH 270
           H            I+H++ +         +E  P TGRTHQLRVH+ H   +GCPIVGD 
Sbjct: 127 H--------GKLGITHWRKLG-VENGMTRVEFTPLTGRTHQLRVHSAHPQGLGCPIVGDR 177

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            Y     G+ T P Q  L LHA Y+   HP+
Sbjct: 178 LY-----GSGTEPGQ--LKLHAGYLCFEHPK 201


>gi|162448280|ref|YP_001610647.1| ribosomal large subunit pseudouridine synthase D [Sorangium
           cellulosum 'So ce 56']
 gi|161158862|emb|CAN90167.1| ribosomal large subunit pseudouridine synthase D [Sorangium
           cellulosum 'So ce 56']
          Length = 356

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 115/234 (49%), Gaps = 29/234 (12%)

Query: 100 ILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSK----GQKP-RLTHR 149
           +++Y D+ + V NKPAG+S      +  +  A  +D  ++  +  +    G+ P  +  R
Sbjct: 112 LVVYADASVVVVNKPAGVSTIPYGDEAPAEQAATLDALVREVLARRDRLRGRAPLGVVQR 171

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHI 208
           LD+ TSG+LV ART AA +HL +  R+R + + Y +L  G +P+       ++L++    
Sbjct: 172 LDKGTSGLLVFARTLAAKKHLAQQLRVRAMHRQYLALAHGAVPRG---TYRSYLVEDR-- 226

Query: 209 GGDYVH-VVKQNEKGANYAISHFKVIDCF--------AQKFCWLEMQPHTGRTHQLRVHA 259
            GD +    +   +    A++H + I+          A     +  +  TGRTHQ+R+H 
Sbjct: 227 -GDGLRGSARDGRREGQLAVTHVEPIEVLRGPQEGAGAGGVTLVACRLETGRTHQIRIHL 285

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G P+VG+  Y  +++G  T     +L LHA  +   HP   R ++  AP P
Sbjct: 286 AEAGHPLVGETVYVRDYRG--TKVPAARLMLHAAELGFDHPADDRPMRFQAPPP 337


>gi|256384025|gb|ACU78595.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           mycoides subsp. capri str. GM12]
 gi|256384857|gb|ACU79426.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           mycoides subsp. capri str. GM12]
 gi|296455719|gb|ADH21954.1| ribosomal large subunit pseudouridine synthase D [synthetic
           Mycoplasma mycoides JCVI-syn1.0]
          Length = 310

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/267 (29%), Positives = 134/267 (50%), Gaps = 21/267 (7%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
           +  NN+I +     + P  N+   I  +  ILD   NL K+ D +   ++Y+D  + V N
Sbjct: 42  ISVNNQIITNNNFVVKP--NSQITITIKDPILDP--NLVKN-DEIDLDIIYQDDDLLVIN 96

Query: 113 KPAGISVQGGSGIAYH--IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAA 166
           K   I+V        +  ++  L S V+        +P + HR+D++T+G+L+VA+    
Sbjct: 97  KQNNITVHPSLSNTNNTIVNALLASDVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKT 156

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
            + L+E F+  +I K Y ++V G+ K  K  I +  + +S I    + V  +N K    A
Sbjct: 157 HKLLSEMFKNHQIYKEYLAIVSGVIKPNKGLI-DAPIGRSQIDRKKMSVTAKNSKQ---A 212

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           I+ F+V++ F  K   ++ Q  TGRTHQ+RVH  ++  P++ D  Y    +  FT   Q 
Sbjct: 213 ITTFEVVERFL-KNTLVKCQIQTGRTHQIRVHFNYINHPVLNDPVYGKKHQ-EFTDFGQ- 269

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLP 312
             YLHA  +   HP     +++ +PLP
Sbjct: 270 --YLHAYKLRFTHPITKKEIELISPLP 294


>gi|33152775|ref|NP_874128.1| pseudouridylate synthase [Haemophilus ducreyi 35000HP]
 gi|34395751|sp|P59831|RLUA_HAEDU RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|33148999|gb|AAP96517.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           ducreyi 35000HP]
          Length = 222

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/217 (31%), Positives = 112/217 (51%), Gaps = 23/217 (10%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           FL+ +  Y D+ I V NKP+G+    G+   Y+ D  + + V  +       HRLD  TS
Sbjct: 13  FLEEV--YRDNHIVVINKPSGLLSVPGNRPEYY-DSVM-TRVQQRYGFAEPAHRLDMATS 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG----GD 211
           GI+++A ++ A + L   FR R  +K Y +L+WG        + + + +   I      D
Sbjct: 69  GIILLALSKVAEKELKRQFRDREPKKHYIALLWG-------KLGDRVGQTGEINFPLICD 121

Query: 212 YVHVVKQN---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           + +  +Q    E+G   A +H++V++  A     ++  P TGR+HQLRVH+L +G PI+G
Sbjct: 122 WENRPRQKICYERGKK-ATTHYEVLEHLANNTTRVKFTPITGRSHQLRVHSLALGHPIIG 180

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           D K+ AN      +P   +L LHA  + + HP    L
Sbjct: 181 D-KFYANPLAKSLAP---RLCLHAESLTIAHPISAEL 213


>gi|259501425|ref|ZP_05744327.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
 gi|302190854|ref|ZP_07267108.1| hypothetical protein LineA_02435 [Lactobacillus iners AB-1]
 gi|259167174|gb|EEW51669.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
          Length = 283

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/279 (26%), Positives = 129/279 (46%), Gaps = 35/279 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKN-----HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           Y+ Y+ +  +E N  +D+  +N      + H  F+ ++K      + V+ K +  N ++ 
Sbjct: 4   YIYYLTISQNENNQNIDQIMRNLLIPRKWRH--FLRIEK-----NILVNNKYLPLNFKVH 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  I V +KPAG   Q
Sbjct: 57  TNDLITI-----KLNHVESLQQKYPASGNMPN--------IIYENDDILVIDKPAG---Q 100

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 101 KTHPNLYETDTALNDCTSYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 160

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQK 239
           + Y++ +            N       IG D + + K+  +     AI+H++V+   A K
Sbjct: 161 RSYFAWIDATNDISDNGTINL-----PIGDDPLDMRKRMVRTDGLKAITHYQVVKKTANK 215

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++ 
Sbjct: 216 IL-VKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQA 253


>gi|227509498|ref|ZP_03939547.1| pseudouridylate synthase RluD [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
 gi|227191041|gb|EEI71108.1| pseudouridylate synthase RluD [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
          Length = 302

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 106/219 (48%), Gaps = 18/219 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED+ + V NK  G        G        L +++ +KG  P + HRLDQETSG ++
Sbjct: 89  ILYEDANLIVINKRRGNKTHPNQPGEVGATINHLAAYLKTKGMLPYMVHRLDQETSGAIL 148

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+  A    L      + I++ Y + V G   + +  I         IG D     K+ 
Sbjct: 149 FAKNPAVVPTLVAKIAAKNIKRTYLAWVVGTDIDSQGII------DFPIGLDPNDKRKRM 202

Query: 220 EKGANYA--ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             G++ A  ++H+ V+      +  L +Q  TGRTHQ+RVH   +G P+VGD  Y  + K
Sbjct: 203 IDGSHPAKSLTHYTVLQK-EDGYSLLAVQLETGRTHQIRVHLAAIGHPLVGDPLYNPDDK 261

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             F       L LH+  + +P P   + ++ITAPLPAH 
Sbjct: 262 HPF-------LLLHSWKLKIPLPFSEQVIEITAPLPAHF 293


>gi|224542885|ref|ZP_03683424.1| hypothetical protein CATMIT_02079 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524215|gb|EEF93320.1| hypothetical protein CATMIT_02079 [Catenibacterium mitsuokai DSM
           15897]
          Length = 322

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 88/334 (26%), Positives = 160/334 (47%), Gaps = 38/334 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V++  +++ R+D++ K          + K+LR   V+V+ KRVK N  + SG  V +  
Sbjct: 4   LVIDQYDDHQRIDKYLKKVLVQAPSSLIYKMLRKKDVKVNGKRVKENYILHSGDEVEL-- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                   + E K  + +  LT +   +   ++YED+ I + +KPAG+ V      + + 
Sbjct: 62  -------FLYEDKFKEYTKPLTIYELPITFKVVYEDAHILIVDKPAGLLVHEDINESVNT 114

Query: 129 IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR- 178
           +   + +++  KG+          P   HRLD+ TSG+++  +   A Q L    + R+ 
Sbjct: 115 LSNQVLTYLHQKGEYDPEKNISFTPGPVHRLDRNTSGLVIFGKDMRALQDLNTMMKTRQG 174

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I+K Y ++  G   + K+   +  +KK+   G  +++VK++  GA   +S   ++    +
Sbjct: 175 IEKKYLTIAMG---HMKDATLSGYVKKNEDEGK-MYLVKKDTPGA---LSMKTIVHVLKR 227

Query: 239 -KFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHAR 293
              C L E+Q  TGRTHQ+R+H    G P++GD KY  +F+ N     +   N  +LHA 
Sbjct: 228 CSTCSLVEVQLITGRTHQIRIHLSATGHPVMGDSKY-GDFEWNKEVKKKFHLNHQFLHAY 286

Query: 294 YMDLPHPEGGRL-----QITAPLPAHMVKTWDSL 322
            +   +P G         +T+ LP  + K    L
Sbjct: 287 RLTFVNPIGSMSYLKGKTVTSQLPEQLEKIQKEL 320


>gi|33519652|ref|NP_878484.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Candidatus Blochmannia floridanus]
 gi|34395754|sp|P59838|RLUD_BLOFL RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|33517315|emb|CAD83700.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Candidatus Blochmannia floridanus]
          Length = 321

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 77/299 (25%), Positives = 143/299 (47%), Gaps = 58/299 (19%)

Query: 51  KRVKFNNRIQS--------GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           K+V  NN++ +        G+++ I  + N  N I K + I+  ++ L          ++
Sbjct: 41  KKVVVNNQVSTLPRKKVVYGELIEIKYINN--NDICKSEDIVPQNIPLN---------II 89

Query: 103 YEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           YED+ I V NK + + V  G G         + Y     LK       ++  +  RLD++
Sbjct: 90  YEDNDILVINKASNMVVHPGIGHYQGTVLNALLYRYPSILKI-----SKQAGIVQRLDKD 144

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G++++A+T +A  +L  SF++R++ K Y ++V+G        + N  +++        
Sbjct: 145 TTGLMIIAKTVSAYDNLLRSFKLRKVVKEYDAIVYG-KFTSNAGVVNQPMRR-------- 195

Query: 214 HVVKQNEKGANY----AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           H  K+     +Y    A++++ V++ F +    + +   TGRTHQ+RVH  ++  P+VGD
Sbjct: 196 HFAKRTFMSVHYTGKSAVTYYSVVEEF-KAHSRVRINLKTGRTHQIRVHMAYINHPLVGD 254

Query: 270 HKYCANFK----GNFTSPIQNKLY------LHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            KY  NF        +  + N L       LHA  + L HP    +++  APLP  +++
Sbjct: 255 QKYKGNFSVFDIKKMSDELNNYLLDFNRQALHACTLQLLHPITQVQMKWNAPLPQDILQ 313


>gi|325273101|ref|ZP_08139401.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas sp.
           TJI-51]
 gi|324101761|gb|EGB99307.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas sp.
           TJI-51]
          Length = 211

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/214 (33%), Positives = 109/214 (50%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED+ I V NKP  + SV G +    + D  +     +      + HRLD ETSGI++
Sbjct: 8   ILHEDAAILVINKPTLLLSVPGRAD--DNKDCLITRLQQNGYPDALIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADSHRELSRQFHDRETEKAYTALCWGQPALDSGSID--LPLRYDPPTKPRHVV-DH 122

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E+G  +A++ +++++      C +E+ P TGR+HQLRVH L +G P++GD  Y AN +  
Sbjct: 123 EQG-KHALTFWRIVE-RCGDHCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY-ANPQAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL+   P P
Sbjct: 180 AA---HERLCLHASMLSFTHPVSGQRLKFECPAP 210


>gi|261344776|ref|ZP_05972420.1| hypothetical protein PROVRUST_06041 [Providencia rustigianii DSM
           4541]
 gi|282567221|gb|EFB72756.1| pseudouridine synthase A [Providencia rustigianii DSM 4541]
          Length = 216

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/206 (33%), Positives = 111/206 (53%), Gaps = 17/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+ +    G    +H D  + S +          HRLD  TSG++VV
Sbjct: 14  ILYQDEHIIVVNKPSELLSVPGKAPEHH-DSII-SRIQRDHPAAESVHRLDMATSGVMVV 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A  +AA + L   FR R  +K Y + VWG  +NK+  I   L+       D+ +  KQ  
Sbjct: 72  ALNKAAERELKRQFREREPKKHYVARVWGHLENKEGLIDLPLI------CDWPNRPKQKV 125

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E G + A + ++V++ + ++   +++ P TGR+HQLRVH L +G PI+GD ++ A+ +
Sbjct: 126 CFETGKS-AQTEYQVLE-YEEQATRVKLSPITGRSHQLRVHMLALGHPILGD-RFYAHEE 182

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
               +P   +L LHA+ + + HP  G
Sbjct: 183 ALALAP---RLQLHAQELYITHPAYG 205


>gi|169349798|ref|ZP_02866736.1| hypothetical protein CLOSPI_00536 [Clostridium spiroforme DSM 1552]
 gi|169293366|gb|EDS75499.1| hypothetical protein CLOSPI_00536 [Clostridium spiroforme DSM 1552]
          Length = 278

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 117/226 (51%), Gaps = 22/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGS---GIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++YED ++ V NKP+G+ S+ GG+     AYH+ G    ++ +K +K ++   HRLD++T
Sbjct: 68  IIYEDKELIVINKPSGLLSISGGNEKEKTAYHLVG---EYLKNKNKKAKVFVIHRLDKDT 124

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+ A+       L  ++     ++ Y +++ G  K K   I N+ L +S     Y+ 
Sbjct: 125 SGVLMFAKNEEIKNKLQNNWNKIVYKRGYLAIIEGRLKEKSGTIKNY-LDESKTQMVYI- 182

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               N K    AI++++V+    +    +E+   TGR +Q+RVH   +G  I+GD KY A
Sbjct: 183 ---TNNKKGKLAITNYRVLKE-TKYNSLVEIFLDTGRKNQIRVHMQSLGHSIIGDKKYGA 238

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAPLPAHMVKTW 319
                 T+PI+ ++ LH+      HP+  +  I  A  P    K +
Sbjct: 239 T-----TNPIK-RMALHSHVFAFVHPDTKKKMIFEAKYPEEFKKIF 278


>gi|332534330|ref|ZP_08410173.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332036240|gb|EGI72713.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 217

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 63/203 (31%), Positives = 108/203 (53%), Gaps = 15/203 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  + + NKP+ +    G     H D  + + V+      R+ HRLD  TSGIL +
Sbjct: 15  ILFQDDDLLIVNKPSELLTVPGKD-PKHADSLI-NRVNRVFPTARIVHRLDMATSGILCL 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A  +AA +HL+  F+ R   K Y + ++G  + +   +   L+       D+ +  KQ  
Sbjct: 73  AMNKAAHRHLSMQFQERETAKRYIARIYGQLEAETGSVDLPLI------CDWPNRPKQMV 126

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      +++HFK+++   +    +E+ P TGR+HQLRVH L +G PI+GD  Y A+ + 
Sbjct: 127 DHDRGKPSLTHFKILE-REENVTRVELTPITGRSHQLRVHMLSLGHPILGDRLY-AHKEA 184

Query: 279 NFTSPIQNKLYLHARYMDLPHPE 301
              +P   +L LHA+ + L HP+
Sbjct: 185 LAAAP---RLQLHAQMLQLKHPK 204


>gi|21672662|ref|NP_660729.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Sg (Schizaphis graminum)]
 gi|25009121|sp|Q8K9E9|RLUD_BUCAP RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|21623299|gb|AAM67940.1| ribosomal large subunit pseudouridine synthase d [Buchnera
           aphidicola str. Sg (Schizaphis graminum)]
          Length = 315

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 115/228 (50%), Gaps = 22/228 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGIL 158
           +YEDS I + NKP G+ V  G+G      ++  L  + + S   +  + HRLD++TSG++
Sbjct: 87  IYEDSNILIINKPPGLVVHPGAGNQDGTILNALLYRYTNISSIPRCGIIHRLDKDTSGLM 146

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A+T  +   L    + R+I + Y  ++ G        I+  ++    +   +  +   
Sbjct: 147 VIAKTIFSYNKLVTLLKKRKIIRKYQGIIKG------NMISGGIVNYPIMRHPFKRICMT 200

Query: 219 NEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY----- 272
            +     +I+H+K+I+ F  KF   +  +  TGRTHQ+RVH LH+G P++GD  Y     
Sbjct: 201 TDSLGKKSITHYKIINRF--KFHTHVSFRLETGRTHQIRVHMLHIGYPLLGDPLYGGIDY 258

Query: 273 -CANFKGNFTSPIQNKLY---LHARYMDLPHPEGGR-LQITAPLPAHM 315
            C  F+ N     +  L+   LHA Y++  HP   + +  +A LP  M
Sbjct: 259 GCNYFQENRNIYRKFNLFRQALHADYIEFIHPFTQKVMSWSASLPQDM 306


>gi|326388573|ref|ZP_08210166.1| pseudouridylate synthase [Novosphingobium nitrogenifigens DSM
           19370]
 gi|326206824|gb|EGD57648.1| pseudouridylate synthase [Novosphingobium nitrogenifigens DSM
           19370]
          Length = 219

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/228 (30%), Positives = 109/228 (47%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED +  V +KPAG+ +         +D  L        ++P   HRLD++TSG L++
Sbjct: 6   ILFEDGEALVIDKPAGLPLDRPRAGGISLDDRLDELRLGFQRRPAPVHRLDRDTSGCLLL 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR   A +    +F  R++ KIY  +V G  +  K  I+  L K S     +  +  +  
Sbjct: 66  ARNPKALKRFAAAFEARKVIKIYLGVVAGPVEGDKGTISLSLSKISSEKNGWRMIPARQG 125

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGN 279
           K    A++H++V+         +E +P TGRTHQ+RVHA   +G  ++GD  Y     G 
Sbjct: 126 KA---AVTHWRVL-ARKDGLTLVEFRPETGRTHQIRVHAASGLGHALLGDPVYGKAVAGT 181

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            T        LHA  + +P      ++  APLPA  V    +LGF  +
Sbjct: 182 RT-------MLHAAQLVIPREGKDTIEAEAPLPADFV----ALGFTIE 218


>gi|297208159|ref|ZP_06924590.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|283470407|emb|CAQ49618.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ST398]
 gi|296887402|gb|EFH26304.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|302332801|gb|ADL22994.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus JKD6159]
 gi|323440971|gb|EGA98678.1| putative RNA pseudouridylate synthase [Staphylococcus aureus O11]
 gi|323442288|gb|EGA99918.1| putative RNA pseudouridylate synthase [Staphylococcus aureus O46]
          Length = 305

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 85/327 (25%), Positives = 150/327 (45%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +     
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYK----- 55

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++   I      + E  IL  ++NL          + YED  + V  KP G+ V    
Sbjct: 56  -VKLNDHIVVTEKEVVEADILPENLNLD---------IYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +   K+     G+ +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAP--IGRNKNDRQSMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQA-----LHAGLIG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G  ++  A LP       D++
Sbjct: 274 FEHPVTGEYIERHAELPQDFEDLLDTI 300


>gi|94497492|ref|ZP_01304062.1| pseudouridylate synthase [Sphingomonas sp. SKA58]
 gi|94423123|gb|EAT08154.1| pseudouridylate synthase [Sphingomonas sp. SKA58]
          Length = 225

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/230 (29%), Positives = 110/230 (47%), Gaps = 18/230 (7%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L   +L+ D +  + +KPAG+ V      +  ++  L S      + P   HRLD++TS
Sbjct: 3   LLTDHVLFLDGEALILDKPAGLPVDAPRDGSMSLENHLASLTFGFQRWPLAVHRLDRDTS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L++AR   A +    +F    + K Y +++ G+P   +  IA  L K S     +  +
Sbjct: 63  GCLLLARNPKAHKRFAAAFEAGTVTKRYIAVLDGVPAETEGTIALSLKKVSTPTQGWRMI 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCA 274
                K    A++H++ +         +   P TGRTHQ+RVHA H +G  I+GD  Y  
Sbjct: 123 AA---KAGKAAVTHWRKL-AERDGRALVAFTPETGRTHQIRVHAQHGLGFGIMGDPVY-- 176

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
              GN   P    + LH+R++ +P  +    + TAPLP    +T+ + GF
Sbjct: 177 ---GNGEGP----MLLHSRFLSVPRGDKPAAEATAPLP----QTFAAAGF 215


>gi|145635746|ref|ZP_01791440.1| hypothetical protein CGSHiAA_07285 [Haemophilus influenzae PittAA]
 gi|145267010|gb|EDK07020.1| hypothetical protein CGSHiAA_07285 [Haemophilus influenzae PittAA]
          Length = 219

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/208 (32%), Positives = 107/208 (51%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+ D  + S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYY-DSVM-SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-----KKECIANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG  +N     K   I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVKLPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD K+ ++
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGD-KFYSH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    SP   +L LHA  + + HP  G
Sbjct: 184 PQTKVMSP---RLCLHAEELTITHPITG 208


>gi|113460513|ref|YP_718577.1| 23S rRNA pseudouridine synthase D [Haemophilus somnus 129PT]
 gi|112822556|gb|ABI24645.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           somnus 129PT]
          Length = 321

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 74/282 (26%), Positives = 134/282 (47%), Gaps = 41/282 (14%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDF----LKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           +IN     +   ++++  V + + S F    L   ++YED  I V NKP    V  G+G 
Sbjct: 47  IINVARTKVYGGELVELCVEIEEESRFEPENLPLNIVYEDEHILVINKPKDFVVHPGAGN 106

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                   + YH    ++  V   G    + HRLD++T+G++VVA+T  A   L +  + 
Sbjct: 107 QRGTVLNALLYHYPKIVE--VPRAG----IVHRLDKDTTGLMVVAKTIPAQTKLVQDLQK 160

Query: 177 RRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           R+I + Y ++ +G+        + ++    K++ +    VH +         A++H++++
Sbjct: 161 RKIIREYEAVAFGVMTQGGKVDQPMSRHPTKRTQMA---VHPL------GKPAVTHYRIM 211

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQN- 286
           + F + +  L ++  TGRTHQ+RVH  H+  P++GD  Y        N    F   +++ 
Sbjct: 212 ERF-RNYTRLRLRLETGRTHQIRVHMAHISHPLLGDQTYGGRPRPPKNASEEFMQVMRDF 270

Query: 287 -KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            +  LHA  + L HP  G  ++  APLP   V   ++L   Y
Sbjct: 271 KRQALHAIMLRLTHPITGEIMEWEAPLPDDFVTLINALKADY 312


>gi|90021296|ref|YP_527123.1| ribosomal large subunit pseudouridine synthase A [Saccharophagus
           degradans 2-40]
 gi|89950896|gb|ABD80911.1| ribosomal large subunit pseudouridine synthase A [Saccharophagus
           degradans 2-40]
          Length = 214

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/221 (31%), Positives = 108/221 (48%), Gaps = 28/221 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGI 157
           LL+ D  I V NKP  + SV G +      D         K Q P   + HRLD  TSG+
Sbjct: 12  LLHCDEDIVVVNKPTDLLSVPGLASPQNLFDRV-------KAQFPTALVVHRLDMATSGL 64

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL----KKSHIGGDYV 213
           ++ A  + A  HL + F  R I+K+Y ++V G+ + +   I++ L+     +     D++
Sbjct: 65  MIFALNKPAQSHLGKQFERRTIKKMYVAVVHGLVEQQSGEISSPLICDWENRPKQKVDWL 124

Query: 214 HVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           H           A++ + V+D   A +   + + PHTGR+HQLRVH   +G PI+GD+ Y
Sbjct: 125 H--------GKPALTQYSVVDRNTAMQATRVHLFPHTGRSHQLRVHMQQIGHPIIGDYFY 176

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                 +  S    +L LHA+ ++L HP  G  +    P P
Sbjct: 177 APQDADSCNS----RLLLHAQTLNLSHPTSGANIHFDCPAP 213


>gi|329944572|ref|ZP_08292712.1| pseudouridine synthase, RluA family [Actinomyces sp. oral taxon 170
           str. F0386]
 gi|328530125|gb|EGF57008.1| pseudouridine synthase, RluA family [Actinomyces sp. oral taxon 170
           str. F0386]
          Length = 314

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/229 (31%), Positives = 111/229 (48%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           LLYED  I V +KPAG++     G     + G LK+    V + G   R  +  RLD  T
Sbjct: 82  LLYEDEDIVVVDKPAGVAAHPSMGWDGPDVLGALKAMHVRVATSGAAERQGIVSRLDVGT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA+   A   L  +FR   + K+Y +LV G        I   + +  H   ++  
Sbjct: 142 SGVMIVAKGERAYSVLKRAFREHMVDKVYHALVQGHLDPSHGTIDAPIGR--HPSREWKM 199

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + +   G   +++H+ VI+      C  E+   TGRTHQ+RVH   +G P VGD  Y A
Sbjct: 200 AIVE---GGRESVTHYDVIEAMPGA-CLAEVHLETGRTHQIRVHMAAVGHPCVGDATYGA 255

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +      + +  + +LHAR + + HP  G  +  T+  PA +V   D +
Sbjct: 256 DPVMTARTGLVRQ-WLHARRLGIAHPITGEHMVFTSDYPADLVHALDVM 303


>gi|254294726|ref|YP_003060749.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254043257|gb|ACT60052.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
          Length = 219

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 73/218 (33%), Positives = 113/218 (51%), Gaps = 20/218 (9%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +++YED    V +KP+G+ SV G      H D  L++   +   + R  HRLD  TSG+ 
Sbjct: 16  VVIYEDEAFLVLDKPSGLLSVPGKP--PEHSD-CLETRAQAVYPEARTVHRLDMATSGVW 72

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+AR  A  +HL   F  R   K Y + VWG  ++ +  I   ++       D+ +  KQ
Sbjct: 73  VMAREHAMMRHLGLQFERRHTSKTYIARVWGDIEDDEGFIDEPII------CDWPNRPKQ 126

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               EKG   + + +KVI+        +E+ P TGRTHQLR+H  H+G PI+ D  Y  +
Sbjct: 127 MICYEKGKP-SQTKWKVIE-RKDGITRVELTPITGRTHQLRLHMQHIGHPILADRIYAHD 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
               F +   ++L LHA  + + HP GG ++  T+P+P
Sbjct: 185 --EAFEA--ADRLQLHAHSITMHHPIGGEKITFTSPVP 218


>gi|24111502|ref|NP_706012.1| hypothetical protein SF0053 [Shigella flexneri 2a str. 301]
 gi|24050255|gb|AAN41719.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
          Length = 228

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 68/210 (32%), Positives = 106/210 (50%), Gaps = 17/210 (8%)

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAY 127
           P  +  N  + E K+   + N  +       ++LY+D  I V NKP+G+ SV G   +  
Sbjct: 6   PAFDRCNASVTEPKMGMENYNPPQEPWL---VILYQDDHIMVVNKPSGLLSVPGR--LEE 60

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           H D  + + +     +    HRLD  TSG++VVA T+AA + L   FR R  +K Y + V
Sbjct: 61  HKDSVM-TRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARV 119

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKFCWLE 244
           WG P   +  +   L+       D+ +  KQ    E G   A + ++V++  A     + 
Sbjct: 120 WGHPSPAEGLVDLPLI------CDWPNRPKQKVCYETG-KPAQTEYEVVEYAADNTARVV 172

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           ++P TGR+HQLRVH L +G PI+GD  Y +
Sbjct: 173 LKPITGRSHQLRVHMLALGHPILGDRFYAS 202


>gi|325269819|ref|ZP_08136429.1| ribosomal large subunit pseudouridine synthase [Prevotella
           multiformis DSM 16608]
 gi|324987792|gb|EGC19765.1| ribosomal large subunit pseudouridine synthase [Prevotella
           multiformis DSM 16608]
          Length = 249

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 106/229 (46%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I +  K  G  VQ        +   ++ W+  K QKP      + HRLD+  S
Sbjct: 28  VLYEDNHIIIVYKEPGEIVQADKSGDEPLSEIVRRWIKEKYQKPGNVFLGVVHRLDRPVS 87

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L   FR   I K YW++V   P + +  + +WL++       Y + 
Sbjct: 88  GLVVFAKTSKALTRLNNMFRNGEIHKTYWAIVTRPPLDPEATLTDWLVRNERQNKSYAY- 146

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  A  ++ H+K I+  + ++  LE+   TGR HQ+R    ++  PI GD KY   
Sbjct: 147 -NHQIPTAKKSVLHYKTINR-SDRYTLLEINLMTGRHHQIRCQLSNIDSPIKGDLKY--- 201

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             G   S     + L +  ++  HP     + + +PLP   +  W ++G
Sbjct: 202 --GAPRSNPDGSISLLSHRVEFVHPVSKENICVESPLPDDAL--WQAIG 246


>gi|170720467|ref|YP_001748155.1| pseudouridine synthase [Pseudomonas putida W619]
 gi|169758470|gb|ACA71786.1| pseudouridine synthase [Pseudomonas putida W619]
          Length = 211

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/214 (33%), Positives = 110/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED+ I V NKP  + SV G +    + D  +    ++      + HRLD ETSGI++
Sbjct: 8   ILHEDAAILVVNKPTLLLSVPGRAD--DNKDCLITRLQENGYPDALIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADSHRELSRQFHDRETEKAYTALCWGQPALDSGSID--LPLRYDPPTKPRHVV-DH 122

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E+G  +A++ +++++      C +E+ P TGR+HQLRVH L +G P++GD  Y AN +  
Sbjct: 123 EQG-KHALTFWRILE-RCGDHCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY-ANPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL+   P P
Sbjct: 180 AA---HERLCLHAAMLSFTHPVSGERLKFECPAP 210


>gi|269127123|ref|YP_003300493.1| pseudouridine synthase, RluA family [Thermomonospora curvata DSM
           43183]
 gi|268312081|gb|ACY98455.1| pseudouridine synthase, RluA family [Thermomonospora curvata DSM
           43183]
          Length = 309

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 113/228 (49%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQ---GGSGIAYHIDGFLKSW--VDSKGQKPR--LTHRLDQE 153
           +LYED  I V +KP G++     G +G    + G L +   V + G   R  + HRLD  
Sbjct: 84  ILYEDEHIVVVSKPVGVAAHPTIGWNGPTV-LGGLLGAGHTVATSGAAERQGIVHRLDAN 142

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G +VVA++  A   L  +F+ RR+ K Y +LV G P   +  I   + +  H  GD  
Sbjct: 143 TTGAMVVAKSEIAYSRLKRAFKERRVDKRYHALVQGHPDPLRGTIDAPIDR--HPSGDGR 200

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V     G   +I+H+  ++ F +    LE+   TGRTHQ+RVH   +  P VGD  Y 
Sbjct: 201 FAVV---AGGRPSITHYDTLEAF-RAASLLEIDLETGRTHQIRVHMSAVRHPCVGDLLYG 256

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           A+        ++ + +LHA  + L HP  G  ++  +P P  + ++ +
Sbjct: 257 ADPTLAARLGVKRQ-WLHAIRLGLEHPTTGEWMEFESPYPEDLTRSLE 303


>gi|153940669|ref|YP_001392256.1| RluA family pseudouridine synthase [Clostridium botulinum F str.
           Langeland]
 gi|152936565|gb|ABS42063.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           Langeland]
 gi|295320251|gb|ADG00629.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           230613]
          Length = 300

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 80/283 (28%), Positives = 136/283 (48%), Gaps = 35/283 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K +R G+V V+K++V   +++    ++ I   +    H    Q I    +N+      
Sbjct: 33  IRKAVRDGRVFVNKEKVIKKHKLSQDDLIEI--YMQEDEH----QNIEPEDMNIE----- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKP--RLTHRL 150
               ++YED+ I V NK  GI V    G   H  G L + +       G+K   RL  RL
Sbjct: 82  ----IVYEDNDIIVINKRPGIVVHPTKG---HPTGTLSNGILYHFKKNGEKSIVRLVSRL 134

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ + +   L         +KIY ++V G  K +KE   N  +       
Sbjct: 135 DRDTSGLIIIAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMK-EKEGRINLPIYNEEESE 193

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +V  +E+G   +I+ ++V++  + K   + ++  TGRTHQ+RVH  H+G P+ GD 
Sbjct: 194 SIKRIV--DERGQE-SITTYEVLEELS-KGSVVRLELETGRTHQIRVHMSHLGHPLYGDS 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
            Y    KG        +  LHA  ++ PHP  G   +LQ + P
Sbjct: 250 LYG---KGEEEKEYIERQALHAYKLEFPHPRTGDILKLQCSLP 289


>gi|297839485|ref|XP_002887624.1| T4O12.25 [Arabidopsis lyrata subsp. lyrata]
 gi|297333465|gb|EFH63883.1| T4O12.25 [Arabidopsis lyrata subsp. lyrata]
          Length = 930

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 87/353 (24%), Positives = 151/353 (42%), Gaps = 81/353 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           +RLD W  +    ++   +Q  +R G V V+ + V K ++ +++G         + +N  
Sbjct: 584 IRLDSWISSRVNGVSRARVQSSIRLGLVTVNGRVVDKVSHNVKAG---------DEVNCT 634

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYH 128
           I E + L +       ++ +   ++YED  + V NKPA + V            +GI +H
Sbjct: 635 ISELQPLKA------EAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGTLVNGILHH 688

Query: 129 I-------------DGFLKSWVDSKGQ-----------KPRLTHRLDQETSGILVVARTR 164
                         D   +++ D +             +P + HRLD+ T+G+LVVA+  
Sbjct: 689 CSLPCVSYSNAEDDDSDEETFSDDEEMTTSSSSYAASVRPGIVHRLDKGTTGLLVVAKDE 748

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            +  HL E F++  I+++Y  +   I ++    I    +     GG            A 
Sbjct: 749 HSHAHLAEQFKLHTIERVYGRIEIPIGRDSSNRIRMAAIPGGLSGGR-----------AR 797

Query: 225 YAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
           +A S +KVI+ FA     L E +  TGRTHQ+R HA +MG P++GD  Y    K    S 
Sbjct: 798 HAASRYKVIETFAGGGSALVEWRLETGRTHQIRAHAKYMGVPLLGDEVY-GGTKSMALSL 856

Query: 284 IQNKLY------------------LHARYMDLPHPEGGRL-QITAPLPAHMVK 317
           +Q ++                   LHA  +   HP  G + + + P P+ + +
Sbjct: 857 LQKRVSRSDQEEIVELISRMDRPCLHAIVLGFTHPCTGEIVKFSCPPPSDLAE 909


>gi|295090745|emb|CBK76852.1| ribosomal large subunit pseudouridine synthase D [Clostridium cf.
           saccharolyticum K10]
          Length = 266

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 115/254 (45%), Gaps = 44/254 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPR-------------- 145
           ++YEDS+I V  KPAG+  Q        +   ++++ V S+ ++ R              
Sbjct: 4   IIYEDSEILVAEKPAGLESQASRKFEPDMVSEIRNYLVRSQKKREREQRRELSTKPSTSL 63

Query: 146 ----------LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNK 194
                     + HRLD+  SG++V A+TR+AA  L+   +  R+ KIY ++V G P  N 
Sbjct: 64  STPAAAPYVGVIHRLDKPVSGVMVYAKTRSAAAFLSRELQAHRVTKIYHAVVCGKPVDNV 123

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTH 253
              + N  + +     +Y  +V +++K    A   ++V+    +K    LE+Q  TGR H
Sbjct: 124 GNFVDNLYMNREE---NYSVLVDKSKKEGKRAELSYRVLSRAEEKNLTLLEIQLKTGRHH 180

Query: 254 QLRVHALHMGCPIVGDHKYCANFKG-------------NFTSPI-QNKLYLHARYMDLPH 299
           Q+RV     G PI GD +Y   F G             +F +P  +  L L A  +  PH
Sbjct: 181 QIRVQLAGHGLPIWGDARYNPQFGGTLPVEEREEKGSESFRTPASRGPLALAAVSLSFPH 240

Query: 300 PEGGRLQITAPLPA 313
           P  G+    +  PA
Sbjct: 241 PSSGKKMTFSIKPA 254


>gi|332828459|gb|EGK01164.1| hypothetical protein HMPREF9455_00204 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 316

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 63/223 (28%), Positives = 114/223 (51%), Gaps = 17/223 (7%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPR----LTHRLDQETS 155
           +++ED +I V +K AG +SV         + G L  +V  K +       + HRLD+E S
Sbjct: 86  IVFEDDEIIVIDKEAGFLSVSTDKEKLRTVYGALNEYVKKKSRNKTDRVFVLHRLDREAS 145

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V AR     +   +++     + IY ++V G P+ ++  + +WL +      +YV +
Sbjct: 146 GLMVFARNAELQEIFQKNWNNLVKEYIYTAVVDGRPEQEEGTVISWLTE----NKNYVMM 201

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               + G   +++H+KVI     ++  L+    T R +QLR+    +G  +VGD KY A+
Sbjct: 202 SSPYDNGGLKSVTHYKVIKSTG-RYSLLDFDLETKRKNQLRIQMQTIGHSVVGDKKYGAS 260

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
                 +PI+ ++ LH R + L HP  G  L+  +P+P  M++
Sbjct: 261 -----NNPIK-RIALHVRELVLKHPVTGEVLEFKSPVPKAMLQ 297


>gi|332975616|gb|EGK12505.1| pseudouridylate synthase for 23S rRNA and tRNAphe(position 32)
           [Psychrobacter sp. 1501(2011)]
          Length = 237

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 105/212 (49%), Gaps = 19/212 (8%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           DF+  + +YED  I + +KPAG+    G  +       L S ++    + +L HRLD +T
Sbjct: 25  DFMTQVTVYEDDDILLVDKPAGLLSIDGKDLKVS----LLSRLERANPEVKLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           SG+++  + +AA  H+++ F  R  QK Y ++V G    P  K E       + S     
Sbjct: 81  SGLMIFGKNKAAQTHISKQFIERIPQKEYQAIVNGTLATPGKKGEINIPVRYEPS---IK 137

Query: 212 YVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             HV   N K   +A++H++V+       +    + + P TGR+HQLRVH +H+G  I+G
Sbjct: 138 PKHVADPNWK--KHALTHYEVLHHELRQGKPVTRVALHPVTGRSHQLRVHMVHLGHVIIG 195

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           D  Y        +S    +L LHA  + L HP
Sbjct: 196 DPIYAEGEALTLSS----RLNLHAHKLRLKHP 223


>gi|283458362|ref|YP_003362985.1| pseudouridylate synthase [Rothia mucilaginosa DY-18]
 gi|283134400|dbj|BAI65165.1| pseudouridylate synthase [Rothia mucilaginosa DY-18]
          Length = 328

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 66/220 (30%), Positives = 111/220 (50%), Gaps = 16/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG------IAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +++ D  I V +KPAG++     G      I+  +   +        ++  + HRLD  T
Sbjct: 99  IVHLDEDIVVVDKPAGVAAHPSPGWHGPTVISALMGEGISVATSGAAERQGIVHRLDVGT 158

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVAR+  A   L  +F+ R + K+Y +LV G+P   +  I   + +  H G ++  
Sbjct: 159 SGLMVVARSERAYTELKRAFKERTVDKVYHTLVQGLPDPLRGTIDAPIGR--HPGNEWKF 216

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V   E G N +I+H+ V++ F      +E+   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 217 AVV--EDGRN-SITHYDVLEAFGPA-SLVEVHLETGRTHQIRVHFSALRHPCCGDLTYGA 272

Query: 275 NFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGRLQITAPLP 312
           + +  F++ +   + +LHA  +   HP  G R+  T+  P
Sbjct: 273 DPR--FSAELGLTRQWLHAHRLGFDHPGTGERVTFTSEYP 310


>gi|329851218|ref|ZP_08265975.1| RNA pseudouridylate synthase family protein [Asticcacaulis
           biprosthecum C19]
 gi|328840064|gb|EGF89636.1| RNA pseudouridylate synthase family protein [Asticcacaulis
           biprosthecum C19]
          Length = 200

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 100/210 (47%), Gaps = 23/210 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++Y D  + V +KPAG+    G G        L + V          HRLD  TSG++V
Sbjct: 1   MIVYADEAMVVADKPAGLLSVPGRGPDKQ--DCLVARVRDTYPDALTVHRLDMATSGLIV 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHV 215
           + R   A + L+++F  RR +K Y ++V G   ++ E     I +W  +           
Sbjct: 59  LGRGPNAQRALSQAFENRRTEKRYIAVVHGHTPDEGEVNLPLITDWPNRPRQ-------- 110

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K +      +++ +++I         +E++P TGR+HQLRVH L +G PIVGD  YC +
Sbjct: 111 -KVDHDIGKPSLTRYRII-SRDDTTSRVELEPVTGRSHQLRVHMLAIGHPIVGDEFYCPD 168

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
                      ++ LHA  + +PHP  G +
Sbjct: 169 IPA-------PRMLLHAERLAVPHPLTGEM 191


>gi|301112595|ref|XP_002998068.1| conserved hypothetical protein [Phytophthora infestans T30-4]
 gi|262112362|gb|EEY70414.1| conserved hypothetical protein [Phytophthora infestans T30-4]
          Length = 214

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 62/203 (30%), Positives = 110/203 (54%), Gaps = 22/203 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK------KRVKFNN 57
           + ++++VV   D+E +RLDRW ++ +P +    +Q  LR  ++R+        +  + N+
Sbjct: 6   LRWMRHVVRAQDQE-LRLDRWLRHQFPTLPQSFVQTQLRKRKIRLQSATASNLEATRANS 64

Query: 58  RIQSGQVVRI----------PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
            ++ G VV I          P V+  +   I  ++ L ++ +  K    LK  ++Y+D++
Sbjct: 65  LLREGSVVAIDAHLFLSKLQPLVVQQVEQDIATRQHLTTAQD--KRLLQLKRCVVYQDAQ 122

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
             V NKP G++VQ GS +   +  +L  W+    Q+ RL HRLD+ETSG+LV+AR+R AA
Sbjct: 123 FVVLNKPHGLAVQDGSTLTESLALYL-PWIAE--QQLRLVHRLDKETSGVLVLARSRLAA 179

Query: 168 QHLTESFRMRRIQKIYWSLVWGI 190
              ++  R   + K Y +LV  +
Sbjct: 180 AKFSKLLRNGAVYKTYEALVEAL 202


>gi|301168827|emb|CBW28418.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae 10810]
          Length = 324

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 121/247 (48%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NK   + V  G+G         + YH    ++  V   G    + HRLD
Sbjct: 85  IVYEDDDIIVINKSKDLVVHPGAGNPNGTVLNALLYHYPPIVE--VPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L    + R+I + Y ++  GI        + +A    K++ +
Sbjct: 139 KDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMARHATKRTLM 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH + +       A++H+++++ + + +  L ++  TGRTHQ+RVH  H+  P++G
Sbjct: 199 A---VHPMGKP------AVTHYRIMENY-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLG 248

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           D  Y        N   +F   ++N  +  LHA  + L HP  G  ++  APLP   V+  
Sbjct: 249 DQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAHPITGEMMEWYAPLPDDFVELL 308

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 309 NALKADY 315


>gi|113969719|ref|YP_733512.1| pseudouridylate synthase [Shewanella sp. MR-4]
 gi|113884403|gb|ABI38455.1| Pseudouridylate synthase [Shewanella sp. MR-4]
          Length = 223

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 101/208 (48%), Gaps = 16/208 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           L Y+D  + + NKP+G+    G   A+  D  L    + + D+      L HRLD  TSG
Sbjct: 16  LRYQDRDLIIINKPSGLLSNPGRA-AHTFDCALTRLQRLYPDTI-----LVHRLDCATSG 69

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I+V AR + A   L   F+ R+ +K+Y + V G+   K   I +  +        Y    
Sbjct: 70  IMVFARNKKAESQLKTQFQDRQNEKVYVAEVMGV-IAKDAGIIDLAIAPDPEHPPYQKTQ 128

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                GA  A +H++V++   +    +E+ P TGRTHQLRVH L +G PI+GD  Y    
Sbjct: 129 MPGTAGAKSAQTHYRVLE-RRENSTLVELTPQTGRTHQLRVHMLALGHPILGDEFY---- 183

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             +     + +L LHA+ +   HP  G+
Sbjct: 184 GDDEVIKARPRLCLHAQSLRFTHPYSGK 211


>gi|310659174|ref|YP_003936895.1| ribosomal large subunit pseudouridine synthase, rlud subfamily
           [Clostridium sticklandii DSM 519]
 gi|308825952|emb|CBH21990.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium sticklandii]
          Length = 306

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 80/312 (25%), Positives = 141/312 (45%), Gaps = 42/312 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVV 65
           +Y +V+ +EE++RLD +  +    ++   +Q +++  +V V+ K  K + ++       +
Sbjct: 6   KYFIVDEEEEDLRLDVFISSALSDLSRTYIQSLIKDKKVTVNDKIEKSSYKVAQLDNICI 65

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            IPP         KE  I    + +          +LYED  + V  K  G+ V  G+G 
Sbjct: 66  LIPPA--------KELVIEAEDIPIE---------ILYEDEDLAVVYKERGMVVHPGAGN 108

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                   + YH  G L S   +   +P + HR+D++TSG+L++A++  A + L+E  + 
Sbjct: 109 ANHTLVNALMYHFKGQLSSI--NGIIRPGIVHRIDKDTSGLLMIAKSDIAHRGLSEQLKE 166

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDC 235
             +Q+ Y  +  G  K      A+     + IG +    +K        +A++H   I  
Sbjct: 167 HTVQRTYTFICHGNIK------ADEFTIDAPIGRNPRDRMKMAVVSDGKHAVTHITKIKS 220

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             + + +      TGRTHQ+RVH    G P+VGD  Y  +   N     Q +L LHA+ +
Sbjct: 221 -NENYSYAMANLETGRTHQIRVHMASKGLPLVGDTLYGPH---NSKFKAQGQL-LHAKTL 275

Query: 296 DLPHPEGGRLQI 307
              HP  G   +
Sbjct: 276 GFVHPVTGEFML 287


>gi|269123861|ref|YP_003306438.1| pseudouridine synthase, RluA family [Streptobacillus moniliformis
           DSM 12112]
 gi|268315187|gb|ACZ01561.1| pseudouridine synthase, RluA family [Streptobacillus moniliformis
           DSM 12112]
          Length = 297

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 105/208 (50%), Gaps = 25/208 (12%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +YED  + + NK AG+ V    G         I Y I     S ++    +P + HRLD+
Sbjct: 78  VYEDKYLAIINKYAGMVVHPSKGHEEDTLVNAIMYKIKDL--SGING-DLRPGIVHRLDK 134

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++++A+       L+E F+ + I+KIY+++V G   NKK      ++ ++      
Sbjct: 135 NTSGLIIIAKDDKTHFKLSEMFKNKEIKKIYYAIVKG-KVNKKSGRIETMIGRNPNDRKK 193

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + VV         AI++F+VID   +KF  L++   TGRTHQ+RVH  H   PI+GD  Y
Sbjct: 194 MAVVDN----GKLAITNFEVIDS-NEKFSLLKVDLETGRTHQIRVHLSHFFFPILGDSVY 248

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
               K  +     ++  LHA  ++  HP
Sbjct: 249 GR--KDEY-----DRQMLHAYMLNFIHP 269


>gi|270159531|ref|ZP_06188187.1| ribosomal large subunit pseudouridine synthase D [Legionella
           longbeachae D-4968]
 gi|289165671|ref|YP_003455809.1| Ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Legionella longbeachae
           NSW150]
 gi|269987870|gb|EEZ94125.1| ribosomal large subunit pseudouridine synthase D [Legionella
           longbeachae D-4968]
 gi|288858844|emb|CBJ12758.1| Ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Legionella longbeachae
           NSW150]
          Length = 321

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 82/334 (24%), Positives = 146/334 (43%), Gaps = 38/334 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +  N R+D    +     +   +   ++ G + ++ +  K  ++++ G ++ I  
Sbjct: 9   LTIPREYHNQRIDTALAHLLSDYSRSQISNWIKCGSIMLNHQSCKPKDKVEDGDLIDINV 68

Query: 70  VINA----LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
             N     L H I E+  L+               ++YED  + V NKPA + V  G+G 
Sbjct: 69  NFNKTDTNLEHCIPEEIPLN---------------IIYEDDDVLVLNKPANMVVHPGAGN 113

Query: 126 AYH-IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             H +   L     S    PR  + HRLD++T+G+L++A+T  A   L    + R I++ 
Sbjct: 114 KEHTLVNALLHHSPSLIHLPRAGIVHRLDKDTTGLLIIAKTLPAHTSLIRQMQAREIKRH 173

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G        I+   +           +    ++    AI+H+ V   +   F  
Sbjct: 174 YITLVQG------HIISGGTIDTGFGRHPRNRLKMAVQEHGRQAITHYAVKKQY-HDFTL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------IQN--KLYLHARY 294
           L++   TGRTHQ+RVH  ++  P+VGD  Y    +    +P       QN  +  LHAR 
Sbjct: 227 LDVNLMTGRTHQIRVHLAYIHHPVVGDPLYGTRMRFPSQAPEHLRTLFQNFKRQALHART 286

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           +   HP+  + L + AP+P       ++L   Y+
Sbjct: 287 LSFYHPKTEKELTLMAPIPDDFKLLLNTLDEHYE 320


>gi|187931810|ref|YP_001891795.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. mediasiatica FSC147]
 gi|187712719|gb|ACD31016.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. mediasiatica FSC147]
          Length = 332

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 142/318 (44%), Gaps = 34/318 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E       +NL          +++ED  I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWIAE------DINLK---------IIFEDDDIIVIDKPVNMIVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +  L  + D + + PR  + HRLD++TSG++V A++  A  +L +    R++ + Y
Sbjct: 117 GTVSNALLHRYKD-QDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC 241
            ++V G      E      + +  IG D  +  K   N +G   AI+H+  I+ +   F 
Sbjct: 176 LAIVEG------EIYQQGTINQP-IGRDPTNRTKMAINYRGKE-AITHYTPIEVY-DGFT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG--NFTSPIQNKLYLHARYMDLPH 299
            +E Q  TGRTHQ+RVH   +  P+VGD  Y  +          I  +  LHA  +   H
Sbjct: 227 LIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSLTKLEKLAITIPTRQALHAYKLSFIH 286

Query: 300 PEGGRL-QITAPLPAHMV 316
           P   ++ +  + LP  M+
Sbjct: 287 PTIAKMVKFKSKLPEDML 304


>gi|90407469|ref|ZP_01215652.1| pseudouridine synthase Rlu family protein [Psychromonas sp. CNPT3]
 gi|90311390|gb|EAS39492.1| pseudouridine synthase Rlu family protein [Psychromonas sp. CNPT3]
          Length = 253

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 115/241 (47%), Gaps = 24/241 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP G+ V       +  +  ++   D  G      HRLD+ TSG+L+ 
Sbjct: 20  ILYQDEAVVAINKPPGLLVHRSWLDPHATEFAIQKLRDQIGVHVYPAHRLDRPTSGVLLF 79

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
              +   + +   F  ++I+K Y ++V G   +  E I ++ LKK      + HV+++ E
Sbjct: 80  LLDKNYLKPVMAQFAEQKIEKRYLAIVRG---HIGEGIIDYALKKKLDKIAHKHVLREPE 136

Query: 221 KGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             A  A++H++          V      ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 137 --AQSAVTHYRNMAHCEVDIGVRPYPTSRYSLVELSPKTGRRHQLRRHMKHVFHPIIGDT 194

Query: 271 -----KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
                K+   F+ NF     ++L LHA  +   HP  G +++I APL        ++LG 
Sbjct: 195 THGDGKHNQMFRDNFEV---SRLLLHAASLTFEHPVSGDKIEIKAPLDNDFKTLLETLGL 251

Query: 325 K 325
           K
Sbjct: 252 K 252


>gi|52079396|ref|YP_078187.1| putative pseudouridine synthase YhcT [Bacillus licheniformis ATCC
           14580]
 gi|52784756|ref|YP_090585.1| YhcT [Bacillus licheniformis ATCC 14580]
 gi|319646823|ref|ZP_08001052.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
 gi|52002607|gb|AAU22549.1| putative Pseudouridine synthase YhcT [Bacillus licheniformis ATCC
           14580]
 gi|52347258|gb|AAU39892.1| YhcT [Bacillus licheniformis ATCC 14580]
 gi|317391411|gb|EFV72209.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
          Length = 305

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 80/277 (28%), Positives = 133/277 (48%), Gaps = 39/277 (14%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           +V+V+ K V  N R++SG  V I       + I+ E   L                +L+E
Sbjct: 44  KVKVNHKSVNHNVRLESGDSVMIDLREEEESGIVPEYGELP---------------VLFE 88

Query: 105 DSKIYVFNKPAGISVQ----GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           D  + + NKPAG++      G +G   ++  F    ++ + +K R  HRLD++TSG +V 
Sbjct: 89  DDHMLIVNKPAGMATHPNEAGQTGTLSNLVAFY-FQMNGEERKVRHVHRLDKDTSGAVVF 147

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A+ R A   L E  + + + + Y ++  G  + K   I+      + IG D  H V++  
Sbjct: 148 AKHRLAHALLDEQLQRKELARTYVAVAEGKFRKKTGTIS------APIGRDKHHPVRRRV 201

Query: 220 EKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                 A++HF+     ++     C L+++  TGRTHQ+RVH   +G P+ GD  Y  + 
Sbjct: 202 SHSGQPAVTHFESKGYDSRHDVTLCRLQLE--TGRTHQIRVHLASIGHPLSGDTLYGGS- 258

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           KG F      +  LHA  +++ HP    R+ + APLP
Sbjct: 259 KGLF-----QRQALHAIEINVTHPITKERVTVAAPLP 290


>gi|260549688|ref|ZP_05823905.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           RUH2624]
 gi|260407205|gb|EEX00681.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           RUH2624]
          Length = 212

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/225 (32%), Positives = 107/225 (47%), Gaps = 21/225 (9%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLD 151
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V     +PR  L HRLD
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLV---AIEPRTLLIHRLD 56

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSGILV   ++     +   F+ R+  KIY +LV G    +       +   S     
Sbjct: 57  RDTSGILVFGLSKRGQSAIARQFQDRQTSKIYEALVAGHLDGEGTVDIPVVYDPSR---P 113

Query: 212 YVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +H+V  +      A++H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVG
Sbjct: 114 PLHIVDASHNKP--ALTHWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVG 171

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           D  Y    +      +  +L LHA+ +   HP  G  L    P+P
Sbjct: 172 DTLYATPEQL-----LVPRLCLHAKQLSFNHPVTGESLTFNCPVP 211


>gi|28211672|ref|NP_782616.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           tetani E88]
 gi|28204114|gb|AAO36553.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           tetani E88]
          Length = 226

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 113/228 (49%), Gaps = 22/228 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS----WVDSKGQK--PRLTHRLDQET 154
           ++YED  I V NK  GI V        H  G L +    + + KG+    RL  RLD++T
Sbjct: 5   IVYEDEDILVINKNPGIVVHPTKS---HPRGTLSNGILYYFEDKGENCIVRLVSRLDRDT 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+ + A   L         +K Y +++ G    KKE   +  + +         
Sbjct: 62  SGLIIIAKNQFAHMALARDMNKDTFKKFYLAIIHG-KLTKKEGTIDLPIYRPE-DSSLKR 119

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV Q  KG   +I+H+KV++ F +    +E    TGRTHQ+RVH  H+G PI+GD  Y  
Sbjct: 120 VVDQ--KGQR-SITHYKVVEEF-KDASLVEFLLETGRTHQIRVHVEHLGHPIIGDSLY-- 173

Query: 275 NFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
              GN    +  N+  LHA  +  PHP  G  L+++  +P+ +  + +
Sbjct: 174 ---GNEDDTMYINRQALHAYKLVFPHPRTGEILELSCDIPSDIKDSME 218


>gi|227114231|ref|ZP_03827887.1| ribosomal large subunit pseudouridine synthase A [Pectobacterium
           carotovorum subsp. brasiliensis PBR1692]
          Length = 217

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/205 (34%), Positives = 105/205 (51%), Gaps = 18/205 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  +   + +        HRLD  TSG++ 
Sbjct: 14  ILYQDQHIMVVNKPSGLLSVPGRA--PEHKDSVMNR-IQADYPTAESVHRLDMATSGVIA 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPKKSYLARVWGHMAQDEGVIDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G   A + ++V+   A     +++ P TGR+HQLRVH L +G PI+GD  Y A+ 
Sbjct: 125 VCFETG-KAAQTEYQVLSRDADGTTRVKLMPITGRSHQLRVHLLALGHPILGDGFY-AHP 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPE 301
                +P   +L LHA+ + + HPE
Sbjct: 183 DAKALAP---RLLLHAQELAITHPE 204


>gi|262278251|ref|ZP_06056036.1| conserved hypothetical protein [Acinetobacter calcoaceticus
           RUH2202]
 gi|262258602|gb|EEY77335.1| conserved hypothetical protein [Acinetobacter calcoaceticus
           RUH2202]
          Length = 212

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/223 (31%), Positives = 107/223 (47%), Gaps = 17/223 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V +   K  L HRLD++
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLV-AIEPKTLLIHRLDRD 58

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     +   F+ R+  KIY +LV G  + +       +   S      +
Sbjct: 59  TSGILVFGLSKRGQSAIARQFQDRQTSKIYEALVAGHLEGEGTVDIPVIYDPSR---PPL 115

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+V  +      A++H++V++ F    Q    +++ P TGR+HQLRVH  ++G PIVGD 
Sbjct: 116 HIVDASHNKP--ALTHWQVLENFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDT 173

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            Y    +      +  +L LHA+ +   HP     L    P+P
Sbjct: 174 LYATPEQQ-----LVPRLCLHAKQLSFNHPVTAETLTFDCPVP 211


>gi|220928045|ref|YP_002504954.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|219998373|gb|ACL74974.1| pseudouridine synthase, RluA family [Clostridium cellulolyticum
           H10]
          Length = 299

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 66/207 (31%), Positives = 106/207 (51%), Gaps = 20/207 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS----WVDSKG--QKPRLTHRLDQET 154
           ++YED  + V NK +GI V   S   YH D  + +    ++  KG  +K R   RLD+ET
Sbjct: 81  VIYEDECMLVLNKQSGIVVHPTS---YHPDNTIANGIVYYLKQKGVTKKVRPVSRLDRET 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI++ A+ +   + L +       +K Y  +V GIP+N +  I   + +K       + 
Sbjct: 138 SGIIIFAKNQFTQEMLIQQMHNNLFKKEYLGIVQGIPQNNEGTINLPIARKP----GSIM 193

Query: 215 VVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           +   +E+GA  +I+H+K++  F +     L  +  TGRTHQ+RVH   MG PI GD  Y 
Sbjct: 194 LRHISEEGAP-SITHYKILKTFPSHNSALLSFKLETGRTHQIRVHCKAMGFPIYGDTLYS 252

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            N     T+   ++  LH+   ++ HP
Sbjct: 253 DN-----TNLFISRQALHSYRTEIIHP 274


>gi|168576177|ref|ZP_02722071.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae MLV-016]
 gi|194398218|ref|YP_002037729.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Streptococcus pneumoniae G54]
 gi|183577907|gb|EDT98435.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae MLV-016]
 gi|194357885|gb|ACF56333.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae G54]
          Length = 298

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 68/219 (31%), Positives = 112/219 (51%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYED    V NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + +K++  +      + +  HTGRTHQ+RVH  ++G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYKIVASYGN-IHLVYIHLHTGRTHQIRVHFSYIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              G+    IQ +  LH  Y+   HP   + LQ+ +PLP
Sbjct: 249 ---GSLEDGIQRQA-LHCHYLSFYHPFLEQDLQLESPLP 283


>gi|255326239|ref|ZP_05367325.1| ribosomal large subunit pseudouridine synthase D [Rothia
           mucilaginosa ATCC 25296]
 gi|255296693|gb|EET76024.1| ribosomal large subunit pseudouridine synthase D [Rothia
           mucilaginosa ATCC 25296]
          Length = 328

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 66/220 (30%), Positives = 111/220 (50%), Gaps = 16/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG------IAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +++ D  I V +KPAG++     G      I+  +   +        ++  + HRLD  T
Sbjct: 99  IVHLDDDIVVVDKPAGVAAHPSPGWHGPTVISALMGEGISVATSGAAERQGIVHRLDVGT 158

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVAR+  A   L  +F+ R + K+Y +LV G+P   +  I   + +  H G ++  
Sbjct: 159 SGLMVVARSERAYTELKRAFKERTVDKVYHTLVQGLPDPLRGTIDAPIGR--HPGNEWKF 216

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V   E G N +I+H+ V++ F      +E+   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 217 AVV--EDGRN-SITHYDVLEAFGPA-SLVEVHLETGRTHQIRVHFSALRHPCCGDLTYGA 272

Query: 275 NFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGRLQITAPLP 312
           + +  F++ +   + +LHA  +   HP  G R+  T+  P
Sbjct: 273 DPR--FSAELGLTRQWLHAHRLGFDHPGTGERVTFTSEYP 310


>gi|327480038|gb|AEA83348.1| pseudouridine synthase RluA [Pseudomonas stutzeri DSM 4166]
          Length = 211

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 110/214 (51%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+ + V NKP  + SV G +    + D  +    ++   + R+ HRLD ETSG++V
Sbjct: 8   IIHQDAALLVINKPTLLLSVPGRA--EDNRDCLVTRLQENGYPEARIVHRLDWETSGLIV 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P+     I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPEQDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ ++V++     +  +E+ P TGR+HQLRVH L +G P++GD  Y      +
Sbjct: 122 HELGKHALTFWRVLE-RCGDYSRVELTPITGRSHQLRVHMLSIGHPLLGDRLYAHEQALH 180

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                  +L LHA  + L HP+ G RL+   P P
Sbjct: 181 ----AHERLCLHASMLTLTHPQTGERLRFECPAP 210


>gi|301155357|emb|CBW14823.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Haemophilus parainfluenzae T3T1]
          Length = 219

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 107/208 (51%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ I V NKP+G+    G+   Y+      S V  K       HRLD  TSGI++ 
Sbjct: 16  IIYQDNHICVVNKPSGLLSVPGNQPEYYDSAM--SRVKEKFGFCEPAHRLDMATSGIILF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC----IANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y +LVWG + ++  E     I +W   +     D+V  
Sbjct: 74  ALSKAADKELKRQFREREPKKYYQALVWGHLEQDSGEINLPMICDW-ENRPRQRIDFVF- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ ++V++        +++ P TGR+HQLR+H L +G PI+GD K+ ++
Sbjct: 132 -------GKRAVTFYEVLERLPTNCTRVKLTPITGRSHQLRLHTLALGHPILGD-KFYSH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    SP   +L LHA  + + HP  G
Sbjct: 184 PQAKSMSP---RLCLHAEELTIMHPITG 208


>gi|299143164|ref|ZP_07036244.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Peptoniphilus sp. oral taxon 386 str. F0131]
 gi|298517649|gb|EFI41388.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Peptoniphilus sp. oral taxon 386 str. F0131]
          Length = 293

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 66/219 (30%), Positives = 111/219 (50%), Gaps = 18/219 (8%)

Query: 101 LLYEDSKIYVFNKPA-GISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGI 157
           ++YED  I V NKP   ++      +   +  F+  + +     +K R+ +RLD++TSGI
Sbjct: 84  IIYEDDDIVVVNKPPYMVTHTAKDDVENTLLNFVAGYFEDNKIRRKVRIVNRLDRDTSGI 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA+   +   + E F    ++K Y ++V GI KN    I     K   I  D +  + 
Sbjct: 144 VIVAKNSFSHSSIQEQFG-DSVKKEYVAIVNGIIKNDSGIIE----KPIDIAKDGIRRIV 198

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             +    Y+ + ++VI      F  ++++ +TGRTHQ+RVH  HMG PI+GD  Y +   
Sbjct: 199 SPD--GKYSKTSYEVIKR-NDFFTLVKLRLYTGRTHQIRVHMSHMGTPILGDALYGS--- 252

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
              TS +  +  LH   M++ HP   + L+  AP+P  M
Sbjct: 253 ---TSNLILRQALHCYEMEIIHPRTKKLLKFIAPVPKDM 288


>gi|284044971|ref|YP_003395311.1| pseudouridine synthase [Conexibacter woesei DSM 14684]
 gi|283949192|gb|ADB51936.1| pseudouridine synthase, RluA family [Conexibacter woesei DSM 14684]
          Length = 299

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 80/312 (25%), Positives = 140/312 (44%), Gaps = 42/312 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD +     P  +    Q+++ +G V VD       +++ +G+ V + P          
Sbjct: 17  RLDLFLAQ--PLGSRARAQRLIDAGLVTVDGAARPKRHKVSAGERVEVTP---------- 64

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            + ++D  V  +  + F    + +ED  + + +KPAG+ V    G   +  G L   +  
Sbjct: 65  -EPVVD--VEPSGDAPF---AVAWEDEHLLIVDKPAGVVVHPAPG---NRTGTLSQALAG 115

Query: 140 K---GQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +   G+ P    + HRLD++TSG+L+VA+T  A + L      R + + Y +LV G P  
Sbjct: 116 RAAGGEDPSRAGIVHRLDRDTSGLLIVAKTEEAHRELKRMIEARDVTREYVALVEGTPPA 175

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQKFCWLEMQPHTGR 251
           +   I       + IG D     + + +  +   A +HF++          L +   TGR
Sbjct: 176 RSGTI------DAPIGRDRRVRTRMSTETDDPRDARTHFRLERALPDS-ALLRVTLETGR 228

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH   +G P+VGD +Y     G F      + +LHA  +   HP    ++ +++P
Sbjct: 229 THQIRVHLEAIGHPVVGDPEY--GRAGRFG---LERQFLHAARLAFAHPLRDEQVDVSSP 283

Query: 311 LPAHMVKTWDSL 322
           LP  +      L
Sbjct: 284 LPPDLAAVLAQL 295


>gi|282892129|ref|ZP_06300604.1| hypothetical protein pah_c207o069 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498024|gb|EFB40368.1| hypothetical protein pah_c207o069 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 283

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/215 (33%), Positives = 109/215 (50%), Gaps = 15/215 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED+ + V  KPAG+ SV      A     FLK     + +K  + HRLDQ+TSG+++
Sbjct: 70  ILYEDAHLVVIEKPAGLLSVATNFDKAKTAHAFLKERY--RPRKVYVVHRLDQDTSGVML 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK-KSHIGGDYVHVVKQ 218
            A T  A   L   F    I + Y ++V G    ++    ++L + K+++    VH  + 
Sbjct: 128 FALTGEAFFGLKALFADHDIDREYTAVVHGKMTQQEGTWQSYLYEDKAYV----VHSTQD 183

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +KG   AI+HFK ++     F  L ++  TG+ +Q+RVH    G PIVGD KY     G
Sbjct: 184 PDKG-ELAITHFKTVEARTH-FSLLNLKLETGKKNQIRVHCEDHGFPIVGDKKYG----G 237

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              S I  +L LHA ++   HP     +   +P+P
Sbjct: 238 EGESHITKRLCLHAHHLGFVHPIYKKEMSFDSPIP 272


>gi|209523615|ref|ZP_03272169.1| pseudouridine synthase, RluA family [Arthrospira maxima CS-328]
 gi|209496020|gb|EDZ96321.1| pseudouridine synthase, RluA family [Arthrospira maxima CS-328]
          Length = 309

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 103/233 (44%), Gaps = 17/233 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILV 159
           ++YED+ I V  KP+G+ V  G G   H    L+       Q  P   HRL + TSG+++
Sbjct: 83  VIYEDADILVVAKPSGLPVIPGGGFLEHT--LLRQLQREYPQDTPIPIHRLGRGTSGLVL 140

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR+     HLT+  R R+I K+Y +L  G        I   + K  H    Y++   + 
Sbjct: 141 LARSTLGRSHLTQQMRHRQITKVYLALAEGCSPRDYFSINCAIGKIPHPIIGYIYGATET 200

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              A    SH +VI     K   +++   TGR HQ+R+H    G P+VGD  Y    K  
Sbjct: 201 GLSAE---SHCQVIKRDTDKMI-VQVTILTGRPHQIRIHLAAAGFPLVGDPLYTIGGKPR 256

Query: 280 FTSPIQN---------KLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
              P  N           YLHA  +   HP+ G  L +TA  P  +   +  +
Sbjct: 257 IPDPTSNHHSTFPGDCGYYLHAYSLSFQHPQTGANLHLTATPPQELSTEYPPM 309


>gi|116051259|ref|YP_789909.1| pseudouridine synthase RluA [Pseudomonas aeruginosa UCBPP-PA14]
 gi|313108585|ref|ZP_07794586.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           aeruginosa 39016]
 gi|115586480|gb|ABJ12495.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|310881088|gb|EFQ39682.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           aeruginosa 39016]
          Length = 211

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 116/214 (54%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D  + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSG++V
Sbjct: 8   IVHQDDALLVVDKPTLLLSVPGRAD--DNKDCLVTRLQENGYPEARIVHRLDWETSGLMV 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG+P+     I   L  +        HVV  +
Sbjct: 66  LARDADSHRELSRQFHDRETEKAYTALCWGLPELDSGRIE--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ ++V++   +++  +E+ P TGR+HQLRVH L +G P++GD  Y AN +  
Sbjct: 122 FEHGRHALTFWRVVERH-ERWSRVELTPITGRSHQLRVHMLSIGHPLLGDRLY-ANPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                  +L LHA  + L HP+ G RL+  +P P
Sbjct: 180 AA---HERLCLHASLLCLTHPQSGERLRFESPAP 210


>gi|255007945|ref|ZP_05280071.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           fragilis 3_1_12]
 gi|313145657|ref|ZP_07807850.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           fragilis 3_1_12]
 gi|313134424|gb|EFR51784.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           fragilis 3_1_12]
          Length = 539

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 68/210 (32%), Positives = 100/210 (47%), Gaps = 24/210 (11%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + V +KP G+ SV G S            + ++ G  P + HRLD  TSG+L+
Sbjct: 338 ILFEDEWLLVIHKPEGLLSVPGKSEELSAYSLLRARYPEATG--PMIVHRLDMATSGLLL 395

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           VA+T+   QHL   F    I+K Y +L+ GI    +  I         I  D +   +Q 
Sbjct: 396 VAKTKEVHQHLQAQFESHSIKKQYTALLEGILPTDEGTI------DLPICPDLLDRPRQK 449

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCA 274
            + +    A++ + VID    +   +   P TGRTHQLRVH+ H   + CPI GD  Y  
Sbjct: 450 ADRESGKKAVTRYCVIDRKNGR-TRIAFFPQTGRTHQLRVHSAHPSGLNCPIAGDELYGK 508

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                       +LYLHA  ++  HP  G+
Sbjct: 509 R---------AERLYLHAERLEFTHPVSGQ 529


>gi|83648561|ref|YP_436996.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83636604|gb|ABC32571.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 319

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 90/348 (25%), Positives = 157/348 (45%), Gaps = 53/348 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q ++V  +    RLD       P  +   +Q  ++ G +RV+ K+VK   ++  G  V +
Sbjct: 7   QSLIVPAELGEQRLDMAASELMPEYSRSRIQNWIKQGALRVNGKQVKPKEKVIEGDQVEL 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              + A      +   LD               +++ED  + V NK A   V   +G   
Sbjct: 67  DVELEAQGDWEAQPIALD---------------VVFEDEHLLVINKQADFVVHPAAG--- 108

Query: 128 HIDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H DG + + V     +  + PR  + HRLD++T+G++V+A+T  A   L E  + R + +
Sbjct: 109 HSDGTVVNAVLHHCPALSELPRAGIVHRLDKDTTGLMVIAKTLIAHNSLVEQLQAREMGR 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKF 240
            Y  +V+G      E     +++ + IG    +  K    +G   A++H+++I  + + F
Sbjct: 169 EYECVVYG------ELTGGGVVEAA-IGRHPQNRQKMAVTRGGKDAVTHYRLIRRW-RGF 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLHA 292
             L ++  TGRTHQ+RVH  H+   I+GD  Y +     KG     I+      +  LHA
Sbjct: 221 THLRLKLETGRTHQIRVHMAHIHHSILGDPLYGSRPRLPKGLSAETIEYLQTFGRQALHA 280

Query: 293 RYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           + ++L HP  G L            +W+ +G   D    + RL S++E
Sbjct: 281 KALELSHPVTGEL-----------LSWE-VGLPEDMINLLNRLDSEEE 316


>gi|117919878|ref|YP_869070.1| pseudouridine synthase [Shewanella sp. ANA-3]
 gi|117612210|gb|ABK47664.1| pseudouridine synthase [Shewanella sp. ANA-3]
          Length = 223

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 101/208 (48%), Gaps = 16/208 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           L Y+D  + + NKP+G+    G   A+  D  L    + + D+      L HRLD  TSG
Sbjct: 16  LRYQDRDLIIINKPSGLLSNPGRA-AHTFDCALTRLQRLYPDTI-----LVHRLDCATSG 69

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I+V AR + A   L   F+ R+ +K+Y + V G    K   I +  +        Y    
Sbjct: 70  IMVFARNKKAESQLKTQFQDRQNEKVYIAEVMGG-IAKDAGIIDLAIAPDPEHPPYQKTQ 128

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                GA  A++H++V++   +    +E+ P TGRTHQLRVH L +G PI+GD  Y    
Sbjct: 129 TPGTAGAKSALTHYRVLE-RRENSTLVELTPQTGRTHQLRVHMLALGHPILGDEFY---- 183

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             +     + +L LHA+ +   HP  G+
Sbjct: 184 GDDEVIKARPRLCLHAQSLRFTHPYSGK 211


>gi|260220462|emb|CBA28023.1| Ribosomal large subunit pseudouridine synthase A [Curvibacter
           putative symbiont of Hydra magnipapillata]
          Length = 224

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/216 (31%), Positives = 109/216 (50%), Gaps = 14/216 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y D  + V NKPAG+    G G +   D   K   D   +   + HRLD++TSG++V+
Sbjct: 18  VVYMDDAMLVLNKPAGLLTVPGRGESKQ-DCLSKRAQDVYPEA-LIVHRLDRDTSGLVVM 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           AR   A + +  SF  R + K Y ++V G+         +W      +  D+ +  K+  
Sbjct: 76  ARGVNAQRAINLSFEKRLVDKRYEAVVIGL----LPVSDDWEEIDLPLLVDWPNRPKRTV 131

Query: 219 NEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           N      A++ ++ I       C  +E++P TGRTHQLRVH   +G P++GD  Y     
Sbjct: 132 NHAEGQQALTRWRCISVDEVIGCSRVELEPVTGRTHQLRVHMQALGHPMLGDTLYATPEA 191

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              +    ++L LHAR + +PHP   + ++ TAP+P
Sbjct: 192 LALS----DRLQLHARSLSIPHPVSAQVVEFTAPVP 223


>gi|225019500|ref|ZP_03708692.1| hypothetical protein CLOSTMETH_03453 [Clostridium methylpentosum
           DSM 5476]
 gi|224947721|gb|EEG28930.1| hypothetical protein CLOSTMETH_03453 [Clostridium methylpentosum
           DSM 5476]
          Length = 299

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/230 (30%), Positives = 113/230 (49%), Gaps = 25/230 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL---KSWVDSKGQKP---RLTHRLDQET 154
           + YED  + + NKPAG  V    G   H +  L    +W  ++ ++    R  +RLD+ T
Sbjct: 82  IAYEDDDLLLVNKPAGTPVHPSPG---HYEDSLANYSAWQYAQRREQLVFRPVNRLDRGT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L VA+   A   L++       ++IY+++V G P      I         IG     
Sbjct: 139 SGLLCVAKNAHAQARLSQQLHTGAFERIYYAVVCGAPSPAAGTI------DLPIGRTPGS 192

Query: 215 VVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+K+  + +GA  A++H++ +      +  L+++  TGRTHQ+RVH  H+GCP+ GD  Y
Sbjct: 193 VLKRRVDPQGAR-AVTHYETVRVNG-AYTLLKIRLETGRTHQIRVHFAHLGCPLFGDFLY 250

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
                G     +     LH+  + L HP  G  ++ + PLPA+M    D+
Sbjct: 251 -----GTERRDVVEGHALHSGEIRLLHPISGEEIRCSVPLPAYMENLMDN 295


>gi|49483360|ref|YP_040584.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257425250|ref|ZP_05601675.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 55/2053]
 gi|257427910|ref|ZP_05604308.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus subsp. aureus 65-1322]
 gi|257430543|ref|ZP_05606925.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus 68-397]
 gi|257433304|ref|ZP_05609662.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257436146|ref|ZP_05612193.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus M876]
 gi|282903750|ref|ZP_06311638.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C160]
 gi|282905514|ref|ZP_06313369.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282908489|ref|ZP_06316319.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WW2703/97]
 gi|282910769|ref|ZP_06318572.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WBG10049]
 gi|282913972|ref|ZP_06321759.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus M899]
 gi|282918894|ref|ZP_06326629.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C427]
 gi|282924017|ref|ZP_06331693.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|283957938|ref|ZP_06375389.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus A017934/97]
 gi|293501005|ref|ZP_06666856.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|293509964|ref|ZP_06668672.1| RNA pseudouridine synthase ylyB [Staphylococcus aureus subsp.
           aureus M809]
 gi|293526552|ref|ZP_06671237.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus M1015]
 gi|295427682|ref|ZP_06820314.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297591359|ref|ZP_06949997.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus MN8]
 gi|49241489|emb|CAG40175.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|257271707|gb|EEV03845.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 55/2053]
 gi|257274751|gb|EEV06238.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus subsp. aureus 65-1322]
 gi|257278671|gb|EEV09290.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus 68-397]
 gi|257281397|gb|EEV11534.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257284428|gb|EEV14548.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus M876]
 gi|282313989|gb|EFB44381.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|282316704|gb|EFB47078.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C427]
 gi|282322040|gb|EFB52364.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus M899]
 gi|282325374|gb|EFB55683.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WBG10049]
 gi|282327551|gb|EFB57834.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WW2703/97]
 gi|282330806|gb|EFB60320.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282595368|gb|EFC00332.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C160]
 gi|283790087|gb|EFC28904.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus A017934/97]
 gi|290920624|gb|EFD97687.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus M1015]
 gi|291096010|gb|EFE26271.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|291466908|gb|EFF09426.1| RNA pseudouridine synthase ylyB [Staphylococcus aureus subsp.
           aureus M809]
 gi|295128040|gb|EFG57674.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297576245|gb|EFH94961.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus MN8]
 gi|312438426|gb|ADQ77497.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|315194083|gb|EFU24476.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus CGS00]
          Length = 305

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 81/308 (26%), Positives = 140/308 (45%), Gaps = 34/308 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +     
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYK----- 55

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++   I      + E  IL  ++NL          + YED  + V  KP G+ V    
Sbjct: 56  -VKLNDHIVVTEKEVVEADILPENLNLD---------IYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKDLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAP--IGRNKNDRQSMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQA-----LHAGLIG 273

Query: 297 LPHPEGGR 304
             HP  G 
Sbjct: 274 FEHPVTGE 281


>gi|197119918|ref|YP_002140345.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
 gi|197089278|gb|ACH40549.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
          Length = 297

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 80/308 (25%), Positives = 140/308 (45%), Gaps = 40/308 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           V+ +    RLD   K  +P  +   +++I+  G   + +  V+  +R ++ G+ + +   
Sbjct: 7   VDAELAGTRLDDAAKTLFPQYSKGEIRRIIDWGGCYLSQTLVRVASRTVKEGEEIAL--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----SGI 125
                 I++ ++ ++ +        + K  LLYED       K AG + Q         +
Sbjct: 64  -----GIMEAERCIELA--------YKKEELLYEDKDFLAVYKAAGFNSQRTPYQLKGTV 110

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            Y ++ ++KS         R+ HRLD+ TSG++   + + AA  ++   +  ++QK YW+
Sbjct: 111 EYAVECYMKSI--GLRDPSRVVHRLDRGTSGVMFFPKHKQAATLISNLLKDGKVQKTYWA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G P  +   +   L K S     + + V  N K A    + F+V+   A     +E 
Sbjct: 169 LVAGSPDQQSWKVDAPLGKVSK----FKYGVALNGKPAR---TLFRVVGEGA-GVTAVEA 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +P TGRTHQ+RVH  H G PI+GD  Y     G   +    ++ LH R M      G  +
Sbjct: 221 KPLTGRTHQIRVHLAHSGFPIIGDETY-----GGIPAA---RMMLHCRGMRFTGARGKVI 272

Query: 306 QITAPLPA 313
           +  AP+ A
Sbjct: 273 EAFAPIDA 280


>gi|253689991|ref|YP_003019181.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251756569|gb|ACT14645.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 217

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/205 (34%), Positives = 106/205 (51%), Gaps = 18/205 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  + S + +        HRLD  TSG++ 
Sbjct: 14  ILYQDQHIMVVNKPSGLLSVPGRA--PEHKDSVM-SRIQADYPTAESVHRLDMATSGVIA 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG  +  +  I   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPKKSYLARVWGHMEQDEGVIDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G   A + ++V+         +++ P TGR+HQLRVH L +G PI+GD  Y A+ 
Sbjct: 125 VCFETG-KAAQTEYQVLSRDDDGTTRVKLMPITGRSHQLRVHLLALGHPILGDGFY-AHP 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPE 301
                +P   +L LHA+ + + HPE
Sbjct: 183 DAKAMAP---RLLLHAQELAITHPE 204


>gi|170766082|ref|ZP_02900893.1| ribosomal large subunit pseudouridine synthase D [Escherichia
           albertii TW07627]
 gi|170125228|gb|EDS94159.1| ribosomal large subunit pseudouridine synthase D [Escherichia
           albertii TW07627]
          Length = 326

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 124/247 (50%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIVDVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+   A   L ES + R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKNVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPV 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F S ++  ++  LHA  + L HP  G  ++  AP+P  MV+  +++
Sbjct: 253 YGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELVEAM 312

Query: 323 GFKYDRN 329
              ++ +
Sbjct: 313 RADFEEH 319


>gi|167753888|ref|ZP_02426015.1| hypothetical protein ALIPUT_02173 [Alistipes putredinis DSM 17216]
 gi|167658513|gb|EDS02643.1| hypothetical protein ALIPUT_02173 [Alistipes putredinis DSM 17216]
          Length = 356

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 81/345 (23%), Positives = 149/345 (43%), Gaps = 60/345 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +  +  +  +RLD++   H    +   +Q    +G + V+ K  K + +++ G  + +  
Sbjct: 30  ITADRGQSPLRLDKFLTIHMERCSRNRIQTAADAGNILVNGKPAKSSYKVKPGDRISL-- 87

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               + +  +E +I+  ++ L          + YED  + + NKPAG+ V  G G     
Sbjct: 88  ---VMPYPKREIEIIPENIPLE---------IPYEDDDLLLVNKPAGMVVHPGHGNYSAT 135

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + Y++             +  L HR+D+ TSG+LV+A+   A   L + F    I 
Sbjct: 136 LVNALTYYLQNL--PLFQEGDMRAGLVHRIDKNTSGLLVIAKNERAHARLAKQFFDHTIT 193

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK--------GANYAISHFKV 232
           + Y +LVWG          N+   +  I G+     K  +K           +A++H++V
Sbjct: 194 RRYVALVWG----------NFEEDEGTITGNIGRSPKDRQKMWVFEDGSDGKHAVTHYRV 243

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN 286
           +  +      +E +  TGRTHQ+RVH    G P+ GD +Y  +   KG     +   I+N
Sbjct: 244 LKRYGY-VTLIECRLETGRTHQIRVHMQWKGHPLFGDERYGGDRILKGTTFNKYKQFIEN 302

Query: 287 ------KLYLHARYMDLPHPEGG-RLQITAPLPAH---MVKTWDS 321
                 +  LHA+ +   HP  G ++   + LP     ++  WD+
Sbjct: 303 CFAAMPRQALHAKSLGFQHPTTGEQVYFESELPEDFRTVLAKWDA 347


>gi|114563871|ref|YP_751385.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114335164|gb|ABI72546.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 217

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 63/198 (31%), Positives = 102/198 (51%), Gaps = 12/198 (6%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  I V NKP+G+    G     H     +  +     +  L HRLD +TSGI++ AR
Sbjct: 18  YKDRDIIVINKPSGLLSNPGRSPDTHDTAITR--LQRCYPEAILIHRLDCDTSGIMIFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           T+ A  HL   F+ R+ +K+Y + V G   ++++   N+ L  +     +  +    +  
Sbjct: 76  TKKAESHLKIQFQNRQAKKVYIAEVIG-HVDEQQGKVNFALGANPDSPPFQMLTDSGKA- 133

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A+++F V++  A     +E++PHTGRTHQLRVH L +G  I+GD  Y      N + 
Sbjct: 134 ---ALTYFSVLEHRAYS-TLMELKPHTGRTHQLRVHMLALGHTILGDEFYGDESTINAS- 188

Query: 283 PIQNKLYLHARYMDLPHP 300
               +L LHA+ + + HP
Sbjct: 189 ---KRLNLHAQSLTITHP 203


>gi|238755741|ref|ZP_04617074.1| Ribosomal large subunit pseudouridine synthase A [Yersinia ruckeri
           ATCC 29473]
 gi|238706033|gb|EEP98417.1| Ribosomal large subunit pseudouridine synthase A [Yersinia ruckeri
           ATCC 29473]
          Length = 217

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/207 (34%), Positives = 105/207 (50%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV    G A      + + + +        HRLD  TSG++V
Sbjct: 14  ILYQDLHIMVVNKPSGLLSV---PGRAPENKDSIMTRIQADFPTAESVHRLDMATSGVMV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG  +  +  I   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPKKSYIARVWGHLEQDEGLIDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + A + ++V+   A     +++ P TGR+HQLRVH L MG PI+GD  Y    
Sbjct: 125 VCYETGKS-AQTEYQVLCRDADGSTRVKLSPITGRSHQLRVHMLAMGHPILGDGFYAHPE 183

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
                S    +L LHA+ + + HPE G
Sbjct: 184 AKAMAS----RLQLHAQELCITHPEFG 206


>gi|237809106|ref|YP_002893546.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
 gi|237501367|gb|ACQ93960.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
          Length = 220

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 68/216 (31%), Positives = 105/216 (48%), Gaps = 16/216 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILV 159
           +LYED  I V NKP+G+    G  +  H D    +W V  +  +    HRLD  TSG+++
Sbjct: 16  ILYEDEHIIVMNKPSGLLSVPGKALE-HADSI--AWRVRQRCPEAGSVHRLDMSTSGVIL 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+   A   L + F+ R+ +K Y++ VWG      E + +  L          HV   N
Sbjct: 73  MAKYSKATGILGKQFQERKTEKFYYAWVWGQVAGT-EGMIDLPLCVDWENRPLQHV---N 128

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +    A +H++ +   A +   +++ P+TGR+HQLRVH   +G PI+GDH Y      +
Sbjct: 129 YEHGRPAQTHWQRVRVEADRTL-MKLTPYTGRSHQLRVHMKELGHPILGDHLYAPKEVQD 187

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG---RLQITAPLP 312
               +Q    LHA  +   HP  G   R +  AP P
Sbjct: 188 LVPHLQ----LHAAMLSFYHPVTGEQMRFEAPAPFP 219


>gi|87119949|ref|ZP_01075845.1| pseudouridine synthase Rlu family protein [Marinomonas sp. MED121]
 gi|86164651|gb|EAQ65920.1| pseudouridine synthase Rlu family protein [Marinomonas sp. MED121]
          Length = 244

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 76/249 (30%), Positives = 116/249 (46%), Gaps = 32/249 (12%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISV-------QGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           SD L  IL Y+D  + V NKP+G+ V       Q    +   ++  L  WV         
Sbjct: 2   SDSLLEIL-YQDDYLVVINKPSGLLVHRTQLASQETDAVVQRLNAQLNKWVYP------- 53

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ TSG LV+A     A+ L E F   +++K Y  LV G  +++   I   L K +
Sbjct: 54  VHRLDRGTSGALVLAFDANTAKLLAEQFSQSQVEKYYLCLVRGHTESRG-TIDYPLAKLN 112

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLR 256
              G     ++  EK    A++H+K I+ F            + C +E++   GR HQ+R
Sbjct: 113 ENKGKSRFKIEGTEKE---AVTHYKKIEGFVLNQAVSKYDTTRCCLVEVKTEQGRKHQIR 169

Query: 257 VHALHMGCPIVGDHKY-CANFKGNFTS-PIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
            H  H+  P++GD +Y C +    F    ++ +L LHA+ +   HP  G +L   A LP 
Sbjct: 170 RHFKHIRFPLIGDTRYGCRHHNKLFRRLGLEQRLMLHAKTLAFKHPVTGHQLDCKASLPD 229

Query: 314 HMVKTWDSL 322
              +T D L
Sbjct: 230 GFKQTLDYL 238


>gi|145224223|ref|YP_001134901.1| RluA family pseudouridine synthase [Mycobacterium gilvum PYR-GCK]
 gi|315444557|ref|YP_004077436.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           Spyr1]
 gi|145216709|gb|ABP46113.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           gilvum PYR-GCK]
 gi|315262860|gb|ADT99601.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           Spyr1]
          Length = 309

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 78/296 (26%), Positives = 142/296 (47%), Gaps = 36/296 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
           G V +D      ++++ +G    VR+PP             + ++ V++          +
Sbjct: 39  GGVDIDGAPAAKSDKLVAGAWLEVRLPP---------PPAPVENTPVDIEGMG------I 83

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYH----IDGFLKSW--VDSKG--QKPRLTHRLDQE 153
           LY D  I   +KP G++    + + +H    + G   +   + + G  ++  + HRLD  
Sbjct: 84  LYSDDDIVAVDKPPGVAAH--ATVGWHGPTVLGGLAAAGFRISTSGIHERQGIVHRLDVG 141

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA +  A   L  +F+ R ++K Y +LV G P      I   + +  H G D+ 
Sbjct: 142 TSGVMVVALSERAYTVLKRAFKQRTVEKRYHALVQGHPDPSSGTIDAPIGR--HRGHDWK 199

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V ++ +   ++I+H+  ++   Q    L+++  TGRTHQ+RVH   +  P  GD  Y 
Sbjct: 200 FAVVEDGR---HSITHYDTLEAH-QAASLLDIELETGRTHQIRVHFAALHHPCCGDLTYG 255

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A+        ++ + +LHAR +   HP +G R++ T+P PA +    D L  ++DR
Sbjct: 256 ADPTLAKKLGLERQ-WLHARSLAFAHPADGRRVEFTSPYPADLQHALDVL-RRHDR 309


>gi|303231392|ref|ZP_07318126.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302513988|gb|EFL55996.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 305

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 88/291 (30%), Positives = 136/291 (46%), Gaps = 47/291 (16%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +Q +++SG V V+ K  K N R+ +   + +          I E +    SV +      
Sbjct: 30  IQSLIKSGHVLVNGKVGKANLRLNADSTISVD---------IPEPE----SVEILPED-- 74

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRL 150
           +    LYED  I + NKP G+ V    G      ++  L    D  G     +P + HRL
Sbjct: 75  IPVEYLYEDHDIIIVNKPRGMVVHPAIGNYSGTLVNALLYHCKDLSGINGEIRPGIVHRL 134

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+++ A+  AA   L E  +    ++ Y +LV G    +K  I      K+ IG 
Sbjct: 135 DKDTSGVMMAAKNDAAHIGLAEQVKAHSAKRTYLALVQGNIVEEKGII------KAPIGR 188

Query: 211 D-----YVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHM 262
                  + VV +N K    A++HFKV++ +       C LE    TGRTHQ+RVH  H+
Sbjct: 189 HPKDRMKMAVVFENSK---EAVTHFKVLERYGYHTLVECVLE----TGRTHQIRVHFAHI 241

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           G P+V D  Y    + +F  PI  +  LH+  +D+ HP  G  +   AP+P
Sbjct: 242 GHPVVNDPFYGYR-RMDF--PIDGQA-LHSHTLDVVHPITGEPMHFEAPVP 288


>gi|297622146|ref|YP_003710283.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
 gi|297377447|gb|ADI39277.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
          Length = 284

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 78/291 (26%), Positives = 138/291 (47%), Gaps = 45/291 (15%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHIIKEQKILDSS 87
           YP  +   L+ +L+  +++VD +  K     ++ GQ++ +          +K+Q ++   
Sbjct: 19  YPDSSKTTLRSLLKEERIKVDGQTCKLGTLSLKKGQILEV----------VKKQNVIAEG 68

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           V +           LY+D  + V  KP+G+ SV         +   LK     K  +  +
Sbjct: 69  VKI-----------LYQDPHLAVVFKPSGLLSVATDFEKNLTLHKILKEHFQPKTVE--V 115

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLK 204
            HRLDQ+TSG++V A  +     L   F    I++ Y ++V G   P++      +W   
Sbjct: 116 VHRLDQDTSGVIVFALDKQTCLKLKILFEKHEIERCYTAIVEGKLTPRS-----GSW--- 167

Query: 205 KSHIGGDYVHVV--KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           +S++  D  +VV    N +    AI+H+ V++ +++KF  L ++  TG+ +Q+RVH    
Sbjct: 168 RSYLHEDENYVVHSTDNARKGKLAITHY-VVEGYSKKFTRLRLKLETGKKNQIRVHCSDA 226

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           G PI GD KY A      +S    +L LHA ++   HP +  ++Q T   P
Sbjct: 227 GHPIAGDTKYGA------SSNPGKRLMLHADHLGFIHPVKRKKMQFTIDPP 271


>gi|71891968|ref|YP_277698.1| pseudouridine synthase [Candidatus Blochmannia pennsylvanicus str.
           BPEN]
 gi|71796074|gb|AAZ40825.1| pseudouridine synthase [Candidatus Blochmannia pennsylvanicus str.
           BPEN]
          Length = 343

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 87/337 (25%), Positives = 155/337 (45%), Gaps = 49/337 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVV 65
           ++ ++V+  +   RLD       P+ +   ++  + S +V V+ + V     ++  G+ +
Sbjct: 27  IKPMIVQESQSGKRLDCILSELLPNYSRSKIKCWILSKKVNVNNQTVIIPKKKMMGGEFI 86

Query: 66  RIPPVINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
            I  ++N  N+ I  Q I LD               ++YED  I V NK   + V  G+G
Sbjct: 87  EIKDIVNIDNNNIVPQDIPLD---------------IVYEDDDIVVINKAKNMVVHPGAG 131

Query: 125 IAYHIDGFLKSWV-----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              H    L + +      ++  +  +  RLD++T+G++VVA+   A   L   F+ R+I
Sbjct: 132 --NHSGTILNALLYKYPAITEVFRSGIVQRLDKDTTGLMVVAKNMIAYHSLLRLFKKRKI 189

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV-HVVKQNEKGAN----YAISHFKVID 234
            + Y ++V G          N+L  +  I      H V +     N     AI+H+ +I+
Sbjct: 190 IREYEAVVLG----------NFLHNEGTINQPIRRHAVHRTRMTVNPMGKSAITHYSIIE 239

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKG-----NFTSPIQN 286
            F   +  + ++  TGRTHQ+RVH  ++  P++GDHKY  +    KG     N    + N
Sbjct: 240 SFGM-YTRIRVRLETGRTHQIRVHMAYINHPLLGDHKYGKSTYFIKGISDTVNDCLHVLN 298

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +  LHA  + L HP    +++   PLP  ++K  + L
Sbjct: 299 RQALHAATLQLCHPITRIKMKWDVPLPKDIIKLINIL 335


>gi|301166302|emb|CBW25878.1| putative pseudouridine Synthase [Bacteriovorax marinus SJ]
          Length = 313

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 64/232 (27%), Positives = 113/232 (48%), Gaps = 18/232 (7%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPR 145
           S+ +    +F +S+L++E++   V NKPA +S    +     ++   L  ++ S G K +
Sbjct: 81  SLPIENKREFKESMLIHEENLFLVANKPAMLSSTATTNSKQDNLHAILTRYI-SGGHKEK 139

Query: 146 ---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KKECIANW 201
              + HR+D ETSG+L+  + ++  +  ++ F  R+++K Y +L+     + K + + N+
Sbjct: 140 YLSIHHRIDFETSGLLIFCKKKSQNKFFSDLFEQRKVKKTYLALIKDPDHSFKDQKVENF 199

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L +        +        G   A ++FK I    +    +E +P TGR HQ+RVH   
Sbjct: 200 LERDPKNKMKMMSTTH----GGKKATTYFKEI-THQEGMTLVEAKPETGRFHQIRVHLAE 254

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +G PI+GD  Y         S    +  LHA  +  PHP+    L+  APLP
Sbjct: 255 LGFPIIGDSIYSQK------SEQFPRTMLHAYKLSFPHPQSDESLEFIAPLP 300


>gi|220917166|ref|YP_002492470.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219955020|gb|ACL65404.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 352

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 82/328 (25%), Positives = 141/328 (42%), Gaps = 49/328 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---P 68
           V  +    RLD       P ++   +Q+++ +G V+VD +  K + R++ G+ + +   P
Sbjct: 28  VPPELAGTRLDAALVRLAPDLSRARVQRLVEAGLVQVDGRGAKASARLRGGEAIALELPP 87

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P  + L                   +  L   +L+ED+ + V +K  G+ V    G  + 
Sbjct: 88  PEPSGLV------------------AQDLPLAVLHEDADLIVLDKAPGMVVHPARGTPHS 129

Query: 129 --IDGFL-----KSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             ++  L            G  PRL   HRLD++TSG LVVA+T AA   L   ++ R +
Sbjct: 130 TVVNALLHRLGLPGAAGPDGGLPRLGLVHRLDKDTSGCLVVAKTEAALAALQAQWKGRSV 189

Query: 180 QKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +K+Y +L  G   P+ + +       +      D +    +    +  A++ ++V + F 
Sbjct: 190 EKVYLALCHGALAPEGRLDTPYGRHPR------DRLRFTGRVTS-SRRALTEWRVREAFG 242

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFTSPIQNKL 288
                 E+  HTGRTHQ+RVH    G P++ D  Y    +             +    + 
Sbjct: 243 AAASLAEVTLHTGRTHQIRVHLSEAGHPLLADAVYGGTRREARLAPADPARRAAEAVGRQ 302

Query: 289 YLHARYMDLPHPEGG-RLQITAPLPAHM 315
            LHA  +   HP  G RL + AP+PA +
Sbjct: 303 ALHALRLGFDHPRTGRRLVVEAPVPADL 330


>gi|29349909|ref|NP_813412.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|29341820|gb|AAO79606.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           thetaiotaomicron VPI-5482]
          Length = 549

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/218 (30%), Positives = 111/218 (50%), Gaps = 37/218 (16%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGIL 158
           +++ED  + V NKP+G +SV G       +   +K+ + ++ G  P + HRLD  TSG+L
Sbjct: 343 IVFEDEWLVVVNKPSGMLSVPGKEEETDSVYHRVKAKYPEATG--PMIVHRLDMATSGLL 400

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKE--------CIANWLLKKSHI 208
           +VA+T+   QHL E F  R I+K Y +L+   G+ +  +E        C+      +  +
Sbjct: 401 LVAKTKEVHQHLQEQFISRSIKKRYVALLDRNGLNQQLEETGTINLPLCLNPLDRPRQMV 460

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCP 265
             +Y             A++ +++++ ++ K+  +   P TGRTHQLRVHA H   +  P
Sbjct: 461 SEEY----------GKPAVTEYRILN-YSDKYIRIAFYPLTGRTHQLRVHAAHHQGLNYP 509

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           I+GD  Y             ++LYLHA Y++  HP  G
Sbjct: 510 ILGDELYGKK---------ADRLYLHAEYIEFRHPVYG 538


>gi|70726718|ref|YP_253632.1| hypothetical protein SH1717 [Staphylococcus haemolyticus JCSC1435]
 gi|68447442|dbj|BAE05026.1| unnamed protein product [Staphylococcus haemolyticus JCSC1435]
          Length = 305

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/269 (26%), Positives = 133/269 (49%), Gaps = 30/269 (11%)

Query: 12  VENDE-ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +EN E    R+D+         +   +Q +++   V V++K +K N +++   ++     
Sbjct: 8   IENQELVGQRIDKLLPEFNNEWSRSQIQDLIKEDLVTVNEKVIKSNYKVKLNDLI----- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                 I+ E++++++ +      + L   + YED  + +  KP G+ V    G      
Sbjct: 63  ------IVTEKEVVEADI----QPENLNLDIYYEDEDVAIVYKPKGMVVHPSPGHYSGTL 112

Query: 129 IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L E    + +++ Y 
Sbjct: 113 VNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMDKSVKRKYT 172

Query: 185 SLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G IP +     A   + ++      + VV   ++    A++HF V++ F   +  +
Sbjct: 173 ALVHGNIPHDYGTIDAP--IGRNEKDRQSMDVVDNGKE----AVTHFNVLEHF-NDYTLI 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           E Q  TGRTHQ+RVH  ++G P+VGD KY
Sbjct: 226 ECQLETGRTHQIRVHMKYIGFPLVGDPKY 254


>gi|212636674|ref|YP_002313199.1| pseudouridine synthase RluD [Shewanella piezotolerans WP3]
 gi|212558158|gb|ACJ30612.1| Pseudouridine synthase, RluD [Shewanella piezotolerans WP3]
          Length = 328

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 88/325 (27%), Positives = 148/325 (45%), Gaps = 53/325 (16%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD+   + +P  +   +++ + SG V +D     K   ++  GQ + +      L  + 
Sbjct: 24  RLDQTLADLFPDYSRTRIKEWILSGAVSIDGNVSDKPRTKVLEGQEIIV------LATLE 77

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
           +E      +++L          ++YED  I V NK AG+ V  G+G         + +H 
Sbjct: 78  EETSAKAEAIDLD---------IVYEDDHILVINKQAGLVVHPGAGNQDGTLMNALLHHC 128

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G     V   G    + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V G
Sbjct: 129 PGI--ELVPRAG----IVHRLDKDTTGLMVVAKTVEAQTHLVTALQAREITREYEAIVQG 182

Query: 190 ---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                    E I     K++H+       V  N K    A++H++V + F +    L ++
Sbjct: 183 GIIAGGTVDEPIDRHPTKRTHMA------VVHNGKP---AMTHYRVAEKF-RAHTRLRLR 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLY-------LHARYMDLP 298
             +GRTHQ+RVH  ++G  +VGD  Y    +     +P   + Y       LHA  ++L 
Sbjct: 233 LESGRTHQIRVHMAYIGHVLVGDPVYAGRPRPPKGAAPDFFETYMGFKRQALHAIRLELA 292

Query: 299 HPEGGRLQI-TAPLPAHMVKTWDSL 322
           HP    +    AP+P  MVK   +L
Sbjct: 293 HPFTCEIMSWQAPVPDDMVKLTKAL 317


>gi|326771685|ref|ZP_08230970.1| ribosomal large subunit pseudouridine synthase D [Actinomyces
           viscosus C505]
 gi|326637818|gb|EGE38719.1| ribosomal large subunit pseudouridine synthase D [Actinomyces
           viscosus C505]
          Length = 306

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 77/290 (26%), Positives = 136/290 (46%), Gaps = 36/290 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++ +  +G+VR   + +  ++R+++G+++ +          + + + ++      +  + 
Sbjct: 32  VEDLCEAGEVRRGGETLAKSSRLRAGELLEVD---------LPDPRPVEPVATPVEGME- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRL 150
               LLYED  I V +KPAG++     G     + G LK+    V + G   R  +  RL
Sbjct: 82  ----LLYEDEDIVVVDKPAGVAAHPSMGWDGPDVLGALKAMHVQVATSGAAERQGIVSRL 137

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+++VA+   A   L  +FR   + K+Y +LV G        I   + +  H   
Sbjct: 138 DVGTSGVMIVAKGERAYSVLKRAFREHTVDKVYHALVQGHLDPSSGTIDAPIGR--HPSR 195

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           ++   + +   G   +I+H+ VI+      C  E+   TGRTHQ+RVH   +G P VGD 
Sbjct: 196 EWKMAIIE---GGRESITHYDVIEAMPGA-CLAEIHLETGRTHQIRVHMAAVGHPCVGDA 251

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
            Y A+   +  + +  + +LHAR + + HP  G          HMV T D
Sbjct: 252 TYGADPVMSARTGLIRQ-WLHARELGIAHPITGE---------HMVFTSD 291


>gi|294675292|ref|YP_003575908.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           ruminicola 23]
 gi|294472360|gb|ADE81749.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           ruminicola 23]
          Length = 459

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/225 (32%), Positives = 105/225 (46%), Gaps = 38/225 (16%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  I    KP+G +SV G +      D  + +W   +     L HRLD  TSGI++
Sbjct: 250 IVYEDEAIAAVYKPSGMLSVPGKTD-----DYSVATWAKERWAASMLPHRLDLMTSGIML 304

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-----ANWLLKKSHIGGDYVH 214
           VA+T  A  HL   F  R I+K Y ++V G  +     I     ++ + +   I  DY H
Sbjct: 305 VAKTPEAYHHLQNQFAARTIKKKYLAVVEGEIQQPHGVIDLPLSSDPMNRPCQI-VDYEH 363

Query: 215 VVKQNEKGANYAISHFKVID-----CFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPI 266
                      AI+ ++V+D        +    L + PHTGRTHQLR+H  H   +GCPI
Sbjct: 364 --------GKRAITEYRVLDRQQSPTTHRPVTLLALYPHTGRTHQLRMHCAHQEGLGCPI 415

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
           +GD  Y             ++LYL A  +   HP  G RL +  P
Sbjct: 416 LGDELYGHK---------ADRLYLQAESIAFEHPTTGKRLHLFCP 451


>gi|194323822|ref|ZP_03057598.1| pseudouridine synthase, RluA family [Francisella tularensis subsp.
           novicida FTE]
 gi|208779913|ref|ZP_03247257.1| pseudouridine synthase, RluA family [Francisella novicida FTG]
 gi|194322186|gb|EDX19668.1| pseudouridine synthase, RluA family [Francisella tularensis subsp.
           novicida FTE]
 gi|208744368|gb|EDZ90668.1| pseudouridine synthase, RluA family [Francisella novicida FTG]
          Length = 317

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 82/308 (26%), Positives = 140/308 (45%), Gaps = 38/308 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D      +   +   +QK L+ G + V+ +  K  + +   + V I   +   N  I 
Sbjct: 9   RIDVVINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEINIELLPTNEWIA 68

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           E       +NL          +++ED  I V +KP  + V  G+G       +  L  + 
Sbjct: 69  E------DINLK---------IIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYK 113

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D + + PR  + HRLD++TSG++V A++  A  +L +    R++ + Y ++V G      
Sbjct: 114 D-QDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEG------ 166

Query: 196 ECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           E      + +  IG D  +  K   N +G   AI+H+  I+ +   F  +E Q  TGRTH
Sbjct: 167 EIYQQGTINQP-IGRDPTNRTKMAINYRGKE-AITHYTPIEVY-DGFTLIECQLETGRTH 223

Query: 254 QLRVHALHMGCPIVGDHKYCANF----KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QIT 308
           Q+RVH   +  P+VGD  Y  +     K   T+P +    LHA  +   HP   ++ +  
Sbjct: 224 QIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITTPTRQA--LHAYKLSFIHPTTAKMVKFK 281

Query: 309 APLPAHMV 316
           + LP  M+
Sbjct: 282 SKLPEDML 289


>gi|120599938|ref|YP_964512.1| RluA family pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|146292126|ref|YP_001182550.1| RluA family pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|120560031|gb|ABM25958.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           W3-18-1]
 gi|145563816|gb|ABP74751.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           putrefaciens CN-32]
 gi|319425422|gb|ADV53496.1| pseudouridine synthase, RluA family [Shewanella putrefaciens 200]
          Length = 324

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 74/234 (31%), Positives = 115/234 (49%), Gaps = 31/234 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NK AG+ V  G+G A   DG L + +          PR  + HRLD++T
Sbjct: 86  IVYEDDHILVINKQAGLVVHPGAGNA---DGTLMNALLHHCPDIEHVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL  + + R I + Y ++V G         E I     K++H+   
Sbjct: 143 TGLMVVAKTVEAQTHLVAALQAREITREYEAIVMGTMTGGGTVDEPIGRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH           A++H++V + F +    L ++  +GRTHQ+RVH  ++G  +VGD  
Sbjct: 201 -VH------HSGKPAVTHYRVAEKF-RNHTRLRLRLESGRTHQIRVHMEYIGHVLVGDPV 252

Query: 272 YCANFK------GNFTSPIQN--KLYLHARYMDLPHPEGGRLQI-TAPLPAHMV 316
           Y    K        F   ++N  +  LHA  ++L HP    +    AP+P  MV
Sbjct: 253 YGGRPKPPKAASPEFFEILKNFKRQALHAVRLELAHPVSCEIMSWQAPIPEDMV 306


>gi|255100096|ref|ZP_05329073.1| putative pseudouridylate synthase [Clostridium difficile QCD-63q42]
          Length = 300

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 112/225 (49%), Gaps = 27/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++Y+D  I + NKP  + V            +GI+Y+ID         +  K R  +RLD
Sbjct: 85  IIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGISYYIDN------QKENVKIRFVNRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG+++VA+   A   L+ +    +++K Y ++V GI K  +  I   + + +    D
Sbjct: 139 MNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGIIKENEGTIDEPIYRPTE---D 195

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  +  +E+G + +++H+KVI+   +    LE+   TGRTHQ+RVH  H+G  I+GD  
Sbjct: 196 SIKRI-IDERGQS-SVTHYKVIERL-ENATVLEVSLETGRTHQIRVHMAHIGHGIIGDEL 252

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           Y     G     + N+  LHA  ++   P    +L+  A +P  M
Sbjct: 253 Y-----GYVDEELINRQALHAYKLEFEQPRTKEKLKFKADIPEDM 292


>gi|15924187|ref|NP_371721.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus subsp. aureus Mu50]
 gi|15926780|ref|NP_374313.1| hypothetical protein SA1040 [Staphylococcus aureus subsp. aureus
           N315]
 gi|57651766|ref|YP_186072.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus COL]
 gi|88194903|ref|YP_499703.1| hypothetical protein SAOUHSC_01163 [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|148267688|ref|YP_001246631.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150393746|ref|YP_001316421.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp.
           aureus JH1]
 gi|151221320|ref|YP_001332142.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus str.
           Newman]
 gi|156979518|ref|YP_001441777.1| hypothetical protein SAHV_1187 [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|221141987|ref|ZP_03566480.1| hypothetical protein SauraJ_10200 [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|253315555|ref|ZP_04838768.1| hypothetical protein SauraC_05302 [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
 gi|253731814|ref|ZP_04865979.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|253733565|ref|ZP_04867730.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|255005984|ref|ZP_05144585.2| hypothetical protein SauraM_05925 [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|257795747|ref|ZP_05644726.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9781]
 gi|258415971|ref|ZP_05682241.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9763]
 gi|258419718|ref|ZP_05682685.1| pseudouridylate synthase [Staphylococcus aureus A9719]
 gi|258438760|ref|ZP_05689913.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9299]
 gi|258444534|ref|ZP_05692863.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus A8115]
 gi|258447633|ref|ZP_05695777.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus A6300]
 gi|258449475|ref|ZP_05697578.1| pseudouridine synthase [Staphylococcus aureus A6224]
 gi|258452494|ref|ZP_05700500.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A5948]
 gi|258454854|ref|ZP_05702818.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A5937]
 gi|262048100|ref|ZP_06020987.1| hypothetical protein SAD30_1876 [Staphylococcus aureus D30]
 gi|262051832|ref|ZP_06024048.1| hypothetical protein SA930_1382 [Staphylococcus aureus 930918-3]
 gi|269202811|ref|YP_003282080.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282892683|ref|ZP_06300918.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8117]
 gi|282919979|ref|ZP_06327708.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|282927537|ref|ZP_06335153.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|284024121|ref|ZP_06378519.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 132]
 gi|295407135|ref|ZP_06816936.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|296275218|ref|ZP_06857725.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus MR1]
 gi|297245979|ref|ZP_06929838.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8796]
 gi|304381241|ref|ZP_07363894.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|13700996|dbj|BAB42292.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           N315]
 gi|14246967|dbj|BAB57359.1| similar to ribosomal large subunit psudouridine synthase D
           [Staphylococcus aureus subsp. aureus Mu50]
 gi|57285952|gb|AAW38046.1| ribosomal large subunit pseudouridine synthases, RluD subfamily
           [Staphylococcus aureus subsp. aureus COL]
 gi|87202461|gb|ABD30271.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           NCTC 8325]
 gi|147740757|gb|ABQ49055.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149946198|gb|ABR52134.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus JH1]
 gi|150374120|dbj|BAF67380.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus str.
           Newman]
 gi|156721653|dbj|BAF78070.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253724413|gb|EES93142.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|253728619|gb|EES97348.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|257789719|gb|EEV28059.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9781]
 gi|257839307|gb|EEV63781.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9763]
 gi|257844303|gb|EEV68685.1| pseudouridylate synthase [Staphylococcus aureus A9719]
 gi|257848019|gb|EEV72012.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9299]
 gi|257850027|gb|EEV73980.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus A8115]
 gi|257853824|gb|EEV76783.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus A6300]
 gi|257857463|gb|EEV80361.1| pseudouridine synthase [Staphylococcus aureus A6224]
 gi|257859712|gb|EEV82554.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A5948]
 gi|257863237|gb|EEV86001.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A5937]
 gi|259160233|gb|EEW45261.1| hypothetical protein SA930_1382 [Staphylococcus aureus 930918-3]
 gi|259163666|gb|EEW48221.1| hypothetical protein SAD30_1876 [Staphylococcus aureus D30]
 gi|262075101|gb|ACY11074.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|269940689|emb|CBI49070.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus TW20]
 gi|282590540|gb|EFB95617.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|282594695|gb|EFB99679.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|282764680|gb|EFC04805.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8117]
 gi|285816879|gb|ADC37366.1| Ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus 04-02981]
 gi|294967988|gb|EFG44016.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|297177143|gb|EFH36397.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8796]
 gi|302751019|gb|ADL65196.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus str. JKD6008]
 gi|304340224|gb|EFM06165.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|312829590|emb|CBX34432.1| pseudouridine synthase, RluA family protein [Staphylococcus aureus
           subsp. aureus ECT-R 2]
 gi|315130988|gb|EFT86972.1| hypothetical protein CGSSa03_05574 [Staphylococcus aureus subsp.
           aureus CGS03]
 gi|320140988|gb|EFW32835.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|329313865|gb|AEB88278.1| Pseudouridine synthase [Staphylococcus aureus subsp. aureus T0131]
 gi|329724740|gb|EGG61245.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21189]
 gi|329727173|gb|EGG63629.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21172]
          Length = 305

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 85/327 (25%), Positives = 150/327 (45%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +     
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKSNYK----- 55

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++   I      + E  IL  ++NL          + YED  + V  KP G+ V    
Sbjct: 56  -VKLNDHIVVTEKEVVEADILPENLNLD---------IYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +   K+     G+ +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAP--IGRNKNDRQSMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQA-----LHAGLIG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G  ++  A LP       D++
Sbjct: 274 FEHPVTGEYIERHAELPQDFEDLLDTI 300


>gi|312875041|ref|ZP_07735059.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
 gi|311089436|gb|EFQ47862.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
          Length = 283

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/279 (25%), Positives = 129/279 (46%), Gaps = 35/279 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKN-----HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           Y+ Y+ +  +E N  +D+  +N      + H  F+ ++K      + V+ K +  N ++ 
Sbjct: 4   YIYYLTISQNENNQNVDQIMRNLLIPRKWRH--FLRIEK-----NILVNDKYLPLNFKVH 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V +KPAG   Q
Sbjct: 57  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENDDVLVIDKPAG---Q 100

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 101 KTHPNLYETDTALNDCASYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 160

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQK 239
           + Y++ +            N       IG D + + K+  +     AI+H++V+   A K
Sbjct: 161 RSYFAWIEATNDISDNGTINL-----PIGDDPLDMRKRMVRTDGLKAITHYQVVKKTANK 215

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++ 
Sbjct: 216 IL-VKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQA 253


>gi|320102049|ref|YP_004177640.1| RluA family pseudouridine synthase [Isosphaera pallida ATCC 43644]
 gi|319749331|gb|ADV61091.1| pseudouridine synthase, RluA family [Isosphaera pallida ATCC 43644]
          Length = 337

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 80/299 (26%), Positives = 135/299 (45%), Gaps = 23/299 (7%)

Query: 34  FVNLQKIL--RSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIKEQKILDSSVNL 90
            V L K++  R G  R        N RI   GQ+   P        ++  + +L  + N 
Sbjct: 25  LVRLDKLVAQRFGLSRRAAGDAVLNGRIDLEGQLCDEP------GRLVPPESVLRFNPNR 78

Query: 91  TKHSDFLKSIL--LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDG-FLKSWVDSKGQKP-- 144
            K    + + L  L+ED  + + NKPAG+ +++  +     + G  LK     +  +P  
Sbjct: 79  PKERKVVTAKLDILFEDRHLLIVNKPAGLLTLETEARETDTLRGRVLKHQSLRRRGRPFV 138

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HRLD+ETSG + +A T  A + L   FR   +++ Y ++V G        +   ++ 
Sbjct: 139 GIVHRLDRETSGAIALALTPEAMKPLQALFRSHAVERRYLAIVAGAVAEDHGVVEAAIV- 197

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            S  G     + +  +  A  A++ F+V++ F      L  +  TGR HQ+RVH   +G 
Sbjct: 198 -SRPGEVRRRLARPGDPDARDALTRFRVLERFGCDASLLACELETGRGHQIRVHLASIGH 256

Query: 265 PIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           P++GD  Y        F+G   + + ++  LHA  + L HP  GG + + AP P    K
Sbjct: 257 PVLGDRLYAPRKDKHAFQGGSGTILFDRQALHAETLGLVHPVAGGTVWVEAPPPGDFRK 315


>gi|51598281|ref|YP_072469.1| hypothetical protein BG0018 [Borrelia garinii PBi]
 gi|51572852|gb|AAU06877.1| conserved hypothetical protein [Borrelia garinii PBi]
          Length = 327

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 55/181 (30%), Positives = 96/181 (53%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS I V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 87  IIYEDSNIIVLNKPQGILSHPGISHWDDTVVNFLLYHIKR-LKINFNEEKVRPGIVHRLD 145

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+       L + F+ +R  K+Y ++V G   +    I +++ +  +    
Sbjct: 146 KDTSGVLICAKNINTLSFLAQQFKDKRTNKVYIAIVKGNFNSFSGSIESFIDRDKYNRKK 205

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F + +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 206 FSVSKDRGKK----ALTEYRLLLNF-RGYSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 260

Query: 272 Y 272
           Y
Sbjct: 261 Y 261


>gi|294011514|ref|YP_003544974.1| pseudouridylate synthase [Sphingobium japonicum UT26S]
 gi|292674844|dbj|BAI96362.1| pseudouridylate synthase [Sphingobium japonicum UT26S]
          Length = 225

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 102/225 (45%), Gaps = 18/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D +  + +KPAG+ V      +  ++  L S      + P   HRLD++TSG L++
Sbjct: 8   VLFIDGEAIILDKPAGLPVDAPRDGSLSLENHLSSLTFGFQRWPLPVHRLDRDTSGCLLL 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR   A +    +F    + K Y ++V G+P      I   L K S     +  +  +  
Sbjct: 68  ARNPKAHKRFAAAFEAGTVAKRYVAVVDGVPAEDSGAIDLSLKKVSTPAQGWRMIPAKAG 127

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGN 279
           K A          D  A     +   P TGRTHQ+R HALH +G  I GD  Y +     
Sbjct: 128 KAAFTEWRKIAEKDGRA----LIVFTPRTGRTHQIRTHALHGLGFGIAGDPVYGSG---- 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
                Q  + LH+R++ +P  E    + TAPLPA    T+ + GF
Sbjct: 180 -----QGPMLLHSRFLSIPRGEKPPAEATAPLPA----TFAAAGF 215


>gi|319440272|ref|ZP_07989428.1| pseudouridylate synthase [Corynebacterium variabile DSM 44702]
          Length = 311

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 112/236 (47%), Gaps = 29/236 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQ---GGSGIAYHIDGFLKSW--VDSKGQKPR--LTHRLDQE 153
           +LY D  + V +KP G++     G  G      G   +   + + G   R  + HRLD  
Sbjct: 87  ILYSDDDVIVVDKPVGVAAHPTIGWEGPTV-TSGLAAAGYRISTSGPPERKGIVHRLDVG 145

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++ VA +  A   L  +FR R + K Y +LV G P      I   + +  H G  + 
Sbjct: 146 TSGVMAVAASERAYTVLKRAFRDRTVDKTYHALVQGHPDPTDGTIDAPIAR--HPGHGWK 203

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH--ALHMGCPIVGDHK 271
             V   + G  +A++H++ I+ F ++   + +   TGRTHQ+RVH  ALH  C   GD  
Sbjct: 204 FAV---QDGGRHAVTHYETIEAF-REATLVRVHLETGRTHQIRVHFSALHHPC--AGDPM 257

Query: 272 YCANFKGNFTSPIQNKL-----YLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           Y ++        +  +L     +LHA ++  PHP+G  + I +P PA +    D L
Sbjct: 258 YGSDPA------LSQRLGLVRQWLHAVHLGFPHPDGRWMDIESPYPADLQTALDRL 307


>gi|254974610|ref|ZP_05271082.1| putative pseudouridylate synthase [Clostridium difficile QCD-66c26]
 gi|255092002|ref|ZP_05321480.1| putative pseudouridylate synthase [Clostridium difficile CIP
           107932]
 gi|255313736|ref|ZP_05355319.1| putative pseudouridylate synthase [Clostridium difficile QCD-76w55]
 gi|255516418|ref|ZP_05384094.1| putative pseudouridylate synthase [Clostridium difficile QCD-97b34]
 gi|255649516|ref|ZP_05396418.1| putative pseudouridylate synthase [Clostridium difficile QCD-37x79]
 gi|306519647|ref|ZP_07405994.1| putative pseudouridylate synthase [Clostridium difficile QCD-32g58]
          Length = 300

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 112/225 (49%), Gaps = 27/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++Y+D  I + NKP  + V            +GI+Y+ID         +  K R  +RLD
Sbjct: 85  IIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGISYYIDN------QKENVKIRFVNRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG+++VA+   A   L+ +    +++K Y ++V GI K  +  I   + + +    D
Sbjct: 139 MNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGIIKENEGTIDEPIYRPTE---D 195

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  +  +E+G + +++H+KVI+   +    LE+   TGRTHQ+RVH  H+G  I+GD  
Sbjct: 196 SIKRI-IDERGQS-SVTHYKVIERL-ENATVLEVSLETGRTHQIRVHMAHIGHGIIGDEL 252

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           Y     G     + N+  LHA  ++   P    +L+  A +P  M
Sbjct: 253 Y-----GYVDEELINRQALHAYKLEFEQPRTKEKLKFKADIPEDM 292


>gi|331085058|ref|ZP_08334145.1| hypothetical protein HMPREF0987_00448 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330408758|gb|EGG88223.1| hypothetical protein HMPREF0987_00448 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 323

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 76/311 (24%), Positives = 140/311 (45%), Gaps = 32/311 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V  +E   RLD+    +          K++R   + ++ K+   N +++ G +V+
Sbjct: 1   MQEIKVTKNEAGQRLDKLLAKYLNEAPKSFFYKMMRKKNIVLNGKKATGNEKLEEGDIVK 60

Query: 67  I---PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +      I   + +    KI  +  NL+         ++YED  + + NKP G+  Q   
Sbjct: 61  LFLADETIRKFSSV----KIQRTKTNLS---------VIYEDQDVVLINKPVGMLSQKAK 107

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                     I+Y +D    S    K  +P + +RLD+ TSGI+V  ++    Q + E F
Sbjct: 108 ESDVSLVEHLISYLLDAGELSEETLKSFRPSICNRLDRNTSGIVVAGKSLPGLQKMGELF 167

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R + K Y  LV G+ + + + +  WL K      + V ++ +    ++  I       
Sbjct: 168 KERTLHKYYRCLVQGVIR-EDQYLKGWLKKDEKT--NKVQILDRPSDPSDQPIETEYHPL 224

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP---IQNKLYLH 291
              +    LE++  TG+THQ+R H    G P++GD+KY      +F      ++++L LH
Sbjct: 225 WTKEGVTLLEVRLITGKTHQIRAHLASEGHPLIGDYKYGDRKLNDFYQKKYGLKSQL-LH 283

Query: 292 ARYMDLPHPEG 302
           A  ++ P  EG
Sbjct: 284 AYRLEFPVMEG 294


>gi|153814854|ref|ZP_01967522.1| hypothetical protein RUMTOR_01069 [Ruminococcus torques ATCC 27756]
 gi|331089624|ref|ZP_08338523.1| hypothetical protein HMPREF1025_02106 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145847885|gb|EDK24803.1| hypothetical protein RUMTOR_01069 [Ruminococcus torques ATCC 27756]
 gi|330404992|gb|EGG84530.1| hypothetical protein HMPREF1025_02106 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 347

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 86/322 (26%), Positives = 144/322 (44%), Gaps = 19/322 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + + ++E   R D++   +        L K+LR   + ++ K+   N  +  G  V+
Sbjct: 1   MKEIEINSNEAGQRFDKFLGKYLDQAPKSFLYKMLRKKNITLNGKKAAGNEILALGDNVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---- 122
           +      +    K  + +   V        +K  +LYED  +   NKP G+  Q      
Sbjct: 61  LFFSDETIKKFSKTSEEVFRPVQKNTAKSKVKLNVLYEDENVIFLNKPVGMLSQKANRED 120

Query: 123 -SGIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            S + Y I+  L S   ++ +     P + +RLD+ TSGI+   +T +A Q L E FR R
Sbjct: 121 TSLVEYLIEYLLDSGQVTREELKTFHPAVCNRLDRNTSGIVAGGKTLSALQILNEMFRTR 180

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  LV G  K+ +  I  +L K +      V   K+  K A    + +  +   +
Sbjct: 181 SLEKYYLCLVSGKIKDGQR-ICGYLKKNTKTNKVSVTKEKRETKEALPIETEYTPL-FVS 238

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---YLHARY 294
                L++   TG+THQ+R H   +G PI+GD+KY  +FK N     +  L    LHA  
Sbjct: 239 DHVTLLKVHLITGKTHQIRAHLAAIGHPIIGDYKY-GDFKINEAYKKKYGLKTQLLHAYQ 297

Query: 295 MDLPHPEGGR----LQITAPLP 312
           +  P  E  +     QI AP+P
Sbjct: 298 LCFPDVELVKNLPNRQIIAPVP 319


>gi|126698644|ref|YP_001087541.1| putative pseudouridylate synthase [Clostridium difficile 630]
 gi|115250081|emb|CAJ67901.1| putative pseudouridylate synthase [Clostridium difficile]
          Length = 300

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 112/225 (49%), Gaps = 27/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++Y+D  I + NKP  + V            +GI+Y+ID         +  K R  +RLD
Sbjct: 85  IIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGISYYIDN------QKENVKIRFVNRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG+++VA+   A   L+ +    +++K Y ++V GI K  +  I   + + +    D
Sbjct: 139 MNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGIIKENEGTIDEPIYRPTE---D 195

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  +  +E+G + +++H+KVI+   +    LE+   TGRTHQ+RVH  H+G  I+GD  
Sbjct: 196 SIKRI-IDERGQS-SVTHYKVIERL-ENATVLEVSLETGRTHQIRVHMAHIGHGIIGDEL 252

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           Y     G     + N+  LHA  ++   P    +L+  A +P  M
Sbjct: 253 Y-----GYVDEELINRQALHAYKLEFEQPRTKEKLKFKADIPEDM 292


>gi|93007115|ref|YP_581552.1| pseudouridine synthase [Psychrobacter cryohalolentis K5]
 gi|92394793|gb|ABE76068.1| ribosomal large subunit pseudouridine synthase A [Psychrobacter
           cryohalolentis K5]
          Length = 237

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 67/222 (30%), Positives = 114/222 (51%), Gaps = 16/222 (7%)

Query: 96  FLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           F K + +YED  I+V +KPAG+ SV G S     +   L + ++      +L HRLD +T
Sbjct: 26  FAKKVTVYEDEDIWVVDKPAGLLSVDGKS-----LKVSLLARLERANPAVKLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+ A+  AA  ++++ F  R  QK Y + V+G   +        +  +        H
Sbjct: 81  SGLLIFAKNAAAQTNISKQFIDRLPQKNYQARVFGQWDSVGATGKISVPVRYEPATKPRH 140

Query: 215 VVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +V  N   + +A++ ++++   +C  Q    + ++P TGR+HQLRVH +H+G  ++GD  
Sbjct: 141 IVDPN--WSKHALTLYEILAHEECDGQIVTRVLLKPVTGRSHQLRVHMVHIGHVMIGDPI 198

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
           Y      +    I  +L LHA+ + L HP  G  +   +P P
Sbjct: 199 YAEGIALD----IAPRLNLHAQQLRLKHPTLGAWMDWESPTP 236


>gi|124267192|ref|YP_001021196.1| ribosomal large subunit pseudouridine synthase D [Methylibium
           petroleiphilum PM1]
 gi|124259967|gb|ABM94961.1| ribosomal large subunit pseudouridine synthase D [Methylibium
           petroleiphilum PM1]
          Length = 334

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 82/297 (27%), Positives = 127/297 (42%), Gaps = 37/297 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPV 70
           V+      RLDRW        +  +LQ ++  GQVR+D + V     R+ +GQ + I   
Sbjct: 26  VDAGAHGERLDRWLATLAGEFSRNHLQTLIEGGQVRIDGQTVTARARRVSAGQQIEI--- 82

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHI 129
              L    + Q      V L          +++ED+ + V +KPAG+ V    G  +  +
Sbjct: 83  --TLLPTPESQAFRPEPVALP---------VVFEDAHLLVIDKPAGLVVHPAPGNWSGTV 131

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L +        PR  + HRLD++TSG++VVA+T  A   L  +   R + + Y +LV
Sbjct: 132 LNGLLAHHAGAAALPRAGIVHRLDKDTSGLMVVAKTLPAMTSLVRAIAAREVHREYLALV 191

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVI---DCFAQKFCWL 243
            G+ +     +       + IG D V  +K     G   A +  ++I   D  +   C L
Sbjct: 192 HGVLRQAVFSV------DAPIGRDPVSRIKMAVLAGGRTARTDVELIAARDAVSAVRCTL 245

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
               HTGRTHQ+RVH    G  ++ D  Y        T     +  LHA  +   HP
Sbjct: 246 ----HTGRTHQIRVHMASRGHALLADALYGGRPGLGLT-----RQALHAHRLGFVHP 293


>gi|238797483|ref|ZP_04640981.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           mollaretii ATCC 43969]
 gi|238718624|gb|EEQ10442.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           mollaretii ATCC 43969]
          Length = 217

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/207 (34%), Positives = 103/207 (49%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G    A      + + + +        HRLD  TSG+++
Sbjct: 14  ILYQDEHIMVVNKPSGLLSVPGR---APENKDSIMTRIQADYPTAESVHRLDMATSGVII 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPKKSYIARVWGHLTQDEGLIDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + A + + V+   A     +++ P TGR+HQLRVH L MG PI+GD  Y    
Sbjct: 125 VCYETGKS-AQTEYHVLSRDADGSTRVKLSPITGRSHQLRVHMLAMGHPILGDGFYAHPE 183

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
                S    +L LHA+ + + HPE G
Sbjct: 184 AKAMAS----RLQLHAQELCITHPEFG 206


>gi|322385565|ref|ZP_08059209.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           cristatus ATCC 51100]
 gi|321270303|gb|EFX53219.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           cristatus ATCC 51100]
          Length = 297

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 68/228 (29%), Positives = 116/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++    D + Q+  +  RLD++TSG+
Sbjct: 78  IVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRQDYENQQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G  + K E   IA        IG D   +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKMIEKRYYALVQGSGELKLEGDIIAP-------IGRDPDSI 190

Query: 216 VKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +   K   YA + +KV+  F   +  ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRCVTKDGKYAHTSYKVVGQFGDIY-LVDIRLHTGRTHQIRVHFAHLGFPLLGDDLYGG 249

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
             +   T   +  L+ H+     P  E  +LQ+ + LP     T  SL
Sbjct: 250 TLEAGIT---RQALHCHSLSFYNPFLE-KQLQLESQLPIDFQNTITSL 293


>gi|317500368|ref|ZP_07958592.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|316898123|gb|EFV20170.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 347

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 86/322 (26%), Positives = 144/322 (44%), Gaps = 19/322 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + + ++E   R D++   +        L K+LR   + ++ K+   N  +  G  V+
Sbjct: 1   MKEIEINSNEAGQRFDKFLGKYLDQAPKSFLYKMLRKKNITLNGKKAAGNEILALGDNVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---- 122
           +      +    K  + +   V        +K  +LYED  +   NKP G+  Q      
Sbjct: 61  LFFSDETIKKFSKTSEEVFRPVQKNTAKSKVKLNVLYEDENVIFLNKPVGMLSQKANRED 120

Query: 123 -SGIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            S + Y I+  L S   ++ +     P + +RLD+ TSGI+   +T +A Q L E FR R
Sbjct: 121 TSLVEYLIEYLLDSGQVTREELKTFHPAVCNRLDRNTSGIVAGGKTLSALQILNEMFRTR 180

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  LV G  K+ +  I  +L K +      V   K+  K A    + +  +   +
Sbjct: 181 SLEKYYLCLVSGKIKDGQR-ICGYLKKNTKTNKVSVTKEKRETKEALPIETEYTPL-FVS 238

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---YLHARY 294
                L++   TG+THQ+R H   +G PI+GD+KY  +FK N     +  L    LHA  
Sbjct: 239 DHVTLLKVHLITGKTHQIRAHLAAIGHPIIGDYKY-GDFKINEAYKKKYGLKTQLLHAYQ 297

Query: 295 MDLPHPEGGR----LQITAPLP 312
           +  P  E  +     QI AP+P
Sbjct: 298 LCFPDVELVKNLPNRQIIAPVP 319


>gi|284799501|ref|ZP_05984156.2| tRNA pseudouridine synthase [Neisseria subflava NJ9703]
 gi|284798057|gb|EFC53404.1| tRNA pseudouridine synthase [Neisseria subflava NJ9703]
          Length = 238

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 109/230 (47%), Gaps = 30/230 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ DS+    NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IIHRDSRTVAVNKPAGMLVHRSWLDKHETRFAVQTLRDQIGQHVYPVHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A    AA+ LT+ F  + I+K YW++V G +P +    + ++ LK      D +    Q 
Sbjct: 64  ALDTEAARLLTQQFENKTIEKTYWAIVRGHLPSD---GLIDYALK---YMPDKI-AEAQT 116

Query: 220 EKGANYAISHFKVIDCFAQ--------------KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           E     A + ++   C AQ              ++ W E+ PHTGR HQLR H  H+  P
Sbjct: 117 EATLQEAQTTYR---CLAQTELPFQSALRYPTSRYSWAELTPHTGRKHQLRRHMKHIFHP 173

Query: 266 IVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPE-GGRLQITAPL 311
           IVGD  Y  + + N          +L LHA+ +     E G R+ + AP+
Sbjct: 174 IVGDTNY-GDLRQNHAVAEHIGTQRLMLHAQSLSFQSIEDGSRMTVQAPI 222


>gi|295696843|ref|YP_003590081.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
 gi|295412445|gb|ADG06937.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
          Length = 327

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 78/278 (28%), Positives = 123/278 (44%), Gaps = 42/278 (15%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSIL----LYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           L+  +    IL+     T   D L   +    LYED  + V NKP G+ V    G+A   
Sbjct: 53  LSERVSAGDILEIRWGETPSDDVLPEPIPFETLYEDEDVLVVNKPPGMLVHPTKGVAAGT 112

Query: 130 --DGFLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFR----------- 175
             +G + +W  +   +P R  +RLD++TSG++++A+ + A Q L+   R           
Sbjct: 113 LANGVVYAWRLTGSYRPFRPLNRLDRDTSGLVLIAKNQFAHQRLSRDLRFVEGGRSPVFG 172

Query: 176 ---------MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANY 225
                    +RR+ + Y +LV G        +A+       I  D  H   +Q       
Sbjct: 173 ADEAERLDGVRRVHREYAALVQG------RVVADRGWIDLPIDRDPNHGNRRQVAPAGRR 226

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           A + F+V +       +L+++  TGRTHQ+RVH   +G P++GD  Y         SP  
Sbjct: 227 ARTRFEVAERVGNA-AYLKVRLQTGRTHQIRVHLAELGHPVIGDTLYGE------PSPWI 279

Query: 286 NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            +  LHA  +   HP  G R+Q+TAP    M + W  L
Sbjct: 280 ERQALHAERLVFDHPRTGKRIQVTAPWFPDMAELWRRL 317


>gi|223935694|ref|ZP_03627610.1| pseudouridine synthase [bacterium Ellin514]
 gi|223895702|gb|EEF62147.1| pseudouridine synthase [bacterium Ellin514]
          Length = 283

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/192 (33%), Positives = 96/192 (50%), Gaps = 21/192 (10%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKS---WVDSKGQK-PRLTHRL 150
           +LYED  +   +KPAG  +      + G  +   +   L +   W  S+  K  R  HRL
Sbjct: 18  ILYEDRSVLAVDKPAGWMLAPDSWDKTGRNLQLALQSSLNAGDFWAHSRNIKFLRYVHRL 77

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-----KKECIANWLLK- 204
           D ET+G+L++ ++  A +   E F  R ++K Y ++V GIPK      K   IA+ ++K 
Sbjct: 78  DAETTGVLLLCKSLGALRAYGELFETRSVEKFYLAVVQGIPKQSEWTCKLPLIADPVVKG 137

Query: 205 KSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           K  +      + K + +G       A +HF+VI     K   +E QP TGRTHQ+RVH  
Sbjct: 138 KMQVVTPGKPLPKSDPRGPQAELKDAETHFRVIQTLQDK-ALVEAQPMTGRTHQIRVHLA 196

Query: 261 HMGCPIVGDHKY 272
             G PIVGD  Y
Sbjct: 197 ASGHPIVGDPLY 208


>gi|163750158|ref|ZP_02157401.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Shewanella benthica KT99]
 gi|161330215|gb|EDQ01197.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Shewanella benthica KT99]
          Length = 324

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 84/319 (26%), Positives = 144/319 (45%), Gaps = 53/319 (16%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD+     +P  +   +++ +  G V +D     K   ++  GQ + +   +      +
Sbjct: 19  RLDQTLAELFPDYSRTRIKEWILDGSVTIDGNVSNKPREKVLEGQEIEVGATL------V 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
           +E      +++L          ++YED  I V NK AG+ V  G+G         + +H 
Sbjct: 73  EETTAKAQAIDLN---------IVYEDDHILVINKQAGLVVHPGAGNSDGTLLNALLHHC 123

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G     V   G    + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V G
Sbjct: 124 PGI--ELVPRAG----IVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAIVMG 177

Query: 190 ---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                    E I     K++H+      VV   +     A++HF+V + F +    L ++
Sbjct: 178 SLISGGTVDEPIDRHPTKRTHMA-----VVLSGKP----AMTHFRVAEKF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLY-------LHARYMDLP 298
             +GRTHQ+RVH  H+G  +VGD  Y    +     +P   +++       LHA  ++L 
Sbjct: 228 LESGRTHQIRVHMAHLGHTLVGDPVYGGRPRPPKAVTPEFFEIFMGFKRQALHAIRLELA 287

Query: 299 HPEGGRLQI-TAPLPAHMV 316
           HP    +    AP+P  MV
Sbjct: 288 HPYTCEIMSWQAPVPEDMV 306


>gi|120601247|ref|YP_965647.1| pseudouridine synthase [Desulfovibrio vulgaris DP4]
 gi|120561476|gb|ABM27220.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           vulgaris DP4]
          Length = 390

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 85/330 (25%), Positives = 134/330 (40%), Gaps = 52/330 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +VV  +E   +L ++    +  +    L + +RSGQVR +  R K  +R++ G  VR+
Sbjct: 4   QAIVVTREEAGQKLLQFLARRF-ALPQAMLHRWIRSGQVRRNGGRCKPFDRLEMGDEVRV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKS---------------------------- 99
           PP   +++       +  SS  +    D   S                            
Sbjct: 63  PPFAASMSERADVGPVSASSDAVRNVPDAAASRPAPSRHDRDGHDAMQPSRQRRPKADTS 122

Query: 100 --------ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                    ++ E   +++F+KPAG++V  G+G    +   L          P   HRLD
Sbjct: 123 LQPARPLPPVVAETPDLFIFDKPAGLAVHPGTGHTDSLTTRLAQHFAKAPFMPTPAHRLD 182

Query: 152 QETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           ++TSG+L+VAR+ A  + L E+F     + K Y + V G  +       +  L K     
Sbjct: 183 RDTSGLLLVARSYAMLRTLHEAFASHDALVKEYLAWVAGCWQPAAPVTLHDRLSKGAEAS 242

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCF--AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +  V   +E GA  A +    + C    Q    L +  HTGRTHQ+RV     G P++G
Sbjct: 243 GFERVASDDE-GAEAACT----VRCLLREQHRSLLLVTLHTGRTHQIRVQLSRRGHPLLG 297

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           D KY          P      LHA  + LP
Sbjct: 298 DRKYGG-------PPRMGGFLLHAVRLCLP 320


>gi|309805623|ref|ZP_07699665.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
 gi|308165061|gb|EFO67302.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
          Length = 311

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/301 (24%), Positives = 139/301 (46%), Gaps = 38/301 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+++E  +RLD++   H   I+   +Q++++   +  +  + K + ++ +   + I  
Sbjct: 9   LVVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNGLQTKLSYKVNTNDKINIE- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                         + S   L+   + L   ++YED  + V NKP G+ V   +G     
Sbjct: 68  --------------IPSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHT 113

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH     K     +  +P + HR+D++TSG+L++A+   A   L +    +  +
Sbjct: 114 LVNGLIYHTKNLAKC---DEILRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINK 170

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V    K+    I +  + ++      + VV   +K    AI+HF V++ F   +
Sbjct: 171 REYIAIVHANFKHSSGVI-DAPIGRNPYQRQQMAVVASGKK----AITHFTVLEQFP-GY 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             ++    TGRTHQ+RVH  ++G PI GD  Y      N      N  +LHA+ +   HP
Sbjct: 225 SLVKCVLETGRTHQIRVHMSYIGHPIAGDPLYGPKKTLN-----GNGQFLHAKTLGFYHP 279

Query: 301 E 301
           +
Sbjct: 280 K 280


>gi|319946086|ref|ZP_08020334.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
 gi|319747732|gb|EFV99977.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
          Length = 278

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 68/213 (31%), Positives = 104/213 (48%), Gaps = 23/213 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  + + NKP G+           +   + ++V   G+   + HRLD+ETSG LV A
Sbjct: 71  LYEDEHLIIVNKPEGMKTHANQPDEIALLNHVSTYV---GKTCYVVHRLDKETSGALVFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           +       L      ++IQ+ YW+L+ G +PK +       L+ K  +G D     K+  
Sbjct: 128 KNPFVLPVLNRLLEDKKIQRDYWALILGSLPKKQ-------LVYKDKLGRDRHDRRKRIV 180

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +   YA +H  ++  F ++   +  Q  TGRTHQ+RVH  H G PIVGD  Y      
Sbjct: 181 DPRKGLYAETHVTILKTF-KRTSLVNCQLQTGRTHQIRVHLSHHGHPIVGDPLYNPE--- 236

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
              +P   +L LHA  + L HP    ++Q+ AP
Sbjct: 237 --RAP---RLMLHAHRLRLSHPFTLEKIQVEAP 264


>gi|304382859|ref|ZP_07365342.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
 gi|304336044|gb|EFM02291.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
          Length = 229

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 67/218 (30%), Positives = 105/218 (48%), Gaps = 18/218 (8%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG----IAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGI 157
           YED+ I + +K +G  VQG       ++  +  +LK      G     + HRLD+   G+
Sbjct: 6   YEDNHIIIVSKRSGEIVQGDKTGDKPLSESVKAYLKEAYAKHGNVFLGVVHRLDRPVEGL 65

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHV 215
           +V A+T  A   L E FR   ++K YW++    P   +  + +WL++  K +    Y H 
Sbjct: 66  VVFAKTSKALSRLNEMFRTGAVRKTYWAITKNRPTTPEGTLIHWLVRNEKQNKSYAYDHE 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  ++K    A   +++I     ++  L ++  TGR HQ+R    H+GCPI GD KY   
Sbjct: 126 VPHSKK----AELQYRII-AQGDRYTLLAIKLLTGRHHQIRCQLSHIGCPIKGDLKY--- 177

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             G   S     + L AR++   HP    L  +TAPLP
Sbjct: 178 --GAPRSNPDGSISLLARHIAFTHPVSKELVSVTAPLP 213


>gi|126174998|ref|YP_001051147.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125998203|gb|ABN62278.1| Pseudouridylate synthase [Shewanella baltica OS155]
          Length = 223

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 63/200 (31%), Positives = 106/200 (53%), Gaps = 12/200 (6%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP+G+    G   A+  D  L + + +   +  L HRLD  TSGI+V AR
Sbjct: 18  YKDRDLIIINKPSGLLSNPGRA-AHTFDCAL-TRLQTLFPETILVHRLDCATSGIMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
            + A  HL   F+ R+ +K+Y + V G +P  +++ + +  +        Y   ++  E 
Sbjct: 76  NKKAESHLKTQFQDRQSKKVYIAEVMGHVP--QEQGMIDLAIAPDTEHPPYQKTLQAGET 133

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           G   A+++++V++   +    +E+ P TGRTHQLRVH L +G  I+GD      F G+  
Sbjct: 134 GGKSALTYYRVLE-RRENSTLVELSPETGRTHQLRVHMLALGHAILGD-----EFYGDAE 187

Query: 282 S-PIQNKLYLHARYMDLPHP 300
               + +L LHA+ + L HP
Sbjct: 188 VIKAKPRLCLHAQSLCLTHP 207


>gi|261212185|ref|ZP_05926471.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. RC341]
 gi|262401594|ref|ZP_06078160.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. RC586]
 gi|260838793|gb|EEX65444.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. RC341]
 gi|262352011|gb|EEZ01141.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. RC586]
          Length = 324

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 120/244 (49%), Gaps = 31/244 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           ++YED  I V NKP    V  G+G A    ++  L  +     + PR  + HRLD++T+G
Sbjct: 86  IVYEDDDIIVINKPRDFVVHPGAGQADSTVLNALLFHY-PPIAEVPRAGIVHRLDKDTTG 144

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++VVA+T  A  HL  + + R + + Y ++V G         A  ++ K  IG    H  
Sbjct: 145 LMVVAKTVPAQTHLVRALQKRDVTREYEAIVIGT------MTAGGMIDKP-IGR---HST 194

Query: 217 KQN----EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K+          +A++H++V + F ++   L ++  TGRTHQ+RVH  ++  P++GD  Y
Sbjct: 195 KRTLMSVSPMGKHAVTHYRVAEHF-REHTRLRLRLETGRTHQIRVHMAYLQHPLLGDTAY 253

Query: 273 CANFK------GNFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
               +         T  I+  ++  LHA  +   HP  G  L+  AP+P  MV+   +L 
Sbjct: 254 GGRARIPKGASEELTEMIRGFDRQALHAVMLKFEHPITGEELEFHAPVPDDMVEM--TLA 311

Query: 324 FKYD 327
            + D
Sbjct: 312 LRED 315


>gi|254757932|ref|ZP_05209959.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Australia 94]
          Length = 249

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/272 (26%), Positives = 128/272 (47%), Gaps = 33/272 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREND 60

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V IP          +E  I    +NL          + YED+ + V NKP G+ V  
Sbjct: 61  EITVTIPEP--------EELDIQPEDMNLE---------IYYEDADVLVVNKPRGMVVHP 103

Query: 122 GSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L     
Sbjct: 104 APGHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLV 163

Query: 176 MRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            + + + Y ++V G IP +K    A     K       V      ++   +A++HF+V++
Sbjct: 164 AKTVTRRYKAIVHGVIPHDKGTIDAPIARDKKERQSMTV------DENGKHAVTHFQVLE 217

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            F + F  +E +  TGRTHQ+RVH  ++G P+
Sbjct: 218 RF-KDFTLVECRLETGRTHQIRVHMKYIGYPL 248


>gi|262202888|ref|YP_003274096.1| pseudouridine synthase [Gordonia bronchialis DSM 43247]
 gi|262086235|gb|ACY22203.1| pseudouridine synthase, RluA family [Gordonia bronchialis DSM
           43247]
          Length = 308

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 92/331 (27%), Positives = 144/331 (43%), Gaps = 38/331 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  + MRLD         ++   +  +   G V VD   V  ++R+ +G 
Sbjct: 1   MRESRMLPVPDGLDGMRLDAALARML-GLSRTVVAGLADDGDVTVDGVAVGKSHRLAAG- 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                    AL H+   +      V  T   D     ++Y DS I V +KP G++     
Sbjct: 59  ---------ALLHVTLPEPERPLQVEPTPVEDL---DVIYHDSDIIVVDKPVGVAAHPSL 106

Query: 124 G-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +    + + G   R  +  RLD  TSG++VVA +  A   L  +F+ R
Sbjct: 107 GWSGPTVLGALDAAGYRISTSGAPERQGIVSRLDVGTSGVMVVAVSERAYSVLKRAFKQR 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G        I   + +  H G D+   V  N K    +I+H++ ++ FA
Sbjct: 167 TVDKGYHALVQGHLDPPTGTIDAPIGR--HPGSDWRFAVTANGK---PSITHYETLEMFA 221

Query: 238 QKFCWLEMQPHTGRTHQLRVH--ALHMGC---PIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                L++   TGRTHQ+RVH  ALH  C   P  G     A   G       ++ +LHA
Sbjct: 222 AA-SLLDIHLETGRTHQIRVHFAALHHPCCGDPTYGGDPVLAKRLG------LDRQWLHA 274

Query: 293 RYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           R +   HP +G R++ T+P P  +    D L
Sbjct: 275 RSLGFAHPADGRRVEFTSPYPHDLQHALDVL 305


>gi|146277612|ref|YP_001167771.1| RluA family pseudouridine synthase [Rhodobacter sphaeroides ATCC
           17025]
 gi|145555853|gb|ABP70466.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides ATCC 17025]
          Length = 349

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 86/343 (25%), Positives = 146/343 (42%), Gaps = 62/343 (18%)

Query: 14  NDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
            ++   RLD+      P    ++   L K++  G VR+    V     R+  GQV  I  
Sbjct: 16  GEDPPERLDKALAREAPEEAALSRSRLMKLIAEGAVRLKGVPVTDPKARVLEGQVYEI-- 73

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               +     E + L  ++ L+         +++ED+ + V +KP G+ V    G     
Sbjct: 74  ----VTGAAAEVEALPEAIPLS---------VVWEDADLIVIDKPVGMVVHPAPGQWTGT 120

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + +H    L      K  +P + HR+D++TSG+LVVA+T  A Q L   F    ++
Sbjct: 121 LVNALLHHCGASLSGIGGEK--RPGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVE 178

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV---------KQNE----KGANYAI 227
           + Y +LV G+P+     +   +   S   G  + +          +Q +    +G  +A+
Sbjct: 179 RRYLALVHGVPEPSDPRL-RGIRGVSFEPGGVLRIATGIARHRTDRQRQAVTFEGGRHAV 237

Query: 228 SHFKVIDCFAQ--KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--- 282
           +  ++++ F        +E +  TGRTHQ+RVH  H+G  ++GD  Y    K +  +   
Sbjct: 238 TRARLLERFGTPPAAALVECRLETGRTHQIRVHMSHVGHGLIGDQTYGGRRKLSAKAVGA 297

Query: 283 ---------PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
                    P Q    LHA  +   HP  G  L   +PLPA M
Sbjct: 298 EAAQAAEAFPRQ---ALHAATLGFCHPVTGEDLSFESPLPADM 337


>gi|255505900|ref|ZP_05348786.3| pseudouridine synthase, RluA family [Bryantella formatexigens DSM
           14469]
 gi|255265256|gb|EET58461.1| pseudouridine synthase, RluA family [Bryantella formatexigens DSM
           14469]
          Length = 342

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 90/336 (26%), Positives = 142/336 (42%), Gaps = 28/336 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++V  +E   RLD+    +        L K+LR   + ++ K+   N        +R
Sbjct: 1   MKEIIVRENEAGQRLDKLLARYLCQAPKSFLYKMLRKKNITLNGKKASGNEITAKEDCIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFL-KSILLYEDSKIYVFNKPAGISVQGGSGI 125
           I      L+    E+          +H+  L K  ++YED  I V NKPAG+  Q     
Sbjct: 61  I-----FLSDETYEKFSAGEEAPPIRHTGALTKEQIIYEDGDILVLNKPAGMLSQKSRPE 115

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               + +  S++   GQ          P + +RLD+ TSG+L+  ++ A  Q + E+ + 
Sbjct: 116 DVSANEYFLSYLLETGQISAQELRTFHPSICNRLDRNTSGLLLAGKSLAGLQAMAEALKD 175

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K Y  LV G    K   +  +L+K        +      +K A   IS   V    
Sbjct: 176 RSLHKYYLCLVSG-SLTKGARLEGFLVKDEAANKVKICATDMGDKEAK-PISTQYVPLWT 233

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF---TSPIQNKLYLHAR 293
             K   L++   TGR HQ+R H   +G PI+GD KY    K  +   T  ++ +L LHA 
Sbjct: 234 DGKVTLLKIWLITGRAHQIRAHLSGIGHPIIGDGKYGDRRKNVYYEKTYHLKGQL-LHAF 292

Query: 294 YMDLPHPEGGRL------QITAPLPAHMVKTWDSLG 323
            M +P P  G L      +  APLP +  K     G
Sbjct: 293 QMKMP-PLTGTLSRLSGQEFIAPLPENFRKILADAG 327


>gi|322412796|gb|EFY03704.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus dysgalactiae subsp. dysgalactiae ATCC
           27957]
          Length = 303

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 64/199 (32%), Positives = 94/199 (47%), Gaps = 13/199 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  + + NKP G+   G       +   + ++    G+   + HRLD ETSG++V A
Sbjct: 92  LYEDDHLIIVNKPEGMKTHGNEPTELALLNHVSAYT---GRTCYVVHRLDMETSGVIVFA 148

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +T      L      R I + YW+LV G   +K+      + +  H     V  VKQ +K
Sbjct: 149 KTPFILPILNRLLEKREISRDYWALVHGTLSSKEVGYREPIGRHRHDRRKRVVDVKQGQK 208

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+  K++  F Q    +  +  TGRTHQ+RVH  + G  ++GD  Y    KG   
Sbjct: 209 ----AITDVKLLKSFKQNVSLINCRLQTGRTHQIRVHLSYHGHALLGDPLYS---KGKAE 261

Query: 282 SPIQNKLYLHARYMDLPHP 300
            P   +L LHA  + L HP
Sbjct: 262 CP---RLMLHAHQLWLRHP 277


>gi|59710878|ref|YP_203654.1| pseudouridine synthase for 23S rRNA and tRNAphe [Vibrio fischeri
           ES114]
 gi|197334224|ref|YP_002155030.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
 gi|59478979|gb|AAW84766.1| pseudouridine synthase for 23S rRNA and tRNAphe [Vibrio fischeri
           ES114]
 gi|197315714|gb|ACH65161.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
          Length = 245

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/210 (32%), Positives = 109/210 (51%), Gaps = 27/210 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           ++Y+D  I V NKP+G+ SV G +    H D     W   K + P  ++ HRLD  TSG+
Sbjct: 16  IVYQDESILVVNKPSGLLSVPGRA--PEHYDSM---WSRLKVEFPDIQVVHRLDMSTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE----CIANWLLKKSHIGGDY 212
           ++ A  + + +HL + F+ R   KIY++ VWG I +++ E     I +W  +        
Sbjct: 71  MLFAMNKYSERHLKKQFQYRLTHKIYYARVWGNIEQDEGEIDLPLICDWENRPKQ----- 125

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V  ++ K +    + ++V+    +K   + + P TGR+HQLRVH L +G PIVGD  Y
Sbjct: 126 -KVCFEHGKPSQ---TRYQVVRR-EEKTTIVRLLPITGRSHQLRVHMLSIGHPIVGDEFY 180

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
                 NF+S    +L LHA  +   HP+ 
Sbjct: 181 ANEEAKNFSS----RLELHAAELSFYHPKS 206


>gi|309805370|ref|ZP_07699419.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
 gi|308165297|gb|EFO67531.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
          Length = 292

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/279 (25%), Positives = 128/279 (45%), Gaps = 35/279 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKN-----HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           Y+ Y+ +  +E N  +D+  +N      + H  F+ ++K      + V+ K +  N ++ 
Sbjct: 13  YIYYLTISQNENNQNVDQIMRNLLIPRKWRH--FLRIEK-----NILVNDKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V +KPAG   Q
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENDDVLVIDKPAG---Q 109

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 110 KTHPNLYETDTALNDCASYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQK 239
           + Y++ +            N       IG D + + K+  +     AI+H++V+     K
Sbjct: 170 RSYFAWIEATNDISDNGTINL-----PIGDDPLDMRKRMVRADGLKAITHYQVVKKIGSK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++ 
Sbjct: 225 IL-VKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQA 262


>gi|260432354|ref|ZP_05786325.1| ribosomal large subunit pseudouridine synthase A [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260416182|gb|EEX09441.1| ribosomal large subunit pseudouridine synthase A [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 215

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 63/205 (30%), Positives = 105/205 (51%), Gaps = 16/205 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED+++ V NKPAG+    G G   H+   L + V +   +  L HRLD++TSG+++ 
Sbjct: 14  VLHEDAQVIVVNKPAGLLSVPGRGA--HLADCLLTRVQAAFPQALLVHRLDRDTSGVMIF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A+T  A ++L + F  R  +K Y + VWG  + K   +   L+       D+ +  +Q  
Sbjct: 72  AQTPHAQKYLGQQFENRLARKTYVARVWGRVEPKTGTVDLPLIV------DWPNRPRQMV 125

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A++ ++V+         + + P TGR+HQLRVH   +G PI+GD  Y      
Sbjct: 126 CHDTGKPAVTDWRVVRHEGDT-TRVRLFPKTGRSHQLRVHMQALGHPILGDPFYAEGPAR 184

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
           +F      +L LH+  + + HPE G
Sbjct: 185 DFP-----RLMLHSEELRIKHPEDG 204


>gi|227504711|ref|ZP_03934760.1| possible pseudouridylate synthase [Corynebacterium striatum ATCC
           6940]
 gi|227198721|gb|EEI78769.1| possible pseudouridylate synthase [Corynebacterium striatum ATCC
           6940]
          Length = 307

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 82/304 (26%), Positives = 135/304 (44%), Gaps = 30/304 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E MR D         I+      +  +G V VD   V  ++R+++G  + +         
Sbjct: 14  EGMRADAALAKLI-GISRGKAADLCAAGDVEVDGTIVGKSDRLEAGGWIDV--------M 64

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKS 135
           +   ++ L     L +  D     +LY D  +   +KP G++     G     + G L++
Sbjct: 65  MPAPEEPLVPKEELVEGMD-----VLYADDDVICVHKPVGVAAHPTLGWEGPTVIGGLRA 119

Query: 136 W---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
               +   G   R  + HRLD  TSG++VVA +  A   L  +F+ R + K Y ++V G+
Sbjct: 120 AGYQLADAGPTERKGIVHRLDVGTSGVMVVAASERAYSQLKAAFKERTVTKTYHAVVQGL 179

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +    G  +  V      G  +A++H+K+++ F ++   LE+   TG
Sbjct: 180 PDPIVGTIDAPIGRHPSSGWKFAVV-----DGGKHAVTHYKLLEAF-REASLLEVHLETG 233

Query: 251 RTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           RTHQ+RVH    G P VGD  Y C          I+   +LHA  +   HP  G+  ++T
Sbjct: 234 RTHQIRVHMSATGHPCVGDPMYGCDPNLAKRVGLIRQ--WLHAVSLGFIHPGTGKHFEVT 291

Query: 309 APLP 312
           AP P
Sbjct: 292 APYP 295


>gi|169629784|ref|YP_001703433.1| pseudouridine synthase RluD [Mycobacterium abscessus ATCC 19977]
 gi|169241751|emb|CAM62779.1| Probable pseudouridine synthase RluD [Mycobacterium abscessus]
          Length = 305

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 113/229 (49%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY D  +   +KPAG++     G     + G L +    + + G   R  + HRLD  T
Sbjct: 83  ILYADDDLVAVDKPAGVAAHASVGWTGPTVLGGLAAAGFRMTTSGVPERKGIVHRLDVGT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA +  A   L  +F+ RR++K Y +LV G P      I   + +  H G D+  
Sbjct: 143 SGVMVVALSEKAYTELKRAFKYRRVEKRYHALVQGHPDPSSGTIDAPIGR--HRGHDWKF 200

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V ++ +   ++I+H+  ++ F      L++   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 201 AVVEDGR---HSITHYDTLEAFVAA-SLLDIHLETGRTHQIRVHFSAIKHPCCGDLTYGA 256

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +        ++ + +LHA+ +   HP  GR ++IT+  P  +    D L
Sbjct: 257 DPTLAAKLGLERQ-WLHAKSLAFAHPGDGRWIEITSEYPEDLAHALDVL 304


>gi|197122401|ref|YP_002134352.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196172250|gb|ACG73223.1| pseudouridine synthase [Anaeromyxobacter sp. K]
          Length = 241

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 112/233 (48%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED+ +   +KPAG + + G  G     +  L++ ++++  +  + HRLD+ TSG+LV
Sbjct: 11  VLHEDAHLLAVDKPAGRLVIPGRDGG----EPSLRAELEARFGRLWVVHRLDRNTSGVLV 66

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHI---------G 209
           +ART AA + L  +F     +K Y +LV G+P  ++   +A    +K  +         G
Sbjct: 67  LARTAAAHRTLNLAFDRGEPRKRYLALVRGVPPAEQRIEVAIAPGRKGRMRPAPPDDPRG 126

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
              V VV++ E    +A+               +E  P TGRTHQ+RVH    G P+  D
Sbjct: 127 KASVTVVRRLEAFPGHALG--------GGPLALVEALPETGRTHQIRVHLAAAGTPLAVD 178

Query: 270 HKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
             Y   A   G     +  +  LHA  + L HP  GR L + APLP  +  T 
Sbjct: 179 PAYGDAAPLLGPGGEAVLARTPLHAARLALRHPADGRELVLEAPLPPDLAGTL 231


>gi|312171317|emb|CBX79576.1| tRNA pseudouridine synthase C [Erwinia amylovora ATCC BAA-2158]
          Length = 255

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 117/242 (48%), Gaps = 21/242 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  +   NKP+G+ V   S +  H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 4   IIYQDRWLVAVNKPSGMLVHR-SWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A +   A  L++ F   ++QK Y ++V G  +           ++  I   +     Q 
Sbjct: 63  MALSSEVAHLLSQQFEQHQLQKTYHAVVRGWLEGADTLDYPLTEERDKIADKF----SQP 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           EK    A++H++ +               ++  +EMQP +GR HQLR H  H+  PI+GD
Sbjct: 119 EKAPQPAVTHWRGVATAELAVPIGRYETSRYSLVEMQPESGRKHQLRRHMTHLRHPIIGD 178

Query: 270 HKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
             +  + K N ++      N+L LHA  ++L HP   G L + A L A   K  +  G++
Sbjct: 179 SAH-GDLKQNRSAAANFGINRLMLHASELNLTHPVTAGPLILRAGLDAVWQKVINQFGWQ 237

Query: 326 YD 327
            +
Sbjct: 238 AE 239


>gi|221638823|ref|YP_002525085.1| Ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides KD131]
 gi|221159604|gb|ACM00584.1| Ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides KD131]
          Length = 322

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 79/314 (25%), Positives = 136/314 (43%), Gaps = 49/314 (15%)

Query: 36  NLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
            L K++  G VR++   V     ++  GQV  I                LD+   +    
Sbjct: 14  RLMKLIGEGAVRLEGAPVTDPKAKVAEGQVYEI---------------ALDAPAEVEARP 58

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL----KSWVDSKGQK-PRLT 147
           + +   +++ED  + V +KP G+ V    G      ++  L    +S     G+K P + 
Sbjct: 59  EAIPLSVVWEDEDLIVIDKPVGMVVHPAPGQWTGTLVNALLHHCGESLSGIGGEKRPGIV 118

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HR+D++TSG+LVVA+T  A Q L   F    +++ Y +LV G+P+     +   +   S 
Sbjct: 119 HRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRYLALVHGVPEVSDPRL-RGVRGTSF 177

Query: 208 IGGDYVHVV---------KQNE----KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRT 252
             G  + +          +Q +    +G  +A++  ++++ F        +E +  TGRT
Sbjct: 178 EPGGVLRIATGLARHRTDRQRQAVTFEGGRHAVTRARLLERFGMPPVLALVECRLETGRT 237

Query: 253 HQLRVHALHMGCPIVGDHKYCANFK-------GNFTSPIQN--KLYLHARYMDLPHP-EG 302
           HQ+RVH  H G  ++GD  Y    K           + ++   +  LHA  +   HP  G
Sbjct: 238 HQIRVHMAHAGHGLIGDQTYGGRRKLSPKALGPEAAAAVEAFPRQALHAASLGFRHPVSG 297

Query: 303 GRLQITAPLPAHMV 316
             L   +PLPA M 
Sbjct: 298 EELSFESPLPADMA 311


>gi|254474013|ref|ZP_05087406.1| 23S rRNA (position 746) and tRNAphe (position 32) specific
           pseudoryidylate sytnthase [Pseudovibrio sp. JE062]
 gi|211956902|gb|EEA92109.1| 23S rRNA (position 746) and tRNAphe (position 32) specific
           pseudoryidylate sytnthase [Pseudovibrio sp. JE062]
          Length = 212

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/216 (32%), Positives = 116/216 (53%), Gaps = 18/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D ++ V NKP+G+ SV G +    H D  L++   S        HRLD +TSG+LV
Sbjct: 7   VVHQDEQLLVLNKPSGLLSVPGRA--EEHKD-CLETRAQSIHPTATTIHRLDMDTSGLLV 63

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +A  + A +H+   F  R  +K Y + VWG  ++  E   +  L+      D+ +  KQ 
Sbjct: 64  MAMNKDAHRHVGLQFEKRMTRKTYIARVWGHLRD-DEGEVDLPLR-----CDWPNRPKQM 117

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +    A++ ++VI+   +    +++ P TGR+HQLRVH L +G PIVGD  Y     
Sbjct: 118 VDHELGRSALTKWEVIN-REEHTTLVKLMPVTGRSHQLRVHMLELGHPIVGDRFYAQGEA 176

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
            +F+     +L+LHA+ ++L HP GG     TA  P
Sbjct: 177 LSFS----ERLHLHAQTLELRHPIGGEYNTFTASCP 208


>gi|288800870|ref|ZP_06406327.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 299 str. F0039]
 gi|288332331|gb|EFC70812.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 299 str. F0039]
          Length = 295

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 74/234 (31%), Positives = 118/234 (50%), Gaps = 19/234 (8%)

Query: 87  SVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQ 142
           S++ TK ++  KS    ++YED+ I V +K AGI S+  G G + ++   L  ++    Q
Sbjct: 67  SISKTKRNNLFKSKYVDIVYEDNHIIVVHKKAGILSMPVGHG-SLNVKTVLDDYLMRSKQ 125

Query: 143 K--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           K    + HRLD+ETSG++V A+ +   +   E +      + Y ++V G  +  +  IAN
Sbjct: 126 KCNAHVVHRLDRETSGLMVYAKDKRVERLFEEDWHNIVYDRRYVAIVSGEVQENEGTIAN 185

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           WL         +V      + G  YA++HF+V    A     +E +  TGR +Q+RVH+ 
Sbjct: 186 WLKDNKM----FVTYSCPFDNGGKYAVTHFQVKKRTAY-HTLVEYKLETGRKNQIRVHSA 240

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
            +G P+ GD KY     GN   PI  +L LHA  +   HP   + L    P+P+
Sbjct: 241 DIGHPVCGDTKY-----GNGDDPI-GRLCLHAYVLAFYHPITHKPLLFETPIPS 288


>gi|145633817|ref|ZP_01789540.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae 3655]
 gi|144985320|gb|EDJ92155.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae 3655]
          Length = 219

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 107/208 (51%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+     +  V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAMAR--VKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC----IANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG + K+  E     I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLEKDYGEVNLPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+   +     +++ P TGR+HQLR+H L +G PI+GD K+ ++
Sbjct: 132 -------GKRAVTKFEVLARLSNNSTRVKLTPVTGRSHQLRLHMLALGHPILGD-KFYSH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    SP   +L LHA  + + HP  G
Sbjct: 184 PQAKAMSP---RLCLHAEELTITHPITG 208


>gi|91223469|ref|ZP_01258734.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           12G01]
 gi|91191555|gb|EAS77819.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           12G01]
          Length = 256

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/261 (27%), Positives = 124/261 (47%), Gaps = 31/261 (11%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
            LT+ S+ ++  ++Y+D      NKPAG+ V       +     +++  D  GQ     H
Sbjct: 5   ELTRSSEPVELEIVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLH 64

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS-- 206
           RLD+ TSG+LV A +   A  +   F   +++K Y ++V G    ++E + ++ LK    
Sbjct: 65  RLDRPTSGVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGW--IEEEGVLDYALKVELD 122

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLR 256
            I   +       EK A  A++ +K +               ++C +EM+P TGR HQLR
Sbjct: 123 KIADKFA----SQEKEAQEAVTEYKPLAKVEVPYSTGKFPTTRYCLVEMKPKTGRKHQLR 178

Query: 257 VHALHMGCPIVGDH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
            H  H+  PIVGD      K+   ++  F S   ++L LHA  +   HP   +  +   +
Sbjct: 179 RHMAHLRHPIVGDTTHGDGKHNKLYRTEFES---HRLLLHASELRFVHPFTDQEIV---M 232

Query: 312 PAHMVKTWDSL--GFKYDRNL 330
            A++ +TW  L   F++D ++
Sbjct: 233 TANLDETWQQLFTRFEWDESM 253


>gi|255068551|ref|ZP_05320406.1| tRNA pseudouridine synthase C [Neisseria sicca ATCC 29256]
 gi|255047187|gb|EET42651.1| tRNA pseudouridine synthase C [Neisseria sicca ATCC 29256]
          Length = 261

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 64/214 (29%), Positives = 98/214 (45%), Gaps = 15/214 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY DS+    NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 30  ILYRDSRTIAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVYPAHRLDRPTSGVLLF 89

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLK-------KSHIGGDY 212
           A    AA+ LT+ F  +  +K YW++V G +P +    + ++ LK       +S      
Sbjct: 90  ALDPEAARLLTQQFEQKTTRKTYWAIVRGYLPDDG---LIDYPLKYQPDKIAESQTEATL 146

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                +  + A   +           ++ W E+ PHTGR HQLR H  H+  PIVGD  Y
Sbjct: 147 QEAQTRYRRLARTELPFQSAARYPTSRYSWAELIPHTGRKHQLRRHMKHIFHPIVGDTNY 206

Query: 273 CANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG 303
             + + N  +       +L LHAR +     E G
Sbjct: 207 -GDLRQNHATAAHLGPTRLMLHARSLSFQSIENG 239


>gi|68249316|ref|YP_248428.1| pseudouridylate synthase [Haemophilus influenzae 86-028NP]
 gi|68057515|gb|AAX87768.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae 86-028NP]
          Length = 219

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 67/208 (32%), Positives = 106/208 (50%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+      S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC----IANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG + K+  E     I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLEKDYGEVNLPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD K+ ++
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGD-KFYSH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    SP   +L LHA  + + HP  G
Sbjct: 184 PQAKAMSP---RLCLHAEELTITHPITG 208


>gi|313899281|ref|ZP_07832797.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
 gi|312955961|gb|EFR37613.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
          Length = 317

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/282 (23%), Positives = 141/282 (50%), Gaps = 35/282 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR- 66
           ++++ END +  R+D++ +     +    + K +R+ +++V++KR + + R+Q G  ++ 
Sbjct: 3   EFIINENDADQ-RVDKFIQKTMKTMPKSLMYKYIRNKKIKVNRKRCEISQRLQVGDTMQC 61

Query: 67  -IPPV---INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            IP     +  +   ++    LD               ++YED  + + NKP G+     
Sbjct: 62  YIPEEFYEVATMRSFLQVPNALD---------------VVYEDDAVLLMNKPKGLRAHSD 106

Query: 123 SG-----IAYHIDGFL--KSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTE 172
           +      +A  +  +L  K   D   ++   P L HR+D+ T G+++ A+T AA + + E
Sbjct: 107 TSEVQDNLADRLLHYLYCKKEYDPTTEQSFTPALCHRIDRNTQGLVIAAKTAAALRCMNE 166

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
              +R+++K Y  +V G  K K++ I  +  K      +   V+ +  +G     + ++V
Sbjct: 167 KIALRQVEKKYLCIVQGKLKKKQDHIVLYHRKNEQ---NTAEVIDREREGYTRMETGYRV 223

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +   A+++  +E++ H+G++HQ+R     +G P++GD KY A
Sbjct: 224 LQ-EAERYSLVEVELHSGKSHQIRALMSWLGHPLLGDVKYGA 264


>gi|296282152|ref|ZP_06860150.1| pseudouridine synthase [Citromicrobium bathyomarinum JL354]
          Length = 225

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 110/225 (48%), Gaps = 16/225 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED +  V +KPAG+S+         +D +L+       + P   HRLD +TSG L++
Sbjct: 8   ILYEDGEALVIDKPAGLSIDRPRKGGPCLDDYLEQLKLGFQRPPSAVHRLDTDTSGCLLL 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR   A +  + +F  +++ K+Y  ++ GIP  ++  +   L K S     +  +  +  
Sbjct: 68  ARNPKAHKRFSAAFEAQQVTKVYHGILAGIPAQEEGVVELALSKISSAEKGWRMIPAKKG 127

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGN 279
           K    +++ ++V+     +   +E +P TGRTHQ+RVHA   +G  +VGD  Y       
Sbjct: 128 K---PSVTAWRVVATHEGR-ALVEFRPATGRTHQIRVHAASGIGIALVGDPVYG------ 177

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
            T     +  LHA  + +       +  T+PLPA     + +LGF
Sbjct: 178 -TKQGAPRTMLHASALTVERESKTDIAATSPLPAD----FQALGF 217


>gi|260682684|ref|YP_003213969.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260686282|ref|YP_003217415.1| putative pseudouridylate synthase [Clostridium difficile R20291]
 gi|260208847|emb|CBA61782.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260212298|emb|CBE03063.1| putative pseudouridylate synthase [Clostridium difficile R20291]
          Length = 281

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 112/225 (49%), Gaps = 27/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++Y+D  I + NKP  + V            +GI+Y+ID         +  K R  +RLD
Sbjct: 66  IIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGISYYIDN------QKENVKIRFVNRLD 119

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG+++VA+   A   L+ +    +++K Y ++V GI K  +  I   + + +    D
Sbjct: 120 MNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGIIKENEGTIDEPIYRPTE---D 176

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  +  +E+G + +++H+KVI+   +    LE+   TGRTHQ+RVH  H+G  I+GD  
Sbjct: 177 SIKRI-IDERGQS-SVTHYKVIERL-ENATVLEVSLETGRTHQIRVHMAHIGHGIIGDEL 233

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           Y     G     + N+  LHA  ++   P    +L+  A +P  M
Sbjct: 234 Y-----GYVDEELINRQALHAYKLEFEQPRTKEKLKFKADIPEDM 273


>gi|148827905|ref|YP_001292658.1| hypothetical protein CGSHiGG_07040 [Haemophilus influenzae PittGG]
 gi|148719147|gb|ABR00275.1| hypothetical protein CGSHiGG_07040 [Haemophilus influenzae PittGG]
          Length = 219

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 104/208 (50%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+      S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG  +N         I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEINLPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD K+ ++
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGD-KFYSH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    SP   +L LHA  + + HP  G
Sbjct: 184 PQAKVMSP---RLCLHAEELTITHPITG 208


>gi|54023755|ref|YP_117997.1| putative RNA pseudouridine synthase [Nocardia farcinica IFM 10152]
 gi|54015263|dbj|BAD56633.1| putative RNA pseudouridine synthase [Nocardia farcinica IFM 10152]
          Length = 308

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/229 (31%), Positives = 111/229 (48%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY D  I   +KP G++   G G     + G L +    + + G   R  + HRLD  T
Sbjct: 84  ILYADDDIVAVDKPVGVAAHTGVGWSGPTVVGGLAAAGYRISTSGAHERQGIVHRLDVGT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA++  A   L  +F+ R + K Y +LV G P      I   + +    G D+  
Sbjct: 144 SGVMVVAQSEHAYTVLKRAFKQRTVSKRYHALVQGHPDPSSGTIDAPIGRAR--GNDWKF 201

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  + +    +++H+  I+ F Q    L++   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 202 AVTADGR---PSVTHYDTIEAF-QAASLLDIHLETGRTHQIRVHFSAIRHPCCGDLTYGA 257

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + +      +Q + +LHAR +   HP  GR L+IT+  P  +    D L
Sbjct: 258 DPRLAERLGLQRQ-WLHARTLGFHHPADGRWLEITSEYPDDLRHALDVL 305


>gi|331004377|ref|ZP_08327850.1| hypothetical protein HMPREF0491_02712 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330411107|gb|EGG90526.1| hypothetical protein HMPREF0491_02712 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 299

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 63/213 (29%), Positives = 111/213 (52%), Gaps = 13/213 (6%)

Query: 103 YEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  I V NKP  + +    +     +   L  +   K    R  +RLD++T+G+ +VA
Sbjct: 83  YEDEDIVVINKPGDMPIHPSLNNYENSLANALMHYYKDKNFVFRCINRLDKDTTGLTIVA 142

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +   +A  L  + + R+I+++Y ++V    +  KE I +  + + +   D +   K +E 
Sbjct: 143 KHFLSAGILNIAMQKRQIKRVYNAIVKDEGRLAKEGIIDLPIAREN---DTLIKRKVSED 199

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           G   A+++FK+I  F + +  +E++  TGRTHQ+RVH  H+G P+ GD+ Y  +  G   
Sbjct: 200 GQR-AVTYFKMIKRFGE-YSLIELRLETGRTHQIRVHMSHIGAPLAGDYLYNESEYGKRN 257

Query: 282 -SPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             P+     LH++ +D  HP  G R+ +   LP
Sbjct: 258 IRPL-----LHSKSLDFIHPVTGERIYLECDLP 285


>gi|320539057|ref|ZP_08038731.1| putative 23S rRNA pseudouridine synthase [Serratia symbiotica str.
           Tucson]
 gi|320030897|gb|EFW12902.1| putative 23S rRNA pseudouridine synthase [Serratia symbiotica str.
           Tucson]
          Length = 325

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 87/326 (26%), Positives = 149/326 (45%), Gaps = 47/326 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V+V+ K   K   ++  G++V I 
Sbjct: 9   ATVAESQLGQRLDQAMAELFPDYSRSRIKEWILDDRVQVNGKTANKPKEKVLGGEIVAIA 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I        +   LD               ++YED  I V NKP    V  G+G   +
Sbjct: 69  AQIEEDPRWEPQDIALD---------------VVYEDCDILVINKPRDRVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + 
Sbjct: 111 PDGTVLNALLHYYPKIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQEREITRE 170

Query: 183 YWSLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H+    V+ + +       A++H+++++ F + 
Sbjct: 171 YEAVAIGTMTAGGTVDEPISRHSTKRTHMA---VYPMGKP------AVTHYRILEHF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LH
Sbjct: 221 HTRLRLRLETGRTHQIRVHMSHINHPLVGDPLYGGRPRSPKGASEAFISTLRGFDRQALH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMV 316
           A  + L HP  G +++  APLP  MV
Sbjct: 281 ATMLRLYHPISGIQMEWHAPLPQDMV 306


>gi|154148379|ref|YP_001406840.1| RluA family pseudouridine synthase [Campylobacter hominis ATCC
           BAA-381]
 gi|153804388|gb|ABS51395.1| pseudouridine synthase, RluA family [Campylobacter hominis ATCC
           BAA-381]
          Length = 357

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 81/289 (28%), Positives = 130/289 (44%), Gaps = 51/289 (17%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------- 140
           NL ++++F   IL YED  + V NKP+G+ V     +    +  L  W+  K        
Sbjct: 81  NLKQNANFDIEIL-YEDDDLLVLNKPSGVVVHPAKSVK---EPTLAEWLKQKKYMLSSIN 136

Query: 141 -GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             ++  + HRLD++TSG ++VA+T  A   L    + + + +IY + +  +   +  C+ 
Sbjct: 137 GDERAGIVHRLDKQTSGAILVAKTDFAHVKLAAQLKDKSMGRIYLAFL-DLALKENVCVD 195

Query: 200 NWL-------LKKSHIGGDYVHVVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQPH-- 248
            ++       LKK+        VV  NE GA  A S F  I  D   Q F  L    +  
Sbjct: 196 RFIARNPSNRLKKA--------VVPPNENGARSAKSAFLNIANDTILQNFKPLNFSQNQT 247

Query: 249 ----------TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
                     TGRTHQ+RVH   +   I+GD  Y   FK +F      +++LHA  +   
Sbjct: 248 NFNLIAAKLFTGRTHQIRVHLSSINRHIIGDFLY--GFKSDFDKI--KRIFLHAYLLYFT 303

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFK---YDRNLYIKRLYSQDECKQ 343
           HP   R + I+A +P+      +   FK   Y++ L    + + D+C Q
Sbjct: 304 HPRTNRQILISAKIPSEFKNLIEKSDFKDEIYEKILPSNLISAFDDCDQ 352


>gi|153816535|ref|ZP_01969203.1| hypothetical protein RUMTOR_02788 [Ruminococcus torques ATCC 27756]
 gi|317502168|ref|ZP_07960343.1| pseudouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331088735|ref|ZP_08337645.1| hypothetical protein HMPREF1025_01228 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145846127|gb|EDK23045.1| hypothetical protein RUMTOR_02788 [Ruminococcus torques ATCC 27756]
 gi|316896433|gb|EFV18529.1| pseudouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330407258|gb|EGG86761.1| hypothetical protein HMPREF1025_01228 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 262

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 69/252 (27%), Positives = 112/252 (44%), Gaps = 50/252 (19%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-------KGQKPRLT--HRL 150
           +++YED +I V +KPAG   Q        ++  LK+ + S       K  +P L   HRL
Sbjct: 8   LIIYEDEQIIVCHKPAGTPTQSSHIGTSDMESLLKNHLFSSRKFHRAKSGEPYLAIIHRL 67

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           DQ   GILV A+T AAA+ L      +   K Y +++ GIP+ ++  + N+L+K +    
Sbjct: 68  DQPVEGILVFAKTPAAAKELNRQLTSQEFGKYYLAVISGIPEPQEGSLENYLVKDTRTNS 127

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFA----QKF-------------------------- 240
               V  +   GA  A  H++ I+ +     +KF                          
Sbjct: 128 SA--VCTKTTPGAKLARLHYRTIETYGAPGNEKFTDSKSTDTPKHTSRNHRQPPLQNESS 185

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--------KLYLHA 292
             +E+   TGR HQ+RV   + G P++GD KY      +  S +Q+        +L+L A
Sbjct: 186 ALIEIHLDTGRHHQIRVQMAYFGHPLIGDRKYGKEITDHMNS-VQSSTKRFQAGQLHLCA 244

Query: 293 RYMDLPHPEGGR 304
             +   HP+ G+
Sbjct: 245 YKLTFHHPKTGK 256


>gi|299769211|ref|YP_003731237.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. DR1]
 gi|298699299|gb|ADI89864.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. DR1]
          Length = 212

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 69/223 (30%), Positives = 107/223 (47%), Gaps = 17/223 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V +   K  L HRLD++
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLV-AIEPKTLLIHRLDRD 58

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     +   F+ R+  KIY +LV G  + +       +   S      +
Sbjct: 59  TSGILVFGLSKRGQSAIARQFQDRQTSKIYEALVAGHLEGEGTVDIPVIYDPSR---PPL 115

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+V  +      A++H++ ++ F    Q    +++ P TGR+HQLRVH  ++G PIVGD 
Sbjct: 116 HIVDASHNKP--ALTHWQAVEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDT 173

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            Y  + +      +  +L LHA+ +   HP     L    P+P
Sbjct: 174 LYATSEQQ-----LVPRLCLHAKQLSFNHPVTAETLTFDCPVP 211


>gi|16272559|ref|NP_438775.1| hypothetical protein HI0617 [Haemophilus influenzae Rd KW20]
 gi|145631647|ref|ZP_01787411.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae R3021]
 gi|260581431|ref|ZP_05849244.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae RdAW]
 gi|260583228|ref|ZP_05851006.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae NT127]
 gi|1175490|sp|P44782|RLUA_HAEIN RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|1573611|gb|AAC22276.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|144982726|gb|EDJ90258.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae R3021]
 gi|260091925|gb|EEW75875.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae RdAW]
 gi|260093730|gb|EEW77640.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae NT127]
 gi|301169333|emb|CBW28932.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Haemophilus influenzae 10810]
          Length = 219

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 104/208 (50%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+      S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG  +N         I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD K+ ++
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGD-KFYSH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    SP   +L LHA  + + HP  G
Sbjct: 184 PQAKVMSP---RLCLHAEELTITHPITG 208


>gi|118581355|ref|YP_902605.1| RluA family pseudouridine synthase [Pelobacter propionicus DSM
           2379]
 gi|118504065|gb|ABL00548.1| pseudouridine synthase, RluA family [Pelobacter propionicus DSM
           2379]
          Length = 310

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 80/334 (23%), Positives = 139/334 (41%), Gaps = 63/334 (18%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RL+ + +   P  +F   +K++RSG V+V+      ++ +     V +    +    I  
Sbjct: 14  RLESYLRLLLPQASFAYPRKLIRSGAVKVNAAPATADSLLTIDDRVTLKESTSLTALIST 73

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E+  LD               +LYED +I + NKP+G+++   +    ++     +++  
Sbjct: 74  ERPGLD---------------ILYEDDQIAIVNKPSGLAMHRTAEQETNLVEQGTAFMAW 118

Query: 140 KGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-------- 189
           +G   +L   +RLD+ TSG +++A++  AA       +   + K+Y +LV G        
Sbjct: 119 RGTPCKLYPVNRLDRGTSGAVILAKSSTAAGIFGRQVKETGLDKLYLALVAGRPDGAGVI 178

Query: 190 -IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
             P + KEC  ++ L     G                              F  LE+ P 
Sbjct: 179 DAPLDGKECRTDYRLLAQGCG------------------------------FSLLELLPF 208

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT 308
           +GR HQ+R H   +G PI+GD +Y                 LH+    L  P+G RL + 
Sbjct: 209 SGRMHQIRRHLEMIGHPILGDQRYSGRVVEELAG-----FALHSFRTGLTMPDGRRLVVC 263

Query: 309 APLPAHMVKTWDSLGFKYDRNL-YIKRL-YSQDE 340
           APL   ++      G + D  L  +KR+  S+DE
Sbjct: 264 APLTDELLALCQQGGIESDSLLPLLKRVALSRDE 297


>gi|319943653|ref|ZP_08017934.1| ribosomal large subunit pseudouridine synthase D [Lautropia
           mirabilis ATCC 51599]
 gi|319742886|gb|EFV95292.1| ribosomal large subunit pseudouridine synthase D [Lautropia
           mirabilis ATCC 51599]
          Length = 332

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 86/326 (26%), Positives = 145/326 (44%), Gaps = 52/326 (15%)

Query: 10  VVVENDEENMRLD----RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           V+   + +  RLD    R+ +     I+   +Q+ +  G VRVD++             V
Sbjct: 18  VIDAREGQGQRLDQFLTRYLQERLDGISRTRIQRWIALGAVRVDQQ-------------V 64

Query: 66  RIPPV-INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           R+P + +  +  I  E + L+S        D +   ++++D+ I V +KPAG+      G
Sbjct: 65  RLPSLRLKGVESIEVEPQPLESDTAFAP--DPVPLAIVHQDADITVIDKPAGLVTHPAPG 122

Query: 125 --IAYHIDGFLKSWVDSKGQK-PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                 ++G L +  D K  + PR  + HRLD++TSG+LV AR+  A   LT     R++
Sbjct: 123 NWRNTLMNGLLHA--DPKAARLPRAGIVHRLDRDTSGLLVCARSERAFASLTAQLASRQM 180

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCF 236
            + Y ++  G    +     N       IG D  + ++           A +H++++   
Sbjct: 181 GRRYLAIACGQTPAQGTVEGN-------IGRDERNRLRMAVVQPPAGKPARTHYRLLAAS 233

Query: 237 AQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
                    C LE    +GRTHQ+RVH  H+G P+VGD  Y       F      +  LH
Sbjct: 234 PDAEAAAILCKLE----SGRTHQIRVHMAHIGHPLVGDTLYGGKPLAGFA-----RQALH 284

Query: 292 ARYMDLPHPEGGRLQI-TAPLPAHMV 316
           A  + L HP   + Q+  AP+P  ++
Sbjct: 285 AWQLQLIHPATQQSQVFVAPIPPDLL 310


>gi|294678331|ref|YP_003578946.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           capsulatus SB 1003]
 gi|294477151|gb|ADE86539.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           capsulatus SB 1003]
          Length = 347

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 110/248 (44%), Gaps = 43/248 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +L+ED  + V +KPAG+ V    G         + +H  G L S +  +  +P + HR+D
Sbjct: 90  VLWEDEDLIVIDKPAGMVVHPAPGSEDGTLVNALLHHFGGRL-SGIGGEA-RPGIVHRID 147

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG+LVVA++  A   L   F    + + Y +LV G+P      +          GG 
Sbjct: 148 KETSGLLVVAKSDRAHHGLAAQFEKHTVHRHYTALVQGVPSAADPRLRGIRGVNFEQGG- 206

Query: 212 YVHVVKQNEK-------------GANYAISHFKVIDCF----AQKFCWLEMQPHTGRTHQ 254
            + +  Q  +             G  +A++  + ++ F    A   CWLE    TGRTHQ
Sbjct: 207 ILKITSQLARHPTDRQRQAVLFTGGRHAVTRARTVEAFGGVAALMDCWLE----TGRTHQ 262

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---------KLYLHARYMDLPHP-EGGR 304
           +RVH  H+G  +VGD  Y    K +  +             +  LHA  +   HP  G  
Sbjct: 263 IRVHMAHVGHGLVGDPTYGGKRKLSVRAVGAAAAEAVANFPRQALHATTLGFTHPVTGEE 322

Query: 305 LQITAPLP 312
           L  T+PLP
Sbjct: 323 LSFTSPLP 330


>gi|254821467|ref|ZP_05226468.1| hypothetical protein MintA_16155 [Mycobacterium intracellulare ATCC
           13950]
          Length = 308

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 116/237 (48%), Gaps = 18/237 (7%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTH 148
           D     +LY D  I   +KPA ++     G     + G L +    + + G   R  + H
Sbjct: 77  DIEGMTILYSDDDIVAVDKPAAVAAHASVGWSGPTVLGGLAAAGYRITTSGVPERQGIVH 136

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++VVA +  A   L  +F+ R + K Y +LV G P      I   + +  H 
Sbjct: 137 RLDVGTSGVMVVALSERAYTLLKRAFKQRTVDKRYHALVQGHPDPSSGTIDAPIGR--HR 194

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH--ALHMGCPI 266
           GG++   + ++ +   ++++H+  ++ F      L++   TGRTHQ+RVH  ALH  C  
Sbjct: 195 GGEWKFAITKDGR---HSLTHYDTVEAFVAA-SLLDVHLETGRTHQIRVHFSALHHPC-- 248

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            GD  Y A+ K      ++ + +LHAR +   HP +G R++I +P P  +    D L
Sbjct: 249 CGDLVYGADPKLAKRLGLERQ-WLHARSLSFAHPADGRRMEIVSPYPPDLQHALDVL 304


>gi|25011477|ref|NP_735872.1| hypothetical protein gbs1435 [Streptococcus agalactiae NEM316]
 gi|24413015|emb|CAD47094.1| unknown [Streptococcus agalactiae NEM316]
          Length = 296

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 111/239 (46%), Gaps = 38/239 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++Y+D  + V NKP G+ V   +G         + YHI    K      G  +P + HR+
Sbjct: 76  IIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHI----KDLSSINGVVRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+   A Q L E  + ++  + Y ++V G   N +  I      ++ IG 
Sbjct: 132 DKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVI------EAPIGR 185

Query: 211 DYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 KQ    KG   AI+ F V++ F   +  +E+   TGRTHQ+RVH  ++G P+ G
Sbjct: 186 SDKDRKKQAVTAKG-KPAITRFHVLERFGD-YTLVELSLETGRTHQIRVHMAYIGHPLAG 243

Query: 269 DHKY----CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           D  Y        KG F         LHA+ +   HP  G  L  +  +P     T D L
Sbjct: 244 DSVYGPRKTLEGKGQF---------LHAQTLGFTHPSNGENLIFSVEVPEIFQTTLDKL 293


>gi|291562536|emb|CBL41352.1| Pseudouridylate synthases, 23S RNA-specific [butyrate-producing
           bacterium SS3/4]
          Length = 266

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 58/187 (31%), Positives = 96/187 (51%), Gaps = 17/187 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----SKGQKP--RLTHRLDQE 153
           +LYED +I V  KPAG+  Q     A  +   +K  +      + G++P   + HRLD+ 
Sbjct: 4   VLYEDDEILVVIKPAGVESQAAKRFAPDMVSEVKKHLVINKSCTPGKEPYVGVIHRLDKP 63

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
            SG++V A+T+ AA  L+E  +  +++KIY ++V G P N  +   ++++K     G+Y 
Sbjct: 64  VSGVMVYAKTKRAAAALSEQIQSHKMKKIYTAVVHGRPVNMVDNYVDYMVKTPD--GNYS 121

Query: 214 HVVKQNEKGANYAISHFKVIDCF--------AQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            VV +   GA  A   ++V+            ++   + +   TGR HQ+RV   H G P
Sbjct: 122 QVVDKGITGAKKAELSYEVLKTIDGEAAGMPGKELSLVRVALKTGRHHQIRVQMAHHGTP 181

Query: 266 IVGDHKY 272
           + GD KY
Sbjct: 182 LYGDMKY 188


>gi|330811143|ref|YP_004355605.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327379251|gb|AEA70601.1| Ribosomal large subunit pseudouridine synthase A [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 211

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 112/214 (52%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D  + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIHQDDAVLVVDKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P+     I   L  +        HVV  +
Sbjct: 66  LARDPDTHRELSRQFHDRETEKAYTALCWGQPELDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ ++V++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEHGKHALTFWRVLE-RCGDWCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPQAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
              P   +L LHA  +   HP+ G RL+   P P
Sbjct: 180 AAWP---RLCLHASMLSFTHPQSGERLRFECPAP 210


>gi|319794365|ref|YP_004156005.1| pseudouridine synthase, rlua family [Variovorax paradoxus EPS]
 gi|315596828|gb|ADU37894.1| pseudouridine synthase, RluA family [Variovorax paradoxus EPS]
          Length = 322

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 89/331 (26%), Positives = 143/331 (43%), Gaps = 41/331 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           VV       RLDR      P  +   LQ+++ +G V    + + K +  +++GQ  RI  
Sbjct: 19  VVSEALHGQRLDRALAALVPEFSRSYLQQLIEAGAVEFQGRTLTKASATVRAGQAGRI-- 76

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L    + Q      ++L         + ++ED  + + +KPAG+ V    G   H 
Sbjct: 77  ---ELRPTPQSQAFRPEPMDL---------VTVFEDEHLRIVDKPAGLVVHPAPG---HW 121

Query: 130 DGFLKSWVDSKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G L + + +   K    PR  + HRLD++TSG++VVARTRAA   L      R +++ Y
Sbjct: 122 SGTLLNGLLALDPKAVLLPRAGIVHRLDRDTSGLMVVARTRAAMDALVALIAAREVKRQY 181

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++      +K    A      + IG D      + VV         A +  + +D  ++
Sbjct: 182 LAI-----GHKPWVGAAARQVDAPIGRDPRNRLRMAVVDLERHSGKTARTLIERLDSHSE 236

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             C +     TGRTHQ+RVH   +G P+VGD  Y     G   +    +  LHA  +   
Sbjct: 237 G-CVVRCTLETGRTHQIRVHMASIGHPLVGDALY-----GGAPAVGLARQALHAFRLAFV 290

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           HP     L+  +  P  +V+   S G  Y+R
Sbjct: 291 HPVTQAALEFHSLPPPDLVQALQSWGLDYNR 321


>gi|254796544|ref|YP_003081380.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Neorickettsia risticii str. Illinois]
 gi|254589781|gb|ACT69143.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Neorickettsia risticii str. Illinois]
          Length = 315

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 74/274 (27%), Positives = 133/274 (48%), Gaps = 36/274 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V E D  N RLD +   + P  +   ++  ++ G+V+ D K             +R+ P
Sbjct: 16  IVAECDVGN-RLDVFLHRYLPFFSRTFIKHCIKGGRVKADGK-------------IRLEP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG---- 124
               L  + +E  +LD  +       F++ + + YED  + V +KPAG+ V  G G    
Sbjct: 62  SKQVL--LGEEYHLLDLPLEQKPRHAFVQPLDVRYEDDSLLVIHKPAGLVVHPGIGNKEQ 119

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + +H      S +DS   +P + HRLD++T+G L+VA+T  +   L+E  +   I
Sbjct: 120 TLVNILEHHYPTEQLSNLDS--SRPGIVHRLDKDTAGFLIVAKTNPSHVRLSEMIKEGVI 177

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQ 238
           ++ Y +LV  +P + +  I     KKS   G    ++   +     A++++ V+     +
Sbjct: 178 RREYLALVHSVPASLRGEI-----KKSIKRGQRKMMI--GKCSGKPALTYYNVLARTVDR 230

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K+  +  +  +GRTHQ+R+H   +GCP+VGD  Y
Sbjct: 231 KYSLVHCKLGSGRTHQIRLHMKSIGCPVVGDKLY 264


>gi|293609771|ref|ZP_06692073.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292828223|gb|EFF86586.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 212

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 70/223 (31%), Positives = 106/223 (47%), Gaps = 17/223 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V +   K  L HRLD++
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLV-AIEPKTLLIHRLDRD 58

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     +   F+ R+  KIY +LV G  + +       +   S      +
Sbjct: 59  TSGILVFGLSKLGQSAIARQFQDRQTSKIYEALVAGHLEGEGTVDIPVIYDPSR---PPL 115

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+V  +      A++H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD 
Sbjct: 116 HIVDASHNKP--ALTHWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDT 173

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            Y    +      +  +L LHA+ +   HP     L    P+P
Sbjct: 174 LYATPEQQ-----LVPRLCLHAKQLSFNHPVTAETLTFDCPVP 211


>gi|255505168|ref|ZP_05344870.3| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Bryantella formatexigens DSM 14469]
 gi|255269406|gb|EET62611.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Bryantella formatexigens DSM 14469]
          Length = 272

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 117/246 (47%), Gaps = 16/246 (6%)

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           Q + D      +  D +  I+ YED ++ V  KPAG++VQ  S     ++  +++++  K
Sbjct: 38  QVLFDFDKQPYRRGDIMPDII-YEDKQLLVCRKPAGLAVQNASFGRMDLESMVRNYLMEK 96

Query: 141 GQKPR----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             KP     + HRLDQ   G+LV A+T AAA  L+   +  R+ K Y ++V G    K+ 
Sbjct: 97  SGKPNPYLGVVHRLDQPVQGLLVFAKTPAAAAALSAQVQDGRMTKEYLAVVCGKLPEKEG 156

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + ++L  K    G+    V +   GA  A   ++V+   A     + ++  TGR HQ+R
Sbjct: 157 ELVHFL--KKEPAGNCSRAVGEKTPGAKRAELSYRVL-AEADGRALVRIKLKTGRHHQIR 213

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           V  +  G P+ GD KY      N  +    +L L A  +   HP GG R++ T   P + 
Sbjct: 214 VQMVACGAPLYGDAKY------NPGAQRGERLALCADRLSFVHPAGGKRVEFTC-RPDNF 266

Query: 316 VKTWDS 321
              W+ 
Sbjct: 267 PAPWEG 272


>gi|198425133|ref|XP_002130987.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4 [Ciona intestinalis]
          Length = 494

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/216 (30%), Positives = 103/216 (47%), Gaps = 31/216 (14%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG---FLKSWVDSK 140
           L S V LTK    L+  ++Y D+K+ +FNKP G+ +  G G    +     FL   V   
Sbjct: 150 LLSDVRLTK---LLRKNVIYADNKLVIFNKPYGLPMHDGDGTKQTVKNVLPFLSKMVYGI 206

Query: 141 GQK-P-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               P  L HRLD+ T+GI + +     A ++   FR RR+ + Y ++V G P+  K  +
Sbjct: 207 NTDIPLHLCHRLDKNTTGITICSTDAEMADYVMGLFRQRRVLRKYLAVVVGEPEPMK-GV 265

Query: 199 ANWLLKKSHIGGDYVH------VVKQNEK--------------GANYAISHFKVIDCFAQ 238
            +  + +S +            ++K + +              G + AI+H++ ID    
Sbjct: 266 VDMPMSESIVSATKSTKRHSRMIIKPDVRYDDATGKEYPLRNAGGHTAITHYRTIDTTGD 325

Query: 239 KFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYC 273
               +E+QP T   HQLRVH A  + CPI+GDHKY 
Sbjct: 326 -LSLVELQPQTTVKHQLRVHMADGLSCPILGDHKYS 360


>gi|162451431|ref|YP_001613798.1| pseudouridylate synthase/ribosomal large subunit pseudouridine
           synthase D [Sorangium cellulosum 'So ce 56']
 gi|161162013|emb|CAN93318.1| Pseudouridylate synthase/ribosomal large subunit pseudouridine
           synthase D [Sorangium cellulosum 'So ce 56']
          Length = 350

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 82/340 (24%), Positives = 146/340 (42%), Gaps = 45/340 (13%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V  + V  +   MRLDR+ +      +     +I+  G    + +R++ ++R++  Q 
Sbjct: 32  SVVTVLRVPPESAGMRLDRFVQTQLKRTSRTRAAEIVARGAYSPEARRLRGSDRVRPEQC 91

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +        L     +++  D+ + +           L+ED  +   +KPAG+ V   + 
Sbjct: 92  I-------LLWREPWDEQAPDTPIPV-----------LHEDDALLAIDKPAGLPVHPTA- 132

Query: 125 IAYHIDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKI 182
             YH    +K    ++ G++  L HRLD+ETSG+L++ RT  A + +   F  R  + K 
Sbjct: 133 -RYHKSTVIKMMEAARPGERLFLAHRLDRETSGVLLLCRTPEADRTVKAQFEERTGVVKR 191

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF------KVIDCF 236
           Y ++ WG P  +++     L  +      Y   ++    G   A +        +     
Sbjct: 192 YAAIAWGWP--ERDTFRVELPLELDDASRYKVKMRVAPPGRGLASATACEVLGRRADPLT 249

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY------- 289
            +++  +     TGR HQ+RVH    G P+VGD  Y  + +G F       L        
Sbjct: 250 GRRYALVRCTLETGRQHQIRVHLAASGLPLVGDKLYGPD-EGMFARGADGVLTDDDRRAL 308

Query: 290 ------LHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                 LHA  ++L HP  G R++I APL   +   WD+L
Sbjct: 309 ELDRHALHAALLELTHPMTGERVRIEAPLSDDLRTFWDAL 348


>gi|203283948|ref|YP_002221688.1| ribosomal large subunit pseudouridine synthase D [Borrelia duttonii
           Ly]
 gi|201083391|gb|ACH92982.1| ribosomal large subunit pseudouridine synthase D [Borrelia duttonii
           Ly]
          Length = 326

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 114/240 (47%), Gaps = 30/240 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  + V  KP GI    G         + + +HI      + ++K  +P + HRLD
Sbjct: 86  ILYEDINVIVIEKPQGILSHPGISNLENTVVNFLLHHISNLRYKFQENK-IRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG+++ A+       L E F+ R ++K+Y ++V G  K     I  ++ +  +    
Sbjct: 145 KETSGVMICAKNLETLNFLFEQFKNRSVKKVYIAIVKGNFKVDSGIIDTFIDRDRYDRKK 204

Query: 212 Y-VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           + VH     +     A++ +KV+    + +  + +QP TGRTHQLRVH  ++  PI+GD 
Sbjct: 205 FTVH-----KNSGKRALTEYKVL-ISMKNYSLVVLQPKTGRTHQLRVHMKYLNHPILGDD 258

Query: 271 KYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            Y      FK       +  L LH+  +++   EG   +  + LP   +   D L   YD
Sbjct: 259 IYSRLDQEFK-------EISLMLHSFKLEISIKEGFLKKFISVLPKRFI---DFLSNFYD 308


>gi|292487216|ref|YP_003530088.1| tRNA pseudouridine synthase C [Erwinia amylovora CFBP1430]
 gi|292900409|ref|YP_003539778.1| tRNA pseudouridylate synthase C [Erwinia amylovora ATCC 49946]
 gi|291200257|emb|CBJ47385.1| tRNA pseudouridylate synthase C [Erwinia amylovora ATCC 49946]
 gi|291552635|emb|CBA19680.1| tRNA pseudouridine synthase C [Erwinia amylovora CFBP1430]
          Length = 255

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 117/242 (48%), Gaps = 21/242 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  +   NKP+G+ V   S +  H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 4   IIYQDRWLVAVNKPSGMLVHR-SWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A +   A  L++ F   ++QK Y ++V G  +           ++  I   +     Q 
Sbjct: 63  MALSSEVAHLLSQQFERHQLQKTYHAVVRGWLEGADTLDYPLTEERDKIADKF----SQP 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           EK    A++H++ +               ++  +EMQP +GR HQLR H  H+  PI+GD
Sbjct: 119 EKAPQPAVTHWRGVATAELAVPIGRYETSRYSLVEMQPESGRKHQLRRHMTHLRHPIIGD 178

Query: 270 HKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
             +  + K N ++      N+L LHA  ++L HP   G L + A L A   K  +  G++
Sbjct: 179 SAH-GDLKQNRSAAANFGINRLMLHASELNLTHPVTAGPLILRAGLDAVWQKVINQFGWQ 237

Query: 326 YD 327
            +
Sbjct: 238 AE 239


>gi|257438386|ref|ZP_05614141.1| pseudouridine synthase, RluA family [Faecalibacterium prausnitzii
           A2-165]
 gi|257199217|gb|EEU97501.1| pseudouridine synthase, RluA family [Faecalibacterium prausnitzii
           A2-165]
          Length = 365

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 83/332 (25%), Positives = 153/332 (46%), Gaps = 27/332 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q+    NDE  +RL R+ ++    +    L K  R+ +V+V+ K+    +R+++G ++ +
Sbjct: 32  QFTATANDE-GVRLSRFVQSVTRDLPTSLLYKSFRNKRVKVNGKKGAPEDRLKAGDLIEL 90

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIA 126
              IN      +  K         K  +  K  ++YED  I V  KP  +      +G A
Sbjct: 91  --YINDEFFPPEGAKPAARKPAPKKQQNQPKVTVIYEDENIAVLYKPTHLLCHSDRTGDA 148

Query: 127 YHIDGFL-----KSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             +D F      K   D+ G+   KP + +RLD+ T G+++ A++ AA + + E  R   
Sbjct: 149 NLVDAFTQYLAQKGEYDAGGENRFKPGICNRLDRGTEGLVIAAKSYAALRDMNEIIRTDL 208

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y+++  GIP++ +     W           +H  +  ++     I+   V+   A 
Sbjct: 209 LKKEYYTITVGIPQSGR--FTAWWEHDEKNNKVSIHAHQSQDERRKQIITDVDVLRT-AG 265

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR--YMD 296
            F   ++   TGRTHQ+R H  ++G P++GD KY  N K N  +  + +     R  ++D
Sbjct: 266 PFALCKIGLVTGRTHQIRAHLAYLGKPVLGDIKY-GNRKMNERTGTRTQALCAVRISFLD 324

Query: 297 LPHP------EGGRLQITAPLPAHMVKTWDSL 322
           +P         G  +++  P    +VK +D+L
Sbjct: 325 IPEENSLRYLSGKVIKLKDP---QIVKQFDAL 353


>gi|291514879|emb|CBK64089.1| ribosomal large subunit pseudouridine synthase D [Alistipes shahii
           WAL 8301]
          Length = 228

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 103/224 (45%), Gaps = 14/224 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
           F    +LYED+ + + NK  G  VQ        ++  +K+++  +  KP      + HR+
Sbjct: 2   FNPDDILYEDNHLLIVNKRCGDLVQPDPSGESALEDQIKAFIKRRDAKPGEVFLGVVHRI 61

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+  SG +V A+T  A   L E  R  RI K+YW+L    P  +   + +++L+      
Sbjct: 62  DRPVSGAVVFAKTSKALVRLNEMIREGRIHKVYWALTEATPDPESGELRHYILRDGRT-- 119

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +        +  A  A   +  +      +  +E++  TGR HQ+R     +GCPI GD 
Sbjct: 120 NRSRACDAPKGDAKEARLRYATLGA-GTNYTLVEVELLTGRHHQIRAQLSKIGCPIRGDL 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           KY     G   S     + LH+R ++  HP     L +TAP+PA
Sbjct: 179 KY-----GARRSLPGGGISLHSRRVEFEHPVRREPLSVTAPVPA 217


>gi|312872998|ref|ZP_07733058.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
 gi|325912701|ref|ZP_08175084.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
 gi|311091520|gb|EFQ49904.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
 gi|325478122|gb|EGC81251.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
          Length = 311

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 73/301 (24%), Positives = 139/301 (46%), Gaps = 38/301 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+++E  +RLD++   H   I+   +Q++++   +  +  + K + ++ +   + I  
Sbjct: 9   LVVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNGLQTKLSYKVNTNDKINIE- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                         + S   L+   + L   ++YED  + V NKP G+ V   +G     
Sbjct: 68  --------------IPSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHT 113

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH     K     +  +P + HR+D++TSG+L++A+   A   L +    +  +
Sbjct: 114 LVNGLIYHTKNLAKC---DEIFRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINK 170

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V    K+    I +  + ++      + VV   +K    AI+HF V++ F   +
Sbjct: 171 REYIAIVHANFKHSSGVI-DAPIGRNPYQRQQMAVVASGKK----AITHFTVLEQFP-GY 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             ++    TGRTHQ+RVH  ++G PI GD  Y      N      N  +LHA+ +   HP
Sbjct: 225 SLVKCVLETGRTHQIRVHMSYIGHPIAGDPLYGPKKTLN-----GNGQFLHAKTLGFYHP 279

Query: 301 E 301
           +
Sbjct: 280 K 280


>gi|332307059|ref|YP_004434910.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332174388|gb|AEE23642.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 233

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 121/243 (49%), Gaps = 32/243 (13%)

Query: 81  QKILDSSV--NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------SGIAYHIDGF 132
           QKI+++ +  +      F    +LY+D  +   NKP+G+    G        + Y I   
Sbjct: 7   QKIVETPIVDSFIAPPCFEAVTVLYQDDYLLAVNKPSGLLSLSGKNPLNKDSVHYRIVKQ 66

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             + +        + HRLD  TSG+L++A  + +   LT+ F+ R ++K Y ++++G  +
Sbjct: 67  FPTAL--------MAHRLDFGTSGVLLLALDKKSNGELTKQFQARSVKKRYSAVLFGKVQ 118

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKF-CWLEMQPH 248
           +++  ++        I  D  +  +Q    E+G   AISH++VI+         +E  P 
Sbjct: 119 DREGRVS------VPIAKDPANFPRQKICFEQGKE-AISHYRVIEYLENPPRTHVEFTPE 171

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQLR+H+L MG PI+G    C  +  + +  +  +L LHA +++  HP   + + I
Sbjct: 172 TGRTHQLRIHSLAMGHPILG----CDLYANDQSEQLAERLLLHASWIEFLHPHSNQPMTI 227

Query: 308 TAP 310
            AP
Sbjct: 228 EAP 230


>gi|238752280|ref|ZP_04613760.1| Ribosomal large subunit pseudouridine synthase A [Yersinia rohdei
           ATCC 43380]
 gi|238709548|gb|EEQ01786.1| Ribosomal large subunit pseudouridine synthase A [Yersinia rohdei
           ATCC 43380]
          Length = 218

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 70/207 (33%), Positives = 104/207 (50%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G    A      + + + +        HRLD  TSG++V
Sbjct: 15  ILYQDEHIMVVNKPSGLLSVPGR---APENKDSIMTRILADFPTAESVHRLDMATSGVMV 71

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ 
Sbjct: 72  VALTKAAERELKRQFREREPKKSYVARVWGHLAQDEGLIDLPLI------CDWPNRPKQK 125

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + + + ++V+   A     +++ P TGR+HQLRVH L +G PI+GD  Y    
Sbjct: 126 VCYETGKS-SQTEYQVLSRDADGSTRVQLSPITGRSHQLRVHMLSIGHPILGDGFYAPPE 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
                S    +L LHA+ + + HPE G
Sbjct: 185 AKAMAS----RLQLHAQELYITHPELG 207


>gi|227872635|ref|ZP_03990967.1| RluA protein [Oribacterium sinus F0268]
 gi|227841522|gb|EEJ51820.1| RluA protein [Oribacterium sinus F0268]
          Length = 340

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 78/332 (23%), Positives = 148/332 (44%), Gaps = 28/332 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++  +E+  +L +  + ++       L K+LR   + ++ K+      ++ G  V++  
Sbjct: 4   ILISQNEKEQKLLKLLQKYFKGQADSFLYKMLRKKNILLNGKKADGKEILRLGDTVQLYF 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
              +L  +I+E++  +  +   K  +F+    LYED    +FNKP G+  +     ++ +
Sbjct: 64  SEESLGKLIQERESGEKELWTQKWQNFI----LYEDKHCILFNKPVGLLSENDGSSSFSV 119

Query: 130 DGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           +  L S++ +KG+         +P + +RLD+ TSGI++  ++    Q   +  +   ++
Sbjct: 120 NSLLLSYMRTKGELSKEQEKSFRPGIANRLDRNTSGIIIFGKSLGGLQAFAKLLQSHDLE 179

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y++LV+G    +K  +    L+K    G    +  +  K    A      ++      
Sbjct: 180 KKYYALVYG--DFQKTGMQEHFLEKDK--GQNKALESERGKRVKSAFEKLACVESSVGSL 235

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDL 297
             L +Q  TG+THQ+R     +  PIVGD KY     N +   T P+  +L LHA  +  
Sbjct: 236 SLLSVQIFTGKTHQIRTQLSLLSHPIVGDDKYGDTRKNARLRKTLPLSYQL-LHAYSLRF 294

Query: 298 PH-PEGGRL------QITAPLPAHMVKTWDSL 322
           P  PE   L         APLP    +   S 
Sbjct: 295 PKLPESSVLFSLSEKCFFAPLPKEYFEILKSF 326


>gi|218198893|gb|EEC81320.1| hypothetical protein OsI_24484 [Oryza sativa Indica Group]
          Length = 445

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 93/379 (24%), Positives = 150/379 (39%), Gaps = 84/379 (22%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V   E   R+D W                 R G   V + R++ +  I++G VV     
Sbjct: 64  AVPAGEGRSRIDAWIS--------------ARLGGGGVSRARIQAS--IRAGLVVVNGRP 107

Query: 71  INALNHIIKEQKILDSSVN----LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           ++ ++H++K   I+  +V+    L    + +   ++YED  + V NKPA + V    G  
Sbjct: 108 VSKVSHMVKGGDIVSCTVSELQPLRAEPEDIPLDIVYEDDHLLVVNKPAHMVVHPAPGNA 167

Query: 125 -------IAYH-------------ID---------------------GFLKSWVDSKGQK 143
                  I +H             ID                     G + S V     +
Sbjct: 168 NGTLVNAILHHCKISTFTCLARNSIDDECPDSSDDDIDVFDIDQFTTGEVSSEVREALVR 227

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD+ TSG+LVVA+   +   L E F++  I+++Y SL  G P      I   + 
Sbjct: 228 PGIVHRLDKGTSGLLVVAKDEHSHAQLAEQFKLHTIRRVYISLTCGAPNPNSGRIEVPIA 287

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHM 262
           +  +     +       + A +A S +KV + FA     L E +  TGRTHQ+R HA ++
Sbjct: 288 RDPNNRIRMIATPGSGHRYARHAASRYKVREVFAGGGSALVEWRLETGRTHQIRAHAKYL 347

Query: 263 GCPIVGDHKYCANFK------------------GNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G P++GD  Y                        N  S I ++  LHA  +   HP  G+
Sbjct: 348 GIPLLGDETYGGTKSMALSLLRPRTPSRYHCDLSNMISKI-DRPCLHAALLGFKHPHSGK 406

Query: 305 -LQITAPLPAHMVKTWDSL 322
            L+ + P P    +  + L
Sbjct: 407 ILEFSCPPPDDFTEVLNEL 425


>gi|134102271|ref|YP_001107932.1| ribosomal large subunit pseudouridine synthase [Saccharopolyspora
           erythraea NRRL 2338]
 gi|291003766|ref|ZP_06561739.1| ribosomal large subunit pseudouridine synthase [Saccharopolyspora
           erythraea NRRL 2338]
 gi|133914894|emb|CAM05007.1| ribosomal large subunit pseudouridine synthase [Saccharopolyspora
           erythraea NRRL 2338]
          Length = 310

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 81/334 (24%), Positives = 148/334 (44%), Gaps = 44/334 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ ++ + V +  + MR+D         ++   +  +  SG V +D      ++R+ +G 
Sbjct: 1   MSGLRTLPVPDGLDGMRVDAGLSKLL-GLSRTIVAGLAESGDVVLDGTPAGKSDRLVAGA 59

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-- 119
              V +PP    L  +    + L                +L++D  I V +KP G++V  
Sbjct: 60  WLEVTLPPAEQPLEVVAVPVEGLR---------------ILHQDDDIVVVDKPIGVAVHP 104

Query: 120 ----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
               +G + +       ++       ++  + HRLD  T+G++VVA++  A   L  +F+
Sbjct: 105 SPGWEGPTVVGGLAAAGVRIATSGASERQGVVHRLDAGTTGVMVVAKSEHAYSTLKRAFK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y +LV G P   +  I   + +  H   DY   V     G   +I+H++ ++ 
Sbjct: 165 ERTVDKRYHALVQGHPDPSRGTIDAPIDR--HPRHDYKFAVV---AGGKPSITHYETVEA 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI------QNKLY 289
           F +    ++++  TGRTHQ+RVH   +  P VGD  Y A+       P+       ++ +
Sbjct: 220 F-RAASLVDVKLETGRTHQIRVHFAAVRHPCVGDLTYGAD-------PVLARRVGLSRQW 271

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           LHAR +   HP  GR +   +  PA +    D L
Sbjct: 272 LHARSLGFEHPSDGRWVSFDSDYPADLAHAVDVL 305


>gi|317132480|ref|YP_004091794.1| pseudouridine synthase, RluA family [Ethanoligenens harbinense
           YUAN-3]
 gi|315470459|gb|ADU27063.1| pseudouridine synthase, RluA family [Ethanoligenens harbinense
           YUAN-3]
          Length = 334

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 74/282 (26%), Positives = 128/282 (45%), Gaps = 31/282 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           + V  ND   +R+D++     P +    L K +R  +++V   R   + R+  G  V + 
Sbjct: 4   FTVGPNDA-GLRVDKFVAKVAPRLPQALLYKYIRLKRIKVGGGRAAISQRLAVGDRVEL- 61

Query: 69  PVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSG 124
                LN    E+K     D+   +          +LYED  I + +K  G+ V +  SG
Sbjct: 62  ----YLNDEFFEEKAATFFDAPTEVD---------ILYEDENILIADKKPGLVVHEDESG 108

Query: 125 IAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            A  + G ++  +  +G+          P L +R+D+ T GI++ A+   A + L E  +
Sbjct: 109 SADTLIGRIQHLLYDRGEYDPERENAFAPALCNRIDRNTGGIVLAAKNAPALRVLNEKIK 168

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R ++K Y  +V G  + + + I  W +K        V V  +   G   A++ ++V+D 
Sbjct: 169 ARELRKQYLCVVHGRMERRNDTITTWQVKDET--EKKVRVYDRPVPGGLTAVTRYRVLDE 226

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                  LE+   TGRTHQ+R    H+G P++GD KY  N +
Sbjct: 227 -QDTLSLLEVDLVTGRTHQIRATFAHIGHPLLGDGKYGDNAR 267


>gi|227327724|ref|ZP_03831748.1| ribosomal large subunit pseudouridine synthase A [Pectobacterium
           carotovorum subsp. carotovorum WPP14]
          Length = 217

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 71/204 (34%), Positives = 105/204 (51%), Gaps = 18/204 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  + S + +        HRLD  TSG++ 
Sbjct: 14  ILYQDQHIMVVNKPSGLLSVPGRA--PEHKDSVM-SRIQADYPTAESVHRLDMATSGVIA 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPKKSYLARVWGHMAQDEGVIDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G   A + ++V+   A     +++ P TGR+HQLRVH L +G PI+GD  Y A+ 
Sbjct: 125 VCFETG-KAAQTEYQVLSRDADGTTRVKLMPITGRSHQLRVHLLALGHPILGDGFY-AHP 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                +P   +L LHA+ + + HP
Sbjct: 183 DAKALAP---RLLLHAQELAITHP 203


>gi|225019205|ref|ZP_03708397.1| hypothetical protein CLOSTMETH_03158 [Clostridium methylpentosum
           DSM 5476]
 gi|224948057|gb|EEG29266.1| hypothetical protein CLOSTMETH_03158 [Clostridium methylpentosum
           DSM 5476]
          Length = 322

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 68/277 (24%), Positives = 134/277 (48%), Gaps = 22/277 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  ++++++   RLD++       +    L K +R  +++++ KR   +  ++ G +V
Sbjct: 11  FMKSFLIDSNDAGQRLDKFVVKVTSGLPKGMLYKAVRKKRIKLNHKRCDCSAMLREGDLV 70

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG---- 121
            +   +N  +    +Q   D + +  K    L   ++YEDS I + +KP G+ V      
Sbjct: 71  EL--YLN--DEFFPKQ---DETFSFLKAPASLS--IVYEDSNILLVDKPVGLRVHSDRAA 121

Query: 122 -GSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
               +   I  +L    +   +K     P L +R+D+ T GI++ A+   A + L E  +
Sbjct: 122 DSDSLVARIQHYLYQKQEYNPEKEHSFAPALCNRIDRNTQGIVIAAKNAPALRILNEKIK 181

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R ++K Y  +V GIP+ +   +  +  K S      V    Q+  G +  ++ + V+  
Sbjct: 182 QRELEKYYLCVVHGIPQPRHAVLTGYWSKDSRRNKALVRDTPQD--GFHEIVTEYTVLRP 239

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +   +E++ HTGR+HQ+R H  H+G P+VGD KY
Sbjct: 240 GVHE-SLVEVRLHTGRSHQIRAHMAHIGHPLVGDAKY 275


>gi|261880461|ref|ZP_06006888.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bergensis DSM 17361]
 gi|270332800|gb|EFA43586.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bergensis DSM 17361]
          Length = 306

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 114/239 (47%), Gaps = 17/239 (7%)

Query: 87  SVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ- 142
           +V+ TK ++ LKS    ++YED+ I V  K  GI        + ++   L  +     Q 
Sbjct: 78  AVSKTKRNNTLKSRYVKIVYEDAYIIVVEKNVGILSMPAGHHSLNVKAVLDEYFHKTKQP 137

Query: 143 -KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +  + HRLD++TSG+++ A+ +     L   ++     + Y ++V G+ +  +  I +W
Sbjct: 138 CQAHVVHRLDRDTSGLMIYAKDKKTEFSLQADWKGTVYDRRYVAVVSGVMEQDEGTIDSW 197

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L         Y       + G  YA++HF  +D   Q    +E +  TGR +Q+RVHA  
Sbjct: 198 LKDNK----SYFSYSSSTDNGGKYAVTHFYTLDRSPQ-HSLVEFKLDTGRKNQIRVHAAD 252

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           MG P+ GD KY     GN   PI  +L LHA  +   HP     ++  A +P + ++ +
Sbjct: 253 MGHPVCGDPKY-----GNGDDPI-GRLCLHAYVLCFYHPVTHEPMEFQARIPQNFIQLF 305


>gi|284030831|ref|YP_003380762.1| pseudouridine synthase, RluA family [Kribbella flavida DSM 17836]
 gi|283810124|gb|ADB31963.1| pseudouridine synthase, RluA family [Kribbella flavida DSM 17836]
          Length = 309

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 83/333 (24%), Positives = 151/333 (45%), Gaps = 42/333 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + ++V +     RLD      +  ++     +++ +G V+VD      + R+ +G 
Sbjct: 1   MSDSRTLMVPDGLAGERLDAALSRLF-GVSRTKAAELIEAGLVQVDGAPAAKSARVSAGV 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ +      L     E  ++  +V   +        ++++D +I V +KP G++     
Sbjct: 60  LLDV-----ELPAPPGEVTVVPETVENLR--------IVHDDDEIVVVDKPVGVAAHPSP 106

Query: 124 G-----IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G     +  H+ G   S + + G   R  + HRLD  TSG++VVA+T  +   L  +F+ 
Sbjct: 107 GWTGPTVIGHLAGAGFS-ISTSGAAERKGIVHRLDVGTSGLMVVAKTEYSYTVLKRAFKE 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R ++KIY +LV G P      +   + +  H   DY   V     G   +I+H++ ++ F
Sbjct: 166 RTVKKIYHALVQGHPDPFTGTVDAPIDR--HPNHDYKFGVV---AGGKPSITHYETLEAF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI------QNKLYL 290
            +    LE+   TGRTHQ+RVH   +G P  GD  Y A+       P+       ++ +L
Sbjct: 221 -RYATLLEITLETGRTHQIRVHMSAIGHPCCGDLTYGAD-------PVLAERLELSRQWL 272

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           HA  +   HP  G   + T+  P  + +  D L
Sbjct: 273 HAMRLGFTHPGSGEYTEFTSQYPDDLDQALDRL 305


>gi|261207216|ref|ZP_05921905.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289566649|ref|ZP_06447067.1| pseudouridine synthase [Enterococcus faecium D344SRF]
 gi|293557194|ref|ZP_06675744.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1039]
 gi|294614335|ref|ZP_06694252.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1636]
 gi|260078844|gb|EEW66546.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289161549|gb|EFD09431.1| pseudouridine synthase [Enterococcus faecium D344SRF]
 gi|291592807|gb|EFF24399.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1636]
 gi|291600646|gb|EFF30948.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1039]
          Length = 285

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 67/206 (32%), Positives = 102/206 (49%), Gaps = 25/206 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + + +KPAG+            +   L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLHEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A+       L      + I + Y ++VWG        IA  +   + IG D     K+ 
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWG-------EIAKDMTITNKIGRDRHDRRKRV 195

Query: 219 -NEKGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            ++K    A++H    KV+    Q +C LE    TGRTHQ+RVH  H G PIVGD  Y  
Sbjct: 196 VDDKNGQSALTHVTVNKVLSEQTQVYCVLE----TGRTHQIRVHLAHKGHPIVGDPLY-- 249

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
               N T+    +L LHA  + + HP
Sbjct: 250 ---QNRTA---ERLMLHALELHMIHP 269


>gi|332654861|ref|ZP_08420603.1| ribosomal large subunit pseudouridine synthase D [Ruminococcaceae
           bacterium D16]
 gi|332516204|gb|EGJ45812.1| ribosomal large subunit pseudouridine synthase D [Ruminococcaceae
           bacterium D16]
          Length = 301

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 82/314 (26%), Positives = 138/314 (43%), Gaps = 39/314 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++   E   RLD +  +    +     Q++L  G V    K +K N +   G VV +  
Sbjct: 4   LILTAQEGGERLDAFVASQVEDLTRSAAQRLLEQGAVTSGGKPLKKNAKTTPGMVVEVLL 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  I+ +   LD               ++YED  + V NKP G+ V    G   H 
Sbjct: 64  PDPQPVEIVPQNIPLD---------------VVYEDDDVIVVNKPVGLVVHPAPG---HP 105

Query: 130 DGFL---------KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           DG L          S     G+ +P + HR+D++TSG+++ A+   A   L    +   +
Sbjct: 106 DGTLVNALLYHCGDSLSGINGELRPGIVHRIDRDTSGLIIAAKNDRAHLALAAQLQDHTL 165

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            ++Y ++  G  K  +  + N  + +  +    + V   + KG   A++H+KV+  +   
Sbjct: 166 ARVYEAVAVGGFKEDRGTV-NAPIGRHPVDRKKMAV---DPKG-RPAVTHWKVLGRYP-G 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              LE +  TGRTHQ+RVH  ++G P++GD  Y A        P      LHAR +   H
Sbjct: 220 CTHLECRLETGRTHQIRVHMAYLGHPLLGDTVYGAKKP----VPGLAGQCLHARRLRFIH 275

Query: 300 PEGGR-LQITAPLP 312
           P  G+ +++  PLP
Sbjct: 276 PTTGQPVEVECPLP 289


>gi|300724802|ref|YP_003714127.1| pseudouridine synthase [Xenorhabdus nematophila ATCC 19061]
 gi|297631344|emb|CBJ92039.1| pseudouridine synthase [Xenorhabdus nematophila ATCC 19061]
          Length = 250

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 113/239 (47%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I   NKPAG  V   S +A H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 4   IIYQDEHIVAVNKPAGWLVHR-SWLARHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A +   A+ L++ F    IQK Y ++V G  +         + +   I   +       
Sbjct: 63  MALSSEVARTLSQQFEFHDIQKTYHAVVRGYVEGDDIIDYALMEQLDKIADKFA----DT 118

Query: 220 EKGANYAISHFKV---IDCFAQ-------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           ++ A  AI+H++    ++C  +       +F  LE+ P TGR HQLR H  H+  PI+GD
Sbjct: 119 DREAQSAITHYRPLAKVECPVEIGRYSTSRFSLLELMPKTGRKHQLRRHMAHIRHPIIGD 178

Query: 270 --HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
             H      +G        +L LHA ++ L HP  G  L +TA         ++  G+K
Sbjct: 179 TTHGDLRQNRGVDKYYQTGRLMLHASHLQLKHPVTGDDLILTARWDTSWQHLFEQFGWK 237


>gi|240144135|ref|ZP_04742736.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis L1-82]
 gi|257203836|gb|EEV02121.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis L1-82]
 gi|291538917|emb|CBL12028.1| Pseudouridylate synthases, 23S RNA-specific [Roseburia intestinalis
           XB6B4]
          Length = 329

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 79/337 (23%), Positives = 148/337 (43%), Gaps = 46/337 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  +E   R D++ K    +     + K+LR   + ++ K+     ++  G  +++    
Sbjct: 6   INENEAGQRFDKYLKKLLGNAPGSFIYKMLRKKNITLNGKKADGTEKLNQGDDIKL---- 61

Query: 72  NALNHIIKEQKILDSSVNLTKHSDF--LKSI------------LLYEDSKIYVFNKPAGI 117
                   ++     S + T  S+F  LK +            ++YED  +   NKP G+
Sbjct: 62  -----FFSDETFEKFSGSGTPDSEFEALKVLSREFTSGKRKLPVVYEDKDVIFINKPTGM 116

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQ 168
             Q         + ++ +++ +KG+         +P + +RLD+ TSG+L   +T    Q
Sbjct: 117 LSQKAKPEDISANEYILAYLIAKGELTESSFRTFRPSICNRLDRNTSGLLAAGKTLKGLQ 176

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            + ++ + R +QK Y  +V G  K +   +  +L K        +   K +E       +
Sbjct: 177 EMAKALKERSVQKYYRCIVKGTVK-EASYLKGYLQKDESSNQVLIRRTKPSEGEWLPIET 235

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSP 283
            +K I C    +   E+   TGR+HQ+R H   +G PI+GD+KY  +     FK N  + 
Sbjct: 236 EYKPIRCMGG-YTEFEVHLMTGRSHQIRAHLASIGHPIIGDYKYGDSGVNVYFKKN--AR 292

Query: 284 IQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           I ++L   +R++     E GR +ITAP  A   + W+
Sbjct: 293 ITSQLLHASRFV----FEDGR-EITAPCGAEFERAWN 324


>gi|301511962|ref|ZP_07237199.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) protein [Acinetobacter
           baumannii AB058]
          Length = 221

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 71/209 (33%), Positives = 107/209 (51%), Gaps = 22/209 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ 
Sbjct: 18  ILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R ++K Y +LV G  K +       I +W  +   I    VH  
Sbjct: 76  AKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLITDWENRPRQI----VHF- 130

Query: 217 KQNEKGANYAISHFK--VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              E G  +A + F+  V D    +   L ++P TGR+HQLRVH +H+G PI+GD  Y  
Sbjct: 131 ---ELG-KHAKTLFQPLVYDATTDQSRVL-LEPVTGRSHQLRVHMMHIGHPIMGDKLYHP 185

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             K        N++ LHA Y+   HP  G
Sbjct: 186 EPKRFHL----NRMALHAAYLAFQHPLKG 210


>gi|260914045|ref|ZP_05920518.1| ribosomal large subunit pseudouridine synthase C [Pasteurella
           dagmatis ATCC 43325]
 gi|260631678|gb|EEX49856.1| ribosomal large subunit pseudouridine synthase C [Pasteurella
           dagmatis ATCC 43325]
          Length = 220

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 69/197 (35%), Positives = 98/197 (49%), Gaps = 26/197 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG---FLKSWVDSKGQKPR--LTHRLDQETS 155
           ++Y+ S   V +KP  ISV        H D     L S V  +   P+  L HRLD+ TS
Sbjct: 6   IVYQHSDFIVIDKPTNISV--------HKDAEKIGLTSLVAQQLNVPQVWLVHRLDKVTS 57

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A  + AA  L+  F   RIQK Y +L    PK K+  I    ++K+  G   +  
Sbjct: 58  GLLILALNQNAASELSRLFAEHRIQKTYLALSTQKPKKKQGLIIGD-MEKARRGAWKLCT 116

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            KQN      AI+ F  ++C      ++ ++P TG+THQLRV    +G PI+GD  Y  N
Sbjct: 117 TKQNP-----AITRFYSVNCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDALYGGN 170

Query: 276 FKGNFTSPIQNKLYLHA 292
           F         N+ YLHA
Sbjct: 171 FDK------VNRTYLHA 181


>gi|184156437|ref|YP_001844776.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|215485059|ref|YP_002327300.1| RNA pseudouridylate synthase family protein [Acinetobacter
           baumannii AB307-0294]
 gi|239503104|ref|ZP_04662414.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) protein [Acinetobacter
           baumannii AB900]
 gi|260557648|ref|ZP_05829862.1| pseudouridylate synthase [Acinetobacter baumannii ATCC 19606]
 gi|332853596|ref|ZP_08434848.1| pseudouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332869273|ref|ZP_08438684.1| pseudouridine synthase A [Acinetobacter baumannii 6013113]
 gi|332875566|ref|ZP_08443379.1| pseudouridine synthase A [Acinetobacter baumannii 6014059]
 gi|183208031|gb|ACC55429.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|193075994|gb|ABO10578.2| dual specificity pseudouridine synthase [Acinetobacter baumannii
           ATCC 17978]
 gi|213988186|gb|ACJ58485.1| RNA pseudouridylate synthase family protein [Acinetobacter
           baumannii AB307-0294]
 gi|260408821|gb|EEX02125.1| pseudouridylate synthase [Acinetobacter baumannii ATCC 19606]
 gi|323516174|gb|ADX90555.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter
           baumannii TCDC-AB0715]
 gi|332728560|gb|EGJ59933.1| pseudouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332732830|gb|EGJ64044.1| pseudouridine synthase A [Acinetobacter baumannii 6013113]
 gi|332736269|gb|EGJ67283.1| pseudouridine synthase A [Acinetobacter baumannii 6014059]
          Length = 221

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 71/209 (33%), Positives = 107/209 (51%), Gaps = 22/209 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ 
Sbjct: 18  ILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R ++K Y +LV G  K +       I +W  +   I    VH  
Sbjct: 76  AKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLITDWENRPRQI----VHF- 130

Query: 217 KQNEKGANYAISHFK--VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              E G  +A + F+  V D    +   L ++P TGR+HQLRVH +H+G PI+GD  Y  
Sbjct: 131 ---ELG-KHAKTLFQPLVYDATTDQSRVL-LEPVTGRSHQLRVHMMHIGHPIMGDKLYHP 185

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             K        N++ LHA Y+   HP  G
Sbjct: 186 EPKRFHL----NRMALHAAYLAFQHPLKG 210


>gi|157150847|ref|YP_001450507.1| 23S rRNA pseudouridine synthase [Streptococcus gordonii str.
           Challis substr. CH1]
 gi|157075641|gb|ABV10324.1| 23S rRNA pseudouridine synthase [Streptococcus gordonii str.
           Challis substr. CH1]
          Length = 295

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 120/231 (51%), Gaps = 27/231 (11%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDS--KGQKPRLTHRLDQET 154
           +++ED    + +KPAG+    SV   + +A ++  +   ++DS  +  +  +  RLD++T
Sbjct: 78  VVFEDDHFLILDKPAGVASIPSVNHSNTMANYVKAY---YIDSGYENHQVHIVTRLDKDT 134

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDY 212
           SG+++ A+   A   L +  + R I+K Y +LV G  + + + E I      +  I    
Sbjct: 135 SGLMLFAKHGYAHARLDKQLQKRAIEKRYLALVKGDGLLEKEGEIILPIARDEDSI---- 190

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             + ++  KG  YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y
Sbjct: 191 --ITRRVAKGGKYAHTSYKVIEQFGNIYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLY 247

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA---HMVKTW 319
                G+ T  I  +  LH   +   +P  G  +   +PLP    H+++T+
Sbjct: 248 G----GSLTEGISRQA-LHCHTLKFYNPFSGEEIGRASPLPTDFEHVIQTF 293


>gi|153812383|ref|ZP_01965051.1| hypothetical protein RUMOBE_02782 [Ruminococcus obeum ATCC 29174]
 gi|149831545|gb|EDM86632.1| hypothetical protein RUMOBE_02782 [Ruminococcus obeum ATCC 29174]
          Length = 293

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 65/223 (29%), Positives = 110/223 (49%), Gaps = 16/223 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQK-P-RLTHRLDQETSGI 157
           +LYED  I V NKPA + V    G     +   + +++++KG+  P R  +RLD++TSG 
Sbjct: 83  VLYEDEDILVVNKPADMPVHPSLGNYTNTLANGVAAYLETKGESCPFRCINRLDRDTSGA 142

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+   +A  L+   R R+I + Y ++V GIP+      A           D V   +
Sbjct: 143 LILAKNALSAAILSVQMRNRQISRTYLAVVEGIPRQSGTISAPI-----SRAADSVIERR 197

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +    AI+H+++++        LE+   TGRTHQ+RVH  ++G P+  D+ Y   + 
Sbjct: 198 IDFENGESAITHYQLLE-VKNNHSLLEIHLETGRTHQIRVHMGYIGHPLPADYLYNPVYD 256

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
                P      LH+  +   HP  G  + + AP+P  M   +
Sbjct: 257 TFKRQP------LHSLQLKFCHPITGTPMCLMAPVPEDMSNAF 293


>gi|73662884|ref|YP_301665.1| pseudouridylate synthase [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72495399|dbj|BAE18720.1| putative pseudouridylate synthase [Staphylococcus saprophyticus
           subsp. saprophyticus ATCC 15305]
          Length = 305

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 71/269 (26%), Positives = 134/269 (49%), Gaps = 30/269 (11%)

Query: 12  VENDEEN-MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +EN E+   R+D+    ++   +   +Q  +++  V+V+ + +K N + +          
Sbjct: 8   IENPEDTGQRIDKLLPEYHSEWSRTQIQDWIKASLVKVNDQVIKSNYKTKMN-------- 59

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
               +HI+  +K    +V      + L   + YED  + +  KP G+ V   +G      
Sbjct: 60  ----DHIVVTEK---ETVEADIQPENLNLDIYYEDDDVAIVYKPKGMVVHPSAGHYTGTL 112

Query: 129 IDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++G +   K+     G+ +P + HR+D++TSG+L+VA+   A + L +    + + + Y 
Sbjct: 113 VNGLMYQMKNLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVDQLVNKTVTRKYV 172

Query: 185 SLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G IP +     A   + ++      + VV   ++    A++HF V++ F  K+  +
Sbjct: 173 ALVHGKIPHDYGTVDAP--IGRNKNDRQSMDVVDDGKE----AVTHFNVLEHF-NKYTLI 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           E Q  TGRTHQ+RVH  ++G P+VGD KY
Sbjct: 226 ECQLETGRTHQIRVHMKYIGYPLVGDPKY 254


>gi|308187865|ref|YP_003931996.1| ribosomal large subunit pseudouridine synthase D [Pantoea vagans
           C9-1]
 gi|308058375|gb|ADO10547.1| ribosomal large subunit pseudouridine synthase D [Pantoea vagans
           C9-1]
          Length = 325

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 122/240 (50%), Gaps = 31/240 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP    V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDFVVHPGAG---NPDGTVLNALLHHYPAIMDVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL +S + R I + Y ++  G        ++ I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVDSLQRREITREYEAVAIGNMTAGGTVEQPISRHSTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMSHISHPLVGDPL 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F + ++  ++  LHA  + L HP  G  ++  A LP  MV    +L
Sbjct: 253 YGGRPRPPKGASEAFITTLRGFDRQALHATMLRLYHPISGIEMEFHAALPQDMVDLIAAL 312


>gi|163802917|ref|ZP_02196805.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. AND4]
 gi|159173324|gb|EDP58150.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. AND4]
          Length = 250

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 69/215 (32%), Positives = 107/215 (49%), Gaps = 26/215 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ED +I   NKP+G+ SV G   +A H D  + S ++ +  + ++ HRLD  TSG++V
Sbjct: 16  IVFEDEQILAVNKPSGLLSVPGR--LAEHHDS-MSSRLEKEYPEIQVVHRLDMSTSGLMV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC----IANW----LLKKSHIGG 210
           +A+ + A   L + F+ R   KIY++ VWG + + + E     I +W    L K     G
Sbjct: 73  LAKNKLAESALKKQFQYRLTHKIYYARVWGHVAQEEGEVDLPLICDWPNRPLQKVCFEDG 132

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                + Q  K   +A            K   + + P TGR+HQLRVH   +G PIVGD 
Sbjct: 133 KPSKTLFQVAKREEHAD---------GLKTTIVRLLPITGRSHQLRVHMQALGHPIVGDE 183

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            Y       F++    +L LHA  +   HPE  +L
Sbjct: 184 FYATEEAQAFST----RLELHATELSFYHPESHQL 214


>gi|46445765|ref|YP_007130.1| putative ribosomal large subunit pseudouridine synthase
           (pseudouridylate synthase), rluA [Candidatus
           Protochlamydia amoebophila UWE25]
 gi|46399406|emb|CAF22855.1| putative ribosomal large subunit pseudouridine synthase
           (pseudouridylate synthase), rluA [Candidatus
           Protochlamydia amoebophila UWE25]
          Length = 243

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 65/214 (30%), Positives = 110/214 (51%), Gaps = 15/214 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED+ + +  KP+G+ SV             LK+    K +K  + HRLDQ+TSG++V
Sbjct: 34  ILYEDADLAIIYKPSGLLSVATAFEKGETTHALLKAHY--KPRKVFVVHRLDQDTSGVMV 91

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A        L + F +  I + Y ++V G   +      ++L + S     +VH   ++
Sbjct: 92  FAFNEKTCNGLKDLFEVHDISRSYTAIVEGQLLSPSGTWKSYLYEDSQY---FVHET-ED 147

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E     AI+H++ +    +K+  +E+   TGR +Q+RVH    G P+VGD KY     G 
Sbjct: 148 ETYGRLAITHYRTLKTL-KKYSLVELTLETGRKNQIRVHCQSAGHPVVGDKKY-----GA 201

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            T+P++ +L LHA  +   HP   + ++I +P+P
Sbjct: 202 HTNPLK-RLCLHAHLLAFKHPISRKIIRIESPIP 234


>gi|332535329|ref|ZP_08411128.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332035242|gb|EGI71749.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 245

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 71/251 (28%), Positives = 117/251 (46%), Gaps = 27/251 (10%)

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------SGI 125
           N+ +    EQ I+       K   F++  +LY+D  I + NKP+G+    G        +
Sbjct: 7   NSTSQTPSEQPIIVDDFVAPKCDGFIE--ILYQDDDILLINKPSGLLSLSGKNPLNWDSV 64

Query: 126 AYHI----DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            Y +     G   ++ ++K     L HRLD  TSGI++V     A++HL + F+ R IQK
Sbjct: 65  HYRLVHGQKGLTAAFAEAK-----LPHRLDLGTSGIMIVGLNAKASKHLNKQFQARTIQK 119

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF- 240
            Y +++ G        I   + K   +       VK  +     A+S + V++   Q   
Sbjct: 120 RYVAMLEGCLAVDVGSITAPIAKDKLL----FPRVKICQTMGKVAVSEYSVLERLKQPCR 175

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             ++  P TGRTHQLR+H+  +G PI+G    C  +K   +  +  +L LHA  +   HP
Sbjct: 176 TLVQFTPVTGRTHQLRIHSQFIGHPILG----CDLYKSAQSEYMAGRLQLHASDLYFEHP 231

Query: 301 E-GGRLQITAP 310
             G ++ I +P
Sbjct: 232 ATGAQIHINSP 242


>gi|297161299|gb|ADI11011.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces bingchenggensis BCW-1]
          Length = 312

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 85/335 (25%), Positives = 149/335 (44%), Gaps = 41/335 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V+VD      ++R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAIARMF-GFSRTKAAELAAAGKVQVDGSVAGKSDRVS 59

Query: 61  SGQVVRI------PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
            G  + +      PPV           +I+   V   +        ++++D  I V +KP
Sbjct: 60  GGAWLEVEMPQAAPPV-----------RIVAEPVEGME--------IVHDDEHIVVVDKP 100

Query: 115 AGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQ 168
            G++     G     + G L +    V + G   R  + HRLD  TSG++VVA++  A  
Sbjct: 101 VGVAAHPSPGWTGPTVIGGLAAAGFRVSTSGAAERQGIVHRLDVGTSGLMVVAKSELAYT 160

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            L + FR R + K Y +LV G P      I   + +  H   DY   V    K    +++
Sbjct: 161 LLKQQFRERTVDKRYQALVQGHPDPLSGTIDAPIGR--HPQHDYKWAVTAEGK---PSVT 215

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NK 287
           H+ +I+ F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +Q  +
Sbjct: 216 HYDLIEAF-RAASLLDIKLETGRTHQIRVHMAAHRHPCVGDLTYGADP--TLAKRLQLTR 272

Query: 288 LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
            +LHA  +   HP GG ++  +  P  + +  D++
Sbjct: 273 QWLHAVRLGFEHPGGGWVEFESRYPDDLQRALDTV 307


>gi|162533083|ref|YP_001621407.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213969739|ref|ZP_03397874.1| Pseudouridine synthase [Pseudomonas syringae pv. tomato T1]
 gi|301382971|ref|ZP_07231389.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato Max13]
 gi|302063259|ref|ZP_07254800.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato K40]
 gi|302131645|ref|ZP_07257635.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato NCPPB 1108]
 gi|118201621|gb|ABK79684.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213925547|gb|EEB59107.1| Pseudouridine synthase [Pseudomonas syringae pv. tomato T1]
 gi|331019062|gb|EGH99118.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. lachrymans str. M302278PT]
          Length = 211

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 68/214 (31%), Positives = 109/214 (50%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIHQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ +KV++      C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEAGKHALTFWKVVE-RHDSHCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              P   +L LHA  +   HP  G RL    P P
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|319775341|ref|YP_004137829.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae F3047]
 gi|317449932|emb|CBY86144.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae F3047]
          Length = 219

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 67/208 (32%), Positives = 106/208 (50%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+ D  + S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYY-DSVM-SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG  +N         I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPEKHYQAIVWGHLENDYGEVNLPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD K+ ++
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGD-KFYSH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    SP   +L LHA  + + HP  G
Sbjct: 184 PQAKAMSP---RLCLHAEELTITHPITG 208


>gi|254994200|ref|ZP_05276390.1| hypothetical protein LmonocytoFSL_15395 [Listeria monocytogenes FSL
           J2-064]
          Length = 296

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 81/299 (27%), Positives = 140/299 (46%), Gaps = 51/299 (17%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQV----VRIPPVINALNHIIKEQKILDSSVNLTK 92
           +Q +L++G + V+ +  K N ++Q G      VR P          +E ++L   + L  
Sbjct: 32  IQLMLKNGDITVNGELAKPNYKVQVGDEIHYEVREP----------EELEVLAEDIPLD- 80

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQK 143
                   + +ED  + V NKP G+ V   +G A         +H D    S ++ K  +
Sbjct: 81  --------IYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL--SGINGK-IR 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    +
Sbjct: 130 PGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPI 188

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++      + VV+  ++    A +HF+V++     +  +  +  TGRTHQ+RVH  ++G
Sbjct: 189 GRAKEDRQKMAVVRDGKE----ARTHFEVLERLP-GYTLINCKLDTGRTHQIRVHLKYIG 243

Query: 264 CPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
            P+ GD KY      KGN         +LHA  +   HP    R+   APLP+   K  
Sbjct: 244 HPLAGDPKYGPKNTIKGNGQ-------FLHAAKLGFDHPTTKERMMFEAPLPSSFEKAL 295


>gi|94264419|ref|ZP_01288209.1| Pseudouridine synthase, RluD [delta proteobacterium MLMS-1]
 gi|93455176|gb|EAT05394.1| Pseudouridine synthase, RluD [delta proteobacterium MLMS-1]
          Length = 310

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 65/221 (29%), Positives = 111/221 (50%), Gaps = 15/221 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYH----IDGFLKSWVDSKG----QKPRLTHRLD 151
           ++LYED  + V +KP G+ V   +G  +H    ++G L    D  G     +P + HRLD
Sbjct: 82  VVLYEDGDLLVISKPPGVVVHPAAG--HHRGTLVNGLLHHCRDLSGISGELRPGIVHRLD 139

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG LVVA+   A + L   F+ R ++KIY +L+ G    ++  +   + +  H    
Sbjct: 140 KDTSGCLVVAKNDRAHRDLLAQFKNREVEKIYLALLSGKLAGEQGRVEGAIGR--HPKQR 197

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V+   +G   A++H+++   F   +  + ++  +GRTHQ+RVH   +G P+ GD  
Sbjct: 198 QKMAVRPAGEG-RAALTHWRLRQRFTAGYTLVSLRLDSGRTHQIRVHMASLGHPVAGDAL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           Y    + +    I  + +LHA  +   HP  G  L+   PL
Sbjct: 257 YGKGGERDRRYGITRQ-WLHAAELAFRHPVSGEPLRCRGPL 296


>gi|313500106|gb|ADR61472.1| Pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 211

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 70/214 (32%), Positives = 109/214 (50%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D+ I V NKP  + SV G +    + D  +    ++      + HRLD ETSGI++
Sbjct: 8   ILFVDAAILVINKPTLLLSVPGRA--EDNKDCLITRLQENGYPDALIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADSHRELSRQFHDRETEKAYTALCWGQPALDSGSID--LPLRYDPPTKPRHVV-DH 122

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E+G  +A++ +++++      C +E+ P TGR+HQLRVH L +G P++GD  Y AN +  
Sbjct: 123 EQG-KHALTFWRIVE-RCGDHCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY-ANPQAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL+   P P
Sbjct: 180 AA---HERLCLHASMLSFTHPVSGQRLKFECPAP 210


>gi|304399171|ref|ZP_07381038.1| pseudouridine synthase, RluA family [Pantoea sp. aB]
 gi|304353225|gb|EFM17605.1| pseudouridine synthase, RluA family [Pantoea sp. aB]
          Length = 325

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 122/240 (50%), Gaps = 31/240 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP    V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDEDIIVINKPRDFVVHPGAG---NPDGTVLNALLHHYPAIMDVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A  HL +S + R I + Y ++  G        ++ I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTHLVDSLQRREITREYEAVAIGNMTAGGTVEQPISRHSTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMSHISHPLVGDPL 252

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F + ++  ++  LHA  + L HP  G  ++  A LP  MV    +L
Sbjct: 253 YGGRPRPPKGASEAFITTLRGFDRQALHATMLRLYHPISGIEMEFHAALPQDMVDLIAAL 312


>gi|203287491|ref|YP_002222506.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           recurrentis A1]
 gi|201084711|gb|ACH94285.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           recurrentis A1]
          Length = 326

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 114/240 (47%), Gaps = 30/240 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  + V  KP GI    G         + + +HI      + ++K  +P + HRLD
Sbjct: 86  ILYEDINVIVIEKPQGILSHLGISNLENTVVNFLLHHISNLRYKFQENK-IRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG+++ A+       L E F+ R ++K+Y ++V G  K     I  ++ +  +    
Sbjct: 145 KETSGVMICAKNLETLNFLFEQFKNRSVKKVYIAIVKGNFKVDSGIIDTFIDRDRYDRKK 204

Query: 212 Y-VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           + VH     +     A++ +KV+    + +  + +QP TGRTHQLRVH  ++  PI+GD 
Sbjct: 205 FTVH-----KNSGKRALTEYKVLIS-MKNYSLVVLQPKTGRTHQLRVHMKYLNHPILGDD 258

Query: 271 KYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            Y      FK       +  L LH+  +++   EG   +  + LP   +   D L   YD
Sbjct: 259 IYSRLDQEFK-------EISLMLHSFKLEISIKEGFLKKFISVLPKRFI---DFLSNFYD 308


>gi|153001327|ref|YP_001367008.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151365945|gb|ABS08945.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 223

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 63/199 (31%), Positives = 105/199 (52%), Gaps = 10/199 (5%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP+G+    G   A+  D  L   + +   +  L HRLD  TSGI+V AR
Sbjct: 18  YKDRDLIIINKPSGLLSNPGRA-AHTFDCALIR-LQTLYPETILVHRLDCATSGIMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
            + A  HL   F+ R+ +K+Y + V G +P  +++ + +  +        Y   ++  E 
Sbjct: 76  NKKAESHLKTQFQDRQSKKVYIAEVMGHVP--QEQGMIDLAIAPDTEHPPYQKTLQAGET 133

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           G   A+++++V++        +E+ P TGRTHQLRVH L +G  I+GD  Y  + +    
Sbjct: 134 GGKSALTYYRVLERRVNS-TLVELSPETGRTHQLRVHMLALGHAILGDEFY-GDAEVIKA 191

Query: 282 SPIQNKLYLHARYMDLPHP 300
           +P   +L LHA+ + L HP
Sbjct: 192 AP---RLCLHAQSLSLSHP 207


>gi|289705615|ref|ZP_06502005.1| pseudouridine synthase, RluA family [Micrococcus luteus SK58]
 gi|289557665|gb|EFD50966.1| pseudouridine synthase, RluA family [Micrococcus luteus SK58]
          Length = 295

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 61/209 (29%), Positives = 105/209 (50%), Gaps = 13/209 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LYED  +   +KP G++     G +   + G L +    + + G   R  + HRLD  T
Sbjct: 92  ILYEDEDLVAVDKPTGVAAHPSPGWVGPTVVGALAALGYHITTSGAPERQGIVHRLDVGT 151

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++VVA+T  A   + + FR R  +K+Y ++V GIP      +   + +  H G  +  
Sbjct: 152 TGVMVVAKTERAYTAMKDQFRERVPEKVYHAVVQGIPDPLSGTVDAPIGR--HPGHHWKF 209

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  + +    +++H++ ++ F  +   LE+   TGRTHQ+RVH   +  P VGD  Y A
Sbjct: 210 AVLDDGR---PSVTHYETLEVFG-RATLLEVHLETGRTHQIRVHTSALRHPCVGDLTYGA 265

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + +      +  + +LHA  +  PHP  G
Sbjct: 266 DPRMAAELGLTRQ-WLHAHRLAFPHPVTG 293


>gi|149916925|ref|ZP_01905426.1| pseudouridine synthase [Plesiocystis pacifica SIR-1]
 gi|149822203|gb|EDM81594.1| pseudouridine synthase [Plesiocystis pacifica SIR-1]
          Length = 255

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 31/246 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +L+ D ++    KP+G+ V  G  +  A  +D  L++ +D     P   HRLD+ TSG+L
Sbjct: 23  ILHRDDRLLAVAKPSGMLVHRGWAADEAVLVD-LLRAQLDGADVFP--LHRLDRGTSGVL 79

Query: 159 VVARTRAAAQHLTESFRMRR--IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +A  + AA  + + F      + K Y +LV G+     +         S  G       
Sbjct: 80  CLALDKEAAAFVGQQFEAHAPPLTKTYLALVRGLAPEAVDVDHGLRPHDSKTG------- 132

Query: 217 KQNEKGANY-----AISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +  K A+      A + F+ I+      + +  ++  P TGRTHQ+R H  H+  PI+G
Sbjct: 133 -KRRKAADALPRIPAQTRFERIEARQIGERSYSLVKALPRTGRTHQIRRHLKHLAHPIIG 191

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
           D +Y        F+ +F     +++ LHA  + L HP+GG L++ AP+PA + +   ++G
Sbjct: 192 DVRYGKGNQNRYFRAHFDF---HRMALHAAALTLEHPDGGALELRAPVPADLREPLRAMG 248

Query: 324 FKYDRN 329
           F+  R 
Sbjct: 249 FETLRT 254


>gi|241760654|ref|ZP_04758746.1| tRNA pseudouridine synthase C [Neisseria flavescens SK114]
 gi|241318835|gb|EER55361.1| tRNA pseudouridine synthase C [Neisseria flavescens SK114]
          Length = 264

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 106/222 (47%), Gaps = 16/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ DS+    NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 30  IIHRDSRTIAVNKPAGMLVHRSWLDKHETRFAVQTLRDQIGQHVYPVHRLDRPTSGVLLF 89

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLK--KSHIGGDYVHVVK 217
           A    AA+ LT+ F  + I+K YW++V G +P +    + ++ LK     I         
Sbjct: 90  ALDTEAARLLTQQFENKTIEKTYWAIVRGYLPSDG---LIDYALKYMPDKIAEAQTEATL 146

Query: 218 QNEKGANYAISHFKV-----IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           Q  + A   ++  ++     +     ++ W E+ P+TGR HQLR H  H+  PIVGD  Y
Sbjct: 147 QEAQTAYRCLAQTELPFQSALRYPTSRYSWAELTPYTGRKHQLRRHMKHIFHPIVGDTNY 206

Query: 273 CANFKGNFTSPIQ---NKLYLHARYMDLPHPE-GGRLQITAP 310
             + + N          +L LHAR +     E G R+ + AP
Sbjct: 207 -GDLRQNHAVAEHIGTQRLMLHARSLSFQSIEDGSRITVNAP 247


>gi|294155914|ref|YP_003560298.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           crocodyli MP145]
 gi|291600512|gb|ADE20008.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           crocodyli MP145]
          Length = 312

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 68/252 (26%), Positives = 117/252 (46%), Gaps = 45/252 (17%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           ++ GQV+ +  +I+   HI  +   LD               + YED  + V  KP+G+ 
Sbjct: 50  VREGQVISVTKLIDKEIHIEAQDIDLD---------------IAYEDEHLLVIKKPSGMV 94

Query: 119 VQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQ 168
           V    G         + +H   F  +  +  G  +P + HR+D++TSG+L+VA+T    Q
Sbjct: 95  VHPAPGHHENTLVNALLFH---FKNNLSNENGLLRPGIVHRIDKDTSGLLIVAKTNEVHQ 151

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            L+E F  + I + Y+++  G+ K+KK  + +  + +       + V   N K   +AI+
Sbjct: 152 LLSEGFSNKSINRKYFAICDGVLKSKKMKL-DLPIGRDVKNRQQMSVTNSNSK---HAIT 207

Query: 229 HFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---------- 275
           + +++  F    Q  C ++    TGRTHQ+RVH  ++  PI GD  Y             
Sbjct: 208 NLEMLKSFYFDNQPKCLVKATLETGRTHQIRVHCAYINNPIFGDSTYGKKVDDFNQRLHA 267

Query: 276 FKGNFTSPIQNK 287
           ++  F  PI NK
Sbjct: 268 YRLEFVHPITNK 279


>gi|260427871|ref|ZP_05781850.1| ribosomal large subunit pseudouridine synthase A [Citreicella sp.
           SE45]
 gi|260422363|gb|EEX15614.1| ribosomal large subunit pseudouridine synthase A [Citreicella sp.
           SE45]
          Length = 215

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 64/208 (30%), Positives = 101/208 (48%), Gaps = 22/208 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D+ + V +KPAG+    G G A  +   L + +++     RL HRLD++TSG++V 
Sbjct: 14  ILHADTDLLVVDKPAGLLSVPGKGEA--LADCLITRLEAAFPTVRLVHRLDRDTSGVMVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKK---ECIANWLLKKSHIGGDYVHV 215
             T  A +HL   F  R+ +K Y + V G   PK        I +W  +          +
Sbjct: 72  GLTAHAQRHLGMQFETRKTRKTYVARVAGRLEPKTGTVDLPLIVDWPNRP---------L 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K   +    A++ +KV    +     + + P TGR+HQLRVH L +G PI+GD  Y  +
Sbjct: 123 QKVCHETGKPALTDYKVTKS-SDTESRVRLHPLTGRSHQLRVHMLALGHPILGDPLYAPD 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
               +      ++ LHA  + L HPE G
Sbjct: 182 TASQY-----PRMMLHAEELRLHHPESG 204


>gi|257464999|ref|ZP_05629370.1| RNA pseudouridine synthase [Actinobacillus minor 202]
 gi|257450659|gb|EEV24702.1| RNA pseudouridine synthase [Actinobacillus minor 202]
          Length = 212

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 64/201 (31%), Positives = 91/201 (45%), Gaps = 30/201 (14%)

Query: 103 YEDSKIYVFNKPAGISVQG---GSGIAYHID---GFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++     V +KP GISV      +G+   I    G  + W         L HRLD+ TSG
Sbjct: 9   FQHPDFIVIDKPEGISVHKDNEATGLTERIAQQLGVPQVW---------LVHRLDKATSG 59

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A T+ AA      F+  +IQK YW+L    PK K+  I   + K  +      H  
Sbjct: 60  LLILALTKEAAVEFYHLFKQHKIQKTYWALSTAKPKKKQGKIVGDMKKSRNSAWKLCHTK 119

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +        AI+ F      A +  W  + PHTGRTHQLRV    +G PI+GD  Y    
Sbjct: 120 E------TPAITQF-TSQSVAPQLRWFTLNPHTGRTHQLRVAMKSLGSPILGDSLYGGE- 171

Query: 277 KGNFTSPIQNKLYLHARYMDL 297
                    ++LYLHA  ++ 
Sbjct: 172 -------KADRLYLHAYQLEF 185


>gi|259500628|ref|ZP_05743530.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
 gi|302191317|ref|ZP_07267571.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners AB-1]
 gi|259168012|gb|EEW52507.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
          Length = 311

 Score = 89.7 bits (221), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 76/301 (25%), Positives = 143/301 (47%), Gaps = 38/301 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+++E  +RLD++   H   I+   +Q++++   +  +  + K + ++ +   + I  
Sbjct: 9   LVVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNGLQTKLSYKVNTNDKINIE- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                         + S   L+   + L   ++YED  + V NKP G+ V   +G   H 
Sbjct: 68  --------------IPSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHT 113

Query: 129 -IDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G +   K+  +     +P + HR+D++TSG+L++A+   A   L +    +  ++ Y
Sbjct: 114 LVNGLIYHTKNLAECDEIFRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINKREY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
            ++V    K+    I +  + ++      + VV   +K    AI+HF V++ F   +   
Sbjct: 174 IAIVHANFKHSSGVI-DAPIGRNPYQRQQMAVVASGKK----AITHFTVLEQFPGYSLVK 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           C LE    TGRTHQ+RVH  ++G PI GD  Y      N      N  +LHA+ +   HP
Sbjct: 229 CILE----TGRTHQIRVHMSYIGHPIAGDPLYGPKKTLN-----GNGQFLHAKTLGFYHP 279

Query: 301 E 301
           +
Sbjct: 280 K 280


>gi|66044855|ref|YP_234696.1| pseudouridine synthase [Pseudomonas syringae pv. syringae B728a]
 gi|63255562|gb|AAY36658.1| Pseudouridine synthase [Pseudomonas syringae pv. syringae B728a]
          Length = 211

 Score = 89.7 bits (221), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 65/204 (31%), Positives = 107/204 (52%), Gaps = 12/204 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIHQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEGGKHALTFWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG 303
              P   +L LHA  +   HP  G
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTG 200


>gi|322506303|gb|ADX01757.1| Dual specificity pseudouridine synthase [Acinetobacter baumannii
           1656-2]
          Length = 221

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 101/207 (48%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ 
Sbjct: 18  ILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R ++K Y +LV G  K +       I +W  +   I    VH  
Sbjct: 76  AKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLITDWENRPRQI----VHF- 130

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            +  K A          +   Q    LE  P TGR+HQLRVH +H+G PI+GD  Y    
Sbjct: 131 -ELGKHAKTLFQPLVYDETTDQSRVLLE--PVTGRSHQLRVHMMHIGHPIMGDKLYHPEP 187

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           K        N++ LHA Y+   HP  G
Sbjct: 188 KRFHL----NRMALHAAYLAFQHPLKG 210


>gi|301346056|ref|ZP_07226797.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) protein [Acinetobacter
           baumannii AB056]
 gi|301596091|ref|ZP_07241099.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) protein [Acinetobacter
           baumannii AB059]
          Length = 221

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 101/207 (48%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ 
Sbjct: 18  ILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R ++K Y +LV G  K +       I +W  +   I    VH  
Sbjct: 76  AKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGRVEVPLITDWENRPRQI----VHF- 130

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            +  K A          +   Q    LE  P TGR+HQLRVH +H+G PI+GD  Y    
Sbjct: 131 -ELGKHAKTLFQPLVYDETTDQSRVLLE--PVTGRSHQLRVHMMHIGHPIMGDKLYHPEP 187

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           K        N++ LHA Y+   HP  G
Sbjct: 188 KRFHL----NRMALHAAYLAFQHPLKG 210


>gi|228475048|ref|ZP_04059776.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus hominis SK119]
 gi|314936640|ref|ZP_07843987.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           hominis subsp. hominis C80]
 gi|228271033|gb|EEK12421.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus hominis SK119]
 gi|313655259|gb|EFS19004.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           hominis subsp. hominis C80]
          Length = 305

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 75/261 (28%), Positives = 123/261 (47%), Gaps = 31/261 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+   +     +   LQ  +++  V V+ K +K N +      V++   I      + 
Sbjct: 17  RIDKLLSDFNSEWSRSQLQDWIKNDLVTVNGKIIKSNYK------VKLNDEIQVTEKEVV 70

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           E  IL  ++NL          + YED  + +  KP G+ V    G      ++G +    
Sbjct: 71  EADILPENLNLD---------IYYEDKDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIK 121

Query: 138 DSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPK 192
           D  G     +P + HR+D++TSG+L+VA+   A + L E    + +++ Y +LV G IP 
Sbjct: 122 DLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRGLVEQLMDKTVKRKYTALVHGNIPH 181

Query: 193 NKKECIAN-WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           +     A     KK     D V   K+       A++HF V++ F   +  +E Q  TGR
Sbjct: 182 DYGTIDAPIGRNKKDRQSMDVVDDGKE-------AVTHFNVLEHF-NDYTLIECQLETGR 233

Query: 252 THQLRVHALHMGCPIVGDHKY 272
           THQ+RVH  ++G P+VGD KY
Sbjct: 234 THQIRVHMKYIGFPLVGDPKY 254


>gi|189461580|ref|ZP_03010365.1| hypothetical protein BACCOP_02239 [Bacteroides coprocola DSM 17136]
 gi|189431690|gb|EDV00675.1| hypothetical protein BACCOP_02239 [Bacteroides coprocola DSM 17136]
          Length = 549

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 76/235 (32%), Positives = 111/235 (47%), Gaps = 21/235 (8%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGF 132
           L H++   ++  + +    H D  K  ++YED  + V NKPAG +SV G   +       
Sbjct: 319 LKHMLVGLQVEKNPLAENIHQD-TKPEIVYEDDWLVVVNKPAGMLSVPGKEALNSVYQFL 377

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            + + ++ G  P L HRLD  TSG+L+ A+ +   Q L   F  R I+K Y +++  I  
Sbjct: 378 HERYPEATG--PMLVHRLDMATSGLLLAAKDKDTHQKLQALFCGREIKKRYTAVLSSIVN 435

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +  I+  L    H   D    +   E G   AI+ +KV++    K   +   P TGRT
Sbjct: 436 ADEGTISLPLCLNFH---DRPRQMVSFEYG-KPAITRYKVLERKNGK-TLIAFYPLTGRT 490

Query: 253 HQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           HQLRVHA H   + CPIVGD  Y             ++LYLHA  +   HP  G 
Sbjct: 491 HQLRVHAAHPQGLACPIVGDELYGKR---------ADRLYLHAAELSFIHPVNGE 536


>gi|152990499|ref|YP_001356221.1| ribosomal large subunit pseudouridine synthase D [Nitratiruptor sp.
           SB155-2]
 gi|151422360|dbj|BAF69864.1| ribosomal large subunit pseudouridine synthase D [Nitratiruptor sp.
           SB155-2]
          Length = 319

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 81/292 (27%), Positives = 143/292 (48%), Gaps = 40/292 (13%)

Query: 37  LQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           ++++++ G VR++ K   K  ++++SG +V +          I E K+   S     H D
Sbjct: 29  IEQLIKQGYVRINGKIEKKAGSKLKSGDLVEV---------TIPEPKV---SQPKDVHFD 76

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---------SKGQKPRL 146
             +   +YED  I V NKPAG+ V     +    +  L  W+          S  ++  +
Sbjct: 77  VER---IYEDEDILVLNKPAGLVVHPAPSVK---EPTLVDWLKANDISLSTLSGEERHGI 130

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ETSG++V+A+     Q L++  + + + + Y ++V   P  K++ I    + ++
Sbjct: 131 VHRLDKETSGLIVIAKNNETHQALSKQLQDKSMGRYYLAIVE--PPLKEDLIIEKPIARN 188

Query: 207 HIGGDYVHVVKQNEKGANYAISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                 + VV    +G  YA S F K+      K+  +  +  TGRTHQ+RVH   +   
Sbjct: 189 PKNRLKMGVV----EGGRYAKSAFVKLTTSKNNKYELIGAKLFTGRTHQIRVHLASINRH 244

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
           I+GD  Y    K + T P   +++LHA  + L HP+ G +++  AP+P  M+
Sbjct: 245 ILGDSLYGFKSK-SVTIP---RVFLHAYILYLKHPKSGEKMRFLAPVPEDML 292


>gi|125625156|ref|YP_001033639.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|124493964|emb|CAL98959.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|300071964|gb|ADJ61364.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris NZ9000]
          Length = 290

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 67/217 (30%), Positives = 107/217 (49%), Gaps = 24/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  + V NKP G+   G +     +   + + ++   Q   + HRLDQ TSG ++ 
Sbjct: 83  ILYEDEHLIVVNKPEGMKTHGNTADEIALQNHVAAAIN---QNVFVVHRLDQATSGAVLF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ +     L + F   +I + Y +LV G    +   I   + +  H     + + K  +
Sbjct: 140 AKNQFVLPILGKMFEENKIHREYLALVAGHFLEETFTINQAIGQNRHEKNKRI-ISKHGQ 198

Query: 221 KGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           K    AI+H ++I  F  K    C L+    TGRTHQ+RVH   +G PI+GD  Y     
Sbjct: 199 K----AITHVQLIQNFTDKSLVKCILD----TGRTHQIRVHLSSLGHPIIGDALY----- 245

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           G  ++   ++L LHA  + +PHP   + L I+AP P+
Sbjct: 246 GQKST---SRLMLHAESIIIPHPFTNQLLNISAPSPS 279


>gi|330999930|ref|ZP_08323628.1| ribosomal large subunit pseudouridine synthase D [Parasutterella
           excrementihominis YIT 11859]
 gi|329573337|gb|EGG54949.1| ribosomal large subunit pseudouridine synthase D [Parasutterella
           excrementihominis YIT 11859]
          Length = 409

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 89/346 (25%), Positives = 149/346 (43%), Gaps = 49/346 (14%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
           + ++   V  D +  RLD+   +    I+   L+ ++  G V+V+ K V K   ++  G 
Sbjct: 38  SKIETFEVTLDLDGERLDKVLASSLKDISRSRLKTLIEDGLVKVNGKTVDKPKEKMSFGD 97

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V I P +  ++ I     I                 ++YED  I V NKPA + V  
Sbjct: 98  EVSVEIKPRLEDMDFIATPMDI----------------DVVYEDDDILVINKPARLVVHP 141

Query: 122 GSGIAYHIDGFLKSWVDSKG----QKPR--LTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +G   H D  L + + +        PR  + HRLD++T+G++VVA+   A   L +  +
Sbjct: 142 AAG---HWDDTLLNGLLAYNPIFRTLPRAGIVHRLDRDTTGLMVVAKNEKAMLDLVQQLQ 198

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID- 234
            R +++ YW+L  G  K   + +    +++         + K     A  A +H + ID 
Sbjct: 199 ARTVKREYWALTRG--KAPADKVIEAAIERDPRNPLRFTIGKGGR--AKPATTHIRCIDQ 254

Query: 235 --CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------- 285
                + F W+  +  TGRTHQ+RVH   +G P++GD  Y    +     P +       
Sbjct: 255 KEVKGKPFSWVACRLKTGRTHQIRVHMESIGLPLIGDPLY----RNKLPKPKEDGSVLNS 310

Query: 286 -NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF-KYDR 328
            ++  LHA  + L HP     ++  A  P       D LGF  +DR
Sbjct: 311 FDRQALHASRLGLIHPVTKETMEWFAEPPQDFRDLMDELGFGPWDR 356


>gi|325103254|ref|YP_004272908.1| pseudouridine synthase [Pedobacter saltans DSM 12145]
 gi|324972102|gb|ADY51086.1| pseudouridine synthase [Pedobacter saltans DSM 12145]
          Length = 238

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 105/229 (45%), Gaps = 24/229 (10%)

Query: 97  LKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            K I+L+ED  I + NKP  +S +    G    +    K +V+      ++ HRLD+ETS
Sbjct: 6   FKDIILFEDEDIIIVNKPPFLSSLDEREGKEISLLKMAKQYVED----AQVCHRLDKETS 61

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LVVA+   A +H++  F  RR+ KIY ++V G    +   +   +L   ++G   V +
Sbjct: 62  GLLVVAKNPEAYRHMSILFERRRVNKIYHAIVDGTHVFEDLLVDLPIL---NVGKGNVVI 118

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +   K A    + F+ ++ F + +  LE +P TGR HQ+R+H       I GD  Y   
Sbjct: 119 SRGEGKRAE---TWFRSLEYF-KHYTLLECRPVTGRMHQIRIHLATQRASITGDKMYGGQ 174

Query: 276 ------------FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                              P+  +  LHAR +    P G  + I A  P
Sbjct: 175 PAFLSKIKRGYKLTDEEEQPVMKRFALHARQLSFVKPNGEEITIEAEYP 223


>gi|271964386|ref|YP_003338582.1| RluA family pseudouridine synthase [Streptosporangium roseum DSM
           43021]
 gi|270507561|gb|ACZ85839.1| RluA family pseudouridine synthase [Streptosporangium roseum DSM
           43021]
          Length = 309

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 82/306 (26%), Positives = 133/306 (43%), Gaps = 27/306 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  E  RLD      +   +     +++ SG V VD      ++R+ +G 
Sbjct: 1   MAEQRSLPVPDGLEGERLDAALSRLF-GFSRTRAAELIVSGDVLVDGSPAAKSDRVHAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +      L         +   V   K        ++YED  I V NKP G++    +
Sbjct: 60  WLDV-----TLPPPPTAPMPVAEPVPGMK--------IVYEDDDIVVVNKPIGVAAHPTT 106

Query: 124 GIAYH--IDGFLKSW--VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      I G L +   V + G   R  + HRLD  T+G +VVA++  A  HL  +F+ R
Sbjct: 107 GWTGPTVIGGLLGTGHRVATSGAAERQGIVHRLDANTTGAMVVAKSEHAYSHLKRAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G P   +  +   + +  H  GD    V     G   +++H+  I+ F 
Sbjct: 167 TVDKRYHALVQGHPDPLRGTVDAPIDR--HPSGDGRFAVV---AGGKESVTHYDTIEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    L+++  TGRTHQ+RVH   +  P VGD  Y A+        +  + +LHA  +  
Sbjct: 221 RAASLLDIKLETGRTHQIRVHMSALRHPCVGDMMYGADPTLAARLGVTRQ-WLHAVSLAF 279

Query: 298 PHPEGG 303
            HP  G
Sbjct: 280 EHPATG 285


>gi|325264047|ref|ZP_08130779.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Clostridium sp. D5]
 gi|324030531|gb|EGB91814.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Clostridium sp. D5]
          Length = 296

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 83/313 (26%), Positives = 148/313 (47%), Gaps = 32/313 (10%)

Query: 12  VENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +  +++ +R++++ +   Y   N V L+K+ +S  V V+    + N R+ +         
Sbjct: 9   IRKNDDGLRVEQYLRRQGYSRQNLVELKKMPQS--VLVNGCFCRLNERLANH-------- 58

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            N L   I+E+   +SS+ +      L   ++YED  I V NKPAG+ V        +  
Sbjct: 59  -NTLTVHIQER---ESSLQIL--PVLLPLDIIYEDEDIIVINKPAGMPVHPSMNNYSNTL 112

Query: 131 GFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               +W   +  KP   R T+RLD++TSG+ V+A+   ++  L+       I + Y ++V
Sbjct: 113 ANGLAWYYQEQGKPFIFRCTNRLDRDTSGLTVIAKHMLSSNILSRMTVRHEITREYLAVV 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  +  +  I   L +K    G  +      E G   A++H+  ++        + +  
Sbjct: 173 RGSVRPSEGIICAPLSRKP---GSIIERTVDFENGEK-AVTHYHAVE-EKNGHSLVSLVL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGRTHQ+R+H  ++G P++GD+ Y  + +      IQ +  LH+  +   HP  G +L+
Sbjct: 228 ETGRTHQIRIHMKYLGFPLIGDYLYNPDMEY-----IQRQA-LHSCRLAFSHPITGEKLE 281

Query: 307 ITAPLPAHMVKTW 319
            TAPLP  M K  
Sbjct: 282 FTAPLPDDMQKVL 294


>gi|187778438|ref|ZP_02994911.1| hypothetical protein CLOSPO_02032 [Clostridium sporogenes ATCC
           15579]
 gi|187772063|gb|EDU35865.1| hypothetical protein CLOSPO_02032 [Clostridium sporogenes ATCC
           15579]
          Length = 299

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 117/236 (49%), Gaps = 33/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKP--RLTHR 149
           ++YEDS I V NK  GI V            +GI YH           KG+K   RL +R
Sbjct: 82  IVYEDSDIIVINKKPGIVVHPTKSHSTGTLSNGILYHFK--------KKGEKSIVRLVNR 133

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG+++VA+ + +   L         +KIY ++V G  K K+  I   + K+ +  
Sbjct: 134 LDRDTSGLVIVAKNQFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEEN-- 191

Query: 210 GDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                 +K+  +E+G   +I+ ++V++  + K   ++++  TGRTHQ+RVH  H+G  + 
Sbjct: 192 ----ESIKRIVDERGQE-SITTYEVLEELS-KGSVVKLELETGRTHQIRVHMSHLGHHLY 245

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           GD  Y     G        +  LHA  ++LPHP  G  L++   LP  + K  + +
Sbjct: 246 GDSLYGM---GEEEKEYIERQALHAYKLELPHPRTGNILKLQCSLPEDIKKLIEKI 298


>gi|302791942|ref|XP_002977737.1| hypothetical protein SELMODRAFT_107344 [Selaginella moellendorffii]
 gi|300154440|gb|EFJ21075.1| hypothetical protein SELMODRAFT_107344 [Selaginella moellendorffii]
          Length = 421

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 64/208 (30%), Positives = 97/208 (46%), Gaps = 33/208 (15%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +P + HRLD+ TSG++VVA+   +   L+E F+ R++++ Y SL  G P      I   +
Sbjct: 212 RPGIVHRLDKGTSGLIVVAKDEQSQLSLSEQFKSRKVRRTYLSLTCGTPSTTSGRIEAEI 271

Query: 203 L-----KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLR 256
           L     +K     D V     + + A +A S +KV+D  A      ++ +  TGRTHQ+R
Sbjct: 272 LRDPRDRKRMTTSDTV----PSARNARFAASRYKVLDVLANGGVALVQWKLETGRTHQIR 327

Query: 257 VHALHMGCPIVGDHKY---------------CANFKGN------FTSPIQNKLYLHARYM 295
           VHA +MG P++GD  Y               CA    +      FTS I+    LHA  +
Sbjct: 328 VHARYMGFPLLGDDVYGGTVGKANSTLLSALCATKTNSRKKIHEFTSDIRRPC-LHAYSL 386

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP   + +  T P P    + W  L
Sbjct: 387 GFEHPATEKYVHFTCPPPEDFEEAWTRL 414


>gi|148825512|ref|YP_001290265.1| hypothetical protein CGSHiEE_02065 [Haemophilus influenzae PittEE]
 gi|229847517|ref|ZP_04467612.1| hypothetical protein CGSHi7P49H1_02889 [Haemophilus influenzae
           7P49H1]
 gi|148715672|gb|ABQ97882.1| hypothetical protein CGSHiEE_02065 [Haemophilus influenzae PittEE]
 gi|229809580|gb|EEP45308.1| hypothetical protein CGSHi7P49H1_02889 [Haemophilus influenzae
           7P49H1]
 gi|309972649|gb|ADO95850.1| Pseudouridine synthase A [Haemophilus influenzae R2846]
          Length = 219

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 104/208 (50%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+      S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG  +N         I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD K+ ++
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGD-KFYSH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    SP   +L LHA  + + HP  G
Sbjct: 184 PQAKAMSP---RLCLHAEELTITHPITG 208


>gi|322387849|ref|ZP_08061457.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           infantis ATCC 700779]
 gi|321141351|gb|EFX36848.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           infantis ATCC 700779]
          Length = 299

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 65/219 (29%), Positives = 113/219 (51%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +L+ED    + NKP G+    SV   + IA  I G+     + + Q+  +  RLD++TSG
Sbjct: 78  ILFEDDHFLIINKPFGVASIPSVNHSNTIANFIKGYYVKQ-NYENQQVHIVTRLDRDTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVH 214
           +++ A+   A   L +  + + I+K Y++LV G    + + E IA     +  I      
Sbjct: 137 LMLFAKHGYAHARLDKQLQKKAIEKRYYALVKGDGHLEPQGEIIAPIARDEDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  KG  YA + ++++  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRRVAKGGKYAHTSYQIVASYGN-IHLVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              G+    IQ +  LH  Y+   HP    +L++  PLP
Sbjct: 249 ---GSLEHGIQRQA-LHCHYLSFYHPFLEEQLELECPLP 283


>gi|313888154|ref|ZP_07821828.1| putative rRNA pseudouridylate synthase C [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312845844|gb|EFR33231.1| putative rRNA pseudouridylate synthase C [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 329

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 78/281 (27%), Positives = 129/281 (45%), Gaps = 30/281 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++V  ++E  RLDR+ K ++       + K LR   + V+ K+ K  + +  G  ++
Sbjct: 1   MREIIVNKNDEGRRLDRFLKIYFEKAPLSFIYKNLRKKNIVVNGKKAKPEDILGEGDEIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          + E+ I     ++ K  +     +LYED  I +  KP  +     S  A
Sbjct: 61  L---------FLAEETIEKFKKDIKKSKNSKLPDILYEDEDIILVKKPINMLTHNDSK-A 110

Query: 127 YHIDGFLKSWVD------------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           Y  D  L   VD             K  +P   +RLD+ TSGIL+ A+   + Q L ++ 
Sbjct: 111 YQ-DNALDRMVDYLIAQGDYNPRLEKSFRPAFVNRLDRNTSGILIGAKNLKSLQDLNDAI 169

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R I+K+Y +LV G  +  K+   +  LKK+   G+ V      E+G   AI+ F V+ 
Sbjct: 170 KKREIKKLYLTLVAG--RVTKDFDVDINLKKT---GNNVMKKSSREEGKR-AITEFNVLK 223

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              + +  L +   TGRTHQ+R      G  IVGD KY  +
Sbjct: 224 S-NKDYSLLSVNLITGRTHQIRASLKEEGLAIVGDRKYGED 263


>gi|309808015|ref|ZP_07701936.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           01V1-a]
 gi|308168744|gb|EFO70841.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           01V1-a]
          Length = 311

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 73/298 (24%), Positives = 142/298 (47%), Gaps = 32/298 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+++E  +RLD++   H   I+   +Q++++   +  +  + K + ++ +   + I  
Sbjct: 9   LVVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNGLQTKLSYKVNTNDKINIE- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                         + S   L+   + L   ++YED  + V NKP G+ V   +G   H 
Sbjct: 68  --------------IPSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHT 113

Query: 129 -IDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G +   K+  +     +P + HR+D++TSG+L++A+   A   L +    +  ++ Y
Sbjct: 114 LVNGLIYHTKNLAECDEIFRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINKREY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V    K+    I +  + ++      + VV   +K    AI+HF V++ F   +  +
Sbjct: 174 IAIVHANFKHSSGVI-DAPIGRNPYQRQQMAVVASGKK----AITHFTVLEQFP-GYSLV 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +    TGRTHQ+RVH  ++G PI GD  Y      N      N  +LHA+ +   HP+
Sbjct: 228 KCVLETGRTHQIRVHMSYIGHPIAGDPLYGPKKTLN-----GNGQFLHAKTLGFYHPK 280


>gi|189424176|ref|YP_001951353.1| pseudouridine synthase [Geobacter lovleyi SZ]
 gi|189420435|gb|ACD94833.1| pseudouridine synthase, RluA family [Geobacter lovleyi SZ]
          Length = 300

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 70/317 (22%), Positives = 138/317 (43%), Gaps = 49/317 (15%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++TY     +  D+   RL+ W +   P       +K+++SG   ++  +   +  + +G
Sbjct: 1   MLTYT----ITADDHCRRLESWLQRLLPTALPAYCRKLIKSGACTLNGTKSSPDTLLSAG 56

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++ +      L  + +    +D               LL++D ++   NKPAG+++   
Sbjct: 57  AIISLKESGQVLELLNRPLPPID---------------LLWQDDRLLAINKPAGLAMHPA 101

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           + +  ++     +W++ K   P   +   RLD+ TSG++++A + + A  L    +   +
Sbjct: 102 AEVDENLADIASAWLEKKANYPVRAYPVNRLDRGTSGVVLLATSSSNAGILGRQVKEEGL 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            KIY ++V G+ +   E                   + Q   G   +IS ++ +    + 
Sbjct: 162 DKIYLTVVEGMLEGIGE-------------------ISQPLDGKE-SISRYRSLS-VGES 200

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
             +L ++P TGRTHQ+R H   +G P++GD +Y A             + LH+    L H
Sbjct: 201 CSFLLVEPVTGRTHQIRRHLSAIGHPVLGDKRYDAQPLATLPG-----IALHSFRTRLQH 255

Query: 300 PEG-GRLQITAPLPAHM 315
           P    RL + APLP  +
Sbjct: 256 PTPETRLTLCAPLPTAL 272


>gi|308235820|ref|ZP_07666557.1| pseudouridine synthase, RluA family protein [Gardnerella vaginalis
           ATCC 14018]
 gi|311114402|ref|YP_003985623.1| ribosomal large subunit pseudouridine synthase D [Gardnerella
           vaginalis ATCC 14019]
 gi|310945896|gb|ADP38600.1| ribosomal large subunit pseudouridine synthase D [Gardnerella
           vaginalis ATCC 14019]
          Length = 310

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 73/282 (25%), Positives = 138/282 (48%), Gaps = 27/282 (9%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           ++  N   ++ SG+ ++  ++ + ++ +Q G V+           +I ++++ D     T
Sbjct: 27  VSRANAISLIDSGKAKILDRKSQKSSTLQDGDVI-----------VINQEEVDDQKEKST 75

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-------IAYHIDGF-LKSWVDSKGQK 143
             S      ++Y D  I V +KP G++     G             G  +K+ V  + +K
Sbjct: 76  SKSTICNIPIVYNDEDIVVVDKPVGVAAHSAKGWDGPTVPECLEASGVEIKTTVCDESRK 135

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             +  RLD  TSG+++V +T  A + + + F    ++KIY +LV G  K  K  I +  +
Sbjct: 136 G-IVSRLDVGTSGLMLVCKTDFAYEEMKKQFANHSVKKIYHALVQGNLKQNKATI-DAPI 193

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++ +  D+   + ++ K    AI+H+ VI+ F +    +++   TGRTHQ+RVH   +G
Sbjct: 194 GRAKVS-DFRFTITKSGK---PAITHWDVIERF-KGATLVKVNLETGRTHQIRVHFSSIG 248

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            P+VGD  Y AN + +    + ++ +LHA  +   HP  G L
Sbjct: 249 HPVVGDPMYGANPQLSEKLGL-SRQWLHAMSLKFKHPRTGEL 289


>gi|306820227|ref|ZP_07453869.1| ribosomal large subunit pseudouridine synthase [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304551724|gb|EFM39673.1| ribosomal large subunit pseudouridine synthase [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 228

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 65/205 (31%), Positives = 102/205 (49%), Gaps = 15/205 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETS 155
           +LYED+ + V  K +GI  Q    G   +   +  ++K   D KG+    L HRLD  TS
Sbjct: 9   VLYEDNHVIVVEKKSGILSQADKSGDVDMLTLVKSYIKEKYDKKGEVFLGLVHRLDTLTS 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V ART  AA  L++  R  ++ K Y ++   + + KK    ++L K S     Y   
Sbjct: 69  GIMVFARTSKAASRLSDDIRQGKMNKKYLAVFEEVIEKKKGSFEDYLAKDSIKNISY--- 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V +++K   Y+   ++V++        +++   TGR+HQ+RV     G  IVGD KY A 
Sbjct: 126 VTKDKKNGKYSKLEYEVLEI-KDGMSLVKINLITGRSHQIRVQFASRGYHIVGDAKYKAK 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                 S  ++K+ LHA  +   HP
Sbjct: 185 ------SKDKDKIALHACELGFYHP 203


>gi|325661187|ref|ZP_08149814.1| hypothetical protein HMPREF0490_00547 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325472694|gb|EGC75905.1| hypothetical protein HMPREF0490_00547 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 323

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 76/311 (24%), Positives = 139/311 (44%), Gaps = 32/311 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V  +E   RLD+    +          K++R   + ++ K+   N +++ G +V+
Sbjct: 1   MQEIKVTKNEAGQRLDKLLAKYLNEAPKSFFYKMMRKKNIVLNGKKATGNEKLEEGDIVK 60

Query: 67  I---PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +      I   + +    KI  +  NL+         ++YED  + + NKP G+  Q   
Sbjct: 61  LFLADETIRKFSSV----KIQRTKTNLS---------VIYEDQDVVLINKPVGMLSQKAK 107

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                     I+Y  D    S    K  +P + +RLD+ TSGI+V  ++    Q + E F
Sbjct: 108 ESDVSLVEHLISYLFDAGELSEETLKSFRPSICNRLDRNTSGIVVAGKSLPGLQKMGELF 167

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R + K Y  LV G+ + + + +  WL K      + V ++ +    ++  I       
Sbjct: 168 KERTLHKYYRCLVQGVIR-EDQYLKGWLKKDEKT--NKVQILDRPSDPSDQPIETEYHPL 224

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP---IQNKLYLH 291
              +    LE++  TG+THQ+R H    G P++GD+KY      +F      ++++L LH
Sbjct: 225 WTKEGVTLLEVRLITGKTHQIRAHLASEGHPLIGDYKYGDRKLNDFYQKKYGLKSQL-LH 283

Query: 292 ARYMDLPHPEG 302
           A  ++ P  EG
Sbjct: 284 AYRLEFPVMEG 294


>gi|311113351|ref|YP_003984573.1| ribosomal large subunit pseudouridine synthase D [Rothia
           dentocariosa ATCC 17931]
 gi|310944845|gb|ADP41139.1| ribosomal large subunit pseudouridine synthase D [Rothia
           dentocariosa ATCC 17931]
          Length = 324

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 118/232 (50%), Gaps = 20/232 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW------VDSKGQKPR--LTHRLDQ 152
           ++Y D  I V +KPAG++     G  +H    L +       V + G   R  + HRLD 
Sbjct: 95  IVYCDDDIVVVDKPAGVAAHPSHG--WHGPTVLSALLGEGVTVATSGAAERQGIVHRLDV 152

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVAR+  A   L  +F+ R ++K+Y +LV G+P      I   + +  H G ++
Sbjct: 153 GTSGLMVVARSERAYTELKRAFKDRTVEKVYHTLVQGLPDPLMGTIDAPIGR--HPGHEW 210

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              V ++ +    +I++++ ++ F      +E+   TGRTHQ+RVH   +  P  GD  Y
Sbjct: 211 KFAVIEDGRS---SITYYETLESFGSA-SLVEVHLETGRTHQIRVHFSSLRHPCCGDLTY 266

Query: 273 CANFKGNFTSPIQ-NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            A+ +  F++ +   + +LHA  +   HP  G R++  +P P  +    ++L
Sbjct: 267 GADPR--FSAELGLTRQWLHAHRLGFTHPTTGERVEFESPYPQDLDYALEAL 316


>gi|294054887|ref|YP_003548545.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
 gi|293614220|gb|ADE54375.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
          Length = 335

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 87/329 (26%), Positives = 138/329 (41%), Gaps = 42/329 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDK--------------KRVKFNNRIQSGQVV--RI 67
           W    YP      L++    G+V +D               KR+      Q   VV  R+
Sbjct: 13  WLAKQYPDSPKKRLKEWFAQGRVTLDGEVITKPHLRLEDPGKRLSMGKPQQVPNVVFKRL 72

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P  I+A  +++     +D+S+ +      L S+ L         N+P+ + +        
Sbjct: 73  PIRIHAQVNLL----YIDNSLAIVNKGPGLLSVPLPGK------NQPSALKILESYFKGK 122

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                 ++ VD     P   HRLDQ TSG+L  A T  A +HL +  R     + Y +L 
Sbjct: 123 GASELERNRVDRATLTPLPVHRLDQYTSGLLCFAMTPQAREHLVKQVRDHSFIREYMALA 182

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--------QK 239
            G    ++    +W   K    G    V  +  +GA  AISH++VID  +        Q 
Sbjct: 183 DGWVDPRRGTWRSWF--KLDKEGMQQAVFDEPTEGATEAISHYEVIDSISWPTRDGKKQT 240

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK----GNFTSPIQNKL-YLHARY 294
              L+++  TG  HQLR+H+   GCP++GD  Y  +FK     N   P   K   LHA +
Sbjct: 241 VSRLKLRLETGLKHQLRIHSARAGCPLLGDRHYNPDFKKAAEANTGQPYGCKRQALHASH 300

Query: 295 MDLPHPEGGRLQ-ITAPLPAHMVKTWDSL 322
           +   HPE G+ +  ++  P  +V+  + L
Sbjct: 301 IGFVHPETGKTKRFSSKFPRDLVELEERL 329


>gi|328948139|ref|YP_004365476.1| pseudouridine synthase, RluA family [Treponema succinifaciens DSM
           2489]
 gi|328448463|gb|AEB14179.1| pseudouridine synthase, RluA family [Treponema succinifaciens DSM
           2489]
          Length = 326

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 87/330 (26%), Positives = 154/330 (46%), Gaps = 46/330 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQV--RVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +RLD++  +  P  N +N  K L+SG V  +V+ K+ K + ++++  ++ I    N  ++
Sbjct: 16  IRLDKYIAS-LP--NGMNRSK-LKSGIVCIQVNGKKQKISCQVKANDIIDIQWEENVPDN 71

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           I  E   LD+               +YED  + V NK  G+     +G      ++  L 
Sbjct: 72  IEPENIPLDT---------------IYEDENVCVVNKKQGMVTHPAAGNWKGTLVNALLY 116

Query: 135 SWVDS------KGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-RRI 179
            W         +GQ        +P + HRLD+ETSGI++ A+     + L+  FR    I
Sbjct: 117 HWGRESIPELKEGQVSKILSNRRPGIVHRLDKETSGIIITAKNHDTEEFLSAQFRNHSSI 176

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y ++  G P+++   I   +++       +  VV   E     A S+++ I C+ + 
Sbjct: 177 VKEYIAICIGRPQHQHGIIQTNIIRDPKERKRFKAVVGTEE--GKPAESYYECISCYGE- 233

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  ++++ +TGRTHQ+RVH  ++ CPI+GD  Y A+    F    +  L L+AR + +  
Sbjct: 234 YSLMKVRINTGRTHQIRVHMKYLNCPILGDGIY-AHQDKKFP---KATLMLNARLLKIKI 289

Query: 300 PEGGRLQI-TAPLPAHMVKTWDSLGFKYDR 328
           P    L I  +P P   ++    L   Y +
Sbjct: 290 PGKEELSIFKSPTPERFIEVMKVLKRDYTK 319


>gi|311264325|ref|XP_003130109.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 1 [Sus scrofa]
          Length = 376

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 79/272 (29%), Positives = 126/272 (46%), Gaps = 47/272 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           ++++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 98  IVHQDKDLLVINKPYGLPVHGGPGVQLCISDVLPILAKILHGHKAEPLHLCHRLDKETTG 157

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P      +   +++K   G    H  
Sbjct: 158 VMVLAWEKEVAHQVQELFRTRQVAKKYWAITVRVPVPSAGVVDIPIIEKEVQGQQQHHKM 217

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  +  + A+ A++ ++V+         LE+QP TG  HQLRVH + 
Sbjct: 218 TLCPSYRMDNGKMVRVRTSRNAHLAVTQYQVLS-STLSSALLELQPVTGIKHQLRVHLSF 276

Query: 261 HMGCPIVGDHKYCANFKGNFTSP-------------IQNK-----LYLHARYMDLPHPEG 302
            + CPI+GDHKY      N  +P              Q+K     L+LHAR + LP  + 
Sbjct: 277 GLDCPILGDHKYS---DWNRLAPQKLSVGVLKKLGLPQSKARHIPLHLHARQLILPALQS 333

Query: 303 GR--LQITAPLPAHMVKTWDSLGFK---YDRN 329
            +  L +    P + V +   LG K   +D+N
Sbjct: 334 RKEELNLVCKPPRYFVHSLRRLGLKMPSHDQN 365


>gi|169824723|ref|YP_001692334.1| putative 23S RNA-specific pseudouridylate synthase [Finegoldia
           magna ATCC 29328]
 gi|167831528|dbj|BAG08444.1| putative 23S RNA-specific pseudouridylate synthase [Finegoldia
           magna ATCC 29328]
          Length = 273

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 80/304 (26%), Positives = 145/304 (47%), Gaps = 51/304 (16%)

Query: 14  NDEENMRLDRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           N ++ +RLD + K NH  H  F+++ K      + ++ K  K N++++ G +V I     
Sbjct: 7   NVDKKIRLDEFLKKNHISHNLFISIYK----DDIFINGKHAKRNSKLEKGDIVTIN---- 58

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHID 130
                +++++     +N+          +LYED  I+V NKP  +++   G   +A    
Sbjct: 59  -----LRDEENKYEPINMDIE-------VLYEDDDIFVLNKPDKLTMNKDGEKSLA---- 102

Query: 131 GFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            F+    + +   QK R  +RLDQ+TSG+++VA+ + A  +    ++    +K Y ++V 
Sbjct: 103 NFVSYLFEQRNIKQKVRFINRLDQDTSGVVMVAKNKIAQAY----YQKNSFKKKYLAIVK 158

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G PK++K       LK+  I  +    + +N K +   + + K    ++     + ++  
Sbjct: 159 GNPKDQK---IELNLKRDGIKTE----IDENGKKSVTILENLKNYGDYS----LVSLELL 207

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT 308
           TGRTHQ+RV   ++ CPIV D  Y    + NFT        LHA  ++    +G    IT
Sbjct: 208 TGRTHQIRVSMEYINCPIVADSLYGEKIE-NFTQ------MLHANEIEFVDMKGEYHNIT 260

Query: 309 APLP 312
             LP
Sbjct: 261 TNLP 264


>gi|167628351|ref|YP_001678850.1| pseudouridine synthase, rlua family [Heliobacterium modesticaldum
           Ice1]
 gi|167591091|gb|ABZ82839.1| pseudouridine synthase, rlua family [Heliobacterium modesticaldum
           Ice1]
          Length = 339

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 80/303 (26%), Positives = 136/303 (44%), Gaps = 51/303 (16%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           LQ + R+   R++ KR   + R++ G ++ +        H  +E  +   ++ L      
Sbjct: 36  LQILTRTDGFRLNGKRAHLDRRVKEGDLLEV------CLHQEEEGNLAPVAMELK----- 84

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF---LKSWVDSKGQKPRLT--HRLD 151
               +LYED+ + + +KP GI V      A         +  +   KG K R+   HRLD
Sbjct: 85  ----VLYEDADLLILDKPPGIEVHPPEQRARFRPTLAHGVAHYFAEKGIKARVRPLHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+GI V A+   A Q L    R   +Q+ Y +++ G+P      I       + IG D
Sbjct: 141 KDTTGICVFAKNAFAHQALDRQLRNGSLQRGYLAILRGLPAELVGVI------DAPIGRD 194

Query: 212 YVHVVKQNEKG-ANYAISHFKVIDCFAQKFCWLEMQP---------------HTGRTHQL 255
             H +++  +     AI+ ++V      +   LEM+                 TGRTHQ+
Sbjct: 195 PEHHMRRMVRDDGERAITRYRVTQVI--EPSGLEMKGAAESEGHWALAEVILETGRTHQI 252

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           RVH  H+G P++GD  Y  +      SP  ++  LH+ ++ L  P  G  +++TA LP  
Sbjct: 253 RVHFRHLGTPLLGDRLYGGD------SPRIDRQALHSAWVTLLQPRSGEAVKVTAELPED 306

Query: 315 MVK 317
           M +
Sbjct: 307 MAR 309


>gi|325925856|ref|ZP_08187225.1| tRNA pseudouridine synthase C [Xanthomonas perforans 91-118]
 gi|325543687|gb|EGD15101.1| tRNA pseudouridine synthase C [Xanthomonas perforans 91-118]
          Length = 296

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 112/237 (47%), Gaps = 26/237 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D  + V +KPAG+ V   S +A   D FL   +  +  KP  L HRLD+ TSG L+
Sbjct: 68  ILYQDDVLAVVDKPAGLMVHD-SKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLL 126

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R +A  L ++   R ++K Y ++  G P  ++     +++     GG    V K  
Sbjct: 127 LAFDRDSASALGKALMAREVEKDYLTVCRGWPAEER-----FIVDHDLDGGPGKPVKKP- 180

Query: 220 EKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 181 ------AVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGD 234

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
             +       +F     +++ LHA  +  PHP GG R+ ITAPL A   K     G+
Sbjct: 235 TSHGDGRHNRSFRMLGIHRMLLHAERLGFPHPGGGRRISITAPLDAEFTKACALFGW 291


>gi|288927126|ref|ZP_06421012.1| ribosomal large subunit pseudouridine synthase A [Prevotella buccae
           D17]
 gi|288336112|gb|EFC74507.1| ribosomal large subunit pseudouridine synthase A [Prevotella buccae
           D17]
          Length = 575

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 104/228 (45%), Gaps = 33/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED+ I V NKPAG+    G      +   L+     + + P + HRLD  TSG+LV 
Sbjct: 364 ILYEDASIVVVNKPAGMLSVPGKTDTPSVYSLLRECC-PQAEGPIIVHRLDMATSGLLVA 422

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG---------IPKNKKECIANWLLKKSHIGGD 211
           A+T  A   L + F  R + K Y +++            PK     +    +    +  D
Sbjct: 423 AKTSKAYFGLQQQFTDRMVTKRYVAVLEANGPRPSSHPAPKTDSSLLPKGAISLP-LSPD 481

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPI 266
           ++   +Q  + +    A++ ++ +         L + PHTGRTHQLRVH  H   +G PI
Sbjct: 482 FMDRPRQKVDREHGRPAVTDYQFVSSDR-----LLLYPHTGRTHQLRVHCAHREGLGRPI 536

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAPL 311
            GD+ Y             ++LYLHA Y+   HP+ G     + +AP 
Sbjct: 537 KGDNLYGTK---------ADRLYLHAEYLSFVHPQTGERVEFECSAPF 575


>gi|242240266|ref|YP_002988447.1| pseudouridine synthase [Dickeya dadantii Ech703]
 gi|242132323|gb|ACS86625.1| pseudouridine synthase, RluA family [Dickeya dadantii Ech703]
          Length = 325

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 122/240 (50%), Gaps = 31/240 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG + + +     +    PR  + HRLD++T
Sbjct: 86  IVYEDEDILVINKPRDLVVHPGAG---NPDGTVLNALLHHYPAIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGD 211
           +G++VVA+   A   L ES + R I + Y ++  G      +  E IA    K++H+   
Sbjct: 143 TGLMVVAKNVPAQTRLVESLQAREITREYEAVANGTMTAGGSVAEPIARHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMAHINHPLVGDPL 252

Query: 272 YCANFK------GNFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           Y    +        F + ++  ++  LHA  + L HP     ++  APLP  MV+   +L
Sbjct: 253 YGGRPRFPKGASDEFLTVLRHFDRQALHATMLRLYHPISCIEMEWHAPLPQDMVELIAAL 312


>gi|42561113|ref|NP_975564.1| ribosomal large subunit pseudouridylate synthase D [Mycoplasma
           mycoides subsp. mycoides SC str. PG1]
 gi|42492610|emb|CAE77206.1| ribosomal large subunit pseudouridylate synthase D [Mycoplasma
           mycoides subsp. mycoides SC str. PG1]
 gi|301320622|gb|ADK69265.1| pseudouridine synthase, RluA family [Mycoplasma mycoides subsp.
           mycoides SC str. Gladysdale]
          Length = 310

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 78/267 (29%), Positives = 133/267 (49%), Gaps = 21/267 (7%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
           +  NN+I +     + P  N+   I  +  ILD   NL K+ D +   ++Y+D  + V N
Sbjct: 42  ISVNNQIITNNNFLVKP--NSQITITIKDPILDP--NLVKN-DEIDLDIIYQDDDLLVIN 96

Query: 113 KPAGISVQGGSGIAYH--IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAA 166
           K   I+V        +  ++  L S V+        +P + HR+D++T+G+L+VA+    
Sbjct: 97  KQNNITVHPSLNNTNNTIVNALLASDVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKT 156

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
            + L+E F+  +I K Y ++V G+ K  K  I +  + +S      + V  +N K    A
Sbjct: 157 HKLLSEMFKNHQIYKEYLAIVTGVIKPNKGLI-DAPIGRSQTDRKKMSVTAKNSKQ---A 212

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           I+ F+V++ F  K   ++ Q  TGRTHQ+RVH  ++  P++ D  Y    +  FT   Q 
Sbjct: 213 ITTFEVVERFF-KNTLVKCQIQTGRTHQIRVHFNYINHPVLNDPVYGKKHQ-EFTDFGQ- 269

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLP 312
             YLHA  +   HP     +++ +PLP
Sbjct: 270 --YLHAYKLKFTHPITKKEIELISPLP 294


>gi|325852028|ref|ZP_08171111.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
 gi|325484584|gb|EGC87500.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
          Length = 319

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 101/216 (46%), Gaps = 14/216 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           ++YED  + V  K  GI        + ++   L  +     QK    + HRLD++TSG++
Sbjct: 108 IVYEDRFLVVVEKNIGILSMAAGHASLNVKSILDDYFYKTRQKCTAHVVHRLDRDTSGLM 167

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A+     Q     +      + Y  +V G  +  +  +ANWL         YV     
Sbjct: 168 IYAKDMQTEQLFEHDWHNIVYDRRYVGVVSGEMEQDEGTVANWLKDNK----AYVTYSSP 223

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            + G  YA++HF V+D     +  +E +  TGR +Q+RVH+  MG P+ GD KY     G
Sbjct: 224 VDNGGKYAVTHFHVLD-RTVAYSLVEYRLETGRKNQIRVHSADMGHPVCGDVKY-----G 277

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           N   P+ ++L LHA  +   HP    R++   P+PA
Sbjct: 278 NGDDPL-HRLCLHAYVLCFHHPVTHQRMEFETPVPA 312


>gi|303257043|ref|ZP_07343057.1| ribosomal large subunit pseudouridine synthase D [Burkholderiales
           bacterium 1_1_47]
 gi|302860534|gb|EFL83611.1| ribosomal large subunit pseudouridine synthase D [Burkholderiales
           bacterium 1_1_47]
          Length = 394

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 89/346 (25%), Positives = 149/346 (43%), Gaps = 49/346 (14%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
           + ++   V  D +  RLD+   +    I+   L+ ++  G V+V+ K V K   ++  G 
Sbjct: 23  SKIETFEVTLDLDGERLDKVLASSLKDISRSRLKTLIEDGLVKVNGKTVDKPKEKMSFGD 82

Query: 64  --VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V I P +  ++ I     I                 ++YED  I V NKPA + V  
Sbjct: 83  EVSVEIKPRLEDMDFIATPMDI----------------DVVYEDDDILVINKPARLVVHP 126

Query: 122 GSGIAYHIDGFLKSWVDSKG----QKPR--LTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +G   H D  L + + +        PR  + HRLD++T+G++VVA+   A   L +  +
Sbjct: 127 AAG---HWDDTLLNGLLAYNPIFRTLPRAGIVHRLDRDTTGLMVVAKNEKAMLDLVQQLQ 183

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID- 234
            R +++ YW+L  G  K   + +    +++         + K     A  A +H + ID 
Sbjct: 184 ARTVKREYWALTRG--KAPADKVIEAAIERDPRNPLRFTIGKGGR--AKPATTHIRCIDQ 239

Query: 235 --CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------- 285
                + F W+  +  TGRTHQ+RVH   +G P++GD  Y    +     P +       
Sbjct: 240 KEVKGKPFSWVACRLKTGRTHQIRVHMESIGLPLIGDPLY----RNKLPKPKEDGSVLNS 295

Query: 286 -NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF-KYDR 328
            ++  LHA  + L HP     ++  A  P       D LGF  +DR
Sbjct: 296 FDRQALHASRLGLIHPVTKETMEWFAEPPQDFRDLMDELGFGPWDR 341


>gi|257068273|ref|YP_003154528.1| ribosomal large subunit pseudouridine synthase D [Brachybacterium
           faecium DSM 4810]
 gi|256559091|gb|ACU84938.1| ribosomal large subunit pseudouridine synthase D [Brachybacterium
           faecium DSM 4810]
          Length = 308

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 74/291 (25%), Positives = 138/291 (47%), Gaps = 29/291 (9%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++ +G V VD +    + R++ G +V +         +  E+  ++    + +       
Sbjct: 36  LVTAGHVLVDGRAPARSTRLEPGVMVHV--------ELPDEKPAVEVRPQIAEGMS---- 83

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQE 153
            L+++D  I V +KP G++    +G     + G L +    + + G   R  +  RLD  
Sbjct: 84  -LIHQDDDIVVIDKPVGVAAHPSAGWSGPTVLGHLAAAGVEIRTSGDPERQGIVSRLDVG 142

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVART  A   L ++FR R + K+Y ++  G P   +  I   + +      DY 
Sbjct: 143 TSGLMVVARTERAYTTLKDAFRAREVGKVYHAICQGTPDQPRGTIEAPIGRSPQ--HDYK 200

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V+++ K   ++++H++ ++   Q    L +   TGRTHQ+RVH   +  P+VGD  Y 
Sbjct: 201 FAVREDGK---HSVTHYETLEEL-QGATLLRIGLETGRTHQIRVHMSALHHPLVGDPLYG 256

Query: 274 ANFK-GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           A+         I+   +LHA  +   HP  GR +  T+  P+ + +  ++L
Sbjct: 257 ADPTLAERVGLIRQ--WLHAMELTFVHPATGREVTYTSQYPSDLAQALEAL 305


>gi|225028953|ref|ZP_03718145.1| hypothetical protein EUBHAL_03243 [Eubacterium hallii DSM 3353]
 gi|224953728|gb|EEG34937.1| hypothetical protein EUBHAL_03243 [Eubacterium hallii DSM 3353]
          Length = 306

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 69/262 (26%), Positives = 127/262 (48%), Gaps = 26/262 (9%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           + ++ KRV    R + GQ++++       +   K+ KI  + +NL          +LYED
Sbjct: 43  ILLNGKRVTVRARGKEGQLLKV----MLEDSQEKQNKIASTKMNLH---------ILYED 89

Query: 106 SKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPR------LTHRLDQETSGIL 158
             +   +KPAGI      G ++  +   ++++ +++G++        L  RLD+ETSGIL
Sbjct: 90  EDLIFVDKPAGIVSHPSKGHLSDSMINGVQAYFENEGREKNERSNIHLIGRLDKETSGIL 149

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            +A+    A+ + +  +   + K Y++LV G P  +          +    GD + +   
Sbjct: 150 GIAKNSVTAERMIKQRQRGILIKEYYALVKGNPPEEGILEIPMEEMRDARDGDKLKMKVG 209

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             + A  A + F+V+  F +KF  + +   TGRTHQ+R H   +GCP++GD     +F G
Sbjct: 210 KSENAKTAKTFFQVVKRF-EKFSLVSLVIETGRTHQIRFHMASIGCPLLGD-----SFYG 263

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
           +      ++  LHA+ +   HP
Sbjct: 264 DGPELGISRTALHAQQLTFTHP 285


>gi|300784875|ref|YP_003765166.1| ribosomal large subunit pseudouridine synthase D [Amycolatopsis
           mediterranei U32]
 gi|299794389|gb|ADJ44764.1| ribosomal large subunit pseudouridine synthase D [Amycolatopsis
           mediterranei U32]
          Length = 309

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 78/325 (24%), Positives = 147/325 (45%), Gaps = 42/325 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +  + MR+D         ++   + ++  SG V +D +    ++R+  G ++ I    
Sbjct: 8   VPDGLDGMRVDAGLAKLL-GLSRTVVAELAESGDVLLDGRPAGKSDRLSGGGLLEI---- 62

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------I 125
             L       +++   V+  +        +L++D  I V +KP G++V    G      +
Sbjct: 63  -TLPEPANPVEVVAQPVDGMQ--------ILHDDDDIVVISKPVGVAVHPSPGWTGPTVV 113

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                  L+       ++  + HRLD  T+G++VVA++  A   L  +F+ R + K Y +
Sbjct: 114 GGLAAAGLRIATSGAAERQGVVHRLDAGTTGVMVVAKSEHAYTVLKRAFKERTVDKGYHA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           +V G P   +  I   + +  H   DY   V Q   G   +++H++V++ F A     ++
Sbjct: 174 IVQGHPDPMRGTIDAPIDR--HPRHDYKFAVVQ---GGRPSVTHYEVVEAFRAASLTHIK 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI------QNKLYLHARYMDLP 298
           ++  TGRTHQ+RVH   +  P VGD  Y A+       P+       ++ +LHA+ +   
Sbjct: 229 LE--TGRTHQIRVHFSALRHPCVGDLTYGAD-------PVLARHLGLSRQWLHAKTLAFA 279

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  GR ++  +  P  + K  + L
Sbjct: 280 HPADGRWVEFESEYPDDLAKALEIL 304


>gi|261364336|ref|ZP_05977219.1| tRNA pseudouridine synthase [Neisseria mucosa ATCC 25996]
 gi|288567596|gb|EFC89156.1| tRNA pseudouridine synthase [Neisseria mucosa ATCC 25996]
          Length = 235

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 103/221 (46%), Gaps = 29/221 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY DS+    NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYRDSRTIAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVYPAHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A    AA+ LT+ F  +  +K YW++V G +P +    + ++ LK      D +    Q 
Sbjct: 64  ALDPEAARLLTQQFEQKTTRKTYWAIVRGYLPDDG---LIDYPLKYQ---PDKI-AESQT 116

Query: 220 EKGANYAISHFKVIDCFAQ--------------KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           E     A + ++   C A+              ++ W E+ PHTGR HQLR H  H+  P
Sbjct: 117 EATLQEAQTQYR---CLARTELPFQSAARYPTSRYSWAELIPHTGRKHQLRRHMKHIFHP 173

Query: 266 IVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG 303
           IVGD  Y  + + N  +       +L LHAR +     E G
Sbjct: 174 IVGDTNY-GDLRQNHATAAHLGTTRLMLHARSISFQSIENG 213


>gi|169824298|ref|YP_001691909.1| putative ribosomal large subunit pseudouridine synthase [Finegoldia
           magna ATCC 29328]
 gi|167831103|dbj|BAG08019.1| putative ribosomal large subunit pseudouridine synthase [Finegoldia
           magna ATCC 29328]
          Length = 321

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 72/277 (25%), Positives = 135/277 (48%), Gaps = 29/277 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ ++N   N R+DR+     P ++  ++QK++R+ +++V+KKR + +  ++   VV 
Sbjct: 1   MRHINIDNSNSNQRVDRFLMKLMPKMSKNHIQKLIRTKKIKVNKKRTEPDYDLKIDDVVN 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I          + ++ I     N    +D     ++YED  + + NK  G+     +   
Sbjct: 61  I---------YLYDEVIEKYQDNKIYTADDFNLDIIYEDDDLILINKKTGVLSHAANPQD 111

Query: 127 Y--HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           Y  +I   + S++    Q          P L +RLD+ TSGI+V A+T  + ++  + F+
Sbjct: 112 YGKNIVDMMVSYLIKTNQFKPTQNSTFTPALVNRLDRNTSGIVVGAKTYDSLKYFNDLFK 171

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I KIY ++V G   N K+   +  L+K +       V+  + K +   + + K    
Sbjct: 172 KHEITKIYETIVVG---NLKDQTIDLALEKDNDKNK--SVINSSGKKSMTKVWNVK---N 223

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           F  K+  + +   TGRTHQ+R H  H+  PI+GD KY
Sbjct: 224 FG-KYSLVNVDLLTGRTHQIRAHLSHINHPIIGDIKY 259


>gi|71066542|ref|YP_265269.1| ribosomal large subunit pseudouridine synthase A [Psychrobacter
           arcticus 273-4]
 gi|71039527|gb|AAZ19835.1| ribosomal large subunit pseudouridine synthase A [Psychrobacter
           arcticus 273-4]
          Length = 237

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 67/222 (30%), Positives = 115/222 (51%), Gaps = 16/222 (7%)

Query: 96  FLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           F K I +YED  I+V +KPAG+ SV G +     +   L + ++      +L HRLD +T
Sbjct: 26  FAKQITVYEDDDIWVVDKPAGLLSVDGKT-----LKVSLLARLERANPAVKLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+ A+  AA  ++++ F  R  QK Y + V+G  ++        +  +        H
Sbjct: 81  SGLLIFAKNAAAQTNISKQFIDRLPQKSYQARVFGQWESAGATGKISVPVRYEPTTKPRH 140

Query: 215 VVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +V  +   + +A++ ++V+   +C  Q    + ++P TGR+HQLRVH +H+G  ++GD  
Sbjct: 141 IVDHD--WSKHALTLYEVLAHEECNGQTVTRVLLKPVTGRSHQLRVHMVHVGHVMIGDPI 198

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
           Y      +    I  +L LHA+ + L HP  G  +   +P P
Sbjct: 199 YAEGQALD----IAPRLNLHAQQLRLKHPTLGAWMDWESPTP 236


>gi|212711202|ref|ZP_03319330.1| hypothetical protein PROVALCAL_02274 [Providencia alcalifaciens DSM
           30120]
 gi|212686370|gb|EEB45898.1| hypothetical protein PROVALCAL_02274 [Providencia alcalifaciens DSM
           30120]
          Length = 216

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 70/206 (33%), Positives = 110/206 (53%), Gaps = 17/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G    +H D  + S +          HRLD  TSG++VV
Sbjct: 14  VLYQDEHIIVVNKPSGLLSVPGKAPEHH-DSIM-SRIQRDHPAAESVHRLDMATSGVMVV 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A  +AA + L   FR R  +K Y + VWG    K E + +  L       D+ +  KQ  
Sbjct: 72  ALHKAAERELKRQFREREPKKHYVARVWGH-LEKPEGLVDLPLI-----CDWPNRPKQKV 125

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E G + A + + V++ + ++   +++ P TGR+HQLRVH L +G PI+GD ++ A+ +
Sbjct: 126 CFETGKS-AQTEYLVLE-YEEQATRVKLSPITGRSHQLRVHMLALGHPILGD-RFYAHEE 182

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
               +P   +L LHA+ + + HPE G
Sbjct: 183 ALALAP---RLQLHAQELYITHPEYG 205


>gi|315652683|ref|ZP_07905658.1| RluA family pseudouridine synthase [Eubacterium saburreum DSM 3986]
 gi|315485061|gb|EFU75468.1| RluA family pseudouridine synthase [Eubacterium saburreum DSM 3986]
          Length = 215

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 63/213 (29%), Positives = 106/213 (49%), Gaps = 21/213 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED+ I V  KP G+  Q  SG    +   +K  +  K     + HRLD+   GI+V 
Sbjct: 5   ILYEDNDIIVVIKPRGVFSQSSSGFEEDMVSLIKKHL-GKDSYIGVVHRLDKPVYGIMVY 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            + + A   L    R + I+KIY +LV G+P   +  + +++ K ++I      VV+++ 
Sbjct: 64  GKNKKATGILCNELRKKNIRKIYEALVEGVPSENRGKLRDFIKKDNNIS----RVVEKDT 119

Query: 221 KGANYAISHFKVIDC--FAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           + A  A+  +++I+    A ++   L++   TGR HQ+R+     G PI+GDHKY     
Sbjct: 120 EDAKEAVLEYEIIETKYSADRYITRLKINLLTGRHHQIRLQCAAHGFPILGDHKYNERV- 178

Query: 278 GNFTSPIQNKL------YLHARYMDLPHPEGGR 304
                 I+ KL       L A  ++  HP+ G+
Sbjct: 179 ------IKEKLDYNKVPALAAVALEFKHPKTGK 205


>gi|255318375|ref|ZP_05359608.1| ribosomal large subunit pseudouridine synthase A [Acinetobacter
           radioresistens SK82]
 gi|262378605|ref|ZP_06071762.1| conserved hypothetical protein [Acinetobacter radioresistens SH164]
 gi|255304367|gb|EET83551.1| ribosomal large subunit pseudouridine synthase A [Acinetobacter
           radioresistens SK82]
 gi|262299890|gb|EEY87802.1| conserved hypothetical protein [Acinetobacter radioresistens SH164]
          Length = 214

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 70/223 (31%), Positives = 108/223 (48%), Gaps = 15/223 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +FL   L++ D    V +KP+GI    G G A   D  L   V  +  K  L HRLD++
Sbjct: 2   GNFLAEHLIHRDEDFMVIHKPSGILSVPGKGEALS-DSVLTRLVAIE-PKTLLIHRLDRD 59

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   +R     +   F+ R+  K Y +LV G  + +       +   +H     +
Sbjct: 60  TSGILVFGLSRRGQNSIARQFQERQTTKTYQALVAGHLQGEGTVDVPVVYDPAH---PPL 116

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+   +      A++H++ I+ F    Q+   +++ P TGR+HQLRVH  ++G  IVGD 
Sbjct: 117 HIADAHHN--KPALTHWQAIEQFEINGQQVTRVKLVPVTGRSHQLRVHMQYLGHAIVGDT 174

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            Y A+ +     P   +L LHA  +   HP+ G  L    P+P
Sbjct: 175 LY-ADLEQQQLMP---RLCLHAEQLGFAHPQTGEALNFYCPVP 213


>gi|169797705|ref|YP_001715498.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter
           baumannii AYE]
 gi|169150632|emb|CAM88541.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter
           baumannii AYE]
          Length = 232

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 71/209 (33%), Positives = 107/209 (51%), Gaps = 22/209 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ 
Sbjct: 29  ILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMF 86

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R ++K Y +LV G  K +       I +W  +   I    VH  
Sbjct: 87  AKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLITDWENRPRQI----VHF- 141

Query: 217 KQNEKGANYAISHFK--VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              E G  +A + F+  V D    +   L ++P TGR+HQLRVH +H+G PI+GD  Y  
Sbjct: 142 ---ELG-KHAKTLFQPLVYDATTDQSRVL-LEPVTGRSHQLRVHMMHIGHPIMGDKLYHP 196

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             K        N++ LHA Y+   HP  G
Sbjct: 197 EPKRFHL----NRMALHAAYLAFQHPLKG 221


>gi|42526592|ref|NP_971690.1| ribosomal large subunit pseudouridine synthase D [Treponema
           denticola ATCC 35405]
 gi|41816785|gb|AAS11571.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Treponema denticola ATCC 35405]
          Length = 345

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 76/327 (23%), Positives = 134/327 (40%), Gaps = 54/327 (16%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D +      H++   L+  L+S  + V+ ++ K +  +Q+G ++ +            
Sbjct: 26  RIDVYCTETLKHLSRSQLKTGLKS--LYVNSQKAKLSRNVQNGDLIEL------------ 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------------- 124
              + D+ +    H   L   ++YED  I V NK  G+      G               
Sbjct: 72  ---VWDNPIPEYAHPQKLPLNIIYEDENIIVVNKERGMVTHPAGGNWDGTLVNALNYYRL 128

Query: 125 --------IAYHIDGFLKSWVDS------KGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
                    A  ++  L   V +      +  +  + HRLD+ETSG+++ AR     + L
Sbjct: 129 YDSRIKDEFAVELNKLLSGEVKNIEKLSLEPYRMGIVHRLDKETSGLIITARNLKTEKLL 188

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              F+ R ++K Y +++ G+P   K  I   + + S     +   V  +      A+S +
Sbjct: 189 KSFFKKRAVKKYYLAVLDGVPPKNKGRIKTSVFRSSSDRKKF--SVSADLSKGKKALSAY 246

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-----NFTSPIQ 285
           KV+     K   +  + +TGRTHQ+R+HA  MGCP+ GD  Y     G            
Sbjct: 247 KVLKSDG-KMSLVLFRIYTGRTHQIRLHAKFMGCPVAGDKVYGKKKTGLEKKTGLAKKTG 305

Query: 286 NKLYLHARYMDLPHPEGGRLQITAPLP 312
             L LHA  + +P     + +  AP+P
Sbjct: 306 MPLMLHAYKLIIPDTVNSKKEFKAPIP 332


>gi|304386318|ref|ZP_07368651.1| ribosomal large subunit pseudouridine synthase [Pediococcus
           acidilactici DSM 20284]
 gi|304327675|gb|EFL94902.1| ribosomal large subunit pseudouridine synthase [Pediococcus
           acidilactici DSM 20284]
          Length = 304

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 74/221 (33%), Positives = 107/221 (48%), Gaps = 28/221 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +L+E+  + V NKPAGI          GS I      FL+++   K       HRLDQ T
Sbjct: 87  VLFENDDLLVVNKPAGIKTHANQPHELGSMI-----NFLQAYFAKKDSNAYNVHRLDQWT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L+VA+       L+     + IQ+ Y  +V G  K++   I         IG D   
Sbjct: 142 SGALLVAKNPVVVPILSRQISQKLIQRTYLCMVEGHLKSRSGTIT------LPIGLDPHD 195

Query: 215 VVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             K+  N  GA  A +H++V+  F ++   L +Q  TGRTHQ+RVH   +G PIVGD  Y
Sbjct: 196 QRKRQINGPGAQPATTHYQVVREFVER-SLLRVQLATGRTHQIRVHLAALGHPIVGDPLY 254

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
            +   G   +P++    LH+  +  P P     Q +TAP+P
Sbjct: 255 NSLADG---APMR----LHSWQVKFPLPFSQSWQTVTAPVP 288


>gi|332678564|gb|AEE87693.1| Ribosomal large subunit pseudouridine synthase D [Francisella cf.
           novicida Fx1]
          Length = 332

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 144/320 (45%), Gaps = 38/320 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E       +NL          +++ED  I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWIAE------DINLK---------IIFEDDDIIVIDKPVNMIVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +  L  + D + + PR  + HRLD++TSG++V A++  A  +L +    R++ + Y
Sbjct: 117 GTVSNALLHRYKD-QDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC 241
            ++V G      E      + +  IG D  +  K   N +G   AI+H+  I+ +   F 
Sbjct: 176 LAIVEG------EIYQEGTINQP-IGRDPTNRTKMAINYRGKE-AITHYTPIEVY-DGFT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF----KGNFTSPIQNKLYLHARYMDL 297
            +E Q  TGRTHQ+RVH   +  P+VGD  Y  +     K    +P +    LHA  +  
Sbjct: 227 LIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAIKTPTRQA--LHAYKLSF 284

Query: 298 PHPEGGRL-QITAPLPAHMV 316
            HP   ++ +  + LP  M+
Sbjct: 285 IHPTTAKMVKFKSKLPEDML 304


>gi|227329204|ref|ZP_03833228.1| 23S rRNA pseudouridine synthase D [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 325

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 76/248 (30%), Positives = 122/248 (49%), Gaps = 39/248 (15%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL--------KSWVDSKGQKPR--L 146
           +K  ++YED  I V NKP  + V  G+G   + DG +           VD     PR  +
Sbjct: 82  IKLDIVYEDQDILVINKPRDLVVHPGAG---NPDGTVLNALLHHYPEIVDV----PRAGI 134

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLL 203
            HRLD++T+G++VVA+T  A   L E+ + R I + Y ++  G        ++ IA    
Sbjct: 135 VHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSMTAGGMVEQPIARHAT 194

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           K++H+    VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+ 
Sbjct: 195 KRTHMA---VHPMGKP------AVTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMAHIN 244

Query: 264 CPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLHARYMDLPHP-EGGRLQITAPLPAH 314
            P+VGD  Y       KG     I+     ++  LHA  +   HP  G  ++  A LP  
Sbjct: 245 HPLVGDQLYGGRPRPPKGASEDFIEMLRGFDRQALHATMLRFYHPITGIHMEWHAELPQD 304

Query: 315 MVKTWDSL 322
           MV   D+L
Sbjct: 305 MVDLIDAL 312


>gi|238758998|ref|ZP_04620169.1| Ribosomal large subunit pseudouridine synthase A [Yersinia aldovae
           ATCC 35236]
 gi|238702809|gb|EEP95355.1| Ribosomal large subunit pseudouridine synthase A [Yersinia aldovae
           ATCC 35236]
          Length = 206

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 71/208 (34%), Positives = 103/208 (49%), Gaps = 18/208 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           I+LY+D  I V NKP+G+ SV G    A      + + + +        HRLD  TSG++
Sbjct: 2   IVLYQDKHIIVINKPSGLLSVPGR---APENKDSVMTRIQADYPTAESVHRLDMATSGVI 58

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + +   FR R  +K Y + VWG     +  I   L+       D+ +  KQ
Sbjct: 59  VVALTKAAEREIKRQFREREPKKCYIARVWGHLAQDEGVIDLPLI------CDWPNRPKQ 112

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G + A + + V+         +++ P TGR+HQLRVH L MG PI+GD  Y   
Sbjct: 113 KVCYETGKS-AQTEYLVLSRDEDGSTRVKLSPITGRSHQLRVHMLAMGHPILGDGFYAHP 171

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 S    +L LHA+ + + HPE G
Sbjct: 172 EAKAMAS----RLQLHAQELCITHPEFG 195


>gi|297588274|ref|ZP_06946917.1| possible RluA protein [Finegoldia magna ATCC 53516]
 gi|297573647|gb|EFH92368.1| possible RluA protein [Finegoldia magna ATCC 53516]
          Length = 321

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 79/281 (28%), Positives = 140/281 (49%), Gaps = 37/281 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ ++N   N R+DR+     P ++  ++QK++R+ +V+V+KKR + +  ++   VV 
Sbjct: 1   MRHINIDNSNSNQRVDRFIMKLMPKMSKNHIQKLIRTKKVKVNKKRTEPDYNLKIDDVVN 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I       + +I  +K  D+ V   +  DF   I +YED  + + NK  G+     +   
Sbjct: 61  IY----LYDEVI--EKYQDNKVYTAE--DFNLDI-IYEDDDLILINKKTGVLSHAANPQD 111

Query: 127 Y--HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           Y  +I   + S++    Q          P L +RLD+ TSGI+V A+T  + ++  + F+
Sbjct: 112 YGKNIVDMMVSYLIKTNQFTPTQNSTFTPALVNRLDRNTSGIVVGAKTYDSLKYFNDLFK 171

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA--ISHFKV- 232
              I KIY ++V G   N K+   +  L+K          + +N+   N +   S  KV 
Sbjct: 172 KHEITKIYETIVVG---NLKDQTIDLALEKD---------IDKNKSVINSSGKKSMTKVW 219

Query: 233 -IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  F  K+  + +   TGRTHQ+R H  H+  PI+GD KY
Sbjct: 220 NVKNFG-KYSLVNVDLLTGRTHQIRAHLSHINHPIIGDIKY 259


>gi|218507605|ref|ZP_03505483.1| putative ribosomal large subunit pseudouridine synthase C
          [Rhizobium etli Brasil 5]
          Length = 67

 Score = 89.4 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 39/67 (58%), Positives = 50/67 (74%)

Query: 4  MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
          M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1  MAGIEHIKVEPDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64 VVRIPPV 70
           VR+PP+
Sbjct: 61 TVRVPPL 67


>gi|37525235|ref|NP_928579.1| 23S rRNA pseudouridine synthase D [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36784662|emb|CAE13562.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (uracil hydrolyase) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 325

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 74/234 (31%), Positives = 119/234 (50%), Gaps = 31/234 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NK   + V  G+G   + DG + + +          PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKSRDLVVHPGAG---NPDGTVLNALLYHYPEIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++V+A+T  A   L ES ++R I + Y ++  G        +E I+    K++H+   
Sbjct: 143 TGLMVIAKTVPAQTRLVESLQLREITREYEAVATGRMTAGGMVEEPISRHPTKRTHMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       AI+H++V++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AITHYRVMEHF-RAHTRLRLRLETGRTHQIRVHMAHISHPLVGDPL 252

Query: 272 YCAN---FKG---NFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           Y       KG    F   ++N  +  LHA  + L HP  G  ++  A LP  MV
Sbjct: 253 YGGRPRPLKGASDEFREVMRNFDRQALHATMLRLYHPITGIEMEWHAELPDDMV 306


>gi|15604676|ref|NP_221194.1| pseudouridylate synthase [Rickettsia prowazekii str. Madrid E]
 gi|3861371|emb|CAA15270.1| SFHB PROTEIN HOMOLOG (sfhB) [Rickettsia prowazekii]
 gi|292572507|gb|ADE30422.1| Ribosomal large subunit pseudouridine synthases RluD subfamily
           protein [Rickettsia prowazekii Rp22]
          Length = 313

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 113/233 (48%), Gaps = 24/233 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD--------SKGQKPRLTHRLDQ 152
           ++YED  + V NK AG++V    GI +H +  + + +            ++P + HRLD+
Sbjct: 81  IIYEDDDLIVINKAAGMTVH--PGIRHHDNTLVNALLHHTKYLSDIGSAERPGIVHRLDK 138

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +T+G++VVA+       L    + R++ + Y +LVWG+  N  E I    + ++      
Sbjct: 139 DTTGLMVVAKNNKTHILLANQIKQRQVIRKYKALVWGVI-NPLEGIIKNNVGRNRNNRKK 197

Query: 213 VHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           + ++K    G   A++++K ++ F       +E +  TGRTHQ+RV   ++   +VGD  
Sbjct: 198 MTILKY---GGKKAVTYYKTLELFYGGTLSMVECKLSTGRTHQIRVQLSNLKHSVVGDQT 254

Query: 272 YCANFKGNFTSP--IQNKLY------LHARYMDLPHPEGGR-LQITAPLPAHM 315
           Y  N +    SP  ++ KL       LH+ Y+   HP     +  +  LP  M
Sbjct: 255 YGNNNRKIINSPPKLKAKLIAFKRQALHSWYLSFTHPTSNDIMAFSCELPRDM 307


>gi|297180864|gb|ADI17069.1| pseudouridylate synthases, 23S RNA-specific [uncultured alpha
           proteobacterium HF0010_30A23]
          Length = 265

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 66/206 (32%), Positives = 99/206 (48%), Gaps = 17/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED+ +   NKP G+    G  +  H D  L + V +   +  + HRLD  TSG++V+
Sbjct: 58  VLFEDAALIALNKPEGLLSVPGRRV-EHQDS-LYTRVRALHPEAMVVHRLDLATSGVIVM 115

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-----IANWLLKKSHIGGDYVHV 215
           A+TR A + L+  F+ R ++K Y ++V G+P     C     I +W  +   I       
Sbjct: 116 AKTREANRALSWQFQQRTVEKTYEAVVEGVPVEASGCVDLPLICDWPNRPRQIVDPVQGK 175

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             Q E  A          D   +    + ++P TGR+HQLRVH   MG  I GD  Y A+
Sbjct: 176 PSQTEWVA------LGAQDVSGRTGTRVRLRPLTGRSHQLRVHMAEMGHAIFGDRFY-AS 228

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE 301
             G   S    +L LHA  + L HP+
Sbjct: 229 EDGAAAS---KRLLLHAHVLTLTHPD 251


>gi|227512368|ref|ZP_03942417.1| pseudouridylate synthase RluD [Lactobacillus buchneri ATCC 11577]
 gi|227084341|gb|EEI19653.1| pseudouridylate synthase RluD [Lactobacillus buchneri ATCC 11577]
          Length = 302

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 105/219 (47%), Gaps = 18/219 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED+ + V NK  G        G        L +++ +K   P + HRLDQETSG ++
Sbjct: 89  ILYEDANLIVINKRRGNKTHPNQPGEVGATINHLAAYLKTKEALPYMVHRLDQETSGAIL 148

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+  A    L      + I++ Y + V G   + +  I         IG D     K+ 
Sbjct: 149 FAKNPAVVPTLVAKIATKNIKRTYLAWVVGTDIDSQGII------DFPIGLDPNDKRKRM 202

Query: 220 EKGANYA--ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             G + A  I+H+ V+      +  L +Q  TGRTHQ+RVH   +G P+VGD  Y  + K
Sbjct: 203 IDGNHPAKSITHYTVLQK-EDGYSLLAVQLETGRTHQIRVHLTAIGHPLVGDPLYNPDDK 261

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             F       L LH+  +++P P   + ++ITAPLPAH 
Sbjct: 262 HPF-------LLLHSWKLNIPLPFSEQVIEITAPLPAHF 293


>gi|254373204|ref|ZP_04988693.1| hypothetical protein FTCG_00787 [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|151570931|gb|EDN36585.1| hypothetical protein FTCG_00787 [Francisella novicida GA99-3549]
          Length = 332

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 144/320 (45%), Gaps = 38/320 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E       +NL          +++ED  I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWIAE------DINLK---------IIFEDDDIIVIDKPVNMIVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +  L  + D + + PR  + HRLD++TSG++V A++  A  +L +    R++ + Y
Sbjct: 117 GTVSNALLHRYKD-QDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC 241
            ++V G      E      + +  IG D  +  K   N +G   AI+H+  I+ +   F 
Sbjct: 176 LAIVEG------EIYQQGTINQP-IGRDPTNRTKMAINYRGKE-AITHYTPIEVY-DGFT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF----KGNFTSPIQNKLYLHARYMDL 297
            +E Q  TGRTHQ+RVH   +  P+VGD  Y  +     K    +P +    LHA  +  
Sbjct: 227 LIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAIKTPTRQA--LHAYKLSF 284

Query: 298 PHPEGGRL-QITAPLPAHMV 316
            HP   ++ +  + LP  M+
Sbjct: 285 IHPTTAKMVKFKSKLPEDML 304


>gi|325268497|ref|ZP_08135127.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           multiformis DSM 16608]
 gi|324989025|gb|EGC20978.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           multiformis DSM 16608]
          Length = 568

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 69/209 (33%), Positives = 95/209 (45%), Gaps = 20/209 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  + V  KP G+    G G    +   LK      G  P + HRLD  TSG+LVV
Sbjct: 356 ILYEDDSLAVVAKPPGLLSVPGKGRQPSVYSLLKERWQRSG-APYMVHRLDMATSGLLVV 414

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           ART  A + L   F  R +QK Y +L+ G  P+ +        L  S    D        
Sbjct: 415 ARTAEAHKALQAQFAARTVQKRYVALLPGSFPEQRFPAEGRIELPLSPCPDDRPRQRVDL 474

Query: 220 EKGANYAISHFKVIDCF-----AQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHK 271
           EKG   AI+ ++V          ++   + + P TGRTHQLR+H  H   +G PI+GD  
Sbjct: 475 EKG-KPAITEYRVAGRTKYGKEGREAVKIILHPLTGRTHQLRMHCAHPDGLGTPIIGDSL 533

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y              +L+LHA ++   HP
Sbjct: 534 YGQR---------AGRLWLHAEHLAFTHP 553


>gi|312873566|ref|ZP_07733613.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
 gi|311090819|gb|EFQ49216.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
          Length = 292

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/279 (25%), Positives = 128/279 (45%), Gaps = 35/279 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKN-----HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           Y+ Y+ +  +E N  +D+  +N      + H  F+ ++K      + V+ K +  N ++ 
Sbjct: 13  YIYYLTISQNENNQNVDQIMRNLLIPRKWRH--FLRIEK-----NILVNDKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V +KPAG   Q
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENDDVLVIDKPAG---Q 109

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 110 KTHPNLYETDTALNDCTSYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQK 239
           + Y++ +            N       IG D + + K+  +     AI+H++V+     K
Sbjct: 170 RSYFAWIDATNDISDNGTINL-----PIGDDPLDMRKRMVRTDGLKAITHYQVVKKIGSK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++ 
Sbjct: 225 IL-VKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQA 262


>gi|262377519|ref|ZP_06070741.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter lwoffii
           SH145]
 gi|262307575|gb|EEY88716.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter lwoffii
           SH145]
          Length = 235

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 69/214 (32%), Positives = 109/214 (50%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + V  KPAG+    G    +H   +L+  V  K  + ++THRLD  TSGIL+ 
Sbjct: 32  IVYEDDDLVVIEKPAGLLSVPGRLPEHHDSAYLR--VLDKYPQAKITHRLDMATSGILMF 89

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ R A   +++ F+ R + K Y +LV G  + +       +    +     VH     E
Sbjct: 90  AKHRDAEVAVSKMFQARTVLKNYVALVQGKLEGEGSVEVPLITDWENRPRQMVHF----E 145

Query: 221 KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            G   A + ++ ++   Q+    + + P TGR+HQLRVH LH+G PI GD  Y    +  
Sbjct: 146 LG-KAAKTLYQALEYLPQQDISRVLLTPITGRSHQLRVHMLHIGHPITGDKIYHPEPQ-- 202

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
             SP+ N++ LHA Y+    P  G  ++I A +P
Sbjct: 203 -RSPL-NRMALHASYLAFTQPLSGVPVEIKAAIP 234


>gi|329122662|ref|ZP_08251241.1| pseudouridine synthase A [Haemophilus aegyptius ATCC 11116]
 gi|327472676|gb|EGF18105.1| pseudouridine synthase A [Haemophilus aegyptius ATCC 11116]
          Length = 219

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 67/208 (32%), Positives = 106/208 (50%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+ D  + S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYY-DSVM-SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG  +N         I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD K+ ++
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGD-KFYSH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    SP   +L LHA  + + HP  G
Sbjct: 184 PQAKAMSP---RLCLHAEELTITHPITG 208


>gi|134301739|ref|YP_001121707.1| pseudouridine synthase, RluA family protein [Francisella tularensis
           subsp. tularensis WY96-3418]
 gi|134049516|gb|ABO46587.1| pseudouridine synthase, RluA family protein [Francisella tularensis
           subsp. tularensis WY96-3418]
          Length = 317

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 80/306 (26%), Positives = 137/306 (44%), Gaps = 34/306 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D      +   +   +QK L+ G + V+ +  K  + +   + V I   +   N  I 
Sbjct: 9   RIDVAINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEINIELLPTNEWIA 68

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV 137
           E       +NL          +++ED  I V +KP  + V  G+G       +  L  + 
Sbjct: 69  E------DINLK---------IIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNTLLHRYK 113

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D + + PR  + HRLD++TSG++V A++  A  +L +    R++ + Y ++V G      
Sbjct: 114 D-QDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEG------ 166

Query: 196 ECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           E      + +  IG D  +  K   N +G   AI+H+  I+ +   F  +E Q  TGRTH
Sbjct: 167 EIYKQGTINQP-IGRDPTNRTKMAINYRGKE-AITHYTPIEVY-DGFTLIECQLETGRTH 223

Query: 254 QLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAP 310
           Q+RVH   +  P+VGD  Y   +         I  +  LHA  +   HP   ++ +  + 
Sbjct: 224 QIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITIPTRQALHAYKLSFIHPTTAKMVKFKSK 283

Query: 311 LPAHMV 316
           LP  M+
Sbjct: 284 LPEDML 289


>gi|76787790|ref|YP_330006.1| ribosomal large subunit pseudouridine synthase A [Streptococcus
           agalactiae A909]
 gi|77408235|ref|ZP_00784979.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
 gi|77412105|ref|ZP_00788430.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|76562847|gb|ABA45431.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus agalactiae A909]
 gi|77161861|gb|EAO72847.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77173176|gb|EAO76301.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
          Length = 296

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 111/239 (46%), Gaps = 38/239 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++Y+D  + V NKP G+ V   +G         + YHI    K      G  +P + HR+
Sbjct: 76  IIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHI----KDLSSINGVVRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+   A Q L E  + ++  + Y ++V G   N +  I      ++ IG 
Sbjct: 132 DKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVI------EAPIGR 185

Query: 211 DYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 KQ    KG   AI+ F V++ F   +  +E+   TGRTHQ+RVH  ++G P+ G
Sbjct: 186 SDKDRKKQAVTAKG-KPAITRFHVLERFGD-YTLVELSLETGRTHQIRVHMAYIGHPLAG 243

Query: 269 DHKY----CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           D  Y        KG F         LHA+ +   HP  G  L  +  +P     T D L
Sbjct: 244 DPVYGPRKTLGGKGQF---------LHAQTLGFTHPSNGENLIFSVEVPEIFQTTLDKL 293


>gi|254823760|ref|ZP_05228761.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
 gi|255521997|ref|ZP_05389234.1| ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes FSL J1-175]
 gi|293592981|gb|EFG00742.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
          Length = 296

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 76/313 (24%), Positives = 148/313 (47%), Gaps = 40/313 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           VE +E+ + L  + K+ +     +   K    G++ V+ K       +++G  VR+  P 
Sbjct: 7   VETEEDGLLLRTFLKSKHISKQLLTAVKFGAEGKIEVNNKEQNVLYHVKAGDKVRLTFPT 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 ++ E   LD               +++ED  + + NKPAG++        YH +
Sbjct: 67  EQQNERLLAEYTDLD---------------IIFEDDFLLIINKPAGMASIPSQ---YHPN 108

Query: 131 GFLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + ++V    +   LT+      RLD+ETSG++++A+ R A   L+   +   +++ Y 
Sbjct: 109 GSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQ 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWL 243
           +   G+   +K  I      ++ IG   V ++++       YA ++++V+  + + F  +
Sbjct: 169 AFTSGVLVEQKGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY-RAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTE 275

Query: 304 R-LQITAPLPAHM 315
           + +    PLPA M
Sbjct: 276 KYMAFDLPLPADM 288


>gi|114771661|ref|ZP_01449065.1| putative Pseudouridine synthase, Rlu [alpha proteobacterium
           HTCC2255]
 gi|114547733|gb|EAU50623.1| putative Pseudouridine synthase, Rlu [alpha proteobacterium
           HTCC2255]
          Length = 341

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 91/341 (26%), Positives = 145/341 (42%), Gaps = 67/341 (19%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRV-KFN 56
           MS    V+  + EN     RLD+   +  P    ++   + K++  G V +  + + K  
Sbjct: 1   MSAPYVVELTLGENPAP--RLDKALASVVPAEVTLSRSRITKLIAEGAVTLAGEPITKLK 58

Query: 57  NRIQSGQVVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
            +  +G + RI  PPV +  N    E   LD               +++ED  + + NKP
Sbjct: 59  YKAPAGSIFRIVMPPVQDYEN-AQPENIPLD---------------IVFEDDHLIIVNKP 102

Query: 115 AGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
           AG+ V    G         + Y+ DG L      K  +P + HR+D++TSG+LVVA++ +
Sbjct: 103 AGMVVHPAPGSENGTLVNALLYYFDGNLSGVGGEK--RPGIVHRIDKDTSGLLVVAKSDS 160

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN------ 219
           A   L + F    I + Y ++  G+P+     +A         GG  V  V  N      
Sbjct: 161 AHAGLAKQFADHSISRRYLAVSKGVPQKSDPRLAGLRGVNFEDGG--VIRVATNIARHKT 218

Query: 220 --------EKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                   +    +AI+   V++ FA      CWLE    TGRTHQ+RVH  H+G  ++G
Sbjct: 219 DRKRMAVVQDAGRHAITRATVLENFAHSALMECWLE----TGRTHQIRVHFSHIGHGLIG 274

Query: 269 DHKYCAN--FKGNFTSPIQ-------NKLYLHARYMDLPHP 300
           D  Y       G+   P         ++  LHA+ +   HP
Sbjct: 275 DPIYGLRKAMPGSVFEPEDMVIVKGFSRQALHAKSIGFIHP 315


>gi|182419830|ref|ZP_02951070.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Clostridium butyricum 5521]
 gi|237666579|ref|ZP_04526564.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum E4 str. BoNT E BL5262]
 gi|182376378|gb|EDT73960.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Clostridium butyricum 5521]
 gi|237657778|gb|EEP55333.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum E4 str. BoNT E BL5262]
          Length = 301

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 76/272 (27%), Positives = 130/272 (47%), Gaps = 36/272 (13%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
           VK N  I  G+V++I    +    I  E+  ++               ++YED  I V N
Sbjct: 48  VKMNRVINEGEVIKIDLAKDESQDIAPEKMDIE---------------IIYEDEDILVVN 92

Query: 113 KPAGISV------QGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTR 164
           K   + V      Q G+     I+ F++S     GQ    RL  RLD  TSG++++A+ +
Sbjct: 93  KKPFMVVHPTKSYQSGTLANGVINYFMES-----GQNCIVRLVSRLDMNTSGLIIIAKNQ 147

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            +   L++     ++ K Y ++V GI +N++  I   + +   I    + +V  +E+G  
Sbjct: 148 FSHGMLSKEMTENKVTKRYLAVVHGILENEEGTIDRPIYRPEGIDFGIMRIV--DERGQR 205

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
            +I+H+KVI+ + +    +E    TGRTHQ+RVH   +G PI GD  Y +   G+    +
Sbjct: 206 -SITHYKVIEKY-ENASLVECTLETGRTHQIRVHLSSIGHPIYGDSLYGS---GDEEQDL 260

Query: 285 QNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            ++  LHA  +D   P  G  L + + LP  +
Sbjct: 261 ISRQALHAYSLDFRSPRTGEILSLKSNLPEDI 292


>gi|85704028|ref|ZP_01035131.1| ribosomal large subunit pseudouridine synthase A [Roseovarius sp.
           217]
 gi|85671348|gb|EAQ26206.1| ribosomal large subunit pseudouridine synthase A [Roseovarius sp.
           217]
          Length = 214

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 63/208 (30%), Positives = 101/208 (48%), Gaps = 22/208 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D +I V NKPAG+    G G   H+   L + V        L HRLD++TSG+++ 
Sbjct: 13  VLHDDHEIVVVNKPAGLLSVPGKG--EHLADCLMARVKDVFPTALLVHRLDRDTSGVMIF 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-----IPKNKKECIANWLLKKSHIGGDYVHV 215
           A T  A +HL   F  R+++K Y + VWG     +       I +W  +          +
Sbjct: 71  ALTPHAQRHLGLQFEKRQVRKTYVARVWGRLEPQVGVVDLPLIVDWPNRP---------L 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K   +    A++ ++V+         + + P TGR+HQLRVH L +G  I+GD  Y   
Sbjct: 122 QKVCHETGRAALTDWRVLRA-GDDETRVRLSPKTGRSHQLRVHMLALGHVILGDPLYAQG 180

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              ++      +L LH+  + L HP+GG
Sbjct: 181 AARDYP-----RLMLHSEELRLRHPDGG 203


>gi|329923371|ref|ZP_08278854.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
 gi|328941362|gb|EGG37655.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
          Length = 353

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 110/250 (44%), Gaps = 44/250 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSG 156
           +LYED  + V NKPAG+ V    G       +G +  W   KG   + R  HRLDQETSG
Sbjct: 86  ILYEDEHLLVLNKPAGVIVHPTHGHYTDTLANGVVHYW-QEKGWNYRFRAVHRLDQETSG 144

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV+A+     QH++E      + K Y + V G P    +           I  D +   
Sbjct: 145 VLVIAKNAYIHQHVSEQMIAGTVDKRYVAFVHGRPSPTGDI-------DGPIDRDPLEPH 197

Query: 217 KQNEKGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--- 272
           ++      Y +++ ++V + +      +E++  TGRTHQ+RVH L +GCP++GD  Y   
Sbjct: 198 RRIVTPEGYPSLTRYRVCETYPSA-SLVELKLETGRTHQIRVHMLSIGCPLIGDQMYRHP 256

Query: 273 ----------------CANFKGNFTSPI----------QNKLYLHARYMDLPHP-EGGRL 305
                            +N       P+           ++  LHA  + L HP EG  +
Sbjct: 257 LYSDQGLLPDAPERDEDSNGAVGSLDPLAATIMRLDGYMDRQALHAASLTLMHPIEGKTM 316

Query: 306 QITAPLPAHM 315
              APLP  M
Sbjct: 317 VFRAPLPEDM 326


>gi|315658516|ref|ZP_07911388.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           lugdunensis M23590]
 gi|315496845|gb|EFU85168.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           lugdunensis M23590]
          Length = 305

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 146/318 (45%), Gaps = 37/318 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT     + +      R+D+   ++    +   +Q  ++   V V+ K +K N++++   
Sbjct: 1   MTTHSIEITDTRHTGQRIDKLLSDYNHDWSRSQIQDWIKHELVIVNGKAIKANHKVKLHD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           +I E++++D+ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  SI-----------VITEKEVVDADIQ----PENLNLDIYYEDKDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L +    +
Sbjct: 106 GHYSGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRSLVDQLVAK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIAN-WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +++ Y +LV G IP +     A     KK     D V      + G + A++HF V++ 
Sbjct: 166 SVKRKYTALVHGNIPHDYGTVDAPIGRNKKDRQSMDVV------DDGKD-AVTHFNVLEH 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +
Sbjct: 219 F-KDYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPKKTLDIGGQA-----LHAGLI 272

Query: 296 DLPHPEGGR-LQITAPLP 312
              HP  G  ++  A LP
Sbjct: 273 GFEHPVTGEYIERQAALP 290


>gi|149019517|ref|ZP_01834836.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP23-BS72]
 gi|147930892|gb|EDK81872.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP23-BS72]
          Length = 237

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 116/236 (49%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 18  IVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 74

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I      ++ IG  
Sbjct: 75  KDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI------EAPIGRS 128

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                KQ    KG   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G  + GD
Sbjct: 129 EKDRKKQAVTAKG-KPAVTRFHVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHSVAGD 186

Query: 270 HKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y      KG+         +LHA+ +   HP  G+ L+  A +P    +T + L
Sbjct: 187 EVYGPRKTLKGHGQ-------FLHAKTLGFTHPRTGKTLEFKADIPEIFKETLERL 235


>gi|284050466|ref|ZP_06380676.1| pseudouridine synthase, RluA family protein [Arthrospira platensis
           str. Paraca]
 gi|291570540|dbj|BAI92812.1| probable pseudouridine synthase [Arthrospira platensis NIES-39]
          Length = 309

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 105/233 (45%), Gaps = 17/233 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILV 159
           ++YED+ I V  KP+G+ V  G G   H    L+       Q  P   HRL + TSG+++
Sbjct: 83  VIYEDADILVVAKPSGLPVIPGGGFLEHT--LLRQLQRKYPQDTPIPIHRLGRGTSGLVL 140

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR+     +LT+  R R+I K+Y +L  G        I   + K  H    Y++   + 
Sbjct: 141 LARSTVGRSYLTKQMRQRQITKVYLALAEGCSPRDYFSINCAIGKIPHPIIGYIYGATET 200

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              A    S+ +VI   + K   +++   TGR HQ+R+H    G P+VGD  Y    K  
Sbjct: 201 GLSAE---SNCQVIRRDSDKMI-VQVTILTGRPHQIRIHLAAAGFPLVGDPLYTIGGKPR 256

Query: 280 FTSPIQN---------KLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
            T P  N           YLHA  +   HP+ G  L +TA  P  +   +  +
Sbjct: 257 ITDPTSNHHSTFPGDCGYYLHAYSLSFQHPQTGANLHLTATPPQELSTEYPPM 309


>gi|281423241|ref|ZP_06254154.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           F0302]
 gi|299140516|ref|ZP_07033654.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           C735]
 gi|281402577|gb|EFB33408.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           F0302]
 gi|298577482|gb|EFI49350.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           C735]
          Length = 299

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 107/228 (46%), Gaps = 17/228 (7%)

Query: 92  KHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRL 146
           +++D  KS    ++YED  + V  K  GI        + ++   L  +     QK    +
Sbjct: 76  RNNDIFKSRYVKIVYEDRHLVVVEKNIGILSMAAGHSSLNVKAVLDDYFKKSRQKCMAHV 135

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ETSG+++ A+ +     L   +      + Y ++V G  + ++  IANWL    
Sbjct: 136 VHRLDRETSGLMLYAKDKETELLLERDWHHIVFDRRYVAVVSGEMEQREGTIANWLKDNK 195

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                Y+      + G  YA++HF V++     +  +E +  TGR +Q+RVH+  MG P+
Sbjct: 196 ----AYITYSSPVDNGGKYAVTHFHVLN-RNDNYSLVEYKLETGRKNQIRVHSADMGHPV 250

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
            GD KY     GN   PI  +L LHA  +   HP     +    P+PA
Sbjct: 251 CGDTKY-----GNGDDPI-GRLCLHAYVLCFYHPITHVPMTFETPIPA 292


>gi|15640728|ref|NP_230358.1| 23S rRNA pseudouridine synthase D [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|153822744|ref|ZP_01975411.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           B33]
 gi|227080889|ref|YP_002809440.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           M66-2]
 gi|229505673|ref|ZP_04395183.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           BX 330286]
 gi|229508754|ref|ZP_04398247.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           B33]
 gi|229519496|ref|ZP_04408939.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC9]
 gi|229608691|ref|YP_002879339.1| 23S rRNA pseudouridine synthase D [Vibrio cholerae MJ-1236]
 gi|254851039|ref|ZP_05240389.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MO10]
 gi|255743834|ref|ZP_05417790.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholera
           CIRS 101]
 gi|262156053|ref|ZP_06029172.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           INDRE 91/1]
 gi|298500820|ref|ZP_07010623.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MAK 757]
 gi|34395835|sp|Q9KU20|RLUD_VIBCH RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|9655151|gb|AAF93874.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|126519727|gb|EAZ76950.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           B33]
 gi|227008777|gb|ACP04989.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           M66-2]
 gi|229344185|gb|EEO09160.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC9]
 gi|229354278|gb|EEO19208.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           B33]
 gi|229357896|gb|EEO22813.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           BX 330286]
 gi|229371346|gb|ACQ61769.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MJ-1236]
 gi|254846744|gb|EET25158.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MO10]
 gi|255738465|gb|EET93854.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholera
           CIRS 101]
 gi|262030089|gb|EEY48734.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           INDRE 91/1]
 gi|297540601|gb|EFH76659.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MAK 757]
          Length = 324

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 86/338 (25%), Positives = 154/338 (45%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G++ V+   + K   ++  G+V+ +  
Sbjct: 10  TVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +        EQ+     + L          ++YED  I V NKP    V  G+G A   
Sbjct: 70  ELE------DEQRWEAQDLPLN---------IVYEDDDIIVINKPRDFVVHPGAGQADKT 114

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L  +     + PR  + HRLD++T+G++VVA+T  A   L  + + R + + Y +
Sbjct: 115 VLNALLFHY-SPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN----EKGANYAISHFKVIDCFAQKFC 241
           +V G         A  ++ K  IG    H  K+          +A++H++V + F ++  
Sbjct: 174 IVIGT------MTAGGMIDKP-IGR---HSTKRTLMSVSPMGKHAVTHYRVAEHF-REHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLHAR 293
            L ++  TGRTHQ+RVH  ++  P++GD  Y    +         T  I+  ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGATEELTEMIRDFDRQALHAV 282

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
            +   HP  G  L+  AP+P  MV+   +L  + D  L
Sbjct: 283 MLKFEHPVTGEELEFHAPVPDDMVEM--TLALREDAKL 318


>gi|290473651|ref|YP_003466523.1| pseudouridine synthase [Xenorhabdus bovienii SS-2004]
 gi|289172956|emb|CBJ79727.1| pseudouridine synthase [Xenorhabdus bovienii SS-2004]
          Length = 250

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/223 (31%), Positives = 107/223 (47%), Gaps = 19/223 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I   NKPAG  V   S +A H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 4   IIYQDDHIVAVNKPAGWLVHR-SWLARHETVFVMQTLRDQIGQHVFPVHRLDKPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A +   A+ L++ F    IQK Y ++V G  +         + +   I   +       
Sbjct: 63  MALSSEVARTLSQQFECHHIQKTYHAIVRGYVEGDGIIDYALMEELDKIADKFA----DT 118

Query: 220 EKGANYAISHFKV---IDCFAQ-------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           ++ A  AI+H++    ++C  +       +F  LE+ P TGR HQLR H  H+  PI+GD
Sbjct: 119 DREAQSAITHYRSLAKVECPVEIGRYPTSRFSLLELMPKTGRKHQLRRHMSHLRHPIIGD 178

Query: 270 --HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
             H      +G        +L LHA  + L HP  G  L +TA
Sbjct: 179 TTHGDLRQNRGVVKYYQTGRLMLHASQLQLAHPVTGEDLLLTA 221


>gi|253577230|ref|ZP_04854549.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251843344|gb|EES71373.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 321

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 109/235 (46%), Gaps = 28/235 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPRL--THRLDQET 154
           ++YED  + + NK AG+ V    G   H  G L + V      KG+K R    HRLDQET
Sbjct: 87  IVYEDEALLIVNKAAGLIVHPTHG---HYTGTLANGVVYYWQEKGEKFRFRPVHRLDQET 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++ +A+     QH++E      + K Y +LV G P   +  I         I  D   
Sbjct: 144 SGLIAIAKNAYVHQHISEQLIAGEVTKKYTALVHGCPAVPEGTI------DGPIDRDPAE 197

Query: 215 VVKQNEKGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             ++    + Y +++++KV + +      +E++  TGRTHQ+RVH   +G P++GD  Y 
Sbjct: 198 PHRRIVTPSGYPSLTYYKVAEAYGDG-ARVELRLGTGRTHQIRVHMTSIGHPLIGDKFYG 256

Query: 274 ANFKGNFTSPIQNKL----------YLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
                   +P + ++           LHA  +   HP  G  L   + LP  M+K
Sbjct: 257 MPGLAELPAPARERIARLDAAIGRQALHASELGFRHPLTGEALTFKSELPEDMLK 311


>gi|46200775|ref|ZP_00056471.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 166

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 53/172 (30%), Positives = 90/172 (52%), Gaps = 12/172 (6%)

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++ R   + + L   F   R++K+YWS+  G P+     +   LLK S  G  +   +K
Sbjct: 1   MILGRHAKSIKRLGRMFEHHRVEKLYWSVCHGSPEGDSGTVDAPLLKVSGRGQGWR--IK 58

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +  G + +I+ + V+        W+E +P TGRTHQ+R+HA H+GCP++GD  Y  + +
Sbjct: 59  VDPAGQS-SITDWSVLG-RGGGLSWIEWRPRTGRTHQIRIHAQHLGCPLLGDAYYGPDPE 116

Query: 278 GNFTSPIQNKLYLHARYMDLP--HPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
                    +L+L AR +  P   P    +++TAP P HMV+     G++ D
Sbjct: 117 ------TMTRLHLLAREVSFPALSPSKDPVRVTAPPPGHMVEALRVCGWRED 162


>gi|282882144|ref|ZP_06290785.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus
           lacrimalis 315-B]
 gi|281298174|gb|EFA90629.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus
           lacrimalis 315-B]
          Length = 295

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 115/229 (50%), Gaps = 18/229 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSW----VDSKGQKPRLTHRLDQET 154
           ++YED  I V +KP  + V  G+G +    ++G L  +     D    +P + HRLD+ T
Sbjct: 77  VIYEDEYIAVISKPQDLVVHIGAGNSSGTLVNGLLYKFKNQLSDLDPLRPGIVHRLDKNT 136

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+   A  +L + F+  +I+K Y ++V G  K  +  I    + ++      + 
Sbjct: 137 SGLMIIAKNNQAHINLVDQFKNSQIKKYYLAIVHG--KTPESGIIAEPIGRNPNDRKKMA 194

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV +N K    AI+ +K +  F Q++  L +   TGRTHQ+RVH  ++G P++GD  Y  
Sbjct: 195 VVYKNSKQ---AITKYKKLKEF-QEYSLLNINLLTGRTHQIRVHMAYIGYPVLGDIIY-- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
              G   S   +K  LH+  +   HP    +++ T   P    K  D +
Sbjct: 249 ---GRKNSLKIDKQMLHSYKLIFNHPITNQKMEFTDEFPIRFKKFIDKI 294


>gi|89256088|ref|YP_513450.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. holarctica LVS]
 gi|115314564|ref|YP_763287.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           OSU18]
 gi|167010773|ref|ZP_02275704.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           FSC200]
 gi|169656565|ref|YP_001428170.2| RNA pseudouridine synthase, RluA family protein [Francisella
           tularensis subsp. holarctica FTNF002-00]
 gi|254367416|ref|ZP_04983442.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. holarctica 257]
 gi|254369095|ref|ZP_04985107.1| hypothetical protein FTAG_00024 [Francisella tularensis subsp.
           holarctica FSC022]
 gi|290954527|ref|ZP_06559148.1| RNA pseudouridine synthase, RluA family protein [Francisella
           tularensis subsp. holarctica URFT1]
 gi|295312043|ref|ZP_06802858.1| RNA pseudouridine synthase, RluA family protein [Francisella
           tularensis subsp. holarctica URFT1]
 gi|89143919|emb|CAJ79138.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. holarctica LVS]
 gi|115129463|gb|ABI82650.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           OSU18]
 gi|134253232|gb|EBA52326.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. holarctica 257]
 gi|157122045|gb|EDO66185.1| hypothetical protein FTAG_00024 [Francisella tularensis subsp.
           holarctica FSC022]
 gi|164551633|gb|ABU61214.2| RNA pseudouridine synthase, RluA family protein [Francisella
           tularensis subsp. holarctica FTNF002-00]
          Length = 332

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 80/318 (25%), Positives = 142/318 (44%), Gaps = 34/318 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E       +NL          +++ED  I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWIAE------DINLK---------IIFEDDDIIVIDKPVNMIVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +  L  + D + + PR  + HRLD++TSG++V A++  A  +L +    R++ + Y
Sbjct: 117 GTVSNALLHRYKD-QDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC 241
            ++V G      E      + +  IG D  +  K   N +G   AI+++  I+ +   F 
Sbjct: 176 LAIVEG------EIYQQGTINQP-IGRDPTNRTKMAINYRGKE-AITYYTPIEVY-DGFT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPH 299
            +E Q  TGRTHQ+RVH   +  P+VGD  Y   +         I  +  LHA  +   H
Sbjct: 227 LIECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITIPTRQALHAYKLSFIH 286

Query: 300 PEGGRL-QITAPLPAHMV 316
           P   ++ +  + LP  M+
Sbjct: 287 PTTAKMVKFKSKLPEDML 304


>gi|114562064|ref|YP_749577.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114333357|gb|ABI70739.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 579

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 115/235 (48%), Gaps = 21/235 (8%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGF 132
           L H++K   + D  + +    D    I+ Y+D  + + NKPA + SV G +         
Sbjct: 351 LTHMLKGMLVDDDPLLINPGKDQHIDII-YQDDAMVIINKPAELLSVPGKNITDSVFSRM 409

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            + + ++ G  P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ G+P 
Sbjct: 410 QQQFPNATG--PLIVHRLDMSTSGLMVIALTKEANKALQQQFIQRSVTKRYIALIEGVPS 467

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +  I+  L        D    +   E G  +A +H++V     Q+   + + P TGRT
Sbjct: 468 QDEGDISLPLRVDL---DDRPKQLVCYEHG-KHAETHWQVYQRQGQR-TLVYLYPKTGRT 522

Query: 253 HQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           HQLR+H  H   +  PIVGD  Y             N+L+LHA+Y+ L HP  G+
Sbjct: 523 HQLRMHCAHHDGLHMPIVGDDLYGV---------ATNRLHLHAQYLSLNHPVSGK 568


>gi|327312402|ref|YP_004327839.1| RluA family pseudouridine synthase [Prevotella denticola F0289]
 gi|326945177|gb|AEA21062.1| pseudouridine synthase, RluA family [Prevotella denticola F0289]
          Length = 319

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 101/216 (46%), Gaps = 14/216 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           ++YED  + V  K  GI        + ++   L  +     QK    + HRLD++TSG++
Sbjct: 108 IVYEDRFLVVVEKNIGILSMAAGHASLNVKSILDDYFYKTRQKCTAHVVHRLDRDTSGLM 167

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A+     Q     +      + Y  +V G  +  +  +ANWL         YV     
Sbjct: 168 IYAKDMQTEQLFEHDWHNIVYDRRYVGVVSGEMEQDEGTVANWLKDNK----AYVTYSSP 223

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            + G  YA++HF V+D     +  +E +  TGR +Q+RVH+  MG P+ GD KY     G
Sbjct: 224 VDNGGKYAVTHFYVLD-RTVAYSLVEYRLETGRKNQIRVHSADMGHPVCGDVKY-----G 277

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           N   P+ ++L LHA  +   HP    R++   P+PA
Sbjct: 278 NGDDPL-HRLCLHAYVLCFHHPVTHQRMEFETPVPA 312


>gi|282877802|ref|ZP_06286615.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
 gi|281300118|gb|EFA92474.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
          Length = 295

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 78/311 (25%), Positives = 141/311 (45%), Gaps = 37/311 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQV 64
           Y +Y V + D     L  W  NH  +++   ++  L    + V+ K + +F+  +++G  
Sbjct: 10  YDRYEVAQADT----LLNWLLNHVTNLSKSKIKATLAGKGIIVNGKCITQFDYPLEAGMK 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +                  S  N+   + +LK  ++YED  + V  K  GI       
Sbjct: 66  IAVSK----------------SKKNINFKNRYLK--IVYEDRYLVVIEKHVGILSMAAGH 107

Query: 125 IAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            + ++   L  +  +  QK    + HRLD+ETSG+++ A+  A  Q L  ++      + 
Sbjct: 108 SSLNVKRVLDDYFRNSKQKCTAHVVHRLDRETSGLMIYAKDMATEQELEHNWHDIVYDRR 167

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G  ++ +  I +WL         YV      + G  +AI+HF  +D    +   
Sbjct: 168 YVAVVSGEMEDDEGVITSWLKDNKA----YVTYSSPVDNGGKFAITHFHTLD-RTTEHSL 222

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGR +Q+RVH+  +G P+ GD KY     GN  +P+ ++L LHA  +   HP  
Sbjct: 223 VEYRLETGRKNQIRVHSADIGHPVCGDFKY-----GNGDNPL-DRLCLHAYMLCFTHPVT 276

Query: 303 GR-LQITAPLP 312
            R ++    +P
Sbjct: 277 RRPMEFETQIP 287


>gi|227486639|ref|ZP_03916955.1| pseudouridylate synthase [Anaerococcus lactolyticus ATCC 51172]
 gi|227235351|gb|EEI85366.1| pseudouridylate synthase [Anaerococcus lactolyticus ATCC 51172]
          Length = 297

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 77/317 (24%), Positives = 143/317 (45%), Gaps = 39/317 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D++  +    I    ++  +++  ++V+ K++K + ++Q G  + I   +  +  I 
Sbjct: 9   IRVDKYISDELDSIPREKIKDFIKASLIKVNDKKIKPSFKLQMGDEIFIDDSLFEVQEIK 68

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK-------PAGISVQGGSGIA----Y 127
            E   LD               ++YE++   + NK       PAG  V G    A    Y
Sbjct: 69  AEDIPLD---------------IVYENNDYAIINKQKNLIVHPAGAIVTGTLVNALLYKY 113

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             DG      D +   P + HRLD++T+G++V+A+   + ++L   F  R+++K Y ++V
Sbjct: 114 GYDGLSHIGGDDR---PGIVHRLDKDTTGLMVIAKNNESYRYLKTLFETRQVRKEYLAIV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G    K   I N++ +  H        V+ +      AIS ++V+      F  +++  
Sbjct: 171 FGNFDEKCGRIENFMDRDPH--NRRKMAVRPS---GRRAISEYEVL-SETDGFSLVKVHI 224

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH   +  P++GD  Y  NFK  F     +   LH  ++     +G  +  
Sbjct: 225 ITGRTHQIRVHMTSINHPLLGDPVY-GNFKHKFN---LDHPLLHCAHLSFEDKDGNEMVF 280

Query: 308 TAPLPAHMVKTWDSLGF 324
              +P    K  + LG 
Sbjct: 281 DKEVPEEFEKYKNILGL 297


>gi|116670141|ref|YP_831074.1| ribosomal large subunit pseudouridine synthase D [Arthrobacter sp.
           FB24]
 gi|116610250|gb|ABK02974.1| ribosomal large subunit pseudouridine synthase D [Arthrobacter sp.
           FB24]
          Length = 308

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 113/235 (48%), Gaps = 26/235 (11%)

Query: 101 LLYEDSKIYVFNKPAGIS------------VQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           +L +D    V +KP G++            V G +G+ Y I            ++  + H
Sbjct: 82  ILLDDEDFVVIDKPVGVAAHPSPGWVGPTVVGGLAGLGYRIS------TSGAPERAGIVH 135

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG +VVA++  A   L  +F+ R + K+Y ++V G+P      I   + +  H 
Sbjct: 136 RLDVGTSGAMVVAKSERAYTALKRAFKERTVDKVYHAVVQGLPDPLAGTIDAPIGR--HP 193

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           G D+   V ++ +    +++H++V++ F  K   +E+   TGRTHQ+RVH   +  P  G
Sbjct: 194 GHDWRFAVIEDGR---ESVTHYEVLEAFG-KASLVEVHLETGRTHQIRVHFSALRHPCAG 249

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           D  Y A+ +   T  +  + +LHAR +    P  G R+ +T+  P  +    + L
Sbjct: 250 DLTYGADPRLAATLGLTRQ-WLHARQLGFDSPRTGERVTVTSDYPQDLAYALEVL 303


>gi|328474367|gb|EGF45172.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus 10329]
          Length = 255

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/249 (28%), Positives = 113/249 (45%), Gaps = 31/249 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       Y     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 17  IVYQDEYFVAVNKPAGMLVHRSWLDKYETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F   +++K Y ++V G    ++E + ++ LK     I   +      
Sbjct: 77  ALSSEVASQVMPMFAEHKMEKTYHAIVRGW--IEEEGVLDYALKVELDKIADKFA----S 130

Query: 219 NEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            EK A  A++ +K +               ++C +EM+P TGR HQLR H  H+  PIVG
Sbjct: 131 QEKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIVG 190

Query: 269 DH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL- 322
           D      K+   F+  F S   ++L LHA  +   HP      +   + A +  TW  L 
Sbjct: 191 DTSHGDGKHNKLFRNEFDS---HRLLLHASELRFVHPFTNEELV---MKASIDDTWQQLF 244

Query: 323 -GFKYDRNL 330
             F++D  L
Sbjct: 245 TRFEWDEEL 253


>gi|225868502|ref|YP_002744450.1| RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
 gi|225701778|emb|CAW99179.1| putative RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
          Length = 298

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 58/205 (28%), Positives = 100/205 (48%), Gaps = 16/205 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    + NKPAG +    +  +  I  F+K++    D   ++  +  RLD++TSG+
Sbjct: 78  IVYEDEHFLILNKPAGYASIPSAIHSNTIANFIKAYYIKQDYPNKQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + R I K Y++LV G  +  ++ E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQQRAINKRYYALVCGQERLPDQGEIIAPIGRTDDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +       YA + +KVI  + +    ++++ HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRTVTPKGKYAKTSYKVIARYPENVSLVDIRLHTGRTHQIRVHFAHLGFPLLGDDLYGGR 251

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                T     +  LH  ++   HP
Sbjct: 252 LDLGMT-----RQALHCHHLSFTHP 271


>gi|195978164|ref|YP_002123408.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
 gi|195974869|gb|ACG62395.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
          Length = 298

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 58/205 (28%), Positives = 100/205 (48%), Gaps = 16/205 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    + NKPAG +    +  +  I  F+K++    D   ++  +  RLD++TSG+
Sbjct: 78  IVYEDEHFLILNKPAGYASIPSAIHSNTIANFIKAYYIKQDYPNKQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + R I K Y++LV G  +  ++ E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQQRAINKRYYALVCGQERLPDQGEIIAPIGRTDDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +       YA + +KVI  + +    ++++ HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRTVTPKGKYAKTSYKVIARYPENVSLVDIRLHTGRTHQIRVHFAHLGFPLLGDDLYGGR 251

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                T     +  LH  ++   HP
Sbjct: 252 LDLGMT-----RQALHCHHLSFTHP 271


>gi|50365205|ref|YP_053630.1| 23S rRNA/tRNA pseudouridine synthase [Mesoplasma florum L1]
 gi|50363761|gb|AAT75746.1| 23S rRNA/tRNA pseudouridine synthase [Mesoplasma florum L1]
          Length = 311

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/222 (31%), Positives = 111/222 (50%), Gaps = 21/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKG--QKPRLTHRLDQE 153
           ++YED  I V NKP  + V  G+G     +   + G    ++ + G  ++P + HR+D++
Sbjct: 81  IVYEDDDILVVNKPNNMVVHPGAGNTEGTMVNALLGRDAEFLSTIGGVERPGIVHRIDKQ 140

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G+L+VA+   + Q LTE  +   I K Y +LVWG  K  K  I +  + +       +
Sbjct: 141 TTGLLIVAKNDKSHQVLTEMLKNHEIYKEYVALVWGEIKEDK-GIIDAPIGRHQNDRKKM 199

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY- 272
            V  +N K   YA+++F+VI     K   ++    TGRTHQ+RVH   +  PIV D  Y 
Sbjct: 200 MVTSKNSK---YAVTNFEVIKRL-DKTTLVKCAIETGRTHQIRVHFNFIKHPIVNDPSYG 255

Query: 273 -CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             A  + +F         LHA  ++  HP    + ++ A LP
Sbjct: 256 KLAEKQTDFGQ------MLHAYKLEFLHPITKEMVKLKAELP 291


>gi|224542059|ref|ZP_03682598.1| hypothetical protein CATMIT_01233 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524992|gb|EEF94097.1| hypothetical protein CATMIT_01233 [Catenibacterium mitsuokai DSM
           15897]
          Length = 276

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 64/215 (29%), Positives = 111/215 (51%), Gaps = 17/215 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILV 159
           LLYED  + V NKP+G+  +      Y    ++   +   K Q+  L HRLDQ+TSG+L+
Sbjct: 66  LLYEDDDMIVINKPSGLVSEETRNNKYQTAFYMVMEYCRKKRQQCYLVHRLDQDTSGVLM 125

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             + +   Q LT ++      + Y +++ G  + K   I N L++   +    + + K+ 
Sbjct: 126 FVKNKKLYQELTHNWNKYVKTRGYVAILEGQCR-KSGTIKNHLVEDKQLK---MRIAKEG 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +     AI+H+K ++  ++ +  +E+   TGR +Q+RVH   +  PI+GD KY     G 
Sbjct: 182 Q----LAITHYKPLEV-SKDYTMMEVFLDTGRKNQIRVHMASLNHPIIGDRKY-----GA 231

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
            T+P++ +L LHA      HP   + +   APLP+
Sbjct: 232 CTNPLK-RLGLHAHEFAFTHPFTHKTMTFKAPLPS 265


>gi|167759623|ref|ZP_02431750.1| hypothetical protein CLOSCI_01981 [Clostridium scindens ATCC 35704]
 gi|167662749|gb|EDS06879.1| hypothetical protein CLOSCI_01981 [Clostridium scindens ATCC 35704]
          Length = 229

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 66/191 (34%), Positives = 90/191 (47%), Gaps = 19/191 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPRLT--HRLDQET 154
           +LYEDS I V  KP G+  Q        ++  +K+ +      KG+ P L   HRLDQ  
Sbjct: 8   ILYEDSHILVCIKPHGVPTQSRRAGTPDMESLIKNHICQSAPEKGE-PYLAVIHRLDQPV 66

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            GILV A+T  AA+ L    +     K Y +L  G P  K+  + ++L+K        V 
Sbjct: 67  KGILVFAKTPFAAKELNRQLQSHGFGKYYRALADGHPSQKEGTLEDYLIKDGRTNTSRVC 126

Query: 215 VVKQNEKGANYAISHFKVID----CFAQK------FCWLEMQPHTGRTHQLRVHALHMGC 264
           V      GA  A  H+ V++     F Q          L+++  TGR HQ+RV   HMGC
Sbjct: 127 V--SGTAGAKLARLHYTVVEQGPFLFDQSKDDDAPRTELDIRLDTGRHHQIRVQLSHMGC 184

Query: 265 PIVGDHKYCAN 275
           PI GD KY  N
Sbjct: 185 PIAGDTKYNPN 195


>gi|42523281|ref|NP_968661.1| ribosomal large subunit pseudouridine synthase C [Bdellovibrio
           bacteriovorus HD100]
 gi|39575486|emb|CAE79654.1| ribosomal large subunit pseudouridine synthase C [Bdellovibrio
           bacteriovorus HD100]
          Length = 231

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 112/231 (48%), Gaps = 15/231 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWV-DSKGQKPRLT--HRLDQETS 155
           +L+ED       KPAG+  Q     +   D F  LK+ + + +G    L   HRLD++TS
Sbjct: 4   ILFEDEFFLAAAKPAGMPSQATVDKSRQ-DFFTALKNQLRNERGDAFYLALHHRLDRDTS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE-CIANWLLKKSHIGGDYVH 214
           G+++ A+T+ A + L + F+  +IQK Y  L     K      + N L++          
Sbjct: 63  GVMIFAKTKEANEPLADLFKTHKIQKTYLCLTKRTQKAADAWEVDNHLVEMKDTKLKKTK 122

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +V+  + G + A + F+ ++ F +    +E QP TGR HQ+RVH    G  I GD  Y A
Sbjct: 123 MVR-TQSGGDRAYTKFRKLEVFPEAL-LIEAQPLTGRMHQIRVHLADRGMGIYGDDIYQA 180

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
                  +P+  +L LHA  ++  HP     ++I   +PA M +   +L F
Sbjct: 181 P-----KNPVAPRLMLHAHALEFTHPFTKEFVRIECAVPADMAQFMKTLTF 226


>gi|170718793|ref|YP_001783975.1| 23S rRNA pseudouridine synthase D [Haemophilus somnus 2336]
 gi|168826922|gb|ACA32293.1| pseudouridine synthase, RluA family [Haemophilus somnus 2336]
          Length = 324

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/247 (27%), Positives = 120/247 (48%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP    V  G+G         + YH    ++  V   G    + HRLD
Sbjct: 85  IVYEDEHILVINKPKDFVVHPGAGNQRGTVLNALLYHYPKIVE--VPRAG----IVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHI 208
           ++T+G++VVA+T  A   L +  + R+I + Y ++ +G+        + ++    K++ +
Sbjct: 139 KDTTGLMVVAKTIPAQTKLVQDLQKRKIIREYEAVAFGVMTQGGKVDQPMSRHPTKRTQM 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               VH +         A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++G
Sbjct: 199 A---VHPL------GKPAVTHYRIMERF-RNYTRLRLRLETGRTHQIRVHMAHISHPLLG 248

Query: 269 DHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           D  Y        N    F   +++  +  LHA  + L HP  G  ++  APLP   V   
Sbjct: 249 DQTYGGRPRPPKNASEEFMQVMRDFKRQALHAIMLCLTHPITGEIMEWEAPLPDDFVTLI 308

Query: 320 DSLGFKY 326
           ++L   Y
Sbjct: 309 NALKADY 315


>gi|303234009|ref|ZP_07320658.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
 gi|302494934|gb|EFL54691.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
          Length = 321

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/277 (25%), Positives = 136/277 (49%), Gaps = 29/277 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ ++N   N R+DR+     P ++  ++QK++R+ +++V+KKR + +  ++   VV 
Sbjct: 1   MRHINIDNSNSNQRVDRFLMKLMPKMSKNHIQKLIRTKKIKVNKKRTEPDYDLKIDDVVN 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I          + ++ I     N    +D     ++YED+ + + NK  G+     +   
Sbjct: 61  I---------YLYDEVIEKYQDNKIYTADDFNLDIIYEDNDLILINKKTGVLSHAANPQD 111

Query: 127 Y--HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           Y  +I   + S++    Q          P L +RLD+ TSGI+V A+T  + ++    F+
Sbjct: 112 YGENIVDMMVSYLIKTNQFKPTQNSTFTPALVNRLDRNTSGIVVGAKTYDSLKYFNGLFK 171

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I KIY ++V G   N K+   ++ L+K +       V+  + K +   + + K    
Sbjct: 172 KHEITKIYETIVVG---NLKDQTIDFALEKDNDKNK--SVINSSGKKSMTKVWNVK---N 223

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           F  K+  + +   TGRTHQ+R H  H+  PI+GD KY
Sbjct: 224 FG-KYSLVNVDLLTGRTHQIRAHLSHINHPIIGDIKY 259


>gi|228938507|ref|ZP_04101115.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228971386|ref|ZP_04132012.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228977999|ref|ZP_04138378.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228781660|gb|EEM29859.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228788253|gb|EEM36206.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228821105|gb|EEM67122.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|326939015|gb|AEA14911.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar chinensis CT-43]
          Length = 307

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 113/228 (49%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGTGTLANLVAFH---FQMQGLEAK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKGKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG N AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-NQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y    K        +   LHA  ++  HP     +++  P P  +
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPTKL 295


>gi|160880920|ref|YP_001559888.1| RluA family pseudouridine synthase [Clostridium phytofermentans
           ISDg]
 gi|160429586|gb|ABX43149.1| pseudouridine synthase, RluA family [Clostridium phytofermentans
           ISDg]
          Length = 346

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/275 (25%), Positives = 123/275 (44%), Gaps = 16/275 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  +E   RLD++   +          K+LR   + ++ K+ +   ++  G +VR
Sbjct: 18  VREITIVQNEAGQRLDKFLAKYLNKAPKSFFYKMLRKKNITLNGKKAEGAEKLIEGDIVR 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +    KE   LD+ VN       +K  +LYEDS + + NKP G+  Q      
Sbjct: 78  LFLAEETIESF-KESYQLDAKVN----QRAVKLDVLYEDSHVVIINKPIGMLSQRAKESD 132

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   L +++   G          KP + +RLD+ TSGI++  ++    Q ++   + R
Sbjct: 133 VSLVELLIAYLLEMGSLTKEELSTFKPSVCNRLDRNTSGIVIAGKSLLGLQEMSAKLQDR 192

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  +V G    K   I  +L K        +     N+  ++Y  + ++ I    
Sbjct: 193 SLHKYYRCIVKGT-MTKGARINGYLAKDEKTNKVRITTNDPNDGESSYIETEYQPI-LSK 250

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +  LE+   TG+THQ+R H   +G PI+GD KY
Sbjct: 251 NGYTLLEVLLITGKTHQIRAHLSSIGHPIIGDTKY 285


>gi|33864307|ref|NP_895867.1| pseudouridine synthase [Prochlorococcus marinus str. MIT 9313]
 gi|33641087|emb|CAE22216.1| Pseudouridine synthase [Prochlorococcus marinus str. MIT 9313]
          Length = 338

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 83/298 (27%), Positives = 140/298 (46%), Gaps = 49/298 (16%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVINALNHIIKEQKILD 85
           HY H +    Q+ L++GQ+R++ + V+ +  + SG  V  + PP + A      E     
Sbjct: 43  HYTHSSRDVWQQRLQAGQIRLNGELVRLDQLLASGDQVCWQRPPWLEAAVPASWE----- 97

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFL--KSWVDSKGQ 142
                          ++++D  + V NKP+G+ V  G G   H + G L  +  +D + +
Sbjct: 98  ---------------VIFDDGDLLVVNKPSGLPVIPGGGFLDHTLTGLLQRRCQLDGESR 142

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-----RRIQKIYWSLV---WGIPKNK 194
            PR  HRL + TSG+L+ AR R     L+  FR      +  +KIY +L      +  ++
Sbjct: 143 LPRPVHRLGRFTSGLLICARQRETRAKLSAMFRRATAGDQGCKKIYRALAHRNLNVHCDE 202

Query: 195 KECIANWLLKKSH--IGGDYV-------HVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
              I   +++ +H  +G  +V       H  KQ+E     A+S  ++++   Q    LE+
Sbjct: 203 VATIRVPIVQTAHPMVGKVWVAADSSRQHDSKQSESRVLTALSTVRLLE-RRQDADLLEV 261

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS---PIQNKLYLHA-RYMDLPH 299
              TGR HQ+R+H   +G P++GD  Y   F G  +S   P      LHA R +D+P+
Sbjct: 262 AIQTGRPHQIRIHLAAIGSPLIGDPLY--GFDGQISSAATPGDGGYCLHAHRLLDVPY 317


>gi|115469990|ref|NP_001058594.1| Os06g0717400 [Oryza sativa Japonica Group]
 gi|75252835|sp|Q5Z8P2|PUS2_ORYSJ RecName: Full=RNA pseudourine synthase 2, chloroplastic; AltName:
           Full=RNA pseudouridylate synthase 2; AltName:
           Full=RNA-uridine isomerase 2; Flags: Precursor
 gi|53791796|dbj|BAD53590.1| ribosomal large subunit pseudouridine synthase-like [Oryza sativa
           Japonica Group]
 gi|54291043|dbj|BAD61720.1| ribosomal large subunit pseudouridine synthase-like [Oryza sativa
           Japonica Group]
 gi|113596634|dbj|BAF20508.1| Os06g0717400 [Oryza sativa Japonica Group]
 gi|215706335|dbj|BAG93191.1| unnamed protein product [Oryza sativa Japonica Group]
 gi|222636236|gb|EEE66368.1| hypothetical protein OsJ_22675 [Oryza sativa Japonica Group]
          Length = 445

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 93/379 (24%), Positives = 149/379 (39%), Gaps = 84/379 (22%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V   E   R+D W                 R G   V + R++ +  I++G VV     
Sbjct: 64  AVPAGEGRSRIDAWIS--------------ARLGGGGVSRARIQAS--IRAGLVVVNGRP 107

Query: 71  INALNHIIKEQKILDSSV----NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           ++ ++H++K   I+  +V     L    + +   ++YED  + V NKPA + V    G  
Sbjct: 108 VSKVSHMVKGGDIVSCTVLELQPLRAEPEDIPLDIVYEDDHLLVVNKPAHMVVHPAPGNA 167

Query: 125 -------IAYH-------------ID---------------------GFLKSWVDSKGQK 143
                  I +H             ID                     G + S V     +
Sbjct: 168 NGTLVNAILHHCKISTFTCLARNSIDDECPDSSDDDIDVFDIDQFTTGEVSSEVREALVR 227

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD+ TSG+LVVA+   +   L E F++  I+++Y SL  G P      I   + 
Sbjct: 228 PGIVHRLDKGTSGLLVVAKDEHSHAQLAEQFKLHTIRRVYISLTCGAPNPNSGRIEVPIA 287

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHM 262
           +  +     +       + A +A S +KV + FA     L E +  TGRTHQ+R HA ++
Sbjct: 288 RDPNNRIRMIATPGSGHRYARHAASRYKVREVFAGGGSALVEWRLETGRTHQIRAHAKYL 347

Query: 263 GCPIVGDHKYCANFK------------------GNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G P++GD  Y                        N  S I ++  LHA  +   HP  G+
Sbjct: 348 GIPLLGDETYGGTKSMALSLLRPRTPSRYHCDLSNMISKI-DRPCLHAALLGFKHPHSGK 406

Query: 305 -LQITAPLPAHMVKTWDSL 322
            L+ + P P    +  + L
Sbjct: 407 ILEFSCPPPDDFTEVLNEL 425


>gi|99079913|ref|YP_612067.1| ribosomal large subunit pseudouridine synthase A [Ruegeria sp.
           TM1040]
 gi|99036193|gb|ABF62805.1| ribosomal large subunit pseudouridine synthase A [Ruegeria sp.
           TM1040]
          Length = 217

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/223 (30%), Positives = 108/223 (48%), Gaps = 33/223 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D+++ V NKPAG+    G G   H+   L + + +   +  L HRLD++TSG++V 
Sbjct: 16  ILHHDAQLLVVNKPAGLLSVPGKGA--HLADCLIARIQAAFPEALLVHRLDRDTSGVMVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKK---ECIANW----LLKKSHIGGD 211
           A T  A +HL   F  R  +K Y + + G   P++       I +W    L K  H  G 
Sbjct: 74  AMTPHAQRHLGLQFEKRMTKKAYVARLTGRLEPRSGTVDLPLIVDWPNRPLQKVCHETGK 133

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             H             + +KVI  + +    + + P TGR+HQLRVH   +G PI+GD  
Sbjct: 134 PAH-------------TDWKVIS-YGENETRVRLSPKTGRSHQLRVHMQSLGHPILGDPL 179

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAPL 311
           Y +        P   ++ LH+  + L HPEGG   + ++ AP 
Sbjct: 180 YASG--AALEHP---RMMLHSEELRLKHPEGGASQKFRVKAPF 217


>gi|253579056|ref|ZP_04856327.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251849999|gb|EES77958.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 299

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/256 (26%), Positives = 126/256 (49%), Gaps = 18/256 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V+   +H+I      +S  N+ +    L   ++YED  I V NKPA + V   +G   + 
Sbjct: 54  VLKPQDHLIVTVPETESGENIIRTKMDLN--IIYEDEDILVINKPADMPVHPSAGNYENT 111

Query: 130 DGFLKSW-VDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                +W    KG+    R  +RLD++T+G L++A+   +A  L+   + R+I + Y +L
Sbjct: 112 LANGIAWYFAEKGEDFVYRCINRLDRDTTGALILAKNPLSAAILSVQMKKRQILRTYLAL 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  +     A      + + G  +   + N      AI+H++ +    +++   E+ 
Sbjct: 172 VDGLLPDSGTINAPI----ARMEGSVI-TREVNFGTGESAITHYERLAA-GKEYSLAELH 225

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
             TGRTHQ+RVH  ++G P+ GD+ Y  +++        N+  LH+  ++  HP  G++ 
Sbjct: 226 LETGRTHQIRVHMKYIGHPLPGDYLYNPDYRR------INRQPLHSYQLEFTHPTTGKVM 279

Query: 307 I-TAPLPAHMVKTWDS 321
           + TAPLP   +  + S
Sbjct: 280 LFTAPLPIDFISAFYS 295


>gi|169632120|ref|YP_001705856.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter
           baumannii SDF]
 gi|169150912|emb|CAO99519.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter
           baumannii]
          Length = 229

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/209 (33%), Positives = 107/209 (51%), Gaps = 22/209 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ 
Sbjct: 26  ILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMF 83

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R ++K Y +LV G  K +       I +W  +   I    VH  
Sbjct: 84  AKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLITDWENRPRQI----VHF- 138

Query: 217 KQNEKGANYAISHFK--VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              E G  +A + F+  V D    +   L ++P TGR+HQLRVH +H+G PI+GD  Y  
Sbjct: 139 ---ELG-KHAKTLFQPLVYDATTDQSRVL-LEPVTGRSHQLRVHMMHIGHPIMGDKLYHP 193

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             K        N++ LHA Y+   HP  G
Sbjct: 194 EPKRFHL----NRMALHAAYLAFQHPLKG 218


>gi|167622731|ref|YP_001673025.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167352753|gb|ABZ75366.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 225

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 62/202 (30%), Positives = 101/202 (50%), Gaps = 15/202 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  I V NKP+G+    G   A+    + +   +    K  + HRLD  TSG++VV
Sbjct: 16  ILHQDKDIMVVNKPSGLLSVPGRDPAHADSTYNRVLAEFPHAK--IVHRLDMATSGVIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A  R+A   L   FR R  +K Y++ V G  K     +   L+       D+ +  KQ  
Sbjct: 74  ALLRSAESELKRQFRDRETEKTYYARVAGHVKETHGTVNLPLI------CDWPNRPKQKV 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + K    + +H++VI    ++   +++ P TGR+HQLRVH + +G PI+GD+ Y      
Sbjct: 128 DHKIGKPSQTHYEVI-SRGKRSTLVKLTPITGRSHQLRVHMMALGHPILGDNFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                   +L LHA+ + + HP
Sbjct: 187 RLAP----RLLLHAQSLTITHP 204


>gi|326386900|ref|ZP_08208514.1| ribosomal large subunit pseudouridine synthase D [Novosphingobium
           nitrogenifigens DSM 19370]
 gi|326208580|gb|EGD59383.1| ribosomal large subunit pseudouridine synthase D [Novosphingobium
           nitrogenifigens DSM 19370]
          Length = 314

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/232 (30%), Positives = 110/232 (47%), Gaps = 27/232 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--DSKGQ--------KPRLTHRL 150
           ++YED+ + V +KPAG+ V   +G   + DG L + +    +GQ        +P + HR+
Sbjct: 84  VVYEDADLIVVDKPAGMVVHPAAG---NPDGTLVNALLHHCRGQLSGIGGVARPGIVHRI 140

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+LVVA+T  A + L   F    I + Y ++  G P      I   + + SH   
Sbjct: 141 DKDTSGLLVVAKTDVAHEGLARQFADHSIVRAYRAVTGGAPTPPAGTIRGAIARSSH--- 197

Query: 211 DYVHVVKQNEKGANYAISHFKV---IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           D   +    E    +A++H++    +D  A   C LE    TGRTHQ+RVH   +G  ++
Sbjct: 198 DRKKMALVEEGRGKHAVTHYRTLERLDSSALVECRLE----TGRTHQVRVHLASIGHSLL 253

Query: 268 GDHKY--C-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           GD  Y  C A  +   +     +  LHA  +   HP  G  L   +  P  M
Sbjct: 254 GDPVYGRCPARLRPVLSRLEFRRQALHAAELGFVHPVSGEHLHFVSATPVDM 305


>gi|310815298|ref|YP_003963262.1| NAD(P) transhydrogenase subunit alpha [Ketogulonicigenium vulgare
           Y25]
 gi|308754033|gb|ADO41962.1| NAD(P) transhydrogenase subunit alpha [Ketogulonicigenium vulgare
           Y25]
          Length = 339

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 88/333 (26%), Positives = 144/333 (43%), Gaps = 62/333 (18%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L K+L  G +R+D   V+    R+  G +V I       +
Sbjct: 17  RLDKALARDVPEEASLSRSRLAKLLDEGAIRIDGTVVQDAKARVTEGALVEITIAEANES 76

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-- 133
           HI+ +   L+               ++YED  + V +KPAG+ V    G     DG L  
Sbjct: 77  HIVGQDIPLN---------------VVYEDDDLIVIDKPAGMVVHPAPGSP---DGTLVN 118

Query: 134 -------KSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                  +S     G K P + HR+D++TSG+LV A+T  A   L   F    I++ Y +
Sbjct: 119 ALIHHCGESLSGVGGMKRPGIVHRIDKDTSGLLVAAKTDRAHHGLAALFEAHDIERRYLA 178

Query: 186 LVWGI-----PKNKKECIANWLLK---KSHIGGDYVHVVKQNE----KGANYAISHFKVI 233
           L +G+     P+ +     N+ L    K     D     +Q +    +G  +A++  +V+
Sbjct: 179 LCYGVLSAADPRVRGLKGVNFELGNILKIQTRLDRHRTDRQRQAVIWEGGRHAVTRARVV 238

Query: 234 DCFAQKF----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL- 288
           + +        CWLE    TGRTHQ+RVH  ++G  ++GD  Y    + +  S  +  + 
Sbjct: 239 EEYNGAASLIECWLE----TGRTHQIRVHMSYVGHGLIGDPTYGGRKRLSPKSLPEAAVA 294

Query: 289 --------YLHARYMDLPHP-EGGRLQITAPLP 312
                    LHA  +   HP  G  ++  +PLP
Sbjct: 295 MAHDFPRQALHAATLGFVHPFTGEEMRFESPLP 327


>gi|187934581|ref|YP_001884790.1| pseudouridine synthase, RluA family [Clostridium botulinum B str.
           Eklund 17B]
 gi|187722734|gb|ACD23955.1| pseudouridine synthase, RluA family [Clostridium botulinum B str.
           Eklund 17B]
          Length = 298

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 84/301 (27%), Positives = 140/301 (46%), Gaps = 50/301 (16%)

Query: 39  KILRSG----QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++RS     ++ V+   V+ N  I++G +++I    N   +I  E+  LD         
Sbjct: 30  RLIRSASKDQRIYVNNSAVRMNYMIKNGDIIKIDLNRNESQNINPEKIDLD--------- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISV------QGGS---GIAYHIDGFLKSWVDSKGQKPR 145
                 ++YED  + V NK   I V      Q G+   GI Y+     ++ +       R
Sbjct: 81  ------IVYEDEDVLVINKQPFIIVHPTKNFQSGTLANGILYYFQETNQNCI------VR 128

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L  RLD  TSG++++A+ + +   L++  +  ++QK Y ++V G  + K+  I   + K 
Sbjct: 129 LVSRLDMNTSGLIIIAKNQFSHSRLSKDMK-EKLQKRYLAIVHGNLEEKEGTIDLPIYKP 187

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHM 262
             I    + VV  +E+G   +I+H+KVI+ F       C LE    TGRTHQ+RVH  H+
Sbjct: 188 EGIEYGSMRVV--DERGQR-SITHYKVIESFEGGDLVECLLE----TGRTHQIRVHLSHL 240

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           G PI GD  Y    + N       +  LHA  ++   P     L + A LP  M +  + 
Sbjct: 241 GHPIYGDELYGVGAEENLIK----RQALHAYGLNFASPRSLKELSLRAELPDDMKELLEK 296

Query: 322 L 322
           +
Sbjct: 297 I 297


>gi|86148440|ref|ZP_01066731.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp.
           MED222]
 gi|218708594|ref|YP_002416215.1| 23S rRNA pseudouridine synthase D [Vibrio splendidus LGP32]
 gi|85833794|gb|EAQ51961.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp.
           MED222]
 gi|218321613|emb|CAV17565.1| ribosomal large subunit pseudouridine synthase D [Vibrio splendidus
           LGP32]
          Length = 324

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 123/250 (49%), Gaps = 35/250 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  + V NKP  + V  G+G     DG + + +        + PR  + HRLD++T
Sbjct: 86  IVYEDDDLLVINKPRDLVVHPGAGTP---DGTILNALLFHYPQIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++VVA+T  A   L  +   RRI + Y ++  G      +  A  +++K    G   H
Sbjct: 143 TGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIG------KMTAGGVVEK----GISRH 192

Query: 215 VVKQ-----NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             K+     NE G   A++H++V + F ++   + ++  TGRTHQ+RVH  ++  P++GD
Sbjct: 193 ATKRTLMDVNELG-KPAVTHYRVAEHF-REHTRIRLRLETGRTHQIRVHMSYLQHPLLGD 250

Query: 270 HKYCANFK------GNFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
             Y    +         T+ I+  ++  LHA  +   HP  G  ++  AP+P  MV   +
Sbjct: 251 IAYGGRARIPKGASEELTTMIRSFDRQALHAVMLKFVHPITGEEVEFHAPVPNDMVVMAE 310

Query: 321 SLGFKYDRNL 330
           +L      N+
Sbjct: 311 ALRVDARENI 320


>gi|109900130|ref|YP_663385.1| pseudouridylate synthase [Pseudoalteromonas atlantica T6c]
 gi|109702411|gb|ABG42331.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           atlantica T6c]
          Length = 218

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 64/215 (29%), Positives = 113/215 (52%), Gaps = 16/215 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D  + V NKP+G+    G  +  H D  L+  V       R+ HRLD  TSG+LV+
Sbjct: 16  IVFKDEYVLVLNKPSGLLTVPGKALE-HKDS-LELRVQRVYPTARIVHRLDMATSGLLVM 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A  +   + L++ F +R+ +K Y + V+G    ++  +   L+       D+ +  KQ  
Sbjct: 74  ALDKDTHRQLSKQFELRQTRKTYIARVFGQVNGERGSVDLPLM------CDWPNRPKQMV 127

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            ++    +++H+++++        +E+ P TGR+HQLRVH L +G PI+GD  Y A+F  
Sbjct: 128 CQQRGKPSLTHWRILE-RNDHTTRMELTPVTGRSHQLRVHMLSLGHPILGDRLY-AHFDA 185

Query: 279 NFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
                + N+L LHA+ +   HP     +   AP+P
Sbjct: 186 ---LAMANRLQLHAQTLGFTHPATNASVDFHAPVP 217


>gi|270290798|ref|ZP_06197022.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
 gi|270280858|gb|EFA26692.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
          Length = 304

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/221 (33%), Positives = 107/221 (48%), Gaps = 28/221 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +L+E+  + V NKPAGI          GS I      FL+++   K       HRLDQ T
Sbjct: 87  VLFENDDLLVVNKPAGIKTHANQPHELGSMI-----NFLQAYFAKKDSNAYNVHRLDQWT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L+VA+       L+     + IQ+ Y  +V G  K++   I         IG D   
Sbjct: 142 SGALLVAKNPVVVPILSRQISQKLIQRTYLCVVEGHLKSRSGTIT------LPIGLDPHD 195

Query: 215 VVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             K+  N  GA  A +H++V+  F ++   L +Q  TGRTHQ+RVH   +G PIVGD  Y
Sbjct: 196 QRKRQINGPGAQPATTHYQVVREFVER-SLLRVQLATGRTHQIRVHLAALGHPIVGDPLY 254

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
            +   G   +P++    LH+  +  P P     Q +TAP+P
Sbjct: 255 NSLADG---APMR----LHSWQVKFPLPFSQSWQTVTAPVP 288


>gi|227522610|ref|ZP_03952659.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
 gi|227090190|gb|EEI25502.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
          Length = 302

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 105/219 (47%), Gaps = 18/219 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED+ + V NK  G        G        L +++ +K   P + HRLDQETSG ++
Sbjct: 89  ILYEDANLIVINKRRGNKTHPNQPGEIGATINHLAAYLKTKEALPYMVHRLDQETSGAIL 148

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+  A    L      + I++ Y + V G   + +  I         IG D     K+ 
Sbjct: 149 FAKNPAVVPTLVAKIATKNIKRTYLAWVVGTDIDSQGII------DFPIGLDPNDKRKRM 202

Query: 220 EKGANYA--ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             G + A  I+H+ V+      +  L +Q  TGRTHQ+RVH   +G P+VGD  Y  + K
Sbjct: 203 IDGNHPAKSITHYTVLQK-EDGYSLLAVQLETGRTHQIRVHLTAIGHPLVGDPLYNPDDK 261

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             F       L LH+  +++P P   + ++ITAPLPAH 
Sbjct: 262 HPF-------LLLHSWKLNIPLPFSEQVIEITAPLPAHF 293


>gi|332290082|ref|YP_004420934.1| 23S rRNA pseudouridine synthase D [Gallibacterium anatis UMN179]
 gi|330432978|gb|AEC18037.1| 23S rRNA pseudouridine synthase D [Gallibacterium anatis UMN179]
          Length = 324

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 83/325 (25%), Positives = 153/325 (47%), Gaps = 43/325 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHII 78
           RLD+     +P  +   ++  + +G V+VD K            +V +P   +     II
Sbjct: 18  RLDQTLAELFPEYSRSRIKTWIEAGLVQVDDK------------IVTVPKEKVFGTEQII 65

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSW 136
            + +I +     T  +  L   ++YED  I V NK   + V  G+G   +  ++  L  +
Sbjct: 66  MQAEI-EEDTRFTPQNIPLD--IVYEDEHILVINKSKDLVVHPGAGNPDNTVLNALLYHY 122

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                + PR  + HRLD++T+G++VVA+T  A   L  + + R+I + Y ++  GI    
Sbjct: 123 -PPIAEVPRAGIVHRLDKDTTGLMVVAKTIEAQTKLVRALQKRQITREYEAIASGIMTKG 181

Query: 195 ---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
               + +A    K++H+    +H +         A++H+++++ F + +  L ++  TGR
Sbjct: 182 GTVDQPMARHPTKRTHMA---IHPL------GKPAVTHYRIMERF-RNYTRLRLRLETGR 231

Query: 252 THQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLHARYMDLPHPEGG 303
           THQ+RVH  ++  P++GD  Y       KG   + ++      +  LHA  + L HP   
Sbjct: 232 THQIRVHMAYIAHPLLGDQTYGGRPKPPKGASEALLEVLRQFQRQALHAIMLRLEHPISR 291

Query: 304 RL-QITAPLPAHMVKTWDSLGFKYD 327
            L +  APLP   V+  ++L   Y+
Sbjct: 292 ELMEWYAPLPDDFVELVNALKTDYE 316


>gi|325104837|ref|YP_004274491.1| ribosomal large subunit pseudouridine synthase D [Pedobacter
           saltans DSM 12145]
 gi|324973685|gb|ADY52669.1| ribosomal large subunit pseudouridine synthase D [Pedobacter
           saltans DSM 12145]
          Length = 342

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 78/338 (23%), Positives = 156/338 (46%), Gaps = 47/338 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  + ++R+D++      + +   +Q  +  G V V+ K +K + +I+    + I  
Sbjct: 21  VVVDKGQSSIRIDKFLMVRLENASRNKIQNAIEQGNVLVNGKAIKPSYKIKPLDDISI-- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L H  ++ ++    + +          ++YED+ + + NK AG+ V  G G     
Sbjct: 79  ---VLPHPPRDTEVYPEDIPID---------IIYEDNDVVLVNKVAGMVVHPGYGNWSGT 126

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + +H     +  +     +P L HR+D++TSG+LV+++   +   L + F    I+
Sbjct: 127 LVNALTHHFSQLPQ--LPGNDGRPGLVHRIDKDTSGLLVISKNEKSMASLAKQFFDHSIK 184

Query: 181 KIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           + Y +LVWG +P   ++ I +  + +S      + +    EKG  ++++H+KV+      
Sbjct: 185 RKYLALVWGDLP---EDGIISGYIGRSIKDRKVMDLYDDPEKG-KWSVTHYKVVKRL-NY 239

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNK 287
              +E Q  TGRTHQ+R H   +G P+  D  Y  +   KG   +           +  +
Sbjct: 240 VTLIECQLETGRTHQIRAHMKAIGHPLFNDTAYGGDKIRKGTIFAKYKQFIDNCFAVMPR 299

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLP---AHMVKTWDS 321
             LHA+ +   HP   + +   + LP   + +++ W+S
Sbjct: 300 QALHAKSLGFIHPTTKKEVYFESELPDDFSQVLEKWES 337


>gi|299783639|gb|ADJ41637.1| Pseudouridine synthase [Lactobacillus fermentum CECT 5716]
          Length = 295

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 66/204 (32%), Positives = 98/204 (48%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYE+  + V +KPAGI S    +G    +   + ++++       + HRLDQETSG ++
Sbjct: 89  VLYENRDLLVVDKPAGIKSHPNQAGEVGTLMNRVAAYLEGTNDAAYMVHRLDQETSGAMI 148

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+       L +      I + Y +LV G+P   +     W L    +G D   V K+ 
Sbjct: 149 VAKNPVVVPILDQLISTGEIHRDYLALVAGVPNPARGI---WDLP---LGQDPTDVRKRK 202

Query: 220 --EKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              K A  A +H++ +     Q    L ++  TGRTHQLRVH    GCPIVGD  Y    
Sbjct: 203 VFGKNAQPARTHYRTLAVNGDQALVVLNLE--TGRTHQLRVHLAAAGCPIVGDPLY---- 256

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
            G   +P   ++YLH    +L  P
Sbjct: 257 -GTVAAP---RMYLHGVAQELVLP 276


>gi|256423396|ref|YP_003124049.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
 gi|256038304|gb|ACU61848.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
          Length = 570

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 64/215 (29%), Positives = 105/215 (48%), Gaps = 20/215 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  + V NKP+G+    G  I   +   LK  +     +P + HRLD +TSG+LVV
Sbjct: 370 IIYQDESVVVVNKPSGLRSVPGVTIQDSVYTRLKHALGDI--EPLIVHRLDMDTSGLLVV 427

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T+AA +H+   F  R + K Y +L+  +    +  I   L          +      +
Sbjct: 428 AKTQAAHKHIQRQFLQRTVSKRYTALLSKVIDTSEGEIDLPLTADLFNRPRQIVCFTTGK 487

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFK 277
           K    +++ +KV+  + Q    ++  P TGRTHQLR+H+ H   +  PIVGD  Y     
Sbjct: 488 K----SVTRWKVVTRY-QAMTKIDFWPLTGRTHQLRMHSAHPLGLNAPIVGDDLYGT--- 539

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
                    ++YLHA +++  HP    R+   AP+
Sbjct: 540 ------AAERMYLHAAHIEFTHPLSRQRISFDAPV 568


>gi|225850427|ref|YP_002730661.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Persephonella marina EX-H1]
 gi|225645814|gb|ACO04000.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Persephonella marina EX-H1]
          Length = 319

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 86/335 (25%), Positives = 152/335 (45%), Gaps = 49/335 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVR--I 67
           +V+ + +  RLD++  + YP  +    QK+++ G V  D K +K  + +++ GQ +   I
Sbjct: 11  MVDEEYDRKRLDQFLSSVYPEYSRSYFQKLIKDGYVFEDGKDIKKPSYKVRKGQEITLVI 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP                    L    + +   +L+ED  I V  KPAG+ V    G   
Sbjct: 71  PP-----------------PETLEIKPENIPVDILFEDEDIAVVYKPAGMVVHPSPG--- 110

Query: 128 HIDGFLKSW-------VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           H  G L +        +   G K R  + HRLD++T+G++++A++  A + L + F+ R 
Sbjct: 111 HTSGTLVNALLYHFRNISEYGGKERAGIVHRLDKDTAGLMIIAKSEFAHKELQKQFQERT 170

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVID-C 235
           + K Y ++V GI +N    I         IG    +  K   +  N   A++ + V +  
Sbjct: 171 VDKRYIAVVTGIVQNDHGFI------DLPIGRSIYNRKKMGTEATNLRDALTEYWVKNRS 224

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHA 292
             +    ++++ HTGRTHQ+RVH   +G P+  D  Y    +  +      I ++   HA
Sbjct: 225 EKENLTVVDIKLHTGRTHQIRVHFSAIGHPLFNDKVYGFKKSQLRSEKMRSISDQTLYHA 284

Query: 293 RY---MDLPHPEGG-RLQIT-APLPAHMVKTWDSL 322
                +   HP  G ++ IT   LP H+ K  +++
Sbjct: 285 LLAYRIAFDHPRTGEKIDITLQKLPEHISKVIEAI 319


>gi|219684788|ref|ZP_03539730.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia garinii PBr]
 gi|219685395|ref|ZP_03540214.1| ribosomal large subunit pseudouridine synthase D [Borrelia garinii
           Far04]
 gi|219671733|gb|EED28788.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia garinii PBr]
 gi|219673168|gb|EED30188.1| ribosomal large subunit pseudouridine synthase D [Borrelia garinii
           Far04]
          Length = 326

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 95/181 (52%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YEDS I V NKP GI    G         + + YHI   LK   + +  +P + HRLD
Sbjct: 86  IIYEDSNIIVLNKPQGILSHPGISHWDDTVVNFLLYHIKR-LKINFNEEKVRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+       L + F+ ++  K+Y ++V G   +    I +++ +  +    
Sbjct: 145 KDTSGVLICAKNINTLSFLAQQFKDKKTNKVYIAIVKGNFNSFSGSIESFIDRDKYNRKK 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + +K    A++ ++++  F   +  L ++P TGRTHQLRVH  ++  PI+GD  
Sbjct: 205 FSVSKDRGKK----ALTEYRLLLNFGG-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEV 259

Query: 272 Y 272
           Y
Sbjct: 260 Y 260


>gi|251778694|ref|ZP_04821614.1| pseudouridine synthase, RluA family [Clostridium botulinum E1 str.
           'BoNT E Beluga']
 gi|243083009|gb|EES48899.1| pseudouridine synthase, RluA family [Clostridium botulinum E1 str.
           'BoNT E Beluga']
          Length = 298

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 84/291 (28%), Positives = 136/291 (46%), Gaps = 50/291 (17%)

Query: 39  KILRSG----QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++RS     ++ V+   V+ N  I++G V++I    N   +I  E+  LD         
Sbjct: 30  RLIRSASKDQRIYVNNSAVRMNYMIKNGDVIKIDLNKNESQNINPEKIDLD--------- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISV------QGGS---GIAYHIDGFLKSWVDSKGQKPR 145
                 ++YED  + V NK   I V      Q G+   GI Y+     ++ +       R
Sbjct: 81  ------IVYEDDDVLVINKQPFIIVHPTKNFQSGTLANGILYYFQETNQNCI------VR 128

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L  RLD  TSG++++A+ + +   L++  +  ++QK Y ++V G  + K+  I   + K 
Sbjct: 129 LVSRLDMNTSGLIIIAKNQFSHSRLSKDMK-EKLQKRYLAIVHGNLEEKEGTIDLPIYKP 187

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHM 262
             I      V+  +E+G   +I+H+KVI+ F       C LE    TGRTHQ+RVH  H+
Sbjct: 188 EGIEYGSRRVI--DERGQR-SITHYKVIESFEGGDLVECLLE----TGRTHQIRVHLSHL 240

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G PI GD  Y    + N       +  LHA  +D   P   + L + A LP
Sbjct: 241 GHPIYGDELYGVGLEENLIK----RQALHAYGLDFESPRSLKPLSLRADLP 287


>gi|160872393|ref|ZP_02062525.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Rickettsiella grylli]
 gi|159121192|gb|EDP46530.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Rickettsiella grylli]
          Length = 325

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 83/321 (25%), Positives = 151/321 (47%), Gaps = 39/321 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +V  D    RLD+     +P  +   LQ+ +   +V VD +  +  ++I+ G  + I  
Sbjct: 12  AIVPEDLAEKRLDQILSQLFPAYSRTRLQQWIHDKRVLVDNEFKRPRDKIKPGAKITI-- 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
           V N           L  +++    ++ L   +++ED  + V NKPAG+ V  G+G  +  
Sbjct: 70  VAN-----------LHEAIDWE--AENLPLDIIFEDDALVVINKPAGLVVHPGAGNRHKT 116

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L   + +  + PR  +  RLD++TSG+L++ +   A   L +  + R +++ Y ++
Sbjct: 117 LVNALLHHLPALKKLPRAGIIQRLDKDTSGLLIIPKILNAHTQLVKQLQARTMKREYTAI 176

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY---AISHFKVIDCFAQKFCWL 243
           + G+       IA   +      G +  + K+     N+   A+SH++VI+ F      +
Sbjct: 177 IQGL------LIAGGSINAP--IGRHPKLRKKMAVTENHGKPAVSHYRVIERF-NHHTLI 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKLYLHARYM 295
            +Q  TGRTHQ+RVH  H+  P+VGD  Y   F      SP+        ++  LHA  +
Sbjct: 228 NVQLETGRTHQIRVHMAHIHHPLVGDKTYSGRFHLPKKASPLLIHCLHHFSRQALHAHCL 287

Query: 296 DLPHPEGGR-LQITAPLPAHM 315
            + HP   + ++  +PLP  M
Sbjct: 288 GITHPISLKPMEWHSPLPEDM 308


>gi|194246668|ref|YP_002004307.1| Pseudouridine synthase [Candidatus Phytoplasma mali]
 gi|193807025|emb|CAP18461.1| Pseudouridine synthase [Candidatus Phytoplasma mali]
          Length = 299

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 83/293 (28%), Positives = 143/293 (48%), Gaps = 38/293 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVN--LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           E+ MRLD +       INF     QK++  G++ V+ K  K +  ++    +++      
Sbjct: 11  EKGMRLDHFLNKK---INFSKNRCQKLIILGKILVNNKPSKKSYILKENDHIKV------ 61

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---SGIAYHID 130
                    I  + +N+ +  D L   ++YED  + V +KP  + +      SG+   I+
Sbjct: 62  --------FIPSTPLNVLQPID-LNLEIIYEDEFLAVIDKPKNLVIHPSITFSGVTL-IN 111

Query: 131 GFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           G L   K++    G +P + HRLD++T+G+++VA++    Q L  S + R I++ YW+L+
Sbjct: 112 GLLFQIKNFRKMDGLRPGIVHRLDKDTTGLILVAKSEEIRQQLQLSIQKREIKRYYWALI 171

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  + + + I   L    H        V +N K    +I++FKV+  F   F  +E Q 
Sbjct: 172 HGHLEKQGKII---LPIGRHPHNRIKMAVVKNGKP---SITYFKVLKYF-NNFSLIECQL 224

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            TGRTHQ+RVH  ++   I+GD  Y    K N  S      +LH++ ++  HP
Sbjct: 225 ETGRTHQIRVHLSYLKHHILGDKLY--GLKENCYS--NESQFLHSKKIEFIHP 273


>gi|225389034|ref|ZP_03758758.1| hypothetical protein CLOSTASPAR_02779 [Clostridium asparagiforme
           DSM 15981]
 gi|225044909|gb|EEG55155.1| hypothetical protein CLOSTASPAR_02779 [Clostridium asparagiforme
           DSM 15981]
          Length = 342

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/275 (25%), Positives = 125/275 (45%), Gaps = 19/275 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q ++V  +E   RLD+    +        L K++R   + ++ K+   + R+  G  +R
Sbjct: 1   MQTLIVTPNEAGQRLDKLLAKYMNQAGKGFLYKMMRKKNITLNGKKCDGSERLGEGDEIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +       K             + K  ++YEDS I V NKPAG+  Q      
Sbjct: 61  LFLADETI------AKFTGGGAAKPISGYYPKPDIIYEDSHILVVNKPAGLLSQKAREDD 114

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             ++  + +++   G+         +P + +RLD+ TSG++V  R+ A  Q +   F+ R
Sbjct: 115 TSLNEAILNYLIDSGRMPVEQLRTFRPSICNRLDRNTSGLVVAGRSLAGLQVMNAVFKDR 174

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I K Y  +V G  K +K+ IA +L K      + V +     + +   ++ +  +  + 
Sbjct: 175 SIHKYYQCIVKGSLK-EKQLIAGFLRKDE--ASNTVDIYPLEVENSVPIMTEYLPL-AWG 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             F  L++   TGR+HQ+R H   +G PI+GD KY
Sbjct: 231 GGFTLLQVTLITGRSHQIRAHLASIGHPILGDFKY 265


>gi|121587761|ref|ZP_01677521.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           2740-80]
 gi|121730333|ref|ZP_01682696.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           V52]
 gi|147673459|ref|YP_001216201.1| 23S rRNA pseudouridine synthase D [Vibrio cholerae O395]
 gi|153215116|ref|ZP_01949823.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           1587]
 gi|153801880|ref|ZP_01956466.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MZO-3]
 gi|153818725|ref|ZP_01971392.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           NCTC 8457]
 gi|153826766|ref|ZP_01979433.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MZO-2]
 gi|153829371|ref|ZP_01982038.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           623-39]
 gi|229525359|ref|ZP_04414764.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           bv. albensis VL426]
 gi|229530513|ref|ZP_04419901.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           12129(1)]
 gi|254224983|ref|ZP_04918597.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           V51]
 gi|254291985|ref|ZP_04962765.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           AM-19226]
 gi|262170005|ref|ZP_06037695.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC27]
 gi|262191805|ref|ZP_06049976.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           CT 5369-93]
 gi|297580830|ref|ZP_06942756.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC385]
 gi|121547988|gb|EAX58068.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           2740-80]
 gi|121627915|gb|EAX60491.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           V52]
 gi|124114907|gb|EAY33727.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           1587]
 gi|124122591|gb|EAY41334.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MZO-3]
 gi|125622370|gb|EAZ50690.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           V51]
 gi|126510747|gb|EAZ73341.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           NCTC 8457]
 gi|146315342|gb|ABQ19881.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           O395]
 gi|148875154|gb|EDL73289.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           623-39]
 gi|149739417|gb|EDM53657.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MZO-2]
 gi|150422124|gb|EDN14091.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           AM-19226]
 gi|227012534|gb|ACP08744.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           O395]
 gi|229332286|gb|EEN97774.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           12129(1)]
 gi|229338940|gb|EEO03957.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           bv. albensis VL426]
 gi|262021739|gb|EEY40450.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC27]
 gi|262032292|gb|EEY50859.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           CT 5369-93]
 gi|297535246|gb|EFH74081.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC385]
 gi|327483506|gb|AEA77913.1| Ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           LMA3894-4]
          Length = 324

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 86/338 (25%), Positives = 154/338 (45%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G++ V+   + K   ++  G+V+ +  
Sbjct: 10  TVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +        EQ+     + L          ++YED  I V NKP    V  G+G A   
Sbjct: 70  ELE------DEQRWEAQDLPLN---------IVYEDDDIIVINKPRDFVVHPGAGQADKT 114

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L  +     + PR  + HRLD++T+G++VVA+T  A   L  + + R + + Y +
Sbjct: 115 VLNALLFHY-PPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN----EKGANYAISHFKVIDCFAQKFC 241
           +V G         A  ++ K  IG    H  K+          +A++H++V + F ++  
Sbjct: 174 IVIGT------MTAGGMIDKP-IGR---HSTKRTLMSVSPMGKHAVTHYRVAEHF-REHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLHAR 293
            L ++  TGRTHQ+RVH  ++  P++GD  Y    +         T  I+  ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGATEELTEMIRDFDRQALHAV 282

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
            +   HP  G  L+  AP+P  MV+   +L  + D  L
Sbjct: 283 MLKFEHPVTGEELEFHAPVPDDMVEM--TLALREDAKL 318


>gi|183597816|ref|ZP_02959309.1| hypothetical protein PROSTU_01145 [Providencia stuartii ATCC 25827]
 gi|188022571|gb|EDU60611.1| hypothetical protein PROSTU_01145 [Providencia stuartii ATCC 25827]
          Length = 217

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/206 (33%), Positives = 109/206 (52%), Gaps = 17/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKP+G+    G    +H D  + S +          HRLD  TSG++VV
Sbjct: 15  VLYQDEHIITVNKPSGLLSVPGKAPEHH-DSIM-SRIQRDHPHAESVHRLDMATSGVMVV 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A  +AA + L   FR R  +K Y + VWG    K+E + +  L       D+ +  KQ  
Sbjct: 73  ALNKAAERELKRQFREREPKKHYIARVWGH-LEKQEGLVDLPLI-----CDWPNRPKQKV 126

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E G   A + ++V++ + ++   +++ P TGR+HQLRVH L +G PI+GD ++ A+ +
Sbjct: 127 CFETG-KAAQTEYQVLE-YEEQATRVKLSPITGRSHQLRVHMLALGHPILGD-RFYAHEQ 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
               +P   +L LHA+ + + HP  G
Sbjct: 184 ARALAP---RLQLHAQELYITHPAYG 206


>gi|77462043|ref|YP_351547.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides 2.4.1]
 gi|126460932|ref|YP_001042046.1| pseudouridine synthase [Rhodobacter sphaeroides ATCC 17029]
 gi|332559970|ref|ZP_08414292.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides WS8N]
 gi|77386461|gb|ABA77646.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides 2.4.1]
 gi|126102596|gb|ABN75274.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides ATCC 17029]
 gi|332277682|gb|EGJ22997.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides WS8N]
          Length = 215

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 110/220 (50%), Gaps = 27/220 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           L++ D++I V +KPAG+    G G     D  ++     +G  P   L HRLD++TSG++
Sbjct: 14  LIHHDAQIVVVDKPAGLLSVPGKG-EDKADCLIERL---RGVFPEILLVHRLDRDTSGVM 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKK---ECIANWLLKKSHIGGDYV 213
           V A T+AA   L + F  R+ +KIY + V G   P+  +       +W  +         
Sbjct: 70  VFALTKAAQGALGQQFEKRQTKKIYVARVAGRLEPREGRVDLPLCVDWPNRPKQ------ 123

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           HV  +N + A    + ++V+  +  K   + + P TGR+HQLRVH    G PI+GD  Y 
Sbjct: 124 HVDPENGRPAQ---TDWRVVK-YLPKETRVRLMPVTGRSHQLRVHMAETGHPILGDALYA 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                +F      +L LHA  + + HP+ G+ L  +AP P
Sbjct: 180 EGAARDFP-----RLMLHAESLRVRHPDTGKSLTYSAPCP 214


>gi|229519979|ref|ZP_04409409.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           TM 11079-80]
 gi|229343031|gb|EEO08019.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           TM 11079-80]
          Length = 324

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 86/338 (25%), Positives = 154/338 (45%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G++ V+   + K   ++  G+V+ +  
Sbjct: 10  TVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +        EQ+     + L          ++YED  I V NKP    V  G+G A   
Sbjct: 70  ELE------DEQRWEAQDLPLN---------IVYEDDDIIVINKPRDFVVHPGAGQADKT 114

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L  +     + PR  + HRLD++T+G++VVA+T  A   L  + + R + + Y +
Sbjct: 115 VLNALLFHY-PPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN----EKGANYAISHFKVIDCFAQKFC 241
           +V G         A  ++ K  IG    H  K+          +A++H++V + F ++  
Sbjct: 174 IVIGT------MTAGGMIDKP-IGR---HSTKRTLMSVSPMGKHAVTHYRVAEHF-REHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLHAR 293
            L ++  TGRTHQ+RVH  ++  P++GD  Y    +         T  I+  ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGATEELTEMIRDFDRQALHAV 282

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
            +   HP  G  L+  AP+P  MV+   +L  + D  L
Sbjct: 283 MLKFDHPVTGEELEFHAPVPDDMVEM--TLALREDAKL 318


>gi|226491450|ref|NP_001140404.1| hypothetical protein LOC100272459 [Zea mays]
 gi|194699356|gb|ACF83762.1| unknown [Zea mays]
          Length = 419

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/270 (25%), Positives = 116/270 (42%), Gaps = 48/270 (17%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN----LTKHSDFLKSILLYEDS 106
            R +    I++G V      ++ ++H +K   ++  +V+    L   ++ +   ++YED 
Sbjct: 86  SRARVQASIRAGLVAVNGRPVSKVSHTVKGGDLVSCTVSELQPLRAEAEDIPLDIVYEDD 145

Query: 107 KIYVFNKPAGISVQGGSGIA---------------------------------------Y 127
            + V NKPA + V    G A                                       +
Sbjct: 146 HVLVVNKPAHMVVHPAPGNAKGTLVNAILHHCKISTFTCLARSSAGDECPDSTDEDTDVF 205

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           H+D F    V S+ +    +P + HRLD+ TSG+LVVA+   +   L E F++  I+++Y
Sbjct: 206 HVDQFAAEDVSSEVRNALVRPGIVHRLDKGTSGLLVVAKDEHSHARLAEQFKLHTIRRVY 265

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            SL  G P      I   + +  +       +     + A  A S +KV + FA     L
Sbjct: 266 ISLTCGAPNPNSGRIEASIARDPNNRIRMTAIAGSGHRYARNAASRYKVREVFAGGGSAL 325

Query: 244 -EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            E +  TGRTHQ+R HA ++G P++GD  Y
Sbjct: 326 VEWRLETGRTHQIRAHAKYIGIPLLGDETY 355


>gi|89097691|ref|ZP_01170579.1| ribosomal large subunit pseudouridine synthase [Bacillus sp. NRRL
           B-14911]
 gi|89087550|gb|EAR66663.1| ribosomal large subunit pseudouridine synthase [Bacillus sp. NRRL
           B-14911]
          Length = 285

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 63/215 (29%), Positives = 103/215 (47%), Gaps = 38/215 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  + + NKPAG+              +  A+H+          + ++ +  HRLD
Sbjct: 67  VLYEDDHMLILNKPAGMDTHPNEPMQEDTLANAAAFHL------LAKGEYRQVKHIHRLD 120

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G ++ A+   A   L +  + R+I++ Y ++  G+ K KK  I      +  IG D
Sbjct: 121 KDTTGAVLFAKHALAGGMLDQLLKERKIKRTYIAMADGVIKQKKGVI------RKPIGRD 174

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCP 265
             H  ++    G   A++H++V   F ++      C LE    TGRTHQ+RVH   MG P
Sbjct: 175 RHHPTRRRVSPGGQDAVTHYEVAAIFPREQQTLVSCRLE----TGRTHQIRVHFSDMGHP 230

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           + GD  Y         SP   +  LHA  +++PHP
Sbjct: 231 LTGDRLYGG-------SPAFPRQALHAAKLEVPHP 258


>gi|242238059|ref|YP_002986240.1| pseudouridine synthase [Dickeya dadantii Ech703]
 gi|242130116|gb|ACS84418.1| pseudouridine synthase [Dickeya dadantii Ech703]
          Length = 217

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/201 (34%), Positives = 103/201 (51%), Gaps = 12/201 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  + S + +        HRLD  TSG++V
Sbjct: 14  VLYQDQHIIVVNKPSGLLSVPGRAD--EHKDSIM-SRIQADIPTAESVHRLDMATSGVMV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG    + E + +  L           V  + 
Sbjct: 71  VALTKAAERELKRQFREREPKKSYLARVWGH-MAQDEGLVDLPLICDWPNRPRQKVCFEQ 129

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K A  A   ++V+   A     +++ P TGR+HQLRVH L +G PI+GD  Y A+    
Sbjct: 130 GKPAQTA---YQVLARDADGTTRVKLMPITGRSHQLRVHMLALGHPILGDGFY-AHPDAK 185

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
             +P   +L LHA+ + + HP
Sbjct: 186 AMAP---RLLLHAQELVITHP 203


>gi|86139411|ref|ZP_01057980.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           MED193]
 gi|85823914|gb|EAQ44120.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           MED193]
          Length = 217

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 115/233 (49%), Gaps = 27/233 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           S + T   D L+  +L+ D++I V NKPAG+    G G   H+   L S V +   +  L
Sbjct: 4   SSDYTPPQDPLE--ILHHDAQILVVNKPAGLLSVPGRG--EHLADCLLSRVQTAFPEALL 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKK---ECIANW 201
            HRLD++TSG++V   T  A +HL+  F  R  +K+Y + + G   P+  +     I +W
Sbjct: 60  VHRLDRDTSGVMVFGVTPHAQRHLSMQFEKRTTRKVYVARLAGHLEPRAGEVDLPLIVDW 119

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
             +   +      V     K    A++ F+V+  + +    + + P TGRTHQLRVH + 
Sbjct: 120 PNRPRQM------VCHDTGKP---ALTDFRVVK-YGEGETRVRLTPKTGRTHQLRVHMMA 169

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAPL 311
           +G  I+GD  Y       ++     ++ LH+  + + HP+ G   + ++ AP 
Sbjct: 170 LGHAILGDPLYATGEDREYS-----RMMLHSEELRIKHPDTGESIKFRVKAPF 217


>gi|167758127|ref|ZP_02430254.1| hypothetical protein CLOSCI_00465 [Clostridium scindens ATCC 35704]
 gi|167664024|gb|EDS08154.1| hypothetical protein CLOSCI_00465 [Clostridium scindens ATCC 35704]
          Length = 333

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 80/305 (26%), Positives = 139/305 (45%), Gaps = 34/305 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++  +E   RLD++ K +        L K+LR   + ++ K+   N ++  G  V++  
Sbjct: 4   IIISQNEAGQRLDKFLKKYLAKAPGSFLYKMLRKKNIVLNGKKATGNEKLGVGDSVKLFL 63

Query: 70  VINALNHI-----IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
             + +        IKE+     SVNL          +++ED+ +   NKPAG+  Q  + 
Sbjct: 64  ADDTIGKFAGLAPIKEE--YQVSVNLD---------IIHEDANVLFINKPAGMLSQKAAK 112

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                    IAY +     +  + +  +P + +RLD+ TSG++V  +T    Q +   F+
Sbjct: 113 DDVSMVEHVIAYLLAEGSITQEELRTFRPSICNRLDRNTSGLIVAGKTLIGLQAMARLFK 172

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R ++K Y   V G  + ++E I  +L K      +  + V   E G     + +  I  
Sbjct: 173 DRTLKKYYLCFVKGGIR-RREHIYGYLAKN-----EKTNKVTIREAGDTPIETEYVPI-A 225

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKL-YLHAR 293
           + Q+   L++   TGRTHQ+R H    G P++GD+KY  A +   F    Q +   LHA 
Sbjct: 226 YNQEMTLLKVHLITGRTHQIRAHLASKGHPLLGDYKYGDAGWNRQFQERYQVRAQQLHAY 285

Query: 294 YMDLP 298
            M LP
Sbjct: 286 QMKLP 290


>gi|116872369|ref|YP_849150.1| ribosomal large subunit pseudouridine synthase [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|116741247|emb|CAK20369.1| ribosomal large subunit pseudouridine synthase [Listeria welshimeri
           serovar 6b str. SLCC5334]
          Length = 296

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 73/296 (24%), Positives = 147/296 (49%), Gaps = 37/296 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VEN+E+ + L  + ++ +     +   K    G++ V++       ++Q+G  VR+    
Sbjct: 7   VENEEDGLLLRTFLRSKHISKQLLTAVKFSADGKIEVNRTEQNVLYQVQTGDNVRLTFPT 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              N     +++L         +++ K  +++ED  + + NKPAG++        YH  G
Sbjct: 67  EQQN-----ERLL---------AEYTKLEVIFEDDFLLIINKPAGMASIPSQ---YHPSG 109

Query: 132 FLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + ++V    +   LT       RLD++TSG++++A+ R A   L+   +   +++ Y +
Sbjct: 110 SVANFVKGHYEAQGLTSAIHIVTRLDRDTSGLMLIAKNRFAHARLSTFLQQGLLKRRYQA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLE 244
           L  G+ + +   I      ++ IG   V ++++       YA ++++V+  + + F  + 
Sbjct: 170 LTSGVLQEEAGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLKRY-RGFDHVA 222

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +Q  TGRTHQ+RVH  ++G P++GD  Y     G  TS +Q +  LH+ ++ L HP
Sbjct: 223 IQLETGRTHQIRVHFSYIGHPLIGDDMY-----GGDTSMLQRQA-LHSCHLHLVHP 272


>gi|256851102|ref|ZP_05556491.1| pseudouridylate synthase [Lactobacillus jensenii 27-2-CHN]
 gi|260660526|ref|ZP_05861441.1| pseudouridylate synthase [Lactobacillus jensenii 115-3-CHN]
 gi|282933759|ref|ZP_06339114.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 208-1]
 gi|297205967|ref|ZP_06923362.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii JV-V16]
 gi|256616164|gb|EEU21352.1| pseudouridylate synthase [Lactobacillus jensenii 27-2-CHN]
 gi|260548248|gb|EEX24223.1| pseudouridylate synthase [Lactobacillus jensenii 115-3-CHN]
 gi|281302138|gb|EFA94385.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 208-1]
 gi|297149093|gb|EFH29391.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii JV-V16]
          Length = 301

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 76/307 (24%), Positives = 138/307 (44%), Gaps = 50/307 (16%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++   H   ++   +Q++L SG + V+ K+ K + ++ +   + +        H+ K
Sbjct: 14  RLDKYISEHS-DLSRSRVQELLGSGDILVNGKQEKPSYKVANNDQITV--------HVPK 64

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSW- 136
                   V L    + +   ++YED  + V NKP G+ V   +G   H  ++  +    
Sbjct: 65  -------LVPLNVEPEDIPLDIVYEDEDVIVVNKPQGMVVHPSAGHPNHTLVNALMNHTK 117

Query: 137 ---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 +G +P + HR+D++TSG+L++A+   A   L      +  +++Y ++V G   N
Sbjct: 118 FLAASPEGFRPGIVHRIDKDTSGLLMIAKNANARTSLESQLAHKTNKRVYLAIVHG---N 174

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPH 248
            KE           I        K  +K     G   A++HF V++ +   +  +  Q  
Sbjct: 175 FKEATGT-------IDAPIARNPKDRKKMAIVEGGKEAVTHFHVLEQYP-GYALVSCQLE 226

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-- 304
           TGRTHQ+RVH  ++G P+ GD  Y      KG+         +LHA+ +    P+ G+  
Sbjct: 227 TGRTHQIRVHMKYIGHPLAGDPLYGPKKTLKGHGQ-------FLHAKILGFKQPKTGQWL 279

Query: 305 -LQITAP 310
             Q+  P
Sbjct: 280 EFQVDPP 286


>gi|94501077|ref|ZP_01307601.1| 23S rRNA pseudouridylate 746 synthase [Oceanobacter sp. RED65]
 gi|94426824|gb|EAT11808.1| 23S rRNA pseudouridylate 746 synthase [Oceanobacter sp. RED65]
          Length = 201

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 64/214 (29%), Positives = 111/214 (51%), Gaps = 18/214 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  + V +KP+G+  Q GS     +D  +   +        L HRLDQ TSG++++
Sbjct: 3   ILYEDKHLLVIDKPSGLLSQQGS-----LDDSVPHRLLKDYAYVGLVHRLDQATSGVMMM 57

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A  + A  HL + F+ R+  K+Y + V+G +P  + +          +     VH+  ++
Sbjct: 58  ALNKKAHGHLAKQFQDRKTFKVYQARVFGSLPGERGQIDLPLRCDWPNRPKQEVHIEGKS 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 +++H++ I+  +Q +  + + PHTGR+HQLRVH   MG PI+GD  Y  +   +
Sbjct: 118 ------SLTHWQCIE-RSQHWSRVALIPHTGRSHQLRVHMAAMGYPILGDRFYAHHEAKS 170

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  + + HP  G R++  + +P
Sbjct: 171 MA----KRLNLHAASLAVNHPISGKRMRFFSSVP 200


>gi|322411665|gb|EFY02573.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus dysgalactiae subsp. dysgalactiae
           ATCC 27957]
          Length = 300

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 58/206 (28%), Positives = 103/206 (50%), Gaps = 18/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V NKP G +    +  +  I  F+K++   K    Q+  +  RLD++TSG+
Sbjct: 78  IVYEDDHFLVINKPVGFASIPSAIHSNTIANFIKAYYVEKSYPNQQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVH 214
           ++ A+   A   L +  + R I+K Y++LV G   +P ++ + +A     K  I      
Sbjct: 138 MLFAKHGYAHARLDKQLQTRAIEKRYFALVSGQGALP-DEGDIVAPIGRSKDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +  +    YA + +KV+  + +    ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRAVDSMGKYAKTSYKVVARYPENVHLVDIKLHTGRTHQIRVHFAHLGFPLLGDDLYGG 250

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
                 T     +  LH  Y++   P
Sbjct: 251 RLDLGIT-----RQALHCHYLNFKDP 271


>gi|297588693|ref|ZP_06947336.1| RluA family pseudouridine synthase [Finegoldia magna ATCC 53516]
 gi|297574066|gb|EFH92787.1| RluA family pseudouridine synthase [Finegoldia magna ATCC 53516]
          Length = 273

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 79/307 (25%), Positives = 138/307 (44%), Gaps = 61/307 (19%)

Query: 16  EENMRLDRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++ +RLD + K NH     F+++ K      + ++ K  K N++++ G  V I       
Sbjct: 9   DKKIRLDEFLKVNHISKNLFLSIYK----DDILINGKHAKRNSKLKPGDKVTID------ 58

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGF 132
              +K+++     +NL          +LYED  I+V NKP  +++   G   +A  +   
Sbjct: 59  ---LKDEENNYEPINLDIE-------VLYEDDDIFVLNKPDKLTMNTDGEESLANFVSYL 108

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +    +  QK R  +RLDQ+TSG+++VA+ + A  +    ++    +K Y ++V G PK
Sbjct: 109 FEQR--NINQKVRFINRLDQDTSGVVMVAKNKIAQAY----YQKTSFEKKYLAIVEGNPK 162

Query: 193 NKK-------ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           N+K       +CI   +      G   V ++K  +   +Y++   K++            
Sbjct: 163 NQKIELNLIRDCIKTEI---DENGKKSVTILKNIKSYGDYSLVSLKLL------------ 207

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              TGRTHQ+RV   ++ CPIV D  Y    +G F+        LHA  +D    +G   
Sbjct: 208 ---TGRTHQIRVSMEYINCPIVADSLYGEKIEG-FSQ------MLHANEIDFVDMKGNEH 257

Query: 306 QITAPLP 312
            I    P
Sbjct: 258 IIATDFP 264


>gi|251796507|ref|YP_003011238.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247544133|gb|ACT01152.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
          Length = 242

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 108/228 (47%), Gaps = 13/228 (5%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---- 145
           +T  +D ++  +LYED+ I    K  GI  Q        +   +K  +  +  KP     
Sbjct: 1   MTAGNDAIQIPVLYEDNHIIAVVKLPGIPSQEDETGDPDMLTLIKQDLKIRHNKPGNVFL 60

Query: 146 -LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HRLD+   G ++ A+T  AA  L+E+ R R   K Y  +V G P  +++ + +++ K
Sbjct: 61  GLIHRLDRPVGGAMLFAKTSKAASRLSEAVRSRTFGKTYVCVVHGKPAKQQDRLRHYIRK 120

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            +    + V V K+    A  AI  ++V    A  +  + ++ HTGR HQ+R    ++GC
Sbjct: 121 DAK--RNQVTVYKEPAADAKEAILEYRVC-AQAGGYSLIAVKLHTGRPHQIRAQMAYIGC 177

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           P+V D KY A    + T      + L +  ++ PHP    LQ    +P
Sbjct: 178 PLVADRKYGAPNTASVTD-----IALWSTSVEAPHPVTKELQCFRSIP 220


>gi|108758129|ref|YP_629362.1| RNA pseudouridine synthase family protein [Myxococcus xanthus DK
           1622]
 gi|108462009|gb|ABF87194.1| RNA pseudouridine synthase family protein [Myxococcus xanthus DK
           1622]
          Length = 329

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 81/324 (25%), Positives = 138/324 (42%), Gaps = 43/324 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VVE +    RLD +       +    LQ ++  G +  +++R+K +  +  G   RI   
Sbjct: 19  VVEPNYAGWRLDEYLGEKLRRMTRERLQGVILRGVI-CEERRLKPSTPVYPGLAFRI--- 74

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                    E+   D+   L          ++++D  + V +KPAG+ +   +   YH  
Sbjct: 75  ----RRRASEEP--DTPTELP---------VVFQDDWLLVLDKPAGLPIHPTA--RYHKG 117

Query: 131 GFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             +    +  G++     HRLD+ETSG++V  RT  + + L   F  R + K Y +L  G
Sbjct: 118 TLVTLLRERFGERFAEPAHRLDRETSGLVVCGRTTESCRVLGRLFVSRDVHKEYLALCEG 177

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFAQ---KFCWLEM 245
            P      +   + +    G + + + V+ +      + + F+V+  F +    F  L  
Sbjct: 178 HPPEDTFTVDAPIAE----GTELIRIAVRIDPVEGKESRTRFQVLQRFTRDGAPFALLRC 233

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQ------NKLYLHAR 293
            P TGR HQ+R+H  H G P+VGD  Y  +      F  +   P         +  LHA 
Sbjct: 234 FPETGRQHQIRIHLCHAGFPLVGDKMYGPDPGYFDRFSKHCLEPEAWPRLRLPRQALHAA 293

Query: 294 YMDLPHPEGGR-LQITAPLPAHMV 316
            +  PHP  G+ +   APLPA + 
Sbjct: 294 RIAFPHPGSGQAVAFEAPLPADLT 317


>gi|261823062|ref|YP_003261168.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
 gi|261607075|gb|ACX89561.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
          Length = 217

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/204 (34%), Positives = 105/204 (51%), Gaps = 18/204 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  + S + +        HRLD  TSG++ 
Sbjct: 14  ILYQDQHIMVVNKPSGLLSVPGRA--PEHKDSVM-SRIQADYPAAESVHRLDMATSGVIA 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPKKCYLARVWGHMAQDEGVIDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + A + ++V+         +++ P TGR+HQLRVH L +G PI+GD  Y A+ 
Sbjct: 125 VCFETGKS-AQTEYQVLSRDDDGTTRVKLMPITGRSHQLRVHLLALGHPILGDGFY-AHP 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                +P   +L LHA+ + + HP
Sbjct: 183 DAKAMAP---RLLLHAQELAITHP 203


>gi|168699207|ref|ZP_02731484.1| pseudouridine synthase, RluA family protein [Gemmata obscuriglobus
           UQM 2246]
          Length = 354

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 61/211 (28%), Positives = 100/211 (47%), Gaps = 29/211 (13%)

Query: 112 NKPAGISVQ---------GGSG---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           NKPAG++           G  G   +   + G L + + +  +     HRLD++TSG++V
Sbjct: 126 NKPAGLTTMRHKEEAEEFGAHGQRFLTKTLAGLLPTLLGTPDRAVTAVHRLDRDTSGLVV 185

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG--GDYVHVVK 217
            ARTRAA ++LT  FR    ++ Y +L  G+PK  +  IA+  +     G  G    +  
Sbjct: 186 FARTRAAGENLTAQFRKHSTERRYLALTRGVPKPGR--IASVFVSDRGDGRRGTTTDLAA 243

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             ++    A++H  V++     F  +E +  TGRTHQ+R+H    G P+ G+  Y     
Sbjct: 244 DGKR----AVTHVAVLEPLG-PFALVECRLETGRTHQVRIHLGEAGAPLCGEGVYDRPID 298

Query: 278 GNFTSPIQN-----KLYLHARYMDLPHPEGG 303
           G    P+ +     +  LHA  +   HP+ G
Sbjct: 299 GQ---PLPDGSGAQRPMLHATRLGFAHPDTG 326


>gi|320528439|ref|ZP_08029601.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
 gi|320131353|gb|EFW23921.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
          Length = 304

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 84/331 (25%), Positives = 149/331 (45%), Gaps = 44/331 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    ++V E+ +E  RLD++  ++   ++   +Q++   G + V+ K  K ++++ +G 
Sbjct: 1   MAKQTWIVSEDTKE--RLDKYLSSNT-ELSRTRVQQLADDGMIFVNGKVAKSSSKVVTGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +      +    I+ E   LD               +LYED  I V NKP G+ V    
Sbjct: 58  EISCDVPEDRPVDILPENIPLD---------------ILYEDHDIIVINKPKGMVVHPAP 102

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HR+D++T+G +V  +   A + + +    +
Sbjct: 103 GNYSNTMVNALLYHCKDLSGINGVIRPGIVHRIDKDTTGCIVACKNDKAHEAIAKQLENK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV--HVVKQNEKGANYAISHFKVIDC 235
              ++Y ++V G          +  L  + IG D      +K  E+ +  A +HF V++ 
Sbjct: 163 TCHRVYKTIVVG------NITHDDGLIDAPIGRDPRDRQRMKVTEENSRDARTHFHVLER 216

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHA 292
           F     +LE +  TGRTHQ+R H  ++  P++GD KY   C           Q ++ LHA
Sbjct: 217 F-NVATYLECRLETGRTHQIRAHMKYINHPVMGDDKYGKPCPYMD------TQGQV-LHA 268

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             + L HP  G  +   APLP++  K  + L
Sbjct: 269 SELTLVHPTTGETMTFHAPLPSYFEKLLEIL 299


>gi|225870507|ref|YP_002746454.1| RNA pseudouridylate synthase [Streptococcus equi subsp. equi 4047]
 gi|225699911|emb|CAW93829.1| putative RNA pseudouridylate synthase [Streptococcus equi subsp.
           equi 4047]
          Length = 300

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 58/205 (28%), Positives = 99/205 (48%), Gaps = 16/205 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    + NKPAG +    +  +  I  F+K++    D   ++  +  RLD++TSG+
Sbjct: 78  IVYEDEHFLILNKPAGYASIPSAIHSNTIANFIKAYYIKQDYPNKQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + R I K Y++LV G  +  ++ E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQQRAINKRYYALVCGQERLPDQGEIIAPIGRTDDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +       YA + +KVI  + +    +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRTVTPKGKYAKTSYKVIARYPENVSLVDITLHTGRTHQIRVHFAHLGFPLLGDDLYGGR 251

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                T     +  LH  ++   HP
Sbjct: 252 LDLGMT-----RQALHCHHLSFTHP 271


>gi|289551021|ref|YP_003471925.1| Ribosomal large subunit pseudouridine synthase D [Staphylococcus
           lugdunensis HKU09-01]
 gi|289180553|gb|ADC87798.1| Ribosomal large subunit pseudouridine synthase D [Staphylococcus
           lugdunensis HKU09-01]
          Length = 305

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 145/318 (45%), Gaps = 37/318 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT     V +      R+D+   ++    +   +Q  ++   V V+ K +K N +++   
Sbjct: 1   MTTHSIEVTDTRHTGQRIDKLLSDYNHDWSRSQIQDWIKHELVIVNGKAIKANYKVKLHD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           +I E++++D+ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  SI-----------VITEKEVVDADIQ----PENLNLDIYYEDKDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L +    +
Sbjct: 106 GHYSGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRSLVDQLVAK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIAN-WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +++ Y +LV G IP +     A     KK     D V      + G + A++HF V++ 
Sbjct: 166 SVKRKYTALVHGNIPHDYGTVDAPIGRNKKDRQSMDVV------DDGKD-AVTHFNVLEH 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +
Sbjct: 219 F-KDYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPKKTLDIGGQA-----LHAGLI 272

Query: 296 DLPHPEGGR-LQITAPLP 312
              HP  G  ++  A LP
Sbjct: 273 GFEHPVTGEYIERQAALP 290


>gi|229512403|ref|ZP_04401877.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           TMA 21]
 gi|229350553|gb|EEO15499.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           TMA 21]
          Length = 324

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 86/338 (25%), Positives = 154/338 (45%), Gaps = 47/338 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G++ V+   + K   ++  G+V+ +  
Sbjct: 10  TVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +        EQ+     + L          ++YED  I V NKP    V  G+G A   
Sbjct: 70  ELE------DEQRWEAQDLPLN---------IVYEDDDIIVINKPRDFVVHPGAGQADKT 114

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L  +     + PR  + HRLD++T+G++VVA+T  A   L  + + R + + Y +
Sbjct: 115 VLNALLFHY-PPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN----EKGANYAISHFKVIDCFAQKFC 241
           +V G         A  ++ K  IG    H  K+          +A++H++V + F ++  
Sbjct: 174 IVIGT------MTAGGMIDKP-IGR---HSTKRTLMSVSPMGKHAVTHYRVAEHF-REHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLHAR 293
            L ++  TGRTHQ+RVH  ++  P++GD  Y    +         T  I+  ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGASEELTEMIRGFDRQALHAV 282

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
            +   HP  G  L+  AP+P  MV+   +L  + D  L
Sbjct: 283 MLKFEHPITGEELEFHAPVPDDMVEM--TLALREDAKL 318


>gi|157961914|ref|YP_001501948.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157846914|gb|ABV87413.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 260

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 75/273 (27%), Positives = 122/273 (44%), Gaps = 47/273 (17%)

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P  N++  I   Q I  ++ N      F +  +L++D  + + NKP+G+    G   A +
Sbjct: 5   PSFNSIESI-SLQLIPTAADNFIAPPCFEEITILFQDEHLLLINKPSGLLSLSGKNPA-N 62

Query: 129 IDG----FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +D      +K + D       L HRLD  TSGI+V+AR +     L   F  R + K Y 
Sbjct: 63  LDSVHYRLVKDFPDCT-----LVHRLDLGTSGIMVIARNKTVNALLCRQFSERSVLKAYT 117

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW-- 242
           +L+ G  KN+   I   + K          ++K  +K    A S ++V+   A++ C   
Sbjct: 118 ALLLGEIKNEDGFIDAPIAKDK----PNFPLMKICDKEGKQARSLYRVL---AKESCASL 170

Query: 243 ----------------------LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                                 +E  P TGRTHQLR+H+ + G PI+G    C  +  +F
Sbjct: 171 DEKTQLLNNKREHIADSVAVTRVEFIPETGRTHQLRIHSQYFGHPIIG----CDLYGSDF 226

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +  + ++L LHA  ++  HP  G R+   +P P
Sbjct: 227 SYRLASRLMLHATRLEFDHPITGERIVANSPCP 259


>gi|221195841|ref|ZP_03568894.1| ribosomal large subunit pseudouridine synthase D [Atopobium rimae
           ATCC 49626]
 gi|221184315|gb|EEE16709.1| ribosomal large subunit pseudouridine synthase D [Atopobium rimae
           ATCC 49626]
          Length = 338

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 113/236 (47%), Gaps = 25/236 (10%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS----------KGQ-KPRLTHRLD 151
           +ED  + V +K AG+      G   HID  L + + +          +G+ +P + HRLD
Sbjct: 90  FEDQYLIVLSKQAGLVCHPSPG---HIDDTLANALVAHCGYEHLGLLQGEDRPGIVHRLD 146

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG++V A++    + L +  R+R + + Y  LV G     +  I   + +      D
Sbjct: 147 MDTSGLMVAAKSDEVQKALQDLIRLRVLDRRYVVLVQGYVAPDEGTIETGIARSIR---D 203

Query: 212 YVHVVKQNEKGANYAISHFKVIDCF-----AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + +   +  GA  AI+ F+ ++ F      + +  LE   +TGRTHQ+RVH  H+G P+
Sbjct: 204 RLKMTVTDAPGAREAITTFRTLERFEAGRRGEGYSLLECHLYTGRTHQIRVHMRHVGHPV 263

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
           VGD  Y    K    +    + +LH+ ++   HP  G  +++T  LP  ++    S
Sbjct: 264 VGDQLY--GRKDERLNLGLKRQFLHSWHIQFEHPVTGETIELTDSLPQDLLAALKS 317


>gi|296117562|ref|ZP_06836146.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           ammoniagenes DSM 20306]
 gi|295969293|gb|EFG82534.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           ammoniagenes DSM 20306]
          Length = 308

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 82/325 (25%), Positives = 144/325 (44%), Gaps = 32/325 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V    + +R+D         ++     ++   G V V+   V  ++R+ +GQ V 
Sbjct: 5   VRTLPVPEGNDGLRIDAALAKML-GLSRTVAAELCAEGAVLVNGTTVSKSDRLTAGQWV- 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG- 124
                        E  + + +  L    + ++ + ++Y D  I   NKP G++     G 
Sbjct: 63  -------------EVTLPEPAAPLVPKEELVEGMDVVYSDDDIIAVNKPVGVAAHPSVGW 109

Query: 125 -IAYHIDGFLKSW--VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                I G   +   + + G   R  + HRLD  TSG++VVA +  A   L  +F+ R +
Sbjct: 110 DGPTVIGGLAAAGFRISNSGPPERKGIVHRLDVGTSGVMVVASSERAYTALKNAFKERTV 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G+P      I   + +  H    +   V ++ K   +AI+H+ +I+ F ++
Sbjct: 170 HKTYHALVQGLPDPIVGTIDAPIGR--HPSSGWKFAVTEDGK---HAITHYSLIEAF-RE 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
              L++   TGRTHQ+RVH    G P  GD  Y ++   N +  +   + +LHA  +   
Sbjct: 224 ASLLDVHLETGRTHQIRVHMSATGHPCCGDPMYGSDP--NLSKRLGLIRQWLHAVKLGFE 281

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  GR ++I    P  +    D L
Sbjct: 282 HPGTGRWIEIETSYPDDLQHALDVL 306


>gi|291086839|ref|ZP_06344600.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium sp. M62/1]
 gi|291077108|gb|EFE14472.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium sp. M62/1]
          Length = 331

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 61/217 (28%), Positives = 110/217 (50%), Gaps = 16/217 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGI 157
           ++YED  + V +KPAG+ V    G  Y+      +W  S+  +P   R  +RLD++T+G+
Sbjct: 103 IIYEDRDLMVIDKPAGMPVHPSQGNFYNTLANGIAWYFSERGEPFTFRAVNRLDRDTTGL 162

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+    A  L+E    + +++ Y ++  G  K  +E      + ++   G  +    
Sbjct: 163 LIIAKHGLCAALLSEMVARKEVRRQYLAIASG--KTDEEGTICAPIARAD--GSTIERCV 218

Query: 218 QNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              +G  YA +H++ +   ++  C  L +   TGRTHQ+RVH  H+G P++GD  Y  ++
Sbjct: 219 DETRG-EYACTHYRRLVYSSENDCSLLLLTLDTGRTHQIRVHMKHIGHPLLGDFLYNPDY 277

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +      +  +  LH+  +   HP  G  L  +APLP
Sbjct: 278 R------LFRRQSLHSFLLSFTHPLTGESLNFSAPLP 308


>gi|317486117|ref|ZP_07944964.1| RNA pseudouridylate synthase [Bilophila wadsworthia 3_1_6]
 gi|316922640|gb|EFV43879.1| RNA pseudouridylate synthase [Bilophila wadsworthia 3_1_6]
          Length = 308

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 91/336 (27%), Positives = 145/336 (43%), Gaps = 59/336 (17%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V   E   +L ++    +     V L + +R+GQVR++  R K  +R++    +R+PP  
Sbjct: 7   VTAAEAGQKLLQFLSRRFEEPQSV-LHRWIRTGQVRINGGRAKPFDRVKLNDEIRVPPFA 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A     K +++  SS         L  I+  E + + VF KP+G+ V  G+G    +  
Sbjct: 66  GAGT---KAERVPASS-----GGKELPPIV-AETADVIVFCKPSGLPVHPGTGHTDSLTT 116

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--RIQKIYWSLV-- 187
            L++        P   HRLD++TSG+L+V +T AA + L+++       + K Y + V  
Sbjct: 117 RLEAAFAGSPFIPAPVHRLDRDTSGLLLVGKTYAAVRRLSDALAAHDGSVAKDYLAWVQG 176

Query: 188 ---WGIPKNKKECIANWLLK----------KSHIGGDYVHVVKQNEKGANYAISHFKVID 234
              W  PK  ++ +A   +           KS  GG        +EK A+  +    V +
Sbjct: 177 ECPWSRPKRLEDHLAKRTVGAQGREKVVAGKSRTGG-------PDEKPASLTVRSLTVRE 229

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA-- 292
             +     L    HTGRTHQ+RV     G P+VGD KY     G       + L LHA  
Sbjct: 230 GRSLVLIRL----HTGRTHQIRVQLSERGFPLVGDVKYGGPRCG-------DGLKLHAVR 278

Query: 293 ------RYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                  Y  LP P  G  ++     AH+   W+ +
Sbjct: 279 LRVGEETYTALP-PWAGPWRV-----AHLPPEWEDV 308


>gi|238924045|ref|YP_002937561.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale ATCC 33656]
 gi|238875720|gb|ACR75427.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale ATCC 33656]
          Length = 324

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 92/339 (27%), Positives = 150/339 (44%), Gaps = 52/339 (15%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++ K   P+ +   + K+LR       KK +K N++  SG    I  V + +
Sbjct: 9   NEAGQRLDKYLKKILPNASMGFIYKMLR-------KKNIKLNDKKASG--TEIVSVDDKI 59

Query: 75  NHIIKEQKILDSSVN---LTKHSDFLKSI------LLYEDSKIYVFNKPAGISVQGGSGI 125
              + +      SVN   L K    L ++      ++YED  I   NKP  +  Q     
Sbjct: 60  KIFLSDDTFAKFSVNEDRLMKDFKALSALKPDGLGVVYEDDDILAANKPVNMLSQKSKET 119

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  ++  +G+         KP + +RLD+ TSG++++ ++    Q+L++  + 
Sbjct: 120 DISANERLIGYLIKEGKLDFDTYKSFKPSVCNRLDRNTSGLILMGKSLHGLQYLSQVLKA 179

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH----FKV 232
           R  +K Y +LV G   ++   I  +L K   +  + V + ++     +  I       K 
Sbjct: 180 RTAEKYYMALVAG-EVDEPMTIEGFLTKDEAV--NKVQITREPISDESLPIKTAYRPLKT 236

Query: 233 IDCFAQ--KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQ 285
           ID  A   K   LE+   TGR+HQ+R H   +G PI+GD KY      A +K N+    Q
Sbjct: 237 IDMSASCHKATLLEVHLITGRSHQIRAHLSSIGHPIIGDIKYGDRRINAFYKENYHVTSQ 296

Query: 286 NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
               LHA ++ LP    GR  I A LP      W  +G 
Sbjct: 297 ---LLHAHHVILPD---GRY-IEAALP----DIWSRVGL 324


>gi|119773744|ref|YP_926484.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119766244|gb|ABL98814.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           amazonensis SB2B]
          Length = 225

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 103/212 (48%), Gaps = 30/212 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           +L++D  I V NKP+G+ SV G   I  H D    +W   K + P  ++ HRLD  TSG+
Sbjct: 17  ILHQDKDIIVINKPSGLLSVPGRDPI--HHDS---AWSRIKAEHPNSQVVHRLDMATSGV 71

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC------IANWLLKKSHIGGD 211
           +V A  ++A   L   FR R   K Y++ V G    K  C      I +W  +       
Sbjct: 72  MVYALRKSAEVELKRQFRDRETHKTYFARVAG--HVKANCSVDLPLICDWPNRPRQ---- 125

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                K + +    +++H  VI  + ++   +++ P TGR+HQLRVH + +G PI+GD  
Sbjct: 126 -----KVDHEIGKPSLTHVDVI-SYGKRSTLVKLTPITGRSHQLRVHMMALGHPILGDGF 179

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           Y      +    + ++L LHA  +   HP  G
Sbjct: 180 YADPLAKS----LADRLLLHAASLSFTHPYSG 207


>gi|255305986|ref|ZP_05350158.1| putative pseudouridylate synthase [Clostridium difficile ATCC
           43255]
          Length = 300

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 111/225 (49%), Gaps = 27/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++Y+D  I + NKP  + V            +GI+Y+ID         +  K R  +RLD
Sbjct: 85  IIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGISYYIDN------QKENVKIRFVNRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG+++VA+   A   L+ +    +++K Y ++V GI K  +  I   + + +    D
Sbjct: 139 MNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGIIKENEGTIDEPIYRPTE---D 195

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  +  +E G + +++H+KVI+   +    LE+   TGRTHQ+RVH  H+G  I+GD  
Sbjct: 196 SIKRI-IDEIGQS-SVTHYKVIERL-ENATVLEVSLETGRTHQIRVHMAHIGHGIIGDEL 252

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           Y     G     + N+  LHA  ++   P    +L+  A +P  M
Sbjct: 253 Y-----GYVDEELINRQALHAYKLEFEQPRTKEKLKFKADIPEDM 292


>gi|253999417|ref|YP_003051480.1| RluA family pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|253986096|gb|ACT50953.1| pseudouridine synthase, RluA family [Methylovorus sp. SIP3-4]
          Length = 353

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 82/328 (25%), Positives = 144/328 (43%), Gaps = 37/328 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIP 68
           +++  D   +RLD+  +   P  +   LQ+ ++ G V ++  + V    ++  G+ +++ 
Sbjct: 9   LIIPQDLGGLRLDQALQKLLPEHSRSRLQQWIKDGLVTLEPAQAVTAKTKVWGGERLQVQ 68

Query: 69  PVINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   H  + + I LD                 YED  I V NKPAG+ V   +G   
Sbjct: 69  VQPSPDEHAFEAEDIPLDVQ---------------YEDEHILVINKPAGLVVHPAAGNWS 113

Query: 126 AYHIDGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++  L  + V     +  + HRLD++TSG+LVVA+T  A   L    + R +++ Y 
Sbjct: 114 GTLLNALLHHAPVVKDLPRAGIVHRLDKDTSGLLVVAKTLTAQTSLVRQLQARTVKREYR 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++VWG      +   N  + +      +        +    A++ ++V++ FA    +L 
Sbjct: 174 AIVWG------QVWQNGRIDQPIGRHPHARTKMAINRNGKPAVTRYEVLERFA-VHTYLR 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQN--KLYLHARYM 295
               TGRTHQ+RVH  H+  P+VGD  Y             +    I N  +  LHA  +
Sbjct: 227 CNLETGRTHQIRVHMQHLKAPLVGDPVYGLGGIVPLRMMPQHLRDTILNFGRQALHAVKL 286

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            L HP  G  ++    LPA M    +++
Sbjct: 287 GLIHPASGEFMEWQVELPADMKSLLEAM 314


>gi|291530266|emb|CBK95851.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           siraeum 70/3]
          Length = 304

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 76/312 (24%), Positives = 135/312 (43%), Gaps = 37/312 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R D++       I       ++  G   V+ K    N ++++G  V +         I+ 
Sbjct: 14  RTDKFLALQDTGITRSAAAALIEQGCCLVNGKIAAKNQKLKTGDTVTLDVPEAQPADILP 73

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHID 130
           E   LD               ++YEDS + V NKP G+ V    G         + YH  
Sbjct: 74  ENIPLD---------------IVYEDSDLLVVNKPKGMVVHPAPGHYSGTLVNALMYHCG 118

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L     +   +P + HR+D++TSG+L+VA+   A   L E  ++    + Y ++V G+
Sbjct: 119 DSLSGI--NGVIRPGIVHRIDRDTSGLLIVAKNDTAHNILAEQIKVHSFTREYMAVVQGV 176

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              K++   +  + +       + V  +N +    AI+H+ V   + +    + ++  TG
Sbjct: 177 I--KEDGTVDAPIGRHKTDRKKMCVTTENSR---EAITHYFVEQTY-RNNTLVRLRLETG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQ+RVH  ++G P+ GD  Y     GN +        LHA+ +   HP+G  ++  + 
Sbjct: 231 RTHQIRVHMAYIGHPVTGDEVY-----GNGSPKWLCGQCLHAKKIGFIHPDGRYMEFDSD 285

Query: 311 LPAHMVKTWDSL 322
           LP +  K   +L
Sbjct: 286 LPDYFKKLLANL 297


>gi|226223587|ref|YP_002757694.1| ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes Clip81459]
 gi|225876049|emb|CAS04755.1| Putative ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes serotype 4b str. CLIP 80459]
          Length = 296

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 76/312 (24%), Positives = 148/312 (47%), Gaps = 38/312 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE +E+ + L  + K+ +     +   K    G++ V+ K       ++ G  VR+    
Sbjct: 7   VETEEDGLLLRTFLKSKHISKQLLTAVKFGAEGKIEVNNKEQNVLYHVKVGDKVRLTFPT 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              N     +++L    NL          +++ED  + + NKPAG++        YH +G
Sbjct: 67  EQQN-----ERLLAEYTNLD---------IIFEDDFLLIINKPAGMASIPSQ---YHPNG 109

Query: 132 FLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + ++V    +   LT+      RLD+ETSG++++A+ R A   L+   +   +++ Y +
Sbjct: 110 SVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLE 244
              G+   +K  I      ++ IG   V ++++       YA ++++V+  + + F  + 
Sbjct: 170 FTSGVLVEQKGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY-RAFDHVA 222

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   +
Sbjct: 223 IQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTEK 276

Query: 305 -LQITAPLPAHM 315
            +    PLPA M
Sbjct: 277 YMAFDLPLPADM 288


>gi|291514728|emb|CBK63938.1| ribosomal large subunit pseudouridine synthase D [Alistipes shahii
           WAL 8301]
          Length = 361

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 83/327 (25%), Positives = 149/327 (45%), Gaps = 43/327 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V  +  +  MRLD++      H +   +Q    SG + V+ K  K + +++    ++I  
Sbjct: 33  VTADKGQTPMRLDKFLTVRMEHCSRNRIQAAADSGNILVNGKAAKSSYKVKPLDRIQI-- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               + +  +E +++   + L          + YED  + + +KPAG+ V  G G     
Sbjct: 91  ---VMPYPRREVELVAEDIPLD---------IPYEDQWLLLVDKPAGLVVHPGVGNYSGT 138

Query: 125 ----IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + +H++   K  + ++ Q +  L HR+D+ TSG+LV+A+       L + F    I
Sbjct: 139 LVNALMHHLN---KQGIPAEEQNRAGLVHRIDKNTSGLLVIAKDEQTHARLAKQFFDHTI 195

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Q+ Y +LVWG   ++ E      + +S      + V      G  +A++H+KV+  +   
Sbjct: 196 QRRYVALVWG-NFDEDEGTITGNIGRSPKDRQKMFVFADGSDG-KHAVTHWKVLKRYGY- 252

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN------K 287
              +E +  TGRTHQ+RVH   +G P+  D +Y  +   KG     +   I+N      +
Sbjct: 253 VTLVECRLETGRTHQIRVHMAWIGHPLFNDERYGGDRILKGTTFAKYRQFIENCFAVMPR 312

Query: 288 LYLHARYMDLPHPEG-GRLQITAPLPA 313
             LHAR +   HP     +   +PLPA
Sbjct: 313 HALHARLLGFEHPATHENVLFESPLPA 339


>gi|329897136|ref|ZP_08271879.1| tRNA pseudouridine synthase C [gamma proteobacterium IMCC3088]
 gi|328921394|gb|EGG28785.1| tRNA pseudouridine synthase C [gamma proteobacterium IMCC3088]
          Length = 239

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 113/240 (47%), Gaps = 44/240 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           ++Y D  +   NKP G+ V   + +  H   F   WV D  GQ+    HRLD+ TSG+L 
Sbjct: 10  VIYSDDNLVAINKPPGMLVHR-TKLDAHETVFALQWVRDHVGQRVYPLHRLDKATSGVLA 68

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A++   A+H ++++    + K Y +LV G P +K               G   H ++  
Sbjct: 69  FAKSSKVARHWSDAWHTDAVHKDYLALVRGWPNSK---------------GTIDHPLRDP 113

Query: 220 EKGANY----AISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +   +     A + F++ID +            +F  L++ P TGR HQLR H  H+  P
Sbjct: 114 DSAPDSPRKEAETTFEIIDKYLININIDRYPMSRFSLLQLSPLTGRRHQLRQHLKHINHP 173

Query: 266 IVGDHKYCANFKGNFTSPIQN-----KLYLHARYMDLPHPEGG--RLQITAPLPAHMVKT 318
           I+GD +Y    KG +    ++     +L+LHA  + L   + G  R+ ITAP   H+ +T
Sbjct: 174 IIGDVRYG---KGTYNRWARDQFGETRLFLHAHQLRL---DDGVTRITITAPPNPHLQQT 227


>gi|145300305|ref|YP_001143146.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142853077|gb|ABO91398.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 218

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/216 (32%), Positives = 108/216 (50%), Gaps = 18/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  I V NKP G+    G G   + D  L   V  +  K    HRLD  T+G++V+
Sbjct: 14  ILFKDKDIMVVNKPTGLLSVPGRG-PENEDSVLHR-VKQQHPKAAAAHRLDMSTTGVIVI 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
             T  + + L+  FR R  +K Y + VWG P+     +   L        D+ +  KQ  
Sbjct: 72  PLTPNSHRELSRQFRERETEKHYLAWVWGEPEADSGQVDLPLCV------DWPNRPKQKV 125

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+G  +A++ ++ +         +++ P TGR+HQLRVH L +G PI+GD+ Y A+  
Sbjct: 126 DFEEG-RHALTLWEKLKV-ENGNSLIKLTPITGRSHQLRVHMLELGHPILGDNLY-AHPD 182

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
               +P    LYLHA  + + HP  G R+   AP P
Sbjct: 183 ALAAAP---HLYLHAAMLTISHPRSGERMTFEAPAP 215


>gi|312884626|ref|ZP_07744329.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           caribbenthicus ATCC BAA-2122]
 gi|309367718|gb|EFP95267.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           caribbenthicus ATCC BAA-2122]
          Length = 256

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/209 (31%), Positives = 107/209 (51%), Gaps = 17/209 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I   NK  G+    G  + +H D      V+ +  + ++ HRLD +TSG++V+
Sbjct: 27  VIYEDDAILAVNKQPGLLSVPGRKVEHH-DSIYTRLVE-RWPEVQVIHRLDMDTSGLMVL 84

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A+ + A + L + F+ R   K+Y++ VWG     +  I   L+       D+ +  KQ  
Sbjct: 85  AKNKPAERALKKQFQYRLTHKVYYARVWGNVAADEGTIDAPLI------CDWPNRPKQKV 138

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E G + + +HF+V+   +Q    + + P TGR+HQLRVH   MG PI+GD  Y +   
Sbjct: 139 CYETGKS-SQTHFQVVKRESQTTI-VRLLPITGRSHQLRVHMQLMGHPILGDEFYASPQA 196

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
              +S    +L LHA  +   HP+   LQ
Sbjct: 197 FALSS----RLDLHAAELSFYHPDSQLLQ 221


>gi|291524781|emb|CBK90368.1| Pseudouridylate synthases, 23S RNA-specific [Eubacterium rectale
           DSM 17629]
          Length = 324

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 92/339 (27%), Positives = 151/339 (44%), Gaps = 52/339 (15%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++ K   P+ +   + K+LR       KK +K N++  SG    I  V + +
Sbjct: 9   NEAGQRLDKYLKKILPNASMGFIYKMLR-------KKNIKLNDKKASG--TEIVSVDDKI 59

Query: 75  NHIIKEQKILDSSVN---LTKHSDFLKSI------LLYEDSKIYVFNKPAGISVQGGSGI 125
              + +      SVN   L K    L ++      ++YED  I   NKP  +  Q     
Sbjct: 60  KIFLSDDTFAKFSVNEDSLMKDFKALGALKPDGLGVVYEDDDILAANKPVNMLSQKSKET 119

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  ++  +G+         KP + +RLD+ TSG++++ ++    Q+L++  + 
Sbjct: 120 DISANERLIGYLIKEGKLDFDTYKSFKPSVCNRLDRNTSGLILMGKSLHGLQYLSQVLKD 179

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH----FKV 232
           R  +K Y +LV G   ++   I  +L K   +  + V + K++    +  I       K 
Sbjct: 180 RTAEKYYMALVAG-EVDEPMTIEGFLTKDEAV--NKVQITKESISDESLPIKTAYRPLKT 236

Query: 233 IDCFAQ--KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQ 285
           I+  A   K   LE+   TGR+HQ+R H   +G PI+GD KY      A +K N+    Q
Sbjct: 237 IEMSASCHKATLLEVHLITGRSHQIRAHLSSIGHPIIGDMKYGDRRINAFYKENYHVTSQ 296

Query: 286 NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
               LHA ++ LP    GR  I A LP      W  +G 
Sbjct: 297 ---LLHAHHVILPD---GRY-IEAALP----DIWSRVGL 324


>gi|269103546|ref|ZP_06156243.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268163444|gb|EEZ41940.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 241

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/203 (32%), Positives = 109/203 (53%), Gaps = 17/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  I   NKP+G+    G   A H D  + S V     K ++ HRLD  TSG++V+
Sbjct: 29  VLHLDRDIIAVNKPSGLLSVPGRDPA-HYDS-IYSRVLRDHPKSQIVHRLDMTTSGLIVL 86

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A  + A +HL   FR R+  K+Y++ VWG  + +   +   L+       D+ +  KQ  
Sbjct: 87  AINKNAERHLKAQFRERQTHKVYYARVWGHLEQQHGSVDLPLI------CDWPNRPKQKV 140

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+G   +++H++V+  + +    + + P TGR+HQLRVH + +G PI+GD ++ A+ +
Sbjct: 141 CYEEGKP-SLTHYEVVR-YEENATLVRLLPVTGRSHQLRVHMMAIGHPILGD-RFYAHDE 197

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               +P   +L LHA  +   HP
Sbjct: 198 AREMAP---RLQLHAAELTFAHP 217


>gi|254438633|ref|ZP_05052127.1| RNA pseudouridine synthase family [Octadecabacter antarcticus 307]
 gi|198254079|gb|EDY78393.1| RNA pseudouridine synthase family [Octadecabacter antarcticus 307]
          Length = 215

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/203 (30%), Positives = 103/203 (50%), Gaps = 12/203 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D +I + NKP+G+    G G   H+   L   V     +  L HRLD++TSG++V 
Sbjct: 14  VIHADHEILIVNKPSGLLSVPGKG--PHLADCLIMRVQVAFPQALLIHRLDRDTSGVMVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A TR A +H+   F  R  +K Y + VWG+ + K   +   L+    +  +   + K   
Sbjct: 72  ALTRHAQRHIGLQFEKRMTKKTYVARVWGMIEPKTGTVDLPLI----VDWENRPLQKVCH 127

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    A + ++V+   A +   + + P TGR+HQLRVH L +G  I+GD  Y       +
Sbjct: 128 ETGKSAQTDWRVLRGDATE-SRVRLMPKTGRSHQLRVHMLSLGHAILGDPFYAVGEAREY 186

Query: 281 TSPIQNKLYLHARYMDLPHPEGG 303
                ++L LH+  + L HP+GG
Sbjct: 187 -----DRLMLHSEELRLRHPDGG 204


>gi|84393596|ref|ZP_00992349.1| ribosomal large subunit pseudouridine synthase D [Vibrio splendidus
           12B01]
 gi|84375805|gb|EAP92699.1| ribosomal large subunit pseudouridine synthase D [Vibrio splendidus
           12B01]
          Length = 324

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 121/242 (50%), Gaps = 35/242 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  + V NKP  + V  G+G     DG + + +        + PR  + HRLD++T
Sbjct: 86  IVYEDDDLLVINKPRDLVVHPGAGTP---DGTILNALLFHYPQIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++VVA+T  A   L  +   RRI + Y ++  G      +  A  +++K    G   H
Sbjct: 143 TGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIG------KMTAGGVVEK----GISRH 192

Query: 215 VVKQ-----NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             K+     NE G   A++H++V + F ++   + ++  TGRTHQ+RVH  ++  P++GD
Sbjct: 193 ATKRTLMDVNELG-KPAVTHYRVAEHF-REHTRIRLRLETGRTHQIRVHMSYLQHPLLGD 250

Query: 270 HKYCANFK------GNFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
             Y    +         T+ I+  ++  LHA  +   HP  G  ++  AP+P  MV   +
Sbjct: 251 IAYGGRARIPKGASEELTTMIRSFDRQALHAVMLKFVHPITGEEVEFHAPVPNDMVVMAE 310

Query: 321 SL 322
           +L
Sbjct: 311 AL 312


>gi|329895229|ref|ZP_08270893.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC3088]
 gi|328922467|gb|EGG29809.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC3088]
          Length = 317

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 85/323 (26%), Positives = 143/323 (44%), Gaps = 41/323 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ ++SG + VD    K    +    V+ +   +    H   
Sbjct: 19  RLDQVAAALWPEFSRGKLQEWIKSGALLVDGNTAKPKQSVDVDSVLTLSADLEPAVHWQP 78

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-- 137
           +   +D               ++YED  + V NKP G+ V   +G   + DG L + +  
Sbjct: 79  QAIPMD---------------IVYEDEDVIVVNKPVGLVVHPAAG---NWDGTLVNALLA 120

Query: 138 --DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              S  Q PR  + HRLD++TSG++VVA+T  +   L E+ + R + + Y ++  G    
Sbjct: 121 HDASLEQVPRAGVVHRLDKDTSGLMVVAKTLQSHTALVEALQQREVSRQYIAIAHG--SM 178

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               + +  + +       + VV   +     A +H+ +   F + F  L ++  TGRTH
Sbjct: 179 TGGGVVDAPIGRHPTMRQKMAVVASGKP----ARTHYSLGQRF-KHFTELHLKLETGRTH 233

Query: 254 QLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKL------YLHARYMDLPHPEGGR- 304
           Q+RVH  H   P+VGD  Y   A   GN    + N +       LHA+ +   HP     
Sbjct: 234 QIRVHMAHKKHPLVGDSVYGGRARVPGNSAPELVNAIREFPRQALHAKALAFFHPISDEW 293

Query: 305 LQITAPLPAHMVKTWDSLGFKYD 327
           +   AP+P  M +  ++L  +YD
Sbjct: 294 MSFDAPIPDDMQQLLETLE-QYD 315


>gi|188590633|ref|YP_001919968.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str.
           Alaska E43]
 gi|188500914|gb|ACD54050.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str.
           Alaska E43]
          Length = 298

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 84/291 (28%), Positives = 136/291 (46%), Gaps = 50/291 (17%)

Query: 39  KILRSG----QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++RS     ++ V+   V+ N  I++G V++I    N   +I  E+  LD         
Sbjct: 30  RLIRSASKDQRIYVNNSVVRMNYMIKNGDVIKIDLNKNESQNINPEKIDLD--------- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISV------QGGS---GIAYHIDGFLKSWVDSKGQKPR 145
                 ++YED  + V NK   I V      Q G+   GI Y+     ++ +       R
Sbjct: 81  ------IVYEDDDVLVINKQPFIIVHPTKNFQSGTLANGILYYFQETNQNCI------VR 128

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L  RLD  TSG++++A+ + +   L++  +  ++QK Y ++V G  + K+  I   + K 
Sbjct: 129 LVSRLDMNTSGLIIIAKNQFSHSRLSKDMK-EKLQKRYLAIVHGNLEEKEGTIDLPIYKP 187

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHM 262
             I      V+  +E+G   +I+H+KVI+ F       C LE    TGRTHQ+RVH  H+
Sbjct: 188 EGIEYGSRRVI--DERGQR-SITHYKVIESFEGGDLVECLLE----TGRTHQIRVHLSHL 240

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G PI GD  Y    + N       +  LHA  +D   P   + L + A LP
Sbjct: 241 GHPIYGDELYGVGLEENLIK----RQALHAYGLDFESPRSLKPLSLRADLP 287


>gi|47096256|ref|ZP_00233854.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|254898858|ref|ZP_05258782.1| hypothetical protein LmonJ_03555 [Listeria monocytogenes J0161]
 gi|254911653|ref|ZP_05261665.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes J2818]
 gi|254935979|ref|ZP_05267676.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|47015401|gb|EAL06336.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|258608567|gb|EEW21175.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|293589602|gb|EFF97936.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes J2818]
          Length = 296

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 76/312 (24%), Positives = 148/312 (47%), Gaps = 38/312 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE +EE + L  + K+ +     +   K    G++ V+ +       ++ G  VR+    
Sbjct: 7   VETEEEGLLLRTFLKSKHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKVGDKVRLTFPT 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              N     +++L    NL          +++ED  + + NKPAG++        YH +G
Sbjct: 67  EQQN-----ERLLAEYTNLD---------IVFEDDFLLIINKPAGMASIPSQ---YHPNG 109

Query: 132 FLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + ++V    +   LT+      RLD+ETSG++++A+ R A   L+   +   +++ Y +
Sbjct: 110 SVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLE 244
            + G+   +K  I      ++ IG   V ++++       YA ++++V+  + + F  + 
Sbjct: 170 FISGVLVEQKGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY-RAFDHVA 222

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP    
Sbjct: 223 IQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTEE 276

Query: 305 -LQITAPLPAHM 315
            +    PLPA M
Sbjct: 277 YMAFDLPLPADM 288


>gi|325289846|ref|YP_004266027.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324965247|gb|ADY56026.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 299

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 93/315 (29%), Positives = 140/315 (44%), Gaps = 39/315 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           Y + ENDE N +L+   +  + H +   +QK+     V +D K    N R +SGQ + I 
Sbjct: 11  YCLTENDE-NRKLEEILRRQF-HFSRKLIQKLKTGEHVWLDGKFSYLNIRGRSGQTLTID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-----ISVQGGS 123
                   +  E   LD               LL+ED  +   NKPAG      SV    
Sbjct: 69  FAEEEDVSVSPEDADLD---------------LLFEDKILLAVNKPAGQVVHPTSVYRSG 113

Query: 124 GIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +A  + G+   W  +    P R   R+D+ TSGI+++A+ R A Q L    +   + K 
Sbjct: 114 TLANAVTGY---WKKNGLSLPFRPISRIDRNTSGIVMIAKNRYAHQQLAWMSQHHLVGKK 170

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  LV G  K+    IA  L     +  D   +V++       +++ +KV++ +   +  
Sbjct: 171 YLGLVHGHLKSSAGEIALPL----RLAPD-SRIVRETHPDGQQSLTLYKVLEEYPY-YSL 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           LE    TGRTHQ+R H   +G  +VGD  Y     G  T  I  +  LHA +    HP  
Sbjct: 225 LEFTLVTGRTHQIRAHCQAIGHSLVGDDLY-----GGQTELIARQA-LHAFHYSFIHPIS 278

Query: 303 GR-LQITAPLPAHMV 316
           G+ ++I APLPA M 
Sbjct: 279 GQPIKIEAPLPADMA 293


>gi|262173056|ref|ZP_06040733.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus MB-451]
 gi|261890414|gb|EEY36401.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus MB-451]
          Length = 559

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 73/232 (31%), Positives = 111/232 (47%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++  ++ D+ +     +D   SI+ Y+D  I V NKPA      G  +   +   L
Sbjct: 332 LAHMLQGMELDDNPLLSNPAADKEISIV-YQDEAIVVVNKPAEFLSVPGVHVHDSVLTRL 390

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           ++   S+ +     HRLD  TSG+LV A TR A +HL + F  R +QK Y +++ G   +
Sbjct: 391 QAQF-SEAEGVFALHRLDMSTSGLLVFALTRRANRHLQKQFITRAVQKRYVAMLEGTLAD 449

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  IA  L       GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 450 AQGEIALPLC------GDLDDRPRQKVCWQQGKPALTHWETV-AVEQGRTRVYLYPHTGR 502

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   + CPIVGD  Y              +L+LHA  +   HP
Sbjct: 503 THQLRVHCAHHLGLNCPIVGDDLYGTQ---------DQRLHLHAEKLSFSHP 545


>gi|254479301|ref|ZP_05092641.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
 gi|214034749|gb|EEB75483.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
          Length = 285

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 85/325 (26%), Positives = 157/325 (48%), Gaps = 54/325 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VVE   E + L+ + K        + + K    G++RV+ ++      ++ G V+    
Sbjct: 3   LVVEKSAEGLTLEGFLKRKGFSTRLIKMYKW--HGEMRVNGEKENVKRVLKEGDVI---- 56

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-------QG- 121
                     E  + D+S ++      L   + YED +I + +KPAG+ V       +G 
Sbjct: 57  ----------ELSLFDTSSDILPQEMDLS--ICYEDDEILIVDKPAGMVVHPTRRYREGT 104

Query: 122 -GSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             +G+AY        + + KG K   R  +RLD+ TSGI++ A+      +L     ++ 
Sbjct: 105 LANGVAY--------YFEKKGIKTLIRPVNRLDKGTSGIVIFAKEPFMQYYLQ---IVKP 153

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y+++V G  K + E I +  +K+      ++ + ++  +  + AI+++K +    +
Sbjct: 154 MSKFYYAIVNG--KLEGEGIIDVPIKRK----SFMTIEREVSEEGDRAITYYKSLKA-TE 206

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +F  L+++  TGRTHQ+RVH  ++G PIVGD  Y     G  TS I+    LHA  +   
Sbjct: 207 EFSLLKIKIATGRTHQIRVHLNYIGHPIVGDDLY-----GEPTSYIERPA-LHAYRVTFF 260

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP   + + + APLP  + + ++ L
Sbjct: 261 HPLKEKVISVYAPLPEDIKRLFELL 285


>gi|124024405|ref|YP_001018712.1| pseudouridine synthase [Prochlorococcus marinus str. MIT 9303]
 gi|123964691|gb|ABM79447.1| Pseudouridine synthase [Prochlorococcus marinus str. MIT 9303]
          Length = 338

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 83/298 (27%), Positives = 140/298 (46%), Gaps = 49/298 (16%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVINALNHIIKEQKILD 85
           HY H +    Q+ L++GQ+R++ + V+ +  + SG  V  + PP + A      E     
Sbjct: 43  HYTHSSRDVWQQRLQAGQIRLNGELVRLDQLLASGDQVCWQRPPWLEAAVPASWE----- 97

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFL--KSWVDSKGQ 142
                          ++++D  + V NKP+G+ V  G G   H + G L  +  +D + +
Sbjct: 98  ---------------VIFDDGDLLVVNKPSGLPVIPGGGFLDHTLTGLLQRRCQLDGESR 142

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-----RRIQKIYWSLV---WGIPKNK 194
            PR  HRL + TSG+L+ AR R     L+  FR      +  +KIY +L      +  ++
Sbjct: 143 LPRPVHRLGRFTSGLLICARQRETRAKLSAMFRRATAGDQGCKKIYRALAHRNLNVHCDE 202

Query: 195 KECIANWLLKKSH--IGGDYV-------HVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
              I   +++ +H  +G  +V       H  KQ+E     A+S  ++++   Q    LE+
Sbjct: 203 VATIRVPIVQTAHPMVGKVWVAADSSRQHDSKQSESRVLTALSTVRLLE-RRQDADLLEV 261

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS---PIQNKLYLHA-RYMDLPH 299
              TGR HQ+R+H   +G P++GD  Y   F G  +S   P      LHA R +D+P+
Sbjct: 262 AIQTGRPHQIRIHLAAIGSPLIGDPLY--GFDGQISSAATPGDGGYCLHAHRLVDVPY 317


>gi|119469549|ref|ZP_01612453.1| putative 23S rRNA pseudouridylate 746 synthase [Alteromonadales
           bacterium TW-7]
 gi|119447084|gb|EAW28354.1| putative 23S rRNA pseudouridylate 746 synthase [Alteromonadales
           bacterium TW-7]
          Length = 235

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 110/220 (50%), Gaps = 17/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKP-----RLTHRLDQET 154
           +LY+D+ I V NKP+G+    G   + + D      V+  KG  P     +L HRLD  T
Sbjct: 24  ILYQDNDILVINKPSGLLSLSGKN-SENWDSVHYRLVNGQKGLTPAFLKAKLVHRLDLGT 82

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI++V+    +++HL + F++R ++K Y +++ G     +  I   + K + +    V 
Sbjct: 83  SGIMLVSLNDVSSKHLNKQFQLRSVKKHYVAVLQGCISEDRGQIDAPIAKDTQL-FPRVK 141

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           + K   K    A++ F VI   A     ++   P TGRTHQLR+H+  +G PI+G    C
Sbjct: 142 ICKLEGKP---AVTEFNVIKRLANPVRTYVHFSPLTGRTHQLRIHSHFIGHPILG----C 194

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             +K   +  +  +L LHA  +   HP   + + I  P P
Sbjct: 195 DLYKSAHSEKLSKRLQLHASDLFFEHPTTNQAIHIHCPSP 234


>gi|302528436|ref|ZP_07280778.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           AA4]
 gi|302437331|gb|EFL09147.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           AA4]
          Length = 308

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 77/306 (25%), Positives = 140/306 (45%), Gaps = 41/306 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +  + MR+D         ++   +  +  +G V +D +    ++R+ +G ++ +    
Sbjct: 8   VPDGLDGMRVDAGLAKLL-GLSRTAVADLAAAGDVLLDGRPAGKSDRLAAGGLLEV---- 62

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
             L    +  +I+   V+  K        +L++D  I V +KP G++V    G     + 
Sbjct: 63  -TLPEPERPAEIVAEPVDGMK--------ILHDDDDIVVISKPVGVAVHPSPGWTGPTVV 113

Query: 131 GFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           G L +    + + G   R  + HRLD  T+G++VVA++  A   L  +F+ R + K Y +
Sbjct: 114 GGLAAAGLRISTSGAAERQGVVHRLDAGTTGVMVVAKSEHAYTVLKRAFKERTVDKGYHA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           +V G P   +  I   + +  H   DY   V     G   +++H++V++ F A     ++
Sbjct: 174 VVQGHPDPTRGTIDAPIDR--HPRHDYKFAVVA---GGRPSVTHYEVVEAFRAASLAHVK 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI------QNKLYLHARYMDLP 298
           ++  TGRTHQ+RVH   +  P  GD  Y A+       P+        + +LHAR +   
Sbjct: 229 LE--TGRTHQIRVHFSALRHPCAGDLTYGAD-------PVLARKLGLTRQWLHARTLGFA 279

Query: 299 HPEGGR 304
           HP  GR
Sbjct: 280 HPADGR 285


>gi|302871648|ref|YP_003840284.1| pseudouridine synthase [Caldicellulosiruptor obsidiansis OB47]
 gi|302574507|gb|ADL42298.1| pseudouridine synthase [Caldicellulosiruptor obsidiansis OB47]
          Length = 311

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/265 (26%), Positives = 125/265 (47%), Gaps = 28/265 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV+ +   +++++  K  YP I    + K+LR G++ V           Q GQV+R    
Sbjct: 6   VVDKELAGVKVEKAIKKKYPTIPMSVIFKMLRKGEIIVSFLPA------QKGQVLRFG-- 57

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            + ++  I+++ +    V + K         +YED  I V +KP GI     S   Y + 
Sbjct: 58  -DTVSFEIEDRFLEHKKVEIIK---------VYEDDNIVVIDKPYGIPSHPDSNNEYSV- 106

Query: 131 GFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               SW++   SKG+ P+L HRLD+ T+G++++A+ R     + +    R I K Y  + 
Sbjct: 107 ---VSWIEDNYSKGELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRTIIKKYLCIT 163

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                 +   + ++L K S     Y+    Q+  G    ++ +K++         ++++ 
Sbjct: 164 KKADLPESGVLVHYLKKDSKKSKVYISDFPQD--GYLEVVTAYKIVRQ-KDDLQLVDVEI 220

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
            TG+THQ+R    H+G  I+GD KY
Sbjct: 221 KTGKTHQIRAQLAHVGLCILGDSKY 245


>gi|190572297|ref|YP_001970142.1| putative tRNA pseudouridine synthase C [Stenotrophomonas
           maltophilia K279a]
 gi|190010219|emb|CAQ43827.1| putative tRNA pseudouridine synthase C [Stenotrophomonas
           maltophilia K279a]
          Length = 246

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 110/234 (47%), Gaps = 15/234 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           LL+ D ++ V NKPAG+ V   S +A   D FL   +  +  +P  L HRLD+ TSG L+
Sbjct: 20  LLHLDERLAVVNKPAGLMVHD-SKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGCLL 78

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV---- 215
           +A  R  A  L ++     + K Y ++  G P         W +     GG    V    
Sbjct: 79  LAFDRETASALGKALMGGEVLKDYLTVCRGWPAE-----LAWQVDHDLDGGPGKPVKKPA 133

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V   ++ A   +S   V +    ++  L  QP TGR  Q+R H  H+   ++GD  +  +
Sbjct: 134 VTDFQRLATGELS-VPVGEFTRSRYALLRCQPQTGRFRQIRRHLKHLSHHMIGDTSH-GD 191

Query: 276 FKGNFTSPIQN--KLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            + N    +Q   ++ LHA  +  PHPEGG + ++APL     K  D  G++ D
Sbjct: 192 GRHNRIFRMQGVHRMLLHAERLRFPHPEGGNVDVSAPLDREFQKALDLFGWQVD 245


>gi|332994526|gb|AEF04581.1| Pseudouridylate synthase [Alteromonas sp. SN2]
          Length = 259

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 115/243 (47%), Gaps = 47/243 (19%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  + S V++      + HRLD  TSGI+V
Sbjct: 18  ILYQDDDILVANKPSGLLSVPGKA--EEHKDSLI-SRVNTVFPTATVVHRLDMATSGIMV 74

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC----IANWLLKKSHIGGDYVH 214
           +A  + + +H+++ F +R+ +K Y++ V+G +  N+ E     I +W  +   +  D+  
Sbjct: 75  MALNKESHRHISKQFELRKTKKRYFARVFGNVKSNQGEVNLPLICDWPNRPKQM-VDF-- 131

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKF------------------------CWLEMQPHTG 250
                E+G   A++H++V+D   +                            + + P TG
Sbjct: 132 -----ERGKK-ALTHYEVVDVIPKASPQPVNSAASASSCASPSTTSELSETLVALYPVTG 185

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           R+HQLRVH L +G PI+GD  Y           +  +L LHA  +   HP     L    
Sbjct: 186 RSHQLRVHMLELGHPILGDRLYAHEEALG----MAERLQLHAESLSFAHPASEDWLTFQT 241

Query: 310 PLP 312
           P+P
Sbjct: 242 PIP 244


>gi|330995758|ref|ZP_08319655.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
 gi|329574488|gb|EGG56053.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
          Length = 522

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 118/248 (47%), Gaps = 30/248 (12%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++   +  ++   +KH D  +  L+YED  +   NKPAG+    G G A  +    
Sbjct: 295 LGHMLQGLDVEPNAHESSKHLDH-EPELVYEDEWMVAVNKPAGMLSVPGKGDAPSV---- 349

Query: 134 KSWVDS---KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            SW  +   +   P L HRLD +TSG+L++A+     + L + F  R I+K Y +L+ G 
Sbjct: 350 WSWARAHFPEATGPLLVHRLDMDTSGVLLIAKDPETHRQLQQLFETRHIKKRYVALLDGT 409

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQPH 248
             + +  I   L        D    +     G   A++ F+V+   C   +  +    P 
Sbjct: 410 VTDDEGFIRLPLCPNP---DDRPRQMVSTAHG-KAAVTRFEVLSRSCGQTRVAFY---PL 462

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           TGRTHQLRVHA H   +  PIVGD     N  G   S    +L+LHA  +   H + GR 
Sbjct: 463 TGRTHQLRVHAAHPEGLDTPIVGD-----NLYGRRAS----RLFLHAETVAFRHFKTGRW 513

Query: 305 LQITAPLP 312
           + ITAP P
Sbjct: 514 VSITAPAP 521


>gi|225859768|ref|YP_002741278.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 70585]
 gi|225720831|gb|ACO16685.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 70585]
          Length = 278

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD  Y +  K  
Sbjct: 182 AKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|187250787|ref|YP_001875269.1| pseudouridine synthase [Elusimicrobium minutum Pei191]
 gi|186970947|gb|ACC97932.1| Pseudouridine synthase [Elusimicrobium minutum Pei191]
          Length = 299

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 83/318 (26%), Positives = 142/318 (44%), Gaps = 55/318 (17%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNHI 77
           RLD +   + P  +   +Q +++ G+V V+ K  K    +  G  V I  P V N     
Sbjct: 15  RLDLFLSENKPDYSRGLIQNLIKQGKVTVNGKERKPAWPLAEGDNVEIEWPSVENKTG-- 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-------AYHID 130
                              LK ++++ED  ++V NKP+G+ V   S +       A+  +
Sbjct: 73  -------------------LKDLIIFEDKNMFVINKPSGMLVHPQSPVWEENPAAAFIGE 113

Query: 131 GFLKSWVDSKGQK--------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             L S + +   K          L HRLD++TSG++++A+       + E F  R + K 
Sbjct: 114 ETLVSLILANPPKNFEKGITRAGLVHRLDKDTSGVMIIAKNSKTQDAMVEMFANREMHKT 173

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G+  + K  I         IG      +K +E G   A++ + V+    +    
Sbjct: 174 YEAIVCGVVPDDKGII------NVPIGRVTGGKIKASELGRE-AVTEYSVLQR-KETVSL 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +++ P TGRT+QLRVH   +G P++GD  Y    KG  T+P   +L LH++  +  HP  
Sbjct: 226 MKLHPVTGRTNQLRVHMSWLGYPVLGDWLY----KGA-TAP---RLMLHSKSAEFEHPFT 277

Query: 303 GR-LQITAPLPAHMVKTW 319
            + ++ T   P     +W
Sbjct: 278 SKPVKFTVAPPKDFKDSW 295


>gi|145640057|ref|ZP_01795653.1| hypothetical protein CGSHiII_01454 [Haemophilus influenzae PittII]
 gi|145270841|gb|EDK10762.1| hypothetical protein CGSHiII_01454 [Haemophilus influenzae PittII]
 gi|309751619|gb|ADO81603.1| Pseudouridine synthase A [Haemophilus influenzae R2866]
          Length = 219

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 103/208 (49%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+      S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG  +N         I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+         +++ P TGR+HQLR+H L  G PI+GD K+ ++
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLASGHPILGD-KFYSH 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +    SP   +L LHA  + + HP  G
Sbjct: 184 PQAKAMSP---RLCLHAEELTITHPITG 208


>gi|194015110|ref|ZP_03053727.1| pseudouridylate synthase [Bacillus pumilus ATCC 7061]
 gi|194014136|gb|EDW23701.1| pseudouridylate synthase [Bacillus pumilus ATCC 7061]
          Length = 288

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/223 (30%), Positives = 112/223 (50%), Gaps = 22/223 (9%)

Query: 101 LLYEDSKIYVFNK-PAGISVQGGSGIAYHI-DGFLKSWVDSKGQKPRLT----HRLDQET 154
           +L+ED  + V NK P   S+       + I +G L  + +   Q  RLT    +RLD++T
Sbjct: 75  ILFEDDHVLVLNKKPYIPSIPSREHPEHSIANGLLHHYAE---QSVRLTVHLVNRLDRDT 131

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA+ R A   L+++ +   +++ Y +   G+ + K   I   + +K    GD + 
Sbjct: 132 SGVMLVAKHRFAHSLLSKAQKSGAVKRTYRAFTHGMIREKHGTIRAKIARK----GDSII 187

Query: 215 VVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               NE G   A++HF V    A+     + +   TGRTHQ+RVH  ++G P++GD  Y 
Sbjct: 188 ERMVNETGQE-AVTHFTVRAVDAELNMSDVRLTLETGRTHQIRVHMQYLGYPLIGDTLYG 246

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                  T+   N+  LH+  +  PHP  G  +  +APLP  M
Sbjct: 247 G------TNERMNRQALHSETLVFPHPMTGEEMTFSAPLPEDM 283


>gi|330942690|gb|EGH45243.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. pisi str. 1704B]
          Length = 211

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/204 (31%), Positives = 106/204 (51%), Gaps = 12/204 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+   V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIHQDAAALVIDKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEGGKHALTFWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG 303
              P   +L LHA  +   HP  G
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTG 200


>gi|229078576|ref|ZP_04211134.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|228704720|gb|EEL57148.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
          Length = 307

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/230 (31%), Positives = 115/230 (50%), Gaps = 32/230 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + V NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLVVNKPEQMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGKI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISSKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           D  Y    K        +   LHA  ++  HP     +++  P P ++ K
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPTNLNK 297


>gi|218132201|ref|ZP_03461005.1| hypothetical protein BACPEC_00058 [Bacteroides pectinophilus ATCC
           43243]
 gi|217992894|gb|EEC58894.1| hypothetical protein BACPEC_00058 [Bacteroides pectinophilus ATCC
           43243]
          Length = 297

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 109/222 (49%), Gaps = 19/222 (8%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPR 145
           D +K  ++YED  I + +KP+G+  Q  S     +  ++  ++   G          +P 
Sbjct: 43  DKIKLKVMYEDEDIVIIDKPSGMLSQKASAGDKSLVEYVTEYLLDTGSLTQKDLITFRPG 102

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK- 204
           + +RLD+ TSG++V  +T    Q ++E+FR R + K Y  +V G   N++  ++ +L++ 
Sbjct: 103 ICNRLDRNTSGLVVAGKTIKGLQEMSEAFRDRTLHKYYICVVAG-RINERSRVSGYLVRD 161

Query: 205 ----KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               KS I  DY   +   E      I    +       F  L+++  TGRTHQ+R H  
Sbjct: 162 EKTNKSTIYADYKEAMDNAEADMINNIETEYIPAVSNDNFTLLKVKLITGRTHQIRAHLA 221

Query: 261 HMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMDLPH 299
            +G PI GD KY +   N + +    I++++ LHA  +D P 
Sbjct: 222 SLGHPIAGDVKYGSRQINKRMSDQYHIKSQM-LHAYELDYPQ 262


>gi|227115223|ref|ZP_03828879.1| 23S rRNA pseudouridine synthase D [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 325

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 85/336 (25%), Positives = 158/336 (47%), Gaps = 55/336 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V+++   + K   ++  G+ V   
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVINKPKEKVLGGESV--- 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
               A++ +I+E+   ++          +K  ++YED  I V NKP  + V  G+G   +
Sbjct: 66  ----AIDALIEEEARWEAQ--------DIKLDIVYEDEDILVINKPRDLVVHPGAG---N 110

Query: 129 IDGFL--------KSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            DG +           VD     PR  + HRLD++T+G++VVA+T  A   L E+ + R 
Sbjct: 111 PDGTVLNALLHHYPEIVDV----PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQARE 166

Query: 179 IQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           I + Y ++  G        ++ IA    K++H+    VH + +       A++H+++++ 
Sbjct: 167 ITREYEAVAIGSMTAGGMVEQPIARHATKRTHMA---VHPMGKP------AVTHYRIMEH 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NK 287
           F +    L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       +F   ++  ++
Sbjct: 218 F-RAHTRLRLRLETGRTHQIRVHMAHINHPLVGDQLYGGRPRPPKGASEDFIETLRGFDR 276

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             LHA  +   HP  G  ++  A LP  MV   ++L
Sbjct: 277 QALHATMLRFYHPITGIHMEWHAELPQDMVDLINAL 312


>gi|332071723|gb|EGI82215.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA17545]
          Length = 286

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD  Y +  K  
Sbjct: 182 AKNGKYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|251778563|ref|ZP_04821483.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum E1 str. 'BoNT E Beluga']
 gi|243082878|gb|EES48768.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum E1 str. 'BoNT E Beluga']
          Length = 302

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 78/320 (24%), Positives = 142/320 (44%), Gaps = 35/320 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIPPV 70
           V  + E +R+D++        +   +Q ++    ++V+ K +K N ++++  ++V   P 
Sbjct: 8   VSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNDKLIKSNYKLKACDEIVITMPE 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
           +  L       K+    ++L          +LYED  + V NK  G+ V    G      
Sbjct: 68  VETL-------KVESEDIDLD---------ILYEDKDVIVVNKEQGMVVHPAPGNYNGTL 111

Query: 129 IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D        +P + HR+D++TSG+LV+A+   +   L    +   + + Y+
Sbjct: 112 VNALLFHCTDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYY 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK-QNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G  KN    I   L      G D  + +K    +    AI+H++V++ +      +
Sbjct: 172 ALVEGRFKNDSGVIDKPL------GRDKKNRLKIAITEDGRRAITHYEVLERYDTGCTLI 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + +  TGRTHQ+RVH   +G P+VGD  Y    K  F    Q    LHA+ +   HP   
Sbjct: 226 KCKLETGRTHQIRVHMASLGHPLVGDPLYGFK-KQRFKLKGQ---MLHAKKLGFIHPTKN 281

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             ++    LP +  +  + L
Sbjct: 282 EYMEFETNLPEYFEEIIEKL 301


>gi|317498384|ref|ZP_07956679.1| RluA family pseudouridine synthase [Lachnospiraceae bacterium
           5_1_63FAA]
 gi|316894278|gb|EFV16465.1| RluA family pseudouridine synthase [Lachnospiraceae bacterium
           5_1_63FAA]
          Length = 323

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/267 (26%), Positives = 127/267 (47%), Gaps = 24/267 (8%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           EE  RLD+    +        + K+LR   ++++ K+   N ++  G  V I    + +N
Sbjct: 10  EEGQRLDKILSKYLNKAPKSFVYKMLRKKNIKLNGKKATGNEKLSQGDQVCIYLAEDTIN 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
              +E K     + L          +LYED  + + NKP GI  Q             I 
Sbjct: 70  KFREEVKAGKQKIKLD---------VLYEDENVIMVNKPWGILSQKSKPEDISINDQIIP 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y ++  L S  + +  KP + +RLD+ T+GI++   +    Q + E  + R ++K Y  +
Sbjct: 121 YAVNQGLISEKELQVVKPSICNRLDRNTTGIIICGISIEGLQTMAEMLKHRDMEKYYLCI 180

Query: 187 VWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G + + +K  ++ +L K      + V V KQ   GA++  + ++ +    ++F  L++
Sbjct: 181 VKGKLERTQK--VSAYLKKDEKT--NKVKVSKQEIAGASHIETAYEPM-ISNEEFTLLKV 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +  TG+THQ+R H   +G P++GD KY
Sbjct: 236 ELITGKTHQIRAHLASIGHPLIGDFKY 262


>gi|242309404|ref|ZP_04808559.1| ribosomal large subunit pseudouridine synthase [Helicobacter
           pullorum MIT 98-5489]
 gi|239523975|gb|EEQ63841.1| ribosomal large subunit pseudouridine synthase [Helicobacter
           pullorum MIT 98-5489]
          Length = 313

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 61/204 (29%), Positives = 106/204 (51%), Gaps = 16/204 (7%)

Query: 79  KEQKILDSSVNL---TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           ++ KIL+  V +      S  LK   L+E+  + +F+KPA + +      A+H    +  
Sbjct: 51  EKNKILEKEVEILLFVPQSKGLKP--LFENEDLAIFDKPAKMLIHPKGRFAHH--SLIDE 106

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             ++ GQ+  L HR+D+ETSG+++V + + + Q L E F  ++I+K Y +LV G  +   
Sbjct: 107 VREACGQESTLIHRIDKETSGLVLVGKHKRSIQELGELFAKKKIKKEYLALVRGEMRGGD 166

Query: 196 ECIANWLLKKSHIGGD-------YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
            C++  L  +   GGD       +  ++K        A S F+++  +      L++ P 
Sbjct: 167 FCLSLPLAMQKK-GGDLSVRSIYWGQILKAQSLNFKAAKSEFEILG-YINGNTLLKVYPI 224

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGRTHQ+R+H   +G PI+GD  Y
Sbjct: 225 TGRTHQIRIHLFALGFPILGDPLY 248


>gi|167768022|ref|ZP_02440075.1| hypothetical protein CLOSS21_02565 [Clostridium sp. SS2/1]
 gi|167710351|gb|EDS20930.1| hypothetical protein CLOSS21_02565 [Clostridium sp. SS2/1]
 gi|291561022|emb|CBL39822.1| pseudouridine synthase, RluA family [butyrate-producing bacterium
           SSC/2]
          Length = 323

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/266 (26%), Positives = 124/266 (46%), Gaps = 22/266 (8%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           EE  RLD+    +        + K+LR   ++++ K+   N ++  G  V I    + +N
Sbjct: 10  EEGQRLDKILSKYLNKAPKSFVYKMLRKKNIKLNGKKATGNEKLSQGDQVCIYLAEDTIN 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
              +E K     + L          +LYED  + + NKP GI  Q             I 
Sbjct: 70  KFREEVKAGKQKIKLD---------VLYEDENVIMVNKPWGILSQKSKPEDISINDQIIP 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y ++  L S  + +  KP + +RLD+ T+GI++   +    Q + E  + R ++K Y  +
Sbjct: 121 YAVNQGLISEKELQVVKPSICNRLDRNTTGIIICGISIEGLQTMAEMLKHRDMEKYYLCI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +  ++  A   LKK     + V V KQ   GA++  + ++ +     +F  L+++
Sbjct: 181 VKGKIEGSQKVSA--YLKKDE-KTNKVKVSKQEIAGASHIETAYEPV-ISNDEFTLLKVE 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
             TG+THQ+R H   +G P++GD KY
Sbjct: 237 LITGKTHQIRAHLASIGHPLIGDFKY 262


>gi|303235055|ref|ZP_07321679.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
 gi|302493910|gb|EFL53692.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
          Length = 273

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 79/302 (26%), Positives = 143/302 (47%), Gaps = 47/302 (15%)

Query: 14  NDEENMRLDRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           N ++  RLD + K NH  H  F+++ K      + ++ K  K N++++ G +V I     
Sbjct: 7   NVDKKTRLDEFLKKNHISHNLFISIYK----DDIFINGKHAKRNSKLEKGDIVTIN---- 58

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHID 130
                +++++     +N+          +LYED  I+V NKP  +++   G   +A  + 
Sbjct: 59  -----LRDEENKYEPINMDIE-------VLYEDDDIFVLNKPDKLTMNKDGEKSLANFVS 106

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              K    +  QK R  +RLDQ+TSG+++VA+ + A  +    ++    +K Y ++V G 
Sbjct: 107 YLFKQR--NIKQKVRFINRLDQDTSGVVMVAKNKIAQAY----YQKNSFKKKYLAIVKGN 160

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           PK++K       LK+  I  +    + +N K +   + + K    ++     + ++  TG
Sbjct: 161 PKDQK---IELNLKRDGIKTE----IDENGKKSVTILENLKNYGDYS----LVSLELLTG 209

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQ+RV   ++ CPIV D  Y    + NF+        LHA  ++    +G    IT  
Sbjct: 210 RTHQIRVSMEYINCPIVADSLYGEKIE-NFSQ------MLHANEIEFVDMKGEYHNITTN 262

Query: 311 LP 312
           LP
Sbjct: 263 LP 264


>gi|229845572|ref|ZP_04465699.1| hypothetical protein CGSHi6P18H1_05160 [Haemophilus influenzae
           6P18H1]
 gi|229811507|gb|EEP47209.1| hypothetical protein CGSHi6P18H1_05160 [Haemophilus influenzae
           6P18H1]
          Length = 219

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/208 (31%), Positives = 100/208 (48%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+      S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG  +N         I +W  +      D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLPMICDWENRPRQC-LDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD  Y   
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGNPILGDKFYSHP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                +S    +L LHA  + + HP  G
Sbjct: 185 QAKAMSS----RLCLHAEELTITHPITG 208


>gi|319745315|gb|EFV97632.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           agalactiae ATCC 13813]
          Length = 296

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 111/239 (46%), Gaps = 38/239 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++Y+D  + V NKP G+ V   +G         + YHI    K      G  +P + HR+
Sbjct: 76  IIYQDDDVAVVNKPQGMVVHSSAGHSSGTLVNALMYHI----KDLSSINGVVRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+   A Q L E  + ++  + Y ++V G   N +  I      ++ IG 
Sbjct: 132 DKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVI------EAPIGR 185

Query: 211 DYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 KQ    KG   AI+ F V++ F   +  +E+   TGRTHQ+RVH  ++G P+ G
Sbjct: 186 SDKDRKKQAVTAKG-KPAITRFHVLERFGD-YTLVELSLETGRTHQIRVHMAYIGHPLAG 243

Query: 269 DHKY----CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           D  Y        KG F         LHA+ +   HP  G  L  +  +P     T + L
Sbjct: 244 DPVYGPRKTLGGKGQF---------LHAQTLGFTHPSNGENLIFSVEVPEIFQTTLEKL 293


>gi|297690649|ref|XP_002822725.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 1 [Pongo abelii]
          Length = 377

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 61/192 (31%), Positives = 95/192 (49%), Gaps = 21/192 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           +L++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 99  ILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P      +   +++K   G    H  
Sbjct: 159 VMVLAWDKDMAHQVQELFRTRQVVKKYWAITVRVPMPSAGVVDIPIVEKEAQGQQQHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-AL 260
                        V  +  + A  A++ ++V+         LE+QP TG  HQLRVH + 
Sbjct: 219 TLSPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSSTLSSAL-LELQPITGIKHQLRVHLSF 277

Query: 261 HMGCPIVGDHKY 272
            + CPI+GDHKY
Sbjct: 278 GLDCPILGDHKY 289


>gi|148989706|ref|ZP_01821015.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP6-BS73]
 gi|147924822|gb|EDK75905.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP6-BS73]
          Length = 291

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD  Y +  K  
Sbjct: 195 AKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDPLYNSKSKT- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|77406381|ref|ZP_00783442.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
 gi|77175005|gb|EAO77813.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
          Length = 296

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 111/239 (46%), Gaps = 38/239 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++Y+D  + V NKP G+ V   +G         + YHI    K      G  +P + HR+
Sbjct: 76  IIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHI----KDLSSINGVVRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+   A Q L E  + ++  + Y ++V G   N +  I      ++ IG 
Sbjct: 132 DKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDQGVI------EAPIGR 185

Query: 211 DYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 KQ    KG   A++ F V++ F   +  +E+   TGRTHQ+RVH  ++G P+ G
Sbjct: 186 SDKDRKKQAVTAKG-KPAVTRFHVLERFGD-YTLVELSLETGRTHQIRVHMAYIGHPLAG 243

Query: 269 DHKY----CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           D  Y        KG F         LHA+ +   HP  G  L  +  +P     T D L
Sbjct: 244 DPVYGPRKTLGGKGQF---------LHAQTLGFTHPSNGENLIFSVEVPEIFQTTLDKL 293


>gi|260914556|ref|ZP_05921024.1| pseudouridine synthase A [Pasteurella dagmatis ATCC 43325]
 gi|260631347|gb|EEX49530.1| pseudouridine synthase A [Pasteurella dagmatis ATCC 43325]
          Length = 228

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 107/203 (52%), Gaps = 16/203 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D    V NKP+G+    G+   Y+      S V  K       HRLD  TSG+++ 
Sbjct: 25  IVHYDDHFVVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPAHRLDMSTSGLILF 82

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A ++AA + L   FR R  +K Y +LVWG  +  +  I   L+       D+ +  +Q  
Sbjct: 83  ALSKAADRELKRQFREREPKKHYQALVWGHLEEDQGKINLPLI------CDWENRPRQKI 136

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+G + A++ ++V++ +      +++ P TGR+HQLR+H L +G PI+GD K+ A+ +
Sbjct: 137 CFERGKS-AVTLYEVLERYPNNTTRVKLTPITGRSHQLRLHMLALGHPILGD-KFYAHPQ 194

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               SP   +L LHA  ++  HP
Sbjct: 195 AKALSP---RLCLHAESLEFSHP 214


>gi|238897770|ref|YP_002923449.1| pseudouridine synthase [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
 gi|229465527|gb|ACQ67301.1| pseudouridine synthase [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
          Length = 325

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/214 (29%), Positives = 112/214 (52%), Gaps = 24/214 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVD-SKGQKPRLTHRLDQETSGI 157
           ++YED+ I V NKP+G+ V  G+G   H  ++  L  + D +   +  + HRLD++T+G+
Sbjct: 86  IIYEDTDILVINKPSGLVVHPGAGNPDHTILNALLDYYPDITHVPRAGIVHRLDKDTTGL 145

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVH 214
           +V+A+T  A   L ++ + R + + Y ++  G      +  E IA    K++H+    VH
Sbjct: 146 MVIAKTLRAQTSLVDALQARLVTREYEAIAVGHITAGGSINEPIARHKSKRTHMA---VH 202

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + ++      A++H++++  F +    L ++  TGRTHQ+RVH  ++  P+VGD  Y  
Sbjct: 203 PLGKS------AVTHYRILQHF-RAHTRLRLRLETGRTHQIRVHFSYIHHPLVGDPLYGR 255

Query: 275 NF---KGNFTSPIQN-----KLYLHARYMDLPHP 300
                KG     I+      +  LHA  + L HP
Sbjct: 256 RLRQPKGALEKLIETLSAFKRQALHATMLRLHHP 289


>gi|225857586|ref|YP_002739097.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae P1031]
 gi|225726338|gb|ACO22190.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae P1031]
 gi|301800771|emb|CBW33421.1| RNA pseudouridylate synthase [Streptococcus pneumoniae OXC141]
          Length = 278

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD  Y +  K  
Sbjct: 182 AKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|15903866|ref|NP_359416.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae R6]
 gi|116515727|ref|YP_817230.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae D39]
 gi|15459512|gb|AAL00627.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae R6]
 gi|116076303|gb|ABJ54023.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae D39]
          Length = 291

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD  Y +  K  
Sbjct: 195 AKNGKYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDPLYNSKSKT- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|67924151|ref|ZP_00517595.1| Pseudouridine synthase, RluD [Crocosphaera watsonii WH 8501]
 gi|67854003|gb|EAM49318.1| Pseudouridine synthase, RluD [Crocosphaera watsonii WH 8501]
          Length = 302

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 80/301 (26%), Positives = 134/301 (44%), Gaps = 38/301 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PP 69
           ++ +   + L  ++  HY H N+    + + SGQV VD++ V     +++GQ +    PP
Sbjct: 11  IKQNHAGLTLIEYYTKHYHHSNYQQWLERIISGQVLVDEQTVDPQTVLKTGQRLSYHRPP 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                    +E ++             L   ++YED  + + NKP+G+ V  G G   H 
Sbjct: 71  --------WQEPEVP------------LSFEIIYEDDNLLIVNKPSGLPVLPGGGFLEHT 110

Query: 130 DGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              L        Q +P   HRL + TSG++++ ++  A  HLT+  R ++I K+Y  L+ 
Sbjct: 111 --LLWQLKKQYPQNEPIPIHRLGRGTSGLMLMGKSAIARSHLTQQMREQKISKVYQGLIG 168

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
                 K  I + + K       Y++  K + K   YA S  +V+  +  K   LE+   
Sbjct: 169 KNNLPDKFSIDHPIGKIPDPVLGYIYGAKVDGK---YAYSECRVLGRYVDK-TLLEVTIL 224

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC------ANFKGN---FTSPIQNKLYLHARYMDLPH 299
           TGR HQ+R+H   +G P++GD  Y         FK +      P     +LHA  +   H
Sbjct: 225 TGRPHQIRIHLATIGYPLLGDPLYVVGGIPKTGFKEDNDTINVPGDCGYFLHAYQLSFVH 284

Query: 300 P 300
           P
Sbjct: 285 P 285


>gi|291545793|emb|CBL18901.1| pseudouridine synthase, RluA family [Ruminococcus sp. SR1/5]
          Length = 298

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/223 (27%), Positives = 108/223 (48%), Gaps = 16/223 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGI 157
           +LYED  I V NKPA + V   +G   +      +W   +  K    R  +RLD++T+G+
Sbjct: 86  ILYEDEDILVLNKPADMPVHPSAGNYENTLANGVAWYYKQQGKAFVYRCINRLDRDTTGV 145

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV+A+   +   L+   + R+I++ Y +L  GIP  +    A      + +    V+   
Sbjct: 146 LVLAKNPLSGALLSAQMKQRQIRRTYLALTDGIPPERGTISAPVARMDASVITREVNF-- 203

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+G   A++H++ +   +  +  +E+   TGRTHQ+RVH  ++GCP+ GD  Y   F 
Sbjct: 204 --ERG-EAAVTHYERL-AVSNGYALVELHLDTGRTHQIRVHMKYIGCPLPGDFLYHPVFD 259

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
                    +  LH+  ++  HP  G  +   AP+P    + +
Sbjct: 260 R------IGRQALHSFQLEFAHPITGEPMCFLAPVPEDFRRAF 296


>gi|254361951|ref|ZP_04978082.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|153093498|gb|EDN74478.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
          Length = 266

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 57/181 (31%), Positives = 97/181 (53%), Gaps = 22/181 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +     + PR  + HRLD++T
Sbjct: 86  IVYEDDDIIVINKPKDLVVHPGAG---NPDGTVLNALLHYYPPIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+   A  HL  + + RRI + Y ++  GI        E +A    K++ +   
Sbjct: 143 TGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMTQGGKVDEPMARHPTKRTAMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 201 -VHPMGKP------AVTHYRIMERF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQL 252

Query: 272 Y 272
           Y
Sbjct: 253 Y 253


>gi|89901092|ref|YP_523563.1| pseudouridine synthase RluD [Rhodoferax ferrireducens T118]
 gi|89345829|gb|ABD70032.1| ribosomal large subunit pseudouridine synthase D [Rhodoferax
           ferrireducens T118]
          Length = 334

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 78/287 (27%), Positives = 123/287 (42%), Gaps = 28/287 (9%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLDR      P  +   LQ+++  G V ++   + K + R+++  V  I      L    
Sbjct: 40  RLDRALVELVPEFSRSYLQQLIDLGGVTINGIVIHKPSTRVKAADVGTI-----ELRPTP 94

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
           + Q     ++ L          +++ED  + V NKPAG+ V    G      ++G L   
Sbjct: 95  QSQAFKPETMALN---------VVFEDEHLMVINKPAGLVVHPAPGNWSGTLLNGLLAR- 144

Query: 137 VDSKGQK-PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            D+K    PR  + HRLD++TSG++VVARTR     L  S   R + + Y +L  G    
Sbjct: 145 -DAKAMNLPRAGIVHRLDKDTSGLMVVARTRPVMDALIRSIAAREVSRQYVALAHGPWTG 203

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            +    N  + +       + VV         A +  +++    Q  CW+    HTGRTH
Sbjct: 204 NRRVEINAPIGRDPRNRLRMAVVDLARNPGKLARTDVELLQNCDQG-CWVLCTLHTGRTH 262

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Q+RVH   +G P+V D  Y    +         +  LHA  +   HP
Sbjct: 263 QIRVHMAMIGHPLVADVLYGGRAEAGM-----QRQALHACRLAFTHP 304


>gi|221232733|ref|YP_002511887.1| RNA pseudouridylate synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225855502|ref|YP_002737014.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae JJA]
 gi|220675195|emb|CAR69781.1| RNA pseudouridylate synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225723486|gb|ACO19339.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae JJA]
          Length = 278

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD  Y +  K  
Sbjct: 182 AKNGKYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|87161600|ref|YP_493787.1| hypothetical protein SAUSA300_1090 [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|161509370|ref|YP_001575029.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|294848190|ref|ZP_06788937.1| RNA pseudouridine synthase ylyB [Staphylococcus aureus A9754]
 gi|87127574|gb|ABD22088.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|160368179|gb|ABX29150.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|294824990|gb|EFG41412.1| RNA pseudouridine synthase ylyB [Staphylococcus aureus A9754]
 gi|315198434|gb|EFU28763.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320144297|gb|EFW36063.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA177]
          Length = 305

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/276 (27%), Positives = 134/276 (48%), Gaps = 29/276 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +     
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKSNYK----- 55

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++   I      + E  IL  ++NL          + YED  + V  KP G+ V    
Sbjct: 56  -VKLNDHIVVTEKEVVEADILPENLNLD---------IYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +   K+     G+ +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAP--IGRNKNDRQSMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY
Sbjct: 220 -KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKY 254


>gi|325298043|ref|YP_004257960.1| pseudouridine synthase [Bacteroides salanitronis DSM 18170]
 gi|324317596|gb|ADY35487.1| pseudouridine synthase [Bacteroides salanitronis DSM 18170]
          Length = 543

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/203 (34%), Positives = 97/203 (47%), Gaps = 18/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + V NKP G+    G  I   +   L +   +    P + HRLD  TSG+L+V
Sbjct: 342 IVYEDEWLIVVNKPEGMLSTPGKLITDSVYTRLHTLYPT-ATGPLIVHRLDMATSGLLLV 400

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T+     L + F  RRIQK Y + + GI     E I N  +   +    Y  V  +  
Sbjct: 401 AKTKEIHYALQKMFASRRIQKRYTAWLNGI-VTTDEGIINLPICPDYDNRPYQMVHSEYG 459

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFK 277
           K    AI+ +KV+     K   +   P TGRTHQLRVHA H   + CPI+GD  Y     
Sbjct: 460 KP---AITRYKVLGRKEGK-TRIAFYPLTGRTHQLRVHAAHPDGLNCPIIGDELYGKK-- 513

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
                   ++LYLHA  +   HP
Sbjct: 514 -------ADRLYLHAAGLSFIHP 529


>gi|242373484|ref|ZP_04819058.1| pseudouridylate synthase RluD [Staphylococcus epidermidis
           M23864:W1]
 gi|242348847|gb|EES40449.1| pseudouridylate synthase RluD [Staphylococcus epidermidis
           M23864:W1]
          Length = 305

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 73/304 (24%), Positives = 139/304 (45%), Gaps = 34/304 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + +  +   R+D+         +   LQ  ++   V+V+ K +K N +++   
Sbjct: 1   METYEFKITDESQVGQRIDKLLSEMNDEWSRSQLQDWIKEDLVKVNDKVIKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           I+ E++++++ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  HI-----------IVTEKEVVEADI----QPEDLNLDIYYEDEDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A     K+      + +V   +     A++HF V++ F
Sbjct: 166 TVKRKYTALVHGNIPHDYGTVDAPIGRNKNDRQA--MAIVDDGKD----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KDYTLIECELETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQA-----LHAGVIG 273

Query: 297 LPHP 300
             HP
Sbjct: 274 FEHP 277


>gi|332071869|gb|EGI82358.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA41301]
          Length = 278

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD  Y +  K  
Sbjct: 182 AKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|297690651|ref|XP_002822726.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 2 [Pongo abelii]
          Length = 346

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 59/177 (33%), Positives = 90/177 (50%), Gaps = 22/177 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           +L++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 99  ILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V+A  +  A  + E FR R++ K YW++   +P      +   ++             
Sbjct: 159 VMVLAWDKDMAHQVQELFRTRQVVKKYWAITVRVPMPSAGVVDIPIV------------- 205

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
              EK A  A++ ++V+         LE+QP TG  HQLRVH +  + CPI+GDHKY
Sbjct: 206 ---EKEAQVAVTQYQVLSSTLSSAL-LELQPITGIKHQLRVHLSFGLDCPILGDHKY 258


>gi|148985947|ref|ZP_01819000.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP3-BS71]
 gi|168492590|ref|ZP_02716733.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC0288-04]
 gi|147921920|gb|EDK73045.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP3-BS71]
 gi|183573261|gb|EDT93789.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC0288-04]
          Length = 291

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD  Y +  K  
Sbjct: 195 AKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDPLYNSKSKT- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|220927804|ref|YP_002504713.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|219998132|gb|ACL74733.1| pseudouridine synthase, RluA family [Clostridium cellulolyticum
           H10]
          Length = 303

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/268 (25%), Positives = 124/268 (46%), Gaps = 26/268 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +  E + E  ++DR  ++ +P++    L K LR   ++V+  R+K +  +  G  + I  
Sbjct: 4   ITAEENHEGKKIDRVVRDFFPNLASGMLYKALRKKDIKVNGVRIKEDYIVSFGDKIDIYI 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAY 127
           + + L               + +  D     ++Y+D  + + NK  GI V        A 
Sbjct: 64  IDDYL---------------IGRDDDGFS--VVYDDDNLLIVNKETGIPVHPDKNQKEAT 106

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            ID     +    G    L HRLD+ TSG++++A+  A  + + E  + R IQK Y  +V
Sbjct: 107 LIDKLQSIY----GPNLALCHRLDRNTSGLVIIAKNPATLEVMLEKIKNREIQKYYTCIV 162

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  + K   + ++L K   +   +++  K   + +   I+ ++++         LE++ 
Sbjct: 163 SGKMEKKNAELVDYLEKNEKLSRVFINPEKT--RNSVQIITRYRILASM-NSLNLLEVEL 219

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            TGRTHQ+R H  + G PI+GD KY  N
Sbjct: 220 VTGRTHQIRAHLAYYGHPIIGDGKYGKN 247


>gi|325479239|gb|EGC82335.1| pseudouridine synthase, RluA family [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 303

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 76/292 (26%), Positives = 145/292 (49%), Gaps = 27/292 (9%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  +    I    ++  ++  +++V+ K VK + ++  G  + I    ++L 
Sbjct: 4   DEIIRIDKFISDELEEIPREKIKDFIKDKKIKVNDKIVKPSFKLSEGDEIEID---DSLF 60

Query: 76  HI-IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG----GSGIAYHID 130
           H+   + + +D  + + ++ D+    ++ +DS + V   PAG  V G    G    Y  D
Sbjct: 61  HVPTIDPEAMDLKI-VYENDDYA---IIDKDSNVIV--HPAGKIVTGTLVNGLLDRYGYD 114

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G      D    +P + HRLD++T+G++ + +   + ++  + F  R++ KIY+++V+G 
Sbjct: 115 GLSHIGGD---DRPGIVHRLDKDTTGLIAITKNNTSYKYFKKMFETRKVDKIYYAIVFGT 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              K + I  ++ +  H     + V     K    AISH++V+      +  ++++  TG
Sbjct: 172 FDKKSDTIETFMDRDPH-NRRKMAVTSSGRK----AISHYEVV-AETNDYSLVKVKIVTG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           RTHQ+RVH  H+  PI+GD  Y  N K NF    Q    LH  Y+     EG
Sbjct: 226 RTHQIRVHMTHLNHPILGDPVY-GNVKHNFNLDHQ---LLHCAYIGFTDMEG 273


>gi|295091133|emb|CBK77240.1| pseudouridine synthase, RluA family [Clostridium cf.
           saccharolyticum K10]
          Length = 314

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 61/217 (28%), Positives = 110/217 (50%), Gaps = 16/217 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGI 157
           ++YED  + V +KPAG+ V    G  Y+      +W  S+  +P   R  +RLD++T+G+
Sbjct: 86  IIYEDRDLMVIDKPAGMPVHPSQGNFYNTLANGIAWYFSERGEPFTFRAVNRLDRDTTGL 145

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+    A  L+E    + +++ Y ++  G  K  +E      + ++   G  +    
Sbjct: 146 LLIAKHGLCAALLSEMVARKEVRRQYLAIASG--KTDEEGTICAPIARAD--GSTIERCV 201

Query: 218 QNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              +G  YA +H++ +   ++  C  L +   TGRTHQ+RVH  H+G P++GD  Y  ++
Sbjct: 202 DETRG-EYACTHYRRLVYSSENDCSLLLLTLDTGRTHQIRVHMKHIGHPLLGDFLYNPDY 260

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +      +  +  LH+  +   HP  G  L  +APLP
Sbjct: 261 R------LFRRQSLHSFLLSFTHPLTGESLNFSAPLP 291


>gi|300771291|ref|ZP_07081167.1| ribosomal large subunit pseudouridine synthase D [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|300761961|gb|EFK58781.1| ribosomal large subunit pseudouridine synthase D [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 348

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/333 (22%), Positives = 149/333 (44%), Gaps = 58/333 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           + V+  +  +R+D++  N   + +   +Q  + +G V V+   +K + +++   ++ +  
Sbjct: 22  IEVDKGQALLRIDKFLMNRVENASRNKIQNAIDAGSVLVNDSVIKSSYKVKPFDIISVVL 81

Query: 68  --PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--- 122
             PP         ++ ++    + L          +++ED ++ V NK AG+ V  G   
Sbjct: 82  PDPP---------RDTEVYPEDIPLD---------IIFEDDEVMVVNKVAGMVVHPGFNN 123

Query: 123 ------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                 + + +H +      +     +P L HR+D++TSG+LV+A++  A  +L + F  
Sbjct: 124 YTGTLVNALTHHFNQL--PTMPGNAGRPGLVHRIDKDTSGLLVIAKSEWAMTYLAKQFFD 181

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY----VHVVKQNEKGANYAISHFKV 232
             I + Y ++VWG        IA       +IG +     V  +  + +   ++++H++V
Sbjct: 182 HSIMRKYVAMVWG-------DIAEDGTVTGYIGRNLKDRRVMTMYDDSEKGKWSVTHYRV 234

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN 286
           ++        +E Q  TGRTHQ+R H   +G P+  D  Y  +   KG     +   ++N
Sbjct: 235 LERLGY-VTLIECQLETGRTHQIRAHMQSIGHPLFNDVAYGGDRILKGTVFNKYRQFVEN 293

Query: 287 ------KLYLHARYMDLPHPEGGR-LQITAPLP 312
                 +  LHA+ +   HP+    L    PLP
Sbjct: 294 CFALLPRQALHAQVLGFEHPKSKEFLTFETPLP 326


>gi|298530973|ref|ZP_07018374.1| pseudouridine synthase, RluA family [Desulfonatronospira
           thiodismutans ASO3-1]
 gi|298508996|gb|EFI32901.1| pseudouridine synthase, RluA family [Desulfonatronospira
           thiodismutans ASO3-1]
          Length = 535

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 83/309 (26%), Positives = 136/309 (44%), Gaps = 43/309 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHI--NFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRI 67
            V+  +   RLDR    + P    +   +Q  +R G + +D    +K  +++ +GQ V  
Sbjct: 8   TVQESQAGSRLDRLVMQNIPRPAPSRSRVQDWIRKGNILLDGTVCLKPAHKLSAGQTV-- 65

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
                         ++L    N        K  ++Y D ++ V NKPAG+SV   S    
Sbjct: 66  --------------QVLAREENEDLEPVAGKLDIVYMDREMVVLNKPAGLSVHPSSSDPA 111

Query: 125 ------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 + Y   G L+   D   Q+P + HRLD++T+G++V A  + A + L   F  RR
Sbjct: 112 PTLVHYLLYACPG-LRLMTDR--QRPGIVHRLDKDTTGLMVAALNQEAKEDLAGQFAGRR 168

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y +LV G  K + E I N  L +       V   ++       A + +KV+     
Sbjct: 169 VHKTYLALVCGALK-QDEGIINVPLARDQQSRARVAPSREGRS----ARTAYKVLKRDPS 223

Query: 239 KF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQNKLYLH 291
                +++Q  TGRTHQ+RVH  H+  P++GD  Y         +K  F S +  +  LH
Sbjct: 224 GLWSLVQVQIFTGRTHQIRVHFSHLNHPVLGDRIYGGTDWDRFGWKKRFLSRLAKRQLLH 283

Query: 292 ARYMDLPHP 300
           +  + + HP
Sbjct: 284 SSCLGIMHP 292


>gi|310659241|ref|YP_003936962.1| ribosomal large subunit pseudouridylate synthase d [Clostridium
           sticklandii DSM 519]
 gi|308826019|emb|CBH22057.1| ribosomal large subunit pseudouridylate synthase D [Clostridium
           sticklandii]
          Length = 301

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 113/230 (49%), Gaps = 17/230 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVD-SKGQKPRLTHRLDQETSGI 157
           LLYED+ + V  K   I V    G   +   +G +K + D S   K R  +RLD++TSGI
Sbjct: 85  LLYEDADLMVIEKEPFIVVHPTKGHQRNTLANGLIKLFKDKSINSKIRFVNRLDRDTSGI 144

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+       LT++  M  ++K Y+++V G   +K   + +  + KS  G   +    
Sbjct: 145 LIVAKNSYCHSILTKNDAMHEMEKKYYAVVSG-HLDKASGVIDLPIDKSEDGIRRI---- 199

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            ++KG   A++ +KVID   +    LE+   TGRTHQ+RVH  H+G P++GD  Y  +  
Sbjct: 200 VSDKGQR-AVTRYKVIDKL-KYATLLEISLETGRTHQIRVHFSHIGHPLLGDELYGGDM- 256

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSLGFKY 326
                 + N+  LH   +    P    +  I + LP  M +  + L   Y
Sbjct: 257 -----SLLNRQALHCFELGFYSPRKSEITYIKSELPHDMRELVEKLSLAY 301


>gi|307297424|ref|ZP_07577230.1| pseudouridine synthase, RluA family [Thermotogales bacterium
           mesG1.Ag.4.2]
 gi|306916684|gb|EFN47066.1| pseudouridine synthase, RluA family [Thermotogales bacterium
           mesG1.Ag.4.2]
          Length = 310

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 83/321 (25%), Positives = 151/321 (47%), Gaps = 38/321 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +Q ++V + E+  RLD+      P  ++   +Q+ +++ +V V+ +  K + +++ G+ +
Sbjct: 2   LQEIIVSSREDGWRLDKVVVEKAPPWVSRTFVQRQIKNSKVFVNSRPRKPSYKVKIGESI 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------ 119
                   L    K   +   ++ L          +++ED  I V NK  GI V      
Sbjct: 62  TF-----DLPEKPKVASVEPEAIPLK---------IVFEDRDIIVVNKDPGIIVHPLPRK 107

Query: 120 QGGSGIAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           Q G+     ++  L    D +G     +P + HRLD++TSGI++VA+   A   L+  F+
Sbjct: 108 QTGT----LVNALLYHCKDLQGIGGVTRPGIVHRLDKDTSGIIIVAKNDLAHVSLSSQFK 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R   K Y +LV G  K       ++ + +  +    + V   NE G   ++++F+ +  
Sbjct: 164 SRLTAKEYIALVRG--KTPPFGKIDYSIARHPVNRLKMSV---NENGKE-SLTYFQTLSN 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F+     + ++P TGRTHQ+RVH    G P++GD  Y    +      I+ ++ LHA  +
Sbjct: 218 FSSIASLIIVRPRTGRTHQIRVHMKEKGFPLLGDAVYGKAREDEIFG-IKRQM-LHAMKL 275

Query: 296 DLPHPEGG-RLQITAPLPAHM 315
            + HP  G R+   A LP  M
Sbjct: 276 TVSHPRSGIRMTFIARLPEDM 296


>gi|257452878|ref|ZP_05618177.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
 gi|317059420|ref|ZP_07923905.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
 gi|313685096|gb|EFS21931.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
          Length = 291

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/262 (27%), Positives = 133/262 (50%), Gaps = 16/262 (6%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE     +R+DR+ +  +P ++  ++ K LR+G+++V+ K+VK N R      ++     
Sbjct: 6   VEEKYVGVRIDRYLRKEFPDLSLGDIFKTLRTGKIKVNGKKVKENYRFLEEDRIQ----- 60

Query: 72  NALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
              N++  E+K   + ++L++     L+  + Y+D+ I VF K AG  +  GS   Y + 
Sbjct: 61  ---NYLQVEEKEKMTFIHLSQEEKKRLEDGIFYQDTDILVFYKKAGELMHKGSSHDYGLA 117

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +++  +  +     +RLD+ETSG+++  +     + L E+ + R I K Y+ ++ G 
Sbjct: 118 EQFQAYFQN--EDFHFVNRLDKETSGLVLGGKCLKIVRELAEAIKKRTIIKKYYIIIEGS 175

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P+     +  +L K    G + V   +  ++      + F VI    +++  LE    TG
Sbjct: 176 PEKNHFSLKTYLKK----GENKVLESQTAKEEYKECSASFSVIRK-NKEYSLLEAVLETG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKY 272
           RTHQLRV    +G PI+GD KY
Sbjct: 231 RTHQLRVQLAGIGFPILGDIKY 252


>gi|291166431|gb|EFE28477.1| ribosomal large subunit pseudouridine synthase family protein
           [Filifactor alocis ATCC 35896]
          Length = 223

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 59/177 (33%), Positives = 91/177 (51%), Gaps = 8/177 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ + V  KP  I  Q  +     +   +K ++  K QKP      L HRLD+ T 
Sbjct: 6   VLYEDNHVIVVVKPYRIPSQEDNSNDTDMLTIVKEYIKEKYQKPGNVFVGLVHRLDRVTG 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  L+E  R  +I+K Y ++V G  K     + +++ K S    + V V
Sbjct: 66  GLMVFAKTSKAASRLSEQIRTNQIEKKYLAVVHGSLKTSSGQLEDFIKKSS--SKNIVSV 123

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +++K A   I ++ VI C    +  + +   TGR+HQ+RV     G  IVGD KY
Sbjct: 124 CSKHDKNAKKCILNYHVISCLPD-YSLINVHLLTGRSHQIRVQFSSRGHSIVGDVKY 179


>gi|167750498|ref|ZP_02422625.1| hypothetical protein EUBSIR_01474 [Eubacterium siraeum DSM 15702]
 gi|167656424|gb|EDS00554.1| hypothetical protein EUBSIR_01474 [Eubacterium siraeum DSM 15702]
          Length = 303

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/312 (24%), Positives = 135/312 (43%), Gaps = 37/312 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R D++       I       ++  G   V+ K    N ++++G  V +         I+ 
Sbjct: 13  RTDKFLALQDTGITRSAAAALIEQGCCLVNGKIAAKNQKLKTGDTVTLDVPEAQPADILP 72

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHID 130
           E   LD               ++YEDS + V NKP G+ V    G         + YH  
Sbjct: 73  ENIPLD---------------IVYEDSDLLVVNKPKGMVVHPAPGHYSGTLVNALMYHCG 117

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L     +   +P + HR+D++TSG+L+VA+   A   L E  ++    + Y ++V G+
Sbjct: 118 DSLSGI--NGVIRPGIVHRIDRDTSGLLIVAKNDTAHNILAEQIKVHSFTREYMAVVQGV 175

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              K++   +  + +       + V  +N +    A++H+ V   + +    + ++  TG
Sbjct: 176 I--KEDGTVDAPIGRHKTDRKKMCVTTENSR---EAVTHYFVEQTY-RNNTLVRLRLETG 229

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQ+RVH  ++G P+ GD  Y     GN +        LHA+ +   HP+G  ++  + 
Sbjct: 230 RTHQIRVHMAYIGHPVTGDEVY-----GNGSPKWLCGQCLHAKKIGFIHPDGRYMEFDSE 284

Query: 311 LPAHMVKTWDSL 322
           LP +  K   +L
Sbjct: 285 LPDYFKKLLANL 296


>gi|226327118|ref|ZP_03802636.1| hypothetical protein PROPEN_00983 [Proteus penneri ATCC 35198]
 gi|225204336|gb|EEG86690.1| hypothetical protein PROPEN_00983 [Proteus penneri ATCC 35198]
          Length = 217

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/201 (32%), Positives = 106/201 (52%), Gaps = 13/201 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I   NKP+G+ SV G +    H D  + S + ++       HRLD  TSG++V
Sbjct: 15  VLYQDEHIIAVNKPSGLLSVPGKA--PEHNDSIM-SRIKAEFPNAECVHRLDMATSGVIV 71

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA  + A + L   FR R  +K Y + VWG    K+E + +  L           V  + 
Sbjct: 72  VALNKEAERELKRQFREREPKKTYIARVWGH-VEKEEGLVDLPLICDWPNRPKQKVCHET 130

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K A    + ++V++ + +    +++ P TGR+HQLRVH L +G PI+GD ++ A+ +  
Sbjct: 131 GKAAQ---TFYEVLE-YEENATRVKLSPITGRSHQLRVHMLALGHPILGD-RFYAHPQAR 185

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
             +P   +L LHA+ + + HP
Sbjct: 186 AMAP---RLQLHAQELFITHP 203


>gi|47093663|ref|ZP_00231418.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|47017959|gb|EAL08737.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|328466988|gb|EGF38091.1| ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes 1816]
          Length = 296

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 76/313 (24%), Positives = 147/313 (46%), Gaps = 40/313 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           VE +E+ + L  + K+ +     +   K    G++ V+ K       ++ G  VR+  P 
Sbjct: 7   VETEEDGLLLRTFLKSKHISKQLLTAVKFGAEGKIEVNNKEQNVLYHVKVGDKVRLTFPT 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 ++ E   LD               +++ED  + + NKPAG++        YH +
Sbjct: 67  EQQNERLLAEYTDLD---------------IIFEDDFLLIINKPAGMASIPSQ---YHPN 108

Query: 131 GFLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + ++V    +   LT+      RLD+ETSG++++A+ R A   L+   +   +++ Y 
Sbjct: 109 GSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQ 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWL 243
           +   G+   +K  I      ++ IG   V ++++       YA ++++V+  + + F  +
Sbjct: 169 AFTSGVLVEQKGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY-RAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTE 275

Query: 304 R-LQITAPLPAHM 315
           + +    PLPA M
Sbjct: 276 KYMAFDLPLPADM 288


>gi|209694254|ref|YP_002262182.1| 23S rRNA pseudouridine synthase D [Aliivibrio salmonicida LFI1238]
 gi|208008205|emb|CAQ78349.1| ribosomal large subunit pseudouridine synthase D [Aliivibrio
           salmonicida LFI1238]
          Length = 324

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 119/239 (49%), Gaps = 29/239 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G     DG + + +     S  + PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAGTP---DGTILNALLFHYPSIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG--GDY 212
           +G++VVA+T  A   L  + + R+I + Y ++V G         A  +++K  IG     
Sbjct: 143 TGLMVVAKTVPAQTRLVRALQKRKITREYEAIVLG------RMTAGGMIEKP-IGRHPQK 195

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             ++  +E G + A++H++V + F +    L ++  TGRTHQ+RVH   +  P+VGD  Y
Sbjct: 196 RTLMAVHELGKD-AVTHYRVAEHF-RIHTRLRLRLETGRTHQIRVHMSFLQHPLVGDTAY 253

Query: 273 CANF---KGNFTSPIQ-----NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                  KG     I      N+  LHA  +   HP  G  ++  AP+P  ++    +L
Sbjct: 254 GGRARIPKGASQELIDMIRGFNRQALHAAMLRFDHPITGEVMEFHAPIPDDIIALAQAL 312


>gi|23006096|ref|ZP_00048580.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 279

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/260 (28%), Positives = 120/260 (46%), Gaps = 36/260 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR     +  ++   LQ ++R G VR D            G V+R P     +    +
Sbjct: 11  RLDRALARAFEDLSRARLQALVRDGLVRCD------------GAVLRDP--ARKVGAGCR 56

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL------ 133
               + + +      + L   +++ED  + V +KPAG+ V   +G   H DG L      
Sbjct: 57  LDLSVPAPLPAEPMGEALPLTVVHEDEDLIVIDKPAGLVVHPAAG---HEDGTLVNRLIA 113

Query: 134 ---KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWS 185
               S     G ++P + HRLD++TSG+LVVA+   A Q L+  F    R   +++ Y +
Sbjct: 114 HCGASLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQFADHGRNGALERAYLA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--IDCFAQKFCWL 243
           LVW +P+ +   I   L +  H   + + VV++ E     AI+H++V  +         L
Sbjct: 174 LVWNVPEPRHGTIRANLARSRH-NREKIAVVREGE--GREAITHYRVEALPGADGVTALL 230

Query: 244 EMQPHTGRTHQLRVHALHMG 263
             +  TGRTHQ+RVH  + G
Sbjct: 231 RCRLETGRTHQIRVHLRNRG 250


>gi|330900138|gb|EGH31557.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. japonica str. M301072PT]
          Length = 211

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/204 (31%), Positives = 106/204 (51%), Gaps = 12/204 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIHQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++      C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEGGKHALTFWKVVE-RHDTHCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG 303
              P   +L LHA  +   HP  G
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTG 200


>gi|266624507|ref|ZP_06117442.1| pseudouridylate synthase [Clostridium hathewayi DSM 13479]
 gi|288863645|gb|EFC95943.1| pseudouridylate synthase [Clostridium hathewayi DSM 13479]
          Length = 320

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 81/324 (25%), Positives = 153/324 (47%), Gaps = 33/324 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++V  +E   RLD+    +        L K++R   + ++ K+   + ++ +G  VR
Sbjct: 1   MRSLIVTENESGQRLDKLLAKYLNLAGKGFLYKMMRKKNITLNGKKCDGSEKLVTGDEVR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---- 122
           +            ++ I   SV+  +    +   ++YED  I + NKP+G+  Q      
Sbjct: 61  L---------FFSDETIGKFSVHTLQEVKKVNLQIIYEDDHILLVNKPSGMLSQKAKDSD 111

Query: 123 -SGIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            S + Y ID  + S   S  Q    +P + +RLD+ TSG++V  ++    Q ++  F+ R
Sbjct: 112 ESLVEYIIDYLVSSGQLSTEQLKSFRPSVCNRLDRNTSGLVVAGKSLPGLQIMSAVFKDR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  +V G   +K+  +    LKK  +  + V +     +G+   ++ ++ +   A
Sbjct: 172 SLHKYYRCVVKGSVTDKQ--VITGFLKKDSVT-NQVTITAAEVEGSVPVMTEYEPLGQ-A 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHA-- 292
           +    L ++  TGRTHQ+R H   +G PI+GD KY     N +      I++++ LH+  
Sbjct: 228 EGCTLLSVKLITGRTHQIRAHLASIGHPILGDFKYGSSAVNEEAKKRWNIRSQM-LHSCT 286

Query: 293 -RYMDLPHPEG---GRLQITAPLP 312
             + +LP P     G+   +APLP
Sbjct: 287 VTFPELPEPLAYLSGK-TFSAPLP 309


>gi|258544489|ref|ZP_05704723.1| tRNA pseudouridine synthase C [Cardiobacterium hominis ATCC 15826]
 gi|258520224|gb|EEV89083.1| tRNA pseudouridine synthase C [Cardiobacterium hominis ATCC 15826]
          Length = 244

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 108/248 (43%), Gaps = 38/248 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D+ +   NKPAG+ V       Y  +  L+   +  G K    HRLD+ TSG+L++
Sbjct: 6   ILYRDAHLIAVNKPAGLLVHRSPLERYADETVLQILQEQTGLKGYPAHRLDRPTSGVLLL 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV---- 216
           A     A+ L E    +R++K Y ++V G           WL +   I     ++     
Sbjct: 66  ALDPTTARLLGELIAQQRLEKTYHAIVRG-----------WLAETGEIDYPLAYLPDKMA 114

Query: 217 ---KQNEKGANYAISHFKVIDCFAQ--------------KFCWLEMQPHTGRTHQLRVHA 259
              +Q EK    A++ ++   C A+              ++   E++P  GR HQLR H 
Sbjct: 115 DRNRQREKPPQEALTRYR---CLARSELPFASDGKHPTSRYSLAELRPLQGRKHQLRRHL 171

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
            H+  PI+GD  +  N +           +L LHA  + LPHP  G  L + AP  AH  
Sbjct: 172 KHIFHPIIGDTTHGDNRQNRVLGERYGALRLMLHASRLQLPHPHTGAPLDLRAPFDAHWA 231

Query: 317 KTWDSLGF 324
           +   +L  
Sbjct: 232 QLAAALTL 239


>gi|255994432|ref|ZP_05427567.1| pseudouridylate synthase [Eubacterium saphenum ATCC 49989]
 gi|255993145|gb|EEU03234.1| pseudouridylate synthase [Eubacterium saphenum ATCC 49989]
          Length = 331

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 112/236 (47%), Gaps = 39/236 (16%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQG----------GSGIAYHIDGFLKSWVDSKGQKPR 145
            LK  +LYED  I V +KPAG+                 I  + +G L +   S   +P 
Sbjct: 103 ILKIGILYEDDYIIVVDKPAGLLTHAKGDKSCECTLSDKILEYTEGSLANG--SGANRPG 160

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-------GIPKNKKECI 198
           + HRLD+ T G++V+A+T  A +HLTE+F  + + K Y ++V+       G+   K E  
Sbjct: 161 VVHRLDRGTCGVMVMAKTDTALKHLTEAFEKQEVSKEYEAIVYDNIVRDSGVITAKIERN 220

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               LK S   GD              A + FKVI+ F  KF ++ +   +GRTHQ+RVH
Sbjct: 221 KKNRLKMS--AGDE----------GREAHTEFKVIERFG-KFTYVSLVIKSGRTHQIRVH 267

Query: 259 ALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             ++  P++GD  Y     K N   P+     L ++ +   HP    +++ TA +P
Sbjct: 268 MNYIHHPVLGDMLYGKRKDKFNLMWPM-----LRSKKIGFLHPITSEKMEFTAAMP 318


>gi|118579004|ref|YP_900254.1| RluA family pseudouridine synthase [Pelobacter propionicus DSM
           2379]
 gi|118501714|gb|ABK98196.1| pseudouridine synthase, RluA family [Pelobacter propionicus DSM
           2379]
          Length = 306

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 103/220 (46%), Gaps = 25/220 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD------SKGQKPRLTHRLD 151
           +  LL+ED  +   NKPAG++ Q      Y + G L+ W           +  R+ HRLD
Sbjct: 78  QEALLHEDDDLIALNKPAGVNTQR---TPYQLKGTLEYWASEYFRRQGNPEPARVIHRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG+++  + + AA  L++ F   +++K Y +LV G P   +  +   + K   I   
Sbjct: 135 RGTSGVMLFPKHKRAAAWLSKRFHDGQVEKRYLALVSGTPGQIEWRVDGPIGK---IASA 191

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              +V     G   A++ F+++   +  +  +E +P TGRTHQ+RVH    G PIVGD  
Sbjct: 192 RYGIVA----GGRSALTEFRLL-AESCGYALVEAKPLTGRTHQIRVHLQSCGLPIVGD-- 244

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                 G +      ++ LH   +      G  + + APL
Sbjct: 245 ------GTYGGEPAARMMLHCASLRFADGGGREIVVEAPL 278


>gi|311264327|ref|XP_003130110.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 2 [Sus scrofa]
          Length = 345

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/255 (29%), Positives = 117/255 (45%), Gaps = 44/255 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSG 156
           ++++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G
Sbjct: 98  IVHQDKDLLVINKPYGLPVHGGPGVQLCISDVLPILAKILHGHKAEPLHLCHRLDKETTG 157

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V+A  +  A  + E FR R++ K YW++   +P      +   ++             
Sbjct: 158 VMVLAWEKEVAHQVQELFRTRQVAKKYWAITVRVPVPSAGVVDIPII------------- 204

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY--- 272
              EK    A++ ++V+         LE+QP TG  HQLRVH +  + CPI+GDHKY   
Sbjct: 205 ---EKEVQVAVTQYQVLS-STLSSALLELQPVTGIKHQLRVHLSFGLDCPILGDHKYSDW 260

Query: 273 --------CANFKGNFTSPIQNK-----LYLHARYMDLPHPEGGR--LQITAPLPAHMVK 317
                             P Q+K     L+LHAR + LP  +  +  L +    P + V 
Sbjct: 261 NRLAPQKLSVGVLKKLGLP-QSKARHIPLHLHARQLILPALQSRKEELNLVCKPPRYFVH 319

Query: 318 TWDSLGFK---YDRN 329
           +   LG K   +D+N
Sbjct: 320 SLRRLGLKMPSHDQN 334


>gi|21282809|ref|NP_645897.1| hypothetical protein MW1080 [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49486036|ref|YP_043257.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|300912239|ref|ZP_07129682.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|21204247|dbj|BAB94945.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49244479|emb|CAG42908.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|300886485|gb|EFK81687.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus TCH70]
          Length = 305

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 84/327 (25%), Positives = 149/327 (45%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +     
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYK----- 55

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++   I      + E  IL  ++NL          + YED  + V  K  G+ V    
Sbjct: 56  -VKLNDHIVVTEKEVVEADILPENLNLD---------IYYEDDDVAVVYKTKGMVVHPSP 105

Query: 124 G--IAYHIDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +   K+     G+ +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++ Y +LV G IP +     A   + ++      + VV   ++    A++HF V++ F
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAP--IGRNKNDRQSMAVVDDGKE----AVTHFNVLEHF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  + 
Sbjct: 220 -KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLDIGGQA-----LHAGLIG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G  ++  A LP       D++
Sbjct: 274 FEHPVTGEYIERHAELPQDFEDLLDTI 300


>gi|296127170|ref|YP_003634422.1| pseudouridine synthase [Brachyspira murdochii DSM 12563]
 gi|296018986|gb|ADG72223.1| pseudouridine synthase [Brachyspira murdochii DSM 12563]
          Length = 216

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/206 (31%), Positives = 97/206 (47%), Gaps = 35/206 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGIL 158
           ++YED      NK AGI V          D  +K   +         L HR+D+ TSGI+
Sbjct: 3   IIYEDDYFIAVNKEAGIEVD---------DNLIKKIKEKHNHINNLYLVHRIDKFTSGIV 53

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR     ++  ESF+ + I K+Y ++  G  KN    I         IG D  +  K+
Sbjct: 54  ILARDENTKKYFEESFKNKTISKVYHAISEGYLKNNSGVI------NISIGIDKKNPNKR 107

Query: 219 ----NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                ++G   A++++KV+    +    LE++P TGRTHQ+RVH  ++G PI+GD  Y  
Sbjct: 108 IPLSVKEGGESAVTYYKVLKKLNE-HTLLELKPVTGRTHQIRVHLSYIGHPIIGDKIYSK 166

Query: 275 N-----FKG--------NFTSPIQNK 287
           N      KG        NF  PI  K
Sbjct: 167 NAGIYKMKGFALIAKEINFVHPITKK 192


>gi|162454208|ref|YP_001616575.1| ribosomal large subunit pseudouridine synthase D [Sorangium
           cellulosum 'So ce 56']
 gi|161164790|emb|CAN96095.1| ribosomal large subunit pseudouridine synthase D [Sorangium
           cellulosum 'So ce 56']
          Length = 345

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 77/315 (24%), Positives = 136/315 (43%), Gaps = 50/315 (15%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +Q+ + +G+V VD +  + +  +++  +V + P   + +    E  ++            
Sbjct: 43  VQRWIAAGRVLVDGEPARASVAVRASALVEVRPEEPSPSPTAAEPDVVIP---------- 92

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIA--------YHIDGFLKSWVDSKGQ----KP 144
               ++YED  + V +KPAG+ V    G A          + GF  +  D +      +P
Sbjct: 93  ----VVYEDEHLLVIDKPAGLVVHPARGHASGTLVNGLLALPGFALAPADPRDPMGHVRP 148

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---------- 194
            + HRLD+ TSG+LVVA+     + L + F    I++ Y ++V G  ++           
Sbjct: 149 GIVHRLDRGTSGLLVVAKDEPTREALKDRFARHAIEREYAAIVAGEARDATYDTLHGRHP 208

Query: 195 --KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +    +W+   +   G +V   ++       A++H +VI+        +     TGRT
Sbjct: 209 TDRLRFTSWIRGGAGAPGSHVAAPRR-------AVTHVRVIERLGDAATVVACSLETGRT 261

Query: 253 HQLRVHALHMG-CPIVGDHKYCANFKGNFTSPIQNKL---YLHARYMDLPHPEGGR-LQI 307
           HQ+RVH    G  P++GD  Y    K      I  +L    LHAR +   HP   + ++ 
Sbjct: 262 HQIRVHLAERGRTPVLGDPLYGKPPKKPAVRAIAEELGRQALHARVLGFIHPATQKPVRW 321

Query: 308 TAPLPAHMVKTWDSL 322
            + LPA M K  D L
Sbjct: 322 ESALPADMRKALDQL 336


>gi|319897782|ref|YP_004135979.1| ribosomal large subunit pseudouridine synthase a [Haemophilus
           influenzae F3031]
 gi|317433288|emb|CBY81663.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae F3031]
          Length = 219

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 102/208 (49%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+      S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC----IANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG + K+  E     I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLEKDYGEVNFPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD  Y   
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGDKFYSHP 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                +S    +L LHA  + + HP  G
Sbjct: 185 QAKAMSS----RLCLHAEELTITHPITG 208


>gi|313676263|ref|YP_004054259.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
 gi|312942961|gb|ADR22151.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
          Length = 548

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/208 (32%), Positives = 106/208 (50%), Gaps = 20/208 (9%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LYED +I V  KPAG+ S+         +    K++  + G  P L HRLD+ TSGI+++
Sbjct: 346 LYEDEQIVVIVKPAGLLSIPSKEIKDSVLTRMQKTYPKATG--PLLAHRLDKMTSGIMLI 403

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           ++   + + L + F  + IQK Y +++ G   +K E   N  L    +  D   + K + 
Sbjct: 404 SKDLDSHKFLQKQFMDKTIQKRYCAVLEGT-LDKSEGEVNLPL---AVDEDNRPMQKVDF 459

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFK 277
           +    A++ +++I    +K   +   P TGRTHQLRVHA H   +  PI+GD  Y     
Sbjct: 460 ESGRKALTKWRLISNNDKK-SMVTFIPVTGRTHQLRVHAAHPKGLDAPIIGDTLY----- 513

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           GN       +L LHA Y+   HP+ GR+
Sbjct: 514 GNKAE----RLMLHAEYIQFKHPQNGRI 537


>gi|313201439|ref|YP_004040097.1| RluA family pseudouridine synthase [Methylovorus sp. MP688]
 gi|312440755|gb|ADQ84861.1| pseudouridine synthase, RluA family [Methylovorus sp. MP688]
          Length = 354

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 81/321 (25%), Positives = 141/321 (43%), Gaps = 37/321 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIP 68
           +++  D   +RLD+  +   P  +   LQ+ ++ G V ++  + V    ++  G+ +++ 
Sbjct: 9   LIIPQDLGGLRLDQALQKLLPEHSRSRLQQWIKDGLVTLEPAQAVTAKTKVWGGERLQVQ 68

Query: 69  PVINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   H  + + I LD                 YED  I V NKPAG+ V   +G   
Sbjct: 69  VQPSPDEHAFEAEDIPLDVQ---------------YEDEHILVINKPAGLVVHPAAGNWS 113

Query: 126 AYHIDGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++  L  + V     +  + HRLD++TSG+LVVA+T  A   L    + R +++ Y 
Sbjct: 114 GTLLNALLHHAPVVKDLPRAGIVHRLDKDTSGLLVVAKTLTAQTSLVRQLQARTVKREYR 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++VWG      +   N  + +      +        +    A++ ++V++ FA    +L 
Sbjct: 174 AIVWG------QVWQNGRIDQPIGRHPHARTKMAINRNGKPAVTRYEVLERFA-VHTYLR 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQN--KLYLHARYM 295
               TGRTHQ+RVH  H+  P+VGD  Y             +    + N  +  LHA  +
Sbjct: 227 CNLETGRTHQIRVHMQHLKAPLVGDPVYGLGGIVPLRMMPQHLRDTVLNFGRQALHAVKL 286

Query: 296 DLPHPEGGR-LQITAPLPAHM 315
            L HP  G  ++    LPA M
Sbjct: 287 GLIHPASGEFMEWQVELPADM 307


>gi|289671918|ref|ZP_06492808.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. syringae FF5]
 gi|330975239|gb|EGH75305.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aptata str. DSM 50252]
          Length = 211

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/204 (31%), Positives = 106/204 (51%), Gaps = 12/204 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIHQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++      C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEGGKHALTFWKVVE-RHDAHCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG 303
              P   +L LHA  +   HP  G
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTG 200


>gi|253689512|ref|YP_003018702.1| pseudouridine synthase, RluA family [Pectobacterium carotovorum
           subsp. carotovorum PC1]
 gi|251756090|gb|ACT14166.1| pseudouridine synthase, RluA family [Pectobacterium carotovorum
           subsp. carotovorum PC1]
          Length = 325

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/248 (30%), Positives = 122/248 (49%), Gaps = 39/248 (15%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL--------KSWVDSKGQKPR--L 146
           +K  ++YED  I V NKP  + V  G+G   + DG +           VD     PR  +
Sbjct: 82  IKLDIVYEDQDILVINKPRDLVVHPGAG---NPDGTVLNALLHHYPEIVDV----PRAGI 134

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLL 203
            HRLD++T+G++VVA+T  A   L E+ + R I + Y ++  G         + IA    
Sbjct: 135 VHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSMTAGGMVDQPIARHST 194

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           K++H+    VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+ 
Sbjct: 195 KRTHMA---VHPMGKP------AVTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMAHIN 244

Query: 264 CPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLHARYMDLPHP-EGGRLQITAPLPAH 314
            P+VGD  Y       +G   + I+     ++  LHA  +   HP  G  ++  A LP  
Sbjct: 245 HPLVGDQLYGGRPRPPRGASEAFIETLRGFDRQALHATMLRFYHPITGIHMEWHAELPQD 304

Query: 315 MVKTWDSL 322
           MV   D+L
Sbjct: 305 MVDLIDAL 312


>gi|126727903|ref|ZP_01743731.1| putative Pseudouridine synthase, Rlu [Rhodobacterales bacterium
           HTCC2150]
 gi|126702844|gb|EBA01949.1| putative Pseudouridine synthase, Rlu [Rhodobacterales bacterium
           HTCC2150]
          Length = 308

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 76/267 (28%), Positives = 114/267 (42%), Gaps = 59/267 (22%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +L+ED  + V NKP G+ V    G         + +H  G L      K  +P + HR+D
Sbjct: 50  ILFEDDDLIVVNKPVGMVVHPAPGSPSGTLVNALLHHFGGNLSGIGGEK--RPGIVHRID 107

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGG 210
           ++TSG+LVVA++ AA   L   F    + + Y ++ +G+P N     A+  LK    +  
Sbjct: 108 KDTSGVLVVAKSDAAHHGLAAQFEAHTVNRKYHAICYGVPDN-----ADPRLKGVRGVSF 162

Query: 211 DYVHVVKQNEKGA----------------NYAISHFKVIDCFAQKF------CWLEMQPH 248
           +  +VVK N + A                 +A++  +++  + +        CWLE    
Sbjct: 163 EGSNVVKINTQLARHRTDRQRQSVYFNQGRHAVTRARLVQRYGKPSVACLVECWLE---- 218

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLHARYMD 296
           TGRTHQ+RVH  H G  ++GD  Y    K    SP               +  LHA  + 
Sbjct: 219 TGRTHQIRVHMTHTGHSLIGDQTYGGRRK---LSPKALSAAAIDAVAAFPRQALHAATLG 275

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSL 322
             HP     L   APLP  M    D L
Sbjct: 276 FVHPITKEELSFDAPLPNDMALLIDLL 302


>gi|327474483|gb|EGF19889.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK408]
          Length = 295

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 115/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++   +G   Q+  +  RLD++TSG+
Sbjct: 78  VIYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRQGYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV   G+ + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGSGLLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +   K   YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRLVTKDGKYAHTSYKVIERFGDVY-LVDIHLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLECGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|317502895|ref|ZP_07960993.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           salivae DSM 15606]
 gi|315666001|gb|EFV05570.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           salivae DSM 15606]
          Length = 300

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 110/238 (46%), Gaps = 18/238 (7%)

Query: 87  SVNLTK-HSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           SV+ TK ++D  KS    ++YED  + V  K  GI          ++   L  +     Q
Sbjct: 70  SVSRTKRNNDIFKSRYVKIVYEDRYLVVVEKNIGILSMAAGHSTLNVKTILDDYFKKSRQ 129

Query: 143 K--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           K    + HRLD++TSG+++ A+ +     L + +      + Y ++V G+ +  +  IAN
Sbjct: 130 KCTAHVVHRLDRDTSGLMIYAKDKQTEMLLEQDWHHIVYDRRYVAVVSGVIEAPEGTIAN 189

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           WL         Y+      + G  YA++HF V+      +  +E +  TGR +Q+RVH+ 
Sbjct: 190 WLKDNKA----YITYSSPVDNGGKYAVTHFHVLGQ-NNDYSLVEYKLETGRKNQIRVHSA 244

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            MG P+ GD KY     GN   PI  +L LHA  +   HP     +    P+P    K
Sbjct: 245 DMGHPVCGDIKY-----GNGDDPI-GRLCLHAYVLCFYHPITHAPMTFETPIPTSFRK 296


>gi|149190361|ref|ZP_01868634.1| 23S rRNA pseudouridine synthase D [Vibrio shilonii AK1]
 gi|148835850|gb|EDL52814.1| 23S rRNA pseudouridine synthase D [Vibrio shilonii AK1]
          Length = 324

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 81/332 (24%), Positives = 153/332 (46%), Gaps = 49/332 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G++ V+ + + K   ++  G+++ +  
Sbjct: 10  TVKDSQLGQRLDQAVAELFADFSRSRLKEWLLDGKIAVNGEVITKPRTKVMGGELITVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +        E++     + L          ++YED  I V NKP    V  G+G     
Sbjct: 70  ELE------DEERFEAQDIPLN---------IVYEDDDIIVINKPRDFVVHPGAGTP--- 111

Query: 130 DGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG + + +     +  + PR  + HRLD++T+G++VVA+T  A   L  + + R I + Y
Sbjct: 112 DGTVLNALLHHFPAIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQK 239
            ++  G      +  A  ++ K+ IG    H  K+     N     A++H++V + F ++
Sbjct: 172 EAIAIG------KMTAGGMVDKA-IGR---HSTKRTLMAVNELGKPAVTHYRVAEHF-RE 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLH 291
              + ++  TGRTHQ+RVH  ++  P++GD  Y    +         T  I+  ++  LH
Sbjct: 221 HTRIRLRLETGRTHQIRVHMSYLQHPLLGDSAYGGRARIPRGASEELTHMIRSFDRQALH 280

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           A  +   HP  G  +   AP+P  MV   ++L
Sbjct: 281 AVMLKFAHPVTGEEMTFHAPIPDDMVVMTEAL 312


>gi|46907201|ref|YP_013590.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|254852463|ref|ZP_05241811.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|254931351|ref|ZP_05264710.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|300764179|ref|ZP_07074174.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
 gi|46880468|gb|AAT03767.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Listeria monocytogenes serotype 4b str. F2365]
 gi|258605772|gb|EEW18380.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|293582902|gb|EFF94934.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|300515169|gb|EFK42221.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
 gi|332311376|gb|EGJ24471.1| Pseudouridylate synthase [Listeria monocytogenes str. Scott A]
          Length = 296

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/313 (23%), Positives = 148/313 (47%), Gaps = 40/313 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           VE +E+ + L  + K+ +     +   K    G++ V+ +       +++G  VR+  P 
Sbjct: 7   VETEEDGLLLRTFLKSKHISKQLLTAVKFGAEGKIEVNNEEQNVLYHVKAGDKVRLTFPT 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 ++ E   LD               +++ED  + + NKPAG++        YH +
Sbjct: 67  EQQNERLLAEYTDLD---------------IIFEDDFLLIINKPAGMASIPSQ---YHPN 108

Query: 131 GFLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + ++V    +   LT+      RLD+ETSG++++A+ R A   L+   +   +++ Y 
Sbjct: 109 GSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQ 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWL 243
           +   G+   +K  I      ++ IG   V ++++       YA ++++V+  + + F  +
Sbjct: 169 AFTSGVLVEQKGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY-RAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTE 275

Query: 304 R-LQITAPLPAHM 315
           + +    PLPA M
Sbjct: 276 KYMAFDLPLPADM 288


>gi|332880211|ref|ZP_08447892.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
 gi|332681860|gb|EGJ54776.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
          Length = 544

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 116/236 (49%), Gaps = 23/236 (9%)

Query: 84  LDSSVNLTKHSDFLK--SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSK 140
           LD   N  ++S  LK    L+YED  +   NKPAG+    G G A  +  + ++ + ++ 
Sbjct: 324 LDVEPNAHENSKHLKHEPELVYEDEWMAAVNKPAGMLSVPGKGDALSVWSWARAHFPEAT 383

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P L HRLD +TSG+L++A+     + L + F  R I+K Y +L+ G   + +  I  
Sbjct: 384 G--PLLVHRLDMDTSGVLLIAKDPETHRQLQQLFETRHIKKRYIALLDGTVTDDEGFIRL 441

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L    +   D    +     G   A++ F+V+   +     +   P TGRTHQLRVHA 
Sbjct: 442 PLCPNPN---DRPRQMVSTAYG-KAAVTRFEVL-SRSHGQTRVAFYPFTGRTHQLRVHAA 496

Query: 261 H---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           H   +  PIVGD+ Y             ++L+LHA  +   H + GR + ITAP P
Sbjct: 497 HPEGLDTPIVGDNLYGRR---------ASRLFLHAETVTFRHFKTGRWVSITAPAP 543


>gi|167625019|ref|YP_001675313.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167355041|gb|ABZ77654.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 572

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/218 (31%), Positives = 103/218 (47%), Gaps = 41/218 (18%)

Query: 98  KSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           KSI +LY+D  + V NKPA      G  +   +   +KS    +   P + HRLD  TSG
Sbjct: 363 KSIEVLYQDEAMAVINKPAEFLSVPGKNVTDSVYARMKSMF-PQATGPLIVHRLDMSTSG 421

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA-----------NWLLKK 205
           ++V+A TR A + L + F  R ++K Y + V G+ + ++  I+             L+  
Sbjct: 422 LMVIALTRDANKSLAQQFIARTVEKRYVAQVAGVVQGEQGEISLPLRVDLDDRPRQLVCY 481

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---M 262
            H  G + H + Q              +   ++K   L + PHTGRTHQLRVH  H   +
Sbjct: 482 KH--GKHAHTLWQ--------------VKSRSEKHTMLYLYPHTGRTHQLRVHCAHHDGL 525

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             PI+GD  Y +           N+L+LHA+ + L HP
Sbjct: 526 HLPIIGDDLYGSK---------ANRLHLHAQKLVLNHP 554


>gi|146281802|ref|YP_001171955.1| pseudouridine synthase RluA [Pseudomonas stutzeri A1501]
 gi|145570007|gb|ABP79113.1| pseudouridine synthase RluA [Pseudomonas stutzeri A1501]
          Length = 244

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/214 (30%), Positives = 109/214 (50%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSG++V
Sbjct: 41  IVHQDAALLVIDKPTLLLSVPGRA--EDNRDCLVTRLQENGYPEARIVHRLDWETSGLIV 98

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 99  LARDADSHRELSRQFHDRETEKAYTALCWGQPDADSGSID--LPLRYDPPTKPRHVV--D 154

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ ++V++        +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 155 PELGKHALTFWRVLE-RCGDHSRVELTPITGRSHQLRVHMLSIGHPLLGDRLYAHEQALR 213

Query: 280 FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
                  +L LHA  + L HP+ G RL+  +P P
Sbjct: 214 ----AHERLCLHASMLTLTHPQTGARLRFESPAP 243


>gi|315126099|ref|YP_004068102.1| 23S rRNA pseudouridine synthase D [Pseudoalteromonas sp. SM9913]
 gi|315014613|gb|ADT67951.1| 23S rRNA pseudouridine synthase D [Pseudoalteromonas sp. SM9913]
          Length = 325

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 91/333 (27%), Positives = 151/333 (45%), Gaps = 52/333 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN---RIQSGQVVRIP 68
           V  D    RLD+     +P  +   ++  +   ++ VD +   FN    ++  G+VV + 
Sbjct: 11  VPTDLGGKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGE--IFNTPREKLLGGEVVAVE 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I A     +E +  D  +N+           +YED  I V NKP G+ V  G+G   +
Sbjct: 69  TTIEA----PREYEAQDIKLNI-----------VYEDDDILVINKPMGLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQK 181
            DG     L  +       PR  + HRLD++T+G++VVA+T  A  HL ++ + R    +
Sbjct: 111 PDGTVLNALLHYYPEIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTHLVKALQKRENFTR 170

Query: 182 IYWSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            Y +L  G        ++ I     +++H+    VH     E G   AI+H++V + F +
Sbjct: 171 EYEALCNGTMTAGGMVEKPIGRHATQRTHMA---VH-----EMG-KPAITHYRVAEKF-R 220

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYL 290
               L ++  TGRTHQ+RVH  ++  P++GD  Y       KG      +      +  L
Sbjct: 221 AHTRLRLRLETGRTHQIRVHMAYLNHPLIGDQSYGGRPRPPKGATPELFELLRSFKRQAL 280

Query: 291 HARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
           HA  + + HP  G +    AP+P  MV+   +L
Sbjct: 281 HAVKLSIAHPITGEMMTWQAPIPDDMVQMTQAL 313


>gi|322378277|ref|ZP_08052759.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M334]
 gi|321280779|gb|EFX57797.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M334]
          Length = 291

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 64/201 (31%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   NKKE     L+ K  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWALVDG-NTNKKE-----LVFKDKIGRDRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F  K   +  +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 195 TKNGQYAETHVSRLKQFPNKTSLVRCKLKTGRTHQIRVHLSHHNFPILGDPLYNSKSKT- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|88858181|ref|ZP_01132823.1| Pseudouridylate synthase, 23S RNA-specific [Pseudoalteromonas
           tunicata D2]
 gi|88819798|gb|EAR29611.1| Pseudouridylate synthase, 23S RNA-specific [Pseudoalteromonas
           tunicata D2]
          Length = 217

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/214 (32%), Positives = 108/214 (50%), Gaps = 15/214 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  I V +K +G+    G   A+  D  L     +  +   L HRLD  TSGI+V 
Sbjct: 16  IVHVDKDIIVIDKQSGLLSNPGRA-AHTFDCALTRLQQAYPET-LLVHRLDCATSGIMVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           AR++ A  HL   F+ R+ +K+Y + V G + +     +A  +  K +     V  + ++
Sbjct: 74  ARSKKAESHLKTQFQDRQNKKVYIAEVAGHLAEPNGTILALLMADKENPPYQKVSPLGKS 133

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 AISH+KV++        +E+   TGRTHQLRVH LH+G PI+GD  Y      N
Sbjct: 134 ------AISHYKVLEQRPDS-SLVELTLETGRTHQLRVHMLHLGHPILGDDFYGDEAIVN 186

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                + +L LHA  + + HP  G+ L  T+P P
Sbjct: 187 ----ARPRLCLHATELSIIHPYSGKTLSFTSPHP 216


>gi|114564164|ref|YP_751678.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114335457|gb|ABI72839.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 219

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/214 (29%), Positives = 104/214 (48%), Gaps = 12/214 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + + NKP G+    G     + D      V        L HRLD  TSGI++V
Sbjct: 15  VLYQDEHLLLINKPTGLLSLSGKN-PLNKDSVHHRLVQDYPSA-TLVHRLDFGTSGIMLV 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +     LT+ F++R + K Y ++++G    +   I   + K S    D   ++K  +
Sbjct: 73  ALNKVINGLLTKQFQLRTVSKTYTAVLYGDLVEQHGDIELPIAKDS----DNFPLMKICQ 128

Query: 221 KGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +    A S ++VI+   Q+    +   P TGRTHQLR+H+L +G PI+G    C  ++  
Sbjct: 129 QTGKPAHSQYQVIERHQQRLSTRVTFTPITGRTHQLRIHSLQIGHPILG----CDLYRNE 184

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           ++  + ++L LHA  +   HP    R+    P P
Sbjct: 185 YSQAMSDRLMLHATSLSFTHPVTEQRIDYVCPSP 218


>gi|300933336|ref|ZP_07148592.1| pseudouridylate synthase [Corynebacterium resistens DSM 45100]
          Length = 339

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 106/233 (45%), Gaps = 23/233 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LY D  + V +KP G++       +G +  A       +       ++  +  RLD  T
Sbjct: 113 ILYSDEDVIVVDKPVGVAAHPTLGWEGPTVTAGLAAAGFRISTSGPPERKGIVQRLDVGT 172

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG +VVA +  A   L  +FR R + K Y +LV G P      I   + +  H    +  
Sbjct: 173 SGAMVVAASERAYSLLKRAFRDREVDKTYHALVQGHPDPTSGTIDAPIAR--HPSAGWRF 230

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V+ + K   +A++H+  ++   Q    L+++  TGRTHQ+RVH   +  P+VGD  Y +
Sbjct: 231 AVRDDGK---HAVTHYDTLEAHRQA-SLLKVKLETGRTHQIRVHFSSLHHPLVGDPMYGS 286

Query: 275 NFKGNFTSPIQNKL-----YLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           +        +  KL     +LHA  +  PHP G  + I +P P  +    D L
Sbjct: 287 DPH------LAEKLGLIRQWLHAVELGFPHPSGKWMTIESPYPKDLAVALDRL 333


>gi|167752914|ref|ZP_02425041.1| hypothetical protein ALIPUT_01176 [Alistipes putredinis DSM 17216]
 gi|167659983|gb|EDS04113.1| hypothetical protein ALIPUT_01176 [Alistipes putredinis DSM 17216]
          Length = 537

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/219 (33%), Positives = 106/219 (48%), Gaps = 29/219 (13%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           LLYED  I    KPAG +SV G S     +D   + +  + G  P + HRLD +TSG+L+
Sbjct: 336 LLYEDRWIAAVFKPAGMLSVPGKSEAPSILDWARERYPAATG--PLVVHRLDMDTSGVLL 393

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKEC-IANWLLKKSHIGGDYVHV 215
           +A T+ A Q L   F+ R ++K Y +L+ G    PK + E  +   L  +     D +H 
Sbjct: 394 LALTKEAHQDLQAQFKHRTVRKRYIALLEGRITPPKGRIELPLRPDLHDRPRQAVDPLH- 452

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKY 272
                     AI+ ++V++ F      +   P TGRTHQLRVHA H   +  PI GD  Y
Sbjct: 453 -------GKPAITEYEVLE-FRNGRTRIAFYPLTGRTHQLRVHAAHPSGLNAPIAGDRLY 504

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
               +         +L LHA  ++  HP  G R+ I  P
Sbjct: 505 GTAGR---------RLLLHAERIEFRHPATGDRIAIEKP 534


>gi|240047580|ref|YP_002960968.1| Pseudouridine synthase [Mycoplasma conjunctivae HRC/581]
 gi|239985152|emb|CAT05162.1| Pseudouridine synthase [Mycoplasma conjunctivae]
          Length = 306

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 83/287 (28%), Positives = 137/287 (47%), Gaps = 42/287 (14%)

Query: 40  ILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           ++ +  V+VD K V K N  ++ GQ + I      LN+  + Q  +++     +  DF  
Sbjct: 36  LIEANSVKVDNKVVNKVNFLLREGQFISI------LNNYQEPQLKVEA-----QKVDFE- 83

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWV----DSKGQ-KPRLTHRLD 151
             ++Y+D+ I V NKP  + V  G+G      ++G L  +     D  G+ +P + HRLD
Sbjct: 84  --IVYQDNDIIVINKPKNLVVHPGNGNWDKTLVNGLLHEFATNLSDVNGEIRPGIVHRLD 141

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGG 210
           ++TSG+L+VA+   A ++L +      I++ Y ++V G IP  K             IG 
Sbjct: 142 KDTSGLLLVAKNNQAHKYLAKQLENHEIERKYIAIVVGKIPHTKMRI-------NLPIGR 194

Query: 211 DYVHVVKQNEKGANY--AISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCP 265
           D  +  K+     N   AI++ ++I+ F  K   F  ++    TGRTHQ+RVH  H+G P
Sbjct: 195 DNQNRTKKVVSSFNSKNAITNVELINTFVYKNEHFSIVKCILETGRTHQIRVHLSHIGYP 254

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           I GD  Y     G     +  +  LHA  +   H +G  +     +P
Sbjct: 255 IYGDPVY-----GKKIDDLGQR--LHAYEITFKHLDGRLMNFKTEMP 294


>gi|145628404|ref|ZP_01784205.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae 22.1-21]
 gi|144980179|gb|EDJ89838.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae 22.1-21]
          Length = 219

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/208 (31%), Positives = 100/208 (48%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+      S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG  +N         I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD  Y   
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGDKFY--- 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                   I ++L LHA  + + HP  G
Sbjct: 182 -SHPQAKAISSRLCLHAEELTITHPITG 208


>gi|325473128|gb|EGC76324.1| ribosomal large subunit pseudouridine synthase [Treponema denticola
           F0402]
          Length = 338

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/322 (23%), Positives = 136/322 (42%), Gaps = 51/322 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D +      +++   L+  L+S  + V+ ++ K +  +Q+G ++ +            
Sbjct: 26  RIDVYCTETLKNLSRSQLKTGLKS--LYVNSQKAKLSRNVQNGDLIEL------------ 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------------- 124
              + D+ +    H   L   ++YED  I V NK  G+      G               
Sbjct: 72  ---VWDNPIPEYAHPQKLPLNIIYEDENIIVVNKERGMVTHPAGGNWDGTLVNALNYYRL 128

Query: 125 --------IAYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHL 170
                    A  ++  L   V +  +      +  + HRLD+ETSG+++ AR     + L
Sbjct: 129 YDSRIKDEFAVELNKLLSGEVKNIEKLSLDPYRMGIVHRLDKETSGLIITARNLKTEKLL 188

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              F+ R ++K Y +++ G+P   K  I   + + S     +   V  +      A+S +
Sbjct: 189 KSFFKKRAVKKYYLAVLDGVPPKNKGRIKTSVFRSSSDRKKF--SVSADLSKGKKALSAY 246

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           KV+     K   +  + +TGRTHQ+R+HA  MGCP+ GD  Y     G   + +   L L
Sbjct: 247 KVLKSDG-KMSLVLFRIYTGRTHQIRLHAKFMGCPVAGDKVYGKKKTGLEKTGMP--LML 303

Query: 291 HARYMDLPHPEGGRLQITAPLP 312
           HA  + +P     + +  AP+P
Sbjct: 304 HAYKLIIPDTVNSKKEFKAPIP 325


>gi|269137963|ref|YP_003294663.1| ribosomal large subunit pseudouridine synthase A [Edwardsiella
           tarda EIB202]
 gi|267983623|gb|ACY83452.1| ribosomal large subunit pseudouridine synthase A [Edwardsiella
           tarda EIB202]
 gi|304558011|gb|ADM40675.1| Ribosomal large subunit pseudouridine synthase A [Edwardsiella
           tarda FL6-60]
          Length = 235

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/177 (36%), Positives = 95/177 (53%), Gaps = 14/177 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D+ I V NKP+G+ SV G   +  H D  L + + ++       HRLD  TSG+LV
Sbjct: 32  VLYQDAHIIVVNKPSGLLSVPGR--LPEHQDSIL-TRIQAQFPGAESVHRLDMATSGVLV 88

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+ A + L   FR R  +K Y + VWG P+  +  I   L+       D+ +  KQ 
Sbjct: 89  VALTKDAERELKRQFREREPKKNYVARVWGHPQQDEGVIDLPLI------CDWPNRPKQK 142

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              E+G   A + ++V+   A     + + P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 143 VCFEQG-KPAQTEYQVLARDADGTARVLLTPITGRSHQLRVHLLALGHPILGDGFYA 198


>gi|271502078|ref|YP_003335104.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270345633|gb|ACZ78398.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 217

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/204 (33%), Positives = 107/204 (52%), Gaps = 18/204 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  + + + +        HRLD  TSG++V
Sbjct: 14  ILYQDQHIMVVNKPSGLLSVPGRA--EEHKDSIM-TRIQTDFPTAESVHRLDMATSGVMV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG     +  +   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPKKSYVARVWGHLAQDEGLVDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E+G   A + + V+   +     +++ P TGR+HQLRVH L +G PI+GD  Y A+ 
Sbjct: 125 VCFEQG-KPAQTDYIVLSRDSDGTTRVKLMPITGRSHQLRVHMLALGHPILGDGFY-AHP 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
           +    +P   +L LHA+ + + HP
Sbjct: 183 EAKALAP---RLLLHAQELAITHP 203


>gi|312793770|ref|YP_004026693.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312180910|gb|ADQ41080.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 311

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 67/265 (25%), Positives = 125/265 (47%), Gaps = 28/265 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V+ +   +++++  K  YP I    + K+LR G++ V           Q GQV+R    
Sbjct: 6   IVDKELAGVKVEKAIKKKYPSIPMSVIFKMLRKGEIIVSFLPA------QKGQVLRFG-- 57

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            + ++  I+++ +    V + K         +YED  I V +KP GI     S   Y + 
Sbjct: 58  -DTVSFEIEDRFLEHKKVEILK---------VYEDDNIVVIDKPYGIPSHPDSNNEYSV- 106

Query: 131 GFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               SW++   SK + P+L HRLD+ T+G++++A+ R     + +    R I+K Y  + 
Sbjct: 107 ---VSWIEDNYSKDELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRAIKKRYLCIT 163

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                 K   + ++L K       Y+    Q+  G +  ++ +K++         ++++ 
Sbjct: 164 KKAELPKSGVLVHYLKKDPKKSKVYISDFPQD--GYSEVVTAYKIVRQ-KDDLQLVDVEI 220

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
            TG+THQ+R    H+G  I+GD KY
Sbjct: 221 KTGKTHQIRAQLAHVGLCILGDSKY 245


>gi|283850426|ref|ZP_06367715.1| pseudouridine synthase, RluA family [Desulfovibrio sp. FW1012B]
 gi|283574452|gb|EFC22423.1| pseudouridine synthase, RluA family [Desulfovibrio sp. FW1012B]
          Length = 558

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/218 (31%), Positives = 103/218 (47%), Gaps = 28/218 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LY D ++ V +KP G++V    G+          +H  G      +  G++P + HRLD
Sbjct: 93  VLYADKELAVLDKPPGLTVHPAPGLPEGTLVNRLLHHFPGLR----EMAGERPGIVHRLD 148

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+VA T      L   F  R++ K Y +LV G P  K   I      +  IG D
Sbjct: 149 KDTSGLLMVALTEPVRLALAADFAARQVHKTYLALVHGRPDGKGGDI------RLPIGRD 202

Query: 212 YVHVVKQN--EKGANYAISHFK-VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +  K     KG   A S ++ V          LE+   TGRTHQ+RVH   +G PI+G
Sbjct: 203 PKYRTKMAVPHKGGRPAHSRWRPVWTAPDGTASLLEVTIFTGRTHQIRVHMAAIGHPIIG 262

Query: 269 D-----HKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
           D     H++ A   +G   + + ++  LHA  +   HP
Sbjct: 263 DAVYGPHQHAAWKRRGGAIARLASRQMLHAWKLSFTHP 300


>gi|282878833|ref|ZP_06287600.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
 gi|281299041|gb|EFA91443.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
          Length = 516

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/220 (30%), Positives = 99/220 (45%), Gaps = 27/220 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + V NKPAG+    G      +   L+  +  +       HRLD  TSG+L+V
Sbjct: 309 MVYEDDDLVVVNKPAGLLSVPGRSSRPSVLTILQEMM-PQDMPLHAVHRLDMATSGLLIV 367

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI----ANWLLKKSHIGGDYVHVV 216
           A+      HL   F+   IQK Y +++ G        I       LL +     D VH  
Sbjct: 368 AKNMKVYHHLQAQFKAHTIQKEYIAVLDGKVTQTDGSINLPLRPDLLDRPRQMVDRVH-- 425

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
                    AI+ ++V+     K   L + P TGRTHQLR+H  H   + CPI+GD  Y 
Sbjct: 426 ------GKSAITFYRVLSVHQGK-TMLALSPMTGRTHQLRMHCAHQEGLNCPILGDELYG 478

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                       ++LYLHA  +   HP  G+ + + AP+P
Sbjct: 479 HQ---------ADRLYLHAASITFIHPTSGKHMTLKAPIP 509


>gi|253990666|ref|YP_003042022.1| 23S rRNA pseudouridine synthase D [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782116|emb|CAQ85280.1| ribosomal large subunit pseudouridine synthase D [Photorhabdus
           asymbiotica]
          Length = 325

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 86/322 (26%), Positives = 154/322 (47%), Gaps = 47/322 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + I  +I       
Sbjct: 19  RLDQALAEMFPDYSRSRIKEWILGDRVQVNGKLINKPKEKVLGGEEISIDAIIE------ 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV- 137
           ++ +    ++ L          ++YED  I V NKP  + V  G+G   + DG + + + 
Sbjct: 73  EDARWEPQNIELN---------IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALL 120

Query: 138 ---DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                    PR  + HRLD++T+G++V+A+T  A   L ES ++R I + Y ++  G   
Sbjct: 121 YRYPEIADVPRAGIVHRLDKDTTGLMVIAKTVPAQTRLVESLQLREITREYEAVATGRMT 180

Query: 193 NK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +E I+    K++H+    VH + +       AI+ ++V++ F +    L ++  T
Sbjct: 181 AGGIVEEPISRHPTKRTHMA---VHPMGKP------AITRYRVMEHF-RAHTRLRLRLET 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN---FKG---NFTSPIQN--KLYLHARYMDLPHP- 300
           GRTHQ+RVH  H+   +VGD  Y       KG    F   ++N  +  LHA  + L HP 
Sbjct: 231 GRTHQIRVHMAHISHSLVGDPLYGGRPRPLKGASDEFREVMRNFDRQALHATMLRLYHPI 290

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
            G  ++  A LP  MV   ++L
Sbjct: 291 TGIEMEWHAELPEDMVILINAL 312


>gi|315185268|gb|EFU19047.1| pseudouridine synthase [Spirochaeta thermophila DSM 6578]
          Length = 300

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/275 (27%), Positives = 118/275 (42%), Gaps = 32/275 (11%)

Query: 9   YVVVEN--DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           Y V E+  D+   RLDR  +    H+    + + LR+G++ ++ KRV  + R+  G  + 
Sbjct: 4   YQVFESGPDDHGKRLDRIVRTLLSHLPLSRVFRALRTGEILLEGKRVPPSTRVSRGARIH 63

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I    + L     +QK   SS+ +           L E   + + NKP G  V G   + 
Sbjct: 64  I--DRSLLPERKPQQKGKASSLPI-----------LLETDHLLILNKPPGAVVHGPGSLT 110

Query: 127 YHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             +  +LK  +  S    P   HRLD+ TSGILV +R+   A+  T++ R  RI+K Y +
Sbjct: 111 DQVRSYLKDRIPPSLAFTPSPLHRLDRLTSGILVFSRSIHGARWFTQALREGRIEKTYLA 170

Query: 186 LVWGIPKNKKECIANW---LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           L+ G         A W   L ++        H      + A   +             C 
Sbjct: 171 LLEGTLAEP----ARWEDLLTREGRRSRPSPH-----GRPALTDVRPLLAAPTATLVLCT 221

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +    HTGR HQ+RV A   G P++GD  Y +  +
Sbjct: 222 I----HTGRMHQIRVQAALRGHPLLGDTAYGSTRR 252


>gi|296140324|ref|YP_003647567.1| pseudouridine synthase [Tsukamurella paurometabola DSM 20162]
 gi|296028458|gb|ADG79228.1| pseudouridine synthase, RluA family [Tsukamurella paurometabola DSM
           20162]
          Length = 308

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 78/299 (26%), Positives = 132/299 (44%), Gaps = 39/299 (13%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           + ++   G V +D   V  ++++++G ++ +      L    +  +I+   V        
Sbjct: 33  VSELAAEGSVTLDGAPVGKSDKLRAGALLDV-----TLPEPARPLEIVAEPVPGMN---- 83

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRL 150
               +LY D  I V +KP G++     G     + G L +    + + G   R  + HRL
Sbjct: 84  ----ILYSDDDIVVVDKPVGVAAHASVGWTGPTVIGGLAAAGFRISTSGAPERQGIVHRL 139

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG++ VA +  A   L  +F+ R + K Y +LV G P      I   + +  H   
Sbjct: 140 DVGTSGVMAVAVSERAYTVLKRAFKQRTVDKRYHALVQGHPDPMSGTIDAPIGR--HRSS 197

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D+   V ++ K    +I+H+  I+ F Q    L++   TGRTHQ+RVH   +  P  GD 
Sbjct: 198 DWKFAVTKDGK---PSITHYDTIEAF-QAATLLDVHLETGRTHQIRVHFAALHHPCCGDQ 253

Query: 271 KYCANFKGNFTSPIQNK------LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            Y ++       P+  K       +LHAR +   HP  G  ++ T+P P  +    D L
Sbjct: 254 TYGSD-------PVLAKKLGLERQWLHARTLGFTHPTKGEYVEFTSPYPDDLQHALDVL 305


>gi|160879192|ref|YP_001558160.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
 gi|160427858|gb|ABX41421.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
          Length = 237

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 53/177 (29%), Positives = 86/177 (48%), Gaps = 7/177 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +L+ED  I V  KP G+  Q G G    +   L+ +  +  +     L HRLD+   G++
Sbjct: 4   ILFEDKHIIVCIKPIGVLSQPGQGEGMDMITLLQEYRKNNKESDYIGLVHRLDRNVGGVM 63

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+T  A + L+ + R R   K Y +++ G P      + + + K S     +  VV +
Sbjct: 64  VFAKTELATKKLSVAIRERNFTKEYMAVIHGRPSESSGILKDLMFKDSSKNKSF--VVNR 121

Query: 219 NEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             KG   A   ++ I+       +F ++ ++ HTGRTHQ+RV       P+VGD KY
Sbjct: 122 MRKGVKEASLEYRTIETIEVAKGEFSFIRVKLHTGRTHQIRVQFASRKLPLVGDGKY 178


>gi|227540505|ref|ZP_03970554.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
 gi|227239587|gb|EEI89602.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
          Length = 348

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 76/333 (22%), Positives = 152/333 (45%), Gaps = 58/333 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
           + V+  +  +R+D++  N   + +   +Q  + +G V V+   +K + +++   ++ +  
Sbjct: 22  IEVDKGQALLRIDKFLMNRVENASRNKIQNAIDAGSVLVNDSVIKSSYKVKPFDIISVVL 81

Query: 68  --PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--- 122
             PP         ++ ++    + L          +++ED ++ V NK AG+ V  G   
Sbjct: 82  PDPP---------RDTEVYPEDIPLD---------IMFEDDEVMVVNKVAGMVVHPGFNN 123

Query: 123 ------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                 + + +H +  L +   + G +P L HR+D++TSG+LV+A++  A  +L + F  
Sbjct: 124 YTGTLVNALTHHFNQ-LPTMPGNAG-RPGLVHRIDKDTSGLLVIAKSEWAMTYLAKQFFD 181

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY----VHVVKQNEKGANYAISHFKV 232
             I + Y ++VWG        IA       +IG +     V  +  + +   ++++H++V
Sbjct: 182 HSIVRKYVAMVWG-------DIAEDGTITGYIGRNLKDRRVMTMYDDPEKGKWSVTHYRV 234

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGN----FTSPIQN 286
           ++        +E Q  TGRTHQ+R H   +G P+  D  Y  +   KG     +   ++N
Sbjct: 235 LERLGY-VTLIECQLETGRTHQIRAHMQSIGHPLFNDAAYGGDRILKGTVFNKYRQFVEN 293

Query: 287 ------KLYLHARYMDLPHPEGGR-LQITAPLP 312
                 +  LHA+ +   HP+    L    PLP
Sbjct: 294 CFALLPRQALHAQVLGFEHPKSKEFLTFETPLP 326


>gi|302380688|ref|ZP_07269153.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
 gi|302311631|gb|EFK93647.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
          Length = 321

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 71/277 (25%), Positives = 135/277 (48%), Gaps = 29/277 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ +++   N R+DR+     P ++  ++QK++R+ +++V+KKR + +  ++   VV 
Sbjct: 1   MRHINIDDSNSNQRVDRFLMKLMPKMSKNHIQKLIRTKKIKVNKKRTEPDYDLKIDDVVN 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I          + ++ I     N    +D     ++YED  + + NK  G+     +   
Sbjct: 61  I---------YLYDEVIEKYQDNKIYTADDFNLDIIYEDDDLILINKKTGVLSHAANPQD 111

Query: 127 Y--HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           Y  +I   + S++    Q          P L +RLD+ TSGI+V A+T  + ++  + F+
Sbjct: 112 YGKNIVDMMVSYLIKTNQFKPTQNSTFTPALVNRLDRNTSGIVVGAKTYDSLKYFNDLFK 171

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I KIY ++V G   N K+   +  L+K +       V+  + K +   + + K    
Sbjct: 172 KHEITKIYETIVVG---NLKDQTIDLALEKDNDKNK--SVINSSGKKSMTKVWNVK---N 223

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           F  K+  + +   TGRTHQ+R H  H+  PI+GD KY
Sbjct: 224 FG-KYSLVNVDLLTGRTHQIRAHLSHINHPIIGDIKY 259


>gi|260574483|ref|ZP_05842487.1| pseudouridine synthase [Rhodobacter sp. SW2]
 gi|259023379|gb|EEW26671.1| pseudouridine synthase [Rhodobacter sp. SW2]
          Length = 215

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 66/219 (30%), Positives = 106/219 (48%), Gaps = 25/219 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D ++ V +KPAG+    G G A   D  + + + +   +  L HRLD +TSG++V 
Sbjct: 14  ILYHDDQVLVVSKPAGLLSVPGKG-ADKADCLI-TRLQAVFPEVLLVHRLDTDTSGVMVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKK---ECIANWLLK-KSHIGGDYVH 214
           A  +AA   L + F  R+ +K+Y + + G+  P+  +     I +W  + + H+  D   
Sbjct: 72  AMNKAAQGALGQQFEKRQTKKVYIARLDGLLEPREGRVDLPLIVDWPNRPRQHVNHDTGR 131

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             + + +   Y  +  +V            + P TGR+HQLRVH   +G PI+GD  Y +
Sbjct: 132 PAQTDWRVVKYGKAETRV-----------RLMPLTGRSHQLRVHMAALGHPILGDALYAS 180

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                       +L LHA  +   HPE G+ L  TAP P
Sbjct: 181 GAACE-----HPRLMLHAESLRFRHPETGKSLTFTAPCP 214


>gi|257093948|ref|YP_003167589.1| pseudouridine synthase [Candidatus Accumulibacter phosphatis clade
           IIA str. UW-1]
 gi|257046472|gb|ACV35660.1| pseudouridine synthase [Candidatus Accumulibacter phosphatis clade
           IIA str. UW-1]
          Length = 230

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 68/217 (31%), Positives = 103/217 (47%), Gaps = 16/217 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y D+ + + NKPAG+    G G        L   V ++     + HRLD  TSG+LV+
Sbjct: 24  VVYSDAALLLVNKPAGLLSVPGRG--EDKQDCLARRVQAEYPDALIVHRLDMATSGLLVL 81

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           AR +A  + L+  F  R++ K Y ++V G+P      I         +  D+ +  +Q  
Sbjct: 82  ARGKAMQRRLSTQFANRQVDKRYVAVVNGLPPLASGEI------DLPLAADWPNRPRQKV 135

Query: 219 NEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +      + + ++V+  D FA     L + P TGRTHQLRVH L +G PIVGD  Y    
Sbjct: 136 DRLAGKPSRTRYQVLSHDPFANT-TRLALWPDTGRTHQLRVHLLAIGHPIVGDGLYAEAG 194

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                +    +L LHA  +   HPE  R +    P P
Sbjct: 195 GAACGA--DARLLLHAESLAFAHPETARPMAFCCPAP 229


>gi|254459281|ref|ZP_05072702.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacterales bacterium GD 1]
 gi|207083894|gb|EDZ61185.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacterales bacterium GD 1]
          Length = 325

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 87/338 (25%), Positives = 155/338 (45%), Gaps = 48/338 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           M+ ++  V +N E   RLD +  +         +  +++   V VD+K V +   +++SG
Sbjct: 1   MSDIKSYVCDNPE---RLDIFLASEIGQTR-SQIASLIKHKCVFVDEKLVTRPGVKLKSG 56

Query: 63  QVVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           Q +++  P          KE   LD   N+          +LYED  + V NKP+G++V 
Sbjct: 57  QNIKVEFPEA--------KESPALDIDFNVE---------ILYEDDDVLVINKPSGVTVH 99

Query: 121 GGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
               +    +  L  W+  KG         ++  + HRLD+ TSG +VVA+   A + L+
Sbjct: 100 PAPSVK---EATLVDWLKHKGIRLSNISGEERHGIVHRLDKGTSGTMVVAKNNEAHEFLS 156

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           E  + + + + Y +++    K++   I   + + +H   + + +   +   + YA + FK
Sbjct: 157 EQLQDKSMGRYYLAVLNPPLKDEITTIEQNIGRSAH---NRLKMTCTDAGKSKYAKTMFK 213

Query: 232 VIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           V+     +K  ++  +  TGRTHQ+RVH   +   I+GDH Y  + K   +     ++ L
Sbjct: 214 VLSLSNDEKQQFVACKLFTGRTHQIRVHLESINRHIIGDHIYALSPKAEKS----ERILL 269

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
           HA  +   HP    +L   APL   M    D L  K+D
Sbjct: 270 HAYMIYFVHPTSKEKLTFVAPLDETM---KDYLDKKFD 304


>gi|258545740|ref|ZP_05705974.1| pseudouridine synthase A [Cardiobacterium hominis ATCC 15826]
 gi|258518985|gb|EEV87844.1| pseudouridine synthase A [Cardiobacterium hominis ATCC 15826]
          Length = 205

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 65/197 (32%), Positives = 96/197 (48%), Gaps = 20/197 (10%)

Query: 103 YEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  IYV NKPAG+ SV G     Y     ++S            HRLD  TSG+L++A
Sbjct: 7   YEDPDIYVINKPAGLLSVPGRGDDKY---DSVQSRCQISAPAAMAAHRLDMATSGLLLIA 63

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
           + +AA +H  + F  RR++K Y ++V G   + +  I   L+       D+    +Q   
Sbjct: 64  KHKAAERHYKQEFAARRVEKRYIAVVHGSLADDRGDIEYPLIT------DWERRPRQKIC 117

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E G   A + ++V+         + + PHTGR+HQLRVH   +G PI+GD      F  
Sbjct: 118 YEHGKT-AHTSYEVL-ARDGATTRVALTPHTGRSHQLRVHLAAIGHPILGD-----EFYA 170

Query: 279 NFTSPIQNKLYLHARYM 295
           +   P   +L LHA  +
Sbjct: 171 DENPPAAPRLLLHAETL 187


>gi|332298344|ref|YP_004440266.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332181447|gb|AEE17135.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 238

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 66/197 (33%), Positives = 94/197 (47%), Gaps = 20/197 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E+ +I + NK  G++VQGG+GI + +D  L   V   G K    HRLD++T+G+LV+
Sbjct: 14  VVFENGEIIIVNKKCGLAVQGGAGIRFSLDRLLSEQV---GYKVYPVHRLDKDTAGLLVL 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH---IGGDYVHVVK 217
           A+T AAA   T       ++K Y +L  GIP  KK      +  K        DYV    
Sbjct: 71  AKTAAAAAVWTNLIASGEVRKEYAALCAGIPPGKKGTFTAPIETKGERKSAVTDYVVC-- 128

Query: 218 QNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              + A         +D         L +   TGR HQ+R+H    GCPIV D KY    
Sbjct: 129 ---RTAETVFPDAPGLDGVQTVPVSLLRLTLGTGRMHQIRIHLAQAGCPIVADDKY---- 181

Query: 277 KGNFTSPIQNKLYLHAR 293
            G+F     NKL+   R
Sbjct: 182 -GDFR---LNKLFRSGR 194


>gi|332535270|ref|ZP_08411072.1| ribosomal large subunit pseudouridine synthase D [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332035301|gb|EGI71805.1| ribosomal large subunit pseudouridine synthase D [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 325

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 89/334 (26%), Positives = 148/334 (44%), Gaps = 46/334 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN---RIQSGQVVRIPPVINALNH 76
           RLD+     +P  +   ++  +   ++ VD +   FN    ++  G+VV +   I A   
Sbjct: 19  RLDQVLAQLFPDYSRSRIKTWILDDKITVDGE--IFNTPREKLLGGEVVSVETTIEA--- 73

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKS 135
             +E +  D  +N+           +YED  I V NKP G+ V  G+G     +   L  
Sbjct: 74  -PREYEAQDIKLNI-----------VYEDDDILVINKPMGLVVHPGAGNPNGTVLNALLH 121

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPK 192
           +       PR  + HRLD++T+G++VVA+T  A  HL  + + R    + Y +L  G   
Sbjct: 122 YYPEIINVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVTALQKRENFTREYEALCNGTMT 181

Query: 193 NK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                ++ I     +++H+    VH + +       AI+H++V + F +    L ++  T
Sbjct: 182 AGGMVEKAIGRHPTQRTHMA---VHELGKP------AITHYRVAEKF-RAHTRLRLRLET 231

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLHARYMDLPHPE 301
           GRTHQ+RVH  H+  P++GD  Y       KG      +      +  LHA  + + HP 
Sbjct: 232 GRTHQIRVHMAHLNHPLIGDQSYGGRPRPPKGATPELFELLRSFRRQALHAVKLSIAHPI 291

Query: 302 GGRLQI-TAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            G +    AP+P  MV    +L      N  I R
Sbjct: 292 TGEMMTWQAPIPDDMVAMTHALREDTKANPDIDR 325


>gi|297559888|ref|YP_003678862.1| pseudouridine synthase [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
 gi|296844336|gb|ADH66356.1| pseudouridine synthase, RluA family [Nocardiopsis dassonvillei
           subsp. dassonvillei DSM 43111]
          Length = 308

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 81/327 (24%), Positives = 147/327 (44%), Gaps = 30/327 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V+ + V +  E  RLD      +  ++     +I+  G V VD      ++R+ +G 
Sbjct: 1   MSDVRSLPVPDGLEGDRLDSAIARMF-GLSRTRAAEIIGDGGVLVDGSEAAKSDRVSAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ--- 120
            + +      L            +V   +        +++ED+ I V +KP G+      
Sbjct: 60  WLEV-----TLPPPPTAPVPRPEAVPGMR--------IVHEDTDIIVVDKPVGVVAHPTV 106

Query: 121 GGSGIAYHIDGFLKSWV----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G +G +  ++G L S V        ++  + HRLD  T+G++VVA++  A   L  +F+ 
Sbjct: 107 GWTGPSV-LEGLLASGVQVATSGAAERQGIVHRLDANTTGLMVVAKSETAYSVLKRAFKE 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K Y +LV G P   +  +   + +  H  GD    V     G   +++H+   + F
Sbjct: 166 RTVDKHYHTLVQGHPDPLRGTVDAPIDR--HPAGDGRWAVV---AGGRPSVTHYDTQEAF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    LE++  TGRTHQ+RVH   +  P VGD  Y A+        ++ + +LHA  + 
Sbjct: 221 -RAASLLEIKLETGRTHQIRVHMSALRHPCVGDMLYGADPTLAERLGVRRQ-WLHAVRLG 278

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP   R ++ ++P P  +    ++L
Sbjct: 279 FDHPTEHRPVEFSSPYPDDLAAAVETL 305


>gi|315641865|ref|ZP_07896857.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           italicus DSM 15952]
 gi|315482433|gb|EFU72973.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           italicus DSM 15952]
          Length = 316

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 68/208 (32%), Positives = 101/208 (48%), Gaps = 29/208 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL---KSWVDSKGQKPRLTHRLDQETSGI 157
           +L+ED  + + NKPAGI            D  L   K+++  K Q+  + HRLD+ETSG+
Sbjct: 109 VLFEDEHLLLVNKPAGIKTHPNQ--PNEDDTLLNDIKAYLAPKQQQAYVVHRLDKETSGV 166

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       L      ++I + Y ++V G  K  K C       +  IG D     K
Sbjct: 167 ILFAKNPLVLPILGRLLEQKKIYRTYQAIVTG--KLTKNCTI-----RKKIGRDRHDRRK 219

Query: 218 Q--NEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +  +E+    A++H +VI   +Q     C LE    TGRTHQ+RVH   +G PI+GD  Y
Sbjct: 220 RVIDERHGQQAVTHVQVIQVHSQTTNITCQLE----TGRTHQIRVHLASIGHPIIGDSLY 275

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
                   T P + +L+LHA  M   HP
Sbjct: 276 Q-------TKPAE-RLFLHAYQMHFIHP 295


>gi|163755956|ref|ZP_02163073.1| hypothetical protein KAOT1_11066 [Kordia algicida OT-1]
 gi|161324127|gb|EDP95459.1| hypothetical protein KAOT1_11066 [Kordia algicida OT-1]
          Length = 300

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 64/206 (31%), Positives = 96/206 (46%), Gaps = 28/206 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLK--SWVDSKGQKPRLTHRLDQETSG 156
           +++ED +I + NKPAG    G     I   +   LK  + +D+    P+  HRLD  TSG
Sbjct: 82  VIFEDDEIAIINKPAGFPTNGNYFKTIENALPHNLKPSNSIDALPF-PKPVHRLDNPTSG 140

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           IL++A+T++A   L + F  + I K Y ++V G  K  KE             G+    V
Sbjct: 141 ILIIAKTKSAQISLYQQFEQQEISKTYQAIVIG--KTDKE-------------GEITSAV 185

Query: 217 KQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            + E   NY     + +          +++ P TGRTHQLR+H   +  PIVGD  Y   
Sbjct: 186 AEKEALTNYET--LQTVSSLQNGHLSLVKLFPKTGRTHQLRIHLASINHPIVGDQLY--- 240

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE 301
             G      +  L+L A  + L HP+
Sbjct: 241 --GKAEENYKKGLFLCATSIQLIHPK 264


>gi|315607191|ref|ZP_07882195.1| ribosomal large subunit pseudouridine synthase A [Prevotella buccae
           ATCC 33574]
 gi|315251245|gb|EFU31230.1| ribosomal large subunit pseudouridine synthase A [Prevotella buccae
           ATCC 33574]
          Length = 575

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 103/228 (45%), Gaps = 33/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED+ I V NKPAG+    G      +   L+     + + P + HRLD  TSG+LV 
Sbjct: 364 ILYEDASIVVVNKPAGMLSVPGKTDTPSVYSLLRECC-PQAEGPIIVHRLDMATSGLLVA 422

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG---------IPKNKKECIANWLLKKSHIGGD 211
           A+T  A   L + F  R + K Y +++            PK     +    +    +  D
Sbjct: 423 AKTSKAYFGLQQQFTDRMVTKRYVAVLEANGPRPSFHPAPKTDSSLLPKGAISLP-LSPD 481

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPI 266
            +   +Q  + +    A++ ++ +         L + PHTGRTHQLRVH  H   +G PI
Sbjct: 482 LMDRPRQKVDREHGRPAVTDYQFVSSDR-----LLLYPHTGRTHQLRVHCAHREGLGRPI 536

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAPL 311
            GD+ Y             ++LYLHA Y+   HP+ G     + +AP 
Sbjct: 537 KGDNLYGTK---------ADRLYLHAEYLSFVHPQTGERVEFECSAPF 575


>gi|149204830|ref|ZP_01881792.1| pseudouridine synthase [Roseovarius sp. TM1035]
 gi|149141700|gb|EDM29755.1| pseudouridine synthase [Roseovarius sp. TM1035]
          Length = 214

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 63/208 (30%), Positives = 101/208 (48%), Gaps = 22/208 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D +I V NKPAG+    G G   H+   L + V        L HRLD++TSG+++ 
Sbjct: 13  VLHDDHEIVVVNKPAGLLSVPGKG--EHLADCLMARVRDVFPTALLVHRLDRDTSGVMIF 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-----IPKNKKECIANWLLKKSHIGGDYVHV 215
           A T  A +HL   F  R+ +K Y + VWG     +       I +W  +          +
Sbjct: 71  ALTPHAQRHLGLQFEKRQTRKTYVARVWGRLEPEVGVVDLPLIVDWPNRP---------L 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K   +    A++ ++V+    ++   + + P TGR+HQLRVH L +G  I+GD  Y + 
Sbjct: 122 QKVCHETGRAALTEWRVLRASDEE-SRVRLSPKTGRSHQLRVHMLALGHVILGDPLYASG 180

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                      +L LH+  + L HP+GG
Sbjct: 181 AARE-----HPRLMLHSEELRLRHPDGG 203


>gi|317154041|ref|YP_004122089.1| RluA family pseudouridine synthase [Desulfovibrio aespoeensis
           Aspo-2]
 gi|316944292|gb|ADU63343.1| pseudouridine synthase, RluA family [Desulfovibrio aespoeensis
           Aspo-2]
          Length = 596

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/272 (25%), Positives = 125/272 (45%), Gaps = 26/272 (9%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILD-SSVNLTKHSDFLKSI-----LLYE 104
            R +    I+SG  +    V+    H +  ++ L      +    D  +++     +++E
Sbjct: 45  SRGRVQEWIESGLALVDGEVVTRGKHKLAGRETLRIGDAGVAPSDDAAQAVPGELEVVFE 104

Query: 105 DSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKG-------QKPRLTHRLDQETS 155
           D+ + V +K AG++     G      ++  L  W D          Q+P + HRLD++TS
Sbjct: 105 DAHVAVIDKRAGLTTHPAPGEPGPTLVNHLLHRWPDVASDISGMDRQRPGIVHRLDKDTS 164

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++VVA T      L   F  RR++K+Y ++V G P      I +  + +       + V
Sbjct: 165 GLMVVALTEGDRLRLAADFAGRRVRKVYLAVVLGRPAQPAGTI-DAPMGRHPSQKTRMAV 223

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V    +G   A+S ++V+    +    L  ++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 224 VA---RGGREAVSDYRVLWTGPRGLASLVAVRIHTGRTHQIRVHMAHIGHPLLGDSAYGP 280

Query: 275 ------NFKGNFTSPIQNKLYLHARYMDLPHP 300
                 + + +  + +  +  LHA ++   HP
Sbjct: 281 RENVEWSRRPDRLAGLAPRQMLHAFHLSFRHP 312


>gi|239826073|ref|YP_002948697.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239806366|gb|ACS23431.1| pseudouridine synthase, RluA family [Geobacillus sp. WCH70]
          Length = 304

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 109/209 (52%), Gaps = 26/209 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQET 154
           +L+ED  + + NK AG+ +       +G   +   F   ++ S+G   K R  HRLD++T
Sbjct: 86  VLWEDEHLLIINKDAGMDIHPSEPSQTGTLANAVAF---YLQSQGILTKVRHIHRLDRDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG ++ A+   A   L      R+I++ Y +LV GI KNK   I+      + IG D  H
Sbjct: 143 SGTILFAKHPLAGATLDRMLAKRQIKRTYVALVHGIMKNKSGTIS------APIGRDRHH 196

Query: 215 VVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             ++  ++ GA  A++H++V+  F  Q+   +E+   TGRTHQ+RVH  ++G P+VGD  
Sbjct: 197 PTRRRVSQTGAK-AVTHYRVLHTFPNQQLSLVELSLDTGRTHQIRVHMSYIGHPLVGDVL 255

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y    +  F     ++  LHA  +   HP
Sbjct: 256 YGG--ENTF-----HRQALHAAKLSFLHP 277


>gi|224370646|ref|YP_002604810.1| TruC [Desulfobacterium autotrophicum HRM2]
 gi|223693363|gb|ACN16646.1| TruC [Desulfobacterium autotrophicum HRM2]
          Length = 260

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 70/221 (31%), Positives = 103/221 (46%), Gaps = 11/221 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL-THRLDQETSGILV 159
           +LY+D  +   NKP G+ V   + +A H   F    V  + Q      HRLD+ T G+L+
Sbjct: 15  ILYQDEDLVAVNKPPGLLVHR-TALATHETRFALQMVRDQTQGHVFPVHRLDRPTQGVLL 73

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQ 218
            AR R  A  ++  F+  +IQK Y ++V G  K +   +     +K         H +K 
Sbjct: 74  FARNRNMATRMSHLFQTGKIQKTYLAVVRGHVKERGTIVHPLKNIKHPQDNKRINHSLKI 133

Query: 219 NEKGANYAISH-----FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           ++   +YA        F V      ++C + + P TGR HQLR H  H+  PIVGD  Y 
Sbjct: 134 DDAVTDYACLASVELPFYVDRYPTTRYCLVALIPKTGRRHQLRRHMKHISHPIVGDTVYG 193

Query: 274 ANFKGNFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPL 311
            +    F +   N   L L AR +   HP+ G  + ITAPL
Sbjct: 194 KSSHNRFFATHLNCTGLLLAARELCFVHPDTGIFITITAPL 234


>gi|223986801|ref|ZP_03636783.1| hypothetical protein HOLDEFILI_04106 [Holdemania filiformis DSM
           12042]
 gi|223961234|gb|EEF65764.1| hypothetical protein HOLDEFILI_04106 [Holdemania filiformis DSM
           12042]
          Length = 225

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 87/181 (48%), Gaps = 8/181 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           +K  +LYED+ + +  KP  ++VQ        +   LK  +  + QKP      L HRLD
Sbjct: 1   MKFKILYEDNHLLIVVKPVNMAVQADDSRDPDLLTLLKQDLKERYQKPGNVYLGLVHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +   G++V A+T  AA  L++  R R ++K Y +++ G P+     + +WL+K      +
Sbjct: 61  RPVGGVMVFAKTSKAASRLSDQVRTRGLKKTYQAVLCGRPQAASATLKDWLIKNEKT--N 118

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V     N   A  AI  ++ I    +     E+Q  TGR HQ+RV       P+ GD +
Sbjct: 119 TVRTAAPNTPKAKEAILSYQ-IQGEKEGLTLAEIQLETGRPHQIRVQFASRRTPLWGDQR 177

Query: 272 Y 272
           Y
Sbjct: 178 Y 178


>gi|319956600|ref|YP_004167863.1| ribosomal large subunit pseudouridine synthase d [Nitratifractor
           salsuginis DSM 16511]
 gi|319419004|gb|ADV46114.1| ribosomal large subunit pseudouridine synthase D [Nitratifractor
           salsuginis DSM 16511]
          Length = 327

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 68/228 (29%), Positives = 113/228 (49%), Gaps = 29/228 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLD 151
           +LYED  + + NKPAG+ V     +    +  L  W+  +G         ++  + HRLD
Sbjct: 83  VLYEDEYLMILNKPAGVVVHPAPSVR---EPTLVHWLVQRGISLSTLAGEERHGIVHRLD 139

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG LV+A+T A  Q L+E  + R + + Y +L+      K++   +  + ++     
Sbjct: 140 KETSGALVIAKTNAVHQALSEELKSREMGRYYLALIDH--PLKEDLTVDAPIARNPANRL 197

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + VV    +G   A + F  +    +    +  + HTGRTHQ+RVH   +G  I+GD  
Sbjct: 198 KMAVV----EGGREARTDFLKLAEGEEGSELIAARLHTGRTHQIRVHLAKIGRHILGDEL 253

Query: 272 YCANFKGNFTSPIQNKL---YLHARYMDLPHPEG-GRLQITAPLPAHM 315
           Y   ++G      Q K+   +LHA  + L HP    RL+++AP+P  M
Sbjct: 254 Y--GYRGA-----QGKIPRVFLHAARLYLTHPATHRRLEVSAPIPEDM 294


>gi|322420987|ref|YP_004200210.1| RluA family pseudouridine synthase [Geobacter sp. M18]
 gi|320127374|gb|ADW14934.1| pseudouridine synthase, RluA family [Geobacter sp. M18]
          Length = 303

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 135/310 (43%), Gaps = 49/310 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D + +N  P   F  L+K++ SG ++++       + ++ GQ++R    +     I +
Sbjct: 14  RVDSFLRNLLPSAQFSYLKKLINSGHLKIN------GSAVEPGQILRFADQVT----IKE 63

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLK 134
             K       LT   D     +L+ED+ I   NKPAG++V          +    +  LK
Sbjct: 64  SSKTAALLARLTPEMD-----ILFEDTWIVCLNKPAGLAVHRTEDPDEITLVDLAEALLK 118

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
              D  G K R  +RLD+ TSG +++A++  AA    +  +   + K+Y ++V G  K +
Sbjct: 119 KR-DGAG-KLRPVNRLDKGTSGAIILAKSAVAAGMFGKMVQEEGLGKLYLAMVEG--KLQ 174

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K+   +  L        Y+ +     +G   A+               L + P TGR HQ
Sbjct: 175 KQGTIDAPLDGKESQTSYLRLF----QGGGVAL---------------LAVYPLTGRMHQ 215

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +R H   +G P++GD +Y       FT        LH+    L HP  G  L I APLP 
Sbjct: 216 IRQHFRMIGHPVLGDKRYGGRGLSGFTGH-----ALHSFRTTLVHPATGEDLDIPAPLPE 270

Query: 314 HMVKTWDSLG 323
            +++     G
Sbjct: 271 QLLRLATRCG 280


>gi|254445726|ref|ZP_05059202.1| pseudouridine synthase, RluA family [Verrucomicrobiae bacterium
           DG1235]
 gi|198260034|gb|EDY84342.1| pseudouridine synthase, RluA family [Verrucomicrobiae bacterium
           DG1235]
          Length = 324

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/221 (30%), Positives = 107/221 (48%), Gaps = 24/221 (10%)

Query: 99  SILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWV-----DSKGQKPRL--THR 149
           + ++Y D  I V NK AG+       S     +D  +  ++     D+K  +  L   HR
Sbjct: 87  AAIVYFDEHIVVVNKAAGLMTVPHPESDETETLDRLVNDYLRIRDPDAKTNRASLGVVHR 146

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D++TSG++V ART  A + L+E FR   I++ Y ++V G  + K + I   L++++  G
Sbjct: 147 IDKDTSGLVVFARTFLAKRALSEQFRAHSIERRYLAIVHG--ELKAQSIRTHLVRETGDG 204

Query: 210 ----GDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHM 262
                       + E+    AI+H  V++  A      C +E    TGRTHQ+R+H   +
Sbjct: 205 LRGSAPKGATNSEGEELGRLAITHVDVVERLAGATLVSCRIE----TGRTHQIRIHLSEI 260

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           G PIVG+  Y   F+G       N+  LHA  +   HP  G
Sbjct: 261 GHPIVGEKVYIRGFEGELIP--ANRAMLHAAELGFIHPGSG 299


>gi|197301688|ref|ZP_03166758.1| hypothetical protein RUMLAC_00414 [Ruminococcus lactaris ATCC
           29176]
 gi|197299128|gb|EDY33658.1| hypothetical protein RUMLAC_00414 [Ruminococcus lactaris ATCC
           29176]
          Length = 340

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 89/327 (27%), Positives = 145/327 (44%), Gaps = 30/327 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++++ +E   R D++   +          K+LR   + ++ K+   N  ++    VR
Sbjct: 10  MKEIIIKKNEAGQRFDKFLAKYMSQAPKSFFYKMLRKKNITLNGKKAAGNEILELNDTVR 69

Query: 67  I---PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +      I   +  I +Q   D    L  H+    SI+ YED      NKPAG+  Q   
Sbjct: 70  LFLSDETIQKFSGTI-QQSPGDPDWILA-HAGKEPSII-YEDESTIFLNKPAGMLSQKAK 126

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                     IAY ++    S  + +   P + +RLD+ TSG++   +T  A Q L+E F
Sbjct: 127 PDDISMVEHLIAYLLNSGQISKEELRTFHPSVCNRLDRNTSGLIAAGKTLQALQQLSEMF 186

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R ++K Y  LV G   +    I+ +L K      + V V +     A+   + + +I 
Sbjct: 187 RDRSLKKYYLCLVRGKVSSDSH-ISGYLKKDPRT--NRVTVSRTPSAAASPIETEYHIIK 243

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---YLH 291
              +    LE+   TG+THQ+R H   +G PI GD+KY  N   N T   +  L    LH
Sbjct: 244 Q-TKDVTLLEVHLITGKTHQIRAHLASIGHPIAGDYKY-GNRAFNETLKKEYGLSSQLLH 301

Query: 292 ARYMDLPHPEGGRL------QITAPLP 312
           A  ++ P   GG L      ++ APLP
Sbjct: 302 AYRLNFPKC-GGDLSLLSGKELQAPLP 327


>gi|239996474|ref|ZP_04716998.1| tRNA pseudouridine synthase A [Alteromonas macleodii ATCC 27126]
          Length = 250

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 72/224 (32%), Positives = 109/224 (48%), Gaps = 29/224 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS------------GIAYHIDGFLKSWVDSKG-QKPRLT 147
           +L+E++ + + NKP GI++   +            G    IDG +          +  L 
Sbjct: 6   VLFENTDLIIVNKPIGIAMHDATSEADVREDIAENGEPEKIDGIVTRLKKQLAVTELHLC 65

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG L +A+  A A  + E F  RR+ K Y +L    PK K+  I   +  K+ 
Sbjct: 66  HRLDTGTSGCLCLAKNAAVAGEIGELFSSRRVSKYYLALSDHKPKKKQGMIMGDM--KNR 123

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            GG  + ++K  E   N AI+ F           ++ ++PH+G+THQ+RV    +G PI+
Sbjct: 124 RGGQRI-LLKTTE---NPAITQFFSSAAKPGTRGFI-VKPHSGKTHQIRVALKSIGAPIL 178

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           GD  Y     G  TS   ++LYLHA ++ LP    G L +TAP 
Sbjct: 179 GDTLY-----GGETS---DRLYLHAWHLRLPL-SSGELSVTAPF 213


>gi|220912349|ref|YP_002487658.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
 gi|219859227|gb|ACL39569.1| pseudouridine synthase, RluA family [Arthrobacter chlorophenolicus
           A6]
          Length = 308

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 63/209 (30%), Positives = 106/209 (50%), Gaps = 15/209 (7%)

Query: 116 GISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G +V GG +G  Y I            ++  + HRLD  TSG++VVA++  A   L  +F
Sbjct: 108 GPTVVGGLAGAGYRIS------TSGSPERAGIVHRLDVGTSGVMVVAKSERAYTALKRAF 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R + K+Y ++V G+P      I   + +  H G D+   V +  +    +++H++V++
Sbjct: 162 KERTVDKVYHAVVQGLPDPLTGTIDAPIGR--HPGHDWRFAVTEEGR---PSVTHYEVLE 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F  K   +E+   TGRTHQ+RVH   +  P  GD  Y A+ +   T  +  + +LHAR 
Sbjct: 217 AFG-KASLVEVHLETGRTHQIRVHFSALRHPCAGDLTYGADPRLAATLGLTRQ-WLHARE 274

Query: 295 MDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +   HP  G R+++T+  P  +    D L
Sbjct: 275 LGFDHPVTGERVRVTSDYPQDLAFALDVL 303


>gi|261493572|ref|ZP_05990092.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261310754|gb|EEY11937.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 242

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 112/244 (45%), Gaps = 24/244 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   NKPAG+ V   S +  H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 5   ILYQDDLLIAINKPAGMLVHR-SWLDKHETVFAMQTLRDQIGQHVFPIHRLDRPTSGVLL 63

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A     A+ ++E F   ++QK Y ++V G  +   +      +    I   +       
Sbjct: 64  FALNSETARVMSEQFEQHQVQKTYLAVVRGYLQGSAQIDYPLTVILDKIADKF-----SQ 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           EK A  AI+ +K +               ++  +E+ P TGR HQLR H  H+  PI+GD
Sbjct: 119 EKEAQAAITDYKGLATVEMPYAVGKHQTARYSLVELSPKTGRKHQLRRHLKHLFHPIMGD 178

Query: 270 HKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKY 326
            KY    +    +     ++L LHA  +   HP+   +++I APL     + W  L   +
Sbjct: 179 SKYGDLHQNRALAEKSGVSRLMLHAHKLQFQHPKNLQKIEIIAPLD----EQWQRLFAFF 234

Query: 327 DRNL 330
           D N 
Sbjct: 235 DWNF 238


>gi|254507230|ref|ZP_05119367.1| pseudouridylate synthase, 23S RNA-specific [Vibrio parahaemolyticus
           16]
 gi|219549940|gb|EED26928.1| pseudouridylate synthase, 23S RNA-specific [Vibrio parahaemolyticus
           16]
          Length = 559

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 74/231 (32%), Positives = 117/231 (50%), Gaps = 21/231 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGF 132
           L H+++  +I D+ +  +   D    I+ YED  + + NKP+G+ SV G +         
Sbjct: 332 LGHMLEGMRIDDNPLEKSWAEDKELEIV-YEDDAMVIVNKPSGLLSVPGKTITDSAYTRL 390

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            K + D++G  P + HRLD  TSGILV A TR A ++L + F  R +QK Y + + G  +
Sbjct: 391 QKRYPDAEG--PFVIHRLDMATSGILVFALTRRANKNLQKQFISRSVQKRYIAQIEGEVQ 448

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +   I N  ++          V  ++ K A    +++++I+  +     L M P TGRT
Sbjct: 449 VQNGTI-NLPMRGDPDDRPRQLVCYEHGKPAE---TYWELIET-SNGQSKLYMHPKTGRT 503

Query: 253 HQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           HQLRVH  H   +  PIVGD  Y             ++L+LHA+ ++L HP
Sbjct: 504 HQLRVHCAHHLGLNMPIVGDALYGTK---------SDRLHLHAQRLELHHP 545


>gi|251788208|ref|YP_003002929.1| pseudouridine synthase [Dickeya zeae Ech1591]
 gi|247536829|gb|ACT05450.1| pseudouridine synthase [Dickeya zeae Ech1591]
          Length = 217

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/204 (33%), Positives = 106/204 (51%), Gaps = 18/204 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  + + + +        HRLD  TSG++V
Sbjct: 14  ILYQDQHIMVVNKPSGLLSVPGRA--EEHKDSIM-TRIQADFPAAESVHRLDMATSGVMV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG        +   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPKKSYIARVWGHLTQDDGLVDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E+G   A +++ V+         +++ P TGR+HQLRVH L +G PI+GD  Y A+ 
Sbjct: 125 VCFEQG-KPAQTNYTVLSRDNDGTTRVKLMPITGRSHQLRVHMLALGHPILGDGFY-AHP 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
           +    +P   +L LHA+ + + HP
Sbjct: 183 EAKALAP---RLLLHAQELAITHP 203


>gi|218263602|ref|ZP_03477676.1| hypothetical protein PRABACTJOHN_03365 [Parabacteroides johnsonii
           DSM 18315]
 gi|218222612|gb|EEC95262.1| hypothetical protein PRABACTJOHN_03365 [Parabacteroides johnsonii
           DSM 18315]
          Length = 551

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/244 (29%), Positives = 112/244 (45%), Gaps = 34/244 (13%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGF 132
           L H+++   + ++ +    H D    I+ YED  + V NKPAG +SV G S +       
Sbjct: 313 LKHMLQGLDVEENPLETDVHRDAELEIV-YEDESLLVVNKPAGMLSVPGKSDVDSVYQRV 371

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            + +  + G  P + HRLD  TSG+++VA+T+   Q+L   F+ R + K Y + + GI +
Sbjct: 372 RRMYPGATG--PMVVHRLDMATSGLMLVAKTKEVHQNLQAQFKNRTVCKRYVAWLDGIVE 429

Query: 193 NKKECIANWLLKKSHIGG----DYVHVVKQNEKGANYAISHFKVIDCFAQKF------CW 242
            K+  +   L            D VH           A++ ++V+     K         
Sbjct: 430 EKEGHLELPLRPDPEDRPRQVVDVVH--------GKPAVTDYRVLRYGGCKGGLRTTPTV 481

Query: 243 LEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +   P TGRTHQLRVH+ H   +  PIVGD  Y             ++LYLHA Y+   H
Sbjct: 482 VSFVPKTGRTHQLRVHSAHPLGLNAPIVGDELYGKK---------ADRLYLHAEYLGFTH 532

Query: 300 PEGG 303
           P  G
Sbjct: 533 PVSG 536


>gi|182412318|ref|YP_001817384.1| pseudouridine synthase [Opitutus terrae PB90-1]
 gi|177839532|gb|ACB73784.1| pseudouridine synthase [Opitutus terrae PB90-1]
          Length = 268

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 111/241 (46%), Gaps = 32/241 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQETSGILV 159
           +L+ED  +  F+KP+G+ +          +  L   V ++ G      HRLD +TSG+L+
Sbjct: 6   ILFEDDAMIAFDKPSGLLIAPDRWDKQREN--LMGLVHARFGHGVANVHRLDADTSGLLL 63

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV---V 216
            A+T+ A   L+  F+ + +QK Y SLV  +P  +   +   +   +    D   V   +
Sbjct: 64  CAKTKPALDFLSGQFQAKTVQKTYLSLVVVLPPEEAMKVVKPIRDDAGGLPDAFQVDLAL 123

Query: 217 KQNE-----------KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            Q+E           +G    ++ F+V++ F  +F  +   P TGRTHQ+RVH    G P
Sbjct: 124 GQDERQPGRMRVFKGRGGKDCVTDFRVLERFG-RFALVSCHPQTGRTHQIRVHLAAAGAP 182

Query: 266 IVGDHKYC------------ANFKG-NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           I+ D  Y               +KG +   P+ ++L LHA  +   HP     L + APL
Sbjct: 183 ILNDPFYGNPEIKLLLSDLKRRYKGRDEEKPLIDRLALHASELTFRHPATRELLTLQAPL 242

Query: 312 P 312
           P
Sbjct: 243 P 243


>gi|49477179|ref|YP_035519.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|49328735|gb|AAT59381.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
          Length = 307

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 71/231 (30%), Positives = 115/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +    S +GG G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPSEKGGMGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV + F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEEYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y    K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 254 DVLYGGGTK------YMSRQALHAMTINFLHPITKEEIEVDVPFPTKLNDT 298


>gi|320539613|ref|ZP_08039277.1| putative pseudouridine synthase for 23S rRNA [Serratia symbiotica
           str. Tucson]
 gi|320030225|gb|EFW12240.1| putative pseudouridine synthase for 23S rRNA [Serratia symbiotica
           str. Tucson]
          Length = 216

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 66/204 (32%), Positives = 104/204 (50%), Gaps = 16/204 (7%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  + D  L + + +     +  HRLD  TSG++
Sbjct: 12  LILYQDQHIMVVNKPSGLLSVPGR--LPENKDSLL-TRIQADFPAAQAVHRLDMATSGVI 68

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  +AA + L   FR R  +K Y + VWG     +  +A  L+       D+ +  +Q
Sbjct: 69  VVALNKAAERELKRQFREREPKKYYIARVWGHLVQDEGVVALPLI------CDWPNRPRQ 122

Query: 219 NE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                    A + ++V+   A     +++ P TGR+HQLRVH L +G PI+GD  Y    
Sbjct: 123 KVCFDTGRAAQTEYRVLSRDADGCTRVKLVPITGRSHQLRVHMLALGHPILGDGFYA--- 179

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
             +    +  +L LHA+ + L HP
Sbjct: 180 -HSQAQALAQRLQLHAQTLHLTHP 202


>gi|325109066|ref|YP_004270134.1| pseudouridine synthase [Planctomyces brasiliensis DSM 5305]
 gi|324969334|gb|ADY60112.1| pseudouridine synthase, RluA family [Planctomyces brasiliensis DSM
           5305]
          Length = 410

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 76/333 (22%), Positives = 148/333 (44%), Gaps = 45/333 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + VE  +  +R D +      + +   +Q++   G + +  + V    R+  G  +++  
Sbjct: 79  LTVEPYQSGLRTDAFLVQQLRNYSLWKIQRLAHWGAITIRHQPVDLMKRLYPGDTIQV-- 136

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYH 128
                       ++++    + +   F   I  YED+ +   NKP G I+   G+  +  
Sbjct: 137 ------------RLVEPPETVYEPEPFPLEIE-YEDAWMLAVNKPPGVIAHPTGNMQSGT 183

Query: 129 IDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +  +L++  D++       KP + HRLD+ETSG++++A+T  A ++  ++F   R+ K Y
Sbjct: 184 LCNYLQAHFDTQSGIPGLLKPGIVHRLDRETSGVMLIAKTHRAHRNFVDAFEHSRVSKTY 243

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L+ G    K+E   +  + ++ +    +   + + K    A +H++V+         +
Sbjct: 244 VALLEG-DVAKEEGTIDLPIGQATVDSKVLMSARGDAKNPKPAKTHWRVLKRLG-SHTLV 301

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL--------------- 288
             +P TGR HQ+RVH   +G P+ GD  Y  +  G F +  ++ L               
Sbjct: 302 AAKPVTGRNHQIRVHFATIGHPLAGDEFY--DRDGQFKAATRDSLEEGRRMTDTRCARTG 359

Query: 289 ----YLHARYMDLPHP-EGGRLQITAPLPAHMV 316
                LHA  +   HP  G  + I A LPA M+
Sbjct: 360 LTRHALHASTIQTAHPITGVWMTIQAGLPADML 392


>gi|167752282|ref|ZP_02424409.1| hypothetical protein ALIPUT_00526 [Alistipes putredinis DSM 17216]
 gi|167660523|gb|EDS04653.1| hypothetical protein ALIPUT_00526 [Alistipes putredinis DSM 17216]
          Length = 236

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 61/223 (27%), Positives = 103/223 (46%), Gaps = 14/223 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
           F    +LYED+ + + NK  G  VQ        ++  +K ++  +  KP      + HR+
Sbjct: 2   FAPEDILYEDNHLLIVNKRCGDLVQPDPSGGDALERQIKEFIRRRDAKPGEVFLGVVHRI 61

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+  SG ++ A+T  A   L E  R   I+K YW+L    P  ++  + +++L+      
Sbjct: 62  DRPVSGAVIFAKTSKALARLNEMIRRGEIKKTYWALTESRPDPEEGELCHYILRNEKT-- 119

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +    +      A  A   ++ +   A ++  +E+   TGR HQ+R     +GCPI GD 
Sbjct: 120 NRSRALDAPRGDAKLAKLRYRTLGASA-RYTLVEVDLLTGRHHQIRAQLSKIGCPIKGDL 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           KY     G   S     + LH+  +D  HP    R+ +TAP+P
Sbjct: 179 KY-----GARRSNPDGGISLHSYRVDFIHPVRRERIVVTAPVP 216


>gi|37524616|ref|NP_927960.1| ribosomal large subunit pseudouridine synthase A (pseudouridylate
           synthase) (uracil hydrolyase) [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|36784040|emb|CAE12909.1| ribosomal large subunit pseudouridine synthase A (pseudouridylate
           synthase) (uracil hydrolyase) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 216

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 110/207 (53%), Gaps = 19/207 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +  A H D  + + +  +       HRLD  TSG++V
Sbjct: 14  VLYQDQYIIVVNKPSGLLSVPGRA--AEHKDSIM-TRIQQQFPAAESVHRLDMATSGVMV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+ A + L   FR R  +K Y + VWG  + +   +   L+       D+ +  KQ 
Sbjct: 71  VALTKDAERELKRQFREREPEKTYIARVWGRLEPETGLVDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + A + ++V+  +  +   +++ P TGR+HQLRVH L +  PI+GD  Y A+ 
Sbjct: 125 VCFETGKS-AQTEYEVL-AYEDEATRIKLSPITGRSHQLRVHMLALEHPILGDQFY-AHQ 181

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    +P   +L LHA+ + + HP  G
Sbjct: 182 QARAMAP---RLQLHAQELYITHPVYG 205


>gi|227499592|ref|ZP_03929699.1| pseudouridylate synthase [Anaerococcus tetradius ATCC 35098]
 gi|227218351|gb|EEI83605.1| pseudouridylate synthase [Anaerococcus tetradius ATCC 35098]
          Length = 328

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 136/286 (47%), Gaps = 32/286 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           ++L+  ++ V+ END    R DR+ + ++ +     +QK +R    +++ KR K ++ + 
Sbjct: 6   INLINMIEIVINENDG-GQRFDRFLRKYFENAPLSLIQKNIRKKNFKINDKRAKKDDFVY 64

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLT--KHSDFLKSILLYEDSKIYVFNKPAGIS 118
            G  V++   IN  ++        D  +  T  K  DF   I+ YED  I + +K  G+ 
Sbjct: 65  PGDSVKM--YINDSDY--------DKWLTRTDFKAQDFNLDIV-YEDDNIIIMDKREGLL 113

Query: 119 VQGGSGIAYH---IDGFLKSWVDSKGQ-------KPRLTHRLDQETSGILVVARTRAAAQ 168
               S   Y    +D  L     +K         KP + +RLD+ T+G+++ A+   A +
Sbjct: 114 THSSSRKDYGNNLVDNMLAYLYKTKSIDMTDKTFKPAVVNRLDRNTAGLVIGAKNAKALR 173

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            L  + R + I K Y ++V G          ++ ++ +    +  + ++++E G    I+
Sbjct: 174 SLNRAIRNKYIDKYYMTIVNG------HIDKDFSIRTTIAKNENKNRIRKSEDGKE-IIT 226

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           HF+ +D   +KF  LE +  TG+THQ+R        PI+GD KY +
Sbjct: 227 HFRPLDS-NKKFTLLECKLETGKTHQIRFSLKENRTPIIGDRKYGS 271


>gi|303228679|ref|ZP_07315504.1| putative Ribosomal large subunit pseudouridine synthase D
           [Veillonella atypica ACS-134-V-Col7a]
 gi|303230316|ref|ZP_07317081.1| putative Ribosomal large subunit pseudouridine synthase D
           [Veillonella atypica ACS-049-V-Sch6]
 gi|302515027|gb|EFL57004.1| putative Ribosomal large subunit pseudouridine synthase D
           [Veillonella atypica ACS-049-V-Sch6]
 gi|302516659|gb|EFL58576.1| putative Ribosomal large subunit pseudouridine synthase D
           [Veillonella atypica ACS-134-V-Col7a]
          Length = 295

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 138/293 (47%), Gaps = 50/293 (17%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRI-QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           N+Q I R       KKRVK N+R+  S +++R   VI               ++ L +  
Sbjct: 30  NVQMIFR-------KKRVKVNSRVAHSKRMLRKGDVI---------------TIELPQDK 67

Query: 95  DFLKSI------LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQ--KPR 145
           D+   +      +LYED    V  K   + V       YH +   +  +   +G+  K R
Sbjct: 68  DYGVEVEKGPIEVLYEDEHTLVVYKSPFMLVHPAGQTKYHTLSNLVAGYYAKRGEVHKIR 127

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD++T+G+++  +TR A Q+ T+  +  RI ++Y  LV G  K   + + N     
Sbjct: 128 PVHRLDRDTTGVIMFGKTREAEQYYTKQLQEGRIHRVYRGLVEG--KITSDGVVN----- 180

Query: 206 SHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
             IG D V   ++  +E G + A++ + VI+ +      LE    TGRTHQ+RVH  H+G
Sbjct: 181 EPIGVDPVFDNRRCVDEFGQD-AVTEYHVIE-YDDVQSLLEFTLLTGRTHQIRVHMAHIG 238

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD-LPHPEGGRLQITAPLPAHM 315
            PI+GD  Y     G    P   +  LHA  +  +P+ +   + + AP+P+ +
Sbjct: 239 HPIIGDAMY-----GMRKKPYTRQA-LHAYSLTFIPYGQSELVTVIAPVPSDL 285


>gi|157149723|ref|YP_001451260.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gordonii str. Challis substr. CH1]
 gi|157074517|gb|ABV09200.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gordonii str. Challis substr. CH1]
          Length = 290

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 94/201 (46%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGTVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + IQ+ YW+LV G      + I    + K  IG D     K+  +
Sbjct: 141 KNPFVLPILNRLLENKDIQREYWALVDG------KFIEKSRIYKDKIGRDRHDRRKRLVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F QK   ++ Q  TGRTHQ+RVH  H G P+VGD  Y  + +G 
Sbjct: 195 NKHGQYAETHVTRLKSFGQK-TLVKCQLKTGRTHQIRVHLSHHGFPLVGDPLYHPHPQG- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 253 -------RLMLHAHRLSFVHP 266


>gi|307128211|ref|YP_003880242.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 670-6B]
 gi|306485273|gb|ADM92142.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 670-6B]
          Length = 278

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +N K  
Sbjct: 182 AKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNFPILGDPLYNSNSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|256829592|ref|YP_003158320.1| RluA family pseudouridine synthase [Desulfomicrobium baculatum DSM
           4028]
 gi|256578768|gb|ACU89904.1| pseudouridine synthase, RluA family [Desulfomicrobium baculatum DSM
           4028]
          Length = 526

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 147/320 (45%), Gaps = 37/320 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           +  YV+ V V +     RLD +++       +    +Q  ++ G+ R++ +   K   R+
Sbjct: 1   MQEYVEKVGVAD--VGQRLDVFWQTCLEEEGVGRSRVQAWIKDGRARINGQVCSKAATRL 58

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             GQ + + P            +  DSSV      D     + + D  + V NK   ++V
Sbjct: 59  MPGQTLTLAP------------EYTDSSVV----PDDGPLNVFFADEDLVVVNKTPAMTV 102

Query: 120 QGGSGIA-----YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                +A     + +     + +   G++P + HRLD++TSG++V+A + +A   LT++F
Sbjct: 103 HPAPSVAEPTLVHRVAHHFPALLSQSGERPGIVHRLDKDTSGLIVLALSESARLSLTQAF 162

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             R + K Y +LV G+P +    ++  L +   I      V    E+G   A + F+++ 
Sbjct: 163 ASREVYKEYLALVAGVP-DSSGTVSLALGRHPSIKTRMAVV----ERGGRAAETRFELLW 217

Query: 235 CFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             A +   L  ++  TGRTHQ+RVH   +G P++GD  Y A+ +    +P Q    LHA 
Sbjct: 218 SAADRSASLVRVRIMTGRTHQIRVHMAALGHPLLGDAVY-ADKQTAARAPRQ---MLHAW 273

Query: 294 YMDLPHPEG-GRLQITAPLP 312
            +   HP     ++  AP P
Sbjct: 274 QLRFEHPRSFESMEFCAPPP 293


>gi|283798477|ref|ZP_06347630.1| ribosomal large subunit pseudouridine synthase family protein
           [Clostridium sp. M62/1]
 gi|291073736|gb|EFE11100.1| ribosomal large subunit pseudouridine synthase family protein
           [Clostridium sp. M62/1]
          Length = 266

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 70/254 (27%), Positives = 114/254 (44%), Gaps = 44/254 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPR-------------- 145
           ++YEDS+I V  KPAG+  Q        +   ++++ V S+ ++ R              
Sbjct: 4   IIYEDSEILVAEKPAGLESQASRKFEPDMVSEIRNYLVRSQKKREREQRRELSTKPSTSL 63

Query: 146 ----------LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNK 194
                     + HRLD+  SG++V A+TR+AA  L+   +  R+ KIY ++V G P  N 
Sbjct: 64  STPAAAPYVGVIHRLDKPVSGVMVYAKTRSAAAFLSRELQAHRVTKIYHAVVCGKPVDNV 123

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTH 253
              + N  + +     +Y  +V +++K    A   ++V+    +K    LE+Q  TGR H
Sbjct: 124 GNFVDNLYMNREE---NYSVLVDKSKKEGKRAELSYRVLSRAEEKNLTLLEIQLKTGRHH 180

Query: 254 QLRVHALHMGCPIVGDHKYCANFKG-------------NFTSPI-QNKLYLHARYMDLPH 299
           Q+RV     G PI GD +Y   F G             +F +P  +  L L A  +   H
Sbjct: 181 QIRVQLAGHGLPIWGDARYNPQFGGTLPVEEREEKGSESFRTPASRGPLALAAVSLSFTH 240

Query: 300 PEGGRLQITAPLPA 313
           P  G+    +  PA
Sbjct: 241 PSSGKKMTFSIKPA 254


>gi|167747168|ref|ZP_02419295.1| hypothetical protein ANACAC_01882 [Anaerostipes caccae DSM 14662]
 gi|317473628|ref|ZP_07932917.1| RluA family pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
 gi|167654128|gb|EDR98257.1| hypothetical protein ANACAC_01882 [Anaerostipes caccae DSM 14662]
 gi|316898918|gb|EFV20943.1| RluA family pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 329

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/276 (24%), Positives = 130/276 (47%), Gaps = 24/276 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + + + EE  RLD+    +        L K+LR   ++++ K+   + +++SG VV 
Sbjct: 1   MKEIRISDREEEQRLDKLLAKYLNKAPKSFLYKMLRKKNIKLNGKKASGSEKLKSGDVVC 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +      +    +E +      +L+         ++Y+DS + + NKP G+  Q      
Sbjct: 61  VYMADATIASFREEPRAERRKADLS---------VIYQDSNVLIINKPYGMLSQKAKPSD 111

Query: 125 -------IAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                  + Y ++ G LK   D +  +P + +RLD+ T+G+L+   +    Q + E  R 
Sbjct: 112 ISVNELIVPYCLEHGILKES-DLELVRPSVCNRLDRNTTGLLIAGISLEGLQTMAEVLRD 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R ++K Y+ +V G+  NKK  I+ ++ K      + V   ++   G +   + ++ +   
Sbjct: 171 RSVRKYYYCIVKGMV-NKKTRISGYICKDHR--ENKVSFSERKISGGSRIETAYEPMAA- 226

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              F  L ++  TG+THQ+R H   MG P+ GD KY
Sbjct: 227 GHGFTLLRVELITGKTHQIRAHLAGMGFPLAGDTKY 262


>gi|291528898|emb|CBK94484.1| Pseudouridylate synthases, 23S RNA-specific [Eubacterium rectale
           M104/1]
          Length = 324

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 92/339 (27%), Positives = 151/339 (44%), Gaps = 52/339 (15%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++ K   P+ +   + K+LR       KK +K N++  SG    I  V + +
Sbjct: 9   NEAGQRLDKYLKKILPNASMGFIYKMLR-------KKNIKLNDKKASG--TEIVSVDDKI 59

Query: 75  NHIIKEQKILDSSVN---LTKHSDFLKSI------LLYEDSKIYVFNKPAGISVQGGSGI 125
              + +      SVN   L K    L ++      ++YED  I V NKP  +  Q     
Sbjct: 60  KIFLSDDTFAKFSVNEDSLMKDFKALGALKPDGLGVVYEDDDILVANKPVNMLSQKSKET 119

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  ++  +G+         KP + +RLD+ TSG++++ ++    Q+L++  + 
Sbjct: 120 DISANERLIGYLIKEGKLDFDTYKSFKPSVCNRLDRNTSGLILMGKSLHGLQYLSQVLKD 179

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH----FKV 232
           R  +K Y +LV G   ++   I  +L K   +  + V + K+     +  I       K+
Sbjct: 180 RTAEKYYMALVAG-EVDEPMTIEGFLTKDEAV--NKVQITKEPISDESLPIKTAYRPIKI 236

Query: 233 IDC--FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQ 285
           I+      K   LE+   TGR+HQ+R H   +G PI+GD KY      A +K N+    Q
Sbjct: 237 IEMSDSCHKATLLEVHLITGRSHQIRAHLSSIGHPIIGDMKYGDKRINAFYKENYHVTSQ 296

Query: 286 NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
               LHA ++ LP    GR  I A LP      W  +G 
Sbjct: 297 ---LLHAHHVILPD---GRY-IEAALP----DIWSRVGL 324


>gi|308806025|ref|XP_003080324.1| RNA pseudouridylate synthases (ISS) [Ostreococcus tauri]
 gi|116058784|emb|CAL54491.1| RNA pseudouridylate synthases (ISS) [Ostreococcus tauri]
          Length = 434

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 57/193 (29%), Positives = 91/193 (47%), Gaps = 32/193 (16%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGI---SVQGGSGIAYHIDGFLKSWVDS-----KGQK 143
           +H D +   +LY+D  I    KPAG+     +GG+  +  +D  L  + D+      G  
Sbjct: 195 EHPDLVNLRVLYDDGSIAAVFKPAGVLTHPAEGGAATSL-MDAALARFGDTGLSDLNGSD 253

Query: 144 PR-LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            R +  RLD+ TSG++++AR  AA   L   F  RR+ K Y  LV G P +++  +   +
Sbjct: 254 KRGIVSRLDKPTSGVILLARHNAAHAKLVTDFYQRRVSKTYIVLVDGAPTDERGTVTAPI 313

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC---WLEMQPHTGRTHQLRVHA 259
             +                    A S +KV++ F    C    + ++P +GR HQ+R H 
Sbjct: 314 DDRP-------------------ATSEYKVLERFNSASCSYALVRVKPKSGRKHQIRRHM 354

Query: 260 LHMGCPIVGDHKY 272
             +GCP+VGD  Y
Sbjct: 355 AMIGCPLVGDTVY 367


>gi|332306836|ref|YP_004434687.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332174165|gb|AEE23419.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 563

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 121/233 (51%), Gaps = 23/233 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           LNH+++   + D+ + L   +D  +  ++Y+D ++ + NKPA +    G  I   +   +
Sbjct: 334 LNHMLQGLSVEDNQL-LQNTADNKQIDIVYQDDEMLIINKPAQLLSVPGKHIQDSVYTRI 392

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+          + HRLD  TSG++V+A + A+ + L + F  R+++K Y +L+ G+ + 
Sbjct: 393 KTLF-PHATGSLIVHRLDMSTSGLMVIALSAASHKALQKQFISRQVEKSYVALIDGLLEK 451

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVID-CFAQKFCWLEMQPHTG 250
           ++  I   L       GD+    +Q   EK    A + + VI+   +Q+   + +QP TG
Sbjct: 452 QQGTITLPL------AGDFYDRPRQCVCEKTGKPAHTTWHVIERRSSQQQTKVLLQPKTG 505

Query: 251 RTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           RTHQLRVH  H   +  PI+GD  Y     GN  S    +L+LHA+ + L HP
Sbjct: 506 RTHQLRVHCAHERGLNMPIIGDDLY-----GNRDS----RLHLHAQSLSLFHP 549


>gi|313677829|ref|YP_004055825.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
 gi|312944527|gb|ADR23717.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
          Length = 300

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 75/294 (25%), Positives = 137/294 (46%), Gaps = 35/294 (11%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINAL 74
           +E+  L +     YP+     L++++  GQ+R++   + +FN+ ++ G  ++I       
Sbjct: 18  QEDTELLKHLTTTYPNKKKALLKQVMGGGQIRINGDVITQFNHPLKKGDEIQI------- 70

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI----SVQGGSGIAYHID 130
           N     +K+    +N+           +YED  +    K AG+    S++  +  A  I 
Sbjct: 71  NWAKPSKKVKLQKLNI-----------IYEDQHLIAIEKEAGLLSVASLKEKTKNAVQIL 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                 +D +  K  + HRL++E SG+L+ A+++   + L   +    I + Y ++V G 
Sbjct: 120 KEHMEAIDPRN-KVYIIHRLEREASGVLLFAKSKEVQEQLQNHWEDYIIDRKYVAVVEGK 178

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K     + N+L    H   + V +V   E  A  AI+HFK++   +  +  LE +  TG
Sbjct: 179 IKESSHTLRNYLRSNKH---NQVFIVNTAE-NATEAITHFKLLKQ-SNAYSMLEFKLETG 233

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             +Q+RV   H G P+ GD KY A       +P+  ++ LHA  ++L HP  G 
Sbjct: 234 FKNQIRVQMAHFGFPVTGDKKYTAK-----KNPLA-RVALHANLIELKHPISGE 281


>gi|229172031|ref|ZP_04299596.1| Pseudouridine synthase [Bacillus cereus MM3]
 gi|228611374|gb|EEK68631.1| Pseudouridine synthase [Bacillus cereus MM3]
          Length = 307

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 115/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKGKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+ +KV   F  Q   ++ +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITFYKVEKYFKNQNVTFVTLQLETGRTHQIRVHMSYHGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y         +   ++  LHA  ++  HP     +++  P PA +  T
Sbjct: 254 DVLYGGQ------TQYMSRQALHAMKINFLHPITKEEIEVDVPFPAKLNDT 298


>gi|22537512|ref|NP_688363.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           agalactiae 2603V/R]
 gi|76797703|ref|ZP_00779971.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
 gi|77414617|ref|ZP_00790757.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
 gi|22534392|gb|AAN00236.1|AE014254_16 ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 2603V/R]
 gi|76586927|gb|EAO63417.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
 gi|77159330|gb|EAO70501.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
          Length = 296

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 111/239 (46%), Gaps = 38/239 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++Y+D  + V NKP G+ V   +G         + YHI    K      G  +P + HR+
Sbjct: 76  IIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHI----KDLSSINGVVRPGIVHRI 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+   A Q L E  + ++  + Y ++V G   N +  I      ++ IG 
Sbjct: 132 DKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVI------EAPIGR 185

Query: 211 DYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 KQ    KG   AI+ F V++ F   +  +E+   TGRTHQ+RVH  ++G P+ G
Sbjct: 186 SDKDRKKQAVTAKG-KPAITRFHVLERFGD-YTLVELSLETGRTHQIRVHMAYIGHPLAG 243

Query: 269 DHKY----CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           D  Y        KG F         LHA+ +   HP  G  L  +  +P     T + L
Sbjct: 244 DPVYGPRKTLGGKGQF---------LHAQTLGFTHPSNGENLIFSVEVPEIFQTTLEKL 293


>gi|210615096|ref|ZP_03290443.1| hypothetical protein CLONEX_02657 [Clostridium nexile DSM 1787]
 gi|210150445|gb|EEA81454.1| hypothetical protein CLONEX_02657 [Clostridium nexile DSM 1787]
          Length = 303

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 63/223 (28%), Positives = 111/223 (49%), Gaps = 22/223 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD----SKGQ--KPRLTHRLDQET 154
           ++YED  + V NKPA + +    G   + D  L + V      KG+    R  +RLD++T
Sbjct: 83  IVYEDEDLMVINKPADMPIHPSQG---NYDNTLANAVAYYYAQKGEPFTYRCINRLDRDT 139

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+L++A+   +A  L++  + R+I + Y ++  G  K     I +  + +  + G  + 
Sbjct: 140 TGLLILAKHMYSASLLSDMVKNRKIHREYLAVAEG--KTPSSGIIDAPIGR--VDGSTIE 195

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                E+G +YA +H+K + C+   +  + +   TGRTHQ+RVH  H+G P+ GD  Y  
Sbjct: 196 RQVDYEQG-DYACTHYKRL-CYKNGYSLVSLTLKTGRTHQIRVHMKHVGHPLPGDFLYNP 253

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           N+       +  +  LH+  +   HP     L  ++PLP  M 
Sbjct: 254 NYH------VIKRQALHSHCLSFEHPITKEPLTFSSPLPDDMA 290


>gi|149920990|ref|ZP_01909450.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
 gi|149818122|gb|EDM77578.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
          Length = 356

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 86/341 (25%), Positives = 147/341 (43%), Gaps = 53/341 (15%)

Query: 5   TYVQYVV-VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNN--RIQ 60
            Y+++ + V    +  RLDR+    +  ++   + K+L +G VR      V   N  R++
Sbjct: 27  VYIEFELEVGPGSDGYRLDRFLSLRFVRMSRTRVHKLLAAGNVRCRSSGEVLTKNALRVR 86

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            GQVV           II+     + +V        L   +++ED  + V +KP  + V 
Sbjct: 87  GGQVV-----------IIRRPAPEEPAV-------ILDYGVVHEDPDVLVLDKPGNLPVH 128

Query: 121 GGSGIAYH---IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   YH   +   ++  +  K     + HR+D+ETSG+++  R +A+   +  SF  R
Sbjct: 129 PTA--RYHRHTLTALMRRRLGPK-HGWEMAHRIDRETSGVIIFGRRKASGPKIKGSFFRR 185

Query: 178 RIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYV-----HVVKQNEKGANYAISH 229
            + K Y ++V G   +P+  +  + +  L  S +G   +       V +    A   I  
Sbjct: 186 EVHKEYLAIVLGRLELPEGPR--LIDMPL-GSAVGSKIMIKMGPRPVDEGGLPAQTTIEV 242

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--------FKGNFT 281
               +   Q    +   P TGRTHQ+RVH   +G PI+GD  Y A           G   
Sbjct: 243 LAHGEHRGQPITLVRCLPRTGRTHQIRVHLAEIGHPILGDKLYAAEEDEFLAVVEDGEPV 302

Query: 282 SPIQNKL-----YLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           + ++ +L      LHAR + LPHP  G  ++  AP P  + 
Sbjct: 303 AELEARLGLWRQALHARALSLPHPTTGDGVRYVAPWPKELA 343


>gi|239623805|ref|ZP_04666836.1| pseudouridine synthase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521836|gb|EEQ61702.1| pseudouridine synthase [Clostridiales bacterium 1_7_47FAA]
          Length = 330

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 126/286 (44%), Gaps = 38/286 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V  +E   R+D+    +        L K++R   + ++ K+   +  ++ G  ++
Sbjct: 1   MQTLTVTPNEAGQRMDKLLAKYLDQAGKGFLYKMMRKKNITLNGKKCDGSEHLEEGDEIQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +     A   I K Q    +    T    + K  ++YED  I V NKP+G+  Q      
Sbjct: 61  L---FMADETIEKFQAAPKAPARSTAGYGYKKLDIIYEDRHILVVNKPSGMLSQKAREGD 117

Query: 127 YHIDGFLKSW-VDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             ++ ++ ++ +DS G         KP + +RLD+ TSG++V  ++ A  Q +   F+ R
Sbjct: 118 MSLNEYILNYLIDSGGLPISQLRTFKPSICNRLDRNTSGLVVAGKSLAGLQVMNGVFKDR 177

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  LV G  K KK  IA +L              +++E      I   +V D   
Sbjct: 178 SLHKYYQCLVAGQIKEKK-LIAGFL--------------RKDEAANTVTIYPLEVEDSVP 222

Query: 238 QKFCWLEMQPH-----------TGRTHQLRVHALHMGCPIVGDHKY 272
               +L +  +           TGR+HQ+R H   +G PIVGD+KY
Sbjct: 223 IMTEYLPLAGNGNHTLLQVTLITGRSHQIRAHLASIGHPIVGDYKY 268


>gi|221640995|ref|YP_002527257.1| Ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides KD131]
 gi|221161776|gb|ACM02756.1| Ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides KD131]
          Length = 224

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 110/220 (50%), Gaps = 27/220 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           L++ D++I V +KPAG+    G G     D  ++     +G  P   L HRLD++TSG++
Sbjct: 23  LIHHDAQIVVVDKPAGLLSVPGKG-EDKADCLIERL---RGVFPEILLVHRLDRDTSGVM 78

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKK---ECIANWLLKKSHIGGDYV 213
           V A T+AA   L + F  R+ +KIY + V G   P+  +       +W  +         
Sbjct: 79  VFALTKAAQGALGQQFEKRQTKKIYVARVAGRLEPREGRVDLPLCVDWPNRPKQ------ 132

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           HV  +N + A    + ++V+  +  K   + + P TGR+HQLRVH    G PI+GD  Y 
Sbjct: 133 HVDHENGRPAQ---TDWRVVK-YLPKETRVRLMPVTGRSHQLRVHMAETGHPILGDALYS 188

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                +F      +L LHA  + + HP+ G+ L  +AP P
Sbjct: 189 EGAARDFP-----RLMLHAESLRVRHPDTGKSLTYSAPCP 223


>gi|254466034|ref|ZP_05079445.1| ribosomal large subunit pseudouridine synthase A [Rhodobacterales
           bacterium Y4I]
 gi|206686942|gb|EDZ47424.1| ribosomal large subunit pseudouridine synthase A [Rhodobacterales
           bacterium Y4I]
          Length = 217

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 63/206 (30%), Positives = 105/206 (50%), Gaps = 18/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D+++   NKPAG+    G G   H+   L + V +   +  L HRLD++TSG++V 
Sbjct: 16  ILHHDAELLAVNKPAGLLSVPGRG--EHLADCLIARVQAVFPEALLVHRLDRDTSGVMVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
             T  A +HL+  F  R  +K Y + V G  + +   +   L+       D+ +  KQ  
Sbjct: 74  GLTPHAQRHLSMQFEKRTAKKAYVARVEGQLEPRSGTVDLPLIV------DWPNRPKQMV 127

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +E G   A++ ++V+ C       + + P TGR+HQLRVH L +G PI+GD  Y +   
Sbjct: 128 CHETG-KPAVTDWRVMKC-EDGATRVRLTPKTGRSHQLRVHMLSLGHPILGDPLYASGAA 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
            +       +L LH+  + + HP+ G
Sbjct: 186 LD-----HPRLMLHSEELRIKHPDSG 206


>gi|153853078|ref|ZP_01994487.1| hypothetical protein DORLON_00472 [Dorea longicatena DSM 13814]
 gi|149753864|gb|EDM63795.1| hypothetical protein DORLON_00472 [Dorea longicatena DSM 13814]
          Length = 340

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/287 (23%), Positives = 128/287 (44%), Gaps = 35/287 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +++ ++E   RLD+  + +        + K+LR   + ++ K+   N  ++ G  V+
Sbjct: 1   MKELIIHDNEAGQRLDKLLRKYLSEAPGSFIYKMLRKKNIVLNGKKATGNEHLKKGDSVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    + +       K ++ S+  T   D     ++YED  +   NKP+G+  Q      
Sbjct: 61  LFLADDTIAKFQAAGKTVEESIKNTVKLD-----VIYEDQNVIFINKPSGMLSQKAKETD 115

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   + +++   GQ         +P + +RLD+ TSG++V  ++ A  Q + E F+ R
Sbjct: 116 VSVVENVTAYLLESGQLTRENLKTFRPSICNRLDRNTSGLIVAGKSLAGLQQMGELFKKR 175

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN----EKGA------NYAI 227
            ++K Y  +V G            + + +HI G  V   K N     KG          I
Sbjct: 176 TLKKYYLCIVKG-----------RITEPAHIRGYLVKDEKTNRVSLSKGGFSKDAKGLPI 224

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               V   + ++   L++   TGRTHQ+R H    G P++GD+KY +
Sbjct: 225 ETEYVPIAWNEEMTLLKVHLITGRTHQIRAHLASTGHPLLGDYKYGS 271


>gi|213420845|ref|ZP_03353911.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 278

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 59/181 (32%), Positives = 95/181 (52%), Gaps = 22/181 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPISRHPTKRTHMS-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH +         A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPM------GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 252

Query: 272 Y 272
           Y
Sbjct: 253 Y 253


>gi|209694302|ref|YP_002262230.1| tRNA pseudouridine synthase C [Aliivibrio salmonicida LFI1238]
 gi|208008253|emb|CAQ78398.1| tRNA pseudouridine synthase C [Aliivibrio salmonicida LFI1238]
          Length = 263

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/217 (30%), Positives = 102/217 (47%), Gaps = 18/217 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y D  +   NKPAG+ V   S +  H   F +++  D  GQ     HRLD+ TSGIL 
Sbjct: 27  IVYRDDDLIAINKPAGMLVHR-SWLDKHETVFAMQTLRDQIGQHVFPLHRLDRPTSGILF 85

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-------IPKNKKECIANWLLKKSHIGGDY 212
            A + A A   +  F  R I+K Y ++V G       +    KE +     KK+    + 
Sbjct: 86  FALSSAVAAQFSPLFASREIKKTYHAIVRGWIEEGDILDYPLKEQLDKIADKKASKDVEA 145

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV----- 267
              + + +  AN  +  +        ++C +E++PHTGR HQLR H  H+  PIV     
Sbjct: 146 KEAITEYKPLANVELP-YSTGKFPTSRYCLMELKPHTGRKHQLRRHMAHLRHPIVGDTTH 204

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GD K+   F+ N  S   ++L LHA  +   HP   +
Sbjct: 205 GDSKHNRLFQNNLDS---HRLLLHASELSFIHPSTNK 238


>gi|227484916|ref|ZP_03915232.1| possible pseudouridylate synthase [Anaerococcus lactolyticus ATCC
           51172]
 gi|227237071|gb|EEI87086.1| possible pseudouridylate synthase [Anaerococcus lactolyticus ATCC
           51172]
          Length = 313

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 66/218 (30%), Positives = 104/218 (47%), Gaps = 27/218 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++YED  I V NKP+G++V         + +AY+   F K+ + SK    RL +RLD  T
Sbjct: 108 IVYEDENIIVVNKPSGLTVNSKNQLSLANLLAYY---FQKNDIKSK---IRLINRLDMNT 161

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA+ R A  +  +     +  K Y + V G   N  E      L K ++  D + 
Sbjct: 162 SGLMMVAKNRYAQAYYQKQIEENKTHKKYLAYVAG-ALNINE------LFKINLEYDEIS 214

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              +N +    AI++FK + C    +  +E    TG+THQ+R     MG PI+GD  Y +
Sbjct: 215 KTYRNSEKGRLAITYFKTLSC-DDDYSLIECDIKTGKTHQIRASLRSMGHPIIGDKLYGS 273

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
            +  NF     ++  LH+ Y+      G    I   LP
Sbjct: 274 AY--NF-----DRFLLHSFYLSFKEFVGQESIILENLP 304


>gi|316931819|ref|YP_004106801.1| pseudouridine synthase [Rhodopseudomonas palustris DX-1]
 gi|315599533|gb|ADU42068.1| pseudouridine synthase [Rhodopseudomonas palustris DX-1]
          Length = 300

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 72/259 (27%), Positives = 106/259 (40%), Gaps = 59/259 (22%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +D +++ +LY D  + V +KP G+ V  G     +++    +      + P L HRLD++
Sbjct: 16  ADEIQARVLYRDGLMLVIDKPPGLPVHRGPKGGPNLEASFDALRYGLPRPPVLAHRLDRD 75

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----------IPKNKKECIANWLL 203
           TSG LV+ R R A   L   F+  RI K YW++V G          +P  K      W  
Sbjct: 76  TSGCLVLGRHRKATATLGLLFKHSRISKTYWAIVEGGPAEDEGSIDLPIGKLNAERGWWQ 135

Query: 204 K-------------------KSHIGGDYVHVVKQN-------------EKGANYAISHFK 231
           K                      + GD   V   +              +    A+S   
Sbjct: 136 KIDQESGLPSLTKWRVMGRSSPPVCGDGSGVGAHSGTPSLGRPHPGPLPQAGEGALSAGA 195

Query: 232 VIDCFAQK------------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
             D  ++K              WL ++P TGRTHQLRVH   MG PI GD+ Y     GN
Sbjct: 196 KGDDLSRKPGAKSGAPPPAQLTWLALEPITGRTHQLRVHCAAMGWPIFGDNIY-----GN 250

Query: 280 FTSPIQNKLYLHARYMDLP 298
                + +L+LHAR + +P
Sbjct: 251 GPRFGEPRLHLHAREIVIP 269


>gi|225028057|ref|ZP_03717249.1| hypothetical protein EUBHAL_02326 [Eubacterium hallii DSM 3353]
 gi|224954657|gb|EEG35866.1| hypothetical protein EUBHAL_02326 [Eubacterium hallii DSM 3353]
          Length = 237

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 62/212 (29%), Positives = 101/212 (47%), Gaps = 12/212 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLT--HRLDQETS 155
           +++ED  + V  KPAG+ VQ        +   LK  +    +  ++P L   HRLD+   
Sbjct: 9   IVFEDDAVIVCEKPAGMPVQSDHTRDMDVLTILKHHIFEEQNSEEEPYLAVVHRLDRPVG 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V+A+T+ AA +L+E  +    +K Y ++V G  +       ++LLK      +   V
Sbjct: 69  GLMVLAKTKEAAANLSEQIQNFEFEKNYQAVVCGNLREDFGTFEDYLLKNGKT--NKTEV 126

Query: 216 VKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           VK    GA  A   +++IDC   K     W+ +  HTGR HQ+RV     G  + GD KY
Sbjct: 127 VKAGTPGARKAELDYELIDCIETKEGVLTWILVILHTGRHHQIRVQFASRGLGLYGDTKY 186

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              F+   T     ++ L++  +   HP  G 
Sbjct: 187 NPKFQK--TKKKYTEIGLYSTRISFNHPVTGE 216


>gi|312622224|ref|YP_004023837.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202691|gb|ADQ46018.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
          Length = 312

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/262 (25%), Positives = 123/262 (46%), Gaps = 21/262 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV+ +   +++++  K  YP I    + K+LR G++ V           Q GQV+R    
Sbjct: 6   VVDKELAGVKVEKAIKKKYPTIPMSVIFKMLRRGEIIVSFLPA------QKGQVLRFGDT 59

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           ++       E + L+      K  + LK   +YED  I V +KP GI     S   Y + 
Sbjct: 60  VS----FEIEDRFLEH-----KKEEILK---VYEDDNIVVIDKPYGIPSHPDSNNEYSVV 107

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            +++    +K + P+L HRLD+ T+G++++A+ R     + +    R I K Y  +    
Sbjct: 108 SWIEDNYSNKEELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRAIIKKYLCITKKA 167

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              +   + ++L K S     Y+    Q+  G +  ++ +K++         ++++  TG
Sbjct: 168 DLPESGVLVHYLKKDSKKSKVYISDFPQD--GYSEVVTAYKIVRQ-KDDLQLVDVEIKTG 224

Query: 251 RTHQLRVHALHMGCPIVGDHKY 272
           +THQ+R    H+G  I+GD KY
Sbjct: 225 KTHQIRAQLAHIGLCILGDSKY 246


>gi|164687826|ref|ZP_02211854.1| hypothetical protein CLOBAR_01470 [Clostridium bartlettii DSM
           16795]
 gi|164603101|gb|EDQ96566.1| hypothetical protein CLOBAR_01470 [Clostridium bartlettii DSM
           16795]
          Length = 307

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 114/233 (48%), Gaps = 24/233 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  + V    G         I YH    L S   +   +P + HR+D
Sbjct: 87  IVYEDDDLLIVNKPQDMVVHPAPGNYENTLVNAILYHCKDNLSSI--NGVIRPGIVHRID 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSGIL++A+   A   L E  +   I + Y  +  G+ K  K    +  + ++     
Sbjct: 145 KDTSGILMIAKNNNAHNSLAEQLKDHSITREYEFICHGVVKEDK-ITVDRPIGRNPKDRL 203

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +VK  ++    A++HF+VI  + + F  ++    TGRTHQ+RVHA  +G P++GD  
Sbjct: 204 KMAIVKDGKR----AVTHFEVIKRY-ENFTHMKANLETGRTHQIRVHAASIGHPLLGDPI 258

Query: 272 YCANFKGNFTSPIQNK-LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           Y     G   S I+ K   LHAR +   HP   + ++  + LP + V+  + +
Sbjct: 259 Y-----GPKNSKIKCKGQTLHARKLGFIHPTTKQYVEFNSDLPDYFVEILNKI 306


>gi|121534815|ref|ZP_01666635.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
 gi|121306610|gb|EAX47532.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
          Length = 301

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 85/299 (28%), Positives = 137/299 (45%), Gaps = 53/299 (17%)

Query: 32  INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I+   L+KI R GQV ++   VK F   + SG  + I                 DS +  
Sbjct: 24  ISLTQLRKIKRQGQVLINGHPVKSFQTPVSSGDEISI-------------DYGDDSCLTP 70

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS---------GIAYHIDGFLKSWVDSKG 141
            K    +   ++YED  + + NKPAG+ V   S         GI Y        ++ SKG
Sbjct: 71  MK----MPLHIVYEDDFLLIVNKPAGLLVHPTSDPTEPTLAHGILY--------YLHSKG 118

Query: 142 QKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                   HRLD+ TSG++ +A+     QH       + ++++Y ++V GIP +    I 
Sbjct: 119 ALGAFHPIHRLDRNTSGLVAIAK-HPHIQHALSGGGAKGLKRLYLAVVTGIPSSLMGRI- 176

Query: 200 NWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                 + IG     ++K+  +     AI+ ++V+  F+     +E++  TGRTHQ+RVH
Sbjct: 177 -----DAPIGRHPNSIIKRVVRSDGQPAITLYRVLSTFSMA-SLVELELLTGRTHQIRVH 230

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
             H+G P++GD  Y     G  T  I+ +  LHA  +   HP   + L +T+PLP  + 
Sbjct: 231 LSHIGHPLLGDDLY-----GGATDLIRRQ-ALHAASLSFRHPATDKVLTLTSPLPPDLA 283


>gi|157165235|ref|YP_001466990.1| RNA pseudouridine synthase family protein [Campylobacter concisus
           13826]
 gi|112800923|gb|EAT98267.1| hypothetical RNA pseudouridine synthase aq_1758 (RNA-uridine
           isomerase) (RNA pseudouridylate synthase) [Campylobacter
           concisus 13826]
          Length = 252

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 71/260 (27%), Positives = 121/260 (46%), Gaps = 46/260 (17%)

Query: 79  KEQKILDSSVNLTKHSDFL-----KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           K QK++ +   +++++ F      K  +++ED  +   NKPA I+ +  S I        
Sbjct: 33  KGQKVMIARALMSENTKFSIEEMPKPSVIFEDENLIAINKPAAITSEKISQI-------- 84

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                    K  L HRLD++TSG+L++ +    A      F+  +++KIY + V GI   
Sbjct: 85  --------YKFPLLHRLDKDTSGVLLLVKNDEFASLAINEFKKMKVEKIYVAAVRGI--M 134

Query: 194 KKECIANW-LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +E + N  +L   +  G +  + K  ++    AIS    +    +K   +++   TGRT
Sbjct: 135 SEEVVVNEPILTIKNKNGAFSKISKDGKE----AISEISPLMVVGKK-TLVKVVIKTGRT 189

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           HQ+RVH   +  PIVGD KY  N          N+++LHA  + L        +  AP+P
Sbjct: 190 HQIRVHLASLNLPIVGDEKYGKNR--------ANRMFLHAYSIALLD-----YKFKAPIP 236

Query: 313 AHMVKTWDSLGFKYDRNLYI 332
               + ++SLGF+      I
Sbjct: 237 ----REFNSLGFELSNKFEI 252


>gi|78045806|ref|YP_361981.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
 gi|78034236|emb|CAJ21881.1| Pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
          Length = 238

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 111/238 (46%), Gaps = 31/238 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D  + V +KPAG+ V   S +A   D FL   +  +  KP  L HRLD+ TSG L+
Sbjct: 10  ILYQDDVLAVVDKPAGLMVHD-SKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLL 68

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R +A  L ++     ++K Y ++  G P  ++     +++     GG    V K  
Sbjct: 69  LAFDRDSASALGKALMAGEVEKDYLTVCRGWPAEER-----FIVDHDLDGGPGKPVKKP- 122

Query: 220 EKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 123 ------AVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGD 176

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT-----WD 320
             +       +F     +++ LHA  +  PHP GG R+ ITAPL A   K      WD
Sbjct: 177 TSHGDGRHNRSFRMLGIHRMLLHAERLGFPHPGGGRRISITAPLDAEFTKACALFGWD 234


>gi|117928240|ref|YP_872791.1| ribosomal large subunit pseudouridine synthase D [Acidothermus
           cellulolyticus 11B]
 gi|117648703|gb|ABK52805.1| ribosomal large subunit pseudouridine synthase D [Acidothermus
           cellulolyticus 11B]
          Length = 314

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 109/224 (48%), Gaps = 18/224 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+D  I V +KPAG++       +G + +   +    +       ++  + HRLD  T
Sbjct: 89  VVYDDPDIVVVDKPAGVAAHPSPGWEGATVLGALLAAGYRVATSGAAERQGIVHRLDVGT 148

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA++  A   L  +FR R + KIY +LV G P   +  I       + I    VH
Sbjct: 149 SGLMVVAKSERAYSTLKRAFREREVHKIYHALVQGHPDPVRGTI------DAPIDRHPVH 202

Query: 215 VVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             +     G   +++H+  ++        LE++  TGRTHQ+RVH   +  P VGD  Y 
Sbjct: 203 EFRFAVVAGGKPSVTHYTTLEALPAA-SLLEIELETGRTHQIRVHMAAIRHPCVGDLMYG 261

Query: 274 ANFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           A+    F + +  ++ +LHA  +   HP  G  +++T+  P  +
Sbjct: 262 AD--PTFAARLGLDRQWLHAVRLRFTHPILGSPIELTSSYPPDL 303


>gi|332308153|ref|YP_004436004.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332175482|gb|AEE24736.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 218

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 111/218 (50%), Gaps = 22/218 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D  + V NKP+G+    G  +  H D  L+  V       ++ HRLD  TSG+LV+
Sbjct: 16  IVFKDEHLLVLNKPSGLLTVPGKALE-HKDS-LELRVQRVYPTAKIVHRLDMATSGLLVM 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A  +   + L++ F +R+ +K Y + V+G    ++       I +W  +   +      V
Sbjct: 74  ALDKDTHRQLSKQFELRQTRKTYIARVYGEVSGERGSVDLPLICDWPNRPKQM------V 127

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +Q  K +   ++H++V++        +E+ P TGR+HQLRVH L +G PI+GD  Y  +
Sbjct: 128 CQQRGKPS---LTHWRVLE-RNDNSTRMELTPVTGRSHQLRVHMLSLGHPILGDRLYAHS 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                      +L LHA+ +   HP     L+++AP+P
Sbjct: 184 DALTMA----QRLQLHAQTLGFTHPVTELPLELSAPVP 217


>gi|332366862|gb|EGJ44603.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1059]
          Length = 295

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 115/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++          +  F+K++   +G   Q+  +  RLD++TSG+
Sbjct: 78  VVYEDEHFLVLDKPAGVASIPSVNHTNTMANFVKAYYIGQGYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +KVI+ F   +  ++++ HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKVIEQFGDVYL-VDIRLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLEHGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|293611211|ref|ZP_06693509.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292826462|gb|EFF84829.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 221

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 67/207 (32%), Positives = 102/207 (49%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ 
Sbjct: 18  ILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R ++K Y +LV G    +       I +W  +   I    VH  
Sbjct: 76  AKHRDAEVAVSKMFQARTVKKHYIALVQGQVAQEGSVEVPLITDWENRPRQI----VHF- 130

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G +       +I         + ++P TGR+HQLRVH +H+G PI+GD  Y    
Sbjct: 131 ---ELGKHAKTLFQPLIYDEKNNQSRVLLEPVTGRSHQLRVHMMHIGHPIMGDKLYHPEP 187

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           K  F     N++ LHA Y+   HP  G
Sbjct: 188 K-RFRL---NRMALHAAYLAFQHPLNG 210


>gi|257462225|ref|ZP_05626642.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
 gi|317059894|ref|ZP_07924379.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
 gi|313685570|gb|EFS22405.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
          Length = 318

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 136/310 (43%), Gaps = 60/310 (19%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV---VRIPP 69
           +  ++  RLD + K   P      L+K++  G V+ D+K +  N +   G+    V IP 
Sbjct: 13  QEKDQGKRLDLFLKEQLPEATRSYLEKLIAEGYVKCDEKVITKNGKKLKGKEAIQVSIP- 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                               +   ++ L   ++YED  + V NK A + V    G     
Sbjct: 72  ----------------EEEEMKMEAEKLPLDIVYEDEYLLVINKAANMVVHPALGNYTGT 115

Query: 128 HIDGFL----KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++  L    +S  D  G  +P + HRLD++T+G++VVA+       L   F+ + IQK 
Sbjct: 116 LVNALLYYCKESLSDVNGTLRPGIVHRLDKDTTGLIVVAKNNQIHHRLALMFQEKTIQKT 175

Query: 183 YWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG----------ANYAISHFK 231
           Y ++V G   + KKE             GD V ++ ++ K              A+SH+K
Sbjct: 176 YLAIVKGRFSEEKKE-------------GDLVTLIARDRKDRKKMAVSQSHGKKAVSHYK 222

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYL 290
           V+    +K   +E+   TGRTHQ+RVH  ++  PI+GD  Y           +Q ++  L
Sbjct: 223 VL-WNGEKHSLVEVNIKTGRTHQIRVHMKYLNHPILGDAVYG-------QEDLQCSRQML 274

Query: 291 HARYMDLPHP 300
           HA  ++  HP
Sbjct: 275 HAYRLEFVHP 284


>gi|229177799|ref|ZP_04305172.1| Pseudouridine synthase [Bacillus cereus 172560W]
 gi|228605590|gb|EEK63038.1| Pseudouridine synthase [Bacillus cereus 172560W]
          Length = 307

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 115/230 (50%), Gaps = 32/230 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGKI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           D  Y    K        +   LHA  ++  HP     +++  P P ++ K
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPTNLNK 297


>gi|327489667|gb|EGF21458.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1058]
          Length = 295

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 115/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++   +G   Q+  +  RLD++TSG+
Sbjct: 78  VVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRQGYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVQGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +K+I+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKIIEQFGDVYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDELYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLEHGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|298713781|emb|CBJ27153.1| ribosomal large subunit pseudouridine synthase A [Ectocarpus
           siliculosus]
          Length = 332

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 68/200 (34%), Positives = 102/200 (51%), Gaps = 27/200 (13%)

Query: 129 IDGFLK-----------SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +DG LK           + V S+  + R  HRLDQ+TSG++V+A T  AA+ +   FR R
Sbjct: 143 VDGHLKKEVGPGVDCLLTRVQSRWPEARHVHRLDQDTSGLVVMALTVEAAREMCRQFRER 202

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVI 233
              K Y +++ G + K  K       L+      D  +  KQ    EKG N A ++++ I
Sbjct: 203 VPSKTYTAVLEGRMAKTPKSGEVTAKLRP-----DTDNRPKQMFCEEKG-NEAHTNWERI 256

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
               +   W++  P TGRTHQ+R+HA+H+G P++GD  Y    +G   S    +L LHAR
Sbjct: 257 K-RKEDRTWVDFTPVTGRTHQIRMHAVHLGHPVMGDSLY-GTPEGTAKS---ERLLLHAR 311

Query: 294 YMDLPHPEGGR-LQITAPLP 312
            +  PHP  G  ++   P P
Sbjct: 312 RISFPHPRTGETVEFECPPP 331


>gi|168703294|ref|ZP_02735571.1| RNA pseudouridylate synthase [Gemmata obscuriglobus UQM 2246]
          Length = 275

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 110/225 (48%), Gaps = 25/225 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-------DSKGQKPRLTHRLDQE 153
           +++ED+ + V +KP+G+       +A   +    ++V            +P + HRLD++
Sbjct: 64  IVHEDAHLVVIDKPSGLLT-----VATESEKLDTAFVRLSDYLRARNAGRPFVVHRLDRD 118

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+L+ AR+      L  ++    + K Y ++V G P++ +  + N+L +   +    V
Sbjct: 119 TSGLLLFARSAEVRDQLQGNWE--ELTKTYLAVVEGRPESSEGGVENYLTEGRDL---RV 173

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               +       A S + V       +  +E++  TGR HQ+RVH   +GCP+ GD  Y 
Sbjct: 174 RASPRPGPDGKRAASRYTVRQTRG-GYSLVEVEIETGRKHQIRVHLAGLGCPVAGDKMY- 231

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
               G  T P++ +L LHA  +   HP    RL++ APLP+ + +
Sbjct: 232 ----GATTDPVR-RLGLHAWRLSFDHPFTLERLELEAPLPSALAR 271


>gi|324991124|gb|EGC23058.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK353]
          Length = 295

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 115/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++   +G   Q+  +  RLD++TSG+
Sbjct: 78  VIYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRQGYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKVIERFGDVYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLEHGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|87123579|ref|ZP_01079430.1| probable pseudouridine synthase [Synechococcus sp. RS9917]
 gi|86169299|gb|EAQ70555.1| probable pseudouridine synthase [Synechococcus sp. RS9917]
          Length = 314

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 83/315 (26%), Positives = 134/315 (42%), Gaps = 49/315 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L  W  + Y H +    ++ L+SG++         N R+  G VV       A    I+ 
Sbjct: 10  LSAWLADRYRHSSAATWRQRLQSGEL-------GLNGRLLQGDVV------VAAGDRIRW 56

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDS 139
           Q+       + +H   L     ++D  + V NKP+G+ V    G   H +   L  W   
Sbjct: 57  QRPPWVEPAIPEHWQTL-----HDDGDVLVINKPSGLPVMPAGGFLVHTLSHQLVLWSRE 111

Query: 140 KGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFR-------MRRIQKIYWSLVWGI 190
           +G+   P+  HRL + TSG+LV AR   +   L+   R           +K+Y +L   +
Sbjct: 112 QGEPLAPKPVHRLGRFTSGLLVCARRPESRAWLSRLLRDSTADGAASACRKVYRALTEPL 171

Query: 191 PKNKKECIANWLLKKSH-----IG-------GDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           P +       W L +S      IG       G+       +   A  + S F +++   +
Sbjct: 172 PPD-------WPLGESREVTVAIGRHPHPLLGEIWCAADPSVATALPSRSSFTLLERRPE 224

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDL 297
             C +E+   +GR HQ+R+HA   G P++GD  Y      +  S P +   +LHA  + L
Sbjct: 225 S-CLVEVVIASGRPHQIRIHAATAGAPLLGDPLYLPGGGASDQSLPGEGGYHLHAHRLQL 283

Query: 298 PHPEGGRLQITAPLP 312
             P+GG L + APLP
Sbjct: 284 ASPDGGLLDLEAPLP 298


>gi|116513066|ref|YP_811973.1| pseudouridylate synthase, 23S RNA-specific [Lactococcus lactis
           subsp. cremoris SK11]
 gi|116108720|gb|ABJ73860.1| Pseudouridylate synthase, 23S RNA-specific [Lactococcus lactis
           subsp. cremoris SK11]
          Length = 290

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 66/217 (30%), Positives = 104/217 (47%), Gaps = 24/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  + V NKP G+   G +     +   +++ ++   Q   + HRLDQ TSG ++ 
Sbjct: 83  ILYEDEHLIVVNKPEGMKTHGNTADEIALQNHVEAAIN---QNVFVVHRLDQATSGAVLF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ +     L + F   +I + Y +LV G    +   I   + +  H     + + K  +
Sbjct: 140 AKNQFVLPILGKMFEENKIHREYLALVAGHFLEETFTINQAIGQNRHEKNKRI-ISKHGQ 198

Query: 221 KGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           K    AI+H ++I  F  K    C L+    TGRTHQ+RVH   +  PI+GD  Y    K
Sbjct: 199 K----AITHVQLIQNFTDKSLVKCILD----TGRTHQIRVHLSSLAHPIIGDALYGQ--K 248

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                    +L LHA  + +PHP   + L I+AP P+
Sbjct: 249 STL------RLMLHAESIIIPHPFTNQLLNISAPSPS 279


>gi|197336758|ref|YP_002158083.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
 gi|197314010|gb|ACH63459.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
          Length = 568

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 68/206 (33%), Positives = 101/206 (49%), Gaps = 24/206 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  + V NKPA      G  I+  +   +++ + ++ G  P + HRLD  TSG+LV
Sbjct: 367 IVYEDDVLVVVNKPAEFLSVSGKYISDSVHARIQARYPNATG--PLIVHRLDMSTSGLLV 424

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +  T  + + + + F  R ++K Y +L+ G  +     I   L       GD     +Q 
Sbjct: 425 LTLTAESNKQVQKQFIERTVEKRYTALLEGNIETDNGTINLPLT------GDMEDRPRQM 478

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCA 274
              K    A +H++VI     K   + + PHTGRTHQLRVH  H   +  PIVGD  Y  
Sbjct: 479 VCHKSGRKAETHYQVI-AQEGKRTKVHLYPHTGRTHQLRVHCAHQAGLNTPIVGDDLY-- 535

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
            FK        N+L+LHA Y+   HP
Sbjct: 536 GFKA-------NRLHLHAGYLKFKHP 554


>gi|254832286|ref|ZP_05236941.1| hypothetical protein Lmon1_13109 [Listeria monocytogenes 10403S]
 gi|284801300|ref|YP_003413165.1| hypothetical protein LM5578_1050 [Listeria monocytogenes 08-5578]
 gi|284994442|ref|YP_003416210.1| hypothetical protein LM5923_1004 [Listeria monocytogenes 08-5923]
 gi|284056862|gb|ADB67803.1| hypothetical protein LM5578_1050 [Listeria monocytogenes 08-5578]
 gi|284059909|gb|ADB70848.1| hypothetical protein LM5923_1004 [Listeria monocytogenes 08-5923]
          Length = 296

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 75/312 (24%), Positives = 148/312 (47%), Gaps = 38/312 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE +E+ + L  + K+ +     +   K    G++ V+ +       ++ G  VR+    
Sbjct: 7   VETEEDGLLLRTFLKSKHISKQLLTAVKFGADGKIEVNSEEQNVLYHVKVGDKVRLTFPT 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              N     +++L    NL          +++ED  + + NKPAG++        YH +G
Sbjct: 67  EQQN-----ERLLAEYTNLD---------IVFEDDFLLIINKPAGMASIPSQ---YHPNG 109

Query: 132 FLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + ++V    +   LT+      RLD+ETSG++++A+ R A   L+   +   +++ Y +
Sbjct: 110 SVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLE 244
            + G+   +K  I      ++ IG   V ++++       YA ++++V+  + + F  + 
Sbjct: 170 FISGVLVEQKGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY-RAFDHVA 222

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP    
Sbjct: 223 IQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTEE 276

Query: 305 -LQITAPLPAHM 315
            +    PLPA M
Sbjct: 277 YMAFDLPLPADM 288


>gi|215403396|ref|ZP_03415577.1| pseudouridylate synthase [Mycobacterium tuberculosis 02_1987]
 gi|215426884|ref|ZP_03424803.1| pseudouridylate synthase [Mycobacterium tuberculosis T92]
 gi|215430434|ref|ZP_03428353.1| pseudouridylate synthase [Mycobacterium tuberculosis EAS054]
 gi|218753261|ref|ZP_03532057.1| pseudouridylate synthase [Mycobacterium tuberculosis GM 1503]
 gi|219557451|ref|ZP_03536527.1| pseudouridylate synthase [Mycobacterium tuberculosis T17]
 gi|254550560|ref|ZP_05141007.1| hypothetical protein Mtube_08877 [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260200601|ref|ZP_05768092.1| hypothetical protein MtubT4_10875 [Mycobacterium tuberculosis T46]
 gi|297634109|ref|ZP_06951889.1| hypothetical protein MtubK4_08307 [Mycobacterium tuberculosis KZN
           4207]
          Length = 294

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 112/228 (49%), Gaps = 14/228 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTH 148
           D     +LY D  I   +KPA ++     G     + G L +    + + G   R  + H
Sbjct: 63  DIEGMTILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRITTSGVHERQGIVH 122

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++VVA +  A   L  +F+ R + K Y +LV G P      I   + +  H 
Sbjct: 123 RLDVGTSGVMVVAISERAYTVLKRAFKYRTVDKRYHALVQGHPDPSSGTIDAPIGR--HR 180

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           G ++   + +N +   ++++H+  ++ F      L++   TGRTHQ+RVH   +  P  G
Sbjct: 181 GHEWKFAITKNGR---HSLTHYDTLEAFVAA-SLLDVHLETGRTHQIRVHFAALHHPCCG 236

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y A+ K      + ++ +LHAR +   HP +G R++I +P PA +
Sbjct: 237 DLVYGADPKLAKRLGL-DRQWLHARSLAFAHPADGRRVEIVSPYPADL 283


>gi|325688842|gb|EGD30850.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK115]
          Length = 291

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 66/202 (32%), Positives = 94/202 (46%), Gaps = 22/202 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK---Q 218
           +       L      R I + YW+LV G   +KK      L+ K  IG D     K   +
Sbjct: 141 KNPFVLPILNRLLEKREISREYWALVQGKFPSKK------LIYKDKIGRDRHDRRKRLVE 194

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +KG  YA +H   I  F Q    ++ Q  TGRTHQ+RVH  H G P++GD  Y    KG
Sbjct: 195 PQKGL-YAETHVTRIKQFGQA-ALVKCQLKTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG 252

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                   +L LHA  +   HP
Sbjct: 253 --------RLMLHAHRLTFTHP 266


>gi|296102445|ref|YP_003612591.1| pseudouridylate synthase [Enterobacter cloacae subsp. cloacae ATCC
           13047]
 gi|295056904|gb|ADF61642.1| pseudouridylate synthase [Enterobacter cloacae subsp. cloacae ATCC
           13047]
          Length = 228

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 69/227 (30%), Positives = 110/227 (48%), Gaps = 17/227 (7%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I+DS +    H D     +L++D  + + NKP+G+    G     ++D      V S   
Sbjct: 4   IIDSFIAPPCHDDIE---ILWQDEHLLLINKPSGLLSLSGKN-PQNLDSVHYRLVQSFPG 59

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD  TSG++V+AR +     L + F  R ++K+Y +L+ G  +N  E I +  
Sbjct: 60  C-TLVHRLDFGTSGLMVIARNKPINAALCQQFSQRSVEKVYSALLCGHLEN-NEGIIDAP 117

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----AQKFCWLEMQPHTGRTHQLRVH 258
           + K       + +   N K A    S ++V++      A     +E+ P TGRTHQLR+H
Sbjct: 118 IAKDPALFPLMSICAVNGKPAR---SRYRVVERLYQNAAMPLTRVELTPETGRTHQLRIH 174

Query: 259 ALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              +G PI+G   Y    + G+ T+P   +L LHA  ++  HP  G 
Sbjct: 175 CQLLGHPILGCDLYGGRTWPGSGTTP---RLMLHASQLNFIHPVSGE 218


>gi|260771763|ref|ZP_05880681.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           metschnikovii CIP 69.14]
 gi|260613055|gb|EEX38256.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           metschnikovii CIP 69.14]
          Length = 324

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 85/330 (25%), Positives = 147/330 (44%), Gaps = 45/330 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +   RLD+     +   +   L++ L  G++ V+   V K   ++  G+      
Sbjct: 10  TVKESQLGQRLDQAVAELFVDFSRSRLKEWLLDGKITVNGTVVTKPRTKVMGGEC----- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            I  L  +  EQ+     + L          ++YED  I V NKP    V  G+G     
Sbjct: 65  -ITVLAELEDEQRWEAQDIPLN---------IVYEDDDILVINKPRDFVVHPGAGTPDRT 114

Query: 129 -IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L  +     + PR  + HRLD++T+G++VVA+T  A   L    + R I + Y +
Sbjct: 115 VLNALLFHY-PPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRDLQKRNITREYEA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQKFC 241
           +  G      +  A  ++ K  IG    H  K+     N     A++H++V + F ++  
Sbjct: 174 IAIG------KMTAGGMIDKP-IGR---HSTKRTLMAVNQMGKPAVTHYRVAEHF-REHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLHAR 293
            + ++  TGRTHQ+RVH  ++  P++GD  Y    +         T  I+  ++  LHA 
Sbjct: 223 RIRLRLETGRTHQIRVHMAYLQHPLLGDSAYGGRARIPKGATPELTEMIRAFDRQALHAV 282

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            +   HP  G  L+  AP+P  MV   ++L
Sbjct: 283 MLKFEHPITGEELEFHAPVPDDMVIMTEAL 312


>gi|225028084|ref|ZP_03717276.1| hypothetical protein EUBHAL_02354 [Eubacterium hallii DSM 3353]
 gi|224954554|gb|EEG35763.1| hypothetical protein EUBHAL_02354 [Eubacterium hallii DSM 3353]
          Length = 422

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 93/376 (24%), Positives = 157/376 (41%), Gaps = 71/376 (18%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +   EE  R D++   + P  +   L K+LR   ++++ K+ +   ++ +G +++
Sbjct: 1   MKEITITKREEGQRFDKFLIKYLPGASSGFLHKMLRKKNIKLNGKKAEGREKLTAGDLIQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVN------------------------------------- 89
           I      L      Q   D S                                       
Sbjct: 61  IFFSDETLEKFQNPQSGRDDSYEADSSMENHKSDRGFGQSGRNRQPDREQAKVYTKDRAG 120

Query: 90  -------LTKHSDFLKSIL--LYEDSKIYVFNKPAGISVQGGSGIA-----YHIDGFLKS 135
                  LTK    L+  +  LY    I VF+KPAG+  Q           Y ID  +++
Sbjct: 121 NGGQERKLTKEERELRKQVRVLYSSEDILVFHKPAGMLSQRAKASDDSLNDYLIDYCIQT 180

Query: 136 WVDSK----GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            + SK    G +P + +RLD+ TSGI++   +    Q L    R R + K Y  LV G  
Sbjct: 181 GIISKEELAGFRPSIANRLDRNTSGIVLAGISIKGLQRLASMLRERTLGKYYLCLVEGKV 240

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K     IA +L K+     + V + K+  +GA+Y  + +KV+     K   L+++  TG+
Sbjct: 241 KEDAR-IAGYLTKEEK--NNKVSLHKEKAEGASYIETEYKVLKS-TDKASLLKIRLITGK 296

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-----NKLYLHARYMDLPHPEGG--R 304
           +HQ+R H   +G P+ GD+KY      +F + I+     N   LH+  + +P   G    
Sbjct: 297 SHQIRGHLASVGHPVFGDYKYGNR---DFNNQIKWKDGVNYQLLHSYELVVPEGTGELFG 353

Query: 305 LQITAPLPA--HMVKT 318
           L I  P+P   H V+T
Sbjct: 354 LHIIDPVPEVFHKVQT 369


>gi|77361542|ref|YP_341117.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity
           [Pseudoalteromonas haloplanktis TAC125]
 gi|76876453|emb|CAI87675.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 233

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 62/202 (30%), Positives = 106/202 (52%), Gaps = 15/202 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + + NKP+ +    G     H D  +   V+      ++ HRLD  TSGIL +
Sbjct: 31  ILYQDEDLLIVNKPSELLTVPGKD-PKHADCLI-GRVNRVFPTAKIVHRLDMATSGILCL 88

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A  +AA +H++  F+ R   K Y + ++G  + +   +   L+       D+ +  KQ  
Sbjct: 89  AMNKAAHRHVSMQFQERETAKRYIARIYGQLEAQTGSVDLPLI------CDWPNRPKQMV 142

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    +++HFK+++        +E+ P TGR+HQLRVH L +G PI+GD  Y A+ + 
Sbjct: 143 DHENGKPSLTHFKILE-REPHATRVELTPITGRSHQLRVHMLSLGHPILGDRLY-AHKEA 200

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
              +P   +L LHA+ + L HP
Sbjct: 201 LAAAP---RLQLHAQMLSLKHP 219


>gi|260587780|ref|ZP_05853693.1| pseudouridylate synthase [Blautia hansenii DSM 20583]
 gi|260542045|gb|EEX22614.1| pseudouridylate synthase [Blautia hansenii DSM 20583]
          Length = 337

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 79/337 (23%), Positives = 147/337 (43%), Gaps = 35/337 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +VV+  E   RLD++   +        L K+LR   + ++ K+   N ++Q    ++
Sbjct: 1   MKQLVVKEIESGQRLDKFLGKYLKEAPKSFLYKMLRKKNITLNGKKATGNEKLQPNDEIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--- 123
           +    + L     E+K           S   +  ++YE++ +   NKP G+  Q      
Sbjct: 61  LFLSDDTLEKFCGEEK----------SSSRTELDIVYENNHVLFVNKPVGMLSQKAEKED 110

Query: 124 -GIAYHIDGFLK-----SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  +I G+L      +  D +  +P + +RLD+ TSGI+   +T    Q +++ F+ R
Sbjct: 111 VSLVEYITGYLLEEKFLTKEDLRTFRPGVCNRLDRNTSGIVAAGKTVQGLQEMSQWFKER 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G    +   +  +L K      + V V ++  +G+    + ++ +    
Sbjct: 171 NLHKYYLTLVKG-KVERPAHVKGYLWKDEK--KNKVAVFQEKREGSLPIETKYEPLGISK 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLHA 292
                L+++  TGR+HQ+R H   +G P++GD KY +     NF+  +    Q    LHA
Sbjct: 228 NGDTLLKVELLTGRSHQIRSHLAGLGHPVIGDWKYGSKEKNENFRKKYGIEFQ---LLHA 284

Query: 293 RYMDLPHPEG-----GRLQITAPLPAHMVKTWDSLGF 324
             +  P  EG         ITA +P    K     G 
Sbjct: 285 WKLSFPKTEGILKELSLKTITADVPEKFQKALKGEGL 321


>gi|206967734|ref|ZP_03228690.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
 gi|206736654|gb|EDZ53801.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
          Length = 307

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 115/230 (50%), Gaps = 32/230 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGKI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFRKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           D  Y    K        +   LHA  ++  HP     +++  P P ++ K
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPTNLNK 297


>gi|152987872|ref|YP_001347260.1| pseudouridine synthase RluA [Pseudomonas aeruginosa PA7]
 gi|150963030|gb|ABR85055.1| pseudouridine synthase RluA [Pseudomonas aeruginosa PA7]
          Length = 211

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 66/215 (30%), Positives = 114/215 (53%), Gaps = 15/215 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D  + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSG++V
Sbjct: 8   IVHQDDALLVVDKPTLLLSVPGRAD--DNKDCLVTRLQENGYPEARIVHRLDWETSGLMV 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + + L+  F  R  +K Y +L WG+P+     I   L  +        HVV  +
Sbjct: 66  LARDADSHRELSRQFHDRETEKAYTALCWGLPELDSGRIE--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ ++V++   +++  +E+ P TGR+HQLRVH L +G P++GD  Y AN +  
Sbjct: 122 FEHGRHALTFWRVLERH-ERWSRVELTPITGRSHQLRVHMLSIGHPLLGDRLY-ANPEAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG---RLQITAPL 311
                 ++L LHA  + L HP  G   R +  AP 
Sbjct: 180 AA---HDRLCLHASLLCLTHPRSGERLRFESAAPF 211


>gi|28849821|gb|AAN64577.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gordonii]
          Length = 290

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 94/201 (46%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + IQ+ YW+LV G      + I    + K  IG D  +  K+  +
Sbjct: 141 KNPFVLPILNRLLENKDIQREYWALVDG------KFIEKSRIYKDKIGRDRHNRRKRLVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F QK   ++ Q  TGRTHQ+RVH  H G P+VGD  Y    +G 
Sbjct: 195 NKHGQYAETHVTRLKSFGQK-TLVKCQLKTGRTHQIRVHLSHHGFPLVGDPLYHPQPQG- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 253 -------RLMLHAYRLSFVHP 266


>gi|108759188|ref|YP_631900.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108463068|gb|ABF88253.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 234

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 113/232 (48%), Gaps = 20/232 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+E   + V +KP G+ V  G      +   L++    + QK  + HRLD++TSG LV 
Sbjct: 6   ILFEGGGVLVVDKPPGMLVIPGREGGPSLRELLET---QRRQKIFVVHRLDRDTSGALVF 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG--DYVHVVKQ 218
           A   A  + L+ +F   +++K Y +LV G         A  ++    + G    + V + 
Sbjct: 63  ALDAAVHRALSGAFETGKVRKRYVALVEG------RVEAPQMVDAPLVAGRKGRMRVARP 116

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC----- 273
            +  A  + +  + ++ F ++   +E +P TGRTHQ+RVH L +G P++ DH+Y      
Sbjct: 117 GDTDAKASRTRVRPVETF-ERASLVEAEPLTGRTHQIRVHLLSLGHPLLVDHQYGREAPL 175

Query: 274 --ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSL 322
              +  G   S + ++  LHA  ++ P   G   + + AP+P  M +  + L
Sbjct: 176 TEKDLGGEGDSVVLSRTPLHAARVEWPALAGVEARAVEAPVPEDMARARELL 227


>gi|289426144|ref|ZP_06427890.1| pseudouridine synthase, RluA family [Propionibacterium acnes SK187]
 gi|289153309|gb|EFD02024.1| pseudouridine synthase, RluA family [Propionibacterium acnes SK187]
          Length = 306

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 78/294 (26%), Positives = 137/294 (46%), Gaps = 32/294 (10%)

Query: 37  LQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +  ++  G V +D ++V + + R+ +GQ++ +      L   +    I    V  T+   
Sbjct: 30  ISSLIEDGGVFLDGQQVSRASVRVATGQMLDVD-----LCDPVATPSITPQIVEGTR--- 81

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQG-----GSGIAYHID--GFLKSWVDSKGQKPRLTH 148
                ++++DS I V +KPAG++        G  +  H+   GF  S      ++  +  
Sbjct: 82  -----IIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS-TSGAPERQGIVQ 135

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++VVA++  A   L ++FR R + K+Y +LV G P      I       + I
Sbjct: 136 RLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI------DAPI 189

Query: 209 GGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           G D+ H  K     G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P  
Sbjct: 190 GRDHRHDWKMAIVDGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAIKHPCC 248

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           GD  Y  +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 249 GDPLYGCDPALAKELGLERQ-WLHAGELSFTHPGSGEWVTFHADLPADLQNALD 301


>gi|254525135|ref|ZP_05137190.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219722726|gb|EED41251.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 247

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 112/234 (47%), Gaps = 15/234 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           LL+ D ++ V NKPAG+ V   S +A   D FL   +  +  +P  L HRLD+ TSG L+
Sbjct: 20  LLHLDERLAVVNKPAGLMVHD-SKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGCLL 78

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R  A  L ++     + K Y ++  G P        +W +     GG    V K  
Sbjct: 79  LAFDRDTASALGKALMGGEVLKDYLTVCRGWPAE-----LSWQVDHDLDGGPGKPVKKPA 133

Query: 220 ----EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               ++ A   +S   + +  + ++  L  QP TGR  Q+R H  H+   ++GD  +  +
Sbjct: 134 ITDFQRLATGELS-VPIGEFSSSRYALLRCQPQTGRFRQIRRHLKHLSHHMIGDTSH-GD 191

Query: 276 FKGNFTSPIQN--KLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            + N    +Q   ++ LHA  +  PHP+GG + + APL A   K  D  G++ D
Sbjct: 192 GRHNRIFRMQGVHRMLLHAERLRFPHPDGGVVDVRAPLDAGFQKALDLFGWQVD 245


>gi|171059743|ref|YP_001792092.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170777188|gb|ACB35327.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
          Length = 256

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 103/225 (45%), Gaps = 27/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  + V  KPAG+    G G   H+   + + V +      + HRLD  TSG++V+
Sbjct: 46  ILHHDDSLLVVRKPAGLLSVPGRG--EHLQDCVAARVQAIWPDALIVHRLDMATSGLMVM 103

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-----ANWLLKKSHIGGDYVHV 215
           AR  AA + L  +F  R + K Y ++V G        +     A+W  +           
Sbjct: 104 ARGPAAQRALGSAFEHRSVTKQYVAVVAGDVAGDAGSVDLPLCADWPNRPRQ-------- 155

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-------LEMQPHTGRTHQLRVHALHMGCPIVG 268
            K +      +++H++      +           LE++P TGR+HQLRVH L +G PI+G
Sbjct: 156 -KVDAAMGRPSLTHWRRATPAHEGSTTGDIDRTRLELEPVTGRSHQLRVHLLALGHPILG 214

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           D  Y  +           +L LHA  + LPHP GG + + +  PA
Sbjct: 215 DTLYAPDAVQRMAP----RLLLHASRIALPHPAGGGICVFSDPPA 255


>gi|119470041|ref|ZP_01612846.1| 23S rRNA pseudouridine synthase [Alteromonadales bacterium TW-7]
 gi|119446751|gb|EAW28024.1| 23S rRNA pseudouridine synthase [Alteromonadales bacterium TW-7]
          Length = 325

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 88/341 (25%), Positives = 154/341 (45%), Gaps = 44/341 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPV 70
           V  D    RLD+     +P  +   ++  +   ++ VD + +     ++  G+V+ +   
Sbjct: 11  VPTDLGGKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEILNTPRTKLLGGEVLNVETT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           I A       ++ L  +++L          ++YED  I V NKP G+ V  G+G      
Sbjct: 71  IEA------PREYLAQNIDLN---------IVYEDDHILVINKPMGLVVHPGAGNPDGTV 115

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWS 185
           ++  L  + D     PR  + HRLD++T+G++VVA+T  A  HL ++ + R    + Y +
Sbjct: 116 LNALLHHYPDII-NVPRAGIVHRLDKDTTGLMVVAKTIQAQTHLVKALQKRENFTREYEA 174

Query: 186 LVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           L  G        ++ I     +++H+    VH     E G   AI+H++V + F +    
Sbjct: 175 LCNGTMTAGGMVEKPIGRHATQRTHMA---VH-----EMG-KPAITHYRVAEKF-RAHTR 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARY 294
           L ++  TGRTHQ+RVH  ++  P++GD  Y    +    +  Q         +  LHA  
Sbjct: 225 LRLRLETGRTHQIRVHMAYLNHPLIGDQSYNGRPRPPKGATPQLFELLRSFKRQALHAVK 284

Query: 295 MDLPHPEGGRLQI-TAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           + + HP  G +    AP+P  MV+   +L      N  I R
Sbjct: 285 LSIAHPITGEMMTWQAPIPDDMVEMTLALREDTQANPDIDR 325


>gi|59713667|ref|YP_206442.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           ES114]
 gi|59481915|gb|AAW87554.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           ES114]
          Length = 576

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 66/206 (32%), Positives = 101/206 (49%), Gaps = 24/206 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  + + NKP       G  I+  +   +++ + ++ G  P + HRLD  TSG+LV
Sbjct: 375 IVYEDDVLVIVNKPVEFLSVSGKYISDSVHARIQARYPNATG--PLIVHRLDMSTSGLLV 432

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +  T  + + + + F  R ++K Y +L+ G  +     I   L       GD     +Q 
Sbjct: 433 LTLTAESNKQVQKQFIERTVEKRYTALLEGNIETDNGTINLPLT------GDMEDRPRQM 486

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCA 274
            N K    A +H++VI     K   + + PHTGRTHQLRVH  H   +  PIVGD  Y  
Sbjct: 487 VNHKSGRKAETHYQVI-AQEGKRTKVHLYPHTGRTHQLRVHCAHQAGLNTPIVGDDLY-- 543

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
            FK        ++L+LHA Y+   HP
Sbjct: 544 GFKA-------DRLHLHAGYLKFKHP 562


>gi|15894548|ref|NP_347897.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|15024193|gb|AAK79237.1|AE007639_10 Pseudouridylate synthase family protein, yabo B.subtilis ortholog
           [Clostridium acetobutylicum ATCC 824]
 gi|325508681|gb|ADZ20317.1| Pseudouridylate synthase family protein [Clostridium acetobutylicum
           EA 2018]
          Length = 299

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 107/219 (48%), Gaps = 16/219 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGI 157
           ++YEDS I V NKPA + V       +  +   L  +   KG+    RL +RLD +TSG+
Sbjct: 83  IVYEDSDIIVLNKPANMIVHPTKNYQHGTLSNGLLYYFREKGENCIVRLVNRLDMDTSGL 142

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA+ + +   L    ++   +K Y ++V G   + K  I   + K+         + +
Sbjct: 143 VLVAKNQFSHMALARDMKLDTFKKEYIAVVRGNLSSLKGTIDKPIYKEEE-----EPIRR 197

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             +     +I+HF+V++ + +    +++   TGRTHQ+RVH   +G PI+GD  Y     
Sbjct: 198 TIDDRGQESITHFEVVERY-KNADKVKLVLETGRTHQIRVHLSSIGNPIIGDSLYGEE-- 254

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
               S +  +  LHA  +  PHP  GR+  I   LP  +
Sbjct: 255 ----SELIKRQALHAFKLQFPHPRDGRIVNIEVKLPEDI 289


>gi|16803009|ref|NP_464494.1| hypothetical protein lmo0969 [Listeria monocytogenes EGD-e]
 gi|224502716|ref|ZP_03671023.1| hypothetical protein LmonFR_09374 [Listeria monocytogenes FSL
           R2-561]
 gi|254827914|ref|ZP_05232601.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL N3-165]
 gi|16410371|emb|CAC99047.1| lmo0969 [Listeria monocytogenes EGD-e]
 gi|258600295|gb|EEW13620.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL N3-165]
          Length = 296

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 75/312 (24%), Positives = 148/312 (47%), Gaps = 38/312 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE +E+ + L  + K+ +     +   K    G++ V+ +       ++ G  VR+    
Sbjct: 7   VETEEDGLLLRTFLKSKHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKVGDKVRLTFPT 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              N     +++L    NL          +++ED  + + NKPAG++        YH +G
Sbjct: 67  EQQN-----ERLLAEYTNLD---------IVFEDDFLLIINKPAGMASIPSQ---YHPNG 109

Query: 132 FLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + ++V    +   LT+      RLD+ETSG++++A+ R A   L+   +   +++ Y +
Sbjct: 110 SVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLE 244
            + G+   +K  I      ++ IG   V ++++       YA ++++V+  + + F  + 
Sbjct: 170 FISGVLVEQKGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY-RAFDHVA 222

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP    
Sbjct: 223 IQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTEE 276

Query: 305 -LQITAPLPAHM 315
            +    PLPA M
Sbjct: 277 YMAFDLPLPADM 288


>gi|269966247|ref|ZP_06180336.1| tRNA pseudouridine synthase C [Vibrio alginolyticus 40B]
 gi|269829162|gb|EEZ83407.1| tRNA pseudouridine synthase C [Vibrio alginolyticus 40B]
          Length = 256

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 70/261 (26%), Positives = 123/261 (47%), Gaps = 31/261 (11%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
            + + S+ ++  ++Y+D      NKPAG+ V       +     +++  D  GQ     H
Sbjct: 5   KIARSSEPVELEIVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLH 64

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS-- 206
           RLD+ TSG+LV A +   A  +   F   +++K Y ++V G    ++E + ++ LK    
Sbjct: 65  RLDRPTSGVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGW--IEEEGVLDYALKVELD 122

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLR 256
            I   +       EK A  A++ +K +               ++C +EM+P TGR HQLR
Sbjct: 123 KIADKFA----SQEKEAQEAVTEYKPLAKVEVPYSTGKFPTTRYCLVEMKPKTGRKHQLR 178

Query: 257 VHALHMGCPIVGDH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
            H  H+  PIVGD      K+   ++  F S   ++L LHA  +   HP   +  +   +
Sbjct: 179 RHMAHLRHPIVGDTTHGDGKHNKLYRTEFDS---HRLLLHASELRFVHPFTDQEIV---M 232

Query: 312 PAHMVKTWDSL--GFKYDRNL 330
            A++ +TW  L   F++D ++
Sbjct: 233 TANLDETWQQLFTRFEWDESM 253


>gi|168334458|ref|ZP_02692629.1| putative pseudouridylate synthase [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 304

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 80/322 (24%), Positives = 148/322 (45%), Gaps = 43/322 (13%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI---PPV 70
           N+  ++R+D++     P      +QK +  G + ++ K      RI++G  +     PP 
Sbjct: 10  NNIADIRVDKFLTEQLPQYTRSYIQKQIELGLLLINGKVAPARTRIKTGDTIEFTIAPP- 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                   +E  I  S + L          ++YEDS I + NKP  + V   +G  ++ D
Sbjct: 69  --------REVDITPSEIKLD---------IIYEDSDILIVNKPKNMVVHPSAG--HYND 109

Query: 131 GFLKSWV----DS----KGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + + +    DS     G+ +P + HR+D++T+G+L+VA+   +   L++  +   I++
Sbjct: 110 TLVNALLFYAKDSLSGINGEIRPGIVHRIDKDTTGLLMVAKNDHSHVFLSDLLKDHNIER 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV+G  K     I   + +        + +V+   +    A++  +V++ F     
Sbjct: 170 KYNALVYGNIKEDFFTIDRPIARNPK-DRKKMAIVENGRR----AVTECRVLERFGNA-T 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+   TGRTHQ+RVH   +G P++GD  Y  + K  F    Q    LHAR +   HP 
Sbjct: 224 HIELSLQTGRTHQIRVHLTSIGHPLLGDPLYGRS-KHLFNLQTQ---MLHARVLGFIHPS 279

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + ++  + LP   + T   L
Sbjct: 280 SQQFMRFESVLPTEFLHTIGRL 301


>gi|328542499|ref|YP_004302608.1| Pseudouridylate synthase for 23S rRNA [polymorphum gilvum
           SL003B-26A1]
 gi|326412246|gb|ADZ69309.1| Pseudouridylate synthase for 23S rRNA [Polymorphum gilvum
           SL003B-26A1]
          Length = 223

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 66/218 (30%), Positives = 108/218 (49%), Gaps = 22/218 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  I V  KP+G+    G G   H D  L+S    +  + R+ HRLD +TSG++V+
Sbjct: 21  VLHADDDILVVVKPSGLLSVPGKGEG-HAD-CLESRARERFAQARIVHRLDMDTSGVMVL 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A   AA +HL   F  RR  K Y + +WG  + +        + +W  +          +
Sbjct: 79  ALNAAAHRHLGLQFERRRTAKAYVARLWGELEGEAGEVDLPLVCDWPNRP---------M 129

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K   +    A++ ++V+    +    + + P TGR+HQLRVH L +G PI+GD+ Y  +
Sbjct: 130 QKVCVETGRPALTRWQVL-ARQRGVTRVRLMPVTGRSHQLRVHMLSLGHPILGDNLYAHD 188

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              +      ++L LHA  +++ HP +G R    AP P
Sbjct: 189 DALSAA----DRLQLHAEDLEIHHPADGRRCAFHAPCP 222


>gi|303287646|ref|XP_003063112.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226455748|gb|EEH53051.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 417

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 96/355 (27%), Positives = 144/355 (40%), Gaps = 81/355 (22%)

Query: 20  RLDRWFKNHYP------HINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI----- 67
           RLD +   H P       I    +   +++G V V+     K + R+  G V+R+     
Sbjct: 87  RLDAYIATHAPPSEGGGGITRARVVASIKAGLVDVNGVVARKASERVSPGDVIRVALKPT 146

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP   A   I  + K                    YED  + V NKPAG+ V    G   
Sbjct: 147 PPTEAAPEDIPLDVK--------------------YEDEHVLVVNKPAGMVVHPAPG--- 183

Query: 128 HIDGFLKSWV-----------------DSKG-QKPRLTHRLDQETSGILVVARTRAAAQH 169
           H  G L + V                  + G  +P + HRLD+ TSG++VVA+  AA   
Sbjct: 184 HSSGTLVNAVLFRCGCPAMRVASGNANTADGVARPGIVHRLDKGTSGLIVVAKNEAAHAS 243

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ----NEKGANY 225
           L E F  R +++ Y ++  G P+  +  +       + IG D    +K       +G   
Sbjct: 244 LCEQFATRVVRRRYLAICLGSPEQGEGRV------DAPIGRDPRDRLKMAVVRRSRGGRR 297

Query: 226 AISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---------N 275
           A S++KV    A+    L E +  TGRTHQ+RVHA  +G PI+GD  Y            
Sbjct: 298 AASNYKVRASLARGNASLVEWRLETGRTHQIRVHAREIGIPILGDETYGGAGNGAEERLR 357

Query: 276 FKGNFT-------SPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            KG  T       + I  +  LHA+ +   HP  G  +   A  P    + +++L
Sbjct: 358 SKGAMTPAEAKRVAKISRRPMLHAQTLGFRHPRTGEEMDFKAEPPEDFAEVFEAL 412


>gi|332290332|ref|YP_004421184.1| tRNA pseudouridine synthase C [Gallibacterium anatis UMN179]
 gi|330433228|gb|AEC18287.1| tRNA pseudouridine synthase C [Gallibacterium anatis UMN179]
          Length = 232

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 65/201 (32%), Positives = 98/201 (48%), Gaps = 29/201 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++ +     V NKP G+SV      QG +       G  + W         L HRLD+ T
Sbjct: 13  IVAQTENFVVINKPCGVSVHKDDNEQGLTTQLAEQLGVEQVW---------LVHRLDKST 63

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+ A  R AA  L+  F   ++QKIY +L  G PK K+  I   +++          
Sbjct: 64  SGLLLCALNRQAAAELSAQFAAHQVQKIYLALATGKPKKKQGLIKGDMIRSRR------A 117

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + K +   +N AI+ F  I C +    ++ ++P TG+THQLRV    +G PI+GD  Y  
Sbjct: 118 MWKLSPSCSNPAITRFYSISCESGLRLFV-LKPQTGKTHQLRVAMKSLGSPILGDPLY-- 174

Query: 275 NFKGNFTSPIQNKLYLHARYM 295
              G+  SP  ++ YLHA  +
Sbjct: 175 ---GD-KSP-ADRCYLHAALL 190


>gi|148978562|ref|ZP_01815014.1| 23S rRNA pseudouridine synthase D [Vibrionales bacterium SWAT-3]
 gi|145962351|gb|EDK27632.1| 23S rRNA pseudouridine synthase D [Vibrionales bacterium SWAT-3]
          Length = 324

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 87/340 (25%), Positives = 156/340 (45%), Gaps = 51/340 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV- 70
           V++ +   RLD+     +   +   +++ L  G+V+VD            G+V+  P V 
Sbjct: 11  VKSSQLGQRLDQAVAELFTDFSRSRIKEWLLDGKVQVD------------GEVITKPRVK 58

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +     II + ++ D        +  +   +++ED  + V NKP    V  G+G     D
Sbjct: 59  VMGGEEIILQAELEDEE---RWEAQDIPLDIVFEDEHLLVINKPRDFVVHPGAGTP---D 112

Query: 131 GFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + + +        + PR  + HRLD++T+G++VVA+T  A   L  +   RRI + Y 
Sbjct: 113 GTVLNALLHHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-----NEKGANYAISHFKVIDCFAQK 239
           ++  G      +  A  +++K    G   H  K+     NE G   A++H++V + F ++
Sbjct: 173 AIAIG------KMTAGGMVEK----GISRHATKRTLMAVNETG-KPAVTHYRVAEHF-RE 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLH 291
              + ++  TGRTHQ+RVH  ++  P++GD  Y    +         T  I+  ++  LH
Sbjct: 221 HTRIRLRLETGRTHQIRVHMSYLQHPLLGDIAYGGRARIPKGASEELTKMIRAFDRQALH 280

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
           A  +   HP  G  ++  AP+P  MV   ++L      NL
Sbjct: 281 AVMLKFVHPITGEEVEFHAPVPNDMVVMAEALRVDARDNL 320


>gi|118476866|ref|YP_894017.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|196046511|ref|ZP_03113736.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|225863254|ref|YP_002748632.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|229183584|ref|ZP_04310807.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|118416091|gb|ABK84510.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|196022695|gb|EDX61377.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|225789436|gb|ACO29653.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|228599827|gb|EEK57424.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
          Length = 307

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 110/226 (48%), Gaps = 22/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++YED  + + NKP  +      +GG G   ++  F    +     K R  HRLD++T+G
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAF-HYQMKGLETKVRHIHRLDKDTTG 145

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D  H  
Sbjct: 146 GVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRDRHHAT 199

Query: 217 KQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           K+  + KG + AI+++KV + F  Q    + +Q  TGRTHQ+RVH  + G P+VGD  Y 
Sbjct: 200 KRRVSPKG-DQAITYYKVEEYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYG 258

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
              K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 259 GQTK------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDT 298


>gi|154174351|ref|YP_001408557.1| ribosomal large subunit pseudouridine synthase C [Campylobacter
           curvus 525.92]
 gi|112803057|gb|EAU00401.1| ribosomal large subunit pseudouridine synthase C [Campylobacter
           curvus 525.92]
          Length = 252

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 104/225 (46%), Gaps = 39/225 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  +   NKPA                F+ S   S+  K  L HRLD+ETSG+L++
Sbjct: 60  VIFEDENLLAINKPA----------------FITSEKISQMYKFPLLHRLDKETSGVLLL 103

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +    A+   E F+  R++KIY + V GI   +       L  KS   G  +  + ++ 
Sbjct: 104 VKNEEFAKRAIEEFKHMRVEKIYIAAVRGILSEETRVSEPILTIKSK--GAAISKISKDG 161

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K A   ++   V+     K   +++   TGRTHQ+R+H   +  PI+GD KY  N     
Sbjct: 162 KEAVSDVTPLMVVG----KKTLVKVAIKTGRTHQIRLHLASINAPIIGDEKYGKNR---- 213

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                 ++YLHA ++ L    G + +   P      K ++ LGF+
Sbjct: 214 ----AKRMYLHAYFIALL---GYKFKADVP------KDFNELGFE 245


>gi|297184482|gb|ADI20596.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium EBAC_27G05]
          Length = 311

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 70/274 (25%), Positives = 132/274 (48%), Gaps = 43/274 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ +D  N+RLD+     +   +   +Q+ + +G + ++ + ++  +++Q G  + + P+
Sbjct: 7   IISSDFHNIRLDQAATALFEDYSRSQIQRWIEAGNLLINGESLRPKDKVQEGDELSLDPI 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
           +   N +  E +  D  +N+            +E+ +  + NKP G+ +  G+G      
Sbjct: 67  LE--NRVSWEAE--DIPLNIH-----------HEEDEFLIINKPYGLVMHPGAGCNNGTL 111

Query: 125 ---IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              +A+H    +        Q PR  + HRLD++TSG+LV+A+T        E  + R I
Sbjct: 112 ANALAFHYPQLI--------QLPRCGIVHRLDKDTSGLLVIAKTEKFRNFFVEKLQNREI 163

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQ 238
            K Y +LV G      + I ++ ++++ I  D  + +K         AISH  +I  F  
Sbjct: 164 FKEYEALVVG------QVIGSFSIEQA-IERDPRNRIKMRTTDFGREAISHISLIK-FYN 215

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  + ++  TGRTHQ+RVH  H   PI+GD  Y
Sbjct: 216 GYSHVAIEIETGRTHQIRVHLSHHKLPIIGDRTY 249


>gi|238918644|ref|YP_002932158.1| hypothetical protein NT01EI_0701 [Edwardsiella ictaluri 93-146]
 gi|238868212|gb|ACR67923.1| conserved hypothetical protein [Edwardsiella ictaluri 93-146]
          Length = 235

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 64/177 (36%), Positives = 94/177 (53%), Gaps = 14/177 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D+ I V NKP+G+ SV G   +  H D  + + + ++       HRLD  TSG+LV
Sbjct: 32  ILYQDAHIIVVNKPSGLLSVPGR--LPEHQDSII-TRIQAQFPDAESVHRLDMATSGVLV 88

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+ A + L   FR R  +K Y + VWG P   +  I   L+       D+ +  KQ 
Sbjct: 89  VALTKDAERELKRQFREREPKKNYVARVWGHPPQDQGVIDLPLI------CDWPNRPKQK 142

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              E+G   A + ++V+   A     + + P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 143 VCFEQG-KPAQTEYQVLAHDADGTARVLLTPITGRSHQLRVHLLALGHPILGDGFYA 198


>gi|145343527|ref|XP_001416372.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144576597|gb|ABO94665.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 332

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 56/180 (31%), Positives = 89/180 (49%), Gaps = 25/180 (13%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +P + HRLD+ TSG++VVA+  +A   L E F  R +++ Y +++ G+P   K  I    
Sbjct: 146 RPGIVHRLDKGTSGVMVVAKDASAHNSLCEQFAARVVRRKYVAILSGVPSPSKGRI---- 201

Query: 203 LKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHA 259
             ++ IG D    ++    + G  +A S+++VI   A     L E +  TGRTHQ+RVHA
Sbjct: 202 --EAPIGRDPRDRLRMAVTQGGGRFAASNYEVIATLANGNASLVEWRLETGRTHQIRVHA 259

Query: 260 LHMGCPIVGDHKYCANFKGNFTS----------------PIQNKLYLHARYMDLPHPEGG 303
            H+G PI+GD  Y        ++                   ++  LHAR +   HP+ G
Sbjct: 260 KHIGHPILGDDTYGGGGGAAVSALSRYGVFDVKEAKALMSTIDRPMLHARTLGFTHPQSG 319


>gi|52144044|ref|YP_082785.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           E33L]
 gi|51977513|gb|AAU19063.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           E33L]
          Length = 307

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 116/235 (49%), Gaps = 32/235 (13%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +    S +GG G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPSEKGGMGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV + F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEEYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           D  Y    K        ++  LHA  ++  HP     +++  P P  +  T  + 
Sbjct: 254 DVLYGGGTK------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDTMKAF 302


>gi|86142154|ref|ZP_01060664.1| ribosomal large subunit pseudouridine synthase D [Leeuwenhoekiella
           blandensis MED217]
 gi|85830906|gb|EAQ49363.1| ribosomal large subunit pseudouridine synthase D [Leeuwenhoekiella
           blandensis MED217]
          Length = 203

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 60/189 (31%), Positives = 92/189 (48%), Gaps = 17/189 (8%)

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTES 173
           +QG       +   +KS++  K  KP      + HRLD+ TSGI++ ART  A   L + 
Sbjct: 1   MQGDKTGDKPLSEVVKSYIAEKYNKPGAVYLGVVHRLDRPTSGIVIFARTSKALPRLNKL 60

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV--VKQNEKGANYAISHFK 231
           F  +  +K YW+LV   P    + + ++L +       Y H+  V  ++KG    I  ++
Sbjct: 61  FAAKEAKKTYWALVKESPPKTSDRLVHYLKRNPKQNKSYSHINEVSDSKKG----ILEYR 116

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V+      +  LE+  HTGR HQ+R     +GCPI GD KY     G   S     ++LH
Sbjct: 117 VLKEL-NNYTLLEVDLHTGRHHQIRSQLSAIGCPIKGDLKY-----GFDRSNPDGSIHLH 170

Query: 292 ARYMDLPHP 300
           +R + L HP
Sbjct: 171 SRKLTLVHP 179


>gi|257457444|ref|ZP_05622614.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
 gi|257445173|gb|EEV20246.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
          Length = 246

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 107/222 (48%), Gaps = 23/222 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKS---WVDSKGQKPRLTHRLDQETS 155
           L+Y D  +   NK AG+ V        A  +D  ++     +     K    HR+D++TS
Sbjct: 8   LIYADDDMVAVNKAAGLLVAADRWDAEAPRLDLLIQKELPQIAPSCNKLYAVHRIDKDTS 67

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GIL+ A    A + L  +F+ R I+K Y  L+ G   ++++   +  L+     GD +H 
Sbjct: 68  GILLYALNAEAHRTLNTAFQNREIKKTYRLLIHG-RVSEEQFTVDLPLRAD---GDALHR 123

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              +++    A++HF V++ F Q F  LE  P TGRTHQ+R H    G PIV D  Y + 
Sbjct: 124 TVVDKRRGKEAVTHFTVLETFRQ-FSLLEACPVTGRTHQIRAHLAAAGYPIVCDSLYGSG 182

Query: 276 -----------FKGNFTS--PIQNKLYLHARYMDLPHPEGGR 304
                      ++G+  +  P+  +L LHA  ++  HP  G+
Sbjct: 183 KPVLLSELKQRWRGDVYTEQPLIGRLALHAYRLEGVHPRSGQ 224


>gi|254504534|ref|ZP_05116685.1| RNA pseudouridine synthase superfamily [Labrenzia alexandrii
           DFL-11]
 gi|222440605|gb|EEE47284.1| RNA pseudouridine synthase superfamily [Labrenzia alexandrii
           DFL-11]
          Length = 200

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/205 (30%), Positives = 103/205 (50%), Gaps = 21/205 (10%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D+ + V +KP+G+    G  + +     +++       + R+ HRLD +TSG++V+A   
Sbjct: 2   DADLLVVDKPSGLLSVPGKALEH--SDCIEARAQQTHPEARIVHRLDMDTSGVMVLAMNA 59

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWG-IPKNKK----ECIANWLLKKSHIGGDYVHVVKQN 219
            A +HL   F  R+ +K Y + VWG I KN        + +W  +   +   + H     
Sbjct: 60  QAHRHLGLQFERRKTEKTYVAEVWGQIEKNAGVIDLPLVCDWPNRPKQM-VSFEH----- 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 A++ ++VI    ++   + + P TGR+HQLRVH L +G PIVGD ++ A     
Sbjct: 114 ---GKPALTRWQVI-MRNERTTRVRLFPFTGRSHQLRVHMLSLGHPIVGD-RFYATGDAL 168

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR 304
             SP   +L LHA  + L HP GG+
Sbjct: 169 EASP---RLRLHAESLTLHHPTGGK 190


>gi|46581593|ref|YP_012401.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           vulgaris str. Hildenborough]
 gi|46451016|gb|AAS97661.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           vulgaris str. Hildenborough]
 gi|311235236|gb|ADP88090.1| pseudouridine synthase [Desulfovibrio vulgaris RCH1]
          Length = 390

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 84/330 (25%), Positives = 137/330 (41%), Gaps = 52/330 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +VV  +E   +L ++    +  +    L + +RSGQVR +  R K  +R++ G  VR+
Sbjct: 4   QAIVVTREEAGQKLLQFLARRF-ALPQAMLHRWIRSGQVRRNGGRCKPFDRLEMGDEVRV 62

Query: 68  PPVINALNHIIKEQKILDSS-------------VNLTKHS----DFLKS----------- 99
           PP   +++       +  +S                ++H     D ++            
Sbjct: 63  PPFAASMSERADVGPVSANSDAVRNVPDAAAPRPAPSRHDRDGHDAMQPSRQRRPKADTS 122

Query: 100 --------ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                    ++ E   +++F+KPAG++V  G+G    +   L          P   HRLD
Sbjct: 123 LQPARPLPPVVAETPDLFIFDKPAGLAVHPGTGHTDSLTTRLAQHFAKAPFMPTPAHRLD 182

Query: 152 QETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           ++TSG+L+VAR+ A  + L E+F     + K Y + V G  +       +  L K     
Sbjct: 183 RDTSGLLLVARSYAMLRTLHEAFASHDALVKEYLAWVAGCWQPAAPVTLHDRLSKGAEAS 242

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCF--AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +  V   +E GA  A +    + C    Q    L +  HTGRTHQ+RV     G P++G
Sbjct: 243 GFERVASDDE-GAEAACT----VRCLLREQHRSLLLVTLHTGRTHQIRVQLSRRGHPLLG 297

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           D KY          P      LHA  + LP
Sbjct: 298 DRKYGG-------PPRMGGFLLHAVRLCLP 320


>gi|312140126|ref|YP_004007462.1| tRNA-pseudouridine synthase i [Rhodococcus equi 103S]
 gi|311889465|emb|CBH48782.1| tRNA-pseudouridine synthase I [Rhodococcus equi 103S]
          Length = 308

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 80/317 (25%), Positives = 141/317 (44%), Gaps = 30/317 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  + MR+D         ++   +  +   G V VD      ++R+ +G 
Sbjct: 1   MRETRSMPVPDGLDGMRVDAGLARLL-GLSRTAVATLTEEGAVLVDGAAAGKSDRLSAGT 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGG 122
            +              E ++ +    LT  ++ ++ + +LY D  I   +KP G++    
Sbjct: 60  WL--------------EVELPEPPRPLTIEAEPVEGMEILYADDDIVAVDKPVGVAAHAS 105

Query: 123 SG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G     + G L +    + + G   R  + HRLD  TSG++VVA +  A   L  +F+ 
Sbjct: 106 VGWTGPTVIGGLAAAGFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTVLKRAFKQ 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I K Y +LV G P      I   + +  H   D+   V  + K    +++H+  ++ F
Sbjct: 166 RTIDKRYHALVQGHPDPSSGTIDAPIGR--HRSNDWKFAVTADGK---PSVTHYDTVEAF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q    L++   TGRTHQ+RVH   +  P  GD  Y A+ +      ++ + +LHAR + 
Sbjct: 221 -QAASLLDIHLETGRTHQIRVHFSALRHPCCGDLTYGADPRLAERLGLERQ-WLHARSLG 278

Query: 297 LPHPEGGR-LQITAPLP 312
             HP  G  ++IT+  P
Sbjct: 279 FAHPADGHWVEITSDYP 295


>gi|228920104|ref|ZP_04083453.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228839560|gb|EEM84852.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 307

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 114/228 (50%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    ++++    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAEKGGTGTLANLVAFH---FQMQGLETR---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGKI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y    K        +   LHA  ++  HP     +++  P PA +
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPAKL 295


>gi|254229488|ref|ZP_04922902.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262393515|ref|YP_003285369.1| tRNA pseudouridine synthase C [Vibrio sp. Ex25]
 gi|151937953|gb|EDN56797.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262337109|gb|ACY50904.1| tRNA pseudouridine synthase C [Vibrio sp. Ex25]
          Length = 256

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 70/261 (26%), Positives = 123/261 (47%), Gaps = 31/261 (11%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
            + + S+ ++  ++Y+D      NKPAG+ V       +     +++  D  GQ     H
Sbjct: 5   EIARSSEPVELEIVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLH 64

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS-- 206
           RLD+ TSG+LV A +   A  +   F   +++K Y ++V G    ++E + ++ LK    
Sbjct: 65  RLDRPTSGVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGW--IEEEGVLDYALKVELD 122

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLR 256
            I   +       EK A  A++ +K +               ++C +EM+P TGR HQLR
Sbjct: 123 KIADKFA----SQEKEAQEAVTEYKPLAKVEVPYSTGKFPTTRYCLVEMKPKTGRKHQLR 178

Query: 257 VHALHMGCPIVGDH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
            H  H+  PIVGD      K+   ++  F S   ++L LHA  +   HP   +  +   +
Sbjct: 179 RHMAHLRHPIVGDTTHGDGKHNKLYRTEFDS---HRLLLHASELRFVHPFTDQDIV---M 232

Query: 312 PAHMVKTWDSL--GFKYDRNL 330
            A++ +TW  L   F++D ++
Sbjct: 233 TANLDETWQQLFTRFEWDESM 253


>gi|315223482|ref|ZP_07865338.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga ochracea F0287]
 gi|314946517|gb|EFS98509.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga ochracea F0287]
          Length = 226

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 62/208 (29%), Positives = 105/208 (50%), Gaps = 18/208 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +   NK  G  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 12  VLYEDNHVIAVNKRVGDIVQGDKTGDTPLSDIVKQYLKQKYNKPGEVFLGVVHRLDRPTT 71

Query: 156 GILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDY 212
           G+++ A+T  A   L   F  ++ +QK YW+LV   P  +++ + +WL++  K +    Y
Sbjct: 72  GVVLFAKTSKALARLNTMFSNKQEVQKTYWALVDAKPPVEEDTLTHWLVRNEKQNKSVAY 131

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              ++Q++K    A+ H+K++  + +++  LE+   TGR HQ+R     +G  I GD KY
Sbjct: 132 NKEMQQSKK----AVLHYKLLKSY-ERYYLLEIDLITGRHHQIRAQLAAIGLHIKGDLKY 186

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
            A       S     + LHA  +   HP
Sbjct: 187 GAK-----RSNPDGGICLHAYSLSFVHP 209


>gi|313791774|gb|EFS39885.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL110PA1]
 gi|313802139|gb|EFS43371.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL110PA2]
 gi|313838471|gb|EFS76185.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL086PA1]
 gi|314963072|gb|EFT07172.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL082PA1]
 gi|315077536|gb|EFT49594.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL053PA2]
 gi|315080320|gb|EFT52296.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL078PA1]
 gi|327452876|gb|EGE99530.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL092PA1]
          Length = 306

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 76/295 (25%), Positives = 138/295 (46%), Gaps = 34/295 (11%)

Query: 37  LQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +  ++  G V +D ++V + + R+ +GQ++ +               + D  V  +    
Sbjct: 30  ISSLIEDGGVFLDGQQVSRASVRVATGQMLDV--------------DLCDPVVTPSITPQ 75

Query: 96  FLKSI-LLYEDSKIYVFNKPAGISVQG-----GSGIAYHID--GFLKSWVDSKGQKPRLT 147
            ++ + ++++DS I V +KPAG++        G  +  H+   GF  S      ++  + 
Sbjct: 76  IVEGMRIIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS-TSGAPERQGIV 134

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
            RLD  TSG++VVA++  A   L ++FR R + K+Y +LV G P      I       + 
Sbjct: 135 QRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI------DAP 188

Query: 208 IGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           IG D+ H  K     G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P 
Sbjct: 189 IGRDHRHDWKMAIVDGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAIKHPC 247

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            GD  Y  +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 248 CGDPLYGCDPALAKELGLERQ-WLHAGELSFTHPGSGEWVTFHADLPADLQNALD 301


>gi|28210692|ref|NP_781636.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           tetani E88]
 gi|28203130|gb|AAO35573.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           tetani E88]
          Length = 320

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 75/283 (26%), Positives = 125/283 (44%), Gaps = 51/283 (18%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   R+D++ +     +    + K +R G V+++ K+VK    +  G +V         
Sbjct: 8   NESGQRMDKFLRKMLTDVPLGAIYKSIRKGDVKINGKKVKEKYSLNLGDIV--------- 58

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSI-------LLYEDSKIYVFNKPAGISVQGGSGIAY 127
                  +I D   N  KH+DF K+I       + YED  + +  K  G+ V      + 
Sbjct: 59  -------EIRDIKTNAEKHNDF-KAIEGANELKVTYEDQNMIIVEKKPGVLVHSDKKNSD 110

Query: 128 -HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  ++ S++  KG           P   +RLD+ T+GI++  +   + + L +  R R
Sbjct: 111 PTLTDYVLSYLYDKGDYVPEEEITFTPASCNRLDRNTAGIIIFGKNYESLKDLNQMIRER 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD------YVHVVKQNEKGANYAISHFK 231
            + K Y +LV G  K+         L K+HI  D      Y+H  K+ +K +       K
Sbjct: 171 HVDKYYQALVCGKIKDG--------LYKAHIVKDEKSNKSYIH--KEPKKNSKEIEMEVK 220

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            I      +  LE+Q  TGR+HQ+R H   +G PIVGD KY +
Sbjct: 221 TIQTCGT-YSLLEIQLITGRSHQIRAHLSSLGNPIVGDKKYGS 262


>gi|15608678|ref|NP_216056.1| hypothetical protein Rv1540 [Mycobacterium tuberculosis H37Rv]
 gi|15841007|ref|NP_336044.1| pseudouridine synthase, RluD-related protein [Mycobacterium
           tuberculosis CDC1551]
 gi|31792726|ref|NP_855219.1| hypothetical protein Mb1567 [Mycobacterium bovis AF2122/97]
 gi|121637461|ref|YP_977684.1| hypothetical protein BCG_1592 [Mycobacterium bovis BCG str. Pasteur
           1173P2]
 gi|148661336|ref|YP_001282859.1| pseudouridine synthase, RluD-related protein [Mycobacterium
           tuberculosis H37Ra]
 gi|148822764|ref|YP_001287518.1| pseudouridylate synthase [Mycobacterium tuberculosis F11]
 gi|224989936|ref|YP_002644623.1| hypothetical protein member of YabO/YceC/YfiL family [Mycobacterium
           bovis BCG str. Tokyo 172]
 gi|253799405|ref|YP_003032406.1| hypothetical protein TBMG_02437 [Mycobacterium tuberculosis KZN
           1435]
 gi|254231769|ref|ZP_04925096.1| conserved hypothetical protein member of yabO/yceC/yfiI family
           [Mycobacterium tuberculosis C]
 gi|254364412|ref|ZP_04980458.1| conserved hypothetical protein member of yabO/yceC/yfiI family
           [Mycobacterium tuberculosis str. Haarlem]
 gi|289442994|ref|ZP_06432738.1| pseudouridylate synthase [Mycobacterium tuberculosis T46]
 gi|289447151|ref|ZP_06436895.1| conserved hypothetical protein [Mycobacterium tuberculosis CPHL_A]
 gi|289554668|ref|ZP_06443878.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN 605]
 gi|289569575|ref|ZP_06449802.1| conserved hypothetical protein [Mycobacterium tuberculosis T17]
 gi|289574224|ref|ZP_06454451.1| pseudouridylate synthase [Mycobacterium tuberculosis K85]
 gi|289745296|ref|ZP_06504674.1| conserved hypothetical protein [Mycobacterium tuberculosis 02_1987]
 gi|289750107|ref|ZP_06509485.1| conserved hypothetical protein [Mycobacterium tuberculosis T92]
 gi|289753627|ref|ZP_06513005.1| conserved hypothetical protein [Mycobacterium tuberculosis EAS054]
 gi|289757656|ref|ZP_06517034.1| pseudouridylate synthase [Mycobacterium tuberculosis T85]
 gi|289761703|ref|ZP_06521081.1| conserved hypothetical protein member of yabO/yceC/yfiI family
           [Mycobacterium tuberculosis GM 1503]
 gi|307079554|ref|ZP_07488724.1| hypothetical protein TMKG_02048 [Mycobacterium tuberculosis
           SUMu011]
 gi|308369471|ref|ZP_07666738.1| hypothetical protein TMBG_00096 [Mycobacterium tuberculosis
           SUMu002]
 gi|308377761|ref|ZP_07668589.1| hypothetical protein TMIG_01808 [Mycobacterium tuberculosis
           SUMu009]
 gi|308378965|ref|ZP_07668871.1| hypothetical protein TMJG_02974 [Mycobacterium tuberculosis
           SUMu010]
 gi|308400685|ref|ZP_07669399.1| hypothetical protein TMLG_00526 [Mycobacterium tuberculosis
           SUMu012]
 gi|313658428|ref|ZP_07815308.1| hypothetical protein MtubKV_08412 [Mycobacterium tuberculosis KZN
           V2475]
 gi|61250913|sp|P0A5T2|Y1540_MYCTU RecName: Full=Uncharacterized RNA pseudouridine synthase
           Rv1540/MT1592; AltName: Full=RNA pseudouridylate
           synthase; AltName: Full=RNA-uridine isomerase
 gi|61250914|sp|P0A5T3|Y1567_MYCBO RecName: Full=Uncharacterized RNA pseudouridine synthase Mb1567;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|1403502|emb|CAA98322.1| CONSERVED HYPOTHETICAL PROTEIN MEMBER OF yabO/yceC/yfiI FAMILY
           [Mycobacterium tuberculosis H37Rv]
 gi|13881216|gb|AAK45858.1| pseudouridine synthase, RluD-related protein [Mycobacterium
           tuberculosis CDC1551]
 gi|31618316|emb|CAD96234.1| CONSERVED HYPOTHETICAL PROTEIN MEMBER OF yabO/yceC/yfiI FAMILY
           [Mycobacterium bovis AF2122/97]
 gi|121493108|emb|CAL71579.1| Conserved hypothetical protein member of yabO/yceC/yfiL family
           [Mycobacterium bovis BCG str. Pasteur 1173P2]
 gi|124600828|gb|EAY59838.1| conserved hypothetical protein member of yabO/yceC/yfiI family
           [Mycobacterium tuberculosis C]
 gi|134149926|gb|EBA41971.1| conserved hypothetical protein member of yabO/yceC/yfiI family
           [Mycobacterium tuberculosis str. Haarlem]
 gi|148505488|gb|ABQ73297.1| pseudouridine synthase, RluD-related protein [Mycobacterium
           tuberculosis H37Ra]
 gi|148721291|gb|ABR05916.1| pseudouridylate synthase [Mycobacterium tuberculosis F11]
 gi|224773049|dbj|BAH25855.1| hypothetical protein member of YabO/YceC/YfiL family [Mycobacterium
           bovis BCG str. Tokyo 172]
 gi|253320908|gb|ACT25511.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN
           1435]
 gi|289415913|gb|EFD13153.1| pseudouridylate synthase [Mycobacterium tuberculosis T46]
 gi|289420109|gb|EFD17310.1| conserved hypothetical protein [Mycobacterium tuberculosis CPHL_A]
 gi|289439300|gb|EFD21793.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN 605]
 gi|289538655|gb|EFD43233.1| pseudouridylate synthase [Mycobacterium tuberculosis K85]
 gi|289543329|gb|EFD46977.1| conserved hypothetical protein [Mycobacterium tuberculosis T17]
 gi|289685824|gb|EFD53312.1| conserved hypothetical protein [Mycobacterium tuberculosis 02_1987]
 gi|289690694|gb|EFD58123.1| conserved hypothetical protein [Mycobacterium tuberculosis T92]
 gi|289694214|gb|EFD61643.1| conserved hypothetical protein [Mycobacterium tuberculosis EAS054]
 gi|289709209|gb|EFD73225.1| conserved hypothetical protein member of yabO/yceC/yfiI family
           [Mycobacterium tuberculosis GM 1503]
 gi|289713220|gb|EFD77232.1| pseudouridylate synthase [Mycobacterium tuberculosis T85]
 gi|308327489|gb|EFP16340.1| hypothetical protein TMBG_00096 [Mycobacterium tuberculosis
           SUMu002]
 gi|308354710|gb|EFP43561.1| hypothetical protein TMIG_01808 [Mycobacterium tuberculosis
           SUMu009]
 gi|308358696|gb|EFP47547.1| hypothetical protein TMJG_02974 [Mycobacterium tuberculosis
           SUMu010]
 gi|308362576|gb|EFP51427.1| hypothetical protein TMKG_02048 [Mycobacterium tuberculosis
           SUMu011]
 gi|308366240|gb|EFP55091.1| hypothetical protein TMLG_00526 [Mycobacterium tuberculosis
           SUMu012]
 gi|323719988|gb|EGB29100.1| hypothetical protein TMMG_00801 [Mycobacterium tuberculosis
           CDC1551A]
 gi|326903170|gb|EGE50103.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           tuberculosis W-148]
 gi|328459155|gb|AEB04578.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN
           4207]
          Length = 308

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 112/228 (49%), Gaps = 14/228 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTH 148
           D     +LY D  I   +KPA ++     G     + G L +    + + G   R  + H
Sbjct: 77  DIEGMTILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRITTSGVHERQGIVH 136

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++VVA +  A   L  +F+ R + K Y +LV G P      I   + +  H 
Sbjct: 137 RLDVGTSGVMVVAISERAYTVLKRAFKYRTVDKRYHALVQGHPDPSSGTIDAPIGR--HR 194

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           G ++   + +N +   ++++H+  ++ F      L++   TGRTHQ+RVH   +  P  G
Sbjct: 195 GHEWKFAITKNGR---HSLTHYDTLEAFVAA-SLLDVHLETGRTHQIRVHFAALHHPCCG 250

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y A+ K      + ++ +LHAR +   HP +G R++I +P PA +
Sbjct: 251 DLVYGADPKLAKRLGL-DRQWLHARSLAFAHPADGRRVEIVSPYPADL 297


>gi|225420028|ref|ZP_03762331.1| hypothetical protein CLOSTASPAR_06371 [Clostridium asparagiforme
           DSM 15981]
 gi|225041284|gb|EEG51530.1| hypothetical protein CLOSTASPAR_06371 [Clostridium asparagiforme
           DSM 15981]
          Length = 254

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 64/232 (27%), Positives = 107/232 (46%), Gaps = 31/232 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD--SKGQKPRLT---------HR 149
           +LYEDS + V  KPAG+  Q   G    +   +++ +   S    P+ T         HR
Sbjct: 4   VLYEDSDVIVVEKPAGVESQSARGFEPDMVSRIRTHIHKLSPTPSPKSTNHPPYVGVIHR 63

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+   G++V A+ + +A +L+   +  +++KIY ++V G P + +    ++LLK    G
Sbjct: 64  LDKPVRGVMVYAKNQKSAANLSAQIQEGKMRKIYAAVVCGKPVDNQGVYVDYLLKNQ--G 121

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHA 259
                +V  +  GA  A   ++V++              +   L+++  TGR HQ+RV  
Sbjct: 122 NSGSEIVDNSVDGAKRAELVYRVLETVKAGRWMAENPEMELSLLDIELMTGRYHQIRVQM 181

Query: 260 LHMGCPIVGDHKYCANFKG-------NFTSPIQNKLYLHARYMDLPHPEGGR 304
              G P+ GD++Y     G        F+ P Q  L L AR +   HP  GR
Sbjct: 182 AGHGTPLFGDNRYGNCLGGGKRAGESGFSGPRQ-PLALCARKLTFYHPSTGR 232


>gi|153840388|ref|ZP_01993055.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|260361363|ref|ZP_05774428.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus K5030]
 gi|260876822|ref|ZP_05889177.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus AN-5034]
 gi|260895884|ref|ZP_05904380.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus Peru-466]
 gi|260900382|ref|ZP_05908777.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus AQ4037]
 gi|149745949|gb|EDM57079.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|308089361|gb|EFO39056.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus Peru-466]
 gi|308091361|gb|EFO41056.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus AN-5034]
 gi|308108565|gb|EFO46105.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus AQ4037]
 gi|308113659|gb|EFO51199.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus K5030]
          Length = 255

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 113/249 (45%), Gaps = 31/249 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 17  IVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F   +++K Y ++V G    ++E + ++ LK     I   +      
Sbjct: 77  ALSSEVASQVMPMFAEHKMEKTYHAIVRGW--IEEEGVLDYALKVELDKIADKFA----S 130

Query: 219 NEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            EK A  A++ +K +               ++C +EM+P TGR HQLR H  H+  PIVG
Sbjct: 131 QEKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIVG 190

Query: 269 DH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL- 322
           D      K+   F+  F S   ++L LHA  +   HP      +   + A +  TW  L 
Sbjct: 191 DTSHGDGKHNKLFRNEFDS---HRLLLHASELRFVHPFTNEELV---MKASIDDTWQQLF 244

Query: 323 -GFKYDRNL 330
             F++D  L
Sbjct: 245 TRFEWDEEL 253


>gi|154252639|ref|YP_001413463.1| pseudouridine synthase [Parvibaculum lavamentivorans DS-1]
 gi|154156589|gb|ABS63806.1| pseudouridine synthase [Parvibaculum lavamentivorans DS-1]
          Length = 226

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 65/214 (30%), Positives = 108/214 (50%), Gaps = 12/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++L++D +I V  K +G+    G  + +     L+S   +     R+ HRLD++TSG+++
Sbjct: 23  VVLHKDDEILVLAKQSGLLCVAGRPVEH--SDCLESRARATFPNARIVHRLDRDTSGVII 80

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A T AA +HL   F  R+I+K Y + VWG  +  +E     L    H       +V  +
Sbjct: 81  MAMTPAAHRHLGLQFERRKIRKTYLARVWG--QLAQEYGRVDLPLACHWPNRPKQMVDVD 138

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 A + ++V++   +    + + P TGR+HQLRVH L +G PI+GD  Y       
Sbjct: 139 --AGRPAQTDWEVVE-REKNATRVRLSPLTGRSHQLRVHMLSLGHPILGDSFYATG--EA 193

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
           F +   ++L LHA  +   HP  GR+ +   P P
Sbjct: 194 FAA--ADRLQLHAETLTFHHPADGRICRFAVPCP 225


>gi|315281680|ref|ZP_07870254.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria marthii FSL S4-120]
 gi|313614674|gb|EFR88244.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria marthii FSL S4-120]
          Length = 296

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 77/314 (24%), Positives = 146/314 (46%), Gaps = 40/314 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
            VE +E  + L  + K+ +     +   K    G++ V+ +       ++SG  VR+  P
Sbjct: 6   TVETEENGLLLRTFLKSKHISKQLLTAVKFSADGKIEVNNEEQNVLYHVKSGDQVRLTFP 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  ++ E   L+               +++ED  + + NKPAG++        YH 
Sbjct: 66  TEQQNERLLAEHTELE---------------IVFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G + ++V    +   LT       RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 HGSVANFVKGHYETQGLTSAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQQGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCW 242
            +   G+   ++  I      ++ IG   V ++++       YA +++ V++ + + F  
Sbjct: 168 QAFTGGVLAEQEGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYAVLERY-RAFDH 220

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + +Q  TGRTHQ+RVH  ++G P++GD  Y     G  T+ +Q +  LH+ ++ L HP  
Sbjct: 221 VAIQLETGRTHQIRVHFSYIGHPLIGDDMY-----GGDTTLLQRQA-LHSCHLHLVHPLT 274

Query: 303 GR-LQITAPLPAHM 315
              +    PLPA M
Sbjct: 275 EEYMAFDLPLPADM 288


>gi|291563059|emb|CBL41875.1| pseudouridine synthase, RluA family [butyrate-producing bacterium
           SS3/4]
          Length = 334

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 114/233 (48%), Gaps = 28/233 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK---SWVDSKGQKP---RLTHRLDQET 154
           +++ED  + V +KPAG+ V    G   H +  L    +W       P   R  +RLD++T
Sbjct: 110 VVFEDEHVLVIDKPAGMPVHPSQG---HYENTLANGIAWYYRNEATPFVFRAVNRLDRDT 166

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+   ++  L+++ +   I + Y ++V G    K +      L  +   G  + 
Sbjct: 167 SGLVLLAKNPYSSCVLSDAVKDHTIHREYAAIVSG----KTDASGTIDLPIARKDGSTIE 222

Query: 215 VVKQNEKGANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V   E+G   A++H++    FA        ++ +   TGRTHQ+RVH   +G P+ GD 
Sbjct: 223 RVCDPERGET-AVTHYRT---FAYNKDADISFIRLLLETGRTHQIRVHMKAIGHPLPGDF 278

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            YC +++        ++  LH+ Y+   HP  G +L+ +A LP  M K +  +
Sbjct: 279 LYCPDYR------FIDRQPLHSTYLRFSHPVTGEKLEFSASLPEDMRKLFPDI 325


>gi|260551283|ref|ZP_05825484.1| dual specificity pseudouridine synthase [Acinetobacter sp. RUH2624]
 gi|260405597|gb|EEW99088.1| dual specificity pseudouridine synthase [Acinetobacter sp. RUH2624]
          Length = 232

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 68/207 (32%), Positives = 100/207 (48%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ 
Sbjct: 29  ILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMF 86

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R ++K Y +LV G  K +       I +W  +   I    VH  
Sbjct: 87  AKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLITDWENRPRQI----VHF- 141

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            +  K A          +   Q    LE  P TGR+HQLRVH +H+G PI+GD  Y    
Sbjct: 142 -ELGKHAKTLFQPLVYDETTDQSRVLLE--PVTGRSHQLRVHMMHIGHPIMGDKLYHPEP 198

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           K         ++ LHA Y+   HP  G
Sbjct: 199 KRFHL----KRMALHAAYLAFQHPLKG 221


>gi|291301467|ref|YP_003512745.1| pseudouridine synthase RluA family [Stackebrandtia nassauensis DSM
           44728]
 gi|290570687|gb|ADD43652.1| pseudouridine synthase, RluA family [Stackebrandtia nassauensis DSM
           44728]
          Length = 312

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 72/299 (24%), Positives = 137/299 (45%), Gaps = 30/299 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V+V +  + +R+D+     +  ++     +++ +G+V VD +    + R+ +G       
Sbjct: 9   VLVPDGLDGLRIDQVISRLF-GLSRTVAAELVSAGEVTVDGQECMKSTRVAAG------- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG---- 124
               L+ ++ E     S+       + ++ + ++Y D  I V +KP G++     G    
Sbjct: 61  --GQLSVLLPEPPKPASA----PEPELVEGLAVIYSDDDIAVVDKPVGVAAHSSPGWNGP 114

Query: 125 --IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             +A       +  V    ++  + HRLD  TSG++ VA++  A   L  +F+ R + K 
Sbjct: 115 TVVAGLAAAGHRISVHGPPERQGIVHRLDVGTSGLMAVAKSERAYSALKRAFKQREVDKR 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +++ G P   +  I   + +  H G D+   V+    G   +I+H+  ++ F      
Sbjct: 175 YRTVIQGHPDPLRGTIDAPIAR--HPGHDFKFAVR---AGGRASITHYDTLEAFPAA-SL 228

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
           L++Q  TGRTHQ+RVH   +  P VGD  Y A+      S +   + +LHA  +   HP
Sbjct: 229 LDVQLETGRTHQIRVHFSALRHPCVGDLIYGADP--TLASKLGLTRQWLHAYRLGFIHP 285


>gi|317401792|gb|EFV82407.1| pseudouridine synthase [Achromobacter xylosoxidans C54]
          Length = 336

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 88/337 (26%), Positives = 139/337 (41%), Gaps = 55/337 (16%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q V V +     RLD+      P  +   LQ  + +G V+V+    K    +  G  +  
Sbjct: 33  QLVTVPSGTRADRLDKVLAGLLPDHSRSRLQGWIEAGNVQVNGAPGKVRQTVGPGDEI-- 90

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                     +  Q   ++     +  DF    ++ E     V NKPAG+ V  G+G   
Sbjct: 91  ---------AVWAQPAPEALAFAPEAIDF---PVVDESPDWIVVNKPAGLVVHPGAGNWS 138

Query: 126 AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + + ++  +  + HRLD++TSG++VVAR   A  HL    + R + + Y 
Sbjct: 139 GTLLNGLLHRYPELAQVARAGIVHRLDKDTSGLMVVARNEIAQTHLVRQLQARSMGREYV 198

Query: 185 SLVWGIPKNKKECIANWLLKKSH----IGGD---YVHVVKQNEKGANYAISHFKV----- 232
           +L  G           WL         IG D    V +  +       A++H+       
Sbjct: 199 ALAHG-----------WLAAAGKVDRPIGRDPRVPVRMSVERPVAPKPAVTHYAPARRGQ 247

Query: 233 IDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKL 288
           ID   +     C LE    TGRTHQ+RVH   +G P++ D  Y   N  G        + 
Sbjct: 248 IDPGGRATEVVCRLE----TGRTHQIRVHLASLGHPLLADTIYGGKNIAG------AQRQ 297

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF 324
            LHAR +    P G G +Q  AP+PA M    +++ +
Sbjct: 298 MLHARALHFDDPGGRGEVQFAAPVPADMTLVQEAIAW 334


>gi|259909472|ref|YP_002649828.1| tRNA pseudouridine synthase C [Erwinia pyrifoliae Ep1/96]
 gi|224965094|emb|CAX56626.1| tRNA pseudouridine synthase C [Erwinia pyrifoliae Ep1/96]
 gi|283479545|emb|CAY75461.1| tRNA pseudouridine synthase C [Erwinia pyrifoliae DSM 12163]
          Length = 265

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 117/242 (48%), Gaps = 21/242 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  +   NKP+G+ V   S +  H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 4   IIYQDRWLVAVNKPSGMLVHR-SWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A +   A+ L++ F   ++QK Y ++V G  +           ++  I   +     Q 
Sbjct: 63  MALSSEVARLLSQQFEQHQLQKTYHAVVRGWLEGADTLDYPLTEEQDKIADKF----SQP 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           EK    A++H++ +               ++  +EM P +GR HQLR H  H+  PI+GD
Sbjct: 119 EKAPQPAVTHWRGVATAELPVPVGRYQTSRYSLVEMLPESGRKHQLRRHMTHLRHPIIGD 178

Query: 270 HKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
             +  + K N ++      N+L LHA  ++L HP     L + A L A   K  + LG++
Sbjct: 179 SAH-GDLKQNRSAAANFGMNRLMLHASELNLTHPVTAEPLMLRAGLDAVWQKVINQLGWQ 237

Query: 326 YD 327
            +
Sbjct: 238 AN 239


>gi|15595160|ref|NP_212949.1| hypothetical protein BB0815 [Borrelia burgdorferi B31]
 gi|2688762|gb|AAC67167.1| conserved hypothetical protein [Borrelia burgdorferi B31]
          Length = 297

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 80/302 (26%), Positives = 144/302 (47%), Gaps = 38/302 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINF--VNLQKILRSGQVRVDKKRVKFNNR 58
           M L  Y+   V+ ND    RLD         +NF   ++ K +R G +R++  +  F+ R
Sbjct: 1   MRLDKYIFLEVLANDN-GKRLDSIL---IKILNFSKASIIKHIRKGDIRLNGLKSHFSCR 56

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +  G  + +   + A N  +   K   S+++      +++  ++YEDS + V +K  GI 
Sbjct: 57  VCKGDKIYLYKSL-AQNLNLTTDKCFKSNIDF----QYIRKRIIYEDSDLLVLDKQKGIL 111

Query: 119 VQGG-SGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           V GG + + + ++ +L S  + S   KP   HRLD+ TSGI++ A+    A+ L+E+F  
Sbjct: 112 VHGGKNSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTARKLSEAFSG 171

Query: 177 RRIQKIYWSLVWGIPKN----KKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHF 230
             I K Y++++ G  K+    K     N  L+K+ +  D  +V+ + +            
Sbjct: 172 GSIIKKYFAILLGEVKSPVVYKNHLFRNKRLRKTFVLEDKNFVNAITKVN---------- 221

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
            ++ C  ++   +E+   TG THQ+R        P++ D KYC  FK       ++  +L
Sbjct: 222 PILSC--KRATLVEIVIETGFTHQIRSQCSFNNHPLINDKKYCNKFK-------KSDYFL 272

Query: 291 HA 292
           HA
Sbjct: 273 HA 274


>gi|28899096|ref|NP_798701.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus RIMD
           2210633]
 gi|34582398|sp|Q87MD4|TRUC_VIBPA RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|28807320|dbj|BAC60585.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           RIMD 2210633]
          Length = 246

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 113/249 (45%), Gaps = 31/249 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 8   IVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F   +++K Y ++V G    ++E + ++ LK     I   +      
Sbjct: 68  ALSSEVASQVMPMFAEHKMEKTYHAIVRGW--IEEEGVLDYALKVELDKIADKFA----S 121

Query: 219 NEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            EK A  A++ +K +               ++C +EM+P TGR HQLR H  H+  PIVG
Sbjct: 122 QEKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIVG 181

Query: 269 DH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL- 322
           D      K+   F+  F S   ++L LHA  +   HP      +   + A +  TW  L 
Sbjct: 182 DTSHGDGKHNKLFRNEFDS---HRLLLHASELRFVHPFTNEELV---MKASIDDTWQQLF 235

Query: 323 -GFKYDRNL 330
             F++D  L
Sbjct: 236 TRFEWDEEL 244


>gi|95931222|ref|ZP_01313943.1| pseudouridine synthase [Desulfuromonas acetoxidans DSM 684]
 gi|95132741|gb|EAT14419.1| pseudouridine synthase [Desulfuromonas acetoxidans DSM 684]
          Length = 295

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 78/323 (24%), Positives = 146/323 (45%), Gaps = 42/323 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            VE +E  +    + + H    +   L+++L+ G+V+  +  V   ++++ G V+     
Sbjct: 5   TVEANEIPLSPLAFLQRHISAASKSYLRQLLKKGKVKGPRGVVSEQDQLKLGDVL----- 59

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG----- 124
                 I+ +   L   +  T      + + +LYE  +I + +KP+G+++    G     
Sbjct: 60  ------ILPDSGRLSELLAATAQPSLEQQLFILYESREILIVDKPSGLAIHSSEGHQDRN 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +A  +D  ++S  D+    P   HRLD ETSG ++  + + A   L + F    ++K Y 
Sbjct: 114 LAALVDELIRSRGDAYQVAP--IHRLDLETSGPVLFGKGKKACSELGKLFMCHEVEKSYL 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G    +        L +S +        K   K A  A   F+ +D   Q    L+
Sbjct: 172 ALVAGKTPGRG-------LIQSEVPS------KGKTKEAQTA---FQALDRNEQA-SLLK 214

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
           +  +TGR HQ+R     +G P+ GD +Y    +G     +  +L+LH   +    P  G 
Sbjct: 215 VTLYTGRQHQIRRQLAELGHPLFGDRRY----RGQQPDAL-PRLFLHCCQLAFIDPFSGA 269

Query: 304 RLQITAPLPAHMVKTWDSLGFKY 326
            ++I +PLPA + +  D++G +Y
Sbjct: 270 PVEINSPLPADLSQFLDTVGLRY 292


>gi|302187306|ref|ZP_07263979.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. syringae 642]
          Length = 211

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/214 (31%), Positives = 108/214 (50%), Gaps = 13/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIHQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L  +        HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSID--LPLRYDPPTKPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ +KVI+      C +E+ P TGR+HQLRVH L +G P++GD  Y A+ +  
Sbjct: 122 HEAGKHALTFWKVIE-RHDTHCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY-AHPQAL 179

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              P   +L LHA  +   HP  G RL      P
Sbjct: 180 AAYP---RLCLHASMLSFTHPGTGERLTFECAAP 210


>gi|298385355|ref|ZP_06994913.1| RNA pseudouridylate synthase [Bacteroides sp. 1_1_14]
 gi|298261496|gb|EFI04362.1| RNA pseudouridylate synthase [Bacteroides sp. 1_1_14]
          Length = 306

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 89/324 (27%), Positives = 145/324 (44%), Gaps = 47/324 (14%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQV 64
           Y  Y V    +E M L  +     P  +   L+ +L    V VD     +FN  +Q G  
Sbjct: 17  YTNYAV----KEPMELMEFLAAKMPDASRTKLKSLLSKRVVLVDNVITTQFNFPLQPGMK 72

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI----SVQ 120
           V+I           KE+   +       H+  LK  ++YED+ I V  K  G+    + +
Sbjct: 73  VQIS----------KEKGKKEF------HNRLLK--IVYEDAYIIVVEKMQGLLSVNTER 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                AY I   L  +V   G++ R  + HRLD++TSG+++ A+     + L +++    
Sbjct: 115 QKERTAYTI---LNEYVQRSGRQHRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHEIV 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHI--GGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + Y ++V G  +   + + +WL  K+      DY       + G + +I+H+K I   
Sbjct: 172 TDRRYVAVVEGTMEKDYDTVVSWLTDKTLYVSSSDY-------DDGGSKSITHYKTIKR- 223

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           A  +  LE+   TGR +Q+RVH  ++G PI+GD +Y      N   PI  +L LHA  + 
Sbjct: 224 ANGYSLLELDLETGRKNQIRVHMQNLGHPIIGDGRYGGEESLN---PI-GRLALHAFKLC 279

Query: 297 LPHPEGGRL-QITAPLPAHMVKTW 319
             HP  G L +   P P    K +
Sbjct: 280 FYHPVTGDLMEFETPYPGEFKKLF 303


>gi|253702213|ref|YP_003023402.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251777063|gb|ACT19644.1| pseudouridine synthase, RluA family [Geobacter sp. M21]
          Length = 297

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 79/308 (25%), Positives = 139/308 (45%), Gaps = 40/308 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           V+ +    RLD   K  +P  +   +++I+  G   + +  V+  +R ++ G+ + +   
Sbjct: 7   VDAELAGTRLDDAAKTLFPQYSKGEIRRIIDWGGCYLSQTLVRVASRTVKEGEEIAL--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----SGI 125
                 I++ ++ ++          + K  LLYED       K AG + Q         +
Sbjct: 64  -----GIMEAERCIELV--------YKKEELLYEDKDFLAVYKAAGFNSQRTPYQLKGTV 110

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            Y ++ ++KS         R+ HRLD+ TSG++   + + AA  ++   +  ++QK YW+
Sbjct: 111 EYAVECYMKSI--GLRDPSRVVHRLDRGTSGVMFFPKHKQAATLISNLLKDGKVQKTYWA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G P  +   +   L K S     + + V  N K A    + F+V+   A     +E 
Sbjct: 169 LVSGSPDQQSWKVEAPLGKVSK----FKYGVALNGKPAR---TLFRVVGEGA-GVTAVEA 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +P TGRTHQ+RVH  + G PI+GD  Y     G   +    ++ LH R M     +G  +
Sbjct: 221 KPLTGRTHQIRVHLAYSGFPIIGDETY-----GGIPA---ARMMLHCRGMRFTGAKGKVI 272

Query: 306 QITAPLPA 313
           +  AP  A
Sbjct: 273 EAFAPADA 280


>gi|189466071|ref|ZP_03014856.1| hypothetical protein BACINT_02441 [Bacteroides intestinalis DSM
           17393]
 gi|189434335|gb|EDV03320.1| hypothetical protein BACINT_02441 [Bacteroides intestinalis DSM
           17393]
          Length = 303

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 110/225 (48%), Gaps = 18/225 (8%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           H+  LK  ++YED+ I V  K  G+    S +     AYHI        + +G    + H
Sbjct: 82  HNKLLK--IVYEDAYIIVVEKMQGLLSVSSERQKERTAYHILNEYVQRSNGRGSNVYIVH 139

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD++TSG+++ A+     + L +++      + Y ++V G  +    CI +WL  ++  
Sbjct: 140 RLDRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVAGEMEKNAGCIISWLTDRTL- 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              YV+    ++ G   +I+H++ I   A  +  +E+   TGR +Q+RVH   +G PIVG
Sbjct: 199 ---YVYSSPTDD-GGQKSITHYRTIKR-ANGYSLVELNLETGRKNQIRVHMQDLGHPIVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
           D +Y         +PI  +L LHA  +   HP  G L Q   P P
Sbjct: 254 DGRYGL----EEVNPI-GRLALHAFKLCFYHPVTGELMQFETPYP 293


>gi|322831582|ref|YP_004211609.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321166783|gb|ADW72482.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 259

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 106/233 (45%), Gaps = 25/233 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   NKPAG+ V   S +  H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 4   ILYQDEHLIAVNKPAGMLVHR-SWLDRHETVFVMQTLRDQIGQHVFTVHRLDKPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A +   A+ L++ F   ++ K+Y ++V G              +   I   +       
Sbjct: 63  LALSSDVARLLSQQFENNQMSKVYHAVVRGYVPQDGTLDYALTEELDKIADKFA----SP 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +K    A++H++V+               ++  +E++P TGR HQLR H  H+  PI+GD
Sbjct: 119 DKAPQPAVTHYRVVAQVEMPVAVGRYDTARYSLVELKPETGRKHQLRRHMSHLRHPIIGD 178

Query: 270 --HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
             H      +G       + L LHA +M LPHP  G        P  +   WD
Sbjct: 179 SAHGDLKQNRGMTQHFGCSGLMLHASHMQLPHPVTGE-------PLSIQARWD 224


>gi|260662398|ref|ZP_05863293.1| pseudouridylate synthase [Lactobacillus fermentum 28-3-CHN]
 gi|260553089|gb|EEX26032.1| pseudouridylate synthase [Lactobacillus fermentum 28-3-CHN]
          Length = 294

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 96/203 (47%), Gaps = 18/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYE+  + V +KPAGI S    +G    +   + ++++       + HRLDQETSG ++
Sbjct: 88  VLYENRDLLVVDKPAGIKSHPNQAGEVGTLMNRVAAYLEGTNDAAYMVHRLDQETSGAMI 147

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+       L        I + Y +LV G+P   +     W L    +G D   V K+ 
Sbjct: 148 VAKNPVVVPILDRLISTGEIHRDYLALVAGVPNPARGI---WDLP---LGQDPTDVRKRK 201

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              K A  A +H++ +     +   + +   TGRTHQLRVH    GCPIVGD  Y     
Sbjct: 202 VFGKNAQPARTHYRTLAVNDDR-ALVVLNLETGRTHQLRVHLAAAGCPIVGDPLY----- 255

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
           G   +P   ++YLH    +L  P
Sbjct: 256 GTVAAP---RMYLHGVAQELVLP 275


>gi|254517296|ref|ZP_05129353.1| tRNA pseudouridine synthase C [gamma proteobacterium NOR5-3]
 gi|219674134|gb|EED30503.1| tRNA pseudouridine synthase C [gamma proteobacterium NOR5-3]
          Length = 248

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 107/224 (47%), Gaps = 19/224 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V +KP G+ V   S I  H   F L+   D  GQ     HRLD+ TSG+L+
Sbjct: 8   VIYQDRDLVVIDKPPGLLVHR-SKIDRHETQFALQMLRDQLGQHVFPVHRLDKPTSGLLI 66

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A +   A  L+E F  R + K Y ++V G      E       K   I    V    + 
Sbjct: 67  FALSSEVATLLSEQFENRAVAKRYLAVVRGYCPQGGEIDHALTEKHDRI----VDKRARA 122

Query: 220 EKGANYAISHFKV---------IDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +K    A++H++          +D + Q ++  +E++P TGR HQLR H  H+G PI+GD
Sbjct: 123 DKAPQEALTHYRTLAQVEWPEAVDRYPQARYSLVELRPQTGRKHQLRRHMKHIGHPIIGD 182

Query: 270 HKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAP 310
             +       F +   +  +L L    ++  HP  G+ LQ++AP
Sbjct: 183 ATHGKGVHNRFFARRFDCGRLLLACTGLEFDHPVTGQPLQLSAP 226


>gi|326333482|ref|ZP_08199724.1| RNA pseudouridine synthase, RluA family [Nocardioidaceae bacterium
           Broad-1]
 gi|325948727|gb|EGD40825.1| RNA pseudouridine synthase, RluA family [Nocardioidaceae bacterium
           Broad-1]
          Length = 313

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 76/302 (25%), Positives = 141/302 (46%), Gaps = 31/302 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V +  E  R+D      +  ++     +++  G V VD   V  ++R+ +G ++    
Sbjct: 11  LLVPDGLEGERVDAAMARLF-GLSRTRAAELIADGLVTVDGSAVAKSDRVSAGSML---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG-IAY 127
                     +  I   +  L    + ++ I ++Y+D    V +KP G++V    G    
Sbjct: 66  ----------DATIPSQADPLEIKPEIVEGIKIIYDDDAFVVIDKPVGVAVHPSPGWQGQ 115

Query: 128 HIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            + G L +    + + G K R  +  RLD  TSG++V+A++  A   L  +FR R + K 
Sbjct: 116 TVVGHLAAAGFRISTSGAKEREGIVQRLDVGTSGVMVIAKSEHAYSVLKNAFRQRTVDKT 175

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC- 241
           Y +LV G P   +  I   + +      DY   V+ + +   ++++H++ ++  A +F  
Sbjct: 176 YHALVQGHPDPLEGTIDAPIGRNPKY--DYKFAVRADGR---HSVTHYETLE--AHRFAS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L++   TGRTHQ+RVH   +  P VGD  Y A+        ++ + +LHA  +   HPE
Sbjct: 229 LLKIHLETGRTHQIRVHMSALKHPCVGDLTYGADPALARRVGLERQ-WLHAVQLGFDHPE 287

Query: 302 GG 303
            G
Sbjct: 288 TG 289


>gi|312876831|ref|ZP_07736808.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796346|gb|EFR12698.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
          Length = 311

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 67/265 (25%), Positives = 125/265 (47%), Gaps = 28/265 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V+ +   +++++  K  YP I    + K+LR G++ V           Q GQV+R    
Sbjct: 6   IVDKELAGVKVEKAIKKKYPSIPMSVIFKMLRKGEIIVSFLPA------QKGQVLRFG-- 57

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            + ++  I+++ +    V + K         +YED  I V +KP GI     S   Y + 
Sbjct: 58  -DTVSFEIEDRFLEHKKVEILK---------VYEDDNIVVIDKPYGIPSHPDSNNEYSV- 106

Query: 131 GFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               SW++   SK + P+L HRLD+ T+G++++A+ R     + +    R I K Y  + 
Sbjct: 107 ---VSWIEDNYSKDELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRAIIKKYLCIT 163

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                 +   + ++L K S     Y+    Q+  G +  ++ +K++         ++++ 
Sbjct: 164 KKADLPESGVLVHYLKKDSKKSKVYISDFPQD--GYSEVVTAYKIVRQ-KDDLQLVDVEI 220

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
            TG+THQ+R    H+G  I+GD KY
Sbjct: 221 KTGKTHQIRAQLAHVGLCILGDSKY 245


>gi|283782368|ref|YP_003373123.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
 gi|283440821|gb|ADB19263.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
          Length = 603

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 112/236 (47%), Gaps = 24/236 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++YED  I V +KPA + +       +H   ++  L+   D   QKPR  HRLD  TSG+
Sbjct: 381 VVYEDEAIAVVHKPAPLPLHASG--RFHRNTLEWILREIYDP--QKPRPVHRLDANTSGL 436

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ ARTR  A+ L + F   +++K Y +LV G P   +      +  ++ + G       
Sbjct: 437 VLFARTRHFAKLLQQQFTQGKVEKFYLALVSGHPVEDRFVSTAPISAEAGVFGSR----S 492

Query: 218 QNEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +E+    A + F+V+        +    +  QP TGRT+Q+RVH   +G PI+G+  Y 
Sbjct: 493 VDEEAGLPAETRFEVLARTTTADGKPVALVRCQPITGRTNQIRVHLWQLGHPIMGEQSYL 552

Query: 274 ANFKGNFT---SPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           A+ K   T   +     L L A  +   HP    R+  T+ LPA     W +L  K
Sbjct: 553 ADQKHGTTQTHTVDDPPLCLLAHQLSFQHPVSRERMTFTSQLPA-----WTNLAEK 603


>gi|254966988|gb|ACT97528.1| ribosomal large subunit pseudouridine synthase D [uncultured
           organism]
          Length = 274

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 109/229 (47%), Gaps = 41/229 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED ++ V NK AG+ V  G+G         +A+H+    +   D+   +  L HR+D
Sbjct: 20  VVYEDDQLMVVNKEAGMVVHPGAGNFHGTLIQAVAWHLRDMPE--FDANDPEVGLVHRID 77

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA+T  A   L + F  +   + Y +LVWG        + +    + +IG D
Sbjct: 78  KDTSGLLVVAKTPTAKTALGKQFFNKTTHRSYHALVWG------NIVEDEGRIEGNIGRD 131

Query: 212 -----YVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMG 263
                 + V   +      A++H+KV++ F       C LE    TGRTHQ+R H  H+G
Sbjct: 132 PKNRLRMKVFDPDSGIGKTAVTHYKVLERFGYTTLVQCVLE----TGRTHQIRAHMKHIG 187

Query: 264 CPIVGDHKYCAN--FKGNFTSP----IQN------KLYLHARYMDLPHP 300
            P+  D  Y      +G  +S     IQN      +  LHA+ +   HP
Sbjct: 188 HPLFMDETYGGTEILRGQRSSSYKAFIQNCFKLCPRQALHAKTLGFVHP 236


>gi|224539550|ref|ZP_03680089.1| hypothetical protein BACCELL_04455 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224518831|gb|EEF87936.1| hypothetical protein BACCELL_04455 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 303

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 113/232 (48%), Gaps = 18/232 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           H++ LK  ++YED+ I V  K  G+    S +     AYHI        + +G    + H
Sbjct: 82  HNNLLK--IVYEDAYIIVVEKMQGLLSVSSERQKERTAYHILNEYVQRSNGRGSNVYIVH 139

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD++TSG+++ A+     + L +++      + Y ++V G  +    C+ +WL  ++  
Sbjct: 140 RLDRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVTGEMEKNAGCVISWLTDRTL- 198

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              YV+    ++ G   AI+H++ I   A  +  +E+   TGR +Q+RVH   +G PI+G
Sbjct: 199 ---YVYSSPTDD-GGQKAITHYRTIKR-ANGYSLVELDLETGRKNQIRVHMQDLGHPIIG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
           D +Y         +PI  +L LHA  +   HP  G L +   P P    K +
Sbjct: 254 DGRYGI----EDVNPI-GRLALHAFKLCFYHPVTGELMKFETPYPNEFKKLF 300


>gi|305665502|ref|YP_003861789.1| hypothetical protein FB2170_04365 [Maribacter sp. HTCC2170]
 gi|88710258|gb|EAR02490.1| hypothetical protein FB2170_04365 [Maribacter sp. HTCC2170]
          Length = 308

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 98/225 (43%), Gaps = 29/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +LYED  +   +KP+GI V G S   I + +   L+         P+  HRLD  T+GIL
Sbjct: 106 MLYEDEHLAAIHKPSGILVSGNSFKTITHALSQNLEPSNLPDSTLPQPVHRLDYATTGIL 165

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ +T +  + L   F  + I+K Y+++  G               K  I G+    +  
Sbjct: 166 LIGKTSSVIRALNGMFERKEIKKTYYAITMG---------------KMEIRGEVTLKIDN 210

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--- 275
               + Y +      + F Q    +++ P TGR HQLR+H   +G PI+GD  Y      
Sbjct: 211 KNAQSKYVVEETVPSERFGQ-LNLVKLTPITGRRHQLRIHMSGIGNPILGDSDYGTKDLI 269

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
            KG         LYLHA  ++  HP    +L I +  P    K +
Sbjct: 270 LKG-------KGLYLHAYSIEFNHPYTNEKLLIKSEFPKRFKKIF 307


>gi|307263793|ref|ZP_07545399.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
 gi|306870914|gb|EFN02652.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
          Length = 319

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 56/181 (30%), Positives = 97/181 (53%), Gaps = 22/181 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +     + PR  + HRLD++T
Sbjct: 86  IVYEDDDIIVINKPKDLVVHPGAG---NPDGTVLNALLHYYPPIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+   A  HL  + + RRI + Y ++  G+        E +A    K++ +   
Sbjct: 143 TGLMVVAKNIPAQTHLVTALQKRRITREYEAVASGVMTQGGKVDEPMARHPTKRTAMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 201 -VHPMGKP------AVTHYRIMERF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQL 252

Query: 272 Y 272
           Y
Sbjct: 253 Y 253


>gi|229829105|ref|ZP_04455174.1| hypothetical protein GCWU000342_01190 [Shuttleworthia satelles DSM
           14600]
 gi|229792268|gb|EEP28382.1| hypothetical protein GCWU000342_01190 [Shuttleworthia satelles DSM
           14600]
          Length = 337

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/275 (24%), Positives = 129/275 (46%), Gaps = 17/275 (6%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++   ++       L K+LR   + +++KR +    +  G  +++  
Sbjct: 4   ISITKEEAGQRLDKFLCKYFRAATTSFLYKMLRKKNIVLNQKRAEGRELLSEGDRIQVFF 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  + +     D +    K  D+    ++YED  I   +KPAG   Q        +
Sbjct: 64  SDETFERM-RGGDHQDQAFFTLKEIDYRHVHVIYEDEDILALDKPAGCLSQRAGQKDISL 122

Query: 130 DGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           +  + +++ +KG           P + +RLD+ TSG+++  +T    Q+L+E  R R + 
Sbjct: 123 NEEMLAYLIAKGALTRESYFLFHPSVANRLDRNTSGLILAGKTLRGQQYLSEQLRDRSVI 182

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE---KGANYAISHFKVIDCFA 237
           K+Y ++V G  +  +E   +  L K  +G + V V ++ E   +GA    + ++ +D   
Sbjct: 183 KLYHTIVRG--RLTEELQLDGYLYKD-VGRNQVLVSEKKEDLPEGAQEIHTAYRPLD-HR 238

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +    LE+   TGR+HQ+R H   +G PI GD KY
Sbjct: 239 KDLTLLEVHLMTGRSHQIRAHLASIGHPIAGDPKY 273


>gi|77359880|ref|YP_339455.1| 23S rRNA pseudouridine synthase D [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874791|emb|CAI86012.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 325

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 93/345 (26%), Positives = 151/345 (43%), Gaps = 52/345 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN---RIQSGQVVRIP 68
           V  D    RLD+     +P  +   ++  +   ++ VD +   FN    ++  G+V+ + 
Sbjct: 11  VPTDLGGKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGE--IFNTPRTKLLGGEVLNVE 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I A    I +   LD               ++YED  I V NKP G+ V  G+G   +
Sbjct: 69  TTIEAPREYIAQDIKLD---------------IVYEDDDILVINKPMGLVVHPGAG---N 110

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQK 181
            DG     L  +       PR  + HRLD++T+G++VVA+T  A  HL  + + R    +
Sbjct: 111 PDGTVLNALLHYHPEIINVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVTALQKRENFTR 170

Query: 182 IYWSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            Y +L  G        ++ I     +++H+    VH     E+G   AI+H++V + F +
Sbjct: 171 EYEALCNGTMTAGGMVEKPIGRHATQRTHMD---VH-----EQG-KPAITHYRVAEKF-R 220

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYL 290
               L ++  TGRTHQ+RVH  ++  P++GD  Y       KG      +      +  L
Sbjct: 221 AHTRLRLRLETGRTHQIRVHMAYLNHPLIGDQSYGGRPRPPKGATPELFELLRSFKRQAL 280

Query: 291 HARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           HA  + + HP  G +    AP+P  MV    +L      N  I R
Sbjct: 281 HAVKLSIAHPITGEMMTWQAPIPDDMVAMTLALREDTKANPDIDR 325


>gi|323350661|ref|ZP_08086322.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis VMC66]
 gi|322123081|gb|EFX94772.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis VMC66]
          Length = 291

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/202 (32%), Positives = 94/202 (46%), Gaps = 22/202 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAILFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK---Q 218
           +       L      R I + YW+LV G   +KK      L+ K  IG D     K   +
Sbjct: 141 KNPFVLPILNRLLEKREISREYWALVQGKFPSKK------LIYKDKIGRDRHDRRKRLVE 194

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +KG  YA +H   +  F Q    ++ Q  TGRTHQ+RVH  H G P++GD  Y    KG
Sbjct: 195 PQKGL-YAETHVTRVKQFGQA-ALVKCQLKTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG 252

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                   +L LHA  +   HP
Sbjct: 253 --------RLMLHAHRLTFTHP 266


>gi|167968095|ref|ZP_02550372.1| pseudouridylate synthase [Mycobacterium tuberculosis H37Ra]
 gi|215445738|ref|ZP_03432490.1| pseudouridylate synthase [Mycobacterium tuberculosis T85]
 gi|260186491|ref|ZP_05763965.1| hypothetical protein MtubCP_10749 [Mycobacterium tuberculosis
           CPHL_A]
 gi|260204826|ref|ZP_05772317.1| hypothetical protein MtubK8_11038 [Mycobacterium tuberculosis K85]
 gi|294996507|ref|ZP_06802198.1| hypothetical protein Mtub2_18881 [Mycobacterium tuberculosis 210]
 gi|297731096|ref|ZP_06960214.1| hypothetical protein MtubKR_08397 [Mycobacterium tuberculosis KZN
           R506]
 gi|308370756|ref|ZP_07422607.2| hypothetical protein TMCG_02690 [Mycobacterium tuberculosis
           SUMu003]
 gi|308371993|ref|ZP_07426975.2| hypothetical protein TMDG_02186 [Mycobacterium tuberculosis
           SUMu004]
 gi|308373178|ref|ZP_07431294.2| hypothetical protein TMEG_01448 [Mycobacterium tuberculosis
           SUMu005]
 gi|308374339|ref|ZP_07435673.2| hypothetical protein TMFG_00637 [Mycobacterium tuberculosis
           SUMu006]
 gi|308375610|ref|ZP_07444499.2| hypothetical protein TMGG_00098 [Mycobacterium tuberculosis
           SUMu007]
 gi|308376755|ref|ZP_07439920.2| hypothetical protein TMHG_00734 [Mycobacterium tuberculosis
           SUMu008]
 gi|308330950|gb|EFP19801.1| hypothetical protein TMCG_02690 [Mycobacterium tuberculosis
           SUMu003]
 gi|308334771|gb|EFP23622.1| hypothetical protein TMDG_02186 [Mycobacterium tuberculosis
           SUMu004]
 gi|308338559|gb|EFP27410.1| hypothetical protein TMEG_01448 [Mycobacterium tuberculosis
           SUMu005]
 gi|308342261|gb|EFP31112.1| hypothetical protein TMFG_00637 [Mycobacterium tuberculosis
           SUMu006]
 gi|308345756|gb|EFP34607.1| hypothetical protein TMGG_00098 [Mycobacterium tuberculosis
           SUMu007]
 gi|308350056|gb|EFP38907.1| hypothetical protein TMHG_00734 [Mycobacterium tuberculosis
           SUMu008]
          Length = 303

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 112/228 (49%), Gaps = 14/228 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTH 148
           D     +LY D  I   +KPA ++     G     + G L +    + + G   R  + H
Sbjct: 72  DIEGMTILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRITTSGVHERQGIVH 131

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++VVA +  A   L  +F+ R + K Y +LV G P      I   + +  H 
Sbjct: 132 RLDVGTSGVMVVAISERAYTVLKRAFKYRTVDKRYHALVQGHPDPSSGTIDAPIGR--HR 189

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           G ++   + +N +   ++++H+  ++ F      L++   TGRTHQ+RVH   +  P  G
Sbjct: 190 GHEWKFAITKNGR---HSLTHYDTLEAFVAA-SLLDVHLETGRTHQIRVHFAALHHPCCG 245

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y A+ K      + ++ +LHAR +   HP +G R++I +P PA +
Sbjct: 246 DLVYGADPKLAKRLGL-DRQWLHARSLAFAHPADGRRVEIVSPYPADL 292


>gi|332518993|ref|ZP_08395460.1| pseudouridine synthase, RluA family [Lacinutrix algicola 5H-3-7-4]
 gi|332044841|gb|EGI81034.1| pseudouridine synthase, RluA family [Lacinutrix algicola 5H-3-7-4]
          Length = 288

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 64/231 (27%), Positives = 102/231 (44%), Gaps = 37/231 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED  + +  KPAGI V G S   I   +   LK         P+  HRLD  TSG+L
Sbjct: 83  VIYEDEYLAIIKKPAGILVSGNSFKTITNALPQNLKPSQLKDATLPQPVHRLDYPTSGLL 142

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +V +T  + + L + F  + I+K Y+++                     IG      + +
Sbjct: 143 LVGKTNTSIRFLNKLFETKTIEKTYYAIT--------------------IGNMQTQGIIK 182

Query: 219 NEKGANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                  +I+H+ V +       +K   +++QP TGR HQLR+H   +  PI+GD +Y  
Sbjct: 183 TPIENKISITHYLVENSVDSKRFEKLNLVKLQPKTGRKHQLRIHLSSLKNPILGDREYGI 242

Query: 275 N---FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
                KG         LYLHA  +   HP   + ++I   LP    K +++
Sbjct: 243 PSLILKG-------KGLYLHAYKLKFTHPFSKKIIEIEDELPKKFKKIFET 286


>gi|330945855|gb|EGH47236.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 216

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 64/198 (32%), Positives = 99/198 (50%), Gaps = 22/198 (11%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD++T+G++VVA+T  A   L    + R + +IY  +V G+     +  A      
Sbjct: 29  IVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAP----- 83

Query: 206 SHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
             IG  G     +   E G   A+SH++V++ F +    + ++  TGRTHQ+RVH  H+ 
Sbjct: 84  --IGRHGQQRQRMAVME-GGKQAVSHYRVLERF-RSHTHVRVKLETGRTHQIRVHMAHIN 139

Query: 264 CPIVGDHKYCANFK----GNFTSPIQNKLY----LHARYMDLPHPEGG-RLQITAPLPAH 314
            P+VGD  Y   F+     + T     K +    LHAR+++L HP  G R+   +PLP  
Sbjct: 140 YPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFLELDHPTTGKRMSWESPLPDD 199

Query: 315 MVKTWDSLGFKYDRNLYI 332
            V  W     K DR  +I
Sbjct: 200 FV--WLLSLLKQDREAFI 215


>gi|307132626|ref|YP_003884642.1| Ribosomal large subunit pseudouridine synthase A [Dickeya dadantii
           3937]
 gi|306530155|gb|ADN00086.1| Ribosomal large subunit pseudouridine synthase A [Dickeya dadantii
           3937]
          Length = 235

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 69/204 (33%), Positives = 107/204 (52%), Gaps = 18/204 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  + + + +        HRLD  TSG++V
Sbjct: 32  ILYQDQHIMVVNKPSGLLSVPGRA--EEHKDSIM-TRIQADFPAAESVHRLDMATSGVMV 88

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG  +     +   L+       D+ +  KQ 
Sbjct: 89  VALTKAAERELKRQFREREPKKSYIARVWGHLEQDDGLVDLPLI------CDWPNRPKQK 142

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E+G   A + + V+   +     +++ P TGR+HQLRVH L +G PI+GD  Y A+ 
Sbjct: 143 VCFEQG-KPAQTGYVVLSRDSDGTTRVKLMPITGRSHQLRVHMLALGHPILGDGFY-AHP 200

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
           +    +P   +L LHA+ + + HP
Sbjct: 201 QAKAMAP---RLLLHAQELAIVHP 221


>gi|302380202|ref|ZP_07268674.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
 gi|302311985|gb|EFK93994.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
          Length = 273

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 78/302 (25%), Positives = 143/302 (47%), Gaps = 47/302 (15%)

Query: 14  NDEENMRLDRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           N ++ +RLD + K NH  H  F+++ K      + ++ K  K N++++ G +V I     
Sbjct: 7   NVDKKIRLDEFLKKNHISHNLFISIYK----DDIFINGKHAKRNSKLEKGDIVTIN---- 58

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHID 130
                +++++     +N+          +LYED  I+V NKP  +++   G   +A  + 
Sbjct: 59  -----LRDEENKYEPINMDIE-------VLYEDDDIFVLNKPDKLTMNKDGEKSLANFVS 106

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              K    +  QK R  +RLDQ+TSG+++VA+ + A  +    ++    +K Y ++V G 
Sbjct: 107 YLFKQR--NIKQKVRFINRLDQDTSGVVMVAKNKIAQAY----YQKNSFKKKYLAIVKGN 160

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           PK++K       LK+  I  +    + +N K +   + + K    ++     + ++  TG
Sbjct: 161 PKDQK---IELNLKRDGIKTE----IDENGKKSVTILENLKNYGDYS----LVSLELLTG 209

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQ+RV   ++ CPIV D  Y    + NF+        LHA  ++    +G    I   
Sbjct: 210 RTHQIRVSMEYINCPIVADSLYGEKIE-NFSQ------MLHANEIEFVDMKGEFHNIATN 262

Query: 311 LP 312
           LP
Sbjct: 263 LP 264


>gi|312127395|ref|YP_003992269.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
 gi|311777414|gb|ADQ06900.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
          Length = 311

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 69/265 (26%), Positives = 125/265 (47%), Gaps = 28/265 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV+ +   +++++  K  YP I    + K+LR G++ V           Q GQV+R    
Sbjct: 6   VVDKELAGVKVEKAIKKKYPIIPMSVIFKMLRRGEIIVSFLPA------QKGQVLRFG-- 57

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            + ++  I+++ +    V + K         +YED  I V +KP GI     S   Y + 
Sbjct: 58  -DTVSFEIEDRFLEHKKVEILK---------VYEDDNIVVIDKPYGIPSHPDSNNEYSV- 106

Query: 131 GFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               SW++   SK + P+L HRLD+ T+G+++VA+ R     + +    R I K Y  + 
Sbjct: 107 ---VSWIEDNYSKNELPQLCHRLDRNTAGLMIVAKNRQVLSEMLKYMSRRAIIKKYLCIT 163

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                 +   + ++L K S     Y+    Q+  G +  ++ +K++         ++++ 
Sbjct: 164 KKADLPESGVLVHYLKKDSKKSKVYISDFPQD--GYSEVVTAYKIVRQ-KDDLQLVDVEI 220

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
            TG+THQ+R    H+G  I+GD KY
Sbjct: 221 KTGKTHQIRAQLAHVGLCILGDSKY 245


>gi|325686709|gb|EGD28735.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK72]
          Length = 291

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 92/201 (45%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      R I + YW+LV G      +  A  L+ K  IG D     K+  +
Sbjct: 141 KNPFVLPILNRLLEKREISREYWALVQG------KFPAKKLIYKDKIGRDRHDRRKRLVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   YA +H   I  F Q    ++ Q  TGRTHQ+RVH  H G P++GD  Y    KG 
Sbjct: 195 PRKGLYAETHVNRIKQFGQA-SLVKCQLKTGRTHQIRVHLAHHGRPLIGDPLYHPQPKG- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 253 -------RLMLHAHRLTFTHP 266


>gi|299822427|ref|ZP_07054313.1| 23S rRNA pseudouridylate synthase RluD [Listeria grayi DSM 20601]
 gi|299815956|gb|EFI83194.1| 23S rRNA pseudouridylate synthase RluD [Listeria grayi DSM 20601]
          Length = 298

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 80/292 (27%), Positives = 138/292 (47%), Gaps = 34/292 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +EE + L  + K  +     +   K    G++ V+        R++SG  V +       
Sbjct: 10  EEEGLLLRTFLKRKHISKLLLTAIKYHEGGRIAVNNATENVLYRVRSGDKVSV------- 62

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             ++ E+K   +   + +H+D     + YED  + V NKPAG+         YH  G + 
Sbjct: 63  --MLPEEK--QNEQLIAEHTDL---DIRYEDDFVIVLNKPAGMPSIPSQ---YHPTGSVA 112

Query: 135 SWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +++    Q+  LT+      RLD+ETSG++++A+TR A   L+   +   +++ Y +L  
Sbjct: 113 NFIKGHYQEQNLTNAVHIVTRLDRETSGLMLIAKTRFAHARLSSFLQKGDLKRKYQALTM 172

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G   NK   I   + + S I    +   K  E G  YA ++++VI  +   F  +++Q  
Sbjct: 173 GDLANKAGYIEAPIGRDSDIS---IMARKVTETG-KYAKTNYQVIASYPD-FEHVDIQLE 227

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+G  ++GD  Y        TS I+    LH+ ++   HP
Sbjct: 228 TGRTHQIRVHFSHIGHSLLGDDMYHGE-----TSLIRRHA-LHSYHLHFIHP 273


>gi|322391936|ref|ZP_08065400.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           peroris ATCC 700780]
 gi|321145162|gb|EFX40559.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           peroris ATCC 700780]
          Length = 299

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 80/307 (26%), Positives = 144/307 (46%), Gaps = 41/307 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVIN 72
           +E++++  + K H   ++   L KI  R G +RV+ +       +  G   V+ IPP   
Sbjct: 8   DEHVKVKTFLKKH--EVSKGLLAKIKFRGGDIRVNGRPQNATYLLDVGDEVVIDIPP--- 62

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI----SVQGGSGIAYH 128
                       +      +  D+   IL +ED    + NKP G+    SV   + IA  
Sbjct: 63  ------------EEGFETLEAIDYPLDIL-FEDDHFLIINKPFGVASIPSVNHSNTIANF 109

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           I G+     + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++L  
Sbjct: 110 IKGYYVKQ-NYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKAIEKHYYALFK 168

Query: 189 GIP--KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           G    + + E IA     +  I      + ++  KG  YA + ++++  +      ++++
Sbjct: 169 GDGHLEPQGEIIAPIARDEDSI------ITRRVAKGGKYAHTSYQIVASYGN-IHLVDIR 221

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
            HTGRTHQ+RVH  H+G P++GD  Y     G+    I+ +  LH  Y+   HP    +L
Sbjct: 222 LHTGRTHQIRVHFSHIGFPLLGDDLYG----GSLEHGIERQA-LHCHYLSFYHPFLEEQL 276

Query: 306 QITAPLP 312
           ++  PLP
Sbjct: 277 ELECPLP 283


>gi|309803986|ref|ZP_07698068.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           11V1-d]
 gi|309807269|ref|ZP_07701239.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
 gi|309809874|ref|ZP_07703724.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
 gi|312871741|ref|ZP_07731829.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
 gi|312874168|ref|ZP_07734202.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
 gi|312875676|ref|ZP_07735677.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
 gi|315653539|ref|ZP_07906459.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
 gi|325912067|ref|ZP_08174465.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
 gi|329920256|ref|ZP_08277040.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
 gi|308163905|gb|EFO66170.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           11V1-d]
 gi|308166329|gb|EFO68538.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
 gi|308169826|gb|EFO71869.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
 gi|311088930|gb|EFQ47373.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
 gi|311090238|gb|EFQ48648.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
 gi|311092683|gb|EFQ51039.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
 gi|315488901|gb|EFU78543.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
 gi|325476017|gb|EGC79185.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
 gi|328936301|gb|EGG32749.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
          Length = 311

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 79/331 (23%), Positives = 148/331 (44%), Gaps = 39/331 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+++E  +RLD++   H   I+   +Q++++   +  +  + K + ++ +   + I  
Sbjct: 9   LVVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNGLQTKLSYKVNTNDKINIE- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                         +     L+   + L   ++YED  + V NKP G+ V   +G     
Sbjct: 68  --------------IPYPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHT 113

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH     K     +  +P + HR+D++TSG+L++A+   A   L +    +  +
Sbjct: 114 LVNGLIYHTKNLAKC---DEIFRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINK 170

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V    K+    I +  + ++      + VV   +K    AI+HF V++ F   +
Sbjct: 171 REYIAIVHDNFKHSSGVI-DAPIGRNPYQRQQMAVVASGKK----AITHFTVLEQFP-GY 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             ++    TGRTHQ+RVH  ++G PI GD  Y      N      N  +LHA+ +   HP
Sbjct: 225 SLVKCVLETGRTHQIRVHMSYIGHPIAGDPLYGPKKTLN-----GNGQFLHAKTLGFYHP 279

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           +  + L+ +   P    K    L  K   NL
Sbjct: 280 KTNQWLEFSISEPQIFAKQLYLLRKKLTNNL 310


>gi|223043754|ref|ZP_03613797.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus capitis SK14]
 gi|222442851|gb|EEE48953.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus capitis SK14]
          Length = 305

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 73/300 (24%), Positives = 141/300 (47%), Gaps = 34/300 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++ + +  +   R+D++        +   LQ  ++   V+V+ K +K N +++    +  
Sbjct: 5   EFKITDETQVGQRIDKFLSESNDAWSRSQLQDWIKEDLVKVNDKVIKSNYKVKLNDHI-- 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                    I+ E++++++ +      + L   + YED  + +  KP G+ V    G   
Sbjct: 63  ---------IVTEKEVVEADI----QPEDLDLDIYYEDDDVAIVYKPKGMVVHPSPGHYT 109

Query: 126 AYHIDGFL---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++G +   K+     G+ +P + HR+D++TSG+L+VA+   A + L E    + +++
Sbjct: 110 GTLVNGLMYQIKNLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMAKSVKR 169

Query: 182 IYWSLVW-GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y +LV   IP +     A     K+      + VV   ++    A++HF VI+ F + +
Sbjct: 170 KYTALVHDNIPHDYGTVDAPIGRNKNDRQA--MAVVDDGKE----AVTHFNVIEHF-KDY 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E +  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +   HP
Sbjct: 223 TLIECELETGRTHQIRVHMKYIGYPLVGDPKYGPKRTLDIGGQA-----LHAGVIGFEHP 277


>gi|184156168|ref|YP_001844508.1| pseudouridylate synthase [Lactobacillus fermentum IFO 3956]
 gi|183227512|dbj|BAG28028.1| pseudouridylate synthase [Lactobacillus fermentum IFO 3956]
          Length = 294

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 96/203 (47%), Gaps = 18/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYE+  + V +KPAGI S    +G    +   + ++++       + HRLDQETSG ++
Sbjct: 88  VLYENRDLLVVDKPAGIKSHPNQAGEVGTLMNRVAAYLEGTNDAAYMVHRLDQETSGAMI 147

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+       L        I + Y +LV G+P   +     W L    +G D   V K+ 
Sbjct: 148 VAKNPVVVPILDRLISTGEIHRDYLALVAGVPNPARGI---WDLP---LGQDPTDVRKRK 201

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              K A  A +H++ +     +   + +   TGRTHQLRVH    GCPIVGD  Y     
Sbjct: 202 VFGKNAQPARTHYRTLAVNDDR-ALVVLNLETGRTHQLRVHLAAAGCPIVGDPLY----- 255

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
           G   +P   ++YLH    +L  P
Sbjct: 256 GTVAAP---RMYLHGVAQELVLP 275


>gi|50122775|ref|YP_051942.1| ribosomal large subunit pseudouridine synthase A [Pectobacterium
           atrosepticum SCRI1043]
 gi|49613301|emb|CAG76752.1| ribosomal large subunit pseudouridine synthase A [Pectobacterium
           atrosepticum SCRI1043]
          Length = 217

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 69/204 (33%), Positives = 104/204 (50%), Gaps = 18/204 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  +   + +        HRLD  TSG++ 
Sbjct: 14  VLYQDQHIMVVNKPSGLLSVPGRA--PEHKDSVMNR-IQADYPTAESVHRLDMATSGVIA 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPKKSYLARVWGHMAQDEGVIDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + A + ++V+         +++ P TGR+HQLRVH L +G PI+GD  Y A+ 
Sbjct: 125 VCFETGKS-AQTEYQVLSRDDDGTTRVKLMPITGRSHQLRVHLLALGHPILGDGFY-AHP 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                +P   +L LHA+ + + HP
Sbjct: 183 DAKAMAP---RLLLHAQELAITHP 203


>gi|49184224|ref|YP_027476.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|65318659|ref|ZP_00391618.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Bacillus
           anthracis str. A2012]
 gi|165870408|ref|ZP_02215063.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|167634370|ref|ZP_02392691.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|167639342|ref|ZP_02397614.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|170686762|ref|ZP_02877982.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|170706270|ref|ZP_02896731.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|177651449|ref|ZP_02934238.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|190568721|ref|ZP_03021625.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|218902499|ref|YP_002450333.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|227815867|ref|YP_002815876.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|228913961|ref|ZP_04077585.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|229604571|ref|YP_002865810.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|254682548|ref|ZP_05146409.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. CNEVA-9066]
 gi|254726210|ref|ZP_05187992.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. A1055]
 gi|254733966|ref|ZP_05191680.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Western North America USA6153]
 gi|254740346|ref|ZP_05198037.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Kruger B]
 gi|254753734|ref|ZP_05205769.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Vollum]
 gi|254758830|ref|ZP_05210857.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Australia 94]
 gi|270000596|ref|YP_003329034.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. Ames]
 gi|291612209|ref|YP_003541023.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. 'Ames Ancestor']
 gi|49178151|gb|AAT53527.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|164713903|gb|EDR19425.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|167512781|gb|EDR88155.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|167530258|gb|EDR92984.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|170128804|gb|EDS97670.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|170669285|gb|EDT20028.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|172082727|gb|EDT67790.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|190560137|gb|EDV14118.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|218535216|gb|ACK87614.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|224552848|gb|ACN55061.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. 'Ames Ancestor']
 gi|227003057|gb|ACP12800.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|228845683|gb|EEM90710.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|229268979|gb|ACQ50616.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|269850296|gb|ACZ49998.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. Ames]
          Length = 307

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 111/226 (49%), Gaps = 22/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++YED  + + NKP  +      +GG G   ++  F    +     K R  HRLD++T+G
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAF-HYQMKGLETKVRHIHRLDKDTTG 145

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D  H  
Sbjct: 146 GVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRDRHHAT 199

Query: 217 KQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           ++  + KG + AI+++KV + F  Q   ++ +Q  TGRTHQ+RVH  + G P+VGD  Y 
Sbjct: 200 RRRVSPKG-DQAITYYKVEEYFKKQNVTFVTLQLETGRTHQIRVHMSYNGNPLVGDVLYG 258

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
              K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 259 GQTK------YMSRQALHAMKINFLHPITKEEIEVDIPFPTKLNDT 298


>gi|307543919|ref|YP_003896398.1| pseudouridine synthase [Halomonas elongata DSM 2581]
 gi|307215943|emb|CBV41213.1| pseudouridine synthase, RluA family [Halomonas elongata DSM 2581]
          Length = 338

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 80/313 (25%), Positives = 138/313 (44%), Gaps = 53/313 (16%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           + +     RLD+     +   +   L+  ++SG + VD    K  +++  G+++ +    
Sbjct: 30  IPDSMAGFRLDQAAAELFSDFSRERLKAWIKSGALTVDGGPAKPKDKVYGGEMLAL---- 85

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
             +  +  + +     + L          +++ED ++ V +KP G+ V   +G   + DG
Sbjct: 86  --VAELEDDARFEPEDIPLE---------VVFEDDEVLVIDKPPGLVVHPAAG---NPDG 131

Query: 132 FLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L + +     S    PR  + HRLD++TSG++VVA+T  A   L E  + R + + Y +
Sbjct: 132 TLLNGLLHHCPSLAMVPRAGIVHRLDKDTSGLMVVAKTLVAQTALVEQLQARTVSREYDA 191

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQKF- 240
           +  G         A   L  + IG    H   +  +  N     A++H++VI+ F     
Sbjct: 192 VAVGA------MTAGGTLD-APIG---RHPRDRKRQAVNASGKPAVTHYRVIERFRAHTH 241

Query: 241 --CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-----GNFTSPIQNKL---YL 290
             C LE    TGRTHQ+RVH  H+  P+VGD  Y    K     G+    +  +     L
Sbjct: 242 VRCRLE----TGRTHQIRVHMAHLRYPLVGDPVYGGRLKLPAGAGDTLKEVLREFPRQAL 297

Query: 291 HARYMDLPHPEGG 303
           HAR +   HP  G
Sbjct: 298 HARKLAFVHPTSG 310


>gi|24212923|ref|NP_710404.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
 gi|45656097|ref|YP_000183.1| hypothetical protein LIC10192 [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|24193592|gb|AAN47422.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
 gi|45599330|gb|AAS68820.1| conserved hypothetical protein [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 312

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 77/277 (27%), Positives = 131/277 (47%), Gaps = 53/277 (19%)

Query: 20  RLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRV--KFNNRIQSGQ--VVRIPPVINAL 74
           RLDR+ K      I+   +QK + +G V+    ++  K + ++++G+  ++ IPP     
Sbjct: 17  RLDRFLKYSLGDEISRATIQKWIEAGYVQGQDGKILDKSSWKVKTGEKYLLSIPP----- 71

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGI 125
                        +NL      L  IL  E     + +KP+GI+   G         +G+
Sbjct: 72  ----------KPPLNLEPIPMELPVIL--ERENFLIIHKPSGIASHSGPGDRSPSLVNGL 119

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            YH     K   +++   P + HRLD+ T G++++A+   A   L+E FR R I+K Y++
Sbjct: 120 IYHFKELSKMGGEAR---PGIVHRLDKPTEGLILIAKNDRAHGKLSELFRKREIEKKYYA 176

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-----NEKGANYAISHFKVIDCF---- 236
            V G P  +   I   + +         H V++     + KG   +I+H+KV+       
Sbjct: 177 WVQGHPPEESGTIDLPIAR---------HPVERLKMTVSPKGRR-SITHYKVLKYINSRS 226

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +KF ++E+   TGRTHQ+RVH  +  CP+VGD  Y 
Sbjct: 227 GRKFSFIEVGLETGRTHQIRVHFQNQRCPVVGDLLYS 263


>gi|25028588|ref|NP_738642.1| putative ribosomal large subunit pseudouridine synthase
           [Corynebacterium efficiens YS-314]
 gi|259507644|ref|ZP_05750544.1| RluA family RNA pseudouridine synthase [Corynebacterium efficiens
           YS-314]
 gi|23493873|dbj|BAC18842.1| putative ribosomal large subunit pseudouridine synthase
           [Corynebacterium efficiens YS-314]
 gi|259164823|gb|EEW49377.1| RluA family RNA pseudouridine synthase [Corynebacterium efficiens
           YS-314]
          Length = 309

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 78/318 (24%), Positives = 140/318 (44%), Gaps = 40/318 (12%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MR+D         I+     ++  +G V VD   V+ ++R+          V +++  +
Sbjct: 16  GMRVDAALSKLL-GISRTTAAELAEAGDVSVDGSAVRKSDRL----------VADSMLDV 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISV------QGGSGIAYHID 130
           +    + + +  L    + +  + +LY D  +   NKP G++       +G + +     
Sbjct: 65  L----LPEPAQPLVPREEIVPGLDILYADDDLIAVNKPVGVAAHPTVGWEGPTVVGGLAA 120

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +       ++  +  RLD  TSG++VVA +      L  +FR R +QK Y +LV G 
Sbjct: 121 AGFRISTSGPPERKGIVQRLDVGTSGVMVVAASERGYTVLKRAFRDRTVQKTYHALVQGH 180

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P   +  I   + +  H    +   V  + K   +A++H++ I+ F Q+   +++   TG
Sbjct: 181 PDPTEGTIEAPIGR--HPSSGWRFAVTTDGK---HAVTHYETIEAF-QEATLVKVHLETG 234

Query: 251 RTHQLRVH--ALHMGC---PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           RTHQ+RVH  ALH  C   P+ G     +   G        + +LHA  +   HP  GR 
Sbjct: 235 RTHQIRVHFSALHHPCCGDPMYGSDPALSERLGLI------RQWLHAVSLGFHHPADGRW 288

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++IT+P P  +    D L
Sbjct: 289 MEITSPYPDDLQHALDVL 306


>gi|253988053|ref|YP_003039409.1| ribosomal large subunit pseudouridine synthase A [Photorhabdus
           asymbiotica subsp. asymbiotica ATCC 43949]
 gi|253779503|emb|CAQ82664.1| ribosomal large subunit pseudouridine synthase A [Photorhabdus
           asymbiotica]
          Length = 230

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/207 (32%), Positives = 110/207 (53%), Gaps = 19/207 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G +    H D  + + +  +       HRLD  TSGI+V
Sbjct: 28  VLYQDQHIIVVNKPSGLLSVPGRA--EEHKDSIM-TRIQQQFPAAESVHRLDMATSGIMV 84

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+ A + L   FR R  +K Y + VWG  K +   +   L+       D+ +  KQ 
Sbjct: 85  VALTKDAERELKRQFREREPKKTYIARVWGYLKPETGTVDLPLI------CDWPNRPKQK 138

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              + G + A + ++V+  +  +   +++ P TGR+HQLRVH L +  PI+GD ++ A+ 
Sbjct: 139 VCFDTGKS-AQTEYEVL-VYEDQATRVKLSPITGRSHQLRVHMLALEHPILGD-RFYAHQ 195

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    +P   +L LHA+ + + HP  G
Sbjct: 196 QARAMAP---RLQLHAQELYITHPAYG 219


>gi|74316676|ref|YP_314416.1| ribosomal large subunit pseudouridine synthase A [Thiobacillus
           denitrificans ATCC 25259]
 gi|74056171|gb|AAZ96611.1| ribosomal large subunit pseudouridine synthase A [Thiobacillus
           denitrificans ATCC 25259]
          Length = 211

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/220 (29%), Positives = 103/220 (46%), Gaps = 24/220 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY D  + VF+KP+G+    G G        L +   +      + HRLD  TSG++V+A
Sbjct: 6   LYADDCLLVFDKPSGLLAVPGRGPDKQ--DCLAARAQACYPDALVVHRLDMATSGLMVMA 63

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--------ECIANWLLKKSHIGGDYV 213
           R   A + L+ +F  R ++K Y ++V G P   +          + +W  +   I    V
Sbjct: 64  RGTYAQRALSRAFAAREVEKRYVAVVAGHPAAPQGAWGTIDLPLVVDWPNRPLRI----V 119

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V+        +++ ++V+         +E++P TGR+HQLRVH   +G PI+GD  Y 
Sbjct: 120 DAVRGKP-----SVTRWRVLGPAGADGTRVELEPVTGRSHQLRVHLREIGHPILGDALYA 174

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                   S    +L LHAR + L HP  G  ++  AP P
Sbjct: 175 PPAVQAQAS----RLLLHARSLGLAHPATGEWMRFEAPQP 210


>gi|295884073|gb|ADG57579.1| RluD [Streptococcus sanguinis]
 gi|332363746|gb|EGJ41526.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK49]
          Length = 291

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 93/201 (46%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSTYV---GETCYVVHRLDKETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      R I + YW+LV G   +KK      L+ K  IG D     K+  +
Sbjct: 141 KNPFVLPILNRLLEKREISREYWALVQGKFPSKK------LIYKDKIGRDRHDRRKRLVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   YA +H   +  F Q    ++ Q  TGRTHQ+RVH  H G P++GD  Y    KG 
Sbjct: 195 PRKGLYAETHVTRLKQFGQA-ALVKCQLKTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 253 -------RLMLHAHRLTFTHP 266


>gi|290893473|ref|ZP_06556457.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J2-071]
 gi|290556974|gb|EFD90504.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J2-071]
          Length = 296

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 74/313 (23%), Positives = 145/313 (46%), Gaps = 40/313 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           VE +E  + L  + K+ +     +   K    G++ V+ +       ++ G  VR+  P 
Sbjct: 7   VETEENGLLLRTFLKSKHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKVGDKVRLTFPT 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 ++ E   LD               +++ED  + + NKPAG++        YH  
Sbjct: 67  EQQNERLLAEYTDLD---------------IVFEDDFLLIINKPAGMASIPSQ---YHPS 108

Query: 131 GFLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + ++V    +   LT+      RLD+ETSG++++A+ R A   L+   +   +++ Y 
Sbjct: 109 GSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRCYQ 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWL 243
           +   G+  +++  I      ++ IG   V ++++       YA ++++V++ +   F  +
Sbjct: 169 AFTSGVLASQEGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLERYT-AFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TTLLKRQALHSCHLHLVHPVTE 275

Query: 304 R-LQITAPLPAHM 315
             +    PLPA M
Sbjct: 276 EYMAFDLPLPADM 288


>gi|313902966|ref|ZP_07836361.1| pseudouridine synthase [Thermaerobacter subterraneus DSM 13965]
 gi|313466690|gb|EFR62209.1| pseudouridine synthase [Thermaerobacter subterraneus DSM 13965]
          Length = 386

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 88/370 (23%), Positives = 143/370 (38%), Gaps = 55/370 (14%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +YVV   DE   RL R  +     +    + ++LR G++ V+ +RV  +  +++G VV  
Sbjct: 27  RYVVTAADE-GQRLHRLARRWLADVPLSAVFRMLRQGRITVNGRRVPRDTVLRAGDVVEA 85

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-------------LLYEDSKIYVFNKP 114
             V++A  H         S     +      S              ++YED  + V NKP
Sbjct: 86  E-VVDAPPHQAAPGAPPPSPAARPRSGPAGSSRAPRLPAPARHEPRVVYEDEHLLVVNKP 144

Query: 115 AGISVQGGSGIAYHIDGFLKSWVDSKGQK-----------PRLTHRLDQETSGILVVART 163
           AG+   G  G     +  L  WV  +  +           P   HRLD+ TSG++   +T
Sbjct: 145 AGLLTHGAGGFGAAREYTLLDWVRDELARRGTLPEGALYQPSPGHRLDRNTSGLVAFGKT 204

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIP----------KNKKECIANWL---------LK 204
           R  A  L +  R     K Y ++V G P          ++++  +   L           
Sbjct: 205 RQGAARLADWMRSGAAVKEYLAIVRGRPPEGVLQHQLQRDRQRRVTRVLPVSVAQKQPAA 264

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              IG   +       + A  A  H  V+   ++ +    ++  TGRTHQ+R      G 
Sbjct: 265 PVEIGEAGLEKAPGAAEQARSATLHLTVVGA-SRGYTLCRIRLLTGRTHQIRAQLAAAGH 323

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           P+ GD KY          P      LH   + LP    G +++ APLPA +++    LG 
Sbjct: 324 PLAGDRKYGGPRVEGLDRPA-----LHCHRLVLP----GGVELVAPLPADLMRLCRRLGL 374

Query: 325 KYDRNLYIKR 334
              +    +R
Sbjct: 375 PVPQGAPGRR 384


>gi|262281369|ref|ZP_06059150.1| dual specificity pseudouridine synthase [Acinetobacter
           calcoaceticus RUH2202]
 gi|262257195|gb|EEY75932.1| dual specificity pseudouridine synthase [Acinetobacter
           calcoaceticus RUH2202]
          Length = 232

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 69/209 (33%), Positives = 106/209 (50%), Gaps = 22/209 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ 
Sbjct: 29  ILFEDDDLVVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMF 86

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R ++K Y ++V G    +       I +W  +   I    VH  
Sbjct: 87  AKHRDAEVAVSKMFQARTVKKHYIAVVQGRVNQEGSVEVPLITDWENRPRQI----VHF- 141

Query: 217 KQNEKGANYAISHFK--VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              E G  +A + F+  V D    +   L ++P TGR+HQLRVH +H+G PI+GD  Y  
Sbjct: 142 ---ELG-KHAKTLFQPLVYDAHTDQTRVL-LEPVTGRSHQLRVHMMHIGHPIMGDKLYHP 196

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             K        N++ LHA Y+   HP  G
Sbjct: 197 EPKQFHL----NRMALHAAYLAFHHPLNG 221


>gi|258647021|ref|ZP_05734490.1| ribosomal large subunit pseudouridine synthase D [Dialister invisus
           DSM 15470]
 gi|260404462|gb|EEW98009.1| ribosomal large subunit pseudouridine synthase D [Dialister invisus
           DSM 15470]
          Length = 562

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 111/230 (48%), Gaps = 40/230 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +LYED  + V NK  G+ +    +GI   +   +  +   KG+K  +   +RLD+ T+G+
Sbjct: 79  ILYEDDTLLVVNKGTGMIIHPTNAGIHDTLVNAVAGYFQKKGEKSGIHPVYRLDRNTTGV 138

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----------IPKNKKE-CIANWLLKKS 206
           +VVA++  A   LT S  +  I + Y ++  G           P  +KE  I  W ++K 
Sbjct: 139 VVVAKSAKAQYALTRSHDL--IHREYIAVAGGYIPGEFGIVDAPIGRKEGSIIEWTVRKD 196

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                  + V ++  G NY +               L++   TGRTHQ+RVHA +MG P+
Sbjct: 197 GRPARTEYTVLRH--GDNYTV---------------LKLHLLTGRTHQIRVHARYMGTPL 239

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           +GD  Y  N        + ++  LHA  + L HPE G  ++ TAP+PA M
Sbjct: 240 LGDDLYGGNHD------LISRQALHAHTVTLTHPETGEAMKFTAPVPADM 283


>gi|319938146|ref|ZP_08012544.1| pseudouridine synthase [Coprobacillus sp. 29_1]
 gi|319806667|gb|EFW03316.1| pseudouridine synthase [Coprobacillus sp. 29_1]
          Length = 279

 Score = 86.7 bits (213), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 66/205 (32%), Positives = 106/205 (51%), Gaps = 19/205 (9%)

Query: 100 ILLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++LYED +I V +KP G+    + +     AY    ++K ++  K +   L HRLDQ TS
Sbjct: 67  VILYEDKEIIVIDKPCGLLSEQTAKENEKTAYQ---YVKQYLYKKKENIFLVHRLDQYTS 123

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GIL+  + +     LT+++      + Y ++V G  K  K  I N+L  +S     Y+  
Sbjct: 124 GILMFVKNKKLYDILTQNWNKYVKTRGYIAIVEGQMKKTKGTIENYLA-ESKTQNVYITT 182

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +Q +K    AI+H+K I    +++  LE+   TGR +Q+RVH   +   IVGD KY A 
Sbjct: 183 KEQGKK----AITHYKQIQS-NKRYSMLEVYLDTGRKNQIRVHLSSLHHSIVGDSKYGAQ 237

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                ++P++ +L LHA      HP
Sbjct: 238 -----SNPLK-RLGLHAHEFMFVHP 256


>gi|218708391|ref|YP_002416012.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           LGP32]
 gi|218321410|emb|CAV17360.1| Ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           LGP32]
          Length = 244

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 63/207 (30%), Positives = 105/207 (50%), Gaps = 15/207 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I V NKPAG+ SV G   +  H D      V  +  + ++ HRLD  TSG+++
Sbjct: 16  IVYQDDDILVVNKPAGLLSVPGR--LPEHYDSMWSRLV-VEFPEIQVVHRLDMSTSGLML 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A +HL + F+ R   K+Y++ VWG     +  I   L+       D+ +  +Q 
Sbjct: 73  LAKHKQAERHLKKQFQYRLTHKLYYARVWGSVGEAEGLIDLPLI------CDWPNRPRQK 126

Query: 220 EKGANYAISHFK-VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                   S  + +++    +   L++ P TGR+HQLRVH + +G PIVGD  Y      
Sbjct: 127 VCFNEGKPSQTRYIVEQQEPQTTLLKLLPITGRSHQLRVHCMELGNPIVGDEFYATPDAF 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRL 305
           N++    ++L LHA  +   HP   + 
Sbjct: 187 NYS----DRLALHACELSFYHPANNQF 209


>gi|262369409|ref|ZP_06062737.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           johnsonii SH046]
 gi|262315477|gb|EEY96516.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           johnsonii SH046]
          Length = 350

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 112/235 (47%), Gaps = 21/235 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKG-QKPRLTHRLDQETSGI 157
           ++YED  I V NKP G+ V  G+G +    ++  L  +  S    +  L HR+D++TSG+
Sbjct: 117 IVYEDDDIIVVNKPVGMVVHPGAGNSSGTLVNALLHHYPKSAELTRAGLVHRIDKDTSGL 176

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LVVA+   A   L++    + + ++Y  +V+G        IA   + +  I    V  VK
Sbjct: 177 LVVAKNLEAQFSLSKQLAKKTVYRVYDLIVYG------NVIAGGTVDEP-IKRHPVDRVK 229

Query: 218 QNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                G   A++H+ V + F Q F  ++ +  TGRTHQ+RVH  ++G  +VGD  Y    
Sbjct: 230 MAVLPGGKDAVTHYNVKERF-QHFTRIQARLETGRTHQIRVHFSYIGFGLVGDPVYMPRV 288

Query: 277 K--GNFTSPIQNKL------YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           +     T  +   L       LHA  + L HP  G  +   AP PA +    D L
Sbjct: 289 RVPAGATELLDETLRGFRRQALHAAELGLKHPRTGEEMLFKAPWPADLATLVDVL 343


>gi|262164736|ref|ZP_06032474.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus VM223]
 gi|262027116|gb|EEY45783.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus VM223]
          Length = 559

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 72/232 (31%), Positives = 111/232 (47%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++  ++ D+ +     +D   SI+ Y+D  I V NKPA      G  +   +   L
Sbjct: 332 LAHMLQGMELDDNPLLSNPAADKEISIV-YQDEAIVVVNKPAEFLSVPGVHVHDSVLTRL 390

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           ++   S+ +     HRLD  TSG+LV A TR A +HL + F  R +QK Y +++ G   +
Sbjct: 391 QAQF-SEAEGVFALHRLDMSTSGLLVFALTRRANKHLQKQFITRAVQKRYVAMLDGTLAD 449

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           ++  I   L       GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 450 EQGEIELPLC------GDLDDRPRQKVCWQQGKPALTHWETV-AVEQGRTRVYLYPHTGR 502

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   + CPIVGD  Y              +L+LHA  +   HP
Sbjct: 503 THQLRVHCAHHLGLNCPIVGDDLYGTQ---------DQRLHLHAEKLSFSHP 545


>gi|117618521|ref|YP_855405.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117559928|gb|ABK36876.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 218

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 106/215 (49%), Gaps = 16/215 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  I V NKP G+    G G   + D  L   V  +  K    HRLD  T+G++V+
Sbjct: 14  ILFKDKDIMVVNKPTGLLSVPGRG-PENEDSVLHR-VKQQHPKAAAAHRLDMSTTGVIVI 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
                + + L+  FR R  +K Y + VWG P+     +   L        D+ +  KQ  
Sbjct: 72  PLNPNSHRELSRQFRERETEKHYLAWVWGEPEAASGQVDLPLCV------DWPNRPKQKV 125

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +   +A++ ++ +         +++ P TGR+HQLRVH L +G PI+GD+ Y A+   
Sbjct: 126 DHEEGRHALTLWEKLKV-ENGNSLIKLTPITGRSHQLRVHMLELGHPILGDNLY-AHPDA 183

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
              +P    LYLHA  + + HP  G R+   AP P
Sbjct: 184 LAAAP---HLYLHAASLTISHPRSGERMTFEAPAP 215


>gi|270264826|ref|ZP_06193090.1| tRNA pseudouridine synthase C [Serratia odorifera 4Rx13]
 gi|270041124|gb|EFA14224.1| tRNA pseudouridine synthase C [Serratia odorifera 4Rx13]
          Length = 257

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 110/237 (46%), Gaps = 31/237 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   NKP+G  V   S +  H   F+   V D  GQ     HRLD+ TSG+L+
Sbjct: 4   ILYQDEHLVAVNKPSGWLVHR-SWLDRHETRFMMQTVRDQIGQHVFTVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A +   A+ L++ F   ++QK Y ++V G  +           +   I   +  V    
Sbjct: 63  MALSSEVARLLSQQFEQHQVQKTYHAVVRGYVQEGATLDYPLTEELDKIADKHTAV---- 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +KG   A++H++ +             + ++  +E++P  GR HQLR H +H+  PI+GD
Sbjct: 119 DKGPQPAVTHYRPLAQVEMPVAIGRYDSARYSLMELKPENGRKHQLRRHMVHLRHPIIGD 178

Query: 270 HKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
            K+           +F  P   +L LHA ++ L HP  G      PLP  +   WD 
Sbjct: 179 SKHGDLRQNRGMAQHFGCP---RLMLHASHLQLNHPVTGE-----PLP--ISARWDE 225


>gi|229068942|ref|ZP_04202236.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|228714226|gb|EEL66107.1| Pseudouridine synthase [Bacillus cereus F65185]
          Length = 307

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 114/230 (49%), Gaps = 32/230 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGKI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           D  Y    K        +   LHA  ++  HP     +++  P P  + K
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPTKLNK 297


>gi|196232099|ref|ZP_03130954.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
 gi|196223821|gb|EDY18336.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
          Length = 265

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 55/176 (31%), Positives = 89/176 (50%), Gaps = 18/176 (10%)

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G +  + +RLD+ETSG+ +VA+ RAAA+ L    + RR++K Y +LVWG P+ +   I  
Sbjct: 59  GGQVSIINRLDRETSGLTLVAKHRAAARELHLQMQGRRVEKEYLALVWGWPERETFTIDA 118

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF------AQKFCWLEMQPHTGRTHQ 254
            +L++       +H+ +        A + F+V   F        +F  +   P TGRTHQ
Sbjct: 119 PILRQGECMPSPIHLKQAVHPDGAAARTRFQVECTFTLETSNGNRFALVRAFPETGRTHQ 178

Query: 255 LRVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQNKLY-----LHARYMDLP 298
           +RVH  H G P+VGD  Y  +        +  +T  + ++L      LH+  + LP
Sbjct: 179 IRVHLAHAGHPVVGDKIYGPDEQCYLEFIRTGWTPELGSRLLLPRHALHSTVLRLP 234


>gi|308068083|ref|YP_003869688.1| Pseudouridylate synthase, 23S RNA-specific [Paenibacillus polymyxa
           E681]
 gi|305857362|gb|ADM69150.1| Pseudouridylate synthase, 23S RNA-specific [Paenibacillus polymyxa
           E681]
          Length = 337

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 62/209 (29%), Positives = 107/209 (51%), Gaps = 16/209 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR----LTHRLDQETSG 156
           +L+ED  I V +K AG+ +   S     +  + +     + + P     + HRLD++TSG
Sbjct: 124 ILHEDEAIIVIHKDAGL-LSVASAQEQEVTAYRQLTAHVRREHPYNRIFVLHRLDRDTSG 182

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++ A++ A  Q + ++++    ++ Y +LV G  K  +  I +W LK+S     Y    
Sbjct: 183 VMMFAKSEAIQQEMQKAWKEVVYERTYIALVEGQVKKAEGTITSW-LKESKTLKMYSSPY 241

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +     +A++H+K++    + F  LE++  TGR +Q+RVH   +G PIVGD KY +  
Sbjct: 242 PND---GQHAVTHYKLLQA-NRHFSLLEVRLETGRKNQIRVHMEDIGHPIVGDKKYGSKS 297

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           K         +L LHAR +   HP  G L
Sbjct: 298 KS------IGRLGLHARLLSFIHPVTGVL 320


>gi|258624340|ref|ZP_05719289.1| conserved hypothetical protein [Vibrio mimicus VM603]
 gi|258583491|gb|EEW08291.1| conserved hypothetical protein [Vibrio mimicus VM603]
          Length = 559

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 72/232 (31%), Positives = 111/232 (47%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++  ++ D+ +     +D   SI+ Y+D  I V NKPA      G  +   +   L
Sbjct: 332 LAHMLQGMELDDNPLLSNPAADKEISIV-YQDEAIVVVNKPAEFLSVPGVHVHDSVLTRL 390

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           ++   S+ +     HRLD  TSG+LV A TR A +HL + F  R +QK Y +++ G   +
Sbjct: 391 QAQF-SEAEGVFALHRLDMSTSGLLVFALTRRANKHLQKQFITRAVQKRYVAMLDGTLAD 449

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           ++  I   L       GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 450 EQGEIELPLC------GDLDDRPRQKVCWQQGKPALTHWETV-AVEQGRTRVYLYPHTGR 502

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   + CPIVGD  Y              +L+LHA  +   HP
Sbjct: 503 THQLRVHCAHHLGLNCPIVGDDLYGTQ---------DQRLHLHAEKLSFSHP 545


>gi|237785359|ref|YP_002906064.1| pseudouridylate synthase [Corynebacterium kroppenstedtii DSM 44385]
 gi|237758271|gb|ACR17521.1| pseudouridylate synthase [Corynebacterium kroppenstedtii DSM 44385]
          Length = 313

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 112/224 (50%), Gaps = 19/224 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY DS + V +KP G++     G     +   L++    V + G   R  +  RLD  T
Sbjct: 84  ILYSDSDVIVVDKPVGVAAHPTMGWDGPTVTSGLRAAGFRVSTSGPPERQGIVQRLDVGT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA +  A   L ++FR R + K Y +LV G P      I   + +  H G  +  
Sbjct: 144 SGVMIVAASERAYSLLKQAFRDRTVDKTYHALVQGHPDPTVGTIDAPIAR--HPGAGWKF 201

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH--ALHMGCPIVGDHKY 272
            V+ + K    A++H+  ++ F ++   + +   TGRTHQ+RVH  ALH  C   GD  Y
Sbjct: 202 AVRSDGK---RAVTHYSTMEAF-REATLVSVHLETGRTHQIRVHFSALHHPC--CGDPMY 255

Query: 273 CANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
            ++ K   T  +  ++ +LHA  +   HP+G  + + +P PA +
Sbjct: 256 GSDPK--LTEHLGLSRQWLHAVSLGFTHPDGHYMVVESPYPADL 297


>gi|217976505|ref|YP_002360652.1| pseudouridine synthase [Methylocella silvestris BL2]
 gi|217501881|gb|ACK49290.1| pseudouridine synthase [Methylocella silvestris BL2]
          Length = 234

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 109/229 (47%), Gaps = 14/229 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L + LLY D  + V +KPAG++V  G     +++           + P L HRLD++TSG
Sbjct: 13  LNARLLYRDGLMLVIDKPAGVAVHRGPKGGANLEAAFHWLRFGLPRSPALAHRLDRDTSG 72

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R   A + L   F+  +I K Y S+V G P  ++  I   L ++    G ++ V 
Sbjct: 73  CLVLGRHHKALEKLGLLFKQGKIGKTYVSIVNGRPGAEEGLIDLPLGRRDETRGWWMKV- 131

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              +     + + ++++         L + P TGRTHQLRVH   MG  I+GD  Y    
Sbjct: 132 ---DPAGQSSQTRWRIL-AKGPAHTLLALTPLTGRTHQLRVHCAAMGFSILGDPIYGE-- 185

Query: 277 KGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
                 P+Q    LHA+ +++P +     +++ AP+P       +S G 
Sbjct: 186 --GGAIPLQ----LHAQKIEIPLYKNKDAVRVEAPIPESFRAALESCGM 228


>gi|328946274|gb|EGG40418.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1087]
          Length = 297

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 119/231 (51%), Gaps = 22/231 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++   +G   Q+  +  RLD++TSG+
Sbjct: 78  VIYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRQGYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV   G+ + + E IA        IG +   +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGSGLLEEQGEIIAP-------IGRNPESI 190

Query: 216 VKQ--NEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + +   E G   YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y
Sbjct: 191 ITRRVTEDGDGKYAHTSYKVIERFGDVYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLY 249

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 250 G----GSLEQGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 295


>gi|298525052|ref|ZP_07012461.1| conserved hypothetical protein [Mycobacterium tuberculosis
           94_M4241A]
 gi|298494846|gb|EFI30140.1| conserved hypothetical protein [Mycobacterium tuberculosis
           94_M4241A]
          Length = 308

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 111/222 (50%), Gaps = 14/222 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY D  I   +KPA ++     G     + G L +    + + G   R  + HRLD  T
Sbjct: 83  ILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRITTSGVHERQGIVHRLDVGT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA +  A   L  +F+ R + K Y +LV G P      I   + +  H G ++  
Sbjct: 143 SGVMVVAISERAYTVLKRAFKYRTVDKRYHALVQGHPDPSSGTIDAPIGR--HRGHEWKF 200

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + +N +   ++++H+  ++ F      L++   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 201 AITKNGR---HSLTHYDTLEAFVAA-SLLDVHLETGRTHQIRVHFAALHHPCCGDLVYGA 256

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           + K      + ++ +LHAR +   HP +G R++I +P PA +
Sbjct: 257 DPKLAKRLGL-DRQWLHARSLAFAHPADGRRVEIVSPYPADL 297


>gi|256420248|ref|YP_003120901.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
 gi|256035156|gb|ACU58700.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
          Length = 247

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 109/233 (46%), Gaps = 27/233 (11%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +  I++ E +   + NKPAG+             + G LK        +    HRLD++T
Sbjct: 3   INDIIIKETADFVILNKPAGMLTIPDRHDNQLDSLQGLLKKHYG----EIFTVHRLDKDT 58

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+   A ++ ++ F  R ++K Y  LV G    +   +   +++   I G  V 
Sbjct: 59  SGVILFAKNEVAHKYYSQLFEGRNVKKFYKGLVNGQLHPETGSVDEAIMEHPTIKGRMV- 117

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH---- 270
               N KG N A + ++V++ F   +  +++Q HTGRTHQ+RVH  H+G PI  D     
Sbjct: 118 ---TNRKGKN-AQTDYQVLEAFGL-YSLVQLQIHTGRTHQIRVHMKHLGHPIAVDELYGT 172

Query: 271 ---KYCANFKGNF--------TSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
               Y +  K N+          P+ ++L LHA  +     +G    I APLP
Sbjct: 173 AAPVYLSAIKKNYKLGKRVEEERPLLSRLGLHAWQLQFKDQQGEENVIEAPLP 225


>gi|228951772|ref|ZP_04113871.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228807894|gb|EEM54414.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
          Length = 307

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 114/230 (49%), Gaps = 32/230 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAERGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGKI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           D  Y    K        +   LHA  ++  HP     +++  P P  + K
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPTKLNK 297


>gi|332652460|ref|ZP_08418205.1| pseudouridine synthase, RluA family [Ruminococcaceae bacterium D16]
 gi|332517606|gb|EGJ47209.1| pseudouridine synthase, RluA family [Ruminococcaceae bacterium D16]
          Length = 327

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 77/283 (27%), Positives = 128/283 (45%), Gaps = 32/283 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++ + +ND    RLDRW     P +     QK +R  +V+V+ K  K + R+Q G V+++
Sbjct: 3   EFTIAKNDA-GQRLDRWLAKTLPLLPAPLAQKYIRLKRVKVNGKGSKRDVRLQVGDVLQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFL-----KSILLYEDSKIYVFNKPAGISVQGG 122
              IN         +  D     T  + FL     K  +LYED  I + +K  G+ V   
Sbjct: 62  --YIN--------DEFFDRP---TPENAFLSLYQPKLNILYEDEHILLLDKRPGLVVHPD 108

Query: 123 -----SGIAYHIDGFL---KSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTE 172
                + +  HI  +L   K W   K     P L +R+D+ T GI++ A+T  A + + +
Sbjct: 109 ETERVNTLLTHIQAYLYQKKEWSPYKENSFAPALCNRIDRNTGGIVIAAKTAEALRVMNQ 168

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
             + R + K Y   V G  + ++  +  ++ K        V+V  + + GA  AI+ +K 
Sbjct: 169 KIKDRELSKFYLCAVLGRMEPREGKLEGFIWKDEV--KKQVYVRSRPQPGAKTAITLYKT 226

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +         +E    TGRTHQ+R      G P++GD KY + 
Sbjct: 227 L-AVQNGLSLVECDLITGRTHQIRAQFAAAGHPLLGDGKYGSE 268


>gi|84500882|ref|ZP_00999117.1| putative Pseudouridine synthase, Rlu [Oceanicola batsensis
           HTCC2597]
 gi|84390949|gb|EAQ03367.1| putative Pseudouridine synthase, Rlu [Oceanicola batsensis
           HTCC2597]
          Length = 339

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 106/245 (43%), Gaps = 31/245 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQE 153
           ++YED+ + V +KP G+ V    G      ++  L    DS       ++P + HR+D++
Sbjct: 89  VVYEDAALIVVDKPVGMVVHPAPGTPEGTLVNALLHHCGDSLSGIGGERRPGIVHRIDKD 148

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+LV A+T  A   L   F     ++ Y ++  G+P      +   +   S   G  +
Sbjct: 149 TSGLLVAAKTDRAHHALAAQFERHSAERAYLAICHGVPDAADPRL-RGVRGASFEPGGVL 207

Query: 214 HVVKQNEK-------------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +  Q  +             G  +A++  +V++ F      LE +  TGRTHQ+RVH  
Sbjct: 208 KLTTQLARHRTDRQRQAVCFEGGRHAVTRARVLEGFGGA-ALLECRLETGRTHQIRVHMA 266

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQN--------KLYLHARYMDLPHPEGGR-LQITAPL 311
           H G  ++GD  Y    +                 +  LHA  +   HPE GR L+  A L
Sbjct: 267 HAGHALIGDAVYGGRRRAGKAMGAAAAEALNGFPRQALHAAVLGFAHPEDGRPLRFEADL 326

Query: 312 PAHMV 316
           PA M 
Sbjct: 327 PADMA 331


>gi|289449856|ref|YP_003475266.1| putative ribosomal large subunit pseudouridine synthase D
           [Clostridiales genomosp. BVAB3 str. UPII9-5]
 gi|289184403|gb|ADC90828.1| putative ribosomal large subunit pseudouridine synthase D
           [Clostridiales genomosp. BVAB3 str. UPII9-5]
          Length = 319

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 121/246 (49%), Gaps = 30/246 (12%)

Query: 82  KILDSSVNLTKH-SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--- 137
           KI  S V + +H ++ L   +++ED  + V NKP G+ V    G   H +G L + +   
Sbjct: 64  KIELSEVAVPRHEAEDLPLDIVFEDEYLLVVNKPRGLVVHPAPG---HANGTLVNALLNY 120

Query: 138 -------DSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                  D  G+ +P + HR+D++TSG+LVVA+  +    L E   +  I ++Y ++V+G
Sbjct: 121 CGGNNLSDINGEFRPGIVHRIDKDTSGLLVVAKDNSIHNKLAELLSVHAINRVYQAIVFG 180

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQP 247
              N  E         + IG D  +  K     KG   A++HF V+      +  L +  
Sbjct: 181 ---NFAETAGKI---DAPIGRDPRNRQKMAVTLKG-KPALTHFTVL-ASRPGYSLLRLNL 232

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-Q 306
            TGRTHQ+RVH  ++G P+VGD  Y A   G   + +  +L LHA  +   HP   R+  
Sbjct: 233 ETGRTHQIRVHLSYIGHPVVGDPLYAA---GRKYADLGGQL-LHAAELHFRHPITQRMID 288

Query: 307 ITAPLP 312
             APLP
Sbjct: 289 CYAPLP 294


>gi|262374552|ref|ZP_06067826.1| dual specificity pseudouridine synthase [Acinetobacter junii SH205]
 gi|262310548|gb|EEY91638.1| dual specificity pseudouridine synthase [Acinetobacter junii SH205]
          Length = 221

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 66/208 (31%), Positives = 105/208 (50%), Gaps = 26/208 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + V NKPAG+    G    +H   +L+  V       ++THRLD  TSG+L+ 
Sbjct: 18  IMYEDEDLVVVNKPAGLLSVMGRLPEHHDSVYLR--VLDLHPTAKVTHRLDMATSGLLMF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R ++K Y +LV G  + +       I +W  +   I    VH  
Sbjct: 76  AKHRDAEVAVSKMFQARTVKKYYEALVQGAIQAEGSVDVPLITDWENRPRQI----VHF- 130

Query: 217 KQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGD---HKY 272
              E G   A + F+++D   +     + ++P TGR+HQLRVH +H+G PI+GD   H  
Sbjct: 131 ---ELGKQ-AKTLFQLMDYDVETDQSRVRLEPVTGRSHQLRVHMMHIGHPIMGDKLYHPE 186

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
            A F          ++ LHA ++   HP
Sbjct: 187 PAKFH-------LKRMALHAAFLSFQHP 207


>gi|258622273|ref|ZP_05717299.1| conserved hypothetical protein [Vibrio mimicus VM573]
 gi|258585597|gb|EEW10320.1| conserved hypothetical protein [Vibrio mimicus VM573]
          Length = 559

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 72/232 (31%), Positives = 111/232 (47%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++  ++ D+ +     +D   SI+ Y+D  I V NKPA      G  +   +   L
Sbjct: 332 LAHMLQGMELDDNPLLSNPAADKEISIV-YQDEAIVVVNKPAEFLSVPGVHVHDSVLTRL 390

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           ++   S+ +     HRLD  TSG+LV A TR A +HL + F  R ++K Y +++ G   +
Sbjct: 391 QAQF-SEAEGVFALHRLDMSTSGLLVFALTRRANKHLQKQFITRAVEKRYVAMLEGTLAD 449

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  IA  L       GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 450 VQGEIALPLC------GDLDDRPRQKVCWQQGKPALTHWETV-AVEQGRTRVYLYPHTGR 502

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   + CPIVGD  Y              +L+LHA  +   HP
Sbjct: 503 THQLRVHCAHHLGLNCPIVGDDLYGTQ---------DQRLHLHAEKLSFSHP 545


>gi|88704640|ref|ZP_01102353.1| tRNA pseudouridine synthase C [Congregibacter litoralis KT71]
 gi|88700961|gb|EAQ98067.1| tRNA pseudouridine synthase C [Congregibacter litoralis KT71]
          Length = 255

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 66/230 (28%), Positives = 101/230 (43%), Gaps = 17/230 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           H D  +  ++Y DS + V NKP G+ V             L+   D  GQ     HRLD+
Sbjct: 2   HPDAERLEIIYRDSDLVVINKPPGLLVHRSKIDRQETRFALQLLRDQIGQHVFPVHRLDK 61

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+LV A     A+ L + F  R + K Y ++V G              K+  I    
Sbjct: 62  PTSGLLVFALNPEMAKRLADQFARREVSKQYLAVVRGYAPGHGTIDHALTEKRDPIADKR 121

Query: 213 VHVVKQNEKGANYAISHFK---------VIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
            +  K  ++    A++H++          +D + Q ++  +E++PHTGR HQLR H  H+
Sbjct: 122 ANTSKAPQE----ALTHYRRLAQIEWPVAVDRYPQARYSLVELRPHTGRKHQLRRHMKHI 177

Query: 263 GCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPH-PEGGRLQITA 309
           G PI+GD  +       F +   N  +L L    +   H   GG L + A
Sbjct: 178 GHPIIGDANHGKGVHNRFFAETLNCPRLLLACTGLSFDHRASGGSLSLRA 227


>gi|153834660|ref|ZP_01987327.1| ribosomal large subunit pseudouridine synthase D [Vibrio harveyi
           HY01]
 gi|156973324|ref|YP_001444231.1| 23S rRNA pseudouridine synthase D [Vibrio harveyi ATCC BAA-1116]
 gi|148868912|gb|EDL67970.1| ribosomal large subunit pseudouridine synthase D [Vibrio harveyi
           HY01]
 gi|156524918|gb|ABU70004.1| hypothetical protein VIBHAR_01005 [Vibrio harveyi ATCC BAA-1116]
          Length = 325

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 84/330 (25%), Positives = 149/330 (45%), Gaps = 45/330 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L +G+V+V+ + V K   R+  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTRVMGGEEITLQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
            +        +   LD               ++YED  I V NKP    V  G+G     
Sbjct: 70  ELEDEERWEAQDIPLD---------------IVYEDEDIIVINKPRDFVVHPGAGTPDGT 114

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L  + D   + PR  + HRLD++T+G++VVA+T  A   L  + + R I + Y +
Sbjct: 115 VLNALLHHYPDI-AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG----ANYAISHFKVIDCFAQKFC 241
           +  G         A   + K  IG    H  K+           A++H++V + F ++  
Sbjct: 174 IAIG------RMTAGGKVDKP-IGR---HSTKRTLMAVAPMGKPAVTHYRVAEHF-REHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLHAR 293
            + ++  TGRTHQ+RVH  ++  P++GD  Y    +         T  I+  ++  LHA 
Sbjct: 223 RIRLRLETGRTHQIRVHMSYLQHPLLGDTAYGGRARIPTGASEELTEMIRGFDRQALHAV 282

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            +   HP  G  L+  AP+P  MV+  ++L
Sbjct: 283 MLRFDHPVTGEELEFHAPVPDDMVEMTEAL 312


>gi|240949614|ref|ZP_04753949.1| tRNA pseudouridine synthase C [Actinobacillus minor NM305]
 gi|240295872|gb|EER46548.1| tRNA pseudouridine synthase C [Actinobacillus minor NM305]
          Length = 242

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 108/225 (48%), Gaps = 20/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V             +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYQDEDLIAINKPAGMLVHRSWLDKAETVFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A+ + E F   +++K Y ++V G  + K     ++ LK   +  D V      E
Sbjct: 65  ALNSDMARTMCELFENHQVKKGYLAIVRGYLEGKARV--DYPLK---VILDKVADRFSQE 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +E+QP TGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAITDYQGLATVEMPYPAGKFQTARYSLVELQPQTGRKHQLRRHLKHLFHPIMGDT 179

Query: 271 KYCANFKGNFTSPIQN---KLYLHARYMDLPHPEG-GRLQITAPL 311
           KY  +   N T   Q+   +L LH+ +M   HP+   +++I APL
Sbjct: 180 KY-GDLHQNRTLAEQSGVERLMLHSHFMQFQHPKTLQKIEIKAPL 223


>gi|325674393|ref|ZP_08154081.1| RluA family RNA pseudouridine synthase [Rhodococcus equi ATCC
           33707]
 gi|325554653|gb|EGD24327.1| RluA family RNA pseudouridine synthase [Rhodococcus equi ATCC
           33707]
          Length = 302

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 79/309 (25%), Positives = 138/309 (44%), Gaps = 30/309 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +  + MR+D         ++   +  +   G V VD      ++R+ +G  +      
Sbjct: 3   VPDGLDGMRVDAGLARLL-GLSRTAVATLTEEGAVLVDGAAAGKSDRLSAGTWL------ 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG-IAYHI 129
                   E ++ +    LT  ++ ++ + +LY D  I   +KP G++     G     +
Sbjct: 56  --------EVELPEPPRPLTIEAEPVEGMEILYADDDIVAVDKPVGVAAHASVGWTGPTV 107

Query: 130 DGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            G L +    + + G   R  + HRLD  TSG++VVA +  A   L  +F+ R I K Y 
Sbjct: 108 IGGLAAAGFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTVLKRAFKQRTIDKRYH 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G P      I   + +  H   D+   V  + K    +++H+  ++ F Q    L+
Sbjct: 168 ALVQGHPDPSSGTIDAPIGR--HRSNDWKFAVTADGK---PSVTHYDTVEAF-QAASLLD 221

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TGRTHQ+RVH   +  P  GD  Y A+ +      ++ + +LHAR +   HP  G 
Sbjct: 222 IHLETGRTHQIRVHFSALRHPCCGDLTYGADPRLAERLGLERQ-WLHARSLGFAHPADGH 280

Query: 305 -LQITAPLP 312
            ++IT+  P
Sbjct: 281 WVEITSDYP 289


>gi|157962835|ref|YP_001502869.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157847835|gb|ABV88334.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 572

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 70/223 (31%), Positives = 108/223 (48%), Gaps = 24/223 (10%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D +  LT  ++     ++Y+D  + V NKPA      G  +   +   +K+    +   
Sbjct: 350 MDENPLLTNPAEGKSLEIIYQDEVMAVVNKPAEFLSVPGKNVTDSVYARMKAQF-PQATG 408

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG++V+A TR A + L + F  R ++K Y + V G+   +K  I   L 
Sbjct: 409 PLIVHRLDMSTSGLMVIALTRDANKSLAQQFIARTVEKRYLAQVPGVVLGEKGEICLPLR 468

Query: 204 KKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
                 GD     +Q    E G  +A++H++V    +     L + PHTGRTHQLRVH  
Sbjct: 469 ------GDIDDRPRQLVCYEHG-KHALTHWQV-KSRSNDATMLYLYPHTGRTHQLRVHCA 520

Query: 261 H---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           H   +  PI+GD  Y             N+L+LHA+ + L HP
Sbjct: 521 HHEGLHLPIIGDDLYGKK---------ANRLHLHAQRLVLNHP 554


>gi|163801775|ref|ZP_02195672.1| pseudouridine synthase Rlu family protein [Vibrio sp. AND4]
 gi|159174283|gb|EDP59087.1| pseudouridine synthase Rlu family protein [Vibrio sp. AND4]
          Length = 255

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 111/244 (45%), Gaps = 29/244 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 17  IIYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F   +++K Y ++V G    ++E + ++ LK     I   +      
Sbjct: 77  ALSSEVASQVMPMFAEHKMEKTYHAIVRGW--IEEEGLLDYALKVELDKIADKFA----S 130

Query: 219 NEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            EK A  A++ +K +               ++C +EM P TGR HQLR H  H+  PIVG
Sbjct: 131 QEKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMNPKTGRKHQLRRHMAHLRHPIVG 190

Query: 269 DH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
           D      K+   ++  F S   ++L LHA  +   HP       T  + A + +TW  L 
Sbjct: 191 DTTHGDGKHNKLYRTEFDS---HRLLLHASELRFVHPFTDE---TIVMRADIDETWQQLF 244

Query: 324 FKYD 327
            ++D
Sbjct: 245 TRFD 248


>gi|314933372|ref|ZP_07840737.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           caprae C87]
 gi|313653522|gb|EFS17279.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           caprae C87]
          Length = 305

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 68/260 (26%), Positives = 130/260 (50%), Gaps = 29/260 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D++        +   LQ  ++   V+V+ K +K N +++    +           I+ 
Sbjct: 17  RIDKFLSESNDAWSRSQLQDWIKEDLVKVNDKVIKSNYKVKLNDHI-----------IVT 65

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL---K 134
           E++++++ +      + L   + YED  + +  KP G+ V    G      ++G +   K
Sbjct: 66  EKEVVEADI----QPEDLDLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIK 121

Query: 135 SWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPK 192
           +     G+ +P + HR+D++TSG+L+VA+   A + L E    + +++ Y +LV G IP 
Sbjct: 122 NLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMNKSVKRKYTALVHGNIPH 181

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           +     A     K+      + VV   ++    A++HF V++ F + +  +E +  TGRT
Sbjct: 182 DYGTVDAPIGRNKNDRQA--MAVVDDGKE----AVTHFNVLEHF-KDYTLIECELETGRT 234

Query: 253 HQLRVHALHMGCPIVGDHKY 272
           HQ+RVH  ++G P+VGD KY
Sbjct: 235 HQIRVHMKYIGFPLVGDPKY 254


>gi|225619928|ref|YP_002721185.1| RsuA/RluD family pseudouridine synthase [Brachyspira hyodysenteriae
           WA1]
 gi|225214747|gb|ACN83481.1| Pseudouridine synthase, RsuA/RluD family [Brachyspira
           hyodysenteriae WA1]
          Length = 217

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 63/184 (34%), Positives = 97/184 (52%), Gaps = 28/184 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED+     +K AGI V         I+   K +  S      L HR+D+ TSGI+++
Sbjct: 3   IIYEDNYFIAIDKEAGIEVDDNL-----INIIKKEY--SHIDNLYLVHRIDKFTSGIVIL 55

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           AR     ++  ++F+ + I K+Y ++V G  K KKE   N  +  S IG D     K+N 
Sbjct: 56  ARDEETKKYFEDAFKNKTINKVYHAIVNG--KVKKE---NGTIDIS-IGID-----KKNP 104

Query: 220 --------EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                   ++G   AI+H+KV+    +    LE++P TGRTHQ+RVH  ++G PI+GD  
Sbjct: 105 NRRIPLSIKEGGESAITHYKVLKRLNE-HTLLELKPLTGRTHQIRVHLSYIGHPIIGDKI 163

Query: 272 YCAN 275
           Y  N
Sbjct: 164 YSKN 167


>gi|29346052|ref|NP_809555.1| RNA pseudouridylate synthase [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|253568538|ref|ZP_04845949.1| RNA pseudouridylate synthase [Bacteroides sp. 1_1_6]
 gi|29337946|gb|AAO75749.1| RNA pseudouridylate synthase [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|251842611|gb|EES70691.1| RNA pseudouridylate synthase [Bacteroides sp. 1_1_6]
          Length = 306

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 89/324 (27%), Positives = 144/324 (44%), Gaps = 47/324 (14%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQV 64
           Y  Y V    +E M L  +     P  +   L+ +L    V VD     +FN  +Q G  
Sbjct: 17  YTNYAV----KEPMELMEFLAAKMPDASRTKLKSLLSKRVVLVDNVITTQFNFPLQPGMK 72

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI----SVQ 120
           V+I           KE+   +       H+  LK  ++YED+ I V  K  G+    + +
Sbjct: 73  VQIS----------KEKGKKEF------HNRLLK--IVYEDAYIIVVEKMQGLLSVNTER 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                AY I   L  +V   G++ R  + HRLD++TSG+++ A+     + L +++    
Sbjct: 115 QKERTAYTI---LNEYVQRSGRQHRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHEIV 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHI--GGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + Y ++V G  +   + + +WL  K+      DY       + G + +I+H+K I   
Sbjct: 172 TDRRYVAVVEGTMEKDYDTVVSWLTDKTLYVSSSDY-------DDGGSKSITHYKTIKR- 223

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           A  +  LE+   TGR +Q+RVH   +G PI+GD +Y      N   PI  +L LHA  + 
Sbjct: 224 ANGYSLLELDLETGRKNQIRVHMQDLGHPIIGDGRYGGEESLN---PI-GRLALHAFKLC 279

Query: 297 LPHPEGGRL-QITAPLPAHMVKTW 319
             HP  G L +   P P    K +
Sbjct: 280 FYHPVTGDLMEFETPYPGEFKKLF 303


>gi|62185009|ref|YP_219794.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           abortus S26/3]
 gi|62148076|emb|CAH63831.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           abortus S26/3]
          Length = 274

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 52/176 (29%), Positives = 91/176 (51%), Gaps = 18/176 (10%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L+  +L+ED+   ++NKP+  S +  + I                 +  + HRLD++T+G
Sbjct: 67  LEPQILWEDAHCCIYNKPSHTSTEDLAKIT----------------RLNIVHRLDRDTTG 110

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            ++ A+  +AA  L+E F+ R+I K Y +LV+G PK     + ++   KS   G  +   
Sbjct: 111 CILFAKHASAANALSELFKKRKIHKQYTALVFGHPKKSSGTVISYTAPKSRRCGSVIFGN 170

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               +G    I+ + ++  + Q +  +  +P TGRTHQ+R+H   +G PIVGD  Y
Sbjct: 171 TPKNQG-KLTITQWSILRTYKQ-YTLMRCEPITGRTHQIRLHMQTLGHPIVGDVDY 224


>gi|134301061|ref|YP_001114557.1| RluA family pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134053761|gb|ABO51732.1| pseudouridine synthase, RluA family [Desulfotomaculum reducens
           MI-1]
          Length = 320

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 67/221 (30%), Positives = 105/221 (47%), Gaps = 24/221 (10%)

Query: 101 LLYEDSKIYVFNKPA-------GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +LYED  + V NKPA       G + +G   +A ++  +LK        +P   HRLD+E
Sbjct: 104 VLYEDDFLLVLNKPAHQLVHPTGQTTRGT--MANYLAYYLKQRNVVSAIRP--VHRLDRE 159

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG ++ A+   +   L +  + R +++ YW+LV GI       I   +     +     
Sbjct: 160 TSGCVIFAKDSRSQFILEQQLKERTLKRTYWALVKGIVHPPSGTIDAPIGPHPSLANRRA 219

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                NE G   +I+H++ +  F +    L++   TGRTHQ+R+H  H+G PI+GD  Y 
Sbjct: 220 ----INEHGEQ-SITHYQTLRSFPE-ISLLKLNLDTGRTHQIRLHLAHLGYPIIGDRMYG 273

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPH-PEGGRLQITAPLPA 313
                   SP  N+  LHA  +   H  E   + + APLP 
Sbjct: 274 VR------SPWINRQALHAYDVSFRHLKENHEIAVHAPLPT 308


>gi|269962553|ref|ZP_06176901.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio harveyi 1DA3]
 gi|269832748|gb|EEZ86859.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio harveyi 1DA3]
          Length = 325

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 83/330 (25%), Positives = 150/330 (45%), Gaps = 45/330 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L +G+V+V+ + V K   ++  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTKVMGGEEITLQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
            +        +   LD               ++YED  I V NKP    V  G+G     
Sbjct: 70  ELEDEERWEAQDIPLD---------------IVYEDEDIIVINKPRDFVVHPGAGTPDGT 114

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L  + D   + PR  + HRLD++T+G++VVA+T  A   L  + + R I + Y +
Sbjct: 115 VLNALLHHYPDI-AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG----ANYAISHFKVIDCFAQKFC 241
           +  G         A   + K  IG    H  K+          +A++H++V + F ++  
Sbjct: 174 IAIG------RMTAGGKVDKP-IGR---HSTKRTLMAVAPMGKHAVTHYRVAEHF-REHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLHAR 293
            + ++  TGRTHQ+RVH  ++  P++GD  Y    +         T  I+  ++  LHA 
Sbjct: 223 RIRLRLETGRTHQIRVHMSYLQHPLLGDTAYGGRARIPTGASQELTEMIRGFDRQALHAV 282

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            +   HP  G  L+  AP+P  MV+  ++L
Sbjct: 283 MLRFEHPVTGEELEFHAPVPDDMVEMTEAL 312


>gi|261418827|ref|YP_003252509.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|297531211|ref|YP_003672486.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|319765643|ref|YP_004131144.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
 gi|261375284|gb|ACX78027.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC61]
 gi|297254463|gb|ADI27909.1| pseudouridine synthase, RluA family [Geobacillus sp. C56-T3]
 gi|317110509|gb|ADU93001.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC52]
          Length = 299

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 67/206 (32%), Positives = 102/206 (49%), Gaps = 22/206 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQ----GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +L+ED  + V NK AGI +     G +G +A  +  +L+S   +   K R  HRLD++TS
Sbjct: 86  ILWEDDHLLVLNKEAGIDIHPSEPGQTGTLANAVAFYLQS--QAILTKVRHIHRLDRDTS 143

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++ A+   A   L      R I++ Y +LV G    K   I+      + IG D  H 
Sbjct: 144 GAILFAKHPLAGATLDRMLAHRAIKRTYVALVHGRLSPKSGTIS------APIGRDRHHP 197

Query: 216 VKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            ++   K    A++H++VI  F      +E+   TGRTHQ+RVH  H+G P+VGD  Y  
Sbjct: 198 TRRRVSKTGAKAVTHYRVIKTFPSTSL-VELSLETGRTHQIRVHLAHLGHPLVGDVLYGG 256

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
                   P+ ++  LHA  +   HP
Sbjct: 257 K-------PVFHRHALHAAKLTFRHP 275


>gi|229189473|ref|ZP_04316490.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|228594064|gb|EEK51866.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
          Length = 307

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 113/228 (49%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGKI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y    K        +   LHA  ++  HP     +++  P P  +
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPTKL 295


>gi|254507454|ref|ZP_05119589.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 16]
 gi|219549710|gb|EED26700.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 16]
          Length = 254

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 109/242 (45%), Gaps = 44/242 (18%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           +++ED  I V NKP+G+ SV G   +  H D     W       P  ++ HRLD +TSG+
Sbjct: 25  IVFEDEHILVANKPSGLLSVPGR--LEEHYDSL---WSRLVAIYPDIQVVHRLDMDTSGL 79

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHI---- 208
           +++A+ + A + L + F+ R   K+Y++ VWG P N         I +W  +   I    
Sbjct: 80  MLLAKHKEAERSLKKQFQYRLTHKVYYARVWGHPTNDNGEIDLPLICDWPNRPRQIVCFD 139

Query: 209 ----GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                     VVK+ E+ +                   + + P TGR+HQLRVH   +G 
Sbjct: 140 DGKPSKTLYQVVKREERTSI------------------VRLLPITGRSHQLRVHMQALGH 181

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           PIVGD  Y       F+    ++L LHA  +   HP    LQ  A +P       +++ F
Sbjct: 182 PIVGDEFYSEGEAFEFS----DRLELHAAELSFYHPHSEALQ-CAFVPCDFYLEAEAMIF 236

Query: 325 KY 326
            Y
Sbjct: 237 NY 238


>gi|325972566|ref|YP_004248757.1| pseudouridine synthase [Spirochaeta sp. Buddy]
 gi|324027804|gb|ADY14563.1| pseudouridine synthase [Spirochaeta sp. Buddy]
          Length = 417

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 105/226 (46%), Gaps = 46/226 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL----------THRL 150
           ++Y+D  I V NKP+G+           + G  +  +DS   + RL          THRL
Sbjct: 208 IVYQDEHIVVVNKPSGL---------LSVPGRTQDKIDSVETRIRLLYPHAPLQCATHRL 258

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW----LLKKS 206
           D +TSG+LVVA  + A   +   FR ++++K Y +L+ G+ K K   I       +  + 
Sbjct: 259 DMDTSGLLVVALNKQAHSRMHIQFREQQVKKSYIALLQGVVKQKSGSITLPFRVDITNRP 318

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALH- 261
           H   D VH          +  +H+  +        +    +  +P TGRTHQLR+H+ H 
Sbjct: 319 HQIYDEVH--------GKWGTTHYTRLGVERTAEGELVTRMLFEPQTGRTHQLRLHSSHP 370

Query: 262 --MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
             +G PIVGD  Y         S +  +LYLHA+ +   HP  G++
Sbjct: 371 KGLGIPIVGDRLY--------GSGMTERLYLHAQRISFSHPISGQM 408


>gi|321474676|gb|EFX85641.1| hypothetical protein DAPPUDRAFT_32502 [Daphnia pulex]
          Length = 250

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 77/243 (31%), Positives = 114/243 (46%), Gaps = 43/243 (17%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL-----THRLDQETSGILVVAR 162
           I   +KP G+      G A  +   L + +    Q  R+      HRLD++T+GIL++A 
Sbjct: 1   IVAIDKPHGLVTTDADGNAKVV---LTNLLPGLSQALRVEKLYTVHRLDRDTTGILLLAS 57

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG------------ 210
            +  A  L + F    IQK Y  +  GIP  ++  I   + +KS IG             
Sbjct: 58  NQTVANKLNKLFLDHEIQKKYMVITKGIPSPREGTIDIPMCEKS-IGDRQRMALRPVLSH 116

Query: 211 --DYVHVVKQNEKGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPI 266
             D +   K N KG ++ AI+HF V    A    ++E++P TG  HQLRVH +  + CP+
Sbjct: 117 SPDSLKSAKYNAKGKSFKAITHFWVKTTNAGT-AFVELEPETGVRHQLRVHLSEGLDCPV 175

Query: 267 VGDHKYCANFKG----------NFTSPIQNK-----LYLHARYMDLP--HPEGGRLQITA 309
           +GDHKY    K           N  +  Q+K     ++LHA +M +P    EG  L I +
Sbjct: 176 LGDHKYSHAEKFAPQKLSQDILNLLAIKQSKARNIPMHLHAAFMAIPGFGQEGQPLCINS 235

Query: 310 PLP 312
           PLP
Sbjct: 236 PLP 238


>gi|315226968|ref|ZP_07868756.1| pseudouridylate synthase [Parascardovia denticolens DSM 10105]
 gi|315121100|gb|EFT84232.1| pseudouridylate synthase [Parascardovia denticolens DSM 10105]
          Length = 337

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/287 (25%), Positives = 134/287 (46%), Gaps = 21/287 (7%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV-----INALNHIIKEQKILDSSVNLTKH 93
           +++  GQ RV+ + V  + +I  G  + +         + +      Q   D        
Sbjct: 39  RLIADGQARVEGRSVPKSGQILPGDFILVSSAGSTAGPSGVRIFTGSQTSKDEKAAGPNQ 98

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLK--SWVDSKGQKPRL 146
           ++    I+ YED  + V +KPAG++    +G     +   +    K  S VDS   +P +
Sbjct: 99  AEASLPIV-YEDDDLVVVDKPAGMASHPAAGWAGPTVVEALQALDKDLSRVDSD-IRPGI 156

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD  TSG+++V ++  A   + E F   +++K Y +LV G     +  +   + +++
Sbjct: 157 VSRLDAGTSGLMLVCKSDRAFVAMKEQFARHQVKKTYQTLVQGHIAQDRATVEAPIARQT 216

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                +   +  + K    AI+H+ V++        L +   TGRTHQ+RVH   +G P+
Sbjct: 217 G-ASSFRFAISPDGK---PAITHWDVLERLPGA-TLLSINLETGRTHQIRVHLSSLGHPL 271

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +GD  Y AN +      + N+ +LH+  ++  HP GGR + + +PLP
Sbjct: 272 IGDTLYGANPRLAEELGL-NRQWLHSIRLEFTHPVGGRTIHLESPLP 317


>gi|291545928|emb|CBL19036.1| pseudouridine synthase, RluA family [Ruminococcus sp. SR1/5]
          Length = 322

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 115/234 (49%), Gaps = 26/234 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDGFLK-----SWVDSKGQKPRLTHRLD 151
           ++YED  I + NKPAG+  Q    G   +  ++ G+L      +  D +  +P + +RLD
Sbjct: 86  IIYEDENILLINKPAGMLSQPADDGTPSLVEYLTGYLLKNGSLTENDLRTFRPSVCNRLD 145

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG++   ++ +  Q L+  F+ R + K Y  LV G+ K ++  I  +L K      +
Sbjct: 146 RNTSGLIAAGKSLSGLQELSGMFKSRELHKYYLCLVEGVLKEER-YIKGYLAKDKK--SN 202

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V + KQ ++ A    + +  +     +   L+++  TGR HQ+R H    G  IVGD K
Sbjct: 203 KVTIYKQEKENALPVETKYYPLGTNGTR-TLLKVELITGRAHQIRAHLASEGHSIVGDPK 261

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEG------GRLQITAPLPAHMVKTW 319
           Y     G     ++ +L LH+  M+ P  +G      G++  TAPLP   ++T 
Sbjct: 262 Y-----GKADKKLKGQL-LHSFRMEFPSMKGSLSYLSGKV-FTAPLPEIFLRTL 308


>gi|228957662|ref|ZP_04119409.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|228802004|gb|EEM48874.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
          Length = 307

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 113/228 (49%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGKI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y    K        +   LHA  ++  HP     +++  P P  +
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPTKL 295


>gi|257066092|ref|YP_003152348.1| pseudouridine synthase, RluA family [Anaerococcus prevotii DSM
           20548]
 gi|256797972|gb|ACV28627.1| pseudouridine synthase, RluA family [Anaerococcus prevotii DSM
           20548]
          Length = 305

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 72/269 (26%), Positives = 135/269 (50%), Gaps = 22/269 (8%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  +    I    ++  ++  +++V+   VK + ++  G  + I    ++L 
Sbjct: 6   DEIIRIDKFISDELEEIPREKIKDFIKDKKIKVNNSFVKPSFKLSEGDEIEID---DSLF 62

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG----GSGIAYHIDG 131
           H+  E K  D  + +   +D     ++ +DS + V   PAG  + G    G    Y  DG
Sbjct: 63  HV-PELKAEDMELKIVYEND--DYAIIDKDSNVIV--HPAGKIITGTLVNGLLGRYGYDG 117

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                 D +   P + HRLD++T+G++ + +T  A ++  + F  R++ K Y+++V+G  
Sbjct: 118 LSHIGGDDR---PGIVHRLDKDTTGLIAITKTNEAYKYFKKMFETRKVDKYYYAIVFGNF 174

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             KK  I N++ +  H   +   +  +N      A+SH++VI    + F  + ++  TGR
Sbjct: 175 DKKKGTIDNFMDRDVH---NRRKMAVRNT--GRRAVSHYEVI-SEVEGFSLVRIKIETGR 228

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNF 280
           THQ+RVH  H+  PI+GD  Y  N K  F
Sbjct: 229 THQIRVHMTHINHPILGDPVY-GNVKHKF 256


>gi|226952242|ref|ZP_03822706.1| RluA-like dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification [Acinetobacter sp. ATCC 27244]
 gi|294648812|ref|ZP_06726269.1| conserved hypothetical protein [Acinetobacter haemolyticus ATCC
           19194]
 gi|226837080|gb|EEH69463.1| RluA-like dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification [Acinetobacter sp. ATCC 27244]
 gi|292825304|gb|EFF84050.1| conserved hypothetical protein [Acinetobacter haemolyticus ATCC
           19194]
          Length = 221

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/207 (31%), Positives = 100/207 (48%), Gaps = 24/207 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  + V NKPAG+    G    +    +L+  V  K    ++THRLD  TSG+L+ 
Sbjct: 18  ILYEDDDLVVVNKPAGLLSVMGRLPEHQDSAYLR--VLEKYPSAKVTHRLDMATSGLLMF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R ++K Y +LV G  + +       I +W  +   +    VH  
Sbjct: 76  AKHRDAEVAVSKMFQARTVKKYYEALVQGKIQAEGSVEVPLITDWENRPRQM----VHFE 131

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD---HKYC 273
                   Y   H+   D    +   + ++P TGR+HQLRVH +H+G PI+GD   H   
Sbjct: 132 LGKPAKTLYQSLHY---DAETDQ-SRVRLEPVTGRSHQLRVHMMHIGHPIMGDKLYHPEP 187

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
           A F          ++ LHA Y+   HP
Sbjct: 188 AKFH-------LKRMALHAAYLAFQHP 207


>gi|156975510|ref|YP_001446417.1| tRNA pseudouridine synthase C [Vibrio harveyi ATCC BAA-1116]
 gi|156527104|gb|ABU72190.1| hypothetical protein VIBHAR_03241 [Vibrio harveyi ATCC BAA-1116]
          Length = 255

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 116/249 (46%), Gaps = 31/249 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 17  IVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F   +++K Y ++V G    ++E + ++ LK     I   +      
Sbjct: 77  ALSSEVASQVMPMFAEHKMEKTYHAIVRGW--IEEEGVLDYALKVELDKIADKFA----S 130

Query: 219 NEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            EK A  A++ +K +               ++C +EM+P TGR HQLR H  H+  PIVG
Sbjct: 131 QEKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIVG 190

Query: 269 DH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL- 322
           D      K+   ++  F S   ++L LHA  +   HP      +   + A++ +TW  L 
Sbjct: 191 DTTHGDGKHNKLYRTEFDS---HRLLLHASELRFVHPFTDEKIV---MKANIDETWQQLF 244

Query: 323 -GFKYDRNL 330
             F++D +L
Sbjct: 245 TRFEWDESL 253


>gi|222529546|ref|YP_002573428.1| pseudouridine synthase [Caldicellulosiruptor bescii DSM 6725]
 gi|222456393|gb|ACM60655.1| pseudouridine synthase [Caldicellulosiruptor bescii DSM 6725]
          Length = 311

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 67/265 (25%), Positives = 125/265 (47%), Gaps = 28/265 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV+ +   +++++  K  YP I    + K+LR G++ V           Q G+V+R    
Sbjct: 6   VVDKELAGLKVEKAIKKKYPTIPMSLIFKMLRRGEIIVSFLPA------QKGEVLRFG-- 57

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            + ++  I+++ +    V + K         +YED  I V +KP GI     S   Y + 
Sbjct: 58  -DTVSFEIEDRFLEHKKVEILK---------VYEDDNIVVIDKPYGIPSHPDSNNEYSV- 106

Query: 131 GFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               SW++   SK + P+L HRLD+ T+G++++A+ R     + +    R I K Y  + 
Sbjct: 107 ---VSWIENNYSKNELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRAIIKKYLCIT 163

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                 +   + ++L K S     Y+    Q+  G +  ++ +K++         ++++ 
Sbjct: 164 KKADLPESGVLVHYLKKDSKKSKVYISDFPQD--GYSEVVTAYKIVRQ-KDDLQLVDVEI 220

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
            TG+THQ+R    H+G  I+GD KY
Sbjct: 221 KTGKTHQIRAQLAHIGLCILGDSKY 245


>gi|71910662|ref|YP_282212.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
 gi|71853444|gb|AAZ51467.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
          Length = 301

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 112/227 (49%), Gaps = 19/227 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSK--GQKPRLTHRLDQETSGI 157
           +++ED    V NKP G +    +  +  I  F+K++ VD+    Q+  +  RLD++TSG+
Sbjct: 78  IVHEDDHFLVINKPIGFASIPSAIHSNTIANFIKAYYVDNHYLDQQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + R I+K Y++LV G  +  ++ + IA     K  I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQTRSIEKRYFALVSGNGMLPDEGDIIAPIGRSKDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +  +    YA + +KV+  +++    ++++ HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRAVDPMGKYAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGFPLLGDDLYGGR 251

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                T     +  LH  Y++   P     +       H+   +DS+
Sbjct: 252 LDLGIT-----RQALHCHYLNFKDP---FTESDCSCAIHLTDDFDSV 290


>gi|300814696|ref|ZP_07094946.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
 gi|300511169|gb|EFK38419.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
          Length = 295

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/229 (28%), Positives = 114/229 (49%), Gaps = 18/229 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQ----KPRLTHRLDQET 154
           ++YED  I V +KP  + V  G+G +    ++G L  + +        +P + HRLD+ T
Sbjct: 77  VIYEDDYIAVISKPQDLVVHIGAGNSSGTLVNGLLYKFKNQLSNLDPLRPGIVHRLDKNT 136

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+   A  +L + F+  +I+K Y ++V G  K  +  I    + ++      + 
Sbjct: 137 SGLMIIAKNNQAHINLVDQFKNSQIKKYYLAIVHG--KTPESGIIEEPIGRNPNDRKKMA 194

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV +N K    AI+ +K +  F Q++  L +   TGRTHQ+RVH  ++G P++GD  Y  
Sbjct: 195 VVYKNSKQ---AITKYKKLKEF-QEYSLLNINLLTGRTHQIRVHMAYIGYPVLGDIIY-- 248

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
              G   S   +K  LH+  +   HP    +++     P    K  D +
Sbjct: 249 ---GRKNSFKIDKQMLHSYKLIFNHPITNQKMEFKDEFPIRFKKFIDKI 294


>gi|293394695|ref|ZP_06638987.1| tRNA pseudouridine synthase C [Serratia odorifera DSM 4582]
 gi|291422821|gb|EFE96058.1| tRNA pseudouridine synthase C [Serratia odorifera DSM 4582]
          Length = 257

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 102/229 (44%), Gaps = 42/229 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKPAG  V              +SW+DS+             GQ     
Sbjct: 4   ILYQDQYLVAVNKPAGWLVH-------------RSWLDSRETVFVMQTVRDQIGQHVFTV 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++A +   A  L++ F   ++QK Y ++V G              ++  
Sbjct: 51  HRLDRPTSGVLLMALSSEVAHLLSQQFEQHQVQKTYHAVVRGFVTQGARLDYPLTQERDK 110

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRV 257
           I   +     + +K    A++H++ +             + ++  +E+QP TGR HQLR 
Sbjct: 111 IADKFA----EQDKEPQPAVTHYRPLAQVEMPVAIGRYDSARYSLMELQPETGRKHQLRR 166

Query: 258 HALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           H  H+  PI+GD K+      +G       ++L LHA ++   HP  G+
Sbjct: 167 HMTHLRHPIIGDSKHGDLRQNRGMAQHFGSSRLMLHASHLQFTHPVTGQ 215


>gi|215411202|ref|ZP_03420010.1| pseudouridylate synthase [Mycobacterium tuberculosis 94_M4241A]
          Length = 303

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 111/222 (50%), Gaps = 14/222 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY D  I   +KPA ++     G     + G L +    + + G   R  + HRLD  T
Sbjct: 78  ILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRITTSGVHERQGIVHRLDVGT 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA +  A   L  +F+ R + K Y +LV G P      I   + +  H G ++  
Sbjct: 138 SGVMVVAISERAYTVLKRAFKYRTVDKRYHALVQGHPDPSSGTIDAPIGR--HRGHEWKF 195

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + +N +   ++++H+  ++ F      L++   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 196 AITKNGR---HSLTHYDTLEAFVAA-SLLDVHLETGRTHQIRVHFAALHHPCCGDLVYGA 251

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           + K      + ++ +LHAR +   HP +G R++I +P PA +
Sbjct: 252 DPKLAKRLGL-DRQWLHARSLAFAHPADGRRVEIVSPYPADL 292


>gi|294787462|ref|ZP_06752715.1| ribosomal large subunit pseudouridine synthase D [Parascardovia
           denticolens F0305]
 gi|294484818|gb|EFG32453.1| ribosomal large subunit pseudouridine synthase D [Parascardovia
           denticolens F0305]
          Length = 325

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/287 (25%), Positives = 134/287 (46%), Gaps = 21/287 (7%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV-----INALNHIIKEQKILDSSVNLTKH 93
           +++  GQ RV+ + V  + +I  G  + +         + +      Q   D        
Sbjct: 27  RLIADGQARVEGRSVPKSGQILPGDFILVSSAGSTAGPSGVRIFTGSQTSKDEKAAGPNQ 86

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLK--SWVDSKGQKPRL 146
           ++    I+ YED  + V +KPAG++    +G     +   +    K  S VDS   +P +
Sbjct: 87  AEASLPIV-YEDDDLVVVDKPAGMASHPAAGWAGPTVVEALQALDKDLSRVDSD-IRPGI 144

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD  TSG+++V ++  A   + E F   +++K Y +LV G     +  +   + +++
Sbjct: 145 VSRLDAGTSGLMLVCKSDRAFVAMKEQFARHQVKKTYQTLVQGHIAQDRATVEAPIARQT 204

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                +   +  + K    AI+H+ V++        L +   TGRTHQ+RVH   +G P+
Sbjct: 205 G-ASSFRFAISPDGK---PAITHWDVLERLPGA-TLLSINLETGRTHQIRVHLSSLGHPL 259

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +GD  Y AN +      + N+ +LH+  ++  HP GGR + + +PLP
Sbjct: 260 IGDTLYGANPRLAEELGL-NRQWLHSIRLEFTHPVGGRTIHLESPLP 305


>gi|228944990|ref|ZP_04107351.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|228814659|gb|EEM60919.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
          Length = 307

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 110/226 (48%), Gaps = 22/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++YED  + + NKP  +      +GG G   ++  F    +     K R  HRLD++T+G
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAF-HYQMKGLETKVRHIHRLDKDTTG 145

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D  H  
Sbjct: 146 GVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRDRHHAT 199

Query: 217 KQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           ++  + KG + AI+++KV + F  Q    + +Q  TGRTHQ+RVH  + G P+VGD  Y 
Sbjct: 200 RRRVSPKG-DQAITYYKVEEYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYG 258

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
              K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 259 GQTK------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDT 298


>gi|149194036|ref|ZP_01871134.1| Pseudouridine synthase, RluD [Caminibacter mediatlanticus TB-2]
 gi|149135989|gb|EDM24467.1| Pseudouridine synthase, RluD [Caminibacter mediatlanticus TB-2]
          Length = 308

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 80/311 (25%), Positives = 145/311 (46%), Gaps = 56/311 (18%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINAL 74
           ++N RLD++  N   +++   ++++++ G V+V++K + K   +++  + V + P+    
Sbjct: 7   DKNKRLDKFLANKL-NVSRNQIEQLIKKGYVKVNEKVITKSGYKLKENEKVEVLPIK--- 62

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                           TK ++F   IL YED  + V NKP GI V        + +  L 
Sbjct: 63  -----------KEEKETKKANFDIPIL-YEDEDLLVINKPPGIVVHPAPS---YKEATLV 107

Query: 135 SWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            W+  KG         ++  + HR+D+ETSG LV+A+     + L+   + + + + Y+ 
Sbjct: 108 DWLKQKGYSLSTIAGEERFGIVHRIDKETSGALVIAKNNKTHEFLSNQLKDKSMGR-YYL 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           ++   P  + +C+      +  IG +      + +VK  ++     +  F   +  A K 
Sbjct: 167 MLLNEPLKEAKCV------EEKIGRNPKNRLKMAIVKNGKEAKTLFVPIFD--NLTAAKL 218

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
                  +TGRTHQ+RVH   +G  I+GD  Y     G     I+ ++ LHAR +   HP
Sbjct: 219 -------YTGRTHQIRVHLTKLGRYILGDTTY-----GKKDQNIK-RVMLHAREIYFTHP 265

Query: 301 EGGRLQITAPL 311
            G +L I APL
Sbjct: 266 NGKKLSIIAPL 276


>gi|187932847|ref|YP_001886621.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum B str. Eklund 17B]
 gi|187721000|gb|ACD22221.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum B str. Eklund 17B]
          Length = 302

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 78/320 (24%), Positives = 141/320 (44%), Gaps = 35/320 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIPPV 70
           V  + E +R+D++        +   +Q ++    ++V+ K +K N ++++  ++V   P 
Sbjct: 8   VSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNDKLIKNNYKLKACDEIVITMPE 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
              L       K+    ++L          +LYED  + V NK  G+ V    G      
Sbjct: 68  AETL-------KVESEDIDLD---------ILYEDKDVIVVNKEQGMVVHPAPGNYNGTL 111

Query: 129 IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D        +P + HR+D++TSG+LV+A+   +   L    +   + + Y+
Sbjct: 112 VNALLFHCTDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYY 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK-QNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G  KN    I   L      G D  + +K    +    AI+H++V++ +      +
Sbjct: 172 ALVEGRFKNDSGIIDKPL------GRDKKNRLKIAITEDGRRAITHYEVLERYDTGCTLI 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + +  TGRTHQ+RVH   +G P+VGD  Y    K  F    Q    LHA+ +   HP   
Sbjct: 226 KCKLETGRTHQIRVHMASLGHPLVGDPLYGFK-KQKFKLKGQ---MLHAKKLGFIHPTKN 281

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             ++    LP +  +  + L
Sbjct: 282 EYMEFETNLPEYFEEIIEKL 301


>gi|15675107|ref|NP_269281.1| hypothetical protein SPy_1127 [Streptococcus pyogenes M1 GAS]
 gi|13622265|gb|AAK34002.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS]
          Length = 301

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 58/205 (28%), Positives = 105/205 (51%), Gaps = 16/205 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSK--GQKPRLTHRLDQETSGI 157
           +++ED    V NKP G +    +  +  I  F+K++ VD+    Q+  +  RLD++TSG+
Sbjct: 78  IVHEDDHFLVINKPIGFASIPSAIHSNTIANFIKAYYVDNHYLDQQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + R I+K Y++LV G  +  ++ + IA     K  I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQTRSIEKRYFALVSGNGMLPDEGDIIAPIGRSKDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +  +    YA + +KV+  +++    ++++ HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRAVDPMGKYAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGFPLLGDDLYGGR 251

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                T     +  LH  Y++   P
Sbjct: 252 LDLGIT-----RQALHCHYLNFKDP 271


>gi|313113934|ref|ZP_07799491.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310623729|gb|EFQ07127.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 335

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 83/333 (24%), Positives = 153/333 (45%), Gaps = 30/333 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           QY    ND+  +RL R+ ++         L K  R+ +V+V+ K+     RIQ+G ++ +
Sbjct: 3   QYTATANDD-GVRLSRFVQSVTRDFPTSLLYKSFRNKRVKVNGKKAVPEYRIQAGDLIEL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIA 126
              IN      +  K +  +    K +   K  ++YED  I V  KP  +      +G A
Sbjct: 62  --YINDEFFPPEGAKTVQKAAPKKKQNQ-PKVNVIYEDENIAVLYKPTHLLCHSDRTGDA 118

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +D F + ++  KG+         KP + +RLD+ T G+++ A++  A + + E  R  
Sbjct: 119 NLVDAFTQ-YLAEKGEYDPHGENRFKPGICNRLDRGTEGLVIAAKSYTALRDMNEIIRTD 177

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y+++  GIP++ +     W           +H  +  ++     I+   V+   A
Sbjct: 178 LLKKEYYTITVGIPQSGR--FTAWWEHDEKNNKVSIHAHQSQDERRKQIITDVDVLRT-A 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR--YM 295
             F   ++   TGRTHQ+R H  ++G P++GD KY  N K N  +  + +     R  ++
Sbjct: 235 GPFALCKIGLVTGRTHQIRAHLAYLGRPVLGDIKY-GNRKMNERTGTKTQALCAVRVTFL 293

Query: 296 DLPHP------EGGRLQITAPLPAHMVKTWDSL 322
           D+P         G  +++  P    +VK +D+L
Sbjct: 294 DIPEENTLHYLSGKVVKLKDP---QIVKQFDAL 323


>gi|256847721|ref|ZP_05553166.1| pseudouridylate synthase [Lactobacillus coleohominis 101-4-CHN]
 gi|256715410|gb|EEU30386.1| pseudouridylate synthase [Lactobacillus coleohominis 101-4-CHN]
          Length = 297

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/274 (26%), Positives = 127/274 (46%), Gaps = 34/274 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           GQ  VD + V+   ++   Q + I      ++    +  +  SS  LT         ++Y
Sbjct: 37  GQFLVDHRHVRPTTQVLPNQTLTI-----QVDAETPDPTVQSSSQPLT---------IVY 82

Query: 104 EDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ED+   V NKP GI+      +    I   + G+L+   D   Q+P L  RLD+ TSG+L
Sbjct: 83  EDANWLVINKPTGIASIPGPTEDNGTILNRVKGYLEKNEDPN-QRPHLITRLDKYTSGLL 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+ R A+  +++      +QK Y ++V G    K+  + +  +K+  + G    ++  
Sbjct: 142 LVAKHRVASSMISQQVEKHTMQKRYLAVVAG-KLTKQHGVIDQPIKR--VAGQTARII-- 196

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +     A + +       + +  +++Q H+GRTHQ+RVH   +G P+VGDH Y    + 
Sbjct: 197 -DPAGQPARTEYWCQQT-NEDYSLVQLQLHSGRTHQIRVHMSFIGHPLVGDHLYGGPLE- 253

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
                I +   LHA  +    P    +LQ  AP+
Sbjct: 254 -----IAHHQVLHASTLSFRDPFTEQQLQFQAPM 282


>gi|319901461|ref|YP_004161189.1| pseudouridine synthase [Bacteroides helcogenes P 36-108]
 gi|319416492|gb|ADV43603.1| pseudouridine synthase [Bacteroides helcogenes P 36-108]
          Length = 549

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 63/214 (29%), Positives = 107/214 (50%), Gaps = 25/214 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILVV 160
           +YED  + V +KPAG+    G      +   ++  + ++ G  P + HRLD  TSG+LV+
Sbjct: 349 VYEDKWLVVVSKPAGMLTVPGKEETVSVYSLMRERYPEADG--PLIVHRLDMATSGLLVI 406

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A+T+   QHL   F+ R ++K Y +L+      K     +W   +  +  + +   +Q  
Sbjct: 407 AKTKQVHQHLQAQFKNRSVKKRYIALL------KDTVTRDWGTIELPLCLNPLDRPRQMV 460

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
           + +    A+++F+V++        +   P TGRTHQLRVH  H   + CPI+GD  Y   
Sbjct: 461 HPEHGKPALTNFEVLERKG-NHTRIAFYPRTGRTHQLRVHTAHPLGLHCPIIGDELYGEK 519

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
                      +LYLHA  ++  HP  G +++I+
Sbjct: 520 ---------AERLYLHAEVLEFIHPITGEKMKIS 544


>gi|315636965|ref|ZP_07892189.1| RluA family ribosomal large subunit pseudouridine synthase
           [Arcobacter butzleri JV22]
 gi|315478795|gb|EFU69504.1| RluA family ribosomal large subunit pseudouridine synthase
           [Arcobacter butzleri JV22]
          Length = 328

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 122/250 (48%), Gaps = 33/250 (13%)

Query: 85  DSSVNLTKHSDFLKSIL-------LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           ++ +N  K  +FLK+ L       +YED  I V NKP  ++V     +    D  L  W+
Sbjct: 63  EAQLNKRKDEEFLKNSLEDKEVEIIYEDDYILVLNKPYNLTVHDAPSVK---DATLVDWL 119

Query: 138 DSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             K          ++  + HRLD+ TSG++V+A+T  A  +L++    + + + Y +++ 
Sbjct: 120 KLKNISLSTISGEERHGIVHRLDKGTSGVMVIAKTNEAHLNLSKQLEDKSMGRYYLAILD 179

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHF-KVIDCFAQKFCWLEMQ 246
              K       N +++K  IG +  + +K + E+   YA S F K+     +KF  +  +
Sbjct: 180 LALK------ENVIIEKP-IGRNPNNRLKMSIEENGRYAKSAFSKIALSDNEKFELIACK 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
            +TGRTHQ+RVH   +   I+GD+ Y   FKG       N+  LHA Y+ L HP    ++
Sbjct: 233 LYTGRTHQIRVHLSSINRHILGDNLYG--FKGELNKI--NRFLLHAYYLYLTHPVTNKQM 288

Query: 306 QITAPLPAHM 315
              A LP  +
Sbjct: 289 CFKANLPEDI 298


>gi|313889381|ref|ZP_07823029.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
 gi|313122213|gb|EFR45304.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
          Length = 296

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 58/206 (28%), Positives = 103/206 (50%), Gaps = 18/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V NKP G +    +  +  I  F+K +    D   ++  +  RLD++TSG+
Sbjct: 78  IVYEDDHFLVINKPVGYASIPSAIHSNTIANFIKGYYVEQDYPNKQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVH 214
           ++ A+   A   L +  + R I+K Y++LV G   +P ++ E IA     K  I      
Sbjct: 138 MLFAKHGYAHARLDKQLQARAIEKRYFALVSGDGQLP-DQGEIIAPIGRSKDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +  +    YA + ++V+  +A+    ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRTVDPMGKYARTSYQVVGRYAENVHLVDIKLHTGRTHQIRVHFSHIGFPLLGDDLYGG 250

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
                 T     +  LH  ++   +P
Sbjct: 251 RLDLGIT-----RQALHCHFLSFHNP 271


>gi|237740892|ref|ZP_04571373.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           4_1_13]
 gi|229431189|gb|EEO41401.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           4_1_13]
          Length = 314

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 81/302 (26%), Positives = 139/302 (46%), Gaps = 46/302 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           V ++ E MRLD++            L+K++ +  V+++ K +  N R ++ G+ + +   
Sbjct: 12  VSSEYEGMRLDKYLSKQIEEATRSYLEKLIDNNYVKINSKVINKNGRKLKLGEKIEVS-- 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                 I KE+ I   + N++         ++YE+    V NK  G+ V    G      
Sbjct: 70  ------IPKEENIDIEAENISLD-------IVYENDDFIVINKSYGMVVHPAYGNYSGTL 116

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + Y+ +    S ++    +P + HRLD++TSG+++VA+   A   L   F  + I K
Sbjct: 117 VNALLYYTNNL--SSING-NIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFTDKTIHK 173

Query: 182 IYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            Y  +V G    +N    I N + + S      + VVK+N K    AIS++KVI+     
Sbjct: 174 TYLCIVKGNFSEENLNGRIENLIGRDSK-DRKKMAVVKENGKT---AISNYKVIEQ-VDG 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------FKGNFTSPIQNKL 288
           +  +E+   TGRTHQ+RVH   +   I+GD  Y              +K  F +P+ NK 
Sbjct: 229 YSLVEIAIETGRTHQIRVHMKSINHVILGDSTYGNEDKNVKRQMLHAYKLEFLNPLDNKE 288

Query: 289 YL 290
           Y+
Sbjct: 289 YI 290


>gi|148977056|ref|ZP_01813702.1| ribosomal large subunit pseudouridine synthase A [Vibrionales
           bacterium SWAT-3]
 gi|145963716|gb|EDK28977.1| ribosomal large subunit pseudouridine synthase A [Vibrionales
           bacterium SWAT-3]
          Length = 560

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 69/211 (32%), Positives = 108/211 (51%), Gaps = 26/211 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++YED +I V NKP       G  I   +   +K+ + ++ G  P + HRLD  TSG+L+
Sbjct: 359 IVYEDEEIVVVNKPEEFLSVPGKFIEDSVYTRIKARYPEATG--PLIIHRLDMSTSGLLI 416

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +A T  + +H+ + F  R ++K Y +L+ G+   +   I+  L       GD     +Q 
Sbjct: 417 LALTAESNKHIQKQFIDRTVEKRYTALLDGVITGESGDISLPL------RGDITDRPRQL 470

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
             +E G N A +H++ +   + K   + + P TGRTHQLRVH  H   +G PI GD  Y 
Sbjct: 471 VCHEHGRN-AETHWQAVSTNSGK-TKVHLYPKTGRTHQLRVHCAHPQGLGVPIRGDDLY- 527

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             +K       + +L+LHA Y+ L HP  G 
Sbjct: 528 -GYK-------RERLHLHAGYLKLIHPTTGE 550


>gi|159045646|ref|YP_001534440.1| ribosomal large subunit pseudouridine synthase A [Dinoroseobacter
           shibae DFL 12]
 gi|157913406|gb|ABV94839.1| ribosomal large subunit pseudouridine synthase A [Dinoroseobacter
           shibae DFL 12]
          Length = 219

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 63/208 (30%), Positives = 100/208 (48%), Gaps = 22/208 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++ED+ + +  KP+G+    G G    +   L S V        L HRLD++TSG++V 
Sbjct: 18  LVHEDAHLLLVEKPSGLLSVPGRG--PELADCLLSRVQGAFPDALLVHRLDRDTSGLMVF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A T  A +HL   F  R+I+K Y + VWG             I +W  +          +
Sbjct: 76  ALTAHAQRHLGLQFEKRQIKKSYVARVWGQVAEATGTVDLPLIVDWPNRP---------L 126

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K + +    A++ ++V+   ++    + + P TGR+HQLRVH   +G PI+GD  Y   
Sbjct: 127 QKVDPETGKAAVTDWRVLKR-SEAETRVRLFPKTGRSHQLRVHMQALGHPILGDPFYAEG 185

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
               F      +L LH+  + L HP+GG
Sbjct: 186 AARAFP-----RLMLHSESLRLRHPDGG 208


>gi|324989625|gb|EGC21569.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK353]
          Length = 291

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/202 (32%), Positives = 94/202 (46%), Gaps = 22/202 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPRELALLNHVSAYV---GETCYVVHRLDKETSGAILFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK---Q 218
           +       L      R I + YW+LV G   +KK      L+ K  IG D     K   +
Sbjct: 141 KNSFVLPILNRLLEKREISREYWALVQGKFPSKK------LIYKDKIGRDRHDRRKRLVE 194

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +KG  YA +H   +  F Q    ++ Q  TGRTHQ+RVH  H G P++GD  Y    KG
Sbjct: 195 PQKGL-YAETHVTRVKQFGQA-ALVKCQLKTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG 252

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                   +L LHA  +   HP
Sbjct: 253 --------RLMLHAHRLTFTHP 266


>gi|196035329|ref|ZP_03102734.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
 gi|195992006|gb|EDX55969.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
          Length = 307

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 110/226 (48%), Gaps = 22/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++YED  + + NKP  +      +GG G   ++  F    +     K R  HRLD++T+G
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAF-HYQMKGLETKVRHIHRLDKDTTG 145

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D  H  
Sbjct: 146 GVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRDRHHAT 199

Query: 217 KQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           ++  + KG + AI+++KV + F  Q    + +Q  TGRTHQ+RVH  + G P+VGD  Y 
Sbjct: 200 RRRVSPKG-DQAITYYKVEEYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYG 258

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
              K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 259 GQTK------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDT 298


>gi|19746076|ref|NP_607212.1| hypothetical protein spyM18_1088 [Streptococcus pyogenes MGAS8232]
 gi|21910322|ref|NP_664590.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28895899|ref|NP_802249.1| hypothetical protein SPs0987 [Streptococcus pyogenes SSI-1]
 gi|50914193|ref|YP_060165.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|71903490|ref|YP_280293.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94988598|ref|YP_596699.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|94990474|ref|YP_598574.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94994396|ref|YP_602494.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|139473780|ref|YP_001128496.1| RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo]
 gi|209559410|ref|YP_002285882.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pyogenes NZ131]
 gi|251782299|ref|YP_002996601.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|19748247|gb|AAL97711.1| conserved hypothetical protein [Streptococcus pyogenes MGAS8232]
 gi|21904518|gb|AAM79393.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28811149|dbj|BAC64082.1| conserved hypothetical protein [Streptococcus pyogenes SSI-1]
 gi|50903267|gb|AAT86982.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|71802585|gb|AAX71938.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94542106|gb|ABF32155.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|94543982|gb|ABF34030.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94547904|gb|ABF37950.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|134272027|emb|CAM30266.1| putative RNA pseudouridylate synthase [Streptococcus pyogenes str.
           Manfredo]
 gi|209540611|gb|ACI61187.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pyogenes NZ131]
 gi|242390928|dbj|BAH81387.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
          Length = 301

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 59/206 (28%), Positives = 106/206 (51%), Gaps = 18/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSK--GQKPRLTHRLDQETSGI 157
           +++ED    V NKP G +    +  +  I  F+K++ VD+    Q+  +  RLD++TSG+
Sbjct: 78  IVHEDDHFLVINKPIGFASIPSAIHSNTIANFIKAYYVDNHYLDQQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVH 214
           ++ A+   A   L +  + R I+K Y++LV G   +P ++ + IA     K  I      
Sbjct: 138 MLFAKHGYAHARLDKQLQTRSIEKRYFALVSGNGTLP-DEGDIIAPIGRSKDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +  +    YA + +KV+  +++    ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRAVDPMGKYAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGFPLLGDDLYGG 250

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
                 T     +  LH  Y++   P
Sbjct: 251 RLDLGIT-----RQALHCHYLNFKDP 271


>gi|331083782|ref|ZP_08332891.1| hypothetical protein HMPREF0992_01815 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330403207|gb|EGG82767.1| hypothetical protein HMPREF0992_01815 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 337

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 79/337 (23%), Positives = 146/337 (43%), Gaps = 35/337 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +VV+  E   RLD++   +        L K+LR   + ++ K+   N ++Q    ++
Sbjct: 1   MKQLVVKEIESGQRLDKFLGKYLKEAPKSFLYKMLRKKNITLNGKKATGNEKLQPNDEIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--- 123
           +    + L     E+K           S   +  ++YE++ +   NKP G+  Q      
Sbjct: 61  LFLSDDTLEKFCGEEK----------SSSRTELDIVYENNHVLFVNKPVGMLSQKAEKED 110

Query: 124 -GIAYHIDGFLK-----SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  +I G+L      +  D +  +P + +RLD+ TSGI+   +T    Q +++ F+ R
Sbjct: 111 VSLVEYITGYLLEEKFLTKEDLRTFRPGVCNRLDRNTSGIVAAGKTVQGLQEMSQWFKER 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G    +   +  +L K      + V V  +  +G+    + ++ +    
Sbjct: 171 NLHKYYLTLVKG-KVERPAHVKGYLWKDEK--KNKVAVFPEKREGSLPIETKYEPLGISK 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLHA 292
                L+++  TGR+HQ+R H   +G P++GD KY +     NF+  +    Q    LHA
Sbjct: 228 NGDTLLKVELLTGRSHQIRSHLAGLGHPVIGDWKYGSKEKNENFRKKYGIEFQ---LLHA 284

Query: 293 RYMDLPHPEG-----GRLQITAPLPAHMVKTWDSLGF 324
             +  P  EG         ITA +P    K     G 
Sbjct: 285 WKLSFPKTEGILKELSLKTITADVPEKFQKALKGEGL 321


>gi|303252861|ref|ZP_07339020.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307247850|ref|ZP_07529886.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|302648291|gb|EFL78488.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306855652|gb|EFM87819.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
          Length = 247

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 117/244 (47%), Gaps = 24/244 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPVHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A+ ++E F   +++K Y ++V G   +K E   ++ LK   +  D +       
Sbjct: 65  ALNSKMARLMSEQFEQHQLEKGYLAVVRGYLLDKGEI--DYPLK---VILDKIADKFSQP 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KEAQQAVTFYQNLASVEMLYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPIIGDT 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
           KY  +   N T   +   ++L LH+ ++   HP+   +++I APL     K W +L   +
Sbjct: 180 KY-GDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLD----KQWQNLFATF 234

Query: 327 DRNL 330
           + N 
Sbjct: 235 NWNF 238


>gi|78484624|ref|YP_390549.1| pseudouridine synthase [Thiomicrospira crunogena XCL-2]
 gi|78362910|gb|ABB40875.1| tRNA pseudouridine synthase C [Thiomicrospira crunogena XCL-2]
          Length = 252

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 112/246 (45%), Gaps = 19/246 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   +KPAG+ V   S I  H   F ++   D   QK    HRLD+ TSG+L+
Sbjct: 12  ILYQDDSLVAVHKPAGLLVHR-SPIDRHETQFAVQMTRDQINQKVYPLHRLDKATSGLLL 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A     A+ + + F    IQK Y ++  G      E       K   +G  +     Q 
Sbjct: 71  FALDSNTARLMGQQFEEHTIQKHYLAICRGWTAEHGEIDHALKHKLDKLGDRHA----QT 126

Query: 220 EKGANYAISHF----------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            K    A+++F          K+    +Q++  +++ P TGR HQLR H  H+  PI+GD
Sbjct: 127 NKPPQEALTNFERLATTDVMHKIGKFDSQRYSLVKLMPKTGRKHQLRRHLNHISHPIIGD 186

Query: 270 HKYCANFKGNF--TSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLGFKY 326
            KY      +F  T   Q++LYL A  +   HP+   R+ + APL     K    L ++ 
Sbjct: 187 VKYGDRHHNHFFNTWLGQHRLYLAATSLTFNHPQTNARMTLNAPLELSYQKATQHLNWQE 246

Query: 327 DRNLYI 332
           +   YI
Sbjct: 247 ETATYI 252


>gi|294101380|ref|YP_003553238.1| pseudouridine synthase, RluA family [Aminobacterium colombiense DSM
           12261]
 gi|293616360|gb|ADE56514.1| pseudouridine synthase, RluA family [Aminobacterium colombiense DSM
           12261]
          Length = 314

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 81/287 (28%), Positives = 138/287 (48%), Gaps = 43/287 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+  +  +P++    + + +R G VRVD ++   + R++ GQ V +P          +
Sbjct: 15  RLDKVIRTLWPNLPLGAMMRGIRKGLVRVDGRKTSCSVRLEDGQSVYVP---------WE 65

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVD 138
           E ++++ SV  TK +  L   ++Y+D  I V NK AG+ +Q   SG    I+   + W++
Sbjct: 66  EPELIEKSVK-TKRTGALS--IVYKDHYIMVLNKEAGLIIQPDQSGEESLIE---RVWLE 119

Query: 139 SKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +   +    HRLD+ T+G++VVA    + + L  +FR   + K Y   V G    + 
Sbjct: 120 VEPEGDFRACAVHRLDRNTTGLVVVALHGQSLRELQRAFRDNDVDKTYLVAVRGQTPLEG 179

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGR 251
           +  A     + H      ++V  +  G   A +H++ I    +C   K   L     TGR
Sbjct: 180 DITAPLQKDRDH------NIVTASPDGLP-AHTHYEKIAGDDECSLLKVSLL-----TGR 227

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +HQ+RVH    G P++GD KY     G+F     NK + H   +D P
Sbjct: 228 SHQIRVHLAISGYPVIGDVKY-----GDFA---LNKQWYHRIRLDHP 266


>gi|303277917|ref|XP_003058252.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226460909|gb|EEH58203.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 508

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 114/242 (47%), Gaps = 30/242 (12%)

Query: 100 ILLYEDSKIYVFNKPAGISV--QGGSGIA--------YHIDGFLKSWVDS-KGQKPR-LT 147
           +++YED      +KPAGI     GG+ +           +D F    V +  G   R + 
Sbjct: 253 VVVYEDDHFAAVSKPAGILTHPTGGASVDKRSVTLVDLALDAFGDEHVSALNGADARGIV 312

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ T+G++V+A+T  A   L  ++  R++QK YW++V G+P  ++         +  
Sbjct: 313 HRLDKPTTGVMVIAKTDVAHALLVTAWYQRKVQKTYWAIVEGVPGRRRPKRRGDAEGEDA 372

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCF--AQKFCWL-EMQPHTGRTHQLRVH-ALHMG 263
              D++  V         A S +KV++ F      C L E+ PHTGR HQ+R H    +G
Sbjct: 373 ETEDHLFGVVDAPADGRPAKSDWKVLEIFNLPDATCSLVEVTPHTGRKHQVRSHMGAILG 432

Query: 264 CPIVGDHKY------------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            P+VGD  Y             A    +   P  + ++LHA  + L HP  G  + ++AP
Sbjct: 433 APLVGDPLYRRGKPAATPAAAAAALTADGAKP-GSVMFLHATSLRLEHPVTGEPMTLSAP 491

Query: 311 LP 312
           +P
Sbjct: 492 VP 493


>gi|94992422|ref|YP_600521.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
 gi|94545930|gb|ABF35977.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
          Length = 275

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 59/206 (28%), Positives = 106/206 (51%), Gaps = 18/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSK--GQKPRLTHRLDQETSGI 157
           +++ED    V NKP G +    +  +  I  F+K++ VD+    Q+  +  RLD++TSG+
Sbjct: 52  IVHEDDHFLVINKPIGFASIPSAIHSNTIANFIKAYYVDNHYLDQQVHIVTRLDRDTSGL 111

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVH 214
           ++ A+   A   L +  + R I+K Y++LV G   +P ++ + IA     K  I      
Sbjct: 112 MLFAKHGYAHARLDKQLQTRSIEKRYFALVSGNGTLP-DEGDIIAPIGRSKDSI------ 164

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +  +    YA + +KV+  +++    ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 165 ITRAVDPMGKYAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGFPLLGDDLYGG 224

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
                 T     +  LH  Y++   P
Sbjct: 225 RLDLGIT-----RQALHCHYLNFKDP 245


>gi|308273177|emb|CBX29780.1| hypothetical protein N47_F14750 [uncultured Desulfobacterium sp.]
          Length = 271

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 69/223 (30%), Positives = 109/223 (48%), Gaps = 23/223 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL----THRLDQETS 155
           +LYED  I V +K +G+ SV+            L ++V     K R+     HRLD+ETS
Sbjct: 44  ILYEDRDIIVIDKSSGLLSVEANYEAENTAHNLLTNYVRKGNPKARINLFVVHRLDRETS 103

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VH 214
           G+L+ A++    +     ++   ++K Y +LV+G    K   I ++L +    G +Y V 
Sbjct: 104 GVLIFAKSLEIREKFAAQWK--NVEKKYIALVYGNLTKKSGIIESYLAE----GDNYKVQ 157

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            VK   +G   AI+ +KVI   ++ +  LE+   TG+ +Q+R H    G PIVGD KY  
Sbjct: 158 SVKNPIEG-KLAITKYKVIKE-SKNYSLLEIDLLTGKKNQIRAHLSENGHPIVGDTKYRE 215

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           N KG        +L LHA  +   HP     +   A +P + +
Sbjct: 216 NTKG--------RLALHAFSIKFKHPFNNEEMMFEAKIPEYFL 250


>gi|228926422|ref|ZP_04089494.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229120931|ref|ZP_04250173.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|228662591|gb|EEL18189.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|228833246|gb|EEM78811.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 307

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 110/226 (48%), Gaps = 22/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++YED  + + NKP  +      +GG G   ++  F    +     K R  HRLD++T+G
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAF-HYQMKGLETKVRHIHRLDKDTTG 145

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D  H  
Sbjct: 146 GVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRDRHHAT 199

Query: 217 KQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           ++  + KG + AI+++KV + F  Q    + +Q  TGRTHQ+RVH  + G P+VGD  Y 
Sbjct: 200 RRRVSPKG-DQAITYYKVEEYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYG 258

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
              K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 259 GQTK------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDT 298


>gi|329117419|ref|ZP_08246136.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
 gi|326907824|gb|EGE54738.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
          Length = 297

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 56/178 (31%), Positives = 93/178 (52%), Gaps = 13/178 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGI 157
           ++YED    V NKP G +    +  +  I  F+K++   K    +  H   RLD++TSG+
Sbjct: 78  IVYEDEHFLVINKPFGFASIPSAIHSNTIANFIKAYYIEKDYPNKQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVH 214
           ++ A+   A   L +  + R I K Y++LV G   +P +  E IA     K  I      
Sbjct: 138 MLFAKHGYAHARLDKQLQARSIDKHYYALVSGPGQLP-DSGEIIAPIGRSKDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + +  +    YA + ++V+  FA+    ++++ HTGRTHQ+RVH  H+G P++GD  Y
Sbjct: 191 ITRAVDPMGKYAKTTYQVVGRFAENVHLVDIKLHTGRTHQIRVHFSHIGFPLLGDDLY 248


>gi|304404981|ref|ZP_07386641.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
 gi|304345860|gb|EFM11694.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
          Length = 337

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 64/212 (30%), Positives = 105/212 (49%), Gaps = 17/212 (8%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGG-SGIAYHIDGFLKSWVDSKGQKPR----LTHRLDQE 153
           ++L+ED  I V  K AG+ S+          +  + +     +   PR    + HRLD++
Sbjct: 115 VILHEDDDIVVVQKDAGLLSISSDKENKENELTAYRQLTAHVRVHNPRNRIFVVHRLDRD 174

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++ A+T AA Q L  +++    ++ Y +LV G  +  +  I +WL + S +     
Sbjct: 175 TSGVMMFAKTEAAQQQLQNNWQEVVKERSYIALVDGKVRKAEGTITSWLRESSTLK---- 230

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                 E    +A++H+K +    Q +  LE+   TGR +Q+RVH   +G PI GD KY 
Sbjct: 231 MYSSFREGDGQHAVTHYKTLQT-NQHYSLLEVHLETGRKNQIRVHMEDIGHPIAGDKKY- 288

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
               G+ +  I  +L LHAR +   HP  G L
Sbjct: 289 ----GSRSREI-GRLGLHARILSFLHPTTGEL 315


>gi|256846833|ref|ZP_05552288.1| pseudouridylate synthase [Fusobacterium sp. 3_1_36A2]
 gi|256717799|gb|EEU31357.1| pseudouridylate synthase [Fusobacterium sp. 3_1_36A2]
          Length = 316

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 81/302 (26%), Positives = 139/302 (46%), Gaps = 46/302 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           V ++ E MRLD++            L+K++ +  V+++ K +  N R ++ G+ + +   
Sbjct: 12  VSSEYEGMRLDKYLSKQIEEATRSYLEKLIDNNYVKINSKVINKNGRKLKLGEKIEVS-- 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                 I KE+ I   + N++         ++YE+    V NK  G+ V    G      
Sbjct: 70  ------IPKEENIDIEAENISLD-------IVYENDDFIVINKSYGMVVHPAYGNYSGTL 116

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + Y+ +    S ++    +P + HRLD++TSG+++VA+   A   L   F  + I K
Sbjct: 117 VNALLYYTNNL--SSING-NIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFTDKTIHK 173

Query: 182 IYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            Y  +V G    +N    I N + + S      + VVK+N K    AIS++KVI+     
Sbjct: 174 TYLCIVKGNFSEENLNGRIENLIGRDSK-DRKKMAVVKENGKT---AISNYKVIEQ-VDG 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------FKGNFTSPIQNKL 288
           +  +E+   TGRTHQ+RVH   +   I+GD  Y              +K  F +P+ NK 
Sbjct: 229 YSLVEIAIETGRTHQIRVHMKSINHVILGDSTYGNEDKNVKRQMLHAYKLEFLNPLDNKE 288

Query: 289 YL 290
           Y+
Sbjct: 289 YI 290


>gi|161502239|ref|YP_001569351.1| hypothetical protein SARI_00264 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160863586|gb|ABX20209.1| hypothetical protein SARI_00264 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 318

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 59/181 (32%), Positives = 96/181 (53%), Gaps = 22/181 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G++VVA+T  A   L ES ++R I + Y ++  G         E I+    K++H+   
Sbjct: 143 TGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPISRHPTKRTHMS-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH + +       A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 201 -VHPMGKP------AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 252

Query: 272 Y 272
           Y
Sbjct: 253 Y 253


>gi|261856729|ref|YP_003264012.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261837198|gb|ACX96965.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
          Length = 222

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 107/215 (49%), Gaps = 18/215 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL E +   +  KP  +  Q G   A+  D  + + V+ +  + R+ HRLD +TSG++V+
Sbjct: 22  LLAETADFLIIAKPTRMLTQPGKE-AHKTDSLI-TRVNQEFPEARIVHRLDWDTSGVMVL 79

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           AR   A + L+ +F+ RR +K Y + V   P   +  I         IG D  H  +   
Sbjct: 80  ARHARAHRALSIAFQDRRTKKCYIAHVDRAPAPPQGLI------DRPIGSDREHRPRYRI 133

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +E+    + + + V++  A  F  L ++P TGR+HQLRVH L +G PI GD  Y  + + 
Sbjct: 134 DEEQGRPSQTRYVVLNETAD-FARLALEPITGRSHQLRVHLLSIGHPIQGDTLYHPHAQN 192

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
           +       +L LHA  +  P P  G  Q  + P+P
Sbjct: 193 H------ARLMLHAESLSFPDPASGITQTFSDPVP 221


>gi|15890930|ref|NP_356602.1| ribosomal large subunit pseudouridine synthase A [Agrobacterium
           tumefaciens str. C58]
 gi|15159240|gb|AAK89387.1| ribosomal large subunit pseudouridine synthase A [Agrobacterium
           tumefaciens str. C58]
          Length = 222

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 62/212 (29%), Positives = 104/212 (49%), Gaps = 10/212 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  + V +KP+G+    G   A  +   L + V  +  K  + +RLD++TSGI+++
Sbjct: 20  IVHRDDDLLVLDKPSGLLSVPGRDPA--LSDSLMTRVQKQFPKALMINRLDKDTSGIVLM 77

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           +  R A   +   F  R  +K Y ++VWG    ++  +   L     I  D     + + 
Sbjct: 78  SLNRKAHAAIAAQFEKRETRKSYVAIVWGTVAGEEGEVDLPL----AIDPDNKPRHRVDH 133

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    A S ++V++        L + P TGRTHQLRVH   +G PI+GD  Y A  +   
Sbjct: 134 ENGKPAQSLWRVLERLPLPATRLALTPLTGRTHQLRVHMKALGHPILGDEFY-AEGEALT 192

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
            +P   +L LHA+ +   HP+G  +  T P P
Sbjct: 193 AAP---RLMLHAQEVGFRHPDGRDVTYTVPCP 221


>gi|325124079|gb|ADY83602.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter
           calcoaceticus PHEA-2]
          Length = 221

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 65/207 (31%), Positives = 101/207 (48%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ 
Sbjct: 18  ILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R ++K Y +LV G    +       I +W  +   I    VH  
Sbjct: 76  AKHRDAEVAVSKMFQARTVKKHYIALVQGQVAQEGSVEVPLITDWENRPRQI----VHF- 130

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G +       ++         + ++P TGR+HQLRVH +H+G PI+GD  Y    
Sbjct: 131 ---ELGKHAKTLFQPLLYDGKTDQSRVLLEPVTGRSHQLRVHMMHIGHPIMGDKLYHPEP 187

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           K        N++ LHA Y+   HP  G
Sbjct: 188 KRFHL----NRMALHAAYLAFQHPLNG 210


>gi|162451128|ref|YP_001613495.1| pseudouridylate synthase/tRNA pseudouridine synthase C [Sorangium
           cellulosum 'So ce 56']
 gi|161161710|emb|CAN93015.1| Pseudouridylate synthase/tRNA pseudouridine synthase C [Sorangium
           cellulosum 'So ce 56']
          Length = 241

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 73/230 (31%), Positives = 113/230 (49%), Gaps = 28/230 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL+ D ++  F KP+G+ V  G G A  +  F+     + G+K    HRLD+ TSG+L+V
Sbjct: 10  LLHLDDRVAAFAKPSGLLVHRGWGDAPVV--FVDLAERALGRKVYPVHRLDRATSGVLLV 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A   AAA  L   F     +K Y +LV G+P     C+               H + + E
Sbjct: 68  ALDPAAAALLCAQFEQGLARKRYLALVRGVPPEHG-CVD--------------HPIPRRE 112

Query: 221 KGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---- 275
            G    A++ F+ +    +++  +E +P TGR HQ+R H  H+  PI+GD  Y       
Sbjct: 113 GGPRVPAVTDFERLHAL-ERYAVVEARPRTGRLHQVRRHLKHISHPIIGDVNYGKGEHNR 171

Query: 276 -FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLG 323
            F+  +     ++L LHA  + + HPE G  L++ APLP  +   +D LG
Sbjct: 172 LFRERYA---LHRLALHAAELAVAHPETGAPLRVAAPLPDDLRGPFDQLG 218


>gi|257095460|ref|YP_003169101.1| RluA family pseudouridine synthase [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257047984|gb|ACV37172.1| pseudouridine synthase, RluA family [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 375

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 109/227 (48%), Gaps = 13/227 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           +++ED  + V +K AG+ V  GSG      ++G L        + PR  + HRLD++T+G
Sbjct: 109 IVFEDDTLIVLDKQAGLVVHPGSGNWRGTLLNGLLHH-APQLARVPRAGIVHRLDKDTTG 167

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++VVA+T  A   L    + R +++ Y +LV GI +     I +  + +       + VV
Sbjct: 168 LMVVAKTLEAQTDLVRQLQARSVKRCYQALVRGIVEGAG--IVDAPIGRHPTVRTRMAVV 225

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                G   A +H++V++ F      +E    TGRTHQ+RVH   +  P+VGD  Y    
Sbjct: 226 ----SGGRPARTHYRVLERFV-ACTLIECALETGRTHQIRVHMTSIAHPLVGDPIYGGGA 280

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
                  +  +  LHA  + L HP  G+  +  + +PA M    D L
Sbjct: 281 SRVPQGAVFPRQALHACRLALVHPASGKAMLWRSGVPADMAALIDRL 327


>gi|332524051|ref|ZP_08400303.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
 gi|332315315|gb|EGJ28300.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 284

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 57/206 (27%), Positives = 104/206 (50%), Gaps = 18/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V NKP G +    +  +  I  F+K +    D   ++  +  RLD++TSG+
Sbjct: 66  IVYEDDHFLVINKPVGYASIPSAIHSNTIANFIKGYYVDQDYPNKQVHIVTRLDRDTSGL 125

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVH 214
           ++ A+   A   L +  + R I+K Y++LV G   +P ++ E +A     K  I      
Sbjct: 126 MLFAKHGYAHARLDKQLQARAIEKRYFALVCGEGQLP-DQGEIVAPIGRSKDSI------ 178

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +  +    YA + ++V+  +A+    ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 179 ITRTVDPMGKYARTTYQVVGRYAENVHLVDIKLHTGRTHQIRVHFSHIGFPLLGDDLYGG 238

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
                 T     +  LH  +++  +P
Sbjct: 239 RLDLGIT-----RQALHCHFLNFHNP 259


>gi|318040274|ref|ZP_07972230.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           CB0101]
          Length = 234

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 63/213 (29%), Positives = 102/213 (47%), Gaps = 10/213 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++   + V NKP G+  Q   G+   +   L S V  +  + +L HRLD++TSG+++V
Sbjct: 25  IVHQAPDLLVLNKPHGLLCQ--PGLGPELADSLISRVQQRWPQAQLVHRLDRDTSGLILV 82

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A      + L+  F  R++QK Y + V G+P      I   + K  H    Y       +
Sbjct: 83  ALASELHRELSRMFAERQVQKRYVADVHGVPDQPHGLIEWPIAKLQHRPPLY-----GVD 137

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                  + ++++     +   LE+QP TGR+HQLRVH   +G PI+GD  Y        
Sbjct: 138 PAGKACSTRWRLLQAHG-RCSRLELQPLTGRSHQLRVHLQAIGHPILGDPLY-GPLASAL 195

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             P+ ++L+LHA  +   HP     L   AP P
Sbjct: 196 DDPLGSRLHLHAAALHWLHPGSSESLAFDAPPP 228


>gi|109898644|ref|YP_661899.1| pseudouridine synthase [Pseudoalteromonas atlantica T6c]
 gi|109700925|gb|ABG40845.1| pseudouridine synthase [Pseudoalteromonas atlantica T6c]
          Length = 567

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 118/233 (50%), Gaps = 23/233 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           LNH+++   + ++ + L   +D  +  ++Y+D ++ + NKPA +    G  I+  +   +
Sbjct: 338 LNHMLEGLTVEENQL-LKNAADGEQIEIIYQDDEMLIINKPAQLLSVPGKHISDSVYTRI 396

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+ +        + HRLD  TSG++V+A + AA + L + F  R++ K Y +L+ GI  +
Sbjct: 397 KAML-PHATGSLIVHRLDMSTSGLMVIALSTAAHKVLQKQFISRQVSKRYMALIDGIVTD 455

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVID-CFAQKFCWLEMQPHTG 250
           +   I   L       GD+    +Q   EK    A + ++VI+     +   + + P TG
Sbjct: 456 ENGVITLPL------AGDFYDRPRQCVCEKTGKPAHTTWQVIERRHKTQQTKVYLHPRTG 509

Query: 251 RTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           RTHQLRVH  H   +  PIVGD  Y    +         +L+LHA+Y+ L HP
Sbjct: 510 RTHQLRVHCAHERGLNMPIVGDDLYGTQAR---------RLHLHAQYLGLFHP 553


>gi|194363955|ref|YP_002026565.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
 gi|194346759|gb|ACF49882.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
          Length = 253

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 69/234 (29%), Positives = 111/234 (47%), Gaps = 15/234 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           LL+ D ++ V NKPAG+ V   S +A   D FL   +  +  +P  L HRLD+ TSG L+
Sbjct: 28  LLHLDERLAVVNKPAGLMVHD-SKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGCLL 86

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV---- 215
           +A  R  A  L ++     + K Y ++  G P        +W +     GG    V    
Sbjct: 87  LAFDRDTASLLGKALMGGEVLKDYLTVCRGWPAE-----LSWRVDHDLDGGPGKPVKKPA 141

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V   ++ A   +S   + +  + ++  L  QP TGR  Q+R H  H+   ++GD  +  +
Sbjct: 142 VTDFQRLATGELS-VPIGEFTSSRYALLRCQPQTGRFRQIRRHLKHLSHHMIGDTSH-GD 199

Query: 276 FKGNFTSPIQN--KLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            + N    +Q   ++ LHA  +  PHP+GG + + APL     K  D  G++ D
Sbjct: 200 GRHNRIFRMQGVHRMLLHAERLRFPHPDGGTVDVRAPLDGGFQKALDLFGWQVD 253


>gi|188590369|ref|YP_001921578.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum E3 str. Alaska E43]
 gi|188500650|gb|ACD53786.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum E3 str. Alaska E43]
          Length = 302

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 78/320 (24%), Positives = 141/320 (44%), Gaps = 35/320 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIPPV 70
           V  + E +R+D++        +   +Q ++    ++V+ K +K N ++++  ++V   P 
Sbjct: 8   VSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNNKLIKSNYKLKACDEIVITMPE 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
              L       K+    ++L          +LYED  + V NK  G+ V    G      
Sbjct: 68  AEIL-------KVESEDIDLD---------ILYEDKDVIVVNKEQGMVVHPAPGNYNGTL 111

Query: 129 IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D        +P + HR+D++TSG+LV+A+   +   L    +   + + Y+
Sbjct: 112 VNALLFHCTDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYY 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK-QNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G  KN    I   L      G D  + +K    +    AI+H++V++ +      +
Sbjct: 172 ALVEGRFKNDSGVIDKPL------GRDKKNRLKIAITEDGRRAITHYEVLERYDTGCTLI 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + +  TGRTHQ+RVH   +G P+VGD  Y    K  F    Q    LHA+ +   HP   
Sbjct: 226 KCKLETGRTHQIRVHMASLGHPLVGDPLYGFK-KQRFKLKGQ---MLHAKKLGFIHPTKN 281

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             ++    LP +  +  + L
Sbjct: 282 EYMEFETNLPEYFEEIIEKL 301


>gi|294806510|ref|ZP_06765351.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|294446373|gb|EFG14999.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
          Length = 281

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 113/226 (50%), Gaps = 20/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 66  IVYEDAYIIVVEKMQGLLSVNTERQKERTAYTI---LNEYVQRSGRQFRVFIVHRLDRDT 122

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+     + L +++      + Y ++V G  +   + + +WL  K+     YV 
Sbjct: 123 SGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTL----YVS 178

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             + ++ G+  +I+H+K I   A  +  LE+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 179 SSEYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRKNQIRVHMQDLGHPIIGDGRYGR 236

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
               N   PI  +L LHA  +   HP  G L +   P PA   K +
Sbjct: 237 EDSPN---PI-GRLALHAFKLCFYHPVTGDLMEFETPYPAEFKKLF 278


>gi|160939065|ref|ZP_02086416.1| hypothetical protein CLOBOL_03959 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438028|gb|EDP15788.1| hypothetical protein CLOBOL_03959 [Clostridium bolteae ATCC
           BAA-613]
          Length = 366

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 75/314 (23%), Positives = 133/314 (42%), Gaps = 61/314 (19%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V  +E   RLD+    +        + K++R   + ++ K+   + R++ G  V+
Sbjct: 1   MQTLTVTQNEAGQRLDKLLTKYLNQAGKGFIYKMMRKKNITLNGKKCDGSERLEEGDQVK 60

Query: 67  IPPVINALNHI-------IKEQKILDSSVNLTKHSDFLKS-------------------I 100
           +      +           ++Q    SS   + H    K+                    
Sbjct: 61  LFLSDETIEKFSVPDMGGYEKQPGDQSSTGASSHEKREKARGKGGEHQGSRDREGGRRLD 120

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLD 151
           ++YED  I V NKP+G+  Q        ++ ++ +++   G+         KP + +RLD
Sbjct: 121 IVYEDQHILVVNKPSGMLSQKAKDSDMSLNEYILNYLIDSGKLPISQLRTFKPSICNRLD 180

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG++V  ++ A  Q + E F+ R I K Y  LV G  K +K+ IA +L         
Sbjct: 181 RNTSGLVVAGKSLAGLQVMNEVFKDRSIHKYYQCLVAGEIK-EKQLIAGFL--------- 230

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFA-----------QKFCWLEMQPHTGRTHQLRVHAL 260
                K++E     +I   +V D              + F  L++   TGR+HQ+R H  
Sbjct: 231 -----KKDESTNTVSIFPLEVEDSVPIMTEYLPLSGNKTFTLLQVTLITGRSHQIRAHLA 285

Query: 261 HMGCPIVGDHKYCA 274
            +G PIVGD+KY +
Sbjct: 286 SIGHPIVGDYKYGS 299


>gi|187477717|ref|YP_785741.1| ribosomal large subunit pseudouridine synthase D [Bordetella avium
           197N]
 gi|115422303|emb|CAJ48827.1| ribosomal large subunit pseudouridine synthase D [Bordetella avium
           197N]
          Length = 320

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 87/322 (27%), Positives = 135/322 (41%), Gaps = 47/322 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  D    RLD+      P  +   LQ  + +G V V+ +  K    +  G V+    
Sbjct: 19  IFIPPDVPADRLDKVLAGLMPGHSRSRLQGWIEAGHVLVNGQAAKVRQPVGPGDVL---- 74

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                   + EQ   +S     +  DF    ++   S   V NKPAG+    G+G     
Sbjct: 75  -------TVWEQPAPESLAFSPEPVDF---DVIDSSSDWIVVNKPAGLVTHPGAGNWTGT 124

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  + + S+  +  + HRLD++TSG++VVAR   A  HL    + R + + Y +L
Sbjct: 125 LLNGLLHRFPELSRVARAGIVHRLDKDTSGLMVVARNELAQTHLVRQLQARSMGREYLAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDY---VHVVKQNEKGANYAISHF--------KVIDC 235
             G        +A        IG D    V +  +    A  AI+H+        +  + 
Sbjct: 185 AHG-------WLAGAGTVDRPIGRDARVPVRMSVERPIAAKPAITHYLPQRRGEAQEGER 237

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             +  C LE    TGRTHQ+RVH   +G P++ D  Y        T     +  LHAR +
Sbjct: 238 VTEVICRLE----TGRTHQIRVHLASLGHPLLADTIYGGRALAGAT-----RQMLHARAL 288

Query: 296 DLPHPEGGRLQIT--APLPAHM 315
               P GGR ++T  A LP  M
Sbjct: 289 HFDDP-GGRGEVTFEAALPPDM 309


>gi|307705695|ref|ZP_07642541.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
 gi|307620709|gb|EFN99799.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
          Length = 278

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 93/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   +K+      L+ K  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDGNISSKE------LVFKDKIGRDRHDRRKRVVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F  K   +  +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 182 TKNGQYAETHVSRLKQFPNKTSLVRCKLKTGRTHQIRVHLSHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|238786690|ref|ZP_04630491.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           frederiksenii ATCC 33641]
 gi|238725058|gb|EEQ16697.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           frederiksenii ATCC 33641]
          Length = 217

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 102/207 (49%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NKP+G+ SV G    A      + + + +        HRLD  TSG++V
Sbjct: 14  ILYQDEHIMVVNKPSGLLSVPGR---APENKDSVMTRIQADFPHAESVHRLDMATSGVIV 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ 
Sbjct: 71  VALTKAAERELKRQFREREPKKSYVARVWGHLAQDEGLIDLPLI------CDWPNRPKQK 124

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E G + + + + V+         +++ P TGR+HQLRVH L +G PI+GD  Y    
Sbjct: 125 VCYETGKS-SQTEYLVLSRDTDGSTRVKLSPITGRSHQLRVHMLAIGHPILGDRFYAHPE 183

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
                S    +L LHA+ + + HPE G
Sbjct: 184 AKAMAS----RLQLHAQELCITHPEFG 206


>gi|167757684|ref|ZP_02429811.1| hypothetical protein CLOSCI_00014 [Clostridium scindens ATCC 35704]
 gi|167664704|gb|EDS08834.1| hypothetical protein CLOSCI_00014 [Clostridium scindens ATCC 35704]
          Length = 305

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 140/310 (45%), Gaps = 32/310 (10%)

Query: 16  EENMRLDRWF-KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           E  +R++++  +  Y   N   L+K+  S  V V+ + +  N R+ SG  +    VI+  
Sbjct: 22  EGGLRIEQFLLRRGYSLQNLTQLKKMKES--VLVNGQWLHLNRRLTSGDEL----VIHIQ 75

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
            H        +SS N+   +  L   ++YED  I V NKPAG+ +        +      
Sbjct: 76  EH--------ESSKNIPAVN--LSLDIVYEDEDIIVINKPAGMPIHPSQNNYRNSLANAL 125

Query: 135 SWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           +W   +  K    R  +RLD++TSG+ VV++   +   L+     R + + Y ++  G  
Sbjct: 126 AWYYQEQGKAFVFRCANRLDRDTSGLTVVSKHMLSGNVLSSMAADRMLHREYLAICRGHI 185

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   L +K    G  +      E+G   AI+H+ V+D        + ++  TGR
Sbjct: 186 TPSAGTIHAPLSRKP---GSIIERTVDWEQGET-AITHYCVVD-EKNGHSLVSLRLETGR 240

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+R+H  H+G P++GD+ Y  + +         +  LH+  +  PHP  G  ++  AP
Sbjct: 241 THQIRIHMKHLGYPLIGDYLYNPDME------YIGRQALHSHKLSFPHPITGEDMEFIAP 294

Query: 311 LPAHMVKTWD 320
           LP  M    D
Sbjct: 295 LPEDMQSVLD 304


>gi|153951567|ref|YP_001397630.1| ribosomal large subunit pseudouridine synthase A [Campylobacter
           jejuni subsp. doylei 269.97]
 gi|152939013|gb|ABS43754.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacter jejuni subsp. doylei 269.97]
          Length = 322

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 108/218 (49%), Gaps = 15/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL--KSWVDSKGQKPR--LTHRLDQET 154
           +LYED  + V NKP+ + V G S +  A  +D  +  K  + + G + R  L HRLD++T
Sbjct: 79  ILYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG +++A+     Q L+E    + + +IY +L+    K  K  +  +L++        + 
Sbjct: 139 SGAILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIA 198

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + K+N+   N   +   V+    +    +  +  TGRTHQ+R H   +   I+GD  Y  
Sbjct: 199 IDKENKFSKNAKSAFINVVKT--ENLTLMAAKLFTGRTHQIRAHLASLNRHILGDSLY-- 254

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
            +KG +      ++ LHA ++   HP+   ++ + APL
Sbjct: 255 GYKGKYDC----RIMLHAYFLYFIHPKTKEQIFVKAPL 288


>gi|331087231|ref|ZP_08336301.1| hypothetical protein HMPREF0987_02604 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330408917|gb|EGG88378.1| hypothetical protein HMPREF0987_02604 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 227

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 102/210 (48%), Gaps = 14/210 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW---VDSKGQKPRL--THRLD 151
           ++S +LYED  + V  KPAG+ VQ        +   LK++    +   ++P L   HRLD
Sbjct: 3   IQSYILYEDRDLIVCRKPAGVPVQTKQIQTKDMVSLLKNYRYQQEGGKEEPYLGVIHRLD 62

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q   GI+V A+T  AA+ L    +     K Y +++  +P+  +  + ++L+K      +
Sbjct: 63  QPVEGIVVFAKTPQAAKELNRQLQAGGFGKYYQAVLCKVPEKAQGQLTDYLVKDGRT--N 120

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              + ++++ GA  A   +K I   A+      +   TGR HQ+RV    MGCPI+GD K
Sbjct: 121 LSKICRKSDAGAKEARLSYK-IQGEAEGKALANIHLDTGRHHQIRVQMSGMGCPILGDVK 179

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           Y    K       + ++ L A  +   HP+
Sbjct: 180 YGGEEKA------RGQIALCASSLTFVHPK 203


>gi|163802429|ref|ZP_02196322.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. AND4]
 gi|159173730|gb|EDP58545.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. AND4]
          Length = 325

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 81/329 (24%), Positives = 148/329 (44%), Gaps = 43/329 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V V+ + V K   R+  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVHVNGEVVTKPRTRVMGGEEITLQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
            +        +   LD               ++YED  I V NKP    V  G+G     
Sbjct: 70  ELEDEERWEAQDIPLD---------------IVYEDEDIIVINKPRDFVVHPGAGTPDCT 114

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L  + D   + PR  + HRLD++T+G++VVA+T  A   L  + + R I + Y +
Sbjct: 115 VLNALLHHYPDI-AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEA 173

Query: 186 LVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           +  G        ++ I     K++ +    +            A++H++V + F ++   
Sbjct: 174 IAIGRMTAGGKVEQPIGRHSTKRTLMAVAPL---------GKPAVTHYRVAERF-REHTR 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLHARY 294
           + ++  TGRTHQ+RVH  ++  P++GD  Y    +         T+ I+  ++  LHA  
Sbjct: 224 IRLRLETGRTHQIRVHMSYLQHPLLGDTAYGGRARIPTGASEELTAMIRGFDRQALHAVM 283

Query: 295 MDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +   HP  G  L+  AP+P  MV+  +SL
Sbjct: 284 LRFEHPITGEELEFHAPIPDDMVEMTESL 312


>gi|295099509|emb|CBK88598.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           cylindroides T2-87]
          Length = 305

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 76/275 (27%), Positives = 126/275 (45%), Gaps = 41/275 (14%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           ++ IL  G + V+    K +  +Q G   +V IP V        +  ++L  ++ L    
Sbjct: 32  VKDILDEGNILVNGSPCKASYILQEGDHLLVNIPEV--------QSLEVLPENIPLN--- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPR 145
                 ++YED  + V NKP G+ V    G   H+ G L + +     D  G     +P 
Sbjct: 81  ------IVYEDDDVIVINKPKGMVVHPAFG---HVSGTLVNALMYHCKDLSGINGVMRPG 131

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HR+D++TSG+LVV +   A   L+E    +   + Y ++V   P + +    N  + +
Sbjct: 132 IVHRIDKDTSGLLVVCKNDKAHLALSEQLSNKTCHREYLAIVHH-PFSHEHGTINAPIGR 190

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  + V   N K    AI+HF V++ F + +  +  +  TGRTHQ+RVH  ++  P
Sbjct: 191 DEKDRQKMAVTANNSK---EAITHFTVLENF-KDYALVRCRLETGRTHQIRVHMQYIKHP 246

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           I GD KY     G+  +   N   LHA  ++  HP
Sbjct: 247 IAGDPKY-----GHRKTIDTNGQLLHACKLEFIHP 276


>gi|257466280|ref|ZP_05630591.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|315917437|ref|ZP_07913677.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|313691312|gb|EFS28147.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
          Length = 318

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 81/302 (26%), Positives = 141/302 (46%), Gaps = 35/302 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVR 66
           +Y V E D+   RLD + K   P      L+K++  G V  ++K +  N R ++  +V++
Sbjct: 9   EYQVGEEDQ-GKRLDLFLKEQLPEATRSYLEKLITEGYVLCNEKVITKNGRKLKGKEVIQ 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +         I+ E   LD               ++YED  + V NK A + V    G  
Sbjct: 68  LAIPEEEKMEIVAENIPLD---------------IVYEDKYLLVVNKQANMVVHPALGNY 112

Query: 125 IAYHIDGFL----KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  L    ++  D  G  +P + HRLD++T+G+++VA+       L   F+ + I
Sbjct: 113 SGTLVNALLYYCKENLSDMNGVIRPGIVHRLDKDTTGLIIVAKNNQVHSKLALMFQEKTI 172

Query: 180 QKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           +K Y ++V G   + KKE     L+ +       + V +   K    AIS+++V+     
Sbjct: 173 RKTYVAIVKGRFSEEKKEGRLETLITRDSKDRKKMTVSQIQGKK---AISNYRVL-LDGD 228

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           K   +E++  TGRTHQ+RVH  ++  PI+GD  Y     G   +  + ++ LHA  ++  
Sbjct: 229 KHSLVEVKIETGRTHQIRVHMKYLNHPILGDIVY-----GQEDTKCKRQM-LHAYRLEFI 282

Query: 299 HP 300
           HP
Sbjct: 283 HP 284


>gi|86144243|ref|ZP_01062575.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp.
           MED222]
 gi|85837142|gb|EAQ55254.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp.
           MED222]
          Length = 560

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 73/218 (33%), Positives = 109/218 (50%), Gaps = 27/218 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++YED +I V NKP       G  I   +   +K+ + D+ G  P + HRLD  TSG+L+
Sbjct: 359 IVYEDDEIVVVNKPEEFLSVPGKFIEDSVYTRIKARYPDATG--PLIIHRLDMSTSGLLI 416

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +A T  + +H+ + F  R ++K Y +L+ G    K   I+  L       GD     +Q 
Sbjct: 417 LALTAESNKHIQKQFIDRTVEKRYIALLDGEIDGKSGDISLPL------RGDITDRPRQL 470

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
             +E G N A +H++ +     K   + + P TGRTHQLRVH  H   +G PI GD  Y 
Sbjct: 471 VCHEHGRN-AETHWEAVSTNNGK-TKVHLYPKTGRTHQLRVHCAHPSGLGVPIRGDDLY- 527

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
             +K       + +L+LHA Y+ L HP  G  L+   P
Sbjct: 528 -GYK-------RERLHLHAGYLKLIHPTTGEWLEFEVP 557


>gi|330831288|ref|YP_004394240.1| ribosomal large subunit pseudouridine synthase A [Aeromonas veronii
           B565]
 gi|328806424|gb|AEB51623.1| Ribosomal large subunit pseudouridine synthase A [Aeromonas veronii
           B565]
          Length = 218

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 66/219 (30%), Positives = 106/219 (48%), Gaps = 24/219 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  I V NKP G+    G G   + D  L   V  +  K    HRLD  T+G++V+
Sbjct: 14  ILFKDKDIMVVNKPTGLLSVPGRG-PENEDSVLHR-VKQQHPKAAAAHRLDMSTTGVIVI 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK------NKKECIANWLLKKSHIGGDYVH 214
                + + L+  FR R  +K Y + VWG P+      +   C+ +W  +          
Sbjct: 72  PLNPNSHRELSRQFRERETEKHYLAWVWGEPELDAGEVDLPLCV-DWPNRPKQ------- 123

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K + +   +A++ ++ +         +++ P TGR+HQLRVH L +G PI+GD+ Y A
Sbjct: 124 --KVDHEEGRHALTLWQKLKV-ENGNSLIKLTPITGRSHQLRVHMLELGHPILGDNLY-A 179

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           +      +P    LYLHA  + + HP  G R+   AP P
Sbjct: 180 HPDALAAAP---HLYLHAAMLTISHPRSGERMTFEAPAP 215


>gi|269215565|ref|ZP_06159419.1| ribosomal large subunit pseudouridine synthase D [Slackia exigua
           ATCC 700122]
 gi|269131052|gb|EEZ62127.1| ribosomal large subunit pseudouridine synthase D [Slackia exigua
           ATCC 700122]
          Length = 316

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 84/334 (25%), Positives = 147/334 (44%), Gaps = 40/334 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ V VE   + MR+D +              + + +G+VRV+   V+ +  ++   VV 
Sbjct: 1   MEAVYVEGSFDGMRIDAFLAAVAAFPTRSAAARRVDAGEVRVNGVVVRKSFTVRISDVVE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
               + A++  + E    D  +++            YED  + V +K AG+      G  
Sbjct: 61  Y---VVAMDARVLELMPADIPLDIR-----------YEDDDVLVLSKQAGLVTHPADGHP 106

Query: 127 YHIDGFLKSWV---------DSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFR 175
              D  + + +         + +G++ RL   HRLD++TSG+++ A+T AA   L E   
Sbjct: 107 EQ-DTLVNALIAHCGREKLCNVQGEQDRLGIVHRLDRDTSGLMLAAKTDAAGLRLMEDIA 165

Query: 176 MRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            R + + Y +LV G IP +    + +  + +S    D + +   + + A  A + F+V+ 
Sbjct: 166 ARDVDRHYLALVHGWIPLDTG--LIDAPIGRS--AKDRLRMCVSDRESARPASTSFRVVR 221

Query: 235 CFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
            F        +  ++ +  TGRTHQ+RVHA ++  P VGD  Y      N     Q   +
Sbjct: 222 RFEPSRRDDGYTLIDCKLFTGRTHQIRVHAEYIKHPCVGDPTYGWPKHDNLGLERQ---F 278

Query: 290 LHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
           LH+  +   HP  G RL     LPA +    D L
Sbjct: 279 LHSYRLAFTHPSTGARLSFEDGLPADLQAVVDEL 312


>gi|302546161|ref|ZP_07298503.1| RluA family RNA pseudouridine synthase [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302463779|gb|EFL26872.1| RluA family RNA pseudouridine synthase [Streptomyces himastatinicus
           ATCC 53653]
          Length = 313

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 84/330 (25%), Positives = 146/330 (44%), Gaps = 34/330 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V+VD      ++R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAIARMF-GFSRTKAAELAAAGKVQVDGSVAGKSDRVS 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPQAAAPVQIVAEP--------------VEGMEIVHDDDDIVVIAKPVGVAA 105

Query: 120 Q---GGSGIAYHIDGFLKSW--VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTE 172
               G SG    I G   +   + + G   R  + HRLD  TSG++VVA++  A   L +
Sbjct: 106 HPSPGWSGTTV-IGGLAAAGFRIATSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKQ 164

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            FR R ++K Y +LV G P      I   + +  H   DY   V  + K    +++H+ +
Sbjct: 165 QFRERTVEKRYHALVQGHPDPLSGTIDAPIGR--HPQHDYKWAVTADGK---PSVTHYDL 219

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLH 291
           I+ F +    L+++  TGRTHQ+RVH      P VGD  Y A+        ++  + +LH
Sbjct: 220 IEAF-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADP--TLAKRLKLTRQWLH 276

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           A  +   HP  G  ++  +P P  + +  D
Sbjct: 277 AMRLGFEHPSDGSWIEFESPYPDDLQRALD 306


>gi|119384947|ref|YP_916003.1| RluA family pseudouridine synthase [Paracoccus denitrificans
           PD1222]
 gi|119374714|gb|ABL70307.1| ribosomal large subunit pseudouridine synthase D [Paracoccus
           denitrificans PD1222]
          Length = 341

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 72/256 (28%), Positives = 112/256 (43%), Gaps = 41/256 (16%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           YED+++ V +KPAG+ V    G         +  H  G L         +P + HR+D+E
Sbjct: 86  YEDAELIVVDKPAGMVVHPAPGAPSGTLVNALLAHCAGSLSGI--GGAARPGIVHRIDKE 143

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKK------------ECIA 199
           TSG+LVVA+T  A Q L   F     ++ Y ++  G+  P + +              + 
Sbjct: 144 TSGLLVVAKTDRAHQGLARQFADHTARRRYLAIAHGMIDPADARLRGLPGVGFEPGGVLR 203

Query: 200 NWLLKKSHIGGDYVHVVK-QNEKGANYAISHFKVIDCFAQKFCWL--EMQPHTGRTHQLR 256
              L   H G      V  QN +   +A++  +V++ F      +  E +  TGRTHQ+R
Sbjct: 204 IATLIGRHPGDRQRQAVSFQNGR---HAVTRARVVETFGTPPAAMLVECRLETGRTHQIR 260

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQN---------KLYLHARYMDLPHPEGGR-LQ 306
           VH  H G  +VGD  Y  N + +  +   +         +  LHA  +   HP  G+ L 
Sbjct: 261 VHMAHAGLGLVGDPVYGGNRRASARALGADAAAAVAAFPRQALHAAELGFEHPVSGQTLT 320

Query: 307 ITAPLPAHMVKTWDSL 322
             +PLPA M     +L
Sbjct: 321 FASPLPADMAGLLATL 336


>gi|312135354|ref|YP_004002692.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
 gi|311775405|gb|ADQ04892.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
          Length = 311

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 67/265 (25%), Positives = 125/265 (47%), Gaps = 28/265 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV+ +   +++++  K  YP I    + K+LR G++ V           Q GQV++    
Sbjct: 6   VVDKELAGVKVEKAIKKKYPTIPMSVIFKMLRKGEIIVSFLPA------QKGQVLKFG-- 57

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            + ++  I+++ +    V + K         +YED  I V +KP GI     S   Y + 
Sbjct: 58  -DTVSFEIEDRFLEHKKVEIIK---------VYEDDNIVVIDKPYGIPSHPDSNNEYSV- 106

Query: 131 GFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               SW++   SK + P+L HRLD+ T+G++++A+ R     + +    R I K Y  + 
Sbjct: 107 ---VSWIEDNYSKDELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRAIIKKYLCIT 163

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                 +   + ++L K S     Y+    Q+  G +  ++ +K++         L+++ 
Sbjct: 164 KKADLPESGVLVHYLKKDSKKSKVYISDFPQD--GYSEVVTAYKIVRQ-KDDLQLLDVEI 220

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
            +G+THQ+R    H+G  I+GD KY
Sbjct: 221 KSGKTHQIRAQLAHVGLCILGDSKY 245


>gi|213965290|ref|ZP_03393487.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           amycolatum SK46]
 gi|213952142|gb|EEB63527.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           amycolatum SK46]
          Length = 327

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 75/285 (26%), Positives = 128/285 (44%), Gaps = 31/285 (10%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQV--VRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +  +  +G + VD   V  ++R++      V +PPV   L  + KE+ +    V      
Sbjct: 51  VADLAAAGDITVDGVSVGKSDRLEENAFLSVLLPPVEKPL--VPKEELVEGMDV------ 102

Query: 95  DFLKSILLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
                  LY DS +   +KP G++       +G + I        +       ++  + H
Sbjct: 103 -------LYHDSDLVAVHKPVGVAAHPSVGWEGPTVIGGLAAAGFRISTSGPPERKGIVH 155

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++VVA +      L  +F+ R + K Y +LV G P      I   + +  H 
Sbjct: 156 RLDVGTSGVMVVACSERGYSVLKRAFKNREVSKTYHALVQGHPDPLSGTIDAPIGR--HP 213

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              +   V+Q+ K   +A++H++ ++ FA     L++   TGRTHQ+RVH   +  P  G
Sbjct: 214 SAGWRFAVRQDGK---HAVTHYETLEAFAPA-TLLKVNLETGRTHQIRVHFSALNHPCCG 269

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           D  Y ++        + N+ +LHA  +   HP  GR ++I  P P
Sbjct: 270 DPMYGSDPALAKRLGL-NRQWLHAVSLGFHHPADGRWMEIECPYP 313


>gi|86149976|ref|ZP_01068204.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni CF93-6]
 gi|88596472|ref|ZP_01099709.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni 84-25]
 gi|218562892|ref|YP_002344671.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|85839422|gb|EAQ56683.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni CF93-6]
 gi|88191313|gb|EAQ95285.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni 84-25]
 gi|112360598|emb|CAL35395.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|284926505|gb|ADC28857.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni IA3902]
 gi|315927093|gb|EFV06444.1| pseudouridine synthase, RluA family protein [Campylobacter jejuni
           subsp. jejuni DFVF1099]
 gi|315928797|gb|EFV08067.1| pseudouridine synthase, RluA family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 322

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 72/279 (25%), Positives = 133/279 (47%), Gaps = 36/279 (12%)

Query: 48  VDKKRVKFNNRIQ--------SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++K  V+ N++IQ        +G ++ I  +   L + IK Q  +D  +++         
Sbjct: 31  IEKDCVQVNDKIQDKNSFKLKNGDIISIASL--KLCNEIKPQFEVDFDIDV--------- 79

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL--KSWVDSKGQKPR--LTHRLDQE 153
             LYED  + V NKP+ + V G S +  A  +D  +  K  + + G + R  L HRLD++
Sbjct: 80  --LYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKD 137

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG +++A+     Q L+E    + + +IY +L+    K  K  +  +L++        +
Sbjct: 138 TSGAILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKI 197

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + K+N+   N   +   V+    +    +  +  TGRTHQ+R H   +   I+GD  Y 
Sbjct: 198 AIDKENKFSKNAKSAFINVVK--TENLTLMAAKLFTGRTHQIRAHLASLNRYILGDSLY- 254

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
             +KG +      ++ LHA ++   HP+   ++ + APL
Sbjct: 255 -GYKGKYDC----RIMLHAYFLYFIHPKTKEQIFVKAPL 288


>gi|332365407|gb|EGJ43168.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK355]
          Length = 277

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 93/201 (46%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG+++ A
Sbjct: 71  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGVVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      R I + YW+LV G      +  A  L+ K  IG D     K+  +
Sbjct: 128 KNPFVLPILNRLLEKREISRQYWALVQG------KFPAKNLIYKDKIGRDRHDRRKRLVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   YA +H   +  F Q    ++ Q  TGRTHQ+RVH  H G P+VGD  Y    +G 
Sbjct: 182 PRKGLYAETHVTRLKQFGQA-TLVQCQLKTGRTHQIRVHLAHHGHPLVGDPLYHPQPQG- 239

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 240 -------RLMLHAHRLTFTHP 253


>gi|308321724|gb|ADO28005.1| RNA pseudouridylate synthase domain-containing protein 4 [Ictalurus
           furcatus]
          Length = 386

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 65/211 (30%), Positives = 101/211 (47%), Gaps = 28/211 (13%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSK--G 141
           SV+    +  L   +LY+D  +   NKP G+ V    GI   I      L   +D    G
Sbjct: 105 SVHPNVFAKALSKSILYQDQNLIAINKPYGVPVYSTGGIGNSIAESLPVLAKIIDCTKGG 164

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            K  + + L+++T+G+L +A T   A+ +    R  + +K Y  +  G+P   +  I   
Sbjct: 165 SKLHVCYNLEKDTTGVLFLAWTEETAERIHNLIRSHQAEKRYMVITVGVPVPSEGVIDIP 224

Query: 202 LLKKSHIG------------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++K  +G                  GD +  V+ N + A  A++ +KV+D  +   C L
Sbjct: 225 IIEKEVMGDQHHFKMGLSPLYRPTEEGDGLVRVRANRQ-AQSAVTRYKVLD--SSSGCSL 281

Query: 244 -EMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
            E QP TG  HQLRVH AL + CPI+GDHKY
Sbjct: 282 VEFQPVTGVKHQLRVHMALALACPILGDHKY 312


>gi|283956675|ref|ZP_06374154.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 1336]
 gi|283791924|gb|EFC30714.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 1336]
          Length = 322

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 108/218 (49%), Gaps = 15/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL--KSWVDSKGQKPR--LTHRLDQET 154
           +LYED  + V NKP+ + V G S +  A  +D  +  K  + + G + R  L HRLD++T
Sbjct: 79  VLYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG +++A+     Q L+E    + + +IY +L+    K  K  +  +L++        + 
Sbjct: 139 SGAILIAKNNFTHQRLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIA 198

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + K+N+   N   +   V+    +    +  +  TGRTHQ+R H   +   I+GD  Y  
Sbjct: 199 IDKENKFSKNAKSAFINVVKT--ENLTLMAAKLFTGRTHQIRAHLASLNRHILGDSLY-- 254

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
            +KG +      ++ LHA ++   HP+   ++ + APL
Sbjct: 255 GYKGKYDC----RIMLHAYFLYFIHPKTKEQIFVKAPL 288


>gi|183603400|ref|ZP_02712152.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1087-00]
 gi|183569583|gb|EDT90111.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1087-00]
          Length = 278

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 182 AKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNLPILGDTLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|171920977|ref|ZP_02696366.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           13 str. ATCC 33698]
 gi|185179169|ref|ZP_02555823.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           5 str. ATCC 27817]
 gi|188024223|ref|ZP_02570294.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           7 str. ATCC 27819]
 gi|188518627|ref|ZP_02556991.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           11 str. ATCC 33695]
 gi|188524489|ref|ZP_02558401.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           12 str. ATCC 33696]
 gi|195867617|ref|ZP_03079619.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           9 str. ATCC 33175]
 gi|198273670|ref|ZP_03206205.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           4 str. ATCC 27816]
 gi|225550414|ref|ZP_03771363.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           2 str. ATCC 27814]
 gi|225551125|ref|ZP_03772071.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           8 str. ATCC 27618]
 gi|171903003|gb|EDT49292.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           13 str. ATCC 33698]
 gi|184208903|gb|EDU05946.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           5 str. ATCC 27817]
 gi|188018878|gb|EDU56918.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           7 str. ATCC 27819]
 gi|188997853|gb|EDU66950.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           11 str. ATCC 33695]
 gi|195659610|gb|EDX52990.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           12 str. ATCC 33696]
 gi|195660674|gb|EDX53929.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           9 str. ATCC 33175]
 gi|198249698|gb|EDY74479.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           4 str. ATCC 27816]
 gi|225378940|gb|EEH01305.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           8 str. ATCC 27618]
 gi|225379568|gb|EEH01930.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           2 str. ATCC 27814]
          Length = 299

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 73/257 (28%), Positives = 125/257 (48%), Gaps = 30/257 (11%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDG 131
           I  EQ ++DS   L   +  L+  +++ED  + V NKP+G+     S Q  + +A  +  
Sbjct: 59  IKNEQCVIDSQKELLPFACPLE--IVFEDQDLLVINKPSGMLVHPTSFQEQNTLANALKH 116

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           +LK+          +THRLD+ TSG++V+ + + A   L + F  + ++K Y+++V    
Sbjct: 117 YLKT------DDFYITHRLDKNTSGLIVICKNQKALCCLQQQFMQKTVKKSYYAIVH--- 167

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
            N+ +      +    IG  Y   ++    + K A  AIS  KVI+ + Q    +E+   
Sbjct: 168 -NRFDMHHLHFMINEPIGHSYQDKLRMKTGDAKNAKEAISIVKVIEQY-QNTALVEVSII 225

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QI 307
           TGRTHQ+RVH  H+  PI  D  Y        T+P +   YLH+ Y+   HP    + + 
Sbjct: 226 TGRTHQIRVHMRHINHPIYNDPLYGI---SKHTTPYEQ--YLHSFYISFIHPSTNEIVEF 280

Query: 308 TAPLP---AHMVKTWDS 321
              +P    +++K W +
Sbjct: 281 KTLMPNEFINLIKEWKT 297


>gi|148554296|ref|YP_001261878.1| pseudouridine synthase [Sphingomonas wittichii RW1]
 gi|148499486|gb|ABQ67740.1| pseudouridine synthase [Sphingomonas wittichii RW1]
          Length = 250

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 104/225 (46%), Gaps = 16/225 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D +  V +KP+G+ V      +  ++  L+S      + P   HRLD++TSG L++
Sbjct: 37  ILFIDGEAMVIDKPSGLPVDPPRDGSISLENHLQSLSFGFKRWPSAVHRLDRDTSGCLLL 96

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR   A +    +F   +++K Y +++ GIP  +   +   L K S     +  V     
Sbjct: 97  ARNPKAHKRYALAFEEGKVEKTYLAILDGIPAQESGLVDLPLAKISTREAGWRMVGDPRG 156

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCANFKGN 279
           K A  A      +D  A     +E +P TGRTHQ+RVH A  +G PI GD  Y    +  
Sbjct: 157 KPATTAWRVVATVDGRA----LVEFRPTTGRTHQIRVHAATGIGLPIHGDPVYGREGQAG 212

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
            T        LHA  + +P      ++  APLPA       +LGF
Sbjct: 213 VT-------LLHASALVVPREGKNPIEAKAPLPARFT----ALGF 246


>gi|332288146|ref|YP_004418998.1| tRNA pseudouridine synthase C [Gallibacterium anatis UMN179]
 gi|330431042|gb|AEC16101.1| tRNA pseudouridine synthase C [Gallibacterium anatis UMN179]
          Length = 242

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 104/233 (44%), Gaps = 23/233 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +  +  ++   D  GQ     HRLD+ TSG+L+ 
Sbjct: 9   ILYQDQALIAVNKPAGMLVHRSWLDKHETEFVMQKLRDQIGQYVFPIHRLDRPTSGVLLF 68

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F  +++QK Y ++V G    ++        K   I   +     Q +
Sbjct: 69  ALSSEIANAVCRQFEQKQVQKQYLAVVRGYLTGQERIDYPLKPKWDKIADKF----SQQD 124

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  + + P TGR HQLR H  H+  PI+GD 
Sbjct: 125 KTPQEAVTDYQGLATLEIPVAVGRYATSRYSLVRLTPQTGRKHQLRRHLKHIFHPIIGDT 184

Query: 271 KYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           +Y        F   F+    N+L LHA  ++L HP   + L+I APL     K
Sbjct: 185 QYGDLHQNRAFSAYFSV---NRLMLHAESLELLHPTTQQVLRICAPLDPSFAK 234


>gi|294634980|ref|ZP_06713497.1| pseudouridine synthase A [Edwardsiella tarda ATCC 23685]
 gi|291091579|gb|EFE24140.1| pseudouridine synthase A [Edwardsiella tarda ATCC 23685]
          Length = 235

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/177 (36%), Positives = 93/177 (52%), Gaps = 14/177 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D+ I V NKP+G+ SV G   +  H D  + + + ++       HRLD  TSG+LV
Sbjct: 32  VLYQDAHIMVVNKPSGLLSVPGR--LPAHQDSIM-TRIQAQFPCAESVHRLDMATSGVLV 88

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+ A + L   FR R  QK Y + VWG P   +  I   L+       D+ +  KQ 
Sbjct: 89  VALTKEAERELKRQFREREPQKNYVARVWGHPTQDEGLIDLPLI------CDWPNRPKQK 142

Query: 220 ---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              E+G   A + ++V+         L + P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 143 VCFEQG-KPAQTAYRVLARDDDGTARLLLTPITGRSHQLRVHLLAIGHPILGDGFYA 198


>gi|221123607|ref|XP_002156005.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4 [Hydra magnipapillata]
          Length = 329

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 117/242 (48%), Gaps = 15/242 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGIL 158
           LY    +   +KP GI V GG  I   I  FL +     G       L HRLD+ TSG+L
Sbjct: 32  LYMKDGLLAIHKPYGIPVHGGPKIKLSIADFLPALEQKHGLLAGSLELAHRLDKNTSGVL 91

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++   +  A++L +    R+I+K Y +++ G   ++   + N  L ++   G +   + +
Sbjct: 92  LLTYKKEMAKYLADLHENRQIEKSYLAILLG-NVSRVTGVLNGELHETLRNGQFKQTINE 150

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEM-QPHTGRTHQLRVHALH-MGCPIVGDHKYCANF 276
                +   +++ ++D   Q  C L + +  TG  HQ+RVHA   + CPI+GDH+Y AN 
Sbjct: 151 ISINKSSVETNYTILDS-NQDTCMLCLFKTFTGNKHQIRVHAYELLKCPILGDHRYHAN- 208

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQI----TAPLPAHMV-KTWDSLGFKYDRNLY 331
           KG  T PI  +L    R   + + E G  +I       LP H++ K+    G    ++L 
Sbjct: 209 KGPQTLPI--RLIQMLRMRGVKNEETGSSKIRPWQRGLLPMHLLTKSIRIPGLDGSKDLT 266

Query: 332 IK 333
           I+
Sbjct: 267 IE 268


>gi|229195588|ref|ZP_04322354.1| Pseudouridine synthase [Bacillus cereus m1293]
 gi|228587837|gb|EEK45889.1| Pseudouridine synthase [Bacillus cereus m1293]
          Length = 307

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/231 (30%), Positives = 114/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +    S +GG G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPSEKGGMGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEKYFRKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y    K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 254 DVLYGGGTK------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDT 298


>gi|116492157|ref|YP_803892.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
 gi|116102307|gb|ABJ67450.1| Pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
          Length = 296

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 77/276 (27%), Positives = 123/276 (44%), Gaps = 30/276 (10%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS-ILLY 103
           +V V+ K V  N  +Q G ++        LN    E    D+ +      DF ++ I+LY
Sbjct: 41  RVLVNGKYVPVNTIVQGGDLIE-------LNF---ESSDFDTPLP-PFDPDFTQAPIILY 89

Query: 104 EDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           E+S + V NKP G+            +  FL+++      +    HRLDQ TSG L+VA+
Sbjct: 90  ENSDLMVVNKPTGVKTHANQPHELGSMMNFLQAYFKDTENEAYNVHRLDQFTSGALLVAK 149

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      + I + Y  +V G  +  K  I         IG D     K+   G
Sbjct: 150 NPVVVPILNRQISTKVINRTYLCVVSGHLEQSKGTI------NVPIGFDPDDKRKRQING 203

Query: 223 AN--YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            N   AI+H++V+  +      +++   TGRTHQ+RVH  ++G PI+GD  Y  +     
Sbjct: 204 LNPLSAITHYQVLAQYENS-SLIQVDLETGRTHQIRVHLSYLGHPIIGDPLYNLDNT--- 259

Query: 281 TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
               Q  + LH+  +  P P     +++TAP+P + 
Sbjct: 260 ----QQPMLLHSWKIRFPLPFNLETIEVTAPIPDYF 291


>gi|169833510|ref|YP_001695365.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae Hungary19A-6]
 gi|168996012|gb|ACA36624.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Hungary19A-6]
          Length = 278

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 182 AKNGQYAETHVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|149011862|ref|ZP_01833010.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP19-BS75]
 gi|194398411|ref|YP_002038593.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Streptococcus pneumoniae G54]
 gi|237650123|ref|ZP_04524375.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae CCRI 1974]
 gi|237821869|ref|ZP_04597714.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae CCRI 1974M2]
 gi|147763817|gb|EDK70750.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP19-BS75]
 gi|194358078|gb|ACF56526.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae G54]
          Length = 291

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 195 AKNGQYAETHVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDPLYNSKSKT- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|257126587|ref|YP_003164701.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
 gi|257050526|gb|ACV39710.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
          Length = 314

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 76/289 (26%), Positives = 133/289 (46%), Gaps = 37/289 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+++ E MRLDR+ + ++       +   +R+G V+V+ K+ K N R+     + I  
Sbjct: 6   VVVDSEMEGMRLDRYLRKNFKDEPLSRIFGAIRAGDVKVNGKKSKENYRLALNDTIVIK- 64

Query: 70  VINALNHIIKEQKILDSSVNLTK----HSDF--LKSILLYEDSKIYVFNKPAGISVQGGS 123
             N  +     +K  + + NL K     SD    K ++++E+   ++ NK   I +  G+
Sbjct: 65  --NLFSENFDNKKSFEKN-NLKKIQIQKSDLEKYKKMIIFENEDFFIVNKSEKIPMHKGT 121

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G  Y +    K     K +     +RLD ETSG+++  +     +++++  R   IQK Y
Sbjct: 122 GHKYGLAEVFKEIF--KNENINFANRLDFETSGLVIGCKNLKFLRYISQKIRDNEIQKKY 179

Query: 184 WSLVWGIPKN---KKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHF-------- 230
           +++V  I  N   K   I N+L    +       +V +N   K +  +I++F        
Sbjct: 180 FAIVHNIKNNIESKIFKIENYLTTTEN-----KVIVSENPISKDSKKSITNFKKILISEL 234

Query: 231 ----KVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               K++D      +    L++   TGR HQ+R    H   PIVGD KY
Sbjct: 235 KNTKKILDLLEKNNKNVFLLDVDLVTGRKHQIRAQLAHQKIPIVGDKKY 283


>gi|237755669|ref|ZP_04584280.1| ribosomal large subunit pseudouridine synthase protein
           [Sulfurihydrogenibium yellowstonense SS-5]
 gi|237692181|gb|EEP61178.1| ribosomal large subunit pseudouridine synthase protein
           [Sulfurihydrogenibium yellowstonense SS-5]
          Length = 270

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 61/215 (28%), Positives = 100/215 (46%), Gaps = 28/215 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  I   +KP  I     S  A   +  L+  +  K  K +  HRLD+ETSG+L+ 
Sbjct: 70  ILYEDDYIIAIDKPPTIVSDKESSSA---EDLLRKKL--KNDKIKAIHRLDKETSGVLLF 124

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+     +   E +  + + KIY ++                   SH   ++      ++
Sbjct: 125 AKDYKIFEKFKEIWEDKNVLKIYLAI-------------------SHNEANFKDFTINHD 165

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGN 279
                AI+H KV+      F + +++  TGR HQ+R H   +  PIVGD  Y    F+ N
Sbjct: 166 IEGKQAITHLKVL-SKGNGFTYFQVRIETGRKHQIRKHLASIRHPIVGDKIYGIKKFENN 224

Query: 280 FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPA 313
               +  ++ LH+  + LPHP    +++ITAP+P+
Sbjct: 225 LVKRVTRQM-LHSHKLVLPHPYLNKKIEITAPIPS 258


>gi|157737249|ref|YP_001489932.1| ribosomal large subunit pseudouridine synthase D [Arcobacter
           butzleri RM4018]
 gi|157699103|gb|ABV67263.1| ribosomal large subunit pseudouridine synthase D [Arcobacter
           butzleri RM4018]
          Length = 328

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 116/249 (46%), Gaps = 31/249 (12%)

Query: 85  DSSVNLTKHSDFLKSIL-------LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           ++ +N  K  +FLK+ L       +YED  I V NKP  ++V     +    D  L  W+
Sbjct: 63  ETQLNKRKDEEFLKNSLEDKEVEIIYEDDYILVLNKPYNLTVHDAPSVK---DATLVDWL 119

Query: 138 DSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             K          ++  + HRLD+ TSG++V+A+T  A  +L++    + + + Y +++ 
Sbjct: 120 KLKNISLSTISGEERHGIVHRLDKGTSGVMVIAKTNEAHLNLSKQLEDKSMGRYYLAILD 179

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF-KVIDCFAQKFCWLEMQP 247
              K       N +++K         +    E+   YA S F K+     +KF  +  + 
Sbjct: 180 LALK------ENVIIEKPIRRNPNNRLKMSIEENGRYAKSAFSKIALSDNEKFELIACKL 233

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
           +TGRTHQ+RVH   +   I+GD+ Y   FKG       N+  LHA Y+ L HP    ++ 
Sbjct: 234 YTGRTHQIRVHLSSINRHILGDNLYG--FKGELNKI--NRFLLHAYYLYLTHPVTNKQMC 289

Query: 307 ITAPLPAHM 315
             A LP  M
Sbjct: 290 FKANLPEDM 298


>gi|283954844|ref|ZP_06372360.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacter jejuni subsp. jejuni 414]
 gi|283793684|gb|EFC32437.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacter jejuni subsp. jejuni 414]
          Length = 322

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 74/279 (26%), Positives = 133/279 (47%), Gaps = 36/279 (12%)

Query: 48  VDKKRVKFNNRIQ--------SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++K  V+ N++IQ        +G VV I   +N  N + K Q  +D  +++         
Sbjct: 31  IEKDCVQVNDKIQDKNSFKLKNGDVVFIAS-LNLCNEV-KPQFEVDFDIDV--------- 79

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL--KSWVDSKGQKPR--LTHRLDQE 153
             LYED  + V NKP+ + V G S +  A  +D  +  K  + + G + R  L HRLD++
Sbjct: 80  --LYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKD 137

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG +++A+     Q L+E    + + +IY +L+    K  K  +  +L++        +
Sbjct: 138 TSGAILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKI 197

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + ++N+   N   +   VI    +    +  +  TGRTHQ+R H   +   I+GD+ Y 
Sbjct: 198 AIDEENKFSKNAKSAFINVIK--TENLTLMAAKLFTGRTHQIRAHLASLNRHILGDNLY- 254

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
             +KG +      ++ LHA ++   HP    ++ + APL
Sbjct: 255 -GYKGKYDC----RIMLHAYFLYFIHPRTKEQIFVKAPL 288


>gi|159027410|emb|CAO86894.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 501

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 112/230 (48%), Gaps = 49/230 (21%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  I   NKPAG+ SV G    +   D  +  +   +G+     HRLD+ETSGIL+
Sbjct: 302 IIYEDEGIIAINKPAGLLSVAGRYQDSQ--DAVVNRF-RRQGKNLIPVHRLDRETSGILL 358

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSL---------------VWGIPKNKKECIANWLLK 204
           +A++    + L++ F+ R ++KIY ++               +WG P+N+     +W  +
Sbjct: 359 LAKSLDIYRCLSQQFQRREVEKIYEAILSEIIERESGIIDLPLWGNPQNRPYQTVDW--Q 416

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MG 263
           +      Y  VV    K  NY+                LE  P+TGRTHQ+RVH+   +G
Sbjct: 417 RGKASQTYFKVVG---KEGNYS---------------RLEFIPYTGRTHQIRVHSQQGLG 458

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
             I+GD  Y  N K +      ++LYLHA+ +   HP+   +L +  P P
Sbjct: 459 IGILGDFLY--NGKQS------DRLYLHAKQLSFRHPQTENKLDLIIPTP 500


>gi|85713493|ref|ZP_01044483.1| pseudouridine synthase [Nitrobacter sp. Nb-311A]
 gi|85699397|gb|EAQ37264.1| pseudouridine synthase [Nitrobacter sp. Nb-311A]
          Length = 298

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 73/261 (27%), Positives = 103/261 (39%), Gaps = 62/261 (23%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ +L+ D  + V +KPAGI+V  G     +++    +      + P L HRLD++TSG
Sbjct: 11  IQARVLHRDGLMLVIDKPAGIAVHRGPKGGANLEASFDALRFGLPRPPVLAHRLDRDTSG 70

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKS 206
            LV+ R R A   L   F+  +I K YW++V G P + +  I            W  K  
Sbjct: 71  CLVLGRHRKATASLGLLFKHGKISKTYWAVVEGGPTDDEGTIDIPLGRMNEERGWWQKPD 130

Query: 207 HIGGDYVHVVKQNEKGA-NYAISHFKVIDC------FAQKF------------------- 240
             G   +   K   +G    A  HF    C       A  F                   
Sbjct: 131 PNGLPSITTWKVLGRGVLTAAGDHFSPSRCGEGPGVGANGFDIPTNHPPPQPSPTREEGA 190

Query: 241 -------------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA----------NFK 277
                         WL ++P TGRTHQLRVH   MG PIVGD  Y             + 
Sbjct: 191 EIPPSDIDRTTLLTWLALEPMTGRTHQLRVHCAAMGWPIVGDSIYGTQASLRRLRNEQYI 250

Query: 278 GNFTSPIQNKLYLHARYMDLP 298
                P    L+LHAR + +P
Sbjct: 251 PRLDDP---GLHLHAREIAVP 268


>gi|146291939|ref|YP_001182363.1| pseudouridylate synthase [Shewanella putrefaciens CN-32]
 gi|145563629|gb|ABP74564.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           putrefaciens CN-32]
          Length = 226

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/207 (31%), Positives = 103/207 (49%), Gaps = 19/207 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +LY+D  I V NKP+G+    G   A H D     +   K + P  ++ HRLD  TSG++
Sbjct: 17  ILYQDKDIIVINKPSGLLSVPGRDPA-HYDSV---YARVKAEHPHCQIVHRLDMATSGVI 72

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A  R+A + L   F  R   K Y + V G  K+    I   L+       D+ +  KQ
Sbjct: 73  VLALIRSAERELKRQFHDRETSKTYIARVAGHIKHDTGSIDYPLI------CDWPNRPKQ 126

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +      +++H++V+   A++   +++ P TGR+HQLRVH + +G PI+GD  Y    
Sbjct: 127 KVDHFVGKPSLTHYQVMS-RAKRSTLVKLTPITGRSHQLRVHMMAIGHPILGDGFYADPL 185

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +       +L LHA  + + HP  G
Sbjct: 186 AKSLAP----RLLLHAAELTIKHPYTG 208


>gi|196040729|ref|ZP_03108028.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
 gi|228932672|ref|ZP_04095546.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|229090345|ref|ZP_04221588.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|196028519|gb|EDX67127.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
 gi|228692928|gb|EEL46646.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|228826990|gb|EEM72750.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 307

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 110/226 (48%), Gaps = 22/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++YED  + + NKP  +      +GG G   ++  F    +     K R  HRLD++T+G
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAF-HYQMKGLETKVRHIHRLDKDTTG 145

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D  H  
Sbjct: 146 GVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRDRHHAT 199

Query: 217 KQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           ++  + KG + AI+++KV + F  Q    + +Q  TGRTHQ+RVH  + G P+VGD  Y 
Sbjct: 200 RRRVSPKG-DQAITYYKVEEYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYG 258

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
              K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 259 GQTK------YMSRQALHAMKINFLHPITKEEIEVDIPFPTKLNDT 298


>gi|47566178|ref|ZP_00237206.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus G9241]
 gi|47556731|gb|EAL15062.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus G9241]
          Length = 307

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 110/226 (48%), Gaps = 22/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++YED  + + NKP  +    S +GG G   ++  F    +     K R  HRLD++T+G
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPSEKGGMGTLANLVAF-HYQMQGLETKVRHIHRLDKDTTG 145

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D  H  
Sbjct: 146 GVVFAKHRIAGAIMDRLLMERKIKRTYVALVEGKVKKKQGTI------DAAIGRDRHHAT 199

Query: 217 KQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VGD  Y 
Sbjct: 200 RRRVSPKG-DQAITYYKVEKYFKNQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYG 258

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
              K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 259 GQTK------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDT 298


>gi|331005540|ref|ZP_08328915.1| tRNA pseudouridine synthase C [gamma proteobacterium IMCC1989]
 gi|330420660|gb|EGG94951.1| tRNA pseudouridine synthase C [gamma proteobacterium IMCC1989]
          Length = 237

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 56/190 (29%), Positives = 91/190 (47%), Gaps = 14/190 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   +KPAG+ V       +     ++   D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   IIYQDEYLVAIHKPAGLLVHKSLIDKHESQYAMQILRDQIGQWVYPLHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             ++  AQ + E F  R +QK YW++V G   NK+  I + +   +    D   +    +
Sbjct: 65  GLSKEVAQLMGEQFEQRLLQKTYWAIVRGY-INKEGIIDHPIKPTADFKRDKQRIA---Q 120

Query: 221 KGANYAISHFKVIDCFAQKFC----------WLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ ++ +      +C           +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 121 KEAQEAITGYRRLGTLELPYCVDQFPISRYSLVELSPQTGRKHQLRKHMKHLSHPIIGDP 180

Query: 271 KYCANFKGNF 280
           KY  +   +F
Sbjct: 181 KYGKSKHNHF 190


>gi|320332730|ref|YP_004169441.1| RluA family pseudouridine synthase [Deinococcus maricopensis DSM
           21211]
 gi|319754019|gb|ADV65776.1| pseudouridine synthase, RluA family [Deinococcus maricopensis DSM
           21211]
          Length = 318

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 73/296 (24%), Positives = 128/296 (43%), Gaps = 35/296 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +  + Y H +  + ++ +  G+V +D   +  +  +Q+GQV+         N    +++ 
Sbjct: 43  YLVSKYRHSSAQDWRERVARGEVTLDGAPIDGHEILQAGQVL-------VWNRPPWDEEA 95

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
              + ++            Y D  +    KP+G+    G G    ++  L S V ++  +
Sbjct: 96  TPRTFDIA-----------YLDDALLAVIKPSGLPTMHGGGF---LENTLLSLVRAQHPE 141

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRL + TSG+++ ART AAA  L+E++RM  ++K Y +L  G+    +  I   + 
Sbjct: 142 ATPLHRLGRATSGLVLFARTHAAASRLSEAWRMHHVEKRYRALASGVLAQDRVTIEAPIG 201

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHAL 260
              H     VH V    K +       + + C  ++      L++   TGR HQ+R+H  
Sbjct: 202 PVPHPRLGTVHGVSATGKAS-------RSVACVLERREDATLLQVDIFTGRPHQIRIHTA 254

Query: 261 HMGCPIVGDHKYCANFK---GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            +G P+VGD  Y    +    N   P      LHA  +   HP  G  L + AP P
Sbjct: 255 FLGHPLVGDPLYGPGGQPKADNPGLPGDGGYLLHAERLAFTHPVTGAPLDVYAPAP 310


>gi|291518263|emb|CBK73484.1| ribosomal large subunit pseudouridine synthase D [Butyrivibrio
           fibrisolvens 16/4]
          Length = 218

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 58/206 (28%), Positives = 104/206 (50%), Gaps = 12/206 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +LYED  I V  KPAG++ Q  +     ++  L +++ SKG+ P +   HRLDQ   G++
Sbjct: 3   VLYEDDSIVVVYKPAGLATQTRNIGEKDMESELSNYLKSKGESPEIHVVHRLDQPVEGVM 62

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+T+ AA +LT        +K Y++++      ++  + ++L+K +    +   VVK+
Sbjct: 63  VFAKTKEAANNLTRQIADHSFKKHYYAIITRESFPEEGDLVDYLVKDNRT--NLSKVVKE 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           ++  A  A   +  +D +  +   L+++  TGR HQ+R+       PI+GD KY     G
Sbjct: 121 SDPRAKKASLKYHTVDEWDDR-KLLDIELFTGRHHQIRIQLASRTAPILGDVKYGGVSTG 179

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR 304
                  + L L +  +   HP  G+
Sbjct: 180 -------HNLALCSYSIGFTHPTSGK 198


>gi|306827367|ref|ZP_07460654.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus pyogenes ATCC
           10782]
 gi|304430514|gb|EFM33536.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus pyogenes ATCC
           10782]
          Length = 301

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 58/206 (28%), Positives = 106/206 (51%), Gaps = 18/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSK--GQKPRLTHRLDQETSGI 157
           +++ED    V NKP G +    +  +  I  F+K++ VD+    Q+  +  RLD++TSG+
Sbjct: 78  IVHEDDHFLVINKPIGFASIPSAIHSNTIANFIKAYYVDNHYLDQQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVH 214
           ++ A+   A   L +  + R ++K Y++LV G   +P ++ + IA     K  I      
Sbjct: 138 MLFAKHGYAHARLDKQLQTRSVEKRYFALVSGNGTLP-DEGDIIAPIGRSKDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +  +    YA + +KV+  +++    ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 191 ITRAVDPMGKYAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGFPLLGDDLYGG 250

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
                 T     +  LH  Y++   P
Sbjct: 251 RLDLGIT-----RQALHCHYLNFKDP 271


>gi|253682033|ref|ZP_04862830.1| pseudouridine synthase, RluA family [Clostridium botulinum D str.
           1873]
 gi|253561745|gb|EES91197.1| pseudouridine synthase, RluA family [Clostridium botulinum D str.
           1873]
          Length = 323

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/272 (27%), Positives = 124/272 (45%), Gaps = 30/272 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI--- 71
           +E   RLD++ +     +    + K LR G +RV+ K+ K N  +Q   ++    +    
Sbjct: 8   NESGQRLDKFCRKWLEDVPLGAIFKALRKGDIRVNGKKAKQNYFLQEEDIIETKYIETYK 67

Query: 72  -NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
            N  +   K Q++  SS+ ++           YED  I +  K  G+ V      G   +
Sbjct: 68  QNKKDIPKKFQEVDFSSIKIS-----------YEDENILIIEKWPGVLVHSDKKNGEPTL 116

Query: 126 AYHIDGFLKSWVDSKGQK-----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             ++  +L    D   QK     P   +RLD+ TSG+++  +     + L    R R+I+
Sbjct: 117 TDYVLSYLFQKGDYDPQKEVTFTPAPCNRLDRNTSGMVIFGKNFKTLKILNAMIRERKIK 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  K K+     ++LK        +H  K+ ++ +       KVID     F
Sbjct: 177 KYYNALVKG--KIKEGYYEAYILKDQVNNISEIH--KEEKQNSKRIAMEVKVIDTVGT-F 231

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +LE+   TGR+HQLR H  ++G PI+GD KY
Sbjct: 232 SFLELDLLTGRSHQLRAHLAYLGNPIIGDDKY 263


>gi|148358865|ref|YP_001250072.1| ribosomal large subunit pseudouridine synthase D [Legionella
           pneumophila str. Corby]
 gi|296106912|ref|YP_003618612.1| ribosomal large subunit pseudouridine synthase D [Legionella
           pneumophila 2300/99 Alcoy]
 gi|148280638|gb|ABQ54726.1| ribosomal large subunit pseudouridine synthase D, RluD [Legionella
           pneumophila str. Corby]
 gi|295648813|gb|ADG24660.1| ribosomal large subunit pseudouridine synthase D [Legionella
           pneumophila 2300/99 Alcoy]
          Length = 321

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 86/323 (26%), Positives = 145/323 (44%), Gaps = 42/323 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q + V  +  N R+D       P  +   +   +++G V ++    K  ++   G ++ I
Sbjct: 7   QQLSVPRELHNQRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCKPKDKALGGDLITI 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                 +NH      I+++  NL K  +    I+ YEDS++ V NKPAG+ V  G+G   
Sbjct: 67  -----NVNH-----TIVNTDFNLCKPENIPIQII-YEDSEVIVVNKPAGLVVHPGAGNKE 115

Query: 128 H--IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           H  ++  L    + +   PR  + HRLD++T+G+L+VA+   +   L    + R I++ Y
Sbjct: 116 HTLVNALLHHCPELQ-LLPRAGIIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVIDCFAQ 238
            +LV G           +++    I   +    K   K A       A++H+  I+   +
Sbjct: 175 LTLVHG-----------YVISGGTIDTGFGRHPKNRLKMAVTDFGRQAVTHYN-INKHYK 222

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKL------YL 290
            F  L +   TGRTHQ+RVH  ++  P+VGD  Y     F  N    I + L       L
Sbjct: 223 DFTLLNVSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKFPPNADEAILSVLKQFKRQAL 282

Query: 291 HARYMDLPHP-EGGRLQITAPLP 312
           HA  +   HP +   + + A LP
Sbjct: 283 HACSISFCHPVKNTEITLNALLP 305


>gi|146292104|ref|YP_001182528.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|145563794|gb|ABP74729.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
          Length = 574

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 76/248 (30%), Positives = 120/248 (48%), Gaps = 31/248 (12%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H++ E  ++D +  LT  ++     +LY+D  + + NKPA      G  I   +   +
Sbjct: 340 LGHML-EGLVVDDNPLLTNPAEGKTLSILYQDEAMAIVNKPAEFLSVPGKEIEDSVYSRM 398

Query: 134 K-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           + ++ ++ G  P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ GIP 
Sbjct: 399 QQTFPNATG--PLIVHRLDMSTSGLMVIALTKDAHKQLQKQFIQRTVTKRYVALLAGIPT 456

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQ---NEKG----ANYAISHFKVIDCFAQKFCWLEM 245
              +  A   +    + GD     +Q   +E G     ++ +SH   +   A+ + +   
Sbjct: 457 AMADKQAAGQISLP-LRGDLDDRPRQLVCHEFGKAAQTHWELSHIDEMARTARVYLF--- 512

Query: 246 QPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-- 300
            P TGRTHQLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP  
Sbjct: 513 -PKTGRTHQLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHPVT 562

Query: 301 -EGGRLQI 307
            E  R QI
Sbjct: 563 REQMRFQI 570


>gi|332365269|gb|EGJ43032.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1059]
          Length = 291

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 64/202 (31%), Positives = 94/202 (46%), Gaps = 22/202 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAILFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK---Q 218
           +       L      R I + YW+LV G   +KK      L+ K  IG D     K   +
Sbjct: 141 KNPFVLPILNRLLEKREISREYWALVQGKFPSKK------LIYKDKIGRDRHDRRKRLVE 194

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +KG  YA +H   +  F Q    ++ Q  TGRTHQ+RVH  H G P++GD  Y    +G
Sbjct: 195 PQKGL-YAETHVTRLKQFGQA-ALVKCQLKTGRTHQIRVHLAHHGHPLIGDPLYHPQPQG 252

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                   +L LHA  +   HP
Sbjct: 253 --------RLMLHAHLLTFTHP 266


>gi|315103148|gb|EFT75124.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL050PA2]
          Length = 306

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 111/229 (48%), Gaps = 18/229 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-----GSGIAYHID--GFLKSWVDSKGQKPRLTHRLDQE 153
           ++++DS I V +KPAG++        G  +  H+   GF  S      ++  +  RLD  
Sbjct: 82  IIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS-TSGAPERQGIVQRLDVG 140

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA++  A   L ++FR R + K+Y +LV G P      I       + IG D+ 
Sbjct: 141 TSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI------DAPIGRDHR 194

Query: 214 HVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           H  K     G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P  GD  Y
Sbjct: 195 HDWKMAIVDGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLY 253

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 254 GCDPALAKELGLERQ-WLHAGELSFTHPGSGEWVTFHADLPADLQNALD 301


>gi|315283354|ref|ZP_07871565.1| ribosomal large subunit pseudouridine synthase D [Listeria marthii
           FSL S4-120]
 gi|313613002|gb|EFR86933.1| ribosomal large subunit pseudouridine synthase D [Listeria marthii
           FSL S4-120]
          Length = 289

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/217 (30%), Positives = 104/217 (47%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP G+        +Y  D     ++ +++  GQ+      HRLDQ TS
Sbjct: 80  IIYEDDFLLVVNKPVGMKTHPND--SYERDTCANAVQYYLEKTGQEANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H KV++   +K   L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHVKVLENDNEKNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 253 -------SPRANRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|196248006|ref|ZP_03146708.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
 gi|196212790|gb|EDY07547.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
          Length = 299

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/232 (26%), Positives = 123/232 (53%), Gaps = 30/232 (12%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + V NKPAG++        GG+   G+ +H   + +  +DS      +  RLD
Sbjct: 84  IVYEDEYVLVVNKPAGLATIPSRHHPGGTLANGLLHH---YRQQQLDSTVH---IITRLD 137

Query: 152 QETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           ++TSG+++VA+ R    HL  + + + ++ + Y ++  G+   ++  I   + +++    
Sbjct: 138 RDTSGLVLVAKHRHV-HHLLSTLQQKGQVTRTYEAVCHGVIDEEEGTIDAPIGRQN---- 192

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D + + ++  +    AI+HF+V++  +  + ++ ++  TGRTHQ+RVH  ++G P+ GD 
Sbjct: 193 DSI-IAREVREDGKRAITHFRVLERLS-GYTYVSLRLETGRTHQIRVHLAYLGHPLAGDE 250

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDS 321
            Y  + +      I  +  LH+R +   HP   +L   TAPLP  M +  ++
Sbjct: 251 LYGGSRE------IIGRQALHSRQLSFFHPFARQLYTFTAPLPDDMARLIEA 296


>gi|206977555|ref|ZP_03238449.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
 gi|217958867|ref|YP_002337415.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|222095026|ref|YP_002529086.1| ribosomal large subunit pseudouridine synthase d [Bacillus cereus
           Q1]
 gi|229138078|ref|ZP_04266676.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|206744273|gb|EDZ55686.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
 gi|217063723|gb|ACJ77973.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|221239084|gb|ACM11794.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           Q1]
 gi|228645423|gb|EEL01657.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
          Length = 307

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/231 (30%), Positives = 114/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +    S +GG G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPSEKGGMGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEKYFRKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y    K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 254 DVLYGGGTK------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDT 298


>gi|50842255|ref|YP_055482.1| pseudouridylate synthase [Propionibacterium acnes KPA171202]
 gi|50839857|gb|AAT82524.1| pseudouridylate synthase [Propionibacterium acnes KPA171202]
 gi|315107090|gb|EFT79066.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL030PA1]
          Length = 306

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 111/229 (48%), Gaps = 18/229 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-----GSGIAYHID--GFLKSWVDSKGQKPRLTHRLDQE 153
           ++++DS I V +KPAG++        G  +  H+   GF  S      ++  +  RLD  
Sbjct: 82  IIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS-TSGAPERQGIVQRLDVG 140

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA++  A   L ++FR R + K+Y +LV G P      I       + IG D+ 
Sbjct: 141 TSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI------DAPIGRDHR 194

Query: 214 HVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           H  K     G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P  GD  Y
Sbjct: 195 HDWKMAIVDGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLY 253

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 254 GCDPALAKELGLERQ-WLHAGELSFTHPGSGEWVTFHADLPADLQNALD 301


>gi|78485000|ref|YP_390925.1| pseudouridine synthase [Thiomicrospira crunogena XCL-2]
 gi|78363286|gb|ABB41251.1| ribosomal large subunit pseudouridine synthase A [Thiomicrospira
           crunogena XCL-2]
          Length = 241

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 61/205 (29%), Positives = 103/205 (50%), Gaps = 21/205 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  I V NKPAG+    G  +   ++  L + V        + HRLD +TSGI+++
Sbjct: 29  VLYEDDDIIVVNKPAGLLSVPGKDLDPEMN--LLAQVQKHVPTALIVHRLDMDTSGIMIL 86

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-----ANWLLKKSHIGGDYVHV 215
           A+ +A+ +HL+  F+ R  +K Y ++ +G P   +  +      +W  +   I       
Sbjct: 87  AKHKASHRHLSIQFQDRLTEKTYQAICFGKPSTSQGHLNLPMRCDWENRPLQI------- 139

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              + K    A +H+K+   +   F  + + P TGR+HQLR+H   +G PI+GD+ Y   
Sbjct: 140 --IDLKQGKAASTHWKLTAQYDNAF-EVNLTPVTGRSHQLRLHMKMLGHPILGDNLYAD- 195

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
              +F +    +L LHA  + + HP
Sbjct: 196 -PQSFAA--SKRLLLHAASLKVTHP 217


>gi|319425400|gb|ADV53474.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 574

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 76/248 (30%), Positives = 120/248 (48%), Gaps = 31/248 (12%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H++ E  ++D +  LT  ++     +LY+D  + + NKPA      G  I   +   +
Sbjct: 340 LGHML-EGLVVDDNPLLTNPAEGKTLSILYQDEAMAIVNKPAEFLSVPGKEIEDSVYSRM 398

Query: 134 K-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           + ++ ++ G  P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ GIP 
Sbjct: 399 QQTFPNATG--PLIVHRLDMSTSGLMVIALTKDAHKQLQKQFIQRTVTKRYVALLAGIPT 456

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQ---NEKG----ANYAISHFKVIDCFAQKFCWLEM 245
              +  A   +    + GD     +Q   +E G     ++ +SH   +   A+ + +   
Sbjct: 457 AMADKQAAGQISLP-LRGDLDDRPRQLVCHEFGKAAQTHWELSHIDEMARTARVYLF--- 512

Query: 246 QPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-- 300
            P TGRTHQLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP  
Sbjct: 513 -PKTGRTHQLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHPVT 562

Query: 301 -EGGRLQI 307
            E  R QI
Sbjct: 563 REQMRFQI 570


>gi|15615410|ref|NP_243713.1| hypothetical protein BH2847 [Bacillus halodurans C-125]
 gi|10175468|dbj|BAB06566.1| BH2847 [Bacillus halodurans C-125]
          Length = 302

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 56/184 (30%), Positives = 97/184 (52%), Gaps = 15/184 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT------HRLDQET 154
           ++YE+    V NKPAG+          H  G L + + +  Q+ ++       +RLD++T
Sbjct: 86  VIYENDHYLVVNKPAGVPTIPSRD---HPQGTLANGLLNYFQRQKMAATFHAVNRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+VA+ + A   L++  R   I++ Y ++V G  + ++  I   + +K     +   
Sbjct: 143 SGLLIVAKHQLAHDQLSKQQRQGNIKRTYMAIVQGEIEQQEGTITAPIARK-----EESL 197

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++  +    AI+HFKVID   Q    +++Q  TGRTHQ+RVH  ++G P+ GD  Y  
Sbjct: 198 ITREVREDGQLAITHFKVIDRLNQG-TIVQVQLETGRTHQIRVHFSYLGYPLFGDDLYGG 256

Query: 275 NFKG 278
             KG
Sbjct: 257 ERKG 260


>gi|313813196|gb|EFS50910.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL025PA1]
          Length = 306

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 111/229 (48%), Gaps = 18/229 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-----GSGIAYHID--GFLKSWVDSKGQKPRLTHRLDQE 153
           ++++DS I V +KPAG++        G  +  H+   GF  S      ++  +  RLD  
Sbjct: 82  IIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS-TSGAPERQGIVQRLDVG 140

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA++  A   L ++FR R + K+Y +LV G P      I       + IG D+ 
Sbjct: 141 TSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI------DAPIGRDHR 194

Query: 214 HVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           H  K     G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P  GD  Y
Sbjct: 195 HDWKMAIVDGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLY 253

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 254 GCDPALAKELGLERQ-WLHAGELSFTHPGSGEWVTFHADLPADLQNALD 301


>gi|289426834|ref|ZP_06428560.1| pseudouridine synthase, RluA family [Propionibacterium acnes J165]
 gi|295130343|ref|YP_003581006.1| Ribosomal large subunit pseudouridine synthase D [Propionibacterium
           acnes SK137]
 gi|289159923|gb|EFD08101.1| pseudouridine synthase, RluA family [Propionibacterium acnes J165]
 gi|291376668|gb|ADE00523.1| Ribosomal large subunit pseudouridine synthase D [Propionibacterium
           acnes SK137]
 gi|313772526|gb|EFS38492.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL074PA1]
 gi|313807256|gb|EFS45743.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL087PA2]
 gi|313809762|gb|EFS47483.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL083PA1]
 gi|313818302|gb|EFS56016.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL046PA2]
 gi|313820064|gb|EFS57778.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL036PA1]
 gi|313823127|gb|EFS60841.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL036PA2]
 gi|313825596|gb|EFS63310.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL063PA1]
 gi|313830671|gb|EFS68385.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL007PA1]
 gi|313833891|gb|EFS71605.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL056PA1]
 gi|314925486|gb|EFS89317.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL036PA3]
 gi|314960263|gb|EFT04365.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL002PA2]
 gi|314968093|gb|EFT12192.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL037PA1]
 gi|314973673|gb|EFT17769.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL053PA1]
 gi|314976266|gb|EFT20361.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL045PA1]
 gi|314978249|gb|EFT22343.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL072PA2]
 gi|314983525|gb|EFT27617.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL005PA1]
 gi|314987713|gb|EFT31804.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL005PA2]
 gi|314990192|gb|EFT34283.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL005PA3]
 gi|315084579|gb|EFT56555.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL027PA2]
 gi|315085915|gb|EFT57891.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL002PA3]
 gi|315088667|gb|EFT60643.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL072PA1]
 gi|315096293|gb|EFT68269.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL038PA1]
 gi|327325929|gb|EGE67719.1| RNA pseudouridine synthase, RluA family [Propionibacterium acnes
           HL096PA2]
 gi|327330628|gb|EGE72374.1| RNA pseudouridine synthase, RluA family [Propionibacterium acnes
           HL097PA1]
 gi|327332198|gb|EGE73935.1| RNA pseudouridine synthase, RluA family [Propionibacterium acnes
           HL096PA3]
 gi|327442820|gb|EGE89474.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL013PA2]
 gi|327446191|gb|EGE92845.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL043PA2]
 gi|327447826|gb|EGE94480.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL043PA1]
 gi|328753730|gb|EGF67346.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL020PA1]
 gi|328760574|gb|EGF74142.1| RNA pseudouridine synthase, RluA family [Propionibacterium acnes
           HL099PA1]
 gi|332675185|gb|AEE72001.1| pseudouridylate synthase [Propionibacterium acnes 266]
          Length = 306

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 111/229 (48%), Gaps = 18/229 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-----GSGIAYHID--GFLKSWVDSKGQKPRLTHRLDQE 153
           ++++DS I V +KPAG++        G  +  H+   GF  S      ++  +  RLD  
Sbjct: 82  IIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS-TSGAPERQGIVQRLDVG 140

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA++  A   L ++FR R + K+Y +LV G P      I       + IG D+ 
Sbjct: 141 TSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI------DAPIGRDHR 194

Query: 214 HVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           H  K     G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P  GD  Y
Sbjct: 195 HDWKMAIVDGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLY 253

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 254 GCDPALAKELGLERQ-WLHAGELSFTHPGSGEWVTFHADLPADLQNALD 301


>gi|299146120|ref|ZP_07039188.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_23]
 gi|298516611|gb|EFI40492.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_23]
          Length = 317

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 86/322 (26%), Positives = 149/322 (46%), Gaps = 43/322 (13%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQV 64
           Y  Y V    +E M L  +     P  +   L+ +L    V VD     +FN  +++G  
Sbjct: 28  YTNYAV----KEPMELMEFLATKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMK 83

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI----SVQ 120
           V+I           K++   + +  L K        ++YED+ I V  K  G+    + +
Sbjct: 84  VQIS----------KQKGKKEFNNRLLK--------IVYEDAYIIVVEKMQGLLSVNTER 125

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                AY I   L  +V   G++ R  + HRLD++TSG+++ A+     + L +++    
Sbjct: 126 QKERTAYTI---LNEYVQRSGRQFRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHDIV 182

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             + Y ++V G  +   + + +WL  K+     YV   + ++ G+  +I+H+K I   A 
Sbjct: 183 TDRRYVAVVEGSMEKDYDTVVSWLTDKTL----YVSSSEYDDGGSK-SITHYKTIKR-AN 236

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  LE+   TGR +Q+RVH   +G PI+GD +Y    + +  +PI  +L LHA  +   
Sbjct: 237 GYSLLELDLETGRKNQIRVHMQDLGHPIIGDGRYG---REDAPNPI-GRLALHAFKLCFY 292

Query: 299 HPEGGRL-QITAPLPAHMVKTW 319
           HP  G L +   P PA   K +
Sbjct: 293 HPVTGDLMEFETPYPAEFKKLF 314


>gi|310766621|gb|ADP11571.1| tRNA pseudouridine synthase C [Erwinia sp. Ejp617]
          Length = 265

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 61/214 (28%), Positives = 105/214 (49%), Gaps = 20/214 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  +   NKP+G+ V   S +  H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 4   IIYQDRWLVAVNKPSGMLVHR-SWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A +   A+ L++ F   ++QK Y ++V G  +           ++  I   +     Q 
Sbjct: 63  MALSSEVARLLSQQFEQHQLQKTYHAVVRGWLEGADTLDYPLTEEQDKIADKF----SQP 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           EK    A++H++ +               ++  +EM P +GR HQLR H  H+  PI+GD
Sbjct: 119 EKAPQPAVTHWRGVATAELPVPVGRYQTSRYSLVEMLPESGRKHQLRRHMTHLRHPIIGD 178

Query: 270 HKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP 300
             +  + K N ++      N+L LHA  ++L HP
Sbjct: 179 SAH-GDLKQNRSAAANFGMNRLMLHASELNLTHP 211


>gi|269960587|ref|ZP_06174959.1| tRNA pseudouridine synthase C [Vibrio harveyi 1DA3]
 gi|269834664|gb|EEZ88751.1| tRNA pseudouridine synthase C [Vibrio harveyi 1DA3]
          Length = 255

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 116/249 (46%), Gaps = 31/249 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 17  IVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F   +++K Y ++V G    ++E + ++ LK     I   +      
Sbjct: 77  ALSSEVASQVMPMFAEHKMEKTYHAIVRGW--IEEEGVLDYALKVELDKIADKFA----S 130

Query: 219 NEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            EK A  A++ +K +               ++C +EM+P TGR HQLR H  H+  PIVG
Sbjct: 131 QEKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIVG 190

Query: 269 DH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL- 322
           D      K+   ++  F S   ++L LHA  +   HP      +   + A++ +TW  L 
Sbjct: 191 DTTHGDGKHNKLYRTEFDS---HRLLLHASELRFVHPFTDEEIV---MKANIDETWQQLF 244

Query: 323 -GFKYDRNL 330
             F++D +L
Sbjct: 245 ARFEWDASL 253


>gi|226952509|ref|ZP_03822973.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. ATCC 27244]
 gi|226836736|gb|EEH69119.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. ATCC 27244]
          Length = 228

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 103/225 (45%), Gaps = 19/225 (8%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L++ D    V +KPAG+    G      +   L + +     K  L HRLD++
Sbjct: 16  SDFLSEYLIHRDEDFMVIHKPAGLLTVPGK--TPDLQDCLINRLLKLEPKTLLIHRLDRD 73

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     ++  F+ R+  KIY +LV G  + +       +   S      V
Sbjct: 74  TSGILVFGLSKFGQSTISRQFQDRQTSKIYQALVAGHLEGQGTVDIPVIYDPSRPPLHIV 133

Query: 214 HVVKQNEKGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                      + AI H ++     Q    +++ P TGR+HQLRVH  ++G PI+GD  Y
Sbjct: 134 DATHHKPALTEWQAIEHLEIQ---GQAVTRVKLIPITGRSHQLRVHMQYLGHPILGDTLY 190

Query: 273 CANFKGNFTSPIQNKLY----LHARYMDLPHPE-GGRLQITAPLP 312
                    +P Q +LY    LHA  +   HP+ G +L    P+P
Sbjct: 191 A--------TPEQQQLYERLCLHATQLSFAHPKTGTQLDFDCPVP 227


>gi|218676329|ref|YP_002395148.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio splendidus
           LGP32]
 gi|218324597|emb|CAV26131.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio splendidus
           LGP32]
          Length = 563

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/211 (33%), Positives = 106/211 (50%), Gaps = 26/211 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++YED +I V NKP       G  I   +   +K+ + D+ G  P + HRLD  TSG+L+
Sbjct: 362 IVYEDDEIVVVNKPEEFLSVPGKFIEDSVYTRIKARYPDATG--PLIIHRLDMSTSGLLI 419

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +A T  + +H+ + F  R ++K Y +L+ G    K   I+  L       GD     +Q 
Sbjct: 420 LALTAESNKHIQKQFIDRTVEKRYTALLDGEIDGKSGDISLPL------RGDITDRPRQL 473

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
             +E G N A +H++ +     K   + + P TGRTHQLRVH  H   +G PI GD  Y 
Sbjct: 474 VCHEHGRN-AETHWEAVSTNNGK-TKVHLYPKTGRTHQLRVHCAHPSGLGVPIRGDDLY- 530

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             +K       + +L+LHA Y+ L HP  G 
Sbjct: 531 -GYK-------RERLHLHAGYLKLIHPTTGE 553


>gi|148379407|ref|YP_001253948.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 3502]
 gi|153932742|ref|YP_001383785.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           ATCC 19397]
 gi|153936684|ref|YP_001387335.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           Hall]
 gi|148288891|emb|CAL82977.1| ribosomal large subunit pseudouridine synthase C [Clostridium
           botulinum A str. ATCC 3502]
 gi|152928786|gb|ABS34286.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 19397]
 gi|152932598|gb|ABS38097.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           Hall]
 gi|322805749|emb|CBZ03314.1| ribosomal large subunit pseudouridine synthase C [Clostridium
           botulinum H04402 065]
          Length = 317

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/274 (25%), Positives = 129/274 (47%), Gaps = 30/274 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  +E   RLD++ +     +    + K +R G+++V+ ++ K  N ++ G +V    
Sbjct: 3   IVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKNFLEEGDIVE--- 59

Query: 70  VINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGS 123
             N  +   K++ + +D+++ +T           YED  + +  K  G+ V     +G S
Sbjct: 60  SFNVKSKGEKKKFVRIDNNLKIT-----------YEDENMVLVEKWPGVLVHSDKKEGES 108

Query: 124 GIAYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            +  ++  +L    D   +      P   +RLD+ TSGI++  +   A + L E  R R+
Sbjct: 109 TLTDYVLSYLYDKGDYTPELEVTFTPASCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRK 168

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I+K Y SLV G     K+ I    + K+    +   +  + +        + K I     
Sbjct: 169 IEKYYSSLVKG---RIKDGIYEAYISKNE-DTNMSKIYNEPKPNTKKIAMNVKTIQTCGS 224

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            F ++E++  TGR+HQLR H  H+G PI+GD KY
Sbjct: 225 -FSFIEIELLTGRSHQLRAHLSHLGNPIIGDSKY 257


>gi|237719529|ref|ZP_04550010.1| RNA pseudouridylate synthase [Bacteroides sp. 2_2_4]
 gi|229451389|gb|EEO57180.1| RNA pseudouridylate synthase [Bacteroides sp. 2_2_4]
          Length = 306

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 86/322 (26%), Positives = 149/322 (46%), Gaps = 43/322 (13%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQV 64
           Y  Y V    +E M L  +     P  +   L+ +L    V VD     +FN  +++G  
Sbjct: 17  YTNYAV----KEPMELMEFLATKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMK 72

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI----SVQ 120
           V+I           K++   + +  L K        ++YED+ I V  K  G+    + +
Sbjct: 73  VQIS----------KQKGKKEFNNRLLK--------IVYEDAYIIVVEKMQGLLSVNTER 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                AY I   L  +V   G++ R  + HRLD++TSG+++ A+     + L +++    
Sbjct: 115 QKERTAYTI---LNEYVQRSGRQFRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHDIV 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             + Y ++V G  +   + + +WL  K+     YV   + ++ G+  +I+H+K I   A 
Sbjct: 172 TDRRYVAVVEGSMEKDYDTVVSWLTDKTL----YVSSSEYDDGGSK-SITHYKTIKR-AN 225

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  LE+   TGR +Q+RVH   +G PI+GD +Y    + +  +PI  +L LHA  +   
Sbjct: 226 GYSLLELDLETGRKNQIRVHMQDLGHPIIGDGRYG---REDAPNPI-GRLALHAFKLCFY 281

Query: 299 HPEGGRL-QITAPLPAHMVKTW 319
           HP  G L +   P PA   K +
Sbjct: 282 HPVTGDLMEFETPYPAEFKKLF 303


>gi|237714573|ref|ZP_04545054.1| RNA pseudouridylate synthase [Bacteroides sp. D1]
 gi|262406439|ref|ZP_06082988.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_22]
 gi|293373837|ref|ZP_06620181.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|298481084|ref|ZP_06999278.1| RNA pseudouridylate synthase [Bacteroides sp. D22]
 gi|229445342|gb|EEO51133.1| RNA pseudouridylate synthase [Bacteroides sp. D1]
 gi|262355142|gb|EEZ04233.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_22]
 gi|292631236|gb|EFF49870.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|295083972|emb|CBK65495.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens
           XB1A]
 gi|298272658|gb|EFI14225.1| RNA pseudouridylate synthase [Bacteroides sp. D22]
          Length = 306

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 87/322 (27%), Positives = 147/322 (45%), Gaps = 43/322 (13%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQV 64
           Y  Y V    +E M L  +     P  +   L+ +L    V VD     +FN  +++G  
Sbjct: 17  YTNYAV----KEPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMK 72

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI----SVQ 120
           V+I           K++   + +  L K        ++YED+ I V  K  G+    + +
Sbjct: 73  VKIS----------KQKGKKEFNNRLLK--------IVYEDAYIIVVEKMQGLLSVNTER 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                AY I   L  +V   G++ R  + HRLD++TSG+++ A+     + L +++    
Sbjct: 115 QKERTAYTI---LNEYVQRSGRQFRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHEIV 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             + Y ++V G  +   + + +WL  K+     YV   + ++ G+  +I+H+K I   A 
Sbjct: 172 TDRRYVAVVEGSMEKDYDTVVSWLTDKTL----YVSSSEYDDGGSK-SITHYKTIKR-AN 225

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  LE+   TGR +Q+RVH   +G PI+GD +Y      N   PI  +L LHA  +   
Sbjct: 226 GYSLLELDLETGRKNQIRVHMQDLGHPIIGDGRYGREDSPN---PI-GRLALHAFKLCFY 281

Query: 299 HPEGGRL-QITAPLPAHMVKTW 319
           HP  G L +   P PA   K +
Sbjct: 282 HPVTGDLMEFETPYPAEFKKLF 303


>gi|120600133|ref|YP_964707.1| pseudouridylate synthase [Shewanella sp. W3-18-1]
 gi|120560226|gb|ABM26153.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           W3-18-1]
          Length = 226

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/207 (31%), Positives = 103/207 (49%), Gaps = 19/207 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +LY+D  I V NKP+G+    G   A H D     +   K + P  ++ HRLD  TSG++
Sbjct: 17  ILYQDKDIIVINKPSGLLSVPGRDPA-HYDSV---YARVKAEHPHCQIVHRLDMATSGVI 72

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A  R+A + L   F  R   K Y + V G  K+    I   L+       D+ +  KQ
Sbjct: 73  VLALIRSAERELKRQFHDRETSKTYIARVAGHIKHDTGSIDYPLI------CDWPNRPKQ 126

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +      +++H++V+   A++   +++ P TGR+HQLRVH + +G PI+GD  Y    
Sbjct: 127 KVDHFVGKPSLTHYQVMS-RAKRSTLVKLTPITGRSHQLRVHMMAIGHPILGDGFYADPL 185

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +       +L LHA  + + HP  G
Sbjct: 186 AKSLAP----RLLLHAAELTIKHPYTG 208


>gi|125718992|ref|YP_001036125.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK36]
 gi|125498909|gb|ABN45575.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Streptococcus sanguinis SK36]
          Length = 299

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 93/201 (46%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 92  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 148

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      R I + YW+LV G   +KK      L+ K  IG D     K+  +
Sbjct: 149 KNPFVLPILNRLLEKREISREYWALVQGKFPSKK------LIYKDKIGRDRHDRRKRLVD 202

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   YA +H   +  F Q    ++ Q  TGRTHQ+RVH  H G P++GD  Y    KG 
Sbjct: 203 PRKGLYAETHVTRVKQFGQA-ALVKCQLKTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG- 260

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 261 -------RLMLHAHRLIFTHP 274


>gi|325695366|gb|EGD37266.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK150]
          Length = 291

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 93/201 (46%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      R I + YW+LV G   +KK      L+ K  IG D     K+  +
Sbjct: 141 KNPFVLPILNRLLEKREISREYWALVQGKFPSKK------LIYKDKIGRDRHDRRKRLVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   YA +H   +  F Q    ++ Q  TGRTHQ+RVH  H G P++GD  Y    +G 
Sbjct: 195 PRKGLYAETHVTRVKQFGQA-ALVKCQLKTGRTHQIRVHLAHHGHPLIGDPLYHPQPQG- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 253 -------RLMLHAHRLTFTHP 266


>gi|217964932|ref|YP_002350610.1| pseudouridine synthase, RluA family [Listeria monocytogenes HCC23]
 gi|217334202|gb|ACK39996.1| pseudouridine synthase, RluA family [Listeria monocytogenes HCC23]
 gi|307570509|emb|CAR83688.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes L99]
          Length = 296

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 74/313 (23%), Positives = 144/313 (46%), Gaps = 40/313 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           VE +E  + L  + K+ +     +   K    G++ V+ +       ++ G  VR+  P 
Sbjct: 7   VETEENGLLLRTFLKSKHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKVGDKVRLTFPT 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 ++ E   LD               +++ED  + + NKPAG++        YH  
Sbjct: 67  EQQNERLLAEYTDLD---------------IVFEDDFLLIINKPAGMASIPSQ---YHPS 108

Query: 131 GFLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + ++V    +   LT+      RLD+ETSG++++A+ R A   L+   +   +++ Y 
Sbjct: 109 GSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQ 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWL 243
           +   G+   ++  I      ++ IG   V ++++       YA ++++V++ +   F  +
Sbjct: 169 AFTSGVLATQEGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLERYT-AFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TTLLKRQALHSCHLHLVHPVTE 275

Query: 304 R-LQITAPLPAHM 315
             +    PLPA M
Sbjct: 276 EYMAFDLPLPADM 288


>gi|86153072|ref|ZP_01071277.1| ribosomal pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|121612140|ref|YP_001000956.1| ribosomal large subunit pseudouridine synthase A [Campylobacter
           jejuni subsp. jejuni 81-176]
 gi|157415544|ref|YP_001482800.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|167005866|ref|ZP_02271624.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|85843957|gb|EAQ61167.1| ribosomal pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|87249616|gb|EAQ72575.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni 81-176]
 gi|157386508|gb|ABV52823.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|307748184|gb|ADN91454.1| Pseudouridine synthase [Campylobacter jejuni subsp. jejuni M1]
 gi|315932431|gb|EFV11374.1| pseudouridine synthase, RluA family protein [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 322

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 80/305 (26%), Positives = 147/305 (48%), Gaps = 32/305 (10%)

Query: 16  EENMRLDRWF-KNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINA 73
           +EN RLD +  K      N V L  ++    V+V DK + K + ++++G ++ I  +   
Sbjct: 7   DENSRLDVFLAKKLNQSRNQVAL--LIEKDCVQVNDKIQDKNSFKLKNGDIISIASL--K 62

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDG 131
           L + IK Q  +D  +++           LYED  + V NKP+ + V G S +  A  +D 
Sbjct: 63  LCNEIKPQFEVDFDIDV-----------LYEDEDLLVLNKPSNLVVHGASSVKNATLVDW 111

Query: 132 FL--KSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  K  + + G + R  L HRLD++TSG +++A+     Q L+E    + + +IY +L+
Sbjct: 112 LIEKKYTLSNLGGEIRAGLVHRLDKDTSGAILIAKNNFTHQKLSEQLADKSMGRIYLALI 171

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
               K  K  +  +L++        + + K+N+   N   +   ++    +    +  + 
Sbjct: 172 DLPLKEDKIIVEKFLMRSPSNAIKKIAIDKENKFSKNAKSAFINIVK--TENLTLMAAKL 229

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            TGRTHQ+R H   +   I+GD  Y   +KG +      ++ LHA ++   HP+   ++ 
Sbjct: 230 FTGRTHQIRAHLASLNRHILGDSLY--GYKGKYDC----RIMLHAYFLYFIHPKTKEQIF 283

Query: 307 ITAPL 311
           + APL
Sbjct: 284 VKAPL 288


>gi|57167607|ref|ZP_00366747.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter coli RM2228]
 gi|305433113|ref|ZP_07402269.1| RluA family pseudouridine synthase [Campylobacter coli JV20]
 gi|57020729|gb|EAL57393.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter coli RM2228]
 gi|304443814|gb|EFM36471.1| RluA family pseudouridine synthase [Campylobacter coli JV20]
          Length = 321

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 110/218 (50%), Gaps = 15/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS--WVDSKGQKPR--LTHRLDQET 154
           +LYED  + V NKP+ + V G   +  A  +D  ++    + + G + R  L HRLD+ET
Sbjct: 78  ILYEDEDLLVLNKPSNLVVHGAKSVRSATLVDWLIEKQYTLSTLGGEVRAGLVHRLDKET 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG +++A+     Q L+E    + + +IY +L+  +P  + + I +  L +S        
Sbjct: 138 SGAILIAKNNFTHQKLSEQLSDKTMGRIYLALI-DLPLKEDKIIIDKALIRSSANAIKKI 196

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V     KG+  A S F V    +++   +  +  TGRTHQ+R H   +   I+GD  Y  
Sbjct: 197 VTNSFVKGSKEAKSAF-VNLAKSEEVSLIGAKLFTGRTHQIRAHLASINRHILGDELY-- 253

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
            ++G +    + ++ LHA ++   HP  G ++ I APL
Sbjct: 254 GYRGKY----ECRIMLHAYFLYFIHPRNGEKIFIQAPL 287


>gi|319425230|gb|ADV53304.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 225

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/207 (31%), Positives = 103/207 (49%), Gaps = 19/207 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +LY+D  I V NKP+G+    G   A H D     +   K + P  ++ HRLD  TSG++
Sbjct: 16  ILYQDKDIIVINKPSGLLSVPGRDPA-HYDSV---YARVKAEHPHCQIVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A  R+A + L   F  R   K Y + V G  K+    I   L+       D+ +  KQ
Sbjct: 72  VLALIRSAERELKRQFHDRETSKTYIARVAGHIKHDTGSIDYPLI------CDWPNRPKQ 125

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +      +++H++V+   A++   +++ P TGR+HQLRVH + +G PI+GD  Y    
Sbjct: 126 KVDHFVGKPSLTHYQVMS-RAKRSTLVKLTPITGRSHQLRVHMMAIGHPILGDGFYADPL 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +       +L LHA  + + HP  G
Sbjct: 185 AKSLAP----RLLLHAAELTIKHPYTG 207


>gi|238916958|ref|YP_002930475.1| ribosomal large subunit pseudouridine synthase C [Eubacterium
           eligens ATCC 27750]
 gi|238872318|gb|ACR72028.1| ribosomal large subunit pseudouridine synthase C [Eubacterium
           eligens ATCC 27750]
          Length = 333

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/289 (23%), Positives = 135/289 (46%), Gaps = 24/289 (8%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           L K+LR   + ++  +   + +++ G +++I            +    + +VN   ++  
Sbjct: 31  LYKMLRKKNITLNNSKATGDEKLKCGDIIKIFFSDETFEKFSADN---NRTVNYDYYNRI 87

Query: 97  LKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRL 146
            + + ++YE+S +   NKP+G+  Q        +  +L + +  KG+         KP +
Sbjct: 88  YRPLDIIYENSDVIFINKPSGMLSQKAKPEDVSLVEYLIAHLIHKGELNAGDLASFKPGI 147

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            +RLD+ TSGI+   +T    Q L+E+F+ R + K Y  +V G   +K+  I  +L K +
Sbjct: 148 CNRLDRNTSGIVAAGKTTKGLQQLSEAFKQRTLGKYYLCIVKG-NVDKRALIKGYLYKDN 206

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                    + + E   +  I    +  C       L++   TGR+HQ+R H   +G P+
Sbjct: 207 KTNK---VTISRTETKDSLPIETEYIPVCSNGNVTLLKIHLLTGRSHQIRAHLASIGHPL 263

Query: 267 VGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           +GD+KY     N   N    +++++ LH+  +D+P  +   + I A +P
Sbjct: 264 IGDYKYGQKSVNDTFNRQYKVKDQM-LHSYELDIPDMD---IHIYAVIP 308


>gi|223935079|ref|ZP_03626997.1| pseudouridine synthase [bacterium Ellin514]
 gi|223895963|gb|EEF62406.1| pseudouridine synthase [bacterium Ellin514]
          Length = 260

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/206 (30%), Positives = 105/206 (50%), Gaps = 14/206 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGI 157
           +++ED+++ V NKPAG+      G  Y     L S V         P L +RLD+ETSGI
Sbjct: 28  VVHEDAELLVINKPAGLVCHPTKGDEY---SSLISRVRLHLGPESHPHLVNRLDRETSGI 84

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA+    A+ L   +  R +QK Y ++V G  + ++  I   L K +      + +  
Sbjct: 85  VIVAKDDTTARGLRRIWEGREVQKEYLAIVHGHVREEQGTIQAALGKDT---SSIIAIKD 141

Query: 218 QNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              +G   + + F V   F+++   F  L + PHTGR HQ+R+H  H+  PIVGD  Y  
Sbjct: 142 TVVEGGAASQTDFTVKKRFSREEGDFTLLRVLPHTGRKHQIRIHLAHIDHPIVGDKMYGG 201

Query: 275 NFKGNFTSPIQNKLYLHA-RYMDLPH 299
           + +  + + +Q++L     + + LPH
Sbjct: 202 D-EDLYMALVQDRLTEEQWKKLILPH 226


>gi|320353226|ref|YP_004194565.1| RluA family pseudouridine synthase [Desulfobulbus propionicus DSM
           2032]
 gi|320121728|gb|ADW17274.1| pseudouridine synthase, RluA family [Desulfobulbus propionicus DSM
           2032]
          Length = 292

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/222 (30%), Positives = 109/222 (49%), Gaps = 25/222 (11%)

Query: 101 LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED +I V +KP G+     + +    + Y +   L    D K ++  + HRLDQ  S
Sbjct: 75  IVYEDKEILVVDKPPGLLTIASASEKTKTMFYKLTACLGERPDGK-ERVFIVHRLDQGAS 133

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LV A+T  A   L +S+   + QK + ++V G P      I + L +        +H 
Sbjct: 134 GLLVFAKTEQAKHALQQSWP--QAQKRFRAIVEGTPCPPSGTIKSLLCESK------IHR 185

Query: 216 VKQNEKGANY---AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V  ++ G+     A + ++VI   A  +  +E+ P T R +QLRVH    G P+ GD KY
Sbjct: 186 VYSDKTGSGAGKPAETRYQVIHT-AGDYALVELIPVTARKNQLRVHLAEQGHPVAGDKKY 244

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
                G  T PI+ +L L A ++   HP  G  ++ +  LPA
Sbjct: 245 -----GAKTDPIK-RLALQASFLSFAHPISGAPMEFSLELPA 280


>gi|261820451|ref|YP_003258557.1| 23S rRNA pseudouridine synthase D [Pectobacterium wasabiae WPP163]
 gi|261604464|gb|ACX86950.1| pseudouridine synthase, RluA family [Pectobacterium wasabiae
           WPP163]
          Length = 325

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 84/336 (25%), Positives = 158/336 (47%), Gaps = 55/336 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   +++ +   +V+++   + K   ++  G+ V   
Sbjct: 9   ATVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVINKPKEKVLGGESV--- 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
               A++ +I+E+   ++          +K  ++YED  I V NK   + V  G+G   +
Sbjct: 66  ----AIDALIEEEARWEAQ--------DIKLDIVYEDQDILVINKSRDLVVHPGAG---N 110

Query: 129 IDGFL--------KSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            DG +           VD     PR  + HRLD++T+G++VVA+T  A   L E+ + R 
Sbjct: 111 PDGTVLNALLHHYPEIVDV----PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQARE 166

Query: 179 IQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           I + Y ++  G        ++ IA    K++H+    VH + +       A++H+++++ 
Sbjct: 167 ITREYEAVAIGSMTAGGMVEQPIARHATKRTHMA---VHPMGKP------AVTHYRIMEH 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NK 287
           F +    L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       +F   ++  ++
Sbjct: 218 F-RAHTRLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDDFIETLRGFDR 276

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             LHA  +   HP  G +++  A LP  MV   ++L
Sbjct: 277 QALHATMLRFYHPITGIQMEWHAALPQDMVDLIEAL 312


>gi|110639592|ref|YP_679802.1| ribosomal large subunit pseudouridine synthase D [Cytophaga
           hutchinsonii ATCC 33406]
 gi|110282273|gb|ABG60459.1| ribosomal large subunit pseudouridine synthase D [Cytophaga
           hutchinsonii ATCC 33406]
          Length = 242

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 112/230 (48%), Gaps = 20/230 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +++ED+ +   NK  G+ VQG       +   +K ++  K  KP      + HR+D+  S
Sbjct: 22  VVFEDNHLIAVNKKNGVLVQGDDTGDKPLSELVKEYLKKKYNKPGNVFAGVIHRIDRPVS 81

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYV 213
           G++++A+T  A + + + F  ++IQK Y  +    P      + +WL K  K +I   + 
Sbjct: 82  GLVLLAKTSKALERMNKQFADKKIQKAYLMVSGSKPNPASAKLVHWLTKDAKRNIAKAHT 141

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             VK+++    Y    + ++   + ++  +E++P TGR+HQ+R     +GC I GD KY 
Sbjct: 142 SEVKESK----YCELSYSLLTS-SDRYFLIEVKPVTGRSHQIRCQMASIGCVIKGDLKY- 195

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
               G   S     + LH+  +   HP  G  +Q+ A  P    + W++L
Sbjct: 196 ----GAPRSNPDGGICLHSHKLSFQHPVTGDNMQLKADPPKG--EPWNAL 239


>gi|159108280|ref|XP_001704412.1| Ribosomal large subunit pseudouridine synthase D [Giardia lamblia
           ATCC 50803]
 gi|157432474|gb|EDO76738.1| Ribosomal large subunit pseudouridine synthase D [Giardia lamblia
           ATCC 50803]
          Length = 250

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 104/225 (46%), Gaps = 27/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG----FLKSW-VDSKGQKPRLTHRLDQETS 155
           +++E+    V NKP  +          HIDG     ++SW + ++G+ PR  ++LD  TS
Sbjct: 4   VVFENDDYTVINKPPNL----------HIDGDYPQTVRSWYLATRGRAPRFVNQLDYPTS 53

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V+A +R AA      F+ R + K Y +LV G      + I+  +   +     +   
Sbjct: 54  GLMVIASSRKAAGFAGREFQARAVAKTYVALVVG--DVASQTISAPIADDAADPRQFCMC 111

Query: 216 VKQNEKGANYAISHFKVIDCFAQK---------FCWLEMQPHTGRTHQLRVHALHMGCPI 266
           + +  K +   +     I    ++         +  + ++P TGR HQLR+H  H+G PI
Sbjct: 112 ISETGKHSETHVERIAAIPEDLRELSPSLPQGLYTLVVLRPVTGRRHQLRLHLAHIGHPI 171

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           VGD  Y            + +L LHA  + +P+  G  L + APL
Sbjct: 172 VGDQLYGGGLTDTNQCGEEERLCLHALMLSIPNLSGLPL-LEAPL 215


>gi|332199087|gb|EGJ13167.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA41317]
          Length = 278

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 182 AKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|145352339|ref|XP_001420507.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580741|gb|ABO98800.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 178

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 58/192 (30%), Positives = 90/192 (46%), Gaps = 18/192 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYE+  + + NKP G+S    S         L++  D++ ++ R  HRLD+ TSG LV 
Sbjct: 2   VLYENDAVVIVNKPPGVSFH--SEFEPGALARLRASRDAREERLRAVHRLDKGTSGTLVF 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T  AA+ L++ F  R I K Y  +    PK K   +   + +            K   
Sbjct: 60  AKTADAAKKLSDGFATRAIVKYYVGISGKKPKKKMGTVTGDMARARR------KAYKLTN 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F  +   A+       +P TG+THQLRV A  +G P++GD  Y        
Sbjct: 114 TKDNPAVTKF--VSFGAKGRRMFIFRPLTGKTHQLRVCAKSLGAPLLGDDVY-------- 163

Query: 281 TSPIQNKLYLHA 292
           +  +  + YLHA
Sbjct: 164 SGAVAERCYLHA 175


>gi|15901834|ref|NP_346438.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae TIGR4]
 gi|148992153|ref|ZP_01821927.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP9-BS68]
 gi|14973521|gb|AAK76078.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae TIGR4]
 gi|147929202|gb|EDK80213.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP9-BS68]
          Length = 291

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 195 AKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNLPILGDPLYNSKSKT- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|86150741|ref|ZP_01068957.1| RluA [Campylobacter jejuni subsp. jejuni 260.94]
 gi|205356297|ref|ZP_03223063.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|315124736|ref|YP_004066740.1| RluA [Campylobacter jejuni subsp. jejuni ICDCCJ07001]
 gi|85841911|gb|EAQ59157.1| RluA [Campylobacter jejuni subsp. jejuni 260.94]
 gi|205345902|gb|EDZ32539.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|315018458|gb|ADT66551.1| RluA [Campylobacter jejuni subsp. jejuni ICDCCJ07001]
          Length = 322

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 72/279 (25%), Positives = 133/279 (47%), Gaps = 36/279 (12%)

Query: 48  VDKKRVKFNNRIQ--------SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++K  V+ N++IQ        +G ++ I  +   L + IK Q  +D  +++         
Sbjct: 31  IEKDCVQVNDKIQDKNSFKLKNGDIISIASL--KLCNEIKPQFEVDFDIDV--------- 79

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL--KSWVDSKGQKPR--LTHRLDQE 153
             LYED  + V NKP+ + V G S +  A  +D  +  K  + + G + R  L HRLD++
Sbjct: 80  --LYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKD 137

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG +++A+     Q L+E    + + +IY +L+    K  K  +  +L++        +
Sbjct: 138 TSGSILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKI 197

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + K+N+   N   +   V+    +    +  +  TGRTHQ+R H   +   I+GD  Y 
Sbjct: 198 AIDKENKFSKNAKSAFINVVK--TENLTLMAAKLFTGRTHQIRAHLASLNRYILGDSLY- 254

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
             +KG +      ++ LHA ++   HP+   ++ + APL
Sbjct: 255 -GYKGKYDC----RIMLHAYFLYFIHPKTKEQIFVKAPL 288


>gi|282854248|ref|ZP_06263585.1| pseudouridine synthase, RluA family [Propionibacterium acnes J139]
 gi|282583701|gb|EFB89081.1| pseudouridine synthase, RluA family [Propionibacterium acnes J139]
 gi|314923234|gb|EFS87065.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL001PA1]
 gi|314967001|gb|EFT11100.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL082PA2]
 gi|314980957|gb|EFT25051.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL110PA3]
 gi|315091688|gb|EFT63664.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL110PA4]
 gi|315093078|gb|EFT65054.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL060PA1]
 gi|327327821|gb|EGE69597.1| RNA pseudouridine synthase, RluA family [Propionibacterium acnes
           HL103PA1]
          Length = 306

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 111/229 (48%), Gaps = 18/229 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-----GSGIAYHID--GFLKSWVDSKGQKPRLTHRLDQE 153
           ++++DS I V +KPAG++        G  +  H+   GF  S      ++  +  RLD  
Sbjct: 82  IIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS-TSGAPERQGIVQRLDVG 140

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA++  A   L ++FR R + K+Y +LV G P      I       + IG D+ 
Sbjct: 141 TSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI------DAPIGRDHR 194

Query: 214 HVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           H  K     G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P  GD  Y
Sbjct: 195 HDWKMAIVDGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLY 253

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 254 GCDPALAKELGLERQ-WLHAGELSFTHPGSGEWVTFHADLPADLQNALD 301


>gi|40889481|pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
           Pseudouridine Synthase Rlud
          Length = 349

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 88/327 (26%), Positives = 148/327 (45%), Gaps = 47/327 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V   
Sbjct: 32  ATVSENQLGQRLDQALAEXFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV--- 88

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             INA   I +E +     + L          ++YED  I + NKP  + V  G+G   +
Sbjct: 89  -AINA--EIEEEARFEPQDIPLD---------IVYEDEDIIIINKPRDLVVHPGAG---N 133

Query: 129 IDGF----LKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG     L  +       PR  + HRLD++T+G+ VVA+T  A   L ES + R I + 
Sbjct: 134 PDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLXVVAKTVPAQTRLVESLQRREITRE 193

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G         E I+    K++H     VH + +       A++H+++ + F + 
Sbjct: 194 YEAVAIGHXTAGGTVDEPISRHPTKRTHXA---VHPMGKP------AVTHYRIXEHF-RV 243

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQ--NKLYLH 291
              L ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F S ++  ++  LH
Sbjct: 244 HTRLRLRLETGRTHQIRVHXAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALH 303

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVK 317
           A  + L HP  G   +  AP+P   V+
Sbjct: 304 ATXLRLYHPISGIEXEWHAPIPQDXVE 330


>gi|111657101|ref|ZP_01407890.1| hypothetical protein SpneT_02001674 [Streptococcus pneumoniae
           TIGR4]
 gi|183603313|ref|ZP_02714103.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae SP195]
 gi|183571639|gb|EDT92167.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae SP195]
 gi|332071803|gb|EGI82293.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA17570]
          Length = 278

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 182 AKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|325288855|ref|YP_004265036.1| ribosomal large subunit pseudouridine synthase D [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964256|gb|ADY55035.1| ribosomal large subunit pseudouridine synthase D [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 312

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 84/330 (25%), Positives = 147/330 (44%), Gaps = 43/330 (13%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
            Y Q++ VE   E +RLD          +   ++ ++  G+V V+ +  K N RI++   
Sbjct: 10  AYEQWLAVEGKPE-VRLDVCLTEKT-GTSRSFIRNMIEEGRVLVNGETKKANYRIRAEDK 67

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I    N      +E K++   + L          ++YED  + V NKP G+ V    G
Sbjct: 68  IGI----NLPKP--RELKVVPQQIPLE---------IIYEDDDLLVVNKPQGMVVHPAPG 112

Query: 125 I--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           +     ++  L    D  G     +P + HR+D++TSG+LVVA+   +   L    +  +
Sbjct: 113 VWEGTLVNALLYHCRDLSGINGIIRPGIVHRIDKDTSGLLVVAKNDESHNQLAGQLKEHK 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           +Q+ Y ++V G+       I   + +          V K +      A++H++V + F  
Sbjct: 173 MQRKYLAVVHGVLSEPSGTIDAPIGRDPKDRKKMAVVFKHSRP----AVTHYEVEERFI- 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-----YLHAR 293
            +  ++    TGRTHQ+RVH  ++  P++GD  Y          P +N L      LHA 
Sbjct: 228 GYTKIKAVLETGRTHQIRVHMAYIRNPVLGDPLY---------GPKKNILGLTGQVLHAH 278

Query: 294 YMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
            +   HP GG+L + +A  P   ++  D L
Sbjct: 279 TLAFLHPRGGKLMEFSADPPREFLEAVDKL 308


>gi|313764724|gb|EFS36088.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL013PA1]
 gi|313815789|gb|EFS53503.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL059PA1]
 gi|314915215|gb|EFS79046.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL005PA4]
 gi|314918556|gb|EFS82387.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL050PA1]
 gi|314919819|gb|EFS83650.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL050PA3]
 gi|314931834|gb|EFS95665.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL067PA1]
 gi|314955990|gb|EFT00388.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL027PA1]
 gi|314958385|gb|EFT02488.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL002PA1]
 gi|315098276|gb|EFT70252.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL059PA2]
 gi|315101033|gb|EFT73009.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL046PA1]
 gi|327451042|gb|EGE97696.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL087PA3]
 gi|327453603|gb|EGF00258.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL083PA2]
 gi|328753075|gb|EGF66691.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL087PA1]
          Length = 285

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 111/229 (48%), Gaps = 18/229 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-----GSGIAYHID--GFLKSWVDSKGQKPRLTHRLDQE 153
           ++++DS I V +KPAG++        G  +  H+   GF  S      ++  +  RLD  
Sbjct: 61  IIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS-TSGAPERQGIVQRLDVG 119

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA++  A   L ++FR R + K+Y +LV G P      I       + IG D+ 
Sbjct: 120 TSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI------DAPIGRDHR 173

Query: 214 HVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           H  K     G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P  GD  Y
Sbjct: 174 HDWKMAIVDGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLY 232

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 233 GCDPALAKELGLERQ-WLHAGELSFTHPGSGEWVTFHADLPADLQNALD 280


>gi|260771109|ref|ZP_05880036.1| ribosomal large subunit pseudouridine synthase D [Vibrio furnissii
           CIP 102972]
 gi|260613706|gb|EEX38898.1| ribosomal large subunit pseudouridine synthase D [Vibrio furnissii
           CIP 102972]
 gi|315179286|gb|ADT86200.1| 23S rRNA pseudouridine synthase D/large subunit [Vibrio furnissii
           NCTC 11218]
          Length = 324

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 119/241 (49%), Gaps = 33/241 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G     DG + + +        + PR  + HRLD++T
Sbjct: 86  IVYEDDDIIVINKPRDLVVHPGAGTP---DGTVLNALLFHFPPIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++VVA+T  A   L    + R I + Y ++  G      +  A  ++ K  IG    H
Sbjct: 143 TGLMVVAKTVPAQTRLVRELQKRNITREYEAIAIG------KMTAGGMIDKP-IGR---H 192

Query: 215 VVKQNEKGAN----YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             K+     +     A++H++V + F ++   + ++  TGRTHQ+RVH  ++  P++GD 
Sbjct: 193 STKRTLMAVSPLGKPAVTHYRVAEHF-REHTRIRLRLETGRTHQIRVHMAYLQHPLLGDT 251

Query: 271 KYCANF---KG---NFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
            Y       KG     T  I+  ++  LHA  +   HP  G  L+  AP+P  MV+  ++
Sbjct: 252 AYGGRARIPKGATQELTDMIRGFDRQALHAVMLRFEHPITGEPLEFHAPVPDDMVEMTEA 311

Query: 322 L 322
           L
Sbjct: 312 L 312


>gi|229154958|ref|ZP_04283072.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|228628516|gb|EEK85229.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
          Length = 307

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/231 (30%), Positives = 114/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +    S +GG G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPSEKGGMGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEKYFKNQNVTLVMLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y    K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 254 DVLYGGQTK------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDT 298


>gi|254428126|ref|ZP_05041833.1| RNA pseudouridine synthase superfamily [Alcanivorax sp. DG881]
 gi|196194295|gb|EDX89254.1| RNA pseudouridine synthase superfamily [Alcanivorax sp. DG881]
          Length = 204

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/223 (31%), Positives = 111/223 (49%), Gaps = 32/223 (14%)

Query: 102 LYEDSKIYVFNKPA-GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +Y D+ I + NKPA  +SV G +    + D  ++  + ++    RL HRLD +TSGI+V 
Sbjct: 1   MYRDAHILLINKPAYLLSVPGRA--PENKDCAVRR-LQAQYADIRLVHRLDLDTSGIMVF 57

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW----LLKKSHIGGD 211
           A T  A   L+  F++R +QK Y ++V G+ ++         IA+W    L K  H    
Sbjct: 58  ALTAQAQSRLSRLFQLRTVQKRYQAVVHGLVEHDSGSIDLPLIADWPNRPLQKVCH---- 113

Query: 212 YVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                   E G N A++H++V++         L + P TGR+HQLR+H   +G PI+G  
Sbjct: 114 --------ETGKN-ALTHYRVLERDIPGNRTRLLLSPVTGRSHQLRIHCRELGHPIIG-- 162

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
             C  +       +  +L LHA ++   HP  G  Q  T+P P
Sbjct: 163 --CDMYAPAEIEALSPRLLLHAEWLAFNHPVTGLWQEFTSPSP 203


>gi|328759180|gb|EGF72796.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL025PA2]
          Length = 285

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 111/229 (48%), Gaps = 18/229 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-----GSGIAYHID--GFLKSWVDSKGQKPRLTHRLDQE 153
           ++++DS I V +KPAG++        G  +  H+   GF  S      ++  +  RLD  
Sbjct: 61  IIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS-TSGAPERQGIVQRLDVG 119

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA++  A   L ++FR R + K+Y +LV G P      I       + IG D+ 
Sbjct: 120 TSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTI------DAPIGRDHR 173

Query: 214 HVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           H  K     G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P  GD  Y
Sbjct: 174 HDWKMAIVDGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLY 232

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 233 GCDPALAKELGLERQ-WLHAGELSFTHPGSGEWVTFHADLPADLQNALD 280


>gi|165976282|ref|YP_001651875.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|165876383|gb|ABY69431.1| probable pseudouridine synthase Rlu family protein [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
          Length = 247

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 117/244 (47%), Gaps = 24/244 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPIHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A+ ++E F   +++K Y ++V G   +K E   ++ LK   +  D +       
Sbjct: 65  ALNSEMARLMSEQFEQHQLEKGYLAVVRGYLLDKGEI--DYPLK---VILDKIADKFSQP 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KEAQQAVTFYQNLASVEMLYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPIMGDT 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
           KY  +   N T   +   ++L LH+ ++   HP+   +++I APL     K W +L   +
Sbjct: 180 KY-GDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLD----KQWQNLFTTF 234

Query: 327 DRNL 330
           + N 
Sbjct: 235 NWNF 238


>gi|327463496|gb|EGF09815.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1057]
          Length = 299

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 93/201 (46%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+       I   +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 92  LYQDQHLIIVNKPEGMKTHANEPIELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 148

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      R I + YW+L+ G   +KK      L+ K  IG D     K+  +
Sbjct: 149 KNPFVLPILNRLLEKREISREYWALIQGKFPSKK------LIYKDKIGRDRHDRRKRLVD 202

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   YA +H   +    Q    ++ Q  TGRTHQ+RVH  H G P++GD  Y    KG 
Sbjct: 203 PRKGLYAETHVTRLKQLGQA-ALVKCQLKTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG- 260

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 261 -------RLMLHAHRLTFTHP 274


>gi|88856520|ref|ZP_01131177.1| ribosomal large subunit pseudouridine synthase [marine
           actinobacterium PHSC20C1]
 gi|88814174|gb|EAR24039.1| ribosomal large subunit pseudouridine synthase [marine
           actinobacterium PHSC20C1]
          Length = 301

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 108/229 (47%), Gaps = 28/229 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQ---GGSGI----AYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           ++Y+D  I V +KPAG++     G  G+    A    G+  S      ++  + HRLD  
Sbjct: 77  IVYDDEHIVVIDKPAGVAAHPSIGWDGVTVLGALAGAGYRIS-TSGAAERAGIVHRLDAG 135

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA++  A   L  +F  R + KIY S+V G P      I   + +  H G  + 
Sbjct: 136 TSGLMVVAKSELAYTELKRAFHDREVNKIYHSIVQGHPDPLMGTIDAPIGR--HPGSSWK 193

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V     G   +I+H++ ++ F      +E+Q  TGRTHQ+RVH      P VGD  Y 
Sbjct: 194 FAVV---AGGKDSITHYETLEAFPSA-SLVEVQLETGRTHQIRVHMAAQRHPCVGDTMYG 249

Query: 274 ANFKGNFTSPIQNKL-----YLHARYMDLPHPEGGRLQIT--APLPAHM 315
           A+        I  KL     +LHA  +   HP   R  +T  +P PA +
Sbjct: 250 AD------PTISAKLGLTRQWLHAHKLGFVHP-ATREPVTFESPYPADL 291


>gi|157372031|ref|YP_001480020.1| tRNA pseudouridine synthase C [Serratia proteamaculans 568]
 gi|157323795|gb|ABV42892.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 256

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/237 (27%), Positives = 107/237 (45%), Gaps = 31/237 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   NKP+G  V   S +  H   F+   V D  GQ     HRLD+ TSG+L+
Sbjct: 4   ILYQDEHLVAVNKPSGWLVHR-SWLDRHETRFVMQTVRDQIGQHVFTVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A +   A+ L++ F   ++QK Y ++V G              +   I   +       
Sbjct: 63  MALSSEVARLLSQQFEQHQMQKTYHAVVRGYVLEGATIDYPLTEELDKIADKFA----SK 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +KG   A++H++ +             + ++  +E++P  GR HQLR H +H+  PI+GD
Sbjct: 119 DKGPQPAVTHYRPLARVEMPVAIGRYESARYSLVELKPENGRKHQLRRHMVHIRHPIIGD 178

Query: 270 HKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
            K+           +F  P   +L LHA ++ L HP  G        P H+   WD 
Sbjct: 179 SKHGDLNQNRGMAQHFGCP---RLMLHASHLQLNHPVTGE-------PLHLSARWDE 225


>gi|118475501|ref|YP_892378.1| ribosomal pseudouridine synthase [Campylobacter fetus subsp. fetus
           82-40]
 gi|118414727|gb|ABK83147.1| ribosomal pseudouridine synthase [Campylobacter fetus subsp. fetus
           82-40]
          Length = 323

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 73/247 (29%), Positives = 118/247 (47%), Gaps = 31/247 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLD 151
           +LYED  I V NKP+ ++V     +    +  L  W+   G          +  + HRLD
Sbjct: 78  ILYEDDDILVLNKPSNLTVHPAPSVK---EATLVEWLKQNGYMLSTLNGDIRAGIVHRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG++VVA+  A+   L      + + ++Y +L+    K+K       L+    IG +
Sbjct: 135 KGTSGVIVVAKNNASHSALAAQLSDKSMGRVYLALIDFNLKDK-------LIIDRPIGRN 187

Query: 212 YVHVVKQNEKGAN--YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             + +K N   AN   A S F  I C       +  +  TGRTHQ+RVH   +   I+GD
Sbjct: 188 PQNRLK-NSVAANGRAAKSAFTNIIC-EDDLNLIAAKLFTGRTHQIRVHLASINRHILGD 245

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           + Y   FK      I+ ++ LHA  ++L HP+ G ++Q  APLP      +D L  K D+
Sbjct: 246 NLY--GFKSK-NCKIK-RVMLHAYILNLTHPKSGEKMQFIAPLPTDF---YDILSKKIDK 298

Query: 329 NLYIKRL 335
            +  +++
Sbjct: 299 EILNEKI 305


>gi|91226723|ref|ZP_01261412.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
 gi|91189020|gb|EAS75303.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
          Length = 559

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/204 (34%), Positives = 103/204 (50%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V NKP+G+    G  I       L++ + D KG  P + HRLD  TSGILV
Sbjct: 358 IIYQDDAMVVVNKPSGLLSVPGKTIKDSAYTRLQAMFPDVKG--PFVIHRLDMATSGILV 415

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A T+ A + L + F  R +QK Y +L+ G+  N+ E   +  ++          V  ++
Sbjct: 416 FALTKRANKSLQKQFMARGVQKRYMALLEGV-LNEPEGEISLPMRGDPDDRPRQLVCFEH 474

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHKYCANF 276
            K A       +V D  ++ +    M P TGRTHQLRVH A HMG   P+VGD  Y    
Sbjct: 475 GKHAETYWQLIEVKDGRSKVY----MYPKTGRTHQLRVHSAHHMGLNMPMVGDGLYGEK- 529

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                    N+L+LHA  ++L HP
Sbjct: 530 --------ANRLHLHAEMLELDHP 545


>gi|68535841|ref|YP_250546.1| pseudouridylate synthase [Corynebacterium jeikeium K411]
 gi|68263440|emb|CAI36928.1| pseudouridylate synthase [Corynebacterium jeikeium K411]
          Length = 323

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 110/236 (46%), Gaps = 29/236 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LY D  + V +KP G++             SG+A    GF  S      ++  +  RLD
Sbjct: 86  ILYSDEDVIVVDKPVGVAAHPTVGWEGPTVTSGLAAA--GFRIS-TSGPPERKGIVQRLD 142

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG+++VA +  A   L  +FR R + K Y +LV G P      I   + +  H    
Sbjct: 143 VGTSGVMIVAASERAYTVLKNAFRDREVSKTYHALVQGHPDPTSGTIDAPIGR--HPSAG 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +   V+++ K   +AI+H+  ++   Q    LE++  TGRTHQ+RVH   +  P+ GD  
Sbjct: 201 WRFSVREDGK---HAITHYDTLEAHRQA-SLLEVKLETGRTHQIRVHFSALHHPLCGDPM 256

Query: 272 YCANFKGNFTSPIQNKL-----YLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           Y ++ K      +  +L     +LHA  +  PHP+G    + +P P  +    D L
Sbjct: 257 YGSDPK------LAERLGLIRQWLHAVELGFPHPDGSWKTVRSPYPEDLQLALDRL 306


>gi|328914578|gb|AEB55411.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           psittaci 6BC]
          Length = 279

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 54/176 (30%), Positives = 91/176 (51%), Gaps = 18/176 (10%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L+  +L+ED    ++NKP+  S +  + I     G              + HRLD++T+G
Sbjct: 71  LEPQILWEDEHYCIYNKPSHTSTEDLAKIT----GL------------NIVHRLDRDTTG 114

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            ++ A+  +AA  L+E F+ R+I K Y +LV+G PK     + ++   KS   G  +   
Sbjct: 115 CILFAKHASAAHALSELFKKRKIHKQYTALVFGHPKKSSGTLISYTAPKSRRCGAVIFGN 174

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            Q   G    I+ + ++ C  +++  +  +P TGRTHQ+R+H   +G PIVGD  Y
Sbjct: 175 TQKNHG-KLTITQWSIL-CAYKQYTLMRCEPITGRTHQIRLHMHTLGHPIVGDVDY 228


>gi|329942738|ref|ZP_08291517.1| RNA pseudouridylate synthase family protein [Chlamydophila psittaci
           Cal10]
 gi|332287335|ref|YP_004422236.1| pseudouridylate synthase protein [Chlamydophila psittaci 6BC]
 gi|313847919|emb|CBY16914.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           psittaci RD1]
 gi|325507344|gb|ADZ18982.1| pseudouridylate synthase protein [Chlamydophila psittaci 6BC]
 gi|328814998|gb|EGF84987.1| RNA pseudouridylate synthase family protein [Chlamydophila psittaci
           Cal10]
          Length = 275

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 54/176 (30%), Positives = 91/176 (51%), Gaps = 18/176 (10%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L+  +L+ED    ++NKP+  S +  + I     G              + HRLD++T+G
Sbjct: 67  LEPQILWEDEHYCIYNKPSHTSTEDLAKIT----GL------------NIVHRLDRDTTG 110

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            ++ A+  +AA  L+E F+ R+I K Y +LV+G PK     + ++   KS   G  +   
Sbjct: 111 CILFAKHASAAHALSELFKKRKIHKQYTALVFGHPKKSSGTLISYTAPKSRRCGAVIFGN 170

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            Q   G    I+ + ++ C  +++  +  +P TGRTHQ+R+H   +G PIVGD  Y
Sbjct: 171 TQKNHG-KLTITQWSIL-CAYKQYTLMRCEPITGRTHQIRLHMHTLGHPIVGDVDY 224


>gi|291518249|emb|CBK73470.1| pseudouridine synthase, RluA family [Butyrivibrio fibrisolvens
           16/4]
          Length = 295

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/302 (23%), Positives = 142/302 (47%), Gaps = 47/302 (15%)

Query: 11  VVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++  + +  ++D++ K   Y   N   ++K+     V +D + V  N ++ +G+++ +  
Sbjct: 8   IISTEYDGFQIDKFLKTQGYSSANITAIKKM--PNNVVIDGEWVHMNRKLSAGELLTV-- 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-------- 121
               ++     +KI    ++L          ++YED  I V NKPAG+ +          
Sbjct: 64  ---NISEEDSSEKIPAVKMDLD---------IVYEDEDIIVINKPAGLPIHPSLNHYEDS 111

Query: 122 -GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             +G+AY+ +   K ++       R  +RLD+ TSG+ V+++   +A  L+   + R   
Sbjct: 112 LANGLAYYYEQQGKPFI------FRCANRLDKNTSGLTVISKHLVSANILSTMVKNREFH 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + Y+++V G  +  +  I       + IG   D +   + + +    A++H+KV+D    
Sbjct: 166 REYYAIVRGTLEQPEGTI------DAPIGRVDDSIITRQVDFENGERAVTHYKVMDE-KN 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               + +   TGRTHQ+RVH  ++G P++GDH Y  +F+         +  LH+  ++  
Sbjct: 219 GHSLVSIHLETGRTHQIRVHFKYIGHPLIGDHLYNPDFE------YMQRQALHSHRIEFV 272

Query: 299 HP 300
           HP
Sbjct: 273 HP 274


>gi|227515296|ref|ZP_03945345.1| pseudouridylate synthase RluD [Lactobacillus fermentum ATCC 14931]
 gi|227086356|gb|EEI21668.1| pseudouridylate synthase RluD [Lactobacillus fermentum ATCC 14931]
          Length = 296

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/203 (31%), Positives = 96/203 (47%), Gaps = 18/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYE+  + V +KPAGI S    +G    +   + ++++       + HRLD+ETSG ++
Sbjct: 90  VLYENRDLLVVDKPAGIKSHPNQAGEVGTLMNRVAAYLEGTNDAAYMVHRLDKETSGAMI 149

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+       L        I + Y +LV G+P   +     W L    +G D   V K+ 
Sbjct: 150 VAKNPVVVPILDRLISTGEIHRDYLALVAGVPNPARGI---WDLP---LGQDPTDVRKRK 203

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              K A  A +H++ +     +   + +   TGRTHQLRVH    GCPIVGD  Y     
Sbjct: 204 VFGKNAQPARTHYRTLAVNDDR-ALVVLNLETGRTHQLRVHLAAAGCPIVGDPLY----- 257

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
           G   +P   ++YLH    +L  P
Sbjct: 258 GTVAAP---RMYLHGVAQELVLP 277


>gi|313113631|ref|ZP_07799215.1| RNA pseudouridine synthase [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310624047|gb|EFQ07418.1| RNA pseudouridine synthase [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 229

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 107/239 (44%), Gaps = 49/239 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAY-----HIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LYED+ + V +KPAG+S + G   A        D F+            + HRLD   S
Sbjct: 3   ILYEDAALVVLDKPAGLSSEEGVPAALRQLWGQPDAFVG-----------VVHRLDTGVS 51

Query: 156 GILVVARTRAAA----QHLTESFRMRRIQ--------------KIYWSLVWGIPKNK--- 194
           G++V ART  AA    + +T+S     +Q              K Y +++ G P      
Sbjct: 52  GLMVFARTPGAAAALSRQITQSQNAYAVQDGRAEGEPEVPQFIKQYRAVIAGGPDEALPA 111

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  + +WL K S  G   V  V +  +G   A+  ++++   A +    E+  HTGRTHQ
Sbjct: 112 ESTLRDWLFKDSRRG--RVFPVSRPRRGVREAVLEYRIVKT-AGEMSLAEITLHTGRTHQ 168

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +RV       P+ GD KY +  KG+        + L +  +   HPE G+ +  T PLP
Sbjct: 169 IRVQFASRKHPLTGDGKYGSRVKGS--------IALQSCGLQFLHPETGKPMAFTLPLP 219


>gi|260578068|ref|ZP_05845990.1| RluA family RNA pseudouridine synthase [Corynebacterium jeikeium
           ATCC 43734]
 gi|258603808|gb|EEW17063.1| RluA family RNA pseudouridine synthase [Corynebacterium jeikeium
           ATCC 43734]
          Length = 323

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 110/236 (46%), Gaps = 29/236 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LY D  + V +KP G++             SG+A    GF  S      ++  +  RLD
Sbjct: 86  ILYSDEDVIVVDKPVGVAAHPTVGWEGPTVTSGLAAA--GFRIS-TSGPPERKGIVQRLD 142

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG+++VA +  A   L  +FR R + K Y +LV G P      I   + +  H    
Sbjct: 143 VGTSGVMIVAASERAYTVLKNAFRDREVSKTYHALVQGHPDPTSGTIDAPIGR--HPSAG 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +   V+++ K   +AI+H+  ++   Q    LE++  TGRTHQ+RVH   +  P+ GD  
Sbjct: 201 WRFSVREDGK---HAITHYDTLEAHRQA-SLLEVKLETGRTHQIRVHFSALHHPLCGDPM 256

Query: 272 YCANFKGNFTSPIQNKL-----YLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           Y ++ K      +  +L     +LHA  +  PHP+G    + +P P  +    D L
Sbjct: 257 YGSDPK------LAERLGLIRQWLHAVELGFPHPDGSWKTVRSPYPEDLQLALDRL 306


>gi|225861831|ref|YP_002743340.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|225728075|gb|ACO23926.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|327389005|gb|EGE87352.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA04375]
          Length = 278

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +N K  
Sbjct: 182 AKNGQYAETYVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNFPILGDPLYNSNSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|149007842|ref|ZP_01831438.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP18-BS74]
 gi|298229086|ref|ZP_06962767.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae str. Canada MDR_19F]
 gi|298254837|ref|ZP_06978423.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae str. Canada MDR_19A]
 gi|298501509|ref|YP_003723449.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|147760692|gb|EDK67665.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP18-BS74]
 gi|298237104|gb|ADI68235.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
          Length = 291

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +N K  
Sbjct: 195 AKNGQYAETYVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNFPILGDPLYNSNSKT- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|30019444|ref|NP_831075.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|229126707|ref|ZP_04255719.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|229143996|ref|ZP_04272412.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|29894988|gb|AAP08276.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|228639393|gb|EEK95807.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|228656647|gb|EEL12473.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
          Length = 307

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 112/228 (49%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGSIMDRLLMERKIKRTYAALVEGKVKKKQGKI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y    K        +   LHA  +   HP     +++  P P  +
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKIHFLHPITKEAIEVDVPFPTKL 295


>gi|54310131|ref|YP_131151.1| 23S rRNA pseudouridine synthase D [Photobacterium profundum SS9]
 gi|90414902|ref|ZP_01222867.1| putative ribosomal large subunit pseudouridine synthase D
           [Photobacterium profundum 3TCK]
 gi|46914570|emb|CAG21349.1| putative ribosomal large subunit pseudouridine synthase D
           [Photobacterium profundum SS9]
 gi|90324016|gb|EAS40610.1| putative ribosomal large subunit pseudouridine synthase D
           [Photobacterium profundum 3TCK]
          Length = 324

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 117/239 (48%), Gaps = 29/239 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPR--LTHRLDQETSGI 157
           ++YED  I V NKP    V  G+G     +   L     +  + PR  + HRLD++T+G+
Sbjct: 86  IVYEDEHILVINKPRDFVVHPGAGTPDRTVLNALLFHCPALAEVPRAGIVHRLDKDTTGL 145

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +VVA+T  A   L  + + R+I + Y ++  G      +      ++K  IG    H  K
Sbjct: 146 MVVAKTIQAQTRLVRALQKRKITREYEAIAMG------KMTGGGTVEKP-IGR---HATK 195

Query: 218 Q-----NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +     +E G   AI+H++V + F ++   L ++  TGRTHQ+RVH  +M  P+VGD  Y
Sbjct: 196 RICMAVHELG-KPAITHYRVAEHF-REHTRLVLRLETGRTHQIRVHMSYMSHPLVGDAIY 253

Query: 273 CANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
               +    +  +        ++  LHAR + L HP  G L +  APLP  ++   D L
Sbjct: 254 GGRPRPPRHASDELILALRSFDRQALHARMLRLSHPITGELMEWRAPLPNDILAMIDIL 312


>gi|320333923|ref|YP_004170634.1| pseudouridine synthase [Deinococcus maricopensis DSM 21211]
 gi|319755212|gb|ADV66969.1| pseudouridine synthase [Deinococcus maricopensis DSM 21211]
          Length = 294

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/252 (27%), Positives = 114/252 (45%), Gaps = 20/252 (7%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +V+    +  L   +L+     +V NKP  + +       + +   L  W  +   +P L
Sbjct: 48  AVSAPTATPILPPEVLFSAESYHVLNKPP-LWLTHQVHARFEVPDAL-GWARATLGEPEL 105

Query: 147 T--HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRLD+ETSG+L++ R+ +AA+     F  RR++K Y ++V G P  ++  +   L  
Sbjct: 106 APAHRLDRETSGVLILTRSSSAARGFHRLFLDRRVEKTYLAIVHGQPAWEEVTLDAPLGF 165

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                 + + V +        A++HF+V+      +  L   P TGR HQLR H  H+G 
Sbjct: 166 LGLSDTNSIRVRQGVVPDGKPAVTHFEVLGRRG-AYALLRCSPRTGRMHQLRAHLAHLGH 224

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLY-------------LHARYMDLPHPEGGRLQITAPL 311
           P+VGD  Y  + +  F   +Q  L              LHA  +  P   G  ++ TAP 
Sbjct: 225 PMVGDKIYGPHPEA-FVQFVQTGLTPALLRTLQLPRQALHAHEVAFPF-GGTTVRHTAPF 282

Query: 312 PAHMVKTWDSLG 323
           PA +   WD+ G
Sbjct: 283 PADLQAFWDAAG 294


>gi|260902224|ref|ZP_05910619.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
 gi|308110528|gb|EFO48068.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
          Length = 559

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/204 (34%), Positives = 104/204 (50%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V NKP+G+    G  I       L++ + D +G  P + HRLD  TSGILV
Sbjct: 358 IIYQDDAMVVVNKPSGLLSVPGKTIKDSAYTRLQAMFPDVEG--PFVIHRLDMATSGILV 415

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A T+ A + L + F  R +QK Y +L+ G+  N+ E   +  ++          V  ++
Sbjct: 416 FALTKRANKSLQKQFMARGVQKRYMALLEGV-LNEPEGEISLPMRGDPDDRPRQLVCFEH 474

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHKYCANF 276
            K A  +    +V D  ++ +    M P TGRTHQLRVH A HMG   P+VGD  Y    
Sbjct: 475 GKHAETSWQLIEVKDGRSKVY----MYPKTGRTHQLRVHSAHHMGLNMPMVGDGLYGEK- 529

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                    N+L+LHA  ++L HP
Sbjct: 530 --------ANRLHLHAEMLELDHP 545


>gi|119775332|ref|YP_928072.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119767832|gb|ABM00403.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
          Length = 224

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/200 (31%), Positives = 94/200 (47%), Gaps = 9/200 (4%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y D  + + NKP+G+      G+A H      + +     +  L HRLD  TSGI+V AR
Sbjct: 18  YIDRDLIIINKPSGL--LSNPGMAAHTHDSAITRLCRLYPEAILVHRLDCATSGIMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           ++ A  +L   F+ R  +K Y + V GI   + E   +  L K      +  V   +   
Sbjct: 76  SKKAESNLKTQFQNRDTEKRYLAQVAGI-IEQDEGTIDLPLGKDRSNPPWQKV---DMAE 131

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNF 280
              A++H++V+    +    + ++P TGRTHQLRVH L +G PI+GD  Y     F    
Sbjct: 132 GRPAVTHYRVL-ARRENSTLVALEPETGRTHQLRVHMLSLGHPILGDDFYGRTQEFGQGT 190

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  +   HP
Sbjct: 191 VEEASPRLCLHAERLSFKHP 210


>gi|313607319|gb|EFR83739.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL F2-208]
          Length = 289

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/217 (30%), Positives = 102/217 (47%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP  +        +Y  D     ++ +++  GQ       HRLDQ TS
Sbjct: 80  IIYEDDFLLVVNKPVDMKTHAND--SYETDTCANAVQYYLEKTGQDANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H KV++   +K   L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHVKVLENDNEKNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 253 -------SPSANRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|190150190|ref|YP_001968715.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|307250101|ref|ZP_07532064.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|307261347|ref|ZP_07543022.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|307263527|ref|ZP_07545142.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|189915321|gb|ACE61573.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|306857898|gb|EFM89991.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306869078|gb|EFN00880.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|306871170|gb|EFN02899.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 247

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 117/244 (47%), Gaps = 24/244 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPIHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A+ ++E F   +++K Y ++V G   +K E   ++ LK   +  D +       
Sbjct: 65  ALNSEMARLMSEQFEQHQLEKGYLAVVRGYLLDKGEI--DYPLK---VILDKIADKFSQP 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KEAQQAVTFYQNLASVEMLYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPIMGDT 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
           KY  +   N T   +   ++L LH+ ++   HP+   +++I APL     K W +L   +
Sbjct: 180 KY-GDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLD----KQWQNLFATF 234

Query: 327 DRNL 330
           + N 
Sbjct: 235 NWNF 238


>gi|327467897|gb|EGF13387.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK330]
          Length = 291

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 92/201 (45%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      R I + YW+LV G      +  A  L+ K  IG D     K+  +
Sbjct: 141 KNPFVLPILNRLLEKREISREYWALVQG------KLPAKNLIYKDKIGRDRHDRRKRLVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   YA +H   +  F Q    ++ Q  TGRTHQ+RVH  H G P+VGD  Y    KG 
Sbjct: 195 PRKGLYAETHVTRLKQFGQA-ALVKCQLKTGRTHQIRVHLGHHGHPLVGDPLYHPQPKG- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 253 -------RLMLHAHRLTFTHP 266


>gi|15639223|ref|NP_218671.1| hypothetical protein TP0231 [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189025464|ref|YP_001933236.1| hypothetical protein TPASS_0231 [Treponema pallidum subsp. pallidum
           SS14]
 gi|3322502|gb|AAC65220.1| conserved hypothetical protein [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189018039|gb|ACD70657.1| hypothetical protein TPASS_0231 [Treponema pallidum subsp. pallidum
           SS14]
 gi|291059635|gb|ADD72370.1| RNA pseudouridine synthase superfamily [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 216

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 115/228 (50%), Gaps = 20/228 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D+ +   +KPAG++VQ G+ +   +   L+  +   G +    HRLD++T+G+L+ 
Sbjct: 5   IIFQDAAVVAVDKPAGLAVQPGARVRVCVVDVLQKQL---GVRLFPLHRLDKDTAGVLLF 61

Query: 161 AR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+  RAAA +      MR I++ Y +L +G P   +EC    +  ++        VV+  
Sbjct: 62  AKHARAAALYQGILGSMRVIKR-YRALCFGRPP--RECGDIRVPIRTGTAARRRQVVR-- 116

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              A+ A    +  D       +LE+  H+GRTHQ+R+H   +GCPI+GD KY  +F  N
Sbjct: 117 --AAHTAYRVLRATD----THTYLELTLHSGRTHQIRIHLAALGCPIIGDDKY-GDFARN 169

Query: 280 FTSPIQ---NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
                     +L L A  + LP      L + A +P H ++  D++  
Sbjct: 170 KACARAWGVKRLQLFAHSLVLPC-ACKPLVLRARMPVHFLRALDAVAL 216


>gi|120599960|ref|YP_964534.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|120560053|gb|ABM25980.1| pseudouridine synthase [Shewanella sp. W3-18-1]
          Length = 574

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/248 (30%), Positives = 120/248 (48%), Gaps = 31/248 (12%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H++ E  ++D +  L   ++     +LY+D  + + NKPA      G  I   +   +
Sbjct: 340 LGHML-EGLVVDDNPLLMNPAEGKTLSILYQDEAMAIVNKPAEFLSVPGKEIEDSVYSRM 398

Query: 134 K-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           + ++ ++ G  P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ GIP 
Sbjct: 399 QQTFPNATG--PLIVHRLDMSTSGLMVIALTKDAHKQLQKQFIQRTVTKRYVALLAGIPT 456

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQ---NEKG----ANYAISHFKVIDCFAQKFCWLEM 245
              + +A   +    + GD     +Q   +E G     ++ +SH   +   A+ + +   
Sbjct: 457 AMADKLAAGQISLP-LRGDLDDRPRQLVCHEFGKAAQTHWELSHIDEMARTARVYLF--- 512

Query: 246 QPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-- 300
            P TGRTHQLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP  
Sbjct: 513 -PKTGRTHQLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHPVT 562

Query: 301 -EGGRLQI 307
            E  R QI
Sbjct: 563 REQMRFQI 570


>gi|298710073|emb|CBJ31789.1| pseudouridine synthase [Ectocarpus siliculosus]
          Length = 541

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 90/351 (25%), Positives = 157/351 (44%), Gaps = 53/351 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV +++    +D       P  +    +K L +G V+VD ++VK   R++ G  + +  
Sbjct: 135 TVVSDEDNKAPIDWVLSRRLPQHSRRFYRKALEAGDVKVDGRKVKRFIRVKRGARISV-- 192

Query: 70  VINALNHIIKEQKILDSSV----------NLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
                  + ++Q+   +S           NL       +  +++ED  ++V  KPAG+  
Sbjct: 193 ------DLGRQQQQQGASAVAAATTTPPPNLVFPQRLPRLRVVFEDDHLFVAMKPAGMIC 246

Query: 120 QGGS---------GIAYHI--DGFLKSWVD---------SKGQKPRLTHRLDQETSGILV 159
           Q  +         G+ YH+   G L+   D         S+G    +  RLD++TSGI+V
Sbjct: 247 QPCAAAPRGTVLHGLMYHMVQSGQLEEGSDITAAAANTLSQG----IVQRLDKQTSGIMV 302

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+T AA+  L+  FR  +++K Y ++  G P      +   L ++S      V   +  
Sbjct: 303 VAKTLAASSKLSALFRKGKVKKQYLAVCHGDP-GFDSVVDAPLYRRSSGKVGAVEPWEAE 361

Query: 220 EKGANYAISHFK-VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---AN 275
              A  A +  + V        C  ++   TGR HQ+RVH   +GCPIVGD +Y    AN
Sbjct: 362 AFRAKEAQTRVRNVATARGLSLCRADI--LTGRMHQVRVHLKWIGCPIVGDREYGDPEAN 419

Query: 276 FKGNFTSPIQ---NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           F+ +  S  +    +  LH+  ++  HP   + +   AP+P  M +T  ++
Sbjct: 420 FRVSKRSAHRVEAQRPLLHSVSLEFIHPFTNKPMSFKAPMPPDMWETAQNI 470


>gi|38492837|pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic
           Module
          Length = 252

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 112/235 (47%), Gaps = 31/235 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP  + V  G+G   + DG     L  +       PR  + HRLD++T
Sbjct: 12  IVYEDEDIIVINKPRDLVVHPGAG---NPDGTVLNALLHYYPPIADVPRAGIVHRLDKDT 68

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGD 211
           +G+ VVA+T  A   L ES + R I + Y ++  G         E I+    K++H    
Sbjct: 69  TGLXVVAKTVPAQTRLVESLQRREITREYEAVAIGHXTAGGTVDEPISRHPTKRTHXA-- 126

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            VH           A++H+++ + F +    L ++  TGRTHQ+RVH  H+  P+VGD  
Sbjct: 127 -VH------PXGKPAVTHYRIXEHF-RVHTRLRLRLETGRTHQIRVHXAHITHPLVGDPV 178

Query: 272 YCANFKG------NFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y    +        F S ++  ++  LHA  + L HP  G   +  AP+P   V+
Sbjct: 179 YGGRPRPPKGASEAFISTLRKFDRQALHATXLRLYHPISGIEXEWHAPIPQDXVE 233


>gi|228907022|ref|ZP_04070887.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228852613|gb|EEM97402.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
          Length = 307

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/228 (30%), Positives = 112/228 (49%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAEKGGNGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G    K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVNKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y    K        +   LHA  ++  HP     +++  P P  +
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPTKL 295


>gi|325694474|gb|EGD36383.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK150]
          Length = 295

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 115/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++      + Q+  +  RLD++TSG+
Sbjct: 78  VVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKVIERFGDVYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLY--- 247

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            +G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 248 -EGSLEHGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|315922777|ref|ZP_07919017.1| RNA pseudouridylate synthase [Bacteroides sp. D2]
 gi|313696652|gb|EFS33487.1| RNA pseudouridylate synthase [Bacteroides sp. D2]
          Length = 317

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/226 (29%), Positives = 115/226 (50%), Gaps = 20/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 102 IVYEDAYIIVVEKMQGLLSVNTERQKERTAYTI---LNEYVQRSGRQFRVFIVHRLDRDT 158

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+     + L +++      + Y ++V G  +   + + +WL  K+     YV 
Sbjct: 159 SGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTL----YVS 214

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             + ++ G+  +I+H+K I   A  +  LE+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 215 SSEYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRKNQIRVHMQDLGHPIIGDGRYG- 271

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
             + +  +PI  +L LHA  +   HP  G L +   P PA   K +
Sbjct: 272 --REDAPNPI-GRLALHAFKLCFYHPVTGDLMEFETPYPAEFKKLF 314


>gi|160884288|ref|ZP_02065291.1| hypothetical protein BACOVA_02266 [Bacteroides ovatus ATCC 8483]
 gi|156110027|gb|EDO11772.1| hypothetical protein BACOVA_02266 [Bacteroides ovatus ATCC 8483]
          Length = 317

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/226 (29%), Positives = 115/226 (50%), Gaps = 20/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 102 IVYEDAYIIVVEKMQGLLSVNTERQKERTAYTI---LNEYVQRSGRQFRVFIVHRLDRDT 158

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+     + L +++      + Y ++V G  +   + + +WL  K+     YV 
Sbjct: 159 SGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTL----YVS 214

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             + ++ G+  +I+H+K I   A  +  LE+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 215 SSEYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRKNQIRVHMQDLGHPIIGDGRYG- 271

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
             + +  +PI  +L LHA  +   HP  G L +   P PA   K +
Sbjct: 272 --REDAPNPI-GRLALHAFKLCFYHPVTGDLMEFETPYPAEFKKLF 314


>gi|296501973|ref|YP_003663673.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
 gi|296323025|gb|ADH05953.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
          Length = 307

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 112/228 (49%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGSIMDRLLMERKIKRTYAALVEGKVKKKQGKI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y    K        +   LHA  +   HP     +++  P P  +
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKIHFLHPITKEAIEVDVPFPTKL 295


>gi|229160344|ref|ZP_04288342.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228623068|gb|EEK79896.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 307

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 114/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VIFEDDHVLIVNKPEQMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DEAITYYKVEKYFKKQDITFVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y    K        +   LHA  ++  HP     +++  P P  +  T
Sbjct: 254 DVLYGGQTK------YMSAQALHAMRINFLHPITKEEIEVDVPFPTKLNNT 298


>gi|255037507|ref|YP_003088128.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
 gi|254950263|gb|ACT94963.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
          Length = 255

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 72/252 (28%), Positives = 111/252 (44%), Gaps = 42/252 (16%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV-------QGGSGIAYHIDGFLKSWVDSKGQKPRL--T 147
            K I+++ED    V NKP  ++        +GGS +             +K   P L   
Sbjct: 20  FKDIIIFEDEDFLVVNKPPHLATLDERTADRGGSVLRL-----------AKEYNPELQAA 68

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ETSG L  A+  AA +HL   F  R + K Y ++V GI  +  E I+ +L     
Sbjct: 69  HRLDKETSGALAFAKNPAAYRHLAMQFEHREVTKRYHAVVNGI--HDLEGISVYLPILPL 126

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             G  V + + + K A    +  +V     + +  +E  P TGR HQ+R+H   +  PIV
Sbjct: 127 KNGTAVKIDRADGKEAETIFNTLQVY----RGYTLVECIPITGRMHQIRIHLSCLKAPIV 182

Query: 268 GDHKY------CANFKGNFT-------SPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
            D +Y       +N K  F         P+  ++ LHAR +      G  +++ AP P  
Sbjct: 183 NDPQYGGEPIFLSNLKRKFNLKKDTEEQPLIQRVALHARSLSFALMNGEDIRVEAPYPKD 242

Query: 315 ---MVKTWDSLG 323
              +VK  +  G
Sbjct: 243 FEVLVKQLNKFG 254


>gi|168205450|ref|ZP_02631455.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
 gi|170662972|gb|EDT15655.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
          Length = 324

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 82/305 (26%), Positives = 136/305 (44%), Gaps = 44/305 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ + +   +    + K LR G +RV+ K+ K    +  G V+ I  
Sbjct: 3   IEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLEGDVIEI-- 60

Query: 70  VINALNHIIKEQK------ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG- 122
               L  ++ ++K      ++DS              ++YED  + +  K  G+ V    
Sbjct: 61  --RYLQSVVTKEKKKPNFQMVDSG----------SLQVVYEDENMLLVEKWPGVLVHSDK 108

Query: 123 -SGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTE 172
            +G A   D ++ S++  KG           P   +RLD+ TSGI+   +     + L E
Sbjct: 109 KNGAATLTD-YVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNE 167

Query: 173 SFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS-HF 230
             R R+++K Y +LV G I   K E    ++ K   +    V+     E+     I    
Sbjct: 168 MIRERKVKKYYCALVKGKIQPGKYEA---YISKDDELNKSTVY---DTERPDTKKIKMDV 221

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           KV+      F  LE++  TGR+HQLR H  H+G PIVGD KY  N   +F    +NK  L
Sbjct: 222 KVLQTNGA-FSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSF---FENKFGL 277

Query: 291 HARYM 295
             +++
Sbjct: 278 TYQFL 282


>gi|42780479|ref|NP_977726.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 10987]
 gi|42736398|gb|AAS40334.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus ATCC 10987]
          Length = 307

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 113/231 (48%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEKYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y    K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 254 DILYGGGTK------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDT 298


>gi|289669903|ref|ZP_06490978.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 272

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 111/236 (47%), Gaps = 26/236 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D  + V +KPAG+     S +A   D FL   +  +  KP  L HRLD+ TSG L+
Sbjct: 44  ILYQDDVLAVVDKPAGLMAHD-SKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLL 102

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  RA+A  L ++     ++K Y ++  G P  ++     +++     GG    V K  
Sbjct: 103 LAFDRASASVLGKALMAGEVEKNYLTVCRGWPAEEQ-----FIVDHDLDGGPGKPVKKP- 156

Query: 220 EKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 157 ------AVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGD 210

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
             +       +F     +++ LHA  ++ PHP +G R+ +TAPL A   K     G
Sbjct: 211 ASHGDGRHNRSFRMLGIHRMLLHAERLEFPHPADGRRISVTAPLDAEFTKACTFFG 266


>gi|157691873|ref|YP_001486335.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
 gi|157680631|gb|ABV61775.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
          Length = 288

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/223 (29%), Positives = 111/223 (49%), Gaps = 22/223 (9%)

Query: 101 LLYEDSKIYVFNK-PAGISVQGGSGIAYHI-DGFLKSWVDSKGQKPRLT----HRLDQET 154
           +L+ED  + V NK P   S+       + I +G L  + +   Q  RLT    +RLD++T
Sbjct: 75  ILFEDEHVLVLNKRPYIPSIPSREHPEHSIANGLLHHYAE---QSVRLTVHLVNRLDRDT 131

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA+ R A   L+++ +   +++ Y +   G+ K K   I   + +K    GD + 
Sbjct: 132 SGVMLVAKHRFAHSLLSKAQKSGAVKRTYRAFTHGMIKEKHGTIRAKIARK----GDSI- 186

Query: 215 VVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           + +  +     A++HF V     +     + +   TGRTHQ+RVH  ++G P++GD  Y 
Sbjct: 187 IERMVDDTGQEAVTHFTVRAVDTELNMSDVALALETGRTHQIRVHMQYLGYPLIGDTLYG 246

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                  T+   N+  LH+  +  PHP  G  +  +APLP  M
Sbjct: 247 G------TNERMNRQALHSETLVFPHPMTGEEMTFSAPLPEDM 283


>gi|56551646|ref|YP_162485.1| RluA family pseudouridine synthase [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241761227|ref|ZP_04759315.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|260752766|ref|YP_003225659.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis NCIMB
           11163]
 gi|59803028|sp|P50513|RLUD_ZYMMO RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|56543220|gb|AAV89374.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241374134|gb|EER63631.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|258552129|gb|ACV75075.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
          Length = 317

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 108/228 (47%), Gaps = 20/228 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED  + V NKPAG+ V   +G         + YH  G L         +P + HR+D
Sbjct: 84  IVFEDEHLLVVNKPAGMVVHPAAGNYDNTLVNALLYHCAGKLSGI--GGVARPGIVHRID 141

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA+T  A   L   F    I + Y ++V G P  +    A   L +S +   
Sbjct: 142 KDTSGLLVVAKTDPAHAGLAAQFADHSINRRYRAIVDGHPSLQGHVDAP--LARSSVNRQ 199

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +V         A++H+++I    +    +E +  TGRTHQ+RVH   +G  ++GD  
Sbjct: 200 KMAIVSDGR--GKRAVTHYRMITPL-KNASLIECRLETGRTHQVRVHMSSIGHSLLGDPV 256

Query: 272 YCANFKGN---FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           Y  + K +     S    +  LHA ++   HP  G ++   A +P  M
Sbjct: 257 YGRSKKAHHALLQSLAFQRQALHAAHLGFIHPISGKQVDFDAEMPQDM 304


>gi|303251277|ref|ZP_07337455.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307252489|ref|ZP_07534385.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|302649819|gb|EFL79997.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306860081|gb|EFM92098.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 247

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 118/246 (47%), Gaps = 24/246 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPVHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A+ ++E F   +++K Y ++V G   +K E   ++ LK   +  D +       
Sbjct: 65  ALNSKMARLMSEQFEQHQLEKGYLAVVRGYLLDKGEI--DYQLK---VILDKIADKFSQP 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KEAQQAVTFYQNLASVEMPYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPIMGDT 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
           KY  +   N T   +   ++L LH+ ++   HP+   +++I APL     + W ++   +
Sbjct: 180 KY-GDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLD----EQWQNVFLTF 234

Query: 327 DRNLYI 332
           + N  I
Sbjct: 235 NWNFPI 240


>gi|301052930|ref|YP_003791141.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           anthracis CI]
 gi|300375099|gb|ADK04003.1| ribosomal large subunit pseudouridylate synthase D [Bacillus cereus
           biovar anthracis str. CI]
          Length = 307

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 109/226 (48%), Gaps = 22/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++YED  + + NKP  +      +GG G   ++  F    +     K R  HRLD++T+G
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAF-HYQMKGLETKVRHIHRLDKDTTG 145

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D  H  
Sbjct: 146 GVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRDRHHAT 199

Query: 217 KQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VGD  Y 
Sbjct: 200 RRRVSPKG-DQAITYYKVEGYFKKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVGDVLYG 258

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
              K        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 259 GQTK------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDT 298


>gi|289664969|ref|ZP_06486550.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 272

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 111/236 (47%), Gaps = 26/236 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D  + V +KPAG+     S +A   D FL   +  +  KP  L HRLD+ TSG L+
Sbjct: 44  ILYQDDVLAVVDKPAGLMAHD-SKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLL 102

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  RA+A  L ++     ++K Y ++  G P  ++     +++     GG    V K  
Sbjct: 103 LAFDRASASVLGKALMAGEVEKNYLTVCRGWPAEEQ-----FIVDHDLDGGPGKPVKKP- 156

Query: 220 EKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 157 ------AVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGD 210

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
             +       +F     +++ LHA  ++ PHP +G R+ +TAPL A   K     G
Sbjct: 211 TSHGDGRHNRSFRMLGIHRMLLHAERLEFPHPADGRRISVTAPLDAEFTKACTLFG 266


>gi|254304341|ref|ZP_04971699.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148324533|gb|EDK89783.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 316

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 80/300 (26%), Positives = 143/300 (47%), Gaps = 52/300 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALN 75
           E MRLD++            L+K++ +  V+V+ K +K N R ++SG+ + +        
Sbjct: 17  EGMRLDKYLSEQIEEATRSYLEKLIDNNFVKVNSKIIKKNGRKLKSGEKIEV-------- 68

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
            +I E++      N+   ++ +   ++YE+    V NK  G+ V    G         + 
Sbjct: 69  -LIPEEE------NIDIEAENIPLDVVYENDDFIVINKNYGMVVHPAYGNYTGTLVNALL 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y+ +    S V+    +P + HRLD++TSG++++A+   A   L   F  + I K Y  +
Sbjct: 122 YYTNNL--SSVNG-NIRPGIIHRLDKDTSGLILIAKNNFAHAKLASMFIDKTIHKTYLCI 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDY-----VHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           V G     +E ++  +  ++ IG D      + VVK+N K    AIS+++VI+   + + 
Sbjct: 179 VKG--NFSEENLSGRI--ENLIGRDIKDRKKMAVVKENGK---IAISNYRVIEQ-VEGYS 230

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------FKGNFTSPIQNKLYL 290
            +E+   TGRTHQ+RVH   +   I+GD  Y              +K  F +P+ NK Y+
Sbjct: 231 LVEVAIETGRTHQIRVHMKSINHVILGDSVYGTEDKNIKRQMLHAYKLEFLNPLDNKEYV 290


>gi|125718029|ref|YP_001035162.1| 23S rRNA pseudouridine synthase [Streptococcus sanguinis SK36]
 gi|125497946|gb|ABN44612.1| 23S rRNA pseudouridine synthase, putative [Streptococcus sanguinis
           SK36]
          Length = 295

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 115/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++      + Q+  +  RLD++TSG+
Sbjct: 78  VVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKVIERFGDVYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLY--- 247

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            +G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 248 -EGSLEHGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|127513571|ref|YP_001094768.1| pseudouridylate synthase [Shewanella loihica PV-4]
 gi|126638866|gb|ABO24509.1| tRNA pseudouridine synthase C [Shewanella loihica PV-4]
          Length = 273

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/239 (28%), Positives = 115/239 (48%), Gaps = 21/239 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  +   +KPAG+ V   S +A     F ++   D  G      HRLD+ TSG+L+
Sbjct: 25  ILYEDDDLVAIHKPAGLLVHR-SYLARREKYFAMQMTRDLVGCHVFPVHRLDRPTSGVLL 83

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVK 217
            A++   A  L E F  + +QK Y +LV G     +  + ++ LK+    +G   V    
Sbjct: 84  FAKSSEMANQLCEQFASKSVQKHYVALVRG--NMHEPGLLDYPLKQELDELGDKNV---D 138

Query: 218 QNEKGANYAISHFKVIDC---------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            N+       S+  +++C          + ++  +++ PHTGR HQLR H  H+  PI+G
Sbjct: 139 PNKAAQEAQTSYHPLLNCEIPYPSGRYASSRYALVQLTPHTGRKHQLRRHMAHLRHPIIG 198

Query: 269 DHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
           D  +    +  F       N+L+L A+ ++  HP  G R+ +   L A  +  ++ LG+
Sbjct: 199 DTTHGDGKQNRFMREHSGINRLWLIAKKLEFNHPRSGERIAVETELEAEWLSLFELLGW 257


>gi|330444402|ref|YP_004377388.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           pecorum E58]
 gi|328807512|gb|AEB41685.1| Ribosomal large subunit pseudouridine synthase C [Chlamydophila
           pecorum E58]
          Length = 275

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/227 (29%), Positives = 109/227 (48%), Gaps = 34/227 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL+ED+   +++KP                 +L +   +K     L HRLD++T+G L+ 
Sbjct: 72  LLWEDAHSCIYDKPP----------------YLTTEEIAKTLGRNLVHRLDRDTTGCLLF 115

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T+ A Q L++ F+ R I K Y +LV+G+PK     +  +   K    G  +       
Sbjct: 116 AKTQDAMQKLSDLFKQRNIHKQYITLVFGLPKQCSGTLTTFTAPKYKRCGAVLFGTTTPS 175

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKG 278
           +G    I+ + V+  + + +  L  +P TGRTHQ+R+H  H+G PIVGD  Y +    KG
Sbjct: 176 QG-KLTITKWTVLQRY-KHYSLLLCEPITGRTHQIRLHMKHLGHPIVGDIDYGSKQQPKG 233

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP-------LPAHMVK 317
            F      +  LHA  +    P  G  + +TA        L AH++K
Sbjct: 234 VF------RPLLHAHSLKFVSPFSGETIYVTASSKKNPRVLAAHLLK 274


>gi|229101991|ref|ZP_04232704.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
 gi|228681378|gb|EEL35542.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
          Length = 307

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 74/231 (32%), Positives = 119/231 (51%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K KK  I      ++ IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKKGTI------EAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F +    ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRVSPKG-DEAITYYKVEKYFKKHNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y     G  T+ +  +  LHA  ++  HP     ++I  P PA +  T
Sbjct: 254 DVLY-----GGQTTYMSGQA-LHAMKINFLHPITKEEIEIDVPFPAKLNNT 298


>gi|226313676|ref|YP_002773570.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226096624|dbj|BAH45066.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
          Length = 306

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 106/218 (48%), Gaps = 18/218 (8%)

Query: 103 YEDSKIYVFNKPAGISVQ--GGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILV 159
           YED  + V  KPAG+ V   G        +G +  W    + +K R  +RLD++TSG+++
Sbjct: 85  YEDEDLMVIAKPAGLVVHPTGNHPSGTLANGMIAYWKKRGENRKFRAVNRLDKDTSGLMI 144

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDYVHVVKQ 218
           VA+ + A +  +   ++R +Q+ Y ++V GI ++    I       + IG  +   + +Q
Sbjct: 145 VAKNQWAHEQFSRMQQIRTLQRTYRAIVQGIVESDDGTI------NTPIGLAENSFITRQ 198

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A++H++V+    +   ++E++  TGRTHQ+RVH    G P+ GD  Y     G
Sbjct: 199 VRPDGQTAVTHYRVL-ARGEGMSFVEVKLETGRTHQIRVHMSSEGHPLAGDDLY-----G 252

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
                I  +  LHA  +   HP  G  +    PLP  M
Sbjct: 253 GEREHI-GRQALHAWGLSFVHPRSGLAMSWEEPLPNDM 289


>gi|149187050|ref|ZP_01865357.1| pseudouridine synthase D large subunit [Erythrobacter sp. SD-21]
 gi|148829339|gb|EDL47783.1| pseudouridine synthase D large subunit [Erythrobacter sp. SD-21]
          Length = 318

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/240 (27%), Positives = 112/240 (46%), Gaps = 27/240 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED+ + V NKPAG+ V   +G         + +H  G L S ++    +P + HR+D
Sbjct: 82  VVFEDAYLLVVNKPAGMVVHPAAGNPDGTLVNALLHHCAGRL-SGINGVA-RPGIVHRID 139

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA++ AA + L + F    I + Y +   G P N      +  + +S     
Sbjct: 140 KDTSGLLVVAKSDAAHEGLAKQFADHSITRRYLAACAGHP-NPPSGTVSGRIGRSDRDRK 198

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + V+  +     +A++H++ +         +E +  TGRTHQ+RVH   +G  ++GD  
Sbjct: 199 KMAVLPDDSTRGKHAVTHYETVRRL-NHAALIECRLETGRTHQVRVHCASIGHALLGDPV 257

Query: 272 YCANFKGNFTSPIQNKL--------YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y     G    P++  L         LHA  +   HP  G  L   A LP  M +    L
Sbjct: 258 Y-----GRTPKPLRATLESLDFQRQALHAARLGFIHPISGESLDFCAELPPDMSELMREL 312


>gi|295101803|emb|CBK99348.1| Pseudouridylate synthases, 23S RNA-specific [Faecalibacterium
           prausnitzii L2-6]
          Length = 334

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 82/332 (24%), Positives = 148/332 (44%), Gaps = 28/332 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           QY    NDE  +RL R+ ++         L K  R+ +++V+ K+    +R+++G ++ +
Sbjct: 3   QYTATANDE-GVRLSRFVQSVTRDFPTSLLYKSFRNKRIKVNGKKGVPEDRLKAGDLIEL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIA 126
              IN       E           K  +  K  ++YED  I V  KP  +      +G A
Sbjct: 62  --YIND-EFFPPEGAKPTRKPAPKKQQNQPKVTVIYEDENIAVLYKPTHLLCHSDRTGDA 118

Query: 127 YHIDGFL-----KSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             +D F      K   D +G+   KP + +RLD+ T G+++ A++  A + + E  R   
Sbjct: 119 NLVDAFTQYLAQKGEYDPQGENRFKPGICNRLDRGTEGLVIAAKSYTALRDMNEIIRTDL 178

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y+++  GIP++ +     W           +H  +  ++     I+   V+   A 
Sbjct: 179 LKKEYYTITVGIPQSGR--FTAWWEHDEKNNKVSIHAHQSQDERRKQIITDVDVLRT-AG 235

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR--YMD 296
            F    +   TGRTHQ+R H  ++G P++GD KY  N K N  +  + +     R  ++D
Sbjct: 236 PFALCRIGLITGRTHQIRAHLAYLGKPVLGDIKY-GNRKMNERTGTRTQALCAVRISFLD 294

Query: 297 LPHP------EGGRLQITAPLPAHMVKTWDSL 322
           +P         G  +++  P    +VK +D L
Sbjct: 295 IPEENTLHYLSGKVIKLKDP---QIVKQFDGL 323


>gi|171059556|ref|YP_001791905.1| RluA family pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170777001|gb|ACB35140.1| pseudouridine synthase, RluA family [Leptothrix cholodnii SP-6]
          Length = 369

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 79/321 (24%), Positives = 143/321 (44%), Gaps = 52/321 (16%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVR 66
           +  VVE      RLD+W     P  +  +LQ ++  G VR  ++ ++ +++ + +GQ + 
Sbjct: 41  RLAVVEAAAHGERLDKWLVRIAPEFSRAHLQGLVEGGHVRCGEQVLRQSHKKVMAGQQI- 99

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                        E  +  ++ +    ++ +   +++ED+ + V +KPAG+ V   +G  
Sbjct: 100 -------------EVALWPTAQSTAFRAEAMTLAVVHEDAHLLVIDKPAGLVVHPAAG-- 144

Query: 127 YHIDGFL----KSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            H  G L     +   +    PR  + HRLD++TSG+++VA++  A   L  +   R ++
Sbjct: 145 -HWSGTLLNGLLAHHAAAAHLPRAGIVHRLDKDTSGLMLVAKSLQAHTALVRAIAARDVK 203

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK----QNEKGANYAISHFKVIDC- 235
           + Y +LV G   +  + I       + +G D V  V+     + K A   +    V +  
Sbjct: 204 REYLALVHGAVMDGLQVI------DAPLGRDPVSRVRMAIVASGKPARTDVRRLAVAELP 257

Query: 236 ------------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
                         ++   +  Q HTGRTHQ+RVH    G P++ D    A + G     
Sbjct: 258 GDGVRQLPGATRAPRQVSAVHCQLHTGRTHQIRVHLASRGHPLLAD----AMYGGAPAFG 313

Query: 284 IQNKLYLHARYMDLPHPEGGR 304
           +Q +  LHA  + L HP  GR
Sbjct: 314 LQRQ-ALHAARLHLLHPIDGR 333


>gi|56419100|ref|YP_146418.1| ribosomal large subunit pseudouridine synthase [Geobacillus
           kaustophilus HTA426]
 gi|56378942|dbj|BAD74850.1| ribosomal large subunit pseudouridine synthase [Geobacillus
           kaustophilus HTA426]
          Length = 299

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/206 (32%), Positives = 101/206 (49%), Gaps = 22/206 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQ----GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +L+ED  + V NK AGI +     G +G +A  +  +L+S   +   K R  HRLD++TS
Sbjct: 86  ILWEDDHLLVLNKEAGIDIHPSEPGQTGTLANAVAFYLQS--QAILTKVRHIHRLDRDTS 143

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++ A+   A   L      R I++ Y +LV G    K   I       + IG D  H 
Sbjct: 144 GAILFAKHPLAGATLDRMLAHRAIKRTYVALVHGRLSPKSGTIF------APIGRDRHHP 197

Query: 216 VKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            ++   K    A++H++VI  F      +E+   TGRTHQ+RVH  H+G P+VGD  Y  
Sbjct: 198 TRRRVSKTGAKAVTHYRVIKTFPSTSL-VELSLETGRTHQIRVHLAHLGHPLVGDVLYGG 256

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
                   P+ ++  LHA  +   HP
Sbjct: 257 K-------PVFHRHALHAAKLTFRHP 275


>gi|308805484|ref|XP_003080054.1| ribosomal large subunit pseudouridine syn (ISS) [Ostreococcus
           tauri]
 gi|116058513|emb|CAL53702.1| ribosomal large subunit pseudouridine syn (ISS) [Ostreococcus
           tauri]
          Length = 422

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 59/185 (31%), Positives = 88/185 (47%), Gaps = 25/185 (13%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D+   +P + HRLD+ TSG++VVA+  +A   L   F  R +++ Y +++ G+PK  K  
Sbjct: 221 DAGSIRPGIVHRLDRGTSGVMVVAKDASAHNSLCNQFASRTVRRRYVAILSGVPKTSKGR 280

Query: 198 IANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQ 254
           I      ++ +G D    ++         YA S+++VI   A     L E +  TGRTHQ
Sbjct: 281 I------EAPVGRDPKDRLRMAVTPGSGRYAASNYEVIATLASGNASLVEWRLETGRTHQ 334

Query: 255 LRVHALHMGCPIVGDHKYCANF---------KGNFTSPIQNKL-------YLHARYMDLP 298
           +RVHA H+G PI+GD  Y             +G F       L        LHAR +   
Sbjct: 335 IRVHAKHIGHPILGDEVYGGGGGAAVDALARRGVFDLKAAKALLSRIDRPMLHARTLGFT 394

Query: 299 HPEGG 303
           HP  G
Sbjct: 395 HPRTG 399


>gi|219119374|ref|XP_002180449.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217407922|gb|EEC47857.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 216

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/227 (29%), Positives = 101/227 (44%), Gaps = 44/227 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----------------KSWVDSKGQKP 144
           ++Y D  + + +KP G++VQGG          L                 S +DS   KP
Sbjct: 1   VIYSDLYLAIIDKPQGMAVQGGENQTLGRSDLLLPLALKPGTKVPWPTQNSILDSALTKP 60

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLL 203
           R+ HRLD  T GILV+A+TR A   L + F  R  +K Y +L++G +PK +    A+   
Sbjct: 61  RVCHRLDAGTGGILVLAKTRVAEVKLKQCFADRACRKRYRALLYGKLPKQEGTIEASLSG 120

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWL---EMQPHTGRTHQLRVHA 259
           K +                     +H+ V+    +  F WL   +++P TGR HQLR H 
Sbjct: 121 KPAE--------------------THYSVLRYVRSLDFGWLTLIDLRPVTGRKHQLRRHM 160

Query: 260 LHMGCPIVGDHKYCANFK---GNFTSPIQNKLYLHARYMDLPHPEGG 303
             MG  I GD +Y    +      +    ++L L A  + LPHP  G
Sbjct: 161 QGMGHAIYGDQRYGPKLEPRPNEGSEDPHSRLCLWAMEIALPHPSTG 207


>gi|160943193|ref|ZP_02090429.1| hypothetical protein FAEPRAM212_00679 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445432|gb|EDP22435.1| hypothetical protein FAEPRAM212_00679 [Faecalibacterium prausnitzii
           M21/2]
          Length = 329

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 75/304 (24%), Positives = 141/304 (46%), Gaps = 21/304 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q+    ND+  +RL R+ ++         L K  R+ +V+V+ K+     R+Q+G ++ +
Sbjct: 3   QFTATANDD-GVRLSRFVQSVTRDFPTSLLYKSFRNKRVKVNGKKAAPEYRLQAGDLIEL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIA 126
              IN      +  K +  +    K  +  K  ++YED  + V  KP  +      +G A
Sbjct: 62  --YINDEFFPPEGAKPVQKAAP-KKQPNQPKVTVIYEDENLAVLYKPTHLLCHSDRTGDA 118

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +D F + ++  KG+         KP + +RLD+ T G+++ A+  AA + + E  R  
Sbjct: 119 NLVDAFTQ-YLTQKGEYDPHGENRFKPGICNRLDRGTEGLVIAAKNYAALRDMNEIIRTD 177

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y+++  GIP++ +     W           +H  +  ++     I+   V+   A
Sbjct: 178 LLKKEYYTITVGIPQSGR--FTAWWEHDEKNNKVSIHAHQSQDERRKQIITDVDVLRT-A 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR--YM 295
             F   ++   TGRTHQ+R H  ++G P++GD KY  N K N  +  + +     R  ++
Sbjct: 235 GPFALCKIGLVTGRTHQIRAHLAYLGKPVLGDIKY-GNRKMNERTGTKTQALCAVRISFL 293

Query: 296 DLPH 299
           D+P 
Sbjct: 294 DVPE 297


>gi|269964797|ref|ZP_06179034.1| Ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
 gi|269830457|gb|EEZ84679.1| Ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
          Length = 225

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/204 (34%), Positives = 103/204 (50%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V NKP+G+    G  I       L++ + D +G  P + HRLD  TSGILV
Sbjct: 24  IIYQDDAMVVVNKPSGLLSVPGKTIKDSAYTRLQAMFPDVEG--PFVIHRLDMATSGILV 81

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A T+ A + L + F  R +QK Y +L+ G+  N+ E   +  ++          V  ++
Sbjct: 82  FALTKRANKSLQKQFMARGVQKRYMALLEGV-LNEPEGEISLPMRGDPDDRPRQLVCFEH 140

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHKYCANF 276
            K A       +V D  ++ +    M P TGRTHQLRVH A HMG   P+VGD  Y    
Sbjct: 141 GKHAETYWQLIEVKDGRSKVY----MYPKTGRTHQLRVHSAHHMGLNMPMVGDGLYGEK- 195

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                    N+L+LHA  ++L HP
Sbjct: 196 --------SNRLHLHAEMLELDHP 211


>gi|222153833|ref|YP_002563010.1| RNA pseudouridylate synthase [Streptococcus uberis 0140J]
 gi|222114646|emb|CAR43689.1| RNA pseudouridylate synthase [Streptococcus uberis 0140J]
          Length = 294

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 59/199 (29%), Positives = 91/199 (45%), Gaps = 14/199 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + V NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 90  LYQDEHLIVVNKPEGMKSHANQPDELALLNHVSAYV---GKTCYIIHRLDKETSGTILFA 146

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       +      R I + YW+ V G  K KK  I   + +  H     V  +KQ +K
Sbjct: 147 KNPFILPIMNRMLENRDISRTYWAFVSGTIKEKKLTIQKPIGRHRHDRRKRVVDMKQGQK 206

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+  K +   +  F  +E    TGRTHQ+RVH   +G P+ GD  Y  +      
Sbjct: 207 ----AITIVKKLKNDSSSFTLVECHLKTGRTHQIRVHMDAIGHPLKGDPLYAPHLP---- 258

Query: 282 SPIQNKLYLHARYMDLPHP 300
                +L LHA+ ++  HP
Sbjct: 259 ---YERLMLHAQQLEFTHP 274


>gi|260174510|ref|ZP_05760922.1| RNA pseudouridylate synthase [Bacteroides sp. D2]
          Length = 306

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/226 (29%), Positives = 115/226 (50%), Gaps = 20/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 91  IVYEDAYIIVVEKMQGLLSVNTERQKERTAYTI---LNEYVQRSGRQFRVFIVHRLDRDT 147

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+     + L +++      + Y ++V G  +   + + +WL  K+     YV 
Sbjct: 148 SGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTL----YVS 203

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             + ++ G+  +I+H+K I   A  +  LE+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 204 SSEYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRKNQIRVHMQDLGHPIIGDGRYG- 260

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
             + +  +PI  +L LHA  +   HP  G L +   P PA   K +
Sbjct: 261 --REDAPNPI-GRLALHAFKLCFYHPVTGDLMEFETPYPAEFKKLF 303


>gi|209809356|ref|YP_002264894.1| putative RNA pseudouridylate synthase [Aliivibrio salmonicida
           LFI1238]
 gi|208010918|emb|CAQ81323.1| putative RNA pseudouridylate synthase [Aliivibrio salmonicida
           LFI1238]
          Length = 561

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 113/236 (47%), Gaps = 25/236 (10%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           L H+++  ++ D+S+  T    + K + ++YED  I + NKPA      G  I   +   
Sbjct: 334 LEHMLEGIELDDNSLKQT--PSYGKDLEIVYEDEAIVIVNKPAEFLSVPGKFITDSVQTR 391

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +K+    +   P + HRLD  TSG+LV+  T    + + + F  R ++K Y +L+ G   
Sbjct: 392 IKARY-PQATGPLIVHRLDMSTSGLLVLTLTAETNKQVQKQFIDRTVEKRYTALLEG--- 447

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                  N  +    + GD     +Q  + K    A + F+VI+    +   + + P TG
Sbjct: 448 ---NIALNDGIIDLPLTGDLEDRPRQMVDHKQGRKAETTFQVIERNNNQ-TKVYLYPKTG 503

Query: 251 RTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RTHQLRVH  H   +G PIVGD  Y   FK        N+L+LHA Y+   HP  G
Sbjct: 504 RTHQLRVHCAHQAGLGTPIVGDDLY--GFKS-------NRLHLHAGYLKFTHPITG 550


>gi|325689674|gb|EGD31678.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK115]
          Length = 295

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 114/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++   +G   Q+  +  RLD++TSG+
Sbjct: 78  VIYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIGQGYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+  P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKVIERFGDVYL-VDIHLHTGRTHQIRVHFSHISFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLEHGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|326438031|gb|EGD83601.1| hypothetical protein PTSG_04209 [Salpingoeca sp. ATCC 50818]
          Length = 293

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/234 (29%), Positives = 108/234 (46%), Gaps = 39/234 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS---GIAYHIDGFLKSWVDSKGQK------------PR 145
           +L+ED  +   NK   + VQGG+    IA  +  +L   +  KG              P 
Sbjct: 17  VLFEDRHVLCINKWPQLVVQGGTNEPSIARALP-YLAQELPPKGSSGRKLVGPNHDFAPS 75

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD++T+G+ V+A+   AA+ L   F   ++ K Y ++  G P  +K  +   +   
Sbjct: 76  IVHRLDKDTTGVTVIAKHAGAARILNNLFAEHQVDKRYLAMTLGAPYPEKGRLDFPIGTN 135

Query: 206 SHIGGD--YVHVVKQNEKGANY----AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH- 258
              G        +  +E+ A      A ++++VID        ++++PHTGR HQLRVH 
Sbjct: 136 KDTGATACITPTMSADERSALTNVVDAATNYRVIDNIDHHIALVDLKPHTGRKHQLRVHC 195

Query: 259 --ALHMGCPIVGDHKYCANFKG----NFTSPIQNK--------LYLHARYMDLP 298
             ALH  CPIVGD+KY             +P + K        L+LHA  + +P
Sbjct: 196 AQALH--CPIVGDNKYGPGVTPWLSLAMRTPSKTKRKELWSPPLFLHAARITIP 247


>gi|313609638|gb|EFR85147.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes FSL F2-208]
          Length = 296

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 74/313 (23%), Positives = 144/313 (46%), Gaps = 40/313 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           VE +E  + L  + K+ +     +   K    G++ V+ +       ++ G  VR+  P 
Sbjct: 7   VETEENGLLLRTFLKSKHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKVGDKVRLTFPT 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 ++ E   LD               +++ED  + + NKPAG++        YH  
Sbjct: 67  EQQNERLLAEYTDLD---------------IVFEDDFLLIINKPAGMASIPSQ---YHPS 108

Query: 131 GFLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + ++V    +   LT+      RLD+ETSG++++A+ R A   L+   +   +++ Y 
Sbjct: 109 GSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQ 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWL 243
           +   G+   ++  I      ++ IG   V ++++       YA ++++V++ +   F  +
Sbjct: 169 AFTSGVLAAQEGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLERYT-AFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TTLLKRQALHSCHLHLVHPVTE 275

Query: 304 R-LQITAPLPAHM 315
             +    PLPA M
Sbjct: 276 EYMAFDLPLPADM 288


>gi|294786018|ref|ZP_06751305.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_27]
 gi|294486355|gb|EFG33718.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_27]
          Length = 316

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 81/302 (26%), Positives = 139/302 (46%), Gaps = 46/302 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           V ++ E MRLD++            L+K++ +  V+++ K +  N R ++ G+ + I   
Sbjct: 12  VSSEYEGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKLKLGEKIEIS-- 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                 I +E+ I   + N++         ++YE+    V NK  G+ V    G      
Sbjct: 70  ------IPEEENIDIEAENISLD-------IVYENDDFIVINKSYGMVVHPAYGNYSGTL 116

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + Y+ +    S ++    +P + HRLD++TSG+++VA+   A   L   F  + I K
Sbjct: 117 VNALLYYTNNL--SSING-NIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFTDKTIHK 173

Query: 182 IYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            Y  +V G    +N    I N L+ +       + VVK+N K    AIS++KVI+     
Sbjct: 174 TYLCIVKGNFSEENLNGRIEN-LIGRGSKDRKKMAVVKENGKT---AISNYKVIEQ-VDG 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------FKGNFTSPIQNKL 288
           +  +E+   TGRTHQ+RVH   +   I+GD  Y              +K  F +P+ NK 
Sbjct: 229 YSLVEIAIETGRTHQIRVHMKSINHVILGDSTYGNEDKNVKRQMLHAYKLEFLNPLDNKE 288

Query: 289 YL 290
           Y+
Sbjct: 289 YI 290


>gi|227484931|ref|ZP_03915247.1| possible RluA protein [Anaerococcus lactolyticus ATCC 51172]
 gi|227237086|gb|EEI87101.1| possible RluA protein [Anaerococcus lactolyticus ATCC 51172]
          Length = 328

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/273 (26%), Positives = 128/273 (46%), Gaps = 27/273 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  ++ N R DR+ + ++ +     + K +R    +++ KR K N+ +  G ++++  
Sbjct: 4   IVISKNQANQRFDRFLRKYFENAPLSVISKNIRKKNFKINDKRAKNNDFVNEGDIIKM-- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-- 127
                 +I  E      +    K  DF   I+ YED  I + +K  G      S   Y  
Sbjct: 62  ------YITDENYKKWLTKTDFKPVDFDLDII-YEDDNILIMDKKCGELTHAASNKDYGN 114

Query: 128 HIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           ++   + S++   G         KP + +RLD+ T+G+++ A+     + L ++ R   I
Sbjct: 115 NLVDKMNSYLYKTGSFDMSDRTFKPAVVNRLDRNTAGLIIGAKNSETLRILNDAIRENSI 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y ++V G  KN      N+ +       +  + VK+ E+G N  +++FK ++    K
Sbjct: 175 DKYYLTIVVGKVKN------NFKIDTYISKNENKNKVKKCEEGKN-ILTYFKPLETNG-K 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           F  LE +  TGRTHQ+R      G PI+GD KY
Sbjct: 227 FSLLECKLITGRTHQIRYSLKENGTPIIGDRKY 259


>gi|169335579|ref|ZP_02862772.1| hypothetical protein ANASTE_01994 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258317|gb|EDS72283.1| hypothetical protein ANASTE_01994 [Anaerofustis stercorihominis DSM
           17244]
          Length = 307

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 87/328 (26%), Positives = 153/328 (46%), Gaps = 39/328 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG--QVVRI 67
           +++  +  +MRLDR+  +    ++   +QK+LR       KK +K N + Q G  +  ++
Sbjct: 4   IIITEEFMDMRLDRFI-SKVTTLSKGEIQKLLR-------KKYIKVNGKKQEGSYRTEKL 55

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             V   L+  + +Q  L S +N    +      ++YED  I + +KP+GI  Q       
Sbjct: 56  DKVQFFLSDEVFKQDNLHSKLNTNNLN------IIYEDKNIILIDKPSGILSQADGSSKE 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            I   L S+++SK     +  RLD  TSGI++  + R A   L E  + + I K Y +LV
Sbjct: 110 DIVSNLISYLNSKS--TGIVTRLDLNTSGIVLAGKNRRALMLLNEMSKNKLIDKRYLTLV 167

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQ 246
            G   +++  + ++ +K +        ++  N+K   ++ +S   +I    +    LE++
Sbjct: 168 RG-DFDREGKVTHYGIKDNKEN----KLILGNKKVDGSFEVSAEFIIKKRYKYHTLLEVR 222

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY-----CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TG+THQ+R     MG P+VGD KY     C N K +F     N+ +LH   + L + E
Sbjct: 223 LITGKTHQIRSQLDKMGFPVVGDRKYNKSKQCGN-KDDFKI---NRQFLHCYKLTLKYSE 278

Query: 302 GGRLQIT------APLPAHMVKTWDSLG 323
             +  +T      + LP  +      LG
Sbjct: 279 KYKEIVTEDKTFYSDLPKDLKNVLKELG 306


>gi|59711171|ref|YP_203947.1| 23S rRNA pseudouridine synthase D [Vibrio fischeri ES114]
 gi|59479272|gb|AAW85059.1| 23S rRNA pseudouridine synthase [Vibrio fischeri ES114]
          Length = 324

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 120/239 (50%), Gaps = 29/239 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  + V NKP    V  G+G     DG + + +     +  + PR  + HRLD++T
Sbjct: 86  IVYEDDDLLVINKPRDFVVHPGAGTP---DGTVLNALLFHYPNIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG--GDY 212
           +G++VVA+T  A   L  + + R+I + Y ++V G         A  +++K  IG   + 
Sbjct: 143 TGLMVVAKTVPAQTRLVRALQKRKITREYEAVVVG------RMTAGGMIEKP-IGRHPNK 195

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             ++  +E G + A++H++V + F +    + ++  TGRTHQ+RVH  ++  P+VGD  Y
Sbjct: 196 RTLMAVHELGKD-AVTHYRVAEHF-RIHTRIRLRLETGRTHQIRVHMSYLQHPLVGDTAY 253

Query: 273 CANF---KGNFTSPIQ-----NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                  KG     I      ++  LHA  +   HP  G  ++  AP+P  M+    +L
Sbjct: 254 GGRARIPKGASQELIDMIRGFDRQALHAAMLRFEHPITGETMEFHAPIPDDMIALSQAL 312


>gi|332307383|ref|YP_004435234.1| pseudouridine synthase Rlu family protein, TIGR01621 [Glaciecola
           agarilytica 4H-3-7+YE-5]
 gi|332174712|gb|AEE23966.1| pseudouridine synthase Rlu family protein, TIGR01621 [Glaciecola
           agarilytica 4H-3-7+YE-5]
          Length = 236

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/224 (30%), Positives = 106/224 (47%), Gaps = 31/224 (13%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQ---GGSGIAYHI---DGFLKSWVDSKGQKPRL 146
           +S F    ++++     + +KP G+SVQ     SGI   +     F K W         L
Sbjct: 3   NSAFPPISVVFDHPDFIIIDKPPGVSVQNEASSSGILPMVCTQHAFDKLW---------L 53

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ TSG+L++A+   AA  L + F  R I+K Y +L    PK K+  +   + K  
Sbjct: 54  VHRLDKVTSGLLILAKHAQAASQLGKLFEAREIEKYYLALGSAKPKKKQGTVTGAMKKIR 113

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              G +      N+ G+  A+S F      A    +L ++P TG+THQLRV    +G PI
Sbjct: 114 D--GKWAF----NQNGSAVAVSQFFSKSVSAGIRLYL-LKPLTGKTHQLRVMLKSLGSPI 166

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           +GD  Y A          Q++ YLHA  +   + +G  +Q+  P
Sbjct: 167 LGDELYKAQ--------AQDRTYLHAYCLRFTY-QGQLVQLVCP 201


>gi|226324582|ref|ZP_03800100.1| hypothetical protein COPCOM_02366 [Coprococcus comes ATCC 27758]
 gi|225207030|gb|EEG89384.1| hypothetical protein COPCOM_02366 [Coprococcus comes ATCC 27758]
          Length = 302

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 109/229 (47%), Gaps = 18/229 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLTHRL 150
           SD   SI+ YED  + V NKPAG+ +    G   +      +W   +  +P   R  +RL
Sbjct: 85  SDLPLSIV-YEDPDLLVINKPAGMPIHPSQGNYDNTLANACAWYFKEKGEPFVYRCINRL 143

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++T+G+L++AR   +A  L+     R I + Y +L  GI        A    K+   G 
Sbjct: 144 DRDTTGLLIIARHLYSASLLSAMMARREIHREYLALATGIVPEDGIITAPIARKE---GS 200

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +V  + K   YA +H++ I        +  + ++  TGRTHQ+RVH  ++G P+ G
Sbjct: 201 TIERMV--DFKHGEYACTHYRRISITNTDPVYSLVALKLDTGRTHQIRVHMNYIGHPLPG 258

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           D  Y  ++         ++  LH+ ++   HP  G  +  TAP+P  M+
Sbjct: 259 DFLYNPDYSH------ISRQALHSHHLRFRHPITGEEMHFTAPVPEDML 301


>gi|32033504|ref|ZP_00133831.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
 gi|126208338|ref|YP_001053563.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae L20]
 gi|126097130|gb|ABN73958.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
          Length = 247

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 117/244 (47%), Gaps = 24/244 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPIHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A+ ++E F   +++K Y ++V G   +K E   ++ LK   +  D +       
Sbjct: 65  ALNSEMARLMSEQFEQHQLKKGYLAVVRGYLLDKGEI--DYPLK---VILDKIADKFSQP 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KEAQQAVTFYQNLASVEMLYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPIMGDT 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
           KY  +   N T   +   ++L LH+ ++   HP+   +++I APL     K W +L   +
Sbjct: 180 KY-GDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLD----KQWQNLFATF 234

Query: 327 DRNL 330
           + N 
Sbjct: 235 NWNF 238


>gi|138894383|ref|YP_001124836.1| ribosomal large subunit pseudouridine synthase D-like protein
           [Geobacillus thermodenitrificans NG80-2]
 gi|134265896|gb|ABO66091.1| ribosomal large subunit pseudouridine synthase D-like protein
           [Geobacillus thermodenitrificans NG80-2]
          Length = 299

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 123/232 (53%), Gaps = 30/232 (12%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + V NKPAG++        GG+   G+ +H   + +  +DS      +  RLD
Sbjct: 84  IVYEDEYVLVVNKPAGLATIPSRHHPGGTLANGLLHH---YRQQQLDSTVH---IITRLD 137

Query: 152 QETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           ++TSG+++VA+ R    HL  + + + ++ + Y ++  G+   ++  I   + +++    
Sbjct: 138 RDTSGLVLVAKHRHV-HHLLSTLQQKGQVTRTYEAVCHGVIDEEEGTIDAPISRQN---- 192

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D + + ++  +    AI+HF+V++  +  + ++ ++  TGRTHQ+RVH  ++G P+ GD 
Sbjct: 193 DSI-IAREVREDGKRAITHFRVLERLS-GYTYVSLRLETGRTHQIRVHLAYLGHPLAGDE 250

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDS 321
            Y  + +      +  +  LH+R +   HP   +L   TAPLP  M +  ++
Sbjct: 251 LYGGSRE------MIGRQALHSRQLSFFHPFARQLYTFTAPLPDDMARLIEA 296


>gi|225572906|ref|ZP_03781661.1| hypothetical protein RUMHYD_01097 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039719|gb|EEG49965.1| hypothetical protein RUMHYD_01097 [Blautia hydrogenotrophica DSM
           10507]
          Length = 221

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 91/181 (50%), Gaps = 7/181 (3%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP----RLTHRLD 151
            L+ +++YED  + V +KPAG++VQ        ++  LK+ +  +  +      + HRLD
Sbjct: 1   MLREVIVYEDEDLIVCHKPAGMAVQSAGIGRMDLESALKNELAMRNPEKLPYVAVIHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q   G++V A+   AA  L+       ++K Y ++        KE + +WL +      +
Sbjct: 61  QPVEGLVVFAKNPKAASGLSSQSARGEMKKCYLAVAQDAKVPDKERLEDWLRRDGR--KN 118

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y  VV +N  G+  A+  ++++     K   L +Q  TGR HQ+RV   H G P++GD K
Sbjct: 119 YSMVVPKNTSGSKRAVLEYRLLKRQNGKM-LLHIQLLTGRHHQIRVQMAHRGMPLLGDRK 177

Query: 272 Y 272
           Y
Sbjct: 178 Y 178


>gi|197335573|ref|YP_002155322.1| ribosomal large subunit pseudouridine synthase D [Vibrio fischeri
           MJ11]
 gi|197317063|gb|ACH66510.1| ribosomal large subunit pseudouridine synthase D [Vibrio fischeri
           MJ11]
          Length = 324

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 120/239 (50%), Gaps = 29/239 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  + V NKP    V  G+G     DG + + +     +  + PR  + HRLD++T
Sbjct: 86  IVYEDDDLLVINKPRDFVVHPGAGTP---DGTVLNALLFHYPNIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG--GDY 212
           +G++VVA+T  A   L  + + R+I + Y ++V G         A  +++K  IG   + 
Sbjct: 143 TGLMVVAKTVPAQTRLVRALQKRKITREYEAVVVG------RMTAGGMIEKP-IGRHPNK 195

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             ++  +E G + A++H++V + F +    + ++  TGRTHQ+RVH  ++  P+VGD  Y
Sbjct: 196 RTLMAVHELGKD-AVTHYRVAEHF-RIHTRIRLRLETGRTHQIRVHMSYLQHPLVGDTAY 253

Query: 273 CANF---KGNFTSPIQ-----NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                  KG     I      ++  LHA  +   HP  G  ++  AP+P  M+    +L
Sbjct: 254 GGRARIPKGASQELIDMIRGFDRQALHAAMLRFEHPITGETMEFHAPIPDDMIALSQAL 312


>gi|195953891|ref|YP_002122181.1| pseudouridine synthase, RluA family [Hydrogenobaculum sp. Y04AAS1]
 gi|195933503|gb|ACG58203.1| pseudouridine synthase, RluA family [Hydrogenobaculum sp. Y04AAS1]
          Length = 308

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 77/297 (25%), Positives = 144/297 (48%), Gaps = 35/297 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVR--IPPVINALNH 76
           R+D    N Y  I+   +++I++   V ++ ++V K + ++    V+   IPP    L+ 
Sbjct: 14  RIDVLISNIYKDISREYIKRIIKENGVLINGEKVFKSSKKVFENDVLEFEIPPP-KKLD- 71

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLK 134
            +K Q I         H D     +LYED+ + V  KP+G+    G G   +  ++  L 
Sbjct: 72  -VKAQDI---------HID-----ILYEDNDLAVVVKPSGMPSHTGPGHDENTLVNALLA 116

Query: 135 SWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            + D       ++P + HRLD+ T G++V+A+   + Q L+  F+ + + K Y ++V+GI
Sbjct: 117 KFGDLSVIGGVERPGIVHRLDRYTHGLMVIAKNDVSHQKLSLMFKNKEVDKHYKAIVYGI 176

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            + K++ I  ++ +      + +     NE     AI+ +  ++   +    L+++ +TG
Sbjct: 177 SRFKEQTIETFIRRHP---TNRLKFEVANE--GKLAITKYS-LEKPLKNASLLDIKIYTG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           RTHQ+RVH  ++G PIVGD  Y    + F       I  +  L A  +   HP+  +
Sbjct: 231 RTHQIRVHMSYIGHPIVGDTLYGYKHSYFDKTLEHMIGKRFLLVAYKLSFLHPKSQK 287


>gi|20808199|ref|NP_623370.1| pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter
           tengcongensis MB4]
 gi|20516793|gb|AAM24974.1| Pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter
           tengcongensis MB4]
          Length = 268

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 77/291 (26%), Positives = 142/291 (48%), Gaps = 52/291 (17%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G++RV+ ++      ++ G V+              E  + D+S ++      L   + Y
Sbjct: 18  GEMRVNGEKENVKRVLKEGDVI--------------ELSLFDTSSDILPQEMDLS--ICY 61

Query: 104 EDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQ 152
           ED +I + +KPAG+ V            +G+AY        + + KG K   R  +RLD+
Sbjct: 62  EDDEILIVDKPAGMVVHPTRRYREGTLANGVAY--------YFEKKGIKTLIRPVNRLDK 113

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++ A+      +L     ++ + K Y+++V G  K + E I +  +K+      +
Sbjct: 114 GTSGIVIFAKEPFMQYYLQ---IVKPMSKFYYAIVNG--KLEGEGIIDVPIKRK----SF 164

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + + ++  +  + AI+++K +    ++F  L+++  TGRTHQ+RVH  ++G PIVGD  Y
Sbjct: 165 MTIEREVSEEGDRAITYYKSLKA-TEEFSLLKIKIATGRTHQIRVHLNYIGHPIVGDDLY 223

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                G  TS I+    LHA  +   HP   + + + APLP  + + ++ L
Sbjct: 224 -----GEPTSYIERPA-LHAYRVTFFHPLKEKVISVYAPLPEDIKRLFELL 268


>gi|326407645|gb|ADZ64716.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis CV56]
          Length = 288

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 64/214 (29%), Positives = 102/214 (47%), Gaps = 26/214 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  + V NKP G+   G +     +   + + ++   Q+  + HRLDQ TSG ++ 
Sbjct: 83  ILYEDEHLIVVNKPEGMKAHGNTADELALQNHVAAAIN---QEVFVVHRLDQATSGAVLF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+ +     L + F   +I + Y +LV G  P+N+   I   + +  H     +   K  
Sbjct: 140 AKNQFVLPILGKMFEGNKIHREYLALVKGHFPENQF-TIDRAIGQNRHDKNKRILSAK-- 196

Query: 220 EKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                 A++H ++I  F  K    C L+    TGRTHQ+RVH   +  PI+GD  Y    
Sbjct: 197 ---GQKAVTHVEIIKKFTDKTLVKCTLD----TGRTHQIRVHLSSLNHPIIGDALYG--- 246

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
                   Q ++ LHA  + +PHP E   L+I+A
Sbjct: 247 -----QKTQERMMLHADKIIIPHPFENKILEISA 275


>gi|260775124|ref|ZP_05884022.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260608825|gb|EEX34987.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 325

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 81/328 (24%), Positives = 145/328 (44%), Gaps = 41/328 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V++ +   RLD+     +   +   L++ L  G+V+V+            G+V+  P  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLVDGKVQVN------------GEVITKPRT 57

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                 II  Q  L+           L   ++YED  I V NKP    V  G+G      
Sbjct: 58  KVMGGEIITLQAELEDEERWEAQDIPLD--IVYEDDDIMVINKPRDFVVHPGAGTPDGTV 115

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           ++  L  + D   + PR  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 116 LNALLHHYPDI-AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAI 174

Query: 187 VWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             G        ++ I     K++ +    +            A++H++V + F ++   +
Sbjct: 175 AIGRMTAGGRVEQPIGRHSTKRTLMAVSPM---------GKPAVTHYRVAEHF-REHTRI 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQ------NKLYLHARYM 295
            ++  TGRTHQ+RVH  ++  P++GD  Y   A      +  +       ++  LHA  +
Sbjct: 225 RLRLETGRTHQIRVHMSYLQHPLLGDSAYGGRARIPSGASEELAEMIRKFDRQALHAVML 284

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSL 322
              HP  G  L+  AP+P  MV+  ++L
Sbjct: 285 KFDHPVTGEELEFHAPVPDDMVEMAEAL 312


>gi|307610038|emb|CBW99572.1| ribosomal large subunit pseudouridine synthase D [Legionella
           pneumophila 130b]
          Length = 321

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 84/323 (26%), Positives = 144/323 (44%), Gaps = 42/323 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q + V  +  N R+DR      P  +   +   +++G V ++    K  ++   G ++  
Sbjct: 7   QQLSVPRELHNQRVDRVIARLLPEYSRSLISNWIKTGAVTLNNLPCKPKDKALGGDLI-- 64

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              IN       +  ++++  N  K  +    I+ YEDS++ V NKPAG+ V  G+G   
Sbjct: 65  --TINV------DHTMVNTDFNFCKPENIPIQII-YEDSEVIVVNKPAGLVVHPGAGNKE 115

Query: 128 H--IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           H  ++  L    + +   PR  + HRLD++T+G+L+VA+   +   L    + R I++ Y
Sbjct: 116 HTLVNALLHHCPELQ-LLPRAGIIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVIDCFAQ 238
            +LV G           +++    I   +    K   K A       A++H+  I+   +
Sbjct: 175 LTLVHG-----------YVISGGTIDTGFGRHPKNRLKMAVTDFGRQAVTHYN-INKHYK 222

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKL------YL 290
            F  L +   TGRTHQ+RVH  ++  P+VGD  Y     F  N    I + L       L
Sbjct: 223 DFTLLNVSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKFPPNADEAILSVLKQFKRQAL 282

Query: 291 HARYMDLPHP-EGGRLQITAPLP 312
           HA  +   HP +   + + A LP
Sbjct: 283 HACSISFCHPVKNTEITLNALLP 305


>gi|217963594|ref|YP_002349272.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes HCC23]
 gi|217332864|gb|ACK38658.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes HCC23]
 gi|307571830|emb|CAR85009.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes L99]
          Length = 289

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/217 (30%), Positives = 102/217 (47%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP  +        +Y  D     ++ +++  GQ       HRLDQ TS
Sbjct: 80  IIYEDDFLLVVNKPVDMKTHAND--SYETDTCANAVQYYLEKTGQDANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H KV++   +K   L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHVKVLENDNEKNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 253 -------SPRANRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|198274965|ref|ZP_03207497.1| hypothetical protein BACPLE_01124 [Bacteroides plebeius DSM 17135]
 gi|198272412|gb|EDY96681.1| hypothetical protein BACPLE_01124 [Bacteroides plebeius DSM 17135]
          Length = 308

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/218 (29%), Positives = 106/218 (48%), Gaps = 18/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +LYED+ + V  K  G+ SV             L  +V    +  R+   HRLD+ETSGI
Sbjct: 95  ILYEDAYLIVVEKKEGLLSVATDHQKERTAQHILNEYVKRTHRNNRIFVVHRLDRETSGI 154

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-KKSHIGGDYVHVV 216
           ++ A+       L +++      + Y S+V G  +  +  + +WL  +K ++    V   
Sbjct: 155 MMYAKDEKTQHTLRDNWHDIVYDRRYVSIVMGDMEKDQGTVRSWLTDRKLYVSSSPV--- 211

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              + G   +I+H++ I   A  +  +E+Q  TGR +Q+RVH   +G P+VGD +Y    
Sbjct: 212 ---DDGGKLSITHYRTIKR-ANGYSLMELQLETGRKNQIRVHMQSLGHPVVGDARY---- 263

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
            G  T P+  +L LHA  +   HP  G R++   P PA
Sbjct: 264 -GCETDPL-GRLALHAFKLCFYHPLTGERMEFETPYPA 299


>gi|324992609|gb|EGC24530.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK405]
 gi|327460012|gb|EGF06351.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1]
 gi|327472158|gb|EGF17595.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK408]
 gi|327488602|gb|EGF20402.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1058]
          Length = 291

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 92/201 (45%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      R I + YW+LV G      +  A  L+ K  IG D     K+  +
Sbjct: 141 KNPFVLPILNRLLEKREISREYWALVQG------KFPAKNLIYKDKIGRDRHDRRKRLVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   YA +H   +  F Q    ++ Q  TGRTHQ+RVH  H G P+VGD  Y    +G 
Sbjct: 195 PRKGLYAETHVTRLKQFGQS-ALVKCQLKTGRTHQIRVHLAHHGHPLVGDPLYHPQPQG- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 253 -------RLMLHAHRLTFTHP 266


>gi|308812997|ref|XP_003083805.1| Pseudouridine synthase, RluD (ISS) [Ostreococcus tauri]
 gi|116055687|emb|CAL57772.1| Pseudouridine synthase, RluD (ISS) [Ostreococcus tauri]
          Length = 383

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/221 (31%), Positives = 100/221 (45%), Gaps = 28/221 (12%)

Query: 101 LLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQE 153
           + YED+ + V NK AG   + +   G        +  W    G +     P + HRLD +
Sbjct: 144 IAYEDATMTVVNKRAGTPSTPRRRVGDDSAASACVARWRTVDGVQGASLVPYVAHRLDLD 203

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW------LLKK-- 205
           TSG LV+ RT A A+ +   F  RR++K YW+L      +  +    W      L+K+  
Sbjct: 204 TSGALVICRTSARAKEVQGWFENRRVEKTYWALCEAR-GDASDDSGEWHTIEFPLVKRAR 262

Query: 206 --SHIGGDYVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +  G  +V  V   E     A  A + F+++   A     +E +P TGRTHQ+R H  
Sbjct: 263 DDAEPGTFFVEAVLTPEDAPEDAKPATTLFRIVSKSAAHVL-VEARPKTGRTHQIRTHLA 321

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             G PIVGD  Y A       S I ++  LHAR +  P  E
Sbjct: 322 AAGLPIVGDTIYGA------PSDIIDRHALHARTLTFPSDE 356


>gi|325663710|ref|ZP_08152114.1| hypothetical protein HMPREF0490_02855 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325470203|gb|EGC73436.1| hypothetical protein HMPREF0490_02855 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 227

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 63/211 (29%), Positives = 102/211 (48%), Gaps = 16/211 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW----VDSKGQKPRL--THRL 150
           ++S +LYED  + V  KPAG+ VQ        +   LK++       KG+ P L   HRL
Sbjct: 3   IQSYILYEDRDLIVCRKPAGVPVQTKQIQTKDMVSLLKNYRYQQEGGKGE-PYLGVIHRL 61

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           DQ   GI+V A+T  AA+ L    +     K Y +++  +P+  +  + ++L+K      
Sbjct: 62  DQPVEGIIVFAKTPQAAKELNRQLQAGDFGKYYQAVLCKVPEKAQGQLTDYLVKDGRT-- 119

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +   + ++++ GA  A   +K I   A+      +   TGR HQ+RV    MGCPI+GD 
Sbjct: 120 NLSKICRKSDAGAKEARLSYK-IQGEAEGKALANIHLDTGRHHQIRVQMSGMGCPILGDV 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           KY    K       + ++ L A  +   HP+
Sbjct: 179 KYGGEEKE------RGQIALCASSLTFVHPK 203


>gi|324325409|gb|ADY20669.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar finitimus YBT-020]
          Length = 307

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/228 (30%), Positives = 112/228 (49%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEKYFRKQNVTLVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y    K        ++  LHA  ++  HP     +++  P P  +
Sbjct: 254 DVLYGGGTK------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKL 295


>gi|298368341|ref|ZP_06979659.1| ribosomal large subunit pseudouridine synthase D [Neisseria sp.
           oral taxon 014 str. F0314]
 gi|298282344|gb|EFI23831.1| ribosomal large subunit pseudouridine synthase D [Neisseria sp.
           oral taxon 014 str. F0314]
          Length = 373

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 139/320 (43%), Gaps = 39/320 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D   +RLD       P  +   L   ++   V V+ K  +   ++  G+ + +  
Sbjct: 30  LTVPLDMAGLRLDSALAKLMPDYSRSRLATWIKEDLVIVNGKPARPKEKLIGGEFITV-- 87

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  +L    + +   ++YED  + V NK AG+ V   +G     
Sbjct: 88  ------------TVRSSEESLAFLPEKMDLDIVYEDDTVIVVNKSAGLVVHPAAGNWSGT 135

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++G L +     GQ PR  + HRLD+ETSG++VVA+T  A   L    + R +++IY +
Sbjct: 136 LLNGLL-AHCPELGQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRA 194

Query: 186 LVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCW 242
           +  GI P + K         ++ IG D  + +K    + G   AI+H KV++ +     +
Sbjct: 195 VANGIVPFDGK--------IETLIGRDPHNRLKMAVVKYGGKPAITHVKVLERYPA-HSY 245

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMD 296
           +E    TGRTHQ+RVH      P+  D  Y      C+         +  +  LHA  + 
Sbjct: 246 IECSLETGRTHQIRVHMREANHPLAADPIYGNPRHPCSEMVKEAVKAL-GRQALHAYRLS 304

Query: 297 LPHPEGGR-LQITAPLPAHM 315
             HP+  + +   A +P  M
Sbjct: 305 FLHPKTQKAVSFEAAIPEDM 324


>gi|50955140|ref|YP_062428.1| ribosomal large subunit pseudouridine synthase [Leifsonia xyli
           subsp. xyli str. CTCB07]
 gi|50951622|gb|AAT89323.1| ribosomal large subunit pseudouridine synthase [Leifsonia xyli
           subsp. xyli str. CTCB07]
          Length = 306

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 79/292 (27%), Positives = 129/292 (44%), Gaps = 30/292 (10%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           ++  SG V VD +    ++R+ +G        ++      +E +I+   V+        +
Sbjct: 34  EVAESGGVTVDGREAGKSDRLPAGSW------LDVTWQPREEPRIVPIVVS--------E 79

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSG-------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
             +++ED  I V +KPAG++     G        A    GF  S      ++  + HRLD
Sbjct: 80  LTIVHEDDDIVVLDKPAGVAAHPSIGWEGPTVLGALAAAGFRIS-TSGAPERAGIVHRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG++VVA++  A   L  +F  R ++KIY ++V G P      I   + +  H   D
Sbjct: 139 AGTSGLMVVAKSEHAYTVLKRAFHDRTVEKIYHAVVQGHPDPLTGTIDAPIGR--HPKSD 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +   V     G   +++H++ I+ F      LE+   TGRTHQ+RVH      P VGD  
Sbjct: 197 WRFAVV---AGGKPSVTHYETIEAFPAA-SLLEIHLETGRTHQIRVHMSAQRHPCVGDAM 252

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           Y A+   +    +  + +LHA  +   HP  G  +  T   PA      D L
Sbjct: 253 YGADPTLSARLGLTRQ-WLHAVQLAFAHPATGEWVTFTTAYPADFRNALDIL 303


>gi|313827835|gb|EFS65549.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL063PA2]
 gi|315108225|gb|EFT80201.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL030PA2]
          Length = 306

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 111/229 (48%), Gaps = 18/229 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-----GSGIAYHID--GFLKSWVDSKGQKPRLTHRLDQE 153
           ++++DS I V +KPAG++        G  +  H+   GF  S      ++  +  RLD  
Sbjct: 82  IIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS-TSGAPERQGIVQRLDVG 140

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA++  A   L ++FR R + K+Y +LV G P      I       + IG D+ 
Sbjct: 141 TSGLMVVAKSEHAYILLKQAFRDRTVDKVYLALVQGHPDPFTGTI------DAPIGRDHR 194

Query: 214 HVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           H  K     G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P  GD  Y
Sbjct: 195 HDWKMAIVDGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLY 253

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 254 GCDPALAKELGLERQ-WLHAGELSFTHPGSGEWVTFHADLPADLQNALD 301


>gi|295105227|emb|CBL02771.1| Pseudouridylate synthases, 23S RNA-specific [Faecalibacterium
           prausnitzii SL3/3]
          Length = 329

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 75/304 (24%), Positives = 141/304 (46%), Gaps = 21/304 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q+    ND+  +RL R+ ++         L K  R+ +V+V+ K+     R+Q+G ++ +
Sbjct: 3   QFTATANDD-GVRLSRFVQSVTRDFPTSLLYKSFRNKRVKVNGKKAAPEYRLQAGDLIEL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIA 126
              IN      +  K +  +    K  +  K  ++YED  + V  KP  +      +G A
Sbjct: 62  --YINDEFFPPEGAKPVQKAAP-KKQPNQPKVTVIYEDENLAVLYKPTHLLCHSDRTGDA 118

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +D F + ++  KG+         KP + +RLD+ T G+++ A+  AA + + E  R  
Sbjct: 119 NLVDAFTQ-YLTQKGEYDPHGENRFKPGICNRLDRGTEGLVIAAKNYAALRDMNEIIRTD 177

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y+++  GIP++ +     W           +H  +  ++     I+   V+   A
Sbjct: 178 LLKKEYYTITVGIPQSGR--FTAWWEHDEKNNKVNIHAHQSQDERRKQIITDVDVLRT-A 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR--YM 295
             F   ++   TGRTHQ+R H  ++G P++GD KY  N K N  +  + +     R  ++
Sbjct: 235 GPFALCKIGLVTGRTHQIRAHLAYLGKPVLGDIKY-GNRKMNERTGTKTQALCAVRISFL 293

Query: 296 DLPH 299
           D+P 
Sbjct: 294 DVPE 297


>gi|228990395|ref|ZP_04150360.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
 gi|228996496|ref|ZP_04156135.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|229004147|ref|ZP_04161948.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228757008|gb|EEM06252.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228763128|gb|EEM12036.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|228768921|gb|EEM17519.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
          Length = 307

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 111/228 (48%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED  + + NKPA +    S +GG+G     +A+H+       +     K R  HRLD
Sbjct: 87  VIFEDDHVLIVNKPAHMDTHPSSKGGTGTLANLVAFHLQ------MQGVETKVRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+   A   +      R I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHGIAGAIMDRLLMERNIKRTYLALVEGKVKKKQGII------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + A++H++V   F  Q    + +Q  TG+THQ+RVH  H G P++G
Sbjct: 195 RHHATRRRVSLKG-DQAVTHYRVEKYFKHQDVTLVTLQLETGKTHQIRVHMSHSGHPLIG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y         S   +   LHA  +   HP     + +  PLP+++
Sbjct: 254 DTLYGGQ------STYMSSQALHAMRIAFLHPITKEEITVEVPLPSYL 295


>gi|289805198|ref|ZP_06535827.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 191

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 56/159 (35%), Positives = 82/159 (51%), Gaps = 14/159 (8%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+    
Sbjct: 33  HRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI---- 88

Query: 208 IGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              D+ +  KQ    E G   A + + V++  A     + ++P TGR+HQLRVH L +G 
Sbjct: 89  --CDWPNRPKQKVCYETG-KPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGH 145

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           PI+GD  Y +    +       +L LHA  + + HP  G
Sbjct: 146 PILGDQFYASPEALSLAP----RLQLHAEMLTITHPAYG 180


>gi|119477573|ref|ZP_01617723.1| putative 23S rRNA pseudouridylate 746 synthase [marine gamma
           proteobacterium HTCC2143]
 gi|119449076|gb|EAW30316.1| putative 23S rRNA pseudouridylate 746 synthase [marine gamma
           proteobacterium HTCC2143]
          Length = 223

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 98/211 (46%), Gaps = 22/211 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+D    + NKP G+    G        + Y +     +          L HRLD  T
Sbjct: 20  VIYQDDSFLLINKPTGLLSLSGKHPRNKDSVHYRLVQDFPTAT--------LVHRLDFGT 71

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI++VA ++    +LT  F+ R ++K Y +L++G   +    I   + K      D   
Sbjct: 72  SGIMLVALSKEVNGNLTRQFQARSVKKTYKALLYGEMADNSGVIDFPIAKDK----DNFP 127

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + K   +    A++ ++VI+  A     +E  P +GRTHQLR+H+  +G PI+G    C 
Sbjct: 128 LQKICYRDGKEAVTRYRVIEKIAGNCTKVEFTPSSGRTHQLRIHSREIGHPILG----CD 183

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            +  +    +  +L LHA  ++  HP  G +
Sbjct: 184 LYGSDEAFVMAERLMLHATTLEFFHPATGEI 214


>gi|332360478|gb|EGJ38289.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK355]
          Length = 295

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 114/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++      + Q+  +  RLD++TSG+
Sbjct: 78  VIYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKVIERFGDVYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLEHGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|302389469|ref|YP_003825290.1| pseudouridine synthase, RluA family [Thermosediminibacter oceani
           DSM 16646]
 gi|302200097|gb|ADL07667.1| pseudouridine synthase, RluA family [Thermosediminibacter oceani
           DSM 16646]
          Length = 291

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 76/246 (30%), Positives = 122/246 (49%), Gaps = 31/246 (12%)

Query: 88  VNLTKHSDFLKSI----LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS----WVDS 139
           V+LT+ S  + S     +LYED  I V NK  G+ V      A+H +  + +    +++ 
Sbjct: 58  VDLTEKSGIVPSPVPINILYEDDHIIVLNKQPGVVVHP---TAFHYNDTIANGVIYYLNQ 114

Query: 140 KGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKE 196
           KG+K      +RLD++T+G+L++A     +QH+    +   R++K Y ++V G+ K  + 
Sbjct: 115 KGKKGGFHPVNRLDRDTTGVLIIA----LSQHMHNLIQTHGRMKKRYIAVVEGVVKENEG 170

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   + ++    G  +     +EKG   AI+ FKV+    +    L+++P TGRTHQ+R
Sbjct: 171 VIVEPIARRE---GSLIERC-VSEKGQK-AITRFKVVKRL-KDLTVLDIEPVTGRTHQIR 224

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           VH    G P+ GD  Y     G     I+ +  LH   M   +P  G  L   APLP  M
Sbjct: 225 VHLSFKGHPVAGDTLY-----GGKNDRIKRQA-LHCAEMTFFYPVTGTYLSFKAPLPEDM 278

Query: 316 VKTWDS 321
           V   +S
Sbjct: 279 VNLINS 284


>gi|294649803|ref|ZP_06727205.1| ribosomal large subunit pseudouridine synthase A [Acinetobacter
           haemolyticus ATCC 19194]
 gi|292824286|gb|EFF83087.1| ribosomal large subunit pseudouridine synthase A [Acinetobacter
           haemolyticus ATCC 19194]
          Length = 228

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 103/225 (45%), Gaps = 19/225 (8%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L++ D    V +KPAG+    G      +   L + +     K  L HRLD++
Sbjct: 16  SDFLSEHLIHRDEDFMVIHKPAGLLTVPGK--TPDLQDCLINRLLKLEPKTLLIHRLDRD 73

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     ++  F+ R+  KIY +LV G  + +       +   S      V
Sbjct: 74  TSGILVFGLSKFGQSTISRQFQDRQTSKIYQALVAGHLEGQGTVDIPVIYDPSRPPLHIV 133

Query: 214 HVVKQNEKGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                      + AI H ++     Q    +++ P TGR+HQLRVH  ++G PI+GD  Y
Sbjct: 134 DATHHKPALTEWQAIEHLEIQ---GQAVTRVKLIPITGRSHQLRVHMQYLGHPILGDTLY 190

Query: 273 CANFKGNFTSPIQNKLY----LHARYMDLPHPE-GGRLQITAPLP 312
                    +P Q +LY    LHA  +   HP+ G +L    P+P
Sbjct: 191 A--------TPEQQQLYERLCLHATQLSFAHPKTGTQLDFDCPVP 227


>gi|307245726|ref|ZP_07527812.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307254697|ref|ZP_07536525.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307256915|ref|ZP_07538693.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|307259139|ref|ZP_07540869.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306853428|gb|EFM85647.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306862370|gb|EFM94336.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306864649|gb|EFM96554.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306866806|gb|EFM98664.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 244

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 118/246 (47%), Gaps = 24/246 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPVHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A+ ++E F   +++K Y ++V G   +K E   ++ LK   +  D +       
Sbjct: 65  ALNSKMARLMSEQFEQHQLEKGYLAVVRGYLLDKGEI--DYPLK---VILDKIADKFSQP 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KEAQQAVTFYQNLASVEMPYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPIMGDT 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
           KY  +   N T   +   ++L LH+ ++   HP+   +++I APL     + W ++   +
Sbjct: 180 KY-GDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLD----EQWQNVFLTF 234

Query: 327 DRNLYI 332
           + N  I
Sbjct: 235 NWNFPI 240


>gi|281420178|ref|ZP_06251177.1| ribosomal large subunit pseudouridine synthase D [Prevotella copri
           DSM 18205]
 gi|281405673|gb|EFB36353.1| ribosomal large subunit pseudouridine synthase D [Prevotella copri
           DSM 18205]
          Length = 315

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 61/223 (27%), Positives = 104/223 (46%), Gaps = 16/223 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLD 151
           S +LK  ++YED  + V  K  GI          ++   L  +     Q  +  + HRLD
Sbjct: 96  SRYLK--IVYEDRYLIVVEKNIGILSMAAGHSTLNVKTVLDDYFHKTRQNCQAHVVHRLD 153

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+ +     L + +      + Y +LV G  ++ +  +ANWL         
Sbjct: 154 RDTSGLMIYAKDKQTELALEDDWHHNVYDRRYVALVSGEMEDDEGTVANWLKDNK----A 209

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y+      + G  YA++++  ++        +E +  TGR +Q+RVH   MG P+ GD K
Sbjct: 210 YITYSSDTDNGGKYAVTYYHTLE-RTTAHSLVEFKLETGRKNQIRVHTADMGHPVCGDIK 268

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           Y     GN   P Q +L LHA  +   HP   + ++   P+PA
Sbjct: 269 Y-----GNGDDPCQ-RLCLHAYVLCFYHPVTHQPMEFETPIPA 305


>gi|213155501|ref|YP_002317546.1| dual specificity pseudouridine synthase [Acinetobacter baumannii
           AB0057]
 gi|213054661|gb|ACJ39563.1| dual specificity pseudouridine synthase [Acinetobacter baumannii
           AB0057]
          Length = 229

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/204 (33%), Positives = 98/204 (48%), Gaps = 18/204 (8%)

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ A+ 
Sbjct: 29  EDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMFAKH 86

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHVVKQN 219
           R A   +++ F+ R ++K Y +LV G  K +       I +W  +   I    VH   + 
Sbjct: 87  RDAEVAVSKMFQARTVKKHYIALVQGQVKQEGRVEVPLITDWENRPRQI----VHF--EL 140

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K A          +   Q    LE  P TGR+HQLRVH +H+G PI+GD  Y    K  
Sbjct: 141 GKHAKTLFQPLVYDETTDQSRVLLE--PVTGRSHQLRVHMMHIGHPIMGDKLYHPEPKRF 198

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG 303
                 N++ LHA Y+   HP  G
Sbjct: 199 HL----NRMALHAAYLAFQHPLKG 218


>gi|162454823|ref|YP_001617190.1| hypothetical protein sce6541 [Sorangium cellulosum 'So ce 56']
 gi|161165405|emb|CAN96710.1| hypothetical protein sce6541 [Sorangium cellulosum 'So ce 56']
          Length = 666

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 101/235 (42%), Gaps = 43/235 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF---LKSWVDSKGQKPR---LTHRLDQET 154
           +L ED  + V +KPAG+S       A  ID     L++++  +G       +  RLD++T
Sbjct: 19  ILAEDGDLIVVDKPAGLSTHAPE--AERIDDMVTRLRAFLRGRGDAEAYLGIHQRLDRDT 76

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI----------------PKNKKECI 198
           SG+L+  R R A   +   F  R +QK Y + V G                 P      +
Sbjct: 77  SGVLLFTRRREANAAVARQFEGRTVQKTYVAAVSGFGDRPPRGTLRHRLVPAPGGAMRAL 136

Query: 199 AN--------WLLKKSHIGGDYVHVVKQNEKGAN--YAISHFKVIDCFAQKFCWLEMQPH 248
           A            ++    G      K+ ++ A+   AI+ +++++    +   LE++P 
Sbjct: 137 AESGGAREDRAAKREDRAAGREDRAAKREDRAASGVLAITRYRLLERRGDR-ALLELRPE 195

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           TGRTHQLRV    +G PI GD  Y          P   +L LHA  + L HP  G
Sbjct: 196 TGRTHQLRVQLAAIGLPIAGDPLYG--------GPEAPRLLLHAAELRLDHPATG 242


>gi|297530964|ref|YP_003672239.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|297254216|gb|ADI27662.1| pseudouridine synthase, RluA family [Geobacillus sp. C56-T3]
          Length = 304

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/258 (25%), Positives = 128/258 (49%), Gaps = 33/258 (12%)

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKS-----ILLYEDSKIYVFNKPAGISV------QG 121
            + H+++  + L       + SD++ +      +LYED  + V NKPAG++        G
Sbjct: 51  TVRHVLRAGETLSVVFPPERTSDWMDAEAMPLDILYEDDYVLVVNKPAGLATIPSRHHPG 110

Query: 122 GS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G+   G+ +H   + K  +DS      +  RLD++TSG+++VA+ R     L+   +   
Sbjct: 111 GTLANGLLHH---YRKQQLDSTVH---IVTRLDRDTSGLVLVAKHRHVHHLLSALQQKGH 164

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + + Y ++  G+    +  I   + ++S    D + + ++  +    A++HF+V++    
Sbjct: 165 VVRTYEAICHGVIVEDEGTIDAPIGRQS----DSI-IAREVREDGKPAVTHFRVLERL-Y 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            + ++ ++  TGRTHQ+RVH  ++G P+ GD  Y  + +      +  +  LH+R +   
Sbjct: 219 GYTYVSLRLETGRTHQIRVHLAYLGHPLAGDELYGGSRE------MIGRQALHSRQLSFF 272

Query: 299 HPEGGR-LQITAPLPAHM 315
           HP  GR    +APLP  M
Sbjct: 273 HPFAGRWYTCSAPLPDDM 290


>gi|110004584|emb|CAK98921.1| probable pseudouridine synthase d protein [Spiroplasma citri]
          Length = 306

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 87/305 (28%), Positives = 145/305 (47%), Gaps = 43/305 (14%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L  +FK +    +   +Q++++  +V+V+            GQVVR   V    +H+I E
Sbjct: 18  LTDYFKTNTTPFSRTKIQELIKQEKVQVN------------GQVVRANYVSQIGDHVIIE 65

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS----- 135
                +S  LT  +  L   +LYEDS + V +KP  + V    G  +  D  + +     
Sbjct: 66  FPSAKAS-ELTPLAIPLT--ILYEDSYLMVIDKPNNLVVHPAPG--HQNDTLVNALLARG 120

Query: 136 --WVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             W  + G Q+P + HR+D++T+G L++A+       L +  + +++Q+ Y +LV G   
Sbjct: 121 VQWSTASGEQRPGIVHRIDRQTTGTLIIAKNDVVHHQLQQQIQTKQLQRRYLALVHG--- 177

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              + I N     + IG D  +  K     K +  A+++  VI+ F   + ++E +  +G
Sbjct: 178 ---QIIENRAKIDAPIGRDPNNRKKMVVTAKNSKKALTNIVVIERF-NDYTYIECELESG 233

Query: 251 RTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
           RTHQ+R H  ++  PIVGD  Y   A+ K +F        YLHA  +   HP     L I
Sbjct: 234 RTHQIRAHLKYINHPIVGDPLYGTVADKKESFGQ------YLHAYQLRFIHPVTKESLTI 287

Query: 308 TAPLP 312
           TA LP
Sbjct: 288 TAALP 292


>gi|90417173|ref|ZP_01225100.1| Pseudouridine synthase, RluD [marine gamma proteobacterium
           HTCC2207]
 gi|90330949|gb|EAS46210.1| Pseudouridine synthase, RluD [marine gamma proteobacterium
           HTCC2207]
          Length = 324

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 81/304 (26%), Positives = 132/304 (43%), Gaps = 51/304 (16%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +   +   LQ  ++SG++ VD ++     ++  G+ + +   + A      
Sbjct: 29  RLDQIAAELFSDYSRSRLQLWIKSGELTVDGQQQPPKFKLLGGETIAVSAQLKAEGDWQA 88

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHID 130
           E   L+               +++ED  I V NKP    V   +G         + +H  
Sbjct: 89  EDIPLN---------------IVFEDEHIIVINKPTNFVVHPAAGNREGTLLNALLFHCP 133

Query: 131 GFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             LKS        PR  + HRLD++T+G++VVA+T AA   L    + R + + Y S+V 
Sbjct: 134 Q-LKSV-------PRAGIVHRLDKDTTGLMVVAKTLAAHTDLVAQLQARTVSREYESVVS 185

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQP 247
           G+       +    L    IG      VK    +    A +H+KV+  F     ++ ++ 
Sbjct: 186 GV-------MTGGGLVDQPIGRHPKQRVKMAVVRDGKEARTHYKVVKRF-DGHTYIRLKL 237

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL------YLHARYMDLPH 299
            TGRTHQ+RVH   +  PIVGD  Y   F+     +  +++ L       LHAR + L H
Sbjct: 238 ETGRTHQIRVHMASIKYPIVGDDTYGGRFRIHKGVSDQLRDSLQYFGRQALHARALGLVH 297

Query: 300 PEGG 303
           P  G
Sbjct: 298 PASG 301


>gi|203284710|ref|YP_002222450.1| RNA pseudouridylate synthase family protein [Borrelia duttonii Ly]
 gi|203284715|ref|YP_002222455.1| RNA pseudouridylate synthase family protein [Borrelia duttonii Ly]
 gi|201084153|gb|ACH93744.1| RNA pseudouridylate synthase family protein [Borrelia duttonii Ly]
 gi|201084158|gb|ACH93749.1| RNA pseudouridylate synthase family protein [Borrelia duttonii Ly]
          Length = 324

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 85/335 (25%), Positives = 146/335 (43%), Gaps = 51/335 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-----LRSGQVRVDKKRVKFNNRI-QSGQVV 65
           V N+++  RLD         I F+ L K      +R+G +R++  +V F+ R+ +  ++ 
Sbjct: 17  VLNNDDGKRLDVVL------IKFLKLPKSKVIKHIRNGDIRLNNLKVSFSQRVLKDDKIY 70

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGG 122
              P++  LN          + V +   +D L+ +   L+YED  + V NK  G+ V G 
Sbjct: 71  LYKPLVQGLNL---------NGVVIKNKTDILRDVESRLVYEDKDLLVINKRKGVLVHGD 121

Query: 123 SGIAYHIDGFLKSWV-----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               Y +D  + +++      S   KP   HRLD+ TSG++V A+   +A+ L+++F   
Sbjct: 122 ---GYSLDVLVNAYLLDENLASLSFKPSAVHRLDRNTSGLIVFAKNIYSARILSKAFSSG 178

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--- 234
            + K Y +L+ G  + K     N+L +   +   +V          N  I+ F  I    
Sbjct: 179 IVTKRYLALLDGEIR-KSLTYKNFLYRDKIVKKTFVM------DNLNSNINKFNAITIVK 231

Query: 235 -CFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                KF  L E+   TG THQ+R         ++ D KY   FK       +N  +LH+
Sbjct: 232 PLLVSKFATLAEVSIKTGFTHQIRAQCAFNNHALIDDKKYNPKFK-------KNNYFLHS 284

Query: 293 RYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
             ++  H    R +      +  VK  +S+   YD
Sbjct: 285 FLINFNHSFFLRNEFFVEPSSDFVKRINSIFGVYD 319


>gi|228984465|ref|ZP_04144642.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
 gi|228775168|gb|EEM23557.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
          Length = 307

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 114/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +    S +GG G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPSEKGGMGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEKYFKNQNVTLVMLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y    +        ++  LHA  ++  HP     +++  P P  +  T
Sbjct: 254 DVLYGGQTR------YMSRQALHAMKINFLHPITKEEIEVDVPFPTKLNDT 298


>gi|203288242|ref|YP_002223257.1| RNA pseudouridylate synthase family protein [Borrelia recurrentis
           A1]
 gi|201085462|gb|ACH95036.1| RNA pseudouridylate synthase family protein [Borrelia recurrentis
           A1]
          Length = 324

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 85/335 (25%), Positives = 146/335 (43%), Gaps = 51/335 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-----LRSGQVRVDKKRVKFNNRI-QSGQVV 65
           V N+++  RLD         I F+ L K      +R+G +R++  +V F+ R+ +  ++ 
Sbjct: 17  VLNNDDGKRLDVVL------IKFLKLPKSKVIKHIRNGDIRLNSLKVSFSQRVLKDDKIY 70

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGG 122
              P++  LN          + V +   +D L+ +   L+YED  + V NK  G+ V G 
Sbjct: 71  LYKPLVQGLNL---------NGVVIKNKTDILRDVESRLVYEDKDLLVINKRKGVLVHGD 121

Query: 123 SGIAYHIDGFLKSWV-----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               Y +D  + +++      S   KP   HRLD+ TSG++V A+   +A+ L+++F   
Sbjct: 122 ---GYSLDVLVNAYLLDENLASLSFKPSAVHRLDRNTSGLIVFAKNIYSARILSKAFSSG 178

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--- 234
            + K Y +L+ G  + K     N+L +   +   +V          N  I+ F  I    
Sbjct: 179 IVTKRYLALLDGEIR-KSLTYKNFLYRDKIVKKTFVM------DNLNSNINKFNAITIVK 231

Query: 235 -CFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                KF  L E+   TG THQ+R         ++ D KY   FK       +N  +LH+
Sbjct: 232 PLLVSKFATLAEVSIKTGFTHQIRAQCAFNNHALIDDKKYNPKFK-------KNNYFLHS 284

Query: 293 RYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
             ++  H    R +      +  VK  +S+   YD
Sbjct: 285 FLINFNHSFFLRNEFFVEPSSDFVKRINSIFGVYD 319


>gi|115375226|ref|ZP_01462492.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|310818943|ref|YP_003951301.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115367788|gb|EAU66757.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|309392015|gb|ADO69474.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 345

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 84/330 (25%), Positives = 141/330 (42%), Gaps = 46/330 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VVE +    RLDR+       ++   +Q+I++ G V   ++R+K +  +  G    I   
Sbjct: 28  VVEPNYAGWRLDRYLGEKIRRLSRPRIQRIIQRGLV--CERRLKPSTLVFPGLTFSIRRS 85

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           ++       E  I+                  Y+D  + V +KPAG+ +      A +  
Sbjct: 86  LSTEPETPTELPIV------------------YQDDWLLVLDKPAGLPIHP---TARYQK 124

Query: 131 GFLKSWVDSK-GQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           G L S +  + G++     HRLD+ETSG++V  RT  A + L   F  R + K Y ++  
Sbjct: 125 GTLVSLLRERFGERFAEPAHRLDRETSGLVVCGRTTEACRVLGRLFLSRDVHKEYLAVCE 184

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ---KFCWLEM 245
           G P      +   + + + +    V + +   K +    + F+V+  F +    F  L  
Sbjct: 185 GHPPEDTFFVDAPIAEGTELIRIAVRIDRAEGKESR---TRFQVLQRFVRDGAPFALLRC 241

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQ------NKLYLHAR 293
            P TGR HQ+R+H    G P+VGD  Y  +      F  +   P         +  LHA 
Sbjct: 242 YPETGRQHQIRIHLHEAGFPLVGDKMYGPDPGYFDRFSKHCLEPEAWERLRLPRHALHAG 301

Query: 294 YMDLPHPEGGRLQIT--APLPAHMVKTWDS 321
           ++  PHP G R  ++  +PLP  +V   D 
Sbjct: 302 HIAFPHP-GTRQAVSFDSPLPGDLVDFMDG 330


>gi|188996912|ref|YP_001931163.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188931979|gb|ACD66609.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 270

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 61/215 (28%), Positives = 99/215 (46%), Gaps = 28/215 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  I   +KP  I     S  A   +  L+  +  K  K +  HRLD+ETSG+L+ 
Sbjct: 70  ILYEDDYIIAIDKPPTIVSDKESSSA---EDILRKKL--KNDKIKAIHRLDKETSGVLLF 124

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+     +   E +  + + KIY ++                   SH   ++       +
Sbjct: 125 AKDYKIFEKFKEIWEDKNVLKIYLAI-------------------SHNEANFKDFTINQD 165

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGN 279
                AI+H KV++     F + +++  TGR HQ+R H   +  PIVGD  Y    F+ N
Sbjct: 166 IDGKQAITHLKVLNK-GNGFTYFQVRIETGRKHQIRKHLASIRHPIVGDKIYSIKKFENN 224

Query: 280 FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPA 313
               +  ++ LH+  + L HP    +++ITAPLP+
Sbjct: 225 LVKRVTRQM-LHSYKLVLTHPYLNKKIEITAPLPS 258


>gi|54297242|ref|YP_123611.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Legionella pneumophila
           str. Paris]
 gi|53751027|emb|CAH12438.1| Ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Legionella pneumophila
           str. Paris]
          Length = 321

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 85/323 (26%), Positives = 144/323 (44%), Gaps = 42/323 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q + V  +  N R+D       P  +   +   +++G V ++    K  ++   G ++  
Sbjct: 7   QQLSVPRELHNQRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCKPKDKALGGDLI-- 64

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              IN       +  I+++  NL K  +    I+ YEDS++ V NKPAG+ V  G+G   
Sbjct: 65  --TINV------DHTIVNTDFNLCKPENIPIQII-YEDSEVIVVNKPAGLVVHPGAGNKE 115

Query: 128 H--IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           H  ++  L    + +   PR  + HRLD++T+G+L+VA+   +   L    + R I++ Y
Sbjct: 116 HTLVNALLHHCPELQ-LLPRAGIIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVIDCFAQ 238
            +LV G           +++    I   +    K   K A       A++H+  I+   +
Sbjct: 175 LTLVHG-----------YVISGGTIDTGFGRHPKNRLKMAVTDFGRQAVTHYN-INKHYK 222

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKL------YL 290
            F  L +   TGRTHQ+RVH  ++  P+VGD  Y     F  N    I + L       L
Sbjct: 223 DFTLLNVSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKFPPNADEAILSVLKQFKRQAL 282

Query: 291 HARYMDLPHP-EGGRLQITAPLP 312
           HA  +   HP +   + + A LP
Sbjct: 283 HACSISFCHPVKNTEITLNALLP 305


>gi|262193432|ref|YP_003264641.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262076779|gb|ACY12748.1| pseudouridine synthase, RluA family [Haliangium ochraceum DSM
           14365]
          Length = 304

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 113/224 (50%), Gaps = 22/224 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           + YED+ + V +KP  +S       + G+ +    + + K   D+      + HR+D+ T
Sbjct: 72  IAYEDAHVVVIDKPVDVSSVPYERRETGTAMDLLREAWRKLRPDAGRTPLHVVHRIDKAT 131

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L  A+T+ A   L   FR   +++ Y  +  G  + ++  I + L++     GD + 
Sbjct: 132 SGLLAFAKTKRAELGLAAQFRQHTLERAYLCVAHGAVRAQR--IESRLVRDR---GDGLR 186

Query: 215 VVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD--HK 271
              +       A++H +V++  A+   C + ++  TG+THQ+R+H    G P+VG+  +K
Sbjct: 187 GSTRAPNQGKRAVTHVEVLEELARASLCQVRLE--TGKTHQIRIHLAERGHPLVGERVYK 244

Query: 272 YCANFKGN--FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             A F+G+    +P   +L LHA  +   HP  G R+ + +PLP
Sbjct: 245 RDAEFRGHTLIDAP---RLMLHAATLGFAHPITGERVFVESPLP 285


>gi|229043131|ref|ZP_04190856.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|228726190|gb|EEL77422.1| Pseudouridine synthase [Bacillus cereus AH676]
          Length = 307

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 111/228 (48%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGSIMDRLLMERKIKRTYAALVEGKVKKKQGKI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTLVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y    K        +   LHA  +   HP     +++  P P  +
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKIHFLHPITKEAIEVDVPFPTKL 295


>gi|198275973|ref|ZP_03208504.1| hypothetical protein BACPLE_02156 [Bacteroides plebeius DSM 17135]
 gi|198271602|gb|EDY95872.1| hypothetical protein BACPLE_02156 [Bacteroides plebeius DSM 17135]
          Length = 539

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/209 (33%), Positives = 103/209 (49%), Gaps = 24/209 (11%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW--VDSKGQKPRLTHRLDQETSGI 157
           +LYED  + V +KPAG +SV G + +    D  L+    +  K   P + HRLD  TSG+
Sbjct: 338 ILYEDEWLLVVHKPAGMLSVPGKNDL----DSILQRLHNLYPKATGPLIVHRLDMATSGL 393

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A+T+   + L   F  R IQK Y +L+ G      E I +  +  + +  D    + 
Sbjct: 394 LLAAKTKEVHKELQALFETRLIQKRYTALLEG-ELETDEGIIDLPICPNPM--DRPRQMV 450

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCA 274
             E G   A++ ++V++        +   PHTGRTHQLRVHA H   +  PIVGD  Y  
Sbjct: 451 SREYGKR-AVTSYRVLERKGGS-TRVTFYPHTGRTHQLRVHAAHPEGLNHPIVGDDLYGQ 508

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                      ++LYLHA  ++  HP  G
Sbjct: 509 P---------SDRLYLHAASLEFVHPVTG 528


>gi|71908482|ref|YP_286069.1| tRNA pseudouridine synthase C [Dechloromonas aromatica RCB]
 gi|71848103|gb|AAZ47599.1| tRNA pseudouridine synthase C [Dechloromonas aromatica RCB]
          Length = 242

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 108/238 (45%), Gaps = 19/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + V +KP+G+ V   S I  H   F ++   D  GQ+    HRLD+ TSG+L+
Sbjct: 7   ILYRDEHVVVIDKPSGLLVHR-SEIDRHETRFAIQILRDQIGQRVWPAHRLDRGTSGVLL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
                A A  L + F    ++K YW++V G P      I + L ++      Y    +Q 
Sbjct: 66  FGLNPAMASQLGKQFEQGTVEKAYWAVVRGYPPASG-SIDHPLTRQR---DPYEFKGEQC 121

Query: 220 EKGANYAISHFK---------VIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
              A  A++HF+          +D + + ++  LE++P TGR HQ+R H  H+  PI+GD
Sbjct: 122 STEAQPALTHFRKLAEIELPVEVDRYPSSRYALLELEPITGRRHQIRRHLKHLAHPIIGD 181

Query: 270 HKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
             Y       + +      +L L    +   HP  G RL I  P+      T    G+
Sbjct: 182 ATYGKGRHNRYFAEQLGCHRLLLACIRLSFNHPVTGLRLDIKTPVSGEFAATLARFGW 239


>gi|170018031|ref|YP_001728950.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
 gi|169804888|gb|ACA83506.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
          Length = 306

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/234 (31%), Positives = 107/234 (45%), Gaps = 37/234 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG------IAYHIDGFLKSWVDSKGQ--KPRLTHRLDQ 152
           +++E+  + V NKPAG+ +   S       + +    F K  + S G   KP + HR+D+
Sbjct: 89  IIFENDDLVVVNKPAGMKMHPHSPSETDTLLNFLAANFSKRHLYSAGAIAKPYMVHRIDR 148

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS-----H 207
           ETSG ++VA+       L    + + IQ+ Y + V GI           LLK S      
Sbjct: 149 ETSGAVIVAKNPVVVPILNRMLKEKVIQRTYLAWVQGI-----------LLKNSGTIDRP 197

Query: 208 IGGDYVHVVKQNEKG--ANYAISH-FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           IG D     ++   G  A +A +H FK+   F      L +Q  TGR HQ+RVH   +  
Sbjct: 198 IGRDISKPFQRQVNGVQAQHAKTHWFKIHTVFQNTL--LRLQLDTGRMHQIRVHLASINH 255

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           PIVGD  Y            Q ++ LHA  + LP P +G +  IT  LP+   K
Sbjct: 256 PIVGDSLYGQRLN-------QQRMMLHAMSLTLPLPFDGPKRIITTSLPSDFPK 302


>gi|89055892|ref|YP_511343.1| ribosomal large subunit pseudouridine synthase D [Jannaschia sp.
           CCS1]
 gi|88865441|gb|ABD56318.1| ribosomal large subunit pseudouridine synthase D [Jannaschia sp.
           CCS1]
          Length = 310

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 77/301 (25%), Positives = 124/301 (41%), Gaps = 55/301 (18%)

Query: 32  INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I+   L +++ +G V ++ + V     R+  G  V I     A    + E   LD     
Sbjct: 7   ISRTRLARLIPAGAVAINGRVVTDPKARVAEGDGVEITVEDAAEVETVAEDIPLD----- 61

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKG 141
                     +++ED  + V NKPAG+ V    G         + +H  G L      K 
Sbjct: 62  ----------IVHEDDDLIVVNKPAGMVVHPAPGSPSGTLVNALLHHFGGKLSGVGGEK- 110

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +P + HR+D++TSG+LVVA++  A   L   F    +++ Y +L  G+P      +   
Sbjct: 111 -RPGIVHRIDKDTSGLLVVAKSDRAHHGLAAQFADHSMEREYLALCHGVPDGSDPRLRG- 168

Query: 202 LLKKSHIGGDYVHVVKQNEK-------------GANYAISHFKVIDC---FAQKFCWLEM 245
            +K     G  V +  Q  +             G  +A++  +V++     A   C LE 
Sbjct: 169 -VKGVSFEGSTVKITTQLARHKTDRQRQAVLFSGGRHAVTRVRVLEAHGPVALVSCRLE- 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL------YLHARYMDLPH 299
              TGRTHQ+RVH  H+G  ++GD  Y    K +   P    +       LHA  +   H
Sbjct: 227 ---TGRTHQIRVHMSHVGHALIGDQTYGGRRKISAKLPGAEAVNAFPRQALHAATLGFVH 283

Query: 300 P 300
           P
Sbjct: 284 P 284


>gi|329117142|ref|ZP_08245859.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
 gi|326907547|gb|EGE54461.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
          Length = 300

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 64/206 (31%), Positives = 92/206 (44%), Gaps = 28/206 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           L+ED  I V NKP G+           +  H+  F +       Q   + HRLD ETSG 
Sbjct: 96  LFEDENIIVVNKPEGMKTHANQPEELALLNHVSAFCQ-------QTCYVVHRLDMETSGA 148

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVV 216
           +V A+       L +    R I + YW+LV G IP+         L+ K  IG       
Sbjct: 149 IVFAKNPFILPILNQLLEKREIHRDYWALVGGQIPQKS-------LVYKDKIGRHRHDRR 201

Query: 217 KQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           K+  + K    AI++   +  +      +  Q  TGRTHQ+RVH  + G PI+GD  Y +
Sbjct: 202 KRVVDPKNGQTAITNLTRLKVYPSNRSLVNCQLETGRTHQIRVHLSYHGFPIIGDPLYQS 261

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           +       P + +L LHA  + L HP
Sbjct: 262 H-------PNKERLMLHAHQLQLVHP 280


>gi|218248702|ref|YP_002374073.1| RluA family pseudouridine synthase [Cyanothece sp. PCC 8801]
 gi|218169180|gb|ACK67917.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8801]
          Length = 306

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 71/264 (26%), Positives = 120/264 (45%), Gaps = 29/264 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PP 69
           V   +  + +  ++   YPH +    Q+ + SGQ+ ++ +    +  +Q GQ +    PP
Sbjct: 12  VNPSDAGLTILAYYTQRYPHSSQGQWQERIISGQILLNGQPTTPDTPLQPGQCLSYHRPP 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                    +E  +             L   +LYED  + V  KP+G+ V  G G   H 
Sbjct: 72  --------WQEPDVP------------LAFEVLYEDVDVLVVAKPSGLPVLPGGGFLEHT 111

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           + G LK       + P   HRL + TSG++++AR+  AA HL+   R  ++ K+Y +LV 
Sbjct: 112 LLGQLKRLYPQ--ETPTPIHRLGRGTSGLMLLARSPLAASHLSHQMRQGQMTKVYHALVG 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
                 +  I   + K  H    YV+    +     +A SH +V+    Q    +E++  
Sbjct: 170 AGDLPHQFSIHQPIGKIPHPVLGYVYGATPD---GLFAHSHCRVLQRSTQG-TLVEVRIF 225

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGR HQ+R+H   +G P++GD  Y
Sbjct: 226 TGRPHQIRIHLASVGYPLLGDPLY 249


>gi|148926270|ref|ZP_01809955.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|145845441|gb|EDK22534.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
          Length = 250

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 105/221 (47%), Gaps = 21/221 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +LYED  + V NKP+ + V G S +    +  L  W+  K       G + R  L HRLD
Sbjct: 7   VLYEDEDLLVLNKPSNLVVHGASSVK---NATLVDWLIEKKYTLSNLGGEIRAGLVHRLD 63

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +++A+     Q L+E    + + +IY +L+    K  K  +  +L++       
Sbjct: 64  KDTSGSILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIK 123

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + + K+N+   N   +   V+    +    +  +  TGRTHQ+R H   +   I+GD  
Sbjct: 124 KIAIDKENKFSKNAKSAFINVVKT--ENLTLMAAKLFTGRTHQIRAHLASLNRYILGDSL 181

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
           Y   +KG +   I     LHA ++   HP+   ++ + APL
Sbjct: 182 Y--GYKGKYDCRIM----LHAYFLYFIHPKTKEQIFVKAPL 216


>gi|294790528|ref|ZP_06755686.1| ribosomal large subunit pseudouridine synthase D [Scardovia
           inopinata F0304]
 gi|294458425|gb|EFG26778.1| ribosomal large subunit pseudouridine synthase D [Scardovia
           inopinata F0304]
          Length = 311

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 114/238 (47%), Gaps = 26/238 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           ++YED  + V +KP G++     G     + G LK+    +   G + R  +  RLD  T
Sbjct: 79  IVYEDGDLVVVDKPVGMAAHQSVGWTGSTVLGSLKARGVHITDYGPQGRQGIVSRLDVGT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++V +++ A + +   F    ++K Y++L  G  K  K  +   + + S    D+  
Sbjct: 139 SGLMLVCKSQMAYKEMRRQFSQHEVKKTYYALAQGNLKEDKATVDAPIGRDS--AADFRF 196

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +    K    AI+H+ VI+ F Q   ++ +   TGRTHQ+RVH   +G P+VGD  Y A
Sbjct: 197 TITPAGK---PAITHWDVIERFGQA-TYISVNLETGRTHQIRVHMSSLGHPLVGDSMYGA 252

Query: 275 NFKGNFTSPI------QNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
           N       P+       ++ +LH+  +D  HP     + + + LP  +    ++L  +
Sbjct: 253 N-------PVLAEQLGLSRQWLHSMKLDFRHPRTHCPVHLESTLPTDLATALETLRLR 303


>gi|226307021|ref|YP_002766981.1| pseudouridine synthase RluD [Rhodococcus erythropolis PR4]
 gi|226186138|dbj|BAH34242.1| putative pseudouridine synthase RluD [Rhodococcus erythropolis PR4]
          Length = 308

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 64/210 (30%), Positives = 100/210 (47%), Gaps = 13/210 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY D  +   +KP G++     G     + G L +    + + G   R  + HRLD  T
Sbjct: 84  ILYADDDVVAVDKPVGVAAHASVGWTGPTVIGGLAAAGFRISTSGAHERQGIVHRLDVGT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA +  A   L  +F+ R I K Y +LV G P      I   + +  H G D+  
Sbjct: 144 SGVMVVATSERAYTLLKRAFKQRTIDKRYHALVQGHPDPSSGTIDAPIGR--HHGNDWRF 201

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  + K    +++H+  I+ F Q    L++   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 202 TVTADGK---PSVTHYDTIEAF-QAASLLDVHLETGRTHQIRVHFSALRHPCCGDLTYGA 257

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           + +      ++ + +LHA  +   HP  GR
Sbjct: 258 DPRLAERLGLERQ-WLHAVSLGFAHPADGR 286


>gi|229490347|ref|ZP_04384188.1| pseudouridine synthase, RluA family [Rhodococcus erythropolis
           SK121]
 gi|229322637|gb|EEN88417.1| pseudouridine synthase, RluA family [Rhodococcus erythropolis
           SK121]
          Length = 308

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 64/210 (30%), Positives = 100/210 (47%), Gaps = 13/210 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY D  +   +KP G++     G     + G L +    + + G   R  + HRLD  T
Sbjct: 84  ILYADDDVVAVDKPVGVAAHASVGWTGPTVIGGLAAAGFRISTSGAHERQGIVHRLDVGT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA +  A   L  +F+ R I K Y +LV G P      I   + +  H G D+  
Sbjct: 144 SGVMVVATSERAYTLLKRAFKQRTIDKRYHALVQGHPDPSSGTIDAPIGR--HHGNDWRF 201

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  + K    +++H+  I+ F Q    L++   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 202 TVTADGK---PSVTHYDTIEAF-QAASLLDVHLETGRTHQIRVHFSALRHPCCGDLTYGA 257

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           + +      ++ + +LHA  +   HP  GR
Sbjct: 258 DPRLAERLGLERQ-WLHAVSLGFAHPADGR 286


>gi|116493188|ref|YP_804923.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
 gi|116103338|gb|ABJ68481.1| Pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
          Length = 294

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 56/177 (31%), Positives = 92/177 (51%), Gaps = 13/177 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +++ED    + NKPAG++   G       +   I G  ++ ++SK   P L  RLD+ TS
Sbjct: 80  IIFEDKNWLLVNKPAGLTAVPGPSDREDTLVNRIKGHWQA-IESKNMMPHLVTRLDRFTS 138

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI +VAR + +   L+E     +I+KIY ++V G+ + +K      L     +  D +H 
Sbjct: 139 GITLVARHQVSNSLLSEQVAHHKIKKIYLAMVDGVVQAEKGTFNQSL----GLAADGIH- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++       A + FKV+  F  +   +++   TGRTHQ+RVH  + G P+VGD  Y
Sbjct: 194 -REVRDDGQQATTSFKVLKRFENQ-TLVQIHLKTGRTHQIRVHFANAGHPLVGDQLY 248


>gi|34556846|ref|NP_906661.1| putative ribosomal pseudouridine synthase [Wolinella succinogenes
           DSM 1740]
 gi|34482561|emb|CAE09561.1| PUTATIVE RIBOSOMAL PSEUDOURIDINE SYNTHASE [Wolinella succinogenes]
          Length = 308

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 57/171 (33%), Positives = 91/171 (53%), Gaps = 14/171 (8%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSK----GQKPRLTHRLDQETSGILVVARTRA 165
           +F+KPA + V       ++      S +D      GQ+  L HR+D+ETSGI+++ R++ 
Sbjct: 81  LFDKPADLLVHPKGTFEHY------SLMDEVRLRFGQEADLAHRIDKETSGIVLITRSKK 134

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
               L  +F  R ++K YW+LV G  K + E I ++ LK      D    ++ +EKG + 
Sbjct: 135 EGAILKINFFNREVKKCYWALVRG--KMEGERILDFPLKAQSKRLDLGVRMRVDEKGKS- 191

Query: 226 AISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +++  K +D  A      +E  P TGRTHQ+R+H  H G PI+GD  Y  +
Sbjct: 192 SLTQIKALDYEALSDTTLVEASPLTGRTHQIRLHLAHAGYPILGDPLYGTS 242


>gi|332360854|gb|EGJ38660.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK49]
          Length = 295

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 114/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++      + Q+  +  RLD++TSG+
Sbjct: 78  VVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKVIERFGDVYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLEHGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|327462178|gb|EGF08505.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1]
          Length = 295

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 114/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++   +G   Q+  +  RLD++TSG+
Sbjct: 78  VIYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRQGYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +KVI+     +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKVIERIGDVYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLEYGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|310640867|ref|YP_003945625.1| pseudouridine synthase, rlua family protein [Paenibacillus polymyxa
           SC2]
 gi|309245817|gb|ADO55384.1| pseudouridine synthase, RluA family protein [Paenibacillus polymyxa
           SC2]
          Length = 293

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 61/209 (29%), Positives = 106/209 (50%), Gaps = 16/209 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR----LTHRLDQETSG 156
           +L+ED  I V +K AG+ +   S     +  + +     + + P     + HRLD++TSG
Sbjct: 80  ILHEDEAIIVIHKDAGL-LSVASAQEQEVTAYRQLTAHVRREHPYNRIFVLHRLDRDTSG 138

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++ A++ A  Q + ++++    ++ Y +LV G  K +   I +W LK+S     Y    
Sbjct: 139 VMMFAKSEAIQQEMQQAWKEVVYERTYIALVEGQVKKETGTITSW-LKESKTLKMYSSPY 197

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +     +A++H+K +    + F  LE++  TGR +Q+RVH   +G PIVGD KY +  
Sbjct: 198 PND---GQHAVTHYKRLQA-NRHFSLLEVRLETGRKNQIRVHMEDIGHPIVGDKKYGSKS 253

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           K         +L LHA+ +   HP  G L
Sbjct: 254 KSI------GRLGLHAKVLSFIHPLTGVL 276


>gi|254361102|ref|ZP_04977247.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261495410|ref|ZP_05991858.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|153092588|gb|EDN73643.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261308915|gb|EEY10170.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
          Length = 242

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 114/244 (46%), Gaps = 24/244 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D+ +   NKPAG+ V   S +  H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 5   ILYQDNSLIAINKPAGVLVHR-SWLDKHETVFAMQTLRDQIGQHVFPIHRLDRPTSGVLL 63

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A     A+ ++E F    +QK Y ++V G  +   +   ++ LK   +  D +      
Sbjct: 64  FALNSETARIMSEQFEQHLVQKTYLAVVRGYLQGSAQI--DYPLK---VILDKIADKFSQ 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           EK A  AI+ +K +               ++  +E+ P TGR HQLR H  H+  PI+GD
Sbjct: 119 EKEAQAAITDYKGLATVEMPYPVGKHQTSRYSLVELSPKTGRKHQLRRHLKHLFHPIMGD 178

Query: 270 HKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKY 326
            KY      +        ++L LHA  +   HP+   +++I A L     + W  L   +
Sbjct: 179 SKYGDLHQNRALVEKSGVSRLMLHAHKLQFQHPKNLQKIEIIASLD----EQWQRLFAFF 234

Query: 327 DRNL 330
           D N 
Sbjct: 235 DWNF 238


>gi|90408903|ref|ZP_01217040.1| putative ribosomal large subunit pseudouridine synthase A
           [Psychromonas sp. CNPT3]
 gi|90309987|gb|EAS38135.1| putative ribosomal large subunit pseudouridine synthase A
           [Psychromonas sp. CNPT3]
          Length = 219

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/209 (31%), Positives = 102/209 (48%), Gaps = 28/209 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPRLTHRLDQETSG 156
           +LY+D  I V NKPAG+    G  I  H D      L+ W ++      + HRLD  TSG
Sbjct: 16  ILYQDDDIVVLNKPAGLLSVPGREIK-HRDSLALRILRVWPNAC-----VVHRLDLATSG 69

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-----ANWLLKKSHIGGD 211
           ++V+A  ++A  H+   F+ + I K Y++ V G  K     +      +W  +   I  D
Sbjct: 70  LIVLAMRKSAQSHIGRQFQQKVIAKTYFARVEGYIKEDAGLVDLPIRCDWENRPRQI-VD 128

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +       E+G + + + +KV+         +E+ P TGRTHQLRVH   +G PI+GD  
Sbjct: 129 F-------EQGKS-SQTQWKVV-SRENDSTLVELTPLTGRTHQLRVHMQQIGHPILGDDF 179

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y +      ++    +L LHA  + L HP
Sbjct: 180 YGSELAKKLST---QRLALHAAKISLIHP 205


>gi|299772005|ref|YP_003734031.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) protein [Acinetobacter
           sp. DR1]
 gi|298702093|gb|ADI92658.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) protein [Acinetobacter
           sp. DR1]
          Length = 221

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 67/208 (32%), Positives = 105/208 (50%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ 
Sbjct: 18  ILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHV- 215
           A+ R A   +++ F+ R ++K Y +LV G    +       I +W  +   I    VH  
Sbjct: 76  AKHRDAEVAVSKMFQARTVKKHYIALVQGQVTEEGSVEVPLITDWENRPRQI----VHFE 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           + ++ K     + + + +D   Q    LE  P TGR+HQLRVH +H+G PI+GD  Y   
Sbjct: 132 LGKHAKTLFQPLVYDEKVD---QTRVLLE--PVTGRSHQLRVHMMHIGHPIMGDKLYHPE 186

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            K    S    ++ LHA ++   HP  G
Sbjct: 187 PKRFHLS----RMALHAAHLAFQHPLKG 210


>gi|88859129|ref|ZP_01133770.1| pseudouridylate synthase for 23S rRNA [Pseudoalteromonas tunicata
           D2]
 gi|88819355|gb|EAR29169.1| pseudouridylate synthase for 23S rRNA [Pseudoalteromonas tunicata
           D2]
          Length = 209

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/219 (28%), Positives = 110/219 (50%), Gaps = 24/219 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----PRLTHRLDQETSG 156
           ++Y+D  + + NKP+G+    G       D      ++ + Q+     ++ HRLD  TSG
Sbjct: 7   IIYQDEDLLILNKPSGLLTVPGK------DPLHADCLEKRAQRVFPTAKIVHRLDMATSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++ +A  +AA  H++  F+ R+ QK Y + V+G    +   +   L+       D+ +  
Sbjct: 61  LICLALNKAAHSHVSRQFQDRKTQKRYIARVFGKLTPETGSVDLPLI------CDWPNRP 114

Query: 217 KQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           KQ  N +    +++H++V++ + +    + + P TGR+HQLRVH L  G  I+GD  Y  
Sbjct: 115 KQMVNFEYGKPSLTHWQVLN-YEEHATRVALTPITGRSHQLRVHMLSQGHVILGDKLYAH 173

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                  S    +L LHA ++ + HP   + L+ TAP P
Sbjct: 174 PEAFQMAS----RLQLHAEWLAITHPVTAQALEFTAPCP 208


>gi|254443316|ref|ZP_05056792.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198257624|gb|EDY81932.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 194

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 60/175 (34%), Positives = 87/175 (49%), Gaps = 17/175 (9%)

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G++    HRLD+ TSG++V+ + R   + L   F  R ++K YW LV G+   + + + +
Sbjct: 22  GRQCWCCHRLDRLTSGVVVLRKGRRFVKELAGQFESRGVRKEYWLLVDGLWDRRIQKMES 81

Query: 201 WLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVH 258
            +   + IG G Y +V    E G   A S F+V+    ++   W+     TGRTHQLR+H
Sbjct: 82  QI---ASIGRGKYANV----ESGGKAAASTFRVLGLDEERRVSWMSGLLKTGRTHQLRLH 134

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           AL  GCP+VGD  Y         S       LHAR + + HP  G  L   A  P
Sbjct: 135 ALKAGCPVVGDPLYG-------KSRDDGLFGLHARSLRMRHPASGEELSFEAEPP 182


>gi|92116023|ref|YP_575752.1| pseudouridine synthase [Nitrobacter hamburgensis X14]
 gi|91798917|gb|ABE61292.1| pseudouridine synthase [Nitrobacter hamburgensis X14]
          Length = 292

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 71/258 (27%), Positives = 104/258 (40%), Gaps = 56/258 (21%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           ++ +++ +L+ D  + V +KPAGI V  G     +++   ++      + P L HRLD++
Sbjct: 8   AEQIQARVLHRDGLMLVIDKPAGIPVHRGPKGGANLEASFEALRFGLPRPPVLAHRLDRD 67

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI----------ANWLL 203
           TSG LV+ R R A   L   F+  +I K YW++V G P   +  I            W  
Sbjct: 68  TSGCLVLGRHRKATASLGLLFKHGKISKTYWAVVEGGPTEDEGTIDIPLGRLNHERGWWQ 127

Query: 204 KKSHIGGDYVHVVKQNEKGANYAIS-HFKVIDCFAQ------------------------ 238
           K    G   V   K   +G   A S  F    C  +                        
Sbjct: 128 KPDPNGLPSVTRWKVLGRGIFTAASDRFSPSPCGVETSEARPEGAGARGNSDGIAPDHPP 187

Query: 239 --------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA----------NFKGNF 280
                   +  WL ++P TGRTHQLRVH   M  PI GD+ Y             +   F
Sbjct: 188 PRAREEGIQLTWLALEPVTGRTHQLRVHCAAMRWPIAGDNIYGTQASLRRLRNEQYIPQF 247

Query: 281 TSPIQNKLYLHARYMDLP 298
             P    L+LHAR + +P
Sbjct: 248 GEP---SLHLHAREIAIP 262


>gi|261419065|ref|YP_003252747.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|319765882|ref|YP_004131383.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
 gi|261375522|gb|ACX78265.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC61]
 gi|317110748|gb|ADU93240.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC52]
          Length = 304

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/258 (25%), Positives = 128/258 (49%), Gaps = 33/258 (12%)

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKS-----ILLYEDSKIYVFNKPAGISV------QG 121
            + H+++  + L       + SD++ +      +LYED  + V NKPAG++        G
Sbjct: 51  TVRHVLRAGETLSVVFPPERTSDWMDAEAMPLDILYEDDYVLVVNKPAGLATIPSRHHPG 110

Query: 122 GS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G+   G+ +H   + K  +DS      +  RLD++TSG+++VA+ R     L+   +   
Sbjct: 111 GTLANGLLHH---YRKQQLDSTVH---IVTRLDRDTSGLVLVAKHRHVHHLLSALQQKGH 164

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + + Y ++  G+    +  I   + ++S    D + + ++  +    A++HF+V++    
Sbjct: 165 VVRTYEAICHGVIVEDEGTIDAPIGRQS----DSI-IAREVREDGKPAVTHFRVLERL-Y 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            + ++ ++  TGRTHQ+RVH  ++G P+ GD  Y  + +      +  +  LH+R +   
Sbjct: 219 GYTYVSLRLETGRTHQIRVHLAYLGHPLAGDELYGGSRE------MIGRQALHSRQLSFF 272

Query: 299 HPEGGR-LQITAPLPAHM 315
           HP  GR    +APLP  M
Sbjct: 273 HPFAGRWYTCSAPLPDDM 290


>gi|189426227|ref|YP_001953404.1| pseudouridine synthase [Geobacter lovleyi SZ]
 gi|189422486|gb|ACD96884.1| pseudouridine synthase, RluA family [Geobacter lovleyi SZ]
          Length = 295

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/216 (30%), Positives = 104/216 (48%), Gaps = 30/216 (13%)

Query: 87  SVNLTKHSDFLKSIL-----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK- 140
           +V   +   FL+ +L     +Y+D ++   NKP+GI+ Q      Y + G L+ WV  + 
Sbjct: 61  TVGFMEQGRFLELLLPPEAIVYQDKELLAINKPSGIASQR---TPYQLKGTLEYWVAEEF 117

Query: 141 -----GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 +  R+ HRLD+ TSG+++  + R AA  L+E F+   IQK Y +LV G P  ++
Sbjct: 118 VRQGIKEPVRVVHRLDRGTSGLMLFPKHRQAAAWLSELFKQGGIQKRYLALVTGKPVEER 177

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 + K   +G     ++ +       A++ F+++         +E  P TGRTHQ+
Sbjct: 178 WSCDGPIGK---LGSARWGIMSEG----RAALTDFRLLAAAEGLAL-VEAFPRTGRTHQI 229

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           RVH    G PIVGD  Y     G   S    +L LH
Sbjct: 230 RVHLSAAGLPIVGDATY-----GGLVS---ERLMLH 257


>gi|313837447|gb|EFS75161.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL037PA2]
 gi|314929343|gb|EFS93174.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL044PA1]
 gi|314971654|gb|EFT15752.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL037PA3]
          Length = 306

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 109/236 (46%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQ--------------GGSGIAYHIDGFLKSWVDSKGQKPRL 146
           ++++DS I V +KPAG++                  +G A    G L        ++  +
Sbjct: 82  IVHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTSGLL--------ERQGI 133

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD  TSG++VVA++  A   L ++FR R + K+Y +LV G P      I       +
Sbjct: 134 VQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRAVDKVYLALVQGHPDPFAGTI------DA 187

Query: 207 HIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            IG D+ H  K     G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P
Sbjct: 188 PIGRDHRHDWKMAIVDGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAVKHP 246

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             GD  Y  +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 247 CCGDPLYGCDPALAKELGLERQ-WLHAAELSFAHPGSGEWVTFHADLPADLQHALD 301


>gi|255655078|ref|ZP_05400487.1| putative pseudouridylate synthase [Clostridium difficile QCD-23m63]
 gi|296451065|ref|ZP_06892807.1| RluA family pseudouridine synthase [Clostridium difficile NAP08]
 gi|296880582|ref|ZP_06904544.1| RluA family pseudouridine synthase [Clostridium difficile NAP07]
 gi|296260072|gb|EFH06925.1| RluA family pseudouridine synthase [Clostridium difficile NAP08]
 gi|296428536|gb|EFH14421.1| RluA family pseudouridine synthase [Clostridium difficile NAP07]
          Length = 300

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 111/225 (49%), Gaps = 27/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++Y+D  I + NK   + V            +GI+Y+ID         +  K R  +RLD
Sbjct: 85  IIYDDFDIIMVNKLPFMVVHPTKSHYDKTIANGISYYIDN------QKENVKIRFVNRLD 138

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG+++VA+   A   L+ +    +++K Y ++V GI K  +  I   + + +    D
Sbjct: 139 MNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGIIKENEGTIDEPIYRPTE---D 195

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  +  +E+G + +++H+KVI+   +    LE+   TGRTHQ+RVH  H+G  I+GD  
Sbjct: 196 SIKRI-IDERGQS-SVTHYKVIERL-ENATVLEVSLETGRTHQIRVHMAHIGHGIIGDEL 252

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           Y     G     + N+  LHA  ++   P    +L+  A +P  +
Sbjct: 253 Y-----GCVDEELINRQALHAYRLEFEQPRTKEKLKFKADIPEDI 292


>gi|153806600|ref|ZP_01959268.1| hypothetical protein BACCAC_00870 [Bacteroides caccae ATCC 43185]
 gi|149131277|gb|EDM22483.1| hypothetical protein BACCAC_00870 [Bacteroides caccae ATCC 43185]
          Length = 306

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 113/226 (50%), Gaps = 20/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 91  IVYEDAYIIVVEKMQGLLSVNTERQKERTAYTI---LNEYVQRSGRQHRVYIVHRLDRDT 147

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+     + L +++      + Y ++V G  +   + + +WL  K+     YV 
Sbjct: 148 SGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTL----YVS 203

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++ G+  +I+H++ I   A  +  +E+   TGR +Q+RVH   +G PI GD +Y  
Sbjct: 204 SSGYDDGGSK-SITHYRTIKR-ANGYSLVELDLETGRKNQIRVHMQDLGHPIAGDGRYGG 261

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
               N+++PI  +L LHA  +   HP  G L +   P P    K +
Sbjct: 262 E---NYSNPI-GRLALHAFKLCFYHPVTGDLMEFETPYPGEFKKLF 303


>gi|56419366|ref|YP_146684.1| hypothetical protein GK0831 [Geobacillus kaustophilus HTA426]
 gi|56379208|dbj|BAD75116.1| hypothetical conserved protein [Geobacillus kaustophilus HTA426]
          Length = 303

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/258 (25%), Positives = 128/258 (49%), Gaps = 33/258 (12%)

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKS-----ILLYEDSKIYVFNKPAGISV------QG 121
            + H+++  + L       + SD++ +      +LYED  + V NKPAG++        G
Sbjct: 51  TVRHVLRAGETLSVVFPPERTSDWMDAEAMPLDILYEDDYVLVVNKPAGLATIPSRHHPG 110

Query: 122 GS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G+   G+ +H   + K  +DS      +  RLD++TSG+++VA+ R     L+   +   
Sbjct: 111 GTLANGLLHH---YRKQQLDSTVH---IVTRLDRDTSGLVLVAKHRHVHHLLSALQQKGH 164

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + + Y ++  G+    +  I   + ++S    D + + ++  +    A++HF+V++    
Sbjct: 165 VVRTYEAICHGVIVEDEGTIDAPIGRQS----DSI-IAREVREDGKPAVTHFRVLERL-Y 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            + ++ ++  TGRTHQ+RVH  ++G P+ GD  Y  + +      +  +  LH+R +   
Sbjct: 219 GYTYVSLRLETGRTHQIRVHLAYLGHPLAGDELYGGSRE------MIGRQALHSRQLSFF 272

Query: 299 HPEGGR-LQITAPLPAHM 315
           HP  GR    +APLP  M
Sbjct: 273 HPFAGRWYTCSAPLPDDM 290


>gi|295108996|emb|CBL22949.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           obeum A2-162]
          Length = 233

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 59/186 (31%), Positives = 95/186 (51%), Gaps = 12/186 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK--GQKPRL--THRLDQ 152
           +++++LYED +I V +K AGI+VQ        ++  LK+++ SK  G  P L   HRLDQ
Sbjct: 5   IENMILYEDKEIIVCHKAAGIAVQSARIGIPDMESTLKNYLASKNPGTMPYLGIVHRLDQ 64

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              G+LV A+ + AA  LT       + K Y ++    P+N +  + ++L K        
Sbjct: 65  PVEGVLVFAKNKRAAAGLTGQITSGSVTKEYLAVTDQKPENVQGHLEDYLKKDGKTNTSA 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ------KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           V   K +   A  A+  ++V++  +       K   + +Q  TGR HQ+RV   H G P+
Sbjct: 125 VVTSKTDR--AKKAVLDYEVLNEVSDERTSTGKRILVRIQLGTGRHHQIRVQMAHAGMPL 182

Query: 267 VGDHKY 272
           +GD KY
Sbjct: 183 LGDRKY 188


>gi|84500695|ref|ZP_00998944.1| ribosomal large subunit pseudouridine synthase A [Oceanicola
           batsensis HTCC2597]
 gi|84391648|gb|EAQ03980.1| ribosomal large subunit pseudouridine synthase A [Oceanicola
           batsensis HTCC2597]
          Length = 215

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 63/209 (30%), Positives = 102/209 (48%), Gaps = 22/209 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED ++ + +KPAG+    G G   H+   L + V +      L HRLD++TSG++V 
Sbjct: 14  VIHEDQELLLVDKPAGLLSVPGKG--EHLADCLLTRVQAAFPTALLVHRLDRDTSGVMVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-----ANWLLKKSHIGGDYVHV 215
           A T  A +HL   F  RR +K Y + V G  + +   +      +W  +   +      V
Sbjct: 72  ALTHHAQRHLGLQFEHRRTRKTYVARVHGHLEPRSGTVDLPLNVDWPNRPRQM------V 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +N + A    + +KV          + + P TGR+HQLRVH L +G PI+GD  Y   
Sbjct: 126 DHENGRAAR---TDWKV-QRHGDGETRVRLMPRTGRSHQLRVHMLALGHPILGDPFYAEG 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              +       +L LH+  + L HP+GG+
Sbjct: 182 AARD-----HPRLMLHSEELRLLHPDGGK 205


>gi|324995861|gb|EGC27772.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK678]
          Length = 291

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 92/201 (45%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      R I + YW+LV G   +KK      L+ K  IG D     K+  +
Sbjct: 141 KNPFVLPILNRLLEKREISREYWALVQGKFPSKK------LIYKDKIGRDRHDRRKRLVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   YA +H   +    Q    ++ Q  TGRTHQ+RVH  H G P++GD  Y    KG 
Sbjct: 195 PRKGLYAETHVTRLKQLGQA-ALVKCQLKTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 253 -------RLMLHAHRLTFTHP 266


>gi|262368495|ref|ZP_06061824.1| pseudouridylate synthase [Acinetobacter johnsonii SH046]
 gi|262316173|gb|EEY97211.1| pseudouridylate synthase [Acinetobacter johnsonii SH046]
          Length = 214

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 67/223 (30%), Positives = 104/223 (46%), Gaps = 15/223 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           S+FL   L++ D    V +KPAGI    G       D  +   V  +  K  L HRLD++
Sbjct: 2   SNFLTEHLIHRDEDFMVIHKPAGILTVPGKTEDLQ-DCMINRLVKLE-PKTLLIHRLDRD 59

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   +R   + ++  F+ R   K Y ++V G    +       +   S      +
Sbjct: 60  TSGILVFGLSRWGQKTISRQFQERLTDKTYQAIVAGHLDGQGTVDVPVIYDPSR---PPL 116

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+ + +      A++ +K I+ F    Q    + + P TGR+HQLRVH   +G PIVGD 
Sbjct: 117 HIAEPSHNKP--AVTEWKAIEHFEIQGQPVTRVALTPITGRSHQLRVHMQFLGHPIVGDT 174

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y A  + +    +  +L LHA  +   HP+   R++   P P
Sbjct: 175 LYAAPDQQD----LMPRLCLHAERLSFHHPQTNERIEFICPAP 213


>gi|237738860|ref|ZP_04569341.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           2_1_31]
 gi|229423963|gb|EEO39010.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           2_1_31]
          Length = 315

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 78/296 (26%), Positives = 139/296 (46%), Gaps = 46/296 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALN 75
           E MRLD++            L+K++ +  V+++ K +  N R ++SG+ + I        
Sbjct: 17  EGMRLDKYLAEQIEEATRSYLEKLIDNSYVKINSKVINKNGRKLKSGEKIEIS------- 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
             I E++      N+   ++ +   +++E+    + NK   + V    G         + 
Sbjct: 70  --IPEEE------NIDIEAENIPLDIVFENDDFILVNKKYNMVVHPAYGNYTGTLVNALL 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y+ +    S V+    +P + HRLD++TSG+++VA+   A   L   F  + I K Y  +
Sbjct: 122 YYTNNL--SSVNG-NIRPGIIHRLDKDTSGLILVAKNNFAHAKLASMFTDKTIHKTYLCI 178

Query: 187 VWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           V G    +N +  I N L+ +       + VVK+N K    AIS+++V++   + +  +E
Sbjct: 179 VKGNFSDENLEGRIEN-LIGRDTKDRKKMAVVKENGK---LAISNYRVVEQ-VKDYSLVE 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------FKGNFTSPIQNKLY 289
           +   TGRTHQ+RVH   +  PI+GD  Y +            FK  F +P+ NK Y
Sbjct: 234 VLIETGRTHQIRVHMKSINHPILGDVIYGSEDKNVKRQMLHAFKLEFLNPLDNKEY 289


>gi|327470007|gb|EGF15471.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK330]
          Length = 295

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 114/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++      + Q+  +  RLD++TSG+
Sbjct: 78  VVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKVIERFGDVYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLEHGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|262283613|ref|ZP_06061378.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           2_1_36FAA]
 gi|262260670|gb|EEY79371.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           2_1_36FAA]
          Length = 290

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 93/201 (46%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + IQ+ YW+LV G     K  + N + K   IG D     K+  +
Sbjct: 141 KNPFVLPILNRLLENKDIQREYWALVDG-----KFPVKNRVFKDK-IGRDRHDRRKRLVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F QK   ++ Q  TGRTHQ+RVH    G P+VGD  Y    +G 
Sbjct: 195 SKHGQYAETHVTRLKSFGQK-TLIKCQLKTGRTHQIRVHLSRHGFPLVGDPLYHPQPQG- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 253 -------RLMLHAHRLSFVHP 266


>gi|59711220|ref|YP_203996.1| tRNA pseudouridine synthase C [Vibrio fischeri ES114]
 gi|59479321|gb|AAW85108.1| tRNA pseudouridine synthase [Vibrio fischeri ES114]
          Length = 259

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 118/250 (47%), Gaps = 29/250 (11%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTH 148
           L + ++ ++  ++Y D  +   NKPAG+ V   S +  H   F +++  D  GQ     H
Sbjct: 14  LEEQAEPIELEIVYRDEHLIAINKPAGMLVHR-SWLDKHETVFAMQTLRDQIGQHVFPLH 72

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSGIL  A +   A  ++  F  R I+K Y ++V G  +       ++ LKK   
Sbjct: 73  RLDRPTSGILFFALSSEIAAQVSPLFASREIKKTYHAIVRGWIEEANTL--DYPLKKE-- 128

Query: 209 GGDYVHVVKQN-EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRV 257
             D +   K + E  A  AI+ +K +               ++C +E++PHTGR HQLR 
Sbjct: 129 -LDKIADKKASQEVEAKEAITEYKPLAKVELPYSTGKFPTTRYCLMELKPHTGRKHQLRR 187

Query: 258 HALHMGCPIVGDH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           H  H+  PIVGD      K+   FK    S   ++L LHA  ++  HP  G   +   + 
Sbjct: 188 HMAHLRHPIVGDTSHGDGKHNRLFKEKLDS---HRLLLHASELNFTHPITGEDIV---IK 241

Query: 313 AHMVKTWDSL 322
           A   +TW  L
Sbjct: 242 ADFDETWKKL 251


>gi|254520113|ref|ZP_05132169.1| ribosomal large subunit pseudouridine synthase C [Clostridium sp.
           7_2_43FAA]
 gi|226913862|gb|EEH99063.1| ribosomal large subunit pseudouridine synthase C [Clostridium sp.
           7_2_43FAA]
          Length = 323

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 73/284 (25%), Positives = 123/284 (43%), Gaps = 47/284 (16%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ +     +    + K LR G V+V+ K+ K N  +Q   VV I  
Sbjct: 3   IEIGTNEAGQRLDKFLRKLLKDVPLSKIFKALRKGDVKVNGKKQKENYSLQIDDVVEIKY 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYH 128
           + +  N    E+K +  +    K        + YEDS + +  K   I V     G    
Sbjct: 63  IQS--NKEKPEEKFIKVNARGMK--------ITYEDSNMLIVEKWPNILVHPDEKGKEAS 112

Query: 129 IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S+++ KG           P   +RLD+ TSGI++  +   A + + E  R  ++
Sbjct: 113 LTDYVLSYLNEKGDYLPENELTFTPAPCNRLDRNTSGIVIFGKNFEALRTMNEMIREGKV 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---- 235
           +K Y +LV G  K+                G Y   + +NE+     I   K+ D     
Sbjct: 173 EKYYNTLVKGKIKD----------------GLYKGYIHKNEEANISRIYDEKITDSKEIA 216

Query: 236 -------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                      + +LE+   TGR+HQ+R H  H+G PI+GD+KY
Sbjct: 217 MEVKTLKTNGAYSFLEIDLITGRSHQIRAHLSHLGTPIIGDNKY 260


>gi|261212690|ref|ZP_05926974.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. RC341]
 gi|260837755|gb|EEX64432.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. RC341]
          Length = 396

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/206 (33%), Positives = 100/206 (48%), Gaps = 24/206 (11%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I V NKP+  +SV G       +      + D++G      HRLD  TSG+LV
Sbjct: 195 IVYQDDAIVVVNKPSEFLSVPGVHVHDSVLSRLQAQFRDAEG--VFALHRLDMSTSGLLV 252

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A TR A +HL + F  R +QK Y +L+ G     +  I      +  + GD     +Q 
Sbjct: 253 FALTRRANKHLQKQFITRAVQKRYVALLEGTLDADRGEI------QLPLCGDLDDRPRQK 306

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCA 274
              +    A++H++VI    Q    + + PHTGRTHQLRVH  H   + CPIVGD  Y  
Sbjct: 307 VCLQQGKPALTHWEVIR-IEQGRTRVYLYPHTGRTHQLRVHCAHQLGLDCPIVGDDLYGQ 365

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
             +         +L+LHA  +   HP
Sbjct: 366 QAQ---------RLHLHAEQLCFTHP 382


>gi|239623515|ref|ZP_04666546.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239521546|gb|EEQ61412.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 297

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 81/287 (28%), Positives = 132/287 (45%), Gaps = 50/287 (17%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G + V  + V   +R+Q G+V+++         ++ E     S V +      L   ++Y
Sbjct: 41  GSLTVKGQPVYTIHRLQPGEVLKV---------VLTEDNPSRSIVPVN-----LPLSIVY 86

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLK---SWVDSKGQKP---RLTHRLDQETSGI 157
           ED  I V NK AG+ +    G   H D  L    +W  S+  +P   R  +RLD++T+G+
Sbjct: 87  EDEDILVINKEAGVPIHPSQG---HHDNTLANAVAWYYSQKGEPFTYRAINRLDRDTTGL 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++AR   +A  L+     RRI++ Y ++V G  ++     A      + + G  +    
Sbjct: 144 LILARHMLSACVLSNDMLNRRIKREYRAIVCGRTRDMGTIDAPI----ARVEGSTIERQV 199

Query: 218 QNEKGANYAISHFKVI--------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             EKG + A +H++ I         C +    WLE    TGRTHQ+RVH   +G P+ GD
Sbjct: 200 DFEKGES-ACTHYRRIAYNEHLDLSCVS---LWLE----TGRTHQIRVHMKSIGHPLPGD 251

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             Y  +++     P      LH+  +   HP  G  ++ TA LP  M
Sbjct: 252 FLYHPDYRYISRQP------LHSCRLSFTHPVTGEPMEFTAGLPEDM 292


>gi|209554367|ref|YP_002284711.1| RluA [Ureaplasma urealyticum serovar 10 str. ATCC 33699]
 gi|209541868|gb|ACI60097.1| RluA [Ureaplasma urealyticum serovar 10 str. ATCC 33699]
          Length = 299

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 72/257 (28%), Positives = 124/257 (48%), Gaps = 30/257 (11%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDG 131
           I  EQ ++DS   L   +  L+  +++ED  + V NKP+G+     S Q  + +A  +  
Sbjct: 59  IKNEQCVIDSQKELLPFACPLE--IVFEDQDLLVINKPSGMLVHPTSFQEQNTLANALKH 116

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           +LK+          +THRLD+ TSG++V+ + + A   L + F  + ++K Y+++V    
Sbjct: 117 YLKT------DDFYITHRLDKNTSGLIVICKNQKALCCLQQQFMQKTVKKSYYAIVH--- 167

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
            N+ +      +    IG  Y   ++    + K    AIS  KVI+ + Q    +E+   
Sbjct: 168 -NRFDMHHLHFMINEPIGHSYQDKLRMKTGDAKNVKEAISIVKVIEQY-QNTALVEVSII 225

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QI 307
           TGRTHQ+RVH  H+  PI  D  Y        T+P +   YLH+ Y+   HP    + + 
Sbjct: 226 TGRTHQIRVHMRHINHPIYNDPLYGI---SKHTTPYEQ--YLHSFYISFIHPSTNEIVEF 280

Query: 308 TAPLP---AHMVKTWDS 321
              +P    +++K W +
Sbjct: 281 KTLMPNEFINLIKEWKT 297


>gi|323143512|ref|ZP_08078192.1| ribosomal large subunit pseudouridine synthase D [Succinatimonas
           hippei YIT 12066]
 gi|322416706|gb|EFY07360.1| ribosomal large subunit pseudouridine synthase D [Succinatimonas
           hippei YIT 12066]
          Length = 323

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 86/337 (25%), Positives = 156/337 (46%), Gaps = 46/337 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           + + ++  N RLD          +   L++ +  G+V VD   + K + ++ SGQ+V + 
Sbjct: 7   LTITDEFHNKRLDAALGGLIDTHSRSTLREYIDEGKVAVDGVVITKPSIKVSSGQIVSV- 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                    I + + LD+     K  D    I+ Y+D  I + NKP    V  G+GI   
Sbjct: 66  --------TIPDPEDLDA-----KPQDLPLDII-YQDDDILIINKPINFVVHPGAGIK-- 109

Query: 129 IDGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            DG + + V          PR  + HRLD++TSG++V+A ++ A Q LT++     + + 
Sbjct: 110 -DGTVMNAVLYHFPQTSSLPRAGIVHRLDKDTSGLMVIALSQLAQQVLTKAIAKHDVVRE 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGD-YVH--VVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G      +  A   +  + IG D YV   +    E     A++H++V++ F + 
Sbjct: 169 YEAIAEG------QITAGGTID-APIGRDPYVRTKMAVMPEGIGREAVTHYRVMERF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-------CANFKGNFTSPIQNKLY--L 290
              L ++  TGRTHQ+RVH   +  P++GD++Y             +  + ++N  +  L
Sbjct: 221 HTRLRLRLETGRTHQIRVHMASIHHPLLGDNQYGGKRLKMLPGADEDLANMLRNYRHQAL 280

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HA +++  HP+    +    P+P  M +  + L   Y
Sbjct: 281 HAVHIEFAHPKTKENMSFDVPIPEEMSELIELLRKDY 317


>gi|92118358|ref|YP_578087.1| pseudouridine synthase, RluD [Nitrobacter hamburgensis X14]
 gi|91801252|gb|ABE63627.1| ribosomal large subunit pseudouridine synthase D [Nitrobacter
           hamburgensis X14]
          Length = 264

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/240 (28%), Positives = 109/240 (45%), Gaps = 35/240 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + V NKP G+ V   +G         +  H  G L         +P + HRLD
Sbjct: 18  IVYEDDDLIVVNKPKGLVVHPAAGHEAGTLVNALIAHCGGSLSGI--GGVCRPGIVHRLD 75

Query: 152 QETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           ++T+G++V A+  AA + L+  F    R   +++ Y +  WG+P N+     +  + +  
Sbjct: 76  KDTTGLMVAAKNDAAHKSLSAQFADHGRTGALRRGYLAFAWGLP-NRPHGTVDAPIDRHP 134

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHM 262
              + + V     +    AI+H++V   F  +        L  Q  TGRTHQ+RVH  H 
Sbjct: 135 YAREKMAVRASGRE----AITHWEVRKAFNGRDGKPVAALLACQLETGRTHQIRVHLAHA 190

Query: 263 GCPIVGDHKYCANF--KGNFTSPIQ-------NKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G P++GD  Y  +F  K N   P          +  LHA  + + HP  G  L+  A LP
Sbjct: 191 GHPLMGDGVYGPHFKTKANQLGPSARTALDALGRQALHAYLLAIEHPRTGEILRWEAALP 250


>gi|229029062|ref|ZP_04185161.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|228732342|gb|EEL83225.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 307

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 114/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  +       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKGKQGTV------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEKYFKKQNVTFVTLQLETGRTHQIRVHMSYHGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y    K + T        LHA  +   HP     +++  P P  +  T
Sbjct: 254 DVLYGGQTK-HMTGQA-----LHAMKIHFLHPITKEEIEVDVPFPTKLNNT 298


>gi|307722069|ref|YP_003893209.1| pseudouridine synthase [Sulfurimonas autotrophica DSM 16294]
 gi|306980162|gb|ADN10197.1| pseudouridine synthase [Sulfurimonas autotrophica DSM 16294]
          Length = 302

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 53/171 (30%), Positives = 89/171 (52%), Gaps = 5/171 (2%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YE+ +  +F+KP+G+ +   +   Y     +       G+   +THR+DQETSG+++ A+
Sbjct: 74  YEEEEFVIFDKPSGVLIHPQN--RYTPYSLIDELKYQYGRDANITHRIDQETSGLVLCAK 131

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            + + + +   F  R ++K Y + V G    K+  +   LL+          VVK +EKG
Sbjct: 132 NKQSERDIKMMFEQRDMKKKYLAFVHG-HFEKELTVEAPLLRAEDESAIVRMVVKVDEKG 190

Query: 223 ANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              + + FK +  F++     +E  P+TGR HQ+RVH  H+  PIVGD  Y
Sbjct: 191 KA-SKTDFKPLQYFSEVDMTLVECSPYTGRQHQIRVHLFHVKHPIVGDPIY 240


>gi|284991670|ref|YP_003410224.1| RluA family pseudouridine synthase [Geodermatophilus obscurus DSM
           43160]
 gi|284064915|gb|ADB75853.1| pseudouridine synthase, RluA family [Geodermatophilus obscurus DSM
           43160]
          Length = 315

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 56/178 (31%), Positives = 93/178 (52%), Gaps = 8/178 (4%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD  T+G++VVA++  A   L  +F+ R ++K Y +LV G P   +  I   + + 
Sbjct: 141 VVHRLDAGTTGLMVVAKSERAYTALKAAFKQRTVEKGYAALVQGHPDPSRGTIDAPIDR- 199

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            H   D+   V Q   G   +++H++V + F      ++++  TGRTHQ+RVH   M  P
Sbjct: 200 -HPKHDWRFAVVQ---GGRPSVTHYEVAEAFPAA-SLVDIRLETGRTHQIRVHFSAMRHP 254

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            VGD  Y A+        + ++ +LHA  + +PHP  G  ++ T+P P  +    D L
Sbjct: 255 CVGDTTYGADPTLAARLGV-SRQWLHAARLGIPHPADGHWMEFTSPFPPDLAGALDIL 311


>gi|15674094|ref|NP_268269.1| pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
 gi|12725167|gb|AAK06210.1|AE006439_7 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 288

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/213 (29%), Positives = 99/213 (46%), Gaps = 24/213 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  + V NKP G+   G +     +   + + ++   Q+  + HRLDQ TSG ++ 
Sbjct: 83  ILYEDEHLIVVNKPEGMKTHGNTADELALQNHVAAAIN---QEVFVVHRLDQATSGAVLF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ +     L + F   +I + Y +LV G     +  I   + +  H     +   K   
Sbjct: 140 AKNQFVLPILGKMFEENKIHREYLALVKGHFSENQFTIDRAIGQNRHDKNKRILSAK--- 196

Query: 221 KGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                A++H ++I  F  K    C L+    TGRTHQ+RVH   +  PI+GD  Y     
Sbjct: 197 --GQKAVTHVEIIKKFTDKTLVKCTLD----TGRTHQIRVHLSSLNHPIIGDALYG---- 246

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
                  Q ++ LHA  + +PHP E   L+I+A
Sbjct: 247 ----QKSQERMMLHAGKIIIPHPFENKILEISA 275


>gi|262067278|ref|ZP_06026890.1| pseudouridine synthase, RluA family [Fusobacterium periodonticum
           ATCC 33693]
 gi|291379004|gb|EFE86522.1| pseudouridine synthase, RluA family [Fusobacterium periodonticum
           ATCC 33693]
          Length = 315

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 78/296 (26%), Positives = 139/296 (46%), Gaps = 46/296 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALN 75
           E MRLD++            L+K++ +  V+++ K +  N R ++SG+ V I        
Sbjct: 17  EGMRLDKYLAEQIEEATRSYLEKLIDNSYVKINSKIINKNGRKLKSGEKVEIS------- 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
             I E++      N+   ++ +   +++E+    + NK   + V    G         + 
Sbjct: 70  --IPEEE------NIDIEAENIPLDIVFENDDFILVNKKYNMVVHPAYGNYTGTLVNALL 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y+ +    S V+    +P + HRLD++TSG+++VA+   A   L   F  + I K Y  +
Sbjct: 122 YYTNNL--SSVNG-NIRPGIIHRLDKDTSGLILVAKNNFAHAKLASMFTDKTIHKTYLCI 178

Query: 187 VWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           V G    +N +  I N L+ +       + +VK+N K    AIS+++V++   + +  +E
Sbjct: 179 VKGNFSDENLEGRIEN-LIGRDTKDRKKMAIVKENGK---LAISNYRVVEQ-VKDYSLVE 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------FKGNFTSPIQNKLY 289
           +   TGRTHQ+RVH   +  PI+GD  Y +            FK  F +P+ NK Y
Sbjct: 234 VLIETGRTHQIRVHMKSINHPILGDVIYGSEDKNVKRQMLHAFKLEFLNPLDNKEY 289


>gi|138894182|ref|YP_001124635.1| ribosomal large subunit pseudouridine synthase D [Geobacillus
           thermodenitrificans NG80-2]
 gi|196250721|ref|ZP_03149409.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
 gi|134265695|gb|ABO65890.1| Ribosomal large subunit pseudouridine synthase D [Geobacillus
           thermodenitrificans NG80-2]
 gi|196209800|gb|EDY04571.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
          Length = 299

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/207 (31%), Positives = 102/207 (49%), Gaps = 24/207 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +L+ED  + + NK AGI +      Q G+ +A  +  +L+S   +   K R  HRLD++T
Sbjct: 86  VLWEDEHLLILNKEAGIDIHPSEPEQTGT-LANAVAFYLQS--QAILTKVRHIHRLDRDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG ++ A+   A   L      R I++ Y +LV G    K   I+      + IG D  H
Sbjct: 143 SGTILFAKHPLAGATLDRMLAHRTIKRTYVALVHGRLSPKSGTIS------APIGRDRHH 196

Query: 215 VVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             ++   K    A++H++V++ F      +E+   TGRTHQ+RVH  H+G P+VGD  Y 
Sbjct: 197 PTRRRVSKTGARAVTHYRVLETFPSA-SLVELNLDTGRTHQIRVHLAHLGHPLVGDMLYG 255

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
                    P  ++  LHA  +   HP
Sbjct: 256 GQ-------PTFHRHALHAVKLTFRHP 275


>gi|6942292|gb|AAF32394.1|AF224466_1 putative pseudouridylate synthase [Haemophilus ducreyi]
          Length = 250

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 55/178 (30%), Positives = 96/178 (53%), Gaps = 22/178 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
           +++ED  I + NKP  + V  G+G   + DG     L  +     + PR  + HRLD++T
Sbjct: 86  IVHEDDDIIIINKPKNLVVHPGAG---NPDGTVLNALLYYYPPIAEVPRAGIIHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
           +G++VVA+   A  HL  + + RRI + Y ++  GI        E +A    K++ +   
Sbjct: 143 TGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMTQGGKVDEPMARHPTKRTAMA-- 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            VH + +       AI+H+++++ F + +  L ++  TGRTHQ+RVH  H+  P++GD
Sbjct: 201 -VHPMGKP------AITHYRIMERF-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGD 250


>gi|302384824|ref|YP_003820646.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
 gi|302195452|gb|ADL03023.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
          Length = 242

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 60/208 (28%), Positives = 100/208 (48%), Gaps = 13/208 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---SKGQKP--RLTHRLDQETS 155
           +LYED +I V  KP G+  Q        +   +K  ++    K  +P   + HRLD+   
Sbjct: 14  ILYEDEEILVAEKPVGMESQSARSFEPDMVSEVKKHINRLSPKQGEPYVGVIHRLDKPVG 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T+ AA+ L+    M +++KIY+++V G P        ++L K      +   +
Sbjct: 74  GVMVYAKTKDAAESLSRQVSMHQMEKIYYAVVCGKPVENFGAYVDYLWKDGK--NNCSKI 131

Query: 216 VKQNEKGANYAISHFKVID--CFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V +  KGA  A   ++++D      + C L ++   TGR HQ+RV     G P+ GD KY
Sbjct: 132 VDKGIKGAKLAELSYQIVDERSIGNEVCSLAKIILKTGRHHQIRVQMAGHGTPLWGDQKY 191

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
              F+  + S     + L A  +   HP
Sbjct: 192 NPLFQKGYRS---GNVALFAYSLTFTHP 216


>gi|322435857|ref|YP_004218069.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX9]
 gi|321163584|gb|ADW69289.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX9]
          Length = 297

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 76/312 (24%), Positives = 134/312 (42%), Gaps = 29/312 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Y    ++ + +    L       YPH +    Q+ L +G+V +D      +  + SGQ++
Sbjct: 6   YAYTTIIGSKQHGWTLLSHLAGLYPHSSAEAWQENLDNGEVTLDGITAAGSELLSSGQIL 65

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                      + K    ++   +  +H +     +L++D  +   NKP+G+    G G 
Sbjct: 66  -----------VWKRPAWIEP--DAPQHFE-----VLFDDLHLLAVNKPSGLPTLPGGGF 107

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              ++  L   V          HRL + T+GI++ A+T  AA  LT  +   R+QKIY +
Sbjct: 108 ---LENTLLRLVHRHSPSANPVHRLGRATTGIVMFAKTAQAAAGLTADWNTPRVQKIYRA 164

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L  G+ + +   I   +    H     +  V     G   + S  KVI   A    + E+
Sbjct: 165 LAQGVARQEAYEILTPIGLVPH---PRLGSVWAASAGGKASKSSAKVISRTAATTTF-EV 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQNKLYLHARYMDLPHP-E 301
           +  +GR HQ+R+H   +G P+VGD  Y +           P      LHA+++   HP  
Sbjct: 221 RLGSGRPHQIRIHLASIGHPLVGDPLYGSTGLPLDDLPGLPGDGGYLLHAQFLKFHHPVT 280

Query: 302 GGRLQITAPLPA 313
           G ++++ A LP+
Sbjct: 281 GEQIELEAALPS 292


>gi|213616279|ref|ZP_03372105.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 165

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 56/159 (35%), Positives = 82/159 (51%), Gaps = 14/159 (8%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+    
Sbjct: 7   HRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI---- 62

Query: 208 IGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              D+ +  KQ    E G   A + + V++  A     + ++P TGR+HQLRVH L +G 
Sbjct: 63  --CDWPNRPKQKVCYETG-KPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGH 119

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           PI+GD  Y +    +       +L LHA  + + HP  G
Sbjct: 120 PILGDQFYASPEALSLAP----RLQLHAEMLTITHPAYG 154


>gi|171909579|ref|ZP_02925049.1| ribosomal large subunit pseudouridine synthase, Rlu family protein
           [Verrucomicrobium spinosum DSM 4136]
          Length = 253

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 125/244 (51%), Gaps = 24/244 (9%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDGF--LKSWVDSKGQK 143
           ++  SD+  +IL  E     V +KPA + +       +G+    DG   L ++  + G +
Sbjct: 1   MSASSDYNFAIL-DETEDWLVVDKPAPLQIHPSKPSDAGLTL-WDGIRELLAYELANGGQ 58

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + +RLD+ETSG+++VA+T  AA+ L ++   R++ K Y ++V G P+ ++  +   +L
Sbjct: 59  VSIINRLDRETSGVVLVAKTGPAARRLGKAMMRRQMDKTYLAVVAGWPEWEETTVTAPIL 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           ++  +    + V ++ ++      SHF+V    +    +F  +E  PHTGR HQLRVH  
Sbjct: 119 RQGDVMDSRIWVKQRVDERGVPCESHFQVRERHETHRGRFSLVECAPHTGRMHQLRVHLA 178

Query: 261 HMGCPIVGDHKYCAN-------FKGNFTSPIQNKLY-----LHARYMDLPHPEGGRLQIT 308
           H+G  +VGD  Y  +        +  +T  ++ +L      LH+  + L   + GR +  
Sbjct: 179 HLGHYVVGDKIYGPSEDCYLEFIETGWTPRLEAQLLLPRQALHSHRLILDDGQ-GRQEWV 237

Query: 309 APLP 312
           APLP
Sbjct: 238 APLP 241


>gi|167950143|ref|ZP_02537217.1| 23S rRNA pseudouridine synthase D [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 306

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 77/286 (26%), Positives = 131/286 (45%), Gaps = 40/286 (13%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T +  V +E  +   RLD+     +   +   LQ+ ++ G++ +D +  K   +++ G+ 
Sbjct: 14  TLISEVALE--QAGRRLDQVVAEQFAQFSRSRLQRWIKDGRLLLDGRPGKPKQKVRGGER 71

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + + P +        EQ++       T     +   +L+ED  + V NKPAG+ V    G
Sbjct: 72  LELVPQL--------EQEV-------TSRPQPIPLDILFEDESLLVVNKPAGLVVHPAVG 116

Query: 125 IAYHIDGFLKS----WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              + DG L +    +  +  Q PR  + HRLD+ETSG+LVVA+T  A   L    + R 
Sbjct: 117 ---NPDGTLVNALLHYFPAISQVPRGGIVHRLDKETSGLLVVAKTLQAQTALVAQLQARS 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFA 237
           +++ Y +   G+       +A      + IG   VH  +         A++H++VI+ + 
Sbjct: 174 MKREYRAFAQGV-------MAAGGKVDAPIGRHPVHRTRMAVVANGKPAVTHYRVIERY- 225

Query: 238 QKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGN 279
            +F   L +Q  TGRTHQ+RVH   +  P  G        AN  G 
Sbjct: 226 -RFHTDLRIQLETGRTHQIRVHMAQIRFPAGGRPGLRWAVANLPGT 270


>gi|120434465|ref|YP_860167.1| RNA pseudouridylate synthase [Gramella forsetii KT0803]
 gi|117576615|emb|CAL65084.1| RNA pseudouridylate synthase [Gramella forsetii KT0803]
          Length = 289

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 64/215 (29%), Positives = 101/215 (46%), Gaps = 37/215 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +L+ED  I V +KP G    G       + + +++     S +D+    P   HRLD  T
Sbjct: 82  VLFEDEHIAVVHKPPGFPTSGNYFKTIENALPHNLSS--SSEIDTLPY-PLPAHRLDNPT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC---IANWLLKKSHIGGD 211
           SGIL+ A+T ++   L E+F  ++IQK Y+++V G  K K E    I   + K   I  +
Sbjct: 139 SGILLCAKTNSSLIKLQEAFAQKQIQKTYYAIVSGEIKEKIEIDSPIDQKISKTILIPIE 198

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +  +  +N                    +  +E+ P TGRTHQLR+H      PI+GD+ 
Sbjct: 199 FYQIENKN--------------------YTLVELNPLTGRTHQLRIHLSENNTPIIGDNL 238

Query: 272 YCANFKGNFTSPIQNK-LYLHARYMDLPHPEGGRL 305
           Y        T+ ++NK +YL A  +   HP   +L
Sbjct: 239 YGK----EETNLLKNKSIYLFAGKISFDHPLSKKL 269


>gi|315924025|ref|ZP_07920252.1| RluA protein [Pseudoramibacter alactolyticus ATCC 23263]
 gi|315622651|gb|EFV02605.1| RluA protein [Pseudoramibacter alactolyticus ATCC 23263]
          Length = 314

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/269 (24%), Positives = 121/269 (44%), Gaps = 15/269 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q  + +N  E  R+DR+     P  +   L K+LR  ++++D  R    + +Q GQV+ 
Sbjct: 2   IQLTISDNAAEQ-RMDRFLIKWLPQASKGFLMKMLRKKRIKLDGHRASPRDYLQKGQVL- 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL---LYEDSKIYVFNKPAGISVQGGS 123
                       ++ +   ++       D LK+++   LYED  +   NKP G+  Q   
Sbjct: 60  ---TFYFSEETYRQFRGQPAAPGEPSLPDSLKALMQPPLYEDDHLIAVNKPVGLLTQPDH 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +     +   S    P   +RLD+ TSGI+++ +     + +  + R   I+K Y
Sbjct: 117 TGTPSLADLAGTLPHSGTFHPAPANRLDRNTSGIVLIPKDYPTQKQIAAAIRSHLIRKSY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++V G  K  +    +  L K+       ++V++   G   A   ++ + C       +
Sbjct: 177 WAIVAG--KITRGAKLHSRLTKN----PRANIVQEETDGQREAWLRYQPL-CSGDAASLI 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++  +GR+HQ+RV    +G PI+GD KY
Sbjct: 230 AIELGSGRSHQIRVQLAGIGHPIIGDPKY 258


>gi|83951260|ref|ZP_00959993.1| ribosomal large subunit pseudouridine synthase A [Roseovarius
           nubinhibens ISM]
 gi|83839159|gb|EAP78455.1| ribosomal large subunit pseudouridine synthase A [Roseovarius
           nubinhibens ISM]
          Length = 222

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/222 (29%), Positives = 107/222 (48%), Gaps = 31/222 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED ++ V NKP+G+    G G   H+   L + +++      L HRLD++TSG++V 
Sbjct: 21  VIHEDHEMLVVNKPSGLLSVPGKG--EHLADCLLARIEAAYPTALLVHRLDRDTSGVMVF 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW----LLKKSHIGGD 211
           A T  A +H+++ F  R  +K Y + V G  + K        I +W    L K  H  G 
Sbjct: 79  ALTPHAQRHMSKQFEKRIPKKTYVARVEGHLEPKTGVVDLPLIVDWPNRPLQKVCHETG- 137

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                         A++ ++V+     +   + + P TGR+HQLRVH L +G  I+GD  
Sbjct: 138 ------------RAALTEYRVLKARDGE-SRVRLSPKTGRSHQLRVHMLALGHVILGDPL 184

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y              +L LH+  + + HP+GG+ +Q  A  P
Sbjct: 185 YATGAAAE-----HPRLMLHSEELRIRHPDGGQGMQFRAKAP 221


>gi|168182364|ref|ZP_02617028.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
 gi|237794773|ref|YP_002862325.1| RluA family pseudouridine synthase [Clostridium botulinum Ba4 str.
           657]
 gi|182674479|gb|EDT86440.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
 gi|229262158|gb|ACQ53191.1| pseudouridine synthase, RluA family [Clostridium botulinum Ba4 str.
           657]
          Length = 317

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 73/277 (26%), Positives = 127/277 (45%), Gaps = 36/277 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  +E   RLD++ +     +    + K +R G+++V+ ++ K  N ++ G +V    
Sbjct: 3   IVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKNFLEEGDIVE--- 59

Query: 70  VINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIA 126
             N  +   K++ + +D+++ +T           YED  + +  K  G+ V      G  
Sbjct: 60  SFNVKSKGEKKKFVRIDNNLKIT-----------YEDENMVLVEKWPGVLVHSDKKEGEP 108

Query: 127 YHIDGFLKSWVDSKGQKPRLT--------HRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              D  L    D     P L         +RLD+ TSGI++  +   A + L E  R R+
Sbjct: 109 TLTDYVLSYLYDKGDYTPELEVTFTPAPCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRK 168

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY---AISHFKVIDC 235
           I+K Y SLV G  + K      ++ K        ++    NE   N    A++   +  C
Sbjct: 169 IEKYYSSLVKG--RIKDGVYEAYISKNEDTNMSKIY----NEPKPNTKKIAMNVKTIQTC 222

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  F ++E++  TGR+HQLR H  H+G PI+GD KY
Sbjct: 223 GS--FSFIEIELLTGRSHQLRAHLSHLGNPIIGDSKY 257


>gi|114569344|ref|YP_756024.1| ribosomal large subunit pseudouridine synthase A [Maricaulis maris
           MCS10]
 gi|114339806|gb|ABI65086.1| ribosomal large subunit pseudouridine synthase A [Maricaulis maris
           MCS10]
          Length = 223

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/206 (30%), Positives = 107/206 (51%), Gaps = 17/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  I V +KP+G+    G+         L++   ++    R+ HRLD +TSG++V+
Sbjct: 21  VIHADDHILVVDKPSGLLTVPGN--RPERADCLEARARAEFPTARIIHRLDMDTSGVIVL 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A T  A  H+ + F  R   K Y + V G    +   +   ++       D+ +  KQ  
Sbjct: 79  ALTTHAQAHIGKQFEKRMTSKSYVARVQGEMTGRSGRVDQPIIT------DWPNRPKQMI 132

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +++G N A++ ++V+D  A     + + P TGR+HQLRVH L +G PI+GD+ Y     
Sbjct: 133 CHDRGRN-AVTDWEVMD-IADGVTRVRLCPLTGRSHQLRVHMLFLGHPILGDNLYAP--P 188

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
              T+   ++L LHA+ +   HP+GG
Sbjct: 189 AALTA--SDRLCLHAQQLGFRHPDGG 212


>gi|295401808|ref|ZP_06811773.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294976175|gb|EFG51788.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 305

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/208 (31%), Positives = 106/208 (50%), Gaps = 24/208 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQET 154
           +L+ED  + + NK AGI +       +G   +   F   ++ ++G   K R  HRLD++T
Sbjct: 87  VLWEDEHLLIINKGAGIDIHPSEPSQTGTLANAVAF---YLQAQGILTKVRHIHRLDRDT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG ++ A+   A   L      R+I++ Y +LV GI K+K   I+      + IG D  H
Sbjct: 144 SGTILFAKHPLAGATLDRMLEKRQIKRTYVALVHGIVKHKSGTIS------APIGRDRHH 197

Query: 215 VVKQN-EKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             ++   K    A++H++V+  F  ++   +E+   TGRTHQ+RVH  ++G P+VGD  Y
Sbjct: 198 PTRRRVSKTGAKAVTHYRVLHTFPDEQTSLVELSLDTGRTHQIRVHMSYIGHPLVGDVLY 257

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
               K  F     ++  LHA  +   HP
Sbjct: 258 GG--KDTF-----HRQALHAVKLSFLHP 278


>gi|294781868|ref|ZP_06747200.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Fusobacterium sp. 1_1_41FAA]
 gi|294481679|gb|EFG29448.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Fusobacterium sp. 1_1_41FAA]
          Length = 318

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 78/296 (26%), Positives = 139/296 (46%), Gaps = 46/296 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALN 75
           E MRLD++            L+K++ +  V+++ K +  N R ++SG+ + I        
Sbjct: 17  EGMRLDKYLAEQIEEATRSYLEKLIDNSYVKINSKVINKNGRKLKSGEKIEIS------- 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
             I E++      N+   ++ +   +++E+    + NK   + V    G         + 
Sbjct: 70  --IPEEE------NIDIEAENIPLDIVFENDDFILVNKKYNMVVHPAYGNYNGTLVNALL 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y+ +    S V+    +P + HRLD++TSG+++VA+   A   L   F  + I K Y  +
Sbjct: 122 YYTNNL--SSVNG-NIRPGIIHRLDKDTSGLILVAKNNFAHAKLASMFTDKTIHKTYLCI 178

Query: 187 VWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           V G    +N +  I N L+ +       + VVK+N K    AIS+++V++   + +  +E
Sbjct: 179 VKGNFSDENLEGRIEN-LIGRDTKDRKKMAVVKENGK---LAISNYRVVEQ-VKDYSLVE 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------FKGNFTSPIQNKLY 289
           +   TGRTHQ+RVH   +  PI+GD  Y +            FK  F +P+ NK Y
Sbjct: 234 VLIETGRTHQIRVHMKSINHPILGDVIYGSEDKNIKRQMLHAFKLEFLNPLDNKEY 289


>gi|158520422|ref|YP_001528292.1| pseudouridine synthase [Desulfococcus oleovorans Hxd3]
 gi|158509248|gb|ABW66215.1| pseudouridine synthase [Desulfococcus oleovorans Hxd3]
          Length = 258

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 106/219 (48%), Gaps = 18/219 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +    KPAG+ VQG S     +    + W+  +  KP      + HRLD+  +
Sbjct: 15  VLYEDNHLLALYKPAGLLVQGDSTGDPTLLELGRCWLKIRYNKPGKVFLGMVHRLDRPVA 74

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++  RT  AA  ++  FR     K Y ++V G+    +  +AN + ++    G   H+
Sbjct: 75  GVVLFCRTSKAAGRISAQFRDGVTAKQYVAVVEGVIPENEGRLANHIFRR----GPTSHI 130

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +      +  A   F VID    +   +++   TGR HQ+RV   H+G P+VGD +Y A 
Sbjct: 131 IDVPTPKSREARLAFHVIDRTDSRTL-VKIDLETGRHHQIRVQFAHLGFPVVGDLRYGA- 188

Query: 276 FKGNFTSPIQNK-LYLHARYMDLPHPE-GGRLQITAPLP 312
                 +P+  + + L AR + + HP  G  L  T+  P
Sbjct: 189 -----PAPLPGRQIALLARRLTVTHPTLGHALTFTSSFP 222


>gi|323487164|ref|ZP_08092469.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323399516|gb|EGA91909.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 298

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/253 (27%), Positives = 122/253 (48%), Gaps = 31/253 (12%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSI-------LLYEDSKIYVFNKPAGISVQGGSGIAY 127
             ++KE  IL  SV L++ +   + I       +LYED  + V NK AG+ V    G   
Sbjct: 52  TRVLKEGNIL--SVRLSEETSSERIIPVPMELSVLYEDEDLMVINKAAGMPVHPSQG--- 106

Query: 128 HIDGFLKS----WVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + D  L +    +   KG+    R  +RLD++T+G+L++A+   +   L+     + I++
Sbjct: 107 NFDNTLANGLAWYFKEKGEAFVFRAVNRLDRDTTGLLLIAKNMLSGAILSSMVSEKTIRR 166

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G+ + +  CI   + +     G  +      E+G  YA + ++ +     K C
Sbjct: 167 EYRAIVSGLTEEEG-CICRPIARAE---GSTIERCVDPERG-EYACTRYRRLGYDRDKDC 221

Query: 242 -WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L +   TGRTHQ+RVH  ++G P++GD  Y  +++         +  LH+  +   HP
Sbjct: 222 SLLLITLDTGRTHQIRVHMKYIGHPLLGDFLYNPDYR------FIKRQSLHSCRLTFTHP 275

Query: 301 -EGGRLQITAPLP 312
             G  +  TAPLP
Sbjct: 276 LTGEAMDFTAPLP 288


>gi|23098304|ref|NP_691770.1| hypothetical protein OB0849 [Oceanobacillus iheyensis HTE831]
 gi|22776530|dbj|BAC12805.1| hypothetical conserved protein [Oceanobacillus iheyensis HTE831]
          Length = 303

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 75/276 (27%), Positives = 128/276 (46%), Gaps = 31/276 (11%)

Query: 36  NLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++ IL  GQV VD     K N  +  G  VRI          +K +  +   V      
Sbjct: 41  SVKSILTRGQVSVDDHIETKHNFMLNKGSTVRI----------LKNKAAIQQDV------ 84

Query: 95  DFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLD 151
            F+   ++YED  I V  K +G+ S+       +     L  +V  +    R+   HRLD
Sbjct: 85  -FVGMSIMYEDDDIIVIEKESGLLSIATEKERKHTALHQLMHYVKQQHPANRVYVVHRLD 143

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+     + L  +++    ++ Y +LV G    +K  I +WL K+S     
Sbjct: 144 KDTSGVMMFAKNERVKRKLQNNWKDIVKERTYVALVEGQVAKEKGYIVSWL-KESATRKM 202

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y   VK +      A + ++V+     ++  LE+Q  TGR +Q+RVH   +G P+VGD +
Sbjct: 203 YSSRVKND---GQRAATRYRVLQT-NNRYSLLELQLETGRKNQIRVHMEELGHPVVGDKR 258

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           Y     G+    +  +L LHA+ +   HP   +L +
Sbjct: 259 Y-----GSKGRSVIGRLGLHAKILSFYHPVTNKLML 289


>gi|28899917|ref|NP_799572.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|260363211|ref|ZP_05776080.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
 gi|260880498|ref|ZP_05892853.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|260898549|ref|ZP_05907045.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|28808200|dbj|BAC61405.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|308084943|gb|EFO34638.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|308092677|gb|EFO42372.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|308111932|gb|EFO49472.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
          Length = 559

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 73/207 (35%), Positives = 108/207 (52%), Gaps = 26/207 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V NKP+G+ SV G +            + D +G  P + HRLD  TSGILV
Sbjct: 358 IIYQDDAMVVVNKPSGLLSVPGKTIKDSAYTRIQAMFPDVEG--PFVIHRLDMATSGILV 415

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A T+ A + L + F  R +QK Y +L+ G+  N+ E   +  ++     GD     +Q 
Sbjct: 416 FALTKRANKSLQKQFMARGVQKRYMALLEGV-LNEPEGEISLPMR-----GDPDDRPRQL 469

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHKYC 273
              E G  +A +++++ID    +   + M P TGRTHQLRVH A HMG   P+VGD  Y 
Sbjct: 470 VCFEHG-KHAETYWQLIDVKDGR-SKVYMYPKTGRTHQLRVHSAHHMGLNMPMVGDGLYG 527

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
                       N+L+LHA  ++L HP
Sbjct: 528 EK---------ANRLHLHAEMLELDHP 545


>gi|323453124|gb|EGB08996.1| hypothetical protein AURANDRAFT_25466 [Aureococcus anophagefferens]
          Length = 361

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 67/237 (28%), Positives = 113/237 (47%), Gaps = 29/237 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDG---FLKSWVDSKGQKPRLTH 148
           +L +D+   V NK AG+      G         +A+   G   F ++       +P + H
Sbjct: 126 VLVDDASFLVVNKAAGMVTHPAPGARRGTLANAVAHRCGGGGVFAEAT-----PRPGIVH 180

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG +VVAR   A + L   F+ R + K+Y +++   P    +  A+ L+  + I
Sbjct: 181 RLDRYTSGAIVVARNARATRRLQAQFKARTVAKLYLAVLARPPPPPPDG-ADELVIDAPI 239

Query: 209 GGDYVHVVKQNE----KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           G    H  ++ +     G   A+S  +V+    ++ C  ++   TGRTHQ+RVH  H+G 
Sbjct: 240 G---RHPARREKMAVVPGGRPAVSRVRVLASDGRR-CVAQVAIDTGRTHQIRVHLAHVGS 295

Query: 265 PIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKT 318
           P++GD  Y           +   N+  LHA  +   HP+ G R+++TAP P  + + 
Sbjct: 296 PVLGDPVYGDAQANARAAAAFAANRTLLHAWRLAFDHPDSGARVEVTAPPPPDLARA 352


>gi|254475763|ref|ZP_05089149.1| ribosomal large subunit pseudouridine synthase A [Ruegeria sp. R11]
 gi|214030006|gb|EEB70841.1| ribosomal large subunit pseudouridine synthase A [Ruegeria sp. R11]
          Length = 217

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 63/206 (30%), Positives = 103/206 (50%), Gaps = 18/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D++I V NKP G+    G G   H+   L S V +   +  L HRLD++TSG+++ 
Sbjct: 16  ILYHDAEIVVVNKPHGLLSVPGRG--EHLADCLISRVQAVFPEALLVHRLDRDTSGVMIF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
             T  A +HL+  F  R  +K Y + V G  + +   +   L+       D+ +  +Q  
Sbjct: 74  GMTAHAQRHLSMQFEKRTTKKAYVARVHGRLEPRSGTVDLPLIV------DWPNRPRQMV 127

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +E G   A++ ++V   + +    + + P TGR+HQLRVH L +G  I+GD  Y     
Sbjct: 128 CHETG-KPAVTDWRVTK-YEEAATRVRLTPKTGRSHQLRVHMLALGHVILGDPIYAEGPA 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
            N       +L LH+  + + HP+ G
Sbjct: 186 RN-----HERLMLHSEELRVKHPDSG 206


>gi|187779918|ref|ZP_02996391.1| hypothetical protein CLOSPO_03514 [Clostridium sporogenes ATCC
           15579]
 gi|187773543|gb|EDU37345.1| hypothetical protein CLOSPO_03514 [Clostridium sporogenes ATCC
           15579]
          Length = 317

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 71/274 (25%), Positives = 123/274 (44%), Gaps = 30/274 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  +E   RLD++ +     +    + K +R G+++V+ K+ K  N ++ G +V    
Sbjct: 3   IVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGKKSKEKNFLEEGDIVE--- 59

Query: 70  VINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIA 126
             N  +   K++ + +D+++ +T           YED  + +  K  G+ V      G  
Sbjct: 60  SFNVKSKGEKKKFVRIDNNLKIT-----------YEDENMVLVEKWPGVLVHSDKKEGEP 108

Query: 127 YHIDGFLKSWVDSKGQKPRLT--------HRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              D  L    D     P L         +RLD+ TSGI++  +   + + L E  R R+
Sbjct: 109 TLTDYVLSYLYDKGDYTPELEVTFTPAPCNRLDRNTSGIVIFGKNYESLKTLNEMIRDRK 168

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I+K Y SLV G     K+ I    + K+    +   +  + +          K I     
Sbjct: 169 IEKYYSSLVKG---RIKDGIYEAYISKNQ-DTNMSKIYNEPKPNTKKIAMEVKTIQTCGS 224

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            F ++E++  TGR+HQLR H  H+G PI+GD KY
Sbjct: 225 -FSFIEIELLTGRSHQLRAHLSHLGNPIIGDSKY 257


>gi|332361173|gb|EGJ38977.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1056]
          Length = 295

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 114/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++      + Q+  +  RLD++TSG+
Sbjct: 78  VVYEDKHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKVIERFGDVYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLEHGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|315639323|ref|ZP_07894485.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
 gi|315480649|gb|EFU71291.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
          Length = 308

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 64/202 (31%), Positives = 102/202 (50%), Gaps = 11/202 (5%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DG 131
           N + K+ +IL   V L  + +  K + ++YE+ +  V  KP+G+ S   G   AY + D 
Sbjct: 47  NLVKKKNEILQGVVELIVYENAPKGVKIVYENEEFAVLEKPSGVLSHPNGRHCAYSLCDE 106

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             + W    G +  + HRLD+ETSG+++VA+T+ +       F  R IQK Y +L  G+ 
Sbjct: 107 IWELW----GMEACVVHRLDKETSGLILVAKTKNSQVEFKTMFEKREIQKEYLALTQGLI 162

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM-QPHTG 250
           K + E      L +++   D V    Q  +    A+S FK +  +      L + +P TG
Sbjct: 163 KEEFEVDLPMRLTQNY---DDVKTRMQICEDGKRALSFFKRVRFYPDLNASLVLCKPFTG 219

Query: 251 RTHQLRVHALHMGCPIVGDHKY 272
           R HQLR+H  H G  I+G+  Y
Sbjct: 220 RQHQLRLHLFHSGHQILGEPLY 241


>gi|296114348|ref|ZP_06833002.1| pseudouridine synthase [Gluconacetobacter hansenii ATCC 23769]
 gi|295979109|gb|EFG85833.1| pseudouridine synthase [Gluconacetobacter hansenii ATCC 23769]
          Length = 293

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 57/193 (29%), Positives = 89/193 (46%), Gaps = 8/193 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHI-DGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L       V +KP G+    G      + D F  + +      P L HRLD++TSG L+
Sbjct: 35  VLLRTRHFIVIDKPPGLPAHAGRAGGPSVEDAF--ALMSRHRNGPWLAHRLDRDTSGCLL 92

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK-- 217
           VA  + A     E F   R  K+YW++  G P      +   LL+++  G   + +    
Sbjct: 93  VALRKQALIAAQECFASGRTTKVYWAITHGHPTAGHGVVDAPLLRRAERGQWRMEITPDG 152

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           Q+ + A   ++   + D       WLE++  TGRTHQ RVH   +GCP++GD +Y     
Sbjct: 153 QDARTAWRCLARGHMPD--GSPASWLELRLETGRTHQARVHCAALGCPVMGDGQY-GRAD 209

Query: 278 GNFTSPIQNKLYL 290
           G     +  +LYL
Sbjct: 210 GKSLHLMSRELYL 222


>gi|166365046|ref|YP_001657319.1| ribosomal large subunit pseudouridine synthase D [Microcystis
           aeruginosa NIES-843]
 gi|166087419|dbj|BAG02127.1| ribosomal large subunit pseudouridine synthase D [Microcystis
           aeruginosa NIES-843]
          Length = 501

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 112/230 (48%), Gaps = 49/230 (21%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  I   NKPAG+ SV G    +   D  +  +   +G+     HRLD+ETSGIL+
Sbjct: 302 IIYEDEGIIAINKPAGLLSVAGRYQDSQ--DAVVNRF-RRQGKNLIPVHRLDRETSGILL 358

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSL---------------VWGIPKNKKECIANWLLK 204
           +A++    + L++ F+ R ++KIY ++               +WG P+N+     +W  +
Sbjct: 359 LAKSLDIYRCLSQQFQRREVEKIYEAILSEIIERESGIIDLPLWGNPQNRPYQTVDW--Q 416

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MG 263
           +      Y  VV    K  NY+                LE  P+TGRTHQ+RVH+   +G
Sbjct: 417 RGKASQTYFKVVG---KEGNYS---------------RLEFIPYTGRTHQIRVHSQQGLG 458

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
             I+GD  Y  N K +      ++L+LHA+ +   HP+   +L +  P P
Sbjct: 459 IGILGDRLY--NGKQS------DRLHLHAKQLSFRHPQTENKLDLIIPTP 500


>gi|53804068|ref|YP_114042.1| ribosomal large subunit pseudouridine synthase A [Methylococcus
           capsulatus str. Bath]
 gi|53757829|gb|AAU92120.1| ribosomal large subunit pseudouridine synthase A [Methylococcus
           capsulatus str. Bath]
          Length = 212

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 60/215 (27%), Positives = 107/215 (49%), Gaps = 10/215 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D+ + V +KP+G+    G G        L + V ++     + HRLD  TSG++V+
Sbjct: 4   VVHTDAALLVLSKPSGLLAVPGRG--QDKQDCLSARVRARYPDALVVHRLDMATSGLMVM 61

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQ 218
           AR  A  + L++SF  R + K Y +LV G+ +   E    W      +  D+ +  + K 
Sbjct: 62  ARGIAVQRILSQSFARREVLKRYEALVHGVLETPPETENGWSSIDLPLLSDWPNRPLQKV 121

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      +++ ++++         +E++P TGR+HQLRVH   +G P++GD  Y      
Sbjct: 122 DPLHGKPSLTRWRILG-HEDGATRVELEPVTGRSHQLRVHLAALGYPVLGDPLYGHEVAK 180

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +       +L LHAR +   HP  G  L+  +P+P
Sbjct: 181 SRA----GRLLLHARTLGFFHPVSGEWLEFESPVP 211


>gi|197334594|ref|YP_002155370.1| tRNA pseudouridine synthase C [Vibrio fischeri MJ11]
 gi|197316084|gb|ACH65531.1| tRNA pseudouridine synthase C [Vibrio fischeri MJ11]
          Length = 259

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 112/239 (46%), Gaps = 29/239 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y D  +   NKPAG+ V   S +  H   F +++  D  GQ     HRLD+ TSGIL 
Sbjct: 25  IVYRDEHLIAINKPAGMLVHR-SWLDKHETVFAMQTLRDQIGQHVFPLHRLDRPTSGILF 83

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A +   A  ++  F  R I+K Y ++V G  +       ++ LKK     D +   K +
Sbjct: 84  FALSSEIAAQVSPLFASREIKKTYHAIVRGWIEEADTL--DYPLKKE---LDKIADKKAS 138

Query: 220 -EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            E  A  AI+ +K +               ++C +E++PHTGR HQLR H  H+  PIVG
Sbjct: 139 QEVEAKEAITEYKPLAKVELPYSTGKFPTTRYCLMELKPHTGRKHQLRRHMAHLRHPIVG 198

Query: 269 DH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           D      K+   FK    S   ++L LHA  ++  HP  G   +   + A   +TW  L
Sbjct: 199 DTSHGDGKHNRLFKEKLDS---HRLLLHASELNFTHPITGENIV---IKADFDETWKKL 251


>gi|318057566|ref|ZP_07976289.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           SA3_actG]
 gi|318081471|ref|ZP_07988794.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           SA3_actF]
          Length = 313

 Score = 84.0 bits (206), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 81/315 (25%), Positives = 136/315 (43%), Gaps = 39/315 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  V+ + V +  E  R+D      +   +     ++   G+V+VD   V  + R++
Sbjct: 1   MSAIPEVRTLPVPDGLEGERVDAALSRMF-GFSRTKAAELAAGGKVQVDGSVVGKSERVR 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P+  A   I+ E                    ++++D  + V  KP G++ 
Sbjct: 60  GGAWLEVEMPLAAAPVQIVAEP--------------VEGMEIVHDDEDVVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +    + + G   R  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGQTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKNQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR+R + K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I
Sbjct: 166 FRVRTVDKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAEGKA---SVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----- 288
           + F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  +L     
Sbjct: 221 EAF-RAASLLDVKLETGRTHQIRVHMSAHRHPCVGDLTYGAD------PTLAKRLGLTRQ 273

Query: 289 YLHARYMDLPHPEGG 303
           +LHA  +   HP  G
Sbjct: 274 WLHAVRLGFTHPGTG 288


>gi|260771000|ref|ZP_05879929.1| ribosomal large subunit pseudouridine synthase A [Vibrio furnissii
           CIP 102972]
 gi|260614237|gb|EEX39427.1| ribosomal large subunit pseudouridine synthase A [Vibrio furnissii
           CIP 102972]
 gi|315179046|gb|ADT85960.1| ribosomal large subunit pseudouridine synthase A [Vibrio furnissii
           NCTC 11218]
          Length = 259

 Score = 84.0 bits (206), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 65/208 (31%), Positives = 100/208 (48%), Gaps = 27/208 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +++ED  I   NKP+G+ SV G   +A H D     W   + Q P +   HRLD  TSG+
Sbjct: 30  VVFEDDYILAVNKPSGLLSVPGR--LAEHHDSM---WSRLQAQYPEIQVVHRLDMSTSGL 84

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDY 212
           ++ A+ +     L + F+ R   KIY++ VWG+    +       I +W  +   +    
Sbjct: 85  MLFAKDKYMEAALKKQFQYRLTHKIYYARVWGVMAQDEGEIDLPLICDWPNRPKQM---- 140

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V  +  K +    + F+V+   A     + + P TGR+HQLRVH   +G PIVGD  Y
Sbjct: 141 --VCHETGKPSQ---TLFQVVKREAHTTV-VRLLPITGRSHQLRVHMQALGHPIVGDEFY 194

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
                 +FT    ++L LHA  +   HP
Sbjct: 195 APQEAIDFT----DRLALHAAELSFYHP 218


>gi|307702537|ref|ZP_07639490.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
 gi|307623883|gb|EFO02867.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
          Length = 278

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 60/209 (28%), Positives = 99/209 (47%), Gaps = 20/209 (9%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SD ++ +  Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD E
Sbjct: 65  SDLVQEV--YQDQHLIIVNKPEGMKTHGNQPGEIALLNHVSAYV---GQTCYVVHRLDME 119

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++ A+       L      + I + YW+L+ G  ++K+      L+ +  IG D  
Sbjct: 120 TSGLVLFAKNPFILPILNRLLEKKEIARDYWALIEGRVESKE------LVFRDKIGRDRH 173

Query: 214 HVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              K+  + K   YA +H   +  F  K   +  +  TGRTHQ+R+H  H   PI+GD  
Sbjct: 174 DRRKRIVDAKNGQYAETHISRLKQFPNKTTLVRCKLKTGRTHQIRIHLSHHKHPILGDPL 233

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y ++ K        ++L LHA  +   HP
Sbjct: 234 YNSSSK-------VSRLMLHAFRLSFTHP 255


>gi|331270027|ref|YP_004396519.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium botulinum BKT015925]
 gi|329126577|gb|AEB76522.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium botulinum BKT015925]
          Length = 302

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 82/315 (26%), Positives = 144/315 (45%), Gaps = 45/315 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE  +E +RL  + KN     +    +K  R G+++V+            G+ VR     
Sbjct: 12  VEIQDEEIRLSHYLKN-VAQCSSRFTRKAAREGRIKVN------------GENVR----- 53

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIY----VFNKPAGISVQGGSGIAY 127
             L++++K   I++  +N  +  D +   +  +         V NKP GI V        
Sbjct: 54  --LSYMLKNDDIVELQINRKEEQDIIPEKMDLDIIYEDDDIIVVNKPKGIVVHP---TKR 108

Query: 128 HIDGFLKSWV----DSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H++G L + V    + K +    RL +RLD +TSG++++A+   +   L+   +     K
Sbjct: 109 HLNGTLSNGVLYYFNDKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFVK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G        I   + +     G    V+  +E+G   +I+ FKV++ + +   
Sbjct: 169 KYLAIVHGNLNEDSGVIDKPIYRVGE--GTLKRVI--DERGQR-SITRFKVVEQY-KNAS 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+   TGRTHQ+RVH   +G PI GD  Y     G       ++  LHA  + +PHP+
Sbjct: 223 LVELTLETGRTHQIRVHLSSIGYPIYGDSLY-----GEEEPQYIDRQALHAYKLQIPHPK 277

Query: 302 GGR-LQITAPLPAHM 315
            G+ L++ + LP  M
Sbjct: 278 DGKILKLESDLPEDM 292


>gi|313159132|gb|EFR58507.1| pseudouridine synthase, RluA family [Alistipes sp. HGB5]
          Length = 362

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 76/312 (24%), Positives = 136/312 (43%), Gaps = 40/312 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV +  +  +RLD++        +   +Q    SG + V+ K  K + +++    ++I  
Sbjct: 34  VVADKGQAPLRLDKFLTVRMEKCSRNRIQAAADSGSILVNGKAAKSSYKVKPLDRIQI-- 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               + +  +E +I+  ++ L          + YED  + + NKPAG+ V  G G     
Sbjct: 92  ---VMPYPRREVEIIPENIPLE---------IPYEDDDLLIVNKPAGLVVHPGHGNYSGT 139

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH+             +  L HR+D+ TSG+LVVA+   +   L + F    I 
Sbjct: 140 LVNALTYHLRNL--PLFQEGDMRAGLVHRIDKNTSGLLVVAKNEQSHARLAKQFFDHTIG 197

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG  +  +  I    + +S      + V +    G  +A++H++V+  +    
Sbjct: 198 RRYVALVWGNFEEDEGTITGN-IGRSPRDRQKMFVFEDGSDG-KHAVTHWRVLKRYGY-V 254

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKL 288
             +E +  TGRTHQ+RVH    G P+  D +Y  +   KG   S           +  + 
Sbjct: 255 TLVECRLETGRTHQIRVHMSWQGHPLFNDERYGGDRILKGTTFSKYKQFIENCFAVMPRH 314

Query: 289 YLHARYMDLPHP 300
            LHA+ +   HP
Sbjct: 315 ALHAQSLGFVHP 326


>gi|257465425|ref|ZP_05629796.1| tRNA pseudouridine synthase C [Actinobacillus minor 202]
 gi|257451085|gb|EEV25128.1| tRNA pseudouridine synthase C [Actinobacillus minor 202]
          Length = 242

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 107/225 (47%), Gaps = 20/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V             +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYQDDDLIAINKPAGMLVHRSWLDKAETVFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A+ + E F   +++K Y ++V G  + K     ++ LK   +  D V      E
Sbjct: 65  ALNSDMARTMCELFENHQVKKGYLAVVRGYLEGKARV--DYPLK---VILDKVADKFSQE 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAITDYQGLATVEMPYPAGKFQTARYSLVELSPQTGRKHQLRRHLKHLFHPIMGDT 179

Query: 271 KYCANFKGNFTSPIQN---KLYLHARYMDLPHPEG-GRLQITAPL 311
           KY  +   N T   Q+   +L LH+ +M   HP+   +++I APL
Sbjct: 180 KY-GDLHQNRTLAEQSGVERLMLHSHFMQFQHPKTLQKIEIKAPL 223


>gi|189485617|ref|YP_001956558.1| pseudouridylate synthase [uncultured Termite group 1 bacterium
           phylotype Rs-D17]
 gi|170287576|dbj|BAG14097.1| pseudouridylate synthase [uncultured Termite group 1 bacterium
           phylotype Rs-D17]
          Length = 296

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 105/225 (46%), Gaps = 44/225 (19%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVD--SKGQ-KPRLTHRLDQETSGILVVARTRAA 166
           V NK +GI V    G   H+ G L + +   S G+  P L HRLD++TSG++V A+T  A
Sbjct: 89  VVNKRSGIVVHPSYG---HLSGTLLNALMGYSAGKYNPYLIHRLDKDTSGVIVFAKTEKA 145

Query: 167 AQHLTESFRMRRIQKIYWSLVWGI---------------PKNKKECIANWLLKKSHIGGD 211
              +++  + R ++KIY++ V G+               PKN+K    N L KK      
Sbjct: 146 KISISKQLQKRVVKKIYYAAVKGVIAENRGIIKAPLGRSPKNRKLVSVNPLAKK------ 199

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                         AI+ FKVI+     +  L+++  TGRTHQ+R H  ++  P++GD +
Sbjct: 200 -------------VAITEFKVIER-KDDYTLLKVRIITGRTHQIRSHMKYINHPVIGDKQ 245

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           Y     G        +  LHA  +   HP   + ++  A LP  M
Sbjct: 246 YGG--PGTIGLKRCERQMLHAHNITFTHPSTSKTVKFIAQLPNDM 288


>gi|170759830|ref|YP_001786858.1| RluA family pseudouridine synthase [Clostridium botulinum A3 str.
           Loch Maree]
 gi|169406819|gb|ACA55230.1| pseudouridine synthase, RluA family [Clostridium botulinum A3 str.
           Loch Maree]
          Length = 317

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 73/277 (26%), Positives = 127/277 (45%), Gaps = 36/277 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  +E   RLD++ +     +    + K +R G+++V+ ++ K  N ++ G +V    
Sbjct: 3   IVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKNFLEEGDIVE--- 59

Query: 70  VINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIA 126
             N  +   K++ + +D+++ +T           YED  + +  K  G+ V      G  
Sbjct: 60  SFNVKSKGEKKKFVRIDNNLKIT-----------YEDENMVLVEKWPGVLVHSDKKEGEP 108

Query: 127 YHIDGFLKSWVDSKGQKPRLT--------HRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              D  L    D     P L         +RLD+ TSGI++  +   A + L E  R R+
Sbjct: 109 TLTDYVLSYLYDKGDYTPELEVTFTPAPCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRK 168

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY---AISHFKVIDC 235
           I+K Y SLV G  + K      ++ K        ++    NE   N    A++   +  C
Sbjct: 169 IEKYYSSLVKG--RIKDGVYEAYISKNEDTNMSKIY----NEPKPNTKKIAMNVKTIQTC 222

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  F ++E++  TGR+HQLR H  H+G PI+GD KY
Sbjct: 223 GS--FSFIEIELLTGRSHQLRAHLSHLGNPIIGDSKY 257


>gi|16804283|ref|NP_465768.1| hypothetical protein lmo2244 [Listeria monocytogenes EGD-e]
 gi|224498988|ref|ZP_03667337.1| hypothetical protein LmonF1_04513 [Listeria monocytogenes Finland
           1988]
 gi|224500956|ref|ZP_03669263.1| hypothetical protein LmonFR_00305 [Listeria monocytogenes FSL
           R2-561]
 gi|254826867|ref|ZP_05231554.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL N3-165]
 gi|254831319|ref|ZP_05235974.1| hypothetical protein Lmon1_08172 [Listeria monocytogenes 10403S]
 gi|16411714|emb|CAD00322.1| lmo2244 [Listeria monocytogenes EGD-e]
 gi|258599247|gb|EEW12572.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL N3-165]
          Length = 289

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 66/217 (30%), Positives = 102/217 (47%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP  +        +Y  D     ++ +++  GQ       HRLDQ TS
Sbjct: 80  IIYEDDFLLVVNKPVDMKTHPND--SYETDTCANAVQYYLEKTGQDANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H KV++   +K   L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHVKVLENDNEKNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 253 -------SPRANRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|46908477|ref|YP_014866.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|47093359|ref|ZP_00231127.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|226224852|ref|YP_002758959.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes Clip81459]
 gi|254825192|ref|ZP_05230193.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
 gi|254931643|ref|ZP_05265002.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|254992053|ref|ZP_05274243.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J2-064]
 gi|46881748|gb|AAT05043.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Listeria monocytogenes serotype 4b str. F2365]
 gi|47018278|gb|EAL09043.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|225877314|emb|CAS06028.1| Putative ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes serotype 4b str. CLIP 80459]
 gi|293583198|gb|EFF95230.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|293594437|gb|EFG02198.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
 gi|328465825|gb|EGF37013.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes 1816]
 gi|328472136|gb|EGF43011.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes 220]
          Length = 289

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 66/217 (30%), Positives = 102/217 (47%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP  +        +Y  D     ++ +++  GQ       HRLDQ TS
Sbjct: 80  IIYEDDFLLVVNKPVDMKTHPND--SYETDTCANAVQYYLEKTGQDANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H KV++   +K   L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHVKVLENDNEKNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 253 -------SPRANRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|295394748|ref|ZP_06804963.1| ribosomal large subunit pseudouridine synthase D [Brevibacterium
           mcbrellneri ATCC 49030]
 gi|294972344|gb|EFG48204.1| ribosomal large subunit pseudouridine synthase D [Brevibacterium
           mcbrellneri ATCC 49030]
          Length = 308

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 76/279 (27%), Positives = 129/279 (46%), Gaps = 44/279 (15%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQV--VRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +  SG V VD  +V  + R+ +G    V +P     L+ + +    ++            
Sbjct: 34  MAESGDVEVDGVKVPKSMRVTTGARIDVTMPKPKEPLSIVAEPVPGMN------------ 81

Query: 98  KSILLYEDSKIYVFNKPAGISVQ---GGSGIAYHIDGFLKSW--VDSKGQKPR--LTHRL 150
              ++Y+D    V +KP G++     G SG    I G   +   + + G   R  + HRL
Sbjct: 82  ---VIYDDDAFVVVDKPVGVAAHAAAGWSGPTV-IGGLAAAGYQIATSGAAERQGIVHRL 137

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG++VVA+   A   L  +F+ R + K Y +LV G+P      I   + +  H   
Sbjct: 138 DVGTSGVMVVAKGEHAYSVLKRAFKNRTVDKTYHALVQGLPDPVVGTIEAPIGR--HPRK 195

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D ++ V+ + K   +A++H++V++ + +    +E++  TGRTHQ+RVH      P  GD 
Sbjct: 196 DGLYAVRTDGK---HAVTHYEVLEAY-RSASLVEVKLETGRTHQIRVHMSATKRPCCGDL 251

Query: 271 KYCANFKGNFTSPI------QNKLYLHARYMDLPHPEGG 303
            Y A+       P+       N+ +LHA  +   HPE G
Sbjct: 252 PYGAD-------PVLAQKLGLNRQWLHAVKLGFEHPETG 283


>gi|293604136|ref|ZP_06686544.1| ribosomal large subunit pseudouridine synthase D [Achromobacter
           piechaudii ATCC 43553]
 gi|292817361|gb|EFF76434.1| ribosomal large subunit pseudouridine synthase D [Achromobacter
           piechaudii ATCC 43553]
          Length = 343

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 87/337 (25%), Positives = 134/337 (39%), Gaps = 55/337 (16%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q V V +     RLD+      P  +   LQ  + SG V V+    K    +  G  +  
Sbjct: 40  QRVTVPSSTRADRLDKVLAGLLPDHSRSRLQGWIESGNVHVNGAPGKIRQTVGPGDQL-- 97

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                    ++  Q   D+     +  +F    ++ E +   V NKPAG+    G+G   
Sbjct: 98  ---------LVWAQPAPDARAFTPEPVEF---TVVDESADWIVVNKPAGLVTHPGAGNWS 145

Query: 126 AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + + +   +  + HRLD++TSG++VVAR   A  HL    + R + + Y 
Sbjct: 146 GTLLNGLLYRYPELAAVARAGIVHRLDKDTSGLMVVARNEKAQTHLVRQLQARSMGREYI 205

Query: 185 SLVWGIPKNKKECIANWLLKKSH----IGGD--------YVHVVKQNEKGANYAISHFKV 232
           +L  G           WL         IG D            V       NYA +    
Sbjct: 206 ALAHG-----------WLAAAGRVDRAIGRDPRVPIRMSVERPVAPKPAITNYAPARRGQ 254

Query: 233 IDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKL 288
           +D      +  C LE    TGRTHQ+RVH   +G P++ D  Y   N  G        + 
Sbjct: 255 VDPGGRVTEVVCRLE----TGRTHQIRVHMASLGHPLLADTIYGGKNIAG------ATRQ 304

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF 324
            LHAR +    P G G +Q  A +PA M    +++ +
Sbjct: 305 MLHARALHFDDPGGSGDVQFAAEVPADMALVQETIAW 341


>gi|284802691|ref|YP_003414556.1| hypothetical protein LM5578_2447 [Listeria monocytogenes 08-5578]
 gi|284995833|ref|YP_003417601.1| hypothetical protein LM5923_2398 [Listeria monocytogenes 08-5923]
 gi|284058253|gb|ADB69194.1| hypothetical protein LM5578_2447 [Listeria monocytogenes 08-5578]
 gi|284061300|gb|ADB72239.1| hypothetical protein LM5923_2398 [Listeria monocytogenes 08-5923]
          Length = 291

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 66/217 (30%), Positives = 102/217 (47%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP  +        +Y  D     ++ +++  GQ       HRLDQ TS
Sbjct: 82  IIYEDDFLLVVNKPVDMKTHPND--SYETDTCANAVQYYLEKTGQDANALAVHRLDQTTS 139

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 140 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 195

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H KV++   +K   L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 196 -RQISPYGQPAVTHVKVLENDNEKNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 254

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 255 -------SPRANRIMLHAEKLHLNHPFKGKEMNFSAP 284


>gi|293364538|ref|ZP_06611261.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           oralis ATCC 35037]
 gi|291316950|gb|EFE57380.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           oralis ATCC 35037]
          Length = 291

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 60/209 (28%), Positives = 99/209 (47%), Gaps = 20/209 (9%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SD ++ +  Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD E
Sbjct: 78  SDLVQEV--YQDQHLIIVNKPEGMKTHGNQPGEIALLNHVSAYV---GQTCYVVHRLDME 132

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++ A+       L      + I + YW+L+ G  ++K+      L+ +  IG D  
Sbjct: 133 TSGLVLFAKNPFILPILNRLLEKKEIARDYWALIEGRVESKE------LVFRDKIGRDRH 186

Query: 214 HVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              K+  + K   YA +H   +  F  K   +  +  TGRTHQ+R+H  H   PI+GD  
Sbjct: 187 DRRKRIVDAKNGQYAETHISRLKQFPNKTTLVRCKLKTGRTHQIRIHLSHHKHPILGDPL 246

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y ++ K        ++L LHA  +   HP
Sbjct: 247 YNSSSKV-------SRLMLHAFRLSFTHP 268


>gi|47096862|ref|ZP_00234442.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|254899054|ref|ZP_05258978.1| hypothetical protein LmonJ_04559 [Listeria monocytogenes J0161]
 gi|254912805|ref|ZP_05262817.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes J2818]
 gi|254937132|ref|ZP_05268829.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|47014781|gb|EAL05734.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|258609734|gb|EEW22342.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|293590800|gb|EFF99134.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes J2818]
          Length = 289

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 66/217 (30%), Positives = 102/217 (47%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP  +        +Y  D     ++ +++  GQ       HRLDQ TS
Sbjct: 80  IIYEDDFLLVVNKPVDMKTHPND--SYETDTCANAVQYYLEKTGQDTNALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H KV++   +K   L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHVKVLENDNEKNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 253 -------SPRANRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|152967132|ref|YP_001362916.1| pseudouridine synthase [Kineococcus radiotolerans SRS30216]
 gi|151361649|gb|ABS04652.1| pseudouridine synthase, RluA family [Kineococcus radiotolerans
           SRS30216]
          Length = 307

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 78/291 (26%), Positives = 134/291 (46%), Gaps = 29/291 (9%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           I  +G V VD + V  ++R+ +G    V +P    A   + +  +       LT   D  
Sbjct: 36  IAAAGHVLVDGRAVGKSDRLTAGAWLEVEVPDAPGAPTAVAERIE------GLTIVHDDD 89

Query: 98  KSILLYEDSKIYVFNKPA--GISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
             +++ +   +     P   G +V GG  G  Y I            ++  + HRLD  T
Sbjct: 90  DLVVVDKPVGVAAHPSPGWTGPTVVGGLMGAGYTI------ATSGSAERQGVVHRLDVGT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA++  A   L  +F+ R ++K+Y +LV G P   +  I   + +  H GG Y  
Sbjct: 144 SGLMVVAKSEHAYSALKRAFKERTVEKVYHALVQGHPDPLRGTIDAPIGR--HPGGTYKF 201

Query: 215 VVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            V    K    +++H++V++ F A   C + ++  TGRTHQ+RVH   +  P VGD  Y 
Sbjct: 202 AVTAEGK---PSVTHYEVLEAFRAAALCEVHLE--TGRTHQIRVHFSALRHPCVGDLNYG 256

Query: 274 ANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           A+      + +   + +LHA  +   HP  G+ ++ T+  P  +    + L
Sbjct: 257 ADP--TLAARLGLTRQWLHAVRLGFEHPGTGQAVEFTSSYPEDLATALERL 305


>gi|322386603|ref|ZP_08060228.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           cristatus ATCC 51100]
 gi|321269276|gb|EFX52211.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           cristatus ATCC 51100]
          Length = 296

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 63/201 (31%), Positives = 92/201 (45%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+   G       +   + S+V   GQ   + HRLD+ETSG ++ A
Sbjct: 84  LYQDEHLIIVNKPNGMKSHGNEPTEVALLNHVSSYV---GQTCYVVHRLDKETSGAILFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+L  G      +  +  ++ K  IG D     K+  +
Sbjct: 141 KNPFVLPILNRLLENKEISREYWALAQG------KFHSKTIVYKDKIGRDRHDRRKRLVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F      ++ Q  TGRTHQ+RVH  H G PIVGD  Y    +G 
Sbjct: 195 PKKGLYAETHVTRLKDFGNT-TLVKCQLKTGRTHQIRVHLAHHGHPIVGDPLYHPQPQG- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  + L HP
Sbjct: 253 -------RLMLHAHRLTLTHP 266


>gi|304407496|ref|ZP_07389148.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
 gi|304343447|gb|EFM09289.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
          Length = 308

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 111/217 (51%), Gaps = 18/217 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQK-P-RLTHRLDQETSGI 157
           +LYED  I V +KPAG+ V     G    +D      +  KG   P R  HRLDQETSG 
Sbjct: 87  VLYEDDSILVMHKPAGVPVHPSRPGERGTLDEAAARHMLKKGDPLPVRHIHRLDQETSGP 146

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ ++   A   L E+ R + I+++Y + V G     +  I       + IG D     +
Sbjct: 147 VLYSKNDLAQLRLDEAMRQKTIERVYLAFVQGKISKPRGVI------DAPIGRDRHQPAR 200

Query: 218 QNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +      ++A++ ++ ++ ++ K   + ++  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 201 RRVIANGDHAVTRYETMERYS-KATLVRIRLETGRTHQIRVHMSHLGHPLIGDSLY---- 255

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            G  T+ ++++  LH   +   HP  G  +++ +PLP
Sbjct: 256 -GGDTALLKHQ-ALHGEMLVFHHPLSGAPVKVFSPLP 290


>gi|227499268|ref|ZP_03929380.1| pseudouridylate synthase [Anaerococcus tetradius ATCC 35098]
 gi|227218677|gb|EEI83908.1| pseudouridylate synthase [Anaerococcus tetradius ATCC 35098]
          Length = 305

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 71/270 (26%), Positives = 136/270 (50%), Gaps = 24/270 (8%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R+D++  +    I    ++  ++   ++V+ K VK + ++  G  + I   + A+ 
Sbjct: 6   DEIIRIDKFISDELEEIAREKIKDFIKDKLIKVNNKAVKPSFKLSEGDEIFIDDSLFAIA 65

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA----YHIDG 131
            I  E   +D  V + ++ D+    ++ +DS + V   PAG  V G    A    Y  DG
Sbjct: 66  EIKAEN--IDLKV-VYENEDYA---VIDKDSDLIV--HPAGKIVTGTLVNALLYKYGYDG 117

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
              S +  +  +P + HRLD++T+G++++ +  A+ ++  + F  R++ K Y+++V+G  
Sbjct: 118 L--SHIGGE-DRPGIVHRLDKDTTGLILITKNNASYKYFKKMFETRKVDKYYYAIVFGNF 174

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQPHTG 250
             K   I  ++ +      D  +  K   + A   A+SH++V+      F  L ++  TG
Sbjct: 175 DKKTGTIETFMDR------DPNNRRKMAVRPAGRRAVSHYEVLRE-VDGFSLLRIKIETG 227

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           RTHQ+RVH  H+  P++GD  Y  N K  F
Sbjct: 228 RTHQIRVHMTHINHPLLGDPVY-GNVKHKF 256


>gi|153854758|ref|ZP_01995992.1| hypothetical protein DORLON_01990 [Dorea longicatena DSM 13814]
 gi|149752665|gb|EDM62596.1| hypothetical protein DORLON_01990 [Dorea longicatena DSM 13814]
          Length = 296

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 103/260 (39%), Gaps = 46/260 (17%)

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I    N          ++  S  LTK        +LYED  I V  KP GI+ Q  S
Sbjct: 6   IISISASANVCLQFFPLHDLISISFVLTKEKYMATLNILYEDPHILVCVKPHGIATQSKS 65

Query: 124 GIAYHIDGFLK------SWVDSKGQKPR---------------LTHRLDQETSGILVVAR 162
                +   +K      S    K   P+               + HRLDQ  +GILV A+
Sbjct: 66  IRYPDMVSLIKNHLAKASGTSGKSGAPKSIGSRTPGSAEPYLAVIHRLDQPVAGILVFAK 125

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           T AAA+ L +  + +   K Y +LV   P  ++  + ++++K +      +   K+N  G
Sbjct: 126 TPAAAKDLNKQLQNQGFGKYYRALVTNAPSEEEGTLEDYMVKDARTNTSRICSAKEN--G 183

Query: 223 ANYAISHFKVIDCFAQKF-----------------------CWLEMQPHTGRTHQLRVHA 259
           A  A  H+  +    + F                         LE+   TGR HQ+RV  
Sbjct: 184 AKIARLHYDTVPDHGRLFSTVSGSSSSVDVSLSSQSQECHETELEIHLDTGRHHQIRVQL 243

Query: 260 LHMGCPIVGDHKYCANFKGN 279
             +GCPIVGD KY     GN
Sbjct: 244 ASIGCPIVGDTKYNPELTGN 263


>gi|323496130|ref|ZP_08101190.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           sinaloensis DSM 21326]
 gi|323318874|gb|EGA71825.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           sinaloensis DSM 21326]
          Length = 245

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 64/212 (30%), Positives = 101/212 (47%), Gaps = 23/212 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ED  I V NKP+G+ SV G   +A H D      V +     ++ HRLD +TSG+++
Sbjct: 16  IVFEDEHILVANKPSGLLSVPGR--LAEHHDSLWSRLVAAYPDI-QVVHRLDMDTSGLML 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVH 214
           +A+ + A + L + F+ R   K+Y++ VWG P   +       I +W  +        V 
Sbjct: 73  LAKHKEAERSLKKQFQYRLTHKVYYARVWGHPAQPQGEVDLPLICDWPNRPRQ----KVC 128

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V        Y ++  +      +    + + P TGR+HQLRVH   +G PIVGD  Y  
Sbjct: 129 FVDGKPSTTLYQVAKRE------EHTSIVRLLPITGRSHQLRVHMQMLGHPIVGDEFYSE 182

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
                F+    ++L LHA  +   HP    LQ
Sbjct: 183 GEAFEFS----DRLALHAAELSFYHPASEVLQ 210


>gi|166710213|ref|ZP_02241420.1| Pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 238

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 110/236 (46%), Gaps = 26/236 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D  + V +KPAG+ V   S +A   D FL   +  +  KP  L HRLD+ TSG L+
Sbjct: 10  ILYQDDVLAVVDKPAGLMVHD-SKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLL 68

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R +A  L +      ++K Y ++  G P  ++     +++     GG    V K  
Sbjct: 69  LAFDRDSASALGKVLMAGEVEKNYLTVCRGWPAEEQ-----FIVDHDLDGGPGKPVKKP- 122

Query: 220 EKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 123 ------AVTHFRRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGD 176

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
             +       +F     +++ LHA  +  PHP +G R+++TAPL A   K     G
Sbjct: 177 TSHGDGRHNRSFRMLGIHRMLLHAERLAFPHPADGRRIRVTAPLDAEFTKACALFG 232


>gi|257784642|ref|YP_003179859.1| pseudouridine synthase, RluA family [Atopobium parvulum DSM 20469]
 gi|257473149|gb|ACV51268.1| pseudouridine synthase, RluA family [Atopobium parvulum DSM 20469]
          Length = 336

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 61/223 (27%), Positives = 105/223 (47%), Gaps = 24/223 (10%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS----------KGQ-KPRLTHRLD 151
           +ED  + V +K  G+      G   H+D  L + + +          +G+ +P + HRLD
Sbjct: 90  FEDQYLIVLSKQIGLVCHPSPG---HVDDTLANALVAHCGYEHLGMLQGEDRPGIVHRLD 146

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+++  ++  A + L +  R+R + + Y  LV G   +    I   + + +    D
Sbjct: 147 MDTSGLMLAVKSDEAQKALQDLIRLRVLDRRYIVLVHGYVAHDSGTIETGIARSTR---D 203

Query: 212 YVHVVKQNEKGANYAISHFKVIDCF-----AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + +   +  GA  AI+ F+ ++ F        +  LE   +TGRTHQ+RVH  H+G P+
Sbjct: 204 RLKMTVSDAPGAREAITTFRTLERFEAGRKGDGYSLLECHLYTGRTHQIRVHMRHIGHPV 263

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           VGD  Y    K    +   N+ +LH+  +   HP  G   I A
Sbjct: 264 VGDQLY--GKKDTSLNLGLNRQFLHSWRVQFEHPFTGENIIVA 304


>gi|47779342|gb|AAT38571.1| predicted ribosomal large subunit pseudouridine synthase D
           [uncultured gamma proteobacterium eBACHOT4E07]
          Length = 311

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 58/197 (29%), Positives = 100/197 (50%), Gaps = 14/197 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGI 157
           +++ED    + NKP+ + +  GSG       +G L  + + +K  +  + HRLD++TSGI
Sbjct: 81  VVHEDENFLIINKPSKLVIHPGSGCDSGTLANGLLFKYPELNKMPRAGIVHRLDKDTSGI 140

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VART     +     + R+++KIY ++V G      + I ++ + +  IG D  + +K
Sbjct: 141 LLVARTEKFRNYFVSLLQERKVKKIYKAVVVG------KIIGSFQINEP-IGRDKTNRIK 193

Query: 218 QNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + +     AIS  K+ +     +  +++   TGRTHQ+RVH  +   PI+GD  Y  N 
Sbjct: 194 MSIRSDGKEAISFVKLHESLGN-YSVVDVSIETGRTHQIRVHLANKKLPIIGDKTY--NS 250

Query: 277 KGNFTSPIQNKLYLHAR 293
            GN       +L    R
Sbjct: 251 AGNIAKETSQELTESIR 267


>gi|91793876|ref|YP_563527.1| pseudouridylate synthase [Shewanella denitrificans OS217]
 gi|91715878|gb|ABE55804.1| Pseudouridylate synthase [Shewanella denitrificans OS217]
          Length = 230

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 60/199 (30%), Positives = 104/199 (52%), Gaps = 14/199 (7%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y D  I V NKP+G+    G     +     +  +     +  L HRLD +TSGI++ AR
Sbjct: 31  YLDRDIIVINKPSGLLSNPGRAPETYDTAITR--LQRLYPETILIHRLDCDTSGIMIFAR 88

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            + A  +L   F+ R+ +K+Y + V G  +++   + N+ L    +   +  V++  +  
Sbjct: 89  NKKAESNLKTQFQNRQAKKVYIAEVSGCFEHQDGKV-NFPLGPDPMTPPFQQVIESGKP- 146

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++++++++  A     +E++PHTGRTHQLRVH   +G  I+GD      F G+ T 
Sbjct: 147 ---ALTYYRLLEHRAST-SLVELKPHTGRTHQLRVHMKALGHTIIGD-----EFYGDETV 197

Query: 283 -PIQNKLYLHARYMDLPHP 300
               ++L LHA+ + L HP
Sbjct: 198 IAASHRLNLHAQSLTLLHP 216


>gi|209693957|ref|YP_002261885.1| ribosomal large subunit pseudouridine synthase A [Aliivibrio
           salmonicida LFI1238]
 gi|208007908|emb|CAQ78038.1| ribosomal large subunit pseudouridine synthase A [Aliivibrio
           salmonicida LFI1238]
          Length = 244

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 108/216 (50%), Gaps = 22/216 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I   NKPAG+    G     H D  + S V ++    +L HRLD  TSG+++ 
Sbjct: 15  IVYQDEAILAVNKPAGLLSNPGRA-PEHYDS-VWSRVVAEFPDAQLVHRLDMSTSGLMIF 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE----CIANWLLKKSHIGGDYVHV 215
           A  + A +H+ + F+ R   K+Y++ VWG + K + +     I +W  +          V
Sbjct: 73  ALYKEAERHIKKQFQYRLTHKVYYARVWGNVEKVEGQIDLPLICDWPNRPRQ------KV 126

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             ++ K +    + ++VI    +K   + + P TGR+HQLRVH +  G  IVGD  Y + 
Sbjct: 127 CYEHGKSSQ---TGYEVIQV-EEKTTLVRLLPITGRSHQLRVHMMEEGHEIVGDEFYASK 182

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
               F+    ++L LH+  +   HPE  + + + AP
Sbjct: 183 EALAFS----DRLQLHSAELSFYHPETDKFISLFAP 214


>gi|332312732|gb|EGJ25827.1| Ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes str. Scott A]
          Length = 291

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 66/217 (30%), Positives = 102/217 (47%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP  +        +Y  D     ++ +++  GQ       HRLDQ TS
Sbjct: 82  IIYEDDFLLVVNKPVDMKTHPND--SYETDTCANAVQYYLEKTGQDANALAVHRLDQTTS 139

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 140 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 195

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H KV++   +K   L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 196 -RQISPYGQPAVTHVKVLENDNEKNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 254

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 255 -------SPRANRIMLHAEKLHLNHPFKGKEMNFSAP 284


>gi|152999592|ref|YP_001365273.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151364210|gb|ABS07210.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 574

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 119/245 (48%), Gaps = 25/245 (10%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++   + D+ + LT  ++     +LY+D  + + NKPA      G  I   +   +
Sbjct: 340 LGHMLEGLAVDDNPL-LTNPAEGKTLAILYQDDSMAIVNKPAEFLSVPGKEIEDSVYSRM 398

Query: 134 K-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           + ++  + G  P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ G+P 
Sbjct: 399 RQTFPHATG--PLIVHRLDMSTSGLMVIALTKEAHKQLQKQFIQRTVTKRYVALLAGMPA 456

Query: 193 --NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--IDCFAQKFCWLEMQPH 248
               K+   N  L       D    +  +E G   A +H+++  +D  A +   + + P 
Sbjct: 457 VMANKQATGNISLPLRGDLDDRPRQLVCHEFG-KAAETHWELSQLDEMA-RTARVYLYPK 514

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP---EG 302
           TGRTHQLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP   E 
Sbjct: 515 TGRTHQLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHPVTRER 565

Query: 303 GRLQI 307
            R Q+
Sbjct: 566 MRFQV 570


>gi|302880095|ref|YP_003848659.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
 gi|302582884|gb|ADL56895.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
          Length = 203

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 67/201 (33%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY D  + V NKPAG+    G G        L S V  K     + HRLD  TSG+LV A
Sbjct: 5   LYRDDWLLVVNKPAGLLSVPGRG--EDKQDCLSSRVQEKFPDALIVHRLDMATSGLLVFA 62

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQN 219
           R     + L+  F  R + K Y ++V G  +  +  I         IG D+    + K +
Sbjct: 63  RGIEMQRQLSAMFHNREVSKRYVAIVAGKLQPDEGEI------NLSIGADWNERPLRKID 116

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E     +++ ++V+   A     +E++P TGRTHQLRVH   +G PI+GD  Y     G 
Sbjct: 117 EATGKPSLTRYRVLSREADT-TRVELEPVTGRTHQLRVHMRAIGHPILGDALY-----GE 170

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
             S    +L LHA+ +   HP
Sbjct: 171 VAS--APRLLLHAQSLSFVHP 189


>gi|184201118|ref|YP_001855325.1| pseudouridine synthase RluD [Kocuria rhizophila DC2201]
 gi|183581348|dbj|BAG29819.1| pseudouridine synthase RluD [Kocuria rhizophila DC2201]
          Length = 325

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 114/229 (49%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           L++ +    V +KPAG++     G     + G L      V + G   R  + HRLD  T
Sbjct: 97  LVHVEPSYVVVDKPAGVAAHPSPGWKGPTVVGALAGAGISVATSGAPERQGIVHRLDVGT 156

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVAR   A   L  +F+ R + K+Y ++V GIP   K  I   + +  H G ++  
Sbjct: 157 SGLMVVAREEGAYSQLKRAFKERTVTKVYHAVVQGIPDPLKGTIDAPIGR--HPGHEWRF 214

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V   E G N +++H++V++ F  +   +E+   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 215 AVM--EDGRN-SVTHYEVLEAFG-RASLVEVHLETGRTHQIRVHFSALQYPCCGDLTYGA 270

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   +    +  + +LHA+ +    P  G+ ++  +P P  +    ++L
Sbjct: 271 DPALSAGLGL-TRQWLHAKRLGFTSPATGQHVEYESPYPTDLAYAVETL 318


>gi|153839865|ref|ZP_01992532.1| pseudouridylate synthase, 23S RNA-specific [Vibrio parahaemolyticus
           AQ3810]
 gi|149746612|gb|EDM57600.1| pseudouridylate synthase, 23S RNA-specific [Vibrio parahaemolyticus
           AQ3810]
          Length = 441

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 73/207 (35%), Positives = 108/207 (52%), Gaps = 26/207 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V NKP+G+ SV G +            + D +G  P + HRLD  TSGILV
Sbjct: 240 IIYQDDAMVVVNKPSGLLSVPGKTIKDSAYTRIQAMFPDVEG--PFVIHRLDMATSGILV 297

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A T+ A + L + F  R +QK Y +L+ G+  N+ E   +  ++     GD     +Q 
Sbjct: 298 FALTKRANKSLQKQFMARGVQKRYMALLEGV-LNEPEGEISLPMR-----GDPDDRPRQL 351

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHKYC 273
              E G  +A +++++ID    +   + M P TGRTHQLRVH A HMG   P+VGD  Y 
Sbjct: 352 VCFEHG-KHAETYWQLIDVKDGR-SKVYMYPKTGRTHQLRVHSAHHMGLNMPMVGDGLYG 409

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
                       N+L+LHA  ++L HP
Sbjct: 410 EK---------ANRLHLHAEMLELDHP 427


>gi|153835569|ref|ZP_01988236.1| ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           HY01]
 gi|148867844|gb|EDL67073.1| ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           HY01]
          Length = 250

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 69/212 (32%), Positives = 99/212 (46%), Gaps = 30/212 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           +++ED +I   NKP+G+ SV G   +A H D     W     Q P  ++ HRLD  TSG+
Sbjct: 16  VVFEDEQILAVNKPSGLLSVPGR--LAEHYDSM---WSRLTEQYPDIQVVHRLDMSTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE----CIANW----LLKKSHI 208
           +V+A+ + A   L + F+ R   KIY++ VWG I + + E     I +W    L K    
Sbjct: 71  MVLAKNKRAESALKKQFQYRLTHKIYYARVWGHIEQEEGEIDLPLICDWPNRPLQKVCFE 130

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            G     + Q  K   +       I         + + P TGR+HQLRVH   +G PIVG
Sbjct: 131 DGKPSKTLFQVAKREEHPDGSKTTI---------VRLLPITGRSHQLRVHMQALGHPIVG 181

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           D  Y       F+     +L LHA  +   HP
Sbjct: 182 DEFYATEEAKVFS----ERLELHAAELSFYHP 209


>gi|317476220|ref|ZP_07935471.1| RluA family pseudouridine synthase [Bacteroides eggerthii
           1_2_48FAA]
 gi|316907631|gb|EFV29334.1| RluA family pseudouridine synthase [Bacteroides eggerthii
           1_2_48FAA]
          Length = 303

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 66/226 (29%), Positives = 110/226 (48%), Gaps = 21/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 88  IVYEDAYIIVVEKMQGLLSVNTERQKERTAYTI---LNEYVQRSGRQHRVYIVHRLDRDT 144

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L +++      + Y ++V G  +N    + +WL  +      YV+
Sbjct: 145 SGLMMFAKDEKTQNTLRDNWHNIVTDRRYVAVVAGEMENNAGMVRSWLTDRKL----YVY 200

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++ G   A++H++ I   A  F  +E+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 201 SSPTDD-GGKEAVTHYRTIKR-ANGFSLVELVLETGRKNQIRVHMQDLGHPIIGDGRYGL 258

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
                  +PI N+L LHA  +   HP  G L Q   P P    K +
Sbjct: 259 ----EEVNPI-NRLALHAFKLCFHHPVTGELMQFETPYPGEFKKLF 299


>gi|261393344|emb|CAX50980.1| putative RNA pseudouridine synthase (RNA-uridine isomerase; RNA
           pseudouridylate synthase) [Neisseria meningitidis 8013]
          Length = 220

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 68/212 (32%), Positives = 103/212 (48%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 6   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 61

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R +A  L+  F  + I+K Y +L    P  K+  I   + +KS  G     + K  
Sbjct: 62  FALNRESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLT 115

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y     G 
Sbjct: 116 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLY-----GG 169

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
             S     ++L+A  +   + +  +++I APL
Sbjct: 170 TES---ETMFLYAWKIQFAY-QNRQIEIVAPL 197


>gi|168209672|ref|ZP_02635297.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
 gi|168213116|ref|ZP_02638741.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE
           str. F4969]
 gi|170712270|gb|EDT24452.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
 gi|170715381|gb|EDT27563.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE
           str. F4969]
          Length = 324

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 80/298 (26%), Positives = 133/298 (44%), Gaps = 30/298 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ + +   +    + K LR G +RV+ K+ K    +  G V+ I  
Sbjct: 3   IEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLDGDVIEI-- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYH 128
               L  ++ ++K      N  +  D     ++YED  + +  K  G+ V       A  
Sbjct: 61  --RYLQSVVTKEK---KKPNF-QMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAPT 114

Query: 129 IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI+   +     + L E  R R++
Sbjct: 115 LTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKV 174

Query: 180 QKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS-HFKVIDCFA 237
           +K Y +LV G I   K E    ++ K   +    V+     E+     I    KV+    
Sbjct: 175 KKYYCALVKGKIQPGKYEA---YISKDDELNKSTVY---DTERPDTKKIKMDVKVLQTNG 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             F  LE++  TGR+HQLR H  H+G PIVGD KY  N   +F    +NK  L  +++
Sbjct: 229 A-FSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSF---FENKFGLTYQFL 282


>gi|156975908|ref|YP_001446815.1| ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           ATCC BAA-1116]
 gi|156527502|gb|ABU72588.1| hypothetical protein VIBHAR_03674 [Vibrio harveyi ATCC BAA-1116]
          Length = 250

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 69/212 (32%), Positives = 100/212 (47%), Gaps = 30/212 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           +++ED +I   NKP+G+ SV G   +A H D     W     Q P  ++ HRLD  TSG+
Sbjct: 16  VVFEDEQILAVNKPSGLLSVPGR--LAEHYDSM---WSRLTEQYPDIQVVHRLDMCTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE----CIANW----LLKKSHI 208
           +V+A+ + A   L + F+ R   KIY++ VWG I + + E     I +W    L K    
Sbjct: 71  MVLAKNKRAESALKKQFQYRLTHKIYYARVWGHIEQEEGEIDLPLICDWPNRPLQKVCFE 130

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            G     + Q  K   ++      I         + + P TGR+HQLRVH   +G PIVG
Sbjct: 131 DGKPSKTLFQVAKREKHSDGSKTTI---------VRLLPITGRSHQLRVHMQALGHPIVG 181

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           D  Y       F+     +L LHA  +   HP
Sbjct: 182 DEFYATEEAKAFS----ERLELHAAELSFYHP 209


>gi|119944340|ref|YP_942020.1| pseudouridine synthase [Psychromonas ingrahamii 37]
 gi|119862944|gb|ABM02421.1| ribosomal large subunit pseudouridine synthase A [Psychromonas
           ingrahamii 37]
          Length = 222

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 70/224 (31%), Positives = 101/224 (45%), Gaps = 33/224 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGS-----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LY+D  I V NKP G+ SV G +      +A  I   L+ W ++      + HRLD  T
Sbjct: 16  ILYQDDDIVVLNKPYGLLSVPGRAKKNRDSLALRI---LRVWPNAS-----VVHRLDMAT 67

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-----ANWLLKKSHIG 209
           SG+L++   ++A  H+   F+ + I K Y++ V GI K     I      +W  +   I 
Sbjct: 68  SGLLILTMRKSAQSHIGRQFQQKIIDKTYYARVEGIIKEDNGVIDLPIRCDWENRPRQI- 126

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            D+        + +         + C         ++P TGRTHQLRVH   +G  IVGD
Sbjct: 127 VDFAEGKSSQTEWSVVKREKLTTLVC---------LKPLTGRTHQLRVHLQAIGHAIVGD 177

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
             Y   F G   SP   +L LHA  + L HP    R+    P P
Sbjct: 178 EFYSTEF-GKKLSP--QRLALHAASITLTHPSTQQRITFNCPPP 218


>gi|315504618|ref|YP_004083505.1| pseudouridine synthase, rlua family [Micromonospora sp. L5]
 gi|315411237|gb|ADU09354.1| pseudouridine synthase, RluA family [Micromonospora sp. L5]
          Length = 314

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 101/215 (46%), Gaps = 25/215 (11%)

Query: 101 LLYEDSKIYVFNKPAGIS------------VQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           ++Y D  I V +KP G++            + G +GI + I            ++  + H
Sbjct: 91  VVYADDDIVVVDKPVGVAAHPSPGWTGPTVIGGLAGIGHRIS------TSGAAERQGVVH 144

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  T+GI+ VA++  A   L  +F+ R ++K Y ++V G P   +  I   + +  H 
Sbjct: 145 RLDVGTTGIMAVAKSERAYTALKRAFKYREVEKRYHAVVQGHPDPLRGTIDAPIDRHPH- 203

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             DY   V     G   +I+H+  ++ F      L+++  TGRTHQ+RVH   M  P VG
Sbjct: 204 -HDYRWAVVS---GGKPSITHYDTLEAFPAA-SLLDVRLETGRTHQIRVHFSSMRHPCVG 258

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           D  Y A+   +    +  + +LHAR +   HP  G
Sbjct: 259 DLTYGADPTLSARLGLSRQ-WLHARSLSFAHPGTG 292


>gi|325678153|ref|ZP_08157783.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
 gi|324110158|gb|EGC04344.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
          Length = 276

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 84/281 (29%), Positives = 122/281 (43%), Gaps = 59/281 (20%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           L K+   G + +D   V+    + +GQ V++            EQ   D +  L      
Sbjct: 34  LTKLKLCGGITLDGDAVRVTVTVCTGQKVQL---------CEPEQSCPDPNPEL------ 78

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETS 155
            K  +LYEDS + VF+KPA + V     I +  D    ++    KG   R  +RLD++T+
Sbjct: 79  -KVPVLYEDSDVIVFDKPANMPVH--ESINHRGDTLANAFAQRCKGMTFRAVNRLDRDTA 135

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK----KECIANWLLKKSHIGGD 211
           G + VA+TR AA  L  S     I K+Y  L   IP  K    + C      ++S I   
Sbjct: 136 GCVCVAKTRFAANALQGS-----ISKVYMGL---IPPTKLSGGRVCAPIARERESVI--- 184

Query: 212 YVHVVKQNEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +  V+ + K   +A + ++V     DC   KF        TGRTHQ+RVH  H+G P++
Sbjct: 185 -LRCVRADGK---FAATCWQVTERRDDCALVKFIL-----ETGRTHQIRVHMAHIGLPLI 235

Query: 268 GDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           GD  Y   C   KG           L    +    PE GRL
Sbjct: 236 GDELYGGDCTKRKGQ---------ALMCGEITFVSPENGRL 267


>gi|261251312|ref|ZP_05943886.1| pseudouridylate synthase LSU rRNA-specific [Vibrio orientalis CIP
           102891]
 gi|260938185|gb|EEX94173.1| pseudouridylate synthase LSU rRNA-specific [Vibrio orientalis CIP
           102891]
          Length = 559

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 65/208 (31%), Positives = 102/208 (49%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + V NKP+G+ SV G +          + + D +G  P + HRLD  TSG+LV
Sbjct: 358 ILFEDESMVVVNKPSGLLSVPGKTITDSAYTRLQQRYPDVEG--PFVIHRLDMATSGLLV 415

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A T+ A + L + F  R ++K Y +L+ G  +  +  I N  ++   +      V  ++
Sbjct: 416 FALTKRANKSLQKQFISRSVKKRYVALLEGSVEETQGDI-NLPMRGDPVDRPRQLVCYEH 474

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANF 276
            K A    +H++ I     +   L + P TGRTHQLRVH  H   +  P+VGD  Y    
Sbjct: 475 GKPAE---THWEAISTIDNR-TKLYLYPKTGRTHQLRVHCAHHLGLNIPMVGDTLYGEK- 529

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                    ++L+LHA  ++  HP  G 
Sbjct: 530 --------ADRLHLHAERLEFDHPYSGE 549


>gi|257452410|ref|ZP_05617709.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|317058953|ref|ZP_07923438.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|313684629|gb|EFS21464.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
          Length = 318

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 79/302 (26%), Positives = 141/302 (46%), Gaps = 35/302 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVR 66
           +Y V E D+   RLD + K   P      L+K++  G V  ++K +  N + ++  +V++
Sbjct: 9   EYQVGEEDQ-GKRLDLFLKEQLPEATRSYLEKLITEGYVLCNEKVITKNGKKLKGKEVIQ 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +         I+ E   LD               ++YED  + V NK A + V    G  
Sbjct: 68  LAIPEEEEMEIVAENIPLD---------------IVYEDKYLLVVNKQANMVVHPALGNY 112

Query: 125 IAYHIDGFL----KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  L    ++  D  G  +P + HRLD++T+G+++VA+       L   F+ + I
Sbjct: 113 SGTLVNALLYYCKENLSDMNGVIRPGIVHRLDKDTTGLIIVAKNNQVHSKLALMFQEKTI 172

Query: 180 QKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           +K Y ++V G   + +KE     L+ +       + V +   K    AIS+++V+     
Sbjct: 173 RKTYVAIVKGRFSEERKEGRLETLITRDPKDRKKMTVSQIQGKK---AISNYRVL-LDGD 228

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           K   +E++  TGRTHQ+RVH  ++  PI+GD  Y     G   +  + ++ LHA  ++  
Sbjct: 229 KHSLVEVKIETGRTHQIRVHMKYLNHPILGDIVY-----GQEDTKCKRQM-LHAYRLEFI 282

Query: 299 HP 300
           HP
Sbjct: 283 HP 284


>gi|152981434|ref|YP_001352926.1| pseudouridylate synthases, 23S RNA-specific [Janthinobacterium sp.
           Marseille]
 gi|151281511|gb|ABR89921.1| Pseudouridylate synthases, 23S RNA-specific [Janthinobacterium sp.
           Marseille]
          Length = 223

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 62/214 (28%), Positives = 102/214 (47%), Gaps = 12/214 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I + NKP+G+    G     ++D      V    Q   + HRLD  TSG+LVV
Sbjct: 19  IIYQDEAILLINKPSGLLTLSGKN-PLNLDSVHHRLVQQFPQA-LMIHRLDLGTSGLLVV 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +A A ++   F++R + K Y +++ G        I    + K  +    + +   + 
Sbjct: 77  ALNKAVAANINRQFQLRTVAKTYQAVLAGQVAEDHGKI-TLPIAKDPLNFPKLKICLASG 135

Query: 221 KGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           K A+   SH++V+D         +   PHTGRTHQLR+H+  +G PI+G    C  +   
Sbjct: 136 KAAS---SHYEVLDRQVDADTTRVLFTPHTGRTHQLRIHSAGIGHPILG----CDLYGTA 188

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            +     +L LHA  ++  HP  G R +  +  P
Sbjct: 189 ESEQGAERLLLHATTLEFDHPLSGARFRGVSACP 222


>gi|297183963|gb|ADI20083.1| pseudouridylate synthases, 23S RNA-specific [uncultured alpha
           proteobacterium EB080_L06A09]
          Length = 217

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 63/207 (30%), Positives = 103/207 (49%), Gaps = 17/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           +LY D  + V NKP+G+    G  + +     L+     K Q P   L HRLD +TSGI+
Sbjct: 15  ILYIDEDVLVVNKPSGLLSVPGKELKHRDSMELRV----KAQYPNSFLVHRLDMDTSGIM 70

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A  +   + L   F  R ++K+Y + V+G  K +   I   L+    +      + K 
Sbjct: 71  IFALNKNTQRLLNMQFEKRMVKKLYEARVFGNMKARNGSINLPLI----VDWPNRPMQKV 126

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    A++H++V+    +    +E+ P TGRTHQLRVH   +G  I+GD      F G
Sbjct: 127 DIENGKSALTHWRVLKK-EKNESRVELMPETGRTHQLRVHMKSLGHTILGDR-----FYG 180

Query: 279 NFTS-PIQNKLYLHARYMDLPHPEGGR 304
           N     + +KL LHA+ + + HP+  +
Sbjct: 181 NAMEISLADKLQLHAKRLIIIHPKSDK 207


>gi|228964349|ref|ZP_04125466.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228795333|gb|EEM42823.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
          Length = 307

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 69/228 (30%), Positives = 112/228 (49%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+      +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAEKGGNRTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y    K        +   LHA  ++  HP     +++  P P  +
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPTKL 295


>gi|168217835|ref|ZP_02643460.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
 gi|182380127|gb|EDT77606.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
          Length = 324

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 80/298 (26%), Positives = 133/298 (44%), Gaps = 30/298 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ + +   +    + K LR G +RV+ K+ K    +  G V+ I  
Sbjct: 3   IEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLEGDVIEI-- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYH 128
               L  ++ ++K      N  +  D     ++YED  + +  K  G+ V       A  
Sbjct: 61  --RYLQSVVTKEK---KKPNF-QMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAPT 114

Query: 129 IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI+   +     + L E  R R++
Sbjct: 115 LTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKV 174

Query: 180 QKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS-HFKVIDCFA 237
           +K Y +LV G I   K E    ++ K   +    V+     E+     I    KV+    
Sbjct: 175 KKYYCALVKGKIQPGKYEA---YISKDDELNKSTVY---DTERPDTKKIKMDVKVLQTNG 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             F  LE++  TGR+HQLR H  H+G PIVGD KY  N   +F    +NK  L  +++
Sbjct: 229 A-FSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSF---FENKFGLTYQFL 282


>gi|149277745|ref|ZP_01883885.1| pseudouridylate synthase [Pedobacter sp. BAL39]
 gi|149231433|gb|EDM36812.1| pseudouridylate synthase [Pedobacter sp. BAL39]
          Length = 240

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 108/245 (44%), Gaps = 31/245 (12%)

Query: 97  LKSILLYEDSKIYVFNKP---AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            K I+L+E+    V NKP   A +  +GGSG   +I    K +        ++ HRLD+E
Sbjct: 6   FKDIILFENDDYIVVNKPPFVASLDERGGSG-EVNILRLAKQY----SPDAQVCHRLDKE 60

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG +++A+T  A +++   F  R+I K Y ++V G      +   N L     I  D  
Sbjct: 61  TSGAIIIAKTPEAYRNVAIQFEKRKINKTYHAIVDG------QFSFNDLFIDLPILNDGN 114

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V  + K    A + F  I  + + +  +E +P TGR HQ+R+H       I GD  Y 
Sbjct: 115 KSVTIDRKEGKRAETIFNSIKNY-RHYTLVECKPITGRMHQIRIHLATQRAAIAGDDMYR 173

Query: 274 AN-------------FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP---AHMVK 317
                           K +   PI  +  LHAR++     +G  + I AP P   A ++K
Sbjct: 174 GKPVYLSSMKKGYRISKDDEEQPIMKRFALHARHLVFKGTDGQDIVIEAPYPKDFATLLK 233

Query: 318 TWDSL 322
             D  
Sbjct: 234 LLDKF 238


>gi|21241018|ref|NP_640600.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21106308|gb|AAM35136.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 244

 Score = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 112/238 (47%), Gaps = 26/238 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D  + V +KPAG+ V   S +A   D FL   +  +  KP  L HRLD+ TSG L+
Sbjct: 10  ILYQDDVLAVVDKPAGLMVHD-SKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLL 68

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R +A  L ++     ++K Y ++  G P  ++     +++     GG    V K  
Sbjct: 69  LAFDRDSASALGKALMAGEVEKQYLTVCRGWPAEER-----FIVDHDLDGGPGKPVKKP- 122

Query: 220 EKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +               ++  L  QP TGR  Q+R H  H+   +VGD
Sbjct: 123 ------AVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMVGD 176

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
             +       +F     +++ LHA  ++ PHP +G R+ +TAPL     K     G++
Sbjct: 177 TSHGDGRHNRSFRMLGIHRMLLHAERLEFPHPADGRRIGVTAPLDVEFSKACALFGWE 234


>gi|323692319|ref|ZP_08106558.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
 gi|323503644|gb|EGB19467.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
          Length = 298

 Score = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 70/253 (27%), Positives = 122/253 (48%), Gaps = 31/253 (12%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSI-------LLYEDSKIYVFNKPAGISVQGGSGIAY 127
             ++KE  IL  SV L++ +   + I       +LYED  + V NK AG+ V    G   
Sbjct: 52  TRVLKEGNIL--SVRLSEETSSERIIPVPMELSVLYEDEDLMVINKAAGMPVHPSQG--- 106

Query: 128 HIDGFLKS----WVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + D  L +    +   KG+    R  +RLD++T+G+L++A+   +   L+     + I++
Sbjct: 107 NFDNTLANGLAWYFKEKGEAFVFRAVNRLDRDTTGLLLIAKNMLSGAILSSMVSEKTIRR 166

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G+ + +  CI   + +     G  +      E+G  YA + ++ +     K C
Sbjct: 167 EYRAIVSGLTEEEG-CICRPIARAE---GSTIERCVDPERG-EYASTRYRRLGYDRDKDC 221

Query: 242 -WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L +   TGRTHQ+RVH  ++G P++GD  Y  +++         +  LH+  +   HP
Sbjct: 222 SLLLITLDTGRTHQIRVHMKYIGHPLLGDFLYNPDYR------FIKRQSLHSCRLTFTHP 275

Query: 301 -EGGRLQITAPLP 312
             G  +  TAPLP
Sbjct: 276 LTGEAMDFTAPLP 288


>gi|311279889|ref|YP_003942120.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308749084|gb|ADO48836.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 232

 Score = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 99/218 (45%), Gaps = 30/218 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +L++D+++ + NKPAG+    G        + Y +                L HRLD  T
Sbjct: 19  ILWQDAQLVIINKPAGLLSLSGKNPQNLDSVHYRLVKLFPGCA--------LVHRLDFGT 70

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVAR +A    L + F  R + K+Y +L+ G    + E   +  + K       + 
Sbjct: 71  SGLIVVARDKAVNAALCQQFSQRAVSKVYTALLCGH-LEENEGTVDAPIAKDPALFPRMS 129

Query: 215 VVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPI 266
           +   + K A    S F+V++ F Q+           + + P TGRTHQLR+H  H+G PI
Sbjct: 130 ICATHGKPAR---SRFQVVERFTQRLEDGRELPLTRVMLTPQTGRTHQLRIHCQHLGHPI 186

Query: 267 VGDHKYCANF-KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +G   Y      G   +P   +L LHA  +   HP  G
Sbjct: 187 LGCDLYGGLLPPGTGRAP---RLMLHASELHFTHPASG 221


>gi|255522642|ref|ZP_05389879.1| hypothetical protein LmonocFSL_15771 [Listeria monocytogenes FSL
           J1-175]
          Length = 279

 Score = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 75/279 (26%), Positives = 132/279 (47%), Gaps = 50/279 (17%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQV----VRIPPVINALNHIIKEQKILDSSVNLTK 92
           +Q +L++G + V+ +  K N ++Q G      VR P          +E ++L   + L  
Sbjct: 32  IQLMLKNGDITVNGELAKPNYKVQVGDEIHYEVREP----------EELEVLAEDIPLD- 80

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQK 143
                   + +ED  + V NKP G+ V   +G A         +H D    S ++ K  +
Sbjct: 81  --------IYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL--SGINGK-IR 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    +
Sbjct: 130 PGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPI 188

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++      + VV+  ++    A +HF+V++     +  +  +  TGRTHQ+RVH  ++G
Sbjct: 189 GRAKEDRQKMAVVRDGKE----ARTHFEVLERLP-GYTLINCKLDTGRTHQIRVHLKYIG 243

Query: 264 CPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHP 300
            P+ GD KY      KGN         +LHA  +   HP
Sbjct: 244 HPLAGDPKYGPKNTIKGNGQ-------FLHAAKLGFDHP 275


>gi|262376261|ref|ZP_06069491.1| dual specificity pseudouridine synthase for 23S rRNA and tRNA-Phe
           modification [Acinetobacter lwoffii SH145]
 gi|262308862|gb|EEY89995.1| dual specificity pseudouridine synthase for 23S rRNA and tRNA-Phe
           modification [Acinetobacter lwoffii SH145]
          Length = 214

 Score = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 105/227 (46%), Gaps = 23/227 (10%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           S+FL   L++ D    V +KPAG+    G       D  +   V  +  K  L HRLD++
Sbjct: 2   SNFLTEHLIHRDDDFMVIHKPAGLLTVPGKTEDLQ-DCLINRLVKLE-PKTLLIHRLDRD 59

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS----HIG 209
           TSGIL    T+   + ++  F+ R+  K Y ++V G  + +       +   S    HI 
Sbjct: 60  TSGILAFGLTKWGQKTISRQFQERQTDKTYQAVVAGTLEGEGTIEVPVVYDPSRPPLHIA 119

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               H           AI+H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PI
Sbjct: 120 DPAHH---------KPAITHWQAIEHFNIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPI 170

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
           +GD  Y    +   +S    +L LHA  +   HP+  +L +   P P
Sbjct: 171 IGDTLYATPEQQQLSS----RLCLHAERLSFYHPQTEQLVEFYCPAP 213


>gi|188534848|ref|YP_001908645.1| tRNA pseudouridine synthase C [Erwinia tasmaniensis Et1/99]
 gi|188029890|emb|CAO97774.1| tRNA pseudouridine synthase C [Erwinia tasmaniensis Et1/99]
          Length = 255

 Score = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/214 (28%), Positives = 104/214 (48%), Gaps = 20/214 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  +   NKP+G+ V   S +  H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 4   IIYQDRWLVAVNKPSGMLVHR-SWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A +   A+ L++ F + ++QK Y ++V G     +        +   I   +     Q 
Sbjct: 63  MALSSDVARLLSQQFELHQLQKTYHAVVRGWLAGAETLDYPLTEELDKIADKF----SQP 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           EK    A++H++ I               ++  +EM P +GR HQLR H  H+  PI+GD
Sbjct: 119 EKAPQPAVTHWRGIATAELPVPVGRYETSRYSLVEMLPESGRKHQLRRHMTHLRHPIIGD 178

Query: 270 HKYCANFKGNFTSPI---QNKLYLHARYMDLPHP 300
             +  + K N ++      ++L LHA  + L HP
Sbjct: 179 SAH-GDLKQNRSAAANFGMDRLMLHASELSLTHP 211


>gi|91217548|ref|ZP_01254506.1| ribosomal large subunit pseudouridine synthase D [Psychroflexus
           torquis ATCC 700755]
 gi|91184228|gb|EAS70613.1| ribosomal large subunit pseudouridine synthase D [Psychroflexus
           torquis ATCC 700755]
          Length = 222

 Score = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 56/178 (31%), Positives = 92/178 (51%), Gaps = 7/178 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +L E++   V NK AG+  +        ++  +   +  K +KP +   HRLD+ TSG+L
Sbjct: 6   VLQENNDYIVVNKMAGLISEKSPYENLTVENQVLHHLLKKKRKPYIGVIHRLDRVTSGVL 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+ ++      E F  R++QK Y ++V   P   K+ + N+L+K +        +V  
Sbjct: 66  VFAKKKSILVGFNELFSGRKVQKTYLAIVQKKPLKSKKTLTNFLVKNNL--EKRADIVSL 123

Query: 219 NEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             K +   I  ++VID     F + LE++P TGR HQ+R    HM  PI+GD KY ++
Sbjct: 124 KSKESLKCILSYQVID--ENNFGYLLEIKPKTGRFHQIRAQLAHMELPIIGDEKYGSD 179


>gi|19553337|ref|NP_601339.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glutamicum ATCC 13032]
 gi|62390974|ref|YP_226376.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           glutamicum ATCC 13032]
 gi|145296099|ref|YP_001138920.1| hypothetical protein cgR_2020 [Corynebacterium glutamicum R]
 gi|21324908|dbj|BAB99531.1| Pseudouridylate synthases, 23S RNA-specific [Corynebacterium
           glutamicum ATCC 13032]
 gi|41326313|emb|CAF20475.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE D [Corynebacterium
           glutamicum ATCC 13032]
 gi|140846019|dbj|BAF55018.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 310

 Score = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 104/234 (44%), Gaps = 24/234 (10%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LY D  +   NKP G++       +G + +        +       ++  +  RLD  T
Sbjct: 86  ILYSDDDVIAVNKPVGVAAHPTVGWEGPTVVGGLAAAGFRISTSGPPERKGIVQRLDVGT 145

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA +      L  +FR R + K Y +LV G P      I   + +    G  +  
Sbjct: 146 SGVMVVAASERGYTVLKRAFRDRTVDKTYHALVQGHPDPLTGTIEAPIGRHPSAGWRFAV 205

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH--ALHMGC---PIVGD 269
             +       +A++H++ ++ F Q+   L++   TGRTHQ+RVH  ALH  C   P+ G 
Sbjct: 206 TTE-----GKHAVTHYETLEAF-QEATLLKIHLETGRTHQIRVHFSALHHPCCGDPMYGS 259

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
               +   G       N+ +LHA  +   HP  GR ++I +P P  +    D L
Sbjct: 260 DPALSERLG------LNRQWLHAVSLGFNHPADGRWMEIVSPYPTDLQHALDVL 307


>gi|302868912|ref|YP_003837549.1| RluA family pseudouridine synthase [Micromonospora aurantiaca ATCC
           27029]
 gi|302571771|gb|ADL47973.1| pseudouridine synthase, RluA family [Micromonospora aurantiaca ATCC
           27029]
          Length = 314

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 101/215 (46%), Gaps = 25/215 (11%)

Query: 101 LLYEDSKIYVFNKPAGIS------------VQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           ++Y D  I V +KP G++            + G +GI + I            ++  + H
Sbjct: 91  VVYADDDIVVVDKPVGVAAHPSPGWTGPTVIGGLAGIGHRIS------TSGAAERQGVVH 144

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  T+GI+ VA++  A   L  +F+ R ++K Y ++V G P   +  I   + +  H 
Sbjct: 145 RLDVGTTGIMAVAKSERAYTALKRAFKYREVEKRYHAVVQGHPDPLRGTIDAPIDRHPHH 204

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             DY   V     G   +I+H+  ++ F      L+++  TGRTHQ+RVH   M  P VG
Sbjct: 205 --DYRWAVVS---GGKPSITHYDTLEAFPAA-SLLDVRLETGRTHQIRVHFSSMRHPCVG 258

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           D  Y A+   +    +  + +LHAR +   HP  G
Sbjct: 259 DLTYGADPTLSARLGLSRQ-WLHARSLSFAHPGTG 292


>gi|238751458|ref|ZP_04612950.1| tRNA pseudouridine synthase C [Yersinia rohdei ATCC 43380]
 gi|238710325|gb|EEQ02551.1| tRNA pseudouridine synthase C [Yersinia rohdei ATCC 43380]
          Length = 257

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 101/233 (43%), Gaps = 23/233 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +     + +
Sbjct: 64  ALSSEVARALSLQFEQHQIQKTYHAVVRGYVLEADTIDYEMTEELDKIADKFA----RPD 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
           K    +++H+K +               +F  LE++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYKPLAKVEVPVAIGRYDTARFSLLELKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 270 -HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
            H      +G       ++L LHA ++ L HP  G        P  +   WD 
Sbjct: 180 AHGDLRQNRGVGQHFDCSRLMLHASHLQLNHPVTGE-------PLSLTARWDE 225


>gi|307718151|ref|YP_003873683.1| ribosomal large subunit pseudouridine synthase C [Spirochaeta
           thermophila DSM 6192]
 gi|306531876|gb|ADN01410.1| ribosomal large subunit pseudouridine synthase C [Spirochaeta
           thermophila DSM 6192]
          Length = 300

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 74/275 (26%), Positives = 113/275 (41%), Gaps = 32/275 (11%)

Query: 9   YVVVEN--DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           Y V E+  D+   RLDR  +    HI    + + LR+G++ ++ KRV  + R+  G  + 
Sbjct: 4   YQVFESGPDDHGKRLDRIVRTLLSHIPLSRVFRALRTGEILLEGKRVPPSTRVSRGARIH 63

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I             + +L       K       ILL  D  + + NKP G  V G   + 
Sbjct: 64  I------------HRSLLPEREPRQKWEPRALPILLETD-HLLILNKPPGAVVHGPGSLT 110

Query: 127 YHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             +  +LK  +  S    P   HRLD+ TSGILV +R+   A+  T + R   I+K Y +
Sbjct: 111 DQVRSYLKDRIPPSLAFTPSPLHRLDRLTSGILVFSRSIHGARWFTRALREGGIEKTYLA 170

Query: 186 LVWGIPKNKKECIANW---LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           L+ G         A W   L ++        H      + A   +             C 
Sbjct: 171 LLEGTLAEP----ARWEDLLTREGRRSRPSPH-----GRPALTDVRPLLAAPTATLALCI 221

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +    HTGR HQ+RV A   G P++GD  Y +  +
Sbjct: 222 I----HTGRMHQIRVQAALRGHPLLGDTAYGSTRR 252


>gi|172079581|ref|ZP_02709037.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1873-00]
 gi|172042644|gb|EDT50690.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1873-00]
 gi|301802690|emb|CBW35457.1| RNA pseudouridylate synthase [Streptococcus pneumoniae INV200]
 gi|332199159|gb|EGJ13238.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA47368]
          Length = 278

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 182 AKNGQYAETYVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|15894302|ref|NP_347651.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|15023925|gb|AAK78991.1|AE007617_3 Pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|325508430|gb|ADZ20066.1| Pseudouridylate synthase [Clostridium acetobutylicum EA 2018]
          Length = 318

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 73/297 (24%), Positives = 131/297 (44%), Gaps = 32/297 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIP 68
           +V+  +E   R+D++ +     +    + K  R G V ++  + K     ++ G V+ I 
Sbjct: 3   IVIGPNEAGQRVDKFIRKWLKDVPLSAIYKAFRKGDVIINGAKCKKEKYSLEEGDVLEI- 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                +    K++K      N           + YED  + +  K  G+ V       + 
Sbjct: 62  ---KYIRSDAKKKKFTRIENNFK---------VTYEDENMLLVEKWPGVLVHSDKEKTSP 109

Query: 128 HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            +  ++ S++  KG           P   +RLD+ TSGI++  +   A + L E  R RR
Sbjct: 110 TLTDYVLSYLYDKGDYAPENEVTFTPSPCNRLDRNTSGIVIYGKNFEALKCLNEMIRERR 169

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I+K Y++LV G     K+ I    +KK  +  +   ++     GA       K ++    
Sbjct: 170 IKKYYYALVKG---KIKDGIYEAYIKKD-VSSNKSEIINTPAPGAKQISMEIKCVETCGT 225

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
            F ++E++  TGR+HQLR H  H+G PI+GD KY      +  S  +NK  L+ +++
Sbjct: 226 -FSFIEIELLTGRSHQLRAHLSHLGNPILGDPKYGIK---DINSYFENKFGLNYQFL 278


>gi|18310186|ref|NP_562120.1| ribosomal large subunit pseudouridine synthase C [Clostridium
           perfringens str. 13]
 gi|110800940|ref|YP_695859.1| RluA family pseudouridine synthase [Clostridium perfringens ATCC
           13124]
 gi|169344395|ref|ZP_02865365.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
 gi|182626167|ref|ZP_02953926.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
 gi|18144865|dbj|BAB80910.1| ribosomal large subunit pseudouridine synthase C [Clostridium
           perfringens str. 13]
 gi|110675587|gb|ABG84574.1| pseudouridine synthase, RluA family [Clostridium perfringens ATCC
           13124]
 gi|169297468|gb|EDS79576.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
 gi|177908523|gb|EDT71051.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
          Length = 324

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 80/298 (26%), Positives = 133/298 (44%), Gaps = 30/298 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ + +   +    + K LR G +RV+ K+ K    +  G V+ I  
Sbjct: 3   IEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLEGDVIEI-- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYH 128
               L  ++ ++K      N  +  D     ++YED  + +  K  G+ V       A  
Sbjct: 61  --RYLQSVVTKEK---KKPNF-QMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAPT 114

Query: 129 IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI+   +     + L E  R R++
Sbjct: 115 LTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKV 174

Query: 180 QKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS-HFKVIDCFA 237
           +K Y +LV G I   K E    ++ K   +    V+     E+     I    KV+    
Sbjct: 175 KKYYCALVKGKIQPGKYEA---YISKDDELNKSTVY---DTERPDTKKIKMDVKVLQTNG 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             F  LE++  TGR+HQLR H  H+G PIVGD KY  N   +F    +NK  L  +++
Sbjct: 229 A-FSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSF---FENKFGLTYQFL 282


>gi|182684947|ref|YP_001836694.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CGSP14]
 gi|303253824|ref|ZP_07339955.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS455]
 gi|303260789|ref|ZP_07346745.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP-BS293]
 gi|303263120|ref|ZP_07349049.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS292]
 gi|303265168|ref|ZP_07351080.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS397]
 gi|303267680|ref|ZP_07353509.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS457]
 gi|303270027|ref|ZP_07355752.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS458]
 gi|182630281|gb|ACB91229.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CGSP14]
 gi|302599211|gb|EFL66226.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS455]
 gi|302635742|gb|EFL66248.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS292]
 gi|302638071|gb|EFL68550.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP-BS293]
 gi|302640439|gb|EFL70861.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS458]
 gi|302642786|gb|EFL73104.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS457]
 gi|302645249|gb|EFL75484.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS397]
          Length = 291

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 195 AKNGQYAETYVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDPLYNSKSKT- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|186681130|ref|YP_001864326.1| pseudouridine synthase [Nostoc punctiforme PCC 73102]
 gi|186463582|gb|ACC79383.1| pseudouridine synthase [Nostoc punctiforme PCC 73102]
          Length = 575

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 112/232 (48%), Gaps = 34/232 (14%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS--- 139
           + +   +L +  + +   ++YED  +   NKP G+           + G  +   DS   
Sbjct: 352 VSEREASLREEREEVTLPIIYEDEWLIAVNKPPGL---------LSVPGRYRDRQDSVLS 402

Query: 140 -------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                   G      HRLDQETSGIL++AR R   + L++ F+ R++ K+Y +++ G+  
Sbjct: 403 RLRHLLPDGMALASVHRLDQETSGILLLARDRQTHKQLSQQFQQRQVHKVYEAILSGVAI 462

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +K  I +  L        Y  V  QN K    +++ F+VI    Q +  +E  P TGRT
Sbjct: 463 AEKGVI-DLPLWGDPENRPYQKVDWQNGKP---SLTQFQVIS-REQDYTRIEFTPLTGRT 517

Query: 253 HQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           HQLRVHA     +G  I+GD  Y  +        + ++LYLHAR +D  HP+
Sbjct: 518 HQLRVHAADVRGLGITILGDRLYGCD-------AVTSRLYLHARELDFEHPQ 562


>gi|332289163|ref|YP_004420015.1| 23S rRNA/tRNA pseudouridine synthase A [Gallibacterium anatis
           UMN179]
 gi|330432059|gb|AEC17118.1| 23S rRNA/tRNA pseudouridine synthase A [Gallibacterium anatis
           UMN179]
          Length = 217

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 64/213 (30%), Positives = 103/213 (48%), Gaps = 15/213 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ I V NK +G+    G+   Y      +  V +K       HRLD  TSGIL+ 
Sbjct: 14  ILYQDNYIAVVNKQSGLLSVPGNQPQYQDSATTR--VANKFGFTEPAHRLDMATSGILLF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A ++AA + L   FR R  +K Y ++VWG  +     +   L+       D+ +  +Q  
Sbjct: 72  ALSKAAEKELKRQFREREPKKHYQAIVWGHLEQDNGIVDLPLI------CDWENRPRQRI 125

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      A + ++V+  +      +++ P TGR+HQLR+H L +G PI+GD  Y      
Sbjct: 126 DFLVGKKAQTQYQVLARYPNNTTRVKLTPITGRSHQLRLHMLALGHPILGDKFYSP---- 181

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                +  +LYLHA  + + HP    R+  T P
Sbjct: 182 PAVRAMAPRLYLHAESLTITHPITQERMTFTCP 214


>gi|307709867|ref|ZP_07646315.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
 gi|307619357|gb|EFN98485.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
          Length = 278

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 60/201 (29%), Positives = 93/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   +K+      L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDGNISSKE------LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F  K   +  +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 182 AKHGQYAETHVNRLKQFPNKTSLVRCKLKTGRTHQIRVHLSHHNFPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|302206504|gb|ADL10846.1| Ribosomal large subunit pseudouridine synthase D [Corynebacterium
           pseudotuberculosis C231]
 gi|308276746|gb|ADO26645.1| Ribosomal large subunit pseudouridine synthase D [Corynebacterium
           pseudotuberculosis I19]
          Length = 307

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 70/276 (25%), Positives = 125/276 (45%), Gaps = 30/276 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-L 101
           +G V VD   V  ++RI  GQ + +                L  + +LT   + ++ + +
Sbjct: 39  AGDVLVDALPVGKSDRIAEGQWLDV---------------TLPETKDLTPREELVEGMDI 83

Query: 102 LYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           LY D  +   NKP G++       +G + I        +       ++  +  RLD  TS
Sbjct: 84  LYSDDDLIAVNKPVGVAAHPTLGWEGPTVIGGLAAAGFRISTSGPPERKGIVQRLDVGTS 143

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V+A +      L  +F+ R + K Y +LV G        I   + +  H    +   
Sbjct: 144 GVMVIAASERGYSVLKRAFKERTVSKTYHALVQGHTDPFTGTIDAPIGR--HPSAGWRFA 201

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  + K   +A++H++ ++ FA+    L++   TGRTHQ+RVH   +  P  GD  Y ++
Sbjct: 202 VTSDGK---HAVTHYETLEAFAEA-SLLKIHLETGRTHQIRVHMSALHHPCCGDPMYGSD 257

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            K +    +  + +LHA  +   HP  GR ++IT+P
Sbjct: 258 PKLSERLGLTRQ-WLHAVSLGFNHPADGRWMEITSP 292


>gi|57238152|ref|YP_179402.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           jejuni RM1221]
 gi|57166956|gb|AAW35735.1| ribosomal large subunit pseudouridine synthases, RluD subfamily
           [Campylobacter jejuni RM1221]
 gi|315058713|gb|ADT73042.1| Ribosomal large subunit pseudouridine synthase D [Campylobacter
           jejuni subsp. jejuni S3]
          Length = 322

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 72/279 (25%), Positives = 132/279 (47%), Gaps = 36/279 (12%)

Query: 48  VDKKRVKFNNRIQ--------SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++K  V+ N++IQ        +G ++ I  +   L + IK Q  +D  +++         
Sbjct: 31  IEKDCVQVNDKIQDKNSFKLKNGDIISIASL--KLCNEIKPQFEVDFDIDV--------- 79

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL--KSWVDSKGQKPR--LTHRLDQE 153
             LYED  + V NKP+ + V G S +  A  +D  +  K  + + G + R  L HRLD++
Sbjct: 80  --LYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKD 137

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG +++A+     Q L+E    + + +IY +L+    K  K  +  +L++        +
Sbjct: 138 TSGSILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKI 197

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + K+N+   N   +   V+    +    +  +  TGRTHQ+R H   +   I+GD  Y 
Sbjct: 198 AIDKENKFSKNAKSAFINVVK--TENLTLMAAKLFTGRTHQIRAHLASLNRHILGDGLYG 255

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
            N K +       ++ LHA ++   HP+   ++ + APL
Sbjct: 256 YNGKYDC------RIMLHAYFLYFIHPKTKEQIFVKAPL 288


>gi|328907008|gb|EGG26774.1| pseudouridine synthase, RluA family [Propionibacterium sp. P08]
          Length = 227

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 109/236 (46%), Gaps = 32/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQ--------------GGSGIAYHIDGFLKSWVDSKGQKPRL 146
           ++++DS I V +KPAG++                  +G A    G L        ++  +
Sbjct: 3   IVHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTSGLL--------ERQGI 54

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD  TSG++VVA++  A   L ++FR R + K+Y +LV G P      I       +
Sbjct: 55  VQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRAVDKVYLALVQGHPDPFAGTI------DA 108

Query: 207 HIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            IG D+ H  K     G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P
Sbjct: 109 PIGRDHRHDWKMAIVDGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAVKHP 167

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
             GD  Y  +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 168 CCGDPLYGCDPALAKELGLERQ-WLHAAELSFAHPGSGEWVTFHADLPADLQHALD 222


>gi|255310907|ref|ZP_05353477.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           6276]
          Length = 303

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 69/259 (26%), Positives = 119/259 (45%), Gaps = 45/259 (17%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINAL 74
           +  +RL  + +   PH+    + + +R    RV+ +  +F + ++Q G  V         
Sbjct: 9   DRQIRLSSFLRTSLPHLPKKTILESVRYHGCRVNGRIERFESYKLQPGDRV--------- 59

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                       S+ + +HS      LL+ED  + ++NKPA    Q    +A+ ++    
Sbjct: 60  ------------SLQIIEHSS---PQLLWEDEHLCIYNKPAK---QTSEDLAHQLNV--- 98

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                      L HRLD++TSG ++ A+   A+  +T+ F+ R I K Y +LV+G P+ +
Sbjct: 99  ----------HLVHRLDRDTSGCILFAKHAKASSLITQLFKNRGIDKRYIALVFGQPRQE 148

Query: 195 KECIANWLLKKSH-IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
              I  +     H IG        QN       I+ ++++  +  K+  L  +P TGRTH
Sbjct: 149 SGIITTYTAPCYHRIGAVLFGNTDQN--SGKITITKWEILTRYP-KYTLLLCRPVTGRTH 205

Query: 254 QLRVHALHMGCPIVGDHKY 272
           Q+R+H   +G PIVGD  Y
Sbjct: 206 QIRLHMKTIGHPIVGDVDY 224


>gi|148998774|ref|ZP_01826211.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP11-BS70]
 gi|168576962|ref|ZP_02722796.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae MLV-016]
 gi|307068624|ref|YP_003877590.1| 23S RNA-specific pseudouridylate synthase [Streptococcus pneumoniae
           AP200]
 gi|147755335|gb|EDK62385.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP11-BS70]
 gi|183577335|gb|EDT97863.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae MLV-016]
 gi|306410161|gb|ADM85588.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           pneumoniae AP200]
          Length = 291

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 195 AKNGQYAETYVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDPLYNSKSKT- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|116748594|ref|YP_845281.1| pseudouridine synthase [Syntrophobacter fumaroxidans MPOB]
 gi|116697658|gb|ABK16846.1| ribosomal large subunit pseudouridine synthase D [Syntrophobacter
           fumaroxidans MPOB]
          Length = 255

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 110/220 (50%), Gaps = 19/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQET 154
           ++YED+ +    KPAG+ VQG  +G A  +D   K W+     KP      + HRLD+  
Sbjct: 13  IIYEDNHLLGLYKPAGLLVQGDRTGEASLLD-LGKKWLKECCGKPGKVFLAMVHRLDRPV 71

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+++  RT  AA  ++  FR  RI+K Y ++  G        + N L  + H     V 
Sbjct: 72  AGVVLFCRTSKAAARISAQFRSGRIRKHYLAVAEGDVTPSAGRLVNQL--ERHDERSSVI 129

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V +   +     +S ++V+D    +   LE++  TGR HQ+R+   H+G PI+GD +Y A
Sbjct: 130 VAEATPRSREARLS-YRVLDVAGSRSL-LEIELETGRHHQIRLQLAHLGFPILGDLRYGA 187

Query: 275 NFKGNFTSPIQNK-LYLHARYMDLPHP-EGGRLQITAPLP 312
                 ++P+  + + L A  ++L HP     L +  PLP
Sbjct: 188 ------SAPLPGRQVALFATQLELEHPTRKESLLLRCPLP 221


>gi|16801409|ref|NP_471677.1| hypothetical protein lin2346 [Listeria innocua Clip11262]
 gi|16414869|emb|CAC97573.1| lin2346 [Listeria innocua Clip11262]
 gi|313617601|gb|EFR89910.1| ribosomal large subunit pseudouridine synthase D [Listeria innocua
           FSL S4-378]
          Length = 289

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 64/217 (29%), Positives = 103/217 (47%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP G+        +Y  D     ++ +++  GQ+      HRLDQ TS
Sbjct: 80  IIYEDDFLLVVNKPVGMKTHAND--SYETDTCANAVQYYLEKTGQEANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H KV++   +    L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHVKVLENDNENNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           + +        N++ LHA  + L HP +G  +  +AP
Sbjct: 253 SSRA-------NRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|238060235|ref|ZP_04604944.1| 50S ribosomal pseudouridine synthase D [Micromonospora sp. ATCC
           39149]
 gi|237882046|gb|EEP70874.1| 50S ribosomal pseudouridine synthase D [Micromonospora sp. ATCC
           39149]
          Length = 311

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 74/304 (24%), Positives = 133/304 (43%), Gaps = 39/304 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +  + MRLD+     +  ++      ++ +G   VD      ++++++G  + +    
Sbjct: 13  VPDGLDGMRLDQAVSRLF-GLSRTAAANLVDAGDALVDGVARPNSHKVKTGSWLDVTLPT 71

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS------------V 119
            A    +  Q +   +V             +Y D  I V +KP G++            +
Sbjct: 72  PAAPPTMVPQAVPGLTV-------------VYADDDIVVVDKPVGVAAHPSPGWTGPTVI 118

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            G +GI + I            ++  + HRLD  T+GI+VVA++  A   L  +F+ R +
Sbjct: 119 GGLAGIGHRIS------TSGAAERQGVVHRLDVGTTGIMVVAKSEQAYTALKRAFKYREV 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++V G P   +  I   + +  H   DY   V     G   +I+H+  ++ F   
Sbjct: 173 EKRYHAVVQGHPDPLRGTIDAPIDRHPH--HDYRWAVVS---GGKPSITHYDTLEAFPSA 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+++  TGRTHQ+RVH   +  P VGD  Y A+   +    +  + +LHAR +   H
Sbjct: 228 -SLLDVRLETGRTHQIRVHFSSLRHPCVGDVTYGADPTLSARLGL-GRQWLHARSLSFLH 285

Query: 300 PEGG 303
           P  G
Sbjct: 286 PRTG 289


>gi|254227499|ref|ZP_04920931.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262396236|ref|YP_003288089.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. Ex25]
 gi|151940111|gb|EDN58937.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262339830|gb|ACY53624.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. Ex25]
          Length = 559

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 70/204 (34%), Positives = 102/204 (50%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V NKP G+    G  I       L++ + D +G  P + HRLD  TSGILV
Sbjct: 358 IIYQDDAMVVVNKPTGLLSVPGKTIKDSAYTRLQAMFPDVEG--PFVIHRLDMATSGILV 415

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A T+ A + L + F  R +QK Y +L+ G+  N+ E   +  ++          V  ++
Sbjct: 416 FALTKRANKSLQKQFMARGVQKRYMALLEGV-LNEPEGEISLPMRGDPDDRPRQLVCFEH 474

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHKYCANF 276
            K A       +V D  ++ +    M P TGRTHQLRVH A HMG   P+VGD  Y    
Sbjct: 475 GKHAETYWQLIEVKDGRSKVY----MYPKTGRTHQLRVHSAHHMGLNMPMVGDGLYGEK- 529

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                    N+L+LHA  ++L HP
Sbjct: 530 --------ANRLHLHAEMLELDHP 545


>gi|284038283|ref|YP_003388213.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283817576|gb|ADB39414.1| pseudouridine synthase [Spirosoma linguale DSM 74]
          Length = 244

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 106/216 (49%), Gaps = 30/216 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LY+D+++   NKP G+ V   S IA     F    + D  GQ+    HRLD++T+G+L+
Sbjct: 13  ILYQDTELVAINKPHGLLVHR-SMIASDASEFAVQLLRDQLGQRVYPVHRLDRKTAGVLL 71

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A + +    + + F    +QK Y ++V G   +  E   ++ L K   G   V V+++ 
Sbjct: 72  FALSESMNAIMQQQFMEGAVQKTYLAIVRGYTPD--ELTIDYPLCKDD-GNGAVGVLQE- 127

Query: 220 EKGANYAISHFKVID------CFAQ----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++H K +        F +    ++  +E+ P TGR HQLR H  H+  PI+GD
Sbjct: 128 ------AVTHLKTLRQTEIPVAFGKHPTSRYSLVELTPTTGRMHQLRRHMAHILHPIIGD 181

Query: 270 HKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
             +  N     FK +F     N + LHA+ ++  HP
Sbjct: 182 RPHGCNKQNKLFKEHFE---MNTMLLHAQRIEFTHP 214


>gi|183603679|ref|ZP_02718812.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC3059-06]
 gi|183575456|gb|EDT95984.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC3059-06]
          Length = 278

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 182 AKNGQYAETYVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|291459169|ref|ZP_06598559.1| pseudouridine synthase, RluA family [Oribacterium sp. oral taxon
           078 str. F0262]
 gi|291418423|gb|EFE92142.1| pseudouridine synthase, RluA family [Oribacterium sp. oral taxon
           078 str. F0262]
          Length = 352

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 70/290 (24%), Positives = 135/290 (46%), Gaps = 31/290 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +  +E   RLD+  + +        L K+LR   + ++ ++      ++ G +++
Sbjct: 1   MRELRIGENEAGQRLDKLLRKYLRRAENGFLYKMLRKKNITLNGRKASGKELLKEGDLLK 60

Query: 67  I-------PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +         +   L  + +E+K  +         +   S ++YED  + +FNKPAG+  
Sbjct: 61  LFFSEESFQKLCAPLTPLPEEKKREEGRAKAEWEGEAFSSRIVYEDENLLLFNKPAGLLS 120

Query: 120 QG-GSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQH 169
           Q  GSG+   ++    S++  KG+         +P   +RLD+ T+G+L+  +T  A Q 
Sbjct: 121 QSDGSGLP-SVNELCLSYLMEKGELGREQLASFRPGAANRLDRNTTGLLLFGKTLPALQE 179

Query: 170 LTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           L+   + R I K Y ++V G  P+  +  I  +L K      + V + ++   GA    S
Sbjct: 180 LSFCLKKRTIGKYYLAVVRGHTPERGR--IEGFLRKDPD--KNRVFLQEEASGGAKEVQS 235

Query: 229 HFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++ +  FA +      F  L +   +G+THQ+R H   +  PI+GD KY
Sbjct: 236 EYRRL--FAGESGEQISFSVLLVHLISGKTHQIRAHLASVSHPILGDPKY 283


>gi|229084380|ref|ZP_04216660.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
 gi|228698920|gb|EEL51625.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
          Length = 307

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 71/226 (31%), Positives = 111/226 (49%), Gaps = 34/226 (15%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED  + + NKPA +    S +GG+G     +A+H+       +     K R  HRLD
Sbjct: 87  VIFEDDHVLIVNKPAHMDTHPSNKGGTGTLANLVAFHLQ------MQGVETKVRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+   A   +      R I++ Y +LV G  + K+  I         IG D
Sbjct: 141 KDTTGGVVFAKHGIAGVIMDRLLMERNIKRTYLALVEGKVRKKQGII------DEAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  ++KG + A++H+K+   F  Q    + +Q  TGRTHQ+RVH  H G P++G
Sbjct: 195 RHHATRRRVSQKG-DRAVTHYKIEKYFKKQDVTLVTLQLETGRTHQIRVHMSHSGHPLIG 253

Query: 269 DHKYCANFKGNFT-SPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           D  Y     G  T  P Q    LHA  +   HP     + + APLP
Sbjct: 254 DVLYG----GQATYMPYQA---LHAMRIHFLHPITKEEITVEAPLP 292


>gi|225378039|ref|ZP_03755260.1| hypothetical protein ROSEINA2194_03699 [Roseburia inulinivorans DSM
           16841]
 gi|225210040|gb|EEG92394.1| hypothetical protein ROSEINA2194_03699 [Roseburia inulinivorans DSM
           16841]
          Length = 294

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 72/258 (27%), Positives = 115/258 (44%), Gaps = 55/258 (21%)

Query: 97  LKSI------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-------- 142
           LKSI      ++YED  + + NKP+G+  Q         + ++ S++  KG         
Sbjct: 51  LKSIDSGRLQVVYEDDDVIIINKPSGMLSQKAVPEDISANEYILSYLIRKGALSEEQFKT 110

Query: 143 -KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            KP + +RLD+ TSG+L+  +T    Q + E+ + R +QK Y  +V G            
Sbjct: 111 FKPSICNRLDRNTSGLLIAGKTLKGLQTMAEALKKRTVQKYYRCIVKG-----------E 159

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--------------CFAQKFCWLEMQP 247
           L +K+H+ G Y+   +QN K     +SH +  +                +  +  LE+  
Sbjct: 160 LREKTHLKG-YLSKDEQNNKVK--VVSHIRPEEKADYLPIETEYRPVAVSNGYTELEVHL 216

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-----EG 302
            TGR+HQ+R H   +G PIVGD KY     G+  +  + +  +H R   L H      E 
Sbjct: 217 ITGRSHQIRAHLASIGHPIVGDGKY-----GDLRTNERFRKEVHVRSQ-LLHAYRIVLED 270

Query: 303 GRLQITAPLPAHMVKTWD 320
           GR ++ AP        WD
Sbjct: 271 GR-EVIAPSGREFEDAWD 287


>gi|77360149|ref|YP_339724.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875060|emb|CAI86281.1| putative 23S rRNA pseudouridylate 746 synthase [Pseudoalteromonas
           haloplanktis TAC125]
          Length = 237

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/208 (29%), Positives = 108/208 (51%), Gaps = 18/208 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYH------IDGFLKSWVDSKGQKPRLTHRLDQE 153
           ++Y D  I + NKP+G+ S+ G + + +       ++G  ++ + +   + +L HRLD  
Sbjct: 26  IVYHDEDILLINKPSGLLSLSGKNPLNWDSVHYRLVNG--QTGITAAYPEAKLPHRLDLG 83

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGI++V    AA++HL + F+ R I+K Y +++ G   + +  I+  + K   +     
Sbjct: 84  TSGIMIVGLNAAASKHLNKQFQARTIKKRYVAMLHGWLIDDEGQISASIAKDKLL----F 139

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             VK  E     A+S +KV+    Q +   ++  P TGRTHQLR+H+  +G PI+G    
Sbjct: 140 PRVKICETTGKTAVSEYKVLQRLTQPQRTLVQFTPITGRTHQLRIHSQFIGHPILG---- 195

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
           C  +    +  +  +L LHA  +   HP
Sbjct: 196 CDLYNNAQSEHMAARLQLHASDLYFQHP 223


>gi|293375853|ref|ZP_06622121.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|325844995|ref|ZP_08168320.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
 gi|292645532|gb|EFF63574.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|325488968|gb|EGC91358.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
          Length = 299

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 78/292 (26%), Positives = 141/292 (48%), Gaps = 35/292 (11%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           H+    + ++  S +V+++ +   FN  ++ G ++ IP V  +     K QK+     NL
Sbjct: 31  HLARKKIHELYMSKKVQLNAQIADFNKILEVGDILLIP-VFESEGIDFKPQKM-----NL 84

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSKG--QKPRL 146
                     ++YED  + + NKPAG+ V      G+   ++G +  + + KG  ++ R 
Sbjct: 85  D---------IVYEDEHLLILNKPAGVMVHPDQKDGLNTLVNG-VAYYYEQKGFNERIRY 134

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HR+D +TSG ++ A+   A   +      ++I++ Y +LV G  K +K  I       +
Sbjct: 135 IHRIDTDTSGGIIFAKHFMAHSLMDYQLSEKQIRRWYLALVSGNLKTRKGRI------DA 188

Query: 207 HIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            IG D  H  ++   K  + A++ ++V   F + +  +E++  TGRTHQ+RVH  H+G P
Sbjct: 189 PIGKDRHHRARRRVAKNGDQAVTLYEVKKQF-KTYSLVELELKTGRTHQIRVHMSHLGHP 247

Query: 266 IVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           ++GD  Y    K G        +  LH+  + + HP     L  + P+P  M
Sbjct: 248 LLGDVLYGGVAKVGKL-----KRQALHSAKIQMQHPMTKENLSFSIPMPLDM 294


>gi|331269001|ref|YP_004395493.1| RluA family pseudouridine synthase [Clostridium botulinum
           BKT015925]
 gi|329125551|gb|AEB75496.1| pseudouridine synthase, RluA family [Clostridium botulinum
           BKT015925]
          Length = 323

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 72/272 (26%), Positives = 121/272 (44%), Gaps = 30/272 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI--- 71
           +E   RLD++ +     +    + K LR G +RV+ K+ K N  +Q   ++    +    
Sbjct: 8   NEAGQRLDKFCRKWLEDVPLGAIFKALRKGDIRVNGKKAKQNYFLQEEDIIETKYIETYK 67

Query: 72  -NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
            N  N   K Q++  SS+ ++           YED  + +  K  G+ V      G   +
Sbjct: 68  QNKKNMPKKFQEVDFSSIKIS-----------YEDENMLIIEKWPGVLVHSDKKDGEPTL 116

Query: 126 AYHIDGFLKSWVDSKGQK-----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             ++  +L    D   QK     P   +RLD+ TSG+++  +     + L    R R+I+
Sbjct: 117 TDYVLSYLFQKGDYDPQKEVTFTPAPCNRLDRNTSGMVIFGKNFKTLKILNAMIRERKIK 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G     KE      + K  +  +   + K+ ++ +        VID     F
Sbjct: 177 KYYNALVKG---KIKEGYYEAYISKDQVN-NISEIHKEKKQNSKKIAMEVNVIDTVGT-F 231

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +LE+   TGR+HQLR H  ++G PI+GD KY
Sbjct: 232 SFLELDLLTGRSHQLRAHLAYLGNPIIGDDKY 263


>gi|328469904|gb|EGF40815.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus 10329]
          Length = 559

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 70/204 (34%), Positives = 102/204 (50%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V NKP+G+    G  I       L++ + D +G  P + HRLD  TSGILV
Sbjct: 358 IIYQDDAMVVVNKPSGLLSVPGKTIKDSAYTRLQAMFPDVEG--PFVIHRLDMATSGILV 415

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A T+ A + L + F  R +QK Y +L+ G+  N  E   +  ++          V  ++
Sbjct: 416 FALTKRANKSLQKQFMARGVQKRYMALLEGV-LNAPEGEISLPMRGDPDDRPRQLVCFEH 474

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHKYCANF 276
            K A       +V D  ++ +    M P TGRTHQLRVH A HMG   P+VGD  Y    
Sbjct: 475 GKHAETYWQLIEVKDGRSKVY----MYPKTGRTHQLRVHSAHHMGLNMPMVGDGLYGEK- 529

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                    N+L+LHA  ++L HP
Sbjct: 530 --------ANRLHLHAEMLELDHP 545


>gi|91227645|ref|ZP_01261922.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           alginolyticus 12G01]
 gi|91188424|gb|EAS74718.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           alginolyticus 12G01]
          Length = 325

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 79/326 (24%), Positives = 149/326 (45%), Gaps = 37/326 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V+VD + V K   ++  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVQVDGEVVTKPRTKVMGGEEITLQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
            +        E++     + L          ++YED  I V NKP    V  G+G     
Sbjct: 70  ELE------DEERWEAQDIPLD---------IVYEDEDIIVINKPRDFVVHPGAGTPDGT 114

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++  L  + D   + PR  + HRLD++T+G++VVA+T  A   L  + + R I + Y +
Sbjct: 115 VLNALLHHYPDI-AEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G  +       +  + +       + V    +     A++H++V + F ++   + +
Sbjct: 174 IAIG--RMTAGGKVDQPIGRHSTKRTLMAVAPMGKP----AVTHYRVAERF-REHTRIRL 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLHARYMDL 297
           +  TGRTHQ+RVH  ++  P++GD  Y    +         T+ I+  ++  LHA  +  
Sbjct: 227 RLETGRTHQIRVHMSYLQHPLLGDIAYGGRARIPTGASEELTAMIRGFDRQALHAVMLRF 286

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  L+  AP+P  MV   ++L
Sbjct: 287 EHPITGEVLEFHAPVPDDMVVMTEAL 312


>gi|1143378|dbj|BAA09443.1| ORFX [Zymomonas mobilis]
          Length = 317

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 107/228 (46%), Gaps = 20/228 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED  + V NKPAG+ V   +G         + YH  G L         +P + HR+D
Sbjct: 84  IVFEDEHLLVVNKPAGMVVHPAAGNYDNTLVNALLYHCAGKLSGI--GGVARPGIVHRID 141

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA+T  A   L   F    I + Y ++V G P  +    A   L +S +   
Sbjct: 142 KDTSGLLVVAKTDPAHAGLAAQFADHSINRRYRAIVDGNPSLQGHVDAP--LARSSVNRQ 199

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +V         A++H+ +I    +    +E +  TGRTHQ+RVH   +G  ++GD  
Sbjct: 200 KMAIVSDGR--GKRAVTHYCMITPL-KNASLIECRLETGRTHQVRVHMSSIGHSLLGDPV 256

Query: 272 YCANFKGN---FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           Y  + K +     S    +  LHA ++   HP  G ++   A +P  M
Sbjct: 257 YGRSKKAHHALLQSLAFQRQALHAAHLGFIHPISGKQVDFDAEMPQDM 304


>gi|332199442|gb|EGJ13518.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA47901]
          Length = 278

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 182 AKNGQYAETYVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|324994489|gb|EGC26402.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK678]
          Length = 295

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 114/228 (50%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++      + Q+  +  RLD++TSG+
Sbjct: 78  VVYEDKHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  K   +A + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTKDGKHAHTSYKVIERFGDVY-LVDIHLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLECGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|153938225|ref|YP_001390782.1| RluA family pseudouridine synthase [Clostridium botulinum F str.
           Langeland]
 gi|168180094|ref|ZP_02614758.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
 gi|170754896|ref|YP_001781073.1| RluA family pseudouridine synthase [Clostridium botulinum B1 str.
           Okra]
 gi|226948698|ref|YP_002803789.1| pseudouridine synthase, RluA family [Clostridium botulinum A2 str.
           Kyoto]
 gi|152934121|gb|ABS39619.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           Langeland]
 gi|169120108|gb|ACA43944.1| pseudouridine synthase, RluA family [Clostridium botulinum B1 str.
           Okra]
 gi|182668924|gb|EDT80900.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
 gi|226843753|gb|ACO86419.1| pseudouridine synthase, RluA family [Clostridium botulinum A2 str.
           Kyoto]
 gi|295318854|gb|ADF99231.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           230613]
          Length = 317

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 73/277 (26%), Positives = 127/277 (45%), Gaps = 36/277 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  +E   RLD++ +     +    + K +R G+++V+ ++ K  N ++ G +V    
Sbjct: 3   IVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKNFLEEGDIVE--- 59

Query: 70  VINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIA 126
             N  +   K++ + +D+++ +T           YED  + +  K  G+ V      G  
Sbjct: 60  SFNVKSKGEKKKFVRIDNNLKIT-----------YEDENMVLVEKWPGVLVHSDKKEGEP 108

Query: 127 YHIDGFLKSWVDSKGQKPRLT--------HRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              D  L    D     P L         +RLD+ TSGI++  +   A + L E  R R+
Sbjct: 109 TLTDYVLSYLYDKGDYTPELEVTFTPASCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRK 168

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY---AISHFKVIDC 235
           I+K Y SLV G  + K      ++ K        ++    NE   N    A++   +  C
Sbjct: 169 IEKYYSSLVKG--RIKDGVYEAYISKNEDTNMSKIY----NEPKPNTKKIAMNVKTIQTC 222

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  F ++E++  TGR+HQLR H  H+G PI+GD KY
Sbjct: 223 GS--FSFIEIELLTGRSHQLRAHLNHLGNPIIGDSKY 257


>gi|304320980|ref|YP_003854623.1| ribosomal large subunit pseudouridine synthase A [Parvularcula
           bermudensis HTCC2503]
 gi|303299882|gb|ADM09481.1| ribosomal large subunit pseudouridine synthase A [Parvularcula
           bermudensis HTCC2503]
          Length = 217

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 70/217 (32%), Positives = 104/217 (47%), Gaps = 22/217 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGG----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LYED  + V +KPAG+ SV G     S     +D F  ++V          HRLD  TS
Sbjct: 17  VLYEDHALIVLDKPAGLLSVPGNISRDSLETRVVDRFPDAYV---------AHRLDMATS 67

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V AR + A   L + F  R  +K Y + VWG     +  I   L  ++      + +
Sbjct: 68  GVIVFARGKQALADLGQQFEHRLTEKRYIADVWGCVSEDEGTID--LPLRTDWPNRPLQM 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  +E+G   A++H++VI   + K   LE++P TGR+HQLR+H   +G PI+GD  Y   
Sbjct: 126 VC-HERG-RPALTHWRVI-TRSPKQTRLELRPVTGRSHQLRIHCRELGHPILGDEWYA-- 180

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
            +G   +                    GR+  TAPLP
Sbjct: 181 -EGEARAAANRLHLHALHLSLTHPTNKGRVTYTAPLP 216


>gi|325129374|gb|EGC52208.1| RNA pseudouridylate synthase family protein [Neisseria meningitidis
           OX99.30304]
          Length = 208

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 101/212 (47%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 4   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R +A  L+  F  + I+K Y +L    P  K+  I   + +KS  G     + K  
Sbjct: 60  FALNRESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLT 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 114 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTE--- 169

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 170 -----SETMFLYAWKIQFAY-QNRQIEIVAPL 195


>gi|311742786|ref|ZP_07716595.1| ribosomal large subunit pseudouridine synthase D [Aeromicrobium
           marinum DSM 15272]
 gi|311314414|gb|EFQ84322.1| ribosomal large subunit pseudouridine synthase D [Aeromicrobium
           marinum DSM 15272]
          Length = 313

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 65/229 (28%), Positives = 111/229 (48%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +++ED  I V +KP G++   G G     + G L +    + + G   R  + HRLD  T
Sbjct: 88  IVHEDDDIVVVDKPVGVAAHPGVGWTGPTVLGALAARGYRISTSGAPERQGIVHRLDVGT 147

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++ VA++  A   L ++FR R + K Y SLV G P      I   + +  H   D+  
Sbjct: 148 SGLMAVAKSEHAYTVLKQAFRDRVVDKTYHSLVQGHPDPHTGTIDAPIAR--HPKHDFKF 205

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V+ + +    +++H+  ++   +    L ++  TGRTHQ+RVH   +  P VGD  Y A
Sbjct: 206 TVRADGRA---SVTHYATLEAH-RYASLLTIKLETGRTHQIRVHMAAIKHPCVGDPLYGA 261

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           +        ++ + +LHA  +   HP  G R+   +  PA +    D++
Sbjct: 262 DPTLAARVGLERQ-WLHALGLGFDHPRTGERVDFASTYPADLQAALDTV 309


>gi|229016637|ref|ZP_04173574.1| Pseudouridine synthase [Bacillus cereus AH1273]
 gi|229022852|ref|ZP_04179372.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228738387|gb|EEL88863.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228744627|gb|EEL94692.1| Pseudouridine synthase [Bacillus cereus AH1273]
          Length = 307

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 71/231 (30%), Positives = 113/231 (48%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +    S + G+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPSEKNGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEKYFNKQNATLVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y    K        +   LHA  ++  HP     + +  P PA +  T
Sbjct: 254 DVLYGGQTK------YMSHQALHAMKINFLHPITKEEIMVDVPFPAKLNNT 298


>gi|218132751|ref|ZP_03461555.1| hypothetical protein BACPEC_00612 [Bacteroides pectinophilus ATCC
           43243]
 gi|217992477|gb|EEC58480.1| hypothetical protein BACPEC_00612 [Bacteroides pectinophilus ATCC
           43243]
          Length = 217

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 88/181 (48%), Gaps = 5/181 (2%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           +K  ++YED  + +  KPAG+  QG       +   L ++   KG+   +   +RLD+  
Sbjct: 1   MKPDIIYEDDGMIICRKPAGVLAQGSRSFDADMVSMLMTYRRKKGEDTYIGVINRLDRPV 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G++V A++   A  L    +     K Y ++VWG     +  + ++L+K +  G +  H
Sbjct: 61  EGLMVFAKSSRDAARLNRLMQQDTFNKTYIAVVWGCIDAVEGTLTDYLVKDA--GNNTSH 118

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V  + E GA  A  +++VI         + +Q  TGR HQ+RV     G  +VGD KY +
Sbjct: 119 VASEGEPGAKRAELNYRVIGSL-DGMSVVRIQLVTGRHHQIRVQFASRGHALVGDAKYGS 177

Query: 275 N 275
           N
Sbjct: 178 N 178


>gi|217974457|ref|YP_002359208.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499592|gb|ACK47785.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 574

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 115/235 (48%), Gaps = 22/235 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H++ E  ++D +  LT  ++     +LY+D  + + NKPA      G  I   +   +
Sbjct: 340 LGHML-EGLVVDENPLLTNPAEGKTLAILYQDDAMAIVNKPAEFLSVPGKEIEDSVYSRI 398

Query: 134 K-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           + ++  + G  P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ GIP 
Sbjct: 399 RQAFPHATG--PLIVHRLDMSTSGLMVIALTKDAHKQLQKQFIQRTVTKRYVALLAGIPA 456

Query: 193 --NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--IDCFAQKFCWLEMQPH 248
               K+   +  L       D    +  +E G   A +H+++  +D  A +   + + P 
Sbjct: 457 VMANKQATGHISLPLRGDLDDRPRQLVCHEFG-KAAETHWELSQLDEMA-RTARVYLYPK 514

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           TGRTHQLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP
Sbjct: 515 TGRTHQLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHP 560


>gi|163814113|ref|ZP_02205505.1| hypothetical protein COPEUT_00266 [Coprococcus eutactus ATCC 27759]
 gi|158450562|gb|EDP27557.1| hypothetical protein COPEUT_00266 [Coprococcus eutactus ATCC 27759]
          Length = 334

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 76/320 (23%), Positives = 146/320 (45%), Gaps = 25/320 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  +E   RL++    +        + +++R   ++++  +   N  +  G V+++  
Sbjct: 4   IVISKNEAGQRLNKLVMKYLNKAPSSFVYRMIRKKNIKLNGGKAVGNEIVYVGDVIQLYL 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
             + ++   ++  I  ++    K     K  ++Y D  + + NKP G+  Q  S   Y I
Sbjct: 64  ADDTIDSF-RDDNIQTAASGSQKK---FKPEIIYHDHNVLIVNKPVGVLSQKASKDDYSI 119

Query: 130 DGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           +  +  ++   G          KP + +RLD+ TSG+++   +    Q L+   R R I 
Sbjct: 120 NESVLDYLLDNGYITSEQLRTYKPSICNRLDRNTSGLVLCGVSLMGNQELSRIIRERNID 179

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSH----IGGDYVHVVKQNEKGANYAISH--FKVID 234
           K Y+++V G  K+ ++  A +L+K       I  D V  +KQ+     +   H  F+ + 
Sbjct: 180 KYYYTIVKGHIKSVQDVTA-YLVKDEKKNTVIVRDGVDEIKQDSGKNEFEKIHTIFEPVR 238

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLH 291
               K+  ++++  TG+THQ+R    HMG PIVGD KY     N     T  ++N+L LH
Sbjct: 239 SNG-KYTEVKVKLITGKTHQIRAQLSHMGYPIVGDQKYGDRETNIYFRQTYKLRNQL-LH 296

Query: 292 ARYMDLPHPEGGRLQITAPL 311
              +   +  GG   +T  +
Sbjct: 297 CGEVKFTNVTGGLDYLTGKI 316


>gi|225549410|ref|ZP_03770382.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           94a]
 gi|225370038|gb|EEG99479.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           94a]
          Length = 315

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 77/302 (25%), Positives = 144/302 (47%), Gaps = 38/302 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINF--VNLQKILRSGQVRVDKKRVKFNNR 58
           M L  Y+   V+ ND    RLD         +NF   ++ K +R G +R++  +  F+ R
Sbjct: 1   MRLDKYIFLEVLANDN-GKRLDSIL---IKILNFSKASIIKHIRKGDIRLNGLKSHFSCR 56

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +  G  + +   + A N  +   +   S+++      +++  ++YEDS + V +K  GI 
Sbjct: 57  VCKGDKIYLYKSL-AQNLNLTMDECFKSNIDFK----YIRKRIIYEDSDLLVLDKQKGIL 111

Query: 119 VQGG-SGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           V GG + + + ++ +L S  + S   KP   HRLD+ TSGI++ A+    ++ L+ +F  
Sbjct: 112 VHGGKNSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTSRKLSAAFSG 171

Query: 177 RRIQKIYWSLVWGIPKN----KKECIANWLLKKSHI--GGDYVHVVKQNEKGANYAISHF 230
             I K Y++++ G  K+    K     N  L+K+ +  G ++V+ + +            
Sbjct: 172 GSIIKKYFAILLGEVKSPVVYKNHLFRNKRLRKTFVLEGKNFVNAITKVN---------- 221

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
            ++ C  ++   +E+   TG THQ+R        P++ D KYC  FK       ++  +L
Sbjct: 222 PILSC--KRATLVEIVIETGFTHQIRSQCSFNNHPLINDKKYCNKFK-------KSDYFL 272

Query: 291 HA 292
           HA
Sbjct: 273 HA 274


>gi|301794949|emb|CBW37412.1| RNA pseudouridylate synthase [Streptococcus pneumoniae INV104]
          Length = 278

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQYLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   N+KE     L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWALVDG-NINRKE-----LVFRDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 182 AKNGQYAETYVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|121635675|ref|YP_975920.1| putative psedouridine synthase [Neisseria meningitidis FAM18]
 gi|254804170|ref|YP_003082391.1| pseudouridylate synthase, 23S RNA-specific [Neisseria meningitidis
           alpha14]
 gi|120867381|emb|CAM11153.1| putative psedouridine synthase [Neisseria meningitidis FAM18]
 gi|254667712|emb|CBA03587.1| pseudouridylate synthase, 23S RNA-specific [Neisseria meningitidis
           alpha14]
 gi|308390117|gb|ADO32437.1| pseudouridylate synthase [Neisseria meningitidis alpha710]
          Length = 236

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 101/212 (47%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 23  ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 78

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R +A  L+  F  + I+K Y +L    P  K+  I   + +KS  G     + K  
Sbjct: 79  FALNRESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLT 132

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 133 RNTENIAVTRFHSISI-AEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGT---- 187

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 188 ----ESETMFLYAWKIQFAY-QNRQIEIVAPL 214


>gi|311895525|dbj|BAJ27933.1| putative ribosomal large subunit pseudouridine synthase D
           [Kitasatospora setae KM-6054]
          Length = 312

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 81/338 (23%), Positives = 150/338 (44%), Gaps = 40/338 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS+    + + V +  E  RLD      +   +     ++   G+V +D      ++R+ 
Sbjct: 1   MSIAAQTRSLPVPDGLEGERLDAALARMF-GFSRTKAAELAAEGKVTLDGAVAGKSDRVT 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +G  + +  P   A   I+ E      +V   +        ++++D  + V +KP G++ 
Sbjct: 60  AGSWLEVEIPAPAAPVQIVAE------AVEGMR--------IIHDDDHVVVIDKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +    + + G   R  + HRLD  TSGI+VVA++  A   L   
Sbjct: 106 HPSPGWTGPTVIGGLAAAGYRISTSGAAERQGVVHRLDVGTSGIMVVAKSERAYTDLKRQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  R  +K Y +LV G P      +   + +  H   D+   V ++ K    +++H+ +I
Sbjct: 166 FHDRVTEKKYNALVQGHPDPLSGTVDAPIGR--HPSSDWKWAVTRDGK---PSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----- 288
           + + +    L+++  TGRTHQ+RVH   +  P VGD  Y A+        +  +L     
Sbjct: 221 EAY-RAASLLDIKLETGRTHQIRVHMSALRHPCVGDLTYGAD------PTLAKRLGLTRQ 273

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +LHA  +   HPE GR ++ ++  P  +    D++  +
Sbjct: 274 WLHAVSLGFEHPEDGRWVEFSSDYPEDLQHALDTIAAE 311


>gi|304388631|ref|ZP_07370694.1| pseudouridine synthase Rlu family protein [Neisseria meningitidis
           ATCC 13091]
 gi|304337403|gb|EFM03574.1| pseudouridine synthase Rlu family protein [Neisseria meningitidis
           ATCC 13091]
 gi|325137288|gb|EGC59876.1| RNA pseudouridylate synthase family protein [Neisseria meningitidis
           ES14902]
          Length = 219

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 101/212 (47%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 6   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 61

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R +A  L+  F  + I+K Y +L    P  K+  I   + +KS  G     + K  
Sbjct: 62  FALNRESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLT 115

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 116 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTE--- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 172 -----SETMFLYAWKIQFAY-QNRQIEIVAPL 197


>gi|293392894|ref|ZP_06637212.1| pseudouridine synthase A [Serratia odorifera DSM 4582]
 gi|291424753|gb|EFE97964.1| pseudouridine synthase A [Serratia odorifera DSM 4582]
          Length = 216

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 99/203 (48%), Gaps = 16/203 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G           +  VD    +    HRLD  TSG++VV
Sbjct: 13  ILYQDEHIIVVNKPSGLLSVPGRAPENKDSLMTRIQVDFPAAES--VHRLDMATSGVIVV 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A  +AA + L   FR R  +K Y + VWG  ++ +  +   L+       D+ +   Q  
Sbjct: 71  ALNKAAERELKRQFREREPKKSYIARVWGHLEHDEGMVDLPLI------CDWPNRPLQKV 124

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E G + A + ++V+   A     +++ P TGR+HQLRVH L +G PI+GD  Y     
Sbjct: 125 CFETGKS-AQTEYQVLSRDADGSTRVKLTPITGRSHQLRVHMLALGHPILGDGFYAHPQA 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               +    +L LHA+ + + HP
Sbjct: 184 KAMAA----RLQLHAQELRITHP 202


>gi|229844088|ref|ZP_04464229.1| tRNA pseudouridine synthase C [Haemophilus influenzae 6P18H1]
 gi|229813082|gb|EEP48770.1| tRNA pseudouridine synthase C [Haemophilus influenzae 6P18H1]
          Length = 239

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 63/238 (26%), Positives = 110/238 (46%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K +      ++   I   +     Q  
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLTVVRGYLQGKAQIDYPLKIQLDKIADKF----SQEN 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG+  AI+ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KGSQEAITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L     K  +  G++
Sbjct: 180 QYGDLHQNRALISHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWKKLINQFGWE 237


>gi|85712033|ref|ZP_01043087.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
 gi|85694219|gb|EAQ32163.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
          Length = 239

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 112/225 (49%), Gaps = 31/225 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V +KP+G+ V   S +A     F ++   D  GQ+    HRLD+ TSG+L+
Sbjct: 9   VVYKDEYLVVIDKPSGLLVHR-SWLASDAKRFAMQMLRDQLGQRVYPVHRLDRPTSGLLI 67

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A +   A+ L E F  R I+K+Y ++V G   +    I ++ LK+ H          Q 
Sbjct: 68  FALSSEIARALNEQFAERDIKKVYHAVVRGYVDDA--GIIDYALKEEH--DKIADKQAQA 123

Query: 220 EKGANYAISHFKVIDCFAQ--------------KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +K A  A++ ++   C A+              ++  +++ P TGR HQLR H  H+  P
Sbjct: 124 DKPAQEAVTEYQ---CVARVELPFKVSKKHDTSRYSLVKLMPLTGRKHQLRRHMSHIRHP 180

Query: 266 IVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           I+GD ++        F+ +F     ++L L +  ++  HP+ G+L
Sbjct: 181 IIGDTRHGEGRHNRFFREHFDC---HRLLLASTAIEFQHPKTGKL 222


>gi|260779409|ref|ZP_05888300.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260604499|gb|EEX30799.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 245

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 72/231 (31%), Positives = 111/231 (48%), Gaps = 24/231 (10%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           ++ED  I V NKP+G+ SV G +    H D     W   K   P +   HRLD  TSG++
Sbjct: 17  VFEDEGILVVNKPSGLLSVPGRA--EEHYDSM---WSRLKDIYPDIQPVHRLDMSTSGLM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A+ +     L + F+ R   K+Y++ VWG  + ++  +   L+       D+ +  KQ
Sbjct: 72  LFAKNKPTESALKKQFQFRLTHKVYYARVWGRVEQQEGEVDLPLI------CDWPNRPKQ 125

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E+G   + + F+V     Q    + + P TGR+HQLRVH   +G PIVGD  Y   
Sbjct: 126 KVCFEQGKP-SKTLFEVAKREEQT-TIVRLLPITGRSHQLRVHMQALGHPIVGDEFYSQG 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
               F+S    +L LHA  +   HP+  RL+    +P       ++L F Y
Sbjct: 184 EAFEFSS----RLELHAAELSFYHPQDERLRSIF-VPCDFYPEAEALIFNY 229


>gi|294626410|ref|ZP_06705011.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
 gi|292599295|gb|EFF43431.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
          Length = 244

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 112/238 (47%), Gaps = 26/238 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D  + V +KPAG+ V   S +A   D FL   +  +  KP  L HRLD+ TSG L+
Sbjct: 10  ILYQDDVLAVVDKPAGLMVHD-SKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLL 68

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R +A  L ++     ++K Y ++  G P  ++     +++     GG    V K  
Sbjct: 69  LAFDRDSASALGKALMAGEVEKQYLTVCRGWPAEER-----FIVDHDLDGGPGKPVKKP- 122

Query: 220 EKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 123 ------AVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGD 176

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
             +       +F     +++ LHA  ++ PHP +G R+ +TAPL     K     G++
Sbjct: 177 TSHGDGRHNRSFRMLGIHRMLLHAERLEFPHPADGRRIGVTAPLDVEFSKACALFGWE 234


>gi|255691622|ref|ZP_05415297.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           finegoldii DSM 17565]
 gi|260622691|gb|EEX45562.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           finegoldii DSM 17565]
          Length = 306

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 85/322 (26%), Positives = 147/322 (45%), Gaps = 43/322 (13%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQV 64
           Y  Y V    +E M L  +     P  +   L+ +L    V VD     +FN  +Q G  
Sbjct: 17  YTNYAV----KEPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLQPGMK 72

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI----SVQ 120
           V+I           KE+   + +  L K        ++YED+ I V  K  G+    + +
Sbjct: 73  VQIS----------KEKGKKEFNNRLLK--------IVYEDAYIIVVEKMQGLLSVNTER 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                AY I   L  +V   G++ R  + HRLD++TSG+++ A+     + L +++    
Sbjct: 115 QKERTAYTI---LNEYVQRSGRQFRVYIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHDIV 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             + Y ++V G  +     + ++L  ++     YV   +Q++ GA  +I+H++ I   A 
Sbjct: 172 TDRRYVAVVEGSMEKDYGTVESFLTDRTL----YVSSSQQDDGGA-LSITHYRTIKR-AN 225

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +E+   TGR +Q+RVH   +G PI+GD +Y      N  +PI  ++ LHA  +   
Sbjct: 226 GYSLIELDLETGRKNQIRVHMQDLGHPIIGDGRYGGE---NTPNPI-GRMALHAFKLCFY 281

Query: 299 HP-EGGRLQITAPLPAHMVKTW 319
           HP  G  ++   P PA   K +
Sbjct: 282 HPITGDLMEFETPYPADFKKLF 303


>gi|170726728|ref|YP_001760754.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169812075|gb|ACA86659.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 238

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 99/216 (45%), Gaps = 26/216 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  I V NKP+G+    G     +ID  +   +        L HRLD  TSGI+V+
Sbjct: 19  ILFEDEHILVINKPSGLLSLSGKH-PLNIDS-VHHRLAKIYPGCTLIHRLDFGTSGIMVL 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +     L + F  RR+ K Y +L+ G  +N    +   + K +    +   +++   
Sbjct: 77  ARNKVINALLCKQFSERRVSKRYTALLQGTVENDSGIVDIGIAKDT----ENFPLMRLCN 132

Query: 221 KGANYAISHFKVIDCFAQK----------------FCWLEMQPHTGRTHQLRVHALHMGC 264
           +    A S ++V+  F Q                    +E +P TGRTHQLR+H+ H+G 
Sbjct: 133 RTGKPAKSQYEVLSRFTQTAQDSFYVDDHRAGERAVSLVEFEPITGRTHQLRLHSKHLGH 192

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           PI+G   Y  +     TS    +L LHA  +   HP
Sbjct: 193 PILGCDLYATDEAFFMTS----RLMLHASLLTFEHP 224


>gi|134299211|ref|YP_001112707.1| RluA family pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134051911|gb|ABO49882.1| pseudouridine synthase, RluA family [Desulfotomaculum reducens
           MI-1]
          Length = 303

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 105/212 (49%), Gaps = 16/212 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQ--GGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGI 157
           +LYED+ +   NKP G+ V            +G L  W+      + R  HRLD+ TSGI
Sbjct: 86  ILYEDAHLLAVNKPPGMLVHPLTNETSGTLANGVLYHWLQQGTIDRFRPVHRLDRNTSGI 145

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++AR     Q L    +  +  + Y +LV G  + ++  I   +  +    G ++   +
Sbjct: 146 VLIARNPYVQQQLQIQMKQGQFVRRYLALVKGKVQPEQGVIQAPIALEE---GSFIK--R 200

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   AISH++V+  F Q    + ++  TGRTHQ+RVH  HMG P++GD  Y     
Sbjct: 201 MISPAGKEAISHYQVLRTFNQA-SLVRVELETGRTHQVRVHMAHMGHPLLGDSLY----- 254

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
           G  TS I+ +  LH  Y+   HP +G R++I+
Sbjct: 255 GGDTSNIKRQ-ALHCAYLAFNHPVQGSRIKIS 285


>gi|325697307|gb|EGD39193.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK160]
          Length = 298

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 93/201 (46%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 92  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 148

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      R I + YW+LV G   +KK      L+ K  IG D     K+  +
Sbjct: 149 KNPFVLPILNRLLEKREISRQYWALVQGKFPSKK------LIYKDKIGRDRHDRRKRLVD 202

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A +H   +  F Q    ++ Q  TGRTHQ+RVH  H G P+VGD  Y    +G 
Sbjct: 203 PRKGLFAETHVTRLKQFGQA-GLVKCQLKTGRTHQIRVHLAHHGHPLVGDPLYHPQPQG- 260

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 261 -------RLMLHAHRLTFTHP 274


>gi|299137599|ref|ZP_07030780.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX8]
 gi|298600240|gb|EFI56397.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX8]
          Length = 298

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 79/314 (25%), Positives = 130/314 (41%), Gaps = 33/314 (10%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Y    ++ +      L     + YPH      Q+ L SG+V ++      +  +  GQ +
Sbjct: 6   YAYTTIIGSKSRGQTLLSHLASLYPHSTLQAWQQNLDSGEVTLNGIIATGSESVTLGQTL 65

Query: 66  --RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
               PP I             DS     +H +     +L +DS +   NKP+G+    G 
Sbjct: 66  VWERPPWIEP-----------DSP----QHFE-----VLLDDSHLLAVNKPSGLPTLPGG 105

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G    ++  L   V  +       HRL + T+GI++ A+T  AA  L+ ++   RIQKIY
Sbjct: 106 GF---MENTLLRLVQKQNPNANPVHRLGRATTGIVLFAKTPQAASQLSANWNTSRIQKIY 162

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L  G+ +     I   +    H     +  V         + S  KVI        + 
Sbjct: 163 RALAQGVAQQDAYEILTPIGLVPH---PLIGSVWAASPSGKPSKSLAKVISRTTSTTTF- 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQNKLYLHARYMDLPHP 300
           E+  H+GR  Q+R+H   +G P+VGD  Y  N    +     P     +LHA+++   HP
Sbjct: 219 EVSLHSGRPQQIRIHLASIGHPLVGDPLYGLNGQPLEDRPGLPGDGGYFLHAQFLRFHHP 278

Query: 301 -EGGRLQITAPLPA 313
             G ++ + A LP+
Sbjct: 279 ITGEQITLEAALPS 292


>gi|332686149|ref|YP_004455923.1| ribosomal large subunit pseudouridine synthase D [Melissococcus
           plutonius ATCC 35311]
 gi|332370158|dbj|BAK21114.1| similar to ribosomal large subunit pseudouridine synthase D
           [Melissococcus plutonius ATCC 35311]
          Length = 290

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 68/213 (31%), Positives = 98/213 (46%), Gaps = 33/213 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +L+ED  + + NKP G+            +  H+  +LK     K Q P + HRLD+ETS
Sbjct: 83  VLFEDEHLIIINKPVGMKTHPNQPDENDTLLNHLTAYLKP----KQQIPYVVHRLDKETS 138

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKECIANWLLKKSHIGGDYVH 214
           G ++ A+       L      ++I + Y ++V GI  KN       W + K  IG D   
Sbjct: 139 GAILFAKNPFVLPILGRMLEKKQIYRCYQAIVDGIVLKN------TWTITKK-IGRDRHD 191

Query: 215 VVKQ--NEKGANYAISHFKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             K+  + K    AI+H +      Q+      C LE    TGRTHQ+RVH  + G PI+
Sbjct: 192 RRKRIIDSKHGMIAITHIQKAFTLTQENKTALLCRLE----TGRTHQIRVHLANAGFPII 247

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           GD  Y  N  GN       +L LHA  + + HP
Sbjct: 248 GDPLYNTNKTGN-----NKRLMLHAYELHIKHP 275


>gi|307710900|ref|ZP_07647326.1| RNA pseudouridylate synthase family protein [Streptococcus mitis
           SK321]
 gi|307617256|gb|EFN96430.1| RNA pseudouridylate synthase family protein [Streptococcus mitis
           SK321]
          Length = 278

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 91/201 (45%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 71  VYQDQHLVIVNKPEGMKTHGNQPNETALLNHVSAYV---GQTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+ V G   N KE +      K  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEISREYWAQVDGYI-NSKEIVF-----KDKIGRDRHDRRKRIVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F  K   +  +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 182 TKNGQYAETHVSRLKQFPNKTSLVRCKLKTGRTHQIRVHLSHHDLPILGDPLYNSKSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|153007158|ref|YP_001381483.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152030731|gb|ABS28499.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 350

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 74/327 (22%), Positives = 131/327 (40%), Gaps = 41/327 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            VE +    RLDR+ +     ++   +Q+++ +     D +R+K + R+ +G    +   
Sbjct: 39  TVEPNYAGWRLDRYLQEKIRRLSRERVQRLIETRLEAEDGRRLKPSTRVVAGLAFAL--- 95

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +          ++ D               ++++D  + V +KPAG+ V   +   Y  +
Sbjct: 96  LKDAEPEPDTPQVFD---------------VVHDDGALLVVDKPAGLPVHPTA--RYSAN 138

Query: 131 GFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            F   +      +K    HRLD+ETSG+L           +   F   R++K Y ++  G
Sbjct: 139 TFTSLARARFPDRKVDPAHRLDRETSGLLACGSAPEWTSRMKRDFAQGRVKKTYLAIAEG 198

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID----CFAQKFCWLEM 245
            P+     +   L   +  G   V V    + G   + + F+V+             L  
Sbjct: 199 APREDTFTVDAPL---ALTGASAVRVRMHVDAGGLASATDFEVLARRVLAGGVPVALLAC 255

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQNKL-----YLHAR 293
           +P TGR HQ+R H  H G P+VGD  Y  +        +   T     +L      LHA 
Sbjct: 256 RPRTGRQHQIRAHLAHAGLPMVGDKIYGPDENIFDRFTRHALTDEDHARLRLPRHALHAW 315

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTW 319
            ++LPHP     + + +PLP  +   W
Sbjct: 316 RLELPHPRTREPVGLESPLPPDLATFW 342


>gi|119898153|ref|YP_933366.1| pseudouridine synthase A [Azoarcus sp. BH72]
 gi|119670566|emb|CAL94479.1| pseudouridine synthase A [Azoarcus sp. BH72]
          Length = 236

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 67/216 (31%), Positives = 106/216 (49%), Gaps = 18/216 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETSGILVV 160
           L+ D    V +KP+G+    G G A   D   +  V        LT HRLD ETSG++V+
Sbjct: 33  LHIDPHFVVVSKPSGLLSVPGRG-AEKQDCLWRRVVHDFPDA--LTVHRLDMETSGLMVL 89

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           AR     + L+  F  R ++K Y ++V G+P + +  I   LL       D+ +  +Q  
Sbjct: 90  ARDAETHRRLSGLFHDRLVEKRYVAMVDGLPTSDRGQIDLPLL------ADWPNRPRQKV 143

Query: 219 NEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           + +G   +++ F+V+  +  +    + + P TGR+HQLRVH L +G PI+GD    A + 
Sbjct: 144 DFEGGKPSLTRFEVMARYPDRDVSRIALMPETGRSHQLRVHLLALGHPILGD----ALYG 199

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                    +L LHA ++   HP  G R+    P P
Sbjct: 200 SPSVQAKAERLLLHAEFLAFRHPHSGARVACECPAP 235


>gi|255283977|ref|ZP_05348532.1| ribosomal large subunit pseudouridine synthase D [Bryantella
           formatexigens DSM 14469]
 gi|255265430|gb|EET58635.1| ribosomal large subunit pseudouridine synthase D [Bryantella
           formatexigens DSM 14469]
          Length = 313

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 115/226 (50%), Gaps = 28/226 (12%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +K  ++YED  + V +KPA + V            +G+AY+ +   +++V       R  
Sbjct: 83  MKLDIVYEDEDLLVIDKPADMPVHPSIHNFDNTLANGLAYYYESRGEAFV------YRCI 136

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
            RLD++T+G+L+VA+   +   L E  + R I + Y ++V G  K + E   +  + +  
Sbjct: 137 TRLDRDTTGLLLVAKNMLSGAFLAEMGKRREIHREYLAIVTG--KTEAEGTVDAPIAR-- 192

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G  +      ++G   A++H++ ++ +   +  + ++  TGRTHQ+RVH  ++G P+ 
Sbjct: 193 VEGSVLERCVDFQRGER-AVTHYRTLE-YRDGYSLVRLKLETGRTHQIRVHMKYIGHPLT 250

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           GD  Y  +++      + +   LH+ Y+   HP  G R++ T+  P
Sbjct: 251 GDFLYNPDYR------LMDHQALHSHYLAFRHPITGERMEFTSQPP 290


>gi|290893595|ref|ZP_06556577.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J2-071]
 gi|290556797|gb|EFD90329.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J2-071]
          Length = 289

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 101/217 (46%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP  +        +Y  D     ++ +++  GQ       HRLDQ TS
Sbjct: 80  IIYEDDFLLVVNKPVDMKTHAND--SYETDTCANAVQYYLEKTGQDANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H KV++   +    L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHVKVLENDNENNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 253 -------SPRANRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|159487279|ref|XP_001701661.1| RNA pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158280880|gb|EDP06636.1| RNA pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 338

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 55/200 (27%), Positives = 88/200 (44%), Gaps = 23/200 (11%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +P + HR+D+ TSG++VVA+T  A   L   F+ R + ++Y S+  G P ++   +   +
Sbjct: 139 RPGIVHRIDKGTSGLIVVAKTETALTRLQAQFKARTVDRLYLSMTVGCPSSRSGRVETNI 198

Query: 203 LKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHA 259
            +     GD   +      G     A S ++V++  A   C L + +  TGRTHQ+RVHA
Sbjct: 199 SRDP---GDRKRMAAAPYGGTRGRTAASSYQVLEPLAGGGCALVQWKLDTGRTHQIRVHA 255

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQ----------------NKLYLHARYMDLPHP-EG 302
            HMG P++ D  Y        ++  +                 +  LHA  +   HP  G
Sbjct: 256 KHMGHPLLADDTYGGGGPAALSAVAKGGARSVEEVKACLERLGRPALHALTLGFSHPVSG 315

Query: 303 GRLQITAPLPAHMVKTWDSL 322
            RL    P P       + L
Sbjct: 316 KRLSFEQPPPEDFASALEQL 335


>gi|58337856|ref|YP_194441.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus NCFM]
 gi|227904506|ref|ZP_04022311.1| pseudouridylate synthase RluD [Lactobacillus acidophilus ATCC 4796]
 gi|58255173|gb|AAV43410.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus NCFM]
 gi|227867761|gb|EEJ75182.1| pseudouridylate synthase RluD [Lactobacillus acidophilus ATCC 4796]
          Length = 281

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 64/224 (28%), Positives = 97/224 (43%), Gaps = 22/224 (9%)

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
           FN ++  G  + I      L+HI   Q+I  +S NL          ++YED  + V NK 
Sbjct: 50  FNEQVFPGDRINI-----KLDHIDSLQQIYPASGNLPN--------IVYEDDDVLVINKN 96

Query: 115 AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            G   Q         D  L       G  P + HRLD  T G+L+VA+  A    L    
Sbjct: 97  KG---QKTHPNLNETDTALNDCATYLGSSPYIVHRLDMLTGGLLLVAKNPAVVPILNREL 153

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVI 233
             +   + Y + V    K K + I ++      IG D     K+  +     A++H++++
Sbjct: 154 TTKMFHREYIAKVNNTDKLKNKGIIDF-----PIGQDPDDQRKRMVRSDGLKAVTHYEIL 208

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                    +++   TGRTHQ+RVH    GCPI+GD  Y  NF+
Sbjct: 209 KTNPDNTGTVKLTLETGRTHQIRVHLAAKGCPIIGDPLYNPNFQ 252


>gi|304404376|ref|ZP_07386037.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
 gi|304346183|gb|EFM12016.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
          Length = 258

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 86/181 (47%), Gaps = 12/181 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ + V  KP G+  Q        +   LK  +  +  KP      L HRLD+   
Sbjct: 20  VLFEDNHLLVVVKPPGVPSQEDDSGDPDMLTLLKEDLKERHNKPGNVFLGLVHRLDRPVG 79

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYV 213
           G +V A+T  AA  L+E+ R R   K Y ++V G P      + +++ K  K ++   + 
Sbjct: 80  GAMVFAKTSKAASRLSETVRSRVFGKTYMAIVHGTPAQPYGTLKHYMRKDNKRNVSETFD 139

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V      A  A+  + V+D        + ++ HTGR+HQ+R     +GCP+ GD KY 
Sbjct: 140 RPVAD----AKEAVLDYAVMDRIGN-LSLVAVKLHTGRSHQIRAQMAAIGCPLYGDAKYG 194

Query: 274 A 274
           A
Sbjct: 195 A 195


>gi|159029331|emb|CAO90197.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 302

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 104/222 (46%), Gaps = 15/222 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +LYED+++ V  KP+G+ V  G G   H  I    + + D     P   HRL + TSGI+
Sbjct: 83  VLYEDTEVLVVAKPSGLPVLAGGGFLEHTLIHLVHQHYADVT---PYPIHRLGRGTSGIV 139

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++A+++ A   L++  R  +I KIY +LV    IP N    I   + K +H    YV+  
Sbjct: 140 LMAKSKPARSKLSQQMREGKITKIYRALVGQGDIPDNF--TINQAIGKIAHPILGYVYGA 197

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CAN 275
             +   A    S  +V+         LE++  TGR HQ+R+H    G P++GD  Y    
Sbjct: 198 LTDGLSAR---SEGRVLKKHLDS-TLLEVEIFTGRPHQIRIHLAFFGHPLIGDPLYSVGG 253

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
                  P     YLHA  +   HP  G R+ I  P P  +V
Sbjct: 254 LPRPDAVPGDCGYYLHANQILFNHPSTGERISICCPAPPELV 295


>gi|325127296|gb|EGC50231.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis N1568]
 gi|325131261|gb|EGC53972.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M6190]
 gi|325135413|gb|EGC58033.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M0579]
 gi|325201344|gb|ADY96798.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M01-240149]
 gi|325208870|gb|ADZ04322.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis NZ-05/33]
          Length = 217

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 101/212 (47%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 4   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R +A  L+  F  + I+K Y +L    P  K+  I   + +KS  G     + K  
Sbjct: 60  FALNRESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLT 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 114 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTE--- 169

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 170 -----SETMFLYAWKIQFAY-QNRQIEIVAPL 195


>gi|254853367|ref|ZP_05242715.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|300763946|ref|ZP_07073942.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
 gi|258606732|gb|EEW19340.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|300515287|gb|EFK42338.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
          Length = 289

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 67/217 (30%), Positives = 103/217 (47%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP  +        +Y  D     ++ +++  GQ       HRLDQ TS
Sbjct: 80  IIYEDDFLLVVNKPVDMKTHPND--SYETDTCANAVQYYLEKTGQDANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H KV++   +K   L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHVKVLENDNEKNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLY-- 250

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
              G F  P  N++ LHA  + L HP +G  +  +AP
Sbjct: 251 ---GGF--PRANRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|302533940|ref|ZP_07286282.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp. C]
 gi|302442835|gb|EFL14651.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp. C]
          Length = 313

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 78/317 (24%), Positives = 135/317 (42%), Gaps = 41/317 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++   G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAIARMF-GFSRTKAAELAAEGKVSVDGSVVGKSERVH 59

Query: 61  SGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
            G    V +P     +  + +    ++               ++++D  + V  KP G++
Sbjct: 60  GGAWLEVEMPAPPRPVELVAEPVPGME---------------IIHDDDDVVVIMKPVGVA 104

Query: 119 VQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTE 172
                G     + G L +    + + G   R  + HRLD  TSG++ VA++  A   L  
Sbjct: 105 AHPSPGWTGTTVIGGLAAAGYRISTSGASERQGIVHRLDVGTSGLMAVAKSERAYTSLKN 164

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            FR R + K Y +LV G P      I   + +  H   DY   V Q+ K    +++H+ +
Sbjct: 165 QFRERVVDKRYHALVQGHPDPMSGTIDAPIGR--HPSADYKWAVTQDGKA---SVTHYDL 219

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---- 288
           I+ F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  +L    
Sbjct: 220 IEAF-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPT------VAKRLGLTR 272

Query: 289 -YLHARYMDLPHPEGGR 304
            +LHA  +   HP  G+
Sbjct: 273 QWLHAVRLGFEHPADGQ 289


>gi|110803565|ref|YP_698546.1| pseudouridylate synthase [Clostridium perfringens SM101]
 gi|110684066|gb|ABG87436.1| pseudouridine synthase, RluA family [Clostridium perfringens SM101]
          Length = 324

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 80/298 (26%), Positives = 132/298 (44%), Gaps = 30/298 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ + +   +    + K LR G +RV+ K+ K    +  G V+ I  
Sbjct: 3   IEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLDGDVIEI-- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYH 128
               L  ++ ++K      N  +  D     ++YED  + +  K  G+ V       A  
Sbjct: 61  --RYLQSVVTKEK---KKPNF-QMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAPT 114

Query: 129 IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI+   +     + L E  R R++
Sbjct: 115 LTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKV 174

Query: 180 QKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS-HFKVIDCFA 237
            K Y +LV G I   K E    ++ K   +    V+     E+     I    KV+    
Sbjct: 175 NKYYCALVKGKIQPGKYEA---YISKDDELNKSTVY---DTERPDTKKIKMDVKVLQTNG 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             F  LE++  TGR+HQLR H  H+G PIVGD KY  N   +F    +NK  L  +++
Sbjct: 229 A-FSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSF---FENKFGLTYQFL 282


>gi|325914340|ref|ZP_08176687.1| tRNA pseudouridine synthase C [Xanthomonas vesicatoria ATCC 35937]
 gi|325539348|gb|EGD10997.1| tRNA pseudouridine synthase C [Xanthomonas vesicatoria ATCC 35937]
          Length = 245

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 112/243 (46%), Gaps = 31/243 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D  + V +KPAG+ V   S +A   D FL   +  +  KP  L HRLD+ TSG L+
Sbjct: 10  ILYQDDVLAVVDKPAGLMVHD-SKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLL 68

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R +A  L ++     + K Y ++  G P   +     +++     GG    V K  
Sbjct: 69  LAFDRDSASALGKALMAGEVDKNYLTVCRGWPAEDR-----FIVDHDLDGGPGKPVKKP- 122

Query: 220 EKGANYAISHFKVIDC---------FA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +           FA  ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 123 ------AVTHFQRLATGELEIPSTGFATSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGD 176

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT-----WDSL 322
             +       +F     +++ LHA  ++ PHP +G R+ + APL     K      WD  
Sbjct: 177 TSHGDGRHNRSFRMLGIHRMLLHAERLEFPHPADGRRISVVAPLDVEFAKACALFGWDVA 236

Query: 323 GFK 325
           G +
Sbjct: 237 GLQ 239


>gi|15602498|ref|NP_245570.1| hypothetical protein PM0633 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|12720907|gb|AAK02717.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 220

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 66/194 (34%), Positives = 96/194 (49%), Gaps = 20/194 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           L+Y+     V +KP GISV             L + V  +   P+  L HRLD+ TSG+L
Sbjct: 6   LIYQHPDFVVIDKPCGISVHKDEEAVG-----LTTLVAQQLDVPQVWLVHRLDKITSGLL 60

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A  + AA+ L+  F   RIQK Y +L    PK K+  I    ++K+  G   +   K 
Sbjct: 61  LLALNQRAARALSLLFAEHRIQKTYLALSQHKPKKKQGLIVGD-MQKARRGAWKLCPTKT 119

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           N      AI+ F  I+C      ++ ++P TG+THQLRV    +G PI+GD  Y  N   
Sbjct: 120 NP-----AITRFHSINCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDALYAGN--- 170

Query: 279 NFTSPIQNKLYLHA 292
              S   ++ YLHA
Sbjct: 171 ---SAKIDRTYLHA 181


>gi|262372045|ref|ZP_06065324.1| 23S RNA-specific pseudouridylate synthase [Acinetobacter junii
           SH205]
 gi|262312070|gb|EEY93155.1| 23S RNA-specific pseudouridylate synthase [Acinetobacter junii
           SH205]
          Length = 228

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 66/218 (30%), Positives = 105/218 (48%), Gaps = 22/218 (10%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L++ D    V +KPAG+    G      +   L + +     K  L HRLD++
Sbjct: 16  SDFLSEHLIHRDEDFMVIHKPAGLLTVPGK--TPDLQDCLINRLLKLEPKTLLIHRLDRD 73

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++    H++  F+ R+  KIY +LV G  + +       +   S      +
Sbjct: 74  TSGILVFGLSKFGQSHISRQFQDRQTSKIYQALVAGHLEGEGIVDIPVIYDPSR---PPL 130

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+V  +      A++ ++VI+    K      +++ P TGR+HQLRVH  ++G PI+GD 
Sbjct: 131 HIVDASHHKP--ALTEWQVIEHLEIKGHPVTRVQLVPITGRSHQLRVHMQYLGHPILGDT 188

Query: 271 KYCANFKGNFTSPIQNKLY----LHARYMDLPHPEGGR 304
            Y         +P Q +LY    LHA  +   HP+  +
Sbjct: 189 LYA--------TPEQQQLYDRLCLHATELSFTHPKTAQ 218


>gi|218896324|ref|YP_002444735.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
 gi|228899971|ref|ZP_04064209.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|218541071|gb|ACK93465.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
 gi|228859657|gb|EEN04079.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
          Length = 307

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 69/228 (30%), Positives = 112/228 (49%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NK   +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKLEQMDTHPAEKGGNGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y    K        +   LHA  ++  HP     +++  P P  +
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPTKL 295


>gi|146278941|ref|YP_001169100.1| pseudouridine synthase [Rhodobacter sphaeroides ATCC 17025]
 gi|145557182|gb|ABP71795.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides ATCC 17025]
          Length = 215

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 68/220 (30%), Positives = 107/220 (48%), Gaps = 27/220 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           L++ D++I V +KPAG+    G G     D  ++     +G  P   L HRLD++TSG++
Sbjct: 14  LIHHDAQIVVVDKPAGLLSVPGKG-EDKADCLIERL---RGVFPEILLVHRLDRDTSGVM 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKK---ECIANWLLKKSHIGGDYV 213
           V A TRAA   L + F  R+ +K+Y + + G   P+  +       +W  +         
Sbjct: 70  VFALTRAAQAALGQQFEKRQTKKVYVARLEGRLEPREGRVDLPLCVDWPNRPRQ------ 123

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           HV   N + A    + ++V+     +   + + P TGR+HQLRVH    G PI+GD  Y 
Sbjct: 124 HVDHVNGRPAQ---TDWRVVKYLPNE-TRVRLMPVTGRSHQLRVHMAETGHPILGDALYA 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           A            +L LHA  + + HP+ G+ L  +AP P
Sbjct: 180 AGAARE-----HPRLMLHAESLRVRHPDTGKSLTYSAPCP 214


>gi|116071041|ref|ZP_01468310.1| putative pseudouridylate synthase [Synechococcus sp. BL107]
 gi|116066446|gb|EAU72203.1| putative pseudouridylate synthase [Synechococcus sp. BL107]
          Length = 219

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 69/217 (31%), Positives = 102/217 (47%), Gaps = 14/217 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +LY D  +   +KP+G+  Q G G     D  + S V +  Q P  RL HRLD++TSG+L
Sbjct: 8   VLYRDRWLLAVDKPSGLLSQPGLG-PDQADSLI-SRVQAHDQAPDWRLVHRLDRDTSGVL 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A    A +  +  F  R + K+Y + V G+   +  CI N L +       Y    + 
Sbjct: 66  VLAAGLEALRRTSALFSNRCVNKLYLAHVHGVLAGRG-CIHNRLARLQRQPPRYGSHPEG 124

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E       S    +   A +   L ++P TGR+HQLR H   +  PI+GD  Y     G
Sbjct: 125 REA------STLWRVRSSAAEVTQLWLRPITGRSHQLRSHLAEIAHPIIGDPIYGDPIDG 178

Query: 279 N--FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +    SP   +L LHA  +   HP  G RL++ +  P
Sbjct: 179 DQAAESPFSQRLRLHAIALSFCHPFTGQRLRLLSADP 215


>gi|313636721|gb|EFS02383.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri FSL S4-171]
          Length = 294

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 101/217 (46%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP G+        +Y  D     ++ +++   Q       HRLDQ TS
Sbjct: 85  VIYEDDFLLVVNKPVGMKTHPND--SYETDTCANAVQYYLEQTNQDANALAVHRLDQTTS 142

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 143 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 198

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H  V++   +K   L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 199 -RQISPYGQPAVTHITVLENDTEKNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 257

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 258 -------SPRANRIMLHAEKLHLNHPFKGKEMNFSAP 287


>gi|296436545|gb|ADH18715.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           G/11222]
          Length = 303

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 77/304 (25%), Positives = 137/304 (45%), Gaps = 54/304 (17%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINAL 74
           +  +RL  + +   PH+    + + +R    RV+ +  +F + ++Q G  V         
Sbjct: 9   DRQIRLSSFLRTSLPHLPKKTILESVRYHGCRVNGRIERFESYKLQPGDRV--------- 59

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                       S+ + +HS      LL+ED  + ++NKPA    Q    +A+ ++    
Sbjct: 60  ------------SLQIIEHSS---PQLLWEDEHLCIYNKPAK---QTSEDLAHQLNV--- 98

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                      L HRLD++TSG ++ A+   A+  +T+ F+ R I K Y +LV+G P+ +
Sbjct: 99  ----------HLVHRLDRDTSGCILFAKHAKASSLITQLFKNREIDKRYIALVFGQPRQE 148

Query: 195 KECIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
              I  +       IG        QN       I+ ++++  +  K+  L  +P TGRTH
Sbjct: 149 SGIITTYTAPCYRRIGAVLFGNTDQN--SGKITITKWEILTRYP-KYTLLLCRPVTGRTH 205

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAP 310
           Q+R+H   +G PIVGD  Y     GN   P +N  +  LHA  +    P    ++++++ 
Sbjct: 206 QIRLHMKTIGHPIVGDVDY-----GNQEQP-KNVVRTLLHAASLAFTSPFSNEKIEVSSL 259

Query: 311 LPAH 314
            P+ 
Sbjct: 260 TPSQ 263


>gi|268319938|ref|YP_003293594.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
 gi|262398313|emb|CAX67327.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
          Length = 282

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 113/239 (47%), Gaps = 24/239 (10%)

Query: 41  LRS-GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           LRS  ++ V+ K +  N  ++ G  + I      L+HI  +Q+   +S  L K       
Sbjct: 36  LRSEKKILVNGKYLPLNFLVKPGDKIEI-----QLDHIESDQQTYPASGKLPK------- 83

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++YED+ I V NKPAG   Q         D  L       G  P + HRLD  TSG+L+
Sbjct: 84  -VVYEDNDILVINKPAG---QKTHPNLNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLL 139

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQ 218
           VA+  A    L      + + + Y + +   P+ K   I +  L   H   D    +V+Q
Sbjct: 140 VAKNPAVVPILNRQLTDKTLHREYLAWISNSPQIKNTGIID--LPIGHDPHDQRKRMVRQ 197

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +      A++H++VI     +   +++   TGRTHQ+RVH   +G PI+GD  Y ++++
Sbjct: 198 D---GQKAVTHYEVIKRDKDRIL-VKLTLETGRTHQIRVHLAALGAPIIGDPLYNSDYQ 252


>gi|295109974|emb|CBL23927.1| pseudouridine synthase, RluA family [Ruminococcus obeum A2-162]
          Length = 330

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 77/321 (23%), Positives = 140/321 (43%), Gaps = 29/321 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           + ++E   R D++      +       K+LR   + ++ K+   N ++++G  +++    
Sbjct: 6   ITDNEAGQRFDKYLAKLLGNAPKSFFYKMLRKKNITLNGKKASGNEKLKNGDQIKLFLSD 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS----GIAY 127
           +      ++++   +  +L          +LYEDS I + +KP G+  Q        +  
Sbjct: 66  DTFAKFSQQEQTARAVTDLD---------ILYEDSDILLISKPVGMLSQPDDTKEPSLVE 116

Query: 128 HIDGFL--KSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           ++ G+L     +  +G +   P + +RLD+ TSGI+   ++ A  Q L+  F  R I K 
Sbjct: 117 YLIGYLLNNGSITEEGLRTFHPSVCNRLDKNTSGIVAAGKSLAGLQELSSLFHDRTIHKD 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  +V GI  + K+ I  +L K + +  + V + K   K A    + ++ +         
Sbjct: 177 YLCIVKGILTDNKQ-IRGYLYKDTKL--NKVTISKIKIKDAQPIETRYEPL-GHTSHMTL 232

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
           L ++  TGRTHQ+R H    G P+ GD KY    F   F      N   LHA  +  P  
Sbjct: 233 LRVRLITGRTHQIRAHLASEGHPLAGDMKYGQKEFNRYFHEKYHLNHQLLHAYRLTFPEL 292

Query: 301 EGGRLQIT-----APLPAHMV 316
            G    ++     APLP   +
Sbjct: 293 TGKLATLSGKCFLAPLPKQFL 313


>gi|294140341|ref|YP_003556319.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293326810|dbj|BAJ01541.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 218

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 63/203 (31%), Positives = 99/203 (48%), Gaps = 14/203 (6%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  I V NKP+G+    G   A   D  L   +  +  +  L HRLD  TSGI+V A 
Sbjct: 18  YQDRDILVINKPSGLLSNPGRA-ANTYDCALTRLL-QRYPEIILVHRLDCATSGIMVFAL 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            + A  ++   F+ R  +K Y + V G   N+ + + +  +K   I      + +  +  
Sbjct: 76  NKKAESNIKTQFQNRMSKKTYIAEVLG-QLNQDQGVIDLAMKADKIRPPLQEIAEDGKVS 134

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-T 281
             Y    +KV++   +    +E++P TGRTHQLR+H L +G PI+GD      F G+   
Sbjct: 135 KTY----YKVLER-RETSTLVELKPVTGRTHQLRLHMLALGHPILGDE-----FYGDADV 184

Query: 282 SPIQNKLYLHARYMDLPHPEGGR 304
               N+L LHA  + + HP  G+
Sbjct: 185 IAASNRLKLHAMSLTIAHPFSGK 207


>gi|294645548|ref|ZP_06723244.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|294808025|ref|ZP_06766800.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|292639122|gb|EFF57444.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|294444778|gb|EFG13470.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
          Length = 615

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 80/262 (30%), Positives = 116/262 (44%), Gaps = 76/262 (29%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ED  + V NKPAG +SV G +      YH     K + ++ G  P + HRLD  TSG
Sbjct: 347 IVFEDEWLLVVNKPAGMLSVPGKAEDRDSVYH--RLKKKYPEATG--PMIVHRLDMATSG 402

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC--IAN--WLLKKSHIGG- 210
           +L+VA+T+   Q L   F  R I+K Y +++ G I K +KE   IA    LL K  +   
Sbjct: 403 LLLVAKTKEVHQDLQAQFANRSIKKRYVAVLDGAIIKTEKETKPIAEKAILLAKETVSTK 462

Query: 211 -----------------------DYVHVVKQNEKGANYAISHFKVI-----------DCF 236
                                  D    +   E G   AI+ +++I           + F
Sbjct: 463 KTAKAERTGNTGRIELPLCLNPLDRPRQMVSREHGKE-AITEYQIISESERITSESENTF 521

Query: 237 ---------------AQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKG 278
                          ++K+  +   P TGRTHQLRVHA H   +GCPI+GD  Y      
Sbjct: 522 NESNRIDESERSINESRKYTRIIFYPLTGRTHQLRVHAAHPEGLGCPILGDELYGKK--- 578

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                  ++LYLHA Y++  HP
Sbjct: 579 ------ADRLYLHAEYIEFRHP 594


>gi|160946974|ref|ZP_02094177.1| hypothetical protein PEPMIC_00936 [Parvimonas micra ATCC 33270]
 gi|158447358|gb|EDP24353.1| hypothetical protein PEPMIC_00936 [Parvimonas micra ATCC 33270]
          Length = 318

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 81/303 (26%), Positives = 141/303 (46%), Gaps = 44/303 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V N++   R+DR+ K +  + +   +QK LR+ +++V++K+V       S  ++    
Sbjct: 4   IEVNNNDSGQRIDRFLKKYLNNASTSMIQKFLRTKKIKVNRKKV------DSNYILAEND 57

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-- 127
           VIN   +  + +K++ S      +S  L   ++YED  I V NKP  +     S   Y  
Sbjct: 58  VINIFIYEEELEKLIVSKSKKYSYSKKLD--IIYEDENIIVMNKPKNLLSHASSKEDYGN 115

Query: 128 HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           ++  F+  ++  KG           P + +RLD+ TSG+++ A+   A + L    +   
Sbjct: 116 NLVDFMIGYLLEKGDYNPRAEKTFVPAIINRLDRNTSGLVIGAKNSKALRELNR-LKENS 174

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I+K Y ++V G  K KK  + N  L+K          + +N K +        + + + +
Sbjct: 175 IEKYYKTIVSG--KVKKNFVINEKLEKDEEKNK--STISKNGKDS--------ITEIYVE 222

Query: 239 K----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLY 289
           K    F  L+++  TGRTHQ+R H    G  I+GD KY        F+ NF    Q   +
Sbjct: 223 KNNDEFSLLKIKLITGRTHQIRSHLSSKGFYIIGDIKYGNAKVNKFFRDNFNLRSQ---F 279

Query: 290 LHA 292
           LHA
Sbjct: 280 LHA 282


>gi|325920613|ref|ZP_08182526.1| tRNA pseudouridine synthase C [Xanthomonas gardneri ATCC 19865]
 gi|325548904|gb|EGD19845.1| tRNA pseudouridine synthase C [Xanthomonas gardneri ATCC 19865]
          Length = 245

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 113/243 (46%), Gaps = 31/243 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +L++D  + V NKPAG+ V   S +A   D FL   +  +  +P  L HRLD+ TSG L+
Sbjct: 10  ILHQDDVLAVVNKPAGLMVHD-SKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGCLL 68

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R +A  L ++     ++K Y ++  G P  ++     +++     GG    V K  
Sbjct: 69  LAFDRESASTLGKALMAGELEKDYLTVCRGWPAEEQ-----FIVDHDLDGGPGKPVKKP- 122

Query: 220 EKGANYAISHFKVIDC---------FA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +           FA  ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 123 ------AVTHFQRLATGELEIPSTGFATSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGD 176

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT-----WDSL 322
             +       +F     +++ LHA  +  PHP +G RL + APL     K      WD  
Sbjct: 177 TSHGDGRHNRSFRMLGIHRMLLHAERLGFPHPADGRRLSVVAPLDVEFAKACALFGWDVA 236

Query: 323 GFK 325
           G +
Sbjct: 237 GLQ 239


>gi|300858799|ref|YP_003783782.1| hypothetical protein cpfrc_01382 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|300686253|gb|ADK29175.1| hypothetical protein cpfrc_01382 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|302331059|gb|ADL21253.1| Putative pseudouridine synthase [Corynebacterium pseudotuberculosis
           1002]
          Length = 307

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 70/276 (25%), Positives = 125/276 (45%), Gaps = 30/276 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-L 101
           +G V VD   V  ++RI  GQ + +                L  + +LT   + ++ + +
Sbjct: 39  AGDVLVDALPVGKSDRIAEGQWLDV---------------TLPETKDLTPREELVEGMDI 83

Query: 102 LYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           LY D  +   NKP G++       +G + I        +       ++  +  RLD  TS
Sbjct: 84  LYSDDDLIAVNKPVGVAAHPTLGWEGPTVIGGLAAAGFRISTSGPPERKGIVQRLDVGTS 143

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V+A +      L  +F+ R + K Y +LV G        I   + +  H    +   
Sbjct: 144 GVMVIAASERGYSVLKRAFKERTVSKTYHALVQGHMDPFTGTIDAPIGR--HPSAGWRFA 201

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  + K   +A++H++ ++ FA+    L++   TGRTHQ+RVH   +  P  GD  Y ++
Sbjct: 202 VTSDGK---HAVTHYETLEAFAEA-SLLKIHLETGRTHQIRVHMSALHHPCCGDPMYGSD 257

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            K +    +  + +LHA  +   HP  GR ++IT+P
Sbjct: 258 PKLSERLGLTRQ-WLHAVSLGFNHPADGRWMEITSP 292


>gi|322388362|ref|ZP_08061965.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           infantis ATCC 700779]
 gi|321140675|gb|EFX36177.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           infantis ATCC 700779]
          Length = 291

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 60/201 (29%), Positives = 92/201 (45%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPDEIALLNHVSAYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G         A  L+ +  IG +     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWALVDG------RLGAKDLIYRDKIGRNRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +K   YA +H   +  F  K   +  +  TGRTHQ+RVH  H G PI+GD  Y  + K  
Sbjct: 195 QKNGQYAETHVTRLKQFQNKTSLVRCRLKTGRTHQIRVHLSHHGHPILGDPLYNPHSKN- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 254 ------KRLMLHAFKLSFIHP 268


>gi|160874211|ref|YP_001553527.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160859733|gb|ABX48267.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315266445|gb|ADT93298.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 574

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 76/248 (30%), Positives = 122/248 (49%), Gaps = 31/248 (12%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H++ E  ++D +  LT  ++     +LY+D  + + NKPA      G  I   +   +
Sbjct: 340 LGHML-EGLVVDENPLLTNPAEGKTLAILYQDDAMAIVNKPAEFLSVPGKEIEDSVYSRM 398

Query: 134 K-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           + ++  + G  P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ G+P 
Sbjct: 399 RQTFPHTTG--PLIVHRLDMSTSGLMVIALTKEAHKQLQKQFIQRTVTKRYVALLAGMPA 456

Query: 193 --NKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKV--IDCFAQKFCWLEM 245
               K+   +  L    + GD     +Q   +E G   A +H+++  +D  A +   + +
Sbjct: 457 VMANKQATGHISLP---LRGDLDDRPRQLVCHEFG-KAAETHWELSQLDEMA-RTARVYL 511

Query: 246 QPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-- 300
            P TGRTHQLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP  
Sbjct: 512 YPKTGRTHQLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHPVT 562

Query: 301 -EGGRLQI 307
            E  R Q+
Sbjct: 563 RERMRFQV 570


>gi|224533460|ref|ZP_03674053.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           CA-11.2a]
 gi|224513422|gb|EEF83780.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           CA-11.2a]
          Length = 313

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 66/260 (25%), Positives = 127/260 (48%), Gaps = 32/260 (12%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R G +R++  +  F+ R+  G  + +   + A N  +   +   S+++      +++  
Sbjct: 37  IRKGDIRLNGLKSHFSCRVCKGDKIYLYKSL-AQNLNLTMDECFKSNIDFK----YIRKR 91

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGIL 158
           ++YEDS + V +K  GI V GG + + + ++ +L S  + S   KP   HRLD+ TSGI+
Sbjct: 92  IIYEDSDLLVLDKQKGILVHGGKNSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGII 151

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN----KKECIANWLLKKSHI--GGDY 212
           + A+    A+ L+ +F    I K Y++++ G  K+    K     N  L+K+ +  G ++
Sbjct: 152 IFAKNINTARKLSAAFSGGSIIKKYFAILLGEVKSPVVYKNHLFRNKRLRKTFVLEGKNF 211

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+ + +             ++ C  ++   +E+   TG THQ+R        P++ D KY
Sbjct: 212 VNAITKVN----------PILSC--KRATLVEIVIETGFTHQIRSQCSFNNHPLINDKKY 259

Query: 273 CANFKGNFTSPIQNKLYLHA 292
           C  FK       ++  +LHA
Sbjct: 260 CNKFK-------KSDYFLHA 272


>gi|313632225|gb|EFR99288.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri FSL N1-067]
          Length = 289

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 101/217 (46%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP G+        +Y  D     ++ +++   Q       HRLDQ TS
Sbjct: 80  VIYEDDFLLVVNKPVGMKTHPND--SYETDTCANAVQYYLEQTNQDANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H  V++   +K   L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHITVLENDTEKNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 253 -------SPRANRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|312148138|gb|ADQ30797.1| RNA pseudouridine synthase family [Borrelia burgdorferi JD1]
          Length = 305

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 67/260 (25%), Positives = 126/260 (48%), Gaps = 32/260 (12%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R G +R++  +  F+ R+  G  + +   + A N  +   K   S+++      +++  
Sbjct: 29  IRKGDIRLNGLKSHFSCRVCKGDKIYLYKSL-AQNLNLTTDKCFKSNIDF----QYIRKR 83

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGIL 158
           ++YEDS + V +K  GI V GG + + + ++ +L S  + S   KP   HRLD+ TSGI+
Sbjct: 84  IIYEDSDLLVLDKQKGILVHGGKNSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGII 143

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN----KKECIANWLLKKSHIGGD--Y 212
           + A+    A+ L+ +F    I K Y++++ G  K+    K     N  L+K+ +  D  +
Sbjct: 144 IFAKNINTARKLSAAFSGGSIIKKYFAILLGEVKSPVVYKNHLFRNKRLRKTFVLEDKNF 203

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+ + +             ++ C  ++   +E+   TG THQ+R        P++ D KY
Sbjct: 204 VNAITKVN----------PILSC--KRATLVEIVIETGFTHQIRSQCSFNNHPLINDKKY 251

Query: 273 CANFKGNFTSPIQNKLYLHA 292
           C  FK       ++  +LHA
Sbjct: 252 CNKFK-------KSDYFLHA 264


>gi|86160593|ref|YP_467378.1| pseudouridine synthase RluD [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85777104|gb|ABC83941.1| Pseudouridine synthase, RluD [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 318

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 78/328 (23%), Positives = 130/328 (39%), Gaps = 41/328 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            VE +    RLDR+ +     ++   +Q+++       D +R+K + R+  G    +   
Sbjct: 10  TVEPNYAGWRLDRYLQEKIRRLSRERVQRLIAQRLETDDGRRLKPSTRVAPGLSFAL--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                       + D+        +F    ++++D  + V +KPAG+ V   +  A +  
Sbjct: 67  ------------LKDAEAEPDTPQEF---GVVHDDGALLVVDKPAGLPVHPTARYAANTF 111

Query: 131 GFLKS--WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             L    + D K       HRLD+ETSG+L         + L   F   R+ K Y +L  
Sbjct: 112 TSLAKLRYPDRKVDP---AHRLDRETSGLLACGTAPEVTKVLKRDFAHARVHKTYLALAL 168

Query: 189 GIPKNKKECI-ANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEM 245
           G P      + A   L  +      +HV  +    + A   ++  +  D        L  
Sbjct: 169 GAPAEDAFTVDAPLALTGASAVRVRMHVAAEGLPSQTAFEVLARRRAPD--GAPVALLAC 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKL----------YLHAR 293
           +P TGR HQ+R H  H G P+VGD  Y  + +    FT                  LHA 
Sbjct: 227 RPRTGRQHQIRAHLAHAGLPMVGDKIYGPDEEIFDRFTRRAMTDADLALLRLPRHALHAW 286

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWD 320
            ++LPHP     +++ APLP  +   W+
Sbjct: 287 RLELPHPLTRAPVRLEAPLPPDLAAFWE 314


>gi|323495785|ref|ZP_08100855.1| pseudouridylate synthase, 23S RNA-specific [Vibrio sinaloensis DSM
           21326]
 gi|323319252|gb|EGA72193.1| pseudouridylate synthase, 23S RNA-specific [Vibrio sinaloensis DSM
           21326]
          Length = 559

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 71/206 (34%), Positives = 104/206 (50%), Gaps = 24/206 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + V NKP+G+    G  I+      L++ + D +G  P + HRLD  TSG+LV
Sbjct: 358 ILYSDDAMVVVNKPSGLLSVPGKTISDSAYTRLQALYPDVEG--PFVIHRLDMATSGLLV 415

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A TR A + L + F  R ++K Y +L+ G      E  A        + GD     +Q 
Sbjct: 416 FALTRRANKSLQKQFISRSVKKRYVALLEG------EVSAQSGDIDLPMRGDPEDRPRQL 469

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCA 274
             E+    A +H+++I+    K   L M P TGRTHQLRVH  H   +  P+VGD  Y  
Sbjct: 470 VCEQHGKPAKTHWQLIETI-DKRSKLYMYPLTGRTHQLRVHCAHHLGLNMPMVGDVLY-- 526

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
              GN      ++L+LHA  +++ HP
Sbjct: 527 ---GNKA----DRLHLHAERLEIDHP 545


>gi|317050965|ref|YP_004112081.1| pseudouridine synthase [Desulfurispirillum indicum S5]
 gi|316946049|gb|ADU65525.1| pseudouridine synthase [Desulfurispirillum indicum S5]
          Length = 273

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 110/240 (45%), Gaps = 23/240 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++Y D  +   +KPAG+ V   S   +     ++   D  GQ     HRLD+ TSG+L+
Sbjct: 12  VIVYRDDHLIAIHKPAGLLVHRSSIDRHETRFAMQLLRDQIGQPVYPVHRLDKPTSGVLL 71

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A     A+ L   F    + K Y ++V G+P   +  I +  L++      Y       
Sbjct: 72  FALNPEVARLLGALFVSAAVAKTYLAVVRGVPP--RSGIIDSPLREER--NRYDDQRTAL 127

Query: 220 EKGANYAISHFK----VIDCFA------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           EK    A++ F+    V   FA       ++  +E+QP TGR HQ+R H  H+  P++GD
Sbjct: 128 EKAPQSAVTRFQTRATVELPFAVGPYPTSRYALVEVQPQTGRRHQIRRHFKHLCHPLIGD 187

Query: 270 HKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            KY        F+ +F      +L L A  + L HP  G  L IT+PL  +  +   +LG
Sbjct: 188 TKYGEGRHNRFFRDHFGC---QRLLLAAVELQLNHPVNGMPLVITSPLEENFRELVTALG 244


>gi|256371990|ref|YP_003109814.1| pseudouridine synthase, RluA family [Acidimicrobium ferrooxidans
           DSM 10331]
 gi|256008574|gb|ACU54141.1| pseudouridine synthase, RluA family [Acidimicrobium ferrooxidans
           DSM 10331]
          Length = 309

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 105/230 (45%), Gaps = 32/230 (13%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHI--------DGFLKSWVDSK---GQKPR--L 146
           ++ YED  + V +KPAG+ V        H+        D  L+ W   +   G   R  L
Sbjct: 79  VVCYEDDDVAVIDKPAGLIVH-----RTHLRDVRPSVADWALERWPSLRALPGDPLRRGL 133

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ TSG++V+A +  A + L  +     +++ Y +LV G+P       A   L + 
Sbjct: 134 VHRLDRGTSGLMVIALSAGAYESLRRAVHDHEVERRYRALVVGVPPQAARIEAP--LGRD 191

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                 V VV     G   A +  +V+         +E+   TGRTHQ+RVH   +G PI
Sbjct: 192 LRDLSRVAVVS----GGRDARTQLRVV-WHGPDTSLVELTLETGRTHQIRVHLSAIGHPI 246

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           VGD  Y   + G    P     +LHA  +   HP   GR+++TA LP  +
Sbjct: 247 VGDEVYGVPY-GGLERP-----FLHATALAFEHPTRPGRVEVTAELPEDL 290


>gi|227874477|ref|ZP_03992652.1| pseudouridylate synthase [Oribacterium sinus F0268]
 gi|227839666|gb|EEJ50121.1| pseudouridylate synthase [Oribacterium sinus F0268]
          Length = 335

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 61/223 (27%), Positives = 104/223 (46%), Gaps = 23/223 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED  I + +KPA +      G     +A  I  +      +        HRLD +TS
Sbjct: 92  IVYEDRDILLLDKPARLPCHPSPGHFEKTLAGAIVFYQMQNSSASSFVCHFIHRLDLDTS 151

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW--LLKKSHIGGDYV 213
           G++++A+ R AA  L +  +  RIQ+ Y +   G P+     I  +  L +K     +Y 
Sbjct: 152 GLILLAKNRLAASVLNKDMKEGRIQRSYLAFCQGNPEFSLGEIQGFTRLEEKKKKEFNYA 211

Query: 214 HVVKQ--------------NEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVH 258
             +                N +    A+S+F V++ F +K +  L++Q  TGRTHQ+RVH
Sbjct: 212 FAISAPIARVEEEKMLRTVNFQKGQEALSYFNVLNYFPEKNYSLLQLQLATGRTHQIRVH 271

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
             ++ CP++GD  Y    +  F+  I  ++  LH+  +   HP
Sbjct: 272 LSYLSCPLLGDSLYGNGEESVFSQNIGLSRQALHSYSISFTHP 314


>gi|297194901|ref|ZP_06912299.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           pristinaespiralis ATCC 25486]
 gi|297152522|gb|EFH31815.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           pristinaespiralis ATCC 25486]
          Length = 313

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 80/311 (25%), Positives = 135/311 (43%), Gaps = 29/311 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V+VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVQVDGSVVGKSERVH 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPQAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIVKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +    + + G   R  + HRLD  TSG++VVA++  A   L + 
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGASERQGIVHRLDVGTSGLMVVAKSERAYTLLKQQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R + K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I
Sbjct: 166 FRERVVDKRYHALVQGHPDPLSGTIDAPIGR--HPTADYKWAVTAEGK---PSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAF-RAASLLDIKLETGRTHQIRVHMAAHRHPCVGDLTYGADPTMAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHPEGGR 304
            +   HP  G+
Sbjct: 279 RLGFEHPSDGQ 289


>gi|268590539|ref|ZP_06124760.1| tRNA pseudouridine synthase [Providencia rettgeri DSM 1131]
 gi|291313926|gb|EFE54379.1| tRNA pseudouridine synthase [Providencia rettgeri DSM 1131]
          Length = 252

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 109/246 (44%), Gaps = 49/246 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y D  +   NKPAG+ V              +SW+DSK             GQ     
Sbjct: 4   IIYHDEYMVAVNKPAGMLVH-------------RSWLDSKETVFVMQTLRDQIGQYVYPI 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSGIL+ A +   A+ L+  F   +++K+Y ++V G    ++      L +   
Sbjct: 51  HRLDRPTSGILLFALSSDVARLLSAQFENHQLEKVYHAVVRGYLTEEQTIDYPLLEELDK 110

Query: 208 IGGDYVHVVKQNEKGANYAISHFK---VIDCF-------AQKFCWLEMQPHTGRTHQLRV 257
           I   +       E      ++H K    ++C          +F  +E++P TGR HQLR 
Sbjct: 111 IADKHA----SREPVLQECVTHCKPIATVECAIAIGRYETSRFSLVELKPETGRKHQLRR 166

Query: 258 HALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           H  H+  PI+GD K+      +G  T    ++L LHA  ++L HP      IT      +
Sbjct: 167 HMSHLRHPIIGDSKHGDLRQNRGVNTHFSVSRLMLHASLLNLNHP------ITKE-NISL 219

Query: 316 VKTWDS 321
           V TWD+
Sbjct: 220 VATWDT 225


>gi|221217613|ref|ZP_03589082.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           72a]
 gi|225550261|ref|ZP_03771220.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           118a]
 gi|221192559|gb|EEE18777.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           72a]
 gi|225369129|gb|EEG98583.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           118a]
          Length = 313

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 66/260 (25%), Positives = 127/260 (48%), Gaps = 32/260 (12%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R G +R++  +  F+ R+  G  + +   + A N  +   +   S+++      +++  
Sbjct: 37  IRKGDIRLNGLKSHFSCRVCKGDKIYLYKSL-AQNLNLTMDECFKSNIDFK----YIRKR 91

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGIL 158
           ++YEDS + V +K  GI V GG + + + ++ +L S  + S   KP   HRLD+ TSGI+
Sbjct: 92  IIYEDSDLLVLDKQKGILVHGGKNSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGII 151

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN----KKECIANWLLKKSHI--GGDY 212
           + A+    A+ L+ +F    I K Y++++ G  K+    K     N  L+K+ +  G ++
Sbjct: 152 IFAKNINTARKLSAAFSGGSIIKKYFAILLGEVKSPVVYKNHLFRNKRLRKTFVLEGKNF 211

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+ + +             ++ C  ++   +E+   TG THQ+R        P++ D KY
Sbjct: 212 VNAITKVN----------PILSC--KRATLVEIVIETGFTHQIRSQCSFNNHPLINDKKY 259

Query: 273 CANFKGNFTSPIQNKLYLHA 292
           C  FK       ++  +LHA
Sbjct: 260 CNKFK-------KSDYFLHA 272


>gi|307707719|ref|ZP_07644198.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus mitis NCTC 12261]
 gi|307616217|gb|EFN95411.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus mitis NCTC 12261]
          Length = 291

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 60/201 (29%), Positives = 92/201 (45%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+ V G   +K+      L+ K  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWAQVDGHINSKE------LVFKDKIGRDRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F  K   +  +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 195 TKNGQYAETHVSRLKQFPNKTSLVRCKLKTGRTHQIRVHLSHHNFPILGDPLYNSKSKT- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|256829455|ref|YP_003158183.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256578631|gb|ACU89767.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 234

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 102/209 (48%), Gaps = 26/209 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ED  + V NKP+G+ SV G +   +  D  L S V    +  +  HRLD  TSG+LV
Sbjct: 18  VIHEDRDMVVVNKPSGLLSVPGRTPELF--DSVL-SRVREIHRGAQAVHRLDLGTSGVLV 74

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVH 214
           VA  R A   L + F+ R  +K+Y + V G+            I +W  +   +      
Sbjct: 75  VATRRKAETILRQQFQDRLTRKLYLARVQGVMSEDSGQVDLPLICDWPNRPMQM------ 128

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V     K A   ++ ++V++   +    L ++PHTGR+HQLRVH   +G PI+GD+ Y  
Sbjct: 129 VCHDTGKPA---LTDYQVLESDGESTLVL-LRPHTGRSHQLRVHMASLGHPILGDNLYGE 184

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              G        +L LHA  + L HP  G
Sbjct: 185 QRPG-------ERLLLHASQLGLYHPYSG 206


>gi|219870928|ref|YP_002475303.1| tRNA pseudouridine synthase C [Haemophilus parasuis SH0165]
 gi|219691132|gb|ACL32355.1| tRNA pseudouridine synthase C, pseudouridylate synthase, 23S
           RNA-specific [Haemophilus parasuis SH0165]
          Length = 242

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 121/246 (49%), Gaps = 20/246 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETS 155
           +K  ++Y+D ++   NKPAG+ V   S +  H   F +++  D  GQ   L HRLD+ TS
Sbjct: 1   MKLEIIYQDDELIAINKPAGMLVHR-SWLDKHETVFAMQTLRDQIGQHVFLIHRLDRPTS 59

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+ A     A+ +++ F+  +IQK Y ++V G  +   E   ++ LK   +  D +  
Sbjct: 60  GVLLFALNSEMARTISQLFKQHQIQKSYLAVVRGYLQG--EGRIDYPLK---VQLDKIAD 114

Query: 216 VKQNEKGANYAISHFKVIDC---------FAQ-KFCWLEMQPHTGRTHQLRVHALHMGCP 265
               EK A  AI+ ++ I           FA  ++  +++ P TGR HQLR H  H+  P
Sbjct: 115 KFSQEKEAQEAITDYRNIATVEMPYPAGKFATARYSLVQLYPKTGRKHQLRRHLKHLFHP 174

Query: 266 IVGDHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           I+GD  Y    +    +     ++L LH+  +   HP+  + ++I APL       +   
Sbjct: 175 IMGDTNYGDLHQNRALTANTGCDRLMLHSNSLQFIHPKTLQTIEIKAPLDEQWKALFTQF 234

Query: 323 GFKYDR 328
           G+ + +
Sbjct: 235 GWNFTK 240


>gi|153802299|ref|ZP_01956885.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-3]
 gi|124122181|gb|EAY40924.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-3]
          Length = 245

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 105/217 (48%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  ++    + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEDTN--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAVTAYRPLAKVELPISTGKFATTRYCLMEMQPRTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFMHP 211


>gi|116624899|ref|YP_827055.1| RluA family pseudouridine synthase [Candidatus Solibacter usitatus
           Ellin6076]
 gi|116228061|gb|ABJ86770.1| pseudouridine synthase, RluA family [Candidatus Solibacter usitatus
           Ellin6076]
          Length = 304

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 83/319 (26%), Positives = 136/319 (42%), Gaps = 43/319 (13%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Y    ++ +      L     + YPH      Q+ L +G+V ++      +  ++SGQ++
Sbjct: 6   YAYTTIISSKYPGQTLLSHLASLYPHSTSEAWQQNLNNGEVTLNGVAATGSESVRSGQIL 65

Query: 66  --RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
               PP I                 ++ KH +     +L+ED  +   NKP+G+    G 
Sbjct: 66  IWNRPPWIEP---------------DVPKHFE-----VLFEDPHLLAVNKPSGLPTLPGG 105

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G    ++  L   V          HRL + TSGI++ ART  AA +L  ++   +I+KIY
Sbjct: 106 GF---LENTLLRLVQKHTPNANPVHRLGRATSGIVLFARTPQAASNLFANWNTPKIRKIY 162

Query: 184 WSLVWGIPKNKKECIAN--WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            +L   I ++    I     L+    IG     V   N  G   + S  KVI   +    
Sbjct: 163 RALAQNIAQHDAYEILTPIGLVPHPRIGS----VWAANPSG-KPSKSLAKVISR-STSTT 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYM 295
             E+  ++GR HQ+R+H   +G P+VGD  Y        N  G    P     +LHA+++
Sbjct: 217 TFEVSLNSGRPHQIRIHLASIGHPLVGDPLYGLTGQPLENLPG---LPGDGGYFLHAQFL 273

Query: 296 DLPHP-EGGRLQITAPLPA 313
              HP  G ++ + A LP+
Sbjct: 274 QFQHPITGEQINLEAALPS 292


>gi|311104863|ref|YP_003977716.1| ribosomal large subunit pseudouridine synthase D [Achromobacter
           xylosoxidans A8]
 gi|310759552|gb|ADP15001.1| ribosomal large subunit pseudouridine synthase D [Achromobacter
           xylosoxidans A8]
          Length = 332

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 85/328 (25%), Positives = 132/328 (40%), Gaps = 55/328 (16%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q+V V +     RLD+      P  +   LQ  + +G V V+ +  K    +  G  + +
Sbjct: 29  QFVTVPSSTRADRLDKVLAGLLPEHSRGRLQGWIEAGNVHVNGRPGKVRQTVGPGDELTV 88

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
            P           Q   +S     +  DF    ++ E     V NKPAG+    G+G   
Sbjct: 89  WP-----------QPAPESLAFAPEPVDF---AVVDESPDWIVVNKPAGLVTHPGAGNWS 134

Query: 126 AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + + ++  +  + HRLD++TSG++VVAR   A  HL    + R + + Y 
Sbjct: 135 GTLLNGLLYRYPELTQVARAGIVHRLDKDTSGLMVVARNETAQTHLVRQLQARSMGREYV 194

Query: 185 SLVWGIPKNKKECIANWLLKKSH----IGGDY---VHVVKQNEKGANYAISHFKVI---- 233
           +L  G           WL         IG D    V +  +       AI+H+       
Sbjct: 195 ALAHG-----------WLAAAGKVDRPIGRDSRVPVRMSVERPVAPKPAITHYAPARRGE 243

Query: 234 ----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKL 288
                   +  C LE    TGRTHQ+RVH   +G P++ D  Y   N  G        + 
Sbjct: 244 ADPGGRVTEVVCRLE----TGRTHQIRVHMASLGHPLLADTLYGGKNIVG------AQRQ 293

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHM 315
            LHAR +    P G G ++  A +P  M
Sbjct: 294 MLHARALHFEDPGGRGEVEFAAAVPPDM 321


>gi|126173232|ref|YP_001049381.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125996437|gb|ABN60512.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 574

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 114/235 (48%), Gaps = 22/235 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H++ E  ++D +  LT  ++     +LY+D  + + NKPA      G  I   +   +
Sbjct: 340 LGHML-EGLVVDDNPLLTNPAEGKTLSILYQDDAMAIVNKPAEFLSVPGKEIEDSVYSRM 398

Query: 134 K-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           + ++  + G  P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ G+P 
Sbjct: 399 RQTFPHATG--PLIVHRLDMSTSGLMVIALTKDAHKQLQKQFIQRTVTKRYVALLAGMPA 456

Query: 193 --NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--IDCFAQKFCWLEMQPH 248
                +   N  L       D    +  +E G   A +H+++  +D  A +   + + P 
Sbjct: 457 VMANTQATGNISLPLRGDLDDRPRQLVCHEFGKT-AETHWELSQLDEMA-RTARVYLYPK 514

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           TGRTHQLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP
Sbjct: 515 TGRTHQLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHP 560


>gi|89894036|ref|YP_517523.1| hypothetical protein DSY1290 [Desulfitobacterium hafniense Y51]
 gi|219668420|ref|YP_002458855.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
 gi|89333484|dbj|BAE83079.1| hypothetical protein [Desulfitobacterium hafniense Y51]
 gi|219538680|gb|ACL20419.1| pseudouridine synthase, RluA family [Desulfitobacterium hafniense
           DCB-2]
          Length = 302

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 104/231 (45%), Gaps = 24/231 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQET 154
           +LYED      NKPAG  V          I   + G+   W+     +P R  HR+D+ T
Sbjct: 85  ILYEDDYFIAINKPAGQVVHPTPRYPRGTIGNAVVGY---WLAKGEARPFRPIHRIDRNT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV 213
           SG++V+ + + A Q +       RI K Y  +V G + +++    A   L          
Sbjct: 142 SGVVVIGKNQFAHQQMAWQHAHGRIHKCYRGIVEGQVMEDQGTIKAPIALAPDSF----- 196

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + +Q     + A++ +KV++ + Q    LE    TGRTHQ+RVH  H+G P++GD  Y 
Sbjct: 197 -IQRQISPEGSPAVTLYKVLERY-QDASLLEFILETGRTHQIRVHCQHLGHPLLGDDLYG 254

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
            N          N+  LH+   +  HP  G L  I APLP  + +    L 
Sbjct: 255 GNLARI------NRQALHSSIYEFNHPLTGELTTIQAPLPEDLQRLLRELA 299


>gi|332668407|ref|YP_004451195.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
 gi|332337221|gb|AEE54322.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
          Length = 243

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 58/184 (31%), Positives = 89/184 (48%), Gaps = 23/184 (12%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HR+D+ETSGILV AR   A + L + F  R ++KIY +LV G P      I   +   
Sbjct: 51  IVHRIDRETSGILVFARNEDAHRALNQQFLDRSVEKIYLALVEGRPMPPTGEINKAIAPH 110

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
             I G  +     + KG + A++ +KV+D + + +  +E    TGRTHQ+RVH   +G P
Sbjct: 111 PSIAGKMI----TSGKGKS-ALTLYKVVDTY-KAYALVEADIKTGRTHQIRVHFASIGHP 164

Query: 266 IVGD----------------HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
           +  D                H++      +    + ++L LHA  + L HP  G R+  T
Sbjct: 165 LAVDPVYGKRAAFFLSEIKTHRFNLKKDQDEEQALVSRLTLHAHKLTLDHPATGERMAFT 224

Query: 309 APLP 312
             LP
Sbjct: 225 CELP 228


>gi|315302419|ref|ZP_07873284.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria ivanovii FSL F6-596]
 gi|313629211|gb|EFR97479.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria ivanovii FSL F6-596]
          Length = 296

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 61/223 (27%), Positives = 113/223 (50%), Gaps = 24/223 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQET 154
           +++ED  + + NKPAG++        YH  G + ++V    +K  LT       RLD+ET
Sbjct: 82  IIFEDEFLLIINKPAGMASIPSQ---YHPSGSVANFVKGHYEKQGLTSAIHIVTRLDRET 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+ R A   L+   +   +++ Y +   G+  N+   I      ++ IG   V 
Sbjct: 139 SGLMLIAKNRFAHARLSTFLQQGLLKRRYQAFTSGVLNNRIGSI------EAPIGRKTVS 192

Query: 215 VVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           ++++       YA ++++V+  + + F  + +Q  TGRTHQ+RVH  ++G P++GD  Y 
Sbjct: 193 IMERFVTPEGKYAKTNYEVLKRY-EAFDHVAIQLETGRTHQIRVHFSYIGHPLIGDDMYG 251

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            +      + +  +  LH+ ++ L HP     L    PLP  M
Sbjct: 252 GD------TTLLKRQALHSCHLHLIHPLTEEYLTFDLPLPKDM 288


>gi|304414221|ref|ZP_07395589.1| 23S rRNA and tRNA pseudouridine synthase [Candidatus Regiella
           insecticola LSR1]
 gi|304283435|gb|EFL91831.1| 23S rRNA and tRNA pseudouridine synthase [Candidatus Regiella
           insecticola LSR1]
          Length = 212

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 64/209 (30%), Positives = 103/209 (49%), Gaps = 22/209 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G          ++  + +   +    HRLD  TSG++VV
Sbjct: 3   VLYQDQHIMVINKPSGLLSVPGRAPENKDSVMMR--IQAAFPQAESVHRLDMATSGVMVV 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A T+AA + L   FR R  +K+Y + V+G  K  +  I   L+       D+ +  KQ  
Sbjct: 61  ALTKAAERELKRQFREREPKKVYVARVYGHVKKDQGLIDLPLI------CDWPNRPKQKV 114

Query: 220 --EKGANYAISHFKVID------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             E G + A + ++V+         +     +++ P TGR+HQLRVH L +G PI+GD  
Sbjct: 115 CYETGKS-AQTEYQVLSRHDETPGHSNSSTRVKLSPITGRSHQLRVHMLALGHPILGDGF 173

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y      +  +    +L LHA+ + + HP
Sbjct: 174 YAPPGAKSMAT----RLQLHAQELYIRHP 198


>gi|269104819|ref|ZP_06157515.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268161459|gb|EEZ39956.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 560

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 61/203 (30%), Positives = 97/203 (47%), Gaps = 18/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  + + NKPA      G  I+  +   +++        P + HRLD  TSG+LV+
Sbjct: 359 IIYQDEAMVIVNKPAEFLSVPGKTISDSVYTRMQAMF-PDADSPLIVHRLDMSTSGLLVI 417

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A T+ A ++L + F  R ++K Y +L+ G+  +  E I +  ++          V  ++ 
Sbjct: 418 ALTKRAHKNLQKQFITRTVEKRYVALLDGL-ADSDEGIISLPMRGDINDRPRQLVCFEHG 476

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFK 277
           K A          D   + + +    P TGRTHQLRVH+ H   M  PI+GD  Y     
Sbjct: 477 KPAETKWQVISRKDGKTKVYYY----PKTGRTHQLRVHSAHPMGMNMPIIGDDLYGQK-- 530

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
                   N+L+LHA Y+ L HP
Sbjct: 531 -------SNRLHLHAEYLSLEHP 546


>gi|42526895|ref|NP_971993.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
 gi|41817210|gb|AAS11904.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
          Length = 305

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 78/323 (24%), Positives = 131/323 (40%), Gaps = 49/323 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  D+   RLDR  +     +    +   +R G++RV+ K+       Q G  + +   +
Sbjct: 10  IGEDDSGRRLDRVIRKFLGKMPLSGVYSAIRRGKIRVNGKKENGAYLTQKGDEISMDLSL 69

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
             L     E +        T +S     +LL  D  +++ NK +G  V G   +   +  
Sbjct: 70  FGLTAPASEDQ--------TNYSISKPDVLLKTDDLLFI-NKRSGELVHGEKSLCEAVLK 120

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           +  S   S   K    HRLD++TSGIL  +++   AQ  + + +  +I K Y  +  G P
Sbjct: 121 YFPSKEKSLSFKVGALHRLDKDTSGILAFSQSLKGAQGFSRALQEGKIGKFYIGITEGRP 180

Query: 192 K--------NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
                    + KEC+   L++           +    K  N ++  F +I          
Sbjct: 181 SLSEFKSIIDGKECLC--LIR-----------ILDFSKEENLSLVLFNLI---------- 217

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL--YLHARYMDLPHPE 301
                TGR HQ+R+     G P++ D KY +  K  F+  +  K   +LHA  +    P 
Sbjct: 218 -----TGRKHQIRIQCSQFGTPLLNDKKYGSKQKKAFSEDLSKKTTYFLHAYKLIFSEPF 272

Query: 302 GGRL--QITAPLPAHMVKTWDSL 322
              L  +ITAPLP +  +   SL
Sbjct: 273 LDDLPKEITAPLPENFKRAVKSL 295


>gi|258621635|ref|ZP_05716667.1| tRNA pseudouridine synthase C [Vibrio mimicus VM573]
 gi|258586107|gb|EEW10824.1| tRNA pseudouridine synthase C [Vibrio mimicus VM573]
          Length = 244

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 63/217 (29%), Positives = 104/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F   +++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASEVMPMFANHKMEKTYHAIVRGWIEEAD--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  AI+ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAITAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFVHP 211


>gi|289435585|ref|YP_003465457.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
 gi|289171829|emb|CBH28375.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
          Length = 289

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 101/217 (46%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP G+        +Y  D     ++ +++   Q       HRLDQ TS
Sbjct: 80  VIYEDDFLLVVNKPVGMKTHPND--SYETDTCANAVQYYLEQTNQDANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H  V++   +K   L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHVTVLENDTEKNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 253 -------SPRANRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|15677843|ref|NP_275010.1| hypothetical protein NMB2018 [Neisseria meningitidis MC58]
 gi|7227280|gb|AAF42341.1| conserved hypothetical protein [Neisseria meningitidis MC58]
 gi|319409672|emb|CBY89973.1| K06177 ribosomal large subunit pseudouridine synthase A [Neisseria
           meningitidis WUE 2594]
 gi|325141436|gb|EGC63913.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis 961-5945]
          Length = 220

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 67/212 (31%), Positives = 103/212 (48%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 6   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 61

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + +A  L+  F  + I+K Y +L    P  K+  I   + +KS  G     + K  
Sbjct: 62  FALNKESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGM-EKSRCG-----MWKLT 115

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y     G 
Sbjct: 116 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLY-----GG 169

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
             S     ++L+A  +   + +  +++I APL
Sbjct: 170 TES---ETMFLYAWKIQFDY-QNRQIEIVAPL 197


>gi|325201066|gb|ADY96521.1| pantetheine-phosphate adenylyltransferase [Neisseria meningitidis
           H44/76]
          Length = 399

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 67/212 (31%), Positives = 103/212 (48%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 185 ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 240

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + +A  L+  F  + I+K Y +L    P  K+  I   + +KS  G     + K  
Sbjct: 241 FALNKESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGM-EKSRCG-----MWKLT 294

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y     G 
Sbjct: 295 RNTENIAVTRFHSIS-IAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLY-----GG 348

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
             S     ++L+A  +   + +  +++I APL
Sbjct: 349 TES---ETMFLYAWKIQFDY-QNRQIEIVAPL 376


>gi|322514573|ref|ZP_08067606.1| tRNA pseudouridine synthase C [Actinobacillus ureae ATCC 25976]
 gi|322119512|gb|EFX91599.1| tRNA pseudouridine synthase C [Actinobacillus ureae ATCC 25976]
          Length = 250

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 114/240 (47%), Gaps = 16/240 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPIHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A+ ++E F   +++K Y ++V G   +K E      +    I  D     K+ +
Sbjct: 65  ALNSEMARLMSEQFEQHQMEKGYLAVVRGYLLDKGEIDYPLKVILDKI-ADKFSQPKEAQ 123

Query: 221 KGANYAISHFKVIDCF------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +   ++ +   V   +        ++  +E+ P TGR HQLR H  H+  PI+GD KY  
Sbjct: 124 QAVTFSQNLASVEMPYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPIMGDTKY-G 182

Query: 275 NFKGNFTSPIQ---NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNL 330
           +   N T   +   ++L LH+ ++   HP+   +++I APL     + W +L   ++ N 
Sbjct: 183 DLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLD----EQWQNLFITFNWNF 238


>gi|221133320|ref|ZP_03559625.1| pseudouridylate synthase [Glaciecola sp. HTCC2999]
          Length = 245

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 69/225 (30%), Positives = 99/225 (44%), Gaps = 20/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQETSGILV 159
           ++Y+D  I   NKP+G+ V   S I  H   F    V +   Q     HRLD+ TSG+LV
Sbjct: 10  IIYQDEHIIAINKPSGLLVHR-SMIDRHETRFAMQMVRNMIDQHVYTVHRLDKPTSGVLV 68

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A +   A+ +TE F  + I K Y +L  G  K++     ++ LK+            Q 
Sbjct: 69  FALSSDVARLMTEQFTEKTIHKTYHALTRGWTKSQ---FVDYALKEK--LDKIADKDAQQ 123

Query: 220 EKGANYAISHFKVIDCFA----------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +K    A +H   +  F            +  W+E+ P TGR HQLR H  H+  PI+GD
Sbjct: 124 DKAPQEAQTHIACLQRFTYPKAVGRYPQARLSWVELNPQTGRKHQLRRHLAHVRHPIMGD 183

Query: 270 HKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPL 311
             +    +  F     N   L LH   M   HP     L ++APL
Sbjct: 184 TTHGDGKQNKFMRDTFNFHHLALHNSSMKFCHPVTQHPLALSAPL 228


>gi|116617201|ref|YP_817572.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
 gi|116096048|gb|ABJ61199.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
          Length = 297

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 118/240 (49%), Gaps = 38/240 (15%)

Query: 91  TKHSDFL----KSI-LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDS 139
           T  S++L    KS+ +++E+  + V +KPAG+ +      +  + + Y    F++  V  
Sbjct: 72  TSESNYLPNHQKSVNIIFENKDLVVIDKPAGMKMHPHSPTETDTLLNYLAGEFIQRKV-- 129

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D+ TSG+++VA+       L      +RI + Y + V G+ ++    IA
Sbjct: 130 -SDQPYMVHRIDRATSGLVIVAKNPVVVPILDRMLADKRIVRTYVTWVSGVVQDNHGTIA 188

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC--WLEMQPHTGRTHQL 255
                   IG D     K+  + K A  A++H+  +      FC   L +Q  TGR HQ+
Sbjct: 189 K------PIGIDARDDRKRAVDGKEAQVAMTHWWRMHTV---FCSSLLRVQLSTGRMHQI 239

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPA 313
           RVH   +G PIVGD  Y   + G        ++ LH+  + +P P  EG R+ IT PLP+
Sbjct: 240 RVHLASIGHPIVGDELYGGVYNG--------RMLLHSATIKIPLPFDEGVRM-ITGPLPS 290


>gi|322376158|ref|ZP_08050666.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C300]
 gi|321278840|gb|EFX55885.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C300]
          Length = 291

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 58/201 (28%), Positives = 94/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPGEIALLNHVSAYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+L+ G  ++K+      L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEIARDYWALIEGRVESKE------LVFRDKIGRDRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F  K   +  +  TGRTHQ+R+H  H   PI+GD  Y +  K  
Sbjct: 195 TKNGQYAETHISRLKQFPNKTTLVRCKLKTGRTHQIRIHLSHHKHPILGDPLYNSRSKV- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|256545099|ref|ZP_05472465.1| RNA pseudouridylate synthase [Anaerococcus vaginalis ATCC 51170]
 gi|256399140|gb|EEU12751.1| RNA pseudouridylate synthase [Anaerococcus vaginalis ATCC 51170]
          Length = 326

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 68/280 (24%), Positives = 133/280 (47%), Gaps = 28/280 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +  ++  + END  N R DR+ + +  +     +QK +R    +++ KR K ++ +++G 
Sbjct: 6   INMIEVKINENDA-NQRFDRFLRKYLQNAPLSLIQKNIRKKNFKINDKRAKKDDFVKNGD 64

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-- 121
           ++ +          +++++         K SDF   I+ YED  I + +K +G+      
Sbjct: 65  IITMYIKDEDYKKWVRKKEF--------KASDFDLDII-YEDENIIIIDKKSGVLSHAAN 115

Query: 122 ----GSGIAYHIDGFL--KSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G+ I   +  +L   + V+S+    KP + +RLD+ T+G+++ A+   A + L ++
Sbjct: 116 KNDYGNNIVDQMTSYLYKTNKVNSRDLTFKPSIVNRLDRNTAGLIIGAKNAKALRSLNKA 175

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R  +I K Y ++V G      E   ++ +       +  ++VK+ E G    I+ F  +
Sbjct: 176 IRQGKINKYYLTIVEG------EIHKDFEIDTRISKNENKNMVKEKEDGKR-IITKFHPL 228

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           +     F  LE +  TG+THQ+R        PI+GD KY 
Sbjct: 229 ET-KNNFTLLECKLITGKTHQIRYSLNKNSTPIIGDRKYS 267


>gi|157375387|ref|YP_001473987.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157317761|gb|ABV36859.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 238

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 106/231 (45%), Gaps = 31/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY+D  + + NKP+G+    G     H D             P  T  HRLD  TSGI+
Sbjct: 19  ILYQDEALILINKPSGLLSLSGK----HPDNKDSVHFRLVQDFPSCTMIHRLDFGTSGIM 74

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA  +     L + F  R + K Y +L+ G  K   E + ++ + K       + V +Q
Sbjct: 75  LVAMNKQVNAQLCKQFSERTVSKRYTALLHGHLK-MDEGLIDFAIAKDTENFPLMKVCQQ 133

Query: 219 NEKGANYAISHFKVIDCFAQK----------------FCWLEMQPHTGRTHQLRVHALHM 262
             K    A+S FKV++ F Q                    +E +P +GRTHQLR+H+  +
Sbjct: 134 TGKP---AVSKFKVLERFVQTHNNAFFQEHKKAGDRAVTRVEFEPVSGRTHQLRLHSQQI 190

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             PI+G   Y  + +  FTS   ++L LHA  +   HP  G R+ I +P P
Sbjct: 191 KHPILGCDLYATD-EAFFTS---SRLLLHASELSFDHPITGERMNIISPSP 237


>gi|302518516|ref|ZP_07270858.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           SPB78]
 gi|333027806|ref|ZP_08455870.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces sp. Tu6071]
 gi|302427411|gb|EFK99226.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           SPB78]
 gi|332747658|gb|EGJ78099.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces sp. Tu6071]
          Length = 313

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 81/315 (25%), Positives = 135/315 (42%), Gaps = 39/315 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  V+ + V +  E  R+D      +   +     ++   G+V+VD   V  + R++
Sbjct: 1   MSAIPEVRTLPVPDGLEGERVDAALSRMF-GFSRTKAAELAAGGKVQVDGSVVGKSERVR 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  + V  KP G++ 
Sbjct: 60  GGAWLEVEMPRAAAPVQIVAEP--------------VEGMEIVHDDEDVVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +    + + G   R  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGQTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKNQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR+R + K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I
Sbjct: 166 FRVRTVDKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAEGKA---SVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----- 288
           + F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  +L     
Sbjct: 221 EAF-RAASLLDVKLETGRTHQIRVHMSAHRHPCVGDLTYGAD------PTLAKRLGLTRQ 273

Query: 289 YLHARYMDLPHPEGG 303
           +LHA  +   HP  G
Sbjct: 274 WLHAVRLGFTHPGTG 288


>gi|126741336|ref|ZP_01757013.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           SK209-2-6]
 gi|126717592|gb|EBA14317.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           SK209-2-6]
          Length = 217

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 63/206 (30%), Positives = 104/206 (50%), Gaps = 18/206 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D++I V NKP G+    G G   H+   L + V     +  L HRLD++TSG++V 
Sbjct: 16  ILHHDAEILVVNKPEGLLSVPGRG--EHLADCLIARVQRVFPEALLVHRLDRDTSGVMVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
             +  A +HL+  F  R  +K Y + + G  + K   +   L+       D+ +  +Q  
Sbjct: 74  GLSPHAQRHLSMQFEKRTTKKTYVARLAGRLEPKSGTVDLPLIV------DWPNRPRQKV 127

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            NE G   A++ +KV+   A++   + + P TGR+HQLRVH L +G  I+GD  Y     
Sbjct: 128 CNESG-KPAVTDWKVVKQSAEE-TRVRLTPKTGRSHQLRVHMLSLGHAILGDPLYAEG-- 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
                P   ++ LH+  + + HP+ G
Sbjct: 184 AALEHP---RMMLHSEELRIKHPQSG 206


>gi|315222228|ref|ZP_07864135.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
 gi|315188731|gb|EFU22439.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
          Length = 286

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 61/200 (30%), Positives = 91/200 (45%), Gaps = 18/200 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  I + NKP G+           +   + ++V   G    + HRLD+ETSG ++ A
Sbjct: 84  LYQDEHITIVNKPEGMKTHANEPTELALLNHVSAYV---GNTCYVVHRLDKETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      + I + YW+LV G    K++   + + +  H   D    +  N+ 
Sbjct: 141 KNPFILPILNRLLENKEISREYWALVQGAFPQKRQIYTDKIGRDRH---DRRKRLVDNKN 197

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           G  YA +H   +  F  K   +  Q  TGRTHQ+RVH  H G PI+GD  Y         
Sbjct: 198 G-QYAETHISKLKEFENK-TLVSCQLKTGRTHQIRVHLAHHGYPIIGDPLY--------- 246

Query: 282 SPIQNK-LYLHARYMDLPHP 300
           +P + K L LHA  +   HP
Sbjct: 247 NPQKAKRLMLHAHRLTFTHP 266


>gi|225551707|ref|ZP_03772651.1| RNA pseudouridine synthase family protein [Borrelia sp. SV1]
 gi|225371734|gb|EEH01160.1| RNA pseudouridine synthase family protein [Borrelia sp. SV1]
          Length = 313

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 77/300 (25%), Positives = 139/300 (46%), Gaps = 44/300 (14%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-----LRSGQVRVDKKRVKFNNRIQ 60
           Y+   V+ ND    RLD         I  +N  K      +R G +R++  +  F+ R+ 
Sbjct: 4   YIFLEVIANDN-GKRLDSIL------IKILNFSKARIIKHIRKGDIRLNGLKSHFSCRVC 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   + A N  +   +   S+++      +++  ++YEDS + V +K  GI V 
Sbjct: 57  KGDKIYLYKSL-AQNLNLTTDECFKSNIDF----QYIRKRIIYEDSDLLVLDKQKGILVH 111

Query: 121 GG-SGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           GG + + +  + +L S  + S   KP   HRLD+ TSGI++ A+    A+ L+E+F    
Sbjct: 112 GGKNSLDFLANAYLLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTARKLSEAFSGGS 171

Query: 179 IQKIYWSLVWGIPKN----KKECIANWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKV 232
           I K Y++++ G  K+    K     N  L+K+ +  D  +V+ + +             +
Sbjct: 172 IIKKYFAILLGEVKSSVVYKNHLFRNKRLRKTFVLEDKNFVNAITKVN----------PI 221

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           + C  ++   +E+   TG THQ+R        P++ D KYC  FK       ++  +LHA
Sbjct: 222 LSC--KRATLVEIVIETGFTHQIRSQCSFNNHPLINDKKYCDKFK-------KSDYFLHA 272


>gi|28897333|ref|NP_796938.1| 23S rRNA pseudouridine synthase D [Vibrio parahaemolyticus RIMD
           2210633]
 gi|153839761|ref|ZP_01992428.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus AQ3810]
 gi|260876296|ref|ZP_05888651.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus AN-5034]
 gi|260895103|ref|ZP_05903599.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus Peru-466]
 gi|260903277|ref|ZP_05911672.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus AQ4037]
 gi|34395767|sp|Q87S65|RLUD_VIBPA RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|28805542|dbj|BAC58822.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|149746714|gb|EDM57702.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus AQ3810]
 gi|308088909|gb|EFO38604.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus Peru-466]
 gi|308092904|gb|EFO42599.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus AN-5034]
 gi|308107949|gb|EFO45489.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus AQ4037]
 gi|328472095|gb|EGF42972.1| 23S rRNA pseudouridine synthase D [Vibrio parahaemolyticus 10329]
          Length = 325

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 113/238 (47%), Gaps = 27/238 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           ++YED  I V NKP    V  G+G      ++  L  + D   + PR  + HRLD++T+G
Sbjct: 86  IVYEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDI-AEVPRAGIVHRLDKDTTG 144

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYV 213
           ++VVA+T  A   L  + + R I + Y ++  G         + I     K++ +    +
Sbjct: 145 LMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDQPIGRHSTKRTLMAVAPL 204

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                       A++H++V + F ++   + ++  TGRTHQ+RVH  ++  P++GD  Y 
Sbjct: 205 ---------GKPAVTHYRVAEHF-REHTRIRLRLETGRTHQIRVHMSYLQHPLLGDTAYG 254

Query: 274 ANFK------GNFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
              +         T  I+  ++  LHA  +   HP  G  L+  AP+P  MV   ++L
Sbjct: 255 GRARIPTGASQELTDMIRGFDRQALHAVMLRFEHPITGEELEFHAPVPDDMVAMTEAL 312


>gi|332525786|ref|ZP_08401930.1| ribosomal large subunit pseudouridine synthase D [Rubrivivax
           benzoatilyticus JA2]
 gi|332109340|gb|EGJ10263.1| ribosomal large subunit pseudouridine synthase D [Rubrivivax
           benzoatilyticus JA2]
          Length = 317

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 83/323 (25%), Positives = 132/323 (40%), Gaps = 42/323 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
           VV+      RLDR   +     +  +LQ ++  G VRVD +     + R+++GQ V +  
Sbjct: 20  VVDTARHGERLDRVLVSIAGEFSRSHLQHLIELGHVRVDGQPASTASRRVKAGQRVEVEL 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
           V    +   + Q               +   +LYED  + V +KPAG+ V    G     
Sbjct: 80  VPTDESRAFRPQP--------------MALAILYEDEHLLVLDKPAGLVVHPAPGNWSGT 125

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++G L     +    PR  + HRLD++TSG+++V ++  A   L      R + + Y +
Sbjct: 126 LLNGLLAHHAAAA-TLPRAGIVHRLDKDTSGVMMVGKSLPAVTALVRDIAARDVHRRYLA 184

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVK----QNEKGANYAISHFKVIDCFAQKFC 241
           L  G    ++          + +G D V  V+     + K A   +      D  +   C
Sbjct: 185 LAHGAVATQR--------IDAPVGRDPVSRVRMAVVASGKPARTDVECLAQHDGVSAVRC 236

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            L    HTGRTHQ+RVH    G  +V D  Y     G   +    +  LHA  ++L HP 
Sbjct: 237 TL----HTGRTHQIRVHLASRGHALVADTLY-----GGRPALGMARQALHAVRLELEHPL 287

Query: 301 EGGRLQITAPLPAHMVKTWDSLG 323
               L    P PA     W ++ 
Sbjct: 288 TRAPLSFVCPPPADFSAAWRAIA 310


>gi|218710322|ref|YP_002417943.1| tRNA pseudouridine synthase C [Vibrio splendidus LGP32]
 gi|218323341|emb|CAV19518.1| tRNA pseudouridine synthase C [Vibrio splendidus LGP32]
          Length = 252

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 111/248 (44%), Gaps = 29/248 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 7   IIYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG----------IPKNKKECIANWLLKKSHIGG 210
           A +   A  +   F    +QK Y ++V G            K + + IA+   K+     
Sbjct: 67  ALSSEVASEVMPMFANHEMQKTYHAIVRGWIEEGDTLDYALKVELDKIADKFAKEDKEPQ 126

Query: 211 DYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           + V V +   K    Y+   F        ++C +EM P TGR HQLR H  H+  PIVGD
Sbjct: 127 EAVTVYEPLAKVEVPYSTGRFPT-----SRYCLVEMMPKTGRKHQLRRHMAHLRHPIVGD 181

Query: 270 H-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL-- 322
                 K+   F+ +  S   ++L LHA  +   HP      +   + A++ +TW  L  
Sbjct: 182 TSHGDGKHNRLFRDDLDS---HRLLLHASELSFIHPFTKEELV---MKANLDETWLRLFE 235

Query: 323 GFKYDRNL 330
            F++D NL
Sbjct: 236 TFEWDANL 243


>gi|254520209|ref|ZP_05132265.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
 gi|226913958|gb|EEH99159.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
          Length = 298

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 85/300 (28%), Positives = 134/300 (44%), Gaps = 48/300 (16%)

Query: 39  KILRSGQVR----VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++RS  +     VD K VK N  ++  + V I  V     +I  E   +D         
Sbjct: 30  RLIRSASIDKRIFVDNKAVKMNYVLKRSEEVLIDLVKEETQNIDPENIPID--------- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQK--PRL 146
                 ++YED  I V NK   + V      Q G+     +   L  +     QK   RL
Sbjct: 81  ------IVYEDEDIIVVNKGPNMVVHPTKRYQSGT-----LANALMYYFKESNQKCIVRL 129

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD +TSG++++A+ + A   L++   +  ++K Y ++V G  +N +  I +  + + 
Sbjct: 130 VSRLDMDTSGLIIIAKNQYAHMELSKEMTLNNVEKRYLTVVHGHMENDEGTI-DLPIYRP 188

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMG 263
              G    VV  +E+G   +I+H+KVI+ F       C LE    TGRTHQ+RVH   +G
Sbjct: 189 EEEGTIRRVV--DERGQR-SITHYKVIERFKDSDLVECLLE----TGRTHQIRVHLSSLG 241

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            PI GD  Y     G   S    +  LHA  +D   P   + L + A +P  + K  + L
Sbjct: 242 HPIWGDTLYGYEEDGEIIS----RQALHAYGLDFKSPRTKKELSLRARVPDDIEKLVEYL 297


>gi|121591256|ref|ZP_01678555.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           2740-80]
 gi|229527559|ref|ZP_04416951.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           12129(1)]
 gi|262401797|ref|ZP_06078362.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. RC586]
 gi|297581352|ref|ZP_06943275.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC385]
 gi|121546902|gb|EAX57056.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           2740-80]
 gi|229335191|gb|EEO00676.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           12129(1)]
 gi|262351769|gb|EEZ00900.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. RC586]
 gi|297534190|gb|EFH73028.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC385]
 gi|327484993|gb|AEA79400.1| Ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           LMA3894-4]
          Length = 245

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 100/203 (49%), Gaps = 17/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I   NKP+G+    G  +  H D      VD      ++ HRLD  TSG+++ 
Sbjct: 16  VIYEDEHIIAANKPSGLLSVPGRPVE-HYDSMWARLVDYCPDV-KVVHRLDMSTSGLILF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A+ +     L + F+ R   KIY++ VWG+   + E   N  L       D+ +  KQ  
Sbjct: 74  AKGKHMESALKKQFQYRLTHKIYYARVWGV-MEQDEGEVNLPL-----CCDWPNRPKQKV 127

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+G + +++ ++V+    +K   + + P TGR+HQLRVH   +G PIVGD  Y     
Sbjct: 128 CFEEGRD-SLTRYQVVK-REEKTTVVRLIPITGRSHQLRVHMQSLGHPIVGDDLYAPQEA 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
             F     ++L LHA  +   HP
Sbjct: 186 VEFA----DRLQLHAAELCFYHP 204


>gi|147673149|ref|YP_001218003.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|153829796|ref|ZP_01982463.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           623-39]
 gi|229513432|ref|ZP_04402896.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           TMA 21]
 gi|254225904|ref|ZP_04919506.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V51]
 gi|254291423|ref|ZP_04962215.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           AM-19226]
 gi|258622801|ref|ZP_05717819.1| Ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM573]
 gi|258625826|ref|ZP_05720705.1| Ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM603]
 gi|262166537|ref|ZP_06034274.1| ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM223]
 gi|262167535|ref|ZP_06035240.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC27]
 gi|262170551|ref|ZP_06038229.1| ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           MB-451]
 gi|125621530|gb|EAZ49862.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V51]
 gi|146315032|gb|ABQ19571.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|148874714|gb|EDL72849.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           623-39]
 gi|150422613|gb|EDN14568.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           AM-19226]
 gi|227014395|gb|ACP10605.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|229349309|gb|EEO14265.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           TMA 21]
 gi|258582064|gb|EEW06934.1| Ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM603]
 gi|258584989|gb|EEW09720.1| Ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM573]
 gi|261891627|gb|EEY37613.1| ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           MB-451]
 gi|262023988|gb|EEY42684.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC27]
 gi|262026253|gb|EEY44921.1| ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM223]
          Length = 245

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 100/203 (49%), Gaps = 17/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I   NKP+G+    G  +  H D      VD      ++ HRLD  TSG+++ 
Sbjct: 16  VIYEDEHIIAANKPSGLLSVPGRPVE-HYDSMWARLVDYCPDV-KVVHRLDMSTSGLILF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A+ +     L + F+ R   KIY++ VWG+   + E   N  L       D+ +  KQ  
Sbjct: 74  AKGKHMESALKKQFQYRLTHKIYYARVWGV-MEQDEGEVNLPL-----CCDWPNRPKQKV 127

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+G + +++ ++V+    +K   + + P TGR+HQLRVH   +G PIVGD  Y     
Sbjct: 128 CFEEGRD-SLTRYQVVK-REEKTTVVRLIPITGRSHQLRVHMQSLGHPIVGDDLYAPQEA 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
             F     ++L LHA  +   HP
Sbjct: 186 VEFA----DRLQLHAAELCFYHP 204


>gi|289167119|ref|YP_003445386.1| 23S_rRNA pseudouridine synthase [Streptococcus mitis B6]
 gi|288906684|emb|CBJ21518.1| 23S rRNA pseudouridine synthase [Streptococcus mitis B6]
          Length = 291

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 92/201 (45%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYV---GQTCYVVHRLDMETSGLILFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      ++I + YW+LV G   +K+      L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKKISREYWALVDGNINSKE------LVFRDKIGRDRHDRRKRVVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K    A +H   +  F  K   +  +  TGRTHQ+RVH  H   PI+GD  Y  N    
Sbjct: 195 TKNGQSAETHISRLKQFPNKTSLVRCKLKTGRTHQIRVHLSHHNFPILGDPLYNNN---- 250

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 251 ---STTSRLMLHAFRLSFTHP 268


>gi|315651177|ref|ZP_07904208.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saburreum DSM 3986]
 gi|315486575|gb|EFU76926.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saburreum DSM 3986]
          Length = 298

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 106/221 (47%), Gaps = 13/221 (5%)

Query: 103 YEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  I V NKP+ + +    +     +   L  +   K    R  +RLD++T+G+ VVA
Sbjct: 83  YEDDDIVVVNKPSDMPIHPSLNNYDNSMANALMYYYRDKNFVFRCINRLDRDTTGLTVVA 142

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +   +A  L  S + R I++IY ++V    ++      +  +       D   + ++   
Sbjct: 143 KHFLSAGILNTSMQRREIKRIYNAIV----EDDGSLTDSGSIDAPISREDNTLIKRRVSA 198

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNF 280
             + AI+H+K++    +    +E+   TGRTHQ+RVH  H+G P+VGD+ Y    +  + 
Sbjct: 199 NGHRAITHYKILKRM-RGASLIELGLETGRTHQIRVHMSHIGHPLVGDYLYNEKYYDKDN 257

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
             P+     LH++ +DL  P  G RL +   LP    +  D
Sbjct: 258 VRPL-----LHSKSLDLLQPLTGKRLHLECELPTDFTERID 293


>gi|297544995|ref|YP_003677297.1| RluA family pseudouridine synthase [Thermoanaerobacter mathranii
           subsp. mathranii str. A3]
 gi|296842770|gb|ADH61286.1| pseudouridine synthase, RluA family [Thermoanaerobacter mathranii
           subsp. mathranii str. A3]
          Length = 285

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/224 (31%), Positives = 118/224 (52%), Gaps = 34/224 (15%)

Query: 103 YEDSKIYVFNKPAGISV------QGGS---GIAYHI-DGFLKSWVDSKGQKPRLTHRLDQ 152
           YED +I + NKPA + V      Q G+   G+A++  D  LK+ +       R  +RLD+
Sbjct: 78  YEDEEILIVNKPANMVVHPTKGYQSGTLANGVAWYFKDKGLKALI-------RPVNRLDR 130

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V A+      +L     ++ + K+Y+++V G  K + E   N  + +    G  
Sbjct: 131 GTSGLVVFAKLPFMQYYLQ---IVKPMSKLYFAVVEG--KMEGEGRINLPISRKPQSGIE 185

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V ++ ++    AI+++KV+   +++F  L+++  TGRTHQ+RVH  H+G PIVGD  Y
Sbjct: 186 RMVSEEGDR----AITNYKVVKS-SERFSLLKVKIETGRTHQIRVHLSHIGHPIVGDTLY 240

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                G+    I+ +  LHA  +   HP E   + + +PLP  M
Sbjct: 241 -----GSSDDYIKRQA-LHAYRLTFVHPLEEKSISVYSPLPQDM 278


>gi|229513013|ref|ZP_04402479.1| tRNA pseudouridine synthase C [Vibrio cholerae TMA 21]
 gi|229349906|gb|EEO14860.1| tRNA pseudouridine synthase C [Vibrio cholerae TMA 21]
          Length = 245

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/215 (30%), Positives = 99/215 (46%), Gaps = 22/215 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG---------IP-KNKKECIANWLLKKSHIGG 210
           A +   A  +   F    ++K Y ++V G          P K + + IA+   K+     
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQDKEAQ 123

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             V   +   K A   IS  K       ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 124 SAVTAYRPLAK-AELPISTGKFATT---RYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
            +        F+ +F++    +L LHA  +   HP
Sbjct: 180 THGDGVHNRLFREHFSA---QRLMLHASELRFMHP 211


>gi|218130909|ref|ZP_03459713.1| hypothetical protein BACEGG_02504 [Bacteroides eggerthii DSM 20697]
 gi|217987253|gb|EEC53584.1| hypothetical protein BACEGG_02504 [Bacteroides eggerthii DSM 20697]
          Length = 303

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 110/226 (48%), Gaps = 21/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 88  IVYEDAYIIVVEKMQGLLSVNTERQKERTAYTI---LNEYVQRSGRQHRVYIVHRLDRDT 144

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L +++      + Y ++V G  +N    + +WL  +      YV+
Sbjct: 145 SGLMMFAKDEKTQNTLRDNWHNIVTDRRYVAVVAGEMENNAGMVRSWLTDRKL----YVY 200

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++ G   +++H++ I   A  F  +E+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 201 SSPTDD-GGKESVTHYRTIKR-ANGFSLVELVLETGRKNQIRVHMQDLGHPIIGDGRYGL 258

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
                  +PI N+L LHA  +   HP  G L Q   P P    K +
Sbjct: 259 ----EEVNPI-NRLALHAFKLCFHHPVTGELMQFETPYPGEFKKLF 299


>gi|148825977|ref|YP_001290730.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittEE]
 gi|148716137|gb|ABQ98347.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittEE]
          Length = 239

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 112/238 (47%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLIAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q  
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQEN 119

Query: 221 KGANYAISHF---KVIDC-------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG+  AI+ +   K+++           ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KGSQEAITDYGGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L     K  +  G++
Sbjct: 180 QYGDLHQNRALISHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWQKLINQFGWE 237


>gi|148982218|ref|ZP_01816647.1| tRNA pseudouridine synthase C [Vibrionales bacterium SWAT-3]
 gi|145960609|gb|EDK25961.1| tRNA pseudouridine synthase C [Vibrionales bacterium SWAT-3]
          Length = 249

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/247 (27%), Positives = 109/247 (44%), Gaps = 27/247 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IIYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    +QK Y ++V G  +          ++   I   +     + +
Sbjct: 64  ALSSEVASEVMPMFANHEMQKTYHAIVRGWIEEGDTLDYALKVELDKIADKFA----KED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EM P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQEAVTAYEPLAKVEVPYSTGRFPTSRYCLVEMLPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 -----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL--G 323
                K+   F+ N  S   ++L LHA  +   HP      +   + A + +TW  L   
Sbjct: 180 SHGDGKHNRLFRENLDS---HRLLLHASELRFIHPFTKEELV---MKASLDETWLQLFET 233

Query: 324 FKYDRNL 330
           F++D NL
Sbjct: 234 FEWDTNL 240


>gi|189463385|ref|ZP_03012170.1| hypothetical protein BACCOP_04104 [Bacteroides coprocola DSM 17136]
 gi|189429814|gb|EDU98798.1| hypothetical protein BACCOP_04104 [Bacteroides coprocola DSM 17136]
          Length = 307

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 106/218 (48%), Gaps = 18/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +LYED+ + V  K  G+ SV             L  +V  + +  R+   HRLD+ETSGI
Sbjct: 94  ILYEDAYLIVVEKKEGLLSVATDHQKEKTAQHILNEYVKRQHRNNRVFVVHRLDRETSGI 153

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-KKSHIGGDYVHVV 216
           ++ A+       L +++      + Y S+V G  +  +  + +WL  +K ++    V   
Sbjct: 154 MMYAKDEKTQHTLRDNWHDIVRDRRYVSIVMGDMEKDQGTVESWLTDRKLYVSSSPV--- 210

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              + G  Y+++H++ I   A  +  +E+Q  TGR +Q+RVH   +G P+VGD +Y    
Sbjct: 211 ---DDGGKYSVTHYRTIKR-ANGYSLVELQLETGRKNQIRVHMQSLGHPVVGDERY---- 262

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
            G   +P+  +L LHA  +   HP  G L +   P P 
Sbjct: 263 -GCEVNPL-GRLALHAFKLCFYHPVTGELMEFETPYPT 298


>gi|304410411|ref|ZP_07392029.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307304503|ref|ZP_07584253.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304350895|gb|EFM15295.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306911905|gb|EFN42329.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 574

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 112/237 (47%), Gaps = 26/237 (10%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGF 132
           L H++ E  ++D +  LT  ++     +LY+D  + + +KPA  +SV G           
Sbjct: 340 LGHML-EGLVVDENPLLTNPAEGKTLTILYQDDAMAIVSKPAEFLSVPGKEIEDSVYSRM 398

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +++  + G  P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ GIP 
Sbjct: 399 CQTFPHATG--PLIVHRLDMSTSGLMVIALTKDAHKQLQKQFIQRTVTKRYVALLAGIPA 456

Query: 193 --NKKECIANWLLKKSHIGGDYVHVVKQNEKG----ANYAISHFKVIDCFAQKFCWLEMQ 246
                +   N  L       D    +  +E G     ++ +SH   +   A+ + +    
Sbjct: 457 VMANTQTTGNISLPLRGDLDDRPRQLVCHEFGKTAETHWDLSHIDEMARTARVYLY---- 512

Query: 247 PHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           P TGRTHQLRVH  H   +  PI+GD  Y             N+L+LHA  + L HP
Sbjct: 513 PKTGRTHQLRVHCAHSEGLNTPIIGDDLYGTR---------ANRLHLHADLLMLQHP 560


>gi|47229673|emb|CAG06869.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 388

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 77/275 (28%), Positives = 125/275 (45%), Gaps = 57/275 (20%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFLKSWVDSKGQK---- 143
           L KH   L   LLY+D  + V NKP G++++  +G+     +   L   +     K    
Sbjct: 110 LAKH---LHRSLLYQDDHVVVINKPYGVALREDTGVTSICSVLPVLSKMMSGNKIKSDFQ 166

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
             P L   L++E SG L++A+    A+++    R  ++Q  YW +  G+P   +  I   
Sbjct: 167 LLPCLG--LEKEASGALLLAKRAEVAENIVNFQRNNQVQITYWVITVGVPVPSEGVIDIP 224

Query: 202 LLKKSHIGGDYVH-------VVKQNEKG-----------ANYAISHFKVIDCFAQKFCWL 243
           ++++  + G   H       + K N+ G           A+ A++ +KV+D      C L
Sbjct: 225 IIER-EVTGPQPHYKMALSPLFKMNDAGDGLTRVRAHRQAHSAVTRYKVLDSSCG--CSL 281

Query: 244 -EMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCANFKGNFTSPI-------------QNK- 287
            E+QP TG  HQ+RVH A  + CPI+GDHKY      N  +P              Q+K 
Sbjct: 282 VELQPSTGVKHQMRVHMAFGLTCPILGDHKYS---HWNKLAPQKLPERVLKKLGLEQSKS 338

Query: 288 ----LYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
               L+LHAR + LP  +   + +  P P +  +T
Sbjct: 339 RHLPLHLHARRLTLPGAQRAGVSVRCPAPKYFTQT 373


>gi|258645458|ref|ZP_05732927.1| pseudouridine synthase, RluA family [Dialister invisus DSM 15470]
 gi|260402809|gb|EEW96356.1| pseudouridine synthase, RluA family [Dialister invisus DSM 15470]
          Length = 313

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 62/204 (30%), Positives = 99/204 (48%), Gaps = 13/204 (6%)

Query: 76  HIIKEQKILDSSVNLTKHSDF-LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           H   E+K  D S    K S F     ++YED  I + +KPAGI  Q  +     ++  L 
Sbjct: 69  HTFSEKKNADPS---QKKSAFPFSRRIIYEDEHILIVDKPAGILTQSDNSNELSLNDALL 125

Query: 135 SWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +    +    KP + +RLD+ TSGI++  +T    Q L E  + R + K Y  +V G  
Sbjct: 126 DYCHYNNHSTAKPSVCNRLDRNTSGIVLCGKTVKGLQMLNEIIKNRTLHKYYRCIVLGET 185

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF--AQKFC-WLEMQPH 248
           K +++ +  +L+K      + V ++ + +  A    + +K I     A   C  LE++  
Sbjct: 186 K-EQDTLKGFLIKNE--SANQVTIITEQKDNAVPIETRYKRISTMERAGNICSLLEVRLI 242

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGR HQ+R H   +G PI+GD KY
Sbjct: 243 TGRPHQIRAHLTSIGHPILGDRKY 266


>gi|317012555|gb|ADU83163.1| hypothetical protein HPLT_03755 [Helicobacter pylori Lithuania75]
          Length = 327

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 58/227 (25%), Positives = 108/227 (47%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W++SK       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVVHKAPSVK---EPTLVDWLESKNYELSNLGLKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHAHLSEQLKTKTMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKATKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N +  F   I  ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN-QALFKEEI--RIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|13508287|ref|NP_110237.1| pseudouridine synthase [Mycoplasma pneumoniae M129]
 gi|2501681|sp|P75230|Y548_MYCPN RecName: Full=Uncharacterized RNA pseudouridine synthase MG370
           homolog; AltName: Full=RNA pseudouridylate synthase;
           AltName: Full=RNA-uridine isomerase
 gi|1673965|gb|AAB95942.1| pseudouridine synthase [Mycoplasma pneumoniae M129]
 gi|301633599|gb|ADK87153.1| pseudouridine synthase, RluA family [Mycoplasma pneumoniae FH]
          Length = 326

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 74/272 (27%), Positives = 123/272 (45%), Gaps = 22/272 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV    EN+R++++     P+I      K+LR G+V ++  + K   R+ SG  +     
Sbjct: 7   VVPKAVENVRIEKFCLKLLPNIKLSQFFKLLRLGKVLLNNTKAKLGQRVSSGDTIVFQFA 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--------- 121
           I    H   E       V+LT+  D L+ I  +ED ++ V +KPAG+  Q          
Sbjct: 67  IEPYLHNHSE------VVDLTQVQDDLQVI--FEDEQLIVVDKPAGVVCQPDAKHELFNL 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            + +  H  G+ + + +S    PR  HR+D+ T G+++ A+T  A Q L   FR   + K
Sbjct: 119 ANSLLKHC-GYNQYFKNSLSFIPRFAHRIDRNTCGLVIGAKTNQALQELEAVFRHNLLMK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KF 240
            Y  LV+G P N K     +  K ++     V V  +    A    + F+      +   
Sbjct: 178 QYQGLVFG-PFNFKGTQKAYWAKDAYQA--LVTVKAKPFPNAKPITTIFENSKYLTKLDL 234

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             L ++  +G+THQ+R     +   +VGD KY
Sbjct: 235 SLLTIRLVSGKTHQIRACLNLLNTQLVGDRKY 266


>gi|319956455|ref|YP_004167718.1| pseudouridine synthase [Nitratifractor salsuginis DSM 16511]
 gi|319418859|gb|ADV45969.1| pseudouridine synthase [Nitratifractor salsuginis DSM 16511]
          Length = 243

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 98/201 (48%), Gaps = 23/201 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D ++   NKPA I        +Y I+  ++          +L HRLD++TSG+L++
Sbjct: 58  IIYQDEQVVAVNKPAFID-------SYEIEEAIEGA--------QLLHRLDRDTSGVLLL 102

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQN 219
           AR  A A+   E+FR R++ K Y + V G+     E  +    +KK   G  +  + K+ 
Sbjct: 103 ARDEAFAKKAIEAFRQRKVHKEYVAWVEGVVVEPFEIDLPIHTIKK---GKAFSKIDKKL 159

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K A   +      D    K   + ++  TGRTHQ+RVH  H+G PIVGD +Y +  +  
Sbjct: 160 GKPALTKVWP----DEVQGKKSKVRIEIETGRTHQIRVHLAHVGHPIVGDEQYGSPTRAK 215

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  K+ L  R  + P P
Sbjct: 216 RPLLHAKKITLLGRSYEAPEP 236


>gi|238763986|ref|ZP_04624942.1| tRNA pseudouridine synthase C [Yersinia kristensenii ATCC 33638]
 gi|238697803|gb|EEP90564.1| tRNA pseudouridine synthase C [Yersinia kristensenii ATCC 33638]
          Length = 257

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 101/232 (43%), Gaps = 23/232 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +     + +
Sbjct: 64  ALSSDVARALSLQFEQHQIQKTYHAVVRGYVLEDGTIDYEMTEELDKIADKF----SRPD 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
           K    +++H+  +               +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYHALAQVEVPIAIGRYDTARFSLMELKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 270 -HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
            H      +G       ++L LHA +++L HP  G        P  +   WD
Sbjct: 180 THGDLRQNRGIAEHFDCSRLMLHASHLNLNHPVTGE-------PLSLTARWD 224


>gi|328461874|gb|EGF34095.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus MTCC 5462]
          Length = 260

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 114/236 (48%), Gaps = 34/236 (14%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V V+ K VK N ++ +G VV +          I E K L +       ++ +   ++YED
Sbjct: 2   VTVNGKPVKANFKVTAGDVVTV---------TIPEVKPLKAV------AEPIPLEIVYED 46

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGI 157
            ++ V NKP G+ V    G   H DG L + +    +        +P + HR+D++TSG+
Sbjct: 47  DQVIVVNKPQGMVVHPAPG---HPDGTLVNGLLYHTKLPGINGVIRPGIVHRIDKDTSGL 103

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+T  A   L+   + +   + Y +LV G  K  +  I       + +G D     +
Sbjct: 104 LMVAKTETAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTI------DAPLGRDPRDRKR 157

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           Q       +A++HF+V++ F   +  ++    TGRTHQ+RVH  ++  P+ GD  Y
Sbjct: 158 QAVVADGRHAVTHFQVLERFTN-YTLVKCILDTGRTHQIRVHMAYIHHPVAGDPLY 212


>gi|167762842|ref|ZP_02434969.1| hypothetical protein BACSTE_01200 [Bacteroides stercoris ATCC
           43183]
 gi|167699182|gb|EDS15761.1| hypothetical protein BACSTE_01200 [Bacteroides stercoris ATCC
           43183]
          Length = 302

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/226 (29%), Positives = 109/226 (48%), Gaps = 21/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ + V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 88  IVYEDAYLIVVEKMQGLLSVNTERQKERTAYTI---LNEYVQRSGRQHRVYIVHRLDRDT 144

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+ A+       L +++      + Y ++V G  +N    + +WL  +      YV+
Sbjct: 145 SGLLMFAKDEKTQNTLRDNWHNIVTDRRYVAVVAGEMENNAGMVRSWLTDRKL----YVY 200

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++ G   AI+H++ I   A  F  +E+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 201 SSPTDD-GGKEAITHYRTIKR-ANGFSLVELMLETGRKNQIRVHMQDLGHPIIGDGRYGL 258

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
                  +PI  +L LHA  +   HP  G L Q   P P    K +
Sbjct: 259 ----EEINPI-GRLALHAFKLCFRHPVTGELMQFETPYPGEFKKLF 299


>gi|262165137|ref|ZP_06032874.1| tRNA pseudouridine synthase C [Vibrio mimicus VM223]
 gi|262024853|gb|EEY43521.1| tRNA pseudouridine synthase C [Vibrio mimicus VM223]
          Length = 244

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/217 (29%), Positives = 104/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  ++    + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEDAD--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  AI+ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAITAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFVHP 211


>gi|229095877|ref|ZP_04226855.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|229114830|ref|ZP_04244243.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228668522|gb|EEL23951.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228687501|gb|EEL41401.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
          Length = 307

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/228 (31%), Positives = 116/228 (50%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEKMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K KK  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKKGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F +    ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRVSPKG-DEAITYYKVEKYFKKHNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y     G  T+ +  +  LHA  ++  HP     ++I  P P  +
Sbjct: 254 DVLY-----GGQTTYMSGQA-LHAMKINFLHPITKEEIEIDVPFPTKL 295


>gi|87311611|ref|ZP_01093729.1| ribosomal large subunit pseudouridine synthase D [Blastopirellula
           marina DSM 3645]
 gi|87285733|gb|EAQ77649.1| ribosomal large subunit pseudouridine synthase D [Blastopirellula
           marina DSM 3645]
          Length = 242

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 105/225 (46%), Gaps = 19/225 (8%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
           +   ++LYED+ +   +KPA ++  G          + K ++     KP      +  R+
Sbjct: 22  YATPLVLYEDNHLLAISKPALLATMGAQEGEPSAAQWAKDYLKRTYNKPGNVYVGIVSRI 81

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D   +G+L+ ART  AA  L+E FR R   K Y +L+   PK +   + +W+ K+     
Sbjct: 82  DAHVTGVLLFARTSKAASRLSEQFRDRSTVKEYAALIPAGPKIRNGELVDWIRKE----- 136

Query: 211 DYVH-VVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVG 268
           D +H +V   E  A+   +  ++++   +  C  L ++  TGR HQ+R+     G PI+G
Sbjct: 137 DRLHRMVIAAEGTADADRAEMEILEQQRRPNCQMLHLRLITGRKHQIRLQLASRGAPILG 196

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
           D KY +      T      + LHA  +   HP     + I APLP
Sbjct: 197 DKKYGS------TDRYSPGIALHAHRLVFTHPTLKTMVTIEAPLP 235


>gi|291560401|emb|CBL39201.1| ribosomal large subunit pseudouridine synthase D
           [butyrate-producing bacterium SSC/2]
          Length = 236

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/222 (28%), Positives = 102/222 (45%), Gaps = 14/222 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDG--FLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+D +I V  KP GI V     G   + + +    F +   D + Q   L HRLD+  
Sbjct: 9   IIYKDDQIVVCEKPKGIPVSSDKTGDMDLLHQLKNQLFFEENTDGEPQL-YLVHRLDRPV 67

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G++V ART+ AA  LTE  +    +K Y +++ G   + +    ++LLK      +   
Sbjct: 68  GGVMVFARTKKAAASLTEQIKDHTFEKDYQAVLTGWLSDDEGTFRDYLLKDPK--NNVSK 125

Query: 215 VVKQNEKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +VK+   GA  AI  ++VID       K+ +  +   TGR HQ+RV     G  I GD K
Sbjct: 126 IVKEGTPGAKEAILDYEVIDMMEDSKMKYTYCLIHLETGRHHQIRVQTSSRGFGIWGDTK 185

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           Y   ++   T     ++ L A  +   HP  G   +    P+
Sbjct: 186 YNPIYQK--TKKKYKEIGLFAARIAFEHPTTGERMVFKADPS 225


>gi|224024089|ref|ZP_03642455.1| hypothetical protein BACCOPRO_00808 [Bacteroides coprophilus DSM
           18228]
 gi|224017311|gb|EEF75323.1| hypothetical protein BACCOPRO_00808 [Bacteroides coprophilus DSM
           18228]
          Length = 307

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/221 (28%), Positives = 110/221 (49%), Gaps = 24/221 (10%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           +LYED+ + V  K  G+    + +     A HI   L  +V  + +  R+   HRLD+ET
Sbjct: 94  ILYEDAYLIVVEKKEGLLSVATEKQKERTAQHI---LNEYVKRQHRNNRVFVVHRLDRET 150

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-KKSHIGGDYV 213
           SGI++ A+       L +++      + Y ++V G  +  +  + +WL  +K ++    V
Sbjct: 151 SGIMMYAKDEKTQHTLRDNWHDIVYDRRYVTIVTGDMEKDQGKVESWLTDRKLYVSSSPV 210

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                 + G  ++++H+  I   A  F  +E+Q  TGR +Q+RVH   +G P+VGD +Y 
Sbjct: 211 ------DDGGKFSVTHYHTIKR-ANGFSLVELQLETGRKNQIRVHMQTLGHPVVGDERY- 262

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
               G   +P+  +L LHA  +   HP  G R++   P PA
Sbjct: 263 ----GCEVNPL-GRLALHAFKLCFYHPVTGERMEFETPYPA 298


>gi|332160586|ref|YP_004297163.1| tRNA pseudouridine synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|318606936|emb|CBY28434.1| tRNA pseudouridine synthase C; tRNA Psi65 [Yersinia enterocolitica
           subsp. palearctica Y11]
 gi|325664816|gb|ADZ41460.1| tRNA pseudouridine synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859592|emb|CBX69932.1| tRNA pseudouridine synthase C [Yersinia enterocolitica W22703]
          Length = 257

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 101/222 (45%), Gaps = 17/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +     + +
Sbjct: 64  ALSSDVARALSLQFEQHQIQKTYHAVVRGYVLEDGTIDYEMTEELDKIADKFA----RPD 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
           K    +++H++ +               +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYQALAQVEVPIAIGRYDTSRFSLMELKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 270 -HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
            H      +G       ++L LHA ++ L HP  G  L +TA
Sbjct: 180 AHGDLRQNRGVAEHFDCSRLMLHASHLHLNHPVTGESLSLTA 221


>gi|316983895|gb|EFV62874.1| RNA pseudouridylate synthase family protein [Neisseria meningitidis
           H44/76]
 gi|325133346|gb|EGC56011.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M13399]
 gi|325139340|gb|EGC61880.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis CU385]
 gi|325143576|gb|EGC65896.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M01-240013]
 gi|325199109|gb|ADY94565.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis G2136]
 gi|325206923|gb|ADZ02376.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M04-240196]
          Length = 218

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/212 (31%), Positives = 103/212 (48%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 4   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + +A  L+  F  + I+K Y +L    P  K+  I   + +KS  G     + K  
Sbjct: 60  FALNKESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGM-EKSRCG-----MWKLT 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y     G 
Sbjct: 114 RNTENIAVTRFHSIS-IAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLY-----GG 167

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
             S     ++L+A  +   + +  +++I APL
Sbjct: 168 TES---ETMFLYAWKIQFDY-QNRQIEIVAPL 195


>gi|281492772|ref|YP_003354752.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
 gi|281376424|gb|ADA65910.1| Ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
          Length = 288

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/213 (28%), Positives = 98/213 (46%), Gaps = 24/213 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  + V NKP G+   G +     +   + + ++   Q+  + HRLD  TSG ++ 
Sbjct: 83  ILYEDEHLIVVNKPEGMKTHGNTADELALQNHVAAAIN---QEVFVVHRLDHATSGAVLF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ +     L + F   +I + Y +LV G     +  I   + +  H     +   K   
Sbjct: 140 AKNQFVLPILGKMFEENKIHREYLALVKGHFSENQFTIDRAIGQNRHDKNKRILSAK--- 196

Query: 221 KGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                A++H ++I  F  K    C L+    TGRTHQ+RVH   +  PI+GD  Y     
Sbjct: 197 --GQKAVTHVEIIKKFTDKTLVKCTLD----TGRTHQIRVHLSSLNHPIIGDALYG---- 246

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
                  Q ++ LHA  + +PHP E   L+I+A
Sbjct: 247 ----QKSQERMMLHADKIIIPHPFENKILEISA 275


>gi|89891166|ref|ZP_01202673.1| ribosomal large subunit pseudouridine synthase A [Flavobacteria
           bacterium BBFL7]
 gi|89516478|gb|EAS19138.1| ribosomal large subunit pseudouridine synthase A [Flavobacteria
           bacterium BBFL7]
          Length = 561

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 117/244 (47%), Gaps = 22/244 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++  ++ D+ + +    D    ++ YED  I + NKP       G  I   +   L
Sbjct: 334 LGHMLEGIEVEDNPLLINPGIDKTMEVI-YEDDAIIIVNKPEEFLSVPGKTIKDSVYSRL 392

Query: 134 KS-WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           K  + D+ G  P L HRLD  TSGILV  +       + E F  R I K Y +L+ G+ +
Sbjct: 393 KELYPDATG--PILVHRLDMSTSGILVATKNLEYYHFIQEQFINRTISKRYVALLNGVLE 450

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           N +  I   L  +  +      +V   E G + A + ++V++   +K   +   P TGRT
Sbjct: 451 NNEGMIE--LPLRVDLDNRPTQLVCY-EYGKS-ARTKYQVLER-REKETLVHFYPITGRT 505

Query: 253 HQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           HQLRVHA H   +  PIVGD  Y     G  T    N+L+LHA ++   HP   + +   
Sbjct: 506 HQLRVHAAHASGLNAPIVGDDLY-----GTAT----NRLHLHAEFIKFIHPITHKTVSFK 556

Query: 309 APLP 312
           AP+P
Sbjct: 557 APVP 560


>gi|117618171|ref|YP_856003.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117559578|gb|ABK36526.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 243

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 69/223 (30%), Positives = 103/223 (46%), Gaps = 22/223 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + + NKP+G+    G     ++D      V +      L HRLD  TSGI++V
Sbjct: 19  ILFEDEHLLLINKPSGLLSLSGKN-PQNLDSVHHRLVQAY-PGCALVHRLDFGTSGIMLV 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +A    L   F  R + K Y +L+ G    K E + +  + K       + +   N 
Sbjct: 77  ARNKAINALLCRQFSQRAVSKAYSALLCGH-LAKDEGVIDAPIAKDPALFPLMSICAVNG 135

Query: 221 KGANYAISHFKVIDCFAQK-------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           K A    S ++VI+  AQ+          + + P TGRTHQLR+H+  +G PI+G   Y 
Sbjct: 136 KPAR---SRYQVIERLAQQIQGQTVPLTSVRLVPETGRTHQLRIHSQQLGHPILGCDLY- 191

Query: 274 ANFKGNFTSPI---QNKLYLHARYMDLPHPEGGR-LQITAPLP 312
               G    P      +L LHA  +D  HP  G  +QI +  P
Sbjct: 192 ----GGLLPPGCERAPRLMLHASELDFVHPVSGEPMQIRSEAP 230


>gi|256830138|ref|YP_003158866.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256579314|gb|ACU90450.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 243

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 74/225 (32%), Positives = 109/225 (48%), Gaps = 29/225 (12%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKGQKPR----LTHRLD 151
           +++YED  I V NKPAG+         +  AY+    L  +V     K R    + HRLD
Sbjct: 17  VIIYEDRDIIVVNKPAGMLTMATETEKTRTAYYA---LTDYVRKGNAKSRYRIFIVHRLD 73

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSGI++ A+T  A + L + +      KIY ++V G     +   A+ +L  SH+   
Sbjct: 74  RETSGIVLFAKTEVAKRTLQDQWE--DTTKIYAAVVHG-----QMGKASGMLS-SHLVES 125

Query: 212 YVHVVKQNEKGA--NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            VH V      A    A + + V+      +  L++   TGR HQ+RV     G PI GD
Sbjct: 126 GVHKVYATRDAALGKLARTAWTVLKERG-GYSLLDVTLLTGRKHQIRVQMADAGHPIAGD 184

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
            KY    KG+  S    +L LHAR +   HP  GR + + AP+P+
Sbjct: 185 KKY--GVKGDTFS----RLALHARSITFAHPFSGRSMTLDAPVPS 223


>gi|153215725|ref|ZP_01950106.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           1587]
 gi|153801105|ref|ZP_01955691.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-3]
 gi|229521570|ref|ZP_04410988.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           TM 11079-80]
 gi|261211068|ref|ZP_05925357.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. RC341]
 gi|262191021|ref|ZP_06049230.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           CT 5369-93]
 gi|124114643|gb|EAY33463.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           1587]
 gi|124123338|gb|EAY42081.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-3]
 gi|229341164|gb|EEO06168.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           TM 11079-80]
 gi|260839569|gb|EEX66180.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. RC341]
 gi|262033084|gb|EEY51613.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           CT 5369-93]
          Length = 245

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 100/203 (49%), Gaps = 17/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I   NKP+G+    G  +  H D      VD      ++ HRLD  TSG+++ 
Sbjct: 16  VIYEDEHIIAANKPSGLLSVPGRPVE-HYDSMWARLVDYCPDV-KVVHRLDMSTSGLILF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A+ +     L + F+ R   KIY++ VWG+   + E   N  L       D+ +  KQ  
Sbjct: 74  AKGKHMESALKKQFQYRLTHKIYYARVWGV-MEQDEGEVNLPL-----CCDWPNRPKQKV 127

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+G + +++ ++V+    +K   + + P TGR+HQLRVH   +G PIVGD  Y     
Sbjct: 128 CFEEGRD-SLTRYQVVK-REEKTTVVRLIPITGRSHQLRVHMQSLGHPIVGDDLYAPPEA 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
             F     ++L LHA  +   HP
Sbjct: 186 VEFA----DRLQLHAAELCFYHP 204


>gi|94986325|ref|YP_605689.1| pseudouridine synthase, RluD [Deinococcus geothermalis DSM 11300]
 gi|94556606|gb|ABF46520.1| Pseudouridine synthase, RluD [Deinococcus geothermalis DSM 11300]
          Length = 301

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 129/318 (40%), Gaps = 61/318 (19%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR--IPPVINALN 75
            + L  +   HY H +  + Q  L  G+V +D         ++ GQV+    PP      
Sbjct: 19  GLTLLAYLTRHYLHSSESDWQARLERGEVCLDGLPAYGPETLRPGQVLEWHRPP------ 72

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
              +E   LD +V             +Y D+ +    KP+G+    G G   H    L +
Sbjct: 73  -WEEEDAPLDFAV-------------VYRDAALLAVAKPSGLPTLPGGGFLKHT---LLA 115

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            V +   + R  HRL + TSG+++ ART  A   L  ++R+R +QK Y +L  G P  ++
Sbjct: 116 QVRTDFPEARPLHRLGRGTSGLVLFARTHEAGAILARAWRVRAVQKRYRALAVGTPLQEE 175

Query: 196 ECIANWLLKKSH--IGGDY------------VHVVKQNEKGANYAISHFKVIDCFAQKFC 241
             I   +    H  +G  +             HV+++    A +A+              
Sbjct: 176 YAITTPIGPVPHPRLGSVFAASAAGKAASSLAHVLERRAATALFAVDI------------ 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTS-PIQNKLYLHARYMDLP 298
                 HTGR HQ+R+H   +G P+VGD  Y +    + +    P      LHA  +   
Sbjct: 224 ------HTGRPHQIRIHLAAIGHPLVGDPLYASGGLPRADLPGLPGDLGYLLHAERLTFL 277

Query: 299 HP-EGGRLQITAPLPAHM 315
           HP  G RL + AP P  +
Sbjct: 278 HPLTGERLSLKAPPPPEL 295


>gi|52841563|ref|YP_095362.1| ribosomal large subunit pseudouridine synthase D, RluD [Legionella
           pneumophila subsp. pneumophila str. Philadelphia 1]
 gi|52628674|gb|AAU27415.1| ribosomal large subunit pseudouridine synthase D, RluD [Legionella
           pneumophila subsp. pneumophila str. Philadelphia 1]
          Length = 321

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 84/323 (26%), Positives = 143/323 (44%), Gaps = 42/323 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q + V  +  N R+D       P  +   +   +++G V ++    K  ++   G ++  
Sbjct: 7   QQLSVPRELHNQRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCKPKDKALGGDLI-- 64

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              IN       +  I+++  N  K  +    I+ YEDS++ V NKPAG+ V  G+G   
Sbjct: 65  --TINV------DHTIVNTDFNYCKPENIPIQII-YEDSEVIVVNKPAGLVVHPGAGNKE 115

Query: 128 H--IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           H  ++  L    + +   PR  + HRLD++T+G+L+VA+   +   L    + R I++ Y
Sbjct: 116 HTLVNALLHHCPELQ-LLPRAGIIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVIDCFAQ 238
            +LV G           +++    I   +    K   K A       A++H+  I+   +
Sbjct: 175 LTLVHG-----------YVISGGTIDTGFGRHPKNRLKMAVTDFGRQAVTHYN-INKHYK 222

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKL------YL 290
            F  L +   TGRTHQ+RVH  ++  P+VGD  Y     F  N    I + L       L
Sbjct: 223 DFTLLNVSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKFPPNADEAILSVLKQFKRQAL 282

Query: 291 HARYMDLPHP-EGGRLQITAPLP 312
           HA  +   HP +   + + A LP
Sbjct: 283 HACSISFCHPVKNTEITLNALLP 305


>gi|183597604|ref|ZP_02959097.1| hypothetical protein PROSTU_00890 [Providencia stuartii ATCC 25827]
 gi|188023103|gb|EDU61143.1| hypothetical protein PROSTU_00890 [Providencia stuartii ATCC 25827]
          Length = 252

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 104/235 (44%), Gaps = 43/235 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKPAG+ V              +SW+DSK             GQ     
Sbjct: 4   IIYQDEYMVAVNKPAGMLVH-------------RSWLDSKETVFVMQTLRDQIGQFVYPI 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L+ A +   A+ L   F   +I+KIY ++V G  +  +      L +   
Sbjct: 51  HRLDRPTSGVLLFALSSDVARQLAAQFESHQIEKIYHAVVRGYVEAPQTIDYPLLEQLDK 110

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVI---DCF-------AQKFCWLEMQPHTGRTHQLRV 257
           I   +       E      ++H + I   +C          +F  LE++P TGR HQLR 
Sbjct: 111 IADKHA----TREPALQECVTHCQPIAQVECSVAIGRYPTSRFSLLELKPETGRKHQLRR 166

Query: 258 HALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           H  H+  PI+GD K+      +G       ++L LHA  + L HP  G R+ + A
Sbjct: 167 HMSHIRHPIIGDSKHGDLRQNRGVSQHFAVSRLMLHASQLVLDHPISGERISLIA 221


>gi|170781776|ref|YP_001710108.1| putative ribosomal large subunit pseudouridine synthase
           [Clavibacter michiganensis subsp. sepedonicus]
 gi|169156344|emb|CAQ01492.1| putative ribosomal large subunit pseudouridine synthase
           [Clavibacter michiganensis subsp. sepedonicus]
          Length = 342

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 57/178 (32%), Positives = 91/178 (51%), Gaps = 8/178 (4%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD  TSG++VVA+T  A   L   F  R ++K+Y ++V G P      I   + + 
Sbjct: 170 IVHRLDAGTSGLMVVAKTERAYTELKRQFHDREVEKVYHAVVQGHPDPLAGTIDAPIGR- 228

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            H   D+   V  + K    +++H++ ++ F ++   LE+   TGRTHQ+RVH      P
Sbjct: 229 -HPRSDWKFAVTADGK---PSVTHYETLEAF-RRAALLEVHLETGRTHQIRVHMAAQRHP 283

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
            VGD  Y A+   +    +Q + +LHA  +D+ HP  G R   ++  PA +    D L
Sbjct: 284 CVGDAMYGADPTISAQLGLQRQ-WLHAMRLDITHPATGDRASFSSTYPADLQHALDVL 340


>gi|153839608|ref|ZP_01992275.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ3810]
 gi|260900301|ref|ZP_05908696.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
 gi|149746879|gb|EDM57867.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ3810]
 gi|308107572|gb|EFO45112.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
          Length = 250

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 100/214 (46%), Gaps = 30/214 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           +++ED  I   NKP+G+ SV G   +A H D     W   + + P  ++ HRLD  TSG+
Sbjct: 16  IVFEDDHILAVNKPSGLLSVPGR--LAEHHDSM---WSRLQEEYPDIQVVHRLDMSTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE----CIANW----LLKKSHI 208
           +V+A+ + A   L + F+ R   KIY++ VWG + + + E     I +W    L K    
Sbjct: 71  MVLAKNKRAESALKKQFQFRLTHKIYYARVWGHVEQEEGEIDLPLICDWPNRPLQKVCFE 130

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            G     + Q  K   +             K   + + P TGR+HQLRVH   +G PIVG
Sbjct: 131 DGKPSKTLFQVAKREEHED---------GTKTTIVRLLPITGRSHQLRVHMQALGHPIVG 181

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           D  Y       F+     +L LHA  +   HP+ 
Sbjct: 182 DEFYATEEAKAFS----ERLELHASELSFYHPKS 211


>gi|302670812|ref|YP_003830772.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
 gi|302395285|gb|ADL34190.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
          Length = 341

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/322 (22%), Positives = 141/322 (43%), Gaps = 41/322 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +V+ N+E + RLD + K++ P+ +   + K+LR   + ++ K+     ++ S  V+ 
Sbjct: 1   MKEIVIGNNESDKRLDGFLKSYLPNASMGFIYKMLRKKNITLNGKKASGTEKLASNDVIC 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI------------------LLYEDSKI 108
           I     A   + K + I   S     +S+    I                  ++YE+  +
Sbjct: 61  I---FFADETLEKFRGISTDSTQSGNNSNSRSDIQDYCKREISSYKKIGELKVIYENKHV 117

Query: 109 YVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
              +KPAG+  Q             I Y +   L +  + +  KP + +RLD+ TSG+++
Sbjct: 118 IFVDKPAGLLSQKSKDTDDSLNDWLIGYMLTNNLITPSELETYKPSICNRLDRNTSGLVI 177

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A++   A+ +    + R + K Y ++V G      E +  +L K       ++      
Sbjct: 178 CAKSLLGARTMNNMLKDRTLHKYYRTIVTGQISESSE-LKGFLYKDEKKNKVFIKTSDPG 236

Query: 220 EKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +   +Y  + +K +  +       LE++  TG+ HQ+R H   +G PI+GD KY      
Sbjct: 237 DDRYSYIETEYKPVRYYYDLDMTLLEVKLITGKPHQIRAHLQSIGHPIIGDVKYGG---- 292

Query: 279 NFTSPIQNKLY--LHARYMDLP 298
              SP++   Y  LH+  + LP
Sbjct: 293 ---SPVKGLKYQLLHSYRLVLP 311


>gi|294497498|ref|YP_003561198.1| pseudouridine synthase, RluA family [Bacillus megaterium QM B1551]
 gi|294347435|gb|ADE67764.1| pseudouridine synthase, RluA family [Bacillus megaterium QM B1551]
          Length = 302

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 78/314 (24%), Positives = 143/314 (45%), Gaps = 38/314 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRI-- 67
            V+N  E + +  + K H   I+  +L  I  R G + V+ K       +Q G  +++  
Sbjct: 10  TVDNSFEGVAVREFLKEH--DISKASLTDIKFRGGAIEVNGKHATVRYILQKGDEIKVAF 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK-PAGISVQGGSGIA 126
           PP   +       + +L  ++ L          ++YED  I V NK P   S+     + 
Sbjct: 68  PPEKAS-------ESLLPRAIPLD---------IVYEDEYILVLNKQPNMPSIPSREHLT 111

Query: 127 YHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +   +  + +         L +RLD++TSG+L+VA+ R      +++ +   I+++Y 
Sbjct: 112 WSLSNAVLYYYEENNINSTVHLVNRLDRDTSGLLIVAKHRHVHYLFSKAQKEHEIKRVYR 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           + V G    K+   A    K+S I      + ++  +   +AI+H+  +  ++  F  + 
Sbjct: 172 AFVHGKLVGKETIEAPIGRKESSI------IEREVREDGQFAITHYTALRQYSS-FTEVA 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TGRTHQ+RVH  + G P++GD  Y        T+ + ++  LH+  +   HP   +
Sbjct: 225 LSLETGRTHQIRVHMAYKGYPLLGDTLYGG------TNHLISRQALHSYELTFFHPFLQK 278

Query: 305 -LQITAPLPAHMVK 317
            L  TAPLP  M K
Sbjct: 279 TLSFTAPLPPDMQK 292


>gi|149912122|ref|ZP_01900709.1| pseudouridine synthase-like protein [Moritella sp. PE36]
 gi|149804799|gb|EDM64840.1| pseudouridine synthase-like protein [Moritella sp. PE36]
          Length = 238

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 102/216 (47%), Gaps = 20/216 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +LY D+ + V NKPAG+ SV   +    H    L+  +        L   HRLD++TSG+
Sbjct: 31  ILYSDNDLVVINKPAGLLSVASANENKQHALAILRKQLSHAKNSVALWPVHRLDRDTSGV 90

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A +R     + E +     +K Y ++V G PK  +  I   L         Y  +V 
Sbjct: 91  LMFATSREMRDAVNEGWS--GAEKTYLAVVEGSPKPSQGRIDQPLRMDPE---KYQMIVG 145

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +  N A++HFK +    ++   LE++  TGR HQ+RVH   +G  ++GD +Y  +  
Sbjct: 146 PHSEAKN-AVTHFKTLRTV-KELTLLEVKLETGRQHQIRVHMAWLGHSVIGDPRYGTDGP 203

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                    ++ LHA  + +  P  G RL   AP P
Sbjct: 204 ---------RMGLHALSLSITRPNTGKRLTFEAPAP 230


>gi|86146894|ref|ZP_01065213.1| pseudouridine synthase Rlu family protein [Vibrio sp. MED222]
 gi|85835346|gb|EAQ53485.1| pseudouridine synthase Rlu family protein [Vibrio sp. MED222]
          Length = 249

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 111/248 (44%), Gaps = 29/248 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IIYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG----------IPKNKKECIANWLLKKSHIGG 210
           A +   A  +   F    +QK Y ++V G            K + + IA+   K+     
Sbjct: 64  ALSSEVASEVMPMFANHEMQKTYHAIVRGWIEEGDTLDYALKVELDKIADKFAKEDKEPQ 123

Query: 211 DYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           + V V +   K    Y+   F        ++C +EM P TGR HQLR H  H+  PIVGD
Sbjct: 124 EAVTVYEPLAKVEVPYSTGRFPT-----SRYCLVEMMPKTGRKHQLRRHMAHLRHPIVGD 178

Query: 270 H-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL-- 322
                 K+   F+ +  S   ++L LHA  +   HP      +   + A++ +TW  L  
Sbjct: 179 TSHGDGKHNRLFRDDLDS---HRLLLHASELRFIHPFTKEELV---MKANLDETWLRLFE 232

Query: 323 GFKYDRNL 330
            F++D NL
Sbjct: 233 TFEWDANL 240


>gi|254391608|ref|ZP_05006807.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           clavuligerus ATCC 27064]
 gi|294812119|ref|ZP_06770762.1| Pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|326440725|ref|ZP_08215459.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces clavuligerus ATCC 27064]
 gi|197705294|gb|EDY51106.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           clavuligerus ATCC 27064]
 gi|294324718|gb|EFG06361.1| Pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
          Length = 313

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 80/311 (25%), Positives = 134/311 (43%), Gaps = 29/311 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTLPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVLVDGAAVGKSERVH 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPQAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIVKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +    + + G   R  + HRLD  TSG++VVA++  A   L + 
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKQQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R + K Y +LV G P      I   + +  H   DY   V    K    +++H+ ++
Sbjct: 166 FRDRTVDKRYHALVQGHPDPMSGTIDAPIGR--HPNHDYKWAVTAEGK---PSVTHYDLL 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAF-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTMAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHPEGGR 304
            +   HP  GR
Sbjct: 279 RLGFEHPSDGR 289


>gi|92115011|ref|YP_574939.1| tRNA pseudouridine synthase C [Chromohalobacter salexigens DSM
           3043]
 gi|91798101|gb|ABE60240.1| tRNA pseudouridine synthase C [Chromohalobacter salexigens DSM
           3043]
          Length = 261

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 116/240 (48%), Gaps = 17/240 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETS 155
           L+  +LY+D ++    KP+G+ V   S IA     F L++  +  G+     HRLD+ TS
Sbjct: 3   LELPVLYQDERMVAVQKPSGMLVHR-SPIARDARVFALQTLRNQLGRHVYPVHRLDRPTS 61

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+ A     AQ L E F   R+ K Y ++V G+    ++ + ++ L++         +
Sbjct: 62  GLLLFALDPEMAQALGEEFTAHRVHKRYLAVVRGV--GPEQDLLDYGLREEDGSRPKAEM 119

Query: 216 VKQNEKGANYAISHFKV---IDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +     A   +   ++   ID + Q ++  +E +P TGR HQ+R H    G PI+GD K
Sbjct: 120 PELEAWTAVRRLDSVELPVRIDRYPQVRYSLMEARPWTGRRHQIRRHLARRGYPIIGDAK 179

Query: 272 YCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +        F+    SP   +L L A  M + HPE  R LQ+ APL   M   +   G++
Sbjct: 180 HGKGAHNRFFRERLDSP---RLLLAAVGMTVWHPEQARTLQLDAPLADDMQALFARFGWQ 236


>gi|88608012|ref|YP_506045.1| ribosomal large subunit pseudouridine synthase A [Neorickettsia
           sennetsu str. Miyayama]
 gi|88600181|gb|ABD45649.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Neorickettsia sennetsu str. Miyayama]
          Length = 330

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 116/246 (47%), Gaps = 36/246 (14%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKP 114
            +RI+S   +++ P    +  + +E  + D  +       F++ + + YED  + V  KP
Sbjct: 37  GSRIESEGKIQLEPSRRVV--VGEEYHLFDLPLERKPRHAFVQPLDVRYEDDCLLVIYKP 94

Query: 115 AGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
           AG+ V  G G         + +H      S +DS   +P + HRLD++T+G L+VA+T  
Sbjct: 95  AGLVVHPGIGNREQTLVNILEHHYPTEKLSSLDS--SRPGIVHRLDKDTAGFLIVAKTNP 152

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK---- 221
           A   L++  +   I++ Y +LV  +P +              + G+    +K+ ++    
Sbjct: 153 AHLSLSQMIKEGVIRREYLALVHSVPAS--------------LSGEIKKPIKRGQRKMMI 198

Query: 222 ---GANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                  A++++ VI     + C L   +  +GRTHQ+R+H   +GCP+VGD  Y  N  
Sbjct: 199 GRCSGKPALTYYGVIARTVDRKCSLVHCRLGSGRTHQIRLHMKSIGCPVVGDKLYGLNRD 258

Query: 278 GNFTSP 283
            +  +P
Sbjct: 259 ADLCAP 264


>gi|313622709|gb|EFR93062.1| ribosomal large subunit pseudouridine synthase D [Listeria innocua
           FSL J1-023]
          Length = 288

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 105/221 (47%), Gaps = 29/221 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP G+        +Y  D     ++ +++  GQ+      HRLDQ TS
Sbjct: 79  IIYEDDFLLVVNKPVGMKTHAND--SYETDTCANAVQYYLEKTGQEANALAVHRLDQTTS 136

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLV---WGIPKNKKECIANWLLKKSHIGGDY 212
           G+++ A+ + A   L+     R I + Y + V   WG+   K        + K  IG D 
Sbjct: 137 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQK--------INKP-IGEDR 187

Query: 213 VHVVK-QNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDH 270
            H  + Q       A++H KV++   +    L E Q  TGRTHQ+RVH   +G PI+GD 
Sbjct: 188 HHGSRRQISPYGQPAVTHVKVLENDNENNTSLVECQIETGRTHQIRVHLSGIGHPIIGDT 247

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
            Y  + +        N++ LHA  + L HP  G  +  +AP
Sbjct: 248 LYGGSSRA-------NRIMLHAEKLHLNHPFIGKEMNFSAP 281


>gi|15642501|ref|NP_232134.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|153817992|ref|ZP_01970659.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           NCTC 8457]
 gi|153822421|ref|ZP_01975088.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|227082624|ref|YP_002811175.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           M66-2]
 gi|229507437|ref|ZP_04396942.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           BX 330286]
 gi|229509638|ref|ZP_04399119.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|229516763|ref|ZP_04406209.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC9]
 gi|229606943|ref|YP_002877591.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MJ-1236]
 gi|254851050|ref|ZP_05240400.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MO10]
 gi|255744517|ref|ZP_05418469.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholera
           CIRS 101]
 gi|262154659|ref|ZP_06028785.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           INDRE 91/1]
 gi|298500664|ref|ZP_07010468.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MAK 757]
 gi|34395834|sp|Q9KP71|RLUA_VIBCH RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|9657087|gb|AAF95647.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|126511427|gb|EAZ74021.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           NCTC 8457]
 gi|126520064|gb|EAZ77287.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|227010512|gb|ACP06724.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           M66-2]
 gi|229345826|gb|EEO10798.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC9]
 gi|229353112|gb|EEO18051.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|229354942|gb|EEO19863.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           BX 330286]
 gi|229369598|gb|ACQ60021.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MJ-1236]
 gi|254846755|gb|EET25169.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MO10]
 gi|255738042|gb|EET93435.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholera
           CIRS 101]
 gi|262030499|gb|EEY49137.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           INDRE 91/1]
 gi|297540833|gb|EFH76890.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MAK 757]
          Length = 245

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 100/203 (49%), Gaps = 17/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I   NKP+G+    G  +  H D      VD      ++ HRLD  TSG+++ 
Sbjct: 16  VIYEDEHIIAANKPSGLLSVPGRPVE-HYDSMWARLVDYCPDV-KVVHRLDMSTSGLILF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A+ +     L + F+ R   KIY++ VWG+   + E   N  L       D+ +  KQ  
Sbjct: 74  AKGKHMESALKKQFQYRLTHKIYYARVWGV-MEQNEGEVNLPL-----CCDWPNRPKQKV 127

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+G + +++ ++V+    +K   + + P TGR+HQLRVH   +G PIVGD  Y     
Sbjct: 128 CFEEGRD-SLTRYQVVK-REEKTTVVRLIPITGRSHQLRVHMQSLGHPIVGDDLYAPPEA 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
             F     ++L LHA  +   HP
Sbjct: 186 VEFA----DRLQLHAAELCFYHP 204


>gi|312112210|ref|YP_003990526.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
 gi|311217311|gb|ADP75915.1| pseudouridine synthase, RluA family [Geobacillus sp. Y4.1MC1]
          Length = 309

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/208 (30%), Positives = 105/208 (50%), Gaps = 24/208 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQET 154
           +L+ED  + + NK AGI +       +G   +   F   ++ ++G   K R  HRLD++T
Sbjct: 86  VLWEDEHLLIINKEAGIDIHPSEPSQTGTLANAVAF---YLQAQGILTKVRHIHRLDRDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG ++ A+   A   L      R+I++ Y +LV GI K+K   I+      + IG D  H
Sbjct: 143 SGTILFAKHPLAGATLDRMLEKRQIKRTYVALVHGIVKHKSGTIS------APIGRDRHH 196

Query: 215 VVKQN-EKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             ++   K    A++H++V+  F   +   +E+   TGRTHQ+RVH  ++G P+VGD  Y
Sbjct: 197 PTRRRVSKTGAKAVTHYRVLHTFLNDQASLVELSLDTGRTHQIRVHMSYIGHPLVGDVLY 256

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
               +  F     ++  LHA  +   HP
Sbjct: 257 GG--ENTF-----HRQALHAVKLSFLHP 277


>gi|227497602|ref|ZP_03927823.1| possible pseudouridylate synthase [Actinomyces urogenitalis DSM
           15434]
 gi|226832928|gb|EEH65311.1| possible pseudouridylate synthase [Actinomyces urogenitalis DSM
           15434]
          Length = 304

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 107/229 (46%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           L+YED  I V +KPAGI+     G     + G LK+    V + G   R  +  RLD  T
Sbjct: 80  LVYEDEDIVVVDKPAGIAAHPSMGWDGPDVLGALKAMHVQVATSGAAERQGIVSRLDVGT 139

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG ++VA+   A   L  +FR   + KIY +LV G        I   + +  H   ++  
Sbjct: 140 SGAMIVAKGERAYSVLKRAFREHEVDKIYHALVQGHLDPSSGTIDAPIGR--HPSREWKM 197

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +     G   +++H+ VI+         E+   TGRTHQ+RVH   +G P VGD  Y A
Sbjct: 198 AIID---GGRESVTHYDVIESMPAADL-AEIHLETGRTHQIRVHMSAVGHPCVGDETYGA 253

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   +  + +  + +LHA  + L HP  G  +   +P P  +V   + L
Sbjct: 254 DAALSQRTGLVRQ-WLHAHRLGLAHPITGEWMTFVSPYPDDLVHALEVL 301


>gi|153830556|ref|ZP_01983223.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 623-39]
 gi|148873954|gb|EDL72089.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 623-39]
          Length = 244

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 105/217 (48%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  ++    + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEDTN--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAVTAYRPLAKVELPISTGKFATTRYCLIEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFMHP 211


>gi|325687489|gb|EGD29510.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK72]
          Length = 295

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 113/228 (49%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++      + Q+  +  RLD++TSG+
Sbjct: 78  VVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHSYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKVIERFGDVYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P     ++  +PLP    +  + L
Sbjct: 249 --GSLEHGIERQA-LHCHSLKFYNPFSSQEVERASPLPEDFKQVIEKL 293


>gi|262273643|ref|ZP_06051456.1| ribosomal large subunit pseudouridine synthase D [Grimontia
           hollisae CIP 101886]
 gi|262222058|gb|EEY73370.1| ribosomal large subunit pseudouridine synthase D [Grimontia
           hollisae CIP 101886]
          Length = 325

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 82/330 (24%), Positives = 151/330 (45%), Gaps = 44/330 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++   RLD+     +P  +   +++ + + +V VD + V K   ++  G+V+    
Sbjct: 10  TVNENQLGQRLDQALAELFPDYSRSRIKEWILADKVSVDGEIVNKPRLKMMGGEVI---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
           V+ A   I  EQ+     + L          ++YED  I V NKP  + V  G+G     
Sbjct: 66  VVQA--EIEDEQRFEAQDIPLN---------IVYEDDDIIVINKPRDLVVHPGAGCPDGT 114

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYW 184
            ++G L  + D   + PR  + HRLD++T+G++VVA+       L  + + R+   + Y 
Sbjct: 115 VLNGLLYHYPDI-AEVPRAGIVHRLDKDTTGLMVVAKNIPTQTRLVRALQKRKKFTREYE 173

Query: 185 SLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        ++ I     K++H+           ++    AI+H++V++ F +   
Sbjct: 174 AIALGNMTGGGMIEKPIGRHSTKRTHMA---------VQELGKPAITHYRVVEHF-RAHT 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQ--NKLYLHAR 293
            L ++  TGRTHQ+RVH  ++  P+VGD  Y        N        ++  ++  LHA 
Sbjct: 224 RLRLRLETGRTHQIRVHMAYLNHPLVGDPLYGGRPRPPRNAGDKLIQTLRQFDRQALHAA 283

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            + + HP     ++  AP+P  MV   + L
Sbjct: 284 MLRIEHPTTKEVMEWHAPIPDDMVNLTEVL 313


>gi|224009936|ref|XP_002293926.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220970598|gb|EED88935.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 337

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 57/179 (31%), Positives = 91/179 (50%), Gaps = 7/179 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG--FLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED  I V NKP+G+    G      ++   F +   +S      + HRL  +TSG++
Sbjct: 94  VVYEDEHIVVINKPSGVLTVPGKDDNPSLNKVVFERFGCESNRMDKMVVHRLGMDTSGLV 153

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVV 216
           V ART +A + L   FR R++ + Y +LV G        I   L++  ++ IG D   V 
Sbjct: 154 VFARTNSALRELNSLFRTRKVTRKYEALVCGHLAKDSGDIDLSLMRDYEALIGLDSGEVG 213

Query: 217 KQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K+  +    +++ F+VI   +   +K   + +   +GRTHQL VH   +G PIVGD  Y
Sbjct: 214 KKLLESPKESMTKFEVISKEEMNGKKVTRIALTSISGRTHQLNVHCAAIGHPIVGDTVY 272


>gi|170766087|ref|ZP_02900898.1| tRNA pseudouridine synthase C [Escherichia albertii TW07627]
 gi|170125233|gb|EDS94164.1| tRNA pseudouridine synthase C [Escherichia albertii TW07627]
          Length = 260

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 116/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKCYHAIVRG-----------WLMEEAE 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N ++       +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSAAEHFGLQRLMLHASKLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDNTWMQALSQFGWR 237


>gi|15604825|ref|NP_219609.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           D/UW-3/CX]
 gi|255348466|ref|ZP_05380473.1| pseudouridine synthetase family protein [Chlamydia trachomatis 70]
 gi|255503008|ref|ZP_05381398.1| pseudouridine synthetase family protein [Chlamydia trachomatis 70s]
 gi|255506680|ref|ZP_05382319.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           D(s)2923]
 gi|3328503|gb|AAC67697.1| predicted pseudouridine synthetase family [Chlamydia trachomatis
           D/UW-3/CX]
 gi|289525149|emb|CBJ14622.1| tRNA pseudouridine synthase A [Chlamydia trachomatis Sweden2]
 gi|296434693|gb|ADH16871.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           E/150]
 gi|296435622|gb|ADH17796.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           G/9768]
 gi|296437482|gb|ADH19643.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           G/11074]
 gi|296438411|gb|ADH20564.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           E/11023]
 gi|297139981|gb|ADH96739.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           G/9301]
 gi|297748235|gb|ADI50781.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D-EC]
 gi|297749115|gb|ADI51793.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D-LC]
          Length = 303

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/259 (26%), Positives = 118/259 (45%), Gaps = 45/259 (17%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINAL 74
           +  +RL  + +   PH+    + + +R    RV+ +  +F + ++Q G  V         
Sbjct: 9   DRQIRLSSFLRTSLPHLPKKTILESVRYHGCRVNGRIERFESYKLQPGDRV--------- 59

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                       S+ + +HS      LL+ED  + ++NKPA    Q    +A+ ++    
Sbjct: 60  ------------SLQIIEHSS---PQLLWEDEHLCIYNKPAK---QTSEDLAHQLNV--- 98

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                      L HRLD++TSG ++ A+   A+  +T+ F+ R I K Y +LV+G P+ +
Sbjct: 99  ----------HLVHRLDRDTSGCILFAKHAKASSLITQLFKNREIDKRYIALVFGQPRQE 148

Query: 195 KECIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
              I  +       IG        QN       I+ ++++  +  K+  L  +P TGRTH
Sbjct: 149 SGIITTYTAPCYRRIGAVLFGNTDQN--SGKITITKWEILTRYP-KYTLLLCRPVTGRTH 205

Query: 254 QLRVHALHMGCPIVGDHKY 272
           Q+R+H   +G PIVGD  Y
Sbjct: 206 QIRLHMKTIGHPIVGDVDY 224


>gi|289578773|ref|YP_003477400.1| pseudouridine synthase [Thermoanaerobacter italicus Ab9]
 gi|289528486|gb|ADD02838.1| pseudouridine synthase, RluA family [Thermoanaerobacter italicus
           Ab9]
          Length = 285

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 121/231 (52%), Gaps = 37/231 (16%)

Query: 103 YEDSKIYVFNKPAGISV------QGGS---GIAYHI-DGFLKSWVDSKGQKPRLTHRLDQ 152
           YED +I + NKPA + V      Q G+   GIA++  D  LK+ +       R  +RLD+
Sbjct: 78  YEDEEILIVNKPANMVVHPTKGYQSGTLANGIAWYFKDKGLKALI-------RPVNRLDR 130

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V A+      +L     ++ + K+Y+++V G  K + E   N  + +    G  
Sbjct: 131 GTSGLVVFAKLPFMQYYLQ---IVKPMSKLYFAVVEG--KMEGEGRINLPISRKPQSGIE 185

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V ++ E     AI+++KV+   +++F  L+++  TGRTHQ+RVH  H+G PIVGD  Y
Sbjct: 186 RMVSEEGE----IAITNYKVVKS-SERFSLLKVKIETGRTHQIRVHLSHIGHPIVGDTLY 240

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP---AHMVKTW 319
                G+    I+ +  LHA  +   HP E   + + +PLP    H++K +
Sbjct: 241 -----GSSDDYIKRQA-LHAYRLTFVHPLEEKSISVYSPLPQDIQHLLKLF 285


>gi|153810096|ref|ZP_01962764.1| hypothetical protein RUMOBE_00477 [Ruminococcus obeum ATCC 29174]
 gi|149834274|gb|EDM89354.1| hypothetical protein RUMOBE_00477 [Ruminococcus obeum ATCC 29174]
          Length = 236

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 56/186 (30%), Positives = 93/186 (50%), Gaps = 12/186 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRL--THRLDQ 152
           ++ ++++ED  I V +K AGI+VQ     A  ++  LK+++  K  +  P L   HRLDQ
Sbjct: 8   IEDMIIFEDKDILVCHKAAGIAVQNARIGAADMESSLKNYLALKNTETVPYLGVVHRLDQ 67

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              G+LV A+ + AA  LT       I K Y ++   + +  +  + ++L+K      + 
Sbjct: 68  PVEGVLVFAKNKKAAAGLTRQITTGNIVKEYLAVTDRMSEKHQGRLEDYLIKNGRT--NT 125

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ------KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             VV     GA  A+  ++VI   +       K   +++   TGR HQ+RV   H G P+
Sbjct: 126 SEVVTSKTSGAKKAVLDYEVIHQISDERTESGKRILIKIHLETGRHHQIRVQMAHAGMPL 185

Query: 267 VGDHKY 272
           +GD KY
Sbjct: 186 LGDRKY 191


>gi|319902371|ref|YP_004162099.1| pseudouridine synthase, RluA family [Bacteroides helcogenes P
           36-108]
 gi|319417402|gb|ADV44513.1| pseudouridine synthase, RluA family [Bacteroides helcogenes P
           36-108]
          Length = 309

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 111/226 (49%), Gaps = 21/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R+   HRLD++T
Sbjct: 88  IVYEDAYIIVIEKMQGLLSVNTERQKERTAYTI---LNEYVQRSGRQHRVYTVHRLDRDT 144

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L +++      + Y ++V G  +     +++WL  ++     YV+
Sbjct: 145 SGLMMFAKDEKTQNTLRDNWHDIVFDRRYVAVVSGEMEKNAGVVSSWLTDRTL----YVY 200

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               N+ G   AI+H++ I   A  +  +E+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 201 SSPTND-GGKEAITHYRTIKR-ANGYSLMELNLETGRKNQIRVHMQDLGHPIIGDGRYGL 258

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
                  +PI  +L LHA  +   HP  G ++    P PA   K +
Sbjct: 259 ----EDINPI-GRLALHAFKLCFYHPVTGEKMSFETPYPADFKKLF 299


>gi|224534166|ref|ZP_03674746.1| RNA pseudouridine synthase family protein [Borrelia spielmanii
           A14S]
 gi|224514591|gb|EEF84905.1| RNA pseudouridine synthase family protein [Borrelia spielmanii
           A14S]
          Length = 315

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 79/306 (25%), Positives = 142/306 (46%), Gaps = 46/306 (15%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-----LRSGQVRVDKKRVKF 55
           M L  Y+   ++ ND    RLD         I  +NL K      +R G +R++  +  F
Sbjct: 1   MRLDKYIFLEILANDN-GKRLDSIL------IKILNLSKARIIKHIRKGDIRLNGIKPHF 53

Query: 56  NNRIQSGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
           + R+  G  + +   +   LN  I E     S ++      +++  ++YEDS + V NK 
Sbjct: 54  SYRVCKGDKIYLYKSLAQGLNLTINE--CYKSDLDFQ----YIRERIIYEDSDLLVLNKQ 107

Query: 115 AGISVQGG-SGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
            GI V G  + + + ++ +L +  + S   KP   HRLD+ TSGI+V A+    A+ L+ 
Sbjct: 108 RGILVHGDRNSLDFLVNAYLSREDLRSLSFKPSAVHRLDRNTSGIIVFAKNIDTARKLSI 167

Query: 173 SFRMRRIQKIYWSLVWGIPKN----KKECIANWLLKKSHI--GGDYVHVVKQNEKGANYA 226
            F    + K Y+++++G  K+    +     N  L+K+ +  G D+++ + +     N  
Sbjct: 168 LFSRGFVTKKYFAILFGEVKSTVVYENHLFRNKRLRKTFVLEGKDFINAITK----VNPI 223

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           +S        +++   +E+   TG THQ+R        P++ D KYC  FK       ++
Sbjct: 224 LS--------SKRATLVEIIIKTGFTHQIRAQCSFNNHPLINDKKYCDKFK-------KS 268

Query: 287 KLYLHA 292
             +LHA
Sbjct: 269 NYFLHA 274


>gi|237721623|ref|ZP_04552104.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_2_4]
 gi|229449419|gb|EEO55210.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_2_4]
          Length = 613

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 77/262 (29%), Positives = 115/262 (43%), Gaps = 76/262 (29%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ED  + V NKPAG +SV G +      YH     K + ++ G  P + HRLD  TSG
Sbjct: 347 IVFEDEWLLVVNKPAGMLSVPGKAEDRDSVYH--RLKKKYPEATG--PMIVHRLDMATSG 402

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNK-------------KECIANW 201
           +L+VA+T+   Q L   F  R I+K Y +++ G  I   K             KE ++  
Sbjct: 403 LLLVAKTKEVHQDLQAQFANRSIKKRYVAVLDGAIIKTEKETKPITEKAILIAKETVSTK 462

Query: 202 LLKKSHIGG--------------DYVHVVKQNEKGANYAISHFKVI-----------DCF 236
              K+   G              D    +  +E G   AI+ +++I           + F
Sbjct: 463 KTAKAERTGNTGRIELPLCLNPLDRPRQMVSSEHGKE-AITEYQIISESERITSESENTF 521

Query: 237 ---------------AQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKG 278
                          ++K+  +   P TGRTHQLRVHA H   +GCPI+GD  Y      
Sbjct: 522 NESNRIDESEKSINESRKYTRIIFYPLTGRTHQLRVHAAHPEGLGCPILGDELYGKK--- 578

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                  ++LYLHA Y++  HP
Sbjct: 579 ------ADRLYLHAEYIEFRHP 594


>gi|302335822|ref|YP_003801029.1| pseudouridine synthase, RluA family [Olsenella uli DSM 7084]
 gi|301319662|gb|ADK68149.1| pseudouridine synthase, RluA family [Olsenella uli DSM 7084]
          Length = 342

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/254 (25%), Positives = 115/254 (45%), Gaps = 26/254 (10%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-----------KGQKPRLTHRLD 151
           +ED  + V +K AG+      G   H+D  L + + +              +P + HRLD
Sbjct: 90  FEDEHLLVLSKQAGLVCHPSPG---HVDDTLANALVAHCGYGHLGMLQGDDRPGIVHRLD 146

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG++V A++    + L +  R+R + + Y  LV G        +   + + +    D
Sbjct: 147 MDTSGLMVAAKSDEVQRALQDLIRLRALDRRYVVLVQGYVAPDAGTVTTGIARSTR---D 203

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + +   ++  A  AI+ F  ++ F      + +  LE   +TGRTHQ+RVH  H+G  +
Sbjct: 204 RLRMAVSDDPMAREAITTFATLERFEASRSDEGYSLLECHLYTGRTHQIRVHMRHIGHQV 263

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL-GF 324
           VGD  Y     G+  +    + +LH+ ++   HP  G  ++    LP  ++   +SL G 
Sbjct: 264 VGDQLY--GRGGDRQNRGLRRQFLHSWHIRFDHPVTGATIERADALPDDLLGILESLKGS 321

Query: 325 KYDRNLYIKRLYSQ 338
              R    +R+  Q
Sbjct: 322 SMGRTEAGERICPQ 335


>gi|315304428|ref|ZP_07874717.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria ivanovii FSL F6-596]
 gi|313627200|gb|EFR96044.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria ivanovii FSL F6-596]
          Length = 289

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/217 (29%), Positives = 101/217 (46%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP G+        +Y  D     ++ +++   Q       HRLDQ TS
Sbjct: 80  VIYEDDFLLVVNKPVGMKTHPND--SYETDTCANAVQYYLEQTNQDANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H  V++   +K    +E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHITVLENDTEKNTSIVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                  SP  N++ LHA  + L HP +G  +  +AP
Sbjct: 253 -------SPRANRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|269963388|ref|ZP_06177716.1| Ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           1DA3]
 gi|269831867|gb|EEZ85998.1| Ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           1DA3]
          Length = 250

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/213 (31%), Positives = 99/213 (46%), Gaps = 30/213 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           +++ED +I   NKP+G+ SV G   +A H D     W     Q P  ++ HRLD  TSG+
Sbjct: 16  VVFEDEQILAVNKPSGLLSVPGR--LAEHHDSM---WSRLTEQYPDIQVVHRLDMCTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW----LLKKSHI 208
           +V+A+ + A   L + F+ R   KIY++ VWG  K ++       I +W    L K    
Sbjct: 71  MVLAKNKRAESALKKQFQYRLTHKIYYARVWGHLKQEEGEIDLPLICDWPNRPLQKVCFE 130

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            G     + Q  K   +       I         + + P TGR+HQLRVH   +G PIVG
Sbjct: 131 DGKPSKTLFQVAKREEHPDGSKTTI---------VRLLPITGRSHQLRVHMQALGHPIVG 181

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           D  Y       F+     +L LHA  +   HP+
Sbjct: 182 DEFYATEEAKAFS----ERLELHAAELSFYHPK 210


>gi|260364018|ref|ZP_05776749.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus K5030]
 gi|308115630|gb|EFO53170.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus K5030]
          Length = 325

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 113/238 (47%), Gaps = 27/238 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           ++YED  I V NKP    V  G+G      ++  L  + D   + PR  + HRLD++T+G
Sbjct: 86  IVYEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDI-AEVPRAGIVHRLDKDTTG 144

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYV 213
           ++VVA+T  A   L  + + R I + Y ++  G         + I     K++ +    +
Sbjct: 145 LMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDQPIGRHSTKRTLMAVAPL 204

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                       A++H++V + F ++   + ++  TGRTHQ+RVH  ++  P++GD  Y 
Sbjct: 205 ---------GKPAVTHYRVAEHF-REHTRIRLRLETGRTHQIRVHMSYLQHPLLGDTAYG 254

Query: 274 ANFK------GNFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
              +         T  I+  ++  LHA  +   HP  G  L+  AP+P  MV   ++L
Sbjct: 255 GRARIPTGASQELTDMIRGFDRQALHAVMLRFEHPITGEELEFHAPVPDDMVAMTEAL 312


>gi|225869691|ref|YP_002745638.1| RNA pseudouridylate synthase [Streptococcus equi subsp. equi 4047]
 gi|225699095|emb|CAW92255.1| RNA pseudouridylate synthase [Streptococcus equi subsp. equi 4047]
          Length = 301

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 94/210 (44%), Gaps = 17/210 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+   G       +   + ++    G+   + HRLD ETSG ++ A
Sbjct: 96  LYQDEHLIIVNKPEGMKTHGNEPTELALLNHVSAYT---GKTCYVVHRLDMETSGAILFA 152

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      R I++ YW+L+ G  + +     + + +  H     V     + K
Sbjct: 153 KNPFILPILNRLLEHRDIKRDYWALIEGQLEQQTVTYRDPIGRHRHDRRKRV----VDSK 208

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+H  ++  F Q  C +  +  TGRTHQ+RVH  H   P++GD  Y         
Sbjct: 209 HGQEAITHLALLQAFDQT-CLVNCRLETGRTHQIRVHLAHHKHPLIGDPLYSRQKA---- 263

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL-QITAP 310
                +L LHA  + L HP    + ++TAP
Sbjct: 264 ----ERLMLHAHQLTLRHPLAQEMIRVTAP 289


>gi|253577780|ref|ZP_04855052.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850098|gb|EES78056.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 341

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 82/341 (24%), Positives = 136/341 (39%), Gaps = 46/341 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++E +E   R D++              K+LR   + ++ K+   N ++  G  +++   
Sbjct: 5   IIEENEAGQRFDKYLAKLLREAPKSFFYKMLRKKNITLNGKKATGNEKLLKGDTIKLFLS 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ----GGSGIA 126
               +      +   +   L          ++YED  I + NKPAG+  Q    G   + 
Sbjct: 65  DETFDKFAGSSQAARAYCELD---------IVYEDPDIIIINKPAGMLSQPAYDGEPSLV 115

Query: 127 YHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            ++ G+L    D   +     +P + +RLD+ TSG++   ++ A  Q L+  F  R + K
Sbjct: 116 EYLTGYLLKKGDLTEEQLKTFRPSVCNRLDRNTSGMVCAGKSLAGLQFLSRIFHDRTLHK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y  L  G            + K  HI G Y+H  K+  K    +   FK       K+C
Sbjct: 176 YYICLTKG-----------KIEKPDHIRG-YLHKDKKTNK-VIVSRQEFKDSLPIETKYC 222

Query: 242 ---------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLH 291
                     LE++  TGRTHQ+R H    G P++GD KY  + F   +         LH
Sbjct: 223 PLGSNGKITLLEVELITGRTHQIRAHLAGTGHPLLGDTKYGDSEFNKQYIRHGVRHQLLH 282

Query: 292 ARYMDLPHPEGGRLQITAPLPAHMVK--TWDSLGFKYDRNL 330
           A  + +P  +       AP P    K    ++L   Y  NL
Sbjct: 283 AYRLVIPETDQ---TFVAPAPELFCKIIKEENLEEAYHENL 320


>gi|255070545|ref|XP_002507354.1| predicted protein [Micromonas sp. RCC299]
 gi|226522629|gb|ACO68612.1| predicted protein [Micromonas sp. RCC299]
          Length = 357

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 86/308 (27%), Positives = 127/308 (41%), Gaps = 66/308 (21%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           ++   +R+  G++V  PP       +  E   LD               +++ED  + V 
Sbjct: 76  KLDIGDRVICGEIVASPP-----TEVAPENIPLD---------------VVFEDDHLVVV 115

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWV-------DSKGQK-------PRL--THRLDQETS 155
           NKP G+ V   +G   H  G L + +        ++G         PRL   HR+D+ TS
Sbjct: 116 NKPPGMVVHPSAG---HAGGSLVNALLFHCNERSNRGDDASKMIDVPRLGVVHRIDKGTS 172

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LV+A+  AA   L   F  R +++ Y ++V G P  +   I       + IG D    
Sbjct: 173 GLLVMAKDAAAQAGLQTQFANRSVRRRYLAIVLGTPARESGRI------DAPIGRDPADR 226

Query: 216 VKQN-EKGAN--YAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +K    +GA    AIS+F V     +    L E Q  TGRTHQ+RVHA  MG PIVGD  
Sbjct: 227 LKMAIVRGATGRQAISNFGVRARLVRGNASLVEWQLETGRTHQIRVHAREMGHPIVGDEA 286

Query: 272 YCANF---------KGNFTSPIQNKL-------YLHARYMDLPHP-EGGRLQITAPLPAH 314
           Y              G  ++    ++        LHAR +   HP  G  +      P  
Sbjct: 287 YGGGGSAAAEFLRRDGAMSAAAAREIVAKCARPMLHARSLGFRHPVTGEEISFAVEPPPD 346

Query: 315 MVKTWDSL 322
            V  +  L
Sbjct: 347 FVDAFTEL 354


>gi|57505358|ref|ZP_00371287.1| ribosomal large subunit pseudouridine synthase C [Campylobacter
           upsaliensis RM3195]
 gi|57016494|gb|EAL53279.1| ribosomal large subunit pseudouridine synthase C [Campylobacter
           upsaliensis RM3195]
          Length = 308

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/202 (31%), Positives = 101/202 (50%), Gaps = 11/202 (5%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DG 131
           N + K+ +IL   V L  + +  K + ++YE+ +  V  KP+G+ S   G   AY + D 
Sbjct: 47  NLVKKKNEILQGVVELIVYENAPKGVKIVYENEEFAVLEKPSGVLSHPNGRHCAYSLCDE 106

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             + W    G +  + HRLD+ETSG+++ A+T+ +       F  R IQK Y +L  G+ 
Sbjct: 107 IWELW----GMEACVVHRLDKETSGLILAAKTKNSQVEFKTMFEKREIQKEYLALTQGLI 162

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM-QPHTG 250
           K + E      L +++   D V    Q  +    A+S FK +  +      L + +P TG
Sbjct: 163 KEEFEVDLPMRLTQNY---DDVKTRMQICEDGKRALSFFKRVRFYPDLNVSLVLCKPFTG 219

Query: 251 RTHQLRVHALHMGCPIVGDHKY 272
           R HQLR+H  H G  I+G+  Y
Sbjct: 220 RQHQLRLHLFHSGHQILGEPLY 241


>gi|218249746|ref|YP_002375313.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           ZS7]
 gi|218164934|gb|ACK74995.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           ZS7]
          Length = 315

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 141/310 (45%), Gaps = 54/310 (17%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINF--VNLQKILRSGQVRVDKKRVKFNNR 58
           M L  Y+   V+ ND    RLD         +NF   ++ K +R G +R++  +  F+ R
Sbjct: 1   MRLDKYIFLEVLANDN-GKRLDSIL---IKILNFSKASIIKHIRKGDIRLNGLKSHFSCR 56

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI--------LLYEDSKIYV 110
           +  G  + +              K L  ++NLT    F  +I        ++YEDS + V
Sbjct: 57  VCKGDKIYL-------------YKSLSQNLNLTMDECFKSNIDFQYIRKRIIYEDSDLLV 103

Query: 111 FNKPAGISVQGG-SGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            +K  GI V GG + + + ++ +L S  + S   KP   HRLD+ TSGI++ A+    A+
Sbjct: 104 LDKQKGILVHGGKNSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTAR 163

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKN----KKECIANWLLKKSHIGGD--YVHVVKQNEKG 222
            L+ +F    I K Y++++ G  K+    K     N  L+K+ +  D  +V+ + +    
Sbjct: 164 KLSAAFSGGSIIKKYFAILLGEVKSPVVYKNHLFRNKRLRKTFVLEDKNFVNAITKVN-- 221

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
                    ++ C  ++   +E+   TG THQ+R        P++ D KYC  FK     
Sbjct: 222 --------PILSC--KRATLVEIVIETGFTHQIRSQCSFNNHPLINDKKYCNKFK----- 266

Query: 283 PIQNKLYLHA 292
             ++  +LHA
Sbjct: 267 --KSDYFLHA 274


>gi|317124659|ref|YP_004098771.1| ribosomal large subunit pseudouridine synthase D [Intrasporangium
           calvum DSM 43043]
 gi|315588747|gb|ADU48044.1| ribosomal large subunit pseudouridine synthase D [Intrasporangium
           calvum DSM 43043]
          Length = 310

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/214 (29%), Positives = 105/214 (49%), Gaps = 23/214 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           ++++D  I V +KP G++     G     + G L +    + + G   R  +  RLD  T
Sbjct: 86  IIHDDEDIVVVDKPVGVAAHPSVGWSGPDVVGGLAAAGYRISTSGAPERQGIVSRLDVGT 145

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA++  A   L ++FR R + K Y +LV G+P      +   + +  H G D+  
Sbjct: 146 SGLMVVAKSEYAYSRLKQAFRTRAVDKNYHALVQGLPDPLVGTVDAPIGR--HPGHDFKF 203

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V +N K    +++H++VI+ F +    L++   TGRTHQ+RVH   +  P  GD  Y A
Sbjct: 204 AVMRNGK---PSVTHYEVIEAF-RHASLLDIHLETGRTHQIRVHMAAIKHPCCGDPLYGA 259

Query: 275 NFKGNFTSPIQNKL-----YLHARYMDLPHPEGG 303
           +        +  KL     +LHA  +   HP  G
Sbjct: 260 D------PTLARKLGLDRQWLHAVGLGFEHPGTG 287


>gi|222153007|ref|YP_002562184.1| RNA pseudouridylate synthase [Streptococcus uberis 0140J]
 gi|222113820|emb|CAR41903.1| putative RNA pseudouridylate synthase [Streptococcus uberis 0140J]
          Length = 301

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 93/178 (52%), Gaps = 13/178 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGI 157
           ++YED    V NKP G +    +  +  I  F+K++   +    +  H   RLD++TSG+
Sbjct: 78  IVYEDDHFLVLNKPVGYASIPSAIHSNTIANFIKAYYFEQNYPNKQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVH 214
           ++ A+   A   L +  + R I+K Y++LV G   +P +  E +      K  I      
Sbjct: 138 MLFAKHGYAHARLDKQLQKRSIEKRYFALVSGNGQLP-DFGEIVEPIGRSKDSI------ 190

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + +  +    YA + ++V+  FA+    ++++ HTGRTHQ+RVH  H+G P++GD  Y
Sbjct: 191 ITRTVDPMGKYAKTTYEVVARFAENVHLVDIKLHTGRTHQIRVHFSHIGFPLLGDDLY 248


>gi|254457748|ref|ZP_05071176.1| pseudouridine synthase D [Campylobacterales bacterium GD 1]
 gi|207086540|gb|EDZ63824.1| pseudouridine synthase D [Campylobacterales bacterium GD 1]
          Length = 308

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 56/178 (31%), Positives = 93/178 (52%), Gaps = 9/178 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           L++  +Y++    VF+KP+G+ +        Y +   LK      G+   + HR+DQETS
Sbjct: 70  LEATAVYDE--FVVFDKPSGVLIHPQNRKTPYSLIDELKYQY---GRDANIAHRIDQETS 124

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + + + +   F  R ++K Y +LV G  K    CI   LL++         V
Sbjct: 125 GLVLCAKNKESERDIKMMFEQRDMKKKYLALVHGELKESI-CIEEPLLRREDESAIVRMV 183

Query: 216 VKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           VK +E+G   + +  + +  FA+     +E  P+TGR HQ+RVH  H+  PIVGD  Y
Sbjct: 184 VKVHEEG-KASKTDIRPLKYFAETDMTLVECSPYTGRQHQIRVHLFHVKHPIVGDPIY 240


>gi|167768426|ref|ZP_02440479.1| hypothetical protein CLOSS21_02985 [Clostridium sp. SS2/1]
 gi|317499212|ref|ZP_07957487.1| RNA pseudouridylate synthase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167709950|gb|EDS20529.1| hypothetical protein CLOSS21_02985 [Clostridium sp. SS2/1]
 gi|316893526|gb|EFV15733.1| RNA pseudouridylate synthase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 236

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/222 (28%), Positives = 102/222 (45%), Gaps = 14/222 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDG--FLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+D +I V  KP GI V     G   + + +    F +   D + Q   L HRLD+  
Sbjct: 9   IIYKDDQIVVCEKPKGIPVSSDKTGDMDLLHQLKNQLFFEENTDGEPQL-YLVHRLDRPV 67

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G++V ART+ AA  LTE  +    +K Y +++ G   + +    ++LLK      +   
Sbjct: 68  GGVMVFARTKKAAASLTEQIKDHTFEKDYQAVLTGWLPDDEGTFRDYLLKDPK--NNVSK 125

Query: 215 VVKQNEKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +VK+   GA  AI  ++VID       K+ +  +   TGR HQ+RV     G  I GD K
Sbjct: 126 IVKEGTPGAKEAILDYEVIDMMEDSKMKYTYCLIHLETGRHHQIRVQTSSRGFGIWGDTK 185

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           Y   ++   T     ++ L A  +   HP  G   +    P+
Sbjct: 186 YNPIYQK--TKKKYKEIGLFAARIAFEHPTTGERMVFKADPS 225


>gi|319954748|ref|YP_004166015.1| pseudouridine synthase [Cellulophaga algicola DSM 14237]
 gi|319423408|gb|ADV50517.1| pseudouridine synthase [Cellulophaga algicola DSM 14237]
          Length = 222

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 55/175 (31%), Positives = 89/175 (50%), Gaps = 7/175 (4%)

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVA 161
           E++   V NK AG   +        I+  L   +  K +KP +   HRLD+ TSG+L+ A
Sbjct: 9   ENNDYIVVNKTAGYISEKNPYEDNTIEDQLFKHLLQKKRKPYIGVIHRLDRVTSGVLIFA 68

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           + ++      E F  R++QK Y ++V   P N K  + N+L+K +        +++   K
Sbjct: 69  KKKSVLVAFNELFSSRQVQKTYLAIVKNKPANTKGDLVNFLVKNNK--DKRADIIQTKSK 126

Query: 222 GANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +      ++VI      F + LE+QP TGR HQ+R    H+G PI+GD KY ++
Sbjct: 127 ESLDCSLSYEVIA--KNNFGYLLEVQPKTGRFHQIRAQLAHIGLPIIGDEKYGSD 179


>gi|121728338|ref|ZP_01681368.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V52]
 gi|121629393|gb|EAX61823.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V52]
          Length = 244

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 104/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEAN--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAVTAYRPLAKVELPIATGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDRVHNRLFREHFSA---QRLMLHASELRFMHP 211


>gi|302840471|ref|XP_002951791.1| hypothetical protein VOLCADRAFT_92295 [Volvox carteri f.
           nagariensis]
 gi|300263039|gb|EFJ47242.1| hypothetical protein VOLCADRAFT_92295 [Volvox carteri f.
           nagariensis]
          Length = 553

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/205 (31%), Positives = 91/205 (44%), Gaps = 40/205 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLK-----SWVDSKGQKPRLTHRLDQET 154
           + YED  + V  KP GI+ QG GSG    + G LK     S +     +P+  HRLD  T
Sbjct: 161 VAYEDDHLAVVIKPPGIATQGSGSGT---VQGRLKYCLRASPLVGALNRPQQVHRLDAPT 217

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---------IPKNKKECIANWLLKK 205
            G+L+VA+T AA + L      RR+ K Y +LV G         +P + K C+ ++ +  
Sbjct: 218 GGLLLVAKTHAAQRRLAGDLHHRRMAKRYCTLVKGERYGSGTIDMPLSGKPCLTSFRVVS 277

Query: 206 SHIGGDYVHVVKQ-------------NEKG-----ANYAISHFKVIDCFAQKFCWLEMQP 247
                    VV                EK         A +  + +D   +   W    P
Sbjct: 278 KRGLSHTTEVVASAAIGARMAAAWTGGEKAVRCGPGPAAAAGRRHLDVLTKILLW----P 333

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
           HTGRTHQLR H  + G PI+GD +Y
Sbjct: 334 HTGRTHQLRKHMAYTGTPILGDPRY 358


>gi|291530201|emb|CBK95786.1| pseudouridine synthase, RluA family [Eubacterium siraeum 70/3]
          Length = 322

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 25/281 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V  ++   R+DR+    +P +    + K+ R   ++++ K+ K +  I    +++
Sbjct: 1   MKEIKVTKNDSGQRIDRFLSKSFP-LGQGQICKLARKNCIKLNGKKCKPDTHIAENDIIK 59

Query: 67  --IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGS 123
             IP  +     +I + K      + T  SD  K  ++YED  I + +KP G+ V +  S
Sbjct: 60  LFIPDEM-----LIPKAK--SDPDDFTAVSD--KIDIVYEDENILLVDKPVGMVVHEDES 110

Query: 124 GIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G +  +   +KS++  KG+          P L +R+D+ T GI++ A+   + + L +  
Sbjct: 111 GDSDTLINRIKSYLYRKGEYHPENELSFAPALCNRIDRNTCGIVIAAKNAESLRILNQKI 170

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R + K+Y  +  G        +  +L K S    + V +  +  K      + +KVI 
Sbjct: 171 RDRELTKLYLCIACGKVTPDSATLTAYLEKNSDT--NTVKISDKKTKSNLTIKTKYKVI- 227

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +  +   L++   TGRTHQ+R H  ++G  ++GD KY  N
Sbjct: 228 AYNGENSLLKVDLLTGRTHQIRAHLAYIGHALLGDGKYGNN 268


>gi|260774106|ref|ZP_05883021.1| pseudouridylate synthase LSU rRNA-specific [Vibrio metschnikovii
           CIP 69.14]
 gi|260611067|gb|EEX36271.1| pseudouridylate synthase LSU rRNA-specific [Vibrio metschnikovii
           CIP 69.14]
          Length = 557

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 74/241 (30%), Positives = 104/241 (43%), Gaps = 41/241 (17%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H++K   + D+ + L   ++  +  ++Y+D  I V NKPA      G  I   +   L
Sbjct: 330 LAHMLKGMPLEDNPL-LVNPAEGKQIEIVYQDEAIVVINKPAEFLSVPGVNIKDSVFTRL 388

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                  G+ P + HRLD  TSG+LV A TR A + L + F  R+I K Y +L+ G    
Sbjct: 389 AEQFPD-GEGPFVLHRLDMSTSGLLVFALTRRANKSLQKQFITRQIDKQYVALLAG---- 443

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQN-----------EKGANYAISHFKVIDCFAQKFCW 242
                     +  H GGD    +  +           E G +      KV     Q    
Sbjct: 444 ----------ELEHDGGDITLPLAADRDDRPRQKVCLETGKSAQTRWEKV--AIEQGQTR 491

Query: 243 LEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           + + PHTGRTHQLRVH  H   +G PIVGD  Y              +L LHA+ +   H
Sbjct: 492 VNLYPHTGRTHQLRVHCAHPDGLGFPIVGDDLY---------GQAAERLCLHAQKLSFYH 542

Query: 300 P 300
           P
Sbjct: 543 P 543


>gi|254721425|ref|ZP_05183214.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. A1055]
          Length = 168

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 54/167 (32%), Positives = 86/167 (51%), Gaps = 14/167 (8%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKS 206
           HR+D++TSG+L+VA+   A + L      + + + Y ++V G IP +K    A     K 
Sbjct: 2   HRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIARDKK 61

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                 V      ++   +A++HF+V++ F + F  +E +  TGRTHQ+RVH  ++G P+
Sbjct: 62  ERQSMTV------DENGKHAVTHFQVLERF-KDFTLVECRLETGRTHQIRVHMKYIGYPL 114

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            GD KY     G   +   N   LHA  +   HP  G  +Q  AP+P
Sbjct: 115 AGDPKY-----GPKKTLDMNGQALHAGILGFDHPRTGEYIQFEAPIP 156


>gi|296111299|ref|YP_003621681.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
 gi|295832831|gb|ADG40712.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
          Length = 306

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/223 (30%), Positives = 104/223 (46%), Gaps = 25/223 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQ 152
           +++E+  + V NKPAG+ +      +  + + Y    FL   V S G   KP + HR+D+
Sbjct: 88  IVFENDDLVVVNKPAGMKMHPHSETEDDTLLNYVAANFLARSVLSAGVPAKPYMVHRIDR 147

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           ETSG +++A+       L      + IQ+ Y + V G    K   I       + IG D 
Sbjct: 148 ETSGAVIIAKNPVVVPILNRLLFEKNIQRTYLAWVDGNMSAKAGVI------DAPIGIDP 201

Query: 213 VHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  K+   G  A  A +H+  +    Q    L +Q  TGR HQ+RVH   MG PIVGD 
Sbjct: 202 QNNRKRLVDGIDAQSAKTHWTRVHVVYQH-TLLRLQLDTGRMHQIRVHLASMGHPIVGDS 260

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            Y +         I  ++ LHA  + +P P +   + I+ P+P
Sbjct: 261 LYASKV-------ITTRMLLHAVSVVIPLPFKNKTVVISCPVP 296


>gi|216263435|ref|ZP_03435430.1| RNA pseudouridine synthase family protein [Borrelia afzelii ACA-1]
 gi|215980279|gb|EEC21100.1| RNA pseudouridine synthase family protein [Borrelia afzelii ACA-1]
          Length = 315

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 84/313 (26%), Positives = 141/313 (45%), Gaps = 60/313 (19%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-----LRSGQVRVDKKRVKF 55
           M L  YV   ++ ND    RLD         I  +NL K      +R G +R++  +  F
Sbjct: 1   MRLDKYVFLEILANDN-GKRLDSIL------IKILNLSKARIIKHIRKGDIRLNGIKSHF 53

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS------DF--LKSILLYEDSK 107
           + R+  G  + +              K L   +NLT +       DF  ++  ++YEDS 
Sbjct: 54  SYRVCKGDKIYL-------------YKSLAQGLNLTMNECYKSNIDFQCIRERIIYEDSD 100

Query: 108 IYVFNKPAGISVQGG-SGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
           + V +K  GI V GG + + + ++ +L K  + S   KP   HRLD+ TSGI+V A+   
Sbjct: 101 LLVLDKQRGILVHGGRNSLDFLVNAYLLKEELRSLSFKPAAVHRLDRNTSGIIVFAKNIN 160

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKN----KKECIANWLLKKSHI--GGDYVHVVKQN 219
            A+ L+ +F    I K Y++++ G  K+    K     N  LKK+ +  G D+++ + + 
Sbjct: 161 TARKLSTAFSSGSITKKYFAILLGEVKSTVVYKNHLFRNKRLKKTFVLDGKDFINAITK- 219

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N  +S        +++    E+   TG THQ+R        P++ D KY   F+  
Sbjct: 220 ---VNPILS--------SKRATLAEIVIETGFTHQIRAQCSFNNHPLINDKKYHDKFE-- 266

Query: 280 FTSPIQNKLYLHA 292
                ++  +LHA
Sbjct: 267 -----KSNYFLHA 274


>gi|237756115|ref|ZP_04584689.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium yellowstonense SS-5]
 gi|237691719|gb|EEP60753.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium yellowstonense SS-5]
          Length = 318

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 82/295 (27%), Positives = 134/295 (45%), Gaps = 36/295 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPV 70
           VE +  N RLD++    YP  +    Q ++ +G V +D   VK  + ++++GQ   I   
Sbjct: 9   VEEEFSNKRLDQFLALVYPEYSRSFYQNLIENGFVLLDNSPVKKPSTKVKTGQEFTIIIP 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 I  E   L+               + YED  + V  KP G+ V    G   H  
Sbjct: 69  PPEPLEIEPENIPLE---------------ICYEDEDLAVVYKPPGMVVHPSVG---HTS 110

Query: 131 GFL--------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G L        K+    +G ++  + HRLD++T+G+L+VA+T  A + L + F+ R I K
Sbjct: 111 GTLVNALLYHFKNVSQYQGKERAGIVHRLDKDTAGLLIVAKTEFAHKELQKMFQDREIDK 170

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KF 240
            Y ++V GI K K   + +  + +S      +  V  N K    A++ + V   F +   
Sbjct: 171 KYKAIVSGIVK-KDHGLIDLPIGRSIYNRQKMGTVSTNLKD---ALTEYWVEKRFEKHNL 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHA 292
             ++++ HTGRTHQ+RVH   +G P+  D  Y    +N        + +KL  HA
Sbjct: 227 TLVDIKLHTGRTHQIRVHFSAIGHPLFNDFVYGFKKSNLSSELAKNLSDKLNYHA 281


>gi|295839444|ref|ZP_06826377.1| RluA family RNA pseudouridine synthase [Streptomyces sp. SPB74]
 gi|197698743|gb|EDY45676.1| RluA family RNA pseudouridine synthase [Streptomyces sp. SPB74]
          Length = 313

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 80/315 (25%), Positives = 134/315 (42%), Gaps = 39/315 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  V+ + V +  E  R+D      +   +     ++   G+V+VD   V  + R++
Sbjct: 1   MSAIPEVRTLPVPDGLEGERVDAALSRMF-GFSRTKAAELAAGGKVQVDGSVVGKSERVR 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  + V  KP G++ 
Sbjct: 60  GGAWLEVEMPAAAAPVRIVAEP--------------VEGMEIVHDDEDVVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +    + + G   R  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGPTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKNQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR+R + K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I
Sbjct: 166 FRVRTVDKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAEGK---PSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----- 288
           + F +    L+++  TGRTHQ+RVH      P  GD  Y A+        +  +L     
Sbjct: 221 EAF-RAASLLDVKLETGRTHQIRVHMAAHRHPCAGDLTYGAD------PTLAKRLGLTRQ 273

Query: 289 YLHARYMDLPHPEGG 303
           +LHA  +   HP  G
Sbjct: 274 WLHAVRLGFTHPGTG 288


>gi|330830420|ref|YP_004393372.1| Pseudouridine synthase [Aeromonas veronii B565]
 gi|328805556|gb|AEB50755.1| Pseudouridine synthase [Aeromonas veronii B565]
          Length = 231

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/213 (31%), Positives = 98/213 (46%), Gaps = 23/213 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILVV 160
           L+ED  + + NKP+G+    G     ++D      V D  G    L HRLD  TSGI+VV
Sbjct: 20  LFEDEHLLLINKPSGLLSLSGKN-PQNLDSVHYRLVQDYPGCT--LVHRLDFGTSGIMVV 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +A    L + F  R + K Y +L+ G   + +  I   + K   +      ++K   
Sbjct: 77  ARNKAINALLCQQFSQRAVSKAYSALLCGHLIDDEGVIDAPIAKDPAL----FPLMKICA 132

Query: 221 KGANYAISHFKVIDCFAQK-------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                A S ++VI+  AQ+          + + P TGRTHQLR+H+  +G PI+G   Y 
Sbjct: 133 ASGKPARSRYRVIERLAQQIQGQTVPLTRVRLVPETGRTHQLRLHSQLLGYPILGCDLY- 191

Query: 274 ANFKGNFTSP---IQNKLYLHARYMDLPHPEGG 303
               G    P      +L LHA  +D  HP  G
Sbjct: 192 ----GGLLPPGCEQAPRLMLHASKLDFTHPVSG 220


>gi|195977301|ref|YP_002122545.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
 gi|195974006|gb|ACG61532.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
          Length = 297

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 94/210 (44%), Gaps = 17/210 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+   G       +   + ++    G+   + HRLD ETSG ++ A
Sbjct: 92  LYQDEHLIIVNKPEGMKTHGNEPTELALLNHVSAYT---GKTCYVVHRLDMETSGAILFA 148

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      R I++ YW+L+ G  + +     + + +  H     V     + K
Sbjct: 149 KNPFILPILNRLLERRDIKRDYWALIEGQLEQQTVTYRDPIGRHRHDRRKRV----VDSK 204

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+H  ++  F Q  C +  +  TGRTHQ+RVH  H   P++GD  Y         
Sbjct: 205 HGQEAITHLALLQAFDQT-CLVNCRLETGRTHQIRVHLAHHKHPLIGDPLYSRQKA---- 259

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL-QITAP 310
                +L LHA  + L HP    + ++TAP
Sbjct: 260 ----ERLMLHAHQLTLRHPLTQEMIRVTAP 285


>gi|91792050|ref|YP_561701.1| pseudouridine synthase [Shewanella denitrificans OS217]
 gi|91714052|gb|ABE53978.1| pseudouridine synthase [Shewanella denitrificans OS217]
          Length = 593

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 119/239 (49%), Gaps = 29/239 (12%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG-F 132
           L+H+++  K+ D +  L   +D  +  ++Y+D  + V +KPA      G  I+  +    
Sbjct: 362 LSHMLEGLKV-DPNPLLENPADDKQITVIYQDEHLLVISKPAEFLSVPGKNISDSVHTRI 420

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           ++ +  + G  P + HRLD  TSG++V+A  + A + L + F +R + K Y +L+ G+  
Sbjct: 421 IRDFPSASG--PIIVHRLDMSTSGLMVIALNKEAHESLQKQFILRTVTKRYIALLDGLLP 478

Query: 193 NKK---ECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           N+    E I +  L+     GD     +Q   +E G + A + +++ID   Q    + + 
Sbjct: 479 NRTAGDEGIISLPLR-----GDLDDRPRQLVCHEHGKS-AETRWQIID-IQQGRTKVFLY 531

Query: 247 PHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           P TGRTHQLRVH  H   +  PIVGD  Y             ++L+LHA  +   HP+ 
Sbjct: 532 PKTGRTHQLRVHCAHSQGLHLPIVGDDHYGVR---------ASRLHLHAESLSFTHPQS 581


>gi|161869184|ref|YP_001598350.1| putative psedouridine synthase [Neisseria meningitidis 053442]
 gi|161594737|gb|ABX72397.1| putative psedouridine synthase [Neisseria meningitidis 053442]
          Length = 236

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/212 (30%), Positives = 101/212 (47%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 23  ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 78

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + +A  L+  F  + I+K Y +L    P  K+  I   + +KS  G     + K  
Sbjct: 79  FALNKESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLT 132

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 133 RNTENIAVTRFHSISI-AEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGT---- 187

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 188 ----ESETMFLYAWRIQFAY-QNRQIEIVAPL 214


>gi|254285561|ref|ZP_04960525.1| pseudouridine synthase Rlu family protein [Vibrio cholerae
           AM-19226]
 gi|150424423|gb|EDN16360.1| pseudouridine synthase Rlu family protein [Vibrio cholerae
           AM-19226]
          Length = 245

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 104/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEAN--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAVTAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFMHP 211


>gi|212710403|ref|ZP_03318531.1| hypothetical protein PROVALCAL_01464 [Providencia alcalifaciens DSM
           30120]
 gi|212686985|gb|EEB46513.1| hypothetical protein PROVALCAL_01464 [Providencia alcalifaciens DSM
           30120]
          Length = 252

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 108/247 (43%), Gaps = 51/247 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKPAG+ V              +SW+DSK             GQ     
Sbjct: 4   IIYQDEYVVAVNKPAGMLVH-------------RSWLDSKETVFVMQTLRDQIGQHVFPI 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L+ A +   A+ L E F   R++K+Y ++V G   +        L +   
Sbjct: 51  HRLDRPTSGVLLFALSSDVARLLAEQFEQHRMEKVYHAIVRGYVMDGDRLDYPLLEELDK 110

Query: 208 IGGDYVHVVKQNEKGANYAISHFK---VIDCF-------AQKFCWLEMQPHTGRTHQLRV 257
           I           E      ++H+K    ++C          +F  +E++P TGR HQLR 
Sbjct: 111 IADKNA----TKEPRLQECVTHYKPLATVECSVAIGRYDTARFSLVELKPETGRKHQLRR 166

Query: 258 HALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP-LPAH 314
           H  H+  PI+GD K+      +G       ++L LHA  +   HP      IT   +P  
Sbjct: 167 HMSHLRHPIIGDSKHGDLRQNRGVAEHFSVSRLMLHASQLIFIHP------ITEEKIP-- 218

Query: 315 MVKTWDS 321
           +V +WD+
Sbjct: 219 LVASWDA 225


>gi|329955144|ref|ZP_08296101.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
 gi|328526143|gb|EGF53162.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
          Length = 297

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/226 (29%), Positives = 108/226 (47%), Gaps = 21/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 82  IVYEDAYIIVVEKMQGLLSVNTERQKERTAYTI---LNEYVQRSGRQHRVYIVHRLDRDT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L +++      + Y ++V G  +N    + +WL  +      YV+
Sbjct: 139 SGLMMFAKDEKTQNTLRDNWHDIVTDRRYVAVVAGEMENNAGMVRSWLTDRKL----YVY 194

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                + G   AI+H++ I   A  F  +E+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 195 S-NPTDDGGKEAITHYRTIKR-ANGFSLVELNLETGRKNQIRVHMQDLGHPIIGDGRYGL 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
                  +PI  +L LHA  +   HP  G L Q   P P    K +
Sbjct: 253 ----EEVNPI-GRLALHAFKLCFYHPVTGELMQFETPYPGDFKKLF 293


>gi|15640904|ref|NP_230535.1| tRNA pseudouridine synthase C [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121588124|ref|ZP_01677871.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 2740-80]
 gi|147674217|ref|YP_001216366.1| tRNA pseudouridine synthase C [Vibrio cholerae O395]
 gi|227081064|ref|YP_002809615.1| pseudouridine synthase Rlu family protein [Vibrio cholerae M66-2]
 gi|229505507|ref|ZP_04395017.1| tRNA pseudouridine synthase C [Vibrio cholerae BX 330286]
 gi|229510823|ref|ZP_04400302.1| tRNA pseudouridine synthase C [Vibrio cholerae B33]
 gi|229517944|ref|ZP_04407388.1| tRNA pseudouridine synthase C [Vibrio cholerae RC9]
 gi|229608526|ref|YP_002879174.1| tRNA pseudouridine synthase C [Vibrio cholerae MJ-1236]
 gi|254848023|ref|ZP_05237373.1| tRNA pseudouridine synthase C [Vibrio cholerae MO10]
 gi|298498990|ref|ZP_07008797.1| tRNA pseudouridine synthase C [Vibrio cholerae MAK 757]
 gi|34582485|sp|Q9KTL4|TRUC_VIBCH RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|9655343|gb|AAF94050.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O1
           biovar El Tor str. N16961]
 gi|121547615|gb|EAX57714.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 2740-80]
 gi|146316100|gb|ABQ20639.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O395]
 gi|227008952|gb|ACP05164.1| pseudouridine synthase Rlu family protein [Vibrio cholerae M66-2]
 gi|227012708|gb|ACP08918.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O395]
 gi|229344659|gb|EEO09633.1| tRNA pseudouridine synthase C [Vibrio cholerae RC9]
 gi|229350788|gb|EEO15729.1| tRNA pseudouridine synthase C [Vibrio cholerae B33]
 gi|229357730|gb|EEO22647.1| tRNA pseudouridine synthase C [Vibrio cholerae BX 330286]
 gi|229371181|gb|ACQ61604.1| tRNA pseudouridine synthase C [Vibrio cholerae MJ-1236]
 gi|254843728|gb|EET22142.1| tRNA pseudouridine synthase C [Vibrio cholerae MO10]
 gi|297543323|gb|EFH79373.1| tRNA pseudouridine synthase C [Vibrio cholerae MAK 757]
          Length = 244

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 104/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEAN--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAVTAYRPLAKVELPIATGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFMHP 211


>gi|317493195|ref|ZP_07951618.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918855|gb|EFV40191.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 256

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 104/219 (47%), Gaps = 24/219 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  +   NKPAG  V   S +  H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 4   IIYQDEHLVALNKPAGWLVHR-SWLDRHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVK 217
           +A +   A+ L+E F  R + K Y ++V G  +   E + ++ L      I   +     
Sbjct: 63  MALSSEVARMLSEQFEQREMNKTYHAVVRGYLEG--EAVIDYALTPELDKIADKF----S 116

Query: 218 QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             +K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+
Sbjct: 117 SPDKAPQTAVTHYRSLATVEMPVAVGKYQTARYSLIELKPETGRKHQLRRHMAHLRHPII 176

Query: 268 GDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG 303
           GD K+  + + N         + L LHA  + L HP  G
Sbjct: 177 GDTKH-GDLRQNRAMSQHFACSGLMLHASELCLEHPITG 214


>gi|226315112|ref|YP_002775008.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226098062|dbj|BAH46504.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
          Length = 310

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 84/327 (25%), Positives = 156/327 (47%), Gaps = 38/327 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS   +++Y V E D   M +++  +    +++   +Q++ RS  + +++K+     +++
Sbjct: 1   MSRKDWIEYTVSEQDT-GMNVEQIVRQKL-NVSGRMMQRLTRSKGILLNRKQPFLQRQVK 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKH---SDFLKSI-LLYEDSKIYVFNKPAG 116
           +G  +       A+  I +++++     + TK    +  + SI +LYED  + + NKPAG
Sbjct: 59  AGDTI-------AVRVIERQEQVPRQPQHDTKPEGPNTPMPSIDILYEDDHLLIANKPAG 111

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESF 174
           + V         +   L + + ++G++  +   HRLD++TSG ++VA++    Q      
Sbjct: 112 MMVHPIKQETDTLVHALAAVLAARGEQTSVHPVHRLDKDTSGAILVAKSSYGHQLADRLL 171

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKV 232
           R   I + Y ++  G+       I       + IG D  H  K+   E G + AI+H++V
Sbjct: 172 REGGIHREYLAVASGVLSEGAGTI------DAPIGRDARHPTKRRVVESG-DPAITHYEV 224

Query: 233 IDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
                +      WLE    TGRTHQ+RVH  H+G P+ GD  Y    +G     +  +  
Sbjct: 225 QQTSEEMTLARVWLE----TGRTHQIRVHFAHIGHPLAGDTMY-GGARG-----LLRRQA 274

Query: 290 LHARYMDLPHP-EGGRLQITAPLPAHM 315
           LHA  +   HP     + + AP+P+ M
Sbjct: 275 LHASKLSFLHPLLEKEIVVEAPIPSDM 301


>gi|197124689|ref|YP_002136640.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196174538|gb|ACG75511.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 323

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 76/327 (23%), Positives = 130/327 (39%), Gaps = 39/327 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            VE +    RLDR+ +     ++   +Q+++       D +R+K + R+  G    +   
Sbjct: 15  TVEPNYAGWRLDRYLQEKIRRLSRERVQRLIEHRLETEDGRRLKPSTRVAPGLSFAL--- 71

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-I 129
                       + D+        +F    ++++D  + V +KPAG+ V   +  A +  
Sbjct: 72  ------------LKDAEAEPDTPQEF---AVVHDDGALLVVDKPAGLPVHPTARYAANTF 116

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               K     +   P   HRLD+ETSG+L    +    + L   F   R+ K Y +L  G
Sbjct: 117 TSLAKLRFPERKVDP--AHRLDRETSGLLACGTSPEVTKVLKRDFAHARVHKTYLALALG 174

Query: 190 IPKNKKECI-ANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQ 246
            P      + A   L  +      +HV  +    + A   ++  +  D        L  +
Sbjct: 175 APVEDAFTVDAPLALTGASAVRVRMHVAAEGLPSQTAFEVLARRRAPD--GAPVALLACR 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQN----------KLYLHARY 294
           P TGR HQ+R H  H G P+VGD  Y  + +    FT               +  LHA  
Sbjct: 233 PRTGRQHQIRAHLAHAGLPMVGDKIYGPDEEIFDRFTRRAMTDEDVALLRLPRHALHAWR 292

Query: 295 MDLPHP-EGGRLQITAPLPAHMVKTWD 320
           ++LPHP     +++  PLP  +   W+
Sbjct: 293 LELPHPLTRAPVRLEVPLPPDLAAFWE 319


>gi|28899453|ref|NP_799058.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|260363379|ref|ZP_05776231.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
 gi|260879313|ref|ZP_05891668.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|260895728|ref|ZP_05904224.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|34395765|sp|Q87LD3|RLUA_VIBPA RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|28807689|dbj|BAC60942.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|308087397|gb|EFO37092.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|308093125|gb|EFO42820.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|308111223|gb|EFO48763.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
          Length = 250

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 100/218 (45%), Gaps = 38/218 (17%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           +++ED  I   NKP+G+ SV G   +A H D     W   + + P  ++ HRLD  TSG+
Sbjct: 16  IVFEDDHILAVNKPSGLLSVPGR--LAEHHDSM---WSRLQEEYPDIQVVHRLDMSTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE----CIANW--------LLK 204
           +V+A+ + A   L + F+ R   KIY++ VWG + + + E     I +W          +
Sbjct: 71  MVLAKNKRAESALKKQFQFRLTHKIYYARVWGHVEQEEGEIDLPLICDWPNRPLQKVCFE 130

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                     V K+ E+      +  +++             P TGR+HQLRVH   +G 
Sbjct: 131 DGKPSKTLFQVAKREEQEDGTKTTIVRLL-------------PITGRSHQLRVHMQALGH 177

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           PIVGD  Y       F+     +L LHA  +   HP+ 
Sbjct: 178 PIVGDEFYATEEAKVFS----ERLELHASELSFYHPKS 211


>gi|213027660|ref|ZP_03342107.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 176

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 45/123 (36%), Positives = 72/123 (58%), Gaps = 7/123 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   +++SG  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLESGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 YHI 129
           + +
Sbjct: 121 FGV 123


>gi|153216000|ref|ZP_01950222.1| tRNA pseudouridine synthase C [Vibrio cholerae 1587]
 gi|124114513|gb|EAY33333.1| tRNA pseudouridine synthase C [Vibrio cholerae 1587]
          Length = 244

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 104/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEAN--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAVTAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFMHP 211


>gi|260425298|ref|ZP_05779278.1| ribosomal large subunit pseudouridine synthase D [Citreicella sp.
           SE45]
 gi|260423238|gb|EEX16488.1| ribosomal large subunit pseudouridine synthase D [Citreicella sp.
           SE45]
          Length = 345

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 84/341 (24%), Positives = 134/341 (39%), Gaps = 55/341 (16%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L +++  G V R  +       R+  G  +          
Sbjct: 16  RLDKALARDVPEEAALSRTRLARLIAEGAVTRAGEALTDPKARVAEGDEI---------- 65

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
            +I   +  DS +      D   SI+ +ED  + V +KPAG+ V    G         + 
Sbjct: 66  -LITVPQAEDSHIG---PEDIPLSIV-WEDEDLVVVDKPAGMVVHPAPGTPSGTLVNALL 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +H  G L S V     +P + HR+D++TSG+LVVA++  A   L   F      + Y ++
Sbjct: 121 HHFGGRL-SGVGGV-ARPGIVHRIDKDTSGLLVVAKSDRAHHGLAAQFEAHSADRAYLAV 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGG-------------DYVHVVKQNEKGANYAISHFKVI 233
           V+G+P      +          GG             D        +    +A +   V+
Sbjct: 179 VYGVPDAGDPRLVGTRGVSMEPGGVIRIQSGLARHKTDRQRQAVYFDGQGRHATTRASVL 238

Query: 234 DCFAQ--KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKLY 289
           + F        ++ +  TGRTHQ+RVH  H G  +VGD  Y    K       P+  +  
Sbjct: 239 ETFGTPPAMALVQCRLETGRTHQIRVHMAHAGHGLVGDPVYGGRRKPPAKAIGPVATEAV 298

Query: 290 -------LHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                  LHA  +   HP  G RL+  +PLP  M    ++L
Sbjct: 299 SGFSRQALHAAELGFDHPVTGERLRFESPLPDDMDALIEAL 339


>gi|27904851|ref|NP_777977.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
 gi|34395768|sp|Q89AD9|RLUD_BUCBP RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|27904249|gb|AAO27082.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
          Length = 317

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 107/227 (47%), Gaps = 19/227 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----PR--LTHRLDQET 154
           ++YED  I V NK     V  G+G   +  G L + +  +       PR  + HRLD++T
Sbjct: 87  VIYEDDDILVINKQDNFVVHPGAG---NTSGTLLNALLHRDSTFFNIPRAGIVHRLDKDT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++V+A+   +   L +  + +++ + Y ++V+G      + I+   + KS I      
Sbjct: 144 TGLMVIAKNNLSYMALIDQIKCKKVIREYQAIVYG------KVISGGTIVKSIIRNPIKR 197

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                 K    AI+H++++  F      L++   TGRTHQ+R H L++  P+VGD  Y  
Sbjct: 198 TTMIVNKCGKRAITHYRILKRFTHH-THLKIILETGRTHQIRTHMLYINFPLVGDKTYGN 256

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
            FK  F   I   L    +          RL +  P+  H+++ W+S
Sbjct: 257 KFK--FYKNISLTLLEQVKKFPRQALHASRLCLYHPVTKHLME-WNS 300


>gi|145642181|ref|ZP_01797749.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae R3021]
 gi|145273105|gb|EDK12983.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae 22.4-21]
          Length = 186

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 57/174 (32%), Positives = 89/174 (51%), Gaps = 16/174 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ + V NKP+G+    G+   Y+      S V  K       HRLD  TSGI+V 
Sbjct: 16  IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKFGFCEPAHRLDMATSGIIVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC----IANWLLKKSHIGGDYVHV 215
           A ++AA + L   FR R  +K Y ++VWG + K+  E     I +W   +     D+V  
Sbjct: 74  ALSKAADRELKRQFREREPKKHYQAIVWGHLEKDYGEVNLPMICDW-ENRPRQRLDFVL- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                     A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD
Sbjct: 132 -------GKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGD 178


>gi|225572464|ref|ZP_03781328.1| hypothetical protein RUMHYD_00761 [Blautia hydrogenotrophica DSM
           10507]
 gi|225040101|gb|EEG50347.1| hypothetical protein RUMHYD_00761 [Blautia hydrogenotrophica DSM
           10507]
          Length = 294

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 60/225 (26%), Positives = 113/225 (50%), Gaps = 18/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGI 157
           +LYED  I V NKPA   +    G     +   +  +  S+G     R  +RLD++T+G 
Sbjct: 83  ILYEDEDILVLNKPADTPIHPSMGNYENTLANGVAHYYQSQGISFVYRCINRLDRDTTGA 142

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+   +A  L+ + + R I + Y +LV G+      C    ++       D   + +
Sbjct: 143 LILAKHAYSAALLSAAMQRREIHRTYLALVQGL------CPECGVIDAPIARKDASVIER 196

Query: 218 Q-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           + N +    A++ ++ +  F Q    ++++  TGRTHQ+RVH  ++G P++GD+ Y  ++
Sbjct: 197 EVNLRTGAPALTRYECL-AFHQGLSLVQLRLETGRTHQIRVHMKYLGYPLLGDYLYNPDY 255

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
                     ++ LH+  +D  HP   + L +TAP+P   ++ W+
Sbjct: 256 SR------IGRVSLHSYQLDFCHPITDKPLCLTAPVPKDFLQAWE 294


>gi|113968627|ref|YP_732420.1| pseudouridine synthase Rlu family protein [Shewanella sp. MR-4]
 gi|113883311|gb|ABI37363.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           sp. MR-4]
          Length = 228

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 59/192 (30%), Positives = 93/192 (48%), Gaps = 19/192 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +++   V +K   +      G A    G +       G K    HRLD  TSG+L++
Sbjct: 4   IIADEADFLVISKSPNVHFHSQDGTA----GVVAQLEQDLGIKLFAVHRLDTPTSGLLLL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+  AAA+ LTE FR  R+QK Y +L  G PK K+  +   + K          +++  E
Sbjct: 60  AKHPAAARQLTELFRAHRVQKYYLALAKGKPKKKQGWVIGDMAKSRR---SMFKLLRTKE 116

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F           +L ++PH+G+THQLRV    +G PI+GD  Y ++     
Sbjct: 117 ---NPAITQFFSTSVGDGLRLYL-LKPHSGKTHQLRVALASLGVPILGDALYGSD----- 167

Query: 281 TSPIQNKLYLHA 292
              + ++ YLHA
Sbjct: 168 ---MADRCYLHA 176


>gi|270293436|ref|ZP_06199644.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M143]
 gi|270278098|gb|EFA23947.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M143]
          Length = 291

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 92/201 (45%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  IYQDQHLIIVNKPEGMKTHGNQPDEIALLNHVSAYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   +K+      L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEIAREYWALVEGQVGSKE------LIFRDKIGRDRHDRRKRVVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +  + +  F  K   +  +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 195 AKSGQYAETQVRRLKQFLNKTSLVRCKLKTGRTHQIRVHLSHHKHPILGDPLYNSRSKA- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 254 ------GRLMLHAFRLSFTHP 268


>gi|33602573|ref|NP_890133.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           bronchiseptica RB50]
 gi|33577012|emb|CAE34092.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           bronchiseptica RB50]
          Length = 320

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 85/334 (25%), Positives = 136/334 (40%), Gaps = 53/334 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD+      P  +   LQ  + +G V V+  + K    +  G V+ +  
Sbjct: 19  LTVPPDTPADRLDKVLAGLLPGHSRSRLQGWIEAGYVLVNGAQAKVRQAVGPGDVLSV-- 76

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                     EQ   +S     +   F    ++ E     V +KPAG+    G+G     
Sbjct: 77  ---------WEQPAPESRAFAPEPVAF---DVVAESPDWIVVDKPAGLVTHPGAGNWSGT 124

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  + + ++  +  + HRLD++TSG++VVAR   A  HL    + R + + Y +L
Sbjct: 125 LLNGLLHRYPELARVARAGIVHRLDKDTSGLMVVARNELAQTHLVRQLQARTMGRQYIAL 184

Query: 187 VWGIPKNKKECIANWLLKKSH----IGGDY---VHVVKQNEKGANYAISHF--KVIDC-- 235
             G           WL         IG D    V +  +       A++HF  +   C  
Sbjct: 185 AHG-----------WLGAAGTVDRPIGRDARVPVRMSVERPIAPKPAVTHFDPRRRGCAE 233

Query: 236 ----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
                ++  C LE    TGRTHQ+RVH   +G P++ D  Y        T     +  LH
Sbjct: 234 GGARVSEVLCRLE----TGRTHQIRVHLASLGHPLLADTLYGGKPLAGAT-----RQMLH 284

Query: 292 ARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF 324
           AR +    P G G +   A +PA M    ++L +
Sbjct: 285 ARALHFDDPGGSGEVSFEAGVPADMSDVQEALAW 318


>gi|332360116|gb|EGJ37930.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1056]
          Length = 290

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 92/201 (45%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      R I + YW+LV G   +KK      L+ K  IG D     K+  +
Sbjct: 141 KNPFVLPILNRLLEKREISREYWALVQGKFPSKK------LIYKDKIGRDRHDRRKRLVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   YA +H   +  F Q    ++ Q  TGRTHQ+RVH  H G  +VGD  Y    +G 
Sbjct: 195 PRKGLYAETHVNRLKQFGQA-SLVKCQLKTGRTHQIRVHLAHHGHQLVGDPLYHPQPQG- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 253 -------RLMLHAHRLTFTHP 266


>gi|315611921|ref|ZP_07886839.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis ATCC 49296]
 gi|315315910|gb|EFU63944.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis ATCC 49296]
          Length = 291

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 59/209 (28%), Positives = 99/209 (47%), Gaps = 20/209 (9%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SD ++ +  Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD E
Sbjct: 78  SDLVQEV--YQDQHLIIVNKPEGMKTHGNQPGEIALLNHVSAYV---GQTCYVVHRLDME 132

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++ A+       L      + I + YW+L+ G  ++K+      L+ +  IG D  
Sbjct: 133 TSGLVLFAKNPFILPILNRLLEKKEIAREYWALIEGRVESKE------LVFRDKIGRDRH 186

Query: 214 HVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              K+  + K   YA +H   +  F  +   +  +  TGRTHQ+R+H  H   PI+GD  
Sbjct: 187 DRRKRIVDAKHGQYAETHVSRLKQFPNQTTLVRCKLKTGRTHQIRIHLSHHNHPILGDPL 246

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y ++ K        ++L LHA  +   HP
Sbjct: 247 YNSSSKV-------SRLMLHAFRLSFTHP 268


>gi|291557011|emb|CBL34128.1| pseudouridine synthase, RluA family [Eubacterium siraeum V10Sc8a]
          Length = 322

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 25/281 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V  ++   R+DR+    +P +    + K+ R   ++++ K+ K +  I    +++
Sbjct: 1   MKEIKVTKNDSGQRIDRFLSKSFP-LGQGQICKLARKNCIKLNGKKCKPDTHIAENDIIK 59

Query: 67  --IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGS 123
             IP  +     +I + K      + T  SD  K  ++YED  I + +KP G+ V +  S
Sbjct: 60  LFIPDEM-----LIPKAK--SDPDDFTAVSD--KIDIVYEDENILLVDKPVGMVVHEDES 110

Query: 124 GIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G +  +   +KS++  KG+          P L +R+D+ T GI++ A+   + + L +  
Sbjct: 111 GDSDTLINRIKSYLYHKGEYRPENELSFAPALCNRIDRNTCGIVIAAKNAESLRILNQKI 170

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R + K+Y  +  G        +  +L K S    + V +  +  K      + +KVI 
Sbjct: 171 RDRELTKLYLCIACGKVTPDSATLTAYLEKNSDT--NTVKISDKKTKSNLTIKTKYKVI- 227

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +  +   L++   TGRTHQ+R H  ++G  ++GD KY  N
Sbjct: 228 AYNGENSLLKVDLLTGRTHQIRAHLAYIGHALLGDGKYGNN 268


>gi|242310704|ref|ZP_04809859.1| ribosomal large subunit pseudouridine synthase [Helicobacter
           pullorum MIT 98-5489]
 gi|239523102|gb|EEQ62968.1| ribosomal large subunit pseudouridine synthase [Helicobacter
           pullorum MIT 98-5489]
          Length = 322

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 83/317 (26%), Positives = 147/317 (46%), Gaps = 39/317 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V + E  MRLD +      +++   + K+L + Q+ +        N+IQ+ +       
Sbjct: 1   MVTSQESGMRLDIFLATKL-NLSRNKINKMLHNKQITL--------NQIQASK------- 44

Query: 71  INALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ--GGSGI 125
            N +  I+KEQ    I  S +   K +  +   +LYED  + V NKP  + V        
Sbjct: 45  -NGI--ILKEQDQIHIFPSLLETAKPTPKIHIPILYEDEDLLVLNKPINLVVHKTNQEDT 101

Query: 126 AYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            Y +  +LK     + + G   R  + HRLD+ TSG +V+A+   + Q L++  + + + 
Sbjct: 102 QYTLHEWLKEQNFKLSNLGDSYREGIIHRLDKTTSGAIVIAKNNHSHQILSQQLKTKEMG 161

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y+  V   P  +   I + L++       Y+   KQ     +   + FK+ID    + 
Sbjct: 162 R-YYLCVINQPLKQDIIIDSPLIRHPKNRLKYITTSKQTPDSKDAKTAFFKIIDNGKTEL 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
              ++   +GRTHQ+R H   +   I+GD  Y  N++GN+T     ++ LH+  + L HP
Sbjct: 221 IGAKL--FSGRTHQIRAHLSKINRHILGDFFY--NYEGNYTQ----RILLHSSLLYLKHP 272

Query: 301 EGGR-LQITAPLPAHMV 316
              + L+I APL   M+
Sbjct: 273 TTQKPLKIYAPLFEDML 289


>gi|325204968|gb|ADZ00422.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M01-240355]
          Length = 217

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/212 (30%), Positives = 101/212 (47%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 4   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + +A  L+  F  + I+K Y +L    P  K+  I   + +KS  G     + K  
Sbjct: 60  FALNKESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLT 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 114 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTE--- 169

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 170 -----SETMFLYAWKIQFAY-QNRQIEIVAPL 195


>gi|320093965|ref|ZP_08025793.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 178 str. F0338]
 gi|319979099|gb|EFW10614.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 178 str. F0338]
          Length = 304

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 107/229 (46%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY+D  I V +KP G++   G G     + G L +    + + G   R  + HRLD  T
Sbjct: 80  ILYDDEDIVVVDKPVGVAAHTGPGWEGPTVLGNLAAAGYRITTHGPPERQGIVHRLDVGT 139

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG ++VA++  A   +  +F+ R + K+Y ++V G        I   + +  H   ++  
Sbjct: 140 SGAMMVAKSELAYSVMKRAFKERTVTKVYHAVVAGHLDPASGTIDAPIGR--HPSREWRM 197

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V     G   AI+H+  ++  A   C  E+   TGRTHQ+RVH   +G P VGD  Y A
Sbjct: 198 AVID---GGKRAITHYDTLEMMAGA-CLAEIHLETGRTHQIRVHMAAVGHPCVGDAFYGA 253

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
           +  G        + +LHA  +   HP  G    + +P P+ +    + L
Sbjct: 254 D-PGQAERLGLVRQWLHAVELSFAHPRTGAPTTVRSPYPSDLAAALEVL 301


>gi|42524230|ref|NP_969610.1| pseudouridylate synthase, 23S RNA-specific [Bdellovibrio
           bacteriovorus HD100]
 gi|39576438|emb|CAE80603.1| Pseudouridylate synthase, 23S RNA-specific [Bdellovibrio
           bacteriovorus HD100]
          Length = 230

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 113/220 (51%), Gaps = 23/220 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPR------LTHRLDQE 153
           +L+ED  + V NK AG+ +V         +   L  +V  KG  PR      + HRLDQ 
Sbjct: 15  ILHEDLDVIVGNKAAGVLTVAAKWDRDNTVHNLLNLYV-RKGN-PRSNKCVYVVHRLDQA 72

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G+L+ A+T      L + ++     K Y+++V G    K   I ++L +  +     V
Sbjct: 73  TTGVLIFAKTEQVQHFLKDDWK--STIKTYYAIVHGKMPKKSGTITSYLEEDENY---VV 127

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H  K ++KG   AI+ ++V+    +KF  L++   TG+ +Q+RVH    G PIVGD KY 
Sbjct: 128 HSSKDSDKG-KLAITEYEVLKE-TEKFSLLKINLLTGKKNQIRVHLAGEGHPIVGDPKY- 184

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
               G  T+ ++ +L LH+  ++  HP    R+ I AP+P
Sbjct: 185 ----GKPTTNLK-ELRLHSASLEFTHPHSKKRITIKAPVP 219


>gi|187917901|ref|YP_001883464.1| ribosomal large subunit pseudouridine synthase D [Borrelia hermsii
           DAH]
 gi|119860749|gb|AAX16544.1| ribosomal large subunit pseudouridine synthase D [Borrelia hermsii
           DAH]
          Length = 326

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 115/240 (47%), Gaps = 28/240 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  + V +KP GI    G         + + +HI     S+ + K  +P + HRLD
Sbjct: 86  ILYEDINVIVVDKPQGILSHPGISNLDNTVVNFLLHHISSLRDSFQEDK-IRPGIVHRLD 144

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG+++ A+       L++ F+ R ++K+Y ++V G  K     I  ++ +  +    
Sbjct: 145 KETSGVMICAKNLTTLNFLSKQFKERFVKKVYVAVVKGNFKIDSGIIETFIDRDRYDRKR 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +     + ++    A++ +KV+      +  + ++P TGRTHQLRVH  H+  PI+GD  
Sbjct: 205 FSVYANRGKR----ALTEYKVLANMGN-YSLVALKPKTGRTHQLRVHMKHLNHPILGDSI 259

Query: 272 YC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           Y      FK       +  L LHA  +++   EG   +  +  P   +   D L   YD+
Sbjct: 260 YTRLDKVFK-------EMSLMLHAFKLEINIEEGSLKKFISAFPQRFI---DFLSIFYDK 309


>gi|146329295|ref|YP_001209214.1| ribosomal large subunit pseudouridine synthase, RluA [Dichelobacter
           nodosus VCS1703A]
 gi|146232765|gb|ABQ13743.1| ribosomal large subunit pseudouridine synthase, RluA [Dichelobacter
           nodosus VCS1703A]
          Length = 203

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 109/217 (50%), Gaps = 22/217 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  +   +KPAG+    G G A   D     W +  +       HRLD  TSGI++
Sbjct: 3   VVYQDEDMIAVDKPAGLLSVPGRG-AEKRDSV--EWRIKQEYCGAAAVHRLDMSTSGIML 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +A+ + A ++   +F  RR++K Y ++  G I +++ E  A  +       GD+V+  KQ
Sbjct: 60  IAKHKDAERYYKTAFEQRRVKKGYVAICHGLIAEDEGEMNAPLI-------GDWVNRPKQ 112

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               E G   A++ F V+    +    + + PHTGR+HQLRVH    G PIVGD     N
Sbjct: 113 KVCYETG-KAALTRFCVLS-RQRDQTRVALFPHTGRSHQLRVHLADKGHPIVGD-----N 165

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
             G+    +  +L LHA ++     +G  ++++  +P
Sbjct: 166 LYGDAADCLLPRLLLHAEWLLFTRRDGAPIKLSTKIP 202


>gi|146318712|ref|YP_001198424.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           05ZYH33]
 gi|146320920|ref|YP_001200631.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           98HAH33]
 gi|253751821|ref|YP_003024962.1| RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|253753644|ref|YP_003026785.1| RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|253755475|ref|YP_003028615.1| RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|145689518|gb|ABP90024.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           05ZYH33]
 gi|145691726|gb|ABP92231.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           98HAH33]
 gi|251816110|emb|CAZ51733.1| putative RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|251817939|emb|CAZ55717.1| putative RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|251819890|emb|CAR45926.1| putative RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|292558391|gb|ADE31392.1| Pseudouridine synthase, RluD [Streptococcus suis GZ1]
 gi|319758173|gb|ADV70115.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           JS14]
          Length = 297

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 108/229 (47%), Gaps = 30/229 (13%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQ 152
           F    ++YED      NKP G +    +  +  I  F+K ++  +  + +  H   RLD+
Sbjct: 74  FFPLDIVYEDDHFLAINKPVGYASIPSALHSSTIANFVKGYLIEQNYENKQVHIVTRLDR 133

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+++ A+   A   L +  + + I K Y++LV G          N  L+++   GD 
Sbjct: 134 DTSGVMLFAKHGYAHARLDKQLQAKLIHKRYYALVKG----------NGQLEET---GDI 180

Query: 213 VHVVKQNE---------KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +  + + E         K   YA + ++V+  +      +++Q HTGRTHQ+RVH  H+G
Sbjct: 181 IAPIGRPEDSIITRCVTKNGKYAHTSYRVVQSWGD-IHLVDIQLHTGRTHQIRVHFSHIG 239

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
            P++GD  Y  + +       +  L+ H    D P     R+ + APLP
Sbjct: 240 FPLLGDDMYGGSLECGIE---RQALHCHNLAFDNPF-SAERIDLEAPLP 284


>gi|258624386|ref|ZP_05719334.1| tRNA pseudouridine synthase C [Vibrio mimicus VM603]
 gi|258583348|gb|EEW08149.1| tRNA pseudouridine synthase C [Vibrio mimicus VM603]
          Length = 244

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 63/217 (29%), Positives = 103/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEAD--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  AI+ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAITAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFVHP 211


>gi|167750591|ref|ZP_02422718.1| hypothetical protein EUBSIR_01567 [Eubacterium siraeum DSM 15702]
 gi|167656517|gb|EDS00647.1| hypothetical protein EUBSIR_01567 [Eubacterium siraeum DSM 15702]
          Length = 322

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 133/281 (47%), Gaps = 25/281 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V  ++   R+DR+    +P +    + K+ R   ++++ K+ K +  I    +++
Sbjct: 1   MKEIKVTKNDSGQRIDRFLSKSFP-LGQGQICKLARKNCIKLNGKKCKPDTHIAENDIIK 59

Query: 67  --IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGS 123
             IP  +     +I + K      + T  SD  K  ++YED  I + +KP G+ V +  S
Sbjct: 60  LFIPDEM-----LIPKAK--SDPDDFTAVSD--KIDIVYEDENILLVDKPVGMVVHEDES 110

Query: 124 GIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G +  +   +KS++  KG+          P L +R+D+ T GI++ A+   + + L +  
Sbjct: 111 GDSDTLINRIKSYLYHKGEYRPENELSFAPALCNRIDRNTCGIVIAAKNAESLRILNQKI 170

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R + K+Y  +  G        +  +L K S    + V +  +  K      + +KVI 
Sbjct: 171 RDRELTKLYLCIACGKVTPDSATLTAYLEKNSDT--NTVKISDKKTKSNLTIKTKYKVI- 227

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +  +   L++   TGRTHQ+R H  ++G  ++GD KY  N
Sbjct: 228 AYNGENSLLKVDLLTGRTHQIRAHLAYIGHALLGDGKYGNN 268


>gi|332883134|gb|EGK03417.1| hypothetical protein HMPREF9456_01484 [Dysgonomonas mossii DSM
           22836]
          Length = 313

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/219 (27%), Positives = 106/219 (48%), Gaps = 15/219 (6%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +++ED  + V  K AG +SV      +  +   L  +V  K +K R+   HRLD+E SG+
Sbjct: 85  IVFEDDDLLVIEKEAGFLSVATDKEKSRTVYNSLNEYVKKKDKKARVYVLHRLDREVSGL 144

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+         +++     +  Y ++V G P  K   + +WL +  +    +V +  
Sbjct: 145 MIFAKDMELQDIFQKNWDNLVPKYSYMAIVEGRPNPKNGTVTSWLTENKN----FVMMSS 200

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             + G   +++H+K        +  L+    T R +Q+RVH   +G PIVGD KY A+  
Sbjct: 201 LIDNGGLKSVTHYKTQKSKGG-YSLLDFDLETRRKNQVRVHMQQIGHPIVGDKKYGAS-- 257

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
               +PI+ ++ LHA  + L HP  G  L+  A +P  M
Sbjct: 258 ---NNPIK-RIALHAGGLILKHPRTGELLEFKAGIPKAM 292


>gi|323351544|ref|ZP_08087198.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis VMC66]
 gi|322122030|gb|EFX93756.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis VMC66]
          Length = 295

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 113/228 (49%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++      + Q+  +  RLD++TSG+
Sbjct: 78  VVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  K    A + +K+I+ F   +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTKDGKCAHTSYKIIEQFGDVY-LVDIHLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLECGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|328471410|gb|EGF42305.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 10329]
          Length = 250

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 100/214 (46%), Gaps = 30/214 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           +++ED  I   NKP+G+ SV G   +A H D     W   + + P  ++ HRLD  TSG+
Sbjct: 16  IVFEDDHILAVNKPSGLLSVPGR--LAEHHDSM---WSRLQEEYPDIQVVHRLDMSTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE----CIANW----LLKKSHI 208
           +V+A+ + A   L + F+ R   KIY++ VWG + + + E     I +W    L K    
Sbjct: 71  MVLAKNKRAESALKKQFQFRLTHKIYYARVWGHVEQEEGEIDLPLICDWPNRPLQKVCFE 130

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            G     + Q  K   +             K   + + P TGR+HQLRVH   +G PIVG
Sbjct: 131 DGKPSKTLFQVAKREEHED---------GTKTTIVRLLPITGRSHQLRVHMQALGHPIVG 181

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           D  Y       F+     +L LHA  +   HP+ 
Sbjct: 182 DEFYATEEAKVFS----ERLELHASELSFYHPKS 211


>gi|261251066|ref|ZP_05943640.1| ribosomal large subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
 gi|260937939|gb|EEX93927.1| ribosomal large subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
          Length = 248

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 68/222 (30%), Positives = 106/222 (47%), Gaps = 27/222 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYH------IDG--------FLKSWVDSKGQKPR 145
           +LY+D  I + NKP+G+ S+ G + + +       ++G           ++VD+K     
Sbjct: 26  ILYQDDDILLINKPSGLLSLSGKNQLNWDSVHYRLVNGQDANQSAKATPAFVDAK----- 80

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD  TSG++VV    AA++ L + F+ R +QK Y +++ G        I+  + K 
Sbjct: 81  LPHRLDLGTSGVMVVGLNSAASKSLNQQFQARTVQKRYLAMLAGWVDGDHGQISAPIAKD 140

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGC 264
             +       VK        AIS ++VI      +   ++  P TGRTHQLR+H+L  G 
Sbjct: 141 KTL----FPRVKICHDTGKSAISDYQVISRLDNPRRTLVQYTPITGRTHQLRIHSLEFGH 196

Query: 265 PIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR 304
           PI+G   Y     G+   T  I  +L LHA  +   HP  G 
Sbjct: 197 PILGCDLYNDPQLGSHHETIDIPQRLMLHASDIYFTHPTTGE 238


>gi|50083937|ref|YP_045447.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. ADP1]
 gi|49529913|emb|CAG67625.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter sp.
           ADP1]
          Length = 219

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/180 (35%), Positives = 95/180 (52%), Gaps = 22/180 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           ++YED  + V +KPAG+ SV G   +  H D    +++  + Q P  R+THRLD  TSG+
Sbjct: 16  MVYEDDDLIVIDKPAGLLSVMGR--LPEHQDS---AYLRIRQQYPLARVTHRLDMATSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A+ R A   +++ F+ R IQK Y +LV G      E  A  +++   I  D+ +  K
Sbjct: 71  LMFAKHRRAEIAISKLFQTRCIQKYYIALVDG------EVQAQGMVEAPLI-TDWPNRPK 123

Query: 218 Q-----NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           Q       K A            F Q    ++++P TGR+HQLRVH  H+G PI+GD  Y
Sbjct: 124 QKIDFVEGKAAKTCYQPLDYNAAFNQ--TRIQLEPITGRSHQLRVHMQHIGHPIMGDKLY 181


>gi|324992871|gb|EGC24791.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK405]
 gi|325696535|gb|EGD38425.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK160]
 gi|327460322|gb|EGF06659.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1057]
          Length = 295

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 113/228 (49%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    V +KPAG++       +  +  F+K++      + Q+  +  RLD++TSG+
Sbjct: 78  VVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAYENQQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    + + E IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +   YA + +KVI+     +  +++  HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVTEDGKYAHTSYKVIERIGDVYL-VDIHLHTGRTHQIRVHFSHIGFPLLGDDLYG-- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             G+    I+ +  LH   +   +P  G  ++  +PLP    +  + L
Sbjct: 249 --GSLEYGIERQA-LHCHSLKFYNPFSGQEVERASPLPEDFKQVIEKL 293


>gi|154509032|ref|ZP_02044674.1| hypothetical protein ACTODO_01549 [Actinomyces odontolyticus ATCC
           17982]
 gi|153798666|gb|EDN81086.1| hypothetical protein ACTODO_01549 [Actinomyces odontolyticus ATCC
           17982]
          Length = 301

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/252 (27%), Positives = 117/252 (46%), Gaps = 28/252 (11%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR- 145
           +K +      +LY+D  I V +KP G++   G G     + G L++    + S G   R 
Sbjct: 65  SKPTPVTDMAILYDDEDIVVVDKPVGVAAHTGPGWEGPTVLGNLEAAGYRITSYGPPERQ 124

Query: 146 -LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HRLD  TSG ++VA++  A   +  +F+ R I+K+Y ++V G        I   + +
Sbjct: 125 GIVHRLDVGTSGAMMVAKSELAYTVMKRAFKERTIEKVYHAVVAGHLDPASGTIDAPIGR 184

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             H   ++   V     G   A++H+  ++  A      E+   TGRTHQ+RVH   +G 
Sbjct: 185 --HPSREWRMAVID---GGKRAVTHYDTLELMAGAQL-TEVHLETGRTHQIRVHMAAVGH 238

Query: 265 PIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           P VGD  Y A+       P Q       + +LHA  +   HP  G  + +++P P  +  
Sbjct: 239 PCVGDTFYGAD-------PTQAERLGLTRQWLHAVRLGFAHPRTGMPMSVSSPYPDDLAD 291

Query: 318 TWDSLGFKYDRN 329
             + L  ++ RN
Sbjct: 292 ALEEL--RHPRN 301


>gi|91791480|ref|YP_561131.1| pseudouridine synthase RluA-like protein [Shewanella denitrificans
           OS217]
 gi|91713482|gb|ABE53408.1| Pseudouridine synthase RluA-like protein [Shewanella denitrificans
           OS217]
          Length = 226

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 60/202 (29%), Positives = 98/202 (48%), Gaps = 23/202 (11%)

Query: 101 LLYEDSKIYVFNKPAGI---SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++ ++S   V +K AG+   S  G +G+   ++  L       G K    HRLD  TSG+
Sbjct: 4   IISDESDFIVIDKYAGVHFHSQDGSAGVVAQLEADL-------GIKLFAVHRLDTPTSGL 56

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+   AA+  TE F   ++QK Y ++  G PK K+  +   + K          +++
Sbjct: 57  LILAKNPLAARRFTEMFTEHKVQKYYLAIAQGKPKKKQGWVIGDMAKARR---SMFKLLR 113

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E   N A++ F           +L ++PH+G+THQLRV    +G PI+GD  Y  N  
Sbjct: 114 STE---NPAVTQFFSHSIVEGLRLYL-LKPHSGKTHQLRVALASIGVPILGDKLYGVN-- 167

Query: 278 GNFTSPIQNKLYLHARYMDLPH 299
               S   ++ YLHA  +D  +
Sbjct: 168 ----SAEHDRCYLHAYCLDFSY 185


>gi|327402055|ref|YP_004342893.1| pseudouridine synthase [Fluviicola taffensis DSM 16823]
 gi|327317563|gb|AEA42055.1| pseudouridine synthase [Fluviicola taffensis DSM 16823]
          Length = 561

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/231 (30%), Positives = 114/231 (49%), Gaps = 21/231 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H++ E + +D +  L   ++     +++ED  I + NKPA      G  I+  +   +
Sbjct: 333 LGHMLGETE-MDENPMLLNPAENKDLEIVFEDDYIVIVNKPAEFLSVPGKSISDSVYTRM 391

Query: 134 KS-WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           K  +  + G  P + HRLD  TSG+LV+A+ +   +HL + F  R +QK Y +L+ GI  
Sbjct: 392 KEKYPHATG--PLIVHRLDMSTSGLLVIAKDKIVHKHLQKQFIKRNVQKRYVALLEGIIS 449

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +   I   L        D    +   E G   A++ ++VI+    +   +   P TGRT
Sbjct: 450 ERLGTIDLPLRVDL---DDRPRQLVCYEHGKR-AVTKWEVIEHRNNQ-TLIYFYPITGRT 504

Query: 253 HQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           HQLRVHA H   +  PI+GD  Y     GN  +    +L+LHA+++   HP
Sbjct: 505 HQLRVHAAHTLGLNAPILGDDLY-----GNRAT----RLHLHAQFLQFTHP 546


>gi|153828997|ref|ZP_01981664.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           623-39]
 gi|148875528|gb|EDL73663.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           623-39]
          Length = 221

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/205 (32%), Positives = 96/205 (46%), Gaps = 22/205 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NKPA      G  +   +   LK+   ++ +     HRLD  TSG+LV 
Sbjct: 20  IVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-TQAEGVFALHRLDMSTSGLLVF 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A TR A + L + F  R IQK Y +L+ G     +  I      +  + GD     +Q  
Sbjct: 79  ALTRRANKQLQKQFISRAIQKRYVALIEGKLSETQGEI------QLPLCGDLDDRPRQKV 132

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
             +    A++H++ +    Q    + + PHTGRTHQLRVH  H   +  PIVGD  Y   
Sbjct: 133 CWQQGKPALTHWETVQV-EQNRTRVYLYPHTGRTHQLRVHCAHHLGLNAPIVGDDLYGLQ 191

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
            K         +L+LHA  +   HP
Sbjct: 192 DK---------RLFLHAEQLSFAHP 207


>gi|256820360|ref|YP_003141639.1| pseudouridine synthase [Capnocytophaga ochracea DSM 7271]
 gi|256581943|gb|ACU93078.1| pseudouridine synthase [Capnocytophaga ochracea DSM 7271]
          Length = 215

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 108/222 (48%), Gaps = 21/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +   NK  G  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 1   MLYEDNHVIAVNKRVGDIVQGDKTGDTPLSDIVKQYLKQKYNKPGEVFLGVVHRLDRPTT 60

Query: 156 GILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDY 212
           G+++ A+T  A   L   F  ++ +QK YW+LV   P  +++ + +WL++  K +    Y
Sbjct: 61  GVVLFAKTSKALARLNTMFANKQEVQKTYWALVDAKPPVEEDTLTHWLVRNEKQNKSVAY 120

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              ++ ++K    A+ H+K++  + +++  LE+   TGR HQ+R     +   I GD KY
Sbjct: 121 NKEMQHSKK----AVLHYKLLKSY-ERYYLLEIDLITGRHHQIRAQLAAIELHIKGDLKY 175

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP---EGGRLQITAPL 311
            A       S     + LHA  +   HP   E  ++   AP 
Sbjct: 176 GAK-----RSNPDGGICLHAYSLSFVHPVKKEPTKIIAEAPF 212


>gi|242279048|ref|YP_002991177.1| pseudouridine synthase, RluA family [Desulfovibrio salexigens DSM
           2638]
 gi|242121942|gb|ACS79638.1| pseudouridine synthase, RluA family [Desulfovibrio salexigens DSM
           2638]
          Length = 549

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 107/237 (45%), Gaps = 21/237 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++Y D KI V NKPAG++           + + +        D    +P + HRLD+ TS
Sbjct: 96  IIYNDGKIAVINKPAGLTTHPAPSCPTGTLVHRMIHHFPEIRDMDEWRPGIVHRLDKFTS 155

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++ VA        ++ +F  R + K Y ++V G+PK +   I         +G   VH 
Sbjct: 156 GLITVALNEHDRLAMSTAFADREVNKAYLAIVHGVPKREFGEI------DQPMGRHPVHK 209

Query: 216 VKQNE--KGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            K     KG   A S ++V+    A +   ++++ +TGRTHQ+RVH  H+G P+VGD  Y
Sbjct: 210 TKMAVVLKGGRDARSEYEVLWSDPAGRASLVKVKIYTGRTHQIRVHMAHIGHPLVGDQVY 269

Query: 273 CANFKGNFT------SPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
            +     +       + +  +  LHA  +   HP+    L  T   P   +    +L
Sbjct: 270 GSMPHAIWEQDQPQLAKLAERQMLHAYSLSFTHPDSEEELSFTQAPPEDFINMLKAL 326


>gi|78044542|ref|YP_359965.1| ribosomal large subunit pseudouridine synthase A [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77996657|gb|ABB15556.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Carboxydothermus hydrogenoformans Z-2901]
          Length = 301

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 80/292 (27%), Positives = 126/292 (43%), Gaps = 54/292 (18%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQS-GQVV-----RIPPVINALNHIIKEQKILDSSVNL 90
           L+K+     V  + + V  N+ + + G+VV      +PP + + N  +K           
Sbjct: 30  LRKLKLQNAVFFNNRPVPLNSHLTTPGEVVIKLPHTLPPAVQSQNAPVK----------- 78

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQ-----KP 144
                     +LYED  + V +KPAG+         A  +     S+   KG+      P
Sbjct: 79  ----------VLYEDDYLIVIDKPAGVLAHPVKNHFAPSMQELTLSYYRDKGRIFEGFYP 128

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW--- 201
              +RLD+ TSG +++A+    A+ L  S R R+I KIY +L+ G P   K  I N    
Sbjct: 129 --IYRLDRNTSGPMLIAKFSLIAEMLNNSLRKRQINKIYLALIEG-PLADKSGIINLPLG 185

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           LL+ S I    V        G   A + ++ +  F      L+++  TGRTHQ+R H   
Sbjct: 186 LLEGSIIKRAVV-------PGGQPACTKYQTVKAFPTH-TLLKVELLTGRTHQIRAHFAA 237

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +G P+ GD  Y           +  +  LH  Y+  PHP   + + + APLP
Sbjct: 238 IGHPLAGDDLYGGKMD------LIERQALHLYYISFPHPITKKTISLYAPLP 283


>gi|293192338|ref|ZP_06609449.1| ribosomal large subunit pseudouridine synthase D [Actinomyces
           odontolyticus F0309]
 gi|292820253|gb|EFF79247.1| ribosomal large subunit pseudouridine synthase D [Actinomyces
           odontolyticus F0309]
          Length = 301

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/252 (27%), Positives = 117/252 (46%), Gaps = 28/252 (11%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR- 145
           +K +      +LY+D  I V +KP G++   G G     + G L++    + S G   R 
Sbjct: 65  SKPTPVTDMAILYDDEDIVVVDKPVGVAAHTGPGWEGPTVLGNLEAAGYRITSYGPPERQ 124

Query: 146 -LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HRLD  TSG ++VA++  A   +  +F+ R I+K+Y ++V G        I   + +
Sbjct: 125 GIVHRLDVGTSGAMMVAKSELAYTVMKRAFKERTIEKVYHAVVAGHLDPASGTIDAPIGR 184

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             H   ++   V     G   A++H+  ++  A      E+   TGRTHQ+RVH   +G 
Sbjct: 185 --HPSREWRMAVID---GGKRAVTHYDTLELMAGAQL-TEVHLETGRTHQIRVHMAAVGH 238

Query: 265 PIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           P VGD  Y A+       P Q       + +LHA  +   HP  G  + +++P P  +  
Sbjct: 239 PCVGDTFYGAD-------PTQAERLGLTRQWLHAVRLGFAHPRTGMPMSVSSPYPDDLAD 291

Query: 318 TWDSLGFKYDRN 329
             + L  ++ RN
Sbjct: 292 ALEEL--RHPRN 301


>gi|229817354|ref|ZP_04447636.1| hypothetical protein BIFANG_02616 [Bifidobacterium angulatum DSM
           20098]
 gi|229785143|gb|EEP21257.1| hypothetical protein BIFANG_02616 [Bifidobacterium angulatum DSM
           20098]
          Length = 314

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 80/303 (26%), Positives = 139/303 (45%), Gaps = 41/303 (13%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++ +GQVRV  + +  +  +Q+G+ V I         +++E+K  +   N          
Sbjct: 34  LIDTGQVRVLDREITKSTTLQAGETVEI--------DLVEERKEPEPIAN--------DM 77

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD------SKGQKPR--LTHRLD 151
            ++YED  + V +KP G++     G  +     L S +D      + G   R  +  RLD
Sbjct: 78  AIVYEDDDVVVVDKPVGVAAHASVG--WTGPTVLGSLLDRGVHITAYGAAGRQGIVSRLD 135

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-- 209
             TSG+++V ++  A   +   F    + K Y +LV G  K  +  I      ++ IG  
Sbjct: 136 VGTSGLMLVCKSDLAYVEMRRQFAEHEVVKTYHALVQGNLKEDRATI------EAPIGRA 189

Query: 210 --GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              D+   V    K    AI+H+ V++ F  +   +++   TGRTHQ+RVH   +G P+V
Sbjct: 190 KVSDFRFCVTPAGK---PAITHWDVMERFGSEATLVKVNLETGRTHQIRVHFSSIGHPLV 246

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           GDH Y AN        I+ + +LHA  ++  HP       +T+  PA +    D++  ++
Sbjct: 247 GDHMYGANPVLAEDLNIERQ-WLHAMQLEFRHPRTHVWTTVTSSYPADLAHALDAMRARH 305

Query: 327 DRN 329
             N
Sbjct: 306 ADN 308


>gi|15827611|ref|NP_301874.1| pseudouridine synthase [Mycobacterium leprae TN]
 gi|221230088|ref|YP_002503504.1| putative pseudouridine synthase [Mycobacterium leprae Br4923]
 gi|4539134|emb|CAB39580.1| putative pseudouridine synthase [Mycobacterium leprae]
 gi|13093162|emb|CAC31581.1| putative pseudouridine synthase [Mycobacterium leprae]
 gi|219933195|emb|CAR71295.1| putative pseudouridine synthase [Mycobacterium leprae Br4923]
          Length = 308

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 77/313 (24%), Positives = 138/313 (44%), Gaps = 30/313 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MR+D         ++   +  +   G V +D  +   ++R+ SG  +++          
Sbjct: 14  GMRVDAGLARLL-GLSRTAVAALAEDGGVELDGVQAGKSDRLTSGAWLQV---------- 62

Query: 78  IKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKS 135
               ++ ++   L     D     +LY D  I   +KPA ++     G A   + G L +
Sbjct: 63  ----RLCEAPAPLENTPVDIEDMTILYSDDDIVAVDKPAAVAAHASVGWAGPTVLGGLAA 118

Query: 136 W---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
               + + G   R  + HRLD  TSG+++VA +  A   L  +F+ R + K Y +LV G 
Sbjct: 119 AGYRITTSGVPERQGIVHRLDVGTSGVMLVAISERAYTVLKRAFKCRTVDKRYHALVQGH 178

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +  H G  +   V ++ +   ++I+H+  ++ F      L++   TG
Sbjct: 179 PDPSSGTIDAPIGR--HRGHTWKFAVTKDGR---HSITHYDTLEAFVAA-SLLDVHLETG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+R H   +  P  GD  Y A+ K      ++ + +LHAR +   HP +G R++I +
Sbjct: 233 RTHQIRAHFAELHRPCCGDLVYGADPKLAKRLGLERQ-WLHARSLSFAHPADGRRVEIVS 291

Query: 310 PLPAHMVKTWDSL 322
             P  +    D L
Sbjct: 292 SYPPDLQHALDVL 304


>gi|91794398|ref|YP_564049.1| pseudouridylate synthase [Shewanella denitrificans OS217]
 gi|91716400|gb|ABE56326.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           denitrificans OS217]
          Length = 225

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/205 (29%), Positives = 99/205 (48%), Gaps = 21/205 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  + V NKP+G+    G   A H D  + S V ++     + HRLD  TSG++VV
Sbjct: 16  ILHQDKDVLVVNKPSGLLSVPGRDPA-HSDS-IYSRVLAQFPNAHIVHRLDMATSGVMVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKK---ECIANWLLKKSHIGGDYVHV 215
           A  R+A + L   F  R  +K+Y++ V G   P + +     I +W  +           
Sbjct: 74  ALRRSAERELKRQFHDRETKKVYYARVAGHLSPVHTRVDLPLICDWPNRPKQ-------- 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K + K    + +  K+I  + ++   +++ P TGR+HQLRVH + +G PI+GD  Y   
Sbjct: 126 -KVDHKLGKPSSTLVKII-SYGKRSTLVKLSPITGRSHQLRVHMMALGHPILGDGFYADA 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                      +L LHA  +   HP
Sbjct: 184 LAKRLAP----RLLLHAAELTFCHP 204


>gi|109897688|ref|YP_660943.1| pseudouridine synthase Rlu family protein [Pseudoalteromonas
           atlantica T6c]
 gi|109699969|gb|ABG39889.1| pseudouridine synthase Rlu family protein, TIGR01621
           [Pseudoalteromonas atlantica T6c]
          Length = 238

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/207 (33%), Positives = 103/207 (49%), Gaps = 22/207 (10%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAA 166
            +V +KP GISVQ          G L      +   K  L HRLD+ TSG+L++A+   A
Sbjct: 18  FFVIDKPHGISVQN----ELDAQGILPVVCAQQAVDKLWLVHRLDKVTSGLLILAKHAQA 73

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           A  L + F  R I+K Y +L    PK K+  I+  + K     G +      ++ GA  A
Sbjct: 74  ASTLGKLFETRAIEKYYLALGGSKPKKKQGTISGAMKKIRD--GKWAF----SQDGAGIA 127

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
            + F      A    +L ++P TG+THQLRV    +GCPI+GD    A +KG      Q+
Sbjct: 128 TTQFFSKSASAGIRLFL-LKPLTGKTHQLRVMLKSLGCPILGD----ALYKGTE----QD 178

Query: 287 KLYLHARYMDLPHPEGGRLQITAPLPA 313
           + YLHA  +   + +G  +Q+T  LP+
Sbjct: 179 RTYLHAYCLRFEY-QGQLIQLTC-LPS 203


>gi|262172099|ref|ZP_06039777.1| tRNA pseudouridine synthase C [Vibrio mimicus MB-451]
 gi|261893175|gb|EEY39161.1| tRNA pseudouridine synthase C [Vibrio mimicus MB-451]
          Length = 244

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 63/217 (29%), Positives = 103/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEAD--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  AI+ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAITAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLILHASELRFVHP 211


>gi|260891446|ref|ZP_05902709.1| pseudouridylate synthase [Leptotrichia hofstadii F0254]
 gi|260858829|gb|EEX73329.1| pseudouridylate synthase [Leptotrichia hofstadii F0254]
          Length = 328

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 73/298 (24%), Positives = 140/298 (46%), Gaps = 45/298 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR----------- 58
           VVV ++ E MRLDR+ + ++       +   +RSG V+++ K+ K N R           
Sbjct: 10  VVVHSEMEGMRLDRYLRKNFKDEPLSRIFGAIRSGDVKINGKKSKENYRLLLNDKITIRN 69

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           + +G   +I  ++N   + IKE KIL+   +L K+    K ++++E+   ++ NK   + 
Sbjct: 70  LSTGNTEKIGEIVNT--YKIKELKILEK--DLEKY----KKMVIFENDDFFIVNKKEKVP 121

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           +  G+G  Y +    K     K       +RLD ETSG+++  +T    +++++  R   
Sbjct: 122 MHKGTGHKYGLAEVFKKIY--KSDNINFANRLDFETSGLVIGCKTLKFLRYISQKIRDNE 179

Query: 179 IQKIYWSLVWG---IPKNKKE----CIANWLLKKSHIGGDYVHVVKQN--EKGANYAISH 229
           + K Y+++V     I +NK E     + ++ ++      +   +V +N   + +  +I++
Sbjct: 180 VHKKYFAVVHNKNIIRRNKLEREKFNLEDFKIENYLTTLENKVIVSENPVSRESKKSITY 239

Query: 230 FK------------VIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           FK            ++  F    +    L+++  TGR HQ+R    H    IVGD KY
Sbjct: 240 FKHVNFNKLKKSKEILKLFEKNNKNILLLDVELITGRKHQIRAQLAHESLFIVGDKKY 297


>gi|153815705|ref|ZP_01968373.1| hypothetical protein RUMTOR_01942 [Ruminococcus torques ATCC 27756]
 gi|317501908|ref|ZP_07960092.1| RluA family Pseudouridine synthase [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|145846946|gb|EDK23864.1| hypothetical protein RUMTOR_01942 [Ruminococcus torques ATCC 27756]
 gi|316896588|gb|EFV18675.1| RluA family Pseudouridine synthase [Lachnospiraceae bacterium
           8_1_57FAA]
          Length = 295

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 79/314 (25%), Positives = 147/314 (46%), Gaps = 34/314 (10%)

Query: 12  VENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           + +  +N+R+D + + H Y   N   L+K+  S  +  + +       +Q+G ++ +   
Sbjct: 9   ITDSGQNIRIDSFLRKHGYSMQNLTLLKKMPES--ILKNGEWSYMQTTLQAGDILTVR-- 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                  I+E+    SS N+   +  L   ++YED  I V NK AG+ +        +  
Sbjct: 65  -------IQEET---SSPNIPAVN--LPIDIVYEDEDIIVINKAAGMPIHPSLNNYRNSL 112

Query: 131 GFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                W   +  KP   R T+RLD++TSG+ VVA+   ++  L+      +I++ Y ++V
Sbjct: 113 ANALMWYYEQQNKPFIFRCTNRLDRDTSGLTVVAKHMVSSNILSSMTARHQIEREYLAIV 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQ 246
            G      E   N  + ++   G  +   K + +   +AI+H+  +  F +     + + 
Sbjct: 173 RG-HVTPFEGTINAPIGRT---GSSLIERKIDFENGEHAITHYHTV--FEKNGLSLVSLI 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  H+G P++GD+ Y  + +      + ++  LH+  +   HP  GR +
Sbjct: 227 LETGRTHQIRVHMKHLGFPLIGDYLYNPDME------LIDRQALHSHCLRFLHPITGRQM 280

Query: 306 QITAPLPAHMVKTW 319
             TA LP  M + +
Sbjct: 281 TFTADLPEDMARLF 294


>gi|229525503|ref|ZP_04414908.1| tRNA pseudouridine synthase C [Vibrio cholerae bv. albensis VL426]
 gi|229339084|gb|EEO04101.1| tRNA pseudouridine synthase C [Vibrio cholerae bv. albensis VL426]
          Length = 245

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 104/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASDVMPMFANHEMEKTYHAIVRGWIEEAN--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAVTAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFMHP 211


>gi|257061765|ref|YP_003139653.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8802]
 gi|256591931|gb|ACV02818.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8802]
          Length = 306

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/264 (26%), Positives = 120/264 (45%), Gaps = 29/264 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PP 69
           V   +  + +  ++   YPH +    Q+ + SGQ+ ++ +    +  +Q GQ +    PP
Sbjct: 12  VNPSDAGLTILAYYTQRYPHSSQGQWQERIISGQILLNGQPTTPDTPLQPGQCLSYHRPP 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                    +E  +             L   +LYED  + V  KP+G+ V  G G   H 
Sbjct: 72  --------WQEPDVP------------LAFEVLYEDVDVLVVAKPSGLPVLPGGGFLEHT 111

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           + G LK       + P   HRL + TSG++++AR+  AA HL++  R  ++ K+Y +LV 
Sbjct: 112 LLGQLKRLYPQ--ETPTPIHRLGRGTSGLMLLARSPLAASHLSKQMRQGQMTKVYHALVG 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
                 +  I   + K  H    YV+    +     +A S  +V+    Q    +E++  
Sbjct: 170 AGDLPHQFSIHQPIGKIPHPVLGYVYGATPD---GLFAHSDCRVLQRSTQG-TLVEVRIF 225

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGR HQ+R+H   +G P++GD  Y
Sbjct: 226 TGRPHQIRIHLASVGYPLLGDPLY 249


>gi|308810719|ref|XP_003082668.1| COG0564: Pseudouridylate synthases, 23S RNA-specific (ISS)
           [Ostreococcus tauri]
 gi|116061137|emb|CAL56525.1| COG0564: Pseudouridylate synthases, 23S RNA-specific (ISS)
           [Ostreococcus tauri]
          Length = 390

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/277 (24%), Positives = 121/277 (43%), Gaps = 37/277 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHI--NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           + VVV++  +   + R      P       + ++  R   +  + + V   +R+ SG V+
Sbjct: 28  ETVVVDDARDGDTVSRTLAVMLPKTFPTATSAKRACRRKTIARNGEIVGSGDRVASGDVL 87

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSG 124
            +      L   +  +      + L K     K ++LYED+   +  KP   +  G GSG
Sbjct: 88  EV------LTRNVPGRGAR-GELGLEKERGARKMVVLYEDAHAAIAVKPDDCATIGPGSG 140

Query: 125 IAYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             +  +  L    +          KP+  HRLD+ T GILV A+TR     L+ +F  R 
Sbjct: 141 GGWSAERMLAISCEVSAADFGVLTKPKPCHRLDEPTGGILVCAKTREGLTTLSSAFASRE 200

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y +++ G             L+K+        VV     G + +  +  V+   ++
Sbjct: 201 VKKRYRAILRG------------RLEKTS------GVVDAPVSGRDASTEYAVVLTRESE 242

Query: 239 KFCWLEMQ---PHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++  L +    P TGRTHQLR H++ +G PI+GD +Y
Sbjct: 243 RYGTLTLVDFFPRTGRTHQLRRHSVALGAPILGDVRY 279


>gi|145629453|ref|ZP_01785251.1| tRNA pseudouridine synthase C [Haemophilus influenzae 22.1-21]
 gi|144978296|gb|EDJ88060.1| tRNA pseudouridine synthase C [Haemophilus influenzae 22.1-21]
 gi|309750918|gb|ADO80902.1| tRNA U65 pseudouridine synthase [Haemophilus influenzae R2866]
          Length = 239

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 110/243 (45%), Gaps = 27/243 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY-------CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +Y          F   F+     +L+LH+  +   HP +  ++ ITA L     +  +  
Sbjct: 180 QYGDLHQNRALTFHLGFS-----RLFLHSNSLSFIHPIKKEQITITAGLDEQWQQLMNQF 234

Query: 323 GFK 325
           G++
Sbjct: 235 GWE 237


>gi|124267382|ref|YP_001021386.1| ribosomal large subunit pseudouridine synthase A [Methylibium
           petroleiphilum PM1]
 gi|124260157|gb|ABM95151.1| ribosomal large subunit pseudouridine synthase A [Methylibium
           petroleiphilum PM1]
          Length = 213

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/222 (31%), Positives = 106/222 (47%), Gaps = 29/222 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSG------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           LY D  + V +KP G+    G G      +A  +    ++W D+     R+ HRLD+ TS
Sbjct: 9   LYRDEALLVVDKPPGLLAVPGRGPLKQDCLAARVQ---RAWPDA-----RVVHRLDEATS 60

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A      + L+ +F  R ++K Y ++V G      E  A  +     +G D+ + 
Sbjct: 61  GLMVFALDVEMQRRLSRAFEQREVEKRYVAVVAG----HVEPAAGRI--DLPLGADWPNR 114

Query: 216 VKQ--NEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +Q  +      A +H++V+    +     LE+ P TGRTHQLRVH + +G  I+GD  Y
Sbjct: 115 PRQQVDHARGKPARTHWQVLSYDTSGDSTRLELTPETGRTHQLRVHLMAIGHAILGDALY 174

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR--LQITAPLP 312
            A       SP   +L LHA  +   HP  GR  L   +P P
Sbjct: 175 -APPSMMARSP---RLLLHASALAFAHPMPGRPALAFESPPP 212


>gi|218767409|ref|YP_002341921.1| putative psedouridine synthase [Neisseria meningitidis Z2491]
 gi|121051417|emb|CAM07710.1| putative psedouridine synthase [Neisseria meningitidis Z2491]
          Length = 220

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/218 (31%), Positives = 103/218 (47%), Gaps = 33/218 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-------IAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +L+        NKP GISV   SG       +A  + G  + W         L HRLD++
Sbjct: 6   ILFRHQDFVAINKPGGISVHQDSGETRLARTLAIQL-GVERVW---------LLHRLDKQ 55

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGIL+ A  R +A  L+  F  + I+K Y +L    P  K+  I   + +KS  G    
Sbjct: 56  TSGILLFALNRESASALSGQFVGKSIKKTYLALSDRKPSKKQGWIKGGM-EKSRCG---- 110

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + K      N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y 
Sbjct: 111 -MWKLTRNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLY- 167

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
               G   S     ++L+A  +   + +  +++I APL
Sbjct: 168 ----GGTES---ETMFLYAWKIQFDY-QNRQIEIVAPL 197


>gi|237715778|ref|ZP_04546259.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D1]
 gi|262408787|ref|ZP_06085333.1| conserved hypothetical protein [Bacteroides sp. 2_1_22]
 gi|229444487|gb|EEO50278.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D1]
 gi|262353652|gb|EEZ02746.1| conserved hypothetical protein [Bacteroides sp. 2_1_22]
          Length = 615

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 77/262 (29%), Positives = 114/262 (43%), Gaps = 76/262 (29%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ED  + V NKPAG +SV G +      YH     K + ++ G  P + HRLD  TSG
Sbjct: 347 IVFEDEWLLVVNKPAGMLSVPGKAEDRDSVYH--RLKKKYPEATG--PMIVHRLDMATSG 402

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNK-------------KECIANW 201
           +L+VA+T+   Q L   F  R I+K Y +++ G  I   K             KE ++  
Sbjct: 403 LLLVAKTKEVHQDLQAQFANRSIKKRYVAVLDGAIIKTEKETKPIAEKAILLAKETVSTK 462

Query: 202 LLKKSHIGG--------------DYVHVVKQNEKGANYAISHFKVI-----------DCF 236
              K+   G              D    +   E G   AI+ +++I           + F
Sbjct: 463 KTAKAERTGNTGRIELPLCLNPLDRPRQMVSREHGKE-AITEYQIISESERITSESENTF 521

Query: 237 ---------------AQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKG 278
                          ++K+  +   P TGRTHQLRVHA H   +GCPI+GD  Y      
Sbjct: 522 NESNRIDESERSINESRKYTRIIFYPLTGRTHQLRVHAAHPEGLGCPILGDELYGKK--- 578

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                  ++LYLHA Y++  HP
Sbjct: 579 ------ADRLYLHAEYIEFRHP 594


>gi|50085931|ref|YP_047441.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter sp. ADP1]
 gi|49531907|emb|CAG69619.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter sp. ADP1]
          Length = 350

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 112/235 (47%), Gaps = 21/235 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGI 157
           ++YED  I V NKPAG+ V  G+G      ++  L  +  + +  +  L HR+D++TSG+
Sbjct: 117 IVYEDQDILVINKPAGMVVHPGAGNPSGTLVNALLYHYPKAVELSRAGLVHRIDKDTSGL 176

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LVVA+   A   L++    + + +IY  +V+G        IA   + +  I    V  +K
Sbjct: 177 LVVAKNLEAQFSLSKQLADKSVYRIYDLVVYG------NIIAGGTIDE-QIKRHPVDRIK 229

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                G   A++H+ V + F Q F  ++ Q  TGRTHQ+RVH  ++G  +VGD  Y +  
Sbjct: 230 MAILPGGREAVTHYNVKERF-QHFTRVQAQLETGRTHQIRVHFSYIGHGLVGDPVYMSRV 288

Query: 277 K--GNFTSPIQNKL------YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           +     +  +   L       LHA  + L HP     +   AP P    +  + L
Sbjct: 289 RVPAGASERLGQTLRGFKRQALHASKLGLVHPRTQEEMMFEAPWPEDFTQLLEVL 343


>gi|313634007|gb|EFS00696.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri FSL N1-067]
          Length = 296

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 75/312 (24%), Positives = 141/312 (45%), Gaps = 38/312 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  + L  + ++ +     +   K    G++ V+         +Q+G  VR+    
Sbjct: 7   VNKEDSGLLLRTFLRSKHISKQLLTAVKFSVDGKIEVNGTEQNVLYEVQTGDEVRLTFPT 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              N  +           L +H+D     +++ED  + + NKPAGI+        YH  G
Sbjct: 67  EQQNERL-----------LAEHTDLE---IVFEDEFLLIINKPAGIASIPSQ---YHPSG 109

Query: 132 FLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + ++V    +   LT       RLD+ETSG++++A+ R A   L+   +   +++ Y +
Sbjct: 110 SVANFVKGHYEAQGLTSAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQQGLLKRSYQA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
            V G    +   I      ++ IG   V ++++       YA ++++V+  + Q F  + 
Sbjct: 170 FVSGELAEQVGSI------EAPIGRKAVSIMERVVTPEGKYAKTNYQVLARY-QAFDHVA 222

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP    
Sbjct: 223 IQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TDLLKRQALHSCHLHLIHPLTEE 276

Query: 305 -LQITAPLPAHM 315
            L    PLP  M
Sbjct: 277 YLAFDLPLPYDM 288


>gi|229530008|ref|ZP_04419398.1| tRNA pseudouridine synthase C [Vibrio cholerae 12129(1)]
 gi|229333782|gb|EEN99268.1| tRNA pseudouridine synthase C [Vibrio cholerae 12129(1)]
          Length = 244

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 104/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASDVMPMFANHEMEKTYHAIVRGWIEEAD--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAVTAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFMHP 211


>gi|169346799|ref|ZP_02865750.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
 gi|169297081|gb|EDS79203.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
          Length = 298

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 82/301 (27%), Positives = 138/301 (45%), Gaps = 52/301 (17%)

Query: 39  KILRSG----QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++RS     +++VD   VK N  +++G+ ++I        +I  E+  ++         
Sbjct: 30  RLIRSAAIDKRIKVDGVSVKMNYVVKTGEEIKIELSKKESQNIEPEKMDIE--------- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPR 145
                 ++YEDS I V NK   + V            +GI Y+   F +S  D      R
Sbjct: 81  ------IVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYY---FKESNQDCI---VR 128

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L  RLD  TSG++++ + + A   L+   +  + QK Y ++V G  + K+  I   + + 
Sbjct: 129 LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRP 188

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHM 262
           +    D +  V  +E+G   +I+H+KVI+ +       C LE    TGRTHQ+RVH   +
Sbjct: 189 AE---DTIKRV-VDERGQE-SITHYKVIESYNGADLVECLLE----TGRTHQIRVHLSSL 239

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           G PI GD  Y     G       ++  LHA  +D   P+  + L + A LP  M +  + 
Sbjct: 240 GHPIFGDSLY-----GTEDEEFISRQALHAYGLDFYSPKTKKPLSLRADLPEDMKELINK 294

Query: 322 L 322
           L
Sbjct: 295 L 295


>gi|148653020|ref|YP_001280113.1| pseudouridine synthase [Psychrobacter sp. PRwf-1]
 gi|148572104|gb|ABQ94163.1| tRNA pseudouridine synthase C [Psychrobacter sp. PRwf-1]
          Length = 256

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 102/226 (45%), Gaps = 37/226 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLT---------- 147
           ++YED  +   NK AG+ V              +SW+D KG+     +LT          
Sbjct: 17  IIYEDEHLVAINKEAGLLVH-------------RSWLD-KGETRFAMQLTRDAVGCHVFP 62

Query: 148 -HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ TSG+L+ A++ A A+ LTE+F  R++ K Y ++V G    +         K  
Sbjct: 63  VHRLDRPTSGVLLFAKSAAVARSLTEAFTERKVTKRYLAVVRGFMTEQGSVDYALSFKPD 122

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFA-------QKFCWLEMQPHTGRTHQLRVHA 259
            I   + ++ K  ++   +  S  ++   FA        ++  + + P TGR HQLR H 
Sbjct: 123 AIADKFANLDKPAQEAVTHWQSLAQIELPFAVSKKHDTSRYSLMRLIPETGRKHQLRRHM 182

Query: 260 LHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG 303
            H+   I+GD  Y       F  T     ++ LHA+ + L HP  G
Sbjct: 183 RHLFHHIIGDTSYGDGRHNKFFRTQYDCTRMLLHAQTLSLTHPVTG 228


>gi|166154327|ref|YP_001654445.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 434/Bu]
 gi|166155202|ref|YP_001653457.1| tRNA pseudouridine synthase A [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|301335578|ref|ZP_07223822.1| tRNA pseudouridine synthase A [Chlamydia trachomatis L2tet1]
 gi|165930315|emb|CAP03801.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 434/Bu]
 gi|165931190|emb|CAP06755.1| tRNA pseudouridine synthase A [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
          Length = 274

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/258 (25%), Positives = 119/258 (46%), Gaps = 43/258 (16%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINAL 74
           + ++RL  + +   PH+    + + +R    RV+ +  +F + ++Q G  V         
Sbjct: 9   DRHIRLSSFLRTSLPHLPKKTILESVRYHGCRVNGRIERFESYKLQPGDRV--------- 59

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                       S+ + +HS      LL+ED  + ++NKPA    Q    +A+ ++    
Sbjct: 60  ------------SLQIIEHSS---PQLLWEDEHLCIYNKPAK---QTSEDLAHQLNV--- 98

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                      L HRLD++TSG ++ A+   A+  +T+ F+ R I K Y +LV+G P+ +
Sbjct: 99  ----------HLVHRLDRDTSGCILFAKHAKASSLITQLFKNREIDKRYIALVFGQPRQE 148

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I  +        G  V     ++      I+ ++++  +  K+  L  +P TGRTHQ
Sbjct: 149 SGIITTYTAPCYRRTGA-VLFGNTDQNSGKITITKWEILTRYP-KYTLLLCRPVTGRTHQ 206

Query: 255 LRVHALHMGCPIVGDHKY 272
           +R+H   +G PIVGD  Y
Sbjct: 207 IRLHMKTIGHPIVGDVDY 224


>gi|323497826|ref|ZP_08102840.1| 23S rRNA pseudouridine synthase D [Vibrio sinaloensis DSM 21326]
 gi|323317173|gb|EGA70170.1| 23S rRNA pseudouridine synthase D [Vibrio sinaloensis DSM 21326]
          Length = 326

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 81/332 (24%), Positives = 155/332 (46%), Gaps = 48/332 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L +G+V+V+ + V K   ++  G+ +    
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTKVMGGEEI---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           ++ A   +  E++     + L          ++YED  I V NKP G  V  G+G     
Sbjct: 66  ILQA--ELEDEERWEAQDIPLD---------IVYEDDDILVINKPRGFVVHPGAGTP--- 111

Query: 130 DGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKI 182
           DG + + +     S  + PR  + HRLD++T+G++VVA+T  A   L  + + +R   + 
Sbjct: 112 DGTVLNALLHHYPSIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFVRE 171

Query: 183 YWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G        ++ I     K++ +    +            AI+H++V + F ++
Sbjct: 172 YEAIAIGRMTAGGRVEQPIGRHSTKRTLMAVSPM---------GKPAITHYRVAEHF-RE 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKL------YLH 291
              + ++  TGRTHQ+RVH  ++  P++GD  Y   A      ++ +  K+       LH
Sbjct: 222 HTRIRLRLETGRTHQIRVHMSYLQHPLLGDSAYGGRARIPSGASNELAEKIRGFDRQALH 281

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           A  +   HP  G  ++  AP+P  MV+  ++L
Sbjct: 282 AVMLKFEHPITGEEVEFHAPVPDDMVEMAEAL 313


>gi|298530696|ref|ZP_07018098.1| pseudouridine synthase [Desulfonatronospira thiodismutans ASO3-1]
 gi|298510070|gb|EFI33974.1| pseudouridine synthase [Desulfonatronospira thiodismutans ASO3-1]
          Length = 318

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 76/296 (25%), Positives = 125/296 (42%), Gaps = 37/296 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            Q  +V + E   +L  + K           L +++R+GQVRV+ KR K  +R+ +G  V
Sbjct: 9   AQQCLVSSTESGQKLFSYLKRRLGREFPGSGLMRLIRTGQVRVNSKRKKPYDRVYAGDTV 68

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP         +    L                +++E+    V +KPAG+ V   SG 
Sbjct: 69  RIPPHFPETGDDPQRAGELQ---------------IVFENPDFTVLDKPAGVPVH--SGT 111

Query: 126 AYHIDGF---LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   D     L+         P L HRLD+ETSG+L+ A+  A  + +   +    ++K 
Sbjct: 112 SARRDNMVLRLRKHYAGADFSPALVHRLDKETSGLLLAAKNYAWLRRIQAMWNKNLVEKT 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y + V G   ++   + + L+K             Q       A+S  + I     K   
Sbjct: 172 YLAWVHGSWPSRWVNLEHRLIK--------TFEKMQPSPEGRPALSRVRSIASSRDKTL- 222

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           ++++  TGRTHQ+R      G P++GD KY  +           ++YLHA  +  P
Sbjct: 223 VQIRIITGRTHQIRTQLSLSGHPVIGDGKYGKDSG-------YAEMYLHAYMLAWP 271


>gi|315038927|ref|YP_004032495.1| ribosomal protein large subunit [Lactobacillus amylovorus GRL 1112]
 gi|312277060|gb|ADQ59700.1| ribosomal protein large subunit [Lactobacillus amylovorus GRL 1112]
 gi|327184070|gb|AEA32517.1| ribosomal protein large subunit [Lactobacillus amylovorus GRL 1118]
          Length = 285

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 83/180 (46%), Gaps = 11/180 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + + NK  G   Q         D  L       G  P + HRLD  T G+L+V
Sbjct: 83  VIYEDDNLLIINKKKG---QKTHPNLNETDTALNDCATYLGSSPYIVHRLDMLTGGLLLV 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A+  A    L      +   + Y + V    K KK    +       IG D     K+  
Sbjct: 140 AKNPAVVPILNRELTTKTFHREYLAKVIHADKLKKNGTIDL-----PIGQDPDDQRKRMV 194

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           N+ G  +A++H++++  ++     +++   TGRTHQ+RVH   +GCPIVGD  Y  +F G
Sbjct: 195 NKTGL-HAVTHYELLKKYSDNTALVKLTLETGRTHQIRVHLAAIGCPIVGDPLYNPDFAG 253


>gi|33597725|ref|NP_885368.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           parapertussis 12822]
 gi|33574153|emb|CAE38483.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           parapertussis]
          Length = 320

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 85/334 (25%), Positives = 136/334 (40%), Gaps = 53/334 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD+      P  +   LQ  + +G V V+  + K    +  G V+ +  
Sbjct: 19  LTVPPDTPADRLDKVLAGLLPGHSRSRLQGWIEAGYVLVNGAQAKVRQAVGPGDVLSV-- 76

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                     EQ   +S     +   F    ++ E     V +KPAG+    G+G     
Sbjct: 77  ---------WEQPAPESRAFAPEPVAF---DVVAESPDWIVVDKPAGLVTHPGAGNWSGT 124

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  + + ++  +  + HRLD++TSG++VVAR   A  HL    + R + + Y +L
Sbjct: 125 LLNGLLHRYPELARVARAGIVHRLDKDTSGLMVVARNELAQTHLVRQLQARTMGRQYIAL 184

Query: 187 VWGIPKNKKECIANWLLKKSH----IGGDY---VHVVKQNEKGANYAISHF--KVIDC-- 235
             G           WL         IG D    V +  +       A++HF  +   C  
Sbjct: 185 AHG-----------WLGAAGTVDRPIGRDARVPVRMSVERPIAPKPAVTHFDPRRRGCAE 233

Query: 236 ----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
                ++  C LE    TGRTHQ+RVH   +G P++ D  Y        T     +  LH
Sbjct: 234 GGARVSEVLCRLE----TGRTHQIRVHLASLGHPLLADTLYGGKPLAGAT-----RQMLH 284

Query: 292 ARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF 324
           AR +    P G G +   A +PA M    ++L +
Sbjct: 285 ARALHFGDPGGAGEVSFEAGVPADMSDVQEALAW 318


>gi|238795199|ref|ZP_04638786.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           intermedia ATCC 29909]
 gi|238725486|gb|EEQ17053.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           intermedia ATCC 29909]
          Length = 196

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/198 (33%), Positives = 97/198 (48%), Gaps = 18/198 (9%)

Query: 110 VFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           V NKP+G+ SV    G A      + + + +        HRLD  TSG+++VA T+AA +
Sbjct: 2   VVNKPSGLLSV---PGRAPENKDSIMTRIQADFPAAESVHRLDMATSGVIIVALTKAAER 58

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANY 225
            L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ    E G + 
Sbjct: 59  ELKRQFREREPKKSYIARVWGHLAEDEGLIDLPLI------CDWPNRPKQKVCYETGKS- 111

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           A + ++V+         +++ P TGR+HQLRVH L MG PI+GD  Y         S   
Sbjct: 112 AQTEYRVLSRDTDGSTRVKLSPITGRSHQLRVHMLAMGHPILGDGFYAHPEAKAMAS--- 168

Query: 286 NKLYLHARYMDLPHPEGG 303
            +L LHA+ + + HPE G
Sbjct: 169 -RLQLHAQELCITHPEFG 185


>gi|256028259|ref|ZP_05442093.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
 gi|289766191|ref|ZP_06525569.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
 gi|289717746|gb|EFD81758.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
          Length = 328

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 77/297 (25%), Positives = 139/297 (46%), Gaps = 46/297 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALN 75
           E MRLD++            L+K++ +  V+++ K +  N R ++ G+ + +        
Sbjct: 17  EGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKLKLGEKIEV-------- 68

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IA 126
            +I E++      N+    + +   ++YE++   V NK  G+ V    G         + 
Sbjct: 69  -LIPEEE------NIDIEPENIPLDIVYENNDFIVINKNYGMVVHPAYGNYTGTLVNALL 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y+ +    S ++    +P + HRLD++TSG+++VA++  A   L   F  + I K Y  +
Sbjct: 122 YYTNNL--SSING-NIRPGIIHRLDKDTSGLILVAKSNYAHAKLASMFIDKTIHKTYLCI 178

Query: 187 VWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           V G    +N    I N + + S      + VVK+N K    AIS++KV++   + +  +E
Sbjct: 179 VKGNFSEENLSGRIENLIGRDSK-DRKKMAVVKENGK---IAISNYKVVEQ-VEGYSLVE 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------FKGNFTSPIQNKLYL 290
           +   TGRTHQ+RVH   +   I+GD  Y              +K  F +P+ NK Y+
Sbjct: 234 VAIETGRTHQIRVHMKSINHVILGDSVYGNEDKNVKRQMLHAYKLEFLNPLDNKEYV 290


>gi|300862110|ref|ZP_07108190.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|300848635|gb|EFK76392.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|315031415|gb|EFT43347.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0017]
 gi|315144507|gb|EFT88523.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2141]
          Length = 283

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/260 (27%), Positives = 116/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q  + +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETNTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG N AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-NSAITHVQVVQVLSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|260772177|ref|ZP_05881094.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           metschnikovii CIP 69.14]
 gi|260613044|gb|EEX38246.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           metschnikovii CIP 69.14]
          Length = 245

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 100/216 (46%), Gaps = 43/216 (19%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW--VDSKGQKPRLTHRLDQETSGI 157
           ++YED  I   NKP+G+ SV G      HI+ +   W  + ++  + ++ HRLD  TSG+
Sbjct: 16  VVYEDEYILAVNKPSGLLSVPGK-----HIEHYDSMWSRLVAEHSEIQVVHRLDMSTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW--------LLK 204
           ++ A+ +     L + F+ R   K+Y++ VWG  + ++       I +W          +
Sbjct: 71  MLFAKNKYMEAALKKQFQYRLTHKVYYARVWGKLEQQQGEVDLPLICDWPNRPRQKVCFE 130

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                     VVKQ E+          ++  F          P TGR+HQLRVH L +G 
Sbjct: 131 HGKASKTLYQVVKQEEQTT--------IVRLF----------PVTGRSHQLRVHMLAIGH 172

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           PIVGD  Y +     F+    ++L LHA  +   HP
Sbjct: 173 PIVGDEFYASPEALAFS----DRLALHAAELSFYHP 204


>gi|110800540|ref|YP_696800.1| RluA family pseudouridine synthase [Clostridium perfringens ATCC
           13124]
 gi|168208824|ref|ZP_02634449.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
 gi|110675187|gb|ABG84174.1| pseudouridine synthase, RluA family [Clostridium perfringens ATCC
           13124]
 gi|170713119|gb|EDT25301.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
          Length = 298

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 82/301 (27%), Positives = 138/301 (45%), Gaps = 52/301 (17%)

Query: 39  KILRSG----QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++RS     +++VD   VK N  +++G+ ++I        +I  E+  ++         
Sbjct: 30  RLIRSAAIDKRIKVDGVAVKMNYVVKTGEEIKIELSKKESQNIEPEKMDIE--------- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPR 145
                 ++YEDS I V NK   + V            +GI Y+   F +S  D      R
Sbjct: 81  ------IVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYY---FKESNQDCI---VR 128

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L  RLD  TSG++++ + + A   L+   +  + QK Y ++V G  + K+  I   + + 
Sbjct: 129 LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRP 188

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHM 262
           +    D +  V  +E+G   +I+H+KVI+ +       C LE    TGRTHQ+RVH   +
Sbjct: 189 AE---DTIKRV-VDERGQE-SITHYKVIESYKGADLVECLLE----TGRTHQIRVHLSSL 239

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           G PI GD  Y     G       ++  LHA  +D   P+  + L + A LP  M +  + 
Sbjct: 240 GHPIFGDSLY-----GTEDEEFISRQALHAYGLDFYSPKTKKPLSLRADLPEDMKELINK 294

Query: 322 L 322
           L
Sbjct: 295 L 295


>gi|33592279|ref|NP_879923.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           pertussis Tohama I]
 gi|33571924|emb|CAE41444.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           pertussis Tohama I]
 gi|332381696|gb|AEE66543.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           pertussis CS]
          Length = 320

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 85/334 (25%), Positives = 136/334 (40%), Gaps = 53/334 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD+      P  +   LQ  + +G V V+  + K    +  G V+ +  
Sbjct: 19  LTVPPDTPADRLDKVLAGLLPGHSRSRLQGWIEAGYVLVNGAQAKVRQAVGPGDVLSV-- 76

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                     EQ   +S     +   F    ++ E     V +KPAG+    G+G     
Sbjct: 77  ---------WEQPAPESRAFAPEPVAF---DVVAESPDWIVVDKPAGLVTHPGAGNWSGT 124

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  + + ++  +  + HRLD++TSG++VVAR   A  HL    + R + + Y +L
Sbjct: 125 LLNGLLHRYPELARVARAGIVHRLDKDTSGLMVVARNERAQTHLVRQLQARTMGRQYIAL 184

Query: 187 VWGIPKNKKECIANWLLKKS----HIGGDY---VHVVKQNEKGANYAISHF--KVIDC-- 235
             G           WL         IG D    V +  +       A++HF  +   C  
Sbjct: 185 AHG-----------WLGAAGTVDRPIGRDARVPVRMSVERPIAPKPAVTHFDPRRRGCAE 233

Query: 236 ----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
                ++  C LE    TGRTHQ+RVH   +G P++ D  Y        T     +  LH
Sbjct: 234 GGARVSEVLCRLE----TGRTHQIRVHLASLGHPLLADTLYGGKPLAGAT-----RQMLH 284

Query: 292 ARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF 324
           AR +    P G G +   A +PA M    ++L +
Sbjct: 285 ARALHFDDPGGAGEVSFEAGVPADMSDVQEALAW 318


>gi|294667753|ref|ZP_06732963.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
 gi|292602379|gb|EFF45820.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
          Length = 244

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 111/238 (46%), Gaps = 26/238 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D  + V +KPAG+ V   S +A   D FL   +  +   P  L HRLD+ TSG L+
Sbjct: 10  ILYQDDVLAVVDKPAGLMVHD-SKLARGEDDFLADRLREQLGNPIFLVHRLDRATSGCLL 68

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R +A  L ++     ++K Y ++  G P  ++     +++     GG    V K  
Sbjct: 69  LAFDRDSASALGKALMAGEVEKQYLTVCRGWPAEER-----FIVDHDLDGGPGKPVKKP- 122

Query: 220 EKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 123 ------AVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGD 176

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
             +       +F     +++ LHA  ++ PHP +G R+ +TAPL     K     G++
Sbjct: 177 TSHGDGRHNRSFRMLGIHRMLLHAERLEFPHPADGRRIGVTAPLDVEFSKACALFGWE 234


>gi|224825896|ref|ZP_03699000.1| pseudouridine synthase [Lutiella nitroferrum 2002]
 gi|224602120|gb|EEG08299.1| pseudouridine synthase [Lutiella nitroferrum 2002]
          Length = 253

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 108/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D ++   +KP+G+ V       +     ++   D  GQ+    HRLD+ TSG+L+ 
Sbjct: 4   ILYRDERLIAIHKPSGLLVHRTVLDRHETRFAIQLLRDQIGQRVYPVHRLDKGTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R   + ++  F  +++ K Y ++V G P  + E I + L ++     D   V ++ +
Sbjct: 64  ALDRDMGREMSWQFERQQVDKRYLAVVRGWPDEQGE-IEHALTRRPD---DLEWVGEKVD 119

Query: 221 KGANYAISHFK---------VIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++ F+          +D +   ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 TAPQAALTRFRRLATVELPYAVDKYPHSRYALVELTPETGRRHQLRRHLKHIAHPIIGDA 179

Query: 271 KYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            Y           +    +L L    M   HP  G  + +TAPL         +LG++
Sbjct: 180 TYGKGRHNRLFGELFGSQRLLLACMEMRFAHPVSGETVTLTAPLADDFAGVVRALGWE 237


>gi|21229703|ref|NP_635620.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66766580|ref|YP_241342.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|21111188|gb|AAM39544.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66571912|gb|AAY47322.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
          Length = 245

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 113/243 (46%), Gaps = 31/243 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D+ + V +KPAG+ V   S +A   D FL   +  +  +P  L HRLD+ TSG L+
Sbjct: 10  ILYQDAVLAVVDKPAGLMVHD-SKLARGEDDFLADRLRVQLGRPIFLVHRLDRATSGCLL 68

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R  A  L ++     ++K Y ++  G P  ++     +++     GG    + K  
Sbjct: 69  LAFDRDTASALGKALMAGEVEKDYLAICRGWPAEER-----FIVDHDLDGGPGKPIKKP- 122

Query: 220 EKGANYAISHFKVIDC---------FA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +           FA  ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 123 ------AVTHFQRLATGELEIPSTGFATSRYALLRCQPQTGRFRQIRRHLKHLSHHMIGD 176

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT-----WDSL 322
             +       +F     +++ LHA  +  PHP +G R+ + APL     K      WD  
Sbjct: 177 TSHGDGRHNRSFRMLGIHRMLLHAERLGFPHPADGRRISVVAPLDVEFAKACALFGWDVA 236

Query: 323 GFK 325
           G +
Sbjct: 237 GLQ 239


>gi|323494676|ref|ZP_08099779.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           brasiliensis LMG 20546]
 gi|323311109|gb|EGA64270.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           brasiliensis LMG 20546]
          Length = 559

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 110/237 (46%), Gaps = 33/237 (13%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGF 132
           L H+++  K+ D+ +      D    IL +ED  + V NKP+G+ SV G +         
Sbjct: 332 LGHMLQGLKVDDNPLEENWAEDKELEIL-FEDDALVVVNKPSGLLSVPGKTITDSAYTRL 390

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            + + D +G  P + HRLD  TSG+LV A T+ A + L + F  R ++K Y +L+ G  +
Sbjct: 391 QQRYPDVEG--PFVIHRLDMATSGLLVFALTKRANKSLQKQFISRSVEKRYVALLEGEVE 448

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------LEMQ 246
            +   I      K  + GD V   +Q          H K  + + +K         L + 
Sbjct: 449 QQNGQI------KLPMRGDPVDRPRQ-----LVCFEHGKPAETYWEKISTINGRSKLYLY 497

Query: 247 PHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           P TGRTHQLRVH  H   +  P+VGD  Y             ++L+LHA  ++  HP
Sbjct: 498 PKTGRTHQLRVHCAHHLGLDLPMVGDGLYGEK---------ADRLHLHAERLEFEHP 545


>gi|52425127|ref|YP_088264.1| tRNA pseudouridine synthase C [Mannheimia succiniciproducens
           MBEL55E]
 gi|52307179|gb|AAU37679.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 236

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 104/225 (46%), Gaps = 19/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG+ V       +     +++  D  G+     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEHIVAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGRLVYPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  L + F  ++++K Y ++V G     +       ++   I   +     Q +
Sbjct: 64  ALSSETANLLCQQFETKQVEKSYLAVVRGYLTGSERIDYPLKIQLDKIADKFA----QED 119

Query: 221 KGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +    +          ++  + + PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTDYEGLKTVEKPYATPRYATSRYALVRLVPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGRLQITAPL 311
           +Y  +   N T       ++L LHA  +   HP +  R +ITA L
Sbjct: 180 QY-GDLHQNRTLTEHTEVSRLMLHAEKLSFIHPIKRQRTEITAGL 223


>gi|254557295|ref|YP_003063712.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254046222|gb|ACT63015.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 300

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 103/220 (46%), Gaps = 25/220 (11%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LY++S + V +KPAG+ S     G    I   L + +    Q P + HRLDQ TSG ++V
Sbjct: 87  LYQNSDLLVVDKPAGVKSHPNQPGETGSILNDLAATLQPTQQVPYMVHRLDQMTSGAMLV 146

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH----IGGDYVHVV 216
           A        L      ++I++ Y++ V G          ++     H    IG D     
Sbjct: 147 ALNPVVVPILDRLISDKQIRRTYYAWVRG----------HFATPTGHFTAPIGHDATDKR 196

Query: 217 KQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           K+  N   A  A++ ++V    A +   +++  HTGRTHQLRVH      PI+GD  Y +
Sbjct: 197 KRWVNTADAQPALTDYEVCATTAHQ-SLVKLTLHTGRTHQLRVHLAASDHPIIGDPLYDS 255

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
             +         +L LHA+ +DL  P    R+ + APLP+
Sbjct: 256 QAES------APRLMLHAQLLDLQLPFSTTRVTVPAPLPS 289


>gi|257888167|ref|ZP_05667820.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,141,733]
 gi|257824221|gb|EEV51153.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,141,733]
          Length = 299

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 142/310 (45%), Gaps = 44/310 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + K+H   + +   +K +  G +     ++KF    Q GQ+     V N L  + K+ K+
Sbjct: 7   YEKDHSQQVKYFLKEKGISKGLL----AKIKF----QGGQIKVNDQVENVLFSLAKDDKV 58

Query: 84  LDSSVNLTKHSDFLKS----ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KS 135
                   +H   L       ++YED  + V NKPAG+S        YH +G +    K+
Sbjct: 59  TIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQ---YHPNGTMANRVKA 115

Query: 136 WVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   +G + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G+  
Sbjct: 116 YYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDTQLREKKFVKKYQALVSGMLS 175

Query: 193 NKKECIANWLLKKSHI----GGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           N        L   SHI      DY  ++K+  +++G +    ++  I+    +   +++Q
Sbjct: 176 N--------LSAHSHIDLPIARDYSSLLKRMVSDEGRSAQTEYW--IEKRLTEIALVDIQ 225

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
            HTGRTHQ+RVH   +GC ++GD  Y     G     I+ +  LH   +   HP     L
Sbjct: 226 LHTGRTHQIRVHFSAIGCALLGDDMYS----GRMDLGIKRQA-LHCYDLRFYHPFTEELL 280

Query: 306 QITAPLPAHM 315
           +   PL A M
Sbjct: 281 EFKQPLAADM 290


>gi|229523315|ref|ZP_04412722.1| tRNA pseudouridine synthase C [Vibrio cholerae TM 11079-80]
 gi|229339678|gb|EEO04693.1| tRNA pseudouridine synthase C [Vibrio cholerae TM 11079-80]
          Length = 244

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 104/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASDVMPMFANHEMEKTYHAIVRGWIEEAD--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +           FA  ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAVTAYRPLAKVELPISTGKFATTRYCLIEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFMHP 211


>gi|323456553|gb|EGB12420.1| hypothetical protein AURANDRAFT_19938 [Aureococcus anophagefferens]
          Length = 283

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 112/232 (48%), Gaps = 36/232 (15%)

Query: 103 YEDSKIYVFNKPAGISV-------QGGSGIAYHIDGFLKSWVDSKG-----QKPRLTHRL 150
           YED  + V  KPAG+          G + +   +   LK     +      ++P+  HRL
Sbjct: 48  YEDDYLAVVVKPAGVPTYSPGGDHGGRANLRSCLPFALKPPASCRAGDEVLRRPQPVHRL 107

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSG+++ A+T+ AA     +F  R ++K Y +++ G P  ++  +   +    ++ G
Sbjct: 108 DKATSGLVLCAKTKLAAVGAARAFATRAVKKRYSAVLLGEPAARRGVVTAPV--PVNVKG 165

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVG 268
             + V+K       YA+    V+D   A K C ++  P TGRTHQLR H A  +G PIVG
Sbjct: 166 --LSVLKSAR--TVYAVE--AVVDSLKASKLCLVKCAPRTGRTHQLRRHFAEALGRPIVG 219

Query: 269 DHKY------CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           D  Y        NF+       ++ L+  AR ++L HP  G RLQ+   LP 
Sbjct: 220 DVLYDGGGPEALNFR-------RSGLFFCARSLELDHPVTGARLQVRTGLPG 264


>gi|149372343|ref|ZP_01891531.1| Ribosomal large subunit pseudouridine synthase D [unidentified
           eubacterium SCB49]
 gi|149354733|gb|EDM43296.1| Ribosomal large subunit pseudouridine synthase D [unidentified
           eubacterium SCB49]
          Length = 300

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 101/232 (43%), Gaps = 38/232 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQETS 155
           +L+ED+ + + +KPAG+ V G     Y I+  L S +    QK     P   HRLD  TS
Sbjct: 89  VLFEDNHLAIIHKPAGVEVSGNK--KYTIENALPSLLKKSNQKDALDRPLPAHRLDYPTS 146

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L++ +T    Q L   F  R I K Y ++  G          N + +          +
Sbjct: 147 GCLLIGKTSETLQALHRMFEKREISKKYIAVTLG----------NQITEGK--------I 188

Query: 216 VKQNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            K  +  A  +++ FK +     K       + + PHTGR HQLR H + +G PI G+  
Sbjct: 189 DKPIDDKA--SLTTFKTLQTITSKKYNALNLVLLTPHTGRRHQLRKHMMQLGNPIFGEKT 246

Query: 272 YC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
           Y   N +G  +      L+LHA  +   HP +   L I +  P    K + S
Sbjct: 247 YGDINDQGKGSG-----LFLHAIALSFKHPIDNKTLIIKSEAPRKFQKLFPS 293


>gi|19704707|ref|NP_604269.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
 gi|296327673|ref|ZP_06870215.1| RluA family pseudouridine synthase [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
 gi|19715021|gb|AAL95568.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
 gi|296155204|gb|EFG95979.1| RluA family pseudouridine synthase [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
          Length = 319

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 78/302 (25%), Positives = 140/302 (46%), Gaps = 46/302 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           V ++ E MRLD++            L+K++ +  V+V+ K +  N R ++ G+ + +   
Sbjct: 17  VNSEYEGMRLDKYLSEQIEEATRSYLEKLIDNNFVKVNSKIINKNGRKLKLGEKIEV--- 73

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                 +I E++      N+    + +   ++YE+    + NK  G+ V    G      
Sbjct: 74  ------LIPEEE------NIDIEPENIPLNIVYENDDFILINKSYGMVVHPAYGNYTGTL 121

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + Y+ +    S V+    +P + HRLD++TSG+++VA+   A   L   F  + I K
Sbjct: 122 VNALLYYTNNL--SSVNG-NIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFIDKTIHK 178

Query: 182 IYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            Y  +V G    +N    I N + + S      + +VK+N K    AIS++KV++   + 
Sbjct: 179 TYLCIVKGNFSEENLSGRIENLIGRDSK-DRKKMTIVKENGK---IAISNYKVVEQ-VEG 233

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------FKGNFTSPIQNKL 288
           +  +E+   TGRTHQ+RVH   +   I+GD  Y              +K  F +P+ NK 
Sbjct: 234 YSLVEVAIETGRTHQIRVHMKSINHVILGDSVYGTEDKNVKRQMLHAYKLEFLNPLDNKK 293

Query: 289 YL 290
           Y+
Sbjct: 294 YI 295


>gi|331265601|ref|YP_004325231.1| 23S rRNA pseudouridine synthase [Streptococcus oralis Uo5]
 gi|326682273|emb|CBY99890.1| 23S rRNA pseudouridine synthase [Streptococcus oralis Uo5]
          Length = 291

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 57/201 (28%), Positives = 95/201 (47%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  IYQDQHLIIVNKPEGMKTHGNQPGEIALLNHVSAYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+L+ G  ++K+      L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEIAREYWALIEGRVESKE------LVFRDKIGRDRHDRRKRIVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F  +   +  +  TGRTHQ+R+H  H   PI+GD  Y ++ K  
Sbjct: 195 AKHGQYAETHVSRLKQFPNQTTLVRCKLKTGRTHQIRIHLSHHNHPILGDPLYNSSSKV- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|260553983|ref|ZP_05826248.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           RUH2624]
 gi|260404869|gb|EEW98374.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           RUH2624]
          Length = 350

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 110/231 (47%), Gaps = 33/231 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED+ I V NKP G+ V  G+G         + YH          ++  +  L HR+D
Sbjct: 117 IVYEDNDILVINKPVGMVVHPGAGNTSGTLVNALLYHFPKL------AELSRAGLVHRID 170

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA+T  A   L++    + + ++Y  +V+G        IA   + +  I   
Sbjct: 171 KDTSGLLVVAKTLEAQFSLSKQLANKSVYRVYDLVVYG------NIIAGGTIDEP-IKRH 223

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V  VK     G   A++H+ V + F + F  ++ +  TGRTHQ+RVH  ++G  ++GD 
Sbjct: 224 PVDRVKMAILPGGRDAVTHYNVKERF-KDFTRVQARLETGRTHQIRVHFSYIGYGLIGDQ 282

Query: 271 KYCANFK---GNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y    +   G     I+      +  LHA  + L HP  G  +   AP P
Sbjct: 283 VYMNRVRVPAGASELLIETLRGFKRQALHAAKLGLKHPRTGEEMLFEAPWP 333


>gi|259502474|ref|ZP_05745376.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           antri DSM 16041]
 gi|259169617|gb|EEW54112.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           antri DSM 16041]
          Length = 289

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/219 (30%), Positives = 110/219 (50%), Gaps = 22/219 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQ---KPRLTHRLDQETSG 156
           ++YED    V +KPAG+ SV G S     +   +K  ++ +G    +P L  RLD+ TSG
Sbjct: 80  VVYEDDSWLVIDKPAGVTSVPGPSITNGTVLNRVKGHLEKQGSEDLRPHLITRLDRFTSG 139

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+VA+   A+  +++  +  R+ K Y ++V G   +    I   ++++    G    ++
Sbjct: 140 LLLVAKHHVASSMISQQVQQHRMLKEYTAVVSGRFADGHGIIDQPIVRRE---GQAARII 196

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             +      A++ + V D   Q+  W  L +Q HTGRTHQ+RVH    G P++GDH Y  
Sbjct: 197 APD---GQQAVTEYWVED---QEPDWARLRLQLHTGRTHQIRVHLASKGHPLIGDHLYG- 249

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              G+ T    +   LHA  +    P    +L  T+PLP
Sbjct: 250 ---GDLTR--ADHQLLHASRLAFLDPFSREQLTFTSPLP 283


>gi|296393841|ref|YP_003658725.1| pseudouridine synthase [Segniliparus rotundus DSM 44985]
 gi|296180988|gb|ADG97894.1| pseudouridine synthase, RluA family [Segniliparus rotundus DSM
           44985]
          Length = 315

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 79/309 (25%), Positives = 137/309 (44%), Gaps = 29/309 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ- 63
           T ++ + V      +RLD         ++     ++  +G   VD K  + ++R+  G  
Sbjct: 6   TALRSLPVPEGLVGLRLDAGLARLL-GVSRTKAAELADAGHALVDGKEARRSDRLVEGAW 64

Query: 64  -VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V +P  + A      E+ + +    L          +L+ D  + V  KPA I+V   
Sbjct: 65  LEVSVPAALPA----PVEEDVPEIIAGLN---------VLFSDEHVVVVEKPAEIAVHPS 111

Query: 123 SG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G     + G LK+    + + G   R  +  RLD  TSG++V+A +  A   L  +F+ 
Sbjct: 112 VGWSGPTVVGGLKALGFRIATSGVAERQGVVQRLDVGTSGVMVLAASEHAYTVLKRAFKH 171

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R ++K Y +LV G P      I   + K+   G  +   V  N +    +++H+  ++ F
Sbjct: 172 REVEKWYEALVQGHPDPSSGTIDAAIGKRP--GPGWRFAVTTNGR---PSVTHYDTLEAF 226

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q    + ++  TGRTHQ+RVH   +  P  GD  Y A+ K      ++ + +LHAR + 
Sbjct: 227 GQA-SLVSIRLETGRTHQIRVHFSALRHPCCGDMLYGADPKLAARLGLRRQ-WLHARKLS 284

Query: 297 LPHPEGGRL 305
             HP  GR+
Sbjct: 285 FAHPGDGRI 293


>gi|255317207|ref|ZP_05358453.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           6276s]
          Length = 303

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 68/259 (26%), Positives = 118/259 (45%), Gaps = 45/259 (17%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINAL 74
           +  +RL  + +   PH+    + + +R    RV+ +  +F + ++Q G  V         
Sbjct: 9   DRQIRLSSFLRTSLPHLPKKTILESVRYHGCRVNGRIERFESYKLQPGDRV--------- 59

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                       S+ + +HS      LL+ED  + ++NKPA    Q    +A+ ++    
Sbjct: 60  ------------SLQIIEHSS---PQLLWEDEHLCIYNKPAK---QTSEDLAHQLNV--- 98

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                      L HRLD++TSG ++ A+   A+  +T+ F+ R I K Y +LV+G P+ +
Sbjct: 99  ----------HLVHRLDRDTSGCILFAKHAKASSLITQLFKNRGIDKRYIALVFGQPRQE 148

Query: 195 KECIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
              I  +       IG        QN       I+ ++++  +  K+  L  +P TGRTH
Sbjct: 149 SGIITTYTAPCYRRIGAVLFGNTDQN--SGKITITKWEILTRYP-KYTLLLCRPVTGRTH 205

Query: 254 QLRVHALHMGCPIVGDHKY 272
           Q+R+H   +G PIVGD  Y
Sbjct: 206 QIRLHMKTIGHPIVGDVDY 224


>gi|327483626|gb|AEA78033.1| tRNA pseudouridine synthase C tRNA Psi65 [Vibrio cholerae
           LMA3894-4]
          Length = 244

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 60/217 (27%), Positives = 102/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASDVMPMFANHEMEKTYHAIVRGWIEEAN--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAVTAYRPLAKVELPIATGKFNTTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFMHP 211


>gi|317052476|ref|YP_004113592.1| pseudouridine synthase [Desulfurispirillum indicum S5]
 gi|316947560|gb|ADU67036.1| pseudouridine synthase [Desulfurispirillum indicum S5]
          Length = 267

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 108/222 (48%), Gaps = 20/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L++D+   V  KPA + VQ  S     +   ++ ++ ++ QKP      +  RLD+  S
Sbjct: 37  VLHQDNHTIVVFKPARVPVQSDSSGDISLLEVVRQYIAAEYQKPGNVFVGMVQRLDRPVS 96

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ART   A  L+E  R  RI K Y +LV G P   +  + + L  +     +   +
Sbjct: 97  GLVVFARTSKGAARLSEQLRQHRIYKHYLALVHGAPSESEGTLRHLLEYR-----EGTAI 151

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             ++ +G   A+ H++V+         L ++  TGR HQ+R     +GCPI+GD +Y A 
Sbjct: 152 AGRHGQGKT-AVLHYRVLQHLPDA-SLLHIRLETGRKHQIRFQLSRIGCPILGDLRYGAR 209

Query: 276 FKGNFTSPIQNK-LYLHARYMDLPHPEGGRLQITAPLPAHMV 316
                 +P+ ++ + L A  +   HP   R  I   LPA ++
Sbjct: 210 ------APLPDQSIALCAWALSYEHPT-SRQPIMVRLPAGLL 244


>gi|110802739|ref|YP_699398.1| pseudouridylate synthase family protein, yabo [Clostridium
           perfringens SM101]
 gi|110683240|gb|ABG86610.1| pseudouridine synthase, RluA family [Clostridium perfringens SM101]
          Length = 298

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 82/301 (27%), Positives = 138/301 (45%), Gaps = 52/301 (17%)

Query: 39  KILRSG----QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++RS     +++VD   VK N  +++G+ ++I        +I  E+  ++         
Sbjct: 30  RLIRSAAIDKRIKVDGVAVKMNYVVKTGEEIKIELSKKESQNIEPEKMDIE--------- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPR 145
                 ++YEDS I V NK   + V            +GI Y+   F +S  D      R
Sbjct: 81  ------IVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYY---FKESNQDCI---VR 128

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L  RLD  TSG++++ + + A   L+   +  + QK Y ++V G  + K+  I   + + 
Sbjct: 129 LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRP 188

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHM 262
           +    D +  V  +E+G   +I+H+KVI+ +       C LE    TGRTHQ+RVH   +
Sbjct: 189 AE---DTIKRV-VDERGQE-SITHYKVIESYNGADLVECLLE----TGRTHQIRVHLSSL 239

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           G PI GD  Y     G       ++  LHA  +D   P+  + L + A LP  M +  + 
Sbjct: 240 GHPIFGDSLY-----GTEDEEFISRQALHAYGLDFYSPKTKKSLSLRADLPEDMKELINK 294

Query: 322 L 322
           L
Sbjct: 295 L 295


>gi|260495646|ref|ZP_05815770.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_33]
 gi|260196829|gb|EEW94352.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_33]
          Length = 328

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 78/302 (25%), Positives = 141/302 (46%), Gaps = 46/302 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           V ++ E MRLD++            L+K++ +  V+++ K +  N R ++ G+ + +   
Sbjct: 12  VNSEYEGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKLKLGEKIEVS-- 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                  I E++      N+    + +   ++YE++   V NK  G+ V    G      
Sbjct: 70  -------IPEEE------NIDIEPENIPLDIVYENNDFIVINKNYGMVVHPAYGNYTGTL 116

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + Y+ +    S ++    +P + HRLD++TSG+++VA++  A   L   F  + I K
Sbjct: 117 VNALLYYTNNL--SSING-NIRPGIIHRLDKDTSGLILVAKSNYAHAKLASMFIDKTIHK 173

Query: 182 IYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            Y  +V G    +N    I N + + S      + VVK+N K    AIS++KV++   + 
Sbjct: 174 TYLCIVKGNFSEENLSGRIENLIGRDSK-DRKKMAVVKENGK---IAISNYKVVEQ-VEG 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------FKGNFTSPIQNKL 288
           +  +E+   TGRTHQ+RVH   +   I+GD  Y              +K  F +P+ NK 
Sbjct: 229 YSLVEVAIETGRTHQIRVHMKSINHVILGDFVYGNEDKNVKRQMLHAYKLEFLNPLDNKE 288

Query: 289 YL 290
           Y+
Sbjct: 289 YV 290


>gi|152974818|ref|YP_001374335.1| RluA family pseudouridine synthase [Bacillus cereus subsp.
           cytotoxis NVH 391-98]
 gi|152023570|gb|ABS21340.1| pseudouridine synthase, RluA family [Bacillus cytotoxicus NVH
           391-98]
          Length = 307

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 72/231 (31%), Positives = 117/231 (50%), Gaps = 32/231 (13%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPR 145
           +F +  +++ED  + + NKP  +    S + G+G     IA+H   F    +++K    R
Sbjct: 81  EFGELDVVFEDDHVLIVNKPEQMDTHPSEKNGTGTLANLIAFH---FQMQGLETK---VR 134

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD++T+G +V A+ R A   + +    R I++ Y +LV G  K +K  I       
Sbjct: 135 HIHRLDKDTTGGVVFAKHRLAGAIMDQLLMERNIKRTYMALVEGKMKKRKGTI------D 188

Query: 206 SHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHM 262
           + IG D  H  ++  + KG + A++H+ V + F  Q    + +Q  TGRTHQ+RVH  + 
Sbjct: 189 AAIGRDRHHATRRRVSPKG-DRAVTHYTVEEYFKRQDTTLVTVQLETGRTHQIRVHMSYN 247

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           G P++GD  Y     GN T    ++  LHA  +   HP   R +I   +PA
Sbjct: 248 GHPLLGDVLYG----GNVT--YMSRQALHAMQIAFLHPI-TREEIIVDIPA 291


>gi|316975348|gb|EFV58793.1| ribosomal large subunit pseudouridine synthase C [Trichinella
           spiralis]
          Length = 372

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 75/276 (27%), Positives = 121/276 (43%), Gaps = 51/276 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +LY  + + V NKP G+ V  G+G+   +      LK  + +K +  R  HRLD+ T+G+
Sbjct: 98  VLYNKNDLIVLNKPYGLPVTNGAGMFVSLKIILPILKELISAKSEILRPVHRLDRCTTGV 157

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN-------------WLLK 204
           L++A ++     L + F+   I+K Y  +   +P      + N               L 
Sbjct: 158 LMLASSKFRFLELKDMFKREEIKKTYICITKLVPNPSSGIVNNEHTHTHIVIRVIEAALG 217

Query: 205 KSHIGGDYVHV-----VKQNEK----GANYAI--SHFKVIDCFAQKFCWLEMQPHT---- 249
           +  I G +        +K  EK    GA+  I  + +  +    +K   ++   +T    
Sbjct: 218 ERRISGRFKTSPLSINLKGKEKCLNSGADAKIVKTEYSTLS-VGEKCALIKCTTYTVFCL 276

Query: 250 GRTHQLRVH-ALHMGCPIVGDHKYCANFKGN----FTSPIQNK------------LYLHA 292
           G  HQ+R H  L  G PIVGDHKY ++F GN      S + +K            LYLHA
Sbjct: 277 GMKHQIRCHMGLCFGHPIVGDHKY-SDFVGNRPQRLPSEMLHKLGIRSSKSRHLPLYLHA 335

Query: 293 RYMDLPH-PEGGRLQITAPLPAHMVKTWDSLGFKYD 327
             +++P  P+   L + APLP   + T   L  +Y 
Sbjct: 336 SEIEIPEFPKQKNLSVKAPLPNFFLYTLKRLRLRYS 371


>gi|219846960|ref|YP_002461393.1| pseudouridine synthase [Chloroflexus aggregans DSM 9485]
 gi|219541219|gb|ACL22957.1| pseudouridine synthase [Chloroflexus aggregans DSM 9485]
          Length = 307

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 87/334 (26%), Positives = 134/334 (40%), Gaps = 60/334 (17%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           + + +  ++V   E  + L     N +        Q  +R G  +   +RV  +   ++G
Sbjct: 1   MSSAIISLIVTEPEAGLSLGAIVANRF---GERGRQAAIRGGLWQ-HGRRVSADTPARAG 56

Query: 63  Q--VVRIPPVIN------ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
           +  +VR+PPV         LNHII                        YED  + V NKP
Sbjct: 57  ETLLVRLPPVGGYRDAPLTLNHII------------------------YEDDDLLVINKP 92

Query: 115 ----AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
                G +     G    +   L +  D       L H+LD  TSGILV+++   A   L
Sbjct: 93  PACYTGDTPWDTQGSVLAVARRLLTERDGLVPTLHLAHQLDAGTSGILVISKHPRANAPL 152

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIAN--------W-LLKKSHIGGDYVHVVKQNEK 221
             +F   ++ K Y +L  G P    E I          W L +++ IG      V  N +
Sbjct: 153 QAAFNHGQVDKRYLALCAGHPPTATELITGHGRAAAGRWRLYEQAEIG-----KVLPNGQ 207

Query: 222 GANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               A +  ++   +      W   +P TGRTHQ+R+H + +GCP++GD +Y        
Sbjct: 208 RVKRAHTQIELRRQYGDVALVW--AKPLTGRTHQIRLHLVALGCPLLGDERYGGPT--TV 263

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
              +     LHA  + LPHP  GR L I  P P+
Sbjct: 264 AGMLIPHPLLHAAELALPHPRSGRLLNIFCPPPS 297


>gi|15603701|ref|NP_246775.1| hypothetical protein PM1836 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|34395822|sp|Q9CK02|RLUA_PASMU RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|12722261|gb|AAK03920.1| RsuA [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 219

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 66/216 (30%), Positives = 109/216 (50%), Gaps = 17/216 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++ T  +D    I+ Y+D  + V NKP+G+    G+   Y+      S V  K       
Sbjct: 4   ISYTPPTDPYLDIVHYDDHFV-VINKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPA 60

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG+++ A ++ A + L   FR R  +K Y +LVWG  +  +  +   L+    
Sbjct: 61  HRLDMSTSGLILFALSKVADRELKRQFREREPKKHYQALVWGHLEEDQGEVNLPLI---- 116

Query: 208 IGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              D+ +  +Q    E+G   A++ ++V+  +      +++ P TGR+HQLR+H L +G 
Sbjct: 117 --CDWENRPRQKICFERGKP-ALTLYEVLARYPNNTTRVKLTPITGRSHQLRLHMLALGH 173

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           PI+GD K+ A  +    SP   +L LHA  +   HP
Sbjct: 174 PILGD-KFYAPPQAKALSP---RLCLHAEQLAFRHP 205


>gi|225867747|ref|YP_002743695.1| RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
 gi|225701023|emb|CAW97796.1| RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
          Length = 289

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 94/210 (44%), Gaps = 17/210 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+   G       +   + ++    G+   + HRLD ETSG ++ A
Sbjct: 84  LYQDEHLIIANKPEGMKTHGNEPTELALLNHVSAYT---GKTCYVVHRLDMETSGAILFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      R I++ YW+L+ G  + +     + + +  H     V     + K
Sbjct: 141 KNPFILPILNRLLERRDIKRDYWALIEGQLEQQTVTYRDPIGRHRHDRRKRV----VDSK 196

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+H  ++  F Q  C +  +  TGRTHQ+RVH  H   P++GD  Y         
Sbjct: 197 HGQEAITHLALLQAFDQT-CLVNCRLETGRTHQIRVHLAHHKHPLIGDPLYSRQKA---- 251

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL-QITAP 310
                +L LHA  + L HP    + ++TAP
Sbjct: 252 ----ERLMLHAHQLTLRHPLTQEMIRVTAP 277


>gi|188989643|ref|YP_001901653.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. B100]
 gi|167731403|emb|CAP49578.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris]
          Length = 258

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 113/243 (46%), Gaps = 31/243 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D+ + V +KPAG+ V   S +A   D FL   +  +  +P  L HRLD+ TSG L+
Sbjct: 22  ILYQDAVLAVVDKPAGLMVHD-SKLARGEDDFLADRLRVQLGRPIFLVHRLDRATSGCLL 80

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R  A  L ++     ++K Y ++  G P  ++     +++     GG    + K  
Sbjct: 81  LAFDRDTASALGKALMAGEVEKDYLAICRGWPAEER-----FIVDHDLDGGPGKPIKKP- 134

Query: 220 EKGANYAISHFKVIDC---------FA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +           FA  ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 135 ------AVTHFQRLATGELEIPSTGFATSRYALLRCQPQTGRFRQIRRHLKHLSHHMIGD 188

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT-----WDSL 322
             +       +F     +++ LHA  +  PHP +G R+ + APL     K      WD  
Sbjct: 189 TSHGDGRHNRSFRMLGIHRMLLHAERLGFPHPADGRRISVVAPLDVEFAKACALFGWDVA 248

Query: 323 GFK 325
           G +
Sbjct: 249 GLQ 251


>gi|299771331|ref|YP_003733357.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           DR1]
 gi|298701419|gb|ADI91984.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           DR1]
          Length = 350

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 111/241 (46%), Gaps = 33/241 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP G+ V  G+G         + YH          S+  +  L HR+D
Sbjct: 117 IVYEDDDILVINKPVGMVVHPGAGNSSGTLVNALLYHFPKL------SELSRAGLVHRID 170

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA++  A   L++    + + ++Y  +V+G        IA   + +  I   
Sbjct: 171 KDTSGLLVVAKSLEAQFSLSKQLANKSVYRVYDLVVYG------NIIAGGTIDEP-IKRH 223

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V  VK     G   A++H+ V + F + F  ++ +  TGRTHQ+RVH  ++G  ++GD 
Sbjct: 224 PVDRVKMAILPGGRDAVTHYNVKERF-KDFTRVQARLETGRTHQIRVHFSYIGYGLIGDQ 282

Query: 271 KYCANFK--GNFTSPIQNKL------YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
            Y    +     +  + + L       LHA  + L HP  G  +   AP P       D 
Sbjct: 283 IYMNRVRVPAGASELLIDTLRGFKRQALHAAKLGLKHPRTGEEMLFEAPWPEDFTHLVDV 342

Query: 322 L 322
           L
Sbjct: 343 L 343


>gi|28379165|ref|NP_786057.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|308181361|ref|YP_003925489.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28272003|emb|CAD64908.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|308046852|gb|ADN99395.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 300

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 103/220 (46%), Gaps = 25/220 (11%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LY++S + V +KPAG+ S     G    I   L + +    Q P + HRLDQ TSG ++V
Sbjct: 87  LYQNSDLLVVDKPAGVKSHPNQPGETGSILNDLAATLQPTQQVPYMVHRLDQMTSGAMLV 146

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH----IGGDYVHVV 216
           A        L      ++I++ Y++ V G          ++     H    IG D     
Sbjct: 147 ALNPVVVPILDRLISDKQIRRTYYAWVRG----------HFATPTGHFTAPIGHDATDKR 196

Query: 217 KQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           K+  N   A  A++ ++V    A +   +++  HTGRTHQLRVH      PI+GD  Y +
Sbjct: 197 KRWVNTADAQPALTDYEVCATTAHQ-SLVKLTLHTGRTHQLRVHLAASDHPIIGDPLYDS 255

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
             +         +L LHA+ +DL  P    R+ + APLP+
Sbjct: 256 QAES------APRLMLHAQLLDLQLPFSTTRVTVPAPLPS 289


>gi|88857987|ref|ZP_01132629.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
 gi|88819604|gb|EAR29417.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
          Length = 325

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 111/237 (46%), Gaps = 38/237 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKPAG+ V  G+G A   DG + + +          PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPAGLVVHPGAGNA---DGTVLNALLHHCPEIANVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           +G++VVA+T  A   L  + + R    + Y ++  G         A  ++ K  IG    
Sbjct: 143 TGLMVVAKTIPAQTRLVANLQARYNFTREYEAICTGT------MTAGGMIDKP-IGR--- 192

Query: 214 HVVKQNEKGANY----AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           H  K+           A++HF+V + F +    L ++  TGRTHQ+RVH  ++  P+VGD
Sbjct: 193 HATKRTHMDVTITGKPAVTHFRVAEKF-RSHTRLRLRLETGRTHQIRVHMSYLTHPLVGD 251

Query: 270 HKYCANFKGNFTSPIQNKLY----------LHARYMDLPHPEGGRLQI-TAPLPAHM 315
             Y  N +         +L+          LHA  + + HP  G +    AP+P  M
Sbjct: 252 QSY--NGRPRPPKKATPELFECLQKFRRQALHAVMLTIEHPITGEMMTWHAPIPDDM 306


>gi|254230257|ref|ZP_04923648.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. Ex25]
 gi|262395163|ref|YP_003287017.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. Ex25]
 gi|269966583|ref|ZP_06180664.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio alginolyticus
           40B]
 gi|151937237|gb|EDN56104.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. Ex25]
 gi|262338757|gb|ACY52552.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. Ex25]
 gi|269828768|gb|EEZ83021.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio alginolyticus
           40B]
          Length = 325

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 114/235 (48%), Gaps = 21/235 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSG 156
           +++ED  I V NKP    V  G+G      ++  L  + D   + PR  + HRLD++T+G
Sbjct: 86  IVFEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDI-AEVPRAGIVHRLDKDTTG 144

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++VVA+T  A   L  + + R I + Y ++  G  +       +  + +       + V 
Sbjct: 145 LMVVAKTVPAQTRLVRALQKRNITREYEAIAIG--RMTAGGKVDQPIGRHSTKRTLMAVA 202

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              +     A++H++V + F ++   + ++  TGRTHQ+RVH  ++  P++GD  Y    
Sbjct: 203 PMGKP----AVTHYRVAERF-REHTRIRLRLETGRTHQIRVHMSYLQHPLLGDIAYGGRA 257

Query: 277 K------GNFTSPIQ--NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +         T+ I+  ++  LHA  +   HP  G  L+  AP+P  MV   ++L
Sbjct: 258 RIPTGASEELTAMIRGFDRQALHAVMLRFEHPITGEVLEFHAPVPDDMVAMTEAL 312


>gi|223932325|ref|ZP_03624328.1| pseudouridine synthase, RluA family [Streptococcus suis 89/1591]
 gi|302023845|ref|ZP_07249056.1| RNA pseudouridylate synthase [Streptococcus suis 05HAS68]
 gi|330832880|ref|YP_004401705.1| RluA family pseudouridine synthase [Streptococcus suis ST3]
 gi|223899006|gb|EEF65364.1| pseudouridine synthase, RluA family [Streptococcus suis 89/1591]
 gi|329307103|gb|AEB81519.1| pseudouridine synthase, RluA family [Streptococcus suis ST3]
          Length = 297

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 108/229 (47%), Gaps = 30/229 (13%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQ 152
           F    ++YED      NKP G +    +  +  I  F+K ++  +  + +  H   RLD+
Sbjct: 74  FFPLDIVYEDDHFLSINKPVGYASIPSALHSSTIANFVKGYLIEQNYENKQVHIVTRLDR 133

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+++ A+   A   L +  + + I K Y++LV G          N  L+++   GD 
Sbjct: 134 DTSGVMLFAKHGYAHARLDKQLQAKLIHKRYYALVKG----------NGQLEET---GDI 180

Query: 213 VHVVKQNE---------KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +  + + E         K   YA + ++V+  +      +++Q HTGRTHQ+RVH  H+G
Sbjct: 181 IAPIGRPEDSIITRCVTKNGKYAHTSYRVVQSWGD-IHLVDIQLHTGRTHQIRVHFSHIG 239

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
            P++GD  Y  + +       +  L+ H    D P     R+ + APLP
Sbjct: 240 FPLLGDDMYGGSLECGIE---RQALHCHNLAFDNPF-SAERIDLEAPLP 284


>gi|261405374|ref|YP_003241615.1| RluA family pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261281837|gb|ACX63808.1| pseudouridine synthase, RluA family [Paenibacillus sp. Y412MC10]
          Length = 302

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/222 (29%), Positives = 108/222 (48%), Gaps = 19/222 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGI 157
           +LYED    V NKPAG++V          ++  + ++ +++G     R  HRLD++T+G 
Sbjct: 84  VLYEDDFCLVVNKPAGLAVHPDNESRETTLNHVVAAYYEAEGIHAAVRHIHRLDKDTTGP 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+   A   L E+ R ++I ++Y ++V G    + + I         IG D  H  +
Sbjct: 144 VLYAKNEYAQLKLDEAMREKKIVRMYAAIVQGRVSQELKRI------DLPIGKDRYHASR 197

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +        AI+H    + +  K   L ++  TGRTHQ+RVH  HMG P++GD  Y    
Sbjct: 198 RRVSLTGQAAITHILSAEAYP-KASLLHIRLETGRTHQIRVHLSHMGHPLLGDVLYGG-- 254

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            G F      +  LH   +   HP  G  +++ AP P  M++
Sbjct: 255 PGTFA-----RQALHGERLLFHHPFTGESIEVPAPWPQDMME 291


>gi|123443491|ref|YP_001007464.1| tRNA pseudouridine synthase C [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090452|emb|CAL13320.1| Conserved hypothetical protein [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 257

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 101/222 (45%), Gaps = 17/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +     + +
Sbjct: 64  ALSSDVARALSLQFEQHQIQKTYHAVVRGYVLEDGTIDYEMTEELDKIADKFA----RPD 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
           K    +++H++ +               +F  ++++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYQALAQVEVPIAIGRYDTSRFSLMQLKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 270 -HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
            H      +G       ++L LHA ++ L HP  G  L +TA
Sbjct: 180 AHGDLRQNRGVAEHFDCSRLMLHASHLHLNHPVTGESLSLTA 221


>gi|116072039|ref|ZP_01469307.1| probable pseudouridine synthase [Synechococcus sp. BL107]
 gi|116065662|gb|EAU71420.1| probable pseudouridine synthase [Synechococcus sp. BL107]
          Length = 315

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 86/308 (27%), Positives = 140/308 (45%), Gaps = 41/308 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINAL 74
           E   L +W  N Y H +       + +G++  + + ++ + ++ SG  +R   PP +   
Sbjct: 32  EGEWLSQWMANRYQHSDVTVWLGRIAAGELHRNGEPLRGDTQLASGDEIRWQRPPWL--- 88

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                E+ I D            +   +++D  + V NKP+G+ V  G G   H    L 
Sbjct: 89  -----EEAIPD------------QWDTIHDDGDLLVINKPSGLPVMPGGGFLEHT---LT 128

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-RRIQKIY--WS-LVWGI 190
           + + S G KP   HRL + TSG+ V ART A    L++ FR   R QKIY  W+  V G+
Sbjct: 129 ALLASTGAKP--VHRLGRFTSGLQVCARTAATRAALSKQFRPDSRCQKIYQAWAHRVEGL 186

Query: 191 PKNKKECIANWLLKKSH--IGGDYVHVVKQNEKGANYAISH--FKVID-CFAQKFCWLEM 245
              K   ++  ++++ H  +G  +    +  E       +H   +++D C A     LE+
Sbjct: 187 EPGKSLVVSTDVVERQHPLLGWLWGPEPRDKEPTRKRLTAHSTVRLLDRCAAGDR--LEV 244

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGR 304
              TGR HQ+R+H   +G P++GD  Y  N K  +  +P      LHA  +D      G 
Sbjct: 245 TIRTGRPHQIRIHLAQLGSPLLGDPLYLLNRKISDHATPGDGGYGLHAWRLD--GLTAGG 302

Query: 305 LQITAPLP 312
           L + A LP
Sbjct: 303 LSLQAALP 310


>gi|42519556|ref|NP_965486.1| hypothetical protein LJ1679 [Lactobacillus johnsonii NCC 533]
 gi|41583845|gb|AAS09452.1| hypothetical protein LJ_1679 [Lactobacillus johnsonii NCC 533]
          Length = 282

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 112/239 (46%), Gaps = 24/239 (10%)

Query: 41  LRS-GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           LRS  ++ V+ K +  N  ++ G  + I      L+HI  +Q+   +S  L K       
Sbjct: 36  LRSEKKILVNGKYLPLNFLVKPGDKIEI-----QLDHIESDQQPYPASGKLPK------- 83

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++YED+ I V NKPAG   Q         D  L       G  P + HRLD  TSG+L+
Sbjct: 84  -VVYEDNDILVINKPAG---QKTHPNLNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLL 139

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQ 218
           VA+  A    L      + + + Y + +   P+ K   I +  L   H   D    +V+Q
Sbjct: 140 VAKNPAVVPILNRQLTDKTLHREYLAWISNSPQIKNTGIID--LPIGHDPHDQRKRMVRQ 197

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +      A++H++VI     +   +++   TGRTHQ+RVH   +G PI+GD  Y + ++
Sbjct: 198 D---GQKAVTHYEVIKRDKDRIL-VKLTLETGRTHQIRVHLAALGAPIIGDPLYNSAYQ 252


>gi|300768616|ref|ZP_07078515.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|300493923|gb|EFK29092.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 300

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 103/220 (46%), Gaps = 25/220 (11%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LY++S + V +KPAG+ S     G    I   L + +    Q P + HRLDQ TSG ++V
Sbjct: 87  LYQNSDLLVVDKPAGVKSHPNQPGETGSILNDLAATLQPTQQVPYMVHRLDQMTSGAMLV 146

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH----IGGDYVHVV 216
           A        L      ++I++ Y++ V G          ++     H    IG D     
Sbjct: 147 ALNPVVVPILDRLISDKQIRRTYYAWVRG----------HFTTPTGHFTAPIGHDATDKR 196

Query: 217 KQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           K+  N   A  A++ ++V    A +   +++  HTGRTHQLRVH      PI+GD  Y +
Sbjct: 197 KRWVNTADAQPALTDYEVCATTAHQ-SLVKLTLHTGRTHQLRVHLAASDHPIIGDPLYDS 255

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
             +         +L LHA+ +DL  P    R+ + APLP+
Sbjct: 256 QAES------APRLMLHAQLLDLQLPFSTTRVTVPAPLPS 289


>gi|239978958|ref|ZP_04701482.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces albus J1074]
 gi|291450838|ref|ZP_06590228.1| ribosomal large subunit pseudouridine synthase [Streptomyces albus
           J1074]
 gi|291353787|gb|EFE80689.1| ribosomal large subunit pseudouridine synthase [Streptomyces albus
           J1074]
          Length = 314

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 83/335 (24%), Positives = 144/335 (42%), Gaps = 40/335 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVLVDGAAVGKSERVH 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPAAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIVKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +    + + G   R  + HRLD  TSG++VVA++  A   L + 
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKQQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R + K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I
Sbjct: 166 FRERTVDKRYHALVQGHPDPMSGTIDAPIGR--HPQHDYKWAVTAEGK---PSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----- 288
           + + +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  +L     
Sbjct: 221 EAY-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPT------LAKRLGLTRQ 273

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +LHA  +   HP +G   + ++  PA +    D++
Sbjct: 274 WLHAVRLGFEHPADGSWAEFSSEYPADLQHALDTV 308


>gi|195941975|ref|ZP_03087357.1| hypothetical protein Bbur8_03759 [Borrelia burgdorferi 80a]
 gi|216264763|ref|ZP_03436755.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           156a]
 gi|226320862|ref|ZP_03796414.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           29805]
 gi|215981236|gb|EEC22043.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           156a]
 gi|226233728|gb|EEH32457.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           29805]
          Length = 313

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 66/260 (25%), Positives = 126/260 (48%), Gaps = 32/260 (12%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R G +R++  +  F+ R+  G  + +   + A N  +   +   S+++      +++  
Sbjct: 37  IRKGDIRLNGLKSHFSCRVCKGDKIYLYKSL-AQNLNLTMDECFKSNIDFK----YIRKR 91

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGIL 158
           ++YEDS + V +K  GI V GG + + + ++ +L S  + S   KP   HRLD+ TSGI+
Sbjct: 92  IIYEDSDLLVLDKQKGILVHGGKNSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGII 151

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN----KKECIANWLLKKSHIGGD--Y 212
           + A+    A+ L+ +F    I K Y++++ G  K+    K     N  L+K+ +  D  +
Sbjct: 152 IFAKNINTARKLSAAFSGGSIIKKYFAILLGEVKSPVVYKNHLFRNKRLRKTFVLEDKNF 211

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+ + +             ++ C  ++   +E+   TG THQ+R        P++ D KY
Sbjct: 212 VNAITKVN----------PILSC--KRATLVEIVIETGFTHQIRSQCSFNNHPLINDKKY 259

Query: 273 CANFKGNFTSPIQNKLYLHA 292
           C  FK       ++  +LHA
Sbjct: 260 CNKFK-------KSDYFLHA 272


>gi|153212875|ref|ZP_01948492.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           1587]
 gi|124116253|gb|EAY35073.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           1587]
          Length = 221

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/205 (31%), Positives = 96/205 (46%), Gaps = 22/205 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NKPA      G  +   +   LK+   ++ +     HRLD  TSG+LV 
Sbjct: 20  IVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-TQAEGVFALHRLDMSTSGLLVF 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A TR A + L + F  R +QK Y +L+ G     +  I      +  + GD     +Q  
Sbjct: 79  ALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEI------QLPLCGDLDDRPRQKV 132

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
             +    A++H++ +    Q    + + PHTGRTHQLRVH  H   +  PIVGD  Y   
Sbjct: 133 CWQQGKPALTHWETVQV-EQNRTRVYLYPHTGRTHQLRVHCAHHLGLNAPIVGDDLYGLQ 191

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
            K         +L+LHA  +   HP
Sbjct: 192 DK---------RLFLHAEQLSFAHP 207


>gi|33863383|ref|NP_894943.1| putative pseudouridylate synthase [Prochlorococcus marinus str. MIT
           9313]
 gi|33640832|emb|CAE21287.1| putative pseudouridylate synthase [Prochlorococcus marinus str. MIT
           9313]
          Length = 207

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 68/220 (30%), Positives = 107/220 (48%), Gaps = 23/220 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK--SWVDSKGQKPRLTHRLDQETSGIL 158
           +L++DS +    KP G+  Q G G+    D  +    ++D +    RL HRLD++TSG+L
Sbjct: 3   ILFQDSWLIAVEKPPGLLSQPGLGVDQQ-DSLIGRMQFIDPEL---RLVHRLDRDTSGLL 58

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR   + +  +  F  RR++K+Y ++V G        I+  + +       Y     +
Sbjct: 59  LLARGAESLRRCSMLFSARRVRKLYLAVVVGRMNRNAGTISFPIARLQKNPPLY----GK 114

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           N +G   + S ++V  C A     L + P TGR+HQLR H   +G PI+GD  Y      
Sbjct: 115 NPQGKE-SRSQWRVRSCHANGST-LWLWPLTGRSHQLRAHLASVGHPILGDPIYGKEV-- 170

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP-LPAH 314
                   ++YLHA  +   HP  G   RL+  AP LPA 
Sbjct: 171 -----FFERMYLHATALSFRHPFTGLRLRLRSRAPFLPAQ 205


>gi|319951753|ref|YP_004163020.1| pseudouridine synthase [Cellulophaga algicola DSM 14237]
 gi|319420413|gb|ADV47522.1| pseudouridine synthase [Cellulophaga algicola DSM 14237]
          Length = 269

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 93/210 (44%), Gaps = 38/210 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +L+ED  + + +KP GI V G S   IA  +   L         KP+  HRLD  T+GIL
Sbjct: 61  VLFEDDYLAIIHKPGGILVSGNSFKTIANALTQNLSPSTLPDATKPQPVHRLDYATTGIL 120

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +  +T ++ + L + F  +++ K Y+++  G                  + G+    +  
Sbjct: 121 LAGKTSSSIRALNKMFEDKKVAKTYYAVTIG---------------TMDVEGEISTTIDD 165

Query: 219 NEKGANYAISHFKVIDCFAQKFCWL---EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
               + Y +    +    +++F  L   ++ P TGR HQLR H   +G PI+GD +Y   
Sbjct: 166 KPSYSMYTV----ITSAPSKRFGTLNLVQLDPKTGRRHQLRKHLSSIGNPILGDKEYGTA 221

Query: 275 ----NFKGNFTSPIQNKLYLHARYMDLPHP 300
               N KG         +YLHA  +   HP
Sbjct: 222 SLILNGKG---------MYLHAYSLQFVHP 242


>gi|227432728|ref|ZP_03914698.1| pseudouridylate synthase RluD [Leuconostoc mesenteroides subsp.
           cremoris ATCC 19254]
 gi|227351520|gb|EEJ41776.1| pseudouridylate synthase RluD [Leuconostoc mesenteroides subsp.
           cremoris ATCC 19254]
          Length = 297

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 119/240 (49%), Gaps = 38/240 (15%)

Query: 91  TKHSDFL----KSI-LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDS 139
           T  S++L    KS+ +++E+  + V +KPAG+ +      +  + + Y    F++  V  
Sbjct: 72  TSESNYLPNHQKSVNIIFENKDLVVIDKPAGMKMHPHSPTETDTLLNYLAGEFIQRKV-- 129

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HR+D+ TSG+++VA+       L      ++I + Y + V G+ ++    IA
Sbjct: 130 -SDQPYMVHRIDRATSGLVIVAKNPVVVPILDRILADKQIVRTYVTWVSGVVQDNHGTIA 188

Query: 200 NWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC--WLEMQPHTGRTHQL 255
                   IG D     K+  + K A  A++H+  +     +FC   L +Q  TGR HQ+
Sbjct: 189 ------KPIGIDARDDRKRAVDGKEAQVAMTHWWRMHT---EFCSSLLRVQLSTGRMHQI 239

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPA 313
           RVH   +G PIVGD  Y   + G        ++ LH+  + +P P  EG R+ IT PLP+
Sbjct: 240 RVHLASIGHPIVGDELYGGVYNG--------RMLLHSATIKIPLPFDEGVRM-ITGPLPS 290


>gi|325846774|ref|ZP_08169689.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481532|gb|EGC84573.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 318

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 73/278 (26%), Positives = 138/278 (49%), Gaps = 30/278 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  + END  N R DR+ + ++ +     +QK +R    +++ KR K ++ ++   +V+
Sbjct: 2   IEVKINENDS-NQRFDRFLRKYFKNAPLSIIQKNIRKKNFKINDKRAKKDDLVKKDDIVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI------SVQ 120
           +       +  +++     S  NL          ++YED  I + +K +G+      S  
Sbjct: 61  MYIKDEDYHKWVRKDDFKASDFNLD---------IIYEDENIIIIDKKSGVLSHAASSSD 111

Query: 121 GGSGIAYHIDGFL--KSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G  +   +  +L   + V+S+    +P + +RLD+ T+G+++ A+   A + L E+ R 
Sbjct: 112 YGKNLVDQMTSYLYKTNKVNSRDLTFRPSIVNRLDRNTAGLIIGAKNTKALRALNEAIRQ 171

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +I K Y +LV G  + KK+ I +  + K     +  ++VK N KG    I+ F  ++  
Sbjct: 172 GKIYKYYLTLVEG--EIKKDFIVDTNISKY----ENKNMVKGN-KGGKRIITKFYPLES- 223

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHM-GCPIVGDHKYC 273
              F  LE +  TG+THQ+R ++LH    PI+GD KY 
Sbjct: 224 KNNFTLLECELITGKTHQIR-YSLHKNSTPIIGDRKYS 260


>gi|220919409|ref|YP_002494713.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219957263|gb|ACL67647.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 323

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 77/329 (23%), Positives = 127/329 (38%), Gaps = 43/329 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            VE +    RLDR+ +     ++   +Q+++       D +R+K + R+  G    +   
Sbjct: 15  TVEPNYAGWRLDRYLQEKIRRLSRERVQRLIEHRLETEDGRRLKPSTRVAPGLSFAL--- 71

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                       + D+         F    ++++D  + V +KPAG+ V   +  A +  
Sbjct: 72  ------------LKDAEAEPDTPQAF---AVVHDDGALLVVDKPAGLPVHPTARYAANTF 116

Query: 131 GFLKS--WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             L    + D K       HRLD+ETSG+L         + L   F   R+ K Y +L  
Sbjct: 117 TSLAKLRYPDRKVDP---AHRLDRETSGLLACGTAPEVTKVLKRDFAHARVHKTYLALAL 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID----CFAQKFCWLE 244
           G P      +   L   +  G   V V          + + F+V+             L 
Sbjct: 174 GAPAEDAFTVDAPL---ALTGASAVRVRMHVAAAGLPSQTAFEVLARRRAPDGAPVALLA 230

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQN----------KLYLHA 292
            +P TGR HQ+R H  H G P+VGD  Y  + +    FT               +  LHA
Sbjct: 231 CRPRTGRQHQIRAHLAHAGLPMVGDKIYGPDEEIFDRFTRRAMTDEDVALLRLPRHALHA 290

Query: 293 RYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
             ++LPHP     +++  PLP  +   W+
Sbjct: 291 WRLELPHPLTRAPVRLEVPLPPDLAAFWE 319


>gi|87300869|ref|ZP_01083711.1| Pseudouridine synthase [Synechococcus sp. WH 5701]
 gi|87284740|gb|EAQ76692.1| Pseudouridine synthase [Synechococcus sp. WH 5701]
          Length = 328

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 106/241 (43%), Gaps = 27/241 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D  +YV +KP+G+ V    G   H    L     +    PR  HRL + TSG+LV 
Sbjct: 88  VIHDDGDLYVIDKPSGLPVLPAGGFLEHTLLRLLERSCAAQALPRPVHRLGRHTSGLLVC 147

Query: 161 AR---TRA-----------------AAQHLTESFRMRRIQKIYWSLVWGIP----KNKKE 196
           AR   +RA                  ++  + + R    +K+Y +L    P      +  
Sbjct: 148 ARRPQSRAWLSARLRESTAQLLNQPGSEARSAATRAGACRKVYRALTVPAPLQLAPGESL 207

Query: 197 CIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
            I   + ++ H G G        ++ GA  A S  ++++   Q    +E+  HTGR HQ+
Sbjct: 208 AITTPIGRRPHAGLGQIWAADGPDDPGALPAWSEMRLLERRPQGHL-VEVSIHTGRPHQI 266

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
           R+H    G P++GD  Y    +    + P      LHA  + LP P GG L + AP+P  
Sbjct: 267 RIHLASAGVPLLGDPLYRPGGEPRPGALPGDGGYLLHAHRLRLPLPAGGWLDLEAPVPPE 326

Query: 315 M 315
           +
Sbjct: 327 L 327


>gi|319650250|ref|ZP_08004396.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317398081|gb|EFV78773.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 265

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 59/211 (27%), Positives = 100/211 (47%), Gaps = 30/211 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS---------GIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +L+ED  + V NKPAG+     S           A+H+       +  + +  +  HRLD
Sbjct: 47  VLFEDDHLLVLNKPAGMDTHPNSPEQNNTLANAAAFHM------QMQGEYRSIKHIHRLD 100

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G ++ A+   A   L +    R I++ Y +LV G     +  I+        IG D
Sbjct: 101 RDTTGAILFAKHALAGAILDKKLEERTIKRTYLALVHGRISKIRGTISEP------IGRD 154

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             H  ++    G   A++++++I+ F   K   ++ +  TGRTHQ+RVH  H+G P+ GD
Sbjct: 155 RHHPARRRVSPGGQPAVTNYELIEYFPNLKLSLIKCRLDTGRTHQIRVHLSHIGHPLAGD 214

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             Y          P   +  LHA  +++PHP
Sbjct: 215 ILYGG-------KPAFPRQALHAVKLEIPHP 238


>gi|302338972|ref|YP_003804178.1| pseudouridine synthase [Spirochaeta smaragdinae DSM 11293]
 gi|301636157|gb|ADK81584.1| pseudouridine synthase, RluA family [Spirochaeta smaragdinae DSM
           11293]
          Length = 319

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 105/226 (46%), Gaps = 28/226 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + V +KP G+ V   +G         + YH     + + +    +P + HRLD
Sbjct: 87  IIYEDEHVIVVDKPQGLVVHPAAGNWSGTLVQGLLYHCRELGERFGEDT-VRPGIVHRLD 145

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+ A+     Q L E F  RR +K Y +LV G   N    + + +++       
Sbjct: 146 KDTSGVLIAAKDPETRQFLAEQFANRRCKKRYIALVKGDLSNATGRMESGIIRDPKNRKR 205

Query: 212 YVHVVKQNEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +   +     G   A++ +  +    DC    F  L     TGRTHQ+RVH L +G P++
Sbjct: 206 FTWTM----SGGKPAVTEYTRLRRGNDCSLAAFNLL-----TGRTHQIRVHTLMLGHPVI 256

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           GD  Y    + N   P    L LH+  +++  P E    +  APLP
Sbjct: 257 GDPIYG---RKNTRFP-DLGLMLHSMSLEILLPGEREPRRFIAPLP 298


>gi|167771389|ref|ZP_02443442.1| hypothetical protein ANACOL_02755 [Anaerotruncus colihominis DSM
           17241]
 gi|167666029|gb|EDS10159.1| hypothetical protein ANACOL_02755 [Anaerotruncus colihominis DSM
           17241]
          Length = 292

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 70/224 (31%), Positives = 108/224 (48%), Gaps = 27/224 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGI 157
           +LYEDS + V+NKPA ++     G+      + F +    + +    RL  RLD++TSG 
Sbjct: 83  ILYEDSDVIVYNKPAAMACHPVRGLRQGTLANVFARDCAANGESCACRLVGRLDRDTSGA 142

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+A+   AA  LT       ++K Y +LV G+P N K  + +  + +         +V 
Sbjct: 143 VVIAKNARAAAVLTG-----HVEKQYIALVTGMP-NPKHGVIDAPIGQPDRKNPRRMIVA 196

Query: 218 QNEKGANYAISHFKV-IDC--FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             +     A++ ++  I C  ++   C L     TGRTHQ+RVH   +GCP++GD  Y  
Sbjct: 197 NGKP----AVTEYETQIRCEGYSVVHCVLR----TGRTHQIRVHMASIGCPLLGDTLY-- 246

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHMVK 317
              G  T  I+ +  LH       HP   RL I  AP+P  M K
Sbjct: 247 ---GGETERIERQ-ALHCMQASFIHPVDKRLCIVHAPIPKDMQK 286


>gi|15600875|ref|NP_232505.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O1 biovar eltor str. N16961]
 gi|121586851|ref|ZP_01676632.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           2740-80]
 gi|121727007|ref|ZP_01680203.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V52]
 gi|147672092|ref|YP_001214876.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|153801249|ref|ZP_01955835.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-3]
 gi|153817723|ref|ZP_01970390.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           NCTC 8457]
 gi|153821627|ref|ZP_01974294.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|254225870|ref|ZP_04919473.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V51]
 gi|254284827|ref|ZP_04959794.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           AM-19226]
 gi|9657491|gb|AAF96018.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|121548894|gb|EAX58935.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           2740-80]
 gi|121630641|gb|EAX63030.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V52]
 gi|124123267|gb|EAY42010.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-3]
 gi|125621597|gb|EAZ49928.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V51]
 gi|126511765|gb|EAZ74359.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           NCTC 8457]
 gi|126520824|gb|EAZ78047.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|146314475|gb|ABQ19015.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|150425612|gb|EDN17388.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           AM-19226]
          Length = 221

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/205 (31%), Positives = 96/205 (46%), Gaps = 22/205 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NKPA      G  +   +   LK+   ++ +     HRLD  TSG+LV 
Sbjct: 20  IVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-TQAEGVFALHRLDMSTSGLLVF 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A TR A + L + F  R +QK Y +L+ G     +  I      +  + GD     +Q  
Sbjct: 79  ALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEI------QLPLCGDLDDRPRQKV 132

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
             +    A++H++ +    Q    + + PHTGRTHQLRVH  H   +  PIVGD  Y   
Sbjct: 133 CWQQGKPALTHWETVQV-EQNRTRVYLYPHTGRTHQLRVHCAHHLGLNAPIVGDDLYGLQ 191

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
            K         +L+LHA  +   HP
Sbjct: 192 DK---------RLFLHAEQLSFAHP 207


>gi|89898424|ref|YP_515534.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           felis Fe/C-56]
 gi|89331796|dbj|BAE81389.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           felis Fe/C-56]
          Length = 274

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 49/172 (28%), Positives = 86/172 (50%), Gaps = 18/172 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED    +++KP   + +  +                K     + HRLD++T+G ++ 
Sbjct: 71  ILWEDQHCCIYDKPTHTTTEDLA----------------KTTGLHIVHRLDRDTTGCILF 114

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+   +A  L+E F+ R+I K Y +LV+G PK     + ++   KS   G  +     ++
Sbjct: 115 AKNTNSAHALSELFKKRKIHKQYTALVFGHPKKSSGTLISYTAPKSRRCGAVI-FGNTDK 173

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                 I+H+ V+  + + +  +  QP TGRTHQ+R+H   +G PIVGD  Y
Sbjct: 174 HSGKLTITHWSVLHSY-KHYTLMLCQPFTGRTHQIRLHMHMLGNPIVGDLDY 224


>gi|315126893|ref|YP_004068896.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
 gi|315015407|gb|ADT68745.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
          Length = 237

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 64/211 (30%), Positives = 106/211 (50%), Gaps = 22/211 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQE 153
           ++Y+D  + V NKP+G+ S+ G + + +  D      V+ +  K       +L HRLD  
Sbjct: 26  IIYQDEALLVINKPSGLLSLSGKNPLNW--DSVHYRLVNGQQGKTAAFAEAKLPHRLDFG 83

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGI++VA    +A++L + F+   I K Y +++ G     K C  +  +    I  D +
Sbjct: 84  TSGIMLVALNSESAKNLNQQFQSHTISKRYVAMLQG-----KVCDNHGQINYP-IAKDKL 137

Query: 214 HV--VKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H   VK        A++H+ V+  F Q     ++  P TGRTHQLR+H+  +G PI+G  
Sbjct: 138 HFPRVKLCNTTGKAALTHYTVLKRFIQPIKTLVQFTPVTGRTHQLRIHSHAIGHPILG-- 195

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             C  +K   +  + ++L LHA  +   HP 
Sbjct: 196 --CDLYKSEQSEQMASRLQLHASDIYFHHPS 224


>gi|256761450|ref|ZP_05502030.1| pseudouridine synthase [Enterococcus faecalis T3]
 gi|256682701|gb|EEU22396.1| pseudouridine synthase [Enterococcus faecalis T3]
          Length = 287

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 71/260 (27%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +V+L    +  +  +LYED
Sbjct: 40  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTVHL---GEATRVKVLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 144 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVQVVQTLSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 258 -----ARLMLHASQLHLLHP 272


>gi|237752561|ref|ZP_04583041.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           winghamensis ATCC BAA-430]
 gi|229376050|gb|EEO26141.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           winghamensis ATCC BAA-430]
          Length = 290

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 54/154 (35%), Positives = 85/154 (55%), Gaps = 16/154 (10%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           L HRLD+ETSGIL++ +  ++  HL   E+F+  ++ K Y ++V GI   + E  A  ++
Sbjct: 132 LLHRLDKETSGILLLVKENSSF-HLKAKEAFKQLQVLKQYTAIVEGILDEECEITAPLII 190

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           KK       V + K NE     AI+H   ++ F +K   L+++  TG+THQ+R H  H+ 
Sbjct: 191 KKGK--SAKVSISKTNE--GQKAITHITPLEIFGKK-TKLDIEIKTGKTHQIRAHLAHIK 245

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            PI+GD  Y A           N++ LHAR++ L
Sbjct: 246 HPIIGDTLYGAK--------PANRILLHARHIAL 271


>gi|254509457|ref|ZP_05121534.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus 16]
 gi|219547619|gb|EED24667.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus 16]
          Length = 326

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 83/333 (24%), Positives = 156/333 (46%), Gaps = 50/333 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L +G+V+V+ + V K   ++  G+ +    
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTKVMGGEEI---- 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           ++ A   +  E++     + L          ++YED  I V NKP G  V  G+G     
Sbjct: 66  ILQA--ELEDEERWEAQDIPLD---------IVYEDDDILVINKPRGFVVHPGAGTP--- 111

Query: 130 DGFLKSWV----DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKI 182
           DG + + +     +  + PR  + HRLD++T+G++VVA+T  A   L  + + +R   + 
Sbjct: 112 DGTVLNALLHHYPNIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFVRE 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQ 238
           Y ++  G         A   +++  IG    H  K+     +     A++H++V + F +
Sbjct: 172 YEAIAIG------RMTAGGRIEQP-IGR---HSTKRTLMAVSPMGKPAVTHYRVAEHF-R 220

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKL------YL 290
           +   + ++  TGRTHQ+RVH  ++  P++GD  Y   A      T  +  K+       L
Sbjct: 221 EHTRIRLRLETGRTHQIRVHMSYLQHPLLGDSAYGGRARIPSGATEELAEKIRSFDRQAL 280

Query: 291 HARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           HA  +   HP  G  ++  AP+P  MV+  ++L
Sbjct: 281 HAVMLKFEHPITGEEVEFHAPVPDDMVEMAEAL 313


>gi|312601410|gb|ADQ90665.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 168]
          Length = 304

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 73/271 (26%), Positives = 130/271 (47%), Gaps = 36/271 (13%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI--QSGQVVRIPPVIN 72
           D+E++R+D             NL +  +  Q  + +K+V  NN +  +  Q+V+    I 
Sbjct: 12  DQEDIRIDILVAK------LANLSR--KVAQDLILEKKVLINNNLVLKKNQIVKTGQKIK 63

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
             N   + +  L+ +       DF    ++++D  + + NKP  + V  G G      ++
Sbjct: 64  IFNDYKRPKPQLEPA-----EVDFE---IIFQDQNMILINKPKNLVVHPGVGNWKNTLVN 115

Query: 131 GFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           G + S  DS  Q    +P + HRLD++T+G+L+VA+   A          R+I++ Y ++
Sbjct: 116 GLI-SHFDSLEQLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFA---QKFC 241
           V G      + +  ++     IG D  + +K+     N   AI++ ++I  F+   Q F 
Sbjct: 175 VIG------KVLHKFMKINLPIGRDLKNPLKKTISFFNSKPAITNVELIKHFSYQNQDFS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++ Q  TGRTHQ+R+H  H+G PI GD  Y
Sbjct: 229 LVKCQLETGRTHQIRLHLAHIGYPIYGDPIY 259


>gi|312149422|gb|ADQ29493.1| RNA pseudouridine synthase family [Borrelia burgdorferi N40]
          Length = 305

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 66/260 (25%), Positives = 126/260 (48%), Gaps = 32/260 (12%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R G +R++  +  F+ R+  G  + +   + A N  +   +   S+++      +++  
Sbjct: 29  IRKGDIRLNGLKSHFSCRVCKGDKIYLYKSL-AQNLNLTMDECFKSNIDFK----YIRKR 83

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGIL 158
           ++YEDS + V +K  GI V GG + + + ++ +L S  + S   KP   HRLD+ TSGI+
Sbjct: 84  IIYEDSDLLVLDKQKGILVHGGKNSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGII 143

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN----KKECIANWLLKKSHIGGD--Y 212
           + A+    A+ L+ +F    I K Y++++ G  K+    K     N  L+K+ +  D  +
Sbjct: 144 IFAKNINTARKLSAAFSGGSIIKKYFAILLGEVKSPVVYKNHLFRNKRLRKTFVLEDKNF 203

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+ + +             ++ C  ++   +E+   TG THQ+R        P++ D KY
Sbjct: 204 VNAITKVN----------PILSC--KRATLVEIVIETGFTHQIRSQCSFNNHPLINDKKY 251

Query: 273 CANFKGNFTSPIQNKLYLHA 292
           C  FK       ++  +LHA
Sbjct: 252 CNKFK-------KSDYFLHA 264


>gi|260583056|ref|ZP_05850838.1| tRNA pseudouridine synthase C [Haemophilus influenzae NT127]
 gi|260093907|gb|EEW77813.1| tRNA pseudouridine synthase C [Haemophilus influenzae NT127]
          Length = 222

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 60/228 (26%), Positives = 107/228 (46%), Gaps = 14/228 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKG 278
           K    A++ ++ +         +++ PHTGR HQLR H  H+  PI+GD +Y      + 
Sbjct: 120 KEPQEAVTDYEGLKI-------VKLIPHTGRKHQLRRHMKHIFHPILGDTQYGDLHQNRA 172

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
             +    ++L+LH+  +   HP    ++ ITA L     +  +  G++
Sbjct: 173 LMSHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 220


>gi|83648421|ref|YP_436856.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83636464|gb|ABC32431.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 248

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 118/241 (48%), Gaps = 26/241 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   +KP+G+ V   S I  H   F ++   D  G++    HRLD+ TSG+L+
Sbjct: 6   ILYQDEWLVAIDKPSGLLVHR-SEIDRHETLFAIQLLRDQIGRRVYPLHRLDKPTSGVLM 64

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVHVVK 217
            A     A+   ES+    + K Y ++V G+P   +E + +  LK+    +G   V    
Sbjct: 65  FALDSDTAKKCGESWETG-VDKAYLAIVRGVPA--EEGVIDKPLKEPWDRLGDRNV---- 117

Query: 218 QNEKGANYAISHF-KVIDCF---------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             +K    A++H+ ++ +C            ++  L+++P TGR HQ+R H   +  P++
Sbjct: 118 SKDKPEQPAVTHYQRLAECELPYAVDRYPTSRYALLKVRPQTGRRHQIRRHFKSLSHPLI 177

Query: 268 GDHKYCANFKGNFTSP---IQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
           GD  Y       F +    +Q +L LHA  M LPHP  G  L + AP+   M +  ++L 
Sbjct: 178 GDTSYGKGVHNRFFAEQFGVQ-RLLLHAAEMRLPHPCSGETLTVCAPVTGEMRRLLETLD 236

Query: 324 F 324
           +
Sbjct: 237 W 237


>gi|306820474|ref|ZP_07454110.1| ribosomal large subunit pseudouridine synthase D [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304551549|gb|EFM39504.1| ribosomal large subunit pseudouridine synthase D [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 300

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 73/301 (24%), Positives = 139/301 (46%), Gaps = 44/301 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            ++ DE  +RLD +  +    ++   +Q ++ SG + ++  + K + ++++G  V     
Sbjct: 6   TLQEDENLIRLDVYLGDKL-ELSRSKIQSLIESGNISLNGNKAKASVKLKTGDTV----Y 60

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----I 125
           +N       E K  D ++++           +YED  + V NKP G+     +G     +
Sbjct: 61  VNYQEENKAEIKAQDIALDI-----------VYEDDDVLVVNKPRGMVTHVANGNHEGTL 109

Query: 126 AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              +  +LK  +  +    R  + HR+D++TSG+LVVA+   ++  LT   +   + ++Y
Sbjct: 110 VNALLYYLKDDISLQNGMYRAGIVHRIDKDTSGLLVVAKNDFSSTELTNQLKDHSMTRVY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD----YVHVVKQNEKGANYAISHFKVIDCFAQK 239
             +  G+       I    + + +IG +      + V ++ K A+  I   ++     +K
Sbjct: 170 TLICNGV-------IDEETVIEQNIGRNPKDRMKYCVIEDGKYAHTTIIPLEIF----EK 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           + + +    TGRTHQ+RVH  H+  PIVGD  Y      N+   I  +L LHA  +   H
Sbjct: 219 YTYAKAILKTGRTHQIRVHLRHINRPIVGDRLYS-----NYKEKIDGQL-LHAGTLGFLH 272

Query: 300 P 300
           P
Sbjct: 273 P 273


>gi|257437725|ref|ZP_05613480.1| pseudouridine synthase, RluD [Faecalibacterium prausnitzii A2-165]
 gi|257200032|gb|EEU98316.1| pseudouridine synthase, RluD [Faecalibacterium prausnitzii A2-165]
          Length = 253

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 111/249 (44%), Gaps = 50/249 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED+ + V +KPAG++ + G   A     G   ++V        + HRLD   SG++V
Sbjct: 3   ILYEDTALVVLDKPAGLTSEEGVPAALRQRWGRPDAYVG-------VIHRLDTGVSGLMV 55

Query: 160 VARTRAAAQHLTESFRMR---------RIQ------------KIYWSLVWGIPKNK---K 195
            ART  AA  LT+              R++            K Y +++ G P  +   +
Sbjct: 56  YARTPGAAAALTKQVTESQQAYAILDGRVEAGPGAPAQPCFLKTYRAVIAGGPDEQLPPE 115

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQ 254
             + ++L K S  G   V  VK+  KG   A+  +++++        L E+  HTGRTHQ
Sbjct: 116 GILRDYLFKDSRKG--RVFPVKRPRKGVREAVLEYRIVETAPDGSLSLAEITLHTGRTHQ 173

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAPL 311
           +RV       P+ GD KY + FKG+        + L +  +   HPE G     Q+  P+
Sbjct: 174 IRVQFASRKHPLYGDGKYGSRFKGD--------IALQSAGLQFVHPETGEKMAFQLEKPI 225

Query: 312 PAHMVKTWD 320
            A     WD
Sbjct: 226 KA----PWD 230


>gi|301168229|emb|CBW27818.1| putative ribosomal large subunit pseudouridine synthase D
           [Bacteriovorax marinus SJ]
          Length = 333

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 60/186 (32%), Positives = 95/186 (51%), Gaps = 10/186 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETS 155
           LK  +++ED ++ + +KP  +S         H+      + +S  +K     HRLD+ETS
Sbjct: 72  LKPSIIFEDDELIIISKPPYMSTHP---TGKHLFNCATVYFESLYKKTVHSIHRLDRETS 128

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA-NWLLKKSHIGGDYV- 213
           G+L++A+T   AQ +T+ F    ++K Y+ + +    N ++    N  L  S  G   V 
Sbjct: 129 GVLMLAKTPKCAQSMTDCFEKDLVRKCYFFIAYNKSWNGEQSFEDNHRLGASEEGLKRVY 188

Query: 214 --HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             H  K++ +G + A + F+VI         L   P TGR HQ+RVHA+  G P+VGD  
Sbjct: 189 INHFPKESSEGKS-ARTLFRVIHSEGDYVLGLAF-PITGRQHQIRVHAMINGLPLVGDKL 246

Query: 272 YCANFK 277
           Y  NFK
Sbjct: 247 YLGNFK 252


>gi|213417523|ref|ZP_03350665.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 122

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 45/121 (37%), Positives = 71/121 (58%), Gaps = 7/121 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   +++SG  VR
Sbjct: 8   VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLESGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPV------RVAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAVHGGSGLS 120

Query: 127 Y 127
           +
Sbjct: 121 F 121


>gi|270263927|ref|ZP_06192195.1| hypothetical protein SOD_f01410 [Serratia odorifera 4Rx13]
 gi|270042120|gb|EFA15216.1| hypothetical protein SOD_f01410 [Serratia odorifera 4Rx13]
          Length = 216

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 66/201 (32%), Positives = 100/201 (49%), Gaps = 12/201 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I V NK +G+ SV G    A      L + + +        HRLD  TSG++V
Sbjct: 13  ILYQDEHIIVVNKASGLLSVPGR---APENKDSLMTRIQADFPAAESVHRLDMATSGVIV 69

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA  +AA + L   FR R  +K Y + VWG  ++  E + +  L           V  + 
Sbjct: 70  VALNKAAERELKRQFREREPKKSYIARVWGHLEH-DEGLVDLPLICDWPNRPLQKVCFET 128

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K A    + + V+   A     +++ P TGR+HQLRVH L +G PI+GD  Y A+ +  
Sbjct: 129 GKAAQ---TEYLVMSRDADGSTRVKLTPITGRSHQLRVHMLALGHPILGDGFY-AHPEAK 184

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
             +P   +L LHA+ + + HP
Sbjct: 185 AMAP---RLQLHAQELRITHP 202


>gi|84394418|ref|ZP_00993135.1| pseudouridine synthase Rlu family protein [Vibrio splendidus 12B01]
 gi|84374951|gb|EAP91881.1| pseudouridine synthase Rlu family protein [Vibrio splendidus 12B01]
          Length = 249

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 71/248 (28%), Positives = 111/248 (44%), Gaps = 29/248 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IIYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG----------IPKNKKECIANWLLKKSHIGG 210
           A +   A  +   F    +QK Y ++V G            K + + IA+   K+     
Sbjct: 64  ALSSEVASQVMPMFANHEMQKTYHAIVRGWIEEGDTLDYALKVELDKIADKFAKEDKEPQ 123

Query: 211 DYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           + V V +   K    Y+   F        ++C +EM P TGR HQLR H  H+  PIVGD
Sbjct: 124 EAVTVYEPLAKVEVPYSTGRFPT-----SRYCLVEMMPKTGRKHQLRRHMAHLRHPIVGD 178

Query: 270 H-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL-- 322
                 K+   F+ +  S   ++L LHA  +   HP   +  +   + A + +TW  L  
Sbjct: 179 TSHGDGKHNRLFRDDLDS---HRLLLHASELRFIHPFTKKELV---MKASLDETWLRLFE 232

Query: 323 GFKYDRNL 330
            F++D +L
Sbjct: 233 TFEWDTSL 240


>gi|145355458|ref|XP_001421978.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582217|gb|ABP00272.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 321

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 84/318 (26%), Positives = 133/318 (41%), Gaps = 95/318 (29%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ +L+ D  + V +KP G++   G+G+   +   L+  +DS+     + HRLD++TSG
Sbjct: 11  IRARVLHADEHVTVVDKPPGLATTRGNGVDVSVYD-LRHALDSE----YVVHRLDRDTSG 65

Query: 157 ILVVARTRAAAQHL------------TESFR--MRR----------IQKIYWSLVWGIPK 192
           +LV+ART  AA  L            TE  R  M R          + K YW+L    P 
Sbjct: 66  VLVLARTAFAANRLNAMFAKKSRMDFTEIMRADMERGDAPSLSNDPVVKTYWALTSNPPP 125

Query: 193 NKKECIANWLLKK-SHIG-GDYVHVV--------------------------KQNEKGA- 223
             +   + W+    + +G GD                               K N+ G+ 
Sbjct: 126 --RGARSGWIEAPLTEVGDGDGYSTARLVGGWRVYDAKGGGVVVGTGESMRDKSNDAGSP 183

Query: 224 --NYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCAN---- 275
               A++HFKV+    +     LE+ P TGR HQLRVH A  +  PI+GD+KY  N    
Sbjct: 184 ASKAAMTHFKVLASAGEDGPTLLELTPITGRKHQLRVHLAKALSSPIIGDYKYGFNDRRA 243

Query: 276 -FKGNFT----SPIQNK---------------------LYLHARYMDLPHPEGG-RLQIT 308
            +K  FT    + ++++                     L+LHAR +   HPE G   ++ 
Sbjct: 244 PWKSRFTDIESADVESEKESDFWRKLRRASLRGVSKIPLHLHARALQFVHPESGVSTRVV 303

Query: 309 APLPAHMVKTWDSLGFKY 326
           A  P H      +   K+
Sbjct: 304 AEPPPHFAAALRAFDLKF 321


>gi|257066386|ref|YP_003152642.1| pseudouridine synthase, RluA family [Anaerococcus prevotii DSM
           20548]
 gi|256798266|gb|ACV28921.1| pseudouridine synthase, RluA family [Anaerococcus prevotii DSM
           20548]
          Length = 318

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 71/274 (25%), Positives = 130/274 (47%), Gaps = 32/274 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           + END  N R DR+ + ++ +     +QK +R    +++ KR K ++ +    +V++   
Sbjct: 6   ISENDG-NQRFDRFLRKYFENAPLSVIQKNIRKKNFKINDKRAKKDDFVYPNDIVKM--- 61

Query: 71  INALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
                  IK++        +  K SDF   I+ YED+ I + +K +G+     S   Y  
Sbjct: 62  ------YIKDEDYDKWITKIDYKPSDFDLDIV-YEDNNIIIMDKKSGLLTHSSSKKDYGN 114

Query: 129 --IDGFL------KSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             +D  L      KS+ +  +  KP + +RLD+ T+G+++ A+   + + L ++ R  +I
Sbjct: 115 NLVDNMLHYLYKTKSFDMSDRTFKPAVVNRLDRNTAGLVIGAKNAESLRSLNKAIRENKI 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            K Y ++V G        +       +HI   D  + V ++  G     ++FK ++   +
Sbjct: 175 DKFYLTIVKG-------YVEKEFSIDTHISKNDNRNRVSKSRNGKRIK-TNFKPLET-NK 225

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           KF  LE +  TG+THQ+R        PI+GD KY
Sbjct: 226 KFSLLECELITGKTHQIRFSLKENSTPIIGDRKY 259


>gi|218289812|ref|ZP_03494012.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
 gi|218240103|gb|EED07288.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
          Length = 314

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 58/230 (25%), Positives = 106/230 (46%), Gaps = 10/230 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILV 159
           +LY D  + V +KP  + V      A  +D  ++  ++ +G  +    HRLD+ T+G ++
Sbjct: 87  VLYSDPSLMVVDKPENLLVHSDGSDAPTLDACVQRLLNEEGAGRAYHVHRLDRGTTGCVL 146

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+     + +       R+++ Y ++  G  + +   ++  + +  H+ G Y   V   
Sbjct: 147 YAKHGLMLRAMDAELAAGRVRRTYLAIACGS-RIRPGVMSAPIGRDRHVSGRYR--VSWT 203

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K A   +      D   +++  + ++  TGR HQ+RVH   MG P+VGD    A + G 
Sbjct: 204 GKAARTHVEVLDEADQGGERWTLVRLRLETGRRHQIRVHLSAMGAPVVGD----ALYGGT 259

Query: 280 FTSPIQ-NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             S +Q  ++ LHA  +   HP  G  + + APLP    K    +G  +D
Sbjct: 260 PHSALQPGQIALHAARLQFRHPYAGEDVDVRAPLPPAWAKLAADVGLSFD 309


>gi|145636754|ref|ZP_01792420.1| hypothetical protein CGSHiHH_06555 [Haemophilus influenzae PittHH]
 gi|145270052|gb|EDK09989.1| hypothetical protein CGSHiHH_06555 [Haemophilus influenzae PittHH]
          Length = 224

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 96/203 (47%), Gaps = 28/203 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+ S   + NKP GISV      QG + +        K W         L HRLD+ T
Sbjct: 5   VVYQHSDFIIINKPEGISVHKDQEEQGLTELVAKQLNVPKVW---------LVHRLDKVT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A    +A   +  F   +I K Y +L    PK K+  I    +KK+  G   + 
Sbjct: 56  SGLLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGD-MKKARDGAWKLC 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K+N      AI+ F  + C      ++ ++P TG+THQLRV    +G PI+GD  Y  
Sbjct: 115 QTKENP-----AITRFASVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDGLYGK 168

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
           N     T  I ++ YLHA  ++ 
Sbjct: 169 N-----TEKI-DRTYLHATQLEF 185


>gi|148825678|ref|YP_001290431.1| hypothetical protein CGSHiEE_03090 [Haemophilus influenzae PittEE]
 gi|229846961|ref|ZP_04467067.1| hypothetical protein CGSHi7P49H1_05916 [Haemophilus influenzae
           7P49H1]
 gi|148715838|gb|ABQ98048.1| hypothetical protein CGSHiEE_03090 [Haemophilus influenzae PittEE]
 gi|229810045|gb|EEP45765.1| hypothetical protein CGSHi7P49H1_05916 [Haemophilus influenzae
           7P49H1]
 gi|309972824|gb|ADO96025.1| Probable pseudouridylate synthase [Haemophilus influenzae R2846]
          Length = 224

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 96/203 (47%), Gaps = 28/203 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+ S   + NKP GISV      QG + +        K W         L HRLD+ T
Sbjct: 5   VVYQHSDFIIINKPEGISVHKDQEEQGLTELVAKQLNVPKVW---------LVHRLDKVT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A    +A   +  F   +I K Y +L    PK K+  I    +KK+  G   + 
Sbjct: 56  SGLLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGD-MKKAREGAWKLC 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K+N      AI+ F  + C      ++ ++P TG+THQLRV    +G PI+GD  Y  
Sbjct: 115 QTKENP-----AITRFASVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDGLYGK 168

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
           N     T  I ++ YLHA  ++ 
Sbjct: 169 N-----TEKI-DRTYLHATQLEF 185


>gi|37675814|ref|NP_936210.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
 gi|37200353|dbj|BAC96180.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
          Length = 565

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 67/205 (32%), Positives = 105/205 (51%), Gaps = 22/205 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V NKP+G+    G  I       L++ + D +G  P + HRLD  TSG+LV
Sbjct: 364 IVYQDEAMVVVNKPSGLLSVPGKTITDSAYARLQALFPDVEG--PFVIHRLDMATSGLLV 421

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            A TR A + L + F  R +QK Y +L+ G +P+++ E      ++          V  +
Sbjct: 422 FALTRRANKSLQKQFISRGVQKRYVALLEGEVPQSQGEI--TLPMRGDPDDRPRQLVCFE 479

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHKYCAN 275
           + K A+      ++ D  ++ + +    P TGRTHQLRVH A H+G   P+VGD  Y   
Sbjct: 480 HGKPAHTDWQLIEIHDGRSKLYLY----PRTGRTHQLRVHCAHHLGLHMPMVGDGLYGEK 535

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                     N+L+LHA  ++L HP
Sbjct: 536 ---------ANRLHLHAESLELDHP 551


>gi|293363941|ref|ZP_06610677.1| pseudouridine synthase, RluA family [Mycoplasma alligatoris A21JP2]
 gi|292552431|gb|EFF41205.1| pseudouridine synthase, RluA family [Mycoplasma alligatoris A21JP2]
          Length = 312

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 80/304 (26%), Positives = 135/304 (44%), Gaps = 71/304 (23%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDK---KRVKFNNRIQSGQVVRIPPVINALNH 76
           R+D++  N+   I+  +++ ++    V V+     + KF+  +  GQV+ I  +I+    
Sbjct: 11  RIDKYISNN-SEISRNDIKSLIEQKAVLVNDIVVNKPKFS--VNEGQVITILKLID---- 63

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAY 127
             KE KI   +++L          + YED  + V  KP+G+ V    G         + Y
Sbjct: 64  --KEIKIEAQNIDLD---------IAYEDEYLLVLKKPSGMVVHPAPGHHENTLVNALLY 112

Query: 128 HIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           H   F  +  +  G  +P + HR+D++TSG+L++A+     + L E F  + I + Y ++
Sbjct: 113 H---FKNNLSNENGLLRPGIVHRIDKDTSGLLLIAKNNEVHKILAEGFATKTINRKYVAI 169

Query: 187 VWGIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
             GI K+ K      L     IG D      + +   N K    A++H +++  F     
Sbjct: 170 CDGILKSPK------LKLDLPIGRDIKNRQLMAITNANSKS---AVTHLELLKSF----- 215

Query: 242 WLEMQP--------HTGRTHQLRVHALHMGCPIVGDHKYCAN----------FKGNFTSP 283
           + E QP         TGRTHQ+RVH  ++  P+ GD  Y             +K  F  P
Sbjct: 216 YYENQPKSLVKATLETGRTHQIRVHCAYIKNPVFGDPVYGRKVDDFNQRLHAYKLEFNHP 275

Query: 284 IQNK 287
           I NK
Sbjct: 276 ITNK 279


>gi|229171950|ref|ZP_04299515.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           MM3]
 gi|228611293|gb|EEK68550.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           MM3]
          Length = 292

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 77/310 (24%), Positives = 140/310 (45%), Gaps = 35/310 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I  R G + V+ +     +++Q+G+ +R+  P
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFRGGAIEVNNQHASVRHQLQAGEELRVFFP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYH 128
           V      +IKE   L                ++YED  + V NK A +S +      A  
Sbjct: 63  VEERSEGMIKEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPAGS 107

Query: 129 IDGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L S  D +       +  RLD++TSG++++A+ R     L++  + + +++ Y ++
Sbjct: 108 VANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAI 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    ++  I   + +KS    D +      E G   A++HF+V+D    K   + ++
Sbjct: 168 VHGEMIEREGTIDAPIGRKS----DSIIERTVCENG-QRAVTHFRVMDSVNHK-THVSLE 221

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
             TGRTHQ+RVH  H+G P++GD  Y           +  +  LH+  +   HP     +
Sbjct: 222 LETGRTHQIRVHMAHIGHPLLGDDLYGGR------RDVIKRQALHSTSLTFYHPILEKEM 275

Query: 306 QITAPLPAHM 315
             T  +P+ M
Sbjct: 276 SFTTTIPSDM 285


>gi|223889337|ref|ZP_03623924.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           64b]
 gi|224532458|ref|ZP_03673084.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           WI91-23]
 gi|226321280|ref|ZP_03796808.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           Bol26]
 gi|223885258|gb|EEF56361.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           64b]
 gi|224512630|gb|EEF83005.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           WI91-23]
 gi|226233312|gb|EEH32063.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           Bol26]
          Length = 313

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 70/268 (26%), Positives = 124/268 (46%), Gaps = 48/268 (17%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R G +R++  +  F+ R+  G  + +              K L  ++NLT    F  +I
Sbjct: 37  IRKGDIRLNGLKSHFSCRVCKGDKIYL-------------YKSLSQNLNLTMDECFKSNI 83

Query: 101 --------LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSW-VDSKGQKPRLTHRL 150
                   ++YEDS + V +K  GI V GG + + + ++ +L S  + S   KP   HRL
Sbjct: 84  DFQYIRKRIIYEDSDLLVLDKQKGILVHGGKNSLDFLVNSYLLSQNLRSLSFKPSAVHRL 143

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN----KKECIANWLLKKS 206
           D+ TSGI++ A+    A+ L+ +F    I K Y++++ G  K+    K     N  L+K+
Sbjct: 144 DRNTSGIIIFAKNINTARKLSAAFSGGSIIKKYFAILLGEVKSPVVYKNHLFRNKRLRKT 203

Query: 207 HIGGD--YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            +  D  +V+ + +             ++ C  ++   +E+   TG THQ+R        
Sbjct: 204 FVLEDKNFVNAITKVN----------PILSC--KRATLVEIVIETGFTHQIRSQCSFNNH 251

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           P++ D KYC  FK       ++  +LHA
Sbjct: 252 PLINDKKYCNKFK-------KSDYFLHA 272


>gi|319897067|ref|YP_004135262.1| tRNA pseudouridine synthase [Haemophilus influenzae F3031]
 gi|317432571|emb|CBY80931.1| tRNA pseudouridine synthase [Haemophilus influenzae F3031]
          Length = 239

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 61/238 (25%), Positives = 109/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|188579049|ref|YP_001915978.1| tRNA pseudouridine synthase C [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188523501|gb|ACD61446.1| tRNA pseudouridine synthase C [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 238

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 110/236 (46%), Gaps = 26/236 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D  + V +K AG+ V   S +A   D FL   +  +  +P  L HRLD+ TSG L+
Sbjct: 10  ILYQDDVLAVVDKTAGLMVHD-SKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGCLL 68

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R  A  L ++     +QK Y ++  G P   +  + + L      GG    V K  
Sbjct: 69  LAFDRETASALGKALMSGDVQKDYLAVCRGWPAEPRFTVDHDL-----DGGPGKPVKKP- 122

Query: 220 EKGANYAISHFKVIDC---------FA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +           FA  ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 123 ------ALTHFQRLATGELQVPSTGFATSRYALLRCQPQTGRFRQIRRHLKHLSHHLIGD 176

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
             +       NF     +++ LHA+ +  PHP +G R+++TAPL     K     G
Sbjct: 177 TSHGDGRHNRNFRMLGIHRMLLHAKRLAFPHPADGRRIRVTAPLDDEFTKACALFG 232


>gi|9971939|gb|AAG10501.1|AF279106_63 predicted ribosomal large subunit pseudouridine synthase D
           [uncultured marine gamma proteobacterium EBAC31A08]
          Length = 310

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 73/269 (27%), Positives = 130/269 (48%), Gaps = 35/269 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ND  +MRLD+     +   +   ++K +  G+V ++ +  +  +++     + + P  
Sbjct: 6   VPNDLSSMRLDKATAEMFTDYSRTQIKKWIEEGRVLINGEVSQPRDKVYENDQIELSPK- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +EQK+   + ++    DF    + +E+    + NKPAG+ +  GSG     DG
Sbjct: 65  -------EEQKVSWEAQDI----DFE---IHFENEDFIIINKPAGLIMHPGSGCY---DG 107

Query: 132 FLKSWVDSKGQK----PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L + +  K  +    PR  + HRLD++TSGIL+VAR  +         + RR+ K Y S
Sbjct: 108 TLANGLIYKFPELINIPRSGIVHRLDKDTSGILLVARNESFRNFFINEMQERRVVKKYTS 167

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWL 243
           +V G        + ++ +++  IG D  +  K    E G + A++  K+ +     +  L
Sbjct: 168 IVIG------STLGSFSIEEP-IGRDKNNRTKMAIREDGKD-ALTFVKLKENIGN-YSVL 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +++  TGRTHQ+RVH      PI+GD  Y
Sbjct: 219 DIRIETGRTHQIRVHLSSKKLPIIGDKTY 247


>gi|71894605|ref|YP_278713.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           synoviae 53]
 gi|71851393|gb|AAZ44002.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           synoviae 53]
          Length = 303

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 71/268 (26%), Positives = 127/268 (47%), Gaps = 39/268 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D++  ++   ++  ++Q++++S  V V+   V      +   +V  P  I  +  + K
Sbjct: 11  RIDKYIASN-SSLSRADIQELIKSKAVFVNNGLV-----CKPSYIVHPPQEIKIIRLLDK 64

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG---------GSGIAYHID 130
             KI   ++ L          ++YED  + + +KP+G+ V            +G+ YH  
Sbjct: 65  TPKIEAQNIKLD---------IIYEDDHLVIIDKPSGLIVHPSPTHYENTLANGLLYH-- 113

Query: 131 GFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            F  +  D+ G  +P + HR+D++TSG+L+V +T A    L E F+   I++ Y ++   
Sbjct: 114 -FKNNLSDTNGLLRPGIVHRIDKDTSGLLIVTKTNAVHIKLAEMFKNHSIKRSYIAICDN 172

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCF---AQKFCWLE 244
              +KK      L     IG D  +  K+      A  AI++ ++I  F    Q    ++
Sbjct: 173 FLTDKK------LRINLPIGLDPKNPQKRKVTNIKAKEAITNVELIKTFYHEKQPKSLVK 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               TGRTHQ+RVH  H+  PI GD+ Y
Sbjct: 227 CNLETGRTHQIRVHLAHINNPIYGDNVY 254


>gi|307331663|ref|ZP_07610770.1| pseudouridine synthase, RluA family [Streptomyces violaceusniger Tu
           4113]
 gi|306882689|gb|EFN13768.1| pseudouridine synthase, RluA family [Streptomyces violaceusniger Tu
           4113]
          Length = 322

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 76/310 (24%), Positives = 139/310 (44%), Gaps = 29/310 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           +S +  ++ + V +  E  R+D      +   +     ++  +G+V++D      ++R+ 
Sbjct: 10  VSTIPEIRTLPVPDGLEGERVDAAIARMF-GFSRTKAAELAAAGKVQLDGTVAGKSDRVS 68

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +      L       +++   V   +        ++++D  I V +KP G++  
Sbjct: 69  GGAWLEV-----ELPQAAPPVRVVAEPVEGME--------IVHDDEDIVVVSKPVGVAAH 115

Query: 121 GGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESF 174
              G     + G L +    V + G   R  + HRLD  TSG++VVA++  A   L ++F
Sbjct: 116 PSPGWTGPTVIGGLAAAGFRVSTSGAAERQGIVHRLDVGTSGLMVVAKSELAYSVLKQAF 175

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R + K Y +LV G P      I   + +  H   DY   V  + K    +++H+ +I+
Sbjct: 176 RERTVDKRYHALVQGHPDPLSGTIDAPIGR--HPQHDYKWAVTADGK---PSVTHYDLIE 230

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHAR 293
            F +    L+++  TGRTHQ+RVH      P VGD  Y A+        ++  + +LHA 
Sbjct: 231 AF-RAASLLDIKLETGRTHQIRVHMAAHRHPCVGDLTYGAD--PTLAKRLKLTRQWLHAM 287

Query: 294 YMDLPHPEGG 303
            +   HP  G
Sbjct: 288 RLGFEHPAHG 297


>gi|212640160|ref|YP_002316680.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
 gi|212561640|gb|ACJ34695.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
          Length = 315

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 112/246 (45%), Gaps = 37/246 (15%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG---------GSGIAYH 128
           IKE++I  +   +  H       +++ED  + V NK A + V            + +A+H
Sbjct: 82  IKEEQIEPTPTYVPLH-------IVFEDDHVLVVNKRAHMDVHPTQPGQTNTLANAVAFH 134

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                    +    K R  HRLD++TSG+++ A+   A   L +    R I++ Y +LV 
Sbjct: 135 FQ------CEGIYSKVRHIHRLDRDTSGVILFAKHALAGAILDQYLAKRTIRRTYIALVH 188

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWL-EMQ 246
           G  K KK  I      ++ IG D  H  ++   K  + AI+H++ +    QK   L  + 
Sbjct: 189 GYVKQKKGTI------EAPIGRDRHHPTRRRVSKTGDTAITHYERLQYDKQKHVSLVRLT 242

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
             TGRTHQ+RVH  ++G P+VGD  Y          P  ++  LHA  +   HP    L 
Sbjct: 243 LDTGRTHQIRVHMSYIGHPLVGDTLYGGK-------PWIDRQALHAFSLSFLHPFTEELI 295

Query: 307 ITAPLP 312
             + LP
Sbjct: 296 TCSALP 301


>gi|182623983|ref|ZP_02951771.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
 gi|177910876|gb|EDT73230.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
          Length = 298

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 82/301 (27%), Positives = 137/301 (45%), Gaps = 52/301 (17%)

Query: 39  KILRSG----QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++RS     +++VD   VK N  +++G+ ++I        +I  E+  ++         
Sbjct: 30  RLIRSAAIDKRIKVDGVAVKMNYVVKTGEEIKIELSKKESQNIEPEKMDIE--------- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPR 145
                 ++YEDS I V NK   + V            +GI Y+   F +S  D      R
Sbjct: 81  ------IVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYY---FKESNQDCI---VR 128

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L  RLD  TSG++++ + + A   L+   +  + QK Y ++V G  + K+  I   + + 
Sbjct: 129 LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRP 188

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHM 262
           +    D +  V  +E+G   +I+H+KVI+ +       C LE    TGRTHQ+RVH   +
Sbjct: 189 AE---DTIKRV-VDERGQE-SITHYKVIESYEGADLVECLLE----TGRTHQIRVHLSSL 239

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           G PI GD  Y     G       ++  LHA  +D   P+    L + A LP  M +  + 
Sbjct: 240 GHPIFGDSLY-----GTEDEDFISRQALHAYGLDFYSPKTKEPLSLRADLPEDMKELINK 294

Query: 322 L 322
           L
Sbjct: 295 L 295


>gi|319940421|ref|ZP_08014771.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319810477|gb|EFW06819.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 286

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 98/222 (44%), Gaps = 26/222 (11%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E+ IL    NL +         LY+D  I + NKP GI           +   + ++V  
Sbjct: 70  EKSILMGKANLVEE--------LYQDEHIIIVNKPEGIKTHANEPTELALLNHVYAYV-- 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G    + HRLD+ETSG ++ A+       L      + I + YW+LV G+   K++   
Sbjct: 120 -GNTCYVVHRLDKETSGAVLFAKNPFILPILNRLLENKEISREYWALVQGVFPKKRQIYT 178

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + + +  H     + V  +N + A   ++  K I       C L+    TGRTHQ+RVH 
Sbjct: 179 DKIGRDRHDRRKRL-VDNKNGQYAETQVTKLKEIGNNTLIKCQLK----TGRTHQIRVHL 233

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHP 300
            H G PIVGD  Y         +P + K L LHA  +   HP
Sbjct: 234 AHHGHPIVGDPLY---------NPQKAKRLMLHAHRLTFTHP 266


>gi|225351455|ref|ZP_03742478.1| hypothetical protein BIFPSEUDO_03050 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225157799|gb|EEG71082.1| hypothetical protein BIFPSEUDO_03050 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 312

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 74/282 (26%), Positives = 130/282 (46%), Gaps = 43/282 (15%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+     +++ SGQ RV  + +  ++ +QSG+ V           I++E+         T
Sbjct: 26  ISRAKAAELIESGQARVLGRDISKSSTLQSGETVEF--------DIVEER---------T 68

Query: 92  KHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD------SKGQKP 144
           +     + + ++YED  + V +KP G++    + + +     L S +D      S G   
Sbjct: 69  EPEPIARDMAVVYEDDDVIVVDKPVGVAAH--ASVGWTGPTVLGSLLDRGVHITSYGAAG 126

Query: 145 R--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           R  +  RLD  TSG+++V ++  A   +   F    + K Y +LV G  K  K  I    
Sbjct: 127 RQGIVSRLDVGTSGLMLVCKSDLAYVEMRRQFAEHEVVKTYHALVQGNLKENKATI---- 182

Query: 203 LKKSHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             ++ IG     D+   V    K    AI+H+ V++ F +    + +   TGRTHQ+RVH
Sbjct: 183 --EAPIGRAKVSDFRFCVTPAGK---EAITHWDVMERFGEA-TLVSVNLETGRTHQIRVH 236

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
              +G P+ GD  Y AN +      ++ + +LHA+ ++  HP
Sbjct: 237 FSSIGHPLAGDAMYGANPQLGEALGLERQ-WLHAKQLEFRHP 277


>gi|254225113|ref|ZP_04918727.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V51]
 gi|125622500|gb|EAZ50820.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V51]
          Length = 245

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 60/217 (27%), Positives = 102/217 (47%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASDVMPMFANHEMEKTYHAIVRGWIEEAN--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVG
Sbjct: 118 QDKEAQSAMTAYRPLAKVELPISTGKFTTTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP 300
           D  +        F+ +F++    +L LHA  +   HP
Sbjct: 178 DTTHGDGVHNRLFREHFSA---QRLMLHASELRFMHP 211


>gi|332716762|ref|YP_004444228.1| ribosomal large subunit pseudouridine synthase A [Agrobacterium sp.
           H13-3]
 gi|325063447|gb|ADY67137.1| ribosomal large subunit pseudouridine synthase A [Agrobacterium sp.
           H13-3]
          Length = 222

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 61/212 (28%), Positives = 104/212 (49%), Gaps = 10/212 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  + V +KP+G+    G   A  +   L + V  +  K  + +RLD++TSGI+++
Sbjct: 20  IVHRDDDLLVLDKPSGLLSVPGRDPA--LSDSLLTRVQKQFPKALMINRLDKDTSGIVLM 77

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           +  R A   +   F  R+ +K Y ++VWG  + ++  +   L     I  +     + + 
Sbjct: 78  SLNRKAHATVAAQFENRQTRKSYVAVVWGEVEGEEGKVDLPLA----IDPENKPRHRVDH 133

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A S ++V++        L + P TGRTHQLRVH   +G PI+GD  Y A  +   
Sbjct: 134 DHGKPAQSLWRVLERLPLPATRLALAPLTGRTHQLRVHMKALGHPILGDEFY-AEGEALA 192

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
            +P   +L LHA  +   HP+G  +  T P P
Sbjct: 193 AAP---RLMLHAEAVGFRHPDGRDVTYTVPCP 221


>gi|293609056|ref|ZP_06691359.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292829629|gb|EFF87991.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 350

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 71/248 (28%), Positives = 114/248 (45%), Gaps = 36/248 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP G+ V  G+G         + YH          ++  +  L HR+D
Sbjct: 117 IVYEDDDILVINKPVGMVVHPGAGNSSGTLVNALLYHFPKL------AELSRAGLVHRID 170

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA++  A   L++    + + ++Y  +V+G        IA   + +  I   
Sbjct: 171 KDTSGLLVVAKSLEAQFSLSKQLANKTVYRVYDLVVYG------NIIAGGTIDE-QIKRH 223

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V  VK     G   A++H+ V + F + F  ++ +  TGRTHQ+RVH  ++G  ++GD 
Sbjct: 224 PVDRVKMAILPGGRDAVTHYNVKERF-KDFTRVQARLETGRTHQIRVHFSYIGYGLIGDQ 282

Query: 271 KYCANFK---GNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITAPLP---AHMVKT 318
            Y    +   G     I+      +  LHA  + L HP  G  +   AP P    H+V  
Sbjct: 283 VYMNRVRVPAGASELLIETLRGFKRQALHAAKLGLKHPRTGEEMLFEAPWPEDFTHLVNV 342

Query: 319 WDSLGFKY 326
             S    Y
Sbjct: 343 LRSENAAY 350


>gi|293449117|ref|ZP_06663538.1| tRNA pseudouridine synthase C [Escherichia coli B088]
 gi|291322207|gb|EFE61636.1| tRNA pseudouridine synthase C [Escherichia coli B088]
          Length = 260

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 116/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG+  A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGSQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|307284559|ref|ZP_07564721.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
 gi|306503236|gb|EFM72490.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
          Length = 283

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHL---GETTRVKVLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|237738430|ref|ZP_04568911.1| LOW QUALITY PROTEIN: conserved hypothetical protein [Fusobacterium
           mortiferum ATCC 9817]
 gi|229420310|gb|EEO35357.1| LOW QUALITY PROTEIN: conserved hypothetical protein [Fusobacterium
           mortiferum ATCC 9817]
          Length = 181

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 54/184 (29%), Positives = 96/184 (52%), Gaps = 14/184 (7%)

Query: 132 FLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           + K+++  K  K ++   HRLD++TSG+++ A++  A   L  ++     ++ Y +LV G
Sbjct: 1   YFKNYLKEKNPKDKIFVVHRLDRDTSGVMIFAKSEKAQDILQTTWNDSVKERTYVALVEG 60

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             K   + I ++L +   +    +     NE+    A+SH+KV+    + +  LE+   T
Sbjct: 61  NVKKDSDTIISYLAENKAM----ITYSTANEEEGKKAVSHYKVLKR-NKNYSLLEVNIET 115

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GR +Q+RVH   +G  +VGD KY     G+  +PI+ +L LHA  +   HP     L  T
Sbjct: 116 GRKNQIRVHMQDLGHSVVGDKKY-----GSTKNPIK-RLGLHAHTIVFKHPITKEVLSFT 169

Query: 309 APLP 312
           + +P
Sbjct: 170 SKIP 173


>gi|27365203|ref|NP_760731.1| tRNA pseudouridine synthase C [Vibrio vulnificus CMCP6]
 gi|34582413|sp|Q8DBG5|TRUC_VIBVU RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|27361350|gb|AAO10258.1| tRNA pseudouridine synthase C [Vibrio vulnificus CMCP6]
          Length = 245

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 106/242 (43%), Gaps = 25/242 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F  + + K Y ++V G  + + E      ++   I   +       E
Sbjct: 64  ALSSEVASQVMPMFAGQEMSKTYHAIVRGWIEEEGELDYALKVELDKIADKFA----SQE 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ +K +               ++  +E++P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQDAITLYKPLAKVEVPYSTSKFPTTRYGLMELKPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 -----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                K+   F+  F +P   +L LHA  +   HP     Q    + A + K W  L  +
Sbjct: 180 THGDGKHNKLFREEFDAP---RLLLHASELRFVHP---YTQQEVVIRAEVDKVWQQLFER 233

Query: 326 YD 327
           ++
Sbjct: 234 FE 235


>gi|266623222|ref|ZP_06116157.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           hathewayi DSM 13479]
 gi|288865005|gb|EFC97303.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           hathewayi DSM 13479]
          Length = 311

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 115/239 (48%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKP--RLTHRLDQETSGI 157
           + YED  + + NK AG+ +    G   +      +W +  KG+    R  +RLD++T+G+
Sbjct: 83  ICYEDRDLLIINKAAGVPIHPSQGNHDNTLANGIAWYLGEKGETAAYRAINRLDRDTTGL 142

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++AR   +A  L+E  R   I++ Y +   G+     E + +  + ++  G   +    
Sbjct: 143 LILARHALSACILSEMVRTHAIRRCYLAAATGL--VPPEGVIDAPIARA--GTSTIERCV 198

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             E+G + A +H++ +       C L E++  TGRTHQ+RVH  H+G P+ GD  Y  ++
Sbjct: 199 DFERG-DSARTHYRTLCYNPDTNCSLVELRLETGRTHQIRVHMKHIGHPLPGDFLYNPDY 257

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           +      +  +  LH+  +D  HP +   L   APLP  M   +   G      LY +R
Sbjct: 258 R------LIGRQALHSWQLDFIHPIKKEPLHFEAPLPDDMRPLF---GMDLPLALYSQR 307


>gi|119472936|ref|ZP_01614809.1| hypothetical protein ATW7_13378 [Alteromonadales bacterium TW-7]
 gi|119444654|gb|EAW25963.1| hypothetical protein ATW7_13378 [Alteromonadales bacterium TW-7]
          Length = 222

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 64/205 (31%), Positives = 91/205 (44%), Gaps = 21/205 (10%)

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           E +  YV  KPA +S     G      GF+        +K    HRLD+ TSG++++AR 
Sbjct: 10  EHADFYVVEKPAELSFHSEDG-----PGFVVLAERQFNEKLYAVHRLDKVTSGLIILARN 64

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
           ++AA   TE F    I K Y ++    PK K+  +   + K     G Y    K      
Sbjct: 65  KSAAATFTELFAQHSIDKFYLAITDSKPKKKQGWVKGDMAKSRR--GTY----KLLASNL 118

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
           N AI+ F  I  F   F    ++P +G+THQLRV    +G PI+GD  Y           
Sbjct: 119 NPAITRFYSI-SFKAGFRAFILKPFSGKTHQLRVALKSIGSPILGDIAYSGT-------- 169

Query: 284 IQNKLYLHARYMDLPHPEGGRLQIT 308
             ++ YLHA  +     +G  LQ T
Sbjct: 170 ASDRTYLHAYALSFTW-QGENLQFT 193


>gi|78213448|ref|YP_382227.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           CC9605]
 gi|78197907|gb|ABB35672.1| putative pseudouridylate synthase [Synechococcus sp. CC9605]
          Length = 195

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 64/192 (33%), Positives = 98/192 (51%), Gaps = 18/192 (9%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
             +KPAG+  Q G G     D  + + +  + Q+ RL HRLD++TSG+L++AR+  A + 
Sbjct: 2   AVDKPAGLLSQPGLG-PEQSDSVI-TRLQQQDQRLRLVHRLDRDTSGVLLLARSADALRR 59

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAIS 228
           L+  F  RRI K+Y ++V G   +   CIA+ L + S     Y      + KG     I 
Sbjct: 60  LSALFAERRINKLYQAVVEG-ELHGCGCIASPLARLSRQPPRY----GSHPKGRLAQTIW 114

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
             + +   + +  WL  +P TGR+HQLR H   +G PIVGD  Y    +         +L
Sbjct: 115 RVRTVGARSTRL-WL--RPLTGRSHQLRAHLAELGHPIVGDPIYGDAGR-------SCRL 164

Query: 289 YLHARYMDLPHP 300
           +LHA+ +   HP
Sbjct: 165 HLHAQSLSFCHP 176


>gi|218232731|ref|YP_002366075.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
 gi|229108847|ref|ZP_04238452.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
 gi|229149592|ref|ZP_04277824.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|218160688|gb|ACK60680.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
 gi|228633938|gb|EEK90535.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|228674616|gb|EEL29855.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
          Length = 307

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 113/228 (49%), Gaps = 32/228 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + + NKP  +      +GG+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVYEDDHVLIVNKPEQMDTHPAEKGGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K KK  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGSIMDRLLMERKIKRTYAALVEGKVKKKKGKI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q   ++ +Q  TGRTHQ+RVH  H G P+VG
Sbjct: 195 RHHATRRRISPKG-DQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHMSHNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           D  Y    K        +   LHA  ++  HP     +++  P P  +
Sbjct: 254 DVLYGGQTK------YMSSQALHAMKINFLHPITKEAIEVDVPFPTKL 295


>gi|325283148|ref|YP_004255689.1| pseudouridine synthase [Deinococcus proteolyticus MRP]
 gi|324314957|gb|ADY26072.1| pseudouridine synthase [Deinococcus proteolyticus MRP]
          Length = 253

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 111/239 (46%), Gaps = 22/239 (9%)

Query: 101 LLYEDSKIYVFNKPA-----GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           LL E    Y  +KPA      +   G S +   +  F +S        P   HRLD+ETS
Sbjct: 15  LLLEHPDFYALHKPALWLTHPVRSHGSSRVP-DVVSFWQSETGESSLGP--PHRLDRETS 71

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+++R   +A+     F  R + K Y ++V G+P      +   L +    GG+ V +
Sbjct: 72  GLLLLSRDSESARRFFVLFGQRLVAKTYRAIVRGVPAWTDYELDAPLGELGLGGGNRVIM 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
            +        A++ F+V++  A     +E +P TGR HQ+R H  H+G P+VGD  Y   
Sbjct: 132 RQGVVPDGRPAVTAFRVLERRA-GHTLIEARPRTGRLHQIRAHLYHLGLPLVGDKIYGPE 190

Query: 275 -----NFKGNFTSP-IQNKL-----YLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                 F+    +P +  +L      LHA  +  P  +G ++++  PLPA M   WD L
Sbjct: 191 RDAFLEFRETGQTPELTRRLGMARQALHAASLHFPW-DGAQVRLHDPLPADMQAFWDGL 248


>gi|260914145|ref|ZP_05920618.1| tRNA pseudouridine synthase C [Pasteurella dagmatis ATCC 43325]
 gi|260631778|gb|EEX49956.1| tRNA pseudouridine synthase C [Pasteurella dagmatis ATCC 43325]
          Length = 241

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 109/238 (45%), Gaps = 19/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYQDDYLVAVNKPAGMLVHRSWLDMHETQFVMQTLRDQIGQHVYPIHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  L   F  ++++K Y ++V G    K+       +K   +   +V    Q +
Sbjct: 65  ALSSEVANLLCLQFEDKQVEKSYLAIVRGYLTGKERIDYPLKVKLDKVADKFV----QED 120

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  + + P TGR HQLR H  H+  PI+GD 
Sbjct: 121 KAPQDAVTDYQGLLTVEMPYSVKKYNTTRYSLVRLLPQTGRKHQLRRHMKHIFHPILGDT 180

Query: 271 KYCANFKGN--FTSPIQNK-LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           +Y  +   N  FT   + K L LHA  +   HP     +++TA L A  +K  +  G+
Sbjct: 181 QY-GDLHQNRAFTEYTEVKRLMLHAETLVFIHPIIREPIKLTAELDADWLKVLEIFGW 237


>gi|323702975|ref|ZP_08114632.1| pseudouridine synthase, RluA family [Desulfotomaculum nigrificans
           DSM 574]
 gi|323532106|gb|EGB21988.1| pseudouridine synthase, RluA family [Desulfotomaculum nigrificans
           DSM 574]
          Length = 293

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 75/278 (26%), Positives = 127/278 (45%), Gaps = 40/278 (14%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V +D + V  N R+  G ++ I  +   ++ I+ E   +D S+             +YED
Sbjct: 40  VLLDGQPVNSNVRVAPGAILEIS-MQQEVSSIVPEP--MDLSI-------------IYED 83

Query: 106 SKIYVFNKPAGISVQ--GGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVA 161
             I   +KP G+ V            +G L  W+  +G   R    HR+D++TSG+++VA
Sbjct: 84  QDIMAVHKPPGMLVHPLTTEPTGTLANGVLYYWLQ-QGSPARFRPVHRIDRDTSGLVLVA 142

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R     Q L        + + Y ++V G    +K  I   + +++  G     VV    K
Sbjct: 143 RNSYVHQQLQSQINQGLMCRRYLAMVTGKLAKQKGTITAPIDREA--GSLIKRVVTPAGK 200

Query: 222 GANYAISHFKVIDCFAQKFCW---LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
               AI+H++V+    ++  W   + ++  TGRTHQ+RVH  H+G P++GD  Y  +   
Sbjct: 201 ---PAITHYRVL----RQLSWGSLVRVELVTGRTHQVRVHMSHIGHPLLGDDLYGGDLS- 252

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
                +  +  LH  Y+   HP  G+L ++  PLP  M
Sbjct: 253 -----LIKRQALHCAYLAFSHPVTGQLIKLACPLPGDM 285


>gi|144227643|gb|AAZ44541.2| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae J]
          Length = 304

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 73/271 (26%), Positives = 130/271 (47%), Gaps = 36/271 (13%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI--QSGQVVRIPPVIN 72
           D+E++R+D             NL +  +  Q  + +K+V  NN +  +  Q+V+    I 
Sbjct: 12  DQEDIRIDILVAK------LANLSR--KVAQDLILEKKVLINNNLVLKKNQIVKTGQKIK 63

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
             N   + +  L+ +       DF    ++++D  + + NKP  + V  G G      ++
Sbjct: 64  IFNDYKRPKPQLEPA-----EIDFE---IIFQDQNMILINKPKNLVVHPGVGNWKNTLVN 115

Query: 131 GFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           G + S  DS  Q    +P + HRLD++T+G+L+VA+   A          R+I++ Y ++
Sbjct: 116 GLI-SHFDSLEQLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFA---QKFC 241
           V G      + +  ++     IG D  + +K+     N   AI++ ++I  F+   Q F 
Sbjct: 175 VIG------KVLHKFMKINLPIGRDLKNPLKKTISFFNSKPAITNVELIKHFSYQNQDFS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++ Q  TGRTHQ+R+H  H+G PI GD  Y
Sbjct: 229 LVKCQLETGRTHQIRLHLAHIGYPIYGDPIY 259


>gi|332686243|ref|YP_004456017.1| ribosomal large subunit pseudouridine synthase D [Melissococcus
           plutonius ATCC 35311]
 gi|332370252|dbj|BAK21208.1| similar to ribosomal large subunit pseudouridine synthase D
           [Melissococcus plutonius ATCC 35311]
          Length = 298

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 79/284 (27%), Positives = 129/284 (45%), Gaps = 39/284 (13%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI----LLYEDS 106
           KR+    + Q G++     + N L ++ K  ++     N  +H   L       +++ED 
Sbjct: 26  KRLLAKIKFQGGKIKVNHQIQNVLFYLTKNDQLQVVIPNEAEHETMLLDTTPIDIIFEDE 85

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTH---RLDQETSGILV 159
              V NKP  I         YH +G +    K++   K    ++ H   RLD++T+G+++
Sbjct: 86  HYLVVNKPVNIP---SIPAQYHPNGTMANRVKAYYKEKNYANQVVHIVTRLDRDTTGLML 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH------IGGDYV 213
            A+   A   L +  R +R+ KIY +LV G        IAN     SH      IG D+ 
Sbjct: 143 FAKHGFAHALLDQELRNKRVVKIYQALVGG-------NIANL---DSHGRIDLPIGRDHS 192

Query: 214 HVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++K Q       AI+ + + + +   F  + +Q HTGRTHQ+RVH   +GCP++GD  Y
Sbjct: 193 SLMKRQVISTGQQAITEYWIEEKYTD-FAAVRIQLHTGRTHQIRVHFSAIGCPLMGDELY 251

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                G     I+ +  LH   +   HP     +++  PLP  M
Sbjct: 252 -----GREKQRIKRQA-LHCSCLYFKHPFTKQEIELKLPLPLDM 289


>gi|296420214|ref|XP_002839670.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295635864|emb|CAZ83861.1| unnamed protein product [Tuber melanosporum]
          Length = 456

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 56/175 (32%), Positives = 85/175 (48%), Gaps = 11/175 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILVV 160
           +YED ++ V NKPAG+ V       Y+ +  ++    D  G  P   +RLD+ TSG++ +
Sbjct: 190 VYEDDRLIVINKPAGVPVHPAG--RYNFNTVIEIMKHDYNGHAPLPCNRLDRLTSGLMFM 247

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+T  AA       + R I+K Y + V G  P  +  C    L     +G + V    + 
Sbjct: 248 AKTPEAANDFMGQLQTRTIKKQYLARVKGKFPAGEVTCSQPILSVSPKLGLNRVRASGKT 307

Query: 220 EKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            K      + FK +    +K +  +E  P TGRTHQ+RVH   +G PI+ D  YC
Sbjct: 308 AK------TLFKRLKYNTEKNYSIVECHPFTGRTHQIRVHLQFLGHPIINDPIYC 356


>gi|255973763|ref|ZP_05424349.1| pseudouridine synthase [Enterococcus faecalis T2]
 gi|255966635|gb|EET97257.1| pseudouridine synthase [Enterococcus faecalis T2]
          Length = 287

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 40  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHL---GETTRVKVLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 144 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 258 -----ARLMLHASQLHLLHP 272


>gi|54020208|ref|YP_115967.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 232]
 gi|53987381|gb|AAV27582.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 232]
          Length = 304

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 73/271 (26%), Positives = 130/271 (47%), Gaps = 36/271 (13%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI--QSGQVVRIPPVIN 72
           D+E++R+D             NL +  +  Q  + +K+V  NN +  +  Q+V+    I 
Sbjct: 12  DQEDIRIDILVAK------LANLSR--KVAQDLILEKKVLINNNLVLKKNQIVKTGQKIR 63

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
             N   + +  L+ +       DF    ++++D  + + NKP  + V  G G      ++
Sbjct: 64  IFNDYKRPKPQLEPA-----EIDFE---IIFQDQNMILINKPKNLVVHPGVGNWKNTLVN 115

Query: 131 GFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           G + S  DS  Q    +P + HRLD++T+G+L+VA+   A          R+I++ Y ++
Sbjct: 116 GLI-SHFDSLEQLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFA---QKFC 241
           V G      + +  ++     IG D  + +K+     N   AI++ ++I  F+   Q F 
Sbjct: 175 VIG------KVLHKFMKINLPIGRDLKNPLKKTISFFNSKPAITNVELIKHFSYQNQDFS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++ Q  TGRTHQ+R+H  H+G PI GD  Y
Sbjct: 229 LVKCQLETGRTHQIRLHLAHIGYPIYGDPIY 259


>gi|157157184|ref|YP_001464113.1| tRNA pseudouridine synthase C [Escherichia coli E24377A]
 gi|191168568|ref|ZP_03030353.1| tRNA pseudouridine synthase C [Escherichia coli B7A]
 gi|193065141|ref|ZP_03046215.1| tRNA pseudouridine synthase C [Escherichia coli E22]
 gi|193071106|ref|ZP_03052031.1| tRNA pseudouridine synthase C [Escherichia coli E110019]
 gi|194426330|ref|ZP_03058885.1| tRNA pseudouridine synthase C [Escherichia coli B171]
 gi|209920242|ref|YP_002294326.1| tRNA pseudouridine synthase C [Escherichia coli SE11]
 gi|218555342|ref|YP_002388255.1| tRNA pseudouridine synthase C [Escherichia coli IAI1]
 gi|218696390|ref|YP_002404057.1| tRNA pseudouridine synthase C [Escherichia coli 55989]
 gi|256019422|ref|ZP_05433287.1| tRNA pseudouridine synthase C [Shigella sp. D9]
 gi|260845437|ref|YP_003223215.1| tRNA pseudouridine synthase [Escherichia coli O103:H2 str. 12009]
 gi|260856901|ref|YP_003230792.1| tRNA pseudouridine synthase [Escherichia coli O26:H11 str. 11368]
 gi|260869469|ref|YP_003235871.1| tRNA pseudouridine synthase [Escherichia coli O111:H- str. 11128]
 gi|300815791|ref|ZP_07096015.1| tRNA pseudouridine synthase [Escherichia coli MS 107-1]
 gi|300820579|ref|ZP_07100730.1| tRNA pseudouridine synthase [Escherichia coli MS 119-7]
 gi|300906681|ref|ZP_07124370.1| tRNA pseudouridine synthase [Escherichia coli MS 84-1]
 gi|300923234|ref|ZP_07139288.1| tRNA pseudouridine synthase [Escherichia coli MS 182-1]
 gi|301304561|ref|ZP_07210671.1| tRNA pseudouridine synthase [Escherichia coli MS 124-1]
 gi|301325733|ref|ZP_07219190.1| tRNA pseudouridine synthase [Escherichia coli MS 78-1]
 gi|307312780|ref|ZP_07592410.1| pseudouridine synthase [Escherichia coli W]
 gi|309795259|ref|ZP_07689678.1| tRNA pseudouridine synthase [Escherichia coli MS 145-7]
 gi|331669526|ref|ZP_08370372.1| tRNA pseudouridine synthase C [Escherichia coli TA271]
 gi|331678771|ref|ZP_08379445.1| tRNA pseudouridine synthase C [Escherichia coli H591]
 gi|332280540|ref|ZP_08392953.1| tRNA pseudouridine synthase C [Shigella sp. D9]
 gi|157079214|gb|ABV18922.1| tRNA pseudouridine synthase C [Escherichia coli E24377A]
 gi|190901415|gb|EDV61179.1| tRNA pseudouridine synthase C [Escherichia coli B7A]
 gi|192927272|gb|EDV81892.1| tRNA pseudouridine synthase C [Escherichia coli E22]
 gi|192955567|gb|EDV86045.1| tRNA pseudouridine synthase C [Escherichia coli E110019]
 gi|194415638|gb|EDX31905.1| tRNA pseudouridine synthase C [Escherichia coli B171]
 gi|209913501|dbj|BAG78575.1| putative pseudouridine synthase [Escherichia coli SE11]
 gi|218353122|emb|CAU98959.1| tRNA pseudouridine synthase [Escherichia coli 55989]
 gi|218362110|emb|CAQ99719.1| tRNA pseudouridine synthase [Escherichia coli IAI1]
 gi|257755550|dbj|BAI27052.1| tRNA pseudouridine synthase [Escherichia coli O26:H11 str. 11368]
 gi|257760584|dbj|BAI32081.1| tRNA pseudouridine synthase [Escherichia coli O103:H2 str. 12009]
 gi|257765825|dbj|BAI37320.1| tRNA pseudouridine synthase [Escherichia coli O111:H- str. 11128]
 gi|300401582|gb|EFJ85120.1| tRNA pseudouridine synthase [Escherichia coli MS 84-1]
 gi|300420473|gb|EFK03784.1| tRNA pseudouridine synthase [Escherichia coli MS 182-1]
 gi|300526843|gb|EFK47912.1| tRNA pseudouridine synthase [Escherichia coli MS 119-7]
 gi|300531720|gb|EFK52782.1| tRNA pseudouridine synthase [Escherichia coli MS 107-1]
 gi|300840165|gb|EFK67925.1| tRNA pseudouridine synthase [Escherichia coli MS 124-1]
 gi|300847483|gb|EFK75243.1| tRNA pseudouridine synthase [Escherichia coli MS 78-1]
 gi|306907215|gb|EFN37721.1| pseudouridine synthase [Escherichia coli W]
 gi|308121230|gb|EFO58492.1| tRNA pseudouridine synthase [Escherichia coli MS 145-7]
 gi|315062072|gb|ADT76399.1| tRNA pseudouridine synthase [Escherichia coli W]
 gi|315256652|gb|EFU36620.1| tRNA pseudouridine synthase [Escherichia coli MS 85-1]
 gi|320202437|gb|EFW77007.1| tRNA pseudouridine synthase C [Escherichia coli EC4100B]
 gi|323154837|gb|EFZ41030.1| RNA pseudouridylate synthase family protein [Escherichia coli
           EPECa14]
 gi|323159892|gb|EFZ45862.1| RNA pseudouridylate synthase family protein [Escherichia coli
           E128010]
 gi|323180223|gb|EFZ65775.1| RNA pseudouridylate synthase family protein [Escherichia coli 1180]
 gi|323183332|gb|EFZ68729.1| RNA pseudouridylate synthase family protein [Escherichia coli 1357]
 gi|323377345|gb|ADX49613.1| pseudouridine synthase [Escherichia coli KO11]
 gi|323946486|gb|EGB42512.1| RNA pseudouridylate synthase [Escherichia coli H120]
 gi|324016355|gb|EGB85574.1| tRNA pseudouridine synthase [Escherichia coli MS 117-3]
 gi|331063194|gb|EGI35107.1| tRNA pseudouridine synthase C [Escherichia coli TA271]
 gi|331073601|gb|EGI44922.1| tRNA pseudouridine synthase C [Escherichia coli H591]
 gi|332102892|gb|EGJ06238.1| tRNA pseudouridine synthase C [Shigella sp. D9]
          Length = 260

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 116/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG+  A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGSQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|307269713|ref|ZP_07551043.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|306513823|gb|EFM82425.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|315034494|gb|EFT46426.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0027]
 gi|315147005|gb|EFT91021.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4244]
 gi|329576828|gb|EGG58313.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1467]
          Length = 283

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHL---GEATRVKVLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|256957449|ref|ZP_05561620.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|257080924|ref|ZP_05575285.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257083608|ref|ZP_05577969.1| pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256947945|gb|EEU64577.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256988954|gb|EEU76256.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|256991638|gb|EEU78940.1| pseudouridine synthase [Enterococcus faecalis Fly1]
          Length = 287

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 40  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHL---GEATRVKVLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 144 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 258 -----ARLMLHASQLHLLHP 272


>gi|168212841|ref|ZP_02638466.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE
           str. F4969]
 gi|170715523|gb|EDT27705.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE
           str. F4969]
          Length = 298

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 82/301 (27%), Positives = 137/301 (45%), Gaps = 52/301 (17%)

Query: 39  KILRSG----QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++RS     +++VD   VK N  +++G+ ++I        +I  E+  ++         
Sbjct: 30  RLIRSAAIDKRIKVDGVAVKMNYVVKTGEEIKIELSKKESQNIEPEKMDIE--------- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPR 145
                 ++YEDS I V NK   + V            +GI Y+   F +S  D      R
Sbjct: 81  ------IVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYY---FKESNQDCI---VR 128

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L  RLD  TSG++++ + + A   L+   +  + QK Y ++V G  + K+  I   + + 
Sbjct: 129 LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRP 188

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHM 262
           +    D +  V  +E+G   +I+H+KVI+ +       C LE    TGRTHQ+RVH   +
Sbjct: 189 AE---DTIKRV-VDERGQE-SITHYKVIESYNGADLVECLLE----TGRTHQIRVHLSSL 239

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           G PI GD  Y     G       ++  LHA  +D   P+    L + A LP  M +  + 
Sbjct: 240 GHPIFGDSLY-----GTEDEEFISRQALHAYGLDFYSPKTKEPLSLRADLPEDMKELINK 294

Query: 322 L 322
           L
Sbjct: 295 L 295


>gi|223039515|ref|ZP_03609803.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter rectus RM3267]
 gi|222879311|gb|EEF14404.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter rectus RM3267]
          Length = 252

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/232 (28%), Positives = 109/232 (46%), Gaps = 39/232 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  +   +KPA                FL S   S+  K  L HRLD+ETSG+L++
Sbjct: 60  VIFEDENLIAVDKPA----------------FLTSEKVSEIYKFPLLHRLDKETSGVLLL 103

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+  R++K Y + V GI  +++  +   ++   + GG +  +   N 
Sbjct: 104 VKNEEFQKKAIEEFKNCRVKKEYVAAVKGIV-SEEFSVNEPIITLKNRGGAFSKI-SPNG 161

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K A   ++   V    A K   ++++  TGRTHQ+RVH  H G  IVGD KY  N     
Sbjct: 162 KDALSIVTPVMV----AGKKSLVKVEIKTGRTHQIRVHLNHAGYGIVGDEKYAKNKAA-- 215

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
                 ++YLHA  ++L         +     +++ + ++ LGF+  RN  I
Sbjct: 216 ------RMYLHAYKIEL---------LGYKFRSNLSEDFNRLGFEISRNFEI 252


>gi|68171700|ref|ZP_00545058.1| Pseudouridine synthase [Ehrlichia chaffeensis str. Sapulpa]
 gi|67998881|gb|EAM85575.1| Pseudouridine synthase [Ehrlichia chaffeensis str. Sapulpa]
          Length = 146

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 48/144 (33%), Positives = 76/144 (52%), Gaps = 11/144 (7%)

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F+ RR++K Y +L  GIPKN    I + ++K        + + K N+     A++ F V
Sbjct: 2   EFKNRRVEKKYLALTQGIPKNDIGQINHSIIKNKR----SLSLDKVNDSYLQEAVTSFSV 57

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-KLYLH 291
           +         LE++P TGR HQ+R+H  H+GC I+GD KY     G F   + N  L LH
Sbjct: 58  LKKLPYGIGLLELKPITGRKHQIRIHLSHIGCSIIGDKKY-----GKFCEHVLNDNLQLH 112

Query: 292 ARYMDLPHPEGGRLQITAPLPAHM 315
           A ++ +   E  ++  T P+P++M
Sbjct: 113 AYFLSINIGE-KKIDFTVPVPSYM 135


>gi|319424672|gb|ADV52746.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           putrefaciens 200]
          Length = 229

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 59/184 (32%), Positives = 89/184 (48%), Gaps = 27/184 (14%)

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           S  G +G+   I+  L       G K    HRLD  TSG+L++A++ AAA+  TE F   
Sbjct: 24  SQDGTAGVVAQIEQDL-------GIKLFAVHRLDTPTSGLLILAKSTAAAKQFTELFTAH 76

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           ++QK Y +L  G PK K+  +   + K          +++  E   N AI+ F  +    
Sbjct: 77  KVQKYYLALAKGKPKKKQGWVIGDMAKSRR---SMFKLLRTKE---NPAITQFFSVSVGD 130

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA----- 292
               +L ++PH+G+THQLRV    +G PI+GD  Y           + ++ YLHA     
Sbjct: 131 GLRLYL-LKPHSGKTHQLRVALASLGVPILGDELYGGA--------VADRCYLHAYCLHF 181

Query: 293 RYMD 296
           RY D
Sbjct: 182 RYQD 185


>gi|108762448|ref|YP_633384.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108466328|gb|ABF91513.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 303

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 102/225 (45%), Gaps = 13/225 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+YED+++ V  KP+G+      G    +   L S+V ++  +    HRL + TSG+++ 
Sbjct: 85  LVYEDAELVVVVKPSGLPTLPSGGF---LKNTLLSFVQARWPEAVPMHRLGRATSGLVLF 141

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            RTR AA  L   +R  R+ K Y +L  G+   +   I   +    H     VH      
Sbjct: 142 TRTRDAAARLASDWREGRVHKRYRALSQGLAAQESYDIRAPIGLVPHPRLGEVHGASARG 201

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FK 277
           K ++   S  +V++   +     E+  HTGR+ Q+R+H   +G P+VGD  +        
Sbjct: 202 KPSH---STARVLERRTEHTL-FEVDIHTGRSEQIRIHLAFIGHPLVGDPLFAVGGLPLA 257

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAPLPAHMVKTW 319
            N   P      LHA  +   HP  G   +LQ  APL   +  +W
Sbjct: 258 ENPGLPGDGGYLLHAESLTFQHPRSGEHVQLQAPAPLELRVQDSW 302


>gi|307109075|gb|EFN57314.1| hypothetical protein CHLNCDRAFT_12398 [Chlorella variabilis]
          Length = 198

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 64/197 (32%), Positives = 96/197 (48%), Gaps = 27/197 (13%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPRLTHRLDQ 152
           L+S LL+ D  +    KPAG++ QGGSG+A+ +D  + +             RL HRLD+
Sbjct: 7   LRSCLLHSDPDLLAVCKPAGLACQGGSGVAHSVDSVMAAAFAHLPGPASHHLRLVHRLDR 66

Query: 153 ETSGILVVARTRAAAQHLTESFR----------------MRRIQKIYWSLVWGIPKNKKE 196
           +T+G L++AR   AA  L  +FR                   IQK YW++V  +P+    
Sbjct: 67  QTTGALLLARGPDAAAWLAAAFRESSGGSGGSGRGDSSSGASIQKQYWAVV-ALPEGGG- 124

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             A+ L     I    V   +     A  A++ ++V+        WLE+ P TGR HQLR
Sbjct: 125 --AHRLPAAGAI-SLPVPGGRGGAAAAQPALTRYRVLH-RGGGLAWLELAPATGRKHQLR 180

Query: 257 VH-ALHMGCPIVGDHKY 272
           +H A  +G  I+GD +Y
Sbjct: 181 LHCAQGLGAAILGDGRY 197


>gi|261344629|ref|ZP_05972273.1| pseudouridine synthase A [Providencia rustigianii DSM 4541]
 gi|282567545|gb|EFB73080.1| pseudouridine synthase A [Providencia rustigianii DSM 4541]
          Length = 232

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/212 (30%), Positives = 100/212 (47%), Gaps = 18/212 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP+G+    G     ++D      V    +   L HRLD  TSG++VVA
Sbjct: 20  LYQDDHLILINKPSGLLSLSGKN-PQNLDSVHHRMVKIFPEC-TLVHRLDFGTSGLMVVA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L   F  R + K+Y +L+ G   +  E + +  + K       + +   N K
Sbjct: 78  RNKAINAALCHQFSQRTVGKMYSALLCG-HLDDDEGVIDAPIAKDPALFPLMSISAINGK 136

Query: 222 GANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            A    SH++VI+ F ++           +++ P TGRTHQLR+H   +G PI+G   Y 
Sbjct: 137 PAR---SHYRVIERFYRELDDGGQLPLTRVQLTPETGRTHQLRIHCQLLGHPILGCDLYG 193

Query: 274 AN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                G   +P   +L LHA  +D  HP  G 
Sbjct: 194 GRLLLGTEQTP---RLMLHACELDFIHPVTGE 222


>gi|86740132|ref|YP_480532.1| ribosomal large subunit pseudouridine synthase D [Frankia sp. CcI3]
 gi|86566994|gb|ABD10803.1| ribosomal large subunit pseudouridine synthase D [Frankia sp. CcI3]
          Length = 313

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 68/234 (29%), Positives = 113/234 (48%), Gaps = 24/234 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY+D  I V +KP G++V    G     + G L +    + + G   R  + HRLD  T
Sbjct: 88  ILYDDDDIIVVDKPVGVAVHPAPGFTGPTVIGALAAAGYRISTSGAAERQGVVHRLDVGT 147

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++VVA++  A   L  +FR R + K Y ++V G P   +  +   + +     G +  
Sbjct: 148 TGVMVVAKSERAYTLLKRAFRDRTVDKRYRAVVQGHPDPLRGTVDAPIDRHPRRPGLFAV 207

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V          +I+H+ + + F +    L ++  TGRTHQ+RVH   +  P VGD  Y A
Sbjct: 208 VADGKP-----SITHYDLQEAF-RAASLLSVRLETGRTHQIRVHMSALRHPCVGDLAYGA 261

Query: 275 NFKGNFTSPIQNKL-----YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +        +  +L     +LHA  +   HP  GGR++ T+P PA + +  + L
Sbjct: 262 DPT------LAERLGLTRQWLHAARLSFDHPGHGGRVEFTSPDPADLAEAVERL 309


>gi|326391214|ref|ZP_08212757.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           JW 200]
 gi|325992718|gb|EGD51167.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           JW 200]
          Length = 285

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 124/231 (53%), Gaps = 37/231 (16%)

Query: 103 YEDSKIYVFNKPAGISV------QGGS---GIAYHI-DGFLKSWVDSKGQKPRLTHRLDQ 152
           YED  + + +KPAG+ V      Q G+   G+A++  D  +K+ +       R  +RLD+
Sbjct: 78  YEDEDVLIVDKPAGVVVHPTKRYQSGTLANGVAWYFKDKGIKALI-------RPVNRLDK 130

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V A+ R   Q+  +   ++ + K+Y+++V G  K + E   +  + +    G  
Sbjct: 131 GTSGLVVFAK-RPFMQYYLQI--VKPMSKLYFAVVEG--KMEGEGRIDLPISRKPQSGIE 185

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V ++ ++    AI+++KVI   +++F  L+++  TGRTHQ+RVH  H+G PIVGD  Y
Sbjct: 186 RMVSEEGDR----AITNYKVIKS-SERFSLLKVKIETGRTHQIRVHLSHIGHPIVGDTLY 240

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP---AHMVKTW 319
                G+    I+ +  LHA  +   HP E   + + +PLP    H++K +
Sbjct: 241 -----GSSDDYIKRQA-LHAYRLTFVHPLEEKSISVYSPLPQDIQHLLKLF 285


>gi|226953430|ref|ZP_03823894.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (uracil hydrolyase) [Acinetobacter sp. ATCC
           27244]
 gi|294649580|ref|ZP_06726999.1| ribosomal large subunit pseudouridine synthase D family protein
           [Acinetobacter haemolyticus ATCC 19194]
 gi|226835813|gb|EEH68196.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (uracil hydrolyase) [Acinetobacter sp. ATCC
           27244]
 gi|292824519|gb|EFF83303.1| ribosomal large subunit pseudouridine synthase D family protein
           [Acinetobacter haemolyticus ATCC 19194]
          Length = 361

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 111/241 (46%), Gaps = 33/241 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NK  G+ V  G+G         + YH          ++  +  L HR+D
Sbjct: 128 IVYEDDDIIVINKDVGMVVHPGAGNPTGTLVNALLYHAPKL------AELARAGLVHRID 181

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA+   A   L++    + + ++Y  +V+G        IA   + +  I   
Sbjct: 182 KDTSGLLVVAKNLEAQFSLSKQLAKKTVYRVYDLVVYG------NIIAGGTIDEP-IKRH 234

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V  VK     G   A++H+ V + F + F  ++ Q  TGRTHQ+RVH  ++G  +VGD 
Sbjct: 235 PVDRVKMAILPGGRDAVTHYNVKERF-RDFTRVQAQLETGRTHQIRVHFSYLGHGLVGDP 293

Query: 271 KYC--ANFKGNFTSPIQNKL------YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            Y     F    ++ + + L       LHA  + L HP  G  +   AP P    +  + 
Sbjct: 294 VYVNRVRFPAGASATLTDMLRGFKRQALHAAKLGLVHPRTGEDMMFEAPWPEDFTQLVEV 353

Query: 322 L 322
           L
Sbjct: 354 L 354


>gi|325957347|ref|YP_004292759.1| ribosomal protein large subunit [Lactobacillus acidophilus 30SC]
 gi|325333912|gb|ADZ07820.1| ribosomal protein large subunit [Lactobacillus acidophilus 30SC]
          Length = 285

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 81/178 (45%), Gaps = 7/178 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + + NK  G   Q         D  L       G  P + HRLD  T G+L+V
Sbjct: 83  VIYEDDNLLIINKKKG---QKTHPNLNETDTALNDCATYLGSSPYIVHRLDMLTGGLLLV 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+  A    L      +   + Y + V    K KK    +  + +     D       N+
Sbjct: 140 AKNPAVVPILNRELTTKTFHREYLAKVIHADKLKKNGTIDLPISQD---PDDQRKRMVNK 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            G  +A++H++++  ++     +++   TGRTHQ+RVH   +GCPIVGD  Y  +F G
Sbjct: 197 TGL-HAVTHYELLKKYSDNTALVKLTLETGRTHQIRVHLAAIGCPIVGDPLYNPDFAG 253


>gi|293392235|ref|ZP_06636569.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952769|gb|EFE02888.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 225

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 63/194 (32%), Positives = 92/194 (47%), Gaps = 22/194 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           ++++     V NKP GISV          D  L   V  +   P+  L HRLD+ TSG+L
Sbjct: 5   IVFQHPDFIVINKPTGISVHKDDA-----DIGLTRLVAQQLGVPQVWLVHRLDKVTSGLL 59

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A     A  L++ F   +IQK Y +L    PK K+  I+   ++K+  G       K 
Sbjct: 60  MLALNEQTAVTLSQKFAHHQIQKTYLALTTHKPKKKQGRISG-DMQKARRGA-----WKL 113

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +   N A++ F V    A       +QP TG+THQLRV    +G PI+GD  YC +   
Sbjct: 114 TQSKENPAVTDF-VSRSLAPNLRLFILQPKTGKTHQLRVAMKSLGSPILGDALYCGDSA- 171

Query: 279 NFTSPIQNKLYLHA 292
                  ++ YLHA
Sbjct: 172 -------DRTYLHA 178


>gi|146291506|ref|YP_001181930.1| pseudouridine synthase Rlu family protein [Shewanella putrefaciens
           CN-32]
 gi|145563196|gb|ABP74131.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           putrefaciens CN-32]
          Length = 229

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 54/161 (33%), Positives = 81/161 (50%), Gaps = 20/161 (12%)

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G K    HRLD  TSG+L++A++ AAA+  TE F   ++QK Y +L  G PK K+  +  
Sbjct: 40  GIKLFAVHRLDTPTSGLLILAKSTAAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIG 99

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + K          +++  E   N AI+ F  +        +L ++PH+G+THQLRV   
Sbjct: 100 DMAKSRR---SMFKLLRTKE---NPAITQFFSVSVGDGLRLYL-LKPHSGKTHQLRVALA 152

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA-----RYMD 296
            +G PI+GD  Y           + ++ YLHA     RY D
Sbjct: 153 SLGVPILGDELYGGA--------VADRCYLHAYCLHFRYQD 185


>gi|262191904|ref|ZP_06050072.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae CT
           5369-93]
 gi|262032204|gb|EEY50774.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae CT
           5369-93]
          Length = 474

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/205 (31%), Positives = 96/205 (46%), Gaps = 22/205 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NKPA      G  +   +   LK+   ++ +     HRLD  TSG+LV 
Sbjct: 273 IVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-TQAEGVFALHRLDMSTSGLLVF 331

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A TR A + L + F  R +QK Y +L+ G     +  I      +  + GD     +Q  
Sbjct: 332 ALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEI------QLPLCGDLDDRPRQKV 385

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
             +    A++H++ +    Q    + + PHTGRTHQLRVH  H   +  PIVGD  Y   
Sbjct: 386 CWQQGKPALTHWETVQV-EQNRTRVYLYPHTGRTHQLRVHCAHHLGLNAPIVGDDLYGLQ 444

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
            K         +L+LHA  +   HP
Sbjct: 445 DK---------RLFLHAEQLSFAHP 460


>gi|116873677|ref|YP_850458.1| ribosomal large subunit pseudouridine synthase D [Listeria
           welshimeri serovar 6b str. SLCC5334]
 gi|116742555|emb|CAK21679.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria welshimeri serovar 6b str. SLCC5334]
          Length = 289

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 63/217 (29%), Positives = 102/217 (47%), Gaps = 21/217 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP G+        +Y  D     ++ +++   Q+      HRLDQ TS
Sbjct: 80  IIYEDDFLLVVNKPVGMKTHPND--SYETDTCANAVQYYLEKTDQEANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + A   L+     R I + Y + V G      + I   + +  H G      
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSR---- 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +Q       A++H KV++   +    L E Q  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 194 -RQISPYGQPAVTHVKVLENDTENNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           + +        N++ LHA  + L HP +G  +  +AP
Sbjct: 253 SNRA-------NRIMLHAEKLHLNHPFKGKEMNFSAP 282


>gi|118580263|ref|YP_901513.1| pseudouridine synthase [Pelobacter propionicus DSM 2379]
 gi|118502973|gb|ABK99455.1| pseudouridine synthase [Pelobacter propionicus DSM 2379]
          Length = 238

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 105/229 (45%), Gaps = 21/229 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPR----LTHRLDQETS 155
           +LYED  I +  KP G+ ++  G      +   L  +V     + R    + HRLD+ETS
Sbjct: 13  VLYEDRDIIIIEKPCGLLTIGTGRDKTRTVHSILNDYVRKGDPRSRNRVYIVHRLDRETS 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GIL++A++ A   +L E +  +   K Y ++V G    K   I+++L + S +       
Sbjct: 73  GILILAKSEANKIYLQEHW--QETDKHYVAVVHGTLALKSGTISSYLAENSAM------R 124

Query: 216 VKQNEKGANYAISHFK-VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V      A   +SH + V+    +    L +   TGR HQ+RVH    G  +VGD KY  
Sbjct: 125 VYSTTDQAQGKLSHTEYVVMKENRGLSLLAIHLLTGRKHQIRVHLSEGGNAVVGDSKYGT 184

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +         +  L LHAR +   HP  G R+ I   +P +  +   S+
Sbjct: 185 DRYA------RANLALHARSLTFTHPVSGRRMAIETGIPDYFTRLVGSI 227


>gi|297172088|gb|ADI23070.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0770_07M15]
          Length = 277

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 57/176 (32%), Positives = 90/176 (51%), Gaps = 8/176 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + V NKPAG+      G     + G L+ +  ++ Q   L +RLD+ETSG++ 
Sbjct: 35  ILHEDDDLLVINKPAGLVCHPTKGDERSSLAGRLRLYRGAE-QSAHLINRLDRETSGVVC 93

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSH--IGGDYVHVV 216
           V +T  AA+ L   +  R + K YW++V G +P+++    A      +   +  D V   
Sbjct: 94  VGKTDEAARELRRLWESREVDKYYWAIVHGHVPESEGTIDAPLGSDDASEVVVKDCVRDD 153

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               +   +    F+  D   +KF WL + P TGR HQ+R+H  H+G  IVGD  Y
Sbjct: 154 GHPSQTRYWTQWKFERDD---EKFTWLRVAPVTGRKHQIRIHLQHLGHAIVGDKLY 206


>gi|315173986|gb|EFU18003.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1346]
          Length = 283

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHL---GEATRVKVLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  DHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|285808641|gb|ADC36159.1| RluA family pseudouridine synthase [uncultured bacterium 162]
          Length = 326

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 78/316 (24%), Positives = 130/316 (41%), Gaps = 39/316 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Y    ++ + +    L     + Y H      Q+ L +G+V VD      +  + SGQ +
Sbjct: 34  YAYTTIISSKDRGRTLLSHLASLYTHSTAQAWQQNLDNGEVTVDGVTANGSESLASGQTL 93

Query: 66  --RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
               PP +                 +  +H +     +L++D  +   NKP+G+    G 
Sbjct: 94  VWNRPPWVEP---------------DAPQHFE-----MLFDDPYLLAVNKPSGLPTLPGG 133

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G    ++  L   V ++       HRL + TSGI++ A+T  AA  L  ++   RIQK+Y
Sbjct: 134 GF---MENTLLRLVQNQCPSANPVHRLGRGTSGIVLFAKTPKAAAELCANWNTPRIQKVY 190

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++  G+ ++    I   +    H     +  V         + S  KVI   A+     
Sbjct: 191 RAVAQGVAEHDAYEILTPIGLVPH---PLIGSVWGASPDGKPSKSVAKVI-SRAESTTTF 246

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDL 297
           E+   +GR HQ+R+H   +G P+VGD  Y        N  G    P      LHA+ +  
Sbjct: 247 EVSLQSGRPHQIRIHLASIGYPLVGDPLYGLGGQPLENLPG---LPGDGGYLLHAQLLKF 303

Query: 298 PHP-EGGRLQITAPLP 312
            HP  G R+++ A LP
Sbjct: 304 QHPISGERIELEAALP 319


>gi|255527608|ref|ZP_05394471.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
 gi|255508709|gb|EET85086.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
          Length = 319

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 73/278 (26%), Positives = 121/278 (43%), Gaps = 47/278 (16%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++ +     +    + K +R G V+V+ K+ K    +  G ++    + +  
Sbjct: 8   NEAGQRLDKFLRKWLKDMPLSAIYKSIRKGDVKVNGKKAKEKYALMEGDLIETRDITS-- 65

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFL 133
           N   K+   +++S        FLK  + YED  + V  K  G+ V   G    + +  ++
Sbjct: 66  NQTKKKFNRIENS--------FLK--IAYEDENMVVIEKWPGVLVHSDGKKKEHTLTDYV 115

Query: 134 KSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            S++  KG           P   +RLD+ TSGI++  +   A + L E  R ++I K Y 
Sbjct: 116 LSYLYDKGDYTPENEVTFTPASCNRLDRNTSGIVIFGKNYEALKLLNEMIREKKIHKYYQ 175

Query: 185 SLVWG----------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +L+ G          I KN+ E I+               V  +  K       + K I 
Sbjct: 176 ALIKGRIKDGLYKAYIHKNESENIS--------------QVYDEPRKDTKEISMNVKNIQ 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                F  +E++  TGR+HQLR H  H+G PI+GD KY
Sbjct: 222 SCGT-FSLVELELLTGRSHQLRAHLNHLGNPILGDTKY 258


>gi|332978702|gb|EGK15396.1| tRNA pseudouridine synthase C [Psychrobacter sp. 1501(2011)]
          Length = 261

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 101/226 (44%), Gaps = 37/226 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLT---------- 147
           ++YED  +   NK AG+ V              +SW+D KG+     +LT          
Sbjct: 22  IIYEDEHLVAINKEAGLLVH-------------RSWLD-KGETRFAMQLTRDAVGCHVVP 67

Query: 148 -HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ TSG+L+ A+  A A+ LTE+F  R++ K Y ++V G    +         K  
Sbjct: 68  VHRLDRPTSGVLLFAKNSAVARSLTEAFTERKVAKQYLAVVRGFMSEEGTVDYALSFKPD 127

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFA-------QKFCWLEMQPHTGRTHQLRVHA 259
            I   + ++ K  ++   +  S  ++   FA        ++  + + P TGR HQLR H 
Sbjct: 128 AIADKFANLNKPAQEAVTHWQSLAQIELPFAVSKKHGTSRYSLMRLIPETGRKHQLRRHM 187

Query: 260 LHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG 303
            H+   I+GD  Y       F  T     ++ LHA+ + L HP  G
Sbjct: 188 RHLFHHIIGDTSYGDGRHNKFFRTQYDCTRMLLHAQTLALSHPVTG 233


>gi|165975689|ref|YP_001651282.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           3 str. JL03]
 gi|165875790|gb|ABY68838.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           3 str. JL03]
          Length = 216

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 61/198 (30%), Positives = 96/198 (48%), Gaps = 24/198 (12%)

Query: 98  KSILLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           K  + ++     V +KP G+SV   +   G+  ++   L++      ++  L HRLD+ T
Sbjct: 4   KLTICFQHHDFVVIDKPVGVSVHKDEEAIGLTENLAEQLQA------EQVWLVHRLDKVT 57

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+ A  + AA H    F   +I+K YW+L    PK K+  I+   ++KS  G   + 
Sbjct: 58  SGLLIFALNKQAAVHFYHLFEQHKIEKTYWALSDQKPKKKQGKISG-DMQKSRNGAWKLS 116

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             KQN      A++ F V            +QP TG+THQLRV    +G PI+GD +Y  
Sbjct: 117 HSKQNP-----AVTQF-VSHSLEPNLRHFILQPKTGKTHQLRVAMKSLGSPILGDQRYAG 170

Query: 275 NFKGNFTSPIQNKLYLHA 292
                      +++YLHA
Sbjct: 171 T--------AADRVYLHA 180


>gi|22538202|ref|NP_689053.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           agalactiae 2603V/R]
 gi|22535113|gb|AAN00926.1|AE014285_8 ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 2603V/R]
          Length = 294

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 60/203 (29%), Positives = 90/203 (44%), Gaps = 23/203 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           LYED  + + NKP G+   G       +  H+  +        GQ   + HRLD ETSG 
Sbjct: 84  LYEDEHLIIVNKPEGMKTHGNQPNEIALLNHVSAY-------SGQTCYVVHRLDMETSGA 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       + +    + I + YW+LV G    K + + + + +  H     + +  
Sbjct: 137 VLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRDKIGRNRHDRRKRI-IDS 195

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +N + A   I   K I   +   C LE    TGRTHQ+RVH  H G P++GD  Y     
Sbjct: 196 KNGQHAMTIIDVLKYIQNSSLIKCRLE----TGRTHQIRVHLSHHGHPLIGDPLYNP--- 248

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               S    +L LHA  + L HP
Sbjct: 249 ----SSNNERLMLHAHRLTLSHP 267


>gi|332670137|ref|YP_004453145.1| RluA family pseudouridine synthase [Cellulomonas fimi ATCC 484]
 gi|332339175|gb|AEE45758.1| pseudouridine synthase, RluA family [Cellulomonas fimi ATCC 484]
          Length = 312

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 55/182 (30%), Positives = 95/182 (52%), Gaps = 8/182 (4%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD  TSG++VVA++  A   L  +F+ R ++K+Y +LV G P+     I   + + 
Sbjct: 137 VVHRLDVGTSGLMVVAKSEHAYTVLKRAFKERTVEKVYHALVQGHPEPTTGTIDAPIGR- 195

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            H   D+   V  + K    +++H++V++        +E+   TGRTHQ+RVH   +  P
Sbjct: 196 -HPSADWKFAVVADGK---PSVTHYEVLEMLPSA-SLVEVHLETGRTHQIRVHFAALRHP 250

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            VGD  Y A+      + +  + +LHA  +   HP  G  L++T+  P  + +  ++LG 
Sbjct: 251 CVGDLTYGADPSLAARTHLSRQ-WLHAVRLGFEHPGTGEWLEVTSEYPQDLARALETLGA 309

Query: 325 KY 326
            Y
Sbjct: 310 GY 311


>gi|313904372|ref|ZP_07837749.1| pseudouridine synthase [Eubacterium cellulosolvens 6]
 gi|313470708|gb|EFR66033.1| pseudouridine synthase [Eubacterium cellulosolvens 6]
          Length = 237

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/222 (29%), Positives = 102/222 (45%), Gaps = 22/222 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQE 153
           +L   DS I V+ KP+G++V+    G   +   I  +L   + S G+K    + +RLDQ 
Sbjct: 3   VLQETDSYIAVY-KPSGLAVESRALGRRTLENEIMKYL--ALKSPGRKTYVAIINRLDQP 59

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP---------KNKKECIA--NWL 202
             GI++ A+T+  A  L+E  +  RI+K Y ++V             K ++E +A  ++L
Sbjct: 60  VEGIVLAAKTQKGAARLSEQLQAHRIKKHYLAVVRVTEDTASQIRTVKEQREEVALTDYL 119

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           LK      +   VV +   G+  A   ++V +        LE+   TGR HQ+RV   H 
Sbjct: 120 LKDGKT--NTTEVVAEGTTGSRRAELRYRVREILDDGRALLEIDLLTGRHHQIRVQLSHA 177

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G PI GD KY             N L L A  +    P+ G+
Sbjct: 178 GLPIAGDRKYGGEITETAGIGAGNSLALCASELAFSDPDSGK 219


>gi|183219523|ref|YP_001837519.1| pseudouridine synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Paris)']
 gi|189909665|ref|YP_001961220.1| pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167774341|gb|ABZ92642.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167777945|gb|ABZ96243.1| Pseudouridine synthase (Uracil hydrolyase) [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 237

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 68/220 (30%), Positives = 115/220 (52%), Gaps = 23/220 (10%)

Query: 101 LLYEDSKIYVFNKPAGI------SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++YED  + V +KPAG+      S +  +  A  +D ++K   +    +  + HRLD++T
Sbjct: 16  IIYEDRDLLVVDKPAGLLTIATESEKSKTAYASLMD-YVKKGSERSKNRIFIVHRLDRDT 74

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK-KSHIGGDYV 213
           SGILV A+T  A Q L +++   + +K Y ++  G  K K+  I ++L + K+H     V
Sbjct: 75  SGILVFAKTEIAKQTLQDNW--DQTKKNYIAVTHGQWKEKQGTIKSYLTESKAH----RV 128

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           + V   ++G  Y+ + +KV+   +  +  LE+   TGR +Q+RVH      PIVGD KY 
Sbjct: 129 YSVDDPKEG-KYSETKYKVLKE-SNLYSLLEIDLITGRKNQIRVHFAENKHPIVGDTKYG 186

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +  K         ++ LH+  +DL HP +   L   A +P
Sbjct: 187 SETKS------YPRMALHSFSIDLIHPFQKKPLSFNAKIP 220


>gi|118444019|ref|YP_877712.1| ribosomal large subunit pseudouridine synthase C [Clostridium novyi
           NT]
 gi|118134475|gb|ABK61519.1| ribosomal large subunit pseudouridine synthase C, putative
           [Clostridium novyi NT]
          Length = 323

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 75/274 (27%), Positives = 127/274 (46%), Gaps = 34/274 (12%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++ +     +    + K LR G +RV+ K+ K N  ++   VV         
Sbjct: 8   NEAGQRLDKFCRKWLEDVPLGAIFKALRKGDIRVNGKKAKQNYFLEEEDVVET------- 60

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGF 132
            +I   +K   +     +  +F    + YED  + +  K  G+ V      G     D +
Sbjct: 61  KYIESYKKNKKNVPKKFQEVNFSSIKIAYEDENMLIIEKWPGVLVHSDKKDGDPTLTD-Y 119

Query: 133 LKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           + S++ +KG+          P   +RLD+ TSG+++  +   + + L E  R R+I K Y
Sbjct: 120 VLSYLFNKGEYIPENEVTFTPAPCNRLDRNTSGMVIFGKNFKSLKLLNEMIRERKISKYY 179

Query: 184 WSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAIS-HFKVIDCFAQ 238
            +LV G I + + E         ++I  D ++ + +   N+K  +  I+   KVID    
Sbjct: 180 NALVKGKIREGRYE---------AYISKDQINNISEIHLNKKPNSKKIAMEVKVIDTVGT 230

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            F +LE+   TGR+HQLR H   +G PI+GD KY
Sbjct: 231 -FSFLELDLITGRSHQLRAHLSFLGNPIIGDDKY 263


>gi|120597084|ref|YP_961658.1| pseudouridine synthase Rlu family protein [Shewanella sp. W3-18-1]
 gi|120557177|gb|ABM23104.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           sp. W3-18-1]
          Length = 229

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 54/161 (33%), Positives = 81/161 (50%), Gaps = 20/161 (12%)

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G K    HRLD  TSG+L++A++ AAA+  TE F   ++QK Y +L  G PK K+  +  
Sbjct: 40  GIKLFAVHRLDTPTSGLLILAKSTAAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIG 99

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + K          +++  E   N AI+ F  +        +L ++PH+G+THQLRV   
Sbjct: 100 DMAKSRR---SMFKLLRTKE---NPAITQFFSVSVGDGLRLYL-LKPHSGKTHQLRVALA 152

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA-----RYMD 296
            +G PI+GD  Y           + ++ YLHA     RY D
Sbjct: 153 SLGVPILGDELYGG--------AVADRCYLHAYCLHFRYQD 185


>gi|270658450|ref|ZP_06222329.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae HK1212]
 gi|270317010|gb|EFA28676.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae HK1212]
          Length = 116

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 47/124 (37%), Positives = 80/124 (64%), Gaps = 8/124 (6%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           +RV+K R+K   ++Q+G VVRIPPV       + E+     S NL K +  L++ +L+ED
Sbjct: 1   MRVNKGRIKPEYKLQTGDVVRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFED 53

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
             + + NKP+GI+V GGSG+ + +   L++ +  + +   L HRLD++TSGIL++A+ R+
Sbjct: 54  DCLIILNKPSGIAVHGGSGLNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRS 112

Query: 166 AAQH 169
           A ++
Sbjct: 113 ALRN 116


>gi|37680745|ref|NP_935354.1| tRNA pseudouridine synthase C [Vibrio vulnificus YJ016]
 gi|320155588|ref|YP_004187967.1| tRNA pseudouridine synthase C/tRNA Psi65 [Vibrio vulnificus
           MO6-24/O]
 gi|37199494|dbj|BAC95325.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
 gi|319930900|gb|ADV85764.1| tRNA pseudouridine synthase C tRNA Psi65 [Vibrio vulnificus
           MO6-24/O]
          Length = 245

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 106/242 (43%), Gaps = 25/242 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F  + + K Y ++V G  + + E      ++   I   +       E
Sbjct: 64  ALSSEVASQVMPMFAGQEMSKTYHAIVRGWIEEEGELDYALKVELDKIADKFA----SQE 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ +K +               ++  +E++P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQDAITLYKPLAKVEVPYSTGKFPTTRYGLMELKPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 -----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                K+   F+  F +P   +L LHA  +   HP     Q    + A + K W  L  +
Sbjct: 180 THGDGKHNKLFREEFEAP---RLLLHASELRFVHP---YTQQEVVIRAEVDKVWQQLFER 233

Query: 326 YD 327
           ++
Sbjct: 234 FE 235


>gi|225619476|ref|YP_002720733.1| ribosomal large subunit pseudouridine synthase C [Brachyspira
           hyodysenteriae WA1]
 gi|225214295|gb|ACN83029.1| ribosomal large subunit pseudouridine synthase C [Brachyspira
           hyodysenteriae WA1]
          Length = 345

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 80/331 (24%), Positives = 152/331 (45%), Gaps = 51/331 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           + E+ EEN R+D++  + + + +    Q ++  G V ++  +VK+   ++ G  +     
Sbjct: 26  IEEDVEENTRIDKYMGDRFSYYSRNKWQDLIGQGLVLLNNSKVKYTRTVKKGDEIAY--- 82

Query: 71  INALNHII--KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                HII  KE ++ D +V            ++Y+D  + + NKPA + V   SG  YH
Sbjct: 83  -----HIIGMKEPEV-DKNVT-----------IVYDDGDLIIANKPANLPVI-PSGKYYH 124

Query: 129 --IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT----------ESFRM 176
             +   +K+ ++S      + +R+D+ETSG +V++R+  +A +            + ++ 
Sbjct: 125 NTLHTIVKNMLNS---NINMLNRIDRETSGCVVLSRSSKSASNFCAMLAGRKVNGKQYKR 181

Query: 177 RRIQKIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVV-KQNEKGANYAISHFKVID 234
             I+K Y +++        K  +  ++L+  H        + K+N +G+ Y+ + FK I 
Sbjct: 182 NSIKKTYIAVIENAKDIEDKFTVEGYMLESGHEYYRRFQTLHKENVEGSKYSKTSFKTIK 241

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-------NF--KGNFTSPIQ 285
                +  +  + +TGR HQ+RVH    G  +VGD  Y         +F  KG       
Sbjct: 242 RIGD-YAVVMARLYTGRMHQIRVHLYSKGFFMVGDKIYGKYGPKVFDDFIEKGIIPEGFF 300

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           N+  LHA  +   HP     +++ APLP  +
Sbjct: 301 NRQALHAYSLKFNHPITDEIIKVKAPLPKDL 331


>gi|110834055|ref|YP_692914.1| ribosomal large subunit pseudouridine synthase A [Alcanivorax
           borkumensis SK2]
 gi|110647166|emb|CAL16642.1| ribosomal large subunit pseudouridine synthase A [Alcanivorax
           borkumensis SK2]
          Length = 229

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 70/223 (31%), Positives = 108/223 (48%), Gaps = 32/223 (14%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +Y D  + + NKPA + SV G +    + D  ++  +  +    RL HRLD +TSGI+V 
Sbjct: 26  IYRDEHLLLINKPAYLLSVPGRA--PENKDCAIRR-LQQRYPDIRLVHRLDLDTSGIMVF 82

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE----CIANW----LLKKSHIGGD 211
             T  A   L+  F++R ++K Y ++V G + KN        IA+W    L K  H    
Sbjct: 83  GLTAFAQSKLSRLFQLRTVKKRYQAIVHGLVEKNAGSIDLPLIADWPKRPLQKVCH---- 138

Query: 212 YVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                   E G N A++H++V++         L + P TGR+HQLR+H   +G PI+G  
Sbjct: 139 --------ETGKN-ALTHYRVLERDIPGNRTRLALSPVTGRSHQLRIHCRELGHPIIG-- 187

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
             C  +       +  +L LHA ++   HP  G  Q  T+P P
Sbjct: 188 --CDMYAPAEIEALSPRLLLHAEWLAFNHPLTGLWQEFTSPCP 228


>gi|332140698|ref|YP_004426436.1| tRNA pseudouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327550720|gb|AEA97438.1| tRNA pseudouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 279

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 60/166 (36%), Positives = 83/166 (50%), Gaps = 16/166 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD  TSG L +A+    A  + E F  RRI K Y +L    PK K+  I   +  K
Sbjct: 85  LCHRLDTGTSGCLCLAKNAKTAAEIGELFSSRRIGKFYLALSEHKPKKKQGAIIGDM--K 142

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +  GG  + +  Q     N AI+ F           ++ ++PH+G+THQ+RV    +G P
Sbjct: 143 NRRGGQRILLKSQE----NPAITQFFSHAAKPGTRGFI-VKPHSGKTHQIRVALKSIGAP 197

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           I+GD  Y     G   S   ++LYLHA ++ LP    G L ITAP 
Sbjct: 198 ILGDSLY-----GGAPS---DRLYLHAWHLRLPL-SAGELTITAPF 234


>gi|261822605|ref|YP_003260711.1| tRNA pseudouridine synthase C [Pectobacterium wasabiae WPP163]
 gi|261606618|gb|ACX89104.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
          Length = 261

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 64/248 (25%), Positives = 112/248 (45%), Gaps = 53/248 (21%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKP+G  V              +SW+D K             GQ     
Sbjct: 4   IIYQDEHLVAVNKPSGWLVH-------------RSWLDRKEKVVVMQTVRDQIGQHVYTV 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++A +   A+ L++ F   ++QK+Y ++V G   +  + + ++ L +  
Sbjct: 51  HRLDRPTSGVLLLALSSEVARALSQQFESHQMQKMYHAVVRGYVLD--DGVIDYALTEEL 108

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQL 255
             I   + +     +K    A++H++ +               ++  +E++P TGR HQL
Sbjct: 109 DKIADKFAN----PDKAPQPAVTHYRALAQVEMPVAIGRYPTARYSLMELKPQTGRKHQL 164

Query: 256 RVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           R H  H+  PI+GD  H    + +G  T     +L LHA  + L HP  G+       P 
Sbjct: 165 RRHMSHLHHPIIGDTAHGDLRHNRGMETHFSCGRLMLHASELQLNHPVSGQ-------PL 217

Query: 314 HMVKTWDS 321
            +   WD+
Sbjct: 218 TLQARWDA 225


>gi|77412972|ref|ZP_00789175.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
 gi|77160984|gb|EAO72092.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
          Length = 342

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 60/203 (29%), Positives = 90/203 (44%), Gaps = 23/203 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           LYED  + + NKP G+   G       +  H+  +        GQ   + HRLD ETSG 
Sbjct: 132 LYEDEHLIIVNKPEGMKTHGNQPNEIALLNHVSAY-------SGQTCYVVHRLDMETSGA 184

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       + +    + I + YW+LV G    K + + + + +  H     + +  
Sbjct: 185 VLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRDKIGRNRHDRRKRI-IDS 243

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +N + A   I   K I   +   C LE    TGRTHQ+RVH  H G P++GD  Y     
Sbjct: 244 KNGQHAMTIIDVLKYIQNSSLIKCRLE----TGRTHQIRVHLSHHGHPLIGDPLYNP--- 296

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               S    +L LHA  + L HP
Sbjct: 297 ----SSNNERLMLHAHRLTLSHP 315


>gi|227517641|ref|ZP_03947690.1| pseudouridylate synthase RluD [Enterococcus faecalis TX0104]
 gi|227074898|gb|EEI12861.1| pseudouridylate synthase RluD [Enterococcus faecalis TX0104]
          Length = 287

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 40  VKINGETTAFHFPVQAGDCVTL---------TFEETDYVRPTIHL---GEATRVKVLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q  + +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETNTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++  G   N+KE   N  + +         +  Q  
Sbjct: 144 AKNPFVLPILGRLLETKQIYRQYQAIAAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H KV+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVKVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 258 -----ARLMLHASQLHLLHP 272


>gi|71893806|ref|YP_279252.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae J]
          Length = 289

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 95/183 (51%), Gaps = 18/183 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQET 154
           ++++D  + + NKP  + V  G G      ++G + S  DS  Q    +P + HRLD++T
Sbjct: 69  IIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLI-SHFDSLEQLDHIRPGIVHRLDKDT 127

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+L+VA+   A          R+I++ Y ++V G      + +  ++     IG D  +
Sbjct: 128 TGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIG------KVLHKFMKINLPIGRDLKN 181

Query: 215 VVKQNEKGANY--AISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +K+     N   AI++ ++I  F+   Q F  ++ Q  TGRTHQ+R+H  H+G PI GD
Sbjct: 182 PLKKTISFFNSKPAITNVELIKHFSYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPIYGD 241

Query: 270 HKY 272
             Y
Sbjct: 242 PIY 244


>gi|18311104|ref|NP_563038.1| hypothetical protein CPE2122 [Clostridium perfringens str. 13]
 gi|168215749|ref|ZP_02641374.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
 gi|18145787|dbj|BAB81828.1| conserved hypothetical protein [Clostridium perfringens str. 13]
 gi|182382353|gb|EDT79832.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
          Length = 298

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 82/301 (27%), Positives = 137/301 (45%), Gaps = 52/301 (17%)

Query: 39  KILRSG----QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++RS     +++VD   VK N  +++G+ ++I        +I  E+  ++         
Sbjct: 30  RLIRSAAIDKRIKVDGVAVKMNYVVKTGEEIKIELSKKESQNIEPEKMDIE--------- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPR 145
                 ++YEDS I V NK   + V            +GI Y+   F +S  D      R
Sbjct: 81  ------IVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYY---FKESNQDCI---VR 128

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L  RLD  TSG++++ + + A   L+   +  + QK Y ++V G  + K+  I   + + 
Sbjct: 129 LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLEEKEGTINRPIYRP 188

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHM 262
           +    D +  V  +E+G   +I+H+KVI+ +       C LE    TGRTHQ+RVH   +
Sbjct: 189 AE---DTIKRV-VDERGQE-SITHYKVIESYNGADLVECLLE----TGRTHQIRVHLSSL 239

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           G PI GD  Y     G       ++  LHA  +D   P+    L + A LP  M +  + 
Sbjct: 240 GHPIFGDSLY-----GTEDEDFISRQALHAYGLDFYSPKTKEPLSLRADLPEDMKELINK 294

Query: 322 L 322
           L
Sbjct: 295 L 295


>gi|331005741|ref|ZP_08329102.1| pseudouridine synthase A [gamma proteobacterium IMCC1989]
 gi|330420458|gb|EGG94763.1| pseudouridine synthase A [gamma proteobacterium IMCC1989]
          Length = 219

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 104/226 (46%), Gaps = 27/226 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG------IAYHIDGF--LKSWVDSKGQKPRLTHRLDQ 152
           +LYED  + + +KPAG+    G G      + + I G   +++  +   +  R+ HRLD 
Sbjct: 6   VLYEDPHLLIVDKPAGLLTVPGRGPDKQDCLIHRIVGHDSIQNNTEQHWETARIIHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKE--CIANWLLKKSHI 208
            TSGI+V+A        + + F  R+I K Y ++V G   P    E   I +W       
Sbjct: 66  ATSGIIVIALDHPVQAAMGKLFAERQINKSYTAVVEGKVRPTATIELPLICDW------- 118

Query: 209 GGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             D     K + +   YA +   ++  C       + + P TGR+HQLRVH L +G  I+
Sbjct: 119 --DNRPKQKVDHEHGKYAKTELALMSYCEQNHTSRVALTPFTGRSHQLRVHMLAIGHHIL 176

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           GD  Y      N +S    +L LHA  +D  HP    +L I +P P
Sbjct: 177 GDFFYAPEDIKNKSS----RLLLHASAIDFIHPMTQEKLSIQSPAP 218


>gi|301170223|emb|CBW29827.1| tRNA pseudouridine synthase [Haemophilus influenzae 10810]
          Length = 239

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 61/238 (25%), Positives = 109/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAITDYEGLKIVEMPYPAGRYQTVRYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALISHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWHQLMNQFGWE 237


>gi|193076604|gb|ABO11275.2| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 17978]
          Length = 350

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/225 (30%), Positives = 109/225 (48%), Gaps = 21/225 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGI 157
           ++YED  I V NKP G+ V  G+G   +  ++  L  S   ++  +  L HR+D++TSG+
Sbjct: 117 IVYEDEDILVINKPVGMVVHPGAGNTSSTLVNALLYHSPKSAELSRAGLVHRIDKDTSGL 176

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LVVA+   A   L++    + + +IY  + +G        IA   + +  I    V  VK
Sbjct: 177 LVVAKNLEAQFSLSKQLGDKSVYRIYDLVTYG------NIIAGGTIDEP-IKRHPVDRVK 229

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                G   A++H+ V + F + F  ++ Q  TGRTHQ+RVH  ++G  +VGD  Y    
Sbjct: 230 MAILPGGRDAVTHYNVKERF-RDFTRVQAQLETGRTHQIRVHFSYIGHGLVGDQVYMNRV 288

Query: 277 K---GNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITAPLP 312
           +   G     I+      +  LHA  + L HP  G  +   AP P
Sbjct: 289 RIPAGASELLIETLRGFKRQALHAAKLGLKHPRTGEEMLFEAPWP 333


>gi|227811730|ref|YP_002811740.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           M66-2]
 gi|254850369|ref|ZP_05239719.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae
           MO10]
 gi|227010872|gb|ACP07083.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           M66-2]
 gi|227014735|gb|ACP10944.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|254846074|gb|EET24488.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae
           MO10]
          Length = 559

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 108/232 (46%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++   + D+ + L+  +      ++Y+D  I V NKPA      G  +   +   L
Sbjct: 332 LAHMLEGMPLEDNPL-LSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRL 390

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+   ++ +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G    
Sbjct: 391 KAQF-TQAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSE 449

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  I      +  + GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 450 TQGEI------QLPLCGDLDDRPRQKVCWQQGKPALTHWETVQV-EQNRTRVYLYPHTGR 502

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   +  PIVGD  Y    K         +L+LHA  +   HP
Sbjct: 503 THQLRVHCAHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHP 545


>gi|25012059|ref|NP_736454.1| hypothetical protein gbs2021 [Streptococcus agalactiae NEM316]
 gi|24413602|emb|CAD47680.1| Unknown [Streptococcus agalactiae NEM316]
          Length = 270

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 60/203 (29%), Positives = 90/203 (44%), Gaps = 23/203 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           LYED  + + NKP G+   G       +  H+  +        GQ   + HRLD ETSG 
Sbjct: 60  LYEDEHLIIVNKPEGMKTHGNQPNEIALLNHVSAY-------SGQTCYVVHRLDMETSGA 112

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       + +    + I + YW+LV G    K + + + + +  H     + +  
Sbjct: 113 VLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRDKIGRNRHDRRKRI-IDS 171

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +N + A   I   K I   +   C LE    TGRTHQ+RVH  H G P++GD  Y     
Sbjct: 172 KNGQHAMTIIDVLKYIQNSSLIKCRLE----TGRTHQIRVHLSHHGHPLIGDPLYNP--- 224

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               S    +L LHA  + L HP
Sbjct: 225 ----SSNNERLMLHAHRLTLSHP 243


>gi|37681108|ref|NP_935717.1| pseudouridylate synthase [Vibrio vulnificus YJ016]
 gi|37199858|dbj|BAC95688.1| pseudouridylate synthase [Vibrio vulnificus YJ016]
          Length = 250

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 95/214 (44%), Gaps = 30/214 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +++ED  I   NKP+G+ SV G   +  H D     W   + Q P +   HRLD  TSG+
Sbjct: 16  IIFEDDHILAVNKPSGLLSVPGR--LPEHHDSM---WSRLQEQYPEIQVVHRLDMSTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW----LLKKSHI 208
           +V A+ + A   L + F+ R   KIY++ VWG  +          I +W    + K  H 
Sbjct: 71  MVFAKNKRAEAALKKQFQYRLTHKIYYARVWGHVETDSGMIDLPLICDWPNRPMQKVCHE 130

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            G       Q  K   +A      I         + + P TGR+HQLRVH   +G PIVG
Sbjct: 131 HGKPSQTEFQVAKREVHANGAQTTI---------MRLLPVTGRSHQLRVHMQALGHPIVG 181

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           D  Y       F+     +L LHA  +   HP+ 
Sbjct: 182 DEFYAQGDAFTFS----ERLELHAAELSFYHPKS 211


>gi|294794409|ref|ZP_06759545.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Veillonella sp. 3_1_44]
 gi|294454739|gb|EFG23112.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Veillonella sp. 3_1_44]
          Length = 301

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 124/285 (43%), Gaps = 54/285 (18%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M++  Y V E  E  + + ++ K  +  ++  ++Q + R       KKRVK N+R+   Q
Sbjct: 13  MSWKTYTVKEPTE--LTVSKYVKERFS-LSSRDIQMMFR-------KKRVKVNSRVAHSQ 62

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GG 122
             R     + L   + + K  D  V++ K        +LYED+   V NK   + V   G
Sbjct: 63  --RALKKGDVLTLELPQDK--DYGVDVEKGP----ITVLYEDAHTLVVNKAPFMLVHPAG 114

Query: 123 SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  +  ++  +   KG   K R  HRLD+ETSG ++  +T+ A Q+ T+  +  RI 
Sbjct: 115 QTKSCTLSNYIAGYYAKKGVVHKVRPVHRLDRETSGCILFGKTKEAQQYYTDELQAGRID 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           +IY  LV G                 HI  D    +     G +    + +VID F Q  
Sbjct: 175 RIYTGLVEG-----------------HIDAD---GMVDEPIGVDPVFDNRRVIDEFGQPA 214

Query: 241 -------------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                          L  +  TGRTHQ+RVH  H+G PI+GD  Y
Sbjct: 215 QTEYTVLGYEGDNTLLRFKLLTGRTHQIRVHMEHIGHPIIGDAMY 259


>gi|297568139|ref|YP_003689483.1| pseudouridine synthase, RluA family [Desulfurivibrio alkaliphilus
           AHT2]
 gi|296924054|gb|ADH84864.1| pseudouridine synthase, RluA family [Desulfurivibrio alkaliphilus
           AHT2]
          Length = 334

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 109/239 (45%), Gaps = 31/239 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           ++YED  + V NKPA +    G     H     +   +  G  KP L +RLD+ETSG++V
Sbjct: 90  VVYEDDDLLVVNKPAPLPCHPGGRYFRHT--LWRLLQERCGVPKPLLVNRLDRETSGLVV 147

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL--------KKSHIGGD 211
           VA+ RAAA+     ++ ++++K Y  LV G      + +A +L         KKS     
Sbjct: 148 VAKKRAAARDCARQWQEQQVEKRYLVLVEGEFPLGAQAVAGFLAPDPASLVRKKSR---- 203

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +    +    GA    + F+++         LE +P TGR HQ+R     +G P+VGD  
Sbjct: 204 FFPADQAAPAGAVSCATAFRLL-ALQGGISLLEARPLTGRCHQIRATLCSLGFPVVGDKI 262

Query: 272 YCANFKGNFTSPIQNKL-------------YLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           Y  + +  F   + ++L              LH+  + + HP   R L+ T PLP  M 
Sbjct: 263 YGLD-EELFLRFLADRLSSDDRRRLRLPRQALHSAGLKMRHPADHRPLEFTCPLPPEMA 320


>gi|327485332|gb|AEA79738.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio cholerae
           LMA3894-4]
          Length = 559

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 108/232 (46%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++   + D+ + L+  +      ++Y+D  I V NKPA      G  +   +   L
Sbjct: 332 LAHMLEGMPLEDNPL-LSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRL 390

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+   ++ +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G    
Sbjct: 391 KAQF-TQAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSE 449

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  I      +  + GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 450 TQGEI------QLPLCGDLDDRPRQKVCWQQGKPALTHWETVQV-EQNRTRVYLYPHTGR 502

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   +  PIVGD  Y    K         +L+LHA  +   HP
Sbjct: 503 THQLRVHCAHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHP 545


>gi|325121171|gb|ADY80694.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           calcoaceticus PHEA-2]
          Length = 350

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 71/248 (28%), Positives = 114/248 (45%), Gaps = 36/248 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP G+ V  G+G         + YH          ++  +  L HR+D
Sbjct: 117 IVYEDDDILVINKPVGMVVHPGAGNSSGTLVNALLYHFPKL------AELSRAGLVHRID 170

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA++  A   L++    + + ++Y  +V+G        IA   + +  I   
Sbjct: 171 KDTSGLLVVAKSLEAQFSLSKQLANKTVYRVYDLVVYG------NIIAGGTIDEP-IKRH 223

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V  VK     G   A++H+ V + F + F  ++ +  TGRTHQ+RVH  ++G  ++GD 
Sbjct: 224 PVDRVKMAILPGGRDAVTHYNVKERF-KDFTRVQARLETGRTHQIRVHFSYIGYGLIGDQ 282

Query: 271 KYCANFK---GNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITAPLP---AHMVKT 318
            Y    +   G     I+      +  LHA  + L HP  G  +   AP P    H+V  
Sbjct: 283 VYMNRVRVPAGASELLIETLRGFKRQALHAAKLGLKHPRTGEEMLFEAPWPEDFTHLVNV 342

Query: 319 WDSLGFKY 326
             S    Y
Sbjct: 343 LRSENAAY 350


>gi|297579761|ref|ZP_06941688.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae
           RC385]
 gi|297535407|gb|EFH74241.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae
           RC385]
          Length = 570

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 108/232 (46%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++   + D+ + L+  +      ++Y+D  I V NKPA      G  +   +   L
Sbjct: 343 LAHMLEGMPLEDNPL-LSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRL 401

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+   ++ +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G    
Sbjct: 402 KAQF-TQAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSE 460

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  I      +  + GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 461 TQGEI------QLPLCGDLDDRPRQKVCWQQGKPALTHWETVQV-EQNRTRVYLYPHTGR 513

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   +  PIVGD  Y    K         +L+LHA  +   HP
Sbjct: 514 THQLRVHCAHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHP 556


>gi|293412139|ref|ZP_06654862.1| conserved hypothetical protein [Escherichia coli B354]
 gi|291468910|gb|EFF11401.1| conserved hypothetical protein [Escherichia coli B354]
          Length = 260

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRMLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|148826937|ref|YP_001291690.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittGG]
 gi|148718179|gb|ABQ99306.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittGG]
          Length = 239

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 109/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|54294221|ref|YP_126636.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Legionella pneumophila
           str. Lens]
 gi|53754053|emb|CAH15526.1| Ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Legionella pneumophila
           str. Lens]
          Length = 321

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 84/323 (26%), Positives = 143/323 (44%), Gaps = 42/323 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q + V  +  N R+D       P  +   +   +++G V ++    K  ++   G ++  
Sbjct: 7   QQLSVPRELHNQRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCKPKDKALGGDLI-- 64

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              IN       +  I ++  NL K  +    I+ YEDS++ V NKPA + V  G+G   
Sbjct: 65  --TINV------DYTIDNTDFNLCKPENIPIQIV-YEDSEVIVVNKPASLVVHPGAGNKE 115

Query: 128 H--IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           H  ++  L    + +   PR  + HRLD++T+G+L+VA+   +  +L    + R I++ Y
Sbjct: 116 HTLVNALLHHCPELQ-LLPRAGIIHRLDKDTTGLLIVAKNLISHTYLIRQMQNREIKRHY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-----NYAISHFKVIDCFAQ 238
            +LV G           +++    I   +    K   K A       A++H+  I+   +
Sbjct: 175 LTLVHG-----------YVISGGTIDTGFGRHPKNRLKMAVTDFGRQAVTHYN-INKHYK 222

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKL------YL 290
            F  L +   TGRTHQ+RVH  ++  P+VGD  Y     F  N    I + L       L
Sbjct: 223 DFTLLNVSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKFPPNADEAILSVLKQFKRQAL 282

Query: 291 HARYMDLPHP-EGGRLQITAPLP 312
           HA  +   HP +   + + A LP
Sbjct: 283 HACSISFCHPVKNTEITLNALLP 305


>gi|282881959|ref|ZP_06290604.1| RluA family pseudouridine synthase [Peptoniphilus lacrimalis 315-B]
 gi|281298234|gb|EFA90685.1| RluA family pseudouridine synthase [Peptoniphilus lacrimalis 315-B]
          Length = 316

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 67/285 (23%), Positives = 128/285 (44%), Gaps = 32/285 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V++  ++ + RLDR+ K ++       + K LR   ++VD K+    + I+ GQ + +  
Sbjct: 4   VIIGPNDSDQRLDRFLKKYFEKAPLSFIYKNLRKKNIKVDGKKASPEDLIKEGQEISLFI 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               +    K++        L ++S     IL YED  I +  KP  +         ++ 
Sbjct: 64  SDETIEKYKKDK--------LARNSQKFPQIL-YEDDNICLMKKPLNMLTHNDKN--FYQ 112

Query: 130 DGFLKSWVD------------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           D  +  ++D                +P + +RLD+ TSGIL+ A+     + + ++ + R
Sbjct: 113 DNMVDRFIDYLIFKEEYSPREENTFRPSICNRLDRNTSGILLGAKNAETLREINKAIKER 172

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y ++V G  K +K    N  L+K+       ++++++ +G +     F +I    
Sbjct: 173 LVDKFYLTIVKG--KVQKPFEINIKLEKTD-----KNIMRKSSQGKDSLTKFFPLIS--N 223

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
            ++  L+++  TGRTHQ+R      G  I+GD KY       F S
Sbjct: 224 GEYSLLKVKLITGRTHQIRASLKEKGLYILGDRKYGTGKDKEFNS 268


>gi|331088277|ref|ZP_08337196.1| hypothetical protein HMPREF1025_00779 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330408521|gb|EGG87987.1| hypothetical protein HMPREF1025_00779 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 245

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 62/224 (27%), Positives = 109/224 (48%), Gaps = 17/224 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGI 157
           ++YED  I V NK AG+ +        +       W   +  KP   R T+RLD++TSG+
Sbjct: 33  IVYEDEDIIVINKAAGMPIHPSLNNYRNSLANALMWYYEQQNKPFIFRCTNRLDRDTSGL 92

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
            VVA+   ++  L+      +I++ Y ++V G      E   N  + ++   G  +   K
Sbjct: 93  TVVAKHMVSSNILSSMTARHQIEREYLAIVRG-HVTPFEGTINAPIGRT---GSSLIERK 148

Query: 218 QNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + +   +AI+H+  +  F +     + +   TGRTHQ+RVH  H+G P++GD+ Y  + 
Sbjct: 149 IDFENGEHAITHYHTV--FEKNGLSLVSLILETGRTHQIRVHMKHLGFPLIGDYLYNPDM 206

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           +      + ++  LH+  +   HP  GR +  TA LP  M + +
Sbjct: 207 E------LIDRQALHSHCLRFLHPITGRQMTFTADLPEDMARLF 244


>gi|256752736|ref|ZP_05493584.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           CCSD1]
 gi|256748374|gb|EEU61430.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           CCSD1]
          Length = 285

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 124/231 (53%), Gaps = 37/231 (16%)

Query: 103 YEDSKIYVFNKPAGISV------QGGS---GIAYHI-DGFLKSWVDSKGQKPRLTHRLDQ 152
           YED  + + +KPAG+ V      Q G+   G+A++  D  +K+ +       R  +RLD+
Sbjct: 78  YEDEDVLIVDKPAGVVVHPTKRYQSGTLANGVAWYFKDKGIKALI-------RPVNRLDK 130

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V A+ R   Q+  +   ++ + K+Y+++V G  K + E   +  + +    G  
Sbjct: 131 GTSGLVVFAK-RPFMQYYLQI--VKPMSKLYFAVVEG--KMEGEGRIDLPISRKPQSGIE 185

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V ++ ++    AI+++KVI   +++F  L+++  TGRTHQ+RVH  H+G PIVGD  Y
Sbjct: 186 RMVSEEGDR----AITNYKVIKS-SERFSLLKVKIETGRTHQIRVHLSHIGHPIVGDTLY 240

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP---AHMVKTW 319
                G+    I+ +  LHA  +   HP E   + + +PLP    H++K +
Sbjct: 241 -----GSSDDYIKRQA-LHAYRLTFVHPLEERSISVYSPLPQDIQHLLKLF 285


>gi|119513806|ref|ZP_01632778.1| ribosomal large chain pseudouridine synthase A [Nodularia spumigena
           CCY9414]
 gi|119461540|gb|EAW42605.1| ribosomal large chain pseudouridine synthase A [Nodularia spumigena
           CCY9414]
          Length = 331

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 80/252 (31%), Positives = 119/252 (47%), Gaps = 26/252 (10%)

Query: 64  VVRIPPVINALNHIIKEQKILDS-------SVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           V R  P++  L   +K Q  + S       S NL   + F   I+ YED  +   NKP G
Sbjct: 83  VERCQPLMGFLLSGLKSQSPVPSTPMQSSLSSNLNDRAGFNLPII-YEDEWLIAVNKPPG 141

Query: 117 ISVQGGSGIAYHIDGFLKSWVD--SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           +    G       D  L  W        +    HRLDQETSGIL++AR R   + L++ F
Sbjct: 142 LLAVPGRYRDTQ-DSVLSRWRYWFPDDAEIMAVHRLDQETSGILLLARVRQIHRQLSQQF 200

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R++ K+Y ++++G   +++  I    L  S     Y  V   N +    +++ F+VI 
Sbjct: 201 QQRQVHKVYEAILFGAVTDEQGVI-ELPLWGSPENRPYQQV---NWQYGKISVTQFRVIG 256

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHA---LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
                +  +E  P TGRTHQLRVHA   L +G  I+GD  Y  N          ++L+LH
Sbjct: 257 -REGNYTRVEFIPVTGRTHQLRVHAADQLGLGMTILGDRLYGCNAAA-------SRLHLH 308

Query: 292 ARYMDLPHPEGG 303
           AR +   HP+ G
Sbjct: 309 ARQLSFKHPQLG 320


>gi|32034411|ref|ZP_00134593.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
 gi|126207717|ref|YP_001052942.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae L20]
 gi|190149500|ref|YP_001968025.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           7 str. AP76]
 gi|303251649|ref|ZP_07337822.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           6 str. Femo]
 gi|303252800|ref|ZP_07338960.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           2 str. 4226]
 gi|307245042|ref|ZP_07527136.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|307247214|ref|ZP_07529264.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|307249442|ref|ZP_07531431.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
 gi|307251759|ref|ZP_07533662.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|307256257|ref|ZP_07538041.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 10
           str. D13039]
 gi|307258451|ref|ZP_07540189.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 11
           str. 56153]
 gi|307262819|ref|ZP_07544444.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 13
           str. N273]
 gi|126096509|gb|ABN73337.1| predicted RNA pseudouridine synthase [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
 gi|189914631|gb|ACE60883.1| predicted RNA pseudouridine synthase [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|302648361|gb|EFL78557.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           2 str. 4226]
 gi|302649491|gb|EFL79674.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           6 str. Femo]
 gi|306854030|gb|EFM86241.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|306856272|gb|EFM88425.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|306858516|gb|EFM90583.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
 gi|306860760|gb|EFM92770.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|306865221|gb|EFM97120.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 10
           str. D13039]
 gi|306867456|gb|EFM99306.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 11
           str. 56153]
 gi|306871834|gb|EFN03553.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 13
           str. N273]
          Length = 216

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 61/198 (30%), Positives = 96/198 (48%), Gaps = 24/198 (12%)

Query: 98  KSILLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           K  + ++     V +KP G+SV   +   G+  ++   L++      ++  L HRLD+ T
Sbjct: 4   KLTICFQHHDFVVIDKPVGVSVHKDEEAIGLTENLAEQLQA------EQVWLVHRLDKVT 57

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+ A  + AA H    F   +I+K YW+L    PK K+  I+   ++KS  G   + 
Sbjct: 58  SGLLIFALNKQAAVHFYHLFEQHKIEKTYWALSDQKPKKKQGKISG-DMQKSRNGAWKLF 116

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             KQN      A++ F V            +QP TG+THQLRV    +G PI+GD +Y  
Sbjct: 117 HSKQNP-----AVTQF-VSHSLEPNLRHFILQPKTGKTHQLRVAMKSLGSPILGDQRYAG 170

Query: 275 NFKGNFTSPIQNKLYLHA 292
                      +++YLHA
Sbjct: 171 T--------AADRVYLHA 180


>gi|256822673|ref|YP_003146636.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
 gi|256796212|gb|ACV26868.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
          Length = 222

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 60/217 (27%), Positives = 110/217 (50%), Gaps = 16/217 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D      NKPAG+    G           +     K +   + HRLD  TSG++++
Sbjct: 16  ILHPDKHFLFVNKPAGLLSIPGRHEENKDCVVTRLQNHPKSKTASIVHRLDMATSGVMIL 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A+T+ A + +++ F +R+  K Y ++V  I +     I   ++       D+ +  KQ  
Sbjct: 76  AQTKFAHREISKQFELRQTDKYYIAVVDAIVEKDSGVIDLPMI------ADWPNRPKQKI 129

Query: 220 --EKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             E+G   A++ ++V++    ++   L+++P TGR+HQLR+H   +G PI+G H Y  N 
Sbjct: 130 DFEEGKK-AVTEWEVLERDLEKQTTRLKLKPITGRSHQLRLHCFELGHPILGCHLYHKN- 187

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            G+ T     +L LHA  + + HP+  + + + +P P
Sbjct: 188 -GSETK--AKRLLLHAASLTITHPKSCKNITVESPCP 221


>gi|293374677|ref|ZP_06620987.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|292646694|gb|EFF64694.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
          Length = 297

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 108/210 (51%), Gaps = 30/210 (14%)

Query: 101 LLYEDSKIYVFNKPAGI----------SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           ++YED  + V NKPAGI               + I Y+ +  + S +          +RL
Sbjct: 83  VVYEDEYLLVINKPAGIPTIPSLRHPEKTLANALIHYYNEHEIASTI-------HFVNRL 135

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+ R     LT+   +++I++ Y++LV G+ +     +   + ++S   G
Sbjct: 136 DRDTSGLLMVAKYRHIHHLLTKD--VKQIKRKYYTLVKGVMEKNSGTVHAPIARESE--G 191

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +    V+ +    + +I+H++V++ + +K   +E +  TGRTHQ+RVH  ++G P+VGD 
Sbjct: 192 NVRRCVRAD---GDDSITHYQVLEVW-EKLTLVECELETGRTHQIRVHMNYLGHPLVGDT 247

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            Y       F   ++    LH+  +   HP
Sbjct: 248 LY-----DEFALELEEGHLLHSYELSFTHP 272


>gi|116627150|ref|YP_819769.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus LMD-9]
 gi|116100427|gb|ABJ65573.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           thermophilus LMD-9]
          Length = 290

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 60/199 (30%), Positives = 88/199 (44%), Gaps = 16/199 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYEDS I V NKP G+   G       +   + ++    GQ   + HRLD ETSG ++ A
Sbjct: 84  LYEDSHIIVVNKPEGMKTHGNKPTEIALLNHVSAYC---GQTCYVVHRLDMETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      + IQ+ YW+L  G  + KK    + + +  H     V V  +  +
Sbjct: 141 KNPFILPILNRLLEDKMIQRQYWALTEGKFQTKKTVYKDKIGRDRHDRRKRV-VDPRKGQ 199

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            A   ++  K  +  +   C L+    TGRTHQ+RVH  H G  I+GD  Y         
Sbjct: 200 SAYTTVTRLKTFEGASLVNCQLK----TGRTHQIRVHLSHHGHAILGDPLYSHQ------ 249

Query: 282 SPIQNKLYLHARYMDLPHP 300
               ++L LHA  +   HP
Sbjct: 250 --PSSRLMLHAHSLSFTHP 266


>gi|229506727|ref|ZP_04396236.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae BX
           330286]
 gi|229510479|ref|ZP_04399959.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae B33]
 gi|229517390|ref|ZP_04406835.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae RC9]
 gi|229605200|ref|YP_002875904.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           MJ-1236]
 gi|298499967|ref|ZP_07009773.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae MAK
           757]
 gi|229345426|gb|EEO10399.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae RC9]
 gi|229352924|gb|EEO17864.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae B33]
 gi|229357078|gb|EEO21996.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae BX
           330286]
 gi|229371686|gb|ACQ62108.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           MJ-1236]
 gi|297541948|gb|EFH77999.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae MAK
           757]
          Length = 570

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 108/232 (46%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++   + D+ + L+  +      ++Y+D  I V NKPA      G  +   +   L
Sbjct: 343 LAHMLEGMPLEDNPL-LSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRL 401

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+   ++ +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G    
Sbjct: 402 KAQF-TQAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSE 460

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  I      +  + GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 461 TQGEI------QLPLCGDLDDRPRQKVCWQQGKPALTHWETVQV-EQNRTRVYLYPHTGR 513

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   +  PIVGD  Y    K         +L+LHA  +   HP
Sbjct: 514 THQLRVHCAHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHP 556


>gi|325297415|ref|YP_004257332.1| pseudouridine synthase, RluA family [Bacteroides salanitronis DSM
           18170]
 gi|324316968|gb|ADY34859.1| pseudouridine synthase, RluA family [Bacteroides salanitronis DSM
           18170]
          Length = 307

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 109/229 (47%), Gaps = 26/229 (11%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDS--KGQKPRL 146
           H   LK  +LYED+ I V  K  G+    + +     A HI   L  +V    KG +  +
Sbjct: 88  HHPMLK--ILYEDAYIIVVEKKEGLLSVATERQKERTAQHI---LNEYVKRIHKGNRIYV 142

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-KK 205
            HRLD+ETSGI++ A+       L +++      + Y ++V G  +  +  + +WL  +K
Sbjct: 143 VHRLDRETSGIMMYAKDEKTQHTLRDNWHDLVRDRRYVTIVQGEMEQDEGTVCSWLTDRK 202

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            ++           + G  Y+++H+  I   A  F  LE+Q  TGR +Q+RVH   +G P
Sbjct: 203 LYVSSS------PTDDGGKYSVTHYHTIK-RANGFSLLELQLETGRKNQIRVHMQSLGHP 255

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +VGD +Y     G   +P+  +L LHA  +   HP     ++   P P 
Sbjct: 256 VVGDERY-----GCEMNPL-GRLALHAFKLCFYHPVTHEWMEFETPYPT 298


>gi|315222714|ref|ZP_07864603.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
 gi|315188400|gb|EFU22126.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
          Length = 296

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 61/218 (27%), Positives = 112/218 (51%), Gaps = 18/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS---KGQKPRLTHRLDQETSGI 157
           ++YED    + NKPAG++       +  +  F+K++  +   + Q+  +  RLD++TSG+
Sbjct: 78  IVYEDEHFLILNKPAGVASIPSVNHSNTMANFVKAYYIANHYENQQIHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    K E   IA    + S I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKVIEKHYYALVKGSAPLKPEGDIIAPIAREGSSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +   K   YA + +KV+  +   +  +++  HTGRTHQ+RVH  ++G P++GD  Y  +
Sbjct: 192 TRCVAKNGKYAHTSYKVLAQYDDIY-LVDIHLHTGRTHQIRVHFSYIGFPLLGDDLYGGS 250

Query: 276 FKGNFTSPIQNKLYLHA-RYMDLPHPEGGRLQITAPLP 312
                T   +  L+ H+ R+ +  H E   +  ++PLP
Sbjct: 251 MTDGIT---RQALHCHSLRFYNPFHEE--VVNKSSPLP 283


>gi|295702869|ref|YP_003595944.1| pseudouridine synthase [Bacillus megaterium DSM 319]
 gi|294800528|gb|ADF37594.1| pseudouridine synthase, RluA family [Bacillus megaterium DSM 319]
          Length = 302

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 77/313 (24%), Positives = 141/313 (45%), Gaps = 36/313 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP- 68
            V++  E + +  + K H   I+  +L  I  R G + V+ K       +Q G  +++  
Sbjct: 10  TVDHSFEGVAVREFLKEH--DISKASLTDIKFRGGAIEVNGKHATVRYILQKGDEIKVAF 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK-PAGISVQGGSGIAY 127
           P   A   ++ +   LD               ++YED  I V NK P   S+     + +
Sbjct: 68  PPEKASESLLPKAIPLD---------------IVYEDEYILVLNKQPNMPSIPSREHLTW 112

Query: 128 HIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +  + +         L +RLD++TSG+L+VA+ R      +++ +   I+++Y +
Sbjct: 113 SLSNAVLYYYEKNNINSTVHLVNRLDRDTSGLLIVAKHRHVHYLFSKAQKEHEIKRVYRA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G    K+   A    K+S I      + ++  +   +AI+H+  +  ++  F  + +
Sbjct: 173 FVHGKLVGKETIEAPIGRKESSI------IEREVREDGQFAITHYTALRQYSS-FTEVAL 225

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
              TGRTHQ+RVH  + G P++GD  Y        T+ + ++  LH+  +   HP   + 
Sbjct: 226 SLETGRTHQIRVHMAYKGYPLLGDTLYGG------TNHLISRQALHSYELTFFHPFLQKT 279

Query: 305 LQITAPLPAHMVK 317
           L  TAPLP  M K
Sbjct: 280 LSFTAPLPPDMQK 292


>gi|328881776|emb|CCA55015.1| Ribosomal large subunit pseudouridine synthase D [Streptomyces
           venezuelae ATCC 10712]
          Length = 313

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 83/335 (24%), Positives = 143/335 (42%), Gaps = 40/335 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    ++ + V +  E  R+D      +   +     ++  +G+V+VD   V  + R+ 
Sbjct: 1   MSTSPEIRTLPVPDGLEGERVDAAIARMF-GFSRTKAAELAAAGKVQVDGSVVGKSERVS 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPGAAAPVQIVAEP--------------VEGMEIVHDDDDIVVIMKPIGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +    + + G   R  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ R + K Y +LV G P      I   + +  H   DY   V  + K    +++H+ +I
Sbjct: 166 FKERTVDKRYHALVQGHPDPMSGTIDAPIGR--HPNHDYKWAVTADGK---PSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----- 288
           + + +    L+++  TGRTHQ+RVH      P VGD  Y A+        I  +L     
Sbjct: 221 EAY-RSASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGAD------PTIAKRLGLTRQ 273

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +LHA  +   HP +G  ++  +  P  + K  D +
Sbjct: 274 WLHAVRLGFEHPGDGSWVEFASTYPEDLQKALDRI 308


>gi|241896391|ref|ZP_04783687.1| pseudouridylate synthase, 23S RNA-specific [Weissella
           paramesenteroides ATCC 33313]
 gi|241870371|gb|EER74122.1| pseudouridylate synthase, 23S RNA-specific [Weissella
           paramesenteroides ATCC 33313]
          Length = 297

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 73/267 (27%), Positives = 124/267 (46%), Gaps = 20/267 (7%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYV 110
           +R+  N + Q    +  P  +  LN + ++    DS   +   S  L+  +LYE+ ++ V
Sbjct: 40  RRIYLNGQYQPTSTILKPYDVLTLNWLPEDFMTPDSQY-VPDDSQSLQ--VLYENDELMV 96

Query: 111 FNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
            NK  G+     S G    +  F ++++  + ++  + HRLD +T+G L++A+       
Sbjct: 97  VNKRKGVKTHPNSPGENGTMMNFAQAYLMKQDKRAYMVHRLDGQTTGALIIAKVPYVVPI 156

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AI 227
           L +    + I++ Y + V G   +    I         IG    +   +   GAN   AI
Sbjct: 157 LNQMLHDKTIKRTYLAWVDGHLTDSTGAIT------LAIGDHPTNSRLRQIDGANAKPAI 210

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +H+  I    Q+   + +Q  TGRTHQ+R+H   +G P+VGD  Y      N  S   + 
Sbjct: 211 THWTKIKSVYQQ-TLVRLQLETGRTHQIRLHMAAIGHPLVGDDLY------NQQSAYADG 263

Query: 288 LYLHARYMDLPHPEGGRLQ-ITAPLPA 313
           L LH+  + LP P    ++ I APLPA
Sbjct: 264 LLLHSASVQLPMPFSSEIKSIGAPLPA 290


>gi|229522777|ref|ZP_04412191.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TM
           11079-80]
 gi|229339994|gb|EEO05002.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TM
           11079-80]
          Length = 570

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 108/232 (46%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++   + D+ + L+  +      ++Y+D  I V NKPA      G  +   +   L
Sbjct: 343 LAHMLEGMPLEDNPL-LSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRL 401

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+   ++ +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G    
Sbjct: 402 KAQF-TQAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSE 460

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  I      +  + GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 461 TQGEI------QLPLCGDLDDRPRQKVCWQQGKPALTHWETVQV-EQNRTRVYLYPHTGR 513

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   +  PIVGD  Y    K         +L+LHA  +   HP
Sbjct: 514 THQLRVHCAHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHP 556


>gi|255033891|ref|YP_003084512.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
 gi|254946647|gb|ACT91347.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
          Length = 228

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 106/239 (44%), Gaps = 30/239 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LY    +   NKP G+ V   S IA   D F    + D   QK    HRLD++TSG+L+
Sbjct: 6   ILYRSDDLVAINKPNGLLVHR-SPIASDADVFAVQLLRDQLSQKVYPAHRLDRKTSGVLL 64

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A        +   F    I K Y ++V G   ++ E              DY   +K++
Sbjct: 65  FALNENVNSEMQGKFMEGEITKTYHAIVRGHTADRGEI-------------DYP--LKRD 109

Query: 220 EKGANYAISHFKVID----CFA------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +     A++HF+ +      FA       ++  +++ P TGR HQLR H  H+  PI+GD
Sbjct: 110 DGVTQDAVTHFETLARAEVPFALGKHATSRYSLVQLNPLTGRMHQLRKHMAHIMHPIIGD 169

Query: 270 HKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
             +  N +  F        ++ LHA  ++  HP  G+ + I AP  +  V+    LG +
Sbjct: 170 RPHGCNKQNRFFKEELGMIQMMLHAVSVEFVHPVSGQHVTIVAPYLSEFVRMRSVLGLE 228


>gi|307265946|ref|ZP_07547494.1| pseudouridine synthase, RluA family [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|306919010|gb|EFN49236.1| pseudouridine synthase, RluA family [Thermoanaerobacter wiegelii
           Rt8.B1]
          Length = 285

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 124/231 (53%), Gaps = 37/231 (16%)

Query: 103 YEDSKIYVFNKPAGISV------QGGS---GIAYHI-DGFLKSWVDSKGQKPRLTHRLDQ 152
           YED  + + +KPAG+ V      Q G+   G+A++  D  +K+ +       R  +RLD+
Sbjct: 78  YEDEDVLIVDKPAGVVVHPTKRYQSGTLANGVAWYFKDKGIKALI-------RPVNRLDK 130

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V A+ R   Q+  +   ++ + K+Y+++V G  K + E   +  + +    G  
Sbjct: 131 GTSGLVVFAK-RPFMQYYLQI--VKPMSKLYFAVVEG--KMEGEGRIDLPISRKPQSGIE 185

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V ++ ++    AI+++KV+   +++F  L+++  TGRTHQ+RVH  H+G PIVGD  Y
Sbjct: 186 RMVSEEGDR----AITNYKVVKS-SERFSLLKVKIETGRTHQIRVHLSHIGHPIVGDTLY 240

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP---AHMVKTW 319
                G+    I+ +  LHA  +   HP E   + + +PLP    H++K +
Sbjct: 241 -----GSSDDYIKRQA-LHAYRLTFVHPLEEKSISVYSPLPQDIQHLLKLF 285


>gi|257415249|ref|ZP_05592243.1| pseudouridine synthase [Enterococcus faecalis AR01/DG]
 gi|257157077|gb|EEU87037.1| pseudouridine synthase [Enterococcus faecalis ARO1/DG]
          Length = 287

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/260 (26%), Positives = 114/260 (43%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 40  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHL---GEATRVTVLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++  G   N+KE   N  + +         +  Q  
Sbjct: 144 AKNPFVLPILGRLLETKQIYRQYQAIAAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 258 -----ARLMLHASQLHLLHP 272


>gi|157376301|ref|YP_001474901.1| pseudouridylate synthase [Shewanella sediminis HAW-EB3]
 gi|157318675|gb|ABV37773.1| pseudouridylate synthase [Shewanella sediminis HAW-EB3]
          Length = 278

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/253 (27%), Positives = 111/253 (43%), Gaps = 28/253 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  +   +KPAG+ V   S +A     F ++   D  G      HRLD+ TSG+L+
Sbjct: 32  ILFEDDDVVAIHKPAGLLVHR-SYLARRERFFAMQLTRDKVGCHVFPVHRLDRPTSGVLL 90

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A++   A  L E F  + + K Y ++V G   N  E        K  +       V  N
Sbjct: 91  FAKSSEMANKLCEQFEAKTVDKHYLAIVRG---NMHEADTLDYALKVELDDHGDKDVDPN 147

Query: 220 EKGANYAISHFKVIDC---------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +   +   S+  +++             ++  +++ PHTGR HQLR H  H+  PIVGD 
Sbjct: 148 KAAQDAVTSYQPLLNTEIPFPSGRYATSRYALVKLTPHTGRKHQLRRHMAHLRHPIVGDT 207

Query: 271 KYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT-----W 319
            +        F+ +F+    N+L+L A+++   HP  G R+ I   L            W
Sbjct: 208 THGDGKQNKFFREHFS---MNRLWLIAKHLSFDHPRSGERITIETELEEQWFTLFEAFGW 264

Query: 320 DSLGFKYDRNLYI 332
           D      DR+ +I
Sbjct: 265 DEEKLATDRSYFI 277


>gi|119896305|ref|YP_931518.1| pseudouridine synthase A [Azoarcus sp. BH72]
 gi|119668718|emb|CAL92631.1| pseudouridine synthase A [Azoarcus sp. BH72]
          Length = 214

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 66/223 (29%), Positives = 105/223 (47%), Gaps = 20/223 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           L   LLY D  + V +KPAG+ SV  G          L   V ++     + HRLD  TS
Sbjct: 4   LTPTLLYTDDSLIVADKPAGLLSVPAGG---EDRQDCLAHRVQAQFDDALIVHRLDAATS 60

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++++AR     + ++  F  R + K Y +LV G        IA  L        D ++ 
Sbjct: 61  GLVLLARGMEMLRRMSLGFEQRVVGKRYVALVHGRVAQDDGEIALPL------AADPLNR 114

Query: 216 VKQNEKGAN--YAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +Q    A    A++ ++V++           LE++P TGR+HQLRVH + +G PIVGD 
Sbjct: 115 PRQIVDAARGRPALTRYRVLERSGAGDAAVSRLELKPMTGRSHQLRVHLMAIGHPIVGDP 174

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y        ++    +++LHA  +   HP+    +Q  +P+P
Sbjct: 175 LYAP----PESAAAHPRMFLHAAGIAFMHPDRRVPMQFDSPVP 213


>gi|260437125|ref|ZP_05790941.1| pseudouridine synthase, RluA family [Butyrivibrio crossotus DSM
           2876]
 gi|292810437|gb|EFF69642.1| pseudouridine synthase, RluA family [Butyrivibrio crossotus DSM
           2876]
          Length = 314

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 76/326 (23%), Positives = 144/326 (44%), Gaps = 31/326 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +Y++ +N E   R D++      +     + K LR+  + ++ K+ K N  ++    VRI
Sbjct: 3   EYIIGKN-EAGQRFDKYIFKLLKNAGTGLIFKQLRNKNIVLNGKKAKGNEILKENDSVRI 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
               + +N      K     ++++K     +  ++YED  I + +KP G+  Q  S    
Sbjct: 62  FMSDDTIN------KFTGGPLHISKTG--FRLDVIYEDDDILLASKPVGVLSQKSSDKDI 113

Query: 128 HIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            ++ +L  ++   G         KP   +RLD+ TSG+++  ++    Q ++E  + R I
Sbjct: 114 SMNEYLIEYLTDNGFGKENLATFKPSFCNRLDRNTSGLMIAGKSLRGLQKMSEIIKDRSI 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI-SHFKVIDCFAQ 238
            K Y ++V GI  +KK  I  +L K      +   V+  N    +Y I + ++ +     
Sbjct: 174 HKFYLTIVKGIV-DKKSVIKGYLRKDEK---NNKVVIYDNPVKDSYEIHTEYEPL-ATKD 228

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDL 297
               L+++  TG+THQ+R H   +  P++GD KY    F   +    + K  LH+  +  
Sbjct: 229 DMTLLKVRLITGKTHQIRAHLAGISHPVLGDFKYGDKVFNEKYG---EKKQLLHSYQVVF 285

Query: 298 PH----PEGGRLQITAPLPAHMVKTW 319
           P     P+        P P +  K +
Sbjct: 286 PKLDDFPDISEKSFNTPYPVNFTKYF 311


>gi|156932726|ref|YP_001436642.1| tRNA pseudouridine synthase C [Cronobacter sakazakii ATCC BAA-894]
 gi|156530980|gb|ABU75806.1| hypothetical protein ESA_00515 [Cronobacter sakazakii ATCC BAA-894]
          Length = 265

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 60/216 (27%), Positives = 100/216 (46%), Gaps = 18/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 5   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G   +        + +   I   +     + +
Sbjct: 65  GLSSEAGRRLAQQFEQHQIQKRYHAIVRGWLTDSAVLDYPLVEELDKIADKF----SRQD 120

Query: 221 KGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +   +Q          ++  +EM P TGR HQLR H  H+  PI+GD 
Sbjct: 121 KEPQPAVTHYRGLATTSQPVAVGRYDSVRYSLVEMLPQTGRKHQLRRHMAHLRHPIIGDS 180

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG 303
           K+  + + N  +      N+L LHA  + L HP  G
Sbjct: 181 KH-GDLRQNRAAAEHFGCNRLMLHASELTLTHPFTG 215


>gi|332876323|ref|ZP_08444096.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6014059]
 gi|322507012|gb|ADX02466.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 1656-2]
 gi|323516880|gb|ADX91261.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332735474|gb|EGJ66528.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6014059]
          Length = 350

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 108/231 (46%), Gaps = 33/231 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP G+ V  G+G         + YH      S   ++  +  L HR+D
Sbjct: 117 IVYEDEDILVINKPVGMVVHPGAGNTSGTLVNALLYH------SPKSAELSRAGLVHRID 170

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA+   A   L++    + + +IY  + +G        IA   + +  I   
Sbjct: 171 KDTSGLLVVAKNLEAQFSLSKQLGDKSVYRIYDLVTYG------NIIAGGTIDEP-IKRH 223

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V  VK     G   A++H+ V + F + F  ++ Q  TGRTHQ+RVH  ++G  +VGD 
Sbjct: 224 PVDRVKMAILPGGRDAVTHYNVKERF-RDFTRVQAQLETGRTHQIRVHFSYIGHGLVGDQ 282

Query: 271 KYCANFK---GNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y    +   G     I+      +  LHA  + L HP  G  +   AP P
Sbjct: 283 VYMNRVRIPAGASELLIETLRGFKRQALHAAKLGLKHPRTGEEMLFEAPWP 333


>gi|170727628|ref|YP_001761654.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169812975|gb|ACA87559.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 285

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 109/237 (45%), Gaps = 19/237 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  I V +KPAG+ V   S +A     F ++   D  G      HRLD+ TSGIL+
Sbjct: 39  ILFEDDDIVVIHKPAGLLVHR-SYLARRERFFAMQMTRDKVGCHVFPVHRLDRPTSGILL 97

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A++   A +L E F  + ++K Y ++V G   N  E        K  +       V  N
Sbjct: 98  FAKSSEMANNLCEQFSAKTVEKQYLAIVRG---NMHEADTLDYALKVELDDHGDKDVDPN 154

Query: 220 EKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            K A  A++ ++ +               ++  +++ PHTGR HQLR H  H+  PIVGD
Sbjct: 155 -KAAQEAVTSYQPLLNTEIPFPSGRYATSRYAMVKLIPHTGRKHQLRRHMAHLRHPIVGD 213

Query: 270 HKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
             +    +  F       N+L+L A+ +   HP  G R+ I   L    +  +++ G
Sbjct: 214 TTHGDGKQNKFFREHFAINRLWLIAKSLAFDHPRSGERITIETELEKEWLTLFEAFG 270


>gi|229514608|ref|ZP_04404069.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TMA 21]
 gi|229348588|gb|EEO13546.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TMA 21]
          Length = 570

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 108/232 (46%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++   + D+ + L+  +      ++Y+D  I V NKPA      G  +   +   L
Sbjct: 343 LAHMLEGMPLEDNPL-LSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRL 401

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+   ++ +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G    
Sbjct: 402 KAQF-TQAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSE 460

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  I      +  + GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 461 TQGEI------QLPLCGDLDDRPRQKVCWQQGKPALTHWETVQV-EQNRTRVYLYPHTGR 513

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   +  PIVGD  Y    K         +L+LHA  +   HP
Sbjct: 514 THQLRVHCAHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHP 556


>gi|229527911|ref|ZP_04417302.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           12129(1)]
 gi|229334273|gb|EEN99758.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           12129(1)]
          Length = 570

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 108/232 (46%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++   + D+ + L+  +      ++Y+D  I V NKPA      G  +   +   L
Sbjct: 343 LAHMLEGMPLEDNPL-LSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRL 401

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+   ++ +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G    
Sbjct: 402 KAQF-TQAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSE 460

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  I      +  + GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 461 TQGEI------QLPLCGDLDDRPRQKVCWQQGKPALTHWETVQV-EQNRTRVYLYPHTGR 513

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   +  PIVGD  Y    K         +L+LHA  +   HP
Sbjct: 514 THQLRVHCAHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHP 556


>gi|312870084|ref|ZP_07730220.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
 gi|311094387|gb|EFQ52695.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
          Length = 289

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 56/180 (31%), Positives = 92/180 (51%), Gaps = 15/180 (8%)

Query: 103 YEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQ---KPRLTHRLDQETSGIL 158
           YED    V +KPAG+S + G +     I   +K +++ +G    +P L  RLD+ TSG+L
Sbjct: 82  YEDDNWLVVDKPAGVSSIPGPTTSNGTILNRVKGYLEEQGSEDLRPHLITRLDRFTSGLL 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+   A+  +++  +  R+ K Y ++V G   +    I   + ++    G    V+  
Sbjct: 142 LVAKHHVASSMISQQVQQHRMLKEYTAVVSGRFADDHGVIDQPIARRE---GQVARVIAP 198

Query: 219 NEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +      A++ + V D   Q   W  L +Q HTGRTHQ+RVH    G P++GDH Y  + 
Sbjct: 199 D---GQRAVTEYWVED---QGVDWARLRLQLHTGRTHQIRVHMASAGHPLIGDHLYGGDM 252


>gi|329123449|ref|ZP_08252013.1| tRNA pseudouridine synthase C [Haemophilus aegyptius ATCC 11116]
 gi|327471031|gb|EGF16486.1| tRNA pseudouridine synthase C [Haemophilus aegyptius ATCC 11116]
          Length = 239

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 61/238 (25%), Positives = 109/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|153825763|ref|ZP_01978430.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae
           MZO-2]
 gi|149740602|gb|EDM54713.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae
           MZO-2]
          Length = 570

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 108/232 (46%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++   + D+ + L+  +      ++Y+D  I V NKPA      G  +   +   L
Sbjct: 343 LAHMLEGMPLEDNPL-LSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRL 401

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+   ++ +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G    
Sbjct: 402 KAQF-TQAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSE 460

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  I      +  + GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 461 TQGEI------QLPLCGDLDDRPRQKVCWQQGKPALTHWETVQV-EQNRTRVYLYPHTGR 513

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   +  PIVGD  Y    K         +L+LHA  +   HP
Sbjct: 514 THQLRVHCAHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHP 556


>gi|145641594|ref|ZP_01797171.1| tRNA pseudouridine synthase C [Haemophilus influenzae R3021]
 gi|145273641|gb|EDK13510.1| tRNA pseudouridine synthase C [Haemophilus influenzae 22.4-21]
          Length = 239

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 110/238 (46%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDAFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|332868375|ref|ZP_08438121.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6013113]
 gi|332733434|gb|EGJ64615.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6013113]
          Length = 350

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 108/231 (46%), Gaps = 33/231 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP G+ V  G+G         + YH      S   ++  +  L HR+D
Sbjct: 117 IVYEDEDILVINKPVGMVVHPGAGNTSGTLVNALLYH------SPKSAELSRAGLVHRID 170

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA+   A   L++    + + +IY  + +G        IA   + +  I   
Sbjct: 171 KDTSGLLVVAKNLEAQFSLSKQLGDKSVYRIYDLVTYG------NIIAGGTIDEP-IKRH 223

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V  VK     G   A++H+ V + F + F  ++ Q  TGRTHQ+RVH  ++G  +VGD 
Sbjct: 224 PVDRVKMAILPGGRDAVTHYNVKERF-RDFTRVQAQLETGRTHQIRVHFSYIGHGLVGDQ 282

Query: 271 KYCANFK---GNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y    +   G     I+      +  LHA  + L HP  G  +   AP P
Sbjct: 283 VYMNRVRIPAGASELLIETLRGFKRQALHAAKLGLKHPRTGEEMLFEAPWP 333


>gi|306826329|ref|ZP_07459662.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|304431442|gb|EFM34425.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
          Length = 291

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 58/201 (28%), Positives = 93/201 (46%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + V NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 84  VYQDQHLIVVNKPEGMKTHGNQPNEIALLNHISAYV---GQTCYVVHRLDMETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G  ++K+      L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEIAREYWALVEGRVESKE------LVFRDKIGRDRHDRRKRVVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   +A +    +  F  K   +  +  TGRTHQ+R+H  H   PI+GD  Y +  K  
Sbjct: 195 PKNGQHAETQVSRLKQFPNKTSLVRCKLKTGRTHQIRIHLSHHKHPILGDPLYNSKSKT- 253

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 254 ------SRLMLHAFRLSFTHP 268


>gi|257418294|ref|ZP_05595288.1| pseudouridine synthase [Enterococcus faecalis T11]
 gi|257160122|gb|EEU90082.1| pseudouridine synthase [Enterococcus faecalis T11]
          Length = 287

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 116/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 40  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q  + +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETNTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 144 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 258 -----ARLMLHASQLHLLHP 272


>gi|194434667|ref|ZP_03066921.1| tRNA pseudouridine synthase C [Shigella dysenteriae 1012]
 gi|194417064|gb|EDX33179.1| tRNA pseudouridine synthase C [Shigella dysenteriae 1012]
 gi|332089085|gb|EGI94195.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           155-74]
          Length = 260

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQYVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|50119965|ref|YP_049132.1| tRNA pseudouridine synthase C [Pectobacterium atrosepticum
           SCRI1043]
 gi|49610491|emb|CAG73936.1| putative RNA pseudouridylate synthase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 261

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 65/248 (26%), Positives = 112/248 (45%), Gaps = 53/248 (21%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKP+G  V              +SW+D K             GQ     
Sbjct: 4   IIYQDEHLVAVNKPSGWLVH-------------RSWLDRKEKIVVMQTVRDQIGQHVYTV 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++A +   A+ L++ F   ++QK+Y ++V G   +  + + ++ L +  
Sbjct: 51  HRLDRPTSGVLLLALSSEVARALSQQFESHQMQKMYHAVVRGYVLD--DGVIDYALTEEL 108

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQL 255
             I   + +     +K    A++H++ +               ++  +E++P TGR HQL
Sbjct: 109 DKIADKFAN----PDKAPQPAVTHYRSLAQAEMPVAIGRYPTARYSLMELKPQTGRKHQL 164

Query: 256 RVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           R H  H+  PI+GD  H    + +G  T     +L LHA  + L HP  G+       P 
Sbjct: 165 RRHMSHLHHPIIGDTAHGDLRHNRGMETHFSCGRLMLHASELQLNHPVSGQ-------PL 217

Query: 314 HMVKTWDS 321
            +   WDS
Sbjct: 218 TLQARWDS 225


>gi|329928505|ref|ZP_08282373.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
 gi|328937764|gb|EGG34172.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
          Length = 302

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 65/222 (29%), Positives = 107/222 (48%), Gaps = 19/222 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGI 157
           +LYED    V NKPAG++V          ++  + ++ +++G     R  HRLD++T+G 
Sbjct: 84  VLYEDDFCLVVNKPAGMAVHPDNESRETTLNHVVAAYYEAEGVHAAVRHIHRLDKDTTGP 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+   A   L E+ R ++I ++Y ++V G    + + I         IG D  H  +
Sbjct: 144 VLYAKNEYAQLKLDEAMREKKIVRMYAAIVQGRVSQELKRI------DLPIGKDRYHASR 197

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +        AI+H    + +  K   L ++  TGRTHQ+RVH  HMG P++GD  Y    
Sbjct: 198 RRVSLTGQAAITHILSAEAYP-KASLLHIRLETGRTHQIRVHLSHMGHPLLGDVLYGG-- 254

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            G F      +  LH   +   HP  G  + + AP P  M++
Sbjct: 255 PGTFA-----RQALHGERLLFHHPFTGESIDVPAPWPQDMME 291


>gi|268607871|ref|ZP_06141602.1| pseudouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 315

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 66/285 (23%), Positives = 127/285 (44%), Gaps = 41/285 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +++V+ +ND    R+D++     P +    + +++R   ++V+ KR + + ++ +  VV 
Sbjct: 2   IKFVINDNDS-GQRVDKFISKALPDLPKSMMYRLIRKKDIKVNGKRCEISTKLMTDDVVT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSIL----LYEDSKIYVFNKPAGISVQ 120
           +          +K++      ++ TK  D  FLK+      +YED  + + NKP G+   
Sbjct: 61  V---------YVKQE------LSGTKQHDMSFLKADTALDTVYEDENVIIVNKPLGLDSH 105

Query: 121 GGSGIAYHIDGFL----KSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAA 167
                  H D  L    K ++ +K +          P L  RLD+ TSG++   +  AA 
Sbjct: 106 SN---GEHNDDTLINRIKLYLYNKNEYQPDEESSFAPALCSRLDRNTSGLVTAVKNAAAL 162

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           + +  + R   + KIY  +    P    + I  +   K     + V +      G     
Sbjct: 163 REINSAIRDGMVHKIYLCITIAQPPKSADIITAY--HKKEDSRNIVRISDHPLDGYKPIK 220

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + ++V+    +    +++   TGRTHQ+R H  H+G P++GD KY
Sbjct: 221 TGYEVLKSH-KGLSLVKVTLFTGRTHQIRAHLSHVGAPLLGDGKY 264


>gi|309778338|ref|ZP_07673264.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Erysipelotrichaceae bacterium 3_1_53]
 gi|308913904|gb|EFP59718.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Erysipelotrichaceae bacterium 3_1_53]
          Length = 293

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 108/254 (42%), Gaps = 31/254 (12%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKS-----ILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
           NH + E+  +   ++L    D +K       +LYED    + NKPA + V      + H 
Sbjct: 53  NHTLHEKDTI--RISLQAEEDTVKPWYKHVEILYEDDLFCIVNKPANLLVHSDGVESEHT 110

Query: 129 IDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +K+   ++G     R  HRLD ETSG+L+  +       L E  + ++I + Y + 
Sbjct: 111 VCNMVKAHYLTEGSNACVRPLHRLDYETSGVLIFCKLPFFQPMLDEMLKSKQIYREYEAF 170

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK----FCW 242
             G    K   I   + +  H        V  N K A          D F ++    F W
Sbjct: 171 AVGRFTQKHYTITRGIARDRHDARRMR--VSDNGKEAR--------TDVFVKQSFSDFTW 220

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-E 301
           +  + HTGRTHQ+RVH + +  P++ D  Y          P   +L LHA  + +PHP  
Sbjct: 221 IRCRLHTGRTHQIRVHLVSLQHPLLSDSLYGKR------DPRCARLALHAARVHIPHPLS 274

Query: 302 GGRLQITAPLPAHM 315
              L I  PLP  M
Sbjct: 275 HTTLNIECPLPEDM 288


>gi|260580730|ref|ZP_05848556.1| tRNA pseudouridine synthase C [Haemophilus influenzae RdAW]
 gi|260092547|gb|EEW76484.1| tRNA pseudouridine synthase C [Haemophilus influenzae RdAW]
          Length = 239

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 61/238 (25%), Positives = 109/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDGFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHVFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|300774785|ref|ZP_07084648.1| tRNA pseudouridine synthase C [Chryseobacterium gleum ATCC 35910]
 gi|300506600|gb|EFK37735.1| tRNA pseudouridine synthase C [Chryseobacterium gleum ATCC 35910]
          Length = 231

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 105/237 (44%), Gaps = 28/237 (11%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LY D  +   NKP+G+    S   G    Y I    K      GQK    HRLD++TSG
Sbjct: 4   ILYRDEHLIAINKPSGLLVHKSFYAGEADTYAIQELKKQI----GQKVYPVHRLDRKTSG 59

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+    +   + ++E F  R ++K Y +++ G  K ++E I   L+ ++ +  + V   
Sbjct: 60  VLLFTLDKDTLRIMSEQFSSREVEKKYLAILRGWTK-EEETIDYDLINENEVRQNAV--- 115

Query: 217 KQNEKGANYAISHFKVIDC-----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                  NY       ID         ++  +E  P TGR HQLR H  H+  PI+G  K
Sbjct: 116 ------TNYRRLQTSEIDLPFLKHQTSRYSLVEAIPETGRFHQLRKHFKHILHPILGCRK 169

Query: 272 YCANFKGNF---TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
           +  N +      T  I NK+ LHA  +   HP    R+ + A +     +  D L F
Sbjct: 170 HGCNKQNKLWLQTFEI-NKMTLHAHQLIFNHPVSNERITVNATIDEEFKRVGDILKF 225


>gi|238792761|ref|ZP_04636392.1| tRNA pseudouridine synthase C [Yersinia intermedia ATCC 29909]
 gi|238727869|gb|EEQ19392.1| tRNA pseudouridine synthase C [Yersinia intermedia ATCC 29909]
          Length = 257

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 100/220 (45%), Gaps = 22/220 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +     + +
Sbjct: 64  ALSSDVARALSAQFEQHQIQKTYHAVVRGYVLEGGTVDYAMSEELDKIADKH----SKQD 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
           K    +++H++ +               +F  LE++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYQPLAQVEVPIAIGRYDTARFSLLELKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 270 -HKYCANFKG---NFTSPIQNKLYLHARYMDLPHPEGGRL 305
            H      +G   +F  P   +L LHA ++ L HP  G +
Sbjct: 180 AHGDLRQNRGIAQHFGCP---RLMLHASHLQLNHPVTGEV 216


>gi|289434238|ref|YP_003464110.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
 gi|289170482|emb|CBH27022.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
          Length = 296

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 73/312 (23%), Positives = 141/312 (45%), Gaps = 38/312 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  + L  + ++ +     +   K    G++ V+         +Q+G  VR+    
Sbjct: 7   VNKEDSGLLLRTFLRSKHISKQLLTAVKFSVDGKIEVNGTEQNVLYEVQTGDEVRLTFPT 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              N     +++L    +L          +++ED  + + NKPAG++        YH  G
Sbjct: 67  EQQN-----ERLLAEYTDLE---------IVFEDDFLLIINKPAGMASIPSQ---YHPSG 109

Query: 132 FLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + ++V    +   LT       RLD+ETSG++++A+ R A   L+   +   +++ Y +
Sbjct: 110 SVANFVKGHYEAQGLTSAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQQGLLKRSYQA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
            V G      E +      ++ IG   V ++++       YA ++++V+  + Q F  + 
Sbjct: 170 FVSG------ELVKQVGSIEAPIGRKAVSIMERVVTPEGKYAKTNYQVLARY-QAFDHVA 222

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP    
Sbjct: 223 LQLETGRTHQIRVHLSYIGHPLIGDDMYGGD------TDLLKRQALHSCHLHLIHPLTEE 276

Query: 305 -LQITAPLPAHM 315
            L    PLP  M
Sbjct: 277 YLAFDLPLPYDM 288


>gi|319746042|gb|EFV98321.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           agalactiae ATCC 13813]
          Length = 294

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 59/203 (29%), Positives = 90/203 (44%), Gaps = 23/203 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           LYED  + + NKP G+   G       +  H+  +        GQ   + HRLD ETSG 
Sbjct: 84  LYEDEHLIIVNKPEGMKTHGNQPNEIALLNHVSAY-------SGQTCYVVHRLDMETSGA 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       + +    + I + YW+LV G    K + + + + +  H     + +  
Sbjct: 137 VLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRDKIGRNRHDRRKRI-IDS 195

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +N + A   I   K I   +   C LE    TGRTHQ+R+H  H G P++GD  Y     
Sbjct: 196 KNGQHAMTIIDVLKYIQNSSLIKCRLE----TGRTHQIRIHLSHHGHPLIGDPLYNP--- 248

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               S    +L LHA  + L HP
Sbjct: 249 ----SSNNERLMLHAHRLTLSHP 267


>gi|172038568|ref|YP_001805069.1| pseudouridine synthase [Cyanothece sp. ATCC 51142]
 gi|171700022|gb|ACB53003.1| probable pseudouridine synthase [Cyanothece sp. ATCC 51142]
          Length = 304

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 110/243 (45%), Gaps = 23/243 (9%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSI-------LLYEDSKIYVFNKPAGISVQGGSGIAY 127
           N ++  + IL +   L+ H    K         L+YED  I V NKP+G+ V  G G   
Sbjct: 52  NQVVTPETILQTGQWLSYHRPPWKEADVPLDFDLIYEDHHILVINKPSGLPVLPGGGFLE 111

Query: 128 H-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           H + G LK     +   P   HRL + TSG++++ +T  A  HLT   R  +++K+Y +L
Sbjct: 112 HTLLGQLKKQYPKEKVFP--IHRLGRGTSGLMLMGKTAIARSHLTRQMREHKMRKVYRTL 169

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           +          I + + K S     Y++  K + K    A S  ++I+ ++ K   +E+ 
Sbjct: 170 IGENNLPDYFNIEHPIGKISDPVLGYIYGAKADGKD---AYSQCQIIERYSDK-TLVEVT 225

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANF---------KGNFTSPIQNKLYLHARYMDL 297
             TGR HQ+R+H   +G P++GD  Y             K     P     +LHA  +  
Sbjct: 226 ILTGRPHQIRIHLATIGYPLLGDPLYVVGGIPKTGFKEQKETVNVPGDCGYFLHAYQLSF 285

Query: 298 PHP 300
            HP
Sbjct: 286 VHP 288


>gi|169634097|ref|YP_001707833.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter baumannii
           SDF]
 gi|169796974|ref|YP_001714767.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter baumannii
           AYE]
 gi|213156621|ref|YP_002318282.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB0057]
 gi|215484435|ref|YP_002326668.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB307-0294]
 gi|239501205|ref|ZP_04660515.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB900]
 gi|260555735|ref|ZP_05827955.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 19606]
 gi|301346835|ref|ZP_07227576.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB056]
 gi|301594459|ref|ZP_07239467.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB059]
 gi|332855566|ref|ZP_08435940.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6013150]
 gi|169149901|emb|CAM87794.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter baumannii
           AYE]
 gi|169152889|emb|CAP01927.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter baumannii]
 gi|213055781|gb|ACJ40683.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB0057]
 gi|213987395|gb|ACJ57694.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB307-0294]
 gi|260410646|gb|EEX03944.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 19606]
 gi|332727390|gb|EGJ58823.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6013150]
          Length = 350

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 108/231 (46%), Gaps = 33/231 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP G+ V  G+G         + YH      S   ++  +  L HR+D
Sbjct: 117 IVYEDEDILVINKPVGMVVHPGAGNTSGTLVNALLYH------SPKSAELSRAGLVHRID 170

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA+   A   L++    + + +IY  + +G        IA   + +  I   
Sbjct: 171 KDTSGLLVVAKNLEAQFSLSKQLGDKSVYRIYDLVTYG------NIIAGGTIDEP-IKRH 223

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V  VK     G   A++H+ V + F + F  ++ Q  TGRTHQ+RVH  ++G  +VGD 
Sbjct: 224 PVDRVKMAILPGGRDAVTHYNVKERF-RDFTRVQAQLETGRTHQIRVHFSYIGHGLVGDQ 282

Query: 271 KYCANFK---GNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y    +   G     I+      +  LHA  + L HP  G  +   AP P
Sbjct: 283 VYMNRVRIPAGASELLIETLRGFKRQALHAAKLGLKHPRTGEEMLFEAPWP 333


>gi|153810915|ref|ZP_01963583.1| hypothetical protein RUMOBE_01301 [Ruminococcus obeum ATCC 29174]
 gi|149832803|gb|EDM87886.1| hypothetical protein RUMOBE_01301 [Ruminococcus obeum ATCC 29174]
          Length = 334

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 113/236 (47%), Gaps = 28/236 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT------HRLDQET 154
           +LYED  I   NKPAG+          H    L + V +  Q+  L+       RLD+ET
Sbjct: 88  ILYEDEDILAVNKPAGVLTHPA---GMHYSDSLANQVAAYFQERNLSVCIRPIGRLDKET 144

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC--IANWLLKKSHIGGD 211
           SGI++ A+ + AAQ L E      ++K Y +LV G +PK++ +     ++ +KK      
Sbjct: 145 SGIVLFAKNQVAAQRLQEQRETGVLEKQYLALVDGNLPKDQDDIWHTIDFPIKKIGNHPL 204

Query: 212 YVHVVKQNEKGANYA-ISH--FKVIDCF-----------AQKFCWLEMQPHTGRTHQLRV 257
            +  VK++    N   I+H     I+CF             K+  ++++  TGRTHQ+RV
Sbjct: 205 RMEAVKKSSSAENEKYIAHQLTDYINCFQAVTHYHVLYSTDKWSAIKLKLDTGRTHQIRV 264

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           H   +G P++GD  Y  +        I  +  LHA  + L  P  GR +++  P+P
Sbjct: 265 HMQAIGHPLLGDSIYNTSTMNREQCTIY-RAALHAWKVRLRQPFNGRKIELEVPVP 319


>gi|306812329|ref|ZP_07446527.1| tRNA pseudouridine synthase C [Escherichia coli NC101]
 gi|305854367|gb|EFM54805.1| tRNA pseudouridine synthase C [Escherichia coli NC101]
          Length = 260

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 71/261 (27%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFARKDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+     N  G     +Q +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKHGDLRQNRSGAEHFSLQ-RLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LAIHAGLDDTWMQALSQFGWR 237


>gi|302669413|ref|YP_003829373.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
 gi|302393886|gb|ADL32791.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
          Length = 257

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 58/235 (24%), Positives = 109/235 (46%), Gaps = 37/235 (15%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV------DSKGQKP---RLTHRLDQ 152
           +YED+ I V +KP+G++ +G       +    ++++       +  +KP      HRLDQ
Sbjct: 7   IYEDNDILVCHKPSGVATEGARTYNMDVVSAARNYIGRQNREKTSDRKPPYVATVHRLDQ 66

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK------- 205
              G+L++A+T+ AA  L    + R  +K Y++L  G   +KK  + N+L++K       
Sbjct: 67  PVEGVLILAKTKKAATKLAAQIKDRTTEKYYYALCKGNFADKKGRLENYLVRKEDGLAAV 126

Query: 206 --------------SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                         +   G+ + ++      A  AI  ++VI    ++   + ++  TGR
Sbjct: 127 VTEEESKKINDNVITRSNGETIRIIGGE---AKKAILEYEVI-AENEETTLVRVKLLTGR 182

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGGR 304
            HQ+RV   ++  PI+GD KY        T  I  ++   +  +Y+ + HP  G+
Sbjct: 183 FHQIRVQMANVDHPIIGDQKYGTEESRTLTDKIGARDVCLVSYKYI-IKHPSTGK 236


>gi|312886597|ref|ZP_07746205.1| pseudouridine synthase [Mucilaginibacter paludis DSM 18603]
 gi|311301000|gb|EFQ78061.1| pseudouridine synthase [Mucilaginibacter paludis DSM 18603]
          Length = 239

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 113/243 (46%), Gaps = 35/243 (14%)

Query: 97  LKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQET 154
            + ++L+E+  I V NKP  IS +    G   ++    K+ W D++     + HRLD+ET
Sbjct: 6   FQDLILFENPDIIVVNKPPFISSLDEREGGEINMLRLAKNYWADAQ-----ICHRLDKET 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L++A+   A + ++  F  RR++KIY +++ G    +   I   +L   + G   V 
Sbjct: 61  SGALIIAKNPEAYRFVSIQFEKRRVRKIYHAIIEGTHVFEDLQIDLPIL---NAGKGNVT 117

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +Q  K A    +HF+ +  F + +  ++ +P TGR HQ+R+H       I GD  Y  
Sbjct: 118 ISRQEGKRAE---THFQSLKYF-KHYTLVQCRPVTGRMHQIRIHLATQRASIAGDEMYKG 173

Query: 275 NFKGNFTS---------------PIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
             K  F S               PI  +  LHA  +     E   + I AP P    K +
Sbjct: 174 --KPVFLSAIKRGYRLGKEQEELPIMKRFALHAYEVTFKTDEDNEITIHAPYP----KDF 227

Query: 320 DSL 322
           D+L
Sbjct: 228 DTL 230


>gi|301511995|ref|ZP_07237232.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB058]
          Length = 350

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 108/231 (46%), Gaps = 33/231 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP G+ V  G+G         + YH      S   ++  +  L HR+D
Sbjct: 117 IVYEDEDILVINKPVGMVVHPGAGNTSGTLVNALLYH------SPKSAELSRAGLVHRID 170

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA+   A   L++    + + +IY  + +G        IA   + +  I   
Sbjct: 171 KDTSGLLVVAKNLEAQFSLSKQLGDKSVYRIYDLVTYG------NIIAGGTIDEP-IKRH 223

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V  VK     G   A++H+ V + F + F  ++ Q  TGRTHQ+RVH  ++G  +VGD 
Sbjct: 224 PVDRVKMAILPGGRDAVTHYNVKERF-RDFTRVQAQLETGRTHQIRVHFSYIGHGLVGDQ 282

Query: 271 KYCANFK---GNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y    +   G     I+      +  LHA  + L HP  G  +   AP P
Sbjct: 283 VYMNRVRIPAGASELLIETLRGFKRQALHAAKLGLKHPRTGEEMLFEAPWP 333


>gi|333001149|gb|EGK20719.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-272]
 gi|333015787|gb|EGK35124.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-227]
          Length = 260

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 114/248 (45%), Gaps = 37/248 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVLMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--- 217
             +  A + L + F   +IQK Y ++V G           WL++++ +  DY  V +   
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAVL--DYPLVEELDK 110

Query: 218 ------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALH 261
                 + +KG   A++H++ +               ++  +E++P TGR HQLR H  H
Sbjct: 111 IADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAH 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           +  PI+GD K+  + + N +        +L LHA  + L HP  G  L I A L    ++
Sbjct: 171 LRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQ 229

Query: 318 TWDSLGFK 325
                G++
Sbjct: 230 ALSQFGWR 237


>gi|219128013|ref|XP_002184218.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217404449|gb|EEC44396.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 325

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 62/214 (28%), Positives = 103/214 (48%), Gaps = 15/214 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +++ED  + V NK A + V   +G     +   +  +L +  +S   +P + HRLD+ T+
Sbjct: 75  IIFEDEHMIVINKAANMVVHPAAGNWDGTVVNALAYYLANRSESISFRPGIVHRLDKGTT 134

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LVVA+T      L+  F  R+++K Y ++  G P   K  + +  + +  +    + V
Sbjct: 135 GVLVVAKTSQTLATLSNFFAARQVKKTYMAITVGNP--GKHVVIDKPIGRHPLHRQRMRV 192

Query: 216 VK---QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V    Q       A+S+   +  F  K   ++++  TGRTHQ+RVH      PI GD  Y
Sbjct: 193 VPDPHQKNSTGRRALSYVDTL-AFDGKLSLVQVRIETGRTHQIRVHLQDRHTPIYGDDIY 251

Query: 273 CA---NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                N K + T  I   L LHA  +++ HP  G
Sbjct: 252 GLADWNKKLSKTHRIVRPL-LHAYKLEINHPVTG 284


>gi|82778170|ref|YP_404519.1| tRNA pseudouridine synthase C [Shigella dysenteriae Sd197]
 gi|309786089|ref|ZP_07680718.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
 gi|81242318|gb|ABB63028.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
 gi|308926200|gb|EFP71678.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
          Length = 260

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 116/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +             + ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPSTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLCHPIIGDSKH-GDLRQNRSGAEHFGLKRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|301308438|ref|ZP_07214392.1| RNA pseudouridylate synthase [Bacteroides sp. 20_3]
 gi|300833908|gb|EFK64524.1| RNA pseudouridylate synthase [Bacteroides sp. 20_3]
          Length = 304

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 109/227 (48%), Gaps = 26/227 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI----AYHIDGFLKSWVDSKGQKPR----LTHRLDQ 152
           +++ED  + V NK  G+       I    AY I   L  +V  K   PR    + HRLD+
Sbjct: 93  IVWEDDDLIVINKREGLLSVSTDRIKERTAYRI---LSDYV--KECDPRNKIFVLHRLDR 147

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSGI++ A+ +   + L  ++     Q+ Y +++ G P+   + I + L++  H+    
Sbjct: 148 DTSGIMMFAKNQKVKEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIVSNLVENKHM---Q 204

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+V +  +     AI+ ++++     ++  +E+   TGR +Q+R     +G PI GD KY
Sbjct: 205 VYVTQDGD--GKEAITRYRLLQT-NNRYSLVELDLETGRKNQIRAQMQSIGHPIAGDSKY 261

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
            A      T+P   +L LHAR +   HP  G  ++    +P     T
Sbjct: 262 GAE-----TNPA-GRLMLHARRLCFIHPVTGEEMRFETRIPEKFTST 302


>gi|222034482|emb|CAP77224.1| tRNA pseudouridine synthase C [Escherichia coli LF82]
 gi|312947318|gb|ADR28145.1| tRNA pseudouridine synthase C [Escherichia coli O83:H1 str. NRG
           857C]
          Length = 260

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMSVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LAIHAGLDDTWMQALSQFGWR 237


>gi|77409155|ref|ZP_00785868.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
 gi|77172239|gb|EAO75395.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
          Length = 342

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 59/203 (29%), Positives = 90/203 (44%), Gaps = 23/203 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           LYED  + + NKP G+   G       +  H+  +        GQ   + HRLD ETSG 
Sbjct: 132 LYEDEHLIIVNKPEGMKTHGNQPNEIALLNHVSAY-------SGQTCYVVHRLDMETSGA 184

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       + +    + I + YW+LV G    K + + + + +  H     + +  
Sbjct: 185 VLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRDKIGRNRHDRRKRI-IDS 243

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +N + A   I   K I   +   C LE    TGRTHQ+R+H  H G P++GD  Y     
Sbjct: 244 KNGQHAMTIIDVLKYIQNSSLIKCRLE----TGRTHQIRIHLSHHGHPLIGDPLYNP--- 296

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               S    +L LHA  + L HP
Sbjct: 297 ----SSNNERLMLHAHRLTLSHP 315


>gi|193216796|ref|YP_002000038.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           arthritidis 158L3-1]
 gi|193002119|gb|ACF07334.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           arthritidis 158L3-1]
          Length = 298

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 138/318 (43%), Gaps = 58/318 (18%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D++  N+   I   ++Q ++  G V V+  ++  N  I               N  I+
Sbjct: 11  RIDKYIANN-SEITRNDIQALIVQGAVFVNSTKINKNKYIVHE------------NDEIE 57

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHID 130
             K+LD   N+   +  L+  ++YE     V NKP+G+ V    G         + YH  
Sbjct: 58  IIKLLDKQQNIEAQNLPLE--IVYECDDYLVINKPSGLVVHPAPGHSSGTLVNSLMYH-- 113

Query: 131 GFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            F  +  D  G  +  + HR+D++TSG+L+VA+      +  +  +   I++ Y+++V G
Sbjct: 114 -FKNNLSDVNGLLRMGIVHRIDKDTSGLLLVAKNNETHNYFAKLLKNHEIKRTYYAIVDG 172

Query: 190 IPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
             +N+   + N  L    IG D        V +QN K A  A+   K ++   Q    ++
Sbjct: 173 HIENR---LINLDLP---IGRDPNNRQKFAVTEQNSKEAFTALEVIKYLNLAGQNKTLVK 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY------LHARYMDLP 298
               TGRTHQ+RVH  ++  P+ GD             P+ NK        LHA+ +D  
Sbjct: 227 CNLKTGRTHQIRVHLAYIKHPVYGD-------------PVYNKKVDDFNQRLHAKELDFV 273

Query: 299 HPEGGRLQITAPLPAHMV 316
              G  +   + LP  M+
Sbjct: 274 DKSGKIMHFESELPQIML 291


>gi|116492962|ref|YP_804697.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
 gi|116103112|gb|ABJ68255.1| Pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
          Length = 253

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 58/223 (26%), Positives = 108/223 (48%), Gaps = 14/223 (6%)

Query: 103 YEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGIL 158
           YED+   + NKP  + +VQ  +     +   +K++      + R+ H   RLDQ+TSG++
Sbjct: 32  YEDADYLIVNKPPFLPTVQSAANQKDTLVNRVKNYYVKNNYESRVVHVVTRLDQDTSGLV 91

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A+ R A   + +  R R+I K+Y ++V G   N+   I   + +       ++  +  
Sbjct: 92  IFAKHRFAHTVMDQDLRQRKINKMYLTIVEGTFTNQHGIIETPIQRDP---DSFIKRMVA 148

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  +++ + V D F + F  L+++ H+GRTHQ+RVH   +G P+VGD  Y     G
Sbjct: 149 PMGEGKPSLTEYWVEDTF-KNFTLLKVKLHSGRTHQIRVHFSSIGHPLVGDELY-----G 202

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWD 320
              + I  +  LH   +   +    ++  I   +P  M++ W+
Sbjct: 203 GMANDILQRQALHCFSLTFKNVFTEKMIDIKTSIPDDMLEYWN 245


>gi|309973117|gb|ADO96318.1| tRNA U65 pseudouridine synthase [Haemophilus influenzae R2846]
          Length = 239

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 110/238 (46%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDAFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K +      ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLTVVRGYLQGKAQIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|312277628|gb|ADQ62285.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 290

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 60/199 (30%), Positives = 88/199 (44%), Gaps = 16/199 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYEDS I V NKP G+   G       +   + ++    GQ   + HRLD ETSG ++ A
Sbjct: 84  LYEDSHIIVVNKPEGMKTHGNKPTEIALLNHVSAYC---GQTCYVVHRLDMETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      + IQ+ YW+L  G  + KK    + + +  H     V V  +  +
Sbjct: 141 KNPFILPILNRLLEDKMIQRQYWALTEGKFQTKKTVYKDKIGRDRHDRRKRV-VDPRKGQ 199

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            A   ++  K  +  +   C L+    TGRTHQ+RVH  H G  I+GD  Y         
Sbjct: 200 SAYTTVTRLKTFEGASLVNCQLK----TGRTHQIRVHLSHHGHAILGDPLYSHQ------ 249

Query: 282 SPIQNKLYLHARYMDLPHP 300
               ++L LHA  +   HP
Sbjct: 250 --PASRLMLHAHSLSFTHP 266


>gi|224013560|ref|XP_002296444.1| hypothetical protein THAPSDRAFT_263801 [Thalassiosira pseudonana
           CCMP1335]
 gi|220968796|gb|EED87140.1| hypothetical protein THAPSDRAFT_263801 [Thalassiosira pseudonana
           CCMP1335]
          Length = 341

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 61/204 (29%), Positives = 100/204 (49%), Gaps = 13/204 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + + NKP+G+ +    G          +  +   ++P+  HRLD+ TSG++VV
Sbjct: 82  VVYEDDHMAIVNKPSGVVLYRAEGGRGGGARDEDTPQNVPLKRPQPVHRLDRPTSGLVVV 141

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T+ AA HL++ F  R+ +K Y ++V GIP  ++  +    ++ + I  D        E
Sbjct: 142 AKTKLAAVHLSQQFEFRKAEKTYVAIVNGIP--RQSGVRAEPMQWNTIDYDL------EE 193

Query: 221 KGANY---AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCANF 276
           K A      +   K +         +EM+P TGR HQLR H A     P+VGD  Y    
Sbjct: 194 KTAVTRWRVLRKVKSLHGNDGTLTLVEMKPKTGRYHQLRRHCAWVCNSPLVGDTTYDGGS 253

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
           +G      +  L+L +  + L HP
Sbjct: 254 EGALRL-RKRGLFLCSSEIALEHP 276


>gi|27364845|ref|NP_760373.1| ribosomal large subunit pseudouridine synthase A [Vibrio vulnificus
           CMCP6]
 gi|34395775|sp|Q8DCG0|RLUA_VIBVU RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|27360990|gb|AAO09900.1| Ribosomal large subunit pseudouridine synthase A [Vibrio vulnificus
           CMCP6]
          Length = 250

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 95/214 (44%), Gaps = 30/214 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +++ED  I   NKP+G+ SV G   +  H D     W   + Q P +   HRLD  TSG+
Sbjct: 16  IIFEDDHILAVNKPSGLLSVPGR--LPEHHDSM---WSRLQEQYPEIQVVHRLDMSTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW----LLKKSHI 208
           +V A+ + A   L + F+ R   K+Y++ VWG  +          I +W    + K  H 
Sbjct: 71  MVFAKNKRAEAALKKQFQYRLTHKVYYARVWGHVEADSGMIDLPLICDWPNRPMQKVCHE 130

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            G       Q  K   +A      I         + + P TGR+HQLRVH   +G PIVG
Sbjct: 131 HGKPSQTAFQVAKREVHANGAQTTI---------MRLLPVTGRSHQLRVHMQALGHPIVG 181

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           D  Y       F+     +L LHA  +   HP+ 
Sbjct: 182 DEFYAQGDAFTFS----ERLELHAAELSFYHPKS 211


>gi|16130698|ref|NP_417271.1| tRNA U65 pseudouridine synthase [Escherichia coli str. K-12 substr.
           MG1655]
 gi|24114075|ref|NP_708585.1| tRNA pseudouridine synthase C [Shigella flexneri 2a str. 301]
 gi|30064136|ref|NP_838307.1| tRNA pseudouridine synthase C [Shigella flexneri 2a str. 2457T]
 gi|74313363|ref|YP_311782.1| tRNA pseudouridine synthase C [Shigella sonnei Ss046]
 gi|89109577|ref|AP_003357.1| tRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           W3110]
 gi|157162245|ref|YP_001459563.1| tRNA pseudouridine synthase C [Escherichia coli HS]
 gi|170018963|ref|YP_001723917.1| tRNA pseudouridine synthase C [Escherichia coli ATCC 8739]
 gi|170082362|ref|YP_001731682.1| tRNA U65 pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170682843|ref|YP_001744955.1| tRNA pseudouridine synthase C [Escherichia coli SMS-3-5]
 gi|187734142|ref|YP_001881468.1| tRNA pseudouridine synthase C [Shigella boydii CDC 3083-94]
 gi|188493340|ref|ZP_03000610.1| tRNA pseudouridine synthase C [Escherichia coli 53638]
 gi|194439667|ref|ZP_03071738.1| tRNA pseudouridine synthase C [Escherichia coli 101-1]
 gi|215488108|ref|YP_002330539.1| tRNA pseudouridine synthase C [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218690914|ref|YP_002399126.1| tRNA pseudouridine synthase C [Escherichia coli ED1a]
 gi|218706287|ref|YP_002413806.1| tRNA pseudouridine synthase C [Escherichia coli UMN026]
 gi|238901929|ref|YP_002927725.1| tRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|253772358|ref|YP_003035189.1| tRNA pseudouridine synthase C [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254037844|ref|ZP_04871902.1| tRNA pseudouridine synthase C [Escherichia sp. 1_1_43]
 gi|254162717|ref|YP_003045825.1| tRNA pseudouridine synthase C [Escherichia coli B str. REL606]
 gi|256024706|ref|ZP_05438571.1| tRNA pseudouridine synthase C [Escherichia sp. 4_1_40B]
 gi|291284120|ref|YP_003500938.1| tRNA pseudouridine synthase C [Escherichia coli O55:H7 str. CB9615]
 gi|293406283|ref|ZP_06650209.1| tRNA pseudouridine synthase C [Escherichia coli FVEC1412]
 gi|293416038|ref|ZP_06658678.1| tRNA pseudouridine synthase C [Escherichia coli B185]
 gi|297517184|ref|ZP_06935570.1| tRNA pseudouridine synthase C [Escherichia coli OP50]
 gi|298382019|ref|ZP_06991616.1| tRNA pseudouridine synthase C [Escherichia coli FVEC1302]
 gi|300898152|ref|ZP_07116515.1| tRNA pseudouridine synthase [Escherichia coli MS 198-1]
 gi|300920353|ref|ZP_07136791.1| tRNA pseudouridine synthase [Escherichia coli MS 115-1]
 gi|300931251|ref|ZP_07146591.1| tRNA pseudouridine synthase [Escherichia coli MS 187-1]
 gi|300936292|ref|ZP_07151224.1| tRNA pseudouridine synthase [Escherichia coli MS 21-1]
 gi|300950522|ref|ZP_07164431.1| tRNA pseudouridine synthase [Escherichia coli MS 116-1]
 gi|300958108|ref|ZP_07170267.1| tRNA pseudouridine synthase [Escherichia coli MS 175-1]
 gi|301026250|ref|ZP_07189710.1| tRNA pseudouridine synthase [Escherichia coli MS 196-1]
 gi|301027548|ref|ZP_07190883.1| tRNA pseudouridine synthase [Escherichia coli MS 69-1]
 gi|301645242|ref|ZP_07245195.1| tRNA pseudouridine synthase [Escherichia coli MS 146-1]
 gi|307139477|ref|ZP_07498833.1| tRNA pseudouridine synthase C [Escherichia coli H736]
 gi|312964939|ref|ZP_07779179.1| RNA pseudouridylate synthase family protein [Escherichia coli
           2362-75]
 gi|312972991|ref|ZP_07787164.1| RNA pseudouridylate synthase family protein [Escherichia coli
           1827-70]
 gi|331643478|ref|ZP_08344609.1| tRNA pseudouridine synthase C [Escherichia coli H736]
 gi|331654276|ref|ZP_08355276.1| tRNA pseudouridine synthase C [Escherichia coli M718]
 gi|331674285|ref|ZP_08375045.1| tRNA pseudouridine synthase C [Escherichia coli TA280]
 gi|92090982|sp|P0AA42|TRUC_SHIFL RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|108936020|sp|P0AA41|TRUC_ECOLI RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|882686|gb|AAB40441.1| corresponds to hypothetical protein from E. carotovora PIR
           Accession Number S45108; 2 ORFs in E. coli; ORF_f260
           [Escherichia coli str. K-12 substr. MG1655]
 gi|1789155|gb|AAC75833.1| tRNA U65 pseudouridine synthase [Escherichia coli str. K-12 substr.
           MG1655]
 gi|24053203|gb|AAN44292.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
 gi|30042392|gb|AAP18117.1| hypothetical protein S2998 [Shigella flexneri 2a str. 2457T]
 gi|73856840|gb|AAZ89547.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|85675610|dbj|BAE76863.1| tRNA pseudouridine synthase [Escherichia coli str. K12 substr.
           W3110]
 gi|157067925|gb|ABV07180.1| tRNA pseudouridine synthase C [Escherichia coli HS]
 gi|169753891|gb|ACA76590.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|169890197|gb|ACB03904.1| tRNA U65 pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170520561|gb|ACB18739.1| tRNA pseudouridine synthase C [Escherichia coli SMS-3-5]
 gi|187431134|gb|ACD10408.1| tRNA pseudouridine synthase C [Shigella boydii CDC 3083-94]
 gi|188488539|gb|EDU63642.1| tRNA pseudouridine synthase C [Escherichia coli 53638]
 gi|194421414|gb|EDX37430.1| tRNA pseudouridine synthase C [Escherichia coli 101-1]
 gi|209761378|gb|ACI79001.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|209761384|gb|ACI79004.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|215266180|emb|CAS10606.1| tRNA pseudouridine synthase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218428478|emb|CAR09404.2| tRNA pseudouridine synthase [Escherichia coli ED1a]
 gi|218433384|emb|CAR14286.1| tRNA pseudouridine synthase [Escherichia coli UMN026]
 gi|226839468|gb|EEH71489.1| tRNA pseudouridine synthase C [Escherichia sp. 1_1_43]
 gi|238863710|gb|ACR65708.1| tRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|242378338|emb|CAQ33115.1| tRNA pseudouridine 65 synthase [Escherichia coli BL21(DE3)]
 gi|253323402|gb|ACT28004.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253974618|gb|ACT40289.1| tRNA pseudouridine synthase [Escherichia coli B str. REL606]
 gi|253978783|gb|ACT44453.1| tRNA pseudouridine synthase [Escherichia coli BL21(DE3)]
 gi|260448158|gb|ACX38580.1| pseudouridine synthase [Escherichia coli DH1]
 gi|281602151|gb|ADA75135.1| tRNA pseudouridine synthase C [Shigella flexneri 2002017]
 gi|284922729|emb|CBG35817.1| tRNA pseudouridine synthase C [Escherichia coli 042]
 gi|290763993|gb|ADD57954.1| tRNA pseudouridine synthase C [Escherichia coli O55:H7 str. CB9615]
 gi|291426289|gb|EFE99321.1| tRNA pseudouridine synthase C [Escherichia coli FVEC1412]
 gi|291432227|gb|EFF05209.1| tRNA pseudouridine synthase C [Escherichia coli B185]
 gi|298277159|gb|EFI18675.1| tRNA pseudouridine synthase C [Escherichia coli FVEC1302]
 gi|299879762|gb|EFI87973.1| tRNA pseudouridine synthase [Escherichia coli MS 196-1]
 gi|300315205|gb|EFJ64989.1| tRNA pseudouridine synthase [Escherichia coli MS 175-1]
 gi|300358142|gb|EFJ74012.1| tRNA pseudouridine synthase [Escherichia coli MS 198-1]
 gi|300394909|gb|EFJ78447.1| tRNA pseudouridine synthase [Escherichia coli MS 69-1]
 gi|300412678|gb|EFJ95988.1| tRNA pseudouridine synthase [Escherichia coli MS 115-1]
 gi|300450155|gb|EFK13775.1| tRNA pseudouridine synthase [Escherichia coli MS 116-1]
 gi|300458544|gb|EFK22037.1| tRNA pseudouridine synthase [Escherichia coli MS 21-1]
 gi|300460905|gb|EFK24398.1| tRNA pseudouridine synthase [Escherichia coli MS 187-1]
 gi|301076512|gb|EFK91318.1| tRNA pseudouridine synthase [Escherichia coli MS 146-1]
 gi|309703149|emb|CBJ02483.1| tRNA pseudouridine synthase C [Escherichia coli ETEC H10407]
 gi|310332933|gb|EFQ00147.1| RNA pseudouridylate synthase family protein [Escherichia coli
           1827-70]
 gi|312290495|gb|EFR18375.1| RNA pseudouridylate synthase family protein [Escherichia coli
           2362-75]
 gi|313647852|gb|EFS12298.1| RNA pseudouridylate synthase family protein [Shigella flexneri 2a
           str. 2457T]
 gi|315137398|dbj|BAJ44557.1| tRNA pseudouridine synthase C [Escherichia coli DH1]
 gi|315615179|gb|EFU95816.1| RNA pseudouridylate synthase family protein [Escherichia coli 3431]
 gi|320173224|gb|EFW48434.1| tRNA pseudouridine synthase C [Shigella dysenteriae CDC 74-1112]
 gi|320640440|gb|EFX09979.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. G5101]
 gi|320645686|gb|EFX14671.1| tRNA pseudouridine synthase C [Escherichia coli O157:H- str.
           493-89]
 gi|320650986|gb|EFX19426.1| tRNA pseudouridine synthase C [Escherichia coli O157:H- str. H
           2687]
 gi|320656482|gb|EFX24378.1| tRNA pseudouridine synthase C [Escherichia coli O55:H7 str. 3256-97
           TW 07815]
 gi|320662378|gb|EFX29775.1| tRNA pseudouridine synthase C [Escherichia coli O55:H7 str. USDA
           5905]
 gi|320667076|gb|EFX34039.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323167869|gb|EFZ53560.1| RNA pseudouridylate synthase family protein [Shigella sonnei 53G]
 gi|323172906|gb|EFZ58537.1| RNA pseudouridylate synthase family protein [Escherichia coli
           LT-68]
 gi|323188791|gb|EFZ74076.1| RNA pseudouridylate synthase family protein [Escherichia coli
           RN587/1]
 gi|323935847|gb|EGB32150.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323941527|gb|EGB37709.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323960691|gb|EGB56315.1| RNA pseudouridylate synthase [Escherichia coli H489]
 gi|323971607|gb|EGB66838.1| RNA pseudouridylate synthase [Escherichia coli TA007]
 gi|324005662|gb|EGB74881.1| tRNA pseudouridine synthase [Escherichia coli MS 57-2]
 gi|331036949|gb|EGI09173.1| tRNA pseudouridine synthase C [Escherichia coli H736]
 gi|331047658|gb|EGI19735.1| tRNA pseudouridine synthase C [Escherichia coli M718]
 gi|331068379|gb|EGI39774.1| tRNA pseudouridine synthase C [Escherichia coli TA280]
 gi|332087547|gb|EGI92675.1| RNA pseudouridylate synthase family protein [Shigella boydii
           5216-82]
 gi|332344684|gb|AEE58018.1| conserved hypothetical protein [Escherichia coli UMNK88]
 gi|332753644|gb|EGJ84023.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-671]
 gi|332754556|gb|EGJ84922.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           2747-71]
 gi|332765743|gb|EGJ95956.1| tRNA pseudouridine 65 synthase [Shigella flexneri 2930-71]
 gi|333015363|gb|EGK34703.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-304]
          Length = 260

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|320194932|gb|EFW69561.1| tRNA pseudouridine synthase C [Escherichia coli WV_060327]
          Length = 260

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMLVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|299535937|ref|ZP_07049256.1| putative RNA pseudouridine synthase yjbO [Lysinibacillus fusiformis
           ZC1]
 gi|298728542|gb|EFI69098.1| putative RNA pseudouridine synthase yjbO [Lysinibacillus fusiformis
           ZC1]
          Length = 311

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 69/220 (31%), Positives = 106/220 (48%), Gaps = 30/220 (13%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +H D     ++YED  I V NKPA  S         + IA  + G+ +           +
Sbjct: 86  EHGDL---TIVYEDDAILVLNKPAHQSTIPSREHPTNSIANLVCGYFQKQ--GLASTAHI 140

Query: 147 THRLDQETSGILVVARTRAAAQHLTE-SFRMRRIQKIYWSLVWG-IPKNKKECIANWLLK 204
             RLD++TSG+L +A+  A   HLT  + R R I + Y ++V G I +N +  IA    K
Sbjct: 141 VTRLDRDTSGLLCIAK-HAHIHHLTGLAQRKREISRQYEAIVHGHIEQNFQSIIAPIGRK 199

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALH 261
           +  I      + ++  +   YA +  KV+  F   A+    + +Q HTGRTHQ+RVH  H
Sbjct: 200 EGSI------IEREVREDGQYAHTDVKVLKRFSLGAEPMTHVRLQLHTGRTHQIRVHMSH 253

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP 300
           +G P+VGD  Y         S +Q ++  LH   + + HP
Sbjct: 254 LGHPLVGDDLYGG-------SRLQIDRQALHCVSLSMEHP 286


>gi|255532415|ref|YP_003092787.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
 gi|255345399|gb|ACU04725.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
          Length = 240

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 110/245 (44%), Gaps = 31/245 (12%)

Query: 97  LKSILLYEDSKIYVFNKP---AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            K ++L+E+    V NKP   A +  +GGSG   +I    K +        ++ HRLD+E
Sbjct: 6   FKDLILFENDDYVVVNKPPFVASLDERGGSG-EVNILRLAKQYT----ADAQVCHRLDKE 60

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG +++A+T  A +++   F  R++ K Y ++V G    K+  I   +L     G   V
Sbjct: 61  TSGAIIIAKTPEAYRNVAMQFEKRKVNKTYHAVVDGQFTFKELFIDLPILND---GNKSV 117

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK-- 271
            + ++  K A    +  K      + +  +E +P TGR HQ+R+H       I GD    
Sbjct: 118 TIDRKEGKRAETIFNTLK----HYRHYTLVECKPITGRMHQIRIHLATQRAAIAGDDMYR 173

Query: 272 ----YCANFKGNF-------TSPIQNKLYLHARYMDLPHPEGGRLQITAPLP---AHMVK 317
               Y ++ K  +         PI  +  LHAR++      G  + I AP P   A ++K
Sbjct: 174 GKPVYLSSLKKGYRLAKDEEEQPIMKRFALHARHLVFKGLNGQDIVIEAPYPKDFATLIK 233

Query: 318 TWDSL 322
             D  
Sbjct: 234 LLDKF 238


>gi|192359752|ref|YP_001982432.1| RNA pseudouridine synthase family protein [Cellvibrio japonicus
           Ueda107]
 gi|190685917|gb|ACE83595.1| RNA pseudouridine synthase family protein [Cellvibrio japonicus
           Ueda107]
          Length = 254

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 110/242 (45%), Gaps = 27/242 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   NKP G+ V   S I  H   F    V D  G++    HRLD+ TSG L+
Sbjct: 7   ILYQDEHLLAVNKPTGLLVHR-SPIDRHETRFALQLVRDQIGRRVYPVHRLDKPTSGALL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A T   A+ L + F   +++K Y ++V G+ + +   I + L ++     D      + 
Sbjct: 66  FALTPDIARQLGQQFEQHQVRKTYVAVVRGLCEGEG-VIDHPLREEIDACADM-----RT 119

Query: 220 EKGANYAISHFKVIDCFAQKFC----------WLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +K +  AI+H+K +      +C           +   P TGR HQ+R H  H+  PI+GD
Sbjct: 120 DKSSQPAITHYKHLASVELPYCVDKYPSSRYSLVRCHPLTGRKHQIRRHLKHINHPIIGD 179

Query: 270 HKYCANFKGNFTSPIQNKLYLH-----ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            K+    KG      Q +L  H     A  +   HP+    +Q+TAPL     +     G
Sbjct: 180 AKHG---KGRHNRLFQQQLDCHRLLLAATELCFTHPQTQESIQLTAPLEQDFYQLLQRFG 236

Query: 324 FK 325
           ++
Sbjct: 237 WE 238


>gi|323447657|gb|EGB03570.1| hypothetical protein AURANDRAFT_15032 [Aureococcus anophagefferens]
          Length = 221

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 62/203 (30%), Positives = 94/203 (46%), Gaps = 17/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---GSGIAYHI--DGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++ E S+  V +KP+G+       G G+   +  D   +   D+   + RL HRLD  TS
Sbjct: 6   VVGETSRWVVVDKPSGVPCHASDKGDGVLTLLRRDAVERGERDAAVAEYRLVHRLDDGTS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L +A+ R  A  L  +FR RR +K Y  L    PK K+  +A  L+K +  G   +  
Sbjct: 66  GCLAIAKDRETATLLGAAFRERRARKAYVGLTDKTPKKKQGVVAGDLVK-ARRGAFKLAR 124

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFC---WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +     A  AI+    +   A        L  +P TG+THQ+RV A  +G P++GD  Y
Sbjct: 125 TRTVGACAVTAITRTAGLGAAAAGDAARKLLVARPVTGKTHQIRVAAKSLGAPLLGDDLY 184

Query: 273 CANFKGNFTSPIQNKLYLHARYM 295
                        ++LYLHA  +
Sbjct: 185 --------GGAAADRLYLHAAAL 199


>gi|315645744|ref|ZP_07898868.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
 gi|315279222|gb|EFU42532.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
          Length = 300

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 108/222 (48%), Gaps = 19/222 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGI 157
           +L+ED    V NKPAG++V          ++  + ++ +++G     R  HRLD++T+G 
Sbjct: 84  VLHEDEFCLVVNKPAGMAVHPDQESEETTLNHVVAAYYEAEGIHTAVRHIHRLDKDTTGP 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+   A   L E+ R ++I +IY ++V G    + + I         IG D  H  +
Sbjct: 144 VLYAKNEYAQLKLDEAMREKKIVRIYAAIVQGRVGQELKVI------DLPIGKDRYHSSR 197

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +        AI+H    + +  +   L +   TGRTHQ+RVH  HMG P++GD  Y    
Sbjct: 198 RRVSLTGQAAITHILSSEVYP-RASLLNISLETGRTHQIRVHLSHMGHPLLGDSLYGG-- 254

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
                  + ++  LH   +   HP  G R+++ AP P  M++
Sbjct: 255 -----PALFSRQALHGERLLFHHPLTGERVEVQAPWPQDMME 291


>gi|295114100|emb|CBL32737.1| pseudouridine synthase, RluA family [Enterococcus sp. 7L76]
          Length = 283

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 36  VKINGETATFHFPVQAGDCVTL---------TFEETDYVFPTIHL---GEATRVKVLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|110642932|ref|YP_670662.1| tRNA pseudouridine synthase C [Escherichia coli 536]
 gi|191171222|ref|ZP_03032772.1| tRNA pseudouridine synthase C [Escherichia coli F11]
 gi|227888331|ref|ZP_04006136.1| TruC protein [Escherichia coli 83972]
 gi|300976014|ref|ZP_07173255.1| tRNA pseudouridine synthase [Escherichia coli MS 45-1]
 gi|300976318|ref|ZP_07173382.1| tRNA pseudouridine synthase [Escherichia coli MS 200-1]
 gi|301049449|ref|ZP_07196408.1| tRNA pseudouridine synthase [Escherichia coli MS 185-1]
 gi|331648518|ref|ZP_08349606.1| tRNA pseudouridine synthase C [Escherichia coli M605]
 gi|331658904|ref|ZP_08359846.1| tRNA pseudouridine synthase C [Escherichia coli TA206]
 gi|110344524|gb|ABG70761.1| hypothetical protein YqcB (putative RNA pseudouridylate synthase)
           [Escherichia coli 536]
 gi|190908522|gb|EDV68111.1| tRNA pseudouridine synthase C [Escherichia coli F11]
 gi|227834600|gb|EEJ45066.1| TruC protein [Escherichia coli 83972]
 gi|281179792|dbj|BAI56122.1| putative pseudouridine synthase [Escherichia coli SE15]
 gi|300298765|gb|EFJ55150.1| tRNA pseudouridine synthase [Escherichia coli MS 185-1]
 gi|300308560|gb|EFJ63080.1| tRNA pseudouridine synthase [Escherichia coli MS 200-1]
 gi|300410152|gb|EFJ93690.1| tRNA pseudouridine synthase [Escherichia coli MS 45-1]
 gi|307554763|gb|ADN47538.1| tRNA pseudouridine synthase C [Escherichia coli ABU 83972]
 gi|315293748|gb|EFU53100.1| tRNA pseudouridine synthase [Escherichia coli MS 153-1]
 gi|315298808|gb|EFU58062.1| tRNA pseudouridine synthase [Escherichia coli MS 16-3]
 gi|324015525|gb|EGB84744.1| tRNA pseudouridine synthase [Escherichia coli MS 60-1]
 gi|331042265|gb|EGI14407.1| tRNA pseudouridine synthase C [Escherichia coli M605]
 gi|331053486|gb|EGI25515.1| tRNA pseudouridine synthase C [Escherichia coli TA206]
          Length = 260

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LAIHAGLDDTWMQALSQFGWR 237


>gi|322391241|ref|ZP_08064713.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           peroris ATCC 700780]
 gi|321145994|gb|EFX41383.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           peroris ATCC 700780]
          Length = 291

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 59/199 (29%), Positives = 93/199 (46%), Gaps = 14/199 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + V NKP G+   G       +   + ++V   GQ   + HRLD+ETSG+++ A
Sbjct: 84  IYQDQHLIVVNKPEGMKTHGNQPDEIALLNHVSAYV---GQTCYVIHRLDKETSGLVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      + I + YW+LV G  + K+    + L +  H     + V  +N +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWALVDGKIEAKELIFRDKLGRNRHDRRKRI-VDPKNGQ 199

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            A   ++  K    F  K   +  +  TGRTHQ+RVH  H G PI+GD  Y  + K    
Sbjct: 200 CAETQVTRLKQ---FQNKTSLVRCKLKTGRTHQIRVHLSHHGHPILGDPLYNPHSKT--- 253

Query: 282 SPIQNKLYLHARYMDLPHP 300
               ++L LHA  +   HP
Sbjct: 254 ----SRLMLHAFKLSFIHP 268


>gi|257877015|ref|ZP_05656668.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|257811181|gb|EEV40001.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
          Length = 284

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 61/209 (29%), Positives = 98/209 (46%), Gaps = 25/209 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK---SWVDSKGQKPRLTHRLDQET 154
           K  +L+ED  + V NKPAG+       +    D  L    +++  K Q+P + HRLD+ET
Sbjct: 80  KVDVLFEDEHLLVLNKPAGVKTHPNQPL--EADTLLNDAAAYLAPKQQQPYVVHRLDKET 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L      ++I + Y + VWG    + + IA  + +  H     + 
Sbjct: 138 SGVVLFAKNPLVLPILGRMLENKQIFRRYQATVWG-KLTQDQTIAKKIGRDRHDRRKRI- 195

Query: 215 VVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               + +    AI+H  +     +    +C L+    TGRTHQ+RVH   +G P+VGD  
Sbjct: 196 ---IDPRNGQSAITHVTIAHTQQKTTDVYCVLD----TGRTHQIRVHLASIGHPVVGDPL 248

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y      N  +P   +L LH   + L HP
Sbjct: 249 Y-----QNKPAP---RLLLHGYELHLEHP 269


>gi|167039932|ref|YP_001662917.1| RluA family pseudouridine synthase [Thermoanaerobacter sp. X514]
 gi|300915271|ref|ZP_07132585.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X561]
 gi|307724743|ref|YP_003904494.1| RluA family pseudouridine synthase [Thermoanaerobacter sp. X513]
 gi|166854172|gb|ABY92581.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X514]
 gi|300888547|gb|EFK83695.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X561]
 gi|307581804|gb|ADN55203.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X513]
          Length = 285

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 119/221 (53%), Gaps = 34/221 (15%)

Query: 103 YEDSKIYVFNKPAGISV------QGGS---GIAYHI-DGFLKSWVDSKGQKPRLTHRLDQ 152
           YED +I + NKPA + V      Q G+   G+A++  D  +K+ +       R  +RLD+
Sbjct: 78  YEDEEILIVNKPANMVVHPTKRYQSGTLANGVAWYFKDKGIKALI-------RPVNRLDK 130

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V A+ R   Q+  +   ++ + K+Y+++V G  K + E   +  + +    G  
Sbjct: 131 GTSGLVVFAK-RPFMQYYLQI--LKPMSKLYFAVVEG--KMEGEGRIDLPISRKPQSGIE 185

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V ++ ++    AI+++KV+   +++F  L+++  TGRTHQ+RVH  H+G PIVGD  Y
Sbjct: 186 RMVSEEGDR----AITNYKVVKS-SKRFSLLKVKIETGRTHQIRVHLSHIGHPIVGDTLY 240

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                G+    I+ +  LHA  +   HP E   + + +PLP
Sbjct: 241 -----GSSDDYIKRQA-LHAYRLTFVHPLEEKSISVYSPLP 275


>gi|220931673|ref|YP_002508581.1| pseudouridine synthase, RluA family [Halothermothrix orenii H 168]
 gi|219992983|gb|ACL69586.1| pseudouridine synthase, RluA family [Halothermothrix orenii H 168]
          Length = 310

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 120/248 (48%), Gaps = 40/248 (16%)

Query: 37  LQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           ++K+ R  ++R++ + VKF   ++ SG ++         N   KE+   D +        
Sbjct: 45  IRKMGREYRIRLNCRYVKFTEVKLNSGDLI-------EFNLNFKEKTYYDPAP------- 90

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRL 146
            L   ++YED  + V NKPA + V            +G+ YH    +++  +    +P  
Sbjct: 91  -LDLDIIYEDRHLLVINKPANMLVHPTPVEKSNTIVNGVLYH----MRNQGNYNLVRP-- 143

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ T+G+L++A+ + A  ++T  F+   I + Y + V G  + KKE I       +
Sbjct: 144 IHRLDRNTTGLLLIAKNQYAHNYITHQFQNNNIHREYLAFVHGNVEFKKESI------NA 197

Query: 207 HIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            IG     ++K+  +      A++H KV+         + ++  TGRTHQ+RVH  H+G 
Sbjct: 198 PIGKTRDSLIKRKVDHTLGKRAVTHIKVVKP-GGLISLIRVKLETGRTHQIRVHLSHLGH 256

Query: 265 PIVGDHKY 272
           P++GD  Y
Sbjct: 257 PLLGDTLY 264


>gi|111115650|ref|YP_710268.1| hypothetical protein BAPKO_0868 [Borrelia afzelii PKo]
 gi|110890924|gb|ABH02092.1| hypothetical protein BAPKO_0868 [Borrelia afzelii PKo]
          Length = 315

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 83/313 (26%), Positives = 140/313 (44%), Gaps = 60/313 (19%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-----LRSGQVRVDKKRVKF 55
           M L  YV   ++ ND    RLD         I  +NL K      +R G +R++  +  F
Sbjct: 1   MRLDKYVFLEILANDN-GKRLDSIL------IKILNLSKARIIKHIRKGDIRLNGIKSHF 53

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS------DF--LKSILLYEDSK 107
           + R+  G  + +              K L   +NLT +       DF  ++  ++YEDS 
Sbjct: 54  SYRVCKGDKIYL-------------YKSLAQGLNLTMNECYKSNIDFQCIRERIIYEDSD 100

Query: 108 IYVFNKPAGISVQGG-SGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
           + V +K  GI V GG + + + ++ +L K  + S   KP   HRLD+ TSGI+V A+   
Sbjct: 101 LLVLDKQRGILVHGGRNSLDFLVNAYLLKEELRSLSFKPAAVHRLDRNTSGIIVFAKNIN 160

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKN----KKECIANWLLKKSHI--GGDYVHVVKQN 219
            A+ L+ +     I K Y++++ G  K+    K     N  LKK+ +  G D+++ + + 
Sbjct: 161 TARKLSTALSSGSITKKYFAILLGEVKSTVVYKNHLFRNKRLKKTFVLDGKDFINAITK- 219

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N  +S        +++    E+   TG THQ+R        P++ D KY   F+  
Sbjct: 220 ---VNPILS--------SKRATLAEIVIETGFTHQIRAQCSFNNHPLINDKKYHDKFE-- 266

Query: 280 FTSPIQNKLYLHA 292
                ++  +LHA
Sbjct: 267 -----KSNYFLHA 274


>gi|91212158|ref|YP_542144.1| tRNA pseudouridine synthase C [Escherichia coli UTI89]
 gi|117625019|ref|YP_854007.1| tRNA pseudouridine synthase C [Escherichia coli APEC O1]
 gi|218559779|ref|YP_002392692.1| tRNA pseudouridine synthase C [Escherichia coli S88]
 gi|237706579|ref|ZP_04537060.1| tRNA pseudouridine synthase C [Escherichia sp. 3_2_53FAA]
 gi|331684413|ref|ZP_08385005.1| tRNA pseudouridine synthase C [Escherichia coli H299]
 gi|91073732|gb|ABE08613.1| hypothetical protein UTI89_C3161 [Escherichia coli UTI89]
 gi|115514143|gb|ABJ02218.1| tRNA pseudouridine synthase [Escherichia coli APEC O1]
 gi|218366548|emb|CAR04301.1| tRNA pseudouridine synthase [Escherichia coli S88]
 gi|226899619|gb|EEH85878.1| tRNA pseudouridine synthase C [Escherichia sp. 3_2_53FAA]
 gi|294489605|gb|ADE88361.1| tRNA pseudouridine synthase C [Escherichia coli IHE3034]
 gi|307625640|gb|ADN69944.1| tRNA pseudouridine synthase C [Escherichia coli UM146]
 gi|315289310|gb|EFU48705.1| tRNA pseudouridine synthase [Escherichia coli MS 110-3]
 gi|323950992|gb|EGB46868.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323957197|gb|EGB52921.1| RNA pseudouridylate synthase [Escherichia coli H263]
 gi|331078028|gb|EGI49234.1| tRNA pseudouridine synthase C [Escherichia coli H299]
          Length = 260

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDLIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|315638897|ref|ZP_07894069.1| RluA family pseudouridine synthase [Campylobacter upsaliensis JV21]
 gi|315481115|gb|EFU71747.1| RluA family pseudouridine synthase [Campylobacter upsaliensis JV21]
          Length = 325

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 109/228 (47%), Gaps = 31/228 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK---SWVDSKGQ-KPRLTHRLDQET 154
           +L+ED  + V NKP  + V G S +  A  ID  L    +  +  G+ +  L HRLD+ET
Sbjct: 78  VLFEDEDVLVLNKPQNLVVHGASSVKEATLIDWLLAKKYALSNLAGELRAGLVHRLDKET 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG----- 209
           SG +++A+   + Q L+E  + + + +IY +L+  +P  + + I N  L +S        
Sbjct: 138 SGAIIIAKNNFSHQRLSEQLQDKSLGRIYLALI-DLPLKEDKIIINKALTRSTQNRIKKI 196

Query: 210 ----GDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                +Y   +K  E K A   ++  K ++  A K         +GRTHQ+R H   +  
Sbjct: 197 AIERENYSPKIKAKEAKSAFINLALAKDVNLIAAKL-------FSGRTHQIRAHLASINR 249

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPL 311
            I+GD  Y   +KGN       ++ LHA ++   HP    L  + APL
Sbjct: 250 HILGDTLY--GYKGNEIC----RVMLHAYFVYFKHPRTKELVFVKAPL 291


>gi|256824745|ref|YP_003148705.1| 23S RNA-specific pseudouridylate synthase [Kytococcus sedentarius
           DSM 20547]
 gi|256688138|gb|ACV05940.1| 23S RNA-specific pseudouridylate synthase [Kytococcus sedentarius
           DSM 20547]
          Length = 316

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 54/158 (34%), Positives = 78/158 (49%), Gaps = 20/158 (12%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK---------ECI 198
           HRLD+ TSG+L+ ART  A + L + F  R++ K Y +LV   P+            E +
Sbjct: 132 HRLDRLTSGVLLCARTPEARRPLQQLFEKRQVAKTYEALVSLPPEEAAGAFSVSPGVEGL 191

Query: 199 ANWLLKKSHIGGDYVHVVKQNE-------KGANYAISHFKVIDC-FAQKFCWLEMQPHTG 250
                 +  IG    H+VK+          G   A++  +V++   A     L + PHTG
Sbjct: 192 GLAERVERAIGEQEHHLVKKRGSQQVVVVPGPPNALTRIEVVEVDEATGRARLRLFPHTG 251

Query: 251 RTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQ 285
           RTHQLRV   H+G PIVGD  Y        G+F++P+Q
Sbjct: 252 RTHQLRVQLAHLGLPIVGDPLYPVQTEQVTGDFSTPLQ 289


>gi|15803313|ref|NP_289346.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 EDL933]
 gi|15832905|ref|NP_311678.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. Sakai]
 gi|168751005|ref|ZP_02776027.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4113]
 gi|168758485|ref|ZP_02783492.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4401]
 gi|168764507|ref|ZP_02789514.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4501]
 gi|168766761|ref|ZP_02791768.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4486]
 gi|168777585|ref|ZP_02802592.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4196]
 gi|168778782|ref|ZP_02803789.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4076]
 gi|168788052|ref|ZP_02813059.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. EC869]
 gi|168802525|ref|ZP_02827532.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. EC508]
 gi|195936394|ref|ZP_03081776.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4024]
 gi|208807818|ref|ZP_03250155.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4206]
 gi|208813945|ref|ZP_03255274.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4045]
 gi|208821365|ref|ZP_03261685.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4042]
 gi|209397015|ref|YP_002272257.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4115]
 gi|217327006|ref|ZP_03443089.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           TW14588]
 gi|254794732|ref|YP_003079569.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           TW14359]
 gi|261226091|ref|ZP_05940372.1| tRNA U65 pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261256654|ref|ZP_05949187.1| tRNA U65 pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK966]
 gi|34582446|sp|Q8X6T6|TRUC_ECO57 RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|12517267|gb|AAG57905.1|AE005507_6 hypothetical protein Z4107 [Escherichia coli O157:H7 str. EDL933]
 gi|13363123|dbj|BAB37074.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|187767213|gb|EDU31057.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4196]
 gi|188014875|gb|EDU52997.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4113]
 gi|189003616|gb|EDU72602.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4076]
 gi|189354717|gb|EDU73136.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4401]
 gi|189363807|gb|EDU82226.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4486]
 gi|189365505|gb|EDU83921.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4501]
 gi|189372179|gb|EDU90595.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. EC869]
 gi|189375502|gb|EDU93918.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. EC508]
 gi|208727619|gb|EDZ77220.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735222|gb|EDZ83909.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4045]
 gi|208741488|gb|EDZ89170.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4042]
 gi|209158415|gb|ACI35848.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4115]
 gi|209761380|gb|ACI79002.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|209761382|gb|ACI79003.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|209761386|gb|ACI79005.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|217319373|gb|EEC27798.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           TW14588]
 gi|254594132|gb|ACT73493.1| tRNA U65 pseudouridine synthase [Escherichia coli O157:H7 str.
           TW14359]
 gi|320189127|gb|EFW63786.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC1212]
 gi|326339134|gb|EGD62949.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. 1044]
 gi|326342983|gb|EGD66751.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. 1125]
          Length = 260

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|238787243|ref|ZP_04631042.1| tRNA pseudouridine synthase C [Yersinia frederiksenii ATCC 33641]
 gi|238724505|gb|EEQ16146.1| tRNA pseudouridine synthase C [Yersinia frederiksenii ATCC 33641]
          Length = 257

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 103/234 (44%), Gaps = 19/234 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +     + +
Sbjct: 64  ALSSDVARALSLQFEQHQIQKTYHAVVRGYVLAGDTIDYEMTEELDKIADKF----SRPD 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
           K    +++H++ +               +F  LE+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYQPLAKVEVPVAIGRYDTARFSLLELLPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 270 -HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
            H      +G       ++L LHA ++ L HP  G   I   L A   ++W  L
Sbjct: 180 AHGDLRQNRGVAQHFGCSRLMLHASHLQLNHPVTGEPLI---LTARWDESWQQL 230


>gi|229546507|ref|ZP_04435232.1| pseudouridylate synthase RluD [Enterococcus faecalis TX1322]
 gi|257089108|ref|ZP_05583469.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|229308407|gb|EEN74394.1| pseudouridylate synthase RluD [Enterococcus faecalis TX1322]
 gi|256997920|gb|EEU84440.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|323479863|gb|ADX79302.1| pseudouridine synthase, RluA family protein [Enterococcus faecalis
           62]
          Length = 287

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 40  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVFPTIHL---GEATRVKVLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 144 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 258 -----ARLMLHASQLHLLHP 272


>gi|332999543|gb|EGK19128.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           VA-6]
          Length = 260

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTV 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|144575467|gb|AAZ53825.2| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 7448]
          Length = 304

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 73/271 (26%), Positives = 129/271 (47%), Gaps = 36/271 (13%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI--QSGQVVRIPPVIN 72
           D+E++R+D             NL +  +  Q  + +K+V  NN +  +  Q+V+    I 
Sbjct: 12  DQEDIRIDILVAK------LANLSR--KVAQDLILEKKVLINNNLVLKKNQIVKTGQKIK 63

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
             N   + +  L+ +       DF    ++++D  + + NKP  + V  G G      ++
Sbjct: 64  IFNDYKRPKPQLEPA-----EIDFE---IIFQDQNMILINKPKNLVVHPGVGNWKNTLVN 115

Query: 131 GFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           G + S  DS  Q    +P + HRLD++T+G+L+VA+   A          R+I++ Y ++
Sbjct: 116 GLI-SHFDSLEQLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFA---QKFC 241
           V G      + +  ++     IG D  + +K+     N   AI++ ++I  F    Q F 
Sbjct: 175 VIG------KVLHKFMKINLPIGRDLKNPLKKTISFFNSKPAITNVELIKHFNYQNQDFS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++ Q  TGRTHQ+R+H  H+G PI GD  Y
Sbjct: 229 LVKCQLETGRTHQIRLHLAHIGYPIYGDPIY 259


>gi|57505439|ref|ZP_00371367.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter upsaliensis RM3195]
 gi|57016264|gb|EAL53050.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter upsaliensis RM3195]
          Length = 325

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 106/225 (47%), Gaps = 25/225 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK---------GQKPRLTHRLD 151
           +L+ED  + V NKP  + V G S +    +  L  W+ +K           +  L HRLD
Sbjct: 78  VLFEDEDVLVLNKPQNLVVHGASSVK---EATLIDWLLAKKYALSNLAGDLRAGLVHRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS---HI 208
           +ETSG +++A+   + Q L+E  + + + +IY +L+  +P  + + I N  L +S    I
Sbjct: 135 KETSGAIIIAKNNFSHQRLSEQLQNKSLGRIYLALI-DLPLKEDKIIINKALTRSTQNRI 193

Query: 209 GGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               +     N K  A  A S F  +   A+    +  +  +GRTHQ+R H   +   I+
Sbjct: 194 KKIAIERENYNPKIKAKEAKSAFINL-ALAKDVNLIAAKLFSGRTHQIRAHLASINRHIL 252

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPL 311
           GD  Y   +KGN       ++ LHA ++   HP    L  + APL
Sbjct: 253 GDTLY--GYKGNEIC----RVMLHAYFVYFKHPRTKELVFVKAPL 291


>gi|307277035|ref|ZP_07558141.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|307289950|ref|ZP_07569879.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|306499016|gb|EFM68505.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|306506279|gb|EFM75443.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|315030583|gb|EFT42515.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4000]
 gi|315159704|gb|EFU03721.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0312]
 gi|315161994|gb|EFU06011.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0645]
 gi|315578744|gb|EFU90935.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0630]
          Length = 283

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVFPTIHL---GEATRVKVLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|227891522|ref|ZP_04009327.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
 gi|227866669|gb|EEJ74090.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
          Length = 315

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 71/248 (28%), Positives = 113/248 (45%), Gaps = 40/248 (16%)

Query: 101 LLYEDSKIYVFNKPAGIS------VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +++E+  + V NKP GI        + G+ + Y     +  ++D++ + P + HRLD  T
Sbjct: 92  IIFENDDLLVVNKPQGIKSHPNQPYETGTLMNY-----IAGYLDARDEHPYMVHRLDMLT 146

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG ++VA+       LT       I++ Y ++  GI  ++KE + +       IG D   
Sbjct: 147 SGAMIVAKNPVVVPILTRLISTHTIKRAYLAITEGI-FDQKEGVIDL-----PIGKD--- 197

Query: 215 VVKQNEK--------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              +N+K        GA  A +H++VI  F      + ++  TGRTHQLRVH   MG PI
Sbjct: 198 ---ENDKRKRKVDGIGALPARTHYQVIKEFGNN-SAVYLRLETGRTHQLRVHLSAMGHPI 253

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           VGD  Y      N  S  +  + LH     L  P   R L++ A +P +     + +   
Sbjct: 254 VGDVLY------NHVSK-EKHMMLHGYKQKLTLPFSMRELELKADIPEYFANYEEKIKEN 306

Query: 326 YDRNLYIK 333
              N Y K
Sbjct: 307 KKLNFYKK 314


>gi|254444612|ref|ZP_05058088.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198258920|gb|EDY83228.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 224

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 67/223 (30%), Positives = 100/223 (44%), Gaps = 30/223 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  I + NKP+G+    G   A ++D      V S      + HRLD  TSGI+V+
Sbjct: 20  ILYRDDAILLINKPSGLLSLSGKNPA-NLDSVHYRLVQSYSGA-LMIHRLDLGTSGIMVL 77

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A ++ A  +L   F+ R + K Y +L+            N  L ++ IG   + ++K  E
Sbjct: 78  ALSKTANANLCLQFKNRSVAKTYTALL------------NGRLAET-IGTIDIPIIKDKE 124

Query: 221 ---------KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                    K    A S ++V+D  A      +   P TGRTHQLR+H+   G  I+G  
Sbjct: 125 NFPYQKTCYKTGKPAQSEYQVLDYDAGNDVSRVLFTPLTGRTHQLRIHSQAFGHSILG-- 182

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
             C  +         N+L LHA  +   HP  G R++   P P
Sbjct: 183 --CDLYASKAIEEKANRLMLHATSLSFDHPTSGKRIEAECPCP 223


>gi|167524080|ref|XP_001746376.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163775138|gb|EDQ88763.1| predicted protein [Monosiga brevicollis MX1]
          Length = 289

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 72/267 (26%), Positives = 125/267 (46%), Gaps = 42/267 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++YED+ +   NK  G++VQ  +G    +  ++D F +   +  G  PRL HRLDQ T+G
Sbjct: 13  VIYEDNHLVALNKWRGLAVQDAAGSPSTVLSNVDVFQQ---NKDGFVPRLAHRLDQNTTG 69

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYV 213
           +LV+A+T  A   L   F++  + K Y +++ G    P    + I   + ++     +  
Sbjct: 70  VLVLAKTAEAVLRLNRLFQLGAVAKTYEAVLAGQVTKPTGTLKGIPELITEEEDANSELT 129

Query: 214 HVVKQNEKGANY----AISHFKVIDCF-------AQKFCWL---EMQPHTGRTHQLRVH- 258
                 +  A++    A SH+ V+          ++   WL   E++P TG  HQLR+  
Sbjct: 130 SNQPLFKTSASWSHSTAQSHYTVLASAQVNDGRPSRTKPWLTRVELRPTTGYKHQLRIQC 189

Query: 259 ALHMGCPIVGDHKYCANFK-------------GNFTS--PIQNKLYLHARYMDLP--HPE 301
           A  +  P++GD +Y    +             G  T+  P    ++LHA+ + +P  + +
Sbjct: 190 ADGLRAPVLGDKRYGGGQEQVSPIILQHLQRHGLRTAAHPYGLVMHLHAKQLVIPGYNWD 249

Query: 302 GGRLQITAPLPAHMVKTWDSLGFKYDR 328
           G  L + A LP HM  T D+ G   D+
Sbjct: 250 GSDLVLRATLPDHMQLTIDACGLHPDQ 276


>gi|27367689|ref|NP_763216.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           CMCP6]
 gi|27359261|gb|AAO08206.1|AE016812_188 Pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           CMCP6]
          Length = 565

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 70/205 (34%), Positives = 105/205 (51%), Gaps = 22/205 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V NKP+G+    G  I       L++ + D +G  P + HRLD  TSG+LV
Sbjct: 364 IVYQDEAMVVVNKPSGLLSVPGKTITDSAYTRLQALFPDVEG--PFVIHRLDMATSGLLV 421

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            A TR A + L + F  R +QK Y +L+ G +P+++ E      L       D    +  
Sbjct: 422 FALTRRANKSLQKQFISRGVQKRYVALLEGEVPQSQGEIT----LPMRGDPDDRPRQLVC 477

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHKYCAN 275
            E G   A + +++I+    +   L + P TGRTHQLRVH A H+G   P+VGD  Y   
Sbjct: 478 FEHG-KPAHTDWQLIETRDGR-SKLYLYPRTGRTHQLRVHCAHHLGLHMPMVGDGLYGEK 535

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                     N+L+LHA  ++L HP
Sbjct: 536 ---------ANRLHLHAESLELDHP 551


>gi|77406648|ref|ZP_00783692.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
 gi|77411850|ref|ZP_00788184.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77162127|gb|EAO73104.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77174748|gb|EAO77573.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
          Length = 325

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 55/203 (27%), Positives = 91/203 (44%), Gaps = 23/203 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           LYED  + + NKP G+   G       +  H+  +        GQ   + HRLD ETSG 
Sbjct: 115 LYEDEHLIIVNKPEGMKTHGNQPNEIALLNHVSAY-------SGQTCYVVHRLDMETSGA 167

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       + +    + I + YW+LV G    K + + + + +  H     +    
Sbjct: 168 VLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRDKIGRNRHDRRKRI---- 223

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + K   +A++   V+  + Q    ++ +  TGRTHQ+R+H  H G P++GD  Y     
Sbjct: 224 IDSKNGQHAMTIIDVLK-YTQNSSLIKCRLETGRTHQIRIHLSHHGHPLIGDPLYNP--- 279

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               S    +L LHA  + L HP
Sbjct: 280 ----SSNNERLMLHAHRLTLSHP 298


>gi|299822133|ref|ZP_07054019.1| ribosomal large subunit pseudouridine synthase D [Listeria grayi
           DSM 20601]
 gi|299815662|gb|EFI82900.1| ribosomal large subunit pseudouridine synthase D [Listeria grayi
           DSM 20601]
          Length = 294

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 63/211 (29%), Positives = 100/211 (47%), Gaps = 28/211 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF---LKSWVDSKGQK---PRLTHRLDQET 154
           ++YED  I V NKPA +        +  ID     +++++++ GQ        HRLD+ T
Sbjct: 80  IVYEDDFILVANKPANLKTHPND--SSEIDSCQQRVQAYLNATGQSGASASPVHRLDEAT 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSL---VWGIPKNKKECIANWLLKKSHIGGD 211
           SG+L+ A+   A    +     R I + Y ++   +W  P       AN+ ++K  I  D
Sbjct: 138 SGLLLFAKNAIALAAFSYQLEQRTIHRHYLAITDNIWKGP-------ANFTIRKP-ISSD 189

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             H  K+    G   A++H  ++    AQ    LE +  TGRTHQ+RVH    G PI+GD
Sbjct: 190 RHHPNKRRVSPGGQTAVTHVAILARHQAQNNTLLECRLDTGRTHQIRVHLSDAGFPIIGD 249

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             Y  + +         +L LHA+ ++  HP
Sbjct: 250 SLYGGSNRA-------ARLLLHAKQLETYHP 273


>gi|116749359|ref|YP_846046.1| pseudouridine synthase [Syntrophobacter fumaroxidans MPOB]
 gi|116698423|gb|ABK17611.1| pseudouridine synthase [Syntrophobacter fumaroxidans MPOB]
          Length = 304

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 55/186 (29%), Positives = 88/186 (47%), Gaps = 12/186 (6%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-----IDGFLKSWVDSKGQKPRL 146
           +H +   + +LY D+ +  ++K AG+  Q     AY+     +  FL     +      L
Sbjct: 80  RHYEIDPARILYRDAHLLAYDKEAGVPSQQTPADAYNNLYAALIRFLAGEARASAPYVAL 139

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ETSG++V A  RA  + L ESF+ +R+ K Y + V G+P   +      + +K 
Sbjct: 140 HHRLDRETSGVMVFALDRAVNRRLGESFQEKRVVKDYLAWVDGVPVLDRWTAVEDICRKD 199

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              G Y    +   +G   A      +   A     +  +P TGRTHQ+R+H    G P+
Sbjct: 200 ---GRY----RTCPQGRGKAARTLLRVLLRAGDRALIAARPVTGRTHQIRLHLAACGHPV 252

Query: 267 VGDHKY 272
           +GD  Y
Sbjct: 253 IGDRLY 258


>gi|315170755|gb|EFU14772.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1342]
          Length = 274

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 116/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 27  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 74

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q  + +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 75  EHLMIVNKPYGIKTHPNQPQETNTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 130

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 131 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 187

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 188 KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 244

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 245 -----ARLMLHASQLHLLHP 259


>gi|226357282|ref|YP_002787022.1| RNA pseudouridine synthase [Deinococcus deserti VCD115]
 gi|226319272|gb|ACO47268.1| putative RNA pseudouridine synthase [Deinococcus deserti VCD115]
          Length = 298

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 83/322 (25%), Positives = 139/322 (43%), Gaps = 41/322 (12%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           TYV  V V        L   +++  P +    L +    G+V+VD   V+ + R+++GQ 
Sbjct: 8   TYVTPVQVSGVSVLDFLSTRYRHSAPEVWAARLAQ----GEVQVDGLTVQGHERLRAGQT 63

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +           +       + SV L  H +     +L+ED+ +   +KP+G+    G G
Sbjct: 64  L-----------VWHRPPWQEESVPL--HFE-----VLHEDASLLAVHKPSGLPTLPGGG 105

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              H    L + V ++       HRL + TSG+++ ART AA   L  ++R + ++K+Y 
Sbjct: 106 FLEHT---LLTVVRAQFPGASPLHRLGRGTSGVVLFARTGAAGSALARAWREQDVRKMYR 162

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWL 243
           +L  G+    +  I   +    H     V       K +    S  +V++ C        
Sbjct: 163 ALASGVATQDETEITVSIGPVPHPRLGEVFAACPTGKPSR---SVARVVERCSGTTL--F 217

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL------YLHARYMDL 297
           ++Q  TGR HQ+R+H   +G P+VGD  Y     G    P    L       LHA  +  
Sbjct: 218 DVQIFTGRPHQIRIHLASIGQPLVGDPLYG---PGGHPLPDLPGLPGDLGYLLHAHTLSF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKT 318
            HP  G+ + +TAP P+ +  T
Sbjct: 275 THPVSGQVITVTAPAPSALEPT 296


>gi|168205929|ref|ZP_02631934.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
 gi|170662629|gb|EDT15312.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
          Length = 298

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 82/301 (27%), Positives = 136/301 (45%), Gaps = 52/301 (17%)

Query: 39  KILRSG----QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +++RS     +++VD   VK N  +++G+ ++I        +I  E+  ++         
Sbjct: 30  RLIRSAAIDKRIKVDGVAVKMNYVVKTGEEIKIELSKKESQNIEPEKMDIE--------- 80

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPR 145
                 ++YEDS I V NK   + V            +GI Y+   F +S  D      R
Sbjct: 81  ------IVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYY---FKESNQDCI---VR 128

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L  RLD  TSG++++ + + A   L+   +  + QK Y ++V G    K+  I   + + 
Sbjct: 129 LVSRLDMNTSGLIIIGKNQYAHMVLSNEMKTDKFQKRYLAIVHGNLAEKEGTINRPIYRP 188

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHM 262
           +    D +  V  +E+G   +I+H+KVI+ +       C LE    TGRTHQ+RVH   +
Sbjct: 189 AE---DTIKRV-VDERGQE-SITHYKVIESYNGADLVECLLE----TGRTHQIRVHLSSL 239

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           G PI GD  Y     G       ++  LHA  +D   P+    L + A LP  M +  + 
Sbjct: 240 GHPIFGDSLY-----GTEDEEFISRQALHAYGLDFYSPKTKEPLSLRADLPEDMKELINK 294

Query: 322 L 322
           L
Sbjct: 295 L 295


>gi|126640893|ref|YP_001083877.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 17978]
          Length = 293

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 69/225 (30%), Positives = 109/225 (48%), Gaps = 21/225 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGI 157
           ++YED  I V NKP G+ V  G+G   +  ++  L  S   ++  +  L HR+D++TSG+
Sbjct: 60  IVYEDEDILVINKPVGMVVHPGAGNTSSTLVNALLYHSPKSAELSRAGLVHRIDKDTSGL 119

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LVVA+   A   L++    + + +IY  + +G        IA   + +  I    V  VK
Sbjct: 120 LVVAKNLEAQFSLSKQLGDKSVYRIYDLVTYG------NIIAGGTIDEP-IKRHPVDRVK 172

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                G   A++H+ V + F + F  ++ Q  TGRTHQ+RVH  ++G  +VGD  Y    
Sbjct: 173 MAILPGGRDAVTHYNVKERF-RDFTRVQAQLETGRTHQIRVHFSYIGHGLVGDQVYMNRV 231

Query: 277 K---GNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITAPLP 312
           +   G     I+      +  LHA  + L HP  G  +   AP P
Sbjct: 232 RIPAGASELLIETLRGFKRQALHAAKLGLKHPRTGEEMLFEAPWP 276


>gi|29832675|ref|NP_827309.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           avermitilis MA-4680]
 gi|29609795|dbj|BAC73844.1| putative pseudouridylate synthase [Streptomyces avermitilis
           MA-4680]
          Length = 314

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 83/331 (25%), Positives = 141/331 (42%), Gaps = 32/331 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVLVDGTVVGKSERVH 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  + V  KP G++ 
Sbjct: 60  GGAWLEVEMPQAPAPVQIVAEP--------------VEGMEIVHDDDDVLVIVKPVGVAA 105

Query: 120 Q---GGSGIAYHIDGFLKSW--VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTE 172
               G SG    I G   +   + + G   R  + HRLD  TSG++VVA++  A   L  
Sbjct: 106 HPSPGWSGTTV-IGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKR 164

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F+ R + K Y +LV G P      I   + +  H   DY   V    K    +++H+ +
Sbjct: 165 QFKERTVDKRYHALVQGHPDPTSGTIDAPIGR--HPNHDYKWAVTAEGK---PSVTHYDL 219

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           I+ F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA
Sbjct: 220 IEAF-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTLGKRLGL-TRQWLHA 277

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +   HP  G  ++     PA + +  D +
Sbjct: 278 VRLGFEHPGDGEWVEFACDYPADLQQALDKV 308


>gi|237745359|ref|ZP_04575840.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           7_1]
 gi|229432588|gb|EEO42800.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           7_1]
          Length = 314

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 76/295 (25%), Positives = 137/295 (46%), Gaps = 46/295 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHI 77
           MRLD++            L+K++ +  V+++ K +  N R ++ G+ + +          
Sbjct: 19  MRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKLKLGEKIEVS--------- 69

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH 128
           I E++      N+    + +   ++YE++   V NK  G+ V    G         + Y+
Sbjct: 70  IPEEE------NIDIEPENIPLDIVYENNDFIVINKNYGMVVHPAYGNYTGTLVNALLYY 123

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +    S ++    +P + HRLD++TSG+++VA++  A   L   F  + I K Y  +V 
Sbjct: 124 TNNL--SSING-NIRPGIIHRLDKDTSGLILVAKSNYAHAKLASMFIDKTIHKTYLCIVK 180

Query: 189 G--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           G    +N    I N + + S      + VVK+N K    AIS++KV++   + +  +E+ 
Sbjct: 181 GNFSEENISGRIENLIGRDSK-DRKKMAVVKENGK---IAISNYKVVEQ-VEGYSLVEVA 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------FKGNFTSPIQNKLYL 290
             TGRTHQ+RVH   +   I+GD  Y              +K  F +P+ NK Y+
Sbjct: 236 IETGRTHQIRVHMKSINHVILGDSVYGNEDKNVKRQMLHAYKLEFLNPLDNKEYV 290


>gi|312904302|ref|ZP_07763464.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
 gi|310632398|gb|EFQ15681.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
          Length = 283

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVFPTIHL---GEATRVKVLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQSQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|238854112|ref|ZP_04644459.1| pseudouridine synthase, RluA family [Lactobacillus gasseri 202-4]
 gi|311110296|ref|ZP_07711693.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus gasseri MV-22]
 gi|238833188|gb|EEQ25478.1| pseudouridine synthase, RluA family [Lactobacillus gasseri 202-4]
 gi|311065450|gb|EFQ45790.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus gasseri MV-22]
          Length = 282

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 105/234 (44%), Gaps = 23/234 (9%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           Q+ ++   +  N  +++G  + I      L+H+  +Q+   +S  L K        ++YE
Sbjct: 41  QILINDHYLPLNFLVKAGDKIDI-----YLDHVESDQQTYPASGKLPK--------VVYE 87

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           DS I V +KP G   Q         D  L       G  P + HRLD  T+G+L+VA+  
Sbjct: 88  DSDILVIDKPTG---QKTHPNLDEKDTALNDCATYLGYSPFIVHRLDMLTNGLLLVAKNP 144

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           A    L      + + + Y  L W    N+ +      L   H   D     +       
Sbjct: 145 AVVPILNRQLTNKTLHREY--LAWVSKSNQLKQSGTISLSIGHDPDD--QRKRMVRLDGQ 200

Query: 225 YAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            AI+H++VI +C  ++   L ++  TGRTHQ+RVH   +G PI+GD  Y  N++
Sbjct: 201 KAITHYEVIKECENKELVKLTLE--TGRTHQIRVHLAALGAPIIGDPLYNPNYQ 252


>gi|170079422|ref|YP_001736060.1| ribosomal large chain pseudouridine synthase A [Synechococcus sp.
           PCC 7002]
 gi|169887091|gb|ACB00805.1| ribosomal large chain pseudouridine synthase A [Synechococcus sp.
           PCC 7002]
          Length = 538

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 69/205 (33%), Positives = 99/205 (48%), Gaps = 24/205 (11%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  +   +KPAG+ S+ G S   Y    F +   D   Q   L HRLDQ+TSGIL+
Sbjct: 341 IIYEDHSLIAIHKPAGLPSIPGRSSQTYD-SAFSRLRRDY--QDIFLVHRLDQDTSGILL 397

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+     Q L   FR R+I K Y +L+    +  +  I   L       GD        
Sbjct: 398 FAKNAETQQDLQTQFRRRKIHKEYEALLEEKIQRPEGMITLPLWADP---GDRPRQKVDA 454

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANF 276
           ++G   + ++F  +D        L+++P TGRTHQLRVH  H   +  PI+GD  Y    
Sbjct: 455 QRG-KPSETYFVKLDSHR-----LKLKPITGRTHQLRVHCAHPNGLNNPILGDRLY---- 504

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPE 301
            GN  +P   +L+L A  +   HPE
Sbjct: 505 -GNRAAP---RLHLQATALTFMHPE 525


>gi|257086040|ref|ZP_05580401.1| pseudouridine synthase [Enterococcus faecalis D6]
 gi|256994070|gb|EEU81372.1| pseudouridine synthase [Enterococcus faecalis D6]
          Length = 287

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 40  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 144 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 258 -----ARLMLHASQLHLLHP 272


>gi|329667795|gb|AEB93743.1| hypothetical protein LJP_1421 [Lactobacillus johnsonii DPC 6026]
          Length = 282

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 112/239 (46%), Gaps = 24/239 (10%)

Query: 41  LRS-GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           LRS  ++ ++ K +  N  ++ G  + I      L+HI  +Q+   +S  L K       
Sbjct: 36  LRSEKKILINGKYLPLNFLVKHGDKIEI-----QLDHIESDQQPYPASGKLPK------- 83

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++YED+ I V NKPAG   Q         D  L       G  P + HRLD  TSG+L+
Sbjct: 84  -VVYEDNDILVINKPAG---QKTHPNLNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLL 139

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQ 218
           VA+  A    L      + + + Y + +   P+ K   I +  L   H   D    +V+Q
Sbjct: 140 VAKNPAVVPILNRQLTDKTLHREYLAWISNSPQIKNTGIID--LPIGHDPHDQRKRMVRQ 197

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +      A++H++VI     +   +++   TGRTHQ+RVH   +G PI+GD  Y + ++
Sbjct: 198 D---GQKAVTHYEVIKRDKDRIL-VKLTLETGRTHQIRVHLAALGAPIIGDPLYNSAYQ 252


>gi|257896942|ref|ZP_05676595.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium Com12]
 gi|293379115|ref|ZP_06625266.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
 gi|257833507|gb|EEV59928.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium Com12]
 gi|292642256|gb|EFF60415.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
          Length = 299

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 82/308 (26%), Positives = 135/308 (43%), Gaps = 40/308 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + K+H   + +   +K +  G +     ++KF    Q GQ+     V N L  + K+ K+
Sbjct: 7   YEKDHSQQVKYFLKEKGISKGLL----AKIKF----QGGQIKVNDQVENVLFSLAKDDKV 58

Query: 84  LDSSVNLTKHSDFLKS----ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KS 135
                   +H   L       ++YED  + V NKPAG+S        YH +G +    K+
Sbjct: 59  TIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQ---YHPNGTMANRVKA 115

Query: 136 WVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   +G + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G+  
Sbjct: 116 YYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDTQLREKKFVKKYQALVSGMLS 175

Query: 193 NKKECIANWLLKKSHI----GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           N        L    HI      DY  ++K+       +      I+    +   +++Q H
Sbjct: 176 N--------LSAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYRIEKRLTEIALVDIQLH 227

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH   +GC ++GD  Y     G     I+ +  LH   +   HP     L+ 
Sbjct: 228 TGRTHQIRVHFSAIGCALLGDDMYS----GRMDLGIKRQA-LHCYDLRFYHPFTEELLEF 282

Query: 308 TAPLPAHM 315
             PL A M
Sbjct: 283 KQPLAADM 290


>gi|110806543|ref|YP_690063.1| tRNA pseudouridine synthase C [Shigella flexneri 5 str. 8401]
 gi|110616091|gb|ABF04758.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
          Length = 260

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFARKDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|116630078|ref|YP_815250.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           ATCC 33323]
 gi|116095660|gb|ABJ60812.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           ATCC 33323]
          Length = 285

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 105/234 (44%), Gaps = 23/234 (9%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           Q+ ++   +  N  +++G  + I      L+H+  +Q+   +S  L K        ++YE
Sbjct: 44  QILINDHYLPLNFLVKAGDKIDI-----YLDHVESDQQTYPASGKLPK--------VVYE 90

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           DS I V +KP G   Q         D  L       G  P + HRLD  T+G+L+VA+  
Sbjct: 91  DSDILVIDKPTG---QKTHPNLDEKDTALNDCATYLGYSPFIVHRLDMLTNGLLLVAKNP 147

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           A    L      + + + Y  L W    N+ +      L   H   D     +       
Sbjct: 148 AVVPILNRQLTNKTLHREY--LAWVSKSNQLKQSGTISLSIGHDPDD--QRKRMVRLDGQ 203

Query: 225 YAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            AI+H++VI +C  ++   L ++  TGRTHQ+RVH   +G PI+GD  Y  N++
Sbjct: 204 KAITHYEVIKECENKELVKLTLE--TGRTHQIRVHLAALGAPIIGDPLYNPNYQ 255


>gi|260437803|ref|ZP_05791619.1| ribosomal large subunit pseudouridine synthase family protein
           [Butyrivibrio crossotus DSM 2876]
 gi|292809827|gb|EFF69032.1| ribosomal large subunit pseudouridine synthase family protein
           [Butyrivibrio crossotus DSM 2876]
          Length = 222

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 55/187 (29%), Positives = 95/187 (50%), Gaps = 12/187 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETS 155
           K I++YED  I V NKP G+  Q        +  ++ +    + +     + +RLD+   
Sbjct: 3   KDIIVYEDDNIIVCNKPVGMPSQSDRTFEQDLVSYVLTHRTEQNEPAYAAIINRLDKPVG 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + AA  L+       I+K Y++LV G P +K E   ++LLK      +   V
Sbjct: 63  GLVLFAKNKKAAAGLSAVSGEHGIEKNYYALVKGSPCDKGE-FTDYLLKDGK--NNISTV 119

Query: 216 VKQNEKGANYAISHF-----KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             ++ KG+  A+  +     K ID   +K+  + ++  TGR HQ+RV   H G P+ GD 
Sbjct: 120 TDKDTKGSKKAVLLYEKLGEKTID--GEKYSLMRVRLLTGRHHQIRVQFSHHGYPLYGDI 177

Query: 271 KYCANFK 277
           KY ++F+
Sbjct: 178 KYNSDFR 184


>gi|327534269|gb|AEA93103.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis OG1RF]
          Length = 283

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 116/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q  + +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETNTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|315025718|gb|EFT37650.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2137]
          Length = 283

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|256854461|ref|ZP_05559825.1| pseudouridine synthase [Enterococcus faecalis T8]
 gi|256710021|gb|EEU25065.1| pseudouridine synthase [Enterococcus faecalis T8]
          Length = 288

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 41  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVFPTIHL---GEATRVKVLYED 88

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 89  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 144

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 145 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 201

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 202 KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 258

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 259 -----ARLMLHASQLHLLHP 273


>gi|163848084|ref|YP_001636128.1| pseudouridine synthase [Chloroflexus aurantiacus J-10-fl]
 gi|222525978|ref|YP_002570449.1| pseudouridine synthase [Chloroflexus sp. Y-400-fl]
 gi|163669373|gb|ABY35739.1| pseudouridine synthase [Chloroflexus aurantiacus J-10-fl]
 gi|222449857|gb|ACM54123.1| pseudouridine synthase [Chloroflexus sp. Y-400-fl]
          Length = 306

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 105/237 (44%), Gaps = 24/237 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++YED+ + V NKP    V        G    +   L +  D       L H+LD  TSG
Sbjct: 77  IIYEDNDVLVVNKPPACYVGDTPWDTQGSVLAVVQRLLTVRDGVPPVLHLAHQLDFGTSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-----D 211
           ILV+++T  A   L  +F      K Y ++  G P    + +          GG     D
Sbjct: 137 ILVLSKTPRANAPLQTAFARGLAMKQYLAVCSGHPPVTADLVTG---HGRAAGGRWRLYD 193

Query: 212 YVHVVKQNEKGANYAISH--FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
              + +    G    ++H  F +   FA     +E  P TGRTHQ+R+H   +GCPI+GD
Sbjct: 194 QADIGRVLPDGQRVRLAHTRFTLRRQFANA-ALVEAMPLTGRTHQIRLHLAALGCPILGD 252

Query: 270 HKY--CANFKG-NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +Y    +  G + T P+     LHA  + LPHP  GR L +  P P+ ++   D L
Sbjct: 253 ERYGGVVDVAGLHLTHPL-----LHAAELQLPHPIHGRSLHLFCPPPSLILTVIDRL 304


>gi|330839025|ref|YP_004413605.1| pseudouridine synthase, RluA family [Selenomonas sputigena ATCC
           35185]
 gi|329746789|gb|AEC00146.1| pseudouridine synthase, RluA family [Selenomonas sputigena ATCC
           35185]
          Length = 301

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 118/247 (47%), Gaps = 34/247 (13%)

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLK 134
           H+ +E +I    + L          +LYED+ + + NKPAG+ V    G   H +   + 
Sbjct: 64  HLAEESRIAPEDIPLE---------ILYEDAALLIVNKPAGMLVHPTGGEYRHTLANAVL 114

Query: 135 SWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP 191
              ++ G+K      HRLD++TSG++++A+  A  QHL  +     I++IY +++ G +P
Sbjct: 115 FHYEAHGEKHAFHPVHRLDRQTSGLVLIAK-EAHVQHLLSAHNA--IERIYLAVIEGKLP 171

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHT 249
           +      A    +   I      + +        A++H+  +   A++     L ++  T
Sbjct: 172 EPCGTIDAPIARRPGSI------IERMVSPAGKCAVTHYATL---AERGGLSLLALRLAT 222

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  H+  P++GD  Y     G  T  I  +  LHA  +   HP  G+ + + 
Sbjct: 223 GRTHQIRVHLAHLAHPLLGDDLY-----GGRTDRIARQ-ALHAHRLRFRHPISGKEITVH 276

Query: 309 APLPAHM 315
           AP PA M
Sbjct: 277 APFPADM 283


>gi|13357873|ref|NP_078147.1| pseudouridine synthase (uracil hydrolase) [Ureaplasma parvum
           serovar 3 str. ATCC 700970]
 gi|11279832|pir||H82907 pseudouridine synthase (uracil hydrolase) UU313 [imported] -
           Ureaplasma urealyticum
 gi|6899289|gb|AAF30722.1|AE002128_10 pseudouridine synthase (uracil hydrolase) [Ureaplasma parvum
           serovar 3 str. ATCC 700970]
          Length = 299

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 57/209 (27%), Positives = 100/209 (47%), Gaps = 18/209 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS--KGQKPRLTHRLDQETSGIL 158
           +++ED  + + NKP+G+ V   S   +H    L + +    K     +THRLD+ TSG++
Sbjct: 81  IIFEDQDLLIVNKPSGMLVHPTS---FHEQNTLANALKYYLKTDNFYITHRLDKNTSGLI 137

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ + + A   L + F  + I+K Y+++V     N+ +      +    IG  Y   ++ 
Sbjct: 138 IICKNQIALNSLQQQFMQKTIRKSYYAIVH----NRFDMQHLHFMINEPIGHSYQDKLRM 193

Query: 219 ---NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              N K    AIS  KV++ +      +E+   TGRTHQ+RVH  ++  P+  D  Y   
Sbjct: 194 KTGNSKNTKEAISIVKVLEQYKNT-ALVEVSIITGRTHQIRVHMRYINHPVYNDPLY--- 249

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             G      + + YLH+ Y+   HP   +
Sbjct: 250 --GISKHTTEYEQYLHSFYISFNHPSTNK 276


>gi|312900272|ref|ZP_07759584.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
 gi|311292633|gb|EFQ71189.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
          Length = 283

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVCPTIHL---GEATRVKVLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|115379301|ref|ZP_01466412.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|310821464|ref|YP_003953822.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115363683|gb|EAU62807.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|309394536|gb|ADO71995.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 232

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 113/236 (47%), Gaps = 28/236 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQETSGILV 159
           +L+E + + V  KP G  V  G G     D  L+  ++++  +K  + HRLD++TSG LV
Sbjct: 6   VLHEGAGLLVVAKPPGTLVIPGRGEG---DTSLREQLEAQLRRKVFVVHRLDRDTSGALV 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVV 216
            A      + L+ +F   R+ K Y +LV G    P+  +E +     +K  +        
Sbjct: 63  FALDAERHRALSMAFEEGRVHKRYLALVEGRVEAPRLVEEALVPA--RKGRM-----RPA 115

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--- 273
           +  E+G   + +  + ++ FAQ    +E +P TGRTHQ+RVH   +G P++ DH+Y    
Sbjct: 116 RPGEEG-KPSRTRIRPVETFAQA-SLVEAEPLTGRTHQIRVHLRSLGHPLLVDHQYGRAE 173

Query: 274 ----ANFKGNFTSPIQNKLYLHARYMD---LPHPEGGRLQITAPLPAHMVKTWDSL 322
                   G   + + ++  LHA  ++   LP  E G   + APLP  M    + L
Sbjct: 174 PLVRRELGGEGEAVVLSRTPLHAARIEWPPLPGVEAG--AVEAPLPGDMALALELL 227


>gi|253687331|ref|YP_003016521.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251753909|gb|ACT11985.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 266

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 64/248 (25%), Positives = 112/248 (45%), Gaps = 53/248 (21%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKP+G  V              +SW+D K             GQ     
Sbjct: 9   IIYQDEHLVAVNKPSGWLVH-------------RSWLDRKEKVVVMQTVRDQIGQHVYTV 55

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++A +   A+ L++ F   ++QK+Y ++V G   +  + + ++ L +  
Sbjct: 56  HRLDRPTSGVLLLALSSEVARALSQQFESHQMQKMYHAVVRGYVLD--DGVIDYALTEEL 113

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQL 255
             I   + +     +K    A++H++ +               ++  +E++P TGR HQL
Sbjct: 114 DKIADKFTN----PDKAPQPAVTHYRSLAQVEMPVAIGRYPTARYSLMELKPQTGRKHQL 169

Query: 256 RVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           R H  H+  PI+GD  H    + +G  T     +L LHA  + L HP  G+       P 
Sbjct: 170 RRHMSHLRHPIIGDTAHGDLRHNRGMETHFSCGRLMLHASELQLNHPVSGQ-------PL 222

Query: 314 HMVKTWDS 321
            +   WD+
Sbjct: 223 TLQARWDA 230


>gi|183602394|ref|ZP_02963760.1| hypothetical protein BIFLAC_05095 [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219683291|ref|YP_002469674.1| pseudouridine synthase RluD [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|241191252|ref|YP_002968646.1| hypothetical protein Balac_1228 [Bifidobacterium animalis subsp.
           lactis Bl-04]
 gi|241196658|ref|YP_002970213.1| hypothetical protein Balat_1228 [Bifidobacterium animalis subsp.
           lactis DSM 10140]
 gi|183218313|gb|EDT88958.1| hypothetical protein BIFLAC_05095 [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219620941|gb|ACL29098.1| pseudouridine synthase RluD [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|240249644|gb|ACS46584.1| hypothetical protein Balac_1228 [Bifidobacterium animalis subsp.
           lactis Bl-04]
 gi|240251212|gb|ACS48151.1| hypothetical protein Balat_1228 [Bifidobacterium animalis subsp.
           lactis DSM 10140]
 gi|289177367|gb|ADC84613.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           animalis subsp. lactis BB-12]
 gi|295794245|gb|ADG33780.1| hypothetical protein BalV_1192 [Bifidobacterium animalis subsp.
           lactis V9]
          Length = 317

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 73/279 (26%), Positives = 127/279 (45%), Gaps = 37/279 (13%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+     +++ +GQ RV  + +  +  +Q+G  V I          ++E++     V+  
Sbjct: 26  ISRAKATELIETGQARVIGRDIHKSATLQAGDTVEID---------VREERREPEPVSN- 75

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFL---KSWVDSKGQKPR-- 145
                 +  + YED  I V +KP G++     G     + G L      + S G   R  
Sbjct: 76  ------EMTIAYEDDDIVVVDKPVGVAAHASVGWTGPTVLGSLIQRGVHITSMGAAGRQG 129

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD  TSG+++V ++  A + +   F    ++K Y +LV G  K  K  I      +
Sbjct: 130 IVSRLDVGTSGLMLVCKSDLAYKEMRRQFSEHEVKKTYHALVQGNLKEDKATI------E 183

Query: 206 SHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + IG     D+   V    K    A++H+ V++ F +      +   TGRTHQ+RVH   
Sbjct: 184 APIGRAKVSDFRFTVTPAGK---EAVTHWDVMERFGEA-TLASINLETGRTHQIRVHFSS 239

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +G P+VGD  Y AN + +    ++ + +LHA  ++  HP
Sbjct: 240 IGHPLVGDPMYGANPRLSQALGLERQ-WLHAMELEFRHP 277


>gi|168186684|ref|ZP_02621319.1| pseudouridine synthase, RluA family [Clostridium botulinum C str.
           Eklund]
 gi|169295320|gb|EDS77453.1| pseudouridine synthase, RluA family [Clostridium botulinum C str.
           Eklund]
          Length = 323

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 76/271 (28%), Positives = 123/271 (45%), Gaps = 28/271 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++ +     +    + K LR G +RV+ K+ K N  ++   VV         
Sbjct: 8   NEAGQRLDKFCRKWLEDVPLGAIFKALRKGDIRVNGKKAKQNYFLEEEDVVET------- 60

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGF 132
            +I   +K  ++     +  +F    + YED  + +  K  G+ V      G     D +
Sbjct: 61  KYIESYKKNKNNVPKKFQEVNFSSIKIAYEDENMLIIEKWPGVLVHSDKKDGDPTLTD-Y 119

Query: 133 LKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           + S++ +KG+          P   +RLD+ TSG+++  +   + + L E  R R+I K Y
Sbjct: 120 VLSYLFNKGEYIPEKEVTFTPAPCNRLDRNTSGMVIFGKNFKSLKLLNEMIRERKISKYY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGG-DYVHVVKQ-NEKGANYAISHFKVIDCFAQKFC 241
            +LV G     KE      + K  I     +H+ K+ N K     +S   VID     F 
Sbjct: 180 NALVKG---KIKEGRYEAYISKDQINNISEIHLDKKPNSKKIAMEVS---VIDTVGT-FS 232

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +LE+   TGR+HQLR H   +G PI+GD KY
Sbjct: 233 FLELDLITGRSHQLRAHLSFLGNPIIGDDKY 263


>gi|256617567|ref|ZP_05474413.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256597094|gb|EEU16270.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
          Length = 287

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 114/260 (43%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +V+L    +  +  +LYED
Sbjct: 40  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTVHL---GEATRVKVLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 144 TKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVQVVQTLSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 258 -----ARLMLHASQLHLLHP 272


>gi|222094929|ref|YP_002528989.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           Q1]
 gi|221238987|gb|ACM11697.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           Q1]
          Length = 297

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 73/280 (26%), Positives = 131/280 (46%), Gaps = 38/280 (13%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           G + V+ +     +++Q+G+ +R+  PV      +I E   L                ++
Sbjct: 41  GSIEVNGQHASVRHQLQAGEELRVFFPVEERSEGMIAEDIPL---------------CIV 85

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQETSG 156
           YED  + V NK A +S         H  G + + + S   K  LT       RLD++TSG
Sbjct: 86  YEDDAVLVINKEANMSTIPSR---EHPAGSVANALLSHYDKRHLTSTVHIVTRLDRDTSG 142

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++++A+ R     L++  + + +++ Y ++V G    K+  I   + +KS    D +   
Sbjct: 143 LMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEKEGTIDAPIGRKS----DSIIER 198

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E+G   A++HF+VID    K   + ++  TGRTHQ+RVH  ++G P++GD     N 
Sbjct: 199 TVCEEG-QRAVTHFRVIDSVNHK-THVSLELDTGRTHQIRVHMAYIGHPLLGD-----NL 251

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH+  +   HP     +  T P+P+ M
Sbjct: 252 YGGKRDEMKRQ-ALHSTSLTFYHPILEKEMSFTTPIPSDM 290


>gi|320155234|ref|YP_004187613.1| ribosomal large subunit pseudouridine synthase A [Vibrio vulnificus
           MO6-24/O]
 gi|319930546|gb|ADV85410.1| ribosomal large subunit pseudouridine synthase A [Vibrio vulnificus
           MO6-24/O]
          Length = 250

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 95/214 (44%), Gaps = 30/214 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +++ED  I   NKP+G+ SV G   +  H D     W   + Q P +   HRLD  TSG+
Sbjct: 16  IIFEDDHILAVNKPSGLLSVPGR--LPEHHDSM---WSRLQEQYPEIQVVHRLDMSTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW----LLKKSHI 208
           +V A+ + A   L + F+ R   KIY++ VWG  +          I +W    + K  H 
Sbjct: 71  MVFAKNKRAEAALKKQFQYRLTHKIYYARVWGHVEADSGMIDLPLICDWPNRPMQKVCHE 130

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            G       Q  K   +A      I         + + P TGR+HQLRVH   +G PIVG
Sbjct: 131 HGKPSQTEFQVAKREVHANGAQTTI---------MRLLPVTGRSHQLRVHMQALGHPIVG 181

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           D  Y       F+     +L LHA  +   HP+ 
Sbjct: 182 DEFYAQGDAFTFS----ERLELHAAELSFYHPKS 211


>gi|319762874|ref|YP_004126811.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|330824953|ref|YP_004388256.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
 gi|317117435|gb|ADU99923.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|329310325|gb|AEB84740.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
          Length = 225

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 62/207 (29%), Positives = 101/207 (48%), Gaps = 19/207 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS---WVDSKGQKPRLTHRLDQETSGIL 158
           ++ D  + V +KPAG+    G G         ++   W D+      + HRLDQ TSG++
Sbjct: 16  VHADDTLLVLDKPAGLLCVPGRGPDKQDSLSTRAQALWPDAL-----IVHRLDQPTSGLV 70

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY----VH 214
           ++AR  A  + L+ +F  R + K Y ++V G+ +  +     W      I  D+    + 
Sbjct: 71  LMARGGAMQRALSHAFAQRLVHKRYQAVVAGLLRPARGSAGEWSEIALPIAADWERRPLR 130

Query: 215 VVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           VV      A+  ++ ++V+    A     +E++P TGRTHQLRVH   +G PI+GD  Y 
Sbjct: 131 VVDAGRGQAS--LTRWRVLAHDEAGGTTRVELEPVTGRTHQLRVHLAALGHPILGDALY- 187

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
           A+      +P   +L LHA  +   HP
Sbjct: 188 ADAATQARAP---RLLLHACALGFGHP 211


>gi|255971139|ref|ZP_05421725.1| pseudouridine synthase [Enterococcus faecalis T1]
 gi|255962157|gb|EET94633.1| pseudouridine synthase [Enterococcus faecalis T1]
          Length = 287

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 63/205 (30%), Positives = 93/205 (45%), Gaps = 20/205 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LYED  + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETS
Sbjct: 83  VLYEDEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETS 138

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G +V A+       L      ++I + Y ++V G   N+KE   N  + +         +
Sbjct: 139 GAIVFAKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRI 197

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             Q  KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y   
Sbjct: 198 DPQ--KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPK 254

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
            +         +L LHA  + L HP
Sbjct: 255 SQA-------ARLMLHASQLHLLHP 272


>gi|227889491|ref|ZP_04007296.1| pseudouridylate synthase RluD [Lactobacillus johnsonii ATCC 33200]
 gi|227849969|gb|EEJ60055.1| pseudouridylate synthase RluD [Lactobacillus johnsonii ATCC 33200]
          Length = 266

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 112/239 (46%), Gaps = 24/239 (10%)

Query: 41  LRS-GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           LRS  ++ V+ K +  N  ++ G  + I      L+HI  +Q+   +S  L K       
Sbjct: 20  LRSEKKILVNGKYLPLNFLVKPGDKIEI-----QLDHIESDQQPYPASGKLPK------- 67

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++YED+ I V NKP G   Q         D  L       G  P + HRLD  TSG+L+
Sbjct: 68  -VVYEDNDILVINKPTG---QKTHPNLNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLL 123

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQ 218
           VA+  A    L      + + + Y + +   P+ K   I +  L   H   D    +V+Q
Sbjct: 124 VAKNPAVVPILNRQLTDKTLHREYLAWISNSPQIKYTGIID--LPIGHDPHDQRKRMVRQ 181

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +      A++H++VI     +   +++   TGRTHQ+RVH   +G PI+GD  Y ++++
Sbjct: 182 D---GQKAVTHYEVIKRDKDRIL-VKLTLETGRTHQIRVHLAALGAPIIGDPLYNSDYQ 236


>gi|257463597|ref|ZP_05627988.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
 gi|317061151|ref|ZP_07925636.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
 gi|313686827|gb|EFS23662.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
          Length = 289

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 104/221 (47%), Gaps = 18/221 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQK--PRLTHRLDQETSG 156
           ++YED  + V NK A +     +    A   +G +  ++ + G+   PR  +RLD  T+G
Sbjct: 75  IVYEDENLLVLNKQANLVTHPTTKKVDATLANGVVAYFLKTTGKTMVPRFYNRLDMNTTG 134

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++V +   +  +L E   +R   K Y ++V G+ +  +  I   + K   +G D   V 
Sbjct: 135 LIIVTKNAYSQAYLQEKTEVR---KSYQTIVKGMVEQDEFYITRPIGK---VGEDLRRVE 188

Query: 217 KQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              EKG   A +  KV+  F QK    LE+   TGRTHQ+R H    G PIVGD  Y   
Sbjct: 189 LPVEKGGQEAKTFVKVLKRFPQKNRTLLEVTLFTGRTHQIRAHLSLEGYPIVGDDLY--- 245

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHM 315
             G     I+ +L LHA  +   +P+    Q I   LP  M
Sbjct: 246 --GGSEETIKRQL-LHAYRLCFQNPKNAEEQEIVIDLPQDM 283


>gi|229548625|ref|ZP_04437350.1| pseudouridylate synthase RluD [Enterococcus faecalis ATCC 29200]
 gi|257420942|ref|ZP_05597932.1| pseudouridine synthase [Enterococcus faecalis X98]
 gi|229306256|gb|EEN72252.1| pseudouridylate synthase RluD [Enterococcus faecalis ATCC 29200]
 gi|257162766|gb|EEU92726.1| pseudouridine synthase [Enterococcus faecalis X98]
          Length = 287

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 40  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 144 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVQVVQTLSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 258 -----ARLMLHASQLHLLHP 272


>gi|270285168|ref|ZP_06194562.1| pseudouridine synthetase family protein [Chlamydia muridarum Nigg]
 gi|301336563|ref|ZP_07224765.1| pseudouridine synthetase family protein [Chlamydia muridarum
           MopnTet14]
          Length = 274

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/257 (27%), Positives = 114/257 (44%), Gaps = 41/257 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +   RL  + +   PH+    + + +R    RV       N RI+  +  ++ P      
Sbjct: 9   DRQTRLACFLRTSLPHLPKKTILESIRYHGCRV-------NGRIERFESYKLHPGDRVCL 61

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
            II+      SS  L           L+ED  + ++NKPA    Q    +A  +      
Sbjct: 62  QIIER-----SSAQL-----------LWEDEHLCIYNKPAK---QTSEALACQLHV---- 98

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                     L HRLD++TSG ++ A+   A   +T+ F+ R+I K Y +LV+G P+ + 
Sbjct: 99  ---------HLVHRLDRDTSGCILFAKHEKAITPITQLFKTRQIDKRYIALVFGHPRQQS 149

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I  +     H     V     +EK     I+ ++V+  ++ K+  L  +P TGRTHQ+
Sbjct: 150 GIITTY-TAPCHRRIGAVLFGNTDEKLGKKTITEWEVLTHYS-KYALLLCRPITGRTHQI 207

Query: 256 RVHALHMGCPIVGDHKY 272
           R+H   +G PIVGD  Y
Sbjct: 208 RLHMKTIGHPIVGDIDY 224


>gi|325578324|ref|ZP_08148459.1| tRNA pseudouridine synthase C [Haemophilus parainfluenzae ATCC
           33392]
 gi|325160060|gb|EGC72189.1| tRNA pseudouridine synthase C [Haemophilus parainfluenzae ATCC
           33392]
          Length = 238

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 58/233 (24%), Positives = 104/233 (44%), Gaps = 17/233 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEYLVAVNKPAGMLVHRSWLDTHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  + + F  + +QK Y ++V G  + K +      ++   I   +     Q +
Sbjct: 64  ALNSEIANLMCQQFEQKTVQKSYLAIVRGYLQGKGQIDYPLKIQLDKIADKFA----QED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ ++              ++  +++ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQEAVTDYEGLNIVEMPYAVGRYQTTRYSLVKLIPQTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
           +Y    +    +      +L+LHA  +   HP    + +I A L    +K  +
Sbjct: 180 QYGDLHQNRALTEHSGCQRLFLHADTLIFEHPIHSTKFEIKANLDEQWMKVME 232


>gi|227552604|ref|ZP_03982653.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecium
           TX1330]
 gi|227178230|gb|EEI59202.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecium
           TX1330]
          Length = 307

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 82/308 (26%), Positives = 135/308 (43%), Gaps = 40/308 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + K+H   + +   +K +  G +     ++KF    Q GQ+     V N L  + K+ K+
Sbjct: 15  YEKDHSQQVKYFLKEKGISKGLL----AKIKF----QGGQIKVNDQVENVLFSLAKDDKV 66

Query: 84  LDSSVNLTKHSDFLKS----ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KS 135
                   +H   L       ++YED  + V NKPAG+S        YH +G +    K+
Sbjct: 67  TIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQ---YHPNGTMANRVKA 123

Query: 136 WVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   +G + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G+  
Sbjct: 124 YYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDTQLREKKFVKKYQALVSGMLS 183

Query: 193 NKKECIANWLLKKSHI----GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           N        L    HI      DY  ++K+       +      I+    +   +++Q H
Sbjct: 184 N--------LSAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYRIEKRLTEIALVDIQLH 235

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH   +GC ++GD  Y     G     I+ +  LH   +   HP     L+ 
Sbjct: 236 TGRTHQIRVHFSAIGCALLGDDMYS----GRMDLGIKRQA-LHCYDLRFYHPFTEELLEF 290

Query: 308 TAPLPAHM 315
             PL A M
Sbjct: 291 KQPLAADM 298


>gi|227536848|ref|ZP_03966897.1| pseudouridine synthase [Sphingobacterium spiritivorum ATCC 33300]
 gi|227243275|gb|EEI93290.1| pseudouridine synthase [Sphingobacterium spiritivorum ATCC 33300]
          Length = 444

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 105/221 (47%), Gaps = 29/221 (13%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDS---KGQKPRLTHRLDQETSG 156
           +LY+D  I V NKPA  +SV G      HI   + + + +   +   P + HRLD  TSG
Sbjct: 243 ILYDDEDIAVVNKPAEFLSVPG-----IHIQDSVYTRMQAAFPEATGPIIVHRLDMSTSG 297

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           IL++A+ + A + + + F    I+K Y +L+ G+ K  +  I   L          +   
Sbjct: 298 ILLIAKHKDAHKFIQQQFINHSIEKRYVALLDGVVKEDEGIIDLPLRLDLDDRPRQMVCY 357

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
           +  +K    A++ ++V+     +   L   P TGRTHQLRVHA H   +  PIVGD  Y 
Sbjct: 358 EYGKK----AVTKYQVLSRTDGQTKIL-FFPVTGRTHQLRVHAAHLLGLHIPIVGDDLYG 412

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAPL 311
                       N+L+LHA Y+   HP   +    ++ AP 
Sbjct: 413 TK---------SNRLHLHAAYLSFVHPRTKKTVVFEVKAPF 444


>gi|157962710|ref|YP_001502744.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157847710|gb|ABV88209.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 284

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 114/244 (46%), Gaps = 31/244 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  I V +KPAG+ V   S +A     F ++   D  G      HRLD+ TSGIL+
Sbjct: 37  VLFEDDDIVVIHKPAGLLVHR-SYLARRERFFAMQLTRDLVGCHVFPVHRLDRPTSGILL 95

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKS--HIGGDYVHVV 216
            A++   A  L E F    + K Y ++V G   N  E    ++ LK+    +G   V   
Sbjct: 96  FAKSSEMANVLCEQFAAHTVDKEYLAIVRG---NMHEAGTLDYALKEELDELGDKDV--- 149

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               K A  A++ +K +               ++  +++ PHTGR HQLR H  H+  PI
Sbjct: 150 -DPNKAAQDAVTSYKPLLNSEIPFSSGRYATSRYALVQLSPHTGRKHQLRRHMAHLRHPI 208

Query: 267 VGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
           +GD  +        F+ +F     N+L+L A+ +   HP  G R+ +   L A  +  ++
Sbjct: 209 LGDTTHGDGKQNKFFRSHFGI---NRLWLIAKKLSFNHPRSGERMSVETELEAEWLSLFE 265

Query: 321 SLGF 324
            LG+
Sbjct: 266 GLGW 269


>gi|194466992|ref|ZP_03072979.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
 gi|194454028|gb|EDX42925.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
          Length = 290

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 76/277 (27%), Positives = 135/277 (48%), Gaps = 34/277 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
            G+  VD ++V+   +I   Q    P  I A      + ++ D +V ++  S      ++
Sbjct: 36  EGEFLVDHRKVRPTTQILPNQ----PLTIRA------QPELADDTVEISNES----LNVV 81

Query: 103 YEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED    V +KPAG++   G       +   + G+L +  +S   +P L  RLD+ T G+
Sbjct: 82  YEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIA-NNSADLRPHLITRLDRFTGGL 140

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+   A+  +++  +  ++ K Y +LV G   ++   I   + +K    G    V+ 
Sbjct: 141 LLIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHGEINKPIGRKD---GQAARVID 197

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +N      A++ + V +  A K+  + ++ HTGRTHQ+RVH   +G P++GDH Y     
Sbjct: 198 EN---GQRALTEYWVEERGA-KWTRVRVRLHTGRTHQIRVHFAAIGHPLIGDHLY----- 248

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           G  TS   ++L LHA  +    P    ++  T+ LPA
Sbjct: 249 GGDTSKYDHQL-LHASKISFNDPFTLKQMTFTSELPA 284


>gi|332530661|ref|ZP_08406593.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
 gi|332039889|gb|EGI76283.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
          Length = 229

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 65/221 (29%), Positives = 104/221 (47%), Gaps = 25/221 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +++ED  + V +KPAG+    G G       +   L  W ++      + HRLDQ TSG+
Sbjct: 13  VVHEDEALVVLDKPAGLLSAPGRGAEKQDCLVARALARWPEAL-----IVHRLDQATSGL 67

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE----------CIANWLLK-KS 206
           +++AR     + L+  F  R + K Y ++V G  +   E           +A+W  + + 
Sbjct: 68  MLLARGPEMQRALSICFAARDVHKRYEAVVDGCVRGSAEHEDEGEIALPLMADWPRRPRQ 127

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +       + + +  A  ++ H    +  A +   L + P TGR+HQLRVH   +G PI
Sbjct: 128 KVDAQGKPSLTRWKVLARDSVGHQSASN--ASQTTRLALFPVTGRSHQLRVHLQAIGHPI 185

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           +GD  Y A+      SP   +L LHA  + LPHP  G L I
Sbjct: 186 LGDALY-ADPATLARSP---RLLLHACELSLPHPRTGALTI 222


>gi|315156668|gb|EFU00685.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0043]
          Length = 283

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVQTLSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|312953063|ref|ZP_07771913.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|310628972|gb|EFQ12255.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|315154025|gb|EFT98041.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0031]
          Length = 283

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNHPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVQTLSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|260887212|ref|ZP_05898475.1| ribosomal large subunit pseudouridine synthase D [Selenomonas
           sputigena ATCC 35185]
 gi|260863274|gb|EEX77774.1| ribosomal large subunit pseudouridine synthase D [Selenomonas
           sputigena ATCC 35185]
          Length = 287

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 118/247 (47%), Gaps = 34/247 (13%)

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLK 134
           H+ +E +I    + L          +LYED+ + + NKPAG+ V    G   H +   + 
Sbjct: 50  HLAEESRIAPEDIPLE---------ILYEDAALLIVNKPAGMLVHPTGGEYRHTLANAVL 100

Query: 135 SWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP 191
              ++ G+K      HRLD++TSG++++A+  A  QHL  +     I++IY +++ G +P
Sbjct: 101 FHYEAHGEKHAFHPVHRLDRQTSGLVLIAK-EAHVQHLLSAHNA--IERIYLAVIEGKLP 157

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHT 249
           +      A    +   I      + +        A++H+  +   A++     L ++  T
Sbjct: 158 EPCGTIDAPIARRPGSI------IERMVSPAGKCAVTHYATL---AERGGLSLLALRLAT 208

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  H+  P++GD  Y     G  T  I  +  LHA  +   HP  G+ + + 
Sbjct: 209 GRTHQIRVHLAHLAHPLLGDDLY-----GGRTDRIARQ-ALHAHRLRFRHPISGKEITVH 262

Query: 309 APLPAHM 315
           AP PA M
Sbjct: 263 APFPADM 269


>gi|332160263|ref|YP_004296840.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|318607167|emb|CBY28665.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325664493|gb|ADZ41137.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|330863027|emb|CBX73159.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica W22703]
          Length = 196

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 57/159 (35%), Positives = 83/159 (52%), Gaps = 14/159 (8%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG     +  I   L+    
Sbjct: 38  HRLDMATSGVIVVALTKAAERELKRQFREREPKKSYVARVWGHLAQDEALIDLPLI---- 93

Query: 208 IGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              D+ +  KQ    E G + + + ++V+   A     +++ P TGR+HQLRVH L +G 
Sbjct: 94  --CDWPNRPKQKVCYETGKS-SQTQYQVLSRDADGSTRVKLSPITGRSHQLRVHMLAIGH 150

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           PI+GD  Y         S    +L LHA+ + + HPE G
Sbjct: 151 PILGDGFYAHPEAKAMAS----RLQLHAQELCITHPEFG 185


>gi|307289628|ref|ZP_07569572.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|306499442|gb|EFM68815.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|315164544|gb|EFU08561.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1302]
          Length = 283

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 63/205 (30%), Positives = 93/205 (45%), Gaps = 20/205 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LYED  + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETS
Sbjct: 79  VLYEDEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETS 134

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G +V A+       L      ++I + Y ++V G   N+KE   N  + +         +
Sbjct: 135 GAIVFAKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRI 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             Q  KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y   
Sbjct: 194 DPQ--KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPK 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
            +         +L LHA  + L HP
Sbjct: 251 SQA-------ARLMLHASQLHLLHP 268


>gi|167971859|ref|ZP_02554136.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 6 str. ATCC 27818]
 gi|168282520|ref|ZP_02690187.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 14 str. ATCC 33697]
 gi|168308674|ref|ZP_02691349.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 1 str. ATCC 27813]
 gi|170762382|ref|YP_001752395.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 3 str. ATCC 27815]
 gi|168827959|gb|ACA33221.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 3 str. ATCC 27815]
 gi|171902645|gb|EDT48934.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 1 str. ATCC 27813]
 gi|182675832|gb|EDT87737.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 14 str. ATCC 33697]
 gi|186700803|gb|EDU19085.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 6 str. ATCC 27818]
          Length = 292

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 57/209 (27%), Positives = 100/209 (47%), Gaps = 18/209 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS--KGQKPRLTHRLDQETSGIL 158
           +++ED  + + NKP+G+ V   S   +H    L + +    K     +THRLD+ TSG++
Sbjct: 74  IIFEDQDLLIVNKPSGMLVHPTS---FHEQNTLANALKYYLKTDNFYITHRLDKNTSGLI 130

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ + + A   L + F  + I+K Y+++V     N+ +      +    IG  Y   ++ 
Sbjct: 131 IICKNQIALNSLQQQFMQKTIRKSYYAIVH----NRFDMQHLHFMINEPIGHSYQDKLRM 186

Query: 219 ---NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              N K    AIS  KV++ +      +E+   TGRTHQ+RVH  ++  P+  D  Y   
Sbjct: 187 KTGNSKNTKEAISIVKVLEQYKNT-ALVEVSIITGRTHQIRVHMRYINHPVYNDPLY--- 242

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             G      + + YLH+ Y+   HP   +
Sbjct: 243 --GISKHTTEYEQYLHSFYISFNHPSTNK 269


>gi|146310754|ref|YP_001175828.1| pseudouridylate synthase [Enterobacter sp. 638]
 gi|145317630|gb|ABP59777.1| Pseudouridylate synthase [Enterobacter sp. 638]
          Length = 232

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 62/213 (29%), Positives = 100/213 (46%), Gaps = 26/213 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG----FLKSWVDSKGQKPRLTHRLDQETSG 156
           +LY+D  + + NKP+G+    G     ++D      +K++         L HRLD  TSG
Sbjct: 19  ILYQDEHLVIINKPSGLLSLSGKN-PQNLDSVHYRLVKTFPGCT-----LIHRLDFGTSG 72

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V+AR +     L + F  R + KIY +L+ G  +N +  I   + K   +    + + 
Sbjct: 73  LMVIARNKTINAALCQQFSQRTVTKIYSALLCGHLENNEGAIDAPIAKDPAL-FPLMSIC 131

Query: 217 KQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               K A    S ++VI+ F +            +E+ P TGRTHQLR+H   +G PI+G
Sbjct: 132 AITGKPAR---SRYRVIERFYRVGEDGAELPLTRVELTPETGRTHQLRIHCQQLGHPILG 188

Query: 269 DHKYCANFK-GNFTSPIQNKLYLHARYMDLPHP 300
              Y    + G   +P   +L LHA  +   HP
Sbjct: 189 CDLYGGLLRPGTEKTP---RLMLHASELHFVHP 218


>gi|331007525|ref|ZP_08330690.1| Ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium IMCC1989]
 gi|330418674|gb|EGG93175.1| Ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium IMCC1989]
          Length = 248

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 108/233 (46%), Gaps = 31/233 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +++ED  I V NKP+G+    G     + D      V    Q P  T  HRLD  TSG++
Sbjct: 25  VVFEDEHILVINKPSGLLSLSGKN-PLNKDSVHYRLVQ---QYPTATMAHRLDFGTSGVM 80

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A  +    HLT  F+ R + K Y +++ G  ++ +  I   ++K ++    Y  V   
Sbjct: 81  VLALNKTVNGHLTGQFQERTVSKTYTAILRGHIESDEGRIDIPIIKDTN-NFPYQKVCYT 139

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEM--QPHTGRTHQLRVHALHMGCPIVG-------- 268
             K A   +SH++V++      C   +   PHTGRTHQLR+H+  +G PI+G        
Sbjct: 140 TGKSA---LSHYQVMERLHTP-CSTRVLFTPHTGRTHQLRIHSQAIGHPILGCDLYGDNE 195

Query: 269 ---DHKYCANFKGNFTS----PIQNKLYLHARYMDLPHPEGGR---LQITAPL 311
              D K+  +   N  +     +  +L LHA  +   HP  G     ++T P 
Sbjct: 196 RDTDEKHSESVDNNNVTVSSLAMAERLLLHATTLGFEHPVSGERLVFEVTCPF 248


>gi|319776302|ref|YP_004138790.1| tRNA pseudouridine synthase [Haemophilus influenzae F3047]
 gi|317450893|emb|CBY87118.1| tRNA pseudouridine synthase [Haemophilus influenzae F3047]
          Length = 239

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 109/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|313683666|ref|YP_004061404.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
 gi|313156526|gb|ADR35204.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
          Length = 305

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 64/204 (31%), Positives = 99/204 (48%), Gaps = 22/204 (10%)

Query: 110 VFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           +++KP+G+SV   S  + Y ++  +K      G +   THR+DQETSG+++V+R + +  
Sbjct: 81  IYDKPSGLSVHPHSRQSPYTLNDEIKHQF---GDEANATHRIDQETSGLVLVSRHKKSES 137

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYA 226
            L   F  R I K Y ++V G  ++  + I   L +K H       VVK + KG  A+  
Sbjct: 138 VLKRLFSERAITKRYLAMVKGCVEHPID-IQEPLYRKDHPNLLISMVVKVDPKGKPAHTV 196

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNF 280
           I+  +           +E  P TGRTHQ+RVH  H+  PI+GD  Y         F    
Sbjct: 197 INPLRYFP--EHDMTLVEASPLTGRTHQIRVHLFHVKHPIIGDPVYGPTEENVIRFIKKE 254

Query: 281 TSPIQ-------NKLYLHARYMDL 297
            SPI+        +L LHA  ++ 
Sbjct: 255 LSPIERMEIGGSTRLLLHAHSLEF 278


>gi|167623992|ref|YP_001674286.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167354014|gb|ABZ76627.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 246

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 108/242 (44%), Gaps = 48/242 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +L++D  + + NKP+G+    G   A ++D      V D  G    L HRLD  TSGI+V
Sbjct: 22  ILFQDEHLLLINKPSGLLSLSGKNPA-NLDSVHYRLVKDFPGCT--LVHRLDLGTSGIMV 78

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG------------IPKNK------KECIANW 201
           +AR +     L + F  R + K Y SL+ G            I K+K      K C    
Sbjct: 79  IARNKQINALLCKQFSERTVLKTYTSLLLGELSHDDGFIDAPIAKDKPNFPLMKICDKEG 138

Query: 202 LLKKS--HIGG--------DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
              +S  H+ G        D   ++  NE+  + ++S  +V           E  P TGR
Sbjct: 139 KTARSLYHVLGLESYSSLDDDAPLLSTNEQAVDRSVSVTRV-----------EFIPQTGR 187

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQLR+H+ + G PI+G    C  +    +  +  +L LHA  ++  HP  G R+   +P
Sbjct: 188 THQLRIHSQYFGHPIIG----CDLYGSETSYRLAPRLMLHATRLEFDHPITGERIFANSP 243

Query: 311 LP 312
            P
Sbjct: 244 SP 245


>gi|307272491|ref|ZP_07553744.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|306510776|gb|EFM79793.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
          Length = 283

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|72080790|ref|YP_287848.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 7448]
          Length = 289

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 94/183 (51%), Gaps = 18/183 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQET 154
           ++++D  + + NKP  + V  G G      ++G + S  DS  Q    +P + HRLD++T
Sbjct: 69  IIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLI-SHFDSLEQLDHIRPGIVHRLDKDT 127

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+L+VA+   A          R+I++ Y ++V G      + +  ++     IG D  +
Sbjct: 128 TGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIG------KVLHKFMKINLPIGRDLKN 181

Query: 215 VVKQNEKGANY--AISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +K+     N   AI++ ++I  F    Q F  ++ Q  TGRTHQ+R+H  H+G PI GD
Sbjct: 182 PLKKTISFFNSKPAITNVELIKHFNYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPIYGD 241

Query: 270 HKY 272
             Y
Sbjct: 242 PIY 244


>gi|304397365|ref|ZP_07379243.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304354983|gb|EFM19352.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 232

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 102/231 (44%), Gaps = 27/231 (11%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGG------SGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           F +   L++D+ + V NKP G+    G        + + + G              L HR
Sbjct: 14  FDEITFLFQDAHLLVINKPGGLLSLSGKNPQNLDSVHHRLVGLFPGCT--------LVHR 65

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++VVAR +A    L + F  R + K Y +L+ G   + +  I   + K   + 
Sbjct: 66  LDFGTSGLMVVARNKAINAALCQQFSQRSVNKTYQALLCGHLSDDEGVIDAAIAKDPALF 125

Query: 210 GDY-VHVVKQNEKGANYAIS---HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
               +  ++     + Y ++   +++  +  A     +E+ P TGRTHQLR+H   +G P
Sbjct: 126 PRMTICTIRGKPARSRYRVTERGYYQGSEGDALPVTRVELTPETGRTHQLRIHCQQLGHP 185

Query: 266 IVGDHKYCANFKGNFTSPIQNK---LYLHARYMDLPHPEGGR-LQITAPLP 312
           I+G   Y     G    P   K   L LHA  +   HP  G  +Q++A  P
Sbjct: 186 ILGCDLY-----GGLLMPGAEKAERLMLHASGLTFIHPVSGEVMQLSAASP 231


>gi|149926150|ref|ZP_01914412.1| ribosomal large subunit pseudouridine synthase D [Limnobacter sp.
           MED105]
 gi|149824968|gb|EDM84180.1| ribosomal large subunit pseudouridine synthase D [Limnobacter sp.
           MED105]
          Length = 388

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 90/342 (26%), Positives = 148/342 (43%), Gaps = 75/342 (21%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD+     +P  +   LQ  L+  +V V+     K N ++Q    + + P +  L H+ 
Sbjct: 30  RLDKVIAELFPQYSRSRLQGWLKEERVLVNGVAAAKGNQKVQGMDRIELSPGV--LAHM- 86

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------IAYHID 130
             Q ++   +NL          ++   ++  V NK AG+ V    G          YH+D
Sbjct: 87  --QALIPEDMNLD---------IVARTNEYTVVNKQAGLVVHPAPGHWTGTLMNGLYHLD 135

Query: 131 GFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             L          PR  + HRLD +T+G++VVART+     L +  + R ++++Y ++VW
Sbjct: 136 PELI-------HVPRAGIVHRLDADTTGLMVVARTQETQVKLVQMLQARIVKRVYLAMVW 188

Query: 189 GIPKNKKECIANWLLKKSHIGGD-----YVHVVKQNEKGANYAISHFKVIDCFAQKF--- 240
           G        I++ L   + +G D      + VV   +     A++HF  +  F +     
Sbjct: 189 G-------RISSPLTVNNPLGRDPRNRLRMAVVDHGKP----AVTHFTPV-AFGELLEVP 236

Query: 241 -----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                C LE    TGRTHQ+RVHA H G  +V D  Y     G+ ++       L    +
Sbjct: 237 VTLMVCRLE----TGRTHQIRVHAQHAGFALVADPVYKIKGAGSHSA-------LRLSSI 285

Query: 296 DLPHPEGGRLQ------ITAPLPAHM-VKTWDSLGFKYDRNL 330
           +LP+ E    Q      ++ P PAH  V+  D     +D +L
Sbjct: 286 ELPNGEKFERQALHATHLSFPDPAHFHVQGSDEAAEDWDESL 327


>gi|152996227|ref|YP_001341062.1| pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150837151|gb|ABR71127.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 242

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 60/210 (28%), Positives = 92/210 (43%), Gaps = 11/210 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  +   NKPAG+ V   +      D  ++   D  G+     HRLD+ TSG+LV+
Sbjct: 5   ILFQDEHLVAVNKPAGLLVHRTNLAKDEEDAVVQRLRDQTGKWVFPVHRLDRGTSGVLVM 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   + QK Y  LV G   N+   I   L K +   G     ++  E
Sbjct: 65  AFSPEVARRLSTQFAESKTQKTYHCLVRGYC-NESGVINYPLAKLNEQKGRSRFKIEGTE 123

Query: 221 KGANYAISHF-------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           + A    +          V    + +  WLE+ P  GR HQ+R H  H   P+VGD  Y 
Sbjct: 124 REAETGFTRLIQYQLPVPVSRYDSMRLSWLEVTPKQGRKHQIRRHFKHHLNPLVGDSCYG 183

Query: 274 ANFKGNFTSPIQN---KLYLHARYMDLPHP 300
                     + +   +L LHA  ++  HP
Sbjct: 184 CRHINKVAKELWSEDFRLMLHASSLEFNHP 213


>gi|115923337|ref|XP_792877.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 3 [Strongylocentrotus purpuratus]
 gi|115953851|ref|XP_001183657.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 3 [Strongylocentrotus purpuratus]
          Length = 373

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 75/286 (26%), Positives = 117/286 (40%), Gaps = 52/286 (18%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQG-----GSGIAYHIDGFLKSWVD-SKGQKPRLTHR 149
           +LK  ++Y+   I   NKP G+ V G            +   +    D +      +   
Sbjct: 81  YLKKNIVYQQDGIVAINKPPGLGVSGKVNEDDESSPLTLSSMMSQVADFTDCPSAEIAQG 140

Query: 150 LDQETSGILVVARTRAAAQHLT----ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L++E SG+L++A  R AA+ L     E+   R+  K Y S+V GIP+ K   ++   L  
Sbjct: 141 LEKEASGLLLLAENRMAAKKLQSKIKEARNRRQFIKTYRSIVCGIPETKIG-VSKMYLGS 199

Query: 206 SHIGGDYVHVVKQNEKGANY-------AISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRV 257
             IGG  + V + N  G          A + ++VI    +  C ++E+QP   + HQL+V
Sbjct: 200 DVIGGINMTVGRHNPSGRQIRDGDVWSAETKYRVISENKELGCAFIELQPLRVKRHQLQV 259

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPI----QNKLYLH-----------ARYMDLPH--- 299
             ++  CPI+GDH Y    +     PI       L +H           A  M  P    
Sbjct: 260 QMVNDLCPILGDHTYSHQVQTILGKPILMDPHQALGVHNIQVLSPGIRKALAMTRPQVSL 319

Query: 300 ------------PEGGRLQ---ITAPLPAHMVKTWDSLGFKYDRNL 330
                       PE    Q   ITAPLP+H  +    LG +   ++
Sbjct: 320 LPLFLHLHHVVLPEWAGHQDVTITAPLPSHFTRALKELGLRSSEDV 365


>gi|76786717|ref|YP_330596.1| ribosomal large subunit pseudouridine synthase A [Streptococcus
           agalactiae A909]
 gi|76561774|gb|ABA44358.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus agalactiae A909]
          Length = 294

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 55/203 (27%), Positives = 91/203 (44%), Gaps = 23/203 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           LYED  + + NKP G+   G       +  H+  +        GQ   + HRLD ETSG 
Sbjct: 84  LYEDEHLIIVNKPEGMKTHGNQPNEIALLNHVSAY-------SGQTCYVVHRLDMETSGA 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       + +    + I + YW+LV G    K + + + + +  H     +    
Sbjct: 137 VLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRDKIGRNRHDRRKRI---- 192

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + K   +A++   V+  + Q    ++ +  TGRTHQ+R+H  H G P++GD  Y     
Sbjct: 193 IDSKNGQHAMTIIDVLK-YTQNSSLIKCRLETGRTHQIRIHLSHHGHPLIGDPLYNP--- 248

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
               S    +L LHA  + L HP
Sbjct: 249 ----SSNNERLMLHAHRLTLSHP 267


>gi|323498626|ref|ZP_08103618.1| tRNA pseudouridine synthase C [Vibrio sinaloensis DSM 21326]
 gi|323316324|gb|EGA69343.1| tRNA pseudouridine synthase C [Vibrio sinaloensis DSM 21326]
          Length = 241

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 108/243 (44%), Gaps = 27/243 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IIFQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +          ++   I   +       +
Sbjct: 64  ALSSEVASQVMPMFANHEMEKTYHAIVRGWIEESGRLDYALKVELDKIADKHA----SQD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EM+P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQEAVTDYRPLAKAEVPHSTGKFPTTRYCLMEMKPLTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 -----KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
                K+   F+  + S   ++L LHA  +   HP  G +L I A + +    TW  L  
Sbjct: 180 THGDGKHNKLFRDVYES---HRLLLHASSLSFIHPFSGEKLVIKAAVDS----TWQRLCE 232

Query: 325 KYD 327
           ++D
Sbjct: 233 EFD 235


>gi|291615429|ref|YP_003525586.1| pseudouridine synthase [Sideroxydans lithotrophicus ES-1]
 gi|291585541|gb|ADE13199.1| pseudouridine synthase [Sideroxydans lithotrophicus ES-1]
          Length = 208

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 61/207 (29%), Positives = 101/207 (48%), Gaps = 28/207 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+Y+D  + + NKPAG+    G G        L + +  +     + HRLD  TSG++V 
Sbjct: 9   LIYQDDYLLLVNKPAGLLAVPGRGADKQ--DCLSARLQLQFPDALVVHRLDMATSGLMVF 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKK---ECIANWLLKKSHIGGDYVHV 215
           AR       L+  FR R + K Y ++V G   P+  +      A+W  +          +
Sbjct: 67  ARGARMQSRLSNMFRDREVGKRYVAVVAGRLEPETGEVDLPIAADWPKRP---------L 117

Query: 216 VKQNEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            K + +    +++ ++++  D  A +   +E++P TGRTHQLRVH   +G PI+GD  Y 
Sbjct: 118 RKIDSELGKPSLTRYRLLELDVSASR---VELEPFTGRTHQLRVHMAAIGHPILGDALY- 173

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
               G+ +S    +L LHA ++   HP
Sbjct: 174 ----GDESS--APRLLLHASWLSFAHP 194


>gi|323491101|ref|ZP_08096291.1| 23S rRNA pseudouridine synthase D [Vibrio brasiliensis LMG 20546]
 gi|323314648|gb|EGA67722.1| 23S rRNA pseudouridine synthase D [Vibrio brasiliensis LMG 20546]
          Length = 326

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 119/242 (49%), Gaps = 34/242 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  I V NKP G  V  G+G     DG + + +     +  + PR  + HRLD++T
Sbjct: 86  IVYEDDDILVINKPRGFIVHPGAGTP---DGTVLNALLHHYPNIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           +G++VVA+T  A   L  + + +R   + Y ++  G         A   +++  IG    
Sbjct: 143 TGLMVVAKTVPAQTRLVRALQKKRNFTREYEAIAIG------RMTAGGRIEQP-IGR--- 192

Query: 214 HVVKQNEKGAN----YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           H  K+     +     A++H++V + F ++   + ++  TGRTHQ+RVH  ++  P++GD
Sbjct: 193 HSTKRTLMAVSPMGKPAVTHYRVAEHF-REHTRIRLRLETGRTHQIRVHMSYLQHPLLGD 251

Query: 270 HKYC------ANFKGNFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
             Y       A       + I+  ++  LHA  +   HP  G  ++  AP+P  MV+  +
Sbjct: 252 SAYGGRARIPAGASEELATMIRQFDRQALHAVMLKFEHPITGEEVEFHAPVPDDMVEMAE 311

Query: 321 SL 322
           +L
Sbjct: 312 AL 313


>gi|256964482|ref|ZP_05568653.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|256954978|gb|EEU71610.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
          Length = 287

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 115/260 (44%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 40  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 144 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 258 -----ARLMLHASQLHLLHP 272


>gi|119717276|ref|YP_924241.1| ribosomal large subunit pseudouridine synthase D [Nocardioides sp.
           JS614]
 gi|119537937|gb|ABL82554.1| ribosomal large subunit pseudouridine synthase D [Nocardioides sp.
           JS614]
          Length = 312

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 72/273 (26%), Positives = 130/273 (47%), Gaps = 28/273 (10%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           +++ +G V VD   V  ++R+  G  V +   + A           D    + +  + +K
Sbjct: 38  ELIAAGNVLVDGAPVGKSDRVLPGSTVAVTIPVEA-----------DPLAVVPEVVEGIK 86

Query: 99  SILLYEDSKIYVFNKPAGISVQ-----GGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQ 152
             +L++D  I V +KP G++V       G  +  H+ G   +       ++  +  RLD 
Sbjct: 87  --ILHDDDDIVVIDKPVGVAVHPSPGWSGPTVVGHLAGAGFRISTSGAPERQGIVQRLDV 144

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V+ ++  A   L  +FR R + K+Y +LV G P   +  I   + +  H   DY
Sbjct: 145 GTSGVMVICKSEHAYSVLKNAFRRRTVDKVYHALVQGHPDPLEGTIDAPIGR--HPKADY 202

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              V  + +   ++++H++ ++  A +F   LE+   TGRTHQ+RVH   +  P VGD  
Sbjct: 203 KFAVMADGR---HSVTHYETLE--AHRFASLLEIHLETGRTHQIRVHMAALKHPCVGDPT 257

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           Y A+        ++ + +LHA  +   HPE G+
Sbjct: 258 YGADPSLARRVGLERQ-WLHAVRLGFEHPETGK 289


>gi|164687176|ref|ZP_02211204.1| hypothetical protein CLOBAR_00817 [Clostridium bartlettii DSM
           16795]
 gi|164603600|gb|EDQ97065.1| hypothetical protein CLOBAR_00817 [Clostridium bartlettii DSM
           16795]
          Length = 326

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/219 (28%), Positives = 106/219 (48%), Gaps = 15/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGI 157
           ++Y+D  + + +KP  + V    S     +   +  ++  KG+  K R  +RLD  TSG+
Sbjct: 111 IIYDDFDLIMVDKPPFMVVHPTKSHFENTMANGVTDYIIKKGEDVKIRFVNRLDMNTSGL 170

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA+   A   L+   +    +K Y ++V GI +  +  I   + + +    D V  V 
Sbjct: 171 VIVAKNPFAQHVLSSEMKDDDFEKKYITVVKGIIEEDEGTINQPIYRPT---DDSVKRV- 226

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +E+G   +I+H+KVI+        +E++  TGRTHQ+RVH  H+G PI+GD  Y     
Sbjct: 227 VDERGQE-SITHYKVIERLNDA-TIVEVKLETGRTHQIRVHMEHIGHPIIGDELY----- 279

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           G     +  +  LHA  +    P     L+  A +P  M
Sbjct: 280 GFVDENLIKRQALHAYSLKFRQPRTKELLEFKADIPEDM 318


>gi|332874770|ref|ZP_08442640.1| pseudouridine synthase A [Acinetobacter baumannii 6014059]
 gi|332737031|gb|EGJ67988.1| pseudouridine synthase A [Acinetobacter baumannii 6014059]
          Length = 196

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/209 (31%), Positives = 101/209 (48%), Gaps = 21/209 (10%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAA 167
           V +KP+ I    G G  +  D  L   V     +PR  L HRLD++TSGILV   ++   
Sbjct: 2   VIHKPSDILSVPGKGDLH--DSVLTRLV---AIEPRTLLIHRLDRDTSGILVFGLSKRGQ 56

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             +   F+ R+  KIY +LV G  + +       +   S      +H+V  +      A+
Sbjct: 57  SAIARQFQDRQTSKIYEALVAGHLEGEGTVDIPVVYDPSR---PPLHIVDASHN--KPAL 111

Query: 228 SHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           +H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD  Y A  +      +
Sbjct: 112 THWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDTLYAAPEQL-----L 166

Query: 285 QNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             +L LHA+ +   HP  G  L    P+P
Sbjct: 167 VPRLCLHAKQLSFNHPVTGESLTFNCPVP 195


>gi|291522040|emb|CBK80333.1| Pseudouridylate synthases, 23S RNA-specific [Coprococcus catus
           GD/7]
          Length = 234

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 65/211 (30%), Positives = 102/211 (48%), Gaps = 19/211 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPR----LTHRLDQETS 155
           +LYED  I V  KPAG++ Q    +   +  +LK++ V  K  K      + HRLD+   
Sbjct: 6   ILYEDKDIIVVVKPAGMASQEERSVDVDMVSWLKTYLVRQKKVKGMPYIGVIHRLDKPVG 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T+ AA  L+E  R  ++ K Y +++ G    K+  + + LL  S+   +   V
Sbjct: 66  GVMVYAKTQQAAAKLSEQVRNNKMTKEYLAVLTGNLPKKEGRLEDMLL--SNGKTNRTEV 123

Query: 216 VKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V     GA  A+  +KV        Q++  + +   TGR HQ+RV   H G  + GD +Y
Sbjct: 124 VDAKTSGAKKAVLEYKVKRTKFEEGQQYSLVNVHLITGRRHQIRVQMAHAGAGLWGDTRY 183

Query: 273 CANF---KGNFTSPIQNKLYLHARYMDLPHP 300
              F   KG F       L L A +++  HP
Sbjct: 184 NPVFTDKKGWFD------LALFAWHLEFDHP 208


>gi|284008525|emb|CBA75052.1| tRNA pseudouridine synthase C [Arsenophonus nasoniae]
          Length = 248

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/222 (30%), Positives = 105/222 (47%), Gaps = 17/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +L++D  +   +KPAG  V   S +  H   F+   V D  GQ     HRLD+ TSG+L+
Sbjct: 1   MLFQDQHLIAIHKPAGWLVHR-SWLDRHETRFVMQTVRDQIGQYVFPVHRLDKPTSGVLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVK 217
           +A +   A  L + F    ++K Y ++V G     +  I ++ LK  K  I   Y   + 
Sbjct: 60  MALSSEVACLLAQQFEYHAVEKKYHAIVRGY--VNEAGIIDYPLKEEKDKIADKYASKIS 117

Query: 218 QNEKGANYAISHFKVIDCFAQ-------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
           Q +    +  S    ++C  +       +F  L ++P TGR HQLR H  H+  PI+GD 
Sbjct: 118 QPQSCITH-YSPLAKVECPIEIGRYPTSRFSLLALKPKTGRKHQLRRHMAHVRHPIIGDT 176

Query: 270 -HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
            H      +G       ++L LHA Y+   HP  G +LQ+ A
Sbjct: 177 THGDLRQNRGVAHHFATSRLMLHASYLSFKHPMTGDKLQLIA 218


>gi|323489453|ref|ZP_08094682.1| putative RNA pseudouridine synthase yhcT [Planococcus donghaensis
           MPA1U2]
 gi|323396947|gb|EGA89764.1| putative RNA pseudouridine synthase yhcT [Planococcus donghaensis
           MPA1U2]
          Length = 281

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/205 (31%), Positives = 94/205 (45%), Gaps = 20/205 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +L+ED    V  KP G++    + G    + I+  L   + + G      HRLDQ TSG+
Sbjct: 79  VLFEDDHFIVARKPKGMATHPNEVGQTDTF-INAILGHIIRNGGSYGEHVHRLDQGTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+   A   L      +++ + Y ++V G   NK   I         IG D  H  +
Sbjct: 138 LMVAKHPVAKNVLDRMLEQKQLVRDYEAVVKGKVHNKSGTI------DFAIGRDRHHPTR 191

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +   +    A++H++V+     K   L +   TGRTHQ+R H  H+G PIVGD  Y    
Sbjct: 192 RMVSQTGQSAVTHYRVLKLMEGK-SLLHLTLETGRTHQIRTHLSHIGHPIVGDTLYDG-- 248

Query: 277 KGNFTSPIQNKLY-LHARYMDLPHP 300
                 P Q+  Y LHA  M   HP
Sbjct: 249 -----PPTQDGAYHLHAFRMSFIHP 268


>gi|116329941|ref|YP_799659.1| pseudouridylate synthase, 23S RNA-specific [Leptospira
           borgpetersenii serovar Hardjo-bovis JB197]
 gi|116123630|gb|ABJ74901.1| Pseudouridylate synthase, 23S RNA-specific [Leptospira
           borgpetersenii serovar Hardjo-bovis JB197]
          Length = 312

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 84/325 (25%), Positives = 143/325 (44%), Gaps = 63/325 (19%)

Query: 20  RLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRV--KFNNRIQSGQ--VVRIPPVINAL 74
           RLDR+ K  +   ++   +QK +  G VR   +++  K + ++++G+   + IPP     
Sbjct: 17  RLDRFLKFSFGDEMSRATIQKWIECGYVRNQDRKICDKSSWKVKTGEQYFLSIPP----- 71

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGF 132
                        +NL      L  +L  ED    + +KP GI+   G G      ++G 
Sbjct: 72  ----------RPPLNLEPIPMTLPVVLERED--YLIIHKPPGIASHSGPGDRSPSLVNGL 119

Query: 133 L---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L   K      G+ +P + HRLD+ T G++++ +   A   L+E FR R I+K Y++ + 
Sbjct: 120 LHHFKELSKVGGEARPGIVHRLDKPTEGLMLIPKNDRAHGKLSELFRKREIEKKYYAWIQ 179

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----AQKFCWLE 244
           G    +   I +  + +  I    + V  +  K    +++H+KV+        +KF ++E
Sbjct: 180 GHLPAETGTI-DLPIARHPIERLKMTVSPKGRK----SVTHYKVLKYVNSRSGRKFSFVE 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------------FKGNFTSP-IQN 286
           +   TGRTHQ+R+H     CP+VGD  Y                    FK  FT   I+ 
Sbjct: 235 VGLETGRTHQIRIHFQSQRCPVVGDLLYSRTGSQFESYGLQLLSYYLKFKDPFTGEMIEA 294

Query: 287 KLYLHARYMDLPHPEGGRLQITAPL 311
            L L  R++        R +  APL
Sbjct: 295 TLALSERFL--------RFEKNAPL 311


>gi|331664352|ref|ZP_08365258.1| tRNA pseudouridine synthase C [Escherichia coli TA143]
 gi|331058283|gb|EGI30264.1| tRNA pseudouridine synthase C [Escherichia coli TA143]
          Length = 260

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFAQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|307260687|ref|ZP_07542377.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 12
           str. 1096]
 gi|306869608|gb|EFN01395.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 12
           str. 1096]
          Length = 216

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/198 (30%), Positives = 96/198 (48%), Gaps = 24/198 (12%)

Query: 98  KSILLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           K  + ++     V +KP G+SV   +   G+  ++   L++      ++  L HRLD+ T
Sbjct: 4   KLTICFQHHDFVVIDKPVGVSVHKDEEAIGLTENLAEQLQA------EQVWLVHRLDKVT 57

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+ A  + AA H    F   +I+K YW+L    PK K+  I+   ++KS  G   + 
Sbjct: 58  SGLLIFALNKQAAVHFYHLFEQHKIEKTYWALSDQKPKKKQGKISG-DMQKSRNGAWKLF 116

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             KQN      A++ F V            +QP TG+THQLRV    +G PI+GD +Y  
Sbjct: 117 HSKQNP-----AVTQF-VSHSLEPNLRHFILQPKTGKTHQLRVAMKSLGSPILGDQRYAG 170

Query: 275 NFKGNFTSPIQNKLYLHA 292
                      +++YLHA
Sbjct: 171 M--------AADRVYLHA 180


>gi|238784871|ref|ZP_04628871.1| tRNA pseudouridine synthase C [Yersinia bercovieri ATCC 43970]
 gi|238714188|gb|EEQ06200.1| tRNA pseudouridine synthase C [Yersinia bercovieri ATCC 43970]
          Length = 257

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 101/222 (45%), Gaps = 17/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +     + +
Sbjct: 64  ALSSDVARALSLQFEQHQIQKTYHAVVRGYVLEGGTVDYEMTEELDKIADKF----SRPD 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
           K    +++H + +               +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHHQPLAQVEMPVAIGRYDTARFSLMELKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 270 -HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
            H      +G       ++L LHA +++L HP  G  L +TA
Sbjct: 180 THGDLRQNRGVAQHFDCSRLMLHASHLELNHPVTGEALSLTA 221


>gi|188996123|ref|YP_001930374.1| pseudouridine synthase, RluA family [Sulfurihydrogenibium sp.
           YO3AOP1]
 gi|188931190|gb|ACD65820.1| pseudouridine synthase, RluA family [Sulfurihydrogenibium sp.
           YO3AOP1]
          Length = 318

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 80/295 (27%), Positives = 134/295 (45%), Gaps = 36/295 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           VE +  N RLD++    YP  +    Q ++ +  V +D   V K + ++++GQ   I   
Sbjct: 9   VEEEFSNKRLDQFLALVYPEYSRSFYQNLIENRFVLLDNNPVRKSSTKVKTGQEFTIIIP 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 I  E   L+               + YED  + V  KP G+ V    G   H  
Sbjct: 69  PPEPLEIEPENIPLE---------------IYYEDEDLAVVYKPPGMVVHPSVG---HTS 110

Query: 131 GFL--------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G L        K+    +G ++  + HRLD++T+G+L+VA++  A + L + F+ R I K
Sbjct: 111 GTLVNALLYHFKNVSQYQGKERAGIVHRLDKDTAGLLIVAKSEFAHKELQKMFQDREIDK 170

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KF 240
            Y ++V GI K K   + +  + +S      +  V  N K    A++ + V   F +   
Sbjct: 171 KYKAIVSGIVK-KDHGLIDLPIGRSIYNRQKMGTVATNPKD---ALTEYWVEKRFEKHNL 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHA 292
             ++++ HTGRTHQ+RVH   +G P+  D  Y    +N   +    + +KL  HA
Sbjct: 227 TLVDIKLHTGRTHQIRVHFSAIGHPLFNDFVYGFKKSNLSSDLAKNLSDKLKYHA 281


>gi|51599066|ref|YP_073254.1| hypothetical protein BG0840 [Borrelia garinii PBi]
 gi|51573637|gb|AAU07662.1| conserved hypothetical protein [Borrelia garinii PBi]
          Length = 315

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 78/306 (25%), Positives = 143/306 (46%), Gaps = 46/306 (15%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-----LRSGQVRVDKKRVKF 55
           M L  Y+   V+ ND    RLD         I  +N  K+     +R G +R++  +  F
Sbjct: 1   MRLDKYIFLEVLANDN-GKRLDSIL------IKILNFSKVRIIKHIRKGDIRLNGLKPHF 53

Query: 56  NNRIQSGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
           + R+  G  + +   ++ +LN  + E     S+++       ++  ++YEDS + V +K 
Sbjct: 54  SYRVCKGDKIYLYKSLVQSLNLAMGE--CYKSNIDFQ----CIRKRIIYEDSDLLVMDKQ 107

Query: 115 AGISVQGG-SGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
            GI V GG + + + ++ +L +  + S   KP   HRLD+ TSGI++ A+   AA+ L+ 
Sbjct: 108 RGILVHGGKNSLDFLVNSYLLREDLRSLSFKPSAVHRLDRNTSGIIIFAKNINAARKLST 167

Query: 173 SFRMRRIQKIYWSLVWGIPKN----KKECIANWLLKKSHI--GGDYVHVVKQNEKGANYA 226
           +F    + K Y++++ G  K+    K     N  LKK+ +    D+++ + +     N  
Sbjct: 168 AFSSGSVTKKYFAILLGEVKSTVLYKNHLFRNQRLKKTFVLEDKDFINAITK----VNPI 223

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           +S        +++    E+   TG THQ+R        P++ D KY   FK       ++
Sbjct: 224 LS--------SKRATLAEIVIETGFTHQIRSQCSFNDHPLINDKKYHDKFK-------KS 268

Query: 287 KLYLHA 292
             +LHA
Sbjct: 269 DYFLHA 274


>gi|320457791|dbj|BAJ68412.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 317

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 71/271 (26%), Positives = 122/271 (45%), Gaps = 36/271 (13%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++ SGQ RV  + V  ++ +Q+G+ V           + +EQ   +              
Sbjct: 31  LVDSGQARVLGREVARSSTLQAGETVEF--------DLAEEQAGPEPIAT--------DM 74

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQE 153
            ++YED  + V +KP G++     G     + G L+     + S G   R  +  RLD  
Sbjct: 75  AVVYEDDDVIVVDKPVGVAAHASVGWTGPTVLGSLRDRGVHIASYGAAGREGIVSRLDVG 134

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG---- 209
           TSG+++V ++  A   +   F    ++K Y +LV G  K  K  I      ++ IG    
Sbjct: 135 TSGLMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQGGLKENKATI------EAPIGRAKV 188

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            D+   V    K    A++H+ V++ F  +   + +   TGRTHQ+RVH   +G P+ GD
Sbjct: 189 SDFRFCVTPAGK---PAVTHWDVLERFGHEATLVSVNLETGRTHQIRVHFSSIGHPLCGD 245

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             Y AN   +    + ++ +LHA  ++  HP
Sbjct: 246 PMYGANPVLSEALGL-DRQWLHAMKLEFRHP 275


>gi|257899597|ref|ZP_05679250.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium Com15]
 gi|293571564|ref|ZP_06682586.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E980]
 gi|257837509|gb|EEV62583.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium Com15]
 gi|291608370|gb|EFF37670.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E980]
          Length = 299

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 76/274 (27%), Positives = 121/274 (44%), Gaps = 32/274 (11%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS----ILLYEDSKIYVFNK 113
           + Q GQ+     V N L  + K+ K+        +H   L       ++YED  + V NK
Sbjct: 33  KFQGGQIKVNDQVENVLFSLAKDDKVTIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNK 92

Query: 114 PAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTH---RLDQETSGILVVARTRAA 166
           PAG+S        YH +G +    K++   +G + ++ H   RLD++TSG+++ A+   A
Sbjct: 93  PAGVSSIPAQ---YHPNGTMANRVKAYYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFA 149

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI----GGDYVHVVKQNEKG 222
              L    R ++  K Y +LV G+  N        L    HI      DY  ++K+    
Sbjct: 150 HAKLDTQLREKKFVKKYQALVSGMLSN--------LSAHGHIDLPIARDYSSLLKRMVSN 201

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              +      I+    +   +++Q HTGRTHQ+RVH   +GC ++GD  Y     G    
Sbjct: 202 EGRSAQTEYWIEKRLTEIALVDIQLHTGRTHQIRVHFSAIGCALLGDDMYS----GRMDL 257

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            I+ +  LH   +   HP     L+   PL A M
Sbjct: 258 GIKRQA-LHCYDLRFYHPFTEELLEFKQPLAADM 290


>gi|116329455|ref|YP_799175.1| pseudouridylate synthase, 23S RNA-specific [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
 gi|116122199|gb|ABJ80242.1| Pseudouridylate synthase, 23S RNA-specific [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
          Length = 312

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 84/325 (25%), Positives = 144/325 (44%), Gaps = 63/325 (19%)

Query: 20  RLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRV--KFNNRIQSGQ--VVRIPPVINAL 74
           RLDR+ K  +   ++   +QK +  G VR   +++  K + ++++G+   + IPP     
Sbjct: 17  RLDRFLKFSFGDEMSRATIQKWIECGYVRNQDRKICDKSSWKVKTGEQYFLSIPP----- 71

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGF 132
                        ++L      L  +L  ED    + +KP GI+   G G      ++G 
Sbjct: 72  ----------RPPLSLEPIPMTLPVVLERED--YLIIHKPPGIASHSGPGDRSPSLVNGL 119

Query: 133 L---KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L   K      G+ +P + HRLD+ T G++++A+   A   L+E FR R I+K Y++ + 
Sbjct: 120 LHHFKELSKVGGEARPGIVHRLDKPTEGLMLIAKNDRAHGKLSELFRKREIEKKYYAWIQ 179

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----AQKFCWLE 244
           G    +   I +  + +  I    + V  +  K    +++H+KV+        +KF ++E
Sbjct: 180 GHLPAETGTI-DLPIARHPIERLKMTVSPKGRK----SVTHYKVLKYVNSRSGRKFSFVE 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----------------FKGNFTSP-IQN 286
           +   TGRTHQ+R+H     CP+VGD  Y                    FK  FT   I+ 
Sbjct: 235 VGLETGRTHQIRIHFQSQRCPVVGDLLYSRTGSQFESYGLQLLSYYLKFKDPFTGEMIEA 294

Query: 287 KLYLHARYMDLPHPEGGRLQITAPL 311
            L L  R++        R +  APL
Sbjct: 295 TLALSERFL--------RFEKNAPL 311


>gi|262280059|ref|ZP_06057844.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           calcoaceticus RUH2202]
 gi|262260410|gb|EEY79143.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           calcoaceticus RUH2202]
          Length = 350

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 113/248 (45%), Gaps = 36/248 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP G+ V  G+G         + YH          S+  +  L HR+D
Sbjct: 117 IVYEDDDILVINKPVGMVVHPGAGNSSGTLVNALLYHFPKL------SELSRAGLVHRID 170

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA++  A   L++    + + ++Y  +V+G        IA   + +  I   
Sbjct: 171 KDTSGLLVVAKSLEAQFSLSKQLANKSVYRVYDLVVYG------NIIAGGTIDEP-IKRH 223

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V  VK     G   A++H+ V + F + F  ++ +  TGRTHQ+RVH  ++G  ++GD 
Sbjct: 224 PVDRVKMAILPGGRDAVTHYNVKERF-RDFTRVQARLETGRTHQIRVHFSYIGYGLIGDQ 282

Query: 271 KYCANFK--GNFTSPIQNKL------YLHARYMDLPHPEGG-RLQITAPLP---AHMVKT 318
            Y    +     +  + + L       LHA  + L HP  G  +    P P    H+V  
Sbjct: 283 IYMNRVRVPAGASELLIDTLRGFKRQALHAAKLGLKHPRTGEEMLFEVPWPEDFTHLVNV 342

Query: 319 WDSLGFKY 326
             S    Y
Sbjct: 343 LRSENAAY 350


>gi|261344742|ref|ZP_05972386.1| hypothetical protein PROVRUST_06000 [Providencia rustigianii DSM
           4541]
 gi|282567184|gb|EFB72719.1| tRNA pseudouridine synthase C [Providencia rustigianii DSM 4541]
          Length = 252

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/246 (26%), Positives = 108/246 (43%), Gaps = 49/246 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKPAG+ V              +SW+DSK             GQ     
Sbjct: 4   IIYQDEFVVAVNKPAGMLVH-------------RSWLDSKETVFVMQTLRDQIGQHVYPI 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L+ A +   A+ L E F   +++K Y ++V G   + +      L +   
Sbjct: 51  HRLDRPTSGVLLFALSSEVARLLAEQFEQHKMEKTYHAVVRGYVTDAQRLDYPLLEELDK 110

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVI---DC-------FAQKFCWLEMQPHTGRTHQLRV 257
           I   +       E      ++H++ +   +C          +F  +E++P TGR HQLR 
Sbjct: 111 IADKHA----SKEPKLQDCVTHYRPLVTAECPVAIGRYETSRFSLVELKPETGRKHQLRR 166

Query: 258 HALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           H  H+  PI+GD K+      +G       ++L LHA  +   HP     QI+      +
Sbjct: 167 HMSHLRHPILGDSKHGDLRQNRGVVEHFGVSRLMLHASQLVFIHPITEE-QIS------L 219

Query: 316 VKTWDS 321
           V +WD+
Sbjct: 220 VASWDA 225


>gi|157148329|ref|YP_001455648.1| tRNA pseudouridine synthase C [Citrobacter koseri ATCC BAA-895]
 gi|157085534|gb|ABV15212.1| hypothetical protein CKO_04146 [Citrobacter koseri ATCC BAA-895]
          Length = 260

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/225 (27%), Positives = 105/225 (46%), Gaps = 36/225 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--- 217
             +  A + L + F   +IQK Y ++V G           WL+ ++ +  DY  V +   
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMDEAVL--DYPLVEELDK 110

Query: 218 ------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALH 261
                 + +KG   A++H++ +               ++  +E++P TGR HQLR H  H
Sbjct: 111 IADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAH 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG 303
           +  PI+GD K+  + + N ++       +L LHA  + L HP  G
Sbjct: 171 LRHPIIGDSKH-GDLRQNRSAAEHFGCQRLMLHASQLTLTHPFTG 214


>gi|324119833|gb|EGC13712.1| RNA pseudouridylate synthase [Escherichia coli E1167]
          Length = 260

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/256 (26%), Positives = 112/256 (43%), Gaps = 69/256 (26%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFVREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGRL 305
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGE- 215

Query: 306 QITAPLPAH--MVKTW 319
               PL  H  +  TW
Sbjct: 216 ----PLTIHACLDDTW 227


>gi|304317468|ref|YP_003852613.1| pseudouridine synthase [Thermoanaerobacterium thermosaccharolyticum
           DSM 571]
 gi|302778970|gb|ADL69529.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 286

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 74/255 (29%), Positives = 125/255 (49%), Gaps = 29/255 (11%)

Query: 71  INALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           I+ +N IIK+  I++      N++   + +   + YED  I V NK AG+ V   +G   
Sbjct: 43  ISIVNRIIKKGDIIELYLDDDNVSVKPEKMDLHICYEDDDILVVNKDAGVVVHPTAG--- 99

Query: 128 HIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H DG L + V      ++     R  +RLD++TSG+++ A+      +L     M+   K
Sbjct: 100 HPDGTLANGVAWYYEKNNINAPIRPVNRLDRDTSGLIIFAKNPFMQNYLQIVCPMK---K 156

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G  +++       L  K   G     +V  +    + A++ F V+    +K  
Sbjct: 157 FYIAIVRGDLEDRGTI---DLPIKRKPGSTIERMVDDD---GDKAVTDFYVLK-RGEKLS 209

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++  TGRTHQ+RVH  H+G PI+GD  Y     G+ TS I+ +  LHA  +    P 
Sbjct: 210 LVKLELKTGRTHQIRVHLSHIGHPIIGDTLY-----GSDTSYIKRQA-LHAYRITFRQPF 263

Query: 302 GGR-LQITAPLPAHM 315
            G+ + I +P+P  M
Sbjct: 264 IGKCISIYSPIPDDM 278


>gi|308187414|ref|YP_003931545.1| ribosomal large subunit pseudouridine synthase A [Pantoea vagans
           C9-1]
 gi|308057924|gb|ADO10096.1| ribosomal large subunit pseudouridine synthase A [Pantoea vagans
           C9-1]
          Length = 243

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 99/226 (43%), Gaps = 17/226 (7%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           F K  LL++D  + V NKP G+    G     ++D      V  +     L HRLD  TS
Sbjct: 25  FDKITLLFQDDHLLVINKPGGLLSLSGKN-PQNLDSVHHRLV-KRFPGCTLVHRLDFGTS 82

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++VVAR +A    L + F  R + K Y +L+ G   + +  I   + K   +    V  
Sbjct: 83  GLMVVARNKAINAALCQQFSQRTVSKTYQALLCGHLADDEGVIDAAIAKDPALFPRMVIC 142

Query: 216 VKQNEKG-ANYAI---SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             Q +   + Y +   S ++  +        +E+ P TGRTHQLR+H   +G PI+G   
Sbjct: 143 AAQGKPARSRYRVTERSFYRRKEGKELPVTRVELTPETGRTHQLRIHCQQLGHPILGCDL 202

Query: 272 YCANFKGNFTSP---IQNKLYLHARYMDLPHPEGGR---LQITAPL 311
           Y     G    P      +L LHA  +   HP  G    L  T+P 
Sbjct: 203 Y-----GGLVLPGAEQAERLMLHASGLTFVHPVSGETLHLSATSPF 243


>gi|297626700|ref|YP_003688463.1| Pseudouridylate synthase, Uncharacterized RNA pseudouridine
           synthase [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
 gi|296922465|emb|CBL57038.1| Pseudouridylate synthase, Uncharacterized RNA pseudouridine
           synthase [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
          Length = 306

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/277 (24%), Positives = 127/277 (45%), Gaps = 39/277 (14%)

Query: 40  ILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           ++  G+V +D   V K + R++ GQ + I      L+   +  ++  + V   +      
Sbjct: 33  LIGEGKVLLDGSTVVKASERVRGGQTIDID-----LSEPTRVARVTPAVVEGMR------ 81

Query: 99  SILLYEDSKIYVFNKPAGIS------------VQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
             ++++D+ I V +KPAG++            V G +G  + I            ++  +
Sbjct: 82  --IVHDDADIVVVDKPAGVAAHPSVGWDGPDVVSGLAGAGFRIS------TSGAAERQGI 133

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  TSG++VVA++  A   L  +FR R + K Y +LV G     +  I   + +  
Sbjct: 134 VHRLDVGTSGLMVVAKSERAYTLLKRAFRDRTVDKYYLTLVQGHLDASEGTIGAPIGR-- 191

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           H G ++   V  + +    +++H++ ++   +    L +   TGRTHQ+RVH   +  P 
Sbjct: 192 HPGSEWKFAVTADGR---PSVTHYETVEMM-RGASLLRVHLETGRTHQIRVHFAALHHPC 247

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           VGD  Y A+        ++ + +LHA  +   HP  G
Sbjct: 248 VGDPLYGADPVLAAQLGLERQ-WLHAADLGFVHPGNG 283


>gi|257866939|ref|ZP_05646592.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257873272|ref|ZP_05652925.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257800995|gb|EEV29925.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257807436|gb|EEV36258.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
          Length = 284

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/209 (28%), Positives = 98/209 (46%), Gaps = 25/209 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK---SWVDSKGQKPRLTHRLDQET 154
           K  +L+ED  + V NKPAG+       +    D  L    +++  K Q+P + HRLD+ET
Sbjct: 80  KVDVLFEDEHLLVLNKPAGVKTHPNQPL--EADTLLNDAAAYLAPKQQQPYVVHRLDKET 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L      ++I + Y + VWG    + + IA  + +  H     + 
Sbjct: 138 SGVVLFAKNPLVLPILGRMLENKQIFRRYQATVWG-KLTQDQTIAKKIGRDRHDRRKRI- 195

Query: 215 VVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               + +    A++H  +     +    +C L+    TGRTHQ+RVH   +G P+VGD  
Sbjct: 196 ---IDPRNGQSAVTHVTIAHTQQKTTDVYCVLD----TGRTHQIRVHLASIGHPVVGDPL 248

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y      N  +P   +L LH   + L HP
Sbjct: 249 Y-----QNKPAP---RLLLHGYELHLEHP 269


>gi|87119362|ref|ZP_01075260.1| putative ribosomal large subunit pseudouridine synthase A
           [Marinomonas sp. MED121]
 gi|86165753|gb|EAQ67020.1| putative ribosomal large subunit pseudouridine synthase A
           [Marinomonas sp. MED121]
          Length = 212

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/210 (31%), Positives = 98/210 (46%), Gaps = 30/210 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSG 156
           +LYED    V NKPA      G G         +  V  + Q    +    HRLD  TSG
Sbjct: 9   ILYEDEWFAVINKPANFLSVPGRGPEK------QDSVTHRAQCLFGEAHAVHRLDFATSG 62

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-----KECIANWLLKKSHIGGD 211
           +++VA+T  + + L+E FR RR+QK Y +++ G    +     K  I +W  +   I   
Sbjct: 63  LILVAKTLESHKRLSEHFRERRVQKEYRAILRGKVLAQEGVVNKPLICDWPNRPRQI--- 119

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            VH      +    A +H+K +          + + P TGR+HQLRVH   M  PI+GD 
Sbjct: 120 -VH-----REWGKAATTHWKKLKTPPGSIHSHVALFPITGRSHQLRVHMQSMSHPILGDE 173

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            Y A      +SP   +L+LHA  ++  HP
Sbjct: 174 FYDA-----LSSPADERLHLHAYRLEFNHP 198


>gi|163744079|ref|ZP_02151445.1| ribosomal large subunit pseudouridine synthase A [Phaeobacter
           gallaeciensis 2.10]
 gi|161382626|gb|EDQ07029.1| ribosomal large subunit pseudouridine synthase A [Phaeobacter
           gallaeciensis 2.10]
          Length = 217

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 111/230 (48%), Gaps = 21/230 (9%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           S + T  +D L   +L+ D+++ V NKP G+    G G   H+   L S + +   +  L
Sbjct: 4   SSDYTPPTDPLD--ILHHDAQLLVVNKPHGLLSVPGRG--EHLADCLLSRLQAVFPEALL 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG++V   T  A +HL+  F  R  +K Y + V G  + +   +   L+   
Sbjct: 60  VHRLDRDTSGVMVFGVTPHAQRHLSMQFEKRSAKKAYVARVDGRLEPRSGTVDLPLIV-- 117

Query: 207 HIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               D+ +  +Q         A++ ++V+  +      + + P TGR+HQLRVH L +G 
Sbjct: 118 ----DWPNRPRQMVCHDTGKEAVTDWRVMK-YEDTATRVRLTPKTGRSHQLRVHMLSLGH 172

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAPL 311
            I+GD  Y      +       ++ LHA  + + HP+ G   + ++ AP 
Sbjct: 173 AILGDPLYAEGHALD-----HPRMMLHAEELRIKHPDSGESMKFRVKAPF 217


>gi|77360598|ref|YP_340173.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875509|emb|CAI86730.1| conserved protein of unknown function ; putative 23S rRNA
           pseudouridylate synthase. In E.coli Pseudouridine
           synthases are responsible for synthesis of pseudouridine
           from uracil in 23S rRNA [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 226

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/197 (30%), Positives = 89/197 (45%), Gaps = 20/197 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++  S  Y+  KPAG++            GF+        +K    HRLD+ TSG+L++
Sbjct: 11  VVHSHSDFYILAKPAGLNFHSEDAA-----GFVVLAEQQLNEKLFAVHRLDKVTSGLLIL 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR + AA   T+ F    I K Y ++    PK K+  I    + KS  G       K   
Sbjct: 66  ARNKLAAAKFTQMFTEHTINKFYLAISDAKPKKKQGWIKG-DMAKSRRG-----TFKLLT 119

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             AN AIS F  +  +   F    ++P++G+THQLRV    +G PI+GD  Y        
Sbjct: 120 TTANPAISRFYSV-SYKPGFRGYILKPYSGKTHQLRVALKSIGAPILGDTSYAGAHSA-- 176

Query: 281 TSPIQNKLYLHARYMDL 297
                 + YLHA  +D 
Sbjct: 177 ------RTYLHAFALDF 187


>gi|319938961|ref|ZP_08013325.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319812011|gb|EFW08277.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 296

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 112/218 (51%), Gaps = 18/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS---KGQKPRLTHRLDQETSGI 157
           ++YED    + NKP+G++       +  +  F+K++  +   + Q+  +  RLD++TSG+
Sbjct: 78  IVYEDKHFLILNKPSGVASIPSVNHSNTMANFVKAYYIANHYENQQIHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G    K E   IA    + S I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQKKVIEKHYYALVKGSAPLKPEGDIIAPIAREDSSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +   K   YA + +KV+  +   +  +++  HTGRTHQ+RVH  ++G P++GD  Y  +
Sbjct: 192 TRCVAKNGKYAHTSYKVLAQYDDIY-LVDIHLHTGRTHQIRVHFSYIGFPLLGDDLYGGS 250

Query: 276 FKGNFTSPIQNKLYLHA-RYMDLPHPEGGRLQITAPLP 312
                T   +  L+ H+ R+ +  H E   +  ++PLP
Sbjct: 251 MTDGIT---RQALHCHSLRFYNPFHEE--VVNKSSPLP 283


>gi|171779340|ref|ZP_02920304.1| hypothetical protein STRINF_01185 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281957|gb|EDT47388.1| hypothetical protein STRINF_01185 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 296

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 109/230 (47%), Gaps = 20/230 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGI 157
           + YED    +FNKP G +       +  I  F+K +   +    +  H   RLD++TSG+
Sbjct: 78  IAYEDDHFLIFNKPHGYASIPSVLHSNTIANFVKYYYMEQNYPNKQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G  +  ++ E IA     +  I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQSKTIEKRYYALVSGQGELEDEGEIIAPIARDEDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++      YA + ++V++ F      ++++ HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVHPSGKYAHTSYRVVERFGD-VALVDIRLHTGRTHQIRVHFAHIGFPLLGDDLYGGC 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                T     +  LH  Y+    P   +  I +   A++   +DS+  K
Sbjct: 251 MDLGIT-----RQALHCHYLRFVDPYTNKEIIQS---ANLTDDFDSVIMK 292


>gi|145354358|ref|XP_001421454.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144581691|gb|ABO99747.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 318

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 74/267 (27%), Positives = 105/267 (39%), Gaps = 56/267 (20%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK----SWVDSKG----------QKPR 145
           + +Y D  +YV NKPA   V     +     G +K    + VD++           +  R
Sbjct: 45  LAVYVDDDVYVLNKPAQTYVHDIERLVER--GMVKCDDATTVDNRATTRDVPFNASESAR 102

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-----KNKKECIAN 200
           + HRLD++TSG LVVAR R A + L+  F    +QK Y +L          ++ +     
Sbjct: 103 VVHRLDRDTSGCLVVARNRDAIRSLSAQFADGTVQKTYVALCAATADYDGVEDHRRVFTG 162

Query: 201 W---------LLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFC--------- 241
           W         L   + IG       K   K A   I   +VI D  A +FC         
Sbjct: 163 WGRAKYGLFRLYDAADIGRALPGNKKVKVKHAETTIIVERVITDGVALRFCEPPTADDAD 222

Query: 242 -------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL------ 288
                       P TGRTHQ+R+H   +G P+VGD +Y          PI          
Sbjct: 223 RRRHRVALARCSPLTGRTHQIRLHCASLGLPLVGDVRYGGPIAATRDGPIDAPFSARRVA 282

Query: 289 --YLHARYMDLPHPEGG-RLQITAPLP 312
              LHA  +   HP+   R+ + AP P
Sbjct: 283 GALLHAERVAFRHPKSNLRVDVHAPRP 309


>gi|239637869|ref|ZP_04678830.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Staphylococcus warneri L37603]
 gi|239596432|gb|EEQ78968.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Staphylococcus warneri L37603]
          Length = 276

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/264 (27%), Positives = 115/264 (43%), Gaps = 42/264 (15%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-- 100
           S  + ++K+  + ++++ SG  V IP           E+K           S++L S   
Sbjct: 34  SKDITINKETSRLSDKVNSGDEVFIP---------TPEEK-----------SNYLPSYRY 73

Query: 101 --LLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
             + YE+    +  KP G+         +  +   L   +DS   +P   HRLDQET G+
Sbjct: 74  AQVYYENDDFAIVLKPKGVKTHPNDLKESNTLMNHLIYTIDSDYVEP--IHRLDQETVGL 131

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+     + L        I +IY + V  +   K + I         IG D  H  K
Sbjct: 132 LIVAKNPLMKKILDRMLEENDITRIYKAHVKALLPIKPQTIDKP------IGKDKFHPNK 185

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +        AI+H    +   +  C LE++  TGRTHQ+RVH   +G P++GD  Y    
Sbjct: 186 KRISNTGQRAITHILSSNMVKENVCELEIKLDTGRTHQIRVHLAEIGHPVIGDPLY---- 241

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
            G+ T     +L LH+  ++L HP
Sbjct: 242 -GDST---LRQLELHSYKIELEHP 261


>gi|210633884|ref|ZP_03297899.1| hypothetical protein COLSTE_01816 [Collinsella stercoris DSM 13279]
 gi|210159053|gb|EEA90024.1| hypothetical protein COLSTE_01816 [Collinsella stercoris DSM 13279]
          Length = 338

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/246 (27%), Positives = 115/246 (46%), Gaps = 30/246 (12%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----------DSKGQ-KPRLTHRLD 151
           YED  + V +K  G+      G   H DG L + +            +G+ +P + HRLD
Sbjct: 87  YEDDYLIVLSKQRGLVCHPAHG---HEDGTLANALVHHCGIEHLGTVQGEDRPGIVHRLD 143

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+     + L    R R + + Y +LV G     +  I   + + +    D
Sbjct: 144 RDTSGLMLAAKDDETQRELQNLIRTRTLDRRYITLVHGEIVMDEGTINTGIARSTR---D 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            V +   ++  A  AI+ F+V++ F      + +  +E   +TGRTHQ+RVH  H+  P+
Sbjct: 201 RVKMAVSDDPFARQAITTFQVLERFEPARGDEGYTLVECHLYTGRTHQIRVHMRHIHHPL 260

Query: 267 VGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
           VGD  Y    KGN    +  ++ +LH+  +   HP  G  +     LP  +    D L  
Sbjct: 261 VGDPLY---GKGNERMNLDLDRQFLHSWSVQFEHPVTGETISCRDELPWDLAAALDEL-- 315

Query: 325 KYDRNL 330
            +DR+L
Sbjct: 316 -HDRSL 320


>gi|89095308|ref|ZP_01168227.1| putative pseudouridine synthase Rlu family protein [Oceanospirillum
           sp. MED92]
 gi|89080427|gb|EAR59680.1| putative pseudouridine synthase Rlu family protein [Oceanospirillum
           sp. MED92]
          Length = 250

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/250 (26%), Positives = 113/250 (45%), Gaps = 40/250 (16%)

Query: 101 LLYEDSKIYVFNKPAGISV-------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +L+ED  +   NKP+G+ V       +G   +A      LK + +  G  P   HRLD+ 
Sbjct: 6   ILFEDDHLIAINKPSGLLVHPSWVAPRGTPNLA----SMLKVYFE--GGSPYTIHRLDRP 59

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGD 211
           TSG+++  +++  AQ +   F  R + K Y  +  G     +    ++ LK+    I   
Sbjct: 60  TSGVILFGKSKEVAQKMNLIFAERDVSKTYLCMCRGY--TPEADTIDYALKEQLDKIADK 117

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFA----------QKFCWLEMQPHTGRTHQLRVHALH 261
           + +     +K A  A+SH++ +               ++  +E++P TGR HQ+R H  H
Sbjct: 118 HAN----QDKEAQEAVSHYRRLGTVELDIPIGRYDKSRYSLVEVKPETGRKHQIRRHMKH 173

Query: 262 MGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           +  PI GD K+  N      K NF      +L L A  +   HP     + ITAP+ ++ 
Sbjct: 174 IFHPIAGDTKHGDNKHNKMLKQNFD---LQRLMLMATNIQFTHPITQEFMDITAPVDSYC 230

Query: 316 VKTWDSLGFK 325
            + +   G+K
Sbjct: 231 DELFAGFGWK 240


>gi|332637468|ref|ZP_08416331.1| pseudouridylate synthase [Weissella cibaria KACC 11862]
          Length = 298

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 105/217 (48%), Gaps = 19/217 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V NK  G+     S G    +  F ++++  +G+   + HRLD +T+G L+
Sbjct: 87  VLFENDDLIVVNKRKGVKTHPNSPGEDGTMMNFAQAYLAEQGKSAYMVHRLDGDTTGALI 146

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+       L +  R + I++ Y + V G         A      + IG + V    + 
Sbjct: 147 IAKNPYVVPMLNQMLRDKTIKRTYLAWVCG------NITATSGTIDAPIGDNPVDSRTRT 200

Query: 220 EKGANY--AISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             G N   A++++ KV   +      L +   TGRTHQ+R+H  H+G P+VGD  Y  N 
Sbjct: 201 VNGPNARPAVTYWHKVHTVYQNTLVRLALA--TGRTHQIRLHMKHLGYPLVGDPLY--NP 256

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
             N++    + L LHA  + LP P    ++ + APLP
Sbjct: 257 DSNYS----DGLLLHAAAIQLPIPFTNDVKSVGAPLP 289


>gi|260579312|ref|ZP_05847194.1| ribosomal large subunit pseudouridine synthase C [Corynebacterium
           jeikeium ATCC 43734]
 gi|258602441|gb|EEW15736.1| ribosomal large subunit pseudouridine synthase C [Corynebacterium
           jeikeium ATCC 43734]
          Length = 269

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/184 (28%), Positives = 95/184 (51%), Gaps = 7/184 (3%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q ++V + + + RLD++ ++    +    L +++R+ Q+ V+  + K + R  +G  VR+
Sbjct: 7   QTLIVSDSQADRRLDKYIRSQVKGVPATVLFRLMRTKQITVNGAKCKPDQRTVAGDKVRL 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P    AL    ++           + +  L   +++ED  + V NKPA I+V  GSG+  
Sbjct: 67  P----ALEVAAEKPTPTGDRKAAEQLARRLSRHIVFEDGALLVVNKPANIAVHVGSGVKA 122

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--RRIQKIYWS 185
            +   L+  +  K ++  L HRLD+ETSG+L+VA+     +HL    R     IQ+ Y +
Sbjct: 123 GVIEALR-VLRPKEKELELAHRLDKETSGLLIVAKNSKMLRHLQGLLRTGGEDIQRYYLA 181

Query: 186 LVWG 189
           +V G
Sbjct: 182 VVAG 185


>gi|82545090|ref|YP_409037.1| tRNA pseudouridine synthase C [Shigella boydii Sb227]
 gi|81246501|gb|ABB67209.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|332091999|gb|EGI97077.1| RNA pseudouridylate synthase family protein [Shigella boydii
           3594-74]
          Length = 260

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVSVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRNQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|16800037|ref|NP_470305.1| hypothetical protein lin0968 [Listeria innocua Clip11262]
 gi|16413427|emb|CAC96199.1| lin0968 [Listeria innocua Clip11262]
          Length = 296

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 73/312 (23%), Positives = 142/312 (45%), Gaps = 38/312 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+N+E+ + L  + K+ +     +   K    G++ V+ +       +++   VR+    
Sbjct: 7   VKNEEDGLLLRTFLKSKHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKTDDKVRLTFPT 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              N  +           L +H+D     +++ED  + + NKPAG++        YH  G
Sbjct: 67  EQQNDRL-----------LAEHTDLE---VVFEDDFLLIINKPAGMASIPSQ---YHPTG 109

Query: 132 FLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + ++V    +   LT       RLD+ETSG++++A+ R A   L+   +   +++ Y +
Sbjct: 110 SVANFVKGHYENQGLTSAIHIVTRLDRETSGLMLIAKNRYAHARLSSFLQQGLLKRRYQA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLE 244
              G  + +   I      ++ IG   V ++++       YA ++++V+  +   F  L 
Sbjct: 170 FTSGTLEEEAGSI------EAPIGRKDVSIMERFVTPEGKYAKTNYEVLMRY-NGFDHLA 222

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  ++G P++GD  Y  +        +  +  LH+ ++ L HP    
Sbjct: 223 IQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------QELLKRQALHSCHLHLVHPVTEE 276

Query: 305 -LQITAPLPAHM 315
            +    PLP  M
Sbjct: 277 YMAFDLPLPEDM 288


>gi|322379039|ref|ZP_08053442.1| Pseudouridine synthase [Helicobacter suis HS1]
 gi|322380804|ref|ZP_08054910.1| pseudouridylate synthase [Helicobacter suis HS5]
 gi|321146808|gb|EFX41602.1| pseudouridylate synthase [Helicobacter suis HS5]
 gi|321148531|gb|EFX43028.1| Pseudouridine synthase [Helicobacter suis HS1]
          Length = 326

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/183 (33%), Positives = 94/183 (51%), Gaps = 21/183 (11%)

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L   V S  Q+ RL HRLD ETSGI++V++ +   ++L   F   +I K Y +LV G   
Sbjct: 134 LYESVYSHNQEARLIHRLDYETSGIILVSQNKEHEKNLRALFSNHQIIKTYTALVQGDMH 193

Query: 193 NKKE---CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQP 247
           N       I   +L+ S++ GD + V  Q  K   ++ +  K++  D F  +   L++ P
Sbjct: 194 NYASGDFSIILPILEPSNLRGD-LGVRSQIHKQGKFSATTIKILCFDAFNNQ-TLLQISP 251

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYC-------------ANFKGNFTSPIQNKLYLHARY 294
            TGRTHQ+R+H   +G PIVG+  Y              A+FKG++ +P +  L L A  
Sbjct: 252 LTGRTHQIRLHLSALGFPIVGEPLYTKDSNARAYLNAKKADFKGSY-APFKPHLALEASG 310

Query: 295 MDL 297
           +D 
Sbjct: 311 LDF 313


>gi|315173724|gb|EFU17741.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1346]
          Length = 297

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 113/233 (48%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLD 151
           +++ED    V NKPAGI+        YH  G + + V  KG   R         +  RLD
Sbjct: 80  IVFEDDHFLVVNKPAGIA---SIPAQYHPSGTMANRV--KGYYKRQNYVNQVIHVVTRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L++K  IG D
Sbjct: 135 RDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLNE---HQLIEKP-IGRD 190

Query: 212 YVHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              ++K Q  +   +A + + +    AQ    + +Q HTGRTHQ+RVH   +GC ++GD 
Sbjct: 191 LSSLLKRQVIETGQFASTEYWLAKRGAQA-AAVRIQLHTGRTHQIRVHFEAIGCSLLGDE 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y     G     I+ +  LH   +   HP     + + +PL   M    D+L
Sbjct: 250 MY----HGEMDQGIERQA-LHCMELIFTHPFTKETVHLISPLAEDMKSVDDTL 297


>gi|227554161|ref|ZP_03984208.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis HH22]
 gi|227176703|gb|EEI57675.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis HH22]
          Length = 297

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 113/233 (48%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLD 151
           +++ED    V NKPAGI+        YH  G + + V  KG   R         +  RLD
Sbjct: 80  IVFEDDHFLVVNKPAGIA---SIPTQYHPSGTMANRV--KGYYKRQNYVNQVIHVVTRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L++K  IG D
Sbjct: 135 RDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLSE---HQLIEKP-IGRD 190

Query: 212 YVHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              ++K Q  +   +A + + +    AQ    + +Q HTGRTHQ+RVH   +GC ++GD 
Sbjct: 191 LSSLLKRQVIETGQFASTEYWLAKRGAQA-AAVRIQLHTGRTHQIRVHFEAIGCSLLGDE 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y     G     I+ +  LH   +   HP     + + +PL   M    D+L
Sbjct: 250 MY----HGKMDQGIERQA-LHCMELIFTHPFTKETVHLISPLAEDMKSVDDTL 297


>gi|145636146|ref|ZP_01791816.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittHH]
 gi|145270668|gb|EDK10601.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittHH]
          Length = 239

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 59/224 (26%), Positives = 104/224 (46%), Gaps = 17/224 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSNSLSFIHPITKEQITITAGL 223


>gi|319774994|ref|YP_004137482.1| pseudouridine synthase [Haemophilus influenzae F3047]
 gi|329123104|ref|ZP_08251674.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           aegyptius ATCC 11116]
 gi|317449585|emb|CBY85790.1| conserved hypothetical pseudouridine synthase [Haemophilus
           influenzae F3047]
 gi|327471659|gb|EGF17101.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           aegyptius ATCC 11116]
          Length = 224

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/203 (31%), Positives = 96/203 (47%), Gaps = 28/203 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+ S   + NK  GISV      QG + +        K W         L HRLD+ T
Sbjct: 5   VVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQLNVPKVW---------LVHRLDKVT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A    +A   +  F   +I K Y +L    PK K+  I   + KK+  G   + 
Sbjct: 56  SGLLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGDM-KKAREGAWKLC 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K+N      AI+ F+ + C      ++ ++P TG+THQLRV    +G PI+GD  Y  
Sbjct: 115 QTKENP-----AITRFESVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDGLYAK 168

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
           N     T  I ++ YLHA  ++ 
Sbjct: 169 N-----TEKI-DRTYLHATQLEF 185


>gi|152998841|ref|YP_001364522.1| pseudouridine synthase Rlu family protein [Shewanella baltica
           OS185]
 gi|151363459|gb|ABS06459.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS185]
          Length = 230

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 94/201 (46%), Gaps = 24/201 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +++   V +K A +      G A    G +       G K    HRLD  TSG+L++
Sbjct: 4   IIADEADFLVISKSAKVHFHSQDGTA----GVVAQAEQDLGIKLFAVHRLDTPTSGLLIL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA+  TE F   ++QK Y +L  G PK K+  +   + K          +++  E
Sbjct: 60  AKSAVAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIGDMAKSRR---SMFKLLRTKE 116

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  +        +L ++PH+G+THQLRV    +G PI+GD  Y        
Sbjct: 117 ---NPAITQFFSLSVSEGLRLYL-LKPHSGKTHQLRVALASLGVPILGDDLY-------- 164

Query: 281 TSPIQNKLYLHA-----RYMD 296
              + ++ YLHA     RY D
Sbjct: 165 GGAVADRCYLHAYCLHFRYGD 185


>gi|238795691|ref|ZP_04639205.1| Pseudouridine synthase [Yersinia mollaretii ATCC 43969]
 gi|238720417|gb|EEQ12219.1| Pseudouridine synthase [Yersinia mollaretii ATCC 43969]
          Length = 232

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 107/233 (45%), Gaps = 23/233 (9%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H    K   LY+D  + + NKPAG+    G     ++D      V    
Sbjct: 3   KIIDTFIAPPCHD---KIETLYQDDHLVLINKPAGLLSLSGKN-PQNLDSVHHRLVQIF- 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   +  E + + 
Sbjct: 58  PGCTLVHRLDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCG-HLDDNEGVIDA 116

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTH 253
            + K       + +   + K A    S ++V++ F  +           +++ P TGRTH
Sbjct: 117 AIAKDPALFPLMSICAIHGKPAR---SGYRVVERFYHELEDGTLLPLTRVQLTPETGRTH 173

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR 304
           QLR+H   +G PI+G    C  + G      +   +L LHA  +   HP GG+
Sbjct: 174 QLRIHCQQLGHPILG----CDLYGGRLLPGTERTLRLMLHASELHFVHPIGGK 222


>gi|256616825|ref|ZP_05473671.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis ATCC 4200]
 gi|256963780|ref|ZP_05567951.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis HIP11704]
 gi|257084358|ref|ZP_05578719.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis Fly1]
 gi|257087643|ref|ZP_05582004.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis D6]
 gi|307271727|ref|ZP_07552998.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|307276911|ref|ZP_07558021.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|256596352|gb|EEU15528.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis ATCC 4200]
 gi|256954276|gb|EEU70908.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis HIP11704]
 gi|256992388|gb|EEU79690.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis Fly1]
 gi|256995673|gb|EEU82975.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis D6]
 gi|295113627|emb|CBL32264.1| pseudouridine synthase, RluA family [Enterococcus sp. 7L76]
 gi|306506334|gb|EFM75494.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|306511605|gb|EFM80604.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|315025558|gb|EFT37490.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2137]
 gi|315032794|gb|EFT44726.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0017]
 gi|315143807|gb|EFT87823.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2141]
 gi|315162164|gb|EFU06181.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0645]
          Length = 297

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 113/233 (48%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLD 151
           +++ED    V NKPAGI+        YH  G + + V  KG   R         +  RLD
Sbjct: 80  IVFEDDHFLVVNKPAGIA---SIPAQYHPSGTMANRV--KGYYKRQNYVNQVIHVVTRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L++K  IG D
Sbjct: 135 RDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLNE---HQLIEKP-IGRD 190

Query: 212 YVHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              ++K Q  +   +A + + +    AQ    + +Q HTGRTHQ+RVH   +GC ++GD 
Sbjct: 191 LSSLLKRQVIETGQFASTEYWLAKRGAQA-AAVRIQLHTGRTHQIRVHFEAIGCSLLGDE 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y     G     I+ +  LH   +   HP     + + +PL   M    D+L
Sbjct: 250 MY----HGEMDQGIERQA-LHCMELIFTHPFTKETVHLISPLAEDMKSVDDTL 297


>gi|227357259|ref|ZP_03841616.1| TruC protein [Proteus mirabilis ATCC 29906]
 gi|227162522|gb|EEI47511.1| TruC protein [Proteus mirabilis ATCC 29906]
          Length = 260

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 104/228 (45%), Gaps = 15/228 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 5   IIYQDEYLVAVNKPAGWLVHRSWLDRHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLLM 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +++K+Y ++V G  +      +  + +   I   +     + +
Sbjct: 65  ALSSEVARTLSVCFEQHQMEKVYHAVVRGYVEEPMIIDSPLVEEHDKIADKFASQPPKIQ 124

Query: 221 KGANYAISHFKVIDCFA------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD--HKY 272
               + +   KV    A       +F  LE++P TGR HQLR H  H+  PI+GD  H  
Sbjct: 125 HCITHCVPLAKVEKEVAIGRYPTSRFSLLELRPETGRKHQLRRHMSHIRHPIIGDTAHGD 184

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +G       ++L LHA  ++L HP      IT   P ++   WD
Sbjct: 185 LRQNRGVVNHFQSHRLMLHASQLNLIHP------ITQQ-PLNLTAKWD 225


>gi|213691700|ref|YP_002322286.1| pseudouridine synthase, RluA family [Bifidobacterium longum subsp.
           infantis ATCC 15697]
 gi|213523161|gb|ACJ51908.1| pseudouridine synthase, RluA family [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 320

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 71/271 (26%), Positives = 122/271 (45%), Gaps = 36/271 (13%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++ SGQ RV  + V  ++ +Q+G+ V           + +EQ   +              
Sbjct: 34  LVDSGQARVLGREVARSSTLQAGETVEF--------DLAEEQAGPEPIAT--------DM 77

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQE 153
            ++YED  + V +KP G++     G     + G L+     + S G   R  +  RLD  
Sbjct: 78  AVVYEDDDVIVVDKPVGVAAHASVGWTGPTVLGSLRDRGVHIASYGAAGREGIVSRLDVG 137

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG---- 209
           TSG+++V ++  A   +   F    ++K Y +LV G  K  K  I      ++ IG    
Sbjct: 138 TSGLMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQGGLKENKATI------EAPIGRAKV 191

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            D+   V    K    A++H+ V++ F  +   + +   TGRTHQ+RVH   +G P+ GD
Sbjct: 192 SDFRFCVTPAGK---PAVTHWDVLERFGHEATLVSVNLETGRTHQIRVHFSSIGHPLCGD 248

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             Y AN   +    + ++ +LHA  ++  HP
Sbjct: 249 PMYGANPVLSEALGL-DRQWLHAMKLEFRHP 278


>gi|324325321|gb|ADY20581.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus thuringiensis serovar finitimus YBT-020]
          Length = 297

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 70/277 (25%), Positives = 130/277 (46%), Gaps = 32/277 (11%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           G + V+ +     +++Q+G+ +R+  PV      +I E   L                ++
Sbjct: 41  GSIEVNGQHASVRHQLQAGEELRVFFPVEERSEGMIAEDIPL---------------CIV 85

Query: 103 YEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGILV 159
           YED  + V NK A +S +      A  +   L S  D +       +  RLD++TSG+++
Sbjct: 86  YEDDAVLVINKEANMSTIPSREHPAGSVANALLSHYDKRHLASTVHIVTRLDRDTSGLML 145

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +      
Sbjct: 146 IAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKS----DSIIERTVC 201

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E+G   A++HF+VID    K   + ++  TGRTHQ+RVH  ++G P++GD     N  G 
Sbjct: 202 EEG-QRAVTHFRVIDSVNHK-THVSLELDTGRTHQIRVHMAYIGHPLLGD-----NLYGG 254

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
               ++ +  LH+  +   HP     +  T P+P+ M
Sbjct: 255 KRDEMKRQ-ALHSTSLTFYHPILEKEMSFTTPIPSDM 290


>gi|255994608|ref|ZP_05427743.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saphenum ATCC 49989]
 gi|255993321|gb|EEU03410.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saphenum ATCC 49989]
          Length = 322

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 82/304 (26%), Positives = 145/304 (47%), Gaps = 34/304 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++ + END    RLDR+FK +Y + +   + K++R   V+V+ K+ K N  + +G  V 
Sbjct: 2   VKFTITENDA-GQRLDRFFKKYYCNASLAYIYKLIRK-DVKVNGKKCKQNFLLNAGDAVH 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I   I+   H  K   + D  V +          +++ED  + V  K AG+   G S   
Sbjct: 60  I--YISDDEH--KRMILKDKGVQIKPSFK-----IIFEDDNLLVVYKRAGLLTHGSSTEK 110

Query: 127 YH-IDGFLKSWVDSKGQ-KPRL--------THRLDQETSGILVVARTRAAAQHLTESFRM 176
              +   +K+++  KG+  P          ++RLD+ T G++ +A+  A+ + L  +F+ 
Sbjct: 111 KRTLLNEVKTYLIQKGEYDPGFEKTFSLATSNRLDRNTEGLIAIAKNAASQRELNAAFKE 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSH----IGGDYVHVVKQN-EKGANYAISHFK 231
            RI++ Y + V G  + + +   ++ L KS     +  D    V  +  K A   +   +
Sbjct: 171 GRIERYYVAEVVG--EVRGDVTIDYPLYKSAKNNTVFADKDGSVPPDVTKEAITKVHPIR 228

Query: 232 V--IDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQ 285
           V  ID    +F +  + ++  TGRTHQ+RVH   +G P+V D KY   AN    + +P +
Sbjct: 229 VNRIDKNGSEFTYTVVRVKLLTGRTHQIRVHLAAIGHPLVNDRKYLKYANVSSKYLNPDK 288

Query: 286 NKLY 289
              Y
Sbjct: 289 RDKY 292


>gi|148273032|ref|YP_001222593.1| putative pseudouridine synthase [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147830962|emb|CAN01907.1| putative pseudouridine synthase [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
          Length = 305

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 55/179 (30%), Positives = 92/179 (51%), Gaps = 10/179 (5%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD  TSG++VVA+T  A   L   F  R ++K+Y ++V G P      I   + + 
Sbjct: 133 IVHRLDAGTSGLMVVAKTERAYTELKRQFHDREVEKVYHAVVQGHPDPLAGTIDAPIGR- 191

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            H   D+   V  + K    +++H++ ++ F ++   LE+   TGRTHQ+RVH      P
Sbjct: 192 -HPRSDWKFAVTADGK---PSVTHYETLEAF-RRAALLEVHLETGRTHQIRVHMAAQRHP 246

Query: 266 IVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
            VGD  Y A+     ++ +  ++ +LHA  +++ HP  G R   ++  PA +    D L
Sbjct: 247 CVGDAMYGADP--TLSAQLDLHRQWLHAMRLEITHPATGDRASFSSSYPADLQHALDVL 303


>gi|227554793|ref|ZP_03984840.1| pseudouridylate synthase RluD [Enterococcus faecalis HH22]
 gi|257077553|ref|ZP_05571914.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|294780463|ref|ZP_06745828.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|227176092|gb|EEI57064.1| pseudouridylate synthase RluD [Enterococcus faecalis HH22]
 gi|256985583|gb|EEU72885.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|294452462|gb|EFG20899.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
          Length = 287

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/260 (26%), Positives = 113/260 (43%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 40  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G    K++ I   +        D        +
Sbjct: 144 AKNPFVLPILGRLLETKQIYRQYQAIVAGHFSQKEQTINQPI---GRDRHDRRKRRIDPQ 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 258 -----ARLMLHASQLHLLHP 272


>gi|168242726|ref|ZP_02667658.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|194451570|ref|YP_002046934.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194409874|gb|ACF70093.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|205338110|gb|EDZ24874.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
          Length = 260

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 110/239 (46%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +     + +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFA----RED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+  + + N ++       +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KH-GDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLMIQAGLDETWMQALTQFGWR 237


>gi|127513457|ref|YP_001094654.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126638752|gb|ABO24395.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 578

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/207 (28%), Positives = 92/207 (44%), Gaps = 18/207 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NKPA      G  +   +   ++     K   P + HRLD  TSG++V+
Sbjct: 377 IIYQDEAIAVVNKPAEFLSVPGKHVTDSVYSRMRQAF-PKATGPLIVHRLDMSTSGLMVI 435

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +  A   L + F  R ++K Y + V G  + ++  I   L          +   +  +
Sbjct: 436 ALSSEANTALVQQFIGRTVEKRYLARVAGEVQGEEGEITLPLRVDLDDRPRQLVCFEHGK 495

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFK 277
               Y +     +    +    L + P TGRTHQLRVH  H   +G PI+GD  Y A   
Sbjct: 496 HAHTYWL-----VKSRGEGTTLLSLFPKTGRTHQLRVHCAHQDGLGMPIIGDDLYGAK-- 548

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR 304
                   N+L+LHA+Y+   HP  G 
Sbjct: 549 -------ANRLHLHAQYLAFNHPISGE 568


>gi|257421756|ref|ZP_05598746.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis X98]
 gi|257163580|gb|EEU93540.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis X98]
 gi|315155543|gb|EFT99559.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0043]
          Length = 297

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 113/233 (48%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLD 151
           +++ED    V NKPAGI+        YH  G + + V  KG   R         +  RLD
Sbjct: 80  IVFEDDHFLVVNKPAGIA---SIPAQYHPSGTMANRV--KGYYKRQNYVNQVIHVVTRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L++K  IG D
Sbjct: 135 RDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLNE---HQLIEKP-IGRD 190

Query: 212 YVHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              ++K Q  +   +A + + +    AQ    + +Q HTGRTHQ+RVH   +GC ++GD 
Sbjct: 191 LSSLLKRQVIETGQFASTEYWLAKRGAQA-AAVRIQLHTGRTHQIRVHFEAIGCSLLGDE 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y     G     I+ +  LH   +   HP     + + +PL   M    D+L
Sbjct: 250 MY----HGEMDQGIERQA-LHCMELIFTHPFTKETVHLISPLAEDMKNVDDTL 297


>gi|312883220|ref|ZP_07742948.1| pseudouridylate synthase, 23S RNA-specific [Vibrio caribbenthicus
           ATCC BAA-2122]
 gi|309369083|gb|EFP96607.1| pseudouridylate synthase, 23S RNA-specific [Vibrio caribbenthicus
           ATCC BAA-2122]
          Length = 556

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 102/207 (49%), Gaps = 26/207 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           +++ED  + V NKP+G+    G  I       L++ + D++G  P + HRLD  TSG+LV
Sbjct: 355 IIFEDDAMVVVNKPSGLLSVPGKTIKDSAYTRLQARYPDAEG--PFVIHRLDMATSGLLV 412

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A T+ A + L + F  RR+QK Y +L+ G        I+        + GD V   +Q 
Sbjct: 413 FALTKRANKSLQKQFISRRVQKRYVALLSGEVSQLSGDIS------LPMRGDPVDRPRQL 466

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
              E G   A +H+++I+    K   L + P TGRTHQLRVH  H   +  PI GD  Y 
Sbjct: 467 VCFEHGKP-AQTHWQLIENMEGK-SKLYLYPKTGRTHQLRVHCAHHLGLNLPIDGDGLYG 524

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
                        +L LHA+ ++  HP
Sbjct: 525 QK---------STRLCLHAQRLEFDHP 542


>gi|270289187|ref|ZP_06195489.1| pseudouridine synthetase family protein [Chlamydia muridarum Weiss]
          Length = 253

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 55/172 (31%), Positives = 87/172 (50%), Gaps = 18/172 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL+ED  + ++NKPA    Q    +A  +                L HRLD++TSG ++ 
Sbjct: 71  LLWEDEHLCIYNKPAK---QTSEALACQLH-------------VHLVHRLDRDTSGCILF 114

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+   A   +T+ F+ R+I K Y +LV+G P+ +   I  +     H     V     +E
Sbjct: 115 AKHEKAITPITQLFKTRQIDKRYIALVFGHPRQQSGIITTY-TAPCHRRIGAVLFGNTDE 173

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K     I+ ++V+  ++ K+  L  +P TGRTHQ+R+H   +G PIVGD  Y
Sbjct: 174 KLGKKTITEWEVLTHYS-KYALLLCRPITGRTHQIRLHMKTIGHPIVGDIDY 224


>gi|229114740|ref|ZP_04244154.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock1-3]
 gi|228668805|gb|EEL24233.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock1-3]
          Length = 292

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/266 (25%), Positives = 126/266 (47%), Gaps = 28/266 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + VD +     +++Q+G+ +R+  P
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVDGQYASVRHQLQAGEQLRVFFP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYH 128
           V      +I E   L                ++YED  + V NK A +S +         
Sbjct: 63  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPEGS 107

Query: 129 IDGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L S+ D +       +  RLD++TSG++++A+ R     L++  + + +++ Y ++
Sbjct: 108 VANALLSYYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAI 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    ++  I   + +KS    D + + +   +    A++HF+VI   +QK   + ++
Sbjct: 168 VHGEMIKREGTIDAPIGRKS----DSI-IERTFCEDGQRAVTHFRVIHSSSQK-THVSLE 221

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
             TGRTHQ+RVH  HMG P++GD  Y
Sbjct: 222 LETGRTHQIRVHMAHMGHPLLGDDLY 247


>gi|150016268|ref|YP_001308522.1| RluA family pseudouridine synthase [Clostridium beijerinckii NCIMB
           8052]
 gi|149902733|gb|ABR33566.1| pseudouridine synthase, RluA family [Clostridium beijerinckii NCIMB
           8052]
          Length = 324

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/270 (24%), Positives = 122/270 (45%), Gaps = 28/270 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++ +     +    + K LR   +RV+  +      +Q G VV I  + +  
Sbjct: 8   NEAGQRLDKFLRKLLKDVPLSAIFKALRKKDIRVNGTKQNEKYFLQEGDVVEIKYIQS-- 65

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGF 132
           N   K++K +       K        + YED  + V  K   + V   S  +    +  +
Sbjct: 66  NKEDKKEKFIKVDPKRIK--------IAYEDENVVVIEKWPDVLVHSDSNNSEEPTLTDY 117

Query: 133 LKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           + S+++ KG           P   +RLD+ TSG+++  +T    + + E+ R   I+K Y
Sbjct: 118 VLSYLNDKGDYIPENEITFTPAACNRLDRNTSGMVMFGKTFEGLKAINEAIREDEIRKYY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK-QNEKGANYAISHFKVIDCFAQKFCW 242
           ++L  G  K +      ++LK        ++  + +N K  +  IS   +++     +  
Sbjct: 178 YALAKG--KIRAGLYEAYILKNPETNTSKIYDTEVKNSKKISMEIS---IVESNGA-YSL 231

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           LE+   TGR+HQ+R H  H+G PI+GD+KY
Sbjct: 232 LEIHLITGRSHQIRAHLAHLGNPIIGDNKY 261


>gi|197286139|ref|YP_002152011.1| tRNA pseudouridine synthase C [Proteus mirabilis HI4320]
 gi|194683626|emb|CAR44534.1| tRNA pseudouridine synthase C [Proteus mirabilis HI4320]
          Length = 259

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 104/228 (45%), Gaps = 15/228 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEYLVAVNKPAGWLVHRSWLDRHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +++K+Y ++V G  +      +  + +   I   +     + +
Sbjct: 64  ALSSEVARTLSVCFEQHQMEKVYHAVVRGYVEEPMIIDSPLVEEHDKIADKFASQPPKIQ 123

Query: 221 KGANYAISHFKVIDCFA------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD--HKY 272
               + +   KV    A       +F  LE++P TGR HQLR H  H+  PI+GD  H  
Sbjct: 124 HCITHCVPLAKVEKEVAIGRYPTSRFSLLELRPETGRKHQLRRHMSHIRHPIIGDTAHGD 183

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +G       ++L LHA  ++L HP      IT   P ++   WD
Sbjct: 184 LRQNRGVVNHFQSHRLMLHASQLNLIHP------ITQQ-PLNLTAKWD 224


>gi|184157114|ref|YP_001845453.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|183208708|gb|ACC56106.1| Pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
          Length = 350

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 107/231 (46%), Gaps = 33/231 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NKP G+ V  G+G         + YH      S   ++  +  L HR+D
Sbjct: 117 IVYEDEDILVINKPVGMVVHPGAGNTSGTLVNALLYH------SPKSAELSRAGLVHRID 170

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LVVA    A   L++    + + +IY  + +G        IA   + +  I   
Sbjct: 171 KDTSGLLVVANNLEAQFSLSKQLGDKSVYRIYDLVTYG------NIIAGGTIDEP-IKRH 223

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V  VK     G   A++H+ V + F + F  ++ Q  TGRTHQ+RVH  ++G  +VGD 
Sbjct: 224 PVDRVKMAILPGGRDAVTHYNVKERF-RDFTRVQAQLETGRTHQIRVHFSYIGHGLVGDQ 282

Query: 271 KYCANFK---GNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y    +   G     I+      +  LHA  + L HP  G  +   AP P
Sbjct: 283 VYMNRVRIPAGASELLIETLRGFKRQALHAAKLGLKHPRTGEEMLFEAPWP 333


>gi|313674292|ref|YP_004052288.1| tRNA pseudouridine synthase c [Marivirga tractuosa DSM 4126]
 gi|312940990|gb|ADR20180.1| tRNA pseudouridine synthase C [Marivirga tractuosa DSM 4126]
          Length = 233

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/230 (26%), Positives = 104/230 (45%), Gaps = 10/230 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  +   NKP G+ V   + IA   D F L+   D  GQ+    HR+D++TSG+L+
Sbjct: 8   IIYQDDYLVAINKPHGLLVHR-TKIATETDVFALQLLRDQLGQRVYPVHRIDRKTSGVLL 66

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A         T  FR ++I+K Y ++V G      E   ++ L+K    G     V   
Sbjct: 67  FALDEENNSKTTALFRDQQIEKTYLAIVRGF--TDSEGTIDYALRKE--SGQLQESVTHY 122

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +  A   I    +      ++  +E++P TGR HQ+R H  H+  PI+ D  +  N +  
Sbjct: 123 KTLAKTEIP-VPLGKFETSRYSLVEVRPETGRMHQIRKHLAHIHHPIIADRPHGCNKQNK 181

Query: 280 FTSP--IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKY 326
                   + + LHA+ +   HP     + I A + +   +T   L F +
Sbjct: 182 LFKEKWAMDSMLLHAKEVIFKHPVSHDVVHIKANISSEFERTLSFLNFDF 231


>gi|224531710|ref|ZP_03672342.1| RNA pseudouridine synthase family protein [Borrelia valaisiana
           VS116]
 gi|224511175|gb|EEF81581.1| RNA pseudouridine synthase family protein [Borrelia valaisiana
           VS116]
          Length = 315

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 86/308 (27%), Positives = 138/308 (44%), Gaps = 50/308 (16%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-----LRSGQVRVDKKRVKF 55
           M L  Y+   V  ND    RLD         I  +NL K+     +R G +R++  +  F
Sbjct: 1   MRLDKYIFLEVFANDN-GKRLDSIL------IKILNLSKVRIIKHIRKGDIRLNGLKSHF 53

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI--------LLYEDSK 107
           + R+  G  + +              K L  S+NLT    +  +I        ++YEDS 
Sbjct: 54  SCRVCKGDKIYL-------------YKSLAQSLNLTMDEYYKSNIDFQCIPKRIIYEDSD 100

Query: 108 IYVFNKPAGISVQGG-SGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRA 165
           + V +K  GI V GG + + + ++ +L    + S   KP   HRLD+ TSGI++ A+   
Sbjct: 101 LLVVDKQRGILVHGGRNSLDFLVNAYLLGENLRSLSFKPSAVHRLDRNTSGIIIFAKNVN 160

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           AA+ L+ +F    I K Y++++ G  K+      N L +   +   +V    +N+K  N 
Sbjct: 161 AARRLSVAFSSGAITKKYFAILLGEVKS-TVVYENHLFRDKRLRKTFVL---ENKKFIN- 215

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGNFTSPI 284
           AI+    I   ++K    E+   TG THQ+R        P++ D KY   F K N+    
Sbjct: 216 AITKVNPI-LSSKKATLAEIVIETGFTHQIRAQCSFNNHPLINDKKYYDKFNKSNY---- 270

Query: 285 QNKLYLHA 292
               +LHA
Sbjct: 271 ----FLHA 274


>gi|315166865|gb|EFU10882.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1341]
 gi|315575307|gb|EFU87498.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309B]
 gi|315581474|gb|EFU93665.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309A]
          Length = 283

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/260 (26%), Positives = 113/260 (43%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L + +      +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHLGEATHVK---VLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G    K++ I   +        D        +
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAGHFSQKEQTINQPI---GRDRHDRRKRRIDPQ 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|255318642|ref|ZP_05359873.1| ribosomal large subunit pseudouridine synthase A [Acinetobacter
           radioresistens SK82]
 gi|255304324|gb|EET83510.1| ribosomal large subunit pseudouridine synthase A [Acinetobacter
           radioresistens SK82]
          Length = 221

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/205 (29%), Positives = 99/205 (48%), Gaps = 20/205 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + + +KPAG+    G    +    +L+     K    ++THRLD  TSGIL+ 
Sbjct: 18  IIYEDDDLIIIDKPAGLLSVPGRLPEHQDSAYLRLL--EKYPHAKITHRLDMATSGILMF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE----CIANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R + K Y +L+ G    +       I +W  +   I    VH  
Sbjct: 76  AKHRDAEVAISKMFQARTVTKRYVALIQGQLNEQGSIDVPLITDWENRPRQI----VHF- 130

Query: 217 KQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              E G + A + F+V+    +     + + P TGR+HQLRVH  ++G PI+GD  Y   
Sbjct: 131 ---ELGKS-AKTLFQVLQYHEEHDMTRVLLTPITGRSHQLRVHMQYIGHPIMGDKLYHPE 186

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G +      ++ LHA Y+    P
Sbjct: 187 PGGFYL----RRMALHASYLAFQQP 207


>gi|329577387|gb|EGG58842.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1467]
          Length = 297

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 113/242 (46%), Gaps = 44/242 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLD 151
           +++ED    V NKPAGI+        YH  G + + V  KG   R         +  RLD
Sbjct: 80  IVFEDDHFLVVNKPAGIA---SIPAQYHPSGTMANRV--KGYYKRQNYVNQVIHVVTRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L++K  IG D
Sbjct: 135 RDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLNE---HQLIEKP-IGRD 190

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWL----------EMQPHTGRTHQLRVHALH 261
              ++K+            +  +CF+ ++ WL           +Q HTGRTHQ+RVH   
Sbjct: 191 LSSLLKRQV---------IETANCFSTEY-WLAKRGAQAAAVRIQLHTGRTHQIRVHFEA 240

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
           +GC ++GD  Y     G     I+ +  LH   +   HP     + + +PL   M    D
Sbjct: 241 IGCSLLGDEMY----HGKMDQGIERQA-LHCMELIFTHPFTKETVHLISPLAEDMKSVDD 295

Query: 321 SL 322
           +L
Sbjct: 296 TL 297


>gi|228475873|ref|ZP_04060583.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Staphylococcus hominis SK119]
 gi|314936097|ref|ZP_07843444.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus hominis subsp. hominis C80]
 gi|228270028|gb|EEK11498.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Staphylococcus hominis SK119]
 gi|313654716|gb|EFS18461.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus hominis subsp. hominis C80]
          Length = 274

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/268 (24%), Positives = 116/268 (43%), Gaps = 43/268 (16%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +L ++  S  + ++++  K  +++ +  VV IP      N++                  
Sbjct: 27  DLHQLNMSKDITINQQSSKLTDKVVTNDVVYIPTPKEKSNYL----------------PS 70

Query: 96  FLKSILLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +  + + YED+ + +  KP G+      ++  + +  H+       +DS   +P   HRL
Sbjct: 71  YRYAQIAYEDNDLAIVVKPKGVKTHPNDLKESNTLMNHV----IYTMDSDYVEP--IHRL 124

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           DQET G+L+VA+     + L       +I +IY + V  +   K + I         IG 
Sbjct: 125 DQETVGLLIVAKNPLMKKILDRMLEENQITRIYRANVKALLPLKPQTI------DMPIGK 178

Query: 211 DYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D  H  K+        AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD
Sbjct: 179 DKFHPNKRRISNTGQRAITHILTSKMIKEGICQLEIKLDTGRTHQIRVHLAEIGHPVIGD 238

Query: 270 HKY---------CANFKGNFTSPIQNKL 288
             Y           ++K  FT P+  +L
Sbjct: 239 PLYGDATLRQLELNSYKIEFTHPLTQEL 266


>gi|237731372|ref|ZP_04561853.1| pseudouridylate synthase [Citrobacter sp. 30_2]
 gi|226906911|gb|EEH92829.1| pseudouridylate synthase [Citrobacter sp. 30_2]
          Length = 232

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/209 (29%), Positives = 98/209 (46%), Gaps = 20/209 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP+G+    G     ++D      V        L HRLD  TSG++VVA
Sbjct: 20  LYQDEHLVLINKPSGLLSLSGKN-PQNLDSVHHRLVQIY-PGCTLVHRLDFGTSGLMVVA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L + F  R + K+Y +L+ G  +N +  I   + K   +    + +   N K
Sbjct: 78  RNKAINAALCQQFSQRTVTKVYSALLCGHLENDEGVIDAAIAKDPAL-FPLMSICALNGK 136

Query: 222 GANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            A    S ++V++ F  +           +++ P TGRTHQLR+H   +G PI+G    C
Sbjct: 137 PAR---SRYQVVERFYHRQEEGTLLPLTRVQLTPETGRTHQLRIHCQQLGHPILG----C 189

Query: 274 ANFKGNFTSPIQ--NKLYLHARYMDLPHP 300
             + G      +  ++L LHA  +   HP
Sbjct: 190 DLYGGRLLPGTEQTSRLMLHASELHFRHP 218


>gi|325841309|ref|ZP_08167410.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
 gi|325489990|gb|EGC92337.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
          Length = 297

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 108/210 (51%), Gaps = 30/210 (14%)

Query: 101 LLYEDSKIYVFNKPAGI----------SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           ++YED  + V NKPAGI               + I Y+ +  + S +          +RL
Sbjct: 83  VVYEDEYLLVINKPAGIPTIPSLRHPEKTLANALIHYYNEHEIASTI-------HFVNRL 135

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L+VA+ R     LT+   +++I++ Y++LV G+ +     +   + ++S   G
Sbjct: 136 DRDTSGLLMVAKYRHIHHLLTKD--VKQIKRKYYTLVKGVMEKNSGTVHAPIARESE--G 191

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +    V+ +    + +I+H++V++ + +K   +E +  TGRTHQ+RVH  ++G P+VGD 
Sbjct: 192 NVRRCVRAD---GDDSITHYQVLEVW-EKSTLVECELETGRTHQIRVHMNYLGHPLVGDT 247

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            Y       F   ++    LH+  +   HP
Sbjct: 248 LY-----DEFALELEEGHLLHSYELSFTHP 272


>gi|315149417|gb|EFT93433.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0012]
          Length = 283

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/260 (26%), Positives = 114/260 (43%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHL---GEATRVKVLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++  G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIAAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L HP
Sbjct: 254 -----ARLMLHASQLHLLHP 268


>gi|55820309|ref|YP_138751.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMG 18311]
 gi|55822199|ref|YP_140640.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus CNRZ1066]
 gi|55736294|gb|AAV59936.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus LMG 18311]
 gi|55738184|gb|AAV61825.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus CNRZ1066]
          Length = 290

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 59/199 (29%), Positives = 88/199 (44%), Gaps = 16/199 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYEDS + V NKP G+   G       +   + ++    GQ   + HRLD ETSG ++ A
Sbjct: 84  LYEDSHLIVVNKPEGMKTHGNKPTEIALLNHVSAYC---GQTCYVVHRLDMETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      + IQ+ YW+L  G  + KK    + + +  H     V V  +  +
Sbjct: 141 KNPFILPILNRLLEDKMIQRQYWALTEGKFQTKKTVYKDKIGRDRHDRRKRV-VDPRKGQ 199

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            A   ++  K  +  +   C L+    TGRTHQ+RVH  H G  I+GD  Y         
Sbjct: 200 SAYTTVTRLKTFEGASLVNCQLK----TGRTHQIRVHLSHHGHAILGDPLYSHQ------ 249

Query: 282 SPIQNKLYLHARYMDLPHP 300
               ++L LHA  +   HP
Sbjct: 250 --PASRLMLHAHSLSFTHP 266


>gi|330684742|gb|EGG96437.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU121]
          Length = 276

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/264 (27%), Positives = 115/264 (43%), Gaps = 42/264 (15%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-- 100
           S  + ++K+  + ++++ SG  V IP           E+K           S++L S   
Sbjct: 34  SKDITINKQTSRLSDKVNSGDEVFIP---------TPEEK-----------SNYLPSYRY 73

Query: 101 --LLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
             + YE+    +  KP G+         +  +   L   +DS   +P   HRLDQET G+
Sbjct: 74  AQVYYENDDFAIVLKPKGVKTHPNDLKESNTLMNHLIYTIDSDYVEP--IHRLDQETVGL 131

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+     + L        I +IY + V  +   K + I         IG D  H  K
Sbjct: 132 LIVAKNPLMKKILDRMLEENDITRIYKAHVKALLPIKPQTI------DMPIGKDKFHPNK 185

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +        AI+H    +   +  C LE++  TGRTHQ+RVH   +G P++GD  Y    
Sbjct: 186 KRISNTGQRAITHILSSNMIKENVCELEIKLDTGRTHQIRVHLAEIGHPVIGDPLY---- 241

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
            G+ T     +L LH+  ++L HP
Sbjct: 242 -GDST---LRQLELHSYKIELEHP 261


>gi|261250364|ref|ZP_05942940.1| ribosomal large subunit pseudouridine synthase D [Vibrio orientalis
           CIP 102891]
 gi|260939480|gb|EEX95466.1| ribosomal large subunit pseudouridine synthase D [Vibrio orientalis
           CIP 102891]
          Length = 326

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 117/242 (48%), Gaps = 34/242 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPR--LTHRLDQET 154
           ++YED  + V NKP G  V  G+G     DG + + +     +  + PR  + HRLD++T
Sbjct: 86  IVYEDDDLLVINKPRGFVVHPGAGTP---DGTVLNALLHHYPNIAEVPRAGIVHRLDKDT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           +G++VVA+T  A   L  + + +R   + Y ++  G         A   +++  IG    
Sbjct: 143 TGLMVVAKTVPAQTRLVRALQKKRNFVREYEAIAIG------RMTAGGRVEQP-IGR--- 192

Query: 214 HVVKQN----EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           H  K+           AI+H++V + F ++   + ++  TGRTHQ+RVH  ++  P++GD
Sbjct: 193 HSTKRTLMAVTPTGKPAITHYRVAEHF-REHTRIRLRLETGRTHQIRVHMSYLQHPLLGD 251

Query: 270 HKYC--ANFKGNFTSPIQNKL------YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
             Y   A      +  + N +       LHA  +   HP  G  ++  AP+P  MV+  +
Sbjct: 252 TAYGGRARIPSGASEELANHIRSFDRQALHAVMLKFEHPITGEEVEFHAPVPDDMVEMAE 311

Query: 321 SL 322
           +L
Sbjct: 312 AL 313


>gi|94501093|ref|ZP_01307617.1| Pseudouridylate synthases, 23S RNA-specific [Oceanobacter sp.
           RED65]
 gi|94426840|gb|EAT11824.1| Pseudouridylate synthases, 23S RNA-specific [Oceanobacter sp.
           RED65]
          Length = 223

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 58/192 (30%), Positives = 92/192 (47%), Gaps = 19/192 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YE     + NKP G+     +G      GF +   D  G      HRLD+ TSG+L+ 
Sbjct: 5   IVYEHQDWILVNKPEGVDFHSQNGEV----GFHRQLCDQLGFNVFPVHRLDKATSGLLLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+++ A + L E F  R+++K Y ++V    K K+  +   ++K  +  G Y    K  +
Sbjct: 61  AKSQDACRGLVELFSQRKVEKYYLAIVSNKLKKKQGKVFGDMVKSRN--GSY----KLTQ 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +  N A + F +       +    ++P TG+THQLRV    +G  IVGD +Y        
Sbjct: 115 ERRNPAFTQF-LSQALKPGYRLALLKPKTGKTHQLRVAMKSLGSAIVGDQRYGGE----- 168

Query: 281 TSPIQNKLYLHA 292
                N+LYLHA
Sbjct: 169 ---SANRLYLHA 177


>gi|298374755|ref|ZP_06984713.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_19]
 gi|298269123|gb|EFI10778.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_19]
          Length = 304

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 108/228 (47%), Gaps = 28/228 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI----AYHI-DGFLKSWVDSKGQKPR----LTHRLD 151
           +++ED  + V NK  G+       I    AY I   +LK         PR    + HRLD
Sbjct: 93  IVWEDDDLIVINKREGLLSVSTDRIKERTAYRILSDYLKEC------DPRNKIFVLHRLD 146

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSGI++ A+ +   + L  ++     Q+ Y +++ G P+   + I + L++  H+   
Sbjct: 147 RDTSGIMMFAKNQKVKEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIVSNLVENKHM--- 203

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V+V +  +     AI+ ++++     ++  +E+   TGR +Q+R     +G PI GD K
Sbjct: 204 QVYVTQDGD--GKEAITRYRLLQT-NNRYSLVELDLETGRKNQIRAQMQSIGHPIAGDSK 260

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           Y A      T+P   +L LHAR +   HP  G  ++    +P     T
Sbjct: 261 YGAE-----TNPA-GRLMLHARRLCFIHPVTGEEMRFETRIPEKFTST 302


>gi|91225595|ref|ZP_01260669.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
 gi|91189715|gb|EAS75989.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
          Length = 250

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/221 (28%), Positives = 100/221 (45%), Gaps = 38/221 (17%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +++ED  I   NKP+G+ SV G   +A H D     W   K   P +   HRLD  TSG+
Sbjct: 16  IVFEDDDILAVNKPSGLLSVPGR--LAEHYDSM---WSRLKELHPEIQVVHRLDMSTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW--------LLK 204
           +++A+ + A + L + F+ R   K+Y++ VWG  ++++       I +W           
Sbjct: 71  MLLAKNKPAERALKKQFQYRLTHKVYYARVWGHVESQEGNIDLPLICDWPNRPRQKVCFD 130

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                     VVK+         +H  V+           + P TGR+HQLRVH + +G 
Sbjct: 131 DGKPSQTLFQVVKREVHPDG---THTTVV----------RLLPITGRSHQLRVHLMAIGH 177

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            IVGD  Y +     F+     +L LHA  +   HP   +L
Sbjct: 178 AIVGDEFYASEEAYQFS----ERLELHAAELSFYHPATDQL 214


>gi|313619655|gb|EFR91288.1| pseudouridine synthase YjbO [Listeria innocua FSL S4-378]
          Length = 296

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 73/312 (23%), Positives = 142/312 (45%), Gaps = 38/312 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+N+E+ + L  + K+ +     +   K    G++ V+ +       +++   VR+    
Sbjct: 7   VKNEEDGLLLRTFLKSKHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKTDDKVRLTFPT 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              N  +           L +H+D     +++ED  + + NKPAG++        YH  G
Sbjct: 67  EQQNERL-----------LAEHTDLE---VVFEDDFLLIINKPAGMASIPSQ---YHPTG 109

Query: 132 FLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + ++V    +   LT       RLD+ETSG++++A+ R A   L+   +   +++ Y +
Sbjct: 110 SVANFVKGHYENQGLTSAIHIVTRLDRETSGLMLIAKNRYAHARLSSFLQQGLLKRRYQA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLE 244
              G  + +   I      ++ IG   V ++++       YA ++++V+  +   F  L 
Sbjct: 170 FTSGTLEEEAGSI------EAPIGRKDVSIMERFVTPEGKYAKTNYEVLMRY-NGFDHLA 222

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  ++G P++GD  Y  +        +  +  LH+ ++ L HP    
Sbjct: 223 IQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------QVLLKRQALHSCHLHLVHPVTEE 276

Query: 305 -LQITAPLPAHM 315
            +    PLP  M
Sbjct: 277 YMAFDLPLPEDM 288


>gi|283833280|ref|ZP_06353021.1| pseudouridine synthase A [Citrobacter youngae ATCC 29220]
 gi|291070917|gb|EFE09026.1| pseudouridine synthase A [Citrobacter youngae ATCC 29220]
          Length = 232

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/213 (30%), Positives = 97/213 (45%), Gaps = 18/213 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + + NKPAG+    G     ++D      V        L HRLD  TSG++V+
Sbjct: 19  ILYQDEHLVLINKPAGLLSLSGKN-PQNLDSVHHRLVQIY-PGCTLVHRLDFGTSGLMVI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +A    L + F  R + K Y +L+ G  +N    I   + K   +    + +   N 
Sbjct: 77  ARNKAINAALCQQFSQRVVTKAYSALLCGHLENDAGVIDAAIAKDPAL-FPRMSICAMNG 135

Query: 221 KGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K A    S ++VI+ F  +           +++ P TGRTHQLR+H   +G PI+G   Y
Sbjct: 136 KPAR---SRYQVIERFLHRQEDGALLPLTRVQLTPETGRTHQLRIHCQQLGHPILGCDLY 192

Query: 273 CANF-KGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                 G   +P   +L LHA  +   HP   R
Sbjct: 193 GGRLWPGTERTP---RLMLHASALHFRHPVSER 222


>gi|262379133|ref|ZP_06072289.1| pseudouridylate synthase [Acinetobacter radioresistens SH164]
 gi|262298590|gb|EEY86503.1| pseudouridylate synthase [Acinetobacter radioresistens SH164]
          Length = 221

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/205 (29%), Positives = 99/205 (48%), Gaps = 20/205 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + + +KPAG+    G    +    +L+     K    ++THRLD  TSGIL+ 
Sbjct: 18  IIYEDDDLIIIDKPAGLLSVPGRLPEHQDSAYLRLL--EKYPHAKITHRLDMATSGILMF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE----CIANWLLKKSHIGGDYVHVV 216
           A+ R A   +++ F+ R + K Y +L+ G    +       I +W  +   I    VH  
Sbjct: 76  AKHRDAEVAISKMFQARTVTKRYVALIQGQLNEQGSIDVPLITDWENRPRQI----VHF- 130

Query: 217 KQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              E G + A + F+V+    +     + + P TGR+HQLRVH  ++G PI+GD  Y   
Sbjct: 131 ---ELGKS-AKTLFQVLQYHEEHDMTRVLLTPITGRSHQLRVHMQYIGHPIMGDKLYHPE 186

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G +      ++ LHA Y+    P
Sbjct: 187 PGGFYL----KRMALHASYLAFQQP 207


>gi|229549211|ref|ZP_04437936.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis ATCC
           29200]
 gi|255971927|ref|ZP_05422513.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T1]
 gi|256957901|ref|ZP_05562072.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis DS5]
 gi|257416850|ref|ZP_05593844.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis AR01/DG]
 gi|257420067|ref|ZP_05597061.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T11]
 gi|300861004|ref|ZP_07107091.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|229305448|gb|EEN71444.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis ATCC
           29200]
 gi|255962945|gb|EET95421.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T1]
 gi|256948397|gb|EEU65029.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis DS5]
 gi|257158678|gb|EEU88638.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis ARO1/DG]
 gi|257161895|gb|EEU91855.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T11]
 gi|300850043|gb|EFK77793.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|315035177|gb|EFT47109.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0027]
 gi|315148637|gb|EFT92653.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4244]
 gi|315159322|gb|EFU03339.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0312]
 gi|315168785|gb|EFU12802.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1341]
 gi|315573843|gb|EFU86034.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309B]
 gi|315580414|gb|EFU92605.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309A]
 gi|323481597|gb|ADX81036.1| pseudouridine synthase, RluA family protein [Enterococcus faecalis
           62]
 gi|327535892|gb|AEA94726.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           OG1RF]
          Length = 297

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 113/233 (48%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLD 151
           +++ED    V NKPAGI+        YH  G + + V  KG   R         +  RLD
Sbjct: 80  IVFEDDHFLVVNKPAGIA---SIPAQYHPSGTMANRV--KGYYKRQNYVNQVIHVVTRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L++K  IG D
Sbjct: 135 RDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLSE---HQLIEKP-IGRD 190

Query: 212 YVHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              ++K Q  +   +A + + +    AQ    + +Q HTGRTHQ+RVH   +GC ++GD 
Sbjct: 191 LSSLLKRQVIETGQFASTEYWLAKRGAQA-AAVRIQLHTGRTHQIRVHFEAIGCSLLGDE 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y     G     I+ +  LH   +   HP     + + +PL   M    D+L
Sbjct: 250 MY----HGKMDQGIERQA-LHCMELIFTHPFTKETVHLISPLAEDMKSVDDTL 297


>gi|145518940|ref|XP_001445342.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|31746352|emb|CAD97486.1| pseudouridine synthase [Paramecium tetraurelia]
 gi|124412786|emb|CAK77945.1| unnamed protein product [Paramecium tetraurelia]
          Length = 350

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/246 (26%), Positives = 125/246 (50%), Gaps = 15/246 (6%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +QK++R+G++ V+ K++K +  +     ++   V+   + + K+       V  T+  + 
Sbjct: 42  VQKLIRNGEINVNNKKIKDHQFL-----LKEGDVVTYWDKLKKQADTQLRPVPNTQAYEE 96

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           LK ++LYE+ +I + NK  G + QGG+   Y+I   L  +     +   + HRLDQ TSG
Sbjct: 97  LKKMILYENDQIIILNKKHGYASQGGANPNYNIPEILNLYF----KNFYIIHRLDQLTSG 152

Query: 157 ILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +L++A+ +  A  ++   + +  I K Y ++V G  K +K  I   LL  ++      + 
Sbjct: 153 LLIIAKNKDIATEISTIIQEKAFITKKYIAVVQGQIKVQKGLIDRPLLFNTNNQKQTCYN 212

Query: 216 VKQNEKGANY-AISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDH 270
            +Q  +G    A + ++VI+ +    + +  L++Q   GR HQ+R H    +  PI+ D 
Sbjct: 213 EEQLLEGKYLPARTSYEVIEEYQYQDEMYSILDLQIFEGRKHQIRAHLSQVLNTPILFDQ 272

Query: 271 KYCANF 276
           KY   F
Sbjct: 273 KYGFQF 278


>gi|84621977|ref|YP_449349.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|84365917|dbj|BAE67075.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 238

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 110/236 (46%), Gaps = 26/236 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D  + V +K AG+ V   S +A   D FL   +  +  +P  L HRLD+ TSG L+
Sbjct: 10  ILYQDDVLAVVDKTAGLMVHD-SKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGCLL 68

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R  A  L ++     +QK Y ++  G P   +  + + L      GG    V K  
Sbjct: 69  LAFDRETASALGKALMSGDVQKDYLAVCRGWPAEPRFTVDHDL-----DGGPGKPVKKP- 122

Query: 220 EKGANYAISHFKVIDC---------FA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +           FA  ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 123 ------ALTHFQRLATGELQVPSTGFATSRYALLRCQPQTGRFRQIRRHLKHLSHHLIGD 176

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
             +       +F     +++ LHA+ +  PHP +G R+++TAPL     K     G
Sbjct: 177 TSHGDGRHNRSFRMLGIHRMLLHAKRLAFPHPADGRRIRVTAPLDDEFTKACALFG 232


>gi|38234158|ref|NP_939925.1| putative pseudouridine synthase [Corynebacterium diphtheriae NCTC
           13129]
 gi|38200420|emb|CAE50108.1| Putative pseudouridine synthase [Corynebacterium diphtheriae]
          Length = 308

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 70/276 (25%), Positives = 122/276 (44%), Gaps = 30/276 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-L 101
           +G V VD   V  ++R+  GQ + +                L    +LT   + ++ + +
Sbjct: 40  AGDVVVDGHCVGKSDRLSEGQWLDV---------------TLPEVRDLTPREELIEGMDI 84

Query: 102 LYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           LY D  +   NKP G++       +G + I        +       ++  +  RLD  TS
Sbjct: 85  LYSDDDVIAVNKPVGVAAHPTLGWEGPTVIGGLAAAGFRISTSGPPERKGIVQRLDVGTS 144

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++VVA +      L  +F+ R + K Y SLV G        I   + +  H    +   
Sbjct: 145 GVMVVAASERGYSVLKRAFKERTVTKTYHSLVQGHMDPLSGTIDAPIGR--HPSAGWRFA 202

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  + K   +A++H++ I+ FA+    L +   TGRTHQ+RVH   +  P  GD  Y ++
Sbjct: 203 VTTDGK---HAVTHYETIEAFAEA-SLLRIHLETGRTHQIRVHMSALHHPCCGDPMYGSD 258

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
              +    + ++ +LHA  +   HP  GR ++I +P
Sbjct: 259 PALSARLGL-DRQWLHAVSLGFHHPADGRWVEIESP 293


>gi|197303693|ref|ZP_03168730.1| hypothetical protein RUMLAC_02422 [Ruminococcus lactaris ATCC
           29176]
 gi|197297213|gb|EDY31776.1| hypothetical protein RUMLAC_02422 [Ruminococcus lactaris ATCC
           29176]
          Length = 295

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/222 (28%), Positives = 107/222 (48%), Gaps = 17/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSG 156
           ++YED  + V NKPAG+ +    +     +   L  +   +G KP   R T+RLD++TSG
Sbjct: 83  IIYEDDDLLVVNKPAGMPIHPSLNNYKNSLANALMYYYKEQG-KPFIFRCTNRLDRDTSG 141

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           + V+A+   ++  L+       I + Y ++V G        I   L +     G  +   
Sbjct: 142 LTVIAKHLVSSSILSFMAVRHEIHREYLAIVRGAVSPASGTINAPLART----GSSIIER 197

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K + +   +A++H+KV+    Q    + +   TGRTHQ+RVH  ++G P+VGD+ Y  + 
Sbjct: 198 KVDFEHGEHAVTHYKVLKEQNQH-SLVSLILETGRTHQIRVHLQYLGHPLVGDYLYNPDM 256

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           +        N+  LH+  +   HP  G  +   APLP  M K
Sbjct: 257 E------YINRQALHSWKLSFIHPITGEAMHFEAPLPEDMRK 292


>gi|76788821|ref|YP_327907.1| tRNA pseudouridine synthase A [Chlamydia trachomatis A/HAR-13]
 gi|237802537|ref|YP_002887731.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/Jali20/OT]
 gi|237804454|ref|YP_002888608.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/TZ1A828/OT]
 gi|76167351|gb|AAX50359.1| tRNA pseudouridine synthase A [Chlamydia trachomatis A/HAR-13]
 gi|231272754|emb|CAX09659.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231273771|emb|CAX10553.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/Jali20/OT]
          Length = 274

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 65/258 (25%), Positives = 118/258 (45%), Gaps = 43/258 (16%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINAL 74
           + ++RL  + +   PH+    + + +R    RV+ +  +F + ++Q G  V         
Sbjct: 9   DRHIRLSSFLRTSLPHLPKKTILESVRYHGCRVNGRIERFESYKLQPGDRV--------- 59

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                       S+ + +HS      LL+ED  + ++NKPA    Q    +A+ ++    
Sbjct: 60  ------------SLQIIEHSS---PQLLWEDEHLCIYNKPAK---QTSEDLAHQLNV--- 98

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                      L HRLD++TSG ++ A+   A+  +T+ F+   I K Y +LV+G P+ +
Sbjct: 99  ----------HLVHRLDRDTSGCILFAKHAKASSLITQLFKNPEIDKRYIALVFGQPRQE 148

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I  +        G  V     ++      I+ ++++  +  K+  L  +P TGRTHQ
Sbjct: 149 SGIITTYTAPCYRRTGA-VLFGNTDQNSGKITITKWEILTRYP-KYTLLLCRPVTGRTHQ 206

Query: 255 LRVHALHMGCPIVGDHKY 272
           +R+H   +G PIVGD  Y
Sbjct: 207 IRLHMKTIGHPIVGDVDY 224


>gi|295110320|emb|CBL24273.1| pseudouridine synthase, RluA family [Ruminococcus obeum A2-162]
          Length = 293

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 76/319 (23%), Positives = 141/319 (44%), Gaps = 40/319 (12%)

Query: 9   YVVVENDEENMRLD----RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           Y + EN++    LD    + F  H       + + + R+GQ      R+    ++ +G  
Sbjct: 7   YQITENEQGTTVLDFLRKKGFSRHILSSMKADKEALTRNGQ------RIGGREQLLAGDH 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
            R+      L   +    I+  S+ L+         +LYED  I V NKPA + V    G
Sbjct: 61  FRV-----RLLETVDSDGIVPVSMPLS---------ILYEDEDILVINKPADMPVHPSIG 106

Query: 125 -IAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                +   + +++D+K +    R  +RLD++TSG L++A+   +A  L+   R R+I++
Sbjct: 107 NYTNTLANGVAAYLDAKDEHSPFRCINRLDRDTSGALILAKNAFSAAVLSTQMRNRQIRR 166

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V GI        A        +   +V  ++        A++H++ ++    +  
Sbjct: 167 TYLAVVEGITPPNGTISAPISRVDDSVIERHVDFLR-----GEPAVTHYERLEV-KNEHS 220

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE+   TGRTHQ+RVH  ++G P+  D+ Y   +      P      LH+  ++  HP 
Sbjct: 221 LLEIHLETGRTHQIRVHMGYIGHPLPADYLYHPVYDCFKRQP------LHSLQLEFRHPV 274

Query: 302 GGR-LQITAPLPAHMVKTW 319
             + + + AP+   M   +
Sbjct: 275 TDKPMCLLAPVSEDMCNAF 293


>gi|255321341|ref|ZP_05362501.1| pseudouridine synthase [Campylobacter showae RM3277]
 gi|255301494|gb|EET80751.1| pseudouridine synthase [Campylobacter showae RM3277]
          Length = 252

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 108/233 (46%), Gaps = 41/233 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  +   +KPA                FL S   S+  K  L HRLD+ETSG+L++
Sbjct: 60  VIFEDENLIAVDKPA----------------FLTSEKVSEIYKFPLLHRLDKETSGVLLL 103

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+  R++K Y + V  I  +++  I   ++   + GG +  +    +
Sbjct: 104 VKNEEFQKKAIEEFKNCRVKKEYVAAVKSIV-SEEFSINEPIITLKNRGGAFSKISPNGK 162

Query: 221 KGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +    A SH  VI    A K   ++++  TGRTHQ+RVH  H G  IVGD KY  N    
Sbjct: 163 E----AFSH--VIPVMVAGKKSLVKVEIKTGRTHQIRVHLNHAGYGIVGDEKYAKNKAA- 215

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
                  ++YLHA  ++L         +     +++   ++ LGF+  RN  I
Sbjct: 216 -------RMYLHAYKIEL---------LGYKFRSNLSSDFNRLGFEISRNFEI 252


>gi|229493462|ref|ZP_04387247.1| RNA pseudouridine synthase family protein [Rhodococcus erythropolis
           SK121]
 gi|229319423|gb|EEN85259.1| RNA pseudouridine synthase family protein [Rhodococcus erythropolis
           SK121]
          Length = 304

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/208 (29%), Positives = 96/208 (46%), Gaps = 13/208 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  I V +KP  + ++  G+ I       L+  +D     P   HRLD+ T+G++V
Sbjct: 90  ILYRDDSILVIDKPHFLATIPRGAHIVESAVVRLRRDLDLPDLAP--VHRLDRMTAGVIV 147

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
              T    +   E F  +RI K Y ++    P+          + K H  G+        
Sbjct: 148 FTVTPDLRRPYQELFAEQRIVKEYEAIAGFAPELTFPRTVRSRINKVH--GEMTATEIAG 205

Query: 220 EKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH---KYCAN 275
           E  +  +I   +VI D   +      + P TGRTHQLR+H   +G PIVGD+   +Y   
Sbjct: 206 EPNSETSIELIEVITDSAGRTLGRYRLLPRTGRTHQLRLHLNSLGVPIVGDNYYPEYLPA 265

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             G+F++P++    L AR ++ P P  G
Sbjct: 266 VPGDFSTPLR----LLARALEYPDPITG 289


>gi|227519595|ref|ZP_03949644.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           TX0104]
 gi|229544944|ref|ZP_04433669.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           TX1322]
 gi|256763299|ref|ZP_05503879.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T3]
 gi|256853972|ref|ZP_05559337.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T8]
 gi|257079838|ref|ZP_05574199.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis JH1]
 gi|257090805|ref|ZP_05585166.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis CH188]
 gi|294779490|ref|ZP_06744886.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|307270621|ref|ZP_07551912.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|307287513|ref|ZP_07567556.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|307290324|ref|ZP_07570239.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|312902437|ref|ZP_07761643.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
 gi|227072945|gb|EEI10908.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           TX0104]
 gi|229309836|gb|EEN75823.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           TX1322]
 gi|256684550|gb|EEU24245.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T3]
 gi|256710915|gb|EEU25958.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T8]
 gi|256987868|gb|EEU75170.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis JH1]
 gi|256999617|gb|EEU86137.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis CH188]
 gi|294453447|gb|EFG21853.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|306498517|gb|EFM68019.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|306501251|gb|EFM70554.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|306512931|gb|EFM81572.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|310634107|gb|EFQ17390.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
 gi|315030281|gb|EFT42213.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4000]
 gi|315164911|gb|EFU08928.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1302]
 gi|315170401|gb|EFU14418.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1342]
 gi|315579152|gb|EFU91343.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0630]
          Length = 297

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 113/233 (48%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLD 151
           +++ED    V NKPAGI+        YH  G + + V  KG   R         +  RLD
Sbjct: 80  IVFEDDHFLVVNKPAGIA---SIPAQYHPSGTMANRV--KGYYKRQNYVNQVIHVVTRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L++K  IG D
Sbjct: 135 RDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLNE---HQLIEKP-IGRD 190

Query: 212 YVHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              ++K Q  +   +A + + +    AQ    + +Q HTGRTHQ+RVH   +GC ++GD 
Sbjct: 191 LSSLLKRQVIETGQFASTEYWLAKRGAQA-AAVRIQLHTGRTHQIRVHFEAIGCSLLGDE 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y     G     I+ +  LH   +   HP     + + +PL   M    D+L
Sbjct: 250 MY----HGKMDQGIERQA-LHCMELIFTHPFTKETVHLISPLAEDMKSVDDTL 297


>gi|212636284|ref|YP_002312809.1| pseudouridylate synthase [Shewanella piezotolerans WP3]
 gi|212557768|gb|ACJ30222.1| Pseudouridylate synthase [Shewanella piezotolerans WP3]
          Length = 278

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 108/242 (44%), Gaps = 21/242 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  +   +KPAG+ V   S +A     F ++   D  G      HRLD+ TSGIL+
Sbjct: 29  ILFEDDDVVAIHKPAGLLVHR-SYLARRERFFAMQLTRDKVGCHVFPVHRLDRPTSGILL 87

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA-NWLLKKSHIGGDYVHVVKQ 218
            A++   A  L E F    I K Y ++V G   N  E    ++ LK+     D       
Sbjct: 88  FAKSSEMANALCEQFAAHSIDKEYLAIVRG---NMHEAATLDYALKEE--LDDVADKDVD 142

Query: 219 NEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             K A  AI+ +K +               ++  + + PHTGR HQLR H  H+  PI+G
Sbjct: 143 PNKAAQDAITSYKPLLNSEIPYASGRYATSRYALVHLSPHTGRKHQLRRHMAHLRHPILG 202

Query: 269 DHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           D  +    +  F       N+L+L A+ +   HP  G R+ +   L    +  +D LG+ 
Sbjct: 203 DTTHGDGKQNKFFREHFGINRLWLIAKKLSFNHPRTGERVAVETELEQEWITLFDELGWD 262

Query: 326 YD 327
            D
Sbjct: 263 DD 264


>gi|317182056|dbj|BAJ59840.1| hypothetical protein HPF57_0766 [Helicobacter pylori F57]
          Length = 327

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 105/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLEFKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  H+   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRAHLEHLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|238763442|ref|ZP_04624405.1| Pseudouridine synthase [Yersinia kristensenii ATCC 33638]
 gi|238763523|ref|ZP_04624485.1| Pseudouridine synthase [Yersinia kristensenii ATCC 33638]
 gi|238698305|gb|EEP91060.1| Pseudouridine synthase [Yersinia kristensenii ATCC 33638]
 gi|238698386|gb|EEP91140.1| Pseudouridine synthase [Yersinia kristensenii ATCC 33638]
          Length = 256

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/208 (30%), Positives = 95/208 (45%), Gaps = 18/208 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKPAG+    G     ++D      V        L HRLD  TSG++V+A
Sbjct: 44  LYQDDHLVLINKPAGLLSLSGKN-PQNLDSVHHRLVQIFPGC-TLVHRLDFGTSGLMVIA 101

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +     L + F  R + K+Y +L+ G   N +  I   + K   +    + +   N K
Sbjct: 102 RNKTINAALCQQFSQRTVTKVYSALLCGHLGNNEGVIDAAIAKDPAL-FPLMSICPINGK 160

Query: 222 GANYAISHFKVIDCFAQKFC--------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            A    SH++VI+ F  K           +++ P TGRTHQLR+H   +G PI G   Y 
Sbjct: 161 PAR---SHYQVIERFYHKLADQKLLPLTRVQLTPETGRTHQLRIHCQQLGHPIWGCDLYG 217

Query: 274 AN-FKGNFTSPIQNKLYLHARYMDLPHP 300
                G   +P   +L LHA  +   HP
Sbjct: 218 GRLLPGTEQTP---RLMLHASELHFVHP 242


>gi|119897756|ref|YP_932969.1| hypothetical protein azo1465 [Azoarcus sp. BH72]
 gi|119670169|emb|CAL94082.1| hypothetical protein azo1465 [Azoarcus sp. BH72]
          Length = 260

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 106/236 (44%), Gaps = 29/236 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   +KP+G+ V   +  A+     ++   D  G+     HRLD+ TSG+LV 
Sbjct: 4   ILYQDEHLVAIHKPSGLLVHRSALDAHEERFAVQLLRDQLGRHVHPVHRLDKGTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV-HVVKQN 219
           A  R  A  L   F  R ++K Y ++V G P      I + L ++     D V HV +  
Sbjct: 64  ALDRDTAGRLATQFETRAVRKQYVAIVRGHPAEAG-TIDHPLSRRF----DPVEHVAEDK 118

Query: 220 EKGANYAISHFK---------VIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 AI+ F+          +D +   ++  L ++P TGR HQ+R H  H+  PI+GD
Sbjct: 119 VFAPQPAITRFRRLATAELPWAVDRYPTSRYALLALEPETGRRHQIRRHLKHISHPIIGD 178

Query: 270 HKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
             +        F+ +F S    ++ L    ++L HP     Q  APL  H     D
Sbjct: 179 STFGKGKHNRMFQAHFGS---ERMLLACTDIELRHP-----QRDAPLQLHAAPAPD 226


>gi|149907559|ref|ZP_01896306.1| Pseudouridylate synthase [Moritella sp. PE36]
 gi|149809229|gb|EDM69158.1| Pseudouridylate synthase [Moritella sp. PE36]
          Length = 251

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 105/226 (46%), Gaps = 43/226 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   +KPAG+ V   S +  H   F    V D  GQ     HRLD+ TSG+L+
Sbjct: 4   ILYQDEYLVAIDKPAGLLVHR-SWLDSHETQFAMQMVRDQIGQHVYTVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A +   A+ ++E F+   + K Y ++V G           W+ +   +  DY   V+ +
Sbjct: 63  FALSSEVARQMSEIFQAHALTKRYLAVVRG-----------WINEAGTL--DYALKVELD 109

Query: 220 ---------EKGANYAISHFKVIDCF-----------AQKFCWLEMQPHTGRTHQLRVHA 259
                    +K A  A++H+K +                ++C +E++P TGR HQLR H 
Sbjct: 110 KIADKQATQDKEAQEAVTHYKPLHQVEIPYPISKNHPTSRYCLMELEPQTGRKHQLRRHM 169

Query: 260 LHMGCPIVGDH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            H+  PIVGD      ++   ++ +F  P   +L L A+ +   HP
Sbjct: 170 KHLFHPIVGDTTHGDGRHNVFYREHFELP---RLLLIAKSLSFIHP 212


>gi|251790751|ref|YP_003005472.1| tRNA pseudouridine synthase C [Dickeya zeae Ech1591]
 gi|247539372|gb|ACT07993.1| pseudouridine synthase [Dickeya zeae Ech1591]
          Length = 260

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 100/227 (44%), Gaps = 46/227 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKPAG  V              +SW+D K             GQ     
Sbjct: 4   IIYQDEHLIAVNKPAGWLVH-------------RSWLDRKEKVVVMQTVRDQIGQHVFTV 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++A +   A+ L + F   R++K Y ++V G     ++ + ++ L +  
Sbjct: 51  HRLDRPTSGVLLMALSADVARLLAQQFEQHRMEKTYHAVVRGY--VMEDGVIDYALTEEL 108

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQL 255
             I   +       +K    A+SH++V+               ++  LE+ P TGR HQL
Sbjct: 109 DRIADKFA----DPDKAPQPAVSHYRVLARAEMPVAIGRYDTARYSLLELSPKTGRKHQL 164

Query: 256 RVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           R H  H+  PI+GD  H      +G        +L LHA  + L HP
Sbjct: 165 RRHMAHLRHPIIGDTTHGDLRQNRGMAAYFGCARLMLHASRLSLTHP 211


>gi|150010359|ref|YP_001305102.1| RNA pseudouridylate synthase [Parabacteroides distasonis ATCC 8503]
 gi|255012377|ref|ZP_05284503.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_7]
 gi|256839209|ref|ZP_05544719.1| RNA pseudouridylate synthase [Parabacteroides sp. D13]
 gi|149938783|gb|ABR45480.1| RNA pseudouridylate synthase [Parabacteroides distasonis ATCC 8503]
 gi|256740128|gb|EEU53452.1| RNA pseudouridylate synthase [Parabacteroides sp. D13]
          Length = 304

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 108/228 (47%), Gaps = 28/228 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI----AYHI-DGFLKSWVDSKGQKPR----LTHRLD 151
           +++ED  + V NK  G+       I    AY I   +LK         PR    + HRLD
Sbjct: 93  IVWEDDDLIVINKREGLLSVSTDRIKERTAYRILSDYLKEC------DPRNKIFVLHRLD 146

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSGI++ A+ +   + L  ++     Q+ Y +++ G P+   + I + L++  H+   
Sbjct: 147 RDTSGIMMFAKNQKVKEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIVSNLVENKHM--- 203

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V+V +  +     AI+ ++++     ++  +E+   TGR +Q+R     +G PI GD K
Sbjct: 204 QVYVTQDGD--GKEAITRYRLLQT-NNRYSLVELDLETGRKNQIRAQMQSIGHPIAGDSK 260

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           Y A      T+P   +L LHAR +   HP  G  ++    +P     T
Sbjct: 261 YGAE-----TNPA-GRLMLHARRLCFIHPVTGEEMRFETRIPEKFTST 302


>gi|303278324|ref|XP_003058455.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226459615|gb|EEH56910.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 417

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 98/227 (43%), Gaps = 49/227 (21%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGI-SVQGGS-----GIAYHIDGFLKSWVDSKGQKPRLT 147
           SD  +  + YED+ + V  KP G+ SV  G+      + Y++    +  V+    +PR  
Sbjct: 166 SDLPRLEIAYEDNHMAVIVKPEGMPSVGDGAWNAERALPYYLRETRR--VEGALSRPRPV 223

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--------------IPKN 193
           HRLD  TSG+LV A+TR A   L+ +F  R  +K Y +++ G               P  
Sbjct: 224 HRLDAATSGLLVCAKTRLAMTSLSVAFARREPKKRYRAVLAGAAGGWESGSEGVADAPLE 283

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K C+  W + +         V   +  G                +   ++  P TGRTH
Sbjct: 284 GKPCVTRWRVDR---------VAPCSRHG----------------RVTLMDFAPETGRTH 318

Query: 254 QLRVHALH-MGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLP 298
           QLR HA   + CPIVGD +Y       F     ++ L+L A  + LP
Sbjct: 319 QLRRHAAESLRCPIVGDFRYTKKSDDAFGGLDDRDGLFLAAVEISLP 365


>gi|197248998|ref|YP_002147874.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197212701|gb|ACH50098.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
          Length = 260

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 108/232 (46%), Gaps = 21/232 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +     + +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFA----RED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
           K+  + + N ++       +L LHA  ++L HP  G+  I   + A + +TW
Sbjct: 180 KH-GDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLI---IQAGLDETW 227


>gi|323966769|gb|EGB62200.1| RNA pseudouridylate synthase [Escherichia coli M863]
 gi|323978598|gb|EGB73680.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
 gi|327251531|gb|EGE63217.1| RNA pseudouridylate synthase family protein [Escherichia coli
           STEC_7v]
          Length = 260

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   IIYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|320527002|ref|ZP_08028191.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
 gi|320132587|gb|EFW25128.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
          Length = 293

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 101/230 (43%), Gaps = 21/230 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHID----GFLKSWVDSKGQKPRLTHRLDQE 153
           K I+LYED+ I V NKPAGI        A H D      LK +        R   RLD+ 
Sbjct: 73  KPIILYEDTDIVVVNKPAGIPSHAS---AEHFDDDMGSILKRYYQDDAFTVRTVGRLDKG 129

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
            SGI+V A+T+  A  L  +   + + K Y ++V G  + K   +   L K+  I G  V
Sbjct: 130 VSGIVVYAKTKQMAALLASACEEQLLHKEYLAIVKGKFEEKWGKLIYTLGKEKGIRGRSV 189

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               Q        I++++VI      F  +++   TGR HQ+R    + G P++GD  Y 
Sbjct: 190 TADGQK------CITNYEVI-TEGNFFSLIKVHIETGRLHQIRAGMAYFGHPLIGDRLYG 242

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +           +  LH   ++  HP+  + + I   LP  M K  D L
Sbjct: 243 GSMHA------MKRPALHCWKVEFIHPKTKKQISIECELPTDMQKVVDKL 286


>gi|207092511|ref|ZP_03240298.1| hypothetical protein HpylHP_06295 [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 327

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 57/227 (25%), Positives = 106/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W+ SK       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVVHKAPSVK---EPTLVDWLKSKNYELSNLGLKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N  G      + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN--GALPKE-EIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|282859900|ref|ZP_06268988.1| pseudouridine synthase, RluA family [Prevotella bivia JCVIHMP010]
 gi|282587303|gb|EFB92520.1| pseudouridine synthase, RluA family [Prevotella bivia JCVIHMP010]
          Length = 577

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/217 (29%), Positives = 103/217 (47%), Gaps = 35/217 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED+ + V +KPAG+    G  +A  +   LK     +  KP + HRLD +TSG++VV
Sbjct: 364 ILFEDNYLAVIDKPAGLLSVPGKKLATSVYALLKQKWQGRC-KPYMVHRLDMDTSGLMVV 422

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLV------WGIPKNKKECIANWLLKKSHIGGDYVH 214
           A+       L + F  R + K Y + +        +P   K  +         +  D   
Sbjct: 423 AKQAHVYHDLQQQFINRTVNKRYTAFLPLSLLDKNLPPKGKIILP--------LTADLFD 474

Query: 215 VVKQ--NEKGANYAISHFKVI------DCFAQKFCWLEMQPHTGRTHQLRVHALH---MG 263
             +Q  +++    AI+ ++++      +   Q    + + PHTGRTHQLRVH  H   +G
Sbjct: 475 RPRQKVDKEVGKIAITTYEIVGKTHYGERLKQLAVRVLLYPHTGRTHQLRVHCAHSEGLG 534

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            PI+GD+ Y     GN      N+L+L+A  +   HP
Sbjct: 535 TPIIGDNLY-----GNKA----NRLHLYADRLRFVHP 562


>gi|182417587|ref|ZP_02948909.1| pseudouridine synthase, RluA family [Clostridium butyricum 5521]
 gi|237668273|ref|ZP_04528257.1| pseudouridine synthase, RluA family [Clostridium butyricum E4 str.
           BoNT E BL5262]
 gi|182378542|gb|EDT76071.1| pseudouridine synthase, RluA family [Clostridium butyricum 5521]
 gi|237656621|gb|EEP54177.1| pseudouridine synthase, RluA family [Clostridium butyricum E4 str.
           BoNT E BL5262]
          Length = 324

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/276 (24%), Positives = 128/276 (46%), Gaps = 30/276 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + + ++E   RLD++ +     +    + K LR   +RV+ K+      ++ G +V I  
Sbjct: 3   IEIGSNEAGQRLDKFLRKLLKDVPLSAIFKALRKKDIRVNGKKQNEKYFLEEGDIVEIKY 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
           +         + K  D +    K  D  +  + +ED  + +  K  GI V   +      
Sbjct: 63  I---------QSKKEDKTQKFIK-VDPKRMKICFEDENMVIVEKWPGILVHSDTNDNKEP 112

Query: 129 -IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            +  ++ S+++ KG           P   +RLD+ TSGI++  +T    + + E+ R   
Sbjct: 113 TLTDYVLSYLNDKGDYLPENEITFTPAACNRLDRNTSGIIMYGKTFEGLKCINEAIREDE 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           ++K Y++L  G  K K      +++K  +++I   Y   VK ++K A        V++  
Sbjct: 173 VKKYYYTLAKG--KVKSGLYEGYIVKNPETNISTVYDKEVKNSKKIA----MDVNVVETN 226

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              + ++E+   TGR+HQ+R H  H+G PI+GD+KY
Sbjct: 227 GA-YSFVEINLITGRSHQIRAHLAHVGNPIIGDNKY 261


>gi|123440998|ref|YP_001004987.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|122087959|emb|CAL10747.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. enterocolitica 8081]
          Length = 196

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 57/159 (35%), Positives = 83/159 (52%), Gaps = 14/159 (8%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG     +  I   L+    
Sbjct: 38  HRLDMATSGVIVVALTKAAERELKRQFREREPKKSYVARVWGHLAQDEGLIDLPLI---- 93

Query: 208 IGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              D+ +  KQ    E G + + + ++V+   A     +++ P TGR+HQLRVH L +G 
Sbjct: 94  --CDWPNRPKQKVCYETGKS-SQTQYQVLSRDADGSTRVKLSPITGRSHQLRVHMLAIGH 150

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           PI+GD  Y         S    +L LHA+ + + HPE G
Sbjct: 151 PILGDGFYAHPEAKAMAS----RLQLHAQELCITHPEFG 185


>gi|260593437|ref|ZP_05858895.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           veroralis F0319]
 gi|260534713|gb|EEX17330.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           veroralis F0319]
          Length = 565

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 74/266 (27%), Positives = 120/266 (45%), Gaps = 52/266 (19%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           ++  L   + E+KI+ S+    K ++ +K   LYED  + V  KP+G+    G G    +
Sbjct: 328 MLKGLQTPLCEEKIVPSN---KKEAERIKLETLYEDDYLAVVVKPSGLLSVPGKGDKPSV 384

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-- 187
              LK+  + K     + HRLD  TSG+LVVAR+    + L   F  R ++K Y +L+  
Sbjct: 385 YSLLKTQWNGKSDV-FIVHRLDMATSGLLVVARSLEIYKALQAQFIQRSVKKTYVALLPM 443

Query: 188 ------------------WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
                               I    ++C+ ++L  K  I  DY HV+ +     +Y   +
Sbjct: 444 SFLDKAYPSSGRIELPLSPDINDRPRQCV-DYLHGKRAI-TDY-HVIGET----SYGKEN 496

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQN 286
              +         +E+ P TGRTHQLR+H  H   +  PI+GD+ Y              
Sbjct: 497 LPAVK--------IELHPLTGRTHQLRIHCAHPDGLDTPIIGDNLYGQR---------AE 539

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPL 311
           +L+LHA +++  +P    R+   APL
Sbjct: 540 RLWLHAEHLEFTYPITQERMVFNAPL 565


>gi|237807990|ref|YP_002892430.1| pseudouridine synthase Rlu family protein [Tolumonas auensis DSM
           9187]
 gi|237500251|gb|ACQ92844.1| pseudouridine synthase Rlu family protein, TIGR01621 [Tolumonas
           auensis DSM 9187]
          Length = 211

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 56/205 (27%), Positives = 97/205 (47%), Gaps = 19/205 (9%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSK----GQKPRLTHRLDQETSGILVVARTRA 165
           VF++P  + V   +GI  H D  +   V       GQ     HRLD+ TSG++++A+ + 
Sbjct: 11  VFDQPDFLVVNKMTGIDMHDDAGVPGLVSRVSAFLGQNVYPVHRLDKVTSGLVLLAKNKE 70

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           A + L+++F  R ++K Y ++    PK K+  I   + K  +     +H         N 
Sbjct: 71  ATRLLSQAFADRLVKKTYLAISDRAPKKKQGWIKGDMAKGRNGSWKLLH------SSDNP 124

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           A++ F+ +     +     + PHTG+THQ+RV    +G PI+GD +Y  +          
Sbjct: 125 AVTRFQSVSLTLPRHRLYIVSPHTGKTHQIRVALKSIGAPILGDERYGGS--------AA 176

Query: 286 NKLYLHARYMDLPHPEGGRLQITAP 310
           ++ YLHA  +   +  G    + AP
Sbjct: 177 DRTYLHAWQLHFTY-AGAEYTVEAP 200


>gi|320527944|ref|ZP_08029110.1| RNA pseudouridine synthase [Solobacterium moorei F0204]
 gi|320131570|gb|EFW24134.1| RNA pseudouridine synthase [Solobacterium moorei F0204]
          Length = 223

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/234 (25%), Positives = 102/234 (43%), Gaps = 21/234 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +    KP  I V         +    K ++  K QKP      L HRLD+   
Sbjct: 4   VLYEDNHVLCVEKPINIPVMEDDSHDMDLLTMCKEYLKEKYQKPGNVYCGLVHRLDRPVG 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  L+E+ R  +++K Y +++ GIP  K + + ++L K +      V  
Sbjct: 64  GVMVFAKTSKAASRLSEAVRTHQLKKEYIAILDGIPIKKADTLEDYLSKDTRTNTVSVTD 123

Query: 216 VKQNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            K  +K   +Y +   K       K   + +   TGR+HQ+RV       P++ D +Y  
Sbjct: 124 AKHGKKCHLSYEVIGQK------SKQSLVHIVLGTGRSHQIRVQFASRKLPLIHDQRYNP 177

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           +         +  + L+A  +  PHP      +    P+  +  W      YD+
Sbjct: 178 HT-------TKGPIGLYAFRLTFPHPTLKTPIVVQATPSQSI--WKEFEVNYDK 222


>gi|239826305|ref|YP_002948929.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239806598|gb|ACS23663.1| pseudouridine synthase, RluA family [Geobacillus sp. WCH70]
          Length = 298

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/283 (24%), Positives = 135/283 (47%), Gaps = 44/283 (15%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           G + VD++ V   +R+  G+ +R+  P  +    ++ E   LD               ++
Sbjct: 41  GAIFVDEQPVTVRHRLCCGETLRVLFPKESPSEGMMPEAIPLD---------------IV 85

Query: 103 YEDSKIYVFNKPAGISV------QGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           YED  + V NKP  ++        GG+    + YH   + K  ++S      +  RLD++
Sbjct: 86  YEDEYVLVVNKPPFMATIPSREHPGGTLANALLYH---YKKQQLESTIH---VVTRLDRD 139

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++VA+ R     L+   +  ++ + Y ++  G     +  I   + +KS    D +
Sbjct: 140 TSGLVLVAKHRHVHHLLSTLQQQGKVTRCYEAICHGCLVEDEGTIDAPIARKS----DSI 195

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + ++  K    A++HF+V+  F +++ ++ ++  TGRTHQ+RVH  H+G P+ GD  Y 
Sbjct: 196 -IEREVRKDGQRAVTHFRVLQRF-REYTYVSLRLETGRTHQIRVHLAHIGHPLAGDELYG 253

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
            + +        ++  LH++ +   HP   ++   + PLP  M
Sbjct: 254 GSREAI------SRQALHSKELSFFHPIKRKIYTFSCPLPDDM 290


>gi|295401674|ref|ZP_06811641.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111991|ref|YP_003990307.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
 gi|294976294|gb|EFG51905.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311217092|gb|ADP75696.1| pseudouridine synthase, RluA family [Geobacillus sp. Y4.1MC1]
          Length = 300

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 76/325 (23%), Positives = 149/325 (45%), Gaps = 42/325 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           + ++V + DE  +  +   +N       ++++     G + V+ + V   +R+  G+ +R
Sbjct: 7   LTWIVTKQDEGKLIREFLKENGISKTALIDIK--FHGGAIYVNDQPVTVRHRLGEGETLR 64

Query: 67  I--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +  PP + +   +  E   LD               ++YED  + V NKP  ++      
Sbjct: 65  VVFPPELPS-EGMAPEAIPLD---------------IVYEDEHVIVVNKPPFMATIPSR- 107

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRR 178
              H  G L + +    +K +LT       RLD++TSG++++A+ R     L+   +  +
Sbjct: 108 --EHPGGTLANALLYHYEKQQLTSTIHVVTRLDRDTSGLVLIAKHRHIHHLLSTLQKQGK 165

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + + Y ++  G     +  I   + +KS    D + + ++  +    A++HF+V+  F +
Sbjct: 166 VARRYEAICHGRVSKDEGTIDAPIARKS----DSI-IAREVREDGQRAVTHFRVLQRF-R 219

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  L +Q  TGRTHQ+RVH  H+G P+ GD  Y     G   + I ++  LH++ +   
Sbjct: 220 DYTHLSLQLETGRTHQIRVHLAHIGHPLAGDELY-----GGSRNAI-DRQALHSKELSFF 273

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSL 322
           HP +      + PLP  M +  + L
Sbjct: 274 HPLKKQAYTFSCPLPDDMQRLIERL 298


>gi|303280505|ref|XP_003059545.1| pseudouridine synthase [Micromonas pusilla CCMP1545]
 gi|226459381|gb|EEH56677.1| pseudouridine synthase [Micromonas pusilla CCMP1545]
          Length = 423

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/183 (34%), Positives = 85/183 (46%), Gaps = 22/183 (12%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-ECIANWLL 203
           R  H+LD  TSG+LV A  + AA    + FR R  +K Y +LV+G P+  +  C A    
Sbjct: 240 RFVHQLDNATSGVLVAASNKRAAGRAAKLFRERAARKAYIALVFGHPREDEWTCDAKLGR 299

Query: 204 KKSHIGGDYVHVVKQNEK---GANYAISHFKVID--CFAQK-------FCWLEMQPHTGR 251
             S   G    VV   E+       + + FKV+    FA +          + + P TGR
Sbjct: 300 DPSDPKGFKERVVVDGEEEGVEGKASETRFKVLQRGTFALRGKHEGADVSKVLVTPITGR 359

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP--EGGRLQITA 309
            HQ+RVH  H G PIVGD  Y  + K  F      + +LHA  + LP    +GG    TA
Sbjct: 360 RHQIRVHLAHGGYPIVGDAAYSED-KDTF------RTFLHAHALTLPFDAKDGGTKTFTA 412

Query: 310 PLP 312
           P P
Sbjct: 413 PEP 415


>gi|254509017|ref|ZP_05121122.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus 16]
 gi|219548052|gb|EED25072.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus 16]
          Length = 240

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 110/239 (46%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IIYQDDYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +          ++   I   +    K+ +
Sbjct: 64  ALSSEVASQVMPMFANHEMEKTYHAIVRGWIEESGRLDYALKVELDKIADKHASQDKEAQ 123

Query: 221 KGAN--YAISHFKVIDCFAQ----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH---- 270
           +     + ++  +V     +    ++C +EM+P TGR HQLR H  H+  PIVGD     
Sbjct: 124 EAITDYWPLAKVEVPHSTGKFPTTRYCLMEMKPLTGRKHQLRRHMAHLRHPIVGDTTHGD 183

Query: 271 -KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
            K+   F+  + S   ++L LHA  ++  HP    +L I A +     +TW +L  ++D
Sbjct: 184 GKHNKLFRDVYDS---HRLLLHASSLEFVHPFTNEKLLIKASVD----ETWQALCQEFD 235


>gi|313889046|ref|ZP_07822704.1| pseudouridine synthase, RluA family [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312844919|gb|EFR32322.1| pseudouridine synthase, RluA family [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 298

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/281 (23%), Positives = 136/281 (48%), Gaps = 35/281 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K ++SG + ++ +  + N  ++ G +V +       N  + EQK LD           
Sbjct: 38  IRKSVKSGNIYLNSRVNRKNKFLKKGDLVSLRFEDEEPNGGV-EQKDLD----------- 85

Query: 97  LKSILLYEDSKIYVFNK-PAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQE 153
               ++YED  + + NK P  ++          +  +L  + + +G  +K R  +RLD++
Sbjct: 86  ----IIYEDDDLVIVNKEPFMVTHTAKDDADGTLLNYLLGYFEEEGLKRKVRFVNRLDRD 141

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDY 212
           TSG++V A+   A   ++  F+   ++K Y ++V G+ + K+  I   +   +  I  + 
Sbjct: 142 TSGLVVAAKNSFAQDKISSDFK-EDVKKKYLAVVEGVFEEKEGLIDGPIATSEDGIRREV 200

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +V+ +       +++ ++V+D + +    + +  HTGRTHQ+RVH  H+G PI+GD  Y
Sbjct: 201 NYVIGKR------SLTSYEVLDEY-KDMSLVLLTLHTGRTHQIRVHMAHIGHPILGDSLY 253

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                    S + N+  LH+  +    P   + +++ A LP
Sbjct: 254 GK------KSDLINRQALHSYSLKFKLPRNNKEIEVYAKLP 288


>gi|299473311|emb|CBN77710.1| pseudouridylate synthases, 23S RNA-specific [Ectocarpus
           siliculosus]
          Length = 256

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 107/215 (49%), Gaps = 18/215 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---KPRLTHRLDQETSGI 157
           +L+ D +I V NKP+ +    G       D          G       + HRLD  TSG 
Sbjct: 52  ILFVDEEIVVCNKPSDLLCVPGR---IEKDSLATRAALELGHYRVDRMIVHRLDMATSGC 108

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++ART AA + L   FR R+++K Y ++V G+    +  +   L +    G   +H+V 
Sbjct: 109 VIMARTDAALKDLNRQFRERQVRKRYVAIVHGVLWADEGEVDLPLCRNR--GCPPLHMV- 165

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            N +    +++ ++V+D  A +   +E+ P +GR+HQLR+H   +G PI+GDH     F 
Sbjct: 166 -NFEHGKPSLTKWRVLDRAADRT-RVELIPVSGRSHQLRLHMNAIGHPILGDH-----FY 218

Query: 278 GNFTS-PIQNKLYLHARYMDLPHPEGG-RLQITAP 310
           G   S  +  +  LHA  + L HP+ G R   TAP
Sbjct: 219 GTTDSLALAGRCLLHAHTLCLRHPKTGERTMFTAP 253


>gi|307253996|ref|ZP_07535844.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
 gi|306863022|gb|EFM94968.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
          Length = 201

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 59/186 (31%), Positives = 92/186 (49%), Gaps = 24/186 (12%)

Query: 110 VFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           + +KP G+SV   +   G+  ++   L++      ++  L HRLD+ TSG+L+ A  + A
Sbjct: 1   MIDKPVGVSVHKDEEAIGLTENLAEQLQA------EQVWLVHRLDKVTSGLLIFALNKQA 54

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           A H    F   +I+K YW+L    PK K+  I+   ++KS  G   +   KQN      A
Sbjct: 55  AVHFYHLFEQHKIEKTYWALSDQKPKKKQGKISG-DMQKSRNGAWKLFHSKQNP-----A 108

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++ F V            +QP TG+THQLRV    +G PI+GD +Y             +
Sbjct: 109 VTQF-VSHSLEPNLRHFILQPKTGKTHQLRVAMKSLGSPILGDQRYAGT--------AAD 159

Query: 287 KLYLHA 292
           ++YLHA
Sbjct: 160 RVYLHA 165


>gi|91789312|ref|YP_550264.1| ribosomal large subunit pseudouridine synthase A [Polaromonas sp.
           JS666]
 gi|91698537|gb|ABE45366.1| ribosomal large subunit pseudouridine synthase A [Polaromonas sp.
           JS666]
          Length = 223

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/217 (29%), Positives = 104/217 (47%), Gaps = 12/217 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D    V  KP+G+    G G        L + V  +  +  + HRLD  TSG++V+
Sbjct: 13  IVHTDDLFLVLRKPSGLLAVPGRG--EDKQDCLSTRVQQQHPEALVVHRLDMGTSGLVVM 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---VVK 217
           AR+R A + L+++F  R + K Y ++V G+     +    W      I  D+      V 
Sbjct: 71  ARSREAQRALSKAFAERAVHKRYVAVVDGLMAAPADSPDGWGRIDLPIIVDWARRPLRVI 130

Query: 218 QNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             E+G   +++ +++     Q+    L ++P TGR+HQLRVH   +G PIVGD  Y    
Sbjct: 131 DAERG-KPSVTRWQIQHHDRQRNTTRLLLEPVTGRSHQLRVHLQAIGHPIVGDALYATPA 189

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                     +L LHA  +   HP GG+ +Q  +P P
Sbjct: 190 VAAGA----GRLLLHACRLAFAHPLGGQWMQFESPPP 222


>gi|26249194|ref|NP_755234.1| tRNA pseudouridine synthase C [Escherichia coli CFT073]
 gi|34582426|sp|Q8FEF9|TRUC_ECOL6 RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|26109601|gb|AAN81804.1|AE016765_206 Hypothetical protein yqcB [Escherichia coli CFT073]
          Length = 260

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/261 (26%), Positives = 113/261 (43%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDY---------VHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY              + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLAEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LAIHAGLDDTWMQALSQFGWR 237


>gi|217958782|ref|YP_002337330.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|217067935|gb|ACJ82185.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
          Length = 297

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 72/280 (25%), Positives = 131/280 (46%), Gaps = 38/280 (13%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           G + V+ +     +++Q+G+ +R+  PV      +I E   L                ++
Sbjct: 41  GSIEVNGQHASVRHQLQAGEELRVFFPVEERSEGMIAEDIPL---------------CIV 85

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQETSG 156
           YED  + V NK A +S         H  G + + + S   K  LT       RLD++TSG
Sbjct: 86  YEDDAVLVINKEANMSTIPSR---EHPAGSVANALLSHYDKRHLTSTVHIVTRLDRDTSG 142

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +   
Sbjct: 143 LMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKS----DSIIER 198

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E+G   A++HF+VID    K   + ++  TGRTHQ+RVH  ++G P++GD     N 
Sbjct: 199 TVCEEG-QRAVTHFRVIDSVNHK-THVSLELDTGRTHQIRVHMAYIGHPLLGD-----NL 251

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH+  +   HP     +  T P+P+ M
Sbjct: 252 YGGKRDEMKRQ-ALHSTSLTFYHPILEKEMSFTTPIPSDM 290


>gi|68248593|ref|YP_247705.1| putative pseudouridine synthase [Haemophilus influenzae 86-028NP]
 gi|68056792|gb|AAX87045.1| conserved hypothetical pseudouridine synthase [Haemophilus
           influenzae 86-028NP]
          Length = 224

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 95/203 (46%), Gaps = 28/203 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+ S   + NK  GISV      QG + +        K W         L HRLD+ T
Sbjct: 5   VVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQLNVPKVW---------LVHRLDKVT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A    +A   +  F   +I K Y +L    PK K+  I    +KKS  G   + 
Sbjct: 56  SGLLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGD-MKKSREGAWKLC 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K+N      AI+ F  + C      ++ ++P TG+THQLRV    +G PI+GD  Y  
Sbjct: 115 QTKENP-----AITRFASVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDGLYGK 168

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
           N     T  I ++ YLHA  ++ 
Sbjct: 169 N-----TEKI-DRTYLHATQLEF 185


>gi|308807815|ref|XP_003081218.1| COG0564: Pseudouridylate synthases, 23S RNA-specific (ISS)
           [Ostreococcus tauri]
 gi|116059680|emb|CAL55387.1| COG0564: Pseudouridylate synthases, 23S RNA-specific (ISS)
           [Ostreococcus tauri]
          Length = 377

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 57/186 (30%), Positives = 92/186 (49%), Gaps = 18/186 (9%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG+++ A T++AA    + FR R+ +K Y ++V+G P+  +      L K
Sbjct: 191 RFCHQLDTATSGVILTAHTKSAAAAAAKLFRDRKAKKTYLAVVYGWPERDEWTTTAKLGK 250

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQ------KFCWLEMQPHTGRTHQL 255
             +    +   V  +E+G   + + FKV+    C         K   L+ +P TGR HQ+
Sbjct: 251 DPNCPKGFRERV--DEEGGKASETRFKVLRRGYCTLDGAHRGIKVTLLQCKPVTGRRHQI 308

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAH 314
           RVH  H G PI+GD  Y +    +F      +++LHA  + +P P E    +   PL   
Sbjct: 309 RVHLQHSGFPILGDIAYYSGVSDSF------RMFLHALELVMPFPDETLTFKTDPPLAFE 362

Query: 315 MVKTWD 320
           +V + D
Sbjct: 363 LVVSAD 368


>gi|77360181|ref|YP_339756.1| ribosomal large subunit pseudouridine synthase A (pseudouridylate
           synthase, 23S RNA-specific) [Pseudoalteromonas
           haloplanktis TAC125]
 gi|76875092|emb|CAI86313.1| ribosomal large subunit pseudouridine synthase A (Pseudouridylate
           synthase, 23S RNA-specific) [Pseudoalteromonas
           haloplanktis TAC125]
          Length = 570

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 94/203 (46%), Gaps = 18/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NKPA      G  I   +   +K+        P + HRLD  TSG+L++
Sbjct: 369 IIYQDQDILVINKPAEFLSVPGVNIEDSVYLRIKTQF-PHATGPLIVHRLDMSTSGLLII 427

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + A + L + F  R I+K Y +LV G        I +  L+          V  Q+ 
Sbjct: 428 ALNKRAHKALQKQFIERTIEKRYVALVAGNVVQNSGTI-DLPLRLDFDDKPRQLVCYQHG 486

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFK 277
           K +   ++ ++V++        L + P TGRTHQLRVH  H   +  PIVGD  Y     
Sbjct: 487 KAS---LTTWQVLE-RKDNITRLHLYPKTGRTHQLRVHCAHKLGLNMPIVGDDHYGEK-- 540

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
                   N+L+LHA Y+   HP
Sbjct: 541 -------ANRLHLHAEYLSFCHP 556


>gi|295095907|emb|CBK84997.1| Pseudouridylate synthases, 23S RNA-specific [Enterobacter cloacae
           subsp. cloacae NCTC 9394]
          Length = 228

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 105/227 (46%), Gaps = 17/227 (7%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I+D+ +    H D     +L++D  + + NKP+G+    G     ++D      V +   
Sbjct: 4   IIDTFIAPPCHDDIE---ILWQDEHLLLINKPSGLLSLSGKN-PQNLDSVHHRLVQTF-P 58

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD  TSG++V+AR +A    L   F  R + K+Y +L+ G  +  +  +   +
Sbjct: 59  GCTLVHRLDFGTSGLMVIARNKAINAALCHQFSQRAVNKVYTALLCGHVEQDEGTVDAPI 118

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ----KFCWLEMQPHTGRTHQLRVH 258
            K   +      ++    +    A S ++V++   Q        +E+ P TGRTHQLR+H
Sbjct: 119 AKDPAL----FPLMTICARTGKPARSRYRVVERIYQDTTMPLTRVELTPETGRTHQLRIH 174

Query: 259 ALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              +G PI+G   Y    + G   +P   +L LHA  ++  HP  G 
Sbjct: 175 CQQLGHPILGCDLYGGLEWPGAEETP---RLMLHASALNFIHPLSGE 218


>gi|255974981|ref|ZP_05425567.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T2]
 gi|307285489|ref|ZP_07565628.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
 gi|255967853|gb|EET98475.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T2]
 gi|306502713|gb|EFM71978.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
          Length = 297

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 82/302 (27%), Positives = 142/302 (47%), Gaps = 35/302 (11%)

Query: 34  FVNLQKILRS--GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           F+N Q + +    +V+    +++ N  +Q+     I P+      ++K   I D + + T
Sbjct: 18  FLNEQGVSKGLLAKVKFQGGKIQVNGTVQNA----IYPL--QTGDVVK-MTIPDEAEHET 70

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR------ 145
             +D     +++ED    V NKPAGI+        YH  G + + V  KG   R      
Sbjct: 71  LLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRV--KGYYKRQNYVNQ 125

Query: 146 ---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L
Sbjct: 126 VIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLSE---HQL 182

Query: 203 LKKSHIGGDYVHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           ++K  IG D   ++K Q  +   +A + + +    A K   + +Q HTGRTHQ+RVH   
Sbjct: 183 IEKP-IGRDLSSLLKRQVIETGQFASTEYWLAKRGA-KAAAVRIQLHTGRTHQIRVHFEA 240

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
           +GC ++GD  Y     G     I+ +  LH   +   HP     + + +PL   M    D
Sbjct: 241 IGCSLLGDEMY----HGKMDQGIERQA-LHCMELIFTHPFTKETVHLISPLAEDMKSVDD 295

Query: 321 SL 322
           +L
Sbjct: 296 TL 297


>gi|315500070|ref|YP_004088873.1| pseudouridine synthase [Asticcacaulis excentricus CB 48]
 gi|315418082|gb|ADU14722.1| pseudouridine synthase [Asticcacaulis excentricus CB 48]
          Length = 205

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/220 (29%), Positives = 110/220 (50%), Gaps = 34/220 (15%)

Query: 102 LYEDSKIYVFNKPAGI-SVQG-----GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           LY D  + VF+KPAG+ SV G        +A  +      W D+      + HRLD  TS
Sbjct: 4   LYADDSVLVFDKPAGLLSVPGRLPENKDSLALRVQAL---WPDAL-----IVHRLDMATS 55

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGG 210
           G++++AR   A + L+ +F  R++ K Y ++V G    ++       I +W  +      
Sbjct: 56  GLILMARGAEAHRSLSIAFAERQVAKRYVAVVAGEVAAEQGEVDLPLICDWPNRPRQ--- 112

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                 K + +    +++ + V+   A +   + ++P TGR+HQLR+H + +G PI+GD 
Sbjct: 113 ------KVDHEVGKPSLTRYAVLAREAGR-TRVALEPVTGRSHQLRLHMMALGHPILGDE 165

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
            Y  + +    SP   +L LHA Y+  PHP +  R+++ A
Sbjct: 166 FYAPD-EVRALSP---RLLLHAEYLAFPHPADERRIEVAA 201


>gi|309799108|ref|ZP_07693361.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus infantis SK1302]
 gi|308117343|gb|EFO54766.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus infantis SK1302]
          Length = 291

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 92/201 (45%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP  +   G       +   + ++V   GQ   + HRLD+ETSG+++ A
Sbjct: 84  VYQDQHLIIVNKPEDMKTHGNQPEEITLLNHVSAYV---GQTCYVVHRLDKETSGLILFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   +K+      L+ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLEKKEISREYWALVEGKVGSKE------LIFRDKIGRDRHDRRKRVVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   YA +H   +  F  K   +  +  TGRTHQ+RVH  H G  I+GD  Y  + K  
Sbjct: 195 FKNGQYAETHVTRLKQFQNKTSLVRCRLKTGRTHQIRVHLSHHGHSILGDPLYNPHSK-- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 253 -----TKRLMLHAFKLSFVHP 268


>gi|251792493|ref|YP_003007219.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           aphrophilus NJ8700]
 gi|247533886|gb|ACS97132.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           aphrophilus NJ8700]
          Length = 238

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/194 (32%), Positives = 92/194 (47%), Gaps = 22/194 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           ++++     V NKP GISV        H D  L   V  +   P+  L HRLD+ TSG+L
Sbjct: 5   IVFQHPDFIVINKPNGISVHKD-----HADVGLTRLVAQQLGVPQVWLVHRLDKVTSGLL 59

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A    AA  L+  F   +IQKIY +L    PK K+  I+   ++K+  G       K 
Sbjct: 60  ILALNEKAAVTLSRKFAEHQIQKIYLALSTQKPKKKQGRISG-DMQKARRGA-----WKL 113

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +   N AI+ F V    A       + P TG+THQ+RV    +G PI+GD  Y      
Sbjct: 114 CQSKENPAITDF-VSHSLAPNLRLFILYPKTGKTHQIRVAMKSLGSPILGDELYGGE--- 169

Query: 279 NFTSPIQNKLYLHA 292
                + ++ YLHA
Sbjct: 170 -----VADRTYLHA 178


>gi|197286814|ref|YP_002152686.1| ribosomal large subunit pseudouridine synthase [Proteus mirabilis
           HI4320]
 gi|194684301|emb|CAR45870.1| putative ribosomal large subunit pseudouridine synthase [Proteus
           mirabilis HI4320]
          Length = 232

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/230 (30%), Positives = 107/230 (46%), Gaps = 27/230 (11%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I+D+ +  T H    K   LY+D  + V NKP+G+    G     +ID      V    +
Sbjct: 4   IIDTFIAPTCHD---KIEYLYQDEHLLVINKPSGLLSLSGKN-PQNIDSVHYRLVPLFPE 59

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD  TSG++V+A  +A  + L + F  R + K Y +L+ G  +N    I    
Sbjct: 60  C-TLVHRLDFGTSGVMVIALNKAINRALCQQFSQRTVTKAYDALLCGHLQNDSGVI---- 114

Query: 203 LKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFC--------WLEMQPHTGRT 252
             ++ I  D  H  +   +      A S+++VI+ F Q            + + P TGRT
Sbjct: 115 --EAPIAKDPQHFPRMSISTTQGKAARSYYQVIERFYQTLADGTRLPLTRVRLTPETGRT 172

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHP 300
           HQLR+H  ++G PI+G    C  + G   S  ++  +L LHA  +   HP
Sbjct: 173 HQLRIHCQYIGHPILG----CDLYGGLLLSGTEHTPRLMLHACELHFIHP 218


>gi|71280071|ref|YP_267294.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
 gi|71145811|gb|AAZ26284.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
          Length = 567

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/211 (30%), Positives = 104/211 (49%), Gaps = 34/211 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D  + V NKPAG+    G  I   +   +K+    +     + HRLD  TSG+L++
Sbjct: 366 IVFQDEHVVVVNKPAGLLSVPGKSIKDSVYTRIKTQF-PQASGGLIVHRLDMATSGLLML 424

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE-CIANWLLKKSHIGGDYVHVVKQ 218
           A    A +HL + F  + I K Y + + G + K   E C+         + GD+    KQ
Sbjct: 425 ALNERAHKHLQQQFMNKEINKRYVATIEGKLEKTSGEICLP--------LRGDFDDRPKQ 476

Query: 219 ---NEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGD 269
              +E G  YA +H+++I   D  ++ F +    P TGRTHQLR+H  H   +  PI+GD
Sbjct: 477 MVCHEHG-KYAETHWQLIEEVDNTSKLFLY----PITGRTHQLRMHCAHPDGLNLPIIGD 531

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             Y  +          ++L+LHA+ +   HP
Sbjct: 532 SLYGHS---------ADRLHLHAQRLSFTHP 553


>gi|88860180|ref|ZP_01134819.1| hypothetical protein PTD2_19250 [Pseudoalteromonas tunicata D2]
 gi|88818174|gb|EAR27990.1| hypothetical protein PTD2_19250 [Pseudoalteromonas tunicata D2]
          Length = 219

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/192 (32%), Positives = 91/192 (47%), Gaps = 20/192 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y  +  Y+FNKPAG+S    +       GF+        +K    HRLD+ TSG+L++
Sbjct: 4   IVYRHTDFYIFNKPAGMSFHSETQA-----GFVVLAEQLCQEKLYSVHRLDKLTSGLLIL 58

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR+  AA   TE F  + I K+Y +L    PK K+  I   ++K     G Y    K   
Sbjct: 59  ARSSEAAARFTEMFSQKLINKVYLALSDQKPKKKQGWIKGDMVKARR--GAY----KLMT 112

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  I        +L ++P +G+THQLRV    +  PI+GD  Y        
Sbjct: 113 SLENPAITRFYSISVSPGLRGYL-LKPFSGKTHQLRVALKSISAPILGDELYGGT----- 166

Query: 281 TSPIQNKLYLHA 292
                ++ YLHA
Sbjct: 167 ---KADRTYLHA 175


>gi|51246876|ref|YP_066760.1| pseudouridine synthase [Desulfotalea psychrophila LSv54]
 gi|50877913|emb|CAG37753.1| related to pseudouridine synthase [Desulfotalea psychrophila LSv54]
          Length = 235

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 102/205 (49%), Gaps = 18/205 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-----GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +L+ED  I V  KP G+   G          Y ++ +++        +  + HRLDQ+TS
Sbjct: 21  ILHEDKDIIVVVKPTGLLTIGTDREKSRTAHYLLNDYVRKGNPKSSNRVYVVHRLDQDTS 80

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+ A++  A + L + +     +K Y ++V G  K K+  I+++L +        V+ 
Sbjct: 81  GLLIFAKSEEAKKFLQKDWE--NTEKHYLAIVCGKLKEKEGTISSYLTENKAYK---VYS 135

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              + KG   + + +KVI    ++   +++   TGR HQ+RVH    G P+ GD KY   
Sbjct: 136 TPDSTKG-KLSKTAYKVIKE-GKEVSLIDIHLLTGRKHQIRVHFAENGHPVAGDKKY--- 190

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G  TS ++ +L LHAR +   HP
Sbjct: 191 --GTGTSGLK-RLALHARSISFTHP 212


>gi|206977693|ref|ZP_03238585.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
 gi|206744121|gb|EDZ55536.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
          Length = 292

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 72/280 (25%), Positives = 131/280 (46%), Gaps = 38/280 (13%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           G + V+ +     +++Q+G+ +R+  PV      +I E   L                ++
Sbjct: 36  GSIEVNGQHASVRHQLQAGEELRVFFPVEERSEGMIAEDIPL---------------CIV 80

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQETSG 156
           YED  + V NK A +S         H  G + + + S   K  LT       RLD++TSG
Sbjct: 81  YEDDAVLVINKEANMSTIPSR---EHPAGSVANALLSHYDKRHLTSTVHIVTRLDRDTSG 137

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +   
Sbjct: 138 LMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKS----DSIIER 193

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E+G   A++HF+VID    K   + ++  TGRTHQ+RVH  ++G P++GD     N 
Sbjct: 194 TVCEEG-QRAVTHFRVIDSVNHK-THVSLELDTGRTHQIRVHMAYIGHPLLGD-----NL 246

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH+  +   HP     +  T P+P+ M
Sbjct: 247 YGGKRDEMKRQ-ALHSTSLTFYHPILEKEMSFTTPIPSDM 285


>gi|42780396|ref|NP_977643.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 10987]
 gi|42736315|gb|AAS40251.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus ATCC 10987]
          Length = 297

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 71/277 (25%), Positives = 128/277 (46%), Gaps = 32/277 (11%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           G + V+ +      ++Q+G+ +R+  PV      +I E   L                ++
Sbjct: 41  GAIEVNGQHASVRYQLQAGEELRVFFPVEERSEGMIAEDIPL---------------CIV 85

Query: 103 YEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGILV 159
           YED  + V NK A +S +      A  +   L S  D +       +  RLD++TSG+++
Sbjct: 86  YEDDAVLVINKEANMSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGLML 145

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +      
Sbjct: 146 IAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKS----DSIIERTVC 201

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E G   A++HF+VID    K   + ++  TGRTHQ+RVH  H+G P++GD     N  G 
Sbjct: 202 EDG-QRAVTHFRVIDSANHK-THVSLELDTGRTHQIRVHMAHIGHPLLGD-----NLYGG 254

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
               ++ +  LH+  +   HP     +  T P+P+ M
Sbjct: 255 KRDEMKRQ-ALHSTSLTFYHPILEKEMSFTTPIPSDM 290


>gi|229137994|ref|ZP_04266592.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST26]
 gi|229195503|ref|ZP_04322271.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           m1293]
 gi|228588043|gb|EEK46093.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           m1293]
 gi|228645339|gb|EEL01573.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST26]
          Length = 292

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 72/280 (25%), Positives = 131/280 (46%), Gaps = 38/280 (13%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           G + V+ +     +++Q+G+ +R+  PV      +I E   L                ++
Sbjct: 36  GSIEVNGQHASVRHQLQAGEELRVFFPVEERSEGMIAEDIPL---------------CIV 80

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQETSG 156
           YED  + V NK A +S         H  G + + + S   K  LT       RLD++TSG
Sbjct: 81  YEDDAVLVINKEANMSTIPSR---EHPAGSVANALLSHYDKRHLTSTVHIVTRLDRDTSG 137

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +   
Sbjct: 138 LMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKS----DSIIER 193

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E+G   A++HF+VID    K   + ++  TGRTHQ+RVH  ++G P++GD     N 
Sbjct: 194 TVCEEG-QRAVTHFRVIDSVNHK-THVSLELDTGRTHQIRVHMAYIGHPLLGD-----NL 246

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH+  +   HP     +  T P+P+ M
Sbjct: 247 YGGKRDEMKRQ-ALHSTSLTFYHPILEKEMSFTTPIPSDM 285


>gi|224419163|ref|ZP_03657169.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
 gi|253828096|ref|ZP_04870981.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
 gi|253511502|gb|EES90161.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
          Length = 319

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 103/220 (46%), Gaps = 47/220 (21%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +YE+    +FNKPA + +       +H    +    +  G +  L HR+D+ETSG+++V 
Sbjct: 75  IYENEDFALFNKPAQMLIHPKGRFFHH--SLMDEVREYFGTEASLIHRIDKETSGLVLVG 132

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV--VKQN 219
           + + +   L E F   RI+K Y +L+ G     K C      K S I GD+  +  +   
Sbjct: 133 KHKRSIVELGELFANNRIKKKYLALIKG-----KMC------KTSKIVGDFCLLMPLSLQ 181

Query: 220 EKGANYAI----------------------SHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           EKG + ++                      S F+++  F      L++ P TGRTHQ+RV
Sbjct: 182 EKGGDLSVRSVFLGQNLRKDSKLLGFRDAKSEFEILGEFGGN-TLLKVYPITGRTHQIRV 240

Query: 258 HALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMD 296
           H   +G PI+GD  Y C ++        Q++ YL + +++
Sbjct: 241 HLFSLGFPILGDPLYGCEDW--------QSREYLDSEFIE 272


>gi|312953695|ref|ZP_07772531.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|310628369|gb|EFQ11652.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|315151826|gb|EFT95842.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0031]
          Length = 297

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 113/233 (48%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLD 151
           +++ED    V NKPAGI+        YH  G + + V  KG   R         +  RLD
Sbjct: 80  IVFEDDHFLVVNKPAGIA---SIPAQYHPSGTMANRV--KGYYKRQNYVNQVIHVVTRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L++K  IG D
Sbjct: 135 RDTSGLMLFAKHGFAHALIDQELREKKLTKIYYALVGGAIEQLSE---HQLIEKP-IGRD 190

Query: 212 YVHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              ++K Q  +   +A + + +    AQ    + +Q HTGRTHQ+RVH   +GC ++GD 
Sbjct: 191 LSSLLKRQVIETGQFASTEYWLAKRGAQA-AAVRIQLHTGRTHQIRVHFEAIGCSLLGDE 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y     G     I+ +  LH   +   HP     + + +PL   M    D+L
Sbjct: 250 MY----HGKMDQGIERQA-LHCMELIFTHPFTKETVHLISPLAEDMKSVDDTL 297


>gi|224372561|ref|YP_002606933.1| ribosomal large subunit pseudouridine synthase D [Nautilia
           profundicola AmH]
 gi|223588812|gb|ACM92548.1| ribosomal large subunit pseudouridine synthase D [Nautilia
           profundicola AmH]
          Length = 311

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 81/336 (24%), Positives = 151/336 (44%), Gaps = 54/336 (16%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINAL 74
           ++N R+D++      +++   +++++++  V V+ K +K    ++Q+G  V +       
Sbjct: 8   DKNERVDKFLSQKL-NVSRNQIEQLIKNSLVSVNSKTIKKGGVKLQAGDTVDVE------ 60

Query: 75  NHIIKEQKIL--DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
              IKE +    D  VN           +LYED  + V NKP GI V     +    +  
Sbjct: 61  ---IKEAESSKEDYEVNFDIP-------VLYEDEDVLVINKPPGIVVHPAPSVK---EAT 107

Query: 133 LKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           L  W+ +K          ++  + HR+D+ETSG L++A+   A + L+   + + + + Y
Sbjct: 108 LVDWLKTKNYRLSTIAGEERFGIVHRIDKETSGALIIAKNNKAHEFLSAQLKDKTMGR-Y 166

Query: 184 WSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           + ++   P  +  C+   + +  K+ +   Y   VK   +     +  ++ +   A+ F 
Sbjct: 167 YIMLLNEPLKEAVCVDKPIARNPKNRLKMAY---VKNGREAKTLFVPVYENV-AAAKLF- 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
                  TGRTHQ+RVH   +G  I+GD  Y    K     P   ++ LHA+ +   HP 
Sbjct: 222 -------TGRTHQIRVHLSTIGRYILGDTLYG---KKEQKLP---RVMLHAKELYFIHPS 268

Query: 302 GGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           G +L I AP+     K     GF Y+    I  +++
Sbjct: 269 GKKLSIIAPMFDDFKKNLPK-GFNYEETDTISDIFT 303


>gi|328861018|gb|EGG10122.1| hypothetical protein MELLADRAFT_94488 [Melampsora larici-populina
           98AG31]
          Length = 341

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 108/230 (46%), Gaps = 23/230 (10%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           ++R+   Q+ R       L H +K ++ L++ +     + F    +LY+D K+ V NKPA
Sbjct: 49  SSRLPRSQIKRAKIAEEKLVHHLKAKEELENRL----RASFRPPEILYDDEKVLVINKPA 104

Query: 116 GISVQGGSGIAYHI------DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           G ++Q   G    I      D F   +      K  L  RLD+ TSG L++AR+ + A+ 
Sbjct: 105 GCALQAEEGSEAFIRWNLIHDHFTNIY-----GKLYLVQRLDKSTSGPLILARSSSVART 159

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNK----KECIANWLLKKSHIGGDYVHVVKQNEKGAN- 224
           +   F+   I+K Y +LV  +P  +    +      +L +     D + + + N  G + 
Sbjct: 160 IGTQFKQSTIKKRYLALVQFLPTKRGPIQEATTQGKVLCRMRNRSDKMVIAEANRTGPDC 219

Query: 225 -YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR-VHALHMGCPIVGDHKY 272
             A + +K++         + + P TGR HQLR V +  +  PIVGD KY
Sbjct: 220 KRAETDWKLVTA-TSTHAIVSLLPTTGRKHQLRLVCSRFLSAPIVGDFKY 268


>gi|323495104|ref|ZP_08100191.1| tRNA pseudouridine synthase C [Vibrio brasiliensis LMG 20546]
 gi|323310655|gb|EGA63832.1| tRNA pseudouridine synthase C [Vibrio brasiliensis LMG 20546]
          Length = 240

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 99/224 (44%), Gaps = 40/224 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--- 217
           A +   A  +   F    ++K Y ++V G           W+L+   +  DY   V+   
Sbjct: 64  ALSSEVASQVMPMFANHEMEKTYHAIVRG-----------WILESGRL--DYPLKVELDK 110

Query: 218 ------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALH 261
                   EK A  AI+ ++ +               ++C +EM+P TGR HQLR H  H
Sbjct: 111 IADKHASQEKEAQEAITDYQPLAQVEIPHSTGRFPTTRYCLMEMKPLTGRKHQLRRHMAH 170

Query: 262 MGCPIVGDH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +  PIVGD      K+   F+  + S   ++L LHA  +   HP
Sbjct: 171 LRHPIVGDTTHGDGKHNKLFREVYDS---HRLLLHASSLKFVHP 211


>gi|282600856|ref|ZP_05979923.2| pseudouridine synthase, RluA family [Subdoligranulum variabile DSM
           15176]
 gi|282571159|gb|EFB76694.1| pseudouridine synthase, RluA family [Subdoligranulum variabile DSM
           15176]
          Length = 320

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 79/320 (24%), Positives = 141/320 (44%), Gaps = 42/320 (13%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ++E  +RL R+ ++    +    + K  R+ +++V+ KR + + R+ +G V+ +      
Sbjct: 8   SNENGVRLSRFVESVTQQLPRSMMYKAFRNKRIKVNGKRAEPDTRLCTGDVIEM------ 61

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDG 131
             +I  E     +  +  K       + ++YED    V  KPA +   +  +G    +D 
Sbjct: 62  --YINDEFFPAHTGTSKPKPPRRQPPVTIVYEDENFAVLYKPAHLLCHRDRTGDPNLVDA 119

Query: 132 FLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           F  +++++KG+          P L +RLD+ T G+++ A+T  A + L E  R   ++K 
Sbjct: 120 F-AAYLEAKGEYNPHAEQRFAPALCNRLDRGTEGLVLAAKTYQALRDLNEIIRTDLMKKE 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++  G P   +     WL        + V +  +  +G    I+   VI   +  F  
Sbjct: 179 YLTITVGAPPAGRHIA--WLQHSEK--NNKVRIHARQSEGYKQIITDVTVIRQ-SGPFAL 233

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY----------------CANFKGNFTSPIQN 286
             +   TGRTHQ+R H  ++G P++GD KY                CA        P +N
Sbjct: 234 CRIGLITGRTHQIRAHLSYLGHPVLGDIKYGNRKMNERTGLKTQALCAQRLTFGRIPPEN 293

Query: 287 KL-YLHARYMDLPHPEGGRL 305
           +L YL  R + L  PE  RL
Sbjct: 294 RLQYLSGRVIKLDDPEIIRL 313


>gi|114797970|ref|YP_759136.1| RNA pseudouridine synthase family protein [Hyphomonas neptunium
           ATCC 15444]
 gi|114738144|gb|ABI76269.1| RNA pseudouridine synthase family protein [Hyphomonas neptunium
           ATCC 15444]
          Length = 215

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/221 (28%), Positives = 100/221 (45%), Gaps = 30/221 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D  + + +KP+G+    G G+        +  V ++       HRLD  TSG+L++A
Sbjct: 14  IYRDDHLILIDKPSGLLSVPGRGVDKADCAITR--VQAEFPDALTVHRLDMATSGLLLMA 71

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW----LLKKSHIGGDY 212
           R++   + L+  F    ++K Y + VWG+P   +       I +W    L K  H  G  
Sbjct: 72  RSKEIQRALSGLFERGEVEKSYLADVWGVPAPARGEIDLPLITDWPNRPLQKVDHEIGKP 131

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              + +     N   +H +           L++ P TGR+HQLRVH   +G PI+GD  Y
Sbjct: 132 SRTLYET---LNPQSAHTR-----------LKLTPLTGRSHQLRVHLAAIGHPILGDEFY 177

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            A      T+  + +L LHA  +   HP  G R+    P P
Sbjct: 178 AAG--EALTA--RPRLALHAARLAFAHPVTGERMDFELPCP 214


>gi|315149952|gb|EFT93968.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0012]
          Length = 297

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 113/233 (48%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLD 151
           +++ED    V NKPAGI+        YH  G + + V  KG   R         +  RLD
Sbjct: 80  IVFEDDHFLVVNKPAGIA---SIPAQYHPSGTMANRV--KGYYKRQNYVNQVIHVVTRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L++K  IG D
Sbjct: 135 RDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLNE---HQLIEKP-IGRD 190

Query: 212 YVHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              ++K Q  +   +A + + +    A K   + +Q HTGRTHQ+RVH   +GC ++GD 
Sbjct: 191 LSSLLKRQVIETGQFASTEYWLAKRGA-KAAAVRIQLHTGRTHQIRVHFEAIGCSLLGDE 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y     G     I+ +  LH   +   HP     + + +PL   M    D+L
Sbjct: 250 MY----HGEMDQGIERQA-LHCMELIFTHPFTKETVHLISPLAEDMKSVDDTL 297


>gi|307243209|ref|ZP_07525382.1| RNA pseudouridine synthase [Peptostreptococcus stomatis DSM 17678]
 gi|306493470|gb|EFM65450.1| RNA pseudouridine synthase [Peptostreptococcus stomatis DSM 17678]
          Length = 226

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 108/210 (51%), Gaps = 19/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  KP  +  Q  +     +    K +V  K +KP      L HRLD+   
Sbjct: 5   VIYEDNHLLVVEKPVNVLSQADNTQDIDMVSMCKVYVKEKYKKPGNVYIGLVHRLDRPVG 64

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  L++  R R ++K Y ++V G  +   +C+ ++L K +    + V +
Sbjct: 65  GVMVFAKTSKAASRLSDQVRTRTMKKTYRTVVVGKCQKAGDCV-DYLYKNTKT--NMVKI 121

Query: 216 V-KQNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           V K N+ G   ++S+ K+ + ++ K    +  LE+  HTGR HQ+RV       P+ GD 
Sbjct: 122 VDKSNKDGKMASLSYKKLGETYSDKDKLDYSLLEVDLHTGRPHQIRVQFSSRNHPLYGDQ 181

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +Y + F     S +  ++ L +  ++L HP
Sbjct: 182 RY-SKF-----SKVGQQIALWSARIELVHP 205


>gi|227543293|ref|ZP_03973342.1| ribosomal pseudouridine synthase [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227180906|gb|EEI61878.1| ribosomal pseudouridine synthase [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 294

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 100/229 (43%), Gaps = 29/229 (12%)

Query: 75  NHIIKEQKILDSSVNL--------TKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSG 124
             +I  ++IL + V++          H  F  SI  +YEDS++ V NKP  + +V  G+ 
Sbjct: 64  GQVIAPEQILAAGVDIFFYRMPAPEPHVPF--SIETVYEDSRVLVVNKPPFLATVPKGAH 121

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           I       L+    ++   P   HRLD+ TSG+L+  ++R       E F  R +QK Y 
Sbjct: 122 ITETAVVRLRRATGNEELSP--AHRLDRHTSGLLLFTKSREFRGAYQEMFARRAVQKTYH 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++  G        +  W  + S + GD   H V        + IS    +   A      
Sbjct: 180 AVSAGPSAVAPGTV--WRSRISKVPGDLQAHTVDGEANAETHVISVSGRVHVLA------ 231

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLY 289
              PHTG+THQLR+H    G PIV D  Y A   +   +FT P+    Y
Sbjct: 232 ---PHTGKTHQLRLHMCEAGVPIVNDPLYPAIRDDLMDDFTRPLGLTAY 277


>gi|90413524|ref|ZP_01221515.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum 3TCK]
 gi|90325456|gb|EAS41939.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum 3TCK]
          Length = 244

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/212 (27%), Positives = 97/212 (45%), Gaps = 17/212 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  +   NKP+G+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILFQDEYLVAVNKPSGMLVHRSWLDRHETVFVMQTLRDQIGQHVFPLHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +   A  +   F  R I K Y ++V G  K+    + ++ LKK        +  +Q  
Sbjct: 65  GLSSEIASQMMPVFSGRDIHKTYHAVVRGWIKDA--AVLDYPLKKELDKIADKNAAEQEA 122

Query: 221 KGANYAISHFKVIDC-------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV-----G 268
           + A  A S    I+           ++C +EM+P TGR HQLR H  H+   I+     G
Sbjct: 123 QDAVTAYSPLATIETNIPVGRYATSRYCLVEMKPETGRKHQLRRHMHHLNHHIIGDVNHG 182

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           D ++   F+ N+     ++L LHA  +   HP
Sbjct: 183 DGRHNRMFRENYDC---HRLMLHASRLQFVHP 211


>gi|330469278|ref|YP_004407021.1| RluA family pseudouridine synthase [Verrucosispora maris AB-18-032]
 gi|328812249|gb|AEB46421.1| RluA family pseudouridine synthase [Verrucosispora maris AB-18-032]
          Length = 314

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/210 (28%), Positives = 105/210 (50%), Gaps = 15/210 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKS---WVDSKGQKPR--LTHRLDQET 154
           ++Y D  I V +KP G++     G     + G L +    + + G   R  + HRLD  T
Sbjct: 91  VVYADDDIVVVDKPVGVAAHPSPGWTGPTVIGGLAAIGHTIATSGAAERQGVVHRLDVGT 150

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++VVA++  A   L  +F+ R ++K Y ++V G     +  I   + +  H   DY  
Sbjct: 151 TGVMVVAKSEQAYSALKRAFKYREVEKRYHAVVQGHLDPLRGTIDAPIDRHPH--HDYRW 208

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  + K    +I+H+  ++ F      ++++  TGRTHQ+RVH   +  P VGD  Y A
Sbjct: 209 AVVSDGK---PSITHYDTLEAFPSA-SLVDVRLETGRTHQIRVHFSTLRHPCVGDLTYGA 264

Query: 275 NFKGNFTSPIQ-NKLYLHARYMDLPHPEGG 303
           +     ++ ++ ++ +LHAR +   HP  G
Sbjct: 265 D--PTLSARLKLDRQWLHARELSFEHPRTG 292


>gi|33866818|ref|NP_898377.1| pseudouridine synthase [Synechococcus sp. WH 8102]
 gi|33639419|emb|CAE08803.1| probable pseudouridine synthase [Synechococcus sp. WH 8102]
          Length = 315

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 74/291 (25%), Positives = 132/291 (45%), Gaps = 38/291 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVINALNHII 78
           L  W    Y H      ++ + SG++  + +R+  + R+  G+ V  R PP +       
Sbjct: 25  LSCWLAERYQHSAGEVWRQRIHSGELDCNGQRLTADRRLAGGEAVLWRRPPWL------- 77

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ I D    +            ++D  + V NKP+G+ V  G G   H    L + ++
Sbjct: 78  -EEAIPDQWETI------------HDDGDLLVINKPSGLPVMPGGGFLLHT---LTALLE 121

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKIYWSLVWGIPKNK 194
             G +P   HRL + TSG+ V AR       L++ FR     R++ + +   V G+ + +
Sbjct: 122 PTGARP--VHRLGRFTSGLQVCARDPMTRAALSKQFRPEGSCRKVYQAWAQRVPGLEQGQ 179

Query: 195 KECIANWLLKKSHIGGDYV---HVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              + N ++++ H    +V     +KQ   +    A S  ++++  A+    L++   TG
Sbjct: 180 TLTVTNDVVERQHPLLGWVWGPEPLKQEPIRKRLTARSELELLERTAEGDR-LQVTITTG 238

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFT-SPIQNKLYLHA-RYMDLPH 299
           R HQ+R+H   +G P++GD  Y  N + + T +P      LHA +   LPH
Sbjct: 239 RPHQIRIHLAQLGSPLLGDPLYLLNREISATATPGDGGYRLHAWQLSGLPH 289


>gi|300215051|gb|ADJ79467.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 311

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 113/248 (45%), Gaps = 40/248 (16%)

Query: 101 LLYEDSKIYVFNKPAGIS------VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +++E+  + V NKP GI        + G+ + Y     +  ++D+K + P + HRLD  T
Sbjct: 88  IIFENEDLLVVNKPQGIKSHPNQPYETGTLMNY-----IAGYLDAKDEHPYMVHRLDMLT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG ++VA+       LT       I++ Y ++  GI  ++KE + +       IG D   
Sbjct: 143 SGAMIVAKNPVVVPILTCLISTHTIKRDYLAITEGI-FDQKEGVIDL-----PIGKD--- 193

Query: 215 VVKQNEK--------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              +N+K        GA  A +H++VI  F      + ++  TGRTHQLRVH   MG PI
Sbjct: 194 ---ENDKRKRKVDGIGALPARTHYQVIKEFGNN-SAVYLRLETGRTHQLRVHLSAMGHPI 249

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           VGD  Y      N  S  +  + LH     L  P   R L++ A +P +     + +   
Sbjct: 250 VGDVLY------NHVSK-EKHMMLHGYKQKLTLPFSMRELELKADIPEYFANYEEKIKEN 302

Query: 326 YDRNLYIK 333
              N Y K
Sbjct: 303 KKLNFYKK 310


>gi|257870826|ref|ZP_05650479.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257804990|gb|EEV33812.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 283

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 70/224 (31%), Positives = 101/224 (45%), Gaps = 30/224 (13%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD--SKGQKPRLTHRLDQETS 155
           K  +L+ED  + V NKPAGI            D  +       S   +P + HRLD+ETS
Sbjct: 80  KITVLFEDEHLIVVNKPAGIKTHPNQ--PNETDTLMNDLAAYLSPETRPYVVHRLDKETS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+       L      ++I + Y + VWG      +   N  ++K  IG D    
Sbjct: 138 GVILFAKNPLVLPILGRMLESKQIYRRYQATVWG------QLDQNQTIRKK-IGRDRHDR 190

Query: 216 VKQ--NEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            K+  + +    A++H ++    AQ    +C L+    TGRTHQ+RVH   +G PIVGD 
Sbjct: 191 RKRVIDPRNGLSAVTHVEIAARNAQTTSIYCVLD----TGRTHQIRVHLASIGHPIVGDP 246

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
            Y              +L LHA  + L HP     LQI A LP 
Sbjct: 247 LYQKKTAA--------RLELHAYELYLTHPFSQESLQIKA-LPG 281


>gi|153954106|ref|YP_001394871.1| RluD2 [Clostridium kluyveri DSM 555]
 gi|219854718|ref|YP_002471840.1| hypothetical protein CKR_1375 [Clostridium kluyveri NBRC 12016]
 gi|146346987|gb|EDK33523.1| RluD2 [Clostridium kluyveri DSM 555]
 gi|219568442|dbj|BAH06426.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 319

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 74/275 (26%), Positives = 128/275 (46%), Gaps = 31/275 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V + ++E   RLD++ +     +    + K +R G ++V+ K+ K    +    +V    
Sbjct: 3   VEIGSNESGQRLDKFLRKWLRDVPISGIYKAIRKGDIKVNGKKTKEKYFLMDKDIVEAQY 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YH 128
           +I+      K +    + VN    S+FLK  + YED  + +  K  G+ V          
Sbjct: 63  IIS------KGKSFEFNKVN----SNFLK--ITYEDENMILVEKWPGVLVHSDKKTDDVT 110

Query: 129 IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI++  +   + + L E  R R I
Sbjct: 111 LTDYVLSYLYDKGDFKPETEVTFTPSPCNRLDRNTSGIVIYGKNYESLKLLNEIIRERNI 170

Query: 180 QKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +K Y +LV G  +  +     ++LK  K++I   Y    K+N K  +  +   KV+    
Sbjct: 171 RKYYQALVKG--RINEGIYEGYILKDRKNNISNVY-DSPKKNTKKISMDV---KVLHTCG 224

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +   E++  TGR+HQLR H  H+G PI+GD KY
Sbjct: 225 T-YSLAELELITGRSHQLRTHLAHLGNPIIGDTKY 258


>gi|145629099|ref|ZP_01784898.1| hypothetical protein CGSHi22121_09865 [Haemophilus influenzae
           22.1-21]
 gi|145633401|ref|ZP_01789131.1| hypothetical protein CGSHi3655_04195 [Haemophilus influenzae 3655]
 gi|145635226|ref|ZP_01790930.1| exonuclease III [Haemophilus influenzae PittAA]
 gi|145639669|ref|ZP_01795272.1| hypothetical protein CGSHiII_09136 [Haemophilus influenzae PittII]
 gi|229845388|ref|ZP_04465519.1| pseudouridine synthase-like protein [Haemophilus influenzae 6P18H1]
 gi|144978602|gb|EDJ88325.1| hypothetical protein CGSHi22121_09865 [Haemophilus influenzae
           22.1-21]
 gi|144985964|gb|EDJ92566.1| hypothetical protein CGSHi3655_04195 [Haemophilus influenzae 3655]
 gi|145267505|gb|EDK07505.1| exonuclease III [Haemophilus influenzae PittAA]
 gi|145271226|gb|EDK11140.1| hypothetical protein CGSHiII_09136 [Haemophilus influenzae PittII]
 gi|229811696|gb|EEP47394.1| pseudouridine synthase-like protein [Haemophilus influenzae 6P18H1]
 gi|301168643|emb|CBW28233.1| conserved hypothetical pseudouridine synthase [Haemophilus
           influenzae 10810]
 gi|309750639|gb|ADO80623.1| Probable pseudouridylate synthase [Haemophilus influenzae R2866]
          Length = 224

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/203 (31%), Positives = 96/203 (47%), Gaps = 28/203 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+ S   + NK  GISV      QG + +        K W         L HRLD+ T
Sbjct: 5   VVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQLNVPKVW---------LVHRLDKVT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A    +A   +  F   +I K Y +L    PK K+  I    +KK+  G   + 
Sbjct: 56  SGLLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGD-MKKAREGAWKLC 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K+N      AI+ F+ + C      ++ ++P TG+THQLRV    +G PI+GD  Y  
Sbjct: 115 QTKENP-----AITRFESVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDGLYGK 168

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
           N     T  I ++ YLHA  ++ 
Sbjct: 169 N-----TEKI-DRTYLHATQLEF 185


>gi|257876751|ref|ZP_05656404.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC20]
 gi|257810917|gb|EEV39737.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC20]
          Length = 299

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 65/232 (28%), Positives = 112/232 (48%), Gaps = 24/232 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTH---RLDQE 153
           ++YED+ + V NKPAGIS        YH  G +    K++  ++  + ++ H   RLD++
Sbjct: 79  IVYEDAHLLVVNKPAGISSIPAQ---YHPTGTMANRVKAYYQAQHYEDQVIHVVTRLDRD 135

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++ A+   A   L    R +++ K Y +LV G    +   ++     +  I  D  
Sbjct: 136 TSGLMLFAKHGFAHAKLDSQLRKKQVVKKYQALVAG----ELPALSAHGEIELPIARDLT 191

Query: 214 HVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            ++K+  +++G      ++  +      F  +++Q HTGRTHQ+RVH   +GCP++GD  
Sbjct: 192 SLLKRKVSDEGKEARTEYW--LKQRNSDFALVDIQLHTGRTHQIRVHFSAIGCPLLGDEM 249

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y     G     I+ +  LH   +   HP     L    PLPA M     ++
Sbjct: 250 Y----GGTMALGIKRQA-LHCCQLQFQHPFTNEPLAFKLPLPADMAAVCSAM 296


>gi|303281963|ref|XP_003060273.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226457744|gb|EEH55042.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 443

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 89/372 (23%), Positives = 131/372 (35%), Gaps = 143/372 (38%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDS------KGQKPRLT-- 147
           L S++LY D  + V NKP+G+ V G G+G A      L + + S         KP LT  
Sbjct: 62  LTSMVLYRDDDVLVLNKPSGLPVVGTGTGNANAAAPSLSAMLASLTFHADAPWKPPLTIV 121

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRR----------------------------I 179
           HRLD++ SG +V+AR   AA+ L  +F  +                             I
Sbjct: 122 HRLDKDASGCVVLARRAVAARTLARAFAAKSASGGEGAREEEEEGLLGGGRAESDALYNI 181

Query: 180 QKIYWSLVWGIPKNKKECIANWLL--------KKSHIGG--------------------- 210
           ++ YW+LV G P   +  I   L          K   GG                     
Sbjct: 182 ERTYWALVAGRPSRDEGVIRAPLRIPGKRNGNTKRRDGGVVFFADDATDERRARLPRPPD 241

Query: 211 -----------DYVHVVKQNEKGANYAISHFKVIDCFAQ----------------KFCWL 243
                        V    +++     A++ ++VI    +                +   L
Sbjct: 242 VAPGGGGGASEGRVEATTEDDPRGVRAVTSYRVIGEVPRDADGDDGDDDEKVTHPRPTLL 301

Query: 244 EMQPHTGRTHQLRVH-ALHMGCPIVGDHKY---------------------------CAN 275
           E+   TGR HQ+RVH A  +G P+VGD+KY                            A 
Sbjct: 302 ELTLSTGRKHQIRVHLASALGTPVVGDYKYGYRDTPRTRRGREIAPPAWMEALRDVEAAA 361

Query: 276 FKGNFT--SPIQN-------------------KLYLHARYMDLPHPEGGR-LQITAPLPA 313
            +G+ T   P                       L+LHAR +  P P GG  +++ APLP 
Sbjct: 362 RRGSGTIRDPASAAAWRARRSLALADDDGGGVPLHLHARSLRFPKPSGGDVVRVVAPLPP 421

Query: 314 HMVKTWDSLGFK 325
           H+    + LG K
Sbjct: 422 HLASALERLGVK 433


>gi|237653878|ref|YP_002890192.1| transaldolase [Thauera sp. MZ1T]
 gi|237625125|gb|ACR01815.1| transaldolase [Thauera sp. MZ1T]
          Length = 648

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 73/263 (27%), Positives = 116/263 (44%), Gaps = 47/263 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LY D  +   +KP+G+ V   S IA H + F    + D  G++    HRLD+ TSG+L+
Sbjct: 4   ILYRDDWLVAIHKPSGLLVHR-SPIAAHEERFAVQLLRDQLGRRVYPAHRLDRGTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R  A+ L + F  + + K Y ++V G P      I + L+++     D V V    
Sbjct: 63  FALDREVARTLAQRFEAQAVDKRYLAVVRGHPPEHG-VIEHALVRRL----DAVEVRSGK 117

Query: 220 EKGANYAI---------------------SHFK---------VIDCF-AQKFCWLEMQPH 248
             GA  A+                     + F+          +D + + ++  +E+ P 
Sbjct: 118 GAGARDALPEDVDDSDSPEAAEPVAQPARTRFRRLATVELPHAVDRYPSSRYALVELLPE 177

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           TGR HQLR H  H+  PI+GD  Y        F+  F S   ++L L    + L HP   
Sbjct: 178 TGRRHQLRRHLKHIAHPIIGDATYGKGRHNRLFQALFGS---HRLLLACTRLALAHPVTE 234

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
           R L+I AP+         +LG++
Sbjct: 235 RPLEIVAPVAEDFAAVLAALGWQ 257


>gi|84387868|ref|ZP_00990882.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           12B01]
 gi|84377214|gb|EAP94083.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           12B01]
          Length = 517

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 68/211 (32%), Positives = 106/211 (50%), Gaps = 26/211 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++YED +I V NKP       G  I   +   +K+ + ++ G  P + HRLD  TSG+L+
Sbjct: 316 IVYEDDEIVVVNKPEEFLSVPGKFIEDSVYTRIKARYPNATG--PLIIHRLDMSTSGLLI 373

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +A T  + +H+ + F  R ++K Y +L+ G    +   I+  L       GD     +Q 
Sbjct: 374 LALTAESNKHIQKQFIDRTVEKRYTALLDGEITGESGDISLPL------RGDITDRPRQL 427

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
             +E G N A ++++ I     K   + + P TGRTHQLRVH  H   +G PI GD  Y 
Sbjct: 428 VCHEHGRN-AETYWEAIGTSNGK-TKVHLYPKTGRTHQLRVHCAHPLGLGVPIRGDDLY- 484

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             +K       + +L+LHA Y+ L +P  G 
Sbjct: 485 -GYK-------RERLHLHAGYLKLINPTTGE 507


>gi|332673452|gb|AEE70269.1| RluA family ribosomal large subunit pseudouridine synthase
           [Helicobacter pylori 83]
          Length = 327

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 106/229 (46%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLEFKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++ +
Sbjct: 257 YGLN---QALPKEETRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLEYF 302


>gi|310764748|gb|ADP09698.1| Pseudouridine synthase [Erwinia sp. Ejp617]
          Length = 232

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/212 (29%), Positives = 98/212 (46%), Gaps = 18/212 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D ++ + NKPAG+    G     +ID      V        L HRLD  TSG++V+
Sbjct: 19  ILYQDDRLVLINKPAGLLSLSGKN-PQNIDSVHYRLVQIF-PGCTLVHRLDFGTSGLMVI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +A    L + F  R + K+Y +L+ G   +  E + +  + K       + +   + 
Sbjct: 77  ARNKAINAALCQQFSQRTVTKVYSALLCG-HLDDNEGVIDAAIAKDPALFPLMSICSIHG 135

Query: 221 KGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K A    S ++V++ F              +++ P TGRTHQLR+H   +G PI+G   Y
Sbjct: 136 KPAR---SRYRVVERFYHPLENRTLLPLTRVQLTPETGRTHQLRIHCQQLGHPILGCDLY 192

Query: 273 CAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 G   +P   +L LHA  +   HP  G
Sbjct: 193 GGRLLPGTERTP---RLMLHASELHFVHPING 221


>gi|256961078|ref|ZP_05565249.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis Merz96]
 gi|293384024|ref|ZP_06629918.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis R712]
 gi|293386837|ref|ZP_06631407.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis S613]
 gi|312908026|ref|ZP_07767009.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|312978446|ref|ZP_07790184.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
 gi|256951574|gb|EEU68206.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis Merz96]
 gi|291078504|gb|EFE15868.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis R712]
 gi|291083671|gb|EFE20634.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis S613]
 gi|310626117|gb|EFQ09400.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|311288595|gb|EFQ67151.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
          Length = 297

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 113/233 (48%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLD 151
           +++ED    V NKPAGI+        YH  G + + V  KG   R         +  RLD
Sbjct: 80  IVFEDDHFLVVNKPAGIA---SIPAQYHPSGTMANRV--KGYYKRQNYVNQVIHVVTRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L++K  IG D
Sbjct: 135 RDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLNE---HQLIEKP-IGRD 190

Query: 212 YVHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              ++K Q  +   +A + + +    AQ    + +Q HTGRTHQ+RVH   +GC ++GD 
Sbjct: 191 LSSLLKRQVIETGQFASTEYWLAKRGAQA-AAVRIQLHTGRTHQIRVHFEAIGCSLLGDE 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y     G     I+ +  LH   +   HP     + + +PL   M    D+L
Sbjct: 250 MY----HGKMDQGIERQA-LHCIELIFTHPFTKETVHLISPLAEDMKSVDDTL 297


>gi|312900037|ref|ZP_07759354.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
 gi|311292794|gb|EFQ71350.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
          Length = 297

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 113/233 (48%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLD 151
           +++ED    V NKPAGI+        YH  G + + V  KG   R         +  RLD
Sbjct: 80  IVFEDDHFLVVNKPAGIA---SIPAQYHPSGTMANRV--KGYYKRQNYVNQVIHVVTRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L++K  IG D
Sbjct: 135 RDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLSE---HQLIEKP-IGRD 190

Query: 212 YVHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              ++K Q  +   +A + + +    A K   + +Q HTGRTHQ+RVH   +GC ++GD 
Sbjct: 191 LSSLLKRQVIETGQFASTEYWLAKRGA-KAAAVRIQLHTGRTHQIRVHFEAIGCSLLGDE 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y     G     I+ +  LH   +   HP     + + +PL   M    D+L
Sbjct: 250 MY----HGKMDQGIERQA-LHCMELIFTHPFTKETVHLISPLAEDMKSVDDTL 297


>gi|160873422|ref|YP_001552738.1| pseudouridine synthase Rlu family protein [Shewanella baltica
           OS195]
 gi|160858944|gb|ABX47478.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS195]
 gi|315265651|gb|ADT92504.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS678]
          Length = 230

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/201 (29%), Positives = 95/201 (47%), Gaps = 24/201 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +++   V +K A +      G A    G +       G K    HRLD  TSG+L++
Sbjct: 4   IIADEADFLVISKSAKVHFHSQDGTA----GVVAQAEQDLGIKLFAVHRLDTPTSGLLIL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA+  TE F   ++QK Y +L  G PK K+  +   + K          +++  E
Sbjct: 60  AKSAGAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIGDMAKSRR---SMFKLLRTKE 116

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  +        +L ++PH+G+THQLRV    +G PI+GD  Y     G  
Sbjct: 117 ---NPAITQFFSLSVSEGLRLYL-LKPHSGKTHQLRVALASLGVPILGDDLY-----GGM 167

Query: 281 TSPIQNKLYLHA-----RYMD 296
            +   ++ YLHA     RY D
Sbjct: 168 AA---DRCYLHAYCLHFRYGD 185


>gi|167037131|ref|YP_001664709.1| RluA family pseudouridine synthase [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|320115551|ref|YP_004185710.1| RluA family pseudouridine synthase [Thermoanaerobacter brockii
           subsp. finnii Ako-1]
 gi|166855965|gb|ABY94373.1| pseudouridine synthase, RluA family [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|319928642|gb|ADV79327.1| pseudouridine synthase, RluA family [Thermoanaerobacter brockii
           subsp. finnii Ako-1]
          Length = 285

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/221 (31%), Positives = 118/221 (53%), Gaps = 34/221 (15%)

Query: 103 YEDSKIYVFNKPAGISV------QGGS---GIA-YHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           YED +I + NKPA + V      Q G+   G+A Y  +  LK+ +       R  +RLD+
Sbjct: 78  YEDEEILIVNKPANMVVHPTKRYQSGTLANGVAWYFKEKGLKALI-------RPVNRLDR 130

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V A+ R   Q+  +   ++ + K+Y+++V G  K + E   +  + +    G  
Sbjct: 131 GTSGLVVFAK-RPFMQYYLQI--IKPMTKLYFAVVEG--KMEGEGRIDLPISRKPQSGIE 185

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V ++ ++    AI+++KV+   +++F  L+++  TGRTHQ+RVH  H+G PIVGD  Y
Sbjct: 186 RMVSEEGDR----AITNYKVVKS-SKRFSLLKVKIETGRTHQIRVHLSHIGHPIVGDTLY 240

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                G+    I+ +  LHA  +   HP E   + + +PLP
Sbjct: 241 -----GSSDDYIKRQA-LHAYRLTFVHPLEEKSISVYSPLP 275


>gi|330723209|gb|AEC45579.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyorhinis MCLD]
          Length = 294

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 79/308 (25%), Positives = 144/308 (46%), Gaps = 38/308 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI--QSGQVVRIPPVINA 73
           +E  RLD + +     ++ V +Q+I+ + QV VD + V   N I  Q  Q+         
Sbjct: 6   DEQTRLDIFLRKKL-ELSRVFVQEIIANNQVWVDNQIVNKKNFILKQGSQI--------E 56

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------IAY 127
           +++  KEQ I+  + ++      LK  +++ED  + V +KP  + V    G      +  
Sbjct: 57  VHYQEKEQNIIAKAQDIE-----LK--IVFEDENVIVVDKPTNMVVHPAPGNYENTLVNA 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  F +    +   +P + HRLD++TSG+++VA+       L +  + R+I++ Y++++
Sbjct: 110 LVYKFAQLSNVNGSLRPGIVHRLDKDTSGLMLVAKNDKMHNFLAQQLKERKIKRKYYAII 169

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLE 244
            G  +N+   I N  + +       + V   N K    AI+H  V   F  K   F ++ 
Sbjct: 170 EGQLENQISHI-NLPIARDEKNRKKMSVSHFNSKE---AITHVFVEKYFHYKKKVFSFVR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQ+RVH  ++  P+ GD  Y     G        +  LHA  ++  + +G  
Sbjct: 226 CELETGRTHQIRVHLAYIKHPVYGDPVY-----GKKVDDFNQR--LHAYEIEFINIDGKT 278

Query: 305 LQITAPLP 312
           L+  + LP
Sbjct: 279 LKFNSKLP 286


>gi|317053991|ref|YP_004118016.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316951986|gb|ADU71460.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 232

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/211 (29%), Positives = 100/211 (47%), Gaps = 18/211 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKPAG+    G     ++D      V        L HRLD  TSG++V+A
Sbjct: 20  LYQDEHLVLINKPAGLLSLSGKN-PQNLDSVHHRLVKIF-PGCTLVHRLDFGTSGLMVIA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L + F  R + K+Y +L+ G  +N  E + +  + K       + +   + K
Sbjct: 78  RNKAINAALCQQFSQRSVTKVYSALLCGHLEN-HEGVIDAAIAKDPARFPLMSICATHGK 136

Query: 222 GANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            A    S ++V++ F  +           +++ P TGRTHQLR+H   +G PI+G   Y 
Sbjct: 137 PAR---SRYQVVERFNHELEEGTLLPLTRVQLIPETGRTHQLRIHCQLLGHPILGCDLYG 193

Query: 274 AN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                G+  +P   +L LHA  ++  HP  G
Sbjct: 194 GRLLPGSEKAP---RLMLHASALNFVHPISG 221


>gi|309776002|ref|ZP_07670994.1| ribosomal large subunit pseudouridine synthase C
           [Erysipelotrichaceae bacterium 3_1_53]
 gi|308916284|gb|EFP62032.1| ribosomal large subunit pseudouridine synthase C
           [Erysipelotrichaceae bacterium 3_1_53]
          Length = 323

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/278 (22%), Positives = 132/278 (47%), Gaps = 24/278 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++ + END +  R+D++ +     +    + K +R+ +++V++KR + + R+  G  ++ 
Sbjct: 3   EFYIGENDADQ-RVDKFIQKTMKTMPKSLMYKYIRNKKIKVNRKRCEISQRLALGDTMQC 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                   +I +E     S     +    L   ++YED  I + NKP G+     +    
Sbjct: 62  --------YIAEEFYETQSMRQFLQVPSTLD--IVYEDEHILLINKPKGLRAHSDTSEVQ 111

Query: 128 H--IDGFLKSWVDSK--------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               D  L    +S+           P L HR+D+ T G+++ A+T AA + + E    R
Sbjct: 112 DNLADRLLHYLYESQEYDPAHEQSFTPALCHRIDRNTQGLVIAAKTAAALRCMNEKIAAR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  ++ G  + +++ I  +  KK     +   V++  ++G     + ++V+    
Sbjct: 172 EVEKKYLCIIQGGLRKQQDHIVLYHRKKEQ--DNIAEVIEHEQEGYARMETSYRVLQDKG 229

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  +E++ H+G++HQ+R     +G P++GD KY A+
Sbjct: 230 -SYSLVEVELHSGKSHQIRALMSWLGHPLLGDVKYGAD 266


>gi|254881959|ref|ZP_05254669.1| RNA pseudouridylate synthase [Bacteroides sp. 4_3_47FAA]
 gi|294775568|ref|ZP_06741078.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|319641038|ref|ZP_07995742.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_40A]
 gi|254834752|gb|EET15061.1| RNA pseudouridylate synthase [Bacteroides sp. 4_3_47FAA]
 gi|294450618|gb|EFG19108.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|317387282|gb|EFV68157.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_40A]
          Length = 308

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/220 (28%), Positives = 103/220 (46%), Gaps = 21/220 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           L+YED+ I V  K  G+    +       A HI   L  +V    +  R+   HRLD+ET
Sbjct: 94  LVYEDAYILVVEKKEGLLSVSTEHQKERTAQHI---LNEYVKRSHRFNRVFVVHRLDRET 150

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L +++      + Y S+V G  +     + +WL  +      YV+
Sbjct: 151 SGLMMYAKDEKTQNTLRDNWHDIVTDRRYVSIVSGDMEKDYGTVESWLTDRKL----YVY 206

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               +     +A++H+K I   A  +  +E+   TGR +Q+RVH L +G P+VGD +Y  
Sbjct: 207 SSPVDNGEGKFAVTHYKTIKR-ANGYSLVELDLETGRKNQIRVHMLDLGHPVVGDRRY-- 263

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
              G+   P+  +L LHA  +   HP    L +   P P 
Sbjct: 264 ---GSECDPL-GRLALHAFKLCFYHPVTKELMEFETPYPT 299


>gi|317010964|gb|ADU84711.1| pseudouridine synthase [Helicobacter pylori SouthAfrica7]
          Length = 326

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 105/227 (46%), Gaps = 17/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W++SK       G K R  + HRLD
Sbjct: 80  VIFEDDDLLVLNKPPNLIVHKAPSVK---EPTLVDWLESKNYQLSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+      K E ++       +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLSRKGEKVSVECYLTRNPNNR 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              +  +NEKG  Y+ S F  +         +  + +TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 LKMMAIKNEKG-RYSKSEFTSLLTSQNNLNLIGAKLYTGRTHQIRTHLEYLNRHIIGDNL 255

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 256 YGLN---EALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 299


>gi|319777728|ref|YP_004137379.1| pseudouridine synthase [Mycoplasma fermentans M64]
 gi|318038803|gb|ADV35002.1| Pseudouridine synthase [Mycoplasma fermentans M64]
          Length = 307

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 75/309 (24%), Positives = 144/309 (46%), Gaps = 46/309 (14%)

Query: 36  NLQKILRSGQVRV-DKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
           ++++++  G V + D  +V K N  ++ GQ + I  ++N      KE KI   ++ L   
Sbjct: 26  DIKELIEQGAVYINDNVQVHKCNYIVREGQEITIVKLLN------KEIKIEPVNIPLD-- 77

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKP 144
                  + YED  + + NKP+ + V            +G+ YH    L +  ++   +P
Sbjct: 78  -------IKYEDDDLVIINKPSNLVVHPSPGHYNDTLVNGLLYHFKNNLSN--ENGLLRP 128

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HR+D++TSG+L++A+       LT+  +   I++ Y ++V G+ +N    I N  + 
Sbjct: 129 GIVHRIDKDTSGLLIIAKNNKMHNSLTDMLKRHEIERSYLAIVRGLIENPLTKI-NLPIA 187

Query: 205 KSHIGGDYVHVVKQNEKGANYA--ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           ++ +    + V K+ ++   +   + HF  +D         E++  TGRTHQ+RVH  ++
Sbjct: 188 RNTVDRKMMSVHKEGKEAITFVHLLKHF-YLDKEPMSLVRCELK--TGRTHQIRVHLSYI 244

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
             P+ GD  Y     G        +  LHA  +   HP   + + + AP+P    K +D 
Sbjct: 245 KHPVYGDPTY-----GKSVDEFNQR--LHAYKLKFIHPLTKKEICVYAPVP----KEFDV 293

Query: 322 LGFKYDRNL 330
             + ++  L
Sbjct: 294 ADYDFNELL 302


>gi|313142669|ref|ZP_07804862.1| conserved hypothetical protein [Helicobacter canadensis MIT
           98-5491]
 gi|313131700|gb|EFR49317.1| conserved hypothetical protein [Helicobacter canadensis MIT
           98-5491]
          Length = 299

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 103/220 (46%), Gaps = 47/220 (21%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +YE+    +FNKPA + +       +H    +    +  G +  L HR+D+ETSG+++V 
Sbjct: 55  IYENEDFALFNKPAQMLIHPKGRFFHH--SLMDEVREYFGTEASLIHRIDKETSGLVLVG 112

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV--VKQN 219
           + + +   L E F   RI+K Y +L+ G     K C      K S I GD+  +  +   
Sbjct: 113 KHKRSIVELGELFANNRIKKKYLALIKG-----KMC------KTSKIVGDFCLLMPLSLQ 161

Query: 220 EKGANYAI----------------------SHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           EKG + ++                      S F+++  F      L++ P TGRTHQ+RV
Sbjct: 162 EKGGDLSVRSVFLGQNLRKDSKLLGFRDAKSEFEILGEFGGN-TLLKVYPITGRTHQIRV 220

Query: 258 HALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMD 296
           H   +G PI+GD  Y C ++        Q++ YL + +++
Sbjct: 221 HLFSLGFPILGDPLYGCEDW--------QSREYLDSEFIE 252


>gi|323342987|ref|ZP_08083218.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322463051|gb|EFY08246.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 291

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/218 (27%), Positives = 109/218 (50%), Gaps = 22/218 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +LYED  I V +KP  + +V                +V  +  K R+   HRLDQ+TSG+
Sbjct: 73  ILYEDKDILVVDKPYKLLTVSNRKEEELTAFRLASDYVKKQDSKNRIFVVHRLDQDTSGV 132

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL--KKSHIGGDYVHV 215
           L+ A++    +   + +     +++Y ++V G+    K+ I ++L   K +H+       
Sbjct: 133 LMFAKSEYVKRLYQDKWSELVDERLYVAIVEGVVPKDKDVIRSFLRQNKTTHMYS----- 187

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     AI++++VI    +    L++Q  TGR +Q+RVH   +G PI+GD KY A 
Sbjct: 188 ----TSSGQEAITNYEVIKR-TENNTILKIQIDTGRKNQIRVHMNDIGHPIIGDKKYDAK 242

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
                T+P++ +L LHA  + + +P+  ++    +PLP
Sbjct: 243 -----TNPLK-RLGLHAYRLRVMNPKTKKMMTFVSPLP 274


>gi|238791583|ref|ZP_04635221.1| Pseudouridine synthase [Yersinia intermedia ATCC 29909]
 gi|238729199|gb|EEQ20715.1| Pseudouridine synthase [Yersinia intermedia ATCC 29909]
          Length = 232

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/211 (28%), Positives = 98/211 (46%), Gaps = 18/211 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + + NKPAG+    G     ++D      V        L HRLD  TSG++V+
Sbjct: 19  ILYQDDHLVLINKPAGLLSLSGKN-PQNLDSVHHRLVQIF-PGCTLVHRLDFGTSGLMVI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +     L + F  R + K+Y +L+ G   +  E + +  + K       + +   + 
Sbjct: 77  ARNKVINAALCQQFSQRTVTKVYSALLCG-HLDDNEGVIDAAIAKDPALFPLMSICSIHG 135

Query: 221 KGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K A    SH++V++ F  +           +++ P TGRTHQLR+H   +G PI+G   Y
Sbjct: 136 KPAR---SHYQVVERFYHELEDSTLLPLTRVQLTPETGRTHQLRIHCQQLGHPILGCDLY 192

Query: 273 CAN-FKGNFTSPIQNKLYLHARYMDLPHPEG 302
                 G   +P   +L LHA  +   HP G
Sbjct: 193 GGRLLPGTERAP---RLMLHASELHFNHPIG 220


>gi|330002097|ref|ZP_08304182.1| pseudouridine synthase, RluA family [Klebsiella sp. MS 92-3]
 gi|328537466|gb|EGF63703.1| pseudouridine synthase, RluA family [Klebsiella sp. MS 92-3]
          Length = 232

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/210 (30%), Positives = 97/210 (46%), Gaps = 20/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LLY+D  + + NKPAG+    G     ++D      V      P L HRLD  TSG++V+
Sbjct: 19  LLYQDEHLVLINKPAGLLSLSGKD-PRNLDSVHHRLVQRFPGCP-LVHRLDFGTSGLMVI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +     L + F  R ++K+Y +L+ G    + E I    + K       + +  ++ 
Sbjct: 77  ARNKGINALLCQQFSQRTVEKVYTALLCGH-LAEDEGIVEAAIAKDPARFPRMALCARHG 135

Query: 221 KGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K A    S ++VID   Q            + + P TGRTHQLR+H   +G PI+G    
Sbjct: 136 KPAR---SRYRVIDRLYQAREGERALALTRVTLTPETGRTHQLRIHCQLLGYPILG---- 188

Query: 273 CANFKGNFT--SPIQNKLYLHARYMDLPHP 300
           C  + G     +   ++L LHA  +   HP
Sbjct: 189 CDLYGGRELPGTECASRLMLHASELRFVHP 218


>gi|291320661|ref|YP_003515926.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           agalactiae]
 gi|290752997|emb|CBH40973.1| Ribosomal large subunit pseudouridine synthaseD [Mycoplasma
           agalactiae]
          Length = 305

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 100/216 (46%), Gaps = 27/216 (12%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQ 152
           YED  + + NKP+G+ V    G         + YH   F  +  D+ G  +  + HR+D+
Sbjct: 80  YEDEYLLILNKPSGLVVHPAPGHLNDTLVNALMYH---FKNNLSDTNGLLRLGIVHRIDK 136

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+L++A+       L +  +  +I++ Y ++  GI  NK   I N  +++       
Sbjct: 137 DTSGLLIIAKDNETHNELAKMLKNHQIKRTYLAICEGILPNKVTKI-NLPIQRDTKNRKL 195

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + + K  +    Y +   K      + +  ++ +  TGRTHQ+RVH  ++  P+ GD  Y
Sbjct: 196 MSIHKDGKSSVTY-VHMLKSFYIDNKPYSLVKCELETGRTHQIRVHLTYIKHPVYGDSIY 254

Query: 273 CAN----------FKGNFTSPIQNKLYLHARYMDLP 298
             +          +K +F  P+ NKL     Y D+P
Sbjct: 255 GKSVDEFNQRLHAYKLSFIHPVTNKLI--EVYSDIP 288


>gi|229166225|ref|ZP_04293984.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228617170|gb|EEK74236.1| Pseudouridine synthase [Bacillus cereus AH621]
          Length = 307

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 115/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED  + + NK   +    S + G+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVFEDDHVLIINKQGQMDTHPSEKNGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYMALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEKYFKKQNATLVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y     G  T+ +  +  LHA  ++  HP     + +  P P ++  T
Sbjct: 254 DVLY-----GGQTTYMSGQA-LHAMKINFLHPITKEEIVVDVPFPTNLNDT 298


>gi|314934014|ref|ZP_07841379.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus caprae C87]
 gi|313654164|gb|EFS17921.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus caprae C87]
          Length = 276

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 73/275 (26%), Positives = 121/275 (44%), Gaps = 50/275 (18%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +L ++  S  + ++ +  K  + +++G  V IP           E+K           S+
Sbjct: 27  DLHQLNMSKDITINNQSAKLTDVVRTGDSVFIP---------TPEEK-----------SN 66

Query: 96  FLKSI----LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +L S     + YED    +  KP G+      ++  + +  H+       VDS+  +P  
Sbjct: 67  YLPSYRYAQVFYEDDDFAIVMKPKGVKTHPNDLKESNTLMNHV----IYTVDSEYVEP-- 120

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLDQET G+L+VA+     + L        I +IY + V  +   K + I        
Sbjct: 121 IHRLDQETVGLLIVAKNPIMKKILDRMLEENEITRIYKANVKALLPIKPQTI------DM 174

Query: 207 HIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            IG D  H  K+        AI+H    +   +  C L+++  TGRTHQ+RVH   +G P
Sbjct: 175 PIGKDKFHPNKRRISNTGQRAITHILNSEMIKEGICQLDIKLDTGRTHQIRVHLAEIGHP 234

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           ++GD  Y     G+ T     KL L++  ++L HP
Sbjct: 235 VIGDPLY-----GDST---LRKLELNSHKIELIHP 261


>gi|254779279|ref|YP_003057384.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
 gi|254001190|emb|CAX29153.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
          Length = 327

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 106/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVVHKAPSVK---EPTLVDWLEFKNYELSNLGLKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MMALKAAKKEKSRYSKSEFSSLLTSPNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N      S  + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN---QALSKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|238810211|dbj|BAH70001.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 315

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 75/309 (24%), Positives = 144/309 (46%), Gaps = 46/309 (14%)

Query: 36  NLQKILRSGQVRV-DKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
           ++++++  G V + D  +V K N  ++ GQ + I  ++N      KE KI   ++ L   
Sbjct: 34  DIKELIEQGAVYINDNVQVHKCNYIVREGQEITIVKLLN------KEIKIEPVNIPLD-- 85

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKP 144
                  + YED  + + NKP+ + V            +G+ YH    L +  ++   +P
Sbjct: 86  -------IKYEDDDLVIINKPSNLVVHPSPGHYNDTLVNGLLYHFKNNLSN--ENGLLRP 136

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HR+D++TSG+L++A+       LT+  +   I++ Y ++V G+ +N    I N  + 
Sbjct: 137 GIVHRIDKDTSGLLIIAKNNKMHNSLTDMLKRHEIERSYLAIVRGLIENPLTKI-NLPIA 195

Query: 205 KSHIGGDYVHVVKQNEKGANYA--ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           ++ +    + V K+ ++   +   + HF  +D         E++  TGRTHQ+RVH  ++
Sbjct: 196 RNTVDRKMMSVHKEGKEAITFVHLLKHF-YLDKEPMSLVRCELK--TGRTHQIRVHLSYI 252

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
             P+ GD  Y     G        +  LHA  +   HP   + + + AP+P    K +D 
Sbjct: 253 KHPVYGDPTY-----GKSVDEFNQR--LHAYKLKFIHPLTKKEICVYAPVP----KEFDV 301

Query: 322 LGFKYDRNL 330
             + ++  L
Sbjct: 302 ADYDFNELL 310


>gi|218547690|ref|YP_002381481.1| tRNA pseudouridine synthase C [Escherichia fergusonii ATCC 35469]
 gi|218355231|emb|CAQ87838.1| tRNA pseudouridine synthase [Escherichia fergusonii ATCC 35469]
 gi|325496166|gb|EGC94025.1| tRNA pseudouridine synthase C [Escherichia fergusonii ECD227]
          Length = 260

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 106/240 (44%), Gaps = 62/240 (25%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++ ++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKYAREDKGPQPAVTQYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGRL 305
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G L
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEL 216


>gi|73662254|ref|YP_301035.1| pseudouridylate synthase [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72494769|dbj|BAE18090.1| putative pseudouridylate synthase [Staphylococcus saprophyticus
           subsp. saprophyticus ATCC 15305]
          Length = 275

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/205 (30%), Positives = 94/205 (45%), Gaps = 28/205 (13%)

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSG 156
           YED  I +  KP G+      ++  + +  H+   +KS +V+         HRLDQET G
Sbjct: 78  YEDDDIAIVMKPKGVKTHPNDLKESNTLMNHVIYTIKSDYVEP-------IHRLDQETVG 130

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+VA+     + L       +I +IY + V  +   K + I         IG D  H  
Sbjct: 131 LLIVAKNPLMKKILDRMLEENKIDRIYKANVHSLLPIKPQTI------DMPIGKDKFHSN 184

Query: 217 KQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           K+        AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y   
Sbjct: 185 KRRVSSTGQSAITHILNSKMIKEDVCELEIKLDTGRTHQIRVHLAEIGHPVIGDPLY--- 241

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             GN T     KL L++  ++  HP
Sbjct: 242 --GNST---LRKLELNSHKIEFIHP 261


>gi|326803085|ref|YP_004320903.1| RNA pseudouridine synthase [Aerococcus urinae ACS-120-V-Col10a]
 gi|326650339|gb|AEA00522.1| RNA pseudouridine synthase [Aerococcus urinae ACS-120-V-Col10a]
          Length = 234

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 105/227 (46%), Gaps = 15/227 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQETS 155
           ++YED+ + +  KP  + VQ  +     +   LK+++  +  KP      L HRLD+   
Sbjct: 5   IIYEDNHLLIVEKPINMPVQEDASGDLDLLSALKAFIKERDHKPGNVYLALLHRLDRPVG 64

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYV 213
           G++   +T  AA  L++ FR  R+++ Y ++V    +    +E   ++L K      + V
Sbjct: 65  GVMAFGKTSKAASRLSDDFRRHRVKRDYLAVVQDQKLTLKNQETWTDYLYKNR--KKNKV 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            VV + +K    A+  ++++    Q    + ++ HTGR+HQ+RV       P+ GD KY 
Sbjct: 123 SVVNKADKRGKKAVLDYQLLKQRKQ-VALVRVRLHTGRSHQIRVQFQSRQHPLWGDQKYG 181

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
             +     S    ++ L A+++ L HP           P    + W+
Sbjct: 182 QKY-----SHKGQQIALWAQHLSLIHPTKKETMTFTSTPPLSKEPWN 223


>gi|324111198|gb|EGC05181.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
          Length = 260

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 106/240 (44%), Gaps = 62/240 (25%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++ ++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKYAREDKGPQPAVTQYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGRL 305
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G L
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEL 216


>gi|182439225|ref|YP_001826944.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces griseus subsp. griseus NBRC 13350]
 gi|326779877|ref|ZP_08239142.1| pseudouridine synthase, RluA family [Streptomyces cf. griseus
           XylebKG-1]
 gi|178467741|dbj|BAG22261.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces griseus subsp. griseus NBRC 13350]
 gi|326660210|gb|EGE45056.1| pseudouridine synthase, RluA family [Streptomyces cf. griseus
           XylebKG-1]
          Length = 313

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 82/335 (24%), Positives = 142/335 (42%), Gaps = 40/335 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    ++ + V +  E  R+D      +   +     ++  +G+V+VD      + R+ 
Sbjct: 1   MSTHPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVQVDGSVAGKSERVH 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPGAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +    + + G   R  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKAQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R + K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I
Sbjct: 166 FRDRVVDKKYHALVQGHPDPMSGTIDAPIGR--HPNHDYKWAVTAEGK---PSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----- 288
           + + +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  +L     
Sbjct: 221 EAY-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPT------LAKRLGLTRQ 273

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +LHA  +   HP  G  ++ ++  PA +    D++
Sbjct: 274 WLHAVRLGFEHPSDGSWVEFSSTYPADLQHALDTI 308


>gi|326795397|ref|YP_004313217.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326546161|gb|ADZ91381.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
          Length = 250

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/225 (26%), Positives = 110/225 (48%), Gaps = 22/225 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G+ V         ++  ++   D  GQ+    HRLD+ TSG+L++
Sbjct: 4   ILYQDDFLVAVNKPSGLLVHRTELARGEMEAAVQLLRDQIGQRVYPVHRLDRGTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
                +A  L E F  R ++K Y +LV G   +    I   L K +   G     ++  E
Sbjct: 64  TLDSESASQLGEQFMNREVKKEYSTLVRGHIHDSG-SIDYPLAKLNEEKGRSRFKIEGTE 122

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +     +SH+++I+ +          + +   ++++P  GR HQ+R H  H+  P++GD 
Sbjct: 123 QE---CVSHYELIEKYTVPIPVSKYPSTRLSHIKVRPEQGRKHQIRRHFKHVFHPLIGDT 179

Query: 271 KY-CAN----FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           +Y C +    F+  +   +  +L LH+  + + HP+ G  L IT+
Sbjct: 180 RYGCRHCNHVFRETYNPDL--RLMLHSASLTVTHPKSGDNLTITS 222


>gi|315634204|ref|ZP_07889493.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           segnis ATCC 33393]
 gi|315477454|gb|EFU68197.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           segnis ATCC 33393]
          Length = 226

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/198 (32%), Positives = 90/198 (45%), Gaps = 30/198 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQ------GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +++  S   V NKP GISV       G + +     G  K W         L HRLD+ T
Sbjct: 5   IVFRHSDFIVINKPNGISVHKDDADVGLTQLVAQQLGVPKVW---------LVHRLDKVT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A    AA  L++ F   +IQK Y +L    PK K+  I+  + K     G +  
Sbjct: 56  SGLLILALNERAAVTLSQKFAQHQIQKTYIALATHKPKKKQGRISGDMQKARR--GTW-- 111

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K  +   N A++ F V    A       +QP TG+THQLRV    +G PI+GD  Y  
Sbjct: 112 --KLCQSKENPAVTDF-VSHSLAPNLRLFILQPKTGKTHQLRVAMKSLGSPILGDELYGG 168

Query: 275 NFKGNFTSPIQNKLYLHA 292
           +           + YLHA
Sbjct: 169 D--------KAERTYLHA 178


>gi|150402179|ref|YP_001329473.1| RluA family pseudouridine synthase [Methanococcus maripaludis C7]
 gi|150033209|gb|ABR65322.1| pseudouridine synthase, RluA family [Methanococcus maripaludis C7]
          Length = 298

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 111/227 (48%), Gaps = 19/227 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS---WVDSKGQKPRLTHRLDQETSGI 157
           ++YED  + + +KP  + V     +         S    ++++  K R  +RLD +T+G+
Sbjct: 84  IIYEDDDLLIVDKPKNMVVHPTKNVLSKTLANAVSNHQKINNQNYKIRFVNRLDMDTTGL 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVV 216
           L++A+   + QHL +      ++KIY ++V G    K+  I + + L    I  +  +V 
Sbjct: 144 LIIAKDPYSHQHLAKQMDEGILEKIYIAVVNGHLDLKEGIIEDSIDLNDDGIKRELSNVG 203

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K        + + +KVI+   +    LE+   TGRTHQ+RVH  ++G PI+GD  Y    
Sbjct: 204 K-------ISKTKYKVIEEL-KNASILEINLLTGRTHQIRVHLSNIGNPIIGDVLYGE-- 253

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                S + N+  LH+  + + HP    +++ ++ LP  +    ++L
Sbjct: 254 ----ISDLINRQALHSHILSIIHPITKEKMKFSSNLPKDIENLIENL 296


>gi|242079953|ref|XP_002444745.1| hypothetical protein SORBIDRAFT_07g027030 [Sorghum bicolor]
 gi|241941095|gb|EES14240.1| hypothetical protein SORBIDRAFT_07g027030 [Sorghum bicolor]
          Length = 439

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 110/231 (47%), Gaps = 36/231 (15%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD---FLKSILLYEDSK 107
           K++K N+ ++ G  + +P  ++     IK++     +  L  + D   +L+ ++++ DS 
Sbjct: 131 KKIKHNDAMEPGMRIHLP--VSVAEGEIKKRYETIPTATLHPNKDEIEYLRRLVIHRDSA 188

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRA 165
           I V NKP  + ++G   +   +D  L +   S G K  P+LT                  
Sbjct: 189 ILVLNKPPKVPMKGHLPVHNSMD-VLAAAALSYGNKEGPKLTW----------------- 230

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--- 222
                 E++    +QK YW+LV G PK ++  I   + K     G    V+  +  G   
Sbjct: 231 --NKACEAY----VQK-YWALVIGTPKEREGVICAPISKVLLDDGKAERVILAHPSGIDG 283

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
           A  AI+ ++V+        W+E++P TGR HQLRVH A  +G PIVGD+KY
Sbjct: 284 AQEAITEYRVMGPTINGCSWIELRPLTGRKHQLRVHCAEALGTPIVGDYKY 334


>gi|212711745|ref|ZP_03319873.1| hypothetical protein PROVALCAL_02820 [Providencia alcalifaciens DSM
           30120]
 gi|212685847|gb|EEB45375.1| hypothetical protein PROVALCAL_02820 [Providencia alcalifaciens DSM
           30120]
          Length = 232

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 109/232 (46%), Gaps = 23/232 (9%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I+D+ +    H D     +LY+D ++ + NKP+G+    G     ++D      V    +
Sbjct: 4   IIDTFIAPPCHEDIE---ILYQDEQLIIINKPSGLLSLSGKN-PQNLDSVHYRLVQIYPE 59

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD  TSG++V AR +A    L + F  R + K Y +L+ G  +N +  I   +
Sbjct: 60  C-TLVHRLDFGTSGVMVAARNKAINAALCQQFSQRTVTKAYHALLCGHVENNEGVIDAPI 118

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQ 254
            K   +    + + + + K A    S++ VI+ F  +           ++  P TGRTHQ
Sbjct: 119 AKDPAL-FPRMSICETHGKSAR---SYYHVIERFYDEQSDGNQLPLTRVKFIPETGRTHQ 174

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGR 304
           LR+H+   G PI+G    C  + G     I+   +L LHA  ++  HP  G+
Sbjct: 175 LRIHSQLFGHPILG----CDLYGGLLPIGIEPAPRLMLHASELNFVHPITGK 222


>gi|196036248|ref|ZP_03103647.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
 gi|195991223|gb|EDX55192.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
          Length = 297

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/269 (25%), Positives = 127/269 (47%), Gaps = 34/269 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+  P
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQAGEEIRVFFP 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 68  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHSSGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 113 VANALLSHYDKQYLAST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 170 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++  TGRTHQ+RVH  H+G P++GD+ Y
Sbjct: 224 SLELDTGRTHQIRVHMAHIGHPLLGDNLY 252


>gi|260767269|ref|ZP_05876210.1| tRNA pseudouridine synthase C [Vibrio furnissii CIP 102972]
 gi|260617777|gb|EEX42955.1| tRNA pseudouridine synthase C [Vibrio furnissii CIP 102972]
          Length = 243

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/213 (28%), Positives = 96/213 (45%), Gaps = 18/213 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ I   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IIYQDAYIVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG---------IP-KNKKECIANWLLKKSHIGG 210
           A +   A ++   F    ++K Y ++V G          P K + + IA+   K+     
Sbjct: 64  ALSSEIAANMMPMFANHEMEKTYHAIVRGWIEVGDVLDYPLKEELDKIADKFAKQDKAPQ 123

Query: 211 DYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D V   +   K    ++   F        ++C +EM+P TGR HQLR H  H+  PIVGD
Sbjct: 124 DAVTAYQPLAKVEVPHSTGKFPTT-----RYCLMEMKPKTGRKHQLRRHMAHLRHPIVGD 178

Query: 270 HKYCANFKGNFTSPIQN--KLYLHARYMDLPHP 300
             +           + +  +L LHA  +   HP
Sbjct: 179 TTHGDGKHNRLYREVYDAHRLMLHASELRFVHP 211


>gi|229496355|ref|ZP_04390075.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas endodontalis ATCC 35406]
 gi|229316933|gb|EEN82846.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas endodontalis ATCC 35406]
          Length = 234

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/191 (30%), Positives = 95/191 (49%), Gaps = 12/191 (6%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---- 145
           L +H   +K  ++YED+ + V +K  G  V         ++  +  ++  K  KP     
Sbjct: 2   LWRHELLMK--VVYEDNHLLVVSKLPGEIVHADKTGDPSLEDMVALYLKKKYNKPGNVFV 59

Query: 146 -LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-ECIANWLL 203
            + HRLD+   G+++ A+T  A   + + F    + K Y ++V   PK  + ECI +WL 
Sbjct: 60  GVVHRLDRPVGGLVLFAKTSKALARMNKLFAEGGVHKTYRAVVQNSPKGTQGECI-DWLW 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           + +     Y+  VK+N   A  A   ++ I   A++F  LE++  TGR HQ+R     MG
Sbjct: 119 RNAKQNKTYI--VKENHPDAKRAHLRWRRI-ATAERFQMLEIELLTGRHHQIRAQLAGMG 175

Query: 264 CPIVGDHKYCA 274
           CPI GD KY A
Sbjct: 176 CPIKGDLKYGA 186


>gi|182415562|ref|YP_001820628.1| pseudouridine synthase [Opitutus terrae PB90-1]
 gi|177842776|gb|ACB77028.1| pseudouridine synthase [Opitutus terrae PB90-1]
          Length = 255

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 105/238 (44%), Gaps = 20/238 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSG-------IAYHIDGFLKSWV-----DSKGQKPRLT 147
           IL  + + +   +KPAG+      G       +  H D   + +V      +  Q+  L 
Sbjct: 20  ILERDPNGLLALSKPAGVLSHPNEGKDQPRSLLTCHFDAVAECYVWTPEGAATSQRWWLL 79

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +RLD  TSG++++A     A+ +   F+ +++ K+Y +LV+G P    E   + ++  + 
Sbjct: 80  NRLDSATSGVILLAANEELAREIRAQFKRKQVTKVYQALVFGKPPRPVELWRD-VVAVTK 138

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            GG            A   +S  +           L+++P TGR+HQLRV       PIV
Sbjct: 139 QGGQIRTTAGAGRVPAECRMSVVRSRGVGEGALALLQLEPRTGRSHQLRVQCAKRHVPIV 198

Query: 268 GDHKYCANFKGN--FTSPI-QNKLYLHARYMDLPHPEGGRLQI---TAPLPAHMVKTW 319
           GD  Y  +F+ N  F     + +L+LH+      +   GR  +    APLPA   + W
Sbjct: 199 GDQTY-GDFRHNREFAKRTGEKRLFLHSLATRFEYAWKGRTHVFAAQAPLPAEFGQVW 255


>gi|86145699|ref|ZP_01064028.1| putative ribosomal large chain pseudouridine synthase A [Vibrio sp.
           MED222]
 gi|85836398|gb|EAQ54527.1| putative ribosomal large chain pseudouridine synthase A [Vibrio sp.
           MED222]
          Length = 570

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 105/207 (50%), Gaps = 26/207 (12%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D  I V +KPAG +SV G +          +   D +G  P + HRLD  TSGIL+
Sbjct: 369 ILFQDDHIVVVHKPAGFLSVPGKTIKDSAYTRVQEMHPDVEG--PFVIHRLDMATSGILI 426

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A TR A + L + F  R ++K Y +++ G+ +  +  +      +  + GD     +Q 
Sbjct: 427 FALTRRANKSLQKQFITREVEKRYVAMIEGVLEQDEGYV------RLPLRGDLYDRPRQI 480

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
              E G   A + ++VI+  +Q    + + P TGRTHQLRVH  H   +  PIVGD  Y 
Sbjct: 481 VCFEHGKP-AETKWEVIE-RSQDTTKVYLHPKTGRTHQLRVHCSHEEGLNMPIVGDGLY- 537

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
               GN      ++L+LHA  + L HP
Sbjct: 538 ----GNKA----DRLHLHAERLALHHP 556


>gi|163739826|ref|ZP_02147233.1| pseudouridine synthase [Phaeobacter gallaeciensis BS107]
 gi|161386860|gb|EDQ11222.1| pseudouridine synthase [Phaeobacter gallaeciensis BS107]
          Length = 207

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/216 (27%), Positives = 105/216 (48%), Gaps = 19/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D+++ V NKP G+    G G   H+   L S + +   +  L HRLD++TSG++V 
Sbjct: 6   ILHHDAQLLVVNKPHGLLSVPGRG--EHLADCLLSRLQAAFPEALLVHRLDRDTSGVMVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
             T  A +HL+  F  R  +K Y + + G  + +   +   L+       D+ +  +Q  
Sbjct: 64  GVTPHAQRHLSMQFEKRSAKKAYVARLDGRLEPRSGTVDLPLIV------DWPNRPRQMV 117

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A++ ++V+  +      + + P TGR+HQLRVH L +G  I+GD  Y      
Sbjct: 118 CHDTGKEAVTDWRVMK-YEDTATRVRLTPKTGRSHQLRVHMLSLGHAILGDPLYAEGRAL 176

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG---RLQITAPL 311
           +       ++ LHA  + + HP+ G   + ++ AP 
Sbjct: 177 D-----HPRMMLHAEELRIKHPDSGESMKFRVKAPF 207


>gi|302846594|ref|XP_002954833.1| RNA pseudouridine synthase mitochondrial precursor [Volvox carteri
           f. nagariensis]
 gi|300259808|gb|EFJ44032.1| RNA pseudouridine synthase mitochondrial precursor [Volvox carteri
           f. nagariensis]
          Length = 343

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 87/201 (43%), Gaps = 19/201 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +P + HRLD+ TSG+LVVA+T  A   L   F+ R + ++Y S+  G P      +   +
Sbjct: 140 RPGIVHRLDKGTSGLLVVAKTEVALTRLQAQFKARTVDRLYDSITVGCPVQPNGRVETNI 199

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALH 261
            +              + +G   A S++ V+   A     L   +  TGRTHQ+RVHA +
Sbjct: 200 CRDPRDRKRMAAAPYGSGRG-RTAGSNYTVMAPLAGGGAALVRWKLDTGRTHQIRVHAKY 258

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQ----------------NKLYLHARYMDLPHP-EGGR 304
           +G P++GD  Y         +  +                 +  LHAR +   HP  G R
Sbjct: 259 IGHPLLGDDTYGGTAPAALAAVSRGSSLDSLSSLEVVEQLGRPALHARTLGFTHPVTGAR 318

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L    P+P   ++    LG +
Sbjct: 319 LSFEQPVPEDFLRALRGLGME 339


>gi|257081816|ref|ZP_05576177.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis E1Sol]
 gi|256989846|gb|EEU77148.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis E1Sol]
          Length = 297

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 110/233 (47%), Gaps = 26/233 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLD 151
           +++ED    V NKPAGI+        YH  G + + V  KG   R         +  RLD
Sbjct: 80  IVFEDDHFLVVNKPAGIA---SIPAQYHPSGTMANRV--KGYYKRQNYVNQVIHVVTRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+   A   + +  R +++ KIY++LV G  +   E   + L++K  IG D
Sbjct: 135 RDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLSE---HQLIEKP-IGRD 190

Query: 212 YVHVVK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              ++K Q  +   +A + + +    AQ    + +Q HTGRTHQ+RVH   +GC ++GD 
Sbjct: 191 LSSLLKRQVIETGQFASTEYWLAKRGAQA-AAVRIQLHTGRTHQIRVHFEAIGCSLLGDE 249

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            Y              +  LH   +   HP     + + +PL   M    D+L
Sbjct: 250 MYHGEMDQGI-----GRQALHCMELIFTHPFTKETVHLISPLAEDMKSVDDTL 297


>gi|210623700|ref|ZP_03293984.1| hypothetical protein CLOHIR_01934 [Clostridium hiranonis DSM 13275]
 gi|210153388|gb|EEA84394.1| hypothetical protein CLOHIR_01934 [Clostridium hiranonis DSM 13275]
          Length = 303

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 103/222 (46%), Gaps = 21/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS------KGQKPRLTHRLDQET 154
           +LY+D  I + +KP  + V        H DG + + V        +  K R  +RLD  T
Sbjct: 85  ILYDDFDIIMVDKPPYMVVHPTKS---HFDGTVANGVTDFIIKKDEKVKVRFVNRLDMNT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA+   A   L+       ++K Y ++V G+ K  K  I   + + +    D + 
Sbjct: 142 SGLVIVAKNAYAHHVLSTDMSENLVEKKYIAVVKGVMKEDKGTIDAPIYRPT---DDSIK 198

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  +E+G   +I+H+ VI+        +E++  TGRTHQ+RVH  H+G  I+GD  Y  
Sbjct: 199 RV-VDERGQR-SITHYSVIERLDDA-TVVELKLETGRTHQIRVHLAHLGYGIIGDELY-- 253

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
              G     +  +  LHA  +    P     L+  A +P  M
Sbjct: 254 ---GYVDENLIKRQALHAYSLKFKQPRTREDLEFKAEIPDDM 292


>gi|73985013|ref|XP_541778.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 3 [Canis familiaris]
          Length = 404

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/194 (30%), Positives = 90/194 (46%), Gaps = 16/194 (8%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD--- 151
           D L++ ++ +   +   NKP G+ V G  G    +   L     S G + R  H +    
Sbjct: 130 DALRAAVVDQKGPLVTLNKPPGLPVTGKPG-ELTLFSVLPELSQSLGLRDRELHVVQASG 188

Query: 152 QETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +ETSG+++++     A HL + F    R RR    YW++  GIP   +  I    LK  H
Sbjct: 189 KETSGLVLLSSCPQTASHLQKFFIYSRRARRPTATYWAITDGIPATSEGNI-QAALKLEH 247

Query: 208 IGG-DYVHVVKQN-----EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           I G D V  VK       ++G    +SHF V+         +++QP T    QL+VH + 
Sbjct: 248 IDGVDLVIPVKSPSRKDFQEGVKRTLSHFHVV-AMGSGCALVQLQPLTVFPSQLQVHMVL 306

Query: 262 MGCPIVGDHKYCAN 275
             CP++GDH Y A 
Sbjct: 307 QLCPVLGDHTYSAR 320


>gi|218676955|ref|YP_002395774.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           splendidus LGP32]
 gi|218325223|emb|CAV27163.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           splendidus LGP32]
          Length = 570

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 105/207 (50%), Gaps = 26/207 (12%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D  I V +KPAG +SV G +          +   D +G  P + HRLD  TSGIL+
Sbjct: 369 ILFQDDHIVVVHKPAGFLSVPGKTIKDSAYTRVQEMHPDVEG--PFVIHRLDMATSGILI 426

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A TR A + L + F  R ++K Y +++ G+ +  +  +      +  + GD     +Q 
Sbjct: 427 FALTRRANKSLQKQFITREVEKRYVAMIEGVLEQDEGYV------RLPLRGDLYDRPRQI 480

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
              E G   A + ++VI+  +Q    + + P TGRTHQLRVH  H   +  PIVGD  Y 
Sbjct: 481 VCFEHGKP-AETKWEVIER-SQDTTKVYLHPKTGRTHQLRVHCSHEEGLNMPIVGDGLY- 537

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
               GN      ++L+LHA  + L HP
Sbjct: 538 ----GNKA----DRLHLHAERLALHHP 556


>gi|148827198|ref|YP_001291951.1| exonuclease III [Haemophilus influenzae PittGG]
 gi|148718440|gb|ABQ99567.1| exonuclease III [Haemophilus influenzae PittGG]
          Length = 224

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/203 (31%), Positives = 96/203 (47%), Gaps = 28/203 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+ S   + NK  GISV      QG + +        K W         L HRLD+ T
Sbjct: 5   VVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQLNVPKVW---------LVHRLDKVT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A    +A   +  F   +I K Y +L    PK K+  I    +KK+  G   + 
Sbjct: 56  SGLLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGD-MKKAREGAWKLC 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K+N      AI+ F+ + C      ++ ++P TG+THQLRV    +G PI+GD  Y  
Sbjct: 115 QTKENP-----AITRFESVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDGLY-- 166

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
              G  T  I ++ YLHA  ++ 
Sbjct: 167 ---GKNTEKI-DRTYLHATQLEF 185


>gi|262373260|ref|ZP_06066539.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           junii SH205]
 gi|262313285|gb|EEY94370.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           junii SH205]
          Length = 349

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 107/231 (46%), Gaps = 33/231 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  I V NK  G+ V  G+G         + YH          ++  +  L HR+D
Sbjct: 116 VVYEDDDIIVINKEVGMVVHPGAGNPSGTLVNALLYHAPKL------AELSRAGLVHRID 169

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+LV+A+   A   L++    + + ++Y  +V+G        IA   + +  I   
Sbjct: 170 KDTSGLLVIAKNLEAQFSLSKQLAKKTVYRVYDLVVYG------NIIAGGTIDEP-IKRH 222

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V  VK     G   A++H+ V + F + F  ++ Q  TGRTHQ+RVH  ++G  +VGD 
Sbjct: 223 PVDRVKMAILPGGREAVTHYNVKERF-RDFTRVQAQLETGRTHQIRVHFSYLGYGLVGDP 281

Query: 271 KYCANFK---GNFTSPIQ-----NKLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y    +   G   + I       +  LHA  + L HP  G  +   AP P
Sbjct: 282 VYVNRVRLPAGASETLIDMLRSFKRQALHAAKLGLVHPRTGEEMMFEAPWP 332


>gi|260582044|ref|ZP_05849839.1| pseudouridylate synthase [Haemophilus influenzae NT127]
 gi|260094934|gb|EEW78827.1| pseudouridylate synthase [Haemophilus influenzae NT127]
          Length = 224

 Score = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/203 (31%), Positives = 96/203 (47%), Gaps = 28/203 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+ S   + NK  GISV      QG + +        K W         L HRLD+ T
Sbjct: 5   VVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQLNVPKVW---------LVHRLDKVT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A    +A   +  F   +I K Y +L    PK K+  I    +KK+  G   + 
Sbjct: 56  SGLLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGD-MKKAREGAWKLC 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K+N      AI+ F+ + C      ++ ++P TG+THQLRV    +G PI+GD  Y  
Sbjct: 115 QTKENP-----AITRFESVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDGLYGK 168

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
           N     T  I ++ YLHA  ++ 
Sbjct: 169 N-----TEKI-DRTYLHATQLEF 185


>gi|307109077|gb|EFN57316.1| hypothetical protein CHLNCDRAFT_143940 [Chlorella variabilis]
          Length = 330

 Score = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 87/335 (25%), Positives = 137/335 (40%), Gaps = 69/335 (20%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           W +   P +    L K+ R   VR+ D    + ++R  S Q        +  +     + 
Sbjct: 17  WLRRRGPPLPESALHKLFRVSTVRLYDPATQRIHSRPSSRQQPGNDGAGSTTSGSTGGRS 76

Query: 83  ILDSSVNLTKHSDF-----------LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
             D+S+   + S             L+S LL+ D  +    KPAG++ QGGSG+++ +D 
Sbjct: 77  SGDTSLAAARASPSRQRASERWAARLRSCLLHSDPDLLAVCKPAGLACQGGSGVSHSVDS 136

Query: 132 FL-KSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--------- 178
            +  ++    G      RL HRLD++T+G L++AR   AA  L  +F+            
Sbjct: 137 VMAAAFAHLPGPASHHLRLVHRLDRQTTGALLLARGPDAAAWLAAAFQESSGGGSSGGGR 196

Query: 179 --------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
                   I+K YW++V  +P    E  A   L  +      V   +     A  A + +
Sbjct: 197 GDSSSGAIIRKQYWAVV-ALP----EGGAAHRLPAAGAISLPVPGGRGGVAAAQPAPTRY 251

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           +V+        WLE+ P TGR HQLR+H A  +G  I+GD +                  
Sbjct: 252 RVLH-RGGGLAWLELAPATGRKHQLRLHCAQGLGAAILGDGRLAVR-------------- 296

Query: 290 LHARYMDLPHPEGGRLQI--TAPLPAHMVKTWDSL 322
                     P  GR Q+  TAPLPA    +W +L
Sbjct: 297 ---------KPGAGRGQVVATAPLPA----SWRAL 318


>gi|33152257|ref|NP_873610.1| tRNA pseudouridine synthase C [Haemophilus ducreyi 35000HP]
 gi|34582379|sp|P59840|TRUC_HAEDU RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|33148479|gb|AAP95999.1| probable pseudouridine synthase Rlu family protein [Haemophilus
           ducreyi 35000HP]
          Length = 243

 Score = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 109/244 (44%), Gaps = 18/244 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D ++   NKPAG+ V             +++  D   Q     HRLD+ TSG+L+ 
Sbjct: 5   ILYRDDELIAINKPAGMLVHRSWLDKAETLFAMQTLRDQINQHVFPIHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A+ ++E F   +++K Y ++V G    K E   ++ LK   +  D +       
Sbjct: 65  ALNSEMARLMSEQFEQHKVEKEYLAIVRGYIAEKGEI--DYPLK---VILDKIADKFSQP 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++  + + P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAAQQAVTFYQNLAKVEMPYSTGKYATTRYSLVALSPKTGRKHQLRRHMKHLFHPIMGDT 179

Query: 271 KYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
           KY    +    +     N+L LHAR +   HP+   ++ I+A L       ++  G+ + 
Sbjct: 180 KYGDLHQNRRLTEKTGCNRLMLHARLLHFTHPKTLQKITISALLDQQWQMLFNQFGWHFT 239

Query: 328 RNLY 331
              Y
Sbjct: 240 DFFY 243


>gi|150390922|ref|YP_001320971.1| RluA family pseudouridine synthase [Alkaliphilus metalliredigens
           QYMF]
 gi|149950784|gb|ABR49312.1| pseudouridine synthase, RluA family [Alkaliphilus metalliredigens
           QYMF]
          Length = 308

 Score = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 109/221 (49%), Gaps = 19/221 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGI 157
           ++YED  + V NK  GI S    S     I    +++++ KG   + R  +RLD +TSG+
Sbjct: 88  VVYEDIDVIVINKEPGIVSHPTKSHPKDTIANAAQNYLEKKGVACRIRFVNRLDMDTSGL 147

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV+A+       +++  +   I K Y + V G+    +  I   + + S         +K
Sbjct: 148 LVIAKNPYTHHIMSQQMKANEITKKYVAFVKGVVVANEGEIDGAIYRSSD------ETIK 201

Query: 218 Q--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +  +++G   +++ F V++ +A     LE+   TGRTHQ+RVH   +G P++GDH Y   
Sbjct: 202 RVVDDRGQQ-SLTKFTVLERYADA-TMLEVSLLTGRTHQIRVHMESIGHPMLGDHLY--- 256

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
             G   + +  +  LHA Y+    P    ++++ A LP  +
Sbjct: 257 --GYVDTELIRRQALHASYLSFLQPRYKEKIEVRASLPKDL 295


>gi|306830219|ref|ZP_07463402.1| ribosomal large subunit pseudouridine synthase [Streptococcus mitis
           ATCC 6249]
 gi|304427586|gb|EFM30683.1| ribosomal large subunit pseudouridine synthase [Streptococcus mitis
           ATCC 6249]
          Length = 278

 Score = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 91/201 (45%), Gaps = 18/201 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + V NKP G+   G       +   + S+V   G    + HRLD ETSG+++ A
Sbjct: 71  VYQDQYLIVVNKPEGMKTHGNQPDEIALLNHVSSYV---GHTCYVVHRLDMETSGLVLFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I + YW+LV G   +K+      L+ +  IG D     K+  +
Sbjct: 128 KNPFILPILNRLLEKKEIAREYWALVEGQVGSKE------LIFRDKIGRDRHDRRKRVVD 181

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K   +A +    +  F  K   +  +  TGRTHQ+RVH  H   PI+GD  Y +  K  
Sbjct: 182 PKNGQHAETQVSRLKQFPNKTSLVRCKLKTGRTHQIRVHLSHHKHPILGDPLYNSQSKT- 240

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 241 ------SRLMLHAFRLSFTHP 255


>gi|239940558|ref|ZP_04692495.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces roseosporus NRRL 15998]
 gi|239987042|ref|ZP_04707706.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces roseosporus NRRL 11379]
 gi|291443991|ref|ZP_06583381.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           roseosporus NRRL 15998]
 gi|291346938|gb|EFE73842.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           roseosporus NRRL 15998]
          Length = 313

 Score = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 82/335 (24%), Positives = 143/335 (42%), Gaps = 40/335 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    ++ + V +  E  R+D      +   +     ++  +G+V+VD      + R+ 
Sbjct: 1   MSTHPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVQVDGSVAGKSERVH 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPGAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +    + + G   R  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKAQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R + K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I
Sbjct: 166 FRDRVVDKRYHALVQGHPDPMSGTIDAPIGR--HPNHDYKWAVTAEGK---PSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----- 288
           + + +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  +L     
Sbjct: 221 EAY-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPT------LAKRLGLTRQ 273

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +LHA  +   HP +G  ++ ++  PA +    D++
Sbjct: 274 WLHAVRLGFEHPADGSWVEFSSTYPADLQHALDTI 308


>gi|319896464|ref|YP_004134657.1| pseudouridine synthase [Haemophilus influenzae F3031]
 gi|317431966|emb|CBY80314.1| conserved hypothetical pseudouridine synthase [Haemophilus
           influenzae F3031]
          Length = 224

 Score = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/203 (31%), Positives = 96/203 (47%), Gaps = 28/203 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+ S   + NK  GISV      QG + +        K W         L HRLD+ T
Sbjct: 5   VVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQLNVPKVW---------LVHRLDKVT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A    +A   +  F   +I K Y +L    PK K+  I    +KK+  G   + 
Sbjct: 56  SGLLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGD-MKKAREGAWKLC 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K+N      AI+ F+ + C      ++ ++P TG+THQLRV    +G PI+GD  Y  
Sbjct: 115 QTKENP-----AITRFESVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDGLYGK 168

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
           N     T  I ++ YLHA  ++ 
Sbjct: 169 N-----TEKI-DRTYLHATQLEF 185


>gi|153003163|ref|YP_001377488.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152026736|gb|ABS24504.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 311

 Score = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 105/242 (43%), Gaps = 31/242 (12%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHR 149
           +L E  ++ V +KPAG++V      +GG+      +  +  + +  G  P         R
Sbjct: 79  VLVETPRLVVVDKPAGVAVHPLAPGEGGT----LANAVVARFPECAGASPEPREGGAVQR 134

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD ETSG +  AR   A Q L      R ++KIY +LV G    +   +    +  +  G
Sbjct: 135 LDLETSGCVTFARDPEAWQELHARLSAREVEKIYLALVAG----RMATVGVSSVPLAQRG 190

Query: 210 GDYVHVV------KQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           G  + V       +   KG     A +H+ V   F +    L ++  TG  HQ+R H  H
Sbjct: 191 GRAIPVPDPETEERLRAKGLRPRPAETHWDVARRF-ETHTLLRVRIVTGVMHQIRAHLAH 249

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
           +G P+ GD  Y  +       P   + +LHA  + L  P+G R++  +PLP  +      
Sbjct: 250 LGHPVAGDALYGGDAA---ALPGLRRQFLHATRLALEGPDGERVEAESPLPPELEAVLAR 306

Query: 322 LG 323
           LG
Sbjct: 307 LG 308


>gi|315180900|gb|ADT87814.1| pseudouridine synthase Rlu family protein [Vibrio furnissii NCTC
           11218]
          Length = 243

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/212 (28%), Positives = 95/212 (44%), Gaps = 16/212 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ I   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IIYQDAYIVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG---------IP-KNKKECIANWLLKKSHIGG 210
           A +   A ++   F    ++K Y ++V G          P K + + IA+   K+     
Sbjct: 64  ALSSEIAANMMPMFANHEMEKTYHAIVRGWIEAGDVLDYPLKEELDKIADKFAKQDKAPQ 123

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D    V   +  A   + H         ++C +EM+P TGR HQLR H  H+  PIVGD 
Sbjct: 124 D---AVTAYQPLAQVEVPH-STGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNFTSPIQN--KLYLHARYMDLPHP 300
            +           + +  +L LHA  +   HP
Sbjct: 180 THGDGKHNRLYREVYDAHRLMLHASELRFVHP 211


>gi|262369254|ref|ZP_06062582.1| pseudouridylate synthase [Acinetobacter johnsonii SH046]
 gi|262315322|gb|EEY96361.1| pseudouridylate synthase [Acinetobacter johnsonii SH046]
          Length = 227

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/210 (30%), Positives = 102/210 (48%), Gaps = 20/210 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++YED  + V  KPAG+    G    +    +L+  V ++    ++THRLD  TSGIL+
Sbjct: 23  VIVYEDDDLVVIEKPAGLLSVPGRLPEHQDSAYLR--VLAQYPHAKITHRLDMATSGILM 80

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IANWLLKKSHIGGDYVHV 215
            A+ R A   +++ F+ R + K Y +LV G    +       I +W  +   I    VH 
Sbjct: 81  FAKHRDAEVAVSKMFQARTVDKHYIALVQGQLDAEGSVEVPLITDWENRPRQI----VHF 136

Query: 216 -VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + +  K    A+S+    D        + + P TGR+HQLRVH  ++G PI GD  Y  
Sbjct: 137 ELGKPAKTLYQALSYDIETDI-----TRVLLTPITGRSHQLRVHMQYIGHPITGDKLYHP 191

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                  SP++ ++ LHA ++    P  G+
Sbjct: 192 E---PTRSPLK-RMALHASFLAFQQPLSGK 217


>gi|332534997|ref|ZP_08410813.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332035564|gb|EGI72057.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 226

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/192 (30%), Positives = 89/192 (46%), Gaps = 20/192 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y  +  Y+  KPAG++     G      GF+        QK    HRLD+ TSG++++
Sbjct: 11  VVYTHNDFYILEKPAGLNFHSEEG-----PGFVVLAEQQLSQKLYAVHRLDKVTSGLIIL 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +AAA   T  F    I K Y ++    PK K+  I    + KS  G       K   
Sbjct: 66  ARNKAAAATFTVMFTEHAIAKFYLAISDAKPKKKQGWIKG-DMAKSRRGS-----FKLLT 119

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  +  +   F    ++P++G+THQLRV    +G  I+GD  Y  +     
Sbjct: 120 STLNPAITRFYSL-SYKPGFRGYILKPYSGKTHQLRVALKSVGAAILGDAMYSGS----- 173

Query: 281 TSPIQNKLYLHA 292
              + N+ YLHA
Sbjct: 174 ---LSNRTYLHA 182


>gi|229010681|ref|ZP_04167879.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
 gi|228750575|gb|EEM00403.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
          Length = 307

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 115/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED  + + NK   +    S + G+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVFEDDHVLIVNKQGQMDTHPSEKNGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYMALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEKYFKKQNATLVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y     G  T+ +  +  LHA  ++  HP     + +  P P ++  T
Sbjct: 254 DVLY-----GGQTTYMSGQA-LHAMKINFLHPITKEEIVVDVPFPTNLNDT 298


>gi|161506492|ref|YP_001573604.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160867839|gb|ABX24462.1| hypothetical protein SARI_04699 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 260

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 108/232 (46%), Gaps = 21/232 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDAWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        L ++  I   +     + +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDALLDYPLLEERDKIADKFA----RED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
           K+  + + N ++       +L LHA  ++L HP  G+  I   + A + +TW
Sbjct: 180 KH-GDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLI---IQAGLDETW 227


>gi|238757890|ref|ZP_04619072.1| Pseudouridine synthase [Yersinia aldovae ATCC 35236]
 gi|238703875|gb|EEP96410.1| Pseudouridine synthase [Yersinia aldovae ATCC 35236]
          Length = 232

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 103/228 (45%), Gaps = 21/228 (9%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H        LY+D  + V NKP G+    G     ++D      V    
Sbjct: 3   KIIDTFIAPPCHDKIEN---LYQDDHLLVINKPTGLLSLSGKN-PQNLDSVHHRLVQIFP 58

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   +  E + + 
Sbjct: 59  SC-TLVHRLDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCG-HLDDNEGVIDA 116

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTH 253
            + K       + +   + K A    S+++V++ F  K           +++ P TGRTH
Sbjct: 117 AIAKDPALFPLMSICAIHGKPAR---SYYRVVERFYHKLEDGTLLPLTRVQLTPETGRTH 173

Query: 254 QLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
           QLR+H   +G PI+G   Y      G   +P   +L LHA  +   HP
Sbjct: 174 QLRIHCQQLGHPILGCDLYGGRLLPGTEQTP---RLMLHASELHFVHP 218


>gi|300361154|ref|ZP_07057331.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           gasseri JV-V03]
 gi|300353773|gb|EFJ69644.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           gasseri JV-V03]
          Length = 285

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 105/236 (44%), Gaps = 23/236 (9%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
             Q+ ++   +  N  +++G  + I      L+H+  EQ+   +S +L +        ++
Sbjct: 42  ENQILINGHYLPLNFLVKAGDKIDI-----YLDHVESEQQTYTASGSLPE--------VV 88

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YEDS I + +KPAG   Q         D  L       G  P + HRLD  T+G+L+VA+
Sbjct: 89  YEDSDILIIDKPAG---QKTHPNLNEKDTALNDCATYLGYSPFIVHRLDMLTNGLLLVAK 145

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
             A    L      + + + Y  L W    N+ +      L   H   D     +     
Sbjct: 146 NPAVVPILNRQLTNKTLHREY--LAWVSKSNQLKQSGTISLPIGHDPND--QRKRMVRPD 201

Query: 223 ANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              AI+H++++ +C  +    L ++  TGRTHQ+RVH   +  PI+GD  Y  N++
Sbjct: 202 GQKAITHYEIVKECENKALVKLTLE--TGRTHQIRVHLAALNAPIIGDPLYNPNYQ 255


>gi|58579971|ref|YP_198987.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|58424565|gb|AAW73602.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
          Length = 290

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 110/236 (46%), Gaps = 26/236 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           +LY+D  + V +K AG+ V   S +A   D FL   +  +  +P  L HRLD+ TSG L+
Sbjct: 62  ILYQDDVLAVVDKTAGLMVHD-SKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGCLL 120

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R  A  L ++     +QK Y ++  G P   +  + + L      GG    V K  
Sbjct: 121 LAFDRETASALGKALMSGDVQKDYLAVCRGWPAEPRFTVDHDL-----DGGPGKPVKKP- 174

Query: 220 EKGANYAISHFKVIDC---------FA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++HF+ +           FA  ++  L  QP TGR  Q+R H  H+   ++GD
Sbjct: 175 ------ALTHFQRLATGELQVPSTGFATSRYALLRCQPQTGRFRQIRRHLKHLSHHLIGD 228

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
             +       +F     +++ LHA+ +  PHP +G R+++TAPL     K     G
Sbjct: 229 TSHGDGRHNRSFRMLGIHRMLLHAKRLAFPHPADGRRIRVTAPLDDEFTKACALFG 284


>gi|325981783|ref|YP_004294185.1| pseudouridine synthase, RluA family [Nitrosomonas sp. AL212]
 gi|325531302|gb|ADZ26023.1| pseudouridine synthase, RluA family [Nitrosomonas sp. AL212]
          Length = 285

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 71/224 (31%), Positives = 106/224 (47%), Gaps = 24/224 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGI 157
           + ED  + + NKPAG+    G+G      ++  L    + K   PR  + HRLD+ T+G+
Sbjct: 60  IEEDETLIIINKPAGLVTHPGNGNWQGTLLNALLHHAPELK-NIPRAGIVHRLDKNTTGL 118

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV+A+T AA   L    + R +++ Y +LV G  K      A        IG   +H  K
Sbjct: 119 LVIAKTLAAQTSLVRQLQQRTVKRDYLALVLGEIKQAGNIDAP-------IGRHPIHRTK 171

Query: 218 Q--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                KG   A ++++VI+ F +    L+    TGRTHQ+RVH   +G  +VGD  Y   
Sbjct: 172 MTITSKG-KPARTNYQVIENF-EGCTLLQCSLETGRTHQIRVHLNAIGHALVGDPVYGGK 229

Query: 276 FKGNFTSPIQNKLY------LHARYMDLPHPEGGRL-QITAPLP 312
             G     I   L       LHA+ + L HP+  ++ Q  AP P
Sbjct: 230 -PGKTARAIAQILTDFPRQALHAQKLALIHPKTEQINQWEAPTP 272


>gi|320011298|gb|ADW06148.1| pseudouridine synthase, RluA family [Streptomyces flavogriseus ATCC
           33331]
          Length = 313

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 83/335 (24%), Positives = 143/335 (42%), Gaps = 40/335 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    V+ + V +  E  R+D      +   +     ++  +G+V+VD      + R+ 
Sbjct: 1   MSTYPEVRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVQVDGAVAGKSERVH 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWMEVEMPQAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +    + + G   R  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKAQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R ++K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I
Sbjct: 166 FRDRVVEKKYHALVQGHPDPMSGTIDAPIGR--HPQHDYKWAVTAEGK---PSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----- 288
           + + +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  +L     
Sbjct: 221 EAY-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGAD------PTLAKRLGLTRQ 273

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +LHA  +   HP +GG ++  +  P  +    D++
Sbjct: 274 WLHAVRLGFEHPADGGWVEFESTYPDDLRHALDTI 308


>gi|78485672|ref|YP_391597.1| pseudouridine synthase RluA-like [Thiomicrospira crunogena XCL-2]
 gi|78363958|gb|ABB41923.1| Pseudouridine synthase, Rlu family protein [Thiomicrospira
           crunogena XCL-2]
          Length = 238

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/221 (27%), Positives = 97/221 (43%), Gaps = 59/221 (26%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLT-------- 147
           L   ++++ ++  V +KPAG++        +H      S  DS GQK P L         
Sbjct: 6   LPITVVFQSTEFIVVDKPAGMN--------FH------SEPDSDGQKQPGLVVFVQQQLG 51

Query: 148 -------HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-- 198
                  HRLD+ TSG+++ A ++A+A+   + F  R+IQK Y ++    PK K+  +  
Sbjct: 52  VEELYPVHRLDKMTSGLVIFALSKASAKAFQQLFESRQIQKFYLAISTHKPKKKQGWVKG 111

Query: 199 -------ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                   +W L K+         + QN +                    W  + PHTG+
Sbjct: 112 DMMPARRGSWKLSKTLENPAITQFISQNTRPGER----------------WFLLNPHTGK 155

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           THQLRV    +G PI GD +Y  + +       +++ YLHA
Sbjct: 156 THQLRVALKSLGAPIAGDARYALSAEAEH----EDRGYLHA 192


>gi|229183506|ref|ZP_04310730.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BGSC 6E1]
 gi|228599916|gb|EEK57512.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BGSC 6E1]
          Length = 292

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 143/313 (45%), Gaps = 41/313 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I  + G + V+ +     +++Q G+ +RI  P
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFQGGAIEVNGQHASVRHQLQVGEELRIFFP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 63  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 107

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 108 VANALLSHYDKQYLAST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 164

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 165 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
            ++  TGRTHQ+RVH  H+G P++GD     N  G     ++ +  LH+  +   HP   
Sbjct: 219 SLELDTGRTHQIRVHMAHIGHPLLGD-----NLYGGKRDEMKRQ-ALHSTSLTFYHPILE 272

Query: 303 GRLQITAPLPAHM 315
             +  TA +P+ M
Sbjct: 273 KEMSFTAMIPSDM 285


>gi|227488548|ref|ZP_03918864.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glucuronolyticum ATCC 51867]
 gi|227543153|ref|ZP_03973202.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glucuronolyticum ATCC 51866]
 gi|227091442|gb|EEI26754.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glucuronolyticum ATCC 51867]
 gi|227180962|gb|EEI61934.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glucuronolyticum ATCC 51866]
          Length = 306

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 57/188 (30%), Positives = 91/188 (48%), Gaps = 11/188 (5%)

Query: 129 IDGFLKSWVDSKGQKPR----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + G   + +D     P     + HRLD  TSG++V+AR+  A   L  +FR R + K Y 
Sbjct: 113 LGGLAAAGIDVTTSGPPERKGIVHRLDVGTSGVMVIARSERAYTLLKRAFRERTVDKTYH 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G P   +  I   + +  H    Y   V +   G   A++H++ ++ F ++   L+
Sbjct: 173 AVVQGHPDPLEGTIEAPIGR--HPKKSYKFAVVE---GGKMAVTHYETLEAF-REASLLK 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TGRTHQ+RVH   +  P VGD  Y  + K      + N+ +LHA  +   HP G  
Sbjct: 227 VHLETGRTHQIRVHFSSLHHPCVGDPMYGCDPKLAKRLGL-NRQWLHAVSLGFDHPNGKH 285

Query: 305 LQITAPLP 312
           L I +  P
Sbjct: 286 LVIESDYP 293


>gi|238855152|ref|ZP_04645474.1| pseudouridine synthase, RluA family [Lactobacillus jensenii 269-3]
 gi|260665529|ref|ZP_05866375.1| ribosomal protein large subunit [Lactobacillus jensenii SJ-7A-US]
 gi|282932565|ref|ZP_06337987.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 208-1]
 gi|238832233|gb|EEQ24548.1| pseudouridine synthase, RluA family [Lactobacillus jensenii 269-3]
 gi|260560650|gb|EEX26628.1| ribosomal protein large subunit [Lactobacillus jensenii SJ-7A-US]
 gi|281303313|gb|EFA95493.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 208-1]
          Length = 287

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 111/249 (44%), Gaps = 33/249 (13%)

Query: 34  FVNLQK-ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           F+ ++K IL +GQ R       FN  +    +  I     +L H+  +Q  +  S +L +
Sbjct: 34  FLRIEKNILINGQYR------NFNELVYPNDLYSI-----SLTHVENQQHPILPSGHLPQ 82

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   ++YED  I V NKP   S Q      +  +  +       G  P + HRLD 
Sbjct: 83  --------IIYEDKNILVINKP---SKQKTHPNLFETNTAMNDVTTYLGYTPYIIHRLDM 131

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T+G+L+ A+  A    L      + +Q+ Y++ V      K + IA      S I  D 
Sbjct: 132 LTNGLLLFAKNPAVVPILNRQLTTKTMQRNYYATV------KLKDIAQKGTISSPIAQDP 185

Query: 213 VHVVKQ--NEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
               K+   + G   A++H++VI    ++    L++   TGRTHQ+RVH   +  PI+GD
Sbjct: 186 TDQRKRIIADNGLK-AVTHYEVIGRDLSKNTMVLKLTLETGRTHQIRVHLASINLPIIGD 244

Query: 270 HKYCANFKG 278
             Y  NF G
Sbjct: 245 PLYNPNFNG 253


>gi|160895409|ref|ZP_02076178.1| hypothetical protein CLOL250_02966 [Clostridium sp. L2-50]
 gi|156862911|gb|EDO56342.1| hypothetical protein CLOL250_02966 [Clostridium sp. L2-50]
          Length = 233

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/216 (27%), Positives = 101/216 (46%), Gaps = 12/216 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLT--HRLD 151
           +K  +LYED+ I V  KP G+  Q     + ++   LK  +   + + ++P L   HRLD
Sbjct: 1   MKIEVLYEDNDILVAVKPYGLPSQPDKKNSENMVSMLKLRIFEKEHRTEEPYLAPIHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +   GI++ A+ + AA  L++      + K Y +++ G   N    I N+L+  +    +
Sbjct: 61  RPVGGIMLFAKNKEAAAKLSKQSEDGEMVKYYQAILTGELPNDAGTITNYLIHDNQT--N 118

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              +V ++  GA  A   ++V+D          ++ +   TGRTHQ+RV        I G
Sbjct: 119 VTRIVDKDTPGAKLAELDYEVLDVMETDDGILSYVLINLITGRTHQIRVQMAGKKAGIWG 178

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           D KY   F+   T     ++ LHA  ++  HP  G 
Sbjct: 179 DTKYNPKFRK--TKKSYKQIGLHASRLEFEHPVTGE 212


>gi|126172548|ref|YP_001048697.1| pseudouridine synthase Rlu family protein [Shewanella baltica
           OS155]
 gi|125995753|gb|ABN59828.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS155]
          Length = 230

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/201 (29%), Positives = 95/201 (47%), Gaps = 24/201 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +++   V +K A +      G A    G +       G K    HRLD  TSG+L++
Sbjct: 4   IIADEADFIVISKSAKVHFHSQDGTA----GVVAQAEQDLGIKLFAVHRLDTPTSGLLIL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA+  TE F   ++QK Y +L  G PK K+  +   + K          +++  E
Sbjct: 60  AKSAVAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIGDMAKSRR---SMFKLLRTKE 116

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  +        +L ++PH+G+THQLRV    +G PI+GD  Y     G  
Sbjct: 117 ---NPAITQFFSLSVSEGLRLYL-LKPHSGKTHQLRVALASLGVPILGDDLY-----GGM 167

Query: 281 TSPIQNKLYLHA-----RYMD 296
            +   ++ YLHA     RY D
Sbjct: 168 AA---DRCYLHAYCLHFRYGD 185


>gi|228990288|ref|ZP_04150255.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           pseudomycoides DSM 12442]
 gi|228769455|gb|EEM18051.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           pseudomycoides DSM 12442]
          Length = 286

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 75/274 (27%), Positives = 131/274 (47%), Gaps = 51/274 (18%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
            + G + VD K     + +Q+ +V+++  PV        + + +L  ++ LT        
Sbjct: 29  FQGGAIEVDGKHATVRHVLQAEEVLQVFFPVEE------RSEGMLAENIPLT-------- 74

Query: 100 ILLYEDSKIYVFNK------------PAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRL 146
            +LYED  + V NK            PAG SV   + + YH D   L S V        +
Sbjct: 75  -VLYEDESVMVINKEPYMSTIPSREHPAG-SV--ANALLYHYDRQNLASTV-------HI 123

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD++TSG++++A+ R     L++  + +++Q+ Y ++V G    +   I   + +K 
Sbjct: 124 VTRLDRDTSGLMLIAKNRFIHHLLSKQHQQKQVQRTYEAIVHGELLEESGTIDAPIGRK- 182

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              GD +      E G   A++HF+V++ F  K   + +Q  TGRTHQ+RVH  ++G P+
Sbjct: 183 ---GDSIIERMVCEDGQK-AVTHFQVMERFPDK-TRVSLQLETGRTHQIRVHMAYLGHPL 237

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +GD  Y     G   S ++ +  LH+  +   HP
Sbjct: 238 LGDDLY-----GGSKSQMKRQ-ALHSTSLTFYHP 265


>gi|167523214|ref|XP_001745944.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163775745|gb|EDQ89368.1| predicted protein [Monosiga brevicollis MX1]
          Length = 512

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 55/182 (30%), Positives = 94/182 (51%), Gaps = 15/182 (8%)

Query: 105 DSKIYVFNKPAGISVQG---GSGIAYHIDGFLKSWVDSKGQ---KP-RLTHRLDQETSGI 157
           D  ++V NK AG+  QG   G  +A ++  +++   D   +   +P  L HRLD+ T+G+
Sbjct: 118 DPFVWVVNKWAGLVTQGEKDGQSLAAYLK-YMRMRHDDDMRLLTRPLSLVHRLDRNTTGV 176

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
             +AR       L +     + QKIY++   G+P  +K  I  +L    H  G  +    
Sbjct: 177 SFIARNPVVHALLQDVLATHQAQKIYYATTLGVPFPRKGEIKGYL--TPHKNGVKLDATP 234

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY---C 273
           QN K + ++ + ++V+D   ++   + ++P TGR HQLR H A  +  PI+GD +Y   C
Sbjct: 235 QN-KNSVFSHTRYQVVDALDREAALVRLEPVTGRRHQLRAHLAQGLRTPILGDTQYGVGC 293

Query: 274 AN 275
           +N
Sbjct: 294 SN 295


>gi|320182406|gb|EFW57303.1| tRNA pseudouridine synthase C [Shigella boydii ATCC 9905]
          Length = 260

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 66/259 (25%), Positives = 112/259 (43%), Gaps = 59/259 (22%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           W ++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WFMEEAV 99

Query: 208 IGGDYVHVVKQ-------NEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTG 250
           +    V  + +        +KG   A++H++ +               ++  +E++P TG
Sbjct: 100 LDYPLVEELDKIADKFACEDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTG 159

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGRLQ 306
           R HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  L 
Sbjct: 160 RKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLT 218

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I A L    ++     G++
Sbjct: 219 IHAGLDDTWMQALSQFGWR 237


>gi|294618813|ref|ZP_06698339.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1679]
 gi|291594936|gb|EFF26287.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1679]
          Length = 299

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 85/310 (27%), Positives = 142/310 (45%), Gaps = 44/310 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + K+H   + +   +K +  G +     ++KF    Q GQ+     V N L  + K+ K+
Sbjct: 7   YEKDHSQQVKYFLKEKGISKGLL----AKIKF----QGGQIKVNDQVENVLFSLAKDDKV 58

Query: 84  LDSSVNLTKHSDFL---KSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KS 135
                   +H   L    SI ++YED  + V NKPAG+S        YH +G +    K+
Sbjct: 59  TIVIPAEGEHETVLLDETSIDIVYEDEHVLVVNKPAGVSSIPAQ---YHPNGTMANRVKA 115

Query: 136 WVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   KG + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G   
Sbjct: 116 YYKKKGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQLREKKFVKKYQALVSGRLS 175

Query: 193 NKKECIANWLLKKSHI----GGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           +        L    HI      DY  ++K+  +++G +    ++  I+    +   +++Q
Sbjct: 176 D--------LSAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYW--IEKRLTEIALVDIQ 225

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
            HTGRTHQ+RVH   +GC ++GD  Y     G     I+ +  LH   +   HP     L
Sbjct: 226 LHTGRTHQIRVHFSAIGCALLGDDMYG----GRMDLGIKRQA-LHCYDLRFYHPFTEELL 280

Query: 306 QITAPLPAHM 315
           +   PL A M
Sbjct: 281 EFKQPLAADM 290


>gi|291545303|emb|CBL18411.1| pseudouridine synthase, RluA family [Ruminococcus sp. SR1/5]
          Length = 380

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 94/192 (48%), Gaps = 12/192 (6%)

Query: 94  SDFLKSI-LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQ--KPRLTHR 149
           S FL  + ++YED  I   NKPAGI     GS  +  +   + S+  SKG+  K R   R
Sbjct: 124 SQFLPELAIIYEDQDILAINKPAGIVTHPSGSHYSDSLANQVASYFRSKGEPTKVRSIGR 183

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHI 208
           LD+ETSGIL+ AR + AA  L         +K Y + V G +P ++        +  +  
Sbjct: 184 LDKETSGILLFARNQTAAARLQNQREEGISEKTYLAAVSGFMPVDEDGAFHRISVPLAPD 243

Query: 209 GGDYVHVVKQNE---KGANYAISHFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHALH 261
             + + +V   +    G+ +A + + V+       A     + ++  TGRTHQ+RVH   
Sbjct: 244 PDNRLKMVVSTDGTLPGSKHAETLYSVLKSTGPDAAAPASLVMLRLKTGRTHQIRVHMAS 303

Query: 262 MGCPIVGDHKYC 273
           +G P++GD  YC
Sbjct: 304 LGHPLLGDSLYC 315


>gi|126642499|ref|YP_001085483.1| putative ribosomal large subunit pseudouridine synthase
           A(RluA-like) [Acinetobacter baumannii ATCC 17978]
          Length = 196

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 65/209 (31%), Positives = 100/209 (47%), Gaps = 21/209 (10%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAA 167
           V +KP+ I    G G  +  D  L   V     +PR  L HRLD++TSGILV   ++   
Sbjct: 2   VIHKPSDILSVPGKGDLH--DSVLTRLV---AIEPRTLLIHRLDRDTSGILVFGLSKRGQ 56

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             +   F+ R+  KIY +LV G  + +       +   S      +H+V  +      A+
Sbjct: 57  SAIARQFQDRQTSKIYEALVAGHLEGEGTVDIPVVYDPSR---PPLHIVDASHN--KPAL 111

Query: 228 SHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           +H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD  Y    +      +
Sbjct: 112 THWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDTLYATPEQL-----L 166

Query: 285 QNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             +L LHA+ +   HP  G  L    P+P
Sbjct: 167 VPRLCLHAKQLSFNHPVTGESLTFNCPVP 195


>gi|148377937|ref|YP_001256813.1| ribosomal large subunit pseudouridine synthaseD [Mycoplasma
           agalactiae PG2]
 gi|148291983|emb|CAL59375.1| Ribosomal large subunit pseudouridine synthaseD [Mycoplasma
           agalactiae PG2]
          Length = 305

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 100/216 (46%), Gaps = 27/216 (12%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQ 152
           YED  + + NKP+G+ V    G         + YH   F  +  D+ G  +  + HR+D+
Sbjct: 80  YEDEYLLILNKPSGLVVHPAPGHLNDTLVNALMYH---FKNNLSDANGLLRLGIVHRIDK 136

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+L++A+       L +  +  +I++ Y ++  GI  NK   I N  +++       
Sbjct: 137 DTSGLLIIAKDNETHNELAKMLKNHQIKRTYLAICEGILPNKTTKI-NLPIQRDTKNRKL 195

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + + K  +    Y +   K      + +  ++ +  TGRTHQ+RVH  ++  P+ GD  Y
Sbjct: 196 MSIHKDGKSSVTY-VHMLKSFYIDNKPYSLVKCELETGRTHQIRVHLAYIKHPVYGDSIY 254

Query: 273 CAN----------FKGNFTSPIQNKLYLHARYMDLP 298
             +          +K +F  P+ NKL     Y D+P
Sbjct: 255 GKSVDEFNQRLHAYKLSFMHPVINKLI--EVYSDIP 288


>gi|104774376|ref|YP_619356.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|116514473|ref|YP_813379.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|103423457|emb|CAI98343.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|116093788|gb|ABJ58941.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|325126179|gb|ADY85509.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           delbrueckii subsp. bulgaricus 2038]
          Length = 282

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/183 (32%), Positives = 85/183 (46%), Gaps = 16/183 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++YED  + V +KP G      QG +G A      L       G  P + HRLD  T G+
Sbjct: 83  VVYEDENVLVIDKPKGQKTHPNQGENGTA------LNDCASYLGYSPYIVHRLDMLTGGL 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+  A    L +    + +++ Y + V     N  + I +       IG D     K
Sbjct: 137 LLVAKNPAVVPILNQQLTSKTLRRDYLATV-----NLNKEIPDQGTIDLPIGQDPADQRK 191

Query: 218 QNEKGANY-AISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +  +     A+SHF+V++    +K   L +   TGRTHQ+RVH    G PIVGD  Y  N
Sbjct: 192 RQVRADGLRAVSHFQVLEKDEVKKKAKLLVTLETGRTHQIRVHLSASGWPIVGDPLYNPN 251

Query: 276 FKG 278
           F G
Sbjct: 252 FAG 254


>gi|328944704|gb|EGG38865.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1087]
          Length = 290

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 91/201 (45%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + ++V   G+   + HRLD+ETSG ++ A
Sbjct: 84  LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRLDKETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      R I + Y +LV G   +KK      L+ K  IG D     K+  +
Sbjct: 141 KNPFVLPILNRLLEKREISREYCALVQGKFPSKK------LIYKDKIGRDRHDRRKRLVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   YA +H   +  F Q    ++ Q  TGRTHQ+RVH  H G  +VGD  Y    +G 
Sbjct: 195 PRKGLYAETHVTRVKQFGQA-SLVKCQLKTGRTHQIRVHLAHHGHQLVGDPLYHPQPQG- 252

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L LHA  +   HP
Sbjct: 253 -------RLMLHAHRLTFTHP 266


>gi|293384999|ref|ZP_06630833.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis R712]
 gi|293389269|ref|ZP_06633731.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis S613]
 gi|312905988|ref|ZP_07765001.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|312909334|ref|ZP_07768190.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
 gi|291077677|gb|EFE15041.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis R712]
 gi|291081433|gb|EFE18396.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis S613]
 gi|310627983|gb|EFQ11266.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|311290358|gb|EFQ68914.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
          Length = 283

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/260 (26%), Positives = 114/260 (43%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 36  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHL---GEATRVKVLYED 83

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 84  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 140 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 196

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 197 KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 253

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L  P
Sbjct: 254 -----ARLMLHASQLHLLQP 268


>gi|332283691|ref|YP_004415602.1| ribosomal large subunit pseudouridine synthase D [Pusillimonas sp.
           T7-7]
 gi|330427644|gb|AEC18978.1| ribosomal large subunit pseudouridine synthase D [Pusillimonas sp.
           T7-7]
          Length = 319

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 81/320 (25%), Positives = 134/320 (41%), Gaps = 46/320 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+      P  +   LQ  + +G V V+            GQ  R+  + N  + ++ 
Sbjct: 29  RLDKVIARLIPEHSRSRLQGWIEAGHVLVN------------GQPGRVKQMANPGDKLVV 76

Query: 80  EQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
            ++    ++  T    DF    ++ + S   V NKPAG+    G+G      ++G L  +
Sbjct: 77  WEQAPPEALAFTPEDVDFQ---VVDQSSDWIVVNKPAGLVTHPGAGNWSGTLLNGLLYRY 133

Query: 137 VD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +   +  + HRLD++TSG+LVVAR   A  HL    + R + + Y +LV G+     
Sbjct: 134 PELATVARAGIVHRLDKDTSGLLVVARHEKAQTHLIRQLQARSVSREYVALVHGLLTRPG 193

Query: 196 ECIANWLLKKSHIGGDY---VHVVKQNEKGANYAISHFKVI-------DCFAQKFCWLEM 245
                    K  IG D    V +  +       A++H+  +           +  C LE 
Sbjct: 194 SV-------KLAIGRDTRVPVRMAVEPAIAPKPAVTHYAPVRAGRIDDAAVTEVACKLE- 245

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL-PHPEGGR 304
              TGRTHQ+RVH + +  P+V D  Y     G       ++  LHAR +    +  G R
Sbjct: 246 ---TGRTHQIRVHMMSLHHPLVADALYGGKALGG-----ASRQLLHARALSFDDYGSGQR 297

Query: 305 LQITAPLPAHMVKTWDSLGF 324
           +   A L A   +  D + +
Sbjct: 298 VSFVASLAADFQQVLDDIAW 317


>gi|78778288|ref|YP_394603.1| pseudouridine synthase, RluD [Sulfurimonas denitrificans DSM 1251]
 gi|78498828|gb|ABB45368.1| Pseudouridine synthase, RluD [Sulfurimonas denitrificans DSM 1251]
          Length = 304

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 82/174 (47%), Gaps = 14/174 (8%)

Query: 105 DSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           + +  VF+KP+G+ +   +    Y +   LK+     G    + HR+DQETSG+++ A+ 
Sbjct: 76  EERFVVFDKPSGMLIHPQNRFTEYSLIDELKAQF---GMNANIAHRIDQETSGLVLCAKD 132

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
           + +   +   F+ R ++K Y ++V G  K +    A  L            VVK +  G 
Sbjct: 133 KKSEVDIKMMFQERDMKKKYLAMVHGELKEELRIDAPLLRYDDEKSALVRMVVKVDPTGK 192

Query: 224 NY-----AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                   + +F + D        +E  PHTGR HQ+RVH  HM  PIVGD  Y
Sbjct: 193 ESLTFVRPLKYFPITDT-----TLVECSPHTGRQHQIRVHMFHMKHPIVGDPVY 241


>gi|110640132|ref|YP_680342.1| ribosomal pseudouridine synthase C large subunit [Cytophaga
           hutchinsonii ATCC 33406]
 gi|110282813|gb|ABG60999.1| ribosomal pseudouridine synthase C, large subunit [Cytophaga
           hutchinsonii ATCC 33406]
          Length = 223

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/217 (29%), Positives = 105/217 (48%), Gaps = 22/217 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDGFLK-SWVDSKGQKPRLTHRLDQETS 155
           +LYED+ I V NKP  + V+    G   +   +  ++K S   +K    +  HRLD+  S
Sbjct: 11  ILYEDNYILVVNKPCSLMVEPDRNGHPNLLQQVQKYVKKSLHPNKEVYVQHIHRLDRPVS 70

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ A+ ++  + L+E F  R ++K Y +L   +  N K  + +W  K S      ++ 
Sbjct: 71  GIVLFAKKKSMLKELSEQFAQRTVKKYYQALTRKVTTNGKGALNHWHFKDSKNKKAILYK 130

Query: 216 VKQNEKGA---NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +Q E  A    Y+ S     D  A    W ++Q +TG+ HQ+R      G PI+GD  Y
Sbjct: 131 EEQQETSAVSLGYSTS-----DYNADYTLW-DIQLNTGKYHQIRAQLSFEGYPILGDECY 184

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP---EGGRLQ 306
            +    +  +P  N + LHA  ++  HP   E  RL+
Sbjct: 185 KST---DVYAP--NAIALHACKLEFVHPVSKESMRLE 216


>gi|227114681|ref|ZP_03828337.1| tRNA pseudouridine synthase C [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 261

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/248 (25%), Positives = 112/248 (45%), Gaps = 53/248 (21%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKP+G  V              +SW+D K             GQ     
Sbjct: 4   IIYQDEHLVAVNKPSGWLVH-------------RSWLDRKEKVVVMQTVRDQIGQHVYTV 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++A +   A+ L++ F   ++QK+Y ++V G   +  + + ++ L +  
Sbjct: 51  HRLDRPTSGVLLLALSSEVARALSQQFESHQMQKMYHAVVRGYVLD--DGVIDYALTEEL 108

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQL 255
             I   + +     +K    A++H++ +               ++  +E++P TGR HQL
Sbjct: 109 DKIADKFTN----PDKAPQPAVTHYRSLAQVEMPVAIGRYPTARYSLMELKPQTGRKHQL 164

Query: 256 RVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           R H  H+  PI+GD  H    + +G  +     +L LHA  + L HP  G+       P 
Sbjct: 165 RRHMSHIHHPIIGDTAHGDLRHNRGMESHFSCGRLMLHASELQLNHPVSGQ-------PL 217

Query: 314 HMVKTWDS 321
            +   WD+
Sbjct: 218 TLQARWDA 225


>gi|260599139|ref|YP_003211710.1| tRNA pseudouridine synthase C [Cronobacter turicensis z3032]
 gi|260218316|emb|CBA33307.1| tRNA pseudouridine synthase C [Cronobacter turicensis z3032]
          Length = 262

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 103/225 (45%), Gaps = 19/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 5   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G   +        + +   I   +     + +
Sbjct: 65  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLTDSAVLDYPLVEELDKIADKF----SRQD 120

Query: 221 KGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +    Q          ++  +EM P TGR HQLR H  H+  PI+GD 
Sbjct: 121 KEPQPAVTHYRGLATTTQPVAVGRYESVRYSLVEMLPQTGRKHQLRRHMAHLRHPIIGDS 180

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGRLQITAPL 311
           K+  + + N  +      ++L LHA  + L HP  G  L I A L
Sbjct: 181 KH-GDLRQNRAAAEHFGCHRLMLHASELTLTHPFTGAPLTIRAGL 224


>gi|118476779|ref|YP_893930.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|196044122|ref|ZP_03111358.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|225863156|ref|YP_002748534.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|118416004|gb|ABK84423.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|196024761|gb|EDX63432.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|225788401|gb|ACO28618.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
          Length = 297

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 143/313 (45%), Gaps = 41/313 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I  + G + V+ +     +++Q G+ +RI  P
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFQGGAIEVNGQHASVRHQLQVGEELRIFFP 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 68  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 113 VANALLSHYDKQYLAST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 170 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
            ++  TGRTHQ+RVH  H+G P++GD     N  G     ++ +  LH+  +   HP   
Sbjct: 224 SLELDTGRTHQIRVHMAHIGHPLLGD-----NLYGGKRDEMKRQ-ALHSTSLTFYHPILE 277

Query: 303 GRLQITAPLPAHM 315
             +  TA +P+ M
Sbjct: 278 KEMSFTAMIPSDM 290


>gi|121594293|ref|YP_986189.1| ribosomal large subunit pseudouridine synthase A [Acidovorax sp.
           JS42]
 gi|120606373|gb|ABM42113.1| ribosomal large subunit pseudouridine synthase A [Acidovorax sp.
           JS42]
          Length = 222

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 66/220 (30%), Positives = 109/220 (49%), Gaps = 23/220 (10%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS---WVDSKGQKPRLTHRL 150
           S+ ++S+  + D  + V +KP+G+    G G         ++   W D+      + HRL
Sbjct: 6   SEGVRSV--HVDDTLLVLDKPSGLLCVPGRGPDKQDALSTRAQALWPDAL-----IVHRL 58

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIG 209
           DQ TSG++++AR  A  + L+ SF  R + K Y ++V G +P         W      I 
Sbjct: 59  DQPTSGLVLMARGAAMQRALSHSFAQRLVHKRYRAVVAGRMPPPDPAHADGWGEIALPIA 118

Query: 210 GDY----VHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            D+    + VV         +++ ++V+    A+    +E++P TGRTHQLRVH   +G 
Sbjct: 119 ADWERRPLRVVDATH--GQPSLTRWRVLAHDAARDTTSVELEPVTGRTHQLRVHLAALGH 176

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
           PI+GD  Y A+      +P   +L LHA  ++  HP +GG
Sbjct: 177 PILGDQLY-ADASVQARAP---RLLLHACVLEFAHPLQGG 212


>gi|2828514|sp|P44197|TRUC_HAEIN RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
          Length = 239

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 107/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDGFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +++ PHTGR H LR H  H+  PI GD 
Sbjct: 120 KEPQEAITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHXLRXHMKHVFHPIXGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|145630664|ref|ZP_01786443.1| hypothetical protein CGSHi22421_01939 [Haemophilus influenzae
           R3021]
 gi|144983790|gb|EDJ91240.1| hypothetical protein CGSHi22421_01939 [Haemophilus influenzae
           R3021]
          Length = 224

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/203 (31%), Positives = 95/203 (46%), Gaps = 28/203 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+ S   + NK  GISV      QG + +        K W         L HRLD+ T
Sbjct: 5   VVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQLNVPKVW---------LVHRLDKVT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A    +A   +  F   +I K Y +L    PK K+  I    +KK+  G   + 
Sbjct: 56  SGLLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGD-MKKAREGAWKLC 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K+N      AI+ F  + C      ++ ++P TG+THQLRV    +G PI+GD  Y  
Sbjct: 115 QTKENP-----AITRFASVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDGLYGK 168

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
           N     T  I ++ YLHA  ++ 
Sbjct: 169 N-----TEKI-DRTYLHATQLEF 185


>gi|24379482|ref|NP_721437.1| putative pseudouridylate synthase [Streptococcus mutans UA159]
 gi|24377420|gb|AAN58743.1|AE014943_6 putative pseudouridylate synthase [Streptococcus mutans UA159]
          Length = 296

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 54/178 (30%), Positives = 92/178 (51%), Gaps = 14/178 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    + +KPAG +          I  F+K +    D   ++  +  RLD++TSG+
Sbjct: 78  IVYEDEHFLILDKPAGYASIPSILHTNTIANFVKYYYLKKDYPNKQIHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVH 214
           +++A+   A   L +  + + I+K Y++LV G   +P ++ E IA     +  I    VH
Sbjct: 138 MLLAKHGYAHARLDKQLQKKTIKKRYYALVSGQGQLP-DQGEIIAPIARPEDSIITRCVH 196

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                     YA + +KV+  +      +++Q HTGRTHQ+RVH  H+G P++GD  Y
Sbjct: 197 ------PSGKYAHTSYKVLARYGD-IALVDIQLHTGRTHQIRVHFAHIGFPLLGDDLY 247


>gi|330448662|ref|ZP_08312310.1| RNA pseudouridylate synthase family protein [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
 gi|328492853|dbj|GAA06807.1| RNA pseudouridylate synthase family protein [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
          Length = 557

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 65/204 (31%), Positives = 99/204 (48%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + + NKPA  +SV G + I          + DS    P + HRLD  TSG++V
Sbjct: 356 IVYQDDDMVIINKPAEFLSVPGKTIIDSVYSRMQAMFPDSDS--PLIVHRLDMSTSGLIV 413

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A T+ A + L + F  R ++K Y +L+ GI     E + ++ ++          V  Q 
Sbjct: 414 IALTKDAHKALQKQFIERTVEKRYVALLEGI-SEADEGLIDFPMRVDLDDRPRQIVCYQY 472

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANF 276
            K A       +  +   + + +    P TGRTHQLRVH+ H   M  PIVGD  Y    
Sbjct: 473 GKPAQTKWQVLERKNGRTKVYYY----PKTGRTHQLRVHSAHIKGMNMPIVGDDLYGQ-- 526

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
           KG       ++L LHA+Y+   HP
Sbjct: 527 KG-------DRLCLHAQYLAFNHP 543


>gi|256959811|ref|ZP_05563982.1| pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256950307|gb|EEU66939.1| pseudouridine synthase [Enterococcus faecalis Merz96]
          Length = 287

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/260 (26%), Positives = 114/260 (43%), Gaps = 32/260 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V+++ +   F+  +Q+G  V +           +E   +  +++L    +  +  +LYED
Sbjct: 40  VKINGETAAFHFPVQAGDCVTL---------TFEETDYVRPTIHL---GEATRVKVLYED 87

Query: 106 SKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
             + + NKP GI       Q    +  H+  +L      K Q P + HRLD+ETSG +V 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAE----KNQVPYVVHRLDKETSGAIVF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+       L      ++I + Y ++V G   N+KE   N  + +         +  Q  
Sbjct: 144 AKNPFVLPILGRLLETKQIYRQYQAIVAG-HFNQKEQTINQPIGRDRHDRRKRRIDPQ-- 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +   
Sbjct: 201 KG-DSAITHVQVVKALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQA-- 257

Query: 281 TSPIQNKLYLHARYMDLPHP 300
                 +L LHA  + L  P
Sbjct: 258 -----ARLMLHASQLHLLQP 272


>gi|300773309|ref|ZP_07083178.1| ribosomal large subunit pseudouridine synthase A [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|300759480|gb|EFK56307.1| ribosomal large subunit pseudouridine synthase A [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 560

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 66/207 (31%), Positives = 100/207 (48%), Gaps = 26/207 (12%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDS---KGQKPRLTHRLDQETSG 156
           +LY+D  I V NKPA  +SV G      HI   + + + +   +   P + HRLD  TSG
Sbjct: 359 ILYDDEDIAVVNKPAEFLSVPG-----VHIQDSVYTRMQAAFPEATGPIIVHRLDMSTSG 413

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           IL++A+ + A + + + F    I+K Y +L+ G+ K  K  I   L          +   
Sbjct: 414 ILLIAKHKDAHKFIQQQFIDHSIEKRYVALLDGVIKEDKGIIDLPLRLDLDDRPRQMVCY 473

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
           +  +K    A++ ++V+     +   L   P TGRTHQLRVHA H   +  PIVGD  Y 
Sbjct: 474 EYGKK----AVTKYQVLSRINGQTKILFF-PVTGRTHQLRVHAAHLLGLHTPIVGDDLYG 528

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
                       N+L+LHA ++   HP
Sbjct: 529 TK---------SNRLHLHAAHLSFVHP 546


>gi|163801533|ref|ZP_02195432.1| putative ribosomal large chain pseudouridine synthase A [Vibrio sp.
           AND4]
 gi|159175022|gb|EDP59822.1| putative ribosomal large chain pseudouridine synthase A [Vibrio sp.
           AND4]
          Length = 559

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/209 (33%), Positives = 96/209 (45%), Gaps = 30/209 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  + V NKP+G+    G  I       L++   +  + P + HRLD  TSGILV 
Sbjct: 358 VLFQDEAMVVVNKPSGLLSVPGKTIKDSAYSRLQAMFPNV-EGPFVIHRLDMATSGILVF 416

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A T+ A + L + F  R +QK Y +L+ G     +  I+        + GD     +Q  
Sbjct: 417 ALTKRANKSLQKQFITRGVQKRYMALLEGTLSEPEGEIS------LPMRGDPEDRPRQ-- 468

Query: 221 KGANYAISHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHK 271
                   H K  D F Q          + M P TGRTHQLRVH A HMG    +VGD  
Sbjct: 469 ---LVCFEHGKPADTFWQLIDVKDGRSRVYMYPKTGRTHQLRVHSAHHMGLNMAMVGDGL 525

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y             N+L+LHA  ++L HP
Sbjct: 526 YGEK---------ANRLHLHAEMLELDHP 545


>gi|325860423|ref|ZP_08173535.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
 gi|325482081|gb|EGC85102.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
          Length = 577

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/218 (31%), Positives = 102/218 (46%), Gaps = 32/218 (14%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILV 159
           LYED  + V  KP G+ SV G  G+        + W   KG+ +P + HRLD  TSG+LV
Sbjct: 363 LYEDDSLAVVAKPPGLLSVPGRDGLPSVYSILKERW---KGRYEPFMVHRLDMATSGLLV 419

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-------IPKNKKECIANWLL-KKSHIGGD 211
           VAR+  A + L   F    ++K Y +L+          P+ + E   + L   +     D
Sbjct: 420 VARSPEAHRALQAQFTNHTVRKQYTALLSPSFLDKHLPPEGRIELPLSPLPDDRPRQCVD 479

Query: 212 YVHVVKQNEKGA--NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPI 266
           YV     N K A   Y ++         Q+   + + P TGRTHQLR+H  H   +G PI
Sbjct: 480 YV-----NGKTAVTEYRVAGKTTYGKTGQEAVKVILYPLTGRTHQLRIHCAHPDGLGTPI 534

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +GD  Y  +           +L+LHA +++  HP  G+
Sbjct: 535 IGDSLYGQH---------AGRLWLHAGHLEFTHPVTGK 563


>gi|163856156|ref|YP_001630455.1| ribosomal large subunit pseudouridine synthase D [Bordetella petrii
           DSM 12804]
 gi|163259884|emb|CAP42185.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           petrii]
          Length = 324

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 78/310 (25%), Positives = 126/310 (40%), Gaps = 45/310 (14%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q++ V       RLD+         +   LQ  + +G V+V+    K    +  G V+  
Sbjct: 22  QFITVPAGTRADRLDKILAALLDGHSRSRLQGWIEAGWVQVNGAPAKVRQVVGPGDVL-- 79

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                     + EQ   +S   L    + +   ++ E     V +KPAG+    G+G   
Sbjct: 80  ---------AVWEQPAPES---LAFTPEPIAFAVVAESPDWIVVDKPAGLVTHPGAGNWS 127

Query: 126 AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + + ++  +  + HRLD++TSG++VVAR   A  HL    + R + + Y 
Sbjct: 128 GTLLNGLLHRYPELARVARAGIVHRLDKDTSGLMVVARNELAQTHLVRQLQARSMGREYI 187

Query: 185 SLVWG-IPKNKKECIANWLLKKSHIGGDY---VHVVKQNEKGANYAISHFKVI------- 233
           +L  G +P   K            IG D    V +  +       AI+H+  +       
Sbjct: 188 ALAHGWLPVAGK--------VDRPIGRDARVPVRMSVERPIAPKPAITHYAPLRRGRAPD 239

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
               +  C LE    TGRTHQ+RVH   +G P++ D  Y        T     +  LHAR
Sbjct: 240 GPVTEVACRLE----TGRTHQIRVHLASLGHPLLADTLYGGRLTAGAT-----RQMLHAR 290

Query: 294 YMDLPHPEGG 303
            +    P GG
Sbjct: 291 ALHFDDPGGG 300


>gi|308190331|ref|YP_003923262.1| pseudouridylate synthase [Mycoplasma fermentans JER]
 gi|307625073|gb|ADN69378.1| pseudouridylate synthase [Mycoplasma fermentans JER]
          Length = 307

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 113/240 (47%), Gaps = 29/240 (12%)

Query: 103 YEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           YED  + + NKP+ + V            +G+ YH    L +  ++   +P + HR+D++
Sbjct: 80  YEDDDLVIINKPSNLVVHPSPGHYNDTLVNGLLYHFKNNLSN--ENGLLRPGIVHRIDKD 137

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+L++A+       LT+  +   I++ Y ++V G+ +N    I N  + ++ +    +
Sbjct: 138 TSGLLIIAKNNKMHNSLTDMLKRHEIERSYLAIVRGLIENPLTKI-NLPIARNTVDRKMM 196

Query: 214 HVVKQNEKGANYA--ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V K+ ++   +   + HF  +D         E++  TGRTHQ+RVH  ++  P+ GD  
Sbjct: 197 SVHKEGKEAITFVHLLKHF-YLDKEPMSLVRCELK--TGRTHQIRVHLSYIKHPVYGDPT 253

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           Y     G        +  LHA  +   HP   + + + AP+P    K +D   + ++  L
Sbjct: 254 Y-----GKSVDEFNQR--LHAYKLKFIHPLTKKEICVYAPVP----KEFDVADYDFNELL 302


>gi|86135056|ref|ZP_01053638.1| ribosomal large subunit pseudouridine synthase A [Polaribacter sp.
           MED152]
 gi|85821919|gb|EAQ43066.1| ribosomal large subunit pseudouridine synthase A [Polaribacter sp.
           MED152]
          Length = 558

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/225 (30%), Positives = 106/225 (47%), Gaps = 28/225 (12%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQ 142
           +DS+  LT  S      +++ED  + V NKPA      G  I   +   +K+ + ++ G 
Sbjct: 340 MDSNSLLTNLSSEKNLEIIFEDDDLIVVNKPAEFLSVPGKTIKDSMYTRIKNQYPNATG- 398

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK----KECI 198
            P + HRLD  TSGILV+ +T+ A + +   F  R ++K Y +L+ G+   +    K  +
Sbjct: 399 -PLIVHRLDMSTSGILVLTKTKEANKIVQSQFINRTVKKRYVALLDGMLTKESGKIKLPL 457

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L  +     D++H      K    +I + K    F          P TGRTHQLRVH
Sbjct: 458 RVDLDDRPKQLVDFIHGKNAETKWTKISIENGKTRVYFY---------PITGRTHQLRVH 508

Query: 259 ALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           + H   +  PI+GD  Y     GN +    N+L+LHA  +   HP
Sbjct: 509 SAHKNGLDTPIIGDDLY-----GNKS----NRLHLHAEQISFIHP 544


>gi|301156232|emb|CBW15703.1| tRNA pseudouridine synthase [Haemophilus parainfluenzae T3T1]
          Length = 238

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 53/212 (25%), Positives = 95/212 (44%), Gaps = 16/212 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEYLVAVNKPAGMLVHRSWLDTHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  + + F  + +QK Y ++V G  + +        ++   I   +     Q +
Sbjct: 64  ALNSEIANLMCQQFEQKTVQKSYLAIVRGYLQGEGRIDYPLKIQLDKIADKFA----QED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ ++              ++  +++ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQEAVTDYEGLNIVEMPYAVGRYQTTRYSLVKLIPQTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNFTSPIQ--NKLYLHARYMDLPHP 300
           +Y    +    +      +L+LHA  +   HP
Sbjct: 180 QYGDLHQNRALTEYSGCQRLFLHADTLIFEHP 211


>gi|290508924|ref|ZP_06548295.1| ribosomal large subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
 gi|289778318|gb|EFD86315.1| ribosomal large subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
          Length = 263

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/209 (30%), Positives = 95/209 (45%), Gaps = 18/209 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LLY+D  + + NKPAG+    G     ++D      V  +     L HRLD  TSG++VV
Sbjct: 50  LLYQDEHLLLINKPAGLLSLSGKD-PRNLDSVHHRLVQ-RFPGCTLVHRLDFGTSGLMVV 107

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +     L + F  R + K+Y +L+ G    + E I    + K       + +  ++ 
Sbjct: 108 ARNKDVNALLCQQFSQRTVAKVYTALLCGH-LAEDEGIVEAAIAKDPARFPRMSLCARHG 166

Query: 221 KGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K A    S ++VID   Q            + + P TGRTHQLR+H   +G PI+G   Y
Sbjct: 167 KPAR---SRYRVIDRLYQSRDGERALALTRVALTPETGRTHQLRIHCQLLGYPILGCDLY 223

Query: 273 CA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
                 G   +P   +L LHA  +   HP
Sbjct: 224 GGRELPGTEQAP---RLMLHASELRFVHP 249


>gi|119469873|ref|ZP_01612711.1| ribosomal large subunit pseudouridine synthase A [Alteromonadales
           bacterium TW-7]
 gi|119446856|gb|EAW28128.1| ribosomal large subunit pseudouridine synthase A [Alteromonadales
           bacterium TW-7]
          Length = 550

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/208 (30%), Positives = 102/208 (49%), Gaps = 28/208 (13%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGIL 158
           ++Y+D  + + NKPA  +SV    GI      FL+      +   P + HRLD  TSG+L
Sbjct: 349 VVYQDDDLVIVNKPAEFLSV---PGITIDDSVFLRMKTQFPEATGPLIVHRLDMSTSGLL 405

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A  + A + + + F  R I+K Y +LV G  + +   I      +  +  D+    +Q
Sbjct: 406 IIALNKRAHKAIQKQFIERTIEKRYVALVDGNIEQESGTI------ELPLTPDFDDKPRQ 459

Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKY 272
               +KG   A++ ++V++        L++ P TGRTHQLRVH  H   +  PI+GD  Y
Sbjct: 460 KVCYQKG-KPALTTWQVLE-RKNNTTRLQLYPKTGRTHQLRVHCAHVLGLNTPIIGDTHY 517

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
                        ++L+LHA Y+   HP
Sbjct: 518 GKK---------ADRLHLHAEYLAFTHP 536


>gi|317009246|gb|ADU79826.1| pseudouridine synthase D [Helicobacter pylori India7]
          Length = 327

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 57/227 (25%), Positives = 105/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W++SK       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVVHKAPSVK---EPTLVDWLESKNYELSNLGLKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KETSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MMALKAAKKEKSRYSKSAFISLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L    PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLHFKVPLLKDMLE 300


>gi|308062067|gb|ADO03955.1| hypothetical protein HPCU_03975 [Helicobacter pylori Cuz20]
          Length = 327

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 106/229 (46%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLEFKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHAHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++ +
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLEYF 302


>gi|113460997|ref|YP_719064.1| tRNA pseudouridine synthase C [Haemophilus somnus 129PT]
 gi|112823040|gb|ABI25129.1| tRNA pseudouridine synthase C [Haemophilus somnus 129PT]
          Length = 234

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 58/214 (27%), Positives = 94/214 (43%), Gaps = 21/214 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 3   ILYQDEFLVVVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----------IANWLLKKSHIGG 210
           A     A  L   F +++++K Y ++V G   + +            IA+   +K  +  
Sbjct: 63  ALNAGIANLLCSQFELKQVKKSYLAIVRGYLSDAQRIDYPLKVQLDKIADKFSRKEELQD 122

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                         Y +  +      + ++  + + PHTGR HQLR H  H+  PI+GD 
Sbjct: 123 AITDYYGLKTVEMPYGVGRYS-----SSRYSLVRLMPHTGRKHQLRRHLKHIFHPILGDT 177

Query: 271 KYCANFKGNFTSPIQN----KLYLHARYMDLPHP 300
           +Y    +    S  QN    +L LHA  +   HP
Sbjct: 178 QYGDLHQNRAFS--QNLGVSRLMLHAEKLCFQHP 209


>gi|332753507|gb|EGJ83887.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           4343-70]
 gi|333000233|gb|EGK19816.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-218]
          Length = 260

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 68/261 (26%), Positives = 115/261 (44%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR +  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRYLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|282862147|ref|ZP_06271210.1| pseudouridine synthase, RluA family [Streptomyces sp. ACTE]
 gi|282563172|gb|EFB68711.1| pseudouridine synthase, RluA family [Streptomyces sp. ACTE]
          Length = 313

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 81/330 (24%), Positives = 144/330 (43%), Gaps = 30/330 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    V+ + V +  E  R+D      +   +     ++  +G+V+VD      + R+ 
Sbjct: 1   MSTYPEVRTLPVPDGLEGERVDAVISRLF-GFSRTKAAELAAAGKVQVDGAVAGKSERVH 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPQAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +    + + G   R  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKAQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R ++K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I
Sbjct: 166 FRDRVVEKKYHALVQGHPDPMSGTIDAPIGR--HPQHDYKWAVTAEGK---PSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + + +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAY-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTMAKRLGL-GRQWLHAV 278

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            +   HP +GG ++ ++  P  + +  +++
Sbjct: 279 RLGFEHPADGGWVEFSSGYPDDLEQALETI 308


>gi|328773939|gb|EGF83976.1| hypothetical protein BATDEDRAFT_85504 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 264

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/209 (29%), Positives = 98/209 (46%), Gaps = 14/209 (6%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           ++++   +  +LY D K+ V NKP  + + G       I+  LK+   +  ++  L H++
Sbjct: 36  SRYNRLFEVSILYNDGKLLVINKPWNVRIDGPVDETTTIEFLLKATFPTY-RRLFLLHQI 94

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+ +   T+  A  +   F  R+IQK Y ++V G   +++E      L       
Sbjct: 95  DYATSGVHMWGLTKHTATIMGRMFLRRQIQKTYLAIVCGT-VDQQEFQIQLPLAPRPEND 153

Query: 211 DYVHVVKQNE--KGANYAISHFKVI--DCFAQK---FCWLEMQPHTGRTHQLRVHALHMG 263
             +HV    E       A +  +V+     A+       LE+QPHTGR HQLRVH   +G
Sbjct: 154 RLMHVPTLGEDVPDTKAAQTFVRVLRRGTLAETQIPVTLLELQPHTGRRHQLRVHLSSIG 213

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            PIV D  Y     G    PI +++ LH+
Sbjct: 214 HPIVNDRVY-----GALNVPIYHRMMLHS 237


>gi|294643719|ref|ZP_06721519.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|292640957|gb|EFF59175.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
          Length = 279

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/198 (29%), Positives = 102/198 (51%), Gaps = 19/198 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 91  IVYEDAYIIVVEKMQGLLSVNTERQKERTAYTI---LNEYVQRSGRQFRVFIVHRLDRDT 147

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+     + L +++      + Y ++V G  +   + + +WL  K+     YV 
Sbjct: 148 SGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTL----YVS 203

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             + ++ G + +I+H+K I   A  +  LE+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 204 SSEYDD-GGSKSITHYKTIKR-ANGYSLLELDLETGRKNQIRVHMQDLGHPIIGDGRYGR 261

Query: 275 NFKGNFTSPIQNKLYLHA 292
               N   PI  +L LHA
Sbjct: 262 EDSPN---PI-GRLALHA 275


>gi|206579623|ref|YP_002237870.1| pseudouridine synthase, RluA family [Klebsiella pneumoniae 342]
 gi|206568681|gb|ACI10457.1| pseudouridine synthase, RluA family [Klebsiella pneumoniae 342]
          Length = 232

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/209 (30%), Positives = 95/209 (45%), Gaps = 18/209 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LLY+D  + + NKPAG+    G     ++D      V  +     L HRLD  TSG++V+
Sbjct: 19  LLYQDEHLLLINKPAGLLSLSGKD-PRNLDSVHHRLVQ-RFPGCTLVHRLDFGTSGLMVI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +     L + F  R + K+Y +L+ G    + E I    + K       + +  ++ 
Sbjct: 77  ARNKGINALLCQQFSQRTVAKVYTALLCGH-LAEDEGIVEAAIAKDPARFPRMSLCARHG 135

Query: 221 KGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K A    S ++VID   Q            + + P TGRTHQLR+H   +G PI+G   Y
Sbjct: 136 KPAR---SRYRVIDRLYQSRDGERALALTRVALTPETGRTHQLRIHCQLLGYPILGCDLY 192

Query: 273 CA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
                 G   +P   +L LHA  +   HP
Sbjct: 193 GGRELPGTEQAP---RLMLHASELRFVHP 218


>gi|304373162|ref|YP_003856371.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyorhinis HUB-1]
 gi|304309353|gb|ADM21833.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyorhinis HUB-1]
          Length = 297

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 77/308 (25%), Positives = 142/308 (46%), Gaps = 38/308 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI--QSGQVVRIPPVINA 73
           +E  RLD + +     ++ V +Q+I+ + QV VD + V   N I  Q  Q+         
Sbjct: 9   DEQTRLDIFLRKKL-ELSRVFVQEIIANNQVWVDNQIVNKKNFILKQGSQI--------E 59

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------IAY 127
           +++  KEQ       N+   +  ++  +++ED  + V +KP  + V    G      +  
Sbjct: 60  VHYQEKEQ-------NINAKAQDIELKIVFEDENVIVVDKPTNMVVHPAPGNYENTLVNA 112

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  F +    +   +P + HRLD++TSG+++VA+       L +  + R+I++ Y++++
Sbjct: 113 LVYKFAQLSNVNGSLRPGIVHRLDKDTSGLMLVAKNDKMHNFLAQQLKERKIKRKYYAII 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLE 244
            G  +N+   I N  + +       + V   N K    AI+H  V   F  K   F ++ 
Sbjct: 173 EGQLENQISHI-NLPIARDEKNRKKMSVSHFNSKE---AITHIFVEKYFHYKKKVFSFVR 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQ+RVH  ++  P+ GD  Y      +F         LHA  ++  + +G  
Sbjct: 229 CELETGRTHQIRVHLAYIKHPVYGDPVYGKKV-DDFNQR------LHAYEIEFINIDGKT 281

Query: 305 LQITAPLP 312
           L+  + LP
Sbjct: 282 LKFNSKLP 289


>gi|290580515|ref|YP_003484907.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
 gi|254997414|dbj|BAH88015.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
          Length = 296

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 54/178 (30%), Positives = 92/178 (51%), Gaps = 14/178 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           ++YED    + +KPAG +          I  F+K +    D   ++  +  RLD++TSG+
Sbjct: 78  IVYEDEHFLILDKPAGYASIPSILHTNTIANFVKYYYLKKDYPNKQIHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVH 214
           +++A+   A   L +  + + I+K Y++LV G   +P ++ E IA     +  I    VH
Sbjct: 138 MLLAKHGYAHARLDKQLQKKTIKKRYYALVSGQGQLP-DQGEIIAPIARPEDSIITRCVH 196

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                     YA + +KV+  +      +++Q HTGRTHQ+RVH  H+G P++GD  Y
Sbjct: 197 ------PSGKYAHTSYKVLARYGD-IALVDIQLHTGRTHQIRVHFAHIGFPLLGDDLY 247


>gi|254785816|ref|YP_003073245.1| pseudouridine synthase for 23S rRNA and tRNAphe [Teredinibacter
           turnerae T7901]
 gi|237686915|gb|ACR14179.1| pseudouridine synthase for 23S rRNA and tRNAphe [Teredinibacter
           turnerae T7901]
          Length = 208

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 100/205 (48%), Gaps = 21/205 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I   NKPAG+ +V G +      D  +    +S     R+ HRLD  TSG+++
Sbjct: 6   IIYQDDHIIAINKPAGLLTVPGLATPDNAFDQLVHQHPNS-----RVVHRLDMATSGLVI 60

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             ++  +       F  R++ K Y + V GI    +  I   L+       D+ +  KQ 
Sbjct: 61  FPQSHESLVRFGRLFEQRKMTKTYTATVAGIVAEDRGEITLPLI------CDWPNRPKQK 114

Query: 220 ---EKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              E+G  +A + +KV++     +   +E+ P TGR+HQLRVH   +G PI+GD    A 
Sbjct: 115 VDLEQG-KHAHTQYKVLERRLDLQTTRIELTPITGRSHQLRVHMQQLGHPILGD----AF 169

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
           +  +      ++L LHA  ++  HP
Sbjct: 170 YAPDAIQQASDRLLLHATTLEFVHP 194


>gi|163939199|ref|YP_001644083.1| RluA family pseudouridine synthase [Bacillus weihenstephanensis
           KBAB4]
 gi|163861396|gb|ABY42455.1| pseudouridine synthase, RluA family [Bacillus weihenstephanensis
           KBAB4]
          Length = 307

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 115/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED  + + NK   +    S + G+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVFEDDHVLIVNKQGQMDTHPSEKNGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEKYFKKQNATLVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y     G  T+ +  +  LHA  ++  HP     + +  P P ++  T
Sbjct: 254 DVLY-----GGQTTYMSGQA-LHAMKINFLHPITKEEIVVDVPFPTNLNDT 298


>gi|228926342|ref|ZP_04089415.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pondicheriensis BGSC 4BA1]
 gi|228833334|gb|EEM78898.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pondicheriensis BGSC 4BA1]
          Length = 292

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/269 (25%), Positives = 127/269 (47%), Gaps = 34/269 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+  P
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQAGEEIRVFFP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 63  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 107

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 108 VANALLSHYDKQYLAST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 164

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 165 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++  TGRTHQ+RVH  H+G P++GD+ Y
Sbjct: 219 SLELDTGRTHQIRVHMAHIGHPLLGDNLY 247


>gi|222823069|ref|YP_002574642.1| ribosomal pseudouridine synthase [Campylobacter lari RM2100]
 gi|222538290|gb|ACM63391.1| putative ribosomal pseudouridine synthase [Campylobacter lari
           RM2100]
          Length = 300

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/209 (28%), Positives = 102/209 (48%), Gaps = 25/209 (11%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQ-GGSGIAYHI-DG 131
           N + ++ K LD  V L  + +  K + +++E+    +  KP+G+     G    Y + D 
Sbjct: 44  NLVEEKNKFLDGLVELIVYENNPKGLEIVFENEDFAIVEKPSGVLTHPNGRNCTYSLCDE 103

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
               W    GQ   + HRLD+ETSG+L++A+ + A   L   F  R +QK Y +LV G  
Sbjct: 104 IWHLW----GQNACVAHRLDKETSGLLLIAKHKNAQIELKTMFEKRLVQKSYLALVKG-- 157

Query: 192 KNKKECIANWLLKKSHIGGDY------VHVVKQNEKGAN--YAISHFKVIDCFAQKFCWL 243
           K K+E I +   K   +  DY      +H+ +  ++     Y + +F+ +D        +
Sbjct: 158 KTKEEFIVD---KSMDLAKDYDAVKTRMHICENGKEALTQFYTLEYFENLDV-----SLI 209

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +P TGR HQ+R+H  H+   I+G+  Y
Sbjct: 210 LAKPLTGRQHQIRLHLFHVKHKILGEPLY 238


>gi|222110929|ref|YP_002553193.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221730373|gb|ACM33193.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 222

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/223 (29%), Positives = 108/223 (48%), Gaps = 29/223 (13%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS---WVDSKGQKPRLTHRL 150
           S+ ++S+  + D  + V  KP+G+    G G         ++   W D+      + HRL
Sbjct: 6   SEGVRSV--HVDDTLLVLEKPSGLLCVPGRGPDKQDALSTRAQALWPDAL-----IVHRL 58

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIG 209
           DQ TSG++++AR  A  + L+ SF  R + K Y ++V G +P         W      I 
Sbjct: 59  DQPTSGLVLMARGAAMQRALSHSFAQRLVHKRYRAVVAGRMPPPDPAHADGWGEIALPIA 118

Query: 210 GDY----VHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            D+    + VV         +++ ++V+    A+    +E++P TGRTHQLRVH   +G 
Sbjct: 119 ADWERRPLRVVDATH--GQPSLTRWRVLAHDAARDTTSVELEPVTGRTHQLRVHLAALGH 176

Query: 265 PIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHP-EGG 303
           PI+GD  Y         +P+Q    +L LHA  ++  HP +GG
Sbjct: 177 PILGDQLYA-------DAPVQARAPRLLLHACVLEFAHPLQGG 212


>gi|308048388|ref|YP_003911954.1| ribosomal large subunit pseudouridine synthase A [Ferrimonas
           balearica DSM 9799]
 gi|307630578|gb|ADN74880.1| ribosomal large subunit pseudouridine synthase A [Ferrimonas
           balearica DSM 9799]
          Length = 219

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 57/178 (32%), Positives = 84/178 (47%), Gaps = 17/178 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  I V +KP+G+    G   A H D       +  G    + HRLD  TSG++V+
Sbjct: 16  VLYEDKDIVVVDKPSGLLSVPGRDPA-HRDSVYSRVAERYGTVYDV-HRLDMATSGVMVL 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKE--CIANWLLKKSHIGGDYVHV 215
           A  + A + L   FR R   K Y + VWG    P+ + +   I +W  +           
Sbjct: 74  ALRKNAERELKRQFRDRETSKTYLARVWGHLAQPEGEIDLPLICDWPNRPKQ-------- 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            K        +++ ++V+         LE+ P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 126 -KVCHDTGKPSLTRYRVLSTDDHS-SLLELTPITGRSHQLRVHLLALGHPILGDGFYA 181


>gi|145300070|ref|YP_001142911.1| tRNA pseudouridine synthase C [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142852842|gb|ABO91163.1| tRNA pseudouridine synthase C [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 246

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 72/269 (26%), Positives = 119/269 (44%), Gaps = 57/269 (21%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK--------------GQ 142
           +K  LLY+D  +   NKP+G+ V              +SW+D                G+
Sbjct: 1   MKLTLLYQDDWLVAVNKPSGLLVH-------------RSWLDKAETRFAMQMTRDLIGGR 47

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HRLD+ TSG+L+ A   A A+ LTE+F  R++ K Y +LV G     ++ + ++ 
Sbjct: 48  HVYPVHRLDRPTSGVLLFALDPAVARILTEAFAARQVHKEYLALVRGW--APEQGVIDYP 105

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------------KFCWLEMQPH 248
           LK+          +   ++ A  A++ F+   C  Q              ++  +++ P 
Sbjct: 106 LKEQ--LDKIADAMSNPDRPAQEAVTAFR---CLHQVELPHAVSKKHPTSRYSLVKLFPK 160

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP-EG 302
           TGR HQLR H  H+  PIVGD  +        F+ +F      +L L AR +   HP   
Sbjct: 161 TGRKHQLRRHMEHLFHPIVGDTTHGDGRHNRFFREHFGC---ERLLLVARTLSFEHPILK 217

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLY 331
             ++I APL   +++ +  LG+    + Y
Sbjct: 218 VPMRIQAPLGLDLLQLFAELGWPGSESDY 246


>gi|145350783|ref|XP_001419777.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580009|gb|ABO98070.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 218

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/196 (30%), Positives = 95/196 (48%), Gaps = 28/196 (14%)

Query: 130 DGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           D   + W++ K  G+  R  H+LD  TSG+++ A TR AA +  + FR R  +K Y ++V
Sbjct: 22  DASCEDWLNLKYPGKHHRFCHQLDTATSGVVLTAHTREAAGNAAKLFRDRLAKKKYLAVV 81

Query: 188 WGIPKNKKECIANWLLKK-SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW---- 242
           +G PK  +  +   L K  + + G    V ++N K +    + FKV+    + +C     
Sbjct: 82  FGWPKEDEWTVNAKLGKDPTDVKGFRERVDEENGKASE---TSFKVL---QRGYCTLDGA 135

Query: 243 --------LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                   LE +P TGR HQ+R+H +H G PI+GD  Y  +           +++LHA  
Sbjct: 136 NRGVEVSRLECRPVTGRRHQIRLHLMHSGHPILGDMAYSDDTD-------SYRMFLHALE 188

Query: 295 MDLPHPEGGRLQITAP 310
           + +P  E      T P
Sbjct: 189 LVMPFEEETLTFATEP 204


>gi|301168062|emb|CBW27648.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteriovorax marinus SJ]
          Length = 327

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 109/237 (45%), Gaps = 43/237 (18%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSG 156
           YED  + + NK AG+ V    G      ++  L    D KG    ++P + HRLD+ TSG
Sbjct: 94  YEDEDLIIVNKAAGMVVHPAPGNYTGTLVNAILYHCKDIKGVGDQRRPGIVHRLDKGTSG 153

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVH 214
           I+VVA+ +   + L + F    I + Y  +  G   P   K         +S+IG    +
Sbjct: 154 IMVVAKNQKCHEGLVKLFSTHDITRRYECIAMGKSFPTGGK--------LESNIGRHPQN 205

Query: 215 VVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH---ALHMGCPIVGD 269
            +K +   K   +A++H++V+  F  K   +E++  TGRTHQ+RVH    LH   PI+ D
Sbjct: 206 RLKMSTESKAGKHALTHYRVLKQF-DKVAHVELKLETGRTHQIRVHLSQLLHR--PILCD 262

Query: 270 HKY-------------CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
             Y              ++  G++  P     +LHA+ +   HP     L  TAP P
Sbjct: 263 PLYGNPKEHLQRIGPELSDIIGDYEHP-----FLHAKELGFIHPITKKELHFTAPPP 314


>gi|227354995|ref|ZP_03839406.1| ribosomal large subunit pseudouridine synthase [Proteus mirabilis
           ATCC 29906]
 gi|227164782|gb|EEI49629.1| ribosomal large subunit pseudouridine synthase [Proteus mirabilis
           ATCC 29906]
          Length = 232

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 64/211 (30%), Positives = 99/211 (46%), Gaps = 24/211 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + V NKP+G+    G     +ID      V    +   L HRLD  TSG++V+A
Sbjct: 20  LYQDEHLLVINKPSGLLSLSGKN-PQNIDSVHYRLVPLFPEC-TLVHRLDFGTSGVMVIA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
             +A  + L + F  R + K Y +L+ G  +N    I      ++ I  D  H  +   +
Sbjct: 78  LNKAINRALCQQFSQRTVTKAYDALLCGHLQNDSGVI------EAPIAKDPQHFPRMSIS 131

Query: 220 EKGANYAISHFKVIDCFAQKFC--------WLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                 A S+++VI+ F Q            + + P TGRTHQLR+H  ++G PI+G   
Sbjct: 132 TTQGKAARSYYQVIERFYQTLADGTRLPLTRVRLTPETGRTHQLRIHCQYIGHPILG--- 188

Query: 272 YCANFKGNFTSPIQN--KLYLHARYMDLPHP 300
            C  + G   S  ++  +L LHA  +   HP
Sbjct: 189 -CDLYGGLLLSGTEHTPRLMLHACELHFIHP 218


>gi|194467694|ref|ZP_03073681.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
 gi|194454730|gb|EDX43627.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
          Length = 301

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 105/229 (45%), Gaps = 20/229 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS------VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++YED    + NKPAG++      V     +   + G+ K   D + Q   +  RLD++T
Sbjct: 80  IIYEDQDFLIMNKPAGVATVPAHNVPVADSLVNRVKGYYKRQ-DYENQVTHVATRLDRDT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V  + R A   L E  +   ++K Y +L+ G     K  + +  +           
Sbjct: 139 SGLVVFPKHRFAHAVLDEQLKKHLVKKNYLALIKG-----KVPVEHGYIDAPIQRDPNSF 193

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V +   K    +++ +   +C  Q    ++++ HTGRTHQ+RVH   +G P++GD  Y  
Sbjct: 194 VKRMVGKEGKASVTEYWCQECNVQA-SLIKIRLHTGRTHQIRVHFASLGFPLIGDKMYGE 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                  S +  +  LH  ++    P +G  + ++APLP+      D L
Sbjct: 253 E------SRLIARQALHCYWLSFYSPFKGENITVSAPLPSDFKNAKDDL 295


>gi|320546661|ref|ZP_08040973.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equinus ATCC 9812]
 gi|320448716|gb|EFW89447.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equinus ATCC 9812]
          Length = 296

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 56/205 (27%), Positives = 97/205 (47%), Gaps = 17/205 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGI 157
           + YED    + NKP G +       +  I  F+K++   +    +  H   RLD+ TSG+
Sbjct: 78  IAYEDEHFLILNKPYGYASIPSILHSNTIANFVKNYYLEQNYPNKQVHIVTRLDKNTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G     ++ E IA     +  I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQNKTIEKRYYALVSGQGDLADEGEIIAPIARDEDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++      YA + +KV++ F      ++++ HTGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 TRRVHPSGKYAHTSYKVVEKFGD-VALVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGR 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                T     +  LH  Y+   +P
Sbjct: 251 MDLGIT-----RQALHCHYLRFVNP 270


>gi|307720729|ref|YP_003891869.1| ribosomal large subunit pseudouridine synthase D [Sulfurimonas
           autotrophica DSM 16294]
 gi|306978822|gb|ADN08857.1| ribosomal large subunit pseudouridine synthase D [Sulfurimonas
           autotrophica DSM 16294]
          Length = 324

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 142/310 (45%), Gaps = 45/310 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           M   Q  + +N E   RLD +  +         +  +++   V VD K+V +   ++++G
Sbjct: 1   MINTQEYICKNPE---RLDTFLTSQIGQTR-SQIAGLIKHECVFVDGKKVPRPGVKLKAG 56

Query: 63  QVVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           QVV++  P          K++K LD + ++          +LYED  + V NKP+G++V 
Sbjct: 57  QVVKVEFPEA--------KQEKALDVNFDVE---------ILYEDDDVLVINKPSGVTVH 99

Query: 121 GGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
               +    +  L  W+  KG         ++  + HRLD+ TSG +VVA+   A + L+
Sbjct: 100 PAPSVK---EATLVDWLKHKGIRLSTISGEERHGIVHRLDKGTSGTMVVAKNNEAHEFLS 156

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           +  + + + + Y +++    K     + + + + SH   + + +    E G  YA + FK
Sbjct: 157 KQLQDKSMGRYYIAVIVPPLKEDITVVESNIGRSSH---NRLKMACGLEHG-KYAKTMFK 212

Query: 232 VIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
            +     +   L   +  TGRTHQ+RVH   M   I+GDH Y  + K   +     ++ L
Sbjct: 213 QLALSEDEHTQLIACKLFTGRTHQIRVHLESMNRHILGDHIYGLSPKQENS----ERILL 268

Query: 291 HARYMDLPHP 300
           HA  +   HP
Sbjct: 269 HAYMIYFIHP 278


>gi|229132186|ref|ZP_04261043.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
 gi|228651234|gb|EEL07212.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
          Length = 307

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 115/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED  + + NK   +    S + G+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVFEDDHVLIVNKQGQMDTHPSEKNGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DKAITYYKVEKYFKKQNATLVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y     G  T+ +  +  LHA  ++  HP     + +  P P ++  T
Sbjct: 254 DVLY-----GGQTTYMSGQA-LHAMKINFLHPITKEEIVVDVPFPTNLNDT 298


>gi|16272017|ref|NP_438215.1| pseudouridine synthase-like protein [Haemophilus influenzae Rd
           KW20]
 gi|260580654|ref|ZP_05848481.1| conserved hypothetical protein [Haemophilus influenzae RdAW]
 gi|1175071|sp|P43930|Y042_HAEIN RecName: Full=Uncharacterized RNA pseudouridine synthase HI_0042;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|1572988|gb|AAC21720.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|260092716|gb|EEW76652.1| conserved hypothetical protein [Haemophilus influenzae RdAW]
          Length = 224

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/203 (31%), Positives = 95/203 (46%), Gaps = 28/203 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+ S   + NK  GISV      QG + +        K W         L HRLD+ T
Sbjct: 5   VVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQLNVPKVW---------LVHRLDKVT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A    +A   +  F   +I K Y +L    PK K+  I    +KK+  G   + 
Sbjct: 56  SGLLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGD-MKKAREGAWKLC 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K N      AI+ F+ + C      ++ ++P TG+THQLRV    +G PI+GD  Y  
Sbjct: 115 QTKDNP-----AITRFESVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDGLYGK 168

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
           N     T  I ++ YLHA  ++ 
Sbjct: 169 N-----TEKI-DRTYLHATQLEF 185


>gi|332857041|ref|ZP_08436347.1| pseudouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332869978|ref|ZP_08438954.1| pseudouridine synthase A [Acinetobacter baumannii 6013113]
 gi|332726856|gb|EGJ58370.1| pseudouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332732478|gb|EGJ63729.1| pseudouridine synthase A [Acinetobacter baumannii 6013113]
          Length = 190

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 64/199 (32%), Positives = 96/199 (48%), Gaps = 20/199 (10%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAA 167
           V +KP+ I    G G  +  D  L   V     +PR  L HRLD++TSGILV   ++   
Sbjct: 2   VIHKPSDILSVPGKGDLH--DSVLTRLV---AIEPRTLLIHRLDRDTSGILVFGLSKRGQ 56

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             +   F+ R+  KIY +LV G  + +       +   S      +H+V  +      A+
Sbjct: 57  SAIARQFQDRQTSKIYEALVAGHLEGEGTVDIPVVYDPSR---PPLHIVDASHN--KPAL 111

Query: 228 SHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           +H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD  Y A        P 
Sbjct: 112 THWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDTLYAA--PEQLLVP- 168

Query: 285 QNKLYLHARYMDLPHPEGG 303
             +L LHA+ +   HP  G
Sbjct: 169 --RLCLHAKQLSFNHPVTG 185


>gi|294140903|ref|YP_003556881.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293327372|dbj|BAJ02103.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 238

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/219 (30%), Positives = 98/219 (44%), Gaps = 26/219 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  I V +KP+G+    G     +ID      V        L HRLD  TSG++++
Sbjct: 19  ILFRDEHILVIDKPSGLLSLSGKH-PLNIDSVHYRLVQDYPTC-TLIHRLDFGTSGVMLL 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +     L + F  RR+ K Y +L+ G  K     +   + K      D   ++K  +
Sbjct: 77  AMNKQINALLCKQFSERRVSKRYTALLHGDLKPDSGLVDCAVAKDI----DNFPLMKLCQ 132

Query: 221 KGANYAISHFKVIDCFAQ----------------KFCWLEMQPHTGRTHQLRVHALHMGC 264
                A S FKV+  F Q                +   +E +P TGRTHQLR+H+ H+G 
Sbjct: 133 DTGKPAQSKFKVLSRFIQTQDDNFFVDDIRAGERQVTRVEFEPVTGRTHQLRLHSQHLGH 192

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           PI+G   Y A  +  F S   ++L LHA  +   HP  G
Sbjct: 193 PILGCDLY-ATDEAYFMS---SRLMLHASQLCFEHPVSG 227


>gi|212635320|ref|YP_002311845.1| 23S RNA-specific pseudouridylate synthase [Shewanella piezotolerans
           WP3]
 gi|212556804|gb|ACJ29258.1| Pseudouridylate synthase, 23S RNA-specific [Shewanella
           piezotolerans WP3]
          Length = 256

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 104/227 (45%), Gaps = 25/227 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + + NKP+G+    G   A ++D      V        L HRLD  TSGI+V+
Sbjct: 39  ILYQDEVMLLINKPSGLLSLSGKNPA-NLDSVHYRLV-KLFPGCSLVHRLDFGTSGIMVI 96

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW---------LLKKSHIGGD 211
           A  +     L   F  R + K Y +++ G  K  K  I            L+K   + G 
Sbjct: 97  ALNKDINALLCRQFSERSVLKRYTAILLGELKEDKGVICAAIAKDKPNFPLMKLCELEGK 156

Query: 212 -----YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                Y  + K+    AN A    + +D        +E+ P TGRTHQLR+H+ ++G PI
Sbjct: 157 AARSLYQVLSKEYLGSANSAAE--RALD--EVSVTRVELTPETGRTHQLRIHSQYIGHPI 212

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +G    C  +   ++  + ++L LHA  ++  HP  G R+   +P P
Sbjct: 213 IG----CDLYGSAYSRQLASRLMLHATRLEFDHPVTGVRVLGYSPCP 255


>gi|91202037|emb|CAJ75097.1| similar to pseudouridine synthase C [Candidatus Kuenenia
           stuttgartiensis]
          Length = 244

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 68/223 (30%), Positives = 108/223 (48%), Gaps = 31/223 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKGQKPR----LTHRLDQ 152
           +LYED  I V +KPAG+   G     +  AY++   L  +V     K R    + HRLD+
Sbjct: 18  ILYEDEDILVIDKPAGLLTMGTDTNKTKTAYYM---LNDYVRKGCVKSRKHVFIIHRLDR 74

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           + SG+L+ A+   +  +L   ++    +K Y ++V G    K   I+ +L +        
Sbjct: 75  DASGLLLFAKNIRSKLNLQSQWQ--NTEKKYLTVVHGRLAKKAGTISTYLAENK---AQV 129

Query: 213 VHVVKQNEKGANYAISH--FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           V+     +KG    +SH  ++V+    + F  LE++  TGR +Q+RVH   +G PIVGD 
Sbjct: 130 VYSTSDTKKGK---LSHTVYRVLKE-TKYFSLLEIKLLTGRKNQIRVHLTELGHPIVGDK 185

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
           KY    KG +      +L LHA  +   HP  G+    +  AP
Sbjct: 186 KYGKE-KGAY-----KRLALHAYSISFKHPFSGKPITFETKAP 222


>gi|237752376|ref|ZP_04582856.1| ribosomal large subunit pseudouridine synthase A [Helicobacter
           winghamensis ATCC BAA-430]
 gi|229375865|gb|EEO25956.1| ribosomal large subunit pseudouridine synthase A [Helicobacter
           winghamensis ATCC BAA-430]
          Length = 353

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 110/245 (44%), Gaps = 29/245 (11%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQ--GGSGIAYHIDGFLKS---WVDSKGQKPR 145
           ++H   L   ++YEDS + + NKPA + V     +   + +  +LK     + + G   R
Sbjct: 84  SQHLQDLNIPIIYEDSDLLILNKPANLIVHRIDENDTQFTLVDYLKQKGFALSNLGDSYR 143

Query: 146 L--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           L   HRLD+ TSG +V+A+  A   HL+   + +++ + Y  ++    KN +      + 
Sbjct: 144 LGIVHRLDKNTSGAIVIAKNNATHAHLSMQIKSKQMGRYYLCIINQPLKNPQTVEIPIM- 202

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH------------TGR 251
              H      ++   N   A  A + F +I             P             TGR
Sbjct: 203 --RHPKQRLKYITTTNNVNAKTAKTAFFMIPTLLDSNFLKTENPKKEIPTLIGAKLFTGR 260

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH   +   I+GD  Y   +KGN+T     ++ LHA ++ L HP+  + L+  AP
Sbjct: 261 THQIRVHLNSINRHILGDGFYG--YKGNYTG----RILLHAHFLHLIHPKTQKLLEFHAP 314

Query: 311 LPAHM 315
           +P  M
Sbjct: 315 IPDDM 319


>gi|15602344|ref|NP_245416.1| tRNA pseudouridine synthase C [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|34582475|sp|Q9CNF3|TRUC_PASMU RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|12720737|gb|AAK02563.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 243

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 57/212 (26%), Positives = 93/212 (43%), Gaps = 16/212 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYQDPYLIAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVYPIHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  L   F  +++QK Y ++V G    +        ++   I   +     Q++
Sbjct: 65  ALSSEVANLLCLQFENKQVQKSYLAIVRGYLVGEGRIDYPLKVQLDKIADKFA----QDD 120

Query: 221 KGANYAISHFKVIDCFAQKFC----------WLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ +  +      +C           + + PHTGR HQLR H  H+  PI+GD 
Sbjct: 121 KAPQEAVTDYLGLAKVEMPYCVKKYPTTRYSLVRLIPHTGRKHQLRRHMKHLFHPILGDT 180

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +Y      +   T     +L LHA  +   HP
Sbjct: 181 QYGDLHQNRALTTHTGVQRLMLHAERLIFTHP 212


>gi|223939788|ref|ZP_03631659.1| pseudouridine synthase [bacterium Ellin514]
 gi|223891564|gb|EEF58054.1| pseudouridine synthase [bacterium Ellin514]
          Length = 269

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/251 (26%), Positives = 111/251 (44%), Gaps = 41/251 (16%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGG--------------SGIAYHIDGFLKSWVDSK 140
           +F +  +LYED  +   +KP+ +                   +GI          W  S+
Sbjct: 15  EFWEISVLYEDEHLLAVDKPSKLLTSPDRYDPKRPNLMKLLHAGIERGT-----PWAKSR 69

Query: 141 GQKPRL-THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-ECI 198
           G    +  HRLD ETSG++++A+ +     +   F   +  K Y +LV   P+ K  E  
Sbjct: 70  GLTYLMNAHRLDFETSGVILLAKDKPMLVAVANLFGSEKPVKTYSALVQRSPEEKSFEVD 129

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A        +G     +++ +EK    + + F++++ FA  +  L+ +P +GR HQ+RVH
Sbjct: 130 AKLAPHPVKLG-----LIRVDEKNGKRSRTQFELVEKFAG-YSLLKCRPLSGRQHQIRVH 183

Query: 259 ALHMGCPIVGDHKYCAN------------FKGNFTS-PIQNKLYLHARYMDLPHP-EGGR 304
             + G PIVGD  Y                K N T  P+ +++ LHA  + L HP     
Sbjct: 184 LQYAGLPIVGDSLYGGQPLMLSSLKRDYRLKPNKTERPLLDRVSLHAEELSLVHPLTNAE 243

Query: 305 LQITAPLPAHM 315
           ++I AP P  +
Sbjct: 244 IKIVAPWPKDL 254


>gi|150005860|ref|YP_001300604.1| putative RNA pseudouridylate synthase [Bacteroides vulgatus ATCC
           8482]
 gi|149934284|gb|ABR40982.1| putative RNA pseudouridylate synthase [Bacteroides vulgatus ATCC
           8482]
          Length = 308

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/220 (28%), Positives = 102/220 (46%), Gaps = 21/220 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           L+YED+ I V  K  G+    +       A HI   L  +V    +  R+   HRLD+ET
Sbjct: 94  LVYEDAYILVVEKKEGLLSVSTEHQKERTAQHI---LNEYVKRSHRFNRVFVVHRLDRET 150

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L +++      + Y S+V G  +     + +WL  +      YV 
Sbjct: 151 SGLMMYAKDEKTQNTLRDNWHDIVTDRRYVSIVSGDMEKDYGTVESWLTDRKL----YVS 206

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               +     +A++H+K I   A  +  +E+   TGR +Q+RVH L +G P+VGD +Y  
Sbjct: 207 SSPVDNGEGKFAVTHYKTIKR-ANGYSLVELDLETGRKNQIRVHMLDLGHPVVGDRRY-- 263

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
              G+   P+  +L LHA  +   HP    L +   P P 
Sbjct: 264 ---GSECDPL-GRLALHAFKLCFYHPVTKELMEFETPYPT 299


>gi|298695119|gb|ADI98341.1| probable RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus ED133]
          Length = 273

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/236 (25%), Positives = 101/236 (42%), Gaps = 34/236 (14%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  N++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMNKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED  + +  KP G+      ++  + +  H+       +DS   +P   HRLDQET G+
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHV----IYTIDSDYVEP--IHRLDQETVGL 131

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+     + L        I +IY + V  +   K + I         IG D  H  K
Sbjct: 132 LIVAKNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTI------DMPIGKDKFHSNK 185

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +        AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y
Sbjct: 186 RRVSPTGQRAITHILTSKMIKETVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLY 241


>gi|237807273|ref|YP_002891713.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
 gi|237499534|gb|ACQ92127.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
          Length = 242

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 102/227 (44%), Gaps = 27/227 (11%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +K  +LY+D  +   NKPAG+ V             ++   D  GQ     HRLD+ TSG
Sbjct: 1   MKLEILYQDEHLVAINKPAGLLVHRSWLDKGETQFAMQMTRDQIGQHVYTVHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVH 214
           IL+ A     A+ LT++F   R+QK Y +LV G    +K    ++ LK+    I   +  
Sbjct: 61  ILLFALDPDTARLLTDAFAGHRMQKEYLALVRGWAPLQK--FLDYPLKEELDRIADKFA- 117

Query: 215 VVKQNEKGANYAISHFKVID----CFA-------QKFCWLEMQPHTGRTHQLRVHALHMG 263
                +K A  A +H + +      FA        ++  +++ P TGR HQLR H  H+ 
Sbjct: 118 ---DQDKPAQPAKTHIRCLGRVELPFAVSPRHPSSRYSLVKLLPLTGRKHQLRRHLAHLR 174

Query: 264 CPIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            PIVGD  +        F+  F+    ++L LH   +   HP    L
Sbjct: 175 HPIVGDTSHGDGRHNRFFRDQFSC---DRLMLHHHQLSFRHPHSNEL 218


>gi|254382579|ref|ZP_04997937.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           Mg1]
 gi|194341482|gb|EDX22448.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           Mg1]
          Length = 313

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 76/313 (24%), Positives = 130/313 (41%), Gaps = 35/313 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAIARMF-GFSRTKAAELAAAGKVSVDGSVVGKSERVH 59

Query: 61  SGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA--G 116
            G    V +P     +  + +    ++   +       +K +       +     P   G
Sbjct: 60  GGAWLEVEMPAPPRPVELVAEPVPGMEIVHDDDDIVVVMKPV------GVAAHPSPGWTG 113

Query: 117 ISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +V GG +   Y I            ++  + HRLD  TSG++ VA++  A   L   FR
Sbjct: 114 TTVIGGLAAAGYRIS------TSGASERQGVVHRLDVGTSGLMAVAKSERAYTSLKNQFR 167

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y +LV G P      I   + +  H   DY   V Q+ K    +++H+ +I+ 
Sbjct: 168 ERVVDKRYHALVQGHPDPMSGTIDAPIGR--HPNADYKWAVTQDGKA---SVTHYDLIEA 222

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-----YL 290
           F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  +L     +L
Sbjct: 223 F-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPT------VAKRLGLTRQWL 275

Query: 291 HARYMDLPHPEGG 303
           HA  +   HP  G
Sbjct: 276 HAVRLGFEHPADG 288


>gi|225165838|ref|ZP_03727617.1| pseudouridine synthase [Opitutaceae bacterium TAV2]
 gi|224799926|gb|EEG18376.1| pseudouridine synthase [Opitutaceae bacterium TAV2]
          Length = 244

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 117/237 (49%), Gaps = 23/237 (9%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKG-QKPRLTHRLD 151
           ++ +++ +++ED ++ V NKP  +      +G    + G ++   ++KG +K  L  RLD
Sbjct: 4   AEEIEAWVVHEDERLLVVNKPGDVVCHPSKAGPWSSLAGAVR---EAKGLEKAHLIFRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG++V A+    A  L  + + RR++K Y +++ G  + ++    +  L        
Sbjct: 61  RETSGVVVFAKDERMASRLQRAMQERRVRKEYLAVLEG--ELREAVTVDQPLGDDLASPV 118

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +V    + +  A  A+SHF  + C A  F  + ++  TGR HQ+R HA  +G P+VGD  
Sbjct: 119 FVKTCVRADGKA--AVSHFYPVAC-AGGFSLVRVRLETGRKHQIRAHASWLGTPVVGDKI 175

Query: 272 YCANFK-------GNFTSPIQNKLY-----LHARYMDLPHPEGGRLQITAPLPAHMV 316
           Y  + +         +T  +  KL+     LH   +DL +  G  L + APL   + 
Sbjct: 176 YGPDARIYLDFIDTGYTPELAAKLHLPRQALHCAEIDL-NEAGVPLVLRAPLAGDLA 231


>gi|188990499|ref|YP_001902509.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. B100]
 gi|167732259|emb|CAP50451.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris]
          Length = 259

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 58/198 (29%), Positives = 93/198 (46%), Gaps = 16/198 (8%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD++TSG++VVART  A   L E    R + + Y ++V G   +     A      
Sbjct: 68  VVHRLDKDTSGVMVVARTLQAQTALVEQLSARDVHRQYLAVVVGALVSGGTADAPI---D 124

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            H        V+ + + A   ++H+++ + F +    LE +  TGRTHQ+RVH  H+  P
Sbjct: 125 RHPRDRLKMAVRDDGRDA---VTHYRLRERF-RAHTALECRLETGRTHQIRVHMAHLKSP 180

Query: 266 IVGDHKYCANFK--GNFTSPIQNKL------YLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           IVGD  Y    K     T  +  +L       LHA  ++  HP  G  ++ +AP+P  + 
Sbjct: 181 IVGDPLYGGALKLPKGATDTLVAELRGFKRQALHAETLEFLHPVSGEPVRASAPVPEDLQ 240

Query: 317 KTWDSLGFKYDRNLYIKR 334
           +   +L     R   + R
Sbjct: 241 RLMSALREDSARAAELAR 258


>gi|257867857|ref|ZP_05647510.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC30]
 gi|257874186|ref|ZP_05653839.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC10]
 gi|257801940|gb|EEV30843.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC30]
 gi|257808350|gb|EEV37172.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC10]
          Length = 299

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 113/235 (48%), Gaps = 30/235 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTH---RLDQE 153
           ++YED+ + V NKPAGIS        YH  G +    K++  ++  + ++ H   RLD++
Sbjct: 79  IVYEDAHLLVVNKPAGISSIPAQ---YHPTGTMANRVKAYYQAQHYEDQVIHVVTRLDRD 135

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++ A+   A   L    R +++ K Y +LV G    +   ++     +  I  D  
Sbjct: 136 TSGLMLFAKHGFAHAKLDSQLRKKQVVKKYQALVAG----ELPALSAHGEIELPIARDLT 191

Query: 214 HVVKQ--NEKGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            ++K+  +++G      ++   +  DC       +++Q HTGRTHQ+RVH   +GCP++G
Sbjct: 192 SLLKRKVSDEGKEARTEYWLKQRNSDC-----ALVDIQLHTGRTHQIRVHFSAIGCPLLG 246

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           D  Y     G     I+ +  LH   +   HP     L    PLPA M     ++
Sbjct: 247 DEMY----GGTMALGIKRQA-LHCCQLQFQHPFTNEPLAFELPLPADMAAVCSAI 296


>gi|223043536|ref|ZP_03613581.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus capitis SK14]
 gi|222443024|gb|EEE49124.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus capitis SK14]
          Length = 276

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 73/275 (26%), Positives = 121/275 (44%), Gaps = 50/275 (18%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +L ++  S  + ++ +  K  + +++G  V IP           E+K           S+
Sbjct: 27  DLHQLNMSKDITINNQSAKLTDVVRTGDSVFIP---------TPEEK-----------SN 66

Query: 96  FLKSI----LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +L S     + YED    +  KP G+      ++  + +  H+       VDS+  +P  
Sbjct: 67  YLPSYRYAQVYYEDDDFAIVMKPKGVKTHPNDLKESNTLMNHV----IYTVDSEYVEP-- 120

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLDQET G+L+VA+     + L        I +IY + V  +   K + I        
Sbjct: 121 IHRLDQETVGLLIVAKNPIMKKILDRMLEENEITRIYKANVKALLPIKPQTI------DM 174

Query: 207 HIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            IG D  H  K+        AI+H    +   +  C L+++  TGRTHQ+RVH   +G P
Sbjct: 175 PIGKDKFHPNKRRISNTGQRAITHILNSEMIKEGICQLDIKLDTGRTHQIRVHLAEIGHP 234

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           ++GD  Y     G+ T     KL L++  ++L HP
Sbjct: 235 VIGDPLY-----GDST---LRKLELNSHKIELIHP 261


>gi|156978129|ref|YP_001449035.1| ribosomal large chain pseudouridine synthase A [Vibrio harveyi ATCC
           BAA-1116]
 gi|156529723|gb|ABU74808.1| hypothetical protein VIBHAR_06934 [Vibrio harveyi ATCC BAA-1116]
          Length = 523

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/204 (32%), Positives = 101/204 (49%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           +L++D  + + NKP+G+    G  I       L++ + D +G  P + HRLD  TSGIL+
Sbjct: 322 ILFQDEAMVIVNKPSGLLSVPGKTIKDSAYTRLQTMFPDVEG--PFVIHRLDMATSGILI 379

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A T+ A + L + F  R +QK Y +L+ G+   + E   +  ++          V  ++
Sbjct: 380 FALTKRANKSLQKQFITRGVQKRYMALLEGV-LTEPEGEISLPMRGDPDDRPRQLVCFEH 438

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHKYCANF 276
            K A       +V D  ++ +    M P TGRTHQLRVH A HMG    +VGD  Y    
Sbjct: 439 GKPAETYWQLIEVKDGRSKVY----MYPKTGRTHQLRVHSAHHMGLNMAMVGDGLYGEK- 493

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                    N+L+LHA  ++L HP
Sbjct: 494 --------ANRLHLHAEMLELDHP 509


>gi|238895332|ref|YP_002920067.1| putative ribosomal large subunit pseudouridine synthase A
           [Klebsiella pneumoniae NTUH-K2044]
 gi|238547649|dbj|BAH64000.1| putative ribosomal large subunit pseudouridine synthase A
           [Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044]
          Length = 232

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/209 (30%), Positives = 95/209 (45%), Gaps = 18/209 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LLY+D  + + NKPAG+    G     ++D      V  +     L HRLD  TSG++V+
Sbjct: 19  LLYQDEHLLLINKPAGLLSLSGKD-PRNLDSVHHRLVQ-RFPGCTLVHRLDFGTSGLMVI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +     L + F  R + K+Y +L+ G    + E I    + K       + +  ++ 
Sbjct: 77  ARNKGINALLCQQFSQRTVDKVYTALLCGH-LAEDEGIVEAAIAKDPARFPRMALCARHG 135

Query: 221 KGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K A    S ++VID   Q            + + P TGRTHQLR+H   +G PI+G   Y
Sbjct: 136 KPAR---SRYRVIDRLYQAREGERALALTRVTLTPETGRTHQLRIHCQLLGYPILGCDLY 192

Query: 273 CA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
                 G   +P   +L LHA  +   HP
Sbjct: 193 GGRELPGTEQAP---RLMLHASELRFVHP 218


>gi|237739111|ref|ZP_04569592.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           2_1_31]
 gi|229423711|gb|EEO38758.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           2_1_31]
          Length = 292

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/223 (29%), Positives = 103/223 (46%), Gaps = 32/223 (14%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-------PRLTHRLDQETS 155
           YED  + + NK   I V         +D  L + V +  +K       PR  +RLD  TS
Sbjct: 81  YEDENLLIVNKEPYIIVHPTQK---KVDKTLANAVVNYFEKTLGKTLVPRFYNRLDMNTS 137

Query: 156 GILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           G++++A+   T+A  Q  TE      ++K Y  +V GI +     I    L    IG D 
Sbjct: 138 GLIIIAKNAYTQAFLQDKTE------VKKTYKVIVSGIIEEDDFFIE---LPIGKIGDDL 188

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             +    E G   A +H KV++   +K   +LE + +TGRTHQ+R H   +G P+VGD  
Sbjct: 189 RRIELSEENGGKSAKTHIKVLERNREKNITFLEARLYTGRTHQIRAHLSLIGHPLVGDEL 248

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP---EGGRLQITAPL 311
           Y  +        +  +  LHA  ++  +P   E  +++I  PL
Sbjct: 249 YGGDMN------LAKRQMLHAYKLEFQNPKTLENLKVEIEIPL 285


>gi|49477132|ref|YP_035440.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|49328688|gb|AAT59334.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
          Length = 297

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 142/313 (45%), Gaps = 41/313 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI  P
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 68  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 113 VANALLSHYDKQYLAST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 170 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
            ++  TGRTHQ+RVH  H+G P++GD     N  G     ++ +  LH+  +   HP   
Sbjct: 224 SLELDTGRTHQIRVHMAHIGHPLLGD-----NLYGGKRDEMKRQ-ALHSTSLTFYHPILE 277

Query: 303 GRLQITAPLPAHM 315
             +  TA +P+ M
Sbjct: 278 KEMSFTAMIPSDM 290


>gi|308063469|gb|ADO05356.1| hypothetical protein HPSAT_03065 [Helicobacter pylori Sat464]
          Length = 327

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 106/229 (46%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLEFKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKTAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++ +
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLEYF 302


>gi|269968014|ref|ZP_06182052.1| Ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
 gi|269827371|gb|EEZ81667.1| Ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
          Length = 250

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 99/222 (44%), Gaps = 38/222 (17%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +++ED  I   NKP+G+ SV G   +A H D     W   K   P +   HRLD  TSG+
Sbjct: 16  IVFEDDDILAVNKPSGLLSVPGR--LAEHYDSM---WSRLKELHPEIQVVHRLDMSTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW--------LLK 204
           +++A+ + A + L + F+ R   K+Y++ VWG  + ++       I +W           
Sbjct: 71  MLLAKNKPAERALKKQFQYRLTHKVYYARVWGHVEPQEGNIDLPLICDWPNRPRQKVCFD 130

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                     VVK+         +H  V+           + P TGR+HQLRVH + +G 
Sbjct: 131 DGKPSQTLFQVVKREVHPDG---THTTVV----------RLLPITGRSHQLRVHLMAIGH 177

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
            I+GD  Y       F+     +L LHA  +   HP   +L+
Sbjct: 178 AIIGDEFYATEEAYQFS----ERLELHAAELSFYHPATDQLR 215


>gi|259907745|ref|YP_002648101.1| Pseudouridine synthase [Erwinia pyrifoliae Ep1/96]
 gi|224963367|emb|CAX54853.1| Pseudouridine synthase [Erwinia pyrifoliae Ep1/96]
 gi|283477602|emb|CAY73518.1| ribosomal large subunit pseudouridine synthase A [Erwinia
           pyrifoliae DSM 12163]
          Length = 232

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 61/212 (28%), Positives = 98/212 (46%), Gaps = 18/212 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D ++ + NKPAG+    G     +ID      V        L HRLD  TSG++V+
Sbjct: 19  ILYQDDRLVLINKPAGLLSLSGKN-PQNIDSVHYRLVQIF-PGCTLVHRLDFGTSGLMVI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +A    L + F  R + K+Y +L+ G   +  E + +  + K       + +   + 
Sbjct: 77  ARNKAINAALCQQFSQRTVTKVYSALLCG-HLDDNEGVIDAAIAKDPALFPLMSICSIHG 135

Query: 221 KGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K +    S ++V++ F              +++ P TGRTHQLR+H   +G PI+G   Y
Sbjct: 136 KPSR---SRYRVVERFYHPLENRTLLPLTRVQLTPETGRTHQLRIHCQQLGHPILGCDLY 192

Query: 273 CAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 G   +P   +L LHA  +   HP  G
Sbjct: 193 GGRLLPGTERTP---RLMLHASELHFVHPING 221


>gi|154505454|ref|ZP_02042192.1| hypothetical protein RUMGNA_02983 [Ruminococcus gnavus ATCC 29149]
 gi|153794247|gb|EDN76667.1| hypothetical protein RUMGNA_02983 [Ruminococcus gnavus ATCC 29149]
          Length = 354

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/224 (26%), Positives = 107/224 (47%), Gaps = 15/224 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGI 157
           ++YED  I V +K AG+ +       Y+      +W   + +KP   R  +RLD++TSG+
Sbjct: 142 IVYEDEDILVIDKQAGMPIHPSLNNYYNSLANALAWYFEQQKKPFIFRCVNRLDRDTSGL 201

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
            ++A+   +A  L+     R I + Y ++V G    +   I   L +K     +      
Sbjct: 202 TIIAKHVVSAAILSSMNARREIHREYRAIVRGHLTPESGVITAPLGRKDSSIIERTVDFD 261

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             EK    A+++++ ++        + ++  TGRTHQ+R+H  ++G P+VGD+ Y  + +
Sbjct: 262 HGEK----AVTYYQFLEE-KNGHSLVSLRLGTGRTHQIRIHMKYIGFPLVGDYLYNPDME 316

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
                    +  LH+  +   HP  G ++  TAPLP  M K  +
Sbjct: 317 ------YITRQALHSYRLTFLHPITGQKMDFTAPLPDDMKKILN 354


>gi|159038967|ref|YP_001538220.1| RluA family pseudouridine synthase [Salinispora arenicola CNS-205]
 gi|157917802|gb|ABV99229.1| pseudouridine synthase, RluA family [Salinispora arenicola CNS-205]
          Length = 314

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 62/210 (29%), Positives = 102/210 (48%), Gaps = 15/210 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           ++Y D  I V NKP G++     G     + G L +    + + G   R  + HRLD  T
Sbjct: 91  VVYADDDIVVVNKPVGVAAHPSPGWSGPTVIGGLAAIGHRIATSGAAERQGVVHRLDVGT 150

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +GI+VVA++  A   L  +F+ R ++K Y ++V G     +  +   + +  H   DY  
Sbjct: 151 TGIMVVAKSEQAYTGLKRAFKYREVEKRYHAVVQGHLDPLRGTVDAPIDRHPH--HDYRW 208

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V     G   +I+H+  ++ F      ++++  TGRTHQ+RVH   +  P VGD  Y A
Sbjct: 209 AVVS---GGKPSITHYDTLEAFPAA-SLVDVRLETGRTHQIRVHFSTLRHPCVGDLTYGA 264

Query: 275 NFKGNFTSPIQ-NKLYLHARYMDLPHPEGG 303
           +      S +  ++ +LHAR +   HP  G
Sbjct: 265 DP--TLASRLGLDRQWLHARELAFRHPRTG 292


>gi|156742179|ref|YP_001432308.1| pseudouridine synthase [Roseiflexus castenholzii DSM 13941]
 gi|156233507|gb|ABU58290.1| pseudouridine synthase [Roseiflexus castenholzii DSM 13941]
          Length = 309

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 70/279 (25%), Positives = 120/279 (43%), Gaps = 35/279 (12%)

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ VR P V   ++  +  Q+  D    + +      +++LYED+ +   +KP    V+
Sbjct: 40  NGRRVRDPDVRLPVDATVVVQRPPD---GIYRDPVVTSAMILYEDADLIALDKPIDTYVE 96

Query: 121 GGSGIAYHIDGFLKSWV-------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                 +  +G L++ +       D       L HRLD++TSG+L++++       L  +
Sbjct: 97  A---TPWDAEGHLRAALAHFLEVRDGSAPPLHLAHRLDRDTSGVLLLSKAPDVNAALQRA 153

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR   ++K Y +L  G+P   +  I     +     G    V    E G   A+     +
Sbjct: 154 FREGAVRKTYLALCAGLPAFDEIEIETGHGRGR---GGVFRVFPHEEIG--RALPQGGTV 208

Query: 234 DCFAQKFCWLE---------MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
                +   +            P TGRTHQ+R+H   +G P++GD KY       +   +
Sbjct: 209 KAMRTRLRVVRRMDDAALACATPLTGRTHQIRLHLAFLGHPLIGDVKYGG--PSTWRGVV 266

Query: 285 QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
               +LHA  ++LPHP  G  L I +P P     TW +L
Sbjct: 267 VQHHHLHAWRLELPHPRSGTALIIESPAP-----TWANL 300


>gi|68250034|ref|YP_249146.1| tRNA pseudouridine synthase C [Haemophilus influenzae 86-028NP]
 gi|145632796|ref|ZP_01788529.1| tRNA pseudouridine synthase C [Haemophilus influenzae 3655]
 gi|229846708|ref|ZP_04466815.1| tRNA pseudouridine synthase C [Haemophilus influenzae 7P49H1]
 gi|68058233|gb|AAX88486.1| tRNA pseudouridine synthase C [Haemophilus influenzae 86-028NP]
 gi|144986452|gb|EDJ93018.1| tRNA pseudouridine synthase C [Haemophilus influenzae 3655]
 gi|229810197|gb|EEP45916.1| tRNA pseudouridine synthase C [Haemophilus influenzae 7P49H1]
          Length = 239

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 58/224 (25%), Positives = 103/224 (45%), Gaps = 17/224 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP G+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPDGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSNSLSFIHPITKEQITITAGL 223


>gi|90412159|ref|ZP_01220165.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum 3TCK]
 gi|90326883|gb|EAS43268.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum 3TCK]
          Length = 228

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/211 (29%), Positives = 97/211 (45%), Gaps = 18/211 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L+++     V NK  G+SV    G    +    K   D   +K  L HRLD+ TSG+L+
Sbjct: 3   TLVHQHPDFLVINKHPGVSVHKDDGDQPLLAEVAKQTGD---EKLYLIHRLDKMTSGLLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R R AA  L+ +F  R ++K Y ++    PK K+  +   + +            K +
Sbjct: 60  LGRNRQAAAELSGNFAKRDVKKFYLAIGTKKPKKKQGVVIGDMSRSRR------SSWKLD 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F        + C+L  +PHTG+THQ+RV    +G  I GD  Y     GN
Sbjct: 114 STKDNPAITQFFSTAAGNGRRCFL-CKPHTGKTHQIRVALRSVGSGITGDEIY-----GN 167

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
             +   ++ YLHA  +  P+    +  I AP
Sbjct: 168 EEA---DRGYLHAYALSFPYKGENQQFICAP 195


>gi|16329580|ref|NP_440308.1| hypothetical protein slr1592 [Synechocystis sp. PCC 6803]
 gi|3915463|sp|P72970|Y1592_SYNY3 RecName: Full=Uncharacterized RNA pseudouridine synthase slr1592;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|1652063|dbj|BAA16988.1| slr1592 [Synechocystis sp. PCC 6803]
          Length = 291

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 74/301 (24%), Positives = 129/301 (42%), Gaps = 35/301 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV---RIPPVINALNHIIKE 80
           ++   Y H      Q+ +  GQ+ VD K V     +Q+GQ +   R P         ++ 
Sbjct: 4   FYSQRYLHSERQAWQERIEQGQIEVDGKTVDPTYPLQAGQTLTYWRSP--------WVEP 55

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDS 139
           +  L  SV             L+ D  ++  +KP+G+ V  G    YH +   LK     
Sbjct: 56  EVPLQLSV-------------LHRDEDLWAIDKPSGLPVLPGGDFVYHTVLEQLKIQYPQ 102

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +   P   HRL   TSG+L++ R+    + L+  FR    +KIY +++      +K    
Sbjct: 103 ESLFP--LHRLGTGTSGLLLLGRSTLGRRELSRQFREHICRKIYRTVIGPCDLPEKFECH 160

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + K  +    Y++    + K A    S+ +++    +K  WLE++  TGR HQ+R+H 
Sbjct: 161 QAIGKIPYPQLGYIYAASSHGKPAQ---SYGRILARSPEK-TWLEVEIRTGRPHQIRIHL 216

Query: 260 LHMGCPIVGDHKYCAN---FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             +G P++GD  Y             P      LH+  +   H    + +++TAPLP  +
Sbjct: 217 ASLGYPLLGDRLYGPGGVPINCRTARPSDGGYTLHSYQLGFLHLHTQQAIKLTAPLPPEL 276

Query: 316 V 316
           +
Sbjct: 277 I 277


>gi|148656758|ref|YP_001276963.1| pseudouridine synthase [Roseiflexus sp. RS-1]
 gi|148568868|gb|ABQ91013.1| pseudouridine synthase [Roseiflexus sp. RS-1]
          Length = 299

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 100/234 (42%), Gaps = 31/234 (13%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-----KGQKP--RLTHRL 150
             ++LYED  +   NKP    V+      +  +G L++ +        G  P   L HRL
Sbjct: 74  PEMILYEDDDLIALNKPIDTYVEA---TPWDAEGHLRAALARFLALRNGTAPPLHLAHRL 130

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+L++++T      L   FR     K Y ++  G+P   +  I           G
Sbjct: 131 DRDTSGVLLISKTPDVNAALQRVFRDGAAHKTYLAICAGLPSFDEIEIET---GHGRGRG 187

Query: 211 DYVHVVKQNEKGANYAI--------SHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHA 259
               V      G             + F+V+   D  A    W    P TGRTHQ+R+H 
Sbjct: 188 GMFRVFPPEAIGRTLPQGGTVKSMRTRFRVVRRLDDAALVRAW----PLTGRTHQIRLHL 243

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
             +G P++GD KY        T    +  +LHA  ++LPHP+ G  L I AP P
Sbjct: 244 AFLGHPLIGDSKYGGLSIWRGTPAFHH--HLHAERLELPHPQSGAPLVIVAPAP 295


>gi|308233940|ref|ZP_07664677.1| pseudouridine synthase, RluA family [Atopobium vaginae DSM 15829]
 gi|328943952|ref|ZP_08241417.1| ribosomal large subunit pseudouridine synthase D [Atopobium vaginae
           DSM 15829]
 gi|327491921|gb|EGF23695.1| ribosomal large subunit pseudouridine synthase D [Atopobium vaginae
           DSM 15829]
          Length = 338

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 68/292 (23%), Positives = 128/292 (43%), Gaps = 29/292 (9%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           +++++V+ N+ +   +  R+       + I   Q+I ++S +    +  +   + YED  
Sbjct: 39  IEQRKVEINDTLALSKSERV----RMGDRICVAQQIDNTSSSHIMPNASIPLDIRYEDDY 94

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-----------KGQKPRLTHRLDQETSG 156
           + V +K  G+      G   H+D  L + + +              +P + HRLD +T+G
Sbjct: 95  LLVISKQTGLVCHPSPG---HVDDTLSNALVAHCGYEHLGLLQGDDRPGIVHRLDMDTTG 151

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V A+     Q L +  R+R   + Y  LV G     +  I   + +      + + + 
Sbjct: 152 LMVAAKDNTTQQALQDLIRLRVFDRRYIVLVQGYVTPDEGTITTGIARSKK---NRLKMC 208

Query: 217 KQNEKGANYAISHFKVIDCFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              +  +  AI+ FK ++ F        +  LE   +TGRTHQ+RVH  ++G  +VGD  
Sbjct: 209 ISKDPASREAITTFKTLERFEAGSKDDGYSLLECHLYTGRTHQIRVHMRYVGHSVVGDPL 268

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y    KG+  +    + +LH+  M   HP     LQ    LP+ + +    L
Sbjct: 269 Y--GRKGDALNQGLQRQFLHSWRMSFDHPITHEHLQFCDKLPSDLSEVLARL 318


>gi|217971508|ref|YP_002356259.1| Rlu family pseudouridine synthase [Shewanella baltica OS223]
 gi|217496643|gb|ACK44836.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS223]
          Length = 230

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 60/201 (29%), Positives = 94/201 (46%), Gaps = 24/201 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++  ++   V +K A +      G A    G +       G K    HRLD  TSG+L++
Sbjct: 4   IIANEADFIVISKSAKVHFHSQDGTA----GVVAQAEQDLGIKLFAVHRLDSPTSGLLIL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA+  TE F   ++QK Y +L  G PK K+  +   + K          +++  E
Sbjct: 60  AKSAVAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIGDMAKSRR---SMFKLLRTKE 116

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  +        +L ++PH+G+THQLRV    +G PI+GD  Y     G  
Sbjct: 117 ---NPAITQFFSLSVSEGLRLYL-LKPHSGKTHQLRVALASLGVPILGDDLY-----GGM 167

Query: 281 TSPIQNKLYLHA-----RYMD 296
            +   ++ YLHA     RY D
Sbjct: 168 AA---DRCYLHAYCLHFRYGD 185


>gi|91204218|emb|CAJ71871.1| similar to pseudouridine synthase C [Candidatus Kuenenia
           stuttgartiensis]
          Length = 274

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 56/212 (26%), Positives = 99/212 (46%), Gaps = 27/212 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D    + +KP GI   G + I    +  L++  +    + +  HRLD++TSG L+ 
Sbjct: 76  ILFNDDCYVIVSKPPGIVTNGQNSI----ERDLRTQFNR--DRIQAVHRLDKDTSGALIF 129

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+   A + + + F+   IQKIY  +V G     K C   + +  S +GG          
Sbjct: 130 AKNENAFEEMKKVFKKHDIQKIYRVIVTG-----KICEPAFTIN-SPVGG---------- 173

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A++H  ++    +   +LE+   TGR HQ+R+H   +G P++G+ +Y      N 
Sbjct: 174 ---QTAVTHITLLKK-GKNTSYLEVATETGRRHQIRIHLASIGHPVIGETEYARKEIENI 229

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
                 +  LHA  +   HP   + + +TAP+
Sbjct: 230 LHREAKRQMLHAHRISFVHPYTKKEISVTAPI 261


>gi|269798694|ref|YP_003312594.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269095323|gb|ACZ25314.1| pseudouridine synthase, RluA family [Veillonella parvula DSM 2008]
          Length = 288

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 114/242 (47%), Gaps = 34/242 (14%)

Query: 42  RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI- 100
           R  Q+   KKRVK N+R+   Q              +K+  +L  ++ L +  D+   + 
Sbjct: 29  RDIQMMFRKKRVKVNSRVAHSQ------------RALKKGDVL--TLELPQDKDYGVDVE 74

Query: 101 -----LLYEDSKIYVFNK-PAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQ 152
                +LYED+   V NK P  +    G   +  +  ++  +   K    K R  HRLD+
Sbjct: 75  KGPITVLYEDAHTLVVNKDPFMLVHPAGQTKSCTLSNYVAGYYAKKNVVHKVRPVHRLDR 134

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG ++  +T+ A Q+ T+  +  RI +IY  LV G         AN ++  + IG D 
Sbjct: 135 DTSGCILFGKTKEAQQYYTDELQAGRIDRIYTGLVEG------RIDANGMV-DAPIGVDP 187

Query: 213 VHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           V   ++  +E G   A + + V+D        L  +  TGRTHQ+RVH  H+G PIVGD 
Sbjct: 188 VFDNRRVIDELGQP-AQTEYIVLDHEGDN-TLLRFKLLTGRTHQIRVHMEHIGHPIVGDA 245

Query: 271 KY 272
            Y
Sbjct: 246 MY 247


>gi|226306673|ref|YP_002766633.1| pseudouridine synthase [Rhodococcus erythropolis PR4]
 gi|226185790|dbj|BAH33894.1| putative pseudouridine synthase [Rhodococcus erythropolis PR4]
          Length = 304

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 60/208 (28%), Positives = 95/208 (45%), Gaps = 13/208 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  I V +KP  + ++  G+ I       L+  +D     P   HRLD+ T+G++V
Sbjct: 90  ILYRDDSILVIDKPHFLATIPRGAHIVESAVVRLRRDLDLPDLAP--VHRLDRMTAGVIV 147

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
              T    +   E F  +RI K Y ++    P+          + K H  G+        
Sbjct: 148 FTVTPDLRRPYQELFAEQRIVKEYEAIAGFDPELTFPRTVRSRINKVH--GEMTATEIDG 205

Query: 220 EKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH---KYCAN 275
           E  +  +I   + I D   +      + P TGRTHQLR+H   +G PIVGD+   +Y   
Sbjct: 206 EPNSETSIELIETITDSAGRTLGRYRLLPRTGRTHQLRLHLNSLGVPIVGDNYYPEYLPA 265

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             G+F++P++    L AR ++ P P  G
Sbjct: 266 VPGDFSTPLR----LLARALEYPDPITG 289


>gi|218701508|ref|YP_002409137.1| tRNA pseudouridine synthase C [Escherichia coli IAI39]
 gi|218371494|emb|CAR19332.1| tRNA pseudouridine synthase [Escherichia coli IAI39]
          Length = 260

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 68/261 (26%), Positives = 114/261 (43%), Gaps = 63/261 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D                Q     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIDQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMEEAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGR 304
           TGR HQLR H  H+  PI+GD K+  + + N +        +L LHA  + L HP  G  
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEP 216

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L I A L    ++     G++
Sbjct: 217 LTIHAGLDDTWMQALSQFGWR 237


>gi|163755084|ref|ZP_02162205.1| ribosomal large subunit pseudouridine synthase D [Kordia algicida
           OT-1]
 gi|161325151|gb|EDP96479.1| ribosomal large subunit pseudouridine synthase D [Kordia algicida
           OT-1]
          Length = 224

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 60/219 (27%), Positives = 104/219 (47%), Gaps = 15/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           +++E+    V NK +G+  +     A  ++  +   +    +KP   + HRLD+ TSG+L
Sbjct: 6   IIHENKDYIVVNKASGLISEKSPYEAVTVEDQVFQHILKSKRKPYVGIIHRLDRVTSGVL 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+ ++      + F  R++QK Y ++V   P   K  + N+L+K +        +V  
Sbjct: 66  ILAKKKSILVAFNKLFSSRKVQKTYLAIVKNKPTKSKGNLVNFLIKNNK--EKKAEIVTT 123

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K A   +  ++VI      +  L ++P TGR HQ+R    ++G PIVGD KY     G
Sbjct: 124 KSKEAQSCMLSYEVIGKNNIGYL-LAVKPKTGRFHQIRAQLANIGLPIVGDSKY-----G 177

Query: 279 NFTSPIQNKLYLHA---RYMDLPHPEGGRLQITAPLPAH 314
           +  S     + LHA    + D+   E    +  A LP H
Sbjct: 178 SDVSYKSLSICLHAWKLTFEDVETKEQKTFE--ASLPNH 214


>gi|325570826|ref|ZP_08146509.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           casseliflavus ATCC 12755]
 gi|325156336|gb|EGC68518.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           casseliflavus ATCC 12755]
          Length = 305

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 111/235 (47%), Gaps = 30/235 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTH---RLDQE 153
           ++YED+ + + NKPAGIS        YH  G +    K++  ++  + ++ H   RLD++
Sbjct: 85  IVYEDAHLLIVNKPAGISSIPAQ---YHPTGTMANRVKAYYQAQHYEDQVIHVVTRLDRD 141

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++ A+   A   L    R +++ K Y +LV G        ++        I  D  
Sbjct: 142 TSGLMLFAKHGFAHAKLDSQLRKKQVVKKYQALVAG----DLSALSAHSEIDLPIARDLT 197

Query: 214 HVVKQ--NEKGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            ++K+  +E+G      ++   +  DC       +++Q HTGRTHQ+RVH   +GCP++G
Sbjct: 198 SLLKRKVSEEGKEARTEYWLKQRNSDC-----ALVDVQLHTGRTHQIRVHFSAIGCPLLG 252

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           D  Y     G     I+ +  LH   +   HP     L    PLPA M     ++
Sbjct: 253 DEMY----GGPMAFGIRRQA-LHCCQLQFQHPFTNEPLAFELPLPADMAAVCSAI 302


>gi|52425225|ref|YP_088362.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52307277|gb|AAU37777.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 217

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 61/214 (28%), Positives = 97/214 (45%), Gaps = 40/214 (18%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQ------GGSGIAYHIDGFLKSWVDSKGQKPR 145
           KH DF+            + +KP G+SV       G +G+        + W         
Sbjct: 9   KHRDFI------------IIDKPNGVSVHRDEAEIGLTGLLAKQLSVAQVW--------- 47

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSG+L++A    +A   +  F    I K Y +L    PK K+  I   + +K
Sbjct: 48  LVHRLDKVTSGLLILALNERSAAEFSLLFARHEISKTYLALSKQKPKKKQGLIIGDM-EK 106

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +  G   +   KQN      A++ F+ + C      ++ ++P TG+THQLRV    +G P
Sbjct: 107 ARRGAWKLCQTKQNP-----AVTRFESVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSP 160

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           I+GD  Y  N + N      ++ YLHA  ++  +
Sbjct: 161 ILGDELYGGNSEKN------DRTYLHAFRLEFTY 188


>gi|229095789|ref|ZP_04226768.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-29]
 gi|228687622|gb|EEL41521.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-29]
          Length = 292

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 69/266 (25%), Positives = 125/266 (46%), Gaps = 28/266 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+  P
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQYASVRHQLQAGEQLRVFFP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYH 128
           V      +I E   L                ++YED  + V NK A +S +         
Sbjct: 63  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPEGS 107

Query: 129 IDGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L S+ D +       +  RLD++TSG++++A+ R     L++  + + +++ Y ++
Sbjct: 108 VANALLSYYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAI 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    ++  I   + +KS    D +      E G   A++HF+VI   +QK   + ++
Sbjct: 168 VHGEMIKREGTIDAPIGRKS----DSIIERTVCEDG-QRAVTHFRVIHSSSQK-THVSLE 221

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
             TGRTHQ+RVH  HMG P++GD  Y
Sbjct: 222 LETGRTHQIRVHMAHMGHPLLGDDLY 247


>gi|127512389|ref|YP_001093586.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126637684|gb|ABO23327.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 217

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 62/205 (30%), Positives = 101/205 (49%), Gaps = 26/205 (12%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           Y+D  I + NKP+G+    G     H   I+  L+ + ++      L HRLD  TSGI+V
Sbjct: 18  YQDRDIIIINKPSGLLSNPGRAAETHDCAINRLLQRFPEAI-----LVHRLDCATSGIMV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + A  HL   F+ R  +K Y + V G+       I   +   S    +   + K  
Sbjct: 73  FALNKKAESHLKTQFQNRTTEKYYVAEVEGLMAQDSGKIELAMKPDS----EQPPLQKIA 128

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E G   A ++F+V++  +     ++++P TGRTHQLR+H   +G  I+GD     +F G+
Sbjct: 129 EDG-KPATTYFEVLERRSNS-TLVKLKPITGRTHQLRLHMKALGHTILGD-----DFYGD 181

Query: 280 ----FTSPIQNKLYLHARYMDLPHP 300
                 +P   +L+LHA ++ + HP
Sbjct: 182 EAIIAAAP---RLHLHAEHLSITHP 203


>gi|288905218|ref|YP_003430440.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
 gi|306831289|ref|ZP_07464449.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus gallolyticus
           subsp. gallolyticus TX20005]
 gi|325978193|ref|YP_004287909.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|288731944|emb|CBI13509.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus gallolyticus UCN34]
 gi|304426525|gb|EFM29637.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus gallolyticus
           subsp. gallolyticus TX20005]
 gi|325178121|emb|CBZ48165.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 296

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 58/205 (28%), Positives = 97/205 (47%), Gaps = 17/205 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGI 157
           + YED    + NKP G +       +  I  F+K +   +    +  H   RLD++TSG+
Sbjct: 78  IAYEDEHFLIINKPHGYASIPSVLHSNTIANFVKHYYLEQNYPNKQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G  +  +K E IA        I    VH 
Sbjct: 138 MLFAKHGYAHARLDKQLQNKTIEKRYYALVSGKGELADKGEIIAPIARSDDSIITRCVH- 196

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                    YA + ++V+  F +    ++++ HTGRTHQ+RVH  H+G P++GD  Y  +
Sbjct: 197 -----PSGKYAHTSYEVVARFGE-VALVDIRLHTGRTHQIRVHFSHIGFPLLGDDMYGGS 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                T     +  LH  Y+   +P
Sbjct: 251 MDYGIT-----RQALHCHYLRFVNP 270


>gi|283835440|ref|ZP_06355181.1| tRNA pseudouridine synthase [Citrobacter youngae ATCC 29220]
 gi|291068616|gb|EFE06725.1| tRNA pseudouridine synthase [Citrobacter youngae ATCC 29220]
          Length = 260

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 105/238 (44%), Gaps = 62/238 (26%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +IQK Y ++V G           WL+  + 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEHHQIQKRYHAIVRG-----------WLMDDAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E+ P 
Sbjct: 100 L--DYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELDPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG 303
           TGR HQLR H  H+  PI+GD K+  + + N ++       +L LHA  ++L HP  G
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSAAEHFGCQRLMLHASQLELIHPFTG 214


>gi|317049313|ref|YP_004116961.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316950930|gb|ADU70405.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 259

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 105/237 (44%), Gaps = 60/237 (25%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKPAG  V              +SW+D K             GQ     
Sbjct: 4   IIYQDEWLVAVNKPAGWLVH-------------RSWLDRKEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +    + L + F   +I+K Y +++ G           WL++   
Sbjct: 51  HRLDRPTSGVLLMGLSSEVGRLLAQQFEQHQIRKTYHAVLRG-----------WLMESGT 99

Query: 208 IGGDYVHVVKQNE---------KGANYAISHFKV---------IDCFAQ-KFCWLEMQPH 248
           +  DY  V + ++         +G   A++ F++         I  +A  ++  +EMQP 
Sbjct: 100 L--DYPLVEELDKIADKFATEPRGPQPAVTDFQMLAHTEMPVAIGRYATARYSLVEMQPR 157

Query: 249 TGRTHQLRVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           TGR HQLR H  H+  PI+GD  H      +G   +   ++L LHA  + L HP  G
Sbjct: 158 TGRKHQLRRHMAHLRHPIIGDTTHGDLRQNRGAAANFGLDRLMLHASALSLNHPVTG 214


>gi|153864749|ref|ZP_01997543.1| pseudouridylate synthase [Beggiatoa sp. SS]
 gi|152145755|gb|EDN72456.1| pseudouridylate synthase [Beggiatoa sp. SS]
          Length = 162

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 56/163 (34%), Positives = 85/163 (52%), Gaps = 7/163 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +YED  + + NKP G++V GGSGI    I+G    + ++   +  L HRLD++TSG L++
Sbjct: 1   MYEDPLLLIINKPTGMAVHGGSGINGGVIEGLRALYPNAPYLE--LVHRLDRDTSGCLMI 58

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+  +  + L    R   I K Y +LV G    +   +   L K     G+   +V+ N 
Sbjct: 59  AKKYSMLRRLHALLREGAIHKQYLALVQGRWDKQTTKVEAPLRKNILQSGE--RIVRVNS 116

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            G + A+S F  I+        L + P TGRTHQ+RVHA + G
Sbjct: 117 DGKS-AVSQFS-IEQRLTTTTLLRVHPLTGRTHQIRVHAAYKG 157


>gi|261838329|gb|ACX98095.1| pseudouridine synthase C [Helicobacter pylori 51]
          Length = 242

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 62/202 (30%), Positives = 99/202 (49%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLLSFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVKKEYLALAQGIIEEEREINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y   
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLY--- 208

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
              N  S    +L LHA  + L
Sbjct: 209 ---NNESSSAKRLMLHAHKIAL 227


>gi|238754814|ref|ZP_04616165.1| tRNA pseudouridine synthase C [Yersinia ruckeri ATCC 29473]
 gi|238706974|gb|EEP99340.1| tRNA pseudouridine synthase C [Yersinia ruckeri ATCC 29473]
          Length = 257

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 99/232 (42%), Gaps = 23/232 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D   Q     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHMVAVNKPAGWLVHRSWLDRNETVFVMQTVRDQIDQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F    ++K+Y ++V G              +   I   +       +
Sbjct: 64  ALSSDVARLLSQQFEQHEVRKVYHAVVRGYVLEDDTLDYALTEELDKIADKF----SSQD 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
           K    A++H++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPKSAVTHYRAMAQAEMPVAIGRYETARYSLMELTPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 270 -HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
            H      +G       ++L LHA ++ L HP  G        P ++   WD
Sbjct: 180 THGDLRQNRGVAQHFDCSRLMLHASHLSLNHPVTGE-------PLNLSARWD 224


>gi|284041381|ref|YP_003391311.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283820674|gb|ADB42512.1| pseudouridine synthase [Spirosoma linguale DSM 74]
          Length = 240

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 104/241 (43%), Gaps = 44/241 (18%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV-------QGGSGI-----AYHIDGFLKSWVDSKGQKP 144
            + ++++E+    + NKP  ++        +GG  I     AYH D              
Sbjct: 5   FEDLIVFENEDYILINKPPHVASLDERTTDRGGQSILRLAKAYHADA------------- 51

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           +L HRLD+ETSGIL +A+   A +HL   F  R + K Y ++  G+  +  E I+ +L  
Sbjct: 52  QLGHRLDKETSGILAIAKNPEAYRHLAMQFEHREVTKRYHAVTNGV--HNFEGISVYLPI 109

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                G  V +    EKG   A + F  +  + +    +E  P TGR HQ+RVH + +  
Sbjct: 110 SPIKDGTAVRI--DREKG-KVAETIFNTLQAY-RTTTLVECMPVTGRMHQIRVHLMCLKA 165

Query: 265 PIVGDHKYCA------------NFK-GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           PIV D  Y              N K G    P+ +++ LHA  +     +G      AP 
Sbjct: 166 PIVNDPTYGGKPVFLSDVKRKFNLKEGTEELPLIHRVALHAHSLTFALLDGEEQTFVAPY 225

Query: 312 P 312
           P
Sbjct: 226 P 226


>gi|111221643|ref|YP_712437.1| pseudouridylate synthase [Frankia alni ACN14a]
 gi|111149175|emb|CAJ60858.1| Pseudouridylate synthase [Frankia alni ACN14a]
          Length = 325

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 110/234 (47%), Gaps = 24/234 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY+D  I V +KP G++     G     + G L +    + + G   R  + HRLD  T
Sbjct: 100 ILYDDDDIVVVDKPPGVAAHPAPGFTGPTVIGALAAAGYRISTSGAAERQGVVHRLDVGT 159

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG +VVA++  A   L  +FR R++ K Y ++V G P      +     +     G +  
Sbjct: 160 SGAMVVAKSERAYTLLKRAFRERQVDKRYRAVVQGHPDPLSGTVDAPTDRHPRRPGLFAV 219

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V          +++H+ +++ F +    L ++  TGRTHQ+RVH   +  P VGD  Y A
Sbjct: 220 VADGKP-----SVTHYDLVEAF-RSASLLSIRLETGRTHQIRVHMSALRHPCVGDLAYGA 273

Query: 275 NFKGNFTSPIQNKL-----YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +        +  +L     +LHA  +   HP  GG ++ T+P PA + +  + L
Sbjct: 274 DPT------LAERLGLTRQWLHAARLSFDHPGHGGPVEFTSPDPADLAEAVERL 321


>gi|307543955|ref|YP_003896434.1| tRNA pseudouridine synthase C [Halomonas elongata DSM 2581]
 gi|307215979|emb|CBV41249.1| tRNA pseudouridine synthase C [Halomonas elongata DSM 2581]
          Length = 256

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 105/236 (44%), Gaps = 21/236 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  +   +KPAG+ V   +         L++  D  GQ+    HRLD+ TSG++V 
Sbjct: 7   ILHHDDHLIAVHKPAGMLVHRSALARGERHFLLQTLRDQIGQRVYPVHRLDRPTSGLMVF 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  L ++F  +R+ K Y ++V G  +  +    ++ L+      D      + E
Sbjct: 67  ALDPEVAGRLADAFATQRVAKRYLAVVRG--QGPEAERLDYALR------DEDGRRPKAE 118

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             A  A +  + +D            + ++  +E +P TGR HQ+R H    G PI+GD 
Sbjct: 119 MPAREARTEVRRLDSVELPVRVDRYPSARYSLMEARPLTGRRHQIRRHLSRRGYPIIGDA 178

Query: 271 KYCANFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
           K+       F +   +  +L L A  +D  HP +G RL +   L A M   +   G
Sbjct: 179 KHGKGVHNRFFAEQLDCPRLLLAAVGLDFEHPVDGRRLTLGCALDAPMTALFQRFG 234


>gi|81428235|ref|YP_395235.1| pseudouridine synthase, 23S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78609877|emb|CAI54924.1| Pseudouridine synthase, 23S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 296

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 86/330 (26%), Positives = 146/330 (44%), Gaps = 62/330 (18%)

Query: 3   LMTYVQYVVVENDEENMR----LDRWF----KNHYPHINFVNLQKILRSGQVRVDKKRVK 54
           ++ Y + V +E D   M     L+ W       H+  IN    ++IL +GQ R       
Sbjct: 1   MIIYQKKVTLETDFSPMSVRGLLNHWLVPQKMQHFLRIN----REILVNGQYRA------ 50

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
           FN  ++ G  +        LN      K+ +  ++ T+        +L+E   + + NKP
Sbjct: 51  FNRNVEPGDEI-------TLNFSEVSVKVQNYELDATQSFS-----VLFESDDLLIVNKP 98

Query: 115 AGISVQ----GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           AGI       G +G   +   F   ++  +G+K  + HR+D+ TSG L++ +T      L
Sbjct: 99  AGIKTHPNRPGENGTLMNQVAF---YLAQQGKKAYMVHRIDEATSGTLLIGKTPIVIGIL 155

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----- 225
                 +++ + Y ++V     + K  +A      S IG D  +     ++  +Y     
Sbjct: 156 NRQLSQKKMARQYIAIV----DDPKHELAEHATINSPIGVDPEN---DRQRCVDYINGLS 208

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           AI+H++V+         L +   TGRTHQ+RVH   +G PI+GD  Y        T+P  
Sbjct: 209 AITHYRVLSRKGAT-AVLAVDLETGRTHQIRVHLASIGHPILGDPLY----NPTDTTP-- 261

Query: 286 NKLYLHA---RYMDLPHPEGGRLQITAPLP 312
            +L LH    RY + P+ +  R  +TAP+P
Sbjct: 262 -RLLLHGQTLRYTE-PYTDQPR-TVTAPVP 288


>gi|196037436|ref|ZP_03104747.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
 gi|196031678|gb|EDX70274.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
          Length = 297

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 142/313 (45%), Gaps = 41/313 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI  P
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 68  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 113 VANALLSHYDKQYLPST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 170 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
            ++  TGRTHQ+RVH  H+G P++GD     N  G     ++ +  LH+  +   HP   
Sbjct: 224 SLELDTGRTHQIRVHMAHIGHPLLGD-----NLYGGKRDEMKRQ-ALHSTSLTFYHPILE 277

Query: 303 GRLQITAPLPAHM 315
             +  TA +P+ M
Sbjct: 278 KEMSFTAMIPSDM 290


>gi|322378406|ref|ZP_08052860.1| RNA pseudouridine synthase [Helicobacter suis HS1]
 gi|322380087|ref|ZP_08054343.1| pseudouridine synthase [Helicobacter suis HS5]
 gi|321147494|gb|EFX42138.1| pseudouridine synthase [Helicobacter suis HS5]
 gi|321149162|gb|EFX43608.1| RNA pseudouridine synthase [Helicobacter suis HS1]
          Length = 342

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 72/269 (26%), Positives = 123/269 (45%), Gaps = 39/269 (14%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLT 147
           LK  +LYED  I V NKP  +++     I+ H +  L  ++ +KG          +  + 
Sbjct: 85  LKIEILYEDEDILVLNKPPYLAMH--PAISLH-EPTLVDYLQAKGVTLSTLSGESRCGIV 141

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--K 205
           HRLD+ TSG +V+A+  A   +L    ++R + + Y +L+   P  K   +   L +  K
Sbjct: 142 HRLDKNTSGAVVIAKNNATHANLATQLQIREMGRYYLALITE-PLKKPMRVECHLGRHPK 200

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           + +    +  ++QN  G  Y+ + F  +   A+    +  + ++GRTHQ+R H   +G  
Sbjct: 201 NRLKMTNLDTLRQNINGGRYSKTDFIPLLSNARGIQLIAAKLYSGRTHQVRAHLESLGRH 260

Query: 266 IVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVK----- 317
           I+GD  Y    N+KG        ++ LHA  + + HP    +L   A +   MV+     
Sbjct: 261 ILGDSLYGKKDNYKG--------RILLHAYLLYMTHPTSQEKLLFKAQILEDMVECLEKE 312

Query: 318 ----TWDSLGFKYDRNLYIKRLYSQDECK 342
                WD L     R  YI  L++   C+
Sbjct: 313 FQGVAWDGL----IRENYILDLFNTTVCE 337


>gi|288934799|ref|YP_003438858.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|288889508|gb|ADC57826.1| pseudouridine synthase [Klebsiella variicola At-22]
          Length = 232

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/209 (30%), Positives = 95/209 (45%), Gaps = 18/209 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LLY+D  + + NKPAG+    G     ++D      V  +     L HRLD  TSG++V+
Sbjct: 19  LLYQDEHLLLINKPAGLLSLSGKD-PRNLDSVHHRLVQ-RFPGCTLVHRLDFGTSGLMVI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +     L + F  R + K+Y +L+ G    + E I    + K       + +  ++ 
Sbjct: 77  ARNKGINALLCQQFSQRTVAKVYTALLCG-HLAEDEGIVEAAIAKVPARFPRMSLCARHG 135

Query: 221 KGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K A    S ++VID   Q            + + P TGRTHQLR+H   +G PI+G   Y
Sbjct: 136 KPAR---SRYRVIDRLYQSRDGERALALTRVALTPETGRTHQLRIHCQLLGYPILGCDLY 192

Query: 273 CA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
                 G   +P   +L LHA  +   HP
Sbjct: 193 GGRELPGTEQAP---RLMLHASELRFVHP 218


>gi|271499489|ref|YP_003332514.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270343044|gb|ACZ75809.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 261

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 101/227 (44%), Gaps = 46/227 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKP+G  V              +SW+D K             GQ     
Sbjct: 4   IVYQDEHLIAVNKPSGWLVH-------------RSWLDRKEKVVVMQTVRDQIGQHVFTV 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++A +   A+ L + F   +++K+Y ++V G   +  + + ++ L +  
Sbjct: 51  HRLDRPTSGVLLMALSSDVARLLAQQFEQHQMEKMYHAVVRGYVMD--DGVIDYALTEEL 108

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQL 255
             I   Y       +K    A+SH++V+               ++  LE+ P TGR HQL
Sbjct: 109 DRIADKYA----DPDKAPQPAVSHYRVLAHAELPVAIGRYDTARYSLLELTPKTGRKHQL 164

Query: 256 RVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           R H  H+  PI+GD  H      +G        +L LHA  + L HP
Sbjct: 165 RRHMAHLRHPIIGDTTHGDLRQNRGMAAHFGCARLMLHASQLSLIHP 211


>gi|184156035|ref|YP_001844375.1| pseudouridylate synthase [Lactobacillus fermentum IFO 3956]
 gi|183227379|dbj|BAG27895.1| pseudouridylate synthase [Lactobacillus fermentum IFO 3956]
          Length = 294

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 70/290 (24%), Positives = 124/290 (42%), Gaps = 42/290 (14%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           +G+ +VD +RV+   +I   Q     P+   +     +  +  S   LT         ++
Sbjct: 36  AGEFQVDHRRVRPTTKILPNQ-----PLTLTVQPEPGDATVATSEEPLT---------IV 81

Query: 103 YEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED    V NKP G++   G       I   + G+L +  D+   +P L  RLD++T+G+
Sbjct: 82  YEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLVA-KDAPDLRPHLITRLDRDTAGL 140

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+   A+  ++       +QK Y ++V G           +      I      +  
Sbjct: 141 LLVAKHNVASSMISPQVEGHTMQKEYRAIVAG----------TFATDHGFIDAPIARIKG 190

Query: 218 QNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           Q E+  N A    K  + +A++    +  + ++ H+GRTHQ+RVH   +G P++GDH Y 
Sbjct: 191 QIEREVNPAGQPAKT-EYWAEESRGDWTLVRLRLHSGRTHQIRVHMASVGHPLLGDHLYG 249

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            +        + +   L+A ++    P     L     +P      WD L
Sbjct: 250 GDLS------MTDHQALYASHLAFTDPFTQTNLAFEVEMPVAFKTLWDGL 293


>gi|152970825|ref|YP_001335934.1| putative ribosomal large subunit pseudouridine synthase A
           [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
 gi|150955674|gb|ABR77704.1| putative ribosomal large subunit pseudouridine synthase A
           [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
          Length = 263

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/209 (30%), Positives = 95/209 (45%), Gaps = 18/209 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LLY+D  + + NKPAG+    G     ++D      V  +     L HRLD  TSG++V+
Sbjct: 50  LLYQDEHLVLINKPAGLLSLSGKD-PRNLDSVHHRLVQ-RYPGCTLVHRLDFGTSGLMVI 107

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +     L + F  R + K+Y +L+ G    + E I    + K       + +  ++ 
Sbjct: 108 ARNKGINALLCQQFSQRTVDKVYTALLCGH-LAEDEGIVEAAIAKDPARFPRMALCARHG 166

Query: 221 KGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K A    S ++VID   Q            + + P TGRTHQLR+H   +G PI+G   Y
Sbjct: 167 KPAR---SRYRVIDRLYQAREGERALALTRVTLTPETGRTHQLRIHCQLLGYPILGCDLY 223

Query: 273 CA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
                 G   +P   +L LHA  +   HP
Sbjct: 224 GGRELPGTEQAP---RLMLHASELRFVHP 249


>gi|329964802|ref|ZP_08301825.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
 gi|328524653|gb|EGF51716.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
          Length = 303

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 108/226 (47%), Gaps = 21/226 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 88  IVYEDAYIIVIEKMQGLLSVNTERQKERTAYTI---LNEYVQRSGRQHRVYIVHRLDRDT 144

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L + +      + Y ++V G  +     +++WL  +      YV+
Sbjct: 145 SGLMMFAKDEKTQNTLRDHWHDIVFDRRYVAVVAGEMEKNVGSVSSWLTDRKL----YVY 200

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++ G   AI+H++ I   A  +  +E+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 201 SSPIDD-GGKEAITHYRTIKR-ANGYSLVELNLETGRKNQIRVHMQDLGHPIIGDGRYGL 258

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
                  +PI  +L LHA  +   HP  G  +    P PA   K +
Sbjct: 259 ----EEVNPI-GRLALHAFKLCFDHPVTGESMHFETPYPADFKKLF 299


>gi|254229275|ref|ZP_04922693.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262393167|ref|YP_003285021.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. Ex25]
 gi|151938199|gb|EDN57039.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262336761|gb|ACY50556.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. Ex25]
          Length = 250

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/221 (28%), Positives = 98/221 (44%), Gaps = 38/221 (17%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +++ED  I   NKP+G+ SV G   +A H D     W   K   P +   HRLD  TSG+
Sbjct: 16  IVFEDDDILAVNKPSGLLSVPGR--LAEHYDSM---WSRLKEVHPEIQVVHRLDMSTSGL 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANW--------LLK 204
           +++A+ + + + L + F+ R   K+Y++ VWG  + ++       I +W           
Sbjct: 71  MLLAKNKPSERALKKQFQYRLTHKVYYARVWGHVEPQEGNIDLPLICDWPNRPRQKVCFD 130

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                     VVK+         +H  V+           + P TGR+HQLRVH + +G 
Sbjct: 131 DGKPSQTLFQVVKREVHSDG---THTTVV----------RLLPITGRSHQLRVHLMAIGH 177

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            IVGD  Y       F+     +L LHA  +   HP   +L
Sbjct: 178 AIVGDEFYATEEAYQFS----ERLELHAAELSFYHPATDQL 214


>gi|225021946|ref|ZP_03711138.1| hypothetical protein CORMATOL_01978 [Corynebacterium matruchotii
           ATCC 33806]
 gi|305681500|ref|ZP_07404307.1| pseudouridine synthase, RluA family [Corynebacterium matruchotii
           ATCC 14266]
 gi|224945232|gb|EEG26441.1| hypothetical protein CORMATOL_01978 [Corynebacterium matruchotii
           ATCC 33806]
 gi|305659705|gb|EFM49205.1| pseudouridine synthase, RluA family [Corynebacterium matruchotii
           ATCC 14266]
          Length = 310

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 79/305 (25%), Positives = 135/305 (44%), Gaps = 28/305 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +MR+D      +     V+   +   G V +D K    +++I  G  + +         +
Sbjct: 16  DMRVDVALSKLFGLSRTVS-ADLATKGDVLIDGKPATKSDKITDGAWLEV--------LL 66

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW 136
            + QK L  +  L    D L+  +LY D  +   +KP G++     G     + G L + 
Sbjct: 67  PEPQKPLVPTEELV---DGLE--ILYADEDLIAVDKPVGVAAHPTVGWDGPTVVGGLAAA 121

Query: 137 ---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
              + + G   R  +  RLD  TSG++VVA +      L  +F+ R + K Y +LV G  
Sbjct: 122 GYRISTSGPPERNGIVQRLDVGTSGVMVVAASERGYSVLKRAFKERTVSKTYHALVQGHM 181

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   + +  H    +   V  + K   +A++H++ ++ F      LE+   TGR
Sbjct: 182 DPLAGTIEANIGR--HPSSGWKFAVTSDGK---HAVTHYETLEAFVAA-SLLEVHLETGR 235

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH   +  P  GD  Y A+ + +    + N+ +LHA  +   HP  GR L+I +P
Sbjct: 236 THQIRVHMSALHHPCCGDPMYGADPQLSARLGL-NRQWLHAVKLGFYHPADGRWLEIESP 294

Query: 311 LPAHM 315
            P  +
Sbjct: 295 YPPDL 299


>gi|300770686|ref|ZP_07080565.1| tRNA pseudouridine synthase C [Sphingobacterium spiritivorum ATCC
           33861]
 gi|300763162|gb|EFK59979.1| tRNA pseudouridine synthase C [Sphingobacterium spiritivorum ATCC
           33861]
          Length = 230

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 105/228 (46%), Gaps = 36/228 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL-THRLDQETSGILV 159
           +LY+D +I   NKP G+ V   S IA     F    +  + Q+     HRLD++T GIL+
Sbjct: 4   ILYQDQEIVAINKPHGLLVHR-SPIARDASEFALQLLRDQLQQRVYPAHRLDRKTGGILL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            + T+   + L + F+ R++ K Y ++V G  ++  +   N+ LKK             +
Sbjct: 63  FSLTKEMDKSLQQLFQDRKMNKSYLAVVRGYTEDDGQI--NYPLKK-------------D 107

Query: 220 EKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++H+K +          +    ++  +E  P TGR HQLR H  H+  PI+GD
Sbjct: 108 NGEEQEALTHYKTLSRSEIDLPTGNFTTSRYSLVEANPETGRMHQLRKHFAHIFHPILGD 167

Query: 270 HKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPL 311
             +  N     +K  F     + + LHA  +   HP  G +  I APL
Sbjct: 168 RPHGCNKQNKLWKERFE---MDTMMLHASQLSFEHPTTGNIVHIKAPL 212


>gi|227515440|ref|ZP_03945489.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus fermentum
           ATCC 14931]
 gi|227086199|gb|EEI21511.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus fermentum
           ATCC 14931]
          Length = 294

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 70/290 (24%), Positives = 126/290 (43%), Gaps = 42/290 (14%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           +G+ +VD +RV+   +I   Q     P+   +     +  +  S   LT         ++
Sbjct: 36  AGEFQVDHRRVRPTTKILPNQ-----PLTLTVQPEPGDATVATSEEPLT---------IV 81

Query: 103 YEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED    V NKP G++   G       I   + G+L +  D+   +P L  RLD++T+G+
Sbjct: 82  YEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLVA-KDAPDLRPHLITRLDRDTAGL 140

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+   A+  ++       +QK Y ++V G    +   I   + +          +  
Sbjct: 141 LLVAKHNVASSMISPQVEGHTMQKEYRAIVAGTFAKEHGIIDTPIAR----------IKG 190

Query: 218 QNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           Q E+  N A    K  + +A++    +  + ++ H+GRTHQ+RVH   +G P++GDH Y 
Sbjct: 191 QIEREVNPAGQPAKT-EYWAEESRGDWTLVRLRLHSGRTHQIRVHMASVGHPLLGDHLYG 249

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            +        + +   L+A ++    P     L     +P      WD L
Sbjct: 250 GDLS------VTDHQALYASHLAFTDPFTQTNLAFDVEMPVAFKTLWDGL 293


>gi|75909345|ref|YP_323641.1| pseudouridine synthase [Anabaena variabilis ATCC 29413]
 gi|75703070|gb|ABA22746.1| Pseudouridine synthase [Anabaena variabilis ATCC 29413]
          Length = 549

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 105/234 (44%), Gaps = 51/234 (21%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           ++YED  +   NKPAG+    G       D  L        Q+  L   HRLDQ+TSGIL
Sbjct: 344 VIYEDEWLIAVNKPAGLLSVPGRYFDTQ-DSVLSRLRRLLTQETMLAAVHRLDQDTSGIL 402

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSL---------------VWGIPKNKKECIANWLL 203
           ++AR R   + L++ F+ R++ K+Y ++               +WG P+N+     +W  
Sbjct: 403 LLARDRQTYRQLSQQFQQRQVHKVYEAILAGVVSTETGIIDLPLWGDPENRPYQQVDWQR 462

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
            K                    ++++F+ I      +  +E  P TGRTHQLRVHA    
Sbjct: 463 GKP-------------------SVTNFRAI-AREGDYTRVEFVPLTGRTHQLRVHASDVQ 502

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAPL 311
            +G  I+GD  Y    K        N+L+LHAR +   HP  G+   LQ+  P 
Sbjct: 503 GLGVVILGDRFYGCTAKA-------NRLHLHARELCFLHPHSGKIIHLQVKTPF 549


>gi|110639414|ref|YP_679623.1| pseudouridylate synthase [Cytophaga hutchinsonii ATCC 33406]
 gi|110282095|gb|ABG60281.1| pseudouridylate synthase [Cytophaga hutchinsonii ATCC 33406]
          Length = 240

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 105/232 (45%), Gaps = 28/232 (12%)

Query: 97  LKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQET 154
           +K ++++E+   +  NKP  IS +   +G A  I    K  W D+     +L HR+D+ET
Sbjct: 6   IKDLIIFENDDYFFINKPPFISSLDERTGGAPSIIRMAKEYWPDA-----QLCHRIDKET 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L VA+  AA +HL+ +F  R + K Y ++V G   +  + +  +L       G    
Sbjct: 61  SGVLAVAKNPAAYRHLSMAFESRNVTKEYHAVVNGT--HDLDGVDVYLPILVLPTG---- 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            VK ++     A + F  I  + +K   +   P TGR HQ+R+H   +G  IVGD  Y  
Sbjct: 115 TVKIDKSKGKLAETIFFTIQAY-KKATLVRCLPITGRMHQIRIHLATLGASIVGDETYGG 173

Query: 275 -------------NFKGNFTS-PIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                        N K +    P+  +  LHA  +         L I AP P
Sbjct: 174 KPLFLSEIKRKKFNLKKDSEERPLIQRFALHANSLIFTDMNEQILDIKAPYP 225


>gi|297379941|gb|ADI34828.1| pseudouridine synthase, RluA family [Helicobacter pylori v225d]
          Length = 327

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 106/229 (46%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLELKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++ +
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLEYF 302


>gi|320157974|ref|YP_004190352.1| pseudouridylate synthase 23S RNA-specific [Vibrio vulnificus
           MO6-24/O]
 gi|319933286|gb|ADV88149.1| pseudouridylate synthase 23S RNA-specific [Vibrio vulnificus
           MO6-24/O]
          Length = 565

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 67/205 (32%), Positives = 102/205 (49%), Gaps = 22/205 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V NKP+G+    G  I       L++ + D +G  P + HRLD  TSG+LV
Sbjct: 364 IVYQDEAMVVVNKPSGLLSVPGKTITDSAYTRLQALFPDVEG--PFVIHRLDMATSGLLV 421

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            A TR A + L + F  R +QK Y +L+ G + +++ E      L       D    +  
Sbjct: 422 FALTRRANKSLQKQFISRGVQKRYVALLEGEVSQSQGEIT----LPMRGDPDDRPRQLVC 477

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
            E G   A + +++I+    +   L + P TGRTHQLRVH  H   +  P+VGD  Y   
Sbjct: 478 FEHG-KPAHTDWQLIETRDGR-SKLYLYPRTGRTHQLRVHCAHHLGLNMPMVGDGLYGEK 535

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                     N+L+LHA  ++L HP
Sbjct: 536 ---------ANRLHLHAESLELDHP 551


>gi|308182904|ref|YP_003927031.1| hypothetical protein HPPC_03775 [Helicobacter pylori PeCan4]
 gi|308065089|gb|ADO06981.1| hypothetical protein HPPC_03775 [Helicobacter pylori PeCan4]
          Length = 327

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 55/229 (24%), Positives = 106/229 (46%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLEFKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+RVH  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRVHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           Y  N         + ++ LHA  ++  HP    +L    PL   M++ +
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLCFKVPLLKDMLEYF 302


>gi|253701860|ref|YP_003023049.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251776710|gb|ACT19291.1| pseudouridine synthase, RluA family [Geobacter sp. M21]
          Length = 302

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 77/307 (25%), Positives = 135/307 (43%), Gaps = 55/307 (17%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D + +N  P   F  L+K++ SG V+V+       + +++ Q+++             
Sbjct: 14  RMDSFMRNLLPTAQFSYLKKLISSGHVKVN------GSSVEAAQLLKY-----------A 56

Query: 80  EQKILDSSVNLTKHSDFLKSI-----LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFL 133
           +Q  L  S   +K + FL  +     +L+EDS I   NK  G+SV +       ++    
Sbjct: 57  DQVTLKES---SKTAAFLARLTPELDILFEDSWIISLNKAPGLSVHRTEDPDEVNLVDLA 113

Query: 134 KSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           ++ +  +    RL   +RLD+ TSG +++A++  AA    +  +   + K+Y +LV G  
Sbjct: 114 ETLLQKRDGVGRLRPVNRLDKGTSGAIILAKSAVAAGMFGKMVQEEGLGKLYLALVEG-- 171

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K +K+ + +  L                  G     S+ ++          L + P TGR
Sbjct: 172 KLQKQGVIDAPL-----------------DGKESQTSYLRLF--HGGGVSLLAVYPITGR 212

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
            HQ+R H   +G PI+GD +Y       FT        LH+    L HP  G  + I AP
Sbjct: 213 MHQIRQHFKMIGHPILGDKRYGGRALTGFTGHA-----LHSFKTTLVHPATGEEVNIPAP 267

Query: 311 LPAHMVK 317
           LP  +++
Sbjct: 268 LPEQLMR 274


>gi|160936866|ref|ZP_02084231.1| hypothetical protein CLOBOL_01755 [Clostridium bolteae ATCC
           BAA-613]
 gi|158440247|gb|EDP17993.1| hypothetical protein CLOBOL_01755 [Clostridium bolteae ATCC
           BAA-613]
          Length = 274

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 67/276 (24%), Positives = 123/276 (44%), Gaps = 43/276 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD------------SKGQKP--RL 146
           +LYED  I V  KPAG+  Q   G A  +   ++ ++             S  Q P   +
Sbjct: 4   ILYEDKDIIVVQKPAGLESQVSRGFAPDMVSEIRRYLHNPQDIHNHPQGVSTAQPPYVGV 63

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+   GI+V A  + +A  L+ + +  +I+K Y ++V G P +K+    ++L    
Sbjct: 64  IHRLDKPVEGIMVYALNQKSAASLSAALQAGKIKKSYLAVVCGKPVDKQGTYVDYLRHCK 123

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCF------AQKFCWLEMQPHTGRTHQLRVHAL 260
               +   +V ++++ +  A+ +++V++         Q    ++++  TGR HQ+RV   
Sbjct: 124 E--NNTSKIVDKSDENSKKAVLNYRVLEVINNPKNQEQILSLIDIELLTGRHHQIRVQFA 181

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNK-------------LYLHARYMDLPHPEGGRLQI 307
               P+ GD +Y        T+   ++             L L AR +  PHP  G++  
Sbjct: 182 GHATPLYGDERYGGGLSTKSTTMTVDRGRKKSSFGDAHRPLALCARRLAFPHPSTGKI-- 239

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQ 343
              +   MV +  +  +  DR    ++L SQ EC +
Sbjct: 240 ---MEFSMVPSSGAFAWFPDR---ARKLISQSECDK 269


>gi|327395022|dbj|BAK12444.1| tRNA pseudouridine synthase C TruC [Pantoea ananatis AJ13355]
          Length = 259

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 108/239 (45%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           ++Y+D+ +   NKPAG  V   S +  H   F+   V D  GQ     HRLD+ TSG+L+
Sbjct: 4   IIYQDAWLVAVNKPAGWLVHR-SWLDRHETQFVMQTVRDQIGQHVFTAHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +  +    + L++ F   +++K Y ++V G  + +       + +   I   +V     +
Sbjct: 63  MGLSSEVGRLLSQQFEHHQMEKTYHAVVRGWLEGRDRLDYPLVEELDKIADKFV----SD 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +    A++ +  +               ++  +E++P TGR HQLR H  H+  PI+GD
Sbjct: 119 PRAPQPAVTDYASLATVEMPVAVSRYPTARYSLIELKPKTGRKHQLRRHMSHLRHPIIGD 178

Query: 270 --HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
             H      +G       N+L LHA  + L HP  G  L I A L     +  D  G++
Sbjct: 179 SAHGDLRQNRGAAAHFGANRLMLHASSLSLSHPVTGEPLVIRAGLDLVWQRVMDQFGWQ 237


>gi|260662712|ref|ZP_05863606.1| pseudouridylate synthase [Lactobacillus fermentum 28-3-CHN]
 gi|260552793|gb|EEX25792.1| pseudouridylate synthase [Lactobacillus fermentum 28-3-CHN]
          Length = 294

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 72/292 (24%), Positives = 125/292 (42%), Gaps = 46/292 (15%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           +G+ +VD +RV+   +I   Q     P+   +     +  +  S   LT         ++
Sbjct: 36  AGEFQVDHRRVRPTTKILPNQ-----PLTLTVQPEPGDATVATSEEPLT---------IV 81

Query: 103 YEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED    V NKP G++   G       I   + G+L +  D+   +P L  RLD++T+G+
Sbjct: 82  YEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLVA-KDAPDLRPHLITRLDRDTAGL 140

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH--IGGDYVHV 215
           L+VA+   A+  ++       +QK Y ++V G               K H  I      +
Sbjct: 141 LLVAKHNVASSMISPQVEGHTMQKEYRAIVAGT------------FAKEHGIIDAPIARI 188

Query: 216 VKQNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             Q E+  N A    K  + +A++    +  + ++ H+GRTHQ+RVH   +G P++GDH 
Sbjct: 189 KGQIEREVNPAGQPAKT-EYWAEESRGDWTLVRLRLHSGRTHQIRVHMASVGHPLLGDHL 247

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y  +        + +   L+A ++    P     L     +P      WD L
Sbjct: 248 YGGDLS------MTDHQALYASHLAFTDPFTQTNLAFDVEMPVAFKTLWDGL 293


>gi|84387506|ref|ZP_00990524.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           splendidus 12B01]
 gi|84377554|gb|EAP94419.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           splendidus 12B01]
          Length = 570

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 104/207 (50%), Gaps = 26/207 (12%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D  I V +KPAG +SV G +          +   D +G  P + HRLD  TSGIL+
Sbjct: 369 ILFQDDHIVVVHKPAGFLSVPGKTIKDSAYTRVQEMHQDVEG--PFVIHRLDMATSGILI 426

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A TR A + L + F  R ++K Y +++ G+ +  +  +      +  + GD     +Q 
Sbjct: 427 FALTRRANKSLQKQFITREVEKRYVAMIEGVLEQDEGYV------RLPLRGDLYDRPRQI 480

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
              E G   A + ++VI+   Q    + + P TGRTHQLRVH  H   +  PIVGD  Y 
Sbjct: 481 VCFEHGKP-AETKWEVIER-NQDTTKVYLHPKTGRTHQLRVHCSHEEGLNMPIVGDGLY- 537

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
               GN      ++L+LHA  + L HP
Sbjct: 538 ----GNKA----DRLHLHAERLALHHP 556


>gi|228932580|ref|ZP_04095460.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar andalousiensis BGSC 4AW1]
 gi|228827098|gb|EEM72852.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar andalousiensis BGSC 4AW1]
          Length = 292

 Score = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 70/269 (26%), Positives = 126/269 (46%), Gaps = 34/269 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI  P
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 63  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 107

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 108 VANALLSHYDKQYLAST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 164

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 165 EAIVHGEMVEREGTIGAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++  TGRTHQ+RVH  H+G P++GD+ Y
Sbjct: 219 SLELDTGRTHQIRVHMAHIGHPLLGDNLY 247


>gi|317014156|gb|ADU81592.1| hypothetical protein HPGAM_03855 [Helicobacter pylori Gambia94/24]
          Length = 327

 Score = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 106/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W+ S+       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVVHKAPSVK---EPTLVDWLKSQNYELSNLGLKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFISLLTSQNGMDLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N      S  + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN---GALSKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|227326531|ref|ZP_03830555.1| tRNA pseudouridine synthase C [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 262

 Score = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 63/248 (25%), Positives = 111/248 (44%), Gaps = 53/248 (21%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKP+G  V              +SW+D K             GQ     
Sbjct: 4   IIYQDEHLVAVNKPSGWLVH-------------RSWLDRKEKVVVMQTVRDQIGQHVYTV 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++A +   A+ L++ F   ++QK Y ++V G   +  + + ++ L +  
Sbjct: 51  HRLDRPTSGVLLLALSSEVARALSQQFESHQMQKTYHAVVRGYVLD--DGVIDYALTEEL 108

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQL 255
             I   + +     +K    A++H++ +               ++  +E++P TGR HQL
Sbjct: 109 DKIADKFTN----PDKAPQPAVTHYRSLAQAEMPVAIGRYPTARYSLMELKPQTGRKHQL 164

Query: 256 RVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           R H  H+  PI+GD  H    + +G  +     +L LHA  + L HP  G+       P 
Sbjct: 165 RRHMTHIHHPIIGDTAHGDLRHNRGMESYFSCGRLMLHASELQLNHPVSGQ-------PL 217

Query: 314 HMVKTWDS 321
            +   WD+
Sbjct: 218 TLQARWDA 225


>gi|168236011|ref|ZP_02661069.1| tRNA pseudouridine synthase C (tRNA-uridine isomerase C)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
 gi|194734776|ref|YP_002115916.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|194710278|gb|ACF89499.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197290820|gb|EDY30174.1| tRNA pseudouridine synthase C (tRNA-uridine isomerase C)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
          Length = 260

 Score = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 109/239 (45%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDQWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +     + +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFA----RED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+  + + N ++       +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KH-GDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLMIQAGLDETWMQALTQFGWR 237


>gi|152971656|ref|YP_001336765.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238896253|ref|YP_002920989.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae NTUH-K2044]
 gi|262041533|ref|ZP_06014730.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|330012185|ref|ZP_08307318.1| RNA pseudouridine synthase [Klebsiella sp. MS 92-3]
 gi|150956505|gb|ABR78535.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae MGH
           78578]
 gi|238548571|dbj|BAH64922.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae
           NTUH-K2044]
 gi|259041094|gb|EEW42168.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|328533887|gb|EGF60555.1| RNA pseudouridine synthase [Klebsiella sp. MS 92-3]
          Length = 264

 Score = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 108/238 (45%), Gaps = 62/238 (26%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   IIYQDDWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L + F   +I+K Y ++V G           WL++++ 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIRKRYHAIVRG-----------WLMEEAL 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         + +KG   A++H++ +               ++  +E++P 
Sbjct: 100 L--DYPLVEELDRIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTSRYGLVELEPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG 303
           TGR HQLR H  H+  PI+GD K+  + + N ++      ++L LHA  + L HP  G
Sbjct: 158 TGRKHQLRRHLAHLRHPILGDSKH-GDLRQNRSAAEHFGCHRLMLHASELSLTHPFTG 214


>gi|157368974|ref|YP_001476963.1| pseudouridine synthase [Serratia proteamaculans 568]
 gi|157320738|gb|ABV39835.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 216

 Score = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 63/200 (31%), Positives = 95/200 (47%), Gaps = 10/200 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G           +   D    +    HRLD  TSG++VV
Sbjct: 13  ILYQDEHIMVVNKPSGLLSVPGRAPENKDSLMTRILADHPAAE--SVHRLDMATSGVIVV 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +AA + L   FR R  +K Y + V G  ++  E + +  L           V  +  
Sbjct: 71  ALNKAAERELKRQFRDREPKKSYIARVSGHLEHD-EGLVDLPLICDWPNRPLQKVCFETG 129

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K A    + + V+   A     +++ P TGR+HQLRVH L +G PI+GD  Y A  +   
Sbjct: 130 KAAQ---TEYLVLSRDADGSTRVKLMPITGRSHQLRVHMLALGHPILGDGFY-APPEVKA 185

Query: 281 TSPIQNKLYLHARYMDLPHP 300
            +P   +L LHA+ + + HP
Sbjct: 186 MAP---RLQLHAQELRITHP 202


>gi|308813053|ref|XP_003083833.1| pseudouridine synthase family protein (ISS) [Ostreococcus tauri]
 gi|116055715|emb|CAL57800.1| pseudouridine synthase family protein (ISS) [Ostreococcus tauri]
          Length = 476

 Score = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 78/322 (24%), Positives = 124/322 (38%), Gaps = 101/322 (31%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L++ + Y D  + V +KP+G++   G+G    +     +      + P + HRLD++TSG
Sbjct: 155 LRARVRYRDEHVVVVDKPSGLATVPGAGNEVSVYDLRHTL-----EAPYVVHRLDRDTSG 209

Query: 157 ILVVARTRAAAQHLTESFRMR------------------------RIQKIYWSLVWGIPK 192
           +LV+ART  AA  L   F+ +                         IQ+ YW++    P 
Sbjct: 210 VLVLARTSFAANKLNAMFQRKSKTDFAAVLRAEMELGKAPRYDDSEIQRTYWAICANPP- 268

Query: 193 NKKECIANWL---LKKSHIG---GDYVHVV--------------------------KQNE 220
             +  +  W+   L  +  G   GD V +V                          K+  
Sbjct: 269 -PRGTLEGWIDAPLADTDEGDGRGDNVRLVGGWRVYDVQNGDVIVGAGEQEFARVNKEEN 327

Query: 221 KGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYC----- 273
             +  A + FKV+          LE+ P TGR HQLRVH +  +  PIVGD+KY      
Sbjct: 328 VSSRAATTRFKVLASAGDDGPTLLELVPITGRKHQLRVHLSKALSSPIVGDYKYGFTDKQ 387

Query: 274 ----ANF--------------------------KGNFTSPIQNKLYLHARYMDLPHPEGG 303
               A F                          + +     +  L+LHA  +   HPEG 
Sbjct: 388 KPWRARFAEIERLERERASSAAADRDDVWRALRRDSLRGASKLPLHLHAHSIKFSHPEGD 447

Query: 304 R-LQITAPLPAHMVKTWDSLGF 324
           R +++ A  P+  V+  D+ G 
Sbjct: 448 RSVRVVAEPPSSFVQALDAFGL 469


>gi|88705946|ref|ZP_01103654.1| ribosomal large subunit pseudouridine synthase A [Congregibacter
           litoralis KT71]
 gi|88699660|gb|EAQ96771.1| ribosomal large subunit pseudouridine synthase A [Congregibacter
           litoralis KT71]
          Length = 233

 Score = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 54/161 (33%), Positives = 80/161 (49%), Gaps = 13/161 (8%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD +TSGI++VAR +     L+  F+ R + K Y + V G   + +  I      +
Sbjct: 74  VVHRLDLDTSGIMMVARGKTTQGALSRLFQERAVDKRYRAWVAGSVSDDEGKI------E 127

Query: 206 SHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
             I  D+ +   Q    +    ++++FKV+D        LE+QP TGRTHQLR+H   MG
Sbjct: 128 LPIARDWENRPLQKICAETGKKSLTYFKVLD-RQNGNSLLELQPATGRTHQLRIHCREMG 186

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            PI+G    C  +          +L LHA  +  PHP  GR
Sbjct: 187 HPILG----CDMYAPPAVLGAAPRLMLHATRIAFPHPVSGR 223


>gi|319949599|ref|ZP_08023642.1| pseudouridine synthase, RluA family protein [Dietzia cinnamea P4]
 gi|319436736|gb|EFV91813.1| pseudouridine synthase, RluA family protein [Dietzia cinnamea P4]
          Length = 308

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 108/237 (45%), Gaps = 30/237 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           ++Y D+ I V +KP G++     G     + G L +    + + G   R  + HRLD  T
Sbjct: 84  VVYSDADIVVVDKPVGVAAHASVGWTGPTVIGGLAAAGYRISTSGPPERKGIVHRLDVGT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA +  A   L  +FR R + K Y +LV G P      I   + +  H   D+  
Sbjct: 144 SGLMVVAASERAYTLLKRAFRDRTVDKTYHALVQGHPDPLSGTIDAPIGR--HTSNDWRF 201

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH--ALHMGCPIVGDHKY 272
            V  + K    +I+H+  ++   Q    +E++  TGRTHQ+RVH  ALH  C   GD  Y
Sbjct: 202 AVISDGK---PSITHYDTLEAH-QAATLVEVKLETGRTHQIRVHFSALHHPC--AGDLTY 255

Query: 273 CANFKGNFTSPI------QNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            A+       P+        + +LHA  +   HP  G R+   +  P  +    D L
Sbjct: 256 GAD-------PVLARRLGLERQWLHAVGLGFEHPGTGARVDFESRYPDDLQHAIDVL 305


>gi|269959540|ref|ZP_06173922.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
 gi|269835727|gb|EEZ89804.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
          Length = 559

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 67/204 (32%), Positives = 100/204 (49%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           +L++D  + + NKP+G+    G  I       L++ + D +G  P + HRLD  TSGILV
Sbjct: 358 ILFQDEAMVIVNKPSGLLSVPGKTIKDSAYTRLQTMFPDVEG--PFVIHRLDMATSGILV 415

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A T+ A + L + F  R +QK Y + + G+   K E   +  ++          V  ++
Sbjct: 416 FALTKRANKSLQKQFITRGVQKRYMAQLEGV-LTKPEGEISLPMRGDPDDRPRQLVCFEH 474

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHKYCANF 276
            K A       +V D  ++ +    M P TGRTHQLRVH A HMG    +VGD  Y    
Sbjct: 475 GKPAETYWQLIEVKDGRSKVY----MYPKTGRTHQLRVHSAHHMGLNMAMVGDGLYGEK- 529

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                    N+L+LHA  ++L HP
Sbjct: 530 --------ANRLHLHAEMLELDHP 545


>gi|119476781|ref|ZP_01617091.1| tRNA pseudouridine synthase C [marine gamma proteobacterium
           HTCC2143]
 gi|119450037|gb|EAW31273.1| tRNA pseudouridine synthase C [marine gamma proteobacterium
           HTCC2143]
          Length = 243

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 110/239 (46%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y D  +   NKP+G+ V   S I  H   F L+   D  GQ     HRLD+ TSG+L+
Sbjct: 7   IIYRDDYLVAINKPSGLLVHR-SNIDRHETQFALQLLRDQLGQHVYPVHRLDKPTSGLLL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A +   A+ ++  F  + I+K Y +LV G    +         +   + G      K+ 
Sbjct: 66  FALSSDVAKTVSLEFSNQTIKKKYLALVRGWCAEQGTIDHALKEQFDKMSGK----PKKQ 121

Query: 220 EKGANYAISHF----KVIDCFA------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
              A  A++HF    KV   FA       ++  +E +P TGR HQ+R H  H+  PI+GD
Sbjct: 122 AIQAKDAVTHFTRLAKVELPFAVDRYPSSRYSLVEARPVTGRKHQIRRHFKHISHPIIGD 181

Query: 270 HKYC-ANFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            K+  ++  G F S    ++L L    M L HP  G  + + A L        D LG+K
Sbjct: 182 AKHGKSSHNGFFQSQFNCHRLMLACTEMTLTHPTTGDMMTLRASLDNTFSDVIDKLGWK 240


>gi|153008381|ref|YP_001369596.1| pseudouridine synthase [Ochrobactrum anthropi ATCC 49188]
 gi|151560269|gb|ABS13767.1| pseudouridine synthase [Ochrobactrum anthropi ATCC 49188]
          Length = 222

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 63/212 (29%), Positives = 108/212 (50%), Gaps = 11/212 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D+   V +KP+G+    G   A  +   L + V  +  + ++ +RLD++TSG++++
Sbjct: 21  ILHRDAGFLVLDKPSGLLSVPGRHPA--LSDSLATRVQEQFPQAQMINRLDKDTSGLVLM 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           +  R A   +   F  R  QK Y ++VWG+ ++  E + +  L           V ++N 
Sbjct: 79  SLNRKAHAAIASQFEARTTQKSYVAVVWGLVED-DEGLIDLPLAIDPDNKPRHRVDRENG 137

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K A    + ++V+D   +    L + P TGRTHQLRVH   +G  I+GD  Y    +G  
Sbjct: 138 KPAQ---TRWRVLDR-DENTTRLRLHPLTGRTHQLRVHMKALGHVILGDEFYA---EGEA 190

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
            +   ++L LHA  +   HP+G  +  TAP P
Sbjct: 191 LA-AADRLLLHAEELSFQHPDGRSVTFTAPCP 221


>gi|47459161|ref|YP_016023.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma mobile
           163K]
 gi|47458490|gb|AAT27812.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma mobile
           163K]
          Length = 298

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 73/307 (23%), Positives = 137/307 (44%), Gaps = 42/307 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           R+D++  N   + +  ++Q+++   QV V+   V K + +I+    + I         +I
Sbjct: 13  RIDKFLANSTDY-SRNDIQQLIDEHQVYVNDILVRKASFKIKENDQIEIKK------QLI 65

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
           KE   +  ++NL          +++E+    + NK +G+ V    G         + +H 
Sbjct: 66  KETNAIAQNINLD---------IVFENEDFLIINKRSGMVVHPAPGNMQDTLVNALLFH- 115

Query: 130 DGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             F  +  +  G+ +P + HR+D++TSG+L+VA+T  A  +     +  +I++ Y +++ 
Sbjct: 116 --FKNNLSNINGEIRPGIVHRIDKDTSGLLLVAKTNEAHNYFALLLKKHQIERKYQAIIV 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G   +    I N  + ++      + V   N K A   I+  K  +  +   C L+    
Sbjct: 174 GKMDHTITNI-NLPIGRNTSSRLKMEVTAHNSKEAFTKITSLKASETHSLIQCELK---- 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT 308
           TGRTHQ+RVH  H+  PI GD+ Y     G        +  LHA  +   + +  +    
Sbjct: 229 TGRTHQIRVHLAHINKPIYGDNIY-----GKKVDDFNQR--LHAYELSFTYKDNKQYSFN 281

Query: 309 APLPAHM 315
            PLP  M
Sbjct: 282 VPLPKEM 288


>gi|317508658|ref|ZP_07966314.1| RluA family pseudouridine synthase [Segniliparus rugosus ATCC
           BAA-974]
 gi|316253061|gb|EFV12475.1| RluA family pseudouridine synthase [Segniliparus rugosus ATCC
           BAA-974]
          Length = 315

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 71/295 (24%), Positives = 131/295 (44%), Gaps = 27/295 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD         ++     ++  +G   +D K    ++R+ +G  + +  V +A +  
Sbjct: 19  GLRLDAGLARLL-GVSRTKAAELADAGHALIDGKEAGRSDRLVAGAWLEVS-VPSAPSAP 76

Query: 78  IKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKS 135
           ++E              + +  + +LY D  + V  KP  I+V    G     + G LK+
Sbjct: 77  VEEDA-----------PEIIPGLNVLYSDEHVVVVEKPPEIAVHPSVGWSGPTVVGGLKA 125

Query: 136 W---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
               + + G   R  +  RLD  TSG++V+A +  A   L  +F+ R ++K Y +LV G 
Sbjct: 126 LGFHIATTGVAERQGVVQRLDVGTSGVMVLAASEHAYTVLKRAFKHREVEKWYEALVQGH 185

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + K+   G  +    +       ++++H+  I+ F      + ++  TG
Sbjct: 186 PDPSSGTIDAPIGKRPGPGWRFAVTTE-----GRHSVTHYDTIEAFGAA-SLVSVKLETG 239

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           RTHQ+RVH   +  P  GD  Y A+ K      ++ + +LHAR +   HP  G++
Sbjct: 240 RTHQIRVHFSALRHPCCGDMLYGADPKLAARLGLRRQ-WLHARRLSFAHPADGKI 293


>gi|158334165|ref|YP_001515337.1| RluA family pseudouridine synthase [Acaryochloris marina MBIC11017]
 gi|158304406|gb|ABW26023.1| pseudouridine synthase, RluA family [Acaryochloris marina
           MBIC11017]
          Length = 306

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 75/297 (25%), Positives = 129/297 (43%), Gaps = 39/297 (13%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            + L  ++   Y H +    Q  + +GQV +D ++   +  ++ GQ        N   H 
Sbjct: 17  GLTLLEFYAQRYRHSSGTEWQVRIETGQVTIDGRQATPDTVLKQGQ--------NLAYHR 68

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
              Q   + +V LT         +LYED+ +   +KP+G+ V  G G   H    L   V
Sbjct: 69  PPWQ---EPTVPLTFD-------VLYEDADVLAIHKPSGLQVLPGGGFLEHT---LLHQV 115

Query: 138 DSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI----P 191
             +  +  P   HRL + TSG++++AR++ A   L++  R R+IQK+Y +L+       P
Sbjct: 116 QQRFPQGTPFPIHRLGRGTSGVVLMARSQQARAALSQQMRNRQIQKVYRALIGPEQTTHP 175

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             ++  I   + K  +    Y++      + A+ A +    I     +   L +   TGR
Sbjct: 176 LEEQFEITQAIGKVPYPELGYIYAATPKGRPAHSACT----ILQRRPEATLLAVTITTGR 231

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLPHP 300
            HQ+R+H   +G P++GD  Y A  +    S        P     +LHA  +   HP
Sbjct: 232 PHQIRIHLATIGYPLLGDPLYVAGGQPQSISSEERSQPVPGDCGYWLHAFSLQFIHP 288


>gi|317012766|gb|ADU83374.1| hypothetical protein HPLT_04870 [Helicobacter pylori Lithuania75]
          Length = 242

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 56/177 (31%), Positives = 91/177 (51%), Gaps = 25/177 (14%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +LV GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVEKEYLALVQGIIEEEREINAPILTFKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLY 208


>gi|258510958|ref|YP_003184392.1| pseudouridine synthase [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
 gi|257477684|gb|ACV58003.1| pseudouridine synthase [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
          Length = 314

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 105/232 (45%), Gaps = 14/232 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILV 159
           +LY D  + V +KP  + V      A  +D  ++  ++ +G  +    HRLD+ T+G ++
Sbjct: 87  VLYNDPSLLVVDKPENLLVHRDGSDAPTLDACVQRLLNEEGAGRAYHVHRLDRGTTGCVL 146

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+     + +       R+++ Y ++  G  + +   ++  + +  H+ G Y     + 
Sbjct: 147 YAKHGLMLRAMDAELAAGRVRRTYLAIASGT-RIRPGVMSAPIGRDRHVSGRY-----RV 200

Query: 220 EKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            +    A +H +V+D   Q   ++  + ++  TGR HQ+RVH   MG P+VGD  Y    
Sbjct: 201 SRTGKVARTHVEVLDEADQGGARWTLVRLRLETGRRHQIRVHLSAMGAPVVGDTLYGGTP 260

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
                     ++ LHA  +   HP  G  +++ APLP    K    +G   D
Sbjct: 261 HPALAP---GQIALHAARLQFCHPYAGEDVEVRAPLPRAWEKLAADVGLSLD 309


>gi|308809467|ref|XP_003082043.1| probable pseudouridine synthase (ISS) [Ostreococcus tauri]
 gi|116060510|emb|CAL55846.1| probable pseudouridine synthase (ISS) [Ostreococcus tauri]
          Length = 300

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 64/256 (25%), Positives = 102/256 (39%), Gaps = 19/256 (7%)

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            AL    ++    D++   +    F + ++L+E   + + NKP G+S       +    G
Sbjct: 28  GALRASTRDDDGRDATARESDAEAFEEMVVLHESEAVVIVNKPRGMSFH-----SEFAPG 82

Query: 132 FLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            L       G++  +   HRLD+ TSGILV A+   A   L+++F  R I K Y  +   
Sbjct: 83  ALARLRTQMGERTAVMSVHRLDKPTSGILVFAKNARARDALSKAFEEREIVKYYVGMSNR 142

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            P+ K   +   + +          +    E  A      F       +       +P T
Sbjct: 143 KPRKKMGTVRGDMTRSRR---KAWMLTSTTESPAETKFVSFGARGMGERALRMFVFRPMT 199

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQIT 308
           G+THQLRV A  +G P++GD  Y             ++ YLHA  + +P    G  +QI 
Sbjct: 200 GKTHQLRVAAKSLGSPLLGDDTYGGERD-------VDRTYLHACAIRIPKSVLGETIQII 252

Query: 309 APLPAHMVKTWDSLGF 324
              P      WD   F
Sbjct: 253 CS-PIGTGDEWDPAAF 267


>gi|327312606|ref|YP_004328043.1| RluA family pseudouridine synthase [Prevotella denticola F0289]
 gi|326945498|gb|AEA21383.1| pseudouridine synthase, RluA family [Prevotella denticola F0289]
          Length = 577

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 69/218 (31%), Positives = 102/218 (46%), Gaps = 32/218 (14%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILV 159
           LYED  + V  KP G+ SV G  G+        + W   KG+ +P + HRLD  TSG+LV
Sbjct: 363 LYEDDSLAVVAKPPGLLSVPGRDGLPSVYSILKERW---KGRYEPFMVHRLDMATSGLLV 419

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVW-------GIPKNKKECIANWLL-KKSHIGGD 211
           VAR+  A + L   F    ++K Y +L+          P+ + E   + L   +     D
Sbjct: 420 VARSPEAHRALQAQFTNHTVRKQYTALLSLSFLDKHLPPEGRIELPLSPLPDDRPRQCVD 479

Query: 212 YVHVVKQNEKGA--NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPI 266
           YV     N K A   Y ++         Q+   + + P TGRTHQLR+H  H   +G PI
Sbjct: 480 YV-----NGKTAVTEYRVAGKTTYGKTGQEAVKVILYPLTGRTHQLRIHCAHPDGLGTPI 534

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +GD  Y  +           +L+LHA +++  HP  G+
Sbjct: 535 IGDSLYGQH---------AGRLWLHAGHLEFTHPVTGK 563


>gi|227489029|ref|ZP_03919345.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glucuronolyticum ATCC 51867]
 gi|227090974|gb|EEI26286.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glucuronolyticum ATCC 51867]
          Length = 294

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 59/193 (30%), Positives = 86/193 (44%), Gaps = 18/193 (9%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +YEDS++ V NKP  + +V  G+ I       L+    ++   P   HRLD+ TSG+L+ 
Sbjct: 98  VYEDSRVLVVNKPPFLATVPKGAHITETAVVRLRRATGNEELSP--AHRLDRHTSGLLLF 155

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQN 219
            ++R       E F  R +QK Y ++  G        +  W  + S + GD   H V   
Sbjct: 156 TKSREFRGAYQEMFARRAVQKTYHAVSAGPSAVVPGTV--WRSRISKVPGDLQAHTVDGE 213

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NF 276
                + IS    +   A         PHTG+THQLR+H    G PIV D  Y A   + 
Sbjct: 214 VNAETHVISVSGRVHVLA---------PHTGKTHQLRLHMCEAGVPIVNDPLYPAIRDDL 264

Query: 277 KGNFTSPIQNKLY 289
             +FT P+    Y
Sbjct: 265 MDDFTRPLGLTAY 277


>gi|330830764|ref|YP_004393716.1| Pseudouridine synthase [Aeromonas veronii B565]
 gi|328805900|gb|AEB51099.1| Pseudouridine synthase [Aeromonas veronii B565]
          Length = 257

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 70/264 (26%), Positives = 120/264 (45%), Gaps = 35/264 (13%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKP 144
           T+    LK  LLY+D  +   NKP+G+ V      +G +  A  +    +  +  +   P
Sbjct: 6   TREESDLKLTLLYQDEWLVAVNKPSGLLVHRSWLDKGETRFAMQMT---RDLIGGRYVYP 62

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRLD+ TSG+L+ A     A+ LTE+F  R++ K Y +LV G     ++ + ++ LK
Sbjct: 63  --VHRLDRPTSGVLLFALDPVIARALTEAFTQRQVHKEYLALVRGW--APEQGVIDYPLK 118

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-----------AQKFCWLEMQPHTGRTH 253
           +          +   ++ A  A++ F+ +                ++  + + P TGR H
Sbjct: 119 EQ--LDKIADAMSNPDRPAQDAVTTFRRLHQVELPHAVSKKHPTSRYSLVRLFPKTGRKH 176

Query: 254 QLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQI 307
           QLR H  H+  PIVGD  +        F+ +F      +L L AR +   HP     ++I
Sbjct: 177 QLRRHMDHLFHPIVGDTTHGDGRHNRFFREHFGC---ERLLLVARTLSFTHPVLKVPMRI 233

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLY 331
            APL   +++ +  LG+    + Y
Sbjct: 234 QAPLGQDVLRLFAELGWPASESDY 257


>gi|262382346|ref|ZP_06075483.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_33B]
 gi|262295224|gb|EEY83155.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_33B]
          Length = 304

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 59/211 (27%), Positives = 105/211 (49%), Gaps = 25/211 (11%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGG---SGIAYHIDGFLKSWVDSKGQKPR----LTHRLDQ 152
           +++ED  + V NK  G+ SV         AY +   L  +V  K   PR    + HRLD+
Sbjct: 93  IVWEDDDLIVINKREGLLSVSTDRVKERTAYRL---LSDYV--KQSDPRNKIFVLHRLDR 147

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSGI++ A+ +   + L  ++     Q+ Y +++ G P+   + I + L++  ++    
Sbjct: 148 DTSGIMMFAKNQGVKEQLQSNWSEMITQRTYVAVIEGRPEKDTDLIVSNLVENKNM---Q 204

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+V  + +     AI+ ++++      +  LE++  TGR +Q+R     +G P+ GD KY
Sbjct: 205 VYVTLEGD--GKEAITRYRLLQT-NNSYSLLELELETGRKNQIRAQMQSIGHPVAGDTKY 261

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            A      T+P   +L LHAR +   HP  G
Sbjct: 262 GAE-----TNPA-GRLMLHARKLCFIHPVTG 286


>gi|189485425|ref|YP_001956366.1| ribosomal large subunit pseudouridine synthase C [uncultured
           Termite group 1 bacterium phylotype Rs-D17]
 gi|170287384|dbj|BAG13905.1| ribosomal large subunit pseudouridine synthase C [uncultured
           Termite group 1 bacterium phylotype Rs-D17]
          Length = 238

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 58/217 (26%), Positives = 106/217 (48%), Gaps = 24/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NKP+G+ V  G  I Y     ++   +   QK  + H +D++ SG+LV 
Sbjct: 7   IIYQDENILVVNKPSGMFVIPGRNI-YENKTLVEILRNQLKQKLWVVHIIDRDASGVLVF 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+     ++++  F   +I+K Y +L+ G+ +  +  I   L+    I G  V +    +
Sbjct: 66  AKNPETHRNISVQFENSKIRKKYIALLSGVLEENEGTINKPLI----ISGKNVRI----D 117

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-------C 273
                +I+ FKV++ F + +  +   P T + HQ+R+H   +G P+  D +Y        
Sbjct: 118 ITGKESITDFKVLENF-RSYTLVNALPLTVKRHQIRIHFWSLGHPLAIDGEYGTLDPIFL 176

Query: 274 ANF-------KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++F       KG   +P+ ++L LHA  + L  P  G
Sbjct: 177 SSFKRGYKIKKGKTENPLISRLTLHAAALTLILPGSG 213


>gi|120597834|ref|YP_962408.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|120557927|gb|ABM23854.1| pseudouridine synthase [Shewanella sp. W3-18-1]
          Length = 236

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 61/208 (29%), Positives = 95/208 (45%), Gaps = 10/208 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+DS I + +KP+G+    G     ++D      V        L HRLD  TSGI++V
Sbjct: 25  VLYQDSDILLIDKPSGLLSLSGKN-PLNLDSVHYRLV-QDFPTATLLHRLDFGTSGIMLV 82

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +     LT+ F+ R ++K Y +L+ G   +    I   + K      D   + K   
Sbjct: 83  ALNKTVNGLLTKQFQARTVEKRYTALLHGHLTDDSGVINLPIAKDV----DNFPLQKICH 138

Query: 221 KGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NF 276
                AIS ++V++   + F   +E  P +GRTHQLR+H+  +G  I+G   Y       
Sbjct: 139 STGKLAISEYRVLERLPEPFATRVEFTPVSGRTHQLRIHSQQLGHSILGCDLYAGVGEKI 198

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             N  +    +L LHA  +   HP  G 
Sbjct: 199 TDNDYALHHTRLMLHATRLAFDHPITGE 226


>gi|217033961|ref|ZP_03439384.1| hypothetical protein HP9810_883g31 [Helicobacter pylori 98-10]
 gi|216943594|gb|EEC23042.1| hypothetical protein HP9810_883g31 [Helicobacter pylori 98-10]
          Length = 242

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 63/202 (31%), Positives = 100/202 (49%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ R  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 100 VLLVRENSEF-HLKAKKAFKNRAVKKEYLALAQGIIEEEQEINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y  N
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYN-N 210

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
             G+       +L LHA  + L
Sbjct: 211 EPGS-----AKRLMLHAHKISL 227


>gi|134095434|ref|YP_001100509.1| 23S rRNA pseudouridylate 746 synthase [Herminiimonas
           arsenicoxydans]
 gi|133739337|emb|CAL62387.1| Ribosomal large subunit pseudouridine synthase A (rRNA-uridine
           isomerase A) (rRNA pseudouridylate synthase A)
           [Herminiimonas arsenicoxydans]
          Length = 223

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 60/207 (28%), Positives = 98/207 (47%), Gaps = 15/207 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           +LY+D  + + NKP+G+    G     ++D      V    Q P   + HRLD  TSG+L
Sbjct: 19  ILYQDEALLLINKPSGLLSLSGKN-PLNLDSVHYRLVQ---QFPTALMLHRLDFGTSGLL 74

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  +  A  +   F++R + K Y +++ G   +    I    + K  +    + +   
Sbjct: 75  VVALNKTVAADIYRQFQLRTVVKTYQAVLAGRMDSDAGDI-ELPIAKDPVNFPKLKICLT 133

Query: 219 NEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             K A+   SHF+V+D         +   P TGRTHQLR+H+  +G PI+G    C  + 
Sbjct: 134 TGKTAS---SHFQVLDRQSGPDTTRVVFTPLTGRTHQLRIHSAGVGHPILG----CDLYG 186

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR 304
              +  + ++L LHA  ++  HP  G 
Sbjct: 187 TPESQQMADRLLLHATTVEFDHPISGE 213


>gi|289550433|ref|YP_003471337.1| Putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus lugdunensis HKU09-01]
 gi|289179965|gb|ADC87210.1| Putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus lugdunensis HKU09-01]
          Length = 278

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 109/247 (44%), Gaps = 42/247 (17%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +L ++  S ++ ++    + +N++ +   V IP           E+K           S+
Sbjct: 27  DLHQLNMSKEITINNAPARLSNQVHTMDCVEIP---------TDEEK-----------SN 66

Query: 96  FLKSI----LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +L S     + YED  + +  KP G+      ++  + +  HI   L    DS+  +P  
Sbjct: 67  YLPSYRYAQIYYEDDDLAIVMKPKGVKTHPNDLKESNTLMNHIIYTL----DSEYAEP-- 120

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLDQET G+L++A+     + L       +I +IY + V  +   K + I        
Sbjct: 121 IHRLDQETVGLLIIAKNPLMKKILDRMLEDNKITRIYKANVNALLPIKPQTI------DM 174

Query: 207 HIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            IG D  H  K+        AI+H        +  C L+++  TGRTHQ+RVH   +G P
Sbjct: 175 PIGKDKFHPNKRRISNTGQRAITHILASTMLKEGVCQLDIKLDTGRTHQIRVHLAEIGHP 234

Query: 266 IVGDHKY 272
           ++GD  Y
Sbjct: 235 VIGDPLY 241


>gi|325115868|emb|CBZ51423.1| putative RNA pseudouridine synthase domain containing protein
            [Neospora caninum Liverpool]
          Length = 6415

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 94/231 (40%), Gaps = 61/231 (26%)

Query: 146  LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----IPKNKKECIANW 201
            L HR D ETSG L++A+TR A + + E FR R + K Y  L  G    +       IA  
Sbjct: 4693 LCHRTDLETSGSLLIAKTRRARESIFEQFRKRLVHKEYLLLCHGRLDKLHARIDHPIATR 4752

Query: 202  LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF------------------------- 236
                S     +  VV  +E G + A++ ++V+  F                         
Sbjct: 4753 DFDSSRSKSHFSEVVGPDE-GGDEALTEYQVVRVFGLRQPVHRKIQAAMSVAARIAASPS 4811

Query: 237  ----------------------------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                                        + +F +  ++ HTGRTHQ+RVH  H+G P+VG
Sbjct: 4812 SSSSSDRARGTGASAPAAGAKTAGSGKGSPEFSFCRVRIHTGRTHQIRVHFRHIGHPLVG 4871

Query: 269  DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP---EGGRLQITAPLPAHMV 316
            D KYC  +K         +++LH+  ++  +P   E   +++  PL   ++
Sbjct: 4872 DTKYCDLYKCTVDRSWCARMFLHSAVLEFDNPDKTETQHVRVVCPLATELL 4922


>gi|260769549|ref|ZP_05878482.1| pseudouridylate synthase LSU rRNA-specific [Vibrio furnissii CIP
           102972]
 gi|260614887|gb|EEX40073.1| pseudouridylate synthase LSU rRNA-specific [Vibrio furnissii CIP
           102972]
          Length = 558

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 105/221 (47%), Gaps = 20/221 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           LD +  L   ++  +  ++Y+D  I V NKPA  +SV G +     +    + + + +G 
Sbjct: 340 LDDNPLLNNPAEGQEIEIVYQDEAIVVINKPAEFLSVPGVNIKDSALTRLEQQFPEVEG- 398

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P + HRLD  TSG+LV A TR A + L + F  R ++K Y +L+ G   + + CI    
Sbjct: 399 -PFVLHRLDMSTSGLLVFALTRRANKSLQKQFITRGVEKRYVALLSGEIAHGEGCI-TLP 456

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH- 261
           L+          V  ++ K A    ++++ I    Q    + + P TGRTHQLRVH  H 
Sbjct: 457 LRPDLDDRPRQMVCFEHGKAAE---TYWQTIGT-EQGRTRVYLFPKTGRTHQLRVHCAHA 512

Query: 262 --MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
                PI+GD  Y             N+L+LHA  +   HP
Sbjct: 513 QGFNTPILGDDLYGEK---------ANRLHLHAESLSFDHP 544


>gi|224824495|ref|ZP_03697602.1| pseudouridine synthase Rlu family protein, TIGR01621 [Lutiella
           nitroferrum 2002]
 gi|224602988|gb|EEG09164.1| pseudouridine synthase Rlu family protein, TIGR01621 [Lutiella
           nitroferrum 2002]
          Length = 229

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 63/210 (30%), Positives = 96/210 (45%), Gaps = 19/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+  D + YV  K  G+S       A  ++  L++ +      P   HRLD+ TSG+L+V
Sbjct: 4   LIATDPRFYVIAKHPGVSFHRQGDEAGLMEA-LRAQLADDALWP--VHRLDRLTSGLLLV 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR+   A  L E+F  R I+K Y +L    P+ K+  +   ++K    GG +    +   
Sbjct: 61  ARSAEVASRLAEAFAAREIEKYYLALSDRKPQKKQGLVRGDMVKGR--GGAW----RLLP 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             AN AI+ F      A       ++PH+G+THQLRV    +  PI+GD  Y        
Sbjct: 115 SSANPAITQFFSF-SLAPGLRLFILRPHSGKTHQLRVALKSLSAPILGDELYGGT----- 168

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                ++ YLHA  +   H +G R     P
Sbjct: 169 ---PSDRGYLHAYSLAF-HLDGERFHFICP 194


>gi|188527412|ref|YP_001910099.1| hypothetical protein HPSH_03105 [Helicobacter pylori Shi470]
 gi|188143652|gb|ACD48069.1| hypothetical protein HPSH_03105 [Helicobacter pylori Shi470]
          Length = 327

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 105/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLEFKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|90962428|ref|YP_536344.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|90821622|gb|ABE00261.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
          Length = 304

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 58/187 (31%), Positives = 92/187 (49%), Gaps = 34/187 (18%)

Query: 101 LLYEDSKIYVFNKPAGIS------VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +++E+  + V NKP GI        + G+ + Y     +  ++D++ + P + HRLD  T
Sbjct: 88  IIFENDDLLVVNKPQGIKSHPNQPYETGTLVNY-----IAGYLDARDEHPYMVHRLDMLT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG ++VA+       LT       I++ Y ++  GI  ++KE + +       IG D   
Sbjct: 143 SGAMIVAKNPVVVPILTRLISTHTIKRDYLAITEGI-FDQKEGVIDL-----PIGKD--- 193

Query: 215 VVKQNEK--------GANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              +N+K        GA  A + ++VI  F      +L ++  TGRTHQLRVH   MG P
Sbjct: 194 ---ENDKRKRKVDGIGALPARTRYQVIKEFENNSVVYLRLE--TGRTHQLRVHLSAMGHP 248

Query: 266 IVGDHKY 272
           IVGD  Y
Sbjct: 249 IVGDVLY 255


>gi|313682856|ref|YP_004060594.1| ribosomal large subunit pseudouridine synthase d [Sulfuricurvum
           kujiense DSM 16994]
 gi|313155716|gb|ADR34394.1| ribosomal large subunit pseudouridine synthase D [Sulfuricurvum
           kujiense DSM 16994]
          Length = 325

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 68/256 (26%), Positives = 117/256 (45%), Gaps = 30/256 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLD 151
           +L+ED  I V NKP+ ++V     +    +  L  W+  KG         ++  + HRLD
Sbjct: 81  ILFEDDDILVINKPSSLTVHPAPSVK---EPTLVDWLKHKGIALSTLSGEERHGIVHRLD 137

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG +V+A+   A + L+   + + + + Y +++    K     I         IG  
Sbjct: 138 RGTSGAMVIAKNNEAHEALSLQLQDKTMGRYYLAIITPAMKETITVIDRP------IGRS 191

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             + +K   +E G N   +  K++    +    +  + +TGRTHQ+RVH   +   I+GD
Sbjct: 192 ANNRLKMAISESGKNAKTAFAKLLPSHDETEELIACKLYTGRTHQIRVHLESISRHIIGD 251

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPL----PAHMVKTWDSLGF 324
           H Y  + K    S    ++ LHA  +   HP    R+  TAPL      ++ K +DS   
Sbjct: 252 HLYGTSAK----SDKMERILLHAYNLYFTHPTTLKRVNFTAPLGDVMEDYLTKHFDSKEL 307

Query: 325 -KYDRNLYIKRLYSQD 339
            +    L I+RL+S +
Sbjct: 308 HELIDPLRIERLFSTE 323


>gi|292489024|ref|YP_003531911.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           CFBP1430]
 gi|292900157|ref|YP_003539526.1| RNA pseudouridylate synthase [Erwinia amylovora ATCC 49946]
 gi|291200005|emb|CBJ47129.1| putative RNA pseudouridylate synthase [Erwinia amylovora ATCC
           49946]
 gi|291554458|emb|CBA21962.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           CFBP1430]
 gi|312173188|emb|CBX81443.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           ATCC BAA-2158]
          Length = 232

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 96/210 (45%), Gaps = 20/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L +D  + + NKPAG+    G     ++D      V        L HRLD  TSG++V+
Sbjct: 19  VLCQDEHLVLINKPAGLLSLSGKN-PQNLDSVHHRLVQIF-PGCTLVHRLDFGTSGLMVI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           ART+A    L + F  R + K+Y +L+ G   N  E + +  + K       + +   + 
Sbjct: 77  ARTKAINAALCQQFSQRTVTKVYCALLCG-HLNDNEGVIDAAIAKDPALFPLMSICSIHG 135

Query: 221 KGANYAISHFKVI--------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K A    S ++V+        D        +E+ P TGRTHQLR+H   +G PI+G    
Sbjct: 136 KPAR---SRYRVLQRCYHALQDGTLLPLTRVELTPETGRTHQLRIHCQQLGYPILG---- 188

Query: 273 CANFKGNFTSPIQ--NKLYLHARYMDLPHP 300
           C  + G      +  ++L LHA  +   HP
Sbjct: 189 CDLYGGRLLPGTERTSRLMLHASELQFVHP 218


>gi|227530166|ref|ZP_03960215.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus vaginalis
           ATCC 49540]
 gi|227349919|gb|EEJ40210.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus vaginalis
           ATCC 49540]
          Length = 291

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 117/238 (49%), Gaps = 29/238 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G+  VD ++V+   +I   Q + I          I + ++ D SV L   SD   +I+ Y
Sbjct: 37  GKFLVDHRKVRPTTKILPNQPLTI----------IAQPELRDLSVKL---SDAPLNIV-Y 82

Query: 104 EDSKIYVFNKPAGIS------VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ED    V +KPAG++      V  G+ +   +   ++    S  Q+P L  RLD+ T G+
Sbjct: 83  EDDNWLVIDKPAGVTSIPGPTVDNGTVLNRAVHYLVEE--KSADQRPHLITRLDRYTGGL 140

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+   A+  +++  +  ++ K Y + V GI   + + I   + ++    G    V+ 
Sbjct: 141 LLIAKHHVASSMISQQVQQHQMLKEYTAFVSGIFDKEHDIIDKPIARRE---GQVQRVIA 197

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           ++      A++ + V +  A  +  L ++ HTGRTHQ+RVH   +  P++GDH Y  +
Sbjct: 198 ED---GQRAVTEYWVEEEGAD-WTKLRVRLHTGRTHQIRVHLASINHPLIGDHLYGGD 251


>gi|261252272|ref|ZP_05944845.1| tRNA pseudouridine synthase C [Vibrio orientalis CIP 102891]
 gi|260935663|gb|EEX91652.1| tRNA pseudouridine synthase C [Vibrio orientalis CIP 102891]
          Length = 240

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 103/240 (42%), Gaps = 21/240 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IVFQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +          ++   I   +       E
Sbjct: 64  ALSSEVASQVMPMFANHEMEKTYHAIVRGWIEESGRLDYALKVELDKIADKHA----SQE 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ +  +               ++C +EM+P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQEAITDYWPLAKVEVPHSTGKFPTTRYCLMEMKPLTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNFTSPI--QNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
            +           +   ++L LHA  ++  HP    +L I A +     +TW  L  ++D
Sbjct: 180 THGDGKHNKLYREVYDSHRLLLHASSLEFVHPFTNEKLLIKAGID----ETWQKLCAEFD 235


>gi|260584109|ref|ZP_05851857.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Granulicatella elegans ATCC 700633]
 gi|260158735|gb|EEW93803.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Granulicatella elegans ATCC 700633]
          Length = 296

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 56/224 (25%), Positives = 113/224 (50%), Gaps = 19/224 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +L+ED  + + NKP G +     +     +A  + G+L++   ++     +  RLD++T+
Sbjct: 79  ILFEDDYLLIVNKPQGTASIPSQLHPDQSMANRVKGYLQT-TRTQDCVTHVVTRLDRDTT 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ R     + ++ R + IQK Y ++V      K++ +    L  + IG     +
Sbjct: 138 GVMMFAKHRVVHAWMDQALRNKTIQKTYHAIV-----TKQDVLKEHDLIDAPIGRTDDSI 192

Query: 216 VKQNEK-GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +  +     +++ + + + + Q    ++++ HTGRTHQ+RVH   +GCP++GD  Y  
Sbjct: 193 INRCVRPDGKPSLTEYWLEETY-QHSQLVKIRLHTGRTHQIRVHFSWLGCPLLGDDLY-- 249

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
              G    P+  +  LH   +D  HP  G ++ + A LP  M +
Sbjct: 250 --GGEKIEPLMRQ-ALHCSQLDFVHPMTGEKMCVKALLPKDMAE 290


>gi|315123230|ref|YP_004065236.1| ribosomal large subunit pseudouridine synthase A (pseudouridylate
           synthase, 23S RNA-specific) [Pseudoalteromonas sp.
           SM9913]
 gi|315016990|gb|ADT70327.1| ribosomal large subunit pseudouridine synthase A (pseudouridylate
           synthase, 23S RNA-specific) [Pseudoalteromonas sp.
           SM9913]
          Length = 563

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 109/233 (46%), Gaps = 25/233 (10%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H++K   + ++ + LT  +      ++Y+D  + V NKPA      G  I   +   +
Sbjct: 336 LGHMLKGLNVEENPL-LTNPAKGKDLTIVYQDDDLLVINKPAEFLSVPGINIDDSVYMRI 394

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPK 192
           K+   +    P + HRLD  TSG+L++A  + A + L + F  R I+K Y +LV G I +
Sbjct: 395 KTQFPA-ASGPLIVHRLDMSTSGLLIIALNKRAHKALQKQFIERTIEKRYVALVAGNITE 453

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           N        +L       D+    +Q    K    +++ + V++        L++ P TG
Sbjct: 454 NSGVINLPLVL-------DFDDKPRQMVCYKTGKPSLTTWHVLE-RKNNTTRLQLYPKTG 505

Query: 251 RTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           RTHQLRVH  H   +  PIVGD  Y    +         +L+LHA Y+   HP
Sbjct: 506 RTHQLRVHCAHQLGLNTPIVGDTHYGEEAE---------RLHLHAEYLAFTHP 549


>gi|297380156|gb|ADI35043.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori v225d]
          Length = 242

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 112/227 (49%), Gaps = 36/227 (15%)

Query: 78  IKEQKILDSSVNLTKHSDFL-----KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           + E+K++ +   L K++ F      K  +++ED  I    KP  I        +Y +  F
Sbjct: 30  VGEKKLMVARKELPKNTHFSVQKVEKPSVIFEDENILALFKPPFIE-------SYDLVSF 82

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGI 190
            K WV        L HRLD+ETSG++++ +  +   HL   ++F+ R ++K Y +L  GI
Sbjct: 83  FKGWV--------LLHRLDKETSGVILLVKENSEF-HLKAKKAFKDRAVKKEYLALAQGI 133

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            + ++E  A  L  K+     +  + K+ ++     I+  K+I+    K   L+ +  TG
Sbjct: 134 IEEEQEINAPILTIKT--TKAFSKISKKGQEAVTI-IAPLKIIN----KKTLLKARIKTG 186

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           RTHQ+RVH  H+  PI+GD  Y  N  G+       +L LHA  + L
Sbjct: 187 RTHQIRVHLKHINHPIIGDTLYN-NEPGS-----AKRLMLHAHKIAL 227


>gi|312885611|ref|ZP_07745247.1| tRNA pseudouridine synthase C [Mucilaginibacter paludis DSM 18603]
 gi|311301923|gb|EFQ78956.1| tRNA pseudouridine synthase C [Mucilaginibacter paludis DSM 18603]
          Length = 234

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 65/223 (29%), Positives = 103/223 (46%), Gaps = 26/223 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y D  +   NKP G+ V   S IA+ +  F L+   D   +     HRLD++T G+L+
Sbjct: 6   IIYHDDYLVAINKPHGLLVHRSS-IAHDVTEFALQILRDQLNRHVFPAHRLDRKTGGVLL 64

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  +   + +   F    ++K Y +LV G   +++E   ++ L+K    G       + 
Sbjct: 65  FALDKETEKLMQTQFMENAVKKKYLALVRGHTPDEQEI--DYPLRKE--NGTLQDAFTRY 120

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +  A   +    + +    ++  +E QP TGR HQLR H  H+  PI+GD  +  N    
Sbjct: 121 KTLARAELK-VPLGNHPTSRYSLIEAQPETGRMHQLRKHFSHIFHPIIGDRTHGCN---- 175

Query: 280 FTSPIQNKLY----------LHARYMDLPHP-EGGRLQITAPL 311
                QNKL+          LHA  +   HP  G +LQI APL
Sbjct: 176 ----KQNKLFKERWGMETMLLHATQLSFTHPVTGEQLQIQAPL 214


>gi|304411759|ref|ZP_07393371.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS183]
 gi|307306189|ref|ZP_07585934.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica BA175]
 gi|304349947|gb|EFM14353.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS183]
 gi|306911062|gb|EFN41489.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica BA175]
          Length = 230

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 54/161 (33%), Positives = 81/161 (50%), Gaps = 20/161 (12%)

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G K    HRLD  TSG+L++A++  AA+  TE F   ++QK Y +L  G PK K+  +  
Sbjct: 40  GIKLFAVHRLDTPTSGLLILAKSAVAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIG 99

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + K          +++  E   N AI+ F  +        +L ++PH+G+THQLRV   
Sbjct: 100 DMAKSRR---SMFKLLRTKE---NPAITQFFSLSVSEGLRLYL-LKPHSGKTHQLRVALA 152

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA-----RYMD 296
            +G PI+GD  Y     G   +   ++ YLHA     RY D
Sbjct: 153 SLGVPILGDDLY-----GGMAA---DRCYLHAYCLHFRYGD 185


>gi|224476909|ref|YP_002634515.1| hypothetical protein Sca_1425 [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222421516|emb|CAL28330.1| conserved hypothetical protein [Staphylococcus carnosus subsp.
           carnosus TM300]
          Length = 275

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 65/270 (24%), Positives = 116/270 (42%), Gaps = 42/270 (15%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           L ++  S +++++    K  +++ +G    IP      N++                  +
Sbjct: 28  LHQLNMSKEIKINNDEAKLTDKVHTGDTAFIPTPDEKSNYL----------------PSY 71

Query: 97  LKSILLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
             + + YED+ I +  KP G+      ++  + +  H+   L    DS+  +P   HRLD
Sbjct: 72  RYAEIFYEDNDIAIIKKPKGVKTHPNDLKESNTLMNHVIYTL----DSEYAEP--IHRLD 125

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           QET G+L+VA+     + L       +I +IY + V      K + I         IG D
Sbjct: 126 QETVGLLIVAKNPLMKKLLDRMLEDNQISRIYKARVKSQLPLKPQTIDKP------IGKD 179

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             H  ++       +AI+H        +  C L+++  TGRTHQ+RVH   +G P++GD 
Sbjct: 180 KFHSNRRRVSPTGQHAITHILDSRMIKENECELDIKLDTGRTHQIRVHLAAIGHPVLGDP 239

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            Y  +           +L LH+  ++  HP
Sbjct: 240 LYGDSK--------LRQLQLHSHQIEFTHP 261


>gi|229815199|ref|ZP_04445535.1| hypothetical protein COLINT_02245 [Collinsella intestinalis DSM
           13280]
 gi|229809209|gb|EEP44975.1| hypothetical protein COLINT_02245 [Collinsella intestinalis DSM
           13280]
          Length = 338

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 115/246 (46%), Gaps = 30/246 (12%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----------DSKGQ-KPRLTHRLD 151
           YED  + V +K  G+      G   H DG L + +            +G+ +P + HRLD
Sbjct: 87  YEDDHLLVLSKQRGLVCHPAHG---HEDGTLANALVYHCGIEHLGTVQGEDRPGIVHRLD 143

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+     + L    R R + + Y +LV G     +  I   + + +    D
Sbjct: 144 RDTSGLMLAAKDDETQRALQNLIRTRTLDRRYITLVHGEIVMDEGTINTGIARSTR---D 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            V +   ++  A  AI+ F+V++ F      + +  +E   +TGRTHQ+RVH  H+  P+
Sbjct: 201 RVKMAVSDDPFARQAITTFQVLERFEPARGDEGYTLVECHLYTGRTHQIRVHMRHIHHPL 260

Query: 267 VGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           VGD  Y    KGN    +  ++ +LH+  +   HP  G  +     LP  +    + L  
Sbjct: 261 VGDPLY---GKGNGRMNLDLDRQFLHSWSVQFEHPITGEVVNCRDELPWDLAAALEEL-- 315

Query: 325 KYDRNL 330
            +DR+L
Sbjct: 316 -HDRSL 320


>gi|152993336|ref|YP_001359057.1| ribosomal large subunit pseudouridine synthase D [Sulfurovum sp.
           NBC37-1]
 gi|151425197|dbj|BAF72700.1| ribosomal large subunit pseudouridine synthase D [Sulfurovum sp.
           NBC37-1]
          Length = 317

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 66/255 (25%), Positives = 118/255 (46%), Gaps = 36/255 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLD 151
           +LYED  + V NKP+G+ V     +    +  L  W+  KG         ++  + HR+D
Sbjct: 77  ILYEDEYLMVVNKPSGLVVHPAPSVK---EPTLVDWLVKKGISLSTISGEERHGIVHRID 133

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ET+G LV+A+     + L+E  + + + + Y +L+      K++ + +  + ++     
Sbjct: 134 KETTGALVIAKDNKVHEMLSEQLQDKSMGRYYLALIDHFL--KEDVVVDKPIGRNPHNRL 191

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + VV   +     A + FK +         +  +  TGRTHQ+RVH   +G  I+GD  
Sbjct: 192 KMDVVPHGKP----AKTAFKKLLTSEYDVELIAAKLFTGRTHQIRVHLNTLGRHILGDDL 247

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
           Y    K +       ++YLHA  + L HP  G +++ TAPL       +D      D  L
Sbjct: 248 YGFKSKRDKIP----RVYLHAYLLYLIHPVTGVKMEFTAPL-------FD------DMKL 290

Query: 331 YIKRLYSQDECKQNI 345
           Y+ + + Q +  + I
Sbjct: 291 YLSKYFDQSDIDEKI 305


>gi|168698081|ref|ZP_02730358.1| ribosomal large subunit pseudouridine synthase D [Gemmata
           obscuriglobus UQM 2246]
          Length = 324

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 58/181 (32%), Positives = 83/181 (45%), Gaps = 9/181 (4%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R+ HRLD+ETSG++V AR+  A + L   FR   + + Y ++V GI     + I + L+ 
Sbjct: 145 RIVHRLDKETSGLVVFARSALAERELGMQFRKHTVVRRYLTVVPGILGT--QTIKSNLVP 202

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               G      +    K A   ++  + +  +    C LE    TGRTHQ+R+H    G 
Sbjct: 203 DRGDGRRGSTKLPGVGKEAVTHVTPEERLPGYTLLSCRLE----TGRTHQIRIHLSEAGH 258

Query: 265 PIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDS 321
           P+ GD  YC    G          +L LHA  +   HP   G L  T PLP  + K  D 
Sbjct: 259 PVCGDKVYCKKANGEVFDDRSGAPRLALHATELGFEHPATSGHLHWTMPLPLDLAKFADR 318

Query: 322 L 322
           L
Sbjct: 319 L 319


>gi|117918741|ref|YP_867933.1| pseudouridine synthase Rlu family protein [Shewanella sp. ANA-3]
 gi|117611073|gb|ABK46527.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           sp. ANA-3]
          Length = 229

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 57/192 (29%), Positives = 91/192 (47%), Gaps = 19/192 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +++   V +K   +      G A    G +       G K    HRLD  TSG+L++
Sbjct: 4   IIADEADFLVISKSPNVHFHSQDGTA----GVVAQLEQDLGIKLFAVHRLDTPTSGLLLL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+  AAA+ LTE F   R+QK Y +L  G PK K+  +   + K          +++  E
Sbjct: 60  AKHPAAARQLTELFSAHRVQKYYLALAKGKPKKKQGWVIGDMAKSRR---SMFKLLRTKE 116

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F           +L ++P +G+THQLRV    +G PI+GD  Y ++     
Sbjct: 117 ---NPAITQFFSTSVGEGLRLYL-LKPLSGKTHQLRVALASLGVPILGDALYGSD----- 167

Query: 281 TSPIQNKLYLHA 292
              + ++ YLHA
Sbjct: 168 ---VADRCYLHA 176


>gi|313229293|emb|CBY23879.1| unnamed protein product [Oikopleura dioica]
          Length = 390

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 47/173 (27%), Positives = 85/173 (49%), Gaps = 3/173 (1%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +  + YV NKP+ + +   +   Y  +  +            + HRLD+ TSG+++ 
Sbjct: 162 VIADTDEFYVVNKPSSLPIHPVA--QYRHNSLIFLIAREYKVNYHVIHRLDRLTSGLVIF 219

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T+  A+ +++    R ++K Y   V G   +K  C  +     +  G   V     +E
Sbjct: 220 AKTKEVAKRVSKEISDRVVRKQYLLRVVGKFPDKAVCDKSLFEISAKKGIYRVAKADDDE 279

Query: 221 KGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K    A++ F++++ F +     +   P TGRTHQ+RVH  ++GCPIV D  Y
Sbjct: 280 KKVKTALTEFELVEYFKEADQSLVRAIPKTGRTHQIRVHTQYLGCPIVNDPVY 332


>gi|288803452|ref|ZP_06408884.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           melaninogenica D18]
 gi|288334062|gb|EFC72505.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           melaninogenica D18]
          Length = 571

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 112/249 (44%), Gaps = 23/249 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKH--SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
           L  I  + K  D + N T+   S+ LK  +LYED  + V  KP+ +    G G    +  
Sbjct: 335 LEGIDVDDKECDRTNNETETVPSEGLK--ILYEDDYLAVVVKPSDMLSVPGKGCQPSVYS 392

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L      K     + HRLD  TSG+LVVART    + L   F  R ++K Y +L+    
Sbjct: 393 ILSERWKGKSDA-FMVHRLDMATSGLLVVARTSEVHKALQAQFIERTVKKKYVALLPLSI 451

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI--DCFAQ---KFCWLEMQ 246
             K+      +     +  D     + +      AI+ +++I    + +   K   +E+ 
Sbjct: 452 LEKQLPAEGRIELPLSLDPDDRPRQRVDRTNGKPAITEYRLIGKTTYGKETLKAVKIELY 511

Query: 247 PHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
           P TGRTHQLRVH  H   +G PI+GD+ Y    +         +L+LHA +++  HP   
Sbjct: 512 PLTGRTHQLRVHCAHPDGLGTPIIGDNLYGQRAE---------RLWLHAAHLEFTHPITQ 562

Query: 303 GRLQITAPL 311
            R+    PL
Sbjct: 563 ERMSFDTPL 571


>gi|261414458|ref|YP_003248141.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261370914|gb|ACX73659.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302326709|gb|ADL25910.1| putative pseudouridine synthase, RluD family [Fibrobacter
           succinogenes subsp. succinogenes S85]
          Length = 321

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 52/178 (29%), Positives = 88/178 (49%), Gaps = 13/178 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ED +  +  KPAG+ V     I Y+     ++   DS+   P   HRLD++T G+++ 
Sbjct: 86  VFEDDEFILVAKPAGVPVHHTGRIFYNTFAAIIRREFDSETATP--MHRLDRDTGGLILF 143

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           AR    A    ++     ++K Y ++V G  P+ + EC  +  L++     D + +   +
Sbjct: 144 ARYGETAARFQKNLDRILLRKFYLAVVRGKFPEGEVEC--HMPLRED--PEDPIRLRMHH 199

Query: 220 EKGANYAISHFKVI---DC--FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +G     + FK++   DC   A +   +E +  TGR HQ+R H   MG PIVGD  Y
Sbjct: 200 REGGKECFTRFKLVRHLDCPEIAPELSLVEAELITGRKHQIRAHLAEMGYPIVGDRLY 257


>gi|313905836|ref|ZP_07839194.1| pseudouridine synthase, RluA family [Eubacterium cellulosolvens 6]
 gi|313469350|gb|EFR64694.1| pseudouridine synthase, RluA family [Eubacterium cellulosolvens 6]
          Length = 326

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 62/247 (25%), Positives = 114/247 (46%), Gaps = 38/247 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK--SWVDSKGQKP---RLTHRLDQETS 155
           ++YED  + + +KPAG ++     I++  D      +W   +   P   R  +RLD++T+
Sbjct: 83  VIYEDEDVLIVDKPAGQAIH--PAISHPADTLANGLAWYYQQKGIPFVVRCINRLDRDTT 140

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVH 214
           G+L+VA+   +A  L +    R I + Y ++  G +P++         L  +   G  + 
Sbjct: 141 GLLIVAKNLVSACVLEQDLLARNIHRTYLAIAEGELPES-----GTINLPIARKEGSLIE 195

Query: 215 VVKQNEKGANYAISHF--------------KVIDCFAQK----FCWLEMQPHTGRTHQLR 256
                ++G + A++HF              + +   + K    +  ++++  TGRTHQ+R
Sbjct: 196 RCVDEDRG-DRAVTHFFRKGYYPPATNASPESVSTGSVKNRNGYSLVQLKLETGRTHQIR 254

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQ-----NKLYLHARYMDLPHP-EGGRLQITAP 310
           VH  H G P++GD  Y  ++      PI      N+  LH+  ++  HP  G  +   AP
Sbjct: 255 VHLSHTGHPLLGDTLYHPDYLRTPEDPIPEGLPINRQALHSWQLEFTHPITGEAMHFEAP 314

Query: 311 LPAHMVK 317
           +P  M K
Sbjct: 315 IPEDMRK 321


>gi|253575685|ref|ZP_04853021.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251845023|gb|EES73035.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 310

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 106/235 (45%), Gaps = 27/235 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGF--------LKSWVDSKGQKPRLTH-- 148
           LLYED    V +KPAG+ V   G  G A   D          +  W  S GQ     H  
Sbjct: 85  LLYEDDFCLVVHKPAGLKVHPDGNEGGASRRDSAPPDTLANRVAGWYASLGQPIAAAHIH 144

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG ++ A+   A   L E+   + I + Y + V G+  +  + I         I
Sbjct: 145 RLDEYTSGPVLFAKNEYAHLKLDEAMSRKEIGRTYIAFVQGVVSSALKII------DQPI 198

Query: 209 GGDYVHVVKQN-EKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           G D  H  ++        AI+H ++++ + + +   + +   TGRTHQ+RVH    G P+
Sbjct: 199 GRDRHHNQRRRVSPTGKPAITHVELMEVYPKHEVSLVRLTLETGRTHQIRVHLSAAGHPL 258

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
           VGD  Y  + K     P Q    LH   +  PHP  G  +++  P P+ +++  D
Sbjct: 259 VGDALYGGSTK---WLPYQA---LHGERLVFPHPLTGETVELDDPWPSAIIQLRD 307


>gi|320536263|ref|ZP_08036307.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
 gi|320146881|gb|EFW38453.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
          Length = 312

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 68/288 (23%), Positives = 129/288 (44%), Gaps = 32/288 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V++N++ + RLDR  +   P +    + K LRSG++RV+ ++   + + +   V+ I  +
Sbjct: 7   VLDNNDSDRRLDRVVRLFLPKMPLSVIYKALRSGKIRVNGQKKHPDYKTKENDVLSIEEL 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +   +  ++E K  ++ +        ++S+ +Y+   + V NKP  I+V G   +A  I 
Sbjct: 67  L--FSSFLQEHKTRNNPIRQ------IESLYIYKGKDLLVLNKPVDIAVHGRGSLAESIA 118

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              K   DS   KP   HRLD+ T GI+  +++   AQ  +   +     K Y  ++ G 
Sbjct: 119 SSYKK--DSLSFKPGPLHRLDKGTEGIICFSQSLKGAQLFSACLKEGTCAKFYLGIIEG- 175

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              KKE +         I    + + +  E+  + A+ H                   TG
Sbjct: 176 -ALKKETVHIEQNTSEEITA-IIPIAQNTEQTLSLAVFHLI-----------------TG 216

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           + HQ+R H   +G  + GD +Y  +   +  + I ++ YL A  + +P
Sbjct: 217 KKHQIRRHCHAIGYQLFGDLRYGGS--KSIQNIIAHRYYLLAWRLYMP 262


>gi|295702688|ref|YP_003595763.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           megaterium DSM 319]
 gi|294800347|gb|ADF37413.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           megaterium DSM 319]
          Length = 303

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 105/239 (43%), Gaps = 33/239 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----------IAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +L+ED  + + NKP  +     S            AY     LK+       KPR  HRL
Sbjct: 85  ILFEDEHVLIVNKPINLDTHPSSEQDQKTLLNAVAAYFQKIGLKT-------KPRHVHRL 137

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D +TSG ++  +   A+    +    R+I + Y ++V GI K K++ I N       IG 
Sbjct: 138 DSDTSGAILFTKHFVASSVFDQLLAERKINRTYIAIVQGIIK-KEDGIIN-----EPIGR 191

Query: 211 DYVHVVKQN-EKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           D  H  ++   +    A + ++V+    A+    +E+   TGRTHQ+RVH  H+G P++G
Sbjct: 192 DRHHATRRRVSRTGQAAKTRYRVLKRNTAKNETLIELSLETGRTHQIRVHMSHIGYPLLG 251

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKY 326
           D  Y            + +  LHA  +   HP    R+   APL   +   +  L F Y
Sbjct: 252 DTLYGGKRLK------EQQQALHAIKLSFLHPFTHQRVSAVAPLTQQVFSPYSKL-FSY 303


>gi|294635111|ref|ZP_06713622.1| tRNA pseudouridine synthase [Edwardsiella tarda ATCC 23685]
 gi|291091488|gb|EFE24049.1| tRNA pseudouridine synthase [Edwardsiella tarda ATCC 23685]
          Length = 264

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 62/230 (26%), Positives = 98/230 (42%), Gaps = 46/230 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKPAG  V              +SW+D K             G+     
Sbjct: 3   IIYQDEHLVAINKPAGWLVH-------------RSWLDRKEKVVVMQTVRDQLGRHVYTV 49

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++  +   A+ L + F   +I K+Y ++V G  +   E + ++ L    
Sbjct: 50  HRLDRPTSGVLLMGLSSEVARALAQQFEQHQIHKVYHAVVRGYLQG--EALLDYPLTPEL 107

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQL 255
             I   +    +  E+G   A +H++ +               +F  +E+ P TGR HQL
Sbjct: 108 DKIADRF----RSAERGPQPAQTHYRGVATAEVPLAIGRYPTARFSLVELTPQTGRKHQL 163

Query: 256 RVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           R H  H+  PI+GD  H      +G         L LHA  + L HP  G
Sbjct: 164 RRHMAHLRHPIIGDTAHGDLRQNRGVAAHFGTAGLMLHASELQLTHPVTG 213


>gi|229526265|ref|ZP_04415669.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae bv.
           albensis VL426]
 gi|229336423|gb|EEO01441.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae bv.
           albensis VL426]
          Length = 570

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 68/232 (29%), Positives = 107/232 (46%), Gaps = 23/232 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H+++   + D+ + L+  +      ++Y+D  I V NKPA      G  +   +   L
Sbjct: 343 LAHMLEGMPLEDNPL-LSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRL 401

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+   ++ +     H LD  TSG+LV A TR A + L + F  R +QK Y +L+ G    
Sbjct: 402 KAQF-TQAEGVFALHCLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSE 460

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +  I      +  + GD     +Q    +    A++H++ +    Q    + + PHTGR
Sbjct: 461 TQGEI------QLPLCGDLDDRPRQKVCWQQGKPALTHWETVQV-EQNRTRVYLYPHTGR 513

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLRVH  H   +  PIVGD  Y    K         +L+LHA  +   HP
Sbjct: 514 THQLRVHCAHHLGLNTPIVGDDLYGLQDK---------RLFLHAEQLSFAHP 556


>gi|239816627|ref|YP_002945537.1| pseudouridine synthase [Variovorax paradoxus S110]
 gi|239803204|gb|ACS20271.1| pseudouridine synthase [Variovorax paradoxus S110]
          Length = 225

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 58/211 (27%), Positives = 104/211 (49%), Gaps = 25/211 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           L++ED+ + V NKPAG+    G G           ++ W D+      + HRLD  TSG+
Sbjct: 6   LIHEDAHLLVLNKPAGLLCVPGRGEDKQDCLSARAMRRWPDAL-----IVHRLDMATSGL 60

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-VV 216
           +++AR  A  + L ++F  RR+ K Y ++V G    + E    W +  + +  D+ +  +
Sbjct: 61  VLMARGAAMQRALGDAFAERRVHKRYEAIVDGAMPVQDE----WSVIDAPLMADWPNRPL 116

Query: 217 KQNEKGANYAISHFKVIDCFAQ------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           ++ +     +++ ++ +   +       +   L ++P TGR+HQLRVH L +G  I+GD 
Sbjct: 117 QKVDPAGKPSLTRWRALSSSSSAPDGNTQASHLLLEPLTGRSHQLRVHLLSIGHSILGDA 176

Query: 271 KY-CANFKGNFTSPIQNKLYLHARYMDLPHP 300
            Y  A+ +         +L LHA  +   HP
Sbjct: 177 LYGSADVQARAP-----RLLLHASELGFVHP 202


>gi|61553985|gb|AAX46489.1| hypothetical protein FLJ14494 [Bos taurus]
          Length = 304

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 88/179 (49%), Gaps = 20/179 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPRLTHRLDQETSG 156
           ++++D ++ V NKP G+ V GG G+   I   L          K +   L HRLD+ET+G
Sbjct: 99  IVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKPLHLCHRLDKETTG 158

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-- 214
           ++V+A  +  A  + E FR R++ K YW++   +P  +   +   +++K   G  + H  
Sbjct: 159 VMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIVEKEAQGQQHHHKM 218

Query: 215 -------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
                        V  ++ + A  A++ ++V+   +     LE+QP TG  HQLRV  L
Sbjct: 219 TLSPSYRMDDGKMVRVRSSRNAQLAVTQYRVLS-SSLSAALLELQPITGIKHQLRVPCL 276


>gi|322378491|ref|ZP_08052942.1| Pseudouridine synthase [Helicobacter suis HS1]
 gi|322380818|ref|ZP_08054919.1| 23S rRNA-specific pseudouridylate synthase [Helicobacter suis HS5]
 gi|321146755|gb|EFX41554.1| 23S rRNA-specific pseudouridylate synthase [Helicobacter suis HS5]
 gi|321149093|gb|EFX43542.1| Pseudouridine synthase [Helicobacter suis HS1]
          Length = 250

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 104/220 (47%), Gaps = 32/220 (14%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETS 155
           LK+ +LY+D ++ V NK            A HID    S+   +  KP +L HRLD+ TS
Sbjct: 54  LKTDVLYQDQELLVLNK------------ATHID----SYTLERQHKPYKLLHRLDKSTS 97

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A+     + L  +F+ R + K Y +L+ GI K  K       ++ +H+  +   V
Sbjct: 98  GLLLLAQATFYTKALL-AFKKREVYKEYLALIEGILKRPKTLTQPLSVRTNHMHFNKGFV 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               +     AI+H   I    Q+   L++   TG THQ+R H  H+G PIVGD  Y  +
Sbjct: 157 KTFVDLKGKPAITHLYPIYHTKQQ-TLLKVVIETGITHQIRAHLSHIGHPIVGDLIYGGS 215

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
              +F        +LHA  + L          +AP+P H 
Sbjct: 216 PNPHF--------FLHAYKLAL-----LEHHFSAPIPPHF 242


>gi|228476465|ref|ZP_04061155.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Streptococcus salivarius SK126]
 gi|228251886|gb|EEK10932.1| ribosomal large subunit pseudouridine synthase, RluD   family
           [Streptococcus salivarius SK126]
          Length = 289

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 60/201 (29%), Positives = 87/201 (43%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  + V NKP G+   G       +   + ++    GQ   + HRLD ETSG ++ A
Sbjct: 84  LYEDQHLIVVNKPEGMKTHGNEPTEIALLNHVSAYC---GQTCYVVHRLDMETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      ++IQ+ YW+L  G  + K+    + + +  H   D    V    K
Sbjct: 141 KNPFILPILNRLLEDKKIQRQYWALAEGKFQTKETVYKDKIGRDRH---DRRKRVVDPRK 197

Query: 222 G--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           G  A   I+  K     +   C L+    TGRTHQ+RVH  H G  I+GD  Y       
Sbjct: 198 GQVAYTTITRLKAFKGASLVNCQLK----TGRTHQIRVHLAHHGHAILGDPLYSHR---- 249

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 250 ----PASRLMLHAHTLSFTHP 266


>gi|242374099|ref|ZP_04819673.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
 gi|242348224|gb|EES39826.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
          Length = 275

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 59/243 (24%), Positives = 110/243 (45%), Gaps = 34/243 (13%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +L ++  S ++++++++ K  +++ +G  V +P      N++                  
Sbjct: 27  DLHQLNMSKEIKINEQQAKLTDKVVTGDEVIVPTPKEKSNYL----------------PS 70

Query: 96  FLKSILLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +  + + YED+ + +  KP G+      ++  + +  HI       +DS   +P   HRL
Sbjct: 71  YRYAQIYYEDNDLAIVMKPKGVKTHPNDLKESNTLMNHI----IYTIDSDYVEP--IHRL 124

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           DQET G+L+VA+     + L       +I ++Y + V  +   K + I         IG 
Sbjct: 125 DQETVGLLIVAKNPIMKKILDRMLEDNQITRVYKANVKALLPIKPQTI------DMPIGK 178

Query: 211 DYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D  H  K+        AI+H        +  C L+++  TGRTHQ+RVH   +G P++GD
Sbjct: 179 DKFHPNKRRISNTGQRAITHILSSQMIKEGVCQLDIKLDTGRTHQIRVHLAEIGHPVIGD 238

Query: 270 HKY 272
             Y
Sbjct: 239 PLY 241


>gi|161615893|ref|YP_001589858.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|168261891|ref|ZP_02683864.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|197262707|ref|ZP_03162781.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|198243086|ref|YP_002216938.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|204928136|ref|ZP_03219336.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205353907|ref|YP_002227708.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207858230|ref|YP_002244881.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|161365257|gb|ABX69025.1| hypothetical protein SPAB_03686 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|197240962|gb|EDY23582.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|197937602|gb|ACH74935.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|204322458|gb|EDZ07655.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205273688|emb|CAR38681.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205349202|gb|EDZ35833.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|206710033|emb|CAR34388.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|322614227|gb|EFY11159.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322620959|gb|EFY17817.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322624022|gb|EFY20856.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322628239|gb|EFY25028.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322633358|gb|EFY30100.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322636065|gb|EFY32773.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322639401|gb|EFY36089.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322643737|gb|EFY40288.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322648849|gb|EFY45296.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322655158|gb|EFY51468.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322658011|gb|EFY54279.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322664112|gb|EFY60311.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322667081|gb|EFY63253.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322673129|gb|EFY69236.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322677880|gb|EFY73943.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322681054|gb|EFY77087.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322685651|gb|EFY81645.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|323194790|gb|EFZ79977.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323196541|gb|EFZ81689.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323205046|gb|EFZ90029.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323207753|gb|EFZ92699.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323212695|gb|EFZ97512.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323214822|gb|EFZ99570.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323222551|gb|EGA06916.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323226431|gb|EGA10639.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323230690|gb|EGA14808.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323234959|gb|EGA19045.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323238998|gb|EGA23048.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323244644|gb|EGA28650.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323247260|gb|EGA31226.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323251792|gb|EGA35657.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323257479|gb|EGA41169.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323263264|gb|EGA46801.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323267516|gb|EGA51000.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323272705|gb|EGA56111.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
 gi|326624702|gb|EGE31047.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
 gi|326629020|gb|EGE35363.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
          Length = 260

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 109/239 (45%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +     + +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFA----RED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+  + + N ++       +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KH-GDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLMIQAGLDETWMQALTQFGWR 237


>gi|225872530|ref|YP_002753985.1| pseudouridine synthase, RluA family [Acidobacterium capsulatum ATCC
           51196]
 gi|225792126|gb|ACO32216.1| pseudouridine synthase, RluA family [Acidobacterium capsulatum ATCC
           51196]
          Length = 301

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 70/291 (24%), Positives = 124/291 (42%), Gaps = 33/291 (11%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVINALNHIIKEQKILDS 86
           YPH +    Q+ L  G++ ++    + +  + +GQV+    PP                 
Sbjct: 29  YPHSSAEVWQQRLSHGEITLNGITAQGSESVAAGQVLVWNCPP----------------- 71

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
               T+    L   +L+ED ++   NKP+G+    GSG    ++  L   V         
Sbjct: 72  ---WTEPDAPLHFDVLFEDDELIAVNKPSGLPTLPGSGF---LENTLLRLVRRYAPHASP 125

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRL + TSGI++ ++T   A  L   +   ++QK+Y ++   + ++++  I   + +  
Sbjct: 126 VHRLGRATSGIVLFSKTAQGAALLEAIWNTSKVQKVYRAVAVNVAEHEEYEIHTPIGRVP 185

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           H     V       K    + S  KV+          E+  H+GR HQ+R+H   +G P+
Sbjct: 186 HPRLGSVWAASSTGK---PSWSSAKVL-ARGTTTTTFEVTLHSGRPHQIRIHLASVGHPL 241

Query: 267 VGDHKYCAN---FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           VGD  Y         +   P      LHA+++   HP  G ++ + APLP+
Sbjct: 242 VGDGLYGPGGLPLADHPGLPGDGGYLLHAQFLAFLHPTSGSQISLEAPLPS 292


>gi|160889892|ref|ZP_02070895.1| hypothetical protein BACUNI_02323 [Bacteroides uniformis ATCC 8492]
 gi|156860884|gb|EDO54315.1| hypothetical protein BACUNI_02323 [Bacteroides uniformis ATCC 8492]
          Length = 303

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 62/224 (27%), Positives = 108/224 (48%), Gaps = 21/224 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 88  IVYEDAYIIVIEKMQGLLSVNTDRQKERTAYTI---LNEYVQRSGKQHRVHIVHRLDRDT 144

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+     + L +++      + Y ++V G  +     + +WL  +      YV+
Sbjct: 145 SGLMMFAKDEKTQRTLRDNWHGIVTDRRYVAVVVGEMEKDAGTVVSWLTDRKL----YVY 200

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++ G   +I+H++ I   A  +  +E+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 201 SSPTDD-GGQESITHYRTIKR-ANGYSLVELNLETGRKNQIRVHMQDLGHPIIGDGRYGL 258

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVK 317
                  +PI  +L LHA  +   HP  G L +   P P    K
Sbjct: 259 ----EDVNPI-GRLALHAFKLCFYHPVTGELMRFETPYPGEFKK 297


>gi|109947567|ref|YP_664795.1| putative ribosomal pseudouridine synthase [Helicobacter acinonychis
           str. Sheeba]
 gi|109714788|emb|CAJ99796.1| putative ribosomal pseudouridine synthase [Helicobacter acinonychis
           str. Sheeba]
          Length = 242

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 62/202 (30%), Positives = 98/202 (48%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K W         L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKDWT--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +LV GI   +KE  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKERAVKKEYLALVQGIVGEEKEINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L+++  TGRTHQ+RVH  H+  PI+GD  Y   
Sbjct: 157 SKKGQEAITI-ITPLKIIN----KKTLLKVEIKTGRTHQIRVHLKHINHPIMGDTLY--- 208

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
              N       +L LHA  + L
Sbjct: 209 ---NNEPSSAKRLMLHAHKIAL 227


>gi|260777893|ref|ZP_05886786.1| pseudouridylate synthase LSU rRNA-specific [Vibrio coralliilyticus
           ATCC BAA-450]
 gi|260605906|gb|EEX32191.1| pseudouridylate synthase LSU rRNA-specific [Vibrio coralliilyticus
           ATCC BAA-450]
          Length = 559

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 64/204 (31%), Positives = 100/204 (49%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + V NKP+G+ SV G +          + + D +G  P + HRLD  TSG+LV
Sbjct: 358 ILFEDEAMVVVNKPSGLLSVPGKTIKDSAYTRLQQRYPDVEG--PFVIHRLDMATSGLLV 415

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A T+ A + L + F  R +QK Y +L+ G      +      L       D    +   
Sbjct: 416 FALTKRANKSLQKQFISRSVQKRYVALLEG---EVNQTSGQIELPMRGDPDDRPRQLVCF 472

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANF 276
           E G   A +++++I+    +   L + P TGRTHQLRVH  H   +  P+VGD  Y    
Sbjct: 473 EHGKP-AETYWELIESRDGR-SKLYLYPKTGRTHQLRVHCAHRLGLNLPMVGDGLYGQR- 529

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                    ++L+LHA+ +++ HP
Sbjct: 530 --------SDRLHLHAQRLEIEHP 545


>gi|254303628|ref|ZP_04970986.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148323820|gb|EDK89070.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 288

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 105/227 (46%), Gaps = 30/227 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-------PRLTHRLDQE 153
           + YED  + + NK   I V         +D  L + V +  +K       PR  +RLD  
Sbjct: 75  IAYEDENLLIVNKEPYIIVHPTQK---KVDKTLANAVVNYFEKTLGKTLVPRFYNRLDMN 131

Query: 154 TSGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           TSG++++A+   T+A  Q  TE      ++K Y  +V GI +     I   + K   IG 
Sbjct: 132 TSGLIIIAKNSYTQAFLQDKTE------VKKTYKVIVSGIIEEDDFFIEKPIGK---IGD 182

Query: 211 DYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D   +    E G   A +H KV++  + +   +LE + +TGRTHQ+R H   +G  +VGD
Sbjct: 183 DLRRIELSEENGGKSAKTHIKVLERNYEKNITFLEARLYTGRTHQIRAHLSLIGHSLVGD 242

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
             Y  N +      +  +  LHA  ++  +P+    L+I   +P  M
Sbjct: 243 ELYGGNME------LAKRQMLHAYKLEFQNPKTLENLKIEIDIPIDM 283


>gi|313894254|ref|ZP_07827819.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313441078|gb|EFR59505.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 288

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 81/285 (28%), Positives = 126/285 (44%), Gaps = 54/285 (18%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M++  Y V E  E  + + ++ K  +  ++  ++Q + R       KKRVK N+R+   Q
Sbjct: 1   MSWKTYTVKEPTE--LTVSKYVKERFS-LSSRDIQMMFR-------KKRVKVNSRVAHSQ 50

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK-PAGISVQGG 122
             R     + L   + + K  D  V++ K        +LYED+   V NK P  +    G
Sbjct: 51  --RSLKKGDVLTLELPQDK--DYGVDVEKGP----ITVLYEDAHTLVINKDPFMLVHPAG 102

Query: 123 SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  +  ++  +   KG   K R  HRLD++TSG ++  +T+ A Q+ T+  +  RI 
Sbjct: 103 QTKSCTLSNYVAGYYAKKGVVHKVRPVHRLDRDTSGCILFGKTKEAQQYYTDELQAGRID 162

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-- 238
           +IY  LV G        I +  +  + IG D V               + +VID F Q  
Sbjct: 163 RIYTGLVEGR-------IDSDGVVDAPIGIDPV-------------FDNRRVIDEFGQPA 202

Query: 239 -----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                          L  +  TGRTHQ+RVH  H+G PIVGD  Y
Sbjct: 203 QTEYIVLSHDGDHTLLRFRLLTGRTHQIRVHMEHIGHPIVGDAMY 247


>gi|299740960|ref|XP_001834124.2| hypothetical protein CC1G_08755 [Coprinopsis cinerea okayama7#130]
 gi|298404490|gb|EAU87719.2| hypothetical protein CC1G_08755 [Coprinopsis cinerea okayama7#130]
          Length = 298

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 77/260 (29%), Positives = 115/260 (44%), Gaps = 37/260 (14%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-----HIDGFLKSWV 137
           IL+  +   K    LKS+L Y D ++ V NKPAG+  Q G  +        +D  LK   
Sbjct: 4   ILERHLAKGKLPTTLKSVL-YLDRQVLVMNKPAGLVSQLGRQLPEMKTRDTLDKVLKQIE 62

Query: 138 DSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                K   R  HRLD  T+G L  A T+ +A+ L++ F   +++K Y +LV G     K
Sbjct: 63  RRLELKEALRPLHRLDTATTGCLAFATTQTSARSLSKQFAQGQVEKSYLALVSG----GK 118

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-------KGANYAISHFKVI-DCFAQKFCWLEMQP 247
           E             G     +K  +        G   +++ + ++          + +  
Sbjct: 119 ETFPG-------TSGRIDTPIKYQDGYFDGLGTGGKLSLTEWSLLASSPVLPISLVRLNL 171

Query: 248 HTGRTHQLRVH-ALHMGCPIVGDHKYCANFKGN---FTSPIQNKLYLHA------RYMDL 297
            TG  HQLR+H A  +G PI+GD +Y ++   +       I+  LYLHA      RY   
Sbjct: 172 LTGNKHQLRIHMAKKLGAPILGDDRYSSSKVASKLLSEGRIKPNLYLHASDIAFVRYRQR 231

Query: 298 PHPEGGRLQITAPLPAHMVK 317
              +  RL ITAPLPAH V+
Sbjct: 232 GPQKRFRLGITAPLPAHFVE 251


>gi|270294141|ref|ZP_06200343.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|317478898|ref|ZP_07938046.1| RluA family pseudouridine synthase [Bacteroides sp. 4_1_36]
 gi|270275608|gb|EFA21468.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|316904932|gb|EFV26738.1| RluA family pseudouridine synthase [Bacteroides sp. 4_1_36]
          Length = 303

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 62/224 (27%), Positives = 108/224 (48%), Gaps = 21/224 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQET 154
           ++YED+ I V  K  G+    + +     AY I   L  +V   G++ R  + HRLD++T
Sbjct: 88  IVYEDAYIIVIEKMQGLLSVNTDRQKERTAYTI---LNEYVQRSGKQHRVHIVHRLDRDT 144

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+     + L +++      + Y ++V G  +     + +WL  +      YV+
Sbjct: 145 SGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVVGEMEKDAGTVVSWLTDRKL----YVY 200

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++ G   +I+H++ I   A  +  +E+   TGR +Q+RVH   +G PI+GD +Y  
Sbjct: 201 SSPTDD-GGQESITHYRTIKR-ANGYSLVELNLETGRKNQIRVHMQDLGHPIIGDGRYGL 258

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVK 317
                  +PI  +L LHA  +   HP  G L +   P P    K
Sbjct: 259 ----EDVNPI-GRLALHAFKLCFYHPVTGELMRFETPYPGEFKK 297


>gi|269303280|gb|ACZ33380.1| RNA pseudouridine synthase family protein [Chlamydophila pneumoniae
           LPCoLN]
          Length = 283

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 49/172 (28%), Positives = 86/172 (50%), Gaps = 18/172 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED    ++ KP  ++ +  +    H+  F               HRLD+ TSG L++
Sbjct: 73  ILWEDDYSIIYEKPPHLTTEQMA----HMTRFFT------------VHRLDKGTSGCLLM 116

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +++ AA  L + F+ R+I K Y +LV+G PK K   + ++        G  +       
Sbjct: 117 GKSKQAATELMKLFKQRKIHKQYMALVFGHPKKKFGTVKSYTAPVYRRCGAVIFGAASPS 176

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +G    I+ + V+D + +++  +  +P TGRTHQ+R+    +G PIVGD  Y
Sbjct: 177 QG-KLTITEWSVLDSY-KRYSLMLCKPITGRTHQIRLQMGLLGHPIVGDVDY 226


>gi|217032147|ref|ZP_03437646.1| hypothetical protein HPB128_186g13 [Helicobacter pylori B128]
 gi|298736447|ref|YP_003728973.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori B8]
 gi|216946137|gb|EEC24746.1| hypothetical protein HPB128_186g13 [Helicobacter pylori B128]
 gi|298355637|emb|CBI66509.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori B8]
          Length = 327

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 105/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W+ SK       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVVHKAPSVK---EPTLVDWLKSKNYELSNLGLKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFISLLASQNGMDLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|254449188|ref|ZP_05062638.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium HTCC5015]
 gi|198261234|gb|EDY85529.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium HTCC5015]
          Length = 217

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 54/203 (26%), Positives = 94/203 (46%), Gaps = 21/203 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D      +KP+G+    G   A      + S +     +  + HRLD +TSG++V+
Sbjct: 15  ILYQDEHCLFIDKPSGLLSVPGRHPANR--DSVASRLQQDFPEAHIVHRLDMDTSGVMVI 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVHV 215
           A    + + L+  F+ RR QK Y ++V   P  ++       I +W  +          +
Sbjct: 73  ALNVESHRFLSRQFQERRSQKRYEAIVSATPTPEQGSVDLPLICDWPNRP---------L 123

Query: 216 VKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            K + +    +++H++    +       + + PHTGR+HQLRVH   +GCPI+GD  Y  
Sbjct: 124 QKVDHEIGKPSLTHYETTGPWQDGAGTRVVLTPHTGRSHQLRVHMAAIGCPILGDSFYAP 183

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
                 T     +L LHA  + +
Sbjct: 184 ----KVTQEAAPRLLLHASELSI 202


>gi|152978874|ref|YP_001344503.1| tRNA pseudouridine synthase C [Actinobacillus succinogenes 130Z]
 gi|150840597|gb|ABR74568.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 238

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 58/213 (27%), Positives = 93/213 (43%), Gaps = 18/213 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFIVAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  L   F  + ++K Y ++V G    +        +++  I   +     Q  
Sbjct: 64  ALHSDIANLLCRQFEGKTVRKSYLAVVRGYLSGEARIDYALKIRRDKIADKF----SQEN 119

Query: 221 KGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ +  +               ++  + + PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEAQAAVTDYTGLQTAEMPWAVGKYQTCRYSLVRLMPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHP 300
           +Y  +   N     Q   ++L LHA  +   HP
Sbjct: 180 QY-GDLHQNRALAEQTQVSRLMLHAEKLAFNHP 211


>gi|300780856|ref|ZP_07090710.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           genitalium ATCC 33030]
 gi|300532563|gb|EFK53624.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           genitalium ATCC 33030]
          Length = 307

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 74/324 (22%), Positives = 148/324 (45%), Gaps = 24/324 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + +VV    ++MR+D      +  ++     +++ +G+V +D  RV  ++R+ +G 
Sbjct: 1   MSRYRSLVVPEGLDSMRVDAAVAKAF-GLSRTVAAELIEAGEVLIDGSRVTKSDRVSTGH 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA--GISVQG 121
            + +  +       + +++I++    LT   D    I++ +   +         G +V G
Sbjct: 60  SLEVT-LPEPKQAPMPKEEIVE---GLTVLYDDDDVIVVDKPVGVAAHPTLGWDGPTVVG 115

Query: 122 G-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G   + Y +            ++  +  RLD  TSG++VVA +      L  +F+ R ++
Sbjct: 116 GLQAMGYQLPDA------GPPERKGIVQRLDVGTSGVMVVANSIPGYSVLKRAFKERTVE 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++V G+P      I   + +    G  +            ++++H++V++ F ++ 
Sbjct: 170 KTYHAVVQGLPDPIVGTIDAPIGRHPSSGWKFAVTAD-----GRHSVTHYEVLEAF-REA 223

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPH 299
             LE+   TGRTHQ+RVH   +G P VGD  Y ++   G     I+   +LHA  +   H
Sbjct: 224 SLLEVHLETGRTHQIRVHMSSVGHPCVGDPMYGSDPNLGKRLGLIRQ--WLHATALGFVH 281

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G  +++ +P P  +    D L
Sbjct: 282 PGTGVWMEVESPYPPDLQHAVDVL 305


>gi|119713310|gb|ABL97374.1| putative ribosomal large subunit pseudouridine synthase D
           [uncultured marine bacterium EB80_02D08]
          Length = 310

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 59/187 (31%), Positives = 87/187 (46%), Gaps = 38/187 (20%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----PR--LTHRLDQETSG 156
           +E+    + NKPAG+ +  GSG     DG L + +  K  +    PR  + HRLD++TSG
Sbjct: 82  FENEDFIIINKPAGLIMHPGSGC---YDGTLANGLIFKFPELVNIPRSGIVHRLDKDTSG 138

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-----------IPKNKKECIANWLLKK 205
           IL+VART +         + RR+ K Y S+V G           I ++K       + + 
Sbjct: 139 ILLVARTESFRNFFINEMQERRVIKKYSSIVIGSTLGSFSIEDPIGRDKNNRTKMAIRED 198

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              G D +  VK  E   NY++               L+++  TGRTHQ+RVH      P
Sbjct: 199 ---GKDALTFVKLKENIGNYSV---------------LDVRIETGRTHQIRVHLASKKLP 240

Query: 266 IVGDHKY 272
           I+GD  Y
Sbjct: 241 IIGDKTY 247


>gi|94989396|ref|YP_597497.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|94993288|ref|YP_601387.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
 gi|94542904|gb|ABF32953.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|94546796|gb|ABF36843.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
          Length = 333

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 61/206 (29%), Positives = 91/206 (44%), Gaps = 19/206 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K   LYED  I + NKP G+   G       +   + ++    GQ   + HRLD+ETSG 
Sbjct: 118 KVTCLYEDEHIIIVNKPEGMKTHGNDPTELALLNHVSAYT---GQTCYVVHRLDKETSGA 174

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+T      L      R I + Y +LV G        + +  +   H  G + H  +
Sbjct: 175 ILFAKTPFILPILNRLLEKRDIHREYLALVHG-------SLDSPRVTYHHPIGRHRHDRR 227

Query: 218 Q---NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +   +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H G  + GD  Y +
Sbjct: 228 KRVVDPINGKKAITEVTLVKNFHKTASLLNCQLQTGRTHQIRVHLAHQGHVLFGDPLY-S 286

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           N K +       +L LHA  + L HP
Sbjct: 287 NGKKDCA-----RLMLHAYQLRLKHP 307


>gi|326431501|gb|EGD77071.1| hypothetical protein PTSG_07411 [Salpingoeca sp. ATCC 50818]
          Length = 418

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 62/252 (24%), Positives = 99/252 (39%), Gaps = 28/252 (11%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLK 134
           ++   ++ D+ +  +     +   ++YED  I   NKP G+ VQ       H  +     
Sbjct: 140 LVDNSRLQDNVIVTSTDPSSIDLDIIYEDEAIVCVNKPPGLPVQPQGADQLHNVLAALHH 199

Query: 135 SWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +  + G     PRL HRLD  TSG+LVVA  R  A  +    + R++ K Y +LV G  
Sbjct: 200 RYRQNDGALDVVPRLVHRLDVNTSGVLVVALDRKIAGRMGALLQSRQVIKQYSALVHGEL 259

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           + +    A          G  +     +  G      +  V          +  +P TGR
Sbjct: 260 RGQGVITAPIARAPKDPEGSRIQKFTVSPHGKPSETEYEGVHASAHWNASLVTFRPRTGR 319

Query: 252 THQLRVHALHMGCPIVGDHKY----------------------CANFKGNFTSPIQ-NKL 288
           THQ+RVH+ H+G P++ D +Y                      C+     F S ++  + 
Sbjct: 320 THQIRVHSHHLGHPLLFDDRYHLHDHQQQAQQQQHEQQQQQSACSQLDNEFASHVRMRRC 379

Query: 289 YLHARYMDLPHP 300
            LH   M   HP
Sbjct: 380 ALHCDSMTFTHP 391


>gi|238760461|ref|ZP_04621598.1| tRNA pseudouridine synthase C [Yersinia aldovae ATCC 35236]
 gi|238701303|gb|EEP93883.1| tRNA pseudouridine synthase C [Yersinia aldovae ATCC 35236]
          Length = 257

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 101/225 (44%), Gaps = 23/225 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I         + +
Sbjct: 64  ALSSEVARTLSLQFEQHQIQKTYHAVVRGYVLESGTVDYAMAEELDKIADKRA----RQD 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
           K    +++H++ +               ++  + ++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYQPVAQVEVPLAIGRYETARYSLVALKPETGRKHQLRRHMAHIRHPIIGDT 179

Query: 270 -HKYCANFKG---NFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
            H      +G   +F  P   +L LHA ++ L HP  G  L +TA
Sbjct: 180 AHGDLRQNRGVAEHFACP---RLMLHASHLQLNHPVTGEALLLTA 221


>gi|218902402|ref|YP_002450236.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|218537046|gb|ACK89444.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
          Length = 292

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 142/313 (45%), Gaps = 41/313 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+  P
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQAGEEIRVFFP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 63  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 107

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 108 VANALLSHYDKQYLAST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 164

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G    ++  I   + +KS    D +      E+G   AI+HF+VI     K   +
Sbjct: 165 EALVHGEMIEQEGTIDAPIGRKS----DSIIERTVCEEG-QRAITHFRVIASANHK-THV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
            ++  TGRTHQ+RVH  H+G P++GD  Y     G     ++ +  LH+  +   HP   
Sbjct: 219 SLELDTGRTHQIRVHMAHIGHPLLGDTLY-----GGKRDEVKRQ-ALHSTSLTFYHPILE 272

Query: 303 GRLQITAPLPAHM 315
             +  TA +P+ M
Sbjct: 273 KEMSFTAMIPSDM 285


>gi|168820315|ref|ZP_02832315.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|205342862|gb|EDZ29626.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|320087390|emb|CBY97155.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Weltevreden str. 2007-60-3289-1]
          Length = 260

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 21/232 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +     + +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFA----RED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPRTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
           K+  + + N ++       +L LHA  ++L HP  G+  I   + A + +TW
Sbjct: 180 KH-GDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLI---IQAGLDETW 227


>gi|163788545|ref|ZP_02182990.1| putative ribosomal large chain pseudouridine synthase A
           [Flavobacteriales bacterium ALC-1]
 gi|159875782|gb|EDP69841.1| putative ribosomal large chain pseudouridine synthase A
           [Flavobacteriales bacterium ALC-1]
          Length = 561

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 62/204 (30%), Positives = 99/204 (48%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           ++YED  + V NKP       G  I   +   +++++ D+ G  P L HRLD  TSG+L+
Sbjct: 360 IIYEDDFLVVLNKPHEFLSVPGKTIKDSVLTRMQNYLPDATG--PLLLHRLDMSTSGLLL 417

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+     ++L + F  R ++K Y +L+ G  +  +  I   L  +  +      +V   
Sbjct: 418 VAKNERTHKNLQKQFIKRIVKKRYVALLNGKLEPSEGTID--LPLRVDLNNRPRQLV--C 473

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANF 276
           ++    A + ++VI+    K   +   P TGRTHQLRVHA H   +  PI+GD  Y    
Sbjct: 474 DEHGKLAKTKYEVIEIKNNK-TRIHFYPITGRTHQLRVHAAHYKGLNMPIIGDDLYGT-- 530

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                    N+L+LHA  +   HP
Sbjct: 531 -------ASNRLHLHAEMLSFEHP 547


>gi|329894521|ref|ZP_08270335.1| Ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium IMCC3088]
 gi|328923046|gb|EGG30371.1| Ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium IMCC3088]
          Length = 217

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 64/210 (30%), Positives = 101/210 (48%), Gaps = 23/210 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +LY+D  +    KP  + SV G   +     I    +++ D+     R+ HRLD +TSG 
Sbjct: 15  ILYQDEHLLFVAKPHFLLSVPGKHPLNKDCLISRLQQTYPDA-----RIVHRLDLDTSGT 69

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+A  +     L+  FR+R++ K Y ++V G  K     I         I  D+ +  +
Sbjct: 70  MVIALGKERHAELSRQFRLRQVAKSYIAVVAGEIKENAGTI------DLPIRADWENRPR 123

Query: 218 QN---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           Q    E+G   +I+HF VI         L + P TGR+HQLR+H L +G PI+G    C 
Sbjct: 124 QKVCFERG-KPSITHFTVI-ARGNNSTRLRLHPVTGRSHQLRLHLLSIGHPILG----CD 177

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +    +    ++L LHA  + L HP  G+
Sbjct: 178 LYADPESLSRSDRLLLHAERLALKHPVTGQ 207


>gi|255017039|ref|ZP_05289165.1| hypothetical protein LmonF_03093 [Listeria monocytogenes FSL
           F2-515]
          Length = 201

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 93/181 (51%), Gaps = 12/181 (6%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    
Sbjct: 27  RPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAP 85

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           + ++      + VV+  ++    A +HF+V++     +  +  +  TGRTHQ+RVH  ++
Sbjct: 86  IGRAKEDRQKMAVVRDGKE----ARTHFEVLERLPG-YTLINCKLDTGRTHQIRVHLKYI 140

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           G P+ GD KY     G   +   N  +LHA  +   HP    R+   APLP+   K   S
Sbjct: 141 GHPLAGDPKY-----GPKNTIKGNGQFLHAAKLGFDHPTTNERMTFEAPLPSSFEKALKS 195

Query: 322 L 322
           L
Sbjct: 196 L 196


>gi|238018437|ref|ZP_04598863.1| hypothetical protein VEIDISOL_00263 [Veillonella dispar ATCC 17748]
 gi|237864908|gb|EEP66198.1| hypothetical protein VEIDISOL_00263 [Veillonella dispar ATCC 17748]
          Length = 289

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 81/296 (27%), Positives = 130/296 (43%), Gaps = 66/296 (22%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M++  Y V E  E  + + ++ K  +  ++  ++Q + R       KKRVK N+R+   Q
Sbjct: 1   MSWKTYTVKEPTE--LTVSKYVKERFS-LSSRDIQMMFR-------KKRVKVNSRVAHSQ 50

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK-------PAG 116
             R     + L   + + K  D  V++ K        +LYED+   V +K       PAG
Sbjct: 51  --RSLKKGDVLTLELPQDK--DYGVDVEKGP----ITVLYEDAHTLVVDKAPFMLVHPAG 102

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              Q  SG    +  ++  +   KG   K R  HRLD++TSG ++  +T+ A Q+ T+  
Sbjct: 103 ---QTKSGT---LSNYVAGYYAKKGVVHKVRPVHRLDRDTSGCILFGKTKEAQQYYTDEL 156

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +  RI +IY  LV G  +   + + +  +                  G +    + +VID
Sbjct: 157 QAGRIDRIYTGLVEG--RINSDGVVDAPI------------------GVDPVFDNRRVID 196

Query: 235 CFAQ-------------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            F Q             +   L+ +  TGRTHQ+RVH  H+G PIVGD  Y    K
Sbjct: 197 EFGQPAQTEYTVLGHEGEHTLLKFKLLTGRTHQIRVHMEHIGHPIVGDAMYGTRNK 252


>gi|156844376|ref|XP_001645251.1| hypothetical protein Kpol_1060p49 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156115910|gb|EDO17393.1| hypothetical protein Kpol_1060p49 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 405

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 103/224 (45%), Gaps = 30/224 (13%)

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PPV      I +E  I++  +            ++YED ++ V NKP+GI V       Y
Sbjct: 93  PPVKQWCTSIEEENSIVEGKIGGID--------IVYEDDELLVVNKPSGIPVHPTG--QY 142

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +++  L   +   G+     +RLD+ TSG+L++A+ +  A  L E  R+  + K+Y + V
Sbjct: 143 YLNT-LTEILKKHGKLVSPCYRLDKTTSGLLIMAKNQIIASKLQEKIRVHDMTKLYLARV 201

Query: 188 WG-------IPKN---KKECIANWLLK---KSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            G       +P +    +E I   ++    KS +  D   +  + +  A  + S     D
Sbjct: 202 EGQFPKILEVPTDLILTQEMILERIMTPALKSSVDSDIFTLELKKQFPAGLSPSREAKTD 261

Query: 235 CFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  K+        +  +P TGRTHQ+R+H   +G PIV DH Y
Sbjct: 262 FYPVKYIPDLDQSIVLCKPLTGRTHQIRIHLARLGFPIVNDHFY 305


>gi|50915102|ref|YP_061074.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|56808190|ref|ZP_00365968.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Streptococcus
           pyogenes M49 591]
 gi|306826523|ref|ZP_07459832.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes ATCC 10782]
 gi|50904176|gb|AAT87891.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|304431250|gb|EFM34250.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes ATCC 10782]
          Length = 303

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 61/206 (29%), Positives = 91/206 (44%), Gaps = 19/206 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K   LYED  I + NKP G+   G       +   + ++    GQ   + HRLD+ETSG 
Sbjct: 88  KVTCLYEDEHIIIVNKPEGMKTHGNDPTELALLNHVSAYT---GQTCYVVHRLDKETSGA 144

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+T      L      R I + Y +LV G        + +  +   H  G + H  +
Sbjct: 145 ILFAKTPFILPILNRLLEKRDIHREYLALVHG-------SLDSPRVTYHHPIGRHRHDRR 197

Query: 218 Q---NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +   +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H G  + GD  Y +
Sbjct: 198 KRVVDPINGKKAITEVTLVKNFHKTASLLNCQLQTGRTHQIRVHLAHQGHVLFGDPLY-S 256

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           N K +       +L LHA  + L HP
Sbjct: 257 NGKKDCA-----RLMLHAYQLRLKHP 277


>gi|299783552|gb|ADJ41550.1| Pseudouridine synthase [Lactobacillus fermentum CECT 5716]
          Length = 329

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 74/292 (25%), Positives = 125/292 (42%), Gaps = 46/292 (15%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           +G+ +VD +RV+   +I   Q     P+   +     +  +  S   LT         ++
Sbjct: 71  AGEFQVDHRRVRPTTKILPNQ-----PLTLTVQPEPGDATVATSEEPLT---------IV 116

Query: 103 YEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED    V NKP G++   G       I   + G+L +  D+   +P L  RLD++T+G+
Sbjct: 117 YEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLVA-KDAPDLRPHLITRLDRDTAGL 175

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH--IGGDYVHV 215
           L+VA+   A+  ++       +QK Y ++V G               K H  I      +
Sbjct: 176 LLVAKHNVASSMISPQVEGHTMQKEYRAIVAGT------------FAKEHGIIDAPIARI 223

Query: 216 VKQNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             Q E+  N A    K  + +A++    +  + ++ H+GRTHQ+RVH   +G P++GDH 
Sbjct: 224 KGQIEREVNPAGQPAKT-EYWAEESRGDWTLVRLRLHSGRTHQIRVHMASVGHPLLGDHL 282

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y     G+ +      LY  A ++    P     L     +P      WD L
Sbjct: 283 YG----GDLSXTDHQALY--ASHLAFTDPFTQTNLAFEVEMPVAFKTLWDGL 328


>gi|270264957|ref|ZP_06193221.1| ribosomal large subunit pseudouridine synthase A [Serratia
           odorifera 4Rx13]
 gi|270041255|gb|EFA14355.1| ribosomal large subunit pseudouridine synthase A [Serratia
           odorifera 4Rx13]
          Length = 232

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 64/231 (27%), Positives = 104/231 (45%), Gaps = 23/231 (9%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H        LY+D  + + NKPAG+    G     ++D      V    
Sbjct: 3   KIIDTFIAPPCHDKIEN---LYQDESLVLINKPAGLLSLSGKN-PQNLDSVHHRLVQIF- 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +     L + F  R + K+Y +L+ G   N +  I   
Sbjct: 58  PGCTLVHRLDFGTSGLMVIARNKTVNAALCQQFSQRTVTKVYSALLCGHLDNDEGVIDAA 117

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF--------CWLEMQPHTGRTH 253
           + K   +    + +   + K A    S ++V++ F ++           +++ P TGRTH
Sbjct: 118 IAKDPAL-FPLMSICATHGKPAR---SGYRVVERFYRELEGGTLLPVTRVQLTPETGRTH 173

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEG 302
           QLR+H   +G PI+G    C  + G      +   +L LHA  +   HP G
Sbjct: 174 QLRIHCQLLGHPILG----CDLYGGRLLPGTERIPRLMLHASELHFVHPIG 220


>gi|71904404|ref|YP_281207.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94991334|ref|YP_599434.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94995246|ref|YP_603344.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|209560185|ref|YP_002286657.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
 gi|71803499|gb|AAX72852.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94544842|gb|ABF34890.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94548754|gb|ABF38800.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|209541386|gb|ACI61962.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
          Length = 333

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 61/206 (29%), Positives = 91/206 (44%), Gaps = 19/206 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K   LYED  I + NKP G+   G       +   + ++    GQ   + HRLD+ETSG 
Sbjct: 118 KVTCLYEDEHIIIVNKPEGMKTHGNDPTELALLNHVSAYT---GQTCYVVHRLDKETSGA 174

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+T      L      R I + Y +LV G        + +  +   H  G + H  +
Sbjct: 175 ILFAKTPFILPILNRLLEKRDIHREYLALVHG-------SLDSPRVTYHHPIGRHRHDRR 227

Query: 218 Q---NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +   +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H G  + GD  Y +
Sbjct: 228 KRVVDPINGKKAITEVTLVKNFHKTASLLNCQLQTGRTHQIRVHLAHQGHVLFGDPLY-S 286

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           N K +       +L LHA  + L HP
Sbjct: 287 NGKKDCA-----RLMLHAYQLRLKHP 307


>gi|229154871|ref|ZP_04282985.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           ATCC 4342]
 gi|228628429|gb|EEK85142.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           ATCC 4342]
          Length = 292

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 114/233 (48%), Gaps = 25/233 (10%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           G + V+ +     +++Q+G+ +R+  PV      +I E   L                ++
Sbjct: 36  GAIEVNGQYASVRHQLQAGEELRVFFPVEERSEGMIAEDIPL---------------CIV 80

Query: 103 YEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGILV 159
           YED  + V NK A +S +      A  +   L S  D +       +  RLD++TSG+++
Sbjct: 81  YEDDAVLVINKEANMSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGLML 140

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +      
Sbjct: 141 IAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKS----DSIIERTVC 196

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           E+G   A++HF+VID    K   + ++  TGRTHQ+RVH  H+G P++GD+ Y
Sbjct: 197 EEG-QRAVTHFRVIDSANHK-THVSLELDTGRTHQIRVHMAHIGHPLLGDNLY 247


>gi|261339742|ref|ZP_05967600.1| pseudouridine synthase A [Enterobacter cancerogenus ATCC 35316]
 gi|288318572|gb|EFC57510.1| pseudouridine synthase A [Enterobacter cancerogenus ATCC 35316]
          Length = 228

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 63/209 (30%), Positives = 97/209 (46%), Gaps = 14/209 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  + + NKP+G+    G     ++D      V +      L HRLD  TSGI+V+
Sbjct: 19  ILWQDDDLILINKPSGLLSLSGKN-PQNLDSVHYRLVQTF-PGCTLVHRLDFGTSGIMVI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +A    L   F  R + K Y +L+ G  K+  E I +  + K       + +   + 
Sbjct: 77  ARNKAINAALCHQFSQRAVSKAYTALLCGHVKD-DEGIIDAPIAKDPALFPLMSICAISG 135

Query: 221 KGANYAISHFKVIDCFAQ----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-N 275
           K A    S F+V++   +        +E+ P TGRTHQLR+H   +G  I+G   Y    
Sbjct: 136 KPAR---SRFRVVERIDKDEELPLTRVELIPETGRTHQLRIHCQQLGHSILGCDLYGGLE 192

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             G   +P   +L LHA  +D  HP  G 
Sbjct: 193 MPGAEGTP---RLMLHASGLDFVHPVSGE 218


>gi|261838022|gb|ACX97788.1| pseudouridine synthase D [Helicobacter pylori 51]
          Length = 327

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 105/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDKDLLVLNKPPNLVVHKAPSVK---EPTLVDWLEFKNYELSNLGLKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKTMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNHLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|157376031|ref|YP_001474631.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157318405|gb|ABV37503.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 218

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 62/206 (30%), Positives = 100/206 (48%), Gaps = 20/206 (9%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           Y+D  I V NKP+G+    G         I+  L+ + ++      L HRLD  TSGI+V
Sbjct: 18  YKDRDIIVINKPSGLLSNPGRAANTFDCAINRLLQRYPEAI-----LVHRLDCATSGIMV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + A  ++   F+ R  +K Y + V G   ++ E +    +K          + ++ 
Sbjct: 73  FALNKKAESNIKTQFQNRMSKKTYIAEVQGHIVDE-EGVIELAMKPDTERPPLQKLAEEG 131

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +    Y    FKV++   +    +E++P TGRTHQLR+H L +G PI+GD     +F G+
Sbjct: 132 KPSKTY----FKVLE-RRKNSTLVELKPVTGRTHQLRLHMLAIGHPILGD-----DFYGD 181

Query: 280 FTSPIQNK-LYLHARYMDLPHPEGGR 304
                 +K L LHA  + + HP  G+
Sbjct: 182 EKVIAASKRLCLHAMSLSITHPYSGK 207


>gi|323704717|ref|ZP_08116295.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323536179|gb|EGB25952.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 286

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 69/222 (31%), Positives = 114/222 (51%), Gaps = 26/222 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK---SWVDSKG--QKP-RLTHRLDQET 154
           + YED  I V NK AGI V   +G   H DG L    +W   K   + P R  +RLD++T
Sbjct: 76  ICYEDEDILVVNKDAGIVVHPTAG---HPDGTLVNGVAWYYEKNNIKAPIRPVNRLDRDT 132

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+      +L     M+   K+Y ++V G   + +  I   + +K    G  + 
Sbjct: 133 SGLIIFAKNPFMQNYLQIVCPMK---KLYIAIVEG-DMDGRGTIDLPIKRKP---GSTIE 185

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +  +E   + A++ F V+   ++K   ++++  TGRTHQ+RVH  H+G PI+GD  Y  
Sbjct: 186 RMVDDE--GDTAVTDFYVLK-RSEKLSLVKLELKTGRTHQIRVHLSHIGHPIIGDTLY-- 240

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
              G+ TS I+ +  LHA  +    P  G+ + + +P+P  M
Sbjct: 241 ---GSDTSYIKRQA-LHAYRLTFRQPFIGKCISLYSPIPDDM 278


>gi|237729755|ref|ZP_04560236.1| tRNA pseudouridine synthase C [Citrobacter sp. 30_2]
 gi|226908361|gb|EEH94279.1| tRNA pseudouridine synthase C [Citrobacter sp. 30_2]
          Length = 260

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 63/238 (26%), Positives = 106/238 (44%), Gaps = 62/238 (26%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKP+G  V              +SW+D               G+     
Sbjct: 4   ILYQDEWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGRHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++  +  A + L++ F   +IQK Y ++V G           WL+  + 
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLSQQFEHHQIQKRYHAIVRG-----------WLMDDAV 99

Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248
           +  DY  V +         +++KG   A++H++ +               ++  +E+ P 
Sbjct: 100 L--DYPLVEELDKIADKFARDDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELDPK 157

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG 303
           TGR HQLR H  H+  PI+GD K+  + + N ++       +L LHA  + L HP  G
Sbjct: 158 TGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSAAEHFGCQRLMLHASQLALTHPFTG 214


>gi|49484092|ref|YP_041316.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257425962|ref|ZP_05602386.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257428627|ref|ZP_05605025.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257431264|ref|ZP_05607641.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257433944|ref|ZP_05610302.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257436860|ref|ZP_05612904.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M876]
 gi|282904425|ref|ZP_06312313.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus C160]
 gi|282906248|ref|ZP_06314103.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282909167|ref|ZP_06316985.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282911473|ref|ZP_06319275.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282914645|ref|ZP_06322431.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M899]
 gi|282919611|ref|ZP_06327346.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           C427]
 gi|282924991|ref|ZP_06332657.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|283958603|ref|ZP_06376054.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Staphylococcus aureus subsp. aureus A017934/97]
 gi|293503717|ref|ZP_06667564.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           58-424]
 gi|293510738|ref|ZP_06669443.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M809]
 gi|293537280|ref|ZP_06671960.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M1015]
 gi|295428428|ref|ZP_06821057.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297590605|ref|ZP_06949243.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus MN8]
 gi|49242221|emb|CAG40928.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257271656|gb|EEV03802.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257275468|gb|EEV06955.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257278212|gb|EEV08860.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257282037|gb|EEV12174.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257284211|gb|EEV14334.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M876]
 gi|282313357|gb|EFB43753.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|282317421|gb|EFB47795.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           C427]
 gi|282321826|gb|EFB52151.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M899]
 gi|282325168|gb|EFB55478.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282327431|gb|EFB57726.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282331540|gb|EFB61054.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282596043|gb|EFC01007.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus C160]
 gi|283471121|emb|CAQ50332.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus ST398]
 gi|283790752|gb|EFC29569.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Staphylococcus aureus subsp. aureus A017934/97]
 gi|290920125|gb|EFD97193.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M1015]
 gi|291095383|gb|EFE25648.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           58-424]
 gi|291466629|gb|EFF09150.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M809]
 gi|295127828|gb|EFG57465.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297575491|gb|EFH94207.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus MN8]
 gi|312437685|gb|ADQ76756.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|315195761|gb|EFU26148.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS00]
          Length = 273

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 60/236 (25%), Positives = 101/236 (42%), Gaps = 34/236 (14%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED  + +  KP G+      ++  + +  H+       VDS   +P   HRLDQET G+
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHV----IYTVDSDYVEP--IHRLDQETVGL 131

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+     + L        I +IY + V  +   K + I         IG D  H  K
Sbjct: 132 LIVAKNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTI------DMPIGKDKFHSNK 185

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +        AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y
Sbjct: 186 RRVSPTGQRAITHILTSKMIKETVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLY 241


>gi|315657924|ref|ZP_07910798.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           lugdunensis M23590]
 gi|315496960|gb|EFU85281.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           lugdunensis M23590]
          Length = 278

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 63/247 (25%), Positives = 109/247 (44%), Gaps = 42/247 (17%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +L ++  S ++ ++    + +N++ +   V IP           E+K           S+
Sbjct: 27  DLHQLNMSKEITINNAPARLSNQVHTMDCVEIP---------TDEEK-----------SN 66

Query: 96  FLKSI----LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +L S     + YED  + +  KP G+      ++  + +  HI   L    DS+  +P  
Sbjct: 67  YLPSYRYAQIYYEDDDLAIVMKPKGVKTHPNDLKESNTLMNHIIYTL----DSEYAEP-- 120

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLDQET G+L++A+     + L       +I +IY + +  +   K + I        
Sbjct: 121 IHRLDQETVGLLIIAKNPLMKKILDRMLEDNKITRIYKANINALLPIKPQTI------DM 174

Query: 207 HIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            IG D  H  K+        AI+H        +  C L+++  TGRTHQ+RVH   +G P
Sbjct: 175 PIGKDKFHPNKRRISNTGQRAITHILASTMLKEGVCQLDIKLDTGRTHQIRVHLAEIGHP 234

Query: 266 IVGDHKY 272
           ++GD  Y
Sbjct: 235 VIGDPLY 241


>gi|313683665|ref|YP_004061403.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
 gi|313156525|gb|ADR35203.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
          Length = 305

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 52/172 (30%), Positives = 90/172 (52%), Gaps = 7/172 (4%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           + + +  V++KP+G+ V   +    Y ++  +K      G +  +THR+DQETSG+++ A
Sbjct: 75  FVEEEFAVYDKPSGLLVHPQNRHTPYSLNDEIKHRF---GHEANITHRIDQETSGLVLAA 131

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R + + + L   F  R+I K Y ++V G  K   + I   LL++         +V+ + +
Sbjct: 132 RNKLSERTLKMMFEERQITKKYIAMVKGHLKEPLD-IQEPLLRREDASSIVRMIVRVHPE 190

Query: 222 GANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           G   + +  K ++ F      L E  P+TGR HQ+RVH  H+  PI+GD  Y
Sbjct: 191 GKP-SRTFIKPLEYFPDTDTTLVEASPYTGRQHQIRVHLFHVEHPIIGDPIY 241


>gi|301299198|ref|ZP_07205485.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300853158|gb|EFK80755.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 304

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 58/187 (31%), Positives = 92/187 (49%), Gaps = 34/187 (18%)

Query: 101 LLYEDSKIYVFNKPAGIS------VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +++E+  + V NKP GI        + G+ + Y     +  ++D++ + P + HRLD  T
Sbjct: 88  IIFENDDLLVVNKPQGIKSHPNQPYETGTLMNY-----IAGYLDARDEHPYMVHRLDMLT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG ++VA+       LT       I++ Y ++  GI  ++KE + +       IG D   
Sbjct: 143 SGAMIVAKNPVVVPILTRLISTHTIKRDYLAITEGI-FDQKEGVIDL-----PIGKD--- 193

Query: 215 VVKQNEK--------GANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              +N+K        GA  A + ++VI  F      +L ++  TGRTHQLRVH   MG P
Sbjct: 194 ---ENDKRKRKVDGIGALPARTRYQVIKEFENNSVVYLRLE--TGRTHQLRVHLSAMGHP 248

Query: 266 IVGDHKY 272
           IVGD  Y
Sbjct: 249 IVGDVLY 255


>gi|291528756|emb|CBK94342.1| Pseudouridylate synthases, 23S RNA-specific [Eubacterium rectale
           M104/1]
          Length = 244

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 110/243 (45%), Gaps = 29/243 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETS 155
           K  ++YED+ I V  KPAGI+ Q        ++ F++++  +K + P   + HRLDQ   
Sbjct: 3   KPDIIYEDNDIIVCYKPAGIATQTRHIGQQDMESFIRNYRAAKNEPPYVGIVHRLDQPVE 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSL-----VWGIPKNKKECIANWLLKKSHIGG 210
           G++V A+ + AA  L+   +    +K Y +      V G  K +    + W     +I  
Sbjct: 63  GVMVFAKNQKAAASLSRQIKEHTTEKYYRAASRGQGVSGADKEEDNHDSAWHTLTDYISF 122

Query: 211 D----YVHVVKQNEKGANYAISHFKVIDCF-----AQKFC---WLEMQPHTGRTHQLRVH 258
           D       +  + ++ A  A+  ++VI        +Q  C     +++  TGR HQ+R+ 
Sbjct: 123 DKRTNTSKITSEKDRLAKKAVLQYRVISVTPDRDSSQNECIRTEFDIKLLTGRHHQIRLQ 182

Query: 259 ALHMGCPIVGDHKY---------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
             H+G P++GD KY           +  G     ++ +L L +  +   HP  G  ++T 
Sbjct: 183 LAHIGYPLIGDTKYGKPASNNSGTGSKSGRTGGGVREQLALCSYKLVFDHPATGE-RMTF 241

Query: 310 PLP 312
            LP
Sbjct: 242 ELP 244


>gi|302333515|gb|ADL23708.1| RluA, Pseudouridylate synthases, 23S RNA-specific [Staphylococcus
           aureus subsp. aureus JKD6159]
          Length = 273

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 60/236 (25%), Positives = 101/236 (42%), Gaps = 34/236 (14%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED  + +  KP G+      ++  + +  H+       VDS   +P   HRLDQET G+
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHV----IYTVDSDYVEP--IHRLDQETVGL 131

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+     + L        I +IY + V  +   K + I         IG D  H  K
Sbjct: 132 LIVAKNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTI------DMPIGKDKFHSNK 185

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +        AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y
Sbjct: 186 RRVSPTGQRAITHILTSKMIKETVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLY 241


>gi|294660309|ref|NP_852991.2| pseudouridine synthase [Mycoplasma gallisepticum str. R(low)]
 gi|284811965|gb|AAP56559.2| Pseudouridine synthase [Mycoplasma gallisepticum str. R(low)]
 gi|284930466|gb|ADC30405.1| Pseudouridine synthase [Mycoplasma gallisepticum str. R(high)]
          Length = 311

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 140/307 (45%), Gaps = 48/307 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQK-----ILRSGQVRVDKKRVKFNNRI-QS 61
           ++  V ND E +RLD +   +      +NL +     ++ +  V+V+KK V  NN + + 
Sbjct: 3   KHTFVNNDSEKIRLDIFLTYN------LNLSRNKTSFLILNDLVKVNKKLVNKNNFVLKV 56

Query: 62  GQVVRIP---PVINAL-NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           G VV +     + N + N I+   K LD               ++YED  + + NKP  +
Sbjct: 57  GDVVELEYEESIFNKVSNEILPFNKKLD---------------IVYEDDDLIIVNKPTNM 101

Query: 118 SVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                +      D  L   +  +K QK  L HRLD++T+G++V  +   A + + E    
Sbjct: 102 LSHPTTH--NEPDTLLNCLMYHNKKQKVYLAHRLDKDTTGLIVATKNFKALEKIQEQI-T 158

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK---QNEKGANYAISHFKVI 233
           +RI K Y+  +   P N+   + +     + IG    H +K   +N K    AI+   V+
Sbjct: 159 KRIMKRYYLAIVHYPFNELRAVID-----APIGYLKDHDLKFGVENTKNPKNAITKIYVL 213

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D   +K+  ++ +  TGRTHQ+RVH   +   I+ D  Y    KG        K +LHA 
Sbjct: 214 DQ-NKKYALIKCELLTGRTHQIRVHMDFIKHNIINDPLYGV--KGE--QRTDYKQFLHAY 268

Query: 294 YMDLPHP 300
            ++L HP
Sbjct: 269 QLELTHP 275


>gi|313246104|emb|CBY35058.1| unnamed protein product [Oikopleura dioica]
          Length = 446

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 51/173 (29%), Positives = 87/173 (50%), Gaps = 7/173 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +  + YV NKP+ + +   +   ++   FL S          + HRLD+ TSG+++ 
Sbjct: 168 VIADTDEFYVVNKPSSLPIHPVAQYRHNSLIFLISR--EYKVNYHVIHRLDRLTSGLVIF 225

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T+  A+ +++    R +QK Y   V G   +K  C  +   K    G   V     +E
Sbjct: 226 AKTKEVAKRVSKEISDRVVQKQYLLRVVGKFPDKAVCDKSGTKK----GIYRVAKADDDE 281

Query: 221 KGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K    A++ F++++ F +     +   P TGRTHQ+RVH  ++GCPIV D  Y
Sbjct: 282 KKVKTALTEFELVEYFKEADQSLVRAIPKTGRTHQIRVHTQYLGCPIVNDPVY 334


>gi|117619994|ref|YP_855705.1| RNA pseudouridine synthase family protein [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
 gi|117561401|gb|ABK38349.1| RNA pseudouridine synthase family protein [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
          Length = 257

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 69/266 (25%), Positives = 118/266 (44%), Gaps = 51/266 (19%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK--------------GQ 142
           L+  LLY+D  +   NKP+G+ V              +SW+D                G+
Sbjct: 12  LQLTLLYQDDWLVAVNKPSGLLVH-------------RSWLDKAETRFAMQMTRDLIGGR 58

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HRLD+ TSG+L+ A   A A+ LTE+F  R++ K Y +LV G     ++ + ++ 
Sbjct: 59  HVYPVHRLDRPTSGVLLFALDPAVARTLTEAFAARQVHKEYLALVRGW--APEQGLIDYP 116

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-----------AQKFCWLEMQPHTGR 251
           LK+          +   ++ A  A++ F+ +                ++  + + P TGR
Sbjct: 117 LKEQ--LDKIADAMSDPDRPAQEAVTAFRRLHQVELPHAVSKKHPTSRYSLVRLFPKTGR 174

Query: 252 THQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPE-GGRL 305
            HQLR H  H+  PIVGD  +        F+ ++     ++L L AR +   HP     +
Sbjct: 175 KHQLRRHMDHLFHPIVGDTTHGDGRHNRFFREHYGC---DRLLLVARTLSFEHPVLKVPM 231

Query: 306 QITAPLPAHMVKTWDSLGFKYDRNLY 331
           +I APL   +++ +  LG+    + Y
Sbjct: 232 RIQAPLGQEVLQLFAELGWPASESDY 257


>gi|228944912|ref|ZP_04107274.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar monterrey BGSC 4AJ1]
 gi|229120827|ref|ZP_04250069.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           95/8201]
 gi|228662487|gb|EEL18085.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           95/8201]
 gi|228814780|gb|EEM61039.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar monterrey BGSC 4AJ1]
          Length = 292

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 70/269 (26%), Positives = 126/269 (46%), Gaps = 34/269 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI  P
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 63  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 107

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 108 VANALLSHYDKQYLAST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 164

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 165 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++  TGRTHQ+RVH  H+G P++GD+ Y
Sbjct: 219 SLELDTGRTHQIRVHMAHIGHPLLGDNLY 247


>gi|188533189|ref|YP_001906986.1| Pseudouridylate synthase [Erwinia tasmaniensis Et1/99]
 gi|188028231|emb|CAO96089.1| Pseudouridylate synthase [Erwinia tasmaniensis Et1/99]
          Length = 232

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/208 (28%), Positives = 95/208 (45%), Gaps = 10/208 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + + NKPAG+    G     +ID      V        L HRLD  TSG++++
Sbjct: 19  ILYQDEHLALINKPAGLLSLSGKN-PQNIDSVHHRLVRIF-PGCTLVHRLDFGTSGLMLI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQN 219
           AR +A    L + F  R++ K+Y +L+ G   N    I   + K   +     +  +   
Sbjct: 77  ARNKAINAALCQQFSQRKVAKMYSALLCGHLDNDGGVIDAAIAKDPALFPLMSICAIHGK 136

Query: 220 EKGANYAIS---HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN- 275
              + Y ++   +  + D        +++ P TGRTHQLR+H   +G PI+G   Y    
Sbjct: 137 PARSRYQVTARFYHALQDGTRLPLTRVQLTPETGRTHQLRIHCQQLGHPILGCDLYGGRL 196

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             G   +P   +L LHA  +   HP GG
Sbjct: 197 LPGTERTP---RLMLHASELHFVHPIGG 221


>gi|56414914|ref|YP_151989.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197363842|ref|YP_002143479.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|56129171|gb|AAV78677.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197095319|emb|CAR60877.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
          Length = 260

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 21/232 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDRWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +     + +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFA----RED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
           K+  + + N ++       +L LHA  ++L HP  G+  I   + A + +TW
Sbjct: 180 KH-GDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLI---IQAGLDETW 227


>gi|298369779|ref|ZP_06981096.1| pseudouridine synthase Rlu family protein [Neisseria sp. oral taxon
           014 str. F0314]
 gi|298282336|gb|EFI23824.1| pseudouridine synthase Rlu family protein [Neisseria sp. oral taxon
           014 str. F0314]
          Length = 215

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/213 (31%), Positives = 104/213 (48%), Gaps = 22/213 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +L+ +      +KPAGI+V    G     D  L +   ++   PRL  THRLD+ TSG+L
Sbjct: 4   ILFRNQDFAAVDKPAGIAVHQEEGA----DNLL-AMAAAQLNVPRLWLTHRLDKPTSGVL 58

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A    AA  L + F  + ++K Y +L    P  KK+ +    ++KS  G   +     
Sbjct: 59  LLALNAQAASELAQQFAAKTMRKTYLALSDRRPA-KKQGLVKGGMEKSRRGAWKL----T 113

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              GAN A++ F      A       +QP TG+THQLRV   ++  PI+GD  Y      
Sbjct: 114 RGDGANLAVTRFHS-QSIAPNLRLFVLQPQTGKTHQLRVAMKNLSSPILGDTLYGG---- 168

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
              +P + +L+LHA  ++  +  GG   + APL
Sbjct: 169 ---TPAE-RLFLHAWRLEFEY-RGGAFSVCAPL 196


>gi|288923211|ref|ZP_06417353.1| pseudouridine synthase, RluA family [Frankia sp. EUN1f]
 gi|288345447|gb|EFC79834.1| pseudouridine synthase, RluA family [Frankia sp. EUN1f]
          Length = 313

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 77/318 (24%), Positives = 141/318 (44%), Gaps = 28/318 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V +  + MRLD      +  ++      ++  GQV VD +    ++R+  G  + +
Sbjct: 9   RSVPVPDGLDGMRLDAALARMF-GLSRTAAVSVVDDGQVSVDGQVRGRSDRVAGGAWLEV 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                AL    +   +  + V            +L++D  I V +KP G++     G   
Sbjct: 68  -----ALPAPPRPVTVDATPVEGLG--------ILHDDDDIVVVDKPVGVAAHPAPGFTG 114

Query: 127 YHIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +    + + G   R  + HRLD  T+GI+VVA++  A   L  +FR R ++K
Sbjct: 115 PTVIGALAAAGYRISTSGAAERQGVVHRLDVGTTGIMVVAKSERAYTLLKRAFRDREVEK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++V G P   +  +   + +     G +  V      G   +++H+   + F +   
Sbjct: 175 VYRAVVQGHPDPLRGTVDAPIDRHPRRPGLFAVVA-----GGKPSVTHYDTEEAF-RSAS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L ++  TGRTHQ+RVH   +  P VGD  Y A+        ++ + +LHA  +   HP 
Sbjct: 229 LLSVRLETGRTHQIRVHLSALRHPCVGDLAYGADPTLAQRLGLERQ-WLHAASLAFAHPS 287

Query: 302 GGR-LQITAPLPAHMVKT 318
            G  ++  +P P  + + 
Sbjct: 288 DGSWVRFVSPDPDDLAEA 305


>gi|16766270|ref|NP_461885.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|167550169|ref|ZP_02343926.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|167993457|ref|ZP_02574551.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|34582459|sp|Q8ZMD5|TRUC_SALTY RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|16421515|gb|AAL21844.1| putative synthase [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
 gi|205324883|gb|EDZ12722.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205328453|gb|EDZ15217.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|261248101|emb|CBG25936.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. D23580]
 gi|267995101|gb|ACY89986.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301159525|emb|CBW19044.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. SL1344]
 gi|312913986|dbj|BAJ37960.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|321225646|gb|EFX50700.1| tRNA pseudouridine synthase C ; tRNA Psi65 [Salmonella enterica
           subsp. enterica serovar Typhimurium str. TN061786]
 gi|323131322|gb|ADX18752.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|332989835|gb|AEF08818.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 260

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 21/232 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +     + +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFA----RED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
           K+  + + N ++       +L LHA  ++L HP  G+  I   + A + +TW
Sbjct: 180 KH-GDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLI---IQAGLDETW 227


>gi|255071781|ref|XP_002499565.1| predicted protein [Micromonas sp. RCC299]
 gi|226514827|gb|ACO60823.1| predicted protein [Micromonas sp. RCC299]
          Length = 318

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 109/240 (45%), Gaps = 35/240 (14%)

Query: 102 LYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDS-----KGQKPR-LTHRLD 151
           L+ED  + V +KPAG+    +   G      ++  L ++ D       G   R + HRLD
Sbjct: 74  LWEDEHLAVVSKPAGMLTHPNEASGGATRTLVEALLDAFGDEGLSAINGADARGIVHRLD 133

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG ++VA+T  A      ++  R++ K Y +LV G+P  ++               +
Sbjct: 134 KPTSGAMLVAKTDLAHAMCVAAWYQRKVTKTYLALVEGVPGRRRGRRRGDDGDAM----E 189

Query: 212 YVHVVKQNEKGANYAISHFKVIDCF-------AQKFCWL-EMQPHTGRTHQLRVH-ALHM 262
              V   + + A    S ++V++ F       A++ C L E+ P TGR HQ+R H  + +
Sbjct: 190 GTCVAPADGRPAR---SDWRVVETFGEEDGDDAEQLCSLVEVTPRTGRRHQIRQHMGMAL 246

Query: 263 GCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP-EGGRLQITAPLPA 313
             P+VGD  Y    + N  +           + L+LH+  + L HP  G  L  + PLPA
Sbjct: 247 DAPLVGDPLYRRGKRPNTPATAAPFLVGKPGSVLFLHSAALALRHPVTGEALSFSDPLPA 306


>gi|314951376|ref|ZP_07854428.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|313596434|gb|EFR75279.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
          Length = 307

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 85/320 (26%), Positives = 144/320 (45%), Gaps = 49/320 (15%)

Query: 19  MRLDRWF-----KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +R+D  F     K+H   + +   +K +  G +     ++KF    Q GQ+     V N 
Sbjct: 5   VRIDMQFTWDYEKDHSQQVKYFLKEKGISKGLL----AKIKF----QGGQIKVNDQVENV 56

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKS----ILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           L  + K+ K+        +H   L       ++YED  + V NKPAG+S        YH 
Sbjct: 57  LFSLAKDDKVTIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQ---YHP 113

Query: 130 DGFL----KSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +G +    K++   +G + ++ H   RLD++TSG+++ A+   A   L    R ++  K 
Sbjct: 114 NGTMANRVKAYYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQLREKKFVKK 173

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHI----GGDYVHVVKQ--NEKGANYAISHFKVIDCF 236
           Y +LV G   +        L    HI      DY  ++K+  +++G +    ++  I+  
Sbjct: 174 YQALVSGRLSD--------LSAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYW--IEKR 223

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
             +   +++Q HTGRTHQ+RVH   +GC ++GD  Y     G     I+ +  LH   + 
Sbjct: 224 LTEIALVDIQLHTGRTHQIRVHFSAIGCALLGDDMYG----GGMDLGIKRQA-LHCYDLR 278

Query: 297 LPHPEGGR-LQITAPLPAHM 315
             HP     L+   PL A M
Sbjct: 279 FYHPFTEELLEFKQPLAADM 298


>gi|153832681|ref|ZP_01985348.1| pseudouridylate synthase, 23S RNA-specific [Vibrio harveyi HY01]
 gi|148871026|gb|EDL69910.1| pseudouridylate synthase, 23S RNA-specific [Vibrio harveyi HY01]
          Length = 559

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 66/204 (32%), Positives = 101/204 (49%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           +L++D  + + NKP+G+    G  I       L++ + D +G  P + HRLD  TSGILV
Sbjct: 358 ILFQDEAMVIVNKPSGLLSVPGKTIKDSAYTRLQAMFPDVEG--PFVIHRLDMATSGILV 415

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A T+ A + L + F  R +QK Y +L+ G+   + E   +  ++          V  ++
Sbjct: 416 FALTKRANKSLQKQFITRGVQKRYMALLEGV-LTEPEGEISLPMRGDPDDRPRQLVCFEH 474

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGC--PIVGDHKYCANF 276
            K A       +V D  ++ +    M P TGRTHQLRVH A HMG    +VGD  Y    
Sbjct: 475 GKPAETYWQLIEVKDGRSKVY----MYPKTGRTHQLRVHSAHHMGLNMAMVGDGLYGEK- 529

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                    ++L+LHA  ++L HP
Sbjct: 530 --------ADRLHLHAEMLELDHP 545


>gi|312870194|ref|ZP_07730326.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
 gi|311094285|gb|EFQ52597.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
          Length = 297

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/220 (28%), Positives = 107/220 (48%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQKPRLTH---RLDQETS 155
           + YED    V NKPAG++      +  A  +   +K +   +  + ++TH   RLD++TS
Sbjct: 80  IAYEDRDFLVLNKPAGVATVPAHNVPVADSLVNRVKYYYRERDYENQVTHVATRLDKDTS 139

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V  + R A   L    +   ++K Y++LV G    +   I       + I  D    
Sbjct: 140 GLVVFPKHRFAHAVLDRQLKRHEVKKNYYALVSGHLHTQHGYI------DAPIRRDPASF 193

Query: 216 VKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VK+        +++ + +    A++   + ++ HTGRTHQ+RVH   +G P+VGD  Y A
Sbjct: 194 VKREVAPDGKDSVTEYWLAQAQAER-SLVRIRLHTGRTHQIRVHFSFLGHPLVGDEMYGA 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                  SP+ ++  LH  +M    P   + + +TAPLPA
Sbjct: 253 PAG----SPLIDRQALHCYWMQFYSPFKEQFITVTAPLPA 288


>gi|52144130|ref|YP_082698.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
 gi|51977599|gb|AAU19149.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
          Length = 297

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 70/269 (26%), Positives = 126/269 (46%), Gaps = 34/269 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI  P
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 68  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 113 VANALLSHYDKQYLAST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 170 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++  TGRTHQ+RVH  H+G P++GD+ Y
Sbjct: 224 SLELDTGRTHQIRVHMAHIGHPLLGDNLY 252


>gi|300813392|ref|ZP_07093743.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
 gi|300512535|gb|EFK39684.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
          Length = 316

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 66/285 (23%), Positives = 127/285 (44%), Gaps = 32/285 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V++  ++ + RLDR+ K ++       + K LR   ++VD K+    + I+ GQ + +  
Sbjct: 4   VIIGPNDSDQRLDRFLKKYFEKAPLSFIYKNLRKKNIKVDGKKASPEDLIKEGQEISLFI 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               +    K++        L ++S     IL YED  I +  KP  +         ++ 
Sbjct: 64  SDETIEKYKKDK--------LARNSQKFPQIL-YEDDNICLMKKPLNMLTHNDKN--FYQ 112

Query: 130 DGFLKSWVD------------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           D  +  ++D                +P + +RLD+ TSGIL+ A+     + + ++ + R
Sbjct: 113 DNMVDRFIDYLIFKEEYSPREENTFRPSICNRLDRNTSGILLGAKNAETLREINKAIKER 172

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y ++V G  K +K    N  L+K+       ++++++  G +     F +I    
Sbjct: 173 LVDKFYLTIVKG--KVQKPFEINIKLEKTD-----KNIMRKSCVGKDSLTKFFPLIS--N 223

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
            ++  ++++  TGRTHQ+R      G  I+GD KY       F S
Sbjct: 224 GEYSLIKVKLITGRTHQIRASLKEKGLYILGDRKYGKGKDKEFNS 268


>gi|295094341|emb|CBK83432.1| ribosomal large subunit pseudouridine synthase D [Coprococcus sp.
           ART55/1]
          Length = 233

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/216 (27%), Positives = 104/216 (48%), Gaps = 12/216 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLT--HRLD 151
           +K  +L+ED+ I V  KP G+  Q     +  +   LK  +   +++ ++P L   HRLD
Sbjct: 1   MKLNILHEDNDIIVAVKPCGVPTQPDKTNSESMVSMLKLRIYEKENRKEEPYLVPIHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +   G++V A+T  AA +L++      + K Y +++ G   N +  + ++LL  +    +
Sbjct: 61  RPVGGVMVFAKTPEAAANLSKQSEDGSMMKYYQAILTGELPNDQGVLKDYLLHDTK--DN 118

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              VV ++  GA Y+   ++V+D          ++ ++  TGR HQ+R       C I G
Sbjct: 119 VTKVVDKDTPGAKYSELEYEVLDVMDTDEGTLTYVLVELITGRHHQIRAQFAKRKCGIWG 178

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           D KY  N K   T     ++ LHA  ++  HP  G 
Sbjct: 179 DTKY--NPKFQKTKKKYKEIGLHASRLEFDHPTTGE 212


>gi|282849742|ref|ZP_06259126.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
 gi|282580679|gb|EFB86078.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
          Length = 289

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 78/291 (26%), Positives = 128/291 (43%), Gaps = 66/291 (22%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M++  Y V E  E  + + ++ K  +  ++  ++Q + R       KKRVK N+R+   Q
Sbjct: 1   MSWKTYTVKEPTE--LTVSKYVKERFS-LSSRDIQMMFR-------KKRVKVNSRVAHSQ 50

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI------LLYEDSKIYVFNKPAGI 117
                        ++K+  +L  ++ L +  D+   +      +LYED+   V NK   +
Sbjct: 51  ------------RVLKKGDVL--TLELPQDKDYGVDVEQGPITVLYEDAHTLVVNKAPFM 96

Query: 118 SVQ-GGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            V   G   +  +  ++  +   K    K R  HRLD++TSG ++  +T+ A Q+ T+  
Sbjct: 97  LVHPAGQTKSCTLSNYVAGYYAKKNVVHKVRPVHRLDRDTSGCILFGKTKEAQQYYTDEL 156

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +  RI +IY  LV G         A+ ++  + IG D V               + +VID
Sbjct: 157 QAGRIDRIYTGLVEG------RIDADGMV-DAPIGVDPV-------------FDNRRVID 196

Query: 235 CFAQKF-------------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            F Q                 L  +  TGRTHQ+RVH  H+G PIVGD  Y
Sbjct: 197 EFGQPAQTEYTVLGYEGDNTLLRFKLLTGRTHQIRVHMEHIGHPIVGDAMY 247


>gi|228984376|ref|ZP_04144555.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar tochigiensis BGSC 4Y1]
 gi|228775345|gb|EEM23732.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar tochigiensis BGSC 4Y1]
          Length = 292

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 69/280 (24%), Positives = 130/280 (46%), Gaps = 32/280 (11%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
            + G + V+ +     +++Q+G+ +R+  PV      +I E   L               
Sbjct: 33  FQGGAIEVNGQHASVRHQLQAGEELRVFFPVEERSEGMIAEDIPL--------------- 77

Query: 100 ILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSG 156
            ++YED  + V NK A +S +      A  +   L +  D +       +  RLD++TSG
Sbjct: 78  CIVYEDDAVLVINKEANMSTIPSREHPAGSVANALLTHYDKQHLASTVHIVTRLDRDTSG 137

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +   
Sbjct: 138 LMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKS----DSIIER 193

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              E+G   A++HF+VID    K   + ++  TGRTHQ+RVH  H+G P++GD     N 
Sbjct: 194 TVCEEG-QRAVTHFRVIDSANHK-THVSLELDTGRTHQIRVHMAHIGHPLLGD-----NL 246

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH+  +   HP     +  T  +P+ M
Sbjct: 247 YGGKRDEMKRQ-ALHSTSLTFYHPILEKEMSFTTTIPSDM 285


>gi|65318577|ref|ZP_00391536.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Bacillus
           anthracis str. A2012]
 gi|165872829|ref|ZP_02217455.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|170708875|ref|ZP_02899309.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|190569145|ref|ZP_03022043.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|164711406|gb|EDR16957.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|170126191|gb|EDS95084.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|190559728|gb|EDV13715.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
          Length = 292

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 70/269 (26%), Positives = 126/269 (46%), Gaps = 34/269 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI  P
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 63  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 107

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 108 VANALLSHYDKQYLPST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 164

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 165 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++  TGRTHQ+RVH  H+G P++GD+ Y
Sbjct: 219 SLELDTGRTHQIRVHLAHIGHPLLGDNLY 247


>gi|162447506|ref|YP_001620638.1| pseudouridylate synthase, 23S RNA-specific [Acholeplasma laidlawii
           PG-8A]
 gi|161985613|gb|ABX81262.1| pseudouridylate synthase, 23S RNA-specific [Acholeplasma laidlawii
           PG-8A]
          Length = 277

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/200 (28%), Positives = 93/200 (46%), Gaps = 18/200 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           ++YED  I + NKP  + V        H+   +       G   ++   HR+D+ET+GI+
Sbjct: 78  IIYEDDDIVIVNKPFNVIVHDDGASEDHLTRRVNMHFQYHGYHHQVLPAHRIDKETTGIV 137

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+   A  +L+  F  R++ K Y  +V    K+K   I + L+K S +    V     
Sbjct: 138 VFAKHFIALAYLSNLFESRQVVKNYICVVENKVKDKTGSIESKLIKDSKLQKMVV----- 192

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  AI+H++++   A +   L++Q  TGRTHQ+R H   +  P+VGD  Y  +   
Sbjct: 193 -SPHGKLAITHYELLGYEATR-SRLKVQIETGRTHQIRAHMASINHPVVGDILYGVS--- 247

Query: 279 NFTSPIQNKLYLHARYMDLP 298
                  ++L LH   +  P
Sbjct: 248 ------SSRLLLHFSEISFP 261


>gi|153810858|ref|ZP_01963526.1| hypothetical protein RUMOBE_01242 [Ruminococcus obeum ATCC 29174]
 gi|149833254|gb|EDM88336.1| hypothetical protein RUMOBE_01242 [Ruminococcus obeum ATCC 29174]
          Length = 288

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/216 (28%), Positives = 103/216 (47%), Gaps = 21/216 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLD 151
           ++YED+ I + NKPAG+  Q        +  +L  ++   G           P + +RLD
Sbjct: 44  IIYEDTDILLINKPAGMLSQPDDTKEPSMVEYLIGYLLQNGSLTEENLRTFHPSVCNRLD 103

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG++   ++ A  Q L+  F  R + K Y  +V G    +   I  +L K +++  +
Sbjct: 104 KNTSGVIAAGKSLAGLQELSTLFHDRTVHKDYLCIVKG-KLTRSRHIRGYLHKDANL--N 160

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V V    EK A    + +  I C  +    L+++  TGRTHQ+R H    G P+ GD K
Sbjct: 161 KVSVSPTKEKDAQPIETQYTPI-CNNEHATLLKVRLITGRTHQIRAHLASEGHPLAGDAK 219

Query: 272 YCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEG 302
           Y +      F+ ++   ++++L LHA  +  P  EG
Sbjct: 220 YGSQEFNRYFRDHYG--LKHQL-LHAYRLTFPELEG 252


>gi|32472413|ref|NP_865407.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica SH 1]
 gi|32443649|emb|CAD73091.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica SH 1]
          Length = 321

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 107/228 (46%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVD-SKGQKPR-LTHRLDQETSGI 157
           +++ED  I V NK AG ++V    G    +   +  ++  SK +K   + HRLD+ETSG+
Sbjct: 86  IVFEDEHIIVVNKSAGTLTVPTDRGEPNSLVDRVSIYLSYSKSKKEAFVVHRLDRETSGL 145

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV  +    A  L E F+ RR  +++ ++V G     +    + L      G +      
Sbjct: 146 LVFGKHEPIADLLIEQFKDRRPTRVFHAIVAGNVSEDEGTFESHLA----TGSNLDRYET 201

Query: 218 QNEKGANYAISHFKVIDCFAQK-------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +  K  + AI+H+KV+   A++          +E Q  T + +Q+RV   + G P++GD 
Sbjct: 202 RPGKDTDQAITHYKVVRRLAERESSHGEETTLIEAQLETSKRNQVRVQFANAGHPVLGDP 261

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           +Y    +       + ++ LHA  +   HP  G  +    PLP+ M K
Sbjct: 262 RYKPK-EATHARWHRKRMALHASTLGFFHPVSGEPVNFDTPLPSAMEK 308


>gi|47568408|ref|ZP_00239109.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus G9241]
 gi|47554956|gb|EAL13306.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus G9241]
          Length = 297

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 114/233 (48%), Gaps = 25/233 (10%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           G + V+ +     +++Q+G+ +R+  PV      +I E   L                ++
Sbjct: 41  GAIEVNGQYASVRHQLQAGEELRVFFPVEERSEGMIAEDIPL---------------CIV 85

Query: 103 YEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGILV 159
           YED  + V NK A +S +      A  +   L S  D +       +  RLD++TSG+++
Sbjct: 86  YEDDAVLVINKEANMSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGLML 145

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +      
Sbjct: 146 IAKNRFMHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKS----DSIIERTVC 201

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           E+G   A++HF+VID    K   + ++  TGRTHQ+RVH  H+G P++GD+ Y
Sbjct: 202 EEG-QRAVTHFRVIDSANHK-THVSLELDTGRTHQIRVHMAHIGHPLLGDNLY 252


>gi|56459957|ref|YP_155238.1| pseudouridylate synthase Rlu family protein [Idiomarina loihiensis
           L2TR]
 gi|56178967|gb|AAV81689.1| Predicted pseudouridylate synthase, Rlu family [Idiomarina
           loihiensis L2TR]
          Length = 236

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 103/231 (44%), Gaps = 28/231 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQETSGILV 159
           ++Y D  + V NKP+G+ V   S IA     F    + ++ G      HRLD+ TSG+L+
Sbjct: 6   VVYLDEHLAVINKPSGLLVHR-SRIASGAREFAMQMLRNQLGCHVYPVHRLDRPTSGLLI 64

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
                  A+ LTE    R + K Y ++V G +P+N      ++ LK+             
Sbjct: 65  FGLNSDVARTLTEQLTAREVSKTYHAVVRGYVPENG---TIDYALKEE--LDKLADKDAD 119

Query: 219 NEKGANYAISHFKVIDCFAQ--------------KFCWLEMQPHTGRTHQLRVHALHMGC 264
            +K    A++H++   C  Q              ++  ++MQP TGR HQLR H  H+  
Sbjct: 120 PDKDKQPAVTHYQ---CLKQIELPYKVSKKHDTTRYSLVQMQPETGRKHQLRRHMAHIRH 176

Query: 265 PIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLP 312
           PIVGD  +      NF     N  +L L A  +   HP  G  + +  PLP
Sbjct: 177 PIVGDTNHGDGRHNNFFREHFNCHRLLLAATGLSFKHPVSGESINLEIPLP 227


>gi|62181474|ref|YP_217891.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|168231056|ref|ZP_02656114.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|168463884|ref|ZP_02697801.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|194443144|ref|YP_002042215.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194468534|ref|ZP_03074518.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|200386574|ref|ZP_03213186.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|224584754|ref|YP_002638552.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|238909744|ref|ZP_04653581.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|62129107|gb|AAX66810.1| putative synthase [Salmonella enterica subsp. enterica serovar
           Choleraesuis str. SC-B67]
 gi|194401807|gb|ACF62029.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194454898|gb|EDX43737.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|195633159|gb|EDX51573.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|199603672|gb|EDZ02217.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|205334611|gb|EDZ21375.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|224469281|gb|ACN47111.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|322715958|gb|EFZ07529.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
          Length = 260

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 21/232 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +     + +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFA----RED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
           K+  + + N ++       +L LHA  ++L HP  G+  I   + A + +TW
Sbjct: 180 KH-GDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLI---IQAGLDETW 227


>gi|228913878|ref|ZP_04077503.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pulsiensis BGSC 4CC1]
 gi|228845817|gb|EEM90843.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pulsiensis BGSC 4CC1]
          Length = 292

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 70/269 (26%), Positives = 126/269 (46%), Gaps = 34/269 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI  P
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 63  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 107

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 108 VANALLSHYDKQYLAST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 164

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 165 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++  TGRTHQ+RVH  H+G P++GD+ Y
Sbjct: 219 SLELDTGRTHQIRVHLAHIGHPLLGDNLY 247


>gi|208434858|ref|YP_002266524.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori G27]
 gi|208432787|gb|ACI27658.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori G27]
          Length = 242

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/202 (29%), Positives = 98/202 (48%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLASFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y ++V GI + ++E  A  L  K+     +  +
Sbjct: 100 VLLVKENSEF-HLKAKKAFKDRAVKKEYLAIVQGIVEEEREINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y   
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYNNE 211

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
                      +L LHA  + L
Sbjct: 212 IGS------AKRLMLHAHKISL 227


>gi|317178694|dbj|BAJ56482.1| hypothetical protein HPF30_0385 [Helicobacter pylori F30]
          Length = 245

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/202 (31%), Positives = 100/202 (49%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 58  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGV 102

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ R  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 103 ILLVRENSEF-HLKAKKAFKDRAVKKEYLALAQGIIEEEQEINAPILTIKT--TKAFSKI 159

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y  N
Sbjct: 160 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYN-N 213

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
             G+       +L LHA  + L
Sbjct: 214 DPGS-----AKRLMLHAHKIAL 230


>gi|301052847|ref|YP_003791058.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           anthracis CI]
 gi|300375016|gb|ADK03920.1| ribosomal large subunit pseudouridylate synthase D [Bacillus cereus
           biovar anthracis str. CI]
          Length = 297

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 70/269 (26%), Positives = 126/269 (46%), Gaps = 34/269 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI  P
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 68  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 113 VANALLSHYDKQYLPST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 170 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++  TGRTHQ+RVH  H+G P++GD+ Y
Sbjct: 224 SLELDTGRTHQIRVHMAHIGHPLLGDNLY 252


>gi|139474518|ref|YP_001129234.1| RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo]
 gi|134272765|emb|CAM31038.1| RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo]
          Length = 272

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/206 (29%), Positives = 91/206 (44%), Gaps = 19/206 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K   LYED  I + NKP G+   G       +   + ++    GQ   + HRLD+ETSG 
Sbjct: 57  KVTCLYEDEHIIIVNKPEGMKTHGNDPTELALLNHVSAYT---GQTCYVVHRLDKETSGA 113

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+T      L      R I + Y +LV G        + +  +   H  G + H  +
Sbjct: 114 ILFAKTPFILPILNRLLEKRDIHREYLALVHG-------SLDSPRVTYHHPIGRHRHDRR 166

Query: 218 Q---NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +   +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H G  + GD  Y +
Sbjct: 167 KRVVDPINGKKAITEVTLVKNFHKTASLLNCQLQTGRTHQIRVHLAHQGHVLFGDPLY-S 225

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           N K +       +L LHA  + L HP
Sbjct: 226 NEKKDCA-----RLMLHAYQLRLKHP 246


>gi|116332841|ref|YP_794368.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
 gi|116098188|gb|ABJ63337.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
          Length = 295

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/223 (28%), Positives = 102/223 (45%), Gaps = 29/223 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQ----GGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LYE + + V NK  G        G  G    H+  +L    D  G  P +  RLDQET+
Sbjct: 86  VLYESADLLVINKTRGSKTHPNQPGERGTTLNHVAAYLGP--DQPG--PYILSRLDQETT 141

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L++ +T A    +      +++Q+ Y + V G          + +     IG D +  
Sbjct: 142 GALLMTKTPAVVPIMVRHIADKQVQRTYLAWVHG------RLTGDGVFTDP-IGRDPLDK 194

Query: 216 VKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            K+   G  A  A++H+ V + + ++   ++++  TGRTHQLRVH    G P++GD  Y 
Sbjct: 195 RKRQVNGDHAQPAVTHYHVCE-YREQATLIQLRLETGRTHQLRVHLAAAGHPLIGDPLYG 253

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP---EGGRLQITAPLPA 313
                  T+   N+L LH   +  P P         +TAP+PA
Sbjct: 254 -------TATDTNRLRLHCWQLTFPQPFTVNDAHTTVTAPVPA 289


>gi|145595716|ref|YP_001160013.1| RluA family pseudouridine synthase [Salinispora tropica CNB-440]
 gi|145305053|gb|ABP55635.1| ribosomal large subunit pseudouridine synthase D [Salinispora
           tropica CNB-440]
          Length = 314

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/209 (29%), Positives = 101/209 (48%), Gaps = 13/209 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           ++Y D  I V +KP G++     G     + G L +    + + G   R  + HRLD  T
Sbjct: 91  VVYADDDIVVVDKPVGVAAHPSPGWTGPTVIGGLAAIGHRISTSGAAERQGVVHRLDVGT 150

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +GI+ VA++  A   L  +F+ R ++K Y ++V G     +  I   + +  H   DY  
Sbjct: 151 TGIMAVAKSEQAYTSLKRAFKYREVEKRYHAVVQGHLDPLRGTIDAPIDRHPH--HDYRW 208

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  + K    +I+H+  ++ F      ++++  TGRTHQ+RVH   +  P VGD  Y A
Sbjct: 209 AVVSDGK---PSITHYDTLEAFPAA-SLVDVRLETGRTHQIRVHFSTLRHPCVGDLTYGA 264

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +     T    ++ +LHAR +   HP  G
Sbjct: 265 D-PTLATRLGLDRQWLHARELRFRHPRTG 292


>gi|254555966|ref|YP_003062383.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254044893|gb|ACT61686.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 293

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 58/180 (32%), Positives = 87/180 (48%), Gaps = 13/180 (7%)

Query: 103 YEDSKIYVFNKPAGI-SVQGGSG----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED+   V NKPAG+ SV G S     +   I G+L +   +  Q+P L  RLD++TSG+
Sbjct: 81  YEDANWLVLNKPAGLTSVPGPSNRTDTLVNRIKGYLIA-SHASNQRPHLITRLDRDTSGL 139

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA+ R A   LTE     ++ K Y + + G        I   + + +      V    
Sbjct: 140 VLVAKHRVAQGMLTEPRIAAQLVKTYQAWIEGTITPASGTIDRPIGRVADSPRRVVTTAG 199

Query: 218 QNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           Q       AI+ ++V  D        L ++  TGRTHQ+RVH   +G P++GD  Y  N 
Sbjct: 200 QR------AITTYQVEADQLQHNVSRLRLELVTGRTHQIRVHLTALGHPLLGDTLYGGNL 253


>gi|145299818|ref|YP_001142659.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142852590|gb|ABO90911.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 232

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/215 (30%), Positives = 96/215 (44%), Gaps = 22/215 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + + NKP+G+    G     ++D      V D  G    L HRLD  TSGI+V
Sbjct: 19  ILFEDEHLLLINKPSGLLSLSGKN-PQNLDSVHYRLVQDYPGCT--LVHRLDFGTSGIMV 75

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VAR +A    L + F  R + K Y +L+     + +  I   + K   +      ++K  
Sbjct: 76  VARNKAINALLCQQFSQRAVSKAYSALLCDHLTDDEGMIDAPIAKDPAL----FPLMKIC 131

Query: 220 EKGANYAISHFKVIDCFA--------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                 A S ++V D           Q    + + P TGRTHQLR+H   +G PI+G   
Sbjct: 132 AASGKPARSRYEVEDRLCRESEHGETQLLTRVRLVPETGRTHQLRIHCQLVGHPILG--- 188

Query: 272 YCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR 304
            C  + G      +   +L LHA  +DL HP  G 
Sbjct: 189 -CDLYGGLLLPGCEQAPRLMLHASELDLVHPVSGE 222


>gi|238922884|ref|YP_002936397.1| putative 23S rRNA pseudouridine synthase [Eubacterium rectale ATCC
           33656]
 gi|238874556|gb|ACR74263.1| probable 23S rRNA pseudouridine synthase [Eubacterium rectale ATCC
           33656]
          Length = 244

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/246 (24%), Positives = 111/246 (45%), Gaps = 35/246 (14%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETS 155
           K  ++YED+ I +  KPAGI+ Q        ++ F++++  +K + P   + HRLDQ   
Sbjct: 3   KPDIIYEDNDIIICYKPAGIATQTRRIGQQDMESFIRNYRAAKNEPPYVGIVHRLDQPVE 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSL-----VWGIPKNKKECIANWLLKKSHIGG 210
           G++V A+ + AA  L+   +    +K Y +      V G  K +    + W     +I  
Sbjct: 63  GVMVFAKNQKAAASLSRQIKEHTTEKYYRAASRGQGVSGADKEEDNHDSAWHTLTDYISF 122

Query: 211 D----YVHVVKQNEKGANYAISHFKVI-----------DCFAQKFCWLEMQPHTGRTHQL 255
           D       +  + ++ A  A+  ++VI           +C   +F   +++  TGR HQ+
Sbjct: 123 DKRTNTSKITSEKDRLAKKAVLQYRVISVTPDRDSSQNECIRTEF---DIKLLTGRHHQI 179

Query: 256 RVHALHMGCPIVGDHKY---------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           R+   H+G P++GD KY           +  G     ++ +L L +  +   HP  G  +
Sbjct: 180 RLQLAHIGYPLIGDTKYGKPASNNSGTGSKSGRTCGGVREQLALCSYKIVFDHPATGE-R 238

Query: 307 ITAPLP 312
           +T  LP
Sbjct: 239 MTFELP 244


>gi|229057021|ref|ZP_04196415.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228720298|gb|EEL71874.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 307

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 114/231 (49%), Gaps = 32/231 (13%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED  + + NK   +    S + G+G     +A+H   F    +++K    R  HRLD
Sbjct: 87  VVFEDDHVLIVNKQGQMDTHPSEKNGTGTLANLVAFH---FQMQGLETK---VRHIHRLD 140

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G +V A+ R A   +      R+I++ Y +LV    K K+  I       + IG D
Sbjct: 141 KDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYMALVEAKVKKKQGTI------DAAIGRD 194

Query: 212 YVHVVKQ--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             H  ++  + KG + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+VG
Sbjct: 195 RHHATRRRVSPKG-DQAITYYKVEKYFKKQNATLVTLQLETGRTHQIRVHMSYNGNPLVG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
           D  Y     G  T+ +  +  LHA  ++  HP     + +  P P ++  T
Sbjct: 254 DVLY-----GGQTTYMSGQA-LHAMKINFLHPITKEEIVVDVPFPTNLNDT 298


>gi|325104427|ref|YP_004274081.1| pseudouridine synthase [Pedobacter saltans DSM 12145]
 gi|324973275|gb|ADY52259.1| pseudouridine synthase [Pedobacter saltans DSM 12145]
          Length = 559

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 113/237 (47%), Gaps = 33/237 (13%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGF 132
           LNH++   ++ ++ + L   +D     ++Y+D  + + NKPA  +SV G +     ++  
Sbjct: 332 LNHMLLGMEVEENPM-LRNPADGKALDIVYDDDYLCIVNKPAEFLSVPGINVTDSVLERI 390

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              + D+ G  P + HRLD  TSGI+++A+++     L   F  R +QK Y +L+ G+ +
Sbjct: 391 KVKYPDATG--PLIVHRLDMSTSGIMLIAKSKDVYIQLQSQFINRTVQKRYIALLDGLVE 448

Query: 193 NKKECIANWL------LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           + +  I   L        +  +  DY    K   +   +     +V         W    
Sbjct: 449 SNEGTIDLPLRVDLEDRPRQLVCYDYGKPAKTKWRALEHKNGKTRV-------HFW---- 497

Query: 247 PHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           P TGRTHQLRVH+ H   + CPIVGD  Y    KG       ++L+LHA ++   HP
Sbjct: 498 PITGRTHQLRVHSAHKSGLNCPIVGDDIYGK--KG-------DRLHLHAEWLQFYHP 545


>gi|88802941|ref|ZP_01118468.1| pseudouridine synthase Rlu family protein [Polaribacter irgensii
           23-P]
 gi|88781799|gb|EAR12977.1| pseudouridine synthase Rlu family protein [Polaribacter irgensii
           23-P]
          Length = 234

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 106/241 (43%), Gaps = 41/241 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-----LKSWV-DSKGQKPRLTHRLDQET 154
           +++ED+ +    KP  I V      AYH         L  W+ + KG K    HRLD++T
Sbjct: 5   IIFEDAYVMCVCKPNNIVVHH----AYHSRSVADERSLLQWILEVKGLKVYPIHRLDRKT 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI+++A+           F    I K Y+ +V G    +K       +  S + G    
Sbjct: 61  SGIILLAKETTYVSEFQALFTENTIDKTYYGVVRGFSPEEK-------IIDSPVKGRDAS 113

Query: 215 VVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           V ++       A++H K +             + ++  +E++P +GRTHQLR+H L +  
Sbjct: 114 VYRE-------ALTHLKTLAQRTLDIPVKPYDSSRYSLVELKPKSGRTHQLRLHTLKISH 166

Query: 265 PIVGDHKYC-ANFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
           P++GD KY   N    +      N L+LHA  ++  HP     L + A  PA     W S
Sbjct: 167 PLIGDSKYGDKNHDLMYAEKFGWNNLFLHAGKLEFQHPFSKENLVLKANFPA----DWTS 222

Query: 322 L 322
           L
Sbjct: 223 L 223


>gi|308179960|ref|YP_003924088.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|308045451|gb|ADN97994.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 293

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 58/180 (32%), Positives = 87/180 (48%), Gaps = 13/180 (7%)

Query: 103 YEDSKIYVFNKPAGI-SVQGGSG----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED+   V NKPAG+ SV G S     +   I G+L +   +  Q+P L  RLD++TSG+
Sbjct: 81  YEDANWLVLNKPAGLTSVPGPSNRTDTLVNRIKGYLIA-SHASNQRPHLITRLDRDTSGL 139

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA+ R A   LTE     ++ K Y + + G        I   + + +      V    
Sbjct: 140 VLVAKHRVAQGMLTEPRIAAQLVKTYQAWIEGTITPASGTIDRPIGRVADSPRRVVTTAG 199

Query: 218 QNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           Q       AI+ ++V  D        L ++  TGRTHQ+RVH   +G P++GD  Y  N 
Sbjct: 200 QR------AITTYQVEADQLQHNVSRLRLELVTGRTHQIRVHLTTLGHPLLGDALYGGNL 253


>gi|254481870|ref|ZP_05095113.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2148]
 gi|214037999|gb|EEB78663.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2148]
          Length = 220

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 51/206 (24%), Positives = 103/206 (50%), Gaps = 17/206 (8%)

Query: 101 LLYEDSKIYVFNKP-AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED+ + +  KP   +S+ G   +       L + +        + HRLD +TSGI++
Sbjct: 18  ILYEDADLLLVRKPDLLLSIPGRHPLN---KDCLITRLQQDYPTASIVHRLDLDTSGIMI 74

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +   +    H++  F+ R ++K Y ++V+G+ +     +      +  I  D+ +   Q 
Sbjct: 75  IPLNKPTHAHISRQFQERLVEKCYHAVVFGLVEQDSGEV------ELPIRCDWENRPLQM 128

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +   +A++ ++V+D  + +   L ++P TGR+HQLR+H   +G PI+G    C  + 
Sbjct: 129 IDHEQGKHALTRYEVLDRLSDRTRLL-LKPVTGRSHQLRIHMRELGHPILG----CDMYA 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
                 + +++ LHA ++   HP  G
Sbjct: 184 HQQALEMADRMLLHASFIGFEHPTSG 209


>gi|206577943|ref|YP_002236857.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae 342]
 gi|288933804|ref|YP_003437863.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|290511116|ref|ZP_06550485.1| tRNA pseudouridine synthase C [Klebsiella sp. 1_1_55]
 gi|206567001|gb|ACI08777.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae 342]
 gi|288888533|gb|ADC56851.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|289776109|gb|EFD84108.1| tRNA pseudouridine synthase C [Klebsiella sp. 1_1_55]
          Length = 264

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 68/267 (25%), Positives = 122/267 (45%), Gaps = 38/267 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDDWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--- 217
             +  A + L + F   +IQK Y ++V G           WL+ ++ +  DY  V +   
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLMDEALL--DYPLVEELDK 110

Query: 218 ------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALH 261
                 + +K    A++H++ +               ++  +E++P TGR HQLR H  H
Sbjct: 111 IADKFAREDKDPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAH 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           +  PI+GD K+  + + N ++      ++L LHA  + L HP  G  L + A      ++
Sbjct: 171 LRHPILGDSKH-GDLRQNRSAAEHFGCHRLMLHASELSLTHPFTGEPLTLRAGFDEVWMR 229

Query: 318 TWDSLGFKYDRNLYIKRLYSQDECKQN 344
                G++    L  +R+   D+C Q+
Sbjct: 230 ALSQFGWRGLLPLN-ERVEFADDCGQD 255


>gi|71911569|ref|YP_283119.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
 gi|71854351|gb|AAZ52374.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
          Length = 333

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/206 (29%), Positives = 91/206 (44%), Gaps = 19/206 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K   LYED  I + NKP G+   G       +   + ++    GQ   + HRLD+ETSG 
Sbjct: 118 KVTCLYEDEHIIIVNKPEGMKTHGNDPTELALLNHVSAYT---GQTCYVVHRLDKETSGA 174

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+T      L      R I + Y +LV G        + +  +   H  G + H  +
Sbjct: 175 ILFAKTPFILPILNRLLEKRDIHREYLALVHG-------SLDSPRVTYHHPIGRHRHDRR 227

Query: 218 Q---NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +   +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H G  + GD  Y +
Sbjct: 228 KRVVDPINGKKAITEVTLVKNFHKTASLLTCQLQTGRTHQIRVHLAHQGHVLFGDPLY-S 286

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           N K +       +L LHA  + L HP
Sbjct: 287 NGKKDCA-----RLMLHAYQLRLKHP 307


>gi|51893029|ref|YP_075720.1| 23S rRNA pseudouridine synthase [Symbiobacterium thermophilum IAM
           14863]
 gi|51856718|dbj|BAD40876.1| 23S rRNA pseudouridine synthase [Symbiobacterium thermophilum IAM
           14863]
          Length = 327

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 82/351 (23%), Positives = 156/351 (44%), Gaps = 67/351 (19%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV+     +RL ++  +    ++   +++   SG + VD +  + +  +  G+VV +   
Sbjct: 4   VVDPSARGLRLSQYLFDRL-KLSRTVVRRAKTSGGILVDGRPARTSLVLAGGEVVEV--- 59

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 + +E ++    + +          ++YED  + V +KPAG+ V     +  ++ 
Sbjct: 60  -----RVAQEGRVEPEPIPIQ---------VVYEDPWLLVVDKPAGMVVHP---VRDYVS 102

Query: 131 GFLKSWVD----SKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + V       G  P  R   R+D+ETSG+++ A+  A A  L      +++++ Y 
Sbjct: 103 GTLANAVAHHLLRSGSDPVARPVQRIDRETSGLVLFAKDPAVAGLLARELERQKLERRYV 162

Query: 185 SL------------------VWGIP------KNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           ++                  VWG P      +  +      LL ++   G     ++++ 
Sbjct: 163 AVVEGAVAADAGTVDRPIRRVWGHPVAREVAEGPRTPEQERLLAEAAAQG---RALREDW 219

Query: 221 KGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
             A   A++H++V+  +      LE++  TGRTHQ+RVH  ++G P++GD  Y     G 
Sbjct: 220 TAAGQPAVTHWRVLRRWPAA-TMLELRLETGRTHQIRVHMAYLGHPLLGDELY-----GG 273

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
             + IQ +  LHA  +   HP     ++ TAPLPA +    + L  + DR 
Sbjct: 274 SRTLIQRQ-ALHAATLAFVHPVTREPVRFTAPLPADL----EDLVARLDRT 319


>gi|21911297|ref|NP_665565.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|21905511|gb|AAM80368.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
          Length = 282

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/206 (29%), Positives = 91/206 (44%), Gaps = 19/206 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K   LYED  I + NKP G+   G       +   + ++    GQ   + HRLD+ETSG 
Sbjct: 67  KVTCLYEDEHIIIVNKPEGMKTHGNDPTELALLNHVSAYT---GQTCYVVHRLDKETSGA 123

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+T      L      R I + Y +LV G        + +  +   H  G + H  +
Sbjct: 124 ILFAKTPFILPILNRLLEKRDIHREYLALVHG-------SLDSPRVTYHHPIGRHRHDRR 176

Query: 218 Q---NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +   +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H G  + GD  Y +
Sbjct: 177 KRVVDPINGKKAITEVTLVKNFHKTASLLNCQLQTGRTHQIRVHLAHQGHVLFGDPLY-S 235

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           N K +       +L LHA  + L HP
Sbjct: 236 NGKKDCA-----RLMLHAYQLRLKHP 256


>gi|88800575|ref|ZP_01116137.1| hypothetical protein MED297_15425 [Reinekea sp. MED297]
 gi|88776720|gb|EAR07933.1| hypothetical protein MED297_15425 [Reinekea sp. MED297]
          Length = 249

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/244 (25%), Positives = 106/244 (43%), Gaps = 22/244 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWV--DSKGQKPRLTHRLDQETS 155
           ++YED  + V +KP+G+ +          D   G  K+++   S+G K    HRLD+ TS
Sbjct: 6   IVYEDDVLLVVDKPSGLLMHPSWLDRRETDTLAGRAKAYLAQQSEGAKVHTVHRLDRPTS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V+ +   AA+ L E F+ + + K YW++  G     +      + +   I   +   
Sbjct: 66  GLVVMCKDDHAAKALVEQFQEKTVNKRYWAICRGFAPVAETLDYPLIEEHDRIADKFA-- 123

Query: 216 VKQNEKGANYAISHFKVIDCFA----------QKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              ++K A  AI+ F+ +               +  W+E  P TGR HQ+R H  H+  P
Sbjct: 124 --DSDKPAQEAITEFRRLGITELAIPVSRYPKMRLSWMECVPVTGRKHQIRRHLKHLRYP 181

Query: 266 IVGDHKYCANFKGNFTSPIQNKLY--LHARYMDLPHPEGGRLQITAPLPAHMVKTW-DSL 322
           I+GD ++              +L+  L A  M   HP    L        ++   W D L
Sbjct: 182 ILGDTRHGCRHLNRAVEGSFGELFMGLRAVEMSFQHPVTNELMTFNVGADNVWSCWLDRL 241

Query: 323 GFKY 326
           G+ +
Sbjct: 242 GWSF 245


>gi|314937995|ref|ZP_07845306.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|314941579|ref|ZP_07848463.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|314948435|ref|ZP_07851823.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
 gi|314991305|ref|ZP_07856784.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|314995356|ref|ZP_07860462.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313590449|gb|EFR69294.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313594078|gb|EFR72923.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|313599599|gb|EFR78442.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|313642670|gb|EFS07250.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|313645160|gb|EFS09740.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
          Length = 307

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 85/320 (26%), Positives = 144/320 (45%), Gaps = 49/320 (15%)

Query: 19  MRLDRWF-----KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +R+D  F     K+H   + +   +K +  G +     ++KF    Q GQ+     V N 
Sbjct: 5   VRIDMQFTWDYEKDHSQQVKYFLKEKGISKGLL----AKIKF----QGGQIKVNDQVENV 56

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKS----ILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           L  + K+ K+        +H   L       ++YED  + V NKPAG+S        YH 
Sbjct: 57  LFSLAKDDKVTIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQ---YHP 113

Query: 130 DGFL----KSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +G +    K++   +G + ++ H   RLD++TSG+++ A+   A   L    R ++  K 
Sbjct: 114 NGTMANRVKAYYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQLREKKFVKK 173

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHI----GGDYVHVVKQ--NEKGANYAISHFKVIDCF 236
           Y +LV G   +        L    HI      DY  ++K+  +++G +    ++  I+  
Sbjct: 174 YQALVSGRLSD--------LSAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYW--IEKR 223

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
             +   +++Q HTGRTHQ+RVH   +GC ++GD  Y     G     I+ +  LH   + 
Sbjct: 224 LTEIALVDIQLHTGRTHQIRVHFSAIGCALLGDDMYG----GRMDLGIKRQA-LHCYDLR 278

Query: 297 LPHPEGGR-LQITAPLPAHM 315
             HP     L+   PL A M
Sbjct: 279 FYHPFTEELLEFKQPLAADM 298


>gi|283770934|ref|ZP_06343826.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
 gi|283461081|gb|EFC08171.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
          Length = 273

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/236 (25%), Positives = 101/236 (42%), Gaps = 34/236 (14%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED  + +  KP G+      ++  + +  H+       VDS   +P   HRLDQET G+
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHV----IYTVDSDYVEP--IHRLDQETVGL 131

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+     + L        I +IY + V  +   K + I         IG D  H  K
Sbjct: 132 LIVAKNPLMKKILDRMLEDNDITRIYKANVNALLPLKPQTI------DMPIGKDKFHSNK 185

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +        AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y
Sbjct: 186 RRVSPTGQRAITHILTSKMIKETVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLY 241


>gi|268678698|ref|YP_003303129.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
 gi|268616729|gb|ACZ11094.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
          Length = 302

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 57/175 (32%), Positives = 88/175 (50%), Gaps = 12/175 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++E     VF+KP+G+ +        Y ++  +KS     G+     HR+D+ TSG+++V
Sbjct: 73  IFETEDFAVFDKPSGVMIHPRKRSDGYTLNDEIKSLY---GKDANAAHRIDKSTSGLVLV 129

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            + + +   L E F  R++QK Y +LV G    K+E + +  LK+          V  +E
Sbjct: 130 GKHKQSEIALKEIFATRKVQKSYIALVKG--HLKEELLIDEKLKRDVETSQIRLKVHVDE 187

Query: 221 KGANYAISHFKVIDC--FAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +G     S  KVI    F  K   L +  P+TGR HQ+RVH  H+  PIVGD  Y
Sbjct: 188 RGKP---SQTKVIPLHYFEDKDATLVQAFPYTGRQHQIRVHLFHVKHPIVGDMIY 239


>gi|148975781|ref|ZP_01812612.1| putative ribosomal large chain pseudouridine synthase A
           [Vibrionales bacterium SWAT-3]
 gi|145964854|gb|EDK30106.1| putative ribosomal large chain pseudouridine synthase A
           [Vibrionales bacterium SWAT-3]
          Length = 570

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 104/207 (50%), Gaps = 26/207 (12%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D  I V +KPAG +SV G +          +   D +G  P + HRLD  TSGIL+
Sbjct: 369 ILFQDEHIVVVHKPAGFLSVPGKTIKDSAYTRVQEMHPDVEG--PFVIHRLDMATSGILI 426

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
            A TR A + L + F  R ++K Y +++ G+    +  +      +  + GD     +Q 
Sbjct: 427 FALTRRANKSLQKQFITREVEKRYVAMIEGVLAEDEGYV------RLPLRGDLYDRPRQI 480

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
              E G   A + ++VI+   Q+   + + P TGRTHQLRVH  H   +  PIVGD  Y 
Sbjct: 481 VCYEHGKP-AETKWEVIER-NQETTKVYLHPKTGRTHQLRVHCSHEEGLYMPIVGDGLY- 537

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
               GN      ++L+LHA  + L HP
Sbjct: 538 ----GNKA----DRLHLHAERLALHHP 556


>gi|49184141|ref|YP_027393.1| pseudouridine synthetase [Bacillus anthracis str. Sterne]
 gi|167636101|ref|ZP_02394406.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|167641221|ref|ZP_02399475.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|170686706|ref|ZP_02877926.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|177654397|ref|ZP_02936294.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|227815949|ref|YP_002815958.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|229600901|ref|YP_002865732.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|254682628|ref|ZP_05146489.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. CNEVA-9066]
 gi|254725424|ref|ZP_05187206.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. A1055]
 gi|254734046|ref|ZP_05191760.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Western North America USA6153]
 gi|254740807|ref|ZP_05198496.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Kruger B]
 gi|254753650|ref|ZP_05205686.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Vollum]
 gi|254758747|ref|ZP_05210774.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Australia 94]
 gi|270000595|ref|YP_003329033.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. Ames]
 gi|291612207|ref|YP_003541021.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. 'Ames Ancestor']
 gi|49178068|gb|AAT53444.1| pseudouridine synthetase [Bacillus anthracis str. Sterne]
 gi|167510862|gb|EDR86254.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|167528455|gb|EDR91220.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|170669229|gb|EDT19972.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|172080681|gb|EDT65763.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|224552858|gb|ACN55068.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. 'Ames Ancestor']
 gi|227004816|gb|ACP14559.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|229265309|gb|ACQ46946.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|269850244|gb|ACZ49984.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. Ames]
          Length = 297

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 70/269 (26%), Positives = 126/269 (46%), Gaps = 34/269 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI  P
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 68  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 113 VANALLSHYDKQYLPST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VID    K   +
Sbjct: 170 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVIDSANHK-THV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++  TGRTHQ+RVH  H+G P++GD+ Y
Sbjct: 224 SLELDTGRTHQIRVHLAHIGHPLLGDNLY 252


>gi|82751504|ref|YP_417245.1| RNA pseudouridylate synthase [Staphylococcus aureus RF122]
 gi|82657035|emb|CAI81472.1| probable RNA pseudouridylate synthase [Staphylococcus aureus RF122]
          Length = 273

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 54/176 (30%), Positives = 80/176 (45%), Gaps = 18/176 (10%)

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED  + +  KP G+      ++  + +  H+       VDS   +P   HRLDQET G+
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHV----IYTVDSDYVEP--IHRLDQETVGL 131

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+     + L        I +IY + V  +   K + I         IG D  H  K
Sbjct: 132 LIVAKNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTI------DMPIGKDKFHSNK 185

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +        AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y
Sbjct: 186 RRVSPTGQRAITHILTSKMIKETVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLY 241


>gi|327538476|gb|EGF25140.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica WH47]
          Length = 321

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 111/230 (48%), Gaps = 20/230 (8%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVD-SKGQKPR-LTHRLDQETSGI 157
           +++ED  I V NK AG ++V    G    +   +  ++  SK +K   + HRLD+ETSG+
Sbjct: 86  IVFEDEHIIVVNKSAGTLTVPTDRGEPNSLVDRVSIYLSYSKSKKEAFVVHRLDRETSGL 145

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI--GGDYVHV 215
           LV  +    A  L E F+ RR  +++ ++V G   N  E    +   +SH+  G +    
Sbjct: 146 LVFGKHEPIADLLIEQFKDRRPTRVFHAIVAG---NVAEDEGTF---ESHLATGSNLDRY 199

Query: 216 VKQNEKGANYAISHFKVIDCFAQK-------FCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +  K  + AI+H+KV+   A++          +E Q  T + +Q+RV   + G P++G
Sbjct: 200 ETRPGKDTDQAITHYKVVRRLAERESSHGEETTLIEAQLETSKRNQVRVQFANAGHPVLG 259

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           D +Y    +       + ++ LHA  +   HP  G  +    PLP+ M K
Sbjct: 260 DPRYKPK-EATHARWHRKRMALHASTLGFFHPVSGEPVNFDTPLPSAMEK 308


>gi|283769208|ref|ZP_06342112.1| RNA pseudouridine synthase [Bulleidia extructa W1219]
 gi|283104184|gb|EFC05563.1| RNA pseudouridine synthase [Bulleidia extructa W1219]
          Length = 225

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 57/205 (27%), Positives = 95/205 (46%), Gaps = 17/205 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  KP  +  Q  +     +   LK  +  + QKP      L HRLD+   
Sbjct: 7   IIYEDNHLLVVEKPVNVLSQADNSQEDDMVSRLKKLIKIRDQKPGQVFIGLVHRLDRPVG 66

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T   A  L++S R    +KIY ++V  +   ++  + ++L K S    + V V
Sbjct: 67  GLMVFAKTSKGASRLSDSIRCHTFKKIYLAIVDSVSLPQEGTLEDYLYKDSQ--KNRVFV 124

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  + K    A  H++V+     K   + +   TGR HQ+RV       P+V D +Y  +
Sbjct: 125 V--DAKKGKLARLHYQVLAKKRGK-SLVRIVLETGRPHQIRVQFASRNWPLVNDQRYHPH 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                  P +  + L A  +  PHP
Sbjct: 182 -------PNRGSICLFAYQLSFPHP 199


>gi|325282268|ref|YP_004254809.1| pseudouridine synthase, RluA family [Deinococcus proteolyticus MRP]
 gi|324314077|gb|ADY25192.1| pseudouridine synthase, RluA family [Deinococcus proteolyticus MRP]
          Length = 305

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 101/225 (44%), Gaps = 9/225 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED+ I   +KP+G+      G    +D  L + +  +       HRL + TSG+++ 
Sbjct: 88  VLYEDAHILAVHKPSGLPTLPAGGF---LDHTLLALLRRQWPAATPLHRLGRGTSGLVLC 144

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           + T AA   LT  +R  RI K Y +L  G+   +K  I   +    H     ++      
Sbjct: 145 SLTPAAGSRLTADWREGRIHKRYRALSAGVAAQEKYDITAPIGLVDHPRLGQIYAATPAG 204

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K +    S  +V++         ++   TGR HQ+R+H    G P++GD  Y    +   
Sbjct: 205 KPSR---SRAQVLE-RRDGSTLFQVDIETGRPHQIRIHLASAGLPLLGDPLYLPGGQARP 260

Query: 281 TS-PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            + P      LHA  ++  HP GG  L ++AP+P  +   + S G
Sbjct: 261 DALPGDLGYLLHAERLEFRHPAGGEHLSLSAPVPPELRSGFSSSG 305


>gi|288929792|ref|ZP_06423635.1| ribosomal large subunit pseudouridine synthase A [Prevotella sp.
           oral taxon 317 str. F0108]
 gi|288328893|gb|EFC67481.1| ribosomal large subunit pseudouridine synthase A [Prevotella sp.
           oral taxon 317 str. F0108]
          Length = 542

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 58/202 (28%), Positives = 102/202 (50%), Gaps = 20/202 (9%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  + V +KP G +SV G  G         + + D+    P + HRLDQ+TSG+++
Sbjct: 336 VVYEDEGLVVVSKPHGMLSVPGKDGGTSVAQMMRQRYPDT--DSPLIVHRLDQDTSGLMI 393

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +A+T+   + L  +F    ++K Y +++ G +P  K+    +  L  +++      V   
Sbjct: 394 IAKTKEMHRTLQLAFENHEVKKRYVAVLDGLLPPEKQRGEISLPLNSNYLDRPRQMVDWL 453

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
           N K    A++ ++VI    +    + + P TGRTHQLRVH  H   +  PI+GD  Y   
Sbjct: 454 NGKS---AVTRYEVIG-HEEGRTIVALYPLTGRTHQLRVHCAHPDGLNLPILGDPLYGRK 509

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
                     +++YLHA  +++
Sbjct: 510 ---------ADRMYLHAEVIEV 522


>gi|327399178|ref|YP_004340047.1| RluA family pseudouridine synthase [Hippea maritima DSM 10411]
 gi|327181807|gb|AEA33988.1| pseudouridine synthase, RluA family [Hippea maritima DSM 10411]
          Length = 301

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/222 (30%), Positives = 107/222 (48%), Gaps = 19/222 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLK---SWVDSKGQKPR--LTHRLDQET 154
           +L+ED  + V  KPAGI V  G+      +   LK     + S G   R  + HR+D++T
Sbjct: 86  ILFEDEDVVVVEKPAGIVVHPGAACEDVSVVSALKYRGVRLSSIGAPLRGGVVHRIDKDT 145

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V+A+   A   L + F    I++ Y  +V    K     I   + +  H     + 
Sbjct: 146 SGVIVLAKNDRAHFFLAKQFFEHSIERRYIGVVGCHLKQNSGEIDKPIGR--HPKNRKLF 203

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V +N K    AI+ +K++    + +  +  +  TGRTHQ+RVH  ++GCP+VGD  Y  
Sbjct: 204 AVVENGK---EAITFYKLLKRL-ENYDVVMFKLQTGRTHQIRVHMKYLGCPLVGDATY-- 257

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
              G     I+ +  LHA  +   HP  G+ L+  + LP  M
Sbjct: 258 ---GGVLKEIKRQA-LHAFVLGFRHPWSGKFLKFYSKLPEDM 295


>gi|312129383|ref|YP_003996723.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
 gi|311905929|gb|ADQ16370.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
          Length = 550

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/204 (31%), Positives = 99/204 (48%), Gaps = 21/204 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + V NKP+G+    G  I   +   L++  D +   P + HRLDQ+TSGILV+
Sbjct: 350 IIYEDDYLAVVNKPSGLLSVPGIQIYDSVYSRLQARWDHEA--PLVVHRLDQDTSGILVM 407

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           AR +   +HL   F  R + K Y +L+ G + ++K E   +  L+          V  ++
Sbjct: 408 ARNKNVHKHLQSQFIRRTVIKHYIALLEGHLVEDKGEI--HLPLRVDLDDRPRQMVCYEH 465

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANF 276
            K A+       +   + +    ++  P TGRTHQLR+HA H   +  PI GD  Y    
Sbjct: 466 GKKAHTIWEKIGIEGPYTR----VKFFPVTGRTHQLRMHAAHHEGLNAPIKGDDMY---- 517

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                     +L LHA Y++  HP
Sbjct: 518 -----GKAAERLCLHAAYLEFLHP 536


>gi|302671097|ref|YP_003831057.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
 gi|302395570|gb|ADL34475.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
          Length = 328

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 112/235 (47%), Gaps = 24/235 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG---FLKSWVDSKGQK--PRLTHRLDQETS 155
           + YED  + + NKP  + V      A++ D    +L  +    GQ+   R   RLD+ETS
Sbjct: 97  IAYEDEDLIIVNKPGEMVVH--PSYAHYKDSLSNYLLGYFIRSGQRHVIRTVGRLDRETS 154

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN---KKECIA--NWLLKKSHIGG 210
           G+++ A+ R AA  + +  +    ++     +   P N   +KE +A  + +  K+H   
Sbjct: 155 GLVIFAKNRHAAALMAQQIKTNDDKENAQDSLGDEPDNMSRRKEYLALCSGVFDKTHDTI 214

Query: 211 DYV-------HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           D          ++++       A++H++V+  +   +  + ++  TGRTHQ+RVH  ++G
Sbjct: 215 DAPIRRRPDERMIREVHPEGKRAVTHYEVVHQY-DDYALVRLRLDTGRTHQIRVHMAYIG 273

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            P++GD+ Y      +       +  LHA Y++   P  G ++ I A +P  M K
Sbjct: 274 HPLLGDNFYGKEIPDDHG---MTRAALHAGYIEFMQPITGEKIVINARMPEDMQK 325


>gi|223992757|ref|XP_002286062.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220977377|gb|EED95703.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 246

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 95/219 (43%), Gaps = 22/219 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  I V +KPA + SV G +  +   D   KS       +  + HRLD +TSGI+V
Sbjct: 23  VLYSDDDIVVIDKPANLRSVPGHASNSPDADDGSKS-----KYQLHVVHRLDCQTSGIMV 77

Query: 160 VARTRAAAQHLTESFRMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV--- 215
           VAR   AA  L  ++R R I QK Y +     P    E ++   +           +   
Sbjct: 78  VARNSTAASKLCHAWRERDIVQKTYLAYCQRWPPYHDEQLSEGTIDLPLAASRTERIKWE 137

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V+  E G     S   V +        LE++P TGRTHQLR+H   +G  IVGD  Y  +
Sbjct: 138 VRALEDGGKPLKSELTV-ERDNDNGVVLELKPITGRTHQLRIHCATIGSGIVGDSLYGDS 196

Query: 276 FKGNFTSPIQN-----------KLYLHARYMDLPHPEGG 303
               F    Q+            L LHA  +  PHP  G
Sbjct: 197 PVEWFGDKPQHGQQTISQSDTQTLRLHAHKLVFPHPSTG 235


>gi|19746943|ref|NP_608079.1| hypothetical protein spyM18_2124 [Streptococcus pyogenes MGAS8232]
 gi|28896670|ref|NP_803020.1| hypothetical protein SPs1758 [Streptococcus pyogenes SSI-1]
 gi|19749193|gb|AAL98578.1| conserved hypothetical protein [Streptococcus pyogenes MGAS8232]
 gi|28811924|dbj|BAC64853.1| conserved hypothetical protein [Streptococcus pyogenes SSI-1]
          Length = 272

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/206 (29%), Positives = 91/206 (44%), Gaps = 19/206 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K   LYED  I + NKP G+   G       +   + ++    GQ   + HRLD+ETSG 
Sbjct: 57  KVTCLYEDEHIIIVNKPEGMKTHGNDPTELALLNHVSAYT---GQTCYVVHRLDKETSGA 113

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+T      L      R I + Y +LV G        + +  +   H  G + H  +
Sbjct: 114 ILFAKTPFILPILNRLLEKRDIHREYLALVHG-------SLDSPRVTYHHPIGRHRHDRR 166

Query: 218 Q---NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +   +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H G  + GD  Y +
Sbjct: 167 KRVVDPINGKKAITEVTLVKNFHKTASLLNCQLQTGRTHQIRVHLAHQGHVLFGDPLY-S 225

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           N K +       +L LHA  + L HP
Sbjct: 226 NGKKDCA-----RLMLHAYQLRLKHP 246


>gi|294783884|ref|ZP_06749206.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           1_1_41FAA]
 gi|294479696|gb|EFG27475.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           1_1_41FAA]
          Length = 288

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 104/227 (45%), Gaps = 30/227 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-------PRLTHRLDQE 153
           + YED  + + NK   I V         +D  L + V +  +K       PR  +RLD  
Sbjct: 75  IAYEDENLLIVNKEPYIIVHPTQK---KVDKTLANAVVNYFEKTLGKTLVPRFYNRLDMN 131

Query: 154 TSGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           TSG++++A+   T+A  Q  TE      ++K Y  +V GI +     I    L    +G 
Sbjct: 132 TSGLIIIAKNAYTQAFLQDKTE------VKKTYKVIVSGIIEEDDFFIE---LPIGKVGD 182

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D   +    E G   A +H KV++   +K   +LE + +TGRTHQ+R H   +G P+VGD
Sbjct: 183 DLRRIELSEENGGKSAKTHIKVLERNREKNITFLEARLYTGRTHQIRAHLSLIGHPLVGD 242

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
             Y  +        +  +  LHA  ++  +P+    L++   +P  M
Sbjct: 243 ELYGGDMN------LAKRQMLHAYKLEFQNPKTLENLKVEIEIPVDM 283


>gi|15645364|ref|NP_207538.1| hypothetical protein HP0745 [Helicobacter pylori 26695]
 gi|3915378|sp|O25441|Y745_HELPY RecName: Full=Uncharacterized RNA pseudouridine synthase HP_0745;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2313872|gb|AAD07795.1| conserved hypothetical protein [Helicobacter pylori 26695]
          Length = 327

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 106/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVVHKALSVK---EPTLVDWLEFKNYELSNLGLKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAVKKEKSRYSKSEFISLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N  G      + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN--GALPKE-EIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|22127019|ref|NP_670442.1| tRNA pseudouridine synthase C [Yersinia pestis KIM 10]
 gi|45442581|ref|NP_994120.1| tRNA pseudouridine synthase C [Yersinia pestis biovar Microtus str.
           91001]
 gi|51597324|ref|YP_071515.1| tRNA pseudouridine synthase C [Yersinia pseudotuberculosis IP
           32953]
 gi|108806509|ref|YP_650425.1| tRNA pseudouridine synthase C [Yersinia pestis Antiqua]
 gi|108813124|ref|YP_648891.1| tRNA pseudouridine synthase C [Yersinia pestis Nepal516]
 gi|145598957|ref|YP_001163033.1| tRNA pseudouridine synthase C [Yersinia pestis Pestoides F]
 gi|149366961|ref|ZP_01888994.1| tRNA pseudouridine synthase C [Yersinia pestis CA88-4125]
 gi|153949809|ref|YP_001399991.1| tRNA pseudouridine synthase C [Yersinia pseudotuberculosis IP
           31758]
 gi|162421605|ref|YP_001607777.1| tRNA pseudouridine synthase C [Yersinia pestis Angola]
 gi|165927134|ref|ZP_02222966.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           F1991016]
 gi|165939825|ref|ZP_02228365.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           IP275]
 gi|166011912|ref|ZP_02232810.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166211483|ref|ZP_02237518.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167399889|ref|ZP_02305407.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167419839|ref|ZP_02311592.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           MG05-1020]
 gi|167425312|ref|ZP_02317065.1| tRNA pseudouridine synthase [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|167468860|ref|ZP_02333564.1| tRNA pseudouridine synthase [Yersinia pestis FV-1]
 gi|170023309|ref|YP_001719814.1| tRNA pseudouridine synthase C [Yersinia pseudotuberculosis YPIII]
 gi|186896429|ref|YP_001873541.1| tRNA pseudouridine synthase C [Yersinia pseudotuberculosis PB1/+]
 gi|218928206|ref|YP_002346081.1| tRNA pseudouridine synthase C [Yersinia pestis CO92]
 gi|229837745|ref|ZP_04457905.1| tRNA U65 pseudouridine synthase [Yersinia pestis Pestoides A]
 gi|229840967|ref|ZP_04461126.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229843068|ref|ZP_04463218.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229903567|ref|ZP_04518680.1| tRNA U65 pseudouridine synthase [Yersinia pestis Nepal516]
 gi|270487346|ref|ZP_06204420.1| tRNA pseudouridine synthase C [Yersinia pestis KIM D27]
 gi|294503055|ref|YP_003567117.1| hypothetical protein YPZ3_0945 [Yersinia pestis Z176003]
 gi|34582458|sp|Q8ZH72|TRUC_YERPE RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|21960067|gb|AAM86693.1|AE013915_2 hypothetical protein y3143 [Yersinia pestis KIM 10]
 gi|45437446|gb|AAS62997.1| Pseudouridylate synthases, 23S RNA-specific [Yersinia pestis biovar
           Microtus str. 91001]
 gi|51590606|emb|CAH22247.1| conserved hypothetical protein [Yersinia pseudotuberculosis IP
           32953]
 gi|108776772|gb|ABG19291.1| tRNA pseudouridine synthase C [Yersinia pestis Nepal516]
 gi|108778422|gb|ABG12480.1| tRNA pseudouridine synthase C [Yersinia pestis Antiqua]
 gi|115346817|emb|CAL19703.1| Conserved hypothetical protein [Yersinia pestis CO92]
 gi|145210653|gb|ABP40060.1| tRNA pseudouridine synthase C [Yersinia pestis Pestoides F]
 gi|149290575|gb|EDM40651.1| tRNA pseudouridine synthase C [Yersinia pestis CA88-4125]
 gi|152961304|gb|ABS48765.1| tRNA pseudouridine synthase [Yersinia pseudotuberculosis IP 31758]
 gi|162354420|gb|ABX88368.1| tRNA pseudouridine synthase [Yersinia pestis Angola]
 gi|165912228|gb|EDR30865.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           IP275]
 gi|165921030|gb|EDR38254.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           F1991016]
 gi|165989178|gb|EDR41479.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166207254|gb|EDR51734.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166962580|gb|EDR58601.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           MG05-1020]
 gi|167050597|gb|EDR62005.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167055712|gb|EDR65496.1| tRNA pseudouridine synthase [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|169749843|gb|ACA67361.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186699455|gb|ACC90084.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
 gi|229679337|gb|EEO75440.1| tRNA U65 pseudouridine synthase [Yersinia pestis Nepal516]
 gi|229689944|gb|EEO82003.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229697333|gb|EEO87380.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229704122|gb|EEO91134.1| tRNA U65 pseudouridine synthase [Yersinia pestis Pestoides A]
 gi|262361091|gb|ACY57812.1| hypothetical protein YPD4_0903 [Yersinia pestis D106004]
 gi|262365333|gb|ACY61890.1| hypothetical protein YPD8_1205 [Yersinia pestis D182038]
 gi|270335850|gb|EFA46627.1| tRNA pseudouridine synthase C [Yersinia pestis KIM D27]
 gi|294353514|gb|ADE63855.1| hypothetical protein YPZ3_0945 [Yersinia pestis Z176003]
 gi|320014170|gb|ADV97741.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 257

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 100/222 (45%), Gaps = 17/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHIVAVNKPAGWLVHRSWLDRNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +     +++
Sbjct: 64  ALSSDVARMLSLQFEQHQIQKTYHAVVRGYVLEGGTVDYAMAEELDKIADKFA----KSD 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
           K    ++SH++ +               ++  + ++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVSHYEALAQVEVPLAIGRYETARYSLVALKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 270 -HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
            H      +G       ++L LHA ++ L HP  G  L +TA
Sbjct: 180 THGDLRQNRGVAQHFGCSRLMLHASHLHLNHPVTGEALTLTA 221


>gi|331090839|ref|ZP_08339685.1| hypothetical protein HMPREF9477_00328 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330399698|gb|EGG79360.1| hypothetical protein HMPREF9477_00328 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 294

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/255 (25%), Positives = 118/255 (46%), Gaps = 25/255 (9%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSI-----LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
           I+ +  IL  ++  T  SD +  +     ++YED  + V NKPA + +        +   
Sbjct: 54  ILHKNDILTVTLLETTSSDNIVPVSLPLDIVYEDEDLMVINKPANMPIHPSQNNYDNTLA 113

Query: 132 FLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              ++  ++ + P   R  +RLD++T+G+L++A+   +A  L++  + R I + Y ++  
Sbjct: 114 NAVAYYYAQKEVPFVYRCINRLDRDTTGLLILAKHMYSASLLSDMVKNRLIHREYIAIAD 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQ 246
           G   +     A     K     D     + N    ++A +H+K   C  +K  +  + ++
Sbjct: 174 GYVDDAGIIDAPIARTK-----DSTIEREVNFSEGDFARTHYK---CLQRKNGYSLVSLK 225

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
             TGRTHQ+RVH  ++G  ++GD  Y  ++          +  LH+  +   HP     L
Sbjct: 226 LETGRTHQIRVHMKYIGHALLGDFLYNPDYT------FIGRQALHSHRLTFMHPITKQHL 279

Query: 306 QITAPLPAHMVKTWD 320
             TAPLP  M K +D
Sbjct: 280 TFTAPLPYDMAKLFD 294


>gi|118362444|ref|XP_001014449.1| pseudouridine synthase, RluD subfamily protein [Tetrahymena
           thermophila]
 gi|89296216|gb|EAR94204.1| pseudouridine synthase, RluD subfamily protein [Tetrahymena
           thermophila SB210]
          Length = 446

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 71/257 (27%), Positives = 110/257 (42%), Gaps = 43/257 (16%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVR------IPPVINALNHIIKEQKILDSSVNLT 91
           Q  +  G++ V+K++   + R +   +         PP+IN L  +I             
Sbjct: 58  QNAIEKGKILVNKQKQNIDYRFKHNDLFEHFTSRVEPPIINLLPKVI------------- 104

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THR 149
                      +ED K+ V +KP  ISV    G  +H +  +       G    L   HR
Sbjct: 105 -----------FEDDKLLVLSKPPYISVHASGG--FHFNSLVGLLKFEMGYNIELYVLHR 151

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-----IPKNKKECIANWLLK 204
           LD+ TSG+L++A+ R   +   ES     I+K Y + V G       + +K     +   
Sbjct: 152 LDKLTSGVLIMAKDRDLTKKFHES-ETELIKKTYLARVHGNFNHQYLEYEKPIYCIYKKV 210

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHM 262
            ++   D     +   KGA  + + FK I  + +K     LE QP TGRTHQ+RVH   +
Sbjct: 211 GTYAVLDTTDEEEIKSKGAKQSKTIFKKI-WYDEKSDSSLLECQPITGRTHQIRVHLSSL 269

Query: 263 GCPIVGDHKYCANFKGN 279
           G PI+ D +Y   F GN
Sbjct: 270 GFPIINDTQYGGQFLGN 286


>gi|296104461|ref|YP_003614607.1| tRNA pseudouridine synthase C [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295058920|gb|ADF63658.1| tRNA pseudouridine synthase C [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 261

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 105/226 (46%), Gaps = 36/226 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 5   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--- 217
             +  A + L + F   +IQK Y ++V G           WL + + +  DY  V +   
Sbjct: 65  GLSSEAGRLLAQQFEQHQIQKRYHAIVRG-----------WLTEAATL--DYPLVEELDK 111

Query: 218 ------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALH 261
                 +++KG   A++ ++ +               ++  +E+ P TGR HQLR H  H
Sbjct: 112 IADKFARDDKGPQPAVTEYRGMATTEMPVATSKFPTTRYSLVELLPKTGRKHQLRRHLKH 171

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGR 304
           +  PI+GD K+  + + N ++      ++L LHA  + L HP  G+
Sbjct: 172 LRHPIIGDSKH-GDLRQNRSAAEHFGCDRLMLHASELSLTHPFTGK 216


>gi|148543809|ref|YP_001271179.1| RluA family pseudouridine synthase [Lactobacillus reuteri DSM
           20016]
 gi|184153213|ref|YP_001841554.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227365096|ref|ZP_03849120.1| RluA family pseudouridine synthase [Lactobacillus reuteri MM2-3]
 gi|325681570|ref|ZP_08161092.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           reuteri MM4-1A]
 gi|148530843|gb|ABQ82842.1| pseudouridine synthase, RluA family [Lactobacillus reuteri DSM
           20016]
 gi|183224557|dbj|BAG25074.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227069874|gb|EEI08273.1| RluA family pseudouridine synthase [Lactobacillus reuteri MM2-3]
 gi|324979111|gb|EGC16056.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           reuteri MM4-1A]
          Length = 301

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 107/230 (46%), Gaps = 22/230 (9%)

Query: 101 LLYEDSKIYVFNKPAGIS------VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++YED    + NKPAG++      V     +   + G+ K   + + Q   +  RLD++T
Sbjct: 80  IIYEDQDFLIMNKPAGVATVPAHNVPVADSLVNRVKGYYKRQ-NYENQVTHVATRLDRDT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V  + R A   L E  +   ++K Y +L+ G      +  A      + I  D   
Sbjct: 139 SGLVVFPKHRFAHAVLDEQLKKHLVKKNYLALIKG------KVPAEHGYIDAPIQRDPNS 192

Query: 215 VVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            VK+   K    +++ +   +C  Q    ++++ HTGRTHQ+RVH   +G P++GD  Y 
Sbjct: 193 FVKRMVGKEGKASVTEYWRQECNVQA-SLIKIRLHTGRTHQIRVHFASLGFPLIGDKMYG 251

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                   S +  +  LH  ++    P +G  + ++APLP+      D L
Sbjct: 252 EE------SGLIARQALHCYWLSFYSPFKGKNITVSAPLPSDFKNAKDDL 295


>gi|126657910|ref|ZP_01729063.1| probable pseudouridine synthase [Cyanothece sp. CCY0110]
 gi|126620850|gb|EAZ91566.1| probable pseudouridine synthase [Cyanothece sp. CCY0110]
          Length = 299

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 77/277 (27%), Positives = 123/277 (44%), Gaps = 41/277 (14%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           L++I+ SGQV ++KK V     +Q GQ          L++     K  D  +N       
Sbjct: 37  LERII-SGQVLLNKKVVTPETILQIGQ---------WLSYHRTPWKEPDVPLNFD----- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR----LTHRLDQ 152
               ++YED  + V NKP+G+ V  G G   H       W   K Q P+      HRL +
Sbjct: 82  ----IIYEDDDLLVINKPSGLPVLPGGGFLEHT----LLW-QLKKQYPKDKVFPIHRLGR 132

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V+ ++  A   LT+  R  +I K+Y +L+          I + + K S     Y
Sbjct: 133 GTSGLMVMGKSAIARSQLTQQMREHKITKVYRTLIGNNNLPDHFNIDHPIGKISDPVLGY 192

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++  K + K   YA S   +++ ++ K   +E+   TGR HQ+R+H   +G P++GD  Y
Sbjct: 193 IYGAKADGK---YAYSECHILERYSDK-TLVEVTILTGRPHQIRIHLATIGYPLLGDPLY 248

Query: 273 C------ANFK---GNFTSPIQNKLYLHARYMDLPHP 300
                    F+        P     +LHA  +   HP
Sbjct: 249 TIGGIPKTGFEEQNDTINVPGDCGYFLHAYQLSFVHP 285


>gi|194364569|ref|YP_002027179.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
 gi|194347373|gb|ACF50496.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
          Length = 204

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/211 (31%), Positives = 107/211 (50%), Gaps = 29/211 (13%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           L Y D  + V  KPAG+ SV G S  A + D  + + + ++       HRLDQ TSG+L+
Sbjct: 4   LHYIDDALLVAEKPAGLLSVPGRS--AENQDCVV-ARLQARYPDALTVHRLDQVTSGLLL 60

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVH 214
            AR +     L+  F  R++ K Y ++V G+ +          I +W  +   +      
Sbjct: 61  HARGKDMQAALSMQFEQRQVGKRYEAIVEGLLEGDAGEVDLPLIVDWPNRPKQM------ 114

Query: 215 VVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               +E+G   A++ ++V+  D  AQ+   + ++P TGR+HQLR+H   +G PIVGD  Y
Sbjct: 115 --VDHERG-KPALTRWRVMARDVEAQR-TRVALEPITGRSHQLRLHMASLGHPIVGDVLY 170

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            A       +P Q +++LHAR +   HP  G
Sbjct: 171 GA-------APAQ-RVHLHARSLQFTHPVTG 193


>gi|302346005|ref|YP_003814358.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
 gi|302149550|gb|ADK95812.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
          Length = 571

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 69/223 (30%), Positives = 102/223 (45%), Gaps = 25/223 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-KSWVDSKGQKPR-LTHRLDQETSGIL 158
           +LYED  + V  KP+G+    G G    I   L + W   KG+    + HRLD  TSG+L
Sbjct: 362 ILYEDDYLAVVVKPSGLLSIPGKGCQASIYSILCERW---KGKSDAFMVHRLDMATSGLL 418

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           VVART    + L   F  R ++K Y +L+   I + +        L  S    D     +
Sbjct: 419 VVARTSEVHKALQAQFIGRTVKKKYVALLPLSILEKQLPAEGRIELPLSPDPDDRPR-QR 477

Query: 218 QNEKGANYAISHFKVIDCF-----AQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGD 269
            +      AI+ +++I        A +   + + P TGRTHQLRVH  H   +G PI+GD
Sbjct: 478 VDRTNGKPAITEYRLIGKTTYGKEALEAVKIALYPLTGRTHQLRVHCAHPDGLGTPIIGD 537

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           + Y              +L+LHA +++  HP    R+    PL
Sbjct: 538 NLYGQR---------AERLWLHATHLEFTHPITQERMSFDTPL 571


>gi|229108765|ref|ZP_04238373.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock1-15]
 gi|229149508|ref|ZP_04277743.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           m1550]
 gi|228633981|gb|EEK90575.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           m1550]
 gi|228674704|gb|EEL29940.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock1-15]
          Length = 292

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 110/220 (50%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           ++YED  + + NK A +S +      A  +   L S  D +       +  RLD++TSG+
Sbjct: 79  IIYEDDAVLIINKEANMSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGL 138

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +    
Sbjct: 139 MLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDAPIGRKS----DSIIERT 194

Query: 218 QNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 195 VCEDG-QRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGDSLY---- 247

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 248 -GGRRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 285


>gi|218234328|ref|YP_002365988.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
 gi|218162285|gb|ACK62277.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
          Length = 297

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 110/220 (50%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           ++YED  + + NK A +S +      A  +   L S  D +       +  RLD++TSG+
Sbjct: 84  IIYEDDAVLIINKEANMSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGL 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +    
Sbjct: 144 MLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDAPIGRKS----DSIIERT 199

Query: 218 QNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 200 VCEDG-QRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHVGHPLLGDSLY---- 252

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 253 -GGRRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 290


>gi|303327488|ref|ZP_07357929.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio sp.
           3_1_syn3]
 gi|302862428|gb|EFL85361.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio sp.
           3_1_syn3]
          Length = 241

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 69/216 (31%), Positives = 99/216 (45%), Gaps = 25/216 (11%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVA 161
           +  ++   KPAG+    G+G   H D       D   Q   KP   HRLD++TSGIL+VA
Sbjct: 5   EGPVWALFKPAGLPTHPGTG---HSDSLATRLADHYAQAAFKPTPAHRLDKDTSGILLVA 61

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            T +A + L E+ R R + K Y   V G  P  +   + + L K    G + +  V    
Sbjct: 62  ATFSALRELQEAIRQRSLIKEYVVWVRGRWPWPEARLLRHQLRKGLERGFEKMRAV-LTA 120

Query: 221 KGANYAISHFKVIDCFAQ--KFC----WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            G   A+       C A+  + C     L ++  TGRTHQ+RV    +G P++GD KY  
Sbjct: 121 AGEERALEAL----CLARPLRICENESLLLIRLFTGRTHQIRVQLASLGHPVLGDVKYGP 176

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
             +     P    +YLHA  + LP   GGR+    P
Sbjct: 177 PEQRVGGGP----MYLHALRVILP---GGRIFACLP 205


>gi|300908288|ref|ZP_07125753.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
 gi|300894535|gb|EFK87892.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
          Length = 325

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 116/234 (49%), Gaps = 20/234 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED    V +KPAG++   G       +   + G+L +  +S   +P L  RLD+ T 
Sbjct: 105 VVYEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIA-NNSADLRPHLITRLDRFTG 163

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A+   A+  +++  +  ++ K Y +LV G   ++   I   + +K    G    V
Sbjct: 164 GLLLIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHGEINKPIGRKD---GQAARV 220

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           + +N      A++ + V +  A K+  + ++ HTGRTHQ+RVH   +G  ++GDH Y   
Sbjct: 221 IDEN---GQRALTEYWVEERGA-KWTRVRVRLHTGRTHQIRVHFAAIGHSLIGDHLY--- 273

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
             G  TS   ++L LHA  +    P    ++  T+ LPA   +      FK +R
Sbjct: 274 --GGDTSKYDHQL-LHASKISFNDPFTLKQMTFTSELPAAFFELVPKCQFKLER 324


>gi|296501895|ref|YP_003663595.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
 gi|296322947|gb|ADH05875.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
          Length = 297

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/220 (27%), Positives = 111/220 (50%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           ++YED  + + NK A +S +      A  +   L S  D +       +  RLD++TSG+
Sbjct: 84  IIYEDDAVLIINKEANMSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGL 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D + + +
Sbjct: 144 MLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDAPIGRKS----DSI-IER 198

Query: 218 QNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              +    A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 199 MVCEDGQRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGDSLY---- 252

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 253 -GGRRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 290


>gi|291618642|ref|YP_003521384.1| TruC [Pantoea ananatis LMG 20103]
 gi|291153672|gb|ADD78256.1| TruC [Pantoea ananatis LMG 20103]
          Length = 259

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 108/239 (45%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           ++Y+D+ +   NKPAG  V   S +  H   F+   V D  GQ     HRLD+ TSG+L+
Sbjct: 4   IIYQDAWLVAVNKPAGWLVHR-SWLDRHETQFVMQTVRDQIGQHVFTAHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +  +    + L++ F   +++K Y ++V G  + +       + +   I   +V     +
Sbjct: 63  MGLSSEVGRLLSQQFEHHQMEKTYHAVVRGWLEGRDRLDYPLVEELDKIADKFV----SD 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +    A++ +  +               ++  +E++P +GR HQLR H  H+  PI+GD
Sbjct: 119 PRAPQPAVTDYASLATVEMPVAVSRYPTARYSLIELKPKSGRKHQLRRHMSHLRHPIIGD 178

Query: 270 --HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
             H      +G       N+L LHA  + L HP  G  L I A L     +  D  G++
Sbjct: 179 SAHGDLRQNRGAAAHFGANRLMLHASSLSLSHPVTGEPLVIRAGLDLVWQRVMDQFGWQ 237


>gi|78776982|ref|YP_393297.1| pseudouridine synthase, RluD [Sulfurimonas denitrificans DSM 1251]
 gi|78497522|gb|ABB44062.1| ribosomal large subunit pseudouridine synthase D [Sulfurimonas
           denitrificans DSM 1251]
          Length = 323

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 108/234 (46%), Gaps = 29/234 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLD 151
           +LYED  I V NKP G++V     +    +  L  W+  KG         ++  + HRLD
Sbjct: 80  ILYEDDDILVINKPTGLTVHPAPSVK---EATLVDWLKHKGMRLSSLSGEERHGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG +V+A+  +  + L++  + + + + Y +++    K++   +   + + SH    
Sbjct: 137 KGTSGAMVIAKNNSTHEFLSDQLQDKSMGRYYLAVINPPLKDELTEVIFPIARSSHNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDH 270
              +    E G  YA S FKV+     +   L   + +TGRTHQ+RVH   +   IVGDH
Sbjct: 197 MAPL----EHG-KYAKSAFKVLAYSNDEANQLIACKLYTGRTHQIRVHLESLNRHIVGDH 251

Query: 271 KYCANFKGNFTSPIQNK---LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            Y         SP Q K   + LHA  +   HP+   R+   A L   M +  D
Sbjct: 252 IYA-------QSPKQEKSERILLHAYIIYFIHPKSKERVSFVASLDKGMQEYID 298


>gi|313885034|ref|ZP_07818786.1| pseudouridine synthase, RluA family [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312619725|gb|EFR31162.1| pseudouridine synthase, RluA family [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 296

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/225 (27%), Positives = 112/225 (49%), Gaps = 19/225 (8%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSG 156
           ++YED    V NKP   +S+         +   +K +   +G   ++ H   RLD++TSG
Sbjct: 80  IVYEDPDCLVVNKPINTVSIPSQKHPDSSMANRIKGYYQQQGYSDQVIHIVTRLDRDTSG 139

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++++A+ R A  +  +  R + I+K Y+++  GI   ++  I       + IG     ++
Sbjct: 140 LMLIAKHRLAHAYFDQQIRNKTIKKYYYAISEGIDWPREGLI------DAPIGRHPDSII 193

Query: 217 KQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           ++  +     A++ F V D + +    L++Q  TGRTHQ+RVH  H+G P+VGD  Y   
Sbjct: 194 QRRVDVSGRPALTRFWVQDKYPEA-TLLKLQLLTGRTHQIRVHLAHLGGPLVGDTLYG-- 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
             G++   IQ +  LH   ++   P    ++ +   LPA M + W
Sbjct: 251 --GSYQDQIQRQA-LHCGQLEFKQPFSHEQIILKQALPADM-QAW 291


>gi|269124164|ref|YP_003306741.1| pseudouridine synthase, RluA family [Streptobacillus moniliformis
           DSM 12112]
 gi|268315490|gb|ACZ01864.1| pseudouridine synthase, RluA family [Streptobacillus moniliformis
           DSM 12112]
          Length = 289

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 74/289 (25%), Positives = 135/289 (46%), Gaps = 47/289 (16%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ--KILDSSVNLTKHSDFLK 98
           LRS +V +D K+++   ++         P I  L  I KE+   I+   +NL        
Sbjct: 30  LRSIEVFLDNKQIRTTTKL---------PKIGILTVIEKEKGSNIVPIKMNLD------- 73

Query: 99  SILLYEDSKIYVFNKPA---------GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             ++YED  + + NK            +     +GI YH   F++ +  +K   PR   R
Sbjct: 74  --IVYEDDDLLIVNKEPYLLTHPTLKKVDKTLANGIVYH---FIEKY--NKNLVPRFISR 126

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++++A+  + +Q   +S +   + K Y +L   + + ++  +   + K    G
Sbjct: 127 LDMNTSGLIMIAKN-SFSQSFIQSGKAN-VTKKYLALAENMFEKEEIIVEEKIYKD---G 181

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +   ++  +++G  YA + FK+I  +       +E +  TGRTHQ+RVH  H+G PI+G
Sbjct: 182 DELARII--DDRG-QYAKTKFKLIKNYPHLDISLIECELFTGRTHQIRVHLKHLGHPIIG 238

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
           D  Y  +   +  + I  +  LH+  +   HP  G R+ +  P+   M+
Sbjct: 239 DSLYNPD---SIFNKIAKRQMLHSYKLSFTHPSSGKRIDVEIPIYHDML 284


>gi|269138083|ref|YP_003294783.1| tRNA pseudouridine synthase C [Edwardsiella tarda EIB202]
 gi|267983743|gb|ACY83572.1| tRNA pseudouridine synthase C [Edwardsiella tarda EIB202]
 gi|304558127|gb|ADM40791.1| tRNA pseudouridine synthase C [Edwardsiella tarda FL6-60]
          Length = 276

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 68/262 (25%), Positives = 110/262 (41%), Gaps = 52/262 (19%)

Query: 96  FLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK------------ 140
           FL  I   ++Y+D  +   NKPAG  V              +SW+D K            
Sbjct: 6   FLSGIGMEIIYQDEHLVAINKPAGWLVH-------------RSWLDRKEKVVVMQTVRDM 52

Query: 141 -GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G+     HRLD+ TSG+L++  +   A+ L + F   +I K+Y ++V G  +   E + 
Sbjct: 53  LGRHVYTVHRLDRPTSGVLLLGLSSEVARALAQQFEQHQIHKVYHAVVRGYLQG--EALL 110

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHT 249
           ++ L             +  ++    A +H++ +               +F  +E+ P T
Sbjct: 111 DYPLTPEL--DKIADRFRSPDRAPQPAQTHYRGLATAEVPLAIGRYPTSRFSLVELMPQT 168

Query: 250 GRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GR HQLR H  H+  PI+GD  +           +F +P    L LHA  + L HP  G 
Sbjct: 169 GRKHQLRRHMAHLRHPIIGDTAHGDLRQNRGVAAHFGTP---GLMLHASELRLTHPVSGE 225

Query: 305 -LQITAPLPAHMVKTWDSLGFK 325
            L + A L     +  D LG++
Sbjct: 226 ALCLRAGLDLRWQELMDGLGWQ 247


>gi|317182255|dbj|BAJ60039.1| hypothetical protein HPF57_0965 [Helicobacter pylori F57]
          Length = 242

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/202 (30%), Positives = 98/202 (48%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVKKEYLALTQGIIEEEQEINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y   
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLY--- 208

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
              N       +L LHA  + L
Sbjct: 209 ---NNEPSSAKRLMLHAHKISL 227


>gi|258423127|ref|ZP_05686021.1| pseudouridine synthase [Staphylococcus aureus A9635]
 gi|257846691|gb|EEV70711.1| pseudouridine synthase [Staphylococcus aureus A9635]
 gi|323438855|gb|EGA96592.1| RNA pseudouridylate synthase [Staphylococcus aureus O11]
 gi|323441699|gb|EGA99344.1| RNA pseudouridylate synthase [Staphylococcus aureus O46]
          Length = 273

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/236 (25%), Positives = 101/236 (42%), Gaps = 34/236 (14%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED  + +  KP G+      ++  + +  H+       +DS   +P   HRLDQET G+
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHV----IYTIDSDYVEP--IHRLDQETVGL 131

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+     + L        I +IY + V  +   K + I         IG D  H  K
Sbjct: 132 LIVAKNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTI------DMPIGKDKFHSNK 185

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +        AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y
Sbjct: 186 RRVSPTGQRAITHILTSKMIKETVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLY 241


>gi|208434657|ref|YP_002266323.1| pseudo uridine synthase D [Helicobacter pylori G27]
 gi|208432586|gb|ACI27457.1| pseudo uridine synthase D [Helicobacter pylori G27]
          Length = 333

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 105/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W++ K       G K R  + HRLD
Sbjct: 86  VIFEDEDLLVLNKPPNLVVHKAPSVK---EPTLVDWLEFKNYELSNLGLKERYGIVHRLD 142

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 143 KDTSGGIVIAKNNFTHVHLSEQLKTKTMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 202

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 203 IIALKAAKKEKSRYSKSEFISLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIMGDNL 262

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 263 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 306


>gi|170717564|ref|YP_001784651.1| tRNA pseudouridine synthase C [Haemophilus somnus 2336]
 gi|168825693|gb|ACA31064.1| pseudouridine synthase [Haemophilus somnus 2336]
          Length = 240

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 57/214 (26%), Positives = 94/214 (43%), Gaps = 21/214 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 9   ILYQDEFLVVVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 68

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----------IANWLLKKSHIGG 210
           A     A  L   F +++++K Y ++V G   + +            IA+   +K  +  
Sbjct: 69  ALNAGIANLLCSQFELKQVKKSYLAIVRGYLSDAQRIDYPLKVQLDKIADKFSRKEELQD 128

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                         Y +  +      + ++  + + P+TGR HQLR H  H+  PI+GD 
Sbjct: 129 AITDYYGLKTVEMPYGVGRYS-----SSRYSLVRLMPYTGRKHQLRRHLKHIFHPILGDT 183

Query: 271 KYCANFKGNFTSPIQN----KLYLHARYMDLPHP 300
           +Y    +    S  QN    +L LHA  +   HP
Sbjct: 184 QYGDLHQNRAFS--QNLGVSRLMLHAEKLCFQHP 215


>gi|213583042|ref|ZP_03364868.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 259

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 21/232 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 3   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +     + +
Sbjct: 63  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLIDDAVLDYPLVEERDKIADKFA----RED 118

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 119 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 178

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
           K+  + + N ++       +L LHA  ++L HP  G+  I   + A + +TW
Sbjct: 179 KH-GDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLI---IQAGLDETW 226


>gi|212693126|ref|ZP_03301254.1| hypothetical protein BACDOR_02633 [Bacteroides dorei DSM 17855]
 gi|237725459|ref|ZP_04555940.1| RNA pseudouridylate synthase [Bacteroides sp. D4]
 gi|265753523|ref|ZP_06088878.1| conserved hypothetical protein [Bacteroides sp. 3_1_33FAA]
 gi|212664231|gb|EEB24803.1| hypothetical protein BACDOR_02633 [Bacteroides dorei DSM 17855]
 gi|229436146|gb|EEO46223.1| RNA pseudouridylate synthase [Bacteroides dorei 5_1_36/D4]
 gi|263235237|gb|EEZ20761.1| conserved hypothetical protein [Bacteroides sp. 3_1_33FAA]
          Length = 308

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 103/220 (46%), Gaps = 21/220 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           L+YED+ I V  K  G+    + +     A HI   L  +V    +  R+   HRLD+ET
Sbjct: 94  LVYEDAYILVVEKKEGLLSVSTERQKERTAQHI---LNEYVKRSHRFNRVFVVHRLDRET 150

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L +++      + Y S+V G  +     + +WL  +      YV 
Sbjct: 151 SGLMMYAKDEKTQNTLRDNWHDIVTDRRYVSIVSGDMEKDYGTVESWLTDRKL----YVS 206

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++    +A++H+K I   A  +  +E+   TGR +Q+RVH   +G P++GD +Y  
Sbjct: 207 SSPVDDGEGKFAVTHYKTIKR-ANGYSLVELDLETGRKNQIRVHMSDLGHPVIGDRRY-- 263

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
              G+   P+  +L LHA  +   HP    L +   P P 
Sbjct: 264 ---GSECDPL-GRLALHAFKLCFYHPVTRELMEFETPYPT 299


>gi|330942730|gb|EGH45266.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. pisi str. 1704B]
          Length = 130

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 41/123 (33%), Positives = 71/123 (57%), Gaps = 8/123 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV      + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG++
Sbjct: 71  IPPV-----RVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSGLS 122

Query: 127 YHI 129
           + +
Sbjct: 123 FGV 125


>gi|32474288|ref|NP_867282.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica SH 1]
 gi|32444826|emb|CAD74828.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica SH 1]
          Length = 256

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 104/222 (46%), Gaps = 21/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
           ++YED+ + V NKP  ++  G +G    H  G    ++     KP      +  RLD  T
Sbjct: 31  VIYEDNHLLVVNKPTKLATMGAAGQPTLHSLGC--DYIRRTCNKPNKVYLGIVSRLDSMT 88

Query: 155 SGILVVARTRAAAQHLTESFRMRR---IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           SG++V+ART  AA  LT  F        +K Y ++V G  + ++  + + + K       
Sbjct: 89  SGVIVMARTSKAASRLTPQFANHSGDGAKKTYLAVVSGRVEQQQGTLVDDVYKDD--AAH 146

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + V   +   A  A   ++V+ C  ++   L ++P TGR HQ+R+    +G PI+GD K
Sbjct: 147 RMRVAHHSRSDAKEARLEYEVLGC-DRELTLLMVKPLTGRKHQIRLQWAEVGFPILGDTK 205

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y +             + LH+  + + HP +  R+   AP+P
Sbjct: 206 YGSERS------WPTGIALHSWRLSIMHPTKKERMTFEAPIP 241


>gi|163748995|ref|ZP_02156246.1| putative 23S rRNA pseudouridylate 746 synthase [Shewanella benthica
           KT99]
 gi|161331371|gb|EDQ02259.1| putative 23S rRNA pseudouridylate 746 synthase [Shewanella benthica
           KT99]
          Length = 238

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/216 (30%), Positives = 97/216 (44%), Gaps = 26/216 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  I V +KP+G+    G     +ID      V        L HRLD  TSGI+++
Sbjct: 19  ILFRDEHILVIDKPSGLLSLSGKH-PLNIDSVHYRLVQDYPTC-TLIHRLDFGTSGIMLL 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +     L + F  RR+ K Y +L+ G  +     +   + K      D   ++K  +
Sbjct: 77  AMNKQINALLCKQFSERRVSKRYTALLHGNLEPDSGLVDCGIAKDV----DNFPLMKLCQ 132

Query: 221 KGANYAISHFKVIDCFAQ----------------KFCWLEMQPHTGRTHQLRVHALHMGC 264
                A S F+VI  F Q                +   +E +P TGRTHQLR+H+ H+G 
Sbjct: 133 DTGKPAQSQFRVISRFIQTDNDNFFLDDTRAGHRQVTRVEFEPVTGRTHQLRLHSQHLGH 192

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           PI+G   Y A  +  F S   ++L LHA  +   HP
Sbjct: 193 PILGCDLY-ATDEAYFMS---SRLMLHASRLCFEHP 224


>gi|114049225|ref|YP_739775.1| pseudouridine synthase Rlu family protein [Shewanella sp. MR-7]
 gi|113890667|gb|ABI44718.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           sp. MR-7]
          Length = 228

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/192 (29%), Positives = 89/192 (46%), Gaps = 19/192 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +++   V +K   +      G A    G +       G K    HRLD  TSG+L++
Sbjct: 4   IIADEADFLVISKSPNVHFHSQDGTA----GVVAQLEQDLGIKLFAVHRLDTPTSGLLLL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+  AAA+ LTE F   ++QK Y +L  G PK K+  +   + K          + K   
Sbjct: 60  AKHPAAARQLTELFSAHQVQKYYLALAKGKPKKKQGWVIGDMAKSRR------SMFKLLR 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A + F           +L ++PH+G+THQLRV    +G PI+GD  Y ++     
Sbjct: 114 TKDNPATTQFFSTSVGDGLRLYL-LKPHSGKTHQLRVALASLGVPILGDALYGSD----- 167

Query: 281 TSPIQNKLYLHA 292
              + ++ YLHA
Sbjct: 168 ---MADRCYLHA 176


>gi|300174185|ref|YP_003773351.1| ribosomal large subunit pseudouridine synthase A [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299888564|emb|CBL92532.1| Ribosomal large subunit pseudouridine synthase A [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 306

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/223 (28%), Positives = 103/223 (46%), Gaps = 25/223 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQ 152
           +++E     V NKPAG+ +      +  + + Y    F +  + S G   +P + HRLD+
Sbjct: 88  IVFESEDFVVVNKPAGMKMHPHTLTENDTLLNYLAADFSERHLVSAGVVARPYMVHRLDR 147

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           ETSG ++VA+       L      + I++ Y + V G      +   N     + IG D 
Sbjct: 148 ETSGAVIVAKNPVVVPILNRMLADKDIKRTYLAWVNG------KMTGNSGTINAPIGVDL 201

Query: 213 VHVVKQNEKGAN--YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               K+   G +   AI+H+  I    QK   L +Q  TGR HQ+RVH   +G PI+GD 
Sbjct: 202 DDDRKRMVNGIDEQLAITHWTQIHMVFQK-TLLRVQLETGRMHQIRVHLAAIGHPIIGDS 260

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
            Y +   G        ++ LHA  ++L  P  G  + ++ P+P
Sbjct: 261 LYGSAM-GTV------RMMLHATSIELTIPFSGDTKMVSVPVP 296


>gi|78776810|ref|YP_393125.1| pseudouridine synthase [Sulfurimonas denitrificans DSM 1251]
 gi|78497350|gb|ABB43890.1| tRNA pseudouridine synthase C [Sulfurimonas denitrificans DSM 1251]
          Length = 241

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/246 (25%), Positives = 112/246 (45%), Gaps = 25/246 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G+ V       +  +  +++  +  G+     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEHLVAINKPSGLLVHRSPIDRHETEFAIQTLRNQLGRFVYPIHRLDKPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + +A+ + E F     +K Y ++V G      E      +K   I          ++
Sbjct: 64  ALDKESAKIMGEKFMAHEAKKSYIAVVRGYTLQSGEIDYALSIKFDKIADK----DSSSD 119

Query: 221 KGANYAISHFKVIDCFA----------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H+K +               ++  +++ P TGR HQLR H  H+   I+GD 
Sbjct: 120 KEPQEALTHYKRLATVELDFEVGKYDKTRYSLVKLNPLTGRKHQLRRHMKHISHHILGDT 179

Query: 271 KYCANFKGNFTSPIQ-----NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           KY    +G     I+     +++ LHA  +++ HP     L I APL    ++ +   G 
Sbjct: 180 KYG---RGEHNKLIRQEFGCHRMLLHAIALEISHPYTKELLYIKAPLDVTFIEMFSFFG- 235

Query: 325 KYDRNL 330
            +D++L
Sbjct: 236 -WDKSL 240


>gi|15924840|ref|NP_372374.1| hypothetical protein SAV1850 [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|15927424|ref|NP_374957.1| hypothetical protein SA1668 [Staphylococcus aureus subsp. aureus
           N315]
 gi|21283520|ref|NP_646608.1| hypothetical protein MW1791 [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49486667|ref|YP_043888.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|57650639|ref|YP_186732.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus COL]
 gi|87160591|ref|YP_494483.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus USA300_FPR3757]
 gi|88195673|ref|YP_500479.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus NCTC 8325]
 gi|148268322|ref|YP_001247265.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH9]
 gi|150394384|ref|YP_001317059.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1]
 gi|151221954|ref|YP_001332776.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|156980166|ref|YP_001442425.1| hypothetical protein SAHV_1835 [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|161510067|ref|YP_001575726.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|253315181|ref|ZP_04838394.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus str. CF-Marseille]
 gi|253735270|ref|ZP_04869435.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|255006638|ref|ZP_05145239.2| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Mu50-omega]
 gi|257793791|ref|ZP_05642770.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9781]
 gi|258413728|ref|ZP_05682001.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9763]
 gi|258420765|ref|ZP_05683704.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9719]
 gi|258438426|ref|ZP_05689710.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9299]
 gi|258443871|ref|ZP_05692210.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8115]
 gi|258447326|ref|ZP_05695473.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A6300]
 gi|258448191|ref|ZP_05696318.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus A6224]
 gi|258452660|ref|ZP_05700659.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus A5948]
 gi|258453376|ref|ZP_05701359.1| pseudouridine synthase [Staphylococcus aureus A5937]
 gi|262050142|ref|ZP_06022996.1| hypothetical protein SAD30_1106 [Staphylococcus aureus D30]
 gi|262052669|ref|ZP_06024861.1| hypothetical protein SA930_0805 [Staphylococcus aureus 930918-3]
 gi|269203487|ref|YP_003282756.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282895148|ref|ZP_06303367.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8117]
 gi|282924181|ref|ZP_06331856.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|282928588|ref|ZP_06336187.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|284024896|ref|ZP_06379294.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 132]
 gi|294850278|ref|ZP_06791013.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9754]
 gi|295406157|ref|ZP_06815965.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|296276018|ref|ZP_06858525.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus MR1]
 gi|297207434|ref|ZP_06923871.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297244920|ref|ZP_06928797.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8796]
 gi|300911518|ref|ZP_07128963.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|13701643|dbj|BAB42936.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           N315]
 gi|14247622|dbj|BAB58012.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|21204961|dbj|BAB95656.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49245110|emb|CAG43576.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|57284825|gb|AAW36919.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus COL]
 gi|87126565|gb|ABD21079.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus USA300_FPR3757]
 gi|87203231|gb|ABD31041.1| ribosomal large subunit pseudouridine synthase, RluD subfamily,
           putative [Staphylococcus aureus subsp. aureus NCTC 8325]
 gi|147741391|gb|ABQ49689.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH9]
 gi|149946836|gb|ABR52772.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1]
 gi|150374754|dbj|BAF68014.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|156722301|dbj|BAF78718.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|160368876|gb|ABX29847.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|253726677|gb|EES95406.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|257787763|gb|EEV26103.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9781]
 gi|257839515|gb|EEV63986.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9763]
 gi|257843369|gb|EEV67779.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9719]
 gi|257848470|gb|EEV72461.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9299]
 gi|257851277|gb|EEV75220.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8115]
 gi|257853913|gb|EEV76869.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A6300]
 gi|257858430|gb|EEV81306.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus A6224]
 gi|257859635|gb|EEV82484.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus A5948]
 gi|257864468|gb|EEV87213.1| pseudouridine synthase [Staphylococcus aureus A5937]
 gi|259159418|gb|EEW44470.1| hypothetical protein SA930_0805 [Staphylococcus aureus 930918-3]
 gi|259161767|gb|EEW46355.1| hypothetical protein SAD30_1106 [Staphylococcus aureus D30]
 gi|262075777|gb|ACY11750.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282589797|gb|EFB94882.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|282592976|gb|EFB97978.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|282762492|gb|EFC02633.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8117]
 gi|285817530|gb|ADC38017.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus 04-02981]
 gi|294822894|gb|EFG39328.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9754]
 gi|294969154|gb|EFG45175.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|296887897|gb|EFH26793.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297178000|gb|EFH37248.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8796]
 gi|300887150|gb|EFK82350.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|312830222|emb|CBX35064.1| RNA pseudouridylate synthase family protein [Staphylococcus aureus
           subsp. aureus ECT-R 2]
 gi|315130506|gb|EFT86492.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS03]
 gi|315196801|gb|EFU27145.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320141300|gb|EFW33145.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320143572|gb|EFW35352.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|329727339|gb|EGG63795.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21172]
 gi|329729507|gb|EGG65909.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21189]
 gi|329732958|gb|EGG69302.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 273

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/236 (25%), Positives = 101/236 (42%), Gaps = 34/236 (14%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED  + +  KP G+      ++  + +  H+       +DS   +P   HRLDQET G+
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHV----IYTIDSDYVEP--IHRLDQETVGL 131

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+     + L        I +IY + V  +   K + I         IG D  H  K
Sbjct: 132 LIVAKNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTI------DMPIGKDKFHSNK 185

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +        AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y
Sbjct: 186 RRVSPTGQRAITHILTSKMIKEAVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLY 241


>gi|228920025|ref|ZP_04083376.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar huazhongensis BGSC 4BD1]
 gi|228839650|gb|EEM84940.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar huazhongensis BGSC 4BD1]
          Length = 292

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/223 (28%), Positives = 110/223 (49%), Gaps = 24/223 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQET 154
           ++YED  + + NK A +S         H  G + + + S   K  L        RLD++T
Sbjct: 79  IVYEDDAVLIINKEANMSTIPSR---EHPTGSVANALLSHYDKQHLASTVHIVTRLDRDT 135

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D + 
Sbjct: 136 SGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDALIGRKS----DSII 191

Query: 215 VVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y 
Sbjct: 192 ERTVCEDGQR-AVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGDSLY- 247

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
               G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 248 ----GGRRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 285


>gi|170726105|ref|YP_001760131.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169811452|gb|ACA86036.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 219

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/203 (29%), Positives = 96/203 (47%), Gaps = 12/203 (5%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + V NKP+G+    G       D  L   +  +  +  L HRLD  TSGI+V A 
Sbjct: 18  YQDRDMIVINKPSGLLSNPGRA-ENTFDCALTRLL-QRYPETILVHRLDCATSGIMVFAL 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            + A  ++   F+ R  +K Y + V G   +K E +    +K          + +  +  
Sbjct: 76  NKKAESNIKTQFQNRLSKKTYIAEVQG-HLDKTEGVIELAMKADSERPPLQKIAEDGKPS 134

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             Y    +KV++   +    +E+ P TGRTHQLR+H L +G PI+GD  Y      + + 
Sbjct: 135 KTY----YKVLEK-RENSTLVELNPVTGRTHQLRLHMLAIGHPILGDDFYGEQEVIDAS- 188

Query: 283 PIQNKLYLHARYMDLPHPEGGRL 305
              ++L LHA  + + HP  G+L
Sbjct: 189 ---HRLCLHAMTLAITHPYSGKL 208


>gi|15675829|ref|NP_270003.1| hypothetical protein SPy_2063 [Streptococcus pyogenes M1 GAS]
 gi|13623058|gb|AAK34724.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS]
          Length = 272

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/203 (29%), Positives = 89/203 (43%), Gaps = 13/203 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K   LYED  I + NKP G+   G       +   + ++    GQ   + HRLD+ETSG 
Sbjct: 57  KVTCLYEDEHIIIVNKPEGMKTHGNDPTELALLNHVSAYT---GQTCYVVHRLDKETSGA 113

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+T      L      R I + Y +LV G   + +    + + +  H     V    
Sbjct: 114 ILFAKTPFILPILNRLLEKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRV---- 169

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H G  + GD  Y +N K
Sbjct: 170 VDPINGKKAITEVTLVKNFHKTASLLTCQLQTGRTHQIRVHLAHQGHVLFGDPLY-SNGK 228

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
            +       +L LHA  + L HP
Sbjct: 229 KDCA-----RLMLHAYQLRLKHP 246


>gi|16761743|ref|NP_457360.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|29143227|ref|NP_806569.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|213162034|ref|ZP_03347744.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
 gi|213424905|ref|ZP_03357655.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213622998|ref|ZP_03375781.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
 gi|213648743|ref|ZP_03378796.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
 gi|289829830|ref|ZP_06547345.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|34582455|sp|Q8Z439|TRUC_SALTI RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|25322427|pir||AG0861 probable RNA pseudouridylate synthase yqcB [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16504044|emb|CAD06078.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhi]
 gi|29138860|gb|AAO70429.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
          Length = 260

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 21/232 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +     + +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLIDDAVLDYPLVEERDKIADKFA----RED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
           K+  + + N ++       +L LHA  ++L HP  G+  I   + A + +TW
Sbjct: 180 KH-GDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLI---IQAGLDETW 227


>gi|268592403|ref|ZP_06126624.1| ribosomal large subunit pseudouridine synthase A [Providencia
           rettgeri DSM 1131]
 gi|291312190|gb|EFE52643.1| ribosomal large subunit pseudouridine synthase A [Providencia
           rettgeri DSM 1131]
          Length = 210

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 54/164 (32%), Positives = 82/164 (50%), Gaps = 16/164 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD  TSG++VVAR +A    L++ F  R + KIY +L+ G   N  E + +  + K
Sbjct: 40  LVHRLDFGTSGLMVVARNKAINAALSQQFSQRSVIKIYQALLCGHLAN-DEGVIDAAIAK 98

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVID--------CFAQKFCWLEMQPHTGRTHQLRV 257
                  + + + N K A    SH++VI+          +     +++ P TGRTHQLR+
Sbjct: 99  DPAQFPRMSLCEVNGKPAR---SHYQVIERLYHPVENGISLPVTRVQLTPETGRTHQLRI 155

Query: 258 HALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
           H   +G PI+G   Y     +G   +P   +L LHA  +   HP
Sbjct: 156 HCQKLGYPILGCDLYGGRLLQGTEQTP---RLLLHASELHFVHP 196


>gi|254671778|emb|CBA09633.1| pseudouridylate synthase, 23S RNA-specific [Neisseria meningitidis
           alpha153]
          Length = 231

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/211 (30%), Positives = 99/211 (46%), Gaps = 19/211 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV    G    +   L + +    +K  L HRLD++T GIL+ 
Sbjct: 18  ILFRHQDFVAINKPQGISVHRSDG-EVSLTATLAAQLGV--EKVWLLHRLDKQTGGILLF 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I   + +KS  G     + K   
Sbjct: 75  ALNSQSAAVLAAQFAERKMKKTYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLTR 128

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F  I   ++K     ++PHTG+THQLRV    +G PI+GD  Y     G  
Sbjct: 129 NMENIAVTQFFSIRI-SEKMRLFILEPHTGKTHQLRVAMKSLGSPILGDRLY-----GGT 182

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
            S      +L+A  +   + +   ++ITAPL
Sbjct: 183 ES---ETTFLYAWKIQFTYQQ-QEIEITAPL 209


>gi|251792621|ref|YP_003007347.1| tRNA pseudouridine synthase C [Aggregatibacter aphrophilus NJ8700]
 gi|247534014|gb|ACS97260.1| tRNA pseudouridine synthase C [Aggregatibacter aphrophilus NJ8700]
          Length = 236

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/212 (26%), Positives = 95/212 (44%), Gaps = 16/212 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDDVLVAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQLVYPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  L + F  ++ +K Y ++V G      E      ++   I   +     Q +
Sbjct: 64  ALNSEIANLLCQQFEQKQTEKQYLAVVRGYVTGHGEIDYPLKIQLDKIADKF----SQQD 119

Query: 221 KGANYAISHFKV---------IDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++          + C+A  ++  + + P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQSAVTFYEGLQTVEMPYGVGCYATSRYSLVRLVPKTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNFTSPIQ--NKLYLHARYMDLPHP 300
           +Y    +    +     ++L LHA  +   HP
Sbjct: 180 QYGDLHQNRALTEHTGCSRLMLHAEKLTFVHP 211


>gi|30019354|ref|NP_830985.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|229126613|ref|ZP_04255626.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-Cer4]
 gi|29894897|gb|AAP08186.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|228656850|gb|EEL12675.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-Cer4]
          Length = 292

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/220 (27%), Positives = 111/220 (50%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           ++YED  + + NK A +S +      A  +   L S  D +       +  RLD++TSG+
Sbjct: 79  IIYEDDAVLIINKEANMSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGL 138

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D + + +
Sbjct: 139 MLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDAPIGRKS----DSI-IER 193

Query: 218 QNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              +    A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 194 MVCEDGQRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGDSLY---- 247

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 248 -GGRRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 285


>gi|229143914|ref|ZP_04272332.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST24]
 gi|228639575|gb|EEK95987.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST24]
          Length = 292

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/220 (27%), Positives = 111/220 (50%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           ++YED  + + NK A +S +      A  +   L S  D +       +  RLD++TSG+
Sbjct: 79  IIYEDDAVLIINKEANMSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGL 138

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D + + +
Sbjct: 139 MLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDAPIGRKS----DSI-IER 193

Query: 218 QNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              +    A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 194 MVCEDGQRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGDSLY---- 247

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 248 -GGRRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 285


>gi|188589626|ref|YP_001921981.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str.
           Alaska E43]
 gi|251780373|ref|ZP_04823293.1| pseudouridine synthase, RluA family [Clostridium botulinum E1 str.
           'BoNT E Beluga']
 gi|188499907|gb|ACD53043.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str.
           Alaska E43]
 gi|243084688|gb|EES50578.1| pseudouridine synthase, RluA family [Clostridium botulinum E1 str.
           'BoNT E Beluga']
          Length = 322

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 71/291 (24%), Positives = 125/291 (42%), Gaps = 29/291 (9%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++ +     +    + K LR   +RV+ K+      ++ G +V I  + +  
Sbjct: 8   NEAGQRLDKFLRKLLKDVPLSAIFKALRKKDIRVNGKKQSEKYFLEEGDIVEIKYIKSNP 67

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFL 133
               K++K +  + +  K +        YED  + V  K  GI V          +  ++
Sbjct: 68  E---KKEKFIQVNFSGMKTA--------YEDENLLVVEKWPGILVHPDKDEKDPTLTDYV 116

Query: 134 KSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            S++  KG           P   +RLD+ TSG+++  +T    + + E+ R  R++K Y 
Sbjct: 117 LSYLKEKGSYVPENEITFTPAPCNRLDRNTSGLVMFGKTFEGLKSINETIREDRVRKYYV 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  K +      ++LK        +  V + E   +  I+           +  LE
Sbjct: 177 ALVKG--KVQDGLHTGYILKNQDTN---ISKVYEKEVPDSKKIAMEVTTTQTNGAYSLLE 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           +   TGR+HQ+R H  H+G PI+GD KY         S  +NK  L  +Y+
Sbjct: 232 INLITGRSHQIRAHLAHLGSPIIGDDKYGDR---KLNSFFKNKYGLEYQYL 279


>gi|84495993|ref|ZP_00994847.1| putative ribosomal large subunit pseudouridine synthase [Janibacter
           sp. HTCC2649]
 gi|84382761|gb|EAP98642.1| putative ribosomal large subunit pseudouridine synthase [Janibacter
           sp. HTCC2649]
          Length = 321

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 58/194 (29%), Positives = 95/194 (48%), Gaps = 20/194 (10%)

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           + + G   R  +  RLD  TSG++VV ++      L  +F+ R ++K Y +LV G+P   
Sbjct: 129 ISTSGASERQGIVSRLDVGTSGLMVVCKSERGYSVLKRAFKERTVEKTYHTLVQGLPDPL 188

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I   + +  H G DY   V ++ K   +A++H+++I+ F +    L+++  TGRTHQ
Sbjct: 189 VGTIDAPIAR--HPGHDYKFAVMESGK---HAVTHYELIEAF-RYASLLDIRLETGRTHQ 242

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-----YLHARYMDLPHPEGGR-LQIT 308
           +RVH   +  P VGD  Y A+        +  KL     +LHA  +   HP  G  +   
Sbjct: 243 IRVHFSALRHPCVGDLTYGAD------PTLAKKLGLERQWLHAVGLGFEHPGSGEWVTFE 296

Query: 309 APLPAHMVKTWDSL 322
           +  PA +    D L
Sbjct: 297 SQYPADLQAALDRL 310


>gi|15645572|ref|NP_207748.1| hypothetical protein HP0956 [Helicobacter pylori 26695]
 gi|3915400|sp|O25610|Y956_HELPY RecName: Full=Uncharacterized RNA pseudouridine synthase HP_0956;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2314093|gb|AAD07999.1| conserved hypothetical protein [Helicobacter pylori 26695]
          Length = 242

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/202 (29%), Positives = 98/202 (48%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K W         L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLASFFKGWA--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 100 VLLVKENSEF-HLKAKKAFKDRAVKKEYLALTQGIIEEEREINAPILTFKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y   
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLY--- 208

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
              N    +  +L LHA  + L
Sbjct: 209 ---NNEPSLAKRLMLHAHKIAL 227


>gi|332673797|gb|AEE70614.1| RNA pseudouridine synthase [Helicobacter pylori 83]
          Length = 242

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/199 (31%), Positives = 99/199 (49%), Gaps = 31/199 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG++++
Sbjct: 58  VIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGVILL 102

Query: 161 ARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            R  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  + K+
Sbjct: 103 VRENSEF-HLKAKKAFKDRAVKKEYLALAQGIIEEEQEINAPILTFKT--TKAFSKISKK 159

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y  N  G
Sbjct: 160 GQEAVTM-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYN-NEPG 213

Query: 279 NFTSPIQNKLYLHARYMDL 297
           +       +L LHA  + L
Sbjct: 214 S-----AKRLMLHAHKIAL 227


>gi|254779554|ref|YP_003057660.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
 gi|254001466|emb|CAX29466.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
          Length = 242

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/199 (30%), Positives = 100/199 (50%), Gaps = 31/199 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG++++
Sbjct: 58  VIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGVILL 102

Query: 161 ARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            +  +   HL   ++F+ R ++K Y ++V GI + ++E  A  L  K+     +  + K+
Sbjct: 103 VKENSEF-HLKAKKAFKDRAVKKEYLAIVQGIVEEEREINAPILTIKT--TKAFSKISKK 159

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y  N  G
Sbjct: 160 GQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYN-NEPG 213

Query: 279 NFTSPIQNKLYLHARYMDL 297
           +       +L LHA  + L
Sbjct: 214 S-----AKRLMLHAHKIAL 227


>gi|22537251|ref|NP_688102.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           agalactiae 2603V/R]
 gi|22534119|gb|AAM99974.1|AE014242_3 ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 2603V/R]
          Length = 294

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 50/177 (28%), Positives = 90/177 (50%), Gaps = 12/177 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    + NKP G +    S  +  I  F+K +  S     Q+  +  RLD++TSG+
Sbjct: 78  IIYEDDHFLILNKPFGFASIPSSIHSNTIANFIKHYYVSNNYANQQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G     +  + IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQAKAIEKRYYALVSGSGDLADSGDIIAPIARDVDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++  +   YA + ++V+  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y
Sbjct: 192 TRRVHESGKYAHTSYQVVARYGD-VRLVDIKLHTGRTHQIRVHFAHIGFPLLGDDLY 247


>gi|322373824|ref|ZP_08048359.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C150]
 gi|321277196|gb|EFX54266.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C150]
          Length = 290

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 87/201 (43%), Gaps = 20/201 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  + V NKP G+   G       +   + ++ D   Q   + HRLD ETSG ++ A
Sbjct: 84  LYEDQHLIVVNKPEGMKTHGNEPTEIALLNHVSAYCD---QTCYVVHRLDMETSGAVLFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      + IQ+ YW+L  G  + K+    + + +  H   D    V    K
Sbjct: 141 KNPFILPILNRLLEDKLIQRQYWALAEGRFQTKETVYKDKIGRDRH---DRRKRVVDPRK 197

Query: 222 G--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           G  A   ++  K  +  +   C L+    TGRTHQ+RVH  H G  I+GD  Y       
Sbjct: 198 GQRAYTTVTRLKTFNGASLVNCQLK----TGRTHQIRVHLAHHGHAILGDPLYSHRHA-- 251

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                 ++L LHA  +   HP
Sbjct: 252 ------SRLMLHAHSLSFTHP 266


>gi|262041866|ref|ZP_06015050.1| ribosomal large subunit pseudouridine synthase A [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|259040771|gb|EEW41858.1| ribosomal large subunit pseudouridine synthase A [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
          Length = 232

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/210 (29%), Positives = 96/210 (45%), Gaps = 20/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LLY+D  + + NKPAG+    G     ++D      V  +     L HRLD  TSG++V+
Sbjct: 19  LLYQDEHLVLINKPAGLLSLSGKD-PRNLDSVHHRLVQ-RFPGCTLVHRLDFGTSGLMVI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +     L + F  R + K+Y +L+ G    + E I    + K       + +  ++ 
Sbjct: 77  ARNKGINALLCQQFSQRTVDKVYTALLCG-HLAEDEGIVEAAIAKDPARFPRMALCARHG 135

Query: 221 KGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K A    S ++VID   Q            + + P TGRTHQLR+H   +G PI+G    
Sbjct: 136 KPAR---SRYRVIDRLYQAREGERALALTRVTLTPETGRTHQLRIHCQLLGYPILG---- 188

Query: 273 CANFKGNFT--SPIQNKLYLHARYMDLPHP 300
           C  + G     +   ++L LHA  +   HP
Sbjct: 189 CDLYGGRELPGTECASRLMLHASELRFVHP 218


>gi|325685780|gb|EGD27854.1| pseudouridine synthase [Lactobacillus delbrueckii subsp. lactis DSM
           20072]
          Length = 282

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/183 (31%), Positives = 84/183 (45%), Gaps = 16/183 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++YED  + V +KP G      QG +G A      L       G  P + HRLD  T G+
Sbjct: 83  VVYEDENVLVIDKPKGQKTHPNQGENGTA------LNDCASYLGYSPYIVHRLDMLTGGL 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+  A    L      + +++ Y + V     +  + I +       IG D     K
Sbjct: 137 LLVAKNPAVVPILNRQLTSKTLRRDYLATV-----DLNKEIPDQGTIDLPIGQDPADQRK 191

Query: 218 QNEKGANY-AISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +  +     A+SHF+V++   +K    L +   TGRTHQ+RVH    G PIVGD  Y  N
Sbjct: 192 RQVRADGLRAVSHFQVLEKDEEKKQAKLLVTLETGRTHQIRVHLSASGWPIVGDPLYNPN 251

Query: 276 FKG 278
           F G
Sbjct: 252 FAG 254


>gi|300812671|ref|ZP_07093082.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
 gi|300496357|gb|EFK31468.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
          Length = 282

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/183 (31%), Positives = 84/183 (45%), Gaps = 16/183 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++YED  + V +KP G      QG +G A      L       G  P + HRLD  T G+
Sbjct: 83  VVYEDENVLVIDKPKGQKTHPNQGENGTA------LNDCASYLGYSPYIVHRLDMLTGGL 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+  A    L      + +++ Y + V     +  + I +       IG D     K
Sbjct: 137 LLVAKNPAVVPILNRQLTSKTLRRDYLATV-----DLNKEIPDQGTIDLPIGQDPADQRK 191

Query: 218 QNEKGANY-AISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +  +     A+SHF+V++   +K    L +   TGRTHQ+RVH    G PIVGD  Y  N
Sbjct: 192 RQVRADGLRAVSHFQVLEKDEEKKQAKLLVTLETGRTHQIRVHLSASGWPIVGDPLYNPN 251

Query: 276 FKG 278
           F G
Sbjct: 252 FAG 254


>gi|229084299|ref|ZP_04216581.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-44]
 gi|228699010|gb|EEL51713.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-44]
          Length = 297

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/213 (30%), Positives = 107/213 (50%), Gaps = 35/213 (16%)

Query: 101 LLYEDSKIYVFNK------------PAGISVQGGSGIAYHIDG-FLKSWVDSKGQKPRLT 147
           ++YED  + V NK            PAG SV   + + YH D   L S V        + 
Sbjct: 86  VVYEDDSVLVMNKAPYMSTIPSREHPAG-SV--ANALLYHYDKQHLASTV-------HIV 135

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
            RLD++TSG+++VA+ R     L++  + +++Q+ Y ++V G    +   I   + +KS 
Sbjct: 136 TRLDRDTSGLMLVAKNRFIHHLLSKQHQEKQVQRTYEAIVHGELVEESGTIDAPIGRKS- 194

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              D +      E G   A++HF+V++ F  K   + +Q  TGRTHQ+RVH  ++G P++
Sbjct: 195 ---DSIIERTVCEDGQK-AVTHFQVLERFPDK-TRVSLQLETGRTHQIRVHMAYVGHPLL 249

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           GD  Y     G  TS ++ +  LH+  +   HP
Sbjct: 250 GDDLY-----GGSTSEMKRQA-LHSTSLTFYHP 276


>gi|114562440|ref|YP_749953.1| pseudouridylate synthase [Shewanella frigidimarina NCIMB 400]
 gi|114333733|gb|ABI71115.1| tRNA pseudouridine synthase C [Shewanella frigidimarina NCIMB 400]
          Length = 293

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 76/271 (28%), Positives = 128/271 (47%), Gaps = 33/271 (12%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSW 136
           I E    D+ ++   H   +   +L+ED  +   +KPAG+ V   S +A     F ++  
Sbjct: 26  IDENATADTELDDDLHPPHID--ILFEDEHLVAIHKPAGLLVHR-SYLARRERFFAMQMT 82

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            D  G      HRLD+ TSG+L+ A++   A+ L E F    I+K Y ++V G   N  E
Sbjct: 83  RDLVGCHVFPVHRLDRPTSGVLLFAKSSEVARALCEQFADHSIKKHYLAIVRG---NMHE 139

Query: 197 C-IANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWL 243
               ++ LK+    +G  +V    QN K A  A++ ++ +               ++  +
Sbjct: 140 SGTLDYALKQEFDDLGDKHV---DQN-KAAQDAVTDYQPLLNTEIPFSSGRYPTSRYGLV 195

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLP 298
           ++ PHTGR HQLR H  H+  PIVGD  +        F+ +FT    N+L+L A+ +   
Sbjct: 196 KLSPHTGRKHQLRRHMAHLRHPIVGDTTHGDGKQNKFFREHFTI---NRLWLIAKSLQFV 252

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           HP   + + I   L A  +  +++ G+  D+
Sbjct: 253 HPVTQQSMHIETELEAEWLTVFNAFGWDDDQ 283


>gi|255084742|ref|XP_002504802.1| predicted protein [Micromonas sp. RCC299]
 gi|226520071|gb|ACO66060.1| predicted protein [Micromonas sp. RCC299]
          Length = 345

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 105/229 (45%), Gaps = 25/229 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS--WVDSKGQ--------KPRLTHR 149
           ++++ED  + V +KPAG+S      +  ++ G L +   + +KG+        +    HR
Sbjct: 64  VVIHEDDDVLVIDKPAGMSFHNDD-LVTNLPGVLSTVRALQAKGELRGSDYAGELHSVHR 122

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ TSGIL++A+    A  L   F  RR+ K Y +L    P  K   +   + +     
Sbjct: 123 LDKITSGILLLAKNERVASWLARQFARRRVHKYYVALSARKPSKKMGTVRGDMAQARR-- 180

Query: 210 GDYVHVVKQNEKGANYAISHF------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           G Y  + + +      A++ F             +    L M+P TG+THQLRV A  +G
Sbjct: 181 GTY-KLTRCSSNSTPAAVTKFVSRGVRGASPGGDRPLRVLLMRPLTGKTHQLRVCAKSLG 239

Query: 264 CPIVGDHKYCA-----NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            P++GD  Y       N   N  +  +++ YLHA  + +  P G  +++
Sbjct: 240 APVLGDAAYGGADTNKNANKNDGAGGEDRGYLHAAALRVAMPGGNVMEV 288


>gi|229101887|ref|ZP_04232601.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-28]
 gi|228681470|gb|EEL35633.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-28]
          Length = 292

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 68/266 (25%), Positives = 125/266 (46%), Gaps = 28/266 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+  P
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQYASVRHQLQAGEQLRVFFP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYH 128
           V      +I E   L                ++YED  + V NK A +S +         
Sbjct: 63  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPEGS 107

Query: 129 IDGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L S+ D +       +  RLD++TSG++++A+ R     L++  + + +++ Y ++
Sbjct: 108 VANALLSYYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAI 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    ++  I   + +KS    D +      E G   A++HF+VI   +QK   + ++
Sbjct: 168 VHGEMIKREGTIDAPIGRKS----DSIIERTVCEDG-QRAVTHFRVIHSSSQK-THVSLE 221

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
             TGRTHQ+RVH  H+G P++GD  Y
Sbjct: 222 LETGRTHQIRVHMAHIGHPLLGDDLY 247


>gi|207091718|ref|ZP_03239505.1| hypothetical protein HpylHP_00901 [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 242

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/202 (30%), Positives = 101/202 (50%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  +    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENVLALFKPPFIE-------SYDLLSFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L+ GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVKKEYLALIQGIIEEEREINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y  N
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYN-N 210

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
             G+       +L LHA  + L
Sbjct: 211 EPGS-----AKRLMLHAHKIAL 227


>gi|323700314|ref|ZP_08112226.1| pseudouridine synthase [Desulfovibrio sp. ND132]
 gi|323460246|gb|EGB16111.1| pseudouridine synthase [Desulfovibrio desulfuricans ND132]
          Length = 214

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/205 (31%), Positives = 101/205 (49%), Gaps = 18/205 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED+ + V +KP+G+    G G A    +   +K+       +P + HRLDQ+TSG+L
Sbjct: 9   IVYEDAVVVVVDKPSGLLSVPGKGEANQDCVVARVKARHPGCIDQPSV-HRLDQDTSGLL 67

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A +  A + L+  F  R + K Y +L+ G+ + +   I      K  +  D       
Sbjct: 68  VLALSAEAHRDLSGQFMDRLVGKRYVALIDGVVEGQGGIIE----LKFRLDPDNRPYQVY 123

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
           +       ++ ++ +     +   +E  PHTGRTHQLR+H+ H   +G PIVGD  Y   
Sbjct: 124 DPVNGKRGVTRWRKLSVEDGR-TRVEFMPHTGRTHQLRLHSAHEKGLGLPIVGDRLY--- 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G  T P Q  L LHA  +   HP
Sbjct: 180 --GTGTGPGQ--LKLHASLLRFRHP 200


>gi|315453361|ref|YP_004073631.1| putative ribosomal pseudouridine synthase [Helicobacter felis ATCC
           49179]
 gi|315132413|emb|CBY83041.1| putative ribosomal pseudouridine synthase [Helicobacter felis ATCC
           49179]
          Length = 247

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 68/217 (31%), Positives = 98/217 (45%), Gaps = 34/217 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSG 156
           K+ +LY+++     NKPAG++                S+   K   P +L HRLD  T+G
Sbjct: 54  KAQILYQETDWLFLNKPAGVN----------------SYALEKQHPPYKLLHRLDLPTTG 97

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L +A+  A AQ L E+F+ R + K Y +LV G+ K  +       ++KSHI      V 
Sbjct: 98  VLALAQNHAHAQGL-EAFKKRAVYKEYIALVQGVIKKPQTLRMPLRVQKSHIEDAKGFVK 156

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              +     A +    +  +  K   L++   TG THQ+R H   +GCPIVGD  Y    
Sbjct: 157 TLLDPAGRPACTKITPLKQYKNK-TLLKVVITTGITHQIRAHLSALGCPIVGDVLYGGRS 215

Query: 277 KGNFTSPIQNKLYLHA-RYMDLPHPEGGRLQITAPLP 312
              F        +LHA R   L H       I APLP
Sbjct: 216 HQYF--------FLHAHRLKILDH------YIQAPLP 238


>gi|167854653|ref|ZP_02477433.1| tRNA pseudouridine synthase C [Haemophilus parasuis 29755]
 gi|167854190|gb|EDS25424.1| tRNA pseudouridine synthase C [Haemophilus parasuis 29755]
          Length = 242

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 118/246 (47%), Gaps = 20/246 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETS 155
           +K  ++Y+D ++   NKPAG+ V   S +  H   F +++  +   Q     HRLD+ TS
Sbjct: 1   MKLEIIYQDDELIAINKPAGMLVHR-SWLDKHETVFAMQTLRNQIRQHVFPIHRLDRPTS 59

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+ A     A+ +++ F   +IQK Y ++V G  +   E   ++ LK   +  D +  
Sbjct: 60  GVLLFALNSEMARTMSQLFEQHQIQKSYLAVVRGYLQG--EGRIDYPLK---VQLDKIAD 114

Query: 216 VKQNEKGANYAISHFKVIDC---------FAQ-KFCWLEMQPHTGRTHQLRVHALHMGCP 265
               EK A  AI+ ++ I           FA  ++  +++ P TGR HQLR H  H+  P
Sbjct: 115 KFSQEKEAQEAITDYRNIATAERPYPAGKFATARYSLVQLYPKTGRKHQLRRHLKHLFHP 174

Query: 266 IVGDHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           I+GD  Y    +    +     ++L LH+  +   HP+  + ++I APL       +   
Sbjct: 175 IMGDTNYGDLHQNRVLTANTGCDRLMLHSNSLQFIHPKTLQTIEIKAPLDEQWKALFTQF 234

Query: 323 GFKYDR 328
           G+ + +
Sbjct: 235 GWNFTK 240


>gi|303233294|ref|ZP_07319965.1| pseudouridine synthase, RluA family [Atopobium vaginae PB189-T1-4]
 gi|302480594|gb|EFL43683.1| pseudouridine synthase, RluA family [Atopobium vaginae PB189-T1-4]
          Length = 338

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/217 (27%), Positives = 98/217 (45%), Gaps = 30/217 (13%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV------DSKGQ-----KPRLTHRLD 151
           YED  + V +K  G+     SG   HID  L + +      D  G+     +P + HRLD
Sbjct: 89  YEDEYLLVISKQKGLVCHPSSG---HIDDTLANALVAHCGFDHLGKLQGDDRPGIVHRLD 145

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +T+G++V A+     + L +  R+R   + Y +LV G     +  I   + +      +
Sbjct: 146 MDTTGLMVAAKDNETQEQLQDLIRLRDFDRRYLALVQGYVSPDEGTITTGIARSKK---N 202

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + +    +  +  AI+ FK +D F        +  LE   +TGRTHQ+RVH  + G  +
Sbjct: 203 RLKMCVSKDPLSRQAITTFKTLDRFEASAHDDGYSLLECHLYTGRTHQIRVHMRYTGHCL 262

Query: 267 VGDHKYCANFKGNFTSPIQNKL---YLHARYMDLPHP 300
           VGD  Y     G     I   L   +LH+ +++  HP
Sbjct: 263 VGDPLY-----GKVGERINLHLKRQFLHSWHINFDHP 294


>gi|145355423|ref|XP_001421961.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582200|gb|ABP00255.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 264

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 69/253 (27%), Positives = 107/253 (42%), Gaps = 36/253 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHI-----------------DGFLKS-WVDSKGQ 142
           +L+ED ++   NK AG +    S +A                    DG L S  V     
Sbjct: 15  ILHEDEEMTCVNKRAGTASTPESRVADSSAASLVVARWRRRLVDAHDGALASNVVLGASL 74

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL-------VWGIPKNKK 195
            P + HRLD ETSG LVV +   AA     +F  R ++K Y +L       V G      
Sbjct: 75  VPYVAHRLDLETSGALVVCKNAKAAARAQGAFERREVEKTYLALCRCDEFDVSG--GGAS 132

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
               +  L K   G  +   V+ +      A + + ++    ++   +  +P TGRTHQ+
Sbjct: 133 SGTIDLALAKRDDGARFF--VETSSADGKPASTEWTIV-ARNRRHALVRCRPKTGRTHQI 189

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAH 314
           RVH   +G PIVGD  Y     G   + + ++  LHA  +  P  +  G  +I AP+P  
Sbjct: 190 RVHLAAIGLPIVGDAAY-----GCLDADVVDRHALHAWTLRFPAKDFAGVPRIVAPVPDD 244

Query: 315 MVKTWDSLGFKYD 327
             +  + +G  +D
Sbjct: 245 FRRACERVGVDFD 257


>gi|157372174|ref|YP_001480163.1| pseudouridine synthase [Serratia proteamaculans 568]
 gi|157323938|gb|ABV43035.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 232

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/230 (28%), Positives = 105/230 (45%), Gaps = 25/230 (10%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H       +LY+D  + + NKP G+    G     ++D      V    
Sbjct: 3   KIIDTFIAPPCHEQIE---ILYQDESLVLINKPTGLLSLSGKN-PQNLDSVHHRLVQ--- 55

Query: 142 QKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           Q P   L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   + +  I 
Sbjct: 56  QFPGCTLIHRLDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLADNEGVID 115

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF--------AQKFCWLEMQPHTGR 251
             + K   +    + +   + K A    S ++VI+ F        +     +++ P TGR
Sbjct: 116 AAIAKDPAL-FPLMSICAIHGKPAR---SGYQVIERFYHELEDGTSLPLTRVQLTPETGR 171

Query: 252 THQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQLR+H   +G PI+G   Y      G   +P   +L LHA  +   HP
Sbjct: 172 THQLRIHCQQLGHPILGCDLYGGLLLPGTERTP---RLMLHASELHFVHP 218


>gi|296272938|ref|YP_003655569.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
 gi|296097112|gb|ADG93062.1| pseudouridine synthase, RluA family [Arcobacter nitrofigilis DSM
           7299]
          Length = 320

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/209 (28%), Positives = 102/209 (48%), Gaps = 21/209 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLD 151
           ++YED  I V NKP  + V   + +    +  L  W+ +K          ++  + HRLD
Sbjct: 78  IIYEDEHILVINKPYNLVVHPAASVK---EPTLVDWLKTKDISLSTISGEERHGIVHRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG++VVA+T  A   L++    + + + Y +++  +P  K   I +  + ++     
Sbjct: 135 KGTSGVMVVAKTNEAHVALSKQLEDKTMGRYYLAII-DLPL-KDNIIIDKPIARNPNNRL 192

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +V   EKG N   +  K+     +K+  +  +  TGRTHQ+RVH   +   I+GD+ 
Sbjct: 193 KMGIV---EKGKNAKTAFAKIALSEDEKYELICCKLFTGRTHQIRVHLNSINRHILGDNL 249

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y   FKG       N+ YLHA  + L HP
Sbjct: 250 Y--GFKGELNKI--NRFYLHAFNLYLIHP 274


>gi|257885366|ref|ZP_05665019.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,501]
 gi|257821222|gb|EEV48352.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,501]
          Length = 299

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 81/306 (26%), Positives = 141/306 (46%), Gaps = 36/306 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + K+H   + +   +K +  G +     ++KF    Q GQ+     V N L  + K+ K+
Sbjct: 7   YEKDHSQQVKYFLKEKGISKGLL----AKIKF----QGGQIKVNDQVENVLFSLAKDDKV 58

Query: 84  LDSSVNLTKHSDFLKS----ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KS 135
                   +H   L       ++YED  + V NKPAG+S        YH +G +    K+
Sbjct: 59  TIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQ---YHPNGTMANRVKA 115

Query: 136 WVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   +G + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G   
Sbjct: 116 YYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQLREKKFVKKYQALVSG--- 172

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              +  A+  +    I  DY  ++K+  +++G +    ++  I+    +   +++Q HTG
Sbjct: 173 RLSDLSAHGRIDLP-IARDYSSLLKRMVSDEGRSAQTEYW--IEKRLTEIALVDIQLHTG 229

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH   +GC ++GD  Y     G     I+ +  LH   +   HP     L+   
Sbjct: 230 RTHQIRVHFSTIGCALLGDDMYG----GRMDLGIKRQA-LHCYDLRFYHPFTEELLEFKQ 284

Query: 310 PLPAHM 315
           PL A M
Sbjct: 285 PLAADM 290


>gi|146312885|ref|YP_001177959.1| tRNA pseudouridine synthase C [Enterobacter sp. 638]
 gi|145319761|gb|ABP61908.1| Pseudouridylate synthase [Enterobacter sp. 638]
          Length = 261

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 104/225 (46%), Gaps = 36/225 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 5   ILYQDEWIVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTVHRLDRPTSGVLLM 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--- 217
             +  A + L++ F   +IQK Y ++V G           WL+ ++ +  DY  V +   
Sbjct: 65  GLSSEAGRLLSQQFEQHQIQKRYHAIVRG-----------WLMDEATL--DYPLVEELDK 111

Query: 218 ------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALH 261
                 +  K    A++ ++ +               ++  +E++P TGR HQLR H  H
Sbjct: 112 IADKFARENKDPQPAVTDYRGLATVEMPVATGKFPTTRYGLVELEPKTGRKHQLRRHLSH 171

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG 303
           +  PI+GD K+  + + N ++      ++L LHA  + L HP  G
Sbjct: 172 LRHPIIGDSKH-GDLRQNRSAAEHFGCDRLMLHASQLSLTHPFTG 215


>gi|257880319|ref|ZP_05659972.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,230,933]
 gi|257882173|ref|ZP_05661826.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,502]
 gi|257890978|ref|ZP_05670631.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,410]
 gi|257894233|ref|ZP_05673886.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,408]
 gi|258614733|ref|ZP_05712503.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Enterococcus faecium DO]
 gi|260562377|ref|ZP_05832891.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium C68]
 gi|293553066|ref|ZP_06673708.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1039]
 gi|293559437|ref|ZP_06675975.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1162]
 gi|293568340|ref|ZP_06679663.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1071]
 gi|294621976|ref|ZP_06701121.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium U0317]
 gi|257814547|gb|EEV43305.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,230,933]
 gi|257817831|gb|EEV45159.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,502]
 gi|257827338|gb|EEV53964.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,410]
 gi|257830612|gb|EEV57219.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,408]
 gi|260073301|gb|EEW61642.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium C68]
 gi|291588949|gb|EFF20774.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1071]
 gi|291598455|gb|EFF29527.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium U0317]
 gi|291602775|gb|EFF32985.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1039]
 gi|291606592|gb|EFF35988.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1162]
          Length = 299

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 140/310 (45%), Gaps = 44/310 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + K+H   + +   +K +  G +     ++KF    Q GQ+     V N L  + K+ K+
Sbjct: 7   YEKDHSQQVKYFLKEKGISKGLL----AKIKF----QGGQIKVNDQVENVLFSLAKDDKV 58

Query: 84  LDSSVNLTKHSDFLKS----ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KS 135
                   +H   L       ++YED  + V NKPAG+S        YH +G +    K+
Sbjct: 59  TIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQ---YHPNGTMANRVKA 115

Query: 136 WVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   +G + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G   
Sbjct: 116 YYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQLREKKFVKKYQALVSGRLS 175

Query: 193 NKKECIANWLLKKSHI----GGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           +        L    HI      DY  ++K+  +++G +    ++  I+    +   +++Q
Sbjct: 176 D--------LSAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYW--IEKRLTEIALVDIQ 225

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
            HTGRTHQ+RVH   +GC ++GD  Y     G     I+ +  LH   +   HP     L
Sbjct: 226 LHTGRTHQIRVHFSAIGCALLGDDMYG----GRMDLGIKRQA-LHCYDLRFYHPFTEELL 280

Query: 306 QITAPLPAHM 315
           +   PL A M
Sbjct: 281 EFKQPLAADM 290


>gi|253578463|ref|ZP_04855735.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850781|gb|EES78739.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 349

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 87/354 (24%), Positives = 148/354 (41%), Gaps = 72/354 (20%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Y+++ + E   E ++++ + K +         Q   R   +  +  R +    I  G V+
Sbjct: 4   YLEFRIDEQTTE-LKMEAFLKKNAGLTKRQISQAKFRPDGITRNGVRCRVTETIYPGDVI 62

Query: 66  RI--------PPVINALNHIIKEQKILD-----SSVNLTKHSDFLKSILLYEDSKIYVFN 112
           R+           +   N  I+ + + D     +S ++++ S  L   +LYED+ I   +
Sbjct: 63  RVCLEEAGTASAHLENYNDGIRSKDLSDFHSNRASASISETSFSLN--ILYEDTDILAVD 120

Query: 113 KPAGISVQGGSGIAY--HIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQ 168
           KPAG+ V   +G+ Y   +   +  +   K ++   R   RLDQETSGI+V A+ + AA 
Sbjct: 121 KPAGM-VTHPTGMHYTDSLSNLVAGYFREKNEQVCVRPVGRLDQETSGIVVFAKNQVAAS 179

Query: 169 HLTESFRMRRIQKIYWSLVWGI-------------------PKN--KKECIANWLLKKSH 207
            L       +I K Y + V G                    P+N  K +  A+  L  S 
Sbjct: 180 RLQSVKSPCKIHKQYLAAVSGTLPVDMPGVWHTLDLPLMQDPENHLKMKTAADLSLHSSA 239

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G               A++H+  +   +Q +  + ++  TGRTHQ+RVH    G P++
Sbjct: 240 LSGKI-----------KTAVTHYHTL-FSSQDWSLITLKLDTGRTHQIRVHMASTGHPLL 287

Query: 268 GDHKY--------CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           GD  Y        CA+F         ++  LHA  +   HP     L + APLP
Sbjct: 288 GDTLYHSDDKISSCASF---------SRAALHAWKVSFQHPFRDEMLLLEAPLP 332


>gi|326800504|ref|YP_004318323.1| pseudouridine synthase [Sphingobacterium sp. 21]
 gi|326551268|gb|ADZ79653.1| pseudouridine synthase [Sphingobacterium sp. 21]
          Length = 245

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 104/227 (45%), Gaps = 26/227 (11%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++++ED  + V NKP  I S+    G   +I    KS+        ++ HR+D+ETSG+L
Sbjct: 16  LIIFEDDNLIVVNKPPFIASLDEREGREINILRMAKSY----HADAQVCHRIDKETSGLL 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+     + ++  F  RR++KIY +++ G    +   +   +L   ++G   V + K 
Sbjct: 72  LIAKNPDTYRSVSIEFEKRRVKKIYHAIIGGTHIFEDLKVDLPIL---NLGNKNVTIDKA 128

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--- 275
           N K A    + FK +  F + +  +E +P TGR HQ+R+H       IVGD  Y      
Sbjct: 129 NGKLAE---TWFKSLAYF-KHYTLVECRPITGRMHQIRIHLATQHASIVGDSLYKGKPVY 184

Query: 276 ----------FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                      KG    PI  +  LHAR +      G      AP P
Sbjct: 185 LSQIKRGYTLSKGQEELPIMKRFALHARALSFS-INGKDYSFEAPYP 230


>gi|261209248|ref|ZP_05923640.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium TC 6]
 gi|289565997|ref|ZP_06446435.1| pseudouridylate synthase, 23S RNA-specific [Enterococcus faecium
           D344SRF]
 gi|294616199|ref|ZP_06695996.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1636]
 gi|260076794|gb|EEW64529.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium TC 6]
 gi|289162195|gb|EFD10057.1| pseudouridylate synthase, 23S RNA-specific [Enterococcus faecium
           D344SRF]
 gi|291590954|gb|EFF22666.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1636]
          Length = 299

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 140/310 (45%), Gaps = 44/310 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + K+H   + +   +K +  G +     ++KF    Q GQ+     V N L  + K+ K+
Sbjct: 7   YEKDHSQQVKYFLKEKGISKGLL----AKIKF----QGGQIKVNDQVENVLFSLAKDDKV 58

Query: 84  LDSSVNLTKHSDFLKS----ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KS 135
                   +H   L       ++YED  + V NKPAG+S        YH +G +    K+
Sbjct: 59  TIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQ---YHPNGTMANRVKA 115

Query: 136 WVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   +G + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G   
Sbjct: 116 YYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQLREKKFVKKYQALVSGRLS 175

Query: 193 NKKECIANWLLKKSHI----GGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           +        L    HI      DY  ++K+  +++G +    ++  I+    +   +++Q
Sbjct: 176 D--------LSAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYW--IEKRLTEIALVDIQ 225

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
            HTGRTHQ+RVH   +GC ++GD  Y     G     I+ +  LH   +   HP     L
Sbjct: 226 LHTGRTHQIRVHFSAIGCALLGDDMYG----GRMDLGIKRQA-LHCYDLRFYHPFTEELL 280

Query: 306 QITAPLPAHM 315
           +   PL A M
Sbjct: 281 EFKQPLAADM 290


>gi|237709871|ref|ZP_04540352.1| RNA pseudouridylate synthase [Bacteroides sp. 9_1_42FAA]
 gi|229455964|gb|EEO61685.1| RNA pseudouridylate synthase [Bacteroides sp. 9_1_42FAA]
          Length = 308

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 103/220 (46%), Gaps = 21/220 (9%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           L+YED+ I V  K  G+    + +     A HI   L  +V    +  R+   HRLD+ET
Sbjct: 94  LVYEDAYILVVEKKEGLLSVSTERQKERTAQHI---LNEYVKRSHRFNRVFVVHRLDRET 150

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L +++      + Y S+V G  +     + +WL  +      YV 
Sbjct: 151 SGLMMYAKDEKTQNTLRDNWHDIVTDRRYVSIVSGNMEKDYGTVESWLTDRKL----YVS 206

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++    +A++H+K I   A  +  +E+   TGR +Q+RVH   +G P++GD +Y  
Sbjct: 207 SSPVDDGEGKFAVTHYKTIKR-ANGYSLVELDLETGRKNQIRVHMSDLGHPVIGDRRY-- 263

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
              G+   P+  +L LHA  +   HP    L +   P P 
Sbjct: 264 ---GSECDPL-GRLALHAFKLCFYHPVTRELMEFETPYPT 299


>gi|166364334|ref|YP_001656607.1| pseudouridine synthase [Microcystis aeruginosa NIES-843]
 gi|166086707|dbj|BAG01415.1| pseudouridine synthase [Microcystis aeruginosa NIES-843]
          Length = 299

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 68/220 (30%), Positives = 101/220 (45%), Gaps = 11/220 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED+++ V  KP+G+ V  G G   H    L     ++   P   HRL + TSGI+++
Sbjct: 83  VLYEDAEVLVVAKPSGLPVLAGGGFLEHTLIHLVHQHYAE-VTPYPIHRLGRGTSGIVLM 141

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           A+++ A   L++  R  +I KIY +LV    IP N     A   +    +G    HV   
Sbjct: 142 AKSKPARAKLSQQMREGKITKIYRALVGQGDIPDNFTINQAIGKIAHPILG----HVYGA 197

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFK 277
              G + A S  +V+         LE++  TGR HQ+R+H    G P++GD  Y      
Sbjct: 198 LTDGLS-ARSDGRVLKKHPDS-TLLEVRIFTGRPHQIRIHLAFFGYPLIGDPLYGLGGLP 255

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
                P     YLHA  +   HP  G R+ I    P  +V
Sbjct: 256 RPDAVPGDCGYYLHANQIVFNHPSTGERISICCQAPPELV 295


>gi|225375309|ref|ZP_03752530.1| hypothetical protein ROSEINA2194_00934 [Roseburia inulinivorans DSM
           16841]
 gi|225212798|gb|EEG95152.1| hypothetical protein ROSEINA2194_00934 [Roseburia inulinivorans DSM
           16841]
          Length = 298

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 101/222 (45%), Gaps = 22/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------RLTHRLDQET 154
           + YED  I V NKPA + +        + D  L + V    Q        R  +RLD++T
Sbjct: 83  ICYEDEDILVVNKPADMPIHPSMN---NYDNTLANAVCHYYQTQGIPYTFRCVNRLDRDT 139

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+ ++A+   ++  L     +R I + Y ++V G  +++    A    K+       + 
Sbjct: 140 TGLTILAKHLISSAILNSEVSVRGISREYLAIVKGFTEDEGTVNAPIGRKEGSTIERQID 199

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+         AI+H+K +  +      + ++  TGRTHQ+RVH   +G P++GD  Y  
Sbjct: 200 VLH-----GETAITHYKRL-AYQDGLSLISLKLETGRTHQIRVHMKSIGHPLIGDFLYNP 253

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           +F         N+  LH+  +   HP   + L  TAPLP  M
Sbjct: 254 DFTK------INRQALHSYRLRFTHPVTKKPLVFTAPLPEDM 289


>gi|124022639|ref|YP_001016946.1| pseudouridylate synthase [Prochlorococcus marinus str. MIT 9303]
 gi|123962925|gb|ABM77681.1| putative pseudouridylate synthase [Prochlorococcus marinus str. MIT
           9303]
          Length = 207

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 104/216 (48%), Gaps = 22/216 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +L++DS +    KP G+  Q G G+     + G L+ + DS+    RL HRLD++TSG+L
Sbjct: 3   VLFQDSWLIAVEKPPGLLSQPGLGVDQQDSLIGRLQ-FFDSE---LRLVHRLDRDTSGLL 58

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR   + +  +  F  RR++K+Y ++V G        I+  + +       Y    + 
Sbjct: 59  LLARGAESLRRCSMLFSARRVRKLYLAVVVGRMNRNAGTISFPMARLQKNPPLYGKHSQG 118

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E     + S ++V  C A     L + P TGR+HQLR H   +G PI+GD  Y      
Sbjct: 119 KE-----SRSQWRVRSCHANGST-LWLWPLTGRSHQLRAHLASVGHPILGDPIYGKKV-- 170

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG---RLQITAPL 311
                   +++LH+  +   HP  G   RL+  AP 
Sbjct: 171 -----FFERMHLHSTALSFRHPFTGLRLRLRSRAPF 201


>gi|261378685|ref|ZP_05983258.1| pseudouridine synthase Rlu family protein [Neisseria cinerea ATCC
           14685]
 gi|269145031|gb|EEZ71449.1| pseudouridine synthase Rlu family protein [Neisseria cinerea ATCC
           14685]
          Length = 223

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/211 (30%), Positives = 100/211 (47%), Gaps = 19/211 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV    G    +   L + +    +K  L HRLD++T GIL+ 
Sbjct: 4   ILFRHQDFVAINKPQGISVHRSDG-EVSLTATLAAQLGV--EKVWLLHRLDKQTGGILLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I   + +KS  G     + K   
Sbjct: 61  ALNPQSAAVLAAQFAERKMKKTYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLTR 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F  I   ++K     ++PHTG+THQLRV    +G PI+GD  Y     G  
Sbjct: 115 NMENIAVTRFFSIRI-SEKMRLFILEPHTGKTHQLRVAMKSLGSPILGDRLY-----GGT 168

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
            S     ++L+A  +   + +   ++ITAPL
Sbjct: 169 ES---ETMFLYAWKIQFTYQQ-QEIEITAPL 195


>gi|224373761|ref|YP_002608133.1| ribosomal large subunit pseudouridine synthase C [Nautilia
           profundicola AmH]
 gi|223589203|gb|ACM92939.1| ribosomal large subunit pseudouridine synthase C [Nautilia
           profundicola AmH]
          Length = 294

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/200 (29%), Positives = 94/200 (47%), Gaps = 35/200 (17%)

Query: 102 LYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++E +   VF+KP+G+++  +  +     +D     W    G    L HRLD+ETSG+++
Sbjct: 72  IFETTHFAVFDKPSGVAIHPKKLANTKSLLDDVRSLW----GNDANLVHRLDKETSGLVM 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-----------IPKNKKECIANWLLKKSHI 208
            ++ + +   L ++F+ + IQK Y +LV G           I  NK E I   ++     
Sbjct: 128 ASKNKFSESVLKKAFQDKEIQKKYLALVKGHLEKDLTIKKPIAVNKDENIKVKVMIHPE- 186

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           G + V ++K  +K     I    +++C           P TGR HQ+RVH   +G PIVG
Sbjct: 187 GKESVTIIKPIKK-----IGENTLVECI----------PLTGRQHQIRVHLFSIGHPIVG 231

Query: 269 DHKYCANFKGNFTSPIQNKL 288
           D  Y  +    F     NKL
Sbjct: 232 DPLYGVD--NEFADRYLNKL 249


>gi|312130454|ref|YP_003997794.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
 gi|311907000|gb|ADQ17441.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
          Length = 250

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 105/229 (45%), Gaps = 21/229 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +K ++++E+    V NKP  +           +   LK   ++ G   +L HRLD+ETSG
Sbjct: 15  IKDLVIFENEHYVVINKPPFVPSLDERTADKSL-SILKLAREAYGDI-QLCHRLDKETSG 72

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+A+   A ++L   F  R +QK Y ++V G   +  + I  +L       G  V + 
Sbjct: 73  ALVLAKNPEAYRNLAMQFEHREVQKEYHAVVNG--AHDFDSIGVFLPIAILKDGTAVRID 130

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV------GDH 270
           +Q  K A    + F  +  F Q+   +   P TGR HQ+RVH   +  PIV      GD+
Sbjct: 131 RQKGKLAE---TIFFTLQKF-QRHTLVRCVPITGRMHQIRVHLQCLNAPIVCDPTYGGDY 186

Query: 271 KYCANFKGNFT-------SPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
            + +  K  F         P+  ++ LHA  +     +G  L ITAP P
Sbjct: 187 IFLSQIKRKFNLKAESEELPLIKRVALHAHKIHFRDVDGTVLSITAPYP 235


>gi|255712643|ref|XP_002552604.1| KLTH0C08756p [Lachancea thermotolerans]
 gi|238933983|emb|CAR22166.1| KLTH0C08756p [Lachancea thermotolerans]
          Length = 610

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 89/180 (49%), Gaps = 20/180 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ED  ++V +KP+GI V       ++ I   L+  ++         +RLD+ TSG++ 
Sbjct: 186 IVFEDQDLFVIDKPSGIPVHPTGRYRFNTITKILQKQINGSVHP---CNRLDRLTSGLMF 242

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK------KECIANWLLKKSHIGGDY 212
           +A+T   A H+    + R ++K Y + V G  P  +       +C+   L     + G  
Sbjct: 243 LAKTPRGADHMANQLKAREVKKEYIARVVGEFPAERISVEKPLKCVEPRLA----LNG-- 296

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V    E+GA  A + F  +  F  +   ++ QPHTGRTHQ+RVH  ++G PI  D  Y
Sbjct: 297 --VCNSEEEGAKEAKTVFTRVS-FDGETSLVKCQPHTGRTHQIRVHLQYLGHPIANDPLY 353


>gi|229004047|ref|ZP_04161850.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           Rock1-4]
 gi|228757200|gb|EEM06442.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           Rock1-4]
          Length = 286

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 75/280 (26%), Positives = 130/280 (46%), Gaps = 63/280 (22%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
            + G + VD K     + +Q+ +V+++  PV        + + +L  ++ LT        
Sbjct: 29  FQGGAIEVDGKHATVRHVLQAEEVLQVFFPVEE------RSEGMLAENIPLT-------- 74

Query: 100 ILLYEDSKIYVFNK------------PAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRL 146
            +LYED  + V NK            PAG SV   + + YH D   L S V        +
Sbjct: 75  -VLYEDESVLVINKAPYMSTIPSREHPAG-SV--ANALLYHYDRQNLASTV-------HI 123

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD++TSG++++A+ R     L++  + +++++ Y ++V G           WL +  
Sbjct: 124 VTRLDRDTSGLMLIAKNRFIHHLLSKQHQQKKVKRTYEAIVHG----------EWLEESG 173

Query: 207 HIG------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            I       GD +      E G   A++HF+V++ F  K   + +Q  TGRTHQ+RVH  
Sbjct: 174 TIDAPIGRKGDSIIERMVCEDGQK-AVTHFQVMERFPDK-TRVSLQLETGRTHQIRVHMA 231

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           ++G P++GD  Y     G   S ++ +  LH+  +   HP
Sbjct: 232 YLGHPLLGDDLY-----GGSKSQMKRQ-ALHSTSLTFYHP 265


>gi|25011211|ref|NP_735606.1| hypothetical protein gbs1160 [Streptococcus agalactiae NEM316]
 gi|76787983|ref|YP_329799.1| ribosomal large subunit pseudouridine synthase A [Streptococcus
           agalactiae A909]
 gi|77405506|ref|ZP_00782598.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
 gi|77408702|ref|ZP_00785434.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
 gi|77410529|ref|ZP_00786890.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77413047|ref|ZP_00789249.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
 gi|23095635|emb|CAD46819.1| unknown [Streptococcus agalactiae NEM316]
 gi|76563040|gb|ABA45624.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus agalactiae A909]
 gi|77160945|gb|EAO72054.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
 gi|77163477|gb|EAO74427.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77172677|gb|EAO75814.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
 gi|77175903|gb|EAO78680.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
 gi|319745122|gb|EFV97447.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus agalactiae
           ATCC 13813]
          Length = 294

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 50/177 (28%), Positives = 90/177 (50%), Gaps = 12/177 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    + NKP G +    S  +  I  F+K +  S     Q+  +  RLD++TSG+
Sbjct: 78  IVYEDDHFLILNKPFGFASIPSSIHSNTIANFIKHYYVSNNYANQQVHIVTRLDRDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G     +  + IA        I      +
Sbjct: 138 MLFAKHGYAHARLDKQLQAKAIEKRYYALVSGSGDLADSGDIIAPIARDVDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++  +   YA + ++V+  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y
Sbjct: 192 TRRVHESGKYAHTSYQVVARYGD-VRLVDIKLHTGRTHQIRVHFAHIGFPLLGDDLY 247


>gi|228996384|ref|ZP_04156026.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           Rock3-17]
 gi|228763347|gb|EEM12252.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           Rock3-17]
          Length = 286

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 75/280 (26%), Positives = 130/280 (46%), Gaps = 63/280 (22%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
            + G + VD K     + +Q+ +V+++  PV        + + +L  ++ LT        
Sbjct: 29  FQGGAIEVDGKHATVRHVLQAEEVLQVFFPVEE------RSEGMLAENIPLT-------- 74

Query: 100 ILLYEDSKIYVFNK------------PAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRL 146
            +LYED  + V NK            PAG SV   + + YH D   L S V        +
Sbjct: 75  -VLYEDESVLVINKAPYMSTIPSREHPAG-SV--ANALLYHYDRQNLASTV-------HI 123

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD++TSG++++A+ R     L++  + +++++ Y ++V G           WL +  
Sbjct: 124 VTRLDRDTSGLMLIAKNRFIHHLLSKQHQQKKVKRTYEAIVHG----------EWLEESG 173

Query: 207 HIG------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            I       GD +      E G   A++HF+V++ F  K   + +Q  TGRTHQ+RVH  
Sbjct: 174 TIDAPIGRKGDSIIERMVCEDGQK-AVTHFQVMERFPDK-TRVSLQLETGRTHQIRVHMA 231

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           ++G P++GD  Y     G   S ++ +  LH+  +   HP
Sbjct: 232 YLGHPLLGDDLY-----GGSKSQMKRQ-ALHSTSLTFYHP 265


>gi|149182747|ref|ZP_01861212.1| hypothetical protein BSG1_15258 [Bacillus sp. SG-1]
 gi|148849561|gb|EDL63746.1| hypothetical protein BSG1_15258 [Bacillus sp. SG-1]
          Length = 294

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 79/315 (25%), Positives = 133/315 (42%), Gaps = 43/315 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQ--VVRI 67
           ++  DE  + +  +   H  HI+   L  I    G++ VD + V     +Q G    V  
Sbjct: 9   IITKDESGVEIKTFLSEH--HISKRMLTDIKFAGGKISVDGQEVTVRYVLQEGNHLTVIF 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP               +      K  D L  I+ YED  + V NKP+ +S         
Sbjct: 67  PP---------------EPKSPTLKPEDILLHII-YEDKDLLVINKPSNMSTIPSR---E 107

Query: 128 HIDGFLKSWVDSKGQKPRL------THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H DG L + V    ++  +        RLD++TSG++++A+ R     ++   + R I++
Sbjct: 108 HPDGSLANAVYGYYRRREIDSAIHIVTRLDRDTSGLVLIAKHRHIHHLMSLQQKKREIKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +   G+   ++  I   + +K     +   + ++       A++H+KVI  +   F 
Sbjct: 168 SYEAFAEGLFSVREGKINEPIGRK-----ETSIIEREVRSDGKTAVTHYKVIGQYG-GFA 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +   TGRTHQ+RVH  + G P++GD  Y     G     I ++  LH   +   HP 
Sbjct: 222 HIGLVLETGRTHQIRVHMSYKGHPLLGDSLY-----GGSREKI-DRQALHCHSLSFFHPT 275

Query: 302 GGR-LQITAPLPAHM 315
            G  L    PLP  M
Sbjct: 276 TGEPLHFHVPLPDDM 290


>gi|54309675|ref|YP_130695.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum SS9]
 gi|46914113|emb|CAG20893.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum SS9]
          Length = 246

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/199 (30%), Positives = 93/199 (46%), Gaps = 18/199 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+++     V NK  G+SV    G    +    K   D   +K  L HRLD+ TSG+L++
Sbjct: 22  LVHQHPDFLVINKHPGVSVHKDDGDQPLLAEVAKQTGD---EKLYLIHRLDKMTSGLLLL 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R R AA  L+ +F  R ++K Y ++    PK K+  +   + +            K + 
Sbjct: 79  GRNRQAAAELSGNFAKRDVEKFYLAIGTKKPKKKQGVVIGDMSRSRR------SSWKLDS 132

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F        + C+L  +PHTG+THQ+RV    +G  I GD  Y     GN 
Sbjct: 133 TKDNPAITQFFSTAAGNGRRCFL-CKPHTGKTHQIRVALKSVGSGITGDEIY-----GNE 186

Query: 281 TSPIQNKLYLHARYMDLPH 299
            +   ++ YLHA  +  P+
Sbjct: 187 EA---DRGYLHAYALSFPY 202


>gi|295097354|emb|CBK86444.1| tRNA pseudouridine synthase C [Enterobacter cloacae subsp. cloacae
           NCTC 9394]
          Length = 261

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 104/225 (46%), Gaps = 19/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 5   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L++ F   ++QK Y ++V G   +        + +   I   +     + +
Sbjct: 65  GLSSEAGRLLSQQFEQHQMQKRYHAIVRGWLTDSATLDYPLVEELDKIADKFA----RED 120

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 121 KGPQPAVTDYRGMATTELPVATSKFPTTRYSLVELLPKTGRKHQLRRHLAHLRHPIIGDS 180

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGRLQITAPL 311
           K+  + + N ++      N+L LHA  + L HP  G  L I A L
Sbjct: 181 KH-GDLRQNRSAAEHFGCNRLMLHASELRLTHPFTGEPLTIRAGL 224


>gi|319427367|gb|ADV55441.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 236

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 63/213 (29%), Positives = 99/213 (46%), Gaps = 20/213 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+DS I + +KP+G+ S+ G + + +  D      V        L HRLD  TSGI++
Sbjct: 25  VLYQDSDILLIDKPSGLLSLSGKNPLNF--DSVHYRLV-QDFPTATLLHRLDFGTSGIML 81

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA  +     LT+ F+ R ++K Y +L+ G   +    I   + K      D   + K  
Sbjct: 82  VALNKTVNGLLTKQFQARTVEKRYTALLHGHLTDDSGVINLPIAKDV----DNFPLQKIC 137

Query: 220 EKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                 AIS ++V++   + F   +E  P +GRTHQLR+H+  +G  I+G    C  + G
Sbjct: 138 HSTGKLAISEYRVLERLTEPFATRVEFTPVSGRTHQLRIHSQQLGHSILG----CDLYGG 193

Query: 279 NFTSPIQN-------KLYLHARYMDLPHPEGGR 304
                  N       +L LHA  +   HP  G 
Sbjct: 194 VGEKITDNDYALHHIRLMLHATRLGFDHPITGE 226


>gi|324519170|gb|ADY47302.1| RNA pseudouridylate synthase domain-containing protein 4 [Ascaris
           suum]
          Length = 331

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 76/330 (23%), Positives = 145/330 (43%), Gaps = 43/330 (13%)

Query: 29  YPHINF-----VNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +P +NF        Q + +  Q ++DK+  K  + + S +VV   P +          +I
Sbjct: 4   FPSLNFDSDSAAMQQPLQKRRQEKLDKQ--KLESAVNSRRVVISEPKLIHEEETTGLNRI 61

Query: 84  LDS-----SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL---KS 135
           LD       +N  +  + +   ++YED  +  F+KP  ++  G       +D  L   K+
Sbjct: 62  LDLIEPVWKMNDAELVELMCKRIIYEDDDLLAFDKPYQMAYSGSKAGQAQMDRILQNLKA 121

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  + Q+  L   LD++ +G+++ A+     + + E ++   +++ Y ++V G+P+  +
Sbjct: 122 SIAPEVQRLCLVKSLDKDLTGVILFAKNELVQKSIMEKYKDGAVEQRYRTIVRGVPEENE 181

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAI-SHFKVI----DCFAQKFCWLEMQPHTG 250
             I   L+KKS+     +  +  N K   + + + ++VI    +C + + C +       
Sbjct: 182 AIINIPLVKKSYKQNFIMRPLMPNSKVRPFHVTTEYRVIKDNGECSSLQ-CII----RND 236

Query: 251 RTHQLRVH-ALHMGCPIVGDHKYCA--NFK-GNFTSPIQNKL------------YLHARY 294
            +HQ+R H  L +GCPI+GD KY     F+     S    +L            YLH   
Sbjct: 237 ISHQVRSHLGLGLGCPIIGDFKYSGYKEFRPPKLPSGTMQRLQLTGNQYRRLPMYLHLSE 296

Query: 295 MDLPHPEGGR--LQITAPLPAHMVKTWDSL 322
           + +P    G   + I +PLPA    T   L
Sbjct: 297 VSIPVASSGSRTINIRSPLPAFFAYTLRKL 326


>gi|261342219|ref|ZP_05970077.1| tRNA pseudouridine synthase [Enterobacter cancerogenus ATCC 35316]
 gi|288315555|gb|EFC54493.1| tRNA pseudouridine synthase [Enterobacter cancerogenus ATCC 35316]
          Length = 261

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/248 (26%), Positives = 113/248 (45%), Gaps = 37/248 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 5   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--- 217
             +  A + L++ F   ++QK Y ++V G           WL +   +  DY  V +   
Sbjct: 65  GLSSEAGRLLSQQFEQHQMQKRYHAIVRG-----------WLTESGTL--DYPLVEELDK 111

Query: 218 ------QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALH 261
                 +++KG   A++ ++ +               ++  +E+ P TGR HQLR H  H
Sbjct: 112 IADKFARDDKGPQPAVTDYRAMATTEMPVATSKFPTTRYSLVELLPKTGRKHQLRRHLAH 171

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           +  PI+GD K+  + + N ++      ++L LHA  + L HP  G  L I A L    ++
Sbjct: 172 LRHPIIGDSKH-GDLRQNRSAAEHFGCHRLMLHASELSLTHPFTGEPLSIRAGLDDVWMQ 230

Query: 318 TWDSLGFK 325
                G++
Sbjct: 231 ALSQFGWR 238


>gi|86133476|ref|ZP_01052058.1| tRNA pseudouridine synthase C [Polaribacter sp. MED152]
 gi|85820339|gb|EAQ41486.1| tRNA pseudouridine synthase C [Polaribacter sp. MED152]
          Length = 234

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 110/238 (46%), Gaps = 25/238 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHI------DGFLKSWVDSKGQKPRLTHRLDQET 154
           ++YED+ +    KP  + V      AYH          L+   +  G K    HRLD++T
Sbjct: 5   IIYEDAYLLCVTKPNNVLVHH----AYHSRNMADEKSLLQLVSEETGLKVYPIHRLDRKT 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG +++A+ +       + F   +IQKIY+ +V G   + K   +    + +++  + + 
Sbjct: 61  SGAILLAKEKEYVAKFQDLFTKNQIQKIYYGVVRGFSPSTKRIDSPVKGRDANVHKEALT 120

Query: 215 VVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +K   K   + A+  +      + ++  +E+ P TGR HQLRVH+  +  P++GD KY 
Sbjct: 121 ELKTLAKITLDIAVKPYD-----SSRYSLIELFPKTGRMHQLRVHSNKISHPLIGDAKYG 175

Query: 274 AN-----FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
                  F+ NF       L+LHA  ++  HP     L + +  P   ++ ++   +K
Sbjct: 176 DKNHDMMFEQNFGF---KNLFLHAGKLEFIHPYTQETLILKSTFPTDWIQLFEKFNWK 230


>gi|297182825|gb|ADI18977.1| pseudouridylate synthases, 23S RNA-specific [uncultured delta
           proteobacterium HF0010_10I05]
          Length = 316

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 55/177 (31%), Positives = 85/177 (48%), Gaps = 27/177 (15%)

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           QK    HRLD+ETSG+++ A+T   AQ +   FR ++I+K Y ++V   P  K+E + + 
Sbjct: 124 QKLYTIHRLDRETSGVVLFAKTHQMAQQMAALFRDKQIRKEYRAVV-TTPLPKEEILVS- 181

Query: 202 LLKKSHIGGDYVHVVK------QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 IG D    ++      ++ K +       K I    ++  +L++ P TGRTHQ+
Sbjct: 182 ----KPIGPDRSSSIRIKQSVCEDGKPSETRFRQLKTI----RECAYLQIHPMTGRTHQI 233

Query: 256 RVHALHMGCPIVGDHKYCANFKGNF-----------TSPIQNKLYLHARYMDLPHPE 301
           R+HA   G PIVGD  Y    K                 + N+  LHA  +D  HP+
Sbjct: 234 RIHAAASGFPIVGDKLYGLAEKDFLRWLEEGEAFLKARNLPNRQLLHAYQIDFIHPQ 290


>gi|317490447|ref|ZP_07948929.1| RluA family pseudouridine synthase [Eggerthella sp. 1_3_56FAA]
 gi|316910440|gb|EFV32067.1| RluA family pseudouridine synthase [Eggerthella sp. 1_3_56FAA]
          Length = 344

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 112/244 (45%), Gaps = 29/244 (11%)

Query: 103 YEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRL--THRLD 151
           +ED  + V +K  G+    SV    G     + YH     ++  + +G+  RL   HRLD
Sbjct: 86  FEDEDLIVLSKQVGLVCHPSVDHDDGTLVNALIYHCGA--ENLCNVQGEDDRLGIVHRLD 143

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+       L    R R + + Y +LV G+  +    I   + +      +
Sbjct: 144 RDTSGLMLAAKNDETGYALMSDIRDRAVDRRYLALVHGVIAHDTGMIDAPIARAEK---E 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              +  ++   A  AI+ F+V++ F        +  ++ +  TGRTHQ+RVH  +   P+
Sbjct: 201 RTRMAVRDTPSAREAITTFRVLERFEHGGRDDGYTLIDCKLFTGRTHQIRVHLEYAKHPL 260

Query: 267 VGDHKYCANFKGNFTSPIQ----NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           VGD  Y +   G  ++P      ++ +LH+  +   HP  G  L+    LP+ + +  D 
Sbjct: 261 VGDPAYTS---GAPSAPAADLGLDRQFLHSFQLSFQHPVTGEGLRFADNLPSDLQEALDD 317

Query: 322 LGFK 325
           L  +
Sbjct: 318 LASR 321


>gi|307129814|ref|YP_003881830.1| tRNA pseudouridine synthase [Dickeya dadantii 3937]
 gi|306527343|gb|ADM97273.1| tRNA pseudouridine synthase [Dickeya dadantii 3937]
          Length = 261

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 100/227 (44%), Gaps = 46/227 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKPAG  V              +SW+D K             GQ     
Sbjct: 4   IVYQDEHLIAVNKPAGWLVH-------------RSWLDRKEKVVVMQTVRDQIGQHVFTV 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++A +   A+ L + F   +++K Y ++V G     ++ + ++ L +  
Sbjct: 51  HRLDRPTSGVLLMALSPEVARLLAQQFEQHQMEKTYHAVVRGY--VMEDGVIDYALTEEL 108

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQL 255
             I   +       +K    A+SH++V+               ++  L++ P TGR HQL
Sbjct: 109 DRIADKFA----DPDKAPQPAVSHYRVLARAEMPVAIGRYDTARYSLLQLNPKTGRKHQL 164

Query: 256 RVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           R H  H+  PI+GD  H      +G        +L LHA  + L HP
Sbjct: 165 RRHMAHLRHPIIGDTTHGDLRQNRGMAAHFDCARLMLHASCLSLTHP 211


>gi|89075424|ref|ZP_01161841.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           sp. SKA34]
 gi|89048840|gb|EAR54410.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           sp. SKA34]
          Length = 245

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/254 (25%), Positives = 115/254 (45%), Gaps = 35/254 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  +   NKPAG+ V      ++     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYRDDYLIAVNKPAGMLVHRSWLDSHETVFVMQTLRDQIGQHVFPLHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
             +   A  +   F  R + K Y ++V G  K  +  + ++ LK      +   +  +N 
Sbjct: 65  GLSSEIASQMMPLFAGRDMHKTYHAVVRGWIK--EAAVLDYPLKV-----ELDKIADKNA 117

Query: 220 --EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             EK A  A++ ++ +               ++C +EM+P TGR HQLR H  H+   I+
Sbjct: 118 SEEKEAQPAVTAYEPLATVETDIAVGRYSTSRYCLVEMKPETGRKHQLRRHMHHLSHHII 177

Query: 268 -----GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
                GD ++   F+ ++     ++L LHA  +   HP  G  + I A +     +TW  
Sbjct: 178 GDVNHGDGRHNRMFREHYDC---HRLMLHASRLQFDHPITGDSIDICADID----ETWHK 230

Query: 322 L--GFKYDRNLYIK 333
           +   F +  NL ++
Sbjct: 231 VMTAFNWSLNLLVR 244


>gi|294792627|ref|ZP_06757774.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Veillonella sp. 6_1_27]
 gi|294456526|gb|EFG24889.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Veillonella sp. 6_1_27]
          Length = 300

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 110/253 (43%), Gaps = 56/253 (22%)

Query: 42  RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI- 100
           R  Q+   KKRVK N+R+   Q              +K+  +L  ++ L +  D+   + 
Sbjct: 41  RDIQMMFRKKRVKVNSRVAHSQ------------RALKKGDVL--TLELPQDKDYGVDVE 86

Query: 101 -----LLYEDSKIYVFNK-PAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQ 152
                +LYED+   V NK P  +    G   +  +  ++  +   K    K R  HRLD+
Sbjct: 87  KGPITVLYEDAHTLVVNKDPFMLVHPAGQTKSCTLSNYVAGYYAKKNVVHKVRPVHRLDR 146

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG ++  +T+ A Q+ T+  +  RI +IY  LV G         A+ ++  + IG D 
Sbjct: 147 DTSGCILFGKTKEAQQYYTDELQAGRIDRIYTGLVEG------RIDADGMV-DAPIGVDP 199

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKF-------------CWLEMQPHTGRTHQLRVHA 259
           V               + +VID F Q                 L  +  TGRTHQ+RVH 
Sbjct: 200 V-------------FDNRRVIDEFGQPAQTEYIVLNHEGDNTLLRFKLLTGRTHQIRVHM 246

Query: 260 LHMGCPIVGDHKY 272
            H+G PIVGD  Y
Sbjct: 247 EHIGHPIVGDAMY 259


>gi|75759795|ref|ZP_00739872.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|218896239|ref|YP_002444650.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
 gi|74492695|gb|EAO55834.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|218543847|gb|ACK96241.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
          Length = 275

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 104/207 (50%), Gaps = 23/207 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQET 154
           ++YED  + + NK A +S         H  G + + + S   K  L        RLD++T
Sbjct: 62  IVYEDDAVLIINKEANMSTIPSR---EHPTGSVANALLSHYDKQHLASTVHIVTRLDRDT 118

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D + 
Sbjct: 119 SGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGMIDAPIGRKS----DSII 174

Query: 215 VVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD    
Sbjct: 175 ERTVCEDG-QRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGD---- 227

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            N  G     ++ +  LH++ +   HP
Sbjct: 228 -NLYGGRRDEMKRQ-ALHSKSLTFYHP 252


>gi|325831406|ref|ZP_08164660.1| pseudouridine synthase, RluA family [Eggerthella sp. HGA1]
 gi|325486660|gb|EGC89108.1| pseudouridine synthase, RluA family [Eggerthella sp. HGA1]
          Length = 344

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 111/244 (45%), Gaps = 29/244 (11%)

Query: 103 YEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRL--THRLD 151
           +ED  + V +K  G+    SV    G     + YH     ++  + +G+  RL   HRLD
Sbjct: 86  FEDEDLIVLSKQVGLVCHPSVDHDDGTLVNALIYHCGA--ENLCNVQGEDDRLGIVHRLD 143

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+       L    R R + + Y +LV G+  +    I   + +      +
Sbjct: 144 RDTSGLMLAAKNDETGYALMSDIRDRAVDRRYLALVHGVIAHDTGMIDAPIARAEK---E 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              +  ++   A  AI+ F+V++ F        +  ++ +  TGRTHQ+RVH  +   P+
Sbjct: 201 RTRMAVRDTPSAREAITTFRVLERFEHGARDDGYTLIDCKLFTGRTHQIRVHLEYAKHPL 260

Query: 267 VGDHKYCANFKGNFTSPIQ----NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
           VGD  Y +   G  ++P      ++ +LH+  +   HP  G  L+    LP  + +  D 
Sbjct: 261 VGDPAYTS---GAPSAPAADLGLDRQFLHSFQLSFQHPVTGESLRFADNLPVDLQEALDD 317

Query: 322 LGFK 325
           L  +
Sbjct: 318 LASR 321


>gi|126335409|ref|XP_001373489.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 1 [Monodelphis domestica]
          Length = 307

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/182 (32%), Positives = 93/182 (51%), Gaps = 13/182 (7%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA    + F+ R++ K Y +LV G  +  +  I + + K
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGRAYKCFKERQVTKAYLALVRGHVQESRMTINHAIGK 120

Query: 205 KSHIGGDYVHVVKQNE--KGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            +  G  ++  ++  E  + A   ++   V++           + +QP TGRTHQLRVH 
Sbjct: 121 NTTEGLTHMMCIEGTEGCENAKPCLTELTVLERGLYDGDPVSKVLLQPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
              G PIVGD  Y  +FK +   P   ++ LHA Y+ +P   G  ++++ P P   V T 
Sbjct: 181 SSSGHPIVGDFTY--SFKKDI-RPF--RMMLHAFYLRIPTC-GELIEVSTPDP--FVPTL 232

Query: 320 DS 321
           D+
Sbjct: 233 DA 234


>gi|89074786|ref|ZP_01161240.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           sp. SKA34]
 gi|89049361|gb|EAR54923.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           sp. SKA34]
          Length = 557

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/204 (30%), Positives = 99/204 (48%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + + NKPA      G  I   +   +++ + DS    P + HRLD  TSG++V
Sbjct: 356 IVYQDDAMVIINKPAEFLSVPGKAITDSVYSRMQTMFPDSDS--PLIVHRLDMSTSGLMV 413

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A T+ A + L + F  R ++K Y +L+ G  ++    I ++ ++          V  Q 
Sbjct: 414 IALTKDAHKALQKQFIERTVEKRYVALLEGNSESDSGLI-DFPIRVDLDDRPRQIVCYQY 472

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANF 276
            K A       +  +   + + +    P TGRTHQLRVH+ H   M  PIVGD  Y    
Sbjct: 473 GKPAQTTWEVLERKNGRTKVYYY----PKTGRTHQLRVHSAHVKGMNMPIVGDDLYGQ-- 526

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
           KG       ++L LHA+Y+   HP
Sbjct: 527 KG-------DRLCLHAQYLAFNHP 543


>gi|220908619|ref|YP_002483930.1| RluA family pseudouridine synthase [Cyanothece sp. PCC 7425]
 gi|219865230|gb|ACL45569.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7425]
          Length = 303

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 77/314 (24%), Positives = 132/314 (42%), Gaps = 39/314 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PP 69
           V+     + L  ++   Y H +    Q  +  GQ+ ++ +      R+Q+GQ +    PP
Sbjct: 12  VDRRHAGLTLLDYYSQRYRHTSSAEWQTRIELGQIHLNGQPAPPTTRLQAGQQLTYHRPP 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                     E ++             LK   +Y D+ + + +KPAG+ V  G G   H 
Sbjct: 72  --------WPEPEVP------------LKFETIYSDADLLIISKPAGLPVLPGGGFLEHT 111

Query: 130 DGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              L        Q+ P   HRL + TSG++++A +  A   L++  R + I+K Y +LV 
Sbjct: 112 --LLWQLQQQYPQETPVPIHRLGRGTSGLMILAISGLAKSALSQQMRDQHIRKTYRALVG 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G     +  I   + K  H    YV+      +   +A S  +V+     +   L +   
Sbjct: 170 GGEMPDRFTIDYPIGKIPHPELGYVYGATPTGR---FAHSECQVLKRTPDR-TLLAVTIL 225

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKL--------YLHARYMDLPH 299
           TGR HQ+R+H    G P++GD  Y       +F +   +K+        +LHA ++   H
Sbjct: 226 TGRPHQIRIHLAAAGYPLLGDPLYINGGIPRSFGATPTDKVAVPGDCGYHLHAHHLAFAH 285

Query: 300 PEGGR-LQITAPLP 312
           P  G  L+  +P P
Sbjct: 286 PRTGEPLEFISPPP 299


>gi|76800233|ref|ZP_00781992.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
 gi|76584552|gb|EAO61413.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
          Length = 267

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 90/179 (50%), Gaps = 12/179 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    + NKP G +    S  +  I  F+K +  S     Q+  +  RLD++TSG+
Sbjct: 69  IVYEDDHFLILNKPFGFASIPSSIHSNTIANFIKHYYVSNNYANQQVHIVTRLDRDTSGL 128

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G     +  + IA        I      +
Sbjct: 129 MLFAKHGYAHARLDKQLQAKAIEKRYYALVSGSGDLADSGDIIAPIARDVDSI------I 182

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            ++  +   YA + ++V+  +      ++++ HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 183 TRRVHESGKYAHTSYQVVARYGD-VRLVDIKLHTGRTHQIRVHFAHIGFPLLGDDLYGG 240


>gi|146294028|ref|YP_001184452.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|145565718|gb|ABP76653.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
          Length = 236

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/212 (29%), Positives = 96/212 (45%), Gaps = 18/212 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+DS I + +KP+G+    G     ++D      V        L HRLD  TSGI++V
Sbjct: 25  VLYQDSDILLIDKPSGLLSLSGKN-PLNLDSVHYRLV-QDFPTATLLHRLDFGTSGIMLV 82

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +     LT+ F+ R ++K Y +L+ G   +    I   + K      D   + K   
Sbjct: 83  ALNKTVNGLLTKQFQARTVEKRYTALLHGHLTDDSGVINLPIAKDV----DNFPLQKICH 138

Query: 221 KGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                AIS ++V++   + F   +E  P +GRTHQLR+H+  +G  I+G    C  + G 
Sbjct: 139 STGKLAISEYRVLERLPEPFATRVEFTPVSGRTHQLRIHSQQLGHSILG----CDLYGGV 194

Query: 280 FTSPIQN-------KLYLHARYMDLPHPEGGR 304
                 N       +L LHA  +   HP  G 
Sbjct: 195 GEKITDNDYALHHIRLMLHATRLAFDHPITGE 226


>gi|255077107|ref|XP_002502205.1| pseudouridine synthase [Micromonas sp. RCC299]
 gi|226517470|gb|ACO63463.1| pseudouridine synthase [Micromonas sp. RCC299]
          Length = 363

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 74/274 (27%), Positives = 118/274 (43%), Gaps = 34/274 (12%)

Query: 64  VVRIPPVINALNHIIKEQKILDSSVN--LTKHSDFLKSI--LLYEDSKIYVFNKPAGISV 119
           V  + P IN L  +    ++   SV+  + +    L+    L++ED+   V NKP  + +
Sbjct: 91  VNEVQPRINYLRFLDDNDRLDGESVSSCIARQPQSLERDFHLVHEDADYAVVNKPWCVRL 150

Query: 120 QGGSG--------IAYHIDGFLKSWVDSK---GQKPRLTHRLDQETSGILVVARTRAAAQ 168
               G          Y  D  ++ W++ +       R  H+LD  TSG+LV A  + AA 
Sbjct: 151 DTPRGWPGKVRFTPKYPGDLSVEDWLERRYPDWDTVRFCHQLDNATSGVLVAASNKRAAG 210

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
              + FR RR +K Y ++V+G P+  +  +   + +       +   V      A    +
Sbjct: 211 AAAKLFRERRARKTYLAIVFGHPEQDEWTVDVPMGRDPDDPKGFRERVDPEHGKA--CET 268

Query: 229 HFKVID----CFAQKF-----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            F+V+         KF       +E+ P TGR HQ+R+H    G PIVGD+ Y  +    
Sbjct: 269 RFRVLKRGRLNLRGKFEGVPVSKVEVTPVTGRRHQIRLHLQFSGHPIVGDNAYSQDTDSF 328

Query: 280 FTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
            T       +LHA  + LP  E  G +Q  AP P
Sbjct: 329 RT-------FLHAHKLTLPFDEPRGTMQFVAPEP 355


>gi|187934776|ref|YP_001887060.1| pseudouridine synthase, RluA family [Clostridium botulinum B str.
           Eklund 17B]
 gi|187722929|gb|ACD24150.1| pseudouridine synthase, RluA family [Clostridium botulinum B str.
           Eklund 17B]
          Length = 322

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 71/291 (24%), Positives = 125/291 (42%), Gaps = 29/291 (9%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++ +     +    + K LR   +RV+ K+      ++ G +V I  + +  
Sbjct: 8   NEAGQRLDKFLRKLLKDVPLSAIFKALRKKDIRVNGKKQSEKYFLEEGDIVEIKYIKSNP 67

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFL 133
               K++K +  + +  K +        YED  + V  K  GI V          +  ++
Sbjct: 68  E---KKEKFIQVNFSGMKTA--------YEDENLLVVEKWPGILVHPDKDEKDPTLTDYV 116

Query: 134 KSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            S++  KG           P   +RLD+ TSG+++  +T    + + E+ R  R++K Y 
Sbjct: 117 LSYLKEKGSYVPENEITFTPAPCNRLDRNTSGLVMFGKTFEGLKSINETIREDRVRKYYV 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  K +      ++LK        +  V + E   +  I+           +  LE
Sbjct: 177 ALVKG--KVQDGLHTGYILKNQDTN---ISKVYEKEVPDSKKIAMEVTTTQTNGAYSLLE 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           +   TGR+HQ+R H  H+G PI+GD KY         S  +NK  L  +Y+
Sbjct: 232 INLITGRSHQIRAHLSHLGSPIIGDDKYGDR---KLNSFFKNKYGLEYQYL 279


>gi|15806687|ref|NP_295407.1| pseudouridine synthase [Deinococcus radiodurans R1]
 gi|6459452|gb|AAF11241.1|AE002010_4 pseudouridine synthase, putative [Deinococcus radiodurans R1]
          Length = 321

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 72/302 (23%), Positives = 127/302 (42%), Gaps = 37/302 (12%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             R+  +    + H +       L +G+V VD   V+ +  ++ GQ             +
Sbjct: 40  GQRVLDFLAQEFRHSDRATWAARLAAGEVTVDGLTVRGDETLRPGQ-------------M 86

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKS 135
           +  Q+   +  +   H D     ++YED+ +   +KP+G+    G G   H  +      
Sbjct: 87  LVWQRPPWAEPDAPLHFD-----VIYEDADLLAVSKPSGLPTMPGGGFLEHTLLHQVRGR 141

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W D+        HRL + TSG+++ + T  A   L + +R  R+QK+Y +L  G+ +  +
Sbjct: 142 WPDASP-----LHRLGRGTSGLVLFSLTSQAGAALLKDWRAGRVQKVYRALSAGVAEQDE 196

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   +   +H     V       K A+   S  +V++   +     E++  TGR HQ+
Sbjct: 197 YDITVPIGPVAHPRLGQVFAASTAGKTAH---SRARVLER-REDTTLFEVEIFTGRPHQI 252

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKL--YLHARYMDLPHPE-GGRLQITAP 310
           R+H   +G P+  D  Y +   G    P  +   L   LHA  +   HP  G  L ++AP
Sbjct: 253 RIHLASLGLPLAVDPLYVS---GGLPRPDALPGDLGYALHASTLTFQHPAHGAALTLSAP 309

Query: 311 LP 312
            P
Sbjct: 310 AP 311


>gi|308184739|ref|YP_003928872.1| hypothetical protein HPSJM_04875 [Helicobacter pylori SJM180]
 gi|308060659|gb|ADO02555.1| hypothetical protein HPSJM_04875 [Helicobacter pylori SJM180]
          Length = 242

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/202 (30%), Positives = 100/202 (49%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVKKEYLALAQGIIEEEREINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y  N
Sbjct: 157 SKKGQEAVTI-IAPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYN-N 210

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
             G+       +L LHA  + L
Sbjct: 211 EPGS-----AKRLMLHAHKIAL 227


>gi|329724870|gb|EGG61373.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU144]
          Length = 274

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 68/271 (25%), Positives = 119/271 (43%), Gaps = 42/271 (15%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +L ++  S ++ ++K+     N +++G  V IP      N++                  
Sbjct: 27  DLHQLNMSKEILINKEYGTLLNNVKTGDHVEIPTPNEVSNYL----------------PS 70

Query: 96  FLKSILLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +  + + YED  + +  KP G+      ++  + +  H+       VDS+  +P   HRL
Sbjct: 71  YRYAQIYYEDDDLAIVMKPKGVKTHPNDLKESNTLMNHV----IYTVDSEYVEP--IHRL 124

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           DQET G+L+VA+     + L        I +IY + V  +   K + I         IG 
Sbjct: 125 DQETVGLLIVAKNPLMKKILDRMLEYNEITRIYKANVKALLPIKPQTI------DMPIGK 178

Query: 211 DYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D  H  K+        AI+H        +  C L+++  TGRTHQ+RVH   +G P++GD
Sbjct: 179 DKFHSNKRRISNTGQRAITHIIDSKMIKEGVCQLDIKLDTGRTHQIRVHLAEIGHPVIGD 238

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             Y        TS ++ +L L++  ++  HP
Sbjct: 239 PLYG-------TSTLR-QLELNSHQIEFTHP 261


>gi|325479486|gb|EGC82582.1| pseudouridine synthase, RluA family [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 318

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 73/282 (25%), Positives = 129/282 (45%), Gaps = 36/282 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  + END  N R DR+ + ++ +     +QK +R    +++ KR K ++ + +   V+
Sbjct: 2   IEIEISENDG-NQRFDRFLRKYFENAPLSVIQKNIRKKNFKINDKRAKKDDFVYANDKVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS----DFLKSILLYEDSKIYVFNKPAGISVQGG 122
           +          IK++   D    LTK      DF  +I+ YED  I + +K  G+     
Sbjct: 61  M---------YIKDE---DYKRWLTKTDFKPQDFDLNII-YEDRNIIIMDKDRGVLTHSS 107

Query: 123 SGIAYH---IDGFL------KSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           S   Y    +D  L      KS+ +  K  KP + +RLD+ T+G+++ A+   + + L +
Sbjct: 108 SKKDYGNNLVDNMLSYLYKTKSFDMSDKTFKPAVVNRLDRNTAGLVIGAKNAKSLRALNK 167

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           + R   I K Y ++V G        IA      ++I  +      +     +   + F+ 
Sbjct: 168 AIRDNLIDKYYLTIVKG-------NIAKEFTIDTNIKKNENKNKIKRATEGSRIRTFFRP 220

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           I+    KF  LE +  TG+THQ+R      G PI+GD KY +
Sbjct: 221 IESNG-KFTLLECKLDTGKTHQIRFSLRENGTPIIGDRKYGS 261


>gi|78185673|ref|YP_378107.1| pseudouridine synthase [Synechococcus sp. CC9902]
 gi|78169967|gb|ABB27064.1| probable pseudouridine synthase [Synechococcus sp. CC9902]
          Length = 315

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 85/313 (27%), Positives = 143/313 (45%), Gaps = 41/313 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPP 69
           V++  E   L +W  N + H       + + +G++  + + +  + ++ SG  +  + PP
Sbjct: 27  VQSHGEGAWLSQWMANRHQHSAAAVWLERIAAGEMHRNGEPLAGDMQLTSGDDICWQRPP 86

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +        E+ I D            +   +++D  + V NKP+G+ V  G G   H 
Sbjct: 87  WL--------EEAIPD------------QWDTIHDDGDLLVINKPSGLPVMPGGGFLEHT 126

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIY--WSL 186
              L + + S G KP   HRL + TSG+ V ART A    L++ FR   R QKIY  W+ 
Sbjct: 127 ---LTALLASTGAKP--VHRLGRFTSGLQVCARTAATRAALSKQFRPESRCQKIYQAWAR 181

Query: 187 -VWGIPKNKKECIANWLLKKSH--IGGDYVHVVKQNEKGANYAISH--FKVID-CFAQKF 240
            V G+   +   ++  ++++ H  +G  +       E       +H   +++D C A   
Sbjct: 182 RVEGLEPGQSLVVSTDVVERQHPLLGWIWGPEPLDQEPTRKRLTAHSTVRLLDRCAAGDR 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-SPIQNKLYLHARYMDLPH 299
             LE+   TGR HQ+R+H   +G P++GD  Y  N K + T +P      LH+  ++   
Sbjct: 242 --LEVTIRTGRPHQIRIHLAQLGSPLLGDPLYLLNRKISETATPGDGGYGLHSWRLNALT 299

Query: 300 PEGGRLQITAPLP 312
             G  L  TAPLP
Sbjct: 300 AAG--LSFTAPLP 310


>gi|167756776|ref|ZP_02428903.1| hypothetical protein CLORAM_02325 [Clostridium ramosum DSM 1402]
 gi|167702951|gb|EDS17530.1| hypothetical protein CLORAM_02325 [Clostridium ramosum DSM 1402]
          Length = 328

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 89/335 (26%), Positives = 155/335 (46%), Gaps = 42/335 (12%)

Query: 11  VVENDEENMRLDRWFKN---HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + END  N R+D++ K    + P+ NF+   K+ R   ++V+ K+V     +     V +
Sbjct: 12  ITENDA-NQRIDKYLKKLLVNAPN-NFI--YKMFRKKDIKVNGKKVDEKYILSLDDEVEM 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
               +      + + I + +   +         +LYED  + +  KPAG+ V   +  + 
Sbjct: 68  FLYDDKFKEFTETKSIYEVNKTFS---------VLYEDKHVLIVFKPAGLLVHEDANESI 118

Query: 128 H-IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           + +   + S++ SK +          P   HRLD+ TSGI++  +T AA Q+L E  + R
Sbjct: 119 NTLTNQVLSYLASKNELDLSRENTFMPGPVHRLDRNTSGIVIFGKTLAALQNLNEMIKQR 178

Query: 178 R-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I+K Y ++  G   N +  +  +++K  +     V +VK++  GA    +  + +  +
Sbjct: 179 HCIEKKYLTICRG-QLNHQRNLHGYMIKLENQAQ--VKLVKKDYPGALTMETIVRPLK-Y 234

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN----FTSPIQNKLYLHA 292
              +  +E+   TGR HQ+RVH   +  PI+GD KY  +F+ N     T  + N+L LHA
Sbjct: 235 NCDYSLVEVTLITGRMHQIRVHLSSIEHPIIGDRKY-GDFELNKYIKKTFGLNNQL-LHA 292

Query: 293 RYMDLPHPEG--GRLQ---ITAPLPAHMVKTWDSL 322
             +      G    LQ   I  P+PA   K   SL
Sbjct: 293 YKIKFVKTFGVLNYLQDKEIICPVPALFEKIEKSL 327


>gi|163749714|ref|ZP_02156960.1| Pseudouridylate synthase, 23S RNA-specific [Shewanella benthica
           KT99]
 gi|161330527|gb|EDQ01485.1| Pseudouridylate synthase, 23S RNA-specific [Shewanella benthica
           KT99]
          Length = 227

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/202 (29%), Positives = 100/202 (49%), Gaps = 20/202 (9%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           Y D  I V NKP+G+    G     +   +   L+ + ++      L HRLD  TSGI+V
Sbjct: 28  YRDRDILVINKPSGLLSNPGRAENTYDCALTRLLQRYPETI-----LVHRLDCATSGIMV 82

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + A  ++   F+ R  +K Y + V G+    +  I   L  K++     +  +  +
Sbjct: 83  FALNKKAESNIKTQFQNRMSKKTYIAEVRGLLSQDQGVIE--LAMKANKTRPPLQEIAAD 140

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K +    +++KV++    +   +E++P TGRTHQLR+H L +G PI+GD     +F G+
Sbjct: 141 GKASK---TYYKVLERRENR-TLVELKPVTGRTHQLRLHMLAIGHPILGD-----DFYGD 191

Query: 280 -FTSPIQNKLYLHARYMDLPHP 300
                  ++L LHA  + + HP
Sbjct: 192 KEVIAASSRLRLHAMSLSIRHP 213


>gi|317014367|gb|ADU81803.1| hypothetical protein HPGAM_04945 [Helicobacter pylori Gambia94/24]
          Length = 242

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/202 (30%), Positives = 98/202 (48%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K W         L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKDWA--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +LV GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVRKEYLALVQGIVEEEREINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y   
Sbjct: 157 SKKGQEAITI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLY--- 208

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
              N       +L LHA  + L
Sbjct: 209 ---NNEPSSAKRLMLHAHKIAL 227


>gi|134082733|emb|CAK42625.1| unnamed protein product [Aspergillus niger]
          Length = 484

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 57/202 (28%), Positives = 96/202 (47%), Gaps = 19/202 (9%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           N ++K  +I+  +++  +     K I +++ED  + V +KPAG+ V   S   YH +  L
Sbjct: 100 NTVVKNGQIISHTLHRHEPPVTGKEIGIIHEDDDLIVIDKPAGVPVH--SAGRYHYNSVL 157

Query: 134 KSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-I 190
           +     +  +  PR  +RLD+ TSG++ + +T  AA+++T   + R +QK Y + V G  
Sbjct: 158 EIMRSQRHPEWVPRPCNRLDRLTSGVMFLGKTAKAAENMTGKLKARTLQKEYVARVKGKF 217

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P     C    +     +G   ++ V+   K A        ++ C           P TG
Sbjct: 218 PDGVIVCDQPIMSVSPKVG---LNRVRATGKEAKTKFRRLAIVHCL----------PLTG 264

Query: 251 RTHQLRVHALHMGCPIVGDHKY 272
           RTHQ+RVH   +G PI  D  Y
Sbjct: 265 RTHQIRVHLQFLGHPISNDPIY 286


>gi|313678812|ref|YP_004056552.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma bovis PG45]
 gi|312950691|gb|ADR25286.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma bovis PG45]
          Length = 305

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 71/293 (24%), Positives = 131/293 (44%), Gaps = 40/293 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV--KFNNRIQSGQVVRIPPVINALNHI 77
           R+D++  ++   I   + + ++    V +D K+   K N  ++ G V+ I      L  +
Sbjct: 11  RIDKYISDN-SEITRNDAKALIEQEAVYIDDKKFVRKPNYMVREGMVITI------LRLL 63

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH 128
            KE  I   +VN+          + YED  + V NKP+G+ V    G         + YH
Sbjct: 64  EKETNI--EAVNMPLD-------IRYEDDNLLVLNKPSGLVVHPAPGHLNDTLVNALMYH 114

Query: 129 IDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              F  +  D+ G  +  + HR+D++TSG+L++A+       L +  +  +I++ Y ++ 
Sbjct: 115 ---FKNNLSDTNGLLRLGIVHRIDKDTSGLLIIAKDNETHNELAKMLKNHQIKRTYIAIC 171

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI  NK   I N  +++       + + K  +    Y +   K      + +  ++ + 
Sbjct: 172 KGILPNKVTKI-NLPIQRDAKNRKLMSIHKDGKSSVTY-VHLLKTFYIDNKPYSLVKCEL 229

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            TGRTHQ+RVH  ++  P+ GD+ Y     G+       +  LHA  +   HP
Sbjct: 230 ETGRTHQIRVHLAYIKHPVYGDNIY-----GSHVDDFNQR--LHAYRLSFIHP 275


>gi|331226410|ref|XP_003325875.1| hypothetical protein PGTG_07077 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
 gi|309304865|gb|EFP81456.1| hypothetical protein PGTG_07077 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
          Length = 380

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 52/201 (25%), Positives = 99/201 (49%), Gaps = 25/201 (12%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPR 145
           + NL K   F    +L+E+ K+ V +KPAG ++Q   G   +I    +  +++ +  K  
Sbjct: 118 TANLEK--SFKPPKILFENEKVVVIDKPAGCALQAELGSEAYIRWKLIMDYLEKRRGKLF 175

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL--L 203
           + HRLD+ T+G L++A++  A++ L+  F+   ++K Y++ +        + + + +  +
Sbjct: 176 IVHRLDKSTTGPLILAKSSTASRTLSTQFKNSTVKKTYYAAI--------QFLGDRIGPI 227

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW-----------LEMQPHTGRT 252
           + +   G     ++ ++     A S+    DC   K  W           + + P TGR 
Sbjct: 228 QDAKSSGQIECRMRDSKDRMVIAESNRTGTDCKQTKTNWELVTATSNHAIVRLTPQTGRK 287

Query: 253 HQLRVH-ALHMGCPIVGDHKY 272
           HQLR+H +  +  PIVGD KY
Sbjct: 288 HQLRLHCSRFLAGPIVGDFKY 308


>gi|256852163|ref|ZP_05557549.1| ribosomal protein large subunit [Lactobacillus jensenii 27-2-CHN]
 gi|260661804|ref|ZP_05862715.1| ribosomal protein large subunit [Lactobacillus jensenii 115-3-CHN]
 gi|282933665|ref|ZP_06339024.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 208-1]
 gi|297205672|ref|ZP_06923068.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii JV-V16]
 gi|256615209|gb|EEU20400.1| ribosomal protein large subunit [Lactobacillus jensenii 27-2-CHN]
 gi|260547551|gb|EEX23530.1| ribosomal protein large subunit [Lactobacillus jensenii 115-3-CHN]
 gi|281302198|gb|EFA94441.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 208-1]
 gi|297150250|gb|EFH30547.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii JV-V16]
          Length = 287

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 84/181 (46%), Gaps = 13/181 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I V NKP+    Q      +  D  +       G  P + HRLD  T+G+L+ 
Sbjct: 83  IIYEDKNILVINKPSN---QKTHPNLFETDTAMNDVTTYLGYTPYIIHRLDMLTNGLLLF 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A+  A    L      + +++ Y++ V      K + I N       I  D     K+  
Sbjct: 140 AKNPAVVPILNRQLTTKIMKRNYYATV------KLKNIPNQGTIDLPIAQDPNDQRKRIV 193

Query: 219 NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           ++ G   AI+H++VI   + Q    L++   TGRTHQ+RVH   +  PI+GD  Y  +F 
Sbjct: 194 DDNGLK-AITHYQVIARNSIQNTMTLKLTLETGRTHQIRVHLASINLPIIGDPLYNPDFN 252

Query: 278 G 278
           G
Sbjct: 253 G 253


>gi|218263542|ref|ZP_03477623.1| hypothetical protein PRABACTJOHN_03310 [Parabacteroides johnsonii
           DSM 18315]
 gi|218222665|gb|EEC95315.1| hypothetical protein PRABACTJOHN_03310 [Parabacteroides johnsonii
           DSM 18315]
          Length = 306

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/211 (27%), Positives = 99/211 (46%), Gaps = 25/211 (11%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR----LTHRLDQ 152
           +++ED  + V NK  G+    S +     A+H+   L  +V  K   PR    + HRLD+
Sbjct: 92  IVWEDDDLIVVNKKEGLLSVSSTRVKERTAFHL---LSGYV--KKTDPRNKIFVLHRLDR 146

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+++ A+     + L  ++      + Y ++V G P+   + I + L + + +    
Sbjct: 147 DTSGLMMFAKNLQVQKALQSNWNSAITARTYVAVVEGRPEKDSDLIISNLTENTKM---- 202

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V    E     AI+ ++++      +  LE+   TGR +Q+R     +G  I GD+KY
Sbjct: 203 -QVYVTTEGDGKEAITRYRLLHSNGA-YSLLELDLETGRKNQIRAQMQSIGHSIAGDYKY 260

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            A      T P   +L LHAR +D  HP  G
Sbjct: 261 GAE-----TDPT-GRLMLHARRLDFIHPVTG 285


>gi|294497315|ref|YP_003561015.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           megaterium QM B1551]
 gi|294347252|gb|ADE67581.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           megaterium QM B1551]
          Length = 303

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 56/184 (30%), Positives = 87/184 (47%), Gaps = 25/184 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----------IAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +L+ED  + + NKP  +     S            AY     LK+       KPR  HRL
Sbjct: 85  ILFEDEHVLIVNKPINLDTHPSSEQDQKTLLNAVAAYFQKIGLKT-------KPRHVHRL 137

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D +TSG ++  +   A+    +    R+I + Y +LV GI K K++ I N       IG 
Sbjct: 138 DSDTSGAILFTKHFVASSVFDQLLAERKINRTYIALVQGIIK-KEDGIIN-----EPIGR 191

Query: 211 DYVHVVKQN-EKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           D  H  ++   +    A + ++V+    A+    +E+   TGRTHQ+RVH  H+G P++G
Sbjct: 192 DRHHATRRRVSRTGQAAKTRYRVLKRNTAKNETLIELSLETGRTHQIRVHMSHIGYPLLG 251

Query: 269 DHKY 272
           D  Y
Sbjct: 252 DTLY 255


>gi|229090249|ref|ZP_04221495.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-42]
 gi|228693095|gb|EEL46810.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-42]
          Length = 292

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 78/313 (24%), Positives = 142/313 (45%), Gaps = 41/313 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI  P
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QGGS 123
           V      +I E   L                ++YED  + V NK A +S         GS
Sbjct: 63  VEERSEGMIAEDIPL---------------CIVYEDDAVLVINKEANMSTIPSREHPSGS 107

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  + K ++ S      +  RLD++TSG++++A+ R     L++  + + +++ Y
Sbjct: 108 VANALLSHYDKQYLAST---VHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTY 164

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    ++  I   + +KS    D +      E+G   A++HF+VI+    K   +
Sbjct: 165 EAIVHGEMVEREGTIDAPIGRKS----DSIIERTVCEEG-QRAVTHFRVINSANHK-THV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
            ++  TGRTHQ+RVH  H+G P++GD     N  G     ++ +  LH+  +   HP   
Sbjct: 219 SLELDTGRTHQIRVHMAHIGHPLLGD-----NLYGGKRDEMKRQ-ALHSTSLTFYHPILE 272

Query: 303 GRLQITAPLPAHM 315
             +  TA +P+ M
Sbjct: 273 KEMSFTAMIPSDM 285


>gi|224100817|ref|XP_002312025.1| predicted protein [Populus trichocarpa]
 gi|222851845|gb|EEE89392.1| predicted protein [Populus trichocarpa]
          Length = 377

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 85/315 (26%), Positives = 125/315 (39%), Gaps = 69/315 (21%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQK-ILDSSVNLTKH--------SDFLKSILLYEDSKI 108
           RI +GQ       I     ++KE K IL   + L  H        + +L  +L YED  +
Sbjct: 61  RIHNGQ-------ITIDGEVVKEPKAILRDGMELVYHRLPWREPDAPYLLQVL-YEDDDM 112

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--------PRLTHRLDQETSGILVV 160
              NKP G+ V  G             W  SKG          P   HRL + TSGIL+ 
Sbjct: 113 VALNKPPGLQVLPGGLFQQRTVLMQLQWRASKGSSSLAIQGSHPVPVHRLGRGTSGILLC 172

Query: 161 ARTRAAAQHLTESF------------------RMRRIQKIYWSLVWGIPKNKKECIANWL 202
           A+T+ A   L   F                  + R+I KIY +LV GI    K  I   +
Sbjct: 173 AKTKVAKTSLAAYFADGTSLIGDSSNANMEQSKRRKISKIYRALVNGILNQDKIIIKQPI 232

Query: 203 LKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
               + G    ++V   + K A   +   +      Q    +E++  +GR HQ+R+H   
Sbjct: 233 GTMRYPGVAKGLYVASPSGKPALSKVEVLERDSQLNQTLVQVEIE--SGRPHQIRIHLSF 290

Query: 262 MGCPIVGDHKY-------CANFK---------GNFTSPIQN-----KLYLHARYMDLPHP 300
           +G P++GD  Y       C + +         G +  P +        YLHA  + L HP
Sbjct: 291 IGHPLLGDPLYDVGGQPMCFDSEHEDESFAEDGGYERPAKPVPGDCGYYLHAHQLVLSHP 350

Query: 301 EGGR--LQITAPLPA 313
                 ++ITAPLP+
Sbjct: 351 TKNEQVIKITAPLPS 365


>gi|159906031|ref|YP_001549693.1| RluA family pseudouridine synthase [Methanococcus maripaludis C6]
 gi|159887524|gb|ABX02461.1| pseudouridine synthase, RluA family [Methanococcus maripaludis C6]
          Length = 297

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/221 (26%), Positives = 105/221 (47%), Gaps = 21/221 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI-----AYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED  + + +KP  + V     +     A  I    K  ++++  K R   RLD +T+
Sbjct: 84  VIYEDDDLLIVDKPKNMVVHPTKNVLSKTLANAISNHQK--INNQNYKIRFVSRLDMDTT 141

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A+   + QHL +      ++KIY ++V G    K+  I + +     +  D +  
Sbjct: 142 GLLIIAKNSYSHQHLAKQMDEGILEKIYVAVVNGRLDLKEGIIEDSI----DLNDDGIK- 196

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++       + + +KVI+   +    LE+   TGRTHQ+RVH   +G  I+GD  Y   
Sbjct: 197 -RELSNSGKISKTKYKVIEEL-KNASVLEINLLTGRTHQIRVHLSSLGNYILGDILYGK- 253

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                TS + ++  LH+  +   HP    R + T+ LP  M
Sbjct: 254 -----TSKLIDRQALHSHILRFIHPITKERKEFTSKLPDDM 289


>gi|172058049|ref|YP_001814509.1| RluA family pseudouridine synthase [Exiguobacterium sibiricum
           255-15]
 gi|171990570|gb|ACB61492.1| pseudouridine synthase, RluA family [Exiguobacterium sibiricum
           255-15]
          Length = 293

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 80/306 (26%), Positives = 133/306 (43%), Gaps = 47/306 (15%)

Query: 22  DRWFKNHY----PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV--VRIPPVINALN 75
           D W   H+     HI+   L  I   G +  +++ V  N  + +G    VR P       
Sbjct: 14  DGWSVGHFCTTRLHISRKMLVSIKHHGDILRNEQHVNVNEPVHAGDRIHVRFP------- 66

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
              +EQ   D       H+   +  +L+ED  + + NKP G+ S+         +  F+ 
Sbjct: 67  ---EEQPAQD------MHATSGELDILFEDDWLLIVNKPPGMASIPSRLHPERSLSNFVL 117

Query: 135 SWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-I 190
            +   + Q P   H   RLD++TSG++V A+   A   L++  +   + + Y +L+ G I
Sbjct: 118 GYY-RQHQIPYAIHIVNRLDRDTSGLVVFAKHSLAHHQLSKMQQNGLLDRRYVALIEGTI 176

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF---KVIDCFAQKFCWLEMQP 247
           P    +              D+  + +   +    AI+H    + I  F+++   L ++ 
Sbjct: 177 PAQTIDLPIGQT--------DHSFMERMVREDGQQAITHILTSEPITAFSRELSRLTIKL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH   +G P+VGD  Y    KG   +P+  +  LH+     PHP  G  + 
Sbjct: 229 ETGRTHQIRVHLAALGHPLVGDTMY----KG---TPLIARQALHSASATFPHPGTGEVMT 281

Query: 307 ITAPLP 312
             APLP
Sbjct: 282 FVAPLP 287


>gi|317180199|dbj|BAJ57985.1| hypothetical protein HPF32_0403 [Helicobacter pylori F32]
          Length = 242

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/202 (30%), Positives = 100/202 (49%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVKKEYLALAQGIIEEEQEINAPILTFKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y  N
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYN-N 210

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
             G+       +L LHA  + L
Sbjct: 211 EPGS-----AKRLMLHAHKISL 227


>gi|227545484|ref|ZP_03975533.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus reuteri
           CF48-3A]
 gi|300908150|ref|ZP_07125618.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus reuteri
           SD2112]
 gi|227184534|gb|EEI64605.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus reuteri
           CF48-3A]
 gi|300894715|gb|EFK88069.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus reuteri
           SD2112]
          Length = 301

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 104/230 (45%), Gaps = 22/230 (9%)

Query: 101 LLYEDSKIYVFNKPAGIS------VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++YED    + NKPAG++      V     +   + G+ K   + + Q   +  RLD++T
Sbjct: 80  IIYEDQDFLIMNKPAGVATVPAHNVPVADSLVNRVKGYYKRQ-NYENQVTHVATRLDRDT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV 213
           SG++V  + R A   L E  +   ++K Y +L+ G +P       A      S       
Sbjct: 139 SGLVVFPKHRFAHAVLDEQLKKHLVKKNYLALIKGKVPAEHGYIDAPIQRDPSSF----- 193

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            V +   K    +++ +   +C  Q    ++++ HTGRTHQ+RVH   +G P++GD  Y 
Sbjct: 194 -VKRMVGKEGKASVTEYWRQECNVQA-SLIKIRLHTGRTHQIRVHFASLGFPLIGDKMYG 251

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                   S +  +  LH  ++    P +G  + + APLP+      D L
Sbjct: 252 EE------SGLIARQALHCYWLSFYSPFKGENITVLAPLPSDFKNAKDDL 295


>gi|154498138|ref|ZP_02036516.1| hypothetical protein BACCAP_02119 [Bacteroides capillosus ATCC
           29799]
 gi|150273128|gb|EDN00285.1| hypothetical protein BACCAP_02119 [Bacteroides capillosus ATCC
           29799]
          Length = 321

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 72/280 (25%), Positives = 119/280 (42%), Gaps = 32/280 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++ + +ND    RLDRW     P +     QK +R  +V+V+ K    + R+Q G  +++
Sbjct: 3   EFTIKKNDA-GQRLDRWLGKTLPLLPAPLAQKYIRLKRVKVNGKGSARDYRLQEGDFLQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-----LLYEDSKIYVFNKPAGISVQGG 122
              IN         +  D+    T  + FL        ++YED  + + +K  GI V   
Sbjct: 62  --YIN--------DEFFDTP---TLENAFLSVFKPRLNIVYEDENLLLVDKQPGIVVHPD 108

Query: 123 -----SGIAYHIDGFL---KSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTE 172
                + +  HI  +L   K W   K     P L +R+D+ T GI++ A+     + + +
Sbjct: 109 ETERVNTLITHIQAYLYQKKEWSPYKENSFAPALCNRIDRNTGGIVIAAKNAETLRIMNQ 168

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
             + R I K Y ++V G   N  E      L K  +    V V          A++ +K 
Sbjct: 169 KIKDREIDKFYLAVVLG-KMNPPEGRLEGFLVKDEVKKQ-VTVYHHPVPDGRTALTVYKT 226

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +         +E +  TGRTHQ+R      G P++GD KY
Sbjct: 227 LKV-GNGLSLVECELLTGRTHQIRAQFADAGHPLLGDGKY 265


>gi|51012815|gb|AAT92701.1| YDL036C [Saccharomyces cerevisiae]
          Length = 462

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 54/173 (31%), Positives = 87/173 (50%), Gaps = 6/173 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP+GI V       Y  +   K   ++ G      +RLD+ TSG++ +
Sbjct: 190 VIFEDDNIMVIDKPSGIPVHPTG--RYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFL 247

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+T   A ++ +  + R + K Y + V G  P+   E I    LK          V + +
Sbjct: 248 AKTPKGADNIGDQLKAREVTKEYVAKVVGEFPET--EVIVEKPLKLIEPRLALNAVCQMD 305

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           EKGA +A + F  I  +  K   ++ +P TGR+HQ+RVH  ++G PI  D  Y
Sbjct: 306 EKGAKHAKTVFNRI-SYDGKTSIVKCKPLTGRSHQIRVHLQYLGHPIANDPIY 357


>gi|257791310|ref|YP_003181916.1| pseudouridine synthase, RluA family [Eggerthella lenta DSM 2243]
 gi|257475207|gb|ACV55527.1| pseudouridine synthase, RluA family [Eggerthella lenta DSM 2243]
          Length = 344

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 111/244 (45%), Gaps = 29/244 (11%)

Query: 103 YEDSKIYVFNKPAGI----SVQGGSG-----IAYHIDGFLKSWVDSKGQKPRL--THRLD 151
           +ED  + V +K  G+    SV    G     + YH     ++  + +G+  RL   HRLD
Sbjct: 86  FEDEDLIVLSKQVGLVCHPSVDHDDGTLVNALIYHCGA--ENLCNVQGEDDRLGIVHRLD 143

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++ A+       L    R R + + Y +LV G+  +    I   + +      +
Sbjct: 144 RDTSGLMLAAKNDETGYALMSDIRDRAVDRRYLALVHGVIAHDTGMIDAPIARAEK---E 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              +  ++   A  AI+ F+V++ F        +  ++ +  TGRTHQ+RVH  +   P+
Sbjct: 201 RTRMAVRDTPSAREAITTFRVLERFEHGARDDGYTLIDCKLFTGRTHQIRVHLEYAKHPL 260

Query: 267 VGDHKYCANFKGNFTSPIQ----NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           VGD  Y +   G  ++P      ++ +LH+  +   HP  G  L+    LP  + +  D 
Sbjct: 261 VGDPAYTS---GAPSAPAADLGLDRQFLHSFQLSFQHPVTGEGLRFADNLPVDLQEALDD 317

Query: 322 LGFK 325
           L  +
Sbjct: 318 LASR 321


>gi|119471760|ref|ZP_01614120.1| tRNA pseudouridine synthase C [Alteromonadales bacterium TW-7]
 gi|119445383|gb|EAW26671.1| tRNA pseudouridine synthase C [Alteromonadales bacterium TW-7]
          Length = 254

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 106/253 (41%), Gaps = 35/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D      NKP+G+ V       +     ++   D  GQ     HRLD+ TSG+L+ 
Sbjct: 15  ILYQDENFVAINKPSGLLVHRSFLDKHETQFAMQMLRDQLGQHVFPVHRLDRPTSGVLLF 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVK 217
           A +  AA+ + + F    I K Y +LV G   +     + +   L K +    D     +
Sbjct: 75  ALSSEAARDMNQLFIEGTIAKRYLALVRGFAPDSVFLDKPLKEELDKIADKFADQNKAPQ 134

Query: 218 QNEKGAN-------------YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           + +   N             Y    + +++CF          P TGR HQ+R H  H+  
Sbjct: 135 EAQTQFNCLYQAALPIPIGKYPTVRYSLVECF----------PKTGRKHQIRRHLKHLSL 184

Query: 265 PIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           PI+GD  +  N     F+ +F      +L L A  +   HP   + + I APL   M++ 
Sbjct: 185 PIIGDVNHGDNQHNQFFRDHFEL---RRLMLFATELSFVHPYTYKAITIKAPLGNDMLQI 241

Query: 319 WDSLGFKYDRNLY 331
            + LG+  +   Y
Sbjct: 242 CEQLGWPNEEKDY 254


>gi|27468449|ref|NP_765086.1| hypothetical protein SE1531 [Staphylococcus epidermidis ATCC 12228]
 gi|57867268|ref|YP_188955.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           epidermidis RP62A]
 gi|251811192|ref|ZP_04825665.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|282875767|ref|ZP_06284634.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|293366172|ref|ZP_06612858.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|27315996|gb|AAO05130.1|AE016749_76 conserved hypothetical protein [Staphylococcus epidermidis ATCC
           12228]
 gi|57637926|gb|AAW54714.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus epidermidis RP62A]
 gi|251805320|gb|EES57977.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|281294792|gb|EFA87319.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|291319694|gb|EFE60054.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|329734308|gb|EGG70623.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU045]
          Length = 274

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 68/271 (25%), Positives = 119/271 (43%), Gaps = 42/271 (15%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +L ++  S ++ ++K+     N +++G  V IP      N++                  
Sbjct: 27  DLHQLNMSKEILINKEYGTLLNNVKTGDHVEIPTPNEVSNYL----------------PS 70

Query: 96  FLKSILLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +  + + YED  + +  KP G+      ++  + +  H+       VDS+  +P   HRL
Sbjct: 71  YRYAQIYYEDDDLAIVMKPKGVKTHPNDLKESNTLMNHV----IYTVDSEYVEP--IHRL 124

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           DQET G+L+VA+     + L        I +IY + V  +   K + I         IG 
Sbjct: 125 DQETVGLLIVAKNPLMKKILDRMLEYNEITRIYKANVKALLPIKPQTI------DMPIGK 178

Query: 211 DYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D  H  K+        AI+H        +  C L+++  TGRTHQ+RVH   +G P++GD
Sbjct: 179 DKFHSNKRRISNTGQRAITHIINSKMIKEGVCQLDIKLDTGRTHQIRVHLAEIGHPVIGD 238

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             Y        TS ++ +L L++  ++  HP
Sbjct: 239 PLYG-------TSTLR-QLELNSHQIEFTHP 261


>gi|2501677|sp|Q47417|TRUC_PECCC RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|496598|emb|CAA55982.1| unnamed protein product [Pectobacterium carotovorum]
          Length = 376

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 63/248 (25%), Positives = 111/248 (44%), Gaps = 53/248 (21%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKP+G  V              +SW+D K             GQ     
Sbjct: 118 IIYQDEHLVAVNKPSGWLVH-------------RSWLDRKEKVVVMQTVRDQIGQHVYTV 164

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++A +   A+ L++ F   ++QK Y ++V G   +  + + ++ L +  
Sbjct: 165 HRLDRPTSGVLLLALSSEVARALSQQFESHQMQKTYHAVVRGYVLD--DGVIDYALTEEL 222

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQL 255
             I   + +     +K    A++H++ +               ++  +E++P TGR HQL
Sbjct: 223 DKIADKFTN----PDKAPQPAVTHYRSLAQAEMPVAIGRYPTARYSLMELKPQTGRKHQL 278

Query: 256 RVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           R H  H+  PI+GD  H    + +G  +     +L LHA  + L HP  G+       P 
Sbjct: 279 RRHMSHIHHPIIGDTAHGDLRHNRGMESHFSCGRLMLHASELQLNHPVSGQ-------PL 331

Query: 314 HMVKTWDS 321
            +   WD+
Sbjct: 332 TLQARWDA 339


>gi|317177743|dbj|BAJ55532.1| hypothetical protein HPF16_0935 [Helicobacter pylori F16]
          Length = 242

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/202 (30%), Positives = 97/202 (48%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVKKEYLALAQGIIEEEQEINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L+    TGRTHQ+RVH  H+  PI+GD  Y   
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKAGIKTGRTHQIRVHLKHINHPIIGDTLY--- 208

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
              N       +L LHA  + L
Sbjct: 209 ---NNEPSSAKRLMLHAHKISL 227


>gi|113953912|ref|YP_730201.1| pseudouridine synthase RluA [Synechococcus sp. CC9311]
 gi|113881263|gb|ABI46221.1| pseudouridine synthase RluA PA3246 [Synechococcus sp. CC9311]
          Length = 220

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/207 (28%), Positives = 98/207 (47%), Gaps = 13/207 (6%)

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           +  V  KP+G+  Q G G +      L + + +   + RL HRLD++TSG+L++AR   +
Sbjct: 24  RFLVVEKPSGLLSQPGLGDSQ--SDSLITRLQAVRPELRLVHRLDRDTSGLLLLARDPES 81

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
            + L   F  R++ K Y + V G PK++   +   L + S       H  +   +    +
Sbjct: 82  LKVLGGLFAERKVHKFYAADVHGHPKSRSGAVRLPLARLS------AHPPRYGPRRDGRS 135

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
                           L + P TGR+HQLR H   +G PI+GD  Y ++  G   SP   
Sbjct: 136 CLTLWRCAQMGSDRSRLWLAPRTGRSHQLRAHLAAIGLPIIGDPIYASSGLG---SP-GE 191

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLP 312
           +L+LHA  +    P  G R+++ + LP
Sbjct: 192 RLHLHALGLSFSDPFSGQRIRVRSSLP 218


>gi|70726113|ref|YP_253027.1| hypothetical protein SH1112 [Staphylococcus haemolyticus JCSC1435]
 gi|68446837|dbj|BAE04421.1| unnamed protein product [Staphylococcus haemolyticus JCSC1435]
          Length = 274

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 53/177 (29%), Positives = 82/177 (46%), Gaps = 20/177 (11%)

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSG 156
           YED  + +  KP G+      ++  + +  H+   L+S +V+         HRLDQET G
Sbjct: 78  YEDDDLAIVMKPKGVKTHPNDLKESNTLMNHVIYTLESDYVEP-------IHRLDQETVG 130

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+VA+     + L        I +IY + V  +   K + I       S IG D  H  
Sbjct: 131 LLIVAKNPLMKKILDRMLEENEITRIYKANVKSLLPIKPQTI------DSPIGKDKFHPN 184

Query: 217 KQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K+        AI+H        +  C L+++  TGRTHQ+RVH   +G P++GD  Y
Sbjct: 185 KRRISNTGQRAITHILSSKMIKEGVCQLDIKLDTGRTHQIRVHLAEIGHPVIGDPLY 241


>gi|332298019|ref|YP_004439941.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332181122|gb|AEE16810.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 336

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 83/343 (24%), Positives = 142/343 (41%), Gaps = 48/343 (13%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI------- 67
           D+   RLD+  +   P+     +   +R   VRV+ K+     R+  G ++ I       
Sbjct: 11  DDARRRLDKIIRKFLPNAPLSAIYSYIRKSLVRVNGKKTDAAARVNEGDLIDIADFLLQP 70

Query: 68  -PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            P  + +     + +     +++    +DFL+           V NKP  I VQG  G  
Sbjct: 71  QPAELPSEPEPARSRPAAFPALDDVFCNDFLR-----------VINKPYDIPVQGCRGAR 119

Query: 127 YHIDGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             I   +++         S   KP   HRLD++T+G+LV +R    A+  + + R   +Q
Sbjct: 120 VSIADIVQAEYAETARASSLSFKPGPLHRLDRKTTGLLVCSRNLEGARWFSAAVRDHLLQ 179

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++V G  + ++  I    +++   G   +H  +++        S  K  D  A   
Sbjct: 180 KRYAAIVQGCLETER--IWTDKIERETEG---LHRFRRS-LACRSGGSEGKTADTRAVPL 233

Query: 241 C--WLEMQPHT--------GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
                E +P T        GRTHQ+R+H    G P++GD  Y     G   S  Q+ +YL
Sbjct: 234 AHGSYEGEPVTLVLFSIGSGRTHQIRLHGGAHGFPLLGDTAY----GGRPISEAQS-IYL 288

Query: 291 HARYMDLPHPEGGRLQ--ITAPLPAHMVKTWDSLGFKYDRNLY 331
           HA  + +P P    L   + AP+  +  K       ++D + Y
Sbjct: 289 HAWQLGIPEPNPVSLPPLLCAPISTNFQKMLKKCLLEWDYSAY 331


>gi|304410331|ref|ZP_07391950.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307301958|ref|ZP_07581716.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304351740|gb|EFM16139.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306913996|gb|EFN44417.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 245

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 98/216 (45%), Gaps = 18/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+DS I + +KP+G+    G     ++D      V        L HRLD  TSGI++V
Sbjct: 26  VLYQDSDILLIDKPSGLLSLSGKN-PLNLDSVHYRLVQDFPTA-TLLHRLDFGTSGIMLV 83

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  ++    LT+ F+ R ++K Y +L+ G        I   + K S    D+  + K   
Sbjct: 84  ALNKSVNGLLTKQFQARTVEKRYTALLHGHIAADSGMINLPIAKDS----DHFPLQKICH 139

Query: 221 KGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NF 276
                AIS ++V++     F   +E  P +GRTHQLR+H+   G  I+G   Y     + 
Sbjct: 140 STGKPAISEYRVLERLTAPFATRVEFTPVSGRTHQLRIHSQQFGHSILGCDLYGGVGESV 199

Query: 277 KGNFTSP--------IQNKLYLHARYMDLPHPEGGR 304
             N  +P          ++L LHA  +   HP  G 
Sbjct: 200 ADNAAAPDPDITKMASNSRLMLHATRLAFDHPITGE 235


>gi|126175503|ref|YP_001051652.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125998708|gb|ABN62783.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 244

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/216 (28%), Positives = 97/216 (44%), Gaps = 18/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+DS I + +KP+G+    G     ++D      V        L HRLD  TSGI++V
Sbjct: 25  VLYQDSDILLIDKPSGLLSLSGKN-PLNLDSVHYRLVQDFPTA-TLLHRLDFGTSGIMLV 82

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  ++    LT+ F+ R ++K Y +L+ G        I   + K      D+  + K   
Sbjct: 83  ALNKSVNGLLTKQFQARTVEKRYTALLHGHIAADSGVINLPIAKDV----DHFPLQKICH 138

Query: 221 KGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALH-----MGCPIVGDHKYCA 274
                AIS ++V++   + F   +E  P +GRTHQLR+H+       +GC + G    C 
Sbjct: 139 STGKPAISEYRVLERLTEPFATRVEFTPVSGRTHQLRIHSQQFGHSILGCDLYGGVGECK 198

Query: 275 NFKGNFTSP------IQNKLYLHARYMDLPHPEGGR 304
               +   P        ++L LHA  +   HP  G 
Sbjct: 199 ADNADAPDPHITEVVSNSRLMLHATRLAFDHPITGE 234


>gi|307637648|gb|ADN80098.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 908]
 gi|325996243|gb|ADZ51648.1| pseudouridine synthase D [Helicobacter pylori 2018]
 gi|325997837|gb|ADZ50045.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 2017]
          Length = 242

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/224 (29%), Positives = 110/224 (49%), Gaps = 36/224 (16%)

Query: 81  QKILDSSVNLTKHSDFL-----KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           QK++ +   L K++ F      K  +++ED  I    KP  I        +Y +  F K 
Sbjct: 33  QKLMVARKELPKNTRFSVQKVEKPSVIFEDENILALFKPPFIE-------SYDLVSFFKD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKN 193
           W         L HRLD+ETSG++++ +  +   HL   ++F+ R ++K Y ++V GI + 
Sbjct: 86  WA--------LLHRLDKETSGVILLVKENSEF-HLKAKKAFKDRAVKKEYLAIVQGIIEE 136

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           ++E  A  L  K+     +  + K+ ++     I+  K+I+    K   L++   TGRTH
Sbjct: 137 EREINAPILTIKT--TKAFSKISKKGQEAITI-ITPLKIIN----KKTLLKVGIKTGRTH 189

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q+RVH  H+  PI+GD  Y  N  G+       +L LHA  + L
Sbjct: 190 QIRVHLKHINHPIIGDTLYN-NEPGS-----AKRLMLHAHKIAL 227


>gi|261493419|ref|ZP_05989944.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261310913|gb|EEY12091.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 217

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/216 (30%), Positives = 100/216 (46%), Gaps = 20/216 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           + Y+     + NKP G+SV         +   +   ++ K  +  L HRLD+ TSG+L++
Sbjct: 7   ICYQHRDFIIINKPEGLSVHKDEA-EIGLTELVARQLNVK--QVWLVHRLDKITSGLLIL 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + AA      F   +I K YW+L    PK K+  I    ++KS  G   +   K+N 
Sbjct: 64  ALNKEAAARFYHLFEQHKIYKTYWALSDKKPKKKQGRIVG-DMQKSRNGAWKLCYSKENP 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               + ISH  V D          +QP TG+THQLRV    +G PI+GD  Y  +     
Sbjct: 123 AVTQF-ISH-SVEDSLRH----FILQPKTGKTHQLRVAMKSLGSPILGDKLYSGS----- 171

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITA-PLPAHM 315
                +++YLHA  +D  + E  ++ + A P   H 
Sbjct: 172 ---QADRVYLHAYQLDFEY-ENEKISVQALPTSGHF 203


>gi|145638949|ref|ZP_01794557.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittII]
 gi|145271921|gb|EDK11830.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittII]
          Length = 232

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 104/232 (44%), Gaps = 27/232 (11%)

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ A +   A  + 
Sbjct: 8   NKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALSSEIANLMC 67

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           E F  + +QK Y ++V G  + K+       ++   I   +     Q +K    A++ ++
Sbjct: 68  EQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQEDKEPQEAVTDYE 123

Query: 232 VIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-------CA 274
            +               ++  +++ PHTGR HQLR H  H+  PI+GD +Y         
Sbjct: 124 GLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDTQYGDLHQNRAL 183

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            F   F+     +L+LH+  +   HP +  ++ ITA L     +  +  G++
Sbjct: 184 TFHLGFS-----RLFLHSNSLSFIHPIKKEQITITAGLDEQWQQLMNQFGWE 230


>gi|313682891|ref|YP_004060629.1| pseudouridine synthase rlu family protein, tigr01621 [Sulfuricurvum
           kujiense DSM 16994]
 gi|313155751|gb|ADR34429.1| pseudouridine synthase Rlu family protein, TIGR01621 [Sulfuricurvum
           kujiense DSM 16994]
          Length = 224

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/192 (30%), Positives = 90/192 (46%), Gaps = 16/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E+    V  KP G++     G A    GF+    +  G      HRLD+ TSG++++
Sbjct: 6   LIFENDTFVVAIKPEGVNFHS-EGEA----GFVVQVSEQLGCPLFPVHRLDKMTSGLVIL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+    A    + F  R I+K Y ++    PK K   I   +       GDY  +V  N 
Sbjct: 61  AKNSETAARFGKMFENREIEKYYLAISMRKPKKKMGWIKGDMASARR--GDYKLLVTMN- 117

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F        +  +L ++PHTG+THQ+RV    +G PI GD +Y    +   
Sbjct: 118 ---NPAITRFISCALRTHERGFL-IKPHTGKTHQIRVALKSLGSPIAGDERYAQADEAR- 172

Query: 281 TSPIQNKLYLHA 292
               +++ YLHA
Sbjct: 173 ---KEDRGYLHA 181


>gi|217032747|ref|ZP_03438231.1| hypothetical protein HPB128_158g26 [Helicobacter pylori B128]
 gi|298736086|ref|YP_003728611.1| pseudouridylate synthase [Helicobacter pylori B8]
 gi|216945563|gb|EEC24218.1| hypothetical protein HPB128_158g26 [Helicobacter pylori B128]
 gi|298355275|emb|CBI66147.1| pseudouridylate synthase [Helicobacter pylori B8]
          Length = 242

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/199 (30%), Positives = 99/199 (49%), Gaps = 31/199 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG++++
Sbjct: 58  VIFEDENILALFKPPFIE-------SYDLLSFFKGWV--------LLHRLDKETSGVILL 102

Query: 161 ARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  + K+
Sbjct: 103 VKENSEF-HLKAKKAFKNRAVKKEYLALTQGIIEEEREINAPILTIKT--TKAFSKISKK 159

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y  N  G
Sbjct: 160 GQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYN-NEPG 213

Query: 279 NFTSPIQNKLYLHARYMDL 297
           +       +L LHA  + L
Sbjct: 214 S-----AKRLMLHAHKIAL 227


>gi|24214190|ref|NP_711671.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
 gi|24195091|gb|AAN48689.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
          Length = 365

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 86/374 (22%), Positives = 149/374 (39%), Gaps = 94/374 (25%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++  +E   RLD +    + + +    QK +  G++ +  K VK    ++ G ++   P+
Sbjct: 18  LISKEESGTRLDHFLSKKFTYHSRTTWQKEITEGRILISSKTVKPGVSLKEGDLISYHPI 77

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 +  + KIL                  YED      +KP  + +   +GI  +  
Sbjct: 78  QKEEPPVRNDYKIL------------------YEDEFFVAVDKPGDLPIHP-AGI--YRK 116

Query: 131 GFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           G L +++   G+   L   HRLD+ETSG+++ A+    A  L++SF +  IQK Y + V 
Sbjct: 117 GNLLTFLKESGKFKDLFTVHRLDRETSGVILFAKNSEIASILSKSFSLGNIQKYYITKVH 176

Query: 189 G-IPKNK------KECIANWLLKKSHIGGDYVHVVKQN----------EKGANYAISHFK 231
           G  PK K      K  +++ + KK        + +K+N          EK    ++++F+
Sbjct: 177 GNFPKRKSAYGILKPDLSSKIRKKRTFVPLKFNFLKRNKKYLFENSLIEKQEEISLTYFQ 236

Query: 232 VI------------------------------------DCFAQKFCWLEMQPHTGRTHQL 255
            I                                    DC++   C    +P TGR HQ+
Sbjct: 237 KIEYDKGRESKFKFSKIEFQFKNVNNEKIKSVFLDQEKDCYSFLLC----KPITGRMHQI 292

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNK------------LYLHARYMDLPHP-EG 302
           R     +G P+ GD  Y  + K  F   I+ K              LH+  + L HP   
Sbjct: 293 RATLFSLGFPLFGDKLYGKDEKV-FLEFIEGKNPDLTTRLGMKRQALHSYAVCLNHPVTN 351

Query: 303 GRLQITAPLPAHMV 316
            +++ITAP+P   +
Sbjct: 352 QKMKITAPIPEDFL 365


>gi|90580967|ref|ZP_01236768.1| putative pseudouridine synthase Rlu family protein [Vibrio angustum
           S14]
 gi|90437845|gb|EAS63035.1| putative pseudouridine synthase Rlu family protein [Vibrio angustum
           S14]
          Length = 245

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 115/253 (45%), Gaps = 33/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  +   NKPAG+ V      ++     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYRDDYLIAVNKPAGMLVHRSWLDSHETVFVMQTLRDQIGQHVFPLHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
             +   A  +   F  R + K Y ++V G  K  +  + ++ LK      +   +  +N 
Sbjct: 65  GLSSEIASQMMPLFAGRDMHKTYHAVVRGWIK--EAAVLDYPLKV-----ELDKIADKNA 117

Query: 220 --EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             EK A  A++ ++ +               ++C +EM+P TGR HQLR H  H+   I+
Sbjct: 118 SEEKEAQPAVTAYEPLATVETDIAVGRYSTSRYCLVEMKPETGRKHQLRRHMHHLSHHII 177

Query: 268 -----GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                GD ++   F+ ++     ++L LHA  +   HP  G       + A + +TW ++
Sbjct: 178 GDVNHGDGRHNRMFREHYDC---HRLMLHASRLQFDHPITGE---AIDIRAGIDETWRNV 231

Query: 323 --GFKYDRNLYIK 333
              F +  NL ++
Sbjct: 232 MAAFNWSPNLLVR 244


>gi|45658116|ref|YP_002202.1| ribosomal large subunit pseudouridine synthase C [Leptospira
           interrogans serovar Copenhageni str. Fiocruz L1-130]
 gi|45601358|gb|AAS70839.1| ribosomal large subunit pseudouridine synthase C [Leptospira
           interrogans serovar Copenhageni str. Fiocruz L1-130]
          Length = 394

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 86/374 (22%), Positives = 149/374 (39%), Gaps = 94/374 (25%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++  +E   RLD +    + + +    QK +  G++ +  K VK    ++ G ++   P+
Sbjct: 47  LISKEESGTRLDHFLSKKFTYHSRTTWQKEITEGRILISSKTVKPGVSLKEGDLISYHPI 106

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 +  + KIL                  YED      +KP  + +   +GI  +  
Sbjct: 107 QKEEPPVRNDYKIL------------------YEDEFFVAVDKPGDLPIHP-AGI--YRK 145

Query: 131 GFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           G L +++   G+   L   HRLD+ETSG+++ A+    A  L++SF +  IQK Y + V 
Sbjct: 146 GNLLTFLKESGKFKDLFTVHRLDRETSGVILFAKNSEIASILSKSFSLGNIQKYYITKVH 205

Query: 189 G-IPKNK------KECIANWLLKKSHIGGDYVHVVKQN----------EKGANYAISHFK 231
           G  PK K      K  +++ + KK        + +K+N          EK    ++++F+
Sbjct: 206 GNFPKRKSAYGILKPDLSSKIRKKRTFVPLKFNFLKRNKKYLFENSLIEKQEEISLTYFQ 265

Query: 232 VI------------------------------------DCFAQKFCWLEMQPHTGRTHQL 255
            I                                    DC++   C    +P TGR HQ+
Sbjct: 266 KIEYDKGRESKFKFSKIEFQFKNVNNEKIKSVFLDQEKDCYSFLLC----KPITGRMHQI 321

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNK------------LYLHARYMDLPHP-EG 302
           R     +G P+ GD  Y  + K  F   I+ K              LH+  + L HP   
Sbjct: 322 RATLFSLGFPLFGDKLYGKDEKV-FLEFIEGKNPDLTTRLGMKRQALHSYAVCLNHPVTN 380

Query: 303 GRLQITAPLPAHMV 316
            +++ITAP+P   +
Sbjct: 381 QKMKITAPIPEDFL 394


>gi|325265622|ref|ZP_08132312.1| tRNA pseudouridine synthase C [Kingella denitrificans ATCC 33394]
 gi|324982892|gb|EGC18514.1| tRNA pseudouridine synthase C [Kingella denitrificans ATCC 33394]
          Length = 242

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 99/233 (42%), Gaps = 28/233 (12%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            IL   D  I V NKPA + V             L++  D  G+     HRLD+ TSGI+
Sbjct: 3   EILAQTDDYIAV-NKPADMLVHRTWLSCGETVFLLQTLRDQLGRHVFPVHRLDRPTSGIM 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK-------SHIGGD 211
           + A  R AAQ+ T  F  R ++K Y ++  G   +   CI ++ LK+        H  GD
Sbjct: 62  LFALHREAAQYFTGQFGSRLVRKTYLAIARGW-TDDAGCI-DYPLKEQLDKIADQHADGD 119

Query: 212 YVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                   E     A S   ++        ++  L + PHTGR HQ+R H  H+  PIVG
Sbjct: 120 KPAQAACTEY-RTLARSELPIVSTPRYATSRYSLLRLMPHTGRKHQIRRHLKHIFHPIVG 178

Query: 269 D--------HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           D        ++    F GN       +L LHA  +    P+   + I AP  A
Sbjct: 179 DTTHGDLRQNRAIHQFYGN------TRLLLHAESLQFTDPQQREIHIAAPTDA 225


>gi|228899885|ref|ZP_04064130.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis IBL 4222]
 gi|228964251|ref|ZP_04125371.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar sotto str. T04001]
 gi|228795446|gb|EEM42933.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar sotto str. T04001]
 gi|228859789|gb|EEN04204.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis IBL 4222]
          Length = 292

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/207 (28%), Positives = 104/207 (50%), Gaps = 23/207 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQET 154
           ++YED  + + NK A +S         H  G + + + S   K  L        RLD++T
Sbjct: 79  IVYEDDAVLIINKEANMSTIPSR---EHPTGSVANALLSHYDKQHLASTVHIVTRLDRDT 135

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D + 
Sbjct: 136 SGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGMIDAPIGRKS----DSII 191

Query: 215 VVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD    
Sbjct: 192 ERTVCEDG-QRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGD---- 244

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            N  G     ++ +  LH++ +   HP
Sbjct: 245 -NLYGGRRDEMKRQ-ALHSKSLTFYHP 269


>gi|226229096|ref|YP_002763202.1| ribosomal large subunit pseudouridine synthase A [Gemmatimonas
           aurantiaca T-27]
 gi|226092287|dbj|BAH40732.1| ribosomal large subunit pseudouridine synthase A [Gemmatimonas
           aurantiaca T-27]
          Length = 476

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/223 (29%), Positives = 101/223 (45%), Gaps = 21/223 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSKGQKPRLTHRLDQET 154
           +  ++YED  + V NKP+G+    G G       +      + D+ GQ   + HRLD +T
Sbjct: 266 EPAVVYEDDHLLVVNKPSGMLTVPGRGPTMQDCVMTRLRARYPDATGQM--VVHRLDLDT 323

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+ A+    A  L   F +R I K Y + + G+  +    I   L          +H
Sbjct: 324 SGLLLAAKDPITASALQRLFSLREIDKHYVAWLDGVVTDDHGHIHLPLRMDVDDRPRNIH 383

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHK 271
               +      A + ++V+         +   PHTGRTHQLRVHA H   +  PIVGD  
Sbjct: 384 ----DPVFGKPAHTEWQVM-ARTDGRTRVRFTPHTGRTHQLRVHAAHPDGLDAPIVGDRL 438

Query: 272 YCANFKGNFTSPIQN-KLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y        T+P ++ +L LHA  +   HP  G ++ +  P P
Sbjct: 439 Y------GRTAPDEDERLQLHAERLAFVHPVSGAKVVVEQPAP 475


>gi|315639721|ref|ZP_07894860.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           italicus DSM 15952]
 gi|315484498|gb|EFU74955.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           italicus DSM 15952]
          Length = 298

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 59/225 (26%), Positives = 100/225 (44%), Gaps = 18/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +++ED  + + NKPA +            +A  + G+ K   +   Q   +  RLD++T+
Sbjct: 80  VVFEDDHLLIVNKPANVPSIPAQYHPNQTMANRVKGYYKRK-NYPNQVVHIVTRLDRDTT 138

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDYVH 214
           G++V A+   A   L    R +   K Y +LV+    ++   + N     + IG  D   
Sbjct: 139 GLMVFAKHGFAHAKLDVQLRDKSFTKKYQALVF----DEANALENHAEIIAPIGRNDASL 194

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +Q      YA + + +   + Q+   +++Q HTGRTHQ+RVH   +GCP++GD  Y  
Sbjct: 195 IQRQVVTDGRYAKTEYWLEKKY-QQIALVDIQLHTGRTHQIRVHFASIGCPLLGDDLYGG 253

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
                       +  LH   +   HP  G  L    PLP  M + 
Sbjct: 254 RLDLGIM-----RQALHCYELHFTHPFSGEALSFVQPLPEDMARV 293


>gi|253732507|ref|ZP_04866672.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|253723788|gb|EES92517.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
          Length = 273

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 58/236 (24%), Positives = 101/236 (42%), Gaps = 34/236 (14%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  + +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDIFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED  + +  KP G+      ++  + +  H+       +DS   +P   HRLDQET G+
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHV----IYTIDSDYVEP--IHRLDQETVGL 131

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+     + L        I +IY + V  +   K + I         IG D  H  K
Sbjct: 132 LIVAKNPLMKKILDRMLEDNDITRIYKAHVKALLPLKPQTI------DMPIGKDKFHSNK 185

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +        AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y
Sbjct: 186 RRVSPTGQRAITHILTSKMIKEAVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLY 241


>gi|259145207|emb|CAY78471.1| Pus9p [Saccharomyces cerevisiae EC1118]
          Length = 462

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/173 (31%), Positives = 87/173 (50%), Gaps = 6/173 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP+GI V       Y  +   K   ++ G      +RLD+ TSG++ +
Sbjct: 190 VIFEDDNIMVIDKPSGIPVHPTG--RYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFL 247

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+T   A ++ +  + R + K Y + V G  P+   E I    LK          V + +
Sbjct: 248 AKTPKGADNIGDQLKAREVTKEYVAKVVGEFPET--EVIVEKPLKLIEPRLALNAVCQMD 305

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           EKGA +A + F  I  +  K   ++ +P TGR+HQ+RVH  ++G PI  D  Y
Sbjct: 306 EKGAKHAKTVFNRI-SYDGKTSIVKCKPLTGRSHQIRVHLQYLGHPIANDPIY 357


>gi|224122944|ref|XP_002318955.1| predicted protein [Populus trichocarpa]
 gi|222857331|gb|EEE94878.1| predicted protein [Populus trichocarpa]
          Length = 261

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 75/254 (29%), Positives = 113/254 (44%), Gaps = 58/254 (22%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           KS +LY+D  +   NKP G+              + ++ +DS  Q   L +RLD++TSG+
Sbjct: 14  KSDVLYQDQWLIAVNKPQGV--------------YCETVLDSVPQL-HLANRLDRDTSGV 58

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECI---------------ANW 201
           +V+ +    A  L ++F   +++K Y +L  G  PK +K  I               A  
Sbjct: 59  MVITKLHKVASKLVKAFTDHKVRKTYIALCIGSAPKWEKITIKSGHGRSKFGAFRVYAAS 118

Query: 202 LLKKSHIGGDYV-------HVVKQNEKGANYAISHF------------KVIDCFAQK-FC 241
            + +S  GG  V        V+  N +G+    S F             VID  A+K   
Sbjct: 119 DVGRSLPGGSTVKDMETSFEVLSINGQGSFREPSEFNSDKNILVVEEKAVIDTDAKKDEI 178

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPH 299
            +   P +GRTHQ+R+H  ++G PI GD KY     +KG       +   LHA  + L H
Sbjct: 179 LVRAFPRSGRTHQIRLHCQYLGIPIRGDVKYEGVCEWKGR----TYDGHELHAESLSLEH 234

Query: 300 PEGGR-LQITAPLP 312
           P  G+ L   APLP
Sbjct: 235 PVTGQPLMFRAPLP 248


>gi|71909763|ref|YP_287350.1| ribosomal large subunit pseudouridine synthase A [Dechloromonas
           aromatica RCB]
 gi|71849384|gb|AAZ48880.1| ribosomal large subunit pseudouridine synthase A [Dechloromonas
           aromatica RCB]
          Length = 218

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/209 (30%), Positives = 101/209 (48%), Gaps = 18/209 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           S +++ D  + V +KPA +    G G    +D  L + V ++       HRLD  TSG+L
Sbjct: 13  SPVIFADEWLIVADKPAELLSVPGRGAG--MDDCLVTRVQNEYPDALSVHRLDMSTSGLL 70

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+AR +   + L+  F+ R++ K Y ++V G+   +   I   L+       D+ +  +Q
Sbjct: 71  VLARGKEIHRQLSRLFQDRQVSKRYIAVVDGLLAEEVGEIDLPLIC------DWPNRPRQ 124

Query: 219 --NEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             +      +++ F+V   D  A     LE++P TGR+HQLRVH   +G PI+GD  Y  
Sbjct: 125 MVDFTIGKPSLTRFRVNGHDTVANT-TRLELEPITGRSHQLRVHMASLGHPILGDDLYGG 183

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              G        +L LHA  +   HP  G
Sbjct: 184 EAHGK-----AGRLLLHAMDLAFVHPATG 207


>gi|295698280|ref|YP_003602935.1| ribosomal large subunit pseudouridine synthase D [Candidatus Riesia
           pediculicola USDA]
 gi|291157095|gb|ADD79540.1| ribosomal large subunit pseudouridine synthase D [Candidatus Riesia
           pediculicola USDA]
          Length = 282

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 72/261 (27%), Positives = 122/261 (46%), Gaps = 62/261 (23%)

Query: 77  IIKEQKILDSSVNLTKHSDFL-KSI---LLYEDSKIYVFNKPAGISVQGGS--------- 123
           I+ E+ IL   ++L K    + K+I   +L+ED  I V +KP  + V  G+         
Sbjct: 21  ILGEKSILIKDIDLEKKIQCIPKNIPLKILHEDDSIIVIDKPYNLCVHPGTHHEKNTLMH 80

Query: 124 GIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            + YH    LK+        PR  + HRLD++TSG+++VA+  +    + + F+ R++ K
Sbjct: 81  ALMYHF-PILKNI-------PRAGIVHRLDKDTSGLMIVAKKSSIQNQMMKLFKSRKVYK 132

Query: 182 IYWSLVWG-----------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            Y ++V+G           I ++  E I N++        D+             A +H+
Sbjct: 133 EYEAIVYGNINSDGTIDKPIKRHPYERIKNFVC-------DF----------GRKAKTHY 175

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY----CANFKGNFTS---- 282
            V + FA  F  + +   +GR HQ RVH  ++G PIVGD+ Y        K N+ S    
Sbjct: 176 YVKEKFAN-FTRIILSLESGRHHQARVHMKYIGHPIVGDYLYQDRQIIRKKKNYISNLIK 234

Query: 283 --PIQNKLYLHARYMDLPHPE 301
              + ++  LHAR + + HP+
Sbjct: 235 IDQVISRQALHARKIKILHPQ 255


>gi|323495007|ref|ZP_08100098.1| pseudouridine synthase Rlu family protein [Vibrio brasiliensis LMG
           20546]
 gi|323310802|gb|EGA63975.1| pseudouridine synthase Rlu family protein [Vibrio brasiliensis LMG
           20546]
          Length = 231

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 56/192 (29%), Positives = 89/192 (46%), Gaps = 17/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+      V NK   +SV    G    ++   K   D+K     L HRLD+ TSGIL++
Sbjct: 4   ILFTHPDFIVINKHPNVSVHKDDGDTMLLEEVAKQTGDNK---LYLIHRLDKMTSGILLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R+ +AA  L+  F  R ++K Y ++    PK K+  I+  + +        V+      
Sbjct: 61  GRSSSAASELSRQFAERSVEKFYLAIGCNKPKKKQGLISGDMQRSRRSAWKLVN------ 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F  +     +  +L  +PHTG+THQ+RV    +G  I GD  Y A+     
Sbjct: 115 SNTNPAVTQFFSLAAMPGERLFL-CKPHTGKTHQIRVALKSLGSAIAGDPIYNASHHA-- 171

Query: 281 TSPIQNKLYLHA 292
                ++ YLHA
Sbjct: 172 -----DRGYLHA 178


>gi|221142167|ref|ZP_03566660.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus str.
           JKD6009]
 gi|304380548|ref|ZP_07363223.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|269941321|emb|CBI49718.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TW20]
 gi|302751659|gb|ADL65836.1| RluA, Pseudouridylate synthase, 23S RNA-specific [Staphylococcus
           aureus subsp. aureus str. JKD6008]
 gi|304340877|gb|EFM06802.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|329314526|gb|AEB88939.1| RluA, Pseudouridylate synthase, 23S RNA-specific [Staphylococcus
           aureus subsp. aureus T0131]
          Length = 273

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 59/236 (25%), Positives = 101/236 (42%), Gaps = 34/236 (14%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED  + +  KP G+      ++  + +  H+       +DS   +P   HRLDQET G+
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHV----IYTIDSDYVEP--IHRLDQETVGL 131

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+     + L        I +IY + V  +   K + I         IG D  H  K
Sbjct: 132 LIVAKNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTI------DMPIGKDKFHSNK 185

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +        AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y
Sbjct: 186 RCVSPTGQRAITHILTSKMIKEAVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLY 241


>gi|134045627|ref|YP_001097113.1| RluA family pseudouridine synthase [Methanococcus maripaludis C5]
 gi|132663252|gb|ABO34898.1| pseudouridine synthase, RluA family [Methanococcus maripaludis C5]
          Length = 298

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 103/230 (44%), Gaps = 39/230 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQET 154
           ++YED  + + +KP  + V     +   + G L + +      +++  K R  +RLD +T
Sbjct: 84  VIYEDDDLLIVDKPKNMVVHPTKNV---LSGTLANAISNHQKINNQNYKIRFVNRLDMDT 140

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+L++A+   + Q L +      ++KIY  +V G   +K+  I +              
Sbjct: 141 TGLLIIAKNSYSHQQLAKQMDEGILEKIYIVVVNGHLDSKEGVIEDS------------- 187

Query: 215 VVKQNEKGANYAISHF--------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +  N+ G    +S F        KVI+ F      LE++  TGRTHQ+RVH    G  I
Sbjct: 188 -IDLNDDGIKRELSTFGKISKTKYKVIEEF-NNVSVLEIKLLTGRTHQIRVHLSSFGNNI 245

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           +GD  Y        T+ +  +  LH+  +   HP     ++I + LP  M
Sbjct: 246 IGDTLYGK------TADLIERQALHSHILRFIHPITKENMEIRSKLPDDM 289


>gi|261839742|gb|ACX99507.1| pseudouridine synthase, RluA family protein [Helicobacter pylori
           52]
          Length = 237

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/202 (30%), Positives = 100/202 (49%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K W         L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWA--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L+ GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVKKEYLALIQGIIEEEQEINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y  N
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYN-N 210

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
             G+       +L LHA  + L
Sbjct: 211 EPGS-----AKRLMLHAHKISL 227


>gi|6320168|ref|NP_010248.1| Pus9p [Saccharomyces cerevisiae S288c]
 gi|3915436|sp|Q12069|PUS9_YEAST RecName: Full=tRNA pseudouridine synthase 9, mitochondrial;
           AltName: Full=tRNA pseudouridylate synthase 9; AltName:
           Full=tRNA-uridine isomerase 9; Flags: Precursor
 gi|1279680|emb|CAA96453.1| unknown [Saccharomyces cerevisiae]
 gi|1431018|emb|CAA98595.1| unnamed protein product [Saccharomyces cerevisiae]
 gi|285810994|tpg|DAA11818.1| TPA: Pus9p [Saccharomyces cerevisiae S288c]
          Length = 462

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/173 (31%), Positives = 87/173 (50%), Gaps = 6/173 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP+GI V       Y  +   K   ++ G      +RLD+ TSG++ +
Sbjct: 190 VIFEDDNIMVIDKPSGIPVHPTG--RYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFL 247

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+T   A ++ +  + R + K Y + V G  P+   E I    LK          V + +
Sbjct: 248 AKTPKGADNIGDQLKAREVTKEYVAKVVGEFPET--EVIVEKPLKLIEPRLALNAVCQMD 305

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           EKGA +A + F  I  +  K   ++ +P TGR+HQ+RVH  ++G PI  D  Y
Sbjct: 306 EKGAKHAKTVFNRI-SYDGKTSIVKCKPLTGRSHQIRVHLQYLGHPIANDPIY 357


>gi|169335105|ref|ZP_02862298.1| hypothetical protein ANASTE_01512 [Anaerofustis stercorihominis DSM
           17244]
 gi|169257843|gb|EDS71809.1| hypothetical protein ANASTE_01512 [Anaerofustis stercorihominis DSM
           17244]
          Length = 305

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 55/168 (32%), Positives = 88/168 (52%), Gaps = 11/168 (6%)

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           ++ K  K R  +RLD +TSGI+V+A+ +     +       +I K Y  +V GI  ++KE
Sbjct: 127 IEKKHFKTRFVNRLDMDTSGIVVIAKNKYVHHFIQNQSINNQIDKKYVLIVDGI-MDQKE 185

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              N  +K++  G     +V ++ K     I+ +KVI+ F +    +E +  TGRTHQLR
Sbjct: 186 GYINAPIKRAE-GHPLRRIVAEDGKEC---ITKYKVIEEF-KNHSLVEAKLITGRTHQLR 240

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           VH  ++G PI+GD  Y  N      S + +   LHA+ +   HP G +
Sbjct: 241 VHFSYVGHPILGDSLYNEN-----KSELISHQALHAKSISFVHPRGNK 283


>gi|160944255|ref|ZP_02091484.1| hypothetical protein FAEPRAM212_01764 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444437|gb|EDP21441.1| hypothetical protein FAEPRAM212_01764 [Faecalibacterium prausnitzii
           M21/2]
          Length = 231

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 111/236 (47%), Gaps = 39/236 (16%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++LYED+ + V +KPAG+S + G      +   L++  ++      + HRLD   SG++V
Sbjct: 1   MILYEDAALVVLDKPAGLSSEEG------VPAALRAHWNAPDAFVGVVHRLDTGVSGLMV 54

Query: 160 VARTRAA----AQHLTESFRMRRIQ--------------KIYWSLVWGIPKNK---KECI 198
            ART AA    ++ +T+S     +Q              K Y +++ G P  +      +
Sbjct: 55  YARTPAAAAALSRQVTQSQDAYAVQDGRAEGKAAAPQFVKQYRAIIAGAPDAQLPAAGVL 114

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            ++L K S  G   V  V +  KG   A+  ++++   A +    E+  HTGRTHQ+RV 
Sbjct: 115 RDYLFKDSRKG--RVFPVSRPRKGVREAVLEYRIL-ATAGENSLAEITLHTGRTHQIRVQ 171

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                 P+ GD KY +  KG+          L +  +   HP+ G+ +  + PLPA
Sbjct: 172 FASRRHPLYGDGKYGSRQKGSIA--------LQSCGLRFVHPDTGKPMAFSLPLPA 219


>gi|93006645|ref|YP_581082.1| pseudouridylate synthase [Psychrobacter cryohalolentis K5]
 gi|92394323|gb|ABE75598.1| tRNA pseudouridine synthase C [Psychrobacter cryohalolentis K5]
          Length = 256

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/226 (27%), Positives = 101/226 (44%), Gaps = 37/226 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLT---------- 147
           ++YED  +   NK AG+ V              +SW+D KG+     +LT          
Sbjct: 17  IIYEDEFLVAINKEAGLLVH-------------RSWLD-KGETRFAMQLTRDAVGCHVFP 62

Query: 148 -HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ TSG+L+ A++ A A+ LTE+F   ++ K Y ++V G    +         +  
Sbjct: 63  VHRLDKPTSGVLLFAKSSAVARSLTEAFTEHKVTKQYLAVVRGYMSEQGTVDYALSFQPD 122

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFA-------QKFCWLEMQPHTGRTHQLRVHA 259
            I   + ++ K  ++   +  S  ++   FA        ++  + + P TGR HQLR H 
Sbjct: 123 AIADKFANLDKPAQEAVTHWQSLAQIELPFAVSKKHDTSRYSLMRLTPETGRKHQLRRHM 182

Query: 260 LHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG 303
            H+   IVGD  +       F  T     ++ LHA+ + L HP  G
Sbjct: 183 RHLFHHIVGDTSHGDGRHNRFFRTQYGCARMLLHAQTLALSHPVTG 228


>gi|120599561|ref|YP_964135.1| pseudouridylate synthase [Shewanella sp. W3-18-1]
 gi|120559654|gb|ABM25581.1| tRNA pseudouridine synthase C [Shewanella sp. W3-18-1]
          Length = 280

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 108/240 (45%), Gaps = 23/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  I   +KPAG+ V   S +A     F ++   D  G      HRLD+ TSG+L+
Sbjct: 32  ILFEDEHIVAIHKPAGLLVHR-SYLARRERFFAMQLTRDLVGCHVFPVHRLDRPTSGVLL 90

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVK 217
            A++   A  L E F    I+K Y +LV G     +  I ++ LK     +G  +     
Sbjct: 91  FAKSSEVANALCEQFAEHSIEKQYLALVRG--NMHESGILDYPLKVELDELGDKHA---- 144

Query: 218 QNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + +K A  A++ FK +               +F  +++ P TGR HQLR H  H+  PI+
Sbjct: 145 RQDKAAQDAVTAFKPLLNAEIPYPSGRYPTSRFALVQLTPKTGRKHQLRRHMAHLRHPIL 204

Query: 268 GDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
           GD  +    +  F       N+L+L A+ +   HP    RL I   L       +  LG+
Sbjct: 205 GDTTHGDGKQNTFFREHFGINRLWLIAKKLTFTHPVTQSRLSIETELEQQWETVFTGLGW 264


>gi|163751074|ref|ZP_02158305.1| tRNA pseudouridine synthase C [Shewanella benthica KT99]
 gi|161329235|gb|EDQ00234.1| tRNA pseudouridine synthase C [Shewanella benthica KT99]
          Length = 284

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 67/240 (27%), Positives = 111/240 (46%), Gaps = 25/240 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+ED  I   +KPAG+ V   S +A     F ++   D  G      HRLD+ TSG+L+ 
Sbjct: 39  LFEDDDIVAIHKPAGLLVHR-SYLARRERFFAMQLTRDKVGCHVFPVHRLDRPTSGVLLF 97

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++   A  L E F  + I+K Y ++V G             ++   +G   V      +
Sbjct: 98  AKSSEMANTLCEQFADKTIEKHYLAIVRGNMHEAATLDYPLKVELDDLGDKNVAA----D 153

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +             + ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 154 KPAQDAMTSYQPLLNTEIPFSSGRYASSRYALVKLTPHTGRKHQLRRHMAHLRHPILGDT 213

Query: 271 KYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
            +        F+ +F+    N+L+L A+ +   HP  G R+ I A L    +  +  LG+
Sbjct: 214 THGDGKQNKFFREHFSV---NRLWLIAKQLTFNHPRTGERMVIEAELEHQWLDLFKGLGW 270


>gi|78221490|ref|YP_383237.1| tRNA pseudouridine synthase C [Geobacter metallireducens GS-15]
 gi|78192745|gb|ABB30512.1| tRNA pseudouridine synthase C [Geobacter metallireducens GS-15]
          Length = 270

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 103/227 (45%), Gaps = 22/227 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  +   +KP G+ V   S I  H   F L+   D  G++    HRLD+ TSG+L+
Sbjct: 3   ILYRDEHLVAVHKPLGLLVHR-SPIDRHETRFALQEVRDLLGRRVYPVHRLDKPTSGVLL 61

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A   A A+ L  +F    + K Y ++V G     +E + +  L +     D     + N
Sbjct: 62  FALDPAFARGLVGAFASGSVTKTYLAVVRGT--MPEEGVIDHPLAEEP---DRFEQGRGN 116

Query: 220 --EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             E+    A++ ++ +               ++  + + P TGR HQLR H  H+  PIV
Sbjct: 117 AGERAPQSAVTGYRRLADVELPVAVGRYPTSRYSLVSLSPRTGRRHQLRRHLKHLFHPIV 176

Query: 268 GDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
           GD KY       F     +  ++ LHA  + +PHP  G  L + AP+
Sbjct: 177 GDTKYGEGRHNRFFREELLTVRMLLHAVELTVPHPATGAPLTVCAPV 223


>gi|308063784|gb|ADO05671.1| hypothetical protein HPSAT_04685 [Helicobacter pylori Sat464]
          Length = 242

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/202 (30%), Positives = 100/202 (49%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRALKKEYLALAQGIIEEEQEINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y  N
Sbjct: 157 SKKGQEAVTI-IAPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYN-N 210

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
             G+       +L LHA  + L
Sbjct: 211 EPGS-----AKRLMLHAHKISL 227


>gi|217972240|ref|YP_002356991.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217497375|gb|ACK45568.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 244

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 98/216 (45%), Gaps = 18/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+DS I + +KP+G+    G     ++D      V        L HRLD  TSGI++V
Sbjct: 25  VLYQDSDILLIDKPSGLLSLSGKN-PLNLDSVHYRLVQDFPTA-TLLHRLDFGTSGIMLV 82

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  ++    LT+ F+ R I+K Y +L+ G        I   + K      D+  + K   
Sbjct: 83  ALNKSVNGLLTKQFQARTIEKRYTALLHGHIAADSGVINLPIAKDV----DHFPLQKICH 138

Query: 221 KGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NF 276
                AIS ++V++   + F   +E  P +GRTHQLR+H+   G  I+G   Y     + 
Sbjct: 139 STGKPAISEYRVLERLTEPFATRVEFTPVSGRTHQLRIHSQQFGHSILGCDLYGGVGESV 198

Query: 277 KGNFTSP--------IQNKLYLHARYMDLPHPEGGR 304
             N  +P          ++L LHA  +   HP  G 
Sbjct: 199 ADNAAAPDPDITKMTSNSRLMLHATRLAFDHPLTGE 234


>gi|328957083|ref|YP_004374469.1| pseudouridylate synthase [Carnobacterium sp. 17-4]
 gi|328673407|gb|AEB29453.1| pseudouridylate synthase [Carnobacterium sp. 17-4]
          Length = 303

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 56/207 (27%), Positives = 102/207 (49%), Gaps = 20/207 (9%)

Query: 101 LLYEDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFL--KSWVDSKGQKPRLTHRLDQE 153
           ++YED    V NKP G++     V     +A  + G+   +++ D   Q   +  RLD++
Sbjct: 80  IVYEDDHYLVVNKPYGVASVPSQVHPEGTMANRVKGYYVRQNYAD---QVIHIVTRLDRD 136

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G+++ A+   A   +    R + I K Y +L+ G     +    +  + ++    D +
Sbjct: 137 TTGLMLFAKHGYAHALMDAKLRAKEITKKYTALISGQLDKAEHGFIDAPIART---TDSI 193

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              + +E G   A++ + +   F Q    +++Q HTGRTHQ+RVH  H+G P++GD  Y 
Sbjct: 194 ITRRAHESGKE-ALTEYWIKGSFPQA-TLVDIQLHTGRTHQIRVHFTHIGHPLMGDDLYG 251

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
              K N+ +    +  LH R ++  HP
Sbjct: 252 GE-KNNWIT----RQALHCRELNFSHP 273


>gi|151941961|gb|EDN60317.1| tRNA-pseudouridine synthase [Saccharomyces cerevisiae YJM789]
          Length = 462

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/173 (31%), Positives = 87/173 (50%), Gaps = 6/173 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP+GI V       Y  +   K   ++ G      +RLD+ TSG++ +
Sbjct: 190 VIFEDDNIMVIDKPSGIPVHPTG--RYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFL 247

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+T   A ++ +  + R + K Y + V G  P+   E I    LK          V + +
Sbjct: 248 AKTPKGADNIGDQLKAREVTKEYVAKVVGEFPET--EVIVEKPLKLIEPRLALNAVCQMD 305

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           EKGA +A + F  I  +  K   ++ +P TGR+HQ+RVH  ++G PI  D  Y
Sbjct: 306 EKGAKHAKTVFNRI-SYDGKTSIVKCKPLTGRSHQIRVHLQYLGHPIANDPIY 357


>gi|319401115|gb|EFV89334.1| RNA pseudouridylate synthase family protein [Staphylococcus
           epidermidis FRI909]
          Length = 274

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 67/271 (24%), Positives = 119/271 (43%), Gaps = 42/271 (15%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +L ++  S ++ ++++     N +++G  V IP      N++                  
Sbjct: 27  DLHQLNMSKEILINEEYGTLLNNVKTGDYVEIPTPNEVSNYL----------------PS 70

Query: 96  FLKSILLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +  + + YED  + +  KP G+      ++  + +  H+       VDS+  +P   HRL
Sbjct: 71  YRYAQIYYEDDDLAIVMKPKGVKTHPNDLKESNTLMNHV----IYTVDSEYVEP--IHRL 124

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           DQET G+L+VA+     + L        I +IY + V  +   K + I         IG 
Sbjct: 125 DQETVGLLIVAKNPLMKKILDRMLEYNEITRIYKANVKALLPIKPQTI------DMPIGK 178

Query: 211 DYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D  H  K+        AI+H        +  C L+++  TGRTHQ+RVH   +G P++GD
Sbjct: 179 DKFHSNKRRISNTGQRAITHIIDSKMIKEGVCQLDIKLDTGRTHQIRVHLAEIGHPVIGD 238

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             Y        TS ++ +L L++  ++  HP
Sbjct: 239 PLYG-------TSTLR-QLELNSHQIEFTHP 261


>gi|261839435|gb|ACX99200.1| hypothetical protein HPKB_0602 [Helicobacter pylori 52]
          Length = 327

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 104/227 (45%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLEFKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNHLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L    PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLCFKVPLLKDMLE 300


>gi|217033764|ref|ZP_03439190.1| hypothetical protein HP9810_7g45 [Helicobacter pylori 98-10]
 gi|216943813|gb|EEC23253.1| hypothetical protein HP9810_7g45 [Helicobacter pylori 98-10]
          Length = 327

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 53/227 (23%), Positives = 105/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLEFKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      +L+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVYLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|15611957|ref|NP_223608.1| hypothetical protein jhp0890 [Helicobacter pylori J99]
 gi|11136009|sp|Q9ZKP5|Y956_HELPJ RecName: Full=Uncharacterized RNA pseudouridine synthase jhp_0890;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|4155455|gb|AAD06458.1| putative [Helicobacter pylori J99]
          Length = 242

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 60/202 (29%), Positives = 98/202 (48%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K W         L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWA--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y ++V GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVKKEYLAIVQGIIEEEREINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y   
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLY--- 208

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
              N       +L LHA  + L
Sbjct: 209 ---NNEPSSAKRLMLHAHKIAL 227


>gi|299537608|ref|ZP_07050901.1| putative RNA pseudouridine synthase yhcT [Lysinibacillus fusiformis
           ZC1]
 gi|298726977|gb|EFI67559.1| putative RNA pseudouridine synthase yhcT [Lysinibacillus fusiformis
           ZC1]
          Length = 279

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/203 (26%), Positives = 92/203 (45%), Gaps = 16/203 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED    + +KP G++         H  ++  +    +  G      HRLD+ T G+L
Sbjct: 78  VVYEDDHCLIVSKPKGMATHPNDARDTHTCMNHIMAHIKEQGGIYAEHVHRLDKGTQGLL 137

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+   A          + I + Y + V G  +     IA        IG D  H  ++
Sbjct: 138 LVAKHPLAKSIFDRMIEEKTIIRTYAAEVQGNLRTSSGTIAEP------IGKDRHHATRR 191

Query: 219 N-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              K   +A++H++V+  + +  C + +   TGRTHQ+RVH  ++G PI+GD  Y A   
Sbjct: 192 VVSKTGQHAVTHYEVVARY-KNSCVVHLILETGRTHQIRVHLAYIGHPIIGDTMYGAR-- 248

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
                 + +   LHA  ++  HP
Sbjct: 249 ----ETVSDDYELHAIQLEFDHP 267


>gi|284931618|gb|ADC31556.1| Pseudouridine synthase [Mycoplasma gallisepticum str. F]
          Length = 311

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 140/307 (45%), Gaps = 48/307 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQK-----ILRSGQVRVDKKRVKFNNRI-QS 61
           ++  V ND E +RLD +   +      +NL +     ++ +  V+V+KK V  NN + + 
Sbjct: 3   KHTFVNNDSEKIRLDIFLTYN------LNLSRNKTSFLILNDLVKVNKKLVNKNNFVLKV 56

Query: 62  GQVVRIP---PVINAL-NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           G VV +     + N + N I+   K LD               ++YED  + + NKP  +
Sbjct: 57  GDVVELEYEESIFNKVSNEILPFNKKLD---------------IVYEDDDLIIVNKPTNM 101

Query: 118 SVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                +      D  L   +  +K QK  L HRLD++T+G++V  +   + + + E    
Sbjct: 102 LSHPTTH--NEPDTLLNCLMYYNKKQKVYLAHRLDKDTTGLIVATKNFKSLEKIQEQI-T 158

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK---QNEKGANYAISHFKVI 233
           +RI K Y+  +   P N+   + +     + IG    H +K   +N K    AI+   V+
Sbjct: 159 KRIMKRYYLAIVHYPFNELRAVID-----APIGYLKDHDLKFGVENTKNPKNAITKIYVL 213

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D   +K+  ++ +  TGRTHQ+RVH   +   I+ D  Y    KG        K +LHA 
Sbjct: 214 DQ-NKKYALIKCELLTGRTHQIRVHMDFIKHNIINDPLYGV--KGE--QRTDYKQFLHAY 268

Query: 294 YMDLPHP 300
            ++L HP
Sbjct: 269 QLELTHP 275


>gi|206967561|ref|ZP_03228517.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
 gi|206736481|gb|EDZ53628.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
          Length = 297

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 109/220 (49%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           ++YED  + + NK A +S +         +   L S  D +       +  RLD++TSG+
Sbjct: 84  IVYEDDAVLIINKEANMSTIPSREHPTRSVANALLSHYDKQHLASTVHIVTRLDRDTSGL 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +    
Sbjct: 144 MLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGRIVEREGMIDAPIGRKS----DSIIERT 199

Query: 218 QNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 200 VCEDG-QRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGDSLY---- 252

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 253 -GGRRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 290


>gi|115529387|ref|NP_001070221.1| RNA pseudouridylate synthase domain-containing protein 1 [Danio
           rerio]
 gi|123908280|sp|Q08C69|RUSD1_DANRE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 1
 gi|115313685|gb|AAI24363.1| Zgc:153465 [Danio rerio]
          Length = 293

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 56/174 (32%), Positives = 84/174 (48%), Gaps = 13/174 (7%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA      F+ RR+ K Y +LV G    +   +   + K
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGQAYRCFKDRRVTKAYLALVRGTVTEENLSLDFAIGK 120

Query: 205 KSHIGGDYVHVVK-----QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            +  G  ++   +     +N K     ++  +       +   + +QP TGRTHQLRVH 
Sbjct: 121 NTTEGKTHMMCTEGTEGCENPKPCQTEVTVLEYGTYDGDQVTKVLLQPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLP 312
             +G PIVGD+ Y         SP   ++ LHA ++ +P H E   + +TAP P
Sbjct: 181 SAIGHPIVGDYTYSLRTDN---SPY--RMMLHAYFLHIPLHNEP--IHVTAPDP 227


>gi|88801890|ref|ZP_01117418.1| ribosomal large subunit pseudouridine synthase A [Polaribacter
           irgensii 23-P]
 gi|88782548|gb|EAR13725.1| ribosomal large subunit pseudouridine synthase A [Polaribacter
           irgensii 23-P]
          Length = 556

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 115/244 (47%), Gaps = 26/244 (10%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H++ E   +D+++ L   S   +  ++YED+ + V +KP  +    G  I   +   +
Sbjct: 329 LTHML-EDLPMDANLLLENLSKDKELEVIYEDAAMIVVHKPTELLSVPGKEIKDAVYTRM 387

Query: 134 KS-WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           K  + ++ G  P + HRLD  TSGIL++ +T+ A + L   F  R I+K Y +L+ G   
Sbjct: 388 KEKYPNATG--PLIVHRLDMSTSGILLLTKTKEANKILQSQFVNRTIKKRYVALLDGNLS 445

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                I      K  +  D     KQ  +      A + ++V+     K   +   P TG
Sbjct: 446 EDSGTI------KLPLRVDLDDRPKQLVDFSYGKAAETTWEVLGRENGK-TRVYFYPVTG 498

Query: 251 RTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
           RTHQLRVHA H   +  PIVGD  Y            +N+L+LHA +++  HP    ++ 
Sbjct: 499 RTHQLRVHAAHKKGLNTPIVGDDLYGTK---------ENRLHLHAEFIEFLHPTTNKKMS 549

Query: 307 ITAP 310
            T P
Sbjct: 550 FTVP 553


>gi|326938929|gb|AEA14825.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar chinensis CT-43]
          Length = 275

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 104/207 (50%), Gaps = 23/207 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQET 154
           ++YED  + + +K A +S         H  G + + + S   K  L        RLD++T
Sbjct: 62  IVYEDDAVLIIDKEANMSTIPSR---EHPTGSVANAILSHYDKQHLASTVHIVTRLDRDT 118

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D + 
Sbjct: 119 SGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGMIDAPIGRKS----DSII 174

Query: 215 VVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD    
Sbjct: 175 ERTVCEDG-QRAVTHFKVIDSTYDKTHVALELE--TGRTHQIRVHMAHIGHPLLGD---- 227

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            N  G     ++ +  LH++ +   HP
Sbjct: 228 -NLYGGRRDEMKRQ-ALHSKSLTFYHP 252


>gi|163801147|ref|ZP_02195047.1| pseudouridine synthase Rlu family protein [Vibrio sp. AND4]
 gi|159175496|gb|EDP60293.1| pseudouridine synthase Rlu family protein [Vibrio sp. AND4]
          Length = 230

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/199 (31%), Positives = 95/199 (47%), Gaps = 17/199 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+      V NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL++
Sbjct: 4   ILHTQPDFLVINKHPNVSVHKDDGDTMLLQEVAKQ---SGDEQLYLIHRLDKMTSGILLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   AA  L+++F  R ++K Y ++    PK K+  +   + +        V     N 
Sbjct: 61  GRNAKAASALSQAFADREVEKFYLAIGSKKPKKKQGLVIGDMERSRRSSWKLV-----NS 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K  N AI+ F  +   + +  +L  +PHTG+THQ+RV    +G  IVGDH Y A   GN 
Sbjct: 116 K-TNPAITQFFSLAAESGERLFL-CKPHTGKTHQIRVALKSVGSGIVGDHIYNA---GND 170

Query: 281 TSPIQNKLYLHARYMDLPH 299
                ++ YLHA  +  P+
Sbjct: 171 A----DRGYLHAFSLCFPY 185


>gi|108563155|ref|YP_627471.1| hypothetical protein HPAG1_0730 [Helicobacter pylori HPAG1]
 gi|107836928|gb|ABF84797.1| pseudouridine synthase D [Helicobacter pylori HPAG1]
          Length = 327

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 104/227 (45%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVVHKAPSVK---EPTLVDWLEFKNYELSNLGLKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      HL+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLARNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++   Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKIRYSKSEFTSLLTSQNGMDLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|325568271|ref|ZP_08144638.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158040|gb|EGC70193.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus ATCC 12755]
          Length = 284

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/208 (29%), Positives = 99/208 (47%), Gaps = 29/208 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK---SWVDSKGQKPRLTHRLDQETSGI 157
           +L+ED  + V NKPA +       +    D  L    +++  K Q+P + HRLD+ETSG+
Sbjct: 83  VLFEDEHLLVLNKPARVKTHPNQPL--EADTLLNDAAAYLAPKQQQPYVVHRLDKETSGV 140

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       L      ++I + Y + V G    + + IA  + +  H   D    + 
Sbjct: 141 VLFAKNPLVLPILGRMLENKQIFRRYQATVLG-KLTQDQTIAKKIGRDRH---DRRKRII 196

Query: 218 QNEKGANYAISHFKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  G + A++H  +    AQ+     +C LE    TGRTHQ+RVH   +G P+VGD  Y
Sbjct: 197 DSRNGQS-AVTHVTI--AHAQQKTTNVYCVLE----TGRTHQIRVHLASIGHPVVGDPLY 249

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
                 N  +P   +L LH   + L HP
Sbjct: 250 -----QNKPAP---RLLLHGYELHLEHP 269


>gi|308183108|ref|YP_003927235.1| hypothetical protein HPPC_04830 [Helicobacter pylori PeCan4]
 gi|308065293|gb|ADO07185.1| hypothetical protein HPPC_04830 [Helicobacter pylori PeCan4]
          Length = 242

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 55/177 (31%), Positives = 90/177 (50%), Gaps = 25/177 (14%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVKKEYLALTQGIIEEEREINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTIY 208


>gi|229189393|ref|ZP_04316412.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           ATCC 10876]
 gi|228594104|gb|EEK51904.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           ATCC 10876]
          Length = 292

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 109/220 (49%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           ++YED  + + NK A +S +         +   L S  D +       +  RLD++TSG+
Sbjct: 79  IVYEDDAVLIINKEANMSTIPSREHPTRSVANALLSHYDKQHLASTVHIVTRLDRDTSGL 138

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +    
Sbjct: 139 MLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDAPIGRKS----DSIIERT 194

Query: 218 QNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 195 VCEDG-QRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGDSLY---- 247

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 248 -GGGRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 285


>gi|190405049|gb|EDV08316.1| tRNA pseudouridine synthase [Saccharomyces cerevisiae RM11-1a]
          Length = 462

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/173 (31%), Positives = 87/173 (50%), Gaps = 6/173 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP+GI V       Y  +   K   ++ G      +RLD+ TSG++ +
Sbjct: 190 VIFEDDNIMVIDKPSGIPVHPTG--RYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFL 247

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+T   A ++ +  + R + K Y + V G  P+   E I    LK          V + +
Sbjct: 248 AKTPRGADNIGDQLKAREVTKEYVAKVVGEFPET--EVIVEKPLKLIEPRLALNAVCQMD 305

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           EKGA +A + F  I  +  K   ++ +P TGR+HQ+RVH  ++G PI  D  Y
Sbjct: 306 EKGAKHAKTVFNRI-SYDGKTSIVKCKPLTGRSHQIRVHLQYLGHPIANDPIY 357


>gi|323450233|gb|EGB06115.1| hypothetical protein AURANDRAFT_29586 [Aureococcus anophagefferens]
          Length = 244

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/186 (33%), Positives = 82/186 (44%), Gaps = 28/186 (15%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN---- 200
           R+ HRLD ETSG+LV A+T AAA  L  SFR    +    +     PK +K  +A     
Sbjct: 68  RVVHRLDFETSGVLVFAKTSAAAAALCASFRADAAEASGAAATAAAPKMRKVYVAAVRGE 127

Query: 201 --------WLLKKSHI-----GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                   W L          G            GA  A + ++     A     L ++P
Sbjct: 128 LAGSGEWAWPLAPDDAARAADGKPRYAACDAGAPGAKAATTLWE-----AAGASRLRLRP 182

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGR+HQLRVH L  G PIVGD  Y     G   +  + +L LHA  +DL HP  G R+ 
Sbjct: 183 QTGRSHQLRVHCLAAGHPIVGDPLY-----GPPPADHEPRLCLHAAELDLTHPGTGDRVT 237

Query: 307 ITAPLP 312
             +P P
Sbjct: 238 FASPAP 243


>gi|313124222|ref|YP_004034481.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ND02]
 gi|312280785|gb|ADQ61504.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ND02]
          Length = 282

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 58/183 (31%), Positives = 83/183 (45%), Gaps = 16/183 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++YED  + V +KP G      QG +G A      L       G  P + HRLD  T G+
Sbjct: 83  VVYEDENVLVIDKPKGQKTHPNQGENGTA------LNDCASYLGYSPYIVHRLDMLTGGL 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+  A    L      + +++ Y + V     +  + I +       IG D     K
Sbjct: 137 LLVAKNPAVVPILNRQLTSKTLRRDYLATV-----DLNKEIPDQGTIDLPIGQDPADQRK 191

Query: 218 QNEKGANY-AISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +  +     A+SHF+V+    +K    L +   TGRTHQ+RVH    G PIVGD  Y  N
Sbjct: 192 RQVRADGLRAVSHFQVLKKDEEKKQAKLLVTLETGRTHQIRVHLSASGWPIVGDPLYNPN 251

Query: 276 FKG 278
           F G
Sbjct: 252 FAG 254


>gi|300865112|ref|ZP_07109937.1| Pseudouridine synthase [Oscillatoria sp. PCC 6506]
 gi|300336883|emb|CBN55087.1| Pseudouridine synthase [Oscillatoria sp. PCC 6506]
          Length = 562

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 111/227 (48%), Gaps = 36/227 (15%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQG-----GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++YED  +   NKP+G+ SV G        +   +   L       G      HRLD ET
Sbjct: 356 IIYEDEWLIAVNKPSGLLSVPGRYRDRQDSVLSRLRQLLPD-----GMNIIPVHRLDLET 410

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS-HIGGDYV 213
           SGI+++AR+    + L+  F+ + ++K+Y +++ G        + ++  + S  + G+  
Sbjct: 411 SGIMLLARSLPIYRELSSQFQHKLVKKVYEAVLSG------NVVNDYCGEISLPLWGNPE 464

Query: 214 HVVKQN---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIV 267
           H   Q    E+G   +++ F+VI     ++  +E  P TGRTHQ+RVHA     +G PI+
Sbjct: 465 HRPYQQVDIERGKP-SLTRFQVI-AREGEYTRVEFMPLTGRTHQIRVHASDKRGLGIPIL 522

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAPL 311
           GD  Y             ++L+LHAR +   HP+ G+   L++  P 
Sbjct: 523 GDRLYGCQADA-------SRLHLHARELYFEHPQLGKNINLEVETPF 562


>gi|86159798|ref|YP_466583.1| pseudouridine synthase RluD [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85776309|gb|ABC83146.1| Pseudouridine synthase, RluD [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 300

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 77/330 (23%), Positives = 130/330 (39%), Gaps = 56/330 (16%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M      + + V  +    RLDRW             + ++ +G+VR+  K    + ++ 
Sbjct: 1   MGTPAAPELLRVPREAAGARLDRWLAAAL-GATAERARWLVETGRVRIRGKTCSPHRKLF 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G                 E+  ++        +      +LY+D+   V  KP G++V+
Sbjct: 60  GG-----------------EEVAVERPAPRAAEASGPALAVLYDDADCLVVAKPPGLAVE 102

Query: 121 GGSGI------------AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            G+              A+ +DG            P L HRLD++TSG L++AR   A  
Sbjct: 103 AGAPGGASAVAAASRLGAFDVDGR---------AAPGLAHRLDRDTSGALLLARHDRALA 153

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK--GANYA 226
            L  +F    I+K Y +LV G P  +           +  G D     +   +      A
Sbjct: 154 ALRAAFEAGAIEKEYLALVAGAPPPEGRL-------DTPYGRDPEDPRRFTTRFPSPRRA 206

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
              +KV     +    L ++  TGRTHQ+RV     G P++GD  Y    +G   +    
Sbjct: 207 RLSWKVERPL-RGAALLRVRLETGRTHQIRVQLAEAGFPVLGDAVY--GVRGEAIA---- 259

Query: 287 KLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           +  LHA  +  P P +G R+++ AP+P  +
Sbjct: 260 RQALHAERLAFPRPSDGARVEVRAPVPEDL 289


>gi|312884948|ref|ZP_07744638.1| tRNA pseudouridine synthase C [Vibrio caribbenthicus ATCC BAA-2122]
 gi|309367425|gb|EFP94987.1| tRNA pseudouridine synthase C [Vibrio caribbenthicus ATCC BAA-2122]
          Length = 241

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 105/242 (43%), Gaps = 25/242 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IVFQDDYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDKPTSGVLIF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    + K Y ++V G  +          ++   I   +  +    +
Sbjct: 64  ALSSEIASSVMPMFANHEMNKTYHAIVRGWIEQAGVLDYPLKVELDKIADKHATL----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ ++ I               ++C +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KEAQDAITDYQPIAKTELPIAMGKFPTTRYCMMELKPRTGRKHQLRRHMAHLRHPIIGDT 179

Query: 271 -----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                K+   F+    S   ++L LHA  +   HP  G    +  + A + +TW  L   
Sbjct: 180 SHGDGKHNKLFRHELDS---HRLLLHASSLSFIHPFTGE---SVVINAGLDETWARLAEV 233

Query: 326 YD 327
           +D
Sbjct: 234 FD 235


>gi|266622468|ref|ZP_06115403.1| ribosomal large subunit pseudouridine synthase family protein
           [Clostridium hathewayi DSM 13479]
 gi|288865823|gb|EFC98121.1| ribosomal large subunit pseudouridine synthase family protein
           [Clostridium hathewayi DSM 13479]
          Length = 239

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 83/180 (46%), Gaps = 10/180 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED +I V  KPAGI  Q        +   +K  ++S   K       + HRLD+   
Sbjct: 7   ILYEDDQIIVVEKPAGIESQSSRTFEPDMVSEVKKHINSLSPKKGDPYVGVIHRLDKPVG 66

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GILV  +T+ AA  L++     + +K Y ++V G P        ++L K      +   +
Sbjct: 67  GILVFGKTKEAAGALSKQISEHQTEKRYLAVVCGKPVENFGTYVDYLWKDGK--NNISKI 124

Query: 216 VKQNEKGANYAISHFKV---IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V +    A  A   ++V   ++      C +E+   TGR HQ+RV     G P++GD KY
Sbjct: 125 VDKGITDAKRAELSYRVLAELEGEGGPLCLMEIDLKTGRHHQIRVQLSGHGTPLLGDLKY 184


>gi|221067278|ref|ZP_03543383.1| pseudouridine synthase [Comamonas testosteroni KF-1]
 gi|220712301|gb|EED67669.1| pseudouridine synthase [Comamonas testosteroni KF-1]
          Length = 220

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 64/213 (30%), Positives = 102/213 (47%), Gaps = 17/213 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +YED  + V +KP+G+    G G     D      +   G    + HRLDQ TSG++++A
Sbjct: 7   VYEDEHLLVLDKPSGLLCVPGRGPDKQ-DCLSLRALQHFGDA-LVVHRLDQATSGLVIMA 64

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC--IANWLLKKSHIGGDY----VHV 215
           R     + L ++F  R++ K Y ++V G  +   E      W L    I  D+    + V
Sbjct: 65  RNPVVQRQLGQAFAERQVDKRYIAVVAGDLQAGPETADAQGWQLIDLPIAADWERRPLRV 124

Query: 216 VKQNEKGANYAISHFKVIDCFAQK--FCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +  N +    + + ++ ++   Q+   C  + + P TGRTHQLR+H    G  I+GD  Y
Sbjct: 125 I--NHENGKSSQTLWQALEQTGQQEMTCTRVLLSPLTGRTHQLRLHMAASGHAILGDALY 182

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            A+      SP   +L LHA  ++L HP  G L
Sbjct: 183 -ADETVASASP---RLLLHATALELVHPVTGTL 211


>gi|146292442|ref|YP_001182866.1| pseudouridylate synthase [Shewanella putrefaciens CN-32]
 gi|145564132|gb|ABP75067.1| tRNA pseudouridine synthase C [Shewanella putrefaciens CN-32]
          Length = 275

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 108/240 (45%), Gaps = 23/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  I   +KPAG+ V   S +A     F ++   D  G      HRLD+ TSG+L+
Sbjct: 27  ILFEDEHIVAIHKPAGLLVHR-SYLARRERFFAMQLTRDLVGCHVFPVHRLDRPTSGVLL 85

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVK 217
            A++   A  L E F    I+K Y +LV G     +  I ++ LK     +G  +     
Sbjct: 86  FAKSSEVANALCEQFAEHSIEKQYLALVRG--NMHESGILDYPLKVELDELGDKHA---- 139

Query: 218 QNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + +K A  A++ FK +               +F  +++ P TGR HQLR H  H+  PI+
Sbjct: 140 RQDKAAQDAVTAFKPLLNAEIPYPSGRYPTSRFALVQLTPKTGRKHQLRRHMAHLRHPIL 199

Query: 268 GDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
           GD  +    +  F       N+L+L A+ +   HP    RL I   L       +  LG+
Sbjct: 200 GDTTHGDGKQNTFFREHFGINRLWLIAKKLTFTHPVTQSRLSIETELEQQWETVFTGLGW 259


>gi|332535815|ref|ZP_08411548.1| tRNA pseudouridine synthase C [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332034793|gb|EGI71331.1| tRNA pseudouridine synthase C [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 254

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 102/245 (41%), Gaps = 35/245 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D      NKP+G+ V       +     ++   D  GQ     HRLD+ TSG+L+ 
Sbjct: 15  ILYQDENYVAINKPSGLLVHRSFLDKHETQFAMQMLRDQLGQHVFPVHRLDRPTSGVLLF 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIP----------KNKKECIANWLL------K 204
           A +  AA+ + + F    I K Y +LV G            K + + IA+         +
Sbjct: 75  ALSSEAARDMNQLFIEGTIAKRYLALVRGFAPESVFLDKPLKEELDKIADKFADQDKAPQ 134

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           ++    + +H          Y    + +++CF          P TGR HQ+R H  H+  
Sbjct: 135 EAQTQFNCLHQAALPIPIGKYPTVRYSLVECF----------PKTGRKHQIRRHLKHLSL 184

Query: 265 PIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           PI+GD  +  N     F+ +F      +L L A  +   HP     + I APL   M++ 
Sbjct: 185 PIIGDVNHGDNQHNQFFREHFEL---RRLMLFATELSFVHPYSNESITIKAPLGEDMLEI 241

Query: 319 WDSLG 323
              LG
Sbjct: 242 CKQLG 246


>gi|88797158|ref|ZP_01112748.1| probable pseudouridine synthase [Reinekea sp. MED297]
 gi|88780027|gb|EAR11212.1| probable pseudouridine synthase [Reinekea sp. MED297]
          Length = 214

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/213 (29%), Positives = 101/213 (47%), Gaps = 26/213 (12%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +IL   D+  +V  KP G +VQ  +     ++     W++ +G      HRLD+ TSG+L
Sbjct: 7   TILTATDA-YFVIVKPTGWTVQRDAQAPSVLE-----WLNDQGHTAFPVHRLDKPTSGLL 60

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VART  A + L+  F   R++K Y ++    P+ K+  +   +         +  + +Q
Sbjct: 61  LVARTTEANRALSLGFAEGRVEKTYLAISDRRPRKKQGWVRGDMAPSRR--SQWKLLREQ 118

Query: 219 NEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           N    N AI+ F+ +  D   + F    + P TG+THQLRV    +G P++GD  Y    
Sbjct: 119 N----NPAITRFRSVSLDDGERGFV---LYPKTGKTHQLRVALKSLGSPMLGDTLYGGT- 170

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
                    ++LYLHA  +     EG RL   A
Sbjct: 171 -------PADRLYLHAWRLAFDF-EGERLSYQA 195


>gi|262276531|ref|ZP_06054340.1| tRNA pseudouridine synthase C [Grimontia hollisae CIP 101886]
 gi|262220339|gb|EEY71655.1| tRNA pseudouridine synthase C [Grimontia hollisae CIP 101886]
          Length = 243

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/218 (27%), Positives = 96/218 (44%), Gaps = 22/218 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  +   NKP+G+ V             +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 7   ILYRDEWLVAVNKPSGMLVHRSWLDKGETRFVMQTLRDQIGQHVFPLHRLDRPTSGVLLF 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F  R I K Y ++V G    ++E   ++ LK+    +   Y      
Sbjct: 67  ALSSEMAAEMMPKFAGRDIHKTYHAVVRGW--IQEEATLDYPLKEELDKVADKYA----T 120

Query: 219 NEKGANYAISHFKVIDCFAQ-----------KFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            E  A  A++ ++ +   A+           ++  +EM+PHTGR HQLR H  H+  PI+
Sbjct: 121 AEPEAKEAVTEYRPV-AHAELPIPLGRYQSCRYTLVEMKPHTGRKHQLRRHMHHLSHPII 179

Query: 268 GDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGG 303
           GD  +           + N  +L LHA      HP  G
Sbjct: 180 GDVNHGDGRHNRLFREVFNCHQLLLHASRTAFQHPVTG 217


>gi|302550785|ref|ZP_07303127.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           viridochromogenes DSM 40736]
 gi|302468403|gb|EFL31496.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           viridochromogenes DSM 40736]
          Length = 314

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 78/329 (23%), Positives = 138/329 (41%), Gaps = 28/329 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++   G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAGGKVTVDGSVVGKSERVH 59

Query: 61  SGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA--G 116
            G    V +P     +  + +  + ++   +        K +       +     P   G
Sbjct: 60  GGAWLEVEMPQAPAPVQVVAEPVEGMEIVHDDDDVVVIAKPV------GVAAHPSPGWTG 113

Query: 117 ISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +V GG +   Y I            ++  + HRLD  TSG++VVA++  A   L   F+
Sbjct: 114 PTVIGGLAAAGYRIS------TSGAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQFK 167

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y +LV G P      I   + +  H   DY   V  + K    +++H+ +I+ 
Sbjct: 168 ERTVDKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTADGK---PSVTHYDLIEA 222

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARY 294
           F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +   + +LHA  
Sbjct: 223 F-RAASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADP--TLAKRLHLTRQWLHAVR 279

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP  G+ ++  +  PA + K  D +
Sbjct: 280 LGFEHPGDGQWVEFASDYPADLQKALDQV 308


>gi|317154375|ref|YP_004122423.1| pseudouridine synthase [Desulfovibrio aespoeensis Aspo-2]
 gi|316944626|gb|ADU63677.1| pseudouridine synthase [Desulfovibrio aespoeensis Aspo-2]
          Length = 215

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/210 (30%), Positives = 96/210 (45%), Gaps = 26/210 (12%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSG------IAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           ++++ D    V +KP G+    G G      +   +   L   +D         HRLDQ+
Sbjct: 9   VIVHRDPLFVVVDKPGGLLSVPGRGPENQDCVVNRLKALLPECLDQPS-----VHRLDQD 63

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+LV+A T  A + L+  F  R + K Y +L+ G+       I             +V
Sbjct: 64  TSGLLVLALTAQAHRALSVQFMERLVGKRYVALIDGVLGPDSGIIELAFRLDPDNRPYHV 123

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDH 270
           +  +Q + G    ++ ++ +    Q    +E  P TGRTHQLR+H+ H   +G PIVGD 
Sbjct: 124 YDPEQGKPG----VTRWRKLGV-EQGRTRVEFMPLTGRTHQLRLHSAHEKGLGHPIVGDR 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            Y     G  T+P Q  L LHA  +   HP
Sbjct: 179 LY-----GTGTAPGQ--LRLHASALRFRHP 201


>gi|228951685|ref|ZP_04113787.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar kurstaki str. T03a001]
 gi|228807970|gb|EEM54487.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar kurstaki str. T03a001]
          Length = 292

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 109/220 (49%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           ++YED  + + NK A +S +         +   L S  D +       +  RLD++TSG+
Sbjct: 79  IVYEDDAVLIINKEANMSTIPSREHPTRSVANALLSHYDKQHLASTVHIVTRLDRDTSGL 138

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +    
Sbjct: 139 MLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDAPIGRKS----DSIIERT 194

Query: 218 QNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 195 VCEDG-QRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGDSLY---- 247

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 248 -GGRRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 285


>gi|149919776|ref|ZP_01908253.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
 gi|149819383|gb|EDM78814.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
          Length = 322

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 83/324 (25%), Positives = 140/324 (43%), Gaps = 35/324 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPP 69
           VV+ DE+   L    +     +++   + ++R+G+V+VD + R     R+++G +V + P
Sbjct: 9   VVDEDEDGATLAAVVRGLMDGLSWNKSRDLVRTGRVQVDGQMRFDPAERLRAGALVEVNP 68

Query: 70  VINALNHI-IKEQKILDSSVNLT---KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                +   + E +++     +    K +  L       D +  +  +   I+++   G 
Sbjct: 69  TGRRRSAPPLPEDRLVFVDSEVVVVRKPAGLLSVPWDDRDDRDTLIER-TRITLREREGT 127

Query: 126 AYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                          G++ RL    RLD++TSG+LV ARTR A + L   FR   I + Y
Sbjct: 128 -------------RSGERDRLGVVQRLDKDTSGLLVFARTRRARKALEAQFRAHTIFRRY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV---IDCFAQKF 240
            +LV G    K     ++L+     G       K   K A  AI+  +V   +D      
Sbjct: 175 VALVHGA--AKAGVHESYLIADRGDGLRGSWRGKSPPKAAKKAITKVRVEEKLDGATLIS 232

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPH 299
           C LE    TGR HQ+R+H    G P+VG+  Y   ++G    +P   +  LHA  +   H
Sbjct: 233 CQLE----TGRQHQIRIHLAEAGHPLVGEPVYGRGYRGRRLPAP---RPMLHAASLGFRH 285

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P G R ++  AP P       + L
Sbjct: 286 PVGDRPVRFEAPPPDDFCAALEQL 309


>gi|15611749|ref|NP_223400.1| hypothetical protein jhp0682 [Helicobacter pylori J99]
 gi|11136015|sp|Q9ZL98|Y745_HELPJ RecName: Full=Uncharacterized RNA pseudouridine synthase jhp_0682;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|4155249|gb|AAD06270.1| putative [Helicobacter pylori J99]
          Length = 327

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 105/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W+ S+       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVVHKAPSVK---EPTLVDWLKSQNYELSNLGLKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+       L+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVCLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNGMDLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N      S  + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN---GVLSKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|219126856|ref|XP_002183664.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217404901|gb|EEC44846.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 235

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 101/230 (43%), Gaps = 35/230 (15%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRL-THRLDQETSGIL 158
           ++Y DS I V NKP  + +V G    +  +D     + ++   K  +  HRLD  TSGI+
Sbjct: 3   IVYHDSDIVVVNKPPDVLTVPGIHSRSCVLDLVHDRFGEAVQDKAHMIVHRLDMATSGIV 62

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSH---------- 207
           +  RT    + +   FR R + K Y +L+ G  P +K     +  L++ H          
Sbjct: 63  LFGRTLNITKRMQAIFRDRLVLKTYQALLMGHFPIDKGTI--DLPLQRDHEYPPFMRIST 120

Query: 208 --IGGDYVHVVKQNE---------KGANYAISHFKVID-CF--AQKFCWLEMQPHTGRTH 253
                D V  VK  +         K    + + F+V+   F     F  +E+ P TGRTH
Sbjct: 121 PTSEADAVQAVKDLQQHGWKKLIRKKPKPSQTSFRVLARSFRNGLPFTRMELVPVTGRTH 180

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           QLRVH   +G PIVGD  Y      +   P +  + LHA  +   HP  G
Sbjct: 181 QLRVHCAALGYPIVGDPTY------DEYVPNEKAMCLHAALLQCEHPTTG 224


>gi|219685683|ref|ZP_03540497.1| RNA pseudouridine synthase family protein [Borrelia garinii Far04]
 gi|219672799|gb|EED29824.1| RNA pseudouridine synthase family protein [Borrelia garinii Far04]
          Length = 315

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 81/305 (26%), Positives = 140/305 (45%), Gaps = 44/305 (14%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-----LRSGQVRVDKKRVKF 55
           M L  Y+   V++ND    RLD         I  +N  K      +R G +R++  +  F
Sbjct: 1   MRLDKYILLEVLDNDN-GKRLDSIL------IKILNFSKARIIKHIRKGDIRLNGLKPSF 53

Query: 56  NNRIQSGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
           + R+  G  + +   ++  L+  + E     S+++       ++  ++YEDS + V +K 
Sbjct: 54  SYRVCKGDKIYLYKSLVQNLHLAMGE--CYKSNIDF----QCIRKRIIYEDSDLLVMDKQ 107

Query: 115 AGISVQGG-SGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
            GI V GG + + + ++ +L +  + S   KP   HRLD+ TSGI++ A+    A+ L+ 
Sbjct: 108 RGILVHGGKNSLDFLVNSYLLREDLRSLSFKPSAVHRLDRNTSGIIIFAKNINVARKLSA 167

Query: 173 SFRMRRIQKIYWSLVWGIPKN----KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           +F    + K Y++++ G  K+    K     N  LKK+ +  D         K +  AI+
Sbjct: 168 AFSSGSVTKKYFAILLGEVKSTVIYKNHLFRNQRLKKTFVLED---------KDSINAIT 218

Query: 229 HFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
             KV    + K   L E+   TG THQ+R        P++ D KY   FK       ++ 
Sbjct: 219 --KVNPILSSKRATLAEIVIETGFTHQIRSQCSFNEHPLINDKKYYNKFK-------KSD 269

Query: 288 LYLHA 292
            +LHA
Sbjct: 270 YFLHA 274


>gi|163814966|ref|ZP_02206353.1| hypothetical protein COPEUT_01116 [Coprococcus eutactus ATCC 27759]
 gi|158449649|gb|EDP26644.1| hypothetical protein COPEUT_01116 [Coprococcus eutactus ATCC 27759]
          Length = 238

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 59/216 (27%), Positives = 102/216 (47%), Gaps = 12/216 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLT--HRLD 151
           +K  +L+EDS I V  KP G+  Q     +  +   LK  +   +++ ++P L   HRLD
Sbjct: 6   MKLNILHEDSDIIVAVKPCGVPTQPDKTNSESMVSMLKLRIYERENRKEEPYLVPIHRLD 65

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +   G++V A+T  AA  L++      + K Y +++ G   N +  + ++LL  +    +
Sbjct: 66  RPVGGVMVFAKTPEAAAALSKQSEDGTMLKYYQAILTGELPNDQGVLKDYLLHDTK--DN 123

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               V ++  GA Y+   ++V+D          ++ ++  TGR HQ+R       C I G
Sbjct: 124 VTKTVDKDTPGAKYSELEYEVLDVMDTDEGVLSYVLVELITGRHHQIRAQFAKRKCGIWG 183

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           D KY  N K   T     ++ LHA  ++  HP  G 
Sbjct: 184 DTKY--NPKFQKTKKKYKEIGLHASRLEFDHPTTGE 217


>gi|226324130|ref|ZP_03799648.1| hypothetical protein COPCOM_01908 [Coprococcus comes ATCC 27758]
 gi|225207679|gb|EEG90033.1| hypothetical protein COPCOM_01908 [Coprococcus comes ATCC 27758]
          Length = 172

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 57/188 (30%), Positives = 92/188 (48%), Gaps = 22/188 (11%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLK 204
           + HRLDQ  SGILV ART AAA++L +  +  + +K Y ++V G +P +    + ++L+K
Sbjct: 1   MIHRLDQPVSGILVFARTPAAAKNLNQQLQNDQFEKYYQAVVCGSLPDSGT--LTDYLVK 58

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMG 263
                 +   +  +N  GA  A+  +++++         +++   TGR HQ+RV     G
Sbjct: 59  DGRT--NTSRICSKNTPGAKKAVLSYEILETSEVTGLSVVQIHLGTGRHHQIRVQMAGAG 116

Query: 264 CPIVGDHKYCANF---KGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
            P+ GD+KY   F   +G F  PI     L A  +   HP  G R++   P        W
Sbjct: 117 APLWGDNKYNPEFVNKRGYF--PIA----LRAFRLSFCHPTTGKRMEFEVPC------NW 164

Query: 320 DSLGFKYD 327
           + L  K D
Sbjct: 165 EQLETKAD 172


>gi|330445141|ref|ZP_08308793.1| tRNA pseudouridine 65 synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328489332|dbj|GAA03290.1| tRNA pseudouridine 65 synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 245

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 64/253 (25%), Positives = 114/253 (45%), Gaps = 33/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  +   NKPAG+ V      ++     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYRDEYLIAVNKPAGMLVHRSWLDSHETVFVMQTLRDQIGQHVFPLHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
             +   A  +   F  R + K Y ++V G  K  +  + ++ LK      +   +  +N 
Sbjct: 65  GLSSEIAAEMMPMFAGRDMHKTYHAVVRGWIK--EAAVLDYPLKV-----ELDKIADKNA 117

Query: 220 --EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             EK A  A++ ++ +               ++C +EM+P TGR HQLR H  H+   I+
Sbjct: 118 SEEKEAQPAVTAYEPLATVETDIAVGRYSTSRYCLVEMKPETGRKHQLRRHMHHLSHHII 177

Query: 268 -----GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                GD ++   F+ ++     ++L LHA  +   HP  G       + A + +TW  +
Sbjct: 178 GDVNHGDGRHNRMFREHYDC---HRLMLHASRLQFAHPITGE---PIDIRADIDETWQRV 231

Query: 323 --GFKYDRNLYIK 333
              F +  +L ++
Sbjct: 232 MSAFNWSSDLLVR 244


>gi|188527777|ref|YP_001910464.1| hypothetical protein HPSH_05040 [Helicobacter pylori Shi470]
 gi|188144017|gb|ACD48434.1| hypothetical protein HPSH_05040 [Helicobacter pylori Shi470]
 gi|308062271|gb|ADO04159.1| hypothetical protein HPCU_05030 [Helicobacter pylori Cuz20]
          Length = 242

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 62/202 (30%), Positives = 100/202 (49%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRALKKEYLALAQGIIEEEQEINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y  N
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYN-N 210

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
             G+       +L LHA  + L
Sbjct: 211 EPGS-----AKRLMLHAHKIAL 227


>gi|153001908|ref|YP_001367589.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151366526|gb|ABS09526.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 245

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 62/216 (28%), Positives = 98/216 (45%), Gaps = 18/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+DS I + +KP+G+    G     ++D      V        L HRLD  TSGI++V
Sbjct: 26  VLYQDSDILLIDKPSGLLSLSGKN-PLNLDSVHYRLVQDFPTA-TLLHRLDFGTSGIMLV 83

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  ++    LT+ F+ R ++K Y +L+ G        I   + K      D+  + K   
Sbjct: 84  ALNKSVNGLLTKQFQARTVEKRYTALLHGHIAADSGVINLPIAKDC----DHFPLQKICH 139

Query: 221 KGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NF 276
                AIS ++V++   + F   +E  P +GRTHQLR+H+   G  I+G   Y     + 
Sbjct: 140 STGKPAISEYRVLERLTEPFATRVEFTPVSGRTHQLRIHSQQFGHSILGCDLYGGVGESV 199

Query: 277 KGNFTSPIQN--------KLYLHARYMDLPHPEGGR 304
             N  +P  +        +L LHA  +   HP  G 
Sbjct: 200 ADNAAAPDPDITKMTNNSRLMLHATRLAFDHPITGE 235


>gi|323356542|ref|YP_004222938.1| pseudouridylate synthase, 23S RNA-specific [Microbacterium
           testaceum StLB037]
 gi|323272913|dbj|BAJ73058.1| pseudouridylate synthase, 23S RNA-specific [Microbacterium
           testaceum StLB037]
          Length = 307

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 58/217 (26%), Positives = 100/217 (46%), Gaps = 14/217 (6%)

Query: 113 KPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           KPAG++       +G + +        +       ++  + HRLD  TSG++VVA+T  A
Sbjct: 94  KPAGVAAHPSVGWEGPTVLGALAAAGFRIATSGPAERRGVVHRLDAGTSGLMVVAKTERA 153

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
              L  +F+ R + KIY ++V G P      I   + +  H    +  V    +     +
Sbjct: 154 YTLLKSAFKEREVDKIYHAVVQGHPDPLSGTIDAPIGRHPHHSWKFAVVPDGKD-----S 208

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++H++ ++ F  +   LE+   TGRTHQ+RVH      P VGD  Y A+   +    ++ 
Sbjct: 209 VTHYETLEAF-PRASLLEIHLETGRTHQIRVHMAAHRHPCVGDPLYGADPTLSARLGLER 267

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + +LHA  +   HP  G  +   +  PA + K  + L
Sbjct: 268 Q-WLHAHRLAFTHPATGEWVGFESAYPADLAKALEIL 303


>gi|194221090|ref|XP_001491378.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 3 [Equus caballus]
          Length = 352

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 55/200 (27%), Positives = 91/200 (45%), Gaps = 14/200 (7%)

Query: 89  NLTKHS--DFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKP 144
           NL++    D L++ ++ +   +   NKP G+ V G  G      +   L   +   GQ+ 
Sbjct: 70  NLSREELVDVLRAAVVDQKGPLVTLNKPQGLPVTGKPGELTLLSVLPELSQGLGLGGQEL 129

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIAN 200
           +L H   +ETSG+++++     A  L + F    R +R    Y ++  GIP   +  I  
Sbjct: 130 QLVHASGKETSGLVLLSTCPQTASRLQKFFIHSRRSQRPTATYCAVTDGIPATSEGKIQA 189

Query: 201 WLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
            L  +   G D V  VK   +     G    +SHF+V+         +++QP T    QL
Sbjct: 190 ALKLEHTDGVDLVVPVKSPSRKDILEGVKRTLSHFRVV-ATGSGCALVQLQPLTAFPSQL 248

Query: 256 RVHALHMGCPIVGDHKYCAN 275
           +VH +   CP++GDH Y A 
Sbjct: 249 QVHMVLELCPVLGDHTYSAR 268


>gi|45358573|ref|NP_988130.1| RluA family pseudouridine synthase [Methanococcus maripaludis S2]
 gi|44921331|emb|CAF30566.1| Pseudouridine synthase:Pseudouridine synthase, Rlu. Related protein
           [Methanococcus maripaludis S2]
          Length = 297

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 72/294 (24%), Positives = 132/294 (44%), Gaps = 55/294 (18%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K  +  ++ V+ K +   ++++  + V +  +   +N+I  E        NLT +   
Sbjct: 36  IKKFDKENKIFVNSKNISLKSKLKENETVSVE-IDYGINNITPE--------NLTLN--- 83

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV------DSKGQKPRLTHRL 150
               ++YED  + + +K   + V     +   + G L + +      +++  K R  +RL
Sbjct: 84  ----VIYEDDDLLIVDKSKNMVVHPTKNV---LSGTLANAISNHQKINNQNYKIRFVNRL 136

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D +T+G+L+VA+   + Q L +      ++KIY ++V G            L  K  I  
Sbjct: 137 DMDTTGLLIVAKNSYSHQQLAKQMDEGILEKIYIAVVNG-----------HLDLKEGIIE 185

Query: 211 DYVHVVKQNEKGANYAISHF--------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           D + +   NE G    +S+F        KVI+   +    LE+   TGRTHQ+RVH    
Sbjct: 186 DSIDL---NENGIKRELSNFGKISKTKYKVIEEL-KNASVLEINLLTGRTHQIRVHLSST 241

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           G  I+GD  Y        TS + ++  LH+  +   HP    +++I + LP  M
Sbjct: 242 GNYIIGDTLYGE------TSKLIDRQALHSHILRFIHPITKEKIEIISKLPDDM 289


>gi|312866863|ref|ZP_07727076.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
 gi|311097646|gb|EFQ55877.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
          Length = 287

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 97/216 (44%), Gaps = 29/216 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + S+V   G    + HRLD+ETSG ++ A
Sbjct: 84  LYQDEHVIIVNKPEGMKTHANEPTEISLLNHVSSYV---GSTCYVVHRLDKETSGAILFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + IQ+ YW+L+ G    K       ++ K  IG D     K+  +
Sbjct: 141 KNPFILPILNRILEDKNIQREYWALIQGSLAQKT------IVYKDKIGRDRHDRRKRLVD 194

Query: 220 EKGANYA---ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            +   YA   ++  K I   +   C L+    TGRTHQ+RVH  H G PIVGD  Y    
Sbjct: 195 PRKGQYAETQVTQLKKIGRNSLVKCQLK----TGRTHQIRVHLSHHGHPIVGDPLY---- 246

Query: 277 KGNFTSPIQ-NKLYLHARYMDLPHPEG-GRLQITAP 310
                +P +  +L LHA  +   +P     +Q+ AP
Sbjct: 247 -----NPARGERLMLHAHRLTFTNPLTLETIQVEAP 277


>gi|149280788|ref|ZP_01886893.1| tRNA pseudouridine synthase C [Pedobacter sp. BAL39]
 gi|149228467|gb|EDM33881.1| tRNA pseudouridine synthase C [Pedobacter sp. BAL39]
          Length = 235

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 101/217 (46%), Gaps = 14/217 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  +   NKP G+ V   S IA     F L+   D   +     HRLD++T GIL+
Sbjct: 4   ILYEDEHLIAINKPHGLLVHRSS-IANDAKEFALQLLRDQVNKHVSPVHRLDRKTGGILL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH--IGGDYVHVVK 217
            A  + A   + + F+   + K Y +++ G   ++ +   N+ L K +  I   +   V 
Sbjct: 63  FAFDKEAEIAMHQQFQNGEVTKKYMAILRGHAPDQMDI--NYPLAKENGTIQEAFTSFVT 120

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +   A  A+   K       ++  +E  P TGR HQLR H  H+  PI+GD K+  N +
Sbjct: 121 LDR--AELAVPFGK---HETSRYSLVEASPTTGRMHQLRRHFAHIFYPIIGDRKHGCNKQ 175

Query: 278 GNFTSPI--QNKLYLHARYMDLPHPEGGR-LQITAPL 311
             F         + LHA  ++  HP   R + I+APL
Sbjct: 176 NRFFKEQWGMTTMLLHASALEFTHPVTKRKIFISAPL 212


>gi|152991961|ref|YP_001357682.1| ribosomal large subunit pseudouridine synthase D [Sulfurovum sp.
           NBC37-1]
 gi|151423822|dbj|BAF71325.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Sulfurovum sp. NBC37-1]
          Length = 245

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 54/197 (27%), Positives = 89/197 (45%), Gaps = 28/197 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  I   NKPA +        +Y I   ++           L HRLD++TSG+L++
Sbjct: 60  ILYEDEDIIAVNKPAQVD-------SYEIQDAIEG--------AELLHRLDRDTSGVLLL 104

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R R   +   + F+ RR++K Y + V G+     E        K    G    ++    
Sbjct: 105 GRNREFIERAIKEFKNRRVEKHYVAWVDGVIYETVEIDEPIFTVKK---GKAFSMIDPVR 161

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               + + H + +     K   +++   TGRTHQ+RVH  H+G PIVGD +Y +  +   
Sbjct: 162 GKKAHTVVHPEEVQG---KKSKVKIDITTGRTHQIRVHLAHIGHPIVGDEQYGSRTQA-- 216

Query: 281 TSPIQNKLYLHARYMDL 297
                 ++ LH+  M +
Sbjct: 217 -----KRILLHSAKMKI 228


>gi|317011193|gb|ADU84940.1| hypothetical protein HPSA_04800 [Helicobacter pylori SouthAfrica7]
          Length = 242

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 54/177 (30%), Positives = 90/177 (50%), Gaps = 25/177 (14%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K W         L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALLKPPFIE-------SYDLVSFFKGWT--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVKKEYLALAQGIVEEEQEINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            K+ ++     I+  K+I+    K   L+++  TGRTHQ+RVH  H+  PI+GD  Y
Sbjct: 157 SKKGQEAITI-IAPLKIIN----KKTLLKVEIKTGRTHQIRVHLKHINHPIIGDTLY 208


>gi|312864071|ref|ZP_07724307.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
 gi|322517537|ref|ZP_08070406.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           vestibularis ATCC 49124]
 gi|311100484|gb|EFQ58691.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
 gi|322123797|gb|EFX95371.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           vestibularis ATCC 49124]
          Length = 289

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 87/205 (42%), Gaps = 28/205 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQGGS----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           LYEDS + V NKP G+   G       +  H+  + +       Q   + HRLD ETSG 
Sbjct: 84  LYEDSHLIVVNKPEGMKTHGNEPTEIALLNHVSAYCR-------QTCYVVHRLDMETSGA 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+       L      + IQ+ YW+L  G  + K+    + + +  H   D    V 
Sbjct: 137 VIFAKNPFILPILNRLLEDKMIQRQYWALTEGKFQTKETVYNDKIGRDRH---DRRKRVV 193

Query: 218 QNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              KG  A   ++  K     +   C L+    TGRTHQ+RVH  H G  I+GD  Y   
Sbjct: 194 DPRKGQVAYTTVTRLKAFKGASLVNCQLK----TGRTHQIRVHLAHHGHAILGDPLYSHR 249

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                     ++L LHA  +   HP
Sbjct: 250 --------PASRLMLHAHTLSFTHP 266


>gi|229177719|ref|ZP_04305094.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           172560W]
 gi|228605774|gb|EEK63220.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           172560W]
          Length = 292

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 109/220 (49%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           ++YED  + + NK A +S +         +   L S  D +       +  RLD++TSG+
Sbjct: 79  IVYEDDAVLIINKEANMSTIPSREHPTRSVANALLSHYDKQHLASTVHIVTRLDRDTSGL 138

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +    
Sbjct: 139 MLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDAPIGRKS----DSIIERT 194

Query: 218 QNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 195 VCEDG-QRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGDSLY---- 247

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 248 -GGRRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 285


>gi|91792903|ref|YP_562554.1| pseudouridylate synthase [Shewanella denitrificans OS217]
 gi|91714905|gb|ABE54831.1| tRNA pseudouridine synthase C [Shewanella denitrificans OS217]
          Length = 298

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 68/239 (28%), Positives = 114/239 (47%), Gaps = 21/239 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I   +KPAG+ V   S +A     F ++   D  G      HRLD+ TSG+L+
Sbjct: 54  ILYQDDDIVAIHKPAGLLVHR-SYLARKERFFAMQLTRDLIGCHVFPVHRLDRPTSGVLL 112

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQ 218
            A++   A++L E F   +I+K Y +LV G   N  E  + ++ L+      D      +
Sbjct: 113 FAKSSEVARNLCEQFAEHKIKKDYLALVRG---NMHEAGLLDYPLRVEL--DDVADKHAK 167

Query: 219 NEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A + ++ +               +F  +++ PHTGR HQLR H  H+  PI+G
Sbjct: 168 ADKPAQEAQTSYQPLLNSEIPFSSGRYPTSRFALIKLSPHTGRKHQLRRHMAHLRHPILG 227

Query: 269 DHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           D  +    +  F+      N+L+L A+ +   HP  G+ + I   +    + T+  LG+
Sbjct: 228 DTTHGDGKQNKFSREHFGVNRLWLIAKRLSFTHPVTGKPMTIETQIEQQWLATFALLGW 286


>gi|238796600|ref|ZP_04640107.1| tRNA pseudouridine synthase C [Yersinia mollaretii ATCC 43969]
 gi|238719578|gb|EEQ11387.1| tRNA pseudouridine synthase C [Yersinia mollaretii ATCC 43969]
          Length = 257

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 99/222 (44%), Gaps = 17/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+      ++QK Y ++V G              +   I   +     + +
Sbjct: 64  ALSSDVARALSLQLEQHQMQKTYHAVVRGYVLEGGTVDYEMTEELDKIADKF----SRPD 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
           K    +++H+  +               +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYLPLAQVEVPVAIGRYETARFSLVELKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 270 -HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
            H      +G       ++L LHA ++ L HP  G  L +TA
Sbjct: 180 THGDLRQNRGIAQHFDCSRLMLHASHLALNHPVTGEALSLTA 221


>gi|222823615|ref|YP_002575189.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           lari RM2100]
 gi|222538837|gb|ACM63938.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           lari RM2100]
          Length = 320

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 95/222 (42%), Gaps = 22/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLD 151
           +LYED  + V NK   I V G S +    +  L  W+  KG          +  L HRLD
Sbjct: 78  ILYEDDDVLVLNKAPNIVVHGASSVK---EATLVDWLLHKGYTLSNLNGEHRAGLVHRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG +++A+   A Q L      + + + Y +L     KN K      +++      +
Sbjct: 135 KGTSGAIIIAKNNQAHQFLANQLLDKSMGRFYLALSELPLKNDKMSNEKAIMR---CPNN 191

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  +  N K      +    I+  + K C L   + +TGRTHQ+R H       I+GD 
Sbjct: 192 RLKKITTNTKNPLAKNAKTDFINLLSAKNCSLIAAKLYTGRTHQIRTHLADFNRYILGDE 251

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPL 311
            Y   +KG       N++ LHA  +   HP    L  I AP+
Sbjct: 252 LY--GYKGKIK---YNRVMLHAYLIYFIHPRTKELMFIKAPM 288


>gi|228938421|ref|ZP_04101031.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar berliner ATCC 10792]
 gi|228971300|ref|ZP_04131928.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar thuringiensis str. T01001]
 gi|228977911|ref|ZP_04138292.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis Bt407]
 gi|228781828|gb|EEM30025.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis Bt407]
 gi|228788450|gb|EEM36401.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar thuringiensis str. T01001]
 gi|228821283|gb|EEM67298.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar berliner ATCC 10792]
          Length = 292

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 104/207 (50%), Gaps = 23/207 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQET 154
           ++YED  + + +K A +S         H  G + + + S   K  L        RLD++T
Sbjct: 79  IVYEDDAVLIIDKEANMSTIPSR---EHPTGSVANAILSHYDKQHLASTVHIVTRLDRDT 135

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D + 
Sbjct: 136 SGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGMIDAPIGRKS----DSII 191

Query: 215 VVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD    
Sbjct: 192 ERTVCEDG-QRAVTHFKVIDSTYDKTHVALELE--TGRTHQIRVHMAHIGHPLLGD---- 244

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            N  G     ++ +  LH++ +   HP
Sbjct: 245 -NLYGGRRDEMKRQ-ALHSKSLTFYHP 269


>gi|90578254|ref|ZP_01234065.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio angustum S14]
 gi|90441340|gb|EAS66520.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio angustum S14]
          Length = 557

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 60/203 (29%), Positives = 96/203 (47%), Gaps = 18/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  + + NKPA      G  I   +   +++        P + HRLD  TSG++V+
Sbjct: 356 IVYQDDAMVIVNKPAEFLSVPGKTITDSVYSRMQAMF-PNSDSPLIVHRLDMSTSGLMVI 414

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A T+ A + L + F  R ++K Y +L+ G  ++    I ++ ++          V  Q  
Sbjct: 415 ALTKDAHKALQKQFIERTVEKRYVALLEGNSESDSGLI-DFPMRVDLDDRPRQIVCYQYG 473

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFK 277
           K A       +  +   + + +    P TGRTHQLRVH+ H   M  PIVGD  Y    K
Sbjct: 474 KPAQTTWEVLERKNGRTKVYYY----PKTGRTHQLRVHSAHIKGMNMPIVGDDLYGQ--K 527

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
           G       ++L LHA+Y+   HP
Sbjct: 528 G-------DRLCLHAQYLAFNHP 543


>gi|317178897|dbj|BAJ56685.1| hypothetical protein HPF30_0588 [Helicobacter pylori F30]
          Length = 327

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 53/227 (23%), Positives = 104/227 (45%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLEFKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      +L+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVYLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L    PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLHFKVPLLKDMLE 300


>gi|269101936|ref|ZP_06154633.1| tRNA pseudouridine synthase C [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268161834|gb|EEZ40330.1| tRNA pseudouridine synthase C [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 259

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 59/218 (27%), Positives = 101/218 (46%), Gaps = 28/218 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G+ V      ++     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 18  ILYQDEYLVAVNKPSGMLVHRSWLDSHETVFVMQTLRDQIGQHVFPLHRLDRPTSGVLLF 77

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A +   A  +   F  R + K Y ++V G    K+  + ++ LKK     +   +  +N 
Sbjct: 78  ALSSEMAAEMMPKFAGRDVHKTYHAVVRGW--VKEAAVLDYPLKK-----ELDKIADKNA 130

Query: 220 --EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             E+ A  A++ +  I               ++  +EM+P TGR HQLR H  H+   I+
Sbjct: 131 SKEQEAQPAVTAYAPIAKVEVPIAVGRYSCSRYSLVEMKPETGRKHQLRRHMHHLSHHII 190

Query: 268 -----GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
                GD ++   F+ N+     ++L LHA  +   HP
Sbjct: 191 GDVNHGDGRHNRMFRDNYDC---HRLMLHASRIQFEHP 225


>gi|229078499|ref|ZP_04211059.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock4-2]
 gi|228704815|gb|EEL57241.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock4-2]
          Length = 292

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 109/220 (49%), Gaps = 18/220 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           ++YED  + + NK A +S +         +   L S  D +       +  RLD++TSG+
Sbjct: 79  IVYEDDAVLIINKEANMSTIPSREHPTRSVANALLSHYDKQHLASTVHIVTRLDRDTSGL 138

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +    
Sbjct: 139 MLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDAPIGRKS----DSIIERT 194

Query: 218 QNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 195 VCEHG-QRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGDSLY---- 247

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 248 -GGRRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 285


>gi|149750888|ref|XP_001496449.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 1 [Equus caballus]
          Length = 316

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 85/181 (46%), Gaps = 9/181 (4%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA      F+ RR+ K Y +LV G  +  +  ++  + +
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYRCFKERRVTKAYLALVRGHIQESQMTVSYAIGR 120

Query: 205 KSHIGGDYVHVVKQNEKGANY--AISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHA 259
            S  G  +   ++  +   N   +++   V++           + +QP TGRTHQLRVH 
Sbjct: 121 NSTEGRAHTMCIEGTQGCENPKPSLTELVVLELGLYAGDPVSKVLLQPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKT 318
             +G P+VGD  Y     G    P   ++ LHA Y+ +P H E   +  + P    +   
Sbjct: 181 SALGHPVVGDLTY-GQASGGEDQPF--RMMLHAFYLRIPTHTECVEVCTSDPFVPALDPC 237

Query: 319 W 319
           W
Sbjct: 238 W 238


>gi|327541913|gb|EGF28421.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification (RluA-like) protein [Rhodopirellula baltica
           WH47]
          Length = 214

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 58/209 (27%), Positives = 98/209 (46%), Gaps = 14/209 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +L++     V NKP G+      G         + +  +      LT  HRLD+  SG++
Sbjct: 4   ILWQCHACVVVNKPVGLPTTSPKGTDSLESCLREQFAQAGNPVSYLTAVHRLDRPVSGLV 63

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++A  + AA+ L+E FR+R +QK Y ++V G  +   K+E   + + K +      V +V
Sbjct: 64  LIALRKKAARLLSEQFRLRHVQKKYIAMVQGNALEACKQEPWHDTIAKLTDEA--RVEIV 121

Query: 217 KQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +      A +    ++  ++     +E++P TGR HQLR+ + H G PIVGD  Y   
Sbjct: 122 GPDSTDGRQAETKVSFLEYDSESDTSRIELRPVTGRMHQLRIQSAHRGHPIVGDPLY--- 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                T+  ++ L L A  +    P  GR
Sbjct: 179 ----GTAEDESTLRLVAAKLSFRDPTNGR 203


>gi|317177424|dbj|BAJ55213.1| hypothetical protein HPF16_0616 [Helicobacter pylori F16]
          Length = 327

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 53/227 (23%), Positives = 105/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLEFKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      +L+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVYLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNHLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|224588366|gb|ACN58990.1| ribosomal large subunit pseudouridine synthase D [uncultured
           bacterium BLR19]
          Length = 171

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 40/129 (31%), Positives = 69/129 (53%), Gaps = 5/129 (3%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+  SG+++ A+ RA  ++L+E F  R+++K Y +    +P + K  + +W  K+  
Sbjct: 13  HRLDRPVSGVVLFAKQRAVLKNLSEQFAGRKVKKFYQAFTEQMPASAKGRLEHWHRKEKK 72

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y   V   EK    A   ++V+   + +F W  ++ HTG+ HQ+R     +GCPI+
Sbjct: 73  KAVLYDKEVPYAEK----ATLEYEVVPISSGRFVW-TIELHTGKYHQIRAQLASVGCPII 127

Query: 268 GDHKYCANF 276
           GD  Y +  
Sbjct: 128 GDIVYGSTL 136


>gi|109947248|ref|YP_664476.1| pseudouridine synthase [Helicobacter acinonychis str. Sheeba]
 gi|109714469|emb|CAJ99477.1| pseudouridine synthase [Helicobacter acinonychis str. Sheeba]
          Length = 326

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 56/230 (24%), Positives = 112/230 (48%), Gaps = 23/230 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W+++K       G K R  + HRLD
Sbjct: 80  VIFEDDDLLVLNKPPNLVVHKAPSVK---EPTLVDWLEAKNYQLSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE---CIANWLLKKSHI 208
           ++TSG +V+A+      +L+E  + + + + Y +L+   P ++KE    +  +L +  + 
Sbjct: 137 KDTSGGIVIAKNNFTHVYLSEQLKTKTMGRYYIALL-STPLSRKEEKISVECYLTRNPN- 194

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             + + ++   ++ + Y+ S F  +         +  + +TGRTHQ+RVH  ++   I+G
Sbjct: 195 --NRLKMMAIKKEKSRYSKSEFTSLLTSQNNLNLIGAKLYTGRTHQIRVHLEYLNRHIIG 252

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           D+ Y  N         + ++ LHA  ++  HP+   +L    PL   M++
Sbjct: 253 DNLYGLN---EALPKEEIRIMLHAYLIEFKHPKSEQKLCFKVPLLKDMLE 299


>gi|120611810|ref|YP_971488.1| ribosomal large subunit pseudouridine synthase A [Acidovorax
           citrulli AAC00-1]
 gi|120590274|gb|ABM33714.1| ribosomal large subunit pseudouridine synthase A [Acidovorax
           citrulli AAC00-1]
          Length = 239

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 103/243 (42%), Gaps = 28/243 (11%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           +N  +  Q + D+               L+ D  + V  KP+G+    G G         
Sbjct: 1   MNAALPAQALADADAGAPPGC-------LHADDDLLVLAKPSGLLCVPGRGPDKQDCLSA 53

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           ++ +   G    + HRLDQ TSGI+V+AR   A + L ++F  R++ K Y ++V   P+ 
Sbjct: 54  RATLHWPGAC--IVHRLDQATSGIVVMARHAQAQRALGDAFAARQVHKRYVAVVHA-PRP 110

Query: 194 KKECIANWLLKKSHIGGDYVH-----VVKQNEKGANYAISHFKVIDCFAQKFCW------ 242
             +  A W      I  D+       VV     G   +++ ++          W      
Sbjct: 111 AGDG-AAWREIDMPIAADWERRPLRVVVPHGAPGGKASLTRWRPAVPGDGAGTWPAADGT 169

Query: 243 --LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++P TGRTHQLRVH   +G PI+GD  Y           +  +L LHA+++   HP
Sbjct: 170 LRVLLEPVTGRTHQLRVHMAAVGQPILGDTLYAL----PAVQALAPRLLLHAQHIAFAHP 225

Query: 301 EGG 303
             G
Sbjct: 226 RTG 228


>gi|269114915|ref|YP_003302678.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hominis]
 gi|268322540|emb|CAX37275.1| Ribosomal large subunit pseudouridine synthaseD (RNA
           pseudouridylate synthase, RNA-uridine isomerase )
           [Mycoplasma hominis ATCC 23114]
          Length = 297

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 74/305 (24%), Positives = 130/305 (42%), Gaps = 37/305 (12%)

Query: 37  LQKILRSGQVRVDK--------KRVKFNNRIQSGQVVRIPPVINALNHIIKE------QK 82
           + KI+ +   R+DK         R      I++G V      IN    ++KE      ++
Sbjct: 1   MLKIISNYSDRIDKYVANNSEISRNDIKELIENGAVFVNSIKINKPKFVVKEGDEILIER 60

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFL 133
           +LD  + +   +  L   ++YE     + NKP+G+ V    G         + YH   F 
Sbjct: 61  LLDKQIKVEPQNIHLD--IVYECDDYLIINKPSGLVVHPAPGHHDNTLVNALMYH---FK 115

Query: 134 KSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +  D  G  +  + HR+D++TSG+L++A+   A  +     +   I++ Y+++V G   
Sbjct: 116 NNLSDVNGLLRMGVVHRIDKDTSGLLLIAKNNKAHNYFASLLKTHEIKRSYYAIVEGKIA 175

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           N++  I   + + +     Y  V + N K A   ++  K      + F  ++    TGRT
Sbjct: 176 NEELHIELPIGRDTKNRQKYA-VSETNSKPAYTIVNVVKYFKMNNKDFSLVKCNLKTGRT 234

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           HQ+RVH  ++  P+ GD  Y     G+       +  LHA  +D     G      A +P
Sbjct: 235 HQIRVHLAYIKHPVYGDPIY-----GHKIDDFNQR--LHAFALDFVDLNGNNKHFEAEMP 287

Query: 313 AHMVK 317
             M K
Sbjct: 288 EIMKK 292


>gi|226941069|ref|YP_002796143.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
 gi|226715996|gb|ACO75134.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 222

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 52/175 (29%), Positives = 87/175 (49%), Gaps = 12/175 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L++D+ + V +KPAG+    G G        L + V +      + HRLD  TSG++V A
Sbjct: 18  LHQDAALLVVDKPAGLLTVPGRGPDKQ--DCLLTRVRADFPDAEIVHRLDMATSGLVVFA 75

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           R     + L  +F  R++ K Y ++V G P + +  I   L+       D+ +  +Q  +
Sbjct: 76  RGLLHQKCLMRAFAERKVDKRYVAVVAGRPPSNRGDINLPLIT------DWPNRPRQKID 129

Query: 220 EKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +    +++ + V+           L+++P TGRTHQLRVH   +G PI+GD  Y
Sbjct: 130 AEAGKPSLTRYLVLASLTDPLPCSRLQLEPVTGRTHQLRVHLDAIGHPILGDPLY 184


>gi|262065871|ref|ZP_06025483.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           periodonticum ATCC 33693]
 gi|291380458|gb|EFE87976.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           periodonticum ATCC 33693]
          Length = 288

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 102/225 (45%), Gaps = 30/225 (13%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-------PRLTHRLDQETS 155
           YED  + + NK   I V         +D  L + V +  +K       PR  +RLD  TS
Sbjct: 77  YEDENLLIVNKEPYIIVHPTQK---KVDKTLANAVVNYFEKTLGKTLVPRFYNRLDMNTS 133

Query: 156 GILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           G++++A+   T+A  Q  TE      ++K Y  +  GI +     I    L    IG D 
Sbjct: 134 GLIIIAKNAYTQAFLQDKTE------VKKTYKVIAGGIIEKDDFFIE---LPIGKIGDDL 184

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             +    E G   A +H KV++   +K   +LE + +TGRTHQ+R H   +G P+VGD  
Sbjct: 185 RRIELSEENGGKSAKTHIKVLERNREKNITFLEARLYTGRTHQIRAHLSLIGHPLVGDEL 244

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           Y  +        +  +  LHA  ++  +P+    L++   +P  M
Sbjct: 245 YGGDIN------LAKRQMLHAYKLEFQNPKTLDDLKVEIEIPLDM 283


>gi|224543798|ref|ZP_03684337.1| hypothetical protein CATMIT_03019 [Catenibacterium mitsuokai DSM
           15897]
 gi|224523289|gb|EEF92394.1| hypothetical protein CATMIT_03019 [Catenibacterium mitsuokai DSM
           15897]
          Length = 282

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 74/127 (58%), Gaps = 10/127 (7%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L +RLD+ETSG++++A++R    H   S  +++++++Y +LV G   N  +   N  +  
Sbjct: 126 LVNRLDKETSGLMMIAKSRYV--HDAFSHDIKQVKRVYHALVKG---NPGQGTVNAPIDH 180

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +   G      ++  +G   AI+H++ I    + +  +E +  TGRTHQ+RVH  ++GCP
Sbjct: 181 AEGHG----TKREVREGGKEAITHYRTIKTTGE-YSLVECKLETGRTHQIRVHMAYLGCP 235

Query: 266 IVGDHKY 272
           +VGD  Y
Sbjct: 236 LVGDPLY 242


>gi|197337902|ref|YP_002158084.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
 gi|197315154|gb|ACH64603.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
          Length = 566

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 66/207 (31%), Positives = 98/207 (47%), Gaps = 26/207 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  + V NKPA      G  I   +   ++  + D+ G    + HRLD  TSG+LV
Sbjct: 365 IVYEDEFMVVVNKPADFLSVPGKNIHDSVYARIQQRYPDATGG--LIIHRLDMATSGLLV 422

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +  T  A + L + F  R ++K Y +L+ G+ +  +  I         + GD     +Q 
Sbjct: 423 LGLTPKAHKRLQQQFINRTVEKRYTALLDGVLEQDEGLIT------LPMRGDLYDRPRQL 476

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
              E G   A + ++VI+    K   + + P TGRTHQLRVH  H   +  PI GD  Y 
Sbjct: 477 VCFEHGKP-AETTYQVIERKESK-TKVYLYPKTGRTHQLRVHCAHYLGLNMPITGDGLYG 534

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
                       N+L+LHA Y+ L HP
Sbjct: 535 KK---------ANRLHLHAGYLSLIHP 552


>gi|116334072|ref|YP_795599.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
 gi|116099419|gb|ABJ64568.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
          Length = 299

 Score = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 72/288 (25%), Positives = 128/288 (44%), Gaps = 26/288 (9%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQS--GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           ++  G  R   K+VKF+  + +  GQ VR+  +  A    +   ++     N      F 
Sbjct: 20  LMAHGVTRTFLKQVKFHGGVVTLDGQPVRV--IAMATPGQVVGLQLPPEPDNPHVTPSFA 77

Query: 98  KSILLYEDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
              +LYED    V NKPAG++     +     +A  + G L + + +      +  RLD+
Sbjct: 78  PLDILYEDEHFLVVNKPAGMASVPSHLYSEDTLANRVKGHLLT-IQAPSTVTHIVTRLDR 136

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGG 210
           +TSG+++ A+   A   L +  ++++I K Y ++  G  +P +++            IG 
Sbjct: 137 DTSGVVLFAKHHFAHSVLDKQLKLKQIDKRYVAVASGRMMPAHQQ--------LTGPIGR 188

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +    +K+  +    A      +   +     L ++ HTGRTHQ+RVH  + G P++GD 
Sbjct: 189 EAGSFIKRTVRPDGRAAETEVWVRATSATASLLAVKLHTGRTHQIRVHCANAGHPLLGDW 248

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
            Y     G  T+P   +  LH   +    P  G+ +   APLP  M +
Sbjct: 249 LY-----GRPTNPWIQRQALHCARVQFFQPFAGKWVTCYAPLPDDMAR 291


>gi|296875626|ref|ZP_06899697.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           parasanguinis ATCC 15912]
 gi|296433423|gb|EFH19199.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           parasanguinis ATCC 15912]
          Length = 274

 Score = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 97/216 (44%), Gaps = 29/216 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + S+V   G    + HRLD+ETSG ++ A
Sbjct: 71  LYQDEHVIIVNKPEGMKTHANEPTEIALLNHVSSYV---GSTCYVVHRLDKETSGAILFA 127

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + IQ+ YW+L+ G    K       ++ K  IG D     K+  +
Sbjct: 128 KNPFILPILNRILEDKNIQREYWALIQGSLAQKT------IVYKDKIGRDRHDRRKRLVD 181

Query: 220 EKGANYA---ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            +   YA   ++  K I   +   C L+    TGRTHQ+RVH  H G PIVGD  Y    
Sbjct: 182 PRKGQYAETQVTQLKKIGRNSLVKCQLK----TGRTHQIRVHLSHHGHPIVGDPLY---- 233

Query: 277 KGNFTSPIQ-NKLYLHARYMDLPHPEG-GRLQITAP 310
                +P +  +L LHA  +   +P     +Q+ AP
Sbjct: 234 -----NPARGERLMLHAHRLTFTNPLTLETIQVEAP 264


>gi|289422501|ref|ZP_06424344.1| ribosomal large subunit pseudouridine synthase family protein
           [Peptostreptococcus anaerobius 653-L]
 gi|289157073|gb|EFD05695.1| ribosomal large subunit pseudouridine synthase family protein
           [Peptostreptococcus anaerobius 653-L]
          Length = 234

 Score = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 56/210 (26%), Positives = 97/210 (46%), Gaps = 19/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  K   I  Q  +     +    K +V  K  KP      L HRLD+   
Sbjct: 13  VIYEDNHLLVVEKIPNILSQSDNTKDVDMLSMCKEYVKIKYNKPGAVFMGLVHRLDRPVG 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ART  AA  L++  R R ++K Y +++ G P    + + ++L K ++   + V  
Sbjct: 73  GVMVFARTSKAASRLSDQVRTRTMKKSYQAIINGNPPKAGDFV-DYLYKDTN--KNMVRC 129

Query: 216 VKQNEKGANYAISHFKVIDCF-----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           V ++  G   A   ++++D        + +  +E+  HTGR HQ+RV        + GD 
Sbjct: 130 VDKSFNGGKEARLSYRLLDSSISPEDKKDYSLVEIDLHTGRPHQIRVQFASRKYALYGDQ 189

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +Y    K         ++ L A  ++L HP
Sbjct: 190 RYSKVAKKG------QQIALWATRLELVHP 213


>gi|237736082|ref|ZP_04566563.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           mortiferum ATCC 9817]
 gi|229421793|gb|EEO36840.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           mortiferum ATCC 9817]
          Length = 289

 Score = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 103/231 (44%), Gaps = 28/231 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           + YED  + + NK   I V            +G+   ++ FLK+    K   PR  +RLD
Sbjct: 76  IAYEDKNLLLINKDPYIIVHPTQKKVDKTLANGV---VNYFLKTT--GKVMVPRFYNRLD 130

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI++V +   A  +L E      + K Y ++V GI + K E + +  + K  IG +
Sbjct: 131 MNTSGIIIVTKNAYAQSYLQEKGI---VNKFYQAIVLGIVE-KDEFLIDRPIGK--IGDE 184

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              V  Q E G   A +  KV+  F +K    +E +  TGRTHQ+R H    G P++GD 
Sbjct: 185 LRRVELQPEDGGQIAQTKVKVLKRFQEKNLTLIEAELLTGRTHQIRAHMALEGYPLLGDE 244

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWD 320
            Y             ++  LH+   +    E G L+ I   LP  M K  +
Sbjct: 245 LYGG------ADNRADRQMLHSYKTEFSDVETGDLKSIEVELPEDMKKLLE 289


>gi|301612808|ref|XP_002935894.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 1
           [Xenopus (Silurana) tropicalis]
          Length = 299

 Score = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 57/173 (32%), Positives = 86/173 (49%), Gaps = 11/173 (6%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  + AA    + F+ R + K Y +LV G    K   I+  + K
Sbjct: 61  RFCHQLDFSTSGALCVALNKEAAGRAYQCFKDRTVTKAYLALVRGTVSEKYMRISLAIGK 120

Query: 205 KSHIGGDYVHVVK-----QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            +  G  ++  V+     +N K     +   +           + +QP TGRTHQLRVH 
Sbjct: 121 NTQEGLTHMMCVEGAPGCKNAKPCQTDLVVLQHGSYKGDPVTKVLLQPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
             +G PIVGD  Y  +FK + + P   ++ LHA Y+ +P  +   +++TAP P
Sbjct: 181 SALGFPIVGDFTY--SFKKD-SEPY--RMMLHAYYLRIPT-DHELIEVTAPDP 227


>gi|294143008|ref|YP_003558986.1| ribosomal pseudouridine synthase Rlu family protein [Shewanella
           violacea DSS12]
 gi|293329477|dbj|BAJ04208.1| ribosomal pseudouridine synthase Rlu family protein [Shewanella
           violacea DSS12]
          Length = 224

 Score = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 58/182 (31%), Positives = 84/182 (46%), Gaps = 26/182 (14%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG+L+ A++  AA   TE F   +IQK Y +L  G PK K+  +   + K   
Sbjct: 47  HRLDSLTSGLLLFAKSSRAAAEFTELFTQHKIQKYYVALATGKPKKKQGWVVGDMAKSRR 106

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  +++  E   N A++ F      A+      ++P +G+THQLRV    +G PI+
Sbjct: 107 ---SMYKLLRTTE---NPALTQF-FSQSVAEGLRLYLLKPLSGKTHQLRVALASLGVPIL 159

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA----------RYMDLPHPEGGRLQITAPLPAHMVK 317
           GDH Y     G   S   ++ YLHA           Y  L +P  G  Q TA      ++
Sbjct: 160 GDHLY-----GGAES---DRGYLHAFSLSFSFRGKDYRYLSYPSQGE-QFTAVDTKKQLQ 210

Query: 318 TW 319
            W
Sbjct: 211 IW 212


>gi|317009613|gb|ADU80193.1| hypothetical protein HPIN_04885 [Helicobacter pylori India7]
          Length = 242

 Score = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 54/174 (31%), Positives = 89/174 (51%), Gaps = 25/174 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG++++
Sbjct: 58  VIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGVVLL 102

Query: 161 ARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  + K+
Sbjct: 103 VKENSEF-HLKAKKAFKDRAVKKEYLALAQGIIEEEREINAPILTIKT--TKAFSKISKK 159

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y
Sbjct: 160 GQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTIY 208


>gi|315586586|gb|ADU40967.1| RluA family ribosomal large subunit pseudouridine synthase
           [Helicobacter pylori 35A]
          Length = 327

 Score = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 53/227 (23%), Positives = 105/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLEFKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      +L+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVYLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIVLKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|327287587|ref|XP_003228510.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Anolis carolinensis]
          Length = 300

 Score = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 57/173 (32%), Positives = 84/173 (48%), Gaps = 11/173 (6%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA    + F+ R + K Y +LV G  +  K  I   + K
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYKCFKERMVTKAYLALVRGHVQEAKLTIEYAIGK 120

Query: 205 KSHIGGDYVHVVKQNEKGANY--AISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            +  G  ++  ++  E   N     S   V++           + +QP TGRTHQLRVH 
Sbjct: 121 NTTEGMTHMMCIEGTEGCENPKPCQSELTVLEHGLYSGDPVSKVLLQPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
             +G PIVGD  Y     G    P   ++ LHA Y+ +P  +   ++++AP P
Sbjct: 181 SAVGHPIVGDFTYSLKTDGG---PF--RMMLHAYYLRIPTAK-ELVEVSAPDP 227


>gi|108563365|ref|YP_627681.1| hypothetical protein HPAG1_0940 [Helicobacter pylori HPAG1]
 gi|107837138|gb|ABF85007.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori HPAG1]
          Length = 242

 Score = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 54/174 (31%), Positives = 89/174 (51%), Gaps = 25/174 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG++++
Sbjct: 58  VIFEDENILALFKPPFIE-------SYDLLSFFKGWV--------LLHRLDKETSGVILL 102

Query: 161 ARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  + K+
Sbjct: 103 VKENSEF-HLKAKKAFKNRAVKKEYLALAQGIIEEEREINAPILTFKT--TKAFSKISKK 159

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y
Sbjct: 160 GQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTIY 208


>gi|329737470|gb|EGG73724.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU028]
          Length = 274

 Score = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 59/204 (28%), Positives = 94/204 (46%), Gaps = 26/204 (12%)

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED  + +  KP G+      ++  + +  H+       VDS+  +P   HRLDQET G+
Sbjct: 78  YEDDDLAIVMKPKGVKTHPNDLKESNTLMNHV----IYTVDSEYVEP--IHRLDQETVGL 131

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+     + L        I +IY + V  +   K + I         IG D  H  K
Sbjct: 132 LIVAKNPLMKKILDRMLEYNEITRIYKANVKALLPIKPQTI------DMPIGKDKFHSNK 185

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +        AI+H        +  C L+++  TGRTHQ+RVH   +G P++GD  Y    
Sbjct: 186 RRISNTGQRAITHIINSKMIKEGVCQLDIKLDTGRTHQIRVHLAEIGHPVIGDPLYG--- 242

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
               TS ++ +L L++  ++  HP
Sbjct: 243 ----TSTLR-QLELNSHQIEFTHP 261


>gi|209809357|ref|YP_002264895.1| putative RNA pseudouridylate synthase [Aliivibrio salmonicida
           LFI1238]
 gi|208010919|emb|CAQ81324.1| putative RNA pseudouridylate synthase [Aliivibrio salmonicida
           LFI1238]
          Length = 561

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 62/207 (29%), Positives = 100/207 (48%), Gaps = 26/207 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  + + NKPA      G  I   +   ++  + ++ G    + HRLD   SG++V
Sbjct: 360 IIYEDEFMLIINKPADFLSVPGKNINDSVYTRVQQRYPNATGG--LIVHRLDMAASGLMV 417

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +  T  A + L + F  R ++K Y +L+ G+  +++  I   L       GD     +Q 
Sbjct: 418 LGLTSKAHKRLQKQFINRTVEKRYTALLDGLLPHREGQITLPLR------GDLYDRPRQL 471

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
              E G   A + + VI+ + +K   + + P TGRTHQLRVH  H   +  PI+GD  Y 
Sbjct: 472 VCFEYGKQ-AETTYNVIE-YKEKQTLVHLYPKTGRTHQLRVHCAHHLGLNMPIIGDGLYG 529

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
                       ++LYLHA Y+ + HP
Sbjct: 530 QK---------ADRLYLHAGYLSVTHP 547


>gi|322390416|ref|ZP_08063937.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           parasanguinis ATCC 903]
 gi|321142874|gb|EFX38331.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           parasanguinis ATCC 903]
          Length = 287

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 96/216 (44%), Gaps = 29/216 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+           +   + S+V   G    + HRLD+ETSG ++ A
Sbjct: 84  LYQDEHVIIVNKPEGMKTHANEPTEIALLNHVSSYV---GSTCYVVHRLDKETSGAILFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + IQ+ YW+L+ G            ++ K  IG D     K+  +
Sbjct: 141 KNPFILPILNRILEDKNIQREYWALIQG------SLAQRTIVYKDKIGRDRHDRRKRLVD 194

Query: 220 EKGANYA---ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            +   YA   ++  K I   +   C L+    TGRTHQ+RVH  H G PIVGD  Y    
Sbjct: 195 PRKGQYAETQVTQLKKIGRNSLVKCQLK----TGRTHQIRVHLSHHGHPIVGDPLY---- 246

Query: 277 KGNFTSPIQ-NKLYLHARYMDLPHPEG-GRLQITAP 310
                +P +  +L LHA  +   +P     +Q+ AP
Sbjct: 247 -----NPARGERLMLHAHRLTFTNPLTLETIQVEAP 277


>gi|303239847|ref|ZP_07326370.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
 gi|302592557|gb|EFL62282.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
          Length = 337

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 53/189 (28%), Positives = 86/189 (45%), Gaps = 37/189 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + V NK   I V            + +AYH+    KS V    +K R   RLD
Sbjct: 81  IIYEDDCLIVINKAPDIVVHPTCSHPDGTLANAVAYHLQ---KSGV---AKKIRPVIRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI--------ANWLL 203
           + TSGI++ A+   + + L      +   K Y  +V+GI KN +  I         + +L
Sbjct: 135 RNTSGIIIFAKNSFSQESLIRQMNTKTFVKEYIGIVYGILKNTRGTIDLPIERKEGSIML 194

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +   + GD              +++HF+ ++        L+ +  TGRTHQ+RVH   +G
Sbjct: 195 RHVSLSGDR-------------SVTHFETLEVL-NNTSLLKFRLETGRTHQIRVHCQAIG 240

Query: 264 CPIVGDHKY 272
            P++GD  Y
Sbjct: 241 HPLIGDTLY 249


>gi|254521992|ref|ZP_05134047.1| ribosomal large subunit pseudouridine synthase A [Stenotrophomonas
           sp. SKA14]
 gi|219719583|gb|EED38108.1| ribosomal large subunit pseudouridine synthase A [Stenotrophomonas
           sp. SKA14]
          Length = 204

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 68/207 (32%), Positives = 108/207 (52%), Gaps = 25/207 (12%)

Query: 103 YEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           Y D  + V  KPAG+ SV G S  A + D  + + + +        HRLDQ TSG+L+ A
Sbjct: 6   YIDDALLVAEKPAGLLSVPGRS--AENQDCVV-ARLQALYPDALTVHRLDQVTSGLLLHA 62

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--- 218
           R +     L+  F  R++ K Y ++V G+ +     +   L+       D+ +  KQ   
Sbjct: 63  RGKDMQAALSMQFEQRQVGKRYEAIVEGLLEGDAGEVDLPLIV------DWPNRPKQMID 116

Query: 219 NEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +E+G   A++ ++V+  D  AQ+   +E++P TGR+HQLR+H   +G PIVGD  Y A  
Sbjct: 117 HERG-KPALTRWRVLARDAGAQR-TRMELEPITGRSHQLRLHMASLGHPIVGDVLYDA-- 172

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
                +P Q +++LHA  +   HP  G
Sbjct: 173 -----APAQ-RVHLHASALAFTHPLTG 193


>gi|284048156|ref|YP_003398495.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
 gi|283952377|gb|ADB47180.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
          Length = 294

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 64/232 (27%), Positives = 107/232 (46%), Gaps = 44/232 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-----GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           LLYED  + V +KPAG+ +          +   + G+ +      G  P   +RLD++T+
Sbjct: 79  LLYEDEDLLVVDKPAGMLIHPTWSGARDTLVQAVGGYFRRTGQHCGIHP--LYRLDRDTT 136

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLV---WGIPKNK--------KECIANWLLK 204
           G+L+VA++  A   LT      +I + Y ++    WGIP+ +         E +  W ++
Sbjct: 137 GVLMVAKSAFAKHALTRDHS--QIYREYLAVCEGRWGIPQGRIEHPIGRVAEGVDRWTVR 194

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                                A++ +++++   Q++  L++   TGRTHQ+RVH  H G 
Sbjct: 195 PD----------------GRPAVTEYRILE-ENQEWTVLKIHLLTGRTHQIRVHFAHEGH 237

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           P+VGD  Y     G     I  +  LHA  +   HP  G  + +TAP+P  M
Sbjct: 238 PLVGDPLY-----GTKDGRIARQA-LHAWTVRFRHPRTGEEILLTAPMPGDM 283


>gi|298252641|ref|ZP_06976435.1| pseudouridylate synthase, 23S RNA-specific [Gardnerella vaginalis
           5-1]
 gi|297533005|gb|EFH71889.1| pseudouridylate synthase, 23S RNA-specific [Gardnerella vaginalis
           5-1]
          Length = 288

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 59/214 (27%), Positives = 105/214 (49%), Gaps = 20/214 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----------IAYHIDGFLKSWVDSKGQKPRLTHRL 150
           ++Y D  + V +KP G++     G           A  ID  +K+ +  + +K  +  RL
Sbjct: 61  IIYNDDDVVVIDKPVGVASHAAKGWSGPTVPECLEAVGID--IKTTLCDESRKG-IVSRL 117

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+++V +T  A + +   F    ++K Y +LV G     K  I +  + ++ +  
Sbjct: 118 DVGTSGLMLVCKTDFAYEVMKNQFAKHIVKKTYHALVQGDLAQDKATI-DAPIGRAKVS- 175

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D+   +  + K    A++H+ V++ F+Q    + +   TGRTHQ+RVH   +G P+VGD 
Sbjct: 176 DFRFTITSDGK---PAVTHWDVLERFSQA-TLVSVNLETGRTHQIRVHFSSIGHPLVGDS 231

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            Y AN        +Q + +LH+  +   HP  G+
Sbjct: 232 MYGANPVLAQKLGLQRQ-WLHSMELTFTHPRTGK 264


>gi|115495425|ref|NP_001069342.1| RNA pseudouridylate synthase domain-containing protein 1 [Bos
           taurus]
 gi|122144661|sp|Q17QT4|RUSD1_BOVIN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 1
 gi|109658212|gb|AAI18197.1| RNA pseudouridylate synthase domain containing 1 [Bos taurus]
 gi|296473482|gb|DAA15597.1| RNA pseudouridylate synthase domain-containing protein 1 [Bos
           taurus]
          Length = 308

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 53/159 (33%), Positives = 79/159 (49%), Gaps = 8/159 (5%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA      F+ RR+ K Y +LV G  +  +  I+  + K
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYRCFKDRRVTKAYLALVRGHVQESRMTISYAIGK 120

Query: 205 KSHIGGDYVHVVKQNEKGANY--AISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            S  G  +   ++  +   N   +++   V++           + +QP TGRTHQLRVH 
Sbjct: 121 NSTEGRTHTMCIEGTQGCENPKPSLTELVVLEHGLYAGDPVSKVLLQPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             +G PIVGD  Y  +  G    P   ++ LHA Y+ +P
Sbjct: 181 SALGHPIVGDLTY-GHALGQEDQPF--RMMLHAFYLRIP 216


>gi|148979501|ref|ZP_01815558.1| pseudouridine synthase Rlu family protein [Vibrionales bacterium
           SWAT-3]
 gi|145961779|gb|EDK27074.1| pseudouridine synthase Rlu family protein [Vibrionales bacterium
           SWAT-3]
          Length = 232

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 65/205 (31%), Positives = 96/205 (46%), Gaps = 33/205 (16%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--T 147
           L  HSDFL            + NK  GISV    G     D  L   V     +P+L   
Sbjct: 5   LLNHSDFL------------LINKHPGISVHKDDG-----DTMLLQEVAKAINEPKLYLV 47

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSGIL++A++ +AA  L++ F  R ++K Y ++    PK K+  I+   +++S 
Sbjct: 48  HRLDKMTSGILLLAKSASAASELSQLFAKREVEKFYLAIGSKKPKKKQGLISG-DMERSR 106

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                +   K+N      AI+ F        +   L  +P TGRTHQ+RV    +G  IV
Sbjct: 107 RSSWKLLTTKENP-----AITQFLSASAEPGERLLL-CKPFTGRTHQIRVAMKSIGSAIV 160

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA 292
           GD  Y  + +        ++ YLHA
Sbjct: 161 GDPIYNPSSEA-------DRGYLHA 178


>gi|224070740|ref|XP_002186856.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 1, partial [Taeniopygia guttata]
          Length = 257

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 55/174 (31%), Positives = 80/174 (45%), Gaps = 13/174 (7%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA    + F+ R + K Y +LV G     +  I   + K
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYKCFKERLVTKAYLALVRGHVSQSRMTIRYAIGK 120

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVI-----DCFAQKFCWLEMQPHTGRTHQLRVHA 259
            +  G  ++  ++  E   N      +++              + +QP TGRTHQLRVH 
Sbjct: 121 NTTEGMTHMMCIEGTEGCENPKPCQSELVVLEHGSYSGDPVTKVLLQPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
             +G PIVGD  Y      N       ++ LHA Y+ +  P G  L ++ AP P
Sbjct: 181 SAIGHPIVGDFTYSQRQDSN-----PYRMMLHAYYLRI--PTGSELIEVCAPDP 227


>gi|126640196|ref|YP_001083180.1| dual specificity pseudouridine synthase [Acinetobacter baumannii
           ATCC 17978]
          Length = 184

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 58/165 (35%), Positives = 86/165 (52%), Gaps = 20/165 (12%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IAN 200
           ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G  K +       I +
Sbjct: 23  KVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLITD 82

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFK--VIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           W  +   I    VH     E G  +A + F+  V D    +   L ++P TGR+HQLRVH
Sbjct: 83  WENRPRQI----VHF----ELG-KHAKTLFQPLVYDATTDQSRVL-LEPVTGRSHQLRVH 132

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +H+G PI+GD  Y    K        N++ LHA Y+   HP  G
Sbjct: 133 MMHIGHPIMGDKLYHPEPKRFHL----NRMALHAAYLAFQHPLKG 173


>gi|293390024|ref|ZP_06634358.1| tRNA pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290950558|gb|EFE00677.1| tRNA pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 237

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 105/236 (44%), Gaps = 22/236 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     ++   D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYQDDVLVAVNKPAGMLVHRSWLDRHETQFVMQILRDQIGQLVYPIHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  +   F  ++ +K Y ++V G    + E      ++   I   +     Q +
Sbjct: 65  ALNSETANLVCHQFEQKQTEKQYLAVVRGYVTGQGEIDYPLKVQLDKIADKFA----QQD 120

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ +  +             A ++  + + P TGR HQLR H  H+  PI+GD 
Sbjct: 121 KAPQSAVTFYDGLKTVEMPYGVGRYAASRYSLVRLTPKTGRKHQLRRHMKHIFHPILGDM 180

Query: 271 KYCANFKGN--FTSPIQ-NKLYLHARYMDLPHPEGGR-LQITAPLPA---HMVKTW 319
           +Y  +   N   T  I  ++L LHA  +   HP  G+ + I A L     H+++T+
Sbjct: 181 QY-GDLHQNRALTEHIGCSRLMLHAEKLTFVHPLTGQPITIEAGLDEQWKHLMRTF 235


>gi|59713668|ref|YP_206443.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           ES114]
 gi|59481916|gb|AAW87555.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           ES114]
          Length = 566

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 66/207 (31%), Positives = 98/207 (47%), Gaps = 26/207 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  + V NKPA      G  I   +   ++  + D+ G    + HRLD  TSG+LV
Sbjct: 365 IVYEDEFMVVVNKPADFLSVPGKNIHDSVYARIQQRYPDATGG--LIIHRLDMATSGLLV 422

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +  T  A + L + F  R ++K Y +L+ G+ +  +  I         + GD     +Q 
Sbjct: 423 LGLTPKAHKRLQQQFINRTVEKRYTALLDGVLEQDEGLIT------LPMRGDLYDRPRQL 476

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
              E G   A + ++VI+    K   + + P TGRTHQLRVH  H   +  PI GD  Y 
Sbjct: 477 VCFEHGKP-AETTYQVIERKENK-TKVYLYPKTGRTHQLRVHCAHYLGLNMPITGDGLYG 534

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
                       N+L+LHA Y+ L HP
Sbjct: 535 KK---------ANRLHLHAGYLSLIHP 552


>gi|50291713|ref|XP_448289.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49527601|emb|CAG61250.1| unnamed protein product [Candida glabrata]
          Length = 457

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 50/176 (28%), Positives = 87/176 (49%), Gaps = 6/176 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED+ I V NKP+GI V       Y  +   K+    +G      +RLD+ TSG++ +
Sbjct: 194 IVFEDNDILVINKPSGIPVHPTG--RYRFNTITKALEKERGYVVHPCNRLDRMTSGLMFL 251

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+T   A  + +  + R ++K Y + V G  P+     + +  LK          V ++ 
Sbjct: 252 AKTSKGADKIGDQLKAREVEKEYLAKVVGEFPEGT--TVVDKPLKLLEPRLTLNVVCEET 309

Query: 220 EKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +  A +A + F+ +     K    ++ +P TGR+HQ+RVH  H+G PI  D  Y +
Sbjct: 310 DPDAKHARTIFERVSVSKDKQTSIVKCKPLTGRSHQIRVHLQHLGHPIANDPIYSS 365


>gi|121604183|ref|YP_981512.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120593152|gb|ABM36591.1| ribosomal large subunit pseudouridine synthase A [Polaromonas
           naphthalenivorans CJ2]
          Length = 233

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 63/208 (30%), Positives = 91/208 (43%), Gaps = 10/208 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  + V NKPAG+    G G        L   V S      + HRLD  TSG++++
Sbjct: 24  IIHADDSLLVLNKPAGLLAVPGRG--EDKQDCLSRRVQSLYPDALIVHRLDMATSGLMLM 81

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R  A  + L + F  R + K Y ++V G      E    W L    I  D+     +  
Sbjct: 82  GRGIAMQRALGQLFERREVYKRYLAVVDGRLAPAPEP-GGWGLIDLPIAVDWPRRPLRII 140

Query: 221 KGANYAISHFK---VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             A+   S  +   V    A     +E++P TGR+HQLRVH   +G PI+GD  Y     
Sbjct: 141 DAASGKPSQTRWRSVAFDAAANSTRVELEPLTGRSHQLRVHLQALGHPILGDALYAPEAV 200

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRL 305
               +    +L LHA  + L HP  G L
Sbjct: 201 QARAA----RLLLHACALRLLHPASGAL 224


>gi|311251719|ref|XP_003124746.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Sus scrofa]
          Length = 312

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 54/163 (33%), Positives = 78/163 (47%), Gaps = 16/163 (9%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA      F+ RR+ K Y +LV G  +  +  I+  + K
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYRCFKDRRVTKAYLALVRGHIQESRVTISYAIGK 120

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVI---------DCFAQKFCWLEMQPHTGRTHQL 255
            S  G  +   ++  +   N   S  +++         D  ++      +QP TGRTHQL
Sbjct: 121 NSTEGRTHTMCIEGTQGCENPKPSLTELVVLEHGLYGGDPVSKVL----LQPLTGRTHQL 176

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           RVH   +G PIVGD  Y     G    P   ++ LHA Y+ +P
Sbjct: 177 RVHCSALGHPIVGDLTY-GQASGREDQPF--RMMLHAFYLRVP 216


>gi|295107941|emb|CBL21894.1| pseudouridine synthase, RluA family [Ruminococcus obeum A2-162]
          Length = 342

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 68/255 (26%), Positives = 112/255 (43%), Gaps = 33/255 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +LYED  I   NKPAGI     G+  A  +   +  +   K    R+    RLD+ETSGI
Sbjct: 88  ILYEDEDILAVNKPAGILTHPSGAHYADTLSNQVAGYFHKKKLSCRVRPIGRLDKETSGI 147

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG------------------IPKNKK---- 195
           ++ A+ + +AQ L        + K Y ++V G                   P  K     
Sbjct: 148 VLFAKNQVSAQRLQTQRESGILHKQYIAVVKGDFSDDTSASSDTAWHTVCFPIRKTADHP 207

Query: 196 ---ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              E I ++    S    D+V  +       + A++H++V+   +  +  + ++  TGRT
Sbjct: 208 LRMEAITDFGSSFSPESADFVAPLVDMATLLS-AVTHYQVLYS-SPNWSVVTLKLDTGRT 265

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTS--PIQNKLYLHARYMDLPHP-EGGRLQITA 309
           HQ+RVH   +G P++GD  Y   F  +  S  P+ ++  LHA  +   HP     + + A
Sbjct: 266 HQIRVHMKALGHPLLGDTLYQKTFPADSVSEQPVFHRTALHAWKIQFRHPFNNAWISLEA 325

Query: 310 PLPAHMVKTWDSLGF 324
           PLP      + ++ F
Sbjct: 326 PLPDDFCNCFQNINF 340


>gi|229068860|ref|ZP_04202155.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           F65185]
 gi|228714278|gb|EEL66158.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           F65185]
          Length = 292

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 103/204 (50%), Gaps = 17/204 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           ++YED  + + NK A +S +         +   L S  D +       +  RLD++TSG+
Sbjct: 79  IVYEDDAVLIINKEANMSTIPSREHPTRSVANALLSHYDKQHLASTVHIVTRLDRDTSGL 138

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D +    
Sbjct: 139 MLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDAPIGRKS----DSIIERT 194

Query: 218 QNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 195 VCEDG-QRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGDSLY---- 247

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
            G     ++ +  LH++ +   HP
Sbjct: 248 -GGRRDEMKRQ-ALHSKSLTFYHP 269


>gi|254360710|ref|ZP_04976858.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261496892|ref|ZP_05993260.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|153091280|gb|EDN73254.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261307416|gb|EEY08751.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
          Length = 217

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 65/216 (30%), Positives = 100/216 (46%), Gaps = 20/216 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           + Y+     + NKP G+SV         +   +   ++ K  +  L HRLD+ TSG+L++
Sbjct: 7   ICYQHRDFIIINKPEGLSVHKDEA-EIGLTELVARQLNVK--QVWLVHRLDKITSGLLIL 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + AA      F   +I K YW+L    PK K+  I    ++KS  G   +   K+N 
Sbjct: 64  ALNKEAAARFYHLFEQHKIYKTYWALSDKKPKKKQGRIVG-DMQKSRNGAWKLCHSKENP 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               + ISH  V D          +QP TG+THQLRV    +G PI+GD  Y  +     
Sbjct: 123 AVTQF-ISH-SVEDSLRH----FILQPKTGKTHQLRVAMKSLGSPILGDKLYSGS----- 171

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITA-PLPAHM 315
                +++YLHA  +D  + E  ++ + A P   H 
Sbjct: 172 ---QADRVYLHAYQLDFEY-ENEKISVQALPTSGHF 203


>gi|149187993|ref|ZP_01866288.1| tRNA pseudouridine synthase C [Vibrio shilonii AK1]
 gi|148837981|gb|EDL54923.1| tRNA pseudouridine synthase C [Vibrio shilonii AK1]
          Length = 258

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 57/215 (26%), Positives = 94/215 (43%), Gaps = 22/215 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V             +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 15  IVYQDQYLVAVNKPAGMLVHRSWLDKNETRFVMQTLRDQIGQHVFPLHRLDRPTSGVLLF 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A      F    I+K Y ++V G             ++   I   +       +
Sbjct: 75  ALSSEIASQAMPMFAEHNIEKTYHAIVRGWITEGDVLDYPLKVELDKIADKFA----SQD 130

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EM+P TGR HQLR H  H+  PI+GD 
Sbjct: 131 KEAQPAVTAYQPLASVEVPYTTGRFPTSRYCLVEMKPKTGRKHQLRRHMHHLSHPIIGDT 190

Query: 271 -----KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
                K+   F+ ++ S   ++L LHA  +   HP
Sbjct: 191 SHGDGKHNRLFREHYDS---HRLLLHASELKFVHP 222


>gi|238749474|ref|ZP_04610979.1| Pseudouridine synthase [Yersinia rohdei ATCC 43380]
 gi|238712129|gb|EEQ04342.1| Pseudouridine synthase [Yersinia rohdei ATCC 43380]
          Length = 232

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 100/229 (43%), Gaps = 21/229 (9%)

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            KI+D+ +    H    K   LY+D  + + NKPAG+    G     ++D      V   
Sbjct: 2   SKIIDTFIAPPCHD---KIETLYQDDHLVLINKPAGLLSLSGKN-PQNLDSVHHRLVQIF 57

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   N +  I  
Sbjct: 58  -PGCTLAHRLDFGTSGLMVIARNKAVNAALCQQFSQRTVTKVYSALLCGHLDNNEGVIDA 116

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRT 252
            + K   +      V+         A S ++V++ F              +++ P TGRT
Sbjct: 117 AIAKDPAL----FPVMSICALHGKPARSGYRVVERFYHPLEDGTLLPLTRVQLTPETGRT 172

Query: 253 HQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
           HQLR+H   +G PI G   Y      G   +P   +L LHA  +   HP
Sbjct: 173 HQLRIHCQLLGHPIWGCDLYGGRLLPGTERTP---RLMLHASELHFIHP 218


>gi|212696916|ref|ZP_03305044.1| hypothetical protein ANHYDRO_01479 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676206|gb|EEB35813.1| hypothetical protein ANHYDRO_01479 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 299

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 109/233 (46%), Gaps = 20/233 (8%)

Query: 101 LLYEDSKIYVFNK-------PAGISVQGG--SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YE+    + +K       PAG  V G   +G+ YH  G+          +P + HRLD
Sbjct: 76  IVYENKDYAIIDKDENVIVHPAGSIVSGTLVNGLLYHF-GYNNLSHIGGDDRPGIVHRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G++V+A++ ++ + L   F  R+I K Y ++  GI K K   I  ++ +  +   +
Sbjct: 135 KDTTGLMVIAKSNSSYKFLKNLFETRKIDKEYLAICNGIFKKKSGEIHTFMDRDPN---N 191

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              +  +N      AIS ++V+      +  ++++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 192 RRKMAVRN--SGRDAISKYEVL-SENDGYSLVKIKILTGRTHQIRVHMTHINHPLLGDPV 248

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           Y  N K  F    Q    LH   +     +G   +  A +     K    LG 
Sbjct: 249 Y-GNVKHKFNLDHQ---LLHCHKLGFTDKDGVYREFEADVHEDFKKYQKVLGL 297


>gi|320590514|gb|EFX02957.1| drap deaminase [Grosmannia clavigera kw1407]
          Length = 528

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 90/180 (50%), Gaps = 10/180 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++++ED  + V NKPAG+ V       Y+ +   LK+  +  G  P   +RLD+ TSGI+
Sbjct: 135 VVIHEDDDMVVINKPAGVPVHPAGRYQYNSVVEMLKAQRE-PGFMPYPCNRLDRLTSGIM 193

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
            +A++ AAA+ L+   + R ++K Y + V G  P  ++ C    L     +G   ++ V+
Sbjct: 194 FLAKSPAAAKRLSLQIQARAVRKEYLARVVGRFPDGQQVCDQPILQISPKLG---LNRVR 250

Query: 218 QNEKGANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            N + A          +  A    + +  +   P TGRTHQ+RVH  ++G PI  D  Y 
Sbjct: 251 ANGRSARTVFQRLAYYEGSAGGRSEGYSVVRCLPVTGRTHQIRVHLQYLGHPIENDPIYA 310


>gi|306833402|ref|ZP_07466529.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus bovis ATCC
           700338]
 gi|304424172|gb|EFM27311.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus bovis ATCC
           700338]
          Length = 296

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 57/205 (27%), Positives = 96/205 (46%), Gaps = 17/205 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGI 157
           + YED    + NK  G +       +  I  F+K +   +    +  H   RLD++TSG+
Sbjct: 78  IAYEDEHFLIINKSYGYASIPSVLHSNTIANFVKYYYLEQNYPNKQVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   L +  + + I+K Y++LV G  +  +K E IA        I    VH 
Sbjct: 138 MLFAKHGYAHARLDKQLQNKTIEKRYYALVSGKGELADKGEIIAPIARSDDSIITRCVH- 196

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                    YA + ++V+  F +    ++++ HTGRTHQ+RVH  H+G P++GD  Y  +
Sbjct: 197 -----PSGKYAHTSYEVVARFGE-VALVDIRLHTGRTHQIRVHFSHIGFPLLGDDMYGGS 250

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
                T     +  LH  Y+   +P
Sbjct: 251 MDYGIT-----RQALHCHYLRFVNP 270


>gi|228469450|ref|ZP_04054458.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           uenonis 60-3]
 gi|228309025|gb|EEK17668.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           uenonis 60-3]
          Length = 232

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 90/189 (47%), Gaps = 25/189 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+DR+  +  PH +   +Q   ++G + VD + VK N +++  + + +  
Sbjct: 48  VRVDPGQTPLRIDRFLVDRMPHTSRHRIQLAAKAGLIWVDGEPVKSNYKVKPLETITM-- 105

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L H  ++  I    + L          ++YED ++ V NKPAG+ V  G G     
Sbjct: 106 ---MLAHPKQDWSITPEDIPLD---------IVYEDDQLLVVNKPAGMVVHPGHGNYSGT 153

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +AY++        D       L HR+D++TSG+L+VA+   A   L   F ++   
Sbjct: 154 LVHALAYYLRN--DPLYDPNDASVGLVHRIDKDTSGLLLVAKRTEAKIRLARQFFLKTTG 211

Query: 181 KIYWSLVWG 189
           + Y +LVWG
Sbjct: 212 RRYQALVWG 220


>gi|126649461|ref|ZP_01721702.1| ribosomal large subunit pseudouridine synthase [Bacillus sp.
           B14905]
 gi|126593786|gb|EAZ87709.1| ribosomal large subunit pseudouridine synthase [Bacillus sp.
           B14905]
          Length = 279

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 52/202 (25%), Positives = 90/202 (44%), Gaps = 14/202 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED    + +KP G++         H  ++  +       G      HRLD+ T G+L
Sbjct: 78  IVYEDDHCLIVSKPKGMATHPNDDRDTHTCMNHVIAHIQQQGGMYAEHVHRLDKGTQGLL 137

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+   A          + I + Y + V G  ++    I+  + K  H     V     
Sbjct: 138 LVAKHPLAKSIFDRMIEEKSIIRTYAAEVQGNIRSSSGTISESIGKDRHHASRRV----- 192

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K   +A++H++V+  + +  C + +   TGRTHQ+RVH  ++G PI+GD  Y A    
Sbjct: 193 VSKTGQHAVTHYEVVSRY-KNSCVVHLILETGRTHQIRVHLAYIGHPIIGDTMYGAR--- 248

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                + +   LHA  ++  HP
Sbjct: 249 ---ETVSDDYELHAIQLEFDHP 267


>gi|242243072|ref|ZP_04797517.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242233530|gb|EES35842.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 274

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 67/271 (24%), Positives = 118/271 (43%), Gaps = 42/271 (15%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +L ++  S ++ ++++     N +++G  V IP      N++                  
Sbjct: 27  DLHQLNMSKEILINEEYGTLLNNVKTGDYVEIPTPNEVSNYL----------------PS 70

Query: 96  FLKSILLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +  + + YED  + +  KP G+      ++  + +  H+       VDS+  +P   HRL
Sbjct: 71  YRYAQIYYEDDDLAIVMKPKGVKTHPNDLKESNTLMNHV----IYTVDSEYVEP--IHRL 124

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           DQET G+L+VA+     + L        I +IY + V  +   K + I         IG 
Sbjct: 125 DQETVGLLIVAKNPLMKKILDRMLEYNEITRIYKANVKALLPIKPQTI------DMPIGK 178

Query: 211 DYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D  H  K+        AI+H        +  C L ++  TGRTHQ+RVH   +G P++GD
Sbjct: 179 DKFHSNKRRISNTGQRAITHIIDSKMIKEGVCQLNIKLDTGRTHQIRVHLAEIGHPVIGD 238

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             Y        TS ++ +L L++  ++  HP
Sbjct: 239 PLYG-------TSTLR-QLELNSHQIEFTHP 261


>gi|242240403|ref|YP_002988584.1| tRNA pseudouridine synthase C [Dickeya dadantii Ech703]
 gi|242132460|gb|ACS86762.1| pseudouridine synthase [Dickeya dadantii Ech703]
          Length = 261

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 98/227 (43%), Gaps = 46/227 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKPAG  V              +SW+D K             G+     
Sbjct: 4   ILYQDDYLVAVNKPAGWLVH-------------RSWLDRKEKVVVMQTVRDQIGRHVFTV 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++A +   A+ L   F   +++K Y ++V G   +  E + ++ L +  
Sbjct: 51  HRLDRPTSGVLLMALSPEVARMLALQFEQHQMEKTYHAVVRGYVAD--EGVIDYALTEEL 108

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQL 255
             I   Y        K    A+S ++ +               ++  LE+ P TGR HQL
Sbjct: 109 DRIADKYA----DPNKAPQPAVSAYRALARAEMPVAIGRYETSRYSLLELHPKTGRKHQL 164

Query: 256 RVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           R H  H+  PI+GD  H      +G  T    ++L LHA  + L HP
Sbjct: 165 RRHMAHIRHPIIGDTTHGDLRQNRGMATHFSCSRLMLHASRLRLNHP 211


>gi|319425744|gb|ADV53818.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 280

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 108/240 (45%), Gaps = 23/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  I   +KPAG+ V   S +A     F ++   D  G      HRLD+ TSG+L+
Sbjct: 32  ILFEDEHIVAIHKPAGLLVHR-SYLARRERFFAMQLTRDLVGCHVFPVHRLDRPTSGVLL 90

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVHVVK 217
            A++   A  L E F    I+K Y +LV G     +  I ++ LK     +G  +     
Sbjct: 91  FAKSSEVANALCEQFAEHSIEKQYLALVRG--NMHESGILDYPLKVELDELGDKHA---- 144

Query: 218 QNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + +K A  A++ FK +               +F  +++ P TGR HQLR H  H+  PI+
Sbjct: 145 RQDKTAQDAVTAFKPLLNTEIPYPSGRYPTSRFALVQLTPKTGRKHQLRRHMAHLRHPIL 204

Query: 268 GDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
           GD  +    +  F       N+L+L A+ +   HP    RL I   L       +  LG+
Sbjct: 205 GDTTHGDGKQNTFFREHFGINRLWLIAKKLTFTHPVTQTRLSIETELEQQWETVFTGLGW 264


>gi|326560902|gb|EGE11267.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 7169]
 gi|326566534|gb|EGE16680.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 12P80B1]
 gi|326569801|gb|EGE19851.1| tRNA pseudouridine synthase C [Moraxella catarrhalis BC8]
          Length = 254

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 104/240 (43%), Gaps = 23/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + + NKPA + V       +     +++  +   Q     HRLD+ TSG+LV 
Sbjct: 15  ILYQDACMVIINKPANMLVHRSWLDKHETCFVVQTLRNQINQHVYPVHRLDRPTSGVLVF 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVHVVKQ 218
           A     A  L + F    IQK Y ++V GI    +    ++ LK     I   +      
Sbjct: 75  ALDSQTAGLLAKQFENHHIQKSYLAVVRGIIGTGR---IDYALKPRLDKIADKF----SN 127

Query: 219 NEKGANYAISHFKVID----------CF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             K +  AI+ ++V+           CF + ++  + + P TGR HQLR H  H+  PIV
Sbjct: 128 PNKASKSAITDYQVLATTQQPFISCRCFDSSRYSLVRLTPITGRKHQLRRHMKHIFHPIV 187

Query: 268 GDHKYCANF--KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
           GD  Y      +         +L LHA  +   HP    + +I APL     +   + G+
Sbjct: 188 GDTTYGDKVQNRAVLAHIGVKRLLLHAHQLQFCHPLYDEMIRIVAPLDTAFCQVMTAFGW 247


>gi|145634988|ref|ZP_01790695.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittAA]
 gi|145267854|gb|EDK07851.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittAA]
          Length = 239

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 57/224 (25%), Positives = 102/224 (45%), Gaps = 17/224 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP G+ V       +     +++  D  GQ     H LD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPDGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHCLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KY--CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           +Y      +   +    ++L+LH+  +   HP    ++ ITA L
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSNSLSFIHPITKEQITITAGL 223


>gi|260906535|ref|ZP_05914857.1| ribosomal large subunit pseudouridine synthase D [Brevibacterium
           linens BL2]
          Length = 307

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 102/208 (49%), Gaps = 15/208 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +++++    V +KP G++     G     + G L +    + + G   R  +  RLD  T
Sbjct: 83  VVHDEDSFVVVDKPVGVAAHPALGWKGRTVVGGLAAAGFRIATSGAPERQGIVQRLDVGT 142

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-V 213
           SG++V+A++  A   L  +F+ R ++K Y ++V G+P      I   + +     G Y V
Sbjct: 143 SGLMVIAKSEYAYSVLKRAFKERTVEKTYHAVVQGLPDPVLGTIDAPIARNPRHDGLYAV 202

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H       G   AI+H++V++   ++   +E+   TGRTHQ+RVH   +  P VGD  Y 
Sbjct: 203 H------SGGKNAITHYEVLEAH-RRASLVEVHLETGRTHQIRVHFSALKRPCVGDLPYG 255

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           A+        ++ + +LHA  +   HPE
Sbjct: 256 ADPTLAKDLHLERQ-WLHAVKLGFHHPE 282


>gi|313891370|ref|ZP_07824986.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
 gi|313120145|gb|EFR43321.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
          Length = 303

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 65/268 (24%), Positives = 123/268 (45%), Gaps = 33/268 (12%)

Query: 12  VENDEENMRLDRWFKNH--YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +D+   RLD + K     PH  F+   K L+  +++V+ K+   N ++++G +V    
Sbjct: 6   ITSDKNGKRLDNYIKEKEKIPHFIFI---KSLKKNKIKVNGKKESGNYKLKTGDIV---- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                ++I  + K     ++ +         + YED  I +  K AGI     +      
Sbjct: 59  ----TSYIENKNKNEKEKIHFS---------INYEDENIIIAEKEAGILCNDTTNKEEKT 105

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   I+ +LK   + +       HR+D  T+G+++ A+   A   L  + + R I+K Y 
Sbjct: 106 LHDEINEYLKGKNEPEAYP---VHRIDLNTTGLVIFAKNMHARAILDRAIKERNIKKYYL 162

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +  G  K K   + + L K +    + V++ ++  KG+  A  ++K +         +E
Sbjct: 163 CVTTGTMKKKSGKLEHQLFKDAK--NNKVYIYEKPCKGSKTATMNYKCLKT-ENGLSLVE 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  TGRTHQ+R    ++G PI+GD KY
Sbjct: 220 CELITGRTHQIRSQLSYIGYPILGDDKY 247


>gi|291523779|emb|CBK89366.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale DSM 17629]
          Length = 241

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 109/243 (44%), Gaps = 32/243 (13%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETS 155
           K  ++YED+ I V  KPAGI+ Q        ++ F++++  +K + P   + HRLDQ   
Sbjct: 3   KPDIIYEDNDIIVCYKPAGIATQTRRIGQQDMESFIRNYRAAKNEPPYVGIVHRLDQPVE 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIANWLLKKSHIGGD-- 211
           G++V A+ + AA  L+   +    +K Y   S   G+     E    W     +I  D  
Sbjct: 63  GVMVFAKNQKAAASLSRQIKEHTTEKYYRAASRGQGVSGTAVEEEEAWHTLTDYISFDKR 122

Query: 212 --YVHVVKQNEKGANYAISHFKVI-----------DCFAQKFCWLEMQPHTGRTHQLRVH 258
                +  + ++ A  A+  ++VI           +C   +F   +++  TGR HQ+R+ 
Sbjct: 123 TNTSKITSEKDRLAKKAVLQYRVISVTPDRDGFKNECIRTEF---DIKLLTGRHHQIRLQ 179

Query: 259 ALHMGCPIVGDHKY---------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
             ++G P++GD KY           +  G     ++ +L L +  +   HP  G  ++T 
Sbjct: 180 LANIGYPLIGDTKYGKPASNNSGTGSKSGRTGGGVREQLALCSYKLVFDHPATGE-RMTF 238

Query: 310 PLP 312
            LP
Sbjct: 239 ELP 241


>gi|295696332|ref|YP_003589570.1| pseudouridine synthase [Bacillus tusciae DSM 2912]
 gi|295411934|gb|ADG06426.1| pseudouridine synthase [Bacillus tusciae DSM 2912]
          Length = 356

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 78/312 (25%), Positives = 127/312 (40%), Gaps = 62/312 (19%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +KIL +G+V    K +K  +R+++            L  I ++    +S+ ++       
Sbjct: 65  KKILVNGRVSFLAKPMKPGDRVEAD-----------LREIGRKAGTTESNPSIP------ 107

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---SKGQK------PRLTH 148
              +LYED  + V +KPAG+ V   +           S  D   S+G        P L H
Sbjct: 108 ---ILYEDDWVLVIDKPAGLVVHAPAPARRTGRPGTTSLADILHSRGAAANPPWVPHLVH 164

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD++T G+L+ A++      L  + R   I +IY  +  G      E I   +      
Sbjct: 165 RLDRDTGGVLLAAKSAHIHARLDRALREGGIHRIYSVVAEGNAMEIPERIELPVAPDPGR 224

Query: 209 GGDYVHVVKQNEKGANYAISH-----FKVIDCFAQK---------------FCWLEMQPH 248
            G +    +  + GA  A++      F  +   A                   +L++   
Sbjct: 225 PGRF-RPAEPGDAGAKPAVTRVCGRRFIPLPAPAAPRGSPLDEPRWSALSGVTFLDVSLE 283

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
           TGRTHQ+RVH   +G PI+GD  Y +             L L AR +  PHP +G  +++
Sbjct: 284 TGRTHQIRVHLSALGHPILGDRWYGSRHP-------NLPLMLFARSLTFPHPADGHSVEV 336

Query: 308 TAPLPAHMVKTW 319
            AP P    +TW
Sbjct: 337 AAPFP----ETW 344


>gi|227539212|ref|ZP_03969261.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
 gi|227240894|gb|EEI90909.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
          Length = 230

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 104/228 (45%), Gaps = 36/228 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL-THRLDQETSGILV 159
           +L++D +I   NKP G+ V   S IA     F    +  + Q+     HRLD++T GIL+
Sbjct: 4   ILHQDQEIVAINKPHGLLVHR-SPIARDASEFALQLLRDQLQQRVYPAHRLDRKTGGILL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            + T+   + L + F+ R++ K Y ++V G  +++               G   + +K+ 
Sbjct: 63  FSLTKEMDKSLQQLFQDRKMNKSYLAVVRGYTEDE---------------GRIDYPLKKE 107

Query: 220 EKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++H+K +          +    ++  +E  P TGR HQLR H  H+  PI+GD
Sbjct: 108 NGEEQEALTHYKTLSRSEIDLPTGNFTTSRYSLVEANPETGRMHQLRKHFAHIFHPILGD 167

Query: 270 HKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
             +  N     +K  F     + + LHA  +   HP  G  + I APL
Sbjct: 168 RPHGCNKQNKLWKERFE---MDTMMLHASQLSFEHPTTGNIILIKAPL 212


>gi|154175159|ref|YP_001407354.1| putative prophage LambdaCh01, recombination protein Bet
           [Campylobacter curvus 525.92]
 gi|112802454|gb|EAT99798.1| putative prophage LambdaCh01, recombination protein Bet
           [Campylobacter curvus 525.92]
          Length = 305

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 53/175 (30%), Positives = 90/175 (51%), Gaps = 12/175 (6%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++E  +  VF+KP+G+ S   G    Y ++   + W    G++  +THRLD+ETSG++VV
Sbjct: 72  IFECDEFAVFDKPSGVLSHPNGRRCEYSLND--EIW-HLYGREAAVTHRLDRETSGLIVV 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY--VHVVKQ 218
           ++  AA + L   F  R ++K Y +L  G     + C    +  K  +  DY  V +  Q
Sbjct: 129 SKNLAAQKELKAMFESRAVKKRYVALAGG-----EICEPFIVDAKMDLASDYDDVKMRMQ 183

Query: 219 NEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +    A++ F+ ++ FA      +   P TGR HQ+R+H  H+   I+G+  Y
Sbjct: 184 ICENGKAAVTEFEPMEYFADIDATLVRAVPLTGRQHQIRLHLFHVKHAIIGEPLY 238


>gi|319794856|ref|YP_004156496.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315597319|gb|ADU38385.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 220

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 55/206 (26%), Positives = 100/206 (48%), Gaps = 20/206 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++ED  + V  KPAG+    G G           +  W D+      + HRLD  TSG++
Sbjct: 9   IHEDVHLLVLEKPAGLLCVPGRGDDKQDCLSARAMHRWPDAL-----IVHRLDMATSGLV 63

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-VVK 217
           V+AR+    + L+ +F  R++ K Y ++V G    ++    +W +  + +  D+    ++
Sbjct: 64  VMARSLEMQRALSAAFADRQVHKRYEAIVDGAMPMRE----DWSIIDAPLMADWPRRPLQ 119

Query: 218 QNEKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +     +++ ++ +    Q       + ++P TGR+HQLRVH L +G PI+GD  Y  
Sbjct: 120 KTDPAGKPSLTRWRALASSMQGEFSATHVLLEPETGRSHQLRVHLLSIGHPILGDALY-G 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           +      +P   +L LHA  +   HP
Sbjct: 179 DAAVQARAP---RLMLHASELAFVHP 201


>gi|307637434|gb|ADN79884.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 908]
 gi|325996024|gb|ADZ51429.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 2018]
 gi|325997619|gb|ADZ49827.1| Ribosomal large subunit pseudouridylate synthase D [Helicobacter
           pylori 2017]
          Length = 327

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 105/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W+ S+       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVVHKAPSVK---EPTLVDWLKSQNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+       L+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVCLSEQLKTKTMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAQKEKSRYSKSEFISLLTSQNGMDLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N      S  + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 257 YGLN---GALSKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|304399240|ref|ZP_07381107.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304353294|gb|EFM17674.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 259

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 99/225 (44%), Gaps = 36/225 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   NKP+G  V   S +  H   F+   V D  GQ     HRLD+ TSG+L+
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHR-SWLDRHETVFVMQTVRDQIGQHVFTAHRLDKPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +  +    + L+  F   ++QK Y ++V G           WL     I  DY  V + +
Sbjct: 63  MGLSSEVGRLLSLQFEQHQMQKTYHAVVRG-----------WLESSGTI--DYPLVEELD 109

Query: 220 E---------KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHAL 260
           +         + A  A++ ++ +               ++  +EM P TGR HQLR H  
Sbjct: 110 KIADKHATEARTAQPAVTDYQSLATVEMPVGIGRYPTSRYSLVEMAPKTGRKHQLRRHMS 169

Query: 261 HMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           H+  PI+GD  H      +G       N+L LHA  + L HP  G
Sbjct: 170 HLRHPIIGDSAHGDLRQNRGAAEHFGANRLMLHASSLALTHPVTG 214


>gi|152974728|ref|YP_001374245.1| RluA family pseudouridine synthase [Bacillus cereus subsp.
           cytotoxis NVH 391-98]
 gi|152023480|gb|ABS21250.1| pseudouridine synthase, RluA family [Bacillus cytotoxicus NVH
           391-98]
          Length = 297

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 66/259 (25%), Positives = 123/259 (47%), Gaps = 35/259 (13%)

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKS-----ILLYEDSKIYVFNKPAGISV------QG 121
            + HI+K  +IL     + + S+ + +      ++YED  + V NK   +S         
Sbjct: 51  TVRHILKTGEILQIFFPVEERSEGMVAEKIPLSIVYEDDAVLVINKEPYMSTIPSREHPT 110

Query: 122 GS---GIAYHIDG-FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           GS    + YH D   L S V        +  RLD++TSG++++A+ R     L++  + +
Sbjct: 111 GSIANALLYHYDTQKLASTV-------HIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           ++++ Y ++V G   N+   I   + +KS    D + + +   +    A++HF+V   ++
Sbjct: 164 QVKRTYEAVVHGRMLNESGTIDAPIGRKS----DSI-IERMVREDGQKAVTHFQVRKRYS 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            K   + +Q  TGRTHQ+RVH  H+G P++GD  Y           +  +  LH++ +  
Sbjct: 219 NK-THVALQLDTGRTHQIRVHMAHIGHPLLGDDLYGGQLD------LIKRQALHSKSLTF 271

Query: 298 PHP-EGGRLQITAPLPAHM 315
            HP     +  +A +P  M
Sbjct: 272 YHPILEKEMSFSADIPTDM 290


>gi|229160262|ref|ZP_04288261.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           R309803]
 gi|228623223|gb|EEK80050.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           R309803]
          Length = 292

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 113/237 (47%), Gaps = 33/237 (13%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           G + V+ +     +++Q+G+ +R+  PV      +I E   L                ++
Sbjct: 36  GAIEVNGQHTSVRHQLQAGEELRVFFPVEERSEGMIAEDIPLS---------------IV 80

Query: 103 YEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           YED  + V NK A +S         GS     +  + K  V S      +  RLD++TSG
Sbjct: 81  YEDEAVLVINKEANMSTIPSREHPTGSVANALLSHYDKQHVAST---VHIVTRLDRDTSG 137

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++++A+ R     L++  + + +++ Y ++V G    +   I   + +KS    D +   
Sbjct: 138 LMLIAKNRFVHHLLSKQHQQKAVRRTYEAVVHGEMIERAGTIDAPIGRKS----DSIIER 193

Query: 217 KQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              E G   A++HF+VID  + +    LE++  TGRTHQ+RVH  +MG P++GD  Y
Sbjct: 194 TVCENGQR-AVTHFRVIDSAYHKTHVSLELE--TGRTHQIRVHMAYMGHPLLGDSLY 247


>gi|260776531|ref|ZP_05885426.1| tRNA pseudouridine synthase C [Vibrio coralliilyticus ATCC BAA-450]
 gi|260607754|gb|EEX34019.1| tRNA pseudouridine synthase C [Vibrio coralliilyticus ATCC BAA-450]
          Length = 241

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 57/215 (26%), Positives = 94/215 (43%), Gaps = 22/215 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   IVFQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    + K Y ++V G  +          ++   I   +       E
Sbjct: 65  ALSSDVASQVMPMFANHEMVKTYHAIVRGWIEEAGRLDYALKVELDKIADKHA----SQE 120

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ +  +               ++C +E++P TGR HQLR H  H+  PIVGD 
Sbjct: 121 KEAQEAITDYHTLAKAEIPYSTGKFPTTRYCLMELKPLTGRKHQLRRHMAHLRHPIVGDT 180

Query: 271 -----KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
                K+   F+  + S   ++L LHA  ++  HP
Sbjct: 181 THGDGKHNKLFREVYDS---HRLLLHASSLEFVHP 212


>gi|163790580|ref|ZP_02185009.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Carnobacterium sp. AT7]
 gi|159874183|gb|EDP68258.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Carnobacterium sp. AT7]
          Length = 310

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 55/204 (26%), Positives = 98/204 (48%), Gaps = 16/204 (7%)

Query: 102 LYEDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +YED    V NKP G++     V     +A  + G+     +   Q   +  RLD++T+G
Sbjct: 90  VYEDEHYLVVNKPFGVASVPSQVHPEGTMANRVKGYYVRQ-NYDDQVIHIVTRLDRDTTG 148

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++ A+   A   + E  R + I K Y +L+ G     +    +  + ++    D +   
Sbjct: 149 LMLFAKHGYAHALMDEKLRAKEITKKYTALISGQFNESEHGFIDAPIART---TDSIITR 205

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           + +E G   A++ + + + F Q    +++Q HTGRTHQ+RVH  H+G P++GD  Y    
Sbjct: 206 RAHESGKE-ALTEYWIKEAFPQA-TLVDIQLHTGRTHQIRVHFAHIGHPLMGDDLY---- 259

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
            G   +    +  LH R ++  HP
Sbjct: 260 -GGKKNEWIVRQALHCRELNFKHP 282


>gi|84391790|ref|ZP_00991692.1| pseudouridine synthase Rlu family protein [Vibrio splendidus 12B01]
 gi|84376503|gb|EAP93382.1| pseudouridine synthase Rlu family protein [Vibrio splendidus 12B01]
          Length = 232

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 64/205 (31%), Positives = 97/205 (47%), Gaps = 33/205 (16%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--T 147
           L  HSDFL            + NK  G+SV    G     D  L   V     +P+L   
Sbjct: 5   LLNHSDFL------------LINKHPGVSVHKDDG-----DTMLLQEVAKAINEPKLYLV 47

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSGIL++A+  +AA  L++ F  R ++K Y ++    PK K+  I+   +++S 
Sbjct: 48  HRLDKMTSGILLLAKNASAASELSQLFAKREVEKYYLAIGSKKPKKKQGLISG-DMERSR 106

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                +   K+N      AI+ F        +  +L  +P+TGRTHQ+RV    +G  IV
Sbjct: 107 RSSWKLLTSKENP-----AITQFLSATAEPGERLFL-CKPYTGRTHQIRVAMKSIGSAIV 160

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA 292
           GD  Y  + +        ++ YLHA
Sbjct: 161 GDPIYNPSSEA-------DRGYLHA 178


>gi|327438734|dbj|BAK15099.1| pseudouridylate synthase [Solibacillus silvestris StLB046]
          Length = 277

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 57/212 (26%), Positives = 96/212 (45%), Gaps = 20/212 (9%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLD 151
           +D     + YED    + +KP G++            ++  ++  +D+ G      HRLD
Sbjct: 70  TDSCDVKIRYEDEHCLIVSKPKGMATHPNEPTDNDTCMNHVMRYIMDNGGHYAEHVHRLD 129

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q T+G+L+VA+   A          + I + Y + V G  +     I       + IG D
Sbjct: 130 QGTNGLLLVAKHPVAKSIFDRMIEEKTIVRTYAAEVQGNLRTDSGTI------NAGIGKD 183

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             H  ++       +A++H++V++ + +  C + +   TGRTHQ+RVH  H+G PIVGD 
Sbjct: 184 RHHNTRRVVSPTGQHAVTHYEVVNRY-KGTCVVHVVLETGRTHQIRVHMAHLGHPIVGDT 242

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHP 300
            Y A     G++         LHA  +   HP
Sbjct: 243 MYGARETASGDYA--------LHAIQLAFMHP 266


>gi|315586901|gb|ADU41282.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori 35A]
          Length = 242

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 61/202 (30%), Positives = 99/202 (49%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENILALFKPPFIE-------SYDLVSFFKGWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y +L  GI + ++E  A  L  K+     +  +
Sbjct: 100 ILLVKENSEF-HLKAKKAFKDRAVKKEYLALAQGIIEEEQEINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L+    TGRTHQ+R+H  H+  PI+GD  Y  N
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKAGIKTGRTHQIRIHLKHINHPIIGDTLYN-N 210

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
             G+       +L LHA  + L
Sbjct: 211 EPGS-----AKRLMLHAHKIAL 227


>gi|210135145|ref|YP_002301584.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori P12]
 gi|210133113|gb|ACJ08104.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori P12]
          Length = 242

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 61/202 (30%), Positives = 99/202 (49%), Gaps = 31/202 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  +    KP  I        +Y +  F K WV        L HRLD+ETSG+
Sbjct: 55  KPSVIFEDENVLALFKPPFIE-------SYDLVSFFKDWV--------LLHRLDKETSGV 99

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +  +   HL   ++F+ R ++K Y  L  GI + ++E  A  L  K+     +  +
Sbjct: 100 VLLVKENSEF-HLKAKKAFKNRAVKKEYLVLAQGIIEEEREINAPILTIKT--TKAFSKI 156

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+ ++     I+  K+I+    K   L++   TGRTHQ+RVH  H+  PI+GD  Y  N
Sbjct: 157 SKKGQEAVTI-ITPLKIIN----KKTLLKVGIKTGRTHQIRVHLKHINHPIIGDTLYN-N 210

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
             G+       +L LHA  + L
Sbjct: 211 EPGS-----AKRLMLHAHKIAL 227


>gi|219121405|ref|XP_002185927.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|209582776|gb|ACI65397.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 193

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 57/181 (31%), Positives = 86/181 (47%), Gaps = 18/181 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSLV--WGIPKNKKE---CIA 199
           + HRLD ETSG+L+ ART  AA  L+ ++R R  +QK Y + V  W +P+        +A
Sbjct: 17  IVHRLDCETSGVLLFARTSEAASRLSRAWREREHVQKTYVAKVYSWRLPETSGRIDLALA 76

Query: 200 -------NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                   W+  K       +  V  +E+ A          D  A+    L + P TGRT
Sbjct: 77  PHPTERIKWIASKEGKPSTTLWTVMPDERKAT---CQNPDSDGCARPVK-LRLIPVTGRT 132

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           HQLR+H    G  I+GD  Y   F        +++L+LH++ + +PHP  G++      P
Sbjct: 133 HQLRIHCCAHGDGILGDTLY-GKFATQSLPGKRSRLFLHSQALSVPHPTTGKMVTFISTP 191

Query: 313 A 313
           A
Sbjct: 192 A 192


>gi|283783562|ref|YP_003374316.1| pseudouridine synthase, RluA family [Gardnerella vaginalis 409-05]
 gi|283441085|gb|ADB13551.1| pseudouridine synthase, RluA family [Gardnerella vaginalis 409-05]
          Length = 321

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 59/214 (27%), Positives = 105/214 (49%), Gaps = 20/214 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----------IAYHIDGFLKSWVDSKGQKPRLTHRL 150
           ++Y D  + V +KP G++     G           A  ID  +K+ +  + +K  +  RL
Sbjct: 94  IIYNDDDVVVIDKPVGVASHAAKGWSGPTVPECLEAVGID--IKTTLCDESRKG-IVSRL 150

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+++V +T  A + +   F    ++K Y +LV G     K  I +  + ++ +  
Sbjct: 151 DVGTSGLMLVCKTDFAYEVMKNQFAKHIVKKTYHALVQGDLAQDKATI-DAPIGRAKVS- 208

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D+   +  + K    A++H+ V++ F+Q    + +   TGRTHQ+RVH   +G P+VGD 
Sbjct: 209 DFRFTITSDGK---PAVTHWDVLERFSQA-TLVSVNLETGRTHQIRVHFSSIGHPLVGDS 264

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            Y AN        +Q + +LH+  +   HP  G+
Sbjct: 265 MYGANPVLAQKLGLQRQ-WLHSMELTFTHPRTGK 297


>gi|257452370|ref|ZP_05617669.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|257465837|ref|ZP_05630148.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|315916994|ref|ZP_07913234.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|317058913|ref|ZP_07923398.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|313684589|gb|EFS21424.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|313690869|gb|EFS27704.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
          Length = 289

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 59/211 (27%), Positives = 100/211 (47%), Gaps = 17/211 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQK--PRLTHRLDQETSG 156
           ++YED  + + NK A +     +    A   +G +  ++ + G+   PR  +RLD  T+G
Sbjct: 75  IVYEDENLLILNKQANLVTHPTTKKVDATLANGVVAYFLKTTGKTMVPRFYNRLDMNTTG 134

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++V +   +  +L E   +R   K Y ++V GI +  +  I   + K   +G D   + 
Sbjct: 135 LIIVTKNAYSQAYLQEKTEVR---KSYQTIVKGIVEQDEFYITKPIGK---VGEDLRRIE 188

Query: 217 KQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               +G   A +  KV+  F ++    L++   TGRTHQ+R H    G PIVGD  Y   
Sbjct: 189 LAVSEGGQEAKTFVKVLKRFPERNRTLLDVTLFTGRTHQIRAHLSLEGYPIVGDDLY--- 245

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
             G     I+ +L LHA  +   +P+ G  Q
Sbjct: 246 --GGADDRIKRQL-LHAYRLTFQNPKNGEQQ 273


>gi|238755849|ref|ZP_04617179.1| Pseudouridine synthase [Yersinia ruckeri ATCC 29473]
 gi|238705934|gb|EEP98321.1| Pseudouridine synthase [Yersinia ruckeri ATCC 29473]
          Length = 232

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 101/234 (43%), Gaps = 33/234 (14%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------SGIAYHIDGFLKS 135
           KI+D+ +    H        LY+D  + + NKPAG+    G        + Y +      
Sbjct: 3   KIIDTFIAPPCHDKIEN---LYQDDHLVLINKPAGLLSLSGKNPQNLDSVHYRLVQIFPG 59

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                     L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   +  
Sbjct: 60  CT--------LVHRLDFGTSGLMVIARNKAINAALCQQFSQRSVTKVYSALLCG-HLDDN 110

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQP 247
           E + +  + K       + +   + K A    S ++V++ F  +           +++ P
Sbjct: 111 EGVIDAAIAKDPALFPRMSICATHGKPAR---SGYRVVERFYHELEDGTLLPLTRVQLTP 167

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            TGRTHQLR+H   +G PI G   Y      G   +P   +L LHA  +   HP
Sbjct: 168 ETGRTHQLRIHCQQLGHPIWGCDLYGGRLLPGTERTP---RLMLHASELHFVHP 218


>gi|134298263|ref|YP_001111759.1| RluA family pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134050963|gb|ABO48934.1| pseudouridine synthase, RluA family [Desulfotomaculum reducens
           MI-1]
          Length = 303

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 81/323 (25%), Positives = 144/323 (44%), Gaps = 37/323 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVR 66
           Q V+     +N +  R F  H   I+   L+K+   G++  +  +V +   + +G +VV 
Sbjct: 7   QVVLCVEASQNGKFLRDFLKHK-DISDRALKKLRNEGEILCNGAKVTWRTIVNTGDKVVL 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I P+     ++  E   LD S+             + ED  I + NK  G+ V     +A
Sbjct: 66  IYPIPPRNQYLPPEP--LDLSI-------------ISEDEDIALVNKQPGMCVH--PTLA 108

Query: 127 YH----IDGFLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           Y      +G +  W+++         +R+D+ TSG+++VA+   +AQ L    + +++ +
Sbjct: 109 YPSGTLANGLVYHWLENNPAPTFHAVNRIDRNTSGLVLVAKNSYSAQKLFLQRKRKQLAR 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G    +   I +  L+K     +     +Q       A++ F+V+  +     
Sbjct: 169 SYVALVHGKIVQRNGYI-DLPLEKC----EGKTTKRQISSTGQQALTRFEVLQ-YITDCT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + + P TGRTHQ+RVH  H+G P+VGD  Y     G   + I  +  LHA  +   HP 
Sbjct: 223 LIRLMPETGRTHQIRVHLSHLGHPLVGDTLY-----GGSIAQI-GRHCLHADKISFLHPR 276

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            G  +    PL   M++    +G
Sbjct: 277 TGHPMSFQIPLAEDMLQVITEMG 299


>gi|315182443|gb|ADT89356.1| ribosomal large chain pseudouridine synthase A [Vibrio furnissii
           NCTC 11218]
          Length = 558

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 103/221 (46%), Gaps = 20/221 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           LD +  L   ++  +  ++Y+D  I V NKPA  +SV G +     +    + + + +G 
Sbjct: 340 LDDNPLLNNPAEGQEIEIVYQDEAIVVINKPAEFLSVPGVNVKDSALTRLEQQFPEVEG- 398

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P + HRLD  TSG+LV A TR A + L + F  R ++K Y +L+ G   +  E I    
Sbjct: 399 -PFVLHRLDMSTSGLLVFALTRRANKSLQKQFITRGVEKRYVALLSGEIAH-GEGIITLP 456

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH- 261
           L+          V  ++ K A    ++++ I    Q    + + P TGRTHQLRVH  H 
Sbjct: 457 LRPDLDDRPRQMVCFEHGKAAE---TYWQTIGT-EQGRTRVYLSPKTGRTHQLRVHCAHA 512

Query: 262 --MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
                PI GD  Y             N+L+LHA  +   HP
Sbjct: 513 QGFNTPIWGDDLYGEK---------ANRLHLHAESLSFDHP 544


>gi|259502332|ref|ZP_05745234.1| ribosomal large subunit pseudouridine synthase [Lactobacillus antri
           DSM 16041]
 gi|259169712|gb|EEW54207.1| ribosomal large subunit pseudouridine synthase [Lactobacillus antri
           DSM 16041]
          Length = 309

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 106/227 (46%), Gaps = 34/227 (14%)

Query: 101 LLYEDSKIYVFNKPAG----ISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +L+E+  + V NKP G     +  G +G   + + G+L            + HRLDQETS
Sbjct: 92  VLFENRDLVVVNKPQGQKSHPNYHGETGTLLNDVAGYLAG----SDCGAFMVHRLDQETS 147

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIAN--WLLKKSHIGG 210
           G ++VA+       L       +I + Y ++V G    +    E I      ++K  +GG
Sbjct: 148 GAMIVAKNPVVVPVLNRLISSGQIHRRYLAVVAGRLTGRGRFTEAIGKDPQDVRKYQVGG 207

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           ++          A  A ++++V+     +   L +Q  TGRTHQ+RVH  H G PI+GD 
Sbjct: 208 EH----------AKPAQTNYQVLANQGDRTLVL-LQLATGRTHQIRVHLAHSGHPIIGDP 256

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
            Y    + NF+     ++ LH    +L  P    R+Q+TAPLP +  
Sbjct: 257 LYS---RDNFS-----RMLLHGAAQELVLPFSFKRIQVTAPLPTYFT 295


>gi|238019027|ref|ZP_04599453.1| hypothetical protein VEIDISOL_00889 [Veillonella dispar ATCC 17748]
 gi|237864511|gb|EEP65801.1| hypothetical protein VEIDISOL_00889 [Veillonella dispar ATCC 17748]
          Length = 322

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 98/230 (42%), Gaps = 32/230 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQKP-RLTHRLDQETSGI 157
           ++YED  I V NK AGI +   S +  H   +G L  +  +         HRLD++TSGI
Sbjct: 104 IVYEDEYILVINKEAGILMHPTSTVRDHTLANGVLHYYQQTNQHYDFHPVHRLDKDTSGI 163

Query: 158 LVVARTRAAAQHLTESFRMR-----------RIQKIYWSLVWGIPKNKKECIANWLLKKS 206
           +++A+T +  QH  +  R             ++   + S+ W I +     I      + 
Sbjct: 164 VIIAKT-SVVQHAFDKKRTHFHKNYDAIVEGQLPTNHISVQWPIGRKPGSIIERCCTNEG 222

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                 + V++ N    N      K+  CF    C L    HTGRTHQ+RVH   +G P+
Sbjct: 223 KPAHTDITVIESNTIVKN------KIEQCFTHVQCLL----HTGRTHQIRVHLSQLGYPL 272

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            GD  Y  +           +  LHA  +   HP     L+I A +P+ M
Sbjct: 273 AGDDLYGGHLD------YIGRQALHASRISFYHPMTDEWLEIQASIPSDM 316


>gi|156537257|ref|XP_001605561.1| PREDICTED: similar to ribosomal pseudouridine synthase [Nasonia
           vitripennis]
          Length = 552

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 113/236 (47%), Gaps = 27/236 (11%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           ++ +R+G + V+ ++V  + R++   +         L +++   ++  +S  +T      
Sbjct: 158 ERCIRAGTLTVNYQKVDVDYRLRHNDL---------LANVVHRHEVPVTSEPIT------ 202

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ D  + V NKPA I V       ++   F+ +  +   +  R  HRLD+ TSGI
Sbjct: 203 ---VIHMDEDVVVVNKPASIPVHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDRLTSGI 258

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVV 216
           L+  RT   A+ +    R R++QK Y   V G  P+ +  C     +    IG     V 
Sbjct: 259 LLFGRTPKKARQMEHQIRNRQVQKQYVCRVEGEFPEEEIVCSEAIEVVSYKIG-----VC 313

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K ++KG +  I+ FK +  +  K   +  +P TGR HQ+RVH  ++G P+V D  Y
Sbjct: 314 KVSDKGKD-CITKFKRLS-YNGKSSVVLCKPQTGRMHQIRVHLQYLGYPVVNDPLY 367


>gi|160876630|ref|YP_001555946.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160862152|gb|ABX50686.1| pseudouridine synthase [Shewanella baltica OS195]
          Length = 245

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 62/216 (28%), Positives = 98/216 (45%), Gaps = 18/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+DS I + +KP+G+    G     ++D      V        L HRLD  TSGI++V
Sbjct: 26  VLYQDSDILLIDKPSGLLSLSGKN-PLNLDSVHYRLVQDFPTA-TLLHRLDFGTSGIMLV 83

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  ++    LT+ F+ R ++K Y +L+ G        I   + K      D+  + K   
Sbjct: 84  ALNKSVNGLLTKQFQARTVEKRYTALLHGHIAADSGVINLPIAKDV----DHFPLQKICH 139

Query: 221 KGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NF 276
                AIS ++V++   + F   +E  P +GRTHQLR+H+   G  I+G   Y     + 
Sbjct: 140 STGKPAISEYRVLERLTEPFATRVEFTPVSGRTHQLRIHSQQFGHSILGCDLYGGVGESV 199

Query: 277 KGNFTSP--------IQNKLYLHARYMDLPHPEGGR 304
             N  +P          ++L LHA  +   HP  G 
Sbjct: 200 ADNADAPEPDITKMTSNSRLMLHATRLAFDHPITGE 235


>gi|225849242|ref|YP_002729406.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225644151|gb|ACN99201.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 318

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 72/297 (24%), Positives = 132/297 (44%), Gaps = 40/297 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK---FNNRIQSGQVVRIP 68
           V  +   +RLD++    YP  +    Q ++  G +  + K +K      ++     V IP
Sbjct: 9   VNEEYAGLRLDQFLAKVYPEYSRSYYQDLIEKGFILKEDKPIKKPSLKVKVGESYTVIIP 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P         +  +++  ++ L          + YED  + V  KP G+ V    G   H
Sbjct: 69  PP--------QPLEVVPENIPLK---------VYYEDEDLAVVYKPPGMVVHPSVG---H 108

Query: 129 IDGFL--------KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             G L        K+    +G ++  + HRLD++T+G+++VA++    + L + F+ R I
Sbjct: 109 TSGTLVNALLYHFKNVSTYQGKERAGIVHRLDKDTAGLIIVAKSEFTHKELQKMFQNREI 168

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            K Y ++V GI K K   I +  + +S      +  V  N +    A++ + V   + + 
Sbjct: 169 DKRYKAIVVGIVK-KDHGIIDLPIGRSIYDRQKMGTVATNLRD---ALTEYWVEKRWEKH 224

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHA 292
               ++++ HTGRTHQ+RVH   +G P++ D  Y    +    +    + N L  HA
Sbjct: 225 NLTMVDIKLHTGRTHQIRVHFSAIGHPLLNDQVYGFKKSKLGSSLAVELSNILNYHA 281


>gi|83644882|ref|YP_433317.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83632925|gb|ABC28892.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 231

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 60/219 (27%), Positives = 102/219 (46%), Gaps = 26/219 (11%)

Query: 117 ISVQGGSGIAYHID----GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           + V    GI++H +    G      D+ G +    HRLD+ TSG+L++ +T A A+ LTE
Sbjct: 16  LVVDKAPGISFHDEEGQPGLCSCVADTLGIRVYPVHRLDKVTSGLLLLPKTPALARELTE 75

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F +R+++K Y +L    P+ K+  I    ++K+  G   +   ++N     +  SH   
Sbjct: 76  QFSLRQVEKYYLALSAHKPQKKQGKIIG-DMEKARAGAWKLTAGRENPAVTQF-FSH--S 131

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           +    + F    ++P TG+THQ+RV    +  PI GD  Y       F     ++ YLHA
Sbjct: 132 LQPGVRAFM---VRPLTGKTHQIRVALKSVSAPIAGDSLYGGRANKEF-----DRTYLHA 183

Query: 293 ----------RYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
                     R   L  P+ G L ++  + A + + W +
Sbjct: 184 YGVRFNYRGNRTAILCPPQNGALFVSEAMSALLEENWGA 222


>gi|238783433|ref|ZP_04627456.1| Pseudouridine synthase [Yersinia bercovieri ATCC 43970]
 gi|238715678|gb|EEQ07667.1| Pseudouridine synthase [Yersinia bercovieri ATCC 43970]
          Length = 267

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 61/208 (29%), Positives = 95/208 (45%), Gaps = 18/208 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKPAG+    G     +ID      V        L HRLD  TSG++V+A
Sbjct: 55  LYQDDHLVLINKPAGLLSLSGKN-PQNIDSVHHRLVQ-IFPGCTLVHRLDFGTSGLMVIA 112

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L + F  R + K+Y +L+ G   + +  I   + K   +    + +   + K
Sbjct: 113 RNKAINAALCQQFSQRTVTKVYSALLCGHLDDNQGVIDAAIAKDPAL-FPLMSICSIHGK 171

Query: 222 GANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            A    S ++V++ F  +           +++ P TGRTHQLR+H   +G PI G   Y 
Sbjct: 172 PAR---SRYRVVERFYHELEDRTLLPLTRVQLTPETGRTHQLRIHCQQLGHPIWGCDLYG 228

Query: 274 AN-FKGNFTSPIQNKLYLHARYMDLPHP 300
                G   +P   +L LHA  +   HP
Sbjct: 229 GRLLPGTERTP---RLMLHASELHFVHP 253


>gi|223039842|ref|ZP_03610126.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Campylobacter rectus RM3267]
 gi|222878851|gb|EEF13948.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Campylobacter rectus RM3267]
          Length = 354

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 74/289 (25%), Positives = 125/289 (43%), Gaps = 41/289 (14%)

Query: 40  ILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           +++SG V ++ K + K + ++  G V+RI              K   S  N  K     +
Sbjct: 50  LIKSGLVSLNGKPLTKPSAKLNLGDVLRI--------------KFEQSEQNAAKFEAEFE 95

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHR 149
             ++YED  + V NKPA + V     +    +  L  W+ +KG          +  + HR
Sbjct: 96  VPIIYEDEDLLVLNKPANLVVHPAPSVK---EPTLVDWLGAKGFLLSNLSGQSRAGIVHR 152

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ TSG +VVA+  AA   L+     + + +IY +L   +P  K+ C   W     +  
Sbjct: 153 LDKGTSGAIVVAKNNAAHAALSSQLSDKSMGRIYLALT-DLPL-KQNCTV-WRAIGRNPA 209

Query: 210 GDYVHVVKQNEKGANYAISH--FKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMG 263
                 +  + + A  A ++  F   D  AQ        +  +  TGRTHQ+RVH   + 
Sbjct: 210 NRLKKAIVPDGRAAKSAFANLLFSEFDGPAQSKNAGVNLIAAKLFTGRTHQIRVHLASLN 269

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
             I+GD  Y    + +  +    ++ LHA  +   HP  GG++   AP+
Sbjct: 270 RHILGDALYGFKSEKDKIA----RVMLHAYGLYFTHPRTGGQMSFVAPI 314


>gi|149910466|ref|ZP_01899106.1| pseudouridine synthase Rlu family protein [Moritella sp. PE36]
 gi|149806426|gb|EDM66398.1| pseudouridine synthase Rlu family protein [Moritella sp. PE36]
          Length = 226

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 62/250 (24%), Positives = 106/250 (42%), Gaps = 44/250 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++++   V NK AGI      G+    DG         G+     HRLD+ TSG+L++
Sbjct: 4   ILFQNNDFLVINKAAGIGFHDEDGV----DGICSIVRKDIGRLVFPVHRLDKVTSGLLLL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA  L + F +  IQK Y  ++   PK K+  +      K  +      + +  +
Sbjct: 60  AKSSEAAAKLAKLFELHEIQKYYLGIIDSKPKKKQGLV------KGDMERSRRSMWRLTK 113

Query: 221 KGANYAISHFKVIDCFAQKFC----WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              + A++ F     F Q        + ++PHTG+THQLRV    +G PI GD  Y +  
Sbjct: 114 TLTSPAVTQF-----FTQSIGDGKRLVVLKPHTGKTHQLRVALNSLGSPICGDPLYQSAD 168

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLY 336
              +     ++ YLHA  +                      T D   F +  + +   L+
Sbjct: 169 AWKY-----DRAYLHAYCLQF--------------------TLDGEDFSFVADEFSGELF 203

Query: 337 SQDECKQNIL 346
           +   CK+ ++
Sbjct: 204 ATPACKEALV 213


>gi|321311023|ref|YP_004193352.1| ribosomal large subunit pseudouridine synthase D (fragment)
           [Mycoplasma haemofelis str. Langford 1]
 gi|319802867|emb|CBY93513.1| ribosomal large subunit pseudouridine synthase D (fragment)
           [Mycoplasma haemofelis str. Langford 1]
          Length = 219

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 64/232 (27%), Positives = 103/232 (44%), Gaps = 26/232 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           +++E+    + NK +GI+V       Y  +  L + V+ K QK    L HR+D+ TSG +
Sbjct: 6   IIFENKNFLIVNKASGIAVHKN---IYDREFNLINEVN-KDQKANYSLVHRIDKYTSGAV 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG---GDYVHV 215
           ++A+ +     L   F    ++K Y +L        KE  A  L     +G    D +  
Sbjct: 62  LIAKNKETLLLLQNLFLNNEVEKHYLALT------SKELPAKKLKITLSLGRSKNDKLRF 115

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +N K    A +  +VID +     +L++   TGRTHQ+R H   + CP++ D  Y   
Sbjct: 116 TNRNAKNYKPACTEVEVIDRY-----FLKILLKTGRTHQIRAHLFSINCPVLNDPIY--- 167

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
             GN     +   YLHA  ++   P     + +TAPLP         L  +Y
Sbjct: 168 --GNRCFNPEFGQYLHAYKLEFTCPITNEFISVTAPLPQEFKDKLSELNIEY 217


>gi|260773303|ref|ZP_05882219.1| tRNA pseudouridine synthase C [Vibrio metschnikovii CIP 69.14]
 gi|260612442|gb|EEX37645.1| tRNA pseudouridine synthase C [Vibrio metschnikovii CIP 69.14]
          Length = 246

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 60/212 (28%), Positives = 98/212 (46%), Gaps = 16/212 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IIYQDPYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  L   F  ++++K Y ++V G    ++  + ++ LK+    I   +    K+
Sbjct: 64  ALSSEVASILMPMFASQQMEKTYHAVVRGW--IEQAGVLDYPLKQELDKIADKFAQQDKE 121

Query: 219 NEKG-------ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +         AN  +  F        ++  +E++P TGR HQLR H  H+  PIVGD  
Sbjct: 122 PQSAITAYQPLANVEVP-FSTGKFATTRYSLMELKPKTGRKHQLRRHMAHLRHPIVGDTT 180

Query: 272 YCANFKGNFTSPIQ---NKLYLHARYMDLPHP 300
           +  + K N     Q    +L LHA  +   HP
Sbjct: 181 H-GDGKHNRLYREQYQVQRLMLHASQLSFIHP 211


>gi|296219230|ref|XP_002755784.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Callithrix jacchus]
          Length = 312

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 53/173 (30%), Positives = 86/173 (49%), Gaps = 9/173 (5%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA     SF+ RR+ K Y +L+ G  +  +  I++ + +
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYRSFKERRVTKAYLALLRGHIQESRVTISHAIGR 120

Query: 205 KSHIGGDYVHVVKQNEKGAN--YAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            S  G  +   ++  +   N   +++   V++           + ++P TGRTHQLRVH 
Sbjct: 121 NSTEGRAHTMCIEGTQGCENPKPSLTELVVLEHGLYAGDPVSKVLLKPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
             +G P+VGD  Y     G    P   ++ LHA Y+ +P  +G  ++   P P
Sbjct: 181 SALGHPVVGDLTY-GEPSGREDRPF--RMMLHALYLRIPT-DGECVEACTPDP 229


>gi|331005130|ref|ZP_08328531.1| Pseudouridylate synthase, 23S RNA-specific [gamma proteobacterium
           IMCC1989]
 gi|330421049|gb|EGG95314.1| Pseudouridylate synthase, 23S RNA-specific [gamma proteobacterium
           IMCC1989]
          Length = 227

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 54/172 (31%), Positives = 83/172 (48%), Gaps = 41/172 (23%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L+ A+T AAA  L++ F+ R+++K Y +L    PK K+  I+        
Sbjct: 20  HRLDKVTSGVLLCAKTSAAASELSQLFQNRQVEKYYLALSDQKPKKKQGLIS-------- 71

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW--------LEMQPHTGRTHQLRVHA 259
             GD    +++  +GA + + H K      Q F +          ++P TG+THQLRV  
Sbjct: 72  --GD----MERGRRGA-WKLCHSKNKPAITQFFSYGLGDGNRLFLLKPKTGKTHQLRVAL 124

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA------------RYMDLPH 299
             +G PI+GD  Y           +   + LHA            RY+DLP+
Sbjct: 125 KSIGSPIIGDRLYGHPLS------LPEGILLHASVLSFEYQGESYRYVDLPN 170


>gi|237734494|ref|ZP_04564975.1| pseudouridine synthase [Mollicutes bacterium D7]
 gi|229382314|gb|EEO32405.1| pseudouridine synthase [Coprobacillus sp. D7]
          Length = 328

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 88/335 (26%), Positives = 156/335 (46%), Gaps = 42/335 (12%)

Query: 11  VVENDEENMRLDRWFKN---HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + END  N R+D++ K    + P+ NF+   K+ R   ++V+ K+V     +     V +
Sbjct: 12  ITENDA-NQRIDKYLKKLLVNAPN-NFI--YKMFRKKDIKVNGKKVDEKYILSLDDEVEM 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
               +      + + I + +   +         +LYED  + +  KPAG+ V   +  + 
Sbjct: 68  FLYDDKFKEFTETKSIYEVNRTFS---------VLYEDKHVLIVFKPAGLLVHEDANESI 118

Query: 128 H-IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           + +   + S++ SK +          P   HRLD+ TSGI++  +T AA Q+L E  + R
Sbjct: 119 NTLTNQVLSYLASKNELDLSRENTFMPGPVHRLDRNTSGIVIFGKTLAALQNLNEMIKQR 178

Query: 178 R-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I+K Y ++  G   +++  +  +++K  +     V +VK++  GA    +  + +  +
Sbjct: 179 HCIEKKYLTICRGQLSHQRN-LHGYMVKLENQAQ--VKLVKKDYPGALTMETIVRPLK-Y 234

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN----FTSPIQNKLYLHA 292
              +  +E+   TGR HQ+RVH   +  PI+GD KY  +F+ N     T  + N+L LHA
Sbjct: 235 NCDYSLVEVTLITGRMHQIRVHLSSIEHPIIGDRKY-GDFELNKYIKKTFGLNNQL-LHA 292

Query: 293 RYMDLPHPEG--GRLQ---ITAPLPAHMVKTWDSL 322
             +      G    LQ   I  P+PA   K   SL
Sbjct: 293 YKIKFVKTFGVLNYLQDKEIICPVPALFEKIEKSL 327


>gi|227544440|ref|ZP_03974489.1| RluA family pseudouridine synthase [Lactobacillus reuteri CF48-3A]
 gi|227185580|gb|EEI65651.1| RluA family pseudouridine synthase [Lactobacillus reuteri CF48-3A]
          Length = 314

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 111/219 (50%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED    V +KPAG++   G       +   + G+L +  +S   +P L  RLD+ T 
Sbjct: 109 VVYEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIA-NNSADLRPHLITRLDRFTG 167

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A+   A+  +++  +  ++ K Y +LV G   ++   I   + +K    G    V
Sbjct: 168 GLLLIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHGEINKPIGRKD---GQAARV 224

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           + +N      A++ + V +  A K+  + ++ HTGRTHQ+RVH   +G  ++GDH Y   
Sbjct: 225 IDEN---GQRALTEYWVEERGA-KWTRVRVRLHTGRTHQIRVHFAAIGHSLIGDHLY--- 277

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
             G  TS   ++L LHA  +    P    ++  T+ LPA
Sbjct: 278 --GGDTSKYDHQL-LHASKISFNDPFTLKQMTFTSELPA 313


>gi|88859724|ref|ZP_01134364.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           tunicata D2]
 gi|88818741|gb|EAR28556.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           tunicata D2]
          Length = 557

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 61/203 (30%), Positives = 106/203 (52%), Gaps = 12/203 (5%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L+H+++  ++ D+ + L   ++ L+  ++Y+D  + V NKPA      G  I   +   +
Sbjct: 330 LSHMLQGLEVDDNPL-LVNPAEGLELSIIYQDDVMLVINKPAEFLSVPGKSITDSVYTRI 388

Query: 134 KS-WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           K+ + ++ G  P + HRLD  TSG++V+A  + + Q L + F +R + K Y +L+ G   
Sbjct: 389 KAQFPNASG--PLIVHRLDMSTSGLMVIALNKRSHQALQKQFILRTVTKRYAALLDGELS 446

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +   I+   L+          V  ++ K A+   ++F+VI   A +   + + P TGRT
Sbjct: 447 VQSGDIS-LPLRVDLADRPRQMVCYEHGKAAH---TYFEVISHQAGR-TKVHLYPKTGRT 501

Query: 253 HQLRVHALH---MGCPIVGDHKY 272
           HQLRVH  H   +  PIVGD  Y
Sbjct: 502 HQLRVHCAHTLGLNTPIVGDDLY 524


>gi|145299458|ref|YP_001142299.1| pseudouridine synthase RluA-like protein [Aeromonas salmonicida
           subsp. salmonicida A449]
 gi|142852230|gb|ABO90551.1| pseudouridine synthase RluA-like protein [Aeromonas salmonicida
           subsp. salmonicida A449]
          Length = 219

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 60/204 (29%), Positives = 98/204 (48%), Gaps = 28/204 (13%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTH 148
           L +H DF+            + NK  G+ +   +G +  ++  L S V +  GQ     H
Sbjct: 5   LAQHKDFM------------LINKGPGLGMHDEAGESGLVNPGLVSRVKADTGQVLYPVH 52

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG++++ART AA + L+ +F  R++ K Y +L    PK K+  +   + K    
Sbjct: 53  RLDKMTSGLVLLARTTAANRALSMAFADRQVSKQYLALSDRKPKKKQGWVKGDMQKGR-- 110

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           GG ++     +    N AIS F  +    +      ++P TG+THQ+RV    +G PI+G
Sbjct: 111 GGSWMLARSLD----NPAISWFDSVPV-REGLRLYRIKPQTGKTHQIRVALKSIGAPILG 165

Query: 269 DHKYCANFKGNFTSPIQNKLYLHA 292
           D +Y             ++ YLHA
Sbjct: 166 DERYGGT--------AADRGYLHA 181


>gi|32471769|ref|NP_864762.1| ribosomal large subunit pseudouridine synthase A [Rhodopirellula
           baltica SH 1]
 gi|32397140|emb|CAD72447.1| ribosomal large subunit pseudouridine synthase A [Rhodopirellula
           baltica SH 1]
          Length = 232

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 58/209 (27%), Positives = 98/209 (46%), Gaps = 14/209 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +L++     V NKP G+      G         + +  +      LT  HRLD+  SG++
Sbjct: 22  ILWQCHACVVVNKPVGLPTTSPKGTDSLESCLREQFAQAGNPVSYLTAVHRLDRPVSGLV 81

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++A  + AA+ L+E FR+R +QK Y ++V G  +   K+E   + + K +      V +V
Sbjct: 82  LIALRKKAARLLSEQFRLRHVQKKYIAMVQGNALEACKQEPWHDTIAKLTDEA--RVEIV 139

Query: 217 KQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +      A +    ++  ++     +E++P TGR HQLR+ + H G PIVGD  Y   
Sbjct: 140 GLDSTDGRQAETKVSFLEYDSESDTSRIELRPVTGRMHQLRIQSAHRGHPIVGDPLY--- 196

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                T+  ++ L L A  +    P  GR
Sbjct: 197 ----GTAEDESALRLVAAKLSFRDPTNGR 221


>gi|114321104|ref|YP_742787.1| tRNA pseudouridine synthase C [Alkalilimnicola ehrlichii MLHE-1]
 gi|114227498|gb|ABI57297.1| tRNA pseudouridine synthase C [Alkalilimnicola ehrlichii MLHE-1]
          Length = 246

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 107/246 (43%), Gaps = 43/246 (17%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---SGIAYHIDGFLKSWVDSKGQ 142
            ++ LT  SD    I+ + D  +   +KPAG+ V       G A      L+   D  GQ
Sbjct: 5   PTIPLTMTSDAPLDII-HRDHDLVAVDKPAGMPVHRSRRHPGDAV----LLQRLRDQLGQ 59

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HRLD  TSG++V A    AA+ L   F+ R ++K Y ++V G           W 
Sbjct: 60  WLWPVHRLDPPTSGLVVFALHPEAARALAAQFQQREVEKRYLAVVRG-----------WP 108

Query: 203 LKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCF----------AQKFCWLEMQPHTGR 251
           L++    G   H +++  +     A++ F  +               ++  LE++P TGR
Sbjct: 109 LEQ----GRVEHPLRRPGRSERQPAVTDFHRLATTELPIPMPPHPTARYALLELRPITGR 164

Query: 252 THQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
            HQLR H  H+  PI+GD  Y        F+  F +   ++L L A  +   HP  G RL
Sbjct: 165 QHQLRRHMKHISHPIIGDTTYGKGPHNRLFRERFGA---SELLLRATRLAFRHPGTGARL 221

Query: 306 QITAPL 311
            +  PL
Sbjct: 222 HLDCPL 227


>gi|89095232|ref|ZP_01168154.1| RluA protein [Oceanospirillum sp. MED92]
 gi|89080486|gb|EAR59736.1| RluA protein [Oceanospirillum sp. MED92]
          Length = 238

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 90/204 (44%), Gaps = 42/204 (20%)

Query: 101 LLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +L + +   + NK  GISV   QG  G+   +   L+        +  L HRLD+ TSG+
Sbjct: 13  ILTQTADFIIINKSPGISVHKDQGDEGLTMLLQRQLEL------DEIFLIHRLDKVTSGV 66

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI---------ANWLLKKSHI 208
           +V A+ R  A  L+  F+ R ++K Y ++    PK K+  +          +W L +S I
Sbjct: 67  MVFAKNRETAADLSMQFQNREVEKFYLAVSANKPKRKQGLVCGDMEKSRRGSWKLLRSKI 126

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                          N A++ F  +      F    ++P TG+THQ+RV     G PI+G
Sbjct: 127 ---------------NPAMTQFVSV-AMKPGFRLFLLKPSTGKTHQIRVALKSEGAPILG 170

Query: 269 DHKYCANFKGNFTSPIQNKLYLHA 292
           D+ Y             ++ YLHA
Sbjct: 171 DNMYGGE--------EADRTYLHA 186


>gi|34763384|ref|ZP_00144336.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
 gi|27886957|gb|EAA24077.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
          Length = 214

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 53/161 (32%), Positives = 81/161 (50%), Gaps = 18/161 (11%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           +P + HRLD++TSG+++VA+   A   L   F  + I K Y  +V G    +N    I N
Sbjct: 33  RPGIIHRLDKDTSGLILVAKNNYAHAKLASMFTDKTIHKTYLCIVKGNFSEENLNGRIEN 92

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + + S      + VVK+N K    AIS++KVI+     +  +E+   TGRTHQ+RVH  
Sbjct: 93  LIGRDSK-DRKKMAVVKENGKT---AISNYKVIEQ-VDGYSLVEIAIETGRTHQIRVHMK 147

Query: 261 HMGCPIVGDHKYCAN-----------FKGNFTSPIQNKLYL 290
            +   I+GD  Y              +K  F +P+ NK Y+
Sbjct: 148 SINHVILGDSTYGNEDKNVKRQMLHAYKLEFLNPLDNKEYI 188


>gi|227363858|ref|ZP_03847963.1| RluA family pseudouridine synthase [Lactobacillus reuteri MM2-3]
 gi|325683068|ref|ZP_08162584.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
 gi|227071085|gb|EEI09403.1| RluA family pseudouridine synthase [Lactobacillus reuteri MM2-3]
 gi|324977418|gb|EGC14369.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
          Length = 297

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 111/219 (50%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED    V +KPAG++   G       +   + G+L +  +S   +P L  RLD+ T 
Sbjct: 87  VVYEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIA-NNSADLRPHLITRLDRFTG 145

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A+   A+  +++  +  ++ K Y +LV G   ++   I   + +K    G    V
Sbjct: 146 GLLLIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHGEINKPIGRKD---GQAARV 202

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           + +N      A++ + V +  A K+  + ++ HTGRTHQ+RVH   +G  ++GDH Y   
Sbjct: 203 IDEN---GQRALTEYWVEERGA-KWTRVRVRLHTGRTHQIRVHFAAIGHSLIGDHLY--- 255

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
             G  TS   ++L LHA  +    P    ++  T+ LPA
Sbjct: 256 --GGDTSKYDHQL-LHASKISFNDPFTLKQMTFTSELPA 291


>gi|116495207|ref|YP_806941.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
 gi|116105357|gb|ABJ70499.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
          Length = 276

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 101/219 (46%), Gaps = 31/219 (14%)

Query: 103 YEDSKIYVFNKPAGI----SVQGGSG-IAYHIDGFLKSWVDSKGQKPRL-THRLDQETSG 156
           YED  + + +KPAG+    ++ G +G +      +L  +       P L THRLD  TSG
Sbjct: 79  YEDDDLLIVDKPAGMKTHPNLPGETGTLMNQAAAYLAPF-------PALITHRLDMATSG 131

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV+A+       +     ++ + + Y +LV        + IA      + IG D     
Sbjct: 132 LLVIAKNPLTQAIINRQLALKTMHRDYIALV-------PQGIAASGTITAPIGHDPDDQR 184

Query: 217 KQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           K+     GA+ AI+HF+ I         + ++  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 185 KRMIRPDGAS-AITHFRRI-AETSTTATVALRLETGRTHQIRVHLASIGYPILGDPLYAP 242

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +           ++YLHA  +    P     L +T+PLP
Sbjct: 243 D------QTTYQRMYLHAFQVRFTKPLSDTTLTVTSPLP 275


>gi|148544733|ref|YP_001272103.1| RluA family pseudouridine synthase [Lactobacillus reuteri DSM
           20016]
 gi|184154085|ref|YP_001842426.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|148531767|gb|ABQ83766.1| pseudouridine synthase, RluA family [Lactobacillus reuteri DSM
           20016]
 gi|183225429|dbj|BAG25946.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
          Length = 290

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 111/219 (50%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED    V +KPAG++   G       +   + G+L +  +S   +P L  RLD+ T 
Sbjct: 80  VVYEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIA-NNSADLRPHLITRLDRFTG 138

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A+   A+  +++  +  ++ K Y +LV G   ++   I   + +K    G    V
Sbjct: 139 GLLLIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHGEINKPIGRKD---GQAARV 195

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           + +N      A++ + V +  A K+  + ++ HTGRTHQ+RVH   +G  ++GDH Y   
Sbjct: 196 IDEN---GQRALTEYWVEERGA-KWTRVRVRLHTGRTHQIRVHFAAIGHSLIGDHLY--- 248

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
             G  TS   ++L LHA  +    P    ++  T+ LPA
Sbjct: 249 --GGDTSKYDHQL-LHASKISFNDPFTLKQMTFTSELPA 284


>gi|332533880|ref|ZP_08409735.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332036688|gb|EGI73152.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 551

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 104/234 (44%), Gaps = 27/234 (11%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L H++K   + D+ + LT  +      ++Y+D  + V NKPA      G  I   +   +
Sbjct: 324 LGHMLKGLDVEDNPL-LTNPAQGKDLSIVYKDDDLLVVNKPAEFLSVPGVNIDDSVYMRI 382

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+    +   P + HRLD  TSG+L++A  +   + L + F  R I K Y +LV G    
Sbjct: 383 KTQF-PEASGPLIVHRLDMSTSGLLMIALNKRVHKALQKQFIERTIDKRYVALVNGNVAE 441

Query: 194 KKECIANWLL----KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               I   L+     K      Y H           +++ ++V++        L++ P T
Sbjct: 442 DSGVIDLPLVLDFDDKPRQMVCYTH--------GKPSLTTWQVLE-RNNNITRLQLYPKT 492

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           GRTHQLRVH  H   +  PI+GD  Y             ++L+LHA Y+   HP
Sbjct: 493 GRTHQLRVHCAHSLGLNMPIIGDTHYGQK---------ADRLHLHAEYLAFTHP 537


>gi|89901537|ref|YP_524008.1| pseudouridine synthase [Rhodoferax ferrireducens T118]
 gi|89346274|gb|ABD70477.1| ribosomal large subunit pseudouridine synthase A [Rhodoferax
           ferrireducens T118]
          Length = 215

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 55/187 (29%), Positives = 97/187 (51%), Gaps = 18/187 (9%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----PRLTH 148
           H+D LK I  Y D  + V +KP G+    G G         +  + ++ Q+      + H
Sbjct: 2   HADELKVI--YADKSLLVLDKPTGLLSVPGRGEDK------QDCLSARAQRLYPDALVVH 53

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++V+AR  AA + L+ +F  R ++K Y ++V G        + +W +    I
Sbjct: 54  RLDMATSGLMVMARGAAAQRALSLAFASRSVRKRYVAIVDG---QLAPSLQDWGVIDLPI 110

Query: 209 GGDYVHVVKQ--NEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
             D+    ++  + +    ++++++V+    + +   +E++P TGR+HQLRVH L +G  
Sbjct: 111 IVDWPERPRRIIDHQRGKPSVTYWRVLAHNTSDETTRVELEPVTGRSHQLRVHLLALGHA 170

Query: 266 IVGDHKY 272
           IVGD  Y
Sbjct: 171 IVGDALY 177


>gi|261868111|ref|YP_003256033.1| tRNA pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413443|gb|ACX82814.1| tRNA pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 237

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 105/236 (44%), Gaps = 22/236 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     ++   D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYQDDVLVAVNKPAGMLVHRSWLDRHETQFVMQILRDQIGQLVYPFHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  +   F  ++ +K Y ++V G    + E      ++   I   +     Q +
Sbjct: 65  ALNSETANLVCHQFEQKQTEKQYLAVVRGYVTGQGEIDYPLKVQLDKIADKFA----QQD 120

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ +  +             A ++  + + P TGR HQLR H  H+  PI+GD 
Sbjct: 121 KAPQSAVTFYDGLKTVEMPYGVGRYAASRYSLVRLTPKTGRKHQLRRHMKHIFHPILGDT 180

Query: 271 KYCANFKGN--FTSPIQ-NKLYLHARYMDLPHPEGGR-LQITAPLPA---HMVKTW 319
           +Y  +   N   T  I  ++L LHA  +   HP  G+ + I A L     H+++T+
Sbjct: 181 QY-GDLHQNRALTEHIGCSRLMLHAEKLTFVHPLTGQPITIEAGLDEQWKHLMRTF 235


>gi|160915826|ref|ZP_02078034.1| hypothetical protein EUBDOL_01842 [Eubacterium dolichum DSM 3991]
 gi|158432302|gb|EDP10591.1| hypothetical protein EUBDOL_01842 [Eubacterium dolichum DSM 3991]
          Length = 313

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 60/285 (21%), Positives = 129/285 (45%), Gaps = 44/285 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  ++ + R+D++     P +    + K +R+ +++V++KR + + R+Q G  +++  
Sbjct: 4   IVIGKNDCDQRVDKFLSKALPTLPKSLMYKAIRNKKIKVNRKRCEISQRLQEGDTMQL-- 61

Query: 70  VINALNHIIKEQKILDSSVNLTK-HSDFLKSI----LLYEDSKIYVFNKPAGISVQGGSG 124
                         L     +T+  + FLK      ++YED  + + NK  G+       
Sbjct: 62  -------------FLAEEFFMTQIDTAFLKVPSELDIVYEDENLLIVNKAKGLLAHRDQK 108

Query: 125 IAYH--IDGFLKSWVDSKGQKPR--------LTHRLDQETSGILVVARTRAAAQHLTESF 174
           +     +D  L      K   PR        L HR+D+ T G+++ A+  A+ + +    
Sbjct: 109 VGQDNLMDRILHYLYIHKEYDPRMENSFVPALCHRIDRNTQGLVIAAKNAASLRAMNAHI 168

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-----ANYAISH 229
           + R+++K Y  +  G+   ++E +   LL       +  H++   ++G      NY I  
Sbjct: 169 KQRKVRKKYVCIAQGVFDKRQEHV---LLYHCKTKDNVAHILPYPKEGYKPIEINYQIKE 225

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            K      +++  +E++  +G++HQ+R    ++  P+ GD KY A
Sbjct: 226 QK------KQYALVEVELLSGKSHQIRAMLAYLSHPLYGDVKYGA 264


>gi|315126704|ref|YP_004068707.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
 gi|315015218|gb|ADT68556.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
          Length = 219

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 56/195 (28%), Positives = 87/195 (44%), Gaps = 20/195 (10%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y     Y+  KPAG++            GF+        +K    HRLD+ TSG++++AR
Sbjct: 6   YTHDDFYIITKPAGLNFHSEES-----PGFVFLAEQQLNEKLFAVHRLDKVTSGLIILAR 60

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            + AA   T+ F    I K Y ++    PK K+  +   + K     G Y  +  Q+   
Sbjct: 61  HKDAAAKFTQMFTEHTINKFYLAVSDSKPKKKQGWVKGDMAKSRR--GTYKLLNSQS--- 115

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
            N AI+ F     F   F    ++P++G+THQLRV    +G  I+GD  Y  +       
Sbjct: 116 -NPAITRFYSF-SFKSGFRAYLLKPYSGKTHQLRVALKSIGAAILGDASYSGS------- 166

Query: 283 PIQNKLYLHARYMDL 297
              ++ YLHA  +D 
Sbjct: 167 -AADRTYLHAFALDF 180


>gi|254673709|emb|CBA09336.1| pseudouridylate synthase, 23S RNA-specific [Neisseria meningitidis
           alpha275]
          Length = 217

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 65/211 (30%), Positives = 98/211 (46%), Gaps = 19/211 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV    G    +   L + +    +K  L HRLD++T GIL+ 
Sbjct: 4   ILFRHQDFVAINKPQGISVHRSDG-EVSLTATLAAQLGV--EKVWLLHRLDKQTGGILLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I   + +KS  G     + K   
Sbjct: 61  ALNPQSAAVLAAQFAERKMKKTYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLTR 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F  I    +K     ++PHTG+THQLRV    +G PI+GD  Y     G  
Sbjct: 115 NMENIAVTRFFSIRI-GEKMRLFILEPHTGKTHQLRVAMKSLGSPILGDRLY-----GGT 168

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
            S      +L+A  +   + +   ++ITAPL
Sbjct: 169 ES---ETTFLYAWKIQFTYQQ-QEIEITAPL 195


>gi|34499206|ref|NP_903421.1| pseudouridine synthase A [Chromobacterium violaceum ATCC 12472]
 gi|34105057|gb|AAQ61413.1| pseudouridine synthase A [Chromobacterium violaceum ATCC 12472]
          Length = 225

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 66/223 (29%), Positives = 109/223 (48%), Gaps = 28/223 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----PRLTHRLDQETSG 156
           ++Y D  + V +KP+G+    G G     D  +     S+ QK        HRLD +TSG
Sbjct: 19  VIYADDCLLVLDKPSGLLSVPGRG-EDKADCLI-----SRAQKVYPDALTVHRLDMDTSG 72

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V+ R     + L+ +F  R+++K Y ++V GI ++    I   L+       D+ +  
Sbjct: 73  LVVMGRGPEMQRALSIAFMDRKVKKRYIAVVDGIIESNSGTIDLPLII------DWPNRP 126

Query: 217 KQN---EKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHM--GCPIVGDH 270
           +Q    ++G   AI+H++VI     +    +E+ P TGR HQLR+H L++  G PI+GD 
Sbjct: 127 RQKVDFDQGKE-AITHYRVILRDTGRNISRVELDPQTGRAHQLRMHMLNLESGHPILGDT 185

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
            Y             ++L LHA  + L HP     ++  AP P
Sbjct: 186 IYAPPEALAKA----DRLLLHASRLVLRHPVTFEEMEFEAPAP 224


>gi|301066771|ref|YP_003788794.1| 23S RNA-specific pseudouridylate synthase [Lactobacillus casei str.
           Zhang]
 gi|300439178|gb|ADK18944.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           str. Zhang]
          Length = 276

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 101/219 (46%), Gaps = 31/219 (14%)

Query: 103 YEDSKIYVFNKPAGI----SVQGGSG-IAYHIDGFLKSWVDSKGQKPRL-THRLDQETSG 156
           YED  + + +KPAG+    ++ G +G +      +L  +       P L THRLD  TSG
Sbjct: 79  YEDDDLLIVDKPAGMKTHPNLPGETGTLMNQAAAYLAPF-------PALITHRLDMATSG 131

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV+A+       +     ++ + + Y +LV        + IA      + IG D     
Sbjct: 132 LLVIAKNPLTQAIINRQLALKTMHRDYIALV-------PQGIAASGTITAPIGHDPDDQR 184

Query: 217 KQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           K+     GA+ AI+HF+ I         + ++  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 185 KRMIRPDGAS-AITHFRRI-AETSTTATVALRLETGRTHQIRVHLASIGYPILGDPLYAP 242

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +           ++YLHA  +    P     L +T+PLP
Sbjct: 243 D------QTTYQRMYLHAFQVRFTKPLSDTTLTVTSPLP 275


>gi|269795564|ref|YP_003315019.1| ribosomal large subunit pseudouridine synthase D [Sanguibacter
           keddieii DSM 10542]
 gi|269097749|gb|ACZ22185.1| ribosomal large subunit pseudouridine synthase D [Sanguibacter
           keddieii DSM 10542]
          Length = 311

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 57/209 (27%), Positives = 103/209 (49%), Gaps = 13/209 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQ------GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+D  + V +KP G++        G + +   I            ++  + HRLD  T
Sbjct: 85  IMYDDDDVVVIDKPVGVAAHPSVGWTGPTVVGALIAAGYTIATSGAAERQGIVHRLDVGT 144

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++VVA++  A   +  +F+ R ++K+Y +LV G P+     I   + +  H   DY  
Sbjct: 145 SGLMVVAKSEHAYSVMKRAFKERTVEKVYHALVQGHPEPTTGTIDAPIGR--HPNHDYKF 202

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  + K    +++H++V++  +     +E+   TGRTHQ+RVH   +  P VGD  Y A
Sbjct: 203 GVVADGK---PSVTHYEVLEMLSAA-SLVEVHLETGRTHQIRVHFSALRHPCVGDLTYGA 258

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + +      +  + +LHA+ +   HP  G
Sbjct: 259 DPRLAEKVSLTRQ-WLHAKRLGFEHPSTG 286


>gi|225850422|ref|YP_002730656.1| RNA pseudouridine synthase family protein [Persephonella marina
           EX-H1]
 gi|225646434|gb|ACO04620.1| RNA pseudouridine synthase family protein [Persephonella marina
           EX-H1]
          Length = 272

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 57/214 (26%), Positives = 97/214 (45%), Gaps = 31/214 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  I    KP  +  +G  G + Y +   L        ++ +  HRLD+ETSG+L+
Sbjct: 73  VIYEDQFILAVQKPPFLESEGRKGSVEYQLRKVL-------DRRLKAIHRLDRETSGVLL 125

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+         + +  + + K+Y S+ +G  K KK+ +   + KK              
Sbjct: 126 FAKNEKIFHRFKDLWHRKEVVKVYLSISYGEAKFKKKVVNMPVDKK-------------- 171

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKG 278
                YA S F      ++ F   E++  TGR HQ+R+H+  +  PIVGD  Y     + 
Sbjct: 172 -----YAKSIF-FTKKISKGFTLFEVEIKTGRKHQIRIHSSKIRHPIVGDKIYGLKKVED 225

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
             T  ++ ++ LH   +   HP  G+ + I AP+
Sbjct: 226 PLTKNVKRQM-LHGYRLRFLHPFTGKVVDIKAPV 258


>gi|117921265|ref|YP_870457.1| tRNA pseudouridine synthase C [Shewanella sp. ANA-3]
 gi|117613597|gb|ABK49051.1| tRNA pseudouridine synthase C [Shewanella sp. ANA-3]
          Length = 284

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 107/242 (44%), Gaps = 27/242 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   +KPAG+ V   S +A     F      D  G      HRLD+ TSG+L+
Sbjct: 32  VLYQDEHLVAIHKPAGLLVHR-SYLARRERFFAMQLTRDLVGCHVFPVHRLDRPTSGVLL 90

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQ 218
            A++   A  L E F    I+K Y +LV G   N  E  + ++ LK      +       
Sbjct: 91  FAKSSEVANALCEQFANHSIEKQYLALVRG---NMHESGVLDYALKVE--LDEVADKFAN 145

Query: 219 NEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +               +F  +++ P TGR HQLR H  H+  PI+G
Sbjct: 146 QDKAAQDAVTQYEPLLNTEIPYPSGRYATSRFALVKLSPKTGRKHQLRRHMAHLRHPIIG 205

Query: 269 DH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           D      K  A F+ +F     N+L+L A+ +   HP    RL I   L       +  L
Sbjct: 206 DTTHGDGKQNAFFRTHFDI---NRLWLIAKKLTFTHPVTQARLSIETELEPEWETVFSGL 262

Query: 323 GF 324
           G+
Sbjct: 263 GW 264


>gi|127511033|ref|YP_001092230.1| pseudouridine synthase Rlu family protein [Shewanella loihica PV-4]
 gi|126636328|gb|ABO21971.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           loihica PV-4]
          Length = 224

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 55/195 (28%), Positives = 90/195 (46%), Gaps = 25/195 (12%)

Query: 101 LLYEDSKIYVFNKPAGI---SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++ +++   V +K  G+   S  G +G+   ++  L   + S        HRLD  TSG+
Sbjct: 4   IIADETDFLVIDKAPGVHFHSQDGSAGVMAQLESDLDIKLYS-------VHRLDTMTSGL 56

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A++  AA   T+ F   ++QK Y +L  G PK K+  I   + K          +++
Sbjct: 57  LLFAKSSEAAAAFTQRFSEHKVQKYYLALAKGKPKKKQGSIVGDMAKSRR---SMYKLLR 113

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E   N AI+ F      A+      ++P +G+THQLRV    +G PI+GD  Y     
Sbjct: 114 SKE---NPAITQF-FSQSVAEGLRLYLLKPLSGKTHQLRVALASLGVPILGDQLYGGE-- 167

Query: 278 GNFTSPIQNKLYLHA 292
                   ++ YLHA
Sbjct: 168 ------DADRGYLHA 176


>gi|329121404|ref|ZP_08250029.1| pseudouridylate synthase [Dialister micraerophilus DSM 19965]
 gi|327469694|gb|EGF15161.1| pseudouridylate synthase [Dialister micraerophilus DSM 19965]
          Length = 303

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 64/265 (24%), Positives = 121/265 (45%), Gaps = 33/265 (12%)

Query: 15  DEENMRLDRWFKNH--YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           D+   RLD + K     PH  F+   K L+  +++V+ K+   N ++++G ++       
Sbjct: 9   DKNGKRLDNYIKEKEKIPHFIFI---KSLKKNKIKVNGKKESGNYKLKTGDII------- 58

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAY 127
             ++I  + K     ++ +         + YED  I +  K AGI     +      +  
Sbjct: 59  -TSYIENKNKNEKEKIHFS---------INYEDENIIIVEKEAGILCNDTTNKEEKTLHD 108

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            I+ +LK   + +       HR+D  T+G+++ A+   A   L  + + R I+K Y  + 
Sbjct: 109 EINEYLKEKNEPEAYP---VHRIDLNTTGLVIFAKNMHARAILDRAIKERNIKKYYLCVT 165

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  K K   + + L K +    + V++ ++  KG+  A  ++K +         +E + 
Sbjct: 166 TGTMKKKSGKLEHQLFKDAK--NNKVYIYEKPCKGSKTATMNYKCLKT-ENGLSLVECEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
            TGRTHQ+R    ++G PI+GD KY
Sbjct: 223 ITGRTHQIRSQLSYIGYPILGDDKY 247


>gi|227534773|ref|ZP_03964822.1| pseudouridine synthase, 23S-rRNA-specific [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
 gi|227187529|gb|EEI67596.1| pseudouridine synthase, 23S-rRNA-specific [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
          Length = 277

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 101/219 (46%), Gaps = 31/219 (14%)

Query: 103 YEDSKIYVFNKPAGI----SVQGGSG-IAYHIDGFLKSWVDSKGQKPRL-THRLDQETSG 156
           YED  + + +KPAG+    ++ G +G +      +L  +       P L THRLD  TSG
Sbjct: 80  YEDDDLLIVDKPAGMKTHPNLPGETGTLMNQAAAYLAPF-------PALITHRLDMATSG 132

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV+A+       +     ++ + + Y +LV        + IA      + IG D     
Sbjct: 133 LLVIAKNPLTQAIINRQLALKTMHRDYIALV-------PQGIAASGTITAPIGHDPDDQR 185

Query: 217 KQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           K+     GA+ AI+HF+ I         + ++  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 186 KRMIRPDGAS-AITHFRRI-AETSTTATVALRLETGRTHQIRVHLASIGYPILGDPLYAP 243

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +           ++YLHA  +    P     L +T+PLP
Sbjct: 244 D------QTTYQRMYLHAFQVRFTKPLSDTTLTVTSPLP 276


>gi|332828687|gb|EGK01379.1| hypothetical protein HMPREF9455_02212 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 242

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 50/182 (27%), Positives = 88/182 (48%), Gaps = 29/182 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D++   H   ++   +Q+   +  + V+   VK N +I+   V+ +      +N   
Sbjct: 41  IRIDKYLAMHIVGVSRNRIQQAAEANCILVNDNPVKSNYKIKPLDVISV-----VMNRPP 95

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHI 129
           +E +I+   + L          ++YED  + V NKP G+ V  G G         +AY  
Sbjct: 96  RELEIIPEDIPLD---------VVYEDDDLMVINKPPGLVVHPGFGNYQGTLVNAVAY-- 144

Query: 130 DGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              LK   +   + PRL   HR+D++TSG++VVA+   A  HL+  F  +  ++ Y +LV
Sbjct: 145 --LLKDTPEYDAKDPRLGIVHRIDKDTSGLIVVAKNAYAKAHLSAQFFNKTTKRQYVALV 202

Query: 188 WG 189
           WG
Sbjct: 203 WG 204


>gi|191638717|ref|YP_001987883.1| Pseudouridine synthase, 23S-rRNA-specific [Lactobacillus casei
           BL23]
 gi|190713019|emb|CAQ67025.1| Pseudouridine synthase, 23S-rRNA-specific [Lactobacillus casei
           BL23]
 gi|327382758|gb|AEA54234.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus casei LC2W]
 gi|327385945|gb|AEA57419.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus casei BD-II]
          Length = 277

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 101/219 (46%), Gaps = 31/219 (14%)

Query: 103 YEDSKIYVFNKPAGI----SVQGGSG-IAYHIDGFLKSWVDSKGQKPRL-THRLDQETSG 156
           YED  + + +KPAG+    ++ G +G +      +L  +       P L THRLD  TSG
Sbjct: 80  YEDDDLLIVDKPAGMKTHPNLPGETGTLMNQAAAYLAPF-------PALITHRLDMATSG 132

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV+A+       +     ++ + + Y +LV        + IA      + IG D     
Sbjct: 133 LLVIAKNPLTQAIINRQLALKTMHRDYIALV-------PQGIAASGTITAPIGHDPDDQR 185

Query: 217 KQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           K+     GA+ AI+HF+ I         + ++  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 186 KRMIRPDGAS-AITHFRRI-AETSTTATVALRLETGRTHQIRVHLASIGYPILGDPLYAP 243

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +           ++YLHA  +    P     L +T+PLP
Sbjct: 244 D------QTTYQRMYLHAFQVRFTKPLSDTTLTVTSPLP 276


>gi|332305526|ref|YP_004433377.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332172855|gb|AEE22109.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 252

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 67/217 (30%), Positives = 100/217 (46%), Gaps = 26/217 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I   +KPAG+ V   S I  H   F ++   D  GQ     HRLD+ TSG+LV
Sbjct: 5   ILYQDEFIVAIHKPAGLLVHR-SMIDRHETQFAMQLLRDQIGQHVFPVHRLDRPTSGVLV 63

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A +   A+ L E F    + K Y+++V G    K     ++ LK+     D +   + N
Sbjct: 64  FALSADIARILGEQFAANTVSKTYFAIVRG--HVKAPGFIDYALKEK---LDKIADKRAN 118

Query: 220 -EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K    A + F  I  F          + ++  +++ P TGR HQLR H  H+  PIVG
Sbjct: 119 QDKDPQEAQTEFVPIKQFELPFAVSRYPSARYTLVKLHPKTGRKHQLRRHMCHINHPIVG 178

Query: 269 DH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           D      K+    +  F+    N L L  + M + HP
Sbjct: 179 DTTHGDGKHNKFMRDQFSF---NGLALTCQQMRITHP 212


>gi|291550480|emb|CBL26742.1| pseudouridine synthase, RluA family [Ruminococcus torques L2-14]
          Length = 295

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 109/224 (48%), Gaps = 25/224 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQ 152
           ++YED  I V NKPAG+ +        + +A   +G +  W  ++  KP   R T+RLD+
Sbjct: 83  IIYEDEDILVVNKPAGMPIHPSLNNYENSLA---NGLM--WYYTEQGKPFIFRCTNRLDR 137

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+ V+A+   ++  L+       I++ Y ++V G        I   L +     G  
Sbjct: 138 DTSGLTVIAKHLISSSILSSMGARHEIKREYLAIVRGSVTPPSGTIDAPLART----GSS 193

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +   K + K    A++H+KV++        + +   TGRTHQ+RVH  ++G P+VGD+ Y
Sbjct: 194 MIERKVDFKHGERAVTHYKVVEE-KNGHSLVSLILETGRTHQIRVHMQYLGFPLVGDYLY 252

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
             + +        ++  LH+  +   HP     ++ TA LP  M
Sbjct: 253 NPDME------YIHRQALHSWKLSFIHPITKEPMEFTAELPEDM 290


>gi|259046558|ref|ZP_05736959.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           adiacens ATCC 49175]
 gi|259036723|gb|EEW37978.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           adiacens ATCC 49175]
          Length = 284

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 101/220 (45%), Gaps = 15/220 (6%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSG 156
           +LYED  + + NKP G  S+       + +   +K +   +G   ++TH   RLD++T+G
Sbjct: 66  ILYEDEYLLIINKPVGTASIPSKLHPDHSMANRVKGYYKRRGYADQITHVVTRLDRDTTG 125

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++ A+ R     + ++ R + IQK Y +LV      +     +  + + H G      V
Sbjct: 126 VMMFAKHRVVHAWMDQALREKTIQKKYLALVHDTSTLEAHGFIDAPIGR-HEGSIINRCV 184

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +E G      ++K       +   +E+  HTGRTHQ+RVH   +G P+V D  Y    
Sbjct: 185 --SEDGKPSLTEYWKKETLVGAEL--VEILLHTGRTHQIRVHFSWIGAPLVADDLY---- 236

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            G       ++  LH   +   HP   + L I APLP  M
Sbjct: 237 -GGVKDEFLDRQALHCHSLTFIHPMTKKELIIEAPLPKDM 275


>gi|254578372|ref|XP_002495172.1| ZYRO0B05082p [Zygosaccharomyces rouxii]
 gi|238938062|emb|CAR26239.1| ZYRO0B05082p [Zygosaccharomyces rouxii]
          Length = 611

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 88/178 (49%), Gaps = 7/178 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + V +KP+GI V       Y  +   K      G+     +RLD+ TSG++ +
Sbjct: 188 VVYEDENLLVIDKPSGIPVHPTG--RYRFNTITKILEKKLGRTVHPCNRLDRLTSGLMFM 245

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+T   A  + +  + R + K Y + V G  P    E + +  LK          V   +
Sbjct: 246 AKTPKGADEMADQLKAREVTKEYVARVVGEFPVG--EVVVDNPLKSLEPKLGLNVVCGMD 303

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           E+GA +A + F+ +  +  +   ++ +P TGRTHQ+RVH  ++G PI  D  Y +N K
Sbjct: 304 EEGAKHAKTVFRRVS-YDGETSIVKCKPLTGRTHQIRVHLQYLGHPIANDPIY-SNLK 359


>gi|326796257|ref|YP_004314077.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326547021|gb|ADZ92241.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
          Length = 211

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 59/203 (29%), Positives = 95/203 (46%), Gaps = 18/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  + V NKP       G G    +D  L       G+     HRLD  TSG+++V
Sbjct: 9   ILYEDEWLLVLNKPENCLSVPGRG-PEKLDSILHRAEQYCGEA-YAVHRLDHATSGLILV 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A++    + + ++FR + + K Y ++V G P  +   +      +  +  D+ +  +Q  
Sbjct: 67  AKSLECQKRMYKAFREKEVDKEYLAIVRGTPIGQCGSV------RKPLRCDWPNRPRQMI 120

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E G + AI+ +K I         + + P TGR+HQLRVH   +G  IVGD      F 
Sbjct: 121 CTEWGKD-AITQWKPIKQVGNNTL-VSLSPITGRSHQLRVHMQSLGHSIVGD-----EFY 173

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
            +  +    +L LHA  ++  HP
Sbjct: 174 DDLYTNQDERLLLHAYRIEFAHP 196


>gi|254457610|ref|ZP_05071038.1| tRNA pseudouridine synthase C [Campylobacterales bacterium GD 1]
 gi|207086402|gb|EDZ63686.1| tRNA pseudouridine synthase C [Campylobacterales bacterium GD 1]
          Length = 250

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 99/222 (44%), Gaps = 36/222 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G+ V       + I   +K   D  GQ     HRLD+ TSG+L+ 
Sbjct: 9   ILYQDGYLVCINKPSGLLVHKSMIDRHEIYFAMKMLRDQIGQWVYPIHRLDKPTSGVLLF 68

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIP----------KNKKECIANWLLKKSHIGG 210
           A  +  A+ ++E F+    +K Y  +V G            K K + IA+   K+     
Sbjct: 69  ALDKETAKLMSEQFKEHTTKKTYICVVRGYTEVFGLIDHALKEKLDKIADKDAKE----- 123

Query: 211 DYVHVVKQNEKGANYAISHFKVIDC----FA------QKFCWLEMQPHTGRTHQLRVHAL 260
                    EK A  A + ++ +D     FA       ++  ++++P TGR HQ+R H  
Sbjct: 124 ---------EKEAQEAATEYERLDTVELDFAVGRYDKTRYSLVKVKPKTGRKHQIRRHMK 174

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHP 300
           H+   I+GD KY       F     +  +L LHA  ++  HP
Sbjct: 175 HISHHILGDTKYGRGEHNVFVREEFDCHRLLLHALSLEFKHP 216


>gi|311278253|ref|YP_003940484.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308747448|gb|ADO47200.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 260

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 104/231 (45%), Gaps = 48/231 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKP+G  V              +SW+D               GQ     
Sbjct: 4   IVYQDQWLVAVNKPSGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++  +  A + L + F   +I K Y ++V G     +E I ++ L +  
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIHKRYHAIVRGW--LSEEGILDYPLVEEL 108

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQL 255
             I   +     + +KG   A++H++ +               ++  +E+ P TGR HQL
Sbjct: 109 DKIADKFA----REDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELDPKTGRKHQL 164

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGG 303
           R H  H+  PI+GD K+  + + N ++      ++L LHA  + L HP  G
Sbjct: 165 RRHLKHLRHPIIGDSKH-GDLRQNRSAAEHFGCDRLMLHASELRLTHPFTG 214


>gi|308187954|ref|YP_003932085.1| tRNA pseudouridine synthase C [Pantoea vagans C9-1]
 gi|308058464|gb|ADO10636.1| tRNA pseudouridine synthase C [Pantoea vagans C9-1]
          Length = 259

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 60/216 (27%), Positives = 96/216 (44%), Gaps = 18/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   NKP+G  V   S +  H   F+   V D  GQ     HRLD+ TSG+L+
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHR-SWLDRHETVFVMQTVRDQIGQHVFTAHRLDKPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +  +    + L+  F   ++QK Y ++V G  ++        + +   I   +       
Sbjct: 63  MGLSSEVGRLLSLQFEQHQMQKTYHAVVRGWLESSGTLDYPLVEELDKIADRHA----TE 118

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            + A  A++ ++ +               ++  +EM P TGR HQLR H  H+  PI+GD
Sbjct: 119 ARTAQPAVTDYQSLATVEMPVGIGRYPTSRYSLVEMAPKTGRKHQLRRHMSHLRHPIIGD 178

Query: 270 --HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             H      +G       N+L LHA  + L HP  G
Sbjct: 179 SAHGDLRQNRGAAEHFGANRLMLHASSLALTHPVTG 214


>gi|28377784|ref|NP_784676.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|28270617|emb|CAD63523.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
          Length = 293

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 57/180 (31%), Positives = 86/180 (47%), Gaps = 13/180 (7%)

Query: 103 YEDSKIYVFNKPAGI-SVQGGSG----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED+   V NK AG+ SV G S     +   I G+L +   +  Q+P L  RLD++TSG+
Sbjct: 81  YEDANWLVLNKTAGLTSVPGPSNRTDTLVNRIKGYLMA-SHASNQRPHLITRLDRDTSGL 139

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA+ R A   LTE     ++ K Y + + G        I   + + +      V    
Sbjct: 140 VLVAKHRVAQGMLTEPRIAAQLVKTYQAWIEGTITPASGTIDRPIGRVADSPRRVVTTAG 199

Query: 218 QNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           Q       AI+ ++V  D        L ++  TGRTHQ+RVH   +G P++GD  Y  N 
Sbjct: 200 QR------AITTYQVEADQLQHNVSRLRLELVTGRTHQIRVHLTTLGHPLLGDALYGGNL 253


>gi|219684906|ref|ZP_03539847.1| RNA pseudouridine synthase family protein [Borrelia garinii PBr]
 gi|219671644|gb|EED28700.1| RNA pseudouridine synthase family protein [Borrelia garinii PBr]
          Length = 315

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 78/301 (25%), Positives = 138/301 (45%), Gaps = 36/301 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-----LRSGQVRVDKKRVKF 55
           M L  Y+   V++ND    RLD         I  +N  K      +R G +R++  +  F
Sbjct: 1   MRLDKYILLEVLDNDN-GKRLDSIL------IKILNFSKARIIKHIRKGDIRLNGLKPSF 53

Query: 56  NNRIQSGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
           + R+  G  + +   ++  L+  + E     S+++       ++  ++YEDS + V +K 
Sbjct: 54  SYRVCKGDKIYLYKSLVQNLHLAMGE--CYKSNIDFQ----CIRKRIIYEDSDLLVMDKQ 107

Query: 115 AGISVQGG-SGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
            GI V GG + + + ++ +L +  + S   KP   HRLD+ TSGI++ A+    A+ L+ 
Sbjct: 108 RGILVHGGKNSLDFLVNSYLLREDLRSLSFKPSAVHRLDRNTSGIIIFAKNINVARKLSA 167

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           +F    + K Y++++ G   N      N L +   +   +V      +K +  AI+  KV
Sbjct: 168 AFSSGSVTKKYFAILLG-EVNSTVIYKNHLFRNQRLKKTFV----LEDKDSINAIT--KV 220

Query: 233 IDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
               + K   L E+   TG THQ+R        P++ D KY   FK       ++  +LH
Sbjct: 221 NPILSSKRATLAEIVIETGFTHQIRSQCSFNEHPLINDKKYYNKFK-------KSDYFLH 273

Query: 292 A 292
           A
Sbjct: 274 A 274


>gi|317180509|dbj|BAJ58295.1| hypothetical protein HPF32_0713 [Helicobacter pylori F32]
          Length = 327

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 53/227 (23%), Positives = 104/227 (45%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + +     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVIHKAPSVK---EPTLVDWLEFKNYELSNLGSKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+      +L+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVYLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L    PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLCFKVPLLKDMLE 300


>gi|229016558|ref|ZP_04173498.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1273]
 gi|229022765|ref|ZP_04179289.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1272]
 gi|228738577|gb|EEL89049.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1272]
 gi|228744734|gb|EEL94796.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1273]
          Length = 292

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 102/210 (48%), Gaps = 29/210 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGS---GIAYHIDG-FLKSWVDSKGQKPRLTHRL 150
           ++YED  + V NK A +S         GS    + YH D   L S V        +  RL
Sbjct: 79  IVYEDDAVLVVNKEAYMSTIPSREHPSGSVANALLYHYDKQNLASTV-------HIVTRL 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ R     L++  + + +++ Y +LV G+   +   I   + +K+    
Sbjct: 132 DRDTSGLMLIAKNRFVHNLLSKQHQQKGVKRTYEALVHGMILEEIGTIDAPIGRKA---- 187

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D +      E G   A++HFKV++  + K   + ++  TGRTHQ+RVH  H+G P++GD 
Sbjct: 188 DSIIERTVCEDG-QRAVTHFKVMESSSNK-THVALELETGRTHQIRVHMAHIGHPLLGDD 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            Y           +  +  LH+  +   HP
Sbjct: 246 LYGGR------RDVMKRQALHSTSLTFYHP 269


>gi|293401387|ref|ZP_06645530.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305025|gb|EFE46271.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 293

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 105/225 (46%), Gaps = 16/225 (7%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG-QKP-RLTHRLD 151
           DF +  + YED  +   NKP+ + V   G   ++ +   ++ +   +G   P R  HRLD
Sbjct: 77  DFTELSICYEDELLLAVNKPSHLLVHSDGVDTSHTLCNRVQGYYLMQGITAPVRPLHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSGI++  +       L    + ++IQ+ Y ++V G    KK+ I   + +  H    
Sbjct: 137 KETSGIVLFCKIPFFQPLLDHMMKEKQIQREYEAIVEGSIHQKKQTITYPIARDRHDARK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V    K A   I+  K    ++    W+  +  TGRTHQ+RVH   +  P++ D  
Sbjct: 197 M--RVSATGKHAKTTITLQKNYGAYS----WIHARLFTGRTHQIRVHLAALKHPLLSDSL 250

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           Y     G  +  I ++L LHA  + L HP    ++Q+T  +P  M
Sbjct: 251 Y-----GTPSDKI-HRLALHASLLTLQHPFTNKKIQVTCEMPLDM 289


>gi|300767769|ref|ZP_07077679.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|300494754|gb|EFK29912.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 293

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/180 (31%), Positives = 86/180 (47%), Gaps = 13/180 (7%)

Query: 103 YEDSKIYVFNKPAGI-SVQGGSG----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED+   V NK AG+ SV G S     +   I G+L +   +  Q+P L  RLD++TSG+
Sbjct: 81  YEDANWLVLNKSAGLTSVPGPSNRTDTLVNRIKGYLIA-SHASNQRPHLVTRLDRDTSGL 139

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA+ R A   LTE     ++ K Y + + G        I   + + +      V    
Sbjct: 140 VLVAKHRVAQGMLTEPRIAAQLVKTYQAWIEGTITPASGTIDRPIGRVADSPRRVVTTAG 199

Query: 218 QNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           Q       AI+ ++V  D        L ++  TGRTHQ+RVH   +G P++GD  Y  N 
Sbjct: 200 QR------AITTYQVEADQLQHNVSRLRLELVTGRTHQIRVHLTALGHPLLGDALYGGNL 253


>gi|315268828|gb|ADT95681.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 268

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 62/216 (28%), Positives = 98/216 (45%), Gaps = 18/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+DS I + +KP+G+    G     ++D      V        L HRLD  TSGI++V
Sbjct: 49  VLYQDSDILLIDKPSGLLSLSGKN-PLNLDSVHYRLVQDF-PTATLLHRLDFGTSGIMLV 106

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  ++    LT+ F+ R ++K Y +L+ G        I   + K      D+  + K   
Sbjct: 107 ALNKSVNGLLTKQFQARTVEKRYTALLHGHIAADSGVINLPIAKDV----DHFPLQKICH 162

Query: 221 KGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NF 276
                AIS ++V++   + F   +E  P +GRTHQLR+H+   G  I+G   Y     + 
Sbjct: 163 STGKPAISEYRVLERLTEPFATRVEFTPVSGRTHQLRIHSQQFGHSILGCDLYGGVGESV 222

Query: 277 KGNFTSP--------IQNKLYLHARYMDLPHPEGGR 304
             N  +P          ++L LHA  +   HP  G 
Sbjct: 223 ADNADAPEPDITKMTSNSRLMLHATRLAFDHPITGE 258


>gi|326692367|ref|ZP_08229372.1| pseudouridylate synthase [Leuconostoc argentinum KCTC 3773]
          Length = 305

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 103/229 (44%), Gaps = 35/229 (15%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQ 152
           +++E+    V +KPAG+ +      +  + + Y    F    + S GQ  +P + HR+D+
Sbjct: 87  IIFENDDFVVVDKPAGMKMHPHAPNEADTLLNYLAADFQARHLMSAGQPARPYMVHRIDR 146

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG ++VA+       L      + I++ Y + V G        I       + IG D 
Sbjct: 147 DTSGAVIVAKNPVVVPILNRLLAQKAIKRTYLAWVQGAVAESAGEI------TTPIGVD- 199

Query: 213 VHVVKQNEK-------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                Q+E+        A  A +H+  +    Q    L +Q  TGR HQ+RVH   +G P
Sbjct: 200 ----PQDERRRVINGLAAQSARTHWARMHTVYQN-SLLRVQLDTGRMHQIRVHLASIGHP 254

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           I+GD  Y     G        ++ LHA  + +P P +GG + I+  +P+
Sbjct: 255 IIGDPLYHPEQPG-------TRMMLHAATLIVPLPFDGGTVTISGAIPS 296


>gi|146319641|ref|YP_001199353.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           05ZYH33]
 gi|146321839|ref|YP_001201550.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           98HAH33]
 gi|253752639|ref|YP_003025780.1| RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|253754465|ref|YP_003027606.1| RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|253756398|ref|YP_003029538.1| RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|145690447|gb|ABP90953.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           05ZYH33]
 gi|145692645|gb|ABP93150.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           98HAH33]
 gi|251816928|emb|CAZ52577.1| RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|251818862|emb|CAZ56705.1| RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|251820711|emb|CAR47473.1| RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|292559258|gb|ADE32259.1| Pseudouridylate synthase [Streptococcus suis GZ1]
 gi|319759055|gb|ADV70997.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           JS14]
          Length = 288

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 66/256 (25%), Positives = 113/256 (44%), Gaps = 28/256 (10%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           QVRV+ + + +   I +G ++ +            ++   + S+ L + +D ++   LY+
Sbjct: 39  QVRVNGELINWQCPITAGDLLEL---------TFDQEDYPEKSIPLGQ-ADLVEE--LYQ 86

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG ++ A+  
Sbjct: 87  DEHLIIVNKPEGMKTHGNDPTEIALLNHVSAYV---GQTCYVVHRLDMETSGAILFAKNP 143

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
                L      + I + Y +L  G  K     I + + +  H   D    V  N KG  
Sbjct: 144 FILPILNRLLEDKVIYRDYLALCQGQLKMTDWTITDKIGRDRH---DRRKRVVDNRKGQT 200

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
            A++  +++     K   +  +  TGRTHQ+RVH  H G  ++GD  Y          P 
Sbjct: 201 -ALTQVRLLKTLG-KNSLVSCRLQTGRTHQIRVHLAHHGHALIGDPLY-----SRVAPP- 252

Query: 285 QNKLYLHARYMDLPHP 300
             +L LHA+ + L HP
Sbjct: 253 --RLMLHAQKLSLTHP 266


>gi|119478011|ref|ZP_01618111.1| 23S rRNA pseudouridylate 746 synthase [marine gamma proteobacterium
           HTCC2143]
 gi|119448924|gb|EAW30166.1| 23S rRNA pseudouridylate 746 synthase [marine gamma proteobacterium
           HTCC2143]
          Length = 221

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 60/206 (29%), Positives = 99/206 (48%), Gaps = 16/206 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  + + NKPAG+    G   A      L + V  +    R+ HRLD +TSGI+V+
Sbjct: 17  ILFTDDDLLLVNKPAGLLSVPGRHPAN--KDCLITRVQRQYADARIVHRLDMDTSGIMVL 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A +  + + L++ F  R+I K Y + V+G   +    I   LL       D+ +  +Q  
Sbjct: 75  ALSADSHRALSQLFAERKIIKEYEANVYGTIIDDHRLIDLPLL------CDWPNRPRQKV 128

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
               G N A +  + +      +  + ++P TGR+HQLRVH   +G PI+G    C  + 
Sbjct: 129 DFHHGKN-AQTWVERVSQHPDGWTRVLLKPVTGRSHQLRVHLAEIGHPILG----CEFYA 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
                 + ++L LHA  ++  HP  G
Sbjct: 184 HQRAVSMADRLQLHATKLEFCHPNSG 209


>gi|157963919|ref|YP_001503953.1| pseudouridine synthase Rlu family protein [Shewanella pealeana ATCC
           700345]
 gi|157848919|gb|ABV89418.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           pealeana ATCC 700345]
          Length = 229

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/195 (29%), Positives = 94/195 (48%), Gaps = 25/195 (12%)

Query: 101 LLYEDSKIYVFNKPAGI---SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++ ++    V NK A +   S  G +G+    +  L       G K    HRLD  TSG+
Sbjct: 4   VIADERDFIVINKSAEVHFHSQDGNAGVVAQAEADL-------GIKLYAVHRLDTMTSGL 56

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A++ +AA   T  F    +QK Y +L  G PK K+     W++         +H + 
Sbjct: 57  IILAKSSSAAAEFTRMFSAHLVQKYYLALAKGKPKKKQ----GWVIGDMAKSRRSMHKLL 112

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +  +  N AI+ F        +  +L ++PH+G+THQLRV    +G PI+GD  Y     
Sbjct: 113 RTTE--NPAITQFFSHSIAEGERLYL-LKPHSGKTHQLRVALASIGVPILGDTLY----- 164

Query: 278 GNFTSPIQNKLYLHA 292
           G  ++   ++ YLHA
Sbjct: 165 GGLSA---DRGYLHA 176


>gi|42527698|ref|NP_972796.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
 gi|41818526|gb|AAS12715.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
          Length = 236

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 55/191 (28%), Positives = 89/191 (46%), Gaps = 27/191 (14%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--------------- 192
           +RLD+  SG++++A + A    L   F+ ++I+K YW++   I +               
Sbjct: 43  NRLDKPVSGLVLIAFSPAMHTKLNNLFKEKKIKKEYWAICKKIEELKSAADSKISDTTPV 102

Query: 193 -NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             KKE   N+L   + I   +V   +Q  K A    S +  +      + +L + P TGR
Sbjct: 103 LYKKEFCENYLEFNTKIQKAFVTESRQRGKKA----SLYWQLAGIGDNYNFLRIFPETGR 158

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+R+   H+G PI GD KY     G   +     + LHA+ +   HPE   R++I+A 
Sbjct: 159 THQIRIQLSHLGMPIKGDIKY-----GFARTEKSGGIRLHAQSLKFEHPESKKRIEISA- 212

Query: 311 LPAHMVKTWDS 321
           LP      W +
Sbjct: 213 LPPSPDTLWSA 223


>gi|320530955|ref|ZP_08031988.1| pseudouridine synthase, RluA family [Selenomonas artemidis F0399]
 gi|320136820|gb|EFW28769.1| pseudouridine synthase, RluA family [Selenomonas artemidis F0399]
          Length = 297

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 106/232 (45%), Gaps = 22/232 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGS-----GIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           L   + YED  + + +KPAG+ V   +      IA  + G   S  D+    P   HRLD
Sbjct: 75  LPLAIAYEDDDLLIIDKPAGMLVHPTTQETRGTIANAVRGLYASRGDTLDFHP--CHRLD 132

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + T+G+L++A+      + T+   +  +++ Y +L+ G      + I   + +   +   
Sbjct: 133 RNTTGLLLIAKRPEVQYYFTK--HLDAVRRAYLALIEGRLTPASDIIDAPIARA--LPSI 188

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  V  + K A    +H+   +    ++  L +   TGRTHQ+RVH  H+G P++GD  
Sbjct: 189 ILRRVAPDGKPAR---THYTT-ERTTGRYSLLRLTLETGRTHQIRVHLAHLGHPLLGDDL 244

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           Y  N     T  I     LHA  + L  P  G  L + +PLP  M +   +L
Sbjct: 245 YGCN-----TDEIARH-ALHAARLSLRLPRTGELLTVESPLPEDMARIAGTL 290


>gi|220918618|ref|YP_002493922.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219956472|gb|ACL66856.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 287

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 73/315 (23%), Positives = 127/315 (40%), Gaps = 38/315 (12%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +    RLDRW             + ++ +G+VR+  K    + ++  G           
Sbjct: 3   REAAGARLDRWLAGAI-GATAERTRWLVETGRVRIRGKTCSPHRKLFGG----------- 50

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF- 132
                 E+  ++        +      +LY+D+   V  KP G++V+  +          
Sbjct: 51  ------EEVAVERPAPRAAEASGPALAVLYDDADCLVVAKPPGLAVEASAPGGASAVAAA 104

Query: 133 --LKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             L S+ D  G+  P L HRLD++TSG L++AR   A   L  +F    ++K Y +LV G
Sbjct: 105 SRLGSF-DVDGRAVPGLPHRLDRDTSGALLLARHDRALAALRAAFEAGAVEKEYLALVGG 163

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK-VIDCFAQKFCWLEMQPH 248
            P  +           +  G D     +   +  +   +     ++   +    L ++  
Sbjct: 164 APPREGRL-------DTPYGRDPADPRRFTTRFPSARRARLSWTVERALRGAALLRVRLE 216

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
           TGRTHQ+RV     G P++GD  Y     G     I  +  LHA  +  P P +G  +++
Sbjct: 217 TGRTHQIRVQLAEAGFPVLGDAAY-----GVRADAIARQ-ALHAARLAFPRPSDGAPVEV 270

Query: 308 TAPLPAHMVKTWDSL 322
            APLP  + +   +L
Sbjct: 271 RAPLPEDLERAIAAL 285


>gi|332876875|ref|ZP_08444629.1| RNA pseudouridine synthase [Capnocytophaga sp. oral taxon 329 str.
           F0087]
 gi|332685158|gb|EGJ58001.1| RNA pseudouridine synthase [Capnocytophaga sp. oral taxon 329 str.
           F0087]
          Length = 202

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 55/191 (28%), Positives = 89/191 (46%), Gaps = 14/191 (7%)

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHL 170
           G  VQG       +   LK+++  K  KP      + HRLD+ T+G+++ A+T  A   L
Sbjct: 2   GDIVQGDKTGDIPLSEHLKAYLKKKYNKPGEAYLGVVHRLDRPTTGVVLFAKTSKALSRL 61

Query: 171 TESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
              F  + ++QK YW+LV  +P   +  + +WL++         H   +  + +  A+ H
Sbjct: 62  NAMFADKAQVQKTYWALVDAMPPATEGTLTHWLVRNEKQNKSVAH--NKEVQHSKKAVLH 119

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           +K++  F   +  LE+   TGR HQ+R     +G  I GD KY A       S     + 
Sbjct: 120 YKLLKSF-DHYHLLEIDLITGRHHQIRAQLAAIGLHIKGDLKYGAK-----RSNPDGGIC 173

Query: 290 LHARYMDLPHP 300
           LHA  +   HP
Sbjct: 174 LHAYKLTFEHP 184


>gi|254282028|ref|ZP_04956996.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium NOR51-B]
 gi|219678231|gb|EED34580.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium NOR51-B]
          Length = 228

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 111/250 (44%), Gaps = 39/250 (15%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYH--IDGF 132
           +I +    DS   L  H+   + I LLY+D+ + +  KP  + SV G   +     +   
Sbjct: 1   MITDPATPDSPPYLVPHTR--EPIRLLYQDNDLLIVEKPTLLLSVPGRHPLNRDSLMTRL 58

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +  + D         HRLD +TSG++VV   R+A   L   F+ RR++K Y ++VWG+  
Sbjct: 59  MPRFPDVAA-----VHRLDLDTSGLMVVPTRRSALSALGRLFQERRVEKEYLAVVWGVLA 113

Query: 193 NKK-----ECIANW----LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +         IA+W    L K  H  G               AI+ + V+     +   L
Sbjct: 114 HDSGTIDLPIIADWHRRPLQKICHDTG-------------KSAITRYTVLKRGTDR-TLL 159

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-G 302
            + P TGR+HQLR+H   +G PI+G    C  +          +L LHA  +  PHP  G
Sbjct: 160 RLNPVTGRSHQLRIHCREIGHPILG----CDLYAHADALAAAPRLLLHATRLAFPHPTLG 215

Query: 303 GRLQITAPLP 312
            RL   +P P
Sbjct: 216 HRLAAVSPAP 225


>gi|12045061|ref|NP_072871.1| RluA family pseudouridine synthase [Mycoplasma genitalium G37]
 gi|255660210|ref|ZP_05405619.1| RluA family pseudouridine synthase [Mycoplasma genitalium G37]
 gi|1351510|sp|P47451|Y209_MYCGE RecName: Full=Uncharacterized RNA pseudouridine synthase MG209;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|3844807|gb|AAC71427.1| pseudouridine synthase, RluA family [Mycoplasma genitalium G37]
 gi|166079007|gb|ABY79625.1| pseudouridine synthase, RluA family [synthetic Mycoplasma
           genitalium JCVI-1.0]
          Length = 308

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 76/310 (24%), Positives = 136/310 (43%), Gaps = 42/310 (13%)

Query: 35  VNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           V + K++ +GQ++V++K + F N +                 I+ +  ++   ++    S
Sbjct: 26  VKVVKLIMNGQIKVNEK-LTFKNSL-----------------IVAKDDVIKVEIHDETTS 67

Query: 95  DFLKSI--------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-R 145
           DF+ S+        +L+ED  + V NKP+G+     +         L + +    + P  
Sbjct: 68  DFITSVEPYNLKLEVLFEDKDLMVINKPSGLLTHPTTF--NEKASLLAACIFHNNKNPVY 125

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD++TSG +VV + +A+  +L    + R +++ Y +LV   P N      N  L  
Sbjct: 126 LVHRLDRDTSGAIVVCKNQASLLNLQNQLQNRTLKRYYVALVH-FPFNALTGSINAPL-- 182

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           + +  + V         A  AI+ FKVI+   +K   + ++  TGRTHQ+RVH   +  P
Sbjct: 183 ARVNNNKVMFKIAQTAKAKQAITKFKVINQ-NEKAALISLELLTGRTHQIRVHLKFIQHP 241

Query: 266 IVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +  D  Y   +  K ++        +LHA  +   HP   + +   APL         SL
Sbjct: 242 VYNDPLYGIKSEKKDSYGQ------FLHANRICFIHPTLNKPMDFHAPLEPKFSTKLKSL 295

Query: 323 GFKYDRNLYI 332
                  L++
Sbjct: 296 NLSLTDPLHV 305


>gi|325847067|ref|ZP_08169893.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481039|gb|EGC84084.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 249

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 54/190 (28%), Positives = 97/190 (51%), Gaps = 17/190 (8%)

Query: 101 LLYEDSKIYVFNK-------PAGISVQGG--SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YE+    + +K       PAG  V G   +G+ YH  G+          +P + HRLD
Sbjct: 26  IVYENEDYAIIDKDENVIVHPAGSIVSGTLVNGLLYHF-GYNNLSHIGGDDRPGIVHRLD 84

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G++V+A++ ++ + L   F  R+I K Y ++  GI K K   I  ++ +  +   +
Sbjct: 85  KDTTGLMVIAKSNSSYKFLKNLFEKRKIDKEYLAICNGIFKKKSGEIHTFMDRDPN---N 141

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              +  +N      AIS ++V+      +  ++++  TGRTHQ+RVH  H+  P++GD  
Sbjct: 142 RRKMAVRN--SGRDAISKYEVL-SENDGYSLVKIKILTGRTHQIRVHMTHINHPLLGDPV 198

Query: 272 YCANFKGNFT 281
           Y  N K  F 
Sbjct: 199 Y-GNVKHKFN 207


>gi|114048209|ref|YP_738759.1| tRNA pseudouridine synthase C [Shewanella sp. MR-7]
 gi|113889651|gb|ABI43702.1| tRNA pseudouridine synthase C [Shewanella sp. MR-7]
          Length = 284

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 107/242 (44%), Gaps = 27/242 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   +KPAG+ V   S +A     F      D  G      HRLD+ TSG+L+
Sbjct: 32  VLYQDEHLVAIHKPAGLLVHR-SYLARRERFFAMQLTRDLVGCHVFPVHRLDRPTSGVLL 90

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQ 218
            A++   A  L E F    I+K Y +LV G   N  E  I ++ LK      +       
Sbjct: 91  FAKSSEVANALCEQFANHSIEKQYLALVRG---NMHESGILDYALKVE--LDEVADKFAN 145

Query: 219 NEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +               +F  +++ P TGR HQLR H  H+  PI+G
Sbjct: 146 QDKAAQDAVTQYEPLLNTEIPYPSGRYATSRFALVKLSPKTGRKHQLRRHMAHLRHPIIG 205

Query: 269 DH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           D      K  A F+ +F     N+L+L A+ +   HP    RL I   L       +  L
Sbjct: 206 DTTHGDGKQNAFFRAHFDI---NRLWLIAKKLTFTHPVTLERLSIETELEPEWETVFAGL 262

Query: 323 GF 324
           G+
Sbjct: 263 GW 264


>gi|304385186|ref|ZP_07367532.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici DSM 20284]
 gi|304329380|gb|EFL96600.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici DSM 20284]
          Length = 301

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 68/285 (23%), Positives = 132/285 (46%), Gaps = 36/285 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
           G++ V+++  + N  + +G    V +PP      H+++ ++ +D               +
Sbjct: 37  GKILVNEQPKRTNEMVTAGDQVTVELPPEPGN-PHVVRSRQPID---------------V 80

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGI 157
           +YED    V NKP  + +VQ        +   +K++   +  + ++ H   RLDQ+TSG+
Sbjct: 81  IYEDQDYLVVNKPPFLPTVQSARNQTDTLVNRVKNYYAERDYESQVVHVVTRLDQDTSGL 140

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+ R A   + +  R  R+QK Y ++  G          +  L  + I  D    +K
Sbjct: 141 VLFAKHRFAHTIMDQDLRQHRVQKYYLAMATG------RFAQSHGLIDAPIERDPASFIK 194

Query: 218 QNEKGANY---AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +    A     + + + V++  A     L++Q HTGRTHQ+RVH   +  P++GD  Y  
Sbjct: 195 RRVASAGNGKPSKTEYWVLEQTATD-SLLKVQLHTGRTHQIRVHFSELHHPLIGDPLYN- 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
             + +F S  +  L+  +   +     G ++ + AP+P  M++ W
Sbjct: 253 --ETSFRSLQRQALHCFSLKFENVF-RGKKIDVQAPIPNDMLEYW 294


>gi|293395440|ref|ZP_06639724.1| ribosomal large subunit pseudouridine synthase A [Serratia
           odorifera DSM 4582]
 gi|291422124|gb|EFE95369.1| ribosomal large subunit pseudouridine synthase A [Serratia
           odorifera DSM 4582]
          Length = 284

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 104/218 (47%), Gaps = 19/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D ++ + +KPAG+    G   A +ID      V        L HRLD  TSG++++
Sbjct: 71  ILYQDEQLVLIDKPAGLLSLSGKN-AQNIDSVHHRLVQIF-PGCTLVHRLDFGTSGLMLI 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +A    L + F  R + K Y +L+ G  ++ +  I   + K   +    + +   + 
Sbjct: 129 ARNKAINAALCQQFSQRTVSKEYHALLCGHLEHNEGVIDAAIAKDPAL-FPLMSICSIHG 187

Query: 221 KGANYAISHFKVID----CFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K A    S ++V++      A++       + + P TGRTHQLR+H   +G PI+G   Y
Sbjct: 188 KPAR---SRYQVVERGYHAVAEQRPVPVTRVRLTPETGRTHQLRIHCQQLGHPILGCDLY 244

Query: 273 CAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
                 G   +P   +L LHA  +   HP   R +ITA
Sbjct: 245 GGRLLPGTEQTP---RLMLHASELQFVHPVSQR-RITA 278


>gi|227892867|ref|ZP_04010672.1| pseudouridylate synthase RluD [Lactobacillus ultunensis DSM 16047]
 gi|227865369|gb|EEJ72790.1| pseudouridylate synthase RluD [Lactobacillus ultunensis DSM 16047]
          Length = 285

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 49/179 (27%), Positives = 79/179 (44%), Gaps = 9/179 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + + NK  G   Q         +  L       G  P + HRLD  T G+L+V
Sbjct: 83  VVYEDKNLLIINKKKG---QKTHPNLNETNTALNDCATYLGSSPYIVHRLDMLTGGLLLV 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+  A    L      +   + Y + V     +  E + +       IG D     K+  
Sbjct: 140 AKNPAVVPILNRELTTKIFHRNYLAKV-----DHAENLKDTGTINVPIGHDPTDQRKRMV 194

Query: 221 KG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +     AI+H+++++        +++   TGRTHQ+RVH  ++G PI+GD  Y  NF G
Sbjct: 195 RNDGQKAITHYQILERNNNGSAIVQLTLETGRTHQIRVHLAYLGAPIIGDPLYNPNFTG 253


>gi|224013728|ref|XP_002296528.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220968880|gb|EED87224.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 405

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 54/172 (31%), Positives = 86/172 (50%), Gaps = 30/172 (17%)

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE------------- 196
           LD+ TSG+LVVA+T+ A   L+  F+ R+++K Y ++V G  + + E             
Sbjct: 181 LDRATSGLLVVAKTKPAMVDLSSQFKHRKVKKTYTAIVNGDIQERPESSISSREAKQLGV 240

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------LEMQPHTG 250
           CI N     SH   D+       E     A++ ++ +D  + ++ W      +E++P TG
Sbjct: 241 CIEN---TGSH---DFRWQFVDEELDGQSAVTIWRTVDKSSLEYAWNNTIAMVELKPKTG 294

Query: 251 RTHQLRVH-ALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHP 300
           R HQLR H A   GC IVGD  Y  + +      ++N+ LYL +  + L HP
Sbjct: 295 RYHQLRRHMAWVYGCSIVGDKSYDGSGQAKL---LRNEGLYLCSNKVTLQHP 343


>gi|317054867|ref|YP_004103334.1| pseudouridine synthase [Ruminococcus albus 7]
 gi|315447136|gb|ADU20700.1| pseudouridine synthase [Ruminococcus albus 7]
          Length = 276

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 99/209 (47%), Gaps = 36/209 (17%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQET 154
            L   +LYED  + VF+KPA + V     I +  D     +    KG   R  +RLD++T
Sbjct: 77  LLDVPVLYEDGDVIVFDKPADMPVH--ESINHRGDTLANFFACRCKGLTFRTVNRLDRDT 134

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK----KECIANWLLKKSHIGG 210
           +G + VA+TR AA  L  S     I K+Y  L   IP  K    + C      ++S I  
Sbjct: 135 AGCVCVAKTRYAANALAGS-----ISKVYCGL---IPLTKLSGGRVCAPIARERESVI-- 184

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             +  V+ + K   Y+ + ++VI+       C   ++  TGRTHQ+RVH  H+G P++GD
Sbjct: 185 --LRCVRADGK---YSATCWQVIERRKDSVLCRFLLE--TGRTHQIRVHMAHIGLPLIGD 237

Query: 270 HKY---CANFKG--------NFTSPIQNK 287
             Y    +N KG        +F SP   K
Sbjct: 238 EMYGGDTSNRKGQALMCSEVSFISPESGK 266


>gi|264678303|ref|YP_003278210.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
 gi|262208816|gb|ACY32914.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
          Length = 214

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 56/187 (29%), Positives = 94/187 (50%), Gaps = 21/187 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPRLTHRLDQETSGI 157
           +YED  + V +KP+G+    G G     D      L+ + D+      + HRLDQ TSG+
Sbjct: 1   MYEDEHLLVLDKPSGLLCVPGRGPDKQ-DCLSLRALRHFGDAL-----VVHRLDQATSGL 54

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN--WLLKKSHIGGDY--- 212
           +V+AR  A  + L+++F  R++ K Y ++V G  +   E   +  W L    I  D+   
Sbjct: 55  VVMARNPAVQRQLSQAFAERKVDKRYIAVVAGELQAHSEAADDRGWQLIDLPIAADWERR 114

Query: 213 -VHVVKQNEKGANYAISHFKVIDCFAQKFCW---LEMQPHTGRTHQLRVHALHMGCPIVG 268
            + V+  N +    + + ++VI+   Q       + + P TGRTHQLR+H   +G P++G
Sbjct: 115 PLRVI--NHETGKSSQTLWQVIEHTVQPGILRTRVLLSPLTGRTHQLRLHMAAIGHPMLG 172

Query: 269 DHKYCAN 275
           D  Y + 
Sbjct: 173 DALYASE 179


>gi|228957577|ref|ZP_04119329.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pakistani str. T13001]
 gi|228802169|gb|EEM49034.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pakistani str. T13001]
          Length = 292

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 62/223 (27%), Positives = 109/223 (48%), Gaps = 24/223 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQET 154
           ++YED  + + NK A +S         H  G + + + S   K  L        RLD++T
Sbjct: 79  IIYEDDAVLIINKEANMSTIPSR---EHPTGSVANALLSHYDKQHLASTVHIVTRLDRDT 135

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+ R     L++  + + +++ Y ++V G    ++  I   + +K     D + 
Sbjct: 136 SGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDAPIGRKP----DSII 191

Query: 215 VVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G P++GD  Y 
Sbjct: 192 ERTVCEDG-QRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGDSLY- 247

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
               G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 248 ----GGRRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 285


>gi|197123853|ref|YP_002135804.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196173702|gb|ACG74675.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 287

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 72/319 (22%), Positives = 124/319 (38%), Gaps = 54/319 (16%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +    RLDRW             + ++ +G+VR+  K    + ++  G           
Sbjct: 3   REAAGARLDRWLAGAI-GATAERTRWLVETGRVRIRGKTCSPHRKLFGG----------- 50

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-------- 125
                 E+  L+        +      +LY+D+   V  KP G++V+  +          
Sbjct: 51  ------EEVALERPAPRAAEASGPALAVLYDDADCLVVAKPPGLAVEASAPGGASAVAAA 104

Query: 126 ----AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
               A+ +DG            P L HRLD++TSG L++AR   A   L  +F    ++K
Sbjct: 105 SRLGAFDVDGR---------AMPGLPHRLDRDTSGALLLARHDRALAALRAAFEAGAVEK 155

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK-VIDCFAQKF 240
            Y +LV G P  +           +  G D     +   +  +   +     ++   +  
Sbjct: 156 EYLALVAGAPPPEGRL-------DTPYGRDPADPRRFTTRFPSARRARLSWTVERALRGA 208

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L ++  TGRTHQ+RV     G P++GD  Y     G     I  +  LHA  +  P P
Sbjct: 209 ALLRVRLETGRTHQIRVQLAEAGFPVLGDAVY-----GVRAEAIARQ-ALHAARLAFPRP 262

Query: 301 -EGGRLQITAPLPAHMVKT 318
            +G  +++ APLP  + + 
Sbjct: 263 SDGAPVEVRAPLPEDLERA 281


>gi|323495632|ref|ZP_08100703.1| pseudouridylate synthase, 23S RNA-specific [Vibrio sinaloensis DSM
           21326]
 gi|323319267|gb|EGA72207.1| pseudouridylate synthase, 23S RNA-specific [Vibrio sinaloensis DSM
           21326]
          Length = 231

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 54/192 (28%), Positives = 92/192 (47%), Gaps = 17/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y      + NK   +SV    G    +    K    S  ++  L HRLD+ TSG+L++
Sbjct: 4   IVYTHPDFILINKHPDVSVHKDDGDTMLLAEVAKR---SGDEQLYLIHRLDKMTSGLLLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R  A+A  L++ F  R ++K Y ++    PK K+  ++  + +        ++  +   
Sbjct: 61  GRNAASASELSQLFSAREVEKYYLAIGSKKPKKKQGLVSGDMERSRRSSWKLINSQR--- 117

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F+ +     +  +L  +PHTG+THQ+RV    +G PI+GD  Y A      
Sbjct: 118 ---NPAITQFQSLAGEPGQRLFL-CKPHTGKTHQIRVALKSIGSPILGDPIYNA------ 167

Query: 281 TSPIQNKLYLHA 292
            S   ++ YLHA
Sbjct: 168 -SSAADRGYLHA 178


>gi|229820887|ref|YP_002882413.1| pseudouridine synthase, RluA family [Beutenbergia cavernae DSM
           12333]
 gi|229566800|gb|ACQ80651.1| pseudouridine synthase, RluA family [Beutenbergia cavernae DSM
           12333]
          Length = 309

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 111/234 (47%), Gaps = 24/234 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           ++Y D  + V +KP G++     G     + G L +    V + G   R  + HRLD  T
Sbjct: 84  IVYSDDDVVVVDKPVGVAAHPSPGWSGPTVIGALAAAGVRVSTSGAAERQGVVHRLDVGT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++ VA++  A   L  +F+ R + K+Y +LV G P      I   + +  H   DY  
Sbjct: 144 SGLMAVAKSERAYSVLKRAFKERTVTKVYHALVQGHPDPSAGTIDAPIGR--HPRHDYKW 201

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  + K    +++H++ ++        LE+   TGRTHQ+RVH   +  P VGD  Y A
Sbjct: 202 AVVADGK---PSVTHYETLEAM-PAASLLEVHLETGRTHQIRVHMAAVKHPCVGDVTYGA 257

Query: 275 NFKGNFTSPIQNKL-----YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + +      +  +L     +LHA  +   HP  G   ++T+  PA +  + ++L
Sbjct: 258 DPR------LAERLGLTRQWLHAVRLGFEHPVTGEWTEVTSDYPADLAASLEAL 305


>gi|169825961|ref|YP_001696119.1| putative RNA pseudouridine synthase yhcT [Lysinibacillus sphaericus
           C3-41]
 gi|168990449|gb|ACA37989.1| Hypothetical RNA pseudouridine synthase yhcT [Lysinibacillus
           sphaericus C3-41]
          Length = 287

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 68/291 (23%), Positives = 129/291 (44%), Gaps = 35/291 (12%)

Query: 15  DEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +E+N+ ++   +NH+      V+  ++ ++  +  D+  V++N  +Q G +V+    I A
Sbjct: 7   NEDNLTIEELLRNHWRLGKKLVHELRMAKAITLENDE-LVQWNTPLQVGTIVKFTFPIPA 65

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDG 131
            ++               K +      ++YED    + +KP G++         H  ++ 
Sbjct: 66  SSY---------------KRTPVCAIDIVYEDDHCLIVSKPKGMATHPNDDRDTHTCMNH 110

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +    +  G      HRLD+ T G+L+VA+   A          + I + Y + V G  
Sbjct: 111 VMAHIQEQGGIYAEHVHRLDKGTQGLLLVAKHPLAKSIFDRMIEEKSIIRTYAAEVQGNI 170

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           ++    I+  + K  H       VV Q      +A++H++V+  + +  C + +   TGR
Sbjct: 171 RSSSGTISESIGKDRHHASR--RVVSQT---GQHAVTHYEVVSRY-KNSCVVHLILETGR 224

Query: 252 THQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHP 300
           THQ+RVH  ++G PI+GD  Y A     G++         LHA  ++  HP
Sbjct: 225 THQIRVHLAYIGHPIIGDTMYGARETASGDYE--------LHAIQLEFDHP 267


>gi|149194782|ref|ZP_01871877.1| Pseudouridine synthase, RluD [Caminibacter mediatlanticus TB-2]
 gi|149135205|gb|EDM23686.1| Pseudouridine synthase, RluD [Caminibacter mediatlanticus TB-2]
          Length = 293

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/191 (29%), Positives = 89/191 (46%), Gaps = 41/191 (21%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSK----GQKPRLTHRLDQETS 155
           ++E     +F+KP        SG+A H       KS +D      G    L HRLD+ETS
Sbjct: 72  IFETDHFAIFDKP--------SGVAIHPKKLANTKSLLDDVRLLYGNDANLVHRLDKETS 123

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-----------IPKNKKECIANWLLK 204
           G+++ ++ + A   L ++F+ + IQK Y +L+ G           I  NK E I   ++ 
Sbjct: 124 GLVIASKNKFAESILKQAFQNKEIQKKYLALIKGHLDKEITIKKPIAVNKDENIKVKVI- 182

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            S  G + + +VK  +K     I    +++C           P TGR HQ+R+H   +G 
Sbjct: 183 ISDEGKESITLVKPIKK-----IGKNTLVECI----------PLTGRQHQIRIHLYSIGH 227

Query: 265 PIVGDHKYCAN 275
           PIVGD  Y  +
Sbjct: 228 PIVGDPLYGVD 238


>gi|313672668|ref|YP_004050779.1| pseudouridine synthase [Calditerrivibrio nitroreducens DSM 19672]
 gi|312939424|gb|ADR18616.1| pseudouridine synthase [Calditerrivibrio nitroreducens DSM 19672]
          Length = 211

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 93/201 (46%), Gaps = 18/201 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I V NK  G+ V       Y  D   LK  +     +  + HRLD  TSGI+V
Sbjct: 5   IVYDDDDILVVNKGHGLLVVPDR---YDKDLPNLKDLLTEIYGRIFVVHRLDYGTSGIMV 61

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+   + + L+  F    + K Y+++  G+      C+    + K +  G Y    K N
Sbjct: 62  FAKNERSHRSLSIQFERSEVDKRYYAICKGVFPADLTCMLP--ISKVNYHGRY----KIN 115

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K    A++ F V+D F+ K   +++ P TGR+HQ+RVH   +G P+  D  Y    +  
Sbjct: 116 FKSGRKALTSFSVLDRFSDK-TLIDVVPLTGRSHQIRVHLKALGYPLYYDFLYNEKRE-- 172

Query: 280 FTSPIQNKLYLHARYMDLPHP 300
                  +L L A Y+   HP
Sbjct: 173 -----DKRLTLQAYYLRFRHP 188


>gi|254515173|ref|ZP_05127234.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium NOR5-3]
 gi|219677416|gb|EED33781.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium NOR5-3]
          Length = 228

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 108/232 (46%), Gaps = 22/232 (9%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP-AGISVQGGSGIAYH--IDGFLK 134
           I + + L+    L  HS     ++ Y D ++ +  KP   +SV G   + +   I    +
Sbjct: 4   IADTQDLEPPPYLVPHSKEPVRVI-YADDELLLIRKPDLLLSVPGRHPLNHDCMITRLQE 62

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           S+ D+      + HRLD +TSGI++VAR +A+   L+  F+ R ++K Y + V G     
Sbjct: 63  SYPDAL-----VVHRLDLDTSGIMMVARGKASQAALSRLFQERAVEKRYRAWVAG----- 112

Query: 195 KECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
               A     +  I  D+ +   Q    +    ++++FKV+    +    LE+ P TGRT
Sbjct: 113 -NVAAEEGKLEYPIARDWENRPLQKICAETGKKSLTYFKVL-MRKEGNSLLELNPATGRT 170

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           HQLR+H   MG PI+G    C  +          +L LHA  +   HP  GR
Sbjct: 171 HQLRIHCREMGHPILG----CDMYAPPAILGAAPRLMLHATRIAFRHPGTGR 218


>gi|301156426|emb|CBW15897.1| unnamed protein product [Haemophilus parainfluenzae T3T1]
          Length = 229

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 62/202 (30%), Positives = 98/202 (48%), Gaps = 22/202 (10%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRL 150
           +  +K  ++Y+     +  KP GISV +  S I       L + +  +   P+  L HRL
Sbjct: 2   TALMKLDIIYQTDDFIIIYKPCGISVHKDQSKIG------LTTLLARQLNVPQVWLVHRL 55

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSG+L++A    +A      F    IQK Y +L    PK K+  +    ++K+  G 
Sbjct: 56  DKVTSGLLILALNAESAAEFFRLFSEHHIQKTYLALSNQKPKKKQGLLVG-DMQKARNGA 114

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +   K+N      AI+ F+ + C      ++ ++P TG+THQLRV    +G PI+GD 
Sbjct: 115 WKLCQSKENP-----AITRFESVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDA 168

Query: 271 KYCANFKGNFTSPIQNKLYLHA 292
            Y  N     T  I ++ YLHA
Sbjct: 169 LYGKN-----TEKI-DRTYLHA 184


>gi|19703986|ref|NP_603548.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
 gi|296327555|ref|ZP_06870101.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
 gi|19714169|gb|AAL94847.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
 gi|296155381|gb|EFG96152.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
          Length = 288

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 104/227 (45%), Gaps = 30/227 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-------PRLTHRLDQE 153
           + YED  + + NK   I V         +D  L + V +  +K       PR  +RLD  
Sbjct: 75  IAYEDENLLIVNKEPYIIVHPTQK---KVDKTLANAVVNYFEKTLGKTLVPRFYNRLDMN 131

Query: 154 TSGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           TSG++++A+   T+A  Q  TE      ++K Y  +  GI +     I   + K   +G 
Sbjct: 132 TSGLIIIAKNAYTQAFLQDKTE------VKKTYKVIASGIIEKDDFFIKIPIGK---VGD 182

Query: 211 DYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D   +    E G   A +H KV++  + +   +LE + +TGRTHQ+R H   +G  +VGD
Sbjct: 183 DLRRIELSEENGGKSAKTHIKVLEKNYEKNITFLEARLYTGRTHQIRAHLSLIGHSLVGD 242

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
             Y  + K      +  +  LHA  ++  +P+    L+I   +P  M
Sbjct: 243 ELYGGDMK------LAKRQMLHAYKLEFQNPKTLENLKIEIDIPVDM 283


>gi|329296365|ref|ZP_08253701.1| tRNA pseudouridine synthase C [Plautia stali symbiont]
          Length = 259

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 95/228 (41%), Gaps = 42/228 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D+ +   NKPAG  V              +SW+D K             GQ     
Sbjct: 4   IIYQDAWLVAVNKPAGWLVH-------------RSWLDRKEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           H LD+ TSG+L++  +    + L + F   +IQK Y ++V G            + +   
Sbjct: 51  HCLDRPTSGVLLMGLSSEIGRLLAQQFEQHQIQKTYHAVVRGWLDGSATLDYPLVEELDK 110

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRV 257
           I   +V       +    A++ ++ +             + ++  +E+ PHTGR HQLR 
Sbjct: 111 IADKFV----TEPRAPQPAVTDYRALAQAELPVAIGKYSSARYTLVELSPHTGRKHQLRR 166

Query: 258 HALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           H  H+  PI+GD  H      +G       ++L LHA  + L HP  G
Sbjct: 167 HMAHLRHPIIGDSSHGDLRQNRGAAAHFGMDRLMLHASALTLTHPVTG 214


>gi|282883125|ref|ZP_06291724.1| pseudouridine synthase, RluA family [Peptoniphilus lacrimalis
           315-B]
 gi|281296937|gb|EFA89434.1| pseudouridine synthase, RluA family [Peptoniphilus lacrimalis
           315-B]
          Length = 300

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 69/283 (24%), Positives = 126/283 (44%), Gaps = 29/283 (10%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +++  R   + V+ KR   N  ++ G  V I     +LN + + + I             
Sbjct: 35  IRRACRENSIYVNGKRTFENVEVKKGDSVAIRFPDESLNALCQYKDI------------- 81

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKG--QKPRLTHRLDQE 153
               + YED  + + NK            +   +  +L  + +     +K R  +RLD++
Sbjct: 82  ---DICYEDYDLLIVNKEYNCVTHTAKDDSKDTLLNYLAGYFEKNNIKRKVRFVNRLDRD 138

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++VA+   A   + + F   ++ KIY ++  G  K K+      ++KK  +  D +
Sbjct: 139 TSGLIIVAKNSYAHAKIMDEFSNNQVDKIYLAICRGDFKEKQ----GEIVKKISLCQDGI 194

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                ++ G  YA + ++V+    +K   ++++  TGRTHQ+RVH   +G PI+GD  Y 
Sbjct: 195 RREVDDDNGK-YAKTKYQVLK-DNKKLALVKLKLFTGRTHQIRVHLKSIGHPIIGDKLYN 252

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHM 315
                N    + N+  LH+  +    P  G L+  TA L   M
Sbjct: 253 ---DSNEEQNLMNRQALHSYSLSFKLPRTGELKTFTAKLSDDM 292


>gi|189218287|ref|YP_001938929.1| pseudouridylate synthase, 23S RNA-specific [Methylacidiphilum
           infernorum V4]
 gi|189185145|gb|ACD82330.1| Pseudouridylate synthase, 23S RNA-specific [Methylacidiphilum
           infernorum V4]
          Length = 268

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 60/194 (30%), Positives = 89/194 (45%), Gaps = 32/194 (16%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           +L HRLD+ETSG+LVVA+  AAA +       R IQK Y ++ WG      E  A++L  
Sbjct: 55  KLIHRLDRETSGLLVVAKNSAAAAYFGRQMEKRLIQKGYLAISWG------ELKADYLKI 108

Query: 205 KSHIGGDYVHVVKQNE---------KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           ++ +G  Y+   K NE          G       + +         W  ++P TG+ HQ+
Sbjct: 109 EAPLG--YLGGAKGNEIVIRQGIVPHGTQSVTEIYPLGHGGGYSLLW--VRPLTGKLHQI 164

Query: 256 RVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQNKLY-----LHARYMDLPHPEGG 303
           RVH   +  P+VGD  Y  N        K  +T  ++  L      LHA Y+     +G 
Sbjct: 165 RVHLSTIRHPVVGDKLYGPNPSFFLEFAKRGWTEEMEKVLLLPRHALHAAYLSF-FWKGD 223

Query: 304 RLQITAPLPAHMVK 317
           + Q  +PLP  + K
Sbjct: 224 KKQFYSPLPEDLKK 237


>gi|187735932|ref|YP_001878044.1| pseudouridine synthase [Akkermansia muciniphila ATCC BAA-835]
 gi|187425984|gb|ACD05263.1| pseudouridine synthase [Akkermansia muciniphila ATCC BAA-835]
          Length = 258

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 59/208 (28%), Positives = 91/208 (43%), Gaps = 36/208 (17%)

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L S+  + G    L +RLD+ETSG+ +VA+ + AA+ L  + + R I K Y ++V   P+
Sbjct: 54  LLSYEIANGAALSLVNRLDRETSGLTLVAKHKRAARELGRAMQRRLIHKEYLAIVQEWPE 113

Query: 193 -NKKECIAN------------WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
             +  C A             W+ +  H  G     V + E+  N       ++ C    
Sbjct: 114 WTETACTAPILRQGEVAESRIWVKQAVHPAGKACTTVFRKERTWNTRRGPLALVRCI--- 170

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGD-------HKYCANFKGNFTSPIQNKLY--- 289
                  P TGR HQ+RVH  H+G PI+GD       H Y    +  ++  ++ +L    
Sbjct: 171 -------PETGRMHQIRVHLAHLGHPILGDKIYGPSEHCYLEYIQHGWSRELEERLVLPR 223

Query: 290 --LHARYMDLPHPEGGRLQITAPLPAHM 315
             LHA  ++ P  E       APLP  M
Sbjct: 224 HALHACRLEFPFDE-ETFTAEAPLPEDM 250


>gi|113970985|ref|YP_734778.1| tRNA pseudouridine synthase C [Shewanella sp. MR-4]
 gi|113885669|gb|ABI39721.1| tRNA pseudouridine synthase C [Shewanella sp. MR-4]
          Length = 284

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 109/242 (45%), Gaps = 27/242 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   +KPAG+ V   S +A     F ++   D  G      HRLD+ TSG+L+
Sbjct: 32  VLYQDEHLVAIHKPAGLLVHR-SYLARRERFFAMQLTRDLVGCHVFPVHRLDRPTSGVLL 90

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQ 218
            A++   A  L E F    I+K Y +LV G   N  E  I ++ LK      +       
Sbjct: 91  FAKSSEVANALCEQFANHSIEKQYLALVRG---NMHESGILDYALKVEL--DEVADKFAN 145

Query: 219 NEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +               +F  +++ P TGR HQLR H  H+  PI+G
Sbjct: 146 QDKAAQDAVTQYEPLLNTEIPYPSGRYATSRFALVKLSPKTGRKHQLRRHMAHLRHPIIG 205

Query: 269 DH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           D      K  A F+ +F     N+L+L A+ +   HP    RL I   L       +  L
Sbjct: 206 DTTHGDGKQNAFFRAHFDI---NRLWLIAKKLTFTHPVTLERLSIETELEPEWETVFAGL 262

Query: 323 GF 324
           G+
Sbjct: 263 GW 264


>gi|294628838|ref|ZP_06707398.1| RluA family RNA pseudouridine synthase [Streptomyces sp. e14]
 gi|292832171|gb|EFF90520.1| RluA family RNA pseudouridine synthase [Streptomyces sp. e14]
          Length = 314

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 76/307 (24%), Positives = 134/307 (43%), Gaps = 21/307 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R++
Sbjct: 1   MSTLPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVLVDGTAVGKSERVR 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   ++ E   L   + +    D +  I+       +     +G +V
Sbjct: 60  GGAWLEVEMPQAPAPVQVVAE---LVEGMEIVHDDDDVVVIVKPVGVAAHPSPGWSGPTV 116

Query: 120 QGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            GG +   Y I            ++  + HRLD  TSG++VVA++  A   L   F+ R 
Sbjct: 117 IGGLAAAGYRIS------TSGAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQFKERT 170

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y +LV G P      I   + +  H   DY   V  + K    +++H+ +I+ F +
Sbjct: 171 VDKRYHTLVQGHPDPTSGTIDAPIGR--HPNHDYKWAVTADGK---PSVTHYDLIEAF-R 224

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDL 297
               L+++  TGRTHQ+RVH      P VGD  Y A+        ++  + +LHA  +  
Sbjct: 225 AASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADP--TLAKRLKLTRQWLHAVRLGF 282

Query: 298 PHPEGGR 304
            HP  G+
Sbjct: 283 EHPGDGQ 289


>gi|224419009|ref|ZP_03657015.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
 gi|253827954|ref|ZP_04870839.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
 gi|313142521|ref|ZP_07804714.1| conserved hypothetical protein [Helicobacter canadensis MIT
           98-5491]
 gi|253511360|gb|EES90019.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
 gi|313131552|gb|EFR49169.1| conserved hypothetical protein [Helicobacter canadensis MIT
           98-5491]
          Length = 265

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 59/199 (29%), Positives = 95/199 (47%), Gaps = 32/199 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D  I   +KPA ++ +        I      W         L HRLD+ETSG+L++
Sbjct: 81  IIFQDENILALSKPAFLTSE-------EIVKLYPQWA--------LLHRLDKETSGVLLL 125

Query: 161 ARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            +  +   HL   E F+  +I K Y ++V GI   ++E     +++K H     V V K+
Sbjct: 126 IKENSPF-HLKAKEEFKKEQIFKQYVAIVEGIIDEEQEITEPLIIQKGHFAK--VIVAKK 182

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           N   A   I+  ++      K   LE+   TGRTHQ+R H  H+  PI+GD      F G
Sbjct: 183 NGIKAYTKITPIEI----ESKKTKLEILIKTGRTHQIRAHLAHIKHPIIGD-----TFYG 233

Query: 279 NFTSPIQNKLYLHARYMDL 297
              +   N++ LHA+ + L
Sbjct: 234 GKPA---NRILLHAQKIAL 249


>gi|295425346|ref|ZP_06818049.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           amylolyticus DSM 11664]
 gi|295065122|gb|EFG56027.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           amylolyticus DSM 11664]
          Length = 279

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 81/178 (45%), Gaps = 10/178 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++EDS + V NK  G   Q      +  +  L       GQ P + HRLD  T G+L+V
Sbjct: 83  IIFEDSNVLVINKRKG---QKTHPNLFETNTALNDCATYLGQSPYIVHRLDMLTGGLLLV 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+  A    L      +   + Y + V     N    + +       IG D     K+  
Sbjct: 140 AKNPAVVPILNRQLTQKIFHREYLAQV-----NLNAALPDHGTISFPIGKDPDDQRKRMV 194

Query: 221 KGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +     A +H++++     +   +++Q  TGRTHQ+RVH   +GCPIVGD  Y  ++K
Sbjct: 195 RSDGLKATTHYQILKK-ENEIALIKLQLETGRTHQIRVHLAAIGCPIVGDPLYNPDYK 251


>gi|119505063|ref|ZP_01627139.1| pseudouridylate synthase for 23S rRNA and tRNA-Phe, dual
           specificity [marine gamma proteobacterium HTCC2080]
 gi|119459045|gb|EAW40144.1| pseudouridylate synthase for 23S rRNA and tRNA-Phe, dual
           specificity [marine gamma proteobacterium HTCC2080]
          Length = 238

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 53/176 (30%), Positives = 91/176 (51%), Gaps = 13/176 (7%)

Query: 101 LLYEDSKIYVFNKP-AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + + +KP   +SV G   +       L + ++         HRLD +TSGILV
Sbjct: 25  ILYADDSLLIIDKPHLLLSVPGRHPLNR---DSLITRLERLFPGVAAAHRLDLDTSGILV 81

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           V R +A    + + F+ R + K Y +LV+G  K+ +  I   L++      D+ +  +Q 
Sbjct: 82  VPRNKATLVAINKQFQDRTVLKTYRALVYGEVKDDQGQIDLPLIR------DWHNRPRQK 135

Query: 220 --EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              +    +++H++V+D        LE++P TGR+HQLR+H + +G PI+G   Y 
Sbjct: 136 ICTETGKPSVTHYRVLD-RQPSATLLELKPITGRSHQLRIHLMALGHPILGCDLYA 190


>gi|187918668|ref|YP_001884235.1| tRNA pseudouridine synthase A [Borrelia hermsii DAH]
 gi|119861516|gb|AAX17311.1| tRNA pseudouridine synthase A [Borrelia hermsii DAH]
          Length = 320

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 68/273 (24%), Positives = 122/273 (44%), Gaps = 27/273 (9%)

Query: 41  LRSGQVRVDKKRVKFNNRI-QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +R+G + ++  +V F++R+ +  Q+    P++  L+  + +  + D    L      +K 
Sbjct: 45  IRNGDILLNNLKVTFSHRVFKDDQIYLYKPLLQGLS--LSKMTVKDEDAILRD----VKR 98

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKGQKPRLTHRLDQET 154
            ++YED  + V NK  G  V G     Y +   + S++     +S   KP   HRLD+ T
Sbjct: 99  RIVYEDEDLLVINKRRGALVHGDK---YSLGALINSYLLDENLESLSFKPSSVHRLDRNT 155

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+   +A+ L+ +F    + K Y +L+ G  K K     N+L +       +V 
Sbjct: 156 SGLIIFAKNIDSARILSRAFSSGIVTKKYLALLDGEIK-KPLTYRNFLYRDRIARKTFV- 213

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               N++G   AI+  K I   ++     E+   TG THQ+R         ++ D KY +
Sbjct: 214 ---VNDEGRCNAITDVKPI-LVSKSSTLAEVSIRTGFTHQIRAQCAFNKHALINDKKYDS 269

Query: 275 NFKGN------FTSPIQNKLYLHARYMDLPHPE 301
            FK N      F       L+L   +   P  +
Sbjct: 270 KFKKNNYFLHSFLIKFNQSLFLRNEFFVEPSSD 302


>gi|12045231|ref|NP_073042.1| RluA family pseudouridine synthase [Mycoplasma genitalium G37]
 gi|1351560|sp|P47610|Y370_MYCGE RecName: Full=Uncharacterized RNA pseudouridine synthase MG370;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|3844958|gb|AAC71597.1| pseudouridine synthase, RluA family [Mycoplasma genitalium G37]
 gi|166078817|gb|ABY79435.1| pseudouridine synthase, RluA family [synthetic Mycoplasma
           genitalium JCVI-1.0]
          Length = 323

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 85/333 (25%), Positives = 139/333 (41%), Gaps = 61/333 (18%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      +V  + EN R+D++     P I   +  K LR G+V ++K + + N R+++  
Sbjct: 1   MRIANKFLVPKESENQRIDQFCLKILPLIKRSDFFKYLRLGKVLLNKTKPQVNTRLKTKD 60

Query: 64  VVR----IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-- 117
            +     I P +   N  +        S++L K  D LK  +++ED  I V +KP GI  
Sbjct: 61  EIAFLFDINPYLQTNNDYL--------SLDLVK--DKLK--IIFEDENIIVVDKPTGIVC 108

Query: 118 ------SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
                 S+   S +     G+ +   +     P+  HR+D+ TSGI++ A+T  A + L 
Sbjct: 109 QPDKKHSIINLSNMLLKHCGYRQFDSNKLNFYPQFAHRIDRNTSGIVIGAKTNKALKELN 168

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--------- 222
           + F+   + K Y  LV+G              + +H+G    +  K N  G         
Sbjct: 169 KVFKNNHLTKRYKGLVFG--------------QFNHLGLQTAYWKKDNNNGIVTVKWKPF 214

Query: 223 --ANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKG 278
             A    + F+     AQK    + ++  +GRTHQ+R         +VGD KY    FK 
Sbjct: 215 PEAKKISTFFENSSYIAQKDMSLITIRLISGRTHQIRACLNLFSNQLVGDKKYSLIQFKN 274

Query: 279 NFTSPIQNKLY----LHARYMDLPHPEGGRLQI 307
                 +N  Y    LHA  +  P  E  +  I
Sbjct: 275 ------RNNKYKHQALHAYELVFPKLETSKFPI 301


>gi|297183636|gb|ADI19762.1| hypothetical protein [uncultured gamma proteobacterium EB000_37F04]
          Length = 322

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 74/320 (23%), Positives = 132/320 (41%), Gaps = 36/320 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V +  D   +RLD    + +P  +   L + +++G+++ + +  +  +++     + + P
Sbjct: 14  VDIPADLHGIRLDAAAAHLFPDFSRSRLAEWIKAGRLQRNHQASRPKDKVAVDDQLLLWP 73

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                     E   LD               +LYED  + V NKPAG+ V   +G     
Sbjct: 74  ETEDRVEWAPEPLPLD---------------ILYEDEHVIVLNKPAGLVVHPATGHQTGT 118

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            ++G L +        PR  + HRLD++TSG+++ AR+  A + L      R + ++Y +
Sbjct: 119 LVNGLL-AHAPEMSALPRGGIVHRLDKDTSGVMLAARSAIAHKSLVAQLADRSVSRLYSA 177

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G         A       H        V ++ K +    +H+++   F+     L +
Sbjct: 178 VCRGTFTGGGTIDAPI---GRHPTSRLKMAVVEDGKPSR---THYRIEKRFS-AHTHLSV 230

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQN--KLYLHARYMDL 297
              TGRTHQ+RVH      P+VGD  Y       A       + +    +  LHAR +  
Sbjct: 231 SLETGRTHQIRVHLAWRKHPLVGDPVYAGRAMRPAGASDQLVAALTGFRRQALHARRLTF 290

Query: 298 PHPEG-GRLQITAPLPAHMV 316
            HP+    +    P+PA M 
Sbjct: 291 LHPQSQDSMTFETPIPADMA 310


>gi|315127084|ref|YP_004069087.1| tRNA pseudouridine synthase C [Pseudoalteromonas sp. SM9913]
 gi|315015598|gb|ADT68936.1| tRNA pseudouridine synthase C [Pseudoalteromonas sp. SM9913]
          Length = 254

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 99/242 (40%), Gaps = 29/242 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D      +KP+G+ V       +     ++   D  GQ     HRLD+ TSG+L+ 
Sbjct: 15  ILYQDENYVAIDKPSGLLVHRSFLDKHETQFAMQMLRDQIGQHVFPVHRLDRPTSGVLLF 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +  AA+ + + F    I K Y +LV G              +   I   +       +
Sbjct: 75  ALSSEAARDMNQLFIEGTITKRYLALVRGFAPESVFLDKPLKEELDKIADKFA----DQD 130

Query: 221 KGANYAISHFKVIDCFAQ-------------KFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           K A  A + F   +C  Q             ++  +E  P TGR HQ+R H  H+  PI+
Sbjct: 131 KAAQEAQTQF---NCLHQAALPIPIGKYPTVRYSLVECFPKTGRKHQIRRHLKHLSLPII 187

Query: 268 GDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           GD  +  N     F+ +F+     +L L A  +   HP     + I APL   M+     
Sbjct: 188 GDVNHGDNQHNQFFREHFSL---RRLMLFASELSFVHPYNNEPITIKAPLGDAMLNICKQ 244

Query: 322 LG 323
           LG
Sbjct: 245 LG 246


>gi|213963503|ref|ZP_03391756.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga sputigena Capno]
 gi|213953783|gb|EEB65112.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga sputigena Capno]
          Length = 201

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 56/193 (29%), Positives = 94/193 (48%), Gaps = 18/193 (9%)

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHL 170
           G  VQG       +   +K+++  K  KP      + HRLD+ T+G+++ A+T  A   L
Sbjct: 2   GDIVQGDKTGDIPLSEIVKAYLKKKYNKPGEVFLGVVHRLDRPTTGVVLFAKTSKALARL 61

Query: 171 TESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAI 227
              F  +  +QK YW+LV  +P  ++  + +WL++  K +    Y   V+ ++K    A+
Sbjct: 62  NAMFANKEEVQKTYWALVDAMPPAEEGTLIHWLVRNEKQNKSVAYNKEVQHSKK----AV 117

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            H+K++  +  ++  LE+   TGR HQ+R     +G  I GD KY A       S     
Sbjct: 118 LHYKLLKTY-DRYYLLEIDLITGRHHQIRAQLAAIGLHIKGDLKYGAK-----RSNPDGG 171

Query: 288 LYLHARYMDLPHP 300
           + LHA  +   HP
Sbjct: 172 ICLHAHSLRFLHP 184


>gi|328786842|ref|XP_624656.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Apis mellifera]
          Length = 535

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 112/236 (47%), Gaps = 27/236 (11%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           ++ +R+G + V+ ++V  + R++   +         L +++   ++  +S  +T      
Sbjct: 156 ERCIRAGTLTVNYQKVDVDYRLRHNDL---------LANVVHRHEVPVTSEPIT------ 200

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ D  + V NKPA I V       ++   F+ +  +   +  R  HRLD+ TSGI
Sbjct: 201 ---VIHMDEDVVVVNKPASIPVHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDRLTSGI 256

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVV 216
           L+  RT   A+ +    R R++ K Y   V G  P+ +  C     +    IG     V 
Sbjct: 257 LLFGRTPKKARQMEHQIRNRQVHKQYVCRVEGEFPEEEVVCSEPIEVVSYKIG-----VC 311

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K +EKG +  ++ FK +  +  K   +  +P TGR HQ+RVH  ++G P+V D  Y
Sbjct: 312 KISEKGKD-CVTRFKRLS-YNGKSSVVLCKPQTGRMHQIRVHLQYLGYPVVNDPLY 365


>gi|285019825|ref|YP_003377536.1| pseudouridine synthase (rna-uridine isomerase) protein [Xanthomonas
           albilineans GPE PC73]
 gi|283475043|emb|CBA17542.1| probable pseudouridine synthase (rna-uridine isomerase) protein
           [Xanthomonas albilineans]
          Length = 276

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 68/249 (27%), Positives = 113/249 (45%), Gaps = 29/249 (11%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTH 148
           +   +DFL+  +LY+D  I V +KPAG+     S +A   D FL   +  +  +P  L H
Sbjct: 1   MNASADFLQ--ILYQDPLIAVVDKPAGLMAHD-SKLARGEDDFLADRLRVQLGRPIFLIH 57

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG L++A  R  A  L ++     + K Y ++  G P   +  + + L      
Sbjct: 58  RLDRATSGCLLLAFDRDTASLLGKALMGGEVDKDYLAICRGWPAEIRFEVDHPL-----D 112

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVH 258
           GG    + K        A + F+ + C             ++  L   P TGR  Q+R H
Sbjct: 113 GGPGKPLKKP-------AQTRFQRLACGELTVPSGEFPTSRYALLRCCPVTGRFRQIRRH 165

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
             H+   ++GD  +  + + N    +Q   ++ LHA  +   HP G R+++ APL A  V
Sbjct: 166 LKHLSHHLIGDTSH-GDGRHNRIFRMQGIHRMLLHAERLAFAHPHGHRVEVRAPLDAQFV 224

Query: 317 KTWDSLGFK 325
           + +   G+ 
Sbjct: 225 RAFGLFGWS 233


>gi|239632089|ref|ZP_04675120.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|239526554|gb|EEQ65555.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
          Length = 277

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 101/219 (46%), Gaps = 31/219 (14%)

Query: 103 YEDSKIYVFNKPAGI----SVQGGSG-IAYHIDGFLKSWVDSKGQKPRL-THRLDQETSG 156
           YED  + + +KPAG+    ++ G +G +      +L  +       P L THRLD  TSG
Sbjct: 80  YEDDDLLIVDKPAGMKTHPNLPGETGTLMNQAAAYLAPF-------PALITHRLDMATSG 132

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV+A+       +     ++ + + Y +LV        + IA      + IG D     
Sbjct: 133 LLVIAKNPLTQAIINRQLALKTMHRDYIALV-------PQGIAASGTITAPIGHDPDDQR 185

Query: 217 KQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           K+     GA+ AI+HF+ I         + ++  TGRTHQ+RVH   +G PI+GD  Y  
Sbjct: 186 KRMIRPDGAS-AITHFRRI-AKTSTTATVALRLETGRTHQIRVHLASIGYPILGDPLYAP 243

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +           ++YLHA  +    P     L +T+PLP
Sbjct: 244 D------QTTYQRMYLHAFQVRFTKPLSDTTLTVTSPLP 276


>gi|303230703|ref|ZP_07317450.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514463|gb|EFL56458.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 306

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 108/232 (46%), Gaps = 29/232 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPRL--THRLDQET 154
           ++YED  I   NK A + +   S +    DG L + V    D   Q       HRLD++T
Sbjct: 81  IVYEDEYILAINKAASVLMHPTSTVR---DGTLANGVLYYYDETEQAHDFHPVHRLDKDT 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK---SHIGGD 211
           SGI+++A+T +  QH  +  R +  QK+Y ++V G   ++   I  W + +   S I   
Sbjct: 138 SGIVIIAKT-SVVQHAFDKQRTK-FQKVYDAIVEGTMPSQSLTI-KWPIGRKAGSIIERC 194

Query: 212 YVHVVKQNEKG----ANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              + K         A + +S    +D      Q    ++   HTGRTHQ+RVH  H+G 
Sbjct: 195 CTSIGKPARTDVTVLARHIVSQPVQMDKNLSTQQILTHVQCVLHTGRTHQIRVHLSHLGF 254

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           P+VGD  Y     G     I+ +  LHA Y+   HP     +++ APLP  M
Sbjct: 255 PLVGDDLY-----GGHLDYIRRQA-LHAGYLAFTHPMTQEYVELRAPLPTDM 300


>gi|118587136|ref|ZP_01544565.1| pseudouridine synthase [Oenococcus oeni ATCC BAA-1163]
 gi|118432415|gb|EAV39152.1| pseudouridine synthase [Oenococcus oeni ATCC BAA-1163]
          Length = 302

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 61/208 (29%), Positives = 103/208 (49%), Gaps = 28/208 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS--KGQKPR-------LTHRLD 151
           +L E     + +KPAG+ +   S      D  L ++V++  KG   R       + HR+D
Sbjct: 86  ILSEKEDYLLVDKPAGMKMHPHS--PNETDTLL-NYVEAQLKGHLSRSCPAHAFMVHRID 142

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG++++A+   A   L +    +RI++ Y + V G  +NKK  I         I  D
Sbjct: 143 RDTSGVVIIAKNPLAVGILDQLLAKKRIKRTYLAWVSGNLENKKGSI------DQAIAVD 196

Query: 212 YVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            ++  K+  ++    A++H+  I    Q    + +   TGRTHQ+RVH   +G PIVGDH
Sbjct: 197 PINPYKRIVDQAGQKAVTHWTKIHTVYQN-TLVRVSLETGRTHQIRVHFAAIGHPIVGDH 255

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLP 298
            Y         SP  ++L LH+  +++P
Sbjct: 256 LYNG-------SPY-SRLLLHSATIEIP 275


>gi|332161266|ref|YP_004297843.1| putative ribosomal large subunit pseudouridine synthase [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|318605161|emb|CBY26659.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325665496|gb|ADZ42140.1| putative ribosomal large subunit pseudouridine synthase [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|330860585|emb|CBX70883.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica W22703]
          Length = 232

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 102/228 (44%), Gaps = 21/228 (9%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H    K   LY+D  + + NKP G+    G     ++D      V    
Sbjct: 3   KIVDTFIAPLCHD---KIEALYQDDHLVLINKPTGLLSLSGKN-PQNLDSVHHRLVQIF- 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   +  E + + 
Sbjct: 58  PGCTLVHRLDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCG-HLDDNEGVIDA 116

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTH 253
            + K       + +   + K A    S ++V++ F  +           +++ P TGRTH
Sbjct: 117 AIAKDPALFPLMSICATHGKPAR---SGYRVVERFYHELEDGRLLPLTRVQLTPETGRTH 173

Query: 254 QLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
           QLR+H   +G PI G   Y      G   +P   +L LHA  +   HP
Sbjct: 174 QLRIHCQQLGHPIWGCDLYGGRLLPGTEQTP---RLMLHASELHFVHP 218


>gi|296129452|ref|YP_003636702.1| pseudouridine synthase, RluA family [Cellulomonas flavigena DSM
           20109]
 gi|296021267|gb|ADG74503.1| pseudouridine synthase, RluA family [Cellulomonas flavigena DSM
           20109]
          Length = 311

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 54/193 (27%), Positives = 94/193 (48%), Gaps = 10/193 (5%)

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           + + G   R  + HRLD  TSG++VVA++  A   L  +F+ R ++K+Y +L  G P   
Sbjct: 125 ISTSGSAERQGVVHRLDAGTSGLMVVAKSEHAYTVLKRAFKERTVEKVYHALAQGHPSPT 184

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I   + +  H   D+   V  + K    +++H++V++        +E+   TGRTHQ
Sbjct: 185 TGTIDAPIGR--HPSSDWKFAVVADGK---PSVTHYEVLEML-PGASLVEVHLETGRTHQ 238

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +   +VGD  Y A+        +  + +LHA  +   HP  G  L++ +  P 
Sbjct: 239 IRVHFAALRHSLVGDLTYGADPALAARLGVSRQ-WLHAVRLGFEHPATGEWLEVASDYPE 297

Query: 314 HMVKTWDSLGFKY 326
            +V   ++L   Y
Sbjct: 298 DLVAALETLRGAY 310


>gi|254993270|ref|ZP_05275460.1| ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes FSL J2-064]
          Length = 243

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/262 (24%), Positives = 123/262 (46%), Gaps = 33/262 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PV 70
           VE +E+ + L  + K+ +     +   K    G++ V+ K       ++ G  VR+  P 
Sbjct: 7   VETEEDGLLLRTFLKSKHISKQLLTAVKFGAEGKIEVNNKEQNVLYHVKVGDKVRLTFPT 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 ++ E   LD               +++ED  + + NKPAG++        YH +
Sbjct: 67  EQQNERLLAEYTDLD---------------IIFEDDFLLIINKPAGMASIPSQ---YHPN 108

Query: 131 GFLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + ++V    +   LT+      RLD+ETSG++++A+ R A   L+   +   +++ Y 
Sbjct: 109 GSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQ 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWL 243
           +   G+   +K  I      ++ IG   V ++++       YA ++++V+  + + F  +
Sbjct: 169 AFTSGVLVEQKGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY-RAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCP 265
            +Q  TGRTHQ+RVH  ++G P
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHP 243


>gi|224007791|ref|XP_002292855.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220971717|gb|EED90051.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 280

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/251 (25%), Positives = 118/251 (47%), Gaps = 26/251 (10%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK--------ILDSSVN 89
           +  + +G++ V  + V    +IQ G         + LNH++   +        I D+   
Sbjct: 40  EAAIDAGRILVSGRPVDREYKIQGG---------DELNHLVHRHEPAVGLSDIIYDNGTI 90

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRL-- 146
              +++     ++YED+ + + +KP+ I++       Y+ +   L  W        RL  
Sbjct: 91  TADYTEHPPVQIVYEDNSLLIVDKPSTIAIHTSGAYNYNSLFEILSYWNPQAYGLGRLFT 150

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWG-IPKNKKECIANWLLK 204
            HRLD+ TSG++++A+T   A+ + +    R   +K+Y + V G  P N  E +A+    
Sbjct: 151 VHRLDRLTSGLVLIAKTPELARSMGKCIMERDGCEKLYLTRVKGKFPLNVMEKVASDGGI 210

Query: 205 KSHIGGDYVHVVKQ-NEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            +    ++ H+ ++ + KG   A + F ++  D  +     L  +P TGRTHQ+R+H   
Sbjct: 211 DAQNDNEHPHLTEEADRKGIKPAQTSFTLLTYDAVSDTSVVL-AKPVTGRTHQIRLHLQQ 269

Query: 262 MGCPIVGDHKY 272
           +G PI  DH Y
Sbjct: 270 LGHPIANDHCY 280


>gi|242817540|ref|XP_002486976.1| DRAP deaminase (Rib2), putative [Talaromyces stipitatus ATCC 10500]
 gi|218713441|gb|EED12865.1| DRAP deaminase (Rib2), putative [Talaromyces stipitatus ATCC 10500]
          Length = 514

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/250 (26%), Positives = 108/250 (43%), Gaps = 31/250 (12%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYED 105
           D+    +   I+ G+V+    V N L+ I+    I+  S +  +H   + S    +++ED
Sbjct: 63  DRTAEYYKQAIEEGRVLISGKVAN-LDTIVPNGAIVSHSTH--RHEPPVSSQPIGIIHED 119

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTR 164
             + V +KPAGI V G     YH +  ++    D  G K    +RLD+ TSG++ +++  
Sbjct: 120 DDMIVIDKPAGIPVHGAG--RYHYNSIIEIMKADRPGSKILPCNRLDRLTSGVMFISKNA 177

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG- 222
            AA+  +   + R +QK Y + V G  P     C    +     +G + V    +  +  
Sbjct: 178 RAAEEFSAQLKERSVQKEYVARVSGRFPDGVVLCDQPIMAVSPKLGLNRVRAAGKEARTK 237

Query: 223 ----ANYAISHFKVIDCFA----------------QKFCWLEMQPHTGRTHQLRVHALHM 262
               A Y +S  K +D                   + +  +   P TGRTHQ+RVH   +
Sbjct: 238 FRRIAYYPVSPKKSVDATTASGDRPATPPATTTEEEGYSIVHCLPLTGRTHQIRVHLQFL 297

Query: 263 GCPIVGDHKY 272
           G PI  D  Y
Sbjct: 298 GYPISNDPIY 307


>gi|325473944|gb|EGC77132.1| RNA pseudouridylate synthase [Treponema denticola F0402]
          Length = 264

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 66/287 (22%), Positives = 115/287 (40%), Gaps = 45/287 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  D+   RLDR  +     +    +   +R G++RV+ K+       Q G  + +   +
Sbjct: 10  IGEDDSGRRLDRVIRKFLGKMPLSGVYSAIRRGKIRVNGKKENGAYLTQKGDEISMDLSL 69

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
             L     E +        T +S     +LL  D  +++ NK +G  V G   +   +  
Sbjct: 70  FGLTAPASEDQ--------TNYSISKPDVLLKTDDLLFI-NKRSGELVHGEKSLCEAVLK 120

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           +  S   S   K    HRLD++TSGIL  +++   AQ  + + +  +I K Y  +  G P
Sbjct: 121 YFPSKEKSLSFKVGALHRLDKDTSGILAFSQSLKGAQGFSRALQEGKIGKFYIGITEGRP 180

Query: 192 K--------NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
                    + KEC+   L++           +    K  N ++  F +I          
Sbjct: 181 SLSEFKSIIDGKECLC--LIR-----------ILDFSKEENLSLVLFNLI---------- 217

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
                TGR HQ+R+     G P++ D KY +  K  F+  +  K Y+
Sbjct: 218 -----TGRKHQIRIQCSQFGTPLLNDKKYGSKQKKAFSEDLSKKNYI 259


>gi|126664148|ref|ZP_01735141.1| pseudouridine synthase [Flavobacteria bacterium BAL38]
 gi|126623862|gb|EAZ94557.1| pseudouridine synthase [Flavobacteria bacterium BAL38]
          Length = 559

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 61/204 (29%), Positives = 95/204 (46%), Gaps = 20/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           +++ED  + V NKPA      G  I+  +   +K  + ++ G  P + HRLD  TSG+++
Sbjct: 354 IVFEDEILAVINKPAEFLSVPGKNISDSVYQRVKELYPNATG--PLIVHRLDMSTSGLML 411

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+       L   F  R I+K Y +L+ G+ + +KE   +  L+          V  ++
Sbjct: 412 IAKDEETYVKLQSQFIKRTIKKRYVALLDGVLE-EKEGFIDLPLRVDLDDRPRQLVCYEH 470

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANF 276
            K A       +V +     + +    P TGRTHQLRVHA H   +  PIVGD  Y    
Sbjct: 471 GKPAQTKWEKIEVRNNQTLVYFY----PITGRTHQLRVHASHELGLKTPIVGDDLYGKK- 525

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
                    N+L+LHA  +   HP
Sbjct: 526 --------ANRLHLHAESLTFEHP 541


>gi|71279393|ref|YP_270735.1| pseudouridine synthase Rlu family protein [Colwellia
           psychrerythraea 34H]
 gi|71145133|gb|AAZ25606.1| pseudouridine synthase Rlu family protein, TIGR01621 [Colwellia
           psychrerythraea 34H]
          Length = 230

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/185 (30%), Positives = 90/185 (48%), Gaps = 16/185 (8%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAA 167
           V +K AG++      I   +   +K  + S+     L   HRLD+ TSG++V A+T A A
Sbjct: 13  VVDKEAGVNFHDEGDIGSGLFSLVKKQLQSQNNNTELYPVHRLDKMTSGLVVFAKTLACA 72

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           Q   + F    I+K Y ++    P  KK+ +    + KS  G     + K      N A+
Sbjct: 73  QIFGQLFNDHDIEKYYLAIGDKKPI-KKQGLIKGDMAKSRRG-----MFKLLRSMENPAV 126

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           + F       ++  +L ++PH+G+THQLRV    +G PIVGD  Y       +T+   ++
Sbjct: 127 TQFFSFSIPNKQRLYL-LKPHSGKTHQLRVALASIGAPIVGDPLY-------YTTSQADR 178

Query: 288 LYLHA 292
            YLHA
Sbjct: 179 GYLHA 183


>gi|261884230|ref|ZP_06008269.1| ribosomal pseudouridine synthase [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 238

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 111/236 (47%), Gaps = 31/236 (13%)

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVAR 162
           NKP+ ++V     +    +  L  W+   G          +  + HRLD+ TSG++VVA+
Sbjct: 4   NKPSNLTVHPAPSVK---EATLVEWLKQNGYMLSTLNGDIRAGIVHRLDKGTSGVIVVAK 60

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
             A+   L      + + ++Y +L+    K+K       L+    IG +  + +K N   
Sbjct: 61  NNASHSALAAQLSDKSMGRVYLALIDFNLKDK-------LIIDRPIGRNPXNRLK-NSVA 112

Query: 223 AN--YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           AN   A S F  I C       +  +  TGRTHQ+RVH   +   I+GD+ Y   FK   
Sbjct: 113 ANGRAAKSAFTNIIC-EDDLNLIAAKLFTGRTHQIRVHLASINRHILGDNLY--GFKSK- 168

Query: 281 TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
              I+ ++ LHA  ++L HP+ G ++Q  APLP      +D L  K D+ +  +++
Sbjct: 169 NCKIK-RVMLHAYILNLTHPKSGEKMQFIAPLPTDF---YDILSKKIDKEILNEKI 220


>gi|317504866|ref|ZP_07962822.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           salivae DSM 15606]
 gi|315664050|gb|EFV03761.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           salivae DSM 15606]
          Length = 522

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/213 (30%), Positives = 101/213 (47%), Gaps = 35/213 (16%)

Query: 102 LYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +YED+ I V  KPAG +SV G +         L    ++ G  P + HRLD  TSG+LVV
Sbjct: 325 IYEDNDIAVVCKPAGMLSVPGKNQRESVRSLVLHRHPEATG--PLIVHRLDMATSGLLVV 382

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIP----KNKKECIA--NWLLKKSHIGGDYVH 214
           A    +  +L + F+   ++K Y +L+  +P    K+ + C+     L  +     D VH
Sbjct: 383 ALNVESYVNLQQQFKQHHVEKQYVALL-SVPHKGAKHGQICLPLRPDLTDRPRQIVDKVH 441

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHK 271
                      A++ ++ +D      C +++ P TGRTHQLR+H  H   +  PI GD  
Sbjct: 442 --------GKEAVTDYQFMDD-----CRVKLYPRTGRTHQLRMHCAHAEGLNNPIRGDEL 488

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           Y    +         +L+LHA  +   HP+ G+
Sbjct: 489 YGTGAQ---------RLFLHAEELAFDHPKTGK 512


>gi|169350066|ref|ZP_02867004.1| hypothetical protein CLOSPI_00806 [Clostridium spiroforme DSM 1552]
 gi|169293279|gb|EDS75412.1| hypothetical protein CLOSPI_00806 [Clostridium spiroforme DSM 1552]
          Length = 322

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 69/273 (25%), Positives = 125/273 (45%), Gaps = 25/273 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           + END  N R+D++ K    +     + K+ R   ++V+ K+V     +++  VV +   
Sbjct: 6   ITENDA-NQRIDKYIKKLLVNAPTNFIYKMFRKKDIKVNGKKVNEKYILKNNDVVEMFLY 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
            +        + I +               +LYED+ + +  KPAG+ V     +  + +
Sbjct: 65  EDKFKEFTATKDIYNVKKTFK---------VLYEDNHVLIVYKPAGLLVHEDKNESVNTL 115

Query: 126 AYHIDGFL--KSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-I 179
              +  +L  K+ +D   +    P   HRLD+ TSGI++  +T  A Q L E  + R  I
Sbjct: 116 TNQVLSYLANKNELDLSRENTFMPGPVHRLDRNTSGIVIFGKTLGALQVLNEMIKQRHCI 175

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++  G   N+K  +  +++K        V +V ++  GA    +  K +  +   
Sbjct: 176 EKSYLTICKG-KVNQKRNLKGYIVKLDDQAQ--VKLVSKDYPGALTMETIVKPVK-YNND 231

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +  +E+   TGR HQ+RVH   +  PI+GD KY
Sbjct: 232 YSKVEVTLVTGRMHQIRVHLSSIDHPIIGDRKY 264


>gi|217974069|ref|YP_002358820.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499204|gb|ACK47397.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 287

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 108/248 (43%), Gaps = 39/248 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LYED  + V +KPAG+ V   S +A     F      D  G      HRLD+ TSG+L+
Sbjct: 32  ILYEDDHLVVIHKPAGLLVHR-SYLARRERFFAMQLTRDLVGCHVFPVHRLDRPTSGVLL 90

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQ 218
            A++   A  L E F    I+K Y +LV G   N  E  I ++ LK        V + + 
Sbjct: 91  FAKSSEVANALCEQFASHTIEKQYLALVRG---NMHESGILDYALK--------VELDEL 139

Query: 219 NEKGANYAISHFKVIDCF----------------AQKFCWLEMQPHTGRTHQLRVHALHM 262
            +K A+   +  + +  +                  +F  + + P TGR HQLR H  H+
Sbjct: 140 GDKNADPNKAAQEAVTAYEPLLNTEIPYPSGRYPTSRFALVRLSPKTGRKHQLRRHMAHL 199

Query: 263 GCPIVGDH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
             PIVGD      K  A F+ +F     N+L+L A+ +   HP    RL I   L     
Sbjct: 200 RHPIVGDTTHGDGKQNAFFREHFGI---NRLWLIAKKLSFTHPVTQVRLSIETELEPEWE 256

Query: 317 KTWDSLGF 324
             +  LG+
Sbjct: 257 TVFAELGW 264


>gi|297180028|gb|ADI16253.1| pseudouridylate synthases, 23S RNA-specific [uncultured bacterium
           HF0010_16H03]
          Length = 309

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 66/267 (24%), Positives = 115/267 (43%), Gaps = 43/267 (16%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N RLD+     +   +   ++K +  G++ V+    K  + +     + I P        
Sbjct: 11  NQRLDKAATELFDEYSRTQIKKWILEGRILVNGDLSKPRDSVHENDEIEINPT------- 63

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
            KE+K+     N+   +        +E     + NKP G+ +  GSG       +G +  
Sbjct: 64  -KERKVSWEPQNINFET-------YHECEDFIIINKPPGLIMHPGSGCYDGTLANGLINK 115

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           + D +   PR  + HRLD++TSG+L+VAR      +  +  + RR+ K Y ++V G    
Sbjct: 116 YPDLENL-PRCGIVHRLDKDTSGVLLVARNEGFRNYFIQLMQERRVTKKYTAIVVGSTLG 174

Query: 194 K---KECIANWLLKKSHI-----GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
               ++ I      ++ +     G + +  VK +E+  NY+I               L++
Sbjct: 175 SFSIEDPIGRDKSNRTKMSVRPDGKEALTFVKTSERIGNYSI---------------LDI 219

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY 272
              TGRTHQ+RVH L    PI+ D  Y
Sbjct: 220 AIETGRTHQIRVHLLSKKLPIIADITY 246


>gi|329728300|gb|EGG64739.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21172]
          Length = 258

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 91/192 (47%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++  L+  +LYED+ I +  KP     Q  +    H+   L   V    Q+   
Sbjct: 39  SVNLIPYARKLE--VLYEDAFIIIVTKPNN---QNCTPSREHLHESLIEQVLYHCQEHGE 93

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 94  NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKVNLKKIYTCLVYGKTHTSGIIEAN 149

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 150 IRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 202

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 203 HIGHPIVGDSLY 214


>gi|81428927|ref|YP_395927.1| pseudouridylate synthase, 23S rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610569|emb|CAI55620.1| Pseudouridylate synthase, 23S rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 300

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 100/220 (45%), Gaps = 17/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSG 156
           +LYED    V NKPAG+ ++ G +     +   +K +    G     P +  RLD +TSG
Sbjct: 81  VLYEDDYWLVVNKPAGLATIPGPTNTTDTLLNRIKGYWQQNGATDLVPHIITRLDFDTSG 140

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I++ A+ + A   L       ++QK Y ++V G    +   I      K+ IG   V   
Sbjct: 141 IVLAAKHQVAQSLLQPQIEQHQLQKFYLAVVAGTGLPEFGTI------KAPIGRVGVEPR 194

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           ++       A + +  +    ++   L++Q HTGRTHQ+RVH   +  P+VGD  Y    
Sbjct: 195 RRVIADGQSAWTDYWRL-AQDERLTVLKVQIHTGRTHQIRVHLSDLDHPLVGDQLYEGPL 253

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                    ++  LHA  +    P    + Q TAP+PA +
Sbjct: 254 GWGI-----DRQALHAYQLTFNDPFSQQKRQFTAPIPADI 288


>gi|254444369|ref|ZP_05057845.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198258677|gb|EDY82985.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 249

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 52/183 (28%), Positives = 83/183 (45%), Gaps = 13/183 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D ++   +KP+G+ V             ++   D  GQ     HR+D+ TSGIL+ 
Sbjct: 16  ILYRDERLVAIHKPSGLLVHRSPIDRRETRFAIQLLRDQIGQHVYPAHRIDRPTSGILLF 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               AA   L+  F+ R IQK Y ++  G +P++    I + L K     G   H+    
Sbjct: 76  GLDEAAGTALSLLFQNREIQKNYLAVTRGHLPESG--LIDSPLHKYEDADG---HIKSSE 130

Query: 220 EKGANYAISHFKVIDCF-------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            + A  A       +           ++  +E+ PHTGR HQ+R H  H+  PI+GD ++
Sbjct: 131 TQEAETAYRRLATTELPYPTERYDTTRYSLVELTPHTGRRHQIRRHLAHIRHPIIGDVRH 190

Query: 273 CAN 275
             N
Sbjct: 191 GCN 193


>gi|154148734|ref|YP_001407253.1| RNA pseudouridine synthase [Campylobacter hominis ATCC BAA-381]
 gi|153804743|gb|ABS51750.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           (RNA pseudouridylate synthase) [Campylobacter hominis
           ATCC BAA-381]
          Length = 304

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/244 (25%), Positives = 110/244 (45%), Gaps = 29/244 (11%)

Query: 35  VNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +N    ++  Q  +DKKR      I  G V            +  + +IL+  + +  + 
Sbjct: 21  INCGFCMKDSQRLIDKKR------IFCGPV-----------SVDTKNEILNGEIFMIDYE 63

Query: 95  DFLKSIL-LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
              + I  ++E+    VF+KP+GI S   G    Y +   + +     G+   + HRLD+
Sbjct: 64  CMSRGIYPIFENDDFAVFDKPSGILSHPNGRHCEYSLCDEIWTLF---GKNANVAHRLDR 120

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           ETSG+L+ ++   +A  L   F  + +QKIY++LV G  +  +  I N  + K++   D 
Sbjct: 121 ETSGLLIASKNPKSADELKNMFEKKTVQKIYFALVSG--RVNENFICNKPIGKAY-SDDE 177

Query: 213 VHVVKQNEKGANYAISHFKVIDCF----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           + +  +       AI+ F  +  +          ++  P TGR HQ+R+H  HM   I G
Sbjct: 178 IGIKMRIRDDGKPAITEFYPLKFYENIGESGATIIKAIPKTGRQHQIRLHLFHMKHKIFG 237

Query: 269 DHKY 272
           D  Y
Sbjct: 238 DPLY 241


>gi|115376321|ref|ZP_01463560.1| ribosomal large subunit pseudouridine synthase A [Stigmatella
           aurantiaca DW4/3-1]
 gi|115366671|gb|EAU65667.1| ribosomal large subunit pseudouridine synthase A [Stigmatella
           aurantiaca DW4/3-1]
          Length = 495

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 100/229 (43%), Gaps = 43/229 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS----------KGQKPRLTHRL 150
           +++ED  + V +KP G+    G G           WVDS              P L HRL
Sbjct: 292 IVFEDDWLVVIDKPCGLLSVPGKGA---------EWVDSVLTRLQARYPHATGPLLVHRL 342

Query: 151 DQETSGILVV---ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           D +TSG+LV    ART AA   L   F  R + K Y + + G  + ++  I   L    H
Sbjct: 343 DLDTSGLLVAALDARTHAA---LQRQFIHREVHKRYVAWIDGRVRGEQGLIDLPLRVDLH 399

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGC 264
                +H    +      A++ ++V++    +   + + P +GRTHQLRVHA H   +G 
Sbjct: 400 DRPRQIH----DPLHGKPAVTEWQVLERQGDR-TRVALFPQSGRTHQLRVHAAHPLGLGA 454

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           PIVGD  Y            + +L LHA  +   HP  G R+    P P
Sbjct: 455 PIVGDRLYGHE---------EVRLLLHAEALSFRHPGTGLRVSFERPAP 494


>gi|312865419|ref|ZP_07725646.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
 gi|311098937|gb|EFQ57154.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
          Length = 287

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 68/258 (26%), Positives = 117/258 (45%), Gaps = 35/258 (13%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           V+ + + + +++++G ++++  + +  N+   ++KIL    NL           LYED  
Sbjct: 42  VNNQAINWQSQVRAGDLIQL--IFDDENY--PKKKILLGQANLVD--------CLYEDQH 89

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + + NKP G+           +   + ++V   G    + HRLD+ETSG+++ A+     
Sbjct: 90  LIIVNKPEGMKTHANQPDEIALLNHVSAYV---GDTCYVVHRLDKETSGLVLFAKNPFVL 146

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANY 225
             L      ++I + YW+L  G    K       +  +  IG D     K+    KG   
Sbjct: 147 PILNRLLEDKQISRQYWALAQGRLAQK------VITYRDKIGRDRHDRRKRLVTNKGQE- 199

Query: 226 AISHFKVIDCF--AQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
           AI+H + +  F  ++  C L + Q  TGRTHQ+RVH  H G  I+GD  Y        + 
Sbjct: 200 AITHIRRLKEFNGSKGPCTLVDCQLETGRTHQIRVHLAHHGHAIIGDPLY--------SK 251

Query: 283 PIQNKLYLHARYMDLPHP 300
               +L LHA  +   HP
Sbjct: 252 IPAKRLMLHAHKLSFVHP 269


>gi|294141898|ref|YP_003557876.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293328367|dbj|BAJ03098.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 567

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/179 (33%), Positives = 92/179 (51%), Gaps = 17/179 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I V NKPA      G  I   +   +K  + ++ G  P + HRLD  TSG++V
Sbjct: 366 IIYQDRDILVINKPAEFLSVPGRNIDDSVYSRIKQLYPEATG--PLIVHRLDMSTSGLMV 423

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +A  +AA + L + F  R ++K Y +L+ G   ++ E I +  L+     GD+    +Q 
Sbjct: 424 IALNKAANKSLQKQFITRTVKKRYVALLTG-ELSQDEGIISLPLR-----GDFDDRPRQL 477

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKY 272
              E G   A + ++VI         + + P TGRTHQLRVH+ H   +  PIVGD  Y
Sbjct: 478 VCFEHG-KPAETKWQVI-SRRDGLTKVHLYPKTGRTHQLRVHSAHPKGLNMPIVGDDLY 534


>gi|152989807|ref|YP_001355529.1| ribosomal large subunit pseudouridine synthase D [Nitratiruptor sp.
           SB155-2]
 gi|151421668|dbj|BAF69172.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Nitratiruptor sp. SB155-2]
          Length = 299

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 100/215 (46%), Gaps = 32/215 (14%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++E     +++KP+GI V   +   ++  ID     +    G +  + HR+D+ETSG+++
Sbjct: 73  IFETKDFVLYDKPSGIMVHPRNRNTHYTLIDEIRYRY----GPQANIVHRIDKETSGLVL 128

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG--GDYVHV-- 215
            +  + A + L + F  ++IQK Y +LV G        I   L+ +  I    DY  +  
Sbjct: 129 ASTNKEAEKALKQMFEHKQIQKRYLALVRG-------NIEKQLVIEEPIALNRDYSKIKL 181

Query: 216 -VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            VK +  G  YA +    +  F   F  +E  P TGR HQ+R+H  H+  PI+GD  Y  
Sbjct: 182 KVKIDPSG-KYAKTIINPLKQFGS-FTLVEAIPITGRQHQIRIHLFHVKHPILGDPIY-- 237

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
                   P  N+     RY+D    E  RL +T 
Sbjct: 238 -------GPSTNE---SIRYLDGLMDEEERLVVTG 262


>gi|12323024|gb|AAG51501.1|AC058785_4 unknown protein [Arabidopsis thaliana]
          Length = 293

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 65/259 (25%), Positives = 116/259 (44%), Gaps = 54/259 (20%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW----VDSKGQKPRLTHRL 150
           +  +  +LYED  +   NKP G+          + +  L+S     +DS  +   L +RL
Sbjct: 42  NLTRDDILYEDEYLMAVNKPKGV----------YCEAVLRSAPQIVLDSSSEY-HLANRL 90

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KKECIANWLLKKSH-- 207
           D++TSG++++ ++   A  L ++F   +I+K Y +L  G   N ++  +++   +  H  
Sbjct: 91  DRDTSGVMIITKSHKVAAKLVKAFTEHKIRKSYIALCIGSSPNWRRVTVSSGHGRSKHGA 150

Query: 208 -------------IGGDYVHVVK-----------QNEKGANYAISHFKVIDCFAQKFCWL 243
                         GG +V  ++           +NE      ++H  V +   +  C  
Sbjct: 151 WRVYAALDVGRVLPGGSFVRDMETTFEVVSVNSVKNESCELEDVNHVIVAEGERELSCGG 210

Query: 244 EMQ---------PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
           +           P +GRTHQ+R+H  ++G PI GD KY   ++ N  +   ++  LHA  
Sbjct: 211 DDDDVVVVVRAFPRSGRTHQIRLHCQYLGIPIRGDVKYHGVYEWNGRTFEGHE--LHAEC 268

Query: 295 MDLPHP-EGGRLQITAPLP 312
           + L HP  G  + I APLP
Sbjct: 269 LSLDHPVTGDSIVIRAPLP 287


>gi|15805985|ref|NP_294685.1| ribosomal large subunit pseudouridine synthase A [Deinococcus
           radiodurans R1]
 gi|6458684|gb|AAF10535.1|AE001948_4 ribosomal large subunit pseudouridine synthase, Rlu family
           [Deinococcus radiodurans R1]
          Length = 257

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 51/188 (27%), Positives = 85/188 (45%), Gaps = 14/188 (7%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ETSG  ++ R   AA+     F+   + K Y ++V G P+  +  +   L     
Sbjct: 71  HRLDRETSGAQLLTRDSDAARTFFTLFKTHLVGKTYLAIVHGEPEWDRRTLDAPLGDLGL 130

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            G + + + +        A++ F+V+   A     +E  P +GR HQ+R H  H+G P+V
Sbjct: 131 GGANKIQIRQAVVPDGKPAVTDFRVVGRRA-GHALIECYPRSGRLHQIRAHLAHLGLPMV 189

Query: 268 GDHKYCAN-------FKGNFTSPIQNKL-----YLHARYMDLPHPEGGRLQITAPLPAHM 315
           GD  Y  +        +   T  +  +L      LHA  +  P   G ++ +  PL   +
Sbjct: 190 GDKIYGRDPQVFLDFMEQGQTPELTARLGLPRQALHAARIAFPW-AGAQMAVEVPLAPDL 248

Query: 316 VKTWDSLG 323
           V  W+ LG
Sbjct: 249 VAYWEGLG 256


>gi|312865090|ref|ZP_07725318.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
 gi|311099201|gb|EFQ57417.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
          Length = 303

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 49/181 (27%), Positives = 91/181 (50%), Gaps = 12/181 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK---GQKPRLTHRLDQETSGI 157
           ++ ED    V NKPAG            +  F+K++ + +    Q+  +  RLD++TSG+
Sbjct: 78  IVAEDEHFLVINKPAGYPSIPSILHDESMANFVKAYYEEQTYENQQIHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   + ++ + + I+K Y++LV G     +  E IA    +   I      +
Sbjct: 138 MLFAKHGYAHSRMDKALQAKTIEKRYYALVSGHKDLLDAGEIIAPIAREAESI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++      YA + ++V+  F      ++++ HTGRTHQ+RVH  H+G P++GD  Y  +
Sbjct: 192 TRRVHPSGKYAHTSYRVLKRFG-PVKLVDIRLHTGRTHQIRVHFSHIGQPLLGDDLYGGS 250

Query: 276 F 276
            
Sbjct: 251 M 251


>gi|312869346|ref|ZP_07729511.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
 gi|311095141|gb|EFQ53420.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
          Length = 309

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 65/223 (29%), Positives = 104/223 (46%), Gaps = 26/223 (11%)

Query: 101 LLYEDSKIYVFNKPAG----ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +L+E+  + V NKP G     +  G +G    +   +  ++ +K     + HRLDQETSG
Sbjct: 92  VLFENRDLVVVNKPQGQKSHPNYHGETGT---LMNDVAGYLTAKDCGAFMVHRLDQETSG 148

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +++A+       L       +I + Y ++V G    + +           +G D   V 
Sbjct: 149 AMIIAKNPVVVPVLNRLISSGQIHRRYLAVVAGNLTGRGKFT-------EPLGKDPRDVR 201

Query: 217 KQNEKGANY--AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           K    G N   A ++++V+     +   L +Q  TGRTHQLRVH  + G PI+GD  Y  
Sbjct: 202 KYCVAGENAKPAQTNYQVLASRHNRTLVL-LQLATGRTHQLRVHLAYHGHPIIGDPLY-- 258

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
              G   SP   ++ LH    +L  P    R+Q+TAPLP++  
Sbjct: 259 ---GRDGSP---RMLLHGATQELVLPFSFKRIQVTAPLPSYFT 295


>gi|17231572|ref|NP_488120.1| ribosomal large chain pseudouridine synthase A [Nostoc sp. PCC
           7120]
 gi|17133215|dbj|BAB75779.1| ribosomal large chain pseudouridine synthase A [Nostoc sp. PCC
           7120]
          Length = 549

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 104/219 (47%), Gaps = 21/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           ++YED  +   NKP+G+    G  I    D  L        ++  L   HRLDQ+TSGIL
Sbjct: 344 VIYEDEWLIAVNKPSGLLSVPGRYIDTQ-DSVLSRLRHMLPEEEMLAAVHRLDQDTSGIL 402

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR     +  ++ F+ R++ K+Y +++ G+  N    I +  L        Y  V  Q
Sbjct: 403 LLARDSQTYRQFSQQFQQRQVYKVYEAILAGV-INTDTGIIDLPLWGDPENRPYQQVDWQ 461

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
             K    ++++F+ I      +  +E  P TGRTHQLRVHA     +G  I+GD  Y   
Sbjct: 462 RGKP---SVTNFREI-AREGDYTRVEFVPLTGRTHQLRVHASDVQGLGVVILGDRFYGCT 517

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAPL 311
            K        N+L+LHAR +   HP  G+   L I  P 
Sbjct: 518 AKA-------NRLHLHARELSFLHPRSGKTIHLHIKTPF 549


>gi|89098123|ref|ZP_01171009.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Bacillus sp. NRRL B-14911]
 gi|89087286|gb|EAR66401.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Bacillus sp. NRRL B-14911]
          Length = 295

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 66/226 (29%), Positives = 103/226 (45%), Gaps = 30/226 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV----------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           ++YED  + V NKPA +S              + I Y+    L S V        +  RL
Sbjct: 84  IVYEDPYVLVVNKPAAMSTIPSREHPRGSLANALIGYYRKIDLASTV-------HIVTRL 136

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+++VA+ R     ++   R  R+++ Y +   G     +  I   + +K     
Sbjct: 137 DRDTSGLVLVAKHRHVHHLMSTLQREGRVKRTYEAFAEGKLFPVEGSIEAPIARKK---- 192

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D +   + N     YA +H+KV      +F + E+   TGRTHQ+RVH  H+G P++GD 
Sbjct: 193 DSIIEREVNFLEGQYACTHYKVKG--TGEFTYAELVLETGRTHQIRVHLSHLGHPLLGDG 250

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            Y  N K   +     +  LH R +   HP   R L  +A LP  M
Sbjct: 251 LYGGN-KNQIS-----RQALHCRELRFFHPFLERELCFSAGLPDDM 290


>gi|302385721|ref|YP_003821543.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
 gi|302196349|gb|ADL03920.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
          Length = 307

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 108/226 (47%), Gaps = 32/226 (14%)

Query: 103 YEDSKIYVFNKPAGISV---QG------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           YED  I V NK AG+ +   QG       +G+AY+     +S+V       R  +RLD++
Sbjct: 85  YEDEHILVVNKEAGVPIHPSQGNFDHTLANGMAYYFMKRGESFVY------RAINRLDRD 138

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G+LV+A+   +A  L++  + R I++ Y ++  G P  +    A      + + G  +
Sbjct: 139 TTGLLVLAKNPLSACILSDMVQKREIRRRYLAITCGKPPLEGTIDAPI----ARVDGSTI 194

Query: 214 HVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                  +G   A +H+K +       Q    L ++  TGRTHQ+RVH   +G P+ GD 
Sbjct: 195 ERCVDFIRGEK-ARTHYKRLYYDPVTGQSLVGLCLE--TGRTHQIRVHLKSIGYPLPGDF 251

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            Y  +++        ++  LH+  +D  HP +   L   APLP  M
Sbjct: 252 LYHPDYR------YISRQALHSFRLDFLHPIKKEPLSFEAPLPKDM 291


>gi|298483420|ref|ZP_07001597.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D22]
 gi|298270368|gb|EFI11952.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D22]
          Length = 612

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 70/262 (26%), Positives = 111/262 (42%), Gaps = 76/262 (29%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ED  + V NKPAG +SV G +      YH     K + ++ G  P + HRLD  TSG
Sbjct: 347 IVFEDEWLLVVNKPAGMLSVPGKAEDRDSVYH--RLKKKYPEATG--PMIVHRLDMATSG 402

Query: 157 ILVVARTRAA-----AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG- 210
           +L+VA+T+       AQ    S + R +  +  +++    + K       L+ K+ +   
Sbjct: 403 LLLVAKTKEVHQDLQAQFANRSIKKRYVAVLDGAIIKTEKETKPIAEKAILIAKNTVSTK 462

Query: 211 -----------------------DYVHVVKQNEKGANYAISHFKVI-----------DCF 236
                                  D    +  +E G   AI+ +++I           + F
Sbjct: 463 KTAKAERTGSTGRIELPLCLNPLDRPRQMVSSEHGKE-AITEYQIISESERITSESENTF 521

Query: 237 ---------------AQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKG 278
                          ++K+  +   P TGRTHQLRVHA H   +GCPI+GD  Y      
Sbjct: 522 NESNRIDESERSINESRKYTRIIFYPLTGRTHQLRVHAAHPEGLGCPILGDELYGKK--- 578

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                  ++LYLHA Y++  HP
Sbjct: 579 ------ADRLYLHAEYIEFRHP 594


>gi|322832332|ref|YP_004212359.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321167533|gb|ADW73232.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 232

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/211 (28%), Positives = 97/211 (45%), Gaps = 18/211 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+    G     ++D      V        L HRLD  TSG++V+A
Sbjct: 20  LYQDEHLVLINKPTGLLSLSGKN-PQNLDSVHHRLVKIF-PGCTLVHRLDFGTSGLMVIA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L   F  R + K+Y +L+ G  ++  E + +  + K       + +   + K
Sbjct: 78  RNKAINAALCHQFSQRTVTKVYSALLCGHLQH-NEGVTDAPIAKDPALFPLMSICAVHGK 136

Query: 222 GANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            A    S ++V++ F ++           + + P TGRTHQLR+H  ++G PI+G   Y 
Sbjct: 137 PAR---SGYRVVERFYREQENGELLPLTRVLLTPQTGRTHQLRIHCQYLGHPILGCDLYG 193

Query: 274 AN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                G   +P   +L LHA  +   HP  G
Sbjct: 194 GRLLPGTEQTP---RLMLHASELHFVHPVSG 221


>gi|289449613|ref|YP_003475167.1| RNA pseudouridine synthase [Clostridiales genomosp. BVAB3 str.
           UPII9-5]
 gi|289184160|gb|ADC90585.1| RNA pseudouridine synthase [Clostridiales genomosp. BVAB3 str.
           UPII9-5]
          Length = 233

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 53/184 (28%), Positives = 87/184 (47%), Gaps = 10/184 (5%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
            ++  ++Y D+ +    KPAG   Q     A  I  + K++V  K  KP      L HRL
Sbjct: 3   LIEPKVIYCDNHLLAVYKPAGYLSQADGTAAPDILAWSKAYVKKKYDKPGDVYLGLVHRL 62

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN--KKECIANWLLKKSHI 208
           D+  +G+LV+ART  AA  L E  R    QKIY ++     +     E   +++ K   +
Sbjct: 63  DRPVAGVLVLARTSKAAGRLAEQIRSHSWQKIYLAICHDEQRTLAAGERWEDYIFKDKRL 122

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +   +V +    A YA  +++ I   +     + ++  TGR+HQ+RV   H G P+  
Sbjct: 123 --NSAAIVDRGHPEAKYAALNYECIQ-HSGDLALVRIKLETGRSHQIRVQFKHHGHPLYA 179

Query: 269 DHKY 272
           D +Y
Sbjct: 180 DRRY 183


>gi|300871600|ref|YP_003786473.1| ribosomal large subunit pseudouridine synthase C [Brachyspira
           pilosicoli 95/1000]
 gi|300689301|gb|ADK31972.1| ribosomal large subunit pseudouridine synthase C [Brachyspira
           pilosicoli 95/1000]
          Length = 330

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 72/321 (22%), Positives = 143/321 (44%), Gaps = 40/321 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E D E+MRLD++  N + + +    Q ++  G V V+ +++K+   I  G         
Sbjct: 26  IEEDIESMRLDKYMGNRFSYYSRNKWQDLIGEGLVLVNGEKIKYTRTISKG--------- 76

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           + +++  K+ K  +  VN        K I ++Y+D  + + NKPA + V       Y+ +
Sbjct: 77  DEISYYFKDMK--EPEVN--------KDIEIIYDDGDLIIVNKPANLPVIPSG--KYYYN 124

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                  +  G    + +R+D+ETSG ++++R    A         +    I  + +  I
Sbjct: 125 TLHTIMQERLGCHLNMINRIDRETSGCVILSRGSLVASKFCAMLANKNNNNIKKTYI-AI 183

Query: 191 PKNKKECIANWLLK--KSHIGGD----YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +N K+   ++ ++     +G      Y  + K+N + + Y+ + FK +      +  L+
Sbjct: 184 VENAKDIEDSFTVEGYMQEVGDKLYRRYQILHKENVEDSKYSKTKFKTVKKIGD-YAILK 242

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY---------LHARYM 295
           ++ +TGR HQ+RVH       +VGD  Y       F S I+  +          LH+  +
Sbjct: 243 IRLYTGRMHQIRVHLHSKNLYMVGDKIYGKYGPKVFNSFIEKSIIPEGFFYRQALHSYML 302

Query: 296 DLPHP-EGGRLQITAPLPAHM 315
           +  HP    R+++ A +P  +
Sbjct: 303 EFNHPITNERIKVKAKIPKDL 323


>gi|331702478|ref|YP_004399437.1| RluA family pseudouridine synthase [Lactobacillus buchneri NRRL
           B-30929]
 gi|329129821|gb|AEB74374.1| pseudouridine synthase, RluA family [Lactobacillus buchneri NRRL
           B-30929]
          Length = 304

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 105/233 (45%), Gaps = 19/233 (8%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLT 147
           N+T  S    +IL YED  + V +K  G        G        L +++ ++   P + 
Sbjct: 79  NVTADSAATVAIL-YEDQNLVVMDKRRGDKTHPNQPGEVGATINHLAAYLATEKTVPYMI 137

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLDQETSG ++  +       L  +   ++I++ Y + V G     +  I         
Sbjct: 138 HRLDQETSGAIIFGKNPVVVPILVANIANKQIKRTYLAWVEGTDLPDEGTI------NLP 191

Query: 208 IGGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           IG D     K+   G  A  A++ ++V+      +  +++   TGRTHQ+RVH   +G P
Sbjct: 192 IGRDPDDKRKRKINGPHAAPALTRYRVLRK-QSGYALVQISLETGRTHQIRVHFAALGHP 250

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           +VGD  Y ++    F       L LH+  +DL  P    R  I AP+P H +K
Sbjct: 251 LVGDPLYNSSNGSPF-------LMLHSWKVDLLMPFTKQRKLIEAPIPDHFIK 296


>gi|328948965|ref|YP_004366302.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
 gi|328449289|gb|AEB15005.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
          Length = 440

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 66/226 (29%), Positives = 103/226 (45%), Gaps = 37/226 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +LY D+ + V NK +G+    G G      I   LK       ++P + HRLD ETSG++
Sbjct: 222 ILYRDNDLIVVNKQSGLLSVPGRGPEKQDCIVNRLKKLFPECIEQPSV-HRLDMETSGLM 280

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A T+ A ++L   F    +QK Y +L+ GI       +A   + +S     Y  +  +
Sbjct: 281 ILAFTKDAHRNLCRQFEEGLVQKKYVALLDGI-------LAKKGIPQSGTMELYFRLDIE 333

Query: 219 NEKG-------ANYAISHFKVIDCFAQKFCWLEMQ---------PHTGRTHQLRVHALH- 261
           N             AI+ +K++D   +    LE +         PHTGRTHQLR+ +   
Sbjct: 334 NRPHQIWDSVYGKKAITEWKILD-VEKYLSPLENKKNVTRVLFIPHTGRTHQLRLASADS 392

Query: 262 --MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              G PI+GD  Y     G        +L LH+ Y+   HP  G++
Sbjct: 393 HGFGVPIIGDTLYGHCEPG-------ERLMLHSCYIKFTHPSTGKV 431


>gi|170078760|ref|YP_001735398.1| putative pseudouridine synthase [Synechococcus sp. PCC 7002]
 gi|169886429|gb|ACB00143.1| putative pseudouridine synthase [Synechococcus sp. PCC 7002]
          Length = 282

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 97/208 (46%), Gaps = 14/208 (6%)

Query: 101 LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D   ++ +KPAG+ V   G+ +   +   LK     +   P   HRL + TSG+++
Sbjct: 62  ILHQDPHFWIIDKPAGLPVLPAGNFLENTLLAQLKRQFPDETPVP--IHRLGRGTSGLMI 119

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R+    Q LT   R  +I KIY +++       +  I   + K  H     +     +
Sbjct: 120 LGRSPLGRQSLTRQLREHQITKIYRAVIPAGDYPDQITITTPIGKIFHPSLGTIFAATAD 179

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----A 274
              A+   S  +V++  A K   +E+Q  TGR HQ+R+H   MG P+VGD  Y      A
Sbjct: 180 GLSAH---SEMRVLERLA-KVSRVEVQIFTGRPHQIRIHMAAMGFPLVGDRLYLPGGLPA 235

Query: 275 NFKGNFTSPIQNKL--YLHARYMDLPHP 300
            ++    SP+       L+A Y+   HP
Sbjct: 236 IYEDANHSPLPGDCGYSLNAYYLKFQHP 263


>gi|77360895|ref|YP_340470.1| tRNA pseudouridine synthase C [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875806|emb|CAI87027.1| tRNA pseudouridine synthase C [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 254

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/253 (25%), Positives = 104/253 (41%), Gaps = 35/253 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D      +KP+G+ V       +     ++   D  GQ     HRLD+ TSG+L+ 
Sbjct: 15  ILYQDENYVAIDKPSGLLVHRSFLDKHETQFAMQMLRDQLGQHVFPVHRLDRPTSGVLLF 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIP----------KNKKECIANWLL------K 204
           A +  AA+ + + F    I K Y +LV G            K + + IA+         +
Sbjct: 75  ALSSEAARDMNQLFIEGTISKRYLALVRGFAPESVFLDKPLKEELDKIADKFADQDKAPQ 134

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           ++    + +H          Y    + +++CF          P TGR HQ+R H  H+  
Sbjct: 135 EAQTQFNCLHQAALPIPIGKYPTVRYSLVECF----------PKTGRKHQIRRHLKHLSL 184

Query: 265 PIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           PI+GD  +  N     F+ +F      +L L A  +   HP     + I APL   M+  
Sbjct: 185 PIIGDVNHGDNQHNQFFREHFEL---RRLMLFATELSFVHPYSNESITIKAPLGDAMLSI 241

Query: 319 WDSLGFKYDRNLY 331
              LG+  +   Y
Sbjct: 242 CKQLGWPDEEKDY 254


>gi|332970317|gb|EGK09309.1| tRNA pseudouridine synthase C [Kingella kingae ATCC 23330]
          Length = 252

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 65/223 (29%), Positives = 107/223 (47%), Gaps = 35/223 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L +     V NKPAG+ V      +      +++  D  GQ     HRLD+ TSG ++ 
Sbjct: 4   ILTQTEHYVVVNKPAGMLVHRSRLDSQETVFLMQTLRDQLGQLVYPVHRLDKPTSGAMLW 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    AA+  T+ F  ++I+K Y ++V G  +N   CI ++ LK+       +H   Q++
Sbjct: 64  ALNSEAARWFTQQFEQKQIRKHYLAIVRGWTENVG-CI-DYPLKEQLDKIADMHA--QSD 119

Query: 221 KGANYAISHFKVI---DC-FA-------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           K A  A + ++ +   +C FA        ++  L + P TGR HQ+R H  H+  PIVGD
Sbjct: 120 KTAQAACTEYQTLQRSECPFASSARYATSRYSLLHITPKTGRKHQIRRHMKHIFHPIVGD 179

Query: 270 ------------HKYCANFK-------GNFTSPI-QNKLYLHA 292
                       +++C+N +        +FT PI Q  + +HA
Sbjct: 180 TTHGDLHQNQAVNQFCSNRRLLLHASSLHFTDPISQQNISIHA 222


>gi|239931821|ref|ZP_04688774.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           ghanaensis ATCC 14672]
 gi|291440189|ref|ZP_06579579.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           ghanaensis ATCC 14672]
 gi|291343084|gb|EFE70040.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           ghanaensis ATCC 14672]
          Length = 314

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 79/328 (24%), Positives = 139/328 (42%), Gaps = 26/328 (7%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVTVDGSVVGKSERVS 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA--GI 117
            G  + +  P   A   ++ E         +    D    +++ +   +     P   G 
Sbjct: 60  GGAWLEVEMPQAPAPVQVVAE-----PVEGMEIVHDDDDVVVIVKPVGVAAHPSPGWTGP 114

Query: 118 SVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +V GG +   Y I            ++  + HRLD  TSG++VVA++  A   L   F+ 
Sbjct: 115 TVIGGLAAAGYRIS------TSGAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQFKE 168

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I+ F
Sbjct: 169 RTVDKRYHTLVQGHPDPTSGTIDAPIGRHPHH--DYKWAVTAEGK---PSVTHYDLIEAF 223

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYM 295
            +    L+++  TGRTHQ+RVH      P VGD  Y A+        ++  + +LHA  +
Sbjct: 224 -RAASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADP--TLAKRLRLTRQWLHAVRL 280

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP  GR  + ++  P  + K  D +
Sbjct: 281 GFEHPGDGRWAEYSSDYPEDLQKALDQV 308


>gi|308048661|ref|YP_003912227.1| tRNA pseudouridine synthase C [Ferrimonas balearica DSM 9799]
 gi|307630851|gb|ADN75153.1| tRNA pseudouridine synthase C [Ferrimonas balearica DSM 9799]
          Length = 247

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/248 (25%), Positives = 111/248 (44%), Gaps = 19/248 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   +KP+G+ V       +     ++   D+ G      HRLD+ TSG+L+ 
Sbjct: 4   ILYQDDHLVAVHKPSGLLVHRSWLDRHETQFAMQMTRDAVGCHVFPVHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            ++   A+ ++E      I K Y +LV G      E   ++ LK      D    +   +
Sbjct: 64  TKSAETARIMSEKMAAHDIDKHYLALVRGYVHEAGEL--DYALKVE--LDDIADKMADKD 119

Query: 221 KGANYAISHFKVID----CFA------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +      FA       ++  + ++P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KAPQEAVTRYRPLAQVELPFAVGRYPTSRYSLMALEPLTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNFTSP---IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            +       F      +Q +L+L A+ +   HP  G  L I APL    +  +++ G+  
Sbjct: 180 THGDGRHNKFYRDHFGVQ-RLWLIAKGLGFAHPVSGEPLWIEAPLEQEWLTLFETFGWST 238

Query: 327 DRNLYIKR 334
            +  Y+ R
Sbjct: 239 AQQDYLIR 246


>gi|293369136|ref|ZP_06615730.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|292635719|gb|EFF54217.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
          Length = 612

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 72/262 (27%), Positives = 112/262 (42%), Gaps = 76/262 (29%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ED  + V NKPAG +SV G +      YH     K + ++ G  P + HRLD  TSG
Sbjct: 347 IVFEDEWLLVVNKPAGMLSVPGKAEDRDSVYH--RLKKKYPEATG--PMIVHRLDMATSG 402

Query: 157 ILVVARTRAA-----AQHLTESFRMRRIQKIYWSLVWGIPKNK----------KECIANW 201
           +L+VA+T+       AQ    S + R +  +  +++    + K          KE +   
Sbjct: 403 LLLVAKTKEVHQDLQAQFANRSIKKRYVAVLDGAIIKTEKEIKPIAEKAILIAKETVLTK 462

Query: 202 LLKKSHIGG--------------DYVHVVKQNEKGANYAISHFKVI-----------DCF 236
              K+   G              D    +  +E G   AI+ +++I           + F
Sbjct: 463 KTAKAERTGNTGRIELPLCLNPLDRPRQMVSSEHGKE-AITEYQIISESERITSESENTF 521

Query: 237 ---------------AQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKG 278
                          ++K+  +   P TGRTHQLRVHA H   +GCPI+GD  Y      
Sbjct: 522 NESNRIDESERNINESRKYTRIVFYPLTGRTHQLRVHAAHPEGLGCPILGDELYGKK--- 578

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                  ++LYLHA Y++  HP
Sbjct: 579 ------ADRLYLHAEYIEFRHP 594


>gi|148267440|ref|YP_001246383.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150393493|ref|YP_001316168.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp.
           aureus JH1]
 gi|257795259|ref|ZP_05644238.1| pseudouridine synthase [Staphylococcus aureus A9781]
 gi|258406908|ref|ZP_05680061.1| pseudouridine synthase [Staphylococcus aureus A9763]
 gi|258421876|ref|ZP_05684797.1| pseudouridine synthase [Staphylococcus aureus A9719]
 gi|258446966|ref|ZP_05695119.1| pseudouridine synthase [Staphylococcus aureus A6300]
 gi|258449944|ref|ZP_05698042.1| pseudouridine synthase [Staphylococcus aureus A6224]
 gi|258455040|ref|ZP_05703003.1| pseudouridine synthase [Staphylococcus aureus A5937]
 gi|282927229|ref|ZP_06334851.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|295405811|ref|ZP_06815620.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|297245402|ref|ZP_06929273.1| RluA family pseudouridine synthase [Staphylococcus aureus A8796]
 gi|147740509|gb|ABQ48807.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus JH9]
 gi|149945945|gb|ABR51881.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus JH1]
 gi|257789231|gb|EEV27571.1| pseudouridine synthase [Staphylococcus aureus A9781]
 gi|257841447|gb|EEV65888.1| pseudouridine synthase [Staphylococcus aureus A9763]
 gi|257842209|gb|EEV66637.1| pseudouridine synthase [Staphylococcus aureus A9719]
 gi|257854298|gb|EEV77248.1| pseudouridine synthase [Staphylococcus aureus A6300]
 gi|257856864|gb|EEV79767.1| pseudouridine synthase [Staphylococcus aureus A6224]
 gi|257862920|gb|EEV85685.1| pseudouridine synthase [Staphylococcus aureus A5937]
 gi|282590918|gb|EFB95993.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|285816686|gb|ADC37173.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus 04-02981]
 gi|294969246|gb|EFG45266.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|297177705|gb|EFH36955.1| RluA family pseudouridine synthase [Staphylococcus aureus A8796]
 gi|315130414|gb|EFT86401.1| pseudouridine synthase, RluA family protein [Staphylococcus aureus
           subsp. aureus CGS03]
          Length = 284

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 91/192 (47%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++  L+  +LYED+ I +  KP     Q  +    H+   L   V    Q+   
Sbjct: 65  SVNLIPYARKLE--VLYEDAFIIIVTKPNN---QNCTPSREHLHESLIEQVLYHCQEHGE 119

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKVNLKKIYTCLVYGKTHTSGIIEAN 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 176 IRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 229 HIGHPIVGDSLY 240


>gi|299532146|ref|ZP_07045540.1| pseudouridine synthase [Comamonas testosteroni S44]
 gi|298719808|gb|EFI60771.1| pseudouridine synthase [Comamonas testosteroni S44]
          Length = 214

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 56/187 (29%), Positives = 94/187 (50%), Gaps = 21/187 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPRLTHRLDQETSGI 157
           +YED  + V +KP+G+    G G     D      L+ + D+      + HRLDQ TSG+
Sbjct: 1   MYEDEHLLVLDKPSGLLCVPGRGPDKQ-DCLSLRALRHFGDAL-----VVHRLDQATSGL 54

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN--WLLKKSHIGGDY--- 212
           +V+AR  A  + L+++F  R++ K Y ++V G  +   E   +  W L    I  D+   
Sbjct: 55  VVMARNPAVQRQLSQAFAERKVDKRYIAVVAGELQAHSEAADDRGWQLIDLPIAADWERR 114

Query: 213 -VHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            + V+  N +    + + ++VI+   Q       + + P TGRTHQLR+H   +G P++G
Sbjct: 115 PLRVI--NHETGKSSQTLWQVIEHTDQPGIPRTRVLLSPLTGRTHQLRLHMAAIGHPMLG 172

Query: 269 DHKYCAN 275
           D  Y + 
Sbjct: 173 DALYASE 179


>gi|238918767|ref|YP_002932281.1| tRNA pseudouridine synthase C [Edwardsiella ictaluri 93-146]
 gi|238868335|gb|ACR68046.1| tRNA pseudouridine synthase C [Edwardsiella ictaluri 93-146]
          Length = 263

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 68/252 (26%), Positives = 110/252 (43%), Gaps = 45/252 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           ++Y+D  +   NKPAG  V              +SW+D K             G+     
Sbjct: 3   IIYQDDHLVAVNKPAGWLVH-------------RSWLDRKEKVVVMQTVRDMIGRHVYTV 49

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS- 206
           HRLD+ TSG+L++  +   A+ L + F   +I K+Y ++V G  +   E + ++ L    
Sbjct: 50  HRLDRPTSGVLLLGLSSEIARALAQQFEQHQIHKVYHAVVRGYLQG--EALLDYPLTPEL 107

Query: 207 -HIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQ----KFCWLEMQPHTGRTHQLRVHA 259
             I   +    +  +    Y   ++  +V     +    +F  +E++P TGR HQLR H 
Sbjct: 108 DKIADRFRSPDRAPQPAQTYYRGLATAEVPLAIGRYPTSRFSLVELRPQTGRKHQLRRHM 167

Query: 260 LHMGCPIVGD--HKYCANFKG---NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
            H+  PI+GD  H      +G   +F +P    L LHA  + L HP  G  L + A L  
Sbjct: 168 AHLRHPIIGDTAHGDLRQNRGIAVHFDTP---GLMLHASELCLTHPVSGEALCLRAGLDL 224

Query: 314 HMVKTWDSLGFK 325
                 D LG++
Sbjct: 225 RWQALMDGLGWQ 236


>gi|30696108|ref|NP_176031.2| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|75140931|sp|Q7XA65|PUS1_ARATH RecName: Full=RNA pseudourine synthase 1; AltName: Full=RNA
           pseudouridylate synthase 1; AltName: Full=RNA-uridine
           isomerase 1
 gi|33589806|gb|AAQ22669.1| At1g56345 [Arabidopsis thaliana]
 gi|110736414|dbj|BAF00174.1| hypothetical protein [Arabidopsis thaliana]
 gi|332195260|gb|AEE33381.1| RNA pseudourine synthase 1 [Arabidopsis thaliana]
          Length = 322

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 65/249 (26%), Positives = 112/249 (44%), Gaps = 46/249 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  +   NKP G+  +     A  I       +DS  +   L +RLD++TSG++++
Sbjct: 77  ILYEDEYLMAVNKPKGVYCEAVLRSAPQI------VLDSSSEY-HLANRLDRDTSGVMII 129

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KKECIANWLLKKSH------------ 207
            ++   A  L ++F   +I+K Y +L  G   N ++  +++   +  H            
Sbjct: 130 TKSHKVAAKLVKAFTEHKIRKSYIALCIGSSPNWRRVTVSSGHGRSKHGAWRVYAALDVG 189

Query: 208 ---IGGDYVHVVK-----------QNEKGANYAISHFKVIDCFAQKFCW---------LE 244
               GG +V  ++           +NE      ++H  V +   +  C          + 
Sbjct: 190 RVLPGGSFVRDMETTFEVVSVNSVKNESCELEDVNHVIVAEGERELSCGGDDDDVVVVVR 249

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
             P +GRTHQ+R+H  ++G PI GD KY   ++ N  +   ++  LHA  + L HP  G 
Sbjct: 250 AFPRSGRTHQIRLHCQYLGIPIRGDVKYHGVYEWNGRTFEGHE--LHAECLSLDHPVTGD 307

Query: 304 RLQITAPLP 312
            + I APLP
Sbjct: 308 SIVIRAPLP 316


>gi|313638581|gb|EFS03722.1| ribosomal large subunit pseudouridine synthase D [Listeria
           seeligeri FSL S4-171]
          Length = 207

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/214 (28%), Positives = 105/214 (49%), Gaps = 24/214 (11%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQETSGILVVART 163
           + NKPAGI+        YH  G + ++V    +   LT       RLD+ETSG++++A+ 
Sbjct: 2   IINKPAGIASIPSQ---YHPSGSVANFVKGHYETQGLTSAIHIVTRLDRETSGLMLIAKN 58

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKG 222
           R A   L+   +   +++ Y + V G    +   I      ++ IG   V ++++     
Sbjct: 59  RFAHARLSTFLQQGLLKRSYQAFVSGELAEQVGSI------EAPIGRKAVSIMERVVTPE 112

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             YA ++++V+  + Q F  + +Q  TGRTHQ+RVH  ++G P++GD  Y  +      +
Sbjct: 113 GKYAKTNYQVLARY-QAFDHVAIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------T 165

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            +  +  LH+ ++ L HP     L    PLP  M
Sbjct: 166 DLLKRQALHSCHLHLIHPLTEEYLAFDLPLPYDM 199


>gi|260103209|ref|ZP_05753446.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DSM 20075]
 gi|260083000|gb|EEW67120.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DSM 20075]
 gi|328464673|gb|EGF36019.1| ribosomal protein large subunit [Lactobacillus helveticus MTCC
           5463]
          Length = 285

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 49/178 (27%), Positives = 76/178 (42%), Gaps = 7/178 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + + NK  G   Q         +  L       GQ P + HRLD  T G+L+V
Sbjct: 83  IIYEDDNLLIINKKKG---QKTHPNLNETNTTLNDCATYLGQSPYIVHRLDMLTGGLLLV 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+  A    L      +   + Y + V    K   +   N  +   H   D     +   
Sbjct: 140 AKNPAVVPILNRELTSKTFHRDYLAKVDHADKLSDQGTINQPI--DHDPED--QRKRMIS 195

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
               +A++H++V+         +++   TGRTHQ+RVH   +G PI+GD  Y  NF G
Sbjct: 196 PAGLHAVTHYQVLKRNDNNTAVVKLTLETGRTHQIRVHLASLGTPIIGDPLYNPNFGG 253


>gi|217968528|ref|YP_002353762.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|217505855|gb|ACK52866.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 217

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/207 (29%), Positives = 99/207 (47%), Gaps = 23/207 (11%)

Query: 102 LYEDSKIYVFNKPAGI-SV-QGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGIL 158
           L+ D  + V +KPAG+ SV  GG G    +   +++ W D+     R+ HRLD  TSG++
Sbjct: 12  LHVDECLLVVDKPAGLLSVPAGGEGRQDCLAARIQARWADA-----RIVHRLDAATSGLV 66

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
           + AR     + ++ +F  R + K Y ++V G + ++  E          +     V  ++
Sbjct: 67  LFARGAEMLRRMSLAFEQRIVGKQYVAVVHGHLAQDDGEIDLPLAEDADNRPRQIVDALR 126

Query: 218 QNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC- 273
                   A++ ++V+D     A     LE++P TGR HQLRVH L +G PI GD  Y  
Sbjct: 127 -----GRRALTRYRVLDRQGAGADACSRLELKPVTGRAHQLRVHLLCLGHPIFGDPLYAP 181

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
                 F      +++LHA  +   HP
Sbjct: 182 PESAARF-----GRMHLHAARIAFMHP 203


>gi|223933756|ref|ZP_03625728.1| pseudouridine synthase [Streptococcus suis 89/1591]
 gi|223897560|gb|EEF63949.1| pseudouridine synthase [Streptococcus suis 89/1591]
          Length = 291

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 56/199 (28%), Positives = 89/199 (44%), Gaps = 16/199 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG ++ A
Sbjct: 84  LYQDEHLIIVNKPEGMKTHGNEPTEIALLNHVSAYV---GQTCYVVHRLDMETSGAILFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      + I + Y +L  G  K     I + + +  H   D    +  N K
Sbjct: 141 KNPFILPILNRLLEDKVIYRDYLALCQGQLKETDWTITDKIGRDRH---DRRKRMVDNRK 197

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           G   A++  +++     K   +  +  TGRTHQ+RVH  H G  ++GD  Y         
Sbjct: 198 G-QAALTQVRLLKPLG-KNSLVSCRLQTGRTHQIRVHLAHHGHALIGDPLY-----SRVA 250

Query: 282 SPIQNKLYLHARYMDLPHP 300
           +P   +L LHA+ + L HP
Sbjct: 251 AP---RLMLHAQKLSLTHP 266


>gi|323466046|gb|ADX69733.1| Ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus H10]
          Length = 285

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 49/178 (27%), Positives = 76/178 (42%), Gaps = 7/178 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + + NK  G   Q         +  L       GQ P + HRLD  T G+L+V
Sbjct: 83  IIYEDDNLLIINKKKG---QKTHPNLNETNTTLNDCATYLGQSPYIVHRLDMLTGGLLLV 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+  A    L      +   + Y + V    K   +   N  +   H   D     +   
Sbjct: 140 AKNPAVVPILNRELTSKTFHRDYLAKVDHADKLSDQGTINQPI--DHDPED--QRKRMIS 195

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
               +A++H++V+         +++   TGRTHQ+RVH   +G PI+GD  Y  NF G
Sbjct: 196 PAGLHAVTHYQVLKRNDNNTAVVKLTLETGRTHQIRVHLASLGTPIIGDPLYNPNFGG 253


>gi|256843689|ref|ZP_05549177.1| ribosomal protein large subunit [Lactobacillus crispatus 125-2-CHN]
 gi|312984138|ref|ZP_07791485.1| pseudouridylate synthase [Lactobacillus crispatus CTV-05]
 gi|256615109|gb|EEU20310.1| ribosomal protein large subunit [Lactobacillus crispatus 125-2-CHN]
 gi|310894492|gb|EFQ43567.1| pseudouridylate synthase [Lactobacillus crispatus CTV-05]
          Length = 285

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 99/240 (41%), Gaps = 28/240 (11%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           Q IL +G  R       FN  I  G  + I      L+H+  +Q+    S  +       
Sbjct: 39  QNILVNGNYRY------FNQNILPGDKIEI-----NLDHVESDQQAYAPSGKMPD----- 82

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              ++YED  + + NK  G   Q         +  L       GQ P + HRLD  T G+
Sbjct: 83  ---VIYEDDNLLIINKKKG---QKTHPNLNETNTALNDCTTYLGQSPYIVHRLDMLTGGL 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+  A    L      +   + Y + V        + +A      + IG D +   K
Sbjct: 137 LLIAKNPAVVPILNRELTSKIFHRDYLAKVIN-----ADHLAERGTINAPIGHDPLDQRK 191

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +  +     A++H++V+         +++   TGRTHQ+RVH   +G PIVGD  Y  +F
Sbjct: 192 RKIDPTGLRAVTHYQVLQKNDDNTAIVKLTLETGRTHQIRVHLASLGSPIVGDPLYNPDF 251


>gi|218709959|ref|YP_002417580.1| RNA pseudouridine synthase [Vibrio splendidus LGP32]
 gi|218322978|emb|CAV19155.1| RNA pseudouridine synthase [Vibrio splendidus LGP32]
          Length = 270

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/205 (31%), Positives = 95/205 (46%), Gaps = 33/205 (16%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--T 147
           L  HSDFL            + NK  G+SV    G     D  L   V     +P+L   
Sbjct: 43  LLNHSDFL------------LINKHPGVSVHKDDG-----DTMLLQEVAKAINEPKLYLV 85

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSGIL++A+   AA  L++ F  R ++K Y ++    PK K+  I+   +++S 
Sbjct: 86  HRLDKMTSGILLLAKDAPAASELSQLFAKREVEKYYLAIGSKKPKKKQGLISG-DMERSR 144

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                +   K+N      AI+ F        +   L  +P+TGRTHQ+RV    +G  IV
Sbjct: 145 RSSWKLLTTKENP-----AITQFLSATAEPGERLLL-CKPYTGRTHQIRVAMKSIGSAIV 198

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA 292
           GD  Y  + +        ++ YLHA
Sbjct: 199 GDPIYNPSNEA-------DRGYLHA 216


>gi|238927181|ref|ZP_04658941.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
 gi|238884963|gb|EEQ48601.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
          Length = 294

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/223 (28%), Positives = 104/223 (46%), Gaps = 23/223 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS-----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED  + V +KPAG  V   +      IA  + G+  +        P   HRLD+ TS
Sbjct: 79  IIYEDDDLLVLDKPAGQLVHPTTKETHGTIANAVRGYYAACGVHLDFHP--CHRLDRNTS 136

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A+       + +   +RR    Y +L+ G     + CI   + +   +    +  
Sbjct: 137 GLLLIAKHPEVQYQIAQQNTLRRE---YLALIAGSLTPPEGCIDVPIARA--LPSIILRC 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V    K A    +H+  +     ++  L +Q  TGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 VSTEGKSA---CTHYVTVQTDG-RYSLLRLQLDTGRTHQIRVHLAHLGHPLLGDDLY--- 244

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
             G   + I     LH+ ++ L HP   + L ++A LPA M +
Sbjct: 245 --GGTRAEIARH-ALHSAHLTLVHPRTKKMLALSALLPADMAR 284


>gi|170097151|ref|XP_001879795.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164645198|gb|EDR09446.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 321

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 108/244 (44%), Gaps = 28/244 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-----GSGIAYHIDGFLKSWVD--SKGQKPRLTHRLDQE 153
           LLY D  + V  KP G+  Q       +G   H +  ++      S    P   HRLD+ 
Sbjct: 30  LLYVDPAVAVVTKPHGLVCQLIHRQLPAGRVNHFNVMMQDLKAHLSLETFPYPVHRLDKS 89

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G  ++A T ++A+ L++ F+ R +QK Y +LV G  K+  E         + + G Y 
Sbjct: 90  TTGAFLLALTESSARQLSQQFQKRTVQKTYLALVRGGEKSFPEKFGEIRTTLNKVDG-YP 148

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
             V  + +G   A     +          LE+   TG  HQLRVH A  +  PI+GD +Y
Sbjct: 149 E-VDLSSQGQPCATDWKLLASSPIAPISLLELNLLTGYKHQLRVHLAKCLHAPILGDAQY 207

Query: 273 CANFKGNFTSPI-------QNKLYLHARYMDL-------PHPEGGRLQITAPLPAHMVKT 318
               K   +S I       +++++LHA  +         PH +  RL + APLP   +K 
Sbjct: 208 S---KKPLSSAITDVVKIPEDRIFLHASEISFLKYKSSGPHKQ-FRLAVRAPLPREFLKL 263

Query: 319 WDSL 322
              L
Sbjct: 264 CKDL 267


>gi|269467869|gb|EEZ79612.1| pseudouridylate synthase, 23S RNA-specific [uncultured SUP05
           cluster bacterium]
          Length = 296

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/180 (32%), Positives = 80/180 (44%), Gaps = 23/180 (12%)

Query: 102 LYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           L+E     VF+KP+GI V              I YH            G++  L HR+D 
Sbjct: 74  LFEVEDFAVFDKPSGIMVHPTRKDTPYCLLDEIRYHF-----------GEEASLAHRIDA 122

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           ETSG+++VA+ + A+  L   F  R   K Y +LV G  KN    I   + K S I G  
Sbjct: 123 ETSGLVLVAKNKQASTVLKNLFENRECNKEYLALVKGQLKNNI-TIDKPISKSSGIIGIK 181

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +    Q+ K +   I   K  +        ++  P TGR HQ+RVH   +G  IVGD  Y
Sbjct: 182 MTCENQDGKASTTHIQPLKFNE--QDNTTLVKAIPVTGRQHQIRVHLDSIGHTIVGDPIY 239


>gi|238789504|ref|ZP_04633289.1| Pseudouridine synthase [Yersinia frederiksenii ATCC 33641]
 gi|238722454|gb|EEQ14109.1| Pseudouridine synthase [Yersinia frederiksenii ATCC 33641]
          Length = 249

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 59/208 (28%), Positives = 94/208 (45%), Gaps = 18/208 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+    G     ++D      V        L HRLD  TSG++V+A
Sbjct: 37  LYQDDHLVLINKPTGLLSLSGKN-PQNLDSVHHRLVQIFPGC-TLVHRLDFGTSGLMVIA 94

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L + F  R + K+Y +++ G   +  E + +  + K       + +   + K
Sbjct: 95  RNKAINAALCQQFSQRTVTKVYSAVLCGH-LDDNEGVIDAAIAKDPALFPLMSICAIHGK 153

Query: 222 GANYAISHFKVIDCF--------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            A    S ++V++ F         Q    +++ P TGRTHQLR+H   +G PI G   Y 
Sbjct: 154 PAR---SRYQVVERFYHELEDKTLQPLTRVQLTPETGRTHQLRIHCQQLGHPIWGCDLYG 210

Query: 274 AN-FKGNFTSPIQNKLYLHARYMDLPHP 300
                G   +P   +L LHA  +   HP
Sbjct: 211 GRLLPGTELTP---RLMLHASELHFVHP 235


>gi|224543721|ref|ZP_03684260.1| hypothetical protein CATMIT_02934 [Catenibacterium mitsuokai DSM
           15897]
 gi|224523374|gb|EEF92479.1| hypothetical protein CATMIT_02934 [Catenibacterium mitsuokai DSM
           15897]
          Length = 289

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 111/240 (46%), Gaps = 31/240 (12%)

Query: 74  LNHIIKEQKILD----SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +N I+    +LD       + T   DF    ++YED  I V NKP GI+V       +  
Sbjct: 54  MNPILHTNDVLDVLAYEHDDETYAPDFQDIDIVYEDDLILVVNKPIGIAVYPDD--PHKT 111

Query: 130 DGF---LKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           D     + ++  ++G     R  HRLD +TSG++V  +      +L  +  ++ IQ+ Y 
Sbjct: 112 DSLSNRVSAYYMTQGYDIPVRYIHRLDNDTSGLVVFCKCHLIQAYLDHALSIKEIQREYL 171

Query: 185 SLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKF 240
           + V G  K  KE  I   L K  H        ++ + KG + A+++++ ++     A   
Sbjct: 172 AYVEGHIKEGKEYKIEQNLGKDRHSPSK----MRVHSKGIS-AVTYYQCLENKEDHALVR 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           C LE    TGR HQ+RVH   +G PI+GD  Y  N   ++      +L LHA Y+    P
Sbjct: 227 CRLE----TGRKHQIRVHMASIGHPILGDSLY--NEGSDYP-----RLALHAAYIKFEEP 275


>gi|296125314|ref|YP_003632566.1| pseudouridine synthase [Brachyspira murdochii DSM 12563]
 gi|296017130|gb|ADG70367.1| pseudouridine synthase [Brachyspira murdochii DSM 12563]
          Length = 336

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 79/326 (24%), Positives = 146/326 (44%), Gaps = 46/326 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           + EN ++++RLD++  + + + +    Q ++  G V ++ K+VK+   I  G  +     
Sbjct: 26  IEENIDDSIRLDKYMGDRFSYYSRNKWQDLIGQGLVLLNGKKVKYTRTINKGDEIEY--- 82

Query: 71  INALNHII--KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                HII  KE ++ D +V            ++Y+D  + + NKPA + V   SG  YH
Sbjct: 83  -----HIIGMKEPEV-DKNVT-----------IIYDDGDLIIANKPANLPVI-PSGKYYH 124

Query: 129 --IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   +K  ++       + +R+D+ETSG +V++R    A         R+  K     
Sbjct: 125 NTLHTIVKQMLNC---NINMLNRIDRETSGCVVMSRGHETASKFCAMIARRKNTKKKIKK 181

Query: 187 VW-GIPKNKKECIANWLLKKSHI--GGDYVH----VVKQNEKGANYAISHFKVIDCFAQK 239
            +  + +N K    N++++   +  G +Y      + K+N +G+ Y+ + FK I      
Sbjct: 182 TYIAVVENAKNIEDNFIVEGYMLESGHEYYRRFQTLHKENIEGSKYSKTAFKTIKRLGD- 240

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY---------L 290
           +  +  + +TGR HQ+RVH       +VGD  Y       F   I+  +          L
Sbjct: 241 YAIVMARLYTGRMHQIRVHLYSKNLYMVGDKIYGKYGPKVFDDFIEKNIIPEGFFHRQAL 300

Query: 291 HARYMDLPHPEGGRL-QITAPLPAHM 315
           HA  ++  HP   +L +I APL   +
Sbjct: 301 HAYSLEFNHPINDKLIKIKAPLAKDL 326


>gi|227878113|ref|ZP_03996093.1| pseudouridylate synthase RluD [Lactobacillus crispatus JV-V01]
 gi|256850157|ref|ZP_05555587.1| ribosomal protein large subunit [Lactobacillus crispatus MV-1A-US]
 gi|262047720|ref|ZP_06020673.1| ribosomal protein large subunit [Lactobacillus crispatus MV-3A-US]
 gi|295693421|ref|YP_003602031.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|227862283|gb|EEJ69822.1| pseudouridylate synthase RluD [Lactobacillus crispatus JV-V01]
 gi|256713129|gb|EEU28120.1| ribosomal protein large subunit [Lactobacillus crispatus MV-1A-US]
 gi|260572005|gb|EEX28572.1| ribosomal protein large subunit [Lactobacillus crispatus MV-3A-US]
 gi|295031527|emb|CBL51006.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
          Length = 285

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 99/240 (41%), Gaps = 28/240 (11%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           Q IL +G  R       FN  I  G  + I      L+H+  +Q+    S  +       
Sbjct: 39  QNILVNGNYRY------FNQNILPGDKIEI-----NLDHVESDQQAYAPSGKMPD----- 82

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              ++YED  + + NK  G   Q         +  L       GQ P + HRLD  T G+
Sbjct: 83  ---VIYEDDNLLIINKKKG---QKTHPNLNETNTALNDCTTYLGQSPYIVHRLDMLTGGL 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+  A    L      +   + Y + V        + +A      + IG D +   K
Sbjct: 137 LLIAKNPAVVPILNRELTSKIFHRDYLAKVIN-----ADHLAERGTINAPIGHDPLDQRK 191

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +  +     A++H++V+         +++   TGRTHQ+RVH   +G PIVGD  Y  +F
Sbjct: 192 RKIDPTGLRAVTHYQVLQKNDDNTAIVKLTLETGRTHQIRVHLASLGSPIVGDPLYNPDF 251


>gi|300814457|ref|ZP_07094719.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
 gi|300511427|gb|EFK38665.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
          Length = 300

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 71/284 (25%), Positives = 129/284 (45%), Gaps = 31/284 (10%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN-LTKHSD 95
           +++  R   + V+ KR   N  ++ G  V I              K  D S+N L ++ D
Sbjct: 35  IRRACRENSIYVNGKRTFENVEVKKGDSVAI--------------KFPDESLNALCQYKD 80

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKG--QKPRLTHRLDQ 152
                + YED  + + NK            +   +  +L ++ +     +K R  +RLD+
Sbjct: 81  I---DICYEDYDLLIVNKEYNCVTHTAKDDSQDTLLNYLAAYFEKNNIKRKVRFVNRLDR 137

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+++VA+   A   + + F   ++ KIY ++  G  K K+      ++KK  +  D 
Sbjct: 138 DTSGLIIVAKNSYAHAKIMDEFSNNQVDKIYLAICRGDFKEKQ----GEIVKKISLCQDG 193

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +     ++ G  YA + ++V+    +K   ++++  TGRTHQ+RVH   +G PI+GD  Y
Sbjct: 194 IRREVDDDNGK-YAKTKYQVLK-DNKKLALVKLKLFTGRTHQIRVHLKSIGHPIIGDKLY 251

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHM 315
                 N    + ++  LH+  +    P  G L+  TA L   M
Sbjct: 252 N---DSNEEQNLLDRQALHSYSLSFKLPRTGELKTFTAKLSDDM 292


>gi|333030807|ref|ZP_08458868.1| pseudouridine synthase [Bacteroides coprosuis DSM 18011]
 gi|332741404|gb|EGJ71886.1| pseudouridine synthase [Bacteroides coprosuis DSM 18011]
          Length = 312

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 114/237 (48%), Gaps = 24/237 (10%)

Query: 101 LLYEDSKIYVFNKPAG---ISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LYED+ + V  K AG   I+V    G + H  ++ +LK   + +GQ   L H+L+ + S
Sbjct: 90  VLYEDAYLIVIEKKAGVLSIAVGKNKGKSAHAILNHYLKK-TNHRGQ-ALLVHKLEVDES 147

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ A+      +L ++++   I   +  LV G  + +     +W+ +++    ++ + 
Sbjct: 148 GIMIFAKDEETKFNLQKNWKELIINHTFVGLVEGDVQEESGLNISWIDEETG-KLNFSNN 206

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           ++   +    AI+ F+ I   A     LE  P   R +++RV    MG PI+GD KY   
Sbjct: 207 LETAPRDPVKAITRFRTIKK-ANGLSMLEFDPREDRNNKIRVQMAEMGHPILGDKKY--- 262

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP---EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
             G F SP++ +  LHA  +   HP   E  + +I+ P      K + SL  K   N
Sbjct: 263 --GEFISPLK-RFALHAFLIRFRHPVTKELMKFEISYP------KEFRSLMMKSSEN 310


>gi|219126101|ref|XP_002183303.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217405059|gb|EEC45003.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 383

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 101/234 (43%), Gaps = 37/234 (15%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID------GFLK----SWVDSKGQKP 144
           D +   +L++D +I V +KP        SG+A+H D      G L          +   P
Sbjct: 92  DDVDVPVLFQDDQILVVHKP--------SGVAHHNDADTGRLGILNLIRHQQTTGRFAYP 143

Query: 145 -RL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE----- 196
            RL   HRLD+ TSGILV+A+T  AAQ LT+++R  R+ K Y  L        K+     
Sbjct: 144 HRLYGVHRLDRVTSGILVLAKTPGAAQILTQAWREDRVTKYYVGLSGNKATTSKQGHVRG 203

Query: 197 -----CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                   +WLL +   G +  H         + A     + +   +    L  +P TGR
Sbjct: 204 RMIRGRRRSWLLTRETHGSNVAHTRFFTAGLGHLAPPSSTLTNVSPKTL--LLFRPTTGR 261

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP----HPE 301
           THQLRV A  +G P+ GD  Y         +   ++  LHA    +P    HPE
Sbjct: 262 THQLRVAAKSVGLPLWGDPVYRDGRHRTENASTPSRTLLHAAGWHVPADDTHPE 315


>gi|332673190|gb|AEE70007.1| pseudouridine synthase D [Helicobacter pylori 83]
          Length = 293

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 75/287 (26%), Positives = 127/287 (44%), Gaps = 45/287 (15%)

Query: 41  LRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           L+  Q  +DK+R+K N + ++  Q+++    I +L H    +K                 
Sbjct: 28  LKEAQRHLDKQRLKQNQQAVRKSQMIQ---GIVSLIHFKPNEKT---------------Q 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  ALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           V +T  +A+ L   F  ++++K Y +LV G+  ++   I   +L   +I  D     K +
Sbjct: 128 VGKTLQSAKDLKTLFMQKKVKKTYLALVHGL-VDRSIVIDKPILTPQNIQKDLRIKSKIS 186

Query: 220 EKGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             G         +S+   +D        L++ P TGRTHQ+R+H   +G  IVG+  Y  
Sbjct: 187 PLGKPSTTLVEPLSYNPFLDI-----SLLKITPITGRTHQIRLHLSSVGHRIVGEGLYGV 241

Query: 275 ---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                      K    +P+   L LHA  ++    +G   +IT+P+P
Sbjct: 242 IDENAREYLQLKRENNAPL---LMLHATSLEFEF-KGAIYKITSPMP 284


>gi|315635420|ref|ZP_07890686.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
 gi|315480178|gb|EFU70845.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
          Length = 300

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 104/228 (45%), Gaps = 38/228 (16%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLT 147
           LK +L +ED    +F+KP  + V   S          I YH            G+   L 
Sbjct: 71  LKPLLEFED--FAIFDKPTNLMVHPISKNTSYSLLDEIRYHF-----------GENANLI 117

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HR+D ETSG+++V + + +   L + F+ ++  K Y ++V G  K + + I   L ++  
Sbjct: 118 HRIDAETSGLVIVGKNKKSEIELKDMFQEKKYHKSYLAIVQGEIKEELK-IDKALDREGK 176

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPI 266
             G  + V  Q E+G   +I+  K I    +K    +E  P TGR HQ+RVH   MG  I
Sbjct: 177 AIGVRMKVCTQ-EEGGKESITIIKPIIYDKEKNLTLVEALPLTGRQHQIRVHLHSMGHTI 235

Query: 267 VGDHKY------CANF-------KGNFTSPIQNKLYLHARYMDLPHPE 301
           +GD  Y        N+       +  F     ++L+LHA Y++  + +
Sbjct: 236 LGDPIYGVDDENAENYLNKTLSKEDRFKVTKSHRLWLHANYLEFNYKD 283


>gi|302307964|ref|NP_984770.2| AEL091Cp [Ashbya gossypii ATCC 10895]
 gi|299789245|gb|AAS52594.2| AEL091Cp [Ashbya gossypii ATCC 10895]
          Length = 609

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 51/172 (29%), Positives = 80/172 (46%), Gaps = 6/172 (3%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +YED  I V +KP+GI         Y  +   K      G      +RLD+ TSG++ +A
Sbjct: 192 VYEDDDILVIDKPSGIPAHPTG--RYRFNSITKILEKQLGYTVHPCNRLDRLTSGLMFLA 249

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           +T   A  + +  + R ++K Y + V G  P    E + +  LK          V    +
Sbjct: 250 KTPKGADEMGDQMKAREVKKEYVARVVGEFPIG--EIVVDMPLKTIEPKLALNMVCDPED 307

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +    A + FK I  +  +   ++ QP+TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 308 EAGKGAKTQFKRIS-YDGQTSIVKCQPYTGRTHQIRVHLQYLGFPIANDPIY 358


>gi|257869733|ref|ZP_05649386.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           gallinarum EG2]
 gi|257803897|gb|EEV32719.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           gallinarum EG2]
          Length = 299

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 106/230 (46%), Gaps = 20/230 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTH---RLDQE 153
           ++YED  + + NKPAGI+        YH +G +    K++   +G + ++ H   RLD++
Sbjct: 80  IVYEDQHLLIVNKPAGIA---SIPAQYHPNGTMANRVKAYYKQQGYQDQVIHVVTRLDRD 136

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++ A+   A   L    R +++ K Y ++V G    + + +A+       I  D  
Sbjct: 137 TSGLMLFAKHGFAHAKLDVQLRQKQLIKKYQAIVAG----QIQELASHGEITYPIARDLS 192

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            ++K+       +      +    Q+   + +  HTGRTHQ+RVH   + CP++GD  Y 
Sbjct: 193 SLLKRKTSLEGKSARTEYWLTKKDQQVAVVTILLHTGRTHQIRVHFAAIHCPLLGDELYG 252

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                       ++  LH   +   HP  G+ L   A LPA M     ++
Sbjct: 253 GAMDLGI-----DRQALHCCELAFTHPFSGKSLHFKADLPADMASIKQAM 297


>gi|320583405|gb|EFW97618.1| DRAP deaminase, putative [Pichia angusta DL-1]
          Length = 569

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 59/223 (26%), Positives = 105/223 (47%), Gaps = 12/223 (5%)

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVF 111
           + N ++ G+V     V N ++ I+K   ++  S  + +H   + S    +++ED ++ V 
Sbjct: 107 YRNALEKGRVTINEKVAN-IDTILKNGDLI--SHRMHRHEPPVTSRPVKIVHEDDELVVI 163

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP+GI V       ++   F+       G K    +RLD+ TSG++ + +T A A+ + 
Sbjct: 164 DKPSGIPVHPTGRYRHNTVTFILER--EMGIKAHPCNRLDRLTSGLMFLGKTAAGAEKMV 221

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           +  R R + K Y + V G    ++E +    L+       +  V ++N K A        
Sbjct: 222 KQMREREVSKEYIAKVVGEFPAQREIVCEEPLRTVDPRIAFNIVDRENGKEAKTVFKRLS 281

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                +   C    +P TGRTHQ+RVH  ++G PIV D  Y +
Sbjct: 282 YDGVTSLVIC----KPLTGRTHQIRVHLQYLGHPIVNDPLYSS 320


>gi|310817977|ref|YP_003950335.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309391049|gb|ADO68508.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 557

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 100/229 (43%), Gaps = 43/229 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS----------KGQKPRLTHRL 150
           +++ED  + V +KP G+    G G           WVDS              P L HRL
Sbjct: 354 IVFEDDWLVVIDKPCGLLSVPGKGA---------EWVDSVLTRLQARYPHATGPLLVHRL 404

Query: 151 DQETSGILVV---ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           D +TSG+LV    ART AA   L   F  R + K Y + + G  + ++  I   L    H
Sbjct: 405 DLDTSGLLVAALDARTHAA---LQRQFIHREVHKRYVAWIDGRVRGEQGLIDLPLRVDLH 461

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGC 264
                +H    +      A++ ++V++    +   + + P +GRTHQLRVHA H   +G 
Sbjct: 462 DRPRQIH----DPLHGKPAVTEWQVLERQGDR-TRVALFPQSGRTHQLRVHAAHPLGLGA 516

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           PIVGD  Y            + +L LHA  +   HP  G R+    P P
Sbjct: 517 PIVGDRLYGHE---------EVRLLLHAEALSFRHPGTGLRVSFERPAP 556


>gi|293380440|ref|ZP_06626509.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
 gi|290923019|gb|EFD99952.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
          Length = 285

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 99/240 (41%), Gaps = 28/240 (11%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           Q IL +G  R       FN  I  G  + I      L+H+  +Q+    S  +       
Sbjct: 39  QNILVNGNYRY------FNQNILPGDKIEI-----NLDHVESDQQAYAPSGKMPD----- 82

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              ++YED  + + NK  G   Q         +  L       GQ P + HRLD  T G+
Sbjct: 83  ---VIYEDDNLLIINKKKG---QKTHPNLNETNTALNDCTTYLGQSPYIVHRLDMLTGGL 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+  A    L      +   + Y + V        + +A      + IG D +   K
Sbjct: 137 LLIAKNPAVVPILNRELTSKIFHRDYLAKVIN-----ADHLAERGTINAPIGHDPLDQRK 191

Query: 218 QN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +  +     A++H++V+         +++   TGRTHQ+RVH   +G PIVGD  Y  +F
Sbjct: 192 RKIDPTGLRAVTHYQVLQKNDDNTTIVKLTLETGRTHQIRVHLASLGSPIVGDPLYNPDF 251


>gi|308184530|ref|YP_003928663.1| hypothetical protein HPSJM_03780 [Helicobacter pylori SJM180]
 gi|308060450|gb|ADO02346.1| hypothetical protein HPSJM_03780 [Helicobacter pylori SJM180]
          Length = 327

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 106/228 (46%), Gaps = 18/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W+ S+       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVVHKAPSVK---EPTLVDWLKSQNYELSNLGLKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +V+A+       L+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIVIAKNNFTHVCLSEQLKTKTMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHV-VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            + + V Q EK + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+
Sbjct: 197 MIALKVAQKEK-SRYSKSEFTSLLASQNGMDLIGAKLFTGRTHQIRAHLEYLNRHIIGDN 255

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
            Y  N         + ++ LHA  ++  HP    +L+   PL   M++
Sbjct: 256 LYGLN---EALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300


>gi|315634350|ref|ZP_07889637.1| tRNA pseudouridine synthase C [Aggregatibacter segnis ATCC 33393]
 gi|315476940|gb|EFU67685.1| tRNA pseudouridine synthase C [Aggregatibacter segnis ATCC 33393]
          Length = 237

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 59/234 (25%), Positives = 100/234 (42%), Gaps = 19/234 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILYQDEHIVAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQLVYPIHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  L   F  ++ +K Y ++V G    + +      ++   I   +     Q +
Sbjct: 65  ALNSETANLLCHQFEQKQTEKEYLAVVRGYVTGQGKIDYPLKVQLDKIADKFA----QQD 120

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ +  +               ++  + + P TGR HQLR H  H+  PI+GD 
Sbjct: 121 KEPQSAVTFYDGLKTVEMPYGVGRYATSRYSLVRLIPKTGRKHQLRRHMKHIFHPILGDT 180

Query: 271 KYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           +Y    +    +     ++L LHA  +   HP     Q +  L A + + W +L
Sbjct: 181 QYGDLHQNRALTEHTGCSRLMLHAEKLTFVHP---LTQQSITLQAGLDEKWQNL 231


>gi|312829403|emb|CBX34245.1| RNA pseudouridylate synthase family protein [Staphylococcus aureus
           subsp. aureus ECT-R 2]
          Length = 284

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 90/192 (46%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++  L+  +LYED+ I +  KP     Q  +    H+   L   V    Q+   
Sbjct: 65  SVNLIPYARKLE--VLYEDAFIIIVTKPNN---QNCTPSREHLHESLIEQVLYHCQEHGE 119

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD  T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 120 NINPHIVTRLDHNTTGIVIFAK----YGHIHHLFSKVNLKKIYTCLVYGKTHTSGIIEAN 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 176 IRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 229 HIGHPIVGDSLY 240


>gi|32491284|ref|NP_871538.1| hypothetical protein WGLp535 [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|25166491|dbj|BAC24681.1| rluD [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 314

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 79/318 (24%), Positives = 144/318 (45%), Gaps = 57/318 (17%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD+     +P  +   ++K + + QV+V D   +     I+ G+ ++I   I+  N++I
Sbjct: 19  RLDKSIAEIFPEYSRNKIKKFIINNQVKVNDICIINPKKNIKGGECIKIK--ISKKNNLI 76

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSW 136
            +++                  L+YED  I V NK   + V  G     +  +   L ++
Sbjct: 77  SKKRKTYK--------------LIYEDDDILVINKYKDVIVHPGCDKHENTLLHDILFNY 122

Query: 137 VDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG------ 189
            DSK   +  + HRLD++T+G++++AR   + + L +  ++R I + Y +++ G      
Sbjct: 123 PDSKNLYRAGIVHRLDKDTTGLMLIARNSFSQKKLIKLLKLRLINREYRAVLLGKIICDG 182

Query: 190 -----IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
                I +N K    N    K HI G               +I+H+K+I  F   F +++
Sbjct: 183 TVSAPIIRNSK----NRTRMKVHISGK-------------ESITHYKIIKNFND-FSYVK 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY------LHARYMDLP 298
           +   +GRTHQ+R+H  ++  P++GD  Y  N K  +   +   ++      LHAR +   
Sbjct: 225 INLESGRTHQIRLHMSYINHPVLGDFVY-GNKKNKYIKTLYKSIFNISRHALHARKIKFI 283

Query: 299 HPEGGRLQI-TAPLPAHM 315
           HP    L +    LP  M
Sbjct: 284 HPINNCLMVHKIDLPDDM 301


>gi|116617792|ref|YP_818163.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
 gi|116096639|gb|ABJ61790.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
          Length = 299

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/239 (25%), Positives = 114/239 (47%), Gaps = 26/239 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
            G + V++K V  ++ +++G +V I  P   + + ++ + K LD               +
Sbjct: 36  GGAILVNEKPVYTSDYLKNGDIVTIVMPTEKSNDLVVPDYKPLD---------------I 80

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYH-----IDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++E+    V +KP GI+   G     H     + G L++ + +    P +  RLD++TSG
Sbjct: 81  IFENEHWLVVDKPYGITTVPGHADRLHTLVNQVKGHLET-IKADDLVPHVVTRLDRDTSG 139

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV-HV 215
           I+++A+ R A   L +  +   ++K Y +   GI  +    I   +     + GD++   
Sbjct: 140 IVLLAKHRFAHAVLDQQLQDHTVEKFYLAYPSGILADDHGDINAPI---GRMDGDFIKRE 196

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+ + K +       +  +   Q    +++Q HTGRTHQ+RVH  ++G P+VGD  Y  
Sbjct: 197 VRDDGKPSRTEYWVERRYEDDEQNMTRVKVQLHTGRTHQIRVHFANIGHPLVGDTLYGG 255


>gi|161507907|ref|YP_001577871.1| ribosomal protein large subunit [Lactobacillus helveticus DPC 4571]
 gi|160348896|gb|ABX27570.1| ribosomal protein large subunit [Lactobacillus helveticus DPC 4571]
          Length = 285

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 49/178 (27%), Positives = 76/178 (42%), Gaps = 7/178 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + + NK  G   Q         +  L       GQ P + HRLD  T G+L+V
Sbjct: 83  IIYEDDNLLIINKKKG---QKTHPNLNETNTTLNDCATYLGQSPYIVHRLDMLTGGLLLV 139

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+  A    L      +   + Y + V    K   +   N  +   H   D     +   
Sbjct: 140 AKNPAVVPILNRELTSKTFHRDYLAKVDHADKLSDQGTINQPI--DHDPED--QRKRMIS 195

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
               +A++H++V+         +++   TGRTHQ+RVH   +G PI+GD  Y  NF G
Sbjct: 196 PAGLHAVTHYQVLKRNDNNTAVVKLTLETGRTHQIRVHLASLGTPIIGDPLYNPNFGG 253


>gi|319955825|ref|YP_004167088.1| pseudouridine synthase [Nitratifractor salsuginis DSM 16511]
 gi|319418229|gb|ADV45339.1| pseudouridine synthase [Nitratifractor salsuginis DSM 16511]
          Length = 324

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 49/170 (28%), Positives = 79/170 (46%), Gaps = 4/170 (2%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
            Y+F+KP+G+ V        +    L       GQ     HR+D+ETSG+L+ +R + + 
Sbjct: 79  FYLFDKPSGVLVHPKKMTTPY--SMLDEVRFHGGQHANAVHRIDKETSGLLLASRHKESE 136

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           + L  +F  + IQK Y +   G  +      A  +L   +  G   H V  + +G     
Sbjct: 137 RFLKGAFERKAIQKSYRAWATGRIEEPFSVDAPIILNNDY--GPTKHKVFIHREGKRAYT 194

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +   +          LE  PHTGRTHQ+R+H  H+  PI+GD  Y  +++
Sbjct: 195 TFLPIQYDERLDATLLECIPHTGRTHQIRIHLFHVKHPILGDPIYGPSYE 244


>gi|196231266|ref|ZP_03130125.1| pseudouridine synthase, RluA family [Chthoniobacter flavus
           Ellin428]
 gi|196224602|gb|EDY19113.1| pseudouridine synthase, RluA family [Chthoniobacter flavus
           Ellin428]
          Length = 289

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 88/180 (48%), Gaps = 14/180 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           + +ED+ + V +KP  +       +    + + +  +L+       ++  + HRLD+ETS
Sbjct: 78  ICFEDAALLVIDKPPDLLTIASEAEQEKTVYFQLTEYLRGNDVHSRERVWIVHRLDRETS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  A   L   +   + +K Y +++ G   N K    ++L +      D   V
Sbjct: 138 GIMVFAKTPQAKGLLQTGWD--KAEKRYQAVIEGSLPNDKGTFRSYLDET-----DPFRV 190

Query: 216 VK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +         +A++H++V+    +    +E+   TGR HQ+RVH    GCPIVGD KY A
Sbjct: 191 ISVPRTPTTRHAVTHYRVLK-RGKGRTLVELTLETGRRHQIRVHLADAGCPIVGDKKYGA 249


>gi|109947518|ref|YP_664746.1| putative ribosomal pseudouridine synthase [Helicobacter acinonychis
           str. Sheeba]
 gi|109714739|emb|CAJ99747.1| putative ribosomal pseudouridine synthase [Helicobacter acinonychis
           str. Sheeba]
          Length = 293

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 71/285 (24%), Positives = 125/285 (43%), Gaps = 41/285 (14%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K     Q+ Q+VR   +I  +  +I  +             +  +  
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQIVRKSQIIQGIVSLIYFK------------PNEKQGK 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     +F+KP  +      G  YH +  L       G+     HRLD ETSG+++V
Sbjct: 71  LVFETKDFGIFDKPTQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLV 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  + + L   F  ++++K Y +LV G+  ++   I   +L   +I  D    ++   
Sbjct: 129 GKTPQSTKDLKALFMQKKVKKTYLALVHGL-MDQNTTIDKPILTPENIQKD----LRIRS 183

Query: 221 KGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-- 274
           K +        +++  A         L++ P TGRTHQ+R+H   M   IVG+  Y    
Sbjct: 184 KISPLGKPSTTLVEPLAYNSFLDVSLLKITPLTGRTHQIRLHLSSMNHRIVGEGLYGVAD 243

Query: 275 -------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                    K    +P+   L LHA  ++    +G   +IT+P+P
Sbjct: 244 ENAREYLQLKRENNAPL---LMLHALSLEFEF-KGAHYKITSPMP 284


>gi|325578565|ref|ZP_08148665.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325159801|gb|EGC71931.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 225

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/202 (30%), Positives = 93/202 (46%), Gaps = 28/202 (13%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQ------GGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +K  ++Y+     +  KP G+SV       G + +     G  + W         L HRL
Sbjct: 1   MKLDIVYQTDDFIIIYKPCGLSVHKDQSEIGLTTLLAEQLGVPQVW---------LVHRL 51

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSG+L++A    +A      F    IQK Y +L    PK K+  I   + K  +  G
Sbjct: 52  DKVTSGLLILALNAESAAEFFRLFSEHHIQKTYLALSNQKPKKKQGLIVGDMQKVRN--G 109

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +    K  +   N AI+ F+ + C      ++ ++P TG+THQLRV    +G PI+GD 
Sbjct: 110 AW----KLCQSKENPAITRFESVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDL 164

Query: 271 KYCANFKGNFTSPIQNKLYLHA 292
            Y  N     T  I ++ YLHA
Sbjct: 165 LYGKN-----TENI-DRTYLHA 180


>gi|300718134|ref|YP_003742937.1| tRNA pseudouridine synthase C [Erwinia billingiae Eb661]
 gi|299063970|emb|CAX61090.1| tRNA pseudouridine synthase C [Erwinia billingiae Eb661]
          Length = 259

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/217 (28%), Positives = 102/217 (47%), Gaps = 18/217 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDQWLVAVNKPAGWLVHRSWLDRHETVFVMQTLRDQIGQHVFTVHRLDRPTSGVLLL 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F    +QK Y ++V G  + ++        +   I   + +     +
Sbjct: 64  ALSSEVARLLSQQFEQHAMQKTYHAVVRGWLEGEETLDYALTEELDKIADKFTN----PD 119

Query: 221 KGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H+K          V    + +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHWKSLAKAELPVAVSRYDSSRFSLVELKPETGRKHQLRRHLRHLRHPIIGDS 179

Query: 271 KYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGR 304
            +  + K N ++       +L LHA  + L HP  G 
Sbjct: 180 AH-GDLKQNRSAAQHFGMKRLMLHASELSLLHPVTGE 215


>gi|119774268|ref|YP_927008.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119766768|gb|ABL99338.1| tRNA pseudouridine synthase C [Shewanella amazonensis SB2B]
          Length = 258

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 108/241 (44%), Gaps = 25/241 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LYED  +   +KPAG+ V   + +A     F      D  G      HRLD+ TSG+L+
Sbjct: 12  ILYEDEAMVAIHKPAGLLVHR-TYLARKEHWFAMQLTRDLVGCHVFPVHRLDRPTSGVLL 70

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A++   A  L   F    I+K Y +LV G        + ++ LK+     +        
Sbjct: 71  FAKSSEVANSLCGQFASHSIRKHYLALVRG--NMFDAGVLDYALKEEL--DELADKDVDP 126

Query: 220 EKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +K A  AI+ ++ +             + +F  + +QP TGR HQLR H  H+  PIVGD
Sbjct: 127 DKPAQEAITAYRPLLNSEIPYSSGRYPSSRFALMHLQPQTGRKHQLRRHMAHLRHPIVGD 186

Query: 270 HKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
             +        F+ +F     N+L+L A+ ++L HP  G  + I   L    +  +  LG
Sbjct: 187 TTHGDGKQNRFFREHFGV---NRLWLIAKRLELTHPLTGAPIAIETELEPEWLDVFSGLG 243

Query: 324 F 324
           +
Sbjct: 244 W 244


>gi|88808956|ref|ZP_01124465.1| putative pseudouridylate synthase [Synechococcus sp. WH 7805]
 gi|88786898|gb|EAR18056.1| putative pseudouridylate synthase [Synechococcus sp. WH 7805]
          Length = 215

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 101/219 (46%), Gaps = 26/219 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+ +  ++ V +KPAG+  Q   G+  H    L S +       RL HRLD++TSG++++
Sbjct: 13  LVLDHPRLMVVDKPAGLLCQ--PGLGSHQQDSLISRLQLACPALRLVHRLDRDTSGLVLL 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQN 219
           A+     + L   F  RR++K+Y + V G  KN    I   L +       Y VH     
Sbjct: 71  AKDPDMLRLLGMFFASRRVRKLYVADVQGQMKNVSGLIGLPLARLKRQPPTYGVH----- 125

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANF 276
             G    ++ ++ +    +    L + P TGR+HQLR H   +  PI+GD  Y   CA  
Sbjct: 126 -PGGKACVTLWRRLK-LMESSTRLWLCPRTGRSHQLRAHLAALHHPIIGDPIYNPGCA-- 181

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPE--GGRLQITAPLPA 313
                      L L A  +  P P+   G++++ AP PA
Sbjct: 182 ---------VGLRLRAMALRFPDPDDPSGQVRVRAPWPA 211


>gi|313899587|ref|ZP_07833096.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
 gi|312955694|gb|EFR37353.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
          Length = 293

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 71/282 (25%), Positives = 117/282 (41%), Gaps = 43/282 (15%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS-----ILLYEDS 106
           RV  NNRI  G            NH+++EQ  +   + L    D ++       +L+ED 
Sbjct: 42  RVSINNRIIHG------------NHMLQEQDTV--RIFLAMEEDTIEPWYEDLEILFEDE 87

Query: 107 KIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVART 163
              + NKPA + V   G   A+ +   +K+    +G     R  HRLD ETSG ++  + 
Sbjct: 88  LFCIVNKPANLLVHSDGIEHAHTVCNLVKAHYLLEGHNTCVRPLHRLDYETSGAMIFCKV 147

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
                 L    + ++I + Y +   G    K   I   + +  H        ++ +E G 
Sbjct: 148 PFLQPLLDAMLKNKQIYREYEAFARGYIAQKHCTITRGIARDRHDARK----MRISEHGK 203

Query: 224 NYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +         D F ++    F W+  + +TGRTHQ+RVH   +  P++ D  Y       
Sbjct: 204 S------ARTDVFVKQNFMDFTWIRCRLYTGRTHQIRVHLAAIQHPLLSDPLY------G 251

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
                  +L LHA  + +PHP     L++  PLP  + +  D
Sbjct: 252 IRDSRCPRLALHACRVSIPHPLSNDMLRVECPLPQDLRQLLD 293


>gi|152996905|ref|YP_001341740.1| pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150837829|gb|ABR71805.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 212

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 58/203 (28%), Positives = 99/203 (48%), Gaps = 18/203 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED    V NKPA      G G    +D  L       G+   + HRLD+ TSG+++V
Sbjct: 11  ILYEDEWFAVINKPANCLSVPGRG-PDKLDSILYRAECLFGEAFAI-HRLDEATSGLILV 68

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A+T    + +   FR R +QK Y +L+ G    +K  +      +  +  D+ +  +Q  
Sbjct: 69  AKTHECQKRMYAHFREREVQKEYRALLRGHLLGEKGEV------RKPLRCDWPNRPRQII 122

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             ++ +  +I++++ +  +      + + P TGR+HQLRVH   +G  I+GD  Y   F+
Sbjct: 123 CTDEWSKDSITYWEKM-AYENNTTRVRLVPFTGRSHQLRVHMQSLGHSIIGDEFYDPEFQ 181

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
            +       +L LHA  ++  HP
Sbjct: 182 ND------PRLLLHAYRLEFRHP 198


>gi|17158025|ref|NP_478072.1| RNA pseudouridylate synthase domain-containing protein 1 [Homo
           sapiens]
 gi|74753357|sp|Q9UJJ7|RUSD1_HUMAN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 1; AltName: Full=Ribosomal large subunit
           pseudouridine synthase C-like protein
 gi|14336724|gb|AAK61255.1|AE006465_1 ribosomal large subunit pseudouridine synthase C like [Homo
           sapiens]
 gi|5748546|emb|CAB53055.1| RNA pseudouridylate synthase domain containing 1 [Homo sapiens]
 gi|15079997|gb|AAH11783.1| RNA pseudouridylate synthase domain containing 1 [Homo sapiens]
 gi|119606118|gb|EAW85712.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_a
           [Homo sapiens]
 gi|119606119|gb|EAW85713.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_a
           [Homo sapiens]
 gi|119606121|gb|EAW85715.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_a
           [Homo sapiens]
 gi|123988657|gb|ABM83844.1| RNA pseudouridylate synthase domain containing 1 [synthetic
           construct]
 gi|123999171|gb|ABM87166.1| RNA pseudouridylate synthase domain containing 1 [synthetic
           construct]
          Length = 312

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 49/159 (30%), Positives = 80/159 (50%), Gaps = 8/159 (5%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA      F+ RR+ K Y +L+ G  +  +  I++ + +
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYRCFKERRVTKAYLALLRGHIQESRVTISHAIGR 120

Query: 205 KSHIGGDYVHVVKQNEKGANY--AISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            S  G  +   ++ ++   N   +++   V++           + ++P TGRTHQLRVH 
Sbjct: 121 NSTEGRAHTMCIEGSQGCENPKPSLTDLVVLEHGLYAGDPVSKVLLKPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             +G P+VGD  Y     G    P   ++ LHA Y+ +P
Sbjct: 181 SALGHPVVGDLTY-GEVSGREDRPF--RMMLHAFYLRIP 216


>gi|88857814|ref|ZP_01132456.1| tRNA pseudouridine synthase C [Pseudoalteromonas tunicata D2]
 gi|88819431|gb|EAR29244.1| tRNA pseudouridine synthase C [Pseudoalteromonas tunicata D2]
          Length = 244

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 98/227 (43%), Gaps = 23/227 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D      +KP+G+ V       +     ++   D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILFQDEHFVAIDKPSGLLVHRSFLDKHETQFAMQMLRDQLGQHVFPVHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +  AA+ + E F   R+ K Y +LV G   + +        +   I   Y     QN 
Sbjct: 64  ALSSDAARKMNEQFSDHRVTKRYLALVRGFAPDYRLLDRPLKEELDKIADKY---ADQN- 119

Query: 221 KGANYAISHFKVIDCFAQ-------------KFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           K    A + F+   C  Q             ++  +E  P TGR HQ+R H   +  PI+
Sbjct: 120 KAPQAAQTEFR---CLQQVTLPIALGKYPTIRYSLVECFPKTGRKHQIRRHLNFLSHPII 176

Query: 268 GDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           GD  +  N   +F      + +L L A+ +   HP  G ++ I APL
Sbjct: 177 GDVNHGDNQHNHFFWQHFERQRLMLFAQRLTFMHPYSGQKIIIEAPL 223


>gi|326571595|gb|EGE21610.1| tRNA pseudouridine synthase C [Moraxella catarrhalis BC7]
          Length = 258

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 101/240 (42%), Gaps = 23/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + + NKPA + V       +     +++  +   Q     HRLD+ TSG+LV 
Sbjct: 19  ILYQDACMVIINKPANMLVHRSWLDKHETCFVMQTLRNQINQHVYPVHRLDRPTSGVLVF 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVHVVKQ 218
           A     A  L + F    IQK Y ++V GI    +    ++ LK     I   +      
Sbjct: 79  ALDSQTAGLLAKQFENHHIQKSYLAVVRGIIGTGR---IDYALKPRLDKIADKF----SN 131

Query: 219 NEKGANYAISHFKVIDCFAQKF-----------CWLEMQPHTGRTHQLRVHALHMGCPIV 267
             K +  AI+ ++V+    Q F             + + P TGR HQLR H  H+  PIV
Sbjct: 132 PNKASKSAITDYQVLATTQQPFISCRRFDSSRYSLVCLTPITGRKHQLRRHMKHIFHPIV 191

Query: 268 GDHKYCANF--KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
           GD  Y      +         +L LHA  +   HP    + +I APL     +   + G+
Sbjct: 192 GDTTYGDKVQNRAVLAHIGVKRLLLHAHQLQFCHPLYDEMIRIVAPLDTAFCQVMTAFGW 251


>gi|315604414|ref|ZP_07879480.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 180 str. F0310]
 gi|315314120|gb|EFU62171.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 180 str. F0310]
          Length = 310

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 107/225 (47%), Gaps = 26/225 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
           +LY+D  I V +KP G++   G G     + G L++    + S G   R  + HRLD  T
Sbjct: 80  ILYDDDDIVVVDKPVGVAAHTGPGWEGPTVLGNLEAAGYRITSHGPPERQGIVHRLDVGT 139

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG ++VA++  A   +  +F+ RRI KIY ++V G        I   + +  H   ++  
Sbjct: 140 SGAMMVAKSELAYSVMKRAFKERRIDKIYHAVVAGHLDPPSGTIDAPIGR--HPSREWRM 197

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V     G   A++H+  ++  A      E+   TGRTHQ+RVH   +G P VGD  Y A
Sbjct: 198 AVID---GGKRAVTHYDTLELMAGAQL-TEVHLETGRTHQIRVHMAAVGHPCVGDTFYGA 253

Query: 275 NFKGNFTSPIQ------NKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +       P Q       + +LHA  +   HP  G  + +++P P
Sbjct: 254 D-------PTQAQRLGLARQWLHAVRLGFAHPRTGMPMTVSSPYP 291


>gi|148926838|ref|ZP_01810517.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|145844563|gb|EDK21670.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
          Length = 244

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 99/201 (49%), Gaps = 17/201 (8%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKS 135
           ++ KIL   V L  + +  K + +++E+    V  K +GI S   G    Y + D     
Sbjct: 48  EKNKILKGDVELIVYENNPKGVEIVFENEDFAVLEKESGILSHPNGRHCKYSLSDEIWHL 107

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W    G+K  + HRLD+ETSG+++VA+ + A   L   F  ++IQK Y +L  G      
Sbjct: 108 W----GKKACVAHRLDKETSGLILVAKHKKAQIELKTMFEKKQIQKEYLALASG------ 157

Query: 196 ECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           E   N+++ ++  +  DY  V    Q  +    AI+ F+V+  + +     L  +P TGR
Sbjct: 158 EIKVNFIVDQAMDLTKDYDDVKTRMQICENGKKAITEFEVLSFYPKLNATLLLCKPLTGR 217

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH  +    I+GD  Y
Sbjct: 218 QHQIRVHLFYKNHKILGDPLY 238


>gi|300854916|ref|YP_003779900.1| putative ribosomal large subunit pseudouridine synthase D
           [Clostridium ljungdahlii DSM 13528]
 gi|300435031|gb|ADK14798.1| predicted ribosomal large subunit pseudouridine synthase D
           [Clostridium ljungdahlii DSM 13528]
          Length = 319

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 77/292 (26%), Positives = 127/292 (43%), Gaps = 32/292 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RLD++ +     +    + + +R G ++V+ K+ K    +  G +V      NA 
Sbjct: 8   NEAGQRLDKFSRKWLRDVPLSGIYRAIRKGDIKVNGKKAKEKYFLLEGDIV------NAE 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGF 132
               KE K     ++    + FLK  ++YED  + +  K  G+ V     S  A   D  
Sbjct: 62  YITSKETKSKFERID----NAFLK--IIYEDKNMLLVEKWPGVLVHSDKNSKDATLTDYV 115

Query: 133 LKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           L    D +G+          P   +RLD+ TSGI++  +   + + L E  R R I+K Y
Sbjct: 116 LSHLYD-RGEFNPEEEVTFTPSPCNRLDRNTSGIVIYGKNYESLKLLNEMIRERSIKKYY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G     K+ +    +KK         V    EK +       K ++     +  +
Sbjct: 175 IALVIG---KIKDGVYEGYIKKDRTNNK-SSVSNTPEKDSKKISMRVKNVNTCGI-YSLI 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           +++  TGR+HQLR H  ++G  IVGD KY  +   N  S   NK  L  +Y+
Sbjct: 230 QLELITGRSHQLRAHLAYLGNAIVGDSKYGVS---NINSFFYNKYGLDYQYL 278


>gi|194041320|ref|XP_001928432.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 3
           isoform 1 [Sus scrofa]
          Length = 352

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 70/284 (24%), Positives = 115/284 (40%), Gaps = 48/284 (16%)

Query: 89  NLTKHS--DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQKP 144
           NL++    D L+  ++ +   +   NKP G+ V G  G    +     L   +    ++ 
Sbjct: 70  NLSREELVDVLREAVVDQKGPLVTLNKPQGLPVTGKPGELTLVSVLPELSQCLGLGEREL 129

Query: 145 RLTHRLDQETSGILVVARTRAAAQHL----TESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           ++     +ETSG+++++     A  L    T S R R+    Y ++  GIP   +  I  
Sbjct: 130 QVVRASGKETSGLVLLSSCPQTASRLQKFFTHSQRARKPTATYCAVTDGIPAASEGKIQA 189

Query: 201 WLLKKSHIGGDYVHVVKQNE-----KGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQ 254
            L  +   G   V  VK        KG  + +SHF+V+   +   C L ++QP T    Q
Sbjct: 190 ALKMEHTDGASLVVPVKSPSRKDFLKGVKWTLSHFRVLA--SGSGCALVQLQPLTAFPSQ 247

Query: 255 LRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQNK--------LYLHARYMDLP---- 298
           L+VH +   CP++GDHKY A         F  P +N           L +R    P    
Sbjct: 248 LQVHMVLQLCPVLGDHKYSACVGTVLGQRFLLPAENTKPQRQVLDEALLSRLHLTPAQAA 307

Query: 299 ----------------HPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                            P    +++ APLP++  +T   LG +Y
Sbjct: 308 QLPLHIHLHRLHLPGTRPRDAPIELLAPLPSYFSRTLQCLGLQY 351


>gi|270291471|ref|ZP_06197693.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus
           acidilactici 7_4]
 gi|270280317|gb|EFA26153.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus
           acidilactici 7_4]
          Length = 301

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 67/285 (23%), Positives = 131/285 (45%), Gaps = 36/285 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
           G++ V+++  + N  + +G    V +PP      H+++ ++ +D               +
Sbjct: 37  GKILVNEQPKRTNEMVTAGDQVTVELPPEPGN-PHVVRSRQPID---------------V 80

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGI 157
           +YED    V NKP  + +VQ        +   +K++   +  + ++ H   RLDQ+TSG+
Sbjct: 81  IYEDQDYLVVNKPPFLPTVQSARNQTDTLVNRVKNYYAERDYESQVVHVVTRLDQDTSGL 140

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+ R A   + +  R  R+QK Y ++  G          +  L  + I  D    +K
Sbjct: 141 VLFAKRRFAHTIMDQDLRQHRVQKYYLAMATG------RFAQSHGLIDAPIERDPASFIK 194

Query: 218 QNEKGANY---AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +    A     + + + V++        L++Q HTGRTHQ+RVH   +  P++GD  Y  
Sbjct: 195 RRVASAGNGKPSKTEYWVLEQ-TDTDSLLKVQLHTGRTHQIRVHFSELHHPLIGDPLYN- 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
             + +F S  +  L+  +   +     G ++ + AP+P  M++ W
Sbjct: 253 --ETSFRSLQRQALHCFSLKFENVF-RGKKIDVQAPIPNDMLEYW 294


>gi|269956094|ref|YP_003325883.1| pseudouridine synthase, RluA family [Xylanimonas cellulosilytica
           DSM 15894]
 gi|269304775|gb|ACZ30325.1| pseudouridine synthase, RluA family [Xylanimonas cellulosilytica
           DSM 15894]
          Length = 310

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 52/167 (31%), Positives = 85/167 (50%), Gaps = 11/167 (6%)

Query: 137 VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           V + G   R  + HRLD  TSG++VVA++ AA   L  +F+ R ++K+Y +L  G P+  
Sbjct: 123 VSTSGAAERQGIVHRLDVGTSGLMVVAKSEAAYTGLKRAFKERTVEKVYHALAQGHPEPT 182

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I   + +  H   D+   V  + K    +++H++V++        +E+   TGRTHQ
Sbjct: 183 VGTIDAPIGR--HPSNDWRFAVVADGK---PSVTHYEVLEMLPAA-SLVEVHLETGRTHQ 236

Query: 255 LRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
           +RVH   +  P+VGD  Y A+      T     + +LHA  +   HP
Sbjct: 237 IRVHFSAVRHPLVGDLTYGADPVLATHTG--LTRQWLHAVRLGFEHP 281


>gi|256845446|ref|ZP_05550904.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_36A2]
 gi|256719005|gb|EEU32560.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_36A2]
          Length = 288

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 103/225 (45%), Gaps = 26/225 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           + YED  + + NK   I V     +    +A  I  + +  +  K   PR  +RLD  TS
Sbjct: 75  IAYEDENLLIVNKEPYIIVHPTQKKVDKTLANAIVNYFEKTL-GKTLVPRFYNRLDMNTS 133

Query: 156 GILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           G++++A+   T+A  Q  TE      ++K Y  +  GI +     I    L    +G D 
Sbjct: 134 GLIIIAKNAYTQAFLQDKTE------VKKTYKVIASGIIEKDDFFIE---LPIGKVGDDL 184

Query: 213 VHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             +    + G   A +H KV++  + +   +LE + +TGRTHQ+R H   +G  +VGD  
Sbjct: 185 KRIELSEKDGGKSAKTHIKVLERNYEKNITFLEARLYTGRTHQIRAHLSLIGHSLVGDEL 244

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           Y  + K      +  +  LHA  ++  +P+    L+I   +P  M
Sbjct: 245 YGGDMK------LAKRQMLHAYKLEFQNPKTLENLKIEIDIPIDM 283


>gi|167748371|ref|ZP_02420498.1| hypothetical protein ANACAC_03115 [Anaerostipes caccae DSM 14662]
 gi|167652363|gb|EDR96492.1| hypothetical protein ANACAC_03115 [Anaerostipes caccae DSM 14662]
          Length = 238

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 60/211 (28%), Positives = 95/211 (45%), Gaps = 12/211 (5%)

Query: 101 LLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETS 155
           +LY+D  I V  KPAG+     + G    +H       + ++  ++P L   HRLD+   
Sbjct: 9   VLYKDQDIAVCEKPAGMPTADDKSGDMDVFHSLKNQLFFEENLDREPELYVVHRLDRPVG 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ART+ AA  L+   R    +K Y ++V G    +     ++LLK      +    
Sbjct: 69  GVMVFARTKEAAAELSRQIREHIFEKDYQAIVNGWLPEEDGVFTDYLLKDDK--KNTSCT 126

Query: 216 VKQNEKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V +  KGA  A   ++V+D       K  +  +   TGR HQ+RV     G  + GD KY
Sbjct: 127 VPEETKGAKKAELSYEVLDMVETGEGKLTYCLIHLMTGRHHQIRVQFAVRGFGLYGDTKY 186

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              F+   T     ++ L+A  +   HP  G
Sbjct: 187 NKKFQK--TKKQYEEIGLYATRISFRHPVTG 215


>gi|326571287|gb|EGE21309.1| tRNA pseudouridine synthase C [Moraxella catarrhalis BC1]
          Length = 254

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 101/240 (42%), Gaps = 23/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + + NKPA + V       +     +++  +   Q     HRLD+ TSG+LV 
Sbjct: 15  ILYQDACMVIINKPANMLVHRSWLDKHETCFVMQTLRNQINQHVYPVHRLDRPTSGVLVF 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVHVVKQ 218
           A     A  L + F    IQK Y ++V GI    +    ++ LK     I   +      
Sbjct: 75  ALDSQTAGLLAKQFENHHIQKSYLAVVRGIIGTGR---IDYALKPRLDKIADKF----SN 127

Query: 219 NEKGANYAISHFKVIDCFAQKF-----------CWLEMQPHTGRTHQLRVHALHMGCPIV 267
             K +  AI+ ++V+    Q F             + + P TGR HQLR H  H+  PIV
Sbjct: 128 PNKASKSAITDYQVLATTQQPFISCRRFDSSRYSLVCLTPITGRKHQLRRHMKHIFHPIV 187

Query: 268 GDHKYCANF--KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
           GD  Y      +         +L LHA  +   HP    + +I APL     +   + G+
Sbjct: 188 GDTTYGDKVQNRAVLAHIGVKRLLLHAHQLQFCHPLYDEMIRIVAPLDTAFCQVMTAFGW 247


>gi|294785258|ref|ZP_06750546.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_27]
 gi|294486972|gb|EFG34334.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_27]
          Length = 288

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 103/225 (45%), Gaps = 26/225 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           + YED  + + NK   I V     +    +A  I  + +  +  K   PR  +RLD  TS
Sbjct: 75  IAYEDENLLIVNKEPYIIVHPTQKKVDKTLANAIVNYFEKTL-GKTLVPRFYNRLDMNTS 133

Query: 156 GILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           G++++A+   T+A  Q  TE      ++K Y  +  GI +     I    L    +G D 
Sbjct: 134 GLIIIAKNAYTQAFLQDKTE------VKKTYKVIASGIIEKDDFFIE---LPIGKVGDDL 184

Query: 213 VHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             +    + G   A +H KV++  + +   +LE + +TGRTHQ+R H   +G  +VGD  
Sbjct: 185 RRIELSEKDGGKSAKTHIKVLERNYEKNITFLEARLYTGRTHQIRAHLSLIGHSLVGDEL 244

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           Y  + K      +  +  LHA  ++  +P+    L+I   +P  M
Sbjct: 245 YGGDMK------LAKRQMLHAYKLEFQNPKTLENLKIEIDIPIDM 283


>gi|307154171|ref|YP_003889555.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7822]
 gi|306984399|gb|ADN16280.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7822]
          Length = 302

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 75/278 (26%), Positives = 118/278 (42%), Gaps = 31/278 (11%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF-------LKSILLYEDSKIY 109
            RIQSGQ++     I+  +     Q +L     LT H          L   + YED ++ 
Sbjct: 38  ERIQSGQIL-----IDGCSQ--DPQTLLQPGQKLTYHRPPWEEPEVPLSFEVFYEDDEVL 90

Query: 110 VFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           V  KP+ + V  G G   H +   L+     +   P   HRL + TSG++++AR+  A  
Sbjct: 91  VVAKPSLLPVLPGGGFLEHTLLSLLQQQYPQRTPIP--VHRLGRGTSGLVLLARSPHARA 148

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           +LTE  R  ++ KIY +LV          I + + K  H    YV     +   A Y+  
Sbjct: 149 NLTEQMRSHQVGKIYRALVGSGNIPDHFVITHPIGKIPHPVLGYVFGATADGMKA-YSEC 207

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK- 287
           H    +        +E++  TGR HQ+R+H    G P++GD  Y          PI  + 
Sbjct: 208 HVLKRN---PTTTLVEVKILTGRPHQIRIHLAVAGYPLIGDPLYQIGGVPRIPEPIAGEK 264

Query: 288 --------LYLHARYMDLPHPEGGRL-QITAPLPAHMV 316
                    +LHA  +   HP  G+L ++  P P  ++
Sbjct: 265 LPVPGDGGYHLHAYGLSFFHPVTGKLIELICPPPTPLI 302


>gi|86150522|ref|ZP_01068746.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|86152341|ref|ZP_01070551.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|315123634|ref|YP_004065638.1| RNA pseudouridylate synthase family [Campylobacter jejuni subsp.
           jejuni ICDCCJ07001]
 gi|85838974|gb|EAQ56239.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|85840638|gb|EAQ57890.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|315017356|gb|ADT65449.1| RNA pseudouridylate synthase family [Campylobacter jejuni subsp.
           jejuni ICDCCJ07001]
          Length = 298

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 99/201 (49%), Gaps = 17/201 (8%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKS 135
           ++ KIL   V L  + +  K + +++E+    V  K +GI S   G    Y + D     
Sbjct: 48  EKNKILKGDVELIVYENNPKGVEIVFENEDFAVLEKESGILSHPNGRHCKYSLSDEIWHL 107

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W    G+K  + HRLD+ETSG+++VA+ + A   L   F  ++IQK Y +L  G      
Sbjct: 108 W----GKKACVAHRLDKETSGLILVAKHKKAQIELKTMFEKKQIQKEYLALASG------ 157

Query: 196 ECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           E   N+++ ++  +  DY  V    Q  +    AI+ F+V+  + +     L  +P TGR
Sbjct: 158 EIKVNFIVDQAMDLTKDYDDVKTRMQICENGKKAITEFEVLSFYPKLNATLLLCKPLTGR 217

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH  +    I+GD  Y
Sbjct: 218 QHQIRVHLFYKNHKILGDPLY 238


>gi|170725275|ref|YP_001759301.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169810622|gb|ACA85206.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 566

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 56/178 (31%), Positives = 91/178 (51%), Gaps = 15/178 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D ++ + NKPA      G  I   +   +K+ + D+ G  P + HRLD  TSG++V
Sbjct: 365 IIYQDEEMAIINKPAEFLSVPGKSIQDSVYLRMKTQFPDATG--PLIVHRLDMSTSGLMV 422

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +A T+ A + L   F  R ++K Y +L+ G  +  +  I+        + GD+    +Q 
Sbjct: 423 IALTKEANKSLQAQFIARTVKKRYTALLTGELREDEGSIS------LPMRGDFDDRPRQL 476

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKY 272
                   A + ++VI+    K   + + P TGRTHQLRVH+ H   +  PIVGD  Y
Sbjct: 477 VCFDHGKPAETKWQVIERKDGK-TKVHLYPKTGRTHQLRVHSAHAQGLNMPIVGDDLY 533


>gi|191638831|ref|YP_001987997.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|190713133|emb|CAQ67139.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|327382880|gb|AEA54356.1| hypothetical protein LC2W_2024 [Lactobacillus casei LC2W]
 gi|327386064|gb|AEA57538.1| hypothetical protein LCBD_2042 [Lactobacillus casei BD-II]
          Length = 287

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 73/263 (27%), Positives = 124/263 (47%), Gaps = 43/263 (16%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           N  +++GQ++R                 + +S  LT   +F    ++YED+   + +KPA
Sbjct: 47  NGPVEAGQIIRFE---------------IPTSKTLT--PEFAPLEVIYEDANWLIVSKPA 89

Query: 116 GISVQGG-----SGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           G++   G     S +   I G+L +  +D+   +P +  RLD++T G LV+A     AQ 
Sbjct: 90  GLTSVPGPHTPNSSLLNRIAGYLVEQKIDAP--QPAIMTRLDRDTVG-LVLAAKHPYAQG 146

Query: 170 LTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
             +    R + K Y ++V G +P  K E  A   L       D +H +   +     A++
Sbjct: 147 RFDQAHQRTLTKHYLAVVSGKLPSPKGEIDAPLKL-----AADGIHRIVAAD--GQTAVT 199

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
            ++V+    +    +++Q  TGRTHQ+RVH   +G P++GDH Y    + +   P Q   
Sbjct: 200 KYRVLK--EKTNTLVDVQLLTGRTHQIRVHFASLGHPLIGDHLYG---QPDARIPYQA-- 252

Query: 289 YLHARYMDLPHPEGGRLQITAPL 311
            L A  ++   P  G+ QITA L
Sbjct: 253 -LQATRLNFTDPFSGK-QITAEL 273


>gi|86147049|ref|ZP_01065366.1| pseudouridine synthase Rlu family protein [Vibrio sp. MED222]
 gi|85835114|gb|EAQ53255.1| pseudouridine synthase Rlu family protein [Vibrio sp. MED222]
          Length = 232

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 63/205 (30%), Positives = 95/205 (46%), Gaps = 33/205 (16%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--T 147
           L  HSDFL            + NK  G+SV    G     D  L   V     +P+L   
Sbjct: 5   LLNHSDFL------------LINKHPGVSVHKDDG-----DTMLLQEVAKAINEPKLYLV 47

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++A+   AA  L++ F  R ++K Y ++    PK K+  I+   +++S 
Sbjct: 48  HRLDKMTSGVLLLAKNAPAASELSQLFAKREVEKYYLAIGSKKPKKKQGLISG-DMERSR 106

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                +   K+N      AI+ F        +   L  +P+TGRTHQ+RV    +G  IV
Sbjct: 107 RSSWKLLTTKENP-----AITQFLSATAEPGERLLL-CKPYTGRTHQIRVAMKSIGSAIV 160

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA 292
           GD  Y  + +        ++ YLHA
Sbjct: 161 GDPIYNPSNEA-------DRGYLHA 178


>gi|290961167|ref|YP_003492349.1| RNA pseudouridine synthase [Streptomyces scabiei 87.22]
 gi|260650693|emb|CBG73809.1| putative RNA pseudouridine synthase [Streptomyces scabiei 87.22]
          Length = 314

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 80/325 (24%), Positives = 137/325 (42%), Gaps = 20/325 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVTVDGSVVGKSERVH 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E       + +    D +  I+       +     +G +V
Sbjct: 60  GGAWLEVEMPQAPAPVQIVAEPV---EGMEIVHDDDDVVVIVKPVGVAAHPSPGWSGPTV 116

Query: 120 QGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            GG +   Y I            ++  + HRLD  TSG++ VA++  A   L   F+ R 
Sbjct: 117 IGGLAAAGYRIS------TSGAAERQGIVHRLDVGTSGLMTVAKSERAYTSLKRQFKERT 170

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I+ F +
Sbjct: 171 VDKRYHALVQGHPDPTSGTIDAPIGR--HPNHDYKWAVTAEGK---PSVTHYDLIEAF-R 224

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               L+++  TGRTHQ+RVH      P VGD  Y A+        I  + +LHA  +   
Sbjct: 225 AASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTLAKRLGI-TRQWLHAVRLGFE 283

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  G  ++  +  PA + K  D +
Sbjct: 284 HPGDGEWVEFESDYPADLQKALDKV 308


>gi|34762661|ref|ZP_00143653.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
 gi|27887682|gb|EAA24759.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
          Length = 292

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 103/225 (45%), Gaps = 26/225 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           + YED  + + NK   I V     +    +A  I  + +  +  K   PR  +RLD  TS
Sbjct: 79  IAYEDENLLIVNKEPYIIVHPTQKKVDKTLANAIVNYFEKTL-GKTLVPRFYNRLDMNTS 137

Query: 156 GILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           G++++A+   T+A  Q  TE      ++K Y  +  GI +     I    L    +G D 
Sbjct: 138 GLIIIAKNAYTQAFLQDKTE------VKKTYKVIASGIIEKDDFFIE---LPIGKVGDDL 188

Query: 213 VHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             +    + G   A +H KV++  + +   +LE + +TGRTHQ+R H   +G  +VGD  
Sbjct: 189 RRIELSEKDGGKSAKTHIKVLERNYEKNITFLEARLYTGRTHQIRAHLSLIGHSLVGDEL 248

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           Y  + K      +  +  LHA  ++  +P+    L+I   +P  M
Sbjct: 249 YGGDMK------LAKRQMLHAYKLEFQNPKTLENLKIEIDIPIDM 287


>gi|259501034|ref|ZP_05743936.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
 gi|302190517|ref|ZP_07266771.1| pseudouridine synthase, RluA family protein [Lactobacillus iners
           AB-1]
 gi|259167728|gb|EEW52223.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
          Length = 300

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 131 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 189

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 190 PIGKKDDPVKRYIM------EGGKESVTKYRVIKQIAGA-SLVELQLLTGRTHQIRVHMQ 242

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F     ++  LH   +    P E  R+++    PA MV+ W
Sbjct: 243 YLGHPLFGDHLY--GVEDDF-----HRQALHCFLLAFDDPLEHKRIEVQIADPADMVQLW 295

Query: 320 DSL 322
             L
Sbjct: 296 QKL 298


>gi|320528517|ref|ZP_08029674.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
 gi|320131103|gb|EFW23676.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
          Length = 287

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 58/233 (24%), Positives = 106/233 (45%), Gaps = 24/233 (10%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           Q+ +++K VK N  + +G V+    VI  LN               T H   ++  +LYE
Sbjct: 41  QMYLNEKPVKVNRVVHTGDVL----VIQELN-----------IETYTLHPSTVRPDILYE 85

Query: 105 DSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           D  + V  KPAG+ S      +   +   L+ +   +    R   RLD++ SGI++ A+ 
Sbjct: 86  DEDVVVVCKPAGMPSHPSHHHLTDDMGTLLRDYYQDEHFVIRPIGRLDKDVSGIMIYAKN 145

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
           + +A  L    +   +QK Y+++V G  ++K   I + + +   +   +        +G 
Sbjct: 146 QLSAARLAAQRKDGILQKHYYAIVEGQLEDKDTLIFSLIKEDGQMAQSF-------NQGG 198

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              ++ ++VI  + Q  C + +   TGRTHQ+R     +G P+ GD  Y  + 
Sbjct: 199 KQCVTEYEVIKHY-QTECLIRVYLKTGRTHQIRAGFAGIGHPLCGDTLYGGSI 250


>gi|311693912|gb|ADP96785.1| tRNA pseudouridine synthase C [marine bacterium HP15]
          Length = 247

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 67/222 (30%), Positives = 99/222 (44%), Gaps = 18/222 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS--KGQKPRLTHRLDQETSGIL 158
           +LY D  +   +KPAG+ V   S I  H   F   +  +   GQ     HRLD+ TSG+L
Sbjct: 7   VLYRDEHLLAVHKPAGLLVHR-SPIDKHETEFALQYARALNGGQHVYPVHRLDRPTSGVL 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH---IGGDYVHV 215
           V AR    A+ L  +     + K Y ++V G P    E I + L ++     + G+   V
Sbjct: 66  VFARDSDTARTLGMALMAGEVTKTYLAMVRGWPPEHGE-IDHPLREEPEDRRLKGEEQPV 124

Query: 216 VKQNEKGANYAISHFKV-IDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                       +   V I+ + + ++  +E+ P TGR HQLR H  H+  PI+GD  + 
Sbjct: 125 RDALTYYRTLTTTEIPVEIEKYPSSRYAVVELNPKTGRKHQLRRHMKHINHPIIGDANHG 184

Query: 274 AN-----FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
                  F   F    Q +L L A  M   HP  G+ L I+A
Sbjct: 185 RGRHNRYFAERFG---QGRLMLAATRMAFQHPVSGKPLTISA 223


>gi|237742173|ref|ZP_04572654.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           4_1_13]
 gi|229429821|gb|EEO40033.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           4_1_13]
          Length = 292

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 103/225 (45%), Gaps = 26/225 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           + YED  + + NK   I V     +    +A  I  + +  +  K   PR  +RLD  TS
Sbjct: 79  IAYEDENLLIVNKEPYIIVHPTQKKVDKTLANAIVNYFEKTL-GKTLVPRFYNRLDMNTS 137

Query: 156 GILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           G++++A+   T+A  Q  TE      ++K Y  +  GI +     I    L    +G D 
Sbjct: 138 GLIIIAKNAYTQAFLQDKTE------VKKTYKVIASGIIEKDDFFIE---LPIGKVGDDL 188

Query: 213 VHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             +    + G   A +H KV++  + +   +LE + +TGRTHQ+R H   +G  +VGD  
Sbjct: 189 KRIELSEKDGGKSAKTHIKVLERNYEKNITFLEARLYTGRTHQIRAHLSLIGHSLVGDEL 248

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           Y  + K      +  +  LHA  ++  +P+    L+I   +P  M
Sbjct: 249 YGGDMK------LAKRQMLHAYKLEFQNPKTLENLKIEIDIPIDM 287


>gi|254445479|ref|ZP_05058955.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198259787|gb|EDY84095.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 262

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 99/201 (49%), Gaps = 27/201 (13%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           L++ +L  D  + + NKPA +      +G    + G  + ++ S  ++  L  RLD+ETS
Sbjct: 15  LETWILQNDDHVLLINKPALLVCHPSKNGPWSSLAGACREYLQS--ERSHLVSRLDRETS 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ A+ R  ++HL  +   R++ K Y +++ G  + K+E + +     + +G D   +
Sbjct: 73  GIVLFAKHRLKSRHLQMALEQRKVSKTYLAILEG--ELKEETLVD-----APLGPDTQSI 125

Query: 216 V----------KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           V          ++ E    Y   H         ++   ++ P TGR HQ+R HALH+G  
Sbjct: 126 VHSKNTVRRDGRKQEAQTKYTPLHSN------GRYTLAKVDPITGRKHQIRAHALHIGHH 179

Query: 266 IVGDHKYCANFKGNFTSPIQN 286
           IVGD  Y  + +G F   I++
Sbjct: 180 IVGDKLYGPD-EGLFLDFIED 199


>gi|321309582|ref|YP_004191911.1| pseudouridylate synthase [Mycoplasma haemofelis str. Langford 1]
 gi|319801426|emb|CBY92072.1| pseudouridylate synthase [Mycoplasma haemofelis str. Langford 1]
          Length = 304

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 56/179 (31%), Positives = 91/179 (50%), Gaps = 13/179 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLK---SWVDSKGQKPRLTHRLDQETSG 156
           +++E   + + +K A + VQ      + H++  L    ++ + +G KP   HRLD  T+G
Sbjct: 84  VVFESENLIIVDKEAKMPVQEDDKHPFNHMNNRLLKHLNYSNREGWKPVFIHRLDLNTTG 143

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS---HIGGDYV 213
           +L+ A+       L +S +  +I+K Y +LV G    KK  I+ +LLKK     I  + V
Sbjct: 144 LLIGAKNYKTFLKLNKSQKSLKIKKSYKALVQGNVSFKKREISCFLLKKDGRVSISREQV 203

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              K+ +  AN+ +  F  I+        LE+   TGRTHQ+R H  ++  PI GD KY
Sbjct: 204 EGAKEAKTIANF-LHFFPSINS-----TLLELTLITGRTHQIRAHMSYIKHPIRGDQKY 256


>gi|229028975|ref|ZP_04185074.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1271]
 gi|228732255|gb|EEL83138.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1271]
          Length = 292

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/235 (25%), Positives = 111/235 (47%), Gaps = 29/235 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           G + V+ +     +++Q+G  +R+  PV      +I E   L                ++
Sbjct: 36  GAIEVNNQHASVRHQLQAGDELRVFFPVEERSEGMIAEDIPL---------------CIV 80

Query: 103 YEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGILV 159
           YED  + V NK A +S +      A  +   L S  D +       +  RLD++TSG+++
Sbjct: 81  YEDDAVLVINKEANMSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGLML 140

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +A+ R     L++  + + +++ Y ++V G      E I       + IG     ++++ 
Sbjct: 141 IAKNRFVHHLLSKQHQQKAVKRTYEAIVHG------EMIEREGTIDAPIGRKPDSIIERI 194

Query: 219 -NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             E G   A++HF+V+D    K   + ++  TGRTHQ+RVH  H+G P++GD  Y
Sbjct: 195 VCEDG-QRAVTHFRVMDSANHK-THVSLELETGRTHQIRVHMAHIGHPLLGDTLY 247


>gi|226939012|ref|YP_002794083.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
 gi|226713936|gb|ACO73074.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 253

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 70/241 (29%), Positives = 106/241 (43%), Gaps = 26/241 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           ++Y D  +   +KPAG+ V   S I  H   F    V D  GQK   +HRLD+ TSG+L+
Sbjct: 8   VIYRDDWLVAVHKPAGLLVHR-SEIDRHETRFALQIVRDQLGQKVWSSHRLDKPTSGLLL 66

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +  T  A + L+ +F  + + K Y ++V G P +    I + L +      D        
Sbjct: 67  LGLTPEAGRSLSMAFEAQAVDKQYLAVVRGWP-DAAGTIDHPLARIV----DAYAPGASR 121

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           E     A++ F  +               ++  +E+ PHTGR HQLR H  H+  PI+GD
Sbjct: 122 EAEPQPAVTGFSTLATTELPWAVDRYPTSRYALVELTPHTGRRHQLRRHLKHVSHPIIGD 181

Query: 270 HKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
             Y  +     F   F     ++L L    M   HP  G RL +  PL     +   +LG
Sbjct: 182 TSYGKSRHNRAFADAFGV---SRLLLACTGMSFTHPVTGERLALDCPLADDFARVVSALG 238

Query: 324 F 324
           +
Sbjct: 239 W 239


>gi|114776527|ref|ZP_01451572.1| pseudouridylate synthase, 23S RNA-specific [Mariprofundus
           ferrooxydans PV-1]
 gi|114553357|gb|EAU55755.1| pseudouridylate synthase, 23S RNA-specific [Mariprofundus
           ferrooxydans PV-1]
          Length = 579

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 66/207 (31%), Positives = 95/207 (45%), Gaps = 24/207 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           ++YED ++ V NKPAG+    G  I    +           Q P LT  HRLD +TSG+L
Sbjct: 376 IVYEDDQLLVVNKPAGLMSTPGREIE---ESLFSRLAQRYPQIPELTLVHRLDMDTSGLL 432

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWS-LVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +VA+     + L + F  R ++K Y + LV  +P    +      L+          V  
Sbjct: 433 LVAKDLRTHKRLQKQFIERSVEKCYEAVLVKRLPAQPDQGRIELPLRVDLDDRPRQMVCY 492

Query: 218 QNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
           Q+ K A    + +++I     +   W    P TGRTHQLRVHA H   +   IVGD    
Sbjct: 493 QHGKPAT---TRWQIIARENNRTRIWF--YPETGRTHQLRVHASHRDGLNAAIVGD---- 543

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
               G +  P + +L LHAR +   HP
Sbjct: 544 ----GLYGLPAE-RLMLHARRLCFTHP 565


>gi|326575127|gb|EGE25055.1| tRNA pseudouridine synthase C [Moraxella catarrhalis CO72]
          Length = 258

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 101/240 (42%), Gaps = 23/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + + NKPA + V       +     +++  +   Q     HRLD+ TSG+LV 
Sbjct: 19  ILYQDACMVIINKPANMLVHRSWLDKHETCFVVQTLRNQINQHVYPVHRLDRPTSGVLVF 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVHVVKQ 218
           A     A  L + F    IQK Y ++V GI    +    ++ LK     I   +      
Sbjct: 79  ALDSQTAGLLAKQFEDHHIQKSYLAVVRGIIGAGR---IDYALKPRLDKIADKF----SN 131

Query: 219 NEKGANYAISHFKVIDCFAQKF-----------CWLEMQPHTGRTHQLRVHALHMGCPIV 267
             K +  AI+ ++V+    Q F             + + P TGR HQLR H  H+  PIV
Sbjct: 132 PNKASKSAITDYQVLATTQQPFISCRRFDSSRYSLVRLTPITGRKHQLRRHMKHIFHPIV 191

Query: 268 GDHKYCANF--KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
           GD  Y      +         +L LHA  +   HP    + +I APL     +   + G+
Sbjct: 192 GDTTYGDKVQNRAVLAHIGVKRLLLHAHQLQFCHPLYDEMIRIVAPLDTAFCQVMTAFGW 251


>gi|291617372|ref|YP_003520114.1| RluA [Pantoea ananatis LMG 20103]
 gi|291152402|gb|ADD76986.1| RluA [Pantoea ananatis LMG 20103]
          Length = 232

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 102/230 (44%), Gaps = 35/230 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LY+D  + + +KP+G+    G        + Y +                L HRLD  T
Sbjct: 19  ILYQDDHLVLIDKPSGLLSLSGKNPQNLDSVHYRLVTIFPGCT--------LVHRLDFGT 70

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV 213
           SG++VVAR +     L++ F  R + K Y +L+ G +P   +E I +  + K       +
Sbjct: 71  SGLIVVARNKTINAALSQQFSARTVAKHYSALLCGHLP--DEEGIIDAPIAKDPARFPRM 128

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCP 265
            +  +  K A    S ++V++ F  K           + + P TGRTHQLR+H   +G P
Sbjct: 129 SICAEWGKPAR---SRYRVVERFNLKRDDARVIPLTRVTLIPETGRTHQLRIHCQLLGHP 185

Query: 266 IVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLP 312
           I+G    C  + G     ++   +L LHA  +   HP  G    I +P P
Sbjct: 186 ILG----CDLYGGLLLPGMEQTPRLMLHASELQFIHPVTGEPFHIVSPSP 231


>gi|154491501|ref|ZP_02031127.1| hypothetical protein PARMER_01111 [Parabacteroides merdae ATCC
           43184]
 gi|154088302|gb|EDN87347.1| hypothetical protein PARMER_01111 [Parabacteroides merdae ATCC
           43184]
          Length = 303

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 101/211 (47%), Gaps = 25/211 (11%)

Query: 101 LLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLKSWVDSKGQKPR----LTHRLDQ 152
           +++ED  + V NK  G+    S +     A H+   L  +V  K   PR    + HRLD+
Sbjct: 92  IVWEDDDLIVVNKKEGLLSVSSTRVKERTALHL---LSEYV--KKTDPRNKIFVLHRLDR 146

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+++ A+     + L  ++      + Y ++V G P+   + I + L + + +    
Sbjct: 147 DTSGLMMFAKNLQVQKALQSNWNSAITARTYVAVVEGRPEKDSDLIVSNLTENAKM---Q 203

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+V  + +     AI+ ++++      +  LE+   TGR +Q+R     +G  I GD+KY
Sbjct: 204 VYVTAEGD--GKEAITRYRLLHSNG-AYSLLELDLETGRKNQIRAQMQSIGHSIAGDYKY 260

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            A      T P   +L LHAR ++  HP  G
Sbjct: 261 GAE-----TDPT-GRLMLHARRLNFIHPVTG 285


>gi|90962453|ref|YP_536369.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|301299242|ref|ZP_07205529.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|90821647|gb|ABE00286.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|300853202|gb|EFK80799.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 296

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 72/272 (26%), Positives = 117/272 (43%), Gaps = 40/272 (14%)

Query: 16  EENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E M L ++ KN    H    +L+K   +G+V VD K+   +  +  G++  I P   + 
Sbjct: 10  DEKMTLKKFLKNKGVSHRTLSSLKK--GNGKVLVDGKKRSLSIEVGKGKITLILPPEKSD 67

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSG--------I 125
            ++   ++ LD               ++YEDS   V +KP  +S V G S         +
Sbjct: 68  ENVKMSKEPLD---------------IIYEDSNWLVVDKPPLLSSVPGPSNRTDTLVNRV 112

Query: 126 AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            +H+      W   SK   P +  RLD++TSG+++VA+ R A   + +      I K Y 
Sbjct: 113 KFHL------WQQKSKDLVPHVITRLDRDTSGLVLVAKHRFAQGLINKQVEEHSIDKKYL 166

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V GI   K   I   L  + +  G  V            A + + V +    K   +E
Sbjct: 167 AVVEGIITEKHGIIDKPLGPRENGIGQMV------TDTGKIAKTEYWVREYLGDKATLVE 220

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + HTGRTHQ+R H   +   +VGD  Y    
Sbjct: 221 CKLHTGRTHQIRAHFSSINHALVGDELYGGRL 252


>gi|255322530|ref|ZP_05363675.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           showae RM3277]
 gi|255300438|gb|EET79710.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           showae RM3277]
          Length = 354

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 81/302 (26%), Positives = 123/302 (40%), Gaps = 39/302 (12%)

Query: 39  KILRSGQVRVDK--------KRVKFNNRIQSGQV------VRIPPVINALNHIIKEQKIL 84
           KIL   Q R D          R +  N I+SG V      +  P V   L  I++  K  
Sbjct: 23  KILDGAQARADAFLATELNVARNQALNLIKSGLVSLNGKPLNKPSVKLNLGDILR-IKFE 81

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--- 141
            S    TK     +  ++YED  + V NKPA + V     +    +  L  W+ +KG   
Sbjct: 82  QSDPETTKFEAEFEVPIIYEDDDLLVLNKPANLVVHPAPSVK---EPTLVDWLGAKGFLL 138

Query: 142 ------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                  +  + HRLD+ TSG +VVA+  AA   L+     + + +IY +L   +P  K+
Sbjct: 139 SNLSGQSRAGIVHRLDKGTSGAIVVAKNNAAHAALSNQLSDKSMGRIYLALT-DLPL-KQ 196

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKG----ANYAISHFK-VIDCFAQKFCWLEMQPHTG 250
            CI    + ++        +V          AN   S F   +         +  +  TG
Sbjct: 197 NCIVERAIGRNPANRLKKAIVSSGRAAKSAFANLLFSEFDGPVQSKNAGVNLIAAKLFTG 256

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           RTHQ+RVH   +   I+GD  Y   FK         ++ LHA  +   HP  G ++   A
Sbjct: 257 RTHQIRVHLASLNRHILGDALY--GFKSEKDK--IGRVMLHAYGLYFTHPRSGEQMSFVA 312

Query: 310 PL 311
           P+
Sbjct: 313 PI 314


>gi|57169014|ref|ZP_00368142.1| RNA pseudouridylate synthase family [Campylobacter coli RM2228]
 gi|57019559|gb|EAL56249.1| RNA pseudouridylate synthase family [Campylobacter coli RM2228]
          Length = 336

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/201 (30%), Positives = 99/201 (49%), Gaps = 17/201 (8%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKS 135
           ++ KIL   V L  + +  K + +++E+    V  K +GI S   G    Y + D     
Sbjct: 86  EKNKILKGDVELIVYENNPKGVEIVFENEDFAVLEKESGILSHPNGRHCKYSLSDEIWHL 145

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W    G+K  + HRLD+ETSG+++VA+ + A   L   F  ++IQK Y +L  G      
Sbjct: 146 W----GKKACVAHRLDKETSGLILVAKHKKAQIELKTMFEKKQIQKEYLALASG------ 195

Query: 196 ECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           E   N+++ ++  +  DY  V    Q  +    AI+ F+V+  + +     L  +P TGR
Sbjct: 196 EIKVNFIVDQAMDLTKDYDDVKTRMQICENGKKAITEFEVLSFYPKLNATLLLCKPLTGR 255

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH  +    I+GD  Y
Sbjct: 256 QHQIRVHLFYKNHKILGDPLY 276


>gi|109391494|gb|ABG33874.1| Yen4 [Yersinia sp. MH-1]
          Length = 232

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 60/210 (28%), Positives = 95/210 (45%), Gaps = 22/210 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP+G+    G     ++D      V        L HRLD  TSG++V+A
Sbjct: 20  LYQDDHLVLINKPSGLLSLSGKN-PQNLDSVHHRLVQIF-PGCTLVHRLDFGTSGLMVIA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L + F  R + K+Y +L+ G   N  E + +  + K       + +     K
Sbjct: 78  RNKAINAALCQQFSRRTVTKVYSALLCGHLDN-DEGVIDAAIAKDAALFPLMSICSIRGK 136

Query: 222 GANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            A    SH++V++ F ++           + + P TGRTHQLR+H   +G PI+G     
Sbjct: 137 PAR---SHYRVVERFYRELEDGRLLPLTRVRLIPETGRTHQLRIHCQQLGHPILG----- 188

Query: 274 ANFKGNFTSPIQN---KLYLHARYMDLPHP 300
            +  G    P      +L LHA  +   HP
Sbjct: 189 CDLYGGLRLPGTEQTARLMLHASELHFVHP 218


>gi|197117385|ref|YP_002137812.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
 gi|197086745|gb|ACH38016.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
          Length = 302

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 76/307 (24%), Positives = 133/307 (43%), Gaps = 55/307 (17%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D + +N  P   F  L+K++ SG V+V+       + +++ Q++R             
Sbjct: 14  RMDSFMRNLLPTAQFSYLKKLISSGHVKVN------GSPVEAAQLLRF-----------A 56

Query: 80  EQKILDSSVNLTKHSDFLKSI-----LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFL 133
           +Q  L  S   +K + FL  +     +L+EDS I   NK  G+SV +       ++    
Sbjct: 57  DQVTLKES---SKTAAFLARLTPELDILFEDSWIISLNKAPGLSVHRTEDPDEVNLVDLA 113

Query: 134 KSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           ++ +  +    RL   +RLD+ TSG +++A++  AA    +  +   + K+Y +LV G  
Sbjct: 114 EALLQKRDGVGRLRPVNRLDKGTSGAIILAKSAVAAGMFGKMVQEEGLGKLYLALVEG-- 171

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K +K+ + +  L                  G     S+ ++          L + P TGR
Sbjct: 172 KLQKQGVIDAPL-----------------DGKESQTSYLRLF--HGGGVSLLAVYPITGR 212

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
            HQ+R H   +G PI+GD +Y       FT        LH+    L HP     + I AP
Sbjct: 213 MHQIRQHFKMIGHPILGDKRYGGRALTGFTGHA-----LHSFKTTLVHPATREEVNIPAP 267

Query: 311 LPAHMVK 317
           L   +++
Sbjct: 268 LSEQLMR 274


>gi|327539595|gb|EGF26204.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica WH47]
          Length = 231

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 103/222 (46%), Gaps = 21/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
           ++YED+ + V NKP  ++  G +G    H  G    ++     KP      +  RLD  T
Sbjct: 6   VIYEDNHLLVVNKPTKLATMGAAGQPTLHSLGC--DYIRRTCNKPNKVYLGIVSRLDSMT 63

Query: 155 SGILVVARTRAAAQHLTESFRMRR---IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           SG++V+ART  AA  LT  F        +K Y ++V G  + ++  + + + K       
Sbjct: 64  SGVIVMARTSKAASRLTPQFANHSGDGAKKTYLAVVPGRVEQQQGTLVDDVYKDD--AAY 121

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + V   +   A  A   ++V   + ++   L+++P TGR HQ+R+     G PI+GD K
Sbjct: 122 RMRVAHHSRSDAKEARLEYEV-SGYDRELTLLKVKPLTGRKHQIRLQWAEAGFPILGDTK 180

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y +             + LH+  + + HP +  R+   AP+P
Sbjct: 181 YGSERS------WPTGIALHSWRLSIMHPTKKERMTFEAPVP 216


>gi|329940930|ref|ZP_08290210.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           griseoaurantiacus M045]
 gi|329300224|gb|EGG44122.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           griseoaurantiacus M045]
          Length = 314

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 74/305 (24%), Positives = 130/305 (42%), Gaps = 19/305 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTLPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELASAGKVHVDGSAVGKSERVH 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   ++ E       + +    + +  ++       +      G +V
Sbjct: 60  GGAWLEVEMPQAAAPVRVVAEPV---EGMEIVYDDEDVVVVVKPVGVAAHPSPGWTGTTV 116

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GG   A    G+  S      ++  + HRLD  TSG++VVA++  A   L   F+ R +
Sbjct: 117 IGGLAAA----GYRVS-TSGAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKRQFKERTV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I+ F + 
Sbjct: 172 DKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAEGK---PSVTHYDLIEAF-RA 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
              L+++  TGRTHQ+RVH      P VGD  Y A+        ++  + +LHA  +   
Sbjct: 226 ASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADP--TLAKRLRLTRQWLHAVRLGFE 283

Query: 299 HPEGG 303
           HP  G
Sbjct: 284 HPGDG 288


>gi|226355886|ref|YP_002785626.1| ribosomal large subunit pseudouridine synthase Rlu family
           [Deinococcus deserti VCD115]
 gi|226317876|gb|ACO45872.1| putative Ribosomal large subunit pseudouridine synthase, Rlu family
           [Deinococcus deserti VCD115]
          Length = 252

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 54/203 (26%), Positives = 94/203 (46%), Gaps = 16/203 (7%)

Query: 135 SWVDSKGQKPRLT--HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +++ ++  +P L   HRLD+ETSG  +++R   AA+     F+   + K Y ++V G P 
Sbjct: 47  TYMQTETGEPDLAPPHRLDRETSGAQILSRDSDAARRFFTLFKTHLVGKTYLAIVHGNPT 106

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            ++  +   L      G + V + +        A++ F+V+D  A     +E  P +GR 
Sbjct: 107 WERYTLDAPLGDLGLGGANRVTIRQAVVPDGRAAVTDFQVVDRRA-GHSLIEAYPRSGRL 165

Query: 253 HQLRVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQNKL-----YLHARYMDLPHP 300
           HQ+R H  H+G P+VGD  Y  +        +   T  +  +L      LHA  +     
Sbjct: 166 HQIRAHLHHLGLPMVGDKIYGRDPQAFLDFMETGQTPALTERLGLPRQALHAARIAFSW- 224

Query: 301 EGGRLQITAPLPAHMVKTWDSLG 323
           +G ++ +  PL   +   WDSL 
Sbjct: 225 DGAQMSVEVPLARDLQAYWDSLA 247


>gi|225076909|ref|ZP_03720108.1| hypothetical protein NEIFLAOT_01960 [Neisseria flavescens
           NRL30031/H210]
 gi|224951795|gb|EEG33004.1| hypothetical protein NEIFLAOT_01960 [Neisseria flavescens
           NRL30031/H210]
          Length = 216

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 56/192 (29%), Positives = 86/192 (44%), Gaps = 17/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E     V NKP G+SV   S     +   L   +    ++  L HRLD+ TSG+L+ 
Sbjct: 4   IVFEHEDFVVINKPCGVSVHSESEGDVCLTASLAQQLGV--ERVWLVHRLDKATSGLLLF 61

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R +A  L+  F  + ++K Y +L    P  K+     W+  K  +        K   
Sbjct: 62  ALNRDSAAALSAQFAEKTMRKTYLALGTHKPAKKQ----GWV--KGGMARSRRGTWKLTR 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N+A++ F              +QP TG+THQLRV    +G PI+GD  Y  +  G+ 
Sbjct: 116 DEDNFAVTRFSS-QSLQPGLRLFVLQPFTGKTHQLRVAMKSIGSPILGDTLYGGDEAGH- 173

Query: 281 TSPIQNKLYLHA 292
                  L+LHA
Sbjct: 174 -------LFLHA 178


>gi|297199052|ref|ZP_06916449.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           sviceus ATCC 29083]
 gi|197715994|gb|EDY60028.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           sviceus ATCC 29083]
          Length = 314

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 77/308 (25%), Positives = 130/308 (42%), Gaps = 25/308 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  SG+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAASGKVTVDGSVVGKSERVH 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA--GI 117
            G  + +  P   A   I+ E         +    D    +++ +   +     P   G 
Sbjct: 60  GGAWLEVEMPQAAAPVQIVAE-----PVEGMEIVHDDDDVVVIVKPVGVAAHPSPGWTGT 114

Query: 118 SVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +V GG +   Y I            ++  + HRLD  TSG++VVA++  A   L   F+ 
Sbjct: 115 TVIGGLAAAGYRIS------TSGAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKRQFKE 168

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I+ F
Sbjct: 169 RTVDKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAEGK---PSVTHYDLIEAF 223

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYM 295
            +    L+++  TGRTHQ+RVH      P VGD  Y A+        ++  + +LHA  +
Sbjct: 224 -RAASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADP--TLAKRLRLTRQWLHAVRL 280

Query: 296 DLPHPEGG 303
              HP  G
Sbjct: 281 GFEHPGDG 288


>gi|322514744|ref|ZP_08067770.1| ribosomal large subunit pseudouridine synthase C [Actinobacillus
           ureae ATCC 25976]
 gi|322119339|gb|EFX91455.1| ribosomal large subunit pseudouridine synthase C [Actinobacillus
           ureae ATCC 25976]
          Length = 216

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 103/218 (47%), Gaps = 29/218 (13%)

Query: 98  KSILLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           K  + ++     V +KP G+SV   +   G+   +   L+       ++  L HRLD+ T
Sbjct: 4   KLTICFQHHDFVVIDKPVGVSVHKDEEAVGLTEKLAEQLQV------EQVWLVHRLDKVT 57

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+    + AA +    F   +I+K YW+L    PK K+  I +  ++KS  G   + 
Sbjct: 58  SGLLIFTLNKQAAVNFYHLFEPHKIEKTYWALSNQKPKKKQGKIIS-DMQKSRNGAWKLC 116

Query: 215 VVKQNEKGANYAISHFK--VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             KQN      A++ F    ++   + F    +QP TG+THQLRV    +G PI+GD  Y
Sbjct: 117 HSKQNP-----AVTQFNSHSVEPNLRHFI---LQPKTGKTHQLRVAMKSLGSPILGDQLY 168

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                   T    +++YLHA  +   + +G    I +P
Sbjct: 169 --------TGSEADRVYLHAYQLKFEY-QGESFCIQSP 197


>gi|283470219|emb|CAQ49430.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus ST398]
          Length = 284

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 58/195 (29%), Positives = 89/195 (45%), Gaps = 28/195 (14%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWV 137
           SVNL  ++  L+  +LYED+ I +  KP   +               + YH        V
Sbjct: 65  SVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYH------CQV 116

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +   P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G        
Sbjct: 117 HGENINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKVNLKKIYTCLVYGKTHTSGII 172

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            AN    K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RV
Sbjct: 173 EANIRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRV 225

Query: 258 HALHMGCPIVGDHKY 272
           H  H+G PIVGD  Y
Sbjct: 226 HFQHIGHPIVGDSLY 240


>gi|227892311|ref|ZP_04010116.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
 gi|227865860|gb|EEJ73281.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
          Length = 297

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 93/201 (46%), Gaps = 22/201 (10%)

Query: 96  FLKSILLYEDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           F+   +LYED    + +KPA ++     +     +   + G+ +     +G  P +  RL
Sbjct: 77  FVPIKILYEDDNYLLVDKPAFVASIPSPLHPNDSLVNRVVGYYQIR-GYRGIIPHIVTRL 135

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSGI++ A+ R A   L    +  +I K Y +++ GI  N      N  +    IG 
Sbjct: 136 DRDTSGIVIFAKHRYAHALLDSQLKEHKISKTYTAILSGILHN------NHYIIDLPIGR 189

Query: 211 DYVHVVKQ----NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           D   ++K+    +EK        F          C +++  HTGRTHQ+RVH  ++G P+
Sbjct: 190 DSTSLIKRKVLFSEKAKRSKTEIFVEERIRDNTLCKIKL--HTGRTHQIRVHCSYLGYPL 247

Query: 267 VGDHKYCANFKGNFTSPIQNK 287
           V D  Y     G  + P+Q +
Sbjct: 248 VSDTLY----GGTISMPLQRQ 264


>gi|241895991|ref|ZP_04783287.1| 23S rRNA pseudouridylate synthase RluD [Weissella paramesenteroides
           ATCC 33313]
 gi|241870722|gb|EER74473.1| 23S rRNA pseudouridylate synthase RluD [Weissella paramesenteroides
           ATCC 33313]
          Length = 305

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 70/279 (25%), Positives = 130/279 (46%), Gaps = 32/279 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
            GQV ++ + V+  + ++ G +V +       N I+                  L   +L
Sbjct: 37  GGQVLLNHRPVRTLDDVEPGDLVEVKMPAEKSNAIVAASD--------------LPIKIL 82

Query: 103 YEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGIL 158
           YED    V +K AG+ SV G +     +   +K ++ S+G +   P +  RLD+ TSG+ 
Sbjct: 83  YEDENWLVVDKVAGVTSVPGKADRETTMVNRVKGYLISEGAEDLVPHVVTRLDRFTSGVA 142

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+ R A   L +  +   + K Y+++V GI  +    I   +     +  D++   ++
Sbjct: 143 LLAKHRFAHGLLDKQLQTHTVDKRYYAIVDGIVPDDHGFIDAPI---GRMDNDFIR--RE 197

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  + + + V++    +   +++Q HTGRTHQ+RVH  ++G P++GD  Y     G
Sbjct: 198 VRADGRPSQTEYWVVNRMPNQ-TLVKVQLHTGRTHQIRVHFKYIGHPLIGDEIYG----G 252

Query: 279 NFTSPIQNKLYLHARYMDL--PHPEGGRLQITAPLPAHM 315
                I+ +  LHA +++   P  E  R  I +PLP  +
Sbjct: 253 PMDRGIERQA-LHAYWLEFYDPFSEIKR-HIQSPLPEDL 289


>gi|59711627|ref|YP_204403.1| 23S rRNA and tRNA pseudouridine synthase (RluA-like) [Vibrio
           fischeri ES114]
 gi|59479728|gb|AAW85515.1| 23S rRNA and tRNA pseudouridine synthase (RluA-like) [Vibrio
           fischeri ES114]
          Length = 228

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 96/210 (45%), Gaps = 18/210 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY++S   V NK   +SV    G    +    K   D   ++  L HRLD+ TSG+L++
Sbjct: 4   ILYQNSDFLVINKHPNVSVHKDDGETSLLIELAKETGD---KQLYLIHRLDKMTSGLLLI 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R +AAA  L++ F  R ++K Y ++    PK K+  +   + +        V+  +   
Sbjct: 61  GRNQAAASELSQLFANRLVEKYYLAIGDKKPKKKQGLVIGDMERSRRASWKLVNSKE--- 117

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F           +L  +PHTG+THQ+RV    +G  I+GD  Y        
Sbjct: 118 ---NPAVTQFFSTAANDGNRLFL-CKPHTGKTHQIRVALKSVGSGILGDPIY-------- 165

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           +S   ++ YLHA  +   + E     I  P
Sbjct: 166 SSSNADRGYLHAYALRFTYQEQAFEFIETP 195


>gi|296112643|ref|YP_003626581.1| tRNA pseudouridine synthase C [Moraxella catarrhalis RH4]
 gi|295920337|gb|ADG60688.1| tRNA pseudouridine synthase C [Moraxella catarrhalis RH4]
 gi|326563862|gb|EGE14113.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 46P47B1]
 gi|326566871|gb|EGE17010.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 103P14B1]
 gi|326576787|gb|EGE26694.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 101P30B1]
          Length = 254

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 101/240 (42%), Gaps = 23/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + + NKPA + V       +     +++  +   Q     HRLD+ TSG+LV 
Sbjct: 15  ILYQDACMVIINKPANMLVHRSWLDKHETCFVVQTLRNQINQHVYPVHRLDRPTSGVLVF 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVHVVKQ 218
           A     A  L + F    IQK Y ++V GI    +    ++ LK     I   +      
Sbjct: 75  ALDSQTAGLLAKQFENHHIQKSYLAVVRGIIGTGR---IDYALKPRLDKIADKF----SN 127

Query: 219 NEKGANYAISHFKVIDCFAQKF-----------CWLEMQPHTGRTHQLRVHALHMGCPIV 267
             K +  AI+ ++V+    Q F             + + P TGR HQLR H  H+  PIV
Sbjct: 128 PNKASKSAITDYQVLATTQQPFISCRRFDSSRYSLVCLTPITGRKHQLRRHMKHIFHPIV 187

Query: 268 GDHKYCANF--KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
           GD  Y      +         +L LHA  +   HP    + +I APL     +   + G+
Sbjct: 188 GDTTYGDKVQNRAVLAHIGVKRLLLHAHQLQFCHPLYDEMIRIVAPLDTAFCQVMTAFGW 247


>gi|227540229|ref|ZP_03970278.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
 gi|227239953|gb|EEI89968.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
          Length = 247

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 58/188 (30%), Positives = 89/188 (47%), Gaps = 13/188 (6%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           S   L K   F   ++++ED  I V NKP  I S+    G   +I    K +        
Sbjct: 4   SEAKLFKFPKFT-DLIIHEDENIIVINKPPFIASLDEREGGEVNILRLAKKYYAD----A 58

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           ++ HRLD+ETSGIL++A+     + ++  F  RR+ K Y +++ G    +   I   +L 
Sbjct: 59  QICHRLDKETSGILLIAKNPETYRLISIEFEKRRVDKTYHAIIEGTHIFQDLKIDLPILN 118

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +   G   V + + N K A    + F  I  F + F  +E +P TGR HQ+R+H      
Sbjct: 119 Q---GNKNVTIDRYNGKPAE---TIFNSIQYF-KHFTLVECKPITGRMHQIRIHLATQHA 171

Query: 265 PIVGDHKY 272
            IVGD  Y
Sbjct: 172 AIVGDSMY 179


>gi|330718647|ref|ZP_08313247.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc fallax KCTC
           3537]
          Length = 301

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 66/269 (24%), Positives = 126/269 (46%), Gaps = 38/269 (14%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
            G + V++K V  ++ ++ G  V I  PV  + + ++ + + +D               +
Sbjct: 36  GGAILVNEKPVYTSDFLKQGDSVTIIMPVEESNDLVVPDYRPMD---------------I 80

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYH-----IDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++E+    + NKP G++   G     H     + G L+  ++++   P +  RLD++TSG
Sbjct: 81  IFENEHWLIVNKPFGVTTVPGHADRLHTLVNQVKGHLEE-IEAEDLVPHVVTRLDRDTSG 139

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHV 215
           ++++A+ R A   L +  +   ++K Y +   GI  +N  E  A        + GD++  
Sbjct: 140 LVLLAKHRFAHAVLDDQLQRHEVEKFYVAYPSGILEQNHGEINA----PIGRMDGDFIK- 194

Query: 216 VKQNEKGANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            ++  +    +++ + V D            +++Q HTGRTHQ+RVH  ++G P+VGD  
Sbjct: 195 -REVREDGKPSLTEYWVEDVIGADTPHPMTRVKVQLHTGRTHQIRVHFSNIGHPLVGDDL 253

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y     G     IQ +  LHA +M    P
Sbjct: 254 YG----GPLVHNIQRQA-LHAYHMRFYDP 277


>gi|255505626|ref|ZP_05347239.3| ribosomal large subunit pseudouridine synthase, RluD family
           [Bryantella formatexigens DSM 14469]
 gi|255266705|gb|EET59910.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Bryantella formatexigens DSM 14469]
          Length = 342

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 56/210 (26%), Positives = 101/210 (48%), Gaps = 26/210 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGI 157
           +LYED  +    K AG+ +    G  +  +  +L+ ++  KG  ++ R   RLD++TSGI
Sbjct: 103 ILYEDEDLICVWKEAGMVLHPAHGHYSDSLANYLQGYLAGKGGQEQVRGIGRLDKDTSGI 162

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN---KKECIANWLLKKSHIGGDYVH 214
           +V AR R AA  L +  +  R QK Y +L  G+  +   ++E   +  ++K     + + 
Sbjct: 163 VVFARNRIAAARLWQQRQSGRFQKEYVALCEGVFPDEAYEREQTIDAPIQKVTGEKNKMC 222

Query: 215 VVKQN--EKGANYAISHFKVI----DCF--------------AQKFCWLEMQPHTGRTHQ 254
           +V++        +A++H++ I     CF               ++   + +   TGRTHQ
Sbjct: 223 IVQERCCPAAGCFAVTHYRAISEKESCFHEAMRLLSAGDLPGPEQASLVRLHLETGRTHQ 282

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           +RVH  ++G P+VGD  Y     G   + +
Sbjct: 283 IRVHMAYIGHPLVGDAVYGRGIAGQTCAKL 312


>gi|300771948|ref|ZP_07081819.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33861]
 gi|300761334|gb|EFK58159.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33861]
          Length = 247

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 58/188 (30%), Positives = 89/188 (47%), Gaps = 13/188 (6%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           S   L K   F   ++++ED  I V NKP  I S+    G   +I    K +        
Sbjct: 4   SEAKLFKFPKFT-DLIIHEDENIIVINKPPFIASLDEREGGEINILRLAKKYYAD----A 58

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           ++ HRLD+ETSGIL++A+     + ++  F  RR+ K Y +++ G    +   I   +L 
Sbjct: 59  QICHRLDKETSGILLIAKNPETYRLISIEFEKRRVDKTYHAIIEGTHIFQDLKIDLPILN 118

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +   G   V + + N K A    + F  I  F + F  +E +P TGR HQ+R+H      
Sbjct: 119 Q---GNKNVTIDRYNGKPAE---TIFNSIQYF-KHFTLVECKPITGRMHQIRIHLATQHA 171

Query: 265 PIVGDHKY 272
            IVGD  Y
Sbjct: 172 AIVGDSMY 179


>gi|332187172|ref|ZP_08388912.1| RNA pseudouridylate synthase family protein [Sphingomonas sp. S17]
 gi|332012872|gb|EGI54937.1| RNA pseudouridylate synthase family protein [Sphingomonas sp. S17]
          Length = 214

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 59/213 (27%), Positives = 98/213 (46%), Gaps = 15/213 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D +  V +KPAG+ V      +  ++  L+S      + P+  HRLD++TSG L++
Sbjct: 6   VLFIDGEALVIDKPAGLPVDPPRDGSLSLENHLESLRFGFKRWPQAVHRLDRDTSGCLLL 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           +R   A     ++F   +++K Y +++ G+ + +   I   L K S     +  V     
Sbjct: 66  SRNPKAHARFQQAFEAGQVEKRYLAVLDGVVEGEG-MIDLALAKVSTREAGWRMVADPAG 124

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCANFKGN 279
           K A       +           +E +P TGRTHQ+RVH A  +G  +VGD  Y A   G 
Sbjct: 125 KAARTGWRALR----HEGGRTLVEFRPETGRTHQIRVHAATGLGAAVVGDPVYGAGEAGG 180

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                   + LHA  + +P  +  +  ITA  P
Sbjct: 181 --------MLLHAASLTVPRGD-AKDPITAEAP 204


>gi|303228397|ref|ZP_07315230.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302516899|gb|EFL58808.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 306

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 110/239 (46%), Gaps = 43/239 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV----DSKGQKPRL--THRLDQET 154
           ++YED  I   NK AG+ +   S +    DG L + V    D   Q       HRLD++T
Sbjct: 81  IVYEDDYILAVNKAAGVLMHPTSTVR---DGTLANGVLYYYDETEQAHDFHPVHRLDKDT 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI----------PKNKKE-------C 197
           SGI+++A+T +  QH  +  R +  +K+Y ++V G           P  +K        C
Sbjct: 138 SGIVIIAKT-SIVQHAFDKQRTK-FKKVYDAIVEGTMPSQSLTIKWPIGRKAGSIIERCC 195

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            +     ++ +     H+V Q  +  N  +S  +V+       C L    HTGRTHQ+RV
Sbjct: 196 TSIGKPARTDVTVLARHIVSQPVQ-MNKNLSTQQVL---THVQCVL----HTGRTHQIRV 247

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           H  H+G P+ GD  Y     G     I+ +  LHA Y+   HP     +++ AP+P  M
Sbjct: 248 HLSHLGYPLAGDDLY-----GGHLDHIRRQA-LHAGYLAFTHPMTQEYIELRAPMPTDM 300


>gi|229056939|ref|ZP_04196335.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH603]
 gi|228720467|gb|EEL72040.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH603]
          Length = 292

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 68/287 (23%), Positives = 131/287 (45%), Gaps = 46/287 (16%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
            R G + V+ +     +++Q+G+ ++I   +   +  ++ ++I                 
Sbjct: 33  FRGGAIEVNGQHTSVRHKLQAGEELQIFFPVEERSEGMEVEEI--------------PLC 78

Query: 101 LLYEDSKIYVFNKPAGISV------QGGS---GIAYHIDG-FLKSWVDSKGQKPRLTHRL 150
           ++YED  + V NK A +S         GS    + YH D   L S V        +  RL
Sbjct: 79  IVYEDDAVLVINKEANMSTIPSREHPSGSIANALLYHYDKQNLASTV-------HIVTRL 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ R     L++  + + +++ Y ++V G    +   I   + +K+    
Sbjct: 132 DRDTSGLMLIAKNRFVHHLLSKQHQQKGVKRTYEAIVHGTILEEVGTIDAPIGRKA---- 187

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D +      E G   A++HF+V++  + K   + ++  TGRTHQ+RVH  ++G P++GD 
Sbjct: 188 DSIIERTVCEDGQR-AVTHFRVMESSSDK-THVALELETGRTHQIRVHMAYIGHPLIGDD 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPAHM 315
            Y           +  +  LH+  +   HP  E G +  T  +P  M
Sbjct: 246 LYGGR------RDVIKRQALHSTSLTFYHPILEKG-MTFTVSIPEDM 285


>gi|123442854|ref|YP_001006830.1| putative ribosomal large subunit pseudouridine synthase [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|122089815|emb|CAL12670.1| putative ribosomal large subunit pseudouridine synthase [Yersinia
           enterocolitica subsp. enterocolitica 8081]
          Length = 232

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 102/228 (44%), Gaps = 21/228 (9%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H    K   LY+D  + + NKP G+    G     ++D      V    
Sbjct: 3   KIVDTFIAPLCHD---KIETLYQDDHLVLINKPTGLLSLSGKN-PQNLDSVHHRLVQIF- 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   +  E + + 
Sbjct: 58  PGCTLVHRLDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCG-HLDDNEGVIDA 116

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF--------AQKFCWLEMQPHTGRTH 253
            + K       + +   + K A    S ++V++ F        +     +++ P TGRTH
Sbjct: 117 AIAKDPALFPLMLICATHGKPAR---SGYRVVERFYHELEDGRSLPLTRVQLIPETGRTH 173

Query: 254 QLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
           QLR+H   +G PI G   Y      G   +P   +L LHA  +   HP
Sbjct: 174 QLRIHCQQLGHPIWGCDLYGGRLLPGTEQTP---RLMLHASELHFVHP 218


>gi|312884566|ref|ZP_07744270.1| pseudouridine synthase Rlu family protein [Vibrio caribbenthicus
           ATCC BAA-2122]
 gi|309367878|gb|EFP95426.1| pseudouridine synthase Rlu family protein [Vibrio caribbenthicus
           ATCC BAA-2122]
          Length = 230

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 58/195 (29%), Positives = 97/195 (49%), Gaps = 23/195 (11%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           + L++D    V NK   +SV    G     D  L   + SK   ++  L HRLD+ TSG+
Sbjct: 5   VFLHDD--FIVINKHPNVSVHKDDG-----DTMLLQEISSKTGDEQLYLVHRLDKMTSGL 57

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++AR   AA+ L+E F +R+++K Y ++  G PK K+  I   +++        V  + 
Sbjct: 58  MLIARHVDAARKLSEQFALRQVEKFYLAIGSGKPKKKQGLICGDMVRSRRSSWKLVKSLD 117

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                  ++IS    +  +    C    +P+TG+THQ+RV    +G  I+GD  Y A+ K
Sbjct: 118 NPATTQFFSISAGPGLRLY---LC----KPYTGKTHQIRVALKSIGGAILGDPIY-ADPK 169

Query: 278 GNFTSPIQNKLYLHA 292
            +      ++ YLHA
Sbjct: 170 AS------DRGYLHA 178


>gi|310287036|ref|YP_003938294.1| Ribosomal large subunit pseudouridine synthase [Bifidobacterium
           bifidum S17]
 gi|291045148|dbj|BAI82361.1| pseudouridine synthase [Bifidobacterium bifidum]
 gi|309250972|gb|ADO52720.1| Ribosomal large subunit pseudouridine synthase [Bifidobacterium
           bifidum S17]
          Length = 313

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 75/281 (26%), Positives = 123/281 (43%), Gaps = 41/281 (14%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+      ++ SGQ RV  + +  +  +  G+ V            I E++     V   
Sbjct: 26  ISRAKAADLIESGQARVLDRAIAKSGTLLYGETVEFD---------IAEERHEPEPV--- 73

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWV--DSKGQKPR-- 145
                L   ++YED  + V +KP G++    +G      +   LK  V   S G   R  
Sbjct: 74  ----CLDMAIVYEDDDVVVVDKPVGVAAHASAGWTGPTVLGSLLKRGVRITSYGAPGRQG 129

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD  TSG+++V ++  A + +   F    + K Y ++V G  K  K  I      +
Sbjct: 130 IVSRLDVGTSGLMLVCKSELAYKEMRRQFSEHEVVKTYHAMVQGNLKEDKATI------E 183

Query: 206 SHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + IG     D+   V  + K    A++H+ V+D F +    + +   TGRTHQ+RVH   
Sbjct: 184 APIGRAKVSDFRFCVTPSGK---PAVTHWDVLDRFGEA-TLVSVNLETGRTHQIRVHFSS 239

Query: 262 MGCPIVGDHKYCAN--FKGNFTSPIQNKLYLHARYMDLPHP 300
           +G P+VGD  Y AN    G       ++ +LHA  ++  HP
Sbjct: 240 IGHPLVGDPMYGANPVLAGELG---LDRQWLHAMKLEFRHP 277


>gi|229488989|ref|ZP_04382855.1| pseudouridylate synthase [Rhodococcus erythropolis SK121]
 gi|229324493|gb|EEN90248.1| pseudouridylate synthase [Rhodococcus erythropolis SK121]
          Length = 307

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 61/208 (29%), Positives = 99/208 (47%), Gaps = 12/208 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  I V +KP  + S   G  IA      L+  ++     P   HRLD+ T+G+L+
Sbjct: 90  ILYRDENILVVDKPHFLASTPRGRYIAESALVRLRRDLELPELSP--AHRLDRVTAGLLL 147

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               +AA +     F  RR+ K Y ++           ++  ++ +S I  +   V+K  
Sbjct: 148 FTVHQAARRDYQTMFAERRVAKEYEAIA-----RHDAQVSTPVVVRSRIVKER-GVLKAA 201

Query: 220 E-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           E +G   + S  ++I+     F    + PHTG+THQLR+H   +G PI GD+ Y  +F  
Sbjct: 202 EIEGEPNSESRIELIET-RDGFARYRLTPHTGKTHQLRLHMTSLGLPIHGDNFY-PDFYD 259

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
                  N L L ++ ++   P+ GRLQ
Sbjct: 260 VAAEDYSNPLRLLSKVLEFEDPKTGRLQ 287


>gi|192361541|ref|YP_001981578.1| ribosomal large subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
 gi|190687706|gb|ACE85384.1| ribosomal large subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
          Length = 221

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 58/204 (28%), Positives = 92/204 (45%), Gaps = 14/204 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL ED    + +KP  +    G           +   D  G    + HRLD +TSG++V+
Sbjct: 20  LLREDEDFLLIHKPTRLLSVPGRHPQNRDSVIARLLPDYPGAT--IVHRLDFDTSGVMVI 77

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
              + A  H+++ F+ R + K Y ++V G+   ++  I   L   S  G  Y    K   
Sbjct: 78  PLNKPALSHISKQFQARSVSKHYTAVVAGLVGQEQGVID--LPIASGEGPTY----KICR 131

Query: 221 KGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                +++ F+V+    A     L + P TGR+HQLR+H   +G PI+G    C  + G 
Sbjct: 132 TSGKPSVTEFRVLARDQAANTSRLVLHPITGRSHQLRLHLQAIGHPILG----CEFYGGT 187

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG 303
           + S    +L LHA  +   HP  G
Sbjct: 188 YAS-AAPRLLLHATDLGFRHPSTG 210


>gi|312874385|ref|ZP_07734416.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
 gi|311090151|gb|EFQ48564.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
          Length = 307

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 138 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 196

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 197 PIGKKDDPVKRYIM------EGGKESVTKYRVIKQVAGA-SLVELQLLTGRTHQIRVHMQ 249

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F     ++  LH   +    P E  R+++    PA MV+ W
Sbjct: 250 YLGHPLFGDHLY--GVEDDF-----HRQALHCFLLAFDDPLEHKRIEVQIADPADMVQLW 302

Query: 320 DSL 322
             L
Sbjct: 303 QKL 305


>gi|90962277|ref|YP_536193.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|90821471|gb|ABE00110.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
          Length = 295

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 93/201 (46%), Gaps = 22/201 (10%)

Query: 96  FLKSILLYEDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           F+   +LYED    + +KPA ++     +     +   + G+ +     +G  P +  RL
Sbjct: 75  FVPIKILYEDDNYLLVDKPAFVASIPSPLHPNDSLVNRVVGYYQIR-GYRGIIPHIVTRL 133

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSGI++ A+ R A   L    +  +I K Y +++ GI  N      N  +    IG 
Sbjct: 134 DRDTSGIVIFAKHRYAHALLDSQLKEHKISKTYTAILSGILHN------NHYIIDLPIGR 187

Query: 211 DYVHVVKQ----NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           D   ++K+    +EK        F          C +++  HTGRTHQ+RVH  ++G P+
Sbjct: 188 DSTSLIKRKVLFSEKAKRSKTEIFVEERIRDNTLCKIKL--HTGRTHQIRVHCSYLGYPL 245

Query: 267 VGDHKYCANFKGNFTSPIQNK 287
           V D  Y     G  + P+Q +
Sbjct: 246 VSDTLY----GGTISMPLQRQ 262


>gi|197336314|ref|YP_002155824.1| pseudouridine synthase Rlu family protein [Vibrio fischeri MJ11]
 gi|197317804|gb|ACH67251.1| pseudouridine synthase Rlu family protein [Vibrio fischeri MJ11]
          Length = 227

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 58/201 (28%), Positives = 90/201 (44%), Gaps = 36/201 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY++S   V NK   +SV    G    +    K   D   ++  L HRLD+ TSG+L++
Sbjct: 4   ILYQNSNFLVINKHPNVSVHKDDGETSLLIELAKETGD---KQLYLIHRLDKMTSGLLLI 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI---------ANWLLKKSHIGGD 211
            R +AAA  L++ F  R ++K Y ++    PK K+  +         A+W L  S     
Sbjct: 61  GRNQAAASELSQLFANRLVEKYYLAIGDKKPKKKQGLVIGDMERSRRASWKLINSKENPA 120

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                    +G N      ++  C          +PHTG+THQ+RV    +G  I+GD  
Sbjct: 121 VTQFFSTAAQGGN------RLFLC----------KPHTGKTHQIRVALKSVGSGILGDPI 164

Query: 272 YCANFKGNFTSPIQNKLYLHA 292
           Y        +S   ++ YLHA
Sbjct: 165 Y--------SSSNADRGYLHA 177


>gi|152999968|ref|YP_001365649.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|160874589|ref|YP_001553905.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|151364586|gb|ABS07586.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|160860111|gb|ABX48645.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315266830|gb|ADT93683.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 287

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 106/247 (42%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LYED  +   +KPAG+ V   S +A     F      D  G      HRLD+ TSG+L+
Sbjct: 32  ILYEDEHLVAIHKPAGLLVHR-SYLARRERFFAMQLTRDLVGCHVFPVHRLDRPTSGVLL 90

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A++   A  L E F    I+K Y +LV G     +  I ++ LK        V + +  
Sbjct: 91  FAKSSEVANALCEQFASHTIEKQYLALVRG--NMHESGILDYALK--------VELDELG 140

Query: 220 EKGANYAISHFKVIDCF----------------AQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +K A+   +  + +  +                  +F  + + P TGR HQLR H  H+ 
Sbjct: 141 DKNADPNKAAQEAVTAYEPLLNTEIPYPSGRYPTSRFALVRLSPKTGRKHQLRRHMAHLR 200

Query: 264 CPIVGDH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            PIVGD      K  A F+ +F     N+L+L A+ +   HP    RL I   L      
Sbjct: 201 HPIVGDTTHGDGKQNAFFREHFGI---NRLWLIAKKLSFTHPVTQVRLSIETELEPQWET 257

Query: 318 TWDSLGF 324
            +  LG+
Sbjct: 258 VFAELGW 264


>gi|305432550|ref|ZP_07401711.1| RNA pseudouridine synthase [Campylobacter coli JV20]
 gi|304444261|gb|EFM36913.1| RNA pseudouridine synthase [Campylobacter coli JV20]
          Length = 334

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 60/201 (29%), Positives = 99/201 (49%), Gaps = 17/201 (8%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKS 135
           ++ KIL   V L  + +  K + +++E+    +  K +GI S   G    Y + D     
Sbjct: 84  EKNKILKGDVELIVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL 143

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W    G+K  + HRLD+ETSG+++VA+ + A   L   F  ++IQK Y +L  G      
Sbjct: 144 W----GKKACVAHRLDKETSGLILVAKHKEAQIELKTMFEKKQIQKEYLALASG------ 193

Query: 196 ECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           E   N+++ ++  +  DY  V    Q  +    AI+ F+V+  + +     L  +P TGR
Sbjct: 194 EIKVNFIVDQAMDLTKDYDDVKTRMQICENGKKAITEFEVLSFYPKLNATLLLCKPLTGR 253

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH  +    I+GD  Y
Sbjct: 254 QHQIRVHLFYKNHKILGDPLY 274


>gi|326577536|gb|EGE27413.1| tRNA pseudouridine synthase C [Moraxella catarrhalis O35E]
          Length = 258

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 101/240 (42%), Gaps = 23/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + + NKPA + V       +     +++  +   Q     HRLD+ TSG+LV 
Sbjct: 19  ILYQDACMVIINKPANMLVHRSWLDKHETCFVVQTLRNQINQHVYPVHRLDRPTSGVLVF 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVHVVKQ 218
           A     A  L + F    IQK Y ++V GI    +    ++ LK     I   +      
Sbjct: 79  ALDSQTAGLLAKQFENHHIQKSYLAVVRGIIGTGR---IDYALKPRLDKIADKF----SN 131

Query: 219 NEKGANYAISHFKVIDCFAQKF-----------CWLEMQPHTGRTHQLRVHALHMGCPIV 267
             K +  AI+ ++V+    Q F             + + P TGR HQLR H  H+  PIV
Sbjct: 132 PNKASKSAITDYQVLATTQQPFISCRRFDSSRYSLVCLTPITGRKHQLRRHMKHIFHPIV 191

Query: 268 GDHKYCANF--KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
           GD  Y      +         +L LHA  +   HP    + +I APL     +   + G+
Sbjct: 192 GDTTYGDKVQNRAVLAHIGVKRLLLHAHQLQFCHPLYDEMIRIVAPLDTAFCQVMTAFGW 251


>gi|228906938|ref|ZP_04070805.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis IBL 200]
 gi|228852686|gb|EEM97473.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis IBL 200]
          Length = 292

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 56/207 (27%), Positives = 104/207 (50%), Gaps = 23/207 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++YED  + + +K A +S         GS     +  + K ++ S      +  RLD++T
Sbjct: 79  IVYEDDAVLIIDKEANMSTIPSREHPTGSVANALLSHYDKQYLAST---VHIVTRLDRDT 135

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS    D + 
Sbjct: 136 SGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGMIDAPIGRKS----DSII 191

Query: 215 VVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                E G   A++HFKVI   + +    LE++  TGRTHQ+RVH  H+G P++GD    
Sbjct: 192 ERTVCEDG-QRAVTHFKVIGSTYHKTHVALELE--TGRTHQIRVHMAHIGHPLLGD---- 244

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            N  G     ++ +  LH++ +   HP
Sbjct: 245 -NLYGGRRDEMKRQ-ALHSKSLTFYHP 269


>gi|311063909|ref|YP_003970634.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           bifidum PRL2010]
 gi|310866228|gb|ADP35597.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           bifidum PRL2010]
          Length = 313

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 75/281 (26%), Positives = 123/281 (43%), Gaps = 41/281 (14%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+      ++ SGQ RV  + +  +  +  G+ V            I E++     V   
Sbjct: 26  ISRAKAADLIESGQARVLNRAIAKSGTLLYGETVEFD---------IAEERHEPEPV--- 73

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWV--DSKGQKPR-- 145
                L   ++YED  + V +KP G++    +G      +   LK  V   S G   R  
Sbjct: 74  ----CLDMAIVYEDDDVVVVDKPVGVAAHASAGWTGPTVLGSLLKRGVRITSYGAPGRQG 129

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD  TSG+++V ++  A + +   F    + K Y ++V G  K  K  I      +
Sbjct: 130 IVSRLDVGTSGLMLVCKSELAYKEMRRQFSEHEVVKTYHAMVQGNLKEDKATI------E 183

Query: 206 SHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + IG     D+   V  + K    A++H+ V+D F +    + +   TGRTHQ+RVH   
Sbjct: 184 APIGRAKVSDFRFCVTPSGK---PAVTHWDVLDRFGEA-TLVSVNLETGRTHQIRVHFSS 239

Query: 262 MGCPIVGDHKYCAN--FKGNFTSPIQNKLYLHARYMDLPHP 300
           +G P+VGD  Y AN    G       ++ +LHA  ++  HP
Sbjct: 240 IGHPLVGDPMYGANPVLAGELG---LDRQWLHAMKLEFRHP 277


>gi|154173855|ref|YP_001407891.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           curvus 525.92]
 gi|112803415|gb|EAU00759.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           curvus 525.92]
          Length = 323

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 106/234 (45%), Gaps = 35/234 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLD 151
           ++YED  I V NKP  I V     +    +  L  W++ KG          +  + HRLD
Sbjct: 78  VIYEDEDILVLNKPPQIVVHQAPSVK---EATLVEWLNQKGFMLSNLNGDLRAGIVHRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG +VVA+  AA   L+     + + +IY +L   +P  K+ECI +  + +S     
Sbjct: 135 KGTSGAIVVAKNNAAHAALSAQLNDKSMGRIYLALT-DLPL-KQECIIDKPIGRSPSNRL 192

Query: 212 YVHVVK--QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            + +V   ++ K A   +     ++  A K         TGRTHQ+R H   +   I+GD
Sbjct: 193 KMGIVTNGRHAKSAFLNLVQTDEVNLIAAKL-------FTGRTHQIRAHLASINRHILGD 245

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           + Y   FK      I+ ++ LHA  +   HP  G +++  A       +TWD  
Sbjct: 246 NLY--GFKSE-NDKIK-RVMLHAYMLYFFHPRSGEKVEFIA-------QTWDDF 288


>gi|116491175|ref|YP_810719.1| pseudouridylate synthase, 23S RNA-specific [Oenococcus oeni PSU-1]
 gi|290890691|ref|ZP_06553761.1| hypothetical protein AWRIB429_1151 [Oenococcus oeni AWRIB429]
 gi|116091900|gb|ABJ57054.1| Pseudouridylate synthase, 23S RNA-specific [Oenococcus oeni PSU-1]
 gi|290479666|gb|EFD88320.1| hypothetical protein AWRIB429_1151 [Oenococcus oeni AWRIB429]
          Length = 299

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 75/278 (26%), Positives = 131/278 (47%), Gaps = 34/278 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
            G++ V+ + V  N+ +++G+ + I  PP         +E   LD+       +D LK  
Sbjct: 36  GGKIVVEGREVFTNDYVKNGEKITIFMPPE--------RENVELDADF-----TDPLK-- 80

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKS-WVDSKGQK--PRLTHRLDQETSG 156
           +++ED    + +KPA ++ V G +     +   +K+  +  K     P +  RLD++TSG
Sbjct: 81  VVFEDKNFLIVDKPAFVTTVPGHADRKTTLVNMIKAHLIQEKADSLVPHVVTRLDRDTSG 140

Query: 157 ILVVARTRAAAQHLTESF-RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           ++++A+ + A   L ++      I+K Y +LV G  +     I   +     I GD++  
Sbjct: 141 LVLLAKHKFAHALLNDALMEHHDIEKFYVALVSGNFQEDHGMIDEPI---GRIEGDFIR- 196

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +Q  +    +++ + V   F   F  L +Q HTGRTHQ+RVH    G P++GD  Y   
Sbjct: 197 -RQVRQDGKRSVTEYWVEKRF-DNFTQLRIQLHTGRTHQIRVHMAWAGHPLIGDVLY--- 251

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
             G   S + ++  LHA  M    P   + Q   A LP
Sbjct: 252 --GGPHSKLISRQALHASEMIFFDPFANKNQHFNAGLP 287


>gi|303289713|ref|XP_003064144.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226454460|gb|EEH51766.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 360

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 65/258 (25%), Positives = 107/258 (41%), Gaps = 39/258 (15%)

Query: 101 LLYEDSKIYVFNKPAGI------SVQGGSGI---AYHIDGFLKSWVDSKG-------QKP 144
           +LYED  +   +KP G+       ++GGS +    +H+ G  +               +P
Sbjct: 39  VLYEDEHVLAVDKPPGVMTYPAHRLRGGSVVNRAVHHLRGVTRDGSGGGAGFGFGAATEP 98

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL--VWGIPKNKKECIANWL 202
              HRLD ETSG+L++A+ + +A  L  +F  R  +K Y ++  +     N  +   +  
Sbjct: 99  IAVHRLDLETSGVLMLAKDKPSASALQGAFERREARKTYLAVCAILEDAANASDESDDDF 158

Query: 203 LKKSHIG-------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             + H G          VH   + + G       F               +P TGRTHQ+
Sbjct: 159 DFERHPGHRRRERRRRAVHT--RGDAGREAREHRFTGKRIVGTALVL--ARPLTGRTHQV 214

Query: 256 RVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           R+H  H G PIVGD  Y  +       G F    + ++ LHA  + + HP     +++  
Sbjct: 215 RLHLAHAGLPIVGDALYGYDDALRPASGGF----EGRMALHAWNLAVKHPRTKNTMRLAV 270

Query: 310 PLPAHMVKTWDSLGFKYD 327
            +PA M      LG + +
Sbjct: 271 DMPADMQALSVGLGLRVE 288


>gi|126173680|ref|YP_001049829.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125996885|gb|ABN60960.1| tRNA pseudouridine synthase C [Shewanella baltica OS155]
          Length = 287

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 107/248 (43%), Gaps = 39/248 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LYED  +   +KPAG+ V   S +A     F      D  G      HRLD+ TSG+L+
Sbjct: 32  ILYEDEHLVAIHKPAGLLVHR-SYLARRERFFAMQLTRDLVGCHVFPVHRLDRPTSGVLL 90

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQ 218
            A++   A  L E F    I+K Y +LV G   N  E  I ++ LK        V + + 
Sbjct: 91  FAKSSEVANALCEQFASHTIEKQYLALVRG---NMHESGILDYALK--------VELDEL 139

Query: 219 NEKGANYAISHFKVIDCF----------------AQKFCWLEMQPHTGRTHQLRVHALHM 262
            +K A+   +  + +  +                  +F  + + P TGR HQLR H  H+
Sbjct: 140 GDKNADPNKAAQEAVTAYEPLLNTEIPYPSGRYPTSRFALVRLSPKTGRKHQLRRHMAHL 199

Query: 263 GCPIVGDH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
             PIVGD      K  A F+ +F     N+L+L A+ +   HP    RL I   L     
Sbjct: 200 RHPIVGDTTHGDGKQNAFFREHFGI---NRLWLIAKKLSFTHPVTQVRLSIETELEPEWE 256

Query: 317 KTWDSLGF 324
             +  LG+
Sbjct: 257 TVFAELGW 264


>gi|312874750|ref|ZP_07734769.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
 gi|311089495|gb|EFQ47920.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
          Length = 302

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 133 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 191

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 192 PIGKKDDPVKRYIM------EGGKESVTKYRVIKQVAGA-SLVELQLLTGRTHQIRVHMQ 244

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F     ++  LH   +    P E  R+++    PA MV+ W
Sbjct: 245 YLGHPLFGDHLY--GVEDDF-----HRQALHCFLLAFDDPLEHKRIEVQIADPADMVQLW 297

Query: 320 DSL 322
             L
Sbjct: 298 QKL 300


>gi|109899489|ref|YP_662744.1| pseudouridylate synthase [Pseudoalteromonas atlantica T6c]
 gi|109701770|gb|ABG41690.1| tRNA pseudouridine synthase C [Pseudoalteromonas atlantica T6c]
          Length = 252

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 63/213 (29%), Positives = 96/213 (45%), Gaps = 18/213 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   +KPAG+ V   S I  H   F ++   D  GQ     HRLD+ TSG+LV
Sbjct: 5   ILYQDECLVAIHKPAGLLVHR-SMIDRHETQFAMQMLRDQIGQHVFPVHRLDRPTSGVLV 63

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A +   A+ L E F    I K Y+++V G    K+  + ++ LK+            + 
Sbjct: 64  FALSADIARLLGEQFAGNTIAKTYFAIVRG--HVKEAGLIDYALKEK--LDKIADKRAKQ 119

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +K A  A + +  +  F          + ++  + + P TGR HQLR H  H+  PIVGD
Sbjct: 120 DKDAQEAQTEYVPLQQFELPFAVSRYPSARYTLVRLHPKTGRKHQLRRHMCHINHPIVGD 179

Query: 270 HKYCANFKGNFTSP--IQNKLYLHARYMDLPHP 300
             +       F       N L L  + M + HP
Sbjct: 180 TTHGDGKHNKFMRDQFSFNGLALTCQQMCMTHP 212


>gi|330833599|ref|YP_004402424.1| pseudouridine synthase [Streptococcus suis ST3]
 gi|329307822|gb|AEB82238.1| pseudouridine synthase [Streptococcus suis ST3]
          Length = 289

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 55/199 (27%), Positives = 89/199 (44%), Gaps = 16/199 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG ++ A
Sbjct: 84  LYQDEHLIIVNKPEGMKTHGNDPTEIALLNHVSAYV---GQTCYVVHRLDMETSGAILFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      + I + Y +L  G  +     I + + +  H   D    V  N K
Sbjct: 141 KNPFILPILNRLLEDKVIYRDYLALCQGQLRKTDWTITDKIGRDRH---DRRKRVVDNRK 197

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           G   A++  +++   + K   +  +  TGRTHQ+RVH  H    ++GD  Y         
Sbjct: 198 G-QVALTQVRLLKTLS-KNSLVTCRLQTGRTHQIRVHLAHHDHALIGDPLY-----SQVA 250

Query: 282 SPIQNKLYLHARYMDLPHP 300
           +P   +L LHA+ + L HP
Sbjct: 251 AP---RLMLHAQKLSLTHP 266


>gi|291535995|emb|CBL09107.1| pseudouridine synthase, RluA family [Roseburia intestinalis M50/1]
          Length = 247

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 101/222 (45%), Gaps = 22/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---SKGQKP---RLTHRLDQET 154
           + YED  I   NKPA + V        H D  L + V    +  + P   R  +RLD++T
Sbjct: 33  ICYEDEDILAVNKPAQMPVHPSLN---HYDHTLANAVCGYYNDQEIPYTFRCVNRLDRDT 89

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+ ++A+   ++  L+ +   R I + Y ++  G  K  +    +  + +  + G  + 
Sbjct: 90  TGLTLIAKHMLSSAILSTAAARREISREYIAIASG--KTPESGTIDAPIGR--VAGSTIE 145

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                E G   AI+H++ +  +      L +   TGRTHQ+RVH   +G P++GD  Y  
Sbjct: 146 RQIDFENGER-AITHYRRL-AYHDGLSLLSLHLETGRTHQIRVHLKSIGHPLIGDFLY-- 201

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
               N T     +  LH+  +   HP  G    +TAPLP  M
Sbjct: 202 ----NPTDTTIKRQALHSYRLTFSHPITGESFVLTAPLPDDM 239


>gi|258539958|ref|YP_003174457.1| ribosomal large subunit 23S pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
 gi|257151634|emb|CAR90606.1| Ribosomal large subunit 23S pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
          Length = 278

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 102/220 (46%), Gaps = 34/220 (15%)

Query: 103 YEDSKIYVFNKPAGISVQ----GGSG-IAYHIDGFLKSWVDSKGQKPRL-THRLDQETSG 156
           YED  + + +KPAG+       G +G +      +L  +       P L THRLD  TSG
Sbjct: 80  YEDDDLLIVDKPAGMKTHPNQPGETGTLMNQAAAYLAPF-------PALITHRLDMATSG 132

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +LV+A+   A   +      + + + Y ++V  GIP+  K  I      ++ IG D    
Sbjct: 133 LLVIAKNPLAQAIINRQLTTKTMHRDYLAVVPSGIPE--KGTI------QAPIGHDPDDK 184

Query: 216 VKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            K+     GA +A++H+  I   A     +E+   TGRTHQ+RVH   +G PI+GD  Y 
Sbjct: 185 RKRMIRADGA-FAVTHYHRIAETADT-ATIELNLETGRTHQIRVHLASIGFPIIGDPLYA 242

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           A            ++ LHA  + L  P     L +T+P P
Sbjct: 243 ATETA-------TRMQLHAFRVRLIRPLTIEPLTVTSPSP 275


>gi|253827544|ref|ZP_04870429.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           canadensis MIT 98-5491]
 gi|313141752|ref|ZP_07803945.1| ribosomal large subunit pseudouridine synthase [Helicobacter
           canadensis MIT 98-5491]
 gi|253510950|gb|EES89609.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           canadensis MIT 98-5491]
 gi|313130783|gb|EFR48400.1| ribosomal large subunit pseudouridine synthase [Helicobacter
           canadensis MIT 98-5491]
          Length = 319

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 105/224 (46%), Gaps = 17/224 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKS---WVDSKGQKPR--LTHRLDQE 153
           +LYED  + + NKP  + V         Y +  +L+     + + G   R  + HRLD+ 
Sbjct: 67  ILYEDEDLLILNKPINLIVHQTHQDDSQYTLQDWLQENNFSLSNLGDSYRQGIIHRLDKT 126

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG +V+A+   A + L++  + + + + Y+  V   P  +   I   L++       Y+
Sbjct: 127 TSGAIVIAKNNYAHEILSQQLKSKEMGR-YYVCVIDSPLKQNILIDAPLIRHPKNRLKYI 185

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              K          + FK+I+    K   +  +  +GRTHQ+R H   +   I+GD  Y 
Sbjct: 186 PTTKDTPLSKEAKTAFFKIIN--NDKIELIGAKLFSGRTHQIRAHLSKIQRHILGDVFY- 242

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
             +KGN+T+    ++ LH+  + L HP    RL+I APL   M+
Sbjct: 243 -GYKGNYTA----RILLHSHLVYLTHPTTKQRLEIYAPLWEDML 281


>gi|309808775|ref|ZP_07702661.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           01V1-a]
 gi|308168011|gb|EFO70143.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           01V1-a]
          Length = 302

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 133 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 191

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 192 PIGKKDDPVKRYIM------EGGKESVTKYRVIKQVAGA-SLVELQLLTGRTHQIRVHMQ 244

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F     ++  LH   +    P E  R+++    PA MV+ W
Sbjct: 245 YLGHPLFGDHLY--GVEDDF-----HRQALHCFLLAFDDPLEHKRIEVQIADPADMVQLW 297

Query: 320 DSL 322
             L
Sbjct: 298 QKL 300


>gi|56964283|ref|YP_176014.1| ribosomal large subunit pseudouridine synthase D [Bacillus clausii
           KSM-K16]
 gi|56910526|dbj|BAD65053.1| ribosomal large subunit pseudouridine synthase D [Bacillus clausii
           KSM-K16]
          Length = 301

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 75/295 (25%), Positives = 134/295 (45%), Gaps = 40/295 (13%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVR--IPPVI 71
           DE+   L R F      ++   L  +  + G +RV++      + +++G +V   +PP  
Sbjct: 11  DEDAPLLLRTFLREKKQVSKRLLAAVKFKGGLLRVNEMEATVRHVVKTGDLVTMVLPP-- 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIA 126
                          S +L+   + L   + YED  + V +KP  ++      + G  +A
Sbjct: 69  --------------ESPSLSLQPEQLLFGIPYEDEHLLVADKPGHMATIPSRDRPGGSLA 114

Query: 127 YHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +G L  +     Q      +RLD+ TSG+L+VA+ R A   L+   +   +++ Y +
Sbjct: 115 ---NGVLHYYKQQHLQATFHAVNRLDRGTSGLLIVAKHRYAHDLLSRLQQQGGVKRCYKA 171

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G+   K   I   + +K    G  +   ++   G   AI+H+KV +  ++    + +
Sbjct: 172 LVTGVLSEKAGIINAPIDRKP---GSIIE--REVGPGGKSAITHYKV-EAESKTHSLVSL 225

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Q  TGRTHQ+RVH  ++G P+VGD  Y     G+    + ++  LH   + L HP
Sbjct: 226 QLETGRTHQIRVHFAYIGHPLVGDGLY-----GDHGEALAHQ-ALHCDRVALTHP 274


>gi|54310089|ref|YP_131109.1| tRNA pseudouridine synthase C [Photobacterium profundum SS9]
 gi|46914528|emb|CAG21307.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum SS9]
          Length = 245

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 59/213 (27%), Positives = 97/213 (45%), Gaps = 18/213 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  +   NKP+G+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 5   ILFQDEYLVAVNKPSGMLVHRSWLDRHETVFVMQTLRDQIGQHVFPLHRLDRPTSGVLLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDYVHVVKQN 219
             +   A  +   F  R I K Y ++V G  K+    + ++ LKK      D     +Q 
Sbjct: 65  GLSSEIASQMMPVFSGREIHKTYHAVVRGWIKDA--AVLDYPLKKELDKIADKNAAEEQE 122

Query: 220 EKGANYAISHFKVIDC-------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV----- 267
            + A  A S    ++           ++C +EM+P TGR HQLR H  H+   I+     
Sbjct: 123 AQEAVTAYSPLATVETNIPVGRYATSRYCLVEMKPETGRKHQLRRHMHHLNHHIIGDVNH 182

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           GD ++   F+ N+     ++L LHA  +   HP
Sbjct: 183 GDGRHNRMFRENYDC---HRLMLHASCLQFVHP 212


>gi|291538489|emb|CBL11600.1| pseudouridine synthase, RluA family [Roseburia intestinalis XB6B4]
          Length = 247

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 101/222 (45%), Gaps = 22/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---SKGQKP---RLTHRLDQET 154
           + YED  I   NKPA + V        H D  L + V    +  + P   R  +RLD++T
Sbjct: 33  ICYEDEDILAVNKPAQMPVHPSLN---HYDHTLANAVCGYYNDQEIPYTFRCVNRLDRDT 89

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+ ++A+   ++  L+ +   R I + Y ++  G  K  +    +  + +  + G  + 
Sbjct: 90  TGLTLIAKHMLSSAILSTAAARREISREYIAIASG--KTPESGTIDAPIGR--VAGSTIE 145

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                E G   AI+H++ +  +      L +   TGRTHQ+RVH   +G P++GD  Y  
Sbjct: 146 RQIDFENGER-AITHYRRL-AYHDGLSLLSLHLETGRTHQIRVHLKSIGHPLIGDFLY-- 201

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
               N T     +  LH+  +   HP  G    +TAPLP  M
Sbjct: 202 ----NPTDTTIKRQALHSYRLTFSHPITGESFVLTAPLPDDM 239


>gi|261337488|ref|ZP_05965372.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           gallicum DSM 20093]
 gi|270277883|gb|EFA23737.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           gallicum DSM 20093]
          Length = 313

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 112/236 (47%), Gaps = 18/236 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD------SKGQKPR--LTHRLDQ 152
           ++YED  + V +KP G++    + + +     L S +D      S G   R  +  RLD 
Sbjct: 80  IVYEDDDVVVVDKPVGVAAH--ASVGWTGPTVLGSLLDRGVHITSYGAAGRQGIVSRLDV 137

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+++V ++  A + +   F    + K Y +LV G  +  K  I +  + ++ +  D+
Sbjct: 138 GTSGLMLVCKSELAYKEMRRQFSEHEVVKTYEALVQGNLQEDKATI-DAPIGRAKVS-DF 195

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +    K    AI+H+ V++ F +      +   TGRTHQ+RVH   +G P+VGD  Y
Sbjct: 196 RFCITPAGK---PAITHWDVLERFGEA-TLARINLETGRTHQIRVHFSSIGHPLVGDPMY 251

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            AN K      +Q + +LHA  +D  HP       +T+ LP  +    D +  + D
Sbjct: 252 GANPKLAQECGLQRQ-WLHAMQLDFRHPRTHVWTTVTSTLPPDLSHALDVMAQRRD 306


>gi|210616986|ref|ZP_03291321.1| hypothetical protein CLONEX_03543 [Clostridium nexile DSM 1787]
 gi|210149509|gb|EEA80518.1| hypothetical protein CLONEX_03543 [Clostridium nexile DSM 1787]
          Length = 227

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 101/210 (48%), Gaps = 17/210 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR------LTHRLDQET 154
           +L+ED+ + V  KPAG+  Q     +  +   LK+++  K QK +      + HRLDQ  
Sbjct: 5   ILFEDTHVIVCYKPAGVPTQTSKIGSQDMVSILKNYL-YKNQKEKKEPYVAVIHRLDQPV 63

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            GILV  +T  AA+ L+   +     K Y ++V G  + K   + ++++K   +  +   
Sbjct: 64  EGILVFGKTPFAAKELSAQMQGAGFGKYYQAVVCGKFEEKSGKLEHYMVKDGRV--NLSK 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           V   + K A  A+  ++V +   +       + ++  TGR HQ+RV     GCPI GD K
Sbjct: 122 VCDPSIKDAKRAVLFYEVEEEGLEDGEERSLVNIKLETGRHHQIRVQMAAAGCPIWGDAK 181

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           Y         S  + K+ L A +++  HP+
Sbjct: 182 YNEK-----QSNGRRKIALCASHLEFLHPK 206


>gi|331085858|ref|ZP_08334941.1| hypothetical protein HMPREF0987_01244 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406781|gb|EGG86286.1| hypothetical protein HMPREF0987_01244 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 298

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 103/226 (45%), Gaps = 30/226 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGI 157
           ++YED  + V NKP+G+ +    G   +      ++  +    P   R  +RLD++T+G+
Sbjct: 83  IVYEDEDLLVINKPSGMPIHPSQGNYENTLANAAAYYFASQNIPFTYRCINRLDRDTTGL 142

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+   +A  L+     R I + Y +   G+ +          + ++ IG      ++
Sbjct: 143 LIIAKHMYSASLLSNMVARREIHREYLAAATGLVEESG-------MIEAPIGRANGSTIE 195

Query: 218 QNEKGA--NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--- 272
           +    A  +YA +HF  +  +   +  + ++  TGRTHQ+RVH  ++G P+ GD  Y   
Sbjct: 196 RCVDFAHGDYACTHFHRL-AYQNGYSLVSLKLETGRTHQIRVHMKYIGHPLPGDFLYHPE 254

Query: 273 --CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
             C + +            LH+  +   HP     L  TAPLP  M
Sbjct: 255 DHCIDRQA-----------LHSYRLSFIHPITKQSLTFTAPLPEDM 289


>gi|157736289|ref|YP_001488972.1| ribosomal large subunit pseudouridine synthase [Arcobacter butzleri
           RM4018]
 gi|157698143|gb|ABV66303.1| ribosomal large subunit pseudouridine synthase [Arcobacter butzleri
           RM4018]
          Length = 300

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 100/228 (43%), Gaps = 38/228 (16%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLT 147
           LK +L +ED    +F+KP  + V   S          I YH            G+   L 
Sbjct: 71  LKPLLEFED--FAIFDKPTNLMVHPISKNTSYSLLDEIRYHF-----------GENANLI 117

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HR+D ETSG+++V + + +   L + F+ ++  K Y ++V G  + K+E   N  L +  
Sbjct: 118 HRIDAETSGLVIVGKNKKSEIELKDMFQEKKYHKSYLAIVQG--EIKEELKINKALDREG 175

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPI 266
                   V   E+G   +I+  K I    +K    +E  P TGR HQ+RVH   MG  I
Sbjct: 176 KAIGVRMKVCTQEEGGKESITIIKPIIYDKEKNLTLVEALPLTGRQHQIRVHLHSMGHTI 235

Query: 267 VGDHKY------CANF-------KGNFTSPIQNKLYLHARYMDLPHPE 301
           +GD  Y        N+       +  F      +L+LHA Y++  + +
Sbjct: 236 LGDPIYGVDDENAENYLNKTLSEEDRFKVTKSYRLWLHANYLEFNYKD 283


>gi|95929488|ref|ZP_01312231.1| Pseudouridine synthase, RluD [Desulfuromonas acetoxidans DSM 684]
 gi|95134604|gb|EAT16260.1| Pseudouridine synthase, RluD [Desulfuromonas acetoxidans DSM 684]
          Length = 303

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 70/261 (26%), Positives = 123/261 (47%), Gaps = 32/261 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD+W       ++   ++K++  G V V+ +RV K +  ++ G  +           + 
Sbjct: 10  RLDQWLATTDRSLSRTVIRKVIDLGGVHVNGRRVRKCSQALKRGDKI----------ELY 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----SGIAYH-IDGFL 133
           ++Q+ L +   L++        +L+ D  + V NKP+G+  Q       G  Y  +  FL
Sbjct: 60  RDQQPL-TPFRLSEED------VLFRDDFLLVVNKPSGVESQPTPSRYKGTLYEALLVFL 112

Query: 134 KSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           K        KP L    RLD+ETSG ++ +      + LTE+++  R++K+Y +LV   P
Sbjct: 113 KDPYRPL-DKPELGMVQRLDRETSGAMIFSIHSRCHKPLTEAWQSHRVRKVYHALVRD-P 170

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
               E     LL ++       + +K   +G   A + ++V+   +  F  +E+Q  TGR
Sbjct: 171 GLDDEGEFISLLARNR----RTNRMKSVARGGKSAHTRYRVLKRLS-GFALVEIQLLTGR 225

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH    G P++GD  Y
Sbjct: 226 MHQIRVHFSEAGAPLLGDKLY 246


>gi|325662008|ref|ZP_08150627.1| hypothetical protein HMPREF0490_01365 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471671|gb|EGC74890.1| hypothetical protein HMPREF0490_01365 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 298

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 58/227 (25%), Positives = 102/227 (44%), Gaps = 32/227 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGI 157
           ++YED  + V NKP+G+ +    G   +      ++  +    P   R  +RLD++T+G+
Sbjct: 83  IVYEDEDLLVINKPSGMPIHPSQGNYENTLANAAAYYFASQNIPFTYRCINRLDRDTTGL 142

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG---GDYVH 214
           L++A+   +A  L+     R I + Y +   G+ +          + ++ IG   G  + 
Sbjct: 143 LIIAKHMYSASLLSNMVARREIHREYLAAATGLVEESG-------MIEAPIGRANGSTIE 195

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-- 272
                  G +YA +HF  +  +   +  + ++  TGRTHQ+RVH  ++G P+ GD  Y  
Sbjct: 196 RCVDFAHG-DYACTHFHRL-AYQNGYSLVSLKLETGRTHQIRVHMKYIGHPLPGDFLYHP 253

Query: 273 ---CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
              C + +            LH+  +   HP     L  TAPLP  M
Sbjct: 254 EDHCIDRQA-----------LHSYRLSFIHPITKQSLTFTAPLPEDM 289


>gi|312898764|ref|ZP_07758153.1| pseudouridine synthase, RluA family [Megasphaera micronuciformis
           F0359]
 gi|310620195|gb|EFQ03766.1| pseudouridine synthase, RluA family [Megasphaera micronuciformis
           F0359]
          Length = 291

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 102/233 (43%), Gaps = 35/233 (15%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED  + V NKP G+ +   S      +A  I  + K         P   HRLD+ TSG+
Sbjct: 78  YEDDYLIVVNKPPGMLMHQTSSERFGTLANAIMYYYKVHGYDHDYHP--VHRLDRNTSGL 135

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
            ++A+  +  QHL +  R+    + Y +L  G         A      + IG D   ++K
Sbjct: 136 CLIAK-ESYVQHLFDKNRLF-YARTYTALAQG------RFPAMLATVHTPIGRDPDSIIK 187

Query: 218 QNE----KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           +N     K A+   +   V D     F  + +  HTGRTHQ+RVH+ ++G P++GD  Y 
Sbjct: 188 RNTREDGKEAHSDFTRLAVCD----DFSLIRITLHTGRTHQIRVHSAYLGHPLIGDDLYG 243

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHM-----VKTWD 320
            + +        N+  LHA  +   HP  G +  +  PLP  M        WD
Sbjct: 244 GSRR------FLNRQALHAGSVRFIHPVTGHMTYVNVPLPTDMQTLVATACWD 290


>gi|304409553|ref|ZP_07391173.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307303911|ref|ZP_07583664.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304352071|gb|EFM16469.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306912809|gb|EFN43232.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 287

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 106/247 (42%), Gaps = 37/247 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILV 159
           +LYED  +   +KPAG+ V   S +A     F      D  G      HRLD+ TSG+L+
Sbjct: 32  ILYEDDHLVAIHKPAGLLVHR-SYLARRERFFAMQLTRDLVGCHVFPVHRLDRPTSGVLL 90

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A++   A  L E F    I+K Y +LV G     +  I ++ LK        V + +  
Sbjct: 91  FAKSSEVANALCEQFASHTIEKQYLALVRG--NMHESGILDYALK--------VELDELG 140

Query: 220 EKGANYAISHFKVIDCF----------------AQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +K A+   +  + +  +                  +F  + + P TGR HQLR H  H+ 
Sbjct: 141 DKNADPNKAAQEAVTAYEPLLNTEIPYPSGRYPTSRFALVRLSPKTGRKHQLRRHMAHLR 200

Query: 264 CPIVGDH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            PIVGD      K  A F+ +F     N+L+L A+ +   HP    RL I   L      
Sbjct: 201 HPIVGDTTHGDGKQNAFFREHFGI---NRLWLIAKKLSFTHPVTQVRLSIETELEPEWET 257

Query: 318 TWDSLGF 324
            +  LG+
Sbjct: 258 VFAELGW 264


>gi|322791282|gb|EFZ15806.1| hypothetical protein SINV_13849 [Solenopsis invicta]
          Length = 360

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 55/173 (31%), Positives = 85/173 (49%), Gaps = 9/173 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  + V NKPA I V       ++   F+ +  +   +  R  HRLD+ TSGIL+ 
Sbjct: 13  VIHMDEDVVVVNKPASIPVHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDRLTSGILLF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            RT   A+ +    R R++ K Y   V G  P+ +  C     +    IG     V K +
Sbjct: 72  GRTPKKARQMEHQIRNRQVHKQYVCRVEGEFPEEEVICSEPIEVVSYKIG-----VCKVS 126

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           EKG +  I+ FK +  +  K   +  +P TGR HQ+RVH  ++G P+V D  Y
Sbjct: 127 EKGKD-CITRFKRLS-YNGKSSVVLCKPQTGRMHQIRVHLQYLGYPVVNDPLY 177


>gi|304437126|ref|ZP_07397088.1| ribosomal large subunit pseudouridine synthase D [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369885|gb|EFM23548.1| ribosomal large subunit pseudouridine synthase D [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 294

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 62/223 (27%), Positives = 104/223 (46%), Gaps = 23/223 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS-----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED  + V +KPAG  V   +      IA  + G+  +        P   HRLD+ TS
Sbjct: 79  IIYEDDDLLVLDKPAGQLVHPTTKETHGTIANAVRGYYAACGVHLDFHP--CHRLDRNTS 136

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A+       + +   ++R    Y +L+ G     + CI   + +   +    +  
Sbjct: 137 GLLLIAKHPEVQYQIAQQNTLKRE---YLALIAGSLTPPEGCIDVPIARA--LPSIILRC 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V    K A    +H+  +     ++  L +Q  TGRTHQ+RVH  H+G P++GD  Y   
Sbjct: 192 VSTEGKSA---CTHYVTVQTDG-RYSLLRLQLDTGRTHQIRVHLAHLGHPLLGDDLY--- 244

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
             G   + I     LH+ ++ L HP   + L ++A LPA M +
Sbjct: 245 --GGTRAEIARH-ALHSAHLTLVHPRTKKMLALSALLPADMAR 284


>gi|291542721|emb|CBL15831.1| pseudouridine synthase, RluA family [Ruminococcus bromii L2-63]
          Length = 291

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 59/217 (27%), Positives = 98/217 (45%), Gaps = 22/217 (10%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGILV 159
           YED    V NKP  + V             + S+  S+  KP   R  +RLD++TSG+++
Sbjct: 84  YEDEHFLVVNKPHSMPVHPVKQHQSDTLANIVSYYCSQNGKPFVFRAINRLDKDTSGLVL 143

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ R  A  +       +  K+Y++L  G      E     ++ K     D   +V+  
Sbjct: 144 IAKNRFTANAVKN-----KTHKVYYALCEG------EINIEGIVDKPMDLRDDSKMVRIV 192

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 A++H+K +    + F  LE+   TGRTHQ+R H  ++G P++GD  Y     G 
Sbjct: 193 RDDGMKAVTHYKPL-VATKDFTLLELWLETGRTHQIRCHMAYLGHPLMGDDLY-----GG 246

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
               I  +  LH   ++  HP +   + +TA +P  M
Sbjct: 247 KLDKISRQA-LHCARLEFYHPIKNEYITVTAEIPEDM 282


>gi|224418218|ref|ZP_03656224.1| ribosomal large subunit pseudouridine synthase A [Helicobacter
           canadensis MIT 98-5491]
          Length = 340

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 105/224 (46%), Gaps = 17/224 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKS---WVDSKGQKPR--LTHRLDQE 153
           +LYED  + + NKP  + V         Y +  +L+     + + G   R  + HRLD+ 
Sbjct: 88  ILYEDEDLLILNKPINLIVHQTHQDDSQYTLQDWLQENNFSLSNLGDSYRQGIIHRLDKT 147

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG +V+A+   A + L++  + + + + Y+  V   P  +   I   L++       Y+
Sbjct: 148 TSGAIVIAKNNYAHEILSQQLKSKEMGR-YYVCVIDSPLKQNILIDAPLIRHPKNRLKYI 206

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              K          + FK+I+    K   +  +  +GRTHQ+R H   +   I+GD  Y 
Sbjct: 207 PTTKDTPLSKEAKTAFFKIIN--NDKIELIGAKLFSGRTHQIRAHLSKIQRHILGDVFY- 263

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
             +KGN+T+    ++ LH+  + L HP    RL+I APL   M+
Sbjct: 264 -GYKGNYTA----RILLHSHLVYLTHPTTKQRLEIYAPLWEDML 302


>gi|12321745|gb|AAG50905.1|AC069159_6 RNA pseudouridylate synthase, putative [Arabidopsis thaliana]
          Length = 254

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 63/255 (24%), Positives = 113/255 (44%), Gaps = 54/255 (21%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +  +  +LYED  +   NKP G+          + +  L+S       +  L +RLD++T
Sbjct: 11  NLTRDDILYEDEYLMAVNKPKGV----------YCEAVLRS-----APQIVLANRLDRDT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KKECIANWLLKKSH------ 207
           SG++++ ++   A  L ++F   +I+K Y +L  G   N ++  +++   +  H      
Sbjct: 56  SGVMIITKSHKVAAKLVKAFTEHKIRKSYIALCIGSSPNWRRVTVSSGHGRSKHGAWRVY 115

Query: 208 ---------IGGDYVHVVK-----------QNEKGANYAISHFKVIDCFAQKFCW----- 242
                     GG +V  ++           +NE      ++H  V +   +  C      
Sbjct: 116 AALDVGRVLPGGSFVRDMETTFEVVSVNSVKNESCELEDVNHVIVAEGERELSCGGDDDD 175

Query: 243 ----LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +   P +GRTHQ+R+H  ++G PI GD KY   ++ N  +   ++  LHA  + L 
Sbjct: 176 VVVVVRAFPRSGRTHQIRLHCQYLGIPIRGDVKYHGVYEWNGRTFEGHE--LHAECLSLD 233

Query: 299 HP-EGGRLQITAPLP 312
           HP  G  + I APLP
Sbjct: 234 HPVTGDSIVIRAPLP 248


>gi|294793936|ref|ZP_06759073.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           3_1_44]
 gi|294455506|gb|EFG23878.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           3_1_44]
          Length = 321

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 82/312 (26%), Positives = 127/312 (40%), Gaps = 65/312 (20%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +++   G + V+ K   +N  I  G   V+++ P          EQ+   S ++L     
Sbjct: 35  RRLRNEGIITVNGKFATWNTLIHGGDHLVMKLTP----------EQEFSLSPMSLD---- 80

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQKP-RLTHRLDQ 152
                ++YED  I V NK AGI +   S +  H   +G L  + ++         HRLD+
Sbjct: 81  -----IIYEDEYILVINKAAGILMHPTSTVRNHTLANGVLHYYQETNQHYDFHPVHRLDK 135

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV------------WGIPKNKKECIAN 200
            TSGI+++A+T +  QH  +  +     KIY ++V            W I +     I  
Sbjct: 136 NTSGIVIIAKT-SVVQHAFDK-KHTHFYKIYDAIVEGHLPSVRISINWPIGRKPDSIIER 193

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANY----------------AISHFKVIDCFAQKFCWLE 244
               +       + VV +N    NY                A +   V + F    C L 
Sbjct: 194 CCTDQGKPARTDITVVSKNTSKFNYSKNNSDDMINNSNICPADNSIIVYNHFTHVQCLL- 252

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              HTGRTHQ+RVH   +G P+ GD  Y     G     IQ +  LHA ++   HP    
Sbjct: 253 ---HTGRTHQIRVHLSQLGYPLAGDDLY-----GGHLEFIQRQA-LHASHVSFYHPITNE 303

Query: 305 -LQITAPLPAHM 315
            L++ A +P  M
Sbjct: 304 WLELHAEMPEDM 315


>gi|116750307|ref|YP_846994.1| RluA family pseudouridine synthase [Syntrophobacter fumaroxidans
           MPOB]
 gi|116699371|gb|ABK18559.1| pseudouridine synthase, RluA family [Syntrophobacter fumaroxidans
           MPOB]
          Length = 300

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 69/292 (23%), Positives = 118/292 (40%), Gaps = 34/292 (11%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVINALN 75
            + +  +    Y H +       L +G+V +D +R + +  ++ GQ +  R PP      
Sbjct: 19  GLTVREYLAAAYRHSSEAEWMARLENGEVCLDGRRARGSVVLKPGQWLAWRRPP------ 72

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
              +E  +             L   +L+ D  +    KP G+      G    +D  L +
Sbjct: 73  --WEEPDV------------PLAYAVLHADEDLLAVAKPRGLPTVPAGGF---LDNTLLA 115

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            V     +    HRL + TSGI+++ART  A   L  + R   + + Y +L  G+P    
Sbjct: 116 LVRRACPEATPVHRLGRGTSGIVLLARTARARSVLAAALRRNEVTRTYRALAGGVPGRDA 175

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQ 254
             + + +    H     VH    + +    A+S  +V++   +  C  + ++  TGR HQ
Sbjct: 176 FTVGSPIGPVPHPLLGSVHAANPSGR---PALSLVEVLE--RRTGCSVVGVRIKTGRPHQ 230

Query: 255 LRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +R+H    G P+VGD  Y       +G    P      LHA  + L HP  G
Sbjct: 231 IRIHLACAGHPLVGDPLYAPGGMIVEGGCALPGDPGYLLHAESLRLLHPATG 282


>gi|260910942|ref|ZP_05917583.1| ribosomal large subunit pseudouridine synthase A [Prevotella sp.
           oral taxon 472 str. F0295]
 gi|260634933|gb|EEX52982.1| ribosomal large subunit pseudouridine synthase A [Prevotella sp.
           oral taxon 472 str. F0295]
          Length = 537

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 55/202 (27%), Positives = 102/202 (50%), Gaps = 20/202 (9%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  + V +KP G +SV G  G         + + D+    P + HRLDQ+TSG+++
Sbjct: 336 VVYEDDALVVVSKPHGMLSVPGKGGGTSVAQLMRERYPDA--DSPLIVHRLDQDTSGLML 393

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +A+T+   + L  +F    ++K Y +++ G +P  +++   +  L  +++      V   
Sbjct: 394 IAKTKEMHRTLQLAFENHEVKKRYVAVLDGLLPPERQQGEISLPLNSNYLDRPRQMV--- 450

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
           +      A++ ++VI    +    + + P TGRTHQLRVH  H   +  PI+GD  Y   
Sbjct: 451 DWLQGKPAVTRYEVIGQ-EEGRTIVALYPLTGRTHQLRVHCAHPDGLNLPILGDPLYGRK 509

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
                     +++YLHA  +++
Sbjct: 510 ---------AHRMYLHAEAIEV 522


>gi|257413757|ref|ZP_04744118.2| pseudouridine synthase, RluA family [Roseburia intestinalis L1-82]
 gi|257202334|gb|EEV00619.1| pseudouridine synthase, RluA family [Roseburia intestinalis L1-82]
          Length = 313

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 76/294 (25%), Positives = 126/294 (42%), Gaps = 38/294 (12%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           YP+  FV L+K   S  V ++        ++ +G  + I      L        IL  S+
Sbjct: 43  YPNAVFVQLKKTPES--VLLNGVWAYMRTKLSAGDELFI-----RLEESTSSAHILPVSM 95

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---SKGQKP- 144
            L+         + YED  I   NKPA + V        H D  L + V    +  + P 
Sbjct: 96  PLS---------ICYEDEDILAVNKPAQMPVHPSLN---HYDHTLANAVCGYYNDQEIPY 143

Query: 145 --RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             R  +RLD++T+G+ ++A+   ++  L+ +   R I + Y ++  G  K  +    +  
Sbjct: 144 TFRCVNRLDRDTTGLTLIAKHMLSSAILSTAAARREISREYIAIASG--KTPESGTIDAP 201

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           + +  + G  +      E G   AI+H++ +  +      L +   TGRTHQ+RVH   +
Sbjct: 202 IGR--VAGSTIKRQIDFENGER-AITHYRRL-AYHDGLSLLSLHLETGRTHQIRVHLKSI 257

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           G P++GD  Y      N T     +  LH+  +   HP  G    +TAPLP  M
Sbjct: 258 GHPLIGDFLY------NPTDTTIKRQALHSYRLTFSHPITGESFVLTAPLPDDM 305


>gi|229552586|ref|ZP_04441311.1| pseudouridylate synthase RluD [Lactobacillus rhamnosus LMS2-1]
 gi|229314138|gb|EEN80111.1| pseudouridylate synthase RluD [Lactobacillus rhamnosus LMS2-1]
          Length = 310

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 65/219 (29%), Positives = 101/219 (46%), Gaps = 32/219 (14%)

Query: 103 YEDSKIYVFNKPAGISVQ----GGSG-IAYHIDGFLKSWVDSKGQKPRL-THRLDQETSG 156
           YED  + + +KPAG+       G +G +      +L  +       P L THRLD  TSG
Sbjct: 112 YEDDDLLIVDKPAGMKTHPNQPGETGTLMNQAAAYLAPF-------PALITHRLDMATSG 164

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +LV+A+   A   +      + + + Y ++V  GIP+  K  I      ++ IG D    
Sbjct: 165 LLVIAKNPLAQAIINRQLTTKTMHRDYLAVVPSGIPE--KGTI------QAPIGHDPDDK 216

Query: 216 VKQNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            K+  +    +A++H+  I   A     +E+   TGRTHQ+RVH   +G PI+GD  Y A
Sbjct: 217 RKRMIRADGAFAVTHYHRIAETADT-ATIELNLETGRTHQIRVHLASIGFPIIGDPLYAA 275

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
                       ++ LHA  + L  P     L +T+P P
Sbjct: 276 TETA-------TRMQLHAFRVRLIRPLTIEPLTVTSPSP 307


>gi|229166145|ref|ZP_04293906.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH621]
 gi|228617367|gb|EEK74431.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH621]
          Length = 292

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 68/287 (23%), Positives = 130/287 (45%), Gaps = 46/287 (16%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
            R G + V+ +     +++Q+G+ ++I   +   +  ++ + I                 
Sbjct: 33  FRGGAIEVNGQHTSVRHKLQAGEELQIFFPVEERSEGMEVEDI--------------PLC 78

Query: 101 LLYEDSKIYVFNKPAGISV------QGGS---GIAYHIDG-FLKSWVDSKGQKPRLTHRL 150
           ++YED  + V NK A +S         GS    + YH D   L S V        +  RL
Sbjct: 79  IVYEDDAVLVINKEANMSTIPSREHPSGSIANALLYHYDKQNLASTV-------HIVTRL 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ R     L++  + + +++ Y ++V G    +   I   + +K+    
Sbjct: 132 DRDTSGLMLIAKNRFVHHLLSKQHQQKGVKRTYEAIVHGTILEEVGTIDAQIGRKA---- 187

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D +      E G   A++HF+V++  + K   + ++  TGRTHQ+RVH  ++G P++GD 
Sbjct: 188 DSIIERTVCEDGQR-AVTHFRVMESSSDK-THVALELETGRTHQIRVHMAYIGHPLLGDD 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPAHM 315
            Y           +  +  LH+  +   HP  E G +  T  +P  M
Sbjct: 246 LYGGR------RDVIKRQALHSTSLTFYHPILEKG-MTFTVSIPEDM 285


>gi|149195656|ref|ZP_01872713.1| tRNA pseudouridine synthase A [Lentisphaera araneosa HTCC2155]
 gi|149141118|gb|EDM29514.1| tRNA pseudouridine synthase A [Lentisphaera araneosa HTCC2155]
          Length = 231

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 52/150 (34%), Positives = 77/150 (51%), Gaps = 19/150 (12%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL---L 203
            HRLD+ TSG+L++AR   + Q L + F  ++I+K Y ++    PK K+     W+   +
Sbjct: 48  VHRLDKVTSGLLLMARNLQSCQELNQLFEAQKIEKFYLAISDRKPKKKQ----GWVIGDM 103

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +KS  GG      K  E   N A++ F        K  +L ++P TG+THQLRV    +G
Sbjct: 104 EKSRRGG-----WKLCESRKNPAVTQFFSYSIGQGKRVYL-LRPRTGKTHQLRVAMKAIG 157

Query: 264 CPIVGDHKYCANF-KGNFTSPIQNKLYLHA 292
            PI GD  Y     KG+     + + YLHA
Sbjct: 158 APICGDPNYYPGLIKGH-----EERCYLHA 182


>gi|313147267|ref|ZP_07809460.1| RNA pseudouridylate synthase [Bacteroides fragilis 3_1_12]
 gi|313136034|gb|EFR53394.1| RNA pseudouridylate synthase [Bacteroides fragilis 3_1_12]
          Length = 305

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 110/226 (48%), Gaps = 20/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++YED+ I V  K  G+   G        A HI   L  +V   G+  R+   HRLD++T
Sbjct: 90  IVYEDAYIIVVEKKEGLLSVGTDRQKERTAQHI---LSEYVGRSGRGNRIFVVHRLDRDT 146

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+     + L + +      + Y ++V G  +   + + +WL  ++     YV 
Sbjct: 147 SGLMMFAKDEKTQRTLRDHWHDIVTDRRYVAVVTGEMEKDSDTVVSWLTDRTL----YVS 202

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++ G+  +I+H++ I   A  +  +E++  TGR +Q+RVH   +G P++GD +Y  
Sbjct: 203 SSSYDDGGSK-SITHYRTIKR-ANGYSLVELRLETGRKNQIRVHMQDLGHPLIGDGRYGI 260

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
           +   N   P+  +L LHA  +   HP   +L +   P P    K +
Sbjct: 261 DGGPN---PL-GRLALHAFKLCFYHPVTDQLMEFETPYPPAFKKLF 302


>gi|262376643|ref|ZP_06069871.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           lwoffii SH145]
 gi|262308353|gb|EEY89488.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           lwoffii SH145]
          Length = 350

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 62/214 (28%), Positives = 101/214 (47%), Gaps = 21/214 (9%)

Query: 112 NKPAGISVQGGSGIAYH--IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQ 168
           NKP G+ V  G+G +    ++  L  +  S    +  L HR+D++TSG+LVVA+   A  
Sbjct: 128 NKPVGMVVHPGAGNSSGTLVNALLHHYPKSAELARAGLVHRIDKDTSGLLVVAKNLEAQF 187

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAI 227
            L++    + + ++Y  +V+G        IA   + +  I    V  VK     G   A+
Sbjct: 188 SLSKQLEKKSVYRLYDLVVYG------NIIAGGTIDEP-IKRHPVDRVKMTVLPGGKDAV 240

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQ 285
           +H+ V + F Q F  ++ +  TGRTHQ+RVH  ++G  +VGD  Y    +     +  + 
Sbjct: 241 THYNVKERF-QHFTRVQARLETGRTHQIRVHFSYIGFGLVGDQVYMPRVRMPAGASQLLD 299

Query: 286 NKL------YLHARYMDLPHPEGG-RLQITAPLP 312
           + L       LHA  + L HP     +   AP P
Sbjct: 300 DTLRGFKRQALHAVQLGLTHPRTKEEMTFEAPWP 333


>gi|152993942|ref|YP_001359663.1| ribosomal large subunit pseudouridine synthase D [Sulfurovum sp.
           NBC37-1]
 gi|151425803|dbj|BAF73306.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Sulfurovum sp. NBC37-1]
          Length = 309

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 81/178 (45%), Gaps = 10/178 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ +    +F KP+G+ V   +    +    L       G     THR+D ETSG+L+ +
Sbjct: 73  LFSNRDFMIFEKPSGVLVHPNTMSTPY--SMLDEIRHISGDNANATHRIDMETSGLLLAS 130

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           + + A  HL  SF  + I+K Y + V G   N+   ++    +K  I  DY  V  +   
Sbjct: 131 KHKKAETHLKNSFEAKTIKKSYLAWVDG-RLNEPFSVS----EKIKINNDYSRVKHKVFI 185

Query: 222 GANYAISHFKVIDC-FAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                 SH   I   + ++     +   P TGRTHQ+RVH  H+  PI+GD  Y   F
Sbjct: 186 SDAGKASHTDFIPLRYNERLDATLVACYPQTGRTHQIRVHLFHVKHPILGDPIYGTTF 243


>gi|329313677|gb|AEB88090.1| Pseudouridine synthase [Staphylococcus aureus subsp. aureus T0131]
          Length = 258

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 90/192 (46%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++  L+  +LYED+ I +  KP     Q  +    H    L   V    Q+   
Sbjct: 39  SVNLIPYARKLE--VLYEDAFIIIVTKPNN---QNCTPSREHPHESLIEQVLYHCQEHGE 93

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 94  NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKVNLKKIYTCLVYGKTHTSGIIEAN 149

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 150 IRRSKDRI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 202

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 203 HIGHPIVGDSLY 214


>gi|167622075|ref|YP_001672369.1| pseudouridine synthase Rlu family protein [Shewanella halifaxensis
           HAW-EB4]
 gi|167352097|gb|ABZ74710.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           halifaxensis HAW-EB4]
          Length = 229

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 52/175 (29%), Positives = 84/175 (48%), Gaps = 17/175 (9%)

Query: 101 LLYEDSKIYVFNKPAGI---SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++ ++    V NK   +   S  G +G+    +  L       G K    HRLD  TSG+
Sbjct: 4   VIADEHDFIVINKSTEVHFHSQDGSAGVVAQAEADL-------GIKLYAVHRLDTLTSGL 56

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A++ AAA   T  F    +QK Y +L  G PK K+     W++         +H + 
Sbjct: 57  IILAKSSAAAAEFTRMFSAHLVQKYYLALAKGKPKKKQ----GWVIGDMAKSRRSMHKLL 112

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++    N AI+ F        +  +L ++PH+G+THQLRV    +G PI+GD  Y
Sbjct: 113 RSTD--NPAITQFFSHSIAEGERLYL-LKPHSGKTHQLRVALASIGVPILGDTLY 164


>gi|157164896|ref|YP_001467348.1| P-protein [Campylobacter concisus 13826]
 gi|112801995|gb|EAT99339.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Campylobacter concisus 13826]
          Length = 323

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 105/240 (43%), Gaps = 47/240 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLD 151
           ++YED  + V NKP  I V     +    +  L  W++ KG          +  + HRLD
Sbjct: 78  IIYEDDDLIVLNKPPQIVVHQAPSVK---EATLVEWLNKKGFMLSNLNGDVRAGIVHRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-------ANWLLK 204
           + TSG +VVA+   A   L+E    + + +IY +L   +P  +   I        N  LK
Sbjct: 135 KGTSGAIVVAKNNFAHAKLSEQLSDKSMGRIYLALT-DLPLKEDIIIDKPIGRNPNNRLK 193

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMG 263
           K+ +              A +A S F  ++  ++     +  +  TGRTHQ+RVH   + 
Sbjct: 194 KAIVA------------DAKFAKSAF--VNLLSEGGVNLIAAKLFTGRTHQIRVHLASIN 239

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
             I+GD  Y    +G+  S    ++ LHA  +   HP  G R++ TA       KT+D  
Sbjct: 240 RHILGDDLYGFKSQGDKIS----RVMLHAYMLYFIHPRTGKRVEFTA-------KTYDDF 288


>gi|45644651|gb|AAS73039.1| predicted pseudouridine synthase D, 23S rRNA-specific [uncultured
           marine gamma proteobacterium EBAC20E09]
          Length = 311

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 58/265 (21%), Positives = 111/265 (41%), Gaps = 25/265 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V  +   MRLD+     +   +   ++K +  G+V ++       + +  G  ++I P+
Sbjct: 6   TVSKEHSKMRLDKVSTIIFEDFSRTQIKKWILEGRVFLNDDIASPRDLVHEGDSIQIDPI 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                  + E+  +D               ++YE+    + NK   + +  G+G +    
Sbjct: 66  AEEKISWVPEEIDID---------------VIYENDDYLIINKQPNLIMHPGAGCSSGTL 110

Query: 130 -DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  + + K   +  + HRLD++TSG+++VAR      +  +  + R + K+Y ++V
Sbjct: 111 ANALLHHYPELKNIARAGIVHRLDKDTSGVILVARNDKFRNYFVDLLQKREVTKLYSAIV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        I         IG D  + VK + +        F  +      +  L++  
Sbjct: 171 VG-------TIIGSFKVTDPIGRDKKNRVKMSIRSDGKESETFVKLKESLGNYSLLDISI 223

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
            TGRTHQ+RVH      PI+GD+ Y
Sbjct: 224 MTGRTHQIRVHLSSKKLPIIGDNTY 248


>gi|255009494|ref|ZP_05281620.1| putative RNA pseudouridylate synthase [Bacteroides fragilis 3_1_12]
          Length = 302

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 110/226 (48%), Gaps = 20/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++YED+ I V  K  G+   G        A HI   L  +V   G+  R+   HRLD++T
Sbjct: 87  IVYEDAYIIVVEKKEGLLSVGTDRQKERTAQHI---LSEYVGRSGRGNRIFVVHRLDRDT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+     + L + +      + Y ++V G  +   + + +WL  ++     YV 
Sbjct: 144 SGLMMFAKDEKTQRTLRDHWHDIVTDRRYVAVVTGEMEKDSDTVVSWLTDRTL----YVS 199

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++ G+  +I+H++ I   A  +  +E++  TGR +Q+RVH   +G P++GD +Y  
Sbjct: 200 SSSYDDGGSK-SITHYRTIKR-ANGYSLVELRLETGRKNQIRVHMQDLGHPLIGDGRYGI 257

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
           +   N   P+  +L LHA  +   HP   +L +   P P    K +
Sbjct: 258 DGGPN---PL-GRLALHAFKLCFYHPVTDQLMEFETPYPPAFKKLF 299


>gi|34496612|ref|NP_900827.1| pseudouridine synthase [Chromobacterium violaceum ATCC 12472]
 gi|34102467|gb|AAQ58832.1| probable pseudouridine synthase [Chromobacterium violaceum ATCC
           12472]
          Length = 224

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 58/193 (30%), Positives = 95/193 (49%), Gaps = 18/193 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L+++D + Y+ +K  G S     G A  +   L++ +D +   P   HRLD+ TSG+++
Sbjct: 3   TLIHQDPRFYLVDKHPGASFHR-EGDAPGLMDALRAGLDDEALWP--VHRLDRITSGLIL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VAR+  AA+ L ++   R ++K Y +L    P  K+  +A  + K    GG +    +  
Sbjct: 60  VARSAEAARALGDALAGREVEKYYLALSDRKPLKKQGRVAGDMAKGR--GGAW----RLT 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E   N A++ F           +L ++P TG+THQLRV     G PI+GD  Y  +    
Sbjct: 114 EGRENPAVTQFFSYALEPGLRLFL-LRPRTGKTHQLRVAMKSQGAPILGDALYGGS---- 168

Query: 280 FTSPIQNKLYLHA 292
                 ++ YLHA
Sbjct: 169 ----EADRGYLHA 177


>gi|229132101|ref|ZP_04260962.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST196]
 gi|228651369|gb|EEL07343.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST196]
          Length = 292

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 68/287 (23%), Positives = 131/287 (45%), Gaps = 46/287 (16%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
            R G + V+ +     +++Q+G+ ++I   +   +  ++ ++I                 
Sbjct: 33  FRGGAIEVNGQHTSVRHKLQAGEELQIFFPVEERSEGMEVEEI--------------PLC 78

Query: 101 LLYEDSKIYVFNKPAGISV------QGGS---GIAYHIDG-FLKSWVDSKGQKPRLTHRL 150
           ++YED  + V NK A +S         GS    + YH D   L S V        +  RL
Sbjct: 79  IVYEDDAVLVINKEANMSTIPSREHPSGSIANALLYHYDKQNLASTV-------HIVTRL 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ R     L++  + + +++ Y ++V G    +   I   + +K+    
Sbjct: 132 DRDTSGLMLIAKNRFVHHLLSKQHQQKGVKRTYEAIVHGTILEEVGTIDAPIGRKA---- 187

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D +      E G   A++HF+V++  + K   + ++  TGRTHQ+RVH  ++G P++GD 
Sbjct: 188 DSIIERTVCEDGQR-AVTHFRVMESSSDK-THVALELETGRTHQIRVHMAYIGHPLLGDD 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPAHM 315
            Y           +  +  LH+  +   HP  E G +  T  +P  M
Sbjct: 246 LYGGR------RDVIKRQALHSTSLTFYHPILEKG-MTFTVSIPEDM 285


>gi|317968138|ref|ZP_07969528.1| pseudouridine synthase [Synechococcus sp. CB0205]
          Length = 318

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 70/314 (22%), Positives = 133/314 (42%), Gaps = 49/314 (15%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQ 81
           ++   Y H +    ++ L +G++  + ++++ +  + +G   +   PP   A   ++ ++
Sbjct: 30  YYAERYGHSDPSVWRERLAAGEIWCNGQQLRADAALAAGDQLIWHRPPWEEAAVPVLSQR 89

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSK 140
            ++                  ++D  + V NKP+G+ V    G   H +   L++W    
Sbjct: 90  AVV------------------FDDGDLLVLNKPSGLPVLPAGGFLEHTLLTQLQTWAPEA 131

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR--------MRRIQKIYWSLVWGIPK 192
               R  HRL + TSG+LV AR R     L+   R         R   K+Y +L   +  
Sbjct: 132 ----RPVHRLGRFTSGLLVCARQRETRGQLSAQLRESTAASAASRGCLKVYRALTEPLAA 187

Query: 193 N----KKECIANWLLKKSH-IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +    +   I   + ++ H + G         +  A  + S   +++   ++ C +EM+ 
Sbjct: 188 DWRCGESRAITVPIGRRPHALLGQLWCAALPGDSSALESRSALTLLERRPER-CLVEMEI 246

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI----QNKLYLHARYMDLPHPEGG 303
            TGR HQ+R+H   +G P++GD  Y     G    P          LHA  + L  P G 
Sbjct: 247 ATGRPHQIRIHTAALGSPLLGDPLY---LPGGVARPEVLPGAGGYQLHAHRLRL-EPRG- 301

Query: 304 RLQITAPLPAHMVK 317
            L + APLP+ +++
Sbjct: 302 -LALEAPLPSGLLE 314


>gi|229043051|ref|ZP_04190781.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH676]
 gi|228726292|gb|EEL77519.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH676]
          Length = 292

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 112/222 (50%), Gaps = 22/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           ++YED  + + NK A +S +      A  +   L S  D +       +  RLD++TSG+
Sbjct: 79  IIYEDDAVLIINKEANMSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGL 138

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     L++  + + +++ Y ++V G    ++  I   + +KS+       +++
Sbjct: 139 MLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKIVEREGMIDAPIGRKSN------SIIE 192

Query: 218 QN--EKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +   E G   A++HFKVID  + +    LE++  TGRTHQ+RVH  H+G  ++GD  Y  
Sbjct: 193 RMICEDG-QRAVTHFKVIDSTYHKTHVALELE--TGRTHQIRVHMAHIGHSLLGDSLY-- 247

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
              G     ++ +  LH++ +   HP     +  T  LP+ M
Sbjct: 248 ---GGRRDEMKRQ-ALHSKSLTFYHPILEKEMSFTIKLPSDM 285


>gi|254506177|ref|ZP_05118321.1| pseudouridine synthase Rlu family protein, TIGR01621 [Vibrio
           parahaemolyticus 16]
 gi|219550995|gb|EED27976.1| pseudouridine synthase Rlu family protein, TIGR01621 [Vibrio
           parahaemolyticus 16]
          Length = 231

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 61/194 (31%), Positives = 88/194 (45%), Gaps = 21/194 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +LY      V  K   +SV    G     +  L   V +K   P+L   HRLD+ TSG+L
Sbjct: 4   ILYTHPDFIVVVKHPNVSVHKDEG-----ETMLLQEVAAKTGDPKLYLVHRLDKMTSGLL 58

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR+  AA  L   F  R I+K Y ++    PK K+  I   + +        ++    
Sbjct: 59  LLARSSKAASALATLFSDREIEKYYLAIGSSKPKKKQGAIIGDMERSRRSTWKLIN---- 114

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             +  N AI+ F       Q    L  +PHTG+THQ+RV    +G  IVGD  Y A+ K 
Sbjct: 115 --RRDNPAITQF-FSTASGQGERLLLCKPHTGKTHQIRVALKSIGSAIVGDAIYNASCKA 171

Query: 279 NFTSPIQNKLYLHA 292
                  ++ YLHA
Sbjct: 172 -------DRGYLHA 178


>gi|118587355|ref|ZP_01544781.1| pseudouridine synthase [Oenococcus oeni ATCC BAA-1163]
 gi|118432179|gb|EAV38919.1| pseudouridine synthase [Oenococcus oeni ATCC BAA-1163]
          Length = 301

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 74/278 (26%), Positives = 131/278 (47%), Gaps = 34/278 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
            G++ V+ + V  N+ +++G+ + I  PP         +E   LD+       +D LK  
Sbjct: 38  GGKIVVEGREVFTNDYVKNGEKITIFMPPE--------RENVELDADF-----TDPLK-- 82

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKS-WVDSKGQK--PRLTHRLDQETSG 156
           +++ED    + +KPA ++ V G +     +   +K+  +  K     P +  RLD++TSG
Sbjct: 83  VVFEDKNFLIVDKPAFVTTVPGHADRKTTLVNMIKAHLIQEKADSLVPHVVTRLDRDTSG 142

Query: 157 ILVVARTRAAAQHLTESF-RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           ++++A+ + A   L ++      I+K Y +LV G  +     I   +     I GD++  
Sbjct: 143 LVLLAKHKFAHALLNDALMEHHDIEKFYVALVSGNFQEDHGMIDEPI---GRIEGDFIR- 198

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +Q  +    +++ + +   F   F  L +Q HTGRTHQ+RVH    G P++GD  Y   
Sbjct: 199 -RQVRQDGKRSVTEYWIEKRF-DNFTQLRIQLHTGRTHQIRVHMAWAGHPLIGDVLY--- 253

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
             G   S + ++  LHA  M    P   + Q   A LP
Sbjct: 254 --GGPHSKLISRQALHASEMIFFDPFANKNQHFNAGLP 289


>gi|325955275|ref|YP_004238935.1| pseudouridine synthase [Weeksella virosa DSM 16922]
 gi|323437893|gb|ADX68357.1| pseudouridine synthase [Weeksella virosa DSM 16922]
          Length = 232

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 102/220 (46%), Gaps = 38/220 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPRLTHRLDQETSG 156
           +LY+DS++   +KP G+ V   S  A  +  F    L++++   GQ     HRLD++T+G
Sbjct: 4   ILYQDSRLVAIHKPPGLLVHR-SYYARDVKQFAVQELRNFLG--GQHVYPIHRLDRKTAG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A  +     + E F  R + K YW++V G    ++E + ++ L      G      
Sbjct: 61  VLLFALDKEMLSLMNEIFNSRAVTKEYWAIVRGY--TEQEGVIDYPLTND--DGQ----- 111

Query: 217 KQNEKGANYAISHFKVIDCFAQ----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +Q+ K     + H ++   F +    ++  ++  P TGR HQLR H  H+  PI+G   +
Sbjct: 112 RQDAKTYYQTLQHAEINLPFGKHATSRYSLVKALPETGRMHQLRKHLRHIAHPILGSRPH 171

Query: 273 CANFKGNFTSPIQNKLYLH----------ARYMDLPHPEG 302
             N         QNKL+L           AR +   HPE 
Sbjct: 172 GCN--------KQNKLWLENFQLEQMMLLARSLRFTHPES 203


>gi|269963462|ref|ZP_06177789.1| pseudouridine synthase Rlu family protein [Vibrio harveyi 1DA3]
 gi|269831862|gb|EEZ85994.1| pseudouridine synthase Rlu family protein [Vibrio harveyi 1DA3]
          Length = 230

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 103/226 (45%), Gaps = 23/226 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL++
Sbjct: 4   ILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAKQ---SGDEQLYLIHRLDKMTSGILLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   AA  L+++F  R ++K Y ++    PK K+  +   + +        V     N 
Sbjct: 61  GRNAKAASALSQAFADREVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV-----NS 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K  N AI+ F  +     +  +L  +PHTG+THQ+RV    +G  IVGD  Y A   GN 
Sbjct: 116 K-TNPAITQFFSLAAEPGERLFL-CKPHTGKTHQIRVALKSVGSGIVGDPIYNA---GNE 170

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                ++ YLHA  +  P+ +     I  P      + + +LG K+
Sbjct: 171 A----DRGYLHAFSLCFPYQDETHCFICDP------REYKALGSKW 206


>gi|255532252|ref|YP_003092624.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
 gi|255345236|gb|ACU04562.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
          Length = 225

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 56/224 (25%), Positives = 94/224 (41%), Gaps = 10/224 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  +   NKP G+ V   S IA     F L+   D   +     HRLD++T G+L+
Sbjct: 4   IVYQDDHLIAINKPHGLLVHRSS-IANDAKEFALQLLRDQVNRHVSPVHRLDRKTGGLLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  +     + + F    +QK Y +++ G   ++         +   I   +   V   
Sbjct: 63  FAFEKDVETAMQQKFMNGEVQKKYLAVLRGYAPDQMAIDYPLAKENGTIQEAFTAFVTLK 122

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               + A            ++  +E  P TGR HQLR H  H+  PI+GD K+  N +  
Sbjct: 123 RAELDIAFGKHPT-----SRYSLVEASPTTGRMHQLRKHFAHIFYPIIGDRKHGCNKQNK 177

Query: 280 FTSPI--QNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
           F         + LHA  +   HP  G ++Q+ A +    ++  D
Sbjct: 178 FFKETWDMTTMLLHASELTFLHPVTGKQVQLKASVQTEFLRVMD 221


>gi|116490290|ref|YP_809834.1| pseudouridylate synthase, 23S RNA-specific [Oenococcus oeni PSU-1]
 gi|290889676|ref|ZP_06552765.1| hypothetical protein AWRIB429_0155 [Oenococcus oeni AWRIB429]
 gi|116091015|gb|ABJ56169.1| Pseudouridylate synthase, 23S RNA-specific [Oenococcus oeni PSU-1]
 gi|290480673|gb|EFD89308.1| hypothetical protein AWRIB429_0155 [Oenococcus oeni AWRIB429]
          Length = 302

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 59/208 (28%), Positives = 101/208 (48%), Gaps = 28/208 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS--KGQKPR-------LTHRLD 151
           +L E     + +KPAG+ +   S      D  L ++V++  KG   R       + HR+D
Sbjct: 86  ILSEKEDYLLVDKPAGMKMHPHS--PNETDTLL-NYVEAQLKGHLSRSCPAHAFMVHRID 142

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG++++A+   A   L +    +RI++ Y + V G  +NKK  I         I  D
Sbjct: 143 RDTSGVVIIAKNPLAVGILDQLLAKKRIKRTYLAWVSGNLENKKGSI------DQAIAVD 196

Query: 212 YVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            ++  K+  ++    A++H+  I    Q    + +   TGRTHQ+RVH   +G PIVGDH
Sbjct: 197 PINPYKRIVDQAGQKAVTHWTKIHTVYQN-TLVRVSLETGRTHQIRVHFAAIGHPIVGDH 255

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLP 298
            Y             ++L LH+  +++P
Sbjct: 256 LY--------NGLAYSRLLLHSATIEIP 275


>gi|329920350|ref|ZP_08277082.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
 gi|328936026|gb|EGG32479.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
          Length = 307

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 56/183 (30%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 138 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 196

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 197 PIGKKDDPVKRYIM------EGGKESVTKYRVIKQVAGA-SLVELQLFTGRTHQIRVHMQ 249

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F  P Q    LH   +    P E  R+++    PA M++ W
Sbjct: 250 YLGHPLFGDHLY--GVEDDF--PRQ---ALHCFLLAFDDPLEHKRIEVQIADPADMLQLW 302

Query: 320 DSL 322
             L
Sbjct: 303 QKL 305


>gi|330829216|ref|YP_004392168.1| Pseudouridine synthase [Aeromonas veronii B565]
 gi|328804352|gb|AEB49551.1| Pseudouridine synthase [Aeromonas veronii B565]
          Length = 219

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 56/193 (29%), Positives = 91/193 (47%), Gaps = 16/193 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILV 159
           +L+E     V +K  GI +         ++  L + V +  G      HRLD+ TSG+++
Sbjct: 4   ILFEHPAFLVIDKQPGIGMHDEKDDGEAVNPGLVNRVKADTGLTLYPVHRLDKMTSGLVL 63

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +ART  A + L+ +F  R + K Y +L    PK K+  +   + K    GG ++ V   +
Sbjct: 64  LARTTEANRELSMAFAAREVSKQYLALSDRKPKKKQGWVKGDMQKGR--GGSWMLVRTLD 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AIS F  +    +      ++P TG+THQ+RV    +G PI+GD +Y       
Sbjct: 122 ----NPAISWFDSVSV-REGLRLYRIKPQTGKTHQIRVALKSIGAPILGDKRYGGT---- 172

Query: 280 FTSPIQNKLYLHA 292
                 ++ YLHA
Sbjct: 173 ----PSDRGYLHA 181


>gi|226308249|ref|YP_002768209.1| pseudouridine synthase [Rhodococcus erythropolis PR4]
 gi|226187366|dbj|BAH35470.1| putative pseudouridine synthase [Rhodococcus erythropolis PR4]
          Length = 323

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 62/208 (29%), Positives = 98/208 (47%), Gaps = 12/208 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  I V +KP  + S   G  IA      L+  +D     P   HRLD+ T+G+L+
Sbjct: 106 ILYRDENILVVDKPHFLASTPRGRYIAESALVRLRRDLDLPELSP--AHRLDRVTAGLLL 163

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               +AA +     F  RR+ K Y ++           ++  ++ +S I  +   V+K  
Sbjct: 164 FTVHQAARRGYQTMFAERRVTKEYEAIA-----RYDAQVSTPVVVRSRIVKER-GVLKAA 217

Query: 220 E-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           E +G   + S  ++I+     F    + PHTG+THQLR+H   +G PI GD+ Y  +F  
Sbjct: 218 EIEGEPNSESRIELIET-RDGFARYRLIPHTGKTHQLRLHMTSLGLPIHGDNFY-PDFYD 275

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
                  N L L ++ ++   P  GRLQ
Sbjct: 276 VAAEDYSNPLRLLSKVLEFEDPTTGRLQ 303


>gi|57650200|ref|YP_185880.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus COL]
 gi|87161458|ref|YP_493609.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88194701|ref|YP_499497.1| hypothetical protein SAOUHSC_00944 [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|151221090|ref|YP_001331912.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|161509205|ref|YP_001574864.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|258452042|ref|ZP_05700058.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A5948]
 gi|262049353|ref|ZP_06022227.1| hypothetical protein SAD30_1651 [Staphylococcus aureus D30]
 gi|262052363|ref|ZP_06024565.1| hypothetical protein SA930_0105 [Staphylococcus aureus 930918-3]
 gi|282923686|ref|ZP_06331365.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|284023934|ref|ZP_06378332.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp.
           aureus 132]
 gi|294847992|ref|ZP_06788739.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9754]
 gi|304381438|ref|ZP_07364089.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|57284386|gb|AAW36480.1| ribosomal large subunit pseudouridine synthases, RluD subfamily
           [Staphylococcus aureus subsp. aureus COL]
 gi|87127432|gb|ABD21946.1| pseudouridine synthases, RluA subfamily [Staphylococcus aureus
           subsp. aureus USA300_FPR3757]
 gi|87202259|gb|ABD30069.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           NCTC 8325]
 gi|150373890|dbj|BAF67150.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|160368014|gb|ABX28985.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|257860257|gb|EEV83089.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A5948]
 gi|259159735|gb|EEW44777.1| hypothetical protein SA930_0105 [Staphylococcus aureus 930918-3]
 gi|259162585|gb|EEW47153.1| hypothetical protein SAD30_1651 [Staphylococcus aureus D30]
 gi|269940506|emb|CBI48884.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus TW20]
 gi|282593072|gb|EFB98072.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|294824792|gb|EFG41214.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9754]
 gi|302750832|gb|ADL65009.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus str. JKD6008]
 gi|304340011|gb|EFM05954.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|315197538|gb|EFU27874.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320141176|gb|EFW33023.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320143233|gb|EFW35023.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|329731131|gb|EGG67502.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21189]
          Length = 284

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 90/192 (46%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++  L+  +LYED+ I +  KP     Q  +    H    L   V    Q+   
Sbjct: 65  SVNLIPYARKLE--VLYEDAFIIIVTKPNN---QNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKVNLKKIYTCLVYGKTHTSGIIEAN 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 176 IRRSKDRI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 229 HIGHPIVGDSLY 240


>gi|328948215|ref|YP_004365552.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
 gi|328448539|gb|AEB14255.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
          Length = 314

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 66/301 (21%), Positives = 138/301 (45%), Gaps = 29/301 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M ++++   E+D+   RLD+  K  +    +   N+ K++R   ++++  +    +RI+S
Sbjct: 1   MEFIEFEAKEDDD-GRRLDKAAKRIFESKGLQPENIFKLIRKTLIKLNNAKSAPEDRIKS 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + I   +   N   K +    S+  +  H D +     +++  +++ NK +GI VQ 
Sbjct: 60  GDKIFIADFLLKENAARKSKTEKKSTQKI--HGD-ISLQTAFKNEHLWIINKQSGIEVQP 116

Query: 122 GSGIAYHIDGFLKSWVD--SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++ +  F+       S   +P   HR+D+ T+G++  +++   A+  +E+ +   I
Sbjct: 117 SKNSSFCLADFVAQNTKNASLSFRPGPLHRIDKFTTGLITFSQSLQGAKWFSENIKNHSI 176

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++V       +  I + + +K+         +K+  +G          I C  ++
Sbjct: 177 KKTYLAVVENFLPENELAIYDTIEEKTA-----CTKIKKIAQG----------IFC-GKE 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDL 297
               ++Q  TGR HQ+R+H    G P++GD  Y       G F+S      +LHA  ++ 
Sbjct: 221 ISLAKIQIETGRKHQIRIHCASRGFPLLGDKLYGGTKIPNGEFSS---CGFFLHAWKLEF 277

Query: 298 P 298
           P
Sbjct: 278 P 278


>gi|226327444|ref|ZP_03802962.1| hypothetical protein PROPEN_01315 [Proteus penneri ATCC 35198]
 gi|225203970|gb|EEG86324.1| hypothetical protein PROPEN_01315 [Proteus penneri ATCC 35198]
          Length = 238

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 63/221 (28%), Positives = 94/221 (42%), Gaps = 36/221 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LY+D  + + NKP G+    G        + Y +                L HRLD  T
Sbjct: 19  ILYQDEHLVIINKPTGLLSLSGKNPQNIDSVHYRLVKLFPGCT--------LVHRLDFGT 70

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VAR +A    L + F  R I KIY +L+ G  K K E + +  + K       + 
Sbjct: 71  SGLMIVARNKAINALLCQQFSQRNITKIYNALLCGHLK-KNEGVIDAPIAKDPALFPRMS 129

Query: 215 VVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPI 266
           +   N K A    S + VI+ F              ++  P TGRTHQLR+H+  +G  I
Sbjct: 130 ICPINGKPAR---SGYHVIERFYHTLEDGTLLPLTRVQFTPETGRTHQLRIHSQFIGHSI 186

Query: 267 VG-------DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +G       D       +G   +P   +L LHA  +   HP
Sbjct: 187 LGCDLYGGCDGGLIEKREGTERTP---RLMLHASELHFVHP 224


>gi|82548298|gb|ABB82988.1| putative RNA pseudouridylate synthase [uncultured organism
           HF10_3D09]
          Length = 294

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 66/280 (23%), Positives = 128/280 (45%), Gaps = 37/280 (13%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           P  +   L+K+L + ++ V++K + +  + + +G+ V I P         K +  ++ + 
Sbjct: 20  PQASTNVLRKMLTNRRITVEEKIIHRAKHPVLAGETVEIRP---------KPKLSIEETR 70

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--- 145
             +  +  L   +++ED  I V  KPAG+       +   +D      V+   +  +   
Sbjct: 71  QTSAETHSLD--IIFEDDAILVVEKPAGLLSVATDRL--EVDTLHNRCVEYCRELKKKAW 126

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLD+ TSG++V A+T    + L E F  R + + Y +LV G+ +  +        
Sbjct: 127 CFIVHRLDKATSGLMVFAKTEDVKRDLQEQFAERLVHRHYVALVEGVAEPGQAI------ 180

Query: 204 KKSHIGGD---YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              H+  D    V V  +  K + +AI+ + +++    +   L +   TGR HQ+RV   
Sbjct: 181 --QHLVEDRNLRVFVSDKKTKTSKHAITTWDILE-KGDESTLLSVVIETGRRHQIRVAMA 237

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             G P++GD  + A      T+ +  ++ LHA  ++  HP
Sbjct: 238 ENGTPVMGDTMHGA------TTNLHGRICLHAVALEFLHP 271


>gi|298694246|gb|ADI97468.1| probable RNA pseudoridylate synthase [Staphylococcus aureus subsp.
           aureus ED133]
          Length = 284

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 58/195 (29%), Positives = 90/195 (46%), Gaps = 28/195 (14%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWV 137
           SVNL  ++  L+  +LYED+ I +  KP   +               + YH        V
Sbjct: 65  SVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCIPSREHPHESLIEQVLYH------CQV 116

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +   P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G   +    
Sbjct: 117 HGENINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKGNLKKIYTCLVYGKTHSSGII 172

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            AN    K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RV
Sbjct: 173 EANIRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRV 225

Query: 258 HALHMGCPIVGDHKY 272
           H  H+G PIVGD  Y
Sbjct: 226 HFQHIGHPIVGDSLY 240


>gi|258423513|ref|ZP_05686403.1| conserved hypothetical protein [Staphylococcus aureus A9635]
 gi|257846214|gb|EEV70238.1| conserved hypothetical protein [Staphylococcus aureus A9635]
          Length = 284

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 90/192 (46%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++  L+  +LYED+ I +  KP     Q  +    H    L   V    Q+   
Sbjct: 65  SVNLIPYARKLE--VLYEDAFIIIVTKPNN---QNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKVNLKKIYTCLVYGKTHTSGIIEAN 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 176 IRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 229 HIGHPIVGDSLY 240


>gi|329769221|ref|ZP_08260640.1| hypothetical protein HMPREF0433_00404 [Gemella sanguinis M325]
 gi|328839352|gb|EGF88932.1| hypothetical protein HMPREF0433_00404 [Gemella sanguinis M325]
          Length = 294

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 71/300 (23%), Positives = 126/300 (42%), Gaps = 45/300 (15%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILD---SSVNLTKHSDF 96
           +L++   R    R+KF+N       +++      + +I+K+  +++    S   ++H  F
Sbjct: 20  LLKNNISRKTLTRIKFDN----DGSIKVNGKEENVRYILKKNDVVEITLPSEEFSEHVRF 75

Query: 97  LKSIL--LYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            +  L  +YED  + + NKPA +          S +   ++G+ K   +     P +  R
Sbjct: 76  FEDKLDIIYEDEYLLIVNKPADLPSIPSRNNEDSSLLEIVNGYFKK--NHYSTIPHIVTR 133

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG------IPKNKKECIANWLL 203
           LD+ T+G++++A+ R    H+   F    I K Y +LV G      I  N K    + + 
Sbjct: 134 LDKNTTGLVLIAKHR----HIHALFSKEEIDKFYLALVVGKVEDGIIEANIKRASDSIIT 189

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +     GDY      +EK              F      ++++  TGRTHQ+RVH     
Sbjct: 190 RCVADDGDYAKTQVWSEKYN------------FKNNISLVKLKLFTGRTHQIRVHMSFSN 237

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            P++GD  Y  N        I ++  LH   +   HP   + +   A LP  M    ++L
Sbjct: 238 NPLLGDELYGGN------KQIIDRQALHCYNLKFKHPITRKNIDAVAQLPEDMNNIVENL 291


>gi|327441282|dbj|BAK17647.1| pseudouridylate synthase, 23S RNA-specific [Solibacillus silvestris
           StLB046]
          Length = 294

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 53/218 (24%), Positives = 102/218 (46%), Gaps = 20/218 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED  + + +KPA +S         + +A  + G+ +           +  RLD++TS
Sbjct: 83  VVYEDEAVLLVDKPAFMSSIPSREHPNNTLANLVYGYFEQQ--QHASTVHIVTRLDRDTS 140

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++++A+ R     ++E  +  +I + Y ++  GI    ++ I   + +K     D   +
Sbjct: 141 GLMLIAKHRHIHHLMSEQQKKGQIHREYEAVAEGIIVQDQQSIIAPIGRK-----DTSII 195

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++      +A +   V+         + ++ HTGRTHQ+RVH  ++G P+VGD  Y   
Sbjct: 196 EREVRPDGQFAHTDVTVL-TRKNNMTHIRLKLHTGRTHQIRVHMAYIGHPLVGDELYGG- 253

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                T    ++  LH RY++  HP    R+   + LP
Sbjct: 254 -----THTFIDRQALHCRYIEFEHPLTKERVHFESKLP 286


>gi|282916259|ref|ZP_06324021.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus D139]
 gi|283770074|ref|ZP_06342966.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
 gi|282319699|gb|EFB50047.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus D139]
 gi|283460221|gb|EFC07311.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
          Length = 284

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 90/192 (46%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++  L+  +LYED+ I +  KP     Q  +    H    L   V    Q+   
Sbjct: 65  SVNLIPYARKLE--VLYEDAFIIIVTKPNN---QNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKVNLKKIYTCLVYGKTHTSGIIEAN 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 176 IRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 229 HIGHPIVGDSLY 240


>gi|90581195|ref|ZP_01236993.1| putative pseudouridine synthase Rlu family protein [Vibrio angustum
           S14]
 gi|90437566|gb|EAS62759.1| putative pseudouridine synthase Rlu family protein [Vibrio angustum
           S14]
          Length = 231

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 59/200 (29%), Positives = 93/200 (46%), Gaps = 20/200 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           L+Y+     V NK  GISV        +    L +  +  G +K  L HRLD+ TSG+L+
Sbjct: 4   LVYQHPDFLVINKHPGISVHKDD----NDQPLLAAVAEQTGDEKLYLIHRLDKMTSGLLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R + AA  L+ +F  R ++K Y ++    PK KK+ +    + +S      +   K+N
Sbjct: 60  LGRNKEAASILSSNFAERVVEKFYVAIGTKKPK-KKQGVVIGDMTRSRRSSWKLESTKEN 118

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 AI+ F        +  +L  +PHTG+THQ+RV    +G  I GD  Y       
Sbjct: 119 P-----AITQFFSTAAGEGRRLFL-CKPHTGKTHQIRVALRSVGSGITGDDIYGTE---- 168

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +  P+
Sbjct: 169 ----ASDRGYLHAYALSFPY 184


>gi|116495316|ref|YP_807050.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
 gi|239629769|ref|ZP_04672800.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|301066888|ref|YP_003788911.1| 23S RNA-specific pseudouridylate synthase [Lactobacillus casei str.
           Zhang]
 gi|116105466|gb|ABJ70608.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           casei ATCC 334]
 gi|239527381|gb|EEQ66382.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|300439295|gb|ADK19061.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           str. Zhang]
          Length = 293

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 62/224 (27%), Positives = 108/224 (48%), Gaps = 36/224 (16%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           N  +++GQ++R                 + +S  LT   +F    ++YED+   + +KPA
Sbjct: 47  NGPVEAGQIIRFE---------------IPTSKTLT--PEFAPLEVIYEDANWLIVSKPA 89

Query: 116 GISVQGG-----SGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           G++   G     S +   I G+L +  +D+   +P +  RLD++T G LV+A     AQ 
Sbjct: 90  GLTSVPGPHTPNSSLLNRIAGYLVEQKIDAP--QPAIMTRLDRDTVG-LVLAAKHPYAQG 146

Query: 170 LTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
             +    R + K Y ++V G +P  K E  A   L       D +H +   +     A++
Sbjct: 147 RFDQAHQRTLTKHYLAVVSGKLPSPKGEIDAPLKL-----AADGIHRIVAAD--GQTALT 199

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++V+    +    +++Q  TGRTHQ+RVH   +G P++GDH Y
Sbjct: 200 KYRVLK--EKTNTLVDVQLLTGRTHQIRVHFASLGHPLIGDHLY 241


>gi|149197335|ref|ZP_01874386.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Lentisphaera araneosa HTCC2155]
 gi|149139353|gb|EDM27755.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Lentisphaera araneosa HTCC2155]
          Length = 218

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 87/178 (48%), Gaps = 12/178 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETS 155
           L+  ++YE   + V NKP  +     +G     D  L+ W +  +G      H+LD +TS
Sbjct: 5   LEKRIIYEKDGLLVLNKPYDLP---STGRKLDDDDCLQYWLIQRQGAMVWAVHQLDADTS 61

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI +    +   ++  E     +  K Y ++V G+P + K+C  +  + K       +H 
Sbjct: 62  GINLFVTEKKLVKYYKELLEQAQADKQYLAIVHGVP-SWKQCEEHGRIGKVDARSLGIHA 120

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             +       A SHF+VI    + F  ++++  TGRTHQ+R+H  H+G P+VG+  YC
Sbjct: 121 EGKT------AHSHFEVIGS-VKDFSLIKVKIFTGRTHQIRIHLSHLGHPLVGEEWYC 171


>gi|15923998|ref|NP_371532.1| hypothetical protein SAV1008 [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|15926596|ref|NP_374129.1| hypothetical protein SA0866 [Staphylococcus aureus subsp. aureus
           N315]
 gi|156979333|ref|YP_001441592.1| hypothetical protein SAHV_1002 [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253316169|ref|ZP_04839382.1| hypothetical protein SauraC_08502 [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
 gi|253731614|ref|ZP_04865779.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|255005796|ref|ZP_05144397.2| hypothetical protein SauraM_04985 [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|258435274|ref|ZP_05689013.1| conserved hypothetical protein [Staphylococcus aureus A9299]
 gi|258441486|ref|ZP_05690846.1| conserved hypothetical protein [Staphylococcus aureus A8115]
 gi|269202622|ref|YP_003281891.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282894033|ref|ZP_06302264.1| hypothetical protein SGAG_01384 [Staphylococcus aureus A8117]
 gi|296275572|ref|ZP_06858079.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus MR1]
 gi|13700811|dbj|BAB42107.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           N315]
 gi|14246778|dbj|BAB57170.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|156721468|dbj|BAF77885.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253724613|gb|EES93342.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|257848935|gb|EEV72918.1| conserved hypothetical protein [Staphylococcus aureus A9299]
 gi|257852276|gb|EEV76202.1| conserved hypothetical protein [Staphylococcus aureus A8115]
 gi|262074912|gb|ACY10885.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282763519|gb|EFC03648.1| hypothetical protein SGAG_01384 [Staphylococcus aureus A8117]
 gi|329728975|gb|EGG65387.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 284

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 90/192 (46%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++  L+  +LYED+ I +  KP     Q  +    H    L   V    Q+   
Sbjct: 65  SVNLIPYARKLE--VLYEDAFIIIVTKPNN---QNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKVNLKKIYTCLVYGKTHTSGIIEAN 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 176 IRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 229 HIGHPIVGDSLY 240


>gi|301300163|ref|ZP_07206378.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300852251|gb|EFK79920.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 295

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 93/201 (46%), Gaps = 22/201 (10%)

Query: 96  FLKSILLYEDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           F+   +LYED    + +KPA ++     +     +   + G+ +     +G  P +  RL
Sbjct: 75  FVPIKILYEDDNYLLVDKPAFVASIPSPLHPNDSLVNRVVGYYQIR-GYRGIIPHIVTRL 133

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSGI++ A+ R A   L    +  +I K Y +++ GI  N      N  +    IG 
Sbjct: 134 DRDTSGIVIFAKHRYAHALLDSQLKEHKISKTYTAILSGILHN------NHYIIDLPIGR 187

Query: 211 DYVHVVKQ----NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           D   ++K+    +EK        F          C +++  HTGRTHQ+RVH  ++G P+
Sbjct: 188 DSTSLIKRKVLFSEKAKRSKTEIFVKERIRDNTLCKIKL--HTGRTHQIRVHCSYLGYPL 245

Query: 267 VGDHKYCANFKGNFTSPIQNK 287
           V D  Y     G  + P+Q +
Sbjct: 246 VSDTLY----GGAISMPLQRQ 262


>gi|253732634|ref|ZP_04866799.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|253729412|gb|EES98141.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
          Length = 284

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 90/192 (46%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++  L+  +LYED+ I +  KP     Q  +    H    L   V    Q+   
Sbjct: 65  SVNLIPYARKLE--VLYEDAFIIIVTKPNN---QNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKVNLKKIYTCLVYGKTHTSGIIEAN 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 176 IRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 229 HIGHPIVGDSLY 240


>gi|154685597|ref|YP_001420758.1| YjbO [Bacillus amyloliquefaciens FZB42]
 gi|154351448|gb|ABS73527.1| YjbO [Bacillus amyloliquefaciens FZB42]
          Length = 297

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 62/225 (27%), Positives = 104/225 (46%), Gaps = 28/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISV---------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  + V NK   +S             +G+  H   + KS V S      L  RLD
Sbjct: 84  ILYEDDHVLVVNKQPYVSSIPSREHPSESIANGVISH---YRKSGVQST---VHLVTRLD 137

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +++A+ R +   L+ + +   + + Y ++V GI   +KE   +  + + H    
Sbjct: 138 RDTSGAMLIAKHRLSHSLLSAAQKKGLVSRRYLAVVHGI-MLQKEGTVDAPIGRKHDSII 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              V  + ++    A++HF+  +     F    ++  TGRTHQ+RVH  ++G P+VGD  
Sbjct: 197 ERMVTPEGQR----AVTHFQT-EKAGHAFTLAALRLETGRTHQIRVHMSYLGHPLVGDTL 251

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           Y    +G        +  LH+  +   HP  G  L   AP+P  M
Sbjct: 252 YGGKNEG------IARQALHSERLSFVHPMTGETLVFHAPVPDDM 290


>gi|302803025|ref|XP_002983266.1| hypothetical protein SELMODRAFT_118202 [Selaginella moellendorffii]
 gi|300148951|gb|EFJ15608.1| hypothetical protein SELMODRAFT_118202 [Selaginella moellendorffii]
          Length = 312

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 70/256 (27%), Positives = 107/256 (41%), Gaps = 56/256 (21%)

Query: 101 LLYEDSKIYVFNKPAGI-------SVQGGSGIAYHI-DGFLKSWVDSKGQKPRLTHRLDQ 152
           ++++D  I V NKP G+       SV    G +Y    GF             L +RLD+
Sbjct: 61  VVFQDEWILVINKPCGVYSEHVLVSVPSLLGDSYSPHRGFF-----------HLANRLDR 109

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSGI+V+AR + AA  LT  F+ R ++K Y +L  G   + K  +      KS  G   
Sbjct: 110 DTSGIIVIARDKVAAGKLTNIFKSRELRKSYVALCVGKAPHWKRAVIESGHGKSRRGCWR 169

Query: 213 VH-------------VVK-------------------QNEKGANYAISHFKVID--CFAQ 238
           V+             VVK                   + + G    +   K++D      
Sbjct: 170 VYSKHDVERSLPDGSVVKDMSTKIEVMPSSLDEAKDSEEDDGEQRIVVEAKMVDPEPGTG 229

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              ++   P TGRTHQ+R+H   +G P+VGD KY      N         +LH+  +   
Sbjct: 230 DEVFIRAVPLTGRTHQIRLHCQFLGLPLVGDVKYGGPLHWNGEK--CQSHFLHSESIAFQ 287

Query: 299 HPEGGR-LQITAPLPA 313
           HP  G  +++ AP P+
Sbjct: 288 HPMTGEVVEVIAPHPS 303


>gi|259503014|ref|ZP_05745916.1| ribosomal large subunit pseudouridine synthase [Lactobacillus antri
           DSM 16041]
 gi|259169025|gb|EEW53520.1| ribosomal large subunit pseudouridine synthase [Lactobacillus antri
           DSM 16041]
          Length = 297

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 104/230 (45%), Gaps = 38/230 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQKPRLTH---RLDQETS 155
           + YED    V NKPAG++      +  A  +   +K +   +G + R+TH   RLD++TS
Sbjct: 80  IAYEDRDFLVLNKPAGVATVPAHNVPVADSLVNRVKRYYREQGYENRVTHVATRLDKDTS 139

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V  + R A   L    +   ++K Y++LV G                  +G  +V++
Sbjct: 140 GLVVFPKHRFAHAVLDRQLKHHAVKKNYYALVNG-----------------RLGSQHVYI 182

Query: 216 VKQNEKGANYAISHF-------KVIDCFAQKFC--W--LEMQPHTGRTHQLRVHALHMGC 264
                +  +  +           V + + ++ C  W  + ++ HTGRTHQ+RVH   +G 
Sbjct: 183 DAPIRRDPDSFVKRVVAPDGKPSVTEYWLERSCTEWSLVRIRLHTGRTHQIRVHFSFLGH 242

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
           P+VGD  Y         S + ++  LH  ++    P   RL  + APLP 
Sbjct: 243 PLVGDRMYGPAAG----SSLIDRQALHCYWLQFYSPFKERLITVRAPLPG 288


>gi|323440839|gb|EGA98547.1| RNA pseudoridylate synthase [Staphylococcus aureus O11]
 gi|323443872|gb|EGB01484.1| RNA pseudoridylate synthase [Staphylococcus aureus O46]
          Length = 284

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 90/192 (46%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++  L+  +LYED+ I +  KP     Q  +    H    L   V    Q+   
Sbjct: 65  SVNLIPYARKLE--VLYEDAFIIIVTKPNN---QNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKGNLKKIYTCLVYGKTHTSGIIEAN 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 176 IRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 229 HIGHPIVGDSLY 240


>gi|294139995|ref|YP_003555973.1| tRNA pseudouridine synthase C [Shewanella violacea DSS12]
 gi|293326464|dbj|BAJ01195.1| tRNA pseudouridine synthase C [Shewanella violacea DSS12]
          Length = 292

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 108/239 (45%), Gaps = 23/239 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+ED  I   +KPAG+ V   S +A     F ++   D  G      HRLD+ TSG+L+ 
Sbjct: 47  LFEDDDIVAIHKPAGLLVHR-SYLARRERFFAMQLTRDKVGCHVFPVHRLDRPTSGVLLF 105

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++   A  L   F  + I+K Y ++V G   N  E        K  +       V Q++
Sbjct: 106 AKSCEMANALCVQFADKTIEKHYLAIVRG---NMHEAATLDYPLKVELDDLGDKDVNQDK 162

Query: 221 KGANYAISHFKVIDC---------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              +   S+  +++           + ++  +++ PHTGR HQLR H  H+  PI+GD  
Sbjct: 163 PAQDAVTSYQPLLNTEIPFTSGRYASSRYALVKLSPHTGRKHQLRRHMAHLRHPILGDTT 222

Query: 272 YCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
           +        F+ +F+    N+L+L A+ +   HP  G R+ I   L       +  LG+
Sbjct: 223 HGDGKQNKFFREHFSV---NRLWLIAKQLTFNHPRTGERMIIETELEQQWFDLFKGLGW 278


>gi|227522958|ref|ZP_03953007.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus hilgardii
           ATCC 8290]
 gi|227089776|gb|EEI25088.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus hilgardii
           ATCC 8290]
          Length = 299

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 68/291 (23%), Positives = 121/291 (41%), Gaps = 37/291 (12%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNHIIKEQKILDSSVNLTKHSD 95
           + I  SGQV ++ +      ++  G  V +  P      N  + EQ I            
Sbjct: 38  KNIKTSGQVLINSRSSDSQTKLADGDQVTVILPDEAGDPNVAVSEQPIK----------- 86

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRL 150
                ++YED    V +KPAG++V  G       +   + G+L     +    P +  RL
Sbjct: 87  -----VVYEDDNWLVVDKPAGLTVVPGPANRDDTLVNRVKGYLVR-AGATDMVPHIITRL 140

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSG++++A+ R A     E    +++ K Y ++V G+       I   + K  +   
Sbjct: 141 DRFTSGLVLIAKHRLANSLANELLAAKQLHKRYLAVVSGVGLPDHGRIQKPIAKDPN--- 197

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            Y  ++  + +   ++ + + V          +E+  HTGRTHQ+RVH   +G P++GD 
Sbjct: 198 GYGQIISDDGR---FSDTEYWVRQRLNDDML-VEVALHTGRTHQIRVHFASIGHPLLGDQ 253

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
            Y             ++  LHA  +    P     +++ +PLP  M    D
Sbjct: 254 LYHGPMNMGI-----DRQALHAVMLGFNDPFSQSEIKLKSPLPKDMSSILD 299


>gi|160916027|ref|ZP_02078235.1| hypothetical protein EUBDOL_02055 [Eubacterium dolichum DSM 3991]
 gi|158432503|gb|EDP10792.1| hypothetical protein EUBDOL_02055 [Eubacterium dolichum DSM 3991]
          Length = 317

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 78/305 (25%), Positives = 130/305 (42%), Gaps = 37/305 (12%)

Query: 37  LQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH-- 93
           +QK L  GQ ++V+++ +  N  +Q   ++RI P                   +L KH  
Sbjct: 42  MQKQLYQGQRIQVNQQTILHNTPLQRKDLIRIQPF---------------PQYDLEKHLI 86

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQK--PRLTHRL 150
             F    +LYED    +  KP+ + V   G+     +   +K +   +G     R  HRL
Sbjct: 87  PCFDPLSILYEDDLFLIVYKPSFMLVHSDGNETETTLYDIVKGYYLLQGLDIPVRAIHRL 146

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ETSG ++  +       L    + ++I + Y +L   +       + + L     IG 
Sbjct: 147 DKETSGAVIFCKIPLLQPLLDYMLQEKQIDRQYLALCAKV-------LNDDLTIDKQIGR 199

Query: 211 DYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D  +  K    K    A +   VI  + Q +  +  + + GRTHQ+RVH   +  P++ D
Sbjct: 200 DRHNAKKMRISKQGKSAKTDVHVIAQY-QDYTLIACKLYQGRTHQIRVHLASITHPLLHD 258

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
             Y     GN+   I N+  LHA  + L HP     + I  PLP  M K  + +    DR
Sbjct: 259 TLY-----GNYDKRI-NRCALHAYRIQLCHPFTQQNITIECPLPTDMKKLVEPINLCNDR 312

Query: 329 NLYIK 333
           +++ K
Sbjct: 313 SIFKK 317


>gi|311742421|ref|ZP_07716230.1| RNA pseudouridine synthase [Aeromicrobium marinum DSM 15272]
 gi|311314049|gb|EFQ83957.1| RNA pseudouridine synthase [Aeromicrobium marinum DSM 15272]
          Length = 283

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 59/192 (30%), Positives = 89/192 (46%), Gaps = 17/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D ++ V +KPA +S +  G  +A  +   L+  +      P   HRLD+ TSG+LV
Sbjct: 62  VLHRDERLVVVDKPAFLSTIPRGRHVAQSVVVRLRDELGLPELSP--VHRLDRVTSGVLV 119

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +    R R A Q +   F+ RR+ K Y +L    P  +        L+K   G   V V 
Sbjct: 120 LTTERRWRGAYQGM---FQHRRVHKAYRALAPLRPDLELPLTVRNHLRKDR-GAWQVTVD 175

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              +  A   +     +D          + P TGRTHQLR H   +G PIVGD  Y A  
Sbjct: 176 PDAQPNAETLVE----LDAVVGGLGVYRLTPRTGRTHQLRAHLCGLGIPIVGDPLYPAVL 231

Query: 277 K---GNFTSPIQ 285
           +    +F++P+Q
Sbjct: 232 EVDVDDFSTPLQ 243


>gi|255029306|ref|ZP_05301257.1| hypothetical protein LmonL_09598 [Listeria monocytogenes LO28]
          Length = 245

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 117/242 (48%), Gaps = 41/242 (16%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQV----VRIPPVINALNHIIKEQKILDSSVNLTK 92
           +Q +L++G + V+ +  K N ++Q G      VR P          +E ++L   + L  
Sbjct: 32  IQLMLKNGDITVNGELAKPNYKVQVGDEIHYEVREP----------EELEVLAEDIPLD- 80

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---------YHIDGFLKSWVDSKGQK 143
                   + +ED  + V NKP G+ V   +G A         +H D    S ++ K  +
Sbjct: 81  --------IYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL--SGINGK-IR 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D++TSG+L+VA+   A + L +  + +   + Y +LV G   ++K  I    +
Sbjct: 130 PGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTI-EAPI 188

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++      + VV+  ++    A +HF+V++     +  +  +  TGRTHQ+RVH  ++G
Sbjct: 189 GRAKEDRQKMAVVRDGKE----ARTHFEVLERLP-GYTLINCKLDTGRTHQIRVHLKYIG 243

Query: 264 CP 265
            P
Sbjct: 244 HP 245


>gi|163750410|ref|ZP_02157650.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           benthica KT99]
 gi|161329900|gb|EDQ00886.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           benthica KT99]
          Length = 599

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 59/179 (32%), Positives = 93/179 (51%), Gaps = 17/179 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+DS + V NKPA      G  I   +   +K  + ++ G  P + HRLD  TSG++V
Sbjct: 398 IIYQDSDMLVVNKPAEFLSVPGRNIDDSVYSRIKQLYPEATG--PLIVHRLDMSTSGLMV 455

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ- 218
           +A  + A + L + F  R ++K Y +L+ G   ++ E I +  L+     GD+    +Q 
Sbjct: 456 IALNKEANKSLQKQFITRTVKKRYVALLTG-DLSQDEGIISLPLR-----GDFDDRPRQL 509

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKY 272
              E G   A + ++VI     +   + + P TGRTHQLRVH+ H   +  PIVGD  Y
Sbjct: 510 VCFEHG-KPAETKWQVISRRDGR-TKVHLYPKTGRTHQLRVHSAHPQGLNMPIVGDDLY 566


>gi|196004434|ref|XP_002112084.1| hypothetical protein TRIADDRAFT_1807 [Trichoplax adhaerens]
 gi|190585983|gb|EDV26051.1| hypothetical protein TRIADDRAFT_1807 [Trichoplax adhaerens]
          Length = 418

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 65/218 (29%), Positives = 103/218 (47%), Gaps = 11/218 (5%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPA 115
           N IQ+G++  +   I + N I+++  ++ ++V+  +       I ++  D  I V NKPA
Sbjct: 58  NAIQNGKIT-VNNKIPSANTIVRDNDVIRNTVHRHEPPVTANPIQIIKMDDDIVVINKPA 116

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            I V       ++   F+ +  D   Q     HRLD+ TSGIL+ ART   AQ L +  R
Sbjct: 117 SIPVHPCGRYRHNSVVFMLAR-DYGLQNLHTIHRLDRLTSGILIFARTLQKAQELEKQVR 175

Query: 176 MRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            R+I+K Y   V G  P    +C     +    +G     V + + KG +      ++  
Sbjct: 176 DRQIEKQYVCRVDGEFPTETIDCKEPIDVVSHKLG-----VCRVSPKGKSCQTIFQRL-- 228

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  K   ++  P TGR HQ+RVH   +G PIV D  Y
Sbjct: 229 SYNGKTSLVKCIPLTGRMHQIRVHLQWLGYPIVNDPIY 266


>gi|300214932|gb|ADJ79348.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 295

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 55/201 (27%), Positives = 93/201 (46%), Gaps = 22/201 (10%)

Query: 96  FLKSILLYEDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           F+   +LYED    + +KPA ++     +     +   + G+ +     +G  P +  RL
Sbjct: 75  FVPIKILYEDDNYLLVDKPAFVASIPSPLHPNDSLVNRVVGYYQIR-GYRGIIPHIVTRL 133

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSGI++ A+ R A   L    +  +I K Y +++ GI  N      N  +    IG 
Sbjct: 134 DRDTSGIVIFAKHRYAHALLDSQLKEHKISKTYTAILSGILHN------NHYIIDLPIGR 187

Query: 211 DYVHVVKQ----NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           D   ++K+    +EK        F          C +++  HTGRTHQ+RVH  ++G P+
Sbjct: 188 DSTSLIKRKVLFSEKAKRSKTEIFVKERIRDNTLCKIKL--HTGRTHQIRVHCSYLGYPL 245

Query: 267 VGDHKYCANFKGNFTSPIQNK 287
           V D  Y     G  + P+Q +
Sbjct: 246 VSDTLY----GGAISMPLQRQ 262


>gi|326795028|ref|YP_004312848.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326545792|gb|ADZ91012.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
          Length = 228

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 52/172 (30%), Positives = 83/172 (48%), Gaps = 13/172 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+ +  +V  KPA  S    SGI +    F +       +     HRLD+ TSG+L+V
Sbjct: 4   VLYQSADFWVVVKPANESFHSESGIGF----FQRLCCAFPNESFFPVHRLDKLTSGLLLV 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +  A  LT+ F   +++K Y ++    P+ K+  +      K  +        K + 
Sbjct: 60  ACNKVMAAKLTKLFMETKVEKRYLAISNKKPRKKQGTV------KGKMAPSRKGQWKLSG 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +G   AI+ F    CF +      ++P TGRTHQ+RV    +G PI+GD +Y
Sbjct: 114 EG-KMAITQFH--SCFVEGKRLFYLRPLTGRTHQIRVALKSVGSPILGDERY 162


>gi|256544688|ref|ZP_05472060.1| RluA family pseudouridine synthase [Anaerococcus vaginalis ATCC
           51170]
 gi|256399577|gb|EEU13182.1| RluA family pseudouridine synthase [Anaerococcus vaginalis ATCC
           51170]
          Length = 299

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 53/190 (27%), Positives = 97/190 (51%), Gaps = 17/190 (8%)

Query: 101 LLYEDSKIYVFNK-------PAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLD 151
           +LYE+    + +K       PAG S+  G+ +   +D F    +   G   +P + HRLD
Sbjct: 76  ILYENEDYAIIDKDENVIVHPAG-SIVSGTLVNGLLDYFGYDNLSHIGGDDRPGIVHRLD 134

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G++V+A+  ++ ++L   F  R+I K Y ++  GI + K   I  ++ +  +   +
Sbjct: 135 KDTTGLMVIAKNNSSYKYLKNLFETRKIDKEYLAICNGIFQKKSGTIHTFMDRDPN---N 191

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              +   N      AIS ++VI      +  ++++  TGRTHQ+RVH  ++  P++GD  
Sbjct: 192 RRKMAVTN--SGRDAISKYEVI-SENNGYSLVKIKILTGRTHQIRVHMTYINHPLLGDPV 248

Query: 272 YCANFKGNFT 281
           Y  N K  F 
Sbjct: 249 Y-GNVKHKFN 257


>gi|224282575|ref|ZP_03645897.1| hypothetical protein BbifN4_01992 [Bifidobacterium bifidum NCIMB
           41171]
 gi|313139732|ref|ZP_07801925.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
           41171]
 gi|313132242|gb|EFR49859.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
           41171]
          Length = 313

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 75/281 (26%), Positives = 122/281 (43%), Gaps = 41/281 (14%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+      ++ SGQ RV  + +  +  +  G+ V            I E++     V   
Sbjct: 26  ISRAKAADLIESGQARVLDRAIAKSGTLLYGETVEFD---------IAEERHEPEPV--- 73

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWV--DSKGQKPR-- 145
                L   + YED  + V +KP G++    +G      +   LK  V   S G   R  
Sbjct: 74  ----CLDMAIAYEDDDVVVVDKPVGVAAHASAGWTGPTVLGSLLKRGVRITSYGAPGRQG 129

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD  TSG+++V ++  A + +   F    + K Y ++V G  K  K  I      +
Sbjct: 130 IVSRLDVGTSGLMLVCKSELAYKEMRRQFSEHEVVKTYHAMVQGNLKEDKATI------E 183

Query: 206 SHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + IG     D+   V  + K    A++H+ V+D F +    + +   TGRTHQ+RVH   
Sbjct: 184 APIGRAKVSDFRFCVTPSGK---PAVTHWDVLDRFGEA-TLVSVNLETGRTHQIRVHFSS 239

Query: 262 MGCPIVGDHKYCAN--FKGNFTSPIQNKLYLHARYMDLPHP 300
           +G P+VGD  Y AN    G       ++ +LHA  ++  HP
Sbjct: 240 IGHPLVGDPMYGANPVLAGELG---LDRQWLHAMKLEFRHP 277


>gi|229520732|ref|ZP_04410155.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TM
           11079-80]
 gi|229342287|gb|EEO07282.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TM
           11079-80]
          Length = 235

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 49/147 (33%), Positives = 74/147 (50%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR   AA  L++ F  R+++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNATAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  +      N AI+ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVNSQE------NPAITQFFSATAAPGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADKSDRGYLHA 178


>gi|229010596|ref|ZP_04167798.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           DSM 2048]
 gi|228750794|gb|EEM00618.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           DSM 2048]
          Length = 292

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 68/287 (23%), Positives = 130/287 (45%), Gaps = 46/287 (16%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
            R G + V+ +     +++Q+G+ ++I   +   +  ++ + I                 
Sbjct: 33  FRGGAIEVNGQHTSVRHKLQAGEELQIFFPVEERSEGMEVEDI--------------PLC 78

Query: 101 LLYEDSKIYVFNKPAGISV------QGGS---GIAYHIDG-FLKSWVDSKGQKPRLTHRL 150
           ++YED  + V NK A +S         GS    + YH D   L S V        +  RL
Sbjct: 79  IVYEDDAVLVINKEANMSTIPSREHPSGSIANALLYHYDKQNLASTV-------HIVTRL 131

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ R     L++  + + +++ Y ++V G    +   I   + +K+    
Sbjct: 132 DRDTSGLMLIAKNRFVHHLLSKQHQQKGVKRTYEAIVHGTILEEVGTIDAPIGRKA---- 187

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D +      E G   A++HF+V++  + K   + ++  TGRTHQ+RVH  ++G P++GD 
Sbjct: 188 DSIIERTVCEDGQR-AVTHFRVMESSSDK-THVALELETGRTHQIRVHMAYIGNPLLGDD 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPAHM 315
            Y           +  +  LH+  +   HP  E G +  T  +P  M
Sbjct: 246 LYGGR------RDVIKRQALHSTSLTFYHPILEKG-MTFTVSIPEDM 285


>gi|326316917|ref|YP_004234589.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
 gi|323373753|gb|ADX46022.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
          Length = 241

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 60/215 (27%), Positives = 94/215 (43%), Gaps = 21/215 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ D  + V  KP+G+    G G         ++ +   G    + HRLDQ TSGI+V+A
Sbjct: 24  LHADDDLLVLAKPSGLLCVPGRGPDKQDCLSARAALHWPGAC--IVHRLDQATSGIVVMA 81

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-----VV 216
           R   A + L ++F  R++ K Y ++V   P    +  A W      I  D+       VV
Sbjct: 82  RHAQAQRALGDAFAARQVHKRYVAVVHA-PHPAGDG-AAWREIDLPIAADWERRPLRVVV 139

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCW--------LEMQPHTGRTHQLRVHALHMGCPIVG 268
                G   +++ ++          W        + ++P TGRTHQLRVH   +  PI+G
Sbjct: 140 PHGAPGGKASLTRWRPAAPGDGAVTWRATEGTLRVLLEPVTGRTHQLRVHMAAVDQPILG 199

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           D  Y           +  +L LHA+++   HP  G
Sbjct: 200 DTLYAP----PAIQALAPRLLLHAQHIAFAHPRTG 230


>gi|195146688|ref|XP_002014316.1| GL19135 [Drosophila persimilis]
 gi|194106269|gb|EDW28312.1| GL19135 [Drosophila persimilis]
          Length = 478

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 60/196 (30%), Positives = 85/196 (43%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 132 KHNDLLANIVHRHEVPVSLQSITIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILAKS 191

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
            +  +  R  HRLD+ TSG+L+  RT   A+ L +  R R++QK Y   V G  P    E
Sbjct: 192 HNL-KNLRTIHRLDRLTSGLLIFGRTSKKARELEQQIRNRQVQKEYICRVEGRFPDGIIE 250

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG   V  V  N K           +   +   C    +P TGR HQ+R
Sbjct: 251 CNEPIQVVSYKIG---VCRVSPNGKDCRTTFRRISEVGDCSIVLC----KPLTGRMHQIR 303

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PIV D  Y
Sbjct: 304 VHLQYLGYPIVNDPLY 319


>gi|255318859|ref|ZP_05360085.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           radioresistens SK82]
 gi|262378883|ref|ZP_06072040.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           radioresistens SH164]
 gi|255304115|gb|EET83306.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           radioresistens SK82]
 gi|262300168|gb|EEY88080.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           radioresistens SH164]
          Length = 350

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 62/214 (28%), Positives = 101/214 (47%), Gaps = 21/214 (9%)

Query: 112 NKPAGISVQ--GGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQ 168
           NK  G+ V    G+G    ++  L  +  S    +  L HR+D++TSG+LVVA+   A  
Sbjct: 128 NKTVGMVVHPGAGNGSGTLVNALLYHYPKSNELARAGLVHRIDKDTSGLLVVAKNLEAQF 187

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAI 227
            L++    + + +IY  +V+G        +A   + +  I    V  VK     G   A+
Sbjct: 188 SLSKQLAKKTVYRIYDLVVYG------NIVAGGTIDEP-IKRHPVDRVKMAILPGGKEAV 240

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQ 285
           +H+ V + F + F  ++ Q  TGRTHQ+RVH  ++G  +VGD  Y +  +     +  + 
Sbjct: 241 THYNVKERF-KDFTRVQAQLETGRTHQIRVHFSYIGYGLVGDPVYMSRVRVPAGASEELA 299

Query: 286 NKL------YLHARYMDLPHPEGGR-LQITAPLP 312
           + L       LHA  + L HP  G  +   AP P
Sbjct: 300 DTLRSFKRQALHAAKLGLVHPRTGENMMFEAPWP 333


>gi|15641672|ref|NP_231304.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O1
           biovar El Tor str. N16961]
 gi|153213916|ref|ZP_01949118.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 1587]
 gi|153817151|ref|ZP_01969818.1| pseudouridine synthase Rlu family protein [Vibrio cholerae NCTC
           8457]
 gi|153821833|ref|ZP_01974500.1| pseudouridine synthase Rlu family protein [Vibrio cholerae B33]
 gi|227081819|ref|YP_002810370.1| pseudouridine synthase Rlu family protein [Vibrio cholerae M66-2]
 gi|229508222|ref|ZP_04397727.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae BX
           330286]
 gi|229511539|ref|ZP_04401018.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae B33]
 gi|229518678|ref|ZP_04408121.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae RC9]
 gi|229607796|ref|YP_002878444.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           MJ-1236]
 gi|254848788|ref|ZP_05238138.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MO10]
 gi|255744905|ref|ZP_05418855.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholera CIRS
           101]
 gi|262161810|ref|ZP_06030828.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae INDRE
           91/1]
 gi|298498251|ref|ZP_07008058.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MAK 757]
 gi|9656182|gb|AAF94818.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O1
           biovar El Tor str. N16961]
 gi|124115654|gb|EAY34474.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 1587]
 gi|126512300|gb|EAZ74894.1| pseudouridine synthase Rlu family protein [Vibrio cholerae NCTC
           8457]
 gi|126520631|gb|EAZ77854.1| pseudouridine synthase Rlu family protein [Vibrio cholerae B33]
 gi|227009707|gb|ACP05919.1| pseudouridine synthase Rlu family protein [Vibrio cholerae M66-2]
 gi|229343367|gb|EEO08342.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae RC9]
 gi|229351504|gb|EEO16445.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae B33]
 gi|229355727|gb|EEO20648.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae BX
           330286]
 gi|229370451|gb|ACQ60874.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           MJ-1236]
 gi|254844493|gb|EET22907.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MO10]
 gi|255737376|gb|EET92771.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholera CIRS
           101]
 gi|262028542|gb|EEY47197.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae INDRE
           91/1]
 gi|297542584|gb|EFH78634.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MAK 757]
          Length = 235

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 49/147 (33%), Positives = 74/147 (50%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR   AA  L++ F  R+++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNATAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  +      N AI+ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVNSQE------NPAITQFFSAAAATGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADESDRGYLHA 178


>gi|154149073|ref|YP_001406285.1| pseudouridine synthase [Campylobacter hominis ATCC BAA-381]
 gi|153805082|gb|ABS52089.1| pseudouridine synthase [Campylobacter hominis ATCC BAA-381]
          Length = 248

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 54/200 (27%), Positives = 91/200 (45%), Gaps = 30/200 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++E+  I V NKP                 F  S    K  K +L +RLD+ETSGI
Sbjct: 55  KPAIVFENDDILVVNKPP----------------FFVSEKLEKIFKFKLLNRLDKETSGI 98

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++ +     +   + F+  R++K Y ++V GI   + E     L  K   G       +
Sbjct: 99  VLLYKNEEFKERAIKEFKNMRVKKTYIAIVQGIVSEEMEFDEPILTIKGKTGA----FSR 154

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +  G +     F ++   + K   ++++  TGRTHQ+RVH  + G  I+GD KY  N  
Sbjct: 155 ISPHGKSAITRIFPLM--ISGKKSLVKIEIDTGRTHQIRVHLSNAGFGIIGDEKYAKN-- 210

Query: 278 GNFTSPIQNKLYLHARYMDL 297
                    +++LHA  ++L
Sbjct: 211 ------SSKRMFLHAYELEL 224


>gi|195051252|ref|XP_001993060.1| GH13297 [Drosophila grimshawi]
 gi|193900119|gb|EDV98985.1| GH13297 [Drosophila grimshawi]
          Length = 562

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 55/173 (31%), Positives = 84/173 (48%), Gaps = 9/173 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  I V NKPA I V       ++   F+ +  +   +  R  HRLD+ TSG+L+ 
Sbjct: 235 IVHMDDDILVVNKPASIPVHPCGRYRHNTMIFILA-KEFNMRNLRTIHRLDRLTSGLLLF 293

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            RT   A+ + +  R R++QK Y   V G  P    EC     +    IG     V K +
Sbjct: 294 GRTAEKAREMEQQIRNRQVQKEYVCCVEGCFPDGNIECNEPIEVVSYKIG-----VCKVS 348

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            KG +   + FK +      +  ++ +P TGR HQ+RVH  ++G PIV D  Y
Sbjct: 349 PKGKDCKTT-FKRLGQVGD-YSIVQCKPLTGRMHQIRVHLQYLGYPIVNDPLY 399


>gi|169826808|ref|YP_001696966.1| putative RNA pseudouridine synthase yjbO [Lysinibacillus sphaericus
           C3-41]
 gi|168991296|gb|ACA38836.1| Hypothetical RNA pseudouridine synthase yjbO [Lysinibacillus
           sphaericus C3-41]
          Length = 293

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 109/236 (46%), Gaps = 29/236 (12%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPR 145
           ++H D     ++YED  I V NKPA  S         + IA  + G+ +           
Sbjct: 67  SEHGDL---AIVYEDDTILVLNKPANQSTIPSREHPTNSIANLVCGYFEQQ--GLASTAH 121

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTE-SFRMRRIQKIYWSLVWG-IPKNKKECIANWLL 203
           +  RLD++TSG+L +A+  A   HLT  + R   I + Y ++V G + ++ +  +A    
Sbjct: 122 IITRLDRDTSGLLCIAK-HAHIHHLTGLAQRNGEISRKYEAIVHGHVHQDSQSIVAPIGR 180

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHAL 260
           K++ I      + ++  +   YA +   VI  F   A+    + +  HTGRTHQ+RVH  
Sbjct: 181 KETSI------IEREVREDGQYAHTDVTVIQRFYLGAEPMTHIGLTLHTGRTHQIRVHMS 234

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            +G P+VGD  Y        +    ++  LH   +++ HP     LQ T+ L   M
Sbjct: 235 SLGHPLVGDELYGG------SRLHMDRQALHCVSLNMTHPLTSEHLQFTSMLNEDM 284


>gi|158316843|ref|YP_001509351.1| RluA family pseudouridine synthase [Frankia sp. EAN1pec]
 gi|158112248|gb|ABW14445.1| pseudouridine synthase, RluA family [Frankia sp. EAN1pec]
          Length = 313

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 75/318 (23%), Positives = 137/318 (43%), Gaps = 38/318 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +  + +RLD      +  ++      ++  GQV VD +    ++R+  G  + +    
Sbjct: 13  VPDGLDGIRLDAAIARMF-GLSRTAAATLVDDGQVSVDGQVRGRSDRVSGGAWLDV---- 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
            AL    +   +  + V   +        +L++D  I V +KP G++     G     + 
Sbjct: 68  -ALPAPPRPLTVEPTPVGGLR--------ILHDDDDIVVVDKPVGVAAHPAPGFTGPTVI 118

Query: 131 GFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           G L +    V + G   R  + HRLD  T+G + VA++  A   L  +FR R ++K Y +
Sbjct: 119 GALAAAGYRVSTSGSAERQGVVHRLDVGTTGAMAVAKSERAYTLLKRAFREREVEKEYRA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G P   +  +   + +     G +  V          +++H+   + F +    L +
Sbjct: 179 VVQGHPDPLRGTVDAPIDRHPRRPGLFAVVAD-----GKPSVTHYDTEEAF-RAASLLSV 232

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-----YLHARYMDLPHP 300
           +  TGRTHQ+RVH   +  P VGD  Y A+        +  +L     +LHA  +   HP
Sbjct: 233 RLETGRTHQIRVHMAALRHPCVGDLAYGADPT------LAQRLGLTRQWLHAARLAFAHP 286

Query: 301 EGGR-LQITAPLPAHMVK 317
             G  ++ T+P P  + +
Sbjct: 287 ADGTWVEFTSPDPDDLAE 304


>gi|297170431|gb|ADI21463.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0070_10G19]
          Length = 312

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 44/132 (33%), Positives = 70/132 (53%), Gaps = 11/132 (8%)

Query: 144 PR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           PR  + HRLD++TSG+LVVA+T     H+   F+ R ++K Y++L+ G        I   
Sbjct: 127 PRCGIVHRLDKDTSGLLVVAKTNEFRNHIVSEFQNRNVKKYYYALIKG-------NILGQ 179

Query: 202 LLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           ++    I  D  + ++   ++    A S  K I+ F   +  +E++  TGRTHQ+RVH  
Sbjct: 180 IIINEPILRDKSNRIRMTVDQAGREATSIVKNIETF-DFYSLVEVEILTGRTHQIRVHMD 238

Query: 261 HMGCPIVGDHKY 272
               PI+GD  Y
Sbjct: 239 FNKTPIIGDKIY 250


>gi|145353632|ref|XP_001421111.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|145357270|ref|XP_001422843.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144581347|gb|ABO99404.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144583087|gb|ABP01202.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 213

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 49/136 (36%), Positives = 71/136 (52%), Gaps = 14/136 (10%)

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           V+    +PR  HRLD+ T G+LV A+TR A   L+ +F  R ++K Y +++ G  ++KK 
Sbjct: 36  VEGALSRPRPVHRLDELTGGLLVCAKTRMAMTALSAAFEKREVRKRYRAVLRGRVESKKG 95

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + +  L       +Y  VV++ E      I    +ID F          P TGRTHQLR
Sbjct: 96  -VVDVPLGGLEALTEY-SVVREYESEEYGGI--LTLIDFF----------PKTGRTHQLR 141

Query: 257 VHALHMGCPIVGDHKY 272
            HA  +  PI+GD KY
Sbjct: 142 RHAKALCAPILGDVKY 157


>gi|325104653|ref|YP_004274307.1| tRNA pseudouridine synthase C [Pedobacter saltans DSM 12145]
 gi|324973501|gb|ADY52485.1| tRNA pseudouridine synthase C [Pedobacter saltans DSM 12145]
          Length = 228

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 59/213 (27%), Positives = 93/213 (43%), Gaps = 29/213 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y D  I   NKP G+ V   S IA   + F L+   D  GQ     HRLD++T G+L+
Sbjct: 4   IIYRDEHIVAVNKPHGLLVHQ-SPIARDAEEFALQILRDQIGQTVWPCHRLDRKTGGLLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  +    +L   F+   +QK Y ++V G    +                DY   + ++
Sbjct: 63  FALDKETEINLQTQFQNGLVQKKYLAIVRGHTMERMTI-------------DYP--IAKD 107

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +     A++HF+ +               ++  +E  P TGR HQLR H  H+  PI+GD
Sbjct: 108 DGKLQDAVTHFRTLSLTEIDLPFGKHATSRYALIEAIPETGRMHQLRRHFAHILHPIIGD 167

Query: 270 HKYCANFKGN-FTSPIQ-NKLYLHARYMDLPHP 300
             +  N +   F    Q + + LHA  +   HP
Sbjct: 168 RPHGCNKQNKLFKEKWQMDTMMLHASELSFEHP 200


>gi|296815982|ref|XP_002848328.1| DRAP deaminase [Arthroderma otae CBS 113480]
 gi|238841353|gb|EEQ31015.1| DRAP deaminase [Arthroderma otae CBS 113480]
          Length = 519

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 69/260 (26%), Positives = 110/260 (42%), Gaps = 43/260 (16%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYED 105
           D+ +  + + I+ G++  I  VI   + II   +++  S  L +H   + S+   +++ED
Sbjct: 73  DRPKGYYTDAIEGGRIT-IDGVIATADSIINNGQVV--SHTLHRHEPPVTSLRIKIIHED 129

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
           + I V +KPAGI V       Y+    +       G  P   +RLD+ TSGI+ + +   
Sbjct: 130 NDIIVIDKPAGIPVHPAGRYNYNSIVEIMRAERGHGWNPYPCNRLDRLTSGIMFIGKHPK 189

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG--------------- 210
           AA+ + ++ R R IQK Y + V G   +        +LK S I G               
Sbjct: 190 AAEQMAQALRSRTIQKEYIARVKGYFPDGVVLCDQPMLKVSPILGLNRVRASGKEATTKF 249

Query: 211 ----------------DYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                           +   VV Q+   + A    S   V + ++   C     P TGRT
Sbjct: 250 RRIAYYPPMKRADNPDETKPVVSQDPETRAATPPPSPADVDEGYSIVHCL----PLTGRT 305

Query: 253 HQLRVHALHMGCPIVGDHKY 272
           HQ+RVH   +G PI  D  Y
Sbjct: 306 HQIRVHLQFLGHPITNDPIY 325


>gi|169349788|ref|ZP_02866726.1| hypothetical protein CLOSPI_00526 [Clostridium spiroforme DSM 1552]
 gi|169293356|gb|EDS75489.1| hypothetical protein CLOSPI_00526 [Clostridium spiroforme DSM 1552]
          Length = 275

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 61/207 (29%), Positives = 97/207 (46%), Gaps = 36/207 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGF-LKSWVDSKGQKPRLTHRL 150
           ++YED    + +KPAGI              + I Y+     LK+ V        L +RL
Sbjct: 77  IIYEDENYLIIDKPAGIPCMPTKRYPNKTIANAIIYYFQMCNLKATV-------HLVNRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++T G++++A+ R A  H   S  +++++++Y  LV GI K   E I +  + K     
Sbjct: 130 DKDTQGLMLIAKNRQA--HYLLSKDIKQVKRVYHCLVEGILKG--EGIIDKPIIK----- 180

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D   V +  +     AI+ ++ +  F  K   +E    TGRTHQ+RVH   +G P+VGD 
Sbjct: 181 DKNSVKRLIDASGKKAITVYRSLKIFDNK-SLIECDLKTGRTHQIRVHLSSIGHPLVGDG 239

Query: 271 KYCA---------NFKGNFTSPIQNKL 288
            Y +         +    F SP  NKL
Sbjct: 240 LYGSMETKTYYLDSVYLEFVSPFTNKL 266


>gi|239832937|ref|ZP_04681266.1| pseudouridine synthase [Ochrobactrum intermedium LMG 3301]
 gi|239825204|gb|EEQ96772.1| pseudouridine synthase [Ochrobactrum intermedium LMG 3301]
          Length = 222

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 63/212 (29%), Positives = 105/212 (49%), Gaps = 11/212 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D+   V +KP+G+    G   A  +   L + V     + ++ +RLD++TSGI+++
Sbjct: 21  ILHRDAGFLVLDKPSGLLSVPGRHPA--LSDSLATRVQETFPQAQMINRLDKDTSGIVLM 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           +  R     +   F  R  QK Y ++VWG  +  +  I   L      G    H V  + 
Sbjct: 79  SLDRKTHAAIAAQFEARTTQKSYIAVVWGNVEEDEGLIDLPLAIDP--GNKPRHRV--DH 134

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    A + ++V+D  +++   L + P TGRTHQLRVH   +G  I+GD  Y    +G  
Sbjct: 135 EHGKPAQTRWQVLDR-SERTTRLRLFPLTGRTHQLRVHMKAIGHVILGDEFYA---EGEA 190

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
            +   ++L LHA  +   HP+G  +  TAP P
Sbjct: 191 LA-AADRLLLHAEELSFRHPDGRAVTFTAPCP 221


>gi|326929074|ref|XP_003210696.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Meleagris gallopavo]
          Length = 310

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 53/159 (33%), Positives = 78/159 (49%), Gaps = 10/159 (6%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA    + F+ R + K Y +LV G     +  I   + K
Sbjct: 68  RFCHQLDFSTSGALCVALNKAAAGSAYKCFKDRLVTKAYLALVRGHVDQSRMTIRYAIGK 127

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVI-----DCFAQKFCWLEMQPHTGRTHQLRVHA 259
            +  G  ++  ++  E   N      ++I              + +QP TGRTHQLRVH 
Sbjct: 128 NTAEGMTHMMCIEGTEGCENPKPCQSELIVLEHGSYSGDPVTKVLLQPLTGRTHQLRVHC 187

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             +G PIVGD  Y  + K + +SP   ++ LHA Y+ +P
Sbjct: 188 SAIGHPIVGDFTY--SHKKD-SSPY--RMMLHAYYLRIP 221


>gi|255323619|ref|ZP_05364749.1| RNA pseudouridine synthase family protein [Campylobacter showae
           RM3277]
 gi|255299333|gb|EET78620.1| RNA pseudouridine synthase family protein [Campylobacter showae
           RM3277]
          Length = 307

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 52/173 (30%), Positives = 86/173 (49%), Gaps = 8/173 (4%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++E  K  VF+KP+G+ S   G    Y ++  + S     G++  + HRLD ETSG++VV
Sbjct: 72  IFECDKFAVFDKPSGVLSHPNGRHCEYSLNDEIWSLY---GREASVAHRLDCETSGLIVV 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            + + A  +L + F  R++ K Y +LV+G         AN  L   +        + ++ 
Sbjct: 129 GKDKNAVVNLKKLFENRQVYKSYVALVYGKISENLHIEANMDLANDYDDVKMRMRICEDG 188

Query: 221 KGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           KG   A++    I+ FA      +   P TGR HQ+R+H  H+   I+G+  Y
Sbjct: 189 KG---AVTEILPIEYFADIDATLVRAVPLTGRQHQIRLHLFHVEHKILGEPLY 238


>gi|163939103|ref|YP_001643987.1| RluA family pseudouridine synthase [Bacillus weihenstephanensis
           KBAB4]
 gi|163861300|gb|ABY42359.1| pseudouridine synthase, RluA family [Bacillus weihenstephanensis
           KBAB4]
          Length = 297

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 68/287 (23%), Positives = 130/287 (45%), Gaps = 46/287 (16%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
            R G + V+ +     +++Q+G+ ++I   +   +  ++ + I                 
Sbjct: 38  FRGGAIEVNGQHTSVRHKLQAGEELQIFFPVEERSEGMEVEDI--------------PLC 83

Query: 101 LLYEDSKIYVFNKPAGISV------QGGS---GIAYHIDG-FLKSWVDSKGQKPRLTHRL 150
           ++YED  + V NK A +S         GS    + YH D   L S V        +  RL
Sbjct: 84  IVYEDDAVLVINKEANMSTIPSREHPSGSIANALLYHYDKQNLASTV-------HIVTRL 136

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+ R     L++  + + +++ Y ++V G    +   I   + +K+    
Sbjct: 137 DRDTSGLMLIAKNRFVHHLLSKQHQQKGVKRTYEAIVHGTILEEVGTIDAPIGRKA---- 192

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D +      E G   A++HF+V++  + K   + ++  TGRTHQ+RVH  ++G P++GD 
Sbjct: 193 DSIIERTVCEDGQR-AVTHFRVMESSSDK-THVALELETGRTHQIRVHMAYIGHPLLGDD 250

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPAHM 315
            Y           +  +  LH+  +   HP  E G +  T  +P  M
Sbjct: 251 LYGGR------RDVIKRQALHSTSLTFYHPILEKG-MTFTVSIPEDM 290


>gi|317496022|ref|ZP_07954384.1| RluA family pseudouridine synthase [Gemella moribillum M424]
 gi|316913926|gb|EFV35410.1| RluA family pseudouridine synthase [Gemella moribillum M424]
          Length = 294

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 63/252 (25%), Positives = 109/252 (43%), Gaps = 38/252 (15%)

Query: 87  SVNLTKHSDFLKSIL--LYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDS 139
           S   ++H  F++  L  +YED    V NKPA +       +G + +   ++ +     ++
Sbjct: 66  SEKFSEHVRFIEGNLDIIYEDEYFLVVNKPANLPSIPSRNEGDASLLEIVNTYFHD--NN 123

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG------IPKN 193
               P +  RLD+ T+G++++A+ R    H+   F    I K Y +L  G      I  N
Sbjct: 124 YVTIPHIVTRLDKNTTGLVLIAKHR----HIHALFGKTDINKFYLALTKGKVADQVIEAN 179

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K    + + +     GDY        K   + + +++  D        ++++  TGRTH
Sbjct: 180 IKREADSIITRCVAEDGDYA-------KTQIWLVKYYEKNDV-----SLVKLKLFTGRTH 227

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Q+RVH  H+G P++GD  Y  N        +  +  LH   +   HP     L + APL 
Sbjct: 228 QIRVHMSHLGHPLLGDELYGGN------KDLIARQALHCHNLQFKHPITQKELSLEAPLA 281

Query: 313 AHMVKTWDSLGF 324
             +    DS+G 
Sbjct: 282 GDIKNITDSIGI 293


>gi|294056443|ref|YP_003550101.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
 gi|293615776|gb|ADE55931.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
          Length = 284

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 103/231 (44%), Gaps = 24/231 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSW-VDSKGQKPRLTHR 149
           +L + +  +    KPAG+ V                YH +     W VD   ++  L +R
Sbjct: 18  VLEHNEDGLVALEKPAGLMVHPNKPEERKFSMLYAHYHYEKECFHWEVDGVSKRVWLINR 77

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D  TSG+++VA   A A+ + + F   R+ K+Y ++V  +P N     ++ L K+ +  
Sbjct: 78  IDSPTSGVVLVALDEALAKEIKQQFATHRVNKVYHAIVKRVPSNHTGTWSDMLTKEVYRA 137

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIV 267
           G  +   ++    A Y     +++      F    L++ P TGRTHQLR+       PIV
Sbjct: 138 GRKIPGGQRIPAKATY-----QLVKSPTGGFPVSLLKLMPVTGRTHQLRIQCQRHRHPIV 192

Query: 268 GDHKYCANFKGN---FTSPIQNKLYLHARYMDLPHPEGGRLQ---ITAPLP 312
           GD  Y  +F  N          ++ LH+    L +   G+L+    ++PLP
Sbjct: 193 GDRSY-GSFSFNREVIAETGVKRMLLHSSETSLKYAFKGKLREFSASSPLP 242


>gi|184199951|ref|YP_001854158.1| putative pseudouridine synthase [Kocuria rhizophila DC2201]
 gi|183580181|dbj|BAG28652.1| putative pseudouridine synthase [Kocuria rhizophila DC2201]
          Length = 326

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 62/212 (29%), Positives = 98/212 (46%), Gaps = 18/212 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  I   +KP G+ S   G  +   +    +   D+   +    HRLD+ T G+L+
Sbjct: 104 VLHEDEWIMAVDKPHGLCSTPKGENVRRSVVVAARCQFDN--DEISALHRLDRSTGGVLL 161

Query: 160 V---ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +   A  R+A   L   F+ R ++K YW+ V G+ +   E       +   I G    VV
Sbjct: 162 LCKRAEDRSAFHRL---FQERTVRKTYWA-VAGVNERVGEQTVRVESRIRKIQG----VV 213

Query: 217 KQ-NEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +   E G   A++  + ++ F      +   E+ P TGRTHQ+RVH   +G P+ GD  Y
Sbjct: 214 QAFEEPGEVNAVTDVRRVETFTDADGTWGLYEIAPLTGRTHQIRVHMTSLGLPLRGDKLY 273

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
               +       +N L L AR ++  HP  GR
Sbjct: 274 PQPRQDFDVEDPENPLQLIARSIEFVHPVTGR 305


>gi|329122013|ref|ZP_08250622.1| RluA family pseudouridine synthase [Dialister micraerophilus DSM
           19965]
 gi|327467065|gb|EGF12577.1| RluA family pseudouridine synthase [Dialister micraerophilus DSM
           19965]
          Length = 290

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 113/222 (50%), Gaps = 24/222 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS-----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED+ + + +K A + +   S      +   I G+ K      G  P   +RLD+ T+
Sbjct: 79  IIYEDNTLLIIDKDADMIIHPTSKTETNTLVNAISGYYKKNNQMSGIHP--IYRLDRNTT 136

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++VVA++      L++      I++ Y ++V G  KNK+  I   + +K   G      
Sbjct: 137 GLIVVAKSAKLQYELSKEHGT--IKREYLAVVEGRFKNKEGSIIYPIGRKE--GSIIEWK 192

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+ + K A    + +KVI+   +  C  L+++ +TGRTHQ+RVH   +G P+VGD  Y  
Sbjct: 193 VRDDGKEAR---TDYKVIE--EKPSCTLLKLRLYTGRTHQIRVHMSFLGHPLVGDDLYGG 247

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           N      S ++ +  LH+ ++   HP+ G  ++  +P+P  M
Sbjct: 248 N-----CSKLKRQA-LHSHHISFIHPDTGECMEFKSPMPYDM 283


>gi|261886282|ref|ZP_06010321.1| RNA pseudouridine synthase [Campylobacter fetus subsp. venerealis
           str. Azul-94]
          Length = 319

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 59/196 (30%), Positives = 92/196 (46%), Gaps = 29/196 (14%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++E  +  VF+KP+G+ S   G    Y + D     W    G+K  + HRLD+ETSG++V
Sbjct: 71  IFECDEFGVFDKPSGVLSHPNGRNCEYSLCDEIWSLW----GKKACVAHRLDRETSGVIV 126

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG----------------IPKNKKECIANW-- 201
           VA+   +A +L +SF  R + K Y + V G                  K+K E   N   
Sbjct: 127 VAKNANSALNLKKSFENRAVAKTYLAFVRGKFDGNGLDKFHINDFEDFKDKLEFFDNIQG 186

Query: 202 --LLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLR 256
             + K   I  DY  +  + E       A++  K+++ + +     +E  P TGR HQ+R
Sbjct: 187 FVIDKNMDITKDYDDIKIRMEICPEGKRAVTVVKLVEYYPKFDISLVECYPLTGRQHQIR 246

Query: 257 VHALHMGCPIVGDHKY 272
           +H  HM   I+GD  Y
Sbjct: 247 LHLFHMKHRILGDPIY 262


>gi|124506351|ref|XP_001351773.1| ribosomal large subunit pseudouridylate synthase, putative
           [Plasmodium falciparum 3D7]
 gi|23504702|emb|CAD51580.1| ribosomal large subunit pseudouridylate synthase, putative
           [Plasmodium falciparum 3D7]
          Length = 487

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 55/186 (29%), Positives = 86/186 (46%), Gaps = 24/186 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YE+    V NKP  I ++ G    I   ++  L  +   K    R+  +LD  TSG+L
Sbjct: 66  IIYENDYFLVLNKPYDIKLEKGKLDDIYPSVETLL--YQKRKLDVFRICGQLDYATSGLL 123

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG------------IPKNKKECIANWLLKKS 206
           +VA+ + +   L  +   + I KIY ++++G            I KNK+     + +K  
Sbjct: 124 IVAKDKLSCNILNYNIESKNISKIYLAILYGHLPLDILHINTPISKNKE----GFKMKLC 179

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           +   DY      N K     I  +K      +K    EM+  TGR HQLR+H+L +G  I
Sbjct: 180 YNYNDYY----DNGKYCYSLIYPYKHSYINNEKVTLCEMRTVTGRRHQLRLHSLSLGSSI 235

Query: 267 VGDHKY 272
           VGD  Y
Sbjct: 236 VGDETY 241


>gi|309791057|ref|ZP_07685593.1| pseudouridine synthase [Oscillochloris trichoides DG6]
 gi|308226912|gb|EFO80604.1| pseudouridine synthase [Oscillochloris trichoides DG6]
          Length = 301

 Score = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 55/186 (29%), Positives = 89/186 (47%), Gaps = 16/186 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSK-GQKP--RLTHRLDQET 154
           S +LYED+ +   NK  G  V      A  H+   L+ ++ ++ G  P   L H+LD++T
Sbjct: 72  SDILYEDAWLIATNKRLGWYVNATPWDAQGHVLAALQRYLHARDGAAPPLHLAHQLDRDT 131

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN--------WLLKKS 206
           SG+L+++R  A    LT +F    + K Y  +V G+P    E  +         W     
Sbjct: 132 SGVLLISREPAINAALTAAFAGGHVAKTYTCIVAGVPDASGEVRSGHGRSAKGLWRTYPL 191

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              G  +       K A+ +    ++++  AQ  C     PHTGRTHQ+R+H   +G P+
Sbjct: 192 EEVGRELPSGGGRVKLAHTSYLRQRILEDAAQVQC----TPHTGRTHQIRLHMALLGHPL 247

Query: 267 VGDHKY 272
           +GD +Y
Sbjct: 248 LGDSRY 253


>gi|195118760|ref|XP_002003904.1| GI18161 [Drosophila mojavensis]
 gi|193914479|gb|EDW13346.1| GI18161 [Drosophila mojavensis]
          Length = 545

 Score = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 56/173 (32%), Positives = 85/173 (49%), Gaps = 9/173 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  I V NKPA I V       ++   F+ +  +   +  R  HRLD+ TSG+L+ 
Sbjct: 226 IVHIDDDILVVNKPASIPVHPCGRYRHNTVIFILA-KEYNLKNLRTIHRLDRLTSGLLLF 284

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            R    A+ + +  R R++QK Y   V G  P    EC     +    IG     V K +
Sbjct: 285 GRNSEKARQMEQQIRNRQVQKEYVCCVEGHFPDGIIECNEPIEVVSYKIG-----VCKVS 339

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +KG +   + FK I   A  +  ++ +P TGR HQ+RVH  ++G PIV D  Y
Sbjct: 340 KKGKDCQTT-FKRI-AQAGDYSIVQCKPLTGRMHQIRVHLQYLGYPIVNDPLY 390


>gi|194761918|ref|XP_001963138.1| GF15796 [Drosophila ananassae]
 gi|190616835|gb|EDV32359.1| GF15796 [Drosophila ananassae]
          Length = 524

 Score = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 68/256 (26%), Positives = 114/256 (44%), Gaps = 37/256 (14%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
             R F+   P +     ++ L +G++ V+ ++V  + +I+   +         L +++  
Sbjct: 163 FSREFRAAPPEV----YERSLEAGKLTVNNEKVPKDYKIKHNDL---------LANVVHR 209

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +T         ++Y D  I V NKPA I V       ++   F+ +  +  
Sbjct: 210 HEVPVTSQPIT---------IVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEHN 259

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
            +  R  HRLD+ TSG+L+  RT   A+ L +  R R++QK Y   V G  P    EC  
Sbjct: 260 LKNLRTIHRLDRLTSGLLLFGRTSDKARELEQQIRNRQVQKEYVCRVEGRFPDGIIECCE 319

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---VIDCFAQKFCWLEMQPHTGRTHQLR 256
              +    IG     V K + KG +   +  +   V DC       +  +P TGR HQ+R
Sbjct: 320 PIDVVSYKIG-----VCKVSPKGKDCKTTFQRIGEVGDCSI-----VHCKPLTGRMHQIR 369

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI  D  Y
Sbjct: 370 VHLQYLGYPISNDPLY 385


>gi|118474442|ref|YP_892925.1| RNA pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40]
 gi|118413668|gb|ABK82088.1| RNA pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40]
          Length = 319

 Score = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 59/196 (30%), Positives = 92/196 (46%), Gaps = 29/196 (14%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++E  +  VF+KP+G+ S   G    Y + D     W    G+K  + HRLD+ETSG++V
Sbjct: 71  IFECDEFGVFDKPSGVLSHPNGRNCEYSLCDEIWSLW----GKKACVAHRLDRETSGVIV 126

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG----------------IPKNKKECIANW-- 201
           VA+   +A +L +SF  R + K Y + V G                  K+K E   N   
Sbjct: 127 VAKNANSALNLKKSFENRAVAKTYLAFVRGKFDGNGLDKFHINDFEDFKDKLEFFDNIQG 186

Query: 202 --LLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLR 256
             + K   I  DY  +  + E       A++  K+++ + +     +E  P TGR HQ+R
Sbjct: 187 FVIDKNMDITKDYDDIKIRMEICPEGKRAVTVVKLVEYYPKFDISLVECYPLTGRQHQIR 246

Query: 257 VHALHMGCPIVGDHKY 272
           +H  HM   I+GD  Y
Sbjct: 247 LHLFHMKHRILGDPIY 262


>gi|223986739|ref|ZP_03636725.1| hypothetical protein HOLDEFILI_04048 [Holdemania filiformis DSM
           12042]
 gi|223961305|gb|EEF65831.1| hypothetical protein HOLDEFILI_04048 [Holdemania filiformis DSM
           12042]
          Length = 295

 Score = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 98/215 (45%), Gaps = 31/215 (14%)

Query: 92  KHSDF----LKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQ--KP 144
           + SDF    +   +LYED  I   +KPAG+ V     G    +   + ++    GQ    
Sbjct: 73  EESDFVPWAIPVRILYEDELILAVSKPAGMIVHPDNKGKTGTLANAVAAYYLRTGQHCTV 132

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  HRLD+ TSGI++ ++       L ++   ++I + Y ++V G+ K K     + L  
Sbjct: 133 RPIHRLDEGTSGIVLFSKCPFFQPKLDQALAQKQIARTYLAVVSGVMKPK-----DRLTL 187

Query: 205 KSHIGGDYVHVVKQNEKG------ANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRV 257
              IG D     + N K          A++H +V+ C   +K   +  Q  TGRTHQ+RV
Sbjct: 188 DKPIGRD-----RHNAKAYRISPTGKPAVTHVEVLRCRQKEKQTLVRCQLETGRTHQIRV 242

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           H   +  P+V D  Y          P+Q ++ LHA
Sbjct: 243 HLASIQRPVVNDPLYNPR-------PVQGRMKLHA 270


>gi|237753351|ref|ZP_04583831.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           winghamensis ATCC BAA-430]
 gi|229375618|gb|EEO25709.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           winghamensis ATCC BAA-430]
          Length = 312

 Score = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 57/194 (29%), Positives = 89/194 (45%), Gaps = 29/194 (14%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGI 157
           L+E+    +FNKP+ + +       +H      S +D    S G K  L HR+D+ETSG+
Sbjct: 53  LFENEDFAIFNKPSKMLIHPKGRFEHH------SLIDEVRASLGLKASLAHRIDRETSGL 106

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLV---WGIPK-NKKECIANWLLKKSHIGGDY- 212
           ++V + + +   L   F    I+K Y +L     GI   N K+   +  +     GGD  
Sbjct: 107 VLVGKHKKSISELGLMFLNNSIKKEYLALTRAKVGIQNVNFKDFCLSLPIAIQEKGGDLC 166

Query: 213 -----VHVVKQNEKGANY----AISHFKVIDCFAQ-----KFCWLEMQPHTGRTHQLRVH 258
                +   +  +K  N     A S F+++          KF   ++ P TGRTHQ+RVH
Sbjct: 167 VRSVSLKNAQMCQKFRNLKFKEAKSEFEILGILENTYKNVKFLLFKVLPKTGRTHQIRVH 226

Query: 259 ALHMGCPIVGDHKY 272
              +G PI+GD  Y
Sbjct: 227 LDALGYPILGDPLY 240


>gi|153834197|ref|ZP_01986864.1| pseudouridine synthase Rlu family protein [Vibrio harveyi HY01]
 gi|148869470|gb|EDL68471.1| pseudouridine synthase Rlu family protein [Vibrio harveyi HY01]
          Length = 230

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 60/199 (30%), Positives = 93/199 (46%), Gaps = 17/199 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL++
Sbjct: 4   ILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAKH---SGDEQLYLIHRLDKMTSGILLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   AA  L+++F  R ++K Y ++    PK K+  +   + +        V     N 
Sbjct: 61  GRNAKAASALSQAFAEREVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV-----NS 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K  N AI+ F  +     +  +L  +PHTG+THQ+RV    +G  IVGD  Y A   GN 
Sbjct: 116 K-TNPAITQFFSLAAEPGERLFL-CKPHTGKTHQIRVALKSVGSGIVGDPIYNA---GNE 170

Query: 281 TSPIQNKLYLHARYMDLPH 299
                ++ YLHA  +  P+
Sbjct: 171 A----DRGYLHAFSLCFPY 185


>gi|283953645|ref|ZP_06371176.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
 gi|283794686|gb|EFC33424.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
          Length = 300

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 60/203 (29%), Positives = 102/203 (50%), Gaps = 17/203 (8%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFL 133
           I ++ KIL+  V L  + +  K + +++E+    V  K +GI S   G    Y + D   
Sbjct: 46  IEEKNKILNGLVELIIYENNPKGVKIVFENEDFAVLEKESGILSHPNGRHCKYSLSDEIW 105

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             W    G++  + HRLD+ETSG+++VA+ + A  +L   F  + +QK Y +L  G    
Sbjct: 106 HLW----GKEACVAHRLDKETSGLILVAKNKKAQINLKSLFEKKLVQKEYLALASG---- 157

Query: 194 KKECIANWLLKKS-HIGGDYVHVVKQNEKGAN--YAISHFKVIDCFAQ-KFCWLEMQPHT 249
             E   N+++ K+  +  +Y  V  + +  A    AI+ F++++ F       L  +P T
Sbjct: 158 --EITENFIVDKAMDLAKNYDDVKTRMQICAQGKQAITEFEILEYFPTLNATLLLCKPLT 215

Query: 250 GRTHQLRVHALHMGCPIVGDHKY 272
           GR HQ+RVH  +    I+GD  Y
Sbjct: 216 GRQHQIRVHLHYKNHTILGDPLY 238


>gi|94985003|ref|YP_604367.1| pseudouridine synthase [Deinococcus geothermalis DSM 11300]
 gi|94555284|gb|ABF45198.1| pseudouridine synthase [Deinococcus geothermalis DSM 11300]
          Length = 251

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 51/181 (28%), Positives = 88/181 (48%), Gaps = 7/181 (3%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLT--HRLDQET 154
           K  +L E    YV +KPA   +     +   +D   + S++ ++  +P L   HRLD+ET
Sbjct: 13  KPRVLVEHPDFYVVHKPA---LWLTHPVRARVDVPDVLSYMRAETGEPDLAPPHRLDRET 69

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG  +++R   AA+     F+   + K Y ++V G P  ++  +   L      G + V 
Sbjct: 70  SGTQLLSRDPDAARRFFTLFKTHLVGKTYLAVVHGSPDWERYTLDAPLGDLGLGGANRVI 129

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +        A++ F+V++     F  +E  P +GR HQ+R H  H+G P+VGD  Y  
Sbjct: 130 IRQAVVPDGRPAVTDFRVVEQRG-GFTLIEAYPRSGRLHQIRAHLSHLGLPLVGDKIYGP 188

Query: 275 N 275
           +
Sbjct: 189 D 189


>gi|309807023|ref|ZP_07701005.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
 gi|308166643|gb|EFO68840.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
          Length = 302

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/183 (30%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 133 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 191

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 192 PIGKKDDPIKRYIM------EGGKDSVTKYRVIKQVAGA-SLVELQLFTGRTHQIRVHMQ 244

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F  P Q    LH   +    P E  R+++    PA M++ W
Sbjct: 245 YLGHPLFGDHLY--GVEDDF--PRQ---ALHCFLLAFDDPLEHKRIEVQIADPADMLQLW 297

Query: 320 DSL 322
             L
Sbjct: 298 QKL 300


>gi|253565801|ref|ZP_04843256.1| RNA pseudouridylate synthase [Bacteroides sp. 3_2_5]
 gi|265764176|ref|ZP_06092744.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_16]
 gi|251946080|gb|EES86487.1| RNA pseudouridylate synthase [Bacteroides sp. 3_2_5]
 gi|263256784|gb|EEZ28130.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_16]
 gi|301163522|emb|CBW23073.1| putative RNA pseudouridylate synthase [Bacteroides fragilis 638R]
          Length = 307

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 109/226 (48%), Gaps = 20/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----IAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++YED+ I V  K  G+   G        A HI   L  +V   G+  R+   HRLD++T
Sbjct: 92  IVYEDAYIIVVEKKEGLLSVGTERQKERTAQHI---LSEYVGRSGRGNRIYVVHRLDRDT 148

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L + +      + Y ++V G  +   + + +WL  ++     YV 
Sbjct: 149 SGLMMFAKDEKTQYTLRDHWHDIVTDRRYVAVVTGEMEKDSDTVVSWLTDRTL----YVS 204

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++ G+  +I+H++ I   A  +  +E++  TGR +Q+RVH   +G P++GD +Y  
Sbjct: 205 SSSYDDGGSK-SITHYRTIKR-ANGYSLVELRLETGRKNQIRVHMQDLGHPLIGDGRYGI 262

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
           +   N   P+  +L LHA  +   HP   +L +   P P    K +
Sbjct: 263 DGGPN---PL-GRLALHAFKLCFYHPVTDQLMEFETPYPPTFKKLF 304


>gi|210134948|ref|YP_002301387.1| pseudouridine synthase D [Helicobacter pylori P12]
 gi|210132916|gb|ACJ07907.1| pseudouridine synthase D [Helicobacter pylori P12]
          Length = 327

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 53/227 (23%), Positives = 102/227 (44%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLD 151
           +++ED  + V NKP  + V     +    +  L  W++ K       G K R  + HRLD
Sbjct: 80  VIFEDEDLLVLNKPPNLVVHKAPSVK---EPTLVDWLEFKNYELSNLGLKERYGIVHRLD 136

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG + +A+       L+E  + + + + Y +L+    K +K  +  +L +  +    
Sbjct: 137 KDTSGGIAIAKNNFTHVCLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLK 196

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + +    ++ + Y+ S F  +         +  +  TGRTHQ+R H  ++   I+GD+ 
Sbjct: 197 MIALKAAKKEKSRYSKSEFISLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNL 256

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           Y  N         + ++ LHA  ++  HP    +L    PL   M++
Sbjct: 257 YGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLHFKVPLLKDMLE 300


>gi|121716811|ref|XP_001275916.1| DRAP deaminase (Rib2), putative [Aspergillus clavatus NRRL 1]
 gi|119404073|gb|EAW14490.1| DRAP deaminase (Rib2), putative [Aspergillus clavatus NRRL 1]
          Length = 538

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 98/229 (42%), Gaps = 33/229 (14%)

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           A N +IK  +I+  S  L +H   +      +++ED+ I V +KPAG+ V       YH 
Sbjct: 98  APNTVIKNGEII--SHTLHRHEPPVTGHEIGVIHEDNDILVIDKPAGVPVHAAG--RYHY 153

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +  ++     +GQ+  PR  +RLD+ TSG++ +A+    A  +T   + R +QK Y + V
Sbjct: 154 NSIVEILRSQRGQEFVPRPCNRLDRLTSGVMFIAKHPQGADMITRKLKQRTVQKEYIARV 213

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
            G  P     C    +     +G + V    ++ K     ++++       +        
Sbjct: 214 KGRFPDGVVVCDQPIMSVSPKLGLNRVRATGKDAKTKFRRLAYYPAASPAPETDEVTASG 273

Query: 240 ----------------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                           +  +   P TGRTHQ+RVH   +G PI  D  Y
Sbjct: 274 ERPATPPPLLANEDEGYSIVHCLPLTGRTHQIRVHLQFLGHPITNDPIY 322


>gi|307174606|gb|EFN65027.1| RNA pseudouridylate synthase domain-containing protein 2
           [Camponotus floridanus]
          Length = 376

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 54/173 (31%), Positives = 85/173 (49%), Gaps = 9/173 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  + V NKPA I V       ++   F+ +  +   +  R  HRLD+ TSGIL+ 
Sbjct: 42  VIHMDEDVVVVNKPASIPVHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDRLTSGILLF 100

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            RT   A+ +    R R++ K Y   V G  P+ +  C     +    IG     V K +
Sbjct: 101 GRTPKKARQMEHQIRNRQVHKQYVCRVEGEFPEEEVICSEPIEVVSYKIG-----VCKVS 155

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           EKG +  ++ FK +  +  K   +  +P TGR HQ+RVH  ++G P+V D  Y
Sbjct: 156 EKGKD-CVTRFKRLS-YNGKSSVVLCKPQTGRMHQIRVHLQYLGYPVVNDPLY 206


>gi|315586335|gb|ADU40716.1| pseudouridine synthase D [Helicobacter pylori 35A]
          Length = 293

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 75/287 (26%), Positives = 126/287 (43%), Gaps = 45/287 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS- 99
           L+  Q  +DK+R+K     Q+ Q VR             + +++   V+L       K+ 
Sbjct: 28  LKEAQCHLDKQRLK-----QNQQAVR-------------KSQMIQGVVSLIHFRPNEKTQ 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  ALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             +T  +A+ L   F  ++++K Y +LV G+  ++   I   +L   +I  D     K +
Sbjct: 128 AGKTLQSAKDLKALFMQKKVKKTYLALVHGL-VDRSIVIDKPILTPQNIQKDLRIKSKIS 186

Query: 220 EKGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             G         +S+   +D        L++ P TGRTHQ+R+H   +G  IVG+  Y  
Sbjct: 187 PLGKPSTTLVEPLSYNPFLD-----ISLLKITPITGRTHQIRLHLSSVGHRIVGEGLYGV 241

Query: 275 ---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                      K    +P+   L LHA  ++    +G   +IT+P+P
Sbjct: 242 IDENAREYLQLKRENNAPL---LMLHASSLEFEF-KGAIHEITSPMP 284


>gi|227534246|ref|ZP_03964295.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
 gi|227188136|gb|EEI68203.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
          Length = 315

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 107/225 (47%), Gaps = 38/225 (16%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           N  +++GQ++R                 + +S  LT   +F    ++YED+   + +KPA
Sbjct: 69  NGPVEAGQIIRFE---------------IPTSKTLT--PEFAPLEVIYEDANWLIVSKPA 111

Query: 116 GISVQGG-----SGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQ 168
           G++   G     S +   I G+L   V+ K    +P +  RLD++T G LV+A     AQ
Sbjct: 112 GLTSVPGPHTPNSSLLNRIAGYL---VEQKIDAPQPAIMTRLDRDTVG-LVLAAKHPYAQ 167

Query: 169 HLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
              +    R + K Y ++V G +P  K E  A   L       D +H +   +     A+
Sbjct: 168 GRFDQAHQRTLTKHYLAVVSGKLPSPKGEIDAPLKL-----AADGIHRIVAAD--GQTAL 220

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + ++V+    +    +++Q  TGRTHQ+RVH   +G P++GDH Y
Sbjct: 221 TKYRVLK--EKTNTLVDVQLLTGRTHQIRVHFASLGHPLIGDHLY 263


>gi|312870695|ref|ZP_07730803.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
 gi|311093806|gb|EFQ52142.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
          Length = 307

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/183 (30%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 138 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 196

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 197 PIGKKDDPIKRYIM------EGGKNSVTKYRVIKQVAGA-SLVELQLLTGRTHQIRVHMQ 249

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F  P Q    LH   +    P E  R+++    PA M++ W
Sbjct: 250 YLGHPLFGDHLY--GVEDDF--PRQ---ALHCFLLAFDDPLEHKRIEVQIADPADMLQLW 302

Query: 320 DSL 322
             L
Sbjct: 303 QKL 305


>gi|28076995|ref|NP_082285.1| RNA pseudouridylate synthase domain-containing protein 1 [Mus
           musculus]
 gi|81901914|sp|Q8VCZ8|RUSD1_MOUSE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 1; AltName: Full=Ribosomal large subunit
           pseudouridine synthase C-like protein
 gi|17390411|gb|AAH18186.1| RNA pseudouridylate synthase domain containing 1 [Mus musculus]
 gi|26340054|dbj|BAC33690.1| unnamed protein product [Mus musculus]
 gi|148690493|gb|EDL22440.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_b
           [Mus musculus]
          Length = 306

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 53/173 (30%), Positives = 83/173 (47%), Gaps = 9/173 (5%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA    + F+ RR+ K Y +LV G  +  +  I   + +
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYKCFKERRVTKAYLALVRGHVQESQVTINYAIGR 120

Query: 205 KSHIGGDYVHVVKQNEKGANY--AISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            S  G  +   ++      N   +++   V++           + ++P TGRTHQLRVH 
Sbjct: 121 NSTEGRTHTMCIEGTHGCENPKPSLTELLVLEHGLYAGDPVSKVLLKPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
             +G PIVGD  Y    +     P   ++ LHA Y+ +P  +  R++   P P
Sbjct: 181 SALGHPIVGDLTY-GQAEDQEDQPF--RMMLHAFYLRIPT-QAERVEACTPDP 229


>gi|302755728|ref|XP_002961288.1| hypothetical protein SELMODRAFT_75008 [Selaginella moellendorffii]
 gi|300172227|gb|EFJ38827.1| hypothetical protein SELMODRAFT_75008 [Selaginella moellendorffii]
          Length = 318

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 72/272 (26%), Positives = 114/272 (41%), Gaps = 60/272 (22%)

Query: 101 LLYEDSKIYVFNKPAGI-------SVQGGSGIAYHI-DGFLKSWVDSKGQKPRLTHRLDQ 152
           ++++D  I V NKP G+       SV    G +Y    GF             L +RLD+
Sbjct: 61  VVFQDEWILVINKPCGVYSEHVLVSVPSLLGDSYSPHRGFF-----------HLANRLDR 109

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP------------KNKKEC-- 197
           +TSGI+V+AR + AA  LT  F+ R ++K Y +L  G  P            K+++ C  
Sbjct: 110 DTSGIIVIARDKVAAGKLTNIFKSRELRKSYVALCVGKAPEWKRAVVESGHGKSRRGCWR 169

Query: 198 ---------------IANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVID--CFAQ 238
                          +   +  K  +    +  VK  E+       +   K++D      
Sbjct: 170 VYSKHDVERSLPDGSVVKDMATKIEVIPSSLDEVKDGEEDDREQRIVVEAKMVDPEPGTG 229

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              ++   P TGRTHQ+R+H   +G P+VGD KY      N         +LH+  +   
Sbjct: 230 DEVFIRAVPLTGRTHQIRLHCQFLGLPLVGDVKYGGPLHWNGEK--CQSHFLHSESIAFQ 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           HP  G  +++ AP P+   K    L F+  +N
Sbjct: 288 HPMTGEVVEVIAPHPSWAAK----LKFQASKN 315


>gi|169824338|ref|YP_001691949.1| pseudouridylate synthase [Finegoldia magna ATCC 29328]
 gi|167831143|dbj|BAG08059.1| pseudouridylate synthase [Finegoldia magna ATCC 29328]
          Length = 307

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 70/299 (23%), Positives = 136/299 (45%), Gaps = 38/299 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++++  +N RLD +  N    ++   +QK +   +V V+ K  K N ++ S   ++    
Sbjct: 6   LIDDSNQNTRLDVFLANEVE-LSRSEIQKFIEDKKVLVNYKPQKKNYKLNSNDKIKF--- 61

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI------SVQGGSG 124
                    + +  D ++   KH       ++YED  + + NK   +      ++   + 
Sbjct: 62  ---------DYEKEDKTIRAQKHD----LDVVYEDDYLAIINKDKDVIVHPTETIYSDTL 108

Query: 125 IAYHIDGFLKSWVDSKGQKPR-LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           + Y +  F K+  D  G   R + HRLD++T+G++++A+       L E  +   I K Y
Sbjct: 109 VNYLMYNF-KNLSDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEIIKTY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             +V G   ++   I  ++ +      D   ++  +E     +IS ++ +D +   +  +
Sbjct: 168 LCIVHG-KIDESGTIKEYMTRNP---KDRKKMMVSDE--GKLSISQYERLD-YNDDYSLV 220

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           ++Q  TGRTHQ+RVH  ++  PI+GD  Y     K  F S +     LHA  +   HP+
Sbjct: 221 KVQIKTGRTHQIRVHMNYIHHPILGDKLYGLKKEKILFDSQV-----LHAYNLQFIHPQ 274


>gi|125623253|ref|YP_001031736.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|124492061|emb|CAL96989.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|300070003|gb|ADJ59403.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris NZ9000]
          Length = 293

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 87/181 (48%), Gaps = 12/181 (6%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSG 156
           +L+ED    V  KPAG  S+ G       +   +K ++  K    +  H   RLD++TSG
Sbjct: 79  VLFEDDHYLVVEKPAGKASITGSLHPTGAMSNAVKGYISRKNYPNQTVHIITRLDRDTSG 138

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVH 214
           I+ +A+ R A   + +      ++K Y++++    +P + +  +       S I      
Sbjct: 139 IMFLAKHRYAHALMVQHKFRDTLEKRYYAIINDGDLPDSGQIDLPIGRRDDSIIE----R 194

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V+ +EK  N   S+  V+         L++  HTGRTHQ+RVH  H+G P+VGD  Y  
Sbjct: 195 QVRFDEKSKNALTSY--VVTERKNDLALLDIILHTGRTHQIRVHFSHLGYPLVGDDLYGG 252

Query: 275 N 275
           N
Sbjct: 253 N 253


>gi|260899347|ref|ZP_05907742.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus AQ4037]
 gi|308110268|gb|EFO47808.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus AQ4037]
          Length = 109

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 37/112 (33%), Positives = 68/112 (60%), Gaps = 6/112 (5%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++++G
Sbjct: 4   IRTQVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKAG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
            +VRIPPV      + K+++ +  S  L K ++ L+ +++YED  + + NKP
Sbjct: 64  DLVRIPPVT-----VEKKEEDVAPSTKLYKVAE-LEHMIIYEDDHMLILNKP 109


>gi|213860017|ref|ZP_03385721.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
          Length = 238

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 51/195 (26%), Positives = 92/195 (47%), Gaps = 21/195 (10%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D  GQ     HRLD+ TSG+L++  +  A + L + F    I+K Y ++V G   +    
Sbjct: 19  DQIGQHVFTAHRLDRPTSGVLLMGLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLIDDAVL 78

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQP 247
               + ++  I   +     + +K    A++ ++ +               ++  +E++P
Sbjct: 79  DYPLVEERDKIADKFA----REDKAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEP 134

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEGGR 304
            TGR HQLR H  H+  PI+GD K+  + + N ++       +L LHA  ++L HP  G+
Sbjct: 135 KTGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQ 193

Query: 305 LQITAPLPAHMVKTW 319
             I   + A + +TW
Sbjct: 194 PLI---IQAGLDETW 205


>gi|125973321|ref|YP_001037231.1| RluA family pseudouridine synthase [Clostridium thermocellum ATCC
           27405]
 gi|256005428|ref|ZP_05430391.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281417524|ref|ZP_06248544.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|125713546|gb|ABN52038.1| pseudouridine synthase, RluA family [Clostridium thermocellum ATCC
           27405]
 gi|255990568|gb|EEU00687.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281408926|gb|EFB39184.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|316940446|gb|ADU74480.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           1313]
          Length = 318

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 72/288 (25%), Positives = 122/288 (42%), Gaps = 59/288 (20%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKS-----ILLYEDSKIYVFNKPAGISVQ------GG 122
           +N ++ E  I++  ++      F++       ++YED  +   NK  GI V       GG
Sbjct: 49  VNAVVCENDIIEVDLDFDDSGIFIQPEDIPIDIIYEDEFLIALNKQPGIVVHPTCSHPGG 108

Query: 123 S---GIAYHID--GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +    +A+H+   G +K        K R   RLD++TSGI++ A+     + L      +
Sbjct: 109 TLANAVAFHLQKKGIVK--------KIRPVIRLDRDTSGIIIFAKNPYCQEFLIRQMNDK 160

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKS------HIGGDYVHVVKQNEKGANYAISHFK 231
              K Y  +V  + +N    I   + +K       HI  D            + A++H+ 
Sbjct: 161 TFIKEYIGIVHKVLENDNGTIDLPIARKPGSIMLRHISPD-----------GDPAVTHYT 209

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGN------- 279
           V++        ++ +  TGRTHQ+RVH   +G P++GD  Y       +  GN       
Sbjct: 210 VLERL-NGATLVKFRLETGRTHQIRVHCQAIGHPLLGDTLYPFEDTPYSLSGNNPHITQA 268

Query: 280 ----FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                TS I  +  LH++     HP   + L+ITAP+P  M    + L
Sbjct: 269 NTPSITSGIITRQALHSQRAVFLHPFTKKILEITAPIPEDMKSALEIL 316


>gi|256846962|ref|ZP_05552408.1| pseudouridine synthase [Lactobacillus coleohominis 101-4-CHN]
 gi|256715626|gb|EEU30601.1| pseudouridine synthase [Lactobacillus coleohominis 101-4-CHN]
          Length = 295

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 72/285 (25%), Positives = 129/285 (45%), Gaps = 34/285 (11%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           I   G +++D +     +++  GQ+V I              ++ D + N  + + F  S
Sbjct: 33  IFHGGSLQIDHQPAWAVDKVLPGQMVGI--------------ELPDETAN-PRITAFPGS 77

Query: 100 I-LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTH---RLDQE 153
             + YED+   V NK AG++      +A    +   +K++        ++TH   RLD++
Sbjct: 78  FQIAYEDADFLVINKDAGVATVPAHNVAVQDSLVNRVKNYYLVHQYPNQVTHVATRLDKD 137

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V  + R A   L    +  +++K Y ++V G   N    I   + +         
Sbjct: 138 TSGLVVFPKHRFAHAVLDRQLKRHQVKKEYVAIVGGQLSNHHGYIYAPISRDPE-----S 192

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            V +Q       +I+ +   +   ++F  + ++ HTGRTHQ+RVH   +G P++GD  Y 
Sbjct: 193 FVKRQVCDDGKESITEYWT-ERTVEQFSVVRIRLHTGRTHQIRVHFSFLGHPLIGDDMYG 251

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
               G F S    +  LH RY+    P +  +++  APLP  M K
Sbjct: 252 GT--GLFMS----RQALHCRYISFYSPFKKQQIECQAPLPDDMNK 290


>gi|163755644|ref|ZP_02162763.1| pseudouridylate synthase, 23S RNA-specific [Kordia algicida OT-1]
 gi|161324557|gb|EDP95887.1| pseudouridylate synthase, 23S RNA-specific [Kordia algicida OT-1]
          Length = 229

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/216 (26%), Positives = 95/216 (43%), Gaps = 30/216 (13%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHID--GFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++LYED  +    KP  I V          D    L+   +   +     HRLD++TSGI
Sbjct: 1   MILYEDDFVIAVAKPNNILVHHSQMARNQSDEQTLLELLFEKFEKNYYPMHRLDRKTSGI 60

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVV 216
           ++ A+ +       + F    IQK+Y+ +V G  P+N         +  S + G   +V 
Sbjct: 61  VLCAKEKRFVSKFQDLFVADAIQKVYYGVVRGFSPENG--------VIDSPVKGRDANVY 112

Query: 217 KQNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           K        A++H+K +               ++  +++ P TGR HQLR+H   +  P+
Sbjct: 113 KS-------ALTHYKTLATKELPIAVQPFETSRYSLVKLLPKTGRMHQLRIHLNKINHPL 165

Query: 267 VGDHKYCANFKGN-FTSPIQ-NKLYLHARYMDLPHP 300
           +GD KY   F    F S  + + L+LHA  +   HP
Sbjct: 166 IGDPKYGDRFHNRMFQSEFEISNLFLHAHSLTFVHP 201


>gi|116511223|ref|YP_808439.1| pseudouridylate synthase, 23S RNA-specific [Lactococcus lactis
           subsp. cremoris SK11]
 gi|116106877|gb|ABJ72017.1| Pseudouridylate synthase, 23S RNA-specific [Lactococcus lactis
           subsp. cremoris SK11]
          Length = 293

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 87/181 (48%), Gaps = 12/181 (6%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSG 156
           +L+ED    V  KPAG  S+ G       +   +K ++  K    +  H   RLD++TSG
Sbjct: 79  VLFEDDHYLVVEKPAGKASITGSLHPTGAMSNAVKGYISRKNYPNQTVHIITRLDRDTSG 138

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVH 214
           I+ +A+ R A   + +      ++K Y++++    +P + +  +       S I      
Sbjct: 139 IMFLAKHRYAHALMVQHKFRETLEKRYYAIINDGDLPDSGQIDLPIGRRDDSIIE----R 194

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V+ +EK  N   S+  V+         L++  HTGRTHQ+RVH  H+G P+VGD  Y  
Sbjct: 195 QVRFDEKSKNALTSY--VVTERKNDLALLDIILHTGRTHQIRVHFSHLGYPLVGDDLYGE 252

Query: 275 N 275
           N
Sbjct: 253 N 253


>gi|60682049|ref|YP_212193.1| putative RNA pseudouridylate synthase [Bacteroides fragilis NCTC
           9343]
 gi|60493483|emb|CAH08269.1| putative RNA pseudouridylate synthase [Bacteroides fragilis NCTC
           9343]
          Length = 305

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 109/226 (48%), Gaps = 20/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----IAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++YED+ I V  K  G+   G        A HI   L  +V   G+  R+   HRLD++T
Sbjct: 90  IVYEDAYIIVVEKKEGLLSVGTERQKERTAQHI---LSEYVGRSGRGNRIYVVHRLDRDT 146

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L + +      + Y ++V G  +   + + +WL  ++     YV 
Sbjct: 147 SGLMMFAKDEKTQYTLRDHWHDIVTDRRYVAVVTGEMEKDSDTVVSWLTDRTL----YVS 202

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++ G+  +I+H++ I   A  +  +E++  TGR +Q+RVH   +G P++GD +Y  
Sbjct: 203 SSSYDDGGSK-SITHYRTIKR-ANGYSLVELRLETGRKNQIRVHMQDLGHPLIGDGRYGI 260

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
           +   N   P+  +L LHA  +   HP   +L +   P P    K +
Sbjct: 261 DGGPN---PL-GRLALHAFKLCFYHPVTDQLMEFETPYPPTFKKLF 302


>gi|229829217|ref|ZP_04455286.1| hypothetical protein GCWU000342_01304 [Shuttleworthia satelles DSM
           14600]
 gi|229792380|gb|EEP28494.1| hypothetical protein GCWU000342_01304 [Shuttleworthia satelles DSM
           14600]
          Length = 341

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 105/245 (42%), Gaps = 33/245 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------RLTHRLDQET 154
           ++YED  I + +KPAG+          H    L + V    QK       R+ +RLD +T
Sbjct: 105 IIYEDEDILLIDKPAGMPSHPSMN---HQKDTLANAVLYYYQKQGIPFVFRIANRLDMDT 161

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH------I 208
           SG++ V++   AA  + +    R+I + Y  +V G             +K  +      I
Sbjct: 162 SGLVAVSKNSLAAARVKQMIDKRQIHREYLCIVEGSFSADSSLAKRDFVKMRYDADGQMI 221

Query: 209 GGDYVHVVKQ----------NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           GG     + +          N      A++ F+++   A K+  L +   TGRTHQ+RVH
Sbjct: 222 GGRIWAPISRREGSVLERRVNASDGQTALTDFEIVQEGA-KYSLLRVWLGTGRTHQIRVH 280

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
             ++G P+  D+ Y   ++     P      LH+  +  PHP  GR +   + LPA M  
Sbjct: 281 MNYLGHPLPADYLYHPVYQDISRQP------LHSAKLRFPHPVSGRQMCFESRLPADMRH 334

Query: 318 TWDSL 322
             D+ 
Sbjct: 335 LLDNF 339


>gi|21282618|ref|NP_645706.1| hypothetical protein MW0889 [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49485783|ref|YP_043004.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|297208359|ref|ZP_06924789.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|300912435|ref|ZP_07129878.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|21204056|dbj|BAB94754.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49244226|emb|CAG42652.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|296887098|gb|EFH26001.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|300886681|gb|EFK81883.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH70]
          Length = 284

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 90/192 (46%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV------DSK 140
           SVNL  ++  L+  +LYED+ I +  KP     Q  +    H    L   V      + +
Sbjct: 65  SVNLIPYARKLE--VLYEDAFIIIVTKPNN---QNCTPSREHPHESLIEQVLYHCQENGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      HL   F    ++KIY  LV+G         AN
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK-YGYIHHL---FSKVNLKKIYTCLVYGKTHTSGIIEAN 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 176 IRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 229 HIGHPIVGDSLY 240


>gi|229826154|ref|ZP_04452223.1| hypothetical protein GCWU000182_01526 [Abiotrophia defectiva ATCC
           49176]
 gi|229789024|gb|EEP25138.1| hypothetical protein GCWU000182_01526 [Abiotrophia defectiva ATCC
           49176]
          Length = 236

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/196 (29%), Positives = 91/196 (46%), Gaps = 25/196 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG--------IAYHIDGFLKSWVDSKGQKP--RLTHRL 150
           +LYED  I V  KP GI  QG           +  H+    +    S G++P   + HRL
Sbjct: 7   ILYEDEDIIVCVKPVGILSQGDKDGNKDLVRELKKHLVISARKNKQSIGKEPYIAVVHRL 66

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+   GI+V A+T  AA  L++     ++ K Y ++V   P+    C     ++K  I  
Sbjct: 67  DRNVRGIMVYAKTGRAAAGLSKQIAENKLTKRYMAVVSFTPER---CTPEINVEKKRI-- 121

Query: 211 DYVH---------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           DY+          + ++  KGA  A  ++KVI     K   +++   TGR HQ+R+    
Sbjct: 122 DYIAADKVKNISTIAEKESKGAERAELNYKVIKTAGNK-ALVQVDLITGRHHQIRLQLSQ 180

Query: 262 MGCPIVGDHKYCANFK 277
           +   IVGD KY  ++K
Sbjct: 181 IFNGIVGDTKYNDDYK 196


>gi|332638678|ref|ZP_08417541.1| ribosomal large subunit pseudouridine synthase D [Weissella cibaria
           KACC 11862]
          Length = 303

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 74/295 (25%), Positives = 130/295 (44%), Gaps = 36/295 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
            G V +  K+V+  + ++ G  V I  PP               + S ++   SD L   
Sbjct: 37  GGAVLLAGKQVRTVDEVKPGDKVTIVMPP---------------EESNDVVAMSD-LPIT 80

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSG 156
           +LYED    V  K AG+ SV G +     +   +K ++   G +   P +  RLD+ TSG
Sbjct: 81  VLYEDENWLVVEKEAGVTSVPGKADRETTMVNRVKGYLARSGAEDLVPHVVTRLDRFTSG 140

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-DYVHV 215
           + ++A+ R A   L +  +   + K Y+++V G      +   ++    + IG  D   +
Sbjct: 141 VALLAKHRFAHGLLDKQLQTHSVDKRYYAIVDG------DLPDDYGFIDAPIGRMDDDFI 194

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +    + + + V+  F  +   + +Q HTGRTHQ+RVH  ++G P++GD  Y   
Sbjct: 195 RREVREDGRPSQTEYWVVKRFGNQ-TLVRVQLHTGRTHQIRVHFKYLGHPLIGDEIYGGP 253

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHMVKTWDSLGFKYDRN 329
                T     +  LHA ++    P     + T + LP  +V   D    + D N
Sbjct: 254 MDRGIT-----RQALHAYWLRFYDPFAQVERTTQSALPQDIVAVLDGYQVEPDEN 303


>gi|227891498|ref|ZP_04009303.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
 gi|227866645|gb|EEJ74066.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
          Length = 296

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 71/272 (26%), Positives = 117/272 (43%), Gaps = 40/272 (14%)

Query: 16  EENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E M L ++ KN    H    +L+K   +G+V VD K+   +  +  G++  I P   + 
Sbjct: 10  DEKMTLKKFLKNKGVSHRTLSSLKK--GNGKVLVDGKKRSLSIEVGKGKITLILPPEKSD 67

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSG--------I 125
            ++   ++ LD               ++YEDS   V +KP  +S V G S         +
Sbjct: 68  ENVKISKEPLD---------------IIYEDSNWLVVDKPPLLSSVPGPSNRTDTLVNRV 112

Query: 126 AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            +H+      W   SK   P +  RLD++TSG+++VA+ R A   + +      I K Y 
Sbjct: 113 KFHL------WQQKSKDLVPHVITRLDRDTSGLVLVAKHRFAQGLINKQVEEHSIDKRYL 166

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V GI   K   I   L  + +  G  V            A + + V +    K   +E
Sbjct: 167 AVVEGIIAEKHGIIDKPLGPRENGIGQMV------TDTGKIAKTEYWVREYLGDKATLVE 220

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + HTGRTHQ+R H   +   ++GD  Y    
Sbjct: 221 CKLHTGRTHQIRAHFSSINHALIGDKLYGGRL 252


>gi|24380298|ref|NP_722253.1| putative pseudouridylate synthase [Streptococcus mutans UA159]
 gi|24378312|gb|AAN59559.1|AE015019_4 putative pseudouridylate synthase [Streptococcus mutans UA159]
          Length = 288

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 93/212 (43%), Gaps = 20/212 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NK  G+           +   + ++V   GQ   + HRLD +TSG ++ A
Sbjct: 84  LYQDEHLIIVNKIEGMKTHANDPNEIALLNHVSAYV---GQTCYVVHRLDMKTSGTVMFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I++ YW+L  G      +   + ++ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLENKSIKREYWALAQG------QFSEHAIIYREPIGRDRHDRRKRVVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K    AI+   ++  F+     ++ Q  TGRTHQ+RVH  +    IVGD  Y     G 
Sbjct: 195 HKHGQTAITQVSLLKHFSNNTSLIKCQLQTGRTHQIRVHLAYHDHAIVGDPLYSQQTAG- 253

Query: 280 FTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
                  +L LHA  +   HP    ++++ AP
Sbjct: 254 -------RLMLHAHQLTFTHPLTLEKIKVEAP 278


>gi|163749894|ref|ZP_02157139.1| hypothetical protein KT99_02081 [Shewanella benthica KT99]
 gi|161330408|gb|EDQ01387.1| hypothetical protein KT99_02081 [Shewanella benthica KT99]
          Length = 224

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 48/145 (33%), Positives = 70/145 (48%), Gaps = 15/145 (10%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG+L+ A++  AA   TE F   ++QK Y +L  G PK K+  +   + K   
Sbjct: 47  HRLDSLTSGLLLFAKSSRAAAEFTELFTQHKVQKYYVALAKGKPKKKQGWVVGDMAKSRR 106

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                +   K      N A++ F      A+      ++P +G+THQLRV    +G PI+
Sbjct: 107 SMYKLLRTTK------NPALTQF-FSQSVAEGLRLYLLKPLSGKTHQLRVALASIGVPIL 159

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA 292
           GD  Y     G   S   ++ YLHA
Sbjct: 160 GDKLY-----GGAES---DRGYLHA 176


>gi|53713831|ref|YP_099823.1| RNA pseudouridylate synthase [Bacteroides fragilis YCH46]
 gi|52216696|dbj|BAD49289.1| RNA pseudouridylate synthase [Bacteroides fragilis YCH46]
          Length = 307

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 109/226 (48%), Gaps = 20/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----IAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++YED+ I V  K  G+   G        A HI   L  +V   G+  R+   HRLD++T
Sbjct: 92  IVYEDAYIIVVEKKEGLLSVGTERQKERTAQHI---LSEYVGRSGRGNRIYVVHRLDRDT 148

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L + +      + Y ++V G  +   + + +WL  ++     YV 
Sbjct: 149 SGLMMFAKDEKTQYTLRDHWHDIVTDRRYVAVVTGEIEKDSDTVVSWLTDRTL----YVS 204

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++ G+  +I+H++ I   A  +  +E++  TGR +Q+RVH   +G P++GD +Y  
Sbjct: 205 SSSYDDGGSK-SITHYRTIKR-ANGYSLVELRLETGRKNQIRVHMQDLGHPLIGDGRYGI 262

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
           +   N   P+  +L LHA  +   HP   +L +   P P    K +
Sbjct: 263 DGGPN---PL-GRLALHAFKLCFYHPVTDQLMEFETPYPPTFKKLF 304


>gi|309810028|ref|ZP_07703875.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
 gi|308169668|gb|EFO71714.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
          Length = 302

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/183 (30%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 133 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 191

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 192 PIGKKDDPIKRYIM------EGGKNSVTKYRVIKQVAGA-SLVELQLLTGRTHQIRVHMQ 244

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F  P Q    LH   +    P E  R+++    PA M++ W
Sbjct: 245 YLGHPLFGDHLY--GVEDDF--PRQ---ALHCFLLAFDDPLEHKRIEVQIADPADMLQLW 297

Query: 320 DSL 322
             L
Sbjct: 298 QKL 300


>gi|297571862|ref|YP_003697636.1| pseudouridine synthase [Arcanobacterium haemolyticum DSM 20595]
 gi|296932209|gb|ADH93017.1| pseudouridine synthase [Arcanobacterium haemolyticum DSM 20595]
          Length = 309

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 52/204 (25%), Positives = 90/204 (44%), Gaps = 9/204 (4%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++ ++ +  V +KP G+ ++  GS +A  +    +   + +       HRLD ET+G+++
Sbjct: 98  VIADEERFIVVDKPHGMATIPRGSHVAQTVTVAARRQFNDEDLV--CAHRLDAETAGLVL 155

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R     +     F  R + K Y ++   IP         W   +  +   Y  +    
Sbjct: 156 LTREPQWRKPYQTLFERRGVGKKYCAVTRDIPG-----FDTWETVELRLERGYRPLATDV 210

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
             G   +++H +++   A      E+ PHTG+THQLRV   H+G PI+GD  Y   F   
Sbjct: 211 VDGEPNSVTHMRIV-ARADGLAQWELIPHTGKTHQLRVTLEHVGAPILGDPLYPRLFTKE 269

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG 303
             +     L LHAR +    P  G
Sbjct: 270 EEAARAYPLQLHARELSFVDPIDG 293


>gi|256026481|ref|ZP_05440315.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
          Length = 288

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 106/226 (46%), Gaps = 28/226 (12%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           + YED  + + NK   I V     +    +A  I  + +  +  K   PR  +RLD  TS
Sbjct: 75  IAYEDENLLIVNKEPYIIVHPTQKKVDKTLANAIVNYFEKTL-GKTLVPRFYNRLDMNTS 133

Query: 156 GILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           G++++A+   T+A  Q  TE      ++K Y  +  GI +     I   + K     GD 
Sbjct: 134 GLIIIAKNAYTQAFLQDKTE------VKKTYKVIASGIIEKDDFFIEIPIGKV----GDN 183

Query: 213 VHVVKQNEK-GANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +  ++ +EK G   A +H KV++  + +   +LE + +TGRTHQ+R H   +G  +VGD 
Sbjct: 184 LRRIELSEKDGGKSAKTHIKVLERNYEKNITFLEARLYTGRTHQIRAHLSLIGHSLVGDE 243

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
            Y  N        +  +  LHA  ++  +P+    L+I   +P  M
Sbjct: 244 LYGGNMN------LAKRQMLHAYKLEFQNPKTLENLKIEIDIPIDM 283


>gi|325911465|ref|ZP_08173877.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
 gi|325476815|gb|EGC79969.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
          Length = 309

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/183 (30%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 140 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 198

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 199 PIGKKDDPIKRYIM------EGGKNSVTKYRVIKQVAGA-SLVELQLLTGRTHQIRVHMQ 251

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F  P Q    LH   +    P E  R+++    PA M++ W
Sbjct: 252 YLGHPLFGDHLY--GVEDDF--PRQ---ALHCFLLAFDDPLEHKRIEVQIADPADMLQLW 304

Query: 320 DSL 322
             L
Sbjct: 305 QKL 307


>gi|90021559|ref|YP_527386.1| copper-resistance protein CopA [Saccharophagus degradans 2-40]
 gi|89951159|gb|ABD81174.1| pseudouridine synthase [Saccharophagus degradans 2-40]
          Length = 209

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 44/151 (29%), Positives = 71/151 (47%), Gaps = 15/151 (9%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ TSG+ + A++  AA    + F  + + K Y ++    P  K+  I   ++K  
Sbjct: 26  AHRLDKPTSGLCIFAKSSGAAAQFGQLFERKLVTKYYLAITSKKPAKKQGAIIGDMVKTR 85

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           +  G +    K      N AI+HF      A     + ++P TG+THQLRV    +G  I
Sbjct: 86  N--GSW----KLTAAKTNPAITHFFSF-ALASGMRLILLKPSTGKTHQLRVALKALGAAI 138

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +GD +Y             ++LYLHA  ++ 
Sbjct: 139 IGDERYGGE--------PSDRLYLHAYQLEF 161


>gi|315453493|ref|YP_004073763.1| putative ribosomal pseudouridine synthase [Helicobacter felis ATCC
           49179]
 gi|315132545|emb|CBY83173.1| putative ribosomal pseudouridine synthase [Helicobacter felis ATCC
           49179]
          Length = 321

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/218 (28%), Positives = 101/218 (46%), Gaps = 34/218 (15%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQ 152
           LYED  + V NKP  ++V     +    +  L  ++ +KG          +  + HRLD+
Sbjct: 78  LYEDEDLLVINKPPHLAVHPAPSLK---EESLVDYLVAKGYQLSNLNGTSRCGIVHRLDK 134

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           ETSG LV+A+  A   HL+   + R++ + Y +L+ G  +         L  + H+G   
Sbjct: 135 ETSGALVIAKNNACHAHLSAQLQSRQMGRYYVALIQGHLREP-------LFVECHLGRHP 187

Query: 213 VHVVKQNE------KGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCP 265
            + +K+        KG   + + F  +  F    C L   + ++GRTHQ+R H   +G P
Sbjct: 188 KNRLKRANLDALKVKGGKPSKTFF--VPLFDGLKCQLVGARLYSGRTHQVRAHLESLGRP 245

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           I+GD  Y A  +G+       +  LHA  + L HP  G
Sbjct: 246 ILGDRLYGAK-EGS-----AKRTMLHAYILYLIHPRTG 277


>gi|326317665|ref|YP_004235337.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
 gi|323374501|gb|ADX46770.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
          Length = 281

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/214 (26%), Positives = 98/214 (45%), Gaps = 12/214 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  +    KPAG  V      A      +++  D  G++    HRLD+ T G+LV+
Sbjct: 14  ILWQDDDLVAVYKPAGWLVHRTGLDAGETRFVMQALRDQMGRRVYPVHRLDKGTCGVLVM 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
                AA+ L+++F   R+ K Y +LV G   ++ +   +  L+      D      Q  
Sbjct: 74  GLHADAARALSQAFEHHRVDKRYLALVRGHAPDRVQV--DHALRPDDAPPD---AAVQPA 128

Query: 221 KGANYAISHFKVIDCFAQKFC-----WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           + A   ++  ++ +    +F       +E  P TGR HQ+R H  H+  PI+GD  +   
Sbjct: 129 RTALRCLARLELPEASDTRFATTRASLVEALPETGRRHQIRRHLKHIAHPILGDATHGKG 188

Query: 276 FKGNFTSPIQN--KLYLHARYMDLPHPEGGRLQI 307
               + +      +L+LHA  + LPHP  G + +
Sbjct: 189 PLNRWWAQRLGLQRLWLHAWRLALPHPATGDMLV 222


>gi|327393813|dbj|BAK11235.1| ribosomal large subunit pseudouridine synthase A RluA [Pantoea
           ananatis AJ13355]
          Length = 232

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 102/230 (44%), Gaps = 35/230 (15%)

Query: 101 LLYEDSKIYVFNKPA------GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LY+D  + + +KP+      G + Q    + Y +                L HRLD  T
Sbjct: 19  ILYQDDHLVLIDKPSELLSLSGKNPQNLDSVHYRLVTIFPGCT--------LVHRLDFGT 70

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV 213
           SG++VVAR +     L++ F  R + K Y +L+ G +P   +E I +  + K       +
Sbjct: 71  SGLMVVARNKTINAALSQQFSARTVAKHYSALLCGHLP--DEEGIIDAPIAKDPARFPRM 128

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCP 265
            +  +  K A    S ++V++ F  K           + + P TGRTHQLR+H   +G P
Sbjct: 129 SICAEWGKPAR---SRYRVVERFNLKRDDARVIPLTRVTLIPETGRTHQLRIHCQLLGHP 185

Query: 266 IVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLP 312
           I+G    C  + G     ++   +L LHA  +   HP  G    I +P P
Sbjct: 186 ILG----CDLYGGLLLPGMEQTPRLMLHASELQFIHPVTGEPFHIVSPSP 231


>gi|227432332|ref|ZP_03914325.1| 23S rRNA pseudouridylate synthase RluD [Leuconostoc mesenteroides
           subsp. cremoris ATCC 19254]
 gi|227351938|gb|EEJ42171.1| 23S rRNA pseudouridylate synthase RluD [Leuconostoc mesenteroides
           subsp. cremoris ATCC 19254]
          Length = 299

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/239 (24%), Positives = 113/239 (47%), Gaps = 26/239 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
            G + V+++ V  ++ +++G +V I  P   + + ++ + K LD               +
Sbjct: 36  GGAILVNERTVYTSDYLKNGDIVTIVMPTEKSNDLVVPDYKPLD---------------I 80

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYH-----IDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++E+    V +KP GI+   G     H     + G L++ + +    P +  RLD++TSG
Sbjct: 81  IFENEHWLVVDKPYGITTVPGHADRLHTLVNQVKGHLET-IKADDLVPHVVTRLDRDTSG 139

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV-HV 215
           I+++A+ R A   L +  +   ++K Y +   GI       I   +     + GD++   
Sbjct: 140 IVLLAKHRFAHAVLDQQLQDHTVEKFYLAYPSGILAYDHGDINAPI---GRMDGDFIKRE 196

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+ + K +       +  +   Q    +++Q HTGRTHQ+RVH  ++G P+VGD  Y  
Sbjct: 197 VRDDGKPSRTEYWVERRYEDDEQNMTRVKVQLHTGRTHQIRVHFANIGHPLVGDTLYGG 255


>gi|88857157|ref|ZP_01131800.1| putative 23S rRNA pseudouridylate 746 synthase [Pseudoalteromonas
           tunicata D2]
 gi|88820354|gb|EAR30166.1| putative 23S rRNA pseudouridylate 746 synthase [Pseudoalteromonas
           tunicata D2]
          Length = 221

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 63/204 (30%), Positives = 94/204 (46%), Gaps = 19/204 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I + NKP+G+    G   A       +   D       L HRLD  TSGI++V
Sbjct: 19  ILYQDEAILLINKPSGLLSLSGKNPANLDSVHYRLCQDFPAAT--LLHRLDFGTSGIMLV 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           A  +     L   F+ R I+K Y +++ G   P N      N  + K+      V + + 
Sbjct: 77  ALNKTINAVLMSQFQQRTIKKSYTAILAGQLTPLNGS---INLPIAKAEFPRHAVCLQRG 133

Query: 219 NEKGANYAI-SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
               ++Y + ++ K  D  + K  +L   P TGRTHQLR+H+  +G PI+G   Y     
Sbjct: 134 KHAQSDYQVHAYCKSTD--STKVTYL---PVTGRTHQLRIHSQAIGHPILGCDLY----- 183

Query: 278 GNFTSPIQN-KLYLHARYMDLPHP 300
           G   S  Q  +L LHA  +   HP
Sbjct: 184 GTVHSLSQAPRLMLHATSLTFTHP 207


>gi|289764495|ref|ZP_06523873.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
 gi|289716050|gb|EFD80062.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
          Length = 292

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 106/226 (46%), Gaps = 28/226 (12%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           + YED  + + NK   I V     +    +A  I  + +  +  K   PR  +RLD  TS
Sbjct: 79  IAYEDENLLIVNKEPYIIVHPTQKKVDKTLANAIVNYFEKTL-GKTLVPRFYNRLDMNTS 137

Query: 156 GILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           G++++A+   T+A  Q  TE      ++K Y  +  GI +     I   + K     GD 
Sbjct: 138 GLIIIAKNAYTQAFLQDKTE------VKKTYKVIASGIIEKDDFFIEIPIGKV----GDN 187

Query: 213 VHVVKQNEK-GANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +  ++ +EK G   A +H KV++  + +   +LE + +TGRTHQ+R H   +G  +VGD 
Sbjct: 188 LRRIELSEKDGGKSAKTHIKVLERNYEKNITFLEARLYTGRTHQIRAHLSLIGHSLVGDE 247

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
            Y  N        +  +  LHA  ++  +P+    L+I   +P  M
Sbjct: 248 LYGGNMN------LAKRQMLHAYKLEFQNPKTLENLKIEIDIPIDM 287


>gi|209694692|ref|YP_002262620.1| RNA psedouridine synthase [Aliivibrio salmonicida LFI1238]
 gi|208008643|emb|CAQ78827.1| RNA psedouridine synthase [Aliivibrio salmonicida LFI1238]
          Length = 228

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 60/210 (28%), Positives = 96/210 (45%), Gaps = 18/210 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY++S   V NK   +SV    G    +    K   D   ++  L HRLD+ TSG+L++
Sbjct: 4   ILYQNSDFLVINKHPNVSVHKDDGDTSLLIELAKVTGD---KQLYLIHRLDKMTSGLLLI 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R ++AA  L++ F  R ++K Y ++    PK K+  +   + +        +     N 
Sbjct: 61  GRHQSAASELSQLFAKRLVEKYYLAIGDKKPKKKQGLVIGDMERSRRASWKLI-----NS 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K  N AI+ F           +L  +PHTG+THQ+RV    +G  I+GD  Y        
Sbjct: 116 K-ENPAITQFFSTAAHNGNRLFL-CKPHTGKTHQIRVALKSVGSGILGDSIY-------- 165

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           +S   ++ YLHA  +   + E     I  P
Sbjct: 166 SSSKADRGYLHAYALRFTYQEQAFEFIETP 195


>gi|327484276|gb|AEA78683.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio cholerae
           LMA3894-4]
          Length = 235

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 49/147 (33%), Positives = 74/147 (50%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR   AA  L++ F  R+++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNVTAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  +      N AI+ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVNSQE------NPAITQFFSAAAATGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADESDRGYLHA 178


>gi|325913175|ref|ZP_08175545.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
 gi|325477596|gb|EGC80738.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
          Length = 309

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/183 (30%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 140 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 198

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 199 PIGKKDDPIKRYIM------EGGKNSVTKYRVIKQVAGA-SLVELQLLTGRTHQIRVHMQ 251

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F  P Q    LH   +    P E  R+++    PA M++ W
Sbjct: 252 YLGHPLFGDHLY--GVEDDF--PRQ---ALHCFLLAFDDPLEHKRIEVQIADPADMLQLW 304

Query: 320 DSL 322
             L
Sbjct: 305 QKL 307


>gi|269468780|gb|EEZ80384.1| pseudouridylate synthase, 23S RNA-specific [uncultured SUP05
           cluster bacterium]
          Length = 277

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/174 (32%), Positives = 88/174 (50%), Gaps = 26/174 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-LTHRLDQETSGILV 159
           LL + +   V+ KPAG+  QG     +     L   V+ K  +P  L HRLD+ TSG+++
Sbjct: 87  LLLDKNDYSVWFKPAGVFSQGSK---WGDHCALTRLVEKKLDRPTFLVHRLDRATSGLML 143

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A T+  A+ L++ F  R I K Y ++V G  K  KE I    L+K   G +        
Sbjct: 144 IAHTKNMARDLSKMFADRNIDKTYLAIVEG--KFTKEKIT---LEKPIDGKN-------- 190

Query: 220 EKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                 A+SH  +++  ++KF   L+++  TGR HQ+R H      PI+GD  Y
Sbjct: 191 ------AVSHVTLLE--SEKFKSLLKVKIETGRKHQIRKHLSEFSHPIIGDRLY 236


>gi|313896082|ref|ZP_07829636.1| pseudouridine synthase, RluA family [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312975507|gb|EFR40968.1| pseudouridine synthase, RluA family [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 297

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 104/227 (45%), Gaps = 22/227 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGS-----GIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           L   + YED  + + +KPAG+ V   +      IA  + G   S  D+    P   HRLD
Sbjct: 75  LPLAIAYEDDDLLIIDKPAGMLVHPTTQETRGTIANAVRGLYASRGDTLDFHP--CHRLD 132

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + T+G+L++A+      + T+      +++ Y +L+ G      + I   + +       
Sbjct: 133 RNTTGLLLIAKCPEVQYYFTK--HRDAVRREYLALIEGRLTPASDIIDAPIARALP---- 186

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              ++++       A +H++ +     ++  L +   TGRTHQ+RVH  H+G P++GD  
Sbjct: 187 -SIILRRVAPEGKPARTHYETV-ASDGRYSLLRLTLETGRTHQIRVHLAHLGHPLLGDDL 244

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           Y  N     T  I     LHA ++ L  P  G  L + +PLP  + +
Sbjct: 245 YGGN-----TDEIARH-ALHAAWLSLRLPHTGELLTVASPLPKDIAR 285


>gi|192358936|ref|YP_001982457.1| ribosomal large subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
 gi|190685101|gb|ACE82779.1| ribosomal large subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
          Length = 212

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 67/205 (32%), Positives = 102/205 (49%), Gaps = 20/205 (9%)

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           NKP+G+    G G       + ++   +     R+ HRLDQ TSGI++        + LT
Sbjct: 19  NKPSGLLTVPGKGPENQHCLYKQALAFNPNA--RIVHRLDQATSGIVMFPLNYPCLKQLT 76

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAIS 228
             F  R I K Y ++V G+    +  +   L+       D+ +  +Q    E G + A +
Sbjct: 77  HQFEARAIHKRYLAVVHGLVGQDEGEVTLPLI------CDWPNRPRQKVCFEHGKS-AHT 129

Query: 229 HFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
            +KVI  D   Q+   LE++P +GRTHQLRVH L +G PI+GD  Y  + +    +P   
Sbjct: 130 RYKVIHRDQGLQQ-TRLELEPVSGRTHQLRVHMLSLGHPILGDRLYAPD-EIIAQAP--- 184

Query: 287 KLYLHARYMDLPHPEGGR-LQITAP 310
           +L LHA+ + L HP   + L I AP
Sbjct: 185 RLLLHAQELWLNHPISAQPLHIKAP 209


>gi|257066371|ref|YP_003152627.1| pseudouridine synthase [Anaerococcus prevotii DSM 20548]
 gi|256798251|gb|ACV28906.1| pseudouridine synthase [Anaerococcus prevotii DSM 20548]
          Length = 277

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 52/187 (27%), Positives = 88/187 (47%), Gaps = 32/187 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGIL 158
           ++YED    V +K A I+V   + I+  +  ++ ++    GQ  K RL +RLD +TSG++
Sbjct: 75  IVYEDDNSLVISKEANITVNSKNQIS--LSNYIANYFIDSGQESKIRLVNRLDMDTSGLM 132

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+ + +  +  +      ++K Y ++V G+                 I   Y +    
Sbjct: 133 LIAKNKYSHAYYQKQLEENTMKKKYLAVVEGML---------------DIDSLYENKFSY 177

Query: 219 NEKGANYAIS--------HFKV--IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           NEK  NY  S        +FK   I+C    F  +E +  TGRTHQ+R     +G PI G
Sbjct: 178 NEKKKNYEPSDKGKISRTYFKSIRINC---DFSIIECEILTGRTHQIRASLTDLGHPIWG 234

Query: 269 DHKYCAN 275
           D  Y ++
Sbjct: 235 DKLYGSD 241


>gi|309803082|ref|ZP_07697181.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           11V1-d]
 gi|308164863|gb|EFO67111.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           11V1-d]
          Length = 307

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/183 (30%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 138 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 196

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 197 PIGKKDDPIKRYIM------EGGKDSVTKYRVIKQVAGA-SLVELQLLTGRTHQIRVHMQ 249

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F  P Q    LH   +    P E  R+++    PA M++ W
Sbjct: 250 YLGHPLFGDHLYGV--EDDF--PRQ---ALHCFLLAFDDPLEHKRIEVQIADPADMLQLW 302

Query: 320 DSL 322
             L
Sbjct: 303 QKL 305


>gi|302332618|gb|ADL22811.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus JKD6159]
          Length = 284

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 89/192 (46%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++   K  +LYED+ I +  KP     Q  +    H    L   V    Q+   
Sbjct: 65  SVNLIPYAR--KVEVLYEDAFIIIVTKPNN---QNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKGNLKKIYTCLVYGKTHTSGIIEAN 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 176 IRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 229 HIGHPIVGDSLY 240


>gi|227530063|ref|ZP_03960112.1| pseudouridylate synthase RluD [Lactobacillus vaginalis ATCC 49540]
 gi|227350031|gb|EEJ40322.1| pseudouridylate synthase RluD [Lactobacillus vaginalis ATCC 49540]
          Length = 300

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 64/220 (29%), Positives = 103/220 (46%), Gaps = 31/220 (14%)

Query: 101 LLYEDSKIYVFNKPAG----ISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LYE+  + V NKP G     +  G +G   + + G+L         +  + HR+D +TS
Sbjct: 91  VLYENRDLLVVNKPRGQKSHPNETGETGTLMNDVAGYLH-------HQAYMVHRIDLQTS 143

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++VA+       L     + +I + Y +LV G  K   E   +W      IG D   +
Sbjct: 144 GAVIVAKNPVVVPILDRLISLGKIHREYLALVEGQIKGSGEW--DW-----PIGNDPSDI 196

Query: 216 VKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            K+   G  +  A + ++ +   + K+  ++++  TGRTHQLRVH  + G PIVGD  Y 
Sbjct: 197 RKRKVNGEHSQRAQTFYQTVKSNS-KYSLVDLRLGTGRTHQLRVHLEYSGHPIVGDPIYN 255

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            +           K++L+     L  P   R + ITAPLP
Sbjct: 256 PSSAA--------KMHLNGYKQRLVVPFSNREITITAPLP 287


>gi|192360612|ref|YP_001982437.1| pseudouridine synthase Rlu family protein [Cellvibrio japonicus
           Ueda107]
 gi|190686777|gb|ACE84455.1| pseudouridine synthase Rlu family protein [Cellvibrio japonicus
           Ueda107]
          Length = 347

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 73/270 (27%), Positives = 110/270 (40%), Gaps = 70/270 (25%)

Query: 67  IPPVINALNHIIKEQKILDS-----------SVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           + PV + L  II   ++  S            +++   SD    ++  ++  + V+ KP 
Sbjct: 71  VQPVADTLVLIIASHRVASSIGLVFSVTSLFFLDVFFMSDVFFQLVDEQEDFLLVYKKP- 129

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTES 173
           G+S     G     +  L   +  +G   +L   HRLD+ TSG+LV A+T  A   L   
Sbjct: 130 GVSFHSEQG-----EPGLFEIIRQRGGYAQLYPVHRLDKVTSGLLVFAKTAEANHQLCAQ 184

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECI---------ANWLLKKSHIGGDYVHVVKQNEKGAN 224
           F  R  QK Y ++  G P  K+  I           W+L ++                 N
Sbjct: 185 FEQRLTQKYYLAISAGKPIKKQGLIKGDMYPARRGAWMLGRTL---------------EN 229

Query: 225 YAISHFKVIDCFAQKFC----WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            AI+ F     F+Q          ++PHTG+THQLRV    +G PIVGD  Y     G  
Sbjct: 230 PAITQF-----FSQGLGNGQRLYVLKPHTGKTHQLRVALKSIGAPIVGDSLYGDRHAG-- 282

Query: 281 TSPIQNKLYLHA------------RYMDLP 298
                +++YLHA            RY +LP
Sbjct: 283 ----IDRVYLHAFSLAFTLNGVAYRYSELP 308


>gi|221134752|ref|ZP_03561055.1| 23S rRNA pseudouridylate synthase [Glaciecola sp. HTCC2999]
          Length = 240

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/203 (28%), Positives = 95/203 (46%), Gaps = 21/203 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS------WVDSKGQKPRLTHRLDQET 154
           +LY+ S  ++  KP G+++   S     +    K+      + +++     L HRLD  T
Sbjct: 3   VLYDHSDFFIIAKPQGVTMHEASNGLPAVLPLFKAALANMAYPEAQYAHLHLVHRLDDHT 62

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L++A+   AA+   E F  +RIQK Y +L     K K   +   ++ K    G +V 
Sbjct: 63  SGCLIIAKHAVAAERFRELFSQQRIQKYYVALSHAKGKRKAGWVKGDMVNKR--KGQWV- 119

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + K  E+    AIS+F              ++P +G+THQ+RV     G  I+GD +Y  
Sbjct: 120 LTKSVERP---AISYF-FRQGLGNGLYLFWVKPFSGKTHQVRVALKSNGSGILGDPQYS- 174

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
                 + P Q ++YLHA  +D 
Sbjct: 175 ------SEPAQ-RMYLHAFALDF 190


>gi|21220553|ref|NP_626332.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           coelicolor A3(2)]
 gi|256788308|ref|ZP_05526739.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           lividans TK24]
 gi|289772202|ref|ZP_06531580.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           lividans TK24]
 gi|5689945|emb|CAB51982.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces coelicolor A3(2)]
 gi|289702401|gb|EFD69830.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           lividans TK24]
          Length = 314

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 73/305 (23%), Positives = 131/305 (42%), Gaps = 19/305 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V+VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVQVDGSVVGKSERVH 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   ++ E       + +    + +  ++       +     +G +V
Sbjct: 60  GGAWLEVEMPQAPAPVQVVAEPV---EGMEIVHDDEDVVVVVKPVGVAAHPSPGWSGPTV 116

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GG   A    G+  S      ++  + HRLD  TSG++ VA++  A   L   F+ R +
Sbjct: 117 IGGLAAA----GYRVS-TSGAAERQGIVHRLDVGTSGLMAVAKSERAYTSLKRQFKERTV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I+ F + 
Sbjct: 172 DKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAEGK---PSVTHYDLIEAF-RA 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
              L+++  TGRTHQ+RVH      P VGD  Y A+        ++  + +LHA  +   
Sbjct: 226 ASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADP--TLAKRLRLTRQWLHAVRLGFE 283

Query: 299 HPEGG 303
           HP  G
Sbjct: 284 HPGTG 288


>gi|205372953|ref|ZP_03225761.1| pseudouridine synthetase [Bacillus coahuilensis m4-4]
          Length = 238

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 53/183 (28%), Positives = 93/183 (50%), Gaps = 15/183 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK---PRLTH---RLDQET 154
           ++YED  + V NKPA ++         H  G L + +    +K   P   H   RLD++T
Sbjct: 23  IVYEDEHVLVVNKPARMNTIPSK---EHPTGSLANALLFYYEKIGLPSTVHIVTRLDRDT 79

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+ +     L+   + +++ + Y +L  G  K     I   + +K     D   
Sbjct: 80  SGLVLIAKHQFVHGKLSLLQQQKKVNREYEALSEGTFKEPYGKIELPIGRK-----DTSI 134

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + ++      YA ++++V+  F QKF  ++++  TGRTHQ+RVH  H+G P+VGD  Y  
Sbjct: 135 IEREVRHDGKYACTYYRVLQNF-QKFSHVKLKLETGRTHQIRVHLSHIGHPLVGDTLYGG 193

Query: 275 NFK 277
             K
Sbjct: 194 GTK 196


>gi|319639018|ref|ZP_07993776.1| pseudouridine synthase Rlu family protein [Neisseria mucosa C102]
 gi|317399922|gb|EFV80585.1| pseudouridine synthase Rlu family protein [Neisseria mucosa C102]
          Length = 219

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 51/175 (29%), Positives = 80/175 (45%), Gaps = 9/175 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E     V NKP G+SV   S     +   L   +    ++  L HRLD+ TSG+L++
Sbjct: 4   IVFEHKDFVVINKPCGVSVHSESEGEVCLTASLAQKLGV--ERVWLVHRLDKATSGLLLL 61

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R +A  L+  F  + ++K Y +L    P  K+     W+  K  +        K   
Sbjct: 62  ALNRDSAAALSTQFAEKTMRKTYLALGTHKPAKKQ----GWV--KGGMARSRRGTWKLTR 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              N+A++ F              +QP TG+THQLRV    +G PI+GD  Y  +
Sbjct: 116 DEDNFAVTRFSS-QSLKPGLRLFVLQPFTGKTHQLRVAMKSIGSPILGDTLYGGD 169


>gi|325111150|ref|YP_004272218.1| hypothetical protein Plabr_4625 [Planctomyces brasiliensis DSM
           5305]
 gi|324971418|gb|ADY62196.1| UPF0176 protein yceA [Planctomyces brasiliensis DSM 5305]
          Length = 621

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 70/296 (23%), Positives = 122/296 (41%), Gaps = 31/296 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ-VVRIPPVINALNHIIKEQK 82
           +  +++PH++  +   +  +G +R   +  + +  +  GQ ++R+ P             
Sbjct: 333 FLADYHPHVSREDWASVCEAGLIRYRDRAWQADQLVWEGQRLLRLEP------------N 380

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
            ++  VN           L+   +++ VF+KPA + V        +    L      +  
Sbjct: 381 TIEPDVNPNIK-------LITWQNQLVVFDKPAPLPVHPCGRFNKNSMTMLLDLAFPE-T 432

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-ECIANW 201
           K R  HRLD  T+G++V    R  +  +   F     +K Y   V G P  +K  C    
Sbjct: 433 KLRPAHRLDANTTGLIVFTSHRDHSLRIQRQFERGEAEKTYLCRVNGQPTEEKFRCDLPI 492

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
               +  G   +     +E+    A + F+V+         +E +P TGRT+Q+RVH  H
Sbjct: 493 SRDTAEAGARCI-----DEENGLSASTEFRVLKRLDDGTALVEAKPLTGRTNQIRVHLWH 547

Query: 262 MGCPIVGDHKYCANFK--GNFTSPIQNK-LYLHARYMDLPHPEGGR-LQITAPLPA 313
           +G PI+ D  Y    K     T  +  + + LH+  + L  PE G  L    PLPA
Sbjct: 548 LGFPILNDSVYLPEQKIGEKITHDVSAQPMCLHSWKLRLREPETGEGLNFETPLPA 603


>gi|312872564|ref|ZP_07732632.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
 gi|311091926|gb|EFQ50302.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
          Length = 300

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/183 (30%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 131 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 189

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 190 PIGKKDDPIKRYIM------EGGKDSVTKYRVIKQVAGA-SLVELQLLTGRTHQIRVHMQ 242

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F  P Q    LH   +    P E  R+++    PA M++ W
Sbjct: 243 YLGHPLFGDHLY--GVEDDF--PRQ---ALHCFLLAFDDPLEHKRIEVQIADPADMLQLW 295

Query: 320 DSL 322
             L
Sbjct: 296 QKL 298


>gi|195434112|ref|XP_002065047.1| GK15252 [Drosophila willistoni]
 gi|194161132|gb|EDW76033.1| GK15252 [Drosophila willistoni]
          Length = 532

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/196 (30%), Positives = 90/196 (45%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L ++              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 195 KHNDLLANVVHRHEVPVTAQPIRIIHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILAK- 253

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  R    A+ L +  R R++QK Y  LV G  P    E
Sbjct: 254 EFNLKDLRTIHRLDRLTSGLLLFGRNANKARELEQQIRQRQVQKEYVCLVEGKFPDGIIE 313

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C  +  +    IG     V + + KG +   + F+ +         L  +P TGR HQ+R
Sbjct: 314 CNESIEVVSYKIG-----VCRVSPKGKDCKTT-FQRLSNVGDSSLVL-CKPLTGRMHQIR 366

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PIV D  Y
Sbjct: 367 VHLQYLGYPIVNDPLY 382


>gi|310777837|ref|YP_003966170.1| pseudouridine synthase, RluA family [Ilyobacter polytropus DSM
           2926]
 gi|309747160|gb|ADO81822.1| pseudouridine synthase, RluA family [Ilyobacter polytropus DSM
           2926]
          Length = 287

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/173 (32%), Positives = 86/173 (49%), Gaps = 28/173 (16%)

Query: 144 PRLTHRLDQETSGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           PR  +RLD  T+GI+VVA+   T+A  Q+  E      ++K Y ++V GI +  +  I  
Sbjct: 121 PRFYNRLDMNTTGIIVVAKNAYTQAFLQYKAE------VKKYYQAIVKGIIEEDEIMIEK 174

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHA 259
            L K+   G +    V   EKG   A +  KVI  + +K    +E++  TGRTHQ+R H 
Sbjct: 175 PLGKE---GDELRRKVMPVEKGGQDAKTFVKVIKRYPEKDLSLVELELFTGRTHQIRAHM 231

Query: 260 LHMGCPIVGDHKYCA-----------NFKGNFTSPIQNKLYLHARYMDLPHPE 301
             +G P++GD  Y A           ++K  FT+P      LH   +++  PE
Sbjct: 232 ESLGHPVLGDELYGAKDDRARRQMLHSYKLEFTNPDN----LHQETVEIELPE 280


>gi|223997012|ref|XP_002288179.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220975287|gb|EED93615.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 175

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 52/164 (31%), Positives = 82/164 (50%), Gaps = 13/164 (7%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMR---RIQKIYWSLVWG-IPKNKKECIANW 201
           + HRLD++TSG+ ++AR   A + L + F+ +   R+ K Y +LV G    +   C+A+ 
Sbjct: 2   VVHRLDRDTSGVFLLARNDEALKTLHDDFKDKTRGRVTKRYVALVCGHWNSDNASCVADR 61

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           +      G   + +V+  E      ++     +        +E+QP TGRTHQLRVH   
Sbjct: 62  MTTDE--GEIDLPLVRDIENPPFMRVA--TTGNEIKLPVTRVELQPITGRTHQLRVHCAA 117

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNK-----LYLHARYMDLPHP 300
           MG PIVGD  Y    +G+    I+       L LHA+ + + HP
Sbjct: 118 MGYPIVGDSIYGYGGEGSPREGIEMDEDECLLCLHAQRLTIFHP 161


>gi|153825491|ref|ZP_01978158.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-2]
 gi|149740903|gb|EDM54988.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-2]
          Length = 235

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 48/147 (32%), Positives = 74/147 (50%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR   +A  L++ F  R+++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNATSASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  +      N AI+ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVNSQE------NPAITQFFSATAAPGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADKSDRGYLHA 178


>gi|145349937|ref|XP_001419383.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144579614|gb|ABO97676.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 243

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 102/242 (42%), Gaps = 32/242 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIA---YHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++E+ +  V NKP  +        +G S ++   +H+DG            P + HRLD
Sbjct: 14  VVFENDEFLVVNKPPNLRFHPNHRFEGNSLLSRALHHMDG----------ATPYIVHRLD 63

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSHIG 209
            +TSG+ V  + +    ++   F+ +  +K Y ++  G+  P      I +  +    I 
Sbjct: 64  MDTSGVAVFVKKQHLVANVAGQFQEKTAKKTYLAVSVGVVPPDCGDSFIVDAPIGDHGIV 123

Query: 210 GDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +   V    E K A             A     + + P TGRTHQ+RVH  H G PIV 
Sbjct: 124 QEARTVDFSGEGKDARTTCEIIARATPPAAVAALVRVTPLTGRTHQIRVHLAHAGLPIVS 183

Query: 269 DHKYCANFK-------GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           D  Y  + +       G   S    +  LHA  ++L HPE G  L   A +P+ M    D
Sbjct: 184 DALYGPHLRWKPYDDWGGALS--IRRQALHAFNLELKHPETGESLTFQAKMPSDMRSVCD 241

Query: 321 SL 322
           +L
Sbjct: 242 AL 243


>gi|330445575|ref|ZP_08309227.1| RNA pseudouridylate synthase family protein [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
 gi|328489766|dbj|GAA03724.1| RNA pseudouridylate synthase family protein [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
          Length = 228

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/200 (29%), Positives = 93/200 (46%), Gaps = 20/200 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           L+Y+     V NK  GISV        +    L +  +  G +K  L HRLD+ TSG+L+
Sbjct: 4   LVYQHPDFLVINKHPGISVHKDD----NDQPLLAAVAEQTGDEKLYLIHRLDKMTSGLLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R + AA  L+ +F  R ++K Y ++    PK KK+ +    + +S      +   K+N
Sbjct: 60  LGRNKEAASILSSNFAERVVEKFYVAIGTKKPK-KKQGVVIGDMSRSRRSSWKLESTKEN 118

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 A++ F        +  +L  +PHTG+THQ+RV    +G  I GD  Y       
Sbjct: 119 P-----AVTQFFSAAAGEGRRVFL-CKPHTGKTHQIRVALRSVGSGITGDDIYGTE---- 168

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +  P+
Sbjct: 169 ----AADRGYLHAYALSFPY 184


>gi|87120482|ref|ZP_01076376.1| Pseudouridine synthase RluA-like [Marinomonas sp. MED121]
 gi|86164125|gb|EAQ65396.1| Pseudouridine synthase RluA-like [Marinomonas sp. MED121]
          Length = 226

 Score = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 94/208 (45%), Gaps = 40/208 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +LY ++  +V NKPAG+S    S       GF++ W+     +      HRLD+ TSG++
Sbjct: 7   VLYREADYWVVNKPAGMSFHAES----EEVGFMQ-WMHQAFPEQVFYPVHRLDRITSGLI 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI---------ANWLLKKSHIG 209
           ++A  + AAQ   + F   ++ K Y ++    PK K+  I          +WLL      
Sbjct: 62  ILAINKRAAQLFGKMFEQHQMAKFYLAISQKKPKKKQGSIKGGMQQGRRGSWLL------ 115

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                    N+   N+A + F           +L ++P TG+THQLRV    +G PI+GD
Sbjct: 116 ---------NQSNENFAHTQFFSTGIKPGLRLFL-LKPKTGKTHQLRVALKSLGSPILGD 165

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDL 297
            +Y             ++ YLHA ++  
Sbjct: 166 VRYGGA--------EADRGYLHAFWLSF 185


>gi|291532509|emb|CBL05622.1| pseudouridine synthase, RluA family [Megamonas hypermegale ART12/1]
          Length = 288

 Score = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 73/269 (27%), Positives = 131/269 (48%), Gaps = 38/269 (14%)

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL--LYEDSKIYVFNKPAGIS 118
           +GQ VR      A   I+K   I++ ++ +T   + ++  L  ++ED    + +K AG+ 
Sbjct: 42  NGQKVR------ATQAIVKPNDIIEYNLPVTSKVEAIQIPLNIVFEDDYFLIVDKIAGML 95

Query: 119 VQG---------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
                        +G+ YH   F K+   + G  P   +RLD+ TSG++V A+       
Sbjct: 96  THPLTFENTQTLANGVMYH---FAKTN-QNVGCHP--LYRLDRNTSGLVVFAKMPQLQHQ 149

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           L  + +  + Q+ Y++LV G    K+  I   + +K     D + + + N++G  +AI++
Sbjct: 150 LANNHQ--KFQRYYYALVHGKLSQKQGQINAPIGRKK----DSIILHEVNDEG-KHAITN 202

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           + VI  F + +  +E+   TGRTHQ+RVH  ++G P++GD  Y    K N  +    +  
Sbjct: 203 YHVIKEF-ENYSLIELWLETGRTHQIRVHMSYLGHPLLGDDLYGG--KLNLIA----RHA 255

Query: 290 LHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           LHA  +   HP     + +++ LP  M K
Sbjct: 256 LHAYKLKFTHPFTHEEICLSSSLPDDMAK 284


>gi|195471882|ref|XP_002088231.1| GE18464 [Drosophila yakuba]
 gi|194174332|gb|EDW87943.1| GE18464 [Drosophila yakuba]
          Length = 939

 Score = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/196 (31%), Positives = 87/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L ++              ++Y D  I V NKPA I V       ++   F+ +  
Sbjct: 597 KHNDLLANVVHRHEVPVTSQPIKIVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 655

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    E
Sbjct: 656 EHNLKNLRTIHRLDRLTSGLLLFGRTAERARELELQIRTRQVQKEYVCRVEGRFPDGTVE 715

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   + FK I         L  +P TGR HQ+R
Sbjct: 716 CNEKIDVVSYKIG-----VCKVSPKGKDCKTT-FKRIGEVGSDSIVL-CKPLTGRMHQIR 768

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI  D  Y
Sbjct: 769 VHLQYLGYPISNDPLY 784


>gi|71002582|ref|XP_755972.1| DRAP deaminase (Rib2) [Aspergillus fumigatus Af293]
 gi|66853610|gb|EAL93934.1| DRAP deaminase (Rib2), putative [Aspergillus fumigatus Af293]
 gi|159130027|gb|EDP55141.1| DRAP deaminase (Rib2), putative [Aspergillus fumigatus A1163]
          Length = 526

 Score = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/200 (25%), Positives = 87/200 (43%), Gaps = 30/200 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           +++ED+ I V +KPAG+ V       YH +  ++     +GQ+  PR  +RLD+ TSG++
Sbjct: 127 IIHEDNDILVIDKPAGVPVHAAG--RYHYNSIVEILRSQRGQEFVPRPCNRLDRLTSGVM 184

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
            +A+   AA  +T   + R +QK Y + V G  P     C    +     +G + V    
Sbjct: 185 FIAKHPKAADAITIKLKQRTVQKEYIARVKGRFPDGVVVCDQPIMSVSPKLGLNRVRATG 244

Query: 218 QNEKGANYAISHFKVIDCFAQK-------------------------FCWLEMQPHTGRT 252
           ++ K     ++++       ++                         +  +   P TGRT
Sbjct: 245 KDAKTKFRRLAYYPPASPAPERDEDEVTASGDRPATPPPLLANESEGYSIVHCLPLTGRT 304

Query: 253 HQLRVHALHMGCPIVGDHKY 272
           HQ+RVH   +G PI  D  Y
Sbjct: 305 HQIRVHLQFLGHPITNDPIY 324


>gi|307108910|gb|EFN57149.1| hypothetical protein CHLNCDRAFT_143494 [Chlorella variabilis]
          Length = 452

 Score = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 42/134 (31%), Positives = 67/134 (50%), Gaps = 6/134 (4%)

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           ++PR  HRLD+ T G++VVA+TR A   L+ +F  RR+ K Y +LVWG  + +   +  +
Sbjct: 205 RRPRHVHRLDEPTGGLVVVAKTRLAQTQLSAAFMQRRVTKRYRALVWG--RLEGRGLVRY 262

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW---LEMQPHTGRTHQLRVH 258
            L       +Y          A   +     +        W   +++ PHTGR HQLR H
Sbjct: 263 CLDGKRCETEYAAAQHTRVDLAALGLRPAAPLAAPQPAI-WVTTVDLWPHTGRKHQLRRH 321

Query: 259 ALHMGCPIVGDHKY 272
              +G P++G+ +Y
Sbjct: 322 MALLGHPLLGETRY 335


>gi|237744692|ref|ZP_04575173.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           7_1]
 gi|229431921|gb|EEO42133.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           7_1]
          Length = 288

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 104/227 (45%), Gaps = 30/227 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKGQK--PRLTHRLDQE 153
           + YED  + + NK   I V         +D  L + V      + G+K  PR  +RLD  
Sbjct: 75  IAYEDENLLIVNKEPYIIVHPTQK---KVDKTLANAVVNYFEKTLGKKLVPRFYNRLDMN 131

Query: 154 TSGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           TSG++++A+   T+A  Q  TE      ++K Y  +  GI +     I   + K   +G 
Sbjct: 132 TSGLIIIAKNAYTQAFLQDKTE------VKKTYKVIASGIIEKDDFFIEIPIGK---VGD 182

Query: 211 DYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D   +    + G   A +H KV++  + +   +LE + +TGRTHQ+R H   +G  +VGD
Sbjct: 183 DLRRIELSEKDGGKSAKTHIKVLERNYEKNITFLEARLYTGRTHQIRAHLSLIGHSLVGD 242

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
             Y  +        +  +  LHA  ++  +P+    L+I   +P  M
Sbjct: 243 ELYGGDMN------LAKRQMLHAYKLEFQNPKTLENLKIEIDIPIDM 283


>gi|199598043|ref|ZP_03211467.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|199591133|gb|EDY99215.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
          Length = 278

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 100/218 (45%), Gaps = 30/218 (13%)

Query: 103 YEDSKIYVFNKPAGISVQ----GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           YED  + + +KPAG+       G +G   +     ++          +THRLD  TSG+L
Sbjct: 80  YEDDDLLIVDKPAGMKTHPNQPGETGTLMN-----QAAAYLAPYPALITHRLDMATSGLL 134

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           V+A+   A   +      + + + Y ++V  GIP+  K  I      ++ IG D     K
Sbjct: 135 VIAKNPLAQAIINRQLATKAMHRDYLAMVPRGIPE--KGTI------QAPIGHDPDDKRK 186

Query: 218 Q--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +     GA  A++H++ I   A     +++   TGRTHQ+RVH   +G PI+GD  Y A 
Sbjct: 187 RMIRADGA-VAVTHYRRIAETATT-ATIQLNLETGRTHQIRVHLASIGFPIIGDPLYAAT 244

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
                      ++ LHA  + L  P     L +T+P P
Sbjct: 245 ETA-------TRMQLHAFRVRLIRPLTIEPLTVTSPSP 275


>gi|42572641|ref|NP_974416.1| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|229891781|sp|Q5M721|PUS5_ARATH RecName: Full=RNA pseudourine synthase 5; AltName: Full=RNA
           pseudouridylate synthase 5; AltName: Full=RNA-uridine
           isomerase 5
 gi|332645400|gb|AEE78921.1| RNA pseudourine synthase 5 [Arabidopsis thaliana]
          Length = 369

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 106/246 (43%), Gaps = 30/246 (12%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAG 116
           RIQ+GQ+     V+   N +++    L  S    K  D   S+ +LYED  +   NKP+G
Sbjct: 55  RIQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDTPYSLEVLYEDDDLIALNKPSG 114

Query: 117 ISVQGGSGIAYHID--------GFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAA 167
           + V  G                G   S++ S+    P   HRL + TSGIL+ A+T+ A 
Sbjct: 115 LQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVPVHRLGRGTSGILLCAKTKLAK 174

Query: 168 QHLTESFRM-----------------RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
             L   F                   R++ KIY +L  GI +  +  I   +    + G 
Sbjct: 175 TKLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADGIVEEDEVVIKQPIGVVRYPGV 234

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGD 269
                V   E     A S   V++   +K C L +++  +GR HQ+R+H  +MG P+VGD
Sbjct: 235 AQGLYVASPE--GKPAFSKVFVLERDREKNCSLVKVEIQSGRPHQIRIHLAYMGHPLVGD 292

Query: 270 HKYCAN 275
             Y A 
Sbjct: 293 PLYVAG 298


>gi|317179260|dbj|BAJ57048.1| hypothetical protein HPF30_0951 [Helicobacter pylori F30]
          Length = 293

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 71/287 (24%), Positives = 125/287 (43%), Gaps = 45/287 (15%)

Query: 41  LRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           L+  Q  +DK+R+K N + ++  Q+++    I +L H    +K                 
Sbjct: 28  LKEAQRHLDKQRLKQNQQAVRKSQMIQ---GIVSLIHFKPNEKT---------------Q 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  ALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-----VH 214
             +T  +A+ L   F  ++++K Y +L  G+  ++   I   +L   +I  D      + 
Sbjct: 128 AGKTLQSAKDLKALFMQKKVKKTYLALAHGL-VDRSIVIDKPILTPQNIQKDLRIRSKIS 186

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + +        +S+   +D        L++ P TGRTHQ+R+H   +G  IVG+  Y  
Sbjct: 187 PLGKPSTTLVEPLSYNPFLDI-----SLLKITPITGRTHQIRLHLSSVGHRIVGEGLYGV 241

Query: 275 ---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                      K    +P+   L LHA  ++    +G   +IT+P+P
Sbjct: 242 IDENAREYLQLKRKNNAPL---LMLHASSLEFEF-KGAIYEITSPMP 284


>gi|190572979|ref|YP_001970824.1| putative ribosomal large subunit pseudouridine synthase A
           [Stenotrophomonas maltophilia K279a]
 gi|190010901|emb|CAQ44510.1| putative ribosomal large subunit pseudouridine synthase A
           [Stenotrophomonas maltophilia K279a]
          Length = 245

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 65/213 (30%), Positives = 106/213 (49%), Gaps = 29/213 (13%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           L Y D  + V  KPAG+ SV G S  A + D  +   + +        HRLDQ TSG+L+
Sbjct: 45  LHYIDDALLVAEKPAGLLSVPGRS--AENQDCVVAR-LQALYPDALTVHRLDQVTSGLLL 101

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIANWLLKKSHIGGDYVH 214
            AR +     L+  F  R++ K Y ++V G+ +          I +W  +   +      
Sbjct: 102 HARGKDMQAALSMQFEQRQVGKRYEAVVQGLLEGDSGEVDLPLIVDWPNRPKQM------ 155

Query: 215 VVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               +E+G   A++ ++V+  D  A++   + ++P TGR+HQLR+H   +G PIVGD  Y
Sbjct: 156 --VDHERG-KPALTRWRVLARDVEARR-TRVALEPITGRSHQLRLHMASIGHPIVGDVLY 211

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            A       +P  ++++LHAR +   HP  G +
Sbjct: 212 DA-------AP-AHRVHLHARSLRFTHPLTGEV 236


>gi|121727329|ref|ZP_01680476.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V52]
 gi|147675726|ref|YP_001217217.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O395]
 gi|262169679|ref|ZP_06037370.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC27]
 gi|121630335|gb|EAX62732.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V52]
 gi|146317609|gb|ABQ22148.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O395]
 gi|227013574|gb|ACP09784.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O395]
 gi|262021913|gb|EEY40623.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC27]
          Length = 235

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 48/147 (32%), Positives = 74/147 (50%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR   +A  L++ F  R+++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNATSASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  +      N AI+ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVNSQE------NPAITQFFSATAAPGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADKSDRGYLHA 178


>gi|195339847|ref|XP_002036528.1| GM18469 [Drosophila sechellia]
 gi|194130408|gb|EDW52451.1| GM18469 [Drosophila sechellia]
          Length = 537

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/196 (31%), Positives = 87/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L ++              ++Y D  I V NKPA I V       ++   F+ +  
Sbjct: 195 KHNDLLANVVHRHEVPVTSQPIKIVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 253

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    E
Sbjct: 254 EHNLKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIRTRQVQKEYVCRVEGRFPDGIVE 313

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   + FK I         L  +P TGR HQ+R
Sbjct: 314 CNEKIDVVSYKIG-----VCKVSPKGKDCKTT-FKRIGEVGSDSIVL-CKPLTGRMHQIR 366

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI  D  Y
Sbjct: 367 VHLQYLGYPISNDPLY 382


>gi|302791938|ref|XP_002977735.1| hypothetical protein SELMODRAFT_107717 [Selaginella moellendorffii]
 gi|300154438|gb|EFJ21073.1| hypothetical protein SELMODRAFT_107717 [Selaginella moellendorffii]
          Length = 191

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 78/181 (43%), Gaps = 33/181 (18%)

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK-----KSHIGGDYVHVVKQNEKGAN 224
           L+E F+ R++++ Y SL  G P      I   +L+     K     D V     + + A 
Sbjct: 9   LSEQFKSRKVRRTYLSLTCGTPSTTSGRIEAEILRDPRDRKRMTTSDTV----PSARNAR 64

Query: 225 YAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGN--- 279
           +A S +KV+D  A     L + +  TGRTHQ+RVHA +MG P++GD  Y     K N   
Sbjct: 65  FAASRYKVLDVLANGGVALVQWKLETGRTHQIRVHARYMGFPLLGDDVYGGTVGKANSTL 124

Query: 280 -----------------FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
                            FTS I+    LHA  +   HP   + +  T P P    + W  
Sbjct: 125 FSALSATKTNSRKKIHEFTSDIRRPC-LHAYSLGFEHPATEKYVHFTCPPPEDFEEAWTR 183

Query: 322 L 322
           L
Sbjct: 184 L 184


>gi|332024709|gb|EGI64898.1| RNA pseudouridylate synthase domain-containing protein 2
           [Acromyrmex echinatior]
          Length = 335

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/169 (31%), Positives = 82/169 (48%), Gaps = 9/169 (5%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  + V NKPA I V       ++   F+ +  +   +  R  HRLD+ TSGIL+  RT 
Sbjct: 2   DEDVVVVNKPASIPVHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDRLTSGILLFGRTP 60

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
             A+ +    R R++ K Y   V G  P+ +  C     +    IG     V K +EKG 
Sbjct: 61  KKARQMEHQIRNRQVHKQYVCRVEGEFPEEEVICSEPIEVVSYKIG-----VCKVSEKGK 115

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +  ++ FK +  +  K   +  +P TGR HQ+RVH  ++G P+V D  Y
Sbjct: 116 D-CVTRFKRLS-YNGKSSVVLCKPQTGRMHQIRVHLQYLGYPVVNDPLY 162


>gi|114561280|ref|YP_748793.1| pseudouridine synthase Rlu family protein [Shewanella frigidimarina
           NCIMB 400]
 gi|114332573|gb|ABI69955.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           frigidimarina NCIMB 400]
          Length = 225

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 46/145 (31%), Positives = 69/145 (47%), Gaps = 15/145 (10%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG+L+VA++  AA   T+ F   ++QK Y ++  G PK K+  I   + K   
Sbjct: 47  HRLDTPTSGLLIVAKSPQAANVFTKMFTEHKVQKYYLAIACGKPKKKQGWIIGDMAKSRR 106

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  + K      N A++ F      A       ++P +G+THQLRV    +G PI+
Sbjct: 107 ------SMYKLLRTTENPAVTQF-FSQSIASGMRMYLLKPLSGKTHQLRVALASIGVPIL 159

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA 292
           GD  Y           + ++ YLHA
Sbjct: 160 GDKLY--------GDELSDRCYLHA 176


>gi|256847649|ref|ZP_05553094.1| pseudouridine synthase [Lactobacillus coleohominis 101-4-CHN]
 gi|256715338|gb|EEU30314.1| pseudouridine synthase [Lactobacillus coleohominis 101-4-CHN]
          Length = 305

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/216 (28%), Positives = 98/216 (45%), Gaps = 19/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V NKPAG        +    +   +  +++       + HR+DQ TSG ++
Sbjct: 90  ILFENRDLLVVNKPAGQKTHPNQPLETGTLMNDVAGYLEGSSAAAYMVHRIDQATSGAVI 149

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+       L       +I + Y ++V G    K     NW      IG +     K+ 
Sbjct: 150 VAKNPVVVPILDHYIAAGKIHRRYVAVVEGTFAQKGGRF-NW-----PIGFNPTDQRKRC 203

Query: 220 EKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             G  A  A++ ++V+   +     +++Q  TGRTHQ+RVH  H G PIVGD  Y  N +
Sbjct: 204 VNGLKAKPAVTDYQVLQT-SDNLSLVQLQLQTGRTHQIRVHLAHSGHPIVGDPLY--NGQ 260

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
            N      +++ LH     L  P    L +I APLP
Sbjct: 261 PN------SRMLLHGIAQQLIVPFKKTLREIYAPLP 290


>gi|83814990|ref|YP_445861.1| ribosomal large subunit pseudouridine synthase A [Salinibacter
           ruber DSM 13855]
 gi|294507771|ref|YP_003571829.1| Ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber M8]
 gi|83756384|gb|ABC44497.1| ribosomal large subunit pseudouridine synthase A [Salinibacter
           ruber DSM 13855]
 gi|294344099|emb|CBH24877.1| Ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber M8]
          Length = 232

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 98/225 (43%), Gaps = 29/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           +L+ D  + V +KP G+  Q   +G    +    +   D     P   L HRLD+  SG+
Sbjct: 3   ILHRDEHLLVVSKPPGLLAQPDQTGDPDVVSRGKEMLSDETEGAPFLGLVHRLDRPASGV 62

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV---- 213
           + +AR+  AA+ L+  FR R ++K Y   V G      + I  W         DY+    
Sbjct: 63  MALARSPEAARELSRQFRERLVEKRYVVAVEGT----LQGIGAWT--------DYIAKPD 110

Query: 214 ---HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +V  +      A   ++V++  +     L++   TGR+HQ+R+ A   G P+VGD 
Sbjct: 111 RQPRLVDPDHPEGKRAALDWQVLES-SSAHTLLQVTLQTGRSHQIRLQAASRGHPVVGDD 169

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAPLPAH 314
           +Y A+      S     + LH   +   HP   R +   AP P H
Sbjct: 170 RYGAS-----DSLPDRAVALHHVLLRADHPARPRRETFVAPPPTH 209


>gi|210631097|ref|ZP_03296753.1| hypothetical protein COLSTE_00638 [Collinsella stercoris DSM 13279]
 gi|210160185|gb|EEA91156.1| hypothetical protein COLSTE_00638 [Collinsella stercoris DSM 13279]
          Length = 227

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 91/222 (40%), Gaps = 20/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLT----HRLDQETS 155
           +LY D  +   +KPAGI V G G+G     D      V S             RLD++T+
Sbjct: 9   VLYRDPWLMAVDKPAGIIVHGDGTGAPTLTDAVRAHLVASGEASASAAAQALQRLDRDTT 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVH 214
           GI++ +  + A          R IQK Y ++V G  P  K  C     L +       + 
Sbjct: 69  GIVLFSLDKEAQPAFDRMIAERSIQKRYLAIVHGRFPAAKTMC---QPLGRDRHDSRRMR 125

Query: 215 VVKQNEKGANYA--ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V +  +     A  I++ K  D  A +   L +  HTGR HQ+RVH  H   P++GD  Y
Sbjct: 126 VSRTGKPAHTDAKRIAYAKA-DARAPERSLLAIDLHTGRKHQIRVHLAHAKFPLLGDSLY 184

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
                          L LHA  +   HP  G    I AP PA
Sbjct: 185 GG-------PSCSGGLMLHASELSFTHPITGAPTHIQAPYPA 219


>gi|156974969|ref|YP_001445876.1| hypothetical protein VIBHAR_02690 [Vibrio harveyi ATCC BAA-1116]
 gi|156526563|gb|ABU71649.1| hypothetical protein VIBHAR_02690 [Vibrio harveyi ATCC BAA-1116]
          Length = 230

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/199 (28%), Positives = 92/199 (46%), Gaps = 17/199 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSG+L++
Sbjct: 4   ILHTHPDFLIINKHPNVSVHKDDGDTMLLHEVAKQ---SGDEQLYLIHRLDKMTSGVLLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   AA  L+++F  R ++K Y ++    PK K+  +   + +        V     N 
Sbjct: 61  GRNAKAASALSQAFADREVEKFYLTIGSKKPKKKQGLVVGDMERSRRSSWKLV-----NS 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K  N AI+ F  +     +  +L  +PHTG+THQ+RV    +G  IVGD  Y A  +   
Sbjct: 116 K-TNPAITQFFSLAAEPGERLFL-CKPHTGKTHQIRVALKSVGSGIVGDPIYNAGNEA-- 171

Query: 281 TSPIQNKLYLHARYMDLPH 299
                ++ YLHA  +  P+
Sbjct: 172 -----DRGYLHAFSLCFPY 185


>gi|119482145|ref|XP_001261101.1| DRAP deaminase (Rib2), putative [Neosartorya fischeri NRRL 181]
 gi|119409255|gb|EAW19204.1| DRAP deaminase (Rib2), putative [Neosartorya fischeri NRRL 181]
          Length = 525

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/200 (25%), Positives = 87/200 (43%), Gaps = 30/200 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           +++ED+ I V +KPAG+ V       YH +  ++     +GQ+  PR  +RLD+ TSG++
Sbjct: 127 IIHEDNDILVIDKPAGVPVHAAG--RYHYNSIVEILRSQRGQEFVPRPCNRLDRLTSGVM 184

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
            +A+   AA  +T   + R +QK Y + V G  P     C    +     +G + V    
Sbjct: 185 FIAKHPKAADAITIKLKQRTVQKEYIARVKGRFPDGVVVCDQPIMSVSPKLGLNRVRATG 244

Query: 218 QNEKGANYAISHFKVIDCFAQK-------------------------FCWLEMQPHTGRT 252
           ++ K     ++++       ++                         +  +   P TGRT
Sbjct: 245 KDAKTKFRRLAYYPPASPAPERDESEVTASGDRPATPPPLLANESEGYSIVHCLPLTGRT 304

Query: 253 HQLRVHALHMGCPIVGDHKY 272
           HQ+RVH   +G PI  D  Y
Sbjct: 305 HQIRVHLQFLGHPITNDPIY 324


>gi|322383212|ref|ZP_08057023.1| RNA pseudouridine synthase [Paenibacillus larvae subsp. larvae
           B-3650]
 gi|321152481|gb|EFX45267.1| RNA pseudouridine synthase [Paenibacillus larvae subsp. larvae
           B-3650]
          Length = 193

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/189 (30%), Positives = 90/189 (47%), Gaps = 21/189 (11%)

Query: 140 KGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           KGQ+ R+   HRLD ET+G ++ A+   +   L E  R++ +++ Y +L  G       C
Sbjct: 14  KGQRCRVRHIHRLDAETTGAVLYAKNEWSHLLLDEGMRLKTVRREYAALAEG-------C 66

Query: 198 IANWL-LKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           I   + +    IG D  H  K+    KG  +A++ + V     Q    L +   TGRTHQ
Sbjct: 67  IEPTVGVIDLPIGRDRHHKSKRRVTLKG-QHAVTRYAVAAQLEQA-ALLHLSLETGRTHQ 124

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           +RVH  H+G P++GD  Y  N      + + ++  LH   +   HP  G  L+I AP P 
Sbjct: 125 IRVHLSHIGHPLLGDSLYGGN------TALISRQALHGERISFSHPITGEDLRIEAPWPG 178

Query: 314 HMVKTWDSL 322
                +  L
Sbjct: 179 DFTALYAKL 187


>gi|146337531|ref|YP_001202579.1| putative RNA pseudouridine synthase [Bradyrhizobium sp. ORS278]
 gi|146190337|emb|CAL74333.1| putative RNA pseudouridine synthase (Uracil hydrolyase)
           [Bradyrhizobium sp. ORS278]
          Length = 300

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 40/99 (40%), Positives = 53/99 (53%), Gaps = 12/99 (12%)

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +GA+ A          A K  WL M+P TGRTHQLRVH+   G PI+GD+ Y     GN 
Sbjct: 198 EGADRATGESAASSGKAPKLTWLAMEPITGRTHQLRVHSAASGWPIIGDNIY-----GNG 252

Query: 281 TSPIQNKLYLHARYMDLP----HPEGGRLQITAPLPAHM 315
               + +L+LHAR + +P     P    +Q+ AP P HM
Sbjct: 253 PRFGEPRLHLHAREISIPLSKNKPP---VQVVAPAPLHM 288



 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 35/98 (35%), Positives = 52/98 (53%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  + V +KPAGI V  G     +++    +      + P L HRLD+ETSG LV+
Sbjct: 15  VLHRDGLMLVIDKPAGIPVHKGPKGGPNLEASFDALRFGLPRPPVLAHRLDKETSGCLVL 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            R R A   L   F+  +I K YW++V G P+  +  I
Sbjct: 75  GRHRKATASLGLLFKHGKISKTYWAVVEGGPEADEGVI 112


>gi|49483170|ref|YP_040394.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257425058|ref|ZP_05601484.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257427722|ref|ZP_05604120.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257430357|ref|ZP_05606739.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257433061|ref|ZP_05609419.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257435958|ref|ZP_05612005.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M876]
 gi|282903554|ref|ZP_06311442.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus C160]
 gi|282905328|ref|ZP_06313183.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282908301|ref|ZP_06316132.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WW2703/97]
 gi|282910585|ref|ZP_06318388.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WBG10049]
 gi|282913781|ref|ZP_06321568.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Staphylococcus aureus subsp. aureus M899]
 gi|282918706|ref|ZP_06326441.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C427]
 gi|282923814|ref|ZP_06331490.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|283957751|ref|ZP_06375202.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Staphylococcus aureus subsp. aureus A017934/97]
 gi|293500819|ref|ZP_06666670.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|293509774|ref|ZP_06668483.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus M809]
 gi|293526360|ref|ZP_06671045.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M1015]
 gi|295427495|ref|ZP_06820127.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297591555|ref|ZP_06950193.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus MN8]
 gi|49241299|emb|CAG39980.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|257272034|gb|EEV04166.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257274563|gb|EEV06050.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257278485|gb|EEV09104.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257281154|gb|EEV11291.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257284240|gb|EEV14360.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M876]
 gi|282313786|gb|EFB44178.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|282316516|gb|EFB46890.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C427]
 gi|282321849|gb|EFB52173.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Staphylococcus aureus subsp. aureus M899]
 gi|282325190|gb|EFB55499.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WBG10049]
 gi|282327966|gb|EFB58248.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WW2703/97]
 gi|282330620|gb|EFB60134.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282595172|gb|EFC00136.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus C160]
 gi|283789900|gb|EFC28717.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Staphylococcus aureus subsp. aureus A017934/97]
 gi|290920432|gb|EFD97495.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M1015]
 gi|291095824|gb|EFE26085.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|291467224|gb|EFF09741.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus M809]
 gi|295127853|gb|EFG57487.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297576441|gb|EFH95157.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus MN8]
 gi|312438620|gb|ADQ77691.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|315193667|gb|EFU24062.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus CGS00]
          Length = 284

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 59/192 (30%), Positives = 90/192 (46%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++  L+  +LYED+ + +  KP     Q  +    H    L   V    Q+   
Sbjct: 65  SVNLIPYARKLE--VLYEDAFVIIVTKPNN---QNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKVNLKKIYTCLVYGKTHTFGIIEAN 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 176 IRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 229 HIGHPIVGDSLY 240


>gi|50312303|ref|XP_456184.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49645320|emb|CAG98892.1| KLLA0F24794p [Kluyveromyces lactis]
          Length = 597

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 53/194 (27%), Positives = 87/194 (44%), Gaps = 16/194 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ED  + V +KP+GI V       Y  +   K     +G      +RLD+ TSG++ +A
Sbjct: 175 VFEDDDLLVIDKPSGIPVHPTG--RYRFNTVTKILEKERGYTVHPCNRLDRLTSGLMFLA 232

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           +    A  + +  + R + K Y + V G  P      + +  L+            K  +
Sbjct: 233 KNPRGADRMADQMKAREVSKEYVARVVGEFPVGL--IVVDKPLRTVDPKVGLNVTCKITD 290

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------- 273
           +GA  A + F+ I  F  K   +  +P TGRTHQ+RVH  H+G PI  D  Y        
Sbjct: 291 EGAKEARTSFERI-SFDGKTSIVRCKPFTGRTHQIRVHLQHLGHPIANDPIYSNPHIWGP 349

Query: 274 ---ANFKGNFTSPI 284
               +++G+F+  I
Sbjct: 350 SLGKDYEGDFSDII 363


>gi|302561137|ref|ZP_07313479.1| RluA family RNA pseudouridine synthase [Streptomyces griseoflavus
           Tu4000]
 gi|302478755|gb|EFL41848.1| RluA family RNA pseudouridine synthase [Streptomyces griseoflavus
           Tu4000]
          Length = 314

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 76/309 (24%), Positives = 130/309 (42%), Gaps = 25/309 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVTVDGSVVGKSERVS 59

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA--GI 117
            G  + +  P   A   I+ E         +    D    +++ +   +     P   G 
Sbjct: 60  GGAWLEVEMPGAPAPVRIVAE-----PVEGMEIVHDDDDVVVIVKPVGVAAHPSPGWTGP 114

Query: 118 SVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +V GG +   Y I            ++  + HRLD  TSG++VVA++  A   L   F+ 
Sbjct: 115 TVIGGLAAAGYRIS------TSGAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQFKE 168

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K Y +LV G P      I   + +  H   DY   V    K    +++H+ +I+ F
Sbjct: 169 RTVDKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAEGK---PSVTHYDLIEAF 223

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYM 295
            +    L+++  TGRTHQ+RVH      P VGD  Y A+        +   + +LHA  +
Sbjct: 224 -RAASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADP--TLAKRLHLTRQWLHAVRL 280

Query: 296 DLPHPEGGR 304
              HP  G+
Sbjct: 281 GFEHPGDGQ 289


>gi|153800993|ref|ZP_01955579.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-3]
 gi|124123463|gb|EAY42206.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-3]
          Length = 235

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 48/147 (32%), Positives = 74/147 (50%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR   +A  L++ F  R+++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNATSASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  +      N AI+ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVNSQE------NPAITQFFSATAAPGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADESDRGYLHA 178


>gi|323488794|ref|ZP_08094034.1| putative RNA pseudouridine synthase yjbO [Planococcus donghaensis
           MPA1U2]
 gi|323397492|gb|EGA90298.1| putative RNA pseudouridine synthase yjbO [Planococcus donghaensis
           MPA1U2]
          Length = 291

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/211 (26%), Positives = 101/211 (47%), Gaps = 23/211 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK---PRLTH---RLDQET 154
           ++YED  + +  KP    +Q       H  G L + V         P   H   RLD++T
Sbjct: 81  IVYEDEVLLIVEKPP---LQNTIPSREHPFGSLANIVAKHFNDHGIPSTLHIATRLDRDT 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV 213
           SG++ +A+ R     +++  + +++++ Y +LV G I K +    A    K + I     
Sbjct: 138 SGLVCIAKNRHIHHMISQQQQEKKMKRRYEALVHGQIDKTEFTITAPIGRKNTSI----- 192

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + ++  +   +A +  +V++   Q +  + +Q +TGRTHQ+RVH  H+G P+VGD  Y 
Sbjct: 193 -IEREVREDGQFAETEVRVLENL-QGYAHVSLQLNTGRTHQIRVHLAHIGHPLVGDDLYG 250

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                     + N+  LH   ++L HP  G+
Sbjct: 251 GK------RDLVNRQALHCTELELIHPVSGK 275


>gi|222110970|ref|YP_002553234.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221730414|gb|ACM33234.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 304

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 100/212 (47%), Gaps = 18/212 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D+ I V +KP  + V   G  +   +   LK  +      P   HR+D++T+G+++
Sbjct: 94  VLYQDAHILVADKPHFLPVVPAGRYLQQTLLVRLKRRLGLSELSP--VHRIDRDTAGLVL 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            +  RA        FR RR+ K+Y ++          CI    L++S       H  + +
Sbjct: 152 FSVQRATRGTYQALFRDRRVHKVYEAVAPWRADLPLPCIHESRLEESG------HFFRMH 205

Query: 220 E-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---N 275
           E  G   A +H  V++  A  +    ++P TG+ HQLRVH   +G P+ GD  Y      
Sbjct: 206 EVPGTPNARTHIDVLEV-ASPWARYRLEPITGKRHQLRVHMAALGLPLRGDAFYPEVNDP 264

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            +G++++P+Q    L AR +    P  G  ++
Sbjct: 265 PEGDYSNPLQ----LLARTLAFTDPLSGEARL 292


>gi|306832623|ref|ZP_07465762.1| ribosomal large subunit pseudouridine synthase [Streptococcus bovis
           ATCC 700338]
 gi|304425231|gb|EFM28358.1| ribosomal large subunit pseudouridine synthase [Streptococcus bovis
           ATCC 700338]
          Length = 286

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/199 (27%), Positives = 86/199 (43%), Gaps = 16/199 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG ++ A
Sbjct: 84  LYQDEHLIIVNKPEGMKTHGNEPNEITLLNHVSAYV---GQTCYVIHRLDMETSGAVMFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      + I + YW+LV G  + K +   + + +  H     V + ++N +
Sbjct: 141 KNPFVLPILNRLLENKDIAREYWALVQGKFEPKHQVFQDKIGRDRHDRRKRV-IDRKNGQ 199

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            A   +   KV        C L+    TGRTHQ+RVH       I+GD  Y        +
Sbjct: 200 TALTIVDRLKVFPNGTLVKCRLK----TGRTHQIRVHLSAHNHAIIGDPLY--------S 247

Query: 282 SPIQNKLYLHARYMDLPHP 300
                +L LHA  +   HP
Sbjct: 248 KIPAKRLMLHAHKLSFTHP 266


>gi|229541367|ref|ZP_04430427.1| pseudouridine synthase, RluA family [Bacillus coagulans 36D1]
 gi|229325787|gb|EEN91462.1| pseudouridine synthase, RluA family [Bacillus coagulans 36D1]
          Length = 290

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 75/303 (24%), Positives = 134/303 (44%), Gaps = 42/303 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +  DE +  L  + K    HI+   L  I  R G + V+ + V    R+Q G    I  
Sbjct: 7   TITEDEAHQELKEFLKAR--HISKRALADIKFRGGMILVNGREVTVRYRLQPGDAAAI-- 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSG 124
                  +  ++     S NLT  +     +  YED  + V +KPA ++         + 
Sbjct: 63  -------VFPKET---PSPNLTPENIPFGHV--YEDESVLVADKPAFMNTIPSREHPSAS 110

Query: 125 IAYHIDG-FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKI 182
           +A  + G + K+ ++S      +  RLD+ TSG++++A+ R    HL    + +  I + 
Sbjct: 111 LANAVLGHYRKNGIESAVH---VVTRLDRNTSGLVLIAKNRYI-HHLCSLMQQKHVICRT 166

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFC 241
           Y +L  G    K   I      ++ IG     ++++  +    +A +H++V+  F   + 
Sbjct: 167 YEALAEGAFTEKSGTI------EAPIGRKETSIIERGVRDDGQFARTHYEVVRQFP-AYA 219

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + ++  TGRTHQ+RVH  ++G P++GD  Y  N    FT     +  LH   +   HP 
Sbjct: 220 HVRLRLDTGRTHQIRVHLSYIGHPLLGDSLYGGN-TSRFT-----RQALHCSELSFQHPV 273

Query: 302 GGR 304
            G+
Sbjct: 274 SGK 276


>gi|332297218|ref|YP_004439140.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332180321|gb|AEE16009.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 244

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 99/229 (43%), Gaps = 20/229 (8%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQ-----KPRLTH 148
           DF +  +LYED+ + V  KPAG+ SV      A      L   +  +G+     +P + H
Sbjct: 15  DFRRLSILYEDASVAVVYKPAGLLSVSYPGSTAKTALDVLCDLMRKRGRVSARVRPAVVH 74

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----IPKNKKECIANWLLK 204
           RLD++TSG++V A T  A   L + +     ++ Y +L       I    +  I + L  
Sbjct: 75  RLDRDTSGVMVFALTAQAKALLMDDWNRLVTERRYRALAENPSGKIALGDRGVIDSPLSY 134

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            +           + E  A  A++ + V+     ++   E++  TGR +Q+R H    G 
Sbjct: 135 NAQHRAYVAKGAGRRENEAVSAVTRYSVVR-RGSRYTLFELELETGRKNQIRAHLASEGF 193

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
            I GD  Y A      + P   +L LHAR +    P  G   R +I  P
Sbjct: 194 VIAGDGSYRAK-----SDPF-GRLCLHARTLAFTQPLTGESLRFEIPEP 236


>gi|323339639|ref|ZP_08079911.1| RluA family pseudouridine synthase [Lactobacillus ruminis ATCC
           25644]
 gi|323092935|gb|EFZ35535.1| RluA family pseudouridine synthase [Lactobacillus ruminis ATCC
           25644]
          Length = 304

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 65/223 (29%), Positives = 104/223 (46%), Gaps = 22/223 (9%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSG----IAYHIDGFLKSWVDSKGQK--PRLTHRLDQE 153
           ++YED    + +KPAGIS V G S     +   + G+L   +D K +   P    RLD+ 
Sbjct: 83  VVYEDENWLLLDKPAGISSVPGPSNDHDTMMNRVKGYL---IDQKSENLVPHAVTRLDRF 139

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++ A+   A   +++  +   ++K Y ++  G  K K   I +  LKK   G  + 
Sbjct: 140 TSGLMLCAKHGFAQGLISKQVQEHSMEKRYLAVCSGFVK-KDHGIIDLPLKKEDNG--FR 196

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +V  +  G N A++ + V + F  +   +E   HTGRTHQ+R H  H   P++ D  Y 
Sbjct: 197 RIVSCD--GQN-AVTEYWVRERFGNEATLVECVLHTGRTHQIRAHFAHFAHPLISDELY- 252

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
               G   +    +  LHA  +    P    RL+   PL   M
Sbjct: 253 ----GGKKNDACKRQALHACCLAFDDPFSCKRLKFELPLENDM 291


>gi|297588316|ref|ZP_06946959.1| RluA family pseudouridine synthase [Finegoldia magna ATCC 53516]
 gi|297573689|gb|EFH92410.1| RluA family pseudouridine synthase [Finegoldia magna ATCC 53516]
          Length = 307

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 73/302 (24%), Positives = 140/302 (46%), Gaps = 44/302 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++++  +N RLD +  N    ++   +QK++   +V V++K  K N ++           
Sbjct: 6   LIDDSNQNTRLDVFLANEVE-LSRSEIQKLIDEKKVLVNEKTQKKNYKLN---------- 54

Query: 71  INALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI------SVQGGS 123
              LN  IK + +  D ++   +H       ++YED  + + NK   +      ++   +
Sbjct: 55  ---LNDKIKFDYEKPDKTIKPQQHD----LDIVYEDDYLAIINKDKNVIVHPTETIYSDT 107

Query: 124 GIAYHIDGFLKSWVDSKGQKPR-LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            + Y +  F ++  D  G   R + HRLD++T+G++++A+       L E  +   I K 
Sbjct: 108 LVNYLMSNF-ENLSDVDGDYRRGIVHRLDKDTTGLIIIAKDNNTHLKLKEIIKNHEITKT 166

Query: 183 YWSLVWGIPKNKKEC--IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           Y  +V G      EC  I  ++ +      D   ++  +E     +IS+++ +D +   +
Sbjct: 167 YLCIVHG---KIDECGTIEEYMTRNP---KDRKKMMISDE--GKLSISNYERLD-YNDDY 217

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPH 299
             +++Q  TGRTHQ+RVH  ++  PI+GD  Y     K  F S +     LHA  +   H
Sbjct: 218 SLVKVQIKTGRTHQIRVHMNYIHHPILGDKLYGLKKEKILFDSQV-----LHAYNLQFIH 272

Query: 300 PE 301
           P+
Sbjct: 273 PQ 274


>gi|254423098|ref|ZP_05036816.1| pseudouridine synthase, RluA family [Synechococcus sp. PCC 7335]
 gi|196190587|gb|EDX85551.1| pseudouridine synthase, RluA family [Synechococcus sp. PCC 7335]
          Length = 328

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 107/245 (43%), Gaps = 34/245 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  ++V NKPAG+ V    G   H     +  V  +  +    HRL + TSG +++
Sbjct: 83  VLYEDEDLWVINKPAGLPVLPSGGFLEHTL-LYQLRVRYRDCQSAPVHRLGRGTSGAMLI 141

Query: 161 ARTRAAAQHLTESFRMRR----------------IQKIYWSLVWGIPKN--KKECIANWL 202
           A++  A   L+E FR R                 + K Y +L+     +  +   I  + 
Sbjct: 142 AKSHIAKVQLSEQFRKRSANLSSNTTPNTASTCTLGKTYRALIAPTTPDQLRDRFICTYP 201

Query: 203 LKK---SHIGGDYVHV--VKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           + K   + +G  Y H+     +EK      +  + S   V+   A     +E+   TGR 
Sbjct: 202 IGKLPHTRLGYIYGHLRDAHSHEKTIGPINSMVSRSEGSVLRRRAHS-TLVEITIQTGRP 260

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGN---FTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           HQ+R+H    G P++GD  Y A    +   +  P     +LHA  +   HP  G+ + IT
Sbjct: 261 HQIRIHLAAAGYPLLGDPLYSAGGVPDPHGYALPGDCGYHLHAHRLQFAHPRTGQSIAIT 320

Query: 309 APLPA 313
           AP PA
Sbjct: 321 APPPA 325


>gi|301622434|ref|XP_002940545.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Xenopus (Silurana) tropicalis]
          Length = 497

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 104/224 (46%), Gaps = 18/224 (8%)

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNK 113
           +    Q+G++      +  LN ++K    L ++V+  +     + + +L E+ ++ V +K
Sbjct: 125 YEQAAQAGRLRLNEETVRDLNVVLKNNDFLRNTVHRHEPPVTAEPLRILAENDEMVVIDK 184

Query: 114 PAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           P+ + V       ++   F L    + KG      HRLD+ TSG+L+ A+T   ++ + E
Sbjct: 185 PSSLPVHPCGRFRHNTVIFILGKEYNLKGL--HTIHRLDRMTSGVLMFAKTLEVSKKIDE 242

Query: 173 SFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH-- 229
             R R+++K Y   V G  PK +  C     +    IG   V    +  K     +S+  
Sbjct: 243 QVRQRQLEKEYVCRVCGEFPKEEVTCEEPIFVVSYKIGVCRVDPKGKPCKTVFQRLSYNG 302

Query: 230 -FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              V+ CF          P+TGRTHQ+RVH  ++G PIV D  Y
Sbjct: 303 KSSVVKCF----------PYTGRTHQIRVHLQYLGHPIVNDPIY 336


>gi|212530788|ref|XP_002145551.1| DRAP deaminase (Rib2), putative [Penicillium marneffei ATCC 18224]
 gi|210074949|gb|EEA29036.1| DRAP deaminase (Rib2), putative [Penicillium marneffei ATCC 18224]
          Length = 511

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 64/248 (25%), Positives = 105/248 (42%), Gaps = 27/248 (10%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSK 107
           D+    +   I+ G+V+    V N L  I+    I+  S +  +     + I +++ED  
Sbjct: 63  DRTPEYYKKAIEDGRVLVGGKVAN-LETIVPNGAIVSHSTHRHEPPVSSRPIGIIHEDDD 121

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           + V +KPAGI V G     YH +  L+    D  G KP   +RLD+ TSG++ +A+   A
Sbjct: 122 MIVIDKPAGIPVHGAG--RYHFNTILEIMKADRPGFKPLPCNRLDRLTSGVMFIAKNPKA 179

Query: 167 AQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           A+      + R +QK Y + V G  P     C    +     +G + V    +  +    
Sbjct: 180 AEKFALQLKSRTLQKEYVARVSGRFPDGVVLCDQPIMSVSPKLGLNRVRATGKEARTKFR 239

Query: 226 AISHFKV---IDCFA------------------QKFCWLEMQPHTGRTHQLRVHALHMGC 264
            I+++      D  +                  + +  +   P TGRTHQ+RVH   +G 
Sbjct: 240 RIAYYPAPPKTDAESATTSGDRPATPPATATEDEGYSIVHCLPLTGRTHQIRVHLQFLGY 299

Query: 265 PIVGDHKY 272
           PI  D  Y
Sbjct: 300 PISNDPIY 307


>gi|296123058|ref|YP_003630836.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
 gi|296015398|gb|ADG68637.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
          Length = 396

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/188 (28%), Positives = 83/188 (44%), Gaps = 25/188 (13%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK---ECIAN- 200
           R  HRLD++TSG++V++R   A   L   F+   + + Y +LVWG  + ++   E I + 
Sbjct: 199 RAAHRLDRQTSGLVVLSRVPEAGAKLYAQFQAHDVLREYEALVWGWIEPQRLESELIRDR 258

Query: 201 -----------WLLKKSHIGGDYVHVVKQNEKGANYAIS----HFKVIDCFAQKFCWLEM 245
                       +L+         + +   +  A   ++    HFK          W+  
Sbjct: 259 GDGRRGSRQPVTMLEAGAEDSPAANPLPAGKMAATNLVASRQGHFKSGTGELAPVSWIRC 318

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
           Q  TGRTHQ+R+H    G PIVGD  Y     G  +     +LYLHA  +   HP  G R
Sbjct: 319 QLETGRTHQVRIHLSEKGNPIVGDDVY-----GTHSLDGVPRLYLHAARLGFIHPMTGKR 373

Query: 305 LQITAPLP 312
           L+ +   P
Sbjct: 374 LEFSLSWP 381


>gi|195384880|ref|XP_002051140.1| GJ14588 [Drosophila virilis]
 gi|194147597|gb|EDW63295.1| GJ14588 [Drosophila virilis]
          Length = 552

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/173 (31%), Positives = 84/173 (48%), Gaps = 9/173 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  I V NKPA I V       ++   F+ +  +   +  R  HR+D+ TSG+L+ 
Sbjct: 228 IVHMDEDILVVNKPASIPVHPCGRYRHNTVIFILAK-EFNLKNLRTIHRIDRLTSGLLLF 286

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            R    A+ + +  R R++QK Y   V G  P    EC     +    IG     V K +
Sbjct: 287 GRNSEKARQMEQQIRNRQVQKEYICCVEGQFPDGIIECNEPIEVVSYKIG-----VCKVS 341

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            KG +   + FK I   A  +  ++ +P TGR HQ+RVH  ++G PIV D  Y
Sbjct: 342 PKGKDCKTT-FKRI-AQAGDYSIVQCKPLTGRMHQIRVHLQYLGYPIVNDPLY 392


>gi|37519752|ref|NP_923129.1| pseudouridine synthase [Gloeobacter violaceus PCC 7421]
 gi|35210743|dbj|BAC88124.1| gll0183 [Gloeobacter violaceus PCC 7421]
          Length = 314

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 72/278 (25%), Positives = 121/278 (43%), Gaps = 29/278 (10%)

Query: 54  KFNNRIQSGQVVRIPPVINALNH-IIKEQKILDSSVNLT-------KHSDFLKSILLYED 105
           ++  RI++GQV+        L+H      ++L S+  LT       + S  L  +++Y D
Sbjct: 51  EWQARIETGQVL--------LDHRSTSSTELLRSAQVLTYCRPPWQEPSVPLDIVIIYAD 102

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
            ++ V  KP G+ V  G G   H   +      +  + P   HRL + TSG++++ART +
Sbjct: 103 EQVLVVAKPGGLPVLPGGGFLEHTLLWQVRRRFAGEEPPVPIHRLGRGTSGLVLLARTHS 162

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH--IGGDYVHVVKQNEKGA 223
           +   L+E  R +RI K+Y +L  G     +  I   + K  H  +G  +          +
Sbjct: 163 SRAALSEQMRRQRIGKLYRALASGTGMRDRFTIRQPIGKVPHPLLGTLWAAAADGLPARS 222

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY----CANFKGN 279
           +  +   +  D        L +   TGR HQ+R+H    G P+VGD  +     A    +
Sbjct: 223 DCVVLRRQCTDSL------LAVAISTGRPHQIRIHLAAAGYPLVGDPLFGPGGVARLDND 276

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
            + P     +LHA  +   HP  G RL +  P P  + 
Sbjct: 277 ASVPGDGGYFLHAHRLSFLHPTSGRRLVLECPPPPELT 314


>gi|258543640|ref|YP_003189073.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256634718|dbj|BAI00694.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256637774|dbj|BAI03743.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-03]
 gi|256640828|dbj|BAI06790.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-07]
 gi|256643883|dbj|BAI09838.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-22]
 gi|256646938|dbj|BAI12886.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-26]
 gi|256649991|dbj|BAI15932.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-32]
 gi|256652981|dbj|BAI18915.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-01-42C]
 gi|256656035|dbj|BAI21962.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-12]
          Length = 168

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/180 (31%), Positives = 81/180 (45%), Gaps = 15/180 (8%)

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D +TSG L +A  +     L ++F  +  QK YW++V   P+     I   L K+S   
Sbjct: 1   MDTDTSGCLAIALRKQPLLALQQAFATKTAQKTYWAVVQTGPQEDTGRIDLPLEKQSSKR 60

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           G    +V      A  A + +KV+    +  CWLE+   TGRTHQ RVH   M  PI+GD
Sbjct: 61  G--WRMVASPSGAA--AATRWKVLG-RNKDLCWLELTLETGRTHQARVHCAAMNWPILGD 115

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
             Y         +P    L+L AR + LP      +   AP    M  T  + G+  D+ 
Sbjct: 116 PLY--------GTPHPQGLHLLARSLTLPF--SPPITAIAPPRTGMKATLQACGWTPDKE 165


>gi|298736716|ref|YP_003729246.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori B8]
 gi|298355910|emb|CBI66782.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori B8]
          Length = 298

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 74/301 (24%), Positives = 127/301 (42%), Gaps = 45/301 (14%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS- 99
           L+  Q  +DK+R+K     Q+ Q VR             + +++   V+L       K+ 
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVR-------------KSQMIQGVVSLIHFKPNEKTQ 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  ALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-----VH 214
             +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D      + 
Sbjct: 128 AGKTLQSAKDLKALFMQKKVKKTYLALAHGL-VDKNIVIDKPILTPQNIQKDLRIRSKIS 186

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + +        +S+   +D        L++ P TGRTHQ+R+H   +G  IVG+  Y  
Sbjct: 187 PLGKPSTTLVEPLSYNPFLDI-----SLLKITPITGRTHQIRLHLSSVGHRIVGEGLYGV 241

Query: 275 ---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                      K    +P+   L LHA  ++    +    +IT+P+P   +     L   
Sbjct: 242 IDENAREYLQLKRENNAPL---LMLHASSLEFEF-KKAFYEITSPMPKRFMPFLKDLALF 297

Query: 326 Y 326
           Y
Sbjct: 298 Y 298


>gi|317010619|gb|ADU84366.1| putative ribosomal pseudouridine synthase [Helicobacter pylori
           SouthAfrica7]
          Length = 293

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 71/287 (24%), Positives = 123/287 (42%), Gaps = 45/287 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK-S 99
           L+  Q  +DK+R+K N +I                  +++ +I+   V+L       K  
Sbjct: 28  LKESQRHLDKQRLKQNQQI------------------VRKSQIIQGVVSLIYFKPNEKQG 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  KLVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-----VH 214
             +T  +A+ L   F  +++QK Y +LV G+  ++   I   +L   +I  D      + 
Sbjct: 128 AGKTLQSAKDLKALFMQKKVQKTYLALVHGL-VDESIIIDKPILTPENIQKDLRIRSQIS 186

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + +        +S+   +D        L++ P TGRTHQ+R+H   +   IVG+  Y  
Sbjct: 187 PLGKPSTTLVEPLSYNSFLDV-----SLLKITPLTGRTHQIRLHLSSVNHRIVGEGLYGV 241

Query: 275 ---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                      K    +P+   L LHA  ++    +G   +I +P+P
Sbjct: 242 IDENAREYLQLKRENNAPL---LMLHATSLEFEF-KGAHYKIASPMP 284


>gi|224436616|ref|ZP_03657625.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
          Length = 359

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 59/223 (26%), Positives = 102/223 (45%), Gaps = 29/223 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---------SKGQKPRLTHRLD 151
           +LYED  I + NKP  + +     +    D  L  W+          S  ++  + HRLD
Sbjct: 99  ILYEDDDILIINKPPHLVIHDAPSVK---DLTLTQWLKLHAHTLHTLSGRERYGIIHRLD 155

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE-------CIANWL-L 203
           ++TSG+L +A++  A + L    + R++ + Y +++    K   +       C  N L +
Sbjct: 156 KQTSGVLCIAKSLLAYEILPNQLKSRQMGRYYLAIIDTPLKQNLQVQCFMGRCPTNRLKM 215

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            K HI  +     +   KG   + S F K+          + ++ HTGRTHQ+R H   +
Sbjct: 216 SKIHIDEN-----ENPPKGVRDSKSSFVKLATSNDGLLELIAIKLHTGRTHQIRTHLESL 270

Query: 263 GCPIVGDHKYCANFKGNFTSPI-QNKLYLHARYMDLPHPEGGR 304
              I+GD  Y   +K +  S   + ++ LHA  + L HP+ G+
Sbjct: 271 SRHILGDSLY--GYKPSAKSFFYEGRILLHAYILYLAHPKNGQ 311


>gi|315638653|ref|ZP_07893827.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
 gi|315481277|gb|EFU71907.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
          Length = 250

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/233 (24%), Positives = 104/233 (44%), Gaps = 55/233 (23%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED KI   NKP           +Y  +G    +      K +L +RLD+ETSG++++
Sbjct: 59  ILFEDEKILAINKP----------YSYISEGLESEF------KAKLLNRLDKETSGLILL 102

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI------GGDYVH 214
            +     +   E FR +R+ K Y +++ G+       +A  L+    I       G +  
Sbjct: 103 CKNEDFKKLCIEEFRKQRVYKSYIAVLDGV-------LAEELVVDEPIRTLKGKNGAFSK 155

Query: 215 VVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + K+ +       S   +I+      K    ++   TGRTHQ+RVH   +  PI+GD KY
Sbjct: 156 IAKEGQ-------SALSIINPLMIQGKKTLAKICIQTGRTHQIRVHTAFVKYPIIGDEKY 208

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                G   +   +++YLH+  + + H E           A++ +++   GF+
Sbjct: 209 -----GKIAA---DRMYLHSYELKILHYE---------FKANLDESFAKFGFE 244


>gi|120610952|ref|YP_970630.1| tRNA pseudouridine synthase C [Acidovorax citrulli AAC00-1]
 gi|120589416|gb|ABM32856.1| tRNA pseudouridine synthase C [Acidovorax citrulli AAC00-1]
          Length = 277

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 101/222 (45%), Gaps = 15/222 (6%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           N  +H     +IL  +D  + V+ KPAG  V      A      +++  D  G++    H
Sbjct: 5   NAPRHPPL--AILRQDDDLVAVY-KPAGWLVHRTGLDAGETRFVMQALRDQLGRRVYPVH 61

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ T G+LV+     AA+ L+++F   R+ K Y +LV G   ++ +   +  L+    
Sbjct: 62  RLDKGTCGVLVMGLHAEAARALSQAFEQHRVDKRYLALVRGHAPDRVQV--DHALRPDDA 119

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-----WLEMQPHTGRTHQLRVHALHMG 263
             D      Q  + A   ++  ++ +    +F       +E  P TGR HQ+R H  H+ 
Sbjct: 120 PPD---AAVQPARTALRCLARLELPEASDARFATTRASLVEALPETGRRHQIRRHLKHIA 176

Query: 264 CPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGG 303
            PI+GD  +       + +      +L+LHA  + LPHP  G
Sbjct: 177 HPILGDATHGKGPLNRWWAQRLGLQRLWLHAWRLALPHPATG 218


>gi|255659830|ref|ZP_05405239.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
 gi|260847905|gb|EEX67912.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
          Length = 302

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 108/224 (48%), Gaps = 24/224 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-----GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LYED    V NKPA + V          + + + G+ +   ++ G  P   +RLD++T+
Sbjct: 79  ILYEDETFLVVNKPADMIVHPTHRAARDTLVHAVAGYFERRGEAAGIHP--LYRLDRDTT 136

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+++A++      +T+     +I + Y +L  G      +C++  +     IG D    
Sbjct: 137 GIVILAKSARIQHAMTKHHG--QIYREYLALAQG----HLDCLSGRI--DMPIGRDITRA 188

Query: 216 VK-QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              Q       A++ ++ I  +   +  L++   TGRTHQ+RVH   +G P++GD  Y  
Sbjct: 189 NHWQVRADGRRALTEYETIASWP-AYSLLKIHLLTGRTHQIRVHFAALGHPLLGDTAYDG 247

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           +     T P Q    LHA  +   HP+ G+ ++I AP+P  M +
Sbjct: 248 SCD---TIPRQA---LHAWRVHFFHPDTGKEIRIEAPIPEDMCR 285


>gi|227545266|ref|ZP_03975315.1| pseudouridylate synthase RluD [Lactobacillus reuteri CF48-3A]
 gi|300908664|ref|ZP_07126127.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
 gi|154705590|gb|ABS84221.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           reuteri]
 gi|227184756|gb|EEI64827.1| pseudouridylate synthase RluD [Lactobacillus reuteri CF48-3A]
 gi|300894071|gb|EFK87429.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
          Length = 306

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 113/233 (48%), Gaps = 31/233 (13%)

Query: 94  SDFLKSI-----LLYEDSKIYVFNKPAG----ISVQGGSGIAYH-IDGFLKSWVDSKGQK 143
           +D++ S+     +LYE+  + V NKP G     +  G +G   + + G+L    ++    
Sbjct: 78  NDYIPSLQSHLEVLYENRDLLVVNKPRGQKTHPNYHGETGTLMNDVAGYLAHSQNNA--- 134

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HR+D +TSG ++VA+       L       +I + Y +LV G  K  +    +W +
Sbjct: 135 -YMVHRIDLQTSGAVIVAKNPIVVPILNRLISDGQIHRQYLALVEG--KMAQSGKFDWAI 191

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++ +     H+ + N + A  A+++++ +    ++   + +   TGRTHQLRVH  H G
Sbjct: 192 GRNPVNP---HLHQVNGQNAQPALTYYETLASNHER-SLVRLHLVTGRTHQLRVHLAHSG 247

Query: 264 CPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHPEGGR-LQITAPLPAH 314
            PIVGD  Y         +P+  + + LH     L  P   + L I+APLP++
Sbjct: 248 HPIVGDPLY---------NPLSTEGMLLHGVAQKLILPFVMKSLNISAPLPSY 291


>gi|306830382|ref|ZP_07463552.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325977346|ref|YP_004287062.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|304427407|gb|EFM30509.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325177274|emb|CBZ47318.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 286

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/199 (27%), Positives = 86/199 (43%), Gaps = 16/199 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG ++ A
Sbjct: 84  LYQDEHLIIVNKPEGMKTHGNEPNEIALLNHVSAYV---GQTCYVIHRLDMETSGAVMFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       +      + I + YW+LV G  + K +   + + +  H     V V ++N +
Sbjct: 141 KNPFVLPIINRLLENKDIAREYWALVQGKFEPKHQVFQDKIGRDRHDRRKRV-VDRKNGQ 199

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            A   +   KV        C L+    TGRTHQ+RVH       I+GD  Y        +
Sbjct: 200 TALTIVDRLKVFPNGTLVKCRLK----TGRTHQIRVHLSAHNHAIIGDPLY--------S 247

Query: 282 SPIQNKLYLHARYMDLPHP 300
                +L LHA  +   HP
Sbjct: 248 KIPAKRLMLHAHKLSFTHP 266


>gi|73959752|ref|XP_547206.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 1 [Canis familiaris]
          Length = 302

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 50/159 (31%), Positives = 76/159 (47%), Gaps = 8/159 (5%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA    + F+ RR+ K Y +LV G  +  +  I   + +
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYKCFKERRVTKAYLALVRGHVQESRMTINYAIGR 120

Query: 205 KSHIGGDYVHVVKQNEKGAN--YAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            S  G  +   ++  E   N   +++   V++           + +QP TGRTHQLRVH 
Sbjct: 121 NSTEGRAHTMCIEGTEGCENPKPSLTELVVLEHGLYAGDPVSKVLLQPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             +  P+VGD  Y          P   ++ LHA Y+ +P
Sbjct: 181 SALSHPVVGDLTY-GQASDQEDQPF--RMMLHAFYLRIP 216


>gi|126336397|ref|XP_001375428.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 3, [Monodelphis domestica]
          Length = 355

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/201 (27%), Positives = 93/201 (46%), Gaps = 31/201 (15%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL--- 150
           ++ +K+ +LY +  +   NKP G++V G  G     +  L S +   GQ   L+  L   
Sbjct: 77  TEVMKTAVLYHNGPLVALNKPPGLAVTGKPG-----ELTLLSVLPEIGQHLGLSQELHIV 131

Query: 151 ---DQETSGILVVARTRAAAQHLTESFR-----MRRIQK---IYWSLVWGIPKNKKECIA 199
               +E+SG+++++    +   +T++F+      RR+QK    YW++  G+P   K  I 
Sbjct: 132 RAPGKESSGLVLLS----SCPRITKTFQNFFIQSRRVQKPTVTYWAVTVGVPATPKGEIQ 187

Query: 200 NWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWL-EMQPHTGRTH 253
             L      G D    VK   +     G    ++ F V D      C L ++QP T   +
Sbjct: 188 VALKLDQVRGADLAVPVKAPSRQTLKEGVKKTLTRFFVEDSTPD--CALVKLQPITAFPN 245

Query: 254 QLRVHALHMGCPIVGDHKYCA 274
           QL VH +   CP++GDH Y A
Sbjct: 246 QLLVHMVLQLCPVLGDHLYSA 266


>gi|261364898|ref|ZP_05977781.1| pseudouridine synthase Rlu family protein [Neisseria mucosa ATCC
           25996]
 gi|288566947|gb|EFC88507.1| pseudouridine synthase Rlu family protein [Neisseria mucosa ATCC
           25996]
          Length = 207

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 101/234 (43%), Gaps = 37/234 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-------IAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +L+        NKP G+SV    G       +A  + G  + W         L HRLD+ 
Sbjct: 4   ILFRHPDFVAINKPCGVSVHQEEGEVSLTQTLAAQL-GLEQIW---------LLHRLDKL 53

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+L+ A    +A  L + F  + ++K Y +L    P  K+  I    ++KS  G    
Sbjct: 54  TSGVLLFALNPQSASALAQQFAAKTMRKTYLALSTDKPSKKQGWIKG-DMEKSRRGA--W 110

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +++  E   N A++ F              + PHTG+THQLRV    +G PI+GD  Y 
Sbjct: 111 KLMRSTE---NPAVTEFNC-QSLEPGLRLFVLHPHTGKTHQLRVAMKSLGSPILGDTLYG 166

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
                       ++++LHA  +   + +    +I APL     + W  L F ++
Sbjct: 167 GK--------AASRMFLHAWKIKFDY-QDQTFEIVAPL----SEEWPPLDFIHE 207


>gi|194862296|ref|XP_001969969.1| GG23644 [Drosophila erecta]
 gi|190661836|gb|EDV59028.1| GG23644 [Drosophila erecta]
          Length = 537

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/196 (31%), Positives = 87/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L ++              ++Y D  I V NKPA I V       ++   F+ +  
Sbjct: 195 KHNDLLANVVHRHEVPVTSQPIKIVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 253

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    E
Sbjct: 254 EHNLKNLRTIHRLDRLTSGLLLFGRTAERARELELQIRTRQVQKEYVCRVEGRFPDGIVE 313

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   + FK I         L  +P TGR HQ+R
Sbjct: 314 CNEKIDVVSYKIG-----VCKVSPKGKDCKTT-FKRIGEVGSDSIVL-CKPLTGRMHQIR 366

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI  D  Y
Sbjct: 367 VHLQYLGYPISNDPLY 382


>gi|261379361|ref|ZP_05983934.1| pseudouridine synthase Rlu family protein [Neisseria subflava
           NJ9703]
 gi|284797801|gb|EFC53148.1| pseudouridine synthase Rlu family protein [Neisseria subflava
           NJ9703]
          Length = 216

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/175 (29%), Positives = 79/175 (45%), Gaps = 9/175 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E     V NKP G+SV   S     +   L   +    ++  L HRLD+ TSG+L+ 
Sbjct: 4   IVFEHKDFVVINKPCGVSVHSESEGDVCLTASLAQQLGV--ERVWLVHRLDKATSGLLLF 61

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R +A  L+  F  + ++K Y +L    P  K+     W+  K  +        K   
Sbjct: 62  ALNRDSAAALSAQFAEKTMRKTYLALGTHKPAKKQ----GWV--KGGMARSRRGTWKLTR 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              N+A++ F              +QP TG+THQLRV    +G PI+GD  Y  +
Sbjct: 116 DEDNFAVTRFSS-QSLKPGLRLFVLQPFTGKTHQLRVAMKSIGSPILGDTLYGGD 169


>gi|10045559|emb|CAC07917.1| putative protein [Arabidopsis thaliana]
          Length = 376

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 71/252 (28%), Positives = 109/252 (43%), Gaps = 33/252 (13%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPA 115
            RIQ+GQ+     V+   N +++    L  S    K  D   S+ +LYED  +   NKP+
Sbjct: 54  QRIQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDTPYSLEVLYEDDDLIALNKPS 113

Query: 116 GISVQGGSGIAYHID--------GFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAA 166
           G+ V  G                G   S++ S+    P   HRL + TSGIL+ A+T+ A
Sbjct: 114 GLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVPVHRLGRGTSGILLCAKTKLA 173

Query: 167 AQHLTESFRM-----------------RRIQKIYWSLVWGI-PKNKKECIANWLLKKSHI 208
              L   F                   R++ KIY +L  GI  +++      +++ K  I
Sbjct: 174 KTKLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADGIVEEDEARPFLLFVVIKQPI 233

Query: 209 GGDYVHVVKQN----EKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMG 263
           G      V Q           A S   V++   +K C L +++  +GR HQ+R+H  +MG
Sbjct: 234 GVVRYPGVAQGLYVASPEGKPAFSKVFVLERDREKNCSLVKVEIQSGRPHQIRIHLAYMG 293

Query: 264 CPIVGDHKYCAN 275
            P+VGD  Y A 
Sbjct: 294 HPLVGDPLYVAG 305


>gi|32266282|ref|NP_860314.1| ribosomal pseudouridine synthase [Helicobacter hepaticus ATCC
           51449]
 gi|32262332|gb|AAP77380.1| ribosomal pseudouridine synthase [Helicobacter hepaticus ATCC
           51449]
          Length = 351

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/249 (23%), Positives = 113/249 (45%), Gaps = 20/249 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD----- 138
           L SS  ++   +     ++Y+D  + + NKP  + +     +    +  L  W+      
Sbjct: 74  LSSSYTISADDERFSIDIVYQDEDVLIINKPPHLVIHHAPSVK---EPTLVDWLKLNAHI 130

Query: 139 ----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               S  ++  + HRLD++TSG L +A++  A   LT+  + R++ + Y +++   P   
Sbjct: 131 LYTLSGEERYGIIHRLDKQTSGALAIAKSNLAYTTLTKELKSRQMGRYYLAII-DTPLKD 189

Query: 195 KECIANWLLKKSH--IGGDYVHVVKQN--EKGANYAISHF-KVIDCFAQKFCWLEMQPHT 249
            + +  ++ +  H  +    +H+   +   KG   + S F K+       F  + ++ HT
Sbjct: 190 NQQVQCFMGRNPHNRLKMSKIHIRSNSPIPKGVRDSKSSFIKIATSDNGAFELIAIKLHT 249

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+R H   +   I+GD  Y    +   T   Q+++ LHA  +   HP+  +     
Sbjct: 250 GRTHQIRAHLESLSRHILGDTLYGYKPQAK-THYYQDRILLHAYILYFIHPKTQQNCTFK 308

Query: 309 APLPAHMVK 317
           AP+   M+K
Sbjct: 309 APILPDMLK 317


>gi|42523026|ref|NP_968406.1| pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
 gi|39575232|emb|CAE79400.1| Pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
          Length = 290

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 66/251 (26%), Positives = 101/251 (40%), Gaps = 37/251 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA----------YHIDGFLKSWVDSKGQKPRLTHRL 150
           LLY+D      NKP+G  V     +           YH    +K  V          HRL
Sbjct: 53  LLYKDEYFIAVNKPSGFHVHPHENVQHRVSRDKICLYHARRMMKQHVYP-------VHRL 105

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+L+ A +  +A  L   F  R   K Y ++V G  K + E      L  +   G
Sbjct: 106 DAGTSGVLLFALSSESASKLCRLFTERATHKTYQAVVRGFVKEEGEVQLPLELDST---G 162

Query: 211 DYV--HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           D V  H   +      + ++  K       ++ W+E+ PHTGR HQ+R H   +  P++G
Sbjct: 163 DLVDAHTSFKRLATVEFPVAVGKKFP--TARYSWVEVTPHTGRYHQIRRHFNRISHPLLG 220

Query: 269 DHKYCANFKGNFTSPIQNK-----LYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           D  +  +    F    +N      L L A  ++  HP  G ++ I AP        W  +
Sbjct: 221 DAVHGDSHHNRF---FRNHLEIEGLCLKALRLEFTHPWSGEKVSIEAP----PCDKWKKI 273

Query: 323 GFKYDRNLYIK 333
              +D  L ++
Sbjct: 274 QLLFDPALPLE 284


>gi|227528997|ref|ZP_03959046.1| RluA family pseudouridine synthase [Lactobacillus vaginalis ATCC
           49540]
 gi|227351009|gb|EEJ41300.1| RluA family pseudouridine synthase [Lactobacillus vaginalis ATCC
           49540]
          Length = 294

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/228 (24%), Positives = 108/228 (47%), Gaps = 19/228 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETS 155
           ++YED    + NKPAG++        +A  +   ++++ + +G +  + H   RLD++TS
Sbjct: 80  IIYEDRDFLILNKPAGVATVPAHHVTVADSLVNRVRNYYERQGYENLVIHVATRLDKDTS 139

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V  + R A   + +  +  +++K Y+++V G  K     I       + I  D    
Sbjct: 140 GLVVFPKHRFAHAVMDQQLKKHQVKKNYYAVVGGQIKAPHGYI------DAPIDRDPEKF 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V +              ++  + +   L ++ HTGRTHQ+RVH  ++G P++GD  Y   
Sbjct: 194 VSRTVISTGKPSVTEYWLEKSSVQMSLLRIRLHTGRTHQIRVHFQYLGHPLIGDEMYGGK 253

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                   I ++  LH  +M    P   + +++ AP+P  M+   +S+
Sbjct: 254 -------QIISRQALHCYWMKFYSPFKQQWIEVHAPVPEDMLNLINSI 294


>gi|254432671|ref|ZP_05046374.1| ribosomal large subunit pseudouridine synthase A [Cyanobium sp. PCC
           7001]
 gi|197627124|gb|EDY39683.1| ribosomal large subunit pseudouridine synthase A [Cyanobium sp. PCC
           7001]
          Length = 206

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 59/202 (29%), Positives = 95/202 (47%), Gaps = 10/202 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ D+ +   +KP+G+  Q G G A        S +  +    RL HRLD++TSG+L++A
Sbjct: 1   MHADAWLLAVHKPSGLLSQPGLGPALRDSAL--SRLQQRWPTARLAHRLDRDTSGLLLLA 58

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
              A+ +HL+  F+   ++K Y + V G    ++ CI   L + S     Y  V      
Sbjct: 59  LDAASHRHLSLQFQRGLVRKAYVAEVHGQLARRRGCIDAPLARVSTRPPRYGVV-----P 113

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           G   +++ ++ +         L + P TGR+HQLR H   +G PI+GD  Y         
Sbjct: 114 GGKPSLTLWRRL-ALGPASTRLLLLPRTGRSHQLRAHLAAIGHPILGDPLY--GPADAAA 170

Query: 282 SPIQNKLYLHARYMDLPHPEGG 303
            P   +L LHA  +   HP  G
Sbjct: 171 DPGSGRLRLHALGLRFHHPHSG 192


>gi|190573986|ref|YP_001971831.1| hypothetical protein Smlt2019 [Stenotrophomonas maltophilia K279a]
 gi|190011908|emb|CAQ45529.1| conserved hypothetical protein [Stenotrophomonas maltophilia K279a]
          Length = 295

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/193 (32%), Positives = 87/193 (45%), Gaps = 20/193 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETSGILV 159
           +L+ D+ + V +KP  + V    G  Y  +  L   V   G       HRLD+ T+G+++
Sbjct: 83  ILHLDAHLLVADKPHFLPVTPAGG--YVRETLLSRLVARTGNTELAPLHRLDRLTAGLVL 140

Query: 160 V---ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
               A TR A Q L   FR RRI+K Y +L   +P      +A  LL+ S +        
Sbjct: 141 FSTQAATRDAYQRL---FRERRIEKTYEALAPALPG-----LAFPLLRDSRLVPGEPFFR 192

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-- 273
                G   A S  + I+  A+   W   ++P TGR HQLRVH   +G PI GD  Y   
Sbjct: 193 MAEVPGEPNARSLIEPIE--AEGPVWRYRLKPETGRKHQLRVHMAMLGAPIEGDDLYPQL 250

Query: 274 -ANFKGNFTSPIQ 285
                  F SP+Q
Sbjct: 251 RPRRDDTFESPLQ 263


>gi|171778899|ref|ZP_02919961.1| hypothetical protein STRINF_00822 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171282545|gb|EDT47969.1| hypothetical protein STRINF_00822 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 286

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/199 (28%), Positives = 89/199 (44%), Gaps = 16/199 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP GI   G       +   + ++V   G+   + HRLD ETSG ++ A
Sbjct: 84  LYQDEHLIIVNKPEGIKTHGNEPNEIALLNHVSAYV---GKTCYVIHRLDMETSGAVMFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      + I + YW+L  G  + K +   + + +  H     V V ++N +
Sbjct: 141 KNPFVLPILNRLLENKDISREYWALAQGKFEPKHQVFQDKIGRDRHDRRKRV-VDRRNGQ 199

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            A   +   KV    +   C L+    TGRTHQ+RVH    G  I+GD  Y         
Sbjct: 200 TALTIVDRLKVFPKGSLVKCRLK----TGRTHQIRVHLSAHGHAIIGDPLYS-------N 248

Query: 282 SPIQNKLYLHARYMDLPHP 300
           +P + +L LHA  +   HP
Sbjct: 249 TPAK-RLMLHAHKLSFTHP 266


>gi|269118930|ref|YP_003307107.1| pseudouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268612808|gb|ACZ07176.1| pseudouridine synthase, RluA family [Sebaldella termitidis ATCC
           33386]
          Length = 283

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 76/274 (27%), Positives = 125/274 (45%), Gaps = 54/274 (19%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI-LDSSVNLTKHSDFLKS 99
           LR+ +V +D K+V+   +I+   ++++       N  IK  KI LD              
Sbjct: 30  LRNIEVFLDGKKVRTTQKIRKQGLLKVVEKEKGTN--IKPIKIPLD-------------- 73

Query: 100 ILLYEDSKIYVFNK---------PAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +++ED  I V NK            + V   +GI Y+   F + +   K   PR  +RL
Sbjct: 74  -IVFEDEDILVVNKQPYLVTHPTKKKVDVTLANGIVYY---FQEKY--GKEMVPRFYNRL 127

Query: 151 DQETSGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           D +TSG++++A+   T+A  Q+  +      ++K Y +LV GI K   E + N     + 
Sbjct: 128 DMDTSGLIIIAKNSFTQAFLQNFGD------VKKYYMALVHGIIK---EEMINIEKPIAR 178

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPI 266
           +G D    +        YA +  K I    +K   L E +  TGRTHQ+RVH  + G PI
Sbjct: 179 VGDDLRRKILDE---GQYAKTVVKTIKRNEEKNITLTECELFTGRTHQIRVHLSNEGYPI 235

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +GD  Y     G+    ++ ++ LH+  +   HP
Sbjct: 236 LGDKLY-----GDMDDNVKRQM-LHSYKVSFIHP 263


>gi|87121539|ref|ZP_01077427.1| RNA pseudouridine synthase family protein [Marinomonas sp. MED121]
 gi|86163071|gb|EAQ64348.1| RNA pseudouridine synthase family protein [Marinomonas sp. MED121]
          Length = 313

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/195 (27%), Positives = 94/195 (48%), Gaps = 12/195 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKG-QKPRLTHRLDQETSG 156
            I+L++D  I V  KP  + V  G GI  +++  L++ +  S G +  +  HRLD+ T+G
Sbjct: 87  EIILFQDQDILVAYKPHFLPVTPG-GI--YVNECLQTRLRRSTGIESLQALHRLDRVTAG 143

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++ +     +Q   E F  R+I K Y ++   + +N+      W +K     G     +
Sbjct: 144 LVIFSVNPETSQCYHELFETRQIDKTYQAIA-KVAENENLIDQEWQVKNRIAKGKPSFRM 202

Query: 217 KQNEKGAN-YAISHFKVIDCFAQ--KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY- 272
           +  E   N    +   +I C  Q  +    E++P TG+THQLR+H   +G PI+ D  Y 
Sbjct: 203 QILEASDNSIQANSLSIIRCTQQVDELALFELKPVTGKTHQLRLHMQSLGLPILNDKYYP 262

Query: 273 --CANFKGNFTSPIQ 285
                   N+ +P+Q
Sbjct: 263 ELAPQTADNYQAPLQ 277


>gi|313143115|ref|ZP_07805308.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
 gi|313128146|gb|EFR45763.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
          Length = 327

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 59/223 (26%), Positives = 102/223 (45%), Gaps = 29/223 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---------SKGQKPRLTHRLD 151
           +LYED  I + NKP  + +     +    D  L  W+          S  ++  + HRLD
Sbjct: 67  ILYEDDDILIINKPPHLVIHDAPSVK---DLTLTQWLKLHAHTLHTLSGRERYGIIHRLD 123

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE-------CIANWL-L 203
           ++TSG+L +A++  A + L    + R++ + Y +++    K   +       C  N L +
Sbjct: 124 KQTSGVLCIAKSLLAYEILPNQLKSRQMGRYYLAIIDTPLKQNLQVQCFMGRCPTNRLKM 183

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            K HI  +     +   KG   + S F K+          + ++ HTGRTHQ+R H   +
Sbjct: 184 SKIHIDEN-----ENPPKGVRDSKSSFVKLATSNDGLLELIAIKLHTGRTHQIRTHLESL 238

Query: 263 GCPIVGDHKYCANFKGNFTSPI-QNKLYLHARYMDLPHPEGGR 304
              I+GD  Y   +K +  S   + ++ LHA  + L HP+ G+
Sbjct: 239 SRHILGDSLY--GYKPSAKSFFYEGRILLHAYILYLAHPKNGQ 279


>gi|224009938|ref|XP_002293927.1| psedouridylate synthase [Thalassiosira pseudonana CCMP1335]
 gi|220970599|gb|EED88936.1| psedouridylate synthase [Thalassiosira pseudonana CCMP1335]
          Length = 329

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/197 (27%), Positives = 91/197 (46%), Gaps = 22/197 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +++ED  I V +KP+G+    G   S  + +   F +   +S      + HRL  +TSG+
Sbjct: 71  VVFEDEHIVVVSKPSGVLTVPGKDESNPSLNKAVFDRYGSESGRMDKMVVHRLGMDTSGL 130

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK------------- 204
           +V ART AA + +   FR R++ + Y +LV G     +  I   L++             
Sbjct: 131 VVFARTNAALRAMNALFRTRKVTRKYEALVCGHVSQDEGSIDLPLMRDYECPPFMRVSTD 190

Query: 205 ---KSHIGGDYVHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVH 258
              ++ I  D   V K+  +    +++ ++V+   D        L +   +GRTHQL VH
Sbjct: 191 DHQRALIELDADEVGKKLLESPKDSLTKYEVVSREDMGGHDVSRLILTSISGRTHQLNVH 250

Query: 259 ALHMGCPIVGDHKYCAN 275
              +G PIVGD  Y  N
Sbjct: 251 CAAIGHPIVGDTVYGYN 267


>gi|198461946|ref|XP_001352285.2| GA19422 [Drosophila pseudoobscura pseudoobscura]
 gi|198142379|gb|EAL42449.2| GA19422 [Drosophila pseudoobscura pseudoobscura]
          Length = 321

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/169 (32%), Positives = 75/169 (44%), Gaps = 9/169 (5%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  I V NKPA I V       ++   F+ +   +  +  R  HRLD+ TSG+L+  RT 
Sbjct: 2   DEDIVVVNKPASIPVHPCGRYRHNTVVFILAKSHNL-KNLRTIHRLDRLTSGLLIFGRTS 60

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
             A+ L +  R R++QK Y   V G  P    EC     +    IG   V  V  N K  
Sbjct: 61  KKARELEQQIRNRQVQKEYVCRVEGRFPDGIIECNEPIQVVSYKIG---VCRVSPNGKDC 117

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                    +   +   C    +P TGR HQ+RVH  ++G PIV D  Y
Sbjct: 118 RTTFRRISEVGDCSIVLC----KPLTGRMHQIRVHLQYLGYPIVNDPLY 162


>gi|28897960|ref|NP_797565.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|153837500|ref|ZP_01990167.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|260364253|ref|ZP_05776956.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           K5030]
 gi|260877117|ref|ZP_05889472.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           AN-5034]
 gi|260895778|ref|ZP_05904274.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           Peru-466]
 gi|260902666|ref|ZP_05911061.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           AQ4037]
 gi|28806174|dbj|BAC59449.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|149749194|gb|EDM59991.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|308088331|gb|EFO38026.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           Peru-466]
 gi|308093765|gb|EFO43460.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           AN-5034]
 gi|308108274|gb|EFO45814.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           AQ4037]
 gi|308111894|gb|EFO49434.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           K5030]
          Length = 230

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/192 (30%), Positives = 91/192 (47%), Gaps = 17/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL++
Sbjct: 4   ILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAKQ---SGDEQLYLIHRLDKMTSGILLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   AA  L+++F  R+++K Y ++    PK K+  +   + +        V     N 
Sbjct: 61  GRNAKAASALSQAFADRQVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV-----NS 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K  N A++ F  +     +  +L  +PHTG+THQ+RV    +G  IVGD  Y A   GN 
Sbjct: 116 KN-NPAVTQFFSLAAEPGERLFL-CKPHTGKTHQIRVALKSVGSGIVGDPIYNA---GNE 170

Query: 281 TSPIQNKLYLHA 292
                ++ YLHA
Sbjct: 171 A----DRGYLHA 178


>gi|262039482|ref|ZP_06012784.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           goodfellowii F0264]
 gi|261746463|gb|EEY34000.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           goodfellowii F0264]
          Length = 293

 Score = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 108/226 (47%), Gaps = 27/226 (11%)

Query: 101 LLYEDSKIYVFNKPAGI---------SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++YED  + V NK   +              +GI Y+   F + +   K   PR  +RLD
Sbjct: 74  IVYEDDDLLVVNKEPFLLTHPTQKKADFTLANGIVYY---FKEKY--EKETVPRFYNRLD 128

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG++++A+  + AQ   ++F     +K Y ++V GI +  +E +     K  +  GD
Sbjct: 129 MNTSGLIIIAKN-SFAQAFLQNFS--NFEKKYLAIVDGIMETDEEIVIE---KPIYRDGD 182

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  +  +E+G  YA +  K +  + +K   L E +  TGRTHQ+RVH   +G  IVGD 
Sbjct: 183 KLERI-IDERG-QYAKTIVKPLKKYPEKNVTLAECELFTGRTHQIRVHLKSVGHTIVGDE 240

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            Y    KG+       + +LHA  +   HP +   +++  PL   M
Sbjct: 241 LYG---KGSDEKRGIKRQFLHAYKVKFTHPVKKEEIELEIPLFNDM 283


>gi|301779327|ref|XP_002925088.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           3-like [Ailuropoda melanoleuca]
 gi|281354153|gb|EFB29737.1| hypothetical protein PANDA_014511 [Ailuropoda melanoleuca]
          Length = 352

 Score = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 57/202 (28%), Positives = 90/202 (44%), Gaps = 18/202 (8%)

Query: 89  NLTKHS--DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR- 145
           NL++    D L++ ++ +   +   NKP G+ V G  G    +   L     S G + R 
Sbjct: 70  NLSREGLVDVLRAAVVDQKGPLVTLNKPPGLPVTGKPG-ELTLCSVLPELSQSLGLRDRE 128

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIA 199
             +     +ETSG+++++     A  L + F    R +R    Y ++  GIP   +  I 
Sbjct: 129 LQIVQASGKETSGLVLLSSCPQTASRLQKFFIHSRRAQRPIATYCAVTDGIPATSEGNI- 187

Query: 200 NWLLKKSHIGG-DYVHVVKQN-----EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
              LK  HI G D V  VK       ++G     SHF V+         +++QP T    
Sbjct: 188 QAALKLEHIDGVDLVIPVKSPSRKDFQEGVKKTFSHFHVV-AMGSGCALVQLQPLTVFPS 246

Query: 254 QLRVHALHMGCPIVGDHKYCAN 275
           QL+VH +   CP++GDH Y A 
Sbjct: 247 QLQVHMVLQLCPVLGDHTYSAR 268


>gi|184154365|ref|YP_001842706.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|183225709|dbj|BAG26226.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
          Length = 309

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 72/286 (25%), Positives = 131/286 (45%), Gaps = 45/286 (15%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQ---SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           + +L +G  R   + V+ N+ IQ    G  +R P    A ++I   Q  L+         
Sbjct: 45  RTVLVNGNYRSMNEIVEKNDNIQLLFCGDEIRTP---TANDYIPSSQSHLE--------- 92

Query: 95  DFLKSILLYEDSKIYVFNKPAG----ISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHR 149
                 +LYE+  + V NKP G     +  G +G   + + G+L    ++      + HR
Sbjct: 93  ------VLYENRDLLVVNKPRGQKTHPNYHGETGTLMNDVAGYLAHSQNNA----YMVHR 142

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D +TSG ++VA+       L       +I + Y ++V G  +  +    +W + ++ + 
Sbjct: 143 IDLQTSGAVIVAKNPIVVPILNRLISDGQIHRQYLAVVEG--EMAQSGKLDWAIGRNPVN 200

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
               H+ + N + A  A+++++ +    ++   ++++  TGRTHQLRVH  H G PIVGD
Sbjct: 201 P---HLHQVNGQNAQPALTYYETLASNHER-SLVKLRLATGRTHQLRVHLAHSGHPIVGD 256

Query: 270 HKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
             Y  ++ +G     +  KL L              L I+APLP++
Sbjct: 257 PLYNPSSTEGMLLHGVSQKLILPFVMKS--------LNISAPLPSY 294


>gi|189439795|ref|YP_001954876.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium longum
           DJO10A]
 gi|189428230|gb|ACD98378.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium longum
           DJO10A]
          Length = 254

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 62/219 (28%), Positives = 94/219 (42%), Gaps = 38/219 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LYED +I V +KP  ++     G+ Y     ++  +  +  +P +T  HRLD+ T+G+L
Sbjct: 13  VLYEDERIIVVDKPHFLATMP-RGMWYRQTALIR--LRERLGEPDITPAHRLDRMTAGVL 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP----------KNKKECIANWLLKKSHI 208
           V  R  A        F+ R+  K+Y  L    P          K +  C    LL++SHI
Sbjct: 70  VFVRDPACRGAYQMLFQNRQAVKVYECLAPCRPISRPRFGTIMKVEPPC-PFPLLRRSHI 128

Query: 209 GGDYVHVVKQNEKGANYAISHFKVID-CFAQ------------------KFCWLEMQPHT 249
             ++  +    E G   A +  +  D CF                      C   + P T
Sbjct: 129 TKEHGTMAAFEEPGLANAETLIERGDLCFPPADGRWREAPEGGPHLGNHPICRYTLHPRT 188

Query: 250 GRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQ 285
           G+THQLRVH   +G PIVGD  Y         +F+ P+Q
Sbjct: 189 GKTHQLRVHMNSLGLPIVGDDFYPRIQTRPYDDFSQPLQ 227


>gi|145348517|ref|XP_001418694.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144578924|gb|ABO96987.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 334

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 67/258 (25%), Positives = 112/258 (43%), Gaps = 47/258 (18%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGI---SVQGGSGIAYHIDGFLKSW----VDSKGQK 143
            K+ D    ++L +   I    KPAG+    V+GG      +D  L  +     D  G  
Sbjct: 91  AKNDDEWSMVVLRDSDGIAAVVKPAGVLTHPVEGGGSELTLMDAALSRFDGQLSDLNGLD 150

Query: 144 PR-LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANW 201
            R +  RLD+ TSG++++A+  A+   L   F  R + K Y +L+ G +P +  E     
Sbjct: 151 KRGIVSRLDKPTSGVVLLAKNNASHAELLTQFYQRCVVKQYCALLDGTLPASGSE----- 205

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVH 258
               + + G               A S ++V++ F   +  +  + ++P +GR HQ+R H
Sbjct: 206 ---STPLDG-------------RSATSEYEVMETFIGPSWSYSLVRVEPKSGRKHQIRRH 249

Query: 259 ALHMGCPIVGDHKY-CANFKGNFTSPIQNKL------------YLHARYMDLPH-PEGGR 304
              +G P+VGD  Y  A  K    +P +  L            +LHA  ++    P G R
Sbjct: 250 MALLGAPLVGDPLYRTARTKQINPNPPECVLKALSVGKPGTIFWLHASAVEYSGMPNGER 309

Query: 305 LQITAPLPAHMVKTWDSL 322
           + ++APLP+       SL
Sbjct: 310 IVVSAPLPSAFETLLASL 327


>gi|34497801|ref|NP_902016.1| pseudouridylate synthase [Chromobacterium violaceum ATCC 12472]
 gi|34103657|gb|AAQ60018.1| probable pseudouridylate synthases [Chromobacterium violaceum ATCC
           12472]
          Length = 249

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 106/240 (44%), Gaps = 23/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  +   +KP+ + V       +     ++   D  G++    HRLD+ TSG L+ 
Sbjct: 4   ILYRDDLLIAIHKPSNLLVHRTELDRHETRFAIQMLRDQIGRRVYPVHRLDKGTSGALLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + A + L+  F  +++ K Y ++V G P +    I + L ++     D   + ++ E
Sbjct: 64  ALDKDAGRELSLQFERQQVYKRYLAVVRGHPDDAGH-IDHPLSRRP---DDLEWIGEKVE 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++ ++ +               ++  LE++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 TAPQPAVTDYRTLARVELPIMVERYPTSRYSLLELEPQTGRKHQLRRHLKHIAHPIIGD- 178

Query: 271 KYCANFKGNFTSPIQNKL-----YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
               + KG       ++L      L    M L HP  G+ L +  PL ++       LG+
Sbjct: 179 --STHGKGRHNRMFADQLGCRRMLLACVEMRLTHPITGQPLLLNCPLESNFSALLARLGW 236


>gi|10952457|gb|AAG24942.1|AF128845_1 RluD [Sinorhizobium meliloti]
          Length = 163

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 46/155 (29%), Positives = 74/155 (47%), Gaps = 22/155 (14%)

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVIDCF 236
           +++ Y ++VWG P+  K  I   L +     GD     V +++   A  AI+H++V++ +
Sbjct: 1   LERAYRAVVWGRPRQLKGKIDAPLGR----AGDRTKRAVKREDSDDAREAITHYEVVERY 56

Query: 237 AQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN---FTSPIQNK 287
            +K         +E    TGRTHQ+RVH  H+G P++GD  Y A F+        P +  
Sbjct: 57  HEKPDGTSLASTVECHLETGRTHQIRVHMAHIGHPLIGDPDYGAAFRTKANLLPEPARAA 116

Query: 288 L------YLHARYMDLPHPEGGR-LQITAPLPAHM 315
           +       LHA  +   HP  G  +    P+PA M
Sbjct: 117 VNRFPRQALHAFMLQFEHPATGETMHFETPVPADM 151


>gi|332844903|ref|XP_510721.3| PREDICTED: RNA pseudouridylate synthase domain-containing protein 1
           [Pan troglodytes]
          Length = 312

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 48/159 (30%), Positives = 79/159 (49%), Gaps = 8/159 (5%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA      F+ RR+ K Y +L+ G  +  +  I++ + +
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYRCFKDRRVTKAYLALLRGHIQESRVTISHAIGR 120

Query: 205 KSHIGGDYVHVVKQNEKGAN--YAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            S  G  +   ++ ++   N   +++   V++           + ++P TGRTHQLRVH 
Sbjct: 121 NSTEGRAHTMCIEGSQGCENPKPSLTELVVLEHGLYAGDPVSKVLLKPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             +G  +VGD  Y     G    P   ++ LHA Y+ +P
Sbjct: 181 SALGHSVVGDLTY-GEVSGREDRPF--RMMLHAFYLRIP 216


>gi|50545681|ref|XP_500379.1| YALI0B01276p [Yarrowia lipolytica]
 gi|49646245|emb|CAG82596.1| YALI0B01276p [Yarrowia lipolytica]
          Length = 337

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 57/214 (26%), Positives = 93/214 (43%), Gaps = 26/214 (12%)

Query: 75  NHIIKEQKILDSSVNLTKHS----DFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHI 129
            H+ K   IL+S V+  + +    D     +++E+  + V +KP GI V   G  +   +
Sbjct: 81  THVFKNGSILESRVHRHEPAVPTRDEKPIRIVFENDALVVVDKPGGIPVHPTGKYLFNSV 140

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              LK     +   P   HRLD+ T+G+LV A+T  +  H+T+    R  +K Y + V G
Sbjct: 141 KEILKHETGLEELYP--AHRLDKNTTGVLVFAKTSESVNHVTQQIMSRSAKKEYLARVKG 198

Query: 190 -IPKNKKEC----IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
             P  + E     + N               +K+N +  +   +  +V     +    + 
Sbjct: 199 RFPPGRVETHHPVVEN--------------TIKRNVQPKDAHTAFERVAYDEHRDLSIVR 244

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             P TGR HQ+R H LH+G PI  D +Y     G
Sbjct: 245 CLPSTGRNHQIRQHLLHLGYPIENDREYNPELAG 278


>gi|148545031|ref|YP_001272401.1| pseudouridine synthase [Lactobacillus reuteri DSM 20016]
 gi|227364179|ref|ZP_03848276.1| pseudouridylate synthase RluD [Lactobacillus reuteri MM2-3]
 gi|325683382|ref|ZP_08162898.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
 gi|148532065|gb|ABQ84064.1| pseudouridine synthase [Lactobacillus reuteri DSM 20016]
 gi|227070818|gb|EEI09144.1| pseudouridylate synthase RluD [Lactobacillus reuteri MM2-3]
 gi|324977732|gb|EGC14683.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
          Length = 306

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 72/286 (25%), Positives = 131/286 (45%), Gaps = 45/286 (15%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQ---SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
           + +L +G  R   + V+ N+ IQ    G  +R P    A ++I   Q  L+         
Sbjct: 42  RTVLVNGNYRSMNEIVEKNDNIQLLFCGDEIRTP---TANDYIPSSQSHLE--------- 89

Query: 95  DFLKSILLYEDSKIYVFNKPAG----ISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHR 149
                 +LYE+  + V NKP G     +  G +G   + + G+L    ++      + HR
Sbjct: 90  ------VLYENRDLLVVNKPRGQKTHPNYHGETGTLMNDVAGYLAHSQNNA----YMVHR 139

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D +TSG ++VA+       L       +I + Y ++V G  +  +    +W + ++ + 
Sbjct: 140 IDLQTSGAVIVAKNPIVVPILNRLISDGQIHRQYLAVVEG--EMAQSGKLDWAIGRNPVN 197

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
               H+ + N + A  A+++++ +    ++   ++++  TGRTHQLRVH  H G PIVGD
Sbjct: 198 P---HLHQVNGQNAQPALTYYETLASNHER-SLVKLRLATGRTHQLRVHLAHSGHPIVGD 253

Query: 270 HKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
             Y  ++ +G     +  KL L              L I+APLP++
Sbjct: 254 PLYNPSSTEGMLLHGVSQKLILPFVMKS--------LNISAPLPSY 291


>gi|256545084|ref|ZP_05472450.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Anaerococcus vaginalis ATCC 51170]
 gi|256399125|gb|EEU12736.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Anaerococcus vaginalis ATCC 51170]
          Length = 286

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 52/182 (28%), Positives = 88/182 (48%), Gaps = 18/182 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +LYED  I   +K A ++V  +G   +A +I  +   W ++   + R  +RLD  TSGI+
Sbjct: 75  ILYEDQDIIAIDKDANLTVNSKGQESLANYISYYF--WKNNIKSQVRFINRLDMNTSGII 132

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR   A  +  +        K Y +LV G          N  + K+ +        K+
Sbjct: 133 LIARNPYAQAYYQKLIENNDFDKEYLALVEG----------NLEIDKTIVLKINYDENKK 182

Query: 219 NEKGAN--YAI-SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             K A+  Y I ++FK I  +  KF  +  +  TG+THQ+R+   ++  PI+GD  Y + 
Sbjct: 183 KMKIADEGYEIKTYFKNIKLY-DKFSLIYCKIFTGKTHQIRISLSNLNHPIIGDKLYGSK 241

Query: 276 FK 277
           +K
Sbjct: 242 YK 243


>gi|328473082|gb|EGF43930.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           10329]
          Length = 230

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 58/192 (30%), Positives = 91/192 (47%), Gaps = 17/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL++
Sbjct: 4   ILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAKQ---SGDEQLYLIHRLDKMTSGILLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   AA  L+++F  R+++K Y ++    PK K+  +   + +        V     N 
Sbjct: 61  GRNAKAASALSQAFADRQVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV-----NS 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K  N A++ F  +     +  +L  +PHTG+THQ+RV    +G  IVGD  Y A   GN 
Sbjct: 116 KN-NPAVTQFFSLAAEPGERLFL-CKPHTGKTHQIRVALKSVGSGIVGDPIYNA---GNE 170

Query: 281 TSPIQNKLYLHA 292
                ++ YLHA
Sbjct: 171 A----DRGYLHA 178


>gi|313624349|gb|EFR94381.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria innocua FSL J1-023]
          Length = 208

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 57/216 (26%), Positives = 103/216 (47%), Gaps = 24/216 (11%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH------RLDQETSGILVVA 161
           + + NKPAG++        YH  G + ++V    +   LT       RLD+ETSG++++A
Sbjct: 1   LLIINKPAGMASIPSQ---YHPTGSVANFVKGHYENQGLTSAIHIVTRLDRETSGLMLIA 57

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NE 220
           + R A   L+   +   +++ Y +   G  +     I      ++ IG   V ++++   
Sbjct: 58  KNRYAHARLSSFLQQGLLKRRYQAFTSGTLEEAAGSI------EAPIGRKDVSIMERFVT 111

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               YA ++++V+  +   F  L +Q  TGRTHQ+RVH  ++G P++GD  Y  +     
Sbjct: 112 PEGKYAKTNYEVLMRY-NGFDHLAIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD----- 165

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
              +  +  LH+ ++ L HP     +    PLP  M
Sbjct: 166 -QELLKRQALHSCHLHLVHPVTEEYMAFDLPLPEDM 200


>gi|259146673|emb|CAY79930.1| Pus6p [Saccharomyces cerevisiae EC1118]
          Length = 404

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 52/191 (27%), Positives = 88/191 (46%), Gaps = 18/191 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP+GI V   +G  Y     +   +   G      +RLD+ TSG+L++
Sbjct: 121 IVFEDESILVIDKPSGIPVHP-TGQFYQ--NTITELLKLHGVDALPCYRLDKITSGLLIL 177

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG------IPKNKKECIANWLLKKSHIGGDYVH 214
           A+   +A  + +S R R + KIY + V G      +  + +          S +  +   
Sbjct: 178 AKNSQSAGEIQKSIRSRDMIKIYLARVKGRFPHSELILDNENAAETTFEDTSKVTVEMTP 237

Query: 215 VVKQNEK--------GANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +   + K         +  AI+ F  I  F+      +  +P TGRTHQ+R+H   +G P
Sbjct: 238 IYSIDPKRQFPVGLSASKDAITKFYPIRYFSHADETVVACKPITGRTHQIRIHLARLGHP 297

Query: 266 IVGDHKYCANF 276
           IV D  YC++ 
Sbjct: 298 IVNDSVYCSHI 308


>gi|116073981|ref|ZP_01471243.1| probable pseudouridine synthase [Synechococcus sp. RS9916]
 gi|116069286|gb|EAU75038.1| probable pseudouridine synthase [Synechococcus sp. RS9916]
          Length = 333

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 68/285 (23%), Positives = 128/285 (44%), Gaps = 33/285 (11%)

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH-SDFLKSIL------LYEDS 106
           ++  R++SG++ R         H+++   +++    ++ H   +L++ +      +++D 
Sbjct: 51  QWKQRLESGELRRD-------GHLLQVDVMVERGERISWHRPPWLEAAVPDQWQTIHDDG 103

Query: 107 KIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVAR- 162
            + V NKP+G+ V  G G   H +   L+     +G+   P+  HRL + TSG+ V AR 
Sbjct: 104 DLLVINKPSGLPVMPGGGFLLHTLTALLEQRSRERGESLAPKPVHRLGRFTSGLQVCARR 163

Query: 163 --TRAA-AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH--IGGDYVHVVK 217
             TRAA + H       R++ + +   V G+       +   ++++ H  +G  +     
Sbjct: 164 PETRAALSAHFRPQGGCRKLYQAWSQRVEGLDLEASVEVCTDVVERPHPLLGWVWGPEPP 223

Query: 218 QNEKGANYAI-------SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            + +G    +       S   ++    Q    L++   TGR HQ+R+H   +G P++GD 
Sbjct: 224 DDARGDATPVRRRRNAHSELTLLQRGEQGDR-LQVAITTGRPHQIRIHLAQLGSPLLGDP 282

Query: 271 KYCANFK-GNFTSPIQNKLYLHA-RYMDLPHPEGGRLQITAPLPA 313
            Y    +     +P     +LHA R   LP      L + APLPA
Sbjct: 283 LYLRGRRLAPSATPGDGGYWLHAWRLEKLPSRGSDGLALEAPLPA 327


>gi|328351783|emb|CCA38182.1| hypothetical protein PP7435_Chr2-0494 [Pichia pastoris CBS 7435]
          Length = 327

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 56/181 (30%), Positives = 86/181 (47%), Gaps = 17/181 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I V NKP G+ V       Y+ +   +K+ +      P   HRLD+ TSGIL+
Sbjct: 75  IVYQDDNILVVNKPCGVPVHPTGKYYYNTMTEIMKNELGVSSLYP--CHRLDRLTSGILI 132

Query: 160 VART-RAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC---IANWLLKKSHIGGDYVH 214
           + +T RAAA++ T+  +   IQK Y + V G  P     C   I N   K+    G    
Sbjct: 133 IGKTPRAAAKYQTQ-LKQNSIQKTYIARVDGEFPMGNIVCSDKIVNIDCKRGKENG---- 187

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +  E   N+    +      +     ++  P TGRTHQ+R+H  ++G PI  D  Y  
Sbjct: 188 ITEPKEALTNFQRLAYST----SLNQSIVKCSPKTGRTHQIRIHLRNLGHPIANDPLYGF 243

Query: 275 N 275
           N
Sbjct: 244 N 244


>gi|331698896|ref|YP_004335135.1| pseudouridine synthase [Pseudonocardia dioxanivorans CB1190]
 gi|326953585|gb|AEA27282.1| pseudouridine synthase [Pseudonocardia dioxanivorans CB1190]
          Length = 252

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 99/231 (42%), Gaps = 35/231 (15%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           S+   +I+L+ED    V +KP G+SV G        D  L +     G+  R  +R+D+ 
Sbjct: 5   SELRSAIVLWEDESCLVVDKPPGLSVMG-----ERHDTDLVTIAADAGEDLRWVNRIDKV 59

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKS----H 207
           TSG +++A+++ A   LT  F+ R + K Y ++    G P   +  I   L+        
Sbjct: 60  TSGAVLLAKSKEAHGALTRQFQQRTVAKSYLAICRPGGFP--TRATIDLPLMTAGSGRIR 117

Query: 208 IGGDYVHVVKQNEK-----GANYAISHFKV-IDCFA----QKFCWLEMQPHTGRTHQLRV 257
           +  D  H+   + +        +A  HF    +C A         +   P TGR HQ+RV
Sbjct: 118 VAADREHIRLDDSRWHVRPEDEHARKHFPSRTECSAIHDDGDTVVVRADPVTGRKHQIRV 177

Query: 258 HALHMGCPIVGD------------HKYCANFKGNFTSPIQNKLYLHARYMD 296
           H   +G  IVGD              Y  +F+  F +P   ++ + AR  D
Sbjct: 178 HLAWVGHAIVGDPLFLRKTDPPEARTYLHSFRVGFRAPSDEEVTVEARPAD 228


>gi|323337472|gb|EGA78720.1| Pus6p [Saccharomyces cerevisiae Vin13]
          Length = 404

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 52/191 (27%), Positives = 88/191 (46%), Gaps = 18/191 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP+GI V   +G  Y     +   +   G      +RLD+ TSG+L++
Sbjct: 121 IVFEDESILVIDKPSGIPVHP-TGQFYQ--NTITELLKLHGVDALPCYRLDKITSGLLIL 177

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG------IPKNKKECIANWLLKKSHIGGDYVH 214
           A+   +A  + +S R R + KIY + V G      +  + +          S +  +   
Sbjct: 178 AKNSQSAGEIQKSIRSRDMIKIYLARVKGRFPHSELILDNENAAETTFEDTSKVTVEMTP 237

Query: 215 VVKQNEK--------GANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +   + K         +  AI+ F  I  F+      +  +P TGRTHQ+R+H   +G P
Sbjct: 238 IYSIDPKRQFPVGLSASKDAITKFYPIRYFSHADETVVACKPITGRTHQIRIHLARLGHP 297

Query: 266 IVGDHKYCANF 276
           IV D  YC++ 
Sbjct: 298 IVNDSVYCSHI 308


>gi|224500659|ref|ZP_03669008.1| hypothetical protein LmonF1_13701 [Listeria monocytogenes Finland
           1988]
          Length = 191

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 50/191 (26%), Positives = 99/191 (51%), Gaps = 17/191 (8%)

Query: 129 IDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +  F+K   +++G      +  RLD+ETSG++++A+ R A   L+   +   +++ Y + 
Sbjct: 6   VANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQAF 65

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEM 245
           + G+   +K  I      ++ IG   V ++++       YA ++++V+  + + F  + +
Sbjct: 66  ISGVLVEQKGSI------EAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY-RAFDHVAI 118

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP     
Sbjct: 119 QLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTEEY 172

Query: 305 LQITAPLPAHM 315
           +    PLPA M
Sbjct: 173 MAFDLPLPADM 183


>gi|326405945|gb|ADZ63016.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis CV56]
          Length = 293

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 87/181 (48%), Gaps = 12/181 (6%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSG 156
           +L+ED    V  KPAG  S+ G       +   +K ++  K    +  H   RLD++TSG
Sbjct: 79  VLFEDDHYLVVEKPAGKPSITGSLHPTGAMSNAVKGYISQKNYANQTVHIITRLDRDTSG 138

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVH 214
           I+ +A+ R A   + +      ++K Y+++V    +P + +  +       S I      
Sbjct: 139 IMFLAKHRYAHALMNQHKFRDTMEKRYFAIVNDQDLPDSGRIDLPIGRRDDSIIQ----R 194

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V+ +EK  +   S+  V+         L++  HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 195 QVRFDEKAKDALTSY--VVAERKNDLALLDIILHTGRTHQIRVHFSHLGYPLIGDDLYGG 252

Query: 275 N 275
           N
Sbjct: 253 N 253


>gi|313891609|ref|ZP_07825216.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
 gi|313119887|gb|EFR43072.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
          Length = 290

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 112/222 (50%), Gaps = 24/222 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS-----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED+ + + +K   + +   S      +   I G+ K      G  P   +RLD+ T+
Sbjct: 79  IIYEDNTLLIIDKDEDMIIHPTSKTETNTLVNAISGYYKKNNQMSGIHP--IYRLDRNTT 136

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++VVA++      L++      I++ Y ++V G  KNK+  I   + +K   G      
Sbjct: 137 GLIVVAKSAKLQYELSKEHGT--IKREYLAVVEGRFKNKEGSIIYPIGRKE--GSIIEWK 192

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+ + K A    + +KVI+   +  C  L+++ +TGRTHQ+RVH   +G P++GD  Y  
Sbjct: 193 VRDDGKEAR---TDYKVIE--EKPSCTLLKLRLYTGRTHQIRVHMSFLGHPLIGDDLYGG 247

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           N      S ++ +  LH+ ++   HP+ G  ++  +P+P  M
Sbjct: 248 N-----CSKLKRQA-LHSHHISFIHPDTGECMEFKSPMPDDM 283


>gi|320544924|ref|NP_001188782.1| RluA-2, isoform B [Drosophila melanogaster]
 gi|318068416|gb|ADV37032.1| RluA-2, isoform B [Drosophila melanogaster]
          Length = 583

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 62/196 (31%), Positives = 86/196 (43%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L ++              ++Y D  I V NKPA I V       ++   F+ +  
Sbjct: 231 KHNDLLANVVHRHEVPVTSQPIKIVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 289

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    E
Sbjct: 290 EHNLKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIRTRQVQKEYVCRVEGRFPDGIVE 349

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   + FK I         L  +P TGR HQ+R
Sbjct: 350 CNEKIDVVSYKIG-----VCKVSPKGKDCKTT-FKRIGEVGSDSIVL-CKPLTGRMHQIR 402

Query: 257 VHALHMGCPIVGDHKY 272
           VH   +G PI  D  Y
Sbjct: 403 VHLQFLGYPISNDPLY 418


>gi|291456224|ref|ZP_06595614.1| RNA pseudouridine synthase [Bifidobacterium breve DSM 20213]
 gi|291381501|gb|EFE89019.1| RNA pseudouridine synthase [Bifidobacterium breve DSM 20213]
          Length = 244

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 101/239 (42%), Gaps = 40/239 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LYED +I V +KP  ++     G+ Y     ++  +  +  +P +T  HRLD+ T+G+L
Sbjct: 3   VLYEDERIIVVDKPHFLATMP-RGMWYRETALIR--LRERLGEPDITPAHRLDRMTAGVL 59

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKSHIG 209
           V  R  A        F+ ++  K+Y  L          +G     +      LL++SHI 
Sbjct: 60  VFVRDPACRGAYQMLFQNKQATKVYECLASCAPIRRPRFGTITQAEPPRPFPLLRRSHIT 119

Query: 210 GDYVHVVKQNEKGANYA---ISHFKVI---------------DCFAQK-FCWLEMQPHTG 250
            +   +    E GA  A   I   ++I                C      C   + P TG
Sbjct: 120 KERGTLAAFEEPGAVNAETLIERGELILTSAGGRWREAPEGGPCLENPPICRYTLHPRTG 179

Query: 251 RTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           +THQLRVH   +G PIVGD  Y         +F+ P+Q    L AR +    P  G+ Q
Sbjct: 180 KTHQLRVHMNSLGLPIVGDDFYPRIQTRLYDDFSQPLQ----LVARVLRFTDPVTGKRQ 234


>gi|151943445|gb|EDN61756.1| pseudouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|190406816|gb|EDV10083.1| conserved hypothetical protein [Saccharomyces cerevisiae RM11-1a]
 gi|323333566|gb|EGA74960.1| Pus6p [Saccharomyces cerevisiae AWRI796]
          Length = 404

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 52/191 (27%), Positives = 88/191 (46%), Gaps = 18/191 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP+GI V   +G  Y     +   +   G      +RLD+ TSG+L++
Sbjct: 121 IVFEDESILVIDKPSGIPVHP-TGQFYQ--NTITELLKLHGVDALPCYRLDKITSGLLIL 177

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG------IPKNKKECIANWLLKKSHIGGDYVH 214
           A+   +A  + +S R R + KIY + V G      +  + +          S +  +   
Sbjct: 178 AKNSQSAGEIQKSIRSRDMIKIYLARVKGRFPHSELILDNENAAETTFEDTSKVTVEMTP 237

Query: 215 VVKQNEK--------GANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +   + K         +  AI+ F  I  F+      +  +P TGRTHQ+R+H   +G P
Sbjct: 238 IYSIDPKRQFPVGLSASKDAITKFYPIRYFSHADETVVACKPITGRTHQIRIHLARLGHP 297

Query: 266 IVGDHKYCANF 276
           IV D  YC++ 
Sbjct: 298 IVNDSVYCSHI 308


>gi|46190854|ref|ZP_00121013.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Bifidobacterium longum DJO10A]
          Length = 244

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 62/219 (28%), Positives = 94/219 (42%), Gaps = 38/219 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LYED +I V +KP  ++     G+ Y     ++  +  +  +P +T  HRLD+ T+G+L
Sbjct: 3   VLYEDERIIVVDKPHFLATMP-RGMWYRQTALIR--LRERLGEPDITPAHRLDRMTAGVL 59

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP----------KNKKECIANWLLKKSHI 208
           V  R  A        F+ R+  K+Y  L    P          K +  C    LL++SHI
Sbjct: 60  VFVRDPACRGAYQMLFQNRQAVKVYECLAPCRPISRPRFGTIMKVEPPC-PFPLLRRSHI 118

Query: 209 GGDYVHVVKQNEKGANYAISHFKVID-CFAQ------------------KFCWLEMQPHT 249
             ++  +    E G   A +  +  D CF                      C   + P T
Sbjct: 119 TKEHGTMAAFEEPGLANAETLIERGDLCFPPADGRWREAPEGGPHLGNHPICRYTLHPRT 178

Query: 250 GRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQ 285
           G+THQLRVH   +G PIVGD  Y         +F+ P+Q
Sbjct: 179 GKTHQLRVHMNSLGLPIVGDDFYPRIQTRPYDDFSQPLQ 217


>gi|315179926|gb|ADT86840.1| pseudouridine synthase Rlu family protein [Vibrio furnissii NCTC
           11218]
          Length = 231

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 48/147 (32%), Positives = 76/147 (51%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR   AA  L++ F  R+++K Y +L    PK K+  I+  + + 
Sbjct: 46  LVHRLDKMTSGILLLARNAKAASELSKGFAERQVEKFYLALGSKKPKKKQGLISGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                 +  +  Q     N A++ F  +     +  +L  +P+TG+THQ+RV    +G  
Sbjct: 106 RR--ASWKLLTSQT----NPAVTQFFSLAAEPGERLFL-CKPYTGKTHQIRVALKSVGSG 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y A  +        ++ YLHA
Sbjct: 159 IVGDPIYNAGNQA-------DRGYLHA 178


>gi|331701048|ref|YP_004398007.1| RluA family pseudouridine synthase [Lactobacillus buchneri NRRL
           B-30929]
 gi|329128391|gb|AEB72944.1| pseudouridine synthase, RluA family [Lactobacillus buchneri NRRL
           B-30929]
          Length = 296

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 101/222 (45%), Gaps = 22/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL---KSWVDSKG---QKPRLTHRLDQET 154
           +++ED    V NKP G++         H+D  +   K +   +G   QK  +  RLD++T
Sbjct: 81  IVHEDPNFLVVNKPYGVASVPAHN---HVDSLVNRVKGYYQRQGYANQKIHIVTRLDKDT 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+   A   L +  + R IQK Y ++V G     +  + ++ +       D   
Sbjct: 138 SGLVIFAKHHFAHSVLDKQLKDRTIQKTYLAIVAG-----RISMPHFEIYLPIGRADDSF 192

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V +Q       +++    +   A++   L+++ HTGRTHQ+RVH   +G P++GD  Y  
Sbjct: 193 VKRQVVDSGKMSVTEAWTVRRLAKQ-TLLKVRLHTGRTHQIRVHMAAIGHPLIGDWLY-- 249

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
               N       +  LH   +    P  GR L   A LP  M
Sbjct: 250 ----NSDDHSMTRQALHCAELTFYDPFAGRLLHCEARLPEDM 287


>gi|326383527|ref|ZP_08205213.1| pseudouridine synthase [Gordonia neofelifaecis NRRL B-59395]
 gi|326197611|gb|EGD54799.1| pseudouridine synthase [Gordonia neofelifaecis NRRL B-59395]
          Length = 291

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 61/214 (28%), Positives = 93/214 (43%), Gaps = 22/214 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  ++    G+ +A      L+  + S    P   HRLD+ T+G+L+
Sbjct: 79  ILHLDDDLAVVDKPHFLATMPRGAHVAETALVRLRRELGSDEVAP--AHRLDRLTAGVLL 136

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQ 218
             R R       E F  RR+ K Y +L        +   I N ++K +   GD    V  
Sbjct: 137 FTRRREVRAAYQELFAQRRVHKEYRALARADDALVERVRIENRIVKTA---GDLRARVVP 193

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY------ 272
            E  A   +S  ++     +      + P TGRTHQLR+H   +G PI+GD  Y      
Sbjct: 194 GEVNA---VSDIELAVRHGEGLAEYRLLPSTGRTHQLRMHMAGLGTPIIGDPLYPEVDHD 250

Query: 273 --CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              A  +G+F+ P    L L A  +    P  GR
Sbjct: 251 LAAAPDRGDFSRP----LALVAHRLSFTDPLSGR 280


>gi|302892903|ref|XP_003045333.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256726258|gb|EEU39620.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 525

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 53/200 (26%), Positives = 86/200 (43%), Gaps = 29/200 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           +++ED  + V NKPAG+ V       Y+ +  ++     +GQ   P L +RLD+ TSGI+
Sbjct: 193 VIHEDEDMIVINKPAGVPVHPAG--RYNYNSVIEIMKSERGQGFLPYLCNRLDRLTSGIM 250

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
            +A+   AA+ L    + R ++K Y + V G  P  +  C    L     +G + V    
Sbjct: 251 FIAKNPPAAEALGIKIKQRTVRKEYIARVMGKFPDGEVVCDQPILQISPKLGLNRVRANG 310

Query: 218 QNEKGANYAISHFKVIDCFAQK------------------------FCWLEMQPHTGRTH 253
           +  +     ++++   D    +                        +  +   P TGRTH
Sbjct: 311 KTARTVFKRLAYYPPPDGEETEGDGRPKTPEEELDEKHHPWINKRGYSIVRCLPVTGRTH 370

Query: 254 QLRVHALHMGCPIVGDHKYC 273
           QLRVH  H+G PI  D  Y 
Sbjct: 371 QLRVHLQHLGHPIQNDPIYA 390


>gi|323348440|gb|EGA82685.1| Pus6p [Saccharomyces cerevisiae Lalvin QA23]
          Length = 404

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 52/191 (27%), Positives = 88/191 (46%), Gaps = 18/191 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP+GI V   +G  Y     +   +   G      +RLD+ TSG+L++
Sbjct: 121 IVFEDESILVIDKPSGIPVHP-TGQFYQ--NTITELLKLHGVDALPCYRLDKITSGLLIL 177

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG------IPKNKKECIANWLLKKSHIGGDYVH 214
           A+   +A  + +S R R + KIY + V G      +  + +          S +  +   
Sbjct: 178 AKNSQSAGEIQKSIRSRDMIKIYLARVKGRFPHSELILDNENAAETTFEDTSKVTVEMTP 237

Query: 215 VVKQNEK--------GANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +   + K         +  AI+ F  I  F+      +  +P TGRTHQ+R+H   +G P
Sbjct: 238 IYSIDPKRQFPVGLSASKDAITKFYPIRYFSHADETVVACKPITGRTHQIRIHLARLGHP 297

Query: 266 IVGDHKYCANF 276
           IV D  YC++ 
Sbjct: 298 IVNDSVYCSHI 308


>gi|256272036|gb|EEU07049.1| Pus6p [Saccharomyces cerevisiae JAY291]
          Length = 404

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 52/191 (27%), Positives = 88/191 (46%), Gaps = 18/191 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP+GI V   +G  Y     +   +   G      +RLD+ TSG+L++
Sbjct: 121 IVFEDESILVIDKPSGIPVHP-TGQFYQ--NTITELLKLHGVDALPCYRLDKITSGLLIL 177

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG------IPKNKKECIANWLLKKSHIGGDYVH 214
           A+   +A  + +S R R + KIY + V G      +  + +          S +  +   
Sbjct: 178 AKNSQSAGEIQKSIRSRDMIKIYLARVKGRFPHSELILDNENAAETTFEDTSKVTVELTP 237

Query: 215 VVKQNEK--------GANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +   + K         +  AI+ F  I  F+      +  +P TGRTHQ+R+H   +G P
Sbjct: 238 IYSIDPKRQFPVGLSASKDAITKFYPIRYFSHADETVVACKPITGRTHQIRIHLARLGHP 297

Query: 266 IVGDHKYCANF 276
           IV D  YC++ 
Sbjct: 298 IVNDSVYCSHI 308


>gi|148690492|gb|EDL22439.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_a
           [Mus musculus]
          Length = 236

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 50/159 (31%), Positives = 77/159 (48%), Gaps = 8/159 (5%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA    + F+ RR+ K Y +LV G  +  +  I   + +
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYKCFKERRVTKAYLALVRGHVQESQVTINYAIGR 120

Query: 205 KSHIGGDYVHVVKQNEKGANY--AISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            S  G  +   ++      N   +++   V++           + ++P TGRTHQLRVH 
Sbjct: 121 NSTEGRTHTMCIEGTHGCENPKPSLTELLVLEHGLYAGDPVSKVLLKPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             +G PIVGD  Y    +     P   ++ LHA Y+ +P
Sbjct: 181 SALGHPIVGDLTY-GQAEDQEDQPF--RMMLHAFYLRIP 216


>gi|329770323|ref|ZP_08261706.1| hypothetical protein HMPREF0433_01470 [Gemella sanguinis M325]
 gi|328836681|gb|EGF86337.1| hypothetical protein HMPREF0433_01470 [Gemella sanguinis M325]
          Length = 254

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 72/266 (27%), Positives = 122/266 (45%), Gaps = 28/266 (10%)

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL--KSILL---YEDSKIYVFNKP 114
           Q    + +   I  LN  + +  +L+ ++ L+K S++L  KSI +   YED  + + +KP
Sbjct: 5   QDNNTILVNNDIAKLNTSLAKNDVLELNIELSK-SNYLTNKSISITKEYEDPYLLIVSKP 63

Query: 115 AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            GI       I+   D  L +++ S  Q     HRLD +T G+++ ++T      L +  
Sbjct: 64  FGIKTHPND-ISIE-DDTLVNYLISDYQYLEPIHRLDIDTCGLVIFSKTPLIKSKLDQML 121

Query: 175 RMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           + R I++ Y +L      PK  K  I   + +K+ +       V    K A   I   + 
Sbjct: 122 KNREIKRYYTALTKNNIKPKTIKTNIGRDIREKNKMA------VTNKGKQATTNILSCEK 175

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLH 291
           ID    KF  + +   TGRTHQ+RVH   +G  I+GD  Y  + +K        +K+YL 
Sbjct: 176 ID--QNKFV-VTISLETGRTHQIRVHLSSIGNAIIGDKLYSNDGYK-------YDKMYLG 225

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMV 316
           A  +   HP    +++I + L    +
Sbjct: 226 ALKVVFNHPVTNDKIEINSSLRTEFI 251


>gi|260768225|ref|ZP_05877159.1| pseudouridylate synthase LSU rRNA-specific [Vibrio furnissii CIP
           102972]
 gi|260616255|gb|EEX41440.1| pseudouridylate synthase LSU rRNA-specific [Vibrio furnissii CIP
           102972]
          Length = 202

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 48/147 (32%), Positives = 76/147 (51%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR   AA  L++ F  R+++K Y +L    PK K+  I+  + + 
Sbjct: 17  LVHRLDKMTSGILLLARNAKAASELSKGFAERQVEKFYLALGSKKPKKKQGLISGDMERS 76

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                 +  +  Q     N A++ F  +     +  +L  +P+TG+THQ+RV    +G  
Sbjct: 77  RR--ASWKLLTSQT----NPAVTQFFSLAAEPGERLFL-CKPYTGKTHQIRVALKSVGSG 129

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y A  +        ++ YLHA
Sbjct: 130 IVGDPIYNAGNQA-------DRGYLHA 149


>gi|207345036|gb|EDZ71984.1| YGR169Cp-like protein [Saccharomyces cerevisiae AWRI1631]
 gi|323354851|gb|EGA86684.1| Pus6p [Saccharomyces cerevisiae VL3]
          Length = 404

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 52/189 (27%), Positives = 87/189 (46%), Gaps = 18/189 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP+GI V   +G  Y     +   +   G      +RLD+ TSG+L++
Sbjct: 121 IVFEDESILVIDKPSGIPVHP-TGQFYQ--NTITELLKFHGVDALPCYRLDKITSGLLIL 177

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG------IPKNKKECIANWLLKKSHIGGDYVH 214
           A+   +A  + +S R R + KIY + V G      +  + +          S +  +   
Sbjct: 178 AKNSQSAGEIQKSIRSRDMIKIYLARVKGRFPHSELILDNENAAETTFEDTSKVTVEMTP 237

Query: 215 VVKQNEK--------GANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +   + K         +  AI+ F  I  F+      +  +P TGRTHQ+R+H   +G P
Sbjct: 238 IYSIDPKRQFPVGLSASKDAITKFYPIRYFSHADETVVACKPITGRTHQIRIHLARLGHP 297

Query: 266 IVGDHKYCA 274
           IV D  YC+
Sbjct: 298 IVNDSVYCS 306


>gi|153952071|ref|YP_001397292.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
 gi|152939517|gb|ABS44258.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
          Length = 300

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 99/201 (49%), Gaps = 17/201 (8%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKS 135
           ++ KIL   V L  + +  K + +++E+    +  K +GI S   G    Y + D     
Sbjct: 48  EKNKILKGLVELIVYENNPKGVEIVFENENFAILEKESGILSHPNGRHCKYSLSDEIWHL 107

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W    G+   + HRLD+ETSG+++VA+ + A   L   F  + +QK Y +L  G      
Sbjct: 108 W----GKGACVAHRLDKETSGLILVAKNKKAQIDLKSLFEKKLVQKEYLALAHG------ 157

Query: 196 ECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           +   N+++ K+ ++  +Y  V    Q  K    AI+ FK+++ F +     L  +P TGR
Sbjct: 158 KIEKNFIVDKAINLAKNYDDVKTRMQICKEGKQAITEFKILEYFPKINATLLLCKPLTGR 217

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH  +    I+GD  Y
Sbjct: 218 QHQIRVHLHYKNHTILGDPLY 238


>gi|291483642|dbj|BAI84717.1| hypothetical protein BSNT_01943 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 299

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 67/258 (25%), Positives = 118/258 (45%), Gaps = 29/258 (11%)

Query: 73  ALNHIIKEQKIL-----DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QG 121
            + +++KE  +L     +  V+ T  ++ +   +LYED  + V NK   +S         
Sbjct: 51  TVKYVLKEGDLLIVKFPEEQVSETLLAEPIPLDILYEDEHVLVINKQPYVSSIPSREHPS 110

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GS     ID + K+ V +      L  RLD++TSG+++VA+ R A   L+ + +   +++
Sbjct: 111 GSIANGIIDHYQKNGVRAT---VHLVTRLDRDTSGVMLVAKHRFAHSILSSAQKNGLVKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKF 240
            Y ++V G     +  +       + IG     ++++        A++HF V  C     
Sbjct: 168 RYAAVVHGRMAQMEGTV------DAPIGRHPDSIIERTVTPDGQKAVTHFYVT-CANDDM 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + +Q  TGRTHQ+RVH  ++G P+ GD  Y        T     +  LH+ ++   HP
Sbjct: 221 TSVALQLETGRTHQIRVHMSYLGHPLCGDTLYGG------TRQEIGRQALHSEHLSFIHP 274

Query: 301 EGGR-LQITAPLPAHMVK 317
              + +   APLP  M K
Sbjct: 275 LTQKNMTFHAPLPQDMRK 292


>gi|115489062|ref|NP_001067018.1| Os12g0560500 [Oryza sativa Japonica Group]
 gi|122203511|sp|Q2QNM3|PUS1_ORYSJ RecName: Full=RNA pseudourine synthase 1; AltName: Full=RNA
           pseudouridylate synthase 1; AltName: Full=RNA-uridine
           isomerase 1
 gi|77556134|gb|ABA98930.1| RNA pseudouridylate synthase, putative, expressed [Oryza sativa
           Japonica Group]
 gi|113649525|dbj|BAF30037.1| Os12g0560500 [Oryza sativa Japonica Group]
 gi|125537021|gb|EAY83509.1| hypothetical protein OsI_38723 [Oryza sativa Indica Group]
 gi|215692563|dbj|BAG87983.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 345

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 68/263 (25%), Positives = 111/263 (42%), Gaps = 63/263 (23%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW------VDSKGQKPRL--THRLDQ 152
           +++ED  + V +KPAG+          + D  L +       +  +  KP L   +RLD+
Sbjct: 86  VVFEDEWLAVVDKPAGV----------YCDALLSALPCSAATLGDEATKPNLHLANRLDR 135

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP---KNKKECIANWLLK----- 204
           +TSG++V+ +    A  L ++F   +++K Y +L  G P   +  K C  +   K     
Sbjct: 136 DTSGLMVITKCNKVAGKLVKAFTEHKVKKTYLALCIGYPPAWEKIKICSGHGRSKHGAWR 195

Query: 205 --------KSHIGGDYV-------HVVKQNEKGANYAISHFKVIDCFA------------ 237
                   +S  GG  V        V+  N KG     S+F+V +  +            
Sbjct: 196 VYAMSDVGRSLPGGSVVRDMSTRFEVLGINGKGQFREPSNFEVDETESITVQEKAADLTS 255

Query: 238 -----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                     +   P +GRTHQ+R+H  ++G PI GD KY    + N      +   LHA
Sbjct: 256 DGDEKNSIILVRAYPQSGRTHQIRLHCQYLGFPIRGDVKYSGVIEWNGVD--YDGHALHA 313

Query: 293 RYMDLPHPEGGRLQIT--APLPA 313
             +   HP  G L +T  +PLP+
Sbjct: 314 ESLSFVHPVTG-LPVTFRSPLPS 335


>gi|119953592|ref|YP_945802.1| tRNA pseudouridine synthase A [Borrelia turicatae 91E135]
 gi|119862363|gb|AAX18131.1| tRNA pseudouridine synthase A [Borrelia turicatae 91E135]
          Length = 331

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 115/242 (47%), Gaps = 21/242 (8%)

Query: 41  LRSGQVRVDKKRVKFNNRI-QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +R+G V ++  +V F++RI +  ++    P++  L+  +    + D    L      +K 
Sbjct: 56  IRNGDVLLNNLKVSFSHRIFKDDKIYLYKPLLQGLS--LNRVTVKDEVAILRD----IKK 109

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--DSKGQ---KPRLTHRLDQET 154
            ++YED+ + V NK  GI V G     Y +D  + +++  +S G    KP   HRLD+ T
Sbjct: 110 RIVYEDADLLVINKRRGILVHGDK---YSLDTLINAYLLDESLGSLSFKPSAVHRLDRNT 166

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+   +A+ L+++F    + K Y +L+ G+   K     N+L +       +V 
Sbjct: 167 SGLIIFAKNINSARILSQAFSSGVVIKKYLALLDGVI-TKPLTYKNFLYRDKIARKTFV- 224

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               N+     A++  K I   ++     E+   TG THQ+R         ++ D KY +
Sbjct: 225 ---INDIDKCNAVTDIKPI-LVSKSSTLAEVSIKTGFTHQIRAQCAFNKHALINDKKYDS 280

Query: 275 NF 276
            F
Sbjct: 281 QF 282


>gi|258405414|ref|YP_003198156.1| pseudouridine synthase Rlu family protein [Desulfohalobium
           retbaense DSM 5692]
 gi|257797641|gb|ACV68578.1| pseudouridine synthase Rlu family protein, TIGR01621
           [Desulfohalobium retbaense DSM 5692]
          Length = 237

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 47/145 (32%), Positives = 76/145 (52%), Gaps = 13/145 (8%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++A+ R  A+ + E F   RI K Y +L    P+ K+  +    +++S 
Sbjct: 47  HRLDKVTSGLLLLAKDRETARSMGELFSAHRIDKFYLALSAKRPRKKQGTVIG-DMRRSR 105

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            G   +   ++N      A++ F        K  +L ++P +G+THQLRV    +G PI+
Sbjct: 106 RGTWRLERSRENP-----AVTQFVSRAWSGGKRAFL-LRPQSGKTHQLRVALKSLGAPIL 159

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA 292
           GD  Y      N +   Q++ YLHA
Sbjct: 160 GDPLYGPR---NHS---QDRCYLHA 178


>gi|205355761|ref|ZP_03222531.1| hypothetical protein Cj8421_0022c [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|205346538|gb|EDZ33171.1| hypothetical protein Cj8421_0022c [Campylobacter jejuni subsp.
           jejuni CG8421]
          Length = 300

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 104/205 (50%), Gaps = 19/205 (9%)

Query: 77  IIKEQK--ILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DG 131
           I+ E+K  IL+  V L  + +  K + +++E+  + +  K +GI S   G    Y + D 
Sbjct: 44  ILVEEKNEILNGLVELIVYENNPKGVEIVFENEDLAILEKESGILSHPNGRHCKYSLSDE 103

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
               W    G++  + HRLD+ETSG+++VA+ + A   L   F  + +QK Y +L  G  
Sbjct: 104 IWHLW----GKEACVAHRLDKETSGLILVAKNKKAQIDLKALFEKKLVQKEYLALANG-- 157

Query: 192 KNKKECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQP 247
               +   N+++ K+ ++  +Y  V    Q  K    AI+ F++++ F +     L  +P
Sbjct: 158 ----KIEENFIIDKAINLAKNYDDVKTRMQICKEGKQAITEFEILEYFPKINATLLLCKP 213

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
            TGR HQ+RVH  +    I+GD  Y
Sbjct: 214 LTGRQHQIRVHLHYKNHTILGDPLY 238


>gi|320544926|ref|NP_001188783.1| RluA-2, isoform C [Drosophila melanogaster]
 gi|318068417|gb|ADV37033.1| RluA-2, isoform C [Drosophila melanogaster]
          Length = 543

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 62/196 (31%), Positives = 86/196 (43%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L ++              ++Y D  I V NKPA I V       ++   F+ +  
Sbjct: 195 KHNDLLANVVHRHEVPVTSQPIKIVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILAK- 253

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    E
Sbjct: 254 EHNLKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIRTRQVQKEYVCRVEGRFPDGIVE 313

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   + FK I         L  +P TGR HQ+R
Sbjct: 314 CNEKIDVVSYKIG-----VCKVSPKGKDCKTT-FKRIGEVGSDSIVL-CKPLTGRMHQIR 366

Query: 257 VHALHMGCPIVGDHKY 272
           VH   +G PI  D  Y
Sbjct: 367 VHLQFLGYPISNDPLY 382


>gi|241760243|ref|ZP_04758339.1| pseudouridine synthase Rlu family protein [Neisseria flavescens
           SK114]
 gi|241319354|gb|EER55819.1| pseudouridine synthase Rlu family protein [Neisseria flavescens
           SK114]
          Length = 216

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 50/175 (28%), Positives = 79/175 (45%), Gaps = 9/175 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E     V NKP G+SV         +   L   +    ++  L HRLD+ TSG+L+ 
Sbjct: 4   IVFEHKDFVVINKPCGVSVHSELEEDVCLTASLTQQLGV--ERVWLVHRLDKATSGLLLF 61

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R +A  L+  F  + ++K Y +L    P  K+     W+  K  +   +    K   
Sbjct: 62  ALNRDSAAALSAQFAEKTVRKTYLALGTHKPAKKQ----GWV--KGGMARSWRGTWKLTR 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              N+A++ F              +QP TG+THQLRV    +G PI+GD  Y  +
Sbjct: 116 DEDNFAVTRFSS-QSLQPGLRLFVLQPFTGKTHQLRVAIKSIGSPILGDTLYGGD 169


>gi|222617295|gb|EEE53427.1| hypothetical protein OsJ_36505 [Oryza sativa Japonica Group]
          Length = 423

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 68/263 (25%), Positives = 111/263 (42%), Gaps = 63/263 (23%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW------VDSKGQKPRL--THRLDQ 152
           +++ED  + V +KPAG+          + D  L +       +  +  KP L   +RLD+
Sbjct: 164 VVFEDEWLAVVDKPAGV----------YCDALLSALPCSAATLGDEATKPNLHLANRLDR 213

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP---KNKKECIANWLLK----- 204
           +TSG++V+ +    A  L ++F   +++K Y +L  G P   +  K C  +   K     
Sbjct: 214 DTSGLMVITKCNKVAGKLVKAFTEHKVKKTYLALCIGYPPAWEKIKICSGHGRSKHGAWR 273

Query: 205 --------KSHIGGDYV-------HVVKQNEKGANYAISHFKVIDCFA------------ 237
                   +S  GG  V        V+  N KG     S+F+V +  +            
Sbjct: 274 VYAMSDVGRSLPGGSVVRDMSTRFEVLGINGKGQFREPSNFEVDETESITVQEKAADLTS 333

Query: 238 -----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                     +   P +GRTHQ+R+H  ++G PI GD KY    + N      +   LHA
Sbjct: 334 DGDEKNSIILVRAYPQSGRTHQIRLHCQYLGFPIRGDVKYSGVIEWNGVD--YDGHALHA 391

Query: 293 RYMDLPHPEGGRLQIT--APLPA 313
             +   HP  G L +T  +PLP+
Sbjct: 392 ESLSFVHPVTG-LPVTFRSPLPS 413


>gi|208434290|ref|YP_002265956.1| pseudo uridine synthase D [Helicobacter pylori G27]
 gi|208432219|gb|ACI27090.1| pseudo uridine synthase D [Helicobacter pylori G27]
          Length = 297

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 74/280 (26%), Positives = 123/280 (43%), Gaps = 31/280 (11%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K     Q+ Q VR   +I  +  +I  +    +              
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVRKSQMIQGVVRLIHFKPNEKAQA------------ 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KPA +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPAQVYTHP-KGYFYH-ESLLDCIQSHLGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  + + L   F  ++++K Y +L  G+   K   I   +L   +I  D + +  Q  
Sbjct: 129 GKTLQSVKDLKALFMQKKVKKTYLALAHGL-VEKSMKIDKPILTLQNIQKD-LRIRSQIS 186

Query: 221 KGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---N 275
                +I+  + +  D F      L++ P TGRTHQ+R+H   +G  IVG+  Y      
Sbjct: 187 PLGKPSITLVESLSYDPFLD-ISLLKITPLTGRTHQIRLHLSSVGHRIVGEGLYGVADEE 245

Query: 276 FKGNFTSPIQNK---LYLHARYMDLPHPEGGRLQITAPLP 312
            +G      +N    L LHA  ++    +G   QI +P+P
Sbjct: 246 ARGYLQLKRENHAPLLMLHAASLEFEF-KGAIYQIASPMP 284


>gi|307107653|gb|EFN55895.1| hypothetical protein CHLNCDRAFT_145520 [Chlorella variabilis]
          Length = 274

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 54/203 (26%), Positives = 86/203 (42%), Gaps = 21/203 (10%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN------- 200
           HRLD   SG +V+A  + AA  L  +FR R++ K Y +L    P  K   +A        
Sbjct: 66  HRLDLICSGCVVLATRQEAAGELIGAFRQRQVHKYYCALSDRRPSKKMGSVAGEMQRGRR 125

Query: 201 --WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLR 256
             W+L +S              K    A++ F        +       ++P TGRTHQLR
Sbjct: 126 GAWMLARSSAAPAADAPAPPVYK----AVTRFTSTAVLGSRPGLRAFLLKPETGRTHQLR 181

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           V    +G P++GD +Y       +    + + YLH   +      G  +Q+  P P H  
Sbjct: 182 VALKSLGSPVLGDERYAQKEAAAW----EERAYLHCAALRF-ELGGAAVQVVCP-PEHGA 235

Query: 317 KTWDSLGFKYDRNLYIKRLYSQD 339
           +  DS GF+   + ++ +   Q+
Sbjct: 236 EFADSPGFRAVFDAWLPQSMEQE 258


>gi|281490911|ref|YP_003352891.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
 gi|281374669|gb|ADA64189.1| Ribosomal large subunit pseudouridine synthase D, RluA family
           [Lactococcus lactis subsp. lactis KF147]
          Length = 293

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 87/181 (48%), Gaps = 12/181 (6%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSG 156
           +L+ED    V  KPAG  S+ G       +   +K ++  K    +  H   RLD++TSG
Sbjct: 79  VLFEDDHYLVVEKPAGKPSITGSLHPTGAMSNAVKGYISQKNYANQTVHIITRLDRDTSG 138

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVH 214
           I+ +A+ R A   + +      ++K Y+++V    +P + +  +       S I      
Sbjct: 139 IMFLAKHRYAHALMNQHKFRDTMEKRYFAIVNDQDLPDSGRIDLPIGRRDDSIIQ----R 194

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V+ +EK  +   S+  V+         L++  HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 195 QVRFDEKAKDALTSY--VVAERKNDLALLDIILHTGRTHQIRVHFSHLGYPLIGDDLYGG 252

Query: 275 N 275
           N
Sbjct: 253 N 253


>gi|332994014|gb|AEF04069.1| tRNA pseudouridine synthase A [Alteromonas sp. SN2]
          Length = 278

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 49/170 (28%), Positives = 86/170 (50%), Gaps = 24/170 (14%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD  TSG L +A+    A  + ++F  R++ K Y ++    PK K+  I   +  K
Sbjct: 89  LCHRLDTGTSGCLCLAKNAQTAALIGDAFASRQVSKYYLAISADKPKKKQGSIVGDM--K 146

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALH 261
           +  GG ++ +  ++    N A++ F     F+Q     +    ++P TG+THQ+RV    
Sbjct: 147 NRRGGQFMLLKSKD----NPAVTQF-----FSQSAKPGYRGFIVKPLTGKTHQIRVALKS 197

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           +G  I+GD  Y         +P  ++L+LHA ++ +P P    + + AP+
Sbjct: 198 VGAAILGDTLYSG-------AP-SDRLHLHAGWLRIPLPS-RTISVKAPI 238


>gi|317482547|ref|ZP_07941562.1| RNA pseudouridylate synthase [Bifidobacterium sp. 12_1_47BFAA]
 gi|316915969|gb|EFV37376.1| RNA pseudouridylate synthase [Bifidobacterium sp. 12_1_47BFAA]
          Length = 254

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 94/218 (43%), Gaps = 36/218 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LYED +I V +KP  ++     G+ Y     ++  +  +  +P +T  HRLD+ T+G+L
Sbjct: 13  VLYEDERIIVVDKPHFLATMP-RGMWYRQTALIR--LRERLGEPDITPAHRLDRMTAGVL 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---------KECIANWLLKKSHIG 209
           V  R  A        F+ R+  K+Y  L    P ++         +      LL++SHI 
Sbjct: 70  VFVRDPACRGAYQMLFQNRQTVKVYECLAPCRPISRPRFGTIMQVEPPRPFPLLRRSHIT 129

Query: 210 GDYVHVVKQNEKGANYAISHFKVID-CFAQ------------------KFCWLEMQPHTG 250
            ++  +    E G   A +  +  D CF                      C   + P TG
Sbjct: 130 KEHGTMAAFEEPGLANAETLIERGDLCFPPADGRWREAPEGGPHPGNHPICRYTLHPRTG 189

Query: 251 RTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQ 285
           +THQLRVH   +G PIVGD  Y         +F+ P+Q
Sbjct: 190 KTHQLRVHMNSLGLPIVGDDFYPRIQTRPYDDFSQPLQ 227


>gi|328774056|gb|EGF84093.1| hypothetical protein BATDEDRAFT_8379 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 379

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 54/208 (25%), Positives = 100/208 (48%), Gaps = 15/208 (7%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           L+++I+   +++++V+  +H   +      ++++   + V NKP+ I V       Y+  
Sbjct: 62  LDYVIRNSDLVENTVH--RHEPVITDTPIEIVHQSDSVLVVNKPSSIPVHPTGRYRYNTV 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG- 189
             L  + ++K     L +R+D+ TSG++++AR +  A ++ +  R RRI K Y + V G 
Sbjct: 120 IHLLEY-ENKMNDLFLVNRIDRLTSGLVLIARDKNKAAYMMQEMRERRIHKTYLARVKGE 178

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            P +  EC       +  +G   V++V    K  +            +   C    +P T
Sbjct: 179 FPADAIECHEPIETVEFKVG---VNIVSPTGKPCSTLFKRLSYNGLTSVVQC----EPLT 231

Query: 250 GRTHQLRVHALHMGCPIVGDHKY-CANF 276
           GRTHQ+RVH   +G PI  D  Y C+ +
Sbjct: 232 GRTHQIRVHLQFLGHPIANDPIYGCSEW 259


>gi|290579729|ref|YP_003484121.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
 gi|254996628|dbj|BAH87229.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
          Length = 288

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 90/212 (42%), Gaps = 20/212 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NK  G+           +     ++V   GQ   + HRLD +TSG ++ A
Sbjct: 84  LYQDEHLIIVNKIEGMKTHANDPNEIALLNHASAYV---GQTCYVVHRLDMKTSGTVMFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           +       L      + I++ YW+L  G      +     ++ +  IG D     K+  +
Sbjct: 141 KNPFILPILNRLLENKSIKREYWALAQG------QFSERAIIYREPIGRDRHDRRKRVVD 194

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K    AI+   ++  F      ++ Q  TGRTHQ+RVH  +    IVGD  Y     G 
Sbjct: 195 HKHGQTAITQVSLLKHFPNNTSLIKCQLQTGRTHQIRVHLAYHDHAIVGDPLYSQQTAG- 253

Query: 280 FTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
                  +L LHA  +   HP    ++++ AP
Sbjct: 254 -------RLMLHAHQLTFTHPLTLEKIKVEAP 278


>gi|254569206|ref|XP_002491713.1| Mitochondrial tRNA pseudouridine synthase involved in
           pseudouridylation of mitochondrial tRNAs [Pichia
           pastoris GS115]
 gi|238031510|emb|CAY69433.1| Mitochondrial tRNA pseudouridine synthase involved in
           pseudouridylation of mitochondrial tRNAs [Pichia
           pastoris GS115]
          Length = 358

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 57/181 (31%), Positives = 86/181 (47%), Gaps = 17/181 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  I V NKP G+ V       Y+ +   +K+ +      P   HRLD+ TSGIL+
Sbjct: 106 IVYQDDNILVVNKPCGVPVHPTGKYYYNTMTEIMKNELGVSSLYP--CHRLDRLTSGILI 163

Query: 160 VART-RAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC---IANWLLKKSHIGGDYVH 214
           + +T RAAA++ T+  +   IQK Y + V G  P     C   I N   K+    G    
Sbjct: 164 IGKTPRAAAKYQTQ-LKQNSIQKTYIARVDGEFPMGNIVCSDKIVNIDCKRGKENG---- 218

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +  E   N+    +       Q    ++  P TGRTHQ+R+H  ++G PI  D  Y  
Sbjct: 219 ITEPKEALTNFQRLAYST--SLNQSI--VKCSPKTGRTHQIRIHLRNLGHPIANDPLYGF 274

Query: 275 N 275
           N
Sbjct: 275 N 275


>gi|19921090|ref|NP_609411.1| RluA-2, isoform A [Drosophila melanogaster]
 gi|16198203|gb|AAL13915.1| LD40728p [Drosophila melanogaster]
 gi|22946170|gb|AAF52961.2| RluA-2, isoform A [Drosophila melanogaster]
 gi|220946196|gb|ACL85641.1| RluA-2-PA [synthetic construct]
 gi|220955960|gb|ACL90523.1| RluA-2-PA [synthetic construct]
          Length = 547

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 62/196 (31%), Positives = 86/196 (43%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L ++              ++Y D  I V NKPA I V       ++   F+ +  
Sbjct: 195 KHNDLLANVVHRHEVPVTSQPIKIVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILAK- 253

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    E
Sbjct: 254 EHNLKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIRTRQVQKEYVCRVEGRFPDGIVE 313

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   + FK I         L  +P TGR HQ+R
Sbjct: 314 CNEKIDVVSYKIG-----VCKVSPKGKDCKTT-FKRIGEVGSDSIVL-CKPLTGRMHQIR 366

Query: 257 VHALHMGCPIVGDHKY 272
           VH   +G PI  D  Y
Sbjct: 367 VHLQFLGYPISNDPLY 382


>gi|183220733|ref|YP_001838729.1| putative ribosomal large subunit pseudouridine synthase [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
 gi|189910834|ref|YP_001962389.1| pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167775510|gb|ABZ93811.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167779155|gb|ABZ97453.1| Putative ribosomal large subunit pseudouridine synthase [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 320

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 61/258 (23%), Positives = 112/258 (43%), Gaps = 34/258 (13%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
            +    +P+ +      ++  G++ V       +  +  G+V+   P+       IKE +
Sbjct: 19  EYLTGKFPYHSLEEWTFLVEEGRITVSGNLASMHKPLLDGEVIEYNPIPGR----IKEPE 74

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +  +   L +  DFL               KP  + +       Y     L S++++K  
Sbjct: 75  VDTNYSILKETEDFL------------FVEKPGNLPMHPAG--RYRTKTLL-SFLETKYP 119

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           K    HRLD+ETSGI++ A++  + + L + F  R + K Y+++V G  K  KE   +  
Sbjct: 120 KIIPVHRLDRETSGIVIFAKSEESRKWLQKKFETRVVYKEYFAIVLG--KFTKEQKLD-- 175

Query: 203 LKKSHIGGDYVHVVKQNE-------KGANYAISHF-KVIDCFAQKFCWLEMQPHTGRTHQ 254
                IG D   V+++           +    +HF  ++    +K   + ++P TGR HQ
Sbjct: 176 ---GFIGRDIHSVIRKKMIFSPVEFPDSKSCATHFVPILYNEDKKISLVLVKPITGRIHQ 232

Query: 255 LRVHALHMGCPIVGDHKY 272
           +R   L++G PI+GD  Y
Sbjct: 233 IRASLLYLGFPIIGDKMY 250


>gi|320109289|ref|YP_004184879.1| RluA family pseudouridine synthase [Terriglobus saanensis SP1PR4]
 gi|319927810|gb|ADV84885.1| pseudouridine synthase, RluA family [Terriglobus saanensis SP1PR4]
          Length = 298

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 78/316 (24%), Positives = 129/316 (40%), Gaps = 37/316 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Y    ++   +    L     + YPH +    Q+ L +G+V V+      +  + SGQ++
Sbjct: 6   YAYTTIIGGKDHGQTLLSHLASLYPHSSPQAWQQNLNNGEVTVNGVIATGSEALTSGQML 65

Query: 66  --RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
               PP I                 +  +H +     +L +D  +   NK          
Sbjct: 66  VWNRPPWIEP---------------DAPQHFE-----VLLDDPHLLAVNK---PGGLPTL 102

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                ++  L   V  +       HRL + T+GI++ A+T  AA +LT  +   RI+KIY
Sbjct: 103 PGGGFMENTLLRLVQKQSPDANPVHRLGRATTGIVLFAKTPQAASNLTADWNTSRIEKIY 162

Query: 184 WSLVWGIP-KNKKECIAN-WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            +L  GI  ++  E +    L+    IG     V   N  G   + S  KVI        
Sbjct: 163 RALAQGIADRDAYEILTPIGLVPHPRIGS----VWAANPDG-KPSKSLAKVISRTTDATT 217

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQNKLYLHARYMDLP 298
           + E+   +GR HQ+R+H   +G P+VGD  Y       +     P     +LHA+++   
Sbjct: 218 F-EVSLGSGRPHQIRIHLASIGHPLVGDPLYGPTGQPLEDLPGLPGDGGYFLHAQFLKFH 276

Query: 299 HP-EGGRLQITAPLPA 313
           HP  G R+ + A LP+
Sbjct: 277 HPITGERIHLEAALPS 292


>gi|241764053|ref|ZP_04762092.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241366658|gb|EER61130.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 198

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 52/164 (31%), Positives = 83/164 (50%), Gaps = 17/164 (10%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLDQ TSG++++AR   A + L+ +F  R++ K Y ++V G+          W    
Sbjct: 35  IVHRLDQATSGLVLMARHIEAQRRLSHAFADRQVHKRYQAVVQGL----LSVDGAWNEID 90

Query: 206 SHIGGDY----VHVVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHA 259
             I  D+    + V+  +      +++ ++ +  D  AQ    +E++P TGRTHQLRVH 
Sbjct: 91  LPIAADWERRPLRVI--DHALGKPSLTRWRALAQDAEAQT-TRIELEPVTGRTHQLRVHL 147

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             MG PI+GD    A +    T  +  +L LHA  +   HP  G
Sbjct: 148 AAMGHPILGD----ALYADAATQAMAPRLLLHASALRFTHPVHG 187


>gi|229553304|ref|ZP_04442029.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus rhamnosus
           LMS2-1]
 gi|258540084|ref|YP_003174583.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
 gi|229313390|gb|EEN79363.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus rhamnosus
           LMS2-1]
 gi|257151760|emb|CAR90732.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
          Length = 289

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 74/264 (28%), Positives = 116/264 (43%), Gaps = 41/264 (15%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           N  IQ+GQ VR    I     +  E+  LD               +LYED    + NKPA
Sbjct: 47  NTAIQAGQTVRF--AIPTTMTVTPEKASLD---------------VLYEDQNWLIINKPA 89

Query: 116 GISVQGGSGIAYH-----IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
            ++   G    +H     I  +L+    ++ Q P +  RLD++T G LV+A     AQ  
Sbjct: 90  HLTSVPGPHDPHHSLLNRIVWYLQQQKVTEPQ-PAIITRLDRDTVG-LVLAAKHPYAQGR 147

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-VVKQNEKGANYAISH 229
            +      ++K Y ++V G   +  E I   +     +G D +H +V +N + A   I+ 
Sbjct: 148 FDQAHHATLKKEYLAVVAGHLSHATETIEAPI----GLGPDGIHRMVTENGQSA---ITK 200

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           ++V+          E+Q  TGRTHQ+RVH   +G P++GD  Y         SP+ +   
Sbjct: 201 YQVLKEAVNTLV--EVQLLTGRTHQIRVHFASLGHPLIGDSLYGQ------ASPLIDHQA 252

Query: 290 LHARYMDLPHP-EGGRLQITAPLP 312
           L A  +    P    R+Q   P+P
Sbjct: 253 LQATRLSFVDPFSEKRIQADLPIP 276


>gi|188527152|ref|YP_001909839.1| hypothetical protein HPSH_01795 [Helicobacter pylori Shi470]
 gi|188143392|gb|ACD47809.1| hypothetical protein HPSH_01795 [Helicobacter pylori Shi470]
          Length = 293

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 107/238 (44%), Gaps = 32/238 (13%)

Query: 41  LRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           L+  Q  +DK+R+K N + ++  Q+++    + +L H    +KI                
Sbjct: 28  LKEAQRHLDKQRLKHNQQAVRKSQMIQ---GVVSLIHFKPNEKI---------------Q 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  I      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  ALVFETKDFGVFDKPPQIYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D     K +
Sbjct: 128 AGKTLQSAKDLKTLFMQKKVKKTYLALAHGL-VDKNIVIDKPILTPQNIQKDLRIRSKIS 186

Query: 220 EKGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             G         +S+   +D        L++ P TGRTHQ+R+H   +G  IVG+  Y
Sbjct: 187 PLGKPSTTLVEPLSYNAFLD-----ISLLKITPLTGRTHQIRLHLSSVGHRIVGEGLY 239


>gi|307195434|gb|EFN77320.1| RNA pseudouridylate synthase domain-containing protein 2
           [Harpegnathos saltator]
          Length = 357

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 53/169 (31%), Positives = 82/169 (48%), Gaps = 9/169 (5%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  + V NKPA I V       ++   F+ +  +   +  R  HRLD+ TSGIL+  RT 
Sbjct: 2   DEDVVVVNKPASIPVHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDRLTSGILLFGRTP 60

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
             A+ +    R R++ K Y   V G  P+ +  C     +    IG     V K ++KG 
Sbjct: 61  KKARQMEHQIRNRQVHKQYVCRVEGEFPEEEVICSEPIEVVSYKIG-----VCKVSDKGK 115

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +  ++ FK +  +  K   +  +P TGR HQ+RVH  ++G P+V D  Y
Sbjct: 116 D-CVTRFKRLS-YNGKSSVVLCKPQTGRMHQIRVHLQYLGYPVVNDPLY 162


>gi|262394573|ref|YP_003286427.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. Ex25]
 gi|262338167|gb|ACY51962.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. Ex25]
          Length = 230

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 58/192 (30%), Positives = 90/192 (46%), Gaps = 17/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL +
Sbjct: 4   ILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAKQ---SGDEQLYLIHRLDKMTSGILFL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   AA  L+++F  R+++K Y ++    PK K+  +   + +        V     N 
Sbjct: 61  GRNAKAASALSQAFADRQVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV-----NS 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K  N A++ F  +     +  +L  +PHTG+THQ+RV    +G  IVGD  Y A   GN 
Sbjct: 116 KN-NPAVTQFFSLAAEPGERLFL-CKPHTGKTHQIRVALKSVGSGIVGDPIYNA---GNE 170

Query: 281 TSPIQNKLYLHA 292
                ++ YLHA
Sbjct: 171 A----DRGYLHA 178


>gi|332298456|ref|YP_004440378.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332181559|gb|AEE17247.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 478

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 66/244 (27%), Positives = 105/244 (43%), Gaps = 43/244 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++Y D    V NKPAG+    G G      A H     + + D   Q     HRLD +TS
Sbjct: 245 IVYRDEHCIVLNKPAGLLSVPGRGEDKQDCAVHR--LRRLYPDCIAQPS--VHRLDMDTS 300

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--------KECIANWLLKKS- 206
           G+LV+A T  A + L+  F    + K Y +L+ G P+          ++ +  +   +S 
Sbjct: 301 GLLVLALTADAHRCLSRQFMEGTVHKEYEALLRGKPRGAAAQSVCADRDGLCGFRAAESG 360

Query: 207 HIGGDYVHVVKQNEKG------ANYAISHFKVID---CFAQK-----FCWLEMQPHTGRT 252
            I   +   V+   +           ++ +++I    C  +         +   P TGRT
Sbjct: 361 RIELPFRLDVENRPRQVFDPVYGKTGVTEWRLIGFERCGKETSSDGVLTRVRFTPLTGRT 420

Query: 253 HQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
           HQLR+H++H   +G PI GD  Y    +G        +L LHA  +   HP  G R+  T
Sbjct: 421 HQLRLHSMHPNGLGAPIRGDRLYGTRLEG-------ERLALHAALLSFTHPVSGERMTFT 473

Query: 309 APLP 312
           + +P
Sbjct: 474 SAVP 477


>gi|288904349|ref|YP_003429570.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus gallolyticus UCN34]
 gi|288731074|emb|CBI12620.1| putative ribosomal large subunit pseudouridine synthase, RluD
           subfamily [Streptococcus gallolyticus UCN34]
          Length = 286

 Score = 67.0 bits (162), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 55/199 (27%), Positives = 85/199 (42%), Gaps = 16/199 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG  + A
Sbjct: 84  LYQDEHLIIVNKPEGMKTHGNEPNEIALLNHVSAYV---GQTCYVIHRLDMETSGAAMFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       +      + I + YW+LV G  + K +   + + +  H     V V ++N +
Sbjct: 141 KNPFVLPIINRLLENKDIAREYWALVQGKFEPKHQVFQDKIGRDRHDRRKRV-VDRKNGQ 199

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            A   +   KV        C L+    TGRTHQ+RVH       I+GD  Y        +
Sbjct: 200 TALTIVDRLKVFPNGTLVKCRLK----TGRTHQIRVHLSAHNHAIIGDPLY--------S 247

Query: 282 SPIQNKLYLHARYMDLPHP 300
                +L LHA  +   HP
Sbjct: 248 KIPAKRLMLHAHKLSFTHP 266


>gi|195578239|ref|XP_002078973.1| GD23709 [Drosophila simulans]
 gi|194190982|gb|EDX04558.1| GD23709 [Drosophila simulans]
          Length = 541

 Score = 67.0 bits (162), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 61/196 (31%), Positives = 87/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L ++              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 195 KHNDLLANVVHRHEVPVTSQPIKIVFMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 253

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    E
Sbjct: 254 EHNLKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIRTRQVQKEYVCRVEGRFPDGIVE 313

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   + FK I         L  +P TGR HQ+R
Sbjct: 314 CNEKIDVVSYKIG-----VCKVSPKGKDCKTT-FKRIGEVGSDSIVL-CKPLTGRMHQIR 366

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI  D  Y
Sbjct: 367 VHLQYLGYPISNDPLY 382


>gi|225848540|ref|YP_002728703.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225644519|gb|ACN99569.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 271

 Score = 67.0 bits (162), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 54/216 (25%), Positives = 95/216 (43%), Gaps = 30/216 (13%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  I   NKP  + S +    + + +         SK  K +  HRLD+ETSGIL+
Sbjct: 72  IIYEDEYIVAVNKPPTLLSDREKDSVEFILRE------KSKNPKIKAIHRLDKETSGILL 125

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+     +   E +  + + K+Y ++                   SH   ++ H+    
Sbjct: 126 LAKDYKVFERFKELWEDKIVFKLYLAI-------------------SHNEANFNHLTVNL 166

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKG 278
                 A+SH K++      F + +++  TGR HQ+R H   +  PIVGD  Y     + 
Sbjct: 167 PVDDKPAVSHIKLVKK-GNGFSYFQVRIETGRKHQIRKHLSSIRHPIVGDKIYGVKKLEH 225

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           N    + N+  LH+  +   HP +  ++ + A +P 
Sbjct: 226 NLLKRV-NRQMLHSYKLSFFHPYKNKKIDLVAEIPT 260


>gi|148240644|ref|YP_001226031.1| pseudouridylate synthase [Synechococcus sp. WH 7803]
 gi|147849183|emb|CAK24734.1| Pseudouridylate synthase [Synechococcus sp. WH 7803]
          Length = 314

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 73/297 (24%), Positives = 125/297 (42%), Gaps = 39/297 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPP 69
           +E  E    L     + Y H +    Q  +R+G++ ++   ++ +  + S  VV  R PP
Sbjct: 19  IERSESGQMLTAVMASRYGHSSRDVWQSRIRTGELLLNGTCLQNDVPVGSKDVVQWRRPP 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +        E  I D            +  ++Y+D  + V NKP+G+ V  G G   H 
Sbjct: 79  WL--------EPAIPD------------RWSVVYDDGDVLVINKPSGLPVMPGGGFLQHT 118

Query: 130 DGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIYWS 185
              L    S +    Q P+  HRL + TSG+ V AR       L+  FR     +K Y  
Sbjct: 119 LSALLMETSRLAGSSQAPKPVHRLGRFTSGLQVCARRPQTRARLSRQFRPEGGCRKTY-- 176

Query: 186 LVW-----GIPKNKKECIANWLLKKSHIGGDYVHVVKQNE----KGANYAISHFKVIDCF 236
           L W     G+  ++   +   ++++SH    +V     ++    +    A S  +++   
Sbjct: 177 LAWAQPMAGLRADQPLVVTTDVVERSHPLLGWVWGPDPSDGEPLRRRLQARSELRLLRRC 236

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHA 292
           +Q    +E+   TGR HQ+R+H   +G P++GD  Y    + N  + P      LHA
Sbjct: 237 SQGDL-VEVAISTGRPHQIRIHLAQLGSPLLGDPLYLPQQRINTAAVPGDGGYRLHA 292


>gi|297285307|ref|XP_001096202.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein 3
           isoform 3 [Macaca mulatta]
          Length = 351

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 57/201 (28%), Positives = 93/201 (46%), Gaps = 18/201 (8%)

Query: 89  NLTKHS--DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QK 143
           NL++    D L++ ++     +   NKP G+ V G SG    +   L     S G   Q+
Sbjct: 69  NLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKSG-ELTLLSVLPELSQSLGLGEQE 127

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHL----TESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            ++     +E+SG+++++     A  L    T S R +R    Y ++  GIP   +  I 
Sbjct: 128 LQVVRASGKESSGLVLLSSCPQTASRLQKFFTHSQRAQRPTATYCAVTNGIPTASEGKI- 186

Query: 200 NWLLKKSHIGGDYVHV-VKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
              LK  HI G  + V VK   +     G    +SHF+V+         +++QP T  + 
Sbjct: 187 QAALKLEHIDGVNLTVPVKAPSRKDILQGVKKTLSHFRVV-ATGSGCALVQLQPLTVFSS 245

Query: 254 QLRVHALHMGCPIVGDHKYCA 274
           QL+VH +   CP++GDH Y A
Sbjct: 246 QLQVHMVLQLCPVLGDHTYSA 266


>gi|291517265|emb|CBK70881.1| Pseudouridylate synthases, 23S RNA-specific [Bifidobacterium longum
           subsp. longum F8]
          Length = 244

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 94/218 (43%), Gaps = 36/218 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LYED +I V +KP  ++     G+ Y     ++  +  +  +P +T  HRLD+ T+G+L
Sbjct: 3   VLYEDERIIVVDKPHFLATMP-RGMWYRQTALIR--LRERLGEPDITPAHRLDRMTAGVL 59

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---------KECIANWLLKKSHIG 209
           V  R  A        F+ R+  K+Y  L    P ++         +      LL++SHI 
Sbjct: 60  VFVRDPACRGAYQMLFQNRQTVKVYECLAPCRPISRPRFGTIMQVEPPRPFPLLRRSHIT 119

Query: 210 GDYVHVVKQNEKGANYAISHFKVID-CFAQ------------------KFCWLEMQPHTG 250
            ++  +    E G   A +  +  D CF                      C   + P TG
Sbjct: 120 KEHGTMAAFEEPGLANAETLIERGDLCFPPADGRWREAPEGGPHPGNHPICRYTLHPRTG 179

Query: 251 RTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQ 285
           +THQLRVH   +G PIVGD  Y         +F+ P+Q
Sbjct: 180 KTHQLRVHMNSLGLPIVGDDFYPRIQTRPYDDFSQPLQ 217


>gi|51246961|ref|YP_066845.1| ribosomal large subunit pseudouridine synthase A [Desulfotalea
           psychrophila LSv54]
 gi|50877998|emb|CAG37838.1| probable ribosomal large subunit pseudouridine synthase A
           [Desulfotalea psychrophila LSv54]
          Length = 211

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 56/205 (27%), Positives = 99/205 (48%), Gaps = 18/205 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++Y D  + V  KP G+ SV G G   +  +   L++ +     +P + HRLD  TSG++
Sbjct: 6   IIYRDDHLVVVIKPGGLLSVPGRGPENSDCVSSRLQAKIPEMITQPAV-HRLDMYTSGLM 64

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A ++   + L+  F+ +++ K Y +L+ G  +     ++  +     +  D   +   
Sbjct: 65  VYAVSKEIHRALSIQFQEQQVDKKYTALLEGCLQE----VSGEIRLPFRVDLDNRPIQIL 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
           + +     I+ ++ +D        +E  P TGRTHQLRVHA H   +G PI+GD  Y + 
Sbjct: 121 DYQHGKMGITLWRKMDE-KNGITRVEFTPMTGRTHQLRVHAAHAKGLGIPIIGDSFYGSG 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP 300
             G       +++ LHA  +   HP
Sbjct: 180 RDG-------DEMMLHAHQLSFTHP 197


>gi|312133201|ref|YP_004000540.1| rlua2 [Bifidobacterium longum subsp. longum BBMN68]
 gi|322690629|ref|YP_004220199.1| ribosomal pseudouridine synthase [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|311772402|gb|ADQ01890.1| RluA2 [Bifidobacterium longum subsp. longum BBMN68]
 gi|320455485|dbj|BAJ66107.1| putative ribosomal pseudouridine synthase [Bifidobacterium longum
           subsp. longum JCM 1217]
          Length = 254

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 94/218 (43%), Gaps = 36/218 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LYED +I V +KP  ++     G+ Y     ++  +  +  +P +T  HRLD+ T+G+L
Sbjct: 13  VLYEDERIIVVDKPHFLATMP-RGMWYRQTALIR--LRERLGEPDITPAHRLDRMTAGVL 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---------KECIANWLLKKSHIG 209
           V  R  A        F+ R+  K+Y  L    P ++         +      LL++SHI 
Sbjct: 70  VFVRDPACRGAYQMLFQNRQAVKVYECLAPCRPISRPRFGTIMQVEPPRPFPLLRRSHIT 129

Query: 210 GDYVHVVKQNEKGANYAISHFKVID-CFAQ------------------KFCWLEMQPHTG 250
            ++  +    E G   A +  +  D CF                      C   + P TG
Sbjct: 130 KEHGTMAAFEEPGLANAETLIERGDLCFPPADGRWREAPEGGPHPGNHPICRYTLHPRTG 189

Query: 251 RTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQ 285
           +THQLRVH   +G PIVGD  Y         +F+ P+Q
Sbjct: 190 KTHQLRVHMNSLGLPIVGDDFYPRIQTRPYDDFSQPLQ 227


>gi|195118758|ref|XP_002003903.1| GI20532 [Drosophila mojavensis]
 gi|193914478|gb|EDW13345.1| GI20532 [Drosophila mojavensis]
          Length = 798

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 58/196 (29%), Positives = 91/196 (46%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 415 KHNDLLANIVHRHEVPVTCQPITIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 473

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V GI P    E
Sbjct: 474 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGIFPDGVVE 533

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K ++KG +   +  K+      K   +  +P TGR HQ+R
Sbjct: 534 CKEPIEVVSYKIG-----VCKVSQKGKDCTTTFQKLSQ--NGKTSVVLCKPLTGRMHQIR 586

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI+ D  Y
Sbjct: 587 VHLQYLGFPILNDPLY 602


>gi|167624902|ref|YP_001675196.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167354924|gb|ABZ77537.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 279

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 101/222 (45%), Gaps = 30/222 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  +   +KPAG+ V   S +A     F ++   D  G      HRLD+ TSGIL+
Sbjct: 27  VLFEDDDVVAIHKPAGLLVHR-SYLARRERFFAMQLTRDKVGCHVFPVHRLDRPTSGILL 85

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKS--HIGGDYVHVV 216
            A++   A  L   F    + K Y ++V G   N  E    ++ LK+    +G   V   
Sbjct: 86  FAKSSEMANALCGQFADHTVDKEYLAIVRG---NMHEAGTLDYALKEELDELGDKDV--- 139

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               K A  A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI
Sbjct: 140 -DPNKAAQDAVTSYQPLLNSEIPFSSGRYATSRYALVQLSPHTGRKHQLRRHMAHLRHPI 198

Query: 267 VGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +GD  +        F+ +F     N+L+L A+ +   HP  G
Sbjct: 199 LGDTTHGDGKQNKFFRSHFGI---NRLWLIAKKLSFNHPRTG 237


>gi|254229878|ref|ZP_04923282.1| pseudouridine synthase Rlu family protein [Vibrio sp. Ex25]
 gi|151937582|gb|EDN56436.1| pseudouridine synthase Rlu family protein [Vibrio sp. Ex25]
          Length = 243

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 59/199 (29%), Positives = 92/199 (46%), Gaps = 17/199 (8%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           + F    +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ 
Sbjct: 10  ASFFMFDILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAKQ---SGDEQLYLIHRLDKM 66

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGIL + R   AA  L+++F  R+++K Y ++    PK K+  +   + +        V
Sbjct: 67  TSGILFLGRNAKAASALSQAFADRQVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV 126

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                N K  N A++ F  +     +  +L  +PHTG+THQ+RV    +G  IVGD  Y 
Sbjct: 127 -----NSKN-NPAVTQFFSLAAEPGERLFL-CKPHTGKTHQIRVALKSVGSGIVGDPIYN 179

Query: 274 ANFKGNFTSPIQNKLYLHA 292
           A   GN      ++ YLHA
Sbjct: 180 A---GNEA----DRGYLHA 191


>gi|300215069|gb|ADJ79485.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 296

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 70/272 (25%), Positives = 116/272 (42%), Gaps = 40/272 (14%)

Query: 16  EENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++ M L ++ KN    H    +L+K   +G+V VD K+      +  G++  I P   + 
Sbjct: 10  DKKMTLKKFLKNKGVSHRTLSSLKK--GNGKVLVDGKKKSLFIEVGKGKITLILPPEKSD 67

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSG--------I 125
            ++   ++ LD               ++YEDS   V +KP  +S V G S         +
Sbjct: 68  ENVKMSKEPLD---------------IIYEDSNWLVVDKPPLLSSVPGPSNRTDTLVNRV 112

Query: 126 AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            +H+      W   SK   P +  RLD++TSG+++VA+ R A   + +      I K Y 
Sbjct: 113 KFHL------WQQKSKDLVPHVITRLDRDTSGLVLVAKHRFAQGLINKQVEEHSIDKRYL 166

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +++ GI   K   I   L  + +  G  V            A + + V +    K   +E
Sbjct: 167 AVIEGIITEKHGIIDKPLGPRENGIGQMV------TDTGKIAKTEYWVREYLGDKATLVE 220

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + HTGRTHQ+R H   +   +VGD  Y    
Sbjct: 221 CKLHTGRTHQIRAHFSSINHALVGDELYGGRL 252


>gi|296131380|ref|YP_003638630.1| pseudouridine synthase [Cellulomonas flavigena DSM 20109]
 gi|296023195|gb|ADG76431.1| pseudouridine synthase [Cellulomonas flavigena DSM 20109]
          Length = 304

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 59/196 (30%), Positives = 91/196 (46%), Gaps = 25/196 (12%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D ++ V +KP  +S +  G  I   +   L++ +D     P   HRLD+ TSG+L+
Sbjct: 95  VLHRDERLVVVDKPPFLSTIPRGRHIVQSVVVRLRAELDLPELSP--LHRLDRATSGVLL 152

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI----GGDY 212
           +A   R RA  Q    +F  R + K Y +L     ++  E  A+    ++HI    G  +
Sbjct: 153 LATEQRWRAPYQ---TAFERRAVDKTYRALAPL--RDDLELPADV---RNHIRKVRGTAH 204

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             VV      A   +   + +D          + P TGRTHQLR+H   +G PIVGD  Y
Sbjct: 205 AEVVPGAPVNAETHVELEREVDGLG----VYRLTPRTGRTHQLRLHLCGLGIPIVGDRLY 260

Query: 273 CANFK---GNFTSPIQ 285
                    +FT P+Q
Sbjct: 261 PVERDLDLDDFTDPLQ 276


>gi|213692876|ref|YP_002323462.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis ATCC
           15697]
 gi|213524337|gb|ACJ53084.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis ATCC
           15697]
          Length = 244

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 100/236 (42%), Gaps = 40/236 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LYED +I V +KP  ++     G+ Y     ++  +  +  +P +T  HRLD+ T+G+L
Sbjct: 3   VLYEDERIIVVDKPHFLATMP-RGMWYRQTALIR--LRERLGEPDITPAHRLDRMTAGVL 59

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKSHIG 209
           V  R  A        F+ R+  K+Y  L          +G            LL++SHI 
Sbjct: 60  VFVRDPACRGAYQMLFQNRQAVKVYECLAPCRPIVRPRYGTVTRIDPPRPFPLLRRSHIV 119

Query: 210 GDYVHVVKQNEKG---ANYAISHFKVIDCF----------------AQKFCWLEMQPHTG 250
            +   +      G   A   I   + +  F                A   C   ++PHTG
Sbjct: 120 KERGVLAAFEMPGLVNAETLIERGEPVSLFPGVKPCMPMAGGPRPSAVPVCRYTLRPHTG 179

Query: 251 RTHQLRVHALHMGCPIVGDHKY-C--ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +THQLRVH   +G PIVGD  Y C  A    +F+ P+Q    L AR +    P  G
Sbjct: 180 KTHQLRVHMNALGLPIVGDDFYPCIQARRYDDFSQPLQ----LVARVLRFTDPVTG 231


>gi|6321608|ref|NP_011685.1| Pus6p [Saccharomyces cerevisiae S288c]
 gi|1723726|sp|P53294|PUS6_YEAST RecName: Full=Pseudouridylate synthase 6; AltName:
           Full=Pseudouridine synthase 6; AltName: Full=Uracil
           hydrolyase; AltName: Full=tRNA pseudouridine 31
           synthase; Short=PSI31 synthase
 gi|1323298|emb|CAA97195.1| unnamed protein product [Saccharomyces cerevisiae]
 gi|285812363|tpg|DAA08263.1| TPA: Pus6p [Saccharomyces cerevisiae S288c]
          Length = 404

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 52/189 (27%), Positives = 87/189 (46%), Gaps = 18/189 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP+GI V   +G  Y     +   +   G      +RLD+ TSG+L++
Sbjct: 121 IVFEDESILVIDKPSGIPVHP-TGQFYQ--NTITELLKLHGVDALPCYRLDKITSGLLIL 177

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG------IPKNKKECIANWLLKKSHIGGDYVH 214
           A+   +A  + +S R R + KIY + V G      +  + +          S +  +   
Sbjct: 178 AKNSQSAGEIQKSIRSRDMIKIYLARVKGRFPHSELILDNENAAETTFEDTSKVTVEMTP 237

Query: 215 VVKQNEK--------GANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +   + K         +  AI+ F  I  F+      +  +P TGRTHQ+R+H   +G P
Sbjct: 238 IYSIDPKRQFPVGLSTSKDAITKFYPIRYFSHADETVVACKPITGRTHQIRIHLARLGHP 297

Query: 266 IVGDHKYCA 274
           IV D  YC+
Sbjct: 298 IVNDSVYCS 306


>gi|315928439|gb|EFV07751.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni DFVF1099]
          Length = 281

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 103/205 (50%), Gaps = 19/205 (9%)

Query: 77  IIKEQK--ILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DG 131
           I+ E+K  IL+  V L  + +  K + +++E+    +  K +GI S   G    Y + D 
Sbjct: 25  ILVEEKNEILNGLVELIVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDE 84

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
               W    G++  + HRLD+ETSG+++VA+ + A   L   F  + +QK Y +L  G  
Sbjct: 85  IWHLW----GKEACVAHRLDKETSGLILVAKNKKAQIDLKTLFEKKLVQKEYLALANG-- 138

Query: 192 KNKKECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQP 247
               +   N+++ K+ ++  +Y  V    Q  K    AI+ F++++ F +     L  +P
Sbjct: 139 ----KIEENFIIDKAINLAKNYDDVKTRMQICKEGKQAITEFEILEYFPKINATLLLCKP 194

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
            TGR HQ+RVH  +    I+GD  Y
Sbjct: 195 LTGRQHQIRVHLHYKNHTILGDPLY 219


>gi|255067175|ref|ZP_05319030.1| pseudouridine synthase Rlu family protein [Neisseria sicca ATCC
           29256]
 gi|255048543|gb|EET44007.1| pseudouridine synthase Rlu family protein [Neisseria sicca ATCC
           29256]
          Length = 207

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 93/218 (42%), Gaps = 33/218 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-------IAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +L+        NKP G+SV    G       +A  + G  + W         L HRLD+ 
Sbjct: 4   ILFRHPDFVAVNKPCGVSVHQEEGEVSLTQTLAAQL-GLEQVW---------LLHRLDKL 53

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+L+ A  + +A  L + F  + ++K Y +L    P  K+  I    ++KS  G    
Sbjct: 54  TSGVLLFALNQQSASELAQQFAAKTMRKTYLALATDKPSKKQGWIKG-DMEKSRRG---- 108

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              K      N A++ F              + PHTG+THQLRV    +G PI+GD  Y 
Sbjct: 109 -AWKLTRGMENPAVTEFGS-HSLEPGLRLFVLHPHTGKTHQLRVAMKSLGSPILGDTLYG 166

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                       ++++LHA  +   + +G   +I A L
Sbjct: 167 GK--------PASRMFLHAWKIKFDY-QGQTFEIVASL 195


>gi|229823324|ref|ZP_04449393.1| hypothetical protein GCWU000282_00622 [Catonella morbi ATCC 51271]
 gi|229787099|gb|EEP23213.1| hypothetical protein GCWU000282_00622 [Catonella morbi ATCC 51271]
          Length = 300

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 107/222 (48%), Gaps = 18/222 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQG----GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED  + + NKP  + S+       S +A  + G+ +   D   Q   +  RLD++T+
Sbjct: 81  VIYEDRDLLIVNKPTDVVSIPSKRIPDSAMANRVKGYYQRQ-DYADQVIHIVTRLDRQTT 139

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++++A+ R A   L +  +  +++K Y ++       K +   + ++ +     +   +
Sbjct: 140 GLMLIAKHRLAHAMLDKQVQGGQVEKYYLAI-----STKADWPDHGVIDRPIARTEDSII 194

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++  +    A++ + +   FA     L+++ HTGRTHQ+RVH    G  +VGD  Y   
Sbjct: 195 TRRVHESGQRAVTEYWLKHRFADS-SLLKLRLHTGRTHQIRVHMQDAGGVLVGDDLYG-- 251

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
             G     I+ +  LH   + L  P  G RL ++APLP  M 
Sbjct: 252 --GPHLEAIRRQA-LHCGELRLTQPFTGQRLVLSAPLPEDMA 290


>gi|160892611|ref|ZP_02073401.1| hypothetical protein CLOL250_00141 [Clostridium sp. L2-50]
 gi|156865652|gb|EDO59083.1| hypothetical protein CLOL250_00141 [Clostridium sp. L2-50]
          Length = 328

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 46/181 (25%), Positives = 84/181 (46%), Gaps = 11/181 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLD 151
           ++Y D  I + +KPAG+  Q  S   Y  +  L  ++   G          +P + +RLD
Sbjct: 91  IIYSDENILIADKPAGVLSQKASKDDYSFNEALIDYLLDSGHITTEELRTYRPSVCNRLD 150

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG+++   +   +Q L+   R   + K Y++LV G    K +  +   L+K +    
Sbjct: 151 RNTSGLILCGVSLTGSQELSRIIREHLLHKYYYTLVRGRLTQKLD--STCYLQKDNAKNK 208

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                +  E+G +  I            +  ++++  TG++HQ+R    H+G P+VGD K
Sbjct: 209 VRISDRPWEQGKSEEIHSIFYPVKKNDDYTLVKVELITGKSHQIRAQLKHLGYPVVGDTK 268

Query: 272 Y 272
           Y
Sbjct: 269 Y 269


>gi|167004717|ref|ZP_02270475.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
          Length = 281

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 57/201 (28%), Positives = 101/201 (50%), Gaps = 17/201 (8%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKS 135
           ++ KIL+  V L  + +  K + +++E+    +  K +GI S   G    Y + D     
Sbjct: 29  EKNKILNGLVELIVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W    G++  + HRLD+ETSG++++A+ + A   L   F  + +QK Y +L  G      
Sbjct: 89  W----GKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALAHG------ 138

Query: 196 ECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           +   N+++ K+ ++  +Y  V    Q  K    AI+ F++++ F +     L  +P TGR
Sbjct: 139 KIEENFIVDKAINLTKNYDDVKTRMQICKEGKQAITEFEILEYFPKINATLLLCKPLTGR 198

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH  +    I+GD  Y
Sbjct: 199 QHQIRVHLHYKNHTILGDPLY 219


>gi|302380682|ref|ZP_07269147.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
 gi|302311625|gb|EFK93641.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
          Length = 307

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 75/302 (24%), Positives = 136/302 (45%), Gaps = 44/302 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSG-QVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++++  +N RLD +           N+ ++ RS  Q  +D K+V  N +IQ         
Sbjct: 6   LIDDSNQNARLDVFL---------ANVVELSRSEIQKLIDDKKVLVNGKIQKKNYK---- 52

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI------SVQGGS 123
            +N  + I  + +  D ++   K        ++YED  + + NK   +      ++   +
Sbjct: 53  -LNLNDKITLDYEKPDKTIKAQKQD----LDIVYEDDYLAIINKDKDVIVHPTETIYSDT 107

Query: 124 GIAYHIDGFLKSWVDSKGQKPR-LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            + Y +  F K+  D  G   R + HRLD++T+G++++A+       L E  +   I K 
Sbjct: 108 LVNYLMYNF-KNLSDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEIIKT 166

Query: 183 YWSLVWGIPKNKKEC--IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           Y  +V G      EC  I  ++   S    D   ++  +E     +IS ++ +D +   +
Sbjct: 167 YLCIVHG---KIDECGTIEEYM---SRNPKDRKKMMVSDE--GKLSISQYERLD-YNDDY 217

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPH 299
             +++Q  TGRTHQ+RVH  ++  PI+GD  Y     K  F S +     LHA  +   H
Sbjct: 218 SLVKVQIKTGRTHQIRVHMNYIHHPILGDKLYGLKKEKILFDSQV-----LHAYNLQFIH 272

Query: 300 PE 301
           P+
Sbjct: 273 PQ 274


>gi|257461315|ref|ZP_05626412.1| pseudouridine synthase [Campylobacter gracilis RM3268]
 gi|257441343|gb|EEV16489.1| pseudouridine synthase [Campylobacter gracilis RM3268]
          Length = 249

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 58/233 (24%), Positives = 103/233 (44%), Gaps = 39/233 (16%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  ++YED  +   NKP                 F+ S    K  K  L +RLD+ETSG+
Sbjct: 56  KPAIIYEDENVLAVNKPP----------------FMSSENLEKIYKFGLLNRLDKETSGV 99

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++ +     +     F+  R++K Y ++V GI   + +     L  K+  G      + 
Sbjct: 100 VLLYKNEEFREAAIAEFKNLRVKKSYIAIVKGIVSEEMKFGEPILTIKTRSGA--FSKIS 157

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            N K A   +    V    + K   ++++  TGRTHQ+RVH  + G  ++GD KY  +  
Sbjct: 158 PNGKSAFSEVYPLMV----SGKKSLVKVRIETGRTHQIRVHLANAGFGVIGDEKYAKSR- 212

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
                    +++LH+   ++       L+  APL     K+++  GF+  ++L
Sbjct: 213 -------AKRMFLHSYETEILG-----LKFKAPLD----KSFNEFGFEIPKDL 249


>gi|255657995|ref|ZP_05403404.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
 gi|260850197|gb|EEX70204.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
          Length = 296

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 68/277 (24%), Positives = 119/277 (42%), Gaps = 30/277 (10%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF----LKSILLYEDS 106
           KR+K +   + G ++      NA    ++   I+  + ++ + SD     L   + YED 
Sbjct: 33  KRIKHSGTFRVGGIL-----CNAARTEVRTGDII--TFDIVRPSDIEPEDLPLDIRYEDD 85

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDG-FLKSWVDSKGQKPRL--THRLDQETSGILVVART 163
            + + NKPAG  V   +  A+   G  +  W  + G+       HRLD+ TSG++++A+ 
Sbjct: 86  YLLIVNKPAGQLVHPTTKEAHGTLGNAVLYWYKAHGEHHAYHPVHRLDRNTSGLVLIAKV 145

Query: 164 RAAAQHLTESFRMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV-KQNEK 221
                 LT      ++  + Y +L+ G      E      L  + I      ++ ++   
Sbjct: 146 PQVQYKLTPRHGEGKLFHREYLALIEG------ELTPPEGLIDAPIARALPSIILRKVSP 199

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               A +H+  +     K   + +   TGRTHQ+RVH  H+G P++GD  Y  N      
Sbjct: 200 DGQTARTHYDTVQTDG-KLSLIHLVLDTGRTHQIRVHLAHLGHPLLGDDLYGGNLARI-- 256

Query: 282 SPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
                +  LHA  +   HP  G  + +  PLP+ M +
Sbjct: 257 ----KRQALHAARLHFRHPMTGAEIDVQVPLPSDMAQ 289


>gi|303234008|ref|ZP_07320657.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
 gi|302494933|gb|EFL54690.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
          Length = 307

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 75/302 (24%), Positives = 136/302 (45%), Gaps = 44/302 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSG-QVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++++  +N RLD +           N+ ++ RS  Q  +D K+V  N +IQ         
Sbjct: 6   LIDDSNQNARLDVFL---------ANVVELSRSEIQKLIDDKKVLVNGKIQKKNYK---- 52

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI------SVQGGS 123
            +N  + I  + +  D ++   K        ++YED  + + NK   +      ++   +
Sbjct: 53  -LNLNDKITLDYEKPDKTIKAQKQD----LDIVYEDDYLAIINKDKDVIVHPTETIYSDT 107

Query: 124 GIAYHIDGFLKSWVDSKGQKPR-LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            + Y +  F K+  D  G   R + HRLD++T+G++++A+       L E  +   I K 
Sbjct: 108 LVNYLMYNF-KNLSDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEIIKT 166

Query: 183 YWSLVWGIPKNKKEC--IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           Y  +V G      EC  I  ++   S    D   ++  +E     +IS ++ +D +   +
Sbjct: 167 YLCIVHG---KIDECGTIEEYM---SRNPKDRKKMMVSDE--GKLSISQYERLD-YNDDY 217

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPH 299
             +++Q  TGRTHQ+RVH  ++  PI+GD  Y     K  F S +     LHA  +   H
Sbjct: 218 SLVKVQIKTGRTHQIRVHMNYIHHPILGDKLYGLKKEKILFDSQV-----LHAYNLQFIH 272

Query: 300 PE 301
           P+
Sbjct: 273 PQ 274


>gi|86153961|ref|ZP_01072163.1| ribosomal large subunit pseudouridylate synthase D [Campylobacter
           jejuni subsp. jejuni HB93-13]
 gi|85842499|gb|EAQ59712.1| ribosomal large subunit pseudouridylate synthase D [Campylobacter
           jejuni subsp. jejuni HB93-13]
 gi|284925325|gb|ADC27677.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni IA3902]
 gi|315057463|gb|ADT71792.1| Putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni S3]
          Length = 281

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 103/205 (50%), Gaps = 19/205 (9%)

Query: 77  IIKEQK--ILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DG 131
           I+ E+K  IL+  V L  + +  K + +++E+    +  K +GI S   G    Y + D 
Sbjct: 25  ILVEEKNEILNGLVELIVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDE 84

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
               W    G++  + HRLD+ETSG+++VA+ + A   L   F  + +QK Y +L  G  
Sbjct: 85  IWHLW----GKEACVAHRLDKETSGLILVAKNKKAQIDLKALFEKKLVQKEYLALANG-- 138

Query: 192 KNKKECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQP 247
               +   N+++ K+ ++  +Y  V    Q  K    AI+ F++++ F +     L  +P
Sbjct: 139 ----KIEENFIIDKAINLAKNYDDVKTRMQICKEGKQAITEFEILEYFPKINATLLLCKP 194

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
            TGR HQ+RVH  +    I+GD  Y
Sbjct: 195 LTGRQHQIRVHLHYKNHTILGDPLY 219


>gi|239622355|ref|ZP_04665386.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis CCUG
           52486]
 gi|239514352|gb|EEQ54219.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis CCUG
           52486]
          Length = 261

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 61/218 (27%), Positives = 93/218 (42%), Gaps = 36/218 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LYED +I V +KP  ++     G+ Y     ++  +  +  +P +T  HRLD+ T+G+L
Sbjct: 20  VLYEDERIIVVDKPHFLATMP-RGMWYRQTALIR--LRERLGEPDITPAHRLDRMTAGVL 76

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKSHIG 209
           V  R  A        F+ R+  KIY  L          +G     +      LL++SHI 
Sbjct: 77  VFVRDSACRGAYQMLFQNRQAVKIYECLAPCRPISGPRFGTIMQVEPPRPFPLLRRSHIT 136

Query: 210 GDYVHVVKQNEKGANYAISHFKVID-CFA------------------QKFCWLEMQPHTG 250
            ++  +    E G   A +  +  D CF                      C   + P TG
Sbjct: 137 KEHGTMAAFEEPGLANAETLIERGDLCFPPAGGRWREAPEGGPHPGNHPICRYTLHPRTG 196

Query: 251 RTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQ 285
           +THQLRVH   +G PIVGD  Y         +F+ P+Q
Sbjct: 197 KTHQLRVHMNSLGLPIVGDDFYPRIQTRPYDDFSQPLQ 234


>gi|317129591|ref|YP_004095873.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
 gi|315474539|gb|ADU31142.1| pseudouridine synthase, RluA family [Bacillus cellulosilyticus DSM
           2522]
          Length = 298

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 68/282 (24%), Positives = 126/282 (44%), Gaps = 48/282 (17%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           GQ+ V+ K       ++ G V+ +      ++  IK  KI              K  +++
Sbjct: 42  GQITVNGKEENVRYTLRLGDVIEVIFPKEKVSRSIKPYKI--------------KLHIIF 87

Query: 104 EDSKIYVFNKPA----------GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           ED  + + NKP           G     G+ +AY+I+  + S   +         RLD++
Sbjct: 88  EDEHVIIINKPPHLPTIPTRNEGEPSLAGAILAYYIENGIPSTFHA-------VSRLDRD 140

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++VA+ R       +  +   I++ Y +LV GI  +    I   + +K+       
Sbjct: 141 TSGLVMVAKHRYMHDLCVKLQKSYEIKRSYVALVEGILSDDYNTIDLPISRKT------T 194

Query: 214 HVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            ++++  NE G + AI+H++V+  ++     L++   TGRTHQ+RVH   +G P++GD  
Sbjct: 195 SIIEREVNEFGKS-AITHYEVLKRYSGA-TLLQLTLETGRTHQIRVHMSAIGHPLLGDTL 252

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y  + +        ++  LH+  +   HP   R      P+P
Sbjct: 253 YGGDVR------YIDRQALHSHQLSFFHPINKREYTFHCPIP 288


>gi|296453676|ref|YP_003660819.1| pseudouridine synthase [Bifidobacterium longum subsp. longum
           JDM301]
 gi|322688643|ref|YP_004208377.1| ribosomal pseudouridine synthase [Bifidobacterium longum subsp.
           infantis 157F]
 gi|296183107|gb|ADG99988.1| pseudouridine synthase [Bifidobacterium longum subsp. longum
           JDM301]
 gi|320459979|dbj|BAJ70599.1| putative ribosomal pseudouridine synthase [Bifidobacterium longum
           subsp. infantis 157F]
          Length = 254

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 61/218 (27%), Positives = 93/218 (42%), Gaps = 36/218 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LYED +I V +KP  ++     G+ Y     ++  +  +  +P +T  HRLD+ T+G+L
Sbjct: 13  VLYEDERIIVVDKPHFLATMP-RGMWYRQTALIR--LRERLGEPDITPAHRLDRMTAGVL 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKSHIG 209
           V  R  A        F+ R+  KIY  L          +G     +      LL++SHI 
Sbjct: 70  VFVRDSACRGAYQMLFQNRQAVKIYECLAPCRPISGPRFGTIMQVEPPRPFPLLRRSHIT 129

Query: 210 GDYVHVVKQNEKGANYAISHFKVID-CFA------------------QKFCWLEMQPHTG 250
            ++  +    E G   A +  +  D CF                      C   + P TG
Sbjct: 130 KEHGTMAAFEEPGLANAETLIERGDLCFPPAGGRWREAPEGGPHPGNHPICRYTLHPRTG 189

Query: 251 RTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQ 285
           +THQLRVH   +G PIVGD  Y         +F+ P+Q
Sbjct: 190 KTHQLRVHMNSLGLPIVGDDFYPRIQTRPYDDFSQPLQ 227


>gi|320459050|dbj|BAJ69671.1| putative ribosomal pseudouridine synthase [Bifidobacterium longum
           subsp. infantis ATCC 15697]
          Length = 254

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 100/236 (42%), Gaps = 40/236 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LYED +I V +KP  ++     G+ Y     ++  +  +  +P +T  HRLD+ T+G+L
Sbjct: 13  VLYEDERIIVVDKPHFLATMP-RGMWYRQTALIR--LRERLGEPDITPAHRLDRMTAGVL 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKSHIG 209
           V  R  A        F+ R+  K+Y  L          +G            LL++SHI 
Sbjct: 70  VFVRDPACRGAYQMLFQNRQAVKVYECLAPCRPIVRPRYGTVTRIDPPRPFPLLRRSHIV 129

Query: 210 GDYVHVVKQNEKG---ANYAISHFKVIDCF----------------AQKFCWLEMQPHTG 250
            +   +      G   A   I   + +  F                A   C   ++PHTG
Sbjct: 130 KERGVLAAFEMPGLVNAETLIERGEPVSLFPGVKPCMPMAGGPRPSAVPVCRYTLRPHTG 189

Query: 251 RTHQLRVHALHMGCPIVGDHKY-CANFK--GNFTSPIQNKLYLHARYMDLPHPEGG 303
           +THQLRVH   +G PIVGD  Y C   +   +F+ P+Q    L AR +    P  G
Sbjct: 190 KTHQLRVHMNALGLPIVGDDFYPCIQARRYDDFSQPLQ----LVARVLRFTDPVTG 241


>gi|281209708|gb|EFA83876.1| putative fatty acid synthase [Polysphondylium pallidum PN500]
          Length = 3329

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 51/186 (27%), Positives = 82/186 (44%), Gaps = 15/186 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+  K  V NKP  I + G     + +  +++S       + R  +R+D  TSGI++ 
Sbjct: 17  IIYKSDKYVVVNKPYDICIDGDDR-EFTVKKYIESCYQEVKGEVRFVNRIDYATSGIVLT 75

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHV-- 215
           A T++ A    + F+ R  +K Y +LVWG      +  E     +     I  D   V  
Sbjct: 76  ATTKSDANVAGQLFQNRATKKHYLALVWGHLHPLYDTNEPDTTEITVDKPIADDKTDVNA 135

Query: 216 ------VKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                 V   +     + +H +V+       +    + + PHTGR HQLRVH   +G  I
Sbjct: 136 FKMCIGVAGTDNPGRPSTTHVRVLQHGYYNGRPVSKVHLIPHTGRRHQLRVHLDTLGHVI 195

Query: 267 VGDHKY 272
           VGD  Y
Sbjct: 196 VGDETY 201


>gi|121613293|ref|YP_999742.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|218561715|ref|YP_002343494.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|112359421|emb|CAL34203.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|121504235|gb|EAQ72031.2| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
          Length = 300

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 57/201 (28%), Positives = 101/201 (50%), Gaps = 17/201 (8%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKS 135
           ++ KIL+  V L  + +  K + +++E+    +  K +GI S   G    Y + D     
Sbjct: 48  EKNKILNGLVELIVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL 107

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W    G++  + HRLD+ETSG++++A+ + A   L   F  + +QK Y +L  G      
Sbjct: 108 W----GKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALAHG------ 157

Query: 196 ECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           +   N+++ K+ ++  +Y  V    Q  K    AI+ F++++ F +     L  +P TGR
Sbjct: 158 KIEENFIVDKAINLTKNYDDVKTRMQICKEGKQAITEFEILEYFPKINATLLLCKPLTGR 217

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH  +    I+GD  Y
Sbjct: 218 QHQIRVHLHYKNHTILGDPLY 238


>gi|42561291|ref|NP_975742.1| RNA pseudouridylate synthase [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
 gi|42492789|emb|CAE77384.1| RNA pseudouridylate synthase [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
 gi|301320799|gb|ADK69442.1| pseudouridine synthase, RluA family [Mycoplasma mycoides subsp.
           mycoides SC str. Gladysdale]
          Length = 302

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 68/282 (24%), Positives = 128/282 (45%), Gaps = 49/282 (17%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV  +++N  L ++ K  +       + K +R+  ++++ KR+   N +   +V  I  V
Sbjct: 5   VVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRISDKNYLL--KVNDIIEV 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            ++   II++Q    S+VNL          ++YED+ I + NKP  + +     +   +D
Sbjct: 63  YDSNKPIIRDQFNYISNVNLD---------IIYEDNNILIVNKPNNLEMHSTYNLC--LD 111

Query: 131 GFLKSW-VDSKGQKPRL--------THRLDQETSGILVVARTRAAAQHLTESFRMR-RIQ 180
             +KS+ VD K     L         HRLD+ TSG+++ A+ + ++  LT +F+++ +I 
Sbjct: 112 DMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSTILTNAFKLKDQIN 171

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y++L          C  +W L +      Y++        +N   +HF +      K+
Sbjct: 172 KYYYALT--------SC--DWNLDEFLQVNGYINY------DSNIKRAHFSLDQKNNYKY 215

Query: 241 CWLE----------MQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           C  E          ++  TG+ HQ+R        PI+ D +Y
Sbjct: 216 CQTEFKLINKNLILVKLITGKKHQIRSVLSFYNHPILNDFRY 257


>gi|170729099|ref|YP_001763125.1| pseudouridine synthase Rlu family protein [Shewanella woodyi ATCC
           51908]
 gi|169814446|gb|ACA89030.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           woodyi ATCC 51908]
          Length = 224

 Score = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 47/145 (32%), Positives = 66/145 (45%), Gaps = 15/145 (10%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG+L+ A++  AA   T  F   R+QK Y +L  G PK K+  I   + K   
Sbjct: 47  HRLDTLTSGLLLFAKSSQAAAEFTRLFTEHRVQKYYLALAKGKPKKKQGSIIGDMAKSRR 106

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  + K      N A + F      A+      ++P +G+THQLRV    +G PI+
Sbjct: 107 ------SMYKLMRTMDNPAKTQF-FSQSVAEGLRLYLLKPLSGKTHQLRVALASIGVPIL 159

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA 292
           GD  Y             ++ YLHA
Sbjct: 160 GDTLYGGE--------ESDRGYLHA 176


>gi|82750620|ref|YP_416361.1| RNA pseudoridylate synthase [Staphylococcus aureus RF122]
 gi|82656151|emb|CAI80562.1| probable RNA pseudoridylate synthase [Staphylococcus aureus RF122]
          Length = 284

 Score = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 59/192 (30%), Positives = 91/192 (47%), Gaps = 22/192 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           SVNL  ++  L+  +LYED+ I +  K   ++ Q  +    H    L   V    Q+   
Sbjct: 65  SVNLIPYARKLE--VLYEDAFIIIVTK---LNNQNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G         AN
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKVNLKKIYTCLVYGKTHTSGIIEAN 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  I      + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 176 IRRSKDSI------ITREVASDGKYAKTSYEVINQ-NDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKY 272
           H+G PIVGD  Y
Sbjct: 229 HIGHPIVGDSLY 240


>gi|323140403|ref|ZP_08075332.1| pseudouridine synthase, RluA family [Phascolarctobacterium sp. YIT
           12067]
 gi|322415088|gb|EFY05878.1| pseudouridine synthase, RluA family [Phascolarctobacterium sp. YIT
           12067]
          Length = 217

 Score = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 60/223 (26%), Positives = 109/223 (48%), Gaps = 20/223 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETS 155
           S+L YED  + + +KPAG+ V    S     +  ++K++ ++ G    +    RLD+ TS
Sbjct: 8   SMLAYEDDFLLIIDKPAGMLVHPTVSERGTTLYDYVKAYYEATGINAVIHPVSRLDRNTS 67

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+       L++    ++++K Y +L  G  +  +  I   + +K    G  +  
Sbjct: 68  GLVIFAKEPIVQHWLSQ----QQVEKEYLALACGRFETSEGIIEAPIARKE---GSIIER 120

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                +G  YA + ++V+  ++     L+++  TGRTHQ+RVH   +G P+V D+ Y   
Sbjct: 121 CVDYTRG-KYAKTAYEVLASYSNH-TLLKVRLFTGRTHQIRVHLASIGHPLVNDNLYG-- 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
                T   Q +  LHA  +   HP     L+IT  LP  ++K
Sbjct: 177 -----TPGPQARHALHAYRLAFKHPVSDVFLEITRSLPNDLLK 214


>gi|317008986|gb|ADU79566.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori India7]
          Length = 293

 Score = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 74/286 (25%), Positives = 123/286 (43%), Gaps = 43/286 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q VR   +I  +  +I  +             +  +  
Sbjct: 28  LKEAQRHLDKQRLKHNQ-----QAVRKSQMIQGVVRLIHFK------------PNEKQGK 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPTQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D     K + 
Sbjct: 129 GKTLQSAKDLKALFMQKKVKKTYLALTHGL-VDKSIIIDKPILTPQNIQKDLRIRSKISP 187

Query: 221 KGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
            G         +S+   +D        L++ P TGRTHQ+R+H   +G  IVG+  Y   
Sbjct: 188 LGKPSTTLVEPLSYNPFLDI-----SLLKITPLTGRTHQIRLHLSSVGHRIVGEGLYGVA 242

Query: 275 --------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                     K    +P+   L LHA  ++    +G   +IT+P+P
Sbjct: 243 DEEAREYLQLKRENHAPL---LMLHAFGLEFEF-KGAIYEITSPMP 284


>gi|261252619|ref|ZP_05945192.1| pseudouridylate synthase LSU rRNA-specific [Vibrio orientalis CIP
           102891]
 gi|260936010|gb|EEX91999.1| pseudouridylate synthase LSU rRNA-specific [Vibrio orientalis CIP
           102891]
          Length = 231

 Score = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 54/192 (28%), Positives = 91/192 (47%), Gaps = 17/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+  +   V +K   +SV    G    +    K   D+K     L HRLD+ TSGIL++
Sbjct: 4   ILHTHTDFIVISKHPNVSVHKDDGDTMLLQEVAKQTGDTK---LYLIHRLDKMTSGILLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R+  AA  L++ F  R ++K Y ++    PK K+  ++  + +       +  +  Q  
Sbjct: 61  GRSSTAASELSQMFAQRSVEKYYLAIGSKKPKKKQGLVSGDMERSRR--ASWKLLTSQT- 117

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F  +     +  +L  +PH+G+THQ+RV    +G  IVGD  Y A  +   
Sbjct: 118 ---NPAVTQFFSLAAEPGERLFL-CKPHSGKTHQIRVALKSVGSGIVGDPIYNAGSE--- 170

Query: 281 TSPIQNKLYLHA 292
                ++ YLHA
Sbjct: 171 ----SDRGYLHA 178


>gi|258508779|ref|YP_003171530.1| ribosomal large subunit 23S pseudouridine synthase D [Lactobacillus
           rhamnosus GG]
 gi|257148706|emb|CAR87679.1| Ribosomal large subunit 23S pseudouridine synthase D [Lactobacillus
           rhamnosus GG]
 gi|259650085|dbj|BAI42247.1| pseudouridylate synthase [Lactobacillus rhamnosus GG]
          Length = 278

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 100/219 (45%), Gaps = 32/219 (14%)

Query: 103 YEDSKIYVFNKPAGISVQ----GGSG-IAYHIDGFLKSWVDSKGQKPRL-THRLDQETSG 156
           YED  + + +K AG+       G +G +      +L  +       P L THRLD  TSG
Sbjct: 80  YEDDDLLIVDKTAGMKTHPNQPGETGTLMNQAAAYLAPF-------PALITHRLDMATSG 132

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +LV+A+   A   +      + + + Y ++V  GIP+  K  I      ++ IG D    
Sbjct: 133 LLVIAKNPLAQAIINRQLATKTMHRDYLAVVPRGIPE--KGTI------QAPIGHDPDDK 184

Query: 216 VKQNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            K+  +    +A++H+  I   A     +E+   TGRTHQ+RVH   +G PI+GD  Y A
Sbjct: 185 RKRMIRADGAFAVTHYHRIAETADT-ATIELNLETGRTHQIRVHLASIGFPIIGDPLYAA 243

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
                       ++ LHA  + L  P     L +T+P P
Sbjct: 244 TETA-------TRMQLHAFRVRLIRPLTIEPLTVTSPSP 275


>gi|90406918|ref|ZP_01215109.1| tRNA pseudouridine synthase A [Psychromonas sp. CNPT3]
 gi|90311960|gb|EAS40054.1| tRNA pseudouridine synthase A [Psychromonas sp. CNPT3]
          Length = 231

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 58/200 (29%), Positives = 92/200 (46%), Gaps = 23/200 (11%)

Query: 101 LLYEDSKIYVFNKPAGI---SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           L+YE+ +  V NK   I   S  G  G+    +  L   + S        HRLD+ TSG+
Sbjct: 10  LVYENEEFIVINKKENINFHSEDGEFGVVVAAEKALNIKLYS-------VHRLDKMTSGL 62

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A++   A HL+  F+  ++QK Y ++    PK K+  I   + K          + K
Sbjct: 63  LLLAKSSHIAAHLSALFKAHQVQKYYIAITDKKPKKKQGLIQGGMQKSRR------SMWK 116

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             +   N AI+ F      A K  ++ ++P TG+THQ+RV    +G  I GD  Y    K
Sbjct: 117 LTKTKENLAITQFFSFTLGAGKRLFI-IKPKTGKTHQIRVALKSIGSAICGDPLYGEKTK 175

Query: 278 GNFTSPIQNKLYLHARYMDL 297
                   ++ YLHA  ++ 
Sbjct: 176 Q------YDRGYLHAYQLEF 189


>gi|255026385|ref|ZP_05298371.1| hypothetical protein LmonocytFSL_08685 [Listeria monocytogenes FSL
           J2-003]
          Length = 180

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 90/169 (53%), Gaps = 15/169 (8%)

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ETSG++++A+ R A   L+   +   +++ Y + + G+   +K  I      ++ I
Sbjct: 17  RLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQAFISGVLVEQKGSI------EAPI 70

Query: 209 GGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           G   V ++++       YA ++++V+  + + F  + +Q  TGRTHQ+RVH  ++G P++
Sbjct: 71  GRKEVSIMERFVTPEGKYAKTNYEVLARY-RAFDHVAIQLETGRTHQIRVHFSYIGHPLI 129

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           GD  Y  +      + +  +  LH+ ++ L HP     +    PLPA M
Sbjct: 130 GDDMYGGD------TNLLKRQALHSCHLHLVHPLTEEYMAFDLPLPADM 172


>gi|221309004|ref|ZP_03590851.1| hypothetical protein Bsubs1_06426 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221313329|ref|ZP_03595134.1| hypothetical protein BsubsN3_06352 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221318253|ref|ZP_03599547.1| hypothetical protein BsubsJ_06296 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221322526|ref|ZP_03603820.1| hypothetical protein BsubsS_06402 [Bacillus subtilis subsp.
           subtilis str. SMY]
          Length = 299

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 67/258 (25%), Positives = 117/258 (45%), Gaps = 29/258 (11%)

Query: 73  ALNHIIKEQKIL-----DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QG 121
            + +++KE  +L     +  V+ T  ++ +   +LYED  + V NK   +S         
Sbjct: 51  TVKYVLKEGDLLIVKFPEEQVSETLLAEPVPLDILYEDEHVLVINKQPYVSSIPSREHPS 110

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GS     ID +  + V +      L  RLD++TSGI++VA+ R A   L+ + +   +++
Sbjct: 111 GSIANGIIDHYQTTGVRAT---VHLVTRLDRDTSGIMLVAKHRFAHSILSSAQKNGLVKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKF 240
            Y ++V G     +  +       + IG     ++++        A++HF V  C     
Sbjct: 168 RYAAVVHGRMAQMEGTV------DAPIGRHPDSIIERTVTPDGQKAVTHFYVT-CANDDM 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + +Q  TGRTHQ+RVH  ++G P+ GD  Y        T     +  LH+ ++   HP
Sbjct: 221 TSVALQLETGRTHQIRVHMSYLGHPLCGDTLYGG------TRQEIGRQALHSEHLSFIHP 274

Query: 301 -EGGRLQITAPLPAHMVK 317
                ++  APLP  M K
Sbjct: 275 LTQENMRFHAPLPQDMSK 292


>gi|304312830|ref|YP_003812428.1| Putative pseudouridine synthase A [gamma proteobacterium HdN1]
 gi|301798563|emb|CBL46793.1| Putative pseudouridine synthase A [gamma proteobacterium HdN1]
          Length = 301

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 53/192 (27%), Positives = 89/192 (46%), Gaps = 37/192 (19%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-LTHRLDQETSGIL 158
           I + ++ +  V+ KPAG+  QG S    H     +  + S  ++   L HR+D+ET+G++
Sbjct: 86  ICISDEGQYSVWYKPAGLLSQG-SEYGDHYSLLRQVELHSNPRREAFLVHRIDRETTGLI 144

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA    AA  L++ F  R ++K Y + V G              + + +G  +   + Q
Sbjct: 145 LVAHNERAAAKLSQLFSGRDVEKHYLACVSG--------------EIAEVGAKF--TIDQ 188

Query: 219 NEKGANYAISHFKVIDCFAQKF------------------CWLEMQPHTGRTHQLRVHAL 260
              G N A+SH  V+D  A                     C L+++  TGR HQ+R H  
Sbjct: 189 AIDGKN-AVSHITVLDSRAPASVQSEPSDRAQDLRKIDHGCLLDVRIETGRKHQIRKHLQ 247

Query: 261 HMGCPIVGDHKY 272
             G P++GDH++
Sbjct: 248 GAGFPVIGDHRF 259


>gi|260818260|ref|XP_002604301.1| hypothetical protein BRAFLDRAFT_88590 [Branchiostoma floridae]
 gi|229289627|gb|EEN60312.1| hypothetical protein BRAFLDRAFT_88590 [Branchiostoma floridae]
          Length = 369

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 58/224 (25%), Positives = 100/224 (44%), Gaps = 16/224 (7%)

Query: 50  KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK-I 108
           +K +K    + +G+ V+       L+ ++K+   + ++V+  +       + + E++  +
Sbjct: 53  EKAIKLGRLLLNGECVK-------LDTVLKDNDFMQNTVHRHEPPVVADPVQIVEETDDL 105

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V NKPA + V    G  ++   F+    +   Q     HRLD+ TSGIL+ A+      
Sbjct: 106 VVINKPASMPVHPCGGYRHNSVIFVLG-KEHGFQNLHPIHRLDRLTSGILIFAKNLETKH 164

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            L    + R ++K+Y + V G    K EC       K  +G     V +   +G     +
Sbjct: 165 RLDAQIKGREVKKVYLARVEGEFPEKAECDKPIFAVKHKLG-----VCRVCPEGKPAKTT 219

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +V   F  K   +   P TGR HQ+RVH  ++G PIV D  Y
Sbjct: 220 FERV--SFDGKSSVVRCFPETGRMHQIRVHLQYLGHPIVNDPLY 261


>gi|121997063|ref|YP_001001850.1| pseudouridine synthase [Halorhodospira halophila SL1]
 gi|121588468|gb|ABM61048.1| tRNA pseudouridine synthase C [Halorhodospira halophila SL1]
          Length = 249

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 99/237 (41%), Gaps = 36/237 (15%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK---PRLT 147
           T   D     +LY D ++    KPAG+ V   S I    D  L+   D  G     P   
Sbjct: 3   TADQDDRSLAILYRDERLIAVYKPAGLLVHR-SNIDRDRDVVLQRLRDQLGGHWVYP--V 59

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ T+G+LV      AA  L  +FR +RI K Y ++V G           W+     
Sbjct: 60  HRLDRATAGVLVFGLDPDAASVLAAAFREQRIGKRYQAVVRG-----------WVEAPGR 108

Query: 208 IGGDYVHVVKQNEKGANYAISHF----------KVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I        +        A++ +           V      +F  L + P TGR HQLR 
Sbjct: 109 IDRPLGAGRRGEGGAPQPAVTDYVPLAWTELPIPVSRYDTARFTRLALHPQTGRQHQLRR 168

Query: 258 HALHMGCPIVGD--HKYCAN---FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
           H   +  PI+GD  H   AN   F+ +F +    +L L A  + +PHP +GG +++ 
Sbjct: 169 HMKAISHPILGDTTHGDGANNRFFREHFGA---RRLLLVATELVVPHPADGGAVRLA 222


>gi|283956200|ref|ZP_06373685.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 1336]
 gi|283792354|gb|EFC31138.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 1336]
          Length = 300

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 57/201 (28%), Positives = 101/201 (50%), Gaps = 17/201 (8%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKS 135
           ++ KIL+  V L  + +  K + +++E+    +  K +GI S   G    Y + D     
Sbjct: 48  EKNKILNGLVELIVYKNNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL 107

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W    G++  + HRLD+ETSG++++A+ + A   L   F  + +QK Y +L  G      
Sbjct: 108 W----GKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALAHG------ 157

Query: 196 ECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           +   N+++ K+ ++  +Y  V    Q  K    AI+ F++++ F +     L  +P TGR
Sbjct: 158 KIEENFIVDKAINLTKNYDDVKTRMQICKEGKQAITEFEILEYFPKINATLLLCKPLTGR 217

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH  +    I+GD  Y
Sbjct: 218 QHQIRVHLHYKNHTILGDPLY 238


>gi|308173127|ref|YP_003919832.1| pseudouridylate synthase [Bacillus amyloliquefaciens DSM 7]
 gi|307605991|emb|CBI42362.1| pseudouridylate synthase [Bacillus amyloliquefaciens DSM 7]
 gi|328554031|gb|AEB24523.1| pseudouridylate synthase [Bacillus amyloliquefaciens TA208]
 gi|328911188|gb|AEB62784.1| pseudouridylate synthase [Bacillus amyloliquefaciens LL3]
          Length = 297

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 103/226 (45%), Gaps = 30/226 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV---------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  + V NK   +S             +G+  H   + K+ V S      L  RLD
Sbjct: 84  ILYEDDHVLVVNKQPYVSSIPSREHPSESIANGVISH---YRKNGVQSTVH---LVTRLD 137

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +++A+ R A   L+ + +   + + Y ++V G+   K+  +   + +K     D
Sbjct: 138 RDTSGAMLIAKHRLAHSLLSAAQKKGLVNRRYLAVVHGVILQKEGTVDAPIGRKP----D 193

Query: 212 YVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            + + +        A++HF+      A     L ++  TGRTHQ+RVH  ++G P+VGD 
Sbjct: 194 SI-IERMVTPEGQKAVTHFQAEKAGHASTLAALRLE--TGRTHQIRVHMSYLGHPLVGDT 250

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            Y    +G        +  LH+  +   HP  G  L   AP+P  M
Sbjct: 251 LYGGKNEG------IARQALHSELLSFVHPMTGETLVFHAPVPDDM 290


>gi|317012185|gb|ADU82793.1| pseudo uridine synthase D [Helicobacter pylori Lithuania75]
          Length = 298

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 76/300 (25%), Positives = 124/300 (41%), Gaps = 43/300 (14%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K     Q+ Q VR   +I  +  +I  +    +              
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVRKSQMIQGVVRLIYFKPNEKAQA------------ 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KPA +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPAQVYTHP-KGYFYH-ESLLDCIQSHLGKNAHPAHRLDYETSGLVLS 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  + + L   F  ++++K Y +L  G+   K   I   +L   +I  D     K + 
Sbjct: 129 GKTLQSVKDLKALFMQKKVKKTYLALAHGL-VEKSMKIDKPILTPQNIQKDLRIRSKISP 187

Query: 221 KGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
            G         +S+   +D        L++ P TGRTHQ+R+H   MG  IVG+  Y   
Sbjct: 188 LGKPSTTLVEPLSYNPFLDI-----SLLKITPLTGRTHQIRLHLSSMGHRIVGEGLYGVA 242

Query: 275 --------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                     K    +P+   L LHA  ++    +    +IT+P+P   +     L   Y
Sbjct: 243 DEEAREYLQLKRENHAPL---LMLHASSLEFEF-KKAFYEITSPMPERFMPFLKDLPLFY 298


>gi|117620216|ref|YP_857174.1| pseudouridine synthase Rlu family protein [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
 gi|117561623|gb|ABK38571.1| pseudouridine synthase Rlu family protein [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
          Length = 219

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 46/145 (31%), Positives = 73/145 (50%), Gaps = 15/145 (10%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG++++ART  A + L+ +F  R + K Y +L    PK K+  +   + K   
Sbjct: 52  HRLDKMTSGLVLLARTTEANRALSMAFAAREVSKQYLALSDRKPKKKQGWVKGDMQKGR- 110

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            GG ++     +    N AIS F  +    +      ++P TG+THQ+RV    +G PI+
Sbjct: 111 -GGSWMLTRTLD----NPAISWFDSVSV-REGLRLYRIKPRTGKTHQIRVALKSVGAPIL 164

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA 292
           GD +Y             ++ YLHA
Sbjct: 165 GDARYGGT--------AADRGYLHA 181


>gi|115375687|ref|ZP_01462942.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|310821153|ref|YP_003953511.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115367335|gb|EAU66315.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|309394225|gb|ADO71684.1| Pseudouridine synthase, RluA family [Stigmatella aurantiaca
           DW4/3-1]
          Length = 298

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 59/220 (26%), Positives = 99/220 (45%), Gaps = 11/220 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+Y D  I   +KP G+    G G   +    L   V  +  +    HRL + TSG+++ 
Sbjct: 84  LVYADEAILAVDKPGGLPTMPGGGFLVNT---LLHVVRERFPEVSPLHRLGRGTSGLVLF 140

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           ART  AA  L+ ++R   ++K Y +L   +       I   + +  H G   + +   + 
Sbjct: 141 ARTHDAAAKLSRAWREHEVEKRYRALSSHVASQDAYDITAPIGEAVHPGRGLLSMALPSG 200

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K +    S  +V+   A    + E+   TGR+ Q+R+H   +G P+ GD  Y        
Sbjct: 201 KASR---SLARVLQRRAASTLF-EVDIQTGRSQQIRIHLAFIGHPLEGDPVYTVGGVPRA 256

Query: 281 TSP--IQNKLY-LHARYMDLPHP-EGGRLQITAPLPAHMV 316
             P  + +  Y LHA  +   HP  G RL++ A LP+ ++
Sbjct: 257 EQPGLLGDTGYLLHAERLCFVHPLTGERLELHATLPSELL 296


>gi|57236934|ref|YP_178049.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
 gi|57165738|gb|AAW34517.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
          Length = 300

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 103/205 (50%), Gaps = 19/205 (9%)

Query: 77  IIKEQK--ILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DG 131
           I+ E+K  IL+  V L  + +  K + +++E+    +  K +GI S   G    Y + D 
Sbjct: 44  ILVEEKNEILNGLVELIVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDE 103

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
               W    G++  + HRLD+ETSG+++VA+ + A   L   F  + +QK Y +L  G  
Sbjct: 104 IWHLW----GKEACVAHRLDKETSGLILVAKNKKAQIDLKALFEKKLVQKEYLALANG-- 157

Query: 192 KNKKECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQP 247
               +   N+++ K+ ++  +Y  V    Q  K    AI+ F++++ F +     L  +P
Sbjct: 158 ----KIEENFIIDKAINLAKNYDDVKTRMQICKEGKQAITEFEILEYFPKINATLLLCKP 213

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
            TGR HQ+RVH  +    I+GD  Y
Sbjct: 214 LTGRQHQIRVHLHYKNHTILGDPLY 238


>gi|195384878|ref|XP_002051139.1| GJ13872 [Drosophila virilis]
 gi|194147596|gb|EDW63294.1| GJ13872 [Drosophila virilis]
          Length = 807

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 58/196 (29%), Positives = 91/196 (46%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 420 KHNDLLANIVHRHEVPVTCQPITIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 478

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V GI P    E
Sbjct: 479 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGIFPDGVVE 538

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K ++KG +   +  K+      K   +  +P TGR HQ+R
Sbjct: 539 CKEPIEVVSYKIG-----VCKVSQKGKDCTTTFQKLSQ--NGKTSVVLCKPLTGRMHQIR 591

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI+ D  Y
Sbjct: 592 VHLQYLGFPILNDPLY 607


>gi|257457321|ref|ZP_05622492.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
 gi|257445243|gb|EEV20315.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
          Length = 231

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 90/225 (40%), Gaps = 53/225 (23%)

Query: 111 FNKPAGISVQGGSGIAYHIDGF---------LKSWVDSKGQ--------KPRLTHRLDQE 153
            NKPAGI V G S I   +              +  D+ G+        KP   HRLD++
Sbjct: 1   MNKPAGIPVHGSSSIDTLLSAASVLTPSAEPPAAVPDTDGRVHLHSLSFKPGPLHRLDKD 60

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDY 212
           T+G+L  +RT A AQ  ++  R + + K Y  +V G +P                     
Sbjct: 61  TTGVLCFSRTLAGAQWFSQCLREKTVGKYYLGVVRGAMPAQP------------------ 102

Query: 213 VHVVKQNEKGAN----YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +  Q+E GA     Y++ + K ID     F  +     TG+ HQ+R H   +G P+ G
Sbjct: 103 --ITAQDENGATMTQCYSVEYCKDIDASLMLFRLI-----TGKKHQIRKHTESVGHPLAG 155

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLP--HPEGGRLQITAPL 311
           D KY     G    P      LHA  +  P   P      I APL
Sbjct: 156 DRKY----HGGNPLPGCKHYLLHAWRLYFPALRPADIPASIEAPL 196


>gi|91225984|ref|ZP_01260911.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           12G01]
 gi|91189425|gb|EAS75702.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           12G01]
          Length = 230

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 58/192 (30%), Positives = 91/192 (47%), Gaps = 17/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL++
Sbjct: 4   ILHTHPDFLIINKHPYVSVHKDDGDTMLLQEVAKQ---SGDEQLYLIHRLDKMTSGILLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   AA  L+++F  R+++K Y ++    PK K+  +   + +        V     N 
Sbjct: 61  GRNAKAASALSQAFADRQVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV-----NS 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K  N A++ F  +     +  +L  +PHTG+THQ+RV    +G  IVGD  Y A   GN 
Sbjct: 116 KN-NPAVTQFFSLAAEPGERLFL-CKPHTGKTHQIRVALKSVGSGIVGDPIYNA---GNE 170

Query: 281 TSPIQNKLYLHA 292
                ++ YLHA
Sbjct: 171 A----DRGYLHA 178


>gi|157786596|ref|NP_001099244.1| RNA pseudouridylate synthase domain-containing protein 1 [Rattus
           norvegicus]
 gi|149052128|gb|EDM03945.1| RNA pseudouridylate synthase domain containing 1 (predicted),
           isoform CRA_a [Rattus norvegicus]
 gi|171847409|gb|AAI61966.1| Rpusd1 protein [Rattus norvegicus]
          Length = 306

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 50/159 (31%), Positives = 76/159 (47%), Gaps = 8/159 (5%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA    + F+ RR+ K Y +LV G  +  +  I   + +
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYKCFKERRVTKAYLALVRGHVQESQVTINYAIGR 120

Query: 205 KSHIGGDYVHVVKQNEKGANY--AISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            S  G  +   ++      N   +++   V++           + ++P TGRTHQLRVH 
Sbjct: 121 NSTEGRTHTMCIEGTHGCENPKPSLTELLVLEHGLYSGDPVSKVLLKPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             +G PIVGD  Y          P   ++ LHA Y+ +P
Sbjct: 181 SALGHPIVGDLTY-GQADDQEDQPF--RMMLHAFYLRIP 216


>gi|226724701|sp|Q0DST9|PUS5_ORYSJ RecName: Full=RNA pseudourine synthase 5; AltName: Full=RNA
           pseudouridylate synthase 5; AltName: Full=RNA-uridine
           isomerase 5
          Length = 397

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 81/319 (25%), Positives = 135/319 (42%), Gaps = 64/319 (20%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL--LYEDSKIYVFNKPA 115
           RI+ GQ+     V    + I++E   L     L     F   +L  LYED  +   NKP+
Sbjct: 72  RIRDGQITVDGEVATDPDMILREGSKLVYH-RLPWQEPFAPHLLDVLYEDDDMIALNKPS 130

Query: 116 GISV------QGGSGIAY-------HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           G+ V      Q  + +A            F     D++   P   HRL + TSG+L+ A+
Sbjct: 131 GLQVLPKGLFQQRTVLAQLQLKDWKMPSSFCSKRKDAQSH-PVPVHRLGRGTSGLLLCAK 189

Query: 163 TRAAAQHLTESF-----------------RMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           T+ A   L   F                 + R+I K Y +LV GI +N +  I   +   
Sbjct: 190 TKLAKAQLAAYFAEGATNAGKSRDETDICKARKISKFYRALVTGILENDEVMITQPIGLV 249

Query: 206 SHIG-GDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMG 263
            + G  + ++    + K A   +S  +V++         ++++ H+GR HQ+R+H  ++G
Sbjct: 250 RYPGVAEGLYAACSSGKPA---MSKVRVLERLKIHNHTLIQVEIHSGRPHQIRIHLAYIG 306

Query: 264 CPIVGDHKYCAN------------------FKGNFTSPIQN-----KLYLHARYMDLPHP 300
            P+V D  Y                     + G +  P+Q        +LHA ++ L HP
Sbjct: 307 HPLVDDPLYGIGGQPKFDEPEPTSTADSFAYDGGYERPLQPVPGDCGYHLHAHWLVLCHP 366

Query: 301 EGGRL-QITAPLPAHMVKT 318
               + +ITAPLP H+++T
Sbjct: 367 TTNEMIKITAPLP-HILQT 384


>gi|194467273|ref|ZP_03073260.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
 gi|194454309|gb|EDX43206.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
          Length = 306

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 110/221 (49%), Gaps = 26/221 (11%)

Query: 101 LLYEDSKIYVFNKPAG----ISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LYE+  + V NKP G     +  G +G   + + G+L   V+S+     + HR+D +TS
Sbjct: 90  VLYENRDLLVVNKPRGQKTHPNYHGETGTLMNDVAGYL---VNSENNA-YMVHRIDLQTS 145

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++VA+       L       +I + Y ++V G  K  +    +W + ++ +     H+
Sbjct: 146 GAVIVAKNPIVVPILNRLISDGQIHRQYLAVVEG--KMAQSGKFDWAIGRNPVNP---HL 200

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            + N + A  A++++  +    ++   ++++  TGRTHQLRVH  + G PIVGD  Y   
Sbjct: 201 HQVNGQNAQPALTYYDTLASNRER-SLVKLRLVTGRTHQLRVHLAYSGHPIVGDPLY--- 256

Query: 276 FKGNFTSPIQNK-LYLHARYMDLPHPEGGR-LQITAPLPAH 314
                 +P+  + + LH     L  P   + L I+APLP++
Sbjct: 257 ------NPLSTEGMLLHGVAQKLILPFVMKSLNISAPLPSY 291


>gi|223038326|ref|ZP_03608620.1| RNA pseudouridine synthase family [Campylobacter rectus RM3267]
 gi|222880183|gb|EEF15270.1| RNA pseudouridine synthase family [Campylobacter rectus RM3267]
          Length = 303

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 63/229 (27%), Positives = 104/229 (45%), Gaps = 24/229 (10%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++E  K  VF+KP G+ S   G    Y ++  + S     G++  + HRLD ETSG++VV
Sbjct: 72  IFECEKFAVFDKPNGVLSHPNGRHCEYSLNDEIWSLY---GREASVAHRLDCETSGLIVV 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            + +    +L + F  R++ K Y +L  G         AN  L   +   D V +  +  
Sbjct: 129 GKDKNTVVNLKKLFENRQVYKSYVALAQGKISENLRIEANMDLANDY---DDVKMRMRIC 185

Query: 221 KGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +    A++    I+ FA      ++  P TGR HQ+R+H  H+   I+G+  Y     G 
Sbjct: 186 EDGKSAVTEISPIEYFADIDATLVQAVPLTGRQHQIRLHLFHVEHKILGEPLY-----GL 240

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHMVKTWDSLGFKYD 327
             S I+       + +D    E  R+  T AP    ++   D + FK+D
Sbjct: 241 MRSQIE-------KILDKEMSEAERILTTGAP---RLLLHADEIRFKFD 279


>gi|257455430|ref|ZP_05620665.1| tRNA pseudouridine synthase C [Enhydrobacter aerosaccus SK60]
 gi|257447392|gb|EEV22400.1| tRNA pseudouridine synthase C [Enhydrobacter aerosaccus SK60]
          Length = 266

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 65/260 (25%), Positives = 107/260 (41%), Gaps = 36/260 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D      NKPAG+ V       +  +  +++  D   Q     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEHCVAVNKPAGMLVHRSWLDRHETEFVMQTLRDQLAQYVYPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKK--SHIGGDYVHVV 216
           A +  +A+ L E F  R++QK Y ++V G      +   + ++ L +    IG       
Sbjct: 64  ALSSESARQLCEQFENRQVQKSYLAIVRGYLTVNAQTSGLIDYPLTQILDKIGDKPSLQA 123

Query: 217 KQNEKGANY------------------AISHFKVIDCFAQ-----------KFCWLEMQP 247
            Q  K ++                   A +H++ +    Q           +F    + P
Sbjct: 124 LQQRKVSSTDMFAEALSSPAELTLLQPAQTHWQCLATTEQPFQARARYPTSRFSLARLTP 183

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPH-PEGGR 304
            TGR HQLR H  H+  PI+GD  Y  + +          ++L LHA  +      +  R
Sbjct: 184 ITGRKHQLRRHMKHVFHPIIGDTSYGDHHQNRAIRQHIGVHRLMLHAHTLAFNRLTDNRR 243

Query: 305 LQITAPLPAHMVKTWDSLGF 324
           + ITAP+    +      GF
Sbjct: 244 VDITAPVDTDWLTMCAQFGF 263


>gi|227834247|ref|YP_002835954.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
 gi|227455263|gb|ACP34016.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
          Length = 353

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 78/189 (41%), Gaps = 16/189 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +L+ED  + V +KP  ++       A HI       +  K     L+  HRLD+ TSGIL
Sbjct: 129 ILFEDEHLLVVDKPPFMATMPR---ARHITETATVRLRRKTGNNELSPAHRLDRLTSGIL 185

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V  + R+        F  RR+ K Y ++    P         W  +     G+    + +
Sbjct: 186 VFTKDRSVRGAYQTLFAERRVTKTYEAIA---PLADVSPGTVWRSRMEKTPGELQGRIVE 242

Query: 219 NEKGANYAISHFKVIDCFA--------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            E  A   ++  + ID            +     ++P TG+THQLR+H L  G PI+GD 
Sbjct: 243 GEVNAITEVAAVEPIDKAPYESIHGSLPELAKYTLKPQTGKTHQLRLHMLQAGVPIIGDP 302

Query: 271 KYCANFKGN 279
            Y   F   
Sbjct: 303 IYPVIFPAE 311


>gi|16078227|ref|NP_389044.1| pseudouridylate synthase [Bacillus subtilis subsp. subtilis str.
           168]
 gi|3915487|sp|O31613|YJBO_BACSU RecName: Full=Uncharacterized RNA pseudouridine synthase yjbO;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2633516|emb|CAB13019.1| pseudouridylate synthase [Bacillus subtilis subsp. subtilis str.
           168]
          Length = 283

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 68/258 (26%), Positives = 118/258 (45%), Gaps = 29/258 (11%)

Query: 73  ALNHIIKEQKIL-----DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------QG 121
            + +++KE  +L     +  V+ T  ++ +   +LYED  + V NK   +S         
Sbjct: 35  TVKYVLKEGDLLIVKFPEEQVSETLLAEPVPLDILYEDEHVLVINKQPYVSSIPSREHPS 94

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GS     ID +  + V +      L  RLD++TSGI++VA+ R A   L+ + +   +++
Sbjct: 95  GSIANGIIDHYQTTGVRAT---VHLVTRLDRDTSGIMLVAKHRFAHSILSSAQKNGLVKR 151

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKF 240
            Y ++V G     +  +       + IG     ++++        A++HF V  C     
Sbjct: 152 RYAAVVHGRMAQMEGTV------DAPIGRHPDSIIERTVTPDGQKAVTHFYVT-CANDDM 204

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + +Q  TGRTHQ+RVH  ++G P+ GD  Y     G     I  +  LH+ ++   HP
Sbjct: 205 TSVALQLETGRTHQIRVHMSYLGHPLCGDTLY-----GGTRQEI-GRQALHSEHLSFIHP 258

Query: 301 -EGGRLQITAPLPAHMVK 317
                ++  APLP  M K
Sbjct: 259 LTQENMRFHAPLPQDMSK 276


>gi|194099471|ref|YP_002002592.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|239999712|ref|ZP_04719636.1| Pseudouridine synthase [Neisseria gonorrhoeae 35/02]
 gi|240081459|ref|ZP_04726002.1| Pseudouridine synthase [Neisseria gonorrhoeae FA19]
 gi|240113658|ref|ZP_04728148.1| Pseudouridine synthase [Neisseria gonorrhoeae MS11]
 gi|240116400|ref|ZP_04730462.1| Pseudouridine synthase [Neisseria gonorrhoeae PID18]
 gi|240118690|ref|ZP_04732752.1| Pseudouridine synthase [Neisseria gonorrhoeae PID1]
 gi|240124238|ref|ZP_04737194.1| Pseudouridine synthase [Neisseria gonorrhoeae PID332]
 gi|240126427|ref|ZP_04739313.1| Pseudouridine synthase [Neisseria gonorrhoeae SK-92-679]
 gi|254494411|ref|ZP_05107582.1| conserved hypothetical protein [Neisseria gonorrhoeae 1291]
 gi|260441622|ref|ZP_05795438.1| Pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|268595524|ref|ZP_06129691.1| conserved hypothetical protein [Neisseria gonorrhoeae 35/02]
 gi|268597560|ref|ZP_06131727.1| conserved hypothetical protein [Neisseria gonorrhoeae FA19]
 gi|268599721|ref|ZP_06133888.1| conserved hypothetical protein [Neisseria gonorrhoeae MS11]
 gi|268602065|ref|ZP_06136232.1| conserved hypothetical protein [Neisseria gonorrhoeae PID18]
 gi|268604405|ref|ZP_06138572.1| conserved hypothetical protein [Neisseria gonorrhoeae PID1]
 gi|268682866|ref|ZP_06149728.1| conserved hypothetical protein [Neisseria gonorrhoeae PID332]
 gi|268685013|ref|ZP_06151875.1| conserved hypothetical protein [Neisseria gonorrhoeae SK-92-679]
 gi|291044997|ref|ZP_06570705.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|193934761|gb|ACF30585.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|226513451|gb|EEH62796.1| conserved hypothetical protein [Neisseria gonorrhoeae 1291]
 gi|268548913|gb|EEZ44331.1| conserved hypothetical protein [Neisseria gonorrhoeae 35/02]
 gi|268551348|gb|EEZ46367.1| conserved hypothetical protein [Neisseria gonorrhoeae FA19]
 gi|268583852|gb|EEZ48528.1| conserved hypothetical protein [Neisseria gonorrhoeae MS11]
 gi|268586196|gb|EEZ50872.1| conserved hypothetical protein [Neisseria gonorrhoeae PID18]
 gi|268588536|gb|EEZ53212.1| conserved hypothetical protein [Neisseria gonorrhoeae PID1]
 gi|268623150|gb|EEZ55550.1| conserved hypothetical protein [Neisseria gonorrhoeae PID332]
 gi|268625297|gb|EEZ57697.1| conserved hypothetical protein [Neisseria gonorrhoeae SK-92-679]
 gi|291011000|gb|EFE02997.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|317164980|gb|ADV08521.1| Pseudouridine synthase [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 177

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 55/175 (31%), Positives = 81/175 (46%), Gaps = 10/175 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV   SG    +   L + +    +K  L HRLD++  GIL+ 
Sbjct: 4   ILFRYQDFVAINKPQGISVHR-SGGEVSLTATLAAQLGV--EKVWLLHRLDKQAGGILLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I   + +KS  G     + K   
Sbjct: 61  ALNPQSAAVLAAQFAERKMKKTYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLTR 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              N A++ F  I   ++K     ++PHTG+THQLRV    +G  I GD  Y   
Sbjct: 115 NMENIAVTRFFSIRI-SEKMRLFILEPHTGKTHQLRVVMKSLGSSIFGDSLYGGT 168


>gi|157414343|ref|YP_001481599.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|157385307|gb|ABV51622.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
          Length = 281

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 56/201 (27%), Positives = 101/201 (50%), Gaps = 17/201 (8%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKS 135
           ++ KIL+  V L  + +  K + +++E+    +  K +GI S   G    Y + D     
Sbjct: 29  EKNKILNGLVELIVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W    G++  + HRLD+ETSG++++A+ + A   L   F  + +QK Y +L  G      
Sbjct: 89  W----GKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALAHG------ 138

Query: 196 ECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           +   N+++ K+ ++  +Y  +    Q  K    AI+ F++++ F +     L  +P TGR
Sbjct: 139 KIEENFIVDKAINLTKNYDDIKTRMQICKEGKQAITEFEILEYFPKINATLLLCKPLTGR 198

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH  +    I+GD  Y
Sbjct: 199 QHQIRVHLHYKNHTILGDPLY 219


>gi|119945062|ref|YP_942742.1| pseudouridine synthase Rlu family protein [Psychromonas ingrahamii
           37]
 gi|119863666|gb|ABM03143.1| pseudouridine synthase Rlu family protein, TIGR01621 [Psychromonas
           ingrahamii 37]
          Length = 242

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 56/197 (28%), Positives = 95/197 (48%), Gaps = 14/197 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E+++  V NK AGI+     G      G + +   +   K    HRLD+ TSG+L++
Sbjct: 18  VVHENNEFIVINKQAGINFHSEDGEF----GVVVAAEKAFSCKLYSVHRLDKMTSGLLLL 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  +A  L+  F   +IQK Y ++    PK K+  I   + K          + K  +
Sbjct: 74  AKSSPSAAQLSALFFEHQIQKYYLAISDKKPKKKQGLIKGGMEKSRR------SMWKLTK 127

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +  N AI+ F        K  ++ ++P TG+THQ+RV    +G  I GD  Y    + + 
Sbjct: 128 QTNNLAITQFFSYSLENGKRLFV-IKPRTGKTHQIRVALNSIGSAICGDPLYA---EKSP 183

Query: 281 TSPIQNKLYLHARYMDL 297
            S   ++ YLHA  +D 
Sbjct: 184 QSAAFDRAYLHAYQIDF 200


>gi|15672346|ref|NP_266520.1| pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
 gi|12723234|gb|AAK04462.1|AE006273_8 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 293

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 51/181 (28%), Positives = 87/181 (48%), Gaps = 12/181 (6%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSG 156
           +L+ED    V  KPAG  S+ G       +   +K ++  K    +  H   RLD++TSG
Sbjct: 79  VLFEDDHYLVVEKPAGKPSITGSLHPTGAMSNAVKGYISQKNYANQTVHIITRLDRDTSG 138

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVH 214
           ++ +A+ R A   + +      ++K Y+++V    +P + +  +       S I      
Sbjct: 139 LMFLAKHRYAHALMNQHKFRDTMEKRYFAIVNDQDLPDSGRIDLPIGRRDDSIIQ----R 194

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V+ +EK  +   S+  V+         L++  HTGRTHQ+RVH  H+G P++GD  Y  
Sbjct: 195 QVRFDEKAKDALTSY--VVAERKNDLALLDIILHTGRTHQIRVHFSHLGYPLIGDDLYGG 252

Query: 275 N 275
           N
Sbjct: 253 N 253


>gi|15644975|ref|NP_207145.1| hypothetical protein HP0347 [Helicobacter pylori 26695]
 gi|3915350|sp|O25114|Y347_HELPY RecName: Full=Uncharacterized RNA pseudouridine synthase HP_0347;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2313436|gb|AAD07404.1| conserved hypothetical protein [Helicobacter pylori 26695]
          Length = 298

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 73/297 (24%), Positives = 126/297 (42%), Gaps = 37/297 (12%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K     Q+ Q VR   +I  +  +I  +    +              
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVRKSQIIQGVVRLIHFKPNEKTQA------------ 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPHQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  + + L   F  ++++K Y +L  G+   K   I   +L   +I  D +H+  +  
Sbjct: 129 GKTLQSVKDLKALFMQKKVKKTYLALAHGL-VEKSMKIDKPILTPQNIQKD-LHIRSKIS 186

Query: 221 KGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---- 274
                +I+  + +  + F      L++ P TGRTHQ+R+H   +   IVG+  Y      
Sbjct: 187 PLGKQSITLVEPLSYNPFLD-ISLLKITPLTGRTHQIRLHLSSVDHRIVGEGLYGVADEN 245

Query: 275 -----NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                  K    +P+   L LHA  ++    +G   +I +P+P   +     L F Y
Sbjct: 246 AREYLQLKRENNAPL---LMLHAASLEFEF-KGAIYKIASPMPERFMPFLKDLSFFY 298


>gi|323334235|gb|EGA75617.1| Pus9p [Saccharomyces cerevisiae AWRI796]
          Length = 276

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 51/164 (31%), Positives = 81/164 (49%), Gaps = 6/164 (3%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           V +KP+GI V       Y  +   K   ++ G      +RLD+ TSG++ +A+T   A +
Sbjct: 2   VIDKPSGIPVHPTG--RYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFLAKTPRGADN 59

Query: 170 LTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           + +  + R + K Y + V G  P+   E I    LK          V + +EKGA +A +
Sbjct: 60  IGDQLKAREVTKEYVAKVVGEFPET--EVIVEKPLKLIEPRLALNAVCQMDEKGAKHAKT 117

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            F  I  +  K   ++ +P TGR+HQ+RVH  ++G PI  D  Y
Sbjct: 118 VFNRI-SYDGKTSIVKCKPLTGRSHQIRVHLQYLGHPIANDPIY 160


>gi|148264981|ref|YP_001231687.1| RluA family pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146398481|gb|ABQ27114.1| pseudouridine synthase, RluA family [Geobacter uraniireducens Rf4]
          Length = 296

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 80/320 (25%), Positives = 135/320 (42%), Gaps = 67/320 (20%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++Y + E D    +++ + +N  P  +   L+K+L +G + V+           SG ++R
Sbjct: 2   LKYEISETDH-CRQVESFLQNLLPSASHSYLRKLLTAGHLAVN------GTPGVSGTILR 54

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-----LLYEDSKIYVFNKPAGISVQG 121
           +   +      +KE          +K S FL+       +L+ED  I +FNK  G+ +  
Sbjct: 55  LGDTVT-----LKES---------SKTSAFLRKARPELDILHEDQWIMIFNKAPGLPMHH 100

Query: 122 GSGI----AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            + +       +   L +  D    K R  +RLD+ TSG +++A++  AA          
Sbjct: 101 AAEVDERNLVDLGTKLLAGRDGGSVKLRPVNRLDRGTSGAVILAKSSMAAAMFGRLIMDE 160

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K+Y +LV G                  +  D V  V    K A    + ++V+  F 
Sbjct: 161 GLGKLYLALVEG-----------------ELAEDGVISVPLEGKEAE---TRYRVL--FH 198

Query: 238 QKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA----NFKGNFTSPIQNKLYLHA 292
           +  C ++ + P TGR HQ+R H   +G PI GD +Y       F GN          LH+
Sbjct: 199 RSDCTFVAVYPVTGRMHQIRQHFKFIGHPIRGDRRYGGQPLPGFAGN---------ALHS 249

Query: 293 RYMDLPHPEGGR-LQITAPL 311
               + HP  G  LQ+ APL
Sbjct: 250 FRTSIVHPATGETLQVFAPL 269


>gi|325955599|ref|YP_004239259.1| pseudouridine synthase [Weeksella virosa DSM 16922]
 gi|323438217|gb|ADX68681.1| pseudouridine synthase [Weeksella virosa DSM 16922]
          Length = 552

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 106/231 (45%), Gaps = 21/231 (9%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           L H++    + D+ + +  + D  K I  LYED  I V NKP       G  +   +   
Sbjct: 325 LGHMLSATLVDDNPLLIDTNKD--KEIEFLYEDDAIIVINKPENFLSVPGIQVKDSVQTR 382

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L+         P + HRLD +TSG++V+A+++ A + L + F  ++++K Y +L+ G   
Sbjct: 383 LQQQYPHISS-PMIVHRLDMQTSGLMVIAKSKIAHEKLQKQFLKKKVKKRYVALLGG-EV 440

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           NK     N  L+          V  Q  K A        + +   + F +    P TGRT
Sbjct: 441 NKYSGEINLPLRVDLEDRPRQLVCYQYGKNAKTLYQVESISNGITRIFFY----PITGRT 496

Query: 253 HQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           HQLRVHA H   +  PI+GD  Y     G   S    +L+LHA  ++  HP
Sbjct: 497 HQLRVHAAHSLGLDSPILGDDLY-----GQKAS----RLFLHAECLEFFHP 538


>gi|319941266|ref|ZP_08015597.1| hypothetical protein HMPREF9464_00816 [Sutterella wadsworthensis
           3_1_45B]
 gi|319805187|gb|EFW02010.1| hypothetical protein HMPREF9464_00816 [Sutterella wadsworthensis
           3_1_45B]
          Length = 457

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 96/225 (42%), Gaps = 20/225 (8%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQK 143
           D  VN          ILL     I VF KP+G+ SV G  G+       L    +  G  
Sbjct: 234 DPRVNSPVTQSLRPRILLEHRDFIAVF-KPSGLLSVPGTGGLPNA----LTIASEMTGTS 288

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD +TSGIL+  +T    + L  +FR  R++K Y +++ G         A   L
Sbjct: 289 LTAVHRLDMDTSGILLYGKTPEGIRSLMAAFREGRVEKRYRAILEGT------LTAECGL 342

Query: 204 KKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH- 261
               I    +  ++Q    G   A + ++ +     +   ++  P TGRTHQLR+HA H 
Sbjct: 343 IDFPITTHPLDRLRQIAALGGRPARTQWRRLSEKNGR-TLVDFLPLTGRTHQLRLHAAHP 401

Query: 262 ---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +  PI GD  Y  +  G      +  L LHA  +  P P+ G
Sbjct: 402 TLGLNAPIAGDPYY--SRPGLLVDRPETPLLLHAAEIIFPDPQNG 444


>gi|291276435|ref|YP_003516207.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
 gi|290963629|emb|CBG39461.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
          Length = 284

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 111/231 (48%), Gaps = 32/231 (13%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           +DK+R+++ +    G+V++   VI         + +LD  V     +  L++I ++ED  
Sbjct: 35  IDKRRLRYPD----GRVIQKSEVICG-------RVLLDEFVP----NGALRAIFVHED-- 77

Query: 108 IYVFNKPAGISVQGGSGIAYHIDG-FL-KSWVDSK----GQKPRLTHRLDQETSGILVVA 161
             VF KP          +  H  G FL  S  DS     G +    HRLD ETSG+++++
Sbjct: 78  FAVFAKP--------HNLLTHPKGRFLHASLCDSIKMQFGMQANPVHRLDFETSGVVLIS 129

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R + A   L   F    ++KIY +LV GI ++++   +  LL K       + +  Q   
Sbjct: 130 RNKRAEIALKTLFERGEVRKIYRALVEGIIEHERCIESRILLPKKEDKSKDLGIKCQIHA 189

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               +I+  + ++    +   LE++P TGRTHQ+R+H   +G  IV +  Y
Sbjct: 190 SGKDSITIIRPLEVRGNQ-TLLEIEPLTGRTHQIRLHLASIGHKIVNEPLY 239


>gi|225450607|ref|XP_002278016.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 313

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 80/295 (27%), Positives = 123/295 (41%), Gaps = 56/295 (18%)

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP+     HI  EQ    S+ + +      +S +L+ED  +   NKP G+  +    I  
Sbjct: 25  PPLPAISKHI--EQSRAMSASSRSSLFSLCRSDILFEDQWLMAVNKPQGVYCET---ILL 79

Query: 128 HIDGFLKSWVDSKGQKP----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            +   L    DS G        L +RLD++TSG++V+ ++   A  L ++F  R++ K Y
Sbjct: 80  SVSRMLD---DSDGHDSCRSLHLANRLDRDTSGVMVITKSHQVAAKLMKAFSDRKVTKTY 136

Query: 184 WSLVWG-IPKNKKECIAN---------W-LLKKSHIG---------GDYV---HVVKQNE 220
            +L  G  P  +K  I +         W +   S +G          D V    V+  N 
Sbjct: 137 LALCIGAAPTWEKITIKSGHGRSKFGAWRVYAASDVGRALPNAPAIKDMVTSFEVLSVNG 196

Query: 221 KG-------------ANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           +G                 +    VID  A Q    +   P +GRTHQ+R+H  ++G  I
Sbjct: 197 QGNVKELPESRKADETVLVVEERSVIDSNARQDEILVRAFPRSGRTHQIRLHCQYLGISI 256

Query: 267 VGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
            GD KY     +KG     I +   LHA  +   HP  G  +   APLP+  V+ 
Sbjct: 257 RGDVKYEGVHEWKGK----IYDGHELHAESLSFEHPVTGVDVAFRAPLPSWAVQA 307


>gi|213403308|ref|XP_002172426.1| DRAP deaminase [Schizosaccharomyces japonicus yFS275]
 gi|212000473|gb|EEB06133.1| DRAP deaminase [Schizosaccharomyces japonicus yFS275]
          Length = 401

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 111/242 (45%), Gaps = 29/242 (11%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           ++ +R+GQV+V+ +    +  IQ+G V+       A  H   E  + D  V +       
Sbjct: 62  ERAIRNGQVKVNNEPGNVDTVIQNGYVISH----AAHRH---EPPVTDEPVRI------- 107

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
               ++ED +  V +KPAGI V   +G   H         ++K       +RLD+ TSG+
Sbjct: 108 ----VHEDEEYVVIDKPAGIPVHP-TGRYNHNTVLHILMHENKCPLLYPCNRLDRLTSGL 162

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKK-ECIANWLLKKSHIGGDYVHV 215
           +  ++T   A+ +      + +QK Y + V G  P  K   C A  L     +G + VH 
Sbjct: 163 MFFSKTPKGAERMRVHMISKDLQKEYVARVVGEFPAEKTITCDAKLLTVAPTLGLNRVHP 222

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             ++      A++ FK +  F      +  +P TGRTHQ+RVH  ++G PI  D  Y AN
Sbjct: 223 DGKD------AVTIFKRL-AFDGHTSLVHCKPLTGRTHQIRVHLQYLGYPIANDPIY-AN 274

Query: 276 FK 277
            +
Sbjct: 275 LR 276


>gi|308061695|gb|ADO03583.1| hypothetical protein HPCU_02050 [Helicobacter pylori Cuz20]
          Length = 293

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 73/287 (25%), Positives = 123/287 (42%), Gaps = 45/287 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS- 99
           L+  Q  +DK+R+K     Q+ Q VR             + +++   V+L       K+ 
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVR-------------KSQMIQGVVSLIHFKPNEKTQ 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  ALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-----VH 214
             +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D      + 
Sbjct: 128 AGKTLQSAKDLKTLFMQKKVKKTYLALAHGL-VDKNIVIDKPILTPQNIQKDLRIRSKIS 186

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + +        +S+    D        L++ P TGRTHQ+R+H   +G  IVG+  Y  
Sbjct: 187 PLGKPSTTLVEPLSYNAFFDI-----SLLKITPLTGRTHQIRLHLSSVGHRIVGEGLYGV 241

Query: 275 ---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                      K    +P+   L LHA  +     +G   +IT+P+P
Sbjct: 242 IDENAREYLQLKRENNAPL---LMLHASSLAFEF-KGAIHEITSPMP 284


>gi|330946151|ref|XP_003306701.1| hypothetical protein PTT_19907 [Pyrenophora teres f. teres 0-1]
 gi|311315680|gb|EFQ85200.1| hypothetical protein PTT_19907 [Pyrenophora teres f. teres 0-1]
          Length = 475

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 108/248 (43%), Gaps = 25/248 (10%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSK 107
           D+    +   I  G+VV     + +   I+K   ++  +++  +     + I +++ED  
Sbjct: 79  DRPAEYYEQAIIDGRVVLNGKPVPSTKTIVKNGDVISHTLHRHEPPCTAQPIGIVHEDDN 138

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRA 165
           + V NKPAG+ V       Y+ +  ++     +G    P   +RLD+ TSGI+ + + + 
Sbjct: 139 MIVINKPAGMPVHPAG--RYNFNSIIEIMRADRGYGWNPLPCNRLDRLTSGIMFIGKHKQ 196

Query: 166 AAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           AA+ L+   R R ++K Y + V G  P+ +  C    L     +G + V    +  K   
Sbjct: 197 AAEELSAQIRGRTVKKEYITRVVGEFPEGEILCEKPILQISPKLGLNRVRANGKEAKTVF 256

Query: 225 YAISHFKVID-----------CFAQKFCWLEMQ--------PHTGRTHQLRVHALHMGCP 265
             ++++   D              Q   W +++        P TGRTHQLRVH   +G P
Sbjct: 257 KRMAYYPPTDHGKRPNGEDSETDPQGQPWKKLRGYSIVRCFPVTGRTHQLRVHLQFLGHP 316

Query: 266 IVGDHKYC 273
           I  D  Y 
Sbjct: 317 ISNDPIYA 324


>gi|262183262|ref|ZP_06042683.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
          Length = 302

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 78/189 (41%), Gaps = 16/189 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +L+ED  + V +KP  ++       A HI       +  K     L+  HRLD+ TSGIL
Sbjct: 78  ILFEDEHLLVVDKPPFMATMPR---ARHITETATVRLRRKTGNNELSPAHRLDRLTSGIL 134

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V  + R+        F  RR+ K Y ++    P         W  +     G+    + +
Sbjct: 135 VFTKDRSVRGAYQTLFAERRVTKTYEAIA---PLADVSPGTVWRSRMEKTPGELQGRIVE 191

Query: 219 NEKGANYAISHFKVIDCFA--------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            E  A   ++  + ID            +     ++P TG+THQLR+H L  G PI+GD 
Sbjct: 192 GEVNAITEVAAVEPIDKAPYESIHGSLPELAKYTLKPQTGKTHQLRLHMLQAGVPIIGDP 251

Query: 271 KYCANFKGN 279
            Y   F   
Sbjct: 252 IYPVIFPAE 260


>gi|301633483|gb|ADK87037.1| pseudouridine synthase, RluA family [Mycoplasma pneumoniae FH]
          Length = 309

 Score = 66.2 bits (160), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 112/234 (47%), Gaps = 13/234 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-LTHRLDQETSGILV 159
           +LYED +I V NKP G+     S      +  L + +     +P  L HRLD++TSG+++
Sbjct: 82  ILYEDEQIMVVNKPNGLISHPTS--FNESESLLGAALFHCNHQPVFLVHRLDRDTSGVIM 139

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-VVKQ 218
           +A+ +++  HL +  + R +++ Y +LV   P +      +  L++  +G + V   V  
Sbjct: 140 LAKNQSSLLHLQKQLQQRVMKRYYLALVH-FPLDSLSGTISAPLER--VGNNKVMWKVGN 196

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +   A  A + F V++   +K   ++ +  TGRTHQ+RVH   +  P+  D  Y    KG
Sbjct: 197 SSNKAKNAFTKFTVLNQ-NEKAALIKCELLTGRTHQIRVHLQFIKHPVYNDPLY--GLKG 253

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLY 331
                 +   YLHA+ +   HP   + +   A L        D+L  K   +LY
Sbjct: 254 E--QATEYGQYLHAQQISFIHPTLNKEMGFEAQLDKTFSDKLDNLNLKIANSLY 305


>gi|296111875|ref|YP_003622257.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
 gi|295833407|gb|ADG41288.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
          Length = 300

 Score = 66.2 bits (160), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 61/241 (25%), Positives = 112/241 (46%), Gaps = 29/241 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSG-QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
            G +  + K+V  ++ +  G QV  I P   + + ++ + K LD               +
Sbjct: 36  GGAILKNDKQVYTSDYLDDGDQVTIIMPTEASNDLVVPDYKPLD---------------I 80

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYH-----IDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++E+    V +KP GI+   G     H     + G L+    ++   P +  RLD++TSG
Sbjct: 81  IFENEHWLVVDKPYGITTVPGHADRLHTLVNQVKGHLEE-THAEDLVPHVVTRLDRDTSG 139

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYV-H 214
           I+++A+ R A   + +  +   ++K Y +   GI P +  +  A        + GD++  
Sbjct: 140 IVLLAKHRFAHAVMDQQLQEHTVEKFYLAYTSGILPDDHGDIQA----PIGRVDGDFIKR 195

Query: 215 VVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            V+ + K +       +  D   Q+    +++Q HTGRTHQ+RVH  ++G P+VGD  Y 
Sbjct: 196 EVRDDGKPSRTEYWVERRYDENGQQPMTRVKVQLHTGRTHQIRVHFQNIGHPLVGDDLYG 255

Query: 274 A 274
            
Sbjct: 256 G 256


>gi|195051256|ref|XP_001993061.1| GH13618 [Drosophila grimshawi]
 gi|193900120|gb|EDV98986.1| GH13618 [Drosophila grimshawi]
          Length = 753

 Score = 66.2 bits (160), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 58/196 (29%), Positives = 92/196 (46%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 375 KHNDLLANIVHRHEVPVTCQPITIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 433

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    E
Sbjct: 434 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGVVE 493

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K ++KG +   + FK +    +    L  +P TGR HQ+R
Sbjct: 494 CKEPIEVVSYKIG-----VCKVSQKGKD-CTTTFKKLSQNGKTSVVL-CKPLTGRMHQIR 546

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI+ D  Y
Sbjct: 547 VHLQYLGYPILNDPLY 562


>gi|312216765|emb|CBX96715.1| hypothetical protein [Leptosphaeria maculans]
          Length = 791

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 62/259 (23%), Positives = 111/259 (42%), Gaps = 46/259 (17%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSK 107
           D+ +  +   I+ G+VV     + + + +IK   ++  +++  +     + I +++ED+ 
Sbjct: 113 DRPKEYYEQAIKDGRVVVNGKPVPSTSTMIKNGDVISHTLHRHEPPCTAQPIGIVHEDND 172

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRA 165
           + V NKPAG+ V       Y+ +  ++     +G    P   +RLD+ TSGI+ + + R 
Sbjct: 173 LIVINKPAGMPVHPAG--RYNFNSIIEIMRADRGYNWNPLPCNRLDRLTSGIMFIGKHRK 230

Query: 166 AAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHV--------- 215
           AA+H++   R R ++K Y + V G  P+ +  C    L     +G + V           
Sbjct: 231 AAEHMSAQIRGRTVKKEYITRVVGEFPEGEVVCEKPILQISPKLGLNRVRADGKEAFTVF 290

Query: 216 --------------------VKQNEKGANYA-ISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                                K +  G  +  +  + ++ CF          P TGRTHQ
Sbjct: 291 KRLAYYPPKEEEAPPEKDARGKADSDGQPWKRLRGYSIVRCF----------PVTGRTHQ 340

Query: 255 LRVHALHMGCPIVGDHKYC 273
           LRVH   +G PI  D  Y 
Sbjct: 341 LRVHLQFLGHPISNDPIYA 359


>gi|145492917|ref|XP_001432455.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124399567|emb|CAK65058.1| unnamed protein product [Paramecium tetraurelia]
          Length = 469

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 69/262 (26%), Positives = 109/262 (41%), Gaps = 56/262 (21%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +  +  G++ V+  RV    +++ G  +      +A   +  E  ILD  V++       
Sbjct: 54  ENAINEGKITVNSVRVSPEYKLEHGMQIE-----HATTRV--EPPILDLPVDI------- 99

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAY-------HIDGFLKSWVDSKGQKPRLTHRL 150
               ++ED    V +KP  + V  G G  Y       H +  LK           + HRL
Sbjct: 100 ----VFEDDSFVVVSKPPSMIVHTGGGYHYNCLSAILHFEHGLKDLY--------VLHRL 147

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-----IPKNKKE--CIANWLL 203
           D+ TSG+L+ ++ R  AQ   ++     +QK Y + V G     I +N K   C++    
Sbjct: 148 DRLTSGLLIFSKNRLLAQKFHDANSKLNVQKTYLARVQGNFSEDIKENNKPQYCVS---- 203

Query: 204 KKSHIGGDYVHVVKQNEKG----ANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRV 257
                  D +      E      A  A + F+ +  D  +     LE +P TGRTHQ+RV
Sbjct: 204 -----MKDAIFACCTEEDAQKLDAKSATTKFEKLWYDPISDS-SLLECKPITGRTHQIRV 257

Query: 258 HALHMGCPIVGDHKYCANFKGN 279
           H   +G PI+ D  Y   F GN
Sbjct: 258 HLADLGHPILNDIGYGGKFIGN 279


>gi|300173026|ref|YP_003772192.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299887405|emb|CBL91373.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 300

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 50/189 (26%), Positives = 96/189 (50%), Gaps = 13/189 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-----IDGFLKSWVDSKGQKPRLTH 148
           +D+    +++E+    V +KP G++   G     H     + G L+  ++++   P +  
Sbjct: 73  ADYNPLTIIFENEHWLVVDKPYGLTTVPGHADRLHTLVNQVKGHLEE-INAEDLVPHVVT 131

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD++TSGI+++A+ R A   + +  +   ++K Y + V GI       I   + +   +
Sbjct: 132 RLDRDTSGIVLLAKHRFAHAVMDQQLQEHTVEKFYVAYVSGILSEDHGDIHAPIGR---M 188

Query: 209 GGDYV-HVVKQNEKGA--NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
             D++   V+ + K +   Y +   +  D   Q    +++Q HTGRTHQ+RVH  ++G P
Sbjct: 189 DDDFIKREVRDDGKPSRTEYWVER-RYDDGGVQPMTRVKVQLHTGRTHQIRVHFQNIGHP 247

Query: 266 IVGDHKYCA 274
           +VGD+ Y  
Sbjct: 248 LVGDNLYGG 256


>gi|221056917|ref|XP_002259596.1| ribosomal large subunit pseudouridylate synthase [Plasmodium
           knowlesi strain H]
 gi|193809668|emb|CAQ40369.1| ribosomal large subunit pseudouridylate synthase, putative
           [Plasmodium knowlesi strain H]
          Length = 504

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 75/280 (26%), Positives = 124/280 (44%), Gaps = 60/280 (21%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQETS 155
           ++YE+    V NKP  I ++ G      +D    S      QK      R+  +LD  TS
Sbjct: 68  IIYENEFFLVVNKPYDIKLEKGK-----LDDVYPSVETLLRQKTNLDVFRICGQLDYATS 122

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----------IPKNKKECIANWLLKK 205
           G+L++A+ + +   L  +   +RI KIY ++++G           P +K +   N+ +K 
Sbjct: 123 GLLIIAKDKLSCNILNYNIESKRISKIYLAILYGHLPLGVLHVNTPISKIK--NNFKMKL 180

Query: 206 SHIGGDYVHVVKQNEKGANYAISH-FKVIDCFA--QKFCWLEMQPHTGRTHQLRVHALHM 262
            +   DY    K       Y  S  +    C+   QK    E++  TGR HQLR+HAL +
Sbjct: 181 CYNYNDYYDTGK-------YCYSLIYPYKQCYLKNQKVTLCELRTITGRRHQLRLHALCL 233

Query: 263 GCPIVGDHKYCANF------KGNFTSPIQNKLYLHA------RYMDLPHPEGGRL-QITA 309
           G  IVGD  Y  +        G+ ++P + ++ L A      R++D    + GR+ +I A
Sbjct: 234 GSGIVGDETYFEDMISNKYKIGSTSNPCEERIGLLAEEDQQDRFLD---TQVGRITKIDA 290

Query: 310 PLPAHMVKTWDSLGFKYDR----------NLYIKRLYSQD 339
                M+  W  L  K D+          N+  K+++ QD
Sbjct: 291 --ERMMLHCWIILKNKADQKKELKKTEDINMLEKKIFDQD 328


>gi|240128906|ref|ZP_04741567.1| Pseudouridine synthase [Neisseria gonorrhoeae SK-93-1035]
 gi|268687291|ref|ZP_06154153.1| conserved hypothetical protein [Neisseria gonorrhoeae SK-93-1035]
 gi|268627575|gb|EEZ59975.1| conserved hypothetical protein [Neisseria gonorrhoeae SK-93-1035]
          Length = 177

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 55/172 (31%), Positives = 81/172 (47%), Gaps = 10/172 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV   SG    +   L + +    +K  L HRLD++  GIL+ 
Sbjct: 4   ILFRYQDFVAINKPQGISVHR-SGGEVSLTATLAAQLGV--EKVWLLHRLDKQAGGILLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I   + +KS  G     + K   
Sbjct: 61  ALNPQSAAVLAAQFAERKMKKTYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLTR 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              N A++ F  I   ++K     ++PHTG+THQLRV    +G  I GD  Y
Sbjct: 115 NMENIAVTRFFSIRI-SEKMRLFILEPHTGKTHQLRVVMKSLGSSIFGDSLY 165


>gi|311067653|ref|YP_003972576.1| pseudouridylate synthase [Bacillus atrophaeus 1942]
 gi|310868170|gb|ADP31645.1| pseudouridylate synthase [Bacillus atrophaeus 1942]
          Length = 298

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 103/222 (46%), Gaps = 22/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDG-FLKSWVDSKGQKPRLTHRLDQET 154
           +LYED  + V NK   +S           IA  I G + K+ V +      L  RLD++T
Sbjct: 84  VLYEDDHVLVINKQPYVSSIPSREHPSGSIANGILGHYKKNGVRAT---VHLVTRLDRDT 140

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++A+ R A   L+   +   +++ Y ++V G  +  +  +   + +K     D + 
Sbjct: 141 SGVMLIAKHRFAHSILSTGQKNGLVKRRYLAVVHGSMEQAEGTVDAPIGRKP----DSI- 195

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +    G   A++HF+V +        + +Q  TGRTHQ+RVH  H+G P+ GD  Y  
Sbjct: 196 IERMVTPGGQRAVTHFQV-NKKTNGLTSVTLQLETGRTHQIRVHMSHLGHPLCGDTLYGG 254

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAPLPAHM 315
                 T    ++  LH+  +   HP      +  AP+P  M
Sbjct: 255 ------TRQKISRQALHSERLSFIHPLTDETMVFYAPVPQDM 290


>gi|268679279|ref|YP_003303710.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
 gi|268617310|gb|ACZ11675.1| pseudouridine synthase, RluA family [Sulfurospirillum deleyianum
           DSM 6946]
          Length = 326

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 101/227 (44%), Gaps = 34/227 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLD 151
           +LYED  I V NKP  ++V G   +    +  L  W+  +G         ++  + HR+D
Sbjct: 77  VLYEDEDILVINKPPFLTVHGAPSVK---EPTLVDWLQHRGISLSTISGEERHGIVHRID 133

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG LV+A+   A   L      + + + Y +++  +P   KE +   L    +    
Sbjct: 134 KETSGALVIAKNNEAHVKLASQLEDKSMGRYYLAII-DLPL--KENVVVDLPIGRNPNHR 190

Query: 212 YVHVVKQNEKGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               V++  + A  A     +SH    +  A K         TGRTHQ+RVH   +   I
Sbjct: 191 LKMAVQREGRSAKSAFCKCSLSHDGKKELIAAKLF-------TGRTHQIRVHLSALSRHI 243

Query: 267 VGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +GD  Y   FK  N T P   ++ LHA  + L HP     L I APL
Sbjct: 244 LGDSLY--GFKSHNGTIP---RVMLHAYILYLKHPRSQEMLYIHAPL 285


>gi|119945260|ref|YP_942940.1| pseudouridine synthase [Psychromonas ingrahamii 37]
 gi|119863864|gb|ABM03341.1| pseudouridine synthase [Psychromonas ingrahamii 37]
          Length = 303

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 55/196 (28%), Positives = 92/196 (46%), Gaps = 15/196 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            K  +L++D  I V +KP  ++V  GG  +   +   L+     +  +    HRLD+ T+
Sbjct: 81  FKETILFQDEHILVAHKPHFLAVTPGGKYVNECLQNRLRRSTGIEALQ--TLHRLDRVTA 138

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ +          + F+ R+I K Y ++   I   +      W +K   + G+    
Sbjct: 139 GLVMFSVNPDTRHRYHQLFKTRQIHKSYQAIA-SISDAENLTGQEWEIKNRIVQGEPRFR 197

Query: 216 VKQNEKGANYAISHFKVIDCFAQ--KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           ++  E  AN   SH  VI C  Q  +    E+ P TG+THQLRVH   +G PI+ D KY 
Sbjct: 198 MRVTEGEAN---SH-SVIRCLRQSAQTALFELTPVTGKTHQLRVHMQALGLPILND-KYY 252

Query: 274 ANFK----GNFTSPIQ 285
              +     N+ +P+Q
Sbjct: 253 PQLEPLSADNYAAPLQ 268


>gi|315931284|gb|EFV10253.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 281

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 56/201 (27%), Positives = 101/201 (50%), Gaps = 17/201 (8%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKS 135
           ++ KIL+  V L  + +  K + +++E+    +  K +GI S   G    Y + D     
Sbjct: 29  EKNKILNGLVELIVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W    G++  + HRLD+ETSG++++A+ + A   L   F  + +QK Y +L  G      
Sbjct: 89  W----GKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALAHG------ 138

Query: 196 ECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           +   N+++ K+ ++  +Y  +    Q  K    AI+ F++++ F +     L  +P TGR
Sbjct: 139 KIEENFIVDKAINLTKNYDDIKTRMQICKEGKQAITEFEILEYFPKINATLLLCKPLTGR 198

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH  +    I+GD  Y
Sbjct: 199 QHQIRVHLHYKNHTILGDPLY 219


>gi|256831089|ref|YP_003159817.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256580265|gb|ACU91401.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 245

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 49/177 (27%), Positives = 86/177 (48%), Gaps = 8/177 (4%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           ++ ++  +L+ D  +   +KPAG+ V   +  A      L+   D  GQ+    HRLD+ 
Sbjct: 4   TELVEIPVLHRDEHLIAVHKPAGLLVHRNAH-AGREPFLLQILRDQLGQRLYPVHRLDRP 62

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDY 212
           TSG++++A +  AA  L   F  + + K Y ++  G +P   +  I + L  +S   G  
Sbjct: 63  TSGLMIMALSPQAAHALALQFASQEVHKTYLAVTRGFVP--PQGLIDDALKSES---GSL 117

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                +  + A   I H  V      ++  + ++P TGRTHQ+R H  H+  P++GD
Sbjct: 118 QEARTEFTRLATAEIPH-PVGPNPTARYSMVRVRPRTGRTHQIRRHFAHIRHPLIGD 173


>gi|297853522|ref|XP_002894642.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297340484|gb|EFH70901.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 321

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 62/244 (25%), Positives = 103/244 (42%), Gaps = 40/244 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  +   NKP G+  +     A  I       V     +  L +RLD++TSG++++
Sbjct: 77  VLYEDEYLMAVNKPKGVYCEAVLRSAPQI-------VLDSSSEFHLANRLDRDTSGVMII 129

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KKECIANWLLKKSH------------ 207
            ++   A  L ++F   +I+K Y +L  G   N +K  +++   +  H            
Sbjct: 130 TKSHKVAAKLVKAFTEHKIRKSYIALCIGSSPNWRKITVSSGHGRSKHGAWRVYAALDVG 189

Query: 208 ---IGGDYV-------HVVKQN-------EKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
               GG +V        VV  N       E      +   + + C       +   P +G
Sbjct: 190 RVLPGGSFVRDMETTFEVVSVNGVETESCEVENVIVVEREQELSCAGDDVVVVRAFPRSG 249

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+R+H  ++G  I GD KY   ++    +   ++  LHA  + L HP     + I A
Sbjct: 250 RTHQIRLHCQYLGISIRGDVKYHGMYEWRGRTFEGHE--LHAECLSLDHPVTDDPIVIRA 307

Query: 310 PLPA 313
           PLP 
Sbjct: 308 PLPC 311


>gi|222056620|ref|YP_002538982.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
 gi|221565909|gb|ACM21881.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
          Length = 296

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 57/230 (24%), Positives = 100/230 (43%), Gaps = 37/230 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI----AYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +L+ED+ I VFNKP G+ +   + +       +   L +  D    K R  +RLD+ TSG
Sbjct: 80  ILFEDTWIVVFNKPPGLPMHRAAEVDDVNLVDVGSRLLNRRDGGNGKLRPVNRLDRGTSG 139

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +++A++  AA       +   + K+Y ++V G  + +                      
Sbjct: 140 AVILAKSSTAAGMFGRQLKEDGLDKLYLAIVDGRLQGEGTITVPL--------------- 184

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                G   A + +K +     +   + + P TGR HQ+R+H   +G PI GD +Y  + 
Sbjct: 185 -----GGKEAETRYKTL-FNGLRHALVAVYPITGRMHQIRLHFKSIGHPICGDVRYGGS- 237

Query: 277 KGNFTSPIQNKL---YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                  I N+L    LH+    + HP  G  +++ APLP   ++   S+
Sbjct: 238 -------ILNELRGHALHSFRSSIIHPATGESVKVFAPLPEDFLQVVKSI 280


>gi|57242694|ref|ZP_00370631.1| ribosomal large subunit pseudouridine synthase, RluD subfamily,
           putative [Campylobacter upsaliensis RM3195]
 gi|57016623|gb|EAL53407.1| ribosomal large subunit pseudouridine synthase, RluD subfamily,
           putative [Campylobacter upsaliensis RM3195]
          Length = 250

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 56/209 (26%), Positives = 95/209 (45%), Gaps = 46/209 (22%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED KI   NKP             +I   L+S       K +L +RLD+ETSG++++
Sbjct: 59  ILFEDEKILAINKPYS-----------YISEELESEF-----KAKLLNRLDKETSGLILL 102

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI------GGDYVH 214
            +     +   E FR +R+ K Y +++ G+       +A  L+    I       G +  
Sbjct: 103 CKNEDFKKLCIEEFRKQRVYKSYIAVLDGV-------LAEELVVDEPIRTLKGKNGAFSK 155

Query: 215 VVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + K+ +       S   +I+      K    ++   TGRTHQ+RVH   +  PI+GD KY
Sbjct: 156 ITKEGQ-------SALSIINPLMIQGKKTLAKICIQTGRTHQIRVHTAFVKHPIIGDEKY 208

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
                G   +   +++YLH+  + + H E
Sbjct: 209 -----GKIAA---DRMYLHSYELKILHYE 229


>gi|330881339|gb|EGH15488.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. glycinea
           str. race 4]
          Length = 126

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 64/121 (52%), Gaps = 12/121 (9%)

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--- 277
           +G   A+SH++V++ F +    + ++  TGRTHQ+RVH  H+  P+VGD  Y   F+   
Sbjct: 8   EGGKQAVSHYRVLERF-RSHTHVRVKLETGRTHQIRVHMAHINYPLVGDPAYGGRFRIPP 66

Query: 278 -GNFTSPIQNKLY----LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLY 331
             + T     K +    LHAR+++L HP  G R+   +PLP   V  W     K DR  +
Sbjct: 67  AASLTMVDSLKTFPRQALHARFLELDHPTTGKRMSWESPLPDDFV--WLLSLLKQDREAF 124

Query: 332 I 332
           I
Sbjct: 125 I 125


>gi|310643591|ref|YP_003948349.1| pseudouridine synthase, rlua family [Paenibacillus polymyxa SC2]
 gi|309248541|gb|ADO58108.1| Pseudouridine synthase, RluA family [Paenibacillus polymyxa SC2]
          Length = 303

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 61/214 (28%), Positives = 99/214 (46%), Gaps = 25/214 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI---AYHIDGFLKSW--VDSKGQKPRLTHRLDQETS 155
           +LYED    V +KPAG++V    G+      +D  + S+  ++      R  HRLD +T+
Sbjct: 84  ILYEDDFCLVVHKPAGMAVHPDGGVKDSPLTLDHAVASYYEINDIHTAVRHVHRLDVDTT 143

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVH 214
           G ++ A+   A   L E  R + I + Y +LV G +P + +    +W + K         
Sbjct: 144 GPVLYAKNEFALLKLDEQMRAKDIGRRYVALVRGKVPPSLRTL--DWPIGKDRHHKQRRR 201

Query: 215 VVKQNEKGANYAISHFKVIDCF-----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           V    +K    A++H +V + +     A    +L ++  TGRTHQ+RVH  H G P++GD
Sbjct: 202 VSPTGQK----AVTHVEVGEVWGSGPSAVSLVYLTLE--TGRTHQIRVHLSHAGYPLLGD 255

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             Y      +F      +  LH   +   HP  G
Sbjct: 256 VLYGGRAV-DF-----GRQALHGERLTFCHPLSG 283


>gi|254431229|ref|ZP_05044932.1| ribosomal large subunit pseudouridine synthase D [Cyanobium sp. PCC
           7001]
 gi|197625682|gb|EDY38241.1| ribosomal large subunit pseudouridine synthase D [Cyanobium sp. PCC
           7001]
          Length = 350

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 75/320 (23%), Positives = 128/320 (40%), Gaps = 51/320 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           + R++   YPH       + + +G++  + ++++ +  +Q G  +           +   
Sbjct: 24  VSRFYAGRYPHSPASVWLERIAAGEIVRNGQQLRADGELQPGDQL-----------VWHR 72

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWV-- 137
              L+ +V      D      L++D  + V  KPAG+ V    G   H +   L+  V  
Sbjct: 73  PPWLEPAV-----PDLPGP--LFDDGDLLVLAKPAGLPVLPAGGYLEHTVLRLLERQVRA 125

Query: 138 ---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR------MRRI--------- 179
              D +   PR  HRL + TSG+LV AR RA+   L+   R       R +         
Sbjct: 126 GRLDGRFGLPRPVHRLGRFTSGLLVCARRRASRAWLSALLRDGTAEASRAVPLELQEMVG 185

Query: 180 ------QKIYWSLVWGIPKNKKECI--ANWLLKKSHIGG-DYVHVVKQNEKGANYAISHF 230
                 +K+Y +L   +P +    +     L   + IG   +  + +    G   A+   
Sbjct: 186 EAPAACRKLYRALAGPLPVSGPGALELGETLRITTPIGRRPHQRLGEVWSAGGRNALPAL 245

Query: 231 KVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNK 287
             I    ++   C +E    TGR HQ+R+H   +G P++GD  Y      N  + P    
Sbjct: 246 TTITLLERRGHGCLVEAAIGTGRPHQIRIHLAAVGAPLLGDPLYRPGGGVNPGALPGDPG 305

Query: 288 LYLHARYMDLPHPEGGRLQI 307
             LHA  + LP P G RL +
Sbjct: 306 YRLHAHRLTLPWPPGQRLAL 325


>gi|328949329|ref|YP_004366666.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
 gi|328449653|gb|AEB15369.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
          Length = 305

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 56/223 (25%), Positives = 97/223 (43%), Gaps = 18/223 (8%)

Query: 101 LLYEDSKIYVFNKPAGI------SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LYED  I V NK +G+        +  + I        K    S+ ++P + HRLD++T
Sbjct: 29  ILYEDKDIVVINKASGLLSVPYPGSKSRTAIELLEKIMRKKGTFSESRRPFVVHRLDRDT 88

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL----LKKSHIGG 210
           SG+++ A      + +  S++     ++Y ++     +N  E   + L    L K+    
Sbjct: 89  SGVMMFALNERVQKKIMSSWKTMVTDRLYRAVAENPRRNHPELTDSGLIDEPLAKNACHQ 148

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            YV     +      A ++F+V+    +     E+   TG+ +Q+R H      P+ GD 
Sbjct: 149 GYVPKKLGDNAETCEARTNFRVV-LRGRTHTLFELSLDTGKKNQIRAHLASRHYPLAGDE 207

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            Y A      T P  ++L LHAR +   HP  G ++    P P
Sbjct: 208 NYRAR-----TDPF-HRLALHARTLAFIHPVTGEKMSFEIPEP 244


>gi|239994623|ref|ZP_04715147.1| pseudouridylate synthase, 23S RNA-specific [Alteromonas macleodii
           ATCC 27126]
          Length = 279

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 60/234 (25%), Positives = 100/234 (42%), Gaps = 10/234 (4%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVD 138
           EQ I    V      + L   +LY+D  I    KP G+ V   S I  H   F +++  D
Sbjct: 23  EQTIGKVDVGEEDSVNALHLPVLYQDEHIIAIEKPPGLLVHR-SPIDRHETVFAVQTLRD 81

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             GQ     HRLD+ TSG+LV + +   A  L +    +++ K Y ++V G   +     
Sbjct: 82  QIGQHVYPAHRLDRPTSGVLVFSFSSEIAAKLGQQMMDKQVVKTYHAIVRGFVHHTGYID 141

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQ----KFCWLEMQPHTGRT 252
                +   I   +    +  +  +    +++ F+V +   +    ++  +++ P TGR 
Sbjct: 142 YALKYRYDKIADKHKRPQQPPQPASTMYQSVAKFEVPEPVGKYQSARYSLVKLSPSTGRK 201

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR 304
           HQLR H +H+  PI+GD  +    +  F       N L L    M   HP  G+
Sbjct: 202 HQLRRHMVHIRHPIIGDTTHGDGKQNKFAKQHFNFNNLALSCTQMGFSHPVTGK 255


>gi|227546352|ref|ZP_03976401.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium longum
           subsp. infantis ATCC 55813]
 gi|227213333|gb|EEI81205.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium longum
           subsp. infantis ATCC 55813]
          Length = 254

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 61/218 (27%), Positives = 93/218 (42%), Gaps = 36/218 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LYED +I V +KP  ++     G+ Y     ++  +  +  +P +T  HRLD+ T+G+L
Sbjct: 13  VLYEDERIIVVDKPHFLATMP-RGMWYRQIALIR--LRERLGEPDITPAHRLDRMTAGVL 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKSHIG 209
           V  R  A        F+ R+  KIY  L          +G     +      LL++SHI 
Sbjct: 70  VFVRDSACRGAYQMLFQNRQAVKIYECLASCRPISGPRFGTIMQVEPPRPFPLLRRSHIT 129

Query: 210 GDYVHVVKQNEKGANYAISHFKVID-CFA------------------QKFCWLEMQPHTG 250
            ++  +    E G   A +  +  D CF                      C   + P TG
Sbjct: 130 KEHGTMAAFEEPGLANAETLIERGDLCFPPAGGRWREAPEGGPHPGNHPICRYTLHPRTG 189

Query: 251 RTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQ 285
           +THQLRVH   +G PIVGD  Y         +F+ P+Q
Sbjct: 190 KTHQLRVHMNSLGLPIVGDDFYPRIQTRPYDDFSQPLQ 227


>gi|34556591|ref|NP_906406.1| putative ribosomal pseudouridine synthase [Wolinella succinogenes
           DSM 1740]
 gi|34482305|emb|CAE09306.1| PUTATIVE RIBOSOMAL PSEUDOURIDINE SYNTHASE [Wolinella succinogenes]
          Length = 320

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 70/296 (23%), Positives = 130/296 (43%), Gaps = 48/296 (16%)

Query: 36  NLQKILRSGQVRVD-KKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTK 92
            ++ ++R G V VD +K  K   +++ G+   V IP        +++E   ++    +  
Sbjct: 29  QVEALVRGGNVWVDGEKSSKGGVKLKGGERIEVEIP--------LLRENPAMEVEFEVE- 79

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QK 143
                   +L+E+    V NKP+G  V G   +    +  L  W+  KG         ++
Sbjct: 80  --------ILHEEEHFIVLNKPSGAVVHGAPSVK---EATLVDWLKKKGISLSTLNGEER 128

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLD+ETSG +V+A++  A + L+   + + + + Y +++   P  + + +  +L 
Sbjct: 129 HGIVHRLDKETSGAIVIAKSNEAHRRLSLQLQEKSMGRYYLAII-DHPLKEDQRVECYLG 187

Query: 204 KKSHIGGDYVHVVK-QNEKGANYAISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           +  H      H +K        YA S F K+ +        +  +  TGRTHQ+R H   
Sbjct: 188 RHPH------HRLKIAKVPVGRYAKSAFVKLEESIDGSKELIAAKLFTGRTHQIRAHLEL 241

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           +G  I+ D  Y       +    + +++LHA  +   HP  G  +   APL   M+
Sbjct: 242 LGRHILHDELY------GYRGTSEGRIFLHAYGLYFDHPMTGESMFFKAPLFEDMI 291


>gi|227509897|ref|ZP_03939946.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
 gi|227190617|gb|EEI70684.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
          Length = 299

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 70/294 (23%), Positives = 126/294 (42%), Gaps = 43/294 (14%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNHIIKEQKILDSSVNLTKHSD 95
           + I  SGQV ++ +      ++  G  V +  P      N  + EQ I            
Sbjct: 38  KNIKTSGQVLINSRSSDSQTKLADGDQVTVILPDEAGDPNVAVSEQPIK----------- 86

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFL-KSWVDSKGQKPRLTHR 149
                ++YED    V +KPAG++V  G       +   + G+L ++ V      P +  R
Sbjct: 87  -----VVYEDDNWLVVDKPAGLTVVPGPANRDDTLVNRVKGYLVRAGVTD--LVPHIITR 139

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSH 207
           LD+ TSG++++A+ R A     E    +++ K Y ++V   G+P + +  I   + K  +
Sbjct: 140 LDRFTSGLVLIAKHRLANSLANELLAAKQLHKRYLAVVSGGGLPDHGR--IQKPIAKDPN 197

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y  ++  + +   ++ + + V          +E+  HTGRTHQ+RVH   +G P++
Sbjct: 198 ---GYGQIISDDGR---FSDTEYWVRQRLNDDML-VEVALHTGRTHQIRVHFASIGHPLL 250

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
           GD  Y             ++  LHA  +    P     +++ +PLP  M    D
Sbjct: 251 GDQLYHGPMNMGI-----DRQALHAVMLGFNDPFSQSEIKLKSPLPKDMSSILD 299


>gi|296271632|ref|YP_003654263.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
 gi|296095807|gb|ADG91757.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
          Length = 300

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 63/257 (24%), Positives = 103/257 (40%), Gaps = 52/257 (20%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLY---------------EDSKIYVFNKPAGISVQGG 122
           I + ++ D + N  K+ D + S L+Y               + +   +F KP+GI V   
Sbjct: 35  ISKGRVFDEAFNTLKYGDIIDSDLIYMAQFEGHTRGLKPLFQTNYFAIFEKPSGIVVHPI 94

Query: 123 SG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           S          + YH            G    L HR+D ETSG+++ A+ R     L   
Sbjct: 95  SKNTEYCLLDEVRYHF-----------GPDANLVHRIDAETSGLIMCAKDRDIESKLKLM 143

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  ++ QK Y ++V G    K+  I +  ++K               K +   I+  K  
Sbjct: 144 FEEKKYQKSYLAIVRG--HIKESVIIDTSIQKEGKNIGVRMAAGAEGKKSKTIINPIKYN 201

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPI------- 284
           +   +    +E  P TGR HQ+RVH   +G PI GD  Y    +F   +   +       
Sbjct: 202 E--KKDLTLIEAIPVTGRQHQIRVHLYSIGHPIFGDPIYGVDDDFADAYLDRLLDDKRRE 259

Query: 285 ----QNKLYLHARYMDL 297
                ++L+LHA Y++ 
Sbjct: 260 EVSGSHRLWLHANYLEF 276


>gi|156095414|ref|XP_001613742.1| ribosomal large subunit pseudouridylate synthase [Plasmodium vivax
           SaI-1]
 gi|148802616|gb|EDL44015.1| ribosomal large subunit pseudouridylate synthase, putative
           [Plasmodium vivax]
          Length = 460

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 104/248 (41%), Gaps = 52/248 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQETS 155
           ++YE+    V NKP  I ++ G      +D    S      QK      R+  +LD  TS
Sbjct: 25  IVYENEFFLVVNKPYDIKLEKGK-----LDDMYPSVETLLRQKTNLDVFRICGQLDYATS 79

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP-------------KNKKECIANW 201
           G+L+VA+ + +   L  +   +RI KIY ++++G +P             KNK +    +
Sbjct: 80  GLLIVAKDKLSCNILNYNIESKRISKIYLAMLYGHLPLGVLHVNTPISKIKNKFKMKLCY 139

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--QKFCWLEMQPHTGRTHQLRVHA 259
                +  G Y + +        Y   H     C+   +K    E++  TGR HQLR+HA
Sbjct: 140 NYNDYYDSGKYCYSLV-------YPYKH-----CYLKNEKVTLCELRTITGRRHQLRLHA 187

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH------PEGGRLQITAPLPA 313
           L +G  IVGD  Y       F   I NK Y   R  +L         EG + +  +P P 
Sbjct: 188 LCLGSGIVGDETY-------FEDMISNK-YKLGRTSNLCEEQTGVLAEGDQQERFSPTPE 239

Query: 314 HMVKTWDS 321
             +   D+
Sbjct: 240 GAIAKIDA 247


>gi|291529049|emb|CBK94635.1| pseudouridine synthase, RluA family [Eubacterium rectale M104/1]
          Length = 295

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/224 (24%), Positives = 102/224 (45%), Gaps = 24/224 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KP---RLTHRLDQETS 155
           + YED  I V NKP  +     +G   H +    + +   G   KP   R  +RLD++T+
Sbjct: 83  IAYEDDDIIVINKPFDMPAHPSAG--NHDNTLANALMYYYGSQNKPFVYRCINRLDRDTT 140

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+ +VA+   A   L  +   R I + Y+++  G       C    +   + I       
Sbjct: 141 GLTIVAKHALAGGILGNAVAKRAIHRTYYAVCSG-------CTPACMRISAPIARKDAST 193

Query: 216 VKQ--NEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +++  + K   YA++ F  I          ++++  TGRTHQ+RVH  ++G P++GD  Y
Sbjct: 194 IERCVDFKRGEYAVTDFIRIKYNPDNNLSLVKLRLLTGRTHQIRVHMKYIGFPLIGDFLY 253

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
             ++         ++  LH+  +   HP  G ++ + + +P+ M
Sbjct: 254 NPDYT------YISRQALHSGRLVFTHPVTGQKMNLISDIPSDM 291


>gi|295397129|ref|ZP_06807237.1| ribosomal large subunit pseudouridine synthase D [Aerococcus
           viridans ATCC 11563]
 gi|294974627|gb|EFG50346.1| ribosomal large subunit pseudouridine synthase D [Aerococcus
           viridans ATCC 11563]
          Length = 294

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 103/227 (45%), Gaps = 19/227 (8%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSG 156
           +L+ED      NKPAG  S+         +   LK++   +    ++ H   RLD++TSG
Sbjct: 79  ILFEDDHYIAVNKPAGYTSIPSQYNPQGSMANILKAYYQRQDYDNQVIHVVTRLDRDTSG 138

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++ A+   A   + +  + + I+K Y ++      +K+    N       I      ++
Sbjct: 139 VMLFAKHAFAHGLIDQQMQQKGIEKTYLAI-----SDKRVSDFNHGFIDDPIARSPRSII 193

Query: 217 KQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           ++  +E G +    ++      A K    ++Q HTGRTHQ+RVH    G P++GD  Y  
Sbjct: 194 ERRVHESGQSALTEYWLAEQVGALKV--YKVQLHTGRTHQIRVHFAFNGAPLIGDDLYG- 250

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
              G     IQ +  LH R +   H   G  ++I APLP  +   +D
Sbjct: 251 ---GQMDHGIQRQA-LHCRSLKFKHQFTGEMIEIQAPLPEDISACFD 293


>gi|238924179|ref|YP_002937695.1| pseudouridine synthase [Eubacterium rectale ATCC 33656]
 gi|238875854|gb|ACR75561.1| pseudouridine synthase [Eubacterium rectale ATCC 33656]
          Length = 295

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/224 (24%), Positives = 102/224 (45%), Gaps = 24/224 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KP---RLTHRLDQETS 155
           + YED  I V NKP  +     +G   H +    + +   G   KP   R  +RLD++T+
Sbjct: 83  IAYEDDDIIVINKPFDMPAHPSAG--NHDNTLANALMYYYGSQNKPFVYRCINRLDRDTT 140

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+ +VA+   A   L  +   R I + Y+++  G       C    +   + I       
Sbjct: 141 GLTIVAKHALAGGILGNAVAKRAIHRTYYAVCSG-------CTPACMRISAPIARKDAST 193

Query: 216 VKQ--NEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +++  + K   YA++ F  I          ++++  TGRTHQ+RVH  ++G P++GD  Y
Sbjct: 194 IERCVDFKRGEYAVTDFIRIKYNPDNNLSLVKLRLLTGRTHQIRVHMKYIGFPLIGDFLY 253

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
             ++         ++  LH+  +   HP  G ++ + + +P+ M
Sbjct: 254 NPDYT------YISRQALHSGRLVFTHPVTGQKMNLISDIPSDM 291


>gi|329767055|ref|ZP_08258583.1| hypothetical protein HMPREF0428_00280 [Gemella haemolysans M341]
 gi|328837780|gb|EGF87405.1| hypothetical protein HMPREF0428_00280 [Gemella haemolysans M341]
          Length = 283

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 68/260 (26%), Positives = 115/260 (44%), Gaps = 34/260 (13%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           ++++    + N+ ++ G ++ +   I+      KE    +S+V++TK          +ED
Sbjct: 41  IKINSNEAELNSPLKVGDILEVN--IDLATSKYKE----NSTVSITKE---------FED 85

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
             + V +KP GI       I    D  L +++ S        HRLD +T G++++A+T  
Sbjct: 86  EYLLVVSKPFGIKTHPND-IELE-DDTLVNYLISNYNYLEPIHRLDIDTCGLVILAKTPL 143

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGAN 224
               L +    R+I++ Y +L   I  N K    N     S+IG D     K    K   
Sbjct: 144 IKAKLDQMLEQRQIKRYYSAL---IKNNIKPQTIN-----SNIGRDSKEKNKMAVTKNGK 195

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSP 283
            AI++    +   Q    + +   TGRTHQ+RVH    G  I+GD  Y  + +K      
Sbjct: 196 NAITNILSCEKIDQNRFLVTVSLETGRTHQIRVHLASNGVAIIGDKLYSKDGYK------ 249

Query: 284 IQNKLYLHARYMDLPHPEGG 303
             +K+YL A  ++  HP  G
Sbjct: 250 -YDKMYLGALKVEFSHPVTG 268


>gi|256062319|ref|XP_002570309.1| ribosomal pseudouridine synthase [Schistosoma mansoni]
 gi|227294250|emb|CAY19151.1| ribosomal pseudouridine synthase, putative [Schistosoma mansoni]
          Length = 875

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 75/292 (25%), Positives = 118/292 (40%), Gaps = 67/292 (22%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  VR+ ++R K N  + +G  + IP   +    I ++   LDS        D  K  LL
Sbjct: 471 SDVVRIIRQRTKLN--LYTGTTLDIPSNKSTSTSIPEK---LDSQGYRIPDEDPYKFDLL 525

Query: 103 YEDSKIYVF--------------NKPAGISVQGGSGIAYHIDGFL--------KSWVDSK 140
            E+    V               NKP GI+ Q G+   ++I   L        K     K
Sbjct: 526 TEEEAAMVLYKSIIEIRENVIALNKPRGIASQPGADCKHNIVDLLPRIESLIRKRNHHGK 585

Query: 141 GQKPRL-----THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G++  +      HRLD+++SGI+++AR + +A  L E+F  R I+K Y  +  GIP++  
Sbjct: 586 GEEKYIGELSTVHRLDKDSSGIILIARNKDSALKLQEAFSRRWIKKDYLCITVGIPRSDY 645

Query: 196 ECIANWLLKKSHIGGDYVH-----------VVKQNEKGANYAISHFKVIDCFA------- 237
             I   L++++  G   +              KQ +   +   + + V D F        
Sbjct: 646 GYIQLPLVERNFNGIRKMCTPQLNRRLQELTCKQTQLDIDNEANEYDVTDAFTVLYDKMR 705

Query: 238 ----QKFCWLEM------------QPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
               Q   W  +               TG  HQ+R H A  +  PI+GDHKY
Sbjct: 706 TNNNQPTTWYNLIDKQNNAALMLCSTLTGIKHQIRAHLAFGLHTPILGDHKY 757


>gi|240014440|ref|ZP_04721353.1| Pseudouridine synthase [Neisseria gonorrhoeae DGI18]
 gi|240016885|ref|ZP_04723425.1| Pseudouridine synthase [Neisseria gonorrhoeae FA6140]
 gi|240120962|ref|ZP_04733924.1| Pseudouridine synthase [Neisseria gonorrhoeae PID24-1]
          Length = 177

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/172 (31%), Positives = 81/172 (47%), Gaps = 10/172 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV   SG    +   L + +    +K  L HRLD++  GIL+ 
Sbjct: 4   ILFRHQDFVAINKPQGISVHR-SGGEVSLTATLAAQLGV--EKVWLLHRLDKQAGGILLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I   + +KS  G     + K   
Sbjct: 61  ALNPQSAAVLAAQFAERKMKKSYLALSDRKPSKKQGWIKGGM-EKSRRG-----MWKLTR 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              N A++ F  I   ++K     ++PHTG+THQLRV    +G  I GD  Y
Sbjct: 115 NMENIAVTRFFSIRI-SEKMRLFILEPHTGKTHQLRVVMKSLGSSIFGDSLY 165


>gi|291524908|emb|CBK90495.1| pseudouridine synthase, RluA family [Eubacterium rectale DSM 17629]
          Length = 295

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/224 (24%), Positives = 102/224 (45%), Gaps = 24/224 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KP---RLTHRLDQETS 155
           + YED  I V NKP  +     +G   H +    + +   G   KP   R  +RLD++T+
Sbjct: 83  IAYEDDDIIVINKPFDMPAHPSAG--NHDNTLANALMYYYGSQNKPFVYRCINRLDRDTT 140

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+ +VA+   A   L  +   R I + Y+++  G       C    +   + I       
Sbjct: 141 GLTIVAKHALAGGILGNAVAKRAIHRTYYAVCSG-------CTPACMRISAPIARKDAST 193

Query: 216 VKQ--NEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +++  + K   YA++ F  I          ++++  TGRTHQ+RVH  ++G P++GD  Y
Sbjct: 194 IERCVDFKRGEYAVTDFIRIKYNPDNNLSLVKLRLLTGRTHQIRVHMKYIGFPLIGDFLY 253

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
             ++         ++  LH+  +   HP  G ++ + + +P+ M
Sbjct: 254 NPDYT------YISRQALHSGRLVFTHPVTGQKMDLISDIPSDM 291


>gi|212639937|ref|YP_002316457.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
 gi|212561417|gb|ACJ34472.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
          Length = 292

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 78/312 (25%), Positives = 140/312 (44%), Gaps = 43/312 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQ--VVRI 67
           +V   ++ M +  + K    HI+   L  I  + G++ V+   V     +++G    V  
Sbjct: 7   IVTQQQDGMLVREFLKQQ--HISKTALTDIKFQGGRIEVNDVPVTVRYVLKAGDEVCVSF 64

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP          EQK      N+   ++ +   ++YED  + V NKP  +S         
Sbjct: 65  PP----------EQK----GANMV--AEPIPLAIVYEDDYVIVINKPPHMSTIPSR---E 105

Query: 128 HIDGFLKSWVDSKGQKPRL------THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H  G L + +    ++ +L        RLD++TSG+++VA+ R     L+E  +  R+++
Sbjct: 106 HPHGTLANALLHHYEQQQLQTTVHVVTRLDRDTSGLVLVAKHRHVHHLLSEQQKQGRVKR 165

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++  G        I   + +K    GD + + ++       A++H++V+     +  
Sbjct: 166 RYEAVCHGYVIQLVGTIDAPIGRK----GDSI-IEREVRLDGQRAVTHYEVLQQ-KNEMT 219

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +Q  TGRTHQ+RVH  H+G P+VGD  Y     G     I ++  LH+  +   HP 
Sbjct: 220 HVSIQLETGRTHQIRVHFSHIGHPLVGDDLY-----GGLREHI-DRQALHSCELTFFHPF 273

Query: 302 GGR-LQITAPLP 312
             + +   APLP
Sbjct: 274 FEKTMTFHAPLP 285


>gi|307746984|gb|ADN90254.1| Pseudouridine synthase [Campylobacter jejuni subsp. jejuni M1]
          Length = 281

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/201 (27%), Positives = 101/201 (50%), Gaps = 17/201 (8%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKS 135
           ++ KIL+  V L  + +  K + +++E+    +  K +GI S   G    Y + D     
Sbjct: 29  EKNKILNGLVELIVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W    G++  + HR+D+ETSG++++A+ + A   L   F  + +QK Y +L  G      
Sbjct: 89  W----GKEACVAHRIDKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALAHG------ 138

Query: 196 ECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           +   N+++ K+ ++  +Y  V    Q  K    AI+ F++++ F +     L  +P TGR
Sbjct: 139 KIEENFIVDKAINLTKNYDDVKTRMQICKEGKQAITEFEILEYFPKINATLLLCKPLTGR 198

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH  +    I+GD  Y
Sbjct: 199 QHQIRVHLHYKNHTILGDPLY 219


>gi|123452968|ref|XP_001314542.1| ribosomal large subunit pseudouridine synthases [Trichomonas
           vaginalis G3]
 gi|121897072|gb|EAY02204.1| ribosomal large subunit pseudouridine synthases, putative
           [Trichomonas vaginalis G3]
          Length = 353

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 64/251 (25%), Positives = 115/251 (45%), Gaps = 37/251 (14%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
           F N +   +    ++ +R+G++ V+ +++  + RI           ++++ HI      +
Sbjct: 57  FTNEFRVASREEYEEKIRNGKIIVNGRKIPVDYRIGP---------LDSIKHICTR---I 104

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYV-FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           ++ V       F K +L   ++  YV + KPA ++V    G  Y+      S V      
Sbjct: 105 EAPV-------FNKPLLKLGETDNYVAYLKPASVTVNTVGGYFYN------SMVKRLPPH 151

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWL 202
             + HRLD+ TSGI+V A+ +AAA +  +     ++ K Y + V G  PK +  C     
Sbjct: 152 LHVVHRLDRVTSGIIVFAKNKAAATNFNQYLVGEKVSKTYIARVIGRFPKGEIIC----- 206

Query: 203 LKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
                +G D+ +H       G   + + FK++    ++   +E  P TGRTHQ+R H  +
Sbjct: 207 --DQPLGTDFNLHRTVVTPTGKP-SKTIFKLLKTNGKE-SIVEAHPITGRTHQIRCHLQY 262

Query: 262 MGCPIVGDHKY 272
           +G PI  D  Y
Sbjct: 263 LGYPITNDEMY 273


>gi|315653906|ref|ZP_07906822.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
 gi|315488602|gb|EFU78248.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
          Length = 300

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 89/183 (48%), Gaps = 18/183 (9%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 131 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 189

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 190 PIGKKDDPIKRYIM------EGGKNSVTKYRVIKQVAGA-SLVELQLLTGRTHQIRVHMQ 242

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           ++G P+ GDH Y    + +F  P Q    LH   +    P E  R+++     A M++ W
Sbjct: 243 YLGHPLFGDHLY--GVEDDF--PRQ---ALHCFLLAFDDPLEHKRIEVQIADSADMLQLW 295

Query: 320 DSL 322
             L
Sbjct: 296 QKL 298


>gi|326424090|ref|NP_761675.2| Pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           CMCP6]
 gi|319999468|gb|AAO11202.2| Pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           CMCP6]
          Length = 231

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/192 (29%), Positives = 88/192 (45%), Gaps = 17/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL++
Sbjct: 4   ILFTHPDFLIINKYPHVSVHKDDGDTMLLQEVAKV---SGDEQLYLIHRLDKMTSGILLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   AA  L++ F  R ++K Y ++    PK K+  +   + +        V+  KQN 
Sbjct: 61  GRNSTAASALSQRFAQREVEKFYLAIGAKKPKKKQGTVIGDMERSRRASWKLVN-SKQNP 119

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                AI+ F  +     +  +L  +P+TG+THQ+RV    +G  IVGD  Y A      
Sbjct: 120 -----AITQFFSLAGEPGERAFL-CKPYTGKTHQIRVALKSVGSSIVGDPIYNAGSD--- 170

Query: 281 TSPIQNKLYLHA 292
                ++ YLHA
Sbjct: 171 ----SDRGYLHA 178


>gi|319789701|ref|YP_004151334.1| pseudouridine synthase [Thermovibrio ammonificans HB-1]
 gi|317114203|gb|ADU96693.1| pseudouridine synthase [Thermovibrio ammonificans HB-1]
          Length = 274

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 63/283 (22%), Positives = 125/283 (44%), Gaps = 56/283 (19%)

Query: 38  QKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++++  G V V+ +K +    R++ G+VVR P         + E      +V L      
Sbjct: 34  KRLIDEGLVSVNGQKELLARRRLKGGEVVRFP---------LTEAPFKPPNVKL------ 78

Query: 97  LKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
                L+ +  ++VF KP  I+  +G   +   +       +       ++ HRLD++T+
Sbjct: 79  -----LFRERGVWVFEKPPFITTNEGEKSLEETVRKLFNPNL-------KVVHRLDKQTT 126

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++   +    +   + F+ R ++K Y  LV G  ++++       +++   G   V +
Sbjct: 127 GPVIAVESEKLFEAFKKQFKRREVKKEYLCLVKGKLRSRQ------TVRRPIDGKSAVSL 180

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V          + HFK         C +E++  TGR HQ+R H   +G P+VG+  Y   
Sbjct: 181 V--------TPLEHFK-----RATLCRVEIE--TGRKHQIRRHLASVGYPVVGEFLY--- 222

Query: 276 FKGNFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           ++G++   +    ++ LH R +   HP  G R+ + + LP  +
Sbjct: 223 YRGSWPEELLFCPRIALHFRKLSFTHPATGKRITVESELPKDL 265


>gi|189237270|ref|XP_973027.2| PREDICTED: similar to ribosomal pseudouridine synthase [Tribolium
           castaneum]
          Length = 487

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 58/196 (29%), Positives = 87/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L ++              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 107 KHNDLLANVVHRHEVPVTSQPITIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 165

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ +    R R +QK Y   V G  P    E
Sbjct: 166 EYNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEHQIRNRLVQKEYVCRVEGEFPDEIIE 225

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +      K+   F  K   +  +P TGR HQ+R
Sbjct: 226 CKEPIEVVSYKIG-----VCKVSPKGKDCNTIFQKL--GFNGKTSIVLCKPKTGRMHQIR 278

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G P+V D  Y
Sbjct: 279 VHLQYLGYPVVNDPLY 294


>gi|284048346|ref|YP_003398685.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
 gi|283952567|gb|ADB47370.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
          Length = 285

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 106/225 (47%), Gaps = 26/225 (11%)

Query: 102 LYEDSKIYV-FNKPAGISVQGGS-----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           + E++++Y+  +KPAG+            ++  +  + ++   S    P    RLD+ETS
Sbjct: 76  ILEETELYLAVDKPAGLVTHNAGKERTPALSRRVAWYFQTHHISSAVHP--VSRLDRETS 133

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+  A   H+       R++K Y +L  G    +   I +W + +    G  V  
Sbjct: 134 GVVLFAKN-ACLHHM---LSRNRLEKTYLALTLGH-WEQPAGILDWPIGRRP--GSIVE- 185

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +Q +     A + ++V+    +    +  Q  TGRTHQ+RVHA   G P++GD  Y   
Sbjct: 186 -RQVDPDGQPARTRYQVLGE-KEGLSLVRFQLETGRTHQIRVHAAAAGHPLLGDTLY--- 240

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
             G   +P   + YLHA  +    P  GR ++ITAPLP    K W
Sbjct: 241 --GTPGAP--GRHYLHAWKVAFREPFTGRPVEITAPLPPDFRKVW 281


>gi|261837781|gb|ACX97547.1| pseudouridine synthase D [Helicobacter pylori 51]
          Length = 293

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 72/287 (25%), Positives = 123/287 (42%), Gaps = 45/287 (15%)

Query: 41  LRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           L+  Q  +DK+R+K N + ++  Q+++    I +L H    +K                 
Sbjct: 28  LKEAQRHLDKQRLKQNQQAVRKSQMIQ---GIVSLIHFKPNEKT---------------Q 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  ALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D     K +
Sbjct: 128 AGKTLQSAKDLKALFMQKKVKKTYLALAHGL-VDKNIVIDKPILTPQNIQKDLSIKSKIS 186

Query: 220 EKGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             G         +S+   +D         ++ P TGRTHQ+R+H   +   IVG+  Y  
Sbjct: 187 PLGKPSTTLVEPLSYNPFLDI-----SLFKITPLTGRTHQIRLHLSSVDHRIVGEGLYGV 241

Query: 275 ---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                      K    +P+   L LHA  ++    +G   +IT+P+P
Sbjct: 242 IDENAREYLQLKRENNAPL---LMLHATSLEFEF-KGAIYKITSPMP 284


>gi|168061155|ref|XP_001782556.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162665963|gb|EDQ52631.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 365

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 97/246 (39%), Gaps = 35/246 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAY----------------HIDGFLKSWVDSKGQ-- 142
           +LYED  +   NKP+G+ V  G                     H+   L S   S     
Sbjct: 100 VLYEDDHLVAINKPSGLQVLPGGLFQQRTVLKQLEWDNEEKEKHLQACLASVSSSDETRL 159

Query: 143 -KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-------------RRIQKIYWSLVW 188
            KP   HRL + TSGIL+ A++ AA   L                   R+I K Y +L  
Sbjct: 160 WKPAPVHRLGRGTSGILLCAKSPAAKSKLAADLAAGTSVSIDRSALIDRKITKTYRALAS 219

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQP 247
           GI   + E  A+  + K    G    +    E G   + S   V+     +    +E+Q 
Sbjct: 220 GI-IMEDEVFADIPIGKVKYSGVAGGLNMATEIGGKPSQSKVTVLWRDIVENQTLVEVQI 278

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           +TGR HQ+R+H   +G P+VGD  Y A  +        N      + MD P  +GG  + 
Sbjct: 279 YTGRPHQIRIHLAALGHPLVGDPLYVAGGRPREDLNTVNAENCEDKSMD-PADDGGYQRP 337

Query: 308 TAPLPA 313
            + LP 
Sbjct: 338 KSVLPG 343


>gi|78224034|ref|YP_385781.1| pseudouridine synthase, RluD [Geobacter metallireducens GS-15]
 gi|78195289|gb|ABB33056.1| Pseudouridine synthase, RluD [Geobacter metallireducens GS-15]
          Length = 296

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 69/318 (21%), Positives = 127/318 (39%), Gaps = 53/318 (16%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           + + + E+D     ++ + +N  P      L K+ R G + V+   V  +  + +G  + 
Sbjct: 2   LTFTITESDH-CRGVESFLRNLLPGAPLAYLGKLTRGGHLTVNGLPVTPDTLLVTGDTMA 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +         +  ++  LD               +L+ED +I V NKP G+ V   +   
Sbjct: 61  LKESGRTRELLAAKRPSLD---------------ILFEDDRIVVVNKPPGLPVHRTAEDE 105

Query: 127 YHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +    + ++  +G   +L   +RLD+ TSG  ++A++  +A       +   + K+Y 
Sbjct: 106 QTLVDVAERFLAQRGTPAKLRPVNRLDRGTSGATILAKSATSAGMFGRFVKETGLGKLYL 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G  K   E   +  L+       Y  + +                    +    L 
Sbjct: 166 AVADG--KLPAEGTIDTPLEGKEAQTQYRTLFQ-------------------GKSAALLL 204

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY----CANFKGNFTSPIQNKLYLHARYMDLPHP 300
           + P TGRTHQ+R H    G P+ GD +Y     A + G+          LHA  +   HP
Sbjct: 205 VTPITGRTHQIRKHLALTGHPVRGDRRYRGAPLAAYPGH---------CLHAFLVSFRHP 255

Query: 301 -EGGRLQITAPLPAHMVK 317
             G  + I APLPA +++
Sbjct: 256 VSGEEIVIHAPLPAALLE 273


>gi|301168046|emb|CBW27632.1| putative tRNA pseudouridylate synthase [Bacteriovorax marinus SJ]
          Length = 254

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 110/232 (47%), Gaps = 26/232 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D ++ +  KP+G+ V          D  ++   D  GQ+    HRLD+  SG+L+ 
Sbjct: 16  ILYQDEQVVIVTKPSGLLVHPYWKETNERDNLMRRVRDQIGQRVYPIHRLDRPVSGVLLF 75

Query: 161 ARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
                  + + E +  + ++ K Y +LV+G  +N+               G +   +  +
Sbjct: 76  GLNGEIVKRIQEHWHDKTKVHKEYLALVFGEIENE---------------GVFDFQLTND 120

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +K    A++ ++ +   +++   +++   TGRTHQ+R H       ++GD K+    KGN
Sbjct: 121 KKIKQDALTKYRPLQS-SERATLMQITIETGRTHQIRRHFSRSRHHLIGDTKHG---KGN 176

Query: 280 FTSPIQ-----NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                +     N+++LH+  + L + +  ++ I +PLP+ + +  D++   Y
Sbjct: 177 INRYYRSEHDFNRIFLHSYRLKL-NLDFLKVDIESPLPSELTELLDTIKIDY 227


>gi|301769635|ref|XP_002920217.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Ailuropoda melanoleuca]
 gi|281341567|gb|EFB17151.1| hypothetical protein PANDA_008946 [Ailuropoda melanoleuca]
          Length = 302

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 54/174 (31%), Positives = 82/174 (47%), Gaps = 11/174 (6%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA    + F+ RR+ K Y +LV G  +  +  I   + +
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYKCFKERRVTKAYLALVRGHVQENRMTINYAIGR 120

Query: 205 KSHIGGDYVHVVKQNEKGANY--AISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            S  G  +   ++      N   +++   V++           + +QP TGRTHQLRVH 
Sbjct: 121 NSTEGRAHTMCIEGTLGCENPKPSLTELVVLEHGLYAGDPVSKVLLQPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLP 312
             +  P+VGD  Y          P   ++ LHA Y+ +P H E  R++   P P
Sbjct: 181 SALSHPVVGDLTY-GQAPDQEDQPF--RMMLHAFYLRIPTHTE--RVEACTPDP 229


>gi|300812735|ref|ZP_07093142.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
 gi|300496275|gb|EFK31390.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
          Length = 297

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 110/231 (47%), Gaps = 24/231 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++ E +   V NKPAG+ S+  G     + I   +  F K  V+    KP +  RLDQ+T
Sbjct: 76  IVEETADYLVINKPAGLLSIPSGFHAEDAVINRVLAYFEKQGVNPAYVKPHIVTRLDQDT 135

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDY 212
           SG++++ +   A    ++  +   I+K Y ++V G   N  E   + L+ K  + +G   
Sbjct: 136 SGLVLLGKNAIAHDRFSKLGKDDFIKK-YHAIVHG---NFAEGDLSGLIDKPLARVGDTV 191

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              V  N KG   A++ ++V+D        +E++  TGRTHQ+R+H   +G  + GD  Y
Sbjct: 192 KREV--NPKGQR-ALTEYRVLDQVPGA-SLIELRLLTGRTHQIRIHMASIGHVLYGDDLY 247

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            A  +  F      +  L+  Y+  P+P GG   +I  P P  M   W  L
Sbjct: 248 GA--RDAFA-----RQALNCFYLAFPNPFGGEEREIEIPDPGDMQGLWRQL 291


>gi|255542880|ref|XP_002512503.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223548464|gb|EEF49955.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 321

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 68/268 (25%), Positives = 118/268 (44%), Gaps = 45/268 (16%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPR-----LTHRLD 151
           +S +LYED  +   NKP G+  +        +        D S+G +       L +RLD
Sbjct: 56  RSDVLYEDQWLIAVNKPQGVYCETVLESVPRVLAASAELTDPSEGAEGNPHEFHLANRLD 115

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECI------------ 198
           ++TSG++V+ ++   A  L ++F   +I+K Y +L  G+ PK +K  I            
Sbjct: 116 RDTSGVMVITKSHKVASKLVKAFTDHKIKKTYIALCIGLAPKWEKITIKSGHGRSKFGVW 175

Query: 199 ---ANWLLKKSHIGGDYV-------HVVKQNEKGANYAISHFK------VIDCFAQKFC- 241
              A   + ++  GG  V        ++  N +G+   +S F+      V++  A K   
Sbjct: 176 RVYAASDVGQTLPGGSTVKDMETSFELLSVNGQGSFKELSEFEKDENILVVEEKAAKNAD 235

Query: 242 ------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                  +   P +GRTHQ+R+H  ++G  I GD KY   ++  +     +   LHA  +
Sbjct: 236 VKKVEILVRAFPQSGRTHQIRLHCQYLGISIRGDVKYEGVYE--WEGRTYDGHELHAETL 293

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSL 322
              HP  G  + + APLP+  ++    L
Sbjct: 294 SFEHPVTGVPVMLRAPLPSWAIQASQPL 321


>gi|321314893|ref|YP_004207180.1| pseudouridylate synthase [Bacillus subtilis BSn5]
 gi|320021167|gb|ADV96153.1| pseudouridylate synthase [Bacillus subtilis BSn5]
          Length = 299

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 102/225 (45%), Gaps = 24/225 (10%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LYED  + V NK   +S         GS     ID +  + V +      L  RLD++T
Sbjct: 84  ILYEDEHVLVINKQPYVSSIPSREHPSGSIANGIIDHYQTTGVRAT---VHLVTRLDRDT 140

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA+ R A   L+ + +   +++ Y ++V G     +  +       + IG     
Sbjct: 141 SGVMLVAKHRFAHSILSSAQKNGLVKRRYAAVVHGRMAQMEGTV------DAPIGRHPDS 194

Query: 215 VVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           ++++        A++HF V  C       + +Q  TGRTHQ+RVH  ++G P+ GD  Y 
Sbjct: 195 IIERTVTPDGQKAVTHFYVT-CANDDMTSVTLQLETGRTHQIRVHMSYLGHPLCGDTLYG 253

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
                  T     +  LH+ ++   HP   + +   APLP  M K
Sbjct: 254 G------TRQEIGRQALHSEHLSFIHPLTQKNMTFHAPLPQDMRK 292


>gi|46111497|ref|XP_382806.1| hypothetical protein FG02630.1 [Gibberella zeae PH-1]
          Length = 512

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/198 (28%), Positives = 87/198 (43%), Gaps = 27/198 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           +++ED  + V NKPAG+ V       Y+ +  ++     +G    P L +RLD+ TSGI+
Sbjct: 182 IIHEDEDMIVINKPAGVPVHPAG--RYNFNSVVEIMKSDRGPAFLPYLCNRLDRLTSGIM 239

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
            +A+   AA+ L    + R ++K Y + V G  P  +  C    L     +G + V    
Sbjct: 240 FIAKNPVAAEALGIKIKDRTVRKEYIARVMGEFPDGEVVCDQPILQISPKLGLNRVRANG 299

Query: 218 QN-----EKGANYAISHFKVIDCFAQKFCWLEMQPH-----------------TGRTHQL 255
           +      +K A Y     + +D   +    L+ + H                 TGRTHQL
Sbjct: 300 KTARTVFKKLAYYPEDENEDVDERPKTPEQLQDETHRPWVNKKGYSIVRCLPVTGRTHQL 359

Query: 256 RVHALHMGCPIVGDHKYC 273
           RVH  H+G PI  D  Y 
Sbjct: 360 RVHLQHLGHPIQNDPIYA 377


>gi|195146686|ref|XP_002014315.1| GL19017 [Drosophila persimilis]
 gi|194106268|gb|EDW28311.1| GL19017 [Drosophila persimilis]
          Length = 644

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 72/267 (26%), Positives = 117/267 (43%), Gaps = 43/267 (16%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ +  + V NKPA I V       ++   F+ +  
Sbjct: 358 KHNDLLANIVHRHEVPVTCQPIKIVHMNEDLVVVNKPASIPVHPCGRYRHNTVVFILAK- 416

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V GI P    E
Sbjct: 417 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGIFPDEIVE 476

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K +++G +   +  K+      K   +  +P TGR HQ+R
Sbjct: 477 CKEPIEVVSYKIG-----VCKVSQRGKDCTTTFQKISQ--NGKTSVVLCKPLTGRMHQIR 529

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ---ITAPLPA 313
           VH  ++G PI+ D  Y     G           L  R+ D+    GG+     I   +  
Sbjct: 530 VHLQYLGYPILNDPLYNHEVFGP----------LKGRFGDI----GGKSDDELIRDLINI 575

Query: 314 HMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           H  + W  LG  YD ++ I +  S+DE
Sbjct: 576 HNAENW--LGIDYDSDISIFK-SSKDE 599


>gi|33865271|ref|NP_896830.1| putative pseudouridylate synthase [Synechococcus sp. WH 8102]
 gi|33632440|emb|CAE07252.1| putative pseudouridylate synthase [Synechococcus sp. WH 8102]
          Length = 213

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 59/206 (28%), Positives = 97/206 (47%), Gaps = 18/206 (8%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  + V  KP+G+  Q G G   H+   L + +        L HRLD++TSG+++VAR  
Sbjct: 16  DPWLLVVLKPSGLLSQPGRG--SHLQDSLITRLQHWSGDHHLVHRLDRDTSGLVLVARGL 73

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            + +  +  F  RR+ K+Y + V G  + +    +    + + +  D        +   +
Sbjct: 74  ESLRRCSAIFAARRVNKLYEAEVVGQLQGRGRIDS----RLARLDRDPPRYGDHPKGRPS 129

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
             +   +     + +  WL  +P TGR+HQLR H   MG PIVGD  Y        T+P+
Sbjct: 130 TTLWRVRARQPNSTQL-WL--RPLTGRSHQLRAHLAGMGHPIVGDPIYGE----ASTTPM 182

Query: 285 QNKLYLHARYMDLPHP-EGGRLQITA 309
           +    LHAR +   HP  G RL+++ 
Sbjct: 183 R----LHARALGFEHPFTGLRLRVST 204


>gi|23098677|ref|NP_692143.1| pseudouridine synthase [Oceanobacillus iheyensis HTE831]
 gi|22776904|dbj|BAC13178.1| pseudouridine synthase [Oceanobacillus iheyensis HTE831]
          Length = 322

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 64/249 (25%), Positives = 112/249 (44%), Gaps = 24/249 (9%)

Query: 78  IKEQKILDSSVNLTKHSDF-----LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           +K + IL  ++   K SD      L   ++YED+   V NKPAG +        ++    
Sbjct: 77  LKREDILTVALPDEKPSDAITPEKLPLDIIYEDAYCLVVNKPAGQACLPSMNHRHNTLAN 136

Query: 133 LKSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             ++   K   P   H   RLD  TSG+++VA+ +      +   +   I ++Y ++V G
Sbjct: 137 GLTYYYQKNSIPSTVHIVTRLDVNTSGLVLVAKNQYVHSLFSRMQQEGNINRVYEAIVHG 196

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQP 247
                   +   + +K    G  +        G  YA ++++V+  D  A    W+E++ 
Sbjct: 197 EVSPTSGIVDAPIARKE---GSIIERTVDMRNG-KYAKTNYRVLYADSIA---SWVEIKL 249

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGRTHQ+RVH  ++G  + GD+ Y        +  I  +  LH + + + HP +   +Q
Sbjct: 250 ETGRTHQIRVHFQYLGHSLYGDNLYGG------SKDIMLRQALHCKQITMMHPIKNQPIQ 303

Query: 307 ITAPLPAHM 315
           + A LP  M
Sbjct: 304 LEASLPEDM 312


>gi|149194110|ref|ZP_01871208.1| Pseudouridine synthase [Caminibacter mediatlanticus TB-2]
 gi|149136063|gb|EDM24541.1| Pseudouridine synthase [Caminibacter mediatlanticus TB-2]
          Length = 252

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/197 (28%), Positives = 85/197 (43%), Gaps = 36/197 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED+ + V +KP                 ++ S   SK  K  L HRLD+ETSGILV+
Sbjct: 60  VIFEDNNLLVIDKPP----------------YITSEEISKRFKYPLLHRLDKETSGILVL 103

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+ + + K Y + V GI     +      + K+  G  +  V    E
Sbjct: 104 TKNEDFRKKAIEEFKNKNVYKEYLAWVSGIVAEPMKIDFPIKVIKTKSGA-FAKVSSDGE 162

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----- 275
           +    AI+  + I  F  K   ++   HTG+THQ+R H   +  PI+GD KY        
Sbjct: 163 E----AITEIEPILAFRTK-SKIKAIIHTGKTHQIRAHLKAIDHPIIGDEKYGGEPYKRV 217

Query: 276 ---------FKGNFTSP 283
                    F  NF SP
Sbjct: 218 MLHHYKFKIFDYNFESP 234


>gi|320547814|ref|ZP_08042098.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           equinus ATCC 9812]
 gi|320447574|gb|EFW88333.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           equinus ATCC 9812]
          Length = 286

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 54/199 (27%), Positives = 84/199 (42%), Gaps = 16/199 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  + + NKP G+   G       +   + ++V   G+   + HRLD ETSG ++ A
Sbjct: 84  LYEDEHLIIVNKPEGMKTHGNEPNEIALLNHVSAYV---GKTCYVIHRLDMETSGAVMFA 140

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L      + I + YW+L  G  + K +   + + +  H     V V ++N +
Sbjct: 141 KNPFVLPILNRLLENKDISREYWALAQGKFEPKHQVFQDKIGRDRHDRRKRV-VDRKNGQ 199

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            A   +   K         C L+    TGRTHQ+RVH       I+GD  Y        +
Sbjct: 200 TALTIVDRLKTFKKGTLVKCRLK----TGRTHQIRVHLSAHNHAIIGDPLY--------S 247

Query: 282 SPIQNKLYLHARYMDLPHP 300
                +L LHA  +   HP
Sbjct: 248 KIPAKRLMLHAHKLSFTHP 266


>gi|297670733|ref|XP_002813514.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           3-like isoform 1 [Pongo abelii]
          Length = 350

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 57/217 (26%), Positives = 97/217 (44%), Gaps = 20/217 (9%)

Query: 89  NLTKHS--DFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKP 144
           NL++    D L++ ++     +   NKP G+ V G  G    + +   L   +    Q+ 
Sbjct: 69  NLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLGKQEL 128

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIAN 200
           ++     +E+SG+++++     A  L + F    R +R    Y ++  GIP   +  I  
Sbjct: 129 QVVRASGKESSGLVLLSSCPQTASRLQKFFTHARRAQRPTATYCAVTDGIPAASEGKI-Q 187

Query: 201 WLLKKSHIGGDYVHV-VKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             LK  HI G  + V VK   +     G    +SHF+V+         +++QP T  + Q
Sbjct: 188 AALKLEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFRVV-ATGSGCALVQLQPLTVFSSQ 246

Query: 255 LRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQNK 287
           L+VH +   CP++GDH Y A         F  P +NK
Sbjct: 247 LQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAENK 283


>gi|319646539|ref|ZP_08000768.1| YjbO protein [Bacillus sp. BT1B_CT2]
 gi|317391127|gb|EFV71925.1| YjbO protein [Bacillus sp. BT1B_CT2]
          Length = 296

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 106/228 (46%), Gaps = 22/228 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------RLTHRLDQET 154
           +L+ED  + V NK   IS         H  G L + +    Q+        L  RLD++T
Sbjct: 84  ILFEDDHVLVLNKQPCISSIPSR---EHPSGSLANGLIHYYQRTGVHATVHLVSRLDRDT 140

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA+ R A   L+   +   +++ Y ++V G+   ++  I   + +KS    +   
Sbjct: 141 SGVMLVAKHRFAHSLLSGLQKKGAVKRQYRAVVHGLIAEEQGTIDAPIGRKSSSIIERA- 199

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+   +K    A++HF V   F+     + ++  TGRTHQ+RVH  H+G P+ GD  Y  
Sbjct: 200 VIPDGQK----AVTHFWVNRRFS-GMTDVSIRLETGRTHQIRVHMSHIGYPLCGDTLYGG 254

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
                 T    N+  LH+  +   HP     L   AP+P  M +  +S
Sbjct: 255 ------TRGFINRQALHSERLTFFHPFTMEELTFQAPVPNDMRQLIES 296


>gi|154345323|ref|XP_001568603.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134065940|emb|CAM43722.1| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 754

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 98/234 (41%), Gaps = 44/234 (18%)

Query: 101 LLYEDSKIYVFNKPAGISV--------QGGSG--------IAYHIDGFLKSWVDSKGQKP 144
           +LYED  + V +KPAG++         Q G+         +A    G L   V  +GQ  
Sbjct: 514 VLYEDDDVLVIDKPAGLATSRHGLSCTQLGTQTTDLISVLLATDRAGALARGVFRQGQ-- 571

Query: 145 RLTHRLDQETSGILVVARTRAAAQHL----TESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              HRLD ETSG L++A++  AA  L      S       KIY +L   +  +       
Sbjct: 572 --VHRLDVETSGCLLIAKSNVAADSLRHQIGTSAAFSHHTKIYHALCVVLEPS------- 622

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHA 259
             L+   + GD +       K      + ++VI  F + +  W+E +   G+ HQ+R H 
Sbjct: 623 --LRNVRLHGDIIDAADPKIK------TRYRVIRFFPKHRIVWVECRIQQGKKHQIRRHL 674

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              G PI+ D  +           I ++  LHA  +   HP  G  +  TAPLP
Sbjct: 675 ASRGFPILADMDHGGAV---CCQSIMSRTALHAHSLSFIHPITGDPIIATAPLP 725


>gi|323304895|gb|EGA58653.1| Pus6p [Saccharomyces cerevisiae FostersB]
 gi|323308935|gb|EGA62166.1| Pus6p [Saccharomyces cerevisiae FostersO]
          Length = 404

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 54/191 (28%), Positives = 91/191 (47%), Gaps = 18/191 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E+  I V +KP+GI V   +G  Y     +   +   G      +RLD+ TSG+L++
Sbjct: 121 IVFENESILVIDKPSGIPVHP-TGQFYQ--NTITELLKLHGVDALPCYRLDKITSGLLIL 177

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK----KECIANWLLK-KSHIGGDYVH 214
           A+   +A  + +S R R + KIY + V G  P ++     E  A    +  S +  +   
Sbjct: 178 AKNSQSAGEIQKSIRSRDMIKIYLARVKGRFPHSELILDNESAAETTFEDTSKVTVEMTP 237

Query: 215 VVKQNEK--------GANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +   + K         +  AI+ F  I  F+      +  +P TGRTHQ+R+H   +G P
Sbjct: 238 IYSIDPKRQFPVGLSASKDAITKFYPIRYFSHADETVVACKPITGRTHQIRIHLARLGHP 297

Query: 266 IVGDHKYCANF 276
           IV D  YC++ 
Sbjct: 298 IVNDSVYCSHI 308


>gi|294792069|ref|ZP_06757217.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           6_1_27]
 gi|294457299|gb|EFG25661.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           6_1_27]
          Length = 321

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 78/337 (23%), Positives = 139/337 (41%), Gaps = 61/337 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRI 67
           ++V++D     ++   K    HI+    +++   G + ++ K   +N  I  G   ++++
Sbjct: 9   LIVDSDVHTQSINHIIKQQ--HISQRMRRRLRSDGIITINGKPATWNTLIHGGDHLIMKL 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P          EQ+   S + L          ++YED  I V NK AGI +   S +  
Sbjct: 67  TP----------EQEFSLSPMELD---------IIYEDEYILVINKAAGILMHPTSTVRD 107

Query: 128 HI--DGFLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHL-----------TES 173
           H   +G L  + ++         HRLD++TSGI+++A+T +  QH             ++
Sbjct: 108 HTLANGVLHYYQETNQHYDFHPVHRLDKDTSGIVIIAKT-SVVQHAFDKKHTYFYKSYDA 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF--- 230
                +  +  S+ W I +     I      +       + V+ +N    NY+ ++    
Sbjct: 167 IVEGHLPSVPISINWPIGRKPGSIIERCCTDQGKPARTDITVISKNTSKINYSKNNSDNL 226

Query: 231 -----------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                       +ID     F  ++   HTGRTHQ+RVH   +G P+ GD  Y     G 
Sbjct: 227 INNSNICPTDNSLID--HNHFTHVQCLLHTGRTHQIRVHLSQLGYPLAGDDLY-----GG 279

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
               IQ +  LHA ++   HP     +++ A +P  M
Sbjct: 280 HLEFIQRQA-LHASHVSFYHPITNEWIELHAEMPEDM 315


>gi|54022650|ref|YP_116892.1| putative RNA pseudouridylate synthase [Nocardia farcinica IFM
           10152]
 gi|54014158|dbj|BAD55528.1| putative RNA pseudouridylate synthase [Nocardia farcinica IFM
           10152]
          Length = 260

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 105/254 (41%), Gaps = 33/254 (12%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           T  S   +  LL ED  +   NKPAGISV G        D  +       G++    HR+
Sbjct: 3   TDWSRLRERCLLAEDDAVLALNKPAGISVTG-----ERHDTDIVELAAGAGERLFPVHRI 57

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIP-------------KNKK 195
           D+ TSG++++A+  AA   LT  F  R  +K Y ++V   G+P             KN+ 
Sbjct: 58  DKVTSGLVLLAKDLAAHGTLTRQFTKRTAEKAYLAVVAGGGLPDRGVIELPLSVGRKNRV 117

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
              A     ++  G  +V            + + F  +   A +   L ++P TGR HQ+
Sbjct: 118 RIAAPRESIRAEDGRWFVDDADLLAVKNYPSRTEFVTLARTADRTV-LALRPVTGRRHQI 176

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA--RYMDLPHPEGGRLQITAPLPA 313
           RVH   +G  IVGD  +         S    + +LH+    +D P      L +TAP  A
Sbjct: 177 RVHLAWIGHAIVGDPLFD-------KSAAHPRAHLHSWRLVLDAPWRTPPELDLTAPPDA 229

Query: 314 HMVKTWDSLGFKYD 327
                W  LG   D
Sbjct: 230 GF---WAPLGAGAD 240


>gi|308184144|ref|YP_003928277.1| hypothetical protein HPSJM_01820 [Helicobacter pylori SJM180]
 gi|308060064|gb|ADO01960.1| hypothetical protein HPSJM_01820 [Helicobacter pylori SJM180]
          Length = 293

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 75/290 (25%), Positives = 125/290 (43%), Gaps = 51/290 (17%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII------KEQKILDSSVNLTKHS 94
           L+  Q  +DK+R+K     Q+ Q VR   +I  +  +I      K+++            
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVRKSQIIQGVVRLIYFKPNEKQER------------ 70

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
                 L++E +    F+KPA I         +H +  L       G+     HRLD ET
Sbjct: 71  ------LVFETNDFGAFDKPAQIYTHPKG--YFHHESLLDCIQSHFGKNAHPAHRLDYET 122

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV 213
           SG+++  +T  +A+ L   F  ++++K Y +L  G I KN K  I   +L   +I  D +
Sbjct: 123 SGLVLAGKTLQSAKDLKALFMQKKVKKTYLALTHGLIEKNMK--IDKPILTPQNIQKD-L 179

Query: 214 HVVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  Q       +I+  + +  + F      L++ P TGRTHQ+R+H   +   IVG+  
Sbjct: 180 RIRSQISPLGKPSITLVEPLSYNPFLD-ISLLKITPLTGRTHQIRLHLSSINHRIVGEGL 238

Query: 272 YCA---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           Y             K    +P    L LHA  ++    +G   QI +P+P
Sbjct: 239 YGVADENAREYLQLKRENNAPT---LMLHAASLEFEF-KGAIYQIASPMP 284


>gi|262276093|ref|ZP_06053902.1| putative pseudouridine synthase Rlu family protein [Grimontia
           hollisae CIP 101886]
 gi|262219901|gb|EEY71217.1| putative pseudouridine synthase Rlu family protein [Grimontia
           hollisae CIP 101886]
          Length = 223

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/174 (31%), Positives = 82/174 (47%), Gaps = 14/174 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGIL 158
           L++++    V +K  GISV          D  L S V  K   +K  L HRLD+ TSG+L
Sbjct: 4   LIFQNDDFLVIDKHPGISVHKDDN-----DQPLLSEVAKKTGNEKLYLIHRLDKMTSGLL 58

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ +   AA  L+  F  + +QK Y +L    P  K+  I   + K          + K 
Sbjct: 59  LLGKHPQAASDLSLMFAEKTVQKFYLALSAKKPGKKQGTIVGDMAKSRR------SMWKL 112

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               +N AI+ F        K  +L  +P+TG+THQ+RV    +G PI+GD  Y
Sbjct: 113 LPTKSNPAITQFFSTAGGEGKRLFL-CKPYTGKTHQIRVALKSVGSPILGDSTY 165


>gi|160897919|ref|YP_001563501.1| pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160363503|gb|ABX35116.1| pseudouridine synthase [Delftia acidovorans SPH-1]
          Length = 319

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 68/263 (25%), Positives = 106/263 (40%), Gaps = 19/263 (7%)

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
           +A  H +  Q     S       D     +L+ D  +    KPAG  V      A+    
Sbjct: 24  SAYTHALMFQPSSIPSPAQPPEPDDAPLHILWRDEHLVAVYKPAGWLVHRTGLDAHETRF 83

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L++  D  G      HRLD+ T G+LV+A    AAQ L ++F  + ++K Y +LV G  
Sbjct: 84  VLQTLRDQLGCHVYPAHRLDKGTCGVLVMALHAQAAQRLGQAFAGQEVRKQYLALVRGWL 143

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-----AQKFCWLEMQ 246
            +  E   +  L+      D      Q  + +   ++  +  + F     A +   +E  
Sbjct: 144 PDAVEV--DHALRPDDAPED---APAQPAQTSLRCLARLEWPEAFDPRHAATRISLVEAL 198

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR 304
           P TGR HQ+R H  H+  PI+GD  +       + +      +L+LHA  ++L HP  G 
Sbjct: 199 PATGRRHQIRRHLKHVAHPIIGDATHGKGPLNRWWAERLGLQRLWLHAHALELAHPMTGE 258

Query: 305 LQITAPLPAHMVKTWDSLGFKYD 327
                  P      W  LG   D
Sbjct: 259 -------PLRFEADWRQLGHVAD 274


>gi|256827075|ref|YP_003151034.1| pseudouridine synthase, RluA family [Cryptobacterium curtum DSM
           15641]
 gi|256583218|gb|ACU94352.1| pseudouridine synthase, RluA family [Cryptobacterium curtum DSM
           15641]
          Length = 347

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 81/334 (24%), Positives = 138/334 (41%), Gaps = 47/334 (14%)

Query: 10  VVVENDEENMRLDRWF--KNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVR 66
           ++V   +  MRLD        YP           RS  V+ ++  +V  N   +S + + 
Sbjct: 7   LIVTQADAGMRLDSLLAVSGAYPS----------RSAAVKQIEAGKVLVNGLARSKRSIV 56

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV------Q 120
            P      + I+ E+  L + + L      L   + +ED  +   +K AG+ V      +
Sbjct: 57  APG-----DTIVYEEIPLATHIPLRGEPIPLD--VRFEDRWMMAISKQAGLCVHPAPGHE 109

Query: 121 GGSGI-----AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           GG+ +     AY  D       D    +P + HRLD +TSG+++ A+       L +  R
Sbjct: 110 GGTLVNALIYAYGRDSLAHVQGD---DRPGIVHRLDMDTSGLMMCAKDDTCGMALQDLVR 166

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             ++ + Y +LV G        I   +     +G D + +       A  A++ F V++ 
Sbjct: 167 DHKVDRRYLTLVHGNIAFDTGQIDEPI---GRVGDDRLRMKISYRPTARNALTTFTVLER 223

Query: 236 FA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLY 289
           F        +  LE + +TGRTHQ+RVH   +G   VGD  Y   N + N      ++ +
Sbjct: 224 FEAGRADNGYTLLECRLYTGRTHQIRVHMEFIGHCCVGDPLYRWGNEQVNLE---LSRQF 280

Query: 290 LHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           LH+  +   HP  G  + +   LP  +     SL
Sbjct: 281 LHSYSLSFNHPMTGDDIALVDGLPPDLFGALRSL 314


>gi|332527619|ref|ZP_08403666.1| putative ribosomal large subunit pseudouridine synthase A
           [Rubrivivax benzoatilyticus JA2]
 gi|332112022|gb|EGJ11999.1| putative ribosomal large subunit pseudouridine synthase A
           [Rubrivivax benzoatilyticus JA2]
          Length = 210

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 57/186 (30%), Positives = 90/186 (48%), Gaps = 23/186 (12%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSKGQKPRLTHRLDQ 152
            L    LY D    V  KPAG+    G G       +      W D+        HRLD 
Sbjct: 1   MLPPDCLYADEHCLVLAKPAGLLAVPGRGPDKQDCLVARAQACWPDAL-----TVHRLDM 55

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGD 211
            TSG++V  R  AA + L+ +F  RR+ K Y ++V G I ++  E  A  +        D
Sbjct: 56  ATSGLMVYGRGAAAQRTLSIAFAERRVDKRYVAVVAGLIAEDTGEVDAPLIC-------D 108

Query: 212 YVHVVKQ---NEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           + +  +Q   +E G   +++ ++V+  D  A +   +E++P TGR+HQLR+H   +G P+
Sbjct: 109 WPNRPRQKVCHEHG-KPSLTRWRVLARDRAAGRT-RVELEPVTGRSHQLRLHLATIGHPM 166

Query: 267 VGDHKY 272
           +GD  Y
Sbjct: 167 LGDDLY 172


>gi|216548145|ref|NP_775930.2| RNA pseudouridylate synthase domain-containing protein 3 isoform 1
           [Homo sapiens]
 gi|294862493|sp|Q6P087|RUSD3_HUMAN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 3
 gi|119584411|gb|EAW64007.1| RNA pseudouridylate synthase domain containing 3, isoform CRA_b
           [Homo sapiens]
          Length = 351

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 53/200 (26%), Positives = 93/200 (46%), Gaps = 16/200 (8%)

Query: 89  NLTKHS--DFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKP 144
           NL++    D L++ ++     +   NKP G+ V G  G    + +   L   +  + Q+ 
Sbjct: 69  NLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLREQEL 128

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIAN 200
           ++     +E+SG+++++     A  L + F    R +R    Y ++  GIP   +  I  
Sbjct: 129 QVVRASGKESSGLVLLSSCPQTASRLQKYFTHARRAQRPTATYCAVTDGIPAASEGKI-Q 187

Query: 201 WLLKKSHIGGDYVHV-VKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             LK  HI G  + V VK   +     G    +SHF+V+         +++QP T  + Q
Sbjct: 188 AALKLEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFRVV-ATGSGCALVQLQPLTVFSSQ 246

Query: 255 LRVHALHMGCPIVGDHKYCA 274
           L+VH +   CP++GDH Y A
Sbjct: 247 LQVHMVLQLCPVLGDHMYSA 266


>gi|258566750|ref|XP_002584119.1| hypothetical protein UREG_04808 [Uncinocarpus reesii 1704]
 gi|237905565|gb|EEP79966.1| hypothetical protein UREG_04808 [Uncinocarpus reesii 1704]
          Length = 537

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 66/277 (23%), Positives = 106/277 (38%), Gaps = 65/277 (23%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           ++ + SG V ++ K    + R+ +G +V                     S  L +H   +
Sbjct: 84  KEAIESGHVAINGKPGNLDTRVMNGDMV---------------------SHTLHRHEPPV 122

Query: 98  KSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQ 152
            S+   +++ED K+ V +KPAG+ V       Y+ +  ++     +G    PR  +RLD+
Sbjct: 123 TSLPIGVIHEDDKMIVIDKPAGVPVHPAG--RYNYNSIIEIMRAERGHSFNPRPCNRLDR 180

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGD 211
            TSG++ + +   AA+ + E  R R +QK Y + V G  P     C    L     +G +
Sbjct: 181 LTSGVMFIGKDPKAAEKIAEGLRARTMQKEYIARVKGKFPDGIILCDQPMLKISPQLGLN 240

Query: 212 YVH--------------------VVKQNEKGANYAISHFKVIDCFAQKF----------- 240
            V                     V K++      A     + D     F           
Sbjct: 241 RVRSSGKEAKTKFRRLAYYPPTAVTKKSSSEDEPATPPATLPDDAPMDFPNNNNKATTTP 300

Query: 241 -----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                  +   P TGRTHQLRVH   +G PI  D  Y
Sbjct: 301 DDEGYSIVHCLPLTGRTHQLRVHLQFLGHPITNDPIY 337


>gi|296089768|emb|CBI39587.3| unnamed protein product [Vitis vinifera]
          Length = 274

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 73/267 (27%), Positives = 112/267 (41%), Gaps = 54/267 (20%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP----RLTHRLD 151
             +S +L+ED  +   NKP G+  +    I   +   L    DS G        L +RLD
Sbjct: 12  LCRSDILFEDQWLMAVNKPQGVYCET---ILLSVSRMLD---DSDGHDSCRSLHLANRLD 65

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIAN---------W 201
           ++TSG++V+ ++   A  L ++F  R++ K Y +L  G  P  +K  I +         W
Sbjct: 66  RDTSGVMVITKSHQVAAKLMKAFSDRKVTKTYLALCIGAAPTWEKITIKSGHGRSKFGAW 125

Query: 202 -LLKKSHIG---------GDYV---HVVKQNEKG-------------ANYAISHFKVIDC 235
            +   S +G          D V    V+  N +G                 +    VID 
Sbjct: 126 RVYAASDVGRALPNAPAIKDMVTSFEVLSVNGQGNVKELPESRKADETVLVVEERSVIDS 185

Query: 236 FA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHA 292
            A Q    +   P +GRTHQ+R+H  ++G  I GD KY     +KG     I +   LHA
Sbjct: 186 NARQDEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVHEWKGK----IYDGHELHA 241

Query: 293 RYMDLPHP-EGGRLQITAPLPAHMVKT 318
             +   HP  G  +   APLP+  V+ 
Sbjct: 242 ESLSFEHPVTGVDVAFRAPLPSWAVQA 268


>gi|227512831|ref|ZP_03942880.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus buchneri ATCC
           11577]
 gi|227083831|gb|EEI19143.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus buchneri ATCC
           11577]
          Length = 299

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 99/218 (45%), Gaps = 19/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED    V +KPAG++V  G       +   + G+L     +    P +  RLD+ TS
Sbjct: 87  VVYEDDNWLVVDKPAGLTVVPGPANRDDTLVNRVKGYLVR-AGATDLVPHIITRLDRFTS 145

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++++A+ R A     E    +++ K Y ++V G+       I   + K  +    Y  +
Sbjct: 146 GLVLIAKHRLANSLANELLAAKQLHKRYLAVVSGVGLPDHGRIQKPIAKDPN---GYGQI 202

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +  + +   ++ + + V          +E+  HTGRTHQ+RVH   +G P++GD  Y   
Sbjct: 203 ISDDGR---FSDTEYWVRQRLNDDML-VEVALHTGRTHQIRVHFASIGHPLLGDQLYHGP 258

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                     ++  LHA  +    P     +++ +PLP
Sbjct: 259 MNMGI-----DRQALHAVMLGFNDPFSQSEIKLKSPLP 291


>gi|160933803|ref|ZP_02081191.1| hypothetical protein CLOLEP_02664 [Clostridium leptum DSM 753]
 gi|156867680|gb|EDO61052.1| hypothetical protein CLOLEP_02664 [Clostridium leptum DSM 753]
          Length = 298

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 106/232 (45%), Gaps = 31/232 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG----FLKSWVDSKGQ--KPRLTHRLDQET 154
           +L+ED  + + NKP  + V    G   H  G    F+  +   KG+  + R  +RLD++T
Sbjct: 81  VLWEDDALLILNKPPLMPVHPCPG---HDRGTVCNFVSYYQKRKGEDWRFRPLNRLDKDT 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+    A  L +      + K Y+++  G    +        LK+ H       
Sbjct: 138 SGLVIGAKDSYTASALND------VGKTYFAVCQGSLPGEGVIDTPIRLKEGH------S 185

Query: 215 VVKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           + ++  +G   A++H+K +       + +  L +   TGRTHQ+RVH   +G P+ GD  
Sbjct: 186 IQREAGEGGKPAVTHWKSLAQGAAAGKSYTLLALTLETGRTHQIRVHLSSIGHPLAGDDF 245

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           Y  + +      + ++  LH   ++L HP    R+ + AP P    K  + L
Sbjct: 246 YGGSRE------LISRQALHCGLVELTHPFFLSRICVKAPFPNDFKKILEFL 291


>gi|268680270|ref|YP_003304701.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
 gi|268618301|gb|ACZ12666.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
          Length = 242

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 51/173 (29%), Positives = 83/173 (47%), Gaps = 24/173 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  I   +KPA                F+ S   ++ +K  L HRLD+ETSG+L++
Sbjct: 58  VLFEDEYIMAVDKPA----------------FITSEEVAEIKKLPLLHRLDRETSGVLLL 101

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQN 219
            +     Q    +F+ R + K Y ++V G      E  A  L +KK +    Y  +    
Sbjct: 102 TKDDEFRQKAVNAFKKREVHKEYIAIVEGKVVEATEVNAPILTIKKGNTA--YSKISPDG 159

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++    AIS+ + +     K   +++   TGRTHQ+RVH   +G  I+GD +Y
Sbjct: 160 KE----AISYIEPL-MIEGKRSKIKVTIETGRTHQIRVHLKSIGASILGDTEY 207


>gi|154302617|ref|XP_001551718.1| hypothetical protein BC1G_09885 [Botryotinia fuckeliana B05.10]
 gi|150855374|gb|EDN30566.1| hypothetical protein BC1G_09885 [Botryotinia fuckeliana B05.10]
          Length = 453

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 103/242 (42%), Gaps = 28/242 (11%)

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVF 111
           + + ++ G +      + +++ IIK   ++  S  L +H   + ++   +++ED  I V 
Sbjct: 82  YKDAMERGAIAVNGKPVESISQIIKNGDVI--SHTLHRHEPPVTALPISIVHEDEDIIVI 139

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           NKP+G+ V       Y+    +       G  P   +RLD+ TSGI+ + +   AA+ L+
Sbjct: 140 NKPSGVPVHPAGRYNYNSVVEIMRAERGHGWNPLPCNRLDRLTSGIMFIGKHAKAAEALS 199

Query: 172 ESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
                R ++K Y + V G  P  +  C    L     +G   ++ V+ N K A       
Sbjct: 200 LQISGRTVRKEYIARVKGKFPDGEVVCDMPILQISPKLG---LNRVRANGKAARTVFKRL 256

Query: 231 ------------------KVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                             K     A++ +  +   P TGRTHQLRVH   +G PI  D  
Sbjct: 257 AYYPPEQAHDNPEQTELDKTRPPMAKEGYSIVRCLPVTGRTHQLRVHLQFLGHPIGNDPI 316

Query: 272 YC 273
           YC
Sbjct: 317 YC 318


>gi|37679587|ref|NP_934196.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
 gi|37198331|dbj|BAC94167.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
          Length = 231

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/192 (28%), Positives = 88/192 (45%), Gaps = 17/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL++
Sbjct: 4   ILFTHPDFLIINKYPHVSVHKDDGDTMLLQEVAKV---SGDEQLYLIHRLDKMTSGILLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   AA  L++ F  R ++K Y ++    PK K+  +   + +        V+  KQN 
Sbjct: 61  GRNSTAASALSQRFAQREVEKFYLAIGAKKPKKKQGTVIGDMERSRRASWKLVN-SKQNP 119

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                AI+ F  +     +  +L  +P+TG+THQ+RV    +G  I+GD  Y A      
Sbjct: 120 -----AITQFFSLAGEPGERAFL-CKPYTGKTHQIRVALKSVGSSIIGDPIYNAGSD--- 170

Query: 281 TSPIQNKLYLHA 292
                ++ YLHA
Sbjct: 171 ----SDRGYLHA 178


>gi|41388987|gb|AAH65741.1| RNA pseudouridylate synthase domain containing 3 [Homo sapiens]
          Length = 343

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 53/200 (26%), Positives = 93/200 (46%), Gaps = 16/200 (8%)

Query: 89  NLTKHS--DFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKP 144
           NL++    D L++ ++     +   NKP G+ V G  G    + +   L   +  + Q+ 
Sbjct: 61  NLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLREQEL 120

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIAN 200
           ++     +E+SG+++++     A  L + F    R +R    Y ++  GIP   +  I  
Sbjct: 121 QVVRASGKESSGLVLLSSCPQTASRLQKYFTHARRAQRPTATYCAVTDGIPAASEGKI-Q 179

Query: 201 WLLKKSHIGGDYVHV-VKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             LK  HI G  + V VK   +     G    +SHF+V+         +++QP T  + Q
Sbjct: 180 AALKLEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFRVV-ATGSGCALVQLQPLTVFSSQ 238

Query: 255 LRVHALHMGCPIVGDHKYCA 274
           L+VH +   CP++GDH Y A
Sbjct: 239 LQVHMVLQLCPVLGDHMYSA 258


>gi|212637673|ref|YP_002314198.1| pseudouridine synthase RluA-like protein [Shewanella piezotolerans
           WP3]
 gi|212559157|gb|ACJ31611.1| Pseudouridine synthase RluA-like protein [Shewanella piezotolerans
           WP3]
          Length = 237

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 44/154 (28%), Positives = 72/154 (46%), Gaps = 17/154 (11%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  TSG+L++A++ A A   T  F   ++QK Y +L  G PK K+     W++   
Sbjct: 59  VHRLDTMTSGLLILAKSSAVAAEFTRQFSEHKVQKYYLALAKGKPKKKQ----GWVIGDM 114

Query: 207 HIGGDYVH-VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                 +H +++  +  A        V D          ++P +G+THQLRV    +G P
Sbjct: 115 AKSRRSMHKLLRSMDNPAKTQFFSHSVGDGLRLYL----LKPLSGKTHQLRVALASIGVP 170

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           I+GD  Y  +          ++ YLHA  ++  +
Sbjct: 171 ILGDELYGGD--------ASDRGYLHAYSLNFSY 196


>gi|21619426|gb|AAH32135.1| RNA pseudouridylate synthase domain containing 3 [Homo sapiens]
 gi|312151418|gb|ADQ32221.1| RNA pseudouridylate synthase domain containing 3 [synthetic
           construct]
          Length = 343

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 53/200 (26%), Positives = 93/200 (46%), Gaps = 16/200 (8%)

Query: 89  NLTKHS--DFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKP 144
           NL++    D L++ ++     +   NKP G+ V G  G    + +   L   +  + Q+ 
Sbjct: 61  NLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLREQEL 120

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIAN 200
           ++     +E+SG+++++     A  L + F    R +R    Y ++  GIP   +  I  
Sbjct: 121 QVVRASGKESSGLVLLSSCPQTASRLQKYFTHARRAQRPTATYCAVTDGIPAASEGKI-Q 179

Query: 201 WLLKKSHIGGDYVHV-VKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             LK  HI G  + V VK   +     G    +SHF+V+         +++QP T  + Q
Sbjct: 180 AALKLEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFRVV-ATGSGCALVQLQPLTVFSSQ 238

Query: 255 LRVHALHMGCPIVGDHKYCA 274
           L+VH +   CP++GDH Y A
Sbjct: 239 LQVHMVLQLCPVLGDHMYSA 258


>gi|326803815|ref|YP_004321633.1| pseudouridine synthase, RluA family [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326651014|gb|AEA01197.1| pseudouridine synthase, RluA family [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 300

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 72/284 (25%), Positives = 123/284 (43%), Gaps = 34/284 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSG-QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
            G + V+ KRV     +  G QV  I P   + + I+     LD               +
Sbjct: 35  GGTIIVNNKRVGSKYFLSLGDQVTIIYPAEGSQDQIMAVDFPLD---------------I 79

Query: 102 LYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGI 157
           LYED    + NKPAG  S+       Y +  F+K++   K  + ++ H   RLD+ TSG 
Sbjct: 80  LYEDRDYLIVNKPAGYTSIPSQFKDEYSMANFVKAYFVRKNYENQVIHVVTRLDRFTSGA 139

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+ + A   + +  +   I K Y +       + +       L ++ IG     +++
Sbjct: 140 MIFAKHKYAHSQIDQLMQSGGINKQYLAFTHSAIGSDQHG-----LIEAPIGRKEGSIIE 194

Query: 218 QNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +  +    +A + + + D  A  + +  +Q HTGRTHQ+RVH  ++G P+ GD  Y  + 
Sbjct: 195 RCIRADGQHAKTEYWLEDSQAGLYRY-RVQLHTGRTHQIRVHFAYLGAPLCGDDLYGGSQ 253

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           +   +        LH + +    P     L I APL +   KTW
Sbjct: 254 EAGLSGQA-----LHCQRLAFKQPLTQEDLVIEAPL-SQDFKTW 291


>gi|52785027|ref|YP_090856.1| YjbO [Bacillus licheniformis ATCC 14580]
 gi|163119352|ref|YP_078456.2| pseudouridine synthase YjbO [Bacillus licheniformis ATCC 14580]
 gi|52347529|gb|AAU40163.1| YjbO [Bacillus licheniformis ATCC 14580]
 gi|145902858|gb|AAU22818.2| Pseudouridine synthase YjbO [Bacillus licheniformis ATCC 14580]
          Length = 291

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 106/228 (46%), Gaps = 22/228 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------RLTHRLDQET 154
           +L+ED  + V NK   IS         H  G L + +    Q+        L  RLD++T
Sbjct: 79  ILFEDDHVLVLNKQPCISSIPSR---EHPSGSLANGLIHYYQRTGVHATVHLVSRLDRDT 135

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA+ R A   L+   +   +++ Y ++V G+   ++  I   + +KS    +   
Sbjct: 136 SGVMLVAKHRFAHSLLSGLQKKGAVKRQYRAVVHGLIAEEQGTIDAPIGRKSSSIIERA- 194

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+   +K    A++HF V   F+     + ++  TGRTHQ+RVH  H+G P+ GD  Y  
Sbjct: 195 VIPDGQK----AVTHFWVNRRFS-GMTDVSIRLETGRTHQIRVHMSHIGYPLCGDTLYGG 249

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
                 T    N+  LH+  +   HP     L   AP+P  M +  +S
Sbjct: 250 ------TRGFINRQALHSERLTFFHPFTMEELTFQAPVPNDMRQLIES 291


>gi|237751452|ref|ZP_04581932.1| conserved hypothetical protein [Helicobacter bilis ATCC 43879]
 gi|229372818|gb|EEO23209.1| conserved hypothetical protein [Helicobacter bilis ATCC 43879]
          Length = 279

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/199 (28%), Positives = 93/199 (46%), Gaps = 29/199 (14%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++ED  I   +K  GI        +Y     LK++   K     L +RLD++TSG+++
Sbjct: 90  VVIFEDDDILALDKSVGIE-------SY---SLLKTYPHYK-----LINRLDKDTSGVIL 134

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+     Q   ++F+ + ++K+Y++L+ G    +         +K      YV     N
Sbjct: 135 LAKNEKMRQKAIQAFKQKEVEKMYFALIEGKVYEEINIEKKISTQKDSKAKSYV----DN 190

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E    YA S    +  F      + +Q  TGRTHQ+R+H   +  PI+GD  Y      N
Sbjct: 191 E--GLYAQSIVTPLQTFTHT-TLVSVQIPTGRTHQIRIHLKSIKHPIIGDIIY------N 241

Query: 280 FTSPIQNK-LYLHARYMDL 297
            TS I+ K L LH +   L
Sbjct: 242 KTSLIKAKRLMLHCQKTSL 260


>gi|323693993|ref|ZP_08108177.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Clostridium symbiosum WAL-14673]
 gi|323501929|gb|EGB17807.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Clostridium symbiosum WAL-14673]
          Length = 272

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/203 (27%), Positives = 93/203 (45%), Gaps = 23/203 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----IAYHIDGFLKSWVDSK-GQKPR---------- 145
           ++YED  I V  KPAG+  Q   G    +   I   LK    S+   KP           
Sbjct: 4   IIYEDHDILVAEKPAGLESQASRGFEPDMVSEIKNHLKRAELSRLSTKPSTKSSTRPVEP 63

Query: 146 ---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              + HRLD+   GI+V A+ + AA  L++  +  R++KIY ++V G   +      ++L
Sbjct: 64  YVGVIHRLDKPVGGIMVYAKNQKAAASLSKQVQDGRMKKIYNAVVCGKLVDIVGNYVDYL 123

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHA 259
           LK      ++  VV ++   +  A   ++ +D   +   +   +E++  +GR HQ+RV  
Sbjct: 124 LKDGR--NNFSFVVDKDTPDSRRAELVYRALDVKTEEEREISLVEIELLSGRHHQIRVQF 181

Query: 260 LHMGCPIVGDHKYCANFKGNFTS 282
              G P+ GD KY   + G   +
Sbjct: 182 AAHGNPLWGDGKYNPEWGGTLPA 204


>gi|51246609|ref|YP_066493.1| ribosomal large subunit pseudouridine synthase D [Desulfotalea
           psychrophila LSv54]
 gi|50877646|emb|CAG37486.1| related to ribosomal large subunit pseudouridine synthase D
           [Desulfotalea psychrophila LSv54]
          Length = 238

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/221 (24%), Positives = 100/221 (45%), Gaps = 19/221 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED+ I + +K AG++     +     AY  +  ++K  V     +  L H +D+E S
Sbjct: 21  IVYEDNDIILVDKVAGLATTSRDKDNENTAYFRLTNYVKKGVAKSSNRVFLIHHVDKEAS 80

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+ A+T  A +HL +++    +   Y + V G+P  + E +    L ++ I   YV V
Sbjct: 81  GLLIFAKTEKARRHLLDNWSDFNVS--YVAAVHGVPV-QTEGVLRANLAENMIHKMYVTV 137

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  + A    S  +     +  +  L ++P T   HQ+RV     G  I+ D  Y   
Sbjct: 138 AGEKTRPAETEYSLLQ----HSANYSLLSLRPKTEVKHQVRVQLADKGHSIIADKIYGVK 193

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
                 S    +L LHA ++ + HP   + +   + +P H 
Sbjct: 194 ------SDEMKRLALHAAHLTITHPHTKKEMSFESRVPGHF 228


>gi|88597629|ref|ZP_01100862.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|88189933|gb|EAQ93909.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
          Length = 281

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/201 (27%), Positives = 100/201 (49%), Gaps = 17/201 (8%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKS 135
           ++ KIL+  V L  + +  K + +++E+    +  K +GI S   G    Y + D     
Sbjct: 29  EKNKILNGLVELIVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           W    G++  + HRLD+ETSG++++ + + A   L   F  + +QK Y +L  G      
Sbjct: 89  W----GKEACVAHRLDKETSGLILITKNKKAQIDLKSLFEKKLVQKEYLALAHG------ 138

Query: 196 ECIANWLLKKS-HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           +   N+++ K+ ++  +Y  V    Q  K    AI+ F++++ F +     L  +P TGR
Sbjct: 139 KIEENFIVDKAINLTKNYDDVKTRMQICKEGKQAITEFEILEYFPKINATLLLCKPLTGR 198

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ+RVH  +    I+GD  Y
Sbjct: 199 QHQIRVHLHYKNHTILGDPLY 219


>gi|323486215|ref|ZP_08091543.1| ribosomal large subunit pseudouridine synthase [Clostridium
           symbiosum WAL-14163]
 gi|323400433|gb|EGA92803.1| ribosomal large subunit pseudouridine synthase [Clostridium
           symbiosum WAL-14163]
          Length = 272

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/203 (27%), Positives = 93/203 (45%), Gaps = 23/203 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----IAYHIDGFLKSWVDSK-GQKPR---------- 145
           ++YED  I V  KPAG+  Q   G    +   I   LK    S+   KP           
Sbjct: 4   IIYEDHDILVAEKPAGLESQASRGFEPDMVSEIKNHLKRAELSRLSTKPSTKSSTRPVEP 63

Query: 146 ---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              + HRLD+   GI+V A+ + AA  L++  +  R++KIY ++V G   +      ++L
Sbjct: 64  YVGVIHRLDKPVGGIMVYAKNQKAAASLSKQVQDGRMKKIYNAVVCGKLVDIVGNYVDYL 123

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHA 259
           LK      ++  VV ++   +  A   ++ +D   +   +   +E++  +GR HQ+RV  
Sbjct: 124 LKDGR--NNFSFVVDKDTPDSRRAELVYRALDVKTEEEREISLVEIELLSGRHHQIRVQF 181

Query: 260 LHMGCPIVGDHKYCANFKGNFTS 282
              G P+ GD KY   + G   +
Sbjct: 182 AAHGNPLWGDGKYNPEWGGTLPA 204


>gi|311029948|ref|ZP_07708038.1| pseudouridylate synthase [Bacillus sp. m3-13]
          Length = 204

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 91/194 (46%), Gaps = 23/194 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    + ++  ++N R+D+         +   +Q+ ++ GQ+ V+ ++ K N +   G 
Sbjct: 1   MTETMTIQIDESQKNDRIDKVLSTQNEEWSRSQVQQWIKEGQILVNGEKTKPNYKCSVGD 60

Query: 64  VVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            + +  P   AL+ ++ E+  LD               + YED+ + V NKP G+ V   
Sbjct: 61  NITVTIPEPEALD-VVPEEMDLD---------------IYYEDADVIVVNKPRGMVVHPA 104

Query: 123 SG--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      
Sbjct: 105 VGHVTGTLVNGLMAHCNDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDFAHEKLVNQLVA 164

Query: 177 RRIQKIYWSLVWGI 190
           + + + Y ++V G+
Sbjct: 165 KTVTRKYQAIVHGV 178


>gi|118473504|ref|YP_886109.1| RNA pseudouridine synthase family protein [Mycobacterium smegmatis
           str. MC2 155]
 gi|118174791|gb|ABK75687.1| RNA pseudouridine synthase family protein [Mycobacterium smegmatis
           str. MC2 155]
          Length = 291

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 97/243 (39%), Gaps = 23/243 (9%)

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-------LLYEDS 106
           +   R  +G  VR   V +    ++ E  +L    ++  + D    +       +LY D 
Sbjct: 35  ELERRFGAGWKVRAGEVFSRDGTVLDESTVLPPGSHVYLYRDLPDEVDVPFDIPVLYRDD 94

Query: 107 KIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
            I V +KP  ++     G +       L+  +D     P   HRLD+ T+G+L+    R 
Sbjct: 95  DIVVVDKPHFLATMPRGGHVTQTALVRLRRELDLPELAP--AHRLDRLTAGVLLFTVRRE 152

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
                   F    +QK Y +   G+PK     IA     +S I      +    E G   
Sbjct: 153 LRGAYQTMFARGDVQKTYLAHAEGVPK-----IALPATLRSRIVKHRGRLQAFEEPGEPN 207

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTS 282
           A ++ + +           + P TGRTHQLRVH   +G PI GD  Y        G+F+ 
Sbjct: 208 AETYVEAVGD-----GLYRLTPRTGRTHQLRVHMASIGLPITGDPFYPTVIDVAPGDFSR 262

Query: 283 PIQ 285
           P+Q
Sbjct: 263 PLQ 265


>gi|302692494|ref|XP_003035926.1| hypothetical protein SCHCODRAFT_30820 [Schizophyllum commune H4-8]
 gi|300109622|gb|EFJ01024.1| hypothetical protein SCHCODRAFT_30820 [Schizophyllum commune H4-8]
          Length = 262

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/179 (30%), Positives = 81/179 (45%), Gaps = 12/179 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETS 155
           +++I   ED  + V  KP G+ V       Y+    L   +  +G    R   RLD+ TS
Sbjct: 90  VRAISQSED--LLVVEKPGGVPVHPVGRYRYNC---LTHMMREQGLPAVRPVSRLDRLTS 144

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVH 214
           G+++      AA  L  + R  R++K Y + V G  P+    C    LL    +G   VH
Sbjct: 145 GVMLFPLNARAAGRLGVALRDGRVRKEYLARVRGRFPREPVLCKEKLLLVHRQLGLSIVH 204

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                E+G   A +  +V          +  +P+TGRTHQ+RVH LH+G PI  D  Y 
Sbjct: 205 -----EEGKPSATAFVRVSYDAKTDTSLVLCRPYTGRTHQIRVHLLHLGHPIPNDPYYA 258


>gi|218675156|ref|ZP_03524825.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli GR56]
          Length = 199

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 52/204 (25%), Positives = 90/204 (44%), Gaps = 36/204 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV-V 65
           ++ V+  ++    RLD W                  + QV  D  R +    I+ GQV +
Sbjct: 3   IRKVLTADETAEGRLDAWL-----------------TAQVGEDFSRSRIKALIKDGQVSM 45

Query: 66  RIPPVINALNHIIKEQK---ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           R  PV +    +         L    + T   + +   +LYED  + V +KPAG+ V   
Sbjct: 46  RGEPVTDPQRKVRVGDSFEITLPEPEDPTPRGEDIPLDILYEDDDLIVISKPAGLVVHPA 105

Query: 123 SG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           SG         + +H    L        ++P + HRLD++T+G++VVA+   A +HL+  
Sbjct: 106 SGNWTGTLVNALIHHCGATLSGI--GGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQ 163

Query: 174 F----RMRRIQKIYWSLVWGIPKN 193
           F    R   +++ Y ++VWG P++
Sbjct: 164 FADHGRTMPLERAYQAIVWGRPRS 187


>gi|282850437|ref|ZP_06259816.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
 gi|282579930|gb|EFB85334.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
          Length = 321

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 131/310 (42%), Gaps = 58/310 (18%)

Query: 37  LQKILRS-GQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKH 93
           +++ LRS G + V+ K   +N  +  G   ++++ P          EQ+   S + L   
Sbjct: 33  MRRRLRSDGIITVNGKPATWNTLVHGGDHLIMKLTP----------EQEFSLSPMELD-- 80

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQKP-RLTHRL 150
                  ++YED  I V NK A I +   S +  H   +G L  + ++         HRL
Sbjct: 81  -------IIYEDEYILVINKAANILMHPTSTVRDHTLANGVLHYYQETNQYYDFHPVHRL 133

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV------------WGIPKNKKECI 198
           D++TSGI+++A+T +  QH  +  +     KIY ++V            W I +     I
Sbjct: 134 DKDTSGIVIIAKT-SVVQHAFDK-KHTHFYKIYDAIVEGHLPSVPISINWPIGRKPGSII 191

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYA--ISHFKVID---CFAQK-------FCWLEMQ 246
                 +       + VV +N    NY+  IS   + +   C A         F  ++  
Sbjct: 192 ERCCTGQGKPARTDITVVSKNISKINYSKNISDDMINNSNICPADNSLIAYNHFTHVQCL 251

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
            HTGRTHQ+RVH   +G P+ GD  Y     G     IQ +  LHA  +   HP     L
Sbjct: 252 LHTGRTHQIRVHLSQLGYPLAGDDLY-----GGHLESIQRQA-LHAARVSFYHPITNEWL 305

Query: 306 QITAPLPAHM 315
           ++ A +P  M
Sbjct: 306 ELHAEMPEDM 315


>gi|242280174|ref|YP_002992303.1| pseudouridine synthase [Desulfovibrio salexigens DSM 2638]
 gi|242123068|gb|ACS80764.1| pseudouridine synthase [Desulfovibrio salexigens DSM 2638]
          Length = 302

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 64/295 (21%), Positives = 126/295 (42%), Gaps = 30/295 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +  +  ++  + ++ +RLD++     P       ++++ +G V V+ +  +   ++  G 
Sbjct: 27  LNEIDRIIAGDSDDGLRLDKFLLKLLPDSGLRERRRLIENGLVMVNGRSCRSGLKMFPGA 86

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +   + A +     + +  S V + K  +   ++  Y+   ++     A I+    S
Sbjct: 87  EVVL---LEAEDRSCAVEIL--SQVKVVKQGEGFGTV--YKPEGLH----SAAIAGSAES 135

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            +   + G         G++P L +RLD  TSG+L++A          E      + K+Y
Sbjct: 136 SVEECLSGIFP------GKEPILANRLDFLTSGMLLIAFGVERENEFRECEDSGTVDKVY 189

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            + V GIP+        +++K S    D       +++      S  +V++ +      L
Sbjct: 190 HAKVHGIPEGP------FVVKNSLDTADRKRTKVLDDQAPEERWSSAEVVERYDDGTSLL 243

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           E++   G  HQ+R H  H G PIVGD  Y     G   S   +++YLH R + LP
Sbjct: 244 EVRIAKGARHQIRAHLAHAGFPIVGDPIY-----GREDS--ADRMYLHHRKIVLP 291


>gi|268608720|ref|ZP_06142447.1| hypothetical protein RflaF_04377 [Ruminococcus flavefaciens FD-1]
          Length = 446

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 81/292 (27%), Positives = 128/292 (43%), Gaps = 46/292 (15%)

Query: 35  VNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL----DSSVNL 90
           V LQ  L  G+  V K+ +    RI  G + R    + +++ + K   I+    D S  L
Sbjct: 14  VTLQNFL-IGEKGVSKRLLTKLKRIDGG-ITRDGKTVRSIDTVNKGDVIVLRFGDDSF-L 70

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PR 145
             + D L    +YE   + VFNKP+G+ V             +K   D+ G K     P 
Sbjct: 71  EPNPD-LDVPAVYESDGVIVFNKPSGMPVHPS----------IKHQGDTLGNKFAAMFPD 119

Query: 146 LT----HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           LT    +RLD++TSG+ VVA+   AA  L       R +K+Y++ V G         A  
Sbjct: 120 LTFRAVNRLDRDTSGLCVVAKNALAANAL-----QGRCEKVYYAAVTGEIPETGTIDAPI 174

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
             ++  I      +++   +    A++H++ I  +  ++   E+   TGRTHQ+RVH  +
Sbjct: 175 ARERESI------IIRCVREDGQRAVTHYRRI-AYNGRYSLAEIHLETGRTHQIRVHFSY 227

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +G P+ GD  Y     G     I  +  LH   M    P  G  + + A LP
Sbjct: 228 IGHPLAGDDLY-----GGTRCDI-GRQALHCGQMSFTDPVTGEEVTVRAELP 273


>gi|260577609|ref|ZP_05845547.1| pseudouridylate synthase [Corynebacterium jeikeium ATCC 43734]
 gi|258604262|gb|EEW17501.1| pseudouridylate synthase [Corynebacterium jeikeium ATCC 43734]
          Length = 297

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/189 (30%), Positives = 83/189 (43%), Gaps = 24/189 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +LY  S   V +KP G+       +   +    +S +  + Q+P L   HRLD++T G+L
Sbjct: 61  VLYSGSDAVVVDKPHGLPSTPNGRL---LRATAQSLMRVRLQEPELVAAHRLDRDTRGLL 117

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW------LLK-------K 205
           V+AR       L   F+ R + K Y +L   IP    E  + W      +LK       K
Sbjct: 118 VLARNPVTRGFLQTQFQRREVSKTYQALAADIP----EIGSQWQDVQLPMLKIKDDPQVK 173

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDC--FAQKFCWLEMQPHTGRTHQLRVHALHMG 263
              G      V +  K A+ A +  + ++           E+QP TG THQLRV   H+G
Sbjct: 174 VVDGERSRLTVTRIRKLASSAGAEARPVEATRAGTPTAVYELQPLTGYTHQLRVLMNHLG 233

Query: 264 CPIVGDHKY 272
            PI GD  Y
Sbjct: 234 APIYGDDTY 242


>gi|195578233|ref|XP_002078970.1| GD22253 [Drosophila simulans]
 gi|194190979|gb|EDX04555.1| GD22253 [Drosophila simulans]
          Length = 555

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/196 (28%), Positives = 88/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 171 KHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 229

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    E
Sbjct: 230 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGIVE 289

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   +  K+             +P TGR HQ+R
Sbjct: 290 CKEPIEVVSYKIG-----VCKVSPKGKDCTTTFQKLSQNGTTSVVLC--KPLTGRMHQIR 342

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI+ D  Y
Sbjct: 343 VHLQYLGYPILNDPLY 358


>gi|308811949|ref|XP_003083282.1| pseudouridine synthase family protein (ISS) [Ostreococcus tauri]
 gi|116055161|emb|CAL57557.1| pseudouridine synthase family protein (ISS) [Ostreococcus tauri]
          Length = 267

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 67/264 (25%), Positives = 106/264 (40%), Gaps = 50/264 (18%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK---------GQKPRLTHRL 150
           +  Y D  ++V  KP    V      A   DG ++   D++         G++ R  HRL
Sbjct: 5   VCAYADDDVFVLVKPTRAYVDDVID-AVRTDGVVRVIRDAREGGRETKLCGEEARCCHRL 63

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG- 209
           D++TSG L+ AR   A + L   F    + K Y +L   +    +    +  L +   G 
Sbjct: 64  DRDTSGALIFARNGNAVKSLAGQFARGTVTKRYVALCAVVDDADEGTWGSGDLVRVESGH 123

Query: 210 -----GDY----VHVVKQNEKGAN------YAISHFKVIDCFAQKFCWLE---------- 244
                G Y    V+ V ++  G N        I   +V++    ++C  E          
Sbjct: 124 GRARYGLYRLYDVNDVDRDLPGNNRVKRCVTTIRVERVVEGVELEYCEPERDGSNARLAL 183

Query: 245 --MQPHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARY 294
               P TGRTHQ+R+H   +G P+ GD +Y        CA+   +    +   L LHA  
Sbjct: 184 ARCSPITGRTHQIRLHCASLGLPLAGDVRYGGPIRVKSCASASTSAIGDLPGAL-LHAEA 242

Query: 295 MDLPHPEGGR-LQITAPLP--AHM 315
           +   HP  G  + +T   P  AH+
Sbjct: 243 ITFRHPRTGEDVTVTVDPPDWAHI 266


>gi|219116402|ref|XP_002178996.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409763|gb|EEC49694.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 424

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 89/205 (43%), Gaps = 44/205 (21%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAY------HIDGFLKSWVDSKGQKPRLTHRL 150
           ++ ED    + NKPAGI V     GG GI         +    K    S  ++P   HRL
Sbjct: 210 VIIEDDHWALVNKPAGIVVYNQRNGGHGIMTVRAALPFVLAPPKVGTISVLRRPASVHRL 269

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC------------- 197
           D+ TSGIL +A+T+ A   L+  F  R ++K Y++++ GIP    E              
Sbjct: 270 DKPTSGILCIAKTKPAMLCLSRQFHDRIVKKTYFAVINGIPTYSNESKISSKTAYELGVD 329

Query: 198 -----IANWLLKKSHIGGDYVHVVKQNEKGANY---AISHFKVIDCFAQKFCWLEMQPHT 249
                + +W L  S +          +EK A      +   K +         +E++P T
Sbjct: 330 VDPNDLDDWQLIDSPL----------DEKKAVTVWRVVRSIKSLHANDGYLTLVELKPKT 379

Query: 250 GRTHQLRVHALHMGC--PIVGDHKY 272
           GR HQLR H +   C  P+VGD +Y
Sbjct: 380 GRYHQLRRH-MAWVCQRPLVGDDEY 403


>gi|158298572|ref|XP_553504.3| AGAP009693-PA [Anopheles gambiae str. PEST]
 gi|157013948|gb|EAL39149.3| AGAP009693-PA [Anopheles gambiae str. PEST]
          Length = 494

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 58/196 (29%), Positives = 87/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 121 KHNDLLANIVHRHEVPVTSQPITIVHMDDDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 179

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ +    R R++QK Y   V G  P    E
Sbjct: 180 EYNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEHQIRNRQVQKEYICRVEGEFPDGIIE 239

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG     +  K+   F      +  +P TGR HQ+R
Sbjct: 240 CKEPIEVVSYKIG-----VCKVSPKGKECTTTFQKL--GFNGNSSVVLCKPLTGRMHQIR 292

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G P+V D  Y
Sbjct: 293 VHLQYLGYPVVNDPLY 308


>gi|207346913|gb|EDZ73262.1| YDL036Cp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 265

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 51/164 (31%), Positives = 81/164 (49%), Gaps = 6/164 (3%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           V +KP+GI V       Y  +   K   ++ G      +RLD+ TSG++ +A+T   A +
Sbjct: 2   VIDKPSGIPVHPTG--RYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFLAKTPKGADN 59

Query: 170 LTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           + +  + R + K Y + V G  P+   E I    LK          V + +EKGA +A +
Sbjct: 60  IGDQLKAREVTKEYVAKVVGEFPET--EVIVEKPLKLIEPRLALNAVCQMDEKGAKHAKT 117

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            F  I  +  K   ++ +P TGR+HQ+RVH  ++G PI  D  Y
Sbjct: 118 VFNRIS-YDGKTSIVKCKPLTGRSHQIRVHLQYLGHPIANDPIY 160


>gi|190346820|gb|EDK38997.2| hypothetical protein PGUG_03095 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 390

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 86/179 (48%), Gaps = 17/179 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V NKP+GI         Y+ +   +K+ +  +   P   HRLD+ TSGIL+
Sbjct: 104 IIYQDPSLIVVNKPSGIPTHPSGNFRYNSVTEIVKAQLHLESIFP--CHRLDKATSGILM 161

Query: 160 VARTRAAAQHLTESFRMRR-IQKIYWSLVWG-IPKNKKECIANWLLKKSHIG----GDYV 213
           +A T AA  ++ +  + R+ ++K Y + V G  P ++        L  S  G    G YV
Sbjct: 162 LATTSAACSNIQKQLQERKDVKKEYIARVKGKFPPSQLVHQDPVFLLNSTAGYIMPGRYV 221

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +       ++   +  K      +     E  PH+G+ HQ+R+H  ++G PIV D  Y
Sbjct: 222 SI------DSSTTFTRLKYNSELDESIVSCE--PHSGKMHQIRIHLRNLGFPIVNDKLY 272


>gi|169775969|ref|XP_001822451.1| DRAP deaminase (Rib2) [Aspergillus oryzae RIB40]
 gi|238502633|ref|XP_002382550.1| DRAP deaminase (Rib2), putative [Aspergillus flavus NRRL3357]
 gi|83771186|dbj|BAE61318.1| unnamed protein product [Aspergillus oryzae]
 gi|220691360|gb|EED47708.1| DRAP deaminase (Rib2), putative [Aspergillus flavus NRRL3357]
          Length = 522

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 59/257 (22%), Positives = 110/257 (42%), Gaps = 42/257 (16%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           ++ L +G+V V+ K    + ++++G V+         +H +   +   +S  +       
Sbjct: 82  REALEAGRVCVNGKPAGPDTKVKNGDVI---------SHTLHRHEPPVTSQEIG------ 126

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETS 155
              +++ED  + V +KPAG+ V   S   YH +  ++     +G    PR  +RLD+ TS
Sbjct: 127 ---IIHEDDGLIVIDKPAGVPVH--SAGRYHYNSVIEILRSERGGGWVPRPCNRLDRLTS 181

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVH 214
           G++ +A+   AA+ +    + R + K Y + V G  P     C    +     +G + V 
Sbjct: 182 GVMFIAKEPKAAEMVARRLKERTVHKEYVTRVKGKFPDGVVVCDQPIMQVSPKLGLNRVR 241

Query: 215 VVKQNEKGANYAISHFKVID----------------CFA---QKFCWLEMQPHTGRTHQL 255
              +  K     ++++   D                 +A   + +  +   P TGRTHQ+
Sbjct: 242 ATGKTAKTKFRRLAYYPPHDPEPVAANKDRAATPPPAYANEEEGYSIVHCLPLTGRTHQI 301

Query: 256 RVHALHMGCPIVGDHKY 272
           RVH   +G PI  D  Y
Sbjct: 302 RVHLQFLGHPITNDPIY 318


>gi|317035512|ref|XP_001397201.2| DRAP deaminase (Rib2) [Aspergillus niger CBS 513.88]
          Length = 518

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 97/229 (42%), Gaps = 39/229 (17%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           N ++K  +I+  +++  +     K I +++ED  + V +KPAG+ V   S   YH +  L
Sbjct: 100 NTVVKNGQIISHTLHRHEPPVTGKEIGIIHEDDDLIVIDKPAGVPVH--SAGRYHYNSVL 157

Query: 134 K--------SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +         WV      PR  +RLD+ TSG++ + +T  AA+++T   + R +QK Y +
Sbjct: 158 EIMRSQRHPEWV------PRPCNRLDRLTSGVMFLGKTAKAAENMTGKLKARTLQKEYVA 211

Query: 186 LVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            V G  P     C    +     +G + V    +  K     +++        Q     E
Sbjct: 212 RVKGKFPDGVIVCDQPIMSVSPKVGLNRVRATGKEAKTKFRRLAYIPPQAPEPQSASDAE 271

Query: 245 MQ---------------------PHTGRTHQLRVHALHMGCPIVGDHKY 272
            +                     P TGRTHQ+RVH   +G PI  D  Y
Sbjct: 272 GRVATPPPIYTNEDEGYSIVHCLPLTGRTHQIRVHLQFLGHPISNDPIY 320


>gi|189200266|ref|XP_001936470.1| DRAP deaminase [Pyrenophora tritici-repentis Pt-1C-BFP]
 gi|187983569|gb|EDU49057.1| DRAP deaminase [Pyrenophora tritici-repentis Pt-1C-BFP]
          Length = 475

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 108/248 (43%), Gaps = 25/248 (10%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSK 107
           D+    +   I  G+VV     + +   I+K   ++  +++  +     + I +++ED  
Sbjct: 79  DRPAEYYEQAIIDGRVVLNGKPVPSTKTIVKNGDVISHTLHRHEPPCTAQPIGIVHEDDN 138

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRA 165
           + V NKPAG+ V       Y+ +  ++     +G    P   +RLD+ TSGI+ + + + 
Sbjct: 139 MIVINKPAGMPVHPAG--RYNFNSIIEIMRADRGYGWNPLPCNRLDRLTSGIMFIGKHKQ 196

Query: 166 AAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           AA+ L+   R R ++K Y + V G  P+ +  C    L     +G + V    +  K   
Sbjct: 197 AAEELSAQIRGRTVKKEYITRVVGEFPEGEILCEKPILQISPKLGLNRVRANGKEAKTVF 256

Query: 225 YAISHFKVID-----------CFAQKFCWLEMQ--------PHTGRTHQLRVHALHMGCP 265
             ++++   D              Q   W +++        P TGRTHQLRVH   +G P
Sbjct: 257 KRMAYYPPKDDGRRPNGEDSETDPQGQPWKKLRGYSIVRCFPVTGRTHQLRVHLQFLGHP 316

Query: 266 IVGDHKYC 273
           I  D  Y 
Sbjct: 317 ISNDPIYA 324


>gi|308070410|ref|YP_003872015.1| RNA pseudouridine synthase (RNA-uridine isomerase) [Paenibacillus
           polymyxa E681]
 gi|305859689|gb|ADM71477.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Paenibacillus polymyxa E681]
          Length = 304

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/215 (28%), Positives = 98/215 (45%), Gaps = 27/215 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI---AYHIDGFLKSWVDSKG--QKPRLTHRLDQETS 155
           +LYED    V +KPAG++V     +      +D  + S+ +  G     R  HRLD +T+
Sbjct: 85  VLYEDDFCLVVHKPAGVAVHPDGAVQDGPLTLDHAVASYYEVNGIHAAVRHVHRLDVDTT 144

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVH 214
           G ++ A+   A   L E  R + I + Y +LV G +P + +    +W      IG D  H
Sbjct: 145 GPVLYAKNEFALLKLDEQMRAKDIGRRYVALVRGKVPPSLRTL--DW-----PIGKDRHH 197

Query: 215 VVKQN-EKGANYAISHFKVIDCF-----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             ++        A++H ++   +     A    +L ++  TGRTHQ+RVH  H G P++G
Sbjct: 198 KQRRRISPTGQKAVTHIELGGVWGSGPSAVSLVYLTLE--TGRTHQIRVHLSHAGYPLLG 255

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           D  Y      +F      +  LH   +   HP  G
Sbjct: 256 DVLYGGRAT-DF-----GRQALHGERLTFCHPLSG 284


>gi|254785984|ref|YP_003073413.1| pseudouridine synthase, Rlu family [Teredinibacter turnerae T7901]
 gi|237683526|gb|ACR10790.1| pseudouridine synthase, Rlu family [Teredinibacter turnerae T7901]
          Length = 231

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 45/145 (31%), Positives = 68/145 (46%), Gaps = 15/145 (10%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+LVVA+  AA ++ +  F  R I K Y +L    P  K+  +   ++K  +
Sbjct: 51  HRLDRTTSGLLVVAKGEAANKYFSTLFEKRAIDKCYLALSAKKPAKKQGAVRGDMVKARN 110

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             G ++     N        S   V     +      ++P TG+THQLRV    +G PI+
Sbjct: 111 --GSWMLTRSLNAPAHTQFFSKGGV-----EGKRLFVLRPITGKTHQLRVAMKSLGAPIL 163

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA 292
           GD +Y             ++ YLHA
Sbjct: 164 GDERYGGG--------DADRCYLHA 180


>gi|221502885|gb|EEE28599.1| RNA pseudouridylate synthase, putative [Toxoplasma gondii VEG]
          Length = 6535

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/84 (33%), Positives = 50/84 (59%), Gaps = 3/84 (3%)

Query: 236  FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
            ++Q+F +  ++ HTGRTHQ+RVH  H+G P+VGD KYC  +K         +++LH+  +
Sbjct: 4924 YSQEFSFCRVRIHTGRTHQIRVHFRHIGHPLVGDTKYCDLYKCTVDRSWCARMFLHSAVL 4983

Query: 296  DLPHP---EGGRLQITAPLPAHMV 316
            +  +P   E   +++  PL   ++
Sbjct: 4984 EFDNPDKTETQHVRVVCPLATELL 5007



 Score = 44.7 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 31/96 (32%), Positives = 46/96 (47%), Gaps = 5/96 (5%)

Query: 146  LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----IPKNKKECIANW 201
            L HR D ETSG L++A+TR A + + E FR R + K Y  L  G    +       IA  
Sbjct: 4761 LCHRTDLETSGSLLIAKTRRARESIFEQFRKRLVHKEYLLLCHGRLDKLHARIDHPIATR 4820

Query: 202  LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
                S     +  VV  +E G + A++ ++V+  F 
Sbjct: 4821 DFDSSRSKSHFSEVVGPDE-GGDEALTEYQVVRVFG 4855


>gi|221482222|gb|EEE20577.1| RNA pseudouridylate synthase, putative [Toxoplasma gondii GT1]
          Length = 6535

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/84 (33%), Positives = 50/84 (59%), Gaps = 3/84 (3%)

Query: 236  FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
            ++Q+F +  ++ HTGRTHQ+RVH  H+G P+VGD KYC  +K         +++LH+  +
Sbjct: 4924 YSQEFSFCRVRIHTGRTHQIRVHFRHIGHPLVGDTKYCDLYKCTVDRSWCARMFLHSAVL 4983

Query: 296  DLPHP---EGGRLQITAPLPAHMV 316
            +  +P   E   +++  PL   ++
Sbjct: 4984 EFDNPDKTETQHVRVVCPLATELL 5007



 Score = 44.7 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 31/96 (32%), Positives = 46/96 (47%), Gaps = 5/96 (5%)

Query: 146  LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----IPKNKKECIANW 201
            L HR D ETSG L++A+TR A + + E FR R + K Y  L  G    +       IA  
Sbjct: 4761 LCHRTDLETSGSLLIAKTRRARESIFEQFRKRLVHKEYLLLCHGRLDKLHARIDHPIATR 4820

Query: 202  LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
                S     +  VV  +E G + A++ ++V+  F 
Sbjct: 4821 DFDSSRSKSHFSEVVGPDE-GGDEALTEYQVVRVFG 4855


>gi|237842261|ref|XP_002370428.1| RNA pseudouridine synthase domain containing protein [Toxoplasma
            gondii ME49]
 gi|211968092|gb|EEB03288.1| RNA pseudouridine synthase domain containing protein [Toxoplasma
            gondii ME49]
          Length = 6535

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/84 (33%), Positives = 50/84 (59%), Gaps = 3/84 (3%)

Query: 236  FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
            ++Q+F +  ++ HTGRTHQ+RVH  H+G P+VGD KYC  +K         +++LH+  +
Sbjct: 4924 YSQEFSFCRVRIHTGRTHQIRVHFRHIGHPLVGDTKYCDLYKCTVDRSWCARMFLHSAVL 4983

Query: 296  DLPHP---EGGRLQITAPLPAHMV 316
            +  +P   E   +++  PL   ++
Sbjct: 4984 EFDNPDKTETQHVRVVCPLATELL 5007



 Score = 44.7 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 31/96 (32%), Positives = 46/96 (47%), Gaps = 5/96 (5%)

Query: 146  LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----IPKNKKECIANW 201
            L HR D ETSG L++A+TR A + + E FR R + K Y  L  G    +       IA  
Sbjct: 4761 LCHRTDLETSGSLLIAKTRRARESIFEQFRKRLVHKEYLLLCHGRLDKLHARIDHPIATR 4820

Query: 202  LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
                S     +  VV  +E G + A++ ++V+  F 
Sbjct: 4821 DFDSSRSKSHFSEVVGPDE-GGDEALTEYQVVRVFG 4855


>gi|328875474|gb|EGG23838.1| Modifier of rudimentary family protein [Dictyostelium fasciculatum]
          Length = 602

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 50/210 (23%), Positives = 92/210 (43%), Gaps = 19/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+       NKP  + + G     + +  F+++         R  +R+D  TSGI++ 
Sbjct: 352 IIYQSDCFISINKPFDVCIDGDDR-EHTVLKFIENRFPELKGLVRFANRIDYATSGIVLT 410

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-------KNKKECIANWLLKKSHIGGDYV 213
           A T+ A       F  R  +K Y ++VWG          N +  I + + +      ++ 
Sbjct: 411 ALTKEATNSAMNLFSSRETKKEYLAIVWGHAHPVYDGNNNTEMTIDSPIAEMQDDPTNFK 470

Query: 214 HV--VKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            V  V  +      +++ ++V++      +    +++ PHTGR HQLRVH   +G  IVG
Sbjct: 471 MVIGVAGSTNAGRASLTKYRVLEHGTLNGKAVSKIQLFPHTGRRHQLRVHMASIGHVIVG 530

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           D  Y          P+  ++ LH+  + LP
Sbjct: 531 DETYGDK------DPLTPRMMLHSWKLMLP 554


>gi|15611389|ref|NP_223040.1| hypothetical protein jhp0321 [Helicobacter pylori J99]
 gi|11136019|sp|Q9ZMA1|Y347_HELPJ RecName: Full=Uncharacterized RNA pseudouridine synthase jhp_0321;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|4154858|gb|AAD05911.1| putative [Helicobacter pylori J99]
          Length = 293

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 74/289 (25%), Positives = 124/289 (42%), Gaps = 49/289 (16%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII------KEQKILDSSVNLTKHS 94
           L+  Q  +DK+R+K     Q+ Q VR   +I  +  +I      K++K            
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQTVRKSQIIQGVVRLIYFKPNEKQEK------------ 70

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
                 L++E     VF+KPA I      G  YH +  L       G+     HRLD ET
Sbjct: 71  ------LVFEAKDFGVFDKPAQIYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYET 122

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++  +T  + + L   F  ++++K Y +L  G+  +K   I   +L   +I  D + 
Sbjct: 123 SGLVLAGKTLQSTKDLKALFMQKKVKKTYLALAHGL-VDKSIIINKPILTPQNIQKD-LR 180

Query: 215 VVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +  Q       +I+  + +  + F      L++ P TGRTHQ+R+H   +   IVG+  Y
Sbjct: 181 IRSQISPLGKPSITLVEPLSYNPFLD-ISLLKITPLTGRTHQIRLHLSSVDHRIVGEGLY 239

Query: 273 CA---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                        K    +P    L LHA  ++    +G   +I +P+P
Sbjct: 240 GVADENAREYLQLKRENNAPT---LMLHAASLEFEF-KGAHYKIASPMP 284


>gi|119776668|ref|YP_929408.1| pseudouridine synthase RluA-like protein [Shewanella amazonensis
           SB2B]
 gi|119769168|gb|ABM01739.1| pseudouridine synthase RluA-like protein [Shewanella amazonensis
           SB2B]
          Length = 224

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 58/195 (29%), Positives = 93/195 (47%), Gaps = 25/195 (12%)

Query: 101 LLYEDSKIYVFNKPAGI---SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           ++ +++   V +K  G+   S  G +G+   ++  L       G      HRLD  TSG+
Sbjct: 4   IIADETDFLVIDKAPGVHFHSQDGSAGVVAQVESDL-------GIDLYPVHRLDTLTSGL 56

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A++ AAA   TE F    +QK Y +L  G PK K+  IA  + K        +  ++
Sbjct: 57  IILAKSSAAAADFTELFSRHGVQKYYLALAKGKPKKKQGKIAGDMAKSRRSQYKLLRTME 116

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                 N A++ F           +L ++P TG+THQLRV    +G PI+GD  Y     
Sbjct: 117 ------NPAVTQFFSASVAEGLRAYL-LKPLTGKTHQLRVALASLGTPILGDTLY----- 164

Query: 278 GNFTSPIQNKLYLHA 292
           G  +S   ++ YLHA
Sbjct: 165 GGESS---DRGYLHA 176


>gi|330948563|gb|EGH48823.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. pisi str. 1704B]
          Length = 75

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/77 (44%), Positives = 53/77 (68%), Gaps = 3/77 (3%)

Query: 112 NKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           NKPAGI+V GGSG+++  I+ F +   D+K  +  L HRLD++TSG+L++A+ R+  +HL
Sbjct: 1   NKPAGIAVHGGSGLSFGVIEAFRQLRPDAK--ELELVHRLDRDTSGLLMIAKKRSMLRHL 58

Query: 171 TESFRMRRIQKIYWSLV 187
            E+ R   + K Y +LV
Sbjct: 59  HEALRGDGVDKRYMALV 75


>gi|255952943|ref|XP_002567224.1| Pc21g01540 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211588935|emb|CAP95051.1| Pc21g01540 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 526

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 62/266 (23%), Positives = 105/266 (39%), Gaps = 58/266 (21%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +K L  G V+V+    +    +++GQV+                     S  L +H   +
Sbjct: 79  RKALEDGLVQVNGVTARPETTLKNGQVI---------------------SHTLHRHEPPV 117

Query: 98  KSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQ 152
            S+   ++YED  + V +KPAG+ V       Y+ +  ++     +G +  PR  +RLD+
Sbjct: 118 TSLPVGIIYEDDDLMVIDKPAGVPVHAAG--RYNFNTVIQILRSERGSEWLPRPCNRLDR 175

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGD 211
            TSGI+ + +    A  +  + + R +QK Y + V G  P     C    +     +G +
Sbjct: 176 LTSGIMFIGKHAKGADKMAAALKARSVQKEYVARVKGKFPDGVVVCDQPIMQVSPKLGLN 235

Query: 212 YVHVVKQ-------------------------NEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            V    +                         +E+ A    S     + ++   C     
Sbjct: 236 RVRATGKEATTKFRRLAYYPPESAKETESSSDDERPATPPASFANETEGYSIVHCL---- 291

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
           P TGRTHQ+RVH   +G PI  D  Y
Sbjct: 292 PLTGRTHQIRVHLQFLGHPISNDPIY 317


>gi|113955599|ref|YP_731829.1| pseudouridine synthase [Synechococcus sp. CC9311]
 gi|113882950|gb|ABI47908.1| Pseudouridine synthase [Synechococcus sp. CC9311]
          Length = 327

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 73/294 (24%), Positives = 128/294 (43%), Gaps = 33/294 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PP 69
           V+  E++ RL       + H      Q+ L SG++ ++      +  +++G  +R   PP
Sbjct: 22  VQPGEQSTRLSAVLALRHRHSCPATWQQRLASGEITLNGLACSDDVEVKAGDWIRWARPP 81

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            + A                     D L+ I  ++D  + V NKP+G+ V  G G   H 
Sbjct: 82  WVEA------------------AVPDQLEVI--HDDGDVLVVNKPSGLPVMPGGGFLVHT 121

Query: 129 IDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIYWS 185
           +   L+    S G+   P+  HRL + TSG+ V AR       L++ FR     +K Y  
Sbjct: 122 LTSLLERSSRSVGEVLVPKPIHRLGRFTSGLQVCARRPETRAALSKQFRPEGDCRKTYLG 181

Query: 186 L---VWGIPKNKKECIANWLLKKSH--IGGDYVHVVKQNEKGANYAISHFKV-IDCFAQK 239
           L   +  + + +   I   ++++ H  +G  +       E       +H +V +    ++
Sbjct: 182 LTHRLESLQQGQTLVIQTDVVERQHPLLGWVWGPEPSTPEPLRRRLSAHSEVQLRERGER 241

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-SPIQNKLYLHA 292
              LE+Q HTGR HQ+R+H   +G P++GD  Y ++     T +P     +LHA
Sbjct: 242 EDLLEVQIHTGRPHQIRIHLAQLGFPLLGDPLYQSDQGLCATATPGDGGYHLHA 295


>gi|78213934|ref|YP_382713.1| pseudouridine synthase [Synechococcus sp. CC9605]
 gi|78198393|gb|ABB36158.1| probable pseudouridine synthase [Synechococcus sp. CC9605]
          Length = 315

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 68/301 (22%), Positives = 134/301 (44%), Gaps = 42/301 (13%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVINALNHIIKEQ 81
           W  + Y H +    Q+ + +G++  +   +  +  +Q G+ +  R PP +        E+
Sbjct: 28  WLADRYRHSDAAVWQQRIAAGELDWNGALLCSDRALQGGEALCWRRPPWL--------EE 79

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            I D            +   +++D  + V NKP+G+ V  G G   H    L + ++  G
Sbjct: 80  AIPD------------QWDTIHDDGDLLVINKPSGLPVMPGGGFLRHT---LMALLEPTG 124

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKIYWSLVWGIPKNKKEC 197
            +P   HRL + TSG+ V A T       ++ FR     R++ + +   V G+   +   
Sbjct: 125 ARP--VHRLGRFTSGLQVCACTPQTRALWSKQFRPDGGCRKVYQAWSQRVPGLELGQCLT 182

Query: 198 IANWLLKKSHI------GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           +++ ++++ H       G + ++     ++ + +  S F++++  A+    L++   TGR
Sbjct: 183 VSSDVVERLHPLLGWIWGPEPLNDAPIRKRLSAH--SEFELLERTAEGDR-LQVTITTGR 239

Query: 252 THQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHA-RYMDLPHPEGGRLQITA 309
            HQ+R+H   +G P++GD  Y  + +     +P      LHA R   LPH      Q+  
Sbjct: 240 PHQIRIHLAQLGSPLLGDPLYLPDREISASATPGDGGYRLHAWRLSGLPHLGDKTFQVNP 299

Query: 310 P 310
           P
Sbjct: 300 P 300


>gi|212696263|ref|ZP_03304391.1| hypothetical protein ANHYDRO_00799 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676892|gb|EEB36499.1| hypothetical protein ANHYDRO_00799 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 282

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 90/189 (47%), Gaps = 34/189 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------GSGIAYHI-DGFLKSWVDSKGQKPRLTHRLDQE 153
           +LYED  I   +KP  ++V         + +AY+  +  +KS +       RL +RLD  
Sbjct: 75  ILYEDKDIVAVDKPPNLTVNSKNQESLSNYLAYYFKENKIKSQI-------RLINRLDMN 127

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK-SHIGGDY 212
           TSGI++VA+   +  +         + K Y +LV G          N ++     I  DY
Sbjct: 128 TSGIMLVAKNPFSHAYYQNQIENNELDKEYLALVEG----------NLIIDDFCEIDIDY 177

Query: 213 VHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               K+N+K       N+  ++FK +  +  KF  +  + +TG+THQ+R+   ++  PI+
Sbjct: 178 D---KENKKMKVVSDKNHVKTYFKTLKNYG-KFSLIYCKIYTGKTHQIRLSLAYLNHPIL 233

Query: 268 GDHKYCANF 276
           GD+ Y + +
Sbjct: 234 GDNLYGSKY 242


>gi|39933287|ref|NP_945563.1| pseudouridine synthase:pseudouridine synthase Rlu [Rhodopseudomonas
           palustris CGA009]
 gi|39652912|emb|CAE25654.1| Pseudouridine synthase:Pseudouridine synthase, Rlu
           [Rhodopseudomonas palustris CGA009]
          Length = 324

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 35/105 (33%), Positives = 54/105 (51%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            D +++ +LY D  + V +KP G+ V  G     +++    +      + P L HRLD++
Sbjct: 16  PDEIQARVLYRDGLMLVIDKPPGLPVHRGPKGGPNLEASFDALRYGLPRPPVLAHRLDRD 75

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           TSG LV+ R R A   L   F+  RI K YW++V G P   +  I
Sbjct: 76  TSGCLVLGRHRKATATLGLLFKHSRISKTYWAIVEGGPTEDQGSI 120



 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/60 (46%), Positives = 38/60 (63%), Gaps = 5/60 (8%)

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +  WL ++P TGRTHQLRVH   MG PI+GD+ Y     GN     + +L+LHAR + +P
Sbjct: 240 QLTWLALEPITGRTHQLRVHCAAMGWPILGDNIY-----GNGPRFGEPRLHLHAREIVIP 294


>gi|323342979|ref|ZP_08083210.1| ribosomal large subunit pseudouridine synthase [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322463043|gb|EFY08238.1| ribosomal large subunit pseudouridine synthase [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 218

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 58/222 (26%), Positives = 95/222 (42%), Gaps = 21/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           + YED+ + V  K      QG       +   +K ++  K  KP      L HRLD+   
Sbjct: 3   IFYEDNHVIVVEKKPNQPSQGDESNDLDLLTEVKEYIKVKYDKPGNVYVGLVHRLDRPVG 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  AA  L++  R R + K Y ++  G    +     + ++K       Y  V
Sbjct: 63  GIMVFAKTSKAAGRLSDQVRTRTLDKTYTAVCTGYV--EPTTFRDTMVKNRKTNTSY--V 118

Query: 216 VKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V +N     YA  H  +I+ +         ++++  TGR+HQ+RV     G  + GD +Y
Sbjct: 119 VDKNHPDGKYAELH--IIEAYYHPTDNLSTVKIKLVTGRSHQIRVQFASRGNALWGDARY 176

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
                 N  S    ++ L A  +   HP    R+  T+  P+
Sbjct: 177 ------NKHSQPGQQIALWATELSFDHPITKERMTFTSHTPS 212


>gi|261367348|ref|ZP_05980231.1| ribosomal large subunit pseudouridine synthase D [Subdoligranulum
           variabile DSM 15176]
 gi|282570108|gb|EFB75643.1| ribosomal large subunit pseudouridine synthase D [Subdoligranulum
           variabile DSM 15176]
          Length = 299

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 71/315 (22%), Positives = 135/315 (42%), Gaps = 49/315 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVR--I 67
           VV ++ E  RL  + +     +    ++ +  +GQ    D + +  + ++ +GQ +   +
Sbjct: 6   VVPSEAEGQRLGLFLRTC--GVTAGLIKSVKHTGQGFFADGQALHTDQKVHAGQCITFAL 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP             ++   + L+         ++YED    V +KPAG++V     + Y
Sbjct: 64  PPE--------PATSVIPQPIPLS---------IVYEDEFAAVLDKPAGLAVH--PTLNY 104

Query: 128 HIDGFLKSWV---DSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                   W+    S+G+    R  +R+D+ TSG+++ A+   AA  L       + +K 
Sbjct: 105 PDHTLANGWIYYLQSQGKNGVFRPVNRIDKNTSGLVLCAQNAFAAPLLAG-----QAKKC 159

Query: 183 YWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y ++V G +P       A    +   I G  V           Y+++ + V+   A+   
Sbjct: 160 YLAIVQGSLPLGPGRVEAPIGRRGDSIIGRCV------TPEGKYSLTEYTVLAASAEH-S 212

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +   P TGRTHQ+RVH  ++G P+ GD  Y  N +         +  LH   +   HP 
Sbjct: 213 LVACIPRTGRTHQIRVHMAYIGHPLAGDTLYGGNIR------RIGRHALHCAVLHFVHPV 266

Query: 302 GGR-LQITAPLPAHM 315
             + ++++ P+P+ M
Sbjct: 267 TRKPIRVSCPMPSDM 281


>gi|254523953|ref|ZP_05136008.1| pseudouridine synthase [Stenotrophomonas sp. SKA14]
 gi|219721544|gb|EED40069.1| pseudouridine synthase [Stenotrophomonas sp. SKA14]
          Length = 295

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/187 (28%), Positives = 85/187 (45%), Gaps = 16/187 (8%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGILVVAR 162
           D+ + V +KP  + V   +    H+   L + + ++   P L   HRLD+ T+G+++ + 
Sbjct: 87  DAHLLVADKPHFLPV---TPAGRHVRETLLARLIARTGNPELVPLHRLDRLTAGLVLFST 143

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
             A        FR RRI+KIY +L   +P       A  L + S +             G
Sbjct: 144 QPATRDAYQRLFRERRIEKIYEALAPAMPGA-----AFPLQRHSRLVPGEPFFRMAEVPG 198

Query: 223 ANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKG 278
              A S  ++I+  A+   W   ++P TGR HQLRVH   +G PI GD  Y    +  +G
Sbjct: 199 EPNARSRIELIE--AEGPIWRFRLRPETGRKHQLRVHMAALGAPIEGDDLYPHLRSRPEG 256

Query: 279 NFTSPIQ 285
               P+Q
Sbjct: 257 AVELPLQ 263


>gi|254443242|ref|ZP_05056718.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198257550|gb|EDY81858.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 244

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 59/222 (26%), Positives = 101/222 (45%), Gaps = 22/222 (9%)

Query: 99  SILLYEDSKIYVFNKPAGI----SVQGGSGIAYHIDGFLK-----SWVDSKGQKPRLTH- 148
           ++L  + + +    KPAG+    + +G    A    G+ +     S +D++  + RL + 
Sbjct: 17  TVLDCDQNGLLAIEKPAGVLSHPNKKGEKAKALLDAGYDEKRQAYSVLDTESGETRLVYL 76

Query: 149 --RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD  TSGI+++A     A+   ++F  + ++K Y +LV+G P+       + L  K 
Sbjct: 77  LNRLDSATSGIVLLALEEGTAKAALKAFETKNVRKTYQALVFGAPRGGPPLWRDRLSVKH 136

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCF--AQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             GG     V+ +  G   A +    ++          L + P TGRTHQLR+       
Sbjct: 137 AEGG-----VRASAGGGLSAETKLVKVELLPGVPLVSRLTLMPITGRTHQLRIQTSKRRI 191

Query: 265 PIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR 304
           PIVGD  Y  +F+ N  +  +   +L LH    +L +   GR
Sbjct: 192 PIVGDRTY-GDFQKNKMAAKKGMKRLCLHCVGTELQYQLSGR 232


>gi|192288639|ref|YP_001989244.1| pseudouridine synthase [Rhodopseudomonas palustris TIE-1]
 gi|192282388|gb|ACE98768.1| pseudouridine synthase [Rhodopseudomonas palustris TIE-1]
          Length = 322

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 35/105 (33%), Positives = 54/105 (51%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            D +++ +LY D  + V +KP G+ V  G     +++    +      + P L HRLD++
Sbjct: 16  PDEIQARVLYRDGLMLVIDKPPGLPVHRGPKGGPNLEASFDALRYGLPRPPVLAHRLDRD 75

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           TSG LV+ R R A   L   F+  RI K YW++V G P   +  I
Sbjct: 76  TSGCLVLGRHRKATATLGLLFKHSRISKTYWAIVEGGPTEDQGSI 120



 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/60 (46%), Positives = 38/60 (63%), Gaps = 5/60 (8%)

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +  WL ++P TGRTHQLRVH   MG PI+GD+ Y     GN     + +L+LHAR + +P
Sbjct: 238 QLTWLALEPITGRTHQLRVHCAAMGWPILGDNIY-----GNGPRFGEPRLHLHAREIVIP 292


>gi|150399091|ref|YP_001322858.1| RluA family pseudouridine synthase [Methanococcus vannielii SB]
 gi|150011794|gb|ABR54246.1| pseudouridine synthase, RluA family [Methanococcus vannielii SB]
          Length = 297

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 52/206 (25%), Positives = 98/206 (47%), Gaps = 22/206 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL------KSWVDSKGQKPRLTHRLDQET 154
           ++YED  + + +KP  + V     +   + G L      +  V+++  K R  +RLD +T
Sbjct: 83  VIYEDEYVMIIDKPKNMVVHETKNV---VSGTLSNAISNRQKVNNQNYKIRFVNRLDMDT 139

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +GIL+VA+   +   +++       +K Y  +V G  + K   I+N L     +G D + 
Sbjct: 140 TGILIVAKNPYSHYLISKQMDEGIFEKKYICVVNGHLRLKSGIISNPL----DLGEDGIK 195

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             ++ +     + + + VI+   +    LE++  TG+THQ+RVH   +G  I+GD  Y  
Sbjct: 196 --RELKNTGKESKTKYTVIEEL-KNASLLEIELFTGKTHQIRVHLSSIGNFIIGDELYGE 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
                  S + ++  LH+  +   HP
Sbjct: 253 ------KSDLIDRQALHSSSLKFIHP 272


>gi|71278963|ref|YP_270317.1| tRNA pseudouridine synthase C [Colwellia psychrerythraea 34H]
 gi|71144703|gb|AAZ25176.1| tRNA pseudouridine synthase C [Colwellia psychrerythraea 34H]
          Length = 304

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 68/268 (25%), Positives = 118/268 (44%), Gaps = 59/268 (22%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   +KPAG+ V         I   L+   D  GQ     HRLD+ TSG+L+ 
Sbjct: 23  ILYQDEYMVAVDKPAGLFVHRSYMDKDEIYFALQLVRDQVGQYVYPVHRLDRPTSGVLLF 82

Query: 161 ARTRAAAQHLTESFRMRRIQKIY---------------------WSLVWGIPKNKKECIA 199
           A T+  A  L+E+F  +  Q  +                      S+  G+  +K    +
Sbjct: 83  ALTKDVATKLSEAFANKSSQAEFKSDTELEGKVHDKTQTGQQGQQSMTEGLTTDKNIDGS 142

Query: 200 NWLLKKSH---------IGGDYV-HVVKQN-----------EKGANYAISHFKV------ 232
           +  + K++         +  D + H +K+            +K A  A S+++V      
Sbjct: 143 DLAMVKTYYALARGHLAVPVDLIDHPLKEKLDKLGDKNVSRDKPAQSAQSYYQVKQQASL 202

Query: 233 ---IDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-- 286
              +  F + ++  +E++P TGR HQ+R H  H+  PI+GD  Y  N +  F   I++  
Sbjct: 203 PIKVGKFDSVRYSLIEVRPITGRRHQIRRHLAHLRHPILGDINYGDNKQNPFF--IEHFG 260

Query: 287 --KLYLHARYMDLPHP-EGGRLQITAPL 311
             +L L A+ ++  HP    R++I+AP 
Sbjct: 261 FKRLMLIAKSLEFNHPINNDRIKISAPF 288


>gi|326492367|dbj|BAK01967.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 346

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 69/292 (23%), Positives = 120/292 (41%), Gaps = 57/292 (19%)

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           PV      + K+ ++  +     +   +  + +++ED  + V +KPAG+  +        
Sbjct: 55  PVSPPYPAVSKDVELRRAMTASARSGAYSSAAVVFEDEWLAVVDKPAGVYCEA------- 107

Query: 129 IDGFLKSWVDSKG---QKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +   L     S G    KP L   +RLD++TSG++V+ +    A  L ++F   +++K Y
Sbjct: 108 LLSALPCSTASSGDPSSKPNLHLANRLDRDTSGLMVITKCNKVAAKLVKAFTEHKVKKTY 167

Query: 184 WSLVWG-IPKNKKECIANWLLKKSH---------------IGGDYV-------HVVKQNE 220
            +L  G +P  +K  + +   +  H                GG  V        V+  + 
Sbjct: 168 LALCIGYLPAWEKVKVCSGHGRSKHGAWRVYAMSDVGRTLPGGSSVRDMSTKFEVLGTDG 227

Query: 221 KGANYAISHFKVIDCFA-----------------QKFCWLEMQPHTGRTHQLRVHALHMG 263
           KG     S+  + D  +                     ++   P +GRTHQ+R+H  ++G
Sbjct: 228 KGQYREPSNVDIDDIESITVQEKAADQTSNVDVKSHMVFVRAYPQSGRTHQIRLHCQYLG 287

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT--APLPA 313
            PI GD KY    + N      +   LHA  +   HP  G L +T  APLP+
Sbjct: 288 IPIRGDVKYGGVIEWNGVD--CDGHALHAESLSFVHPVTG-LPVTFQAPLPS 336


>gi|328725051|ref|XP_001944933.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Acyrthosiphon pisum]
          Length = 522

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 58/206 (28%), Positives = 89/206 (43%), Gaps = 41/206 (19%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L ++              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 164 KHNDLLANVVHRHEVPVTNDPITIVHMDDDIVVVNKPASIPVHPCGRYRHNTVVFVLA-K 222

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  RT   A+ +    R R++ K Y   V G  P+   E
Sbjct: 223 EHNLRNLRTIHRLDRLTSGLLMFGRTPRYARIMEAQIRNRQVNKQYVCRVEGRFPEQTIE 282

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAIS----------HFKVIDCFAQKFCWLEMQ 246
           C     +    IG     V K + KG N + +          +  V+ CF          
Sbjct: 283 CNHPIEVVSYKIG-----VCKVSNKGKNCSTTFQLVGYNEKTNISVVLCF---------- 327

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
           PH+GR HQ+RVH  ++G P+  D  Y
Sbjct: 328 PHSGRMHQIRVHLQYLGFPVKNDPLY 353


>gi|227505675|ref|ZP_03935724.1| ribosomal pseudouridine synthase [Corynebacterium striatum ATCC
           6940]
 gi|227197643|gb|EEI77691.1| ribosomal pseudouridine synthase [Corynebacterium striatum ATCC
           6940]
          Length = 329

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 63/260 (24%), Positives = 97/260 (37%), Gaps = 53/260 (20%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSI------- 100
           D        R  +G+VV            +++Q +L     LTK  D F   I       
Sbjct: 52  DDNAAALQARFDAGEVV------------LRDQTVLKPETLLTKDQDVFFYRIPAPEEPV 99

Query: 101 -----LLYEDSKIYVFNKPAGIS--------VQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
                +L+ED  + V +KP  ++        VQ  +     I G     +D         
Sbjct: 100 PYDIPILFEDKHLLVVDKPPFMATMPRAKHIVQSATVQMRRITG-----IDDLSP----A 150

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSGILV  +T+         F  RR+ K Y ++    P +     A W  +   
Sbjct: 151 HRLDRLTSGILVFTKTKEIRGAYQTLFAERRVHKTYEAIA---PLSDVPVGAMWESRIEK 207

Query: 208 IGGDYVHVVKQNEKGANYAIS--------HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             G+    +   E  A   ++         ++ I           ++P TG+THQLR+H 
Sbjct: 208 TPGEIQGRLVAGEPNAFTEVAGVNPVDNEPYEAIHGPQPPLAKYTLKPKTGKTHQLRLHM 267

Query: 260 LHMGCPIVGDHKYCANFKGN 279
              G PI+GD  Y   F  +
Sbjct: 268 WEAGVPILGDPVYPVTFPAD 287


>gi|157163990|ref|YP_001467817.1| disulfide isomerase [Campylobacter concisus 13826]
 gi|112801796|gb|EAT99140.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           (RNA pseudouridylate synthase) [Campylobacter concisus
           13826]
          Length = 307

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 99/231 (42%), Gaps = 20/231 (8%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++E     VF+KP+G+ S   G    Y ++  + +     G+   + HRLD ETSG++VV
Sbjct: 72  IFECESFAVFDKPSGVLSHPNGRHCEYSLNDEIYTLF---GRDASVAHRLDCETSGVIVV 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            + R +   L + F  R + K Y ++V G  + +    A   L  ++        + +N 
Sbjct: 129 GKDRNSTIKLKKIFENREVFKSYVAMVQGKIEREFTIDAKMDLANNYDDVKMRMQICENG 188

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K A   I   K  D        +   P TGR HQ+R+H  H+   I+G+  Y        
Sbjct: 189 KSAVTKILPIKYFDDIDT--TLVRAIPLTGRQHQIRLHLFHVKHKILGEPLY------GL 240

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLY 331
           + P   K+      +D    E  R+ +T      ++   D + FK+D   Y
Sbjct: 241 SRPQIEKI------LDKEMSERERINLTD--AKRLLLHSDEISFKFDEIFY 283


>gi|45201401|ref|NP_986971.1| AGR305Wp [Ashbya gossypii ATCC 10895]
 gi|44986335|gb|AAS54795.1| AGR305Wp [Ashbya gossypii ATCC 10895]
          Length = 381

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 104/228 (45%), Gaps = 30/228 (13%)

Query: 63  QVVRIPPVINALNHIIKEQKILDSSV--------------NLTKHSDFLKSILLYEDSKI 108
           Q++R   V+NA   +IK + +  S                N+  ++  LK  +++ED+ +
Sbjct: 57  QLLRDGVVLNANTELIKNKDVFQSKQHNHEPPVLQWPLLHNVAHNTAGLK--VVFEDNDL 114

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V +KP GI +   +   ++ +   +   D++G      +RLD+ TSG+L+ A+T+  A 
Sbjct: 115 LVIDKPCGIPIHPTA--YFYKNTLTEVLEDARGYPLFPCYRLDKITSGLLIFAKTQQTAS 172

Query: 169 HLTESFRMRRIQKIYWSLVWG-IPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGAN 224
            L    R + + K Y + V G    NKK     I  +  KKS + G +  V     + A 
Sbjct: 173 RLQSQIRDQNMNKWYLARVDGNFDFNKKTASSPIYTFEPKKS-LKGAFAPV-----RDAL 226

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               H    +   Q       +P TGRTHQ+R+H   +G PIV D  Y
Sbjct: 227 TEFYHVAYNEELNQSLVL--CKPLTGRTHQIRIHLARLGHPIVNDPFY 272


>gi|315453301|ref|YP_004073571.1| ribosomal pseudouridine synthase [Helicobacter felis ATCC 49179]
 gi|315132353|emb|CBY82981.1| ribosomal pseudouridine synthase [Helicobacter felis ATCC 49179]
          Length = 302

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 51/166 (30%), Positives = 81/166 (48%), Gaps = 19/166 (11%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----IPKNKKECIAN 200
           RL HRLD ETSG+++V+  +     L E F  R+I+K Y + V G      +     I  
Sbjct: 113 RLIHRLDYETSGLVMVSTQKRYENALRELFSARQIKKTYEAWVQGDVRAYAQGPFSVILR 172

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHA 259
            L  K  I    + +  Q  K    + +  ++++ C   +   L++ P +GRTHQ+R+H 
Sbjct: 173 ILEPKIKIKHADLAIRCQIAKEGKPSATTIEILNFCPHTQRTHLKITPLSGRTHQIRLHL 232

Query: 260 LHMGCPIVGDHKYC-------------ANFKGNFTSPIQNKLYLHA 292
             +G PIVG+  Y              A+F+G+F S +Q +L L A
Sbjct: 233 SALGFPIVGEPLYTDDAHARAYLDAKKADFQGSFKS-LQTQLALEA 277


>gi|262375387|ref|ZP_06068620.1| pseudouridylate synthase [Acinetobacter lwoffii SH145]
 gi|262309641|gb|EEY90771.1| pseudouridylate synthase [Acinetobacter lwoffii SH145]
          Length = 302

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/204 (26%), Positives = 97/204 (47%), Gaps = 21/204 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+    V +KP  +++   G  +   +   LK    ++   P   HRLD+ET+G+++
Sbjct: 95  ILFENEHFMVVDKPHFLTMSPTGQYVQETLLVRLKKQTGNEHLTP--IHRLDRETAGVVL 152

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY--VHVVK 217
           +++   +     + F  R++QK Y ++    P  K   I    ++K   G  +  +HV+ 
Sbjct: 153 ISKCVESRGIYQQMFATRQVQKTYHAIAAYHPDLKFPLITRLRMEK---GQPFYTMHVLD 209

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWL--EMQPHTGRTHQLRVHALHMGCPIVGDHKY--- 272
                         VID       W   E++PHTG+ HQLRVH  H+G PI  D  Y   
Sbjct: 210 GTPNSET-------VIDLLKHNTEWAKYELKPHTGKQHQLRVHLNHLGIPIQHDPFYPQV 262

Query: 273 CANFKGNFTSPIQNKLYLHARYMD 296
               + +F++P+ + L  H +++D
Sbjct: 263 AHKAEDDFSAPL-SLLAKHIQFVD 285


>gi|293331663|ref|NP_001167875.1| hypothetical protein LOC100381582 [Zea mays]
 gi|223944581|gb|ACN26374.1| unknown [Zea mays]
          Length = 237

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 38/94 (40%), Positives = 53/94 (56%), Gaps = 4/94 (4%)

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG---ANYAISHFKVIDCFAQK 239
           YW+LV G PK ++  I+  + K     G    V+  +  G   A  AI+ ++V+      
Sbjct: 39  YWALVIGTPKEREGVISAPISKVLLDDGKAERVILAHPSGIDGAQEAITEYRVMGPTING 98

Query: 240 FCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
             W+E+QP TGR HQLRVH A  +G PIVGD+KY
Sbjct: 99  CSWIELQPLTGRKHQLRVHCAEALGTPIVGDYKY 132


>gi|329939071|ref|ZP_08288445.1| ribosomal pseudouridine synthase [Streptomyces griseoaurantiacus
           M045]
 gi|329301956|gb|EGG45849.1| ribosomal pseudouridine synthase [Streptomyces griseoaurantiacus
           M045]
          Length = 312

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 103/216 (47%), Gaps = 31/216 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           ++Y D+ + V +KP  ++    GS +A      L+  +D     P LT  HRLD+ T+G+
Sbjct: 97  VVYRDAHVLVADKPHFLATTPRGSHVAETALARLRRELD----LPALTAAHRLDRLTAGL 152

Query: 158 LVVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           ++       R A Q L   FR RR+ K Y +L    P +    +   +  +S +  +   
Sbjct: 153 VLFTLRPEERGAYQTL---FRDRRVHKEYEALA---PYDPALALPRTV--RSRLVKERGE 204

Query: 215 VVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +  +   G   A+S  +++  D    ++  L   P TG+THQLRVH   +G PI+GD  Y
Sbjct: 205 LRAREVPGEPNAVSRVELVEHDGTVGRYRLL---PRTGQTHQLRVHMCALGLPILGDPLY 261

Query: 273 ----CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                A   G+FT P++    L AR ++   P  GR
Sbjct: 262 PVVEPAAAPGDFTRPLR----LLARALEFTDPVTGR 293


>gi|108562767|ref|YP_627083.1| hypothetical protein HPAG1_0342 [Helicobacter pylori HPAG1]
 gi|107836540|gb|ABF84409.1| pseudouridine synthase D [Helicobacter pylori HPAG1]
          Length = 293

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 72/282 (25%), Positives = 123/282 (43%), Gaps = 35/282 (12%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K     Q+ Q VR   +I  +  +I  +    + V            
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVRKSQMIQGVVSLIHFKPNEKTQV------------ 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPHQVYTHP-KGYFYH-ESLLDCIQSHLGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  + + L   F  ++++K Y +L  G+   K   I   +L   +I  D + +  Q  
Sbjct: 129 GKTLQSVKDLKALFMQKKVKKTYLALAHGL-VEKSMKIDKPILTPQNIQKD-LRIRSQIS 186

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA----- 274
                +I+  + ++         L++ P TGRTHQ+R+H  +MG  IVG+  Y       
Sbjct: 187 PLGKPSITLVEPLNYNPFLDISLLKITPLTGRTHQIRLHLSNMGHRIVGEGLYGVADEEA 246

Query: 275 ----NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                 K    +P+   L LHA  ++    +G   +IT+ +P
Sbjct: 247 RGYLQLKRENHAPL---LMLHAASLEFEF-KGANYKITSQIP 284


>gi|313893624|ref|ZP_07827192.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313441768|gb|EFR60192.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 322

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 78/341 (22%), Positives = 139/341 (40%), Gaps = 67/341 (19%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ--VVRI 67
           ++V++D     ++   K    HI+    +++   G + V+ +   +N  +  G   V+++
Sbjct: 9   LIVDSDVHTQSMNHIIKQQ--HISQRMRRRLRNEGIITVNDEPATWNTLVHGGDHLVMKL 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P          EQ+   S ++L          ++YED  I V NK AG+ +   S +  
Sbjct: 67  TP----------EQEFSLSPMDLD---------IVYEDEHILVINKAAGVLMHPTSTVRD 107

Query: 128 HI--DGFLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQH-----------LTES 173
           H   +G L  + ++         HRLD++TSGI+++A+T +  QH             ++
Sbjct: 108 HTLANGVLYYYQETHQHYDFHPVHRLDKDTSGIVIIAKT-SVVQHAFDKKHTHFYKTYDA 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
               ++  +  ++ W I +     I      +       + V+  N   ++  I +   I
Sbjct: 167 IVEGKLPAVPLTINWPIGRKPGSIIERCCTNEGKPARTDITVISHNSINSSNTIVYGSPI 226

Query: 234 ---------------DC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                          +C   F    C L    HTGRTHQ+RVH   +G P+ GD  Y   
Sbjct: 227 SDSNTIIGSNNMADENCETHFTHVQCLL----HTGRTHQIRVHVSQLGYPLAGDDLY--- 279

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             G     IQ +  LHA  +   HP     L+++A +P  M
Sbjct: 280 --GGHLDYIQRQA-LHAARVSFHHPMTNEWLELSADMPQDM 317


>gi|269967021|ref|ZP_06181090.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           40B]
 gi|269828375|gb|EEZ82640.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           40B]
          Length = 230

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/192 (29%), Positives = 89/192 (46%), Gaps = 17/192 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+      + NK   +SV    G    +    K    S  +   L HRLD+ TSGIL++
Sbjct: 4   ILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAKQ---SGDEHLYLIHRLDKMTSGILLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   A   L+++F  R+++K Y ++    PK K+  +   + +        V     N 
Sbjct: 61  GRNAKAGSALSQAFADRQVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV-----NS 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K  N A++ F  +     +  +L  +PHTG+THQ+RV    +G  IVGD  Y A   GN 
Sbjct: 116 KN-NPAVTQFFSLAAEPGERLFL-CKPHTGKTHQIRVALKSVGSGIVGDPIYNA---GNE 170

Query: 281 TSPIQNKLYLHA 292
                ++ YLHA
Sbjct: 171 A----DRGYLHA 178


>gi|42563248|ref|NP_177732.2| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|332197668|gb|AEE35789.1| RNA pseudourine synthase 2 [Arabidopsis thaliana]
          Length = 313

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 52/217 (23%), Positives = 97/217 (44%), Gaps = 50/217 (23%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           +V+  +  +RLD W  +    ++   +Q  +R G V V+ + V K ++ ++SG       
Sbjct: 74  IVDAAKGKIRLDSWISSRINGVSRARVQSSIRLGLVTVNGRVVDKVSHNVKSG------- 126

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
             + +N  I E + L +       ++ +   ++YED  + V NKPA + V    G     
Sbjct: 127 --DEVNCTISELQPLKA------EAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGT 178

Query: 128 HIDGFL---------------------KSWVD-----------SKGQKPRLTHRLDQETS 155
            ++G L                     +++ D           +   +P + HRLD+ T+
Sbjct: 179 LVNGILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRPGIVHRLDKGTT 238

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           G+LVVA+   +  HL E F++  I+++Y SL  G+P 
Sbjct: 239 GLLVVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPS 275


>gi|13508031|ref|NP_109980.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           pneumoniae M129]
 gi|2501680|sp|P75485|Y292_MYCPN RecName: Full=Uncharacterized RNA pseudouridine synthase MG209
           homolog; AltName: Full=RNA pseudouridylate synthase;
           AltName: Full=RNA-uridine isomerase
 gi|1674240|gb|AAB96191.1| ribosomal large subunit pseudouridine synthase D-like protein
           [Mycoplasma pneumoniae M129]
          Length = 309

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 111/234 (47%), Gaps = 13/234 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-LTHRLDQETSGILV 159
           +LYED +I V NKP G+     S      +  L + +     +P  L HRLD++TSG+++
Sbjct: 82  ILYEDEQIMVVNKPNGLISHPTS--FNESESLLGAALFHCNHQPVFLVHRLDRDTSGVIM 139

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-VVKQ 218
           +A+ +++  HL +  + R +++ Y +LV   P +      +  L++  +G + V   V  
Sbjct: 140 LAKNQSSLLHLQKQLQQRVMKRYYLALV-HFPLDSLSGTISAPLER--VGNNKVMWKVGN 196

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +   A  A + F V++   +K   ++ +  TGRTHQ+RVH   +  P+  D  Y    + 
Sbjct: 197 SSNKAKNAFTKFTVLNQ-NEKAALIKCELLTGRTHQIRVHLQFIKHPVYNDPLYGLKSE- 254

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLY 331
                 +   YLHA+ +   HP   + +   A L        D+L  K   +LY
Sbjct: 255 ---QATEYGQYLHAQQISFIHPTLNKEMGFEAQLDKTFSDKLDNLNLKIANSLY 305


>gi|323309473|gb|EGA62684.1| Pus9p [Saccharomyces cerevisiae FostersO]
          Length = 265

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 51/164 (31%), Positives = 81/164 (49%), Gaps = 6/164 (3%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           V +KP+GI V       Y  +   K   ++ G      +RLD+ TSG++ +A+T   A +
Sbjct: 2   VIDKPSGIPVHPTG--RYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFLAKTPRGADN 59

Query: 170 LTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           + +  + R + K Y + V G  P+   E I    LK          V + +EKGA +A +
Sbjct: 60  IGDQLKAREVTKEYVAKVVGEFPET--EVIVEKPLKLIEPRLALNAVCQMDEKGAKHAKT 117

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            F  I  +  K   ++ +P TGR+HQ+RVH  ++G PI  D  Y
Sbjct: 118 VFNRIS-YDGKTSIVKCKPLTGRSHQIRVHLQYLGHPIANDPIY 160


>gi|194761916|ref|XP_001963137.1| GF14093 [Drosophila ananassae]
 gi|190616834|gb|EDV32358.1| GF14093 [Drosophila ananassae]
          Length = 755

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/196 (28%), Positives = 88/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 374 KHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 432

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    E
Sbjct: 433 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGVVE 492

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   +  K+             +P TGR HQ+R
Sbjct: 493 CKEPIEVVSYKIG-----VCKVSPKGKDCTTTFQKLSQNGTTSVVLC--KPLTGRMHQIR 545

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI+ D  Y
Sbjct: 546 VHLQYLGYPILNDPLY 561


>gi|149916984|ref|ZP_01905485.1| ribosomal large subunit pseudouridine synthase A [Plesiocystis
           pacifica SIR-1]
 gi|149822262|gb|EDM81653.1| ribosomal large subunit pseudouridine synthase A [Plesiocystis
           pacifica SIR-1]
          Length = 509

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/175 (32%), Positives = 82/175 (46%), Gaps = 16/175 (9%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWL 202
           PRL HRLD  TSG+L+ A+ R A   L   F  R+I K Y +LV G +P    E     L
Sbjct: 344 PRLVHRLDLATSGLLIAAKHREAYVALQRQFSSRQIGKRYVALVRGPLPDALGEGGEIEL 403

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALH 261
                +  D     K + +    A + ++++    +     + + PHTGRTHQLR+HA H
Sbjct: 404 PLARDL--DDRPRQKVDRREGKVARTRWQLLAHEPEHAASRVALYPHTGRTHQLRLHAAH 461

Query: 262 ---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              +  P+VGD  Y              +L LHA  +   HP  G  +++ +P P
Sbjct: 462 PEGLDAPLVGDLLYGYGEGA--------RLMLHAERLTFLHPTRGEPMELRSPCP 508


>gi|195471884|ref|XP_002088232.1| GE13593 [Drosophila yakuba]
 gi|194174333|gb|EDW87944.1| GE13593 [Drosophila yakuba]
          Length = 738

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/196 (28%), Positives = 89/196 (45%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 355 KHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 413

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    E
Sbjct: 414 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGIVE 473

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   +  K+    +        +P TGR HQ+R
Sbjct: 474 CKEPIEVVSYKIG-----VCKVSSKGKDCTTTFQKLSQNGSTSVVLC--KPLTGRMHQIR 526

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI+ D  Y
Sbjct: 527 VHLQYLGYPILNDPLY 542


>gi|241889793|ref|ZP_04777091.1| ribosomal large subunit pseudouridine synthase D [Gemella
           haemolysans ATCC 10379]
 gi|241863415|gb|EER67799.1| ribosomal large subunit pseudouridine synthase D [Gemella
           haemolysans ATCC 10379]
          Length = 251

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 65/221 (29%), Positives = 98/221 (44%), Gaps = 28/221 (12%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILVVA 161
           YED  I V +KP GI       I    D  +   + D    +P   HRLD +T G++++A
Sbjct: 52  YEDDYILVVSKPFGIKTHPND-IETENDTLVNYLIADYSYLEP--IHRLDIDTCGLVILA 108

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH----VVK 217
           +T      L +    R I++ Y +L   I  N K    N     ++IG D        V 
Sbjct: 109 KTPLIKAKLDQMLEQRAIKRYYTAL---IKNNIKPQTIN-----TNIGRDSKEKNKMAVT 160

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-F 276
           +N K A   I     +D    +F  L +   TGRTHQ+RVH   +G  I+GD  Y  + +
Sbjct: 161 RNGKNAITNILECSKLD--QNRFSVL-ISLETGRTHQIRVHLASIGVSIIGDKLYSKDGY 217

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           K        +K+YL A  ++  HP  G  L+I + +    +
Sbjct: 218 K-------YDKMYLGALKVNFQHPVTGNTLEIKSSIEKDFI 251


>gi|320156659|ref|YP_004189038.1| pseudouridylate synthase 23S RNA-specific [Vibrio vulnificus
           MO6-24/O]
 gi|319931971|gb|ADV86835.1| pseudouridylate synthase 23S RNA-specific [Vibrio vulnificus
           MO6-24/O]
          Length = 262

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 49/147 (33%), Positives = 74/147 (50%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++ R   AA  L++ F  R ++K Y ++    PK K+  +   + + 
Sbjct: 77  LIHRLDKMTSGILLLGRNSTAASALSQRFAQREVEKFYLAIGAKKPKKKQGTVIGDMERS 136

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  KQN      AI+ F  +     +  +L  +P+TG+THQ+RV    +G  
Sbjct: 137 RRASWKLVN-SKQNP-----AITQFFSLAGEPGERAFL-CKPYTGKTHQIRVALKSVGSS 189

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y     G   S   ++ YLHA
Sbjct: 190 IVGDPIY----NGGSDS---DRGYLHA 209


>gi|227495588|ref|ZP_03925904.1| ribosomal pseudouridine synthase [Actinomyces coleocanis DSM 15436]
 gi|226830820|gb|EEH63203.1| ribosomal pseudouridine synthase [Actinomyces coleocanis DSM 15436]
          Length = 358

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 64/224 (28%), Positives = 92/224 (41%), Gaps = 24/224 (10%)

Query: 110 VFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           V NKP  I S   GS I       L+    +    P   HRLD+ TSG+L+         
Sbjct: 140 VINKPKDIASTPRGSYIVRTATIALRRQEGNADLTP--AHRLDRATSGLLLFTERPELRG 197

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKN------------KKECIANWLLKKSHIGGDYVHVV 216
              + F+ R++ K Y +    I  N              E    W+  +S I        
Sbjct: 198 MYQDLFQNRQVTKTYRATAKAIDFNYIKSSALVKITVDPEEQPGWVKIESRIEKRPGDPG 257

Query: 217 KQNEKGANYAISHF---KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            Q+  G   A+++    K +    Q+F   E+QP TG+THQ+R+H   +G P+VGD  Y 
Sbjct: 258 AQHAFGKINAVTYLRPVKTVTIEGQQFVEYEVQPQTGKTHQIRLHFASLGAPLVGDPLY- 316

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
               G F +       + A Y +L H E  RL+   P    MVK
Sbjct: 317 ----GGFNAAPFGLEKVPAGYQEL-HLEACRLEFKDPQTQEMVK 355


>gi|157377520|ref|YP_001476120.1| pseudouridine synthase Rlu family protein [Shewanella sediminis
           HAW-EB3]
 gi|157319894|gb|ABV38992.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           sediminis HAW-EB3]
          Length = 224

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 51/182 (28%), Positives = 79/182 (43%), Gaps = 26/182 (14%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG+L+ A++  AA   T+ F   ++QK Y ++  G PK K+  +   + K   
Sbjct: 47  HRLDTLTSGLLLFAKSSRAAAEFTQLFTEHKVQKYYVAIAKGKPKKKQGWVVGDMAKSRR 106

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  + K      N A++ F      A+      ++P +G+THQLRV    +G PI+
Sbjct: 107 ------SMYKLMRTMENPAMTQF-FSQSVAEGVRLYLLKPLSGKTHQLRVALASIGVPIL 159

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA----------RYMDLPHPEGGRLQITAPLPAHMVK 317
           GD  Y             ++ YLHA           Y  L +P  G  + T P     ++
Sbjct: 160 GDRLYGGG--------EADRGYLHAFSLSFIFRAKAYQYLNYPAQGA-EFTTPDAIKQLQ 210

Query: 318 TW 319
            W
Sbjct: 211 IW 212


>gi|308182516|ref|YP_003926643.1| hypothetical protein HPPC_01740 [Helicobacter pylori PeCan4]
 gi|308064701|gb|ADO06593.1| hypothetical protein HPPC_01740 [Helicobacter pylori PeCan4]
          Length = 293

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 74/287 (25%), Positives = 124/287 (43%), Gaps = 45/287 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS- 99
           L+  Q  +DK+R+K     Q+ Q VR             + +++   V+L       K+ 
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVR-------------KSQMIQGVVSLIHFKPNEKTQ 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  ALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D     K +
Sbjct: 128 AGKTLQSAKDLKALFMQKKVKKTYLALAHGL-VDKNIVIDKPILTPQNIQKDLRIRSKIS 186

Query: 220 EKGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             G         +S+   +D        L++ P TGRTHQ+R+H   +G  IVG+  Y  
Sbjct: 187 PLGKPSTTLVKPLSYNPFLDI-----SLLKITPLTGRTHQIRLHLSSVGHRIVGEGLYGV 241

Query: 275 ---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                      K    +P+   L LHA  ++    +G   +IT+ +P
Sbjct: 242 IDENAREYLQLKRENNAPL---LMLHASSLEFEF-KGAIHEITSQMP 284


>gi|292669466|ref|ZP_06602892.1| ribosomal large subunit pseudouridine synthase D [Selenomonas noxia
           ATCC 43541]
 gi|292648919|gb|EFF66891.1| ribosomal large subunit pseudouridine synthase D [Selenomonas noxia
           ATCC 43541]
          Length = 290

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 66/280 (23%), Positives = 122/280 (43%), Gaps = 30/280 (10%)

Query: 51  KRVKFNNR--IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKI 108
           KR+K +    +    V+    V+ A + +  E  ++ S +      + L   ++YED+ +
Sbjct: 32  KRIKHSGTFAVNGMPVIAARTVLRAGDMVSYELPVISSVI-----PEQLPLTVVYEDADL 86

Query: 109 YVFNKPAG-----ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
            V +K AG      + +    +A  + G   +     G  P   HRLD+ T+G+L++A+ 
Sbjct: 87  LVIDKSAGQLVHPTTKEAHGTVANAVLGLYAARRAPLGFHP--CHRLDRNTTGLLLIAKH 144

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
                 +    R   + + Y +L+ G+   +K CI   + +   +    +  V  + K A
Sbjct: 145 PEVQYQIA---RQDTLTREYLALIKGMLSPEKGCIDAPIARA--LPSIILRHVAPDGKPA 199

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
               +H++  +        L +   TGRTHQ+RVH  H+G P++GD  Y  N        
Sbjct: 200 R---THYQT-EQTDGTHTLLRLHLETGRTHQIRVHLAHLGHPLLGDDLYGGNADEI---- 251

Query: 284 IQNKLYLHARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
              +  LH+  + L HP   ++ +  +PLP  M +    L
Sbjct: 252 --KRHALHSARLTLSHPRTQKMLVFESPLPPDMARIAKQL 289


>gi|260949943|ref|XP_002619268.1| hypothetical protein CLUG_00427 [Clavispora lusitaniae ATCC 42720]
 gi|238846840|gb|EEQ36304.1| hypothetical protein CLUG_00427 [Clavispora lusitaniae ATCC 42720]
          Length = 432

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 112/228 (49%), Gaps = 28/228 (12%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  +LN I+++ ++++++            ++LYED  I V NKPAG+     +GI +  
Sbjct: 127 VGGSLNGIVQKWRVVENT------------LVLYEDENILVVNKPAGVPTHP-NGI-FRR 172

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--IQKIYWSLV 187
           +   +      G      HRLD+ TSG+LV+A+T+   + L E  + ++  ++K Y + V
Sbjct: 173 NSLTEIVRFELGVSVYPCHRLDKGTSGVLVLAKTKTG-KMLQEVLQNKKSHVEKWYVARV 231

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-----KFCW 242
            G          + +   +  G  Y+++    E+    + +HFK++    +      FC 
Sbjct: 232 RGKFPFASCSYTSPVFSINTAGTGYLNI-PNAERVPATSSTHFKMVSYSPELDESIVFC- 289

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLY 289
              +P +G+ HQ+RVH  +MG PI  D  Y A N  G+  + ++ +LY
Sbjct: 290 ---RPISGKMHQIRVHLRNMGYPISNDPLYNAENGLGHAKNQLEKELY 334


>gi|170017524|ref|YP_001728443.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
 gi|169804381|gb|ACA82999.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
          Length = 300

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 50/188 (26%), Positives = 93/188 (49%), Gaps = 13/188 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-----IDGFLKSWVDSKGQKPRLTHR 149
           D+    +++E+    V +KP G++   G     H     + G L+  ++++   P +  R
Sbjct: 74  DYRPLDIIFENEHWLVVDKPYGVTTVPGHADRLHTLVNQVKGHLEE-INAEDLVPHVVTR 132

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSGI+++A+ R A   L +  +   ++K Y +   GI       I   +     + 
Sbjct: 133 LDRDTSGIVLLAKHRFAHAVLDQQLQDHTVEKFYLAYPSGILTEDHGDINAPI---GRVE 189

Query: 210 GDYV-HVVKQNEKGA--NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           GD++   V+ + K +   Y +   +  +   Q    +++Q HTGRTHQ+RVH  ++G P+
Sbjct: 190 GDFIKREVRDDGKPSRTEYWVER-RYDENGEQPMTRVKVQLHTGRTHQIRVHFKNIGHPL 248

Query: 267 VGDHKYCA 274
           VGD  Y  
Sbjct: 249 VGDDLYGG 256


>gi|83319852|ref|YP_424674.1| ribosomal large subunit pseudouridine synthase A [Mycoplasma
           capricolum subsp. capricolum ATCC 27343]
 gi|90110089|sp|P45614|Y714_MYCCT RecName: Full=Uncharacterized RNA pseudouridine synthase MCAP_0714;
           AltName: Full=ORF2; AltName: Full=RNA pseudouridylate
           synthase; AltName: Full=RNA-uridine isomerase
 gi|83283738|gb|ABC01670.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma capricolum subsp. capricolum ATCC 27343]
          Length = 302

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 65/282 (23%), Positives = 128/282 (45%), Gaps = 49/282 (17%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  +++N  L ++ K  +       + K +R+  ++++ KRV  N++    ++  +  V
Sbjct: 5   IVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRV--NDKNYLLKINDVVEV 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            ++   II++Q    S+VNL          ++YED+ I + NKP  + +     +   +D
Sbjct: 63  YDSNKPIIRDQFNYISNVNLD---------IVYEDNNILIVNKPNNLEMHSIYNLC--LD 111

Query: 131 GFLKSW-VDSKGQKPRL--------THRLDQETSGILVVARTRAAAQHLTESFRMR-RIQ 180
             +KS+ VD K     L         HRLD+ TSG+++ A+ + ++  LT +F+ + +I 
Sbjct: 112 DMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSIILTNAFKTKDQIN 171

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y++L             +W L       D++ V       +N   + F +++    K+
Sbjct: 172 KYYYAL----------TSYDWNL------NDFLQVNGYINYNSNTQKADFSLVEKNNYKY 215

Query: 241 CWLE----------MQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           C  E          ++  TG+ HQ+R        PI+ D +Y
Sbjct: 216 CQTEFKLVNKNLILVKLITGKKHQIRSVLSFYNNPILNDFRY 257


>gi|269955480|ref|YP_003325269.1| pseudouridine synthase [Xylanimonas cellulosilytica DSM 15894]
 gi|269304161|gb|ACZ29711.1| pseudouridine synthase [Xylanimonas cellulosilytica DSM 15894]
          Length = 309

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 56/193 (29%), Positives = 91/193 (47%), Gaps = 17/193 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  ++    G  +   +   L+  +D     P   HRLD+ T+G+LV
Sbjct: 97  VLHRDENLLVVDKPHLVATMPRGRWVTQTVLVHLRRTLDLPELAP--AHRLDRPTAGVLV 154

Query: 160 V---ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +   A  R A Q L   F+ RR++K+Y + V  +P +  E        +S I        
Sbjct: 155 LTVRASVRGAYQDL---FQERRVRKVYEA-VAPLPGDGVELPTTV---RSRIVKHRGVAP 207

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-- 273
            Q E G   A S   +I     +   L  ++PHTG+THQLR+H   +G PI+ D  +   
Sbjct: 208 AQEEPGEPNAESRIDLIGRDEGRGLGLYRLEPHTGKTHQLRLHLASLGMPILHDPFWPVL 267

Query: 274 -ANFKGNFTSPIQ 285
             +  G+  +P+Q
Sbjct: 268 RPDSDGDPATPLQ 280


>gi|291277548|ref|YP_003517320.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
 gi|290964742|emb|CBG40597.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
          Length = 245

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 50/176 (28%), Positives = 79/176 (44%), Gaps = 23/176 (13%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +L++D  +    KPA +        +Y +      WV        L HRLD+ETSG+
Sbjct: 56  KPEILFQDENLLALIKPAFLE-------SYDLAEMFDGWV--------LLHRLDKETSGV 100

Query: 158 LVVARTRAAA-QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++ R  +   +   ++F+ + + K Y +LV G     +   A  L  K       +H  
Sbjct: 101 ILLVRGESDFHKRAKKAFKDQEVYKEYIALVSGFLSEPQTITAPILTTKKGFAKSRIH-- 158

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            Q+   A   I   K+I     K   ++    TGRTHQ+RVH  H+G  I+GD  Y
Sbjct: 159 -QDGLSAVTYIDPLKIIG----KKTLIKAVIQTGRTHQIRVHLKHIGHSIIGDRLY 209


>gi|149198149|ref|ZP_01875196.1| tRNA pseudouridine synthase [Lentisphaera araneosa HTCC2155]
 gi|149138751|gb|EDM27157.1| tRNA pseudouridine synthase [Lentisphaera araneosa HTCC2155]
          Length = 246

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 68/248 (27%), Positives = 110/248 (44%), Gaps = 20/248 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGIL 158
            LYED  + V  K A ISV             L + V +K  GQ     HRLD+  SG L
Sbjct: 9   FLYEDEYLVVAKKLAKISVHRSEMCRDRRT--LLTMVRNKLGGQYVYAVHRLDRPVSGPL 66

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A++    + L + F  + ++K Y +LV G  + K + +   LLKKS+  G     + +
Sbjct: 67  LFAKSPEMCRELQKQFNEKTVEKKYIALVRGWLEGKGK-VDKQLLKKSN--GTIQDCLTR 123

Query: 219 NEKGANYAISH----FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               A   I      F  +     ++  +E++P TGR HQLR H   +  PI+GD     
Sbjct: 124 YRGLATAEIDEPLGKFPTV-----RYGLVELEPVTGRYHQLRRHMRDLAYPIIGDSTDGD 178

Query: 275 NFKGNFTSPI--QNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYDRNLY 331
           + +  F        +L LH  Y+   HP    L +I       +++ ++ LG  Y++   
Sbjct: 179 SHQNRFFREKFELRRLMLHCFYLSFKHPVSQELIKIYLEPDRDLLRIYEQLGM-YEQFKQ 237

Query: 332 IKRLYSQD 339
           ++R Y  +
Sbjct: 238 LEREYEDE 245


>gi|88799662|ref|ZP_01115237.1| putative RNA pseudouridylate synthase [Reinekea sp. MED297]
 gi|88777556|gb|EAR08756.1| putative RNA pseudouridylate synthase [Reinekea sp. MED297]
          Length = 309

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 67/268 (25%), Positives = 114/268 (42%), Gaps = 33/268 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +F   +PH+N   L   + +G+V  D            G  V   PV   L   I  Q+ 
Sbjct: 36  FFVARFPHLNPQALAAKIAAGRVYYD-----------DGSPV---PVDAPL---IPGQRF 78

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQ 142
                N  +      + +LYED +I V +KP  +S    G  + + +   L++   +   
Sbjct: 79  WYFRENPNEPDIPFDADILYEDEQILVVDKPHFLSTTPVGQFMKHTVTTRLRNRTGNMAI 138

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P   HRLD+ T+G+L++ + RA  +     F  R ++K Y +L    P+  ++   N  
Sbjct: 139 TP--AHRLDRATAGVLLLTKQRAVREAYQSLFLRREVEKTYHALCHPNPELPEQFEINLH 196

Query: 203 LKKSHIGGDYVHVV--KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           LK++     +V V+    N   +   ++     D +       E++P +GR HQLR    
Sbjct: 197 LKEN-TDNMFVRVLDAPPNSHTSAKRLARHSTGDLY-------ELRPSSGRKHQLRCQMA 248

Query: 261 HMGCPIVGDHKYCA---NFKGNFTSPIQ 285
           H+G  IV D  Y         +F+ P+Q
Sbjct: 249 HLGAGIVNDIWYPVAQDPSPDDFSRPLQ 276


>gi|325846771|ref|ZP_08169686.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481529|gb|EGC84570.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 264

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 57/208 (27%), Positives = 95/208 (45%), Gaps = 34/208 (16%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG------GSGIAYHI-DGFLK 134
           KIL    NL       K  +LYED  I   +KP  ++V         + +AY+  +  +K
Sbjct: 56  KILIEDENLNYEPINKKIKILYEDKDIVAVDKPPNLTVNSKNQESLSNYLAYYFKENKIK 115

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           S +       RL +RLD  TSGI++VA+   +  +         + K Y +LV G     
Sbjct: 116 SQI-------RLINRLDMNTSGIMLVAKNPFSHAYYQNQIENNELDKEYLALVEG----- 163

Query: 195 KECIANWLLKK-SHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPH 248
                N ++     I  DY    K+N+K       N+  ++FK +  +  KF  +  + +
Sbjct: 164 -----NLIIDDFCEIDIDYD---KENKKMKVVSDKNHVKTYFKTLKNYG-KFSLIYCKIY 214

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANF 276
           TG+THQ+R+   ++  PI+GD  Y + +
Sbjct: 215 TGKTHQIRLSLAYLNHPILGDDLYGSKY 242


>gi|199598482|ref|ZP_03211900.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|258508901|ref|YP_003171652.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus GG]
 gi|199590666|gb|EDY98754.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|257148828|emb|CAR87801.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus GG]
 gi|259650194|dbj|BAI42356.1| pseudouridylate synthase [Lactobacillus rhamnosus GG]
          Length = 285

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 77/287 (26%), Positives = 126/287 (43%), Gaps = 42/287 (14%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
            +K+L +  + +D  R   N  IQ+GQ VR    I     +  E+  LD           
Sbjct: 29  FKKMLANHLLWLDGHRTG-NTAIQAGQTVRF--AIPTTMTVTPEKASLD----------- 74

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-----IDGFLKSWVDSKGQKPRLTHRLD 151
               +LYED    + NKPA ++   G    +H     I  +L+    ++ Q P +  RLD
Sbjct: 75  ----VLYEDQNWLIINKPAHLTSVPGPHDPHHSLLNRIVWYLQQQKITEPQ-PAIITRLD 129

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T G LV+A     AQ   +      ++K Y ++V G   +    I   +     +G D
Sbjct: 130 RDTVG-LVLAAKHPYAQGRFDQAHHATLKKEYLAVVAGHLSHATGTIEAPI----GLGPD 184

Query: 212 YVH-VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +H +V +N + A   I+ ++V+          ++Q  TGRTHQ+RVH   +G P++GD 
Sbjct: 185 GIHRMVTENGQSA---ITKYQVLKEAVNTLV--DVQLLTGRTHQIRVHFASLGHPLIGDS 239

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
            Y         SP+ +   L A ++    P    R+Q   P+P   V
Sbjct: 240 LYGQ------ASPLIDHQALQATHLSFVDPFSEKRIQADLPIPDDFV 280


>gi|171678031|ref|XP_001903966.1| hypothetical protein [Podospora anserina S mat+]
 gi|170937084|emb|CAP61743.1| unnamed protein product [Podospora anserina S mat+]
          Length = 479

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 52/200 (26%), Positives = 88/200 (44%), Gaps = 29/200 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGIL 158
           +++ED  + V NKP+G+ V       YH +  ++     +G    PR  +RLD+ TSGI+
Sbjct: 146 VIHEDDDMIVINKPSGVPVHPAG--RYHYNSVVEIMKAERGPTFAPRPCNRLDRLTSGIM 203

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
            +A+T  AA+ L+     R ++K Y + V G  P  +  C    L     +G + V    
Sbjct: 204 FIAKTAKAAESLSAQIFRRSVRKEYLARVVGRFPDGEVVCDQPILQISPKLGLNRVRANG 263

Query: 218 QNEKGANYAISHFKVI---------------------DCFAQK---FCWLEMQPHTGRTH 253
           ++ K     ++++                        D F ++   +  +   P TGRTH
Sbjct: 264 KSAKTVFKRLAYYPSPIIKPSSSNSPSPDEAETGGPEDQFTRETEGYSIVRCLPVTGRTH 323

Query: 254 QLRVHALHMGCPIVGDHKYC 273
           Q+RVH   +G P+  D  Y 
Sbjct: 324 QIRVHLQFLGHPVQNDPIYA 343


>gi|28316862|gb|AAO39454.1| RH45372p [Drosophila melanogaster]
          Length = 739

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 56/196 (28%), Positives = 88/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 356 KHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 414

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    E
Sbjct: 415 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGIVE 474

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   +  K+             +P TGR HQ+R
Sbjct: 475 CKEPIEVVSYKIG-----VCKVSAKGKDCTTTFQKLSQNGTTSVVLC--KPLTGRMHQIR 527

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI+ D  Y
Sbjct: 528 VHLQYLGYPILNDPLY 543


>gi|156846788|ref|XP_001646280.1| hypothetical protein Kpol_1032p14 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156116955|gb|EDO18422.1| hypothetical protein Kpol_1032p14 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 612

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 48/172 (27%), Positives = 78/172 (45%), Gaps = 6/172 (3%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ED  I V +KP+GI V       +  +   K      G      +RLD+ TSG++ +A
Sbjct: 193 VFEDDNILVIDKPSGIPVHPTG--RFRFNTITKILEKKLGYSVHPCNRLDKLTSGLMFLA 250

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           +T   A  + +  + R + K Y + V G  P    E      +K          V    +
Sbjct: 251 KTPKGADEMADQLKAREVTKEYVARVVGEFPVG--EVTVEKPVKTVDPRVSLNSVCSLED 308

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + A +A + F  +  +  K   ++ +P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 309 ENAKHAKTIFNRV-SYDGKTSIVKCKPLTGRTHQIRVHLQYIGFPIANDPIY 359


>gi|257438416|ref|ZP_05614171.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Faecalibacterium prausnitzii A2-165]
 gi|257198995|gb|EEU97279.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Faecalibacterium prausnitzii A2-165]
          Length = 305

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 71/294 (24%), Positives = 122/294 (41%), Gaps = 52/294 (17%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
            D   +  N R+Q+GQ +R    + A    ++ Q  +   V             +YED+ 
Sbjct: 42  ADDAPILANRRVQAGQTIRF--ALPADGSGVEPQPEIPVRV-------------VYEDAF 86

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFL---KSWVDSKGQKP--RLTHRLDQETSGILVVAR 162
             V  KP  ++V     + Y  D       +W  + G+ P  R  +R+D++TSG+++ A+
Sbjct: 87  AVVLEKPPHLAVH--PTLNYPRDTLANGYAAWAVAHGESPVFRPVNRIDKDTSGLVLAAK 144

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
              AA  L E      ++K+Y+++V G +P       A    +   I G  V    +  +
Sbjct: 145 NGYAAPLLAEG-----VEKLYYAIVEGELPLGPGVIDAPIGRRGDSIIGRCVTPEGKPSR 199

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--------- 272
                 + + ++   AQ        P TGRTHQ+R H   +G P+ GD  Y         
Sbjct: 200 ------TEYTILRA-AQGLSLAACVPVTGRTHQIRAHFASIGHPLAGDDLYGGHRDRIAR 252

Query: 273 ----CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
               CA  + +F  P   ++    R ++ P  E  R + + +PLP  M    D+
Sbjct: 253 QALHCA--RQSFRVPAYTEVPGGIR-LETPVGEHARTIAVESPLPEDMRALLDA 303


>gi|24583445|ref|NP_723592.1| RluA-1, isoform A [Drosophila melanogaster]
 gi|24583447|ref|NP_723593.1| RluA-1, isoform B [Drosophila melanogaster]
 gi|24583449|ref|NP_723594.1| RluA-1, isoform C [Drosophila melanogaster]
 gi|22946167|gb|AAF52959.2| RluA-1, isoform A [Drosophila melanogaster]
 gi|22946168|gb|AAF52960.2| RluA-1, isoform B [Drosophila melanogaster]
 gi|22946169|gb|AAN10755.1| RluA-1, isoform C [Drosophila melanogaster]
 gi|206725570|gb|ACI16540.1| FI04540p [Drosophila melanogaster]
          Length = 739

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 56/196 (28%), Positives = 88/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 356 KHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 414

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    E
Sbjct: 415 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGIVE 474

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   +  K+             +P TGR HQ+R
Sbjct: 475 CKEPIEVVSYKIG-----VCKVSAKGKDCTTTFQKLSQNGTTSVVLC--KPLTGRMHQIR 527

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI+ D  Y
Sbjct: 528 VHLQYLGYPILNDPLY 543


>gi|195434114|ref|XP_002065048.1| GK15253 [Drosophila willistoni]
 gi|194161133|gb|EDW76034.1| GK15253 [Drosophila willistoni]
          Length = 761

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 57/196 (29%), Positives = 90/196 (45%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 374 KHNDLLANIVHRHEVPVTCQPITIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 432

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V GI P    E
Sbjct: 433 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGIFPDGIVE 492

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + +G +   +  K+      K   +  +P TGR HQ+R
Sbjct: 493 CKEPIEVVSYKIG-----VCKVSPRGKDCTTTFQKLSQ--NGKTSVVLCKPLTGRMHQIR 545

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI+ D  Y
Sbjct: 546 VHLQYLGYPILNDPLY 561


>gi|269102975|ref|ZP_06155672.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268162873|gb|EEZ41369.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 238

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 79/158 (50%), Gaps = 15/158 (9%)

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           +K  L HRLD+ TSG+L++ R + AA  L+ +F  R ++K Y ++    PK KK+ I   
Sbjct: 53  EKLYLIHRLDKMTSGLLLLGRNKEAAAELSGNFANRVVEKFYVAIGSKKPK-KKQGIVIG 111

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            + +S      +   K N      AI+ F        +  +L  +PHTG+THQ+RV    
Sbjct: 112 DMTRSRRSSWKLESSKHNP-----AITQFFSTAAGNGRRLFL-CKPHTGKTHQIRVALKS 165

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +G  I GD  Y     GN  +   ++ YLHA  +  P+
Sbjct: 166 VGSGITGDDIY-----GNEAA---DRGYLHAYALSFPY 195


>gi|149052129|gb|EDM03946.1| RNA pseudouridylate synthase domain containing 1 (predicted),
           isoform CRA_b [Rattus norvegicus]
          Length = 234

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 44/133 (33%), Positives = 66/133 (49%), Gaps = 5/133 (3%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA    + F+ RR+ K Y +LV G  +  +  I   + +
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYKCFKERRVTKAYLALVRGHVQESQVTINYAIGR 120

Query: 205 KSHIGGDYVHVVKQNEKGANY--AISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            S  G  +   ++      N   +++   V++           + ++P TGRTHQLRVH 
Sbjct: 121 NSTEGRTHTMCIEGTHGCENPKPSLTELLVLEHGLYSGDPVSKVLLKPLTGRTHQLRVHC 180

Query: 260 LHMGCPIVGDHKY 272
             +G PIVGD  Y
Sbjct: 181 SALGHPIVGDLTY 193


>gi|115387957|ref|XP_001211484.1| DRAP deaminase [Aspergillus terreus NIH2624]
 gi|114195568|gb|EAU37268.1| DRAP deaminase [Aspergillus terreus NIH2624]
          Length = 507

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 49/199 (24%), Positives = 83/199 (41%), Gaps = 29/199 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           +++ED  + V +KPAG+ V       YH +  ++   +  G +  PR  +RLD+ TSG++
Sbjct: 108 IIHEDDDLLVIDKPAGVPVHAAG--RYHYNSIIEILRNENGVEWMPRPCNRLDRLTSGVM 165

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
            + +T   A+ +    + R +QK Y + V G  P     C    +     +G + V    
Sbjct: 166 FIGKTAKGAEKMCAKLQQRTVQKEYIARVKGRFPDGVVICDQPIMQVSPKLGLNRVRATG 225

Query: 218 QNEK------------------------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           ++ K                        G   A +    +    + +  +   P TGRTH
Sbjct: 226 KDAKTKFRRIAYYPPAAPAAGEEDSQGEGEERAATPPPALANEDEGYSIVHCLPLTGRTH 285

Query: 254 QLRVHALHMGCPIVGDHKY 272
           Q+RVH   +G PI  D  Y
Sbjct: 286 QIRVHLQFLGHPITNDPIY 304


>gi|195339845|ref|XP_002036527.1| GM11650 [Drosophila sechellia]
 gi|194130407|gb|EDW52450.1| GM11650 [Drosophila sechellia]
          Length = 739

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 56/196 (28%), Positives = 88/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 355 KHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 413

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    E
Sbjct: 414 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGIVE 473

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   +  K+             +P TGR HQ+R
Sbjct: 474 CKEPIEVVSYKIG-----VCKVSPKGKDCTTTFQKLSQNGTTSVVLC--KPLTGRMHQIR 526

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI+ D  Y
Sbjct: 527 VHLQYLGYPILNDPLY 542


>gi|241766964|ref|ZP_04764762.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241362555|gb|EER58438.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 224

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 100/230 (43%), Gaps = 35/230 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  +    KPAG  V      A      +++  +  GQ     HRLD+ T G+LV+
Sbjct: 6   ILWRDEHLVAVYKPAGWLVHRTGLDAGETRFVMQALRNQLGQHVFPVHRLDKGTCGVLVM 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE---------CIANWLLKKSHIG-G 210
           A    AA+ L+++F  +   K Y +LV G    + E           A+  ++ +H    
Sbjct: 66  ALHSDAARALSQAFEQQATTKRYLALVRGWAPARAEVDHALKPDDAPAHAPVQDAHTRFR 125

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD- 269
               +V      A +A +   +++            P TGR HQ+R H  H+  PI+GD 
Sbjct: 126 RLAQLVLPEPSDARFATTRASLVEAV----------PTTGRRHQIRRHLKHLAHPIIGDA 175

Query: 270 -------HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
                  +++ A   G+       +L+LHA  + +PHP  G RL + + L
Sbjct: 176 THGKGPLNRWWAERLGH------QRLWLHAWQLTVPHPVTGARLTLDSGL 219


>gi|283778696|ref|YP_003369451.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
 gi|283437149|gb|ADB15591.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
          Length = 341

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 45/161 (27%), Positives = 77/161 (47%), Gaps = 7/161 (4%)

Query: 144 PRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           PR+   HRLD++TSG++V ART  A+  L + F+   + + Y ++V G P  +K  I  +
Sbjct: 158 PRIFAVHRLDRDTSGLMVFARTPEASTALIKLFKKHHVTRAYVAVVHGTPVEQK--IETY 215

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L++    G        +  + A  A++H +++      +  +E +  TGRTHQ+R+H   
Sbjct: 216 LVRDRGDGLRGSSPAGKVAEEAQRAVTHVRLMQTIG-PYSVVECRLETGRTHQIRIHLAE 274

Query: 262 MGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLPHP 300
            G  + G+  Y      K         +  LHA  +   HP
Sbjct: 275 AGHMLCGEKVYTHKLGEKSQRDESGAPRQALHAAELGFVHP 315


>gi|302765707|ref|XP_002966274.1| hypothetical protein SELMODRAFT_168290 [Selaginella moellendorffii]
 gi|300165694|gb|EFJ32301.1| hypothetical protein SELMODRAFT_168290 [Selaginella moellendorffii]
          Length = 359

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 70/266 (26%), Positives = 111/266 (41%), Gaps = 59/266 (22%)

Query: 101 LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGI 157
           +LYED  +   NKP+G+ V  GG      +   L+  V  + ++  P   HRL + TSG+
Sbjct: 96  ILYEDEHLLAINKPSGLQVLPGGLFQQRTVLSQLQWRVTDQVERNHPTPVHRLGRGTSGV 155

Query: 158 LVVARTRA----------------AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA-N 200
            V   +                   A+     +R   + K+Y +LV GI ++ K  I+ +
Sbjct: 156 YVCGTSLTKTFVYFKYLHFSGVLLCAKSDQARYRFEMLSKVYRALVCGIVQDDKVIISID 215

Query: 201 WLLKKSHI----GGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTH 253
             + ++H     GG Y+ V K          SH KV        +    +E++  +GR H
Sbjct: 216 QAIGRAHYPGVRGGLYMAVAKGKP-------SHSKVTTLKRNTEENSTVVEVEIFSGRAH 268

Query: 254 QLRVHALHMGCPIVGDHKYCANFK-----------------GNFTSPIQNKL------YL 290
           Q+R+H   +G P+VGD  Y    +                 G +  P +N L      +L
Sbjct: 269 QIRIHLASIGHPLVGDPLYVRGGQPSMQVVSTLERASVAEDGGYERP-ENPLPGDCGYHL 327

Query: 291 HARYMDLPHP-EGGRLQITAPLPAHM 315
           HA  +   HP    RL+I APLP  +
Sbjct: 328 HAHRLTFHHPVTNQRLEIVAPLPPEL 353


>gi|108758087|ref|YP_634154.1| ribosomal large subunit pseudouridine synthase A [Myxococcus
           xanthus DK 1622]
 gi|108461967|gb|ABF87152.1| ribosomal large subunit pseudouridine synthase A [Myxococcus
           xanthus DK 1622]
          Length = 559

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 98/229 (42%), Gaps = 43/229 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +++ED  + V  KP G+       ++   D  L      + + P      L HRLD +TS
Sbjct: 356 IVFEDEWLVVVEKPEGLLSVPAKDVSVE-DSVLARL---RARAPEAAGTMLAHRLDLDTS 411

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LV A+       L   F  R + K Y + V G  + ++  I            D+   
Sbjct: 412 GLLVAAKDARTYAALQRQFAGREVHKRYAAWVEGNVQGERGTI------------DFPMR 459

Query: 216 VKQNEKG--------ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGC 264
           V  +++            A++ + V++  +     + + P TGRTHQLRVHA H   +G 
Sbjct: 460 VDLDDRPRQIHDPVHGKPAVTEWHVLE-RSHGRTKVALFPLTGRTHQLRVHAAHPLGLGA 518

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           PIVGD  Y          P   +L+LHA  +   HP  G RL +  P P
Sbjct: 519 PIVGDRLY------GHPGP---RLHLHAEALSFQHPVTGQRLTLERPAP 558


>gi|330721752|gb|EGG99744.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC2047]
          Length = 287

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 54/174 (31%), Positives = 81/174 (46%), Gaps = 16/174 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-LTHRLDQETSGILV 159
           ++ ++    V+ KP G+  QG S    H   +    V+ K +KP  L HRLD+  +G+++
Sbjct: 88  MIADEGAYSVWYKPYGMRSQG-SKWGDHCALYRWVEVNHKPEKPAFLVHRLDRAATGLIL 146

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA ++ AA  LT+ F  R + K Y  +V G      E    W  K++             
Sbjct: 147 VAHSKKAAVALTKLFEERNVDKRYQVIVVG---QFSEQSGVWAKKQTFTA---------- 193

Query: 220 EKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           E     A SH + +   A+K    LE+   TGR HQ+R H    G P+VGD  Y
Sbjct: 194 EVDGKAATSHARCLAYDAEKDRSLLEVTIETGRKHQIRYHLAAAGFPVVGDRLY 247


>gi|219110967|ref|XP_002177235.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217411770|gb|EEC51698.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 168

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 49/172 (28%), Positives = 81/172 (47%), Gaps = 9/172 (5%)

Query: 105 DSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           D+ +YV NKP+ + V   G  ++  +   +++ V  +    +  HR D+ TSG+ +  ++
Sbjct: 1   DAAVYVCNKPSSVPVHPAGPFLSNSLTIMVEAQVGLQCGSLKPVHRTDRVTSGLTLCCKS 60

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            A A+          + K+Y + V G  P    E      L  +    D  + V+  +  
Sbjct: 61  SAVARIFHRCLSEGTVDKLYVARVHGKFPSTNSE----MHLDAAVHTLDPANGVRIVDSA 116

Query: 223 ANYAISHFKVIDCF--AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              + S FK++D F  A+    +  QP TGR HQLRVH   +G PIV D +Y
Sbjct: 117 GKPSKSVFKLVD-FNQAENVSVIACQPITGRNHQLRVHLQMLGYPIVNDTQY 167


>gi|330846924|ref|XP_003295235.1| hypothetical protein DICPUDRAFT_160487 [Dictyostelium purpureum]
 gi|325074072|gb|EGC28238.1| hypothetical protein DICPUDRAFT_160487 [Dictyostelium purpureum]
          Length = 533

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 45/148 (30%), Positives = 72/148 (48%), Gaps = 24/148 (16%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-------IPK-----NKK 195
           HRLD+ TSG+L++ART  AA+      +   + K Y++ V G       +P      N+ 
Sbjct: 301 HRLDRLTSGLLMLARTPDAAKKRASQIQSGDVSKQYFAKVVGKFPIGTDLPDGTVIVNQP 360

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM-QPHTGRTHQ 254
             I N  L  +H+G           +G   +++HFK+     +    + +  P TGRTHQ
Sbjct: 361 IVIQNMRLGINHVG-----------EGGKPSVTHFKLYSYDEKSNQSIVLCSPKTGRTHQ 409

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTS 282
           +RVH   +G PI  D  Y  +F+ +F +
Sbjct: 410 IRVHLKWLGYPITNDPLYNNDFRDSFKA 437


>gi|320528188|ref|ZP_08029353.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
 gi|320131536|gb|EFW24101.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
          Length = 296

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 56/214 (26%), Positives = 97/214 (45%), Gaps = 23/214 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGIL 158
           ++YED+ IY+ +K AG+ + G  G    ++ +   +  + G  Q  R  HRLD++T G++
Sbjct: 85  VVYEDAFIYIVHKDAGMIIHGDPGDTTCLNAYAARYQINHGIKQPVRPIHRLDKDTVGLV 144

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
           + ++              ++I + Y ++  G I  + +  I   L +  H  G Y    +
Sbjct: 145 IYSKIPFFQPWFDAQLSSKKIHRHYLAITNGNIDPSFRMTINKPLGRDRHNSGMY----R 200

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +  G   AI++ + +  + Q +  L     TGRTHQ+RVH   +  PIV D  Y    K
Sbjct: 201 VSSTGVE-AITYVEALGNY-QSYSLLGCTLETGRTHQIRVHLASIDHPIVNDILYGVKTK 258

Query: 278 G-----------NFTSPIQNKLYLHARYMDLPHP 300
                        F +PI NK +   +  D P+P
Sbjct: 259 DFPAMGLWANWIEFKNPITNKKH---KIFDQPNP 289


>gi|237735851|ref|ZP_04566332.1| pseudouridine synthase [Mollicutes bacterium D7]
 gi|229381596|gb|EEO31687.1| pseudouridine synthase [Coprobacillus sp. D7]
          Length = 278

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 49/184 (26%), Positives = 92/184 (50%), Gaps = 19/184 (10%)

Query: 103 YEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILV 159
           YED    V +KPAG+ S+         +   +  +  S+G K    L +RLD++T G+L+
Sbjct: 78  YEDENFLVIDKPAGLPSIPTKRYPRNTLANAVVYYYQSQGIKATVHLVNRLDKDTQGLLL 137

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+   A  H   S  +++++++Y  +V G+   +    A  +  K  +    +H     
Sbjct: 138 IAKNSYA--HYLLSRDIKQVRRVYHCVVEGVLTGQGTITAPIIKDKKSVK-RLIH----- 189

Query: 220 EKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                +A++H++ ++  A +    C LE    TGRTHQ+RVH   +  P+VGD  Y + +
Sbjct: 190 -PAGKFAVTHYRGLEVSANQSKIECILE----TGRTHQIRVHLSSINHPLVGDTLYDSIY 244

Query: 277 KGNF 280
           + ++
Sbjct: 245 QESY 248


>gi|194862300|ref|XP_001969970.1| GG10383 [Drosophila erecta]
 gi|190661837|gb|EDV59029.1| GG10383 [Drosophila erecta]
          Length = 721

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 56/196 (28%), Positives = 88/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 338 KHNDLLANIVHRHEVPVTSQPIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 396

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    E
Sbjct: 397 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGIVE 456

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG +   +  K+             +P TGR HQ+R
Sbjct: 457 CKEPIEVVSYKIG-----VCKVSSKGKDCTTTFQKLSQNGTTSVVLC--KPLTGRMHQIR 509

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI+ D  Y
Sbjct: 510 VHLQYLGYPILNDPLY 525


>gi|323464082|gb|ADX76235.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus pseudintermedius ED99]
          Length = 276

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 80/180 (44%), Gaps = 20/180 (11%)

Query: 101 LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLK-SWVDSKGQKPRLTHRLDQET 154
           + YED  + +  KP G+      ++  + +  H+   L   +V+         HRLDQET
Sbjct: 76  IAYEDDFLAIVYKPKGVKTHPNDLKESNTLMNHVIYTLNHPYVEP-------IHRLDQET 128

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G+L+VA+     + L        I +IY + V  +   K + I         IG D  H
Sbjct: 129 VGLLIVAKHPIIKKILDRMLENNDIHRIYKAQVKSLLPIKPQTI------DLPIGKDKFH 182

Query: 215 VVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             K+        A++H    +   +  C + ++  TGRTHQ+RVH   +G P++GD  Y 
Sbjct: 183 PNKRRVSPTGQRAVTHILSSEMIEEGVCEVMLKLDTGRTHQIRVHLAEIGYPVLGDPLYS 242


>gi|217033363|ref|ZP_03438794.1| hypothetical protein HP9810_9g116 [Helicobacter pylori 98-10]
 gi|216944304|gb|EEC23729.1| hypothetical protein HP9810_9g116 [Helicobacter pylori 98-10]
          Length = 293

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 75/293 (25%), Positives = 127/293 (43%), Gaps = 57/293 (19%)

Query: 41  LRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           L+  Q  +DK+R+K N + ++  Q+++    + +L H    +K                 
Sbjct: 28  LKEAQRHLDKQRLKQNQQAVRKSQMIQ---GVVSLIHFRPNEKT---------------Q 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD------SKGQKPRLTHRLDQE 153
            L++E     VF+KP  +      G  YH     +S +D      SK   P   HRLD E
Sbjct: 70  ALVFETKDFGVFDKPPQVYTHP-KGYFYH-----ESLLDCIQSYFSKNAHP--AHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  + + L   F  ++++K Y +L  G+  +K   I   +L   +I  D  
Sbjct: 122 TSGLVLAGKTLQSTKDLKMLFMQKKVKKTYLALAHGL-VDKNIVIDKPILTPQNIQKDLR 180

Query: 214 HVVKQNEKGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              K +  G         +S+   +D        L++ P TGRTHQ+R+H   +G  IVG
Sbjct: 181 IKSKISPLGKPSTTLVEPLSYNPFLDI-----SLLKITPITGRTHQIRLHLSSVGHRIVG 235

Query: 269 DHKYCA---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           +  Y             K    +P+   L LHA  ++    +G   +IT+P+P
Sbjct: 236 EGLYGVIDENAREYLQLKRENNAPL---LMLHASSLEFEF-KGAIHEITSPMP 284


>gi|297379564|gb|ADI34451.1| Hypothetical protein HPV225_0363 [Helicobacter pylori v225d]
          Length = 293

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 71/287 (24%), Positives = 124/287 (43%), Gaps = 45/287 (15%)

Query: 41  LRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           L+  Q  +DK+R+K N + ++  Q+++    + +L H    +K                 
Sbjct: 28  LKEAQRHLDKQRLKHNQQAVRKSQMIQ---GVVSLIHFKPNEKT---------------Q 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  VLVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D     K +
Sbjct: 128 AGKTLQSAKDLKALFMQKKVKKTYLALAHGL-VDKNIVIDKPILTPQNIQKDLRIRSKIS 186

Query: 220 EKGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             G         +S+   +D        L++ P TGRTHQ+R+H   +   IVG+  Y  
Sbjct: 187 PLGKPSTTLVEPLSYNPFLDI-----SLLKITPLTGRTHQIRLHLSSVNHRIVGEGLYGV 241

Query: 275 ---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                      K    +P+   L LHA  ++    +G   +IT+ +P
Sbjct: 242 IDENAREYLQLKRENNAPL---LMLHASSLEFEF-KGAIHEITSQMP 284


>gi|310792938|gb|EFQ28399.1| RluA family pseudouridine synthase [Glomerella graminicola M1.001]
          Length = 476

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 101/229 (44%), Gaps = 35/229 (15%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           +H++K   +++ +++  +     + I +++ED ++ V +KP+G+ V       Y  +  +
Sbjct: 118 DHVVKNGDLVNHTIHRHEPPVTGEPIRIIHEDDEMIVVDKPSGVPVHPAG--RYKYNSLI 175

Query: 134 KSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-I 190
           +     +G+   P   HRLD+ TSGIL + +T  AA  LT   R   ++K Y + V G  
Sbjct: 176 EIMKAERGEHFLPYPCHRLDRLTSGILFIGKTPQAAVKLTAQIRAHTVRKEYLARVAGKF 235

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF----------------KVID 234
           P  +  C    L     +G   ++ V+ N K A                       K  +
Sbjct: 236 PDGEVVCDQPILQISPRLG---LNRVRANGKSARTVFKRLAYYPPDKQDALPMEQPKTPE 292

Query: 235 CFAQ--KFCWLEMQ--------PHTGRTHQLRVHALHMGCPIVGDHKYC 273
             A+  +  W++ +        P TGRTHQ+RVH   +G PI  D  Y 
Sbjct: 293 QLAEEKRRPWIKKEGYSIVRCLPLTGRTHQIRVHLQFLGHPIQNDPLYA 341


>gi|294054835|ref|YP_003548493.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
 gi|293614168|gb|ADE54323.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
          Length = 260

 Score = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 88/186 (47%), Gaps = 20/186 (10%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----SKGQKPRLTHR 149
           D L++ +L +D ++ V NKP  +            +G L S V      +  +K  L  R
Sbjct: 15  DALQAWILRDDEELLVINKPGWLVCHPSK------NGPLSSLVGAVRELTGAEKLHLVAR 68

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKS 206
           LD+ETSG++V A+  AAA+    + + R + K Y +++ G  +      + IA       
Sbjct: 69  LDRETSGLVVFAKRPAAARKYQMAIQNRIVAKTYLAILEGTLEESILVDQSIARRKQGLV 128

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           H+  +  +V     +GA  AI+ +  I      +    ++P TGR HQ+RVHA  +   +
Sbjct: 129 HVKNEVSYV-----RGAQSAITRYVPI-AHGGGYTLARVEPETGRKHQIRVHAEWLEHRV 182

Query: 267 VGDHKY 272
           VGD  Y
Sbjct: 183 VGDKIY 188


>gi|167757078|ref|ZP_02429205.1| hypothetical protein CLORAM_02627 [Clostridium ramosum DSM 1402]
 gi|167703253|gb|EDS17832.1| hypothetical protein CLORAM_02627 [Clostridium ramosum DSM 1402]
          Length = 278

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 49/186 (26%), Positives = 93/186 (50%), Gaps = 19/186 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGI 157
           + YED    V +KPAG+ S+         +   +  +  S+G K    L +RLD++T G+
Sbjct: 76  ICYEDENFLVIDKPAGLPSIPTKRYPRNTLANAVVYYYQSQGIKATVHLVNRLDKDTQGL 135

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+   A  H   S  +++++++Y  +V G+   +    A  +  K  +    +H   
Sbjct: 136 LLIAKNSYA--HYLLSRDIKQVRRVYHCVVEGVLTGQGTITAPIIKDKKSVK-RLIH--- 189

Query: 218 QNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                  +A++H++ ++  A +    C LE    TGRTHQ+RVH   +  P+VGD  Y +
Sbjct: 190 ---PAGKFAVTHYRGLEVSANQSKIECILE----TGRTHQIRVHLSSINHPLVGDTLYDS 242

Query: 275 NFKGNF 280
            ++ ++
Sbjct: 243 IYQESY 248


>gi|317181687|dbj|BAJ59471.1| hypothetical protein HPF57_0397 [Helicobacter pylori F57]
          Length = 293

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 124/286 (43%), Gaps = 43/286 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K     Q+ Q VR   +I  +  +I             K ++  ++ 
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVRKSQMIQGVVSLI-----------FFKPNEKTQA- 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  +A+ L   F  ++++K Y  L  G+  +K   I   +L   +I  D     K + 
Sbjct: 129 GKTLQSAKDLKALFMQKKVKKTYLVLAHGL-VDKNIVIDKPILTPQNIQKDLRIKSKISP 187

Query: 221 KGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
            G         +++   +D        L++ P TGRTHQ+R+H   +   IVG+  Y   
Sbjct: 188 LGKPSTTLVEPLNYNPFLDI-----SLLKITPITGRTHQIRLHLSSVNHRIVGEGLYGVI 242

Query: 275 --------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                     K    +P+   L LHA  ++    +G   +IT+P+P
Sbjct: 243 DENAREYLQLKRENNAPL---LMLHATSLEFEF-KGAIYKITSPMP 284


>gi|297243790|ref|ZP_06927720.1| pseudouridylate synthase, 23S RNA-specific [Gardnerella vaginalis
           AMD]
 gi|296888211|gb|EFH26953.1| pseudouridylate synthase, 23S RNA-specific [Gardnerella vaginalis
           AMD]
          Length = 288

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 46/159 (28%), Positives = 80/159 (50%), Gaps = 7/159 (4%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD  TSG++++ +T  A + +   F    ++K Y +LV G     K  I +  + +
Sbjct: 113 IVSRLDVGTSGLMIICKTDFAYEVMKNQFAKHIVKKTYHALVQGDLAQDKATI-DAPIGR 171

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           + +  D+   +  + K    A++H+ V++ F Q      +   TGRTHQ+RVH   +G P
Sbjct: 172 AKVS-DFRFTITSDGK---PAVTHWDVLERFGQA-TLASVNLETGRTHQIRVHFSSIGHP 226

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +VGD  Y AN        +Q + +LH+  +   HP  G+
Sbjct: 227 LVGDSMYGANPVLAQKLGLQRQ-WLHSMELTFTHPRTGK 264


>gi|291457515|ref|ZP_06596905.1| RNA pseudouridine synthase, RluA family [Bifidobacterium breve DSM
           20213]
 gi|291381350|gb|EFE88868.1| RNA pseudouridine synthase, RluA family [Bifidobacterium breve DSM
           20213]
          Length = 314

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 47/159 (29%), Positives = 78/159 (49%), Gaps = 14/159 (8%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD  TSG+++V ++  A   +   F    ++K Y +LV G  K  K  I      +
Sbjct: 130 IVSRLDVGTSGLMLVCKSELAYTEMRRQFAEHEVKKTYHALVQGGLKEDKATI------E 183

Query: 206 SHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + IG     D+   +    K    AI+H+ V++ F  +   + +   TGRTHQ+RVH   
Sbjct: 184 APIGRAKVSDFRFCITPAGK---PAITHWDVLERFDHEATLVSVNLETGRTHQIRVHFSS 240

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +G P+ GD  Y AN   +    + ++ +LHA  ++  HP
Sbjct: 241 IGHPLCGDPMYGANPVLSEALGL-DRQWLHAMKLEFRHP 278


>gi|194377234|dbj|BAG63178.1| unnamed protein product [Homo sapiens]
          Length = 524

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 100/212 (47%), Gaps = 26/212 (12%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  LN ++K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++ 
Sbjct: 173 VQDLNIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNT 232

Query: 130 DGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V
Sbjct: 233 VIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRV 289

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW---- 242
            G  P  +  C    L+    +G     V + + +G        K  +   Q+  +    
Sbjct: 290 EGEFPTEEVTCKEPILVVSYKVG-----VCRVDPRG--------KPCETVFQRLSYNGQS 336

Query: 243 --LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +  +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 337 SVVRCRPLTGRTHQIRVHLQFLGHPILNDPIY 368


>gi|56753585|gb|AAW24995.1| SJCHGC01427 protein [Schistosoma japonicum]
          Length = 567

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 96/226 (42%), Gaps = 53/226 (23%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFL---KSWVDSKGQKPR-----------LTHRLDQE 153
           + + NKP GI+ Q G+   ++I   L   +S +  +  +               HRLD++
Sbjct: 247 VIIMNKPYGIASQPGADCKHNIVDLLPRIESMIRKRNHRASKVKEETVDELSTVHRLDKD 306

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH------ 207
           ++G +++AR R A+  L E+F  R I+K Y  +  GIP+++   I   L++++       
Sbjct: 307 STGAMLIARNRDASLKLQEAFARRWIKKDYLCITVGIPRSEYGYIQLPLVERNFKEFHKM 366

Query: 208 -IGGDYVHV----VKQNEKGANYAISHFKVIDCFA------------QKFCWLEMQPH-- 248
            I     H+     KQ +   N   + + V D F+            Q   W  +     
Sbjct: 367 CIPKLDRHLQELACKQTQLDENDETNEYDVTDAFSVLYNKMQTNNNNQPVTWYHLLDQRN 426

Query: 249 ----------TGRTHQLRVH-ALHMGCPIVGDHKYCANFKGNFTSP 283
                     TG  HQ+R H A  +  PI+GDHKY     G + +P
Sbjct: 427 DAGLMLCSTLTGIKHQVRAHLAFGLQTPILGDHKYS---HGEYLAP 469


>gi|319892885|ref|YP_004149760.1| ribosomal large subunit pseudouridine synthase D, YhcT
           [Staphylococcus pseudintermedius HKU10-03]
 gi|317162581|gb|ADV06124.1| ribosomal large subunit pseudouridine synthase D, YhcT
           [Staphylococcus pseudintermedius HKU10-03]
          Length = 276

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 80/180 (44%), Gaps = 20/180 (11%)

Query: 101 LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLK-SWVDSKGQKPRLTHRLDQET 154
           + YED  + +  KP G+      ++  + +  H+   L   +V+         HRLDQET
Sbjct: 76  IAYEDDFLAIVYKPKGVKTHPNDLKESNTLMNHVIYTLNHPYVEP-------IHRLDQET 128

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G+L+VA+     + L        I +IY + V  +   K + I         IG D  H
Sbjct: 129 VGLLIVAKHPIIKKILDRMLENNDIHRIYKAQVKSLLPIKPQTI------DLPIGKDKFH 182

Query: 215 VVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             K+        A++H    +   +  C + ++  TGRTHQ+RVH   +G P++GD  Y 
Sbjct: 183 PNKRRVSPTGQRAVTHILSSEMIEEGVCEVMLKLDTGRTHQIRVHLAEIGYPVLGDPLYS 242


>gi|146418802|ref|XP_001485366.1| hypothetical protein PGUG_03095 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 390

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 86/179 (48%), Gaps = 17/179 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  + V NKP+GI         Y+ +   +K+ +  +   P   HRLD+ TSGIL+
Sbjct: 104 IIYQDPSLIVVNKPSGIPTHPSGNFRYNSVTEIVKAQLHLESIFP--CHRLDKATSGILM 161

Query: 160 VARTRAAAQHLTESFRMRR-IQKIYWSLVWG-IPKNKKECIANWLLKKSHIG----GDYV 213
           +A T AA  ++ +  + R+ ++K Y + V G  P ++        L  S  G    G YV
Sbjct: 162 LATTSAACSNIQKQLQERKDVKKEYIARVKGKFPPSQLVHQDPVFLLNSTAGYIMPGRYV 221

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +       ++   +  K      +     E  PH+G+ HQ+R+H  ++G PIV D  Y
Sbjct: 222 SI------DSSTTFTRLKYNLELDESIVSCE--PHSGKMHQIRIHLRNLGFPIVNDKLY 272


>gi|314933208|ref|ZP_07840573.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus caprae C87]
 gi|313653358|gb|EFS17115.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus caprae C87]
          Length = 284

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 56/214 (26%), Positives = 96/214 (44%), Gaps = 30/214 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQ-KPRLTHRLDQETSGI 157
           +++ED  I + NKP   +        +   ++  L   ++   Q  P +  RLD+ TSG+
Sbjct: 77  IVFEDEFILIVNKPQSQNCAPSREHPHESLVEQVLAYLMNKDVQTNPHIVTRLDRNTSGL 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+      H+   F   + +K Y  L +G  + + E +    + +     D +   K
Sbjct: 137 VLFAK----FGHIHHLFSKVKFEKEYICLAYG--RTQPEGVVEAPIARD---SDSIITRK 187

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY----- 272
            ++KG     S++ ++       C +++  HTGRTHQ+RVH   MG PIVGD  Y     
Sbjct: 188 VSDKGKYAKTSYYTIVQNNTLSLCKVKL--HTGRTHQIRVHFQFMGHPIVGDDLYGGVHH 245

Query: 273 --------CANFKGNFTSPI-QNKLYLHARYMDL 297
                   C + K  F  PI  NK+ ++  Y  L
Sbjct: 246 LVKGQSLQCCSLK--FVHPINHNKISINIDYKQL 277


>gi|294461273|gb|ADE76199.1| unknown [Picea sitchensis]
          Length = 386

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 81/316 (25%), Positives = 128/316 (40%), Gaps = 65/316 (20%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           LQ+I  +GQ+ VD K V      +   V+RI P            K++   ++  +    
Sbjct: 47  LQRI-HNGQITVDGKTVN-----EPDTVLRIGP------------KLVYHRLSWREPIAP 88

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGG----------------SGIAYHIDGFLKSWVDSK 140
            K  +L+ED  +   NKP+G+ V  G                S  + +     K+  D +
Sbjct: 89  CKLYVLFEDDHLLAVNKPSGLQVLPGGLFQQRTVLTQLKWKASQSSKYRSVAGKAVADFQ 148

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-------------------MRRIQK 181
             +P   HRL + TSGIL+ A++  A   L   F                     RRI K
Sbjct: 149 ESQPVPVHRLGRGTSGILLCAKSEIAKSQLAADFADGTSFISRNSSSDIDAGEIKRRIYK 208

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            Y +L  GI +  K  I   + K  + G   G YV      +     A S   V+     
Sbjct: 209 TYRALADGIIEQNKIAIKQPIGKMRYPGVRSGLYVASPTGKQ-----AESRITVLSRDKN 263

Query: 239 KFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + C L E++ ++GR HQ+R+H   +G P++GD  Y A  + + T    +  Y  +R  D 
Sbjct: 264 RNCTLVEVEIYSGRPHQIRIHLSFIGHPLLGDPLYVAGGRPSITV---SDSYSESREGDN 320

Query: 298 PHPEGGRLQITAPLPA 313
              +GG  +   P+P 
Sbjct: 321 FAEDGGYQKPLNPVPG 336


>gi|239620840|ref|ZP_04663871.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|322689550|ref|YP_004209284.1| hypothetical protein BLIF_1367 [Bifidobacterium longum subsp.
           infantis 157F]
 gi|322691511|ref|YP_004221081.1| hypothetical protein BLLJ_1322 [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|239516416|gb|EEQ56283.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|320456367|dbj|BAJ66989.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|320460886|dbj|BAJ71506.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           infantis 157F]
          Length = 309

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 47/159 (29%), Positives = 78/159 (49%), Gaps = 14/159 (8%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD  TSG+++V ++  A   +   F    ++K Y +LV G  K  K  I      +
Sbjct: 119 IVSRLDVGTSGLMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQGGLKENKATI------E 172

Query: 206 SHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + IG     D+   V    K    A++H+ V++ F  +   + +   TGRTHQ+RVH   
Sbjct: 173 APIGRAKVSDFRFCVTPAGK---PAVTHWDVLERFGHEATLVSVNLETGRTHQIRVHFSS 229

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +G P+ GD  Y AN   +    + ++ +LHA  ++  HP
Sbjct: 230 IGHPLCGDPMYGANPVLSEALGL-DRQWLHAMKLEFRHP 267


>gi|184155038|ref|YP_001843378.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
 gi|227514836|ref|ZP_03944885.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus fermentum
           ATCC 14931]
 gi|260663582|ref|ZP_05864471.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
 gi|183226382|dbj|BAG26898.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
 gi|227086826|gb|EEI22138.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus fermentum
           ATCC 14931]
 gi|260551808|gb|EEX24923.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
 gi|299783021|gb|ADJ41019.1| Pseudouridine synthase [Lactobacillus fermentum CECT 5716]
          Length = 296

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 67/301 (22%), Positives = 131/301 (43%), Gaps = 59/301 (19%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           I   GQ+R++ +     ++++ G VV          +++   +  + ++ ++  +     
Sbjct: 33  IFHGGQMRINDRVAWAIDQVEPGDVV----------YLVVPNEPANPTITVSDQT----F 78

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTH---RLDQET 154
            + YED    V NK AG++      +A    +   +K +   +    ++TH   RLD++T
Sbjct: 79  EIAYEDEDFLVINKEAGVATVPAHHVAVQDSLVNRVKGYYQRQNYPNQVTHVATRLDKDT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V  + R A   L    + R+++K Y ++V G     +  +++  +  + I  D   
Sbjct: 139 SGLVVFPKHRFAHAVLDRQLKARQVKKEYLAMVQG-----RLTVSHGYI-DAPIRRDPDS 192

Query: 215 VVKQ--NEKGANYAISHF--KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            VK+     G   A  ++  +V D  +     + ++ HTGRTHQ+RVH   +G P++GD 
Sbjct: 193 FVKRLVAPDGKASATEYWCERVTDTTS----LVRVRLHTGRTHQIRVHFSFLGHPLLGDD 248

Query: 271 KYCANF----------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
            Y   F          + +F SP + K+                + + APLP    +  D
Sbjct: 249 MYGTGFGMPRQALHCQRVSFYSPFKQKV----------------ISVAAPLPTDFQRAED 292

Query: 321 S 321
            
Sbjct: 293 E 293


>gi|157116527|ref|XP_001658535.1| ribosomal pseudouridine synthase [Aedes aegypti]
 gi|108883445|gb|EAT47670.1| ribosomal pseudouridine synthase [Aedes aegypti]
          Length = 516

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 57/196 (29%), Positives = 87/196 (44%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 121 KHNDLLANIVHRHEVPVTSQPITIVHMDDDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 179

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ +    R R++QK Y   V G  P    E
Sbjct: 180 EYNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEHQIRNRQVQKEYICRVEGEFPDGIIE 239

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K + KG     +  K+   +      +  +P TGR HQ+R
Sbjct: 240 CKEPIEVVSYKIG-----VCKVSPKGKECTTTFQKL--GYNGTSSVVLCKPLTGRMHQIR 292

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G P+V D  Y
Sbjct: 293 VHLQYLGYPVVNDPLY 308


>gi|23464749|ref|NP_695352.1| hypothetical protein BL0123 [Bifidobacterium longum NCC2705]
 gi|227546864|ref|ZP_03976913.1| possible pseudouridylate synthase [Bifidobacterium longum subsp.
           infantis ATCC 55813]
 gi|317481580|ref|ZP_07940616.1| RluA family pseudouridine synthase [Bifidobacterium sp.
           12_1_47BFAA]
 gi|23325319|gb|AAN23988.1| widely conserved hypothetical protein in the Rlu family of
           pseudouridine synthases [Bifidobacterium longum NCC2705]
 gi|227212826|gb|EEI80707.1| possible pseudouridylate synthase [Bifidobacterium longum subsp.
           infantis ATCC 55813]
 gi|316916940|gb|EFV38326.1| RluA family pseudouridine synthase [Bifidobacterium sp.
           12_1_47BFAA]
          Length = 320

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 47/159 (29%), Positives = 78/159 (49%), Gaps = 14/159 (8%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD  TSG+++V ++  A   +   F    ++K Y +LV G  K  K  I      +
Sbjct: 130 IVSRLDVGTSGLMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQGGLKENKATI------E 183

Query: 206 SHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + IG     D+   V    K    A++H+ V++ F  +   + +   TGRTHQ+RVH   
Sbjct: 184 APIGRAKVSDFRFCVTPAGK---PAVTHWDVLERFGHEATLVSVNLETGRTHQIRVHFSS 240

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +G P+ GD  Y AN   +    + ++ +LHA  ++  HP
Sbjct: 241 IGHPLCGDPMYGANPVLSEALGL-DRQWLHAMKLEFRHP 278


>gi|319763272|ref|YP_004127209.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|317117833|gb|ADV00322.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
          Length = 316

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 55/220 (25%), Positives = 98/220 (44%), Gaps = 34/220 (15%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +  +LY+D  I V +KP  + V   G  + + +   LK  +  +   P   HR+D++T+
Sbjct: 90  FQETVLYQDEHILVADKPHFLPVVPAGRYLQHTLLVRLKRRLGLRELSP--VHRIDRDTA 147

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ +  RA        FR R+++K+Y            E +A W   ++ +     H 
Sbjct: 148 GLVLFSVQRATRGRYQALFRDRQVRKVY------------EAVAPW---RADLRFPRTHA 192

Query: 216 VKQNEKGANYAI-------SHFKVIDCFAQKFCWLE--MQPHTGRTHQLRVHALHMGCPI 266
            +  E G  + +       +    +D   Q   W    ++P TG+ HQLRVH   +G P+
Sbjct: 193 SRLQESGHFFRMHEVPGEPNAVTTMDVAEQAGGWARYRLEPVTGKRHQLRVHMAALGLPL 252

Query: 267 VGDHKYCA---NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            GD  Y       +G++++P+Q    L AR +    P  G
Sbjct: 253 CGDGFYPEVNDPPEGDYSNPLQ----LLARTLSFTDPVTG 288


>gi|256383973|gb|ACU78543.1| 23S rRNA pseudouridine synthase [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|256384805|gb|ACU79374.1| 23S rRNA pseudouridine synthase [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|296455605|gb|ADH21840.1| 23S rRNA pseudouridine synthase [synthetic Mycoplasma mycoides
           JCVI-syn1.0]
          Length = 302

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 68/279 (24%), Positives = 131/279 (46%), Gaps = 43/279 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV  +++N  L ++ K  +       + K +R+  ++++ KR+          +++I  V
Sbjct: 5   VVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRIS-----DKNYLLKINDV 59

Query: 71  INALNH---IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           I   +    II++Q    S+VNL          ++YED+ I + NKP  + +     +  
Sbjct: 60  IEVYDSNKPIIRDQFNYISNVNLD---------IVYEDNNILIVNKPNNLEMHSTYNLC- 109

Query: 128 HIDGFLKSW-VDSKGQKPRL--------THRLDQETSGILVVARTRAAAQHLTESFRMR- 177
            +D  +KS+ VD K     L         HRLD+ TSG+++ A+ + ++  LT +F+ + 
Sbjct: 110 -LDDMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSTILTNAFKSKD 168

Query: 178 RIQKIYWSLV---WGIPKNKKECIANWLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVI 233
           +I K Y++L    W + +  +  +  ++   S+I   D+    K N K   Y  + FK+I
Sbjct: 169 QINKYYYALTSSDWSLDEFLQ--VNGYINYDSNIKKADFSLDKKNNYK---YCQTEFKLI 223

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +        + ++  TG+ HQ+R        PI+ D +Y
Sbjct: 224 NK-----NLILVKLITGKKHQIRSVLSFYNHPILNDFRY 257


>gi|154482915|ref|ZP_02025363.1| hypothetical protein EUBVEN_00612 [Eubacterium ventriosum ATCC
           27560]
 gi|149736199|gb|EDM52085.1| hypothetical protein EUBVEN_00612 [Eubacterium ventriosum ATCC
           27560]
          Length = 204

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 44/197 (22%), Positives = 98/197 (49%), Gaps = 17/197 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + +  ++   R D++   ++       + K+LR   + ++ K+     ++  G  ++
Sbjct: 1   MQEIKITENQAGQRFDKFLFKYFKEATSGFIYKMLRKKNIVLNGKKSDGKEKLNVGDSIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I     A + I+K +   ++ V++ K  D     ++YED  I + NKP+G+  Q      
Sbjct: 61  I---FMADDTILKFRG--ETKVDIVKPIDL---DIVYEDDNILIINKPSGMLSQKAEASD 112

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             ++ ++ S++ S  +         KP + +RLD+ TSG+++  ++    Q +++ F+ R
Sbjct: 113 VSVNEYIISYLVSTNKLSEEQLKTFKPGVCNRLDRNTSGLIIAGKSLKGLQTMSKMFKER 172

Query: 178 RIQKIYWSLVWGIPKNK 194
            + K Y++LV G  +NK
Sbjct: 173 TMDKYYFALVNGKIENK 189


>gi|317013785|gb|ADU81221.1| hypothetical protein HPGAM_01875 [Helicobacter pylori Gambia94/24]
          Length = 293

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 60/223 (26%), Positives = 100/223 (44%), Gaps = 20/223 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KPA +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFEAKDFGVFDKPAQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  + + L   F  ++++K Y +L  G+  +K   I   +L   +I  D + +  Q  
Sbjct: 129 GKTLQSVKDLKALFMQKKVKKTYLALAHGL-VDKSIIINKPILTPQNIQKD-LRIRSQIS 186

Query: 221 KGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---- 274
                +I+  + +  + F      L++ P TGRTHQ+R+H   +   IVG+  Y      
Sbjct: 187 PLGKPSITLVEPLSYNPFLD-ISLLKITPLTGRTHQIRLHLSSINHRIVGEGLYGVADEN 245

Query: 275 -----NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                  K    +P    L LHA  ++    +G   QI +P+P
Sbjct: 246 AREYLQLKRENNAPT---LMLHAASLEFEF-KGAIYQIASPMP 284


>gi|152995953|ref|YP_001340788.1| pseudouridine synthase Rlu family protein [Marinomonas sp. MWYL1]
 gi|150836877|gb|ABR70853.1| pseudouridine synthase Rlu family protein, TIGR01621 [Marinomonas
           sp. MWYL1]
          Length = 223

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 58/195 (29%), Positives = 91/195 (46%), Gaps = 25/195 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+     ++  KPAG+S    S     +     S+ D   Q     HRLD+ TSG+L+V
Sbjct: 4   ILFRSVDYWIVEKPAGMSFHAESEGLGVMQTLAISYPD---QNFYPVHRLDKMTSGLLIV 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A   AAA    + F    ++K Y +L    PK K+  I+  +       G +  + + NE
Sbjct: 61  ACHAAAAAEFGKMFERHEMEKRYLALSAKKPKKKQGTISGGMAPSRR--GQW-KLTQDNE 117

Query: 221 KGANYAISHFKVIDCFAQKFCWLE---MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              N+A++ F     F+  F  L    ++P TG+THQ+RV    +G PI+GD +Y     
Sbjct: 118 ---NFAVTQF-----FSSAFHGLRVFIVRPLTGKTHQIRVALKSLGSPILGDLRYSGE-- 167

Query: 278 GNFTSPIQNKLYLHA 292
                   ++ YLHA
Sbjct: 168 ------GADRGYLHA 176


>gi|88809883|ref|ZP_01125389.1| probable pseudouridine synthase [Synechococcus sp. WH 7805]
 gi|88786267|gb|EAR17428.1| probable pseudouridine synthase [Synechococcus sp. WH 7805]
          Length = 298

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 56/211 (26%), Positives = 93/211 (44%), Gaps = 17/211 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKG--QKPRLTHRLDQETSGI 157
           ++Y+D  + V NKP+G+ V  G G   H +   L     S G  Q P+  HRL + TSG+
Sbjct: 64  VVYDDGDVLVINKPSGLPVMPGGGFLQHTLSALLMEASRSAGASQVPKPVHRLGRFTSGL 123

Query: 158 LVVARTRAAAQHLTESFR----MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI----- 208
            V AR       L+  FR     R+    + + V G+  ++   +   ++++ H      
Sbjct: 124 QVCARRPQTRAELSRQFRPEGGCRKTYLAWANPVKGLRADQPLVVTTDVVERVHPLLGWV 183

Query: 209 -GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            G D         +   +A S  +++    Q    +E+   TGR HQ+R+H   +G P++
Sbjct: 184 WGPDPFDGEPLRRR--LHARSELRLLKRCDQGDL-VEVAISTGRPHQIRIHLAQLGSPLL 240

Query: 268 GDHKYCANFKGNFTS-PIQNKLYLHARYMDL 297
           GD  Y    + N  + P      LHA  + L
Sbjct: 241 GDPLYLPQQRINAAAVPGDGGYRLHAHTLAL 271


>gi|326919876|ref|XP_003206203.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Meleagris gallopavo]
          Length = 479

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 43/126 (34%), Positives = 69/126 (54%), Gaps = 8/126 (6%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKS 206
           HRLD+ TSG+L+ A+T   ++ + E  R R+++K Y   V G  P+++  C    L+   
Sbjct: 198 HRLDRMTSGVLMFAKTVEVSKRIDEQVRERQLEKEYVCRVVGEFPEHEVVCEEPILVVSY 257

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +G     V + + KG     + F+ +  +  K   ++  PHTGRTHQ+RVH  ++G PI
Sbjct: 258 KVG-----VCRVDPKG-KCCKTIFQRLS-YNGKSSVVKCLPHTGRTHQIRVHLQYLGYPI 310

Query: 267 VGDHKY 272
           V D  Y
Sbjct: 311 VNDPIY 316


>gi|309804686|ref|ZP_07698751.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
 gi|308166078|gb|EFO68296.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
          Length = 274

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 43/132 (32%), Positives = 69/132 (52%), Gaps = 10/132 (7%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           KP +  RLD++TSG+++V +   A      S + R I+K Y ++V G   P   +  I  
Sbjct: 133 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKK-YHAIVHGNFSPSQLQGVIDA 191

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + KK      Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  
Sbjct: 192 PIGKKDDPIKRYI------MEGGKNSVTKYRVIKQVAGA-SLVELQLLTGRTHQIRVHMQ 244

Query: 261 HMGCPIVGDHKY 272
           ++G P+ GDH Y
Sbjct: 245 YLGHPLFGDHLY 256


>gi|332994209|gb|AEF04264.1| Pseudouridylate synthase [Alteromonas sp. SN2]
          Length = 265

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 105/235 (44%), Gaps = 19/235 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I   +KP G+ V   S I  H   F +++  D   +     HRLD+ TSG+L+
Sbjct: 30  ILYQDEHIVAIDKPPGLLVHR-SPIDRHETRFAVQTLRDQLNKHVFPAHRLDRPTSGVLL 88

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            +     A  L +    +++QK Y ++V G  K+    + ++ LK  +      H   Q 
Sbjct: 89  FSFDSKTAALLGQQLMNKQVQKQYHAIVRGYVKH--SGLIDYALKYRYDKIADKHKRPQQ 146

Query: 220 ---------EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                    E  ANY +  F V      ++  +++ P TGR HQLR H +H+  PI+GD 
Sbjct: 147 APQQATTVYESLANYELP-FAVGKYETARYSLVKLLPSTGRKHQLRRHMVHIRHPILGDT 205

Query: 271 KYCANFKGNFTS---PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            +    +  F       QN L L    M   HP  G+ L +   + + M +  D+
Sbjct: 206 THGDGKQNKFLQTHFSFQN-LALSCTQMGFYHPITGKWLSVFVRMHSEMQRVLDA 259


>gi|317177158|dbj|BAJ54947.1| hypothetical protein HPF16_0350 [Helicobacter pylori F16]
          Length = 293

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 73/287 (25%), Positives = 123/287 (42%), Gaps = 45/287 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS- 99
           L+  Q  +DK+R+K     Q+ Q VR             + +++   V+L       K+ 
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVR-------------KSQMIQGVVSLIHFRPNEKTQ 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  ALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             +T  +A+ L   F  ++++K Y  L  G+  ++   I   +L   +I  D     K +
Sbjct: 128 AGKTLQSAKDLKALFMQKKVKKTYLVLAHGL-VDRSIVIDKPILTPQNIQKDLRIKSKIS 186

Query: 220 EKGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             G         +S+   +D        L++ P TGRTHQ+R+H   +   IVG+  Y  
Sbjct: 187 PLGKPSTTLVEPLSYNPFLDI-----SLLKITPITGRTHQIRLHLSSVNHRIVGEGLYGV 241

Query: 275 ---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                      K    +P+   L LHA  ++    +G   +IT+P+P
Sbjct: 242 IDENAREYLQLKRENNAPL---LMLHAASLEFEF-KGAIYKITSPMP 284


>gi|260222881|emb|CBA32891.1| hypothetical protein Csp_B16300 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 308

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 58/213 (27%), Positives = 98/213 (46%), Gaps = 28/213 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           ++++D  + V +KP  + V        H+   L + +  +   P L+  HR+D++T+G++
Sbjct: 93  VIWQDEHLLVVDKPHFLPVVPSGK---HVRETLLARLQLRLNLPDLSPVHRIDKDTAGLV 149

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-------LLKKSHIGGD 211
           +     A        FR RR+ K Y            ECIA W       + ++S IG D
Sbjct: 150 MFTTQPAGRNAYQALFRERRVSKTY------------ECIAPWKPGLVWPVHRESRIG-D 196

Query: 212 YVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             H ++Q E  G   AI+  ++++  A  +    ++P TG+ HQLRVH   +G PI+ D 
Sbjct: 197 AEHFMQQAEVPGEVNAITDIELLEV-AGDWARYALRPLTGQRHQLRVHMHALGLPILFDG 255

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            Y        T+  +  L L AR ++   P  G
Sbjct: 256 IYPV-LTPEGTNDYRRPLQLLARTLEFVDPLSG 287


>gi|330825467|ref|YP_004388770.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
 gi|329310839|gb|AEB85254.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
          Length = 316

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 55/220 (25%), Positives = 98/220 (44%), Gaps = 34/220 (15%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +  +LY+D  I V +KP  + V   G  + + +   LK  +  +   P   HR+D++T+
Sbjct: 90  FQETVLYQDEHILVADKPHFLPVVPAGRYLQHTLLVRLKRRLGLRELSP--VHRIDRDTA 147

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ +  RA        FR R+++K+Y            E +A W   ++ +     H 
Sbjct: 148 GLVLFSVQRATRGRYQALFRDRQVRKVY------------EAVAPW---RADLRFPRTHA 192

Query: 216 VKQNEKGANYAI-------SHFKVIDCFAQKFCWLE--MQPHTGRTHQLRVHALHMGCPI 266
            +  E G  + +       +    +D   Q   W    ++P TG+ HQLRVH   +G P+
Sbjct: 193 SRLQESGHFFRMHEVPGEPNAVTAMDVAEQAGGWARYRLEPVTGKRHQLRVHMAALGLPL 252

Query: 267 VGDHKYCA---NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            GD  Y       +G++++P+Q    L AR +    P  G
Sbjct: 253 CGDGFYPEVNDPPEGDYSNPLQ----LLARTLSFTDPVTG 288


>gi|50311419|ref|XP_455734.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49644870|emb|CAG98442.1| KLLA0F14553p [Kluyveromyces lactis]
          Length = 377

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 67/258 (25%), Positives = 111/258 (43%), Gaps = 32/258 (12%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           K+LR G+       +K  + + + Q    PPV N    I  E+ I+   +          
Sbjct: 64  KLLREGKQLEGDPIIKNKDILLTYQHNHEPPVKNWGEPICDEKHIMGIPI---------- 113

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGI 157
              +++D ++ V NKP GI V      AY     L   + DS G      +RLD+ TSG+
Sbjct: 114 ---VHQDEQLLVINKPNGIPVHP---TAYFYKNTLTELLKDSLGYPVHPCYRLDKITSGL 167

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKN--KKECIANWLLKKSHIGGDYVH 214
           L++A+    A  +    R R ++K Y + V G  P+    K  I    LK   I  + + 
Sbjct: 168 LILAKNPIDANRVQSKIRDRDMKKYYLARVKGKFPETAVDKSPIYTCDLK---IKSEPLS 224

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +K  +    + +  +  +   +   C    +P TGRTHQ+R+H    G PI  D  Y  
Sbjct: 225 PLK--DAHTEFELMEYDAVTDQSIVLC----KPFTGRTHQIRIHLARQGHPITNDPFYNL 278

Query: 275 NFKGNFTSPIQNKLYLHA 292
           +   N T P++++  +  
Sbjct: 279 D---NSTYPLRSRFIIET 293


>gi|171742473|ref|ZP_02918280.1| hypothetical protein BIFDEN_01585 [Bifidobacterium dentium ATCC
           27678]
 gi|283456441|ref|YP_003361005.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           dentium Bd1]
 gi|306822383|ref|ZP_07455762.1| RluA family RNA pseudouridine synthase [Bifidobacterium dentium
           ATCC 27679]
 gi|309802127|ref|ZP_07696236.1| pseudouridine synthase, RluA family [Bifidobacterium dentium
           JCVIHMP022]
 gi|171278087|gb|EDT45748.1| hypothetical protein BIFDEN_01585 [Bifidobacterium dentium ATCC
           27678]
 gi|283103075|gb|ADB10181.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           dentium Bd1]
 gi|304554381|gb|EFM42289.1| RluA family RNA pseudouridine synthase [Bifidobacterium dentium
           ATCC 27679]
 gi|308221207|gb|EFO77510.1| pseudouridine synthase, RluA family [Bifidobacterium dentium
           JCVIHMP022]
          Length = 312

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 49/159 (30%), Positives = 79/159 (49%), Gaps = 15/159 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD  TSG+++V ++  A   +   F    + K Y +LV G  K  K  I      +
Sbjct: 130 IVSRLDVGTSGLMLVCKSELAYVEMRRQFAEHEVVKTYHALVQGNLKEDKATI------E 183

Query: 206 SHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + IG     D+   V    K    AI+H+ V++ F +    + +   TGRTHQ+RVH   
Sbjct: 184 APIGRAKVSDFRFCVTPAGK---EAITHWDVMERFGEA-TLVSVNLETGRTHQIRVHFSS 239

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +G P+VGD  Y AN + +    ++ + +LHA  ++  HP
Sbjct: 240 IGHPLVGDPMYGANPQLSEALGLERQ-WLHAMQLEFRHP 277


>gi|331703735|ref|YP_004400422.1| RNA pseudouridylate synthase [Mycoplasma mycoides subsp. capri LC
           str. 95010]
 gi|328802290|emb|CBW54444.1| RNA pseudouridylate synthase [Mycoplasma mycoides subsp. capri LC
           str. 95010]
          Length = 302

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 67/276 (24%), Positives = 132/276 (47%), Gaps = 37/276 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV  +++N  L ++ K  +       + K +R+  ++++ KR+   N +   ++  +  V
Sbjct: 5   VVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRISDKNYLL--EINDVIEV 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            ++   II++Q    S+VNL          ++YED+ I + NKP  + +     +   +D
Sbjct: 63  YDSNKPIIRDQFNYISNVNLD---------IVYEDNNILIVNKPNNLEMHSTYNLC--LD 111

Query: 131 GFLKSW-VDSKGQKPRL--------THRLDQETSGILVVARTRAAAQHLTESFRMR-RIQ 180
             +KS+ VD K     L         HRLD+ TSG+++ A+ + ++  LT +F+ + +I 
Sbjct: 112 DMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSTILTNAFKSKDQIN 171

Query: 181 KIYWSLV---WGIPKNKKECIANWLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCF 236
           K Y++L    W + +  +  +  ++   S+I   D+    K N K   Y  + FK+I+  
Sbjct: 172 KYYYALTSSDWNLDEFLQ--VNGYINYDSNIKKADFSLDKKNNYK---YCQTEFKLINK- 225

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                 + ++  TG+ HQ+R        PI+ D +Y
Sbjct: 226 ----NLILVKLITGKKHQIRSVLSFYNHPILNDFRY 257


>gi|239940134|ref|ZP_04692071.1| putative ribosomal pseudouridine synthase [Streptomyces roseosporus
           NRRL 15998]
 gi|239986622|ref|ZP_04707286.1| putative ribosomal pseudouridine synthase [Streptomyces roseosporus
           NRRL 11379]
          Length = 292

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 63/211 (29%), Positives = 99/211 (46%), Gaps = 23/211 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG-IL 158
           ++Y D +I V +KP  ++    G  I       L+  +D    +P   HRLD+ T+G +L
Sbjct: 80  VVYRDERIVVADKPHFLATMPRGRHITETAVARLRRELDLPVLQP--AHRLDRLTAGLVL 137

Query: 159 VVART--RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            V R+  R A Q L   FR RR++K Y ++    P +    +   +  +S I  +   + 
Sbjct: 138 FVVRSQDRGAYQTL---FRDRRVRKEYEAVA---PYDPGVALPRTV--RSRIVKERGVLA 189

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---- 272
            + E G   + SH ++++          + P TGRTHQLRVH   +G PIV D  Y    
Sbjct: 190 AREEPGEANSESHVELVERRG-ALGRYRLVPATGRTHQLRVHMNALGLPIVHDPLYPVVA 248

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 +F+ P+Q    L AR ++   P GG
Sbjct: 249 AEASADDFSRPLQ----LLARVLEFTDPVGG 275


>gi|223944597|gb|ACN26382.1| unknown [Zea mays]
          Length = 307

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 67/260 (25%), Positives = 109/260 (41%), Gaps = 60/260 (23%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-----VDSKGQKPRL--THRLDQE 153
           +++ED  + V +KPAG+          + D  L S+      ++   KP L   +RLD++
Sbjct: 49  VVFEDEWLAVVDKPAGV----------YCDALLTSFPCSAVSENPATKPNLHLANRLDRD 98

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP---KNKKECIANWLLK------ 204
           TSG++V+ +    A  L ++F   +++K Y +L  G P   +  K C  +   K      
Sbjct: 99  TSGLMVITKCNKVAGKLVKAFTDHKVKKTYLALCIGFPPAWEKIKICSGHGRSKHGAWRV 158

Query: 205 -------KSHIGGDYV-------HVVKQNEKG---ANYA-----ISHFKVIDCFAQKFC- 241
                  +S  GG  V        V+  N KG     Y+     I    V +    + C 
Sbjct: 159 YAMSDVGRSLPGGSVVRDMSTRFEVLGVNGKGQFREPYSLDTDDIEPITVQEKATDQTCG 218

Query: 242 --------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                    +   P +GRTHQ+R+H  ++G PI GD KY    + +          LHA 
Sbjct: 219 GDANSSVILVRAYPQSGRTHQIRLHCQYLGLPIRGDVKYGGVIEWDGVE--CEGHALHAE 276

Query: 294 YMDLPHP-EGGRLQITAPLP 312
            +   HP  G  + + +PLP
Sbjct: 277 SLSFVHPITGLPITLRSPLP 296


>gi|318040646|ref|ZP_07972602.1| pseudouridine synthase [Synechococcus sp. CB0101]
          Length = 349

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 101/243 (41%), Gaps = 33/243 (13%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++ ++++D  + V NKP+G+ V    G   H +   L+ W        R  HRL + TSG
Sbjct: 94  EASVVFDDGDLLVLNKPSGLPVLPAGGFLEHTLLAQLQGWAPEA----RPVHRLGRFTSG 149

Query: 157 ILVVARTRAAAQHLTESFRMRRIQ---------------------KIYWSLVWGIPKN-- 193
           +LV AR   +   L+   R                          KIY +L   +P +  
Sbjct: 150 LLVCARRAESRAWLSAQLRESTAAAQPHGDQEYFGAEEHPHSGCLKIYRALTQPLPADWQ 209

Query: 194 --KKECIANWLLKKSH-IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             +   +   + ++ H + G+       + + A  + S F +++   +  C +E+   TG
Sbjct: 210 VGESRDVTTAIGRRPHPLLGEIWCAADVSPRAALPSRSCFTLLERRPES-CLVEVAIATG 268

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNF-TSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           R HQ+R+HA  +G P+ GD  Y A  + +    P      LHA    L  P    L + A
Sbjct: 269 RPHQIRIHAAAIGAPLEGDPLYRAGGRADPQVLPGDGGYLLHACRFVLRPPARAPLHLEA 328

Query: 310 PLP 312
           P P
Sbjct: 329 PPP 331


>gi|302417027|ref|XP_003006345.1| DRAP deaminase [Verticillium albo-atrum VaMs.102]
 gi|261355761|gb|EEY18189.1| DRAP deaminase [Verticillium albo-atrum VaMs.102]
          Length = 549

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 54/200 (27%), Positives = 82/200 (41%), Gaps = 30/200 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGIL 158
           +++ED+   + NKPAG+ V       Y+ +  ++     +G    PR  HRLD+ TSGIL
Sbjct: 216 VIHEDNDYLIVNKPAGVPVHPAG--RYNFNSVVEILKSERGAHFMPRPCHRLDRLTSGIL 273

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIG-------G 210
              +T  AA  L+   + R ++K Y + V G  P  +  C    L     +G       G
Sbjct: 274 CFGKTAQAATDLSRQIQARMVRKEYVARVIGHFPDGEVVCDQPLLQISPRLGLNRVRANG 333

Query: 211 DYVHVV------------------KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +   V                  +Q  K    A    +      + +  +   P TGRT
Sbjct: 334 KFARTVFKRLAYYPPPLSDVDGGPEQRPKTPEEAADEEQRPWTAKKGYSIVRCLPLTGRT 393

Query: 253 HQLRVHALHMGCPIVGDHKY 272
           HQ+RVH   +G PI  D  Y
Sbjct: 394 HQIRVHLQFLGYPIQNDPIY 413


>gi|260792462|ref|XP_002591234.1| hypothetical protein BRAFLDRAFT_106462 [Branchiostoma floridae]
 gi|229276437|gb|EEN47245.1| hypothetical protein BRAFLDRAFT_106462 [Branchiostoma floridae]
          Length = 244

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 48/160 (30%), Positives = 76/160 (47%), Gaps = 12/160 (7%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  HRLD  TSG + +A  + AA H  ++F  +++ K Y +LV G        I N  + 
Sbjct: 64  RFVHRLDYSTSGPICIALNKKAAGHAGKAFSQKQVIKQYLALVRGHISEDHLSI-NKAIG 122

Query: 205 KSHIGGDYVHVVKQNEKGANY---AISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVH 258
           +       V +  +   G  +   A++   V++      Q    + + P TGR HQLRVH
Sbjct: 123 EQGTPDAPVPMCVEGTPGCQHLRDAVTQLTVVEKGLYEGQPATKVNLCPMTGRRHQLRVH 182

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              +G PIVGD+ Y        T+P   ++ LHA+ + +P
Sbjct: 183 CQSIGHPIVGDYTYSCR---QDTTPY--RMMLHAQRLVIP 217


>gi|23308689|ref|NP_689473.1| RNA pseudouridylate synthase domain-containing protein 2 [Homo
           sapiens]
 gi|158563848|sp|Q8IZ73|RUSD2_HUMAN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 2
 gi|16550833|dbj|BAB71059.1| unnamed protein product [Homo sapiens]
 gi|119612834|gb|EAW92428.1| RNA pseudouridylate synthase domain containing 2 [Homo sapiens]
 gi|127796558|gb|AAH16967.2| RNA pseudouridylate synthase domain containing 2 [Homo sapiens]
          Length = 545

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 100/212 (47%), Gaps = 26/212 (12%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  LN ++K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++ 
Sbjct: 194 VQDLNIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNT 253

Query: 130 DGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V
Sbjct: 254 VIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRV 310

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW---- 242
            G  P  +  C    L+    +G     V + + +G        K  +   Q+  +    
Sbjct: 311 EGEFPTEEVTCKEPILVVSYKVG-----VCRVDPRG--------KPCETVFQRLSYNGQS 357

Query: 243 --LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +  +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 358 SVVRCRPLTGRTHQIRVHLQFLGHPILNDPIY 389


>gi|26553585|ref|NP_757519.1| pseudouridine synthase [Mycoplasma penetrans HF-2]
 gi|26453591|dbj|BAC43923.1| pseudouridine synthase [Mycoplasma penetrans HF-2]
          Length = 298

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 110/245 (44%), Gaps = 44/245 (17%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKS 135
           I+KE+KI++ +  LT     ++  ++YED  I + NKP  I V   S  ++  +   +K 
Sbjct: 52  ILKEEKIVEETKVLTPWKKDIE--IVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKY 109

Query: 136 WVDSK-----GQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             DSK     G   R+   HRLD+ T G+++VA++  +    T+ F  ++I+K Y +L+ 
Sbjct: 110 IFDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLH 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHV---VKQNEKGANYAISH----------FKVIDC 235
                            +H+    V V   +K+ E      +S           FK I+ 
Sbjct: 170 -----------------NHLQTRTVEVDAPIKRVETSTRREVSRDIDAKEARTIFKEINK 212

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           + + F   E++  TGRTHQ+RVHA  +   ++ D  Y        T   Q   YL A  +
Sbjct: 213 Y-KNFTLAEVELFTGRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYGQ---YLVAYKL 268

Query: 296 DLPHP 300
              HP
Sbjct: 269 KFIHP 273


>gi|255660399|ref|ZP_05405808.1| RluA family pseudouridine synthase [Mycoplasma genitalium G37]
          Length = 210

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 54/198 (27%), Positives = 93/198 (46%), Gaps = 24/198 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      +V  + EN R+D++     P I   +  K LR G+V ++K + + N R+++  
Sbjct: 1   MRIANKFLVPKESENQRIDQFCLKILPLIKRSDFFKYLRLGKVLLNKTKPQVNTRLKTKD 60

Query: 64  VVR----IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-- 117
            +     I P +   N  +        S++L K  D LK  +++ED  I V +KP GI  
Sbjct: 61  EIAFLFDINPYLQTNNDYL--------SLDLVK--DKLK--IIFEDENIIVVDKPTGIVC 108

Query: 118 ------SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
                 S+   S +     G+ +   +     P+  HR+D+ TSGI++ A+T  A + L 
Sbjct: 109 QPDKKHSIINLSNMLLKHCGYRQFDSNKLNFYPQFAHRIDRNTSGIVIGAKTNKALKELN 168

Query: 172 ESFRMRRIQKIYWSLVWG 189
           + F+   + K Y  LV+G
Sbjct: 169 KVFKNNHLTKRYKGLVFG 186


>gi|18855035|gb|AAL79727.1|AC091774_18 putative ribosomal large subunit pseudouridine synthase [Oryza
           sativa Japonica Group]
          Length = 275

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 52/190 (27%), Positives = 87/190 (45%), Gaps = 25/190 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V   E   R+D W                 R G   V + R++ +  I++G VV     
Sbjct: 64  AVPAGEGRSRIDAWIS--------------ARLGGGGVSRARIQAS--IRAGLVVVNGRP 107

Query: 71  INALNHIIKEQKILDSSV----NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           ++ ++H++K   I+  +V     L    + +   ++YED  + V NKPA + V    G A
Sbjct: 108 VSKVSHMVKGGDIVSCTVLELQPLRAEPEDIPLDIVYEDDHLLVVNKPAHMVVHPAPGNA 167

Query: 127 YH--IDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
               ++  L   K    +   +P + HRLD+ TSG+LVVA+   +   L E F++  I++
Sbjct: 168 NGTLVNAILHHCKISTFTSLVRPGIVHRLDKGTSGLLVVAKDEHSHAQLAEQFKLHTIRR 227

Query: 182 IYWSLVWGIP 191
           +Y SL  G P
Sbjct: 228 VYISLTCGAP 237


>gi|281423381|ref|ZP_06254294.1| RNA pseudouridine synthase family protein [Prevotella oris F0302]
 gi|281402717|gb|EFB33548.1| RNA pseudouridine synthase family protein [Prevotella oris F0302]
          Length = 522

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 90/226 (39%), Gaps = 25/226 (11%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D   N  + +D      +YED  I V  KPAG+    G  +  ++   ++     +   
Sbjct: 307 IDIEENPLERADQQALEWIYEDKDIVVVCKPAGMLSVPGKSLRENVRSLVRQ-RHPEATG 365

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+LVVA    +   L   F    +QK Y +L+       +    +  L
Sbjct: 366 PMIVHRLDMATSGLLVVALNLKSYIDLQRQFEEHSVQKRYVALLSRPHHGARSGQISLPL 425

Query: 204 KKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           +          V  V   +   NY  +    ++ +          P TGRTHQLR+H  H
Sbjct: 426 RPDLYDRPRQIVDAVHGRKAVTNYQQTGENRMNLY----------PLTGRTHQLRMHCAH 475

Query: 262 ---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              +  PI GD  Y              +LYLHA  +   HP  G+
Sbjct: 476 ADGLNNPIKGDELYGTR---------DERLYLHAEELSFVHPGTGK 512


>gi|294788439|ref|ZP_06753682.1| RNA pseudouridine synthase [Simonsiella muelleri ATCC 29453]
 gi|294483870|gb|EFG31554.1| RNA pseudouridine synthase [Simonsiella muelleri ATCC 29453]
          Length = 306

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 45/163 (27%), Positives = 85/163 (52%), Gaps = 13/163 (7%)

Query: 148 HRLDQETSGILVVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           HRLD++T+G+++++   +TRA  Q L   F+ + I+KIY +L       + +     L++
Sbjct: 147 HRLDKDTAGVILLSHNPKTRAIYQQL---FQEKNIRKIYHALA----PTRLDLAYPLLVR 199

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              + GD   + K  +   N + +  ++++    K    E++P TG+ HQLRVH + +G 
Sbjct: 200 SRLVRGDEFFLTKTVDGEPN-SETEIRLLENRG-KISLYELKPITGKKHQLRVHMMSLGM 257

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           P++ D  Y    +   T   +  L L A+ ++L  P  G L++
Sbjct: 258 PLLNDMLYPI-VQPVGTEDFEKPLKLLAKRIELIDPVSGSLKV 299


>gi|270015056|gb|EFA11504.1| hypothetical protein TcasGA2_TC014218 [Tribolium castaneum]
          Length = 289

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 57/191 (29%), Positives = 89/191 (46%), Gaps = 40/191 (20%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG------------------ 189
           HRLD  TSG++ V   + A Q  +++ + R+ +K Y +LV G                  
Sbjct: 101 HRLDYSTSGLMCVPVHKKACQVASQAIQQRKCKKYYIALVRGYLSSNLLDLNFPIGRDNS 160

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I   +K C+ +    +S      + VV +N    NY  S  KV+           ++P T
Sbjct: 161 ITDIEKMCVTHDSNSRS---ARTLIVVLENGLFENYPSS--KVL-----------IRPIT 204

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
           GR HQ+RVH  H+G  IVGD+ Y +N K   T+P   ++YLH+  + +P+  E   +Q +
Sbjct: 205 GRRHQIRVHCAHIGHTIVGDYTY-SNKKD--TTP--ERMYLHSLRLVIPNKIEDINVQTS 259

Query: 309 APLPAHMVKTW 319
            P      K W
Sbjct: 260 DPFSEKGAKCW 270


>gi|242083792|ref|XP_002442321.1| hypothetical protein SORBIDRAFT_08g018120 [Sorghum bicolor]
 gi|241943014|gb|EES16159.1| hypothetical protein SORBIDRAFT_08g018120 [Sorghum bicolor]
          Length = 315

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 73/270 (27%), Positives = 112/270 (41%), Gaps = 70/270 (25%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-------------KGQKPRL- 146
           +++ED  + V +KPAG+          + D FL S   S                KP L 
Sbjct: 49  VVFEDEWLAVVDKPAGV----------YCDAFLTSLPSSVVSGKYFLRLAEDPATKPNLH 98

Query: 147 -THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP---KNKKECIANWL 202
             +RLD++TSG++V+ +    A  L ++F   +++K Y +L  G P   +  K C  +  
Sbjct: 99  LANRLDRDTSGLMVITKCNKVAGKLVKAFTDHKVKKTYLALCIGCPPTWEKIKICSGHGR 158

Query: 203 LK-------------KSHIGGDYV-------HVVKQNEKGA-----NY---AISHFKVID 234
            K             +S  GG  V        V+  N K       N+    I    V +
Sbjct: 159 SKHGAWRVYAMSDVGRSLPGGSVVRDMSTQFEVLGVNGKCQFREPYNFDTDDIESITVQE 218

Query: 235 CFAQKFCWLEMQ---------PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
             A + C  ++          P +GRTHQ+R+H  ++G PI GD KY    + N      
Sbjct: 219 KAADQTCSGDVNNSAILVRAYPQSGRTHQIRLHCQYLGFPIRGDVKYGGVIEWNGVE--C 276

Query: 286 NKLYLHARYMDLPHPEGGRLQIT--APLPA 313
           +   LHA  +   HP  G L IT  +PLP+
Sbjct: 277 DGHALHAESLSFVHPITG-LPITFRSPLPS 305


>gi|169614099|ref|XP_001800466.1| hypothetical protein SNOG_10184 [Phaeosphaeria nodorum SN15]
 gi|160707276|gb|EAT82519.2| hypothetical protein SNOG_10184 [Phaeosphaeria nodorum SN15]
          Length = 474

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 66/256 (25%), Positives = 108/256 (42%), Gaps = 41/256 (16%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYED 105
           D+    +   I  G+VV     + +    IK   I+  S  L +H     +    +++ED
Sbjct: 79  DRPAEYYEKAIVEGRVVVNGQPVPSTKTTIKNGDII--SHTLHRHEPPCTATPIGIVHED 136

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVART 163
             + V NKPAG+ V       Y+ +  ++     +G    P   +RLD+ TSGI+ + + 
Sbjct: 137 DNLIVINKPAGMPVHPAG--RYNFNSIIEILRADRGYGWNPLPCNRLDRLTSGIMFIGKH 194

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           R AA+ ++   R R ++K Y + V G  P+ +  C    L     +G   ++ V+ N K 
Sbjct: 195 RQAAEDMSAQIRTRTVKKEYITRVAGEFPEGEVVCEKPILQISPKLG---LNRVRANGK- 250

Query: 223 ANYAISHFKVIDCFAQK-------------------------FCWLEMQPHTGRTHQLRV 257
              A++ FK +  +  K                         +  +   P TGRTHQLRV
Sbjct: 251 --EALTVFKRLAYYPPKDDGKPGEEQDVEEGPDGQPWKKLRGYSIVRCFPVTGRTHQLRV 308

Query: 258 HALHMGCPIVGDHKYC 273
           H   +G PI  D  Y 
Sbjct: 309 HLQFLGHPISNDPIYA 324


>gi|307721677|ref|YP_003892817.1| pseudouridine synthase [Sulfurimonas autotrophica DSM 16294]
 gi|306979770|gb|ADN09805.1| pseudouridine synthase [Sulfurimonas autotrophica DSM 16294]
          Length = 244

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 52/171 (30%), Positives = 80/171 (46%), Gaps = 21/171 (12%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++E+  I V +KPA ++       +  I+   K  V        L HRLD+ETSG+L++ 
Sbjct: 61  IFENDDIIVVDKPAHVN-------SDEIERQFKPAV--------LLHRLDRETSGVLMLV 105

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +     Q   + FR  ++ K Y + V GI     E       +K +    Y +V   + K
Sbjct: 106 KNEDFRQRAIKEFRDDKVYKEYIAWVEGIMTEPIEVDKAITTQKKN-NKAYSNV---SPK 161

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           G       F   D  + K   ++   H GRTHQ+RVHA ++  PIVGD +Y
Sbjct: 162 GKPARTEFFP--DIVSAKKTKVKCIIHNGRTHQIRVHARYIDHPIVGDEQY 210


>gi|148239908|ref|YP_001225295.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           WH 7803]
 gi|147848447|emb|CAK23998.1| Ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           WH 7803]
          Length = 197

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 62/223 (27%), Positives = 94/223 (42%), Gaps = 47/223 (21%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + V +KPAG+  Q G G+  H    L S +       RL HRLD++TSG++++A+     
Sbjct: 1   MLVVDKPAGLLCQPGLGV--HQRDSLISRLQHACPDLRLVHRLDRDTSGLVLLAKDADTQ 58

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYA 226
           + L   F  RR+ K+Y + V G                  + G   + + + N +   Y 
Sbjct: 59  RVLGALFAARRVGKLYLADVQG--------------SMGAVSGRIDLPLARLNRQPPTYG 104

Query: 227 ISHFKVIDCFAQKFCWLEMQ-----------PHTGRTHQLRVHALHMGCPIVGDHKY--- 272
           + H     C      W  +Q           P TGR+HQLR H   +  PI+GD  Y   
Sbjct: 105 V-HPDGKACLT---LWRRLQRMETRTRLWLCPRTGRSHQLRAHLAALHHPIIGDPIYNPG 160

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPE--GGRLQITAPLPA 313
           CA             L L A  +  P P+  G ++++ AP PA
Sbjct: 161 CA----------AGGLRLRAIALRFPDPDQPGSQVRVRAPWPA 193


>gi|78184312|ref|YP_376747.1| putative pseudouridylate synthase [Synechococcus sp. CC9902]
 gi|78168606|gb|ABB25703.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           CC9902]
          Length = 214

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 60/213 (28%), Positives = 97/213 (45%), Gaps = 11/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  +   +KP+G+  Q G G         +     +G   RL HRLD++TSG+L++
Sbjct: 8   ILHQDRWLLAVDKPSGLLSQPGLGPEQADSLISRVQAHDEGPDWRLVHRLDRDTSGVLLL 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    A +  +  F  R + K+Y + V G+   +   I N L +       Y    +  E
Sbjct: 68  AAGLEALRRTSALFSSRSVNKLYLAHVCGVMAGRGS-INNRLARLQRQPPRYGSHPEGRE 126

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A + ++V    A     L ++P TGR+HQLR H   +  PI+GD  Y        
Sbjct: 127 -----ACTLWRVRSS-AAGVTQLWLRPITGRSHQLRSHLAEIAHPILGDPIYGDQSVDRL 180

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                 +L+LHA  +   HP  G RL++ +  P
Sbjct: 181 R---LQRLHLHAIALSFSHPFTGQRLRLVSADP 210


>gi|332235181|ref|XP_003266785.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 2
           [Nomascus leucogenys]
          Length = 545

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 100/212 (47%), Gaps = 26/212 (12%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  LN ++K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++ 
Sbjct: 194 VQDLNVVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNT 253

Query: 130 DGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V
Sbjct: 254 VIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRV 310

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW---- 242
            G  P  +  C    L+    +G     V + + +G        K  +   Q+  +    
Sbjct: 311 EGEFPTEEVTCKEPILVVSYKVG-----VCRVDPRG--------KPCETVFQRLSYNGQS 357

Query: 243 --LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +  +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 358 SVVRCRPLTGRTHQIRVHLQFLGHPILNDPIY 389


>gi|308063206|gb|ADO05093.1| hypothetical protein HPSAT_01720 [Helicobacter pylori Sat464]
          Length = 293

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 106/238 (44%), Gaps = 32/238 (13%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS- 99
           L+  Q  +DK+R+K     Q+ Q VR             + +++   V+L       K+ 
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVR-------------KSQMIQGVVSLIHFKPNEKTQ 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  ALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D     K +
Sbjct: 128 AGKTLQSAKDLKVLFMQKKVKKTYLALAHGL-VDKNIVIDKPILTPQNIQKDLRIRSKIS 186

Query: 220 EKGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             G         +S+   +D        L++ P TGRTHQ+R+H   +G  IVG+  Y
Sbjct: 187 PLGKPSTTLVEPLSYNPFLDI-----SLLKITPLTGRTHQIRLHLSSVGHRIVGEGLY 239


>gi|327404189|ref|YP_004345027.1| pseudouridine synthase [Fluviicola taffensis DSM 16823]
 gi|327319697|gb|AEA44189.1| pseudouridine synthase [Fluviicola taffensis DSM 16823]
          Length = 227

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 97/226 (42%), Gaps = 29/226 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           L+YED    V +KP+ + V          +  L   +  +G  +    HRLD++TSG+++
Sbjct: 8   LIYEDEYCLVVSKPSNLIVHHSYYARNIEETSLTDLIREQGCLEACPVHRLDRKTSGLIL 67

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+         + F    I+K Y +L+ G  + +               G     VK +
Sbjct: 68  FAKKAEWVADFQKLFENGEIEKKYLALLRGHLEAE---------------GSIDSPVKND 112

Query: 220 EKGANYAISHFKVIDCFA----------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A++ +  ++ F           Q++  +E+ P TGR HQLR+HA  +  PI+ D
Sbjct: 113 RGNYKDALTKYTCLEHFERAYVIPPYEKQRYSLVELTPITGRMHQLRIHANKIAHPIIND 172

Query: 270 HKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
            KY      ++   +   ++L+LHA+ +    P  G L  +  P P
Sbjct: 173 PKYGNRHHNHYFQEVLGIHELFLHAQSLKFKQPFTGELVWLQEPFP 218


>gi|194376328|dbj|BAG62923.1| unnamed protein product [Homo sapiens]
          Length = 538

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 100/212 (47%), Gaps = 26/212 (12%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  LN ++K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++ 
Sbjct: 187 VQDLNIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNT 246

Query: 130 DGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V
Sbjct: 247 VIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRV 303

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW---- 242
            G  P  +  C    L+    +G     V + + +G        K  +   Q+  +    
Sbjct: 304 EGEFPTEEVTCKEPILVVSYKVG-----VCRVDPRG--------KPCETVFQRLSYNGQS 350

Query: 243 --LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +  +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 351 SVVRCRPLTGRTHQIRVHLQFLGHPILNDPIY 382


>gi|28378819|ref|NP_785711.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|300768863|ref|ZP_07078757.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308181018|ref|YP_003925146.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28271656|emb|CAD64562.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|300493596|gb|EFK28770.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308046509|gb|ADN99052.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 300

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 103/222 (46%), Gaps = 20/222 (9%)

Query: 101 LLYEDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LYED    + NKPAG++         + +A  + G+ ++      +   +T RLD++TS
Sbjct: 80  ILYEDRDYLIVNKPAGVASVPAHALPDNTLANRVKGYYQA-AHYDNEVVHITTRLDRDTS 138

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ A+   A   +    +   ++K+Y ++V G    +      WL   + IG      
Sbjct: 139 GIVLFAKHHFAHSIIDHQLKAHAMRKMYLAVVSG----ELTTDHGWL--DAPIGRAADSF 192

Query: 216 VKQNEK-GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +K+  +     +++ + V+    +    + ++ HTGRTHQ+RVH    G P++GD  Y  
Sbjct: 193 IKRTTRPDGKPSLTEYWVVKRL-RNMTVVRVRLHTGRTHQIRVHFAASGHPLIGDALY-- 249

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHM 315
              G    P   +  LH   ++   P   +   T APLPA +
Sbjct: 250 ---GGPRDPWIQRQALHCMQLEFDDPFISQTLTTFAPLPADL 288


>gi|39995777|ref|NP_951728.1| ribosomal large subunit pseudouridine synthase C [Geobacter
           sulfurreducens PCA]
 gi|39982541|gb|AAR34001.1| ribosomal large subunit pseudouridine synthase C [Geobacter
           sulfurreducens PCA]
 gi|298504786|gb|ADI83509.1| RNA pseudouridine synthase, RluA family [Geobacter sulfurreducens
           KN400]
          Length = 296

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 69/301 (22%), Positives = 128/301 (42%), Gaps = 47/301 (15%)

Query: 22  DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           + + +N  P      ++K++ +G ++++   V  +  + +G    I         +   +
Sbjct: 16  ESFLRNLLPAAPSAYIRKLISAGHLKINGGAVAPDTLLAAGNTATIKESDRTRQLLAAAK 75

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWVDS 139
             LD               +L+ED    + NKPAG+ V     +G A  ++   + ++  
Sbjct: 76  PQLD---------------ILWEDDYCVIVNKPAGLPVHRTAEAGEANLVE-LAEHFMAG 119

Query: 140 KGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +G   K R  +RLD+ TSG  ++A++ ++A  L    +   + K+Y ++  G   +    
Sbjct: 120 RGTAVKLRPVNRLDRGTSGATILAKSSSSAGMLGRYVKEEGLDKLYLAVTDGSLPDAGTI 179

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                 K +H   D+  + +      + A+S   VI             P +GR HQ+R 
Sbjct: 180 DTPLDGKDAHT--DFRTLAR------DTAVSFALVI-------------PISGRMHQIRK 218

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +G P+ GD +Y    +G   +     L LHA  + L HP  GR L + APLP   +
Sbjct: 219 HLSAIGHPVRGDRRY----RGTLLTGYPGHL-LHAFRVALIHPVTGRKLIVHAPLPPAFI 273

Query: 317 K 317
           +
Sbjct: 274 Q 274


>gi|300859437|ref|YP_003784420.1| hypothetical protein cpfrc_02020 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|300686891|gb|ADK29813.1| hypothetical protein cpfrc_02020 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|302207115|gb|ADL11457.1| Ribosomal pseudouridine synthase [Corynebacterium
           pseudotuberculosis C231]
          Length = 327

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 54/188 (28%), Positives = 77/188 (40%), Gaps = 26/188 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +YED  + V NKP  ++    G  I       ++    +    P   HRLD+ TSGILV 
Sbjct: 111 IYEDDNLLVVNKPPFLATMPRGKHITQTATVQMRRATGNGDLSP--AHRLDRLTSGILVF 168

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI---GGDYVHVVK 217
            + R         F  R++ K Y +    I    ++   N L +   I   G    H+V 
Sbjct: 169 TKNRKVRGAYQSLFAERKVTKTYHA----IAPFSEDLTGNTLWRDHMIKTPGDMQGHIVP 224

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLE-------------MQPHTGRTHQLRVHALHMGC 264
                    +    V +  AQ+   L+             +QPHTGRTHQLR+H    G 
Sbjct: 225 GPPNAETLLVD---VTELDAQETAQLQKLHHVTTPLARYTLQPHTGRTHQLRLHMWAAGV 281

Query: 265 PIVGDHKY 272
           PI+GD  Y
Sbjct: 282 PILGDPAY 289


>gi|291443564|ref|ZP_06582954.1| ribosomal pseudouridine synthase [Streptomyces roseosporus NRRL
           15998]
 gi|291346511|gb|EFE73415.1| ribosomal pseudouridine synthase [Streptomyces roseosporus NRRL
           15998]
          Length = 312

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 63/211 (29%), Positives = 99/211 (46%), Gaps = 23/211 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG-IL 158
           ++Y D +I V +KP  ++    G  I       L+  +D    +P   HRLD+ T+G +L
Sbjct: 100 VVYRDERIVVADKPHFLATMPRGRHITETAVARLRRELDLPVLQP--AHRLDRLTAGLVL 157

Query: 159 VVART--RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            V R+  R A Q L   FR RR++K Y ++    P +    +   +  +S I  +   + 
Sbjct: 158 FVVRSQDRGAYQTL---FRDRRVRKEYEAVA---PYDPGVALPRTV--RSRIVKERGVLA 209

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---- 272
            + E G   + SH ++++          + P TGRTHQLRVH   +G PIV D  Y    
Sbjct: 210 AREEPGEANSESHVELVERRG-ALGRYRLVPATGRTHQLRVHMNALGLPIVHDPLYPVVA 268

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 +F+ P+Q    L AR ++   P GG
Sbjct: 269 AEASADDFSRPLQ----LLARVLEFTDPVGG 295


>gi|332843544|ref|XP_510311.3| PREDICTED: RNA pseudouridylate synthase domain-containing protein 2
           isoform 2 [Pan troglodytes]
          Length = 545

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 100/212 (47%), Gaps = 26/212 (12%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  LN ++K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++ 
Sbjct: 194 VQDLNIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNT 253

Query: 130 DGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V
Sbjct: 254 VIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRV 310

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW---- 242
            G  P  +  C    L+    +G     V + + +G        K  +   Q+  +    
Sbjct: 311 EGEFPTEEVTCKEPILVVSYKVG-----VCRVDPRG--------KPCETVFQRLSYNGQS 357

Query: 243 --LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +  +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 358 SVVRCRPLTGRTHQIRVHLQFLGHPILNDPIY 389


>gi|302795552|ref|XP_002979539.1| hypothetical protein SELMODRAFT_36043 [Selaginella moellendorffii]
 gi|300152787|gb|EFJ19428.1| hypothetical protein SELMODRAFT_36043 [Selaginella moellendorffii]
          Length = 229

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 50/209 (23%), Positives = 88/209 (42%), Gaps = 32/209 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-- 68
            +  +  + R+D W     PH +   +Q  +R G   V+            G+ +  P  
Sbjct: 12  TIPEETVSTRIDVWLSGQLPHTSRARVQDSIRKGLALVN------------GKTITKPSF 59

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
           PVI     +      L  +  L    + ++  +++ED  + V NK A + V    G    
Sbjct: 60  PVIGGDEVVC----TLCGAAPLEATPEKIQLDIVHEDDHVIVVNKAADMVVHPAPGHYGG 115

Query: 125 -----IAYHIDGFLKSWVDSKGQKP----RLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                I +H  G   +    +G +P     + HRLD+ TSG++VVA+   +   L+E F+
Sbjct: 116 TLVNAILHHC-GLPATPSRFRGPRPVIRPGIVHRLDKGTSGLIVVAKDEQSQLSLSEQFK 174

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            R++++ Y SL  G P      I   +L+
Sbjct: 175 SRKVRRTYLSLTCGTPSTTSGRIEAEILR 203


>gi|50285951|ref|XP_445404.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49524708|emb|CAG58310.1| unnamed protein product [Candida glabrata]
          Length = 584

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 85/178 (47%), Gaps = 15/178 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTH---RLDQETSG 156
           +++E+  I V +KP GI V       Y+ I   L+       Q  R  H   RLD+ TSG
Sbjct: 165 IVFENDDILVIDKPGGIPVHPTGRYRYNTITKILEK------QMKRSVHPCNRLDRLTSG 218

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++ +A+T   A  + +  + R + K Y + V G     +  +   L  KS+     ++++
Sbjct: 219 LMFLAKTPEGADQMADQMKTREVTKEYIARVVGEFPTGEITVEKPL--KSYDPKVSLNII 276

Query: 217 --KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               NE  A  A + F+ I  F  +   ++ +P TGRTHQ+RVH   +G PI  D  Y
Sbjct: 277 CDDTNEDDAKPAKTVFQRI-SFDGQTSIVKCKPLTGRTHQIRVHLQFLGHPIANDPIY 333


>gi|257470632|ref|ZP_05634722.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
 gi|317064838|ref|ZP_07929323.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
 gi|313690514|gb|EFS27349.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
          Length = 296

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 49/146 (33%), Positives = 69/146 (47%), Gaps = 9/146 (6%)

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           FLK+    K   PR  +RLD  TSG+++VA+   A   L E      + K Y ++V G  
Sbjct: 112 FLKTT--GKIMVPRFYNRLDMNTSGLIIVAKNSFAQSFLQEK---GIVNKFYKAIVKGTV 166

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           + K E + +  + K  IG D        E G   A +  KVI  F +    +E +  TGR
Sbjct: 167 E-KDEFLIDRPIGK--IGDDLRRREISVEDGGQEAQTKIKVIKRF-KDLTLIEAELLTGR 222

Query: 252 THQLRVHALHMGCPIVGDHKYCANFK 277
           THQ+R H    G P++GD  Y    K
Sbjct: 223 THQIRAHMALEGYPLLGDELYGGEDK 248


>gi|145612127|ref|XP_362534.2| hypothetical protein MGG_08117 [Magnaporthe oryzae 70-15]
 gi|145019360|gb|EDK03588.1| hypothetical protein MGG_08117 [Magnaporthe oryzae 70-15]
          Length = 487

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 53/195 (27%), Positives = 88/195 (45%), Gaps = 19/195 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED ++ V NKP+G+ V       ++    +     S+  K    +RLD+ TSGI+ +
Sbjct: 154 VLHEDDEMIVINKPSGMPVHPAGRYNFNSVVEVMRSERSRDFKAYPCNRLDRLTSGIMFI 213

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+T  AA  + E    R ++K Y + V G  P  +  C    L     +G + V    ++
Sbjct: 214 AKTPQAACKMGEQIMGRTVRKEYLARVIGRFPDGEVICNEPILQISPKLGLNRVRANGRH 273

Query: 220 EKGANYAISHFKVIDCFA-----------------QKFCWLEMQPHTGRTHQLRVHALHM 262
            +     ++++   +                    Q +  +   P TGRTHQ+RVH  H+
Sbjct: 274 ARTVFKRLAYYPPAEGQGNEAKPGEAANGRPWRNKQGYSIVRCLPVTGRTHQIRVHLQHL 333

Query: 263 GCPIVGDHKYCANFK 277
           G PI  D  Y AN+K
Sbjct: 334 GHPIENDPIY-ANYK 347


>gi|126139263|ref|XP_001386154.1| DRAP deaminase [Scheffersomyces stipitis CBS 6054]
 gi|126093436|gb|ABN68125.1| DRAP deaminase [Scheffersomyces stipitis CBS 6054]
          Length = 585

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 63/252 (25%), Positives = 106/252 (42%), Gaps = 49/252 (19%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVV------RIPPVINALNHIIKEQKILDSSVNLT 91
           +K + +GQV ++KK    ++ +++G ++      + PPV +      +E KI+       
Sbjct: 124 KKAIDAGQVTLNKKPANLDSIVRNGDLISHRTYRKEPPVSS------REIKIV------- 170

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                      YED  +   +KP+GI V       Y  +   K +    G+     +RLD
Sbjct: 171 -----------YEDDDLIAIDKPSGIPVHPTG--RYRYNTITKIFQHEMGKVVHPCNRLD 217

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGG 210
           + TSG++ + +T   A  L +  R R ++K Y + V G  P  + E           +G 
Sbjct: 218 RLTSGLMFLGKTAKGADKLVKQIRERSVRKEYIARVKGEFPLEEVEVDQPMRTIAHKLGL 277

Query: 211 DYVHV-----VKQNEKGANYAISH-FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           + + +      K   K  +Y   H   ++ C           P TGRTHQ+RVH  ++G 
Sbjct: 278 NRIDLKEGKDAKTAFKRVSYDPEHDTSIVKCI----------PLTGRTHQIRVHLQYLGH 327

Query: 265 PIVGDHKYCANF 276
           PI  D  Y   F
Sbjct: 328 PIANDPIYSNKF 339


>gi|189233766|ref|XP_001814310.1| PREDICTED: similar to AGAP004401-PA [Tribolium castaneum]
          Length = 274

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 57/191 (29%), Positives = 89/191 (46%), Gaps = 40/191 (20%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG------------------ 189
           HRLD  TSG++ V   + A Q  +++ + R+ +K Y +LV G                  
Sbjct: 86  HRLDYSTSGLMCVPVHKKACQVASQAIQQRKCKKYYIALVRGYLSSNLLDLNFPIGRDNS 145

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I   +K C+ +    +S      + VV +N    NY  S  KV+           ++P T
Sbjct: 146 ITDIEKMCVTHDSNSRS---ARTLIVVLENGLFENYPSS--KVL-----------IRPIT 189

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
           GR HQ+RVH  H+G  IVGD+ Y +N K   T+P   ++YLH+  + +P+  E   +Q +
Sbjct: 190 GRRHQIRVHCAHIGHTIVGDYTY-SNKKD--TTP--ERMYLHSLRLVIPNKIEDINVQTS 244

Query: 309 APLPAHMVKTW 319
            P      K W
Sbjct: 245 DPFSEKGAKCW 255


>gi|58336973|ref|YP_193558.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus NCFM]
 gi|227903532|ref|ZP_04021337.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus ATCC 4796]
 gi|58254290|gb|AAV42527.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus NCFM]
 gi|227868419|gb|EEJ75840.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus ATCC 4796]
          Length = 300

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 110/229 (48%), Gaps = 23/229 (10%)

Query: 105 DSKIYVF-NKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++K Y+  NKPA +       +    I   + G+     + K  KP +  RLD++TSG++
Sbjct: 85  ETKNYILVNKPANVLSIPSRYEDDDAIVNRLMGYFMEKKE-KDLKPHVITRLDRDTSGLV 143

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V +   A    ++  + + I+K Y ++V G   ++K E + +  + K  I       V 
Sbjct: 144 LVGKNSIAHARFSKIGKEKFIKK-YHAIVHGNFAEDKLEGLIDQPIGK--IDAGVKRGVV 200

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            N K A    + ++V+D  +     +E++  TGRTHQ+RVH +++G P+ GD  Y  +  
Sbjct: 201 LNGKSAQ---TEYRVLDQVSGA-SLVELRLLTGRTHQIRVHMMYLGHPLYGDPLYGID-- 254

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITA-PLPAHMVKTWDSLGFK 325
            NF+     +  L+  Y+  P P   + +I     P  M K W  L +K
Sbjct: 255 DNFS-----RQALNCFYLSFPDPFDNKDKIIKIDDPLDMRKLWQKLKYK 298


>gi|256831008|ref|YP_003159736.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256580184|gb|ACU91320.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 232

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 47/150 (31%), Positives = 72/150 (48%), Gaps = 20/150 (13%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ TSG+L++AR+R  A  L   FR R +QK Y +L    P  K+  +   +++  
Sbjct: 51  VHRLDKATSGLLLLARSREWAAALAGLFRERAVQKYYIALSDLTPGKKQGLVQGDMVRSR 110

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              G +  + +  E+ A      + V            ++P +GRTHQLRV    +G PI
Sbjct: 111 R--GSW-KLARSMERPARTRFLSWSV----RPGMRLFVLKPMSGRTHQLRVAMKSLGAPI 163

Query: 267 VGDHKYCANFKGNFTSPI----QNKLYLHA 292
           +GD  Y          PI     +++YLHA
Sbjct: 164 LGDSLY---------HPIVPDWPDRMYLHA 184


>gi|156055472|ref|XP_001593660.1| hypothetical protein SS1G_05088 [Sclerotinia sclerotiorum 1980]
 gi|154702872|gb|EDO02611.1| hypothetical protein SS1G_05088 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 399

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 97/226 (42%), Gaps = 25/226 (11%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAY 127
           + + + IIK   ++  S  L +H   + ++   +++ED  I V NKP+G+ V       Y
Sbjct: 41  VESTSQIIKNGDVI--SHTLHRHEPPVTALPISIVHEDEDIIVINKPSGVPVHPAGRYNY 98

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +    +       G  P   +RLD+ TSGI+ + +   AA+ L+     R ++K Y + V
Sbjct: 99  NSVVEIMRAERGHGWNPLPCNRLDRLTSGIMFIGKHAKAAEALSLQISGRTVRKEYIARV 158

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-----ANYAISHFKVIDCFAQK-- 239
            G  P  +  C    L     +G + V    +  +      A Y   + + ++  ++   
Sbjct: 159 KGKFPDGEVVCDMPILQISPKLGLNRVRASGKAARTVFKRLAYYPPENLEQVEDSSEPME 218

Query: 240 ------------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                       +  +   P TGRTHQLRVH   +G PI  D  YC
Sbjct: 219 PDKSKPSMNKEGYSIVRCLPVTGRTHQLRVHLQFLGHPIGNDPIYC 264


>gi|300175850|emb|CBK21846.2| Pseudouridylate synthase [Blastocystis hominis]
          Length = 273

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 62/247 (25%), Positives = 113/247 (45%), Gaps = 34/247 (13%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK--EQKILDSSVNLTKHSD 95
           ++ +R+G++RV+ +RV  ++ +++G         + + H +   E  +  S V       
Sbjct: 41  EEAIRNGRIRVNGERVTRDHILKNG---------DRITHTVHRHEPPVPYSPV------- 84

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQET 154
               ++L E   I   NKPA + V       Y+ ++  L+   ++K  +    HRLD+ T
Sbjct: 85  ----VILGETDDIIAVNKPAALPVHPCGAYRYNSLETILRK--ENKLSEFYFIHRLDRVT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-V 213
           SG++++A+ +  A  L+E        K+Y +   G    K E    +  +++ I  D  +
Sbjct: 139 SGVMLLAKRKDIASKLSEQLVKGGFHKVYLAEAEGNCFEKPEIPGVFYTQQNGIAVDRNI 198

Query: 214 HVVKQ-------NEKGANYAISH-FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            VV Q       +EK    A ++ F +          +E  P TGRTHQ+R+H  ++G P
Sbjct: 199 AVVSQKEGIFKVDEKEGKPAYTYLFPLYYSKQSNTTLMECVPITGRTHQIRLHLKYIGHP 258

Query: 266 IVGDHKY 272
           I  D  Y
Sbjct: 259 IDDDVNY 265


>gi|326472889|gb|EGD96898.1| DRAP deaminase [Trichophyton tonsurans CBS 112818]
          Length = 528

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 69/272 (25%), Positives = 113/272 (41%), Gaps = 56/272 (20%)

Query: 34  FVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
            + LQK  +  G++ +D K    ++ I +GQV+                     S  L +
Sbjct: 86  LIILQKAAIDGGRITIDGKVATADSIINNGQVI---------------------SHTLHR 124

Query: 93  HSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLT 147
           H   + S    +++ED  I V +KPAGI V       Y+ +  ++     +G    P   
Sbjct: 125 HEPPVTSRPIKIIHEDEDIIVIDKPAGIPVHPAG--RYNYNSIIEIMRSERGLGWIPYPC 182

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +RLD+ TSGI+ + +   +A+ + +S R R ++K Y + V G   +        +LK S 
Sbjct: 183 NRLDRLTSGIMFLGKHPKSAEQMAQSLRSRTLRKEYIARVKGYFPDGVVLCDQPMLKVSP 242

Query: 208 I---------GGD----------YVHVVKQNEKGA--------NYAISHFKVIDCFAQKF 240
           I         G D          Y  V K+N+ G         + A +   +     + +
Sbjct: 243 ILGLNRVRATGKDAQTKFRRIAYYPPVEKENKNGETTGSQGPDSRASTPPPLPADVDEGY 302

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +   P TGRTHQ+RVH   +G PI  D  Y
Sbjct: 303 SIVHCLPLTGRTHQIRVHLQFLGHPITNDPIY 334


>gi|326692754|ref|ZP_08229759.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc argentinum
           KCTC 3773]
          Length = 300

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 50/189 (26%), Positives = 93/189 (49%), Gaps = 15/189 (7%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-----IDGFLKSWVDSKGQKPRLTHR 149
           D+    +++E+    V +KP G++   G     H     + G L+   +++   P +  R
Sbjct: 74  DYKPLNIIFENEHWLVVDKPYGVTTVPGHADRLHTLVNQVKGHLEE-TNAEDLVPHVVTR 132

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHI 208
           LD++TSGI+++A+ R A   L +  +   ++K Y +   GI P++  +  A        +
Sbjct: 133 LDRDTSGIVLLAKHRFAHAVLDQQLQEHTVEKFYLAYTSGILPEDHGDINA----PIGRV 188

Query: 209 GGDYV-HVVKQNEKGA--NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            GD++   V+ + K +   Y +   +  +        + +Q HTGRTHQ+RVH  ++G P
Sbjct: 189 EGDFIKREVRDDGKPSRTEYWVER-RYDEDGDNPMTRVRVQLHTGRTHQIRVHFQNIGHP 247

Query: 266 IVGDHKYCA 274
           +VGD  Y  
Sbjct: 248 LVGDDLYGG 256


>gi|260779060|ref|ZP_05887952.1| pseudouridylate synthase LSU rRNA-specific [Vibrio coralliilyticus
           ATCC BAA-450]
 gi|260605224|gb|EEX31519.1| pseudouridylate synthase LSU rRNA-specific [Vibrio coralliilyticus
           ATCC BAA-450]
          Length = 231

 Score = 63.2 bits (152), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 53/161 (32%), Positives = 77/161 (47%), Gaps = 32/161 (19%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN----- 200
           L HRLD+ TSG+L++AR  AAA  L+  F  RR++K Y ++    PK K+  ++      
Sbjct: 46  LVHRLDKMTSGLLLLARNAAAASELSTQFAQRRVEKFYLAIGSKKPKKKQGLVSGDMERS 105

Query: 201 ----WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
               W L  SH               +N AI+ F        +  +L  +PHTG+THQ+R
Sbjct: 106 RRSAWKLTSSH---------------SNPAITQFLSTSAEPGERLFL-CKPHTGKTHQIR 149

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           V    +G PIVGD  Y    K        ++ YLHA  ++ 
Sbjct: 150 VALKSVGSPIVGDAIYTPASKS-------DRGYLHAFALEF 183


>gi|227889588|ref|ZP_04007393.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
 gi|227849890|gb|EEJ59976.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
          Length = 299

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 86/180 (47%), Gaps = 12/180 (6%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           KP +  RLD++TSG+++V R   A    ++  +   I+K Y ++V G   N +E      
Sbjct: 127 KPHVITRLDRDTSGLVLVGRNAVAHARFSKMEKNEFIKK-YHAIVHG---NFEEAQRQGT 182

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           +  + IG     V +        +++ ++V+D   +    +E+Q  TGRTHQ+RVH  ++
Sbjct: 183 ID-APIGKIDTGVKRGIVNNGQRSVTKYRVLDQ-VKGASLIELQLLTGRTHQIRVHMQYL 240

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G P+ GD  Y    K NF     N  YL     D P  E  R +I    P  M + W +L
Sbjct: 241 GHPLFGDPLY--GIKDNFKRQALNCFYLE---FDDPFSE-KRQKIEIADPIDMKRLWKNL 294


>gi|311269242|ref|XP_003132405.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 3
           isoform 2 [Sus scrofa]
          Length = 337

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 58/217 (26%), Positives = 89/217 (41%), Gaps = 44/217 (20%)

Query: 152 QETSGILVVARTRAAAQHL----TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +ETSG+++++     A  L    T S R R+    Y ++  GIP   +  I   L  +  
Sbjct: 122 KETSGLVLLSSCPQTASRLQKFFTHSQRARKPTATYCAVTDGIPAASEGKIQAALKMEHT 181

Query: 208 IGGDYVHVVKQNE-----KGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALH 261
            G   V  VK        KG  + +SHF+V+   +   C L ++QP T    QL+VH + 
Sbjct: 182 DGASLVVPVKSPSRKDFLKGVKWTLSHFRVLA--SGSGCALVQLQPLTAFPSQLQVHMVL 239

Query: 262 MGCPIVGDHKYCAN----FKGNFTSPIQNK--------LYLHARYMDLP----------- 298
             CP++GDHKY A         F  P +N           L +R    P           
Sbjct: 240 QLCPVLGDHKYSACVGTVLGQRFLLPAENTKPQRQVLDEALLSRLHLTPAQAAQLPLHIH 299

Query: 299 ---------HPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                     P    +++ APLP++  +T   LG +Y
Sbjct: 300 LHRLHLPGTRPRDAPIELLAPLPSYFSRTLQCLGLQY 336


>gi|221194862|ref|ZP_03567919.1| ribosomal large subunit pseudouridine synthase D [Atopobium rimae
           ATCC 49626]
 gi|221185766|gb|EEE18156.1| ribosomal large subunit pseudouridine synthase D [Atopobium rimae
           ATCC 49626]
          Length = 248

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 58/227 (25%), Positives = 94/227 (41%), Gaps = 26/227 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----------IAYHIDGFLKSWVDSKG-----QKPR 145
           ++Y+DS I   NKPAGI +                A  +    + ++++ G     Q  +
Sbjct: 3   IIYQDSYILAVNKPAGIIIHSDGTSHAGERADMCAAETLTDLARVYLENNGCVQQAQDVQ 62

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD++T+GI++ +  +       E  R R + K Y ++V G     ++ I   + + 
Sbjct: 63  ALHRLDKDTTGIVLFSLDKETQPLFDELIRSRNVHKTYLAVVKGEFPEGEQDITLPIGRD 122

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            H     +HV K   K A   +   +V          +  +  TGR HQ+RVH   +G P
Sbjct: 123 RH-DARRMHVSKTG-KAALTHVRRLEVQRRGQSTRSLMLAELGTGRKHQIRVHFSALGFP 180

Query: 266 IVGDHKYCANFKGNF---------TSPIQNKLYLHARYMDLPHPEGG 303
           IVGD  Y    + +           +  Q  L LHA  +   HP  G
Sbjct: 181 IVGDGLYGPIARDSMYGRAPSTRTAAFTQASLMLHAYELSFVHPVTG 227


>gi|290981670|ref|XP_002673553.1| predicted protein [Naegleria gruberi]
 gi|284087137|gb|EFC40809.1| predicted protein [Naegleria gruberi]
          Length = 483

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 56/192 (29%), Positives = 88/192 (45%), Gaps = 21/192 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY++S + V +KPA   +       Y  +       ++      + HRLD  TSG+LV+
Sbjct: 123 ILYDESDLLVVDKPASFPIHPCG--RYRKNSLTYILEENGYGTLHVVHRLDHSTSGVLVL 180

Query: 161 ARTRAAAQHLTESFRMRR--IQKIYWSLVWGIPKNKKEC------IANWLLK-------K 205
           A+ +  +  + E  + R   I K Y ++V G  K + E       + N  +K       K
Sbjct: 181 AKNKKVSGEIVEMIKTREKAIGKYYLAVVKGKWKGEYEVSGLVKDLNNSFVKCEKKVYCK 240

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM-QPHTGRTHQLRVHALHMGC 264
           +H  G +      +E G   AI+ F  I    +K   L M +P TGRTHQ+R+H   +G 
Sbjct: 241 NHKNGTWS---ADDELGTFEAITLFSGIVYNKEKDISLIMCKPITGRTHQIRIHLESIGN 297

Query: 265 PIVGDHKYCANF 276
           PI+ D  Y   F
Sbjct: 298 PIINDFFYNEQF 309


>gi|302331676|gb|ADL21870.1| Ribosomal pseudouridine synthase [Corynebacterium
           pseudotuberculosis 1002]
          Length = 325

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 54/188 (28%), Positives = 77/188 (40%), Gaps = 26/188 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +YED  + V NKP  ++    G  I       ++    +    P   HRLD+ TSGILV 
Sbjct: 109 IYEDDNLLVVNKPPFLATMPRGKHITQTATVQMRRATGNGDLSP--AHRLDRLTSGILVF 166

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI---GGDYVHVVK 217
            + R         F  R++ K Y +    I    ++   N L +   I   G    H+V 
Sbjct: 167 TKNRKVRGAYQSLFAERKVTKTYHA----IAPFSEDLTGNTLWRDHMIKTPGDMQGHIVP 222

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLE-------------MQPHTGRTHQLRVHALHMGC 264
                    +    V +  AQ+   L+             +QPHTGRTHQLR+H    G 
Sbjct: 223 GPPNAETLLVD---VTELDAQETAQLQKLHHVTTPLARYTLQPHTGRTHQLRLHMWAAGV 279

Query: 265 PIVGDHKY 272
           PI+GD  Y
Sbjct: 280 PILGDPAY 287


>gi|222151816|ref|YP_002560976.1| ribosomal large subunit pseudouridine synthase homolog [Macrococcus
           caseolyticus JCSC5402]
 gi|222120945|dbj|BAH18280.1| ribosomal large subunit pseudouridine synthase homolog [Macrococcus
           caseolyticus JCSC5402]
          Length = 273

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 51/175 (29%), Positives = 77/175 (44%), Gaps = 14/175 (8%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILV 159
           YED  + +  KP G+            +  L   +   DS+  +P   HRLDQET G+L+
Sbjct: 78  YEDEYLAILVKPKGVKTHPND--MSESNTLLNHAIYTLDSEYVEP--IHRLDQETVGLLL 133

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+     + L      R I++ Y + V      K + I         IG D  H  K+ 
Sbjct: 134 VAKNPFIKKILDRMLEERLIKRTYRAKVKSHLPLKHQTI------DMPIGKDKFHPNKRR 187

Query: 220 -EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             +  + A++H             +E+Q  TGRTHQ+RVH   +G P++GD  Y 
Sbjct: 188 VSQTGDRAVTHIVSSKANRDGTADVELQLETGRTHQIRVHLAEIGHPVIGDPLYS 242


>gi|207341390|gb|EDZ69458.1| YOL066Cp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 589

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 106/226 (46%), Gaps = 8/226 (3%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSK 107
           D++   ++  I  G+V       N L+ II++  ++   V+  +     K I +++ED  
Sbjct: 111 DREPSYYSKTIAEGKVYLNDEPAN-LDTIIRDGDLITHKVHRHEPPVTSKPIDIVFEDED 169

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I V +KP+ I V       Y  +   K      G      +RLD+ TSG++ +A+T   A
Sbjct: 170 ILVIDKPSSIPVHPTG--RYRFNTITKMLERQLGYSVHPCNRLDKPTSGLMFLAKTPLGA 227

Query: 168 QHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
             + +  + R + K Y + V G  P    E   +  ++  +       V + +++ A +A
Sbjct: 228 DRMGDQMKAREVTKEYVARVKGEFPIGIVE--VDKPVRSVNPKVALNAVCEMSDENAKHA 285

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            + F+ +  +  +   ++ +P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 286 KTVFQRVS-YDGQTSIVKCKPLTGRTHQIRVHLQYLGFPIANDPIY 330


>gi|84370153|ref|NP_001033650.1| RNA pseudouridylate synthase domain-containing protein 3 [Bos
           taurus]
 gi|122137054|sp|Q2TBK7|RUSD3_BOVIN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 3
 gi|83638710|gb|AAI10001.1| RNA pseudouridylate synthase domain containing 3 [Bos taurus]
          Length = 344

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 66/277 (23%), Positives = 108/277 (38%), Gaps = 48/277 (17%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLD 151
           D L++ ++     +   NKP G+ V G  G    +   L     S G   Q+ ++     
Sbjct: 70  DVLRAAVVDSKGPLVTLNKPQGLPVTGKPG-ELTLLSVLPELSRSLGLGEQEVQVVRASG 128

Query: 152 QETSGILVVARTRAAAQHL----TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +E SG+++++     A  L    T S R R+    Y ++  GIP   +  I    LK  H
Sbjct: 129 KEASGLVLLSSCSQTASRLQKFFTHSRRARKPTATYCAVTDGIPVTSEGKI-QAALKLEH 187

Query: 208 IGGDYVHVVKQNE------KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           I G  + V  Q+       +G    +SHF+V+         +++QP T    QL+ H   
Sbjct: 188 IDGVNLVVPVQSPSRKDIMEGVKRTLSHFRVV-ATGSGCALVQLQPLTVFPSQLQAHMAL 246

Query: 262 MGCPIVGDHKYCAN----FKGNFTSPIQN--------------KLYLHARYMDL------ 297
             CP++GDH Y A         F  P+++              +L L A           
Sbjct: 247 QLCPVLGDHTYSARVGTVLGQRFLLPVESTKPQRQVLDEALLGRLCLTASQAARLPLHLH 306

Query: 298 --------PHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                     P    +++ APLP++  +T   LG  Y
Sbjct: 307 LHCLRLPGARPRDPPIELLAPLPSYFSRTLQCLGLHY 343


>gi|289805997|ref|ZP_06536626.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 201

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 50/203 (24%), Positives = 91/203 (44%), Gaps = 18/203 (8%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++  +  A 
Sbjct: 3   LVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 62

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           + L + F    I+K Y ++V G   +        + ++  I   +     + +K    A+
Sbjct: 63  RRLAQQFEQHHIRKRYHAIVRGWLIDDAVLDYPLVEERDKIADKFA----REDKAPQPAV 118

Query: 228 SHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           + ++ +               ++  +E++P TGR HQLR H  H+  PI+GD K+  + +
Sbjct: 119 TQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDSKH-GDLR 177

Query: 278 GNFTSPIQ---NKLYLHARYMDL 297
            N ++       +L LHA  ++L
Sbjct: 178 QNRSAAEHFACRRLMLHASRLEL 200


>gi|238018444|ref|ZP_04598870.1| hypothetical protein VEIDISOL_00271 [Veillonella dispar ATCC 17748]
 gi|237864915|gb|EEP66205.1| hypothetical protein VEIDISOL_00271 [Veillonella dispar ATCC 17748]
          Length = 334

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 65/258 (25%), Positives = 109/258 (42%), Gaps = 65/258 (25%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LYED  + + +KPAG++V         +G+AY+   F ++ +    +K R  +RLD++T
Sbjct: 93  ILYEDDDLLIVDKPAGVTVNSKDQVSLANGVAYY---FKENGI---KRKVRFLNRLDRDT 146

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI------------------------ 190
           +G +V+A++  A     +       +K Y + V GI                        
Sbjct: 147 TGCIVIAKSGLAQSLYQQQMDDNTFEKWYMATVEGIVEADEDSLVLPMDRSTDGIHYEVN 206

Query: 191 PKNKK----------------ECIANWLLKKSHIGGDYVHVVKQN--EKGANYAISHFKV 232
           PK K+                +   + L+K   I  + V +  QN  + G N   S    
Sbjct: 207 PKGKETRTDFSFLCRHSSQPVDNSVHKLVKSVDIAQENVDIELQNVDKHGVNVDKSVHNS 266

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLH 291
             C    +  + ++ +TG+THQ+RV   H+G P+VGD  Y A   G  F    Q  ++ H
Sbjct: 267 SKC---GYTEVLVRLYTGKTHQIRVAFSHIGHPLVGDTLYGAQPTGQPFQLRAQKVVFTH 323

Query: 292 ARYMDLPHPEGGRLQITA 309
            R        G R+ +TA
Sbjct: 324 MR-------TGERITVTA 334


>gi|189439004|ref|YP_001954085.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium longum
           DJO10A]
 gi|189427439|gb|ACD97587.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium longum
           DJO10A]
          Length = 258

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 47/159 (29%), Positives = 78/159 (49%), Gaps = 14/159 (8%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD  TSG+++V ++  A   +   F    ++K Y +LV G  K  K  I      +
Sbjct: 68  IVSRLDVGTSGLMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQGGLKENKATI------E 121

Query: 206 SHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + IG     D+   V    K    A++H+ V++ F  +   + +   TGRTHQ+RVH   
Sbjct: 122 APIGRAKVSDFRFCVTPAGK---PAVTHWDVLERFGHEATLVSVNLETGRTHQIRVHFSS 178

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +G P+ GD  Y AN   +    + ++ +LHA  ++  HP
Sbjct: 179 IGHPLCGDPMYGANPVLSEALGL-DRQWLHAMKLEFRHP 216


>gi|152991248|ref|YP_001356970.1| ribosomal large subunit pseudouridine synthase D [Nitratiruptor sp.
           SB155-2]
 gi|151423109|dbj|BAF70613.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Nitratiruptor sp. SB155-2]
          Length = 242

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 55/189 (29%), Positives = 80/189 (42%), Gaps = 43/189 (22%)

Query: 98  KSILLYEDSKIYVFNKPAGIS---VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           K  +L+ED KI   NKPA I+   ++  SG                     L HRLD+ET
Sbjct: 56  KPEILFEDEKILAINKPAHITSEEIKEDSGY-------------------ELLHRLDKET 96

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-V 213
           SG+L++ +  A  +   E FR  R+ K Y + V GI     E              DY +
Sbjct: 97  SGVLLLVKNEAFRKKAIEEFRKSRVYKEYVAWVEGIVAEPYEI-------------DYPI 143

Query: 214 HVVKQNEKG-ANYAISHFKVIDCFAQ------KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             +K++ K  +  + S  K    + +      K   ++    TGRTHQ+RVH      PI
Sbjct: 144 LTIKKDGKAKSRLSASKGKPAKTYVEPLEIHGKKSKVKAVIETGRTHQIRVHLARTDHPI 203

Query: 267 VGDHKYCAN 275
           +GD  Y   
Sbjct: 204 LGDTLYGGK 212


>gi|296475055|gb|DAA17170.1| RNA pseudouridylate synthase domain-containing protein 3 [Bos
           taurus]
          Length = 344

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 66/277 (23%), Positives = 108/277 (38%), Gaps = 48/277 (17%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLD 151
           D L++ ++     +   NKP G+ V G  G    +   L     S G   Q+ ++     
Sbjct: 70  DVLRAAVVDRKGPLVTLNKPQGLPVTGKPG-ELTLLSVLPELSRSLGLGEQEVQVVRASG 128

Query: 152 QETSGILVVARTRAAAQHL----TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +E SG+++++     A  L    T S R R+    Y ++  GIP   +  I    LK  H
Sbjct: 129 KEASGLVLLSSCSQTASRLQKFFTHSRRARKPTATYCAVTDGIPVTSEGKI-QAALKLEH 187

Query: 208 IGGDYVHVVKQNE------KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           I G  + V  Q+       +G    +SHF+V+         +++QP T    QL+ H   
Sbjct: 188 IDGVNLVVPVQSPSRKDIMEGVKRTLSHFRVV-ATGSGCALVQLQPLTVFPSQLQAHMAL 246

Query: 262 MGCPIVGDHKYCAN----FKGNFTSPIQN--------------KLYLHARYMDL------ 297
             CP++GDH Y A         F  P+++              +L L A           
Sbjct: 247 QLCPVLGDHTYSARVGTVLGQRFLLPVESTKPQRQVLDEALLGRLCLTASQAARLPLHLH 306

Query: 298 --------PHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                     P    +++ APLP++  +T   LG  Y
Sbjct: 307 LHCLRLPGARPRDPPIELLAPLPSYFSRTLQCLGLHY 343


>gi|305433225|ref|ZP_07402381.1| RNA pseudouridine synthase [Campylobacter coli JV20]
 gi|304443926|gb|EFM36583.1| RNA pseudouridine synthase [Campylobacter coli JV20]
          Length = 250

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 59/225 (26%), Positives = 105/225 (46%), Gaps = 39/225 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I   NKP           AY  +   K +        +L +RLD+ETSG++++
Sbjct: 59  VIFEDENIIAINKP----------YAYISEELEKKF------NAKLLNRLDKETSGVILL 102

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+ +R+ K Y +++ GI   + E     L  K+  G     + K ++
Sbjct: 103 CKNEDFRKICIEEFKKQRVYKSYIAVLDGILAEEIEIDEPILTIKTKNGA----LSKISK 158

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +G + A+S F  I   A+K    ++   TGRTHQ+RVHA  +   I+GD KY        
Sbjct: 159 EGLS-AVSIFTPIMMQAKK-TLAKIIIKTGRTHQIRVHAKFIKHGIIGDEKY-----AKI 211

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           +S   +++YLH+  + +         +     A +  ++  LGF+
Sbjct: 212 SS---DRMYLHSHEIRI---------LNYQFKAELDSSFSKLGFE 244


>gi|295396998|ref|ZP_06807115.1| ribosomal large subunit pseudouridine synthase [Aerococcus viridans
           ATCC 11563]
 gi|294974746|gb|EFG50456.1| ribosomal large subunit pseudouridine synthase [Aerococcus viridans
           ATCC 11563]
          Length = 156

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 43/156 (27%), Positives = 74/156 (47%), Gaps = 9/156 (5%)

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V A+T  AA  L++  R   +++ Y ++V   PK     + N+L K      + V +V 
Sbjct: 1   MVFAKTSKAASRLSDQVRRNAMERTYLAVVNEKPKQASSRLVNYLYKNRQ--KNKVSIVS 58

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           ++ K    A+  + VI         L ++  TGR HQ+RV    +G  I GD KY A + 
Sbjct: 59  EHHKEGKKAVLDYSVI-ASRDGLSLLSVKLQTGRPHQIRVQLAGIGTSIWGDQKYGAQY- 116

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
               S +  ++ L A  + + HP +   + + +PLP
Sbjct: 117 ----SKVGQQIALWANSLTISHPVQKTPISVASPLP 148


>gi|57167720|ref|ZP_00366860.1| ribosomal large subunit pseudouridine synthase C, putative
           [Campylobacter coli RM2228]
 gi|57020842|gb|EAL57506.1| ribosomal large subunit pseudouridine synthase C, putative
           [Campylobacter coli RM2228]
          Length = 208

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 59/225 (26%), Positives = 105/225 (46%), Gaps = 39/225 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I   NKP           AY  +   K +        +L +RLD+ETSG++++
Sbjct: 17  VIFEDENIIAINKPY----------AYISEELEKKF------NAKLLNRLDKETSGVILL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+ +R+ K Y +++ GI   + E     L  K+  G     + K ++
Sbjct: 61  CKNEDFRKICIEEFKKQRVYKSYIAVLDGILAEEIEIDEPILTIKTKNGA----LSKISK 116

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +G + A+S F  I   A+K    ++   TGRTHQ+RVHA  +   I+GD KY        
Sbjct: 117 EGLS-AVSIFTPIMMQAKK-TLAKIIIKTGRTHQIRVHAKFIKHGIIGDEKY-----AKI 169

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           +S   +++YLH+  + +         +     A +  ++  LGF+
Sbjct: 170 SS---DRMYLHSHEIRI---------LNYQFKAELDSSFSKLGFE 202


>gi|332970065|gb|EGK09063.1| ribosomal large subunit pseudouridine synthase D [Desmospora sp.
           8437]
          Length = 300

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 111/227 (48%), Gaps = 18/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQ--KPRLTHRLDQETSG 156
           +++ED  + + +K  G+ V      +     +G    W   +G+    R   RLD++TSG
Sbjct: 84  VVHEDEDLIILDKQPGVVVHPTRNYSEGTLANGLAAYW-QERGEFHLVRPVTRLDKDTSG 142

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V A+   A   L+     +R  + Y ++V G  + ++  +   + + S    +  H+ 
Sbjct: 143 LIVFAKHPHAHAVLSGQMERKRYLREYLAVVHGSLEMEEGRVEEPIARSS----ETPHLR 198

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             + +GA  A + ++V+  + +    + ++  TGRTHQ+RVH  H+G P+ GD  Y    
Sbjct: 199 TVSPEGAP-ARTQYRVVRRWPEA-TLVRLRLETGRTHQIRVHMAHLGHPLYGDTLY---- 252

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
            G  T+ I ++  LHA  + L HP  G+ +   +PLP  +    +SL
Sbjct: 253 -GGRTAGI-DRQALHAVRLSLIHPRDGKKRCWESPLPEDIHLLMESL 297


>gi|316971885|gb|EFV55608.1| pseudouridylate synthase 6 [Trichinella spiralis]
          Length = 404

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 68/265 (25%), Positives = 115/265 (43%), Gaps = 38/265 (14%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK--EQKILDSSVNLTKHS 94
            ++ + +G+V V+ +    +  +++G ++R         H+    E  +LDS+V++   +
Sbjct: 87  FEEAILAGRVTVNGQPTSVDYVVENGDLIR---------HMCHRHELPVLDSAVDIVTDT 137

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQE 153
           +            I V NKP  I V       YH +  +       G     T HRLD+ 
Sbjct: 138 E-----------DILVVNKPCSIPVHPCG--RYHFNSLVLYLKHIGGMDNLKTFHRLDRL 184

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDY 212
           TSG+++  +     + L +     +I+K Y  LV G  P+ +  C     +    +G  Y
Sbjct: 185 TSGLVIFLKNEKIEKKLRQQMIENQIKKEYLCLVDGEFPEEEVVCDKPLDVLSQSMGIMY 244

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +         A+   S  K    F+  K   L+  P TGRTHQ+RVH  ++G PIV D+ 
Sbjct: 245 I--------TADGKPSLTKFYKLFSDGKTSILKCCPETGRTHQIRVHLQYLGYPIVNDYI 296

Query: 272 YCANFKGNFTSPIQNKLYLHARYMD 296
           Y  N    F  P + KL  + + +D
Sbjct: 297 Y--NNSDAF-GPNKGKLCDYGKSLD 318


>gi|238882595|gb|EEQ46233.1| DRAP deaminase [Candida albicans WO-1]
          Length = 589

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 48/183 (26%), Positives = 79/183 (43%), Gaps = 19/183 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  + V +KP GI V       Y  +   K +   KG+     +RLD+ TSG++ +
Sbjct: 173 IVFEDDDLLVIDKPGGIPVHPTG--RYRYNTVTKIFEHEKGKIVHPCNRLDRLTSGLMFL 230

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            ++   A ++    R R + K Y + V G  P ++         K   +  + V +    
Sbjct: 231 GKSSKGANNMMSQIRDRNVTKEYIARVKGEFPLDRIIVDKPLSTKSPKLTLNVVDMENGK 290

Query: 220 EKGANY------AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           E    +       I++  V+ C           P TGRTHQ+RVH   +G PI  D  Y 
Sbjct: 291 EAKTEFQRVSYDPITNTSVVKC----------HPLTGRTHQIRVHLQFLGYPIANDPIYS 340

Query: 274 ANF 276
           + F
Sbjct: 341 SEF 343


>gi|323331668|gb|EGA73082.1| Rib2p [Saccharomyces cerevisiae AWRI796]
 gi|323335647|gb|EGA76930.1| Rib2p [Saccharomyces cerevisiae Vin13]
 gi|323346638|gb|EGA80923.1| Rib2p [Saccharomyces cerevisiae Lalvin QA23]
 gi|323352328|gb|EGA84863.1| Rib2p [Saccharomyces cerevisiae VL3]
          Length = 591

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 106/226 (46%), Gaps = 8/226 (3%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSK 107
           D++   ++  I  G+V       N L+ II++  ++   V+  +     K I +++ED  
Sbjct: 111 DREPSYYSKTIAEGKVYLNDEPAN-LDTIIRDGDLITHKVHRHEPPVTSKPIDIVFEDED 169

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I V +KP+ I V       Y  +   K      G      +RLD+ TSG++ +A+T   A
Sbjct: 170 ILVIDKPSSIPVHPTG--RYRFNTITKMLERQLGYSVHPCNRLDKPTSGLMFLAKTPLGA 227

Query: 168 QHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
             + +  + R + K Y + V G  P    E   +  ++  +       V + +++ A +A
Sbjct: 228 DRMGDQMKAREVTKEYVARVKGEFPIGIVE--VDKPVRSVNPKVALNAVCEMSDENAKHA 285

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            + F+ +  +  +   ++ +P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 286 KTVFQRVS-YDGQTSIVKCKPLTGRTHQIRVHLQYLGFPIANDPIY 330


>gi|85075514|ref|XP_955780.1| hypothetical protein NCU03846 [Neurospora crassa OR74A]
 gi|28916789|gb|EAA26544.1| hypothetical protein NCU03846 [Neurospora crassa OR74A]
          Length = 473

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 61/252 (24%), Positives = 110/252 (43%), Gaps = 31/252 (12%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSK 107
           D+    + N +++G VV     +    H++K   ++  + +  +     + I +++ED+ 
Sbjct: 94  DRPAEYYRNAVETGLVVVNGKAVGP-EHVLKNGDLISHTTHRHEPPVTAEPIRVIHEDND 152

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + V NKP+G+ V       Y+    +       G  PR  +RLD+ TSGI+ +A+++ AA
Sbjct: 153 LIVINKPSGVPVHPAGRYNYNSVVEIIKSERGPGFLPRPCNRLDRLTSGIMFLAKSQHAA 212

Query: 168 QHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           + L      R ++K Y + V G  P  +  C    L     +    ++ V+ N K A   
Sbjct: 213 ERLVAQISQRSVRKEYIARVVGRFPDGEVVCDQPILQISPKL---TLNRVRANGKAARTV 269

Query: 227 ---ISHFKVIDC----------------FAQK------FCWLEMQPHTGRTHQLRVHALH 261
              ++++  +D                  AQ+      +  +   P TGRTHQ+RVH   
Sbjct: 270 FKRLAYYPPVDPPTKGQTEQPAMPDAEQAAQRRGEGEGYSIVRCLPVTGRTHQIRVHLQF 329

Query: 262 MGCPIVGDHKYC 273
           +G PI  D  Y 
Sbjct: 330 LGHPIQNDPIYA 341


>gi|291279974|ref|YP_003496809.1| ribosomal large subunit pseudouridine synthase A [Deferribacter
           desulfuricans SSM1]
 gi|290754676|dbj|BAI81053.1| ribosomal large subunit pseudouridine synthase A [Deferribacter
           desulfuricans SSM1]
          Length = 219

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 58/218 (26%), Positives = 96/218 (44%), Gaps = 25/218 (11%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +T+ S+F    ++Y+D+ I V NK   I V   +    I       +K+ +  +  +  +
Sbjct: 1   MTQSSEFS---IVYQDNDIIVLNKSHSILVIPDRYNKNIPS-----IKNILQREFNEIYV 52

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  T G++V A+ R + + L+  F   +I K Y  +  G+ K     +    + K 
Sbjct: 53  VHRLDFGTGGLIVFAKNRYSHKSLSTQFSKNQIVKKYLCITDGVIKYPFTSL--LPISKR 110

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           +  G Y    K N K    +I+ F  I+ +  K+  +E  P TGR+HQ+RVH      P+
Sbjct: 111 NYHGKY----KINFKSGRKSITTFIPIN-YNNKYSLIEAIPKTGRSHQIRVHLKAYKAPL 165

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             D  Y              +L L A Y+   HP   +
Sbjct: 166 YQDFLYNKKID-------DKRLTLFAYYLSFTHPTKNK 196


>gi|14043412|gb|AAH07697.1| RPUSD2 protein [Homo sapiens]
          Length = 554

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 100/212 (47%), Gaps = 26/212 (12%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  LN ++K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++ 
Sbjct: 203 VQDLNIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNT 262

Query: 130 DGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V
Sbjct: 263 VIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRV 319

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW---- 242
            G  P  +  C    L+    +G     V + + +G        K  +   Q+  +    
Sbjct: 320 EGEFPTEEVTCKEPILVVSYKVG-----VCRVDPRG--------KPCETVFQRLSYNGQS 366

Query: 243 --LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +  +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 367 SVVRCRPLTGRTHQIRVHLQFLGHPILNDPIY 398


>gi|254557025|ref|YP_003063442.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254045952|gb|ACT62745.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 300

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 58/225 (25%), Positives = 105/225 (46%), Gaps = 26/225 (11%)

Query: 101 LLYEDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +LYED    + NKPAG++         + +A  + G+ ++      +   +T RLD++TS
Sbjct: 80  ILYEDRDYLIVNKPAGVASVPAHALPDNTLANRVKGYYQA-AHYDNEVVHITTRLDRDTS 138

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ A+   A   +    +   ++K+Y ++V G    +      WL   + IG      
Sbjct: 139 GIVLFAKHHFAHSIIDHQLKAHAMRKMYLAVVSG----ELTTDHGWL--DAPIGRAADSF 192

Query: 216 VKQNEK-GANYAISHFKVIDCFAQKFC---WLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +K+  +     +++ + V+    ++ C    + ++ HTGRTHQ+RVH    G P++GD  
Sbjct: 193 IKRTTRPDGKPSLTEYWVV----KRLCNMTVVRVRLHTGRTHQIRVHFAASGHPLIGDAL 248

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHM 315
           Y     G    P   +  LH   ++   P   +   T APLPA +
Sbjct: 249 Y-----GGPRDPWIQRQALHCMRLEFDDPFISQTLTTFAPLPADL 288


>gi|229829765|ref|ZP_04455834.1| hypothetical protein GCWU000342_01862 [Shuttleworthia satelles DSM
           14600]
 gi|229791754|gb|EEP27868.1| hypothetical protein GCWU000342_01862 [Shuttleworthia satelles DSM
           14600]
          Length = 312

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 34/100 (34%), Positives = 55/100 (55%), Gaps = 2/100 (2%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQE 153
            +++ ++YED+ I+V  KPAG + Q  S +   +   LK++  S+G+     L  RLDQ 
Sbjct: 1   MMRTEIIYEDADIFVCYKPAGFATQTASALQADLVSELKNYRKSRGESDYIGLIGRLDQP 60

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             G++V+A+   AA  L  +    RI K Y +L  G+PK 
Sbjct: 61  VEGLMVIAKNPRAAGKLEAAQAKGRIDKYYLALTQGLPKG 100



 Score = 40.8 bits (94), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 40/87 (45%), Gaps = 11/87 (12%)

Query: 221 KGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           KGA  A   ++++D    K       L +   TGR HQ+R+    +G PI+GD +Y A+ 
Sbjct: 205 KGARKARLEYQILDHSKTKDGRALALLRVHLLTGRRHQIRLQLSGLGSPILGDARYGAD- 263

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 P    L L A  +  PHP  G
Sbjct: 264 ------PNGQPLALCACQLSFPHPGTG 284


>gi|195621906|gb|ACG32783.1| RNA binding protein [Zea mays]
          Length = 379

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 80/321 (24%), Positives = 125/321 (38%), Gaps = 70/321 (21%)

Query: 4   MTYVQ-YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +TY   +   + D     ++ +  NH          K +R+GQ+ VD            G
Sbjct: 25  LTYTDTFRCADADAATTLIEFYSTNHKSSAPLPGWIKRIRNGQITVD------------G 72

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKH-----SDFLKSIL--LYEDSKIYVFNKPA 115
           +VV  P           +  ++D S  L  H       F   +L  LYED  +   NKP+
Sbjct: 73  EVVTDP-----------DMTLVDGS-KLVYHRFPWQEPFAPYLLEVLYEDDDMVALNKPS 120

Query: 116 GISV------QGGSGIAYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVV 160
           G+ V      Q  + +A      LK W  +   +         P   HRL + TSG+L+ 
Sbjct: 121 GLQVLPKGLFQQRTVLAQLQ---LKDWKMASSCRFKRKDVQSHPVPVHRLGRGTSGLLLC 177

Query: 161 ARTRAAAQHLTESF-----------------RMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           A+T+ A   L   F                   R+I K Y +LV GI  +  E +    +
Sbjct: 178 AKTKVAKVRLASYFAEGAINAAKKRDKSEFSEERKISKFYRALVTGI-LDDDEVVVTQPI 236

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHM 262
              H  G    +      G   A+S   V++  A Q    ++++ H+GR HQ+R+H  ++
Sbjct: 237 GLVHYPGVAEGLYAACSSGKP-AMSKVCVLERLAHQNHTLVQVEIHSGRPHQIRIHLAYI 295

Query: 263 GCPIVGDHKYCANFKGNFTSP 283
           G P+V D  Y      NF  P
Sbjct: 296 GHPLVDDPLYGIGGHPNFVEP 316


>gi|68482658|ref|XP_714726.1| hypothetical protein CaO19.10687 [Candida albicans SC5314]
 gi|68482929|ref|XP_714595.1| hypothetical protein CaO19.3177 [Candida albicans SC5314]
 gi|46436176|gb|EAK95543.1| hypothetical protein CaO19.3177 [Candida albicans SC5314]
 gi|46436316|gb|EAK95680.1| hypothetical protein CaO19.10687 [Candida albicans SC5314]
          Length = 589

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 48/183 (26%), Positives = 79/183 (43%), Gaps = 19/183 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  + V +KP GI V       Y  +   K +   KG+     +RLD+ TSG++ +
Sbjct: 173 IVFEDDDLLVIDKPGGIPVHPTG--RYRYNTVTKIFEHEKGKIVHPCNRLDRLTSGLMFL 230

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            ++   A ++    R R + K Y + V G  P ++         K   +  + V +    
Sbjct: 231 GKSSKGANNMMSQIRDRNVTKEYIARVKGEFPLDRIIVDKPLSTKSPKLTLNVVDMENGK 290

Query: 220 EKGANY------AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           E    +       I++  V+ C           P TGRTHQ+RVH   +G PI  D  Y 
Sbjct: 291 EAKTEFQRVSYDPITNTSVVKC----------HPLTGRTHQIRVHLQFLGYPIANDPIYS 340

Query: 274 ANF 276
           + F
Sbjct: 341 SEF 343


>gi|74000106|ref|XP_544620.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 2 [Canis familiaris]
          Length = 518

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 98/220 (44%), Gaps = 44/220 (20%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGS 123
           + E+ + D S+ L K +DFL++               LL E+  + V +KP+ I V    
Sbjct: 162 LNEEPVQDLSIML-KDNDFLRNRVHRHEPPVTAEPVRLLAENEDVVVVDKPSSIPVHPCG 220

Query: 124 GIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++   F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K
Sbjct: 221 RFRHNTVIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEK 277

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI--------SHFKV 232
            Y   V G  P  +  C    L+    +G     V + + +G              H  V
Sbjct: 278 EYVCRVEGEFPTEEVTCKEPILVVSYKVG-----VCRVDTRGKPCETVFQRLSYNGHSSV 332

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + C          +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 333 VRC----------RPLTGRTHQIRVHLQFLGHPILNDPIY 362


>gi|6324506|ref|NP_014575.1| Rib2p [Saccharomyces cerevisiae S288c]
 gi|2501674|sp|Q12362|RIB2_YEAST RecName: Full=Bifunctional protein RIB2; Includes: RecName:
           Full=tRNA pseudouridine synthase 8, cytoplasmic;
           AltName: Full=tRNA pseudouridylate synthase 8; AltName:
           Full=tRNA-uridine isomerase 8; Includes: RecName:
           Full=Diaminohydroxyphosphoribosylaminopyrimidine
           deaminase; Short=DRAP deaminase; AltName:
           Full=Riboflavin-specific deaminase
 gi|642221|emb|CAA79742.1| DRAP deaminase [Saccharomyces cerevisiae]
 gi|1419887|emb|CAA99076.1| RIB2 [Saccharomyces cerevisiae]
 gi|285814824|tpg|DAA10717.1| TPA: Rib2p [Saccharomyces cerevisiae S288c]
          Length = 591

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 106/226 (46%), Gaps = 8/226 (3%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSK 107
           D++   ++  I  G+V       N L+ II++  ++   V+  +     K I +++ED  
Sbjct: 111 DREPSYYSKTIAEGKVYLNDEPAN-LDTIIRDGDLITHKVHRHEPPVTSKPIDIVFEDED 169

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I V +KP+ I V       Y  +   K      G      +RLD+ TSG++ +A+T   A
Sbjct: 170 ILVIDKPSSIPVHPTG--RYRFNTITKMLERQLGYSVHPCNRLDKPTSGLMFLAKTPLGA 227

Query: 168 QHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
             + +  + R + K Y + V G  P    E   +  ++  +       V + +++ A +A
Sbjct: 228 DRMGDQMKAREVTKEYVARVKGEFPIGIVE--VDKPVRSVNPKVALNAVCEMSDENAKHA 285

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            + F+ +  +  +   ++ +P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 286 KTVFQRVS-YDGQTSIVKCKPLTGRTHQIRVHLQYLGFPIANDPIY 330


>gi|190407280|gb|EDV10547.1| DRAP deaminase [Saccharomyces cerevisiae RM11-1a]
          Length = 591

 Score = 62.8 bits (151), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 106/226 (46%), Gaps = 8/226 (3%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSK 107
           D++   ++  I  G+V       N L+ II++  ++   V+  +     K I +++ED  
Sbjct: 111 DREPSYYSKTIAEGKVYLNDEPAN-LDTIIRDGDLITHKVHRHEPPVTSKPIDIVFEDED 169

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I V +KP+ I V       Y  +   K      G      +RLD+ TSG++ +A+T   A
Sbjct: 170 ILVIDKPSSIPVHPTG--RYRFNTITKMLERQLGYSVHPCNRLDKPTSGLMFLAKTPLGA 227

Query: 168 QHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
             + +  + R + K Y + V G  P    E   +  ++  +       V + +++ A +A
Sbjct: 228 DRMGDQMKAREVTKEYVARVKGEFPIGIVE--VDKPVRSVNPKVALNAVCEMSDENAKHA 285

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            + F+ +  +  +   ++ +P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 286 KTVFQRVS-YDGQTSIVKCKPLTGRTHQIRVHLQYLGFPIANDPIY 330


>gi|151945568|gb|EDN63809.1| DRAP deaminase [Saccharomyces cerevisiae YJM789]
 gi|256273956|gb|EEU08875.1| Rib2p [Saccharomyces cerevisiae JAY291]
 gi|323303146|gb|EGA56948.1| Rib2p [Saccharomyces cerevisiae FostersB]
 gi|323307078|gb|EGA60361.1| Rib2p [Saccharomyces cerevisiae FostersO]
          Length = 591

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 106/226 (46%), Gaps = 8/226 (3%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSK 107
           D++   ++  I  G+V       N L+ II++  ++   V+  +     K I +++ED  
Sbjct: 111 DREPSYYSKTIAEGKVYLNDEPAN-LDTIIRDGDLITHKVHRHEPPVTSKPIDIVFEDED 169

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I V +KP+ I V       Y  +   K      G      +RLD+ TSG++ +A+T   A
Sbjct: 170 ILVIDKPSSIPVHPTG--RYRFNTITKMLERQLGYSVHPCNRLDKPTSGLMFLAKTPLGA 227

Query: 168 QHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
             + +  + R + K Y + V G  P    E   +  ++  +       V + +++ A +A
Sbjct: 228 DRMGDQMKAREVTKEYVARVKGEFPIGIVE--VDKPVRSVNPKVALNAVCEMSDENAKHA 285

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            + F+ +  +  +   ++ +P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 286 KTVFQRVS-YDGQTSIVKCKPLTGRTHQIRVHLQYLGFPIANDPIY 330


>gi|19113793|ref|NP_592881.1| tRNA pseudouridylate synthase (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|1175381|sp|Q09709|YA32_SCHPO RecName: Full=Uncharacterized protein C18B11.02c
 gi|929888|emb|CAA90587.1| tRNA pseudouridylate synthase (predicted) [Schizosaccharomyces
           pombe]
          Length = 394

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 106/237 (44%), Gaps = 28/237 (11%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +K +R+GQV+V+ +    +  I++G +V      +A  H   E  + D  V +       
Sbjct: 62  EKAIRNGQVKVNNQIGNVDTLIENGYIVSH----HAHRH---EPPVSDQPVGI------- 107

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
               ++ED    V +KPAG+ V   +G   H         ++K       +RLD+ TSG+
Sbjct: 108 ----VHEDESYVVIDKPAGVPVHP-TGRYNHNTVLHILMKENKCSLLYPCNRLDRLTSGL 162

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHV 215
           +  +++  AA+ +      + ++K Y + V G   N  E  C A  L     +G + +H 
Sbjct: 163 MFFSKSPKAAEEMRVHMISKSLKKEYVARVIGEFPNSGEVICDAPLLTVAPTLGLNRIH- 221

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                     A + FK I  F      +  +P TGRTHQLRVH  ++G PI  D  Y
Sbjct: 222 -----PDGKEASTVFKRI-AFDGHTSLVLCKPLTGRTHQLRVHLQYLGYPIANDPIY 272


>gi|219113125|ref|XP_002186146.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|209582996|gb|ACI65616.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 175

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 51/184 (27%), Positives = 86/184 (46%), Gaps = 23/184 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLT------HRLDQE 153
           +++ED  I V +KP+G+ +V     +       L   V    Q   +T      HRL  +
Sbjct: 3   IVHEDEHIIVVDKPSGVLTVPSDKNVPS-----LAQAVFDHCQPTEVTLDQMVVHRLGMD 57

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V+A+T    + +   FR R+I + Y +LV G        I+  L++      DY 
Sbjct: 58  TSGLIVLAKTMDTVRQMNALFRTRKITRQYEALVVGHLPQHGGLISLPLMR------DYE 111

Query: 214 H--VVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           H   +++  +    +++ ++V+   D        + +   +GRTHQL VH    G PIVG
Sbjct: 112 HPPYMRKLLEMPKESLTKYEVVNREDMDGTPVSRVALTSISGRTHQLNVHLAAFGHPIVG 171

Query: 269 DHKY 272
           D  Y
Sbjct: 172 DSVY 175


>gi|295100993|emb|CBK98538.1| Pseudouridylate synthases, 23S RNA-specific [Faecalibacterium
           prausnitzii L2-6]
          Length = 303

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 66/266 (24%), Positives = 112/266 (42%), Gaps = 54/266 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKR-VKF--------------NNRIQSGQVV--RIPPVIN 72
           P  + + L+  LR   V  D  R VKF              N R+++GQV+   +PP   
Sbjct: 9   PEADGMLLRGFLRRCSVSTDLSRAVKFRGSGFFADGVPVLANRRVEAGQVISFELPPEGE 68

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
            +                    D +   ++YED+   V  KP  ++V     + Y +D  
Sbjct: 69  GV-----------------APQDDIPVDVVYEDAFALVVEKPPHLAVH--PTLNYPLDTL 109

Query: 133 L---KSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                +W   +G+ P  R  +R+D++TSG+++ A+   AA  L +     R++K+Y+++ 
Sbjct: 110 ANGYAAWALRQGRSPVFRPVNRIDKDTSGLVLAAQNGYAAPLLAQ-----RVEKLYYAVA 164

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            G +P       A    +   I G     V  + K +    +  +  +  +   C     
Sbjct: 165 EGELPLGPGVIDAPIGRQGESIIG---RCVTPDGKPSRTEYTILRAENGLSLAACV---- 217

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
           P TGRTHQ+RVH   +G P+ GD  Y
Sbjct: 218 PVTGRTHQIRVHFASIGHPLAGDDLY 243


>gi|319948901|ref|ZP_08023012.1| ribosomal pseudouridine synthase [Dietzia cinnamea P4]
 gi|319437439|gb|EFV92448.1| ribosomal pseudouridine synthase [Dietzia cinnamea P4]
          Length = 332

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 62/144 (43%), Gaps = 11/144 (7%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ T+G+LV     A      + F  RR+ K Y ++         + +A    + S 
Sbjct: 142 HRLDRLTAGVLVFTADPAYRGAYQDLFAARRVTKTYLAVA-----PAPDGVATVRERSSR 196

Query: 208 I---GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           I    G         E  A+  I+          +     ++P TGRTHQLRVH   +G 
Sbjct: 197 ILKTRGVLQATEVDGEPDAHTRITLLDTRGAGPDRLGLYRLEPTTGRTHQLRVHMNALGT 256

Query: 265 PIVGDHKYCANF---KGNFTSPIQ 285
           PI+GD  Y        G+FT P+Q
Sbjct: 257 PILGDDLYPDVLDMTPGDFTRPLQ 280


>gi|291403226|ref|XP_002717836.1| PREDICTED: RNA pseudouridylate synthase domain containing 2
           [Oryctolagus cuniculus]
          Length = 561

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 98/220 (44%), Gaps = 44/220 (20%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGS 123
           + E+ + D S+ L K +DFL++               LL E+  + V +KP+ I V    
Sbjct: 206 LNEEPVQDLSIVL-KDNDFLRNTVHRHEPPVTAEPIRLLAENDDVVVVDKPSSIPVHPCG 264

Query: 124 GIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++   F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K
Sbjct: 265 RFRHNTVIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEK 321

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI--------SHFKV 232
            Y   V G  P  +  C    L+    +G     V + + +G              H  V
Sbjct: 322 EYVCRVEGEFPVEEVTCKEPILVVSYKVG-----VCRVDPRGKPCETVFQRLSYNGHSSV 376

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + C          +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 377 VRC----------RPLTGRTHQIRVHLQFLGHPILNDPIY 406


>gi|313665599|ref|YP_004047470.1| pseudouridine synthase, RluA family [Mycoplasma leachii PG50]
 gi|312949399|gb|ADR23995.1| pseudouridine synthase, RluA family [Mycoplasma leachii PG50]
          Length = 302

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 68/276 (24%), Positives = 130/276 (47%), Gaps = 37/276 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  +++N  L ++ K  +       + K +R+  ++++ KR+  N++    +V  I  V
Sbjct: 5   IVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRI--NDKNYLLKVNDIIEV 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            ++   II++Q    S+VNL          ++YED+ I + NK   + +     +   +D
Sbjct: 63  YDSNKPIIRDQFNYISNVNLD---------IVYEDNNILIVNKSNNLEMHSTYNLC--LD 111

Query: 131 GFLKSW-VDSKGQKPRL--------THRLDQETSGILVVARTRAAAQHLTESFRMR-RIQ 180
             +KS+ VD K     L         HRLD+ TSG+++ A+ + ++  LT +F+   +I 
Sbjct: 112 DMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSTILTNAFKSNDQIN 171

Query: 181 KIYWSLV---WGIPKNKKECIANWLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCF 236
           K Y++L    W +  N    +  ++   S+    D+  V K N K   Y  + FK+I+  
Sbjct: 172 KYYYALTSYDWNL--NDFLQVNGYISYDSNTQKADFSLVEKNNYK---YCQTEFKLINK- 225

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                 + ++  TG+ HQ+R        PI+ D +Y
Sbjct: 226 ----NLILVKLITGKKHQIRSVLSFYNNPILNDFRY 257


>gi|194670657|ref|XP_583460.4| PREDICTED: RNA pseudouridylate synthase domain containing 2 isoform
           1 [Bos taurus]
          Length = 505

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 61/215 (28%), Positives = 98/215 (45%), Gaps = 34/215 (15%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGS 123
           + E+ + D S+ L K +DFL++               LL E+  + V +KP+ I V    
Sbjct: 149 LNEEPVQDLSIVL-KDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCG 207

Query: 124 GIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++   F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K
Sbjct: 208 RFRHNTVIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEK 264

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS---HFKVIDCFA 237
            Y   V G  P  +  C    L+    +G   V    +  +     +S   H  V+ C  
Sbjct: 265 EYVCRVVGEFPTEEVTCKEPILVVSYKVGVCRVDPQGKPCESVFQRLSYNGHSSVVRC-- 322

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                   +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 323 --------RPLTGRTHQIRVHLQFLGHPILNDPIY 349


>gi|149189891|ref|ZP_01868170.1| pseudouridine synthase Rlu family protein [Vibrio shilonii AK1]
 gi|148836206|gb|EDL53164.1| pseudouridine synthase Rlu family protein [Vibrio shilonii AK1]
          Length = 228

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 55/190 (28%), Positives = 81/190 (42%), Gaps = 17/190 (8%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YE+    V NK  G+SV    G    +       +        L HRLD+ TSG+L++A+
Sbjct: 6   YENEDFVVINKYPGVSVHKDDGDTMLVSDVA---IAIGASSLHLVHRLDKMTSGLLILAK 62

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
               A   +  F  R I K Y ++    PK K+  I   + +        V     N K 
Sbjct: 63  RAEVAAQFSRLFEQRDIDKYYLAIGSKKPKKKQGTIIGDMERSRRSSWKLV-----NSKN 117

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
            N A++ F        +  +L  +P +G+THQ+RV    +G PI GD  Y        TS
Sbjct: 118 -NPAVTQFFSAAAENGERVFL-CKPLSGKTHQIRVALKSIGSPIKGDAIYN-------TS 168

Query: 283 PIQNKLYLHA 292
              ++ YLHA
Sbjct: 169 DSSDRGYLHA 178


>gi|294155753|ref|YP_003560137.1| ribosomal large subunit pseudouridylate synthase C [Mycoplasma
           crocodyli MP145]
 gi|291600008|gb|ADE19504.1| ribosomal large subunit pseudouridylate synthase C [Mycoplasma
           crocodyli MP145]
          Length = 280

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 76/308 (24%), Positives = 133/308 (43%), Gaps = 56/308 (18%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-------VKFNNRI 59
           ++ ++  +++    L +    +  ++    ++K+ R   ++V+  R       + FN++I
Sbjct: 1   MKTIIATSNDAGRTLYKLITKYLDNVPLSRIEKLFRKKDIKVNGIRTNQKDYTIAFNDQI 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +          I  L  I KE+  L SS +  K         +YED+ I + +KP GI V
Sbjct: 61  E----------IYGLIDIKKEEAPLISSFSFKK---------IYEDNNILIIDKPNGIEV 101

Query: 120 QGGSG-IAYHIDGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 +   +  +LK   VDS   KP    RLD+ETSGI++ A+   A ++L ++  M 
Sbjct: 102 HSSPNCLDNQVLAYLKFKQVDS--FKPSHVGRLDKETSGIMLYAKNYQALKYLNDN--ME 157

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLK---KSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            I K Y +      +  K+ +  +L K   K  +   +  V       +  + +HF +  
Sbjct: 158 NIIKTY-TFKSDFNEESKD-VELYLYKDEDKKRMAASFTKV-----PYSKLSKTHFYLES 210

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              +K+  L     +GR HQ+RV  + +G PI GD KY     G        +L LH   
Sbjct: 211 --NKKYATLS----SGRKHQIRVSLMKLGKPIYGDFKYGGKKAG--------RLMLHCLQ 256

Query: 295 MDLPHPEG 302
           +     EG
Sbjct: 257 IKFQQLEG 264


>gi|317472094|ref|ZP_07931426.1| RNA pseudouridylate synthase [Anaerostipes sp. 3_2_56FAA]
 gi|316900498|gb|EFV22480.1| RNA pseudouridylate synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 180

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 47/161 (29%), Positives = 74/161 (45%), Gaps = 7/161 (4%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+   G++V ART+ AA  L+   R    +K Y ++V G    +     ++LLK 
Sbjct: 1   MIHRLDRPVGGVMVFARTKEAAAELSRQIREHIFEKDYQAIVNGWLPEEDGVFTDYLLKD 60

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALHM 262
           +    +    V +  KGA  A   ++V+D       K  +  +   TGR HQ+RV     
Sbjct: 61  NK--KNTSCTVPEETKGAKKAELSYEVLDMVETGEGKLTYCLIHLMTGRHHQIRVQFAAR 118

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           G  + GD KY   F+   T     ++ L+A  +   HP  G
Sbjct: 119 GFGLYGDTKYNKKFQK--TKKQYEEIGLYATRISFRHPVTG 157


>gi|224373533|ref|YP_002607905.1| ribosomal pseudouridine synthase [Nautilia profundicola AmH]
 gi|223589983|gb|ACM93719.1| ribosomal pseudouridine synthase [Nautilia profundicola AmH]
          Length = 253

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 46/153 (30%), Positives = 71/153 (46%), Gaps = 20/153 (13%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HRLD+ETSG+L++ +     +   E F+ + + K Y + V GI     +      + 
Sbjct: 87  ELLHRLDKETSGVLILVKNDEFKKKAIEEFKKQNVYKEYITWVSGIVAEPMKIDLPIKVI 146

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           K+  G     + K ++ G + A++  + I  F  K   ++   HTGRTHQ+R H   +  
Sbjct: 147 KTKSGA----LAKISKDGED-AVTEIEPILAFRTK-SKVKAVIHTGRTHQIRAHLKAVEH 200

Query: 265 PIVGDHKYCAN--------------FKGNFTSP 283
           PI+GD KY                 F  NFTSP
Sbjct: 201 PILGDEKYGGEPFKRVMLHHHKFKIFDYNFTSP 233


>gi|218513991|ref|ZP_03510831.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli 8C-3]
          Length = 136

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 41/124 (33%), Positives = 62/124 (50%), Gaps = 16/124 (12%)

Query: 215 VVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           V + + + A+ AI+H++VI+ F +          +E +  TGRTHQ+RVH  H+G P++G
Sbjct: 11  VKRPDSQDADEAITHYEVIERFHETPDATALASLVECRLETGRTHQIRVHMAHIGHPLLG 70

Query: 269 DHKYCANF--KGNFTSPIQNKLY-------LHARYMDLPHPEGGRL-QITAPLPAHMVKT 318
           D  Y A F  K N       K+        LHA  +   HP  G L     PLP  M++ 
Sbjct: 71  DTVYGAGFRTKANLLPEDIRKVVNRFDRQALHAFMLQFEHPRSGELMHFEVPLPDDMMEL 130

Query: 319 WDSL 322
            ++L
Sbjct: 131 VEAL 134


>gi|75764363|ref|ZP_00743883.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|74488148|gb|EAO51844.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
          Length = 103

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/95 (38%), Positives = 54/95 (56%), Gaps = 8/95 (8%)

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +E G N A++HF+V++ F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY     G
Sbjct: 4   DENGKN-AVTHFQVLERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKY-----G 56

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              +   N   LHA  +   HP  G  +Q  AP+P
Sbjct: 57  PKKTLDMNGQALHAGILGFDHPRTGEYIQFEAPIP 91


>gi|148251982|ref|YP_001236567.1| putative RNA pseudouridine synthase [Bradyrhizobium sp. BTAi1]
 gi|146404155|gb|ABQ32661.1| putative RNA pseudouridine synthase (Uracil hydrolyase)
           [Bradyrhizobium sp. BTAi1]
          Length = 295

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/98 (35%), Positives = 51/98 (52%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  + V +KPAGI V  G     +++    +      + P L HRLD+ETSG LV+
Sbjct: 5   VLHRDGLMLVIDKPAGIPVHKGPKGGANLEASFDALRFGLPRPPVLAHRLDKETSGCLVL 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            R R A   L   F+  +I K YW++V G P   +  I
Sbjct: 65  GRHRKATASLGLLFKHGKISKTYWAVVEGGPDADEGVI 102



 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 36/83 (43%), Positives = 47/83 (56%), Gaps = 12/83 (14%)

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           + +  WL M+P TGRTHQLRVHA   G PIVGD+ Y     GN     + +L+LHAR + 
Sbjct: 209 SPRLTWLAMEPITGRTHQLRVHAASQGWPIVGDNIY-----GNGPRFGEPRLHLHAREIS 263

Query: 297 LP----HPEGGRLQITAPLPAHM 315
           +P     P    + + AP P HM
Sbjct: 264 IPLSKNKPP---VHVVAPAPMHM 283


>gi|328870665|gb|EGG19038.1| hypothetical protein DFA_02281 [Dictyostelium fasciculatum]
          Length = 579

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 51/182 (28%), Positives = 84/182 (46%), Gaps = 8/182 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETS 155
           L+  L+ E     V +KP  I V       ++   FL       G    L  HRLD+ TS
Sbjct: 214 LEPTLIAETLDYLVVDKPPSIPVHPAGPYRHNSLTFL--LARQFGYTNLLACHRLDRLTS 271

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVH 214
           G++V+A+   A+  L + F+   I KIY + V G+ P  ++  +A  ++  + I G  V 
Sbjct: 272 GVVVLAKNSTASGRLGKVFKKGDIDKIYLAKVKGMFPYLEETMVAKPIMVLNEITGLGVE 331

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             +       + ++H+      +  +C    +P TGR HQ+R+H   +G PI  D  Y  
Sbjct: 332 DARGKPSTTFFKLAHYNKESDTSIIWC----RPITGRGHQIRIHLKSIGFPITNDPLYND 387

Query: 275 NF 276
           +F
Sbjct: 388 DF 389


>gi|194206789|ref|XP_001501154.2| PREDICTED: similar to RPUSD2 protein [Equus caballus]
          Length = 559

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 98/220 (44%), Gaps = 44/220 (20%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGS 123
           + E+ + D S+ L K +DFL++               LL E+  + V +KP+ I V    
Sbjct: 203 LNEEPVQDLSIVL-KDNDFLRNTVHRHEPPVTAEPVRLLAENEDMVVVDKPSSIPVHPCG 261

Query: 124 GIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++   F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K
Sbjct: 262 RFRHNTVIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEK 318

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI--------SHFKV 232
            Y   V G  P  +  C    L+    +G     V + + +G              H  V
Sbjct: 319 EYVCRVEGEFPTEEVTCKEPILVVSYKVG-----VCRVDTRGKPCETVFQRLSYNGHSSV 373

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + C          +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 374 VRC----------RPLTGRTHQIRVHLQFLGHPILNDPIY 403


>gi|226952693|ref|ZP_03823157.1| 23S RNA-specific pseudouridylate synthase [Acinetobacter sp. ATCC
           27244]
 gi|226836561|gb|EEH68944.1| 23S RNA-specific pseudouridylate synthase [Acinetobacter sp. ATCC
           27244]
          Length = 302

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 90/202 (44%), Gaps = 37/202 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + V +KP  +++   G  +   +   LK     K   P   HRLD+ET+G+++
Sbjct: 94  ILFEDEHLLVVDKPHFLTMSPTGQYVQETLLVRLKKQTGYKELTP--IHRLDRETAGVVL 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLV-----WGIPKNKKECIANWL--------LKKS 206
             +  +A     + F  R++QKIY ++         P+  K  +   L        L+K 
Sbjct: 152 FCKKASARGIYQQLFAERKVQKIYHAIAVYRPELHFPQTVKLHLEKGLPFYTMQVNLEKP 211

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                ++ +++ N+  A Y                   ++P TG+ HQLRVH  ++G PI
Sbjct: 212 SNTETFIELLEHNKSHAKYL------------------LKPQTGKQHQLRVHLNYLGIPI 253

Query: 267 VGDHKY---CANFKGNFTSPIQ 285
           + D  Y         +F+SP+Q
Sbjct: 254 LNDEFYPDIAHKSSDDFSSPLQ 275


>gi|326569279|gb|EGE19340.1| putative pseudouridylate synthase [Moraxella catarrhalis BC7]
          Length = 298

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 50/190 (26%), Positives = 87/190 (45%), Gaps = 12/190 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           ++YED  + V +KP  ++V    G   ++   L + +      P L+  HRLD++T+G++
Sbjct: 86  IIYEDQTLLVVDKPHFLTVSPAGG---YVQQTLLTRLKQTTGNPHLSPAHRLDKQTAGLM 142

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +  +T  + +     F  R+I KIY ++      ++     +  L +      Y   V  
Sbjct: 143 IFTKTCESRRAYQSLFNDRQINKIYHAIAPMTQAHQFPLQVSLPLVRGE--PFYTMAVGI 200

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---N 275
            E   +  I    V +    K+   E++P TG+ HQLRVH  ++G PI  D  Y      
Sbjct: 201 GEPNTHTDIDILAVSE--DGKWAKYELKPTTGKLHQLRVHLNYLGIPIAHDSFYPKVMHR 258

Query: 276 FKGNFTSPIQ 285
            K +F  P+Q
Sbjct: 259 AKDDFDKPLQ 268


>gi|270007545|gb|EFA03993.1| hypothetical protein TcasGA2_TC014142 [Tribolium castaneum]
          Length = 552

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 51/173 (29%), Positives = 79/173 (45%), Gaps = 9/173 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++ D  + V +KP  + V       ++   F+ +  +   +  R  HRLD+ TSG+L+ 
Sbjct: 193 LIHVDEDLVVLDKPCSLPVHPCGRYRHNTVVFILAK-EYNLKNLRTIHRLDRLTSGLLLF 251

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            R+   A+ +    R R +QK Y   V G  P    EC     +    IG     V K +
Sbjct: 252 GRSPKKARQMEHQIRNRLVQKEYVCRVEGEFPDEIIECKEPIEVVSYKIG-----VCKVS 306

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            KG +      K+   F  K   +  +P TGR HQ+RVH  ++G P+V D  Y
Sbjct: 307 PKGKDCNTIFQKL--GFNGKTSIVLCKPKTGRMHQIRVHLQYLGYPVVNDPLY 357


>gi|296112286|ref|YP_003626224.1| pseudouridine synthase [Moraxella catarrhalis RH4]
 gi|295919980|gb|ADG60331.1| pseudouridine synthase [Moraxella catarrhalis RH4]
 gi|326561795|gb|EGE12130.1| putative pseudouridylate synthase [Moraxella catarrhalis 7169]
 gi|326562263|gb|EGE12589.1| putative pseudouridylate synthase [Moraxella catarrhalis 103P14B1]
 gi|326563232|gb|EGE13499.1| putative pseudouridylate synthase [Moraxella catarrhalis 46P47B1]
 gi|326564758|gb|EGE14971.1| putative pseudouridylate synthase [Moraxella catarrhalis 12P80B1]
 gi|326568979|gb|EGE19048.1| putative pseudouridylate synthase [Moraxella catarrhalis BC1]
 gi|326571956|gb|EGE21961.1| putative pseudouridylate synthase [Moraxella catarrhalis BC8]
 gi|326575466|gb|EGE25391.1| putative pseudouridylate synthase [Moraxella catarrhalis 101P30B1]
 gi|326576445|gb|EGE26353.1| putative pseudouridylate synthase [Moraxella catarrhalis CO72]
 gi|326577916|gb|EGE27780.1| putative pseudouridylate synthase [Moraxella catarrhalis O35E]
          Length = 298

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 50/190 (26%), Positives = 87/190 (45%), Gaps = 12/190 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           ++YED  + V +KP  ++V    G   ++   L + +      P L+  HRLD++T+G++
Sbjct: 86  IIYEDQTLLVVDKPHFLTVSPAGG---YVQQTLLTRLKQTTGNPHLSPAHRLDKQTAGLM 142

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +  +T  + +     F  R+I KIY ++      ++     +  L +      Y   V  
Sbjct: 143 IFTKTCESRRAYQSLFNDRQINKIYHAIAPMTQAHQFPLQVSLPLVRGE--PFYTMAVGI 200

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---N 275
            E   +  I    V +    K+   E++P TG+ HQLRVH  ++G PI  D  Y      
Sbjct: 201 GEPNTHTDIDILAVSE--DGKWAKYELKPTTGKLHQLRVHLNYLGIPIAHDSFYPKVMHR 258

Query: 276 FKGNFTSPIQ 285
            K +F  P+Q
Sbjct: 259 AKDDFDKPLQ 268


>gi|209529662|ref|NP_001129317.1| RNA pseudouridylate synthase domain-containing protein 2 [Rattus
           norvegicus]
 gi|149022995|gb|EDL79889.1| RNA pseudouridylate synthase domain containing 2 (predicted)
           [Rattus norvegicus]
          Length = 553

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 56/206 (27%), Positives = 100/206 (48%), Gaps = 14/206 (6%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  LN ++K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++ 
Sbjct: 207 VQDLNIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENDDVVVIDKPSSIPVHPCGRFRHNT 266

Query: 130 DGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V
Sbjct: 267 VIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSEKIHEQVRDRQLEKEYVCRV 323

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            G  P  +  C    L+    +G     V + + +G        ++   +  +   ++ +
Sbjct: 324 AGEFPDKEVICKEPILVVSYKVG-----VCRVDPQGKPCETVFQRL--SYNGRSSVVQCR 376

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
           P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 377 PLTGRTHQIRVHLQFLGHPILNDPIY 402


>gi|109730743|gb|AAI17829.1| RNA pseudouridylate synthase domain containing 2 [Mus musculus]
 gi|109734876|gb|AAI17828.1| RNA pseudouridylate synthase domain containing 2 [Mus musculus]
          Length = 553

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 102/218 (46%), Gaps = 40/218 (18%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGS 123
           + E+ + D S+ L K +DFL++               LL E++ + V +KP+ I V    
Sbjct: 202 LNEEPVQDLSIVL-KDNDFLRNTVHRHEPPVTAEPIRLLAENNDVVVIDKPSSIPVHPCG 260

Query: 124 GIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++   F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K
Sbjct: 261 RFRHNTVIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSEKIHEQVRDRQLEK 317

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y   V G  P  +  C    L+    +G     V + + +G        K  +   Q+ 
Sbjct: 318 EYVCRVAGEFPDKEVICKEPILVVSYKVG-----VCRVDPRG--------KPCETMFQRL 364

Query: 241 CW------LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +      ++ +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 365 SYNGRSSVVQCRPLTGRTHQIRVHLQFLGHPILNDPIY 402


>gi|224476102|ref|YP_002633708.1| putative pseudouridylate synthase [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222420709|emb|CAL27523.1| putative pseudouridylate synthase [Staphylococcus carnosus subsp.
           carnosus TM300]
          Length = 294

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 43/144 (29%), Positives = 77/144 (53%), Gaps = 13/144 (9%)

Query: 131 GFLKSWV-DSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           G+LK    D   Q  P +  RLD++TSGI++ A+      HL        ++K+Y  +  
Sbjct: 112 GYLKDQAADGNYQSIPHIVTRLDRDTSGIVLFAK----HGHLHHRMSSTEMKKVYHCICN 167

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  +N  + +A  +       GD + + ++ ++   YA + ++ I+  ++++   E++ H
Sbjct: 168 GKLENTSKIVAPIMR-----AGDSI-IERKVDQAGKYAATSYQPINA-SEQYTLCEVRLH 220

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGRTHQ+RVH  ++  PIVGD  Y
Sbjct: 221 TGRTHQIRVHFQYINHPIVGDGLY 244


>gi|257458049|ref|ZP_05623208.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
 gi|257444762|gb|EEV19846.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
          Length = 240

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 62/214 (28%), Positives = 101/214 (47%), Gaps = 26/214 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQ-GGSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQE 153
           +LYED  + V NKP+G+ SV   GS +    D  L+  + SKG      +P   HRLD++
Sbjct: 14  ILYEDPSLIVINKPSGLLSVPYQGSSVRTAAD-ILERIMRSKGAYSKHHRPFAVHRLDRD 72

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE-CIANWLLKKSHIGGDY 212
           TSG+++ A           S+     ++IY +    + +N  E  +A+  +  + +  + 
Sbjct: 73  TSGVMLFALNERTKDEFMRSWHTLVTERIYRA----VAENPAEGGLADSGIIDAPLAYNA 128

Query: 213 VH--VVKQNEKGANY----AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +   V   EK A++    A + +K+I+  A  +   E+   TG+ +Q+R H    G PI
Sbjct: 129 YNRAFVPTAEKHAHFDTVAARTRYKIIERGAA-YTLFELSLDTGKKNQIRAHLAANGYPI 187

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            GD    A      T P   +L LHAR +   HP
Sbjct: 188 AGDPIGHAR-----TDPF-GRLALHARSLAFTHP 215


>gi|68536479|ref|YP_251184.1| putative pseudouridylate synthase [Corynebacterium jeikeium K411]
 gi|68264078|emb|CAI37566.1| putative pseudouridylate synthase [Corynebacterium jeikeium K411]
          Length = 291

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/190 (28%), Positives = 80/190 (42%), Gaps = 26/190 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +LY  S   V +KP G+       +   +    +S +  + Q+P L   HRLD++T G+L
Sbjct: 61  VLYSGSDAVVVDKPHGLPSTPNGRL---LRATAQSLMRVRLQEPELVAAHRLDRDTRGLL 117

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW---LLKKSHIGGDYVHV 215
           V+AR       L   F+ R + K Y +L   IP    E  + W    L    I  D    
Sbjct: 118 VLARNPVTRGFLQTQFQRREVSKTYQALAADIP----EIGSQWQEAQLPMLKIKDDPQVK 173

Query: 216 VKQNEKGANYAISHFKVIDCFA-------------QKFCWLEMQPHTGRTHQLRVHALHM 262
           V   E+ +   ++  + +   A                   E+QP TG THQLRV   H+
Sbjct: 174 VVDGER-SRLTVTRIRKLASRAGMGVTPSEDTHAGTPTAVYELQPLTGYTHQLRVLMNHL 232

Query: 263 GCPIVGDHKY 272
           G PI GD  Y
Sbjct: 233 GAPIYGDDTY 242


>gi|311029802|ref|ZP_07707892.1| pseudouridine synthase, RluA family protein [Bacillus sp. m3-13]
          Length = 302

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/236 (25%), Positives = 104/236 (44%), Gaps = 33/236 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV-------QGGSGIA----YHIDGFLKSWVDSKGQKPRLTHR 149
           +++ED  + V NKPAG++         G    A    YH+ G   +          +  R
Sbjct: 84  IVFEDEYVLVVNKPAGMASIPSREHRHGTLANAVLGYYHLKGICATI--------HIVTR 135

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG++++A+ R A    +   +   +++ Y +LV G            +   + IG
Sbjct: 136 LDRDTSGLMLIAKHRHAHHLFSLQQKEFGVKRRYEALVHGEMTGDAGSACGKV--DAPIG 193

Query: 210 -GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TGRTHQLRVHALHMGCPI 266
             D   + ++       A++H++V+   A    W  +  H  TGRTHQ+RVH  H+G P+
Sbjct: 194 RKDSSIIEREVRSDGQRAVTHYEVLRVGAG---WSHVTLHLETGRTHQIRVHMAHLGHPL 250

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
           +GD  Y  +  G  +     +  LH+  +   HP E   +     LP  M +  + 
Sbjct: 251 LGDTLYGGSMFGGMS-----RQALHSCELRFFHPVEEQDMTFRCELPEDMKRVLEE 301


>gi|148695986|gb|EDL27933.1| RNA pseudouridylate synthase domain containing 2 [Mus musculus]
          Length = 553

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 102/218 (46%), Gaps = 40/218 (18%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGS 123
           + E+ + D S+ L K +DFL++               LL E++ + V +KP+ I V    
Sbjct: 202 LNEEPVQDLSIVL-KDNDFLRNTVHRHEPPVTAEPIHLLAENNDVVVIDKPSSIPVHPCG 260

Query: 124 GIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++   F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K
Sbjct: 261 RFRHNTVIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSEKIHEQVRDRQLEK 317

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y   V G  P  +  C    L+    +G     V + + +G        K  +   Q+ 
Sbjct: 318 EYVCRVAGEFPDKEVICKEPILVVSYKVG-----VCRVDPRG--------KPCETMFQRL 364

Query: 241 CW------LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +      ++ +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 365 SYNGRSSVVQCRPLTGRTHQIRVHLQFLGHPILNDPIY 402


>gi|114775713|ref|ZP_01451281.1| RNA pseudouridine synthase family protein [Mariprofundus
           ferrooxydans PV-1]
 gi|114553824|gb|EAU56205.1| RNA pseudouridine synthase family protein [Mariprofundus
           ferrooxydans PV-1]
          Length = 291

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/206 (26%), Positives = 95/206 (46%), Gaps = 29/206 (14%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRL 146
           F  + L+++   +Y+ +K +G   Q             +A H++        ++  + R 
Sbjct: 80  FTPAQLVWQQPPLYLIHKKSGQYAQEALHRSRGTLPDELARHLE-----LTPAQASELRP 134

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG+++ + + A  QHL   +    ++K Y ++V   P    + I   + +  
Sbjct: 135 VHRLDRDTSGLMLFSASAAMLQHLQAHWH-DAVEKRYLAVVSPAPDWDDQRIRLAIDRNR 193

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              G Y H+            S   V++    +   +E+ PHTGR+HQLRVH   +GCPI
Sbjct: 194 DAHGRY-HL----SPDGRACDSEAHVVERRDNR-ALVELVPHTGRSHQLRVHLSALGCPI 247

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHA 292
           +GD +Y     G    P   +L LHA
Sbjct: 248 LGDSRY-----GGKPHP---RLMLHA 265


>gi|256079649|ref|XP_002576098.1| ribosomal pseudouridine synthase [Schistosoma mansoni]
 gi|238661358|emb|CAZ32333.1| ribosomal pseudouridine synthase, putative [Schistosoma mansoni]
          Length = 455

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/190 (28%), Positives = 81/190 (42%), Gaps = 25/190 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
            +++   I V NKP  I +       Y ++          G +P R THRLD+ TSG+L+
Sbjct: 151 FVHDSDDILVVNKPPSIPIHPCG--QYTLNSITHILAKDYGLRPLRFTHRLDRMTSGLLL 208

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KEC----IANWLLKKSHIGGDY- 212
           +A+    +  L      + + K Y   V G    +   +C    I N ++  S   G   
Sbjct: 209 IAKNYDTSVRLQSQISSKEVAKYYICHVEGCFPTEPIDQCTGFEINNGVVVCSQPVGPIS 268

Query: 213 ----VHVVKQNEKGANYAISHF------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
               VH V     G  +A +HF       V D  +   C L     TGRTHQ+R+H  ++
Sbjct: 269 RRMGVHGVLPESAGGKFARTHFLRLSYNPVTDT-SLVICRL----FTGRTHQIRIHVQYL 323

Query: 263 GCPIVGDHKY 272
           G PIV D  Y
Sbjct: 324 GYPIVDDPLY 333


>gi|149196356|ref|ZP_01873411.1| ribosomal large subunit pseudouridine synthase C [Lentisphaera
           araneosa HTCC2155]
 gi|149140617|gb|EDM29015.1| ribosomal large subunit pseudouridine synthase C [Lentisphaera
           araneosa HTCC2155]
          Length = 328

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 65/265 (24%), Positives = 110/265 (41%), Gaps = 22/265 (8%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +   N I+K   ++   V      D  +   ++YED  I +  K   + V      ++  
Sbjct: 64  VEDYNAILKAGDVISLDVTKIPEPDIDRDFKVVYEDDDILMVEKTGDLPVHPAG--SFFK 121

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +      V   G    + +RLD+ETSG++++AR   AA  L + F  R++ K Y  LV G
Sbjct: 122 NTLWYMLVKQFGN-VHIMNRLDRETSGLVLIARHHKAASVLGKQFERRQVGKEYDVLVEG 180

Query: 190 IPKNKKECIANWL--LKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEM 245
           +    +     ++     S I   +     ++  + G + A + F V+   + +   L  
Sbjct: 181 LVSWDQYDALGYMGPAVSSKIRKKFSFTEAEDWQDYGKHSARTEFSVLRR-SHELSHLHC 239

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQNKL-----YLHAR 293
           + HTGRTHQ+R   L +G P+VGD  Y  +         G  T     K+      LH  
Sbjct: 240 RLHTGRTHQIRATLLSLGFPLVGDKIYGLDEQFFLSFIDGALTEQDYQKMRLRRQALHCS 299

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVK 317
            M   HP  G  +   + LP  + +
Sbjct: 300 LMSFTHPMSGEDVVFESSLPKELAE 324


>gi|121594845|ref|YP_986741.1| tRNA pseudouridine synthase C [Acidovorax sp. JS42]
 gi|120606925|gb|ABM42665.1| tRNA pseudouridine synthase C [Acidovorax sp. JS42]
          Length = 268

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 100/218 (45%), Gaps = 24/218 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL++D+ +    KPAG  V      A      +++  D  GQ     HRLD+ T G+LV+
Sbjct: 10  LLWQDAHMVAVFKPAGWLVHRTGLDAGETRFVMQALRDQIGQHVYPVHRLDKGTCGVLVM 69

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A   AAA+ L ++F    ++K Y +LV G    + E   +  L+      D      Q  
Sbjct: 70  ALHPAAARALADAFARHAVRKQYLALVRGWAPAQAEV--DHPLRPDDAPPD---APTQPA 124

Query: 221 KGANYAISHFKVIDCFAQKFC-----WLEMQPHTGRTHQLRVHALHMGCPIVGD------ 269
                 ++  ++ +C   +F       +  +P TGR HQ+R H  H+  PI+GD      
Sbjct: 125 HTRLTRLARLELPECSDPRFATTRASLVRAEPTTGRRHQIRRHLKHLAHPILGDATHGKG 184

Query: 270 --HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
             +++ A   G       ++L+LHA  + LPHP  GRL
Sbjct: 185 PLNRWWAQRLG------LHRLWLHAWQLSLPHPADGRL 216


>gi|82617847|gb|ABB84841.1| RNA pseudouridylate synthase [uncultured delta proteobacterium
           DeepAnt-32C6]
          Length = 197

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 90/201 (44%), Gaps = 36/201 (17%)

Query: 133 LKSWV----DSKGQKPRLTHRLDQETSGILVVA---RTRAAAQH-LTESFRMRRIQKIYW 184
           L +W     D+ G  P   HR+D+ TSG+L+ +   R RA   H L +     ++ K Y 
Sbjct: 16  LMTWARTHFDAPGLAP--AHRIDKATSGLLLCSPDPRVRARVGHWLAQG----QVHKEYR 69

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQKFCWL 243
           +LV+G                +H  G     +    +G    A + F+ +   A +  +L
Sbjct: 70  ALVFG---------------HTHRSGRIDRPLMDRRRGRRLDACTRFRRL-ATASQLSYL 113

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            + P TGR HQ+R H   +G  IVGD +Y    +         +L+LH R ++L  PEG 
Sbjct: 114 AVYPETGRKHQIRRHLRGLGHAIVGDTRYGPTHQRPLPG-CPGRLWLHLRQLEL--PEG- 169

Query: 304 RLQITAPLPAHMVKTWDSLGF 324
            L   APLP  +V   + LG 
Sbjct: 170 -LTFEAPLPPALVAHLERLGI 189


>gi|126278380|ref|XP_001381115.1| PREDICTED: similar to RPUSD2 protein [Monodelphis domestica]
          Length = 503

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 60/220 (27%), Positives = 97/220 (44%), Gaps = 44/220 (20%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGS 123
           + EQ + D  V L K +DFL++               LL E+  + V +KP+ + V    
Sbjct: 150 LNEQPVRDLGVIL-KDNDFLRNTVHRHEPPVTAEPIHLLAENDDVVVVDKPSSMPVHPCG 208

Query: 124 GIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++   F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K
Sbjct: 209 RFRHNTVIFV---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEK 265

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI--------SHFKV 232
            Y   V G  P  +  C    L+    +G     + + + +G              H  V
Sbjct: 266 EYVCRVEGEFPSEEVTCKEPILVVSYKVG-----LCRVDPRGKPCETVFQRLSYNGHSSV 320

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + C          +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 321 VRC----------RPLTGRTHQIRVHLQFLGHPIINDPIY 350


>gi|330824854|ref|YP_004388157.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
 gi|329310226|gb|AEB84641.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
          Length = 256

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 58/214 (27%), Positives = 90/214 (42%), Gaps = 16/214 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL++D  +    KPAG  V      A      +++  D  G+     HRLD+ T G+LV+
Sbjct: 11  LLWQDEHMVALYKPAGWLVHRTGLDAGETRFVVQALRDQIGRHVYPVHRLDKGTCGVLVM 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
               AAA+ L  SF    + K Y +LV  W  P    +      L+      D      Q
Sbjct: 71  GLHPAAARALAGSFARHAVHKRYLALVRGWAPPLADVDHP----LRPDDAPQD---APAQ 123

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEM-----QPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                   ++  ++ +    +F          +P TGR HQ+R H  H   PI+GD  + 
Sbjct: 124 PAHTLLTRLARLELPESSDPRFATTRASLVLAEPTTGRRHQIRRHLKHAAHPILGDATHG 183

Query: 274 ANFKGNFTSPIQN--KLYLHARYMDLPHPEGGRL 305
                 + +      +L+LHA  + LPHP+ GR+
Sbjct: 184 KGPLNRWWAERLGLQRLWLHAWRLRLPHPQDGRM 217


>gi|242309086|ref|ZP_04808241.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pullorum MIT 98-5489]
 gi|239524510|gb|EEQ64376.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pullorum MIT 98-5489]
          Length = 257

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 57/199 (28%), Positives = 99/199 (49%), Gaps = 32/199 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  I   +KPA ++ +        I     +W         L HRLD+ETSGIL++
Sbjct: 73  ILFQDDNILALSKPAFLTSE-------EIAKLYPNWA--------LLHRLDKETSGILLL 117

Query: 161 ARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            +  +   HL   E+F+  ++ K Y ++V GI + ++E  A  +++K    G++  V+  
Sbjct: 118 IKENSPF-HLKAKEAFKKEQVFKQYIAIVEGIIEEEQEITAPLIIQK----GNFAKVLVS 172

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            ++G   A +    I+   +K   LE+   TG+THQ+R H  H+  PI+GD  Y      
Sbjct: 173 KKEGIR-AYTKITPIEIIGKK-TKLEIIIKTGKTHQIRAHLAHIKHPIIGDTFYGGK--- 227

Query: 279 NFTSPIQNKLYLHARYMDL 297
                  N++ LHA+ + L
Sbjct: 228 -----PANRILLHAQKISL 241


>gi|223042701|ref|ZP_03612749.1| pseudouridylate synthase, 23S RNA-specific [Staphylococcus capitis
           SK14]
 gi|222443555|gb|EEE49652.1| pseudouridylate synthase, 23S RNA-specific [Staphylococcus capitis
           SK14]
          Length = 284

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 58/217 (26%), Positives = 98/217 (45%), Gaps = 36/217 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-----IDGFLKSWVDSKGQ-KPRLTHRLDQET 154
           ++YED  I + NKP    +Q  +    H     ++  L   ++   Q  P +  RLD+ T
Sbjct: 77  IVYEDEFILIVNKP---QLQNCAPSREHPHESLVEQVLAYLMNKDEQTNPHIVTRLDRNT 133

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+      H+   F   + +K Y  L +G  + + E +    + +     + + 
Sbjct: 134 SGLVLFAK----FGHIHHLFSKVKFEKEYICLAYG--RTQSEGVIEAPIARD---NESII 184

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-- 272
             K ++KG     S++ +        C +++  HTGRTHQ+RVH   MG PIVGD  Y  
Sbjct: 185 TRKVSDKGKYAKTSYYTIAQNNNLSLCKVKL--HTGRTHQIRVHFQFMGHPIVGDDLYGG 242

Query: 273 -----------CANFKGNFTSPIQ-NKLYLHARYMDL 297
                      C + K  F  PI+ NK+ ++  Y  L
Sbjct: 243 IHPLVKGQSLQCCSLK--FVHPIKHNKITINVDYKQL 277


>gi|326480203|gb|EGE04213.1| DRAP deaminase [Trichophyton equinum CBS 127.97]
          Length = 517

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 66/264 (25%), Positives = 109/264 (41%), Gaps = 55/264 (20%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS- 99
           +  G++ +D K    ++ I +GQV+                     S  L +H   + S 
Sbjct: 83  IDGGRITIDGKVATADSIINNGQVI---------------------SHTLHRHEPPVTSR 121

Query: 100 --ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETS 155
              +++ED  I V +KPAGI V       Y+ +  ++     +G    P   +RLD+ TS
Sbjct: 122 PIKIIHEDEDIIVIDKPAGIPVHPAG--RYNYNSIIEIMRSERGLGWIPYPCNRLDRLTS 179

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI------- 208
           GI+ + +   +A+ + +S R R ++K Y + V G   +        +LK S I       
Sbjct: 180 GIMFLGKHPKSAEQMAQSLRSRTLRKEYIARVKGYFPDGVVLCDQPMLKVSPILGLNRVR 239

Query: 209 --GGD----------YVHVVKQNEKGA--------NYAISHFKVIDCFAQKFCWLEMQPH 248
             G D          Y  V K+N+ G         + A +   +     + +  +   P 
Sbjct: 240 ATGKDAQTKFRRIAYYPPVEKENKNGETTGSQGPDSRASTPPPLPADVDEGYSIVHCLPL 299

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGRTHQ+RVH   +G PI  D  Y
Sbjct: 300 TGRTHQIRVHLQFLGHPITNDPIY 323


>gi|27734094|ref|NP_775626.1| RNA pseudouridylate synthase domain-containing protein 2 [Mus
           musculus]
 gi|158564131|sp|Q149F1|RUSD2_MOUSE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 2
 gi|26336789|dbj|BAC32077.1| unnamed protein product [Mus musculus]
 gi|126540740|emb|CAM45958.1| RNA pseudouridylate synthase domain containing 2 [Mus musculus]
          Length = 553

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 101/212 (47%), Gaps = 28/212 (13%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGS 123
           + E+ + D S+ L K +DFL++               LL E++ + V +KP+ I V    
Sbjct: 202 LNEEPVQDLSIVL-KDNDFLRNTVHRHEPPVTAEPIHLLAENNDVVVIDKPSSIPVHPCG 260

Query: 124 GIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++   F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K
Sbjct: 261 RFRHNTVIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSEKIHEQVRDRQLEK 317

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y   V G  P  +  C    L+    +G     V + + +G        ++   +  + 
Sbjct: 318 EYVCRVAGEFPDKEVICKEPILVVSYKVG-----VCRVDPRGKPCETVFQRL--SYNGRS 370

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             ++ +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 371 SVVQCRPLTGRTHQIRVHLQFLGHPILNDPIY 402


>gi|297479512|ref|XP_002690866.1| PREDICTED: RNA pseudouridylate synthase domain containing 2 [Bos
           taurus]
 gi|296483299|gb|DAA25414.1| RNA pseudouridylate synthase domain containing 2 [Bos taurus]
          Length = 518

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/215 (28%), Positives = 98/215 (45%), Gaps = 34/215 (15%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGS 123
           + E+ + D S+ L K +DFL++               LL E+  + V +KP+ I V    
Sbjct: 162 LNEEPVQDLSIVL-KDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCG 220

Query: 124 GIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++   F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K
Sbjct: 221 RFRHNTVIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEK 277

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS---HFKVIDCFA 237
            Y   V G  P  +  C    L+    +G   V    +  +     +S   H  V+ C  
Sbjct: 278 EYVCRVVGEFPTEEVTCKEPILVVSYKVGVCRVDPQGKPCESVFQRLSYNGHSSVVRC-- 335

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                   +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 336 --------RPLTGRTHQIRVHLQFLGHPILNDPIY 362


>gi|302497041|ref|XP_003010521.1| hypothetical protein ARB_03222 [Arthroderma benhamiae CBS 112371]
 gi|291174064|gb|EFE29881.1| hypothetical protein ARB_03222 [Arthroderma benhamiae CBS 112371]
          Length = 482

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 69/269 (25%), Positives = 112/269 (41%), Gaps = 56/269 (20%)

Query: 37  LQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           LQK  +  G++ +D K    ++ I +GQV+                     S  L +H  
Sbjct: 43  LQKAAIDGGRITIDGKVATADSIINNGQVI---------------------SHTLHRHEP 81

Query: 96  FLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRL 150
            + S    +++ED  I V +KPAGI V       Y+ +  ++     +G    P   +RL
Sbjct: 82  PVTSRPIKIIHEDEDIIVIDKPAGIPVHPAG--RYNYNSIIEIMRSERGLGWIPYPCNRL 139

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI-- 208
           D+ TSGI+ + +   AA+ + +S R R ++K Y + V G   +        +LK S I  
Sbjct: 140 DRLTSGIMFLGKHPKAAEQMAQSLRSRTLRKEYIARVKGYFPDGVVLCDQPMLKVSPILG 199

Query: 209 -------GGD----------YVHVVKQNEKGA--------NYAISHFKVIDCFAQKFCWL 243
                  G D          Y  V K+++ G         + A +   +     + +  +
Sbjct: 200 LNRVRATGKDAQTKFRRIAYYPPVEKEDKNGEATGTQGPDSRASTPPPLPADVDEGYSIV 259

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              P TGRTHQ+RVH   +G PI  D  Y
Sbjct: 260 HCLPLTGRTHQIRVHLQFLGHPITNDPIY 288


>gi|269798210|ref|YP_003312110.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269094839|gb|ACZ24830.1| pseudouridine synthase, RluA family [Veillonella parvula DSM 2008]
          Length = 324

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 103/244 (42%), Gaps = 35/244 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQKP-RLTHRLDQETSGI 157
           ++YED  I V NK AGI +   S I  H   +G L  + ++         HRLD++TSGI
Sbjct: 81  IIYEDEYILVINKAAGILMHPTSTIRDHTLANGVLHYYQETNQHYDFHPVHRLDKDTSGI 140

Query: 158 LVVARTRAAAQ-------HLTESFRM---RRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +++A+T            H  +S+       +  +  S+ W I +     I      +  
Sbjct: 141 VIIAKTSVVQHAFDKKHTHFYKSYDAIVEGHLPSVPISINWPIGRKPGSIIERCCTVQGK 200

Query: 208 IGGDYVHVVKQN-EKGANYAISHFKVID-------CFA-------QKFCWLEMQPHTGRT 252
                + ++ +N  K ++  I+   VI        C          +F  ++   HTGRT
Sbjct: 201 PARTDITIISKNTSKISSGKINSDDVITLNNNSNICSTDSSLTSYSQFTHVKCLLHTGRT 260

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           HQ+RVH   +G P+ GD  Y     G     IQ +  LHA  +   HP     L++ A +
Sbjct: 261 HQIRVHLSQLGYPLAGDDLY-----GGHLESIQRQA-LHAARVSFYHPITNEWLELHAEM 314

Query: 312 PAHM 315
           P  M
Sbjct: 315 PEDM 318


>gi|253582659|ref|ZP_04859880.1| pseudouridylate synthase [Fusobacterium varium ATCC 27725]
 gi|251835529|gb|EES64069.1| pseudouridylate synthase [Fusobacterium varium ATCC 27725]
          Length = 289

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 43/134 (32%), Positives = 62/134 (46%), Gaps = 7/134 (5%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           PR  +RLD  TSG+++VA+   A   L E      + K Y ++V GI +  +  I   + 
Sbjct: 123 PRFYNRLDMNTSGLIIVAKNSYAQSFLQEKGI---VNKFYKAIVKGIIEKDEFLIDKPIG 179

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           K   +G D        E G   A +  KVI    +    +E +  TGRTHQ+R H    G
Sbjct: 180 K---VGDDLRRREISVENGGQEAQTKIKVIKRL-KDLTLIEAELLTGRTHQIRAHMALEG 235

Query: 264 CPIVGDHKYCANFK 277
            P++GD  Y    K
Sbjct: 236 YPLLGDELYGGEDK 249


>gi|227877169|ref|ZP_03995243.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus crispatus
           JV-V01]
 gi|227863223|gb|EEJ70668.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus crispatus
           JV-V01]
          Length = 304

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 113/245 (46%), Gaps = 30/245 (12%)

Query: 92  KHSDFLK------SILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQK- 143
           K +DFLK      SI+L E+    V NKPAG+ S+         +   L  +   KGQK 
Sbjct: 71  KKNDFLKPSNNPVSIVL-ENKNYLVVNKPAGVLSIPSRYEDDDAVVNRLLGYFAQKGQKN 129

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIA 199
             P +  RLD++TSG+++V +   +    ++  + + ++K Y ++V G   P      I 
Sbjct: 130 LKPHVITRLDRDTSGLVLVGKNAISHARFSKIGKEKFVKK-YHAIVHGNFAPNELTGLID 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + KK   G      V  + K A  A   ++V+D        +E++  TGRTHQ+RVH 
Sbjct: 189 QPIGKK---GSGVKRAVVADGKDAQTA---YRVLDQVTGA-SLVELRLLTGRTHQIRVHM 241

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL--PAHMVK 317
            ++G P+ GD  Y    +  F+     +  L+  Y++ P P   +   T  L  P  M +
Sbjct: 242 AYLGHPLYGDPLY--GIQDGFS-----RQALNCFYLNFPDPFSQQKCKTIELNDPKDMQE 294

Query: 318 TWDSL 322
            W  L
Sbjct: 295 LWQKL 299


>gi|256848967|ref|ZP_05554401.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus MV-1A-US]
 gi|295692522|ref|YP_003601132.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|312977754|ref|ZP_07789501.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus CTV-05]
 gi|256714506|gb|EEU29493.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus MV-1A-US]
 gi|295030628|emb|CBL50107.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|310895493|gb|EFQ44560.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus CTV-05]
          Length = 301

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 113/245 (46%), Gaps = 30/245 (12%)

Query: 92  KHSDFLK------SILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQK- 143
           K +DFLK      SI+L E+    V NKPAG+ S+         +   L  +   KGQK 
Sbjct: 68  KKNDFLKPSNNPVSIVL-ENKNYLVVNKPAGVLSIPSRYEDDDAVVNRLLGYFAQKGQKN 126

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIA 199
             P +  RLD++TSG+++V +   +    ++  + + ++K Y ++V G   P      I 
Sbjct: 127 LKPHVITRLDRDTSGLVLVGKNAISHARFSKIGKEKFVKK-YHAIVHGNFAPNELTGLID 185

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + KK   G      V  + K A  A   ++V+D        +E++  TGRTHQ+RVH 
Sbjct: 186 QPIGKK---GSGVKRAVVADGKDAQTA---YRVLDQVTGA-SLVELRLLTGRTHQIRVHM 238

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL--PAHMVK 317
            ++G P+ GD  Y    +  F+     +  L+  Y++ P P   +   T  L  P  M +
Sbjct: 239 AYLGHPLYGDPLY--GIQDGFS-----RQALNCFYLNFPDPFSQQKCKTIELNDPKDMQE 291

Query: 318 TWDSL 322
            W  L
Sbjct: 292 LWQKL 296


>gi|332971512|gb|EGK10462.1| RNA pseudouridine synthase [Kingella kingae ATCC 23330]
          Length = 305

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 39/128 (30%), Positives = 71/128 (55%), Gaps = 12/128 (9%)

Query: 148 HRLDQETSGILVVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           HRLD++T+G+++++   +TRAA Q L   F+ + IQK Y +L       + +      ++
Sbjct: 146 HRLDKDTAGVMLLSHNPQTRAAYQQL---FQQKVIQKTYHALA----PTRLDLAYPLTVQ 198

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              + GD   + KQ +   N + +  ++++    K    E++P TG+ HQLRVH +H+G 
Sbjct: 199 SRLVRGDSFFLTKQIDGEPN-SQTEIRLLEQRG-KHSLYELRPITGKKHQLRVHMMHLGM 256

Query: 265 PIVGDHKY 272
           P++ D  Y
Sbjct: 257 PLLNDALY 264


>gi|32266140|ref|NP_860172.1| ribosomal pseudouridine synthase [Helicobacter hepaticus ATCC
           51449]
 gi|32262190|gb|AAP77238.1| ribosomal pseudouridine synthase [Helicobacter hepaticus ATCC
           51449]
          Length = 245

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 98/220 (44%), Gaps = 37/220 (16%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +L+ D  I    KP  I        +Y +    + W         L HRLD+ETSG+
Sbjct: 57  KPKVLFTDEHILALEKPPFIE-------SYDLSNMFEGW--------HLLHRLDRETSGV 101

Query: 158 LVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ +   +A H+   E+F+ + + K Y  LV GI  +  E   N  +  +  G     +
Sbjct: 102 ILLIK-EGSAFHIKAKEAFKNQEVYKEYVCLVHGILADSIEI--NKAISTTKRGFAKSRI 158

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              ++KG N A++    +    +K   L+    TGRTHQ+RVH   +  PI+GD  Y  N
Sbjct: 159 ---DKKGLN-ALTLLTPLSIMGKK-TLLKALIKTGRTHQIRVHCQSINHPILGDRIYGKN 213

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
            +         +L LHA  + L   E      T+PLP  +
Sbjct: 214 DEA-------KRLMLHAHKIALLGYE-----FTSPLPKEL 241


>gi|218659525|ref|ZP_03515455.1| pseudouridine synthase, RluA family protein [Rhizobium etli IE4771]
          Length = 45

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/35 (62%), Positives = 31/35 (88%)

Query: 290 LHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           +HAR++D+PHP GGRL+++APLP HMV+TW+ LG 
Sbjct: 1   MHARHIDIPHPSGGRLRVSAPLPPHMVQTWNLLGL 35


>gi|120555026|ref|YP_959377.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120324875|gb|ABM19190.1| tRNA pseudouridine synthase C [Marinobacter aquaeolei VT8]
          Length = 245

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 96/219 (43%), Gaps = 33/219 (15%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS--KGQKPRLTHRLDQETSGILV 159
           +Y D  +   +KPAG+ V   S I  H   F   +  +   G+     HRLD+ TSG+L+
Sbjct: 8   IYRDDWLLAVHKPAGLLVHR-SPIDKHETEFALQYARAMNGGEHVYPVHRLDRPTSGVLL 66

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            AR    A+ L  +     + K Y ++V G     ++ + +  L++          +K  
Sbjct: 67  FARDPETARALGLAMMAGAVSKTYLAMVRGW--APEQGVIDHPLREE----PEDRRLKGQ 120

Query: 220 EKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           E+    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD
Sbjct: 121 EQPVREALTRYRRLATTELPVAIERYPTSRYSLVELKPETGRKHQLRRHMKHINHPIIGD 180

Query: 270 --------HKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
                   ++Y A   G      Q +L L A  + L HP
Sbjct: 181 ANHGRGRHNRYFAERFG------QGRLMLAATELRLRHP 213


>gi|297819936|ref|XP_002877851.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297323689|gb|EFH54110.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 387

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 99/241 (41%), Gaps = 30/241 (12%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAG 116
           RIQ+GQ+     V+   N +++    L       K  D   S+ +LYED  +   NKP+G
Sbjct: 58  RIQNGQIQIDGEVVKDPNTLLRSGSKLVYHRLPWKEPDTPYSLQVLYEDDDLIALNKPSG 117

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAA 167
           + V  G             W   K            P   HRL + TSGIL+ A+T+ A 
Sbjct: 118 LQVLPGGLFQQRTVLTQLQWCFRKNDSYTGSRESPHPVPVHRLGRGTSGILLCAKTKLAK 177

Query: 168 QHLTESF-----------------RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
             L   F                 + R++ KIY +L  GI +  +  I   L    + G 
Sbjct: 178 TKLAAYFAEGTSLVGSGNLEQECGKGRKLSKIYRALADGIVEEDEVVIKQPLGVVRYPGV 237

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGD 269
                V   E     A S   V++   QK C L +++  +GR HQ+R+H  +MG P++  
Sbjct: 238 AKGLYVASPE--GKPAFSKVAVLERDKQKNCTLVKVEIQSGRPHQIRIHLAYMGHPLLAS 295

Query: 270 H 270
           +
Sbjct: 296 Y 296


>gi|320197496|gb|EFW72110.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           WV_060327]
          Length = 132

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/93 (39%), Positives = 53/93 (56%), Gaps = 4/93 (4%)

Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  I V NKP+G+ SV G   +  H D  + + +     +    HRLD  TSG++
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           VVA T+AA + L   FR R  +K Y + VWG P
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHP 104


>gi|268319849|ref|YP_003293505.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
 gi|262398224|emb|CAX67238.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
          Length = 299

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 86/180 (47%), Gaps = 12/180 (6%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           KP +  RLD++TSG+++V +   A    ++  +   I+K Y ++V G   N +E      
Sbjct: 127 KPHVITRLDRDTSGLVLVGKNAVAHARFSKMEKNEFIKK-YHAIVHG---NFEEAQRQGT 182

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           +  + IG     V +        +++ ++V+D   +    +E+Q  TGRTHQ+RVH  ++
Sbjct: 183 ID-APIGKIDTGVKRGVVNNGQRSVTKYRVLDQ-VKGASLIELQLLTGRTHQIRVHMQYL 240

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G P+ GD  Y    K NF     N  YL     D P  E  R +I    P  M + W +L
Sbjct: 241 GHPLFGDPLY--GIKDNFKRQALNCFYLE---FDDPFSE-KRQKIEIADPIDMKRLWKNL 294


>gi|212715527|ref|ZP_03323655.1| hypothetical protein BIFCAT_00425 [Bifidobacterium catenulatum DSM
           16992]
 gi|212660894|gb|EEB21469.1| hypothetical protein BIFCAT_00425 [Bifidobacterium catenulatum DSM
           16992]
          Length = 312

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 47/159 (29%), Positives = 79/159 (49%), Gaps = 15/159 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD  TSG+++V ++  A   +   F    + K Y +LV G  +  K  I      +
Sbjct: 130 IVSRLDVGTSGLMLVCKSDLAYVEMRRQFAEHEVVKTYHALVQGNLRENKATI------E 183

Query: 206 SHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + IG     D+   V    K    A++H+ V++ F +    + +   TGRTHQ+RVH   
Sbjct: 184 APIGRAKVSDFRFCVTPAGK---EAVTHWDVMERFGEA-TLVSVNLETGRTHQIRVHFSS 239

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +G P+ GD  Y AN + + T  ++ + +LHA  ++  HP
Sbjct: 240 IGHPLAGDAMYGANPQLSETLGLERQ-WLHAMQLEFRHP 277


>gi|227499607|ref|ZP_03929714.1| possible pseudouridylate synthase [Anaerococcus tetradius ATCC
           35098]
 gi|227218366|gb|EEI83620.1| possible pseudouridylate synthase [Anaerococcus tetradius ATCC
           35098]
          Length = 280

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 47/177 (26%), Positives = 84/177 (47%), Gaps = 12/177 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGIL 158
           +L+ED+   V +K + ++V   + +  ++  +L  +        K RL +RLD  TSG++
Sbjct: 75  VLFEDANSLVVSKTSNLTVNSKNQV--NLSNYLAYYFKENDIRNKIRLVNRLDMNTSGLM 132

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+ + A  +         I+K Y ++V   P    +     LL ++ I  D  +    
Sbjct: 133 LVAKNKYAHAYYQRQVENNLIKKKYLAVVD--PNTDLD-----LLYEARISYDEENKKYI 185

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  A ++FK ID     +  +E +  TG+THQ+RV    +G PI GD  Y ++
Sbjct: 186 ASNNGKLARTYFKTIDK-NDSYSLIECEIFTGKTHQIRVSLQSLGHPIYGDKLYGSD 241


>gi|320168624|gb|EFW45523.1| RNA pseudouridylate synthase domain-containing protein 2
           [Capsaspora owczarzaki ATCC 30864]
          Length = 515

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 105/231 (45%), Gaps = 33/231 (14%)

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVF 111
           F+  I+ G+V     V+ A ++II++  +L  + +  +H   + +    ++ E   + V 
Sbjct: 143 FDQAIRDGRVTVNGKVV-APSYIIQDSDVLVHTAH--RHEPPVTAAPIRVIAETDDLVVI 199

Query: 112 NKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRL-THRLDQETSGILVVARTRAAAQH 169
           +KPA I V        H +   +KS +   G    L  HRLD+ TSG+LV+A+ RAAA  
Sbjct: 200 DKPASIPVHVAGRFNVHTVISIMKSEM---GYSNLLGCHRLDRLTSGVLVMAKNRAAAAA 256

Query: 170 LTESFRMRRIQKIYWSLVWGI-PKNKKECIANWL-------LKKSHIGGDYVHVVKQNEK 221
           +T     R ++K Y   V G+ P+ +  C    L       L      G     V   E+
Sbjct: 257 VTRLITEREVEKFYICRVTGVFPQEQVTCTEPLLSFCPKFGLNGVDPSGKPAETVFVREQ 316

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             N  IS   ++ CF          P TGR HQ+RVH  ++G PI  D  Y
Sbjct: 317 -TNGVIS---IVKCF----------PKTGRAHQIRVHLQYLGYPIENDPIY 353


>gi|302663414|ref|XP_003023349.1| hypothetical protein TRV_02451 [Trichophyton verrucosum HKI 0517]
 gi|291187343|gb|EFE42731.1| hypothetical protein TRV_02451 [Trichophyton verrucosum HKI 0517]
          Length = 517

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 66/264 (25%), Positives = 109/264 (41%), Gaps = 55/264 (20%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS- 99
           +  G++ +D K    ++ I +GQV+                     S  L +H   + S 
Sbjct: 83  IDGGRITIDGKVATADSIINNGQVI---------------------SHTLHRHEPPVTSR 121

Query: 100 --ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETS 155
              +++ED  I V +KPAGI V       Y+ +  ++     +G    P   +RLD+ TS
Sbjct: 122 PIKIIHEDEDIIVIDKPAGIPVHPAG--RYNYNSIIEIMRSERGLGWIPYPCNRLDRLTS 179

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI------- 208
           GI+ + +   AA+ + +S R R ++K Y + V G   +        +LK S I       
Sbjct: 180 GIMFLGKHPKAAEQMAQSLRSRTLRKEYIARVKGYFPDGVVLCDQPMLKVSPILGLNRVR 239

Query: 209 --GGD----------YVHVVKQNEKGA--------NYAISHFKVIDCFAQKFCWLEMQPH 248
             G D          Y  V K+++ G         + A +   +     + +  +   P 
Sbjct: 240 ATGKDAQTKFRRIAYYPPVEKEDKNGEATGSQGPDSRASTPPPLPADVDEGYSIVHCLPL 299

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGRTHQ+RVH   +G PI  D  Y
Sbjct: 300 TGRTHQIRVHLQFLGHPITNDPIY 323


>gi|111017875|ref|YP_700847.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
 gi|110817405|gb|ABG92689.1| possible pseudouridylate synthase [Rhodococcus jostii RHA1]
          Length = 297

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/211 (26%), Positives = 100/211 (47%), Gaps = 18/211 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  + ++  G+ I       L+  +D     P   HRLD+ T+G+LV
Sbjct: 90  ILHRDDHLVVIDKPHFLATIPRGAHITETAVVRLRRALDLPDLTP--AHRLDRMTAGVLV 147

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               R   +   E F  +++ K Y ++    P      +A     +S I  ++  +    
Sbjct: 148 FLIRREDRRPYQELFVSQQVTKEYEAVAGHDP-----ALAFPRTIRSRIVKEHGIMTATE 202

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-- 277
           E G   + +   ++D    +  +  + P TGRTHQLR+H   +G PI GD+ Y  +F+  
Sbjct: 203 EPGEPNSETVVDLLDTRDGRARY-RLLPKTGRTHQLRLHMSSLGLPIEGDN-YYPDFRRS 260

Query: 278 --GNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
             G+F++P++    L AR ++   P  G ++
Sbjct: 261 EPGDFSTPLR----LLARAIEFTDPRSGEVR 287


>gi|327183169|gb|AEA31616.1| Pseudouridine synthase [Lactobacillus amylovorus GRL 1118]
          Length = 301

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 107/243 (44%), Gaps = 26/243 (10%)

Query: 92  KHSDFLKSI-----LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKG 141
           K +DFLK        + E     + NKPAG+       +    I   + G+  +   +K 
Sbjct: 68  KKNDFLKPSNNPVEPVLETKNYIILNKPAGVLSIPSRYEDNDAIVNRLMGYF-TRKGAKD 126

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            KP +  RLD++TSG+++V +   A    ++  + R I+K Y ++V G   N +      
Sbjct: 127 LKPHVITRLDRDTSGLVLVGKNAVAHARFSKIGKERFIKK-YHAIVHG---NFESTELTG 182

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L+ +  IG     V +        A + +KV+         +E++  TGRTHQ+RVH  +
Sbjct: 183 LIDEP-IGKIDSGVKRGVIPDGKSAQTEYKVLKQVPGA-SLVELRLLTGRTHQIRVHMAY 240

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL--PAHMVKTW 319
           +G P+ GD  Y    K +F+     +  L+  Y+  P P       T  +  P+ M   W
Sbjct: 241 LGHPLYGDQLYGV--KDSFS-----RQALNCFYLSFPDPVNSEKDKTVEISDPSDMQNLW 293

Query: 320 DSL 322
             L
Sbjct: 294 QKL 296


>gi|319778799|ref|YP_004129712.1| ribosomal large subunit pseudouridine synthase A-like protein
           [Taylorella equigenitalis MCE9]
 gi|317108823|gb|ADU91569.1| ribosomal large subunit pseudouridine synthase A-like protein
           [Taylorella equigenitalis MCE9]
          Length = 289

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 61/218 (27%), Positives = 96/218 (44%), Gaps = 34/218 (15%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  I   +KP  + SV GG  +       L+  +++    P   HRLD+ET+G+LV
Sbjct: 64  ILYEDDLIVAIDKPHLLASVPGGYHLHESALIKLRRLLNNININP--IHRLDRETAGVLV 121

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN--------WLLKKSHI--G 209
             +           F+ R I K Y            ECIA          L++KS+I   
Sbjct: 122 FCKQSKYRNAYQVMFQDRVINKSY------------ECIAPKPIDLSIFPLVRKSYICRS 169

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            ++  +++  E   N + +  + +           + P TG+ HQLRVH   +G PIV D
Sbjct: 170 NNFFTMIENTELIPN-SETRIEFVHTVKGGNALYRLFPSTGKKHQLRVHMSGLGLPIVHD 228

Query: 270 HKYCANF----KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + Y        K +F++P+Q    L AR ++   P  G
Sbjct: 229 NFYPVLLAQRDKNDFSNPLQ----LLARSIEFKDPISG 262


>gi|118474954|ref|YP_892206.1| pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40]
 gi|118414180|gb|ABK82600.1| pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40]
          Length = 254

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/201 (24%), Positives = 88/201 (43%), Gaps = 29/201 (14%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K +   K +++YED  I   NKP                 F+ S   ++  K  L +RLD
Sbjct: 51  KVTKLAKPVMIYEDDNIVAVNKPP----------------FITSEKVAEIFKFPLLNRLD 94

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG++++ +     +   + F   +++K Y ++V GI  ++          K+  G  
Sbjct: 95  KETSGVILLYKNEEFQKAAIKEFANNKVKKTYLAIVRGIVVDEFSVELPISTVKTKSGA- 153

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                K +      AI+H   +    +K   +++   TGRTHQ+R H  + G  ++GD K
Sbjct: 154 ---FSKIDLSRGKTAITHVSPLMVEGKK-SLIKVGIETGRTHQIRCHLAYSGYGVIGDEK 209

Query: 272 YCANFKGNFTSPIQNKLYLHA 292
           Y  N           ++YLH+
Sbjct: 210 YAKN--------SSKRVYLHS 222


>gi|327334511|gb|EGE76222.1| RNA pseudouridylate synthase family protein [Propionibacterium
           acnes HL097PA1]
          Length = 281

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 61/213 (28%), Positives = 93/213 (43%), Gaps = 20/213 (9%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LY D +I V +KP  +S +  G  +   +   L++ +      P LT  HRLD+ T+G+
Sbjct: 64  ILYSDERILVVDKPHFLSSIPRGRHVLESVVVRLRTQLGL----PELTVAHRLDRVTAGV 119

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA---NWLLKKSHIGGDYVH 214
           L++ R R   +   E F  R + K Y  +   +    +E I    N    +S I  +   
Sbjct: 120 LLLTRERKWRRPYQEMFERREVVKKYRLVAPVVHDPAREGIGATKNGWQVRSRIIKERGI 179

Query: 215 VVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           +  +   G   A++   +I  C        E  P TGRTHQ+R+H   +G PIV D  Y 
Sbjct: 180 LQAREVPGVPNAVTDIVLIGKCGG--LGLYEASPRTGRTHQIRLHMQRLGAPIVNDPFYP 237

Query: 274 ANFK---GNFTSPIQNKLYLHARYMDLPHPEGG 303
                   +FT P+Q    L A  M    P  G
Sbjct: 238 TVLDTPVDDFTHPLQ----LQAWRMGFTDPVSG 266


>gi|323466963|gb|ADX70650.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 321

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 104/227 (45%), Gaps = 21/227 (9%)

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +E     V NKPAG+       +    +   + G+     + K  KP +  RLD++TSG+
Sbjct: 107 FETKNYIVLNKPAGVLSIPSRYEDNDAVVNRLMGYFLQQ-NKKDLKPHVITRLDRDTSGL 165

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV-HV 215
           ++V +   A    ++  +   ++K Y ++V G   +++   I +  + K    GD V   
Sbjct: 166 VLVGKNAIAHARFSKIGKDNFVKK-YHAIVHGNFAEDELTGIIDEPIGKE---GDGVKRA 221

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  N K A    + ++V+    +    +E++  TGRTHQ+RVH  ++G P+ GD  Y  N
Sbjct: 222 VVANGKKAQ---TRYRVLKQ-VEGASLVELRLLTGRTHQIRVHMAYLGYPLFGDPLYGIN 277

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
              NF+    N  YL   + D P     + +I    P  M K W  L
Sbjct: 278 --DNFSRQALNCFYL--AFPD-PFDNERKQEIQIKDPEDMSKLWQKL 319


>gi|119026149|ref|YP_909994.1| hypothetical protein BAD_1131 [Bifidobacterium adolescentis ATCC
           15703]
 gi|154488937|ref|ZP_02029786.1| hypothetical protein BIFADO_02246 [Bifidobacterium adolescentis
           L2-32]
 gi|118765733|dbj|BAF39912.1| hypothetical protein [Bifidobacterium adolescentis ATCC 15703]
 gi|154083074|gb|EDN82119.1| hypothetical protein BIFADO_02246 [Bifidobacterium adolescentis
           L2-32]
          Length = 309

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/159 (30%), Positives = 78/159 (49%), Gaps = 15/159 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD  TSG+++V ++  A   +   F    + K Y +LV G  K  K  I      +
Sbjct: 130 IVSRLDVGTSGLMLVCKSDLAYVEMRRQFAEHEVVKTYHALVQGNLKEDKATI------E 183

Query: 206 SHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + IG     D+   V    K    AI+H+ V++ F +    + +   TGRTHQ+RVH   
Sbjct: 184 APIGRAKVSDFRFCVTPAGK---EAITHWDVMERFGEA-TLVSVNLETGRTHQIRVHFSS 239

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +G P+ GD  Y AN + +    ++ + +LHA  ++  HP
Sbjct: 240 IGHPLAGDAMYGANPQLSEALGLERQ-WLHAMQLEFRHP 277


>gi|119963365|ref|YP_946570.1| RNA pseudouridine synthase [Arthrobacter aurescens TC1]
 gi|119950224|gb|ABM09135.1| putative RNA pseudouridine synthase [Arthrobacter aurescens TC1]
          Length = 309

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 51/196 (26%), Positives = 85/196 (43%), Gaps = 17/196 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +L++D  I V +KP  +    G     +I       + +    P L   HRLD+ T+G+L
Sbjct: 90  ILHQDEHILVVDKPHFLPTTPG---GTYIQESALVRLRNLLNLPDLIPMHRLDRMTAGLL 146

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++    TR   Q L   F  R++QK Y  +    P      +    + ++ +     ++
Sbjct: 147 LLSTNPETRGKYQVL---FEKRQVQKEYECVSAATPAAGFPAVEFPAVVRNRMTKSRSYL 203

Query: 216 VKQ---NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + +    E  A   I   K  D    +     ++PHTG+THQLRVH   +G  IV D  Y
Sbjct: 204 LAEVIDGEPNAETRIEQTKTFDAGTHQRALYRLEPHTGKTHQLRVHMASLGLGIVNDAFY 263

Query: 273 ---CANFKGNFTSPIQ 285
                    ++T P+Q
Sbjct: 264 PDLLDKAPDDYTKPLQ 279


>gi|114778309|ref|ZP_01453168.1| hypothetical protein SPV1_13252 [Mariprofundus ferrooxydans PV-1]
 gi|114551411|gb|EAU53967.1| hypothetical protein SPV1_13252 [Mariprofundus ferrooxydans PV-1]
          Length = 298

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 66/264 (25%), Positives = 118/264 (44%), Gaps = 23/264 (8%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-------KHSDFLKSILLY 103
           +R  + +R+++G++       + L +II           L        +H    +  +L+
Sbjct: 38  ERAIWQHRLEAGKIT------DELGNIITTDTSFRPHARLRYFREVAYEHPIPFREQILF 91

Query: 104 EDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           ++  I V +KP  + V  GGS +   +   LK     +   P   HRLD+ET+G+++   
Sbjct: 92  QNDSILVADKPHFLPVTPGGSYVNECLLHRLKRSTGLEHLVP--AHRLDRETAGLVLFTV 149

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            +   Q   + FR   I K Y ++    P   ++    WL++ S I      +  +N  G
Sbjct: 150 DKKQRQPWFDLFRHGAISKSYEAIA-ATPAESQQ--REWLVE-SRIERGEPWIRFRNTVG 205

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A S  ++I+         E+QP TG+THQLR+H   +G  IVGD ++  +++     
Sbjct: 206 EINARSRIRIIES-KGSLSRFELQPITGKTHQLRLHMGLIGAHIVGD-RFYPDYQSPTDP 263

Query: 283 P-IQNKLYLHARYMDLPHPEGGRL 305
           P   N L L A+ +    P  G++
Sbjct: 264 PSYDNPLQLLAKRLAFTDPVSGQM 287


>gi|317180758|dbj|BAJ58544.1| hypothetical protein HPF32_0962 [Helicobacter pylori F32]
          Length = 293

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 70/287 (24%), Positives = 122/287 (42%), Gaps = 45/287 (15%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS- 99
           L+  Q  +DK+R+K     Q+ Q VR             + +++   V+L       K+ 
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVR-------------KSQMIQGVVSLIHFKPNEKTQ 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  +      G  YH +  L        +     HRLD ETSG+++
Sbjct: 70  ALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFDKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-----VH 214
             +T  + + L   F  ++++K Y +L  G+  +K   I   +L   +I  D      + 
Sbjct: 128 AGKTLQSVKDLKALFMQKKVKKTYLALAHGL-VDKNIVIDKPILTPQNIQKDLRIRSKIS 186

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + +        +S+   +D        L++ P TGRTHQ+R+H   +   IVG+  Y  
Sbjct: 187 PLGKPSTTLVEPLSYNPFLDI-----SLLKIAPLTGRTHQIRLHLSSVNHRIVGEGLYGV 241

Query: 275 ---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                      K    +P+   L LHA  ++    +G   +IT+P+P
Sbjct: 242 IDENAREYLQLKRENNAPL---LMLHATSLEFEF-KGAIYKITSPIP 284


>gi|161507179|ref|YP_001577133.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DPC 4571]
 gi|160348168|gb|ABX26842.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DPC 4571]
          Length = 298

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 105/228 (46%), Gaps = 21/228 (9%)

Query: 102 LYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++E     V NKPAG+       +    +   + G+     + K  KP +  RLD++TSG
Sbjct: 83  VFETKNYIVLNKPAGVLSIPSRYEDNDAVVNRLMGYFLQQ-NKKDLKPHVITRLDRDTSG 141

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV-H 214
           +++V +   A    ++  +   ++K Y ++V G   +++   I +  + K    GD V  
Sbjct: 142 LVLVGKNAIAHARFSKIGKDNFVKK-YHAIVHGNFAEDELTGIIDEPIGKE---GDGVKR 197

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  N K A    + ++V+    +    +E++  TGRTHQ+RVH  ++G P+ GD  Y  
Sbjct: 198 AVVANGKKAQ---TRYRVLKQ-VEGASLVELRLLTGRTHQIRVHMAYLGHPLFGDPLYGI 253

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           N   NF+    N  YL   + D P     + +I    P  M K W  L
Sbjct: 254 N--DNFSRQALNCFYL--AFPD-PFDNERKQEIQIKDPEDMSKLWQKL 296


>gi|104773696|ref|YP_618676.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103422777|emb|CAI97416.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|325125343|gb|ADY84673.1| Ribosomal large subunit pseudouridine synthase [Lactobacillus
           delbrueckii subsp. bulgaricus 2038]
          Length = 302

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 109/231 (47%), Gaps = 24/231 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++ E +   V NKPAG+ S+  G     + I   +  F K  V+    KP +  RLDQ+T
Sbjct: 81  IVEETADYLVINKPAGLLSIPSGFHAEDAVINRVLAYFEKQGVNPAYVKPHIVTRLDQDT 140

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDY 212
           SG++++ +   A    ++  +   I+K Y ++V G   N  E   + L+ K  + +G   
Sbjct: 141 SGLVLLGKNAIAHDRFSKLGKDAFIKK-YHAIVHG---NFAEGDLSGLIDKPLARVGDTV 196

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              V  N KG   A++ ++V++        +E++  TGRTHQ+R+H   +G  + GD  Y
Sbjct: 197 KREV--NPKGQR-ALTEYRVLNQVPGA-SLVELRLLTGRTHQIRIHMASIGHVLYGDDLY 252

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            A  +  F      +  L+  Y+  P+P  G   +I  P P  M   W  L
Sbjct: 253 GA--RDAFA-----RQALNCFYLAFPNPFSGEEREIEIPDPGDMQGLWRQL 296


>gi|327299994|ref|XP_003234690.1| DRAP deaminase [Trichophyton rubrum CBS 118892]
 gi|326463584|gb|EGD89037.1| DRAP deaminase [Trichophyton rubrum CBS 118892]
          Length = 517

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 66/264 (25%), Positives = 109/264 (41%), Gaps = 55/264 (20%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS- 99
           +  G++ +D K    ++ I +GQV+                     S  L +H   + S 
Sbjct: 83  IDGGRITIDGKVATADSIINNGQVI---------------------SHTLHRHEPPVTSR 121

Query: 100 --ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETS 155
              +++ED  I V +KPAGI V       Y+ +  ++     +G    P   +RLD+ TS
Sbjct: 122 PIKIIHEDEDIIVIDKPAGIPVHPAG--RYNYNSIIEIMRSERGLGWIPYPCNRLDRLTS 179

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI------- 208
           GI+ + +   AA+ + +S R R ++K Y + V G   +        +LK S I       
Sbjct: 180 GIMFLGKHPKAAEQMAKSLRSRTLRKEYIARVKGYFPDGVVLCDQPMLKVSPILGLNRVR 239

Query: 209 --GGD----------YVHVVKQNEKGA--------NYAISHFKVIDCFAQKFCWLEMQPH 248
             G D          Y  V K+++ G         + A +   +     + +  +   P 
Sbjct: 240 ATGKDAQTKFRRIAYYPPVEKEDKNGEATSSQGPDSRASTPPPLPADVDEGYSIVHCLPL 299

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGRTHQ+RVH   +G PI  D  Y
Sbjct: 300 TGRTHQIRVHLQFLGHPITNDPIY 323


>gi|319401727|gb|EFV89935.1| pseudouridine synthase, RluA family protein [Staphylococcus
           epidermidis FRI909]
          Length = 284

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 57/206 (27%), Positives = 97/206 (47%), Gaps = 26/206 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK----SWVDSKGQK--PRLTHRLDQET 154
           ++YED+ + + NKP    +Q  +    H  G L     ++   KG+K  P +  RLD+ T
Sbjct: 77  VIYEDAYLIIVNKP---QMQNCAPSREHPHGSLVEQVLAYYTKKGEKINPHIVTRLDRNT 133

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V A+      H+   F   + +K Y +L +G  ++    I   + + S    D + 
Sbjct: 134 SGLVVFAK----FGHVHHLFSKVKFKKEYVALAYGQTQSSG-VIEAPIARLS----DSII 184

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             + NEKG      + K++       C +++   TGRTHQ+RVH  ++G P++GD  Y  
Sbjct: 185 KREVNEKGKCAKTVYQKLMQNETASLCKIKLL--TGRTHQIRVHFEYIGHPLIGDDLYGG 242

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           N       P  +   LH   ++  HP
Sbjct: 243 N------HPCVHGQALHCCSVEFIHP 262


>gi|210134539|ref|YP_002300978.1| pseudouridine synthase D [Helicobacter pylori P12]
 gi|210132507|gb|ACJ07498.1| pseudouridine synthase D [Helicobacter pylori P12]
          Length = 297

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 73/289 (25%), Positives = 123/289 (42%), Gaps = 49/289 (16%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII------KEQKILDSSVNLTKHS 94
           L+  Q  +DK+R+K     Q+ Q VR   +I  +  +I      K++K            
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVRKSQMIQGVVRLIYFKPNEKQEK------------ 70

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
                 L++E     VF+KP  I      G  YH +  L       G+     HRLD ET
Sbjct: 71  ------LVFETKDFGVFDKPTQIYTHP-KGYFYH-ESLLDCIQSHLGKNAHPAHRLDYET 122

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++  +T  + + L   F  ++++K Y +L  G+   K   I   +L   +I  D + 
Sbjct: 123 SGLVLAGKTLQSVKDLKALFMQKKVKKTYLALAHGL-VEKSMKIDKPILTPQNIQKD-LR 180

Query: 215 VVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +  Q       +I+  + +  + F      L++ P TGRTHQ+R+H   +   IVG+  Y
Sbjct: 181 IRSQISPLGKPSITLVEPLSYNPFLD-ISLLKITPLTGRTHQIRLHLSSINHRIVGEGLY 239

Query: 273 CA---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                        K    +P+   L LHA  ++    +G   +IT+ +P
Sbjct: 240 GVADENAREYLQLKRENNAPL---LMLHAASLEFEF-KGANYKITSQIP 284


>gi|194365401|ref|YP_002028011.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
 gi|194348205|gb|ACF51328.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
          Length = 292

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/170 (29%), Positives = 74/170 (43%), Gaps = 11/170 (6%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETSGILVVART 163
           D+ + V +KP  + V    G  Y  +  L   V S G    +  HRLD+ T+G+++ +  
Sbjct: 84  DAHLLVADKPHFLPVTPAGG--YVRETLLARLVASTGNTDLVPLHRLDRLTAGLVLFSTQ 141

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
            A+       FR RRI K Y +L   +P      +   L + S +             G 
Sbjct: 142 AASRDAYQRLFRERRIDKTYEALAPALP-----AVTFPLHRHSRLAPAEPFFRMAEVPGE 196

Query: 224 NYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             A S  ++I+   +   W   + P TGR HQLRVH   +G PI GD  Y
Sbjct: 197 PNARSRIELIE--GEGPIWRYRLLPETGRKHQLRVHMAMLGAPIEGDDLY 244


>gi|315042395|ref|XP_003170574.1| DRAP deaminase [Arthroderma gypseum CBS 118893]
 gi|311345608|gb|EFR04811.1| DRAP deaminase [Arthroderma gypseum CBS 118893]
          Length = 516

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 67/264 (25%), Positives = 107/264 (40%), Gaps = 54/264 (20%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS- 99
           + +G++ +D K    ++ I +GQV+                     S  L +H   + S 
Sbjct: 83  IDNGRITIDGKIATADSIINNGQVI---------------------SHTLHRHEPPVTSQ 121

Query: 100 --ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ED  I V +KPAGI V       Y+    +       G  P   +RLD+ TSGI
Sbjct: 122 RIKIIHEDDDIIVIDKPAGIPVHPAGRYNYNSIIEILRAERGVGWVPYPCNRLDRLTSGI 181

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG------- 210
           + + +   AA+ +  S R R +QK Y + V G   +        +LK S I G       
Sbjct: 182 MFLGKHPKAAEQMAHSLRSRTLQKEYIARVKGYFPDGVVLCDQPMLKVSPILGLNRVRAT 241

Query: 211 -----------DYVHVVKQNEKGANYAISHFKVIDCFA-----------QKFCWLEMQPH 248
                       Y   VK+ ++ +N   ++ +  D  A           + +  +   P 
Sbjct: 242 GKDAQTKFRRIAYYPPVKKGDE-SNGETANSQDPDSRASTPPPSPADVDEGYSIVHCLPL 300

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGRTHQ+RVH   +G PI  D  Y
Sbjct: 301 TGRTHQIRVHLQFLGHPITNDPIY 324


>gi|297198479|ref|ZP_06915876.1| ribosomal pseudouridine synthase [Streptomyces sviceus ATCC 29083]
 gi|197717376|gb|EDY61410.1| ribosomal pseudouridine synthase [Streptomyces sviceus ATCC 29083]
          Length = 317

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 97/212 (45%), Gaps = 25/212 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL- 158
           ++Y D  + V +KP  ++    GS +A      L+  +D         HRLD+ T+G++ 
Sbjct: 99  VIYRDEHLVVADKPHFLATTPRGSHVAETALARLRRQLDIPALG--AAHRLDRLTAGLVM 156

Query: 159 --VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIANWLLKKSHIGGDYVHV 215
             V    R A Q L   FR RR+ K Y ++    P       + + ++K+  +      +
Sbjct: 157 FTVRPEERGAYQSL---FRDRRVAKEYEAVARYDPTLPLPHTVRSRIVKERGV------L 207

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--- 272
             Q   G   A+S  ++++   ++  +  + P TG+THQLRVH   +G PI+GD  Y   
Sbjct: 208 AAQEVDGEPNAVSRVELLEHRGERARY-RLTPGTGQTHQLRVHMSALGVPILGDPLYPVV 266

Query: 273 -CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 G+F  P+Q    L AR ++   P  G
Sbjct: 267 TAPVAPGDFRRPLQ----LLARVLEFTDPVTG 294


>gi|47230110|emb|CAG10524.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 516

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 86/179 (48%), Gaps = 9/179 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L +D ++ V +KPA I V       ++   F+    +    +    HRLD+ TSG+L+ 
Sbjct: 180 VLVDDGEVLVVDKPASIPVHPCGRFRHNTVIFILGK-ELGISELHTVHRLDRLTSGVLLF 238

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           ART   ++ L +  R R+++K Y   V G  P+ +  C    L+    +G     + + +
Sbjct: 239 ARTLETSKKLDQLVRDRKLEKEYVCRVEGEFPEEEVICEQPILVVSFKVG-----LCRVD 293

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            KG        ++   F  K   +   P TGRTHQ+RVH  ++G PI+ D  Y ++  G
Sbjct: 294 PKGKECRTVFQRL--SFNGKTSVVRCLPVTGRTHQIRVHLQYLGFPILNDPIYGSSAWG 350


>gi|116513692|ref|YP_812598.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|116093007|gb|ABJ58160.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
          Length = 297

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 109/231 (47%), Gaps = 24/231 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++ E +   V NKPAG+ S+  G     + I   +  F K  V+    KP +  RLDQ+T
Sbjct: 76  IVEETADYLVINKPAGLLSIPSGFHAEDAVINRVLAYFEKQGVNPAYVKPHIVTRLDQDT 135

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDY 212
           SG++++ +   A    ++  +   I+K Y ++V G   N  E   + L+ K  + +G   
Sbjct: 136 SGLVLLGKNAIAHDRFSKLGKDAFIKK-YHAIVHG---NFAEGDLSGLIDKPLARVGDTV 191

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              V  N KG   A++ ++V++        +E++  TGRTHQ+R+H   +G  + GD  Y
Sbjct: 192 KREV--NPKGQR-ALTEYRVLNQVPGA-SLVELRLLTGRTHQIRIHMASIGHVLYGDDLY 247

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            A  +  F      +  L+  Y+  P+P  G   +I  P P  M   W  L
Sbjct: 248 GA--RDAFA-----RQALNCFYLAFPNPFSGEEREIEIPDPGDMQGLWRQL 291


>gi|324509347|gb|ADY43935.1| Unknown [Ascaris suum]
          Length = 386

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/196 (28%), Positives = 86/196 (43%), Gaps = 22/196 (11%)

Query: 92  KHSDFLKSILLYEDSK-IYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHR 149
           +H    K I   E++  + V NKP  + V        H + G L +  +  G   R+ HR
Sbjct: 89  EHPILAKPIEFIENNDDLLVVNKPPSMPVHACGQYRLHTVMGLLHTEHNITGL--RVLHR 146

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHI 208
           LD+ TSG+L+ A+   +     E+ +   + K Y   V G+ P N +E I    +  S +
Sbjct: 147 LDRTTSGVLIFAKNYESDLEFKEALKSGELHKEYVCKVEGVFPGNGEEVICEEPIG-SLV 205

Query: 209 GGDYVHVVKQNEKGAN------YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
               +  V+ + K A       ++     V+ CF            TGRTHQ+RVH  ++
Sbjct: 206 LTMGIQCVRNDGKPARTRFKRLWSDGKISVVKCFLD----------TGRTHQIRVHLQYL 255

Query: 263 GCPIVGDHKYCANFKG 278
           G PIV D  Y  +  G
Sbjct: 256 GFPIVDDELYNTDVWG 271


>gi|296332584|ref|ZP_06875045.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305673865|ref|YP_003865537.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
 gi|296150502|gb|EFG91390.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305412109|gb|ADM37228.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
          Length = 299

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 103/226 (45%), Gaps = 30/226 (13%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  + V NK   +S         GS   GI +H   + K+ V +      L  RLD
Sbjct: 84  ILYEDEHVLVINKQPYVSSIPSREHPSGSIANGIIHH---YQKNGVRAT---VHLVTRLD 137

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+++VA+ R A   L+ + +   +++ Y ++V G     +  I       + IG  
Sbjct: 138 RDTSGVMLVAKHRFAHSILSSAQKNGLVKRRYAAVVHGRLTQAEGTI------DAPIGRH 191

Query: 212 YVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              ++++        A++HF V  C       + +Q  TGRTHQ+RVH  ++G P+ GD 
Sbjct: 192 PDSIIERTVTPDGQKAVTHFYVT-CANDDMTSVTLQLETGRTHQIRVHMSYLGHPLCGDT 250

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            Y     G     I  +  LH+  +   HP    ++   A LP  M
Sbjct: 251 LY-----GGTRREI-GRQALHSEQLSFIHPLTQEKMTFHASLPQDM 290


>gi|223946633|gb|ACN27400.1| unknown [Zea mays]
          Length = 315

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 68/259 (26%), Positives = 110/259 (42%), Gaps = 50/259 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQG--GSGIAYHIDG--FLKSWVDSKGQKPRL--THRLDQET 154
           +++ED  + V +KPAG+       S     + G  FL+   ++   KP L   +RLD++T
Sbjct: 49  VVFEDEWLAVVDKPAGVYCDALLTSFPCSAVSGKHFLR-LAENPATKPNLHLANRLDRDT 107

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP---KNKKECIANWLLK------- 204
           SG++V+ +    A  L ++F   +++K Y +L  G P   +  K C  +   K       
Sbjct: 108 SGLMVITKCNKVAGKLVKAFTDHKVKKTYLALCIGFPPAWEKIKICSGHGRSKHGAWRVY 167

Query: 205 ------KSHIGGDYV-------HVVKQNEKG---ANYA-----ISHFKVIDCFAQKFC-- 241
                 +S  GG  V        V+  N KG     Y+     I    V +    + C  
Sbjct: 168 AMSDVGRSLPGGSVVRDMSTRFEVLGVNGKGQFREPYSLDTDDIEPITVQEKATDQTCGG 227

Query: 242 -------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                   +   P +GRTHQ+R+H  ++G PI GD KY    + +          LHA  
Sbjct: 228 DANSSVILVRAYPQSGRTHQIRLHCQYLGLPIRGDVKYGGVIEWDGVE--CEGHALHAES 285

Query: 295 MDLPHP-EGGRLQITAPLP 312
           +   HP  G  + + +PLP
Sbjct: 286 LSFVHPITGLPITLRSPLP 304


>gi|330881340|gb|EGH15489.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           glycinea str. race 4]
          Length = 190

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/177 (28%), Positives = 82/177 (46%), Gaps = 24/177 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +   +   L   ++ G++ VD   ++  + +  G V+           +I 
Sbjct: 19  RLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVL----------ELIA 68

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW--- 136
           EQ+     V      D     ++YED +I V NKPAG+ V   +G   H DG L +    
Sbjct: 69  EQEAQGEWVAQDIELD-----IIYEDDQILVINKPAGLVVHPAAG---HADGTLLNALLH 120

Query: 137 -VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY  +V G+
Sbjct: 121 HVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGV 177


>gi|182439619|ref|YP_001827338.1| putative ribosomal pseudouridine synthase [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|178468135|dbj|BAG22655.1| putative ribosomal pseudouridine synthase [Streptomyces griseus
           subsp. griseus NBRC 13350]
          Length = 312

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 60/207 (28%), Positives = 94/207 (45%), Gaps = 15/207 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG-IL 158
           ++Y D +I V +KP  ++    G  I       L+  ++    +P   HRLD+ T+G +L
Sbjct: 100 VVYRDERIVVADKPHFLATMPRGRHITETAAARLRRELELPALQP--AHRLDRLTAGLVL 157

Query: 159 VVART--RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            V R   R A Q L   FR RR++K Y +L    P +    +   +  +S I  +   + 
Sbjct: 158 FVVRPEDRGAYQTL---FRDRRVRKEYEALA---PYDPDVALPRTV--RSRIVKERGVLA 209

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + E G   + S  ++++       +  + P TGRTHQLRVH   +G PIV D  Y    
Sbjct: 210 AREEPGEANSESRVELVERRGGVGRY-RLLPATGRTHQLRVHMNALGLPIVHDPLYPVVA 268

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +          L L AR ++   P GG
Sbjct: 269 EEGAPDDFSRPLQLLARVLEFADPVGG 295


>gi|242242285|ref|ZP_04796730.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242234241|gb|EES36553.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 284

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 102/207 (49%), Gaps = 28/207 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK----SWVDSKGQK--PRLTHRLDQET 154
           ++YED+ + + NKP    +Q  +    H  G L     ++   KG+K  P +  RLD+ T
Sbjct: 77  VIYEDAYLIIVNKP---QMQNCAPSREHPHGSLVEQVLAYYTKKGEKINPHIVTRLDRNT 133

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V A+      H+   F   + +K Y +L +G  ++    I   + ++S    D + 
Sbjct: 134 SGLVVFAK----FGHVHHLFSKVKFKKEYVALAYGHTQSSG-VIEAPIARRS----DSII 184

Query: 215 VVKQNEKGANYAISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             + N+KG  YAI+ + +++       C +++   TGRTHQ+RVH  ++G P++GD  Y 
Sbjct: 185 KREVNDKG-KYAITVYQRLMQNETASLCKVKLL--TGRTHQIRVHFEYIGHPLIGDDLYG 241

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            N       P  +   LH   ++  HP
Sbjct: 242 GN------HPCVHGQALHCCSVEFIHP 262


>gi|311112905|ref|YP_003984127.1| RNA pseudouridine synthase [Rothia dentocariosa ATCC 17931]
 gi|310944399|gb|ADP40693.1| RNA pseudouridine synthase [Rothia dentocariosa ATCC 17931]
          Length = 365

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 97/237 (40%), Gaps = 45/237 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LYED  +   +KP  + V   G+ IA       K  V  +   P LT  HRLD+ T+GI
Sbjct: 110 VLYEDEHLLAVDKPHYLPVTPRGAYIAQ--TALTKLRV--RKNNPLLTPVHRLDRPTAGI 165

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGD----- 211
           L+ A+TR A       F+ R++ K Y ++     ++ +E  +   +  +SHI  D     
Sbjct: 166 LLFAKTRDARGPFQTMFQNRQVTKTYLAIAPAPSEDLRESMLGEGVQVRSHIDKDRNILQ 225

Query: 212 -------------------------YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                                     ++   Q+    + A + +       ++    E+ 
Sbjct: 226 VRQYSARECERAGLSVNAETLVRIREIYQAPQSVPLKSGAQNPYLPYPAPGEELALYELT 285

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHP 300
           PHTG+ HQLR H   +G PI GD  Y         + + P+Q    L A  +D  HP
Sbjct: 286 PHTGKMHQLRAHLNLLGTPIFGDVLYPQVLPTAPNDASVPLQ----LLAHRLDCVHP 338


>gi|77919951|ref|YP_357766.1| 23S RNA-specific pseudouridylate synthase [Pelobacter carbinolicus
           DSM 2380]
 gi|77546034|gb|ABA89596.1| 23S RNA-specific pseudouridylate synthase [Pelobacter carbinolicus
           DSM 2380]
          Length = 296

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 73/283 (25%), Positives = 119/283 (42%), Gaps = 41/283 (14%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           L+++LRSG++R +   +  N  ++  + +++P      +     +   D    LT     
Sbjct: 31  LRQLLRSGKIRCNGSILTENICLRGHESLQLP------DSKRLREVCTDRVPELT----- 79

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLT--HRLDQE 153
              ILL  D  + VF KPAG++V    G    ++   LK+W+       R+   HRLD  
Sbjct: 80  ---ILLETDEFLAVF-KPAGLAVHSSVGHTEDNLTDRLKAWIKQCKAPYRIAPVHRLDIG 135

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG ++  + R A   L    +   + K Y +LV G P                  G  V
Sbjct: 136 TSGPVIFGKGRKATAELGRLLQNGHMSKTYLALVNGHPPET---------------GMMV 180

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V+   K    A + F+V+   A           +GR HQ+R      G P+ GDH+Y 
Sbjct: 181 TSVRVQGK-PKQAATRFRVLGRHASAALLELEL-LSGRKHQIRQQCADAGWPLYGDHRY- 237

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHM 315
               G    P +++L+LH   +  P   +    +IT+PLP  +
Sbjct: 238 ----GGPELPGRDRLFLHCWQLAWPIQGDQPSHRITSPLPEEL 276


>gi|82752903|ref|XP_727467.1| hypothetical protein [Plasmodium yoelii yoelii str. 17XNL]
 gi|23483320|gb|EAA19032.1| hypothetical protein [Plasmodium yoelii yoelii]
          Length = 588

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/212 (25%), Positives = 88/212 (41%), Gaps = 57/212 (26%)

Query: 103 YEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           YE+    V NKP  I ++ G    I   ++  L+          R+  +LD  TSG+L++
Sbjct: 68  YENDYFLVVNKPYDIKLEKGKLDDIYPSVETLLRK--KRNLNTFRMCGQLDYATSGLLII 125

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ + ++  L  +   + I KIY ++++G                 H+  D +H+     
Sbjct: 126 AKDKLSSNILNYNIESKNISKIYLAILYG-----------------HLPLDVLHINVPIS 168

Query: 221 KGANYAISHFKVIDCF-------AQKFCW------------------LEMQPHTGRTHQL 255
           K  N     FK+  C+         K+C+                   E++  TGR HQL
Sbjct: 169 KVKN----EFKMKLCYNYNDYYDTGKYCYSLIYPYKHTYLKNEKVTLCELRTITGRRHQL 224

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           R+H++ +G  IVGD  Y       F   I+NK
Sbjct: 225 RLHSICLGSGIVGDETY-------FEDMIENK 249


>gi|290967748|ref|ZP_06559303.1| pseudouridine synthase, RluA family [Megasphaera genomosp. type_1
           str. 28L]
 gi|290782264|gb|EFD94837.1| pseudouridine synthase, RluA family [Megasphaera genomosp. type_1
           str. 28L]
          Length = 301

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 72/301 (23%), Positives = 124/301 (41%), Gaps = 53/301 (17%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++I  SG    + + +   N + +G  + I  PV          Q      +  T+    
Sbjct: 30  RRIKHSGTCTCNGQVIGLQNFVHTGDTICISLPV---------RQAFAPEPLAFTR---- 76

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                +YED  + V NKPAG+ +   +G     +A  +  +  +        P   HRLD
Sbjct: 77  -----VYEDRHLLVINKPAGLLMHPTAGQRSGTLANAVSYYYITSNQHCAYHP--VHRLD 129

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG+ ++A+     Q L +    R  +++Y +L  G        +       S +G  
Sbjct: 130 KNTSGLCMIAK-NPYVQSLFDHAPNRYYKRLYLALSTGYFPTPTATV------HSPVGRA 182

Query: 212 YVHVVKQ----NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              ++K+    + + A+         D ++     L++  HTGRTHQ+RVH  ++G P++
Sbjct: 183 ENSIIKRCVCLDGQKAHTDFVRLAAADTYS----LLQVSLHTGRTHQIRVHCSYLGFPLL 238

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT-----WDS 321
           GD  Y        T  + ++  LHA  M   HP     +++ A  PA M        WDS
Sbjct: 239 GDDLY------GGTHELLSRQALHAYAMLFIHPITHKEIRLFALPPADMQALITEAGWDS 292

Query: 322 L 322
           L
Sbjct: 293 L 293


>gi|255732273|ref|XP_002551060.1| DRAP deaminase [Candida tropicalis MYA-3404]
 gi|240131346|gb|EER30906.1| DRAP deaminase [Candida tropicalis MYA-3404]
          Length = 590

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/176 (27%), Positives = 75/176 (42%), Gaps = 5/176 (2%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YE+  I V +KP+GI V       Y  +   K      G+     +RLD+ TSG++ +
Sbjct: 172 IVYENDDILVIDKPSGIPVHPTG--RYRYNTVTKIIEQEFGKTVHPCNRLDRLTSGLMFL 229

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            ++   A  +    R R + K Y + V G    ++  I   L   S I       V   E
Sbjct: 230 GKSSKGANEMMSQIRDRNVSKEYIARVKGEFPIERIVIEKPL---STIAPKLTLNVVDEE 286

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            G        ++          ++  P TGRTHQ+RVH  ++G PI  D  Y + F
Sbjct: 287 NGKEAKTEFQRISYDPITDTSVVKCHPLTGRTHQIRVHLQYIGHPIANDPMYSSQF 342


>gi|326317327|ref|YP_004234999.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
 gi|323374163|gb|ADX46432.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
          Length = 328

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 93/219 (42%), Gaps = 30/219 (13%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +  +LY+D  + V +KP  + V   G  + + +   LK  +   G  P   HR+D++T+
Sbjct: 112 FEETVLYQDEHLVVADKPHFLPVVPTGRYLQHTLLVRLKRRLGLDGLSP--VHRIDRDTA 169

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-------KKSHI 208
           G+++ +  RA        FR R + K Y            E +A W +       + S I
Sbjct: 170 GLVLFSVQRATRGRYQALFRDRAVDKTY------------EAVAPWRVDVAFPRERSSRI 217

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                        G   +++  +V+D     +    + P TGR HQLRVH   +G P+ G
Sbjct: 218 EESPQFFRMHEVPGEANSLTRMEVLDVDG-AWARYRLSPVTGRRHQLRVHMAALGLPLRG 276

Query: 269 DHKYCA---NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           D  Y       +G+F+ P+Q    L AR +    P  GR
Sbjct: 277 DAFYPEVNDPPEGDFSRPLQ----LLARAIAFTDPVTGR 311


>gi|313678868|ref|YP_004056608.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma bovis PG45]
 gi|312950295|gb|ADR24890.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma bovis PG45]
          Length = 284

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 81/300 (27%), Positives = 128/300 (42%), Gaps = 64/300 (21%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVRIPP 69
           V   ++   +L ++  + +  +    + K+LR   V+++ KR+  +N I   G  V I  
Sbjct: 5   VAHKNDGGRKLIKYISSLFKDLPESRIYKLLRQKCVKINGKRITDSNHIINEGDEVVI-- 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                 + IKEQ    +++ +      L S ++YED  I + NK AG  V G       +
Sbjct: 63  ------YGIKEQ----ATIYIYDVGLQLDSKIIYEDDNILIINKKAGKVVHGE---LLCL 109

Query: 130 DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           D  + S++  K     KP    RLD+ TSG++V A+   A + L +  ++    KIY   
Sbjct: 110 DNQVLSYLKFKQNSSFKPSHVGRLDKWTSGLIVYAKNYKALRELND--KIGFFDKIY--- 164

Query: 187 VWGIPKNKKECIANWLLKKSHIGGD-----YVH--------VVKQNEKGANYAISHFKV- 232
                           LK  + GGD     Y+H        +V +N  G N  I   K+ 
Sbjct: 165 ---------------TLKSDYNGGDNVVSAYIHHDEKMQKMIVTKNPAGLNNQIVKTKIY 209

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           +D        L  Q  TGR HQ+R    ++G PI GD KY    K N       ++YLH+
Sbjct: 210 VDSNK-----LYAQLLTGRKHQIRATMEYLGYPIYGDIKYGWRKKTN------KRIYLHS 258


>gi|169846844|ref|XP_001830136.1| tRNA-pseudouridine synthase [Coprinopsis cinerea okayama7#130]
 gi|116508906|gb|EAU91801.1| tRNA-pseudouridine synthase [Coprinopsis cinerea okayama7#130]
          Length = 583

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 54/182 (29%), Positives = 86/182 (47%), Gaps = 10/182 (5%)

Query: 94  SDFLKSILLYEDSKIY-VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLD 151
           +D    IL  +D + + V +KP  I V       Y+ +  ++  V   G +K    +RLD
Sbjct: 142 TDTPVRILHRDDEREFIVVDKPGSIPVHASG--RYYKNTLIEILVHDFGIKKCYPANRLD 199

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGG 210
           + TSG++++  +   A+ LTE F    ++K Y + V G  P+    C    L     +G 
Sbjct: 200 RLTSGLMIMPLSPERARTLTEEFTAGTVKKEYVARVKGKFPEGSVVCEQPLLTVDRQMGL 259

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           + VH   +  K     I + +  +    K C    +PHTGR+HQLRVH  ++G PI  D 
Sbjct: 260 NIVHPDGKPAKTVFTLIRYDENTNSSVVK-C----EPHTGRSHQLRVHLQYLGHPIANDP 314

Query: 271 KY 272
            Y
Sbjct: 315 IY 316


>gi|301167669|emb|CBW27252.1| putative pseudouridine synthase [Bacteriovorax marinus SJ]
          Length = 276

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/191 (28%), Positives = 88/191 (46%), Gaps = 29/191 (15%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           V+ KPAG+  QG     +     +   V+       L  RLD+ETSG++++A T   A+ 
Sbjct: 98  VWYKPAGVLSQG---TKFGDQASILRHVEKNVPNAYLIQRLDRETSGLMIIAYTDKVARI 154

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
            T + + R I+K Y + V G  + ++  IA  L  KS                   A + 
Sbjct: 155 FTNAMKNRLIRKFYQAEVLGTLRQEQGEIAFDLDGKS-------------------AKTL 195

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           ++V + F Q    LE++  TGR HQ+R H   +  P++GD KY  + K +      + L 
Sbjct: 196 YQVHEEFEQS-TLLEIEIITGRFHQIRKHFEKIKHPVIGDPKYGRHNKND------DGLK 248

Query: 290 LHARYMDLPHP 300
           L A  ++L  P
Sbjct: 249 LVAHKLELKDP 259


>gi|294867086|ref|XP_002764957.1| tRNA pseudouridine synthase C, putative [Perkinsus marinus ATCC
           50983]
 gi|239864810|gb|EEQ97674.1| tRNA pseudouridine synthase C, putative [Perkinsus marinus ATCC
           50983]
          Length = 417

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 41/152 (26%), Positives = 82/152 (53%), Gaps = 8/152 (5%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL-LK 204
           + HRLD++TSG +++AR   + + +   F+  ++ K Y  LV GI  N    I + + ++
Sbjct: 54  MCHRLDKQTSGPVLIARKLESWKFIRRQFQKEQVTKRYVCLVDGICANDSGMIDSPIRVR 113

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMG 263
           ++     +      +   ++ A S ++V++ + +    + ++  TG THQ+RVH A  +G
Sbjct: 114 RTE---KHTSAEIGSGPASSSAHSEYRVLERYEEGCTLMSVRITTGVTHQIRVHMAQGLG 170

Query: 264 CPIVGDHKYCANFKGN---FTSPIQNKLYLHA 292
            PIVGD KY  + +G+     + +  +++LH 
Sbjct: 171 HPIVGDKKYTPSGRGSELPCATRMPGRVFLHC 202


>gi|38234813|ref|NP_940580.1| hypothetical protein DIP2277 [Corynebacterium diphtheriae NCTC
           13129]
 gi|38201077|emb|CAE50801.1| Conserved hypothetical protein [Corynebacterium diphtheriae]
          Length = 349

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 59/225 (26%), Positives = 93/225 (41%), Gaps = 29/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  + V +KP  ++    G  I       L+         P   HRLD+ TSG+L+
Sbjct: 129 VVYEDDTLLVADKPPFLATMPRGKHITNSATVQLRRSTGIDELSP--AHRLDRLTSGLLL 186

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
                R R A Q L   F  R ++K Y +     P      I  W    +   G+    +
Sbjct: 187 FTKRKRVRGAYQTL---FSERNVRKTYVATAQYNPSITPGTI--WRSHMTKTAGEIQGHI 241

Query: 217 KQNEKGANYAISHFKVIDCFAQK-----------FCWLEMQPHTGRTHQLRVHALHMGCP 265
                 A   +S  + ID   Q+                ++PHTG+THQLR+H L  G P
Sbjct: 242 IDAPPNAETLVSAIERIDAPTQQHLHALHGTDVDLAHYTLKPHTGKTHQLRLHMLAAGVP 301

Query: 266 IVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           I+GD  Y    A    +++ P    ++L +  ++   P  GR ++
Sbjct: 302 ILGDTIYPTILAEDAEDYSRP----MHLTSTELEFIDPLTGRPRL 342


>gi|314929196|gb|EFS93027.1| RNA pseudouridine synthase [Propionibacterium acnes HL044PA1]
          Length = 281

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 59/213 (27%), Positives = 94/213 (44%), Gaps = 20/213 (9%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LY D +I V +KP  +S +  G  +   +   L++ +      P LT  HRLD+ T+G+
Sbjct: 64  ILYSDERILVVDKPHFLSSIPRGRHVLESVVVRLRTQLG----LPELTMAHRLDRVTAGV 119

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIAN--WLLKKSHIGGDYV 213
           L++ R R   +   E F  R + K Y  +   +  P  +   + N  W ++ S I  +  
Sbjct: 120 LLLTRERQWRRPYQELFERREVVKKYRLVAPAVHDPAGEGAVVTNNGWQVR-SRIVKERG 178

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY- 272
            +  +   G   A++   ++          E  P TGRTHQ+R+H   +G PIV D  Y 
Sbjct: 179 ILQAREVPGEPNAVTDIVLVSEHG-GLGLYEASPRTGRTHQIRLHMQRLGAPIVNDPFYP 237

Query: 273 --CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                   +FT P+Q    L A  M    P  G
Sbjct: 238 IVLGTQIDDFTHPLQ----LQAWQMGFTDPVSG 266


>gi|301754896|ref|XP_002913309.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Ailuropoda melanoleuca]
          Length = 511

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 98/220 (44%), Gaps = 44/220 (20%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGS 123
           + E+ + D S+ L K +DFL++               LL E+  + V +KP+ I V    
Sbjct: 155 LNEEPVQDLSIVL-KDNDFLRNRVHRHEPPVTAEPVRLLAENEDMVVVDKPSSIPVHPCG 213

Query: 124 GIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++   F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K
Sbjct: 214 RFRHNTVIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEK 270

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI--------SHFKV 232
            Y   V G  P  +  C    L+    +G     V + + +G              H  V
Sbjct: 271 EYVCRVEGEFPTEEVICKEPILVVSYKVG-----VCRVDARGKPCETVFQRLSYNGHSSV 325

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + C          +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 326 VRC----------RPLTGRTHQIRVHLQFLGHPILNDPIY 355


>gi|282852228|ref|ZP_06261580.1| S4 domain protein [Lactobacillus gasseri 224-1]
 gi|282556647|gb|EFB62257.1| S4 domain protein [Lactobacillus gasseri 224-1]
          Length = 163

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 48/179 (26%), Positives = 88/179 (49%), Gaps = 27/179 (15%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT   ++V+E  EE  RLD+        ++   +++++    + V+ K  K + ++Q+G 
Sbjct: 1   MTENYHLVIE--EEKGRLDKVIAEKLKDLSRTKIKELVNDKNILVNHKAEKVSYKVQAGD 58

Query: 64  VVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            + I  PP         K   +   ++NL          ++YED+ + V NKP G+ V  
Sbjct: 59  SIDITVPPA--------KPLSLEAQNLNLD---------IVYEDADVIVVNKPQGMVVHP 101

Query: 122 GSGIAYH--IDGFL---KSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            +G   H  ++G L       DS +G +P + HR+D++TSG+L+VA+   A + L +  
Sbjct: 102 SAGHPDHTLVNGLLYHTHELADSPEGFRPGIVHRIDKDTSGLLMVAKNDKARESLEKQL 160


>gi|194696406|gb|ACF82287.1| unknown [Zea mays]
          Length = 242

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 87/211 (41%), Gaps = 44/211 (20%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESF-----------------RMRRIQKIYWSL 186
           P   HRL + TSG+L+ A+T+ A   L   F                   R+I K Y +L
Sbjct: 16  PVPVHRLGRGTSGLLLCAKTKVAKVRLASYFAEGAINAAKKRDKSEFSEERKISKFYRAL 75

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEM 245
           V GI  +  E +    +   H  G    +      G   A+S   V++  A Q    +++
Sbjct: 76  VTGI-LDDDEVVVTQPIGLVHYPGVAEGLYAACSSG-KPAMSKVCVLERLAHQNHTLVQV 133

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----------------- 288
           + H+GR HQ+R+H  ++G P+V D  Y      NF  P                      
Sbjct: 134 EIHSGRPHQIRIHLAYIGHPLVDDPLYGIGGHPNFVEPESTGTDSSFASDGGYERPLQPV 193

Query: 289 ------YLHARYMDLPHPEGGRL-QITAPLP 312
                 +LHA ++ L HP   ++ +ITAPLP
Sbjct: 194 PGDCGYHLHAHWLVLCHPTTNKMVKITAPLP 224


>gi|72058953|ref|XP_781802.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
 gi|115955042|ref|XP_001182766.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
          Length = 613

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 55/198 (27%), Positives = 86/198 (43%), Gaps = 10/198 (5%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIY-VFNKPAGISVQGGSGIAYHIDGFLKS 135
           I+K    + S V+  +     + I +  D++ Y V NKP+ I V       ++   F+  
Sbjct: 95  ILKNNDFMQSKVHRHEPPVSGEPIQIIADTQDYLVINKPSSIPVHPCGKYRHNTIVFILG 154

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
             D   +     HRLD+ TSG+L+ ART   +  L    R R+++K Y     G  P   
Sbjct: 155 K-DYGFKGLHTIHRLDRLTSGLLLFARTLQVSHRLDAYVRERKLEKTYVCKAHGEFPSTP 213

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             C     +    IG   V  VK++ K              +  +   ++  PHTGR HQ
Sbjct: 214 VVCEEPIFIVSHKIG---VCRVKEDGKPCKTRFERLS----YDGETSIIKCHPHTGRMHQ 266

Query: 255 LRVHALHMGCPIVGDHKY 272
           +RVH  ++G PI+ D  Y
Sbjct: 267 IRVHLQYLGFPIINDPLY 284


>gi|254779038|ref|YP_003057143.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
 gi|254000949|emb|CAX28893.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
          Length = 298

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 77/306 (25%), Positives = 126/306 (41%), Gaps = 55/306 (17%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K     Q+ Q VR   +I  +  +I  +    +              
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVRKSQMIQGVVRLIHFKPNEKTQA------------ 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD------SKGQKPRLTHRLDQET 154
           L++E     VF+KPA +      G  YH     +S +D      SK   P   HRLD ET
Sbjct: 71  LVFETKDFGVFDKPAQVYTHP-KGYFYH-----ESLLDCIQSHFSKNAHP--AHRLDYET 122

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++  +T  + + L   F  ++++K Y +L  G+   K   I   +L   +I  D   
Sbjct: 123 SGLVLAGKTLQSVKDLKALFMQKKVKKTYLALAHGL-VEKSMKIDKPILTPQNIQKDLRI 181

Query: 215 VVKQNEKGANY-----AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             K +  G         +S+   +D        L++ P TGRTHQ+R+H   +   IVG+
Sbjct: 182 RSKISPLGKPSITLVEPLSYNPFLDI-----SLLKIIPLTGRTHQIRLHLSSINHRIVGE 236

Query: 270 HKYCA---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
             Y             K    +P+   L LHA  ++    +G   +I +P+P   +    
Sbjct: 237 GLYGVADENAREYLQLKRKNNAPL---LMLHAASLEFEF-KGAIYKIASPMPERFMPFLK 292

Query: 321 SLGFKY 326
            L   Y
Sbjct: 293 DLPLFY 298


>gi|319762713|ref|YP_004126650.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|317117274|gb|ADU99762.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
          Length = 282

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 58/214 (27%), Positives = 90/214 (42%), Gaps = 16/214 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL++D  +    KPAG  V      A      +++  D  G+     HRLD+ T G+LV+
Sbjct: 37  LLWQDEHMVALYKPAGWLVHRTGLDAGETRFVVQALRDQIGRHVYPVHRLDKGTCGVLVM 96

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
               AAA+ L  SF    + K Y +LV  W  P    +      L+      D      Q
Sbjct: 97  GLHPAAARALAGSFARHAVHKRYLALVRGWAPPLADVDHP----LRPDDAPQD---APAQ 149

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEM-----QPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                   ++  ++ +    +F          +P TGR HQ+R H  H   PI+GD  + 
Sbjct: 150 PAHTLLTRLARLELPESSDPRFATTRASLVLAEPTTGRRHQIRRHLKHAAHPILGDATHG 209

Query: 274 ANFKGNFTSPIQN--KLYLHARYMDLPHPEGGRL 305
                 + +      +L+LHA  + LPHP+ GR+
Sbjct: 210 KGPLNRWWAERLGLQRLWLHAWRLRLPHPQDGRM 243


>gi|241955527|ref|XP_002420484.1| DRAP deaminase, putative; pseudouridine synthase, putative [Candida
           dubliniensis CD36]
 gi|223643826|emb|CAX41563.1| DRAP deaminase, putative [Candida dubliniensis CD36]
          Length = 589

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 47/176 (26%), Positives = 76/176 (43%), Gaps = 5/176 (2%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  + V +KP+GI V       Y  +   K +    G+     +RLD+ TSG++ +
Sbjct: 173 IVFEDDDLLVIDKPSGIPVHPTG--RYRYNTITKVFEHEMGKIVHPCNRLDRLTSGLMFL 230

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            ++   A ++    R R + K Y + V G    ++  +   L  KS         V   E
Sbjct: 231 GKSSKGANNMMSQIRDRNVTKEYIARVKGEFPLERLIVDKPLSTKSP---KLTLNVVDTE 287

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            G        +V          ++  P TGRTHQ+RVH   +G PI  D  Y + F
Sbjct: 288 NGKEAKTEFQRVSYDPMTNTSVVKCHPLTGRTHQIRVHLQFLGYPIANDPLYSSEF 343


>gi|45402|emb|CAA78140.1| putative protein of unknown function [Pseudomonas aeruginosa PAO1]
          Length = 185

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 48/177 (27%), Positives = 82/177 (46%), Gaps = 24/177 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   L   ++ G++ VD   V+  + + SG  + +     A    + 
Sbjct: 19  RLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAVVRPRDIVHSGAQLVLEAEQEAQGEWLA 78

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW--- 136
           +   L+               ++YED  I V +KPAG+ V   +G   H DG L +    
Sbjct: 79  QDIELE---------------IVYEDEHILVIDKPAGLVVHPAAG---HQDGTLLNALLY 120

Query: 137 -VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            V      PR  + HRLD++T+G++VVA+T  A   L    + R + +IY ++V G+
Sbjct: 121 HVPDIANVPRAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGV 177


>gi|241888711|ref|ZP_04776018.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Gemella haemolysans ATCC 10379]
 gi|241864734|gb|EER69109.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Gemella haemolysans ATCC 10379]
          Length = 293

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 66/278 (23%), Positives = 125/278 (44%), Gaps = 36/278 (12%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-----LLYEDS 106
           R+KF+    S   +++      + +++K+  I++ ++     S+F++ I     ++YED+
Sbjct: 32  RIKFD----SDGSIKVNGKEENVRYLLKKNDIVEITLPSENFSEFVRFIDKDINIIYEDA 87

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGILVV 160
              + NK   +       +    D  L   V+   +K      P +  RLD+ TSG++++
Sbjct: 88  YFLIVNKEINLPSIPSRNLE---DESLLEIVNYYFKKKNINTIPHIVTRLDKNTSGLVLI 144

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ R    H+   F    I K Y +LV G  K+ +   A      S I      + ++  
Sbjct: 145 AKHR----HVHALFSNMEIDKFYTALVSGKVKDNEIIEAPIRRVTSSI------IEREVG 194

Query: 221 KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +G  +A + + + D    K    ++++ +TGRTHQ+RVH  +   P++GD  Y     G 
Sbjct: 195 EGGEFAKTEYWLDDYIVDKDISVVKLKLYTGRTHQIRVHMKYKDYPLLGDELY-----GG 249

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
             S I  +  LH   +   HP     + + A LP  ++
Sbjct: 250 DVSNISRQA-LHCTNLKFIHPITDEVVNVRADLPEDII 286


>gi|229918468|ref|YP_002887114.1| pseudouridine synthase, RluA family [Exiguobacterium sp. AT1b]
 gi|229469897|gb|ACQ71669.1| pseudouridine synthase, RluA family [Exiguobacterium sp. AT1b]
          Length = 287

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 66/282 (23%), Positives = 117/282 (41%), Gaps = 51/282 (18%)

Query: 44  GQVRVDKKRVKFNNRIQSGQ--VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
           G + V+       + ++ G    VR PP   +L+ +  E+ I                 +
Sbjct: 38  GDIEVNGMHRTVRHELEPGDEVSVRFPPESPSLDMVASERPIR----------------I 81

Query: 102 LYEDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           LYED  +   +KPAGI+     +     +A  + G+ +    S      + +RLD++TSG
Sbjct: 82  LYEDDTLLAVDKPAGIATIPSRLHPTDTLANAVLGYYQRIGLSSAIH--VINRLDRDTSG 139

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIA---NWLLKKSHIGGD 211
           +++ A+        +E  +   + + Y +LV     P+     I    N ++++      
Sbjct: 140 VVLFAKYGFIHHRFSELQKANGLMRTYKALVEEEVTPQTIDAPIGRAENSIMERV----- 194

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              V  + ++    AI+H      F      L ++  TGRTHQ+RVH  H+G  ++GD  
Sbjct: 195 ---VTTEGQR----AITHILACQPFGSG-SLLTIRLETGRTHQIRVHLRHIGHSLIGDSM 246

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y    +         +  LH+      HP  G  +QI AP+P
Sbjct: 247 YGGTAR-------MPRHALHSASARFIHPMTGDTIQIEAPIP 281


>gi|328905742|gb|EGG25518.1| RNA pseudouridine synthase [Propionibacterium sp. P08]
          Length = 322

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 72/286 (25%), Positives = 120/286 (41%), Gaps = 28/286 (9%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           +P +    ++K+LR G  RVD+   +      +G+  R        +     Q  +    
Sbjct: 39  WPTMRAYLVEKLLRVGGPRVDEMLDEGRFVDDAGRAFR-------QDSPFTPQTFVFFHR 91

Query: 89  NLTKHSDFLKSI-LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +L   +     I +LY D +I V +KP  +S +  G  +   +   L++ +      P L
Sbjct: 92  DLPTETPVPAGIGILYSDERILVVDKPHFLSSIPRGRHVLESVVVRLRTQLG----LPEL 147

Query: 147 T--HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIAN-- 200
           T  HRLD+ T+G+L++ R R   +   E F  R + K Y  +   +  P  +   + N  
Sbjct: 148 TMAHRLDRVTAGVLLLTRERQWRRPYQELFERREVVKKYRLVAPAVHDPAGEGAVVTNNG 207

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           W ++ S I  +   +  +   G   A++   ++          E  P TGRTHQ+R+H  
Sbjct: 208 WQVR-SRIVKERGILQAREVPGEPNAVTDIVLVSEHG-GLGLYEASPRTGRTHQIRLHMQ 265

Query: 261 HMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +G PIV D  Y         +FT P+Q    L A  M    P  G
Sbjct: 266 RLGAPIVNDPFYPIVLGTQIDDFTHPLQ----LQAWQMGFTDPVSG 307


>gi|291221038|ref|XP_002730528.1| PREDICTED: hypothetical protein [Saccoglossus kowalevskii]
          Length = 375

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 66/279 (23%), Positives = 117/279 (41%), Gaps = 49/279 (17%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGS---GIAYHIDGFLKSWVDSK---GQK-PRLTH 148
           +LKS ++Y++  +   NKPAG+ V         A H    L+   D K   G+K  +   
Sbjct: 89  YLKSQIVYDEDGVLALNKPAGLGVHSQREDLDTADHQWSLLEVLPDLKHQIGEKHLQFVK 148

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQ----KIYWSLVWGIPKNK----KECIAN 200
             +++ SG+ ++A+T   A  +  S +  R++    +++W++  G+P       K  + N
Sbjct: 149 APEKDCSGVTLLAKTPEIAADIDRSLKEARLRQVFTRVFWAVTVGVPSPLSGLIKVPVTN 208

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANY--AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            ++   H         K++ K  N    ++ ++VI   + +   +E+ P      QLRVH
Sbjct: 209 EVVDDEHQVSPVKDSSKRSYKMRNTRKLLTKYRVIS-ESNQCALVELMPLKAYKDQLRVH 267

Query: 259 ALHMGCPIVGDHKYCANFKG----------------------------NFTSPIQNK--L 288
                C I+GDH Y +  +                             N TS + +   L
Sbjct: 268 MTTKLCRILGDHVYSSRIQTILGIPVLIDARNAMPGTQVLSEEVRHRMNLTSAVIDSIPL 327

Query: 289 YLHARYMDLPH-PEGGRLQITAPLPAHMVKTWDSLGFKY 326
           +LH   M LP   +   L I+APLP +  KT   L  ++
Sbjct: 328 HLHCVAMTLPSWKKKEDLIISAPLPKYFWKTLKLLDIEH 366


>gi|89900681|ref|YP_523152.1| pseudouridine synthase [Rhodoferax ferrireducens T118]
 gi|89345418|gb|ABD69621.1| pseudouridine synthase [Rhodoferax ferrireducens T118]
          Length = 302

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 59/214 (27%), Positives = 104/214 (48%), Gaps = 26/214 (12%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++L++D ++ V +KP  + V    G +A  +   LK  +      P   HR+D++T+G++
Sbjct: 92  VILFQDEQLIVVDKPHFLPVMPSGGYLAETVLVRLKQKLGIDTLVP--VHRIDRDTAGLV 149

Query: 159 ---VVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIANWLLKKSHIGGDYVH 214
              V   TRAA   L   F  R ++K Y ++  W      +E +A  + ++S I  +  H
Sbjct: 150 MFSVQPETRAAYHAL---FSQRSVKKTYEAIAPW------REGLALPMTRQSRIV-EAGH 199

Query: 215 VVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY- 272
            + Q+E  G    ++  +V+          ++QP TG+ HQLRVH   +G PI+GD  Y 
Sbjct: 200 FMLQHEVSGPPNTVTRIEVLQVQG-GLARYQLQPVTGKRHQLRVHMAALGLPILGDGLYP 258

Query: 273 --CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                 + ++  P+Q    L AR ++   P  G+
Sbjct: 259 TLTPEGQVDYEHPLQ----LLARRIEFVDPVSGQ 288


>gi|89074028|ref|ZP_01160529.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           sp. SKA34]
 gi|89050166|gb|EAR55677.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           sp. SKA34]
          Length = 231

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 59/205 (28%), Positives = 92/205 (44%), Gaps = 30/205 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG----FLKSWVDSKG-QKPRLTHRLDQETS 155
           L+Y+     V NK  GISV        H D      L +  +  G +K  L HRLD+ TS
Sbjct: 4   LVYQHPDFLVINKHPGISV--------HKDDNDQPLLAAVAEQTGDEKLYLIHRLDKMTS 55

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSL-VWGIPKNKKECIANWLLKKSHIGGDYVH 214
           G+L++ R + AA  L+ +F  R ++K Y ++      K +   I +  + +S      + 
Sbjct: 56  GLLLLGRNKEAASILSSNFAERVVEKFYVAIGTKKPKKKQVVVIGD--MTRSRRSSWKLE 113

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K+N      AI+ F        +  +L  +PHTG+THQ+RV    +G  I GD  Y  
Sbjct: 114 STKENP-----AITQFFSTAAGEGRRLFL-CKPHTGKTHQIRVALRSVGSGITGDDIYGT 167

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPH 299
                      ++ YLHA  +  P+
Sbjct: 168 E--------ASDRGYLHAYALSFPY 184


>gi|148243361|ref|YP_001228518.1| pseudouridylate synthases, 23S RNA-specific [Synechococcus sp.
           RCC307]
 gi|147851671|emb|CAK29165.1| Pseudouridylate synthases, 23S RNA-specific [Synechococcus sp.
           RCC307]
          Length = 323

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 62/270 (22%), Positives = 122/270 (45%), Gaps = 15/270 (5%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           R  +  R+Q+G+       + A   + ++ ++L       + +   +   + +D  + V 
Sbjct: 41  RATWAQRLQAGECQLNGAPVQAEQVLQRDDELLWQRPPWLEPAIPDQWETIVDDGDLLVI 100

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           NKP+G+ V  G G   H    L + ++  G KP   HRL + TSG+ V AR       L+
Sbjct: 101 NKPSGLPVMPGGGFLQHT---LTALLEPTGAKP--VHRLGRFTSGLQVCARRPETRAQLS 155

Query: 172 ESFRMRR-IQKIYWSLVWGIPK-NKKECIA--NWLLKKSHIGGDYVHVVKQNE----KGA 223
              + +   +K+Y +    +P  +  +C+A    ++++ H    ++   + ++    +  
Sbjct: 156 RQMQPQGGCRKLYQAWAQRVPALDVGQCLAITTAVVERQHPLLGWIWGPRADDLELLRRQ 215

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTS 282
             A S  ++++  A     L++  HTGR HQ+R+H   +G P++GD  Y A  +     +
Sbjct: 216 LSAHSEIRLLERAAIGDR-LDVVIHTGRPHQIRIHLAQIGSPLLGDPLYLAEQRIAEHAT 274

Query: 283 PIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           P      LHA+ +      G  L++ A  P
Sbjct: 275 PGDGGYRLHAQQLGGLEHNGQTLKLMASPP 304


>gi|162456191|ref|YP_001618558.1| hypothetical protein sce7908 [Sorangium cellulosum 'So ce 56']
 gi|161166773|emb|CAN98078.1| rluD4 [Sorangium cellulosum 'So ce 56']
          Length = 326

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 50/190 (26%), Positives = 80/190 (42%), Gaps = 19/190 (10%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-- 201
           P    RLD   SG ++ A      +H+       RI ++Y     G+   + E    W  
Sbjct: 117 PHAASRLDVGVSGAVLCATGARGRRHVVAMREAGRIARVYV----GVAGGRVEGSGTWDA 172

Query: 202 -LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRV 257
            +      GG  +  V   +  A  A +H++ +            L + P TGRTHQLRV
Sbjct: 173 PIGAARARGGRSLPAVGGAD--AKDASTHYRAVASAGGGAAPATLLRLDPVTGRTHQLRV 230

Query: 258 HALHMGCPIVGDH-----KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           HA H G P++GD      +     +G    P+ +++ LHA  + +P   G      AP+P
Sbjct: 231 HAAHAGAPLLGDRDHGGARSVTTARGRVI-PL-SRVALHALRVTVPDERGELCAAIAPVP 288

Query: 313 AHMVKTWDSL 322
             + + W +L
Sbjct: 289 DELRELWVAL 298


>gi|118091027|ref|XP_426389.2| PREDICTED: similar to RPUSD2 protein [Gallus gallus]
          Length = 480

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 42/126 (33%), Positives = 68/126 (53%), Gaps = 8/126 (6%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKS 206
           HRLD+ TSG+L+ A+T   ++ + E  R R+++K Y   V G  P+++  C    L+   
Sbjct: 198 HRLDRMTSGVLMFAKTVEVSKRIDEQVRERQLEKEYVCRVVGEFPEHEVVCEEPILVVSY 257

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +G     V + + KG     + F+ +  +  K   ++  P TGRTHQ+RVH  ++G PI
Sbjct: 258 KVG-----VCRVDPKG-KCCKTIFQRLS-YNGKSSVVKCLPRTGRTHQIRVHLQYLGYPI 310

Query: 267 VGDHKY 272
           V D  Y
Sbjct: 311 VNDPIY 316


>gi|332140394|ref|YP_004426132.1| pseudouridylate synthase, 23S RNA-specific [Alteromonas macleodii
           str. 'Deep ecotype']
 gi|327550416|gb|AEA97134.1| pseudouridylate synthase, 23S RNA-specific [Alteromonas macleodii
           str. 'Deep ecotype']
          Length = 265

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 54/209 (25%), Positives = 91/209 (43%), Gaps = 10/209 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  I   +KP G+ V   S I  H   F +++  D  GQ     HRLD+ TSG+LV
Sbjct: 30  VLYQDEHIIAIDKPPGLLVHR-SPIDKHETVFAVQTLRDQIGQHVFPAHRLDRPTSGVLV 88

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            + +   A  L +    +++ K Y ++V G   +          +   I   +    +  
Sbjct: 89  FSFSADTAAKLGKQMMDKQVVKQYHAIVRGFVHHTGYIDYALKYRYDKIADKHKRPQQPP 148

Query: 220 EKGANY--AISHFKVIDCFAQ----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           +  +    +++ F V +   +    ++  + + P TGR HQLR H +H+  PI+GD  + 
Sbjct: 149 QPASTMYESLAKFDVPEPVGRYQSARYSLVRLSPSTGRKHQLRRHMVHIRHPIIGDTTHG 208

Query: 274 ANFKGNFTSPIQN--KLYLHARYMDLPHP 300
              +  F     N   L L    M   HP
Sbjct: 209 DGKQNKFAKSHFNFTHLALSCTQMGFSHP 237


>gi|57866557|ref|YP_188179.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           epidermidis RP62A]
 gi|57637215|gb|AAW54003.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus epidermidis RP62A]
          Length = 284

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 57/206 (27%), Positives = 96/206 (46%), Gaps = 26/206 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK----SWVDSKGQK--PRLTHRLDQET 154
           ++YED+ + + NKP    +Q  +    H  G L     ++   KG+K  P +  RLD+ T
Sbjct: 77  VIYEDAYLIIVNKP---QMQNCAPSREHPHGSLVEQVLAYYTKKGEKINPHIVTRLDRNT 133

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V A+      H+   F   + +K Y +L +G  ++    I   + + S    D + 
Sbjct: 134 SGLVVFAK----FGHVHNLFSKVKFKKEYVALAYGQTQSSG-VIEVPIARLS----DSII 184

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             + NEKG      + K++       C + +   TGRTHQ+RVH  ++G P++GD  Y  
Sbjct: 185 KREVNEKGKYAKTVYQKLMQNETASLCKINLL--TGRTHQIRVHFEYIGHPLIGDDLYGG 242

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           N       P  +   LH   ++  HP
Sbjct: 243 N------HPCVHGQALHCCSVEFIHP 262


>gi|325684453|gb|EGD26617.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp. lactis
           DSM 20072]
          Length = 302

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 75/289 (25%), Positives = 131/289 (45%), Gaps = 38/289 (13%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
            G + V+  R   + R++ G VV          H +  Q+ ++  + +++    L   ++
Sbjct: 37  GGMMLVNHHRRNGSYRLKEGDVV----------HFLMGQEPVNPWLKVSR----LPLDIV 82

Query: 103 YEDSKIYVFNKPAGI-SVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
            E +   V NKPAG+ S+  G     + I   +  F K  V+    KP +  RLDQ+TSG
Sbjct: 83  EETADYLVINKPAGLLSIPSGFHAEDAVINRVLAYFEKQGVNPAYVKPHIVTRLDQDTSG 142

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVH 214
           ++++ +   A    ++  +   I+K Y ++V G   N  E   + L+ K  + +G     
Sbjct: 143 LVLLGKNAIAHDRFSKLGKDAFIKK-YHAIVHG---NFAEGDLSGLIDKPLARVGDTVKR 198

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  N KG   A++ ++V+D        +E++  TGRTHQ+R+H   +G  + GD  Y A
Sbjct: 199 EV--NPKGQR-ALTEYRVLDQVPGA-SLVELRLLTGRTHQIRIHMASIGHVLYGDDLYGA 254

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             +  F      +  L+  Y+   +P  G   +I  P P  M   W  L
Sbjct: 255 --RDAFA-----RQALNCFYLSFTNPFSGEEREIEIPDPGDMQGLWRQL 296


>gi|298252221|ref|ZP_06976024.1| pseudouridine synthase [Ktedonobacter racemifer DSM 44963]
 gi|297546813|gb|EFH80681.1| pseudouridine synthase [Ktedonobacter racemifer DSM 44963]
          Length = 348

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 73/305 (23%), Positives = 121/305 (39%), Gaps = 76/305 (24%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-------QGGS---GIAYHIDG-F 132
           L +S+ +  + + +   +LY+D  + + NKPAG+ +        GG+    +  H++   
Sbjct: 33  LAASIPILPNMEEMGITILYQDHYLLIVNKPAGMVIHPTYKHTDGGTMWDALLRHLEAQE 92

Query: 133 LKSW------------------------------VDSKGQKPR--LTHRLDQETSGILVV 160
            + W                              +  +G  PR  L HRLD++TSG++ +
Sbjct: 93  PEQWSPPALADDPAWARAPLEIQDMLRERRRAQILQEEGLLPRPCLVHRLDKDTSGVVAL 152

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH------ 214
           ART  +  HL   F    I K Y ++V     +  +  A   +   H G    H      
Sbjct: 153 ARTERSRTHLVHQFHDHTIVKSYLAVVEPGSPDWTQPRAPLSVAFPHNGRVLTHFPTSFI 212

Query: 215 --VVKQNE--------------------KGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +V   E                    +G   A +  +V+   A +   LE++P TGRT
Sbjct: 213 QELVPDTEFLIDGPLWRDPDDRRRCVVIEGGQEARTWVRVLAHEAGR-SLLEVRPVTGRT 271

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           HQ+R H   +G  I GD  Y      +    +  + +LHAR + L H    R +  TAPL
Sbjct: 272 HQIRAHLAALGQAIAGDPVYRELQPSDL---VLGRQFLHARSLTLRHYVDNRVMTFTAPL 328

Query: 312 PAHMV 316
            A ++
Sbjct: 329 TADLL 333


>gi|242373163|ref|ZP_04818737.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
 gi|242349114|gb|EES40715.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
          Length = 284

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 64/246 (26%), Positives = 111/246 (45%), Gaps = 40/246 (16%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHS 94
            +  I R+G + V+K+ V     +  G  + +  P+    +++I  QK L+         
Sbjct: 26  TISAIKRNGALIVNKQPVTVRKEMSFGDHLEVHMPIEQPSSNLIPYQKALE--------- 76

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-----IDGFLKSWVDSKGQK--PRLT 147
                 +++ED  + + NKP     Q  +    H     ++  L +++ +KG+K  P + 
Sbjct: 77  ------IIFEDDFLVIVNKP---QYQNCAPSREHPHESLVEQVL-AYLINKGEKSNPHIV 126

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
            RLD+ T GI+V A+      H+   F   + +K Y  L +G  K+K    A        
Sbjct: 127 TRLDRNTMGIVVFAK----YGHVHHLFSKVKFEKEYVCLAYGRTKSKGVIEAPIARDNKS 182

Query: 208 IGGDYVHVVKQNEKGANYA-ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           I      + ++  K   YA  S++ ++       C +++  HTGRTHQ+RVH  H+  PI
Sbjct: 183 I------ITRKISKDGKYAKTSYYTLVQKDNASLCKVKL--HTGRTHQIRVHFQHIEHPI 234

Query: 267 VGDHKY 272
           VGD  Y
Sbjct: 235 VGDDLY 240


>gi|42518750|ref|NP_964680.1| hypothetical protein LJ0825 [Lactobacillus johnsonii NCC 533]
 gi|41583036|gb|AAS08646.1| hypothetical protein LJ_0825 [Lactobacillus johnsonii NCC 533]
          Length = 299

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 103/226 (45%), Gaps = 16/226 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQ---KPRLTHRLDQETSG 156
           +++E     V NK AGI S+      +  +   L  +   + Q   KP +  RLD++TSG
Sbjct: 81  IVFEQKDYLVINKDAGILSIPSRYEDSDAVVNRLLHYFQQQKQTDLKPHVITRLDRDTSG 140

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++V +   A    ++  +   I+K Y ++V G   N +E      +  + IG     V 
Sbjct: 141 LVLVGKNAVAHARFSKMEKNEFIKK-YHAIVHG---NFEEAQRQGTID-APIGKIDAGVK 195

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +        +++ ++V+D   +    +E+Q  TGRTHQ+RVH  ++G P+ GD  Y    
Sbjct: 196 RGVVNNGQRSVTKYRVLDQ-VKGASLIELQLLTGRTHQIRVHMQYLGHPLFGDPLY--GI 252

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           K NF     N  YL     D P  E  R +I    P  M   W +L
Sbjct: 253 KDNFKRQALNCFYLE---FDDPFSE-KRQKIEIADPIDMEILWKNL 294


>gi|68067749|ref|XP_675809.1| ribosomal large subunit pseudouridylate synthase, [Plasmodium
           berghei strain ANKA]
 gi|56495204|emb|CAI05271.1| ribosomal large subunit pseudouridylate synthase, putative
           [Plasmodium berghei]
          Length = 523

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 53/212 (25%), Positives = 89/212 (41%), Gaps = 57/212 (26%)

Query: 103 YEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           YE+    V NKP  I ++ G    I   ++  L+   +      R+  +LD  TSG+L++
Sbjct: 70  YENDFFLVVNKPYDIKLEKGKLDDIYPSVETLLRKKRNLNT--FRMCGQLDYATSGLLII 127

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ + ++  L  +   + I KIY ++++G                 H+  D +H+     
Sbjct: 128 AKDKLSSNILNYNIESKNISKIYLAILYG-----------------HLPLDVLHINVPIS 170

Query: 221 KGANYAISHFKVIDCF-------AQKFCW------------------LEMQPHTGRTHQL 255
           K  N     FK+  C+         K+C+                   E++  TGR HQL
Sbjct: 171 KVKN----EFKMKLCYNYNDYYDTGKYCYSLIYPYKHTYLKNEKVTLCELRTITGRRHQL 226

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           R+H++ +G  IVGD  Y       F   I+NK
Sbjct: 227 RLHSICLGSGIVGDETY-------FEDMIENK 251


>gi|221065999|ref|ZP_03542104.1| pseudouridine synthase [Comamonas testosteroni KF-1]
 gi|220711022|gb|EED66390.1| pseudouridine synthase [Comamonas testosteroni KF-1]
          Length = 250

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 101/231 (43%), Gaps = 36/231 (15%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           H+ FL   +L++D  +    KPAG  V      A+     +++  D  G+     HRLD+
Sbjct: 6   HNPFLH--ILWQDEHLVAVYKPAGWLVHRTGLDAHETRFVMQTLRDQLGRHVWPVHRLDK 63

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L++A  + AAQ L   F     +K Y +LV G           WL +   +    
Sbjct: 64  GTCGVLLMALNKEAAQALAARFAAHETRKEYRALVRG-----------WLPEVVEVD--- 109

Query: 213 VHVVKQNEKGANYAISHFKV-IDCFAQKFCW---------------LEMQPHTGRTHQLR 256
            H +K ++   +  +      + C A +  W               +E  P TGR HQ+R
Sbjct: 110 -HPLKPDDAPEDAPVQEAHTRLRCLA-RLSWPESWDGRHPETRISLVEALPTTGRRHQIR 167

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGGRL 305
            H  H+  PI+GD  +       + +    Q +L+LHAR +++ HP  G+L
Sbjct: 168 RHLKHVAHPIIGDATHGKGPLNRWWAERLGQQRLWLHARALEIAHPVSGQL 218


>gi|239624699|ref|ZP_04667730.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239521085|gb|EEQ60951.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 250

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 54/247 (21%), Positives = 110/247 (44%), Gaps = 27/247 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-----------KGQKPR---L 146
           +LYED  I V +KPAG+  Q   G A  +   ++ ++ +            G +P    +
Sbjct: 4   ILYEDKDIIVVHKPAGLESQSSRGFAPDMVSEIRRYLHNPQDIHRPAAGISGSQPPYVGV 63

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+   G++V A+ + +A  L+ + +  +++K Y +++ G   +K+    ++L +  
Sbjct: 64  IHRLDKPVEGVMVYAKNQKSAAALSAALQDGKMEKFYMAVICGQLVDKQGVYVDYLRQDR 123

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCF------AQKFCWLEMQPHTGRTHQLRVHAL 260
               +   +V ++ K A  A   ++ ++         +    ++++  TGR HQ+RV   
Sbjct: 124 K--NNTSEIVDKSVKDAKKAALKYREMEVIHSPEDKEKMLSLIDIELLTGRHHQIRVQFA 181

Query: 261 HMGCPIVGDHKYCANFKG-----NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
             G P+ GD +Y  +           + ++  L L A ++   HP  G   +    P+  
Sbjct: 182 GHGTPLYGDGRYGGDISTIVDIKKEPAAVRRPLALCACHLAFLHPVTGEKLVFEIRPSGG 241

Query: 316 VKTWDSL 322
              W S+
Sbjct: 242 AFNWFSV 248


>gi|329729823|gb|EGG66216.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU144]
          Length = 284

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 55/206 (26%), Positives = 98/206 (47%), Gaps = 26/206 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK----SWVDSKGQK--PRLTHRLDQET 154
           ++YED+ + + NKP    +Q  +    H  G L     ++   KG+K  P +  RLD+ T
Sbjct: 77  VIYEDAYLIIVNKP---QMQNCAPSREHPHGSLVEQVLAYYTKKGEKINPHIVTRLDRNT 133

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V A+      H+   F   + +K Y +L +G  ++    I   + ++S    D + 
Sbjct: 134 SGLVVFAK----FGHVHHLFSKVKFKKEYVALAYGHTQSSG-VIEEPIARRS----DSII 184

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             + N+KG      + +++       C +++   TGRTHQ+RVH  ++G P++GD  Y  
Sbjct: 185 KREVNDKGKYAKTVYQRLMQNETASLCKVKLL--TGRTHQIRVHFEYIGHPLIGDDLYGG 242

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           N       P  +   LH   ++  HP
Sbjct: 243 N------HPCVHGQALHCCSVEFIHP 262


>gi|281338228|gb|EFB13812.1| hypothetical protein PANDA_001071 [Ailuropoda melanoleuca]
          Length = 545

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 98/220 (44%), Gaps = 44/220 (20%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGS 123
           + E+ + D S+ L K +DFL++               LL E+  + V +KP+ I V    
Sbjct: 189 LNEEPVQDLSIVL-KDNDFLRNRVHRHEPPVTAEPVRLLAENEDMVVVDKPSSIPVHPCG 247

Query: 124 GIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++   F+   +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K
Sbjct: 248 RFRHNTVIFI---LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEK 304

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI--------SHFKV 232
            Y   V G  P  +  C    L+    +G     V + + +G              H  V
Sbjct: 305 EYVCRVEGEFPTEEVICKEPILVVSYKVG-----VCRVDARGKPCETVFQRLSYNGHSSV 359

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + C          +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 360 VRC----------RPLTGRTHQIRVHLQFLGHPILNDPIY 389


>gi|313123295|ref|YP_004033554.1| pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
 gi|312279858|gb|ADQ60577.1| Pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
          Length = 297

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 75/289 (25%), Positives = 131/289 (45%), Gaps = 38/289 (13%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
            G + V+  R   + R++ G VV          H +  Q+ ++  + +++    L   ++
Sbjct: 32  GGMMLVNHHRRNGSYRLKEGDVV----------HFLMGQEPVNPWLKVSR----LPLDIV 77

Query: 103 YEDSKIYVFNKPAGI-SVQGG-----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
            E +   V NKPAG+ S+  G     + I   +  F K  V+    KP +  RLDQ+TSG
Sbjct: 78  EETADYLVINKPAGLLSIPSGFHAEDAVINRVLAYFEKQGVNPAYVKPHIVTRLDQDTSG 137

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVH 214
           ++++ +   A    ++  +   I+K Y ++V G   N  E   + L+ K  + +G     
Sbjct: 138 LVLLGKNAIAHDRFSKLGKDAFIKK-YHAIVHG---NFAEGDLSGLIDKPLARVGDTVKR 193

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  N KG   A++ ++V+D        +E++  TGRTHQ+R+H   +G  + GD  Y A
Sbjct: 194 EV--NPKGQR-ALTEYRVLDQVPGA-SLVELRLLTGRTHQIRIHMASIGHVLYGDDLYGA 249

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             +  F      +  L+  Y+   +P  G   +I  P P  M   W  L
Sbjct: 250 --RDAFA-----RQALNCFYLSFTNPFSGEEREIEIPDPGDMQGLWRQL 291


>gi|183233062|ref|XP_001913799.1| hypothetical protein [Entamoeba histolytica HM-1:IMSS]
 gi|169801746|gb|EDS89422.1| hypothetical protein, conserved [Entamoeba histolytica HM-1:IMSS]
          Length = 356

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 65/221 (29%), Positives = 95/221 (42%), Gaps = 32/221 (14%)

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIY-VFNKPAGISVQ-GGSGIAYHID 130
            +N +I+E  IL S  +L +    +K I + E++  Y V NKP+GI V   G      I 
Sbjct: 60  TINSVIEEHDILISKCHLHEPPVPIKEIQIIENTNEYLVINKPSGIPVHPTGRYNQNCII 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--------RIQKI 182
             L +       KP   +RLD+ TSGIL+ A+T+  A       + +         +QKI
Sbjct: 120 NILLNEYHFSHLKP--VYRLDKNTSGILLFAKTKIFASSFQSILKEKSSVISSTSSLQKI 177

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI--------SHFKVID 234
           Y + V G   +  E   N  L     G +    + ++   A  +         S+  VI+
Sbjct: 178 YLARVVGYFPDSIE--VNLPLHLVRFGTESQSCICEDGIEARSSFKRLFFDKDSNTSVIE 235

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           C           PHTGRTHQLR+H   +  PI  D  Y  N
Sbjct: 236 CV----------PHTGRTHQLRLHLKAIHHPIANDSAYLLN 266


>gi|228477070|ref|ZP_04061708.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Streptococcus salivarius SK126]
 gi|228251089|gb|EEK10260.1| ribosomal large subunit pseudouridine synthase, RluD   family
           [Streptococcus salivarius SK126]
          Length = 298

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 80/166 (48%), Gaps = 12/166 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V NKP G +          +  F+K    S     Q+  +  RLD++TSG+
Sbjct: 78  IVYEDDNFLVINKPYGYASIPSVNHDNTMANFVKHHFVSNNYPNQRVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   + +  + + I+K Y++LV G  K   + E IA        I      +
Sbjct: 138 MLFAKHGYAHARMDKQLQQKSIKKHYYALVEGDTKLEEQGEIIAPIARDVDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            ++  K   YA + ++++  +  +   +++  HTGRTHQ+RVH  H
Sbjct: 192 TRRVHKSGKYAHTSYRLVADYG-RVKLVDINLHTGRTHQIRVHFAH 236


>gi|220934229|ref|YP_002513128.1| tRNA pseudouridine synthase C [Thioalkalivibrio sp. HL-EbGR7]
 gi|219995539|gb|ACL72141.1| tRNA pseudouridine synthase C [Thioalkalivibrio sp. HL-EbGR7]
          Length = 235

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 67/229 (29%), Positives = 101/229 (44%), Gaps = 14/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  +   NKP  + V   S I+      L+   D  GQ+    HRLD+ TSG+L+ 
Sbjct: 9   ILHQDDDLVAINKPEQMLVHR-SPISRDEVFVLQRLRDQLGQRVYTVHRLDRPTSGVLLF 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
               AAA  +   F    + K Y ++V G  +   E I + L  +S  G      V +  
Sbjct: 68  GLHPAAATAMARQFEAGEVHKRYLAVVRGYTEESGE-IDHPL--ESEDGRGLQQAVTRYR 124

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----- 275
           + A   +    V      ++  LE+ P +GR HQ+R H  H+  P+ GD  Y        
Sbjct: 125 RLATVELD-IPVGRYPVARYSLLEVWPRSGRRHQIRRHFKHIFHPLAGDTTYGEGRHNRL 183

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           F+ +F      +L LHA ++ L HP  G  L + APLP         LG
Sbjct: 184 FREHFGV---ERLLLHASHLSLRHPSTGEALNLHAPLPEAFSVLLQRLG 229


>gi|50365380|ref|YP_053805.1| 23S rRNA pseudouridine synthase [Mesoplasma florum L1]
 gi|50363936|gb|AAT75921.1| 23S rRNA pseudouridine synthase [Mesoplasma florum L1]
          Length = 323

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 69/315 (21%), Positives = 134/315 (42%), Gaps = 47/315 (14%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +++N  L ++ K +Y       + K LR G ++++ KR+K  + +           I A 
Sbjct: 30  NDDNQSLFKFLKKNYKTTPLSVIYKWLRKGDIKINGKRIKDKDYL-----------IKAN 78

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSI-----LLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           + II    + D++  + +  DF K       ++YEDS + +  KP  + V   S +   +
Sbjct: 79  DEII----VYDNNKPVLR-DDFKKITNYDIDVIYEDSNLLIVKKPYNVEVH--SPVKTSM 131

Query: 130 DGFLKSWV-DSKGQKPRLT--------HRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           D  +K+++ D+    P           HRLD+ TSG+++ A+ +     + E+ + +   
Sbjct: 132 DDIVKNYLFDTNQYNPSEENSYVISHIHRLDKLTSGLIMYAKNKQTHDIMVEAIQDKEKI 191

Query: 181 KIYWSLVWGIPKNKKECIANWL-----LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           + Y+     +P  +      W+     ++KS    ++    K+       A + F V+  
Sbjct: 192 EKYYRCRIDVPVTESLIAKGWIKYDPIIQKSVFSEEFRSDYKE-------ATTIFNVVSL 244

Query: 236 -FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHA 292
               +   LE+Q  TGR HQ+R    + G  I+ D +Y      N        NKL  + 
Sbjct: 245 DVTNEQTELEVQILTGRKHQIRATLEYYGASIINDSRYSGTIINNEKMIFLFANKLVFNG 304

Query: 293 RYMDLPHPEGGRLQI 307
              +L +  G  ++I
Sbjct: 305 FEGNLENLNGKIIEI 319


>gi|67462777|ref|XP_648050.1| RNA pseudouridylate synthase [Entamoeba histolytica HM-1:IMSS]
 gi|56463954|gb|EAL42664.1| RNA pseudouridylate synthase, putative [Entamoeba histolytica
           HM-1:IMSS]
          Length = 373

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 65/221 (29%), Positives = 95/221 (42%), Gaps = 32/221 (14%)

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIY-VFNKPAGISVQ-GGSGIAYHID 130
            +N +I+E  IL S  +L +    +K I + E++  Y V NKP+GI V   G      I 
Sbjct: 77  TINSVIEEHDILISKCHLHEPPVPIKEIQIIENTNEYLVINKPSGIPVHPTGRYNQNCII 136

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--------RIQKI 182
             L +       KP   +RLD+ TSGIL+ A+T+  A       + +         +QKI
Sbjct: 137 NILLNEYHFSHLKP--VYRLDKNTSGILLFAKTKIFASSFQSILKEKSSVISSTSSLQKI 194

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI--------SHFKVID 234
           Y + V G   +  E   N  L     G +    + ++   A  +         S+  VI+
Sbjct: 195 YLARVVGYFPDTIE--VNLPLHLVRFGTESQSCICEDGIEARSSFKRLFFDKDSNTSVIE 252

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           C           PHTGRTHQLR+H   +  PI  D  Y  N
Sbjct: 253 CV----------PHTGRTHQLRLHLKAIHHPIANDSAYLLN 283


>gi|296214181|ref|XP_002753587.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Callithrix jacchus]
          Length = 484

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 58/209 (27%), Positives = 91/209 (43%), Gaps = 43/209 (20%)

Query: 89  NLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
            L K +DFL++               LL E+  + V +KP+ I V       ++   F+ 
Sbjct: 138 GLRKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFI- 196

Query: 135 SWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP 191
             +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G  P
Sbjct: 197 --LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFP 254

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI--------SHFKVIDCFAQKFCWL 243
             +  C    L+    +G     V + + +G              H  V+ C        
Sbjct: 255 NEEVTCKEPILVVSYKVG-----VCRVDPQGKPCETVFQRLSYNGHSSVVQC-------- 301

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 302 --RPLTGRTHQIRVHLQFLGHPILNDPIY 328


>gi|264679457|ref|YP_003279364.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
 gi|262209970|gb|ACY34068.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
          Length = 255

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 69/263 (26%), Positives = 109/263 (41%), Gaps = 48/263 (18%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + +  + D S N   H       +L++D  + V  KPAG  V      A+     +++  
Sbjct: 1   MPDTALPDGSANPPLH-------ILWQDEHMVVVYKPAGWLVHRTGLDAHETRFVMQTLR 53

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D  G      HRLD+ T G+L++A  + AAQ L  SF     +K Y +LV G        
Sbjct: 54  DQLGHHVWPVHRLDKGTCGVLLMALHKQAAQALAASFAAHETRKEYRALVRG-------- 105

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCW-------------- 242
              WL +   +     H +K ++   +  +      + C A +  W              
Sbjct: 106 ---WLPETLEVD----HPLKPDDAPEDAPVQDAHTHLRCLA-RLSWPESYDGRHPETRIS 157

Query: 243 -LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYMDLPH 299
            +E  P TGR HQ+R H  H+  PI+GD  +       + +    Q +L+LHAR +++ H
Sbjct: 158 LVEALPTTGRRHQIRRHLKHVAHPIIGDATHGKGPLNRWWAERLGQQRLWLHARALEIAH 217

Query: 300 PEGGRLQITAPLPAHMVKTWDSL 322
           P  G+L        H    W SL
Sbjct: 218 PVSGQLM-------HFEADWSSL 233


>gi|312863550|ref|ZP_07723788.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
 gi|311101086|gb|EFQ59291.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
          Length = 298

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 80/166 (48%), Gaps = 12/166 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V NKP G +          +  F+K    S     Q+  +  RLD++TSG+
Sbjct: 78  IVYEDDNFLVINKPYGYASIPSVNHDNTMANFVKYHFVSNNYPNQRVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   + +  + + I+K Y++LV G  K   + E IA        I      +
Sbjct: 138 MLFAKHGYAHARMDKQLQQKSIKKHYYALVEGDTKLEQQGEIIAPIARDVDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            ++  K   YA + ++++  +  +   +++  HTGRTHQ+RVH  H
Sbjct: 192 TRRVHKSGKYAHTSYRLVGDYG-RVKLVDINLHTGRTHQIRVHFAH 236


>gi|116628160|ref|YP_820779.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus LMD-9]
 gi|116101437|gb|ABJ66583.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           thermophilus LMD-9]
          Length = 298

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 80/166 (48%), Gaps = 12/166 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V NKP G +          +  F+K    S     Q+  +  RLD++TSG+
Sbjct: 78  IVYEDDNFLVINKPYGYASIPSVNHDNTMANFVKHHFVSNNYPNQRVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   + +  + + I+K Y++LV G  K   + E IA        I      +
Sbjct: 138 MLFAKHGYAHARMDKQLQQKSIKKHYYALVEGETKLEQEGEIIAPIARDVDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            ++  K   YA + ++++  +  +   +++  HTGRTHQ+RVH  H
Sbjct: 192 TRRVHKSGKYAHTSYRLVGDYG-RVKLVDINLHTGRTHQIRVHFAH 236


>gi|55821440|ref|YP_139882.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMG 18311]
 gi|55823366|ref|YP_141807.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus CNRZ1066]
 gi|55737425|gb|AAV61067.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus LMG 18311]
 gi|55739351|gb|AAV62992.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus CNRZ1066]
 gi|312278771|gb|ADQ63428.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 298

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 80/166 (48%), Gaps = 12/166 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V NKP G +          +  F+K    S     Q+  +  RLD++TSG+
Sbjct: 78  IVYEDDNFLVINKPYGYASIPSVNHDNTMANFVKHHFVSNNYPNQRVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   + +  + + I+K Y++LV G  K   + E IA        I      +
Sbjct: 138 MLFAKHGYAHARMDKQLQQKSIKKHYYALVEGETKLEQQGEIIAPIARDVDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            ++  K   YA + ++++  +  +   +++  HTGRTHQ+RVH  H
Sbjct: 192 TRRVHKSGKYAHTSYRLVGDYG-RVKLVDINLHTGRTHQIRVHFAH 236


>gi|50555826|ref|XP_505321.1| YALI0F12199p [Yarrowia lipolytica]
 gi|49651191|emb|CAG78128.1| YALI0F12199p [Yarrowia lipolytica]
          Length = 605

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 81/183 (44%), Gaps = 12/183 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  + V +KP+G+ V       ++    +   V+     P   +RLD+ TSG++ +
Sbjct: 172 IVHEDDDLVVIDKPSGMPVHPAGRYRFNTAVNILKHVNGLHVHP--CNRLDRLTSGLMFM 229

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV------ 213
           A+   +A       R R++QK Y + V G  P  +     N       IG + V      
Sbjct: 230 AKNPKSADKFGAQLRDRQVQKQYVARVVGKFPDGEISVDENLCTLDPKIGFNIVTTKVDR 289

Query: 214 --HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             H    +      A + FK I    +    L  +P+TGRTHQ+RVH   +G PI  D  
Sbjct: 290 DHHRALMDRATEREAKTVFKRISYDGETSIVL-CKPYTGRTHQIRVHLQFLGHPIANDPL 348

Query: 272 YCA 274
           Y +
Sbjct: 349 YSS 351


>gi|325956350|ref|YP_004291762.1| Pseudouridine synthase [Lactobacillus acidophilus 30SC]
 gi|325332915|gb|ADZ06823.1| Pseudouridine synthase [Lactobacillus acidophilus 30SC]
          Length = 301

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 63/243 (25%), Positives = 106/243 (43%), Gaps = 26/243 (10%)

Query: 92  KHSDFLKSI-----LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKG 141
           K +DFLK        + E     + NKP G+       +    I   + G+  +   +K 
Sbjct: 68  KKNDFLKPSNNPVEPVLETKNYIILNKPVGVLSIPSRYEDNDAIVNRLMGYF-TRKGAKD 126

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            KP +  RLD++TSG+++V +   A    ++  + R I+K Y ++V G   N +      
Sbjct: 127 LKPHVITRLDRDTSGLVLVGKNAVAHARFSKMGKERFIKK-YHAIVHG---NFESTELTG 182

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L+ +  IG     V +        A + +KV+         +E++  TGRTHQ+RVH  +
Sbjct: 183 LIDEP-IGKIDSGVKRGVIPDGKSAQTEYKVLKQVPGA-SLVELRLLTGRTHQIRVHMAY 240

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL--PAHMVKTW 319
           +G P+ GD  Y    K +F+     +  L+  Y+  P P       T  +  P+ M   W
Sbjct: 241 LGHPLYGDQLYGV--KDSFS-----RQALNCFYLSFPDPVNSEKDKTVEISDPSDMQNLW 293

Query: 320 DSL 322
             L
Sbjct: 294 QKL 296


>gi|257487594|ref|ZP_05641635.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 100

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 38/100 (38%), Positives = 57/100 (57%), Gaps = 8/100 (8%)

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           HVV  + +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y 
Sbjct: 7   HVV--DHEGGKHALTFWKVVE-RHDTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLY- 62

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           A+ +     P   +L LHA  +   HP  G RL    P P
Sbjct: 63  AHPEALAAYP---RLCLHASMLSFTHPGTGERLTFECPAP 99


>gi|294659113|ref|XP_461454.2| DEHA2F25652p [Debaryomyces hansenii CBS767]
 gi|202953627|emb|CAG89871.2| DEHA2F25652p [Debaryomyces hansenii]
          Length = 433

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 67/261 (25%), Positives = 124/261 (47%), Gaps = 27/261 (10%)

Query: 50  KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIY 109
           +++++  + I + + +  P V   L  + K  K   +S +LT  S      +++E+ ++ 
Sbjct: 83  ERKIQSQDLIYNSKHIHEPSVAQGLELVKKSSKC--TSQDLTDLS------IIFENDEML 134

Query: 110 VFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           V +KPAGI         Y+ I   +K  ++ +   P   HRLD+ TSGIL++  T+  ++
Sbjct: 135 VIDKPAGIPTHPKGNYRYNSITELVKHDLNLENVWP--CHRLDKVTSGILILGTTKQGSK 192

Query: 169 HLTESFRMRR--IQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
             +      R  I K Y + V G  PK+  E + N  +   +  G Y+          N 
Sbjct: 193 IYSTIINNERDRISKQYVARVMGEFPKD--EFVMNCPIFLVNTSGGYIMPSNSRNVPKN- 249

Query: 226 AISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP- 283
           + + F+ ++   +     +  +P TGR HQ+R+H  + G PIV D++Y  N +G+ T   
Sbjct: 250 STTIFRRLNYNKELNQSIVLCKPITGRMHQIRIHLRNTGHPIVNDYEY--NPQGDATRSH 307

Query: 284 ---IQNKLYLHAR---YMDLP 298
              ++N++ L      Y+D P
Sbjct: 308 IQRLRNQIELQMYENIYLDFP 328


>gi|168037108|ref|XP_001771047.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162677735|gb|EDQ64202.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 324

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 69/308 (22%), Positives = 114/308 (37%), Gaps = 78/308 (25%)

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + + P    L+  ++ Q+ L +   +       +  +L+ED  + + NKP G+  +    
Sbjct: 20  IPLSPFAGELSKEVELQRALVAEAAMKAGPAIGQESVLFEDDWLMIVNKPRGLYCE---- 75

Query: 125 IAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              H+   + S   S   +  L   +RLD++TSGI+V+ + + AA  LT +F  R +QK 
Sbjct: 76  ---HVLATIPSLCRSSETQLHLHMANRLDRDTSGIMVITKCKEAAAKLTRAFTNREVQKT 132

Query: 183 YWS-LVWGIPKNKKECIAN---------WLLKKSH---------------------IGG- 210
           Y +      P  +K  I +         W +   H                     I G 
Sbjct: 133 YLAQCARAKPTWRKTRIESGHGRSRYGAWRVYAKHDIGRRLPGGSTVRDMVTRVEIIAGT 192

Query: 211 -------------DYVHVV-----------KQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                        D+V VV            + E G+        V+  F          
Sbjct: 193 NSLKQDPQPSPEHDFVEVVVGREDEVRLGKDEVEDGSLRETQELTVVRAF---------- 242

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           P TGRTHQ+R+H  ++G  + GD KY         S   +   LHA  +   HP     +
Sbjct: 243 PETGRTHQIRLHCQYLGLSLCGDVKYGGPLVWQGLS--YDSHALHAESLAFRHPITKEPI 300

Query: 306 QITAPLPA 313
            +  P P+
Sbjct: 301 SVVTPCPS 308


>gi|116629980|ref|YP_815152.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           ATCC 33323]
 gi|238853582|ref|ZP_04643952.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           202-4]
 gi|282851411|ref|ZP_06260776.1| pseudouridine synthase, RluA family [Lactobacillus gasseri 224-1]
 gi|311110388|ref|ZP_07711785.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           gasseri MV-22]
 gi|116095562|gb|ABJ60714.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           ATCC 33323]
 gi|238833800|gb|EEQ26067.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           202-4]
 gi|282557379|gb|EFB62976.1| pseudouridine synthase, RluA family [Lactobacillus gasseri 224-1]
 gi|311065542|gb|EFQ45882.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           gasseri MV-22]
          Length = 299

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 101/226 (44%), Gaps = 16/226 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSG 156
           +++E     V NK AG+ S+         +   L  +    GQK   P +  RLD++TSG
Sbjct: 81  IVFEQHDYLVVNKEAGVLSIPSRYEDNDAVVNRLIYYFQKNGQKDLKPHVITRLDRDTSG 140

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++V +   A    +E  +   I+K Y ++V G    ++E         + IG     V 
Sbjct: 141 LVLVGKNAVAHARFSEMGKDCFIKK-YHAIVHGNFSKEQETGT----IDAPIGKLDAGVK 195

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +        +I+ ++V++        +E+Q  TGRTHQ+RVH  ++G P+ GD  Y    
Sbjct: 196 RGIVANGQRSITKYRVLEQ-VNGASLVELQLLTGRTHQIRVHMQYLGHPLYGDPLY--GI 252

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           K NF     N  YL     D P  E  + +IT   P  M   W SL
Sbjct: 253 KDNFKRQALNCFYLK---FDDPFSE-LKQEITISEPVDMKCLWQSL 294


>gi|326780284|ref|ZP_08239549.1| pseudouridine synthase [Streptomyces cf. griseus XylebKG-1]
 gi|326660617|gb|EGE45463.1| pseudouridine synthase [Streptomyces cf. griseus XylebKG-1]
          Length = 312

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 61/207 (29%), Positives = 93/207 (44%), Gaps = 15/207 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG-IL 158
           ++Y D +I V +KP  ++    G  I       L+  ++    +P   HRLD+ T+G +L
Sbjct: 100 VVYRDERIVVADKPHFLATMPRGRHITETAVARLRRELELPALQP--AHRLDRLTAGLVL 157

Query: 159 VVART--RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            V R   R A Q L   FR RR++K Y +L    P +    +   +  +S I  +   + 
Sbjct: 158 FVVRPEDRGAYQTL---FRDRRVRKEYEALA---PYDPDVALPRTV--RSRIVKERGVLA 209

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + E G   + S  ++++       +  + P TGRTHQLRVH   +G PIV D  Y    
Sbjct: 210 AREEPGEANSESRVELVERRGGVGRY-RLLPATGRTHQLRVHMNALGLPIVHDPLYPVVV 268

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
                      L L AR +D   P GG
Sbjct: 269 PEAAVENWDRPLQLLARVLDFTDPVGG 295


>gi|221484026|gb|EEE22330.1| RNA pseudouridylate synthase domain-containing protein, putative
            [Toxoplasma gondii GT1]
          Length = 2255

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 44/132 (33%), Positives = 65/132 (49%), Gaps = 9/132 (6%)

Query: 148  HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWL---L 203
            HRLD  TSG L+VA++ A    L       R +K+Y +LV+G +P  +K  + + L    
Sbjct: 2021 HRLDTPTSGPLLVAKSYAGLAFLRAQLASWRPKKVYLALVFGAVPLREKVHLVHPLRPTF 2080

Query: 204  KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHAL 260
            +    G   + V   N   A  A+S    I  ++   + F    ++P TGRTHQ+R    
Sbjct: 2081 EAGKTGKKEMEVA--NTVDAKIALSFLSGITHYSYGGRDFTLCRVEPVTGRTHQIRAQLA 2138

Query: 261  HMGCPIVGDHKY 272
            H+G PIV D  Y
Sbjct: 2139 HIGHPIVADPIY 2150


>gi|322516374|ref|ZP_08069299.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           vestibularis ATCC 49124]
 gi|322125107|gb|EFX96500.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           vestibularis ATCC 49124]
          Length = 298

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 80/166 (48%), Gaps = 12/166 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V NKP G +          +  F+K    S     Q+  +  RLD++TSG+
Sbjct: 78  IVYEDDNFLVINKPYGYASIPSVNHDNTMANFVKYHFVSNNYPNQRVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   + +  + + I+K Y++LV G  K   + E IA        I      +
Sbjct: 138 MLFAKHGYAHARMDKQLQQKSIKKHYYALVEGDTKLEQQGEIIAPIARDVDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            ++  K   YA + ++++  +  +   +++  HTGRTHQ+RVH  H
Sbjct: 192 TRRVHKSGKYAHTSYRLVGDYG-RVKLVDINLHTGRTHQIRVHFAH 236


>gi|313771117|gb|EFS37083.1| RNA pseudouridine synthase [Propionibacterium acnes HL074PA1]
          Length = 281

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 55/197 (27%), Positives = 91/197 (46%), Gaps = 20/197 (10%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LY D +I V +KP  +S +  G  +   +   L++ +      P LT  HRLD+ T+G+
Sbjct: 64  ILYSDERILVVDKPHFLSSIPRGRHVLESVVVRLRTQLGL----PELTVAHRLDRVTAGV 119

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI----ANWLLKKSHIGGDYV 213
           L++ R R   +   E F  R + K Y  +   +  +  E +    + W ++ S I  +  
Sbjct: 120 LLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDSAGEGVTATKSGWQVR-SRIIKERG 178

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  +   G   A++   +I    +   W   E  P TGRTHQ+R+H   +G PIV D  
Sbjct: 179 ILQAREVPGVPNAVTDIALI---GEHGGWGLYEASPRTGRTHQIRLHMQRLGAPIVNDPF 235

Query: 272 YCANFK---GNFTSPIQ 285
           Y         +FT P+Q
Sbjct: 236 YPVVLDTPVDDFTHPLQ 252


>gi|330861062|emb|CBX71331.1| hypothetical protein YEW_JI40630 [Yersinia enterocolitica W22703]
          Length = 122

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 68/121 (56%), Gaps = 7/121 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +  N    +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLNKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  VPPVRVA------EREEIQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 Y 127
           +
Sbjct: 121 F 121


>gi|322373374|ref|ZP_08047910.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus sp. C150]
 gi|321278416|gb|EFX55485.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus sp. C150]
          Length = 298

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 80/166 (48%), Gaps = 12/166 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGI 157
           ++YED    V NKP G +          +  F+K    S     Q+  +  RLD++TSG+
Sbjct: 78  IVYEDDNFLVVNKPYGYASIPSVNHDNTMANFVKYHFVSNNYPNQRVHIVTRLDKDTSGL 137

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHV 215
           ++ A+   A   + +  + + I+K Y++LV G  K   + E IA        I      +
Sbjct: 138 MLFAKHGYAHARMDKQLQQKSIKKHYYALVEGDTKLEEQGEIIAPIARDVDSI------I 191

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            ++  K   YA + ++++  +  +   +++  HTGRTHQ+RVH  H
Sbjct: 192 TRRVHKSGKYAHTSYRLVGDYG-RVKLVDINLHTGRTHQIRVHFAH 236


>gi|289615384|emb|CBI57785.1| unnamed protein product [Sordaria macrospora]
          Length = 476

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/198 (26%), Positives = 81/198 (40%), Gaps = 27/198 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           +++ED  + V NKP+G+ V       Y+ +  ++     +G    PR  +RLD+ TSGI+
Sbjct: 146 VIHEDDDLIVINKPSGVPVHPAG--RYNYNSVVEIIKSQRGPDFLPRPCNRLDRLTSGIM 203

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWL-------LKKSHIGG 210
            +A+ + AA+ L      R ++K Y + V G  P  +  C    L       L +    G
Sbjct: 204 FLAKNQRAAERLVAQISQRSVRKEYIARVVGRFPDGEVVCDQPILQISPKLTLNRVRANG 263

Query: 211 DYVHVV---------------KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                V                Q E+ A              + +  +   P TGRTHQ+
Sbjct: 264 KSARTVFKRLAYYPPPDAAGKDQTEQPATPDAEQTAQRRGEGEGYSIVRCLPVTGRTHQI 323

Query: 256 RVHALHMGCPIVGDHKYC 273
           RVH   +G PI  D  Y 
Sbjct: 324 RVHLQFLGHPIQNDPIYA 341


>gi|326499976|dbj|BAJ90823.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326504092|dbj|BAK02832.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 389

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 82/329 (24%), Positives = 134/329 (40%), Gaps = 79/329 (24%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R+GQ+ VD            GQVV  P +I +    +   +       L+    F   +
Sbjct: 67  IRNGQITVD------------GQVVTDPDIILSEGSKLVYHR-------LSWKEPFAPYL 107

Query: 101 L--LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------------PRL 146
           L  LYED  +   NKP+G+ V                W + K               P  
Sbjct: 108 LQVLYEDDDMLALNKPSGLQVLPKGLFQQRTVLAQLQWKEWKMPPSSCSKKKNVQLHPVP 167

Query: 147 THRLDQETSGILVVARTRAAAQHL-----------------TESFRMRRIQKIYWSLVWG 189
            HRL + TSG+L+ A+T+ A   L                 TE  +  +I K Y +LV G
Sbjct: 168 VHRLGRGTSGLLLCAKTKLAKVQLASYFAEGAANAEKKRDGTEVGKEWKISKFYRALVTG 227

Query: 190 IPKNKKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQP 247
           I ++ ++ I   +    + G  + ++V   + K    A+S   V++  A Q    ++++ 
Sbjct: 228 ILEHDEDVITQPIGLVHYPGVAEGLYVACSSGKP---AMSKVCVLERLAHQNQTLVQVEI 284

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCAN------------------FKGNFTSPIQN--- 286
           H+GR HQ+R+H  ++G P+V D  Y                     + G +  P+Q    
Sbjct: 285 HSGRPHQIRIHLAYIGHPLVDDPLYGIGGQPKFHDLEPTSTDISFAYDGGYERPLQPVPG 344

Query: 287 --KLYLHARYMDLPHPEGGR-LQITAPLP 312
               +LHA ++ L HP   + L+ITA LP
Sbjct: 345 DCGYHLHAHWLVLCHPTTNKMLKITAHLP 373


>gi|331702115|ref|YP_004399074.1| RluA family pseudouridine synthase [Lactobacillus buchneri NRRL
           B-30929]
 gi|329129458|gb|AEB74011.1| pseudouridine synthase, RluA family [Lactobacillus buchneri NRRL
           B-30929]
          Length = 292

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 67/280 (23%), Positives = 117/280 (41%), Gaps = 41/280 (14%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
            GQ RV  ++V     +++G  V +  P   +  N  +  Q I                 
Sbjct: 36  GGQFRVGGRKVDATVVLRAGDQVTVDFPAEASDPNVAVSRQPI----------------S 79

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQK--PRLTHRLDQE 153
           ++YED    + +KPAG++V  G       +   + G L   V++  +   P +  RLD+ 
Sbjct: 80  VIYEDDNWLIVDKPAGLTVVPGPANRDDTLVNRVKGHL---VENGAEDLVPHIITRLDRF 136

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++++A+ R A     E    + + K Y ++V G+   K   I   + K       Y 
Sbjct: 137 TSGLVLIAKHRLANSLANEMLAAKTLHKQYQAVVAGVGLQKHGFIDRPIAKDPT---GYG 193

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             +  + K A    + + V   +  +   +++  HTGRTHQ+RVH   +  P++GD  Y 
Sbjct: 194 QRITADGKPAQ---TEYWVDQAYEDR-TLVDVVLHTGRTHQIRVHFASIDHPLLGDALYH 249

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              +         +  LHA  ++   P   R L   + LP
Sbjct: 250 GPMELGI-----GRQALHATQLNFEDPFSNRALSFKSQLP 284


>gi|221505297|gb|EEE30951.1| RNA pseudouridylate synthase domain-containing protein, putative
            [Toxoplasma gondii VEG]
          Length = 2273

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 44/132 (33%), Positives = 65/132 (49%), Gaps = 9/132 (6%)

Query: 148  HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWL---L 203
            HRLD  TSG L+VA++ A    L       R +K+Y +LV+G +P  +K  + + L    
Sbjct: 2039 HRLDTPTSGPLLVAKSYAGLAFLRAQLASWRPKKVYLALVFGAVPLREKVRLVHPLRPTF 2098

Query: 204  KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHAL 260
            +    G   + V   N   A  A+S    I  ++   + F    ++P TGRTHQ+R    
Sbjct: 2099 EAGKTGKKEMEVA--NTVDAKIALSFLSGITHYSYGGRDFTLCRVEPVTGRTHQIRAQLA 2156

Query: 261  HMGCPIVGDHKY 272
            H+G PIV D  Y
Sbjct: 2157 HIGHPIVADPIY 2168


>gi|237836503|ref|XP_002367549.1| RNA pseudouridylate synthase domain-containing protein [Toxoplasma
            gondii ME49]
 gi|211965213|gb|EEB00409.1| RNA pseudouridylate synthase domain-containing protein [Toxoplasma
            gondii ME49]
          Length = 2257

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 44/132 (33%), Positives = 65/132 (49%), Gaps = 9/132 (6%)

Query: 148  HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWL---L 203
            HRLD  TSG L+VA++ A    L       R +K+Y +LV+G +P  +K  + + L    
Sbjct: 2023 HRLDTPTSGPLLVAKSYAGLAFLRAQLASWRPKKVYLALVFGAVPLREKVRLVHPLRPTF 2082

Query: 204  KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHAL 260
            +    G   + V   N   A  A+S    I  ++   + F    ++P TGRTHQ+R    
Sbjct: 2083 EAGKTGKKEMEVA--NTVDAKIALSFLSGITHYSYGGRDFTLCRVEPVTGRTHQIRAQLA 2140

Query: 261  HMGCPIVGDHKY 272
            H+G PIV D  Y
Sbjct: 2141 HIGHPIVADPIY 2152


>gi|209483640|gb|ACI47296.1| pseudouridine synthase 1 [Toxoplasma gondii]
          Length = 2117

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 44/132 (33%), Positives = 65/132 (49%), Gaps = 9/132 (6%)

Query: 148  HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWL---L 203
            HRLD  TSG L+VA++ A    L       R +K+Y +LV+G +P  +K  + + L    
Sbjct: 1883 HRLDTPTSGPLLVAKSYAGLAFLRAQLASWRPKKVYLALVFGAVPLREKVRLVHPLRPTF 1942

Query: 204  KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHAL 260
            +    G   + V   N   A  A+S    I  ++   + F    ++P TGRTHQ+R    
Sbjct: 1943 EAGKTGKKEMEVA--NTVDAKIALSFLSGITHYSYGGRDFTLCRVEPVTGRTHQIRAQLA 2000

Query: 261  HMGCPIVGDHKY 272
            H+G PIV D  Y
Sbjct: 2001 HIGHPIVADPIY 2012


>gi|224011685|ref|XP_002295617.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|209583648|gb|ACI64334.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 344

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 54/189 (28%), Positives = 74/189 (39%), Gaps = 47/189 (24%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS-----------------LVWGI 190
           HRLD+ TSG+L++A+  + A  L   FR   + K Y +                 +V G 
Sbjct: 117 HRLDRVTSGVLLLAKDSSVANELITKFRQGEVSKYYMAISGKKPKKKKQGWVKGQMVMGR 176

Query: 191 PKNKKECIANWLLKKSHIGGDYVH---VVKQNEKGANYAISHFKVIDCFAQKFCWLE--- 244
             + K    N  +     G D V     V Q +K   YA++ F        +   L    
Sbjct: 177 RGSYKLVNENRDVLDEGDGDDEVEDGGEVSQVKKKGGYAVTRFYTAGLGDLQLAPLPKCD 236

Query: 245 -----------------MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN- 286
                             QPHTG+THQLRV A   G PI+GD +Y     G  T   +N 
Sbjct: 237 GDESNDDELLIPKTAILFQPHTGKTHQLRVAAKSAGIPILGDVRYGG---GTVTQREENA 293

Query: 287 ---KLYLHA 292
              + YLHA
Sbjct: 294 NFDRTYLHA 302


>gi|299530540|ref|ZP_07043960.1| pseudouridine synthase [Comamonas testosteroni S44]
 gi|298721516|gb|EFI62453.1| pseudouridine synthase [Comamonas testosteroni S44]
          Length = 255

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 65/246 (26%), Positives = 105/246 (42%), Gaps = 41/246 (16%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + +  + D S N   H       +L++D  + V  KPAG  V      A+     +++  
Sbjct: 1   MPDTALPDGSANPPLH-------ILWQDEHMVVVYKPAGWLVHRTGLDAHETRFVMQTLR 53

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D  G      HRLD+ T G+L++A  + AAQ L  SF     +K Y +LV G        
Sbjct: 54  DQLGHHVWPVHRLDKGTCGVLLMALHKQAAQALAASFAAHETRKEYRALVRG-------- 105

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCW-------------- 242
              WL +   +     H +K ++   +  +      + C A +  W              
Sbjct: 106 ---WLPETLEVD----HPLKPDDAPEDAPVQDAHTHLRCLA-RLSWPESYDGRHPETRIS 157

Query: 243 -LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYMDLPH 299
            +E  P TGR HQ+R H  H+  PI+GD  +       + +    Q +L+LHAR +++ H
Sbjct: 158 LVEALPTTGRRHQIRRHLKHVAHPIIGDATHGKGPLNRWWAERLGQQRLWLHARALEIAH 217

Query: 300 PEGGRL 305
           P  G+L
Sbjct: 218 PVSGQL 223


>gi|297696328|ref|XP_002825346.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Pongo abelii]
          Length = 484

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 57/207 (27%), Positives = 93/207 (44%), Gaps = 39/207 (18%)

Query: 89  NLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
            L K +DFL++               LL E+  + V +KP+ I V       ++   F+ 
Sbjct: 138 GLRKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFI- 196

Query: 135 SWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP 191
             +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G  P
Sbjct: 197 --LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFP 254

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------LEM 245
             +  C    L+    +G     V + + +G        K  +   Q+  +      +  
Sbjct: 255 TEEVTCKEPILVVSYKVG-----VCRVDPRG--------KPCETVFQRLSYNGQSSVVRC 301

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 302 RPLTGRTHQIRVHLQFLGHPILNDPIY 328


>gi|329667702|gb|AEB93650.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus johnsonii
           DPC 6026]
          Length = 299

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 103/226 (45%), Gaps = 16/226 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQ---KPRLTHRLDQETSG 156
           +++E     V NK AGI S+      +  +   L  +   + Q   KP +  RLD++TSG
Sbjct: 81  IVFEQKDYLVINKDAGILSIPSRYEDSDAVVNRLLHYFQQQKQTDLKPHVITRLDRDTSG 140

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++V +   A    ++  +   I+K Y ++V G   N +E      +  + IG     V 
Sbjct: 141 LVLVGKNAVAHARFSKMEKNEFIKK-YHAIVHG---NFEEAQRQGTID-APIGKIDTGVK 195

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +        +++ ++V+D   +    +E+Q  TGRTHQ+RVH  ++G P+ GD  Y    
Sbjct: 196 RGVVNNGQRSVTKYRVLDQ-VKGASLIELQLLTGRTHQIRVHMQYLGHPLFGDPLY--GI 252

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           K NF     N  YL     D P  E  R +I    P  M   W +L
Sbjct: 253 KDNFKRQALNCFYLE---FDDPFLE-KRQKIEIADPIDMEILWKNL 294


>gi|315037877|ref|YP_004031445.1| Pseudouridine synthase [Lactobacillus amylovorus GRL 1112]
 gi|312276010|gb|ADQ58650.1| Pseudouridine synthase [Lactobacillus amylovorus GRL 1112]
          Length = 301

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 107/242 (44%), Gaps = 24/242 (9%)

Query: 92  KHSDFLKSI-----LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQK-- 143
           K +DFLK        + E     + +KPAG+ S+         I   L  +   +G+K  
Sbjct: 68  KKNDFLKPSNNPVEPVLETKNYIILSKPAGVLSIPSRYEDDDAIVNRLMCYFIKEGKKDL 127

Query: 144 -PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P +  RLD++TSG+++V +   A    ++  + R I+K Y ++V G  +N  E      
Sbjct: 128 KPHVITRLDRDTSGLVLVGKNAVAHARFSKIGKERFIKK-YHAIVHGNFEND-ELTG--- 182

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L    IG     V +        A + +KV+   +     +E++  TGRTHQ+RVH  ++
Sbjct: 183 LVDEPIGKIDSGVKRGVIPDGKSAQTEYKVLKQVSGA-SLVELRLLTGRTHQIRVHMAYL 241

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA--PLPAHMVKTWD 320
           G P+ GD  Y    K  F+     +  L+  Y+  P P       T   P PA M K W 
Sbjct: 242 GHPLYGDQLY--GIKDPFS-----RQALNCFYLSFPDPFNSEKNKTVEIPDPADMQKLWQ 294

Query: 321 SL 322
            L
Sbjct: 295 GL 296


>gi|262047145|ref|ZP_06020104.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus MV-3A-US]
 gi|293380273|ref|ZP_06626351.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
 gi|260572722|gb|EEX29283.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus MV-3A-US]
 gi|290923182|gb|EFE00107.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
          Length = 301

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 112/245 (45%), Gaps = 30/245 (12%)

Query: 92  KHSDFLK------SILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQK- 143
           K +DFLK      SI+L E+    V NKPAG+ S+         +   L  +   KGQK 
Sbjct: 68  KKNDFLKPSNNPVSIVL-ENKNYLVVNKPAGVLSIPSRYEDDDAVVNRLLGYFAQKGQKN 126

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIA 199
             P +  RLD+ TSG+++V +   +    ++  + + ++K Y ++V G   P      I 
Sbjct: 127 LKPHVITRLDRYTSGLVLVGKNAISHARFSKIGKEKFVKK-YHAIVHGNFAPNELTGLID 185

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + KK   G      V  + K A  A   ++V+D        +E++  TGRTHQ+RVH 
Sbjct: 186 QPIGKK---GSGVKRAVVADGKDAQTA---YRVLDQVTGA-SLVELRLLTGRTHQIRVHM 238

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL--PAHMVK 317
            ++G P+ GD  Y    +  F+     +  L+  Y++ P P   +   T  L  P  M +
Sbjct: 239 AYLGHPLYGDPLY--GIQDGFS-----RQALNCFYLNFPDPFSQQKCKTIELNDPKDMQE 291

Query: 318 TWDSL 322
            W  L
Sbjct: 292 LWQKL 296


>gi|27467615|ref|NP_764252.1| hypothetical protein SE0697 [Staphylococcus epidermidis ATCC 12228]
 gi|251810369|ref|ZP_04824842.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|282875499|ref|ZP_06284370.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|293367012|ref|ZP_06613686.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|27315159|gb|AAO04294.1|AE016746_84 conserved hypothetical protein [Staphylococcus epidermidis ATCC
           12228]
 gi|251806106|gb|EES58763.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|281295526|gb|EFA88049.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|291318867|gb|EFE59239.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|329733393|gb|EGG69726.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU028]
 gi|329738101|gb|EGG74319.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU045]
          Length = 284

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 55/206 (26%), Positives = 98/206 (47%), Gaps = 26/206 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK----SWVDSKGQK--PRLTHRLDQET 154
           ++YED+ + + NKP    +Q  +    H  G L     ++   KG+K  P +  RLD+ T
Sbjct: 77  VIYEDAYLIIVNKP---QMQNCAPSREHPHGSLVEQVLAYYTKKGEKINPHIVTRLDRNT 133

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V A+      H+   F   + +K Y +L +G  ++    I   + ++S    D + 
Sbjct: 134 SGLVVFAK----FGHVHHLFSKVKFKKEYVALAYGHTQSSG-VIEAPIARRS----DSII 184

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             + N+KG      + +++       C +++   TGRTHQ+RVH  ++G P++GD  Y  
Sbjct: 185 KREVNDKGKYAKTVYQRLMQNETASLCKVKLL--TGRTHQIRVHFEYIGHPLIGDDLYGG 242

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP 300
           N       P  +   LH   ++  HP
Sbjct: 243 N------HPCVHGQALHCCSVEFIHP 262


>gi|260772679|ref|ZP_05881595.1| pseudouridylate synthase LSU rRNA-specific [Vibrio metschnikovii
           CIP 69.14]
 gi|260611818|gb|EEX37021.1| pseudouridylate synthase LSU rRNA-specific [Vibrio metschnikovii
           CIP 69.14]
          Length = 261

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 49/147 (33%), Positives = 75/147 (51%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSG+L++AR  AAA  L+ +F  R+++K Y ++    PK K+  I+  + + 
Sbjct: 75  LVHRLDKMTSGLLLLARNAAAASELSRAFAKRKVEKYYLAIGAKKPKKKQGLISGDMQRS 134

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V          N AI+ F  +     +  +L  +PHTG+THQ+RV    +G P
Sbjct: 135 RRASWKLVPTYD------NPAITQFFSLPAEPGERLFL-CKPHTGKTHQIRVALKSIGSP 187

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y    +        ++ YLHA
Sbjct: 188 IVGDPIYLPTSQA-------DRGYLHA 207


>gi|313811717|gb|EFS49431.1| RNA pseudouridine synthase [Propionibacterium acnes HL083PA1]
 gi|313832484|gb|EFS70198.1| RNA pseudouridine synthase [Propionibacterium acnes HL007PA1]
 gi|313832710|gb|EFS70424.1| RNA pseudouridine synthase [Propionibacterium acnes HL056PA1]
 gi|314975148|gb|EFT19243.1| RNA pseudouridine synthase [Propionibacterium acnes HL053PA1]
 gi|314977558|gb|EFT21653.1| RNA pseudouridine synthase [Propionibacterium acnes HL045PA1]
 gi|314985095|gb|EFT29187.1| RNA pseudouridine synthase [Propionibacterium acnes HL005PA1]
 gi|315096956|gb|EFT68932.1| RNA pseudouridine synthase [Propionibacterium acnes HL038PA1]
 gi|327332450|gb|EGE74185.1| RNA pseudouridylate synthase family protein [Propionibacterium
           acnes HL096PA2]
 gi|327446775|gb|EGE93429.1| RNA pseudouridine synthase [Propionibacterium acnes HL043PA2]
 gi|327448784|gb|EGE95438.1| RNA pseudouridine synthase [Propionibacterium acnes HL043PA1]
 gi|328759846|gb|EGF73436.1| RNA pseudouridylate synthase family protein [Propionibacterium
           acnes HL099PA1]
          Length = 281

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 55/197 (27%), Positives = 91/197 (46%), Gaps = 20/197 (10%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LY D +I V +KP  +S +  G  +   +   L++ +      P LT  HRLD+ T+G+
Sbjct: 64  ILYSDERILVVDKPHFLSSIPRGRHVLESVVVRLRTQLGL----PELTVAHRLDRVTAGV 119

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI----ANWLLKKSHIGGDYV 213
           L++ R R   +   E F  R + K Y  +   +  +  E +    + W ++ S I  +  
Sbjct: 120 LLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDSAGEGVTATKSGWQVR-SRIIKERG 178

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  +   G   A++   +I    +   W   E  P TGRTHQ+R+H   +G PIV D  
Sbjct: 179 ILQAREVPGVPNAVTDIALI---GEHGGWGLYEASPRTGRTHQIRLHMQRLGAPIVNDPF 235

Query: 272 YCANFK---GNFTSPIQ 285
           Y         +FT P+Q
Sbjct: 236 YPVVLDTPVDDFTHPLQ 252


>gi|257461210|ref|ZP_05626308.1| RNA pseudouridine synthase family protein [Campylobacter gracilis
           RM3268]
 gi|257441584|gb|EEV16729.1| RNA pseudouridine synthase family protein [Campylobacter gracilis
           RM3268]
          Length = 470

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 36/89 (40%), Positives = 51/89 (57%), Gaps = 4/89 (4%)

Query: 102 LYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++E      F+KP+GI S   G    Y++  + + W    GQ   + HRLD ETSGIL+V
Sbjct: 72  IFECDAFAAFDKPSGILSHPSGRNSPYNM--YDEIW-SLYGQDACVAHRLDLETSGILIV 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           A+ + AA+ L E F  RR+ K Y +LV G
Sbjct: 129 AKDKDAARELKECFEQRRVMKSYLALVQG 157


>gi|227874155|ref|ZP_03992360.1| pseudouridylate synthase [Oribacterium sinus F0268]
 gi|227840002|gb|EEJ50427.1| pseudouridylate synthase [Oribacterium sinus F0268]
          Length = 206

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 49/183 (26%), Positives = 85/183 (46%), Gaps = 15/183 (8%)

Query: 132 FLKSWVDSKGQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV- 187
           + ++ +DS+   P+     HRLD+  SG+L+  + + AA  L+     ++I+K Y  +V 
Sbjct: 13  YKEAGLDSEKDAPKDCLPIHRLDKVASGLLLYGKNKEAAAALSRQLTEKKIKKRYHIVVP 72

Query: 188 ---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
               G    ++ C  ++L K S         VK   KG   AI  +K+++   + +  L+
Sbjct: 73  KGEEGKALPEEGCFQDYLYKDSK--KQKCFPVKSLRKGVKEAILRYKILEENGE-WMLLD 129

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL-----HARYMDLPH 299
           ++  TGR HQ+R      G P+ GD KY +  KG          +L       R  ++ +
Sbjct: 130 VELETGRFHQIRAQFASRGFPLYGDGKYGSRQKGTVGLHCYQLSFLDVKTGEERGFEIKN 189

Query: 300 PEG 302
           PEG
Sbjct: 190 PEG 192


>gi|146102317|ref|XP_001469333.1| hypothetical protein [Leishmania infantum]
 gi|134073702|emb|CAM72439.1| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 741

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 61/235 (25%), Positives = 97/235 (41%), Gaps = 44/235 (18%)

Query: 101 LLYEDSKIYVFNKPAGISV--------QGGSGIAYHID--------GFLKSWVDSKGQKP 144
           +LYED  + V +KPAG++         Q G+     I         G L   +  +GQ  
Sbjct: 514 VLYEDDDVLVVDKPAGLATSRHGLSCTQLGTPTTDLISVLLATDRVGALARGIFRQGQ-- 571

Query: 145 RLTHRLDQETSGILVVARTRAAAQ----HLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              HRLD ETSG L++A++  AA      L  S       KIY +L   +  +       
Sbjct: 572 --VHRLDAETSGCLLIAKSDVAADSLRHQLGTSAAFSHHSKIYHALCVVLEPS------- 622

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHA 259
             L+   +  D +       +      + ++VI  F + +  W+E +   G+ HQLR H 
Sbjct: 623 --LRNVRLHDDIIDAADPKIR------TRYRVIRFFPKHRVAWVECRIQQGKKHQLRRHL 674

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
              G PI+ D ++           + +++ LHA  +   HP     +   APLPA
Sbjct: 675 ASRGLPILADLEHGGAV---CCQSMISRVALHAHSLSFIHPVTADPITAAAPLPA 726


>gi|319787217|ref|YP_004146692.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317465729|gb|ADV27461.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
          Length = 282

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 47/151 (31%), Positives = 76/151 (50%), Gaps = 21/151 (13%)

Query: 148 HRLDQETSGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           HRLD++T+G+++ +    TR A Q L   FR RRI+K+Y ++   +P      ++   L 
Sbjct: 127 HRLDRDTAGLVMFSTQPATRGAYQAL---FRERRIRKLYRAVAPPLP-----GLSFPHLH 178

Query: 205 KSHI-GGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWL-EMQPHTGRTHQLRVHALH 261
           +S +  G+    +++ E   N       VID   +    W  +++P TGR HQLRVH   
Sbjct: 179 RSRLEAGEPFFRMREVEGEPNSET----VIDVLERNGPTWTYQLEPVTGRKHQLRVHMAA 234

Query: 262 MGCPIVGDHKYC---ANFKGNFTSPIQNKLY 289
           +G PI+GD  Y         +  +P+Q   Y
Sbjct: 235 LGAPIIGDRYYPKLQPQDTDDLAAPLQLTAY 265


>gi|156089749|ref|XP_001612281.1| RNA pseudouridylate synthase family protein [Babesia bovis]
 gi|154799535|gb|EDO08713.1| RNA pseudouridylate synthase family protein [Babesia bovis]
          Length = 465

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 99/231 (42%), Gaps = 36/231 (15%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKS 135
           ++ EQ  LDSSV +           L+ED      +KP+ + +       Y+ +   LK+
Sbjct: 143 LVHEQMALDSSVRI-----------LHEDDDYIAVSKPSSLPLYHTGTYYYNTLVEVLKN 191

Query: 136 WVDSKGQKPRL-THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN- 193
            V     +     HRLD+ TSG++++A++  AA    E  R  R +K+Y + V G   N 
Sbjct: 192 EVFKDSARTLYPVHRLDKLTSGVIILAKSSKAASEFCEGIRNSRFRKVYIARVKGDFTNV 251

Query: 194 --KKECIA----------------NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
               ECI+                 ++   SH    +   +   +K    A + F+++  
Sbjct: 252 FGDHECISINDGIGVGNGSVACCHGFMRCVSHKLSMHEFTLDDTKKDVKVAETRFRMLSY 311

Query: 236 FAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
            +      L   P TGRTHQ+R H  ++G PI  D   C N  G  +S ++
Sbjct: 312 NSSLDESLLLCYPVTGRTHQIRAHLKYLGYPISNDK--CYN-DGELSSSVE 359


>gi|168024645|ref|XP_001764846.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162683882|gb|EDQ70288.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 327

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 33/122 (27%), Positives = 65/122 (53%), Gaps = 10/122 (8%)

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V + PV + L++ ++ Q+ L +   +       +  +L+ED  + + NKP G+       
Sbjct: 20  VPLSPVPSQLSNEVELQRALVAEAAMKSRPAIGRESVLFEDEWLIIVNKPRGL------- 72

Query: 125 IAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            + H+   + S   S G+ P    + +RLD++TSGI+++ + + AA +LT S+  R++ K
Sbjct: 73  YSGHVFETMPSLCSSSGETPLHLHMANRLDRDTSGIMIITKCKVAAANLTRSYMNRKVHK 132

Query: 182 IY 183
            Y
Sbjct: 133 TY 134



 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 43/80 (53%), Gaps = 7/80 (8%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           P TGRTHQ+R+H  ++G P+ GD KY       + S   +   LHA  + L HP   + L
Sbjct: 245 PETGRTHQIRLHCQYLGLPLCGDVKYGGPL--FWQSVHYDSHTLHAESLALRHPMTNQLL 302

Query: 306 QITAPLPAHMVKTWDSLGFK 325
           Q+ AP P+  V+    LG K
Sbjct: 303 QVVAPYPSWAVQ----LGVK 318


>gi|325973143|ref|YP_004250207.1| tRNA pseudouridine synthase [Mycoplasma suis str. Illinois]
 gi|323651745|gb|ADX97827.1| tRNA pseudouridine synthase [Mycoplasma suis str. Illinois]
          Length = 231

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 50/192 (26%), Positives = 86/192 (44%), Gaps = 26/192 (13%)

Query: 119 VQGGSGIAYHIDGFLK---SWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           V   SGI  H D + +   + +D      G+   L +RLD+ TSG+L++A+ + +   L 
Sbjct: 15  VDKDSGILVHKDKYTRGKDTLIDILKEEYGEDIYLVNRLDKNTSGLLLIAKGKLSLLTLK 74

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F  ++I K Y +++     + K  I   L +     G  +     N K    A+++ +
Sbjct: 75  ALFEEQKIDKKYLAILSSPLPHPKIKITFSLGRDK---GKKLRFTATNSKKYKTALTYAE 131

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL--- 288
            I+    +   L ++  TGRTHQLR H   + CP++ D  Y          P++N     
Sbjct: 132 TINS---QLVLLSLK--TGRTHQLRAHLFTLSCPVLNDSVYGV--------PLENDSFGQ 178

Query: 289 YLHARYMDLPHP 300
           YLH+  +    P
Sbjct: 179 YLHSYSLSFVDP 190


>gi|291059569|gb|ADD72304.1| putative S4 domain protein [Treponema pallidum subsp. pallidum str.
           Chicago]
          Length = 404

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 65/275 (23%), Positives = 113/275 (41%), Gaps = 42/275 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+      ++   R+DR  +   P    V +   LR   +R++ + V+   R+Q G V+ 
Sbjct: 77  VECFRCTKNDAGRRVDRVLRILLPACPRVGVYAALRRTAIRLNGRPVQPAKRVQVGDVLS 136

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P    +L         L S +  T     L S++ ++   +  F+KPAG+ V G     
Sbjct: 137 LP---ESLCRARAASSRL-SKMPGTPKLRVLPSVV-FKTQDLLFFHKPAGLCVHGPRS-- 189

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 L +WV  +G+         +P   HRLD+ T G++  +R+   AQ  + + +  
Sbjct: 190 ------LDAWVRGQGRAHVPPALSFRPGPLHRLDRGTEGLIAFSRSLRGAQWFSAALQQH 243

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  L       +    A  L++     G+  HV  Q    +  +    +VI    
Sbjct: 244 TLRKFY--LAITAAPARTAAAARTLVRP----GEVTHV--QTVLHSCDSALVLRVI---- 291

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                    P TG+ HQ+R +    G P+VGD  Y
Sbjct: 292 --------VPVTGKKHQIRRYCAAQGFPLVGDRTY 318


>gi|313894448|ref|ZP_07828013.1| RNA pseudouridine synthase [Veillonella sp. oral taxon 158 str.
           F0412]
 gi|313441272|gb|EFR59699.1| RNA pseudouridine synthase [Veillonella sp. oral taxon 158 str.
           F0412]
          Length = 261

 Score = 60.1 bits (144), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 59/256 (23%), Positives = 108/256 (42%), Gaps = 61/256 (23%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LYED  + + +KPAG++V         +G+AY+   F ++ +    +K R  +RLD++T
Sbjct: 20  ILYEDDDLLIVDKPAGVTVNSKDQVSLVNGVAYY---FKENGIK---RKVRFLNRLDRDT 73

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG----- 209
           +G + +A++  A     +       +K Y + V GI +  ++ +    +++S  G     
Sbjct: 74  TGCIAIAKSGLAQSLYQQQMDDNTFEKWYMATVEGIVEADEDSLV-LSMERSADGIHYEV 132

Query: 210 --------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP-------------- 247
                    DY  + +   +  + +++  K     A K   +E+                
Sbjct: 133 NPKGKETRTDYSVLCRHQSQPVDNSVNKSKNSVDIASKNVDIELSDVDKSGQNVDKSVYN 192

Query: 248 -------------HTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHAR 293
                        +TG+THQ+RV   H+G P+VGD  Y A   G  F    Q  ++ H R
Sbjct: 193 SQECGYTEVLVRLYTGKTHQIRVAFSHIGHPLVGDTLYGAQPTGQPFQLRAQKVVFTHMR 252

Query: 294 YMDLPHPEGGRLQITA 309
                   G R+ +TA
Sbjct: 253 -------TGERITVTA 261


>gi|309813100|ref|ZP_07706824.1| RNA pseudouridine synthase [Dermacoccus sp. Ellin185]
 gi|308432904|gb|EFP56812.1| RNA pseudouridine synthase [Dermacoccus sp. Ellin185]
          Length = 286

 Score = 60.1 bits (144), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 55/200 (27%), Positives = 88/200 (44%), Gaps = 32/200 (16%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED +I V +KP  + S+  G  +   +    ++ +D     P   HRLD+ T+G+L+
Sbjct: 67  VLHEDERIVVVDKPHFLASIPRGRHVTQSVVVKARAMLDEPTLVP--VHRLDRLTAGVLL 124

Query: 160 VART---RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-------IG 209
           + R    RAA Q +   F  R++ K Y ++    P  +        ++K H       + 
Sbjct: 125 LTREPRWRAAYQGI---FEARQVSKTYEAVAAYDPSLELPRRVESHIRKQHGLAQAFEVP 181

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           G  V+ +   E G                      + P TGRTHQLR+H   +G PIVGD
Sbjct: 182 GAPVNAITDIELGQVRG------------DVATYRLTPATGRTHQLRLHLNGLGIPIVGD 229

Query: 270 ----HKYCANFKGNFTSPIQ 285
               H    +   +FT P+Q
Sbjct: 230 PLYPHVRLDDDIDDFTRPLQ 249


>gi|304438848|ref|ZP_07398773.1| RluA family ribosomal large subunit pseudouridine synthase
           [Peptoniphilus duerdenii ATCC BAA-1640]
 gi|304372689|gb|EFM26270.1| RluA family ribosomal large subunit pseudouridine synthase
           [Peptoniphilus duerdenii ATCC BAA-1640]
          Length = 313

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 68/289 (23%), Positives = 127/289 (43%), Gaps = 52/289 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR------VKFNNRIQ 60
           ++ +++ +++++ RLDR+   +  +     + K +R   + V+ K+      +K N+R++
Sbjct: 1   MKEIIINSNDKDQRLDRFMGKYLQNAKKSLIMKSIRKKNITVNNKKSAPEYILKENDRVE 60

Query: 61  ---SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
              S +   I       NH+                 DF    ++YED  I +  KP G+
Sbjct: 61  IYFSDET--IEKFTKIKNHV---------------KRDF--PDIIYEDENIALVKKPRGL 101

Query: 118 SVQGGSGIAYH---IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRA 165
                    Y    +D F+ S++  KG+         +P   +RLD+ TSGIL+  +   
Sbjct: 102 LTHNDKK-DYEKNALDMFV-SYMIHKGEYVPRVEKSFRPSFCNRLDRNTSGILIGCKNAQ 159

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV-HVVKQNEKGAN 224
           A + + ++ + R I+K Y +LV G        I   +   S++  D   + V  NE+G  
Sbjct: 160 ALREINDAIKRREIEKHYMALVDG-------SIDEEIHDISYLEKDREKNKVSLNERGDG 212

Query: 225 YAISH-FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             I    + ++   + +  +++   TGRTHQ+R         IVGD KY
Sbjct: 213 KEIETIIRPMEKLGE-YTLVDINLITGRTHQIRATLKKYNRSIVGDLKY 260


>gi|227893162|ref|ZP_04010967.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus ultunensis
           DSM 16047]
 gi|227865028|gb|EEJ72449.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus ultunensis
           DSM 16047]
          Length = 310

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 73/328 (22%), Positives = 140/328 (42%), Gaps = 39/328 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +MT +  ++V+  +         KN + H   +  +     G + V+ KR   + R+++G
Sbjct: 9   IMTSLFKLIVQERDPKKLGSFLLKNGFSHQALIKAR--YHHGMILVNHKRRYLSFRLRTG 66

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI----- 117
             V         N  +K              S+ +K +L  E     V +KPAG+     
Sbjct: 67  DEVIFISGEEKKNEFLKPS------------SNPVKPVL--ETKNYIVLDKPAGVLSIPS 112

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +    I   + G+  +  +    KP +  RLD++TSG+++V +   A    ++  + +
Sbjct: 113 RYEDNDAIVNRLMGYF-AKKNMSNLKPHVITRLDRDTSGLVLVGKNAIAHARFSKIGKEK 171

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            ++K Y ++V G   ++K   + +  + K   G     V +   +G   A + ++V+   
Sbjct: 172 FVKK-YHAIVHGNFSEDKLTGVIDAPIGKKGSG-----VKRAVVEGGKKAQTKYRVLKQV 225

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           +     +E++  TGRTHQ+RVH  ++G P+ GDH Y    + +F+    N  YL      
Sbjct: 226 SGA-SLVELRLLTGRTHQIRVHMAYLGHPLYGDHLY--GIEDDFSRQALNCFYL-----S 277

Query: 297 LPHPEGGR--LQITAPLPAHMVKTWDSL 322
            P P       +I+   P  M + W  +
Sbjct: 278 FPDPFDNEKIKEISIEEPTDMNELWQKM 305


>gi|325989585|ref|YP_004249284.1| pseudouridine synthase, RluA family [Mycoplasma suis KI3806]
 gi|323574670|emb|CBZ40326.1| similar to pseudouridine synthase, RluA family [Mycoplasma suis]
          Length = 231

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 50/192 (26%), Positives = 86/192 (44%), Gaps = 26/192 (13%)

Query: 119 VQGGSGIAYHIDGFLK---SWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           V   SGI  H D + +   + +D      G+   L +RLD+ TSG+L++A+ + +   L 
Sbjct: 15  VDKDSGILVHKDKYTRGKDTLIDILKEEYGENIYLVNRLDKNTSGLLLIAKGKLSLLTLK 74

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F  ++I K Y +++     + K  I   L +     G  +     N K    A+++ +
Sbjct: 75  ALFEEQKIDKKYLAILSSPLPHPKIKITFSLGRDK---GKKLRFTATNSKKYKTALTYAE 131

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL--- 288
            I+    +   L ++  TGRTHQLR H   + CP++ D  Y          P++N     
Sbjct: 132 TINS---QLVLLSLK--TGRTHQLRAHLFTLSCPVLNDSVYGV--------PLENDSFGQ 178

Query: 289 YLHARYMDLPHP 300
           YLH+  +    P
Sbjct: 179 YLHSYSLSFIDP 190


>gi|222823998|ref|YP_002575572.1| ribosomal large subunit pseudouridine synthase [Campylobacter lari
           RM2100]
 gi|222539220|gb|ACM64321.1| putative ribosomal large subunit pseudouridine synthase
           [Campylobacter lari RM2100]
          Length = 250

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 49/177 (27%), Positives = 82/177 (46%), Gaps = 24/177 (13%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K+ +L+ED KI   NKP G            I   L+   ++K     L +RLD+ETSG+
Sbjct: 56  KAKILFEDDKIIALNKPYG-----------EISENLEDVYNAK-----LINRLDKETSGV 99

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++++         + ++ + + K Y ++V G+   + E        K+  G       K
Sbjct: 100 LLLSKDEEFRLKCIQEYKKQNVYKSYLAIVDGVIAEELEICEKITTIKNKSGA----FSK 155

Query: 218 QNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            ++ G     +H +V+      K   ++    TGRTHQ+RVH  H+   I+GD KY 
Sbjct: 156 IDKFGLE---AHTQVVPLMVNAKKTLIKAIIKTGRTHQIRVHLNHIKHGIIGDEKYA 209


>gi|321475493|gb|EFX86456.1| hypothetical protein DAPPUDRAFT_313092 [Daphnia pulex]
          Length = 670

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 51/196 (26%), Positives = 84/196 (42%), Gaps = 23/196 (11%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              ++Y+D  + V +KP  + V       ++   F+ +  
Sbjct: 228 KHNDLLANIVHRHEVPVESKIIEIVYQDDDMIVIDKPCSVPVHPCGRYRHNTVAFILAK- 286

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  R +  A+ +    R R + K Y   V G  P     
Sbjct: 287 EHNLRNLRTIHRLDRLTSGLLMFGRNQEKARQMEVQIRTRLVSKEYVCRVGGEFPSGHIM 346

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V + + KG +      ++   +  K   +  +P TGR HQ+R
Sbjct: 347 CTEPIEVVSYKIG-----VCRVSPKGKDCQTEFERL--SYNGKTSVVLCKPRTGRMHQIR 399

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI  D  Y
Sbjct: 400 VHLQYLGYPIANDPLY 415


>gi|194375494|dbj|BAG56692.1| unnamed protein product [Homo sapiens]
          Length = 484

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 57/207 (27%), Positives = 93/207 (44%), Gaps = 39/207 (18%)

Query: 89  NLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
            L K +DFL++               LL E+  + V +KP+ I V       ++   F+ 
Sbjct: 138 GLRKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFI- 196

Query: 135 SWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP 191
             +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G  P
Sbjct: 197 --LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFP 254

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------LEM 245
             +  C    L+    +G     V + + +G        K  +   Q+  +      +  
Sbjct: 255 TEEVTCKEPILVVSYKVG-----VCRVDPRG--------KPCETVFQRLSYNGQSSVVRC 301

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 302 RPLTGRTHQIRVHLQFLGHPILNDPIY 328


>gi|227499062|ref|ZP_03929199.1| pseudouridine synthase [Acidaminococcus sp. D21]
 gi|226904511|gb|EEH90429.1| pseudouridine synthase [Acidaminococcus sp. D21]
          Length = 296

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 102/215 (47%), Gaps = 23/215 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRL--THRLDQETSG 156
           +LYED  +   +K  G+ V   SG+     +   +  +    G K  L    RLD+ETSG
Sbjct: 77  ILYEDEVLLAVHKEQGLLVHN-SGLTQESSLSRRVLFYYREHGIKAALHPVSRLDRETSG 135

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I++ A+  A    LT++     ++K+Y +L  G  +     IA  + +K   G      V
Sbjct: 136 IVLFAKNAALHHMLTKA----PMKKLYLALSHGPWEKFSGVIAQPIARKD--GSLIERCV 189

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               K A    + ++V+   A K   +    +TGRTHQ+RVHA  MG P++GD  Y A  
Sbjct: 190 APQGKPAR---TRYRVLWQDAAKSV-VAFHLYTGRTHQIRVHAAFMGHPLLGDTLYGA-- 243

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           KG+     Q    LHA  +   HP  G+ ++IT P
Sbjct: 244 KGS-----QKAHALHAMRLQFRHPLSGKDVKITDP 273


>gi|325295044|ref|YP_004281558.1| pseudouridine synthase [Desulfurobacterium thermolithotrophum DSM
           11699]
 gi|325065492|gb|ADY73499.1| pseudouridine synthase [Desulfurobacterium thermolithotrophum DSM
           11699]
          Length = 280

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 59/216 (27%), Positives = 103/216 (47%), Gaps = 36/216 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED    V NKP  I+              ++S +  + +   + HRLD++TSG L++
Sbjct: 74  ILYEDEYFLVVNKPPFINSNKNFPD-------VESLLRKRFKSIYVAHRLDKQTSGALII 126

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+++   +     F+ + ++K Y +LV G + KN  +        K  I G         
Sbjct: 127 AKSKEVFELFKLKFKKKEVKKKYLALVAGNLKKNSGKI-------KFSIDG--------- 170

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 AIS ++V++    K  +LE++  TGR HQ+R H + +  PI+G+  Y   +K  
Sbjct: 171 ----KEAISRYQVVERVG-KTDFLEVEILTGRKHQIRKHFVSVNHPIIGEFVY---WKRT 222

Query: 280 FTSPI---QNKLYLHARYMDLPHP-EGGRLQITAPL 311
           F   I     ++ LHA+ +   HP +   +++ APL
Sbjct: 223 FPQKIHLFSPRIMLHAKLLKFKHPIKEHHVEVKAPL 258


>gi|219122503|ref|XP_002181583.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406859|gb|EEC46797.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 271

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 110/243 (45%), Gaps = 32/243 (13%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK-HSDFLKS 99
           ++ G++RV  ++V     I+S  V         L H +      + +V +++  + F+K 
Sbjct: 50  IQQGRIRVGNEKVDVAYTIRSNDV---------LTHTVHRH---EPAVAVSQPQAPFVKV 97

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +   E     V +KP  + V      AYH++  L    ++ G K    HRLD+ TSG+++
Sbjct: 98  VANSE--TWLVVDKPGTMPVHPSG--AYHLNSLLPILENTYG-KLYPIHRLDRLTSGLVI 152

Query: 160 VARTRAAAQHLTESFRMR-RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
           + +T  AA+ L ++ + R    K+Y + V G  P N    + N    KS+        V 
Sbjct: 153 LGKTPEAARQLGKAIKERDSCTKLYIARVRGRFPFNCASHVPNLSSHKSYPPRYGEWSVL 212

Query: 218 QNEKG--------ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           Q+  G         ++A+  F      +   C    +P TGRTHQ+R+H  ++G PI  D
Sbjct: 213 QDMDGKKDMKAAETSFALLKFDAKSDSSVVLC----RPATGRTHQIRLHLQYLGHPIAND 268

Query: 270 HKY 272
             Y
Sbjct: 269 PNY 271


>gi|329900914|ref|ZP_08272646.1| 23S rRNA pseudouridylate synthase [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327549326|gb|EGF33898.1| 23S rRNA pseudouridylate synthase [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 112

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 34/93 (36%), Positives = 49/93 (52%), Gaps = 9/93 (9%)

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-------KGNFTSPIQNKLYL 290
           + F +LE +  TGRTHQ+RVHA   G PI GD KY  +F       K +       +++L
Sbjct: 9   ENFAFLEAELKTGRTHQIRVHAASSGFPIAGDDKY-GDFALNRLLQKADGKRVALKRMFL 67

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           HA  +   HPE G+ + + APL    ++   SL
Sbjct: 68  HAHQITFVHPESGKPMTLNAPLTPECLRFLASL 100


>gi|294628458|ref|ZP_06707018.1| RNA pseudouridylate synthase [Streptomyces sp. e14]
 gi|292831791|gb|EFF90140.1| RNA pseudouridylate synthase [Streptomyces sp. e14]
          Length = 324

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 57/212 (26%), Positives = 96/212 (45%), Gaps = 22/212 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++++ D  I V +KP  ++    GS +       L+  +D         HRLD+ T+G++
Sbjct: 103 VVVHRDEHIVVVDKPHFLATTPRGSHVTETALARLRRELDLPTLG--AAHRLDRLTAGLV 160

Query: 159 ---VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
              V    R A Q L   FR RR++K Y ++    P +    +   +  +S I  +   +
Sbjct: 161 LFTVRPEERGAYQTL---FRDRRVRKEYEAVA---PYDPDLALPRTV--RSRIVKERGVL 212

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
             +   G   A++  +++           + P TG+THQLRVH   +G PI+GD  Y A 
Sbjct: 213 TAEEVPGEPNAVTDVELVGRRPGGPARYRLTPRTGQTHQLRVHMNALGVPILGDPLYPAV 272

Query: 275 ---NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 G+F+ P+Q    L AR ++   P  G
Sbjct: 273 TPDGPPGDFSRPLQ----LLARALEFTDPVTG 300


>gi|283956117|ref|ZP_06373604.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 1336]
 gi|283792437|gb|EFC31219.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 1336]
          Length = 250

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 51/192 (26%), Positives = 86/192 (44%), Gaps = 30/192 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED KI   NKP           AY  +   K +        +L +RLD+ETSG++++
Sbjct: 59  IIFEDDKIIAINKP----------YAYVSEDLEKKF------NAKLLNRLDKETSGVILL 102

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+  R+ K Y +++ G+   + E        K+  G      + +  
Sbjct: 103 CKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKCGA-----LSKVS 157

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K    A+S    I     K    ++   TGRTHQ+RVHA  +   +VGD KY        
Sbjct: 158 KDGLSALSIITPI-MLQSKKTLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY-----AKI 211

Query: 281 TSPIQNKLYLHA 292
           +S   +++YLH+
Sbjct: 212 SS---DRMYLHS 220


>gi|313113493|ref|ZP_07799082.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310624220|gb|EFQ07586.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 349

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 50/177 (28%), Positives = 83/177 (46%), Gaps = 18/177 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQKP--RLTHRLDQETSG 156
           ++YED+   V  KP  ++V       Y    +G+  +W   +G  P  R  +R+D++TSG
Sbjct: 124 VVYEDAFAVVLEKPPHLAVHPTLNYPYDTLANGY-AAWAAQQGISPVFRPVNRIDKDTSG 182

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ A+   AA  L      R ++K+Y+++V G +P       A    +   I G     
Sbjct: 183 LVLAAKHAYAAPLLA-----RNVEKLYYAVVEGELPLGPGVIDAPIGRQAESIIG---RC 234

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V  + K +    +  K  +  +   C     P TGRTHQ+RVH   +G P+ GD  Y
Sbjct: 235 VTPDGKPSRTEYTILKAENGLSLAACV----PVTGRTHQIRVHFASIGHPLAGDDLY 287


>gi|120611342|ref|YP_971020.1| pseudouridine synthase [Acidovorax citrulli AAC00-1]
 gi|120589806|gb|ABM33246.1| pseudouridine synthase [Acidovorax citrulli AAC00-1]
          Length = 307

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 56/219 (25%), Positives = 92/219 (42%), Gaps = 30/219 (13%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +  +LY+D  + V +KP  + V   G  + + +   LK  +      P   HR+D++T+
Sbjct: 90  FEEAVLYQDEHLVVADKPHFLPVVPTGRYLQHTLLVRLKRRLGLDELSP--VHRIDRDTA 147

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-------KKSHI 208
           G+++ +  RA        FR R + K Y            E +A W +       + S I
Sbjct: 148 GLVLFSVQRATRGRYQALFRDRAVDKTY------------EAVAPWRVDVAFPRERASRI 195

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                        G   +++  +V+D     +    + P TGR HQLRVH   +G P+ G
Sbjct: 196 EESPQFFRMHEVPGEANSLTRMEVLDVDG-AWARYRLSPVTGRRHQLRVHMAALGLPLRG 254

Query: 269 DHKYCA---NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           D  Y       +G+F+ P+Q    L AR +    P  GR
Sbjct: 255 DAFYPEVNDPPEGDFSRPLQ----LLARAIAFTDPVTGR 289


>gi|81429051|ref|YP_396051.1| pseudouridine synthase, 23S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610693|emb|CAI55744.1| Pseudouridine synthase, 23S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 306

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 75/327 (22%), Positives = 133/327 (40%), Gaps = 41/327 (12%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRI---PP 69
            D E   L  + + H   I+   L KI    GQ+ V+ +    N R+    VV +   P 
Sbjct: 8   TDSEGCILRNFLRRH--EISRSQLSKIKFSGGQILVNGQEAHTNIRLVQNDVVTVYLAPE 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYH 128
           V  A+ H+I  +  L                + YED    + +KPA + S+   +     
Sbjct: 66  V--AVEHVIPVKGDLK---------------IAYEDDHFLIVDKPAFVASLPAPNHPNNT 108

Query: 129 IDGFLKSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  F+K ++  +  +    H   RLD++TSG+++  +   A   L    + + +QK Y +
Sbjct: 109 MANFVKQYLIDEQAESLAVHVVTRLDRDTSGLMMFTKHGFAHSLLDRQLQSKELQKTYIA 168

Query: 186 LVWGIPKNKKECIAN--WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +  G   + +E +    W+ +      ++       E G      +++           L
Sbjct: 169 IASG---DMREDLPQHAWIDRPIKRSEEFYMRRVVGEGGKRSLTEYWQAAHGDGATLVKL 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
           ++   TGRTHQ+RVH   +G  ++GD+ Y    + N   P Q    LH R +   HP E 
Sbjct: 226 KLL--TGRTHQIRVHFASLGHSLIGDNLYG---ESNDLLPRQA---LHCRQLTFYHPFEE 277

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRN 329
             + + +P+PA          F +D  
Sbjct: 278 RTITVKSPVPADFSAVLAQRQFDFDET 304


>gi|261839194|gb|ACX98959.1| RNA pseudouridine synthase family protein [Helicobacter pylori 52]
          Length = 298

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 106/243 (43%), Gaps = 42/243 (17%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K     Q+ Q VR   +I  +  +I  +    +              
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVRKSQMIQGVVRLIHFKPNEKTQA------------ 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD------SKGQKPRLTHRLDQET 154
           L++E     VF+KPA +      G  YH     +S +D      SK   P   HRLD ET
Sbjct: 71  LVFETKDFGVFDKPAQVYTHP-KGYFYH-----ESLLDCIQSHFSKNAHP--AHRLDYET 122

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY-- 212
           SG+++  +T  + + L   F  ++++K Y +LV G+   K   I   +L   +I  D   
Sbjct: 123 SGLVLAGKTLQSVKDLKALFMQKKVKKTYLALVHGL-IEKSMKIDKPILTPQNIQKDLHI 181

Query: 213 ---VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
              +  + +        +S+   +D        L++ P TGRTHQ+R+H   +   IVG+
Sbjct: 182 RSKISPLGKPSTTLVEPLSYNPFLDI-----SLLKITPLTGRTHQIRLHLSSVDHRIVGE 236

Query: 270 HKY 272
             Y
Sbjct: 237 GLY 239


>gi|258507862|ref|YP_003170613.1| pseudouridine synthase [Lactobacillus rhamnosus GG]
 gi|257147789|emb|CAR86762.1| Pseudouridine synthase [Lactobacillus rhamnosus GG]
 gi|259649190|dbj|BAI41352.1| pseudouridylate synthase [Lactobacillus rhamnosus GG]
          Length = 300

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 101/242 (41%), Gaps = 46/242 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           + YED    V NKPAG++     G     +A  +  +L     ++ Q   +  RLD++TS
Sbjct: 79  ICYEDDDYLVVNKPAGVASIPAVGRRNDSMANMVKAYLIK-THAESQAVHVVTRLDRDTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWLLKKSHIGGDYV 213
           G++V A+   A   L          K Y +LV       K  ++   W++    +   + 
Sbjct: 138 GLMVFAKHSLAHSLLDRQLHSENFLKQYLALV-----TSKSLLSAHGWIVLPIGVSTGFY 192

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY- 272
                +E G   +++ ++ +   +     L +  HTGRTHQ+RVH   +G P+ GD  Y 
Sbjct: 193 MRRVVSETGKP-SVTEYQTLAQNSHAAAVL-VTLHTGRTHQIRVHFAAIGHPLFGDDLYN 250

Query: 273 ------------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                       CA+ +  F  P+Q K      ++DL           APLP  M K  D
Sbjct: 251 RQADDFKRQALHCAHLR--FWQPLQKK------WVDL----------HAPLPTDMAKLSD 292

Query: 321 SL 322
            L
Sbjct: 293 HL 294


>gi|296454474|ref|YP_003661617.1| RluA family pseudouridine synthase [Bifidobacterium longum subsp.
           longum JDM301]
 gi|296183905|gb|ADH00787.1| pseudouridine synthase, RluA family [Bifidobacterium longum subsp.
           longum JDM301]
          Length = 317

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 67/270 (24%), Positives = 117/270 (43%), Gaps = 34/270 (12%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++ SGQ RV  + V  ++ +Q+G+ V           + +EQ   +        +D    
Sbjct: 31  LVDSGQARVLGREVARSSTLQAGETVEF--------DLAEEQAGPEPIA-----TDMAVV 77

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW---VDSKGQKPR--LTHRLDQET 154
               +   +      A  +  G +G    + G L+     + S G   R  +  RLD  T
Sbjct: 78  YEDDDVVVVDKPVGVAAHASVGWTGPT--VLGSLRDRGVHIASYGAAGREGIVSRLDVGT 135

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG----G 210
           SG+++V ++  A   +   F    ++K Y +LV G  K  K  I      ++ IG     
Sbjct: 136 SGLMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQGGLKENKATI------EAPIGRAKVS 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D+   V    K    A++H+ V++ F  +   + +   TGRTHQ+RVH   +G P+ GD 
Sbjct: 190 DFRFCVTPAGK---PAVTHWDVLERFGHEATLVSVNLETGRTHQIRVHFSSIGHPLCGDP 246

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            Y AN   +    + ++ +LHA  ++  HP
Sbjct: 247 MYGANPVLSEALGL-DRQWLHAMKLEFRHP 275


>gi|182414459|ref|YP_001819525.1| pseudouridine synthase [Opitutus terrae PB90-1]
 gi|177841673|gb|ACB75925.1| pseudouridine synthase [Opitutus terrae PB90-1]
          Length = 279

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/213 (24%), Positives = 97/213 (45%), Gaps = 29/213 (13%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           ++ L++ +++ED ++ V  KP  +      +G    + G ++ +         L  RLD+
Sbjct: 36  AEELRTWIVHEDERLLVVAKPGDVVCHPSKAGPWSSLVGAVREFTGLATVH--LVFRLDR 93

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-------IPKNKKECIANWLLKK 205
           ETSGI+V+A+    A  L  + + R+I K Y +++ G       + +   + +A+ +  K
Sbjct: 94  ETSGIVVLAKDPKTASRLQVAMQERKIGKAYVAILTGAMREPVTVDQPLGDDVASPVFVK 153

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGC 264
           S +  D              +++HF  I   A   F  + +   TGR HQ+R HA  +G 
Sbjct: 154 SAVRAD-----------GQRSVTHFSPITVAADDAFSLVRVVTETGRKHQIRAHAQWLGH 202

Query: 265 PIVGDHKYCANFK-------GNFTSPIQNKLYL 290
            +VGD  Y  + +         +T  + +KL L
Sbjct: 203 SLVGDKIYGPDARCYLDFIDTGWTPALADKLLL 235


>gi|332843546|ref|XP_003314668.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 2
           isoform 1 [Pan troglodytes]
          Length = 484

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 57/207 (27%), Positives = 93/207 (44%), Gaps = 39/207 (18%)

Query: 89  NLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
            L K +DFL++               LL E+  + V +KP+ I V       ++   F+ 
Sbjct: 138 GLRKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFI- 196

Query: 135 SWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP 191
             +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G  P
Sbjct: 197 --LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFP 254

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------LEM 245
             +  C    L+    +G     V + + +G        K  +   Q+  +      +  
Sbjct: 255 TEEVTCKEPILVVSYKVG-----VCRVDPRG--------KPCETVFQRLSYNGQSSVVRC 301

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 302 RPLTGRTHQIRVHLQFLGHPILNDPIY 328


>gi|42522740|ref|NP_968120.1| methyltransferase [Bdellovibrio bacteriovorus HD100]
 gi|39573936|emb|CAE79113.1| methyltransferase [Bdellovibrio bacteriovorus HD100]
          Length = 521

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 83/183 (45%), Gaps = 17/183 (9%)

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G ++ + +   +K    HRLD+ TSG LV A +   A  LT++F   +++K Y  L    
Sbjct: 35  GCVEIYEEELDRKLYTVHRLDKATSGALVFATSSEIAAQLTQAFEQHKVEKKYLFLT--- 91

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
               K+        +S I  +    V ++ +  N   S FK +        W E  PHTG
Sbjct: 92  ---DKKIARTEFTYESFIQKEKNVFVSRDTQEPNSKTS-FKWVKALGPYQLW-EAVPHTG 146

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           + HQ+R+HA   G  ++GD  +  N   +F      +L LH++ +      G +++   P
Sbjct: 147 KPHQIRLHAEANGIAVLGDSDH--NGTNHF------RLCLHSQVLGF-ELNGQKVRYETP 197

Query: 311 LPA 313
           LP 
Sbjct: 198 LPG 200


>gi|72549946|ref|XP_843613.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|323364132|emb|CBZ13139.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 741

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 61/235 (25%), Positives = 98/235 (41%), Gaps = 44/235 (18%)

Query: 101 LLYEDSKIYVFNKPAGISV--------QGGSG--------IAYHIDGFLKSWVDSKGQKP 144
           +LYED  + V +KPAG++         Q G+         +A    G L   V  +GQ  
Sbjct: 514 VLYEDDDVLVVDKPAGLATSRHGLSCTQLGTPTTDLISVLLATDRAGALARGVFRQGQ-- 571

Query: 145 RLTHRLDQETSGILVVARTRAAAQ----HLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              HRLD ETSG L++A++  AA      L  S       KIY +L   +  +       
Sbjct: 572 --VHRLDAETSGCLLIAKSDVAADSLRHQLGTSAAFSHHSKIYHALCVVLEPS------- 622

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHA 259
             L+   +  D +       +      + ++VI  F + +  W+E +   G+ HQ+R H 
Sbjct: 623 --LRNVRLHDDIIDAADPKIR------TRYRVIRFFPKHRVAWVECRIQQGKKHQIRRHL 674

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
              G PI+ D ++           + +++ LHA  +   HP     +   APLPA
Sbjct: 675 ASRGFPILADLEHGGAV---CCQSMISRVALHAHSLSFIHPVTADPITAAAPLPA 726


>gi|283458768|ref|YP_003363408.1| pseudouridylate synthase [Rothia mucilaginosa DY-18]
 gi|283134823|dbj|BAI65588.1| pseudouridylate synthase [Rothia mucilaginosa DY-18]
          Length = 377

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 54/200 (27%), Positives = 90/200 (45%), Gaps = 32/200 (16%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LYED  +   +KP  + +   G+ IA      L+     + Q P L   HRLD+ T+G+
Sbjct: 137 VLYEDEHVLAIDKPHFLPTTPRGAYIAQTALTKLRV----REQNPLLIPIHRLDRPTAGV 192

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIY---WSLVWGIPKNKKECIANWLLKKSHIGG--DY 212
           L+ A+T  A +     F+ RR+ K Y     +       ++   A  L  +SHI    D 
Sbjct: 193 LLFAKTVEARRPFQMMFQHRRVSKTYRAVAPVPADPAAAERALSAEGLQVRSHIQKIRDQ 252

Query: 213 VHVVKQNEKGANY------AISHFKVIDCFA--------------QKFCWLEMQPHTGRT 252
           + V + +E+           ++  K++  F               +++   ++ PHTG+T
Sbjct: 253 LQVQQLSEEQCAAQGVEPNTLTTAKILQTFTPSAQAVEGWRAEPNREWALYDLAPHTGKT 312

Query: 253 HQLRVHALHMGCPIVGDHKY 272
           HQLR H   +G PI+GD  Y
Sbjct: 313 HQLRAHLNMLGSPILGDVLY 332


>gi|218132473|ref|ZP_03461277.1| hypothetical protein BACPEC_00332 [Bacteroides pectinophilus ATCC
           43243]
 gi|217992583|gb|EEC58585.1| hypothetical protein BACPEC_00332 [Bacteroides pectinophilus ATCC
           43243]
          Length = 229

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/231 (22%), Positives = 105/231 (45%), Gaps = 37/231 (16%)

Query: 20  RLDRWFKNHYPHINFVN---LQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINAL 74
           R+DR+       ++ ++   LQK+++ G V V+   +K N +++   ++ I  P      
Sbjct: 16  RIDRYMAQEREELSDLSRSYLQKLIQDGNVLVNGCNIKANYKLKKADIIDITLPD----- 70

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------I 125
              IKE +I   ++ L          +LYED  I V NKP G+ V   +G         +
Sbjct: 71  ---IKEPQIEAENIPLD---------ILYEDEDIIVINKPKGMVVHPAAGHYSGTLVNAL 118

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            YH    L     +   +P + HR+D  T+G+LV  +   A   ++    +  I + Y +
Sbjct: 119 MYHCRDNLSGI--NGVMRPGIVHRIDMNTTGVLVACKNDFAHNAISAQLSVHSITRKYEA 176

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           +V+    N++    +  + +SH     + + + N +    A++H+++++ F
Sbjct: 177 IVYN-RFNEESGTVDAPIGRSHNDRKKMAIDRDNGR---RAVTHYRLLENF 223


>gi|116494411|ref|YP_806145.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
 gi|116104561|gb|ABJ69703.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
          Length = 300

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 58/221 (26%), Positives = 97/221 (43%), Gaps = 20/221 (9%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED    + NKPAG++     G     +A  +  +L     ++ Q   +  RLD++TSG+
Sbjct: 81  YEDDDYLIVNKPAGVASIPAVGRQNNSMANMVKAYLIK-TKAESQAVHVVTRLDRDTSGL 139

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDYVHVV 216
           +V A+   A   L +    +   K Y ++V             W++    +  G Y+  V
Sbjct: 140 MVFAKHGLAHSLLDQQLHSQDFVKQYVAIVTA---QTPLATHGWIVLPIGVSDGFYMRRV 196

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +   A+  ++ ++ +D        L +  HTGRTHQ+RVH   +G  + GD  Y  + 
Sbjct: 197 VTDTGKAS--VTEYRTLDENTAGAMML-VTLHTGRTHQIRVHFAAIGHALYGDGLYSPDT 253

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMV 316
            G       N+  LH  ++    P   +L  + APLPA M 
Sbjct: 254 HGF------NRQALHCAHLRFWQPLKHKLIDLHAPLPADMA 288


>gi|42522844|ref|NP_968224.1| pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
 gi|39574040|emb|CAE79217.1| Pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
          Length = 228

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 101/219 (46%), Gaps = 15/219 (6%)

Query: 100 ILLYEDSKIY-VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           I + E SK + V NKP+G+SV         +    K       Q     HRLD+ETSG+L
Sbjct: 10  IPIVEKSKHWLVINKPSGVSVHNDPPDVRTL--LKKQLTPGTYQDIHPVHRLDKETSGLL 67

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +V      A +L+  F+  +++K Y++L+ G    +     +W    + I  D     K 
Sbjct: 68  LVGLDAETAANLSGQFQEHKVEKTYYALLRG----ELPVSTDWQEWNTPIS-DKAEGRKN 122

Query: 219 NE---KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-A 274
            +   K    A + +KV++   + F  +E++  TGR HQ+R H   +   IVGD +Y   
Sbjct: 123 PQGLLKDRVEARTLYKVLEA-NKYFSLVEVRLITGRQHQIRKHTALIRHAIVGDTRYGDP 181

Query: 275 NFKGNFTSPIQNK-LYLHARYMDLPHPEGGRLQITAPLP 312
            +     +  Q K ++LHA  M +    G +    APLP
Sbjct: 182 KYNERMANIYQTKRMFLHAARMTV-MINGYKHSFEAPLP 219


>gi|312138349|ref|YP_004005685.1| tRNA-pseudouridine synthase i [Rhodococcus equi 103S]
 gi|311887688|emb|CBH47000.1| putative tRNA-pseudouridine synthase I [Rhodococcus equi 103S]
          Length = 297

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 53/205 (25%), Positives = 91/205 (44%), Gaps = 12/205 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  + S   G+ +       L+  +D     P   HRLD+ T+G+L+
Sbjct: 90  VLHRDQDLLVVDKPHFLASTPRGAYVVESALVRLRRELDLPELTP--AHRLDRITAGVLL 147

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQ 218
               R A +     F  RR  K+Y +L    P  +    + + ++K+  +      +  +
Sbjct: 148 FTVRREARRAYQSLFDERRATKVYEALARHDPSLHLPVTVRSRIIKERGV------LQAR 201

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              G   A S  +++D          + P TG+THQLR+H   +G PI+GD+ Y   F  
Sbjct: 202 EVDGEPNAESRIELLDV-RDGVGHYRLLPRTGKTHQLRLHMCSLGVPIIGDNFY-PRFYD 259

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
             +    + L L AR ++   P  G
Sbjct: 260 VASDDYSDPLRLLARSLEFDDPYTG 284


>gi|86151843|ref|ZP_01070057.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|86153369|ref|ZP_01071573.1| hypothetical RNA pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni HB93-13]
 gi|121612323|ref|YP_001000404.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|167005346|ref|ZP_02271104.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|315124210|ref|YP_004066214.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|85841472|gb|EAQ58720.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|85843095|gb|EAQ60306.1| hypothetical RNA pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni HB93-13]
 gi|87249488|gb|EAQ72448.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|315017932|gb|ADT66025.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
          Length = 250

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/194 (26%), Positives = 86/194 (44%), Gaps = 34/194 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED KI   NKP           AY  +   K +        +L +RLD+ETSG++++
Sbjct: 59  IIFEDDKIIAINKP----------YAYVSEDLEKKF------NAKLLNRLDKETSGVILL 102

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+  R+ K Y +++ G+   + E        K+  GG    V K   
Sbjct: 103 CKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAK-GGALSKVSKD-- 159

Query: 221 KGANYAISHFKVID--CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                 +S   +I       K    ++   TGRTHQ+RVHA  +   +VGD KY      
Sbjct: 160 -----GLSALSIITPIMMQSKKTLTKIVIQTGRTHQIRVHAKFIKHGVVGDEKY-----A 209

Query: 279 NFTSPIQNKLYLHA 292
             +S   +++YLH+
Sbjct: 210 KISS---DRMYLHS 220


>gi|227535627|ref|ZP_03965676.1| pseudouridine synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|239631158|ref|ZP_04674189.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|227186757|gb|EEI66824.1| pseudouridine synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|239525623|gb|EEQ64624.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
          Length = 300

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 58/221 (26%), Positives = 97/221 (43%), Gaps = 20/221 (9%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED    + NKPAG++     G     +A  +  +L     ++ Q   +  RLD++TSG+
Sbjct: 81  YEDDDYLIVNKPAGVASIPAVGRQNNSMANMVKAYLIK-TKAESQAVHVVTRLDRDTSGL 139

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDYVHVV 216
           +V A+   A   L +    +   K Y ++V             W++    +  G Y+  V
Sbjct: 140 MVFAKHGLAHSLLDQQLHSQDFVKQYVAIVTA---QTPLATHGWIVLPIGVSDGFYMRRV 196

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +   A+  ++ ++ +D        L +  HTGRTHQ+RVH   +G  + GD  Y  + 
Sbjct: 197 VTDTGKAS--VTEYRTLDQNTAGAMML-VTLHTGRTHQIRVHFAAIGHALYGDGLYSPDT 253

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMV 316
            G       N+  LH  ++    P   +L  + APLPA M 
Sbjct: 254 HGF------NRQALHCAHLRFWQPLKHKLIDLHAPLPADMA 288


>gi|57237010|ref|YP_178812.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
 gi|57165814|gb|AAW34593.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
          Length = 250

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/194 (26%), Positives = 86/194 (44%), Gaps = 34/194 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED KI   NKP           AY  +   K +        +L +RLD+ETSG++++
Sbjct: 59  IIFEDDKIIAINKP----------YAYVSEDLEKKF------NAKLLNRLDKETSGVILL 102

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+  R+ K Y +++ G+   + E        K+  GG    V K   
Sbjct: 103 CKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAK-GGALSKVSKD-- 159

Query: 221 KGANYAISHFKVID--CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                 +S   +I       K    ++   TGRTHQ+RVHA  +   +VGD KY      
Sbjct: 160 -----GLSALSIITPIMMQSKKTLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY-----A 209

Query: 279 NFTSPIQNKLYLHA 292
             +S   +++YLH+
Sbjct: 210 KISS---DRMYLHS 220


>gi|157414995|ref|YP_001482251.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|157385959|gb|ABV52274.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|307747633|gb|ADN90903.1| Pseudouridine synthase [Campylobacter jejuni subsp. jejuni M1]
 gi|315931909|gb|EFV10864.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 250

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/194 (26%), Positives = 86/194 (44%), Gaps = 34/194 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED KI   NKP           AY  +   K +        +L +RLD+ETSG++++
Sbjct: 59  IIFEDDKIIAINKP----------YAYVSEDLEKKF------NAKLLNRLDKETSGVILL 102

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+  R+ K Y +++ G+   + E        K+  GG    V K   
Sbjct: 103 CKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAK-GGALSKVSKD-- 159

Query: 221 KGANYAISHFKVID--CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                 +S   +I       K    ++   TGRTHQ+RVHA  +   +VGD KY      
Sbjct: 160 -----GLSALSIITPIMMQSKKTLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY-----A 209

Query: 279 NFTSPIQNKLYLHA 292
             +S   +++YLH+
Sbjct: 210 KISS---DRMYLHS 220


>gi|149036915|gb|EDL91533.1| RNA pseudouridylate synthase domain containing 3 (predicted),
           isoform CRA_b [Rattus norvegicus]
          Length = 346

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 88/200 (44%), Gaps = 14/200 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR 145
           + L + +  L++ ++ +   +   NKP G+ V G  G      +  +L   +  + Q+ +
Sbjct: 65  LGLEELAQVLRAAVVDQKGPLVTLNKPQGLPVTGRPGELTLLSVLPWLSQALGLEHQELQ 124

Query: 146 LTHRLDQETSGILVVARTRAAAQHL----TESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           +     +E SG+++++       HL    T S R +R    Y ++  G+P+  +  +   
Sbjct: 125 VVRAPGKEASGLVLLSSCPQTTSHLQKFFTHSRRAQRPTATYCAITDGVPEPSEGTVHIA 184

Query: 202 LLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQL 255
           L  +   G D    V     K  ++G    +SHF V        C L ++QP T    QL
Sbjct: 185 LRLERMDGIDLAVPVTSPSRKDIQEGVKRTLSHFHVTATGC--GCALVQLQPLTVFPSQL 242

Query: 256 RVHALHMGCPIVGDHKYCAN 275
           +VH     CPI+GDH Y A 
Sbjct: 243 QVHMALQLCPILGDHTYAAR 262


>gi|34558398|ref|NP_908213.1| putative ribosomal pseudouridine synthase [Wolinella succinogenes
           DSM 1740]
 gi|34484117|emb|CAE11113.1| PUTATIVE RIBOSOMAL PSEUDOURIDINE SYNTHASE [Wolinella succinogenes]
          Length = 244

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 45/155 (29%), Positives = 75/155 (48%), Gaps = 20/155 (12%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTES-FRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           L HRLD+ETSG++++ +  +  Q   ++ F+ +++ K Y ++V G+   ++E     L  
Sbjct: 90  LLHRLDKETSGVILLVQEGSEFQKSAKAEFKAQKVYKEYVAIVEGMIPEEREITKPILTT 149

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--QKFCWLEMQPHTGRTHQLRVHALHM 262
           K H       + K+ E       S +  I+  A   K   L++   TGRTHQ+RVH   +
Sbjct: 150 KGHFAKS--KISKEGE-------SAYTKIEPLAYEGKQTQLKVIIKTGRTHQIRVHLASI 200

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             PI+GD  Y              ++ LHAR + L
Sbjct: 201 NHPIIGDTLYGGKN--------AKRILLHARKIAL 227


>gi|325674660|ref|ZP_08154347.1| RNA pseudouridine synthase [Rhodococcus equi ATCC 33707]
 gi|325554246|gb|EGD23921.1| RNA pseudouridine synthase [Rhodococcus equi ATCC 33707]
          Length = 297

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 53/205 (25%), Positives = 91/205 (44%), Gaps = 12/205 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  + S   G+ +       L+  +D     P   HRLD+ T+G+L+
Sbjct: 90  VLHRDQDLLVVDKPHFLASTPRGAYVVESALVRLRRELDLPELTP--AHRLDRITAGVLL 147

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQ 218
               R A +     F  RR  K+Y +L    P  +    + + ++K+  +      +  +
Sbjct: 148 FTVRREARRAYQSLFDERRATKVYEALARHDPSLHLPVTVRSRIIKERGV------LQAR 201

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              G   A S  +++D          + P TG+THQLR+H   +G PI+GD+ Y   F  
Sbjct: 202 EVDGEPNAESRIELLDV-RDGVGHYRLLPRTGKTHQLRLHMCSLGVPIIGDNFY-PRFYD 259

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
             +    + L L AR ++   P  G
Sbjct: 260 VASDDYSDPLRLLARSLEFDDPYTG 284


>gi|315058171|gb|ADT72500.1| Ribosomal large subunit pseudouridine synthase D [Campylobacter
           jejuni subsp. jejuni S3]
          Length = 250

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 52/194 (26%), Positives = 86/194 (44%), Gaps = 34/194 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED KI   NKP           AY  +   K +        +L +RLD+ETSG++++
Sbjct: 59  IIFEDDKIIAINKP----------YAYVSEDLEKKF------NAKLLNRLDKETSGVILL 102

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+  R+ K Y +++ G+   + E        K+  GG    V K   
Sbjct: 103 CKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAK-GGALSKVSKD-- 159

Query: 221 KGANYAISHFKVID--CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                 +S   +I       K    ++   TGRTHQ+RVHA  +   +VGD KY      
Sbjct: 160 -----GLSALSIITPIMMQSKKTLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY-----A 209

Query: 279 NFTSPIQNKLYLHA 292
             +S   +++YLH+
Sbjct: 210 KISS---DRMYLHS 220


>gi|319785749|ref|YP_004145224.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317464261|gb|ADV25993.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
          Length = 273

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 57/236 (24%), Positives = 98/236 (41%), Gaps = 25/236 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  + V +KPAG+ V      A   D          G++  L HRLD+ TSG L++
Sbjct: 41  VLHADQWLAVVDKPAGLMVHDSVLAADETDFAADRLRAQFGRQVFLVHRLDRATSGCLLL 100

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R  A  L ++   +++ K Y ++  G P+        + +     GG         +
Sbjct: 101 AFDRDTASALGKAVMAQQLDKRYLAVCRGWPEE------GFTIDHPLDGG-------PGK 147

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++ F+ + C             ++  LE  P TGR  Q+R H  H    ++GD 
Sbjct: 148 PQKKPAVTRFRRLACGELDEPSAGFPTSRYALLECAPVTGRFRQIRRHLKHASHHLIGDT 207

Query: 271 KYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            +        F     +++ LHA  +  PHP+ G+ + + AP     +K     G+
Sbjct: 208 SHGDGRHNRAFRMRGVHRMLLHAWQLGFPHPKDGQEMTVVAPPSGEFLKAMALFGW 263


>gi|257460774|ref|ZP_05625875.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           gracilis RM3268]
 gi|257442105|gb|EEV17247.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           gracilis RM3268]
          Length = 495

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 47/178 (26%), Positives = 83/178 (46%), Gaps = 27/178 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD +  +    I+   +  +++S  VRV+   + K   ++ +G++VRI    +A     
Sbjct: 11  RLDVFLSSQL-GISRNQISNLIKSAAVRVNGAVQTKPGYKLSAGELVRIDYPASAPQQTS 69

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+   D  +             LYED  + V NKPAG++V   + +    +  L  W+ 
Sbjct: 70  AERLNFDVEI-------------LYEDDDLLVVNKPAGLTVHPAASVK---EPTLVDWLK 113

Query: 139 SKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           S+G          +  + HRLD+ TSG L+VA+  AA   L+     + + +IY +L+
Sbjct: 114 SRGYLLSTLGGELRAGIVHRLDKLTSGALLVAKNNAAHAALSAQLSDKSMGRIYLALI 171



 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 81/198 (40%), Gaps = 10/198 (5%)

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           S ++   D  L +  D+   K   TH      +G   +   RA       +  M+   KI
Sbjct: 269 SAVSTGKDKILNASRDADASKILATHASANPNAGTDKILNNRADNVDEISNNCMQSADKI 328

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANY--AISHFKVIDCFAQK 239
                  IP N+ +     L   + +  D     +  E K  N+     ++K+     + 
Sbjct: 329 LIQSADKIPNNRADNADKIL--TADMSADQTQTARLAENKALNFKNPAQNYKLPPINLKS 386

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           F  +  +  TGRTHQ+RVH   +   I+GDH Y   FK        +++ LHA  +   H
Sbjct: 387 FNLVAAKLFTGRTHQIRVHLSSINRHILGDHLY--GFKSENAK--ISRILLHAYLLYFIH 442

Query: 300 PEGGR-LQITAPLPAHMV 316
           P  G+ ++I A LP+  +
Sbjct: 443 PRSGKEVKICAGLPSEFL 460


>gi|196005647|ref|XP_002112690.1| hypothetical protein TRIADDRAFT_25933 [Trichoplax adhaerens]
 gi|190584731|gb|EDV24800.1| hypothetical protein TRIADDRAFT_25933 [Trichoplax adhaerens]
          Length = 247

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 57/228 (25%), Positives = 96/228 (42%), Gaps = 28/228 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS-----GIAYHIDGFLKSWVD-SKGQKPRLTHRLDQET 154
           ++++ +   + NKP  + +          +A  +   L + VD S     R  +RLD  T
Sbjct: 12  IVHQTNSYVIINKPFDMHINSNEEDVKPTVATQLAELLPTLVDKSICFGFRFVNRLDYAT 71

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG----- 209
           SG+L +A  + AA    + F    + K Y +LV GI         + L++K+ IG     
Sbjct: 72  SGLLCIAFDKRAANMARKLFEANHVSKKYLALVRGILSRDN---GDILVRKA-IGLDRRD 127

Query: 210 --------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
                    D+   + Q+ K A   I          +    + + P TGR HQLRVH L 
Sbjct: 128 PRGFRMCIPDHNPHLCQSPKAAETLIRILGYGKYDGEDITKISLSPVTGRRHQLRVHCLT 187

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           +G  IVGD+ Y      N       ++ LH+  + +P  +   +++T 
Sbjct: 188 LGHCIVGDYTY-----SNEVDSKPYRMMLHSYSLKIPLQDCPAIEVTT 230


>gi|295396160|ref|ZP_06806342.1| RNA pseudouridine synthase [Brevibacterium mcbrellneri ATCC 49030]
 gi|294970948|gb|EFG46841.1| RNA pseudouridine synthase [Brevibacterium mcbrellneri ATCC 49030]
          Length = 315

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 47/151 (31%), Positives = 71/151 (47%), Gaps = 21/151 (13%)

Query: 148 HRLDQETSGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKN------KKECI 198
           HRLD+ T+G+L+++R   TR A Q L   F+ R++ K Y +L   +P +       +EC 
Sbjct: 146 HRLDRVTAGLLILSRNPDTRGAYQRL---FQDRKVDKTYEALAV-LPPDFDPAAFPRECE 201

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRV 257
           +     K   G   V         A   I    V+  +         + PHTG+THQLRV
Sbjct: 202 SRIEKDKGTRGVKEV----DGPINARSRIEFSHVVGTYEGDPVGRFVLTPHTGKTHQLRV 257

Query: 258 HALHMGCPIVGDHKYCANFKG---NFTSPIQ 285
           H L  G PI+GD  Y  +      +F+ P++
Sbjct: 258 HMLGAGVPILGDPVYPHDLDQDPYDFSHPLR 288


>gi|240047291|ref|YP_002960679.1| Ribosomal large subunit pseudouridine synthase [Mycoplasma
           conjunctivae HRC/581]
 gi|239984863|emb|CAT04854.1| Ribosomal large subunit pseudouridine synthase [Mycoplasma
           conjunctivae]
          Length = 284

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 106/230 (46%), Gaps = 31/230 (13%)

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           KE KI+   +NL      +K  +LYEDS I V  KP   ++       + +D  +  +++
Sbjct: 64  KEAKIVKPDINLAYIK--VKFDILYEDSNILVVIKPRQTAMHSHK---FSLDNQVHKYLN 118

Query: 139 SKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTES--FRMRRIQKIYWSLVWGIPKN 193
            K     KP    RLD++T+GI++ A+    A  + +   F ++R     +     I   
Sbjct: 119 IKMADIFKPAHIGRLDKDTTGIVIYAKNYQTALEMNKKQHFFVKR-----YVFKSDIDLK 173

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +K  +  W+ K   +    + V ++  + +  AI+   +I     K   L+    TG+ H
Sbjct: 174 EKVDVKLWIKKNDDLKK--MEVSQEKTQNSQLAITSLFLIG--NNKIAQLQ----TGKKH 225

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           Q+R+   H+G PI GD KY + FK     P    ++LH  ++ L + EG 
Sbjct: 226 QIRLTLSHLGYPIYGDQKYSS-FK---LMP----MFLHCFFLQLNNLEGN 267


>gi|303228653|ref|ZP_07315478.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302516633|gb|EFL58550.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 335

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 57/243 (23%), Positives = 103/243 (42%), Gaps = 54/243 (22%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LYED  + + +KPAG++V         +GIA++   F++  +    +K R  +RLD++T
Sbjct: 94  ILYEDDDLLIVDKPAGVTVNSKDQVSLANGIAHY---FMEHGI---KRKVRFLNRLDRDT 147

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G +V+A++  A     +       +K Y ++V G+ ++  + +    + +S  G  Y  
Sbjct: 148 TGCIVIAKSGLAQSLYQQQMDDNTFEKWYMAIVEGLVESDSDSLV-LPMDRSIDGIHYEV 206

Query: 215 VVKQNEKGANYAISHF--------------KVIDCFAQKFCW------------------ 242
             K  E   ++ + H                ++D   +                      
Sbjct: 207 NSKGKETRTDFTVLHRYPDGAVDNSVHNLQNIVDISHENVDSTVNTVDKQGGIVDNSVHN 266

Query: 243 LEMQP--------HTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHAR 293
           LE QP        +TG+THQ+RV   H+G P++GD  Y A   G  F       ++ H R
Sbjct: 267 LENQPCTAVAVRLYTGKTHQIRVAFSHIGHPLLGDTLYGAKSTGEPFALRAMKVVFTHMR 326

Query: 294 YMD 296
             D
Sbjct: 327 SGD 329


>gi|297296167|ref|XP_001096617.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Macaca mulatta]
          Length = 484

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 57/207 (27%), Positives = 93/207 (44%), Gaps = 39/207 (18%)

Query: 89  NLTKHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
            L K +DFL++               LL E+  + V +KP+ I V       ++   F+ 
Sbjct: 138 GLRKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFI- 196

Query: 135 SWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP 191
             +  + Q   L   HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G  P
Sbjct: 197 --LGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFP 254

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------LEM 245
             +  C    L+    +G     V + + +G        K  +   Q+  +      +  
Sbjct: 255 TEEVTCKEPILVVSYKVG-----VCRVDTRG--------KPCETVFQRLSYNGQSSVVRC 301

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +P TGRTHQ+RVH   +G PI+ D  Y
Sbjct: 302 RPLTGRTHQIRVHLQFLGHPILNDPIY 328


>gi|261200229|ref|XP_002626515.1| DRAP deaminase [Ajellomyces dermatitidis SLH14081]
 gi|239593587|gb|EEQ76168.1| DRAP deaminase [Ajellomyces dermatitidis SLH14081]
 gi|239607533|gb|EEQ84520.1| DRAP deaminase [Ajellomyces dermatitidis ER-3]
 gi|327352524|gb|EGE81381.1| DRAP deaminase [Ajellomyces dermatitidis ATCC 18188]
          Length = 549

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 67/284 (23%), Positives = 108/284 (38%), Gaps = 72/284 (25%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           QK +  G V ++ K V  + +IQ+G V+                     S  L +H   +
Sbjct: 82  QKAIEDGAVCINGKAVSIDTKIQNGDVI---------------------SHTLHRHEPPV 120

Query: 98  KSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQ 152
            S    +++ED+ + V +KPAG+ V       Y+ +  L+     +G    P   +RLD+
Sbjct: 121 TSQPIGIIHEDNDMIVIDKPAGVPVHPAG--RYNYNSVLEIMKAERGNGWVPYPCNRLDR 178

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-- 210
            TSG++ + +    A+ + E  R R ++K Y + V G   +        +LK S I G  
Sbjct: 179 LTSGVMFIGKHPKGAEQIGEKLRSRTVRKEYVARVKGKFPDGVVLCDQPMLKISPILGLN 238

Query: 211 ----------------DYVHVVKQNEKGANYAIS----------HFKVIDCFA------- 237
                            Y    KQ EK +  +               + D          
Sbjct: 239 RARASGKEARTKFRRIAYYPPHKQAEKTSGSSTGPATPPATLPDQMNISDSPTDTPTGAT 298

Query: 238 ---------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                    + +  +   P TGRTHQLRVH  ++G PI  D  Y
Sbjct: 299 TPIPMSLDEEGYSIVHCLPLTGRTHQLRVHLQYLGHPITNDPIY 342


>gi|314959443|gb|EFT03545.1| RNA pseudouridine synthase [Propionibacterium acnes HL002PA1]
          Length = 281

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 55/197 (27%), Positives = 90/197 (45%), Gaps = 20/197 (10%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LY D +I V +KP  +S +  G  +   +   L++ +      P LT  HRLD+ T+G+
Sbjct: 64  ILYSDERILVVDKPHFLSSIPRGRHVLESVVVRLRTQLGL----PELTVAHRLDRVTAGV 119

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI----ANWLLKKSHIGGDYV 213
           L++ R R   +   E F  R + K Y  +   +     E +    + W ++ S I  +  
Sbjct: 120 LLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTATKSGWQVR-SRIIKERG 178

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  +   G   A++   +I    +   W   E  P TGRTHQ+R+H   +G PIV D  
Sbjct: 179 ILQAREVPGVPNAVTDIALI---GEHGGWGLYEASPRTGRTHQIRLHMQRLGAPIVNDPF 235

Query: 272 YCANFK---GNFTSPIQ 285
           Y         +FT P+Q
Sbjct: 236 YPVVLDTPVDDFTHPLQ 252


>gi|313765077|gb|EFS36441.1| RNA pseudouridine synthase [Propionibacterium acnes HL013PA1]
 gi|313792621|gb|EFS40707.1| RNA pseudouridine synthase [Propionibacterium acnes HL110PA1]
 gi|313803157|gb|EFS44353.1| RNA pseudouridine synthase [Propionibacterium acnes HL110PA2]
 gi|313806800|gb|EFS45298.1| RNA pseudouridine synthase [Propionibacterium acnes HL087PA2]
 gi|313817590|gb|EFS55304.1| RNA pseudouridine synthase [Propionibacterium acnes HL046PA2]
 gi|313821584|gb|EFS59298.1| RNA pseudouridine synthase [Propionibacterium acnes HL036PA1]
 gi|313824472|gb|EFS62186.1| RNA pseudouridine synthase [Propionibacterium acnes HL036PA2]
 gi|313826817|gb|EFS64531.1| RNA pseudouridine synthase [Propionibacterium acnes HL063PA1]
 gi|313829136|gb|EFS66850.1| RNA pseudouridine synthase [Propionibacterium acnes HL063PA2]
 gi|313839569|gb|EFS77283.1| RNA pseudouridine synthase [Propionibacterium acnes HL086PA1]
 gi|314916163|gb|EFS79994.1| RNA pseudouridine synthase [Propionibacterium acnes HL005PA4]
 gi|314917426|gb|EFS81257.1| RNA pseudouridine synthase [Propionibacterium acnes HL050PA1]
 gi|314921765|gb|EFS85596.1| RNA pseudouridine synthase [Propionibacterium acnes HL050PA3]
 gi|314926247|gb|EFS90078.1| RNA pseudouridine synthase [Propionibacterium acnes HL036PA3]
 gi|314930967|gb|EFS94798.1| RNA pseudouridine synthase [Propionibacterium acnes HL067PA1]
 gi|314955362|gb|EFS99767.1| RNA pseudouridine synthase [Propionibacterium acnes HL027PA1]
 gi|314961609|gb|EFT05710.1| RNA pseudouridine synthase [Propionibacterium acnes HL002PA2]
 gi|314963927|gb|EFT08027.1| RNA pseudouridine synthase [Propionibacterium acnes HL082PA1]
 gi|314969134|gb|EFT13232.1| RNA pseudouridine synthase [Propionibacterium acnes HL037PA1]
 gi|314979975|gb|EFT24069.1| RNA pseudouridine synthase [Propionibacterium acnes HL072PA2]
 gi|314987166|gb|EFT31258.1| RNA pseudouridine synthase [Propionibacterium acnes HL005PA2]
 gi|314990633|gb|EFT34724.1| RNA pseudouridine synthase [Propionibacterium acnes HL005PA3]
 gi|315079107|gb|EFT51114.1| RNA pseudouridine synthase [Propionibacterium acnes HL053PA2]
 gi|315081549|gb|EFT53525.1| RNA pseudouridine synthase [Propionibacterium acnes HL078PA1]
 gi|315083025|gb|EFT55001.1| RNA pseudouridine synthase [Propionibacterium acnes HL027PA2]
 gi|315086559|gb|EFT58535.1| RNA pseudouridine synthase [Propionibacterium acnes HL002PA3]
 gi|315087963|gb|EFT59939.1| RNA pseudouridine synthase [Propionibacterium acnes HL072PA1]
 gi|315102262|gb|EFT74238.1| RNA pseudouridine synthase [Propionibacterium acnes HL046PA1]
 gi|315107443|gb|EFT79419.1| RNA pseudouridine synthase [Propionibacterium acnes HL030PA1]
 gi|315109736|gb|EFT81712.1| RNA pseudouridine synthase [Propionibacterium acnes HL030PA2]
 gi|327334072|gb|EGE75787.1| RNA pseudouridylate synthase family protein [Propionibacterium
           acnes HL096PA3]
 gi|327444523|gb|EGE91177.1| RNA pseudouridine synthase [Propionibacterium acnes HL013PA2]
 gi|327454203|gb|EGF00858.1| RNA pseudouridine synthase [Propionibacterium acnes HL087PA3]
 gi|327456261|gb|EGF02916.1| RNA pseudouridine synthase [Propionibacterium acnes HL083PA2]
 gi|327457465|gb|EGF04120.1| RNA pseudouridine synthase [Propionibacterium acnes HL092PA1]
 gi|328755960|gb|EGF69576.1| RNA pseudouridine synthase [Propionibacterium acnes HL087PA1]
 gi|328758029|gb|EGF71645.1| RNA pseudouridine synthase [Propionibacterium acnes HL020PA1]
 gi|328758923|gb|EGF72539.1| RNA pseudouridine synthase [Propionibacterium acnes HL025PA2]
          Length = 281

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 55/197 (27%), Positives = 90/197 (45%), Gaps = 20/197 (10%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LY D +I V +KP  +S +  G  +   +   L++ +      P LT  HRLD+ T+G+
Sbjct: 64  ILYSDERILVVDKPHFLSSIPRGRHVLESVVVRLRTQLGL----PELTVAHRLDRVTAGV 119

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI----ANWLLKKSHIGGDYV 213
           L++ R R   +   E F  R + K Y  +   +     E +    + W ++ S I  +  
Sbjct: 120 LLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTATKSGWQVR-SRIIKERG 178

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  +   G   A++   +I    +   W   E  P TGRTHQ+R+H   +G PIV D  
Sbjct: 179 ILQAREVPGVPNAVTDIALI---GEHGGWGLYEASPRTGRTHQIRLHMQRLGAPIVNDPF 235

Query: 272 YCANFK---GNFTSPIQ 285
           Y         +FT P+Q
Sbjct: 236 YPVVLDTPVDDFTHPLQ 252


>gi|218887114|ref|YP_002436435.1| pseudouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|218758068|gb|ACL08967.1| pseudouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
          Length = 393

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 63/223 (28%), Positives = 91/223 (40%), Gaps = 37/223 (16%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + V  KPAG++VQ G+G    +   L +        P   HRLD++TSG+L+VA + A  
Sbjct: 159 LLVLLKPAGLAVQPGTGHDDCVTARLAAQYAGADFLPTPAHRLDRDTSGLLLVATSYARL 218

Query: 168 QHLTESFRMRR-IQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           + L+++F  R  + K Y + V G  P      + + L K+   G   V  V   E     
Sbjct: 219 RALSDAFAAREGLVKEYLAWVAGRWPHEGARTLHDRLEKQGAPGRQKVRRVG-GEGSVPR 277

Query: 226 AISHFKVI---------------------DCFAQKF------CWLEMQPHTGRTHQLRVH 258
           A S  + +                      C             L ++ HTGRTHQ+RV 
Sbjct: 278 AASGNEAVRVESGTDAAHAAAGADAGRHAACTVTPLRRGDGASLLLVRLHTGRTHQIRVQ 337

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
               G PI+GD KY     G         + LHA  + LP  E
Sbjct: 338 LAERGHPIMGDRKYGGPACG-------QGMLLHAVRLTLPDGE 373


>gi|303231322|ref|ZP_07318057.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514002|gb|EFL56009.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 335

 Score = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 57/243 (23%), Positives = 103/243 (42%), Gaps = 54/243 (22%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LYED  + + +KPAG++V         +GIA++   F++  +    +K R  +RLD++T
Sbjct: 94  ILYEDDDLLIVDKPAGVTVNSKDKVSLANGIAHY---FMEHGI---KRKVRFLNRLDRDT 147

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G +V+A++  A     +       +K Y ++V G+ ++  + +    + +S  G  Y  
Sbjct: 148 TGCIVIAKSGLAQSLYQQQMDDNTFEKWYMAIVEGLVESDSDSLV-LPMDRSIDGIHYEV 206

Query: 215 VVKQNEKGANYAISHF--------------KVIDCFAQKFCW------------------ 242
             K  E   ++ + H                ++D   +                      
Sbjct: 207 NSKGKETRTDFTVLHRYPDGAVDNSVHNLQNIVDISHENVDSTVNTVDKQGGIVDNSVHN 266

Query: 243 LEMQP--------HTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHAR 293
           LE QP        +TG+THQ+RV   H+G P++GD  Y A   G  F       ++ H R
Sbjct: 267 LENQPCTAVAVRLYTGKTHQIRVAFSHIGHPLLGDTLYGAKSTGEPFALRAMKVVFTHMR 326

Query: 294 YMD 296
             D
Sbjct: 327 SGD 329


>gi|323339779|ref|ZP_08080049.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           ruminis ATCC 25644]
 gi|323092858|gb|EFZ35460.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           ruminis ATCC 25644]
          Length = 301

 Score = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 53/208 (25%), Positives = 100/208 (48%), Gaps = 21/208 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK---SWVDSKGQKPRLTH---RLDQET 154
           +LYED    + +KPA ++        +  D  +     + + +G K  + H   RLD++T
Sbjct: 81  ILYEDRDFLIVDKPAHLATIPSPDKKHRYDSLVNRVVGYYELRGIKDTVVHVITRLDRDT 140

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +GI+++A+ R A   + +      I+K Y +L+ G   +++    N       IG +   
Sbjct: 141 TGIVLIAKHRYAHALIDKQVHDHSIKKEYLALLSG-KVDRRHFFVNL-----PIGREPGS 194

Query: 215 VVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++K+   E G   +  +F  ++   +      ++ H+GRTHQ+RVH+  +G P+V D  Y
Sbjct: 195 MIKRTITEDGKPSSSEYF--LEKKLRDASLYRVRLHSGRTHQIRVHSKAIGHPLVADTLY 252

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
                G  + P+Q +  LH  ++   HP
Sbjct: 253 ----DGKNSLPLQRQ-GLHCFHLVFYHP 275


>gi|305680267|ref|ZP_07403075.1| RNA pseudouridine synthase [Corynebacterium matruchotii ATCC 14266]
 gi|305659798|gb|EFM49297.1| RNA pseudouridine synthase [Corynebacterium matruchotii ATCC 14266]
          Length = 339

 Score = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 55/220 (25%), Positives = 89/220 (40%), Gaps = 25/220 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ED ++ V +KP  ++    G  I       L+    +    P   HRLD+ TSG+LV 
Sbjct: 116 IFEDERLLVVDKPPFLATMPRGKHITQSATVQLRKLTGNGELSP--AHRLDRLTSGVLVF 173

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN-WLLKKSHIGGDYVHVVKQN 219
            +TR       + F  R  +K Y ++    P N K      W  + +   G+        
Sbjct: 174 TKTREVRGAYQQLFARREAEKTYEAIARYDPVNPKAQPGMVWRDRMTKNPGELQGYFVPG 233

Query: 220 EKGANYAISHFKVIDC-------------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           E  A   +   + +                 Q+  ++ +QP TGRTHQLR+H    G PI
Sbjct: 234 EPNAITTVIAVEPVPTERMRALRATHGSELPQQARYV-LQPATGRTHQLRLHMWKAGVPI 292

Query: 267 VGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +GD  Y       + +F  P    ++L A+ +    P  G
Sbjct: 293 LGDPAYPTVLPEAEEDFAVP----MHLRAKMLRFTDPLSG 328


>gi|312374039|gb|EFR21691.1| hypothetical protein AND_16535 [Anopheles darlingi]
          Length = 912

 Score = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 43/129 (33%), Positives = 61/129 (47%), Gaps = 8/129 (6%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLL 203
           R  HRLD+ TSG+L+  R+   A+ +    R R++QK Y   V G  P    EC     +
Sbjct: 40  RTIHRLDRLTSGLLLFGRSPKKARQMEHQIRNRQVQKEYICRVEGEFPDGVIECKEPIEV 99

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
               IG     V K + KG     +  K+   F      +  +P TGR HQ+RVH  ++G
Sbjct: 100 VSYKIG-----VCKVSPKGKECTTTFQKL--GFNGSSSVVLCKPLTGRMHQIRVHLQYLG 152

Query: 264 CPIVGDHKY 272
            P+V D  Y
Sbjct: 153 YPVVNDPLY 161


>gi|149237721|ref|XP_001524737.1| DRAP deaminase [Lodderomyces elongisporus NRRL YB-4239]
 gi|146451334|gb|EDK45590.1| DRAP deaminase [Lodderomyces elongisporus NRRL YB-4239]
          Length = 622

 Score = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 49/178 (27%), Positives = 76/178 (42%), Gaps = 9/178 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  + V +KP+GI         Y  +   K      G      +RLD+ TSG++ +
Sbjct: 191 IVYQDDDLLVIDKPSGIPAHPSG--RYRYNSVTKILQHEMGIVLHPCNRLDRLTSGLMFL 248

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            +T   +  L    + R + K Y + V G  PK         L     +  + V  VK  
Sbjct: 249 GKTAKGSTKLMTQIKDRNVSKEYIARVKGKFPKESITVDQPLLTLNPRLTLNVVDFVKGK 308

Query: 220 EKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           E     A + FK I    +     ++  P TGRTHQ+RVH  ++G PI  D  Y   +
Sbjct: 309 E-----ASTEFKRISYDPKTNTSVIKCHPLTGRTHQIRVHLQYIGYPIANDPIYSNGY 361


>gi|32266234|ref|NP_860266.1| hypothetical protein HH0735 [Helicobacter hepaticus ATCC 51449]
 gi|32262284|gb|AAP77332.1| conserved hypothetical protein [Helicobacter hepaticus ATCC 51449]
          Length = 303

 Score = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 60/239 (25%), Positives = 105/239 (43%), Gaps = 40/239 (16%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF---LKSI 100
            Q  +DKKR++ +NR+                  I + +I+   V L++       L+ +
Sbjct: 31  AQKVLDKKRLRQHNRV------------------IAKNEIICGQVELSEFEACDIELEPL 72

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
              ED    V++KP  +     G    Y ++  LK      G      HRLD++TSG+++
Sbjct: 73  FFNED--FCVYDKPHNLLTHPKGRFYHYSLNDALKLRF---GNYANAIHRLDKQTSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK-KSHIGGDY-----V 213
            A    +   L E    R+I K Y+++V G  K  +EC+ +  +  + + G D      +
Sbjct: 128 CAINPQSEPELKELISTRQILKTYYAIVEG--KLTQECLIDEPIALQKYKGTDLSIKSII 185

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               +  +   Y +++    D        + + P TGRTHQ+R+H  H+G  I+GD  Y
Sbjct: 186 SPYGKPSRTKLYPLAYHSPTDS-----TLIRVLPLTGRTHQIRLHCAHIGHRILGDPLY 239


>gi|256831879|ref|YP_003160606.1| pseudouridine synthase [Jonesia denitrificans DSM 20603]
 gi|256685410|gb|ACV08303.1| pseudouridine synthase [Jonesia denitrificans DSM 20603]
          Length = 362

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 46/180 (25%), Positives = 72/180 (40%), Gaps = 13/180 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  +YV +KP  ++     G        ++   D+   +    HRLD+ T+G+LV 
Sbjct: 133 VLFEDDDLYVIDKPHFLA-STPKGRYVTETALVRLRKDTGNPELSPAHRLDRLTAGVLVF 191

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH--------IGGDY 212
            + R       E F  R++ K+Y ++    P           + K H         G   
Sbjct: 192 TKRRELRGAYQELFAQRQVTKVYQAVAPTNPAVDLPATVRSRIVKEHGIMRAHTMPGEPN 251

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +      A     H    D   Q      + PHTG+THQLR+H   +G  IV D+ Y
Sbjct: 252 TETLVTLTDTATLPAGH----DVAVQDVGLYTLYPHTGKTHQLRIHMASLGLGIVYDNYY 307


>gi|22331748|ref|NP_190794.2| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|56744228|gb|AAW28554.1| At3g52260 [Arabidopsis thaliana]
 gi|332645401|gb|AEE78922.1| RNA pseudourine synthase 5 [Arabidopsis thaliana]
          Length = 294

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 103/238 (43%), Gaps = 30/238 (12%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPA 115
            RIQ+GQ+     V+   N +++    L  S    K  D   S+ +LYED  +   NKP+
Sbjct: 54  QRIQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDTPYSLEVLYEDDDLIALNKPS 113

Query: 116 GISVQGGS-----GIAYHID---GFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAA 166
           G+ V  G       +   +    G   S++ S+    P   HRL + TSGIL+ A+T+ A
Sbjct: 114 GLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVPVHRLGRGTSGILLCAKTKLA 173

Query: 167 AQHLTESFRM-----------------RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
              L   F                   R++ KIY +L  GI +  +  I   +    + G
Sbjct: 174 KTKLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADGIVEEDEVVIKQPIGVVRYPG 233

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPI 266
                 V   E     A S   V++   +K C L +++  +GR HQ+R+H  +MG P+
Sbjct: 234 VAQGLYVASPE--GKPAFSKVFVLERDREKNCSLVKVEIQSGRPHQIRIHLAYMGHPL 289


>gi|300780235|ref|ZP_07090091.1| probable ribosomal pseudouridine synthase [Corynebacterium
           genitalium ATCC 33030]
 gi|300534345|gb|EFK55404.1| probable ribosomal pseudouridine synthase [Corynebacterium
           genitalium ATCC 33030]
          Length = 339

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 60/200 (30%), Positives = 85/200 (42%), Gaps = 27/200 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  I V NKP  ++     S I       L+    ++   P   HRLD+ TSG+L+
Sbjct: 110 VVYEDDAIMVVNKPPFLATMPRASHITESATVRLRRSTGNEELTP--AHRLDRMTSGLLL 167

Query: 160 V---ARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHV 215
               A  R A Q L   F  R + K+Y ++   I P       AN  L   H      H+
Sbjct: 168 FTKKASVRGAYQQL---FASRAVAKLYEAVADDIGPSLPARPSANSPLVWEH------HI 218

Query: 216 VK-QNEKGANYAISHFKVIDCFAQKFCWLE-------MQPHTGRTHQLRVHALHMGCPIV 267
           VK + E  ++  +        +      L+       +QP TGRTHQLRV     G PI 
Sbjct: 219 VKREGELASSITVDAIPNSLTYVTDITPLQGGAARYLLQPVTGRTHQLRVQMHAAGAPIH 278

Query: 268 GDHKYCANFKG---NFTSPI 284
           GD  Y         +FT+P+
Sbjct: 279 GDPVYPELLPASAEDFTNPM 298


>gi|226360008|ref|YP_002777786.1| pseudouridine synthase [Rhodococcus opacus B4]
 gi|226238493|dbj|BAH48841.1| putative pseudouridine synthase [Rhodococcus opacus B4]
          Length = 297

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 101/212 (47%), Gaps = 20/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  + ++  G+ I       L+  +D     P   HRLD+ T+G+LV
Sbjct: 90  VLHRDDHLVVIDKPHFLATIPRGAHITETAVVRLRRALDLPDLTP--AHRLDRMTAGVLV 147

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIANWLLKKSHIGGDYVHVVKQ 218
                   +   E F  +++ K Y ++    P  +    I + ++K+  I      +   
Sbjct: 148 FLIRPEDRRAYQELFVSQQVTKEYEAVAGHDPALEFPRTIRSRIVKEHGI------MTAT 201

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK- 277
            E G   + +   +I+    +  +  + P TGRTHQLR+H   +G PI GD+ Y  +F+ 
Sbjct: 202 EEPGEPNSETVVDLIESRDGRARY-RLLPKTGRTHQLRLHMSSLGLPIEGDN-YYPDFRR 259

Query: 278 ---GNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
              G+F++P++    L AR ++   P  GR++
Sbjct: 260 SEPGDFSTPLR----LLARAIEFTDPRSGRVR 287


>gi|191637795|ref|YP_001986961.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|301065920|ref|YP_003787943.1| 23S RNA-specific pseudouridylate synthase [Lactobacillus casei str.
           Zhang]
 gi|190712097|emb|CAQ66103.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|300438327|gb|ADK18093.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           str. Zhang]
 gi|327381861|gb|AEA53337.1| Uncharacterized RNA pseudouridine synthase yhcT [Lactobacillus
           casei LC2W]
 gi|327385023|gb|AEA56497.1| Uncharacterized RNA pseudouridine synthase yhcT [Lactobacillus
           casei BD-II]
          Length = 300

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 57/221 (25%), Positives = 98/221 (44%), Gaps = 20/221 (9%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           YED    + NKPAG++     G     +A  +  +L     ++ Q   +  RLD++TSG+
Sbjct: 81  YEDDDYLIVNKPAGVASIPAVGRQNNSMANMVKAYLIK-TKAESQAVHVVTRLDRDTSGL 139

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDYVHVV 216
           +V A+   A   L +    +   K Y ++V             W++    +  G Y+  V
Sbjct: 140 MVFAKHGLAHSLLDQQLHSQDFVKQYVAIVTA---QTPLATHGWIVLPIGVSDGFYMRRV 196

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +   A+  ++ ++ +D   +    + +  HTGRTHQ+RVH   +G  + GD  Y  + 
Sbjct: 197 VTDTGKAS--VTEYRTLDQ-NKAGAMMLVTLHTGRTHQIRVHFAAIGHALYGDGLYSPDT 253

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMV 316
            G       N+  LH  ++    P   +L  + APLPA M 
Sbjct: 254 HGF------NRQALHCAHLRFWQPLKHKLIDLHAPLPADMA 288


>gi|332704296|ref|ZP_08424384.1| pseudouridine synthase [Desulfovibrio africanus str. Walvis Bay]
 gi|332554445|gb|EGJ51489.1| pseudouridine synthase [Desulfovibrio africanus str. Walvis Bay]
          Length = 278

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 65/285 (22%), Positives = 114/285 (40%), Gaps = 42/285 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR  +   P ++    ++++  G+  VD +      ++  GQ + +            
Sbjct: 19  RLDRLLERIVPELSLRGRRRLIDLGKALVDGQPKPAGFKVGPGQTITV------------ 66

Query: 80  EQKILDSSVNLTKHSDFLKS--ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                   ++ T  SD   S   ++  D +     KPAG+  +  +G    +D  L   +
Sbjct: 67  -------RMDDTPASDASASGPYVVQADERFAAVYKPAGMHSESLAGGGQGLDALLPELL 119

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNK 194
                  RL +RLD  TSGI++ A    A Q   +     +++K Y  LV G   +P   
Sbjct: 120 GRT--DARLVNRLDLPTSGIVLAALGADAEQEFRKLENAGQVRKEYAVLVHGRVEVPTVL 177

Query: 195 KECIANWLLKKSH-IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +  +     KK   +GGD    ++  E      +++  ++D    +   L      G  H
Sbjct: 178 RLALDTSDRKKVRALGGDSPDPLRWTEI---EPVAYDAILDRTRLRAVIL-----MGARH 229

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           Q+R H      PIVGD  Y  + +G        +LYLH   +++P
Sbjct: 230 QIRAHLAMHDHPIVGDTLYGPDAEG-------ERLYLHHGRLEMP 267


>gi|295131837|ref|YP_003582500.1| RNA pseudouridine synthase [Propionibacterium acnes SK137]
 gi|291375421|gb|ADD99275.1| RNA pseudouridine synthase [Propionibacterium acnes SK137]
          Length = 322

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 68/270 (25%), Positives = 117/270 (43%), Gaps = 28/270 (10%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           +P +    ++K+ R G  RVD+   +     +SG+  R        +     Q  +    
Sbjct: 39  WPTMRDYLVEKLPRMGGQRVDEMLDEGRFVDESGRTFR-------RDSPFTPQTFVFFHR 91

Query: 89  NLTKHSDFLKSI-LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +L   +     I +LY D +I V +KP  +S +  G  +   +   L++ +      P L
Sbjct: 92  DLPTETPVPAGIGILYSDERILVVDKPHFLSSIPRGRHVLESVVVRLRTQLG----LPEL 147

Query: 147 T--HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI----AN 200
           T  HRLD+ T+G+L++ R R   +   E F  R + K Y  +   +  +  E +    + 
Sbjct: 148 TVAHRLDRVTAGVLLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDSAGEGVTATKSG 207

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVH 258
           W ++ S I  +   +  +   G   A++   +I    +   W   E  P TGRTHQ+R+H
Sbjct: 208 WQVR-SRIIKERGILQAREVPGVPNAVTDIALI---GEHGGWGLYEASPRTGRTHQIRLH 263

Query: 259 ALHMGCPIVGDHKYCANFK---GNFTSPIQ 285
              +G PIV D  Y         +FT P+Q
Sbjct: 264 MQRLGAPIVNDPFYPVVLDTPVDDFTHPLQ 293


>gi|238916039|ref|YP_002929556.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           eligens ATCC 27750]
 gi|238871399|gb|ACR71109.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           eligens ATCC 27750]
          Length = 225

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 85/180 (47%), Gaps = 8/180 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---LTHRLDQETSGI 157
           +++E   I + NKPAG   QG  G    +   + ++  S+G KP    + +RLD+  SG+
Sbjct: 4   IIHETKDIIIVNKPAGQLSQGAKGFDLDLVSEVMTYNASQG-KPAYAAIINRLDRPVSGL 62

Query: 158 LVVARTR-AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV--H 214
           +++A+ + AAA++ T   +     K Y +L+ G     K    ++L K        +   
Sbjct: 63  VLIAKNKSAAAKYSTLMQKEGGFNKQYEALICGKLSESKGTFVDYLKKDGRTNTSAIVPA 122

Query: 215 VVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               N+K A  +   ++VI     K    + +   TGR HQ+RV       P+VGD+KY 
Sbjct: 123 DAAANDKEAKLSKLEYEVISYDEVKDITHVRIHLITGRHHQIRVQFASRRHPLVGDYKYA 182


>gi|317122830|ref|YP_004102833.1| pseudouridine synthase [Thermaerobacter marianensis DSM 12885]
 gi|315592810|gb|ADU52106.1| pseudouridine synthase [Thermaerobacter marianensis DSM 12885]
          Length = 414

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/235 (22%), Positives = 92/235 (39%), Gaps = 49/235 (20%)

Query: 4   MTYVQYVVVENDEENM--RLDR-WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  ++YVV   DE     RL R W ++    +    + ++LR G++ V+ +R   +  ++
Sbjct: 1   MPRLRYVVTPADEGQKLHRLARRWLRD----VPLSAVFRLLRQGRITVNGRRAPRDAVLR 56

Query: 61  SGQVVRI----------------------PPVINALNHIIKEQKILDSSVNLTKHSDF-- 96
           +G V+                        P    A  H    +        L   +    
Sbjct: 57  AGDVIEAELERVEGPGPDPSGLRPGAAGRPGPRPAAPHPPGPRPAAPQPPGLRPAAPHPP 116

Query: 97  -----------LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--- 142
                      L  +++YED  + V NKPAG+   G     + +  +++  +  +G    
Sbjct: 117 APHVPGPRVPELDPVIVYEDDHVLVVNKPAGMLTHGDGHAEWTLLAWVRDQLARRGTLPA 176

Query: 143 ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
               +P   HRLD+ TSG++   +TR  A  L E+ R  +  K Y ++V G P  
Sbjct: 177 GALFQPSPAHRLDRNTSGLVAFGKTRHGAARLAEALRSGQAIKEYLAVVRGRPPE 231



 Score = 40.0 bits (92), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 33/76 (43%), Gaps = 9/76 (11%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT 308
           TGRTHQ+R      G P+ GD KY     G    P   +  LH   + LP    G + + 
Sbjct: 339 TGRTHQIRAQLAATGHPLAGDRKY-----GGPKVPGLQRPALHCYRLVLP----GGVDVV 389

Query: 309 APLPAHMVKTWDSLGF 324
           APLP  +      LG 
Sbjct: 390 APLPPDLTGLCRRLGL 405


>gi|321455306|gb|EFX66443.1| hypothetical protein DAPPUDRAFT_332203 [Daphnia pulex]
          Length = 309

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 44/159 (27%), Positives = 75/159 (47%), Gaps = 12/159 (7%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD  TSG+L +A  + AA   + +F  R+ +K Y +L+ G   ++   I+  +   
Sbjct: 98  FVHRLDYSTSGVLCLATNKKAANLGSTAFSARKTRKYYLALLRGHVSHELIDISLPIGAD 157

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVHA 259
           S  G  +  +   +++   Y  + F  +    + F        + M+P TGR HQLR+H 
Sbjct: 158 SRPGHSH-KMCSSDKQFCQYPKAAFTRLLVLQKGFYDGFPVTKVMMKPVTGRRHQLRIHC 216

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             +G  IVGD  Y      N    +  +++LH+  + LP
Sbjct: 217 SSLGHTIVGDFTY-----SNGKDVLPYRMFLHSHRLILP 250


>gi|72386765|ref|XP_843807.1| hypothetical protein [Trypanosoma brucei TREU927]
 gi|62359821|gb|AAX80250.1| hypothetical protein, conserved [Trypanosoma brucei]
 gi|70800339|gb|AAZ10248.1| hypothetical protein, conserved [Trypanosoma brucei brucei strain
           927/4 GUTat10.1]
          Length = 828

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 71/281 (25%), Positives = 113/281 (40%), Gaps = 63/281 (22%)

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL-----LYEDSKIYVFNKPAGIS 118
           VVR+PP          E + + ++  + +  D LKS L     +YED  + V NKP  ++
Sbjct: 572 VVRLPP----------EHECVRAAETM-RAGDPLKSPLPIFPVVYEDDDLLVINKPPHVA 620

Query: 119 V-------------QGGSGIAYHID----GFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
                         +    ++  +     G +   V  +GQ     HRLD ETSG L++A
Sbjct: 621 TSRHALSCSQLCDDKATDIVSLQLTCKKRGDVMRRVFRQGQ----VHRLDTETSGCLIMA 676

Query: 162 RTRAAAQHLT----ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++  AA  L      S    +  KIY +L   +  N      N +L+             
Sbjct: 677 KSDVAASSLRHQMGTSAAYSQSSKIYLALCAVVESNLTNIPLNGVLRDP----------A 726

Query: 218 QNEKGANYAISHFKVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    Y I HF       ++F    +E +   G+ HQ+R H   +G PI+ D ++   
Sbjct: 727 DAKITTKYRIVHFY------KRFRVALVEARIQQGKKHQIRRHLAAVGLPILQDVEHGG- 779

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
                 SP+  ++ LHA  + + HP     L   APLP  M
Sbjct: 780 --AACCSPLLQRVALHASSVTVVHPRTAEVLTCVAPLPEDM 818


>gi|322495754|emb|CBZ31060.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 741

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 61/235 (25%), Positives = 98/235 (41%), Gaps = 44/235 (18%)

Query: 101 LLYEDSKIYVFNKPAGISV--------QGGSG--------IAYHIDGFLKSWVDSKGQKP 144
           +LYED  + V +KPAG++         Q G+         +A    G L   V  +GQ  
Sbjct: 514 VLYEDDDVLVVDKPAGLATSRHGLSCTQLGTPTTDLISVLLARDRAGALARGVFRQGQ-- 571

Query: 145 RLTHRLDQETSGILVVARTRAAAQ----HLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              HRLD ETSG L++A++  AA      L  S       KIY +L   +  +       
Sbjct: 572 --VHRLDAETSGCLLIAKSDVAADSLRHQLGTSAAFSHHSKIYHALCVVLEPS------- 622

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHA 259
             L+   +  D +       +      + ++VI  F + +  W+E +   G+ HQ+R H 
Sbjct: 623 --LRNVRLHDDIIDAADPKIR------TRYRVIRFFPKHRVAWVECRIQQGKKHQIRRHL 674

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
              G PI+ D ++           + +++ LHA  +   HP     +   APLPA
Sbjct: 675 ASRGFPILADLEHGGAV---CCQSMISRVALHAHSLSFIHPVTADPIIAAAPLPA 726


>gi|227509368|ref|ZP_03939417.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
 gi|227191080|gb|EEI71147.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
          Length = 297

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 105/225 (46%), Gaps = 27/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +++ED    V NK AG++      +    +   + G+ +       QK  +  RLD++TS
Sbjct: 81  IVFEDEHFLVVNKSAGVASVPAHNRANDSLVNRVKGYYQRN-HYANQKIHIVTRLDKDTS 139

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+   A   L +  +  +I+K Y ++V G+       I  +L  K   G     +
Sbjct: 140 GLVIFAKHHFAHSVLDKQLKDHQIKKTYLAIVEGVFSTTHFEI--YLPIKRAAGS----L 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           VK+ + G    +S   V + + ++       L++Q HTGRTHQ+RVH   +G P+VGD  
Sbjct: 194 VKR-QVGFPGKMS---VTEAWTKQRLRQHTLLKLQIHTGRTHQIRVHMTAIGHPLVGDWL 249

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           Y    K   + P Q    LH   +   +P  G  +   APLP  M
Sbjct: 250 YNPEDK---SFPRQA---LHCAGLRFFNPFAGHFVDCRAPLPDDM 288


>gi|91974996|ref|YP_567655.1| pseudouridine synthase [Rhodopseudomonas palustris BisB5]
 gi|91681452|gb|ABE37754.1| pseudouridine synthase [Rhodopseudomonas palustris BisB5]
          Length = 298

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 33/102 (32%), Positives = 54/102 (52%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ +L+ D  + V +KPAG+ V  G     +++   +       + P L HRLD++TSG
Sbjct: 19  IQARVLHRDGLMLVIDKPAGLPVHRGPKGGPNLETSFEFLRFGLPRPPVLAHRLDRDTSG 78

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            LV+ R R A   L   F+  +I K YW++V G P+     I
Sbjct: 79  CLVLGRHRKATATLGLLFKHSKISKTYWAIVEGGPEQDHGTI 120



 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/61 (49%), Positives = 39/61 (63%), Gaps = 5/61 (8%)

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++  WL ++P TGRTHQLRVH   MG PIVGD+ Y     GN     + KL+LHAR + +
Sbjct: 213 KRLTWLALEPITGRTHQLRVHCAAMGWPIVGDNIY-----GNGPRFGEPKLHLHAREIVI 267

Query: 298 P 298
           P
Sbjct: 268 P 268


>gi|330686161|gb|EGG97779.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU121]
          Length = 284

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/193 (26%), Positives = 91/193 (47%), Gaps = 24/193 (12%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVDSKG 141
           S NLT +   L   +L+ED  I + +KP G +           +   + G+L      KG
Sbjct: 65  SANLTPYMKPLD--ILFEDDYIIIVSKPNGQNCAPSREHPHESLVEQVLGYLHH----KG 118

Query: 142 QK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           ++  P +  RLD+ T+GI++ A+      HL   F   ++ K+Y  L +G+ +       
Sbjct: 119 ERTNPHIVTRLDRNTTGIVLFAK-YGYIHHL---FSKAKMDKVYTCLAYGMTE------P 168

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + +++      D   + +   +   YA + F+ +       C  E+Q  TGRTHQ+RVH 
Sbjct: 169 SGMIEAPIARSDESIIERCVSENGKYAKTVFRTLKQKENVSCC-EVQLCTGRTHQIRVHF 227

Query: 260 LHMGCPIVGDHKY 272
            ++G P++GD  Y
Sbjct: 228 QYIGHPLIGDTLY 240


>gi|329768061|ref|ZP_08259571.1| hypothetical protein HMPREF0428_01268 [Gemella haemolysans M341]
 gi|328838329|gb|EGF87939.1| hypothetical protein HMPREF0428_01268 [Gemella haemolysans M341]
          Length = 293

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 64/286 (22%), Positives = 125/286 (43%), Gaps = 30/286 (10%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +L +   R    R+KF+N       +++      + +I+KE  I++ ++    +S+F++ 
Sbjct: 20  LLENNISRKTLTRIKFDN----DGSIKVNSKEENVRYILKEGDIVEITLPSENYSEFVRF 75

Query: 100 I-----LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLD 151
           I     ++YED    V NK   + S+   +     +   +  +   K     P +  RLD
Sbjct: 76  IDKPIDIVYEDDYFLVVNKEINLPSIPSRNAEDESLLERVNYYFREKNINSIPHIVTRLD 135

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG++++A+ R    H+   F    I K Y +L+ G  K+     A      S I   
Sbjct: 136 KNTSGLVLIAKHR----HIHALFSNMEIDKYYTALINGKIKDHGILEAPIRRVSSSI--- 188

Query: 212 YVHVVKQNEKGANYAISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              + ++  +G  YA + +             + ++ +TG+THQ+RVH  ++G P++GD 
Sbjct: 189 ---IEREVGEGGEYAKTEYWSEKHNIKNDINVIRLKLYTGKTHQIRVHMKYLGYPLLGDE 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
            Y  +        + ++  LH   +   HP    ++ +   LP  M
Sbjct: 246 LYGGDIS------LISRQALHCSNLAFIHPISREKVNVCTNLPDDM 285


>gi|256842723|ref|ZP_05548211.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus 125-2-CHN]
 gi|256614143|gb|EEU19344.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus 125-2-CHN]
          Length = 301

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 111/245 (45%), Gaps = 30/245 (12%)

Query: 92  KHSDFLK------SILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQK- 143
           K +DFLK      SI+L E+    V NKPAG+ S+         +   L  +   KGQK 
Sbjct: 68  KKNDFLKPSNNPVSIVL-ENKNYLVVNKPAGVLSIPSRYEDDDAVVNRLLGYFAQKGQKN 126

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIA 199
             P +  RLD+ TSG+++V +   +    ++  + + ++K Y ++V G   P      I 
Sbjct: 127 LKPHVITRLDRYTSGLVLVGKNAISHARFSKIGKEKFVKK-YHAIVHGNFAPNELTGLID 185

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + KK   G      V  + K A  A   ++V+D        +E+   TGRTHQ+RVH 
Sbjct: 186 QPIGKK---GSGVKRAVVADGKDAQTA---YRVLDQVTGA-SLVELCLLTGRTHQIRVHM 238

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL--PAHMVK 317
            ++G P+ GD  Y    +  F+     +  L+  Y++ P P   +   T  L  P  M +
Sbjct: 239 AYLGHPLYGDPLY--GIQDGFS-----RQALNCFYLNFPDPFSQQKCKTIELNDPKDMQE 291

Query: 318 TWDSL 322
            W  L
Sbjct: 292 LWQKL 296


>gi|222624713|gb|EEE58845.1| hypothetical protein OsJ_10432 [Oryza sativa Japonica Group]
          Length = 458

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 65/259 (25%), Positives = 109/259 (42%), Gaps = 37/259 (14%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL--LYEDSKIYVFNKPA 115
           RI+ GQ+     V    + I++E   L     L     F   +L  LYED  +   NKP+
Sbjct: 72  RIRDGQITVDGEVATDPDMILREGSKLVYH-RLPWQEPFAPHLLDVLYEDDDMIALNKPS 130

Query: 116 GISV------QGGSGIA------YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           G+ V      Q  + +A      + +     S        P   HRL + TSG+L+ A+T
Sbjct: 131 GLQVLPKGLFQQRTVLAQLQLKDWKMPSSFCSKRKDAQSHPVPVHRLGRGTSGLLLCAKT 190

Query: 164 RAAAQHLTESF-----------------RMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
           + A   L   F                 + R+I K Y +LV GI +N +  I   +    
Sbjct: 191 KLAKAQLAAYFAEGATNAGKSRDETDICKARKISKFYRALVTGILENDEVMITQPIGLVR 250

Query: 207 HIG-GDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGC 264
           + G  + ++    + K A   +S  +V++         ++++ H+GR HQ+R+H  ++G 
Sbjct: 251 YPGVAEGLYAACSSGKPA---MSKVRVLERLKIHNHTLIQVEIHSGRPHQIRIHLAYIGH 307

Query: 265 PIVGDHKYCANFKGNFTSP 283
           P+V D  Y    +  F  P
Sbjct: 308 PLVDDPLYGIGGQPKFDEP 326


>gi|437185|gb|AAA64631.1| C-terminal sequence of ORF C product shows homology to several
           bacterial ORFs (accession numbers M87501, M59757,
           D10483, M62747, M96791, X57620, Z12154) and human EST
           cDNA (Z13254) [Leishmania donovani]
          Length = 741

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 97/235 (41%), Gaps = 44/235 (18%)

Query: 101 LLYEDSKIYVFNKPAGISV--------QGGSGIAYHID--------GFLKSWVDSKGQKP 144
           +LYED  + V +KPAG++         Q G+     I         G L   +  +GQ  
Sbjct: 514 VLYEDDDVLVVDKPAGLATSRHGLSCTQLGTPTTDLISVLLATDRVGALARGIFRQGQ-- 571

Query: 145 RLTHRLDQETSGILVVARTRAAAQ----HLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              HRLD ETSG L++A++  AA      L  S       KIY +L   +  +       
Sbjct: 572 --VHRLDAETSGCLLIAKSDVAADSLRHQLGTSAAFSHHSKIYHALCVVLEPS------- 622

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHA 259
             L+   +  D +       +      + ++VI  F + +  W+E +   G+ HQ+R H 
Sbjct: 623 --LRNVRLHDDIIDAADPKIR------TRYRVIRFFPKHRVAWVECRIQQGKKHQIRRHL 674

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
              G PI+ D ++           + +++ LHA  +   HP     +   APLPA
Sbjct: 675 ASRGLPILADLEHGGAV---CCQSMISRVALHAHSLSFIHPVTADPITAAAPLPA 726


>gi|331217838|ref|XP_003321597.1| hypothetical protein PGTG_03134 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
 gi|309300587|gb|EFP77178.1| hypothetical protein PGTG_03134 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
          Length = 572

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 42/129 (32%), Positives = 65/129 (50%), Gaps = 7/129 (5%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWG-IPKNKKECIANWLLK 204
           ++RLD+ TSG++V A T  A++ L++ F     ++K Y +   G  P ++  C    L  
Sbjct: 236 SNRLDRLTSGVMVCALTVEASRGLSKFFSTEGAVKKEYIARCRGNFPDDEVTCEEPLLTI 295

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              IG + VH   ++ K     +S+    D        L  +P TGR+HQLRVH   +G 
Sbjct: 296 DRQIGLNVVHPEGKHAKTIFKKLSYDPESDS-----SVLHCRPITGRSHQLRVHLQFLGF 350

Query: 265 PIVGDHKYC 273
           PI+ D  YC
Sbjct: 351 PILNDTIYC 359


>gi|86747487|ref|YP_483983.1| pseudouridine synthase [Rhodopseudomonas palustris HaA2]
 gi|86570515|gb|ABD05072.1| Pseudouridine synthase [Rhodopseudomonas palustris HaA2]
          Length = 300

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 33/105 (31%), Positives = 55/105 (52%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           ++ ++S +L+ D  + V +KP G+ V  G     +++   +       + P L HRLD++
Sbjct: 16  AEDIQSRVLHRDGLMLVIDKPPGLPVHRGPKGGPNLETSFEFLRFGLPRPPVLAHRLDRD 75

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           TSG LV+ R R A   L   F+  +I K YW++V G P   +  I
Sbjct: 76  TSGCLVLGRHRKATATLGLLFKHSKISKTYWAIVEGGPLEDQGTI 120



 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 36/60 (60%), Gaps = 5/60 (8%)

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              WL ++P TGRTHQLRVH   MG PI GD+ Y     GN     + KL+LHAR + +P
Sbjct: 216 PLTWLALEPITGRTHQLRVHCAAMGWPIFGDNIY-----GNGPRFGEPKLHLHAREITIP 270


>gi|314936786|ref|ZP_07844133.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus hominis subsp. hominis C80]
 gi|313655405|gb|EFS19150.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus hominis subsp. hominis C80]
          Length = 288

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 53/207 (25%), Positives = 89/207 (42%), Gaps = 34/207 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS---WVDSKGQK-----PRLTHRLDQ 152
           +LYED+ + + +KP  ++        +  D  ++    +++    K     P +  RLD+
Sbjct: 77  ILYEDTYLIIVSKPVHLNCAPSREHPH--DSLIERVMYYLNHSTNKVQYIVPHIVTRLDR 134

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T+GI++  +      HL  +F    I K Y  + +G  K +    A     K  I    
Sbjct: 135 NTTGIVIFTK-HGHIHHLMSTFE---IDKRYICVCYGKTKEQSMIEAPIGRNKDSI---- 186

Query: 213 VHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             + +       YA + +K +    +   C  E++ HTGRTHQ+RVH  H+G P++GD  
Sbjct: 187 --ITRCITPSGKYAKTEYKTLSSHHSASLC--EVKLHTGRTHQIRVHFKHIGHPLIGDDL 242

Query: 272 Y-----------CANFKGNFTSPIQNK 287
           Y              +K  F  PI NK
Sbjct: 243 YDGFHPRIQTQSLQCYKVKFIHPIYNK 269


>gi|311693193|gb|ADP96066.1| protein containing pseudouridine synthase domain [marine bacterium
           HP15]
          Length = 273

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 97/219 (44%), Gaps = 31/219 (14%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSG 156
           K ILL    +  V+ KP G+  QG S    H    L    + + ++P  L HRLD + +G
Sbjct: 79  KPILLENAGRYTVWFKPHGLLAQG-SQWGDHCS--LLRLAEIQLEQPCHLIHRLDADAAG 135

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++++A    AA  L++ F  R + K Y + V G+   +++ +   +  K+ +    V  +
Sbjct: 136 LMLIAHDSKAAGALSQCFSGRTMTKHYKARVAGLIDAREQLVDAPVEGKAAV--SRVSTL 193

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           + +E G    +                E+   TGR HQ+R H   +G PI+GD  Y    
Sbjct: 194 ELDETGETSLV----------------EVSIETGRKHQIRRHLAGLGHPIIGDRLY---- 233

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
                 P    L L A +++   P   R ++T  LPA +
Sbjct: 234 ----GRPAGAPLQLLAFFLEFDCPLNKR-KMTFELPAEL 267


>gi|323697656|ref|ZP_08109568.1| pseudouridine synthase [Desulfovibrio sp. ND132]
 gi|323457588|gb|EGB13453.1| pseudouridine synthase [Desulfovibrio desulfuricans ND132]
          Length = 275

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 75/306 (24%), Positives = 125/306 (40%), Gaps = 52/306 (16%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M +     ++   + +RLDR  +   P       +++   G++ VD +  K   R+++GQ
Sbjct: 1   MLFEGTFSIDASGDGLRLDRALEAVMPGSGLRLRRRLCDEGRILVDGRARKPGYRVRTGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V +           KE +       +T   +    I+ +ED      NKP G+     S
Sbjct: 61  LVEV-----------KEGR------EMTTPGELGVRIVKWEDG-FAAVNKPGGVH----S 98

Query: 124 GIAYHIDGFLKSWVDS------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            I   I G  +  V++       G +P L +RLD+ TSG+L+VA T  A     E     
Sbjct: 99  AI---ISGRDEPCVEAVLPALFPGMEPVLLNRLDRLTSGLLLVALTPEARDAYLEYEDQG 155

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-----YAISHFKV 232
            I+K Y + V G    + + I +   +          V+ + ++ A       A+SH   
Sbjct: 156 AIKKFYLARVRG----RLDGIVSVRNRLDTDDRKTTRVLAEPDEDARRWTGVTALSHDNA 211

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            D    + C +      G  HQ+R H   +G PIVGD  Y     G   SP    L L  
Sbjct: 212 ADTSLVR-CLIT----KGARHQIRAHLASIGHPIVGDPLY-----GGGESP--RGLMLQH 259

Query: 293 RYMDLP 298
           + +++P
Sbjct: 260 QRLEMP 265


>gi|314965704|gb|EFT09803.1| RNA pseudouridine synthase [Propionibacterium acnes HL082PA2]
          Length = 281

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 59/215 (27%), Positives = 94/215 (43%), Gaps = 24/215 (11%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LY D +I V +KP  +S +  G  +   +   L++ +      P LT  HRLD+ T+G+
Sbjct: 64  ILYSDERILVVDKPPFLSSIPRGRHVLESVVVRLRTQLGL----PELTVAHRLDRVTAGV 119

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI----ANWLLKKSHIGGDYV 213
           L++ R R   +   E F  R + K Y  +   +     E +    + W ++ S I  +  
Sbjct: 120 LLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTATKSGWQVR-SRIIKERG 178

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  +   G    ++   +I    +   W   E  P TGRTHQ+R+H   +G PIV D  
Sbjct: 179 ILQAREVPGVPNTVTDIALI---GEHGGWGLYEASPRTGRTHQIRLHMQRLGAPIVNDPF 235

Query: 272 YCANFK---GNFTSPIQNKLYLHARYMDLPHPEGG 303
           Y         +FT P+Q    L A  M    P  G
Sbjct: 236 YPVVLDIPVDDFTHPLQ----LQAWRMGFTDPVSG 266


>gi|228474393|ref|ZP_04059128.1| pseudouridine synthase YjbO [Staphylococcus hominis SK119]
 gi|228271752|gb|EEK13099.1| pseudouridine synthase YjbO [Staphylococcus hominis SK119]
          Length = 288

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 53/207 (25%), Positives = 89/207 (42%), Gaps = 34/207 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS---WVDSKGQK-----PRLTHRLDQ 152
           +LYED+ + + +KP  ++        +  D  ++    +++    K     P +  RLD+
Sbjct: 77  ILYEDTYLIIVSKPVHLNCAPSREHPH--DSLIERVMYYLNHSTNKVQYVVPHIVTRLDR 134

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T+GI++  +      HL  +F    I K Y  + +G  K +    A     K  I    
Sbjct: 135 NTTGIVIFTK-HGHIHHLMSTFE---IDKRYICVCYGKTKEQSMIEAPIGRNKDSI---- 186

Query: 213 VHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             + +       YA + +K +    +   C  E++ HTGRTHQ+RVH  H+G P++GD  
Sbjct: 187 --ITRCITPSGKYAKTEYKTLSSHHSASLC--EVKLHTGRTHQIRVHFKHIGHPLIGDDL 242

Query: 272 Y-----------CANFKGNFTSPIQNK 287
           Y              +K  F  PI NK
Sbjct: 243 YDGFHPRIQTQSLQCYKVKFIHPIYNK 269


>gi|332285853|ref|YP_004417764.1| pseudouridine synthase [Pusillimonas sp. T7-7]
 gi|330429806|gb|AEC21140.1| pseudouridine synthase [Pusillimonas sp. T7-7]
          Length = 306

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 59/216 (27%), Positives = 101/216 (46%), Gaps = 27/216 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +L+ D  + V +KP  + S+ GG    Y  +  L     S G  P L+  HRLD++T+G+
Sbjct: 99  VLFRDDHLVVADKPHFLASIPGGR---YLKETALVRLRQSLGL-PELSPIHRLDRDTAGV 154

Query: 158 LVV---ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           L+      +R   Q L   F+ R ++K Y ++        +  +A  L+ +S +     H
Sbjct: 155 LLFCADPESRGVYQAL---FQTRNVRKEYEAIA-----PLRSDLAFPLVHRSSMAARPGH 206

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-- 272
              +   G   + +  ++++    K+    ++PHTGR HQLRVH   +G PI  D  Y  
Sbjct: 207 FTMREVPGEPNSETQIELMEAMG-KWGRYRLRPHTGRKHQLRVHMSALGMPIRHDDFYPE 265

Query: 273 --CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
                   +F+ P+Q    L AR ++   P  G+L+
Sbjct: 266 LKAYARDDDFSRPLQ----LLARSIEFVDPVSGQLR 297


>gi|295426413|ref|ZP_06819063.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           amylolyticus DSM 11664]
 gi|295063781|gb|EFG54739.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           amylolyticus DSM 11664]
          Length = 294

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 48/188 (25%), Positives = 90/188 (47%), Gaps = 18/188 (9%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +  G KP +  RLD++TSG++++ +   A    ++  +   ++K +  +      N+ + 
Sbjct: 122 NEAGLKPHVVTRLDRDTSGLVLIGKNSVAHARFSKMDKENFVKKYHAIVAGNFSSNELKG 181

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQL 255
           + +  + K   G     V +Q       A + ++V+   AQK     +E++  TGRTHQ+
Sbjct: 182 LIDQPIGKEGSG-----VKRQVMSTGQKAQTEYQVL---AQKNNASLVELRLLTGRTHQI 233

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAH 314
           RVH  ++G P++GD  Y         S I  +  L+  Y+    P +  +++     PA 
Sbjct: 234 RVHMAYIGHPLLGDKLYGG-------SNIFFRQALNCFYLAFTDPFDQEQVEEKISDPAD 286

Query: 315 MVKTWDSL 322
           M K W+SL
Sbjct: 287 MQKLWNSL 294


>gi|84998092|ref|XP_953767.1| (RNA) pseudouridylate synthase [Theileria annulata]
 gi|65304764|emb|CAI73089.1| (RNA) pseudouridylate synthase, putative [Theileria annulata]
          Length = 441

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 58/227 (25%), Positives = 106/227 (46%), Gaps = 26/227 (11%)

Query: 72  NALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHI 129
           N L+HI+K  ++IL  ++     +   K  ++YED +  V +KP  I V Q G+     +
Sbjct: 108 NVLDHILKPNERILHEAIVHEPVALNSKVPVVYEDDQYIVVSKPTSIPVYQTGTYNYNSL 167

Query: 130 DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              +K  + S +  K    HR+D+  SG++  A++   A +L+++ R   ++K+Y + V 
Sbjct: 168 MEIMKREIPSCRDLKLFTVHRIDRLVSGLVAFAKSSQDASNLSQAIRDNEVKKVYIARVK 227

Query: 189 G----------IPKNKKECIANWLLKKSHIGGDYVHVVK----------QNEKGANY--A 226
           G              + +  A+  L+       Y+ V+           +N++  +Y  +
Sbjct: 228 GDFSYLINTSNSDNKESDGDADNSLENVFESIGYMRVISKKEGKYEFVGENDEDESYKRS 287

Query: 227 ISHFKVIDCFAQKFCWLEM-QPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++ FK+I         L +  P TGRTHQ+R H  ++G PI  D  Y
Sbjct: 288 VTRFKLIKYNKDLHESLVLCSPITGRTHQIRAHLKYLGYPISNDPWY 334


>gi|290961710|ref|YP_003492892.1| RNA pseudouridine synthase [Streptomyces scabiei 87.22]
 gi|260651236|emb|CBG74358.1| putative RNA pseudouridine synthase [Streptomyces scabiei 87.22]
          Length = 305

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 59/212 (27%), Positives = 93/212 (43%), Gaps = 24/212 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           ++Y D  I V +KP  ++    +    HI     + +  +   P L+  HRLD+ T+G++
Sbjct: 76  IVYRDDHIVVVDKPHFLAT---TPRGSHITETALARLRRELAVPTLSAAHRLDRLTAGLV 132

Query: 159 ---VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
              V    R A Q L   FR R + K Y ++    P     C       +S I  +   +
Sbjct: 133 LFTVRPGERGAYQSL---FRDRLVTKEYEAVAPYDPSVVLPCTV-----RSRIVKERGVM 184

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-- 273
             +  +G   A+S  +++D  A       + P TG+THQLR H   +G PI+GD  Y   
Sbjct: 185 AAREVEGEPNAVSGVELLDRRAGGPARYRLLPRTGQTHQLRAHMASLGLPILGDPLYPLV 244

Query: 274 --ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 G+F  P+Q    L AR ++   P  G
Sbjct: 245 RDPVPPGDFRRPLQ----LLARALEFTDPVTG 272


>gi|168010811|ref|XP_001758097.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162690553|gb|EDQ76919.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 361

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 56/211 (26%), Positives = 91/211 (43%), Gaps = 28/211 (13%)

Query: 102 LYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSK---GQKPRLTHRLDQETS 155
           LYED  I   +KP  + V   +  S +    + FLK+ V+++   GQK    HRLD+  S
Sbjct: 69  LYEDQYIIGVSKPGTLLVHNNKASSPLEKQRNAFLKNMVEAQLTAGQKVSPVHRLDRPAS 128

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++ +++  A +    S       K Y  L  G          ++ +    +       
Sbjct: 129 GAIIFSKSAVATRAAQASLSHPACIKEYVVLARGT-------TPDFFICDEPVN------ 175

Query: 216 VKQNEKGA-NYAISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              +EKGA   A+S   K++D    +   L++   TGR HQ+R H  H    +VGD K+ 
Sbjct: 176 ---DEKGAPKSAVSQCEKILDLPESRCSLLKVVIKTGRWHQIRKHLNHRAHHVVGDVKHG 232

Query: 274 ANFKGNFTSP----IQNKLYLHARYMDLPHP 300
                 F       +  +++LHA  +  PHP
Sbjct: 233 KGKTNRFFRENHKMLSGRIFLHAARLTFPHP 263


>gi|229551713|ref|ZP_04440438.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus rhamnosus
           LMS2-1]
 gi|258539108|ref|YP_003173607.1| pseudouridine synthase [Lactobacillus rhamnosus Lc 705]
 gi|229314918|gb|EEN80891.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus rhamnosus
           LMS2-1]
 gi|257150784|emb|CAR89756.1| Pseudouridine synthase [Lactobacillus rhamnosus Lc 705]
          Length = 300

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 101/242 (41%), Gaps = 46/242 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           + YED    V NKPAG++     G     +A  +  +L     ++ Q   +  RLD++TS
Sbjct: 79  ICYEDDDYLVVNKPAGVASIPAVGRRNDSMANMVKAYLIK-THAESQAVHVVTRLDRDTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWLLKKSHIGGDYV 213
           G++V A+   A   L          K Y +LV       K  ++   W++    +   + 
Sbjct: 138 GLMVFAKHSLAHSLLDRQLHSENFLKQYLALV-----TSKSLLSAHGWIILPIGVSTGFY 192

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY- 272
                +E G   +++ ++ +   +     L +  HTGRTHQ+RVH   +G P+ GD  Y 
Sbjct: 193 MRRVVSETGKP-SVTEYQTLAQNSHAAAVL-VTLHTGRTHQIRVHFAAIGHPLFGDDLYN 250

Query: 273 ------------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                       CA+ +  F  P+Q +      ++DL           APLP  M K  D
Sbjct: 251 RQADDFKRQALHCAHLR--FWQPLQKQ------WVDL----------HAPLPTDMAKLSD 292

Query: 321 SL 322
            L
Sbjct: 293 HL 294


>gi|50843747|ref|YP_056974.1| putative RNA pseudouridylate synthase [Propionibacterium acnes
           KPA171202]
 gi|50841349|gb|AAT84016.1| putative RNA pseudouridylate synthase [Propionibacterium acnes
           KPA171202]
          Length = 295

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/197 (27%), Positives = 90/197 (45%), Gaps = 20/197 (10%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LY D +I V +KP  +S +  G  +   +   L++ +      P LT  HRLD+ T+G+
Sbjct: 78  ILYSDERILVVDKPHFLSSIPRGRHVLESVVVRLRTQLGL----PELTVAHRLDRVTAGV 133

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI----ANWLLKKSHIGGDYV 213
           L++ R R   +   E F  R + K Y  +   +     E +    + W ++ S I  +  
Sbjct: 134 LLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTATKSGWQVR-SRIIKERG 192

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  +   G   A++   +I    +   W   E  P TGRTHQ+R+H   +G PIV D  
Sbjct: 193 ILQAREVPGVPNAVTDIALI---GEHGGWGLYEASPRTGRTHQIRLHMQRLGAPIVNDPF 249

Query: 272 YCANFK---GNFTSPIQ 285
           Y         +FT P+Q
Sbjct: 250 YPVVLDTPVDDFTHPLQ 266


>gi|239817699|ref|YP_002946609.1| pseudouridine synthase [Variovorax paradoxus S110]
 gi|239804276|gb|ACS21343.1| pseudouridine synthase [Variovorax paradoxus S110]
          Length = 303

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 62/225 (27%), Positives = 93/225 (41%), Gaps = 36/225 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL- 158
           +L++D ++ V +KP  + V   G  +   +   LK  +      P   HR+D+ T+G++ 
Sbjct: 92  VLFQDDELVVADKPPFLPVTPTGKYLQESLLVRLKRKLKLDDLVP--LHRIDRSTAGLVL 149

Query: 159 --VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV--- 213
             V   TR A Q +   F  RRI K Y            E +  W    S + G Y    
Sbjct: 150 FSVRPETRGAYQAM---FPERRIDKHY------------EAVVPWQPGVSSVPGTYRSRL 194

Query: 214 ----HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
               H ++  E+           +   A     LE+ P TGR HQLRVH + +G PIV D
Sbjct: 195 VDDDHFMRVKEEAGEPNSETRIALRKTAGGHALLELSPVTGRKHQLRVHCMALGMPIVND 254

Query: 270 HKYCANFK---GNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAP 310
             Y         +F  P+Q    L A+ +    P  G L+  T+P
Sbjct: 255 PFYPTLLPPDSDDFDKPLQ----LLAKSVAFQDPVSGELRSFTSP 295


>gi|158292130|ref|XP_313685.4| AGAP004401-PA [Anopheles gambiae str. PEST]
 gi|157017288|gb|EAA09234.5| AGAP004401-PA [Anopheles gambiae str. PEST]
          Length = 300

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 84/186 (45%), Gaps = 25/186 (13%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD  TSGIL +   + A + + + F  +R +K Y +L+ G     +E I       
Sbjct: 104 FAHRLDFATSGILCIPLNKNACKEVCQVFEEQRARKYYLALLRGHTDFDEEVI------D 157

Query: 206 SHIGGDY--------VHVVKQNEKGAN--YAISHFKVID---CFAQKFCWLEMQPHTGRT 252
             IG D         +  + ++E   N   +I+   V+D      +    + ++P TGR 
Sbjct: 158 IAIGEDVRFKDTSKKMCTILEDELCQNPRRSITKVLVLDRGYYNGKPVTKVLLRPITGRR 217

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           HQLR+H   +G  IVGD+ Y        TSP   +++LHA  + LP+  E   +Q   P 
Sbjct: 218 HQLRLHCSQIGHVIVGDYTYSLKID---TSP--PRMFLHAFRLVLPNTIENLDIQTDDPF 272

Query: 312 PAHMVK 317
               +K
Sbjct: 273 TEKALK 278


>gi|116330669|ref|YP_800387.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116124358|gb|ABJ75629.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 377

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 61/259 (23%), Positives = 111/259 (42%), Gaps = 39/259 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  D+  +RLD +    + + +    QK +  G++ V  K+VK    ++ G  V   P
Sbjct: 14  IFISKDDVGIRLDHFLSKKFTYHSRNVWQKEINEGRISVLGKKVKSGILLREGDTVVYQP 73

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +      + K+ KIL                  YED      +KP  + V        + 
Sbjct: 74  IERKEPPVRKDYKIL------------------YEDEFFVAVDKPGDLPVHPAGK---YR 112

Query: 130 DGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            G L + +   G+   L   HRLD+ETSG+++ A+   AA  L+  F  R+IQK Y + V
Sbjct: 113 KGNLLTLLKESGKFENLFTVHRLDRETSGVVLFAKDSKAASLLSGLFSSRKIQKYYITKV 172

Query: 188 WG-IPKNK------KECIANWLLKKSHIGGDYVHVVKQNEK---------GANYAISHFK 231
           +G  P+ K      K  +++ + KK        + +K+N+K            + ++ F+
Sbjct: 173 YGDFPRRKIAYGVLKPDVSSIIRKKRKFFLLKSNFLKRNKKYFLENSFSPEEEFCLTAFR 232

Query: 232 VIDCFAQKFCWLEMQPHTG 250
            I+ +  K  + E++   G
Sbjct: 233 KIESYFIKTQFQEIESDVG 251


>gi|116669183|ref|YP_830116.1| pseudouridine synthase [Arthrobacter sp. FB24]
 gi|116609292|gb|ABK02016.1| pseudouridine synthase [Arthrobacter sp. FB24]
          Length = 314

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 51/200 (25%), Positives = 91/200 (45%), Gaps = 20/200 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D  I V +KP  + +  GG+ I       L++ +D     P   HRLD+ T+GIL+
Sbjct: 90  ILHQDDHILVVDKPHFLPTTPGGTYIQESALVRLRNQLDLPDLIP--MHRLDRMTAGILL 147

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++    TR   Q L   F  R++QK Y  +    P      +   ++ ++ +     +++
Sbjct: 148 LSTNPETRGKYQVL---FEKRQVQKEYECVSAAEPAAGYPAVGFPVVVRNRMTKSRSYLL 204

Query: 217 KQNEKGANYAISHFKVIDCF--------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +   G   A +  ++   F          +     ++PH+G+THQLRVH   +G  IV 
Sbjct: 205 AEVVDGEPNAETRIELTKTFDAGTHASEPARRGLYRLEPHSGKTHQLRVHMASLGLGIVN 264

Query: 269 DHKY---CANFKGNFTSPIQ 285
           D  Y         ++T P+Q
Sbjct: 265 DAFYPELLDKAPDDYTRPLQ 284


>gi|199599112|ref|ZP_03212517.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|199590005|gb|EDY98106.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
          Length = 300

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 63/244 (25%), Positives = 100/244 (40%), Gaps = 46/244 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           + YED    V NKPAG++     G     +A  +  +L     ++ Q   +  RLD++TS
Sbjct: 79  ICYEDDDYLVVNKPAGVASIPAVGRRNDSMANMVKAYLIK-THAESQAVHVVTRLDRDTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWLLKKSHIGGDYV 213
           G++V A+   A   L          K Y +LV       K  ++   W++    +   + 
Sbjct: 138 GLMVFAKHSLAHSLLDRQLHSENFLKQYLALV-----TSKSLLSAHGWIILPIGVSTGFY 192

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY- 272
                 E G   +++ ++ +   +     L +  HTGRTHQ+RVH   +G P+ GD  Y 
Sbjct: 193 MRRVVIETGKP-SVTEYQTLAQNSDAAAVL-VTLHTGRTHQIRVHFAAIGHPLFGDDLYN 250

Query: 273 ------------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                       CA+ +  F  P+Q K      ++DL           APLP  M K  D
Sbjct: 251 RQADDFKRQALHCAHLR--FWQPLQKK------WVDL----------HAPLPTDMAKLSD 292

Query: 321 SLGF 324
            L  
Sbjct: 293 HLNL 296


>gi|148926673|ref|ZP_01810354.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|145845192|gb|EDK22287.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
          Length = 251

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/192 (26%), Positives = 87/192 (45%), Gaps = 30/192 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED KI   NKP           AY  +   K +        +L +RLD+ETSG++++
Sbjct: 60  IIFEDDKIIAINKP----------YAYVSEDLEKKF------NAKLLNRLDKETSGVILL 103

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+  R+ K Y +++ G+   + E   N  +    + G  +  V ++ 
Sbjct: 104 CKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEV--NEPIFTIKVKGGALSKVSKDG 161

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             A   I+          K    ++   TGRTHQ+RVHA  +   +VGD KY        
Sbjct: 162 LSALSIITPI----MMQSKKTLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY-----AKI 212

Query: 281 TSPIQNKLYLHA 292
           +S   +++YLH+
Sbjct: 213 SS---DRMYLHS 221


>gi|282849749|ref|ZP_06259133.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
 gi|282580686|gb|EFB86085.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
          Length = 372

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 59/256 (23%), Positives = 110/256 (42%), Gaps = 61/256 (23%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LYED+ + + +KP G++V         +G+A++   F +  +    +K R  +RLD++T
Sbjct: 131 ILYEDTDLLIVDKPCGLTVNSKDQVSLANGVAHY---FKEHGI---KRKVRFLNRLDRDT 184

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G +V+A++  A     +       +K Y + V GI +  ++ +  + +++S  G  Y  
Sbjct: 185 TGCIVIAKSGLAQSLYQQQMDDNTFEKWYMATVEGIVEADEDSLV-FPMERSADGIHYEV 243

Query: 215 VVKQNEKGANYAI----SHFKVIDCFAQKFCWLEMQP----------------------- 247
            VK  E   ++++    S   V +   +    +++ P                       
Sbjct: 244 NVKGKETRTDFSVLCRHSSQAVDNSVNKSKNSVDIAPKNVDINLGDVDKSSQNVDKTVYK 303

Query: 248 -------------HTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHAR 293
                        +TG+THQ+RV   H+G P+VGD  Y A   G  F    Q  ++ H R
Sbjct: 304 SNKCGYSKVLVRLYTGKTHQIRVAFSHIGHPLVGDILYGAQPTGQPFQLRAQKVVFTHMR 363

Query: 294 YMDLPHPEGGRLQITA 309
                   G R+ +TA
Sbjct: 364 T-------GERITVTA 372


>gi|293363350|ref|ZP_06610172.1| pseudouridine synthase, RluA family [Mycoplasma alligatoris A21JP2]
 gi|292553019|gb|EFF41770.1| pseudouridine synthase, RluA family [Mycoplasma alligatoris A21JP2]
          Length = 280

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 109/243 (44%), Gaps = 38/243 (15%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           ++K+ R   ++++ +R    + I +   V+ I  +I+      KE+  L +S +  K   
Sbjct: 31  VEKLFRKKDIKINGQRTNQKDYIIAFNDVIEIYGLIDTK----KEEAPLLTSFSFKK--- 83

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLK-SWVDSKGQKPRLTHRLDQE 153
                 +YED+ + + +KP GI V      +   +  +LK   VDS   KP    RLD+E
Sbjct: 84  ------IYEDANVLIIDKPNGIEVHSAPNCLDNQVLAYLKYKQVDS--FKPSHIGRLDKE 135

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK---KSHIGG 210
           TSGI++ A+   A ++L +   M  I+K Y +         KE +  +L K   K  +  
Sbjct: 136 TSGIMLYAKNYQALKYLND--YMENIKKTY-TFKSDFNDESKE-VELFLYKDEEKKRMAA 191

Query: 211 DYVHV-VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +  V   +  K   Y  S+ K    F            +GR HQ+RV  + +G PI GD
Sbjct: 192 SFTKVPYSKLSKTHLYTESNKKYATLF------------SGRKHQIRVTLMKLGKPIYGD 239

Query: 270 HKY 272
            KY
Sbjct: 240 FKY 242


>gi|224371098|ref|YP_002605262.1| RluC [Desulfobacterium autotrophicum HRM2]
 gi|223693815|gb|ACN17098.1| RluC [Desulfobacterium autotrophicum HRM2]
          Length = 295

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 55/222 (24%), Positives = 101/222 (45%), Gaps = 23/222 (10%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYH 128
           IN  NHI  + +   + +  T   + +++      +      KP+G+SV    GS +   
Sbjct: 38  INLSNHIYAQTRQKITPMETTNSVEIVRT-----GNGWLCAEKPSGMSVHNHPGSDLLCV 92

Query: 129 IDGFLKSWVD-------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           ++  +++  D        +G +    HRLDQETSG+++VA      ++L+  F+   +QK
Sbjct: 93  LERQIRADEDLMVALGAQEGFQIHPVHRLDQETSGLILVATDPDRLRYLSNLFQQGAVQK 152

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI---SHFKVIDCFAQ 238
            Y +LV G      +    W    S   G      + + +G    +   + ++++D  + 
Sbjct: 153 HYIALVHGNFDPPCDPFQVWDTPLSKQAGG-----RTDPRGKGKRVRSETRYRIMDQ-SP 206

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            +  LE++  TGR HQ+R HA   G P+ GD +Y +     F
Sbjct: 207 HYTLLEIELVTGRKHQIRRHAKLAGHPVTGDTRYGSKRSVEF 248


>gi|317495180|ref|ZP_07953550.1| RNA pseudouridylate synthase [Gemella moribillum M424]
 gi|316914602|gb|EFV36078.1| RNA pseudouridylate synthase [Gemella moribillum M424]
          Length = 282

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 87/207 (42%), Gaps = 42/207 (20%)

Query: 103 YEDSKIYVFNKPAGISV-------QGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQE 153
           YED  + + +KP GI         +  + + Y I  +           P L   HRLD +
Sbjct: 83  YEDDYLLIASKPFGIKTHPNDITDENNTLVNYLITDY-----------PYLEPIHRLDTD 131

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T G+++ A+T      L +    R I++ Y +LV       K  I    +  ++IG D  
Sbjct: 132 TCGLVIFAKTPFVKSKLDQMLEHRVIKRFYTALV-------KNNIHVQTIN-TNIGRDNR 183

Query: 214 HVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD-- 269
              K     KG N AI++    +   Q      +   TGRTHQ+R+H  + G PI+GD  
Sbjct: 184 EKNKMAVTNKGKN-AITNILSCEKIEQNKFATTISLETGRTHQIRIHLAYKGNPIIGDKL 242

Query: 270 -----HKYCANFKGN----FTSPIQNK 287
                HKY   + G     F  P+ NK
Sbjct: 243 YSNDGHKYEKMYLGALKVIFNHPVTNK 269


>gi|291276623|ref|YP_003516395.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
 gi|290963817|emb|CBG39653.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
          Length = 322

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 61/257 (23%), Positives = 113/257 (43%), Gaps = 40/257 (15%)

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G+ ++I   IN L    +  KIL+S  +L   +       +YED  + + NKP+ + +
Sbjct: 48  KGGKELKIGDRINILAPTSRP-KILESKTSLEIDT-------IYEDDHLLILNKPSDLVI 99

Query: 120 QGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHL 170
                        L  W+ +KG         ++  + HRLD++T+G + +A+   A   L
Sbjct: 100 HPAPSQKAET---LLDWLKAKGYTLSTISGEERCGIVHRLDKDTTGAIAIAKNNLAHNSL 156

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE------KGAN 224
               + R + + Y +++        + I   L    H+G +  + +K  +        A 
Sbjct: 157 ANQLQTRTMGRYYLAII-------DQPIKEALSIHCHMGRNPKNRLKMCKLDPLVFPQAR 209

Query: 225 YAISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
            + S F  +       +  + ++  TGRTHQ+RVH   +   I+GD  Y   ++GNF+  
Sbjct: 210 ESKSLFLPLFLSHNHSYQLVAIKLFTGRTHQIRVHLESISRHILGDGLY--GYRGNFS-- 265

Query: 284 IQNKLYLHARYMDLPHP 300
              ++ LHA  + L HP
Sbjct: 266 --KRIMLHAFLLYLIHP 280


>gi|307191610|gb|EFN75107.1| RNA pseudouridylate synthase domain-containing protein 1
           [Harpegnathos saltator]
          Length = 269

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 54/216 (25%), Positives = 89/216 (41%), Gaps = 41/216 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS-----GIAYHIDGFLKSWVDSK-GQKPRLTHRLDQET 154
           +++      V NKP  + +   +      +   +   L   V+ K   +    HRLD  T
Sbjct: 21  VVHRSENFLVVNKPYDMYINSNNPDRRNTLQLELKKMLPDLVNPKLCHEFHFVHRLDYPT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++ +A  + AA+  + +F    +QK Y +LV G           +++    IG D   
Sbjct: 81  SGVICIALNKKAARAASVAFENHTVQKFYLALVHG------HVHEPYIVIDKAIGDDI-- 132

Query: 215 VVKQNEKGANYAISHFKVIDCFAQK-----FCWLE-------------MQPHTGRTHQLR 256
                EK +N+ +     I C   +        LE             + P TGR HQLR
Sbjct: 133 ----REKNSNHKMCTSDSIFCEKPRRSTTVLVVLEHGFWKSKPATKILLAPSTGRRHQLR 188

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           VH  H+G  ++GD+ Y    +G    P  ++ YLH+
Sbjct: 189 VHCHHIGHTVIGDYTYS---EGKDIEP--HRTYLHS 219


>gi|326508344|dbj|BAJ99439.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 394

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 65/271 (23%), Positives = 111/271 (40%), Gaps = 37/271 (13%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK--EQKILDSSVNLTKHSDFLK 98
           ++ G+++VD++ V+ +  ++S Q          ++H +   E  +L  ++          
Sbjct: 73  VKCGRLQVDEQMVQADYIVKSSQ---------KISHFLHRHEPPVLGGNI---------- 113

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL-THRLDQETSGI 157
            ++L  +  +    KPA + V       Y  +  +       G  P    HRLD+  SG+
Sbjct: 114 -VILQNEVDVVTVCKPASVPVHPCG--QYRKNTVVGIMEAEHGLTPLFPVHRLDRLVSGL 170

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVV 216
           L+ A++   A+   +      +QK Y + V G+ P+ ++   AN        G   V V 
Sbjct: 171 LIFAKSAERAERFRQQIEANLLQKEYVAKVVGVFPEGEQTVDANVNFNARE-GRSTVEVS 229

Query: 217 KQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               K       A + F+ I C       +  +P TGRTHQ+RVH  H+G PI  D  Y 
Sbjct: 230 NGPGKAIPSGKQACTKFQRI-CTDGNHSIVLCKPVTGRTHQIRVHLKHLGYPIANDELY- 287

Query: 274 ANFKGNFTSPIQNKLYLH---ARYMDLPHPE 301
               GNF         +H   +    LP P+
Sbjct: 288 --VSGNFCPRSSKGTSIHRATSLVCSLPSPD 316


>gi|119476986|ref|ZP_01617267.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2143]
 gi|119449793|gb|EAW31030.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2143]
          Length = 280

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/168 (29%), Positives = 81/168 (48%), Gaps = 28/168 (16%)

Query: 110 VFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           ++ KP G+  QG   G    ID  ++ +     ++  L HRLD+ T+G++++A ++  A 
Sbjct: 89  IWYKPYGVLCQGSKWGDHCTIDRMIEIYTQ---KRSYLVHRLDRATTGLMIIAHSKDMAA 145

Query: 169 HLTESFRMRRIQKIYWSLVWG-IPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
            L++ FR R I K Y ++V G  P   KK+ I + L  K                    A
Sbjct: 146 KLSKLFRDRAIDKRYLAIVDGDFPYCEKKQTITSTLDGKK-------------------A 186

Query: 227 ISHFKVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ISH + +  ++Q+     +++   TGR HQ+R      G PIVGD  Y
Sbjct: 187 ISHMRRLR-YSQRHHQSLIDVNIETGRKHQIRRQLSDQGYPIVGDRLY 233


>gi|157116207|ref|XP_001652796.1| hypothetical protein AaeL_AAEL007487 [Aedes aegypti]
 gi|108876584|gb|EAT40809.1| conserved hypothetical protein [Aedes aegypti]
          Length = 300

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 84/186 (45%), Gaps = 25/186 (13%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD  TSGIL +   + A + + + F  +R +K Y +L+ G     +E I       
Sbjct: 104 FAHRLDFATSGILCIPLNKNACKEVCQVFEEQRARKYYLALLRGHTDFDEEVI------D 157

Query: 206 SHIGGDY--------VHVVKQNEKGAN--YAISHFKVID---CFAQKFCWLEMQPHTGRT 252
             IG D         +  + ++E   N   +I+   V+D      +    + ++P TGR 
Sbjct: 158 IAIGEDIRFKDTSKKMCTILEDELCQNPRRSITKVLVLDRGYYNGKPVTKVLLRPITGRR 217

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           HQLR+H   +G  IVGD+ Y        TSP   +++LHA  + LP+  E   +Q   P 
Sbjct: 218 HQLRLHCSQIGHVIVGDYTYSLKID---TSP--PRMFLHAFRLVLPNSFENIDIQTEDPF 272

Query: 312 PAHMVK 317
               +K
Sbjct: 273 TEKALK 278


>gi|289424437|ref|ZP_06426220.1| RNA pseudouridine synthase [Propionibacterium acnes SK187]
 gi|289427345|ref|ZP_06429058.1| RNA pseudouridine synthase [Propionibacterium acnes J165]
 gi|289155134|gb|EFD03816.1| RNA pseudouridine synthase [Propionibacterium acnes SK187]
 gi|289159275|gb|EFD07466.1| RNA pseudouridine synthase [Propionibacterium acnes J165]
 gi|332676702|gb|AEE73518.1| putative RNA pseudouridylate synthase [Propionibacterium acnes 266]
          Length = 322

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 68/270 (25%), Positives = 116/270 (42%), Gaps = 28/270 (10%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           +P +    ++K+ R G  RVD+   +     +SG+  R        +     Q  +    
Sbjct: 39  WPTMRDYLVEKLPRMGGQRVDEMLDEGRFVDESGRTFR-------RDSPFTPQTFVFFHR 91

Query: 89  NLTKHSDFLKSI-LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +L   +     I +LY D +I V +KP  +S +  G  +   +   L++ +      P L
Sbjct: 92  DLPTETPVPAGIGILYSDERILVVDKPHFLSSIPRGRHVLESVVVRLRTQLGL----PEL 147

Query: 147 T--HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI----AN 200
           T  HRLD+ T+G+L++ R R   +   E F  R + K Y  +   +     E +    + 
Sbjct: 148 TVAHRLDRVTAGVLLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTATKSG 207

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVH 258
           W ++ S I  +   +  +   G   A++   +I    +   W   E  P TGRTHQ+R+H
Sbjct: 208 WQVR-SRIIKERGILQAREVPGVPNAVTDIALI---GEHGGWGLYEASPRTGRTHQIRLH 263

Query: 259 ALHMGCPIVGDHKYCANFK---GNFTSPIQ 285
              +G PIV D  Y         +FT P+Q
Sbjct: 264 MQRLGAPIVNDPFYPVVLDTPVDDFTHPLQ 293


>gi|116335030|ref|YP_802525.1| ribosomal large subunit pseudouridine synthase [Candidatus
           Carsonella ruddii PV]
 gi|116235311|dbj|BAF35159.1| ribosomal large subunit pseudouridine synthase [Candidatus
           Carsonella ruddii PV]
          Length = 204

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 56/199 (28%), Positives = 90/199 (45%), Gaps = 29/199 (14%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y D+ I V NKP GI V+    +      F+K  ++ K     + +RLD+ TSG+++VA+
Sbjct: 8   YFDNNIIVINKPIGIEVKNLLNV-----NFIK--LNDKIPNFGILNRLDKYTSGLILVAK 60

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEK 221
                 +  +      I+K Y S V     NKK       +KK  +  D +        K
Sbjct: 61  NFYFYFYFKKLIVKNLIKKNYISFV-----NKK-------IKKGFVNVDIFKKKKSSIIK 108

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               +I+++K+I    + F +L +   TGRTHQ+R+H +H+   I  D  Y   +  N T
Sbjct: 109 NNKKSITYYKIIKE-KKNFSFLNICIKTGRTHQIRLHMMHIEKKIFNDFYYNKTYLLNNT 167

Query: 282 SPIQNKLYLHARYMDLPHP 300
                   LH + M   +P
Sbjct: 168 --------LHFKKMMFYYP 178


>gi|153952563|ref|YP_001398347.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
 gi|152940009|gb|ABS44750.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
          Length = 250

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/194 (25%), Positives = 86/194 (44%), Gaps = 34/194 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED KI   NKP           AY  +   K +        +L +RLD+ETSG++++
Sbjct: 59  IIFEDDKIIAINKP----------YAYVSEDLEKKF------NAKLLNRLDKETSGVILL 102

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+  R+ K Y +++ G+   + E        K+  GG    V K   
Sbjct: 103 CKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAK-GGALSKVSKD-- 159

Query: 221 KGANYAISHFKVID--CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                 +S   +I       K    ++   TGRTHQ+R+HA  +   ++GD KY      
Sbjct: 160 -----GLSALSIITPIMMQSKKTLAKIVIQTGRTHQIRIHAKFIKHGVIGDEKY-----A 209

Query: 279 NFTSPIQNKLYLHA 292
             +S   +++YLH+
Sbjct: 210 KISS---DRMYLHS 220


>gi|311063917|ref|YP_003970642.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           bifidum PRL2010]
 gi|310866236|gb|ADP35605.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           bifidum PRL2010]
          Length = 253

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 98/231 (42%), Gaps = 38/231 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED+ I V +KP  ++     G+ Y       L+   D     P   HRLD+ T+GI+
Sbjct: 20  VVYEDAGIIVIDKPHFLATTP-RGMWYRQTALIRLREMFDEPDITP--AHRLDRLTAGIV 76

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKSHIG 209
           V  R  A        F+ R+I K Y  L          +G  +     +   L ++SHI 
Sbjct: 77  VFVRDPALRGAYQMMFQGRKISKTYECLAPCRPTTRPRYGTVERLDPPVVFPLRRRSHIT 136

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL--------------EMQPHTGRTHQL 255
                V++  E+     ++   VID  A ++  +              E+ P TG+THQL
Sbjct: 137 -KLRGVLQAFEEPQT--VNAETVIDLAAGEYPSMGGRLCHGKNGLRAYELHPLTGKTHQL 193

Query: 256 RVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G PI GD  Y         +F++P++    L AR +    P  G
Sbjct: 194 RVHMNSIGLPIHGDDFYPRIVERAYDDFSTPLE----LVARSLRFTDPVSG 240


>gi|116334307|ref|YP_795834.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
 gi|116099654|gb|ABJ64803.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
          Length = 294

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 91/219 (41%), Gaps = 20/219 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +L+E+    V +KPAG++V  G       +   I G+ ++   ++   P +  RLD+ TS
Sbjct: 78  VLFENRDWLVVDKPAGLNVVPGPANRTDTLVNRIKGYWEA-EHAENLVPHILTRLDRFTS 136

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++ VAR R A    ++     +I K Y ++V G  +     I   L          V  
Sbjct: 137 GVVWVARHRLANSLASQLQAAHQIDKRYLAVVSGRLEADHAVIDAPLASDPTGYNQMVSP 196

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  +   +    F      A K        HTGRTHQ+R H   +G P++GD  Y   
Sbjct: 197 TGKPARTEYWVQQRFATATVVAVKL-------HTGRTHQIRAHFASLGHPLLGDALYDGP 249

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
             G       N+  L A  +    P    + Q T+ LPA
Sbjct: 250 VTG------INRQALQALSLTFKDPFTDEQRQFTSELPA 282


>gi|328724994|ref|XP_001952731.2| PREDICTED: hypothetical protein LOC100168337, partial
           [Acyrthosiphon pisum]
          Length = 1131

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 52/197 (26%), Positives = 92/197 (46%), Gaps = 23/197 (11%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           SL T+   +  EN E  +R+D+   +  P  +   +Q  ++ G V V+ K +K N +   
Sbjct: 472 SLNTFEFKIETEN-EIGVRIDKLLPDLNPDWSRNQIQDWIKLGLVEVNGKVIKANYK--- 527

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
               ++  VI A   +I+E  I+   + +          + YED  + V  KP G+ V  
Sbjct: 528 ---TKLNDVIVATEKVIEEVDIVAEDLGIE---------VYYEDKDVAVVYKPKGMVVHP 575

Query: 122 GSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++G +    D  G     +P + HR+D++TSG+L++A+   A + L E   
Sbjct: 576 APGHYTGTLVNGLMYVIKDLSGINGEIRPGIVHRIDKDTSGLLMIAKNDIAHRGLVEQLV 635

Query: 176 MRRIQKIYWSLVWG-IP 191
            + + + Y +LV G IP
Sbjct: 636 DKTVTREYTALVHGNIP 652


>gi|260102907|ref|ZP_05753144.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DSM 20075]
 gi|260083278|gb|EEW67398.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DSM 20075]
          Length = 275

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 54/195 (27%), Positives = 93/195 (47%), Gaps = 18/195 (9%)

Query: 103 YEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +E     V NKPAG+       +    +   + G+     + K  KP +  RLD++TSG+
Sbjct: 84  FETKNYIVLNKPAGVLSIPSRYEDNDAVVNRLMGYFLQQ-NKKDLKPHVITRLDRDTSGL 142

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV-HV 215
           ++V +   A    ++  +   ++K Y ++V G   +++   I +  + K    GD V   
Sbjct: 143 VLVGKNAIAHARFSKIGKDNFVKK-YHAIVHGNFAEDELTGIIDEPIGKE---GDGVKRA 198

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  N K A    + ++V+    +    +E++  TGRTHQ+RVH  ++G P+ GD  Y  N
Sbjct: 199 VVANGKKAQ---TRYRVLKQ-VEGASLVELRLLTGRTHQIRVHMAYLGHPLFGDPLYGIN 254

Query: 276 FKGNFTSPIQNKLYL 290
              NF+    N  YL
Sbjct: 255 --DNFSRQALNCFYL 267


>gi|163785435|ref|ZP_02180045.1| hypothetical protein HG1285_12602 [Hydrogenivirga sp. 128-5-R1-1]
 gi|159879297|gb|EDP73191.1| hypothetical protein HG1285_12602 [Hydrogenivirga sp. 128-5-R1-1]
          Length = 179

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/188 (26%), Positives = 91/188 (48%), Gaps = 32/188 (17%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVR--IP 68
           V++  +N RLD++  + YP  +    QK+++ G V   +K +K  + +++ GQ +   IP
Sbjct: 10  VDSQYKNKRLDQFLASVYPEFSRSYYQKLIKQGNVLEGEKELKKPSLKLKEGQEITLIIP 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P         +E ++   ++ L          + YED  + V  KP  + V    G   H
Sbjct: 70  PP--------EEIEVKPENIPLD---------IYYEDEDLAVVYKPPHMVVHPSVG---H 109

Query: 129 IDGFLKSW-------VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             G L +        V + G + R  + HRLD+ET+G+L++A++  A + L   F+ R +
Sbjct: 110 TSGTLVNALLYHFKNVSTYGGRERAGIVHRLDKETAGLLIIAKSEFAHKELQRQFQERTV 169

Query: 180 QKIYWSLV 187
            K Y ++V
Sbjct: 170 DKRYKAIV 177


>gi|86149810|ref|ZP_01068039.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|88597099|ref|ZP_01100335.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|218562347|ref|YP_002344126.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|85839628|gb|EAQ56888.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|88190788|gb|EAQ94761.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|112360053|emb|CAL34845.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|284925964|gb|ADC28316.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni IA3902]
 gi|315926823|gb|EFV06197.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni DFVF1099]
 gi|315929636|gb|EFV08817.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 250

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/192 (26%), Positives = 87/192 (45%), Gaps = 30/192 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED KI   NKP           AY  +   K +        +L +RLD+ETSG++++
Sbjct: 59  IIFEDDKIIAINKP----------YAYVSEDLEKKF------NAKLLNRLDKETSGVILL 102

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+  R+ K Y +++ G+   + E   N  +    + G  +  V ++ 
Sbjct: 103 CKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEV--NEPIFTIKVKGGALSKVSKDG 160

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             A   I+          K    ++   TGRTHQ+RVHA  +   +VGD KY        
Sbjct: 161 LSALSIITPI----MMQSKKTLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY-----AKI 211

Query: 281 TSPIQNKLYLHA 292
           +S   +++YLH+
Sbjct: 212 SS---DRMYLHS 220


>gi|294650008|ref|ZP_06727396.1| RNA pseudouridine synthase [Acinetobacter haemolyticus ATCC 19194]
 gi|292824101|gb|EFF82916.1| RNA pseudouridine synthase [Acinetobacter haemolyticus ATCC 19194]
          Length = 302

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 47/189 (24%), Positives = 92/189 (48%), Gaps = 11/189 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V +KP  +++   G  +   +   LK     K   P   HRLD+ET+G+++
Sbjct: 94  ILFENEDLLVVDKPHFLTMSPTGQYVQETLLVRLKKQTGYKELTP--IHRLDRETAGVVL 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             +  +A     + F  R++QKIY ++    P+          L+K    G   + ++ N
Sbjct: 152 FCKKASARGIYQQLFAERKVQKIYHAIAAYCPELHFPQTVKLHLEK----GLPFYTMQVN 207

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANF 276
            +  +   +  ++++       +L ++P TG+ HQLRVH  ++G PI+ D  Y       
Sbjct: 208 LEKPSNTETLIELLEHNKSHAKYL-LKPQTGKQHQLRVHLNYLGIPILNDEFYPVIAHKS 266

Query: 277 KGNFTSPIQ 285
             +F++P+Q
Sbjct: 267 SDDFSNPLQ 275


>gi|310287045|ref|YP_003938303.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium bifidum
           S17]
 gi|309250981|gb|ADO52729.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium bifidum
           S17]
          Length = 253

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 98/231 (42%), Gaps = 38/231 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED+ I V +KP  ++     G+ Y       L+   D     P   HRLD+ T+GI+
Sbjct: 20  VVYEDAGIIVIDKPHFLATTP-RGMWYRQTALIRLREMFDEPDITP--AHRLDRLTAGIV 76

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKSHIG 209
           V  R  A        F+ R++ K Y  L          +G  +         L ++SHI 
Sbjct: 77  VFVRDPALRGAYQMMFQGRKVSKTYECLAPCRPTTRPRYGTVERLDPPAVFPLRRRSHIT 136

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL--------------EMQPHTGRTHQL 255
                V++  E+    A++   VID  A+ +  +              E+ P TG+THQL
Sbjct: 137 -KLRGVLQAFEE--PQAVNAETVIDLAAEGYPSMGGRLCHGRNGLRAYELHPLTGKTHQL 193

Query: 256 RVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G PI GD  Y         +F++P++    L AR +    P  G
Sbjct: 194 RVHMNSIGLPIHGDDFYPRIVERAYDDFSTPLE----LVARSLRFADPVSG 240


>gi|325116888|emb|CBZ52441.1| RNA pseudouridylate synthase domain-containing protein [Neospora
            caninum Liverpool]
          Length = 2211

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/151 (28%), Positives = 67/151 (44%), Gaps = 7/151 (4%)

Query: 148  HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA-----NWL 202
            HRLD  TSG L+VA++ A    L       R +K+Y +LV+G    ++E +         
Sbjct: 1964 HRLDTPTSGPLLVAKSYAGLAFLRAQLASWRPKKVYLALVFGAVPLRRETVRLVHPLRPT 2023

Query: 203  LKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
             +    G   + V    + K A   ++         + F    ++P TGRTHQ+R    H
Sbjct: 2024 FEARQAGKKEMEVASTIDAKIALLFLTALAQYSYAGRDFTLCRVEPVTGRTHQIRAQLAH 2083

Query: 262  MGCPIVGDHKYCANFKGN-FTSPIQNKLYLH 291
            +G PIV D  Y  +         + N+L+LH
Sbjct: 2084 IGHPIVADPIYVKDPADRALGRSLSNRLFLH 2114


>gi|258511645|ref|YP_003185079.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478371|gb|ACV58690.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 333

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 104/245 (42%), Gaps = 27/245 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           + YED  + V NKPAG+        + GS +A         ++  +G  P   HRLD+ T
Sbjct: 74  ICYEDDDVIVVNKPAGMLTHPSPHERRGSLLA-----AAAHYLRDRGGVPHAVHRLDKYT 128

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW---GIPKNKKECIANWLLKKSHIGGD 211
           SG +++A+   A   L  + R   + + Y ++V+   G    +     + L    H    
Sbjct: 129 SGAVLIAKHAHAHHQLDRALRQGLVDRRYVAIVYAPEGCETGRWLTFVDGLAPNPHRPSR 188

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              +V   ++G + A++H   +   A     + +   TGRTHQ+R      G P+VGD  
Sbjct: 189 --RIVVPPDRG-DRAVTHALPL-VQAGPLALVALVLETGRTHQIRAQMAFHGMPLVGDRD 244

Query: 272 YC---ANFK-----GNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           Y    AN +      +F      +  LHA  +  P  E   + ++ A +   M + W ++
Sbjct: 245 YTYALANRRDPLGQASFYEKAFGRQALHAYALSWPRVEDRAMCKVRARVADDMRELWQTV 304

Query: 323 GFKYD 327
             + D
Sbjct: 305 AGRDD 309


>gi|324999146|ref|ZP_08120258.1| RNA pseudouridylate synthase [Pseudonocardia sp. P1]
          Length = 308

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 47/145 (32%), Positives = 66/145 (45%), Gaps = 17/145 (11%)

Query: 148 HRLDQETSGILV-VART--RAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLL 203
           HRLD+ T+G+L+ VAR   R A Q L   F   R+ K Y ++    P         + ++
Sbjct: 134 HRLDRATAGVLLLVARPELRGAYQML---FAEGRVGKTYEAITRHDPSLTLPRTEVSRIV 190

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           K+  I   +  V +     A   I     +D          + P TGRTHQLRVH   +G
Sbjct: 191 KRPGI---FAAVTEPGTPNAETRIE----LDTHRAGLARYRLFPRTGRTHQLRVHLNELG 243

Query: 264 CPIVGDHKYCA---NFKGNFTSPIQ 285
            PI+GD  Y        G+FT P+Q
Sbjct: 244 VPILGDDVYPELRQRPDGDFTRPLQ 268


>gi|242024726|ref|XP_002432777.1| Ribosomal large subunit pseudouridine synthase A, putative
           [Pediculus humanus corporis]
 gi|212518286|gb|EEB20039.1| Ribosomal large subunit pseudouridine synthase A, putative
           [Pediculus humanus corporis]
          Length = 227

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 46/157 (29%), Positives = 81/157 (51%), Gaps = 15/157 (9%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++ VA ++ +    + +F+ +  +K Y +L+ G   +K+E   N  + ++ 
Sbjct: 40  HRLDYSTSGVMCVALSKKSCAAASIAFQEKTTKKYYLALLRG-HVSKREIELNAPIGETI 98

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVI-----DCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             G  + ++    KGA  A S   V+     D +      L  +P TGR HQLRVH   +
Sbjct: 99  KKG--LKIMSSEVKGALPACSRLLVLERGIYDSYPATKVLL--RPLTGRRHQLRVHCNII 154

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           G  I+GD+ Y    K + + P   +++LH+  + +P+
Sbjct: 155 GHTIIGDYTYSQ--KKDVSPP---RMFLHSIRLIIPN 186


>gi|291520763|emb|CBK79056.1| pseudouridine synthase, RluA family [Coprococcus catus GD/7]
          Length = 310

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 58/246 (23%), Positives = 114/246 (46%), Gaps = 30/246 (12%)

Query: 43  SGQVRVDKKRVKF--NNRIQSGQVVRIPPVINALNHII------KEQKILDSSVNLTKHS 94
           +G  R   + VKF  N  + +GQ V    V++A + ++      + QK++ +   ++   
Sbjct: 25  AGLSRAFLRSVKFRENGILINGQRVTTRGVLHAGDSLVFNMPNDRTQKVVPAEGPVS--- 81

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLT--HRLD 151
                 +++E+  I + NKPA + +    G  +  +  +L  +     ++P L    RLD
Sbjct: 82  ------IVFENEDIVLVNKPARLVIHPCHGHYSDTLLSYLAWYYRLLPEQPLLCPIGRLD 135

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIG 209
           ++TSG++++A+ + AAQ L        + ++Y +L  G    ++K   I   + K     
Sbjct: 136 KDTSGLILIAKNKYAAQQLERQRANHTLSRVYLALAEGHWTNQSKSGLIDRPIEKVPECF 195

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPI 266
             Y     Q       + + ++V+  F  +   F  + ++  TGRTHQ+RVH   +  P+
Sbjct: 196 NRY-----QVADTGRPSRTEYEVLSEFTYEETPFSLVRLKLQTGRTHQIRVHMASLSHPL 250

Query: 267 VGDHKY 272
           +GD  Y
Sbjct: 251 LGDSIY 256


>gi|222110555|ref|YP_002552819.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221729999|gb|ACM32819.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 268

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/218 (28%), Positives = 99/218 (45%), Gaps = 24/218 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL++D+ +    KPAG  V      A      +++  D  GQ     HRLD+ T G+LV+
Sbjct: 10  LLWQDAHMVAVFKPAGWLVHRTGLDAGETRFVMQALRDQIGQHVYPVHRLDKGTCGVLVM 69

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A   AAA+ L ++F    ++K Y +LV G    + E   +  L+      D      Q  
Sbjct: 70  ALHPAAARALADAFARHAVRKQYLALVRGWAPAQAEV--DHPLRPDDAPPD---APTQPA 124

Query: 221 KGANYAISHFKVIDCFAQKFC-----WLEMQPHTGRTHQLRVHALHMGCPIVGD------ 269
                 ++  ++ +    +F       +  +P TGR HQ+R H  H+  PI+GD      
Sbjct: 125 HTRLTRLARLELPESSDPRFATTRASLVRAEPTTGRRHQIRRHLKHLAHPILGDATHGKG 184

Query: 270 --HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
             +++ A   G       ++L+LHA  + LPHP  GRL
Sbjct: 185 PLNRWWAQRLG------LHRLWLHAWQLSLPHPADGRL 216


>gi|300361258|ref|ZP_07057435.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus gasseri
           JV-V03]
 gi|300353877|gb|EFJ69748.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus gasseri
           JV-V03]
          Length = 299

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 53/183 (28%), Positives = 84/183 (45%), Gaps = 12/183 (6%)

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           K  KP +  RLD++TSG+++V +   A    +E  +   I+K Y ++V G    ++E   
Sbjct: 124 KDLKPHVITRLDRDTSGLVLVGKNAVAHARFSEMGKDCFIKK-YHAIVHGNFSKEQEIG- 181

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +  + IG     V +        +I+ ++V+D        +E+Q  TGRTHQ+RVH 
Sbjct: 182 ---IIDAPIGKLDASVKRGIVANGQRSITKYRVLDQ-VNGASLVELQLLTGRTHQIRVHM 237

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
            ++  P+ GD  Y    K NF     N  YL     D P  E  + ++T   P  M   W
Sbjct: 238 QYLDHPLFGDPLY--GIKDNFKRQALNCFYLK---FDDPFSE-RKQEVTISEPVDMKCLW 291

Query: 320 DSL 322
             L
Sbjct: 292 QRL 294


>gi|254458808|ref|ZP_05072232.1| pseudouridine synthase [Campylobacterales bacterium GD 1]
 gi|207084574|gb|EDZ61862.1| pseudouridine synthase [Campylobacterales bacterium GD 1]
          Length = 244

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 49/171 (28%), Positives = 79/171 (46%), Gaps = 21/171 (12%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++E+ +I V +KPA ++       +  I+  LK  V        L HRLD+ETSG+L++ 
Sbjct: 61  IFENDEIIVVDKPAFVN-------SDEIERQLKPAV--------LLHRLDRETSGVLMLV 105

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +     Q   + F+   + K Y + V GI     E     L +K +    Y +V   + K
Sbjct: 106 KDEEFRQKAIKEFKKDNVYKEYIAWVEGIISEPVEVDKPILTQKKN-NKAYSNV---SGK 161

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           G       F   D  +     ++   H GRTHQ+R H  ++  PI+GD +Y
Sbjct: 162 GKPARTEFFP--DLVSANKTKIKCIIHHGRTHQIRTHLRYIDHPIIGDEQY 210


>gi|71893374|ref|YP_278820.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyopneumoniae J]
 gi|71851501|gb|AAZ44109.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyopneumoniae J]
          Length = 281

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 120/281 (42%), Gaps = 51/281 (18%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +++V  +N +   +L +  K      N+  +QK  R+       K++K NN  Q      
Sbjct: 2   IKFVATKN-QSGQKLIQLIKKILLKSNYNEIQKYFRT-------KKIKVNNTFQEK---- 49

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI--------LLYEDSKIYVFNKPAGIS 118
                   N+IIKE+ I+    +  K   F K +        ++Y+D  I + +KP  + 
Sbjct: 50  --------NYIIKEKDII-LIFSQEKLKTFSKKVPEFKLNLKIIYQDENILLVDKPQNLQ 100

Query: 119 VQGGSGIAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           V GG    +++D  L  W      +++  KP    RLD++TSGI++      +   L + 
Sbjct: 101 VHGGR---FNLD--LAVWNYLKIPENQVFKPSHIGRLDKKTSGIILYGLNYQSVVELNQ- 154

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + +  +KIY    +    N K  I   +  + +   ++   ++   K  N   +     
Sbjct: 155 -KQKFFEKIY---TFKSDINLKNTIKTDVFIRKN---NFQQKMEVTLKSPNSFFASTTFY 207

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               +KF  L    HTG+ HQ+RV   H+G PI GD KY  
Sbjct: 208 SKNQKKFAIL----HTGKKHQIRVSLSHLGFPIFGDEKYGG 244


>gi|299148873|ref|ZP_07041935.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_23]
 gi|298513634|gb|EFI37521.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_23]
          Length = 612

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/67 (43%), Positives = 39/67 (58%), Gaps = 12/67 (17%)

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           ++K+  +   P TGRTHQLRVHA H   +GCPI+GD  Y             ++LYLHA 
Sbjct: 537 SRKYTRIVFYPLTGRTHQLRVHAAHPEGLGCPILGDELYGKK---------ADRLYLHAE 587

Query: 294 YMDLPHP 300
           Y++  HP
Sbjct: 588 YIEFRHP 594



 Score = 53.1 bits (126), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 54/94 (57%), Gaps = 8/94 (8%)

Query: 101 LLYEDSKIYVFNKPAG-ISVQGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +++ED  + V NKPAG +SV G +      YH     K + ++ G  P + HRLD  TSG
Sbjct: 347 IVFEDEWLLVVNKPAGMLSVPGKAEDRDSVYH--RLKKKYPEATG--PMIVHRLDMATSG 402

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           +L+VA+T+   + L   F  R I+K Y +++ G+
Sbjct: 403 LLLVAKTKEVHRDLQAQFANRSIKKRYVAVLDGV 436


>gi|167391242|ref|XP_001739694.1| ribosomal pseudouridine synthase [Entamoeba dispar SAW760]
 gi|165896535|gb|EDR23920.1| ribosomal pseudouridine synthase, putative [Entamoeba dispar
           SAW760]
          Length = 378

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/223 (27%), Positives = 99/223 (44%), Gaps = 36/223 (16%)

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS-KIYVFNKPAGISVQGGSGIAYHIDG 131
           +L+ +I+E  IL S  +L +    +K I + E++ +  V NKP+GI V       Y+ + 
Sbjct: 77  SLHSVIEEHDILISKCHLHEPPVPIKEIKIIENTPEFLVINKPSGIPVHPTG--RYNQNC 134

Query: 132 FLKSWVDS---KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--------RIQ 180
            L   ++       KP   +RLD+ TSG+L+ A+T+  A       + +         +Q
Sbjct: 135 ILNILLNEHHFSHLKP--VYRLDKNTSGVLLFAKTKKFASSFQSFLKEKSSVFSSPSSLQ 192

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI--------SHFKV 232
           KIY + V G   +  E   N  L     G +  + + ++   A  +         S+  V
Sbjct: 193 KIYLARVVGYFPDFIE--VNLPLHLIRFGTESQNSICEDGVEAKSSFKRLFFDKDSNTSV 250

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           I+C           PHTGRTHQLR+H   +  PI  D  Y  N
Sbjct: 251 IECI----------PHTGRTHQLRLHLKAINHPIANDSAYLLN 283


>gi|300744294|ref|ZP_07073313.1| RNA pseudouridine synthase [Rothia dentocariosa M567]
 gi|300380019|gb|EFJ76583.1| RNA pseudouridine synthase [Rothia dentocariosa M567]
          Length = 365

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 56/235 (23%), Positives = 95/235 (40%), Gaps = 41/235 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  +   +KP  + V   G+ +A      L+   ++    P   HRLD+ T+GIL+
Sbjct: 110 VLYEDEHLLAVDKPHYLPVTPRGAYVAQTALTKLRVRENNPLLTP--VHRLDRPTAGILL 167

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGD------- 211
            A+TR A       F+ R++ K Y ++     ++ +E  +   +  +S I  D       
Sbjct: 168 FAKTREARGPFQTMFQNRQVTKTYLAIAPAPSEDLRESMLGEGVQVRSRIDKDRNILQVR 227

Query: 212 -----------------------YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
                                   ++   Q+    + A + +       ++    E+ PH
Sbjct: 228 QYSARECERAGLTMNAETLVRIREIYQAPQSVPLKSGAQNPYLPYPAPGEEVALYELTPH 287

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHP 300
           TG+ HQLR H   +G PI GD  Y         + + P+Q    L A  +D  HP
Sbjct: 288 TGKMHQLRAHLNLLGTPIFGDVLYPQVLPTAPNDASVPLQ----LLAHRLDCVHP 338


>gi|168054605|ref|XP_001779721.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162668919|gb|EDQ55517.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 401

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/218 (26%), Positives = 91/218 (41%), Gaps = 44/218 (20%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS--KGQKPR-LTHRLD 151
           D+L  ++   DS + V +KPAG+SV    G   +++    ++V    K +KP  LTH++D
Sbjct: 139 DWLSRVIAETDSFV-VVDKPAGVSV---GGTVDNLEEMCATFVSRALKLKKPLILTHQID 194

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI--- 208
             T G +V A+T+A + H     R R+++K Y +L            A  +    H+   
Sbjct: 195 TCTEGCVVFAKTKAFSTHFHMLLRERKVRKEYTALA-----------AAPVAPGHHVHYM 243

Query: 209 -GGDYVHVVKQNEKGANYAISHFKVIDC-------------FAQKFCWLEMQPH------ 248
               Y   +  N   +++      V+ C             F    C  E + H      
Sbjct: 244 RSDRYAPRMVSNNDYSDWMNCELNVLGCRQVKWPSSSVEKQFRIAHCGWESREHAYECNV 303

Query: 249 ---TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
              TGRTHQ+RV    +  P+VGD  Y  +      SP
Sbjct: 304 RLLTGRTHQIRVQFAALDAPLVGDSVYMPSVVARKKSP 341


>gi|294792637|ref|ZP_06757784.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           6_1_27]
 gi|294456536|gb|EFG24899.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           6_1_27]
          Length = 300

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 59/255 (23%), Positives = 110/255 (43%), Gaps = 61/255 (23%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LYED  +++ +KP+G++V         +G+A++   F +  +    +K R  +RLD++T
Sbjct: 59  VLYEDEDLFIVDKPSGVTVNSKDQLSLANGVAHY---FKEHGI---KRKVRFLNRLDRDT 112

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G +V+A++  A     +       +K Y + V GI +  ++ +  + +++S  G  Y  
Sbjct: 113 TGCIVIAKSGLAQSLYQQQMDDNTFEKWYMATVEGIVEADEDTLV-FPMERSADGIHYEV 171

Query: 215 VVKQNEKGANYAI---------------SHFKV--------------------IDCFAQK 239
             K  E   ++++               S   V                    +D    K
Sbjct: 172 NAKGKETRTDFSVLCRHSSQPVDNSVNKSENSVHIGLKNVDIELVDVDKNNPNVDKTVYK 231

Query: 240 F-----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHAR 293
           F       + ++ +TG+THQ+RV   H+G P+VGD  Y A   G  F    Q  ++ H R
Sbjct: 232 FNKCGYTEVLVRLYTGKTHQIRVAFSHLGHPLVGDTLYGAQPTGQPFQLRAQKVVFTHMR 291

Query: 294 YMDLPHPEGGRLQIT 308
                   G R+ +T
Sbjct: 292 -------TGERITVT 299


>gi|262372214|ref|ZP_06065493.1| pseudouridylate synthase [Acinetobacter junii SH205]
 gi|262312239|gb|EEY93324.1| pseudouridylate synthase [Acinetobacter junii SH205]
          Length = 303

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 66/288 (22%), Positives = 116/288 (40%), Gaps = 44/288 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIP 68
           V + ND   + +  +    +PHI  +  Q+    G +   D  ++   +R      +   
Sbjct: 21  VFLPNDVSELTIFEYLCVQFPHIQAIEWQQRFEDGLIYASDGMKLSIQDRYTPNTFIFYY 80

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +    H+  E +IL                  +ED  + V +KP  +++   S    +
Sbjct: 81  RFLAHEIHVPFEHQIL------------------FEDEHLLVVDKPHFLTM---SPTGQY 119

Query: 129 IDGFLKSWVDSKGQKPRLT--HRLDQETSGILVV---ARTRAAAQHLTESFRMRRIQKIY 183
           +   L   +  +     LT  HRLD+ET+G+++    A +R   Q L   F  R++QK Y
Sbjct: 120 VQETLLVRLKKQTGYAELTPIHRLDRETAGVVLFCKKAESRGIYQQL---FAERKVQKTY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKF-- 240
            ++    P+ K        ++K H      + ++ N +K AN        I+     F  
Sbjct: 177 HAIAAYRPEIKFPMSLELHMEKGHP----FYTMRVNYDKTANTE----TFIELLEHNFQH 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQ 285
              ++ P TG+ HQLRVH  H+  PI+ D  Y         +F  P+Q
Sbjct: 229 AKYQLSPKTGKQHQLRVHLNHLNIPILNDPFYPTVLHKADDDFNHPLQ 276


>gi|71894118|ref|YP_278226.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           synoviae 53]
 gi|71850906|gb|AAZ43515.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           synoviae 53]
          Length = 281

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 64/267 (23%), Positives = 120/267 (44%), Gaps = 38/267 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +   +NDE N  L +    ++P++    ++K+ R  +++V+ KR+     + S     
Sbjct: 2   VSFKASKNDE-NRSLFKLICKYFPNLTIATIEKLFRKKEIKVNSKRITDKKFVVSE---- 56

Query: 67  IPPVINALNHIIKEQKILDSSVNLTK----HSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
                   N +++   I +S++NL +      DF    ++YED+ I + +K   + + G 
Sbjct: 57  --------NDLVEVYGISESNLNLPQIKKVSFDFQ---IIYEDANILIIDKKENLVIHGE 105

Query: 122 GSGIAYHIDGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE-SFRMRRI 179
            + +   +  +LK   +DS   KP    RLD+ETSG++V A+     + L E SF  +++
Sbjct: 106 DNSLDNQVLSYLKHKQIDS--FKPSHVGRLDKETSGLIVYAKNYLTLKQLNEKSFNFKKV 163

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            +     +   P   K     +  K  +         K+N K A ++I + +    FAQ 
Sbjct: 164 YQFKSDFLSSSPLELKL----YFYKDENNKTKISKTQKENSKLA-HSIFYCENNKKFAQI 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPI 266
                    TGR HQ+R+   ++  PI
Sbjct: 219 I--------TGRKHQIRLSLAYLNKPI 237


>gi|296086047|emb|CBI31488.3| unnamed protein product [Vitis vinifera]
          Length = 347

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/248 (25%), Positives = 99/248 (39%), Gaps = 50/248 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPRL-------THRLDQ 152
           +LYED  +   NKP+G+ V  G             W  + +   P          HRL +
Sbjct: 95  ILYEDDDVIALNKPSGLQVLPGGLFQQRTVLTQLQWRANKQNSLPACQESHSVPVHRLGR 154

Query: 153 ETSGILVVARTRAAAQHLTESF------------------RMRRIQKIYWSLVWGIPKNK 194
            TSGIL+ A+T+ A   L   F                   MR+I KIY +LV GI  +K
Sbjct: 155 GTSGILLCAKTKLAKTRLAAYFADGTSVVGGNRDADMKSRTMRKISKIYRALVNGI-LDK 213

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTH 253
            E +    +      G    +   +  G   A+S   +++   Q     ++++  +GR H
Sbjct: 214 DEIVIEQPIGMVQYPGVAKGLYVASPSGKP-ALSKVSILERDVQGDHMIVQVEIQSGRPH 272

Query: 254 QLRVHALHMGCPIVGDHKY-------CAN---------FKGNFTSPIQN-----KLYLHA 292
           Q+R+H   +G P++GD  Y       C +           G +  P++        +LHA
Sbjct: 273 QIRIHLSFIGHPLLGDPLYVPGGQPKCCDAEFTNESYALDGGYQRPVKPVPGDCGYHLHA 332

Query: 293 RYMDLPHP 300
             + L HP
Sbjct: 333 HQLVLSHP 340


>gi|256828761|ref|YP_003157489.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256577937|gb|ACU89073.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 281

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/195 (30%), Positives = 84/195 (43%), Gaps = 32/195 (16%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRL--THRLDQETSGILVVARTRAA 166
           V+NKPA +  QG +  A H    L     +K G +  L   HRLD+E  GI+++A    A
Sbjct: 96  VWNKPAAVLSQG-TRFADHCT--LPRLAQAKLGSRNELHPVHRLDREARGIMLLAHDGKA 152

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           A  L E FR   + K Y ++V GIP                   D+  +          A
Sbjct: 153 AAKLGELFRQGAVVKEYAAIVRGIP-------------------DWTDIEVNEPLDGKEA 193

Query: 227 ISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
            S F V+    A     L  +  TGR HQ+R H   +G P++GD +Y     G  T  +Q
Sbjct: 194 RSRFHVVQSDPASDMTLLLARIDTGRKHQIRRHLNGLGHPVMGDPRY-----GRGTRQVQ 248

Query: 286 NKLYLHARYMDLPHP 300
            +L L AR +    P
Sbjct: 249 -ELQLVARSLAFTCP 262


>gi|157738183|ref|YP_001490867.1| ribosomal large subunit pseudouridine synthase [Arcobacter butzleri
           RM4018]
 gi|315636326|ref|ZP_07891576.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
 gi|157700037|gb|ABV68197.1| ribosomal large subunit pseudouridine synthase [Arcobacter butzleri
           RM4018]
 gi|315479415|gb|EFU70098.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
          Length = 251

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 51/193 (26%), Positives = 89/193 (46%), Gaps = 26/193 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KPA ++                  V  K +   L +RLD+ETSG+++ 
Sbjct: 62  VIFEDKDILVVDKPAFLTA---------------DEVCKKFENAILLNRLDKETSGVMMF 106

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+     +   + F+  R+ K Y ++V G   ++ E I   +L     G     +  +  
Sbjct: 107 AKNEEFQKKAIKEFQANRVYKEYVAIVEGKVVDEIE-IDKPILTTKDRGMAKSKIDVKRG 165

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K A   +    V    ++    +E    +GRTHQ+RVH   +G PI+GD  Y     G  
Sbjct: 166 KPAKSTVYPLLVEGNKSKIKVVIE----SGRTHQIRVHLNSVGLPIIGDAIY-----GRV 216

Query: 281 TSPIQNKLYLHAR 293
           +S + N++ LH++
Sbjct: 217 SSNV-NRVLLHSK 228


>gi|308051432|ref|YP_003914998.1| pseudouridine synthase Rlu family protein, TIGR01621 [Ferrimonas
           balearica DSM 9799]
 gi|307633622|gb|ADN77924.1| pseudouridine synthase Rlu family protein, TIGR01621 [Ferrimonas
           balearica DSM 9799]
          Length = 235

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 59/199 (29%), Positives = 92/199 (46%), Gaps = 25/199 (12%)

Query: 97  LKSILLYEDSKIYVFNKPAGI---SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           L   ++++     V  KPAG+   S  G +G+   ++  L   +          HRLD  
Sbjct: 14  LTPSVIHQHPDFVVVVKPAGVHFHSQDGNAGLVAQLEAQLNESLYP-------VHRLDTP 66

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+LV+AR  AAA  LT  F   +++K Y +L    PK K+  +   + K     G + 
Sbjct: 67  TSGLLVLARHPAAAATLTALFTAHQVEKRYLALSGHKPKKKQGTVKGGMAKARR--GAWK 124

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               Q     N+AI+ F   +       +L ++P +GRTHQ+RV    +G PI+GD  Y 
Sbjct: 125 LTPGQE----NWAITQFVSHNLRPGIRAFL-LRPRSGRTHQIRVALKSLGAPILGDALYG 179

Query: 274 ANFKGNFTSPIQNKLYLHA 292
            +          ++ YLHA
Sbjct: 180 GSDA--------DRTYLHA 190


>gi|331007320|ref|ZP_08330519.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC1989]
 gi|330418882|gb|EGG93349.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC1989]
          Length = 308

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 47/175 (26%), Positives = 79/175 (45%), Gaps = 24/175 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---LTHRLDQETSGI 157
           LL++  +  ++ KP G+ +  GS    H    +  WV+   Q  R   L HRLD+ TSGI
Sbjct: 91  LLHDHGQYSIWYKPHGM-LSHGSKWGDHCS--ITRWVEQYHQPQRPSFLVHRLDRATSGI 147

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A  +  A +L   F  R+  K Y ++V G   + K  + + +  K+      +H + 
Sbjct: 148 MLIAHNKKVAANLCAQFENRQTDKRYHAVVEGELPSGKHTLTDPIDNKA--AHSEIHTIA 205

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            + +                 K   +++   TGR HQ+R H    G PI+GD  Y
Sbjct: 206 YDAEN----------------KSSLVDITIKTGRKHQIRRHLSQFGYPILGDKLY 244


>gi|323448452|gb|EGB04350.1| hypothetical protein AURANDRAFT_6163 [Aureococcus anophagefferens]
          Length = 166

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 38/126 (30%), Positives = 58/126 (46%), Gaps = 19/126 (15%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD++ SG +V+A+TRAA   L   F  RR++K Y ++  G         A W    
Sbjct: 60  VVHRLDRDASGAMVLAKTRAAHALLVREFAARRVRKTYLAVGRG--------AATW---- 107

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                D    V  + +G   A     +          L+ +  TGR HQ+R+H   +G P
Sbjct: 108 -----DGARAVDDDVQGKPAATEVAALA--AGGDRVLLDCRARTGRKHQVRLHCAALGLP 160

Query: 266 IVGDHK 271
           +VGD +
Sbjct: 161 LVGDPR 166


>gi|17978940|gb|AAL47436.1| AT3g52260/T25B15_30 [Arabidopsis thaliana]
          Length = 294

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 103/242 (42%), Gaps = 38/242 (15%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPA 115
            RIQ+GQ+     V+   N +++    L  S    K  D   S+ +LYED  +   NKP+
Sbjct: 54  QRIQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDTPYSLEVLYEDDDLIALNKPS 113

Query: 116 GISVQGGSGIAYHID--------GFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAA 166
           G+ V  G                G   S++ S+    P   HRL + TSGIL+ A+T+ A
Sbjct: 114 GLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVPVHRLGRGTSGILLCAKTKLA 173

Query: 167 AQHLTESFRM-----------------RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
              L   F                   R++ KIY +L  GI +  +  I      K  IG
Sbjct: 174 KTKLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADGIVEEDEVVI------KQPIG 227

Query: 210 GDYVHVVKQNEKGANY----AISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGC 264
                 V Q    A+     A S   V++   +K C L +++  +GR HQ+R+H  +MG 
Sbjct: 228 VVRYPGVAQGLYVASPEWKPAFSKVFVLERDREKNCSLVKVEIQSGRPHQIRIHLAYMGH 287

Query: 265 PI 266
           P+
Sbjct: 288 PL 289


>gi|226364380|ref|YP_002782162.1| pseudouridine synthase [Rhodococcus opacus B4]
 gi|226242869|dbj|BAH53217.1| putative pseudouridine synthase [Rhodococcus opacus B4]
          Length = 302

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 58/211 (27%), Positives = 91/211 (43%), Gaps = 24/211 (11%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  + S   G+ +A      L+  +D     P   HRLD+ T+G+L+
Sbjct: 93  ILHRDENLLVVDKPHFLASTPRGAYVAESALVRLRRDLDLPELTP--AHRLDRLTAGVLI 150

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW---LLKKSHIGGDYVH-- 214
               R   +     F  RR+ K Y            E +A +   LL  + +    V   
Sbjct: 151 FTVRREVRRDYQSLFDQRRVTKEY------------EAVARYDPDLLLPATVRSRIVKER 198

Query: 215 -VVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            V+K  E  G   + S  ++++       +  + PHTG+THQLRVH   +G PI GD+ Y
Sbjct: 199 GVLKAYEVDGPANSESRIELLEVHGAAARY-RLLPHTGKTHQLRVHMSSLGIPIHGDNFY 257

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +F           L L AR ++   P  G
Sbjct: 258 -PDFYDVAADDYSTPLRLLARSVEFADPCSG 287


>gi|15639147|ref|NP_218593.1| hypothetical protein TP0154 [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189025387|ref|YP_001933159.1| hypothetical protein TPASS_0154 [Treponema pallidum subsp. pallidum
           SS14]
 gi|3322421|gb|AAC65144.1| conserved hypothetical protein [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189017962|gb|ACD70580.1| hypothetical protein TPASS_0154 [Treponema pallidum subsp. pallidum
           SS14]
          Length = 345

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 62/275 (22%), Positives = 110/275 (40%), Gaps = 42/275 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+      ++   R+DR  +   P    V +   +R   +R++ + V+   R+Q G V+ 
Sbjct: 18  VECFRCTKNDAGRRVDRVLRILLPACPRVGVYARVRRTAIRLNGRPVQPAKRVQVGDVLS 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P    +L         L S +  T     L S++ ++   +  F+KPAG+ V G     
Sbjct: 78  LP---ESLCRARAASSRL-SKMPGTPKLRVLPSVV-FKTQDLLFFHKPAGLCVHGPRS-- 130

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 L +WV  +G+         +P   HRLD+ T G++  +R+   AQ  + + +  
Sbjct: 131 ------LDAWVRGQGRAHVPPALSFRPGPLHRLDRGTEGLIAFSRSLRGAQWFSAALQQH 184

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  L       +    A  L++     G+  HV                V+    
Sbjct: 185 TLRKFY--LAITAAPARTAAAARTLVRP----GEVTHVQ--------------TVLHSCD 224

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                  + P TG+ HQ+R +    G P+VGD  Y
Sbjct: 225 SALVLRVIVPVTGKKHQIRRYCAAQGFPLVGDRTY 259


>gi|262191836|ref|ZP_06050006.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae CT
           5369-93]
 gi|262032263|gb|EEY50831.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae CT
           5369-93]
          Length = 235

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 75/147 (51%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR  AAA  L++ F  R+++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  +      N AI+ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVNSQE------NPAITQFFSATAAPGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADKSDRGYLHA 178


>gi|309803449|ref|ZP_07697543.1| RNA pseudouridine synthase [Lactobacillus iners LactinV 11V1-d]
 gi|308164458|gb|EFO66711.1| RNA pseudouridine synthase [Lactobacillus iners LactinV 11V1-d]
          Length = 225

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 56/241 (23%), Positives = 104/241 (43%), Gaps = 34/241 (14%)

Query: 6   YVQYVVVENDEENMRLDRWFKN-----HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           Y+ Y+ +  +E N  +D+  +N      + H  F+ ++K      + V+ K +  N ++ 
Sbjct: 13  YIYYLTISQNENNQNVDQIMRNLLIPRKWRH--FLRIEK-----NILVNDKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE++ + V NKPAG   Q
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENADVLVINKPAG---Q 109

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 110 KTHPNLYETDTALNDCASYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQK 239
           + Y++ +            N       IG D + + K+  +     AI+H++V+     K
Sbjct: 170 RSYFAWIEATNDISDNGTINL-----PIGDDPLDMRKRMVRADGLKAITHYQVVKKQLIK 224

Query: 240 F 240
           F
Sbjct: 225 F 225


>gi|254491987|ref|ZP_05105165.1| RNA pseudouridine synthase family [Methylophaga thiooxidans DMS010]
 gi|224462802|gb|EEF79073.1| RNA pseudouridine synthase family [Methylophaga thiooxydans DMS010]
          Length = 279

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 58/204 (28%), Positives = 93/204 (45%), Gaps = 28/204 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---LTHRLDQETSGI 157
           L+ +  +  ++NKP G+  QG S    H    +  W +      R   + HRLD+  +G+
Sbjct: 87  LIADMGQYSIWNKPYGMLSQG-SKWGDHCT--ITRWAEQHLTPQRNAFVVHRLDRAANGL 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA  + AA  L+  F+ R+I+K Y   V G   +++  + N +     + G       
Sbjct: 144 IIVAHEKKAAALLSGLFQSRQIEKRYQIWVEG-EFSEQATVDNPVKVDLDLDG------- 195

Query: 218 QNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                  +A+S F  +   A K    L+++  TGR HQ+R HA  +G P+VGD  Y    
Sbjct: 196 ------RHAVSFFTRLKFDASKQQSLLDVRIETGRKHQIRQHAASLGHPVVGDRLY---- 245

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP 300
            GN     Q  L L A +M    P
Sbjct: 246 -GNILQ--QENLQLKAYFMAFRCP 266


>gi|227503769|ref|ZP_03933818.1| RNA pseudouridylate synthase family protein [Corynebacterium
           striatum ATCC 6940]
 gi|227199593|gb|EEI79641.1| RNA pseudouridylate synthase family protein [Corynebacterium
           striatum ATCC 6940]
          Length = 271

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/193 (29%), Positives = 89/193 (46%), Gaps = 27/193 (13%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + V +KP  + +   G  +   +   L+  +D+    P   HRLD+ T+G++V
Sbjct: 74  VLYADEHLLVVDKPHFLPTTSNGRIVRETLQTRLRVDMDNDEIVP--LHRLDRLTAGVVV 131

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +   RTR   QH+   F+ R++ K Y + V      + E +    + K H G   V V 
Sbjct: 132 CSVNPRTRGLYQHM---FQDRQMHKTYRARVTQ--PLQFEGMVTLRMAKPH-GSRQVVVD 185

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                   +  +  K +          E+QP TG THQLRV   H+G PI GD  Y  + 
Sbjct: 186 PAGTPTQTFVRASGKDV----------ELQPLTGHTHQLRVLLNHLGSPICGDDTYPVD- 234

Query: 277 KG----NFTSPIQ 285
           KG    +F+ P+Q
Sbjct: 235 KGLDLYDFSEPLQ 247


>gi|167949147|ref|ZP_02536221.1| Pseudouridylate synthase [Endoriftia persephone 'Hot96_1+Hot96_2']
          Length = 154

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 37/105 (35%), Positives = 56/105 (53%), Gaps = 2/105 (1%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I   NKPAG+ V       Y     +K   D  G+     HRLD+ TSG+L+ 
Sbjct: 6   IIYQDQAIVAINKPAGLLVHPSLVDRYETRSAMKLLRDQLGRWVYPVHRLDKPTSGVLLF 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           A     AQ L E F  R ++K Y ++V G P +++E I ++ LK+
Sbjct: 66  ALNSEVAQRLGEQFEGRGVEKRYLAVVRGHP-DQQEVI-DYPLKE 108


>gi|294954338|ref|XP_002788118.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239903333|gb|EER19914.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 393

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 102/237 (43%), Gaps = 41/237 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLT-HRLDQETSGIL 158
           ++ E   +   +KP+G+ V  G G   + +   LK    S+      T HRLD+ TSGI+
Sbjct: 123 IVGETDDVVAVDKPSGMPVHSGGGHRVNCLSAILKEQDPSRFSLAIHTLHRLDRLTSGIV 182

Query: 159 VVARTRAAAQHLTESFRM--RRIQKIYWSLVWG-------IPKNKKEC----IANWLLKK 205
           ++ +    A+  +E+F+   + IQK Y + V G       + +    C    +  ++L K
Sbjct: 183 ILGKNPDVARAFSEAFKKHDQEIQKCYLARVKGKFEGSNVVVEGFMRCVDFRVGKFILVK 242

Query: 206 SHIG--------GDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQ-------- 246
           S+ G        GD        +  +  A+    + D ++Q      W + Q        
Sbjct: 243 SNKGTASEDANQGDAPTSTPSGDDKS--AVEEEHIEDKWSQTSFDKVWYDEQNDETIIKC 300

Query: 247 -PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH   +G PI  D  Y   +K +   P    L  HA   ++P  EG
Sbjct: 301 YPKTGRTHQIRVHLESIGHPIANDSCYGGEYKADH--PFAFPLAPHAN--NVPPKEG 353


>gi|319796006|ref|YP_004157646.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315598469|gb|ADU39535.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 305

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 55/210 (26%), Positives = 95/210 (45%), Gaps = 20/210 (9%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSK 140
           + LD  V++       +  +L++D ++ V +KP  + V   G  +   +   LK  ++  
Sbjct: 80  RTLDGEVHIP-----FEEQVLFQDDELVVADKPPFLPVTPTGKYLQESLLVRLKRKLNID 134

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIA 199
              P   HR+D+ TSG+++ +  R       + F  RRI K Y ++V W      +E ++
Sbjct: 135 DLVP--LHRIDRSTSGLVLFSVRRETRGAYQQMFPERRIAKHYEAVVPW------QEGVS 186

Query: 200 NWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               + +S +  D   +  + E G   + +  +V +    +   L + P TGR HQLRVH
Sbjct: 187 TVPDIYRSRLVDDEHFMRMREEPGEPNSETRIEVQEIRGGR-ALLRLSPVTGRKHQLRVH 245

Query: 259 ALHMGCPIVGDHKYCANFKGN---FTSPIQ 285
            L +G PI  D  Y      N   F  P+Q
Sbjct: 246 CLALGMPIENDPIYPVLLPENTDDFDKPLQ 275


>gi|325995626|gb|ADZ51031.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 2018]
 gi|325997222|gb|ADZ49430.1| putative RNA pseudouridylate synthase [Helicobacter pylori 2017]
          Length = 293

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 71/289 (24%), Positives = 121/289 (41%), Gaps = 49/289 (16%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII------KEQKILDSSVNLTKHS 94
           L+  Q  +DK+R+K     Q+ Q VR   +I  +  +I      K+++            
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVRKSQIIQGVVSLIYFKPNEKQER------------ 70

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
                 L++E      F+KPA I      G   H +  L       G+     HRLD ET
Sbjct: 71  ------LVFEAKDFGAFDKPAQIYTHP-KGYFDH-ESLLDCIQSHFGKNAHPAHRLDYET 122

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++  +T  + + L   F  ++++K Y  L  G+  +K   I   +L   +I  D + 
Sbjct: 123 SGLVLAGKTLQSTKDLKALFMQKKVKKTYLVLTHGL-VDKSIIIDKPILTPENIQKD-LR 180

Query: 215 VVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +  Q       +I+  + +  + F      L++ P TGRTHQ+R+H   +   IVG+  Y
Sbjct: 181 IRSQISPLGKPSITLVEPLSYNPFLD-ISLLKITPLTGRTHQIRLHLSSVNHRIVGEGLY 239

Query: 273 CA---------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                        K    +P    L LHA  ++    +G   +I +P+P
Sbjct: 240 GVADENAREYLQLKRENNAPT---LMLHAASLEFEF-KGAHYKIASPMP 284


>gi|218192587|gb|EEC75014.1| hypothetical protein OsI_11092 [Oryza sativa Indica Group]
          Length = 461

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 54/214 (25%), Positives = 93/214 (43%), Gaps = 34/214 (15%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIA------YHIDGFLKSWVDSKGQKPRLTH 148
           +LYED  +   NKP+G+ V      Q  + +A      + +     S        P   H
Sbjct: 119 VLYEDDDMIALNKPSGLQVLPKGLFQQRTVLAQLQLKDWKMPSSFCSKRKDAQSHPVPVH 178

Query: 149 RLDQETSGILVVARTRAAAQHLTESF-----------------RMRRIQKIYWSLVWGIP 191
           RL + TSG+L+ A+T+ A   L   F                 + R+I K Y +LV GI 
Sbjct: 179 RLGRGTSGLLLCAKTKLAKAQLAAYFAEGATNAGKSRDETDICKARKISKFYRALVTGIL 238

Query: 192 KNKKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHT 249
           +N +  I   +    + G  + ++    + K A   +S  +V++         ++++ H+
Sbjct: 239 ENDEVMITQPIGLVRYPGVAEGLYAACSSGKPA---MSKVRVLERLKIHNHTLIQVEIHS 295

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
           GR HQ+R+H  ++G P+V D  Y    +  F  P
Sbjct: 296 GRPHQIRIHLAYIGHPLVDDPLYGIGGQPKFDEP 329


>gi|114564709|ref|YP_752223.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114336002|gb|ABI73384.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 326

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/200 (28%), Positives = 90/200 (45%), Gaps = 23/200 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D+   +  KP  + V  GG+ +   +   L+         P   HRLD++T+G+++
Sbjct: 109 VLYQDNDTIIVYKPHFLPVTPGGNYVNECLVHRLRIATQIDTVAP--AHRLDKDTAGVML 166

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN-------WLLKKSHIG 209
           +    +TR A   L   F   +I K Y ++    P    E   N       W +K   + 
Sbjct: 167 MTLNPQTRHAYHQL---FLDDKITKDYQAIAKLTPTLLSEFADNTCMLPIHWTVKNRIVA 223

Query: 210 GDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +    ++  E  AN   SH ++ +      F   E+ P TG+THQLRVH   +G PI+ 
Sbjct: 224 ANPSFTMQVVEGEAN---SHSEISLVAVKNGFGLFELSPITGKTHQLRVHMQSLGMPILH 280

Query: 269 DHKYCANF-KG--NFTSPIQ 285
           D  Y     KG  NF  P+Q
Sbjct: 281 DRFYPVLLPKGPDNFDKPLQ 300


>gi|282852992|ref|ZP_06262329.1| RNA pseudouridine synthase [Propionibacterium acnes J139]
 gi|282582445|gb|EFB87825.1| RNA pseudouridine synthase [Propionibacterium acnes J139]
 gi|314982992|gb|EFT27084.1| RNA pseudouridine synthase [Propionibacterium acnes HL110PA3]
 gi|315091497|gb|EFT63473.1| RNA pseudouridine synthase [Propionibacterium acnes HL110PA4]
 gi|315094599|gb|EFT66575.1| RNA pseudouridine synthase [Propionibacterium acnes HL060PA1]
 gi|315105253|gb|EFT77229.1| RNA pseudouridine synthase [Propionibacterium acnes HL050PA2]
 gi|327328883|gb|EGE70643.1| RNA pseudouridylate synthase family protein [Propionibacterium
           acnes HL103PA1]
          Length = 281

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 58/215 (26%), Positives = 90/215 (41%), Gaps = 24/215 (11%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LY D +I V +KP  +S +  G  +   +   L++ +      P LT  HRLD+ T+G+
Sbjct: 64  ILYSDERILVVDKPHFLSSIPRGRHVLESVVVRLRTQLGL----PELTVAHRLDRVTAGV 119

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI----ANWLLKKSHIGGDYV 213
           L++ R R   +   E F  R + K Y  +   +     E +    + W ++   I    +
Sbjct: 120 LLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTATKSGWQVRSRIIKERGI 179

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              ++     N        I    +   W   E  P TGRTHQ+R+H   +G PIV D  
Sbjct: 180 LQAREVPGVPNTVTD----IALIGEHGGWGLYEASPRTGRTHQIRLHMQRLGAPIVNDPF 235

Query: 272 YCANFK---GNFTSPIQNKLYLHARYMDLPHPEGG 303
           Y         +FT P+Q    L A  M    P  G
Sbjct: 236 YPVVLDIPVDDFTHPLQ----LQAWRMGFTDPVSG 266


>gi|218290916|ref|ZP_03494973.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|218239081|gb|EED06284.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
          Length = 333

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 80/181 (44%), Gaps = 18/181 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           + YED  + V NKPAG+        + GS +A         ++  +G  P   HRLD+ T
Sbjct: 74  ICYEDDDVIVVNKPAGMLTHPSPHERRGSLLA-----AAAHYLRDRGGVPHAVHRLDKYT 128

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW---GIPKNKKECIANWLLKKSHIGGD 211
           SG +++A+   A   L  + R   + + Y ++V+   G    +     + L    H    
Sbjct: 129 SGAVLIAKHAHAHHQLDRALRQGLVDRRYVAIVYAPEGCETGRWLTFVDGLAPNPHRPSR 188

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              +V   ++G + A++H   +   A     + +   TGRTHQ+R      G P+VGD  
Sbjct: 189 --RIVVPPDRG-DRAVTHALPL-VQAGPLALVALVLETGRTHQIRAQMAFHGMPLVGDRD 244

Query: 272 Y 272
           Y
Sbjct: 245 Y 245


>gi|225449104|ref|XP_002276664.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 348

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 62/249 (24%), Positives = 99/249 (39%), Gaps = 51/249 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPRL-------THRLDQ 152
           +LYED  +   NKP+G+ V  G             W  + +   P          HRL +
Sbjct: 95  ILYEDDDVIALNKPSGLQVLPGGLFQQRTVLTQLQWRANKQNSLPACQESHSVPVHRLGR 154

Query: 153 ETSGILVVARTRAAAQHLTESF-------------------RMRRIQKIYWSLVWGIPKN 193
            TSGIL+ A+T+ A   L   F                    MR+I KIY +LV GI  +
Sbjct: 155 GTSGILLCAKTKLAKTRLAAYFADGTSVVGGNRLDADMKSRTMRKISKIYRALVNGI-LD 213

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRT 252
           K E +    +      G    +   +  G   A+S   +++   Q     ++++  +GR 
Sbjct: 214 KDEIVIEQPIGMVQYPGVAKGLYVASPSGKP-ALSKVSILERDVQGDHMIVQVEIQSGRP 272

Query: 253 HQLRVHALHMGCPIVGDHKY-------CAN---------FKGNFTSPIQN-----KLYLH 291
           HQ+R+H   +G P++GD  Y       C +           G +  P++        +LH
Sbjct: 273 HQIRIHLSFIGHPLLGDPLYVPGGQPKCCDAEFTNESYALDGGYQRPVKPVPGDCGYHLH 332

Query: 292 ARYMDLPHP 300
           A  + L HP
Sbjct: 333 AHQLVLSHP 341


>gi|312084667|ref|XP_003144368.1| hypothetical protein LOAG_08790 [Loa loa]
 gi|307760466|gb|EFO19700.1| hypothetical protein LOAG_08790 [Loa loa]
          Length = 379

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 51/171 (29%), Positives = 80/171 (46%), Gaps = 11/171 (6%)

Query: 105 DSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILVVAR 162
           D+ I V +KPA + V   G    + + G L+   + +G +  R+ HRLD+ TSG+L+ AR
Sbjct: 79  DNNIIVVDKPASMPVHPCGRYCVHTVLGMLR---EQRGLRDLRVVHRLDRTTSGVLLFAR 135

Query: 163 TRAAAQHLTESFRMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
                  L +  R+  +  K Y   V G+    KE I +  +    +    +  ++ + K
Sbjct: 136 NSETDTKLKKMLRVGEVWHKEYLCKVEGVFPADKEIICDRPIGPLVLSMG-IQCIRDDGK 194

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            A             +   C LE    TGRTHQ+RVH  ++G PIV D+ Y
Sbjct: 195 CARSRFWRLWTDGQTSIVRCMLE----TGRTHQIRVHLQYLGYPIVDDYIY 241


>gi|256851497|ref|ZP_05556886.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii 27-2-CHN]
 gi|260660920|ref|ZP_05861835.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii 115-3-CHN]
 gi|282931931|ref|ZP_06337399.1| pseudouridine synthase YjbO [Lactobacillus jensenii 208-1]
 gi|297206310|ref|ZP_06923705.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii JV-V16]
 gi|256616559|gb|EEU21747.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii 27-2-CHN]
 gi|260548642|gb|EEX24617.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii 115-3-CHN]
 gi|281303947|gb|EFA96081.1| pseudouridine synthase YjbO [Lactobacillus jensenii 208-1]
 gi|297149436|gb|EFH29734.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii JV-V16]
          Length = 297

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 62/246 (25%), Positives = 109/246 (44%), Gaps = 30/246 (12%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQ- 142
           N  K S+    I+L  D+ + V NKPA +       +    +   + G+      S+   
Sbjct: 70  NFLKASNKSVKIVLETDNYL-VINKPAAVLSIPSRYEDKDAVVNRVMGYFAKKKSSEQAF 128

Query: 143 -KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIA 199
            KP +  RLD++TSG+++V +   A    +E  +     K Y ++V G    +++K  I 
Sbjct: 129 LKPHIVTRLDRDTSGLVLVGKNAVAHSKFSE-LKKDVFVKEYHAIVHGNFNSEHQKGLIT 187

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRV 257
             + K       YV            +++ ++V+   AQK     ++++  TGRTHQ+RV
Sbjct: 188 APIGKIDDSVKRYV------TPNGQKSVTQYEVL---AQKDDASLVKLRLFTGRTHQIRV 238

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           H  H+G P+ GD  Y +    NFT     +  L+  ++  P P    ++ +    P  M 
Sbjct: 239 HMAHIGHPLFGDKLYGS--VDNFT-----RQALNCSHLSFPDPFTDEKVTVEIDDPEDMA 291

Query: 317 KTWDSL 322
             W +L
Sbjct: 292 HLWQNL 297


>gi|229515060|ref|ZP_04404520.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TMA 21]
 gi|229347765|gb|EEO12724.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TMA 21]
          Length = 235

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 75/147 (51%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR  AAA  L++ F  R+++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  +      N AI+ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVNSQE------NPAITQFFSAAAATGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADESDRGYLHA 178


>gi|110004533|emb|CAK98870.1| hypothetical rna pseudouridylate synthase c protein [Spiroplasma
           citri]
          Length = 312

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 70/285 (24%), Positives = 120/285 (42%), Gaps = 25/285 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RI 59
           M   T V   V  ND  N  +  + K  +       + K+ R+ +++V+ K +K  N ++
Sbjct: 1   MEPKTVVTLTVKANDV-NQTIFNFIKKMFQTTPLSVIYKLFRNKKIKVNNKVMKERNYKL 59

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q G  +    +I   N ++ E+    +  N+    + L   ++YED  I V +KP G  V
Sbjct: 60  QLGDQI----IIFDKNLVVTERNQAVTYNNV----ETLPLQVVYEDDNILVVDKPHG--V 109

Query: 120 QGGSGIAYHIDGFLKSWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           +  S     +D  ++ ++         D +       HRLD+ T G+++ A+ +     L
Sbjct: 110 EMYSKFHTSLDAMVQHYLIQKHEYHPEDEQSFVISHVHRLDKLTRGLVLYAKNKITLDLL 169

Query: 171 TESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
                 +  I+K Y +   GI K     +  +L K        +   K  +  A    +H
Sbjct: 170 LAKINQKESIEKKYLAKCEGIIKETDFTLTGYLYKNE--DKQKMVFTKTVQPHAKVVKTH 227

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           F+V         WLE+   TGR HQ+R    ++  PIV D KY A
Sbjct: 228 FRVQHQLTNA-TWLEVTLITGRKHQIRASLSYLHHPIVNDIKYGA 271


>gi|254285389|ref|ZP_04960354.1| pseudouridine synthase Rlu family protein [Vibrio cholerae
           AM-19226]
 gi|150424661|gb|EDN16597.1| pseudouridine synthase Rlu family protein [Vibrio cholerae
           AM-19226]
          Length = 235

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 75/147 (51%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR  AAA  L++ F  R+++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  +      N AI+ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVNSQE------NPAITQFFSATAAPGERMFL-CKPHTGKTHQIRVALKSIGSS 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADESDRGYLHA 178


>gi|260945269|ref|XP_002616932.1| hypothetical protein CLUG_02376 [Clavispora lusitaniae ATCC 42720]
 gi|238848786|gb|EEQ38250.1| hypothetical protein CLUG_02376 [Clavispora lusitaniae ATCC 42720]
          Length = 590

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 102/230 (44%), Gaps = 9/230 (3%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSK 107
           DK+   +   I +GQV+ +      L+ I++   ++    +  + +   + I +++ED+ 
Sbjct: 124 DKEPEFYRRAIAAGQVL-LNKTPTTLDSIVRNGDLISHRCHRHEPAVSSRPIEIVFEDAD 182

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
               NKP+GI V       Y  +   K +    G+     +RLD+ TSG++ + +    A
Sbjct: 183 KIAINKPSGIPVHPTG--RYRYNTITKIFQHEFGKTVHPCNRLDRLTSGLMFLGKNARGA 240

Query: 168 QHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           +   +  R R ++K Y + V G  P    E   +  L    +   +   V  +EKG    
Sbjct: 241 EFFVKQIRERTVRKEYIARVKGKFPLG--ELTVDEPLHT--VSPKHALNVVDHEKGKEAK 296

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               ++          ++ +P TGRTHQ+RVH  ++G PI  D  Y + +
Sbjct: 297 TLFSRISYDPESDTSVVKCRPLTGRTHQIRVHLQYIGHPIANDPIYSSEY 346


>gi|229529302|ref|ZP_04418692.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           12129(1)]
 gi|229333076|gb|EEN98562.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           12129(1)]
          Length = 235

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 75/147 (51%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR  AAA  L++ F  R+++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  +      N AI+ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVNSQE------NPAITQFFSATAAPGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADKSDRGYLHA 178


>gi|229523755|ref|ZP_04413160.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae bv.
           albensis VL426]
 gi|229337336|gb|EEO02353.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae bv.
           albensis VL426]
          Length = 235

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 75/147 (51%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR  AAA  L++ F  R+++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  +      N AI+ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVNSQE------NPAITQFFSATAAPGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADESDRGYLHA 178


>gi|258650803|ref|YP_003199959.1| pseudouridine synthase [Nakamurella multipartita DSM 44233]
 gi|258554028|gb|ACV76970.1| pseudouridine synthase [Nakamurella multipartita DSM 44233]
          Length = 299

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 58/216 (26%), Positives = 95/216 (43%), Gaps = 34/216 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ DS + V +KP  ++    G  I       L+  +D     P   HRLD+ T+G+LV
Sbjct: 89  ILHRDSDLLVVDKPHFLATMPRGLHIVESALVRLRRELDLPELSP--IHRLDRVTAGVLV 146

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWG------IPKNKKECIANWLLKKSHIGG 210
            +     R A Q L   F  R++ K Y+  V G      +P   +  I  +    +    
Sbjct: 147 FSLRPANRGAYQTL---FAQRKVTK-YYEAVAGHRADLTLPTTVESRIVKFRGTPT---- 198

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                  Q   G   A +  + +    ++  +  + PHTG+ HQLR+H   +G PIVGD+
Sbjct: 199 ------AQQVPGEPNARTVVERLAARGERALY-GLHPHTGKVHQLRLHMTSLGVPIVGDN 251

Query: 271 KYCA---NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            Y       + +++ P+Q    L AR ++ P P  G
Sbjct: 252 FYPTLLDTPRDDYSDPLQ----LLARSIEFPDPFTG 283


>gi|73663086|ref|YP_301867.1| RNA pseudouridylate synthase [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72495601|dbj|BAE18922.1| putative RNA pseudouridylate synthase [Staphylococcus saprophyticus
           subsp. saprophyticus ATCC 15305]
          Length = 284

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 49/175 (28%), Positives = 85/175 (48%), Gaps = 14/175 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           +L+ED  + V +KP   +       + Y I   +  +++ K  G  P +  RLD+ TSGI
Sbjct: 77  ILFEDDYLIVVSKPPYQNCAPSRDHLHYSIVEQVLGYLNEKQPGINPHIVTRLDRNTSGI 136

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+      HL  +     I K Y  + +G  K +KE + +  + +         + +
Sbjct: 137 VILAK-HGFIHHLMSNLN---IDKKYLCICYG--KTEKEGVIDAPIARH----PESIIQR 186

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + +     A + FK ++ + + F   E+   TGRTHQ+RVH  H+G  IVGD  Y
Sbjct: 187 RVDAAGKTAQTRFKRVE-YKEGFSMCEVTLLTGRTHQIRVHFQHIGHSIVGDALY 240


>gi|225682103|gb|EEH20387.1| DRAP deaminase [Paracoccidioides brasiliensis Pb03]
          Length = 525

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 67/284 (23%), Positives = 109/284 (38%), Gaps = 72/284 (25%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +K +  G V ++ K V  + +IQ+G V+                     S  L +H   +
Sbjct: 81  KKAIEDGAVCINGKAVTIDTKIQNGDVI---------------------SHTLHRHEPPV 119

Query: 98  KSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQ 152
            S    +++ED+ + V +KPAG+ V       Y+ +  L+     +G    P   +RLD+
Sbjct: 120 TSQPIGVIHEDNDMIVIDKPAGVPVHPAG--RYNYNSVLEIMKAERGHGWVPYPCNRLDR 177

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-- 210
            TSG++ V +    A+ + E  R R ++K Y + V G   +        +LK S I G  
Sbjct: 178 LTSGVMFVGKHPKGAEQIGEKLRSRTVRKEYVARVKGKFPDGVVLCDQPMLKISPILGLN 237

Query: 211 ----------------DYVHVVKQNEKGA-----------------NYAISHFKVIDCFA 237
                            Y    +  EKG+                 N + S        A
Sbjct: 238 RARASGKEARTKFRRIAYYPPYEPAEKGSVSSTEPATPPATLPDEMNISNSSTATPTGVA 297

Query: 238 ---------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                    + +  +   P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 298 TPLPKSSDEEGYSIVHCLPLTGRTHQIRVHLQYLGYPITNDPIY 341


>gi|261326897|emb|CBH09870.1| hypothetical protein, conserved [Trypanosoma brucei gambiense
           DAL972]
          Length = 828

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 70/281 (24%), Positives = 112/281 (39%), Gaps = 63/281 (22%)

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL-----LYEDSKIYVFNKPAGIS 118
            VR+PP          E + + ++  + +  D LKS L     +YED  + V NKP  ++
Sbjct: 572 AVRLPP----------EHECVRAAETM-RAGDPLKSPLPIFPVVYEDDDLLVINKPPHVA 620

Query: 119 V-------------QGGSGIAYHID----GFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
                         +    ++  +     G +   V  +GQ     HRLD ETSG L++A
Sbjct: 621 TSRHALSCSQLCDDKATDIVSLQLTCKKRGDVMRRVFRQGQ----VHRLDTETSGCLIMA 676

Query: 162 RTRAAAQHLT----ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++  AA  L      S    +  KIY +L   +  N      N +L+             
Sbjct: 677 KSDVAASSLRHQMGTSAAYSQSSKIYLALCAVVESNLTNIPLNGVLRDP----------A 726

Query: 218 QNEKGANYAISHFKVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    Y I HF       ++F    +E +   G+ HQ+R H   +G PI+ D ++   
Sbjct: 727 DAKITTKYRIVHFY------KRFRVALVEARIQQGKKHQIRRHLAAVGLPILQDVEHGG- 779

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
                 SP+  ++ LHA  + + HP     L   APLP  M
Sbjct: 780 --AACCSPLLQRVALHASSVTVVHPRTAEVLTCVAPLPEDM 818


>gi|219683568|ref|YP_002469951.1| pseudouridine synthase [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|219621218|gb|ACL29375.1| pseudouridine synthase [Bifidobacterium animalis subsp. lactis
           AD011]
          Length = 230

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 96/224 (42%), Gaps = 28/224 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           ++YE+ +I V +KP  ++     G+ Y     ++  +  + ++P +   HRLD+ T+GI+
Sbjct: 1   MVYENERIIVVDKPHFLATTP-RGMWYRETALMR--LRERYREPNIIPAHRLDRPTAGIV 57

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV----WGIPKNKKECIAN----W-LLKKSHIG 209
           V  R  AA       F+  R +K Y  L        P+       +    W L+++S I 
Sbjct: 58  VFVRDPAARGAYQMLFQEHRTRKCYECLAPIRPLATPRTGTVVHGSPPRIWPLVRRSRIR 117

Query: 210 GDYVHVVKQNEKG---ANYAIS----HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                +  Q   G   A  AI     H ++            + P TG+THQLRVH   +
Sbjct: 118 KTRGVLCAQEIPGQVNAETAIELEALHARMSARMGMSIGVYRLLPRTGKTHQLRVHMNSL 177

Query: 263 GCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           G PIVGD  Y         +F+ P+Q    L AR +    P  G
Sbjct: 178 GLPIVGDDFYPRIEERAYDDFSQPLQ----LVARSLAFTDPFTG 217


>gi|262171321|ref|ZP_06038999.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus MB-451]
 gi|261892397|gb|EEY38383.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus MB-451]
          Length = 233

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 51/147 (34%), Positives = 75/147 (51%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR  AAA  L++ F  R ++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNAAAASELSQGFAKRTVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                 +  V  QN    N A++ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RR--SSWKLVNSQN----NPAVTQFFSATAVPGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADESDRGYLHA 178


>gi|254820676|ref|ZP_05225677.1| RNA pseudouridine synthase family protein [Mycobacterium
           intracellulare ATCC 13950]
          Length = 271

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 59/245 (24%), Positives = 98/245 (40%), Gaps = 26/245 (10%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-------LLYEDSKIYVFNKPAGISVQG- 121
           V+ A   +I  + +L +  ++  + +    +       +LY D  I V +KP  ++    
Sbjct: 23  VVGADGAVIDAKTVLPAGASVYLYRELPDEVPVPFEIPVLYRDDDIVVVDKPHFVATMPR 82

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G  +A      L+  +D     P   HRLD+ T+G+L+    R         F    + K
Sbjct: 83  GRHVAQSALVRLRRELDLPELSP--AHRLDRLTAGVLMFTARREVRGAFQTLFSRGLVDK 140

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +     P  +   +      KS I      +    E GA  A +  +++        
Sbjct: 141 TYLARAAVDPALRLPRVV-----KSRIVKRRGQLQAVCEPGAANAETLVELV----SPDG 191

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQNKLYLHARYMDLP 298
              + P TGRTHQLRVH   +G PI GD  Y         +F++P++    L AR ++  
Sbjct: 192 LYRLTPRTGRTHQLRVHMASLGIPIEGDPLYPNVIDVAPDDFSTPLR----LLARRIEFT 247

Query: 299 HPEGG 303
            P  G
Sbjct: 248 DPRSG 252


>gi|23465740|ref|NP_696343.1| ribosomal pseudouridine synthase [Bifidobacterium longum NCC2705]
 gi|23326424|gb|AAN24979.1| possible ribosomal pseudouridine synthase [Bifidobacterium longum
           NCC2705]
          Length = 233

 Score = 57.4 bits (137), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 49/170 (28%), Positives = 69/170 (40%), Gaps = 31/170 (18%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKEC 197
            HRLD+ T+G+LV  R  A        F+ R+  KIY  L          +G     +  
Sbjct: 37  AHRLDRMTAGVLVFVRDSACRGAYQMLFQNRQAVKIYECLAPCRPISGPRFGTIMQVEPP 96

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQ------------------ 238
               LL++SHI  ++  +    E G   A +  +  D CF                    
Sbjct: 97  RPFPLLRRSHITKEHGTMAAFEEPGLANAETLIERGDLCFPPAGGRWREAPEGGPHPGNH 156

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQ 285
             C   + P TG+THQLRVH   +G PIVGD  Y         +F+ P+Q
Sbjct: 157 PICRYTLHPRTGKTHQLRVHMNSLGLPIVGDDFYPRIQTRPYDDFSQPLQ 206


>gi|170578286|ref|XP_001894351.1| Hypothetical 50.0 kDa protein K07E8.7 in chromosome IV, putative
           [Brugia malayi]
 gi|158599118|gb|EDP36813.1| Hypothetical 50.0 kDa protein K07E8.7 in chromosome IV, putative
           [Brugia malayi]
          Length = 430

 Score = 57.4 bits (137), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 49/170 (28%), Positives = 77/170 (45%), Gaps = 9/170 (5%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           D+ + V +KP  + V      + H + G L+     +G   R+ HRLD+ TSG+L+ AR 
Sbjct: 130 DNDMLVVDKPPSMPVHPCGRYSVHTVLGMLREQRGLRGL--RVVHRLDRTTSGVLLFARN 187

Query: 164 RAAAQHLTESFRMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                 L +  R+  I  K Y   V G+    KE + +  +    +    +  ++ + K 
Sbjct: 188 AETDTKLKKMLRVGEIWHKEYICKVEGVFPGDKEIVCDRPIGPLVVSMG-IQCIRDDGKS 246

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           A             +   C LE    TGRTHQ+RVH  ++G PIV D+ Y
Sbjct: 247 ARSRFWRLWTDGQTSIVRCMLE----TGRTHQIRVHLQYLGYPIVDDYIY 292


>gi|153828845|ref|ZP_01981512.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 623-39]
 gi|148875641|gb|EDL73776.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 623-39]
          Length = 235

 Score = 57.4 bits (137), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 75/147 (51%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR  AAA  L++ F  R+++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+  +      N AI+ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVNSQE------NPAITQFFSATAAPGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y        T+   ++ YLHA
Sbjct: 159 IVGDPIYN-------TADKSDRGYLHA 178


>gi|302533507|ref|ZP_07285849.1| ribosomal pseudouridine synthase [Streptomyces sp. C]
 gi|302442402|gb|EFL14218.1| ribosomal pseudouridine synthase [Streptomyces sp. C]
          Length = 322

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 55/207 (26%), Positives = 86/207 (41%), Gaps = 14/207 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ D  + V +KP  ++    G+ +       L+  +D     P   HRLD+ T+G+++
Sbjct: 100 VVHRDRHLLVVDKPHFLATTPRGTHVTETALARLRRELDLPALSP--AHRLDRMTAGLVM 157

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +     R A Q L   F+ RR+ K Y +L    P      +    L +SHI      + 
Sbjct: 158 FSIRPEDRGAYQLL---FQQRRVHKEYEALAAHAP-----SLELPRLVRSHIEKTRGVMA 209

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                GA         +           + PHTGRTHQLRVH   +G PI+GD  Y    
Sbjct: 210 AVEVPGAEPNAESLVELTGVRDGLGRYRLTPHTGRTHQLRVHMNSLGLPILGDPVYPVVA 269

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    +  +  L L AR +    P  G
Sbjct: 270 EAADPADYRRPLQLLARTLAFTDPVTG 296


>gi|303314793|ref|XP_003067405.1| ribosomal large subunit pseudouridine synthase D, putative
           [Coccidioides posadasii C735 delta SOWgp]
 gi|240107073|gb|EER25260.1| ribosomal large subunit pseudouridine synthase D, putative
           [Coccidioides posadasii C735 delta SOWgp]
          Length = 531

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 63/272 (23%), Positives = 106/272 (38%), Gaps = 61/272 (22%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           + SG V ++ K    ++++++G VV                     S  L +H   + S+
Sbjct: 81  IESGHVTINGKPGGVDSKVKNGDVV---------------------SHTLHRHEPPVTSL 119

Query: 101 ---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ED ++ V +KPAG+ V       Y+    +       G  P   +RLD+ TSG+
Sbjct: 120 PIGVIHEDDEMIVIDKPAGVPVHPAGRYNYNSIIEIMRAERGHGFNPLPCNRLDRLTSGV 179

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGGDYVHVV 216
           + + +   AA+ ++   R R +QK Y + V G   +        +LK SH +G + V   
Sbjct: 180 MFIGKDPKAAERISHGLRARTMQKEYIARVKGKFPDGIILCDQPMLKISHQLGLNRVRAS 239

Query: 217 KQNEKG-----ANYAISHFK-------------------------------VIDCFAQKF 240
            +  K      A Y  +  K                               +     + +
Sbjct: 240 GKEAKSKFRRLAYYPATAVKKASSSEDDPATPPATLADDVPLDFGNNGKATISPPEDEGY 299

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +   P TGRTHQLRVH   +G PI  D  Y
Sbjct: 300 SIVHCLPLTGRTHQLRVHLQFLGHPITNDPIY 331


>gi|119175237|ref|XP_001239884.1| hypothetical protein CIMG_09505 [Coccidioides immitis RS]
 gi|320037744|gb|EFW19681.1| DRAP deaminase [Coccidioides posadasii str. Silveira]
          Length = 531

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 63/272 (23%), Positives = 106/272 (38%), Gaps = 61/272 (22%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           + SG V ++ K    ++++++G VV                     S  L +H   + S+
Sbjct: 81  IESGHVTINGKPGGVDSKVKNGDVV---------------------SHTLHRHEPPVTSL 119

Query: 101 ---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ED ++ V +KPAG+ V       Y+    +       G  P   +RLD+ TSG+
Sbjct: 120 PIGVIHEDDEMIVIDKPAGVPVHPAGRYNYNSIIEIMRAERGHGFNPLPCNRLDRLTSGV 179

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGGDYVHVV 216
           + + +   AA+ ++   R R +QK Y + V G   +        +LK SH +G + V   
Sbjct: 180 MFIGKDPKAAERISHGLRARTMQKEYIARVKGKFPDGIILCDQPMLKISHQLGLNRVRAS 239

Query: 217 KQNEKG-----ANYAISHFK-------------------------------VIDCFAQKF 240
            +  K      A Y  +  K                               +     + +
Sbjct: 240 GKEAKSKFRRLAYYPATAVKKASSSEDDPATPPATLADDVPLDFGNNGKATISPPEDEGY 299

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +   P TGRTHQLRVH   +G PI  D  Y
Sbjct: 300 SIVHCLPLTGRTHQLRVHLQFLGHPITNDPIY 331


>gi|322705188|gb|EFY96776.1| DRAP deaminase [Metarhizium anisopliae ARSEF 23]
          Length = 513

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 52/211 (24%), Positives = 89/211 (42%), Gaps = 40/211 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           +++ED  + V NKP+G+ V       Y  +  L+     +GQ+  P   +RLD+ TSGI+
Sbjct: 159 IIHEDDDMIVINKPSGVPVHPAG--RYKFNSVLEIMKAERGQEFMPYPCNRLDRLTSGIM 216

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
            VA++  AA+ L    + R ++K Y + V G  P+ +  C    L     +G + V    
Sbjct: 217 FVAKSVKAAEALGNQIKSRTVRKEYMARVVGEFPEGEIVCDQPILSISPKLGLNRVRAEG 276

Query: 218 QNEKGANYAISHFK-------------VIDCFAQKFCWLEMQ------------------ 246
           +  +     ++++              V +   ++   L  +                  
Sbjct: 277 KAARTVFKRLAYYPPRGDAEANGQQGGVPEPTDKELSRLPAEEGDESNGKPWINKRGYSI 336

Query: 247 ----PHTGRTHQLRVHALHMGCPIVGDHKYC 273
               P TGRTHQ+RVH  ++G PI  D  Y 
Sbjct: 337 VRCLPVTGRTHQIRVHLQYLGHPIQNDPIYA 367


>gi|116328674|ref|YP_798394.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116121418|gb|ABJ79461.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
          Length = 377

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 84/382 (21%), Positives = 143/382 (37%), Gaps = 101/382 (26%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  D+  +RLD +    + + +    QK +  G++ V  K+VK    ++ G  V   P
Sbjct: 14  IFISKDDVGIRLDHFLSKKFTYHSRNVWQKEINEGRISVLGKKVKSGILLREGDTVVYQP 73

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +      + K+ KIL                  YED      +KP  + V        + 
Sbjct: 74  IERKEPPVRKDYKIL------------------YEDEFFVAVDKPGDLPVHPA---GKYR 112

Query: 130 DGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            G L + +   G+   L   HRLD+ETSG+++ A+   AA  L+  F   +IQK Y + V
Sbjct: 113 KGNLLTLLKESGKFENLFTVHRLDRETSGVVLFAKDSKAASLLSGLFSSGKIQKYYITKV 172

Query: 188 WG-IPKNK------KECIANWLLKKSHIGGDYVHVVKQNEK---------GANYAISHFK 231
           +G  P+ K      K  +++ + KK        + +K+N+K            + ++ F+
Sbjct: 173 YGDFPRRKIAYGVLKPDVSSIIRKKRKFFLLKSNFLKRNKKYFLENSFSPEEEFCLTAFR 232

Query: 232 VIDCFAQKFCWLEMQ--------------------------------------------- 246
            I+ +  K  + E++                                             
Sbjct: 233 KIESYFIKTQFQEIESDVGELKVRSRKKKLNFESLQTQNEKNEEPKVRSIYPKHEFYSFV 292

Query: 247 ---PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK------------LYLH 291
              P TGR HQ+R     +G PI GD  Y  + +  F   I+ K              LH
Sbjct: 293 LCKPITGRMHQIRAVLYGLGFPIWGDKLYGKD-EEVFLEFIEGKNPDLTERLGMERQALH 351

Query: 292 ARYMDLPHPEGGR-LQITAPLP 312
           A  +   HP   R ++I A +P
Sbjct: 352 AYAIRFNHPITNRKMKIVASVP 373


>gi|254561887|ref|YP_003068982.1| hypothetical protein METDI3488 [Methylobacterium extorquens DM4]
 gi|254269165|emb|CAX25131.1| hypothetical protein METDI3488 [Methylobacterium extorquens DM4]
          Length = 135

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 49/95 (51%), Gaps = 9/95 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           LLY D+ + V +KPAG+ V    +GG  +  H+D           ++P   HRLD++TSG
Sbjct: 14  LLYRDALMLVIDKPAGLPVHPGPKGGPTLTDHLDALRFGLP----RRPEAAHRLDRDTSG 69

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            LV+ R   A   L   F   ++ K YW+L W  P
Sbjct: 70  CLVLGRHAKALARLNRLFADGKVDKTYWAL-WRSP 103


>gi|269798687|ref|YP_003312587.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269095316|gb|ACZ25307.1| pseudouridine synthase [Veillonella parvula DSM 2008]
          Length = 372

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 54/240 (22%), Positives = 106/240 (44%), Gaps = 54/240 (22%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LYED  +++ +KP+G++V         +G+A++   F +  +    +K R  +RLD++T
Sbjct: 131 VLYEDEDLFIVDKPSGVTVNSKDRLSLANGVAHY---FKEHGI---KRKVRFLNRLDRDT 184

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G +V+A++  A     +       +K Y + V GI +  ++ +  + +++S  G  Y  
Sbjct: 185 TGCIVIAKSGLAQSLYQQQMDDNTFEKWYMATVEGIVEADEDTLV-FPMERSADGIHYEV 243

Query: 215 VVKQNEKGANYAI--------------------------SHFKVIDCF------------ 236
             K  E   ++++                             +++D              
Sbjct: 244 NAKGKETRTDFSVLCRHSSQPVDNSVNKSENSVDIGLKNVDIELVDVDKNNLNVDKTVYK 303

Query: 237 AQKFCWLE--MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHAR 293
           + K  + E  ++ +TG+THQ+RV   H+G P+VGD  Y A   G  F    Q  ++ H R
Sbjct: 304 SNKCGYTEVLVRLYTGKTHQIRVAFSHIGHPLVGDTLYGAQPTGQPFQLRAQKVVFTHIR 363


>gi|269796147|ref|YP_003315602.1| 23S RNA-specific pseudouridylate synthase [Sanguibacter keddieii
           DSM 10542]
 gi|269098332|gb|ACZ22768.1| 23S RNA-specific pseudouridylate synthase [Sanguibacter keddieii
           DSM 10542]
          Length = 303

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 45/163 (27%), Positives = 71/163 (43%), Gaps = 12/163 (7%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ T+G+LV+   R       + F  R I K Y ++    P+          + K 
Sbjct: 128 AHRLDRITAGVLVLTTRREVRGAYQQLFASRTIHKTYEAVARVDPRLDLPRTVRSRIVKE 187

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMG 263
           H  G  V      E  A   +S  +V        +      ++PHTG+THQLR+H   +G
Sbjct: 188 H--GTLVAQEVPGEPNAESRVSLAEVAPGAGDGGEALGRYVLEPHTGKTHQLRLHMASLG 245

Query: 264 CPIVGDHKYCANF---KGNFTSPIQNKLYLHARYMDLPHPEGG 303
            PI+ D+ Y   +     ++++P+Q    L AR +    P  G
Sbjct: 246 LPILNDNFYPRFYDVAPDDYSAPLQ----LLARSISFTDPLSG 284


>gi|50290395|ref|XP_447629.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49526939|emb|CAG60566.1| unnamed protein product [Candida glabrata]
          Length = 411

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 69/266 (25%), Positives = 108/266 (40%), Gaps = 50/266 (18%)

Query: 39  KILRSGQ----VRVDKKRVKFNNRIQSGQVVRIPPVI----NALNHIIKEQKILDSSVNL 90
           K++R GQ    + V    +K N++++S      PPV+    N  N  I  +KI    +  
Sbjct: 61  KLIRDGQYLDNLSVLDTPIKNNDKLESTVHKHEPPVLQWCSNEAN--IPGKKIAGIDI-- 116

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
                      +YED  + V NKP GI +   +G+ Y     L   +   G      +RL
Sbjct: 117 -----------VYEDENLLVINKPCGIPIHP-TGLYY--GNTLTEILKVNGVHALPAYRL 162

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--------------------I 190
           D+ TSG+L++++    A  + +  R   +QK Y + V G                    +
Sbjct: 163 DKVTSGLLILSKDTGTASMVQKKIRSHEMQKWYLARVEGAFPHVNEVPHIETLEIQRLDL 222

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY---AISHFKVIDCFAQK-FCWLEMQ 246
           P  ++    N +L         V   KQ   G +    A + F  I  F  K    +  +
Sbjct: 223 PIEEQIIQDNSILTIEDSDVYTVEPKKQYPSGLSVPRSAKTIFYPIKYFPHKNESIVACR 282

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
           P TGRTHQ+R+H   +  PIV D  Y
Sbjct: 283 PITGRTHQIRIHLARLNHPIVNDTIY 308


>gi|225573997|ref|ZP_03782642.1| hypothetical protein RUMHYD_02093 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038727|gb|EEG48973.1| hypothetical protein RUMHYD_02093 [Blautia hydrogenotrophica DSM
           10507]
          Length = 310

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 96/230 (41%), Gaps = 47/230 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKGQKPRLTHRLDQETS 155
           +LYED  + V  K +G  V   SG+ Y  D      V       +    R+  RLD++TS
Sbjct: 83  VLYEDESLVVVEKRSG-QVCHPSGMHYR-DSLANQLVWHFQNRQENTSVRIIGRLDKDTS 140

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG------------IPKNKKECIANWLL 203
           GI+V A+ + AAQ L+         K Y +LV G            I + +   +   + 
Sbjct: 141 GIVVAAKHKIAAQKLSWQRDRGIFGKEYLALVHGEFSDFDGFLREPIARVQGHPLKMKVC 200

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            +        HV+ QN     YA+     + C          + +TGRTHQ+RVH   +G
Sbjct: 201 AQGKPAKTQYHVIAQNR---GYAL-----VSC----------RLYTGRTHQIRVHMQSIG 242

Query: 264 CPIVGDHKYCANFKGNFTSPIQN----------KLYLHARYMDLPHPEGG 303
            P+V D  Y    + +F   ++N          KL LHA  + + HP  G
Sbjct: 243 HPLVNDVIYGLGEQDDFAKTLENEQKIAGDRHKKLGLHAAKVWMRHPLSG 292


>gi|213965321|ref|ZP_03393517.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           amycolatum SK46]
 gi|213951937|gb|EEB63323.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           amycolatum SK46]
          Length = 342

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 47/189 (24%), Positives = 78/189 (41%), Gaps = 20/189 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           ++++D  + V +KP+ ++         HI       +  +   P L   HRLD+ TSG+L
Sbjct: 100 IVFQDDNLVVVDKPSFLATMPR---GRHITETAVVRLRRELGNPELVPAHRLDRLTSGLL 156

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLL----KKSHIGGDY 212
           +    R         F    + K Y +L    P      E +    L    ++  I G  
Sbjct: 157 IFTARREVRGAYQGLFASGEVTKRYHALTSPTPIAGGASEALPETPLELRTRQHKIAGQM 216

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ---------KFCWLEMQPHTGRTHQLRVHALHMG 263
                + E  A+  I H  ++D  +          +    +++P TGRTHQLR+H   +G
Sbjct: 217 QAYTLEGEPNAHTIIEHISLVDVPSDADGLAADSGRVALWQLKPITGRTHQLRLHLSELG 276

Query: 264 CPIVGDHKY 272
            PI+GD  Y
Sbjct: 277 FPILGDQYY 285


>gi|71009880|ref|XP_758324.1| hypothetical protein UM02177.1 [Ustilago maydis 521]
 gi|46098066|gb|EAK83299.1| hypothetical protein UM02177.1 [Ustilago maydis 521]
          Length = 1096

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 52/171 (30%), Positives = 78/171 (45%), Gaps = 9/171 (5%)

Query: 104 EDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           +D  I V  KP  I V   G  + + + G L+S  +        T+RLD+ TSGI+V + 
Sbjct: 64  DDEGILVIVKPGSIPVHAAGRYLRHTLVGLLQS--EHGVDMVYTTNRLDRLTSGIMVCST 121

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
            +  A  L   F   ++ K Y   V G  P+ +  C    L      G + VH   ++ +
Sbjct: 122 KKETASRLGAQFAAGQVNKAYVCRVRGKFPQGEVVCKQPILTIDRQSGVNIVHPKGKHCE 181

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                +S +   D  +  FC    +P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 182 TIFVRLS-YDASDDSSVVFC----RPITGRTHQIRVHVQYLGHPICNDPIY 227


>gi|262404083|ref|ZP_06080638.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. RC586]
 gi|262349115|gb|EEY98253.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. RC586]
          Length = 235

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 47/131 (35%), Positives = 69/131 (52%), Gaps = 15/131 (11%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR  AAA  L++ F MR+++K Y ++    PK K+  I       
Sbjct: 46  LVHRLDKMTSGILLLARNAAAASELSQGFAMRKVEKFYLAIGSKKPKKKQGLIC------ 99

Query: 206 SHIGGDYVHVVKQNEK----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
               GD     + + K     +N A++ F        +  +L  +PHTG+THQ+RV    
Sbjct: 100 ----GDMERSRRSSWKLLNSQSNPAVTQFFSATAALGERLFL-CKPHTGKTHQIRVALKS 154

Query: 262 MGCPIVGDHKY 272
           +G  IVGD  Y
Sbjct: 155 IGSAIVGDPIY 165


>gi|225022032|ref|ZP_03711224.1| hypothetical protein CORMATOL_02064 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945153|gb|EEG26362.1| hypothetical protein CORMATOL_02064 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 300

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 54/220 (24%), Positives = 89/220 (40%), Gaps = 25/220 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ED ++ V +KP  ++    G  I       L+    +    P   HRLD+ TSG+LV 
Sbjct: 77  IFEDERLLVVDKPPFLATMPRGKHITQSATVQLRKLTGNGELSP--AHRLDRLTSGVLVF 134

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIANWLLKKSHIGGDYVHVVKQN 219
            +TR       + F  R  +K Y ++    P N   +    W  + +   G+        
Sbjct: 135 TKTREVRGAYQQLFARREAEKTYEAIARYDPTNPMAQPGMVWRDRMAKNPGELQGYFIPG 194

Query: 220 EKGANYAISHFKVIDC-------------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           E  A   +   + +                 Q+  ++ +QP TGRTHQLR+H    G PI
Sbjct: 195 EPNAITTVIAVEPVPPERMRALRATHESELPQQARYV-LQPATGRTHQLRLHMWKAGVPI 253

Query: 267 VGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +GD  Y       + +F  P    ++L A+ +    P  G
Sbjct: 254 LGDPAYPVVLPEAEEDFAVP----MHLRAKTLRFTDPLSG 289


>gi|156538671|ref|XP_001607742.1| PREDICTED: similar to conserved hypothetical protein [Nasonia
           vitripennis]
          Length = 272

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 71/180 (39%), Gaps = 65/180 (36%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----------IP---- 191
             HRLD  TSG++ +A  + +AQ  + +F  R ++K Y +LV G          IP    
Sbjct: 72  FVHRLDYATSGVMCLALNKQSAQAASSAFEERTVRKYYLALVHGHIDKYSMVIDIPIGHD 131

Query: 192 -------------------KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
                              K +K C A  +L+K +I    V                 KV
Sbjct: 132 VRELNGNRKMCTKDDDFCEKARKSCTALLVLEKGYIDDRPVT----------------KV 175

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           +           + P TGR HQLRVH  H+G  IVGD+ Y        T    ++ +LHA
Sbjct: 176 L-----------LYPKTGRRHQLRVHCAHIGHIIVGDYTYSGK-----TDTKPHRTFLHA 219


>gi|332008660|gb|AED96043.1| RNA pseudourine synthase 7 [Arabidopsis thaliana]
          Length = 410

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 55/204 (26%), Positives = 85/204 (41%), Gaps = 8/204 (3%)

Query: 100 ILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++L+++  +    KPA + V   G      I G L +  D     P   HRLD+  SG+L
Sbjct: 137 VILHQEPDVVTVCKPASVPVHPCGQYRKNTIVGILDAEHDLGTLFP--IHRLDRLVSGLL 194

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSH---IGGDYVH 214
           ++ART A A    +      ++K Y + V G+ P+++    AN     S       D   
Sbjct: 195 IIARTAAKADFFRQQIEGGMVKKRYIAKVIGVFPEDEMIVDANINYNGSEGRSTAEDANS 254

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                +     A + F  ID        +  +P TGRTHQ+RVH  + G PI  D  Y  
Sbjct: 255 SGDDKKVKGKPACTKFTRIDTNGTH-SLVSCEPVTGRTHQIRVHLQYTGHPIANDPLYLN 313

Query: 275 NFKGNFTSPIQNKLYLHARYMDLP 298
               N  + I  ++    R +  P
Sbjct: 314 QHIDNLETYIAKRIDAGERKIVSP 337


>gi|313139743|ref|ZP_07801936.1| pseudouridine synthase [Bifidobacterium bifidum NCIMB 41171]
 gi|313132253|gb|EFR49870.1| pseudouridine synthase [Bifidobacterium bifidum NCIMB 41171]
          Length = 246

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 97/231 (41%), Gaps = 38/231 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED+ I V +KP  ++     G+ Y       L+   D     P   HRLD+ T+GI+
Sbjct: 13  VVYEDAGIIVIDKPHFLATTP-RGMWYRQTALIRLREMFDEPDITP--AHRLDRLTAGIV 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKSHIG 209
           V  R  A        F+ R++ K Y  L          +G  +         L ++SHI 
Sbjct: 70  VFVRDPALRGAYQMMFQGRKVSKTYECLAPCRPTTRPRYGTVERLDPPAVFPLRRRSHIT 129

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL--------------EMQPHTGRTHQL 255
                V++  E+    A++   VID  A  +  +              E+ P TG+THQL
Sbjct: 130 -KLRGVLQAFEE--PQAVNAETVIDLAAGGYPSMGGRLCHGRNGLRAYELHPLTGKTHQL 186

Query: 256 RVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G PI GD  Y         +F++P++    L AR +    P  G
Sbjct: 187 RVHMNSIGLPIHGDDFYPRIVERAYDDFSTPLE----LVARSLRFTDPVSG 233


>gi|300785329|ref|YP_003765620.1| RNA pseudouridylate synthase [Amycolatopsis mediterranei U32]
 gi|299794843|gb|ADJ45218.1| putative RNA pseudouridylate synthase [Amycolatopsis mediterranei
           U32]
          Length = 311

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 59/226 (26%), Positives = 100/226 (44%), Gaps = 20/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ D  + V +KP  + ++  G  I       L+  +D     P   HRLD+ T+G+++
Sbjct: 92  VVHRDEHLLVVDKPHFLATIPRGQHILETALVRLRRELDLPQLSP--AHRLDRVTAGLVM 149

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
              T  +       FR RR+ K Y ++    P +    +   +  +S I  +   +  Q 
Sbjct: 150 FVITPESRGKYQTLFRDRRVHKEYEAIA---PHDPALTLPRTV--RSRIVKERGVLAAQE 204

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANF 276
             G   A ++  +++  A       + P TGRTHQLR+H   +G PI+GD  Y       
Sbjct: 205 VPGEPNAETYVDLLEHRA-GLGRYRLVPATGRTHQLRLHLSGLGVPILGDDFYPQLREKP 263

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
            G+FT P+Q    L A+ +D   P  G   + T+   A  +  WD 
Sbjct: 264 LGDFTKPLQ----LLAKVLDFDDPLTGAHRRFTS---ARRLSAWDD 302


>gi|170724937|ref|YP_001758963.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169810284|gb|ACA84868.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 306

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 53/213 (24%), Positives = 92/213 (43%), Gaps = 13/213 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D +I V  KP  +++   G+ I   +   L+     +   P   HRLD+ T+G+++
Sbjct: 88  VIYQDERIIVAFKPHFLALHPSGNVINECLVNRLRIKTGLETIVP--AHRLDRATAGLVL 145

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-------KNKKECIANWLLKKSHIGGDY 212
           +       Q   + F+  +I+K Y +L    P       + +     NW +K   + G+ 
Sbjct: 146 LCLHPEHRQRYHDLFKFGQIRKEYQALAKLTPELLLKHQRGELSLPLNWTVKNRMVKGEP 205

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              ++      N   S  ++I+   +      + P TGRTHQLRVH   +G PI+ D  Y
Sbjct: 206 TFTMRVAPGEPNTH-SEIQLIEINGE-LGVFNLSPITGRTHQLRVHMQSLGMPILNDRCY 263

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
               +          L L AR +    P  G+L
Sbjct: 264 -PELQPKAPDDYSKPLKLLARRLTFTDPVSGQL 295


>gi|323452498|gb|EGB08372.1| hypothetical protein AURANDRAFT_26183 [Aureococcus anophagefferens]
          Length = 91

 Score = 57.0 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 7/61 (11%)

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           LE++PHTGR HQLR H   +G PI+GD  Y A+ +G       ++L+LHA+ +    P  
Sbjct: 26  LELEPHTGRLHQLRAHCAAIGHPILGDDIYGADAEG-------SRLHLHAKALRFAEPSS 78

Query: 303 G 303
           G
Sbjct: 79  G 79


>gi|198477421|ref|XP_002136622.1| GA24957 [Drosophila pseudoobscura pseudoobscura]
 gi|198142914|gb|EDY71626.1| GA24957 [Drosophila pseudoobscura pseudoobscura]
          Length = 540

 Score = 57.0 bits (136), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 51/187 (27%), Positives = 86/187 (45%), Gaps = 23/187 (12%)

Query: 92  KHSDFLKSI--------------LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +I              +++ +  + V NKPA I V       ++   F+ +  
Sbjct: 358 KHNDLLANIVHRHEVPVTCQPIKIVHMNEDLVVVNKPASIPVHPCGRYRHNTVVFILAK- 416

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V GI P    E
Sbjct: 417 EFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGIFPDEIVE 476

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K +++G +   +  K+      K   +  +P TGR HQ+R
Sbjct: 477 CKEPIEVVSYKIG-----VCKVSQRGKDCTTTFQKISQ--NGKTSVVLCKPLTGRMHQIR 529

Query: 257 VHALHMG 263
           VH  ++G
Sbjct: 530 VHLQYLG 536


>gi|237808063|ref|YP_002892503.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
 gi|237500324|gb|ACQ92917.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
          Length = 316

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 49/192 (25%), Positives = 95/192 (49%), Gaps = 18/192 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + + +KP  + V   G  ++  +   L + +++   +P   HR+D+ T+G+++
Sbjct: 109 ILYMDEHLLIADKPHFLPVTPAGDYVSQTLLARLVARLNNFELQP--LHRIDRHTAGLVM 166

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +   ++RAA Q L   FR R+I+K Y ++   +P+     IA   ++ + I       +
Sbjct: 167 FSVQKKSRAAYQAL---FRDRKIEKRYEAIAPALPQ-----IAFPHIRATRIERGEPFFL 218

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-- 274
            Q   G   + +   VI+  A  + +  + P TG+ HQLR+H   +G PI  D  Y +  
Sbjct: 219 SQETAGTANSQTIIDVIERRADLWKY-ALNPVTGKKHQLRLHMSALGAPIYNDAFYPSVN 277

Query: 275 -NFKGNFTSPIQ 285
            +   ++  P+Q
Sbjct: 278 DDVADDYQKPLQ 289


>gi|219119925|ref|XP_002180713.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217408186|gb|EEC48121.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 200

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 55/180 (30%), Positives = 79/180 (43%), Gaps = 15/180 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQ---GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           L Y+D  + V NKPAG+S     G     + +   LK  +    +K    HRLD  TSG 
Sbjct: 1   LCYQDRWVCV-NKPAGMSTHRSGGNRSNQFVVSTLLKRQLS---RKVFPVHRLDHRTSGA 56

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A        L ++ R +  +K Y  LV G   N  E     + K   + G       
Sbjct: 57  LLFAFDSEMCASLHDALREQSARKTYVCLVRGFWDNFFESDTATVDKALTVDGTKRSATT 116

Query: 218 QNEKGANYAISHFKVIDCFAQK----FCWLEMQ-PHTGRTHQLRVHALHMGCPIVGDHKY 272
              K A+  I +      + +K     C L +  P TGRTHQ+R HA  MG P++GD ++
Sbjct: 117 VFTKLASTIILNNSA---YGEKNVPISCSLILAVPTTGRTHQIRRHASAMGMPVLGDTQH 173


>gi|113971866|ref|YP_735659.1| pseudouridine synthase [Shewanella sp. MR-4]
 gi|113886550|gb|ABI40602.1| pseudouridine synthase [Shewanella sp. MR-4]
          Length = 308

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 45/150 (30%), Positives = 76/150 (50%), Gaps = 16/150 (10%)

Query: 148 HRLDQETSGILVVARTRAAAQHLT-ESFRMRRIQKIYWSLVWGIPK-------NKKECIA 199
           HRLD+ET+G++++  TR   +H+  + F    I+K Y ++    P+        +     
Sbjct: 134 HRLDRETAGVILMT-TRPETRHIYHQLFVDDAIRKDYQAIAKLTPEIMAQYACGELTLPL 192

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +W +K      +    +K  E  AN   +H ++ +     +F   E+ P TG+THQLRVH
Sbjct: 193 HWTVKNRMQRSEPSFTMKIVEGEAN---THSEISLVAVKGEFGLFELSPITGKTHQLRVH 249

Query: 259 ALHMGCPIVGDHKYCANF-KG--NFTSPIQ 285
            L +G P++ D  Y   + KG  +FT P+Q
Sbjct: 250 MLSLGMPLLNDRFYPTLYPKGLDDFTKPLQ 279


>gi|290976301|ref|XP_002670879.1| predicted protein [Naegleria gruberi]
 gi|284084442|gb|EFC38135.1| predicted protein [Naegleria gruberi]
          Length = 464

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 62/225 (27%), Positives = 100/225 (44%), Gaps = 36/225 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D +  V +KP+ I V   G  +   +   L+S   + G+K  L HRLD+ TSG+L+
Sbjct: 157 VLYHDDEFLVIDKPSSIPVHPAGRFVKNSLHYLLES---ALGRKLFLIHRLDKVTSGVLI 213

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGD---YVH- 214
                A A+   ++ +   ++K Y + V+G  P+ +     + LL       D   ++H 
Sbjct: 214 HTWNAALAKSYQDTMKEGNVRKCYLAQVYGEFPETENMSGEHVLLNGQSFHKDKEGFIHV 273

Query: 215 ----VVKQNE-------------------KGANYAISHFKVI--DCFAQKFCWLEMQPHT 249
               V KQN+                   K  + A +  K I  D  + +   + + P T
Sbjct: 274 KNKMVYKQNDWTFIWRADSSENGSDSTDPKNTDTAYTLVKRIYYDPASSRSIVIAI-PIT 332

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHAR 293
           GRTHQ+R H   MG PI+ D  +    KG N+ +P   K  +  R
Sbjct: 333 GRTHQIREHLRVMGYPIINDVGFELVDKGENWENPWPEKWEIMKR 377


>gi|242044020|ref|XP_002459881.1| hypothetical protein SORBIDRAFT_02g012960 [Sorghum bicolor]
 gi|241923258|gb|EER96402.1| hypothetical protein SORBIDRAFT_02g012960 [Sorghum bicolor]
          Length = 246

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 43/148 (29%), Positives = 64/148 (43%), Gaps = 11/148 (7%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVR----------VDKKRVKFNNRIQSG 62
           E    N    RW +   PH+    +QK+ R  +V+           D    +   R  S 
Sbjct: 84  EGSRSNSTAIRWVRRCCPHLPASLVQKLFRLRKVKKNLVTADTSSTDSIAQQLRLRRVSA 143

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQG 121
           +   +P  I  L   I+E  + +      K+  DFL+S+ +Y+D  I V NKP G+ VQG
Sbjct: 144 KDELVPGDILFLPDNIQESSVTEKKKFGNKNEIDFLRSLEIYKDRAIIVLNKPPGMPVQG 203

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           G GI   ID     + D   + PRL  +
Sbjct: 204 GVGIKNSIDILAPMFEDGSSEAPRLLKK 231


>gi|183602524|ref|ZP_02963889.1| pseudouridine synthase [Bifidobacterium animalis subsp. lactis
           HN019]
 gi|241190598|ref|YP_002967992.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|241196004|ref|YP_002969559.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|183218165|gb|EDT88811.1| pseudouridine synthase [Bifidobacterium animalis subsp. lactis
           HN019]
 gi|240248990|gb|ACS45930.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|240250558|gb|ACS47497.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|295793585|gb|ADG33120.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium animalis
           subsp. lactis V9]
          Length = 242

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 56/206 (27%), Positives = 90/206 (43%), Gaps = 24/206 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           ++YE+ +I V +KP  ++     G+ Y     ++  +  + ++P +   HRLD+ T+GI+
Sbjct: 13  VVYENERIIVVDKPHFLATTP-RGMWYRETALMR--LRERYREPNIIPAHRLDRPTAGIV 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV----WGIPKNKKECIAN----W-LLKKSHIG 209
           V  R  AA       F+  R +K Y  L        P+       +    W L+++S I 
Sbjct: 70  VFVRDPAARGAYQMLFQEHRTRKCYECLAPIRPLATPRTGTVVHGSPPRIWPLVRRSRIR 129

Query: 210 GDYVHVVKQNEKG---ANYAIS----HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                +  Q   G   A  AI     H ++            + P TG+THQLRVH   +
Sbjct: 130 KTRGVLCAQEIPGQVNAETAIELEALHARMSARMGMSIGVYRLLPRTGKTHQLRVHMNSL 189

Query: 263 GCPIVGDHKYC---ANFKGNFTSPIQ 285
           G PIVGD  Y         +F+ P+Q
Sbjct: 190 GLPIVGDDFYPRIEERAYDDFSQPLQ 215


>gi|294794416|ref|ZP_06759552.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           3_1_44]
 gi|294454746|gb|EFG23119.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           3_1_44]
          Length = 300

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 57/256 (22%), Positives = 110/256 (42%), Gaps = 61/256 (23%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +LYED+ + + +KP+G++V         +G+A++   F +  +    +K R  +RLD++T
Sbjct: 59  ILYEDTDLLIVDKPSGVTVNSKDQVSLANGVAHY---FKEHGI---KRKVRFLNRLDRDT 112

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G +V+A++  A     +       +K Y + V GI +  ++ +  + +++S  G  Y  
Sbjct: 113 TGCIVIAKSGLAQSIYQQQMDDNTFEKWYMATVEGIVEADEDSLV-FPMERSVDGIHYEV 171

Query: 215 VVKQNEKGANYAI----SHFKVIDCFAQKFCWLEMQP----------------------- 247
             K  E   ++++    S   V +   +    +++ P                       
Sbjct: 172 NPKGKETRTDFSVLCRHSSETVDNSVNKSKNSVDIAPKNVDINLGDVDKSNQNVDKTVYK 231

Query: 248 -------------HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                        +TG+THQ+RV   H+G P+VGD  Y A        P +    L A+ 
Sbjct: 232 SNKCGYSEVLVRLYTGKTHQIRVAFSHIGHPLVGDTLYGAQ-------PTEQPFQLRAQK 284

Query: 295 MDLPHPEGG-RLQITA 309
           +   H   G R+ +TA
Sbjct: 285 VVFTHMRTGERITVTA 300


>gi|212637300|ref|YP_002313825.1| pseudouridine synthase [Shewanella piezotolerans WP3]
 gi|212558784|gb|ACJ31238.1| Pseudouridine synthase [Shewanella piezotolerans WP3]
          Length = 319

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 41/166 (24%), Positives = 72/166 (43%), Gaps = 14/166 (8%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS-------LVWGIPKNKKECIA 199
           +HRLD+ T+G+++++ +        + F+   I K Y +       L+  I  +      
Sbjct: 147 SHRLDRATAGVMLLSLSVDTRHDYHQLFKTGNITKTYQAIARLSDELMAKIAADALVLPI 206

Query: 200 NWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +W +K   +  D  ++  +   E  ++  I+  +V       F   E+ P TGRTHQLR+
Sbjct: 207 SWTVKNRLVKADPSFMMKISVGESNSHSEITLLQV----KGGFGLFELTPVTGRTHQLRL 262

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           H + +G PI+ D  Y             N L L A+ +    P  G
Sbjct: 263 HMMSLGMPILNDRLY-PELLDKAADDFDNPLKLMAKRLAFTDPITG 307


>gi|150865938|ref|XP_001385357.2| DRAP deaminase and pseudouridylate synthase [Scheffersomyces
           stipitis CBS 6054]
 gi|149387194|gb|ABN67328.2| DRAP deaminase and pseudouridylate synthase [Scheffersomyces
           stipitis CBS 6054]
          Length = 425

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 46/176 (26%), Positives = 82/176 (46%), Gaps = 8/176 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++E+  + V +KP+GI         Y+ +   LK  ++ K   P   HRLD+ TSGIL+
Sbjct: 117 IVFENEDMLVVDKPSGIPTHPTGNYYYNTMTEILKHDLNMKNVWP--FHRLDKVTSGILI 174

Query: 160 VARTRAAAQHLTESFRMRR--IQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVV 216
             +++ A    +  F+  +  I K Y + + G  P    E + N  +   +  G Y+  +
Sbjct: 175 FGKSKTACDTYSSIFQNEKDNISKQYLARIEGEFPTT--EVMVNCPIFSVNSTGGYIKPL 232

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +    N      ++          +  +P TGR HQ+R+H  ++G PIV D+ Y
Sbjct: 233 NADMLPINSTTVFKRLRYSKELNQSIVICRPLTGRMHQIRIHLRNIGHPIVNDYLY 288


>gi|71649760|ref|XP_813593.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70878491|gb|EAN91742.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 733

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 99/237 (41%), Gaps = 37/237 (15%)

Query: 101 LLYEDSKIYVFNKPAGISV------------QGGSGIAYHIDGFLKSWVDSKGQ-KPRLT 147
           +++ED+ I V NKP  ++             +  + +   I    K+   ++G  +    
Sbjct: 510 VIFEDNDILVLNKPPHLASSRHALSCTQMNDKTATDVVSLILASTKNGETTRGVFRQGQV 569

Query: 148 HRLDQETSGILVVARTRAAAQHLT----ESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           HRLD ETSG LV+A+T  AA  L      S    +  K+Y +L   +  + +      +L
Sbjct: 570 HRLDAETSGCLVMAKTDCAADSLRHQMGTSAAYSQCNKVYLALCAVMEPDLRRIPLRGVL 629

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
           +       Y               + ++VI  F + +   LE +   G+ HQ+R H    
Sbjct: 630 RDPMDPKIY---------------TKYRVIRFFRKARVALLECRIQQGKKHQIRRHLAAA 674

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           G PI+ D ++        T+P+ +++ LHA  + L HP     +   APL     +T
Sbjct: 675 GLPILQDVEHGG---AACTTPLIDRVALHAAALTLVHPRTAEVVTFVAPLAMDFAET 728


>gi|157962549|ref|YP_001502583.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157847549|gb|ABV88048.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 305

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 44/200 (22%), Positives = 92/200 (46%), Gaps = 32/200 (16%)

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           H+   Q +LD +V          + LL+++ +  V+ KP G+  QG     +     +  
Sbjct: 92  HLYYNQAVLDETVT--------DAELLFDEEQYSVWYKPFGMRCQGSK---WSDHTTINR 140

Query: 136 WVDSKGQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +++++   PR   + HRLD   +G++V+  T+     + + F  R + K Y  +V G   
Sbjct: 141 FIETQLTPPRNAYIIHRLDLAATGLIVLGHTKKVTAAIAQLFETRALDKFYQVIVEGKFP 200

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +  I   +  K  +   + H+++ N +     ++  KV           +++  +GR 
Sbjct: 201 EGQVTINTDVDNKKALS--HAHILEYNSE-----LNQSKV-----------QVKIESGRK 242

Query: 253 HQLRVHALHMGCPIVGDHKY 272
           HQ+R+H   +G P++GD ++
Sbjct: 243 HQIRIHMASLGHPVIGDRQH 262


>gi|15241389|ref|NP_199927.1| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|75264240|sp|Q9LU60|PUS7_ARATH RecName: Full=RNA pseudourine synthase 7; AltName: Full=RNA
           pseudouridylate synthase 7; AltName: Full=RNA-uridine
           isomerase 7
 gi|8843850|dbj|BAA97376.1| unnamed protein product [Arabidopsis thaliana]
 gi|332008659|gb|AED96042.1| RNA pseudourine synthase 7 [Arabidopsis thaliana]
          Length = 395

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 55/204 (26%), Positives = 85/204 (41%), Gaps = 8/204 (3%)

Query: 100 ILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++L+++  +    KPA + V   G      I G L +  D     P   HRLD+  SG+L
Sbjct: 137 VILHQEPDVVTVCKPASVPVHPCGQYRKNTIVGILDAEHDLGTLFP--IHRLDRLVSGLL 194

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSH---IGGDYVH 214
           ++ART A A    +      ++K Y + V G+ P+++    AN     S       D   
Sbjct: 195 IIARTAAKADFFRQQIEGGMVKKRYIAKVIGVFPEDEMIVDANINYNGSEGRSTAEDANS 254

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                +     A + F  ID        +  +P TGRTHQ+RVH  + G PI  D  Y  
Sbjct: 255 SGDDKKVKGKPACTKFTRIDTNGTH-SLVSCEPVTGRTHQIRVHLQYTGHPIANDPLYLN 313

Query: 275 NFKGNFTSPIQNKLYLHARYMDLP 298
               N  + I  ++    R +  P
Sbjct: 314 QHIDNLETYIAKRIDAGERKIVSP 337


>gi|325119975|emb|CBZ55528.1| hypothetical protein NCLIV_059530 [Neospora caninum Liverpool]
          Length = 830

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 66/274 (24%), Positives = 109/274 (39%), Gaps = 52/274 (18%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           H+ F+  Q+         D+     + R+ +G +V  P   +AL+H    ++I   S  L
Sbjct: 244 HVKFLRKQR---------DRPEASKDARVNAGDLVYFPRGSDALHHA---KEISRPSAGL 291

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGI---SVQGGSGIAYHIDGFLKSWVD-------SK 140
                 L+  LLY+D+     +KP G+    ++     A   D    S +        S 
Sbjct: 292 D-----LRERLLYKDTDFLAIDKPFGLCTGQLRPRGRRAPKKDTEKASVLSLAHQLRFSL 346

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI-YWSLVWG-IPKNKKECI 198
            + P+L HRL  E +G+L++ RT+  A    + FR      + + +LV G  P  ++E +
Sbjct: 347 DETPKLLHRLGDEVTGVLLLGRTKQTAALALDRFRGGTFGTVTFLALVHGRPPGGRREGV 406

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISH---FKVIDCFAQKFCWLEMQPHTGRT--- 252
               L ++  G   V V    ++G    ++     KV     +  C  E   H       
Sbjct: 407 IRIPLAENEAG---VMVPTAVQRGGAAVVTRWRLLKVASAAGRHGCDRESDAHGSAGLGF 463

Query: 253 -------------HQLRVHALH-MGCPIVGDHKY 272
                        HQ R H L+ + CPIVGD  Y
Sbjct: 464 SLIELEIDQQQCRHQARAHCLYGLCCPIVGDRVY 497


>gi|289178336|gb|ADC85582.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           animalis subsp. lactis BB-12]
          Length = 249

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 96/224 (42%), Gaps = 28/224 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           ++YE+ +I V +KP  ++     G+ Y     ++  +  + ++P +   HRLD+ T+GI+
Sbjct: 20  VVYENERIIVVDKPHFLATTP-RGMWYRETALMR--LRERYREPNIIPAHRLDRPTAGIV 76

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV----WGIPKNKKECIAN----W-LLKKSHIG 209
           V  R  AA       F+  R +K Y  L        P+       +    W L+++S I 
Sbjct: 77  VFVRDPAARGAYQMLFQEHRTRKCYECLAPIRPLATPRTGTVVHGSPPRIWPLVRRSRIR 136

Query: 210 GDYVHVVKQNEKG---ANYAIS----HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                +  Q   G   A  AI     H ++            + P TG+THQLRVH   +
Sbjct: 137 KTRGVLCAQEIPGQVNAETAIELEALHARMSARMGMSIGVYRLLPRTGKTHQLRVHMNSL 196

Query: 263 GCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           G PIVGD  Y         +F+ P+Q    L AR +    P  G
Sbjct: 197 GLPIVGDDFYPRIEERAYDDFSQPLQ----LVARSLAFTDPFTG 236


>gi|270284361|ref|ZP_05965988.2| RNA pseudouridine synthase [Bifidobacterium gallicum DSM 20093]
 gi|270276723|gb|EFA22577.1| RNA pseudouridine synthase [Bifidobacterium gallicum DSM 20093]
          Length = 232

 Score = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 60/225 (26%), Positives = 95/225 (42%), Gaps = 31/225 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED +I V +KP  ++     G+ Y     +++     G++  L HRLD+ T+G+LV+
Sbjct: 1   MLYEDERIIVVDKPHFLASMP-RGMWYRQTVLMRAR-QQFGEQVTLAHRLDRLTAGVLVL 58

Query: 161 ART---RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL---------KKSHI 208
            R    R A Q L   F  RR  KIY  L    P  +        L         ++S I
Sbjct: 59  VRDPQFRGAYQTL---FEQRRTTKIYECLAPLKPARRPPTGTVRALEPPRSFPLERRSRI 115

Query: 209 GGDYVHVVKQNEKGANYAISHFK-------VIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
                 +  + ++G   A++  +       +     +      + P TG+THQLRVH   
Sbjct: 116 VKMRGVLQAREQRGQVNAVTLIEREELAPGITVADGRAVARYRLHPCTGKTHQLRVHMNS 175

Query: 262 MGCPIVGDHKYCANFK---GNFTSPIQNKLYLHARYMDLPHPEGG 303
           +G P++ D  Y         +F+ P    L L AR +    P  G
Sbjct: 176 LGLPMLNDPWYPRVLDVPYDDFSRP----LALVARELQFVDPVSG 216


>gi|224282585|ref|ZP_03645907.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium bifidum
           NCIMB 41171]
          Length = 253

 Score = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 97/231 (41%), Gaps = 38/231 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED+ I V +KP  ++     G+ Y       L+   D     P   HRLD+ T+GI+
Sbjct: 20  VVYEDAGIIVIDKPHFLATTP-RGMWYRQTALIRLREMFDEPDITP--AHRLDRLTAGIV 76

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKSHIG 209
           V  R  A        F+ R++ K Y  L          +G  +         L ++SHI 
Sbjct: 77  VFVRDPALRGAYQMMFQGRKVSKTYECLAPCRPTTRPRYGTVERLDPPAVFPLRRRSHIT 136

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL--------------EMQPHTGRTHQL 255
                V++  E+    A++   VID  A  +  +              E+ P TG+THQL
Sbjct: 137 -KLRGVLQAFEE--PQAVNAETVIDLAAGGYPSMGGRLCHGRNGLRAYELHPLTGKTHQL 193

Query: 256 RVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G PI GD  Y         +F++P++    L AR +    P  G
Sbjct: 194 RVHMNSIGLPIHGDDFYPRIVERAYDDFSTPLE----LVARSLRFTDPVSG 240


>gi|289449819|ref|YP_003475504.1| RluA family pseudouridine synthase [Clostridiales genomosp. BVAB3
           str. UPII9-5]
 gi|289184366|gb|ADC90791.1| pseudouridine synthase, RluA family [Clostridiales genomosp. BVAB3
           str. UPII9-5]
          Length = 354

 Score = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 62/246 (25%), Positives = 110/246 (44%), Gaps = 28/246 (11%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           H + + ++++   G++ +D K        QSGQ +    V+  ++   +  + +++  ++
Sbjct: 25  HFSRLLIKRVKLHGRMEIDGKPELMKTPAQSGQKI----VVFYMDPAGEVNRPIEAQPDI 80

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
                     +L++D    + NKPA +          H    L + + S    P   +RL
Sbjct: 81  P---------ILFQDEWFIICNKPANLVTHP---TYLHHANNLTARLCSDLLHP--VNRL 126

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++++A+   A   LT       I K Y +LV G        I+   L  +   G
Sbjct: 127 DRDTSGLVILAKNGYAHHALTTV----SIAKRYLALVHGTHVPDAGEIS---LPIARSPG 179

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             +  +++       AIS F  +  + A +   LE  P TGRTHQLR+H+L    PIVG+
Sbjct: 180 SII--LREINASGQTAISRFICLKRWPAAQVSLLEYTPVTGRTHQLRLHSLMSSWPIVGE 237

Query: 270 HKYCAN 275
             Y  N
Sbjct: 238 TLYGCN 243


>gi|67900736|ref|XP_680624.1| hypothetical protein AN7355.2 [Aspergillus nidulans FGSC A4]
 gi|40742536|gb|EAA61726.1| hypothetical protein AN7355.2 [Aspergillus nidulans FGSC A4]
          Length = 1054

 Score = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 62/267 (23%), Positives = 108/267 (40%), Gaps = 57/267 (21%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK--EQKILDSSVNLTKHSD 95
           +K L SG V V+ K    +  +++G+V+         +H +   E  +  + + +     
Sbjct: 564 KKALESGNVCVNGKPAGPHTVLKNGEVI---------SHTLHRHEPPVTGNEIGI----- 609

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQE 153
                 ++E   + V +KPAG+ V   S   YH +  ++      G    PR  +RLD+ 
Sbjct: 610 ------IHETDDLLVIDKPAGVPVH--STGRYHYNSVMEILRIQNGGAYVPRPCNRLDRL 661

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS-HIGGDY 212
           TSG++ V +T   A  +T   + R +QK Y + V G   +    +   ++  S  +G + 
Sbjct: 662 TSGVMFVGKTAQGADRMTVKLKERTVQKEYVARVKGRFPDGVVVVDQPIMSVSPKVGLNR 721

Query: 213 VHVV--------------------------KQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V                              +N + A    S+    + ++   C+    
Sbjct: 722 VRATGKEAKTKFRRLAYYPPPSPTTSTSDEGENARPATPPPSYVNESEGYSIVHCF---- 777

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC 273
           P TGRTHQ+RVH   +G PI  D  Y 
Sbjct: 778 PLTGRTHQIRVHLQFLGHPISNDPIYS 804


>gi|254564943|ref|XP_002489582.1| DRAP deaminase, catalyzes the third step of the riboflavin
           biosynthesis pathway [Pichia pastoris GS115]
 gi|238029378|emb|CAY67301.1| DRAP deaminase, catalyzes the third step of the riboflavin
           biosynthesis pathway [Pichia pastoris GS115]
 gi|328350006|emb|CCA36406.1| DRAP deaminase [Pichia pastoris CBS 7435]
          Length = 547

 Score = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 46/177 (25%), Positives = 72/177 (40%), Gaps = 7/177 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           + YED +I V NKP+GI V       Y  +          G      +RLD+ TSGI+ +
Sbjct: 136 IAYEDDEITVINKPSGIPVHPTG--RYRHNSITMIMKQEMGTIAHTCNRLDRLTSGIMFL 193

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            +T      + +  + R + K+Y +   G  P   +      L     +  + V +    
Sbjct: 194 GKTAMKTAKMVQQIKERNVGKVYIAKCKGKFPLGLQVVDKPLLTIDPRLTFNLVDLEDGK 253

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           E    +    +   D  +   C     P TGRTHQ+RVH   +G PI  D  Y + +
Sbjct: 254 EAKTLFRRISYDTKDNTSIVKC----MPLTGRTHQIRVHLQFIGYPIANDPVYSSPY 306


>gi|197117718|ref|YP_002138145.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
 gi|197087078|gb|ACH38349.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
          Length = 293

 Score = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 68/262 (25%), Positives = 118/262 (45%), Gaps = 22/262 (8%)

Query: 52  RVKFNNRIQSGQVV--RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIY 109
           R  +  RI  G+V+     P+ +A ++  +++      +   K   F + IL +++ ++ 
Sbjct: 35  RSCWERRIAQGKVLGEDGTPITSASSYAPQKRIFYFREIENEKVIPFAEEIL-FQNDELL 93

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETSGILVVARTRAAAQ 168
           V  KP  + V  G    Y     L    +S G    +  HR+D+ET+GI++ +       
Sbjct: 94  VACKPHFLPVTPGG--EYLSQSLLHRLRESTGIHDLVPLHRIDRETAGIVLFSANPKTRG 151

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
              E FR   I+K Y + +   P    +  A WL++   + G+    ++  E+G   A S
Sbjct: 152 RYGELFREGSIEKSYEA-ISAAPVEPGQ--AEWLVENRLVHGEPWFTMR-TEQGPPNARS 207

Query: 229 HFKVIDC--FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSP 283
             ++++    A +F   ++ P TG+THQLRVH   +G  I+ D  Y         +F  P
Sbjct: 208 LIRLVEQRDGAARF---QLTPVTGKTHQLRVHMSGLGLQILHDRLYPQLQPQQPDDFDRP 264

Query: 284 IQNKLYLHARYMDLPHPEGGRL 305
           +Q    L AR +    P  GRL
Sbjct: 265 LQ----LLARRVRFRDPLSGRL 282


>gi|326675673|ref|XP_693475.4| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Danio rerio]
          Length = 599

 Score = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 41/126 (32%), Positives = 66/126 (52%), Gaps = 8/126 (6%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKS 206
           HRLD+ TSG+L+ ART   ++ L    R R+++K Y   V G  P+ +  C    L+   
Sbjct: 307 HRLDRLTSGVLLFARTLEVSKKLDVMVRERQLEKEYVCRVEGEFPEAEVVCEEPILVVSF 366

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +G     + + + KG   + + F+ +  F  +   +  +P TGRTHQ+RVH   +G PI
Sbjct: 367 RVG-----LCRVDPKGKE-SRTIFQRLS-FNGRSSVVRCRPLTGRTHQIRVHLQFLGFPI 419

Query: 267 VGDHKY 272
           + D  Y
Sbjct: 420 LNDPIY 425


>gi|227512235|ref|ZP_03942284.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus buchneri ATCC
           11577]
 gi|227524034|ref|ZP_03954083.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus hilgardii
           ATCC 8290]
 gi|227084629|gb|EEI19941.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus buchneri ATCC
           11577]
 gi|227088773|gb|EEI24085.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus hilgardii
           ATCC 8290]
          Length = 297

 Score = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 62/221 (28%), Positives = 98/221 (44%), Gaps = 19/221 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           +++ED    V NK +GI+      +    +   + G+ +       QK  +  RLD++TS
Sbjct: 81  IVFEDEHFLVVNKLSGIASVPAHNRANDSLVNRVKGYYQRN-HYANQKIHIVTRLDKDTS 139

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+   A   L +  +  +I+K Y ++V G        I  +L  K     D   V
Sbjct: 140 GLVIFAKHHFAHSVLDKQLKDHQIKKTYLAIVEGTFSTTHFEI--YLPIKR---ADGSLV 194

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +Q       +I+         Q    L++Q HTGRTHQ+RVH   +G P+VGD  Y   
Sbjct: 195 KRQVGFPGKMSITEAWTKQRLRQH-TLLKLQIHTGRTHQIRVHMTAIGHPLVGDWLYNPE 253

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            K   + P Q    LH   +   +P  G  +   APLP  M
Sbjct: 254 DK---SFPRQA---LHCAGLRFFNPFAGHFVDCRAPLPDDM 288


>gi|328721920|ref|XP_001945972.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Acyrthosiphon pisum]
          Length = 565

 Score = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 55/196 (28%), Positives = 87/196 (44%), Gaps = 22/196 (11%)

Query: 92  KHSDFLKSIL--------------LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           KH+D L +++              ++ D  I V NKP+ I V       ++   F+ +  
Sbjct: 191 KHNDLLANVVHRHEVPVASSTIDVIHLDDDIVVVNKPSSIPVHPCGRYRHNTMVFVLAK- 249

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +   +  +  HRLD+ TSG+L+  RT+  A+ L    R R + K Y   V G      EC
Sbjct: 250 EYGLRDLKTIHRLDRLTSGVLMFGRTQNRARTLEAQIRDRVVNKQYVCRVEGKFPESVEC 309

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM-QPHTGRTHQLR 256
                +    IG     V K +  G   + S F++I    Q    + + +P +GR HQ+R
Sbjct: 310 EQPIEVISYKIG-----VCKVSPNGKQCSTS-FQLIGYNEQANTSVVLCKPRSGRMHQIR 363

Query: 257 VHALHMGCPIVGDHKY 272
           VH  ++G PI  D  Y
Sbjct: 364 VHLQYLGHPIQNDPLY 379


>gi|156401575|ref|XP_001639366.1| predicted protein [Nematostella vectensis]
 gi|156226494|gb|EDO47303.1| predicted protein [Nematostella vectensis]
          Length = 418

 Score = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 64/268 (23%), Positives = 109/268 (40%), Gaps = 51/268 (19%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N  L   F+  +   +    +K + SG++ V+ ++V     ++   V+R        N +
Sbjct: 25  NRELLDIFREEFRSESISYYEKAIESGKITVNGEKVLPTTVLRGNDVLR--------NRV 76

Query: 78  IK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            + E  + D  + +  ++D            I V NKP+ I V       ++   FL   
Sbjct: 77  HRHEPPVTDQPLEIICNTD-----------DIVVLNKPSSIPVHPCGRYRHNTVVFLL-- 123

Query: 137 VDSKGQKPRL-----THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-I 190
               G++  L      HR+D+ TSGIL+ A+T   A+ L    R R+++K Y   V G  
Sbjct: 124 ----GKEHNLRNLYTIHRIDRLTSGILMFAKTLTRARMLEAQVRDRQVEKEYLCRVQGEF 179

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF------KVIDCFAQKFCWLE 244
           P    +C    ++    +G   +  V  + K      +         V+ C         
Sbjct: 180 PSEPVDCEQPIIVVSHKVG---ICRVSPDGKSCRTVFTKLHSNGKSSVVKCI-------- 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             P+TGR HQ+RVH   +G PI+ D  Y
Sbjct: 229 --PYTGRMHQIRVHLQWLGYPIIDDPIY 254


>gi|54019984|ref|YP_115530.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyopneumoniae 232]
 gi|53987157|gb|AAV27358.1| ribosomal large subunit pseudouridine synthase [Mycoplasma
           hyopneumoniae 232]
          Length = 281

 Score = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 102/237 (43%), Gaps = 43/237 (18%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI--------LL 102
           K++K NN  Q              N+IIKE+ I+    +  K   F K +        ++
Sbjct: 38  KKIKVNNTFQEK------------NYIIKEKDII-LIFSQEKLKTFSKKVPEFKLNLKII 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGI 157
           Y+D  I + +KP  + V GG    +++D  L  W      +++  KP    RLD++TSGI
Sbjct: 85  YQDENILLVDKPQNLQVHGG---KFNLD--LAVWNYLKIPENQVFKPSHIGRLDKKTSGI 139

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++      +   L +  + +  +KIY    +    N K  I   +  + +   ++   ++
Sbjct: 140 ILYGLNYQSVVELNQ--KQKFFEKIY---TFKSDINLKNTIKTDVFIRKN---NFQQKME 191

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              K  N   +         +KF  L    HTG+ HQ+RV   H+G PI GD KY  
Sbjct: 192 VTLKSPNSFFASTTFYSKNQKKFAIL----HTGKKHQIRVSLSHLGFPIFGDEKYGG 244


>gi|241949279|ref|XP_002417362.1| DRAP deaminase, putative; hydrolase, putative [Candida dubliniensis
           CD36]
 gi|223640700|emb|CAX45011.1| DRAP deaminase, putative [Candida dubliniensis CD36]
          Length = 405

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 54/188 (28%), Positives = 90/188 (47%), Gaps = 19/188 (10%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRL 150
           ++D +KSI  YED++I V +KP+GI     +G  YH    L   +  +     +   HRL
Sbjct: 103 YNDIIKSI--YEDNEILVVDKPSGIPTHP-TGNYYH--NSLSEIIKQQYNMDSIWTCHRL 157

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRR--IQKIYWSLVWG-IPKNKKECIANWLLKKSH 207
           D+ TSG+LV+A+T+      ++  R  +   +K Y + V G  P    E I  +      
Sbjct: 158 DKVTSGVLVLAKTKNGGVKFSKLMRDSKQHTKKTYLARVSGKFP----EGIHQYRCPIFA 213

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +  +   +    E+    + + F+ I    C  Q    ++  P TG+ HQ+R+H  ++G 
Sbjct: 214 VNMNGYLMSGNMEELPTDSTTVFEQIKYNACLDQSL--IKCIPITGKFHQIRIHLRNLGF 271

Query: 265 PIVGDHKY 272
           PIV D  Y
Sbjct: 272 PIVNDSFY 279


>gi|67478945|ref|XP_654854.1| RNA pseudouridylate synthase [Entamoeba histolytica HM-1:IMSS]
 gi|56471941|gb|EAL49468.1| RNA pseudouridylate synthase, putative [Entamoeba histolytica
           HM-1:IMSS]
          Length = 389

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 51/183 (27%), Positives = 80/183 (43%), Gaps = 17/183 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED+ + V NKP+GI    G    Y  +  ++     +  K    HRLD+ TSG+L++
Sbjct: 141 IIYEDNDVIVVNKPSGIPTHSGG--RYTENTVIRILEKERNIKLFGVHRLDRLTSGVLLI 198

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-LLKKSHIGGDYVHVVKQN 219
           A++   A  +   F      K Y   V G   +   CI N  +++ S I    V V  + 
Sbjct: 199 AKSSEIANEIQRHFI--NAYKKYICRVIGYMDS---CIVNKPIIETSCITKQRVTVGCEG 253

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD------HKYC 273
            K +       +  +       W    P TGR HQ+RVH  +   PI  D      ++YC
Sbjct: 254 -KASTTIFEQIQYDEKTDTTLLW--AIPKTGRMHQIRVHLSYENHPIANDSMYRNKNEYC 310

Query: 274 ANF 276
            +F
Sbjct: 311 THF 313


>gi|259483290|tpe|CBF78558.1| TPA: DRAP deaminase (Rib2), putative (AFU_orthologue; AFUA_2G16360)
           [Aspergillus nidulans FGSC A4]
          Length = 572

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 62/266 (23%), Positives = 108/266 (40%), Gaps = 57/266 (21%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK--EQKILDSSVNLTKHSD 95
           +K L SG V V+ K    +  +++G+V+         +H +   E  +  + + +     
Sbjct: 82  KKALESGNVCVNGKPAGPHTVLKNGEVI---------SHTLHRHEPPVTGNEIGI----- 127

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQE 153
                 ++E   + V +KPAG+ V   S   YH +  ++      G    PR  +RLD+ 
Sbjct: 128 ------IHETDDLLVIDKPAGVPVH--STGRYHYNSVMEILRIQNGGAYVPRPCNRLDRL 179

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS-HIGGDY 212
           TSG++ V +T   A  +T   + R +QK Y + V G   +    +   ++  S  +G + 
Sbjct: 180 TSGVMFVGKTAQGADRMTVKLKERTVQKEYVARVKGRFPDGVVVVDQPIMSVSPKVGLNR 239

Query: 213 VHVV--------------------------KQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V                              +N + A    S+    + ++   C+    
Sbjct: 240 VRATGKEAKTKFRRLAYYPPPSPTTSTSDEGENARPATPPPSYVNESEGYSIVHCF---- 295

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
           P TGRTHQ+RVH   +G PI  D  Y
Sbjct: 296 PLTGRTHQIRVHLQFLGHPISNDPIY 321


>gi|299142544|ref|ZP_07035675.1| ribosomal large subunit pseudouridine synthase A [Prevotella oris
           C735]
 gi|298575979|gb|EFI47854.1| ribosomal large subunit pseudouridine synthase A [Prevotella oris
           C735]
          Length = 522

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 57/206 (27%), Positives = 84/206 (40%), Gaps = 23/206 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +YED  I V  KP G+    G     ++   ++     +   P + HRLD  TSG+LVVA
Sbjct: 325 IYEDKDIVVVCKPVGMLSVPGKIQRENVRSLVRQ-RHPEATGPMIVHRLDMATSGLLVVA 383

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
               +   L   F    +QK Y +L+   P +        L  +  +      +V     
Sbjct: 384 LNLKSYIDLQCQFEEHSVQKRYVALL-SRPHHGARSGQICLPLRPDLHDRPRQIVD---- 438

Query: 222 GANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFK 277
               A+   K +  + Q     + + P TGRTHQLR+H  H   +  PI GD  Y    +
Sbjct: 439 ----AVHGRKAVTNYQQTGENRMNLYPLTGRTHQLRMHCAHADGLNNPIKGDELYGTRAE 494

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
                    +LYLHA  +   HP  G
Sbjct: 495 ---------RLYLHAEELSFVHPGTG 511


>gi|58266206|ref|XP_570259.1| hypothetical protein [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|134111034|ref|XP_775981.1| hypothetical protein CNBD3880 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50258647|gb|EAL21334.1| hypothetical protein CNBD3880 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|57226492|gb|AAW42952.1| conserved hypothetical protein [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 520

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 69/268 (25%), Positives = 122/268 (45%), Gaps = 23/268 (8%)

Query: 18  NMRLDRWFKNHY-PHINFVNLQKILR------SGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           N RL R+ K+++ P+  FV  + I R      + + R D+    + + ++SG V R+  V
Sbjct: 17  NPRL-RYIKSYWWPYKTFVKQRWIGRQLLEVITTEFR-DRSMEYYRHALESG-VTRVNGV 73

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLY---EDSKIYVFNKPAGISVQGGSGIAY 127
           +   + I++    +D++V+  +       IL+     + +  V +KP  + V        
Sbjct: 74  VAQPDLILRNGDRIDNTVHRHEPPVTNDPILVLHIDREREFIVISKPGSLPVHAAGRYFK 133

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           H    L+      G K    +RLD+ TSG++++A +  AA  L   F   +++K Y + V
Sbjct: 134 HT--VLEMMESDYGLKCYSVNRLDRLTSGLMILALSGKAASKLAREFVEGKVKKEYVARV 191

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI--DCFAQKFCWLE 244
            G  PK +       +     +G     V+   E  +  A++ F  I  D    +   + 
Sbjct: 192 KGKFPKEEITVDKPMMTVDRQMG----LVIITPEGKSQDAVTIFNRIAYDPVRDQSV-VR 246

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 247 CRPQTGRTHQIRVHLQYLGHPIANDPLY 274


>gi|170055019|ref|XP_001863394.1| conserved hypothetical protein [Culex quinquefasciatus]
 gi|167875138|gb|EDS38521.1| conserved hypothetical protein [Culex quinquefasciatus]
          Length = 252

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 83/186 (44%), Gaps = 25/186 (13%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD  TSGIL +   + A + + + F  +R +K Y +L+ G      E I       
Sbjct: 56  FAHRLDFATSGILCIPLNKNACKEVCQVFEEQRARKYYLALLRGHTDFDDEVI------D 109

Query: 206 SHIGGDY--------VHVVKQNEKGAN--YAISHFKVID---CFAQKFCWLEMQPHTGRT 252
             IG D         +  + ++E   N   +I+   V+D      +    + ++P TGR 
Sbjct: 110 IAIGEDIRFKDTSKKMCTILEDELCQNPRRSITKVLVLDRGYYNGKPVTKVLLRPITGRR 169

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           HQLR+H   +G  IVGD+ Y        TSP   +++LHA  + LP+  E   +Q   P 
Sbjct: 170 HQLRLHCSQIGHVIVGDYTYSLKID---TSP--PRMFLHAFRLVLPNSFENIDIQTDDPF 224

Query: 312 PAHMVK 317
               +K
Sbjct: 225 TEKALK 230


>gi|159466816|ref|XP_001691594.1| pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158278940|gb|EDP04702.1| pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 694

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 40/149 (26%), Positives = 63/149 (42%), Gaps = 19/149 (12%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
           T+RLD+  SG+L++AR+ A A  +      R   K Y + V G+  +        ++  +
Sbjct: 249 TYRLDKPVSGVLLLARSSAVAGRMRVLLEERGCAKAYVARVQGVFPDTSSLSGGVMVVDT 308

Query: 207 HIG--GDYVHVVKQNEKG----------------ANYAISHFKVIDCFAQKFCWL-EMQP 247
            +G      H       G                A  A +HF+ +         + E  P
Sbjct: 309 PLGWEAKTNHATPVPASGLAADGATALPPALVASAKPAETHFRRLSVSPDGLTSVVEAVP 368

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            TGRTHQ+RVH  H+G PI  D +Y  ++
Sbjct: 369 KTGRTHQIRVHLQHVGHPIANDTQYGGSY 397


>gi|16974566|gb|AAL31256.1| AT5g51140/MWD22_8 [Arabidopsis thaliana]
 gi|23507777|gb|AAN38692.1| At5g51140/MWD22_8 [Arabidopsis thaliana]
          Length = 367

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 63/255 (24%), Positives = 105/255 (41%), Gaps = 30/255 (11%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK--EQKILDSSVNLTKHSDFLK 98
           ++SG+++VD + V  +  ++S Q          + H +   E  ++   V          
Sbjct: 68  VKSGRIKVDGEIVPVSYIVKSSQ---------KITHFLHRHEPPVMIDDV---------- 108

Query: 99  SILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
            ++L+++  +    KPA + V   G      I G L +  D     P   HRLD+  SG+
Sbjct: 109 -VILHQEPDVVTVCKPASVPVHPCGQYRKNTIVGILDAEHDLGTLFP--IHRLDRLVSGL 165

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSH---IGGDYV 213
           L++ART A A    +      ++K Y + V G+ P+++    AN     S       D  
Sbjct: 166 LIIARTAAKADFFRQQIEGGMVKKRYIAKVIGVFPEDEMIVDANINYNGSEGRSTAEDAN 225

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                 +     A + F  ID        +  +P TGRTHQ+RVH  + G PI  D  Y 
Sbjct: 226 SSGDDKKVKGKPACTKFTRIDTNGTH-SLVSCEPVTGRTHQIRVHLQYTGHPIANDPLYL 284

Query: 274 ANFKGNFTSPIQNKL 288
                N  + I  ++
Sbjct: 285 NQHIDNLETYIAKRI 299


>gi|332645402|gb|AEE78923.1| RNA pseudourine synthase 5 [Arabidopsis thaliana]
          Length = 416

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 54/194 (27%), Positives = 85/194 (43%), Gaps = 29/194 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS-----GIAYHID---GFLKSWVDSKGQK-PRLTHRLD 151
           +LYED  +   NKP+G+ V  G       +   +    G   S++ S+    P   HRL 
Sbjct: 129 VLYEDDDLIALNKPSGLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVPVHRLG 188

Query: 152 QETSGILVVARTRAAAQHLTESFRM-----------------RRIQKIYWSLVWGIPKNK 194
           + TSGIL+ A+T+ A   L   F                   R++ KIY +L  GI +  
Sbjct: 189 RGTSGILLCAKTKLAKTKLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADGIVEED 248

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTH 253
           +  I   +    + G      V   E     A S   V++   +K C L +++  +GR H
Sbjct: 249 EVVIKQPIGVVRYPGVAQGLYVASPE--GKPAFSKVFVLERDREKNCSLVKVEIQSGRPH 306

Query: 254 QLRVHALHMGCPIV 267
           Q+R+H  +MG P+V
Sbjct: 307 QIRIHLAYMGHPLV 320


>gi|319935050|ref|ZP_08009493.1| hypothetical protein HMPREF9488_00324 [Coprobacillus sp. 29_1]
 gi|319810068|gb|EFW06437.1| hypothetical protein HMPREF9488_00324 [Coprobacillus sp. 29_1]
          Length = 301

 Score = 56.2 bits (134), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 56/209 (26%), Positives = 89/209 (42%), Gaps = 26/209 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------RLTHRLDQET 154
           ++YED  + V NKP  +SV   +    H D  L + V +  Q+       R  HRLD ET
Sbjct: 83  IIYEDEFLLVVNKPPFLSVFPDN--LSHTDS-LANRVSAYYQQCGYNIPVRYIHRLDYET 139

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV 213
           +G+ +  +       +     ++ IQ+ Y ++V G +   K+  I   + +  H     +
Sbjct: 140 TGLTLFCKCSFIQPLMDYQLSIKEIQRKYLAIVKGKLTGYKQHSICQPIGRDRHHNQRMI 199

Query: 214 HVVKQNEKGANYAISHFKVIDCFA--QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V    ++   Y         C A  Q    +E    TGR HQ+RVH   +G P++GD  
Sbjct: 200 -VSSSGKRACTYY-------QCIATNQDLSVVECTLDTGRKHQIRVHMSAIGHPLLGDCL 251

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Y         S + N+  LHA  +   HP
Sbjct: 252 YGEK------SHLMNRQALHAFQLIFTHP 274


>gi|148377981|ref|YP_001256857.1| ribosomal large subunit pseudouridine synthaseC [Mycoplasma
           agalactiae PG2]
 gi|148292027|emb|CAL59419.1| Ribosomal large subunit pseudouridine synthaseC [Mycoplasma
           agalactiae PG2]
          Length = 284

 Score = 56.2 bits (134), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 68/259 (26%), Positives = 117/259 (45%), Gaps = 34/259 (13%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRI-QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           + ++ R   ++V+ KR+  +N + ++G  + I  + +  + +I      D+S  L     
Sbjct: 31  IYRLFRQKSIKVNNKRITDSNYVVKTGDEIIIYGIKDEPSFVI-----YDNSWKLD---- 81

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
              S ++YED  I + NK AG  V G S  +   +  + K +  +   +P    RLD+ T
Sbjct: 82  ---SEIVYEDDNILLINKKAGTIVHGDSNCLDNQVFSYFK-FRQNSAFRPSHVGRLDKWT 137

Query: 155 SGILVVARTRAAAQHLTE-SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           SG+++ A+     Q LTE + +   + KIY   V     N  + I +  +    +    V
Sbjct: 138 SGLIMYAKN---YQTLTELNHKTEFLDKIY---VLKSDYNPHDEIVSVYIHHDELQQKMV 191

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               +N +  N  I+  +    F +K   L  Q  TGR HQ+R    ++G PI GD KY 
Sbjct: 192 --ATKNMQHPNDKIAKTR----FFKKDNKLYAQLFTGRKHQIRATLEYLGYPIYGDSKYG 245

Query: 274 ANFKGNFTSPIQNKLYLHA 292
           +  KG        ++YLH 
Sbjct: 246 SKTKGT------KRVYLHC 258


>gi|56755719|gb|AAW26038.1| SJCHGC01065 protein [Schistosoma japonicum]
          Length = 438

 Score = 56.2 bits (134), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 81/185 (43%), Gaps = 15/185 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
            +++   + V NKP  I +       Y ++          G +P R THRLD+ TSG+L+
Sbjct: 134 FIHDSHDMLVINKPPSIPIHPCG--RYTLNSITHILAKDYGLRPLRFTHRLDRMTSGLLL 191

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE-C----IANWLLKKSHIGGDY- 212
           +A+    +  L      + + K Y   V G  P    + C    I N ++  S   G   
Sbjct: 192 IAKDYDTSVRLQSQIASKEVTKHYICHVDGCFPTEPIDHCTGFEINNGVVVCSQPVGPIS 251

Query: 213 ----VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM-QPHTGRTHQLRVHALHMGCPIV 267
               +H V     G   A +HF  ++  +     L + +  TGRTHQ+R+H  ++G PIV
Sbjct: 252 PKMGIHAVLPESAGGKPARTHFLRLNYNSVTNTSLVICRLFTGRTHQIRIHTQYLGYPIV 311

Query: 268 GDHKY 272
            D  Y
Sbjct: 312 EDPIY 316


>gi|322697720|gb|EFY89497.1| DRAP deaminase [Metarhizium acridum CQMa 102]
          Length = 512

 Score = 56.2 bits (134), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 52/211 (24%), Positives = 88/211 (41%), Gaps = 40/211 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           +++ED  + V NKP+G+ V       Y  +  L+     +G +  P   +RLD+ TSGI+
Sbjct: 159 IIHEDEDMIVINKPSGVPVHPAG--RYKFNSVLEIMKAERGPEFMPYPCNRLDRLTSGIM 216

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYV---- 213
            VA++  AA+ L    + R ++K Y + V G  P+ +  C    L     +G + V    
Sbjct: 217 FVAKSVKAAEALGNQIKSRTVRKEYMARVVGEFPEGEIVCDQPILSISPKLGLNRVRAEG 276

Query: 214 -----------------HVVKQNEKGANYAISHFKVIDCFAQK--------------FCW 242
                            H     ++G     +  ++    A++              +  
Sbjct: 277 KAARTVFKRLAYYPPRAHAEANGQQGGVPEPTDKELSRLPAEEGDESNGKPWINKRGYSI 336

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           +   P TGRTHQ+RVH  ++G PI  D  Y 
Sbjct: 337 VRCLPVTGRTHQIRVHLQYLGHPIQNDPIYA 367


>gi|319935762|ref|ZP_08010192.1| hypothetical protein HMPREF9488_01023 [Coprobacillus sp. 29_1]
 gi|319809311|gb|EFW05752.1| hypothetical protein HMPREF9488_01023 [Coprobacillus sp. 29_1]
          Length = 277

 Score = 56.2 bits (134), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 61/279 (21%), Positives = 121/279 (43%), Gaps = 50/279 (17%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Y + ++V  +   +R+D +   H  HI+   L+ I + G + V+ +       +  G  V
Sbjct: 2   YKRELIVTKENHQLRIDDFAYQH--HISRKALKVIKQCGDILVNGEHQTVRYVLNEGDYV 59

Query: 66  RI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV---- 119
               PP         ++ +I+  +V L          ++YED  + + +KP G++     
Sbjct: 60  VFIYPP---------EDNQIIPENVPLY---------IVYEDDFLLIVDKPKGMACFPTR 101

Query: 120 -----QGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                   + ++Y+     L S V          +RLD++T+G++++A+ R     + ++
Sbjct: 102 SHPCQTLANALSYYYHSIELDSTV-------HFVNRLDKDTAGLMMIAKYREIHDMMCQN 154

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                IQ IY      +    ++ + +  + K   G +   ++ +N K +       +  
Sbjct: 155 -----IQHIYRRYQAHVEGQVEQGVIDLPIHKD--GQNMRRIIDENGKDSRTYYRCLEYS 207

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           D  ++  C LE    TGRTHQ+RVH   +G P++GD  Y
Sbjct: 208 DGISRVECILE----TGRTHQIRVHMAAIGHPLIGDLLY 242


>gi|240171345|ref|ZP_04750004.1| pseudouridine synthase [Mycobacterium kansasii ATCC 12478]
          Length = 272

 Score = 56.2 bits (134), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 90/227 (39%), Gaps = 22/227 (9%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-------LLYEDSKIYVFNKPAGISVQG- 121
           V+++   +I    +L     +  + D    +       +LY+D  I V +KP  ++    
Sbjct: 29  VVDSRGAVIDRDTVLPPGSFVHLYRDLPDEVPVPFEMPVLYQDDDIVVADKPHFLATMPR 88

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G  +A      L+  +      P   HRLD+ T+G+L+    R         F    + K
Sbjct: 89  GRHVAQTALVRLRCELGLPELSP--AHRLDRLTAGVLLFTTRRELRGRYQTLFACGAVHK 146

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +     P      +    + K    G    V +  E  A        +++  + +  
Sbjct: 147 TYLARAAVNPAVVLPRVVRSRIVKRR--GQLQAVCEPGEPNAE------TLVELISPQGL 198

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQ 285
           +  + P TGRTHQLRVH   +G PI GD  Y        G+F+SP+Q
Sbjct: 199 Y-RLTPRTGRTHQLRVHMASLGLPITGDPLYPKVLQEVDGDFSSPLQ 244


>gi|149923247|ref|ZP_01911658.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
 gi|149815904|gb|EDM75423.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
          Length = 401

 Score = 56.2 bits (134), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 76/343 (22%), Positives = 126/343 (36%), Gaps = 82/343 (23%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +V++ V   D    R D       P ++    + + R+G +RVD  +   + R + GQV+
Sbjct: 14  HVEHTVTAEDA-GERADVILGRRVPALSRRQARSLARAGHLRVDGLKRPPSTRAREGQVL 72

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+     AL+          SS  L    D L+  +L E       +KPAG+       +
Sbjct: 73  RL-----ALDD-------EPSSPELAARLDALE--VLAETPDFVYVHKPAGVHTVA---L 115

Query: 126 AYHIDGFLKS-----WVDSKG--QKPR---LTHRLDQETSGILVVARTRAAAQHLTESFR 175
                G L +     W +  G  + PR     HRLD+ TSG++  AR+        ++F 
Sbjct: 116 TPQQPGVLATAVAERWPECAGASEDPREGGAVHRLDRPTSGVVAFARSPEIWARARKAFS 175

Query: 176 MRRIQKIYW-------------SLVWGIPKNKKECIANWLL-------KKSHIG------ 209
             +++K Y              ++ W  P   +  +  W+L        ++ +G      
Sbjct: 176 AEQVRKRYLAVCLDLGARERGAAMTW-PPALPEGGLRGWVLPAEVEAHPRAELGSLAGID 234

Query: 210 ------------GDYVHVVKQNEKGANYAI-----SHFKVIDCFAQKFC-------W-LE 244
                            V ++ E  ++ A+         V+   AQ          W L 
Sbjct: 235 TATATHPSFRVRAPLGRVAREAEIPSHTAVRLDGQRASSVVHPLAQASATSTGAQPWLLA 294

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           ++  TGR HQ R H   +G PIVGD  Y    +   T P    
Sbjct: 295 LELETGRRHQARCHLAWIGLPIVGDSLY--GPRAGATPPTSGS 335


>gi|330502423|ref|YP_004379292.1| pseudouridine synthase [Pseudomonas mendocina NK-01]
 gi|328916709|gb|AEB57540.1| pseudouridine synthase [Pseudomonas mendocina NK-01]
          Length = 293

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 50/213 (23%), Positives = 103/213 (48%), Gaps = 20/213 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +L++D  + V +KP  + V        +++  L + +  +   P L   HR+D+ T+G++
Sbjct: 84  VLWQDEHLLVADKPHFLPVMPA---GEYVEQTLLARLIKRTGNPDLVPIHRIDRLTAGLV 140

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + +   A+       FR R ++K Y ++   +P+ +      +L +   + G+    +++
Sbjct: 141 LFSVNPASRGQYQALFRQRAVEKCYEAIAPALPQLQ----FPYLHRSRMVEGEPFFRMQE 196

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-----C 273
               AN + +  +V++   + + +  + P TGR HQLRVH   +G PIVGD  Y      
Sbjct: 197 VAGEAN-SETRIEVLERRGELWRY-GLSPVTGRKHQLRVHLAGLGAPIVGDDFYPQLRES 254

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
            N   +++ P++    L AR +    P  G+++
Sbjct: 255 RNQPDDYSKPLK----LLARGLLFADPVSGQVR 283


>gi|257457504|ref|ZP_05622672.1| ribosomal large subunit pseudouridine synthase family protein
           [Treponema vincentii ATCC 35580]
 gi|257445127|gb|EEV20202.1| ribosomal large subunit pseudouridine synthase family protein
           [Treponema vincentii ATCC 35580]
          Length = 276

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 42/176 (23%), Positives = 74/176 (42%), Gaps = 28/176 (15%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC------IANW 201
           +RLD   SGI+++A +  A   L+++F+   ++K YW++      +  E       + +W
Sbjct: 44  NRLDTPVSGIILLAFSAQAQTLLSQAFKTGSVEKEYWAICERTAADTTEEEPGIHRLEHW 103

Query: 202 L-----LKKSHIGGDYVHVVKQNEKGANYAISH------------FKVIDCFAQKFCWLE 244
           L      +K+ +G   + +   N   A                  +  +     ++ ++ 
Sbjct: 104 LGFHTKTQKAFVGAAPIDITLTNTTAAGITKPKKHKKPALKKAVLYWTLCGKGDRYDFIR 163

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           + P TGRTHQ+RV     G PI GD KY     G   S     + LH+  +   HP
Sbjct: 164 ISPETGRTHQIRVQMAAAGHPIKGDLKY-----GARRSETGGGIRLHSYKLSFSHP 214


>gi|331697825|ref|YP_004334064.1| pseudouridine synthase [Pseudonocardia dioxanivorans CB1190]
 gi|326952514|gb|AEA26211.1| pseudouridine synthase [Pseudonocardia dioxanivorans CB1190]
          Length = 309

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 48/190 (25%), Positives = 85/190 (44%), Gaps = 14/190 (7%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ D  + V +KP  +S +  G  +       L+  +D     P   HRLD+ T+G+L+
Sbjct: 93  VVHRDEHLLVVDKPHFLSTIPRGRHVVETALVRLRRDLDLPELSP--AHRLDRVTAGLLM 150

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIANWLLKKSHIGGDYVHVVKQ 218
               R         FR RR+ K Y ++    P       + + ++K+  I      +V +
Sbjct: 151 FVVRREDRGAYQTMFRDRRVAKTYEAIAPHDPALLLPRTVTSRIVKERGI------IVAR 204

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---N 275
              G   A ++ ++++          + P TGRTHQLR+H   +  PI+GDH Y      
Sbjct: 205 EVDGPPNAETYVELVE-HRDGLGRYRLTPATGRTHQLRLHMAALNVPILGDHFYPELHDK 263

Query: 276 FKGNFTSPIQ 285
              ++T P+Q
Sbjct: 264 PLDDYTRPLQ 273


>gi|169630733|ref|YP_001704382.1| pseudouridine synthase [Mycobacterium abscessus ATCC 19977]
 gi|169242700|emb|CAM63728.1| Pseudouridine synthase [Mycobacterium abscessus]
          Length = 277

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 57/208 (27%), Positives = 89/208 (42%), Gaps = 16/208 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  ++    G  +       L+  +D     P   HRLD+ T+G+L+
Sbjct: 70  VLHWDENVLVVDKPHFLATMPRGRHVTETALVRLRKMLDLPELAP--AHRLDRLTAGVLL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               R A       F  R++ KIY +L        K  ++  L  +S I      +    
Sbjct: 128 FTVRRDARAAYHSLFAQRQVVKIYEALA-----PVKPGLSLPLTVRSRIVKRRSILQAVE 182

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-- 277
           E G   A +  +++D          + P TG+THQLRVH   MG PI+ D  Y    +  
Sbjct: 183 EPGPANAETRVELVDRH-HAVGRYRLTPSTGQTHQLRVHMNSMGVPILNDPLYPDVVEVP 241

Query: 278 -GNFTSPIQNKLYLHARYMDLPHPEGGR 304
             +FT P+Q    L AR +    P  G+
Sbjct: 242 PDDFTRPLQ----LLARTLAFRDPLNGK 265


>gi|281211774|gb|EFA85936.1| pseudouridine synthase family protein [Polysphondylium pallidum
           PN500]
          Length = 530

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 42/138 (30%), Positives = 65/138 (47%), Gaps = 16/138 (11%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG------IPKNKKECIANW 201
           HRLD+ TSG+L++AR+ AAA   +E+     + K Y + V G      I  ++   + N 
Sbjct: 279 HRLDRLTSGLLILARSPAAATKKSEAIMSGNVTKRYVAQVRGRFPDGDITVDQPLKVQNH 338

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            L  + +  D    +    + +  A +   V+ C           P TGRTHQ+R+H   
Sbjct: 339 RLGLNQVSPDGKPALTVITRLSYDAETDTSVVSCL----------PKTGRTHQIRLHLQW 388

Query: 262 MGCPIVGDHKYCANFKGN 279
           +G PI  D  Y  +FK N
Sbjct: 389 IGHPITNDPLYNEHFKLN 406


>gi|111021862|ref|YP_704834.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
 gi|110821392|gb|ABG96676.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
          Length = 338

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 54/205 (26%), Positives = 87/205 (42%), Gaps = 12/205 (5%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  + S   G+ +A      L+   D     P   HRLD+ T+G+L+
Sbjct: 129 ILHRDEDLLVVDKPHFLASTPRGAYVAESALVRLRRDFDLPELTP--AHRLDRLTAGVLI 186

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               R   +     F  RR+ K Y ++    P  +        + K         V+K  
Sbjct: 187 FTVRREVRRDYQSLFDQRRVVKEYEAVARYDPDLRLPATVRSRIVKER------GVLKAY 240

Query: 220 E-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           E  G   + S  ++++       +  + PHTG+THQLR+H   +G PI GD+ Y  +F  
Sbjct: 241 EMDGPANSESRIELLEIHGDAARY-RLLPHTGKTHQLRLHMSSLGIPIHGDNFY-PDFYD 298

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
                    L L AR ++   P  G
Sbjct: 299 VAADDYSTPLRLLARSVEFVDPYSG 323


>gi|302526188|ref|ZP_07278530.1| ribosomal pseudouridine synthase [Streptomyces sp. AA4]
 gi|302435083|gb|EFL06899.1| ribosomal pseudouridine synthase [Streptomyces sp. AA4]
          Length = 309

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 99/227 (43%), Gaps = 20/227 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  + ++  G  +       L+  +D     P   HRLD+ T+G+++
Sbjct: 93  VLHRDDHLLVVDKPHFLATIPRGRHVLETALVRLRRSLDLPALSP--AHRLDRVTAGLVM 150

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
              T +A       FR R + K Y ++    P  +   +      +S I  +   +  Q 
Sbjct: 151 FVITPSARGAYQTMFRDRLVHKEYEAIAPYDPTLELPRVV-----RSRIVKERGVLAAQE 205

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-- 277
             G   A S  ++++          + P TGRTHQLRVH   +G PI+GD  Y    +  
Sbjct: 206 VPGPPNAESTVELLE-HRDGLGRYRLTPATGRTHQLRVHMCSLGIPILGDDFYPELHEKP 264

Query: 278 -GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             +FT P+Q    L A+ ++   P  G   + T+      +  WDSL
Sbjct: 265 LNDFTKPLQ----LLAKVLEFDDPLTGEHRRFTS---RRTLSAWDSL 304


>gi|321257772|ref|XP_003193704.1| hypothetical protein CGB_D5020C [Cryptococcus gattii WM276]
 gi|317460174|gb|ADV21917.1| Conserved hypothetical protein [Cryptococcus gattii WM276]
          Length = 497

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 68/268 (25%), Positives = 122/268 (45%), Gaps = 23/268 (8%)

Query: 18  NMRLDRWFKNHY-PHINFVNLQKILR------SGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           N RL R+ K+++ P+  FV  + I R      + + R D+    + + ++SG V R+  V
Sbjct: 17  NPRL-RYIKSYWWPYKTFVKQRWIGRQLLEVITTEFR-DRSMEYYRHALESG-VTRVNGV 73

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLY---EDSKIYVFNKPAGISVQGGSGIAY 127
           +   + I++    +D++V+  +       IL+     + +  V +KP  + V        
Sbjct: 74  VARPDLILRNGDRIDNTVHRHEPPVTNDPILILHIDREREFIVISKPGSLPVHAAGRYFK 133

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           H    L+      G K    +RLD+ TSG++++A +  AA  L   F   +++K Y + V
Sbjct: 134 HT--VLEMMESDYGLKCYSVNRLDRLTSGLMILALSGKAASKLAREFVEGKVKKEYVARV 191

Query: 188 WG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI--DCFAQKFCWLE 244
            G  P+ +       +     +G     V+   E  +  A++ F  I  D    +   + 
Sbjct: 192 KGKFPEEEVTVDKPMMTVDRQMG----LVIITPEGKSQDAVTIFNRIAYDPVRDQSV-VR 246

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 247 CRPQTGRTHQIRVHLQYLGYPIANDPLY 274


>gi|323453198|gb|EGB09070.1| hypothetical protein AURANDRAFT_53496 [Aureococcus anophagefferens]
          Length = 430

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 42/168 (25%), Positives = 74/168 (44%), Gaps = 17/168 (10%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D+++   +KP  + +      +YH +  L S +          HRLD+ TSG++++AR+ 
Sbjct: 173 DARVLAVDKPGTVPMHPCG--SYHYNA-LSSLLAEDFTPRSFVHRLDRLTSGLVLLARSA 229

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            AA  L +     R +K Y + V G              +++          + +E  + 
Sbjct: 230 EAATELCDCIGAGRARKTYVARVAG-----------RFPERAPAATRGPDAARPDEDASR 278

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              + F+++   A     +E  P TGRTHQ+R+H   +G PI  D  Y
Sbjct: 279 ---TRFRLLHRHADGTSTVECHPRTGRTHQIRLHLQWLGHPIANDPNY 323


>gi|315658673|ref|ZP_07911543.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           lugdunensis M23590]
 gi|315496304|gb|EFU84629.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           lugdunensis M23590]
          Length = 284

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 83/181 (45%), Gaps = 20/181 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQET 154
           ++YED  + +  KP   S+Q  +    H    L   V      +     P +  RLD+ T
Sbjct: 77  IVYEDDYLLIVCKP---SIQNCAPSREHPHESLIEQVIAYCHENDNDFTPHIVTRLDRNT 133

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++++A+      H+       +I K Y +L  G    + E I    + ++    D + 
Sbjct: 134 TGLVLLAK----HGHIHHLLSHIKINKRYIALCHG--ATQPEGIIEAPIARA---NDSI- 183

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +Q      YA S ++ ++   Q     E+  HTGRTHQ+RVH  ++G P++GD  Y  
Sbjct: 184 ITRQVSSTGKYAKSTYRTLNS-KQNVSLCEVTLHTGRTHQIRVHFQYIGHPLIGDALYGG 242

Query: 275 N 275
           N
Sbjct: 243 N 243


>gi|260809809|ref|XP_002599697.1| hypothetical protein BRAFLDRAFT_119379 [Branchiostoma floridae]
 gi|229284978|gb|EEN55709.1| hypothetical protein BRAFLDRAFT_119379 [Branchiostoma floridae]
          Length = 418

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 63/267 (23%), Positives = 101/267 (37%), Gaps = 60/267 (22%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILV 159
           ++Y+D  I   NK AG+ VQG +     I+  L     + +     +   LD   SGI++
Sbjct: 172 IVYDDGHIVAINKLAGLPVQGQTPEQLSINSLLPELGAALEASDLSIVKPLDWHLSGIVL 231

Query: 160 VART---RAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKECIA---NWLLKKSHIGGDY 212
           +ART   RA   ++T++ R R +  + YW +V G     ++C +   N    +   G + 
Sbjct: 232 LARTPEARAEVFNVTKAARQRDKFYRKYWGVVIGNLDPSEDCTSVKPNPSCSEKEGGSEL 291

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              ++  + GA        +   F                 QL+VH     C I+GDH Y
Sbjct: 292 SDEIQGPQSGAG-------ICPVFVD---------------QLQVHLTTKLCSILGDHVY 329

Query: 273 CANFKGNFTSPI------------------------------QNKLYLHARYMDLPHPEG 302
            +        P                               +  ++LH   M LP   G
Sbjct: 330 SSRVGSVAGMPALMEPTNVGPRTQRVPKDILKKMNLRAIQMHKVPVHLHCGEMLLPGYRG 389

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRN 329
             ++ITAPLP H + T   LG +   N
Sbjct: 390 RDVRITAPLPKHFLWTLQLLGLEDPTN 416


>gi|312600987|gb|ADQ90242.1| Ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyopneumoniae 168]
          Length = 281

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 68/281 (24%), Positives = 120/281 (42%), Gaps = 51/281 (18%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +++V  +N +   +L +  K      ++  +QK  R+       K++K NN  Q      
Sbjct: 2   IKFVATKN-QSGQKLIQLIKKILLKSDYNEIQKYFRT-------KKIKVNNTYQEK---- 49

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI--------LLYEDSKIYVFNKPAGIS 118
                   N+IIKE+ I+    +  K   F K +        ++Y+D  I + +KP  + 
Sbjct: 50  --------NYIIKEKDII-LIFSQEKLKTFSKKVPEFKLNLKIIYQDENILLVDKPQNLQ 100

Query: 119 VQGGSGIAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           V GG    +++D  L  W      +++  KP    RLD++TSGI++      +   L + 
Sbjct: 101 VHGG---KFNLD--LAVWNYLKIPENQVFKPSHIGRLDKKTSGIILYGLNYQSVVELNQ- 154

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + +  +KIY    +    N K  I   +  + +   ++   ++   K  N   +     
Sbjct: 155 -KQKFFEKIY---TFKSDINLKNTIKTDVFIRKN---NFQQKMEVTLKSPNSFFASTTFY 207

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               +KF  L    HTG+ HQ+RV   H+G PI GD KY  
Sbjct: 208 SKNQKKFAIL----HTGKKHQIRVSLSHLGFPIFGDEKYGG 244


>gi|294954492|ref|XP_002788195.1| RNA pseudouridylate synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239903410|gb|EER19991.1| RNA pseudouridylate synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 309

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 101/237 (42%), Gaps = 41/237 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLT-HRLDQETSGIL 158
           ++ E   +   +KP+G+ V  G G   + +   LK    S+      T HRLD+ TSGI+
Sbjct: 39  IVGETDDVVAVDKPSGMPVHSGGGHRVNCLSAILKEQDPSRFSLAIHTLHRLDRLTSGIV 98

Query: 159 VVARTRAAAQHLTESFRM--RRIQKIYWSLVWG-------IPKNKKEC----IANWLLKK 205
           ++ +    A+  +E+F+   + IQK Y + V G       + +    C    +  ++L  
Sbjct: 99  ILGKNPDVARAFSEAFKKHDQEIQKCYLARVKGKFEGSNVVVEGFMRCVDFRVGKFILVN 158

Query: 206 SHIG--------GDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQ-------- 246
           S+ G        GD        +  +  A+    + D ++Q      W + Q        
Sbjct: 159 SNKGTASEDANQGDAPTSTPSGDDKS--AVEEDHIEDKWSQTSFDKVWYDEQNDETIIKC 216

Query: 247 -PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            P TGRTHQ+RVH   +G PI  D  Y   +K +   P    L  HA   ++P  EG
Sbjct: 217 YPKTGRTHQIRVHLESIGHPIANDSCYGGEYKADH--PFAFPLAPHAN--NVPPKEG 269


>gi|289666985|ref|ZP_06488060.1| putative pseudouridylate synthase [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 296

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 54/204 (26%), Positives = 94/204 (46%), Gaps = 18/204 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y D+++ V  KP  + V   G+ +   +   L   +D+    P   HR+D+ET+G+++
Sbjct: 89  VVYADAQLVVACKPHFLPVAPAGAYVRETLLTRLVRRLDNPALVP--LHRIDRETAGLVL 146

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            +   A        FR RRI+K Y ++   +P+ +   +   LL+     G+    +++ 
Sbjct: 147 FSANPATRGIYQALFRQRRIRKHYLAVAPPLPQLRFPHVHRSLLEP----GEPFFRMREG 202

Query: 220 EKGANYAISHFKVIDCFAQKF-CWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC---A 274
               N       VI+  A+    W   ++P TGR HQLRVH   +G PI+ +  Y    A
Sbjct: 203 VGEPNSET----VIEVVARNADTWTYRLEPVTGRKHQLRVHMAALGAPILHERFYPELEA 258

Query: 275 NFKGNFTSPIQNKLYLHARYMDLP 298
               +   P+Q  L+ H    D P
Sbjct: 259 QRPDDPERPLQ--LFAHTLAFDDP 280


>gi|160899685|ref|YP_001565267.1| pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160365269|gb|ABX36882.1| pseudouridine synthase [Delftia acidovorans SPH-1]
          Length = 305

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 91/200 (45%), Gaps = 26/200 (13%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            ++ +L+ D+ + V +KP  + V   G  +   +   LK   D     P   HR+D++T+
Sbjct: 90  FEAEVLHRDAHLLVADKPHFLPVVPAGKYLQQTLLVRLKREFDLPELSP--IHRIDRDTA 147

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW----LLKKSHIG-- 209
           G++V +  RA        FR R I K Y            E +A W    +  ++H    
Sbjct: 148 GLVVFSVQRATRGIYQALFRDRAIHKTY------------EAVAPWREDVVFPRTHESRM 195

Query: 210 GDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +  H  + +E  G     +H +V++    ++    ++P +G+ HQLRVH   +G P+ G
Sbjct: 196 EESGHFFRMHEVAGTPNTRTHMQVLEQHG-RWARYRLEPESGKRHQLRVHMAALGLPLWG 254

Query: 269 DHKYCANF---KGNFTSPIQ 285
           D  Y       +G+++ P+Q
Sbjct: 255 DGFYPEVHDMPEGDYSRPLQ 274


>gi|148262340|ref|YP_001229046.1| pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146395840|gb|ABQ24473.1| pseudouridine synthase [Geobacter uraniireducens Rf4]
          Length = 293

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 95/210 (45%), Gaps = 19/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D +I V  KP  + V  GG  +   +   L+         P   HR+D+ET+G+++
Sbjct: 85  ILFLDDEILVACKPHFLPVTPGGRYVDECLLNRLRGSTGIADLAP--LHRIDRETAGLVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            +  + +     + F    I+K Y +L    P  +    A+W ++     G+    +K  
Sbjct: 143 FSVNKKSRGLYGKLFLNGLIEKTYQALSACQPLQE---TASWDIRNRIERGEPWFRMKTA 199

Query: 220 EKGANY--AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---A 274
             G N   AI+  +V    A+      +QP TG+THQLR+H   +G  I+ D  Y    A
Sbjct: 200 PGGVNARSAINLVEVKGGMAR----FTLQPRTGKTHQLRIHMSGLGFGILNDRYYPELQA 255

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             + NF +P+Q    L A+ +    P  GR
Sbjct: 256 ESEDNFDTPLQ----LVAQMLRFKDPLSGR 281


>gi|78049978|ref|YP_366153.1| putative pseudouridylate synthase [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|78038408|emb|CAJ26153.1| putative pseudouridylate synthase [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
          Length = 296

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 56/204 (27%), Positives = 95/204 (46%), Gaps = 18/204 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ D+++ V  KP  + V   G+ +   +   L   +D+    P   HR+D+ET+G+++
Sbjct: 89  VVHADAQLVVACKPHFLPVAPAGAYVRETLLTRLVRRLDNPALVP--LHRIDRETAGLVL 146

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            +   A        FR RRI+K Y ++   +P+ +   +   LL+    G  +  +    
Sbjct: 147 FSANPATRGIYQALFRQRRIRKHYLAVAPPLPQLRFPHVHRSLLEP---GEPFFRM---- 199

Query: 220 EKGANYAISHFKVIDCFAQKF-CWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC---A 274
            +G   A S   VI+  A+    W   ++P TGR HQLRVH   +G PI+ D  Y    A
Sbjct: 200 HEGVGEANSE-TVIEVVARNADTWTYRLEPVTGRKHQLRVHMAALGAPILHDRFYPELEA 258

Query: 275 NFKGNFTSPIQNKLYLHARYMDLP 298
               +   P+Q  L+ H    D P
Sbjct: 259 QRPDDPERPLQ--LFAHTLAFDDP 280


>gi|312376036|gb|EFR23246.1| hypothetical protein AND_13247 [Anopheles darlingi]
          Length = 327

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 54/207 (26%), Positives = 87/207 (42%), Gaps = 40/207 (19%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI------- 198
             HRLD  TSGIL +   + A + + + F  +R +K Y +L+ G     +E I       
Sbjct: 104 FAHRLDFATSGILCIPLNKNACKEVCQVFEEQRARKYYLALLRGHTDFDEEVIDIAIGKR 163

Query: 199 --------------ANWLLKKSHIGGDY--------VHVVKQNEKGAN--YAISHFKVID 234
                          N+ +  S  G D         +  + + E+  N   +I+   V+D
Sbjct: 164 SDGSSIGTCVPERLTNFTILSSVPGEDVRFKDTSKKMCTILEEERCQNPRRSITKVLVLD 223

Query: 235 ---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
                 +    + ++P TGR HQLR+H   +G  IVGD+ Y        TSP   +++LH
Sbjct: 224 RGYYNGKPVTKVLLRPITGRRHQLRLHCAQIGHVIVGDYTYSLKID---TSP--PRMFLH 278

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVK 317
           A  + LP+  E   +Q   P     +K
Sbjct: 279 AFRLVLPNTIENLDIQTDDPFTEKALK 305


>gi|238854907|ref|ZP_04645237.1| pseudouridine synthase, RluA family [Lactobacillus jensenii 269-3]
 gi|313472401|ref|ZP_07812893.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 1153]
 gi|238832697|gb|EEQ25004.1| pseudouridine synthase, RluA family [Lactobacillus jensenii 269-3]
 gi|239529732|gb|EEQ68733.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 1153]
          Length = 297

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 58/234 (24%), Positives = 102/234 (43%), Gaps = 29/234 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQE 153
           ++ E     V NKPA +       + G  +   + G+      S+    KP +  RLD++
Sbjct: 81  IVLETDNYLVINKPANVLSIPSRYEDGDAVVNRVMGYFSKKKSSEQAFLKPHIVTRLDRD 140

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSHIGGD 211
           TSG+++V +   A    +E  +     K Y ++V     P+ +   I   + K       
Sbjct: 141 TSGLVLVGKNAVAHSKFSE-LKKDVFVKEYHAIVHSNFNPEEQAGLIDAPIGKIDDSVKR 199

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           YV  +   +K    +++ ++V+   AQK     ++++  TGRTHQ+RVH  H+G P+ GD
Sbjct: 200 YV--IPNGQK----SLTQYEVL---AQKEGASLVKLRLFTGRTHQIRVHMAHIGHPLFGD 250

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHMVKTWDSL 322
             Y  +   NF      +  L+  ++  P P     +I     P  M   W +L
Sbjct: 251 KLYGID--DNFA-----RQALNCSHLSFPDPFTNEEKIVEVSDPQDMTDLWRNL 297


>gi|302550275|ref|ZP_07302617.1| ribosomal pseudouridine synthase [Streptomyces viridochromogenes
           DSM 40736]
 gi|302467893|gb|EFL30986.1| ribosomal pseudouridine synthase [Streptomyces viridochromogenes
           DSM 40736]
          Length = 317

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 52/172 (30%), Positives = 81/172 (47%), Gaps = 24/172 (13%)

Query: 144 PRLT--HRLDQETSGILVVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           P LT  HRLD+ T+G+++       R A Q L   FR RR++K Y ++    P +    +
Sbjct: 126 PALTAAHRLDRLTAGLVLFTVRLEDRGAYQTL---FRDRRVRKEYEAVA---PHDPGLAL 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL---EMQPHTGRTHQL 255
              +  +S I  +   +  +   G   A+S  ++++  A     L    + P TG+THQL
Sbjct: 180 PRTV--RSRIVKERGVLTAREVAGEPNAVSRIELVEHRAAGSGGLARYRLVPGTGQTHQL 237

Query: 256 RVHALHMGCPIVGDHKY----CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G PI+GD  Y         G+F  P+Q    L AR ++   P  G
Sbjct: 238 RVHMTALGVPILGDPLYPEVTAPVPAGDFRRPLQ----LLARTLEFTDPVTG 285


>gi|197120696|ref|YP_002132647.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196170545|gb|ACG71518.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 312

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 98/239 (41%), Gaps = 23/239 (9%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKP 144
              D   S+LL E  +  V  KPAG++V     +A    G L + V ++         +P
Sbjct: 71  PQPDAPLSVLL-ERPRYLVVEKPAGVAVHP---LAPGEGGTLANAVAARHPECAEASPEP 126

Query: 145 R---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           R      RLD ETSG ++ AR   A + L        + K+Y +L  G       C    
Sbjct: 127 REGGAVQRLDLETSGCVLFARDPEAWEALHAQLGAHTVDKVYLALAVGRLPAGGVCSVPL 186

Query: 202 LLKKSHI--GGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             +   +    D     +   +G     A +H++    FA     L ++  TG  HQ+R 
Sbjct: 187 AQRGGRVVPAPDLEAEERLQARGLRPRPAETHYEPERRFAD-HTLLRVRIVTGVMHQIRA 245

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           H   +G P+ GD  Y     G    P   + +LHA  +    P+G GR+ + +PLP  +
Sbjct: 246 HLALLGHPVAGDALYGGAAAG---LPGLERQFLHAWRLAFDDPDGAGRVAVESPLPPEL 301


>gi|282931619|ref|ZP_06337112.1| pseudouridine synthase YjbO [Lactobacillus jensenii 208-1]
 gi|281304230|gb|EFA96339.1| pseudouridine synthase YjbO [Lactobacillus jensenii 208-1]
          Length = 290

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 58/234 (24%), Positives = 102/234 (43%), Gaps = 29/234 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQE 153
           ++ E     V NKPA +       + G  +   + G+      S+    KP +  RLD++
Sbjct: 74  IVLETDNYLVINKPANVLSIPSRYEDGDAVVNRVMGYFSKKKSSEQAFLKPHIVTRLDRD 133

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSHIGGD 211
           TSG+++V +   A    +E  +     K Y ++V     P+ +   I   + K       
Sbjct: 134 TSGLVLVGKNAVAHSKFSE-LKKDVFVKEYHAIVHSNFNPEEQAGLIDAPIGKIDDSVKR 192

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           YV  +   +K    +++ ++V+   AQK     ++++  TGRTHQ+RVH  H+G P+ GD
Sbjct: 193 YV--IPNGQK----SLTQYEVL---AQKEGASLVKLRLFTGRTHQIRVHMAHIGHPLFGD 243

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHMVKTWDSL 322
             Y  +   NF      +  L+  ++  P P     +I     P  M   W +L
Sbjct: 244 KLYGID--DNFA-----RQALNCSHLSFPDPFTNEEKIVEVSDPQDMTDLWRNL 290


>gi|212636064|ref|YP_002312589.1| pseudouridine synthase [Shewanella piezotolerans WP3]
 gi|212557548|gb|ACJ30002.1| Pseudouridine synthase [Shewanella piezotolerans WP3]
          Length = 281

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 56/245 (22%), Positives = 113/245 (46%), Gaps = 38/245 (15%)

Query: 60  QSGQVVRIPPVINALN--HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           Q+ ++ R+  V++  +  H+   Q +LD SV          + LL+++ +  V+ KP G+
Sbjct: 50  QTNRLRRVKKVLSQGDELHLYYNQTVLDESVP--------NAELLFDEGQYSVWYKPFGM 101

Query: 118 SVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             QG     +  I+ F ++ ++   +   + HRLD   +G++V+  ++     + + F  
Sbjct: 102 RCQGSKWSDHTTINRFAETHLEP-ARSAYIIHRLDLAATGLIVLGHSKKTTAAIAKLFET 160

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K Y  +V G   + K  I   +  KS                   A+SH  +++  
Sbjct: 161 RALDKYYQVIVEGEFPDSKVTIDTDVDGKS-------------------ALSHAHLLEYN 201

Query: 237 AQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           A+     ++++  +GR HQ+R+H   +G P++GD  +     GN ++P    L L + Y+
Sbjct: 202 AELNQSKVQVKIESGRKHQIRLHMASVGHPVIGDRLHG---NGNESTP---NLQLTSCYL 255

Query: 296 DLPHP 300
           +   P
Sbjct: 256 NFICP 260


>gi|255066777|ref|ZP_05318632.1| RNA pseudouridine synthase [Neisseria sicca ATCC 29256]
 gi|255048852|gb|EET44316.1| RNA pseudouridine synthase [Neisseria sicca ATCC 29256]
          Length = 309

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/125 (23%), Positives = 64/125 (51%), Gaps = 6/125 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A  +     F+ + ++K Y ++       + + +    +    
Sbjct: 150 HRLDKDTAGVMLLSHNPATRRDYQTMFQEKSVRKTYHAVA----PTRTDLVYPLDVVSRM 205

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++++   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 206 VRGERFFTTQETEGEPN-AHTTVELLENRGE-FSLYRLTPHTGKKHQLRVHMMRLGMPLL 263

Query: 268 GDHKY 272
            D  Y
Sbjct: 264 NDALY 268


>gi|255319550|ref|ZP_05360764.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter
           radioresistens SK82]
 gi|262378429|ref|ZP_06071586.1| RNA pseudouridylate synthase [Acinetobacter radioresistens SH164]
 gi|255303490|gb|EET82693.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter
           radioresistens SK82]
 gi|262299714|gb|EEY87626.1| RNA pseudouridylate synthase [Acinetobacter radioresistens SH164]
          Length = 303

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 52/194 (26%), Positives = 88/194 (45%), Gaps = 22/194 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E  +  V +KP  +++   G  +   +   LK     +   P   HRLD+ET+G+++
Sbjct: 96  ILHETDEFLVVDKPHFLTMSPTGQYVQETLLVRLKKQTGIETLTP--IHRLDRETAGVVL 153

Query: 160 VAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            ++   TR   Q L   F  R+++K Y ++    P           L K    G+  + +
Sbjct: 154 FSKRPETRGLYQKL---FAERKVEKTYHAVAPFKPDLNFPINLKLRLDK----GEPFYTM 206

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +  E   N       +ID    +  W   +++P TG+ HQLRVH  H+G PI  D  Y  
Sbjct: 207 QIVEGEPNTET----LIDLLDVRAHWAKYQLKPRTGKQHQLRVHLNHLGIPIQNDSFYPI 262

Query: 275 ---NFKGNFTSPIQ 285
                  +FT+P+Q
Sbjct: 263 VQHKSDNDFTAPLQ 276


>gi|306823384|ref|ZP_07456759.1| possible pseudouridylate synthase [Bifidobacterium dentium ATCC
           27679]
 gi|309802642|ref|ZP_07696746.1| RNA pseudouridine synthase [Bifidobacterium dentium JCVIHMP022]
 gi|304553091|gb|EFM41003.1| possible pseudouridylate synthase [Bifidobacterium dentium ATCC
           27679]
 gi|308220706|gb|EFO77014.1| RNA pseudouridine synthase [Bifidobacterium dentium JCVIHMP022]
          Length = 264

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 98/231 (42%), Gaps = 45/231 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +LYED  I V +KP  ++     G+ Y     ++  +  +  +P +   HRLD+ T+G++
Sbjct: 37  VLYEDDGIIVIDKPHFLATTP-RGMWYRETALIR--LRERYGEPDIVPAHRLDRLTAGVV 93

Query: 159 VVART---RAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKS 206
           V  R    R A Q L   F+  R  K Y  L          +G            L+++S
Sbjct: 94  VFVRKPELRGAYQML---FQEHRTVKTYECLAPLAPVVRPRYGTVTRIDRNQPFPLVRRS 150

Query: 207 HIGGD-----------YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           HI  D            V+     E+G N  I    V+  +        + P TG+THQL
Sbjct: 151 HIAKDRGRLQAYEIPAAVNAESLIERGDNPHIIDGNVVINYV-------LHPKTGKTHQL 203

Query: 256 RVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G PI+GD  Y    +    +F+ P++    L AR ++   P  G
Sbjct: 204 RVHMNSLGLPILGDDFYPDVIQRPYDDFSRPLE----LVARRLEFDDPVTG 250


>gi|225456408|ref|XP_002280549.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 376

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 68/259 (26%), Positives = 106/259 (40%), Gaps = 42/259 (16%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR------IPPVINALNHIIKEQKI 83
           P+  +VN    ++SG+++VD + V  +  ++S Q +        PPV+            
Sbjct: 58  PYDYYVNA---VQSGRIQVDGEMVPVSYIVRSSQKISHFVHRHEPPVL-----------A 103

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQ 142
           LD SV L K  D L               KPA + V   G      + G L++     G 
Sbjct: 104 LDVSV-LQKEPDVL------------TICKPASVPVHPCGQYRKNTVVGILQA---EHGL 147

Query: 143 KPRLT-HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            P    HRLD+  SG+L++AR+ + A    +      +QK Y + V G+  + ++ +   
Sbjct: 148 APLFPIHRLDRLVSGLLILARSASKADSFRQQIEAGMVQKQYIAKVTGVFPDDEQVVNVN 207

Query: 202 LLKKSHIGGDYVHV---VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +   +  G   V V             A + F  I         L  +P TGRTHQ+RVH
Sbjct: 208 VNYNAREGRSTVEVGNCCGNTPLKGKSACTKFTRISTNGTHSIVL-CEPITGRTHQIRVH 266

Query: 259 ALHMGCPIVGDHKYCANFK 277
             + G PI  D  Y + F 
Sbjct: 267 LQYTGHPIANDMLYLSEFS 285


>gi|82540405|ref|XP_724523.1| RNA pseudouridylate synthase [Plasmodium yoelii yoelii str. 17XNL]
 gi|23479192|gb|EAA16088.1| RNA pseudouridylate synthase, putative [Plasmodium yoelii yoelii]
          Length = 1254

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/87 (29%), Positives = 45/87 (51%)

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           K I+ + ++F    ++ HTGRTHQ+RVH  H+G P+V D KY      N       +++L
Sbjct: 522 KDIETYTKEFTLCNVKIHTGRTHQIRVHMRHIGHPLVSDKKYLNTSLSNLDKFWCFRMFL 581

Query: 291 HARYMDLPHPEGGRLQITAPLPAHMVK 317
           H+  ++  +P+     +   +P    K
Sbjct: 582 HSIILEFNNPDYYFYNLNDDIPKKRTK 608



 Score = 45.8 bits (107), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 30/50 (60%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K KK
Sbjct: 165 LCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYILLCHGRIKKKK 214


>gi|325927184|ref|ZP_08188446.1| 23S RNA-specific pseudouridylate synthase [Xanthomonas perforans
           91-118]
 gi|325542445|gb|EGD13925.1| 23S RNA-specific pseudouridylate synthase [Xanthomonas perforans
           91-118]
          Length = 300

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 57/206 (27%), Positives = 93/206 (45%), Gaps = 22/206 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           +++ D+++ V  KP  + V      AY  +  L   V   D+    P   HR+D+ET+G+
Sbjct: 89  VVHADAQLVVACKPHFLPVAPAG--AYVRETLLTRLVRRLDNPALVP--LHRIDRETAGL 144

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ +   A        FR RRI+K Y ++   +P+ +   +   LL    + G+    + 
Sbjct: 145 VLFSANPATRGIYQALFRQRRIRKHYLAVAPPLPQLRFPHVHRSLL----VPGEPFFRMH 200

Query: 218 QNEKGANYAISHFKVIDCFAQKF-CWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-- 273
           +    AN       VI+  A+    W   ++P TGR HQLRVH   +G PI+ D  Y   
Sbjct: 201 EGVGEANSE----TVIEVVARNADTWTYRLEPVTGRKHQLRVHMAALGAPILHDRFYPEL 256

Query: 274 -ANFKGNFTSPIQNKLYLHARYMDLP 298
            A    +   P+Q  L+ H    D P
Sbjct: 257 EAQRPDDPERPLQ--LFAHTLAFDDP 280


>gi|302822493|ref|XP_002992904.1| hypothetical protein SELMODRAFT_136149 [Selaginella moellendorffii]
 gi|300139249|gb|EFJ05993.1| hypothetical protein SELMODRAFT_136149 [Selaginella moellendorffii]
          Length = 415

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 63/248 (25%), Positives = 101/248 (40%), Gaps = 28/248 (11%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           D+   I+  E+S + V NKPAG+SV G       I     +   +  Q    TH+LD  T
Sbjct: 126 DWRSRIIANEESFV-VLNKPAGVSVGGSVDNVEEICSTFATRALNLEQPLVTTHQLDNCT 184

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK-----------KECIAN-- 200
            G L++A+    A       +  +++K Y +L    +P  K              ++N  
Sbjct: 185 EGCLLLAKNNEFASRFHRFLKENKVEKFYLALAAAPVPLGKTAHYMRSDKYPPRIMSNNE 244

Query: 201 ---WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--FAQKFCW-LEMQPHTGRTHQ 254
              W L   H     V   KQ    +  A+S ++V  C     KF +   ++  TG THQ
Sbjct: 245 RLGWQLCVMH-----VLECKQVPWPSEAALSEYQVQPCGWTKSKFAYECRVKLLTGLTHQ 299

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
           LR     +G P++GD  Y         +P  +  +L  R  ++   E G ++ +      
Sbjct: 300 LRAQFSALGSPLIGDSLYMPAAAARLENPELDP-FLDTRKKEIADEEAG-IEKSPAESKQ 357

Query: 315 MVKTWDSL 322
           + K W SL
Sbjct: 358 LEKKWISL 365


>gi|313835228|gb|EFS72942.1| RNA pseudouridine synthase [Propionibacterium acnes HL037PA2]
 gi|314970851|gb|EFT14949.1| RNA pseudouridine synthase [Propionibacterium acnes HL037PA3]
          Length = 174

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 46/165 (27%), Positives = 72/165 (43%), Gaps = 13/165 (7%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIAN--W 201
           + HRLD+ T+G+L++ R R   +   E F  R + K Y  +   +  P  +   + N  W
Sbjct: 1   MAHRLDRVTAGVLLLTRERQWRRPYQELFERREVVKKYRLVAPAVHDPAGEGAVVTNNGW 60

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            ++ S I  +   +  +   G   A++   ++          E  P TGRTHQ+R+H   
Sbjct: 61  QVR-SRIVKERGILQAREVPGEPNAVTDIVLVSEHG-GLGLYEASPRTGRTHQIRLHMQR 118

Query: 262 MGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +G PIV D  Y         +FT P+Q    L A  M    P  G
Sbjct: 119 LGAPIVNDPFYPIVLGTQIDDFTHPLQ----LQAWQMGFTDPVSG 159


>gi|302796789|ref|XP_002980156.1| hypothetical protein SELMODRAFT_112010 [Selaginella moellendorffii]
 gi|300152383|gb|EFJ19026.1| hypothetical protein SELMODRAFT_112010 [Selaginella moellendorffii]
          Length = 415

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 63/248 (25%), Positives = 101/248 (40%), Gaps = 28/248 (11%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           D+   I+  E+S + V NKPAG+SV G       I     +   +  Q    TH+LD  T
Sbjct: 126 DWRSRIIANEESFV-VLNKPAGVSVGGSVDNVEEICSTFATRALNLEQPLVTTHQLDNCT 184

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK-----------KECIAN-- 200
            G L++A+    A       +  +++K Y +L    +P  K              ++N  
Sbjct: 185 EGCLLLAKNNEFASRFHRLLKENKVEKFYLALAAAPVPLGKTAHYMRSDKYPPRIMSNNE 244

Query: 201 ---WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--FAQKFCW-LEMQPHTGRTHQ 254
              W L   H     V   KQ    +  A+S ++V  C     KF +   ++  TG THQ
Sbjct: 245 RLGWQLCVMH-----VLECKQVPWPSEAALSEYQVQPCGWTKSKFAYECRVKLLTGLTHQ 299

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
           LR     +G P++GD  Y         +P  +  +L  R  ++   E G ++ +      
Sbjct: 300 LRAQFSALGSPLIGDSLYMPAAAARLENPELDP-FLDTRKKEIADEEAG-IEKSPAESKQ 357

Query: 315 MVKTWDSL 322
           + K W SL
Sbjct: 358 LEKKWISL 365


>gi|87121619|ref|ZP_01077507.1| RNA pseudouridine synthase family protein [Marinomonas sp. MED121]
 gi|86163151|gb|EAQ64428.1| RNA pseudouridine synthase family protein [Marinomonas sp. MED121]
          Length = 289

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 43/164 (26%), Positives = 76/164 (46%), Gaps = 24/164 (14%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---LTHRLDQETSGILVVARTRAA 166
           V+ KP G+  QG     +     +  W  +     R   + HRLD+  +G++++A T+AA
Sbjct: 92  VWYKPYGMLSQGSK---WSDHTTISRWAQTHLTPERPVFIVHRLDRAATGLIIIAHTKAA 148

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           A+ L+  F    ++K Y  +V G                +H   D   V+ Q   G + A
Sbjct: 149 ARALSGMFEQHALEKHYQIIVHG----------------NHSEHDQPEVITQEIDGKS-A 191

Query: 227 ISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            S F  ++   +     ++++  +GR HQ+R+HA  +G P+V D
Sbjct: 192 QSTFNCLEHAPSSNLSLIDVKIDSGRKHQIRLHAAGIGLPVVAD 235


>gi|68488860|ref|XP_711730.1| hypothetical protein CaO19.2788 [Candida albicans SC5314]
 gi|46433052|gb|EAK92508.1| hypothetical protein CaO19.2788 [Candida albicans SC5314]
          Length = 402

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 51/194 (26%), Positives = 91/194 (46%), Gaps = 31/194 (15%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLD 151
           H+D +KS+  YED +I V +KP+GI         Y+ +   +K  ++         HRLD
Sbjct: 103 HNDIIKSV--YEDDEILVVDKPSGIPTHPTGNYYYNSLSEIIKQQLNMDS--IWTCHRLD 158

Query: 152 QETSGILVVARTRAAAQHLTESFRMRR--IQKIYWSLVWG-IPK--NKKEC------IAN 200
           + TSG+LV+A+T+      ++  R  +   +K Y + V G  P+  ++  C      +  
Sbjct: 159 KVTSGVLVLAKTKNGGVRFSKLMRDSKQHTEKTYLARVSGKFPEGIHRYRCPIFAVNMNG 218

Query: 201 WLLKKS--HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +L+  +   +  D   + ++ +  A+   S  K +             P TG+ HQ+R+H
Sbjct: 219 YLMSGNMEELPTDSTTIFERIKYNASLDQSLVKCV-------------PITGKFHQIRIH 265

Query: 259 ALHMGCPIVGDHKY 272
             ++G PIV D  Y
Sbjct: 266 LRNLGFPIVNDSFY 279


>gi|283953926|ref|ZP_06371455.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
 gi|283794531|gb|EFC33271.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
          Length = 250

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 48/192 (25%), Positives = 88/192 (45%), Gaps = 30/192 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED KI   NKP     +            L+  +++K     L +RLD+ETSG++++
Sbjct: 59  IIFEDDKIIAINKPYSCVSED-----------LEKKINAK-----LLNRLDKETSGVILL 102

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +     +   E F+  R+ K Y +++ G+   + E        K+  G     + K ++
Sbjct: 103 CKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEIEVNEPIFTIKAKGGA----LSKVSK 158

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            G N +     ++     K    ++   TGRTHQ+RVH   +   +VGD KY        
Sbjct: 159 DGLNASSIITPIM--MQSKKTLAKIVIQTGRTHQIRVHTKFIKHGVVGDEKY-----AKI 211

Query: 281 TSPIQNKLYLHA 292
           +S   +++YLH+
Sbjct: 212 SS---DRMYLHS 220


>gi|224001856|ref|XP_002290600.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220974022|gb|EED92352.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 596

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 77/296 (26%), Positives = 113/296 (38%), Gaps = 87/296 (29%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-----------------SVQGG------ 122
           S   +T H D L++I  Y D  I V NKP+G+                  V GG      
Sbjct: 263 SKTKVTIH-DHLQTI--YFDKDIVVTNKPSGLLCVPGVNHYRSLLDLVYEVYGGGANPND 319

Query: 123 ---SGIAYHIDGFLKSWVDSKGQKPRL-THRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              S      D    + ++   QK  +  HRLD +TSGI+V ARTR A   L +SFR R 
Sbjct: 320 KGISTTQQTTDESATTTLEEPLQKDSMIAHRLDMDTSGIVVFARTRLAMSKLHKSFRERT 379

Query: 179 -IQKIYWSLV--------WGIPKNKKE------CIANWLLKKSHIGGDYVHV-------- 215
             +K Y +L+        W    N         C A      + +GG  +++        
Sbjct: 380 GTRKRYEALLVGWLDTATWASSANNSSNNNYLGCNAGDTTADTDLGGGEINLPLQRDHKH 439

Query: 216 -------VKQNEKGANYAI--------------------SHFKVID---CFAQKFCWLEM 245
                    ++E  A  A+                    + F+++            +E+
Sbjct: 440 PPFMRVSTPESEVEAAMAVRDLNHAGWKKLVAKRPKPSTTQFRILAHEVWMDHPITRVEL 499

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY--C--ANFKGNFTSPIQNKLYLHARYMDL 297
            P TGRTHQLRVH   +G PI+GD  Y  C  A+  G F   +  ++      M+L
Sbjct: 500 TPITGRTHQLRVHCAAIGHPILGDPAYGWCGEAHPNGGFCEEVMRQMSPTCAGMEL 555


>gi|226944123|ref|YP_002799196.1| RNA pseudouridine synthase family protein [Azotobacter vinelandii
           DJ]
 gi|226719050|gb|ACO78221.1| RNA pseudouridine synthase family protein [Azotobacter vinelandii
           DJ]
          Length = 301

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 46/176 (26%), Positives = 87/176 (49%), Gaps = 15/176 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +L+ D  + V +KP  + V   + +  +++  L + +  +   P L   HR+D+ T+G++
Sbjct: 87  VLHADDHLVVADKPHFLPV---APVGEYVEQTLLARLVRRLGNPDLVPLHRIDRLTAGLV 143

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGGDYVHVVK 217
           + +   A+       FR RRI+K+Y ++   +P      ++  LL++S  + G+   +++
Sbjct: 144 LFSCNPASRGRYQALFRERRIRKVYAAIAPALPG-----LSFPLLRRSRLVKGEPFFLMR 198

Query: 218 QNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + E   N   S  +V     +   W   + P TG+THQLRVH   +G  I  D  Y
Sbjct: 199 EAEGEPN---SETRVEPGERRGELWRYVLHPVTGKTHQLRVHMATLGAGICNDPLY 251


>gi|289551172|ref|YP_003472076.1| Putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus lugdunensis HKU09-01]
 gi|289180704|gb|ADC87949.1| Putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus lugdunensis HKU09-01]
          Length = 284

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 83/181 (45%), Gaps = 20/181 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQET 154
           ++YED  + +  KP   S+Q  +    H    L   V      +     P +  RLD+ T
Sbjct: 77  IVYEDDYLLIVCKP---SLQNCAPSREHPHESLIEQVLAYCHENDNDFTPHIVTRLDRNT 133

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G++++A+      H+       +I K Y +L  G    + E I    + ++    D + 
Sbjct: 134 TGLVLLAK----HGHIHHLLSHIKINKRYIALCHG--ATQPEGIIEAPIARA---NDSI- 183

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + +Q      YA S ++ ++   Q     E+  HTGRTHQ+RVH  ++G P++GD  Y  
Sbjct: 184 ITRQVSSTGKYAKSTYRTLNS-KQNVSLCEVTLHTGRTHQIRVHFQYIGHPLIGDALYGG 242

Query: 275 N 275
           N
Sbjct: 243 N 243


>gi|19173607|ref|NP_597410.1| similarity to HYPOTHETICAL PROTEIN OF THE FAMILY OF PSEUDOURIDINE
           SYNTHASES YD36_YEAST [Encephalitozoon cuniculi GB-M1]
 gi|19170813|emb|CAD26587.1| similarity to HYPOTHETICAL PROTEIN OF THE FAMILY OF PSEUDOURIDINE
           SYNTHASES YD36_YEAST [Encephalitozoon cuniculi GB-M1]
          Length = 318

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 55/199 (27%), Positives = 88/199 (44%), Gaps = 34/199 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSG 156
           ++ E+    V NKP GI          H  G  + +  +K     +K    +RLD   SG
Sbjct: 85  VIKEEGDYIVVNKPPGIPC--------HPTGGYREYCVTKALFGDEKVACINRLDMPVSG 136

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG---GDYV 213
           +L++A  R  ++ L     +R  +KIY + V+G+  +K +           IG   G Y 
Sbjct: 137 VLILA-VRNHSKCLEA---IRDAKKIYVAKVYGMFPDKVDV-------DKRIGCTEGRYR 185

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           HV      G    ++ F+ ++ +   +  +E +P TGRTHQ+R+H   +G PI  D  Y 
Sbjct: 186 HV----NAGGKACLTLFRRLE-YRDGYSLVECRPVTGRTHQIRIHLQSIGFPIANDIMY- 239

Query: 274 ANFKGNFTSPIQNKLYLHA 292
               G    P QN    +A
Sbjct: 240 --GDGEAPPPPQNDGVCNA 256


>gi|297734463|emb|CBI15710.3| unnamed protein product [Vitis vinifera]
          Length = 374

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 70/258 (27%), Positives = 109/258 (42%), Gaps = 42/258 (16%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR------IPPVINALNHIIKEQKI 83
           P+  +VN    ++SG+++VD + V  +  ++S Q +        PPV+            
Sbjct: 58  PYDYYVNA---VQSGRIQVDGEMVPVSYIVRSSQKISHFVHRHEPPVL-----------A 103

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQ 142
           LD SV L K  D L               KPA + V   G      + G L++     G 
Sbjct: 104 LDVSV-LQKEPDVL------------TICKPASVPVHPCGQYRKNTVVGILQA---EHGL 147

Query: 143 KPRLT-HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            P    HRLD+  SG+L++AR+ + A    +      +QK Y + V G+  + ++ +   
Sbjct: 148 APLFPIHRLDRLVSGLLILARSASKADSFRQQIEAGMVQKQYIAKVTGVFPDDEQVVNVN 207

Query: 202 LLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +   +  G   V     N   KG + A + F  I         L  +P TGRTHQ+RVH 
Sbjct: 208 VNYNAREGRSTVGNCCGNTPLKGKS-ACTKFTRISTNGTHSIVL-CEPITGRTHQIRVHL 265

Query: 260 LHMGCPIVGDHKYCANFK 277
            + G PI  D  Y + F 
Sbjct: 266 QYTGHPIANDMLYLSEFS 283


>gi|291299500|ref|YP_003510778.1| pseudouridine synthase [Stackebrandtia nassauensis DSM 44728]
 gi|290568720|gb|ADD41685.1| pseudouridine synthase [Stackebrandtia nassauensis DSM 44728]
          Length = 254

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 52/194 (26%), Positives = 76/194 (39%), Gaps = 30/194 (15%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L ++ ++   NKP GISV G        D  +       G K    HR+D+ TSG+++ A
Sbjct: 15  LVDNDQVLALNKPTGISVMG-----ERHDTDVARLAAEAGDKLHPVHRIDKATSGLVLFA 69

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG--DYVHVVKQN 219
           R       LT  F  R + K Y ++V     N  E  A   +      G  + V V    
Sbjct: 70  RDLKCHGVLTRQFNKRTVDKTYLAVV-----NSAEVPAAARIDLPLSVGRKNRVRVAAPR 124

Query: 220 E----KGANYAI------SHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALH 261
           E     G ++ +      +H K      +            L ++P +GR HQ+RVH   
Sbjct: 125 EAITNTGTDWTVPETDVFTHVKTYPSVTEYDTLWTGDGLSLLAVRPISGRRHQIRVHLAW 184

Query: 262 MGCPIVGDHKYCAN 275
            G  I GD  Y  N
Sbjct: 185 TGFAITGDSLYDKN 198


>gi|220911522|ref|YP_002486831.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
 gi|219858400|gb|ACL38742.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
          Length = 326

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 52/210 (24%), Positives = 90/210 (42%), Gaps = 30/210 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D  + V +KP  + +  GG+ I       L++ +D     P   HRLD+ T+G+L+
Sbjct: 90  ILHQDEHLLVVDKPHFLPTTPGGTYIQESALVRLRNQLDLPDLIP--MHRLDRMTAGVLL 147

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV- 215
            +   +TR   Q L   F  R++QK Y  +    P      +   ++ ++ +     ++ 
Sbjct: 148 FSTNPQTRGKYQVL---FEKRQVQKEYECVSAADPAPGHPAVEFPVVVRNRMTKSRSYLL 204

Query: 216 --VKQNEKGANYAISHFKVIDCFAQ---------------KFCWLEMQPHTGRTHQLRVH 258
             V + E  A   I   +  D  A                +     ++PHTG+THQLRVH
Sbjct: 205 AEVVEGEPNAETRIERLETFDGGASPDTNGSTAAVPGSPTRLARYRLEPHTGKTHQLRVH 264

Query: 259 ALHMGCPIVGDHKY---CANFKGNFTSPIQ 285
              +G  IV D  Y         ++  P+Q
Sbjct: 265 MASLGLGIVNDAFYPDLLDKAPDDYAKPLQ 294


>gi|328868208|gb|EGG16588.1| pseudouridine synthase family protein [Dictyostelium fasciculatum]
          Length = 558

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/126 (30%), Positives = 67/126 (53%), Gaps = 6/126 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L++A++  +AQ ++ +     + K Y +LV G   N +  +   L  ++H
Sbjct: 296 HRLDRLTSGLLILAKSTESAQKMSGAIMKGEVSKRYVALVKGKFSNDEVVVDQPLKVQNH 355

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             G  +++V  + K +      F ++   A+     +   P TGRTHQ+R+H   +G PI
Sbjct: 356 RLG--LNMVAPDGKPSTTV---FNIVSYDAETDTSVVCATPKTGRTHQIRLHLQWLGHPI 410

Query: 267 VGDHKY 272
           + D  Y
Sbjct: 411 LNDPLY 416


>gi|23272995|gb|AAH38081.1| Rpusd3 protein [Mus musculus]
          Length = 331

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/198 (23%), Positives = 87/198 (43%), Gaps = 12/198 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR 145
           + L + +  L++ ++ +   +   NKP G+ V G  G      +   L   +  + Q+ +
Sbjct: 50  LGLEELAHVLRAAVVDQKGPLVTLNKPQGLPVTGRPGELTLLSVLPQLSQALGLEHQELQ 109

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANW 201
           +     +E SG+++++     A  L + F    R +R    Y ++  GIP+  +  +   
Sbjct: 110 VVRAPGKEASGLVLLSSCPQTASRLQKFFIHSRRAQRPTATYCAVTDGIPEPSEGTVCMP 169

Query: 202 LLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           L  +     D    V     K  ++G    +S F V+    +    +++QP T   +QL+
Sbjct: 170 LKMEQMNDVDLAVPVMSPSRKDIQEGVKRTLSRFHVM-ATGRGCALVQLQPLTVFPNQLQ 228

Query: 257 VHALHMGCPIVGDHKYCA 274
           VH     CPI+GDH Y A
Sbjct: 229 VHMALQLCPILGDHTYAA 246


>gi|226724697|sp|Q0E0Y3|PUS7_ORYSJ RecName: Full=RNA pseudourine synthase 7; AltName: Full=RNA
           pseudouridylate synthase 7; AltName: Full=RNA-uridine
           isomerase 7
 gi|222622934|gb|EEE57066.1| hypothetical protein OsJ_06883 [Oryza sativa Japonica Group]
          Length = 393

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/238 (23%), Positives = 100/238 (42%), Gaps = 30/238 (12%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK--EQKILDSSVNLTKHSDFLK 98
           ++ G+++VD + V  +  +QS Q          ++H +   E  +L   + +        
Sbjct: 71  VKCGRLQVDDQMVHADYVVQSSQ---------KISHFLHRHEPPVLGGDITI-------- 113

Query: 99  SILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRL-THRLDQETSG 156
              L  ++ +    KPA + V   G      + G L++     G  P    HRLD+  SG
Sbjct: 114 ---LQNEADVVTVCKPASVPVHPCGQYRKNTVVGILQA---EHGLVPLFPVHRLDRLVSG 167

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A+    A+   +      +QK Y + V G+  + ++ +   +   +  G     V 
Sbjct: 168 LLIFAKNADKAESFRQQIEASLLQKEYVAKVVGVFPDGEQTVNANVHFNAREGRSTAEVC 227

Query: 217 KQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             + K      A + F+ I C       +  +P TGRTHQ+RVH  H+G PI  D  Y
Sbjct: 228 DGDGKAPIGKQACTKFQRI-CTDGIHSIVLCKPVTGRTHQIRVHLKHIGYPIANDEVY 284


>gi|312139708|ref|YP_004007044.1| tRNA-pseudouridine synthase i [Rhodococcus equi 103S]
 gi|311889047|emb|CBH48360.1| tRNA-pseudouridine synthase I [Rhodococcus equi 103S]
          Length = 288

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 43/159 (27%), Positives = 73/159 (45%), Gaps = 13/159 (8%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ T+G+L+        +   E F  RR++K+Y ++        +  I      +S 
Sbjct: 127 HRLDRMTAGVLLCTADPRLRRPYQEMFERRRVRKVYEAIA-----PYRGDIEFPRTVRSR 181

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           I   +  +    E G   + +  ++++          + P TGRTHQLR+H   +G PIV
Sbjct: 182 IVKVHGELTAYEEAGEPNSETLIELVERRGD-LARYRLHPRTGRTHQLRLHLNAIGAPIV 240

Query: 268 GDHKYCA---NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           GD+ Y       + +FT P++    L AR ++   P  G
Sbjct: 241 GDNFYPQFRRRDRDDFTVPLR----LLARSLEFDDPVTG 275


>gi|218190831|gb|EEC73258.1| hypothetical protein OsI_07380 [Oryza sativa Indica Group]
          Length = 393

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/238 (23%), Positives = 100/238 (42%), Gaps = 30/238 (12%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK--EQKILDSSVNLTKHSDFLK 98
           ++ G+++VD + V  +  +QS Q          ++H +   E  +L   + +        
Sbjct: 71  VKCGRLQVDDQMVHADYVVQSSQ---------KISHFLHRHEPPVLGGDITI-------- 113

Query: 99  SILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRL-THRLDQETSG 156
              L  ++ +    KPA + V   G      + G L++     G  P    HRLD+  SG
Sbjct: 114 ---LQNEADVVTVCKPASVPVHPCGQYRKNTVVGILQA---EHGLVPLFPVHRLDRLVSG 167

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A+    A+   +      +QK Y + V G+  + ++ +   +   +  G     V 
Sbjct: 168 LLIFAKNADKAESFRQQIEASLLQKEYVAKVVGVFPDGEQTVNANVHFNAREGRSTAEVC 227

Query: 217 KQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             + K      A + F+ I C       +  +P TGRTHQ+RVH  H+G PI  D  Y
Sbjct: 228 DGDGKAPIGKQACTKFQRI-CTDGIHSIVLCKPVTGRTHQIRVHLKHIGYPIANDEVY 284


>gi|281354950|ref|ZP_06241444.1| pseudouridine synthase [Victivallis vadensis ATCC BAA-548]
 gi|281317830|gb|EFB01850.1| pseudouridine synthase [Victivallis vadensis ATCC BAA-548]
          Length = 321

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 67/281 (23%), Positives = 123/281 (43%), Gaps = 32/281 (11%)

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
           ++ +RI +G+++    + +    +    +I     ++ +    L   + YED  + V +K
Sbjct: 43  EWRDRIAAGEIMLNGELSDPERRLELHDRIEYFPADIAEPEADLDYRIAYEDDALLVVDK 102

Query: 114 PAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE- 172
           P  + V        H    L   + SK  K  L +RLD+ETSG+LV A+   AA  L + 
Sbjct: 103 PGNLCVHPSGPFFKHT---LWHLLSSKYGKIHLVNRLDRETSGLLVAAKNPKAAAKLGKP 159

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKEC-------IANWLLKKSHIGGDYVHVVKQNEKGANY 225
            + MR   K Y +LV+G   ++ E        +A+ + KK      +V   +  E     
Sbjct: 160 GWPMR---KEYLALVFGNFADRIEAYGFLVPDLASVVRKKRR----FVAGERPPEGAVRP 212

Query: 226 AISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKG 278
             +   ++     +++  +   P TGR HQ+R     +G P++GD  Y  +       + 
Sbjct: 213 ESARTVLLPARSGERYSLVRALPETGRLHQIRATLFSLGFPLLGDKLYGPDDGIFLKIRS 272

Query: 279 N-FTSPIQNKLY-----LHARYMDLPHPEGGR-LQITAPLP 312
           N  T+  + +L      LH+  +   HP+ G  + + +PLP
Sbjct: 273 NAITAADRERLILLRQALHSAKLAFRHPDTGETVAVESPLP 313


>gi|119025492|ref|YP_909337.1| pseudouridine synthase [Bifidobacterium adolescentis ATCC 15703]
 gi|118765076|dbj|BAF39255.1| pseudouridine synthase [Bifidobacterium adolescentis ATCC 15703]
          Length = 228

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/220 (25%), Positives = 93/220 (42%), Gaps = 25/220 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGILV 159
           +YED  I V +KP  ++     G+ Y     ++  +  +  +P +T  HRLD+ T+G++V
Sbjct: 1   MYEDENIIVIDKPHFLATTP-RGMWYRETALVR--LCERYDEPNITPAHRLDRLTAGVVV 57

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC---------IANWLLKKSHIGG 210
             R  +A       F+ R+  K Y  L    P  +            +   L+++SHI  
Sbjct: 58  FVRNPSARGAYQMLFQNRKTVKTYECLAPLAPTQRPRYGTAVRIDRHLPFPLVRRSHINK 117

Query: 211 DYVHV---VKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           D   +      +   A   I     I   A + +    + P TG+THQLRVH   +G  I
Sbjct: 118 DRGRLQAYESADVPNAETLIERGSGIRFVAGRPYVNYTLHPKTGKTHQLRVHMNSLGLAI 177

Query: 267 VGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +GD  Y         +F+ P++    L AR +    P  G
Sbjct: 178 LGDDFYPDIVQRAYDDFSQPLE----LVARELRFDDPLNG 213


>gi|307171499|gb|EFN63340.1| RNA pseudouridylate synthase domain-containing protein 1
           [Camponotus floridanus]
          Length = 246

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 71/165 (43%), Gaps = 35/165 (21%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD  TSGI+ +A  + AA+  + +F  +++QK Y +LV G  +     I       
Sbjct: 97  FVHRLDYPTSGIMCIALNKKAARAASFAFENQKVQKFYLALVHGHIREPHVII------N 150

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------------------LEMQP 247
             IG D        EK  N+ +     + C   +  +                  + + P
Sbjct: 151 KPIGDDI------REKNGNHKMCTNDSVFCEKPRNSYTVLMVLEHGFWKNKPATKILLAP 204

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            TGR HQLRVH  ++G  ++GD+ Y     G    P  ++ YLH+
Sbjct: 205 GTGRRHQLRVHCHYIGHTVIGDYTYS---DGKDIQP--HRTYLHS 244


>gi|239636478|ref|ZP_04677480.1| pseudouridylate synthase, 23S RNA-specific [Staphylococcus warneri
           L37603]
 gi|239597833|gb|EEQ80328.1| pseudouridylate synthase, 23S RNA-specific [Staphylococcus warneri
           L37603]
          Length = 284

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 86/185 (46%), Gaps = 23/185 (12%)

Query: 96  FLKSI-LLYEDSKIYVFNKP-----AGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLT 147
           +LK + +L+ED  I + +KP     A         +   + G+L      KG+   P + 
Sbjct: 71  YLKPLDILFEDDYIIIVSKPNRQNCAPSCEHPHESLVEQVLGYLLH----KGEHTNPHIV 126

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
            RLD+ T+GI++ A+      HL   F   ++ K+Y  L  GI +      A     ++ 
Sbjct: 127 TRLDRNTTGIVLFAK-YGYIHHL---FSKTKMDKVYTCLAHGITEPSGVIEAPIARNEAS 182

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           I      + +Q  +   YA + ++ I       C  E+Q  TGRTHQ+RVH  ++G P++
Sbjct: 183 I------IERQVSENGKYAKTLYRTIKQKENVSCC-EVQLCTGRTHQIRVHFQYIGHPLI 235

Query: 268 GDHKY 272
           GD  Y
Sbjct: 236 GDTLY 240


>gi|171741038|ref|ZP_02916845.1| hypothetical protein BIFDEN_00104 [Bifidobacterium dentium ATCC
           27678]
 gi|283455575|ref|YP_003360139.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           dentium Bd1]
 gi|171276652|gb|EDT44313.1| hypothetical protein BIFDEN_00104 [Bifidobacterium dentium ATCC
           27678]
 gi|283102209|gb|ADB09315.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           dentium Bd1]
          Length = 264

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 98/231 (42%), Gaps = 45/231 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +LYED  I V +KP  ++     G+ Y     ++  +  +  +P +   HRLD+ T+G++
Sbjct: 37  VLYEDDGIIVIDKPHFLATTP-RGMWYRETALIR--LRERYGEPDIVPAHRLDRLTAGVV 93

Query: 159 VVART---RAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKS 206
           V  R    R A Q L   F+  R  K Y  L          +G            L+++S
Sbjct: 94  VFVRKPELRGAYQML---FQEHRTVKTYECLAPLAPVVRPRYGTVTRIDRNQPFPLVRRS 150

Query: 207 HIGGD-----------YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           HI  D            V+     E+G N  I    V+  +        + P TG+THQL
Sbjct: 151 HIAKDRGRLQAYEIPAAVNAESLIERGDNPRIIDGNVVINYV-------LHPKTGKTHQL 203

Query: 256 RVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G PI+GD  Y    +    +F+ P++    L AR ++   P  G
Sbjct: 204 RVHMNSLGLPILGDVFYPDVIQRPYDDFSRPLE----LVARRLEFDDPVTG 250


>gi|226494518|ref|NP_001028376.1| RNA pseudouridylate synthase domain-containing protein 3 [Mus
           musculus]
 gi|123796151|sp|Q14AI6|RUSD3_MOUSE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 3
 gi|109732980|gb|AAI16828.1| RNA pseudouridylate synthase domain containing 3 [Mus musculus]
 gi|109733482|gb|AAI16826.1| RNA pseudouridylate synthase domain containing 3 [Mus musculus]
          Length = 344

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/198 (23%), Positives = 87/198 (43%), Gaps = 12/198 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR 145
           + L + +  L++ ++ +   +   NKP G+ V G  G      +   L   +  + Q+ +
Sbjct: 63  LGLEELAHVLRAAVVDQKGPLVTLNKPQGLPVTGRPGELTLLSVLPQLSQALGLEHQELQ 122

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANW 201
           +     +E SG+++++     A  L + F    R +R    Y ++  GIP+  +  +   
Sbjct: 123 VVRAPGKEASGLVLLSSCPQTASRLQKFFIHSRRAQRPTATYCAVTDGIPEPSEGTVCMP 182

Query: 202 LLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           L  +     D    V     K  ++G    +S F V+    +    +++QP T   +QL+
Sbjct: 183 LKMEQMNDVDLAVPVMSPSRKDIQEGVKRTLSRFHVM-ATGRGCALVQLQPLTVFPNQLQ 241

Query: 257 VHALHMGCPIVGDHKYCA 274
           VH     CPI+GDH Y A
Sbjct: 242 VHMALQLCPILGDHTYAA 259


>gi|261331318|emb|CBH14308.1| RNA pseudouridylate synthase protein, putative [Trypanosoma brucei
            gambiense DAL972]
          Length = 1279

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 53/193 (27%), Positives = 88/193 (45%), Gaps = 36/193 (18%)

Query: 112  NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR------LTHRLDQETSGILVVARTRA 165
            +KPAG+S     G  + +D FL   +  KG          L +R+D  TSG+++VA T A
Sbjct: 1003 DKPAGMSTTLHVGHPHLLD-FLAGNLPWKGPSAPVLFQHGLVNRIDLGTSGLVLVADTEA 1061

Query: 166  AAQHLTESFRMRR-IQKIYWSLVWGIPK-----NKKECIANWLLKKSHI--------GGD 211
            + +    +  + R ++K+Y +LV   P      +  EC   W L    I        G D
Sbjct: 1062 SLEEARRASIVERCVEKVYRALVLHCPPPISRIDTSEC---WYLNPCGIIMCDVLANGAD 1118

Query: 212  Y---VHVVKQNEKGA--------NYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHA 259
            +   +     ++ GA          A + ++V+  F +    +LE+  HTGR HQ+R H 
Sbjct: 1119 FSLQIAAYNSSKGGALPVGAMDRRSATTTYRVLQYFPRSGVYYLEIHLHTGRRHQIRQHF 1178

Query: 260  LHMGCPIVGDHKY 272
              +  P++GD +Y
Sbjct: 1179 ARLCHPLLGDGRY 1191


>gi|71744882|ref|XP_827071.1| RNA pseudouridylate synthase protein [Trypanosoma brucei TREU927]
 gi|70831236|gb|EAN76741.1| RNA pseudouridylate synthase protein, putative [Trypanosoma brucei]
          Length = 1279

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 53/193 (27%), Positives = 88/193 (45%), Gaps = 36/193 (18%)

Query: 112  NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR------LTHRLDQETSGILVVARTRA 165
            +KPAG+S     G  + +D FL   +  KG          L +R+D  TSG+++VA T A
Sbjct: 1003 DKPAGMSTTLHVGHPHLLD-FLAGNLPWKGPSAPVLFQHGLVNRIDLGTSGLVLVADTEA 1061

Query: 166  AAQHLTESFRMRR-IQKIYWSLVWGIPK-----NKKECIANWLLKKSHI--------GGD 211
            + +    +  + R ++K+Y +LV   P      +  EC   W L    I        G D
Sbjct: 1062 SLEEARRASIVERCVEKVYRALVLHCPPPISRIDTSEC---WYLNPCGIIMCDVLANGAD 1118

Query: 212  Y---VHVVKQNEKGA--------NYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHA 259
            +   +     ++ GA          A + ++V+  F +    +LE+  HTGR HQ+R H 
Sbjct: 1119 FSLQIAAYNSSKGGALPVGAMDRRSATTTYRVLQYFPRSGVYYLEIHLHTGRRHQIRQHF 1178

Query: 260  LHMGCPIVGDHKY 272
              +  P++GD +Y
Sbjct: 1179 ARLCHPLLGDGRY 1191


>gi|297579243|ref|ZP_06941171.1| pseudouridine synthase Rlu family protein [Vibrio cholerae RC385]
 gi|297536837|gb|EFH75670.1| pseudouridine synthase Rlu family protein [Vibrio cholerae RC385]
          Length = 235

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/131 (35%), Positives = 68/131 (51%), Gaps = 15/131 (11%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR  AAA  L++ F  R+++K Y ++    PK K+  I       
Sbjct: 46  LVHRLDKMTSGILLLARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLIC------ 99

Query: 206 SHIGGDYVHVVKQNEK----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
               GD     + + K     +N A++ F        +  +L  +PHTG+THQ+RV    
Sbjct: 100 ----GDMERSRRSSWKLLNSQSNPAVTQFFSATAAPGERLFL-CKPHTGKTHQIRVALKS 154

Query: 262 MGCPIVGDHKY 272
           +G  IVGD  Y
Sbjct: 155 IGSAIVGDPIY 165


>gi|294952723|ref|XP_002787432.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Perkinsus marinus ATCC 50983]
 gi|239902404|gb|EER19228.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Perkinsus marinus ATCC 50983]
          Length = 602

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/170 (26%), Positives = 75/170 (44%), Gaps = 18/170 (10%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN----KKECIAN 200
           RL ++LD  TSG LV+   + A +  +  F+ R  +K+Y ++  G   +    K   I  
Sbjct: 373 RLANQLDFATSGALVLTLNKTADRETSALFQFRLTKKVYIAVCEGWVGDDELMKPRIITT 432

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +   S  GG     +         +  H    D     +    ++  TGR HQLR+H  
Sbjct: 433 GI--SSEGGGKMSSTI-----AVPVSTGHLLCDDIKCTVYI---LRLLTGRRHQLRLHLS 482

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE----GGRLQ 306
           ++G PI+GD+ Y  +       P   ++ LHA  + LP  +    GG+L+
Sbjct: 483 YIGHPILGDYTYSTHLPKGGRGPTLPRMLLHAWRLTLPFGDLLHCGGKLR 532


>gi|148667049|gb|EDK99465.1| mCG132976, isoform CRA_e [Mus musculus]
          Length = 331

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/198 (23%), Positives = 87/198 (43%), Gaps = 12/198 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR 145
           + L + +  L++ ++ +   +   NKP G+ V G  G      +   L   +  + Q+ +
Sbjct: 50  LGLEELAHVLRAAVVDQKGPLVTLNKPQGLPVTGRPGELTLLSVLPQLSQALGLEHQELQ 109

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANW 201
           +     +E SG+++++     A  L + F    R +R    Y ++  GIP+  +  +   
Sbjct: 110 VVRAPGKEASGLVLLSSCPQTASRLQKFFIHSRRAQRPTATYCAVTDGIPEPSEGTVCMP 169

Query: 202 LLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           L  +     D    V     K  ++G    +S F V+    +    +++QP T   +QL+
Sbjct: 170 LKMEQMNDVDLAVPVMSPSRKDIQEGVKRTLSRFHVM-ATGRGCALVQLQPLTVFPNQLQ 228

Query: 257 VHALHMGCPIVGDHKYCA 274
           VH     CPI+GDH Y A
Sbjct: 229 VHMALQLCPILGDHTYAA 246


>gi|153824295|ref|ZP_01976962.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
 gi|126518181|gb|EAZ75406.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
          Length = 95

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/75 (40%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPE 301
           ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP 
Sbjct: 11  VQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVHPA 70

Query: 302 G-GRLQITAPLPAHM 315
              +L+I APL AH+
Sbjct: 71  SEKKLEIHAPLEAHL 85


>gi|149910060|ref|ZP_01898708.1| putative pseudouridylate synthase [Moritella sp. PE36]
 gi|149806928|gb|EDM66889.1| putative pseudouridylate synthase [Moritella sp. PE36]
          Length = 315

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 48/182 (26%), Positives = 85/182 (46%), Gaps = 16/182 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  I V  KP  ++V   G  +   +   L+  + +  +     HRLD+ T+G+++
Sbjct: 87  VIYEDDNIMVAYKPHFLAVSPSGQFVNECLVNRLR--IKTGIETLVTAHRLDRATAGLML 144

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHIGGDY 212
           +++         + F+   I K Y ++    P+        +     +W +K   + G+ 
Sbjct: 145 LSKHPEQRHLYHDLFKYANITKHYQAIARLTPELYQQHQQGELALPLHWTVKNRIVKGEP 204

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              +K  +  AN   SH + I+  A K  F    + P TG+THQLR+H L +G P+V D 
Sbjct: 205 SFTMKIADGEAN---SHSE-IELIAVKGEFGLFRLSPITGKTHQLRLHMLSLGLPLVNDR 260

Query: 271 KY 272
            Y
Sbjct: 261 LY 262


>gi|124506149|ref|XP_001351672.1| RNA pseudouridylate synthase, putative [Plasmodium falciparum 3D7]
 gi|74862473|sp|Q8I3Z1|MLRR1_PLAF7 RecName: Full=MATH and LRR domain-containing protein PFE0570w
 gi|23504600|emb|CAD51479.1| RNA pseudouridylate synthase, putative [Plasmodium falciparum 3D7]
          Length = 10061

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 45/80 (56%)

Query: 222  GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
              +Y ++  K I+ + ++F    ++ HTGRTHQ+RVH  H+G P+V D KY      N  
Sbjct: 7375 SEDYFLTDPKEIENYTKEFTLCNVKIHTGRTHQIRVHMRHIGHPLVSDKKYLNPSLSNLD 7434

Query: 282  SPIQNKLYLHARYMDLPHPE 301
                 +++LH+  ++  +P+
Sbjct: 7435 KFWCFRMFLHSLILEFNNPD 7454



 Score = 47.4 bits (111), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 31/50 (62%)

Query: 146  LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            L HR+D ETSG L++A+T+ A + L + FR R + K Y  L  G  K KK
Sbjct: 7082 LCHRIDLETSGSLIIAKTKEAREFLFDQFRKRNVYKEYILLCHGRIKKKK 7131


>gi|224076324|ref|XP_002304926.1| predicted protein [Populus trichocarpa]
 gi|222847890|gb|EEE85437.1| predicted protein [Populus trichocarpa]
          Length = 470

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 50/214 (23%), Positives = 83/214 (38%), Gaps = 31/214 (14%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           KS +++      V +KPAG SV G +           +         R TH++D  T G 
Sbjct: 205 KSRIIHVTESFVVLDKPAGTSVGGTTDNIEESCATFATRALGLTAPLRTTHQIDNCTEGC 264

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVV 216
           +V+ARTR          R + ++K+Y +L    +P      + N  ++  ++    V   
Sbjct: 265 VVLARTREDCSVFHGKIREKTVKKLYIALAASPVPIG----VVNHYMRPINMAPRLV--- 317

Query: 217 KQNEKGANYAISHFKVIDC---------FAQKFC-----W--------LEMQPHTGRTHQ 254
              E    + +   +V++C           +K+C     W         ++   TGRTHQ
Sbjct: 318 -SEEFIKGWHLCQLEVMECKRVPWPDAVMEEKYCVQDCGWPSKDHAYECKINLLTGRTHQ 376

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
           +R     +G P+VGD  Y         SP  N  
Sbjct: 377 IRAQLAALGAPLVGDSMYMPAAVAEMVSPGCNPF 410


>gi|75764813|ref|ZP_00744194.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|74487697|gb|EAO51532.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
          Length = 192

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/181 (24%), Positives = 83/181 (45%), Gaps = 23/181 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVRIPPVINALN 75
           +N R+D++        +   +Q+ ++   V V+ K VK N ++ +  ++    P   AL+
Sbjct: 14  KNERIDKFVAGINNEWSRSQVQQWIKDDVVTVNGKAVKVNYKVKEEDEITVTIPDPEALD 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                  I    +NL          + YED+ + V NKP G+ V    G      ++G +
Sbjct: 74  -------IQPEDMNLE---------IYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLM 117

Query: 134 KSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y ++V G
Sbjct: 118 HHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLLNQLVAKTVTRRYKAIVHG 177

Query: 190 I 190
           +
Sbjct: 178 V 178


>gi|258621886|ref|ZP_05716916.1| pseudouridine synthase Rlu family protein [Vibrio mimicus VM573]
 gi|258627415|ref|ZP_05722196.1| pseudouridine synthase Rlu family protein [Vibrio mimicus VM603]
 gi|258580221|gb|EEW05189.1| pseudouridine synthase Rlu family protein [Vibrio mimicus VM603]
 gi|258585824|gb|EEW10543.1| pseudouridine synthase Rlu family protein [Vibrio mimicus VM573]
          Length = 233

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/147 (33%), Positives = 73/147 (49%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR  AAA  L++ F  R ++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNAAAASELSQGFAKRTVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+         N A++ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVN------SQHNPAVTQFFSATAAPGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y A  +        ++ YLHA
Sbjct: 159 IVGDPIYNAADES-------DRGYLHA 178


>gi|114561967|ref|YP_749480.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114333260|gb|ABI70642.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 281

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/199 (23%), Positives = 86/199 (43%), Gaps = 36/199 (18%)

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           H+   Q ILD  V   +        LL+++++  ++ KP G+  QG     +     +  
Sbjct: 68  HLYYNQYILDEQVTPAE--------LLFDEAEYSIWYKPYGMRCQGSK---WSDHTTINR 116

Query: 136 WVDSKGQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IP 191
           + +   Q  R   + HRLD+  +G+LV+  ++ A   + + F  R ++K Y  +V G  P
Sbjct: 117 YAELNMQPQRNAFIIHRLDRAATGLLVLGHSKKATAAIAKLFETRELEKYYQVIVEGEFP 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTG 250
            N                     V          A+SH  ++   ++     ++++  TG
Sbjct: 177 SNP--------------------VTINTPVDNKPALSHATLLTYNSELNQSKVQVKIDTG 216

Query: 251 RTHQLRVHALHMGCPIVGD 269
           R HQ+R+H   +G P+VGD
Sbjct: 217 RKHQIRIHMASLGHPVVGD 235


>gi|297670735|ref|XP_002813515.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           3-like isoform 2 [Pongo abelii]
          Length = 335

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/150 (29%), Positives = 70/150 (46%), Gaps = 16/150 (10%)

Query: 152 QETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +E+SG+++++     A  L + F    R +R    Y ++  GIP   +  I    LK  H
Sbjct: 121 KESSGLVLLSSCPQTASRLQKFFTHARRAQRPTATYCAVTDGIPAASEGKI-QAALKLEH 179

Query: 208 IGGDYVHV-VKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           I G  + V VK   +     G    +SHF+V+         +++QP T  + QL+VH + 
Sbjct: 180 IDGVNLTVPVKAPSRKDILEGVKKTLSHFRVV-ATGSGCALVQLQPLTVFSSQLQVHMVL 238

Query: 262 MGCPIVGDHKYCAN----FKGNFTSPIQNK 287
             CP++GDH Y A         F  P +NK
Sbjct: 239 QLCPVLGDHMYSARVGTVLGQRFLLPAENK 268


>gi|302822543|ref|XP_002992929.1| hypothetical protein SELMODRAFT_136180 [Selaginella moellendorffii]
 gi|300139274|gb|EFJ06018.1| hypothetical protein SELMODRAFT_136180 [Selaginella moellendorffii]
          Length = 428

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 54/204 (26%), Positives = 90/204 (44%), Gaps = 43/204 (21%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRL-THRLD 151
           KS +L E+    V +KPAG+SV GGS     +D   +S V    +      P L TH++D
Sbjct: 149 KSRILAENDLFVVLDKPAGVSV-GGS-----VDNLEESCVTFASRALGMAFPLLVTHQID 202

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIANWLLKKSHIGG 210
             T G +V+A+ +    +     R R++ K Y  L  + +P      I +  ++  H   
Sbjct: 203 NCTEGCVVLAKDKDFVSNFNRLLRTRKVDKRYLVLAAFPVPLG----IVSHYMRPDHFAP 258

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKF-------------CWLEMQPH--------- 248
              H++ Q+++   + +   +V+ C   ++             C LE   H         
Sbjct: 259 ---HLLSQDKR-QGWHLCSMEVLQCHQVEWPSEARLRENGVSNCELEHDGHAYECEVKLL 314

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TG+THQ+R     +G PI+GD  Y
Sbjct: 315 TGKTHQVRAQFAALGAPILGDTIY 338


>gi|294142528|ref|YP_003558506.1| ribosomal pseudouridine synthase family protein [Shewanella
           violacea DSS12]
 gi|293328997|dbj|BAJ03728.1| ribosomal pseudouridine synthase family protein [Shewanella
           violacea DSS12]
          Length = 316

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 39/133 (29%), Positives = 62/133 (46%), Gaps = 9/133 (6%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIA 199
            HRLD+ T+GI+++     A     + F+  +I K Y +L    P+        +     
Sbjct: 141 AHRLDRATAGIVLMILNPEARTQYHDLFKNHQITKEYQALAKLTPELLASHQAGELALPI 200

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +W +K   + G+   ++K  E   N   S   +ID       + ++ P TGRTHQLRVH 
Sbjct: 201 HWTVKNRMVKGEPSFIMKVVEGEPNTH-SEISLIDIKGDNGLF-KLSPITGRTHQLRVHM 258

Query: 260 LHMGCPIVGDHKY 272
             +G PI+ D  Y
Sbjct: 259 HSLGMPIINDRCY 271


>gi|262165841|ref|ZP_06033578.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus VM223]
 gi|262025557|gb|EEY44225.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus VM223]
          Length = 233

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/147 (33%), Positives = 73/147 (49%), Gaps = 14/147 (9%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR  AAA  L++ F  R ++K Y ++    PK K+  I   + + 
Sbjct: 46  LVHRLDKMTSGILLLARNAAAASELSQGFAKRTVEKFYLAIGSKKPKKKQGLICGDMERS 105

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V+         N A++ F        +  +L  +PHTG+THQ+RV    +G  
Sbjct: 106 RRSSWKLVN------SQHNPAVTQFFSATAAPGERLFL-CKPHTGKTHQIRVALKSIGSA 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           IVGD  Y A  +        ++ YLHA
Sbjct: 159 IVGDPIYNAADES-------DRGYLHA 178


>gi|297285309|ref|XP_001096088.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein 3
           isoform 2 [Macaca mulatta]
          Length = 336

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/134 (30%), Positives = 65/134 (48%), Gaps = 12/134 (8%)

Query: 152 QETSGILVVARTRAAAQHL----TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +E+SG+++++     A  L    T S R +R    Y ++  GIP   +  I    LK  H
Sbjct: 121 KESSGLVLLSSCPQTASRLQKFFTHSQRAQRPTATYCAVTNGIPTASEGKI-QAALKLEH 179

Query: 208 IGGDYVHV-VKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           I G  + V VK   +     G    +SHF+V+         +++QP T  + QL+VH + 
Sbjct: 180 IDGVNLTVPVKAPSRKDILQGVKKTLSHFRVV-ATGSGCALVQLQPLTVFSSQLQVHMVL 238

Query: 262 MGCPIVGDHKYCAN 275
             CP++GDH Y A 
Sbjct: 239 QLCPVLGDHTYSAR 252


>gi|120402627|ref|YP_952456.1| pseudouridine synthase [Mycobacterium vanbaalenii PYR-1]
 gi|119955445|gb|ABM12450.1| pseudouridine synthase [Mycobacterium vanbaalenii PYR-1]
          Length = 285

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 56/215 (26%), Positives = 94/215 (43%), Gaps = 23/215 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  ++    GS +A      ++  +D     P   HRLD+ T+G+LV
Sbjct: 84  VLHRDDNLVVVDKPHFLATMPRGSHVAQTALVRMRRELDLPQLSP--AHRLDRLTAGVLV 141

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWS-LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
               R         F    + K Y +    G  ++    + + ++K+    G    V + 
Sbjct: 142 FTTRREVRGAYQTMFARGGVSKTYLAQSSAGTDRDFPITVRSRIIKRR---GTLQAVEEP 198

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK- 277
            E  A   +     +D    +     + P TGRTHQLRVH   +G PI GD  Y      
Sbjct: 199 GEPNAETLVER---VDDRTYR-----LMPRTGRTHQLRVHMNSLGLPIAGDPLYPNVIDV 250

Query: 278 --GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
             G+F++P++    L A+ ++   P  G RL+ T+
Sbjct: 251 AVGDFSTPLK----LLAQCLEFTDPLAGVRLRFTS 281


>gi|237801044|ref|ZP_04589505.1| pseudouridine synthase [Pseudomonas syringae pv. oryzae str. 1_6]
 gi|331023901|gb|EGI03958.1| pseudouridine synthase [Pseudomonas syringae pv. oryzae str. 1_6]
          Length = 296

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 52/178 (29%), Positives = 81/178 (45%), Gaps = 19/178 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 89  ILYADDHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 145

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TRAA Q L   F  RRI K Y ++   +P      +    L +S +       
Sbjct: 146 LFSANRQTRAAYQTL---FPTRRIDKFYEAIAPALPD-----LEFPRLHESRLVEGEPFF 197

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             Q   GA+   +H +V++   Q+  W   + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 198 RMQEGPGASNTQTHIEVLE--RQEQLWRYGLHPVTGKKHQLRVHMAALGAAICNDPFY 253


>gi|294786685|ref|ZP_06751939.1| RNA pseudouridine synthase [Parascardovia denticolens F0305]
 gi|315226296|ref|ZP_07868084.1| 23S RNA-specific pseudouridylate synthase [Parascardovia
           denticolens DSM 10105]
 gi|294485518|gb|EFG33152.1| RNA pseudouridine synthase [Parascardovia denticolens F0305]
 gi|315120428|gb|EFT83560.1| 23S RNA-specific pseudouridylate synthase [Parascardovia
           denticolens DSM 10105]
          Length = 263

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 60/249 (24%), Positives = 94/249 (37%), Gaps = 36/249 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYEDS+I V +KP  +      G+ Y     ++       +     HRLD+ T+GI+V 
Sbjct: 13  VLYEDSRIIVVDKPHFLPTTP-RGMWYRSTALIRLREKYGDEAITPAHRLDRMTAGIVVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----------------ECIANW-- 201
            R     +     F+ R+ +K Y  L    P  +                   C  +   
Sbjct: 72  VRDPRYRRDYQLLFQNRQARKKYVCLAPAKPVVRPALGTLFPLIDDQSGLRLSCPDDRRL 131

Query: 202 ---LLKKSHIGGDYVHVVKQNEKGANYAISHFKVI------DCFAQKFCWLEMQPHTGRT 252
              L++ SHI      +    E     A++  ++           +     ++ P TG+T
Sbjct: 132 FFPLIRSSHITKTRGVLQACEEADKPNAVTIIRLSADQPRGQTLEKGLRSYDLFPRTGKT 191

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-------RL 305
           +QLRVH   +G PIVGD  Y             + L L A+ +D   P  G       R 
Sbjct: 192 YQLRVHMNSLGLPIVGDPLYPEILPEAAYDDFSDPLRLVAQELDFADPVSGQDFHFRSRW 251

Query: 306 QITAPLPAH 314
            +T P PA 
Sbjct: 252 TVTDPGPAE 260


>gi|68488811|ref|XP_711752.1| hypothetical protein CaO19.10304 [Candida albicans SC5314]
 gi|46433075|gb|EAK92530.1| hypothetical protein CaO19.10304 [Candida albicans SC5314]
          Length = 402

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 51/194 (26%), Positives = 91/194 (46%), Gaps = 31/194 (15%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLD 151
           H+D +KS+  YED +I V +KP+GI         ++ +   +K  ++         HRLD
Sbjct: 103 HNDIIKSV--YEDDEILVVDKPSGIPTHPTGNYYFNSLSEIIKQQLNMDS--IWTCHRLD 158

Query: 152 QETSGILVVARTRAAAQHLTESFRMRR--IQKIYWSLVWG-IPK--NKKEC------IAN 200
           + TSG+LV+A+T+      ++  R  +   +K Y + V G  P+  ++  C      +  
Sbjct: 159 KVTSGVLVLAKTKNGGVRFSKLMRDSKQYTEKTYLARVSGKFPEGIHRYRCPIFAVNMNG 218

Query: 201 WLLKKS--HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +L+  +   +  D   + ++ +  A+   S  K +             P TG+ HQ+RVH
Sbjct: 219 YLMSGNMEELPTDSTTIFERIKYNASLDQSLVKCV-------------PITGKFHQIRVH 265

Query: 259 ALHMGCPIVGDHKY 272
             ++G PIV D  Y
Sbjct: 266 LRNLGFPIVNDSFY 279


>gi|329120090|ref|ZP_08248760.1| RNA pseudouridine synthase [Neisseria bacilliformis ATCC BAA-1200]
 gi|327463621|gb|EGF09939.1| RNA pseudouridine synthase [Neisseria bacilliformis ATCC BAA-1200]
          Length = 377

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/180 (24%), Positives = 80/180 (44%), Gaps = 13/180 (7%)

Query: 101 LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLK-----SWVDSKGQKPRLTHRLDQET 154
           +LY D  +   +KP  + V  GG  +   +   L+        D  G  P   HR+D++T
Sbjct: 166 ILYADKHLLAVDKPHFLPVVPGGRFLRETLLTRLRLHPELQDADPDGLAP--LHRIDKDT 223

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+++  R R + +     F+ RR++K Y ++       ++  +   L  +S I      
Sbjct: 224 AGVVLFCRRRESRRAYQMLFQARRVEKSYEAVA-----AERAGMTFPLHIRSRIERGEPF 278

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + +   GA  A +  +  +          ++P +G+ HQLRVH   +G PI+ D  Y A
Sbjct: 279 FLMRETGGAANAHTVVEAAEPLGGGLARYRLRPVSGKKHQLRVHMAALGLPILNDPLYPA 338


>gi|86156693|ref|YP_463478.1| pseudouridine synthase RluD [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85773204|gb|ABC80041.1| Pseudouridine synthase, RluD [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 312

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 96/233 (41%), Gaps = 28/233 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-----GQKPR-----LTHRL 150
           +L E  +  V +KPAG++V     +A    G L + V ++     G  P         RL
Sbjct: 79  VLLERPRYLVVDKPAGVAVHP---LAPGEGGTLANAVAARHPECAGASPEPREGGAVQRL 135

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI-- 208
           D ETSG ++ AR   A + L        + K+Y +L  G       C      +   +  
Sbjct: 136 DLETSGCVLFARDPEAWEALHAQLGAHTVDKVYLALAVGRVPAGGVCSVPLAQRGGRVLP 195

Query: 209 GGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             D     +   +G     A +H++    FA     L ++  TG  HQ+R H   +G P+
Sbjct: 196 APDAEAEERLRARGLRPRPAETHYEPERRFA-GHTLLRVRIVTGVMHQIRAHLALLGHPV 254

Query: 267 VGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            GD  Y    A   G        + +LHA  +    P+ GGR+ + +PLPA +
Sbjct: 255 AGDALYGGAAAELAG------LERQFLHAWRLAFDDPDGGGRVAVESPLPAEL 301


>gi|253744794|gb|EET00944.1| Ribosomal large subunit pseudouridine synthase D [Giardia
           intestinalis ATCC 50581]
          Length = 196

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/153 (30%), Positives = 69/153 (45%), Gaps = 17/153 (11%)

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC--IANWLLKKSHIGGDYVHV 215
           +++A  + AA      F+MR + K+Y +LV G   ++     IA+ +             
Sbjct: 1   MILAANKKAAGSAGREFQMRAVTKVYVALVAGDVNSQTISLPIADDVSDPHQFRMCVSST 60

Query: 216 VKQNEKGANYAISHFK-VIDCFAQKFC----WLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            K++E       S  K + D  A   C     + ++P TGR HQLRVH  H+G PIVGD 
Sbjct: 61  GKRSETHVKRIASISKDICDALALSPCESYTLVVLRPVTGRRHQLRVHLAHVGHPIVGDQ 120

Query: 271 KYCANFKGNFTSPI-----QNKLYLHARYMDLP 298
            Y     GN    I     + +L LHA  + +P
Sbjct: 121 LY-----GNAIEDIHHVNGEQRLCLHAFMLSIP 148


>gi|259505649|ref|ZP_05748551.1| ribosomal pseudouridine synthase [Corynebacterium efficiens YS-314]
 gi|259166731|gb|EEW51285.1| ribosomal pseudouridine synthase [Corynebacterium efficiens YS-314]
          Length = 308

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 92/223 (41%), Gaps = 28/223 (12%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++ED  + V +KP  ++     G        +K  V +  Q+    HRLD+ TSG+LV
Sbjct: 81  LIIHEDEDLLVVDKPPYLATMP-RGRHITETALVKMRVLTGHQELTPAHRLDRLTSGVLV 139

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWLLKKSHI----GGDYV 213
           + +           F  R   K Y +    I   + E +     L+ +SHI    G    
Sbjct: 140 MVKRPELRGMYQTLFARREATKTYEA----IGDYRPELVPGDEPLIWESHIEKVRGQVQA 195

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLE----------MQPHTGRTHQLRVHALHMG 263
           +V  +        +S   V D    +   L           + P TG+THQLR+H    G
Sbjct: 196 YVTDEEPNTRTRVVSVTPVTDDEQAQLEALHGHLPRQGRYVLAPETGKTHQLRIHMRDAG 255

Query: 264 CPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            PI+GD  Y    A    ++T+P    ++L AR +    P+ G
Sbjct: 256 VPILGDPLYPVLHAVDDEDYTTP----MHLIARTLTFIDPQSG 294


>gi|72080357|ref|YP_287415.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyopneumoniae 7448]
 gi|71913481|gb|AAZ53392.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyopneumoniae 7448]
          Length = 281

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 47/179 (26%), Positives = 81/179 (45%), Gaps = 22/179 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETS 155
           ++Y+D  I + +KP  + V GG    +++D  L  W      +++  KP    RLD++TS
Sbjct: 83  IIYQDENILLVDKPQNLQVHGG---KFNLD--LAVWNYLKIPENQVFKPSHIGRLDKKTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++      +   L +  + +  +KIY    +    + K  I   +  K +   ++   
Sbjct: 138 GIILYGLNYQSVVELNQ--KQKFFEKIY---TFKSDIDLKNTIKTDVFIKKN---NFQQK 189

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           ++   K  N   +         +KF  L    HTG+ HQ+RV   H+G PI GD KY  
Sbjct: 190 MEVTLKSPNSFFASTTFYSKNQKKFAIL----HTGKKHQIRVSLSHLGFPIFGDEKYGG 244


>gi|291450450|ref|ZP_06589840.1| ribosomal pseudouridine synthase [Streptomyces albus J1074]
 gi|291353399|gb|EFE80301.1| ribosomal pseudouridine synthase [Streptomyces albus J1074]
          Length = 318

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/214 (27%), Positives = 96/214 (44%), Gaps = 24/214 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETS 155
             ++L+ D  + V +KP  ++    +    H+     + + ++ + P L+  HRLD+ T+
Sbjct: 93  PPVVLFRDEHLVVVDKPHFLAT---TPRGRHVTQTALALLRTRLELPELSPAHRLDRLTA 149

Query: 156 G-ILVVART--RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           G +L+  R   RAA Q L   F  R ++K Y ++    P      +A     +S I  + 
Sbjct: 150 GLVLLTVRPAERAAYQRL---FSDRLVRKEYEAVAGYDP-----GLALPRTVRSRIVKER 201

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +  Q   G   A +  +++           + PHTGRTHQLRVH   +G PI+GD  Y
Sbjct: 202 GVIAAQEVPGEPNAETRVELL-AHRGTLGRYRLLPHTGRTHQLRVHLNSLGVPILGDPVY 260

Query: 273 ---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                    +F  P+Q    L AR ++   P  G
Sbjct: 261 PHLTDPAPDDFRRPLQ----LLARTVEFTDPVTG 290


>gi|260664193|ref|ZP_05865046.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii SJ-7A-US]
 gi|260562079|gb|EEX28048.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii SJ-7A-US]
          Length = 297

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/234 (24%), Positives = 101/234 (43%), Gaps = 29/234 (12%)

Query: 101 LLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQE 153
           ++ E     V NKPA +       + G  +   + G+      S+    KP +  RLD++
Sbjct: 81  IVLETDNYLVINKPANVLSIPSRYEDGDAVVNRVMGYFSKKKSSEQAFLKPHIVTRLDRD 140

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSHIGGD 211
           TSG+++V +   A    +E  +     K Y ++V     P+ +   I   + K       
Sbjct: 141 TSGLVLVGKNAVAHSKFSE-LKKDVFVKEYHAIVHSNFNPEEQAGLIDAPIGKIDDSVKR 199

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           YV  +   +K     ++ ++V+   AQK     ++++  TGRTHQ+RVH  H+G P+ GD
Sbjct: 200 YV--IPNGQK----FLTQYEVL---AQKEGASLVKLRLFTGRTHQIRVHMAHIGHPLFGD 250

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APLPAHMVKTWDSL 322
             Y  +   NF      +  L+  ++  P P     +I     P  M   W +L
Sbjct: 251 KLYGID--DNFA-----RQALNCSHLSFPDPFTNEEKIVEVSDPQDMTDLWRNL 297


>gi|239978554|ref|ZP_04701078.1| ribosomal pseudouridine synthase [Streptomyces albus J1074]
          Length = 280

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/214 (27%), Positives = 96/214 (44%), Gaps = 24/214 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETS 155
             ++L+ D  + V +KP  ++    +    H+     + + ++ + P L+  HRLD+ T+
Sbjct: 55  PPVVLFRDEHLVVVDKPHFLAT---TPRGRHVTQTALALLRTRLELPELSPAHRLDRLTA 111

Query: 156 G-ILVVART--RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           G +L+  R   RAA Q L   F  R ++K Y ++    P      +A     +S I  + 
Sbjct: 112 GLVLLTVRPAERAAYQRL---FSDRLVRKEYEAVAGYDP-----GLALPRTVRSRIVKER 163

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +  Q   G   A +  +++           + PHTGRTHQLRVH   +G PI+GD  Y
Sbjct: 164 GVIAAQEVPGEPNAETRVELL-AHRGTLGRYRLLPHTGRTHQLRVHLNSLGVPILGDPVY 222

Query: 273 ---CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                    +F  P+Q    L AR ++   P  G
Sbjct: 223 PHLTDPAPDDFRRPLQ----LLARTVEFTDPVTG 252


>gi|261211789|ref|ZP_05926076.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. RC341]
 gi|260839139|gb|EEX65771.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. RC341]
          Length = 235

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 50/151 (33%), Positives = 75/151 (49%), Gaps = 22/151 (14%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSGIL++AR  AAA  L++ F  R ++K Y ++    PK K+  ++      
Sbjct: 46  LVHRLDKMTSGILLLARNAAAASELSQGFAKRSVEKFYLAIGSKKPKKKQGLVS------ 99

Query: 206 SHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
               GD     + + K  N     A++ F        +  +L  +PHTG+THQ+RV    
Sbjct: 100 ----GDMERSRRSSWKLLNSQHNPAVTQFFSTTAAPGERLFL-CKPHTGKTHQIRVALKS 154

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           +G  IVGD  Y        T+   ++ YLHA
Sbjct: 155 IGSAIVGDPIYN-------TADEADRGYLHA 178


>gi|25029349|ref|NP_739403.1| hypothetical protein CE2793 [Corynebacterium efficiens YS-314]
 gi|23494637|dbj|BAC19603.1| conserved hypothetical protein [Corynebacterium efficiens YS-314]
          Length = 340

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 92/223 (41%), Gaps = 28/223 (12%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++ED  + V +KP  ++     G        +K  V +  Q+    HRLD+ TSG+LV
Sbjct: 113 LIIHEDEDLLVVDKPPYLATMP-RGRHITETALVKMRVLTGHQELTPAHRLDRLTSGVLV 171

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWLLKKSHI----GGDYV 213
           + +           F  R   K Y +    I   + E +     L+ +SHI    G    
Sbjct: 172 MVKRPELRGMYQTLFARREATKTYEA----IGDYRPELVPGDEPLIWESHIEKVRGQVQA 227

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLE----------MQPHTGRTHQLRVHALHMG 263
           +V  +        +S   V D    +   L           + P TG+THQLR+H    G
Sbjct: 228 YVTDEEPNTRTRVVSVTPVTDDEQAQLEALHGHLPRQGRYVLAPETGKTHQLRIHMRDAG 287

Query: 264 CPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            PI+GD  Y    A    ++T+P    ++L AR +    P+ G
Sbjct: 288 VPILGDPLYPVLHAVDDEDYTTP----MHLIARTLTFIDPQSG 326


>gi|290977304|ref|XP_002671378.1| predicted protein [Naegleria gruberi]
 gi|284084946|gb|EFC38634.1| predicted protein [Naegleria gruberi]
          Length = 272

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 96/237 (40%), Gaps = 41/237 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH---------IDGFLKSWVDSKGQKP-----RL 146
           ++++   + V +KP  + + G   +            ++  L+      G  P     + 
Sbjct: 15  IIFKSRDVLVIDKPNDLHIDGDYELTVEKLINNYYPEMENPLEEIQHKPGHTPSRRKLKF 74

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA------ 199
            H+LD  TSGIL +A TR +   +T  F+ R  QK Y +++ G +  N  E +       
Sbjct: 75  CHQLDYATSGILCLAFTRESCAKITYPFQQRTAQKQYLAVLRGHVLINDFEILTFIGEDP 134

Query: 200 ----NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------------- 242
                + ++  ++G +   + + N +         +    F    C              
Sbjct: 135 SDERKFRMRNFYLGREKTLLSELNTEEEIQEAKKSRESLTFGSVLCRGFYHKDNDTIPVT 194

Query: 243 -LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            + ++P TGR HQLR+H   +G PI+GD  Y  +  G       +++ LHA  + LP
Sbjct: 195 KVLLRPKTGRRHQLRLHTQLLGFPILGDATY--SLLGRDGEEGVHRMMLHAWNLTLP 249


>gi|299769556|ref|YP_003731582.1| putative pseudouridylate synthase [Acinetobacter sp. DR1]
 gi|298699644|gb|ADI90209.1| putative pseudouridylate synthase [Acinetobacter sp. DR1]
          Length = 302

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 52/206 (25%), Positives = 94/206 (45%), Gaps = 12/206 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V +KP  +++   G  +   +   LK    ++   P   HRLD+ET+G+++
Sbjct: 94  ILFENDDLLVVDKPHFLTISPTGQYVQETLLVRLKKQTGNEFLTP--IHRLDRETAGVVL 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             +   +     + F  R++ KIY +    I   KK+      L      G   + ++  
Sbjct: 152 FCKRVESRGIYQQLFAERQVNKIYHA----IAPYKKDLNFPQTLHLHLDKGHPFYTMRVI 207

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NF 276
           E       ++ ++I+   Q +    + P TG+ HQLRVH  H+G PI  D  Y       
Sbjct: 208 ENAKTNTETYIELIE-HNQIWAKYRLTPTTGKQHQLRVHLSHLGIPIKNDPFYPVVQHKA 266

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEG 302
           + +F+ P+Q  L  H  ++D    EG
Sbjct: 267 EDDFSEPLQ-LLAKHISFIDPLTKEG 291


>gi|157960378|ref|YP_001500412.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157845378|gb|ABV85877.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 312

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 53/218 (24%), Positives = 96/218 (44%), Gaps = 24/218 (11%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           F +  LL  D  + VF KP  ++V   G+ +   +   L+  + +  Q+    HRLD+ T
Sbjct: 84  FKEKCLLQTDEFLLVF-KPHFLAVNPSGNFVNECLVNRLR--LKTGNQQIVAAHRLDRAT 140

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-------WGIPKNKKECIANWLLKK-- 205
           +G++++++         E F+  +IQK Y ++          + +       +W +K   
Sbjct: 141 AGVMLLSQKSETRHDYHELFKSGQIQKTYQAVAPLNNQIKQMLEQGSLTLPMHWTVKNRI 200

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           S     +   +   E  ++   S  ++I+ F   +   E+ P TGRTHQLRVH + +G  
Sbjct: 201 SKTTPSFRMCISDGEANSH---SEIRLIETFG-GYGLFELVPVTGRTHQLRVHMMSLGMS 256

Query: 266 IVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHP 300
           I+ D  Y         +F  P++    L AR +    P
Sbjct: 257 ILNDRLYPELLDKAADDFAKPLK----LMARRLSFTDP 290


>gi|308807064|ref|XP_003080843.1| Pseudouridine synthase, RluD (ISS) [Ostreococcus tauri]
 gi|116059304|emb|CAL55011.1| Pseudouridine synthase, RluD (ISS) [Ostreococcus tauri]
          Length = 472

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 64/284 (22%), Positives = 109/284 (38%), Gaps = 55/284 (19%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS------SVNLTKHSDFLKSILL 102
           D KR+ F  R   G   R+ P   A    +   ++  +      +V L +    L   ++
Sbjct: 109 DVKRMCFRARDGMGDGERMTPEACAAALGVPTGRVKTTLRRASLAVELARDDAPLD--VV 166

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDG---FLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +ED +  V NKP  +         +  +G     ++   +KG+ P + HRLD +TSG+ V
Sbjct: 167 HEDDEFLVVNKPPNLRFHPN----HRFEGNSLLSRALHHTKGETPYIVHRLDMDTSGVAV 222

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV------ 213
             + ++    +   F  +  +K Y ++  G+      C  +  +  + IG   V      
Sbjct: 223 FVKKQSLVSDVARQFHEKTARKTYLAISVGV--TPPGC-GDGFVVDAPIGDHGVVKEARN 279

Query: 214 --------------HVVKQNEKGANYAISHFKVIDCFAQK----------------FCWL 243
                          V+ + E  A + IS   V      K                   +
Sbjct: 280 VDFSGEGKEARTVCEVISRKET-ALFDISDETVAATTTPKGVSATSETNDSSPSATAALV 338

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++P TGRTHQ+RVH  H G PIV D  Y  + +    S  +N+
Sbjct: 339 LVKPMTGRTHQIRVHLAHAGLPIVSDALYGPHIRWGAQSADENE 382


>gi|68066382|ref|XP_675174.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56494204|emb|CAH93561.1| conserved hypothetical protein [Plasmodium berghei]
          Length = 895

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 42/71 (59%)

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           K I+ + ++F    ++ HTGRTHQ+RVH  H+G P+V D KY  +   N       +++L
Sbjct: 340 KDIETYTKEFTLCNVKIHTGRTHQIRVHMRHIGHPLVSDKKYLNSSLSNLDKFWCFRMFL 399

Query: 291 HARYMDLPHPE 301
           H+  ++  +P+
Sbjct: 400 HSIILEFNNPD 410



 Score = 45.8 bits (107), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 30/50 (60%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K KK
Sbjct: 36  LCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYILLCHGRIKKKK 85


>gi|229524488|ref|ZP_04413893.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           bv. albensis VL426]
 gi|229338069|gb|EEO03086.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           bv. albensis VL426]
          Length = 177

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 47/90 (52%), Gaps = 2/90 (2%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I   NKP+G+    G  +  H D      VD      ++ HRLD  TSG+++ 
Sbjct: 16  VIYEDEHIIAANKPSGLLSVPGRPVE-HYDSMWARLVD-YCPDVKVVHRLDMSTSGLILF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           A+ +     L + F+ R   KIY++ VWG+
Sbjct: 74  AKGKHMESALKKQFQYRLTHKIYYARVWGV 103


>gi|325479463|gb|EGC82559.1| pseudouridine synthase, RluA family [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 279

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 46/177 (25%), Positives = 84/177 (47%), Gaps = 12/177 (6%)

Query: 101 LLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED    V +K   I+V  +G   +A +I  + KS  ++   K R  +RLD +TSG++
Sbjct: 75  IIYEDRDTLVISKDPNITVNSKGQISLANNIAYYFKS--NNINSKVRFVNRLDMDTSGLI 132

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+ + A     +      + K Y ++V   P    + +  +  K ++      +VV +
Sbjct: 133 LVAKNKYAHAFYQKQIENNEMIKKYIAIVD--PNANLDML--YEEKFAYDEKSKSYVVSE 188

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           + K A       K++    +    +E Q  TG+THQ+R     +  PI GD  Y ++
Sbjct: 189 DGKTAKTIFKPLKLL----KDRTIVECQILTGKTHQIRASLSSLDYPIFGDKLYGSD 241


>gi|121609561|ref|YP_997368.1| pseudouridine synthase [Verminephrobacter eiseniae EF01-2]
 gi|121554201|gb|ABM58350.1| pseudouridine synthase [Verminephrobacter eiseniae EF01-2]
          Length = 314

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 99/227 (43%), Gaps = 40/227 (17%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
               LL++D  + V +KP  + V   G  + + +   LK  +      P   HR+D++T+
Sbjct: 99  FAPTLLHQDPHLVVADKPHFMPVTPSGRYLQHTLLVRLKRQLGLPQLSP--VHRIDRDTA 156

Query: 156 GILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW----LLKKSHI 208
           G+++++    TR A Q L   FR RRI K Y            E IA W    +  + H 
Sbjct: 157 GLVLLSVQQCTRGAYQAL---FRERRITKHY------------EAIAPWRADVVFPRDHT 201

Query: 209 -----GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                G  +  +  Q   G   + +H +++   A  +    + P TG+ HQLRVH   +G
Sbjct: 202 SRIEPGPQFFRM--QEVPGPPNSHTHMQLL-AVAGDWAHYRLSPSTGKRHQLRVHMAALG 258

Query: 264 CPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            P+  D  Y        G+++ P+Q    L AR ++   P  G  ++
Sbjct: 259 LPLRNDPFYPVVDDPPPGDYSRPLQ----LLARALEFVDPLSGERRV 301


>gi|297619316|ref|YP_003707421.1| pseudouridine synthase [Methanococcus voltae A3]
 gi|297378293|gb|ADI36448.1| pseudouridine synthase [Methanococcus voltae A3]
          Length = 372

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 59/250 (23%), Positives = 104/250 (41%), Gaps = 49/250 (19%)

Query: 101 LLYEDSKIYVFNKPAGI------SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++YED  I V NKP  +      +++ G+     +D    +  +S+  K R  +R+D +T
Sbjct: 106 IMYEDMDILVVNKPKNMVVHPTKTIKSGTLANAIMDYQNHNKSESERFKIRFINRIDMDT 165

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWL---LKKSHIG 209
           +GI+++A+   A Q +   F+   ++K Y +++ G     N    + N L   L  +   
Sbjct: 166 TGIVLIAKNSFAHQKIANQFQ-GCMKKEYLAVISGNMDVDNLDTNLNNSLDTELNNNLND 224

Query: 210 GDY-------VHVVKQN---------EKGANYAISH--FKVIDC--------------FA 237
             Y       + + K+N         ++  +  I H  F++I                 +
Sbjct: 225 EKYNLPLNLRLKIYKENNSKFSVIIFDRDTDELIEHTNFEIIKNTKDTKDNKDNKDTEIS 284

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKLYLHARYM 295
             F  ++    TG+THQ+R H  ++G  IVGD  Y  N     NF +     L LH+   
Sbjct: 285 NNFTLIKASLITGKTHQIRRHLAYLGFSIVGDELYTNNNELNDNFKNY---SLMLHSYKT 341

Query: 296 DLPHPEGGRL 305
              HP    L
Sbjct: 342 TFIHPRTNEL 351


>gi|89093809|ref|ZP_01166755.1| hypothetical protein MED92_04904 [Oceanospirillum sp. MED92]
 gi|89081939|gb|EAR61165.1| hypothetical protein MED92_04904 [Oceanospirillum sp. MED92]
          Length = 313

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 52/182 (28%), Positives = 85/182 (46%), Gaps = 17/182 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           L++E  ++   NKP  + V   +   Y     L S V  +   P  +L HRLD ETSG++
Sbjct: 80  LVWESDELMAINKPPLLPVSRTTRNLYMT---LISLVRRQTPYPDAQLLHRLDTETSGLI 136

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY---VHV 215
           ++A+ R A +           +K+Y + V G P      +   L +K+  G D    V+V
Sbjct: 137 LLAKNREADRKWKPQLAKLIRRKVYQAWVHGSPNWDHLLMECELSEKA--GSDIRSQVYV 194

Query: 216 VKQNEKGANY-----AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           V + +  + Y     + + F V+     K   ++ +  TGR HQ+R    H+G PI+GD 
Sbjct: 195 V-EPQSDSQYLKPRPSKTEFLVLQRAGSK-SLIQCELFTGRKHQIRAQLAHLGHPIIGDK 252

Query: 271 KY 272
            Y
Sbjct: 253 IY 254


>gi|240976679|ref|XP_002402471.1| ribosomal pseudouridine synthase, putative [Ixodes scapularis]
 gi|215491192|gb|EEC00833.1| ribosomal pseudouridine synthase, putative [Ixodes scapularis]
          Length = 263

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/207 (26%), Positives = 92/207 (44%), Gaps = 28/207 (13%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  HRLD  TSG+L +A  + +A+    +F  R  +K Y +++ G  ++      + +L 
Sbjct: 65  RFCHRLDFSTSGVLCLALHKQSARSAQRAFHQRLAKKYYVAILEGHVRD------DHVLV 118

Query: 205 KSHIGGDY--VHVVKQNEKGANYAIS----HFKVIDCF-----AQKFCWLEMQPHTGRTH 253
            S IG D    H  K      +Y +S      +++  +      +    + ++P TGR H
Sbjct: 119 DSPIGEDKRPQHSHKMCTADKDYCVSPRGAQTRLLVLWRGLLKGRPATKVLLRPVTGRRH 178

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           QLRVH   +G  IVGD  Y  +           +++LHA  + LP  E   L +  P P 
Sbjct: 179 QLRVHCASLGHTIVGDFTYGEDASS-------RRMFLHACRLVLP-TEVETLDVETPDP- 229

Query: 314 HMVKTWDSLGFKYDRNLYIKRLYSQDE 340
                +D+ G  Y + +    L+ + E
Sbjct: 230 -FAADFDA-GSDYGQTVPTASLFEELE 254


>gi|170727493|ref|YP_001761519.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169812840|gb|ACA87424.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 283

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 38/161 (23%), Positives = 73/161 (45%), Gaps = 23/161 (14%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+  +G++++  +++    L + F +R + K Y  +V G   + +E +       
Sbjct: 132 IVHRLDRAATGLVLIGHSKSITAALAKLFELRELDKYYQVIVEGRFNSGREEV------- 184

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGC 264
                    V   ++     A SH K+++  A Q    ++++  +GR HQ+R+H   +G 
Sbjct: 185 ---------VTVDSDVDNKSACSHAKLLEYDAKQNRSLVQVKIDSGRKHQIRIHMASLGH 235

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           P+VGD  +         S     L L + Y+  P P  G +
Sbjct: 236 PVVGDRLH------GIASGSDINLQLTSCYLKFPCPVTGEI 270


>gi|225444351|ref|XP_002264641.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|302144082|emb|CBI23187.3| unnamed protein product [Vitis vinifera]
          Length = 472

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/227 (25%), Positives = 87/227 (38%), Gaps = 52/227 (22%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           D+   I+   +S + V +KPAG SV G +           +         R TH++D  T
Sbjct: 209 DWKSRIIAVTESYV-VLDKPAGTSVGGTTDNIEESCATFATRALGLTTPLRTTHQIDNCT 267

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-----GI------PKNKKECIANWLL 203
            G +V+ART+          R ++++K+Y +L       GI      P N    IA  L+
Sbjct: 268 EGCVVLARTKEYCSVFHGKIREKKVKKLYRALAAAPMPIGIVTHYMRPVN----IAPRLI 323

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---------FAQKFC-----W------- 242
            +  I G Y              +   +V++C           +K+C     W       
Sbjct: 324 SEDFIKGWY--------------LCQLEVLECKEVPWPSTLIEEKYCIEDRGWPLKNSAF 369

Query: 243 -LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
             ++   TGRTHQ+R      G PIVGD  Y        TSP  N  
Sbjct: 370 KCKINLLTGRTHQIRAQLAACGAPIVGDSMYMPAAIAEITSPGLNPF 416


>gi|289662056|ref|ZP_06483637.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 349

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/204 (26%), Positives = 93/204 (45%), Gaps = 18/204 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ D+ + V  KP  + V   G+ +   +   L   +D+    P   HR+D++T+G+++
Sbjct: 142 VVHADADLVVACKPHFLPVAPAGAYVRETLLTRLVRRLDNPALVP--LHRIDRDTAGLVL 199

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            +   A        FR RRI+K Y ++   +PK     +    L+     G+    +++ 
Sbjct: 200 FSANPATRGVYQALFRERRIRKQYLAVAPPLPKLTFPYVHRSRLEP----GEPFFRMREG 255

Query: 220 EKGANYAISHFKVIDCFAQ-KFCWLEM-QPHTGRTHQLRVHALHMGCPIVGDHKYC---A 274
           E   N       VID  A+ +  W  + +P TGR HQLRVH   +G PI+ D  Y    A
Sbjct: 256 EGEPNSET----VIDVVARAEDTWTYLLEPVTGRKHQLRVHMAALGAPILHDRFYPDLEA 311

Query: 275 NFKGNFTSPIQNKLYLHARYMDLP 298
               +   P+Q  L+ H    D P
Sbjct: 312 QRPDDPERPLQ--LFAHTLAFDDP 333


>gi|242212124|ref|XP_002471897.1| predicted protein [Postia placenta Mad-698-R]
 gi|220728995|gb|EED82877.1| predicted protein [Postia placenta Mad-698-R]
          Length = 435

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 37/127 (29%), Positives = 61/127 (48%), Gaps = 6/127 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKS 206
           +RLD+ TSG++++  + + A  LT+ F    I+K Y +   G  PK +  C    L    
Sbjct: 136 NRLDRLTSGLMIIPLSSSMANTLTQEFAAGTIRKEYIARCRGQFPKEELACEVPLLTIDR 195

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +G + VH   +  K   +   H+      +   C    +P TGR+HQ+RVH  ++G P+
Sbjct: 196 QMGLNVVHPEGKPAKTI-FKRMHYDANTDTSVVHC----KPLTGRSHQIRVHLQYLGHPV 250

Query: 267 VGDHKYC 273
             D  Y 
Sbjct: 251 ANDPIYS 257


>gi|213420423|ref|ZP_03353489.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 101

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 34/101 (33%), Positives = 60/101 (59%), Gaps = 1/101 (0%)

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +V GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R +
Sbjct: 2   AVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREK 60

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            +QK Y +LV G  ++  + +   LLK     G+ +  V Q
Sbjct: 61  GMQKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQ 101


>gi|169350972|ref|ZP_02867910.1| hypothetical protein CLOSPI_01749 [Clostridium spiroforme DSM 1552]
 gi|169292034|gb|EDS74167.1| hypothetical protein CLOSPI_01749 [Clostridium spiroforme DSM 1552]
          Length = 310

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 57/221 (25%), Positives = 102/221 (46%), Gaps = 24/221 (10%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQK--PRLTHRLDQETSGILV 159
           YE+  I + NKP   ++   +    + +  ++ ++     Q    R  HRLD++T+G+++
Sbjct: 96  YENDFILIVNKPINTTIYPETKKELNTLCNYVANYYLETNQYLLIRHIHRLDKDTTGLVL 155

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQ 218
             +       L      + I++ Y ++  GI       I + L     I  D +V+ ++ 
Sbjct: 156 FCKCPLLQPILDNMMANKLIKRSYIAICKGI-------IDHDLTINRDIARDRHVNKMRI 208

Query: 219 NEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             KG   AI+  K+I    QK    C  +++  TGR HQ+RVH   +  P++ D  Y   
Sbjct: 209 TNKGLK-AITEIKIIKHDKQKNYTVCKCDLK--TGRKHQIRVHLASINHPLLSDPLY--- 262

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
             GN  S + ++L LHA  ++  HP    ++ + A LP  M
Sbjct: 263 --GN-KSKLIDRLALHAYKLEFIHPVTKQQIIVKADLPQDM 300


>gi|226324971|ref|ZP_03800489.1| hypothetical protein COPCOM_02763 [Coprococcus comes ATCC 27758]
 gi|225206319|gb|EEG88673.1| hypothetical protein COPCOM_02763 [Coprococcus comes ATCC 27758]
          Length = 121

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 31/97 (31%), Positives = 54/97 (55%), Gaps = 6/97 (6%)

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           NEK    A++H++V++ F   + ++  +  TGRTHQ+RVH   +  P++GD   C     
Sbjct: 18  NEKNGRNAVTHYRVLERFGD-YTYIACELETGRTHQIRVHMASIHHPLLGD---CVYGPA 73

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
                +Q +  LHA+ + + HP  G+ ++  APLP +
Sbjct: 74  KCPWTLQGQT-LHAKILGIIHPRTGKYMEFDAPLPEY 109


>gi|149212744|ref|NP_439586.2| hypothetical protein HI1435 [Haemophilus influenzae Rd KW20]
 gi|262021233|gb|AAC23084.2| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
          Length = 182

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 39/161 (24%), Positives = 72/161 (44%), Gaps = 14/161 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDGFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGR 251
           K    AI+ ++ +               ++  +++ PHTG+
Sbjct: 120 KEPQEAITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGQ 160


>gi|322418714|ref|YP_004197937.1| pseudouridine synthase [Geobacter sp. M18]
 gi|320125101|gb|ADW12661.1| pseudouridine synthase [Geobacter sp. M18]
          Length = 293

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 44/157 (28%), Positives = 69/157 (43%), Gaps = 6/157 (3%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HR+D+ET+GI++ +          E FR   I+K Y +L  GI     E    W ++   
Sbjct: 131 HRIDRETAGIVLFSVNPQTRGRYGELFRDGSIEKSYRALSAGIAAAGGE---EWQVENRL 187

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+    +   + G   A S  ++I+          + P TG+THQLRVH   +G PI+
Sbjct: 188 VHGEPWFTMT-TQPGPPNARSQIRLIEERG-GVSHFSLTPLTGKTHQLRVHMSGLGMPIM 245

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            D  Y    K       +  L L A+ +    P  G+
Sbjct: 246 HDRLY-PQLKPRHPDDFEKPLQLLAQRLRFKDPVSGK 281


>gi|237750038|ref|ZP_04580518.1| pseudouridine synthase D [Helicobacter bilis ATCC 43879]
 gi|229374449|gb|EEO24840.1| pseudouridine synthase D [Helicobacter bilis ATCC 43879]
          Length = 326

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 70/317 (22%), Positives = 136/317 (42%), Gaps = 41/317 (12%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI--LDSSVNLTKHSDFLK 98
           + S  V++++K  K +  ++ G  + I  + N    I  ++ I  LD  V          
Sbjct: 33  IESNLVKMNEKNTKKSQILKKGACIEIYTIKNTSKVINTDELIQGLDIEV---------- 82

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHR 149
              ++E+S   + NKP  + V     +    +  L  ++ +K  +           + HR
Sbjct: 83  ---IHENSDYLILNKPRNLVVHHAPSVK---EVTLTDYLSAKNYELSTINGEMRFGIVHR 136

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSH 207
           LD++TSG ++VA+  A+     E  + R + +IY  ++    ++    EC   ++ +  +
Sbjct: 137 LDKDTSGAILVAKNNASHLRFAEMLQNRTMGRIYICVINKALQHNTFVEC---YMGRNPN 193

Query: 208 IGGDYVHVVKQNEKGANYAISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                  + K+    A  + S F K+++     F  + ++  +GRTHQ+RVH   +   I
Sbjct: 194 NRLKMAKLDKEKYPFARDSKSEFRKIMESKNGVFELIGVRLFSGRTHQIRVHLSTLQRYI 253

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
            GD  Y      N  S  + K+ LHA+   L + +G     +A +P  ++K  +     Y
Sbjct: 254 YGDMLYSPE---NLKSTYKTKMLLHAQ---LLYFDGNVF--SAKIPKDLLKFLNENFINY 305

Query: 327 DRNLYIKRLYSQDECKQ 343
           +  L       QDE ++
Sbjct: 306 ESKLEAFLSQWQDELRK 322


>gi|168018525|ref|XP_001761796.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162686851|gb|EDQ73237.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 346

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 53/233 (22%), Positives = 104/233 (44%), Gaps = 16/233 (6%)

Query: 50  KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL---KSILLYEDS 106
           + R  +   ++ G++ R+   + A ++++++ + +   V+  +H   +   + I+L E  
Sbjct: 36  RPREYYEEAVKRGRI-RVEGKVVAPSYVVRDSQTMSHFVH--RHEPPVLAGRVIVLEEGP 92

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL-THRLDQETSGILVVARTRA 165
            I V +KPA + V       Y  +  +          P    HRLD+  SG+L++AR   
Sbjct: 93  DIIVVSKPATVPVHPCG--QYRKNSVISILEAEHKTGPLFPVHRLDRLVSGLLILARNSR 150

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLL-----KKSHIGGDYVHVVKQN 219
            A    +      +QK Y + V G+ P  + E  A  +      + S    + + V  ++
Sbjct: 151 TADFFRQEIEAGVVQKQYVAKVKGVFPAEEVELNAAVIYDPREGRSSVEVQNNLEVTPES 210

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +  +  + + F+ +         ++  P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 211 DAKSKESCTKFRRLSTDGVD-SIVQCMPLTGRTHQIRVHLQYLGFPIANDDLY 262


>gi|307069601|ref|YP_003878078.1| putative pseudouridine synthase, RluA family [Candidatus Zinderia
           insecticola CARI]
 gi|306482861|gb|ADM89732.1| putative pseudouridine synthase, RluA family [Candidatus Zinderia
           insecticola CARI]
          Length = 242

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 51/173 (29%), Positives = 90/173 (52%), Gaps = 11/173 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ED  I + NKP  +SV  G  I  ++  FLK   + K     L HR+D++ SGIL+++
Sbjct: 18  IFEDKYIIIINKPNYLSVHSGYKIKLNLIEFLKKKYNLK--LINLIHRIDKDISGILLLS 75

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGGDYVHVVKQN 219
           +++   + + + F+ ++I+K Y S+V G     NKK  +            +Y++   +N
Sbjct: 76  KSKKILKIINKKFKNKKIKKNYLSIVHGNLNFINKKIKLFFKKNNNFINKKNYIN---RN 132

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            K     IS  K+     + F  + ++  TG+ HQ+R+H   +G PI+ D KY
Sbjct: 133 GKKTYSIISLIKI----YKNFSLINIKLITGKMHQIRMHLNFLGFPIIFDKKY 181


>gi|116201645|ref|XP_001226634.1| hypothetical protein CHGG_08707 [Chaetomium globosum CBS 148.51]
 gi|88177225|gb|EAQ84693.1| hypothetical protein CHGG_08707 [Chaetomium globosum CBS 148.51]
          Length = 475

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 53/212 (25%), Positives = 86/212 (40%), Gaps = 44/212 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           +++ED  + V NKP+G+ V       Y+ +  ++     +G    PR  +RLD+ TSGI+
Sbjct: 136 IIHEDDDMIVINKPSGVPVHPAG--RYNYNSIVEIMKAERGLDFTPRPCNRLDRLTSGIM 193

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
            +A+   AA+ L      R ++K Y + V G  P  +  C    L     +G   ++ V+
Sbjct: 194 FIAKHTKAAEQLGVQIFQRSVRKEYVARVIGKFPDGEVVCDQPILQISPKLG---LNRVR 250

Query: 218 QNEKGANYA---ISHFKVIDCFA---------------------------------QKFC 241
            N K A      ++++      A                                 + + 
Sbjct: 251 ANGKAARTVFKRLAYYPPASGLAVSPNDGGTTGPAEEPVSGRSESAPRPTGGRKADEGYS 310

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +   P TGRTHQLRVH   +G PI  D  Y 
Sbjct: 311 IVRCLPVTGRTHQLRVHLQFLGHPIQNDPIYA 342


>gi|114045928|ref|YP_736478.1| pseudouridine synthase [Shewanella sp. MR-7]
 gi|113887370|gb|ABI41421.1| pseudouridine synthase [Shewanella sp. MR-7]
          Length = 308

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 44/150 (29%), Positives = 75/150 (50%), Gaps = 16/150 (10%)

Query: 148 HRLDQETSGILVVARTRAAAQHLT-ESFRMRRIQKIYWSLVWGIPK-------NKKECIA 199
           HRLD+ET+G++++  TR   +H+  + F    I+K Y ++    P+        +     
Sbjct: 134 HRLDRETAGVILMT-TRPETRHIYHQLFVDDAIRKDYQAIAKLTPEIMAQYACGELTLPL 192

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +W +K      +    +K  E  AN   +H ++ +     +F   E+ P TG+THQLRVH
Sbjct: 193 HWTVKNRMQRSEPSFTMKIVEGEAN---THSEISLVAVKGEFGLFELSPITGKTHQLRVH 249

Query: 259 ALHMGCPIVGDHKYCANF-KG--NFTSPIQ 285
              +G P++ D  Y   + KG  +FT P+Q
Sbjct: 250 MQSLGMPLLNDRFYPTLYPKGPDDFTKPLQ 279


>gi|325676532|ref|ZP_08156210.1| RNA pseudouridine synthase [Rhodococcus equi ATCC 33707]
 gi|325552710|gb|EGD22394.1| RNA pseudouridine synthase [Rhodococcus equi ATCC 33707]
          Length = 332

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 52/186 (27%), Positives = 85/186 (45%), Gaps = 19/186 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ D  + V +KP  + +  GG  +       L++ +D+    P   HRLD+ T+G+++
Sbjct: 96  IVHVDDDLVVIDKPHFLPTTPGGRYLRESALVRLRTRLDNPDLTP--IHRLDRATAGLVM 153

Query: 160 VAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-----LLKKSHI--- 208
            +    TR A Q L   F  RR+ K+Y ++    P  K +  A       +L ++HI   
Sbjct: 154 FSARPATRGAYQSL---FEKRRVTKVYEAVSALPPAWKPDVPALGGHPVPVLYRNHIEAR 210

Query: 209 -GGDYVHVVKQNEKGANYAIS-HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            G   V V       +   I  H   +    +      ++PHTGR HQLRVH   +G  I
Sbjct: 211 RGELRVAVDPSRPPNSETLIEVHGTGVSASGRTVLHTILRPHTGRMHQLRVHLAALGAGI 270

Query: 267 VGDHKY 272
           +GD  Y
Sbjct: 271 LGDSWY 276


>gi|302796533|ref|XP_002980028.1| hypothetical protein SELMODRAFT_111763 [Selaginella moellendorffii]
 gi|300152255|gb|EFJ18898.1| hypothetical protein SELMODRAFT_111763 [Selaginella moellendorffii]
          Length = 428

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 54/204 (26%), Positives = 89/204 (43%), Gaps = 43/204 (21%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRL-THRLD 151
           KS +L E+    V +KPAG+SV GGS     +D   +S V    +      P L TH++D
Sbjct: 149 KSRILAENDLFVVLDKPAGVSV-GGS-----VDNLEESCVTFASRALGMAFPLLVTHQID 202

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGG 210
             T G +V+A+ +    +     R R++ K Y  L    +P      I +  ++  H   
Sbjct: 203 NCTEGCVVLAKDKDFVSNFNRLLRTRKVDKRYLVLAASPVPLG----IVSHYMRPDHFAP 258

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKF-------------CWLEMQPH--------- 248
              H++ Q+++   + +   +V+ C   ++             C LE   H         
Sbjct: 259 ---HLLSQDKR-QGWHLCSMEVLQCHQVEWPSEARLRENGVSNCELEHDGHAYECEVKLL 314

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TG+THQ+R     +G PI+GD  Y
Sbjct: 315 TGKTHQVRAQFAALGAPILGDTIY 338


>gi|300933570|ref|ZP_07148826.1| putative pseudouridylate synthase [Corynebacterium resistens DSM
           45100]
          Length = 224

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 55/219 (25%), Positives = 95/219 (43%), Gaps = 17/219 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++ E   + V NKP G+ S   G  +       L+  V  +       HRLD+ T G+LV
Sbjct: 5   VIAETPDVLVVNKPHGLPSTPNGRFMRACAQTMLR--VRREESDLVAIHRLDRLTGGVLV 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSL-VWGIPKNKKECIANWL---LKKSHIGGD-YVH 214
           ++R      +L   F+ R ++K+Y ++  + +P      ++ W    ++ + I  D  V 
Sbjct: 63  LSRRPETRSYLQTQFQNRTVRKVYEAVSAYRLPH-----LSQWTRFEVEMTKIPHDPQVK 117

Query: 215 VVKQNEKGANYAISHFKVI--DCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           V + N K     +     +  D   +   W  E++P TG THQ+R    H+G P++GD  
Sbjct: 118 VGQGNGKTTETWVRLLGPVASDQRKEAASWRYEVRPKTGHTHQIRALMNHLGAPLIGDDT 177

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           Y   ++      +   + L A  + L  P G      AP
Sbjct: 178 Y-PEYQPRPAEKLDPTMGLQAVELTLCLPGGEEAIFRAP 215


>gi|78776648|ref|YP_392963.1| pseudouridine synthase [Sulfurimonas denitrificans DSM 1251]
 gi|78497188|gb|ABB43728.1| Pseudouridine synthase [Sulfurimonas denitrificans DSM 1251]
          Length = 244

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 91/212 (42%), Gaps = 36/212 (16%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++E+  + V +KPA ++       +  I+   K  V        L HRLD+ETSG+L++ 
Sbjct: 61  IFENDDLVVVDKPAHVN-------SDEIERQFKPAV--------LLHRLDKETSGVLMLV 105

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-KKSHIGGDYVHVVKQNE 220
           +     +   + F+  R+ K Y + + GI     +     L  KK++     V     + 
Sbjct: 106 KNEEFREKAIQEFKKDRVYKEYIAWIEGILSEPVDIDRPILTTKKNNRASSNV-----SS 160

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG       F   D  +     ++   H GRTHQ+RVH  ++  PIVGD +Y        
Sbjct: 161 KGKPARTEVFP--DLVSANKTKVKCIIHHGRTHQIRVHLRYIEHPIVGDEQYGGRR---- 214

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                 ++ LHA  + L       ++ TAP P
Sbjct: 215 ----AKRVMLHAHKVRLLG-----MEFTAPEP 237


>gi|50085467|ref|YP_046977.1| putative pseudouridylate synthase [Acinetobacter sp. ADP1]
 gi|49531443|emb|CAG69155.1| putative pseudouridylate synthase [Acinetobacter sp. ADP1]
          Length = 304

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 49/204 (24%), Positives = 90/204 (44%), Gaps = 26/204 (12%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           H  F  SIL +E+  + V +KP  +++   G  +   +   LK    ++   P   HRLD
Sbjct: 89  HVPFEHSIL-FENHDLLVVDKPHFLTISPTGKYVQETLLVRLKQQTGNEDLTP--IHRLD 145

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIY-----WSLVWGIPKNKKECIANWLLKKS 206
           +ET+G+++  +   +       F  R + KIY     ++ +   P+  + C+        
Sbjct: 146 RETAGVVLFCKRPESRGIYQTLFAKREVHKIYHAIAAYNPLITFPQTLRLCLEK------ 199

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE--MQPHTGRTHQLRVHALHMGC 264
              G+  + ++ N  G    ++    I+C A    W +  + P TG+ HQLR+H   +  
Sbjct: 200 ---GNPFYTMQVNPNGQ---VNSETRIECLAHNQQWAKYRLSPSTGKQHQLRLHLSFLNI 253

Query: 265 PIVGDHKYCA---NFKGNFTSPIQ 285
           PI  D  Y         +F++P+Q
Sbjct: 254 PIKNDPFYPVVEHKADDDFSAPLQ 277


>gi|127514276|ref|YP_001095473.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126639571|gb|ABO25214.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 313

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 99/226 (43%), Gaps = 19/226 (8%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQE 153
           F +SIL Y D +I + NKP  +++  G  +   I+  L + +  +     L   HRLD+ 
Sbjct: 92  FSESIL-YLDEQIVLANKPHFMALHPGGEV---INQCLINRLRERTGCETLIAAHRLDRA 147

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN-------WLLKKS 206
           T+GI+++ +   +       FR  +I K Y +L    P+   E  A        W +K  
Sbjct: 148 TAGIVLLVKQSDSRDAYHGLFRHGQITKEYQALARLTPELLAEYHAGKLSLPRRWTVKNR 207

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              G     ++  +  AN   SH ++ +     +    E+ P TG+THQLR+H   +G P
Sbjct: 208 IDKGTPSFTMRIVDGEAN---SHSEIALVSVEGEIGRFELMPITGKTHQLRLHMNSLGMP 264

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           I+ D+ Y           +   + L AR +    P  GR L I  P
Sbjct: 265 ILNDNFY-PTLLPRSAEDVAQPMKLLARRLAFTDPVTGRKLDICLP 309


>gi|198414279|ref|XP_002128102.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 2 [Ciona intestinalis]
          Length = 456

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 54/217 (24%), Positives = 96/217 (44%), Gaps = 9/217 (4%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED-SKIYVFNKPAGI 117
           ++ G  V + PV+ +L+  +++  ++ + ++  +       + + ED SK  V NKP+ I
Sbjct: 143 LEGGVKVNLKPVV-SLDVKLRDNDMISARLHRHEAPVLDTKVEIIEDNSKYVVVNKPSSI 201

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRL-THRLDQETSGILVVARTRAAAQHLTESFRM 176
            +       +  +  +       G +  L  HR+D+ TSGI++  +T+  A  + +    
Sbjct: 202 PIHPCG--RFRNNSLVYILAKDLGYQGLLGCHRIDRLTSGIVIFGKTKNIAHKVAKEISE 259

Query: 177 RRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           R+++K Y   V G  P     C     L    +G  Y    K        A + F  +  
Sbjct: 260 RKVEKQYVCKVVGEFPSTDIVCNEPVSLFNRKLG--YAVAWKVEGVVGKEASTWFTRMSY 317

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                  L  +P TGRTHQ+RVH  ++G PI+ D  Y
Sbjct: 318 DGTNSVVL-CKPKTGRTHQIRVHLQYLGFPIINDPIY 353


>gi|114049531|emb|CAJ75876.1| hypothetical protein [Lactobacillus plantarum subsp. plantarum]
          Length = 122

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 37/105 (35%), Positives = 51/105 (48%), Gaps = 11/105 (10%)

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKG 278
           K    A++HFKV+  + Q +  +  +  TGRTHQ+RVH   +G P+VGD  Y      KG
Sbjct: 19  KTGRPAVTHFKVLKRY-QHYTLISCRLETGRTHQIRVHLQSIGHPLVGDPLYGPKKTIKG 77

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           +         +LHA+ +   HP  G  L   APLP     T   L
Sbjct: 78  HGQ-------FLHAKLLGFKHPVTGDLLTFEAPLPPIFTTTLAKL 115


>gi|260905406|ref|ZP_05913728.1| ribosomal pseudouridine synthase [Brevibacterium linens BL2]
          Length = 332

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 100/222 (45%), Gaps = 55/222 (24%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQ----KPRLT--HRLDQE 153
           +++ED  + V +KP  + S   G         F++  V ++ +    +P L   HRLD+ 
Sbjct: 100 VVFEDDDLLVVDKPHFLASTPNGR--------FVRECVVTRARLDFDQPDLVAIHRLDRV 151

Query: 154 TSGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI-- 208
           T+G+L++++   TR   Q L   F+ R + K Y +L    P +    +   L+K+S +  
Sbjct: 152 TAGLLILSKRPETRGRYQRL---FQDRLVTKTYRALAAMPPAD----LELPLVKESRLVK 204

Query: 209 --GGDYVHVVKQNEKGANYAISHF--------------------KVIDCFAQKFCWLEMQ 246
             GG  V  V + E  A   IS                       V +C        +++
Sbjct: 205 PRGGRQVLEV-EGEPNAFSKISLLGERTPPSPRWSDATEPPPRRSVGEC--PSIGEYQLE 261

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKG---NFTSPIQ 285
           P TG+THQLRVH   +G PI+GD  Y  +      +F+SP+Q
Sbjct: 262 PLTGKTHQLRVHMNSLGLPILGDPVYPVDRAPDPYDFSSPLQ 303


>gi|241758655|ref|ZP_04756769.1| YabO/YceC/SfhB family protein [Neisseria flavescens SK114]
 gi|241321166|gb|EER57362.1| YabO/YceC/SfhB family protein [Neisseria flavescens SK114]
          Length = 307

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 37/163 (22%), Positives = 77/163 (47%), Gaps = 13/163 (7%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A  +     F+ + +QK Y ++       + +      L    
Sbjct: 148 HRLDKDTAGVMLLSLNPATRRDYQTMFQEKTVQKTYEAVA----PTRTDLDYPLDLSSRM 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             G+   + ++ E   N A +  ++I+     F    + PHTG+ HQLRVH + +  P++
Sbjct: 204 ERGEKFFLTRETEGEPN-AHTTIELIENRGA-FSLYRLTPHTGKKHQLRVHMMSLNMPLM 261

Query: 268 GDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    A    ++  P++    L A+ ++   P  G +++
Sbjct: 262 NDALYPNPLAAGDEDYDRPLK----LLAKRIEFTDPVSGEIRV 300


>gi|224438280|ref|ZP_03659207.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
 gi|313144719|ref|ZP_07806912.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
 gi|313129750|gb|EFR47367.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
          Length = 245

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 92/211 (43%), Gaps = 41/211 (19%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           ++  K  +++ED +I   +KP  I        +Y +    + W         L HRLD++
Sbjct: 53  AEIKKPKVIFEDKQILALDKPPFIE-------SYDLSDMFEGW--------SLLHRLDKQ 97

Query: 154 TSGILVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPK-----NKKECIANWLLKKS 206
           TSG++++ +  +   HL   E+F+ + + K Y  L+ GI       NK          KS
Sbjct: 98  TSGVILLIQENSPF-HLKAKEAFKKQAVYKEYICLLHGILADSITINKPISTIKKGFAKS 156

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            I         +N   A+  ++   ++    Q    +     TGRTHQ+RVH   +  PI
Sbjct: 157 RID--------KNGLSAHTQLTPLSIVGKKTQAQAIIT----TGRTHQIRVHCQSINHPI 204

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           VGD  Y     GN T+    +L LHA  + L
Sbjct: 205 VGDTLY-----GN-TNDNAKRLMLHAHKIRL 229


>gi|167624728|ref|YP_001675022.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167354750|gb|ABZ77363.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 281

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 46/203 (22%), Positives = 90/203 (44%), Gaps = 38/203 (18%)

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----SGIAYHID 130
           H+   Q +LD +V         ++ LL++  +  ++ KP G+  QG      + I  +I+
Sbjct: 68  HLYYNQAVLDETVT--------EAELLFDQEQYSIWYKPFGMRCQGSKWSDHTTINRYIE 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L     +  +   L HRLD   +G++V+   +     + + F  R + K Y  +V G 
Sbjct: 120 THL-----NPARNAYLIHRLDLAATGLIVLGHNKKVTAAIAKLFETRALDKFYQVIVEGK 174

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHT 249
             + K  I   +  KS                   A+SH + ++  ++     ++++  +
Sbjct: 175 FPDGKVTIDTDVDNKS-------------------ALSHAERLEYNSELNQSKVQVKIES 215

Query: 250 GRTHQLRVHALHMGCPIVGDHKY 272
           GR HQ+R+H   +G P+VGD ++
Sbjct: 216 GRKHQIRIHMASLGHPVVGDRQH 238


>gi|322817842|gb|EFZ25435.1| hypothetical protein TCSYLVIO_8401 [Trypanosoma cruzi]
          Length = 733

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 61/241 (25%), Positives = 102/241 (42%), Gaps = 45/241 (18%)

Query: 101 LLYEDSKIYVFNKPAGIS--------VQGGSGIAYHI---------DGFLKSWVDSKGQK 143
           +++ED+ I V NKP  ++         Q     A  +         +G     V  +GQ 
Sbjct: 510 VIFEDNDILVLNKPPHLASSRHALSCTQMNDKRATDVVSLILASTKNGETMRGVFRQGQ- 568

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLT----ESFRMRRIQKIYWSLVWGIPKNKKECIA 199
               HRLD ETSG LV+A+T  AA  L      S    +  K+Y +L   +  +      
Sbjct: 569 ---VHRLDAETSGCLVMAKTDCAADSLRHQMGTSAAYSQCNKVYLALCAVMEPD------ 619

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVH 258
              L++  + G     V ++      + + ++VI  F + +   LE +   G+ HQ+R H
Sbjct: 620 ---LRRIPLRG-----VLRDPMDPKIS-TKYRVIRFFRKARVALLECRIQQGKKHQIRRH 670

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
               G PI+ D ++        T+P+ +++ LHA  + L HP     +   APL     +
Sbjct: 671 LAAAGLPILQDVEHGG---AACTTPLIDRVALHAAALTLVHPRTAEVVTFVAPLAMDFAE 727

Query: 318 T 318
           T
Sbjct: 728 T 728


>gi|297795919|ref|XP_002865844.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297311679|gb|EFH42103.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 392

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 51/194 (26%), Positives = 81/194 (41%), Gaps = 8/194 (4%)

Query: 100 ILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++L+++  +    KPA + V   G      + G L +  D     P   HRLD+  SG+L
Sbjct: 134 VILHQEPDVVTVCKPASVPVHPCGQYRKNTVVGILDAEHDLGTLFP--IHRLDRLVSGLL 191

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSH---IGGDYVH 214
           ++ART A A    +      ++K Y + V G+ P+++    AN     S       D   
Sbjct: 192 IIARTAAKADFFRQQIEGGMVKKRYIAKVIGVFPEDEMIVDANINYNGSEGRSTAEDPDS 251

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                +     A +    ID        +  +P TGRTHQ+RVH  + G PI  D  Y  
Sbjct: 252 SGDDKKVKGKPACTKLTRIDTNG-THSLVSCEPVTGRTHQIRVHLQYTGHPIANDPLYLN 310

Query: 275 NFKGNFTSPIQNKL 288
               N  + I  ++
Sbjct: 311 QHIDNLETYIAKRI 324


>gi|242212896|ref|XP_002472279.1| predicted protein [Postia placenta Mad-698-R]
 gi|220728646|gb|EED82536.1| predicted protein [Postia placenta Mad-698-R]
          Length = 448

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 58/234 (24%), Positives = 100/234 (42%), Gaps = 25/234 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L SG   ++ K  K +  +Q+G   RI  V++       E  +  + V +  H       
Sbjct: 46  LESGVTTINGKIAKPDTIVQNGD--RIENVVHR-----HEPPVTATPVRIIHHD------ 92

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
               + +  + +KP  I V   G      +   LK+  D   +K    +RLD+ TSG+++
Sbjct: 93  ---REREFIIIDKPGSIPVHASGRFFRNSLVEILKN--DFGFKKVYTINRLDRLTSGLMI 147

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +  + + A  LT+ F    I+K Y +   G  P+ +  C    L     +G + VH   +
Sbjct: 148 IPLSSSMANTLTQEFAAGTIRKEYIARCRGQFPEEELACEVPLLTIDRQMGLNVVHPEGK 207

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             K   +   H+      +   C    +P TGR+HQ+RVH  ++G P+  D  Y
Sbjct: 208 PAKTI-FKRMHYDANTDTSVVHC----EPLTGRSHQIRVHLQYLGHPVANDPIY 256


>gi|238878813|gb|EEQ42451.1| conserved hypothetical protein [Candida albicans WO-1]
          Length = 402

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 102/229 (44%), Gaps = 39/229 (17%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLD 151
           H+D +KS+  YED +I V +KP+GI         Y+ +   +K  ++         HRLD
Sbjct: 103 HNDIIKSV--YEDDEILVVDKPSGIPTHPTGNYYYNSLSEIIKQQLNIDS--IWTCHRLD 158

Query: 152 QETSGILVVARTRAAAQHLTESFRMRR--IQKIYWSLVWG-IPK--NKKEC------IAN 200
           + TSG+LV+A+T+      ++  R  +   +K Y + V G  P+  ++  C      +  
Sbjct: 159 KVTSGVLVLAKTKNGGVRFSKLMRDSKQYTEKTYLARVSGKFPEGIHRYRCPIFAVNMNG 218

Query: 201 WLLKKS--HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +L+  +   +  D   + ++ +  A+   S  K +               TG+ HQ+R+H
Sbjct: 219 YLMSGNMEELPTDSTTIFERIKYNASLDESLIKCVSI-------------TGKFHQIRIH 265

Query: 259 ALHMGCPIVGDHKYCAN------FKGNFTSPIQNKLYLHARYMDLPHPE 301
             ++G PIV D  Y          K N    + NKL+  A+Y    H E
Sbjct: 266 LRNLGFPIVNDSFYQPEQDQLTIQKCNIERQLYNKLF--AKYPQFKHFE 312


>gi|26345624|dbj|BAC36463.1| unnamed protein product [Mus musculus]
          Length = 315

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 48/199 (24%), Positives = 88/199 (44%), Gaps = 14/199 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKPR 145
           + L + +  L++ ++ +   +   NKP G+ V G  G      +   L   +  + Q+ +
Sbjct: 63  LGLEELAHVLRAAVVDQKGPLVTLNKPQGLPVTGRPGELTLLSVLPQLSQALGLEHQELQ 122

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANW 201
           +     +E SG+++++     A  L + F    R +R    Y ++  GIP+  +  +   
Sbjct: 123 VVRAPGKEASGLVLLSSCPQTASRLQKFFIHSRRAQRPTATYCAVTDGIPEPSEGTVCMP 182

Query: 202 LLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQL 255
           L  +     D    V     K  ++G    +S F V+     + C L ++QP T   +QL
Sbjct: 183 LKMEQMNDVDLAVPVMSPSRKDIQEGVKRTLSRFHVMA--TGRGCALVQLQPLTVFPNQL 240

Query: 256 RVHALHMGCPIVGDHKYCA 274
           +VH     CPI+GDH Y A
Sbjct: 241 QVHMALQLCPILGDHTYAA 259


>gi|291320720|ref|YP_003515985.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           agalactiae]
 gi|290753056|emb|CBH41032.1| Ribosomal large subunit pseudouridine synthaseC [Mycoplasma
           agalactiae]
          Length = 284

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 65/260 (25%), Positives = 110/260 (42%), Gaps = 36/260 (13%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRI-QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           + ++ R   ++V+ KR+  +N + ++G  + I  + +  + +I      D+S  L     
Sbjct: 31  IYRLFRQKSIKVNNKRIADSNYVVKTGDEIIIYGIKDEPSFVI-----YDNSWKLD---- 81

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
              S ++YED  I + NK AG  V G S  +   +  +LK +  +   +P    RLD+ T
Sbjct: 82  ---SDIVYEDDNILLINKKAGTIVHGDSNCLDNQVFSYLK-FKQNSAFRPSHVGRLDKWT 137

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+   A   L    +   + KIY   V     N  + I +  +    +    V 
Sbjct: 138 SGLIMYAKNYPALAELNR--KTEFLDKIY---VLKSDYNPHDEIVSVYVHHDELQQKMVA 192

Query: 215 VVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                      A + F   D   +AQ F        TGR HQ+R    ++  PI GD KY
Sbjct: 193 TKNMQHPDDKMAKTRFFKKDNKLYAQLF--------TGRKHQIRATLEYLEYPIYGDSKY 244

Query: 273 CANFKGNFTSPIQNKLYLHA 292
            +  KG        ++YLH 
Sbjct: 245 GSKAKGT------KRVYLHC 258


>gi|306837150|ref|ZP_07470087.1| RNA pseudouridine synthase [Corynebacterium accolens ATCC 49726]
 gi|304566998|gb|EFM42626.1| RNA pseudouridine synthase [Corynebacterium accolens ATCC 49726]
          Length = 313

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 56/231 (24%), Positives = 94/231 (40%), Gaps = 24/231 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED  I V +KP  ++       A HI     ++    +   +    HRLD+ TSG+L
Sbjct: 91  IIYEDDNILVADKPPFMATMPR---ARHIVETATVRLRRSTGNNELVPAHRLDRLTSGLL 147

Query: 159 VVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +  +    R A Q L   F  +++ K Y ++       +      W  + +   G+    
Sbjct: 148 LFTKHKDVRGAYQSL---FAEKKVHKTYRAVAEF---RRLPTPLQWSSRLTKTPGEIQGR 201

Query: 216 VKQNEKGANYAISHFKVIDCFA--------QKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + + E  A   +     ID                  ++P TG+THQLR+H    G PI+
Sbjct: 202 IAEGEPNAFTTLESVDPIDKAPYEKVHGPLPDLGLYTLKPQTGKTHQLRLHMWQAGIPIL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVK 317
           GD  Y   F       +   ++L A  ++   P  G+ +  T+ LP  M K
Sbjct: 262 GDPVYPTIFPEEAED-MSVPMHLTATDLEFTDPLSGKPRHFTSGLPLAMHK 311


>gi|255711220|ref|XP_002551893.1| KLTH0B02376p [Lachancea thermotolerans]
 gi|238933271|emb|CAR21455.1| KLTH0B02376p [Lachancea thermotolerans]
          Length = 397

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 47/182 (25%), Positives = 81/182 (44%), Gaps = 13/182 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E   + V +KP+GI +   +G  Y     L   + S G+    +HRLD+ TSG+L++
Sbjct: 115 VVHECEDLLVIDKPSGIPIHP-TGQYYQ--NTLVEVLKSHGKTVFPSHRLDKITSGVLIL 171

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLLKKSHIGGDYVHVVK 217
            +    A  +    R R + KIY + V G   +              K+      ++ V+
Sbjct: 172 TKNPHMANKIQHQIRQRTMSKIYLARVDGAFPMADTLGSLTPFESPDKTQTVDSAIYTVE 231

Query: 218 -QNEKGANYAISHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            + +  A ++         +  K+        +  QP TGRTHQ+R+H   +G PIV D 
Sbjct: 232 LKKQFPAAFSPPREAKTKFYPLKYYPKSDETLVACQPITGRTHQIRIHLARLGHPIVNDP 291

Query: 271 KY 272
            Y
Sbjct: 292 FY 293


>gi|70947911|ref|XP_743527.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56523063|emb|CAH79456.1| conserved hypothetical protein [Plasmodium chabaudi chabaudi]
          Length = 1071

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 41/71 (57%)

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           K I+ + ++F    ++ HTGRTHQ+RVH  H+G P+V D KY      N       +++L
Sbjct: 385 KDIETYTKEFTLCNVKIHTGRTHQIRVHMRHIGHPLVSDKKYLDASLSNLDKFWCFRMFL 444

Query: 291 HARYMDLPHPE 301
           H+  ++  +P+
Sbjct: 445 HSIILEFNNPD 455



 Score = 45.4 bits (106), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 30/50 (60%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K KK
Sbjct: 77  LCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYILLCHGRIKKKK 126


>gi|332298538|ref|YP_004440460.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332181641|gb|AEE17329.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 296

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 65/248 (26%), Positives = 98/248 (39%), Gaps = 47/248 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-------------------------IDGFLKS 135
           +LY D+ + V  K AG   +  S  A H                         I+  L S
Sbjct: 6   VLYADTDLAVVVKYAGEVCELPSAAAAHSADRPAAESPAAAEAPCLADVVRPEIEAALGS 65

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNK 194
            V   G      HRLD   SG+ V+A  R  A  L+  F  R  ++K Y + V  + KN 
Sbjct: 66  PVPFCG----CVHRLDLPVSGLCVLALNRDCAALLSAQFANRDSVEKTYLA-VTELKKNG 120

Query: 195 KECI-----ANWLLKKSHIGGD----YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            + +     +   L   H+  D       +V +  + A  A   +++     +++ ++ +
Sbjct: 121 DDSVHSGTPSPETLLSCHMIFDPKARKARIVAETTRKAKKAELAYRIAG-TGERYSFVTV 179

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
           +  TGRTHQ+R      G P+ GD KY     G   S     + LHA  +   HP  G R
Sbjct: 180 RLLTGRTHQIRCQLAAEGMPVKGDVKY-----GARRSDPLGGIRLHAYRLRFTHPVTGKR 234

Query: 305 LQITAPLP 312
              TAP P
Sbjct: 235 CDFTAPPP 242


>gi|241765468|ref|ZP_04763435.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241364778|gb|EER59767.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 303

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 62/258 (24%), Positives = 112/258 (43%), Gaps = 49/258 (18%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL--------TKHSDFLKSILL 102
            R ++  R+++G VV      +     +  Q+  +  + L          H  F +++L 
Sbjct: 43  PRGEWLQRMEAGDVV------DERGEPVLPQRRFEPGIRLYYYRHLQAEPHIPFEETVL- 95

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGILVV 160
           Y+D  + V +KP  + V   +    ++   L   +  +   P L+  HR+D++T+G+++ 
Sbjct: 96  YQDEHLLVADKPHFMPV---TPTGRYLQHTLLVRLKRRLGLPELSPLHRIDRDTAGLVLF 152

Query: 161 A---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW----LLKKSHIG--GD 211
           +   RTR   Q L   FR R+I K Y            + +A W       + HI    +
Sbjct: 153 SVQRRTRGTYQAL---FRDRQISKHY------------DAVAPWHADVPFPREHISRMEE 197

Query: 212 YVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                + +E  GA  + +H +V    A  +    + P TG+ HQLRVH   +G P+  D 
Sbjct: 198 SPQFFRMHEVAGAPNSHTHMEV-QAVAGGWALYRLSPITGKRHQLRVHMAALGLPLRNDP 256

Query: 271 KYCA---NFKGNFTSPIQ 285
            Y       +G+F+ P+Q
Sbjct: 257 FYPLVNDPPEGDFSRPLQ 274


>gi|330723753|gb|AEC46123.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyorhinis MCLD]
          Length = 289

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 63/250 (25%), Positives = 109/250 (43%), Gaps = 43/250 (17%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K+ R  +++V+KK       +Q   +++I    N     +K Q++ + +         
Sbjct: 31  IEKLFRKKEIKVNKKPQTKKYIVQQDDIIQI--YTNEKLDKLKTQELENQTKKYIPRKIK 88

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLD 151
               ++YED  I V NK   ++V  G    + +D  +  ++  K QK     P    RLD
Sbjct: 89  FDFDVIYEDENILVLNKHINVAVHDG---VWSLDNQVSKYL--KTQKINSFTPSHIGRLD 143

Query: 152 QETSGILVVARTRAAAQHLTES---------FRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           + TSG+++ A+   +   L +          F+     K  + +   I KN+K       
Sbjct: 144 KATSGLIIYAKNYFSLVELNKKQNSFLKYYIFQSDIEIKKKFEVKIKIEKNEK------- 196

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           LKK  +          N++ A  A++HF     F+ K   +  Q  TG+ HQ+RV   H+
Sbjct: 197 LKKMQVT---------NKETATVALTHF-----FSSKNLKI-AQILTGKKHQIRVSLEHL 241

Query: 263 GCPIVGDHKY 272
           G PI GD KY
Sbjct: 242 GYPIYGDTKY 251


>gi|190347088|gb|EDK39300.2| hypothetical protein PGUG_03398 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 611

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 49/173 (28%), Positives = 80/173 (46%), Gaps = 7/173 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  +   +KP+GI V       Y  +   K +    G+     +RLD+ TSG++ +
Sbjct: 192 IVHEDDDVIAIDKPSGIPVHPVG--RYRYNTITKIFQHEFGRVVHPCNRLDRLTSGLMFL 249

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T   A    +  + R ++K Y + V G  K   E I   +  K+      +++V  + 
Sbjct: 250 GKTPKGADKFVQQIKDRTVRKEYIARVIG--KFPCEEITVEVPIKTVSPKHTLNMV--DP 305

Query: 221 KGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K    A + FK I    A     ++  P TGRTHQ+RVH  H+G  I  D  Y
Sbjct: 306 KNGKEAKTKFKRISYDPASNTSIVKCYPLTGRTHQIRVHLQHIGHAIANDPIY 358


>gi|255324086|ref|ZP_05365210.1| RNA pseudouridine synthase family protein [Corynebacterium
           tuberculostearicum SK141]
 gi|255298787|gb|EET78080.1| RNA pseudouridine synthase family protein [Corynebacterium
           tuberculostearicum SK141]
          Length = 316

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 49/215 (22%), Positives = 88/215 (40%), Gaps = 15/215 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  I V +KP  ++       I       L+    +    P   HRLD+ TSGIL+
Sbjct: 91  ILFEDEHILVADKPPFMATMPRARHIVQTATVQLRRMTGNDELAP--AHRLDRLTSGILL 148

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             + R         F  +++QK Y ++       +      W    +   G+    +   
Sbjct: 149 FTKHRDVRGAYQTLFAEKKVQKTYQAIAE---YRRFPTPLQWASHLTKTPGEIQGRIGDG 205

Query: 220 EKGANYAISHFKVIDCFA--------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              A   ++  ++ID            +     ++P TG+THQLR+H    G PI+GD  
Sbjct: 206 IPNAFTTLTAVELIDNAPYEKIHGELPQLGKYTLKPTTGKTHQLRLHMWQAGIPILGDPV 265

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           Y   +  +    ++  ++L A +++   P  G+ Q
Sbjct: 266 YPEIYPEDAED-MRIPMHLTATHIEFTDPLSGKYQ 299


>gi|304373355|ref|YP_003856564.1| Ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyorhinis HUB-1]
 gi|304309546|gb|ADM22026.1| Ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyorhinis HUB-1]
          Length = 289

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 63/250 (25%), Positives = 109/250 (43%), Gaps = 43/250 (17%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K+ R  +++V+KK       +Q   +++I    N     +K Q++ + +         
Sbjct: 31  IEKLFRKKEIKVNKKPQTKKYIVQQDDIIQI--YTNEKLDKLKTQELENQTKKYIPRKIK 88

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLD 151
               ++YED  I V NK   ++V  G    + +D  +  ++  K QK     P    RLD
Sbjct: 89  FDFDVIYEDENILVLNKHINVAVHDG---VWSLDNQVSKYL--KTQKINSFTPSHIGRLD 143

Query: 152 QETSGILVVARTRAAAQHLTES---------FRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           + TSG+++ A+   +   L +          F+     K  + +   I KN+K       
Sbjct: 144 KATSGLIIYAKNYFSLVELNKKQNSFLKYYIFQSDIEIKKKFEVKIKIEKNEK------- 196

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           LKK  +          N++ A  A++HF     F+ K   +  Q  TG+ HQ+RV   H+
Sbjct: 197 LKKMQVT---------NKETATVALTHF-----FSSKNLKI-AQILTGKKHQIRVSLEHL 241

Query: 263 GCPIVGDHKY 272
           G PI GD KY
Sbjct: 242 GYPIYGDTKY 251


>gi|332529225|ref|ZP_08405189.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
 gi|332041448|gb|EGI77810.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
          Length = 319

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 48/177 (27%), Positives = 87/177 (49%), Gaps = 13/177 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL- 158
           ++++D+ + V +KP  + V   G  +   +   LKS    +   P   HR+D+ET+G++ 
Sbjct: 98  IVFQDAHLIVADKPHFMPVTPTGRYVRNSLLVRLKSATGLETLSP--VHRIDRETAGLVL 155

Query: 159 --VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
             V  + R A Q L   FR + + K+Y ++     +     +    L +S I  D     
Sbjct: 156 FSVRPQDRGAYQAL---FRTQAVDKVYEAIAPLRAQGSDRPLPA--LHRSRIEVDPEQFF 210

Query: 217 KQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +Q E +G   + +  ++++       +  ++P +G+THQLRVH   +G PIVGD  Y
Sbjct: 211 RQRETEGEPNSETALELVESRPPHALY-RLRPRSGKTHQLRVHMNALGRPIVGDLFY 266


>gi|312130287|ref|YP_003997627.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
 gi|311906833|gb|ADQ17274.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
          Length = 206

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 96/224 (42%), Gaps = 31/224 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++E+    + +KP+GI+ Q   G     D  L ++         +  RLD+  SG++V+A
Sbjct: 3   IFENDNYIILDKPSGIASQDEPG---KNDSILSAFPGC-----HVLTRLDKRVSGLMVLA 54

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           ++   A   +      +  K Y  +V      K+  + +W+ K+      + H V+    
Sbjct: 55  KSAEVAARWSP----EKYSKTYHCIVNLPGPGKEGVLKHWIKKQGLKAKVFDHAVE---- 106

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           GA  AI  ++ +   +Q++    ++  TGR HQ+R     +G P+VGD KY     G   
Sbjct: 107 GAKQAILRYQ-LRGNSQRYALYAVKIETGRFHQIRAQFSKVGFPLVGDLKY-----GYKR 160

Query: 282 SPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           S     ++L    +  P       ++  PLP      W   GF+
Sbjct: 161 STPDGSIFLSCTQIKGPD-----FEVEIPLPF----LWAKYGFE 195


>gi|319637809|ref|ZP_07992575.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317400964|gb|EFV81619.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 307

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 38/174 (21%), Positives = 77/174 (44%), Gaps = 35/174 (20%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A  +     F+ + +QK Y            E +A      + 
Sbjct: 148 HRLDKDTAGVMLLSLNPATRRDYQTMFQEKTVQKTY------------EAVA-----PTR 190

Query: 208 IGGDY-VHVVKQNEKGANYAISH--------FKVIDCFAQK--FCWLEMQPHTGRTHQLR 256
              DY +H+  + E+G  + ++            I+    +  F    + PHTG+ HQLR
Sbjct: 191 TDLDYPLHISSRMERGEKFFLTRETEGKPNAHTTIELIENRGAFSLYRLTPHTGKKHQLR 250

Query: 257 VHALHMGCPIVGDHKYCANFKG---NFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           VH + +  P++ D  Y         ++  P++    L A+ ++   P  G +++
Sbjct: 251 VHMMSLNMPLMNDALYPTPLAAGDEDYDKPLK----LLAKRIEFTDPVSGEIRV 300


>gi|298707166|emb|CBJ29939.1| RNA pseudouridylate synthase domain containing 1 [Ectocarpus
           siliculosus]
          Length = 453

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 38/128 (29%), Positives = 63/128 (49%), Gaps = 6/128 (4%)

Query: 66  RIPPVINALNHIIKEQKILDSS---VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           R P    AL   +  Q+ L  +   +  ++    + +  L  D    V NKPA + + G 
Sbjct: 8   RSPIRCQALADTVMAQRGLSMTSRELAASRQCGDIPTETLSLDDDFVVINKPADVRMDGN 67

Query: 123 SGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             +A  +D  ++ W  + + ++ +  H+LD  TSG+L VA  R AA    E+FR RR +K
Sbjct: 68  FDVA--VDKLIRYWCPTLEDKELKWVHQLDFATSGVLCVALHREAAARGCEAFRERRAKK 125

Query: 182 IYWSLVWG 189
            Y ++V G
Sbjct: 126 SYLAVVQG 133



 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 35/53 (66%), Gaps = 6/53 (11%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           M+PHTGR HQLR+HALHMG PI+GD  Y      + T P   ++ LHA+ + L
Sbjct: 315 MRPHTGRRHQLRLHALHMGHPILGDTTYG---DADHTIP---RMCLHAQSLTL 361


>gi|295661807|ref|XP_002791458.1| RNA pseudouridylate synthase domain-containing protein
           [Paracoccidioides brasiliensis Pb01]
 gi|226280015|gb|EEH35581.1| RNA pseudouridylate synthase domain-containing protein
           [Paracoccidioides brasiliensis Pb01]
          Length = 525

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 65/289 (22%), Positives = 108/289 (37%), Gaps = 82/289 (28%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +K +  G V ++ K V  + +IQ+G V+                     S  L +H   +
Sbjct: 81  KKAIEDGAVCINGKAVTIDTKIQNGDVI---------------------SHTLHRHEPPV 119

Query: 98  KSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQ 152
            S    L++ED+ + V +KPAG+ V       Y+ +  L+     +G    P   +RLD+
Sbjct: 120 TSQPIGLIHEDNDMIVIDKPAGVPVHPAG--RYNYNSVLEIMKAERGHGWVPYPCNRLDR 177

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++ + +    A+ + E  R R ++K Y + V G   +        +LK S I G  
Sbjct: 178 LTSGVMFIGKHPRGAEQIGEKLRSRTVRKEYVARVKGKFPDGVVLCDQPMLKISPILG-- 235

Query: 213 VHVVKQNEKGANYAISHFKVIDCF-----AQKFCWLEMQPHT------------------ 249
              + +       A + F+ I  +     A+K      +P T                  
Sbjct: 236 ---LNRARASGKEARTKFRRIAYYPPYEPAEKSSVSSAEPATPPATLPNEMNISNSSTAT 292

Query: 250 --------------------------GRTHQLRVHALHMGCPIVGDHKY 272
                                     GRTHQ+RVH  ++G PI  D  Y
Sbjct: 293 PTGVATPVPKSSDEEGYSIVHCLPLTGRTHQIRVHLQYLGYPITNDPIY 341


>gi|298715052|emb|CBJ27759.1| RNA pseudouridylate synthase domain-containing protein [Ectocarpus
           siliculosus]
          Length = 527

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 94/229 (41%), Gaps = 36/229 (15%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           SS+   + S  L+  +L+++    V +KP G+        +   D  ++   D  G++  
Sbjct: 122 SSLESPQQSPPLE--VLHQNEHFAVVSKPPGMHCHRPEFGSRDPDFVMQKARDQLGRRVF 179

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ TSG L+V  +  AA+ L ++       K Y ++V G                
Sbjct: 180 LPHRLDRATSGCLLVGFSSQAAKVLHQTLAQPDSSKTYVAIVRG---------------- 223

Query: 206 SHIGGDYV--------HVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQ 254
              GG +V          +K  +K    A + F  +   +    + C +  QP TGR HQ
Sbjct: 224 --SGGAFVGKGWFTVDRPIKDEKKILREASTRFLFVRGGNDPDPRCCLVLAQPSTGRFHQ 281

Query: 255 LRVHALHMGCPIVGD--HKYC---ANFKGNFTSPIQNKLYLHARYMDLP 298
           +R H   +  PIVGD  H  C        +  S    +L LH   + LP
Sbjct: 282 IRRHLNGLSHPIVGDSVHGDCRFNREVADHRNSAPAGRLMLHCLRLSLP 330


>gi|311029949|ref|ZP_07708039.1| pseudouridine synthase [Bacillus sp. m3-13]
          Length = 105

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 37/95 (38%), Positives = 50/95 (52%), Gaps = 8/95 (8%)

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           NE   N A++HF+VI+ F + F  +E Q  TGRTHQ+RVH  ++G P+ GD KY     G
Sbjct: 5   NENSRN-AVTHFRVIERF-KDFSHIECQLETGRTHQIRVHMKYIGYPLAGDPKY-----G 57

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              S       LHA  +   HP     ++  AP P
Sbjct: 58  PKKSLDIEGQALHAGILGFIHPRTEEYMEFEAPNP 92


>gi|21536736|gb|AAM61068.1| unknown [Arabidopsis thaliana]
          Length = 395

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 44/155 (28%), Positives = 66/155 (42%), Gaps = 5/155 (3%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKS 206
           HRLD+  SG+L++ART A A    +      ++K Y + V G+ P+++    AN     S
Sbjct: 184 HRLDRLVSGLLIIARTAAKADFFRQQIEGGMVKKRYIAKVIGVFPEDEMIVDANINYNGS 243

Query: 207 H---IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                  D        +     A + F  ID        +  +P TGRTHQ+RVH  + G
Sbjct: 244 EGRSTAEDANSSGDDKKVKGKPACTKFTRIDTNGTH-SLVSCEPVTGRTHQIRVHLQYTG 302

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            PI  D  Y      N  + I  ++    R +  P
Sbjct: 303 HPIANDPLYLNQHIDNLETYIAKRIDAGERKIVSP 337


>gi|149200226|ref|ZP_01877248.1| Pseudouridine synthase [Lentisphaera araneosa HTCC2155]
 gi|149136668|gb|EDM25099.1| Pseudouridine synthase [Lentisphaera araneosa HTCC2155]
          Length = 290

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 46/189 (24%), Positives = 87/189 (46%), Gaps = 12/189 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KP  + +   G  +   +   L+   ++    P   HR+D+ T+G++ 
Sbjct: 83  ILYEDENLLLVDKPHFLPIHPAGPYVKETLVYRLRESQNNPDISP--LHRIDRLTAGLVF 140

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            ++  +  +     F  R ++K Y ++  G   ++      W LK     G+   +    
Sbjct: 141 FSKKVSIRKDYQLLFENRLVEKTYHAISAGPAPDQ----GYWHLKNRIEAGEPWFLSAIK 196

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-- 277
           E  AN + S+  VI+         E++P +G+ HQLRVH   +G PI+ D  Y +  +  
Sbjct: 197 EGKAN-SESYINVIEA-KDNLVKFELKPISGKKHQLRVHLASIGYPILHDPLYPSFVEKP 254

Query: 278 -GNFTSPIQ 285
             N+  P+Q
Sbjct: 255 PDNYEKPMQ 263


>gi|157872395|ref|XP_001684746.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|68127816|emb|CAJ06253.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 453

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 35/65 (53%), Gaps = 11/65 (16%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-----------KLYLHAR 293
           + PHTGR HQLRVH   +G PIVGD  YCA+       P+ +           ++YLHA 
Sbjct: 326 LAPHTGRRHQLRVHCRAIGFPIVGDTSYCADLPWCTALPLGSSPSTWVTAGARRMYLHAW 385

Query: 294 YMDLP 298
            + LP
Sbjct: 386 RLLLP 390



 Score = 37.4 bits (85), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 27/99 (27%), Positives = 46/99 (46%), Gaps = 17/99 (17%)

Query: 108 IYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKG----------------QKPRLTHRL 150
           + V NKP GI + G   I    ++  +   + ++G                ++ +  H+L
Sbjct: 1   MLVVNKPPGILMDGDESIYGRTVESLVCEHMKARGIFDETHEQLQKEKKRKKQLKFVHQL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           D  TSG+L +A T+  A  L   F MR ++K Y +L+ G
Sbjct: 61  DFGTSGVLCLAFTKDMAARLAHCFEMRLVRKYYVALLHG 99


>gi|38566140|gb|AAH62362.1| RPUSD3 protein [Homo sapiens]
 gi|119584410|gb|EAW64006.1| RNA pseudouridylate synthase domain containing 3, isoform CRA_a
           [Homo sapiens]
          Length = 328

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 65/133 (48%), Gaps = 12/133 (9%)

Query: 152 QETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +E+SG+++++     A  L + F    R +R    Y ++  GIP   +  I    LK  H
Sbjct: 113 KESSGLVLLSSCPQTASRLQKYFTHARRAQRPTATYCAVTDGIPAASEGKI-QAALKLEH 171

Query: 208 IGGDYVHV-VKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           I G  + V VK   +     G    +SHF+V+         +++QP T  + QL+VH + 
Sbjct: 172 IDGVNLTVPVKAPSRKDILEGVKKTLSHFRVV-ATGSGCALVQLQPLTVFSSQLQVHMVL 230

Query: 262 MGCPIVGDHKYCA 274
             CP++GDH Y A
Sbjct: 231 QLCPVLGDHMYSA 243


>gi|216548152|ref|NP_001136019.1| RNA pseudouridylate synthase domain-containing protein 3 isoform 2
           [Homo sapiens]
          Length = 336

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 40/134 (29%), Positives = 65/134 (48%), Gaps = 12/134 (8%)

Query: 152 QETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +E+SG+++++     A  L + F    R +R    Y ++  GIP   +  I    LK  H
Sbjct: 121 KESSGLVLLSSCPQTASRLQKYFTHARRAQRPTATYCAVTDGIPAASEGKI-QAALKLEH 179

Query: 208 IGGDYVHV-VKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           I G  + V VK   +     G    +SHF+V+         +++QP T  + QL+VH + 
Sbjct: 180 IDGVNLTVPVKAPSRKDILEGVKKTLSHFRVV-ATGSGCALVQLQPLTVFSSQLQVHMVL 238

Query: 262 MGCPIVGDHKYCAN 275
             CP++GDH Y A 
Sbjct: 239 QLCPVLGDHMYSAR 252


>gi|167933175|ref|ZP_02520262.1| pseudouridine synthase, RluA family protein [candidate division TM7
           single-cell isolate TM7b]
          Length = 94

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 8/80 (10%)

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +++QP TGRTHQLRVH  ++  PI+GD  Y          P + +++LHA  +++   
Sbjct: 22  SLIKLQPKTGRTHQLRVHMQYLNTPILGDLVYGGK-------PAE-RMFLHAESLEVTLL 73

Query: 301 EGGRLQITAPLPAHMVKTWD 320
            G R    APLP   +  ++
Sbjct: 74  SGERKVFKAPLPDDFINFFN 93


>gi|294790685|ref|ZP_06755843.1| RNA pseudouridine synthase [Scardovia inopinata F0304]
 gi|294458582|gb|EFG26935.1| RNA pseudouridine synthase [Scardovia inopinata F0304]
          Length = 252

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 92/237 (38%), Gaps = 35/237 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  I   +KP  +      G+ Y     +     +        HRLD+ T+G+L++
Sbjct: 12  ILYEDQAIIAVDKPHFLPTMP-RGMWYKSTAVMTMRERTGNDSLIPAHRLDRMTAGVLIL 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSL----------------VW---GIPKNKKECIANW 201
            +     +     F+ R++ K Y  L                VW   G   N    + N 
Sbjct: 71  VKEPQYRKMYQMLFQSRQVHKTYQCLAPIRPASRPRLGLVGHVWSRKGEDNNLTVDVTNL 130

Query: 202 ---LLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-----CFAQKFCWLEMQPHTGRTH 253
              LL+ SHI      +    E  A  A+S   +          +      + P TG+TH
Sbjct: 131 SFPLLRSSHITKKRGILQAYEEAEAINAVSLITISSHQSSHALNKGLRAYTLHPLTGKTH 190

Query: 254 QLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           QLRVH   +G PI GD+ Y         +F+ P+Q    L AR +    P  G+ +I
Sbjct: 191 QLRVHMTSLGLPIDGDNWYPQVEERAYDDFSHPLQ----LIAREISFTDPLTGQERI 243


>gi|257487593|ref|ZP_05641634.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 108

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 30/92 (32%), Positives = 51/92 (55%), Gaps = 3/92 (3%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D+ + V +KP  + SV G +    + D  +    ++   + R+ HRLD ETSGI++
Sbjct: 8   IIYQDAAVLVIDKPTLLLSVPGRAD--DNKDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           +AR     + L+  F  R  +K Y +L WG P
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQP 97


>gi|219363655|ref|NP_001136977.1| hypothetical protein LOC100217137 [Zea mays]
 gi|194697832|gb|ACF83000.1| unknown [Zea mays]
          Length = 386

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 39/135 (28%), Positives = 61/135 (45%), Gaps = 6/135 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+  SG+L+ A+    A+   +      +QK Y + V G+  + ++ +   +   + 
Sbjct: 161 HRLDRLVSGLLIFAKNADRAECFRQQIEAGLLQKEYVAKVVGVFPDGEQTVDANVNFNAR 220

Query: 208 IGGDYVHVV--KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            G   V +      E     A++ F+ I C       +  +P TGRTHQ+RVH    G P
Sbjct: 221 EGRSTVEISGGAGEEPNGKQALTRFQRI-CTDGTHSIVLCKPVTGRTHQIRVHLKQAGYP 279

Query: 266 IVGDHKYCANFKGNF 280
           I  D  Y     GNF
Sbjct: 280 IANDELY---LSGNF 291


>gi|213023142|ref|ZP_03337589.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 150

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 69/147 (46%), Gaps = 10/147 (6%)

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + +   LLK     G+ +  V Q  K +    + FKV + +A  F
Sbjct: 5   KDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQEGKPSE---TRFKVEERYA--F 59

Query: 241 CWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQN--KLYLHARYMD 296
             L    P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  + 
Sbjct: 60  ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALK 119

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSL 322
             HP  G  ++I AP+   + +  + L
Sbjct: 120 FTHPGTGDVMRIEAPMDKQLKRCLEVL 146


>gi|146093778|ref|XP_001467000.1| hypothetical protein [Leishmania infantum JPCM5]
 gi|134071364|emb|CAM70050.1| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 453

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 35/65 (53%), Gaps = 11/65 (16%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-----------KLYLHAR 293
           + PHTGR HQLRVH   +G PIVGD  YCA+       P+ +           ++YLHA 
Sbjct: 326 LAPHTGRRHQLRVHCRAIGFPIVGDTSYCADLPWCAALPLGSSTSTWAAAGARRMYLHAW 385

Query: 294 YMDLP 298
            + LP
Sbjct: 386 RLLLP 390



 Score = 36.2 bits (82), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 26/42 (61%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           H+LD  TSG+L +A T+  A  L   F MR ++K Y +L+ G
Sbjct: 58  HQLDFGTSGVLCLAFTKDMAARLAHCFEMRTVRKYYVALLHG 99


>gi|226289283|gb|EEH44795.1| RNA pseudouridylate synthase domain-containing protein
           [Paracoccidioides brasiliensis Pb18]
          Length = 525

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 65/289 (22%), Positives = 108/289 (37%), Gaps = 82/289 (28%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +K +  G V ++ K V  + +IQ+G V+                     S  L +H   +
Sbjct: 81  KKAIEDGAVCINGKAVTIDTKIQNGDVI---------------------SHTLHRHEPPV 119

Query: 98  KSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQ 152
            S    +++ED+ + V +KPAG+ V       Y+ +  L+     +G    P   +RLD+
Sbjct: 120 TSQPIGVIHEDNDMIVIDKPAGVPVHPAG--RYNYNSVLEIMKAERGHGWVPYPCNRLDR 177

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++ V +    A+ + E  R R ++K Y + V G   +        +LK S I G  
Sbjct: 178 LTSGVMFVGKHPKGAEQIGEKLRSRTVRKEYVARVKGKFPDGVVLCDQPMLKISPILG-- 235

Query: 213 VHVVKQNEKGANYAISHFKVIDCF-----AQKFCWLEMQPHT------------------ 249
              + +       A + F+ I  +     A+K      +P T                  
Sbjct: 236 ---LNRARASGKEARTKFRRIAYYPPYEPAEKSSVSSTEPATPPATLPDEMNISNSSTAT 292

Query: 250 --------------------------GRTHQLRVHALHMGCPIVGDHKY 272
                                     GRTHQ+RVH  ++G PI  D  Y
Sbjct: 293 PTGVATPVPKSSDEEGYSIVHCLPLTGRTHQIRVHLQYLGYPITNDPIY 341


>gi|322501097|emb|CBZ36174.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 453

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 35/65 (53%), Gaps = 11/65 (16%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-----------KLYLHAR 293
           + PHTGR HQLRVH   +G PIVGD  YCA+       P+ +           ++YLHA 
Sbjct: 326 LAPHTGRRHQLRVHCRAIGFPIVGDTSYCADLPWCAALPLGSSTSTWAAAGARRMYLHAW 385

Query: 294 YMDLP 298
            + LP
Sbjct: 386 RLLLP 390



 Score = 36.2 bits (82), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 26/42 (61%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           H+LD  TSG+L +A T+  A  L   F MR ++K Y +L+ G
Sbjct: 58  HQLDFGTSGVLCLAFTKDMAARLAHCFEMRTVRKYYVALLHG 99


>gi|220905224|ref|YP_002480536.1| pseudouridine synthase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|219869523|gb|ACL49858.1| pseudouridine synthase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 493

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 42/200 (21%), Positives = 82/200 (41%), Gaps = 12/200 (6%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +    Q   V++    +RLD+  ++  PH+     ++   +G V V+ +  K + R++ G
Sbjct: 87  IAAATQEFCVDHQHAGLRLDQALEHLLPHMGLRGRRRCAENGGVSVNGRAAKASRRMRQG 146

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA---GISV 119
            VVR+         +   +++  ++ +           +L    +   F+KPA     S+
Sbjct: 147 DVVRLHNAEARKKKVALGREVSGTAFSCGSAVAACGLRMLGRQGEYCFFSKPARMHSASL 206

Query: 120 QGGSGIAYH--IDGFLKSWVDSKGQKPR-------LTHRLDQETSGILVVARTRAAAQHL 170
            G SG++           W +  G           L  RLD  TSG+L  A + +AA+  
Sbjct: 207 AGISGVSVEALAPALAVRWTEKSGSGNEFDLAALTLMQRLDFGTSGLLCAALSTSAAEDF 266

Query: 171 TESFRMRRIQKIYWSLVWGI 190
             +      +K Y +L+ G+
Sbjct: 267 RAAEAAGLCEKRYVALLSGV 286


>gi|325265762|ref|ZP_08132449.1| RNA pseudouridine synthase [Kingella denitrificans ATCC 33394]
 gi|324982745|gb|EGC18370.1| RNA pseudouridine synthase [Kingella denitrificans ATCC 33394]
          Length = 309

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 62/125 (49%), Gaps = 6/125 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A+     + F  + +QK Y +L        +  +   L  +S 
Sbjct: 150 HRLDKDTAGVMLLSHNPASRAAYQQMFAEKTVQKTYHALA-----PTRLDLPYPLTVQSR 204

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +       + Q   G   A +  ++++       + E++P TG+ HQLRVH + +G P++
Sbjct: 205 LVRGESFFLTQEVDGTPNAQTEIRLLEMHGDVSLY-ELKPLTGKKHQLRVHMMKLGMPLL 263

Query: 268 GDHKY 272
            D  Y
Sbjct: 264 NDALY 268


>gi|225556035|gb|EEH04325.1| DRAP deaminase [Ajellomyces capsulatus G186AR]
          Length = 545

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 38/154 (24%), Positives = 72/154 (46%), Gaps = 22/154 (14%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           QK +  G V ++ K V  + +IQ+G V+         +H +   +   +S  ++      
Sbjct: 82  QKAIEDGAVCINGKAVSIDTKIQNGDVI---------SHTLHRHEPPVTSQPIS------ 126

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETS 155
              +++ED  + V +KPAG+ V       Y+ +  L+     +G    P   +RLD+ TS
Sbjct: 127 ---IIHEDDDMIVIDKPAGVPVHPAG--RYNYNSILEIMKAERGNGWVPYPCNRLDRLTS 181

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           G++ + +    A+ + E  R R ++K Y + V G
Sbjct: 182 GVMFIGKHPKGAEQIGEKLRSRTVRKEYVARVKG 215


>gi|171060976|ref|YP_001793325.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170778421|gb|ACB36560.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
          Length = 310

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 43/172 (25%), Positives = 76/172 (44%), Gaps = 31/172 (18%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESF-RMRRIQKIY-----WSLVWGIPKNKKECI--- 198
           HRLD+ET+G+++    + A +H  +S  R R ++K+Y     W     +P  +   +   
Sbjct: 140 HRLDRETAGVVLFT-VQPATRHAYQSLLRDRSVEKVYEAVAPWRADLALPLTRCSRLQER 198

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+  ++ + + G         E  A  +I   + +   A+      ++P TG+ HQLR H
Sbjct: 199 ADAFMQMAEVAG---------EPNAQTSIELIRRV-AAAEPLALYRLRPRTGQKHQLRAH 248

Query: 259 ALHMGCPIVGDHKY-------CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +G PI GD  Y           + +++ P+Q    L AR +    P  G
Sbjct: 249 MAALGLPIRGDRIYPVLQPDLAEGAQPDYSRPLQ----LLARSIAFTDPVSG 296


>gi|78486049|ref|YP_391974.1| pseudouridine synthase [Thiomicrospira crunogena XCL-2]
 gi|78364335|gb|ABB42300.1| Pseudouridine synthase Rlu family protein [Thiomicrospira crunogena
           XCL-2]
          Length = 300

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 46/188 (24%), Positives = 78/188 (41%), Gaps = 29/188 (15%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK---GQKPR-----LTHRLD 151
           +L+ +     V+ KP G+  QG S    H    L  W+++     + P      + HRLD
Sbjct: 99  VLIEDADDFSVWYKPKGVLSQG-SKWGDHTT--LNRWIETHYLFKEPPEKRPCWIVHRLD 155

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + T G++++A  + +AQ L   F   +I K Y + V G                    G+
Sbjct: 156 KATDGLILIAHNKKSAQMLARRFEAHQIGKSYQAWVKGK------------------FGE 197

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              V  Q+  G        +++         +++   TGR HQ+R+H    G PI+GD  
Sbjct: 198 TERVFDQDVNGKTALSKAHQLVYNSDNDCSLVQVTIATGRKHQIRIHLSKAGFPIIGDRL 257

Query: 272 YCANFKGN 279
           Y    +G+
Sbjct: 258 YGDAQEGD 265


>gi|145351767|ref|XP_001420235.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580469|gb|ABO98528.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 357

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 51/190 (26%), Positives = 77/190 (40%), Gaps = 25/190 (13%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGI 157
           +L   D  + V+ KPA + V       Y  +  L     S+    RL   HRLD+  SG+
Sbjct: 83  VLTVNDDVVSVW-KPATVPVHPTG--QYRRNTVLALLAASRRDLGRLFPIHRLDKNVSGL 139

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---------------IPKNKKECIANWL 202
           L++AR+  AA  +      R ++K Y + V G               +  + K  +A W 
Sbjct: 140 LLLARSSEAANEMRVKMEAREMRKEYVARVRGAFNDGDATPVSNVESLGFDSKGRVAIWR 199

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            KK     D     ++  K    A + F  I         +  +P TGR+HQ+R H   +
Sbjct: 200 GKKGVTDLD-----ERTLKSFKDASTKFTCIKTLVDGTSLVRCEPFTGRSHQIRAHLAML 254

Query: 263 GCPIVGDHKY 272
           G PI  D  Y
Sbjct: 255 GYPIANDVAY 264


>gi|147861752|emb|CAN83167.1| hypothetical protein VITISV_021912 [Vitis vinifera]
          Length = 208

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 38/132 (28%), Positives = 58/132 (43%), Gaps = 21/132 (15%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNK-KECIANWLLKK 205
           HRLD+  SG+L++AR+ + A    +      +QK Y + V G+ P ++   C  N  LK 
Sbjct: 5   HRLDRLVSGLLILARSASKADSFRQQIEAGMVQKQYIAKVTGVFPDDEVGNCCGNTPLKG 64

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                 +  +            +H  V+            +P TGRTHQ+RVH  + G P
Sbjct: 65  KSACTKFTRISTNG--------THSIVL-----------CEPITGRTHQIRVHLQYTGHP 105

Query: 266 IVGDHKYCANFK 277
           I  D  Y + F 
Sbjct: 106 IANDMLYLSEFS 117


>gi|239932294|ref|ZP_04689247.1| ribosomal pseudouridine synthase [Streptomyces ghanaensis ATCC
           14672]
          Length = 299

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 48/164 (29%), Positives = 76/164 (46%), Gaps = 19/164 (11%)

Query: 147 THRLDQETSGIL---VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            HRLD+ T+G++   V    R A Q L   FR RR+ K Y ++    P +    +   + 
Sbjct: 124 AHRLDRLTAGLVLFTVRPGERGAYQTL---FRDRRVHKEYEAVA---PYDPGLDLPRTV- 176

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            +S I  +   +  +  +G   A++  ++ +  A       + P TG+THQLRVH   +G
Sbjct: 177 -RSRIVKERGELAAREVEGEPNALTLVELTEHRADGPGRYRLVPGTGQTHQLRVHMSALG 235

Query: 264 CPIVGDHKY----CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            PI+GD  Y         G+F  P+Q    L AR ++   P  G
Sbjct: 236 VPILGDPLYPEVTAPVPAGDFRRPLQ----LLARVLEFTDPVTG 275


>gi|21245032|ref|NP_644614.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21110760|gb|AAM39150.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 298

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 47/177 (26%), Positives = 84/177 (47%), Gaps = 13/177 (7%)

Query: 101 LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ D+++ V  KP  + V   G+ +   +   L   +D+    P   HR+D+ET+G+++
Sbjct: 89  VVHADAQLVVACKPHFLPVAPAGAYVRETLLTRLVRRLDNPALVP--LHRIDRETAGLVL 146

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            +   A        FR RRI+K Y ++   +P+ +   +    L+     G+    +++ 
Sbjct: 147 FSANPATRGIYQALFRERRIRKHYLAVAAPLPELRFPYVHRSRLEP----GEPFFRMREG 202

Query: 220 EKGANYAISHFKVIDCFAQKF-CWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               N       VI+  A+    W   ++P TGR HQLRVH   +G PI+ D  Y A
Sbjct: 203 VGEPNSET----VIEVVARNADTWTYRLEPVTGRKHQLRVHMAALGAPILHDRFYPA 255


>gi|291440659|ref|ZP_06580049.1| ribosomal pseudouridine synthase [Streptomyces ghanaensis ATCC
           14672]
 gi|291343554|gb|EFE70510.1| ribosomal pseudouridine synthase [Streptomyces ghanaensis ATCC
           14672]
          Length = 319

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 48/164 (29%), Positives = 76/164 (46%), Gaps = 19/164 (11%)

Query: 147 THRLDQETSGIL---VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            HRLD+ T+G++   V    R A Q L   FR RR+ K Y ++    P +    +   + 
Sbjct: 144 AHRLDRLTAGLVLFTVRPGERGAYQTL---FRDRRVHKEYEAVA---PYDPGLDLPRTV- 196

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            +S I  +   +  +  +G   A++  ++ +  A       + P TG+THQLRVH   +G
Sbjct: 197 -RSRIVKERGELAAREVEGEPNALTLVELTEHRADGPGRYRLVPGTGQTHQLRVHMSALG 255

Query: 264 CPIVGDHKY----CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            PI+GD  Y         G+F  P+Q    L AR ++   P  G
Sbjct: 256 VPILGDPLYPEVTAPVPAGDFRRPLQ----LLARVLEFTDPVTG 295


>gi|145296955|ref|YP_001139776.1| hypothetical protein cgR_2855 [Corynebacterium glutamicum R]
 gi|140846875|dbj|BAF55874.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 322

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 53/202 (26%), Positives = 81/202 (40%), Gaps = 23/202 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP  ++     G        +K  V +        HRLD+ TSG+LV+
Sbjct: 97  VIHEDDDILVIDKPPYLATMP-RGRHITETALVKMRVLTGNNDLTPAHRLDRLTSGVLVM 155

Query: 161 ART---RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
            +    R A Q L   F  R   K Y ++   +P       A W  +     G     V 
Sbjct: 156 VKKPELRGAYQTL---FARREASKTYEAIAEFVPGLLDNGPAIWESRIEKERGIVQAFVV 212

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQ------------PHTGRTHQLRVHALHMGCP 265
           +    A   +     +D  A++    EM             P TG+THQLR+H      P
Sbjct: 213 EGPVNARTELVSVTPVDD-AEQSILEEMHGPLPRQARYVLAPSTGKTHQLRIHMRDFAAP 271

Query: 266 IVGDHKYC---ANFKGNFTSPI 284
           I+GD  Y    A    ++T+P+
Sbjct: 272 ILGDPLYPVLHAVDDEDYTTPM 293


>gi|215413178|ref|ZP_03421879.1| hypothetical protein Mtub9_17501 [Mycobacterium tuberculosis
           94_M4241A]
          Length = 305

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 85/189 (44%), Gaps = 15/189 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D+ I V +KP  ++    G  +A      L+  +      P   HRLD+ T+G+L+
Sbjct: 87  VLHQDADIVVVDKPHFLATMPRGRHVAQTALVRLRRELGLPELSP--AHRLDRLTAGVLL 144

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               R         F    ++K Y +     P      +A   L +S I     H+    
Sbjct: 145 FTTRREVRGSYQTMFARGLVRKTYLARAPVAPG-----LALPRLVRSRIVKRRGHLQAVC 199

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANF 276
           E G   A +   +++  A+   +  + P TGRTHQLRVH   +G PI+GD  Y    +  
Sbjct: 200 EPGVPNAET---LVERIARDGLY-RLTPTTGRTHQLRVHMAALGIPIMGDPLYPNVISVA 255

Query: 277 KGNFTSPIQ 285
             +F++P+Q
Sbjct: 256 AHDFSTPLQ 264


>gi|104782764|ref|YP_609262.1| pseudouridylate synthase [Pseudomonas entomophila L48]
 gi|95111751|emb|CAK16475.1| putative pseudouridylate synthase [Pseudomonas entomophila L48]
          Length = 294

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 58/205 (28%), Positives = 101/205 (49%), Gaps = 24/205 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +L+ D  + V +KP  + V   +    +++  L   +  +   P L   HR+D+ T+G++
Sbjct: 88  ILHVDEHLVVADKPHFLPV---TPTGEYVEQTLLRRLIRRLDNPHLVPLHRIDRHTAGLV 144

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR A Q L   F  RRI K Y ++   +P++    +    L    + G+    
Sbjct: 145 LFSANPQTRGAYQCL---FPERRIDKHYQAIAAAMPQHMFPLVHRSRL----VHGEPFFR 197

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY-- 272
           + + E GA+ + +H  V++   Q   W   + P TG+THQLRVH   +G  I  D  Y  
Sbjct: 198 MHEVE-GADNSETHACVLE--KQGELWRYGLSPVTGKTHQLRVHMASLGAAICNDPFYPQ 254

Query: 273 CANFKGNFTSPIQNKLYLHA-RYMD 296
            AN + ++T P+  KL  H+ R+ D
Sbjct: 255 LANEQDDYTRPL--KLLAHSLRFKD 277


>gi|42522902|ref|NP_968282.1| pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
 gi|39574098|emb|CAE79275.1| Pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
          Length = 239

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 93/225 (41%), Gaps = 27/225 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG-FLKSWVDSKGQKPRL--THRLDQETSGI 157
           ++Y+D   +  +KP+G  V       Y +    +  W   K  +  +   HRLD  TSGI
Sbjct: 9   IIYQDENFFAIDKPSGFFVHPPELSPYPVPKERICLWHLRKMFRKDVFPVHRLDAPTSGI 68

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---------IPKNKKECIANWLLKKSHI 208
           ++ A +R  A+ L   F  RR+ K Y ++V G         +P    E     +++   +
Sbjct: 69  VLFAMSRQDARELNFLFAERRMHKTYHAVVRGFVPASGSIDLPLEVDE--GQSIVEAQTV 126

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 V      G  Y  S + ++          +  P TGR HQ+R H   +  P++G
Sbjct: 127 FRSLAQVELPYAVGKKYPTSRYSLV----------QAHPVTGRWHQIRRHFDRIAHPLLG 176

Query: 269 DHKYCANFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAP 310
           D ++  +    F     N   L L A  +++  P  G R+ I AP
Sbjct: 177 DIEHGDSHHNRFFRDTLNIKGLCLKATKIEMESPWNGQRVVIEAP 221


>gi|257784215|ref|YP_003179432.1| pseudouridine synthase [Atopobium parvulum DSM 20469]
 gi|257472722|gb|ACV50841.1| pseudouridine synthase [Atopobium parvulum DSM 20469]
          Length = 246

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 59/233 (25%), Positives = 91/233 (39%), Gaps = 34/233 (14%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-------LKSWVDSKGQKPRLTHRLDQET 154
           LY+D  +   NKPAG+ V         +          L+S       + +  +RLD+ET
Sbjct: 13  LYQDDYLLAVNKPAGMIVHSDGTNEPSLTDLVCEKLCALESSNKIDLSQVQALNRLDKET 72

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +GI++ +  +       +    + + K Y ++V G      +   N LL    IG D   
Sbjct: 73  TGIVLFSLKKETQPQFDQLIASKELSKEYLAVVKG------DFGLNKLLIDKAIGKDRHD 126

Query: 215 V----VKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                +    K +   +   KV      Q    L +   TGR HQ+RVH   +G P+VGD
Sbjct: 127 AQKMRISDTGKPSQTEVRLIKVASSAQGQIQSLLLVNLLTGRKHQIRVHLSSLGFPLVGD 186

Query: 270 HKYCANFKGNFTSPIQNK---------LYLHARYMDLPHP-EGGRLQITAPLP 312
             Y         S +Q K         L LHA  +   HP  G ++ I   +P
Sbjct: 187 VLYGG------MSSLQRKTKKKHRPQPLMLHAYRIGFIHPVTGAKIVIKTDIP 233


>gi|31794480|ref|NP_856973.1| hypothetical protein Mb3328c [Mycobacterium bovis AF2122/97]
 gi|31620076|emb|CAD95420.1| CONSERVED HYPOTHETICAL PROTEIN [Mycobacterium bovis AF2122/97]
          Length = 305

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 85/189 (44%), Gaps = 15/189 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D+ I V +KP  ++    G  +A      L+  +      P   HRLD+ T+G+L+
Sbjct: 87  VLHQDADIVVVDKPHFLATMPRGRHVAQTALVRLRRELGLPELSP--AHRLDRLTAGVLL 144

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               R         F    ++K Y +     P      +A   L +S I     H+    
Sbjct: 145 FTTRREVRGSYQTMFARGLVRKTYLARAPVAPG-----LALPRLVRSRIVKRRGHLQAVC 199

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANF 276
           E G   A +   +++  A+   +  + P TGRTHQLRVH   +G PI+GD  Y    +  
Sbjct: 200 EPGVPNAET---LVERIARDGLY-RLTPTTGRTHQLRVHMAALGIPIMGDPLYPNVISVA 255

Query: 277 KGNFTSPIQ 285
             +F++P+Q
Sbjct: 256 AHDFSTPLQ 264


>gi|26450633|dbj|BAC42428.1| putative RNA pseudouridylate synthase [Arabidopsis thaliana]
          Length = 148

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 34/50 (68%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +P + HRLD+ T+G+LVVA+   +  HL E F++  I+++Y SL  G+P 
Sbjct: 61  RPGIVHRLDKGTTGLLVVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPS 110


>gi|254385032|ref|ZP_05000366.1| ribosomal pseudouridine synthase [Streptomyces sp. Mg1]
 gi|194343911|gb|EDX24877.1| ribosomal pseudouridine synthase [Streptomyces sp. Mg1]
          Length = 324

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 57/209 (27%), Positives = 87/209 (41%), Gaps = 19/209 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y D  + V +KP  ++    GS +       L+  +D     P   HRLD+ T+G+++
Sbjct: 99  VVYRDEHLLVADKPHFLATTPRGSHVTQTALARLRDELDLPALSP--AHRLDRLTAGLVM 156

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +     R A Q L   F+ RR+ K Y +L    P +    +   L  +S I      + 
Sbjct: 157 FSIRPEDRGAYQLL---FQNRRVGKQYEALA---PLDPALALPRTL--RSRIEKTRGVIA 208

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                G          +           + PHTGRTHQLRVH   +G PI+GD  Y    
Sbjct: 209 AAEIPGGEPNAETLVELAESKGDTGRYRLTPHTGRTHQLRVHMNSLGLPILGDPVYP--- 265

Query: 277 KGNFTSPI--QNKLYLHARYMDLPHPEGG 303
           K     P+  +  L L AR ++   P  G
Sbjct: 266 KVTDPDPLDYRRPLQLLARVLEFTDPVTG 294


>gi|255554955|ref|XP_002518515.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223542360|gb|EEF43902.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 476

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 54/212 (25%), Positives = 91/212 (42%), Gaps = 16/212 (7%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           D+   I+   D  + V +KPAG SV G +           +         + TH++D  T
Sbjct: 209 DWKSRIIAVTDCYV-VLDKPAGTSVGGTADNIEESCATFATRALGLTTPLKTTHQIDNCT 267

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-----GIPKN--KKECIANWLLKKSH 207
            G +V+AR++          R ++++K+Y +L       G+ KN  +   IA  LL +  
Sbjct: 268 EGCVVLARSKEYCSVFHGKIREKKVKKLYLALAASPVPVGVIKNYMRPVNIAPRLLSEEF 327

Query: 208 IGGDYVHVVKQNE----KGANYAISH-FKVIDCF--AQKFCW-LEMQPHTGRTHQLRVHA 259
           + G ++  ++  E       + AI   + V DC   ++ F +  ++   TGRTHQ+R   
Sbjct: 328 VNGWHLCQLEVLECRKVPWPDAAIEEKYSVEDCGWPSKDFAYECKINLLTGRTHQIRAQL 387

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
              G P+VGD  Y         +P  N    H
Sbjct: 388 AASGAPLVGDSMYMPAAVAEMANPGLNPFGKH 419


>gi|21324194|dbj|BAB98819.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Corynebacterium glutamicum
           ATCC 13032]
          Length = 252

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 61/240 (25%), Positives = 99/240 (41%), Gaps = 45/240 (18%)

Query: 35  VNLQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
           V LQK+L        R  ++ +D+ RV+ N+RI + Q VR+ P     N +I+   +   
Sbjct: 12  VRLQKVLAQAGVASRRHAEILIDQGRVEVNDRIVTTQGVRVDPN----NDVIRVDGV--- 64

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
                        I + ED + +V NKP G+       +     G L S   + GQ+   
Sbjct: 65  ------------RIHINEDLEYFVLNKPRGMHSTMSDELGRPCVGDLVSEKTASGQRLFH 112

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD +T G+L++      A  L        + K Y + V G   NK       L+   
Sbjct: 113 VGRLDADTEGLLLLTNDGELANRLMHP--KYEVSKTYLATVRGEATNK-------LVSAL 163

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             G +    ++     A++A    ++ID F  K   L ++ H GR H +R     +G P+
Sbjct: 164 RDGVE----LEDGPAKADFA----QIIDVFQGK-SLLRIEIHEGRKHIVRRLFDELGFPV 214


>gi|225076837|ref|ZP_03720036.1| hypothetical protein NEIFLAOT_01888 [Neisseria flavescens
           NRL30031/H210]
 gi|224951823|gb|EEG33032.1| hypothetical protein NEIFLAOT_01888 [Neisseria flavescens
           NRL30031/H210]
          Length = 307

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 38/165 (23%), Positives = 77/165 (46%), Gaps = 17/165 (10%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A  +     F+ + +QK Y ++             N+ L  S 
Sbjct: 148 HRLDKDTAGVMLLSLNPATRRDYQTMFQEKTVQKTYEAVA------PTRTDLNYPLDISS 201

Query: 208 --IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
               G+   + ++ E   N A +  ++I+     F    + PHTG+ HQLRVH + +  P
Sbjct: 202 RMERGEKFFLTRETEGEPN-AHTTIELIENRGA-FSLYRLTPHTGKKHQLRVHMMSLNMP 259

Query: 266 IVGDHKYCANFKG---NFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           ++ D  Y         ++  P++    L A+ ++   P  G +++
Sbjct: 260 LMNDALYPTPLAAGDEDYDKPLK----LLAKRIEFTDPVSGEIRV 300


>gi|15610436|ref|NP_217817.1| hypothetical protein Rv3300c [Mycobacterium tuberculosis H37Rv]
 gi|121639189|ref|YP_979413.1| hypothetical protein BCG_3329c [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|121639223|ref|YP_979447.1| hypothetical protein BCG_3365c [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148663163|ref|YP_001284686.1| hypothetical protein MRA_3341 [Mycobacterium tuberculosis H37Ra]
 gi|148824502|ref|YP_001289256.1| hypothetical protein TBFG_13329 [Mycobacterium tuberculosis F11]
 gi|167968932|ref|ZP_02551209.1| hypothetical protein MtubH3_13227 [Mycobacterium tuberculosis
           H37Ra]
 gi|215405313|ref|ZP_03417494.1| hypothetical protein Mtub0_16781 [Mycobacterium tuberculosis
           02_1987]
 gi|215428786|ref|ZP_03426705.1| hypothetical protein MtubT9_21303 [Mycobacterium tuberculosis T92]
 gi|218755082|ref|ZP_03533878.1| hypothetical protein MtubG1_17389 [Mycobacterium tuberculosis GM
           1503]
 gi|219559362|ref|ZP_03538438.1| hypothetical protein MtubT1_19482 [Mycobacterium tuberculosis T17]
 gi|224991682|ref|YP_002646371.1| hypothetical protein JTY_3325 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|224991701|ref|YP_002646390.1| hypothetical protein JTY_3345 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|224991720|ref|YP_002646409.1| hypothetical protein JTY_3365 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253800343|ref|YP_003033344.1| hypothetical protein TBMG_03348 [Mycobacterium tuberculosis KZN
           1435]
 gi|254233908|ref|ZP_04927233.1| conserved hypothetical protein [Mycobacterium tuberculosis C]
 gi|254365921|ref|ZP_04981966.1| conserved hypothetical protein [Mycobacterium tuberculosis str.
           Haarlem]
 gi|254552402|ref|ZP_05142849.1| hypothetical protein Mtube_18458 [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260188348|ref|ZP_05765822.1| hypothetical protein MtubCP_20308 [Mycobacterium tuberculosis
           CPHL_A]
 gi|260202462|ref|ZP_05769953.1| hypothetical protein MtubT4_20818 [Mycobacterium tuberculosis T46]
 gi|260206652|ref|ZP_05774143.1| hypothetical protein MtubK8_20352 [Mycobacterium tuberculosis K85]
 gi|289444882|ref|ZP_06434626.1| conserved hypothetical protein [Mycobacterium tuberculosis T46]
 gi|289448989|ref|ZP_06438733.1| conserved hypothetical protein [Mycobacterium tuberculosis CPHL_A]
 gi|289555578|ref|ZP_06444788.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN 605]
 gi|289571527|ref|ZP_06451754.1| conserved hypothetical protein [Mycobacterium tuberculosis T17]
 gi|289576020|ref|ZP_06456247.1| conserved hypothetical protein [Mycobacterium tuberculosis K85]
 gi|289747118|ref|ZP_06506496.1| conserved hypothetical protein [Mycobacterium tuberculosis 02_1987]
 gi|289751996|ref|ZP_06511374.1| conserved hypothetical protein [Mycobacterium tuberculosis T92]
 gi|289763488|ref|ZP_06522866.1| conserved hypothetical protein [Mycobacterium tuberculosis GM 1503]
 gi|294993759|ref|ZP_06799450.1| hypothetical protein Mtub2_04411 [Mycobacterium tuberculosis 210]
 gi|297635954|ref|ZP_06953734.1| hypothetical protein MtubK4_17602 [Mycobacterium tuberculosis KZN
           4207]
 gi|297732951|ref|ZP_06962069.1| hypothetical protein MtubKR_17757 [Mycobacterium tuberculosis KZN
           R506]
 gi|313660283|ref|ZP_07817163.1| hypothetical protein MtubKV_17757 [Mycobacterium tuberculosis KZN
           V2475]
 gi|2181957|emb|CAB09445.1| CONSERVED HYPOTHETICAL PROTEIN [Mycobacterium tuberculosis H37Rv]
 gi|121494837|emb|CAL73318.1| Conserved hypothetical protein [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|121494871|emb|CAL73354.1| Conserved hypothetical protein [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|124599437|gb|EAY58541.1| conserved hypothetical protein [Mycobacterium tuberculosis C]
 gi|134151434|gb|EBA43479.1| conserved hypothetical protein [Mycobacterium tuberculosis str.
           Haarlem]
 gi|148507315|gb|ABQ75124.1| conserved hypothetical protein [Mycobacterium tuberculosis H37Ra]
 gi|148723029|gb|ABR07654.1| conserved hypothetical protein [Mycobacterium tuberculosis F11]
 gi|224774797|dbj|BAH27603.1| hypothetical protein JTY_3325 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|224774816|dbj|BAH27622.1| hypothetical protein JTY_3345 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|224774835|dbj|BAH27641.1| hypothetical protein JTY_3365 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253321846|gb|ACT26449.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN
           1435]
 gi|289417801|gb|EFD15041.1| conserved hypothetical protein [Mycobacterium tuberculosis T46]
 gi|289421947|gb|EFD19148.1| conserved hypothetical protein [Mycobacterium tuberculosis CPHL_A]
 gi|289440210|gb|EFD22703.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN 605]
 gi|289540451|gb|EFD45029.1| conserved hypothetical protein [Mycobacterium tuberculosis K85]
 gi|289545281|gb|EFD48929.1| conserved hypothetical protein [Mycobacterium tuberculosis T17]
 gi|289687646|gb|EFD55134.1| conserved hypothetical protein [Mycobacterium tuberculosis 02_1987]
 gi|289692583|gb|EFD60012.1| conserved hypothetical protein [Mycobacterium tuberculosis T92]
 gi|289710994|gb|EFD75010.1| conserved hypothetical protein [Mycobacterium tuberculosis GM 1503]
 gi|326902472|gb|EGE49405.1| hypothetical protein TBPG_00317 [Mycobacterium tuberculosis W-148]
 gi|328460077|gb|AEB05500.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN
           4207]
          Length = 305

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 85/189 (44%), Gaps = 15/189 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D+ I V +KP  ++    G  +A      L+  +      P   HRLD+ T+G+L+
Sbjct: 87  VLHQDADIVVVDKPHFLATMPRGRHVAQTALVRLRRELGLPELSP--AHRLDRLTAGVLL 144

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               R         F    ++K Y +     P      +A   L +S I     H+    
Sbjct: 145 FTTRREVRGSYQTMFARGLVRKTYLARAPVAPG-----LALPRLVRSRIVKRRGHLQAVC 199

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANF 276
           E G   A +   +++  A+   +  + P TGRTHQLRVH   +G PI+GD  Y    +  
Sbjct: 200 EPGVPNAET---LVERIARDGLY-RLTPTTGRTHQLRVHMAALGIPIMGDPLYPNVISVA 255

Query: 277 KGNFTSPIQ 285
             +F++P+Q
Sbjct: 256 AHDFSTPLQ 264


>gi|255729940|ref|XP_002549895.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
 gi|240132964|gb|EER32521.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
          Length = 392

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 52/193 (26%), Positives = 88/193 (45%), Gaps = 10/193 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETSGILVV 160
           +YED ++ V +KP+G+         Y+ +   +   D  G +   T HRLD+ TSG+L+ 
Sbjct: 109 VYEDDELLVVDKPSGVPTHPTGN--YYFNSVSEMVKDQFGLEAIWTCHRLDKVTSGVLIF 166

Query: 161 ARTRAAAQHLTESFRMRRIQ--KIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
            +T++A    +   +  + Q  K Y + V G  P  K +   N  +   ++ G Y+    
Sbjct: 167 GKTKSAGSKFSRLIKDHKDQTEKTYLARVVGEFPNGKLQ--YNCPIFAVNLNG-YLVPGN 223

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NF 276
             E   +      KV    +     ++  P TG+ HQ+R+H  ++G PIV D  Y   N 
Sbjct: 224 SEELPLDSTTIFQKVSYNASLNQSLVKCIPITGKFHQIRIHLRNLGFPIVNDSFYRGDNE 283

Query: 277 KGNFTSPIQNKLY 289
             N    I+ +LY
Sbjct: 284 LTNRRCSIEEELY 296


>gi|330958926|gb|EGH59186.1| pseudouridine synthase [Pseudomonas syringae pv. maculicola str.
           ES4326]
          Length = 296

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 94/208 (45%), Gaps = 18/208 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + V +KP  + V   G  +   +   L   +D+    P   HR+D+ T+G+++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAGEYVEQTLLRRLIHRLDNPDLVP--LHRIDRHTAGLVL 146

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +   +TR+A Q L   F  RRI K Y ++   +P  +   +    L +   G  +  + 
Sbjct: 147 FSANRQTRSAYQAL---FPTRRIDKFYEAIAPALPGLEFPRVHESRLVE---GEPFFRM- 199

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            Q   GA+   +  +V++   Q+  W   + P TG+ HQLRVH   +G  I  D  Y   
Sbjct: 200 -QEGPGASNTQTRIEVLE--RQEHLWRYGLYPVTGKKHQLRVHMAALGAAICNDPFYPDA 256

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            K N     QN L L A+ +    P  G
Sbjct: 257 LK-NPLDDYQNPLKLLAKGLRFVDPLSG 283


>gi|282851241|ref|ZP_06260606.1| RNA pseudouridine synthase [Lactobacillus gasseri 224-1]
 gi|282557209|gb|EFB62806.1| RNA pseudouridine synthase [Lactobacillus gasseri 224-1]
          Length = 151

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 62/125 (49%), Gaps = 7/125 (5%)

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G+L+VA+  A    L      + + + Y  L W    N+ +      L   H   D  
Sbjct: 3   TNGLLLVAKNPAVVPILNRQLTNKTLHREY--LAWVSKSNQLKQSGTISLSIGHDPDDQR 60

Query: 214 HVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             + + +     AI+H++VI +C  ++   L ++  TGRTHQ+RVH   +G PI+GD  Y
Sbjct: 61  KRMVRLD--GQKAITHYEVIKECENKELVKLTLE--TGRTHQIRVHLAALGAPIIGDPLY 116

Query: 273 CANFK 277
             N++
Sbjct: 117 NPNYQ 121


>gi|330870692|gb|EGH05401.1| pseudouridine synthase [Pseudomonas syringae pv. aesculi str.
           0893_23]
          Length = 264

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 92/210 (43%), Gaps = 20/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 57  ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 113

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  R+I K Y ++   +P      +    L +S +       
Sbjct: 114 LFSANQQTRSAYQAL---FPTRQIDKFYEAIAPALP-----GLEFPRLHESRLVEGEPFF 165

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y A
Sbjct: 166 RMQEGAGASNTRTQIEVLE--RQDQLWRYGLYPVTGKKHQLRVHMAALGAGICNDPFYPA 223

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             K N     QN L L A+ +    P  G+
Sbjct: 224 VVK-NPVDDYQNPLKLLAKGLRFIDPLSGK 252


>gi|256823775|ref|YP_003147738.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
 gi|256797314|gb|ACV27970.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
          Length = 282

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 94/224 (41%), Gaps = 35/224 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           K  L+ ++    V+NKP G+  QG   G    I   ++   D   Q   + HRLD+   G
Sbjct: 91  KPELIADEGDYSVWNKPNGVWSQGSKWGDHCSISRLVEEHFDYNRQT-YVVHRLDKAARG 149

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A  + AA  L+  F  R ++K Y + V G                     D + + 
Sbjct: 150 LLILAHNKEAAAALSAMFAKRTVEKHYLAWVNG-----------------QFPHDSITID 192

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K  +     +I   K  D    +   L +Q  TGR HQ+R+H   +G PI+GD  +    
Sbjct: 193 KPIDNKPAKSIVTLKEYDADKDRSL-LSVQILTGRKHQIRIHLSSLGFPIIGDRLHG--- 248

Query: 277 KGNFTSPIQNK-LYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
                 P Q++ L L A  +D   P      IT    A+ +KTW
Sbjct: 249 -----EPTQSQDLQLMAYKLDFQCP------ITGDKKAYQLKTW 281


>gi|298526776|ref|ZP_07014185.1| pseudouridine synthase [Mycobacterium tuberculosis 94_M4241A]
 gi|298496570|gb|EFI31864.1| pseudouridine synthase [Mycobacterium tuberculosis 94_M4241A]
          Length = 297

 Score = 52.8 bits (125), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 85/189 (44%), Gaps = 15/189 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D+ I V +KP  ++    G  +A      L+  +      P   HRLD+ T+G+L+
Sbjct: 79  VLHQDADIVVVDKPHFLATMPRGRHVAQTALVRLRRELGLPELSP--AHRLDRLTAGVLL 136

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               R         F    ++K Y +     P      +A   L +S I     H+    
Sbjct: 137 FTTRREVRGSYQTMFARGLVRKTYLARAPVAPG-----LALPRLVRSRIVKRRGHLQAVC 191

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANF 276
           E G   A +   +++  A+   +  + P TGRTHQLRVH   +G PI+GD  Y    +  
Sbjct: 192 EPGVPNAET---LVERIARDGLY-RLTPTTGRTHQLRVHMAALGIPIMGDPLYPNVISVA 247

Query: 277 KGNFTSPIQ 285
             +F++P+Q
Sbjct: 248 AHDFSTPLQ 256


>gi|308370221|ref|ZP_07420688.2| hypothetical protein TMBG_01995 [Mycobacterium tuberculosis
           SUMu002]
 gi|308371305|ref|ZP_07424495.2| hypothetical protein TMCG_01723 [Mycobacterium tuberculosis
           SUMu003]
 gi|308372495|ref|ZP_07428863.2| hypothetical protein TMDG_02135 [Mycobacterium tuberculosis
           SUMu004]
 gi|308373700|ref|ZP_07433364.2| hypothetical protein TMEG_03697 [Mycobacterium tuberculosis
           SUMu005]
 gi|308374836|ref|ZP_07437561.2| hypothetical protein TMFG_00509 [Mycobacterium tuberculosis
           SUMu006]
 gi|308376065|ref|ZP_07445963.2| hypothetical protein TMGG_02848 [Mycobacterium tuberculosis
           SUMu007]
 gi|308377296|ref|ZP_07441776.2| hypothetical protein TMHG_02521 [Mycobacterium tuberculosis
           SUMu008]
 gi|308378264|ref|ZP_07482058.2| hypothetical protein TMIG_02817 [Mycobacterium tuberculosis
           SUMu009]
 gi|308379478|ref|ZP_07486410.2| hypothetical protein TMJG_03484 [Mycobacterium tuberculosis
           SUMu010]
 gi|308325101|gb|EFP13952.1| hypothetical protein TMBG_01995 [Mycobacterium tuberculosis
           SUMu002]
 gi|308329322|gb|EFP18173.1| hypothetical protein TMCG_01723 [Mycobacterium tuberculosis
           SUMu003]
 gi|308333153|gb|EFP22004.1| hypothetical protein TMDG_02135 [Mycobacterium tuberculosis
           SUMu004]
 gi|308336840|gb|EFP25691.1| hypothetical protein TMEG_03697 [Mycobacterium tuberculosis
           SUMu005]
 gi|308340673|gb|EFP29524.1| hypothetical protein TMFG_00509 [Mycobacterium tuberculosis
           SUMu006]
 gi|308344407|gb|EFP33258.1| hypothetical protein TMGG_02848 [Mycobacterium tuberculosis
           SUMu007]
 gi|308348411|gb|EFP37262.1| hypothetical protein TMHG_02521 [Mycobacterium tuberculosis
           SUMu008]
 gi|308353248|gb|EFP42099.1| hypothetical protein TMIG_02817 [Mycobacterium tuberculosis
           SUMu009]
 gi|308356988|gb|EFP45839.1| hypothetical protein TMJG_03484 [Mycobacterium tuberculosis
           SUMu010]
          Length = 294

 Score = 52.8 bits (125), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 85/189 (44%), Gaps = 15/189 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D+ I V +KP  ++    G  +A      L+  +      P   HRLD+ T+G+L+
Sbjct: 76  VLHQDADIVVVDKPHFLATMPRGRHVAQTALVRLRRELGLPELSP--AHRLDRLTAGVLL 133

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               R         F    ++K Y +     P      +A   L +S I     H+    
Sbjct: 134 FTTRREVRGSYQTMFARGLVRKTYLARAPVAPG-----LALPRLVRSRIVKRRGHLQAVC 188

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANF 276
           E G   A +   +++  A+   +  + P TGRTHQLRVH   +G PI+GD  Y    +  
Sbjct: 189 EPGVPNAET---LVERIARDGLY-RLTPTTGRTHQLRVHMAALGIPIMGDPLYPNVISVA 244

Query: 277 KGNFTSPIQ 285
             +F++P+Q
Sbjct: 245 AHDFSTPLQ 253


>gi|260435147|ref|ZP_05789117.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           WH 8109]
 gi|260413021|gb|EEX06317.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           WH 8109]
          Length = 120

 Score = 52.8 bits (125), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 53/101 (52%), Gaps = 2/101 (1%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL  D  +   +KPAG+  Q G G     D  +   +  +    RL HRLD++TSG+L++
Sbjct: 3   LLLRDPWLMAVDKPAGLLSQPGLG-QEQGDSVITR-LQQQDPSLRLVHRLDRDTSGVLLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           AR+  A + L+  F  RRI K+Y + V G    +   ++ W
Sbjct: 61  ARSADALRRLSALFTERRINKLYQADVEGELHGRGCIVSPW 101


>gi|310823851|ref|YP_003956209.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309396923|gb|ADO74382.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 575

 Score = 52.8 bits (125), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 92/219 (42%), Gaps = 22/219 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWV--DSKGQKPRLTHRLDQETSGI 157
           L+YED  +   +KP G+ SV G    +   D  L        +  +P + H L+ +TSG+
Sbjct: 371 LVYEDPWLLAVDKPCGLLSVPGRH--SPQRDSVLTRLRRRAPEAPEPLIVHPLESDTSGL 428

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+  +       L   F  +   K Y + + G        I   L  ++H       +V 
Sbjct: 429 LLATKDAETHAALQRQFARKEADKHYIAWLEGPVLGDHGVIE--LPLRAHPEERPRQIV- 485

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCA 274
            +      A++ ++V+     +   +   P TG  HQLRVHA H   +G PI GD  Y +
Sbjct: 486 -DPVHGKRAVTEWRVLRRRGPQ-TQVSFLPRTGHPHQLRVHAAHPLGLGAPIAGDRLYGS 543

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           +           +L LHA  + + HP  G RL +  P P
Sbjct: 544 SGG--------TRLMLHAESLTVLHPRTGERLHLECPAP 574


>gi|154275958|ref|XP_001538824.1| hypothetical protein HCAG_06429 [Ajellomyces capsulatus NAm1]
 gi|150413897|gb|EDN09262.1| hypothetical protein HCAG_06429 [Ajellomyces capsulatus NAm1]
          Length = 545

 Score = 52.8 bits (125), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 40/157 (25%), Positives = 70/157 (44%), Gaps = 28/157 (17%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           QK +  G V ++ K V  + +IQ+G V+                     S  L +H   +
Sbjct: 82  QKAIEDGAVCINGKAVSIDTKIQNGDVI---------------------SHTLHRHEPPV 120

Query: 98  KSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQ 152
            S    +++ED  + V +KPAG+ V       Y+ +  L+     +G    P   +RLD+
Sbjct: 121 TSQPIGIIHEDDDMIVIDKPAGVPVHPAG--RYNYNSILEIMKAERGNGWVPYPCNRLDR 178

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            TSG++ + +    A+ + E  R R ++K Y + V G
Sbjct: 179 LTSGVMFIGKHPKGAEQIGEKLRSRTVRKEYVARVKG 215


>gi|126667503|ref|ZP_01738474.1| Pseudouridylate synthases, 23S RNA-specific [Marinobacter sp.
           ELB17]
 gi|126628095|gb|EAZ98721.1| Pseudouridylate synthases, 23S RNA-specific [Marinobacter sp.
           ELB17]
          Length = 304

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 83/185 (44%), Gaps = 16/185 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
           LL + S+  V+ KP G+  QG S    H    L    + +  +P  L HRLD + +G+++
Sbjct: 81  LLEDKSRYSVWFKPHGLLAQG-SQWGDHCS--LLRVAEVQLNRPCFLIHRLDADAAGLML 137

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK---SHIGGDYVHVV 216
           +A    AA  L++ F  R I K Y + V G+   +++ I   +  K   SH+   Y +  
Sbjct: 138 IAHDSKAAAALSQLFAGRAIIKQYLADVTGVLDVEEQTIDGDIDGKAAISHVSTLYSNAG 197

Query: 217 KQNEKGANYAISHFKVIDCFA---------QKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             N    N   ++   I+  +              + ++  TGR HQ+R H   +G PIV
Sbjct: 198 SINTSAVNSNSTNASSINASSINTKAEDTDASTSRVNVRIETGRKHQIRRHLASIGHPIV 257

Query: 268 GDHKY 272
            D  Y
Sbjct: 258 ADRLY 262


>gi|149002475|ref|ZP_01827409.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP14-BS69]
 gi|147759412|gb|EDK66404.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP14-BS69]
          Length = 127

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 31/107 (28%), Positives = 56/107 (52%), Gaps = 12/107 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKG----QKPRLTHRLD 151
           ++Y+D  + V NKP G+ V   +G   H  G L + +     D  G     +P + HR+D
Sbjct: 9   IVYQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNALMYHIKDLSGINGVLRPGIVHRID 65

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           ++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I
Sbjct: 66  KDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVI 112


>gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylate synthase [Herbaspirillum
           seropedicae SmR1]
 gi|300074785|gb|ADJ64184.1| 23S RNA-specific pseudouridylate synthase protease protein
           [Herbaspirillum seropedicae SmR1]
          Length = 299

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 39/149 (26%), Positives = 68/149 (45%), Gaps = 7/149 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ET+G++V +   A+       F+ R + K+Y ++        +  +    + +S 
Sbjct: 138 HRLDRETAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIA-----PLRSDLELPRVHRSR 192

Query: 208 IGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           +        K +E +GA  + +H  +I+       +  ++P TGR HQLRVH   +G PI
Sbjct: 193 VEEIPEQFFKMHEAEGAPNSETHISLIEARGALGLY-RLEPVTGRRHQLRVHMAALGIPI 251

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           + D  Y           +   L L AR +
Sbjct: 252 LNDLFYPEAVPVGVADDLDKPLKLLARSL 280


>gi|146416095|ref|XP_001484017.1| hypothetical protein PGUG_03398 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 611

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 49/173 (28%), Positives = 79/173 (45%), Gaps = 7/173 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  +   +KP GI V       Y  +   K +    G+     +RLD+ TSG++ +
Sbjct: 192 IVHEDDDVIAIDKPLGIPVHPVG--RYRYNTITKIFQHEFGRVVHPCNRLDRLTSGLMFL 249

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T   A    +  + R ++K Y + V G  K   E I   +  K+      +++V  + 
Sbjct: 250 GKTPKGADKFVQQIKDRTVRKEYIARVIG--KFPCEEITVEVPIKTVSPKHTLNMV--DP 305

Query: 221 KGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           K    A + FK I    A     ++  P TGRTHQ+RVH  H+G  I  D  Y
Sbjct: 306 KNGKEAKTKFKRISYDPASNTSIVKCYPLTGRTHQIRVHLQHIGHAIANDPIY 358


>gi|115372594|ref|ZP_01459901.1| pseudouridylate synthase, 23S RNA-specific [Stigmatella aurantiaca
           DW4/3-1]
 gi|115370315|gb|EAU69243.1| pseudouridylate synthase, 23S RNA-specific [Stigmatella aurantiaca
           DW4/3-1]
          Length = 555

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 92/219 (42%), Gaps = 22/219 (10%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWV--DSKGQKPRLTHRLDQETSGI 157
           L+YED  +   +KP G+ SV G    +   D  L        +  +P + H L+ +TSG+
Sbjct: 351 LVYEDPWLLAVDKPCGLLSVPGRH--SPQRDSVLTRLRRRAPEAPEPLIVHPLESDTSGL 408

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+  +       L   F  +   K Y + + G        I   L  ++H       +V 
Sbjct: 409 LLATKDAETHAALQRQFARKEADKHYIAWLEGPVLGDHGVIE--LPLRAHPEERPRQIV- 465

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCA 274
            +      A++ ++V+     +   +   P TG  HQLRVHA H   +G PI GD  Y +
Sbjct: 466 -DPVHGKRAVTEWRVLRRRGPQ-TQVSFLPRTGHPHQLRVHAAHPLGLGAPIAGDRLYGS 523

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           +           +L LHA  + + HP  G RL +  P P
Sbjct: 524 SGG--------TRLMLHAESLTVLHPRTGERLHLECPAP 554


>gi|308232412|ref|ZP_07415966.2| hypothetical protein TMAG_02753 [Mycobacterium tuberculosis
           SUMu001]
 gi|308380643|ref|ZP_07490629.2| hypothetical protein TMKG_02560 [Mycobacterium tuberculosis
           SUMu011]
 gi|308406115|ref|ZP_07495174.2| hypothetical protein TMLG_02074 [Mycobacterium tuberculosis
           SUMu012]
 gi|308214050|gb|EFO73449.1| hypothetical protein TMAG_02753 [Mycobacterium tuberculosis
           SUMu001]
 gi|308360844|gb|EFP49695.1| hypothetical protein TMKG_02560 [Mycobacterium tuberculosis
           SUMu011]
 gi|308364529|gb|EFP53380.1| hypothetical protein TMLG_02074 [Mycobacterium tuberculosis
           SUMu012]
          Length = 297

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 85/189 (44%), Gaps = 15/189 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D+ I V +KP  ++    G  +A      L+  +      P   HRLD+ T+G+L+
Sbjct: 79  VLHQDADIVVVDKPHFLATMPRGRHVAQTALVRLRRELGLPELSP--AHRLDRLTAGVLL 136

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               R         F    ++K Y +     P      +A   L +S I     H+    
Sbjct: 137 FTTRREVRGSYQTMFARGLVRKTYLARAPVAPG-----LALPRLVRSRIVKRRGHLQAVC 191

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANF 276
           E G   A +   +++  A+   +  + P TGRTHQLRVH   +G PI+GD  Y    +  
Sbjct: 192 EPGVPNAET---LVERIARDGLY-RLTPTTGRTHQLRVHMAALGIPIMGDPLYPNVISVA 247

Query: 277 KGNFTSPIQ 285
             +F++P+Q
Sbjct: 248 AHDFSTPLQ 256


>gi|149002476|ref|ZP_01827410.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP14-BS69]
 gi|147759413|gb|EDK66405.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP14-BS69]
          Length = 93

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/97 (31%), Positives = 52/97 (53%), Gaps = 7/97 (7%)

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y     G   +   +
Sbjct: 1   MTRFHVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGDEVY-----GPRKTLKGH 54

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +LHA+ +   HP  G+ L+  A +P    +T + L
Sbjct: 55  GQFLHAKTLGFTHPRTGKTLEFKADIPEIFKETLERL 91


>gi|145630740|ref|ZP_01786518.1| hypothetical protein CGSHi22421_10087 [Haemophilus influenzae
           R3021]
 gi|144983622|gb|EDJ91082.1| hypothetical protein CGSHi22421_10087 [Haemophilus influenzae
           R3021]
          Length = 152

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 49/95 (51%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           A +   A  + E F  + +QK Y ++V G  + K+
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKE 98


>gi|314922786|gb|EFS86617.1| RNA pseudouridine synthase [Propionibacterium acnes HL001PA1]
          Length = 209

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 70/171 (40%), Gaps = 19/171 (11%)

Query: 144 PRLT--HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI--- 198
           P LT  HRLD+ T+G+L++ R R   +   E F  R + K Y  +   +     E +   
Sbjct: 32  PELTVAHRLDRVTAGVLLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTAT 91

Query: 199 -ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQL 255
            + W ++   I    +   ++     N        I    +   W   E  P TGRTHQ+
Sbjct: 92  KSGWQVRSRIIKERGILQAREVPGVPNTVTD----IALIGEHGGWGLYEASPRTGRTHQI 147

Query: 256 RVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKLYLHARYMDLPHPEGG 303
           R+H   +G PIV D  Y         +FT P+Q    L A  M    P  G
Sbjct: 148 RLHMQRLGAPIVNDPFYPVVLDIPVDDFTHPLQ----LQAWRMGFTDPVSG 194


>gi|298486671|ref|ZP_07004728.1| RNA pseudouridylate synthase [Pseudomonas savastanoi pv. savastanoi
           NCPPB 3335]
 gi|298158754|gb|EFH99817.1| RNA pseudouridylate synthase [Pseudomonas savastanoi pv. savastanoi
           NCPPB 3335]
          Length = 296

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 92/210 (43%), Gaps = 20/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 145

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  R+I K Y ++   +P      +    L +S +       
Sbjct: 146 LFSANQQTRSAYQAL---FPTRQIDKFYEAIAPALPG-----LEFPRLHESRLVEGEPFF 197

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y A
Sbjct: 198 RMQEGAGASNTRTQIEVLE--RQDQLWRYGLYPVTGKKHQLRVHMAALGAGICNDPFYPA 255

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             K N     QN L L A+ +    P  G+
Sbjct: 256 VVK-NPVDDYQNPLKLLAKGLRFIDPLSGK 284


>gi|307069602|ref|YP_003878079.1| putative pseudouridine synthase, RluA family [Candidatus Zinderia
           insecticola CARI]
 gi|306482862|gb|ADM89733.1| putative pseudouridine synthase, RluA family [Candidatus Zinderia
           insecticola CARI]
          Length = 291

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 39/139 (28%), Positives = 71/139 (51%), Gaps = 14/139 (10%)

Query: 144 PRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           PRL   +R+D+ T G++++ +   +  +    F+   I+K Y  LVWG  KN      N+
Sbjct: 108 PRLGIINRIDKNTFGLIIIIKNIYSYFYFIYQFKFNTIKKKYICLVWGKVKN--NNFINF 165

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-----CWLEMQPHTGRTHQLR 256
            + K+    + + +V +N+K     I+ +K+I+    KF       L ++  TG+ HQ+R
Sbjct: 166 SIIKNKKKYNKM-IVNKNKKSN--IITKYKIIN--YNKFNNLYISLLNIKLITGKMHQIR 220

Query: 257 VHALHMGCPIVGDHKYCAN 275
           +H  ++   I+GD  Y  N
Sbjct: 221 IHMKNIKHSILGDILYEKN 239


>gi|302845024|ref|XP_002954051.1| pseudouridine synthase mitochondrial precursor [Volvox carteri f.
           nagariensis]
 gi|300260550|gb|EFJ44768.1| pseudouridine synthase mitochondrial precursor [Volvox carteri f.
           nagariensis]
          Length = 955

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 59/169 (34%), Gaps = 54/169 (31%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQ---------------------------------- 168
           +PRL HRLDQ  SG++ ++R R   +                                  
Sbjct: 713 EPRLVHRLDQAASGVMALSRERRGGEDRDPNDEDEEAGGFGGRGGDPARRGRVGPGGLAL 772

Query: 169 ----HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
                +     M  I + YW+ + G             L+    G   + VV        
Sbjct: 773 NRDERVGRDGEMPAIHRTYWAFLAGD------------LQPRQSGRVSLPVVVDGVLCPA 820

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
                 K   C      W+E+ P TGR HQLR+H A  +G PI+GD +Y
Sbjct: 821 VTAYRVKATGC---GVSWVELTPETGRRHQLRIHCARKLGAPIIGDGRY 866


>gi|289623665|ref|ZP_06456619.1| pseudouridine synthase [Pseudomonas syringae pv. aesculi str.
           NCPPB3681]
          Length = 296

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 92/210 (43%), Gaps = 20/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 145

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  R+I K Y ++   +P      +    L +S +       
Sbjct: 146 LFSANQQTRSAYQAL---FPTRQIDKFYEAIAPALPG-----LEFPRLHESRLVEGEPFF 197

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y A
Sbjct: 198 RMQEGAGASNTRTQIEVLE--RQDQLWRYGLYPVTGKKHQLRVHMAALGAGICNDPFYPA 255

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             K N     QN L L A+ +    P  G+
Sbjct: 256 VVK-NPVDDYQNPLKLLAKGLRFIDPLSGK 284


>gi|146306485|ref|YP_001186950.1| pseudouridine synthase [Pseudomonas mendocina ymp]
 gi|145574686|gb|ABP84218.1| pseudouridine synthase [Pseudomonas mendocina ymp]
          Length = 293

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 49/217 (22%), Positives = 103/217 (47%), Gaps = 20/217 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQET 154
            ++ +L++D  + V +KP  + V        +++  L + +  +   P L   HR+D+ T
Sbjct: 80  FEARVLWQDEHLLVADKPHFLPVMPA---GEYVEQTLLARLIKRTGNPDLVPIHRIDRLT 136

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+++ +   ++       FR R ++K Y ++   +P+ +   +     +   + G+   
Sbjct: 137 AGLVLFSVAPSSRGQYQALFRQRAVEKRYEAIAPALPQLQFPHVH----RSRMVEGEPFF 192

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-- 272
            +++    AN + +  +V++   + + +  + P TGR HQLRVH   +G PIVGD  Y  
Sbjct: 193 RMQEVAGEAN-SETRIEVLERRGELWRY-GLSPVTGRKHQLRVHLAGLGAPIVGDDFYPE 250

Query: 273 ---CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
                N   ++  P++    L AR +    P  G+L+
Sbjct: 251 LHESRNQPDDYAKPLK----LLARGLRFVDPLSGQLR 283


>gi|196011042|ref|XP_002115385.1| expressed hypothetical protein [Trichoplax adhaerens]
 gi|190582156|gb|EDV22230.1| expressed hypothetical protein [Trichoplax adhaerens]
          Length = 267

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 57/248 (22%), Positives = 99/248 (39%), Gaps = 37/248 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILV 159
           LL     +   NKP GI+     GI Y+     +   +D   Q   L+H LD+  +GIL+
Sbjct: 29  LLVNSYNVIAINKPYGIASHDNPGIGYNCHSIYRELNLDDDSQPVYLSHVLDRNCTGILI 88

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
              ++A    + ++ +              IP  + + +    LK    G     +  + 
Sbjct: 89  --GSKAITVGIPKAIKG----------TIDIPIVEDKTLKRVKLKMQDEGASKQEIAYKY 136

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCA---- 274
                 A +++KV+         +E +  T    Q+RVHA   +GCP++GDH+Y +    
Sbjct: 137 GGRVRLASTNYKVLSKSEIGCALIEFETKTYYKKQIRVHAADALGCPVLGDHQYSSKKIG 196

Query: 275 -------------NFKGNFTSPIQNKLYLHARYMDLPH-PEGGR---LQITAPLPAHMVK 317
                        N  G  T+ +  K++LH R + +   P  G+   L I A      ++
Sbjct: 197 HNQVVSPKIGQALNLIGGNTNTL--KMHLHLRKVTISKWPASGKVINLAIVASPSYEFMQ 254

Query: 318 TWDSLGFK 325
           T + L  K
Sbjct: 255 TLEMLQLK 262


>gi|255519723|ref|ZP_05386960.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Listeria monocytogenes FSL J1-175]
          Length = 68

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/68 (42%), Positives = 38/68 (55%), Gaps = 8/68 (11%)

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
           E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L HP +G
Sbjct: 1   ECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLNHPFKG 53

Query: 303 GRLQITAP 310
             +  +AP
Sbjct: 54  KEMNFSAP 61


>gi|91788766|ref|YP_549718.1| pseudouridine synthase [Polaromonas sp. JS666]
 gi|91697991|gb|ABE44820.1| pseudouridine synthase [Polaromonas sp. JS666]
          Length = 303

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 45/178 (25%), Positives = 81/178 (45%), Gaps = 11/178 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +  +L++D  + V +KP  + V   G  +   +   LK+ +      P   HR+D+ET+
Sbjct: 91  FEETVLHQDEHLVVADKPHFLPVTPSGHYLQETLLVRLKNRLGIDSLVP--IHRIDRETA 148

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIANWLLKKSHIGGDYVH 214
           G+++ +   A        FR   + K Y +L  W      +E +   L +KS I  D   
Sbjct: 149 GLVLFSVNPAERDAYQALFRQHAVSKHYEALAPW------REDLRFPLTRKSRIVQDEPF 202

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             ++   G   + +H +++    ++  +  + P TG+ HQLRVH   +G PI  D  Y
Sbjct: 203 FRQREVPGEPNSETHLELLQISGEQARY-ALSPVTGKKHQLRVHMNALGLPITNDRMY 259


>gi|62391784|ref|YP_227186.1| ribosomal pseudouridine synthase [Corynebacterium glutamicum ATCC
           13032]
 gi|41327126|emb|CAF20969.1| Putative ribosomal pseudouridine synthase [Corynebacterium
           glutamicum ATCC 13032]
          Length = 338

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 59/220 (26%), Positives = 91/220 (41%), Gaps = 29/220 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP  ++     G        +K  V +        HRLD+ TSG+LV+
Sbjct: 113 VIHEDDDILVIDKPPYLATMP-RGRHITETALVKMRVLTGNNDLTPAHRLDRLTSGVLVM 171

Query: 161 ART---RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK-KSHIGGDYVHVV 216
            +    R A Q L   F  R   K Y ++   +P    +  A W  + +   G     VV
Sbjct: 172 VKKPELRGAYQTL---FARREASKTYEAIAEFVPGLLDDGPAIWESRIEKERGIVQAFVV 228

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEM------------QPHTGRTHQLRVHALHMGC 264
           +         +S   V D  A++    EM             P TG+THQLR+H      
Sbjct: 229 EGPVNARTELVSVTPVED--AEQSILEEMHGPLPRQARYVLAPSTGKTHQLRIHMRDFAA 286

Query: 265 PIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           PI+GD  Y    A    ++T+P    ++L AR +    P+
Sbjct: 287 PILGDPLYPVLHAVDDEDYTTP----MHLIARTLTFVDPQ 322


>gi|307243145|ref|ZP_07525319.1| conserved domain protein [Peptostreptococcus stomatis DSM 17678]
 gi|306493505|gb|EFM65484.1| conserved domain protein [Peptostreptococcus stomatis DSM 17678]
          Length = 84

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/82 (36%), Positives = 45/82 (54%), Gaps = 6/82 (7%)

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE- 301
           + ++  TGRTHQ+RVH  H+G PI+GD  Y     G   S + ++  LHA  +    P  
Sbjct: 1   VNLRLETGRTHQIRVHLSHIGHPIMGDDLY-----GRPDSSLIDRQALHAYKLIFDQPRL 55

Query: 302 GGRLQITAPLPAHMVKTWDSLG 323
           G R+++ + LP  MV   + LG
Sbjct: 56  GDRIELKSSLPKDMVGLLEKLG 77


>gi|289647117|ref|ZP_06478460.1| pseudouridine synthase [Pseudomonas syringae pv. aesculi str. 2250]
          Length = 324

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 92/210 (43%), Gaps = 20/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 117 ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 173

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  R+I K Y ++   +P      +    L +S +       
Sbjct: 174 LFSANQQTRSAYQAL---FPTRQIDKFYEAIAPALPG-----LEFPRLHESRLVEGEPFF 225

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y A
Sbjct: 226 RMQEGAGASNTRTQIEVLE--RQDQLWRYGLYPVTGKKHQLRVHMAALGAGICNDPFYPA 283

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             K N     QN L L A+ +    P  G+
Sbjct: 284 VVK-NPVDDYQNPLKLLAKGLRFIDPLSGK 312


>gi|188578461|ref|YP_001915390.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae PXO99A]
 gi|188522913|gb|ACD60858.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae PXO99A]
          Length = 206

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 79/178 (44%), Gaps = 19/178 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           +L+ D+ + V  KP  + V      AY  +  L   V   D+    P   HR+D+ET+G+
Sbjct: 39  VLHADANLVVACKPHFLPVAPAG--AYVHETLLTRLVRRLDNPALVP--LHRIDRETAGL 94

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-ANWLLKKSHIGGDYVHVV 216
           ++ +   A        FR RRI+K Y  +   +P+     +  +WL       G+    +
Sbjct: 95  VLFSANPATRGIYQALFRERRIRKQYLVVAPPLPELSFPYVHRSWLEP-----GEPFFRM 149

Query: 217 KQNEKGANYAISHFKVIDCFAQKF-CWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++     N       VID  A     W   ++P TGR HQLRVH   +G PI+ D  Y
Sbjct: 150 REGVGEPNSE----TVIDVVAPGADTWTYRLEPVTGRKHQLRVHMAALGAPILHDRFY 203


>gi|255540129|ref|XP_002511129.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223550244|gb|EEF51731.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 385

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 46/176 (26%), Positives = 75/176 (42%), Gaps = 7/176 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +    KPA + V   G      + G L++  +     P   HRLD+  SG+L+
Sbjct: 120 VLYKDPDVVTVYKPATVPVHPCGQYRKNTVVGILQAEHNLAPLFP--VHRLDRLVSGLLI 177

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA---NWLLKKSHIGGDYVHVV 216
           +AR    A    +      +QK Y + V G+    ++ +    N+  ++     +  +  
Sbjct: 178 LARNALKADLFRQEIEAGMVQKQYVAKVVGVFPEDEQVVGVNINYNAREGRSTAEVGNSC 237

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +      A + F  I         L  +P TGRTHQ+RVH  + G PI  D  Y
Sbjct: 238 VDSPPKGKTACTKFTRISTNGTHSIVL-CKPITGRTHQIRVHLQYTGHPIANDFLY 292


>gi|153820593|ref|ZP_01973260.1| RNA pseudouridine synthase family protein [Vibrio cholerae NCTC
           8457]
 gi|126508864|gb|EAZ71458.1| RNA pseudouridine synthase family protein [Vibrio cholerae NCTC
           8457]
          Length = 115

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/67 (40%), Positives = 38/67 (56%), Gaps = 8/67 (11%)

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHAR 293
           ++C +EMQP TGR HQLR H  H+  PIVGD  +        F+ +F++    +L LHA 
Sbjct: 19  RYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDTTHGDGVHNRLFREHFSA---QRLMLHAS 75

Query: 294 YMDLPHP 300
            +   HP
Sbjct: 76  ELRFMHP 82


>gi|309808140|ref|ZP_07702052.1| RNA pseudouridine synthase [Lactobacillus iners LactinV 01V1-a]
 gi|308168609|gb|EFO70715.1| RNA pseudouridine synthase [Lactobacillus iners LactinV 01V1-a]
          Length = 194

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 47/197 (23%), Positives = 83/197 (42%), Gaps = 22/197 (11%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
            + V+ K +  N ++ +  ++ I      LNH+   Q+   +S N+          ++YE
Sbjct: 19  NILVNDKYLPLNFKVHTNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYE 65

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           +  + V NKPAG   Q      Y  D  L       G  P + HRLD  T+G+L+VA+  
Sbjct: 66  NDDVLVINKPAG---QKTHPNLYETDTALNDCASYLGYSPYIVHRLDMLTNGLLLVAKNP 122

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           A    L +    + + + Y++ +            N       IG D + + K+  +   
Sbjct: 123 AVVPILNKQLIDKTLSRSYFAWIEATNDISDNGTINL-----PIGDDPLDMRKRMVRADG 177

Query: 225 Y-AISHFKVIDCFAQKF 240
             AI+H++V+     KF
Sbjct: 178 LKAITHYQVVKKQLIKF 194


>gi|296141678|ref|YP_003648921.1| pseudouridine synthase [Tsukamurella paurometabola DSM 20162]
 gi|296029812|gb|ADG80582.1| pseudouridine synthase [Tsukamurella paurometabola DSM 20162]
          Length = 305

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 46/189 (24%), Positives = 82/189 (43%), Gaps = 12/189 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ D +I V +KP  ++    G+ +       L+  +      P   HRLD+ T+G+L+
Sbjct: 98  IIHADDRIVVVDKPHFLATMPRGARVVQSALVRLRRELGEPSLSP--AHRLDRLTAGVLL 155

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             R  A      + F     +K Y +L    P  +   +   +  +       +   + N
Sbjct: 156 FTRDPAVRGPYQQLFAQGLARKEYAALA---PLRRDLELPATVESRIEKTPGIMRAYEVN 212

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---F 276
             G   A SH + ++          ++P TG+THQLR+H   +G PI+GD  Y       
Sbjct: 213 --GPVNARSHVE-LEAELGTIARYRLRPETGKTHQLRLHMSRLGVPILGDPLYPEPREVI 269

Query: 277 KGNFTSPIQ 285
            G+FT P++
Sbjct: 270 DGDFTDPLR 278


>gi|302837881|ref|XP_002950499.1| hypothetical protein VOLCADRAFT_90941 [Volvox carteri f.
           nagariensis]
 gi|300264048|gb|EFJ48245.1| hypothetical protein VOLCADRAFT_90941 [Volvox carteri f.
           nagariensis]
          Length = 535

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/66 (43%), Positives = 39/66 (59%), Gaps = 7/66 (10%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           PHTGRTHQ+RVH  H+G PI+GD  Y        T P   +  LHA  +   HP  G+ +
Sbjct: 415 PHTGRTHQIRVHLHHVGHPILGDDIY------GVTGPWMGRQALHAAELRFTHPLTGQVM 468

Query: 306 QITAPL 311
           +++APL
Sbjct: 469 RLSAPL 474


>gi|294141810|ref|YP_003557788.1| ribosomal large subunit pseudouridine synthase family protein
           [Shewanella violacea DSS12]
 gi|293328279|dbj|BAJ03010.1| ribosomal large subunit pseudouridine synthase family protein
           [Shewanella violacea DSS12]
          Length = 287

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 41/172 (23%), Positives = 83/172 (48%), Gaps = 21/172 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           L+++  +  ++ KP G+  QG   G    I+ + ++ + S  +   + HRLD+  +G+++
Sbjct: 88  LIFDGGQYSIWYKPYGMLCQGSKWGDHTTINRYAETHL-SPDRPAFIIHRLDRAATGLVL 146

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +  ++     L + F +R + K Y  +V G     ++E +         IG D       
Sbjct: 147 IGHSKKTTAALAKLFELRLLDKYYQVIVEGQFNLGQQESVT--------IGTDV------ 192

Query: 219 NEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                  A SH K++   A++    ++++  +GR HQ+R+H   +G P+VGD
Sbjct: 193 ---DGKAACSHAKLLQYDAERGRSLVQVKIESGRKHQIRIHMESIGYPVVGD 241


>gi|319441171|ref|ZP_07990327.1| putative pseudouridylate synthase [Corynebacterium variabile DSM
           44702]
          Length = 328

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 53/199 (26%), Positives = 75/199 (37%), Gaps = 29/199 (14%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           LLY D  I V +KP  +S +  G  I        +         P   HRLD+ T G+L+
Sbjct: 79  LLYRDENILVADKPPFMSTLPRGQHITETAVVRARRQFGIDDLSP--VHRLDRLTRGVLL 136

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK----NKKECIAN--------------- 200
               R       + F  R +QK Y ++    P      + E  A                
Sbjct: 137 FTVRREVRGAYQQLFERRLVQKTYDAVTPRPPGWTDLTQVEVPAGALHLGSPASALAAPS 196

Query: 201 ----WLLKKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
               W+L+   I   G     V + +  +  A+   +  D    K  W  +QPH+GRTHQ
Sbjct: 197 AAEPWVLRHRLIKDRGHLATYVAEGDANSETAVVGIRPSDLDDSKLVW-TLQPHSGRTHQ 255

Query: 255 LRVHALHMGCPIVGDHKYC 273
           LRV+      PIV D  Y 
Sbjct: 256 LRVNMRLFKTPIVDDPIYT 274


>gi|297581272|ref|ZP_06943196.1| tRNA pseudouridine synthase C [Vibrio cholerae RC385]
 gi|297534588|gb|EFH73425.1| tRNA pseudouridine synthase C [Vibrio cholerae RC385]
          Length = 172

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 38/67 (56%), Gaps = 8/67 (11%)

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHAR 293
           ++C +EMQP TGR HQLR H  H+  PIVGD  +        F+ +F++    +L LHA 
Sbjct: 75  RYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDTTHGDGVHNRLFREHFSA---QRLMLHAS 131

Query: 294 YMDLPHP 300
            +   HP
Sbjct: 132 ELRFMHP 138


>gi|19554131|ref|NP_602133.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glutamicum ATCC 13032]
 gi|21325718|dbj|BAC00339.1| Pseudouridylate synthases, 23S RNA-specific [Corynebacterium
           glutamicum ATCC 13032]
          Length = 322

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 55/203 (27%), Positives = 84/203 (41%), Gaps = 25/203 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V +KP  ++     G        +K  V +        HRLD+ TSG+LV+
Sbjct: 97  VIHEDDDILVIDKPPYLATMP-RGRHITETALVKMRVLTGNNDLTPAHRLDRLTSGVLVM 155

Query: 161 ART---RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK-KSHIGGDYVHVV 216
            +    R A Q L   F  R   K Y ++   +P    +  A W  + +   G     VV
Sbjct: 156 VKKPELRGAYQTL---FARREASKTYEAIAEFVPGLLDDGPAIWESRIEKERGIVQAFVV 212

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQ------------PHTGRTHQLRVHALHMGC 264
           +         +S   V D  A++    EM             P TG+THQLR+H      
Sbjct: 213 EGPVNARTELVSVTPVED--AEQSILEEMHGPLPRQARYVLAPSTGKTHQLRIHMRDFAA 270

Query: 265 PIVGDHKYC---ANFKGNFTSPI 284
           PI+GD  Y    A    ++T+P+
Sbjct: 271 PILGDPLYPVLHAVDDEDYTTPM 293


>gi|284799465|ref|ZP_06390155.1| ribosomal large subunit pseudouridine synthase [Neisseria subflava
           NJ9703]
 gi|284797936|gb|EFC53283.1| ribosomal large subunit pseudouridine synthase [Neisseria subflava
           NJ9703]
          Length = 125

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 35/115 (30%), Positives = 59/115 (51%), Gaps = 14/115 (12%)

Query: 215 VVKQNEKGANYAISHFKVIDCFA---------QKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +V+ +E G + A + F+V++ F+             ++E    TGRTHQ+RVH     CP
Sbjct: 1   MVRVSEDGQS-AHTIFRVLNRFSDGLLHQVGLSDLTFVEATLKTGRTHQIRVHLQSQDCP 59

Query: 266 IVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           I GD +Y  +++ N         +++LHA  + L HP  G +L + A LP  + +
Sbjct: 60  IAGDERY-GDYQANKRLQKLGLKRMFLHASELHLAHPLTGEKLILKAHLPQELAQ 113


>gi|260549352|ref|ZP_05823571.1| pseudouridylate synthase [Acinetobacter sp. RUH2624]
 gi|260407461|gb|EEX00935.1| pseudouridylate synthase [Acinetobacter sp. RUH2624]
          Length = 302

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 49/191 (25%), Positives = 86/191 (45%), Gaps = 15/191 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V +KP  +++   G  +   +   LK    ++   P   HRLD+ET+G+++
Sbjct: 94  ILFENDDLLVVDKPHFLTISPTGQYVQETLLVRLKKQTGNEFLTP--IHRLDRETAGVVL 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY--VHVVK 217
             +   +     + F  R + KIY ++     + K   I    L K   G  +  + V+ 
Sbjct: 152 FCKRPQSRGIYQQLFADREVHKIYHAIAAYKAELKFPQILKLYLDK---GTPFYTMQVIA 208

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--- 274
             +      I   +    +A K+C   + P TG+ HQLRVH  H+G PI  D  Y     
Sbjct: 209 HTKTNTETKIELIEHNHSWA-KYC---LTPTTGKQHQLRVHLNHLGIPIKNDPFYPIVQH 264

Query: 275 NFKGNFTSPIQ 285
               +F+ P+Q
Sbjct: 265 KADDDFSQPLQ 275


>gi|269861115|ref|XP_002650272.1| diaminohydroxyphosphoribosylaminopyrimidine deaminase
           [Enterocytozoon bieneusi H348]
 gi|220066286|gb|EED43774.1| diaminohydroxyphosphoribosylaminopyrimidine deaminase
           [Enterocytozoon bieneusi H348]
          Length = 331

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/183 (26%), Positives = 80/183 (43%), Gaps = 21/183 (11%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D +I V NKP GI        AYH     K+    K +     +RLD   SG+L++ 
Sbjct: 81  IYIDDEITVVNKPFGIPCHPVG--AYHYYTVTKTIF--KNKPVGCVNRLDIPVSGVLIIN 136

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-- 219
                  H      +   +KIY + V G      E +    ++K    G  + +V ++  
Sbjct: 137 TCNQKRIHE----YLLNSKKIYIAKVIGQFIFSDEQLHKLGIEKRISNGKSIIIVNKSLL 192

Query: 220 ----------EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                          +A +HF+++  +  ++  ++  P TGRTHQ+RVH  ++G PI+ D
Sbjct: 193 LDPKTKKQKISDDGKFAETHFELVS-YQNQYSMIKCYPITGRTHQIRVHLAYIGFPILYD 251

Query: 270 HKY 272
             Y
Sbjct: 252 TLY 254


>gi|325141924|gb|EGC64364.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis 961-5945]
          Length = 173

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 40/157 (25%), Positives = 66/157 (42%), Gaps = 37/157 (23%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD       P  +   L   ++ G V V+ K  +  +++  G+ +R+            
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKPSQPKDKMIGGEQIRV------------ 87

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              +  S  NL    + +   ++YED  + V NKPAG+ V   +G          +W   
Sbjct: 88  --TVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAG----------NWEGD 135

Query: 140 KGQKP-------------RLTHRLDQETSGILVVART 163
             Q+P              + HRLD+ETSG++VVA+T
Sbjct: 136 AAQRPVGALSRIEPSTACSIVHRLDKETSGLMVVAKT 172


>gi|56807623|ref|ZP_00365522.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Streptococcus
           pyogenes M49 591]
          Length = 112

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 5/76 (6%)

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           YA + +KV+  +++    ++++ HTGRTHQ+RVH  H+G P++GD  Y        T   
Sbjct: 12  YAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGFPLLGDDLYGGRLDLGIT--- 68

Query: 285 QNKLYLHARYMDLPHP 300
             +  LH  Y++   P
Sbjct: 69  --RQALHCHYLNFKDP 82


>gi|255067494|ref|ZP_05319349.1| ribosomal large subunit pseudouridine synthase C [Neisseria sicca
           ATCC 29256]
 gi|255048289|gb|EET43753.1| ribosomal large subunit pseudouridine synthase C [Neisseria sicca
           ATCC 29256]
          Length = 125

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 35/115 (30%), Positives = 60/115 (52%), Gaps = 14/115 (12%)

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKF---------CWLEMQPHTGRTHQLRVHALHMGCP 265
           +V+ +E+G + A + F+V++ F+              ++    TGRTHQ+RVH     CP
Sbjct: 1   MVRVSEEGQS-AHTIFRVLNRFSDDLLHQVGLSHLTLVQATLKTGRTHQIRVHLQSQHCP 59

Query: 266 IVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
           I GD +Y  +++ N         +++LHA  + L HP  G +L + APLP  + +
Sbjct: 60  IAGDERY-GDYQANKRLQKLGLKRMFLHAAELHLDHPLTGEKLILKAPLPQDLAQ 113


>gi|281211459|gb|EFA85621.1| hypothetical protein PPL_00850 [Polysphondylium pallidum PN500]
          Length = 616

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 41/134 (30%), Positives = 63/134 (47%), Gaps = 37/134 (27%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYH------IDGFLKSWVDSKG-------Q 142
           ++YED  + V NKPAG+ V     +GG            ++G L  +  +KG       +
Sbjct: 156 VIYEDEWLAVVNKPAGLLVHPTPQRGGDDSNSENQTHTLVNGLLHKY-GAKGLSTMGGLE 214

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFR------------------MRRIQKIYW 184
           +P + HRLD++T+GILV+A+T A  Q L +  +                    +IQK Y 
Sbjct: 215 RPGIVHRLDKDTAGILVIAKTDAIHQQLKDMLQEHTEDSISETKKSSSGGGSTKIQKKYR 274

Query: 185 SLVWGIPKNKKECI 198
            LV G PK ++  I
Sbjct: 275 CLVAGKPKEQRGLI 288



 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 5/79 (6%)

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           +  +  L++  HTGRTHQ+RVH+L  G PIVGD  Y     G  T  +   L L + Y+ 
Sbjct: 458 SSSYALLDITLHTGRTHQIRVHSLSEGMPIVGDPIYS----GKSTQFMVPYLLLASVYLC 513

Query: 297 LPHP-EGGRLQITAPLPAH 314
             HP    + + T P P H
Sbjct: 514 FVHPVTKEKKEFTIPNPPH 532


>gi|240278475|gb|EER41981.1| DRAP deaminase [Ajellomyces capsulatus H143]
          Length = 545

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 40/157 (25%), Positives = 70/157 (44%), Gaps = 28/157 (17%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           QK +  G V ++ K V  + +IQ+G V+                     S  L +H   +
Sbjct: 82  QKAVEDGAVCINGKAVSIDTKIQNGDVI---------------------SHTLHRHEPPV 120

Query: 98  KSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQ 152
            S    +++ED  + V +KPAG+ V       Y+ +  L+     +G    P   +RLD+
Sbjct: 121 TSQPIGIIHEDDDMIVIDKPAGVPVHPAG--RYNYNSILEIMKAERGNGWVPYPCNRLDR 178

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            TSG++ + +    A+ + E  R R ++K Y + V G
Sbjct: 179 LTSGVMFIGKHPKGAEQIGEKLRSRTVRKEYVARVKG 215


>gi|170117367|ref|XP_001889871.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164635211|gb|EDQ99522.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 478

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 49/183 (26%), Positives = 85/183 (46%), Gaps = 12/183 (6%)

Query: 101 LLYED--SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGI 157
           +LY D   +  V +KP  I V       Y+ +  ++  V+  G +K    +RLD+ TSG+
Sbjct: 100 VLYHDVEREFLVVDKPGSIPVHASG--RYYRNTLIEILVNDFGYKKCYPANRLDRLTSGL 157

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVH-- 214
           +++  +   A+ LT+ F    ++K Y + V G  P  +  C    L     +G + VH  
Sbjct: 158 MIIPLSPDRARVLTDEFTTGTVRKEYVARVRGRFPAQEIVCEEPLLTVDRQMGLNIVHPE 217

Query: 215 --VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V+  + + A    +  +  +        +  +P TGR+HQLRVH  ++G PI  D  Y
Sbjct: 218 GKVLFIHLQPAKTVFNLIRYDENTNSSV--VRCEPLTGRSHQLRVHLQYLGFPIANDPIY 275

Query: 273 CAN 275
             +
Sbjct: 276 SES 278


>gi|313681623|ref|YP_004059361.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
 gi|313154483|gb|ADR33161.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
          Length = 245

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 44/196 (22%), Positives = 86/196 (43%), Gaps = 29/196 (14%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++E+  + V +KPA ++                  ++ + +  +L HRLD+ETSG+L++ 
Sbjct: 61  IFENDDLIVVDKPAFVN---------------SDEIERQFKGSQLLHRLDRETSGVLMLV 105

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +         + F+   + K Y + V G+  ++   +   L+ +      Y  V K+ + 
Sbjct: 106 KNEEFRLKAIQEFKKDNVYKEYVAWVEGLV-SEPFVVDQPLITEKKGNKAYTKVAKKGKP 164

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+    ++   +K   +++  H GRTHQ+R H      PI+GD  Y         
Sbjct: 165 ----AITEVTPLEVSGKK-TKVQLIIHHGRTHQIRAHMKFAQHPIIGDESYGGR------ 213

Query: 282 SPIQNKLYLHARYMDL 297
                ++ LHA+ + L
Sbjct: 214 --QSKRVMLHAKKVTL 227


>gi|212696244|ref|ZP_03304372.1| hypothetical protein ANHYDRO_00780 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676873|gb|EEB36480.1| hypothetical protein ANHYDRO_00780 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 195

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 44/193 (22%), Positives = 94/193 (48%), Gaps = 20/193 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  + END  N R DR+ + +  +     +QK +R    +++ KR K ++ ++   +V+
Sbjct: 2   IEVKINENDS-NQRFDRFLRKYLKNAPLSIIQKNIRKKNFKINDKRAKKDDLVKKDDIVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI------SVQ 120
           +       +  +++     S+ NL          ++YED  I + +K +G+      S  
Sbjct: 61  MYIKDEDYHKWVRKDDFKASNFNLD---------IIYEDENIIIIDKKSGVLSHAASSSD 111

Query: 121 GGSGIAYHIDGFL--KSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G  +   +  +L   + V+S+    +P + +RLD+ T+G+++ A+   + + L E+ R 
Sbjct: 112 YGKNLVDQMTSYLYKTNKVNSRDLTFRPSIVNRLDRNTAGLIIGAKNAKSLRALNEAIRQ 171

Query: 177 RRIQKIYWSLVWG 189
            +I K Y +LV G
Sbjct: 172 GKIYKYYLTLVEG 184


>gi|406497|gb|AAD12509.1| Homology to M62747 [Mycoplasma genitalium]
          Length = 119

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 39/121 (32%), Positives = 63/121 (52%), Gaps = 4/121 (3%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD++TSG +VV + +A+  +L    + R +++ Y +LV   P N      N  L +
Sbjct: 2   LVHRLDRDTSGAIVVCKNQASLLNLQNQLQNRTLKRYYVALVH-FPFNALTGSINAPLAR 60

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
             +  + V         A  AI+ FKVI+   +K   + ++  TGRTHQ+RVH   +  P
Sbjct: 61  --VNNNKVMFKIAQTAKAKQAITKFKVINQ-NEKAALISLELLTGRTHQIRVHLKFIQHP 117

Query: 266 I 266
           +
Sbjct: 118 V 118


>gi|145225398|ref|YP_001136076.1| pseudouridine synthase [Mycobacterium gilvum PYR-GCK]
 gi|145217884|gb|ABP47288.1| pseudouridine synthase [Mycobacterium gilvum PYR-GCK]
          Length = 286

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 84/211 (39%), Gaps = 22/211 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  I V +KP  ++    GS +A      L+  +D     P   HRLD+ T+G+L+
Sbjct: 82  VLHRDDDIVVVDKPHFLATMPRGSHVAQTALVRLRRELDLPELSP--AHRLDRLTAGVLL 139

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWS-LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
               R         F      K Y +       +     I N L+K     G    V + 
Sbjct: 140 FTVRREVRGAYQTLFVRGEAAKTYVAHSSHATDREFPMTIRNRLVKHR---GSLQAVEEP 196

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-- 276
            E  A   + +               + P TGRTHQLRVH   +G PI GD  Y      
Sbjct: 197 GEPNAETVVEYLDE--------GMYRLTPRTGRTHQLRVHMAGLGIPITGDPLYPDVVDV 248

Query: 277 -KGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
             G+F SP++    L A+ ++   P  G L+
Sbjct: 249 PPGDFGSPLR----LLAQALEFTDPISGELR 275


>gi|330973980|gb|EGH74046.1| pseudouridine synthase [Pseudomonas syringae pv. aceris str.
           M302273PT]
          Length = 296

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 90/208 (43%), Gaps = 18/208 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + V +KP  + V   G  +   +   L   +D+    P   HR+D+ T+G+++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAGEYVEQTLLRRLIHRLDNPDMVP--LHRIDRHTAGLVL 146

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +   +TR+A Q L   F  RRI K Y ++   +P      +A   L +S +        
Sbjct: 147 FSANRQTRSAYQGL---FPTRRIDKFYQAIAPALPG-----LAFPRLHESRLVEGEPFFR 198

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y   
Sbjct: 199 MQEGIGASNTRTQIEVLE--RQDKLWRYGLYPMTGKKHQLRVHMAALGAAICNDPFYPDV 256

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            K       QN L L A  +    P  G
Sbjct: 257 VKDPVDD-YQNPLKLLASSLRFVDPLSG 283


>gi|313111139|ref|ZP_07796964.1| putative pseudouridylate synthase [Pseudomonas aeruginosa 39016]
 gi|310883466|gb|EFQ42060.1| putative pseudouridylate synthase [Pseudomonas aeruginosa 39016]
          Length = 275

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 45/180 (25%), Positives = 79/180 (43%), Gaps = 15/180 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETS 155
            ++ +LY D  + V +KP  + V    G  Y     L     S G +  +  HR+D+ T+
Sbjct: 60  FEARILYRDEHLLVADKPHFLPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTA 117

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGGDYVH 214
           G+++ +    +       FR RRI K Y ++   +P+     +   LL+++  + G+   
Sbjct: 118 GLVLFSTNPGSRGRYQALFRERRIDKYYEAIAPALPR-----LDFPLLRRTRLVPGEPFF 172

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +++ E   N        I+   +   W    + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 173 RMREGEGEPNSETR----IEVAERNGRWWRYRLYPVTGKKHQLRVHLAALGAGIQNDGFY 228


>gi|320197497|gb|EFW72111.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           WV_060327]
          Length = 79

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/67 (41%), Positives = 40/67 (59%), Gaps = 5/67 (7%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++P TGR+HQLRVH L +G PI+GD  Y A+ +    +P   +L LHA  + + HP  G 
Sbjct: 14  LKPITGRSHQLRVHMLALGHPILGDRFY-ASPEARAMAP---RLLLHAEMLTITHPAYGN 69

Query: 304 RLQITAP 310
            +   AP
Sbjct: 70  SMTFKAP 76


>gi|311740341|ref|ZP_07714170.1| RNA pseudouridine synthase [Corynebacterium pseudogenitalium ATCC
           33035]
 gi|311304525|gb|EFQ80599.1| RNA pseudouridine synthase [Corynebacterium pseudogenitalium ATCC
           33035]
          Length = 336

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/213 (22%), Positives = 85/213 (39%), Gaps = 15/213 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  I V +KP  ++       I       L+    +    P   HRLD+ TSGIL+
Sbjct: 111 ILFEDEHILVADKPPFMATMPRARHIVQTATVQLRRMTGNDELAP--AHRLDRLTSGILL 168

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             + R         F  +++ K Y ++       +      W    +   G+    +   
Sbjct: 169 FTKHRDVRGAYQTLFAEKKVHKTYQAIAE---YRRFPTPLQWASHLTKTPGEIQGRIGDG 225

Query: 220 EKGANYAISHFKVIDCFA--------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              A   ++   +ID            +     ++P TG+THQLR+H    G PI+GD  
Sbjct: 226 SPNAFTTLAAVDLIDNAPYEKIHGELPQLGKYTLKPTTGKTHQLRLHMWQAGIPILGDPV 285

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           Y   F  +    ++  ++L A +++   P  G+
Sbjct: 286 YPEIFPEDAED-MRIPMHLTATHIEFTDPLSGK 317


>gi|240127829|ref|ZP_04740490.1| Pseudouridine synthase [Neisseria gonorrhoeae SK-93-1035]
 gi|268686227|ref|ZP_06153089.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-93-1035]
 gi|268626511|gb|EEZ58911.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-93-1035]
          Length = 307

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 38/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       K +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTKTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAE-GVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|239998629|ref|ZP_04718553.1| Pseudouridine synthase [Neisseria gonorrhoeae 35/02]
 gi|268594485|ref|ZP_06128652.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae 35/02]
 gi|268547874|gb|EEZ43292.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae 35/02]
 gi|317163901|gb|ADV07442.1| hypothetical protein NGTW08_0470 [Neisseria gonorrhoeae
           TCDC-NG08107]
          Length = 307

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 38/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       K +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTKTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAE-GVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|146320632|ref|YP_001200343.1| YlyB [Streptococcus suis 98HAH33]
 gi|145691438|gb|ABP91943.1| YlyB [Streptococcus suis 98HAH33]
          Length = 243

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 55/238 (23%), Positives = 108/238 (45%), Gaps = 40/238 (16%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNH 76
            +RLD+   +       V  ++I ++GQV V+ +  K    +Q G V+    P +  +++
Sbjct: 9   GIRLDKALSDLTDLSRSVANEQI-KAGQVLVNGQPKKAKYSVQVGDVLTYQIPEVEEIDY 67

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           + ++  +                 ++++D  + V NKP G+ V   +G   H  G L + 
Sbjct: 68  VAEDIPLE----------------IVFQDEDVAVVNKPQGMVVHPSAG---HTSGTLVNA 108

Query: 137 V-----DSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +     D  G     +P + HR+D++TSG+L++A+   A   L    + ++  + YW++V
Sbjct: 109 LLYHVKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWL 243
            G   N +  I      ++ IG       KQ    KG   A++ F+V++ F   + W+
Sbjct: 169 HGNLPNDRGVI------EAPIGRSEKDRKKQAVTAKGKE-AVTRFQVLERFGD-YTWV 218


>gi|218892001|ref|YP_002440868.1| putative pseudouridylate synthase [Pseudomonas aeruginosa LESB58]
 gi|218772227|emb|CAW28006.1| putative pseudouridylate synthase [Pseudomonas aeruginosa LESB58]
          Length = 300

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 45/180 (25%), Positives = 79/180 (43%), Gaps = 15/180 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETS 155
            ++ +LY D  + V +KP  + V    G  Y     L     S G +  +  HR+D+ T+
Sbjct: 85  FEARILYRDEHLLVADKPHFLPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTA 142

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGGDYVH 214
           G+++ +    +       FR RRI K Y ++   +P+     +   LL+++  + G+   
Sbjct: 143 GLVLFSTNPGSRGRYQALFRERRIDKCYEAIAPALPQ-----LDFPLLRRTRLVPGEPFF 197

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +++ E   N        I+   +   W    + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 198 RMREGEGEPNSETR----IEVVERNGGWWRYRLYPVTGKKHQLRVHLAALGAGIQNDGFY 253


>gi|53690306|ref|ZP_00121875.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Bifidobacterium longum DJO10A]
          Length = 180

 Score = 52.0 bits (123), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 41/148 (27%), Positives = 71/148 (47%), Gaps = 14/148 (9%)

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG----GDY 212
           +++V ++  A   +   F    ++K Y +LV G  K  K  I      ++ IG     D+
Sbjct: 1   MMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQGGLKENKATI------EAPIGRAKVSDF 54

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              V    K A   ++H+ V++ F  +   + +   TGRTHQ+RVH   +G P+ GD  Y
Sbjct: 55  RFCVTPAGKPA---VTHWDVLERFGHEATLVSVNLETGRTHQIRVHFSSIGHPLCGDPMY 111

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
            AN   +    + ++ +LHA  ++  HP
Sbjct: 112 GANPVLSEALGL-DRQWLHAMKLEFRHP 138


>gi|262200450|ref|YP_003271658.1| pseudouridine synthase [Gordonia bronchialis DSM 43247]
 gi|262083797|gb|ACY19765.1| pseudouridine synthase [Gordonia bronchialis DSM 43247]
          Length = 317

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/204 (26%), Positives = 84/204 (41%), Gaps = 28/204 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  I V +KP  ++    G  +       L+  + S    P   HRLD+ T+G+L+
Sbjct: 95  ILYADENIVVVDKPHFLATMPRGRHVTETALVRLRRQLGSDDVAP--AHRLDRLTAGVLL 152

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
                  RAA Q L   F  R   K Y +L         + +   +  ++ I      + 
Sbjct: 153 FTLRREVRAAYQDL---FATRAATKEYRALAP-----VDDALTTTVTIRNRIEKTAGDLR 204

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            +   G   AIS   ++           + PHTGRTHQLR+H   +  PIV D  Y    
Sbjct: 205 ARVVDGPVNAISDITLL----SDAGLYRLVPHTGRTHQLRLHMASLRVPIVDDPLYPDVR 260

Query: 277 K--------GNFTSPIQNKLYLHA 292
                    G+F++P+  +L  HA
Sbjct: 261 PELAQRPDVGDFSAPL--RLVAHA 282


>gi|167386039|ref|XP_001737591.1| ribosomal pseudouridine synthase [Entamoeba dispar SAW760]
 gi|165899521|gb|EDR26097.1| ribosomal pseudouridine synthase, putative [Entamoeba dispar
           SAW760]
          Length = 389

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 83/185 (44%), Gaps = 21/185 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED+ + V NKP+GI    G    Y  +  +      +  K    HRLD+ TSG+L++
Sbjct: 141 IIHEDNDVIVVNKPSGIPTHSGG--RYTENTVINILEKERNIKLFGVHRLDRLTSGVLII 198

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-LLKKSHIGGDYVHVVKQN 219
           A++   A  +   F      K Y   V G   +   CI N  +++ + I    V V  + 
Sbjct: 199 AKSSEIANEIQRHF--ISAHKKYICRVIGYMGS---CIVNKPIIETTCITKQRVTVGSE- 252

Query: 220 EKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGD------HK 271
                 + + F+ I  + QK     L   P TGR HQ+RVH  +   PI  D      ++
Sbjct: 253 ---GKISTTIFEQIQ-YDQKTDTTLLWAIPKTGRMHQIRVHLSYENHPIANDSMYRNKNE 308

Query: 272 YCANF 276
           YC +F
Sbjct: 309 YCIHF 313


>gi|59800875|ref|YP_207587.1| hypothetical protein NGO0433 [Neisseria gonorrhoeae FA 1090]
 gi|194098179|ref|YP_002001227.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|240016189|ref|ZP_04722729.1| Pseudouridine synthase [Neisseria gonorrhoeae FA6140]
 gi|240115283|ref|ZP_04729345.1| Pseudouridine synthase [Neisseria gonorrhoeae PID18]
 gi|240117570|ref|ZP_04731632.1| Pseudouridine synthase [Neisseria gonorrhoeae PID1]
 gi|268600964|ref|ZP_06135131.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID18]
 gi|268603274|ref|ZP_06137441.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID1]
 gi|59717770|gb|AAW89175.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
 gi|193933469|gb|ACF29293.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|268585095|gb|EEZ49771.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID18]
 gi|268587405|gb|EEZ52081.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID1]
          Length = 307

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       K +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTKTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAE-GVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|240013751|ref|ZP_04720664.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae DGI18]
 gi|240120819|ref|ZP_04733781.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID24-1]
          Length = 307

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/160 (23%), Positives = 72/160 (45%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L        +  +   L   S 
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA-----PTRTDLPYPLDVVSR 202

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +         Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 203 LARGEKFFTTQEAEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDAFYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|330999262|ref|ZP_08322979.1| RNA pseudouridine synthase [Parasutterella excrementihominis YIT
           11859]
 gi|329575120|gb|EGG56671.1| RNA pseudouridine synthase [Parasutterella excrementihominis YIT
           11859]
          Length = 257

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 60/219 (27%), Positives = 93/219 (42%), Gaps = 34/219 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V +KP  +            +  L+   D  G++    +RLD+ TSGIL+ 
Sbjct: 6   ILYQDEDLVVVSKPEKMLTHRTEIANGDTEFALQLLRDQIGRRVSPVYRLDRGTSGILMF 65

Query: 161 ARTR----AAAQHLTESFRMRRIQKIYWSLVWG-IPKN------KKECIANWLLKKSHIG 209
              R    A +Q   E+F  R     Y+++V G  P++       K  +  +L  +    
Sbjct: 66  GLNREIVSALSQQTHETFHKR-----YYAVVRGWAPEDIEVRHALKPPVDPYLRVQKTEA 120

Query: 210 GD---YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            D   Y+H V ++E      +S  K  D        LE+   TGR HQLR H  H+  PI
Sbjct: 121 QDALSYLHRVAESE----VPVSSGK-FDTTRLSLVLLELA--TGRRHQLRRHLKHLAHPI 173

Query: 267 VGDHKYCANFKGNFTSPIQ-----NKLYLHARYMDLPHP 300
           +GD  Y    KG     +      ++L LH   +   HP
Sbjct: 174 IGDATYG---KGPLNRVLAEYFGGDRLLLHCGRISFIHP 209


>gi|145589394|ref|YP_001155991.1| pseudouridine synthase [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
 gi|145047800|gb|ABP34427.1| pseudouridine synthase [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
          Length = 299

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 49/194 (25%), Positives = 90/194 (46%), Gaps = 20/194 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  I V +KP  + V   SG+  H     +    +  Q     HR+D++T+G+++ +
Sbjct: 88  LYQDEHILVADKPHFLPVTP-SGLYLHQTLLNRLKKKTGIQTLSPIHRIDRDTAGLVIFS 146

Query: 162 ---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
                RA  Q+L   FR R + K+Y ++    P +K+      L  +S +      +  Q
Sbjct: 147 INPYERANYQNL---FRDRTVTKVYEAIA---PYSKELANKLPLTYRSRLEESEHFLQMQ 200

Query: 219 NEKGANYAISHFKVIDCFA--QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-- 274
             +G   A ++ ++++      ++C   + P +G+ HQLR H   +G PI  D  Y    
Sbjct: 201 EVEGEANADTYIELLEASEPWARYC---LGPGSGKKHQLRCHLNALGAPIKHDQIYPVLT 257

Query: 275 ---NFKGNFTSPIQ 285
               +  +F+ P+Q
Sbjct: 258 PYQEYDLDFSKPLQ 271


>gi|319891978|ref|YP_004148853.1| hypothetical protein SPSINT_0688 [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317161674|gb|ADV05217.1| hypothetical protein SPSINT_0688 [Staphylococcus pseudintermedius
           HKU10-03]
 gi|323464932|gb|ADX77085.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           pseudintermedius ED99]
          Length = 284

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 47/178 (26%), Positives = 75/178 (42%), Gaps = 20/178 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQET 154
           +LYED+ + +  KP   S Q  +    H    L     +  QK      P +  RLD+ T
Sbjct: 77  ILYEDTWLLIVAKP---SHQNTAPSREHPHESLVEQALAHMQKRGERGIPHIVTRLDRNT 133

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            GI+++A++R    H+        I+K Y  +   +   K E           I    V 
Sbjct: 134 MGIVIIAKSR----HMHHLMNQCDIEKYYECICERVLTAKGEIDQPIARASDSIINRIVS 189

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +  +   + + +FK        + W  ++  TGRTHQ+RVH   +G P+VGD  Y
Sbjct: 190 EQGKRARTIYWPLKNFKT-------YTWCRVKLETGRTHQIRVHFQWLGAPLVGDTLY 240


>gi|240123126|ref|ZP_04736082.1| Pseudouridine synthase [Neisseria gonorrhoeae PID332]
 gi|260440900|ref|ZP_05794716.1| Pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|268681754|ref|ZP_06148616.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID332]
 gi|291044222|ref|ZP_06569931.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|268622038|gb|EEZ54438.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID332]
 gi|291011116|gb|EFE03112.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
          Length = 307

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       K +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTKTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAE-GVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|225389449|ref|ZP_03759173.1| hypothetical protein CLOSTASPAR_03197 [Clostridium asparagiforme
           DSM 15981]
 gi|225044484|gb|EEG54730.1| hypothetical protein CLOSTASPAR_03197 [Clostridium asparagiforme
           DSM 15981]
          Length = 165

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 7/70 (10%)

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH   +G P+ GD  YC +++      + N+  LH+  ++  HP  G+ ++
Sbjct: 53  ETGRTHQIRVHMASIGHPLPGDFLYCPDYR------LINRQPLHSWRLEFCHPVTGKPIE 106

Query: 307 ITAPLPAHMV 316
            TAPLP  M 
Sbjct: 107 FTAPLPQDMA 116


>gi|237747439|ref|ZP_04577919.1| pseudouridine synthase [Oxalobacter formigenes HOxBLS]
 gi|229378790|gb|EEO28881.1| pseudouridine synthase [Oxalobacter formigenes HOxBLS]
          Length = 318

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 50/198 (25%), Positives = 89/198 (44%), Gaps = 11/198 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +  +LY+D  + V +KP  + V   G  +   +   LK  +      P   HR+D+ET+
Sbjct: 93  FQETVLYQDEWLVVADKPHFLPVTPSGKYVRETLLVRLKQKLGIDSLTP--VHRIDRETA 150

Query: 156 GILVVARTRAAAQHLTES-FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           G LV+  T+   ++L +  FR   + K Y ++        ++ ++  L  KS +      
Sbjct: 151 G-LVLFSTKPEGRNLYQRLFRENLVSKHYEAIA-----PYRDDLSFPLRYKSRLVQGDSF 204

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +  Q   G   A +  +++    + +    ++P TGR HQLRV    +G PI+ D  Y  
Sbjct: 205 MRMQTVSGKPNAETEIRLLQQLGE-WGHYRLKPVTGRKHQLRVQMCSLGIPILNDRIYPD 263

Query: 275 NFKGNFTSPIQNKLYLHA 292
           +F    T  +Q + Y H 
Sbjct: 264 HFPEAVTQEMQTEEYRHP 281


>gi|78356022|ref|YP_387471.1| pseudouridylate synthase 23S RNA-specific-like protein
           [Desulfovibrio desulfuricans subsp. desulfuricans str.
           G20]
 gi|78218427|gb|ABB37776.1| Pseudouridylate synthases 23S RNA-specific-like protein
           [Desulfovibrio desulfuricans subsp. desulfuricans str.
           G20]
          Length = 305

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 59/244 (24%), Positives = 100/244 (40%), Gaps = 27/244 (11%)

Query: 58  RIQSGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           R Q+G V+ I  P  N   HI+   +    +  L + +D+         + I+   KP G
Sbjct: 58  RTQTGDVIDIVCPCRNKTQHILPAAQ----AEVLCRTADY---------AAIF---KPEG 101

Query: 117 I-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           + S +  +  A  ++  L S    +   P L +RLD+ TSG+++ A    AA+   +  +
Sbjct: 102 LHSARIAASPAPSVEDQLDSLFAGE-TPPVLVNRLDRPTSGMVLAAFGSHAAEAFRKFEQ 160

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVID 234
             +++K+Y ++V G  K    C     ++   +     H  +   +      +       
Sbjct: 161 AGQVEKLYLAVVLGHMKAPVACRNELNMQNRQVTTVLPHEAQDPLRHTTVLPLRALPAES 220

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              QK   +    H G  HQ+R H  H G PI GD  Y +N            LYLH   
Sbjct: 221 MDGQKTTLVLAAIHRGARHQIRAHLAHAGHPIAGDCVYGSNQA-------DGTLYLHHFK 273

Query: 295 MDLP 298
           +D+P
Sbjct: 274 IDMP 277


>gi|240112543|ref|ZP_04727033.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae MS11]
 gi|240125374|ref|ZP_04738260.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-92-679]
 gi|268598611|ref|ZP_06132778.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae MS11]
 gi|268683976|ref|ZP_06150838.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-92-679]
 gi|268582742|gb|EEZ47418.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae MS11]
 gi|268624260|gb|EEZ56660.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-92-679]
          Length = 307

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/160 (23%), Positives = 72/160 (45%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L        +  +   L   S 
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA-----PTRTDLPYPLDVVSR 202

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +         Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 203 LARGEKFFTTQEAEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDAFYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|107101470|ref|ZP_01365388.1| hypothetical protein PaerPA_01002511 [Pseudomonas aeruginosa PACS2]
          Length = 295

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/178 (24%), Positives = 84/178 (47%), Gaps = 11/178 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETS 155
            ++ +LY D  + V +KP  + V    G  Y     L     S G +  +  HR+D+ T+
Sbjct: 80  FEARILYRDEHLLVADKPHFLPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTA 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGGDYVH 214
           G+++ +    +       FR RRI K Y ++   +P+     +   LL+++  + G+   
Sbjct: 138 GLVLFSTNPGSRGRYQALFRERRIDKCYEAIAPALPQ-----LDFPLLRRTRLVPGEPFF 192

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +++ E   N + +  +V++   + + +  + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 193 RMREGEGEPN-SETRIEVVERNGRWWRY-RLYPVTGKKHQLRVHLAALGAGIQNDGFY 248


>gi|325962091|ref|YP_004239997.1| 23S RNA-specific pseudouridylate synthase [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323468178|gb|ADX71863.1| 23S RNA-specific pseudouridylate synthase [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 327

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 51/205 (24%), Positives = 82/205 (40%), Gaps = 50/205 (24%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D  + V +KP  + +  GG+ I       L++ ++     P   HRLD+ T+G+L+
Sbjct: 90  ILHQDHHLLVVDKPHFLPTTPGGTYIQESALVRLRNQLELPDLIP--MHRLDRMTAGVLL 147

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +   +TR   Q L   F  R++QK Y            EC++       H   D+  VV
Sbjct: 148 FSTNPQTRGKYQVL---FEKRQVQKEY------------ECVSAAEPAPGHAAVDFPVVV 192

Query: 217 K---------------QNEKGANYAISHFKVIDCFAQ--------------KFCWLEMQP 247
           +                 E  A   I   +  D                  +     ++P
Sbjct: 193 RNRMTKSRSYLLAEVVDGEPNAETRIERLETFDAGTSLGAAGAAAAPGDPARLARYRLEP 252

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY 272
           HTG+THQLRVH   +G  I+ D  Y
Sbjct: 253 HTGKTHQLRVHMASLGLGIINDAFY 277


>gi|302695171|ref|XP_003037264.1| hypothetical protein SCHCODRAFT_47965 [Schizophyllum commune H4-8]
 gi|300110961|gb|EFJ02362.1| hypothetical protein SCHCODRAFT_47965 [Schizophyllum commune H4-8]
          Length = 263

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 50/186 (26%), Positives = 86/186 (46%), Gaps = 17/186 (9%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD +T+G L++  T A  + L+  FR R ++K Y +LV G   +    I+  + +   
Sbjct: 32  HRLDMDTTGALLLGLTEARTRDLSAQFRNRTVKKTYLALVHG-GIDAFSSISGQIREPIF 90

Query: 208 I-GGDYVHVVKQNEK-GANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALH-MG 263
           +  G  VH  + N +     A + ++++   +      L+++  TG  HQLRVH  H + 
Sbjct: 91  LRDGQPVHHSRANARCEMKEAATDWELLGSSSIAPLSVLKLKLLTGYKHQLRVHLAHRLK 150

Query: 264 CPIVGDHKYCANFK----GNFTSPIQNKLYLHA------RYMDLPHPEGGR--LQITAPL 311
            PI GD  Y             +    +++LH+      RY      +G R  L + APL
Sbjct: 151 TPIFGDALYSPKTGSVELARVVTHSPERMFLHSAELGIHRYRSEGPTKGKRYELNVCAPL 210

Query: 312 PAHMVK 317
           P+  ++
Sbjct: 211 PSDFLQ 216


>gi|302561569|ref|ZP_07313911.1| pseudouridylate synthase [Streptomyces griseoflavus Tu4000]
 gi|302479187|gb|EFL42280.1| pseudouridylate synthase [Streptomyces griseoflavus Tu4000]
          Length = 299

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 46/164 (28%), Positives = 76/164 (46%), Gaps = 19/164 (11%)

Query: 147 THRLDQETSGIL---VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            HRLD+ T+G++   V    R A Q L   FR R ++K Y ++    P + +  +   + 
Sbjct: 124 AHRLDRLTAGLVLFTVRPGERGAYQTL---FRDRLVRKEYEAVA---PYDPELVLPRTV- 176

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            +S I  +   +  +   G   A++  ++ +  +       + P TG+THQLRVH   +G
Sbjct: 177 -RSRIVKERGVLTAREVAGEPNALTRVEIAERRSDGPARYRLVPGTGQTHQLRVHMNGLG 235

Query: 264 CPIVGDHKY----CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            PI+GD  Y         G+F  P+Q    L AR ++   P  G
Sbjct: 236 VPILGDPLYPEVTGPGPAGDFRRPLQ----LLARTLEFTDPVTG 275


>gi|66045373|ref|YP_235214.1| pseudouridine synthase [Pseudomonas syringae pv. syringae B728a]
 gi|63256080|gb|AAY37176.1| Pseudouridine synthase [Pseudomonas syringae pv. syringae B728a]
          Length = 313

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 90/208 (43%), Gaps = 18/208 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + V +KP  + V   G  +   +   L   +D+    P   HR+D+ T+G+++
Sbjct: 106 ILYADEHLVVADKPHFLPVTPAGEYVEQTLLRRLIHRLDNPDMVP--LHRIDRHTAGLVL 163

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +   +TR+A Q L   F  RRI K Y ++   +P      +A   L +S +        
Sbjct: 164 FSANRQTRSAYQAL---FPTRRIDKFYQAIAPALPG-----LAFPRLHESRLVEGEPFFR 215

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y   
Sbjct: 216 MQEGIGASNTRTQIEVLE--RQDKLWRYGLYPVTGKKHQLRVHMAALGAAICNDPFYPDV 273

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            K       QN L L A  +    P  G
Sbjct: 274 VKDPVDD-YQNPLKLLASSLRFVDPLSG 300


>gi|325676842|ref|ZP_08156515.1| RNA pseudouridine synthase [Rhodococcus equi ATCC 33707]
 gi|325552390|gb|EGD22079.1| RNA pseudouridine synthase [Rhodococcus equi ATCC 33707]
          Length = 288

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 35/125 (28%), Positives = 59/125 (47%), Gaps = 6/125 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ T+G+L+        +   E F  RR++K+Y ++        +  I      +S 
Sbjct: 127 HRLDRMTAGVLLCTADPRLRRPYQEMFERRRVRKVYEAIA-----PYRGDIDFPRTVRSR 181

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           I   +  +    E G   + +  ++++          + P TGRTHQLR+H   +G PIV
Sbjct: 182 IVKVHGELTAYEEAGEPNSETLIELVERRGD-LARYRLHPRTGRTHQLRLHLNAIGAPIV 240

Query: 268 GDHKY 272
           GD+ Y
Sbjct: 241 GDNFY 245


>gi|154341671|ref|XP_001566787.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134064112|emb|CAM40306.1| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 452

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/107 (31%), Positives = 48/107 (44%), Gaps = 13/107 (12%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-----------KGNFTSPIQNKLYLHAR 293
           + PHTGR HQLRVH   +G PIVGD  YC +               +T+    ++YLHA 
Sbjct: 325 LAPHTGRRHQLRVHCRAIGFPIVGDTLYCTDLPWCAALPLGPSASTWTTVEARRMYLHAW 384

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
            + LP      L  T  +     +  ++LG     N  +    S+DE
Sbjct: 385 RLLLPGTAARHLDETERVALKKKRRRETLGLSEQGNASVS--ASRDE 429



 Score = 42.0 bits (97), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 32/117 (27%), Positives = 52/117 (44%), Gaps = 18/117 (15%)

Query: 108 IYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKG----------------QKPRLTHRL 150
           + V NKP GI + G   I    I+     ++ ++G                ++ +  H+L
Sbjct: 1   MLVVNKPPGIPMGGDEAIYGRTIESLAYDYMKARGIFDEAHEQLQQARKRKKQLKFVHQL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKS 206
           D  TSG+L +A T+  A  L   F MR ++K Y +L+ G +P       A  L  +S
Sbjct: 61  DFGTSGVLCLAFTKDMAARLAHCFEMRTVRKYYIALLHGHVPCETAPPEAGALCDQS 117


>gi|119475020|ref|ZP_01615373.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2143]
 gi|119451223|gb|EAW32456.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2143]
          Length = 297

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/211 (26%), Positives = 96/211 (45%), Gaps = 13/211 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLK--SWVDSKGQKPRLTHRLDQETSGI 157
           +L++D  + V +KP  +++  GG  +   +   L+  + +DS     +  HRLD+ T+G 
Sbjct: 85  ILFQDEHLLVAHKPHFLALTPGGVFVNECLQNRLRLRTGIDSL----QALHRLDRVTAG- 139

Query: 158 LVVARTRAAAQHLT-ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           LV+  T    +HL  + F  R+I+K Y ++       +K     W +K + +        
Sbjct: 140 LVLFSTNPTTRHLYHQLFSHRQIEKTYHAIA-QTDSRQKLTTKEWQVK-NRLEPSAQRFR 197

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            Q   G   + S  + +     K    E++P TG+THQLRVH   +G PI+ D KY    
Sbjct: 198 MQVVAGEANSHSFIRSLRQNGDK-ALFELKPITGKTHQLRVHMQTIGWPILND-KYYPRL 255

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           +       +  L L A+ +    P   ++Q 
Sbjct: 256 EQQSADDFEKPLQLLAKQLRFIDPVSQKMQF 286


>gi|254493346|ref|ZP_05106517.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae 1291]
 gi|226512386|gb|EEH61731.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae 1291]
          Length = 307

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/160 (23%), Positives = 72/160 (45%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L        +  +   L   S 
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA-----PTRTDLPYPLDVVSR 202

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +         Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 203 LARGEKFFTTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDAFYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|15597239|ref|NP_250733.1| hypothetical protein PA2043 [Pseudomonas aeruginosa PAO1]
 gi|9948049|gb|AAG05431.1|AE004630_8 hypothetical protein PA2043 [Pseudomonas aeruginosa PAO1]
          Length = 300

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/178 (24%), Positives = 84/178 (47%), Gaps = 11/178 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETS 155
            ++ +LY D  + V +KP  + V    G  Y     L     S G +  +  HR+D+ T+
Sbjct: 85  FEARILYRDEHLLVADKPHFLPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTA 142

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGGDYVH 214
           G+++ +    +       FR RRI K Y ++   +P+     +   LL+++  + G+   
Sbjct: 143 GLVLFSTNPGSRGRYQALFRERRIDKCYEAIAPALPQ-----LDFPLLRRTRLVPGEPFF 197

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +++ E   N + +  +V++   + + +  + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 198 RMREGEGEPN-SETRIEVVERNGRWWRY-RLYPVTGKKHQLRVHLAALGAGIQNDGFY 253


>gi|19552642|ref|NP_600644.1| 16S rRNA uridine-516 pseudouridylate synthase [Corynebacterium
           glutamicum ATCC 13032]
 gi|62390310|ref|YP_225712.1| 16S rRNA uridine-516 pseudouridylate synthase or related
           pseudouridylate synthase [Corynebacterium glutamicum
           ATCC 13032]
 gi|41325647|emb|CAF21436.1| 16S rRNA uridine-516 pseudouridylate synthase or related
           pseudouridylate synthase [Corynebacterium glutamicum
           ATCC 13032]
          Length = 320

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 100/240 (41%), Gaps = 45/240 (18%)

Query: 35  VNLQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
           V LQK+L        R  ++ +D+ RV+ N+RI + Q VR+ P     N +I+   +   
Sbjct: 80  VRLQKVLAQAGVASRRHAEILIDQGRVEVNDRIVTTQGVRVDPN----NDVIRVDGV--- 132

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
                        I + ED + +V NKP G+       +     G L S   + GQ+   
Sbjct: 133 ------------RIHINEDLEYFVLNKPRGMHSTMSDELGRPCVGDLVSEKTASGQRLFH 180

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD +T G+L++      A  L        + K Y + V G   NK   + + L    
Sbjct: 181 VGRLDADTEGLLLLTNDGELANRLMHP--KYEVSKTYLATVRGEATNK---LVSALR--- 232

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               D V +     K A++A    ++ID F  K   L ++ H GR H +R     +G P+
Sbjct: 233 ----DGVELEDGPAK-ADFA----QIIDVFQGK-SLLRIEIHEGRKHIVRRLFDELGFPV 282


>gi|296314658|ref|ZP_06864599.1| RNA pseudouridine synthase [Neisseria polysaccharea ATCC 43768]
 gi|296838567|gb|EFH22505.1| RNA pseudouridine synthase [Neisseria polysaccharea ATCC 43768]
          Length = 307

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 62/125 (49%), Gaps = 6/125 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G++++++  A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSQNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKY 272
            D  Y
Sbjct: 262 NDALY 266


>gi|254240477|ref|ZP_04933799.1| hypothetical protein PA2G_01128 [Pseudomonas aeruginosa 2192]
 gi|126193855|gb|EAZ57918.1| hypothetical protein PA2G_01128 [Pseudomonas aeruginosa 2192]
          Length = 300

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/178 (24%), Positives = 84/178 (47%), Gaps = 11/178 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETS 155
            ++ +LY D  + V +KP  + V    G  Y     L     S G +  +  HR+D+ T+
Sbjct: 85  FEARILYRDEHLLVADKPHFLPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTA 142

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGGDYVH 214
           G+++ +    +       FR RRI K Y ++   +P+     +   LL+++  + G+   
Sbjct: 143 GLVLFSTNPGSRGRYQALFRERRIDKCYEAIAPALPQ-----LDFPLLRRTRLVPGEPFF 197

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +++ E   N + +  +V++   + + +  + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 198 RMREGEGEPN-SETRIEVVERNGRWWRY-RLYPVTGKKHQLRVHLAALGAGIQNDGFY 253


>gi|49084528|gb|AAT51207.1| PA2043 [synthetic construct]
          Length = 301

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/178 (24%), Positives = 84/178 (47%), Gaps = 11/178 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETS 155
            ++ +LY D  + V +KP  + V    G  Y     L     S G +  +  HR+D+ T+
Sbjct: 85  FEARILYRDEHLLVADKPHFLPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTA 142

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGGDYVH 214
           G+++ +    +       FR RRI K Y ++   +P+     +   LL+++  + G+   
Sbjct: 143 GLVLFSTNPGSRGRYQALFRKRRIDKCYEAIAPALPQ-----LDFPLLRRTRLVPGEPFF 197

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +++ E   N + +  +V++   + + +  + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 198 RMREGEGEPN-SETRIEVVERNGRWWRY-RLYPVTGKKHQLRVHLAALGAGIQNDGFY 253


>gi|328881321|emb|CCA54560.1| Ribosomal large subunit pseudouridine synthase A [Streptomyces
           venezuelae ATCC 10712]
          Length = 308

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 50/160 (31%), Positives = 74/160 (46%), Gaps = 19/160 (11%)

Query: 147 THRLDQETSG-ILVVART--RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            HRLD+ T+G +L V R   R A Q L   FR RR++K Y ++    P      +   + 
Sbjct: 144 AHRLDRLTAGLVLCVVRPEDRGAYQTL---FRDRRVRKEYEAVAPYDP-----AVGLPVT 195

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            +S I  +   +  +   G   A S  +++   A       + P TGRTHQLRVH   +G
Sbjct: 196 VRSRIEKERGVMAARELPGEPNAESRIELVGR-AGGLGRYRLVPETGRTHQLRVHMNGLG 254

Query: 264 CPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            PI+ D  Y    A+   +F  P+Q    L AR ++   P
Sbjct: 255 LPILHDPIYPVVRADGPEDFGRPLQ----LLARTLEFTDP 290


>gi|227501848|ref|ZP_03931897.1| ribosomal pseudouridine synthase [Corynebacterium accolens ATCC
           49725]
 gi|227077342|gb|EEI15305.1| ribosomal pseudouridine synthase [Corynebacterium accolens ATCC
           49725]
          Length = 327

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 56/231 (24%), Positives = 93/231 (40%), Gaps = 24/231 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED  I V +KP  ++       A HI     ++    +   +    HRLD+ TSG+L
Sbjct: 105 IIYEDDNILVADKPPFMATMPR---ARHIVETATVRLRRSTGNNELVPAHRLDRLTSGLL 161

Query: 159 VVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +  +    R A Q L   F  +++ K Y ++       +      W    +   G+    
Sbjct: 162 LFTKHKDVRGAYQSL---FAEKKVHKTYQAVAEF---RRLPTPLQWSSHLTKTPGEIQGR 215

Query: 216 VKQNEKGANYAISHFKVIDCFA--------QKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +   E  A   +   + ID                  ++P TG+THQLR+H    G PI+
Sbjct: 216 IADGEPNAFTTLESVQPIDKAPYEKVHGPLPDLGLYTLKPQTGKTHQLRLHMWQAGIPIL 275

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVK 317
           GD  Y   F       +   ++L A  ++   P  G+ +  T+ LP  M K
Sbjct: 276 GDPVYPTIFPEEAED-MAIPMHLTATDLEFTDPLSGKPRHFTSGLPLAMHK 325


>gi|153823687|ref|ZP_01976354.1| RNA pseudouridine synthase family protein [Vibrio cholerae B33]
 gi|126518790|gb|EAZ76013.1| RNA pseudouridine synthase family protein [Vibrio cholerae B33]
          Length = 124

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 38/67 (56%), Gaps = 8/67 (11%)

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHAR 293
           ++C +EMQP TGR HQLR H  H+  PIVGD  +        F+ +F++    +L LHA 
Sbjct: 28  RYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDTTHGDGVHNRLFREHFSA---QRLMLHAS 84

Query: 294 YMDLPHP 300
            +   HP
Sbjct: 85  ELRFMHP 91


>gi|127513475|ref|YP_001094672.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126638770|gb|ABO24413.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 287

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 48/222 (21%), Positives = 94/222 (42%), Gaps = 38/222 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPR-LTHRLDQETSGIL 158
           L+ +  +  ++ KP  +  QG     +  I+ F+++ +    Q+P  + HRLD+  +G++
Sbjct: 89  LILDKGEYSIWYKPYAMLCQGSKWSDHTTINRFVETHLTP--QRPAFIIHRLDRAATGLV 146

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++  ++     L   F  R + K Y  +V G  PK  +                      
Sbjct: 147 IIGHSKTITAALAAQFEHRELDKQYRVIVKGEFPKATRTIT------------------- 187

Query: 218 QNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             E     A SH  +++  ++     ++++  TGR HQ+R+H   +G P+VGD ++    
Sbjct: 188 -TEVDGKPACSHASLVEYDSELDMSLVQVKIETGRKHQIRIHMASIGFPVVGDRQHGGAE 246

Query: 277 KG-----------NFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            G           +FT P+ N+  LH    +   P    L++
Sbjct: 247 TGDVNLQLTACFLDFTCPL-NQQPLHVALPEALQPSLAALKV 287


>gi|221057129|ref|XP_002259702.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
            knowlesi strain H]
 gi|193809774|emb|CAQ40478.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
            knowlesi strain H]
          Length = 10549

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 41/71 (57%)

Query: 231  KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
            K ++ + ++F    ++ HTGRTHQ+RVH  H+G P+V D KY      N       +++L
Sbjct: 7603 KEVENYTKEFTLCNVKIHTGRTHQIRVHMRHIGHPLVADKKYLNPSLSNLDKYWCFRMFL 7662

Query: 291  HARYMDLPHPE 301
            H+  ++  +P+
Sbjct: 7663 HSVILEFNNPD 7673



 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 32/53 (60%)

Query: 146  LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K KK CI
Sbjct: 7280 LCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYLLLCHGRIKKKKGCI 7332


>gi|116049993|ref|YP_791196.1| putative pseudouridylate synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|296389546|ref|ZP_06879021.1| putative pseudouridylate synthase [Pseudomonas aeruginosa PAb1]
 gi|115585214|gb|ABJ11229.1| putative pseudouridylate synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
          Length = 300

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 45/180 (25%), Positives = 79/180 (43%), Gaps = 15/180 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETS 155
            ++ +LY D  + V +KP  + V    G  Y     L     S G +  +  HR+D+ T+
Sbjct: 85  FEARILYRDEHLLVADKPHFLPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTA 142

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGGDYVH 214
           G+++ +    +       FR RRI K Y ++   +P+     +   LL+++  + G+   
Sbjct: 143 GLVLFSTNPGSRGRYQALFRERRIDKYYEAIAPALPR-----LDFPLLRRTRLVPGEPFF 197

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +++ E   N        I+   +   W    + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 198 RMREGEGEPNSETR----IEVAERNGRWWRYRLYPVTGKKHQLRVHLAALGAGIQNDGFY 253


>gi|15842891|ref|NP_337928.1| hypothetical protein MT3399 [Mycobacterium tuberculosis CDC1551]
 gi|13883223|gb|AAK47742.1| RNA pseudouridylate synthase family protein [Mycobacterium
           tuberculosis CDC1551]
 gi|323718169|gb|EGB27351.1| hypothetical protein TMMG_02448 [Mycobacterium tuberculosis
           CDC1551A]
          Length = 305

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/192 (27%), Positives = 86/192 (44%), Gaps = 21/192 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D+ I V +KP  ++    G  +A      L+  +      P   HRLD+ T+G+L+
Sbjct: 87  VLHQDADIVVVDKPHFLATMPRGRHVAQTALVRLRRELGLPELSP--AHRLDRLTAGVLL 144

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
               R         F    ++K Y +     P      +A   L +S I     H+    
Sbjct: 145 FTTRREVRGSYQTMFARGLVRKTYLARAPVAPG-----LALPRLVRSRIVKRRGHLQAVC 199

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY------C 273
           E G   A +   +++  A+   +  + P TGRTHQLRVH   +G PI+GD  Y       
Sbjct: 200 EPGVPNAET---LVERIARDGLY-RLTPTTGRTHQLRVHMAALGIPIMGDPLYPNVISVA 255

Query: 274 ANFKGNFTSPIQ 285
           A++   F++P+Q
Sbjct: 256 AHY---FSTPLQ 264


>gi|317486123|ref|ZP_07944968.1| RNA pseudouridylate synthase [Bilophila wadsworthia 3_1_6]
 gi|316922608|gb|EFV43849.1| RNA pseudouridylate synthase [Bilophila wadsworthia 3_1_6]
          Length = 339

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 56/238 (23%), Positives = 91/238 (38%), Gaps = 48/238 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
           L+Y+D  I    KPAG+     +G ++  ++  L   + S+  G   RL +RLD  TSG+
Sbjct: 105 LVYKDGGIAALYKPAGMHTAALAGSLSPSLETLLGDLLPSEEEGYASRLLNRLDAPTSGL 164

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--------------KNKKECI----- 198
           ++ + T    +    + R+    K+Y +L+ G P              +NK         
Sbjct: 165 VLASCTDGGERRWYRAERIGNTDKLYLALIEGQPLYDFTVARRLDTDTRNKTRVRHTDDP 224

Query: 199 -----ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                 +  L      GD   +V+ ++  A        ++ C  +K          G  H
Sbjct: 225 DPVRHTDVTLLAPLTAGDVPGLVESDDPDAP-----LMLVGCRIRK----------GARH 269

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           Q+R H    G P+ GD  Y A        P  +   LH   + LP  +  RL    PL
Sbjct: 270 QIRAHLAAAGHPLAGDSLYGAEL------PCPSGFLLHHGRVSLPDFQAFRLPAWLPL 321


>gi|326429138|gb|EGD74708.1| hypothetical protein PTSG_06069 [Salpingoeca sp. ATCC 50818]
          Length = 224

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/106 (30%), Positives = 52/106 (49%), Gaps = 1/106 (0%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           S+ ++      L+++L Y+D  +   NK   +SVQ        +   L         +PR
Sbjct: 3   SATSVISRRGLLRAVL-YQDHNVIALNKWRSLSVQDELQSDNTLLNNLHLLQLKHNDEPR 61

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L HRLDQ T+G+L++ R   A   ++  F+ R IQK Y ++V   P
Sbjct: 62  LLHRLDQNTTGVLLIGRKPQATAAISTLFQHRLIQKTYLAVVVATP 107


>gi|253701551|ref|YP_003022740.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251776401|gb|ACT18982.1| pseudouridine synthase [Geobacter sp. M21]
          Length = 293

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 108/243 (44%), Gaps = 20/243 (8%)

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P+ +A ++  +++      +   K   F + IL +++ ++ V  KP  + V  G G  Y 
Sbjct: 54  PITSASSYAPQKRIFYYREIENEKVIPFAEEIL-FQNDELLVACKPHFLPVTPGGG--YL 110

Query: 129 IDGFLKSWVDSKGQKPRLT-HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               L    +S G    +  HR+D+ET+GI++ +            FR   I+K Y ++ 
Sbjct: 111 SQSLLHRLRESTGIHDLVPLHRIDRETAGIVLFSVNPKTRGLYGGVFRDGSIEKSYEAIS 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--FAQKFCWLEM 245
                  +   A WL++   + G+    V+  +   N A S  ++++    A +F   ++
Sbjct: 171 AA---RIEPGQAEWLVENRLVQGEPWFRVRTGDGPPN-ARSLIRLVEQRDGAARF---QL 223

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            P TG+THQLRVH   +G  I+ D  Y         +F  P+Q    L AR +    P  
Sbjct: 224 TPVTGKTHQLRVHMSGLGLQILHDRLYPQLMPRQPDDFDRPLQ----LLARRVRFRDPLS 279

Query: 303 GRL 305
           G+L
Sbjct: 280 GKL 282


>gi|269218864|ref|ZP_06162718.1| RNA pseudouridylate synthase family protein [Actinomyces sp. oral
           taxon 848 str. F0332]
 gi|269211975|gb|EEZ78315.1| RNA pseudouridylate synthase family protein [Actinomyces sp. oral
           taxon 848 str. F0332]
          Length = 306

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/133 (33%), Positives = 64/133 (48%), Gaps = 20/133 (15%)

Query: 147 THRLDQETSGILVVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK----ECIA 199
            HRLD  T G+L++    R RA  Q L   F  R ++K Y ++    P + +    + +A
Sbjct: 148 AHRLDAATRGVLLLTLAKRWRAPYQML---FERREVRKAYLAVA---PADDRFVEAQTVA 201

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L K    G     VV     G   A++  ++ D   +     E++P TGRTHQ+RV  
Sbjct: 202 LALAKPR--GSLKALVVD----GQPNAVTTVRLADER-RGLGLYEIEPKTGRTHQIRVTM 254

Query: 260 LHMGCPIVGDHKY 272
            H+G PIVGD  Y
Sbjct: 255 SHLGIPIVGDWLY 267


>gi|254673322|emb|CBA08488.1| pseudouridylate synthase [Neisseria meningitidis alpha275]
 gi|325202346|gb|ADY97800.1| RNA pseudouridine synthase [Neisseria meningitidis M01-240149]
 gi|325207901|gb|ADZ03353.1| RNA pseudouridine synthase [Neisseria meningitidis NZ-05/33]
          Length = 307

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|261379850|ref|ZP_05984423.1| RNA pseudouridine synthase [Neisseria subflava NJ9703]
 gi|284797545|gb|EFC52892.1| RNA pseudouridine synthase [Neisseria subflava NJ9703]
          Length = 307

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/174 (21%), Positives = 76/174 (43%), Gaps = 35/174 (20%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + +QK Y            E +A      + 
Sbjct: 148 HRLDKDTAGVMLLSLNPATRCDYQTMFQEKTVQKTY------------EAVA-----PTR 190

Query: 208 IGGDY-VHVVKQNEKGANYAISH--------FKVIDCFAQK--FCWLEMQPHTGRTHQLR 256
              DY +H+  + E+G  + ++            I+    +  F    + PHTG+ HQLR
Sbjct: 191 TDLDYPLHISSRMERGEKFFLTRETEGEPNAHTTIELIENRGAFSLYRLTPHTGKKHQLR 250

Query: 257 VHALHMGCPIVGDHKYCANFKG---NFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           VH + +  P++ D  Y         ++  P++    L A+ ++   P  G +++
Sbjct: 251 VHMMSLNMPLMNDALYPTPLAAGDEDYDKPLK----LLAKRIEFTDPVSGEIRV 300


>gi|159482266|ref|XP_001699192.1| pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158273039|gb|EDO98832.1| pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 303

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/213 (25%), Positives = 91/213 (42%), Gaps = 18/213 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-----KSWVDSKGQKPRLTHRLDQETS 155
           ++YED+ +   +KP+G+ V   +   +H    L     + ++D     P   HRL + TS
Sbjct: 98  VVYEDADMVALSKPSGLQVLPAA--MFHQRTVLSLLRRRQYLDV----PAPVHRLGRGTS 151

Query: 156 GI-LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           G          ++   + S     ++K Y +LV G  K  +  +   +    H G D   
Sbjct: 152 GCGAAALAALISSAPASGSGCQLPLRKFYRALVQGRVKADQGRVDVPIGPIPHPGVDRGL 211

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                +     A S ++   C   +   +E++  TGR HQ+R+H   MG P+VGD  Y A
Sbjct: 212 FAATPD--GKPAASVWRA-GCMEAECTLMEVEILTGRPHQIRIHMAAMGHPLVGDPLYGA 268

Query: 275 NFKGNFTSPIQNK---LYLHARYMDLPHPEGGR 304
             +      +       YLH+  + LPHP  G+
Sbjct: 269 GGRPKVRYRLYGSDCGYYLHSLELHLPHPITGQ 301


>gi|152981592|ref|YP_001355201.1| RNA pseudouridylate synthase family protein [Janthinobacterium sp.
           Marseille]
 gi|151281669|gb|ABR90079.1| RNA pseudouridylate synthase family protein [Janthinobacterium sp.
           Marseille]
          Length = 316

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/222 (24%), Positives = 95/222 (42%), Gaps = 38/222 (17%)

Query: 100 ILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  +   +KP  + V   G  +   +   LK  +D     P   HR+D+ET+G++
Sbjct: 106 VVLYQDDYLVAVDKPHFLPVTPAGRYLQETLLVRLKRSLDIDTLAP--MHRIDRETAGLV 163

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLV-----WGIPKNKKECI--ANWLLKKSHI 208
           +     +TR   Q L   FR R + K Y ++        +P   +  +  +   +K   +
Sbjct: 164 LFTIQPQTRNLYQTL---FRERSVSKEYEAIAPLRADLELPTTYRSRLLESEAFMKMCEV 220

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            G         E  +  AIS  +    F +      +QP +G+ HQLR H   +G PIV 
Sbjct: 221 AG---------EANSETAISLLETRGNFGRYL----LQPVSGQKHQLRAHMAALGIPIVN 267

Query: 269 DHKYCANFKG-----NFTSPIQNKLYLHARYMDLPHPEGGRL 305
           D  Y   +       +++ P+Q    L A+ +    P  G+L
Sbjct: 268 DRIYPHLYPDEGATQDYSQPLQ----LLAKSISFTDPLSGKL 305


>gi|255327672|ref|ZP_05368738.1| pseudouridylate synthase [Rothia mucilaginosa ATCC 25296]
 gi|255295346|gb|EET74697.1| pseudouridylate synthase [Rothia mucilaginosa ATCC 25296]
          Length = 383

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 98/231 (42%), Gaps = 33/231 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LYED  +   +KP  + +   G+ IA      L+     + Q P L   HRLD+ T+G+
Sbjct: 143 VLYEDEHVLAIDKPHFLPTTPRGAYIAQTALTKLRV----REQNPLLIPIHRLDRPTAGV 198

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIY---WSLVWGIPKNKKECIANWLLKKSHIGG--DY 212
           L+ A+T  A +     F+ R++ K Y     +       ++   A  L  +SHI    D 
Sbjct: 199 LLFAKTVEARRPFQMMFQHRQVSKTYRAVAPVPADAAAAEQALSAEGLQVRSHIQKIRDQ 258

Query: 213 VHVVKQNEKGANY------AISHFKVIDCFA--------------QKFCWLEMQPHTGRT 252
           + V + +E+           ++  K++  F               +++   ++ PHTG+T
Sbjct: 259 LQVQQLSEQECAAQGVEPNTLTTAKILRTFTPSAQAVAGWRAEPNREWALYDLAPHTGKT 318

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           HQLR H   +  PI+GD  Y          P +  L L A  +   HP  G
Sbjct: 319 HQLRAHLNMLSSPILGDVLYPQVLPDAPDRP-EYPLQLLAYSLHFEHPITG 368


>gi|152983735|ref|YP_001348604.1| RNA pseudouridine synthase family protein [Pseudomonas aeruginosa
           PA7]
 gi|150958893|gb|ABR80918.1| RNA pseudouridine synthase family protein [Pseudomonas aeruginosa
           PA7]
          Length = 275

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/217 (23%), Positives = 92/217 (42%), Gaps = 18/217 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-HRLDQETS 155
            ++ +L++D  + V +KP  + V    G  Y     L     S G +  +  HR+D+ T+
Sbjct: 60  FEARILHQDEHLLVADKPHFLPVMPAGG--YVEQTLLARLARSTGNRELVPLHRIDRHTA 117

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGGDYVH 214
           G+++ +    +       FR RRI K Y ++   +P+     +   LL+K+  + G+   
Sbjct: 118 GLVLFSTNPGSRGRYQALFRERRIDKYYEAIAPALPR-----LDFPLLRKTRLVPGEPFF 172

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +++ +   N        I+   +   W    + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 173 RMREGDGEPNSETR----IEVAERNGRWWRYRLYPVTGKKHQLRVHLAALGAAIQNDGFY 228

Query: 273 CANFKGNFTSP--IQNKLYLHARYMDLPHPEGGRLQI 307
                    SP   +  L L AR +    P  G  ++
Sbjct: 229 PGLLDAE-DSPDDYRRPLKLLARGLRFDDPLSGEARV 264


>gi|295104735|emb|CBL02279.1| Pseudouridylate synthases, 23S RNA-specific [Faecalibacterium
           prausnitzii SL3/3]
          Length = 303

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 98/243 (40%), Gaps = 45/243 (18%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVR--IPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
            R G    D   V  N RI  GQ++   +PP                    +T   +   
Sbjct: 38  FRGGGFFADGVPVLANRRIYPGQMLSFALPP----------------EGDGVTPQPEIPV 81

Query: 99  SILLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRL 150
            ++ YED+   V  KP  ++V       GG+      +G+      + G  P  R  +R+
Sbjct: 82  KVV-YEDAFAVVLEKPPQLAVHPTLNYPGGT----LANGYAAWAA-AHGHSPVFRPVNRI 135

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIG 209
           D++TSG+++ A+   AA  L       R+ K+Y+++  G +P  +    A    +   I 
Sbjct: 136 DKDTSGLVLAAKNAYAAPLLAG-----RVTKLYYAIAQGALPLGEGAIDAPIGRRGDSII 190

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           G     V    K +    +  K  +  +   C     P TGRTHQ+RVH   +G P+ GD
Sbjct: 191 G---RCVTPEGKPSRTEYTIIKEENGLSLAACV----PVTGRTHQIRVHFASIGHPLAGD 243

Query: 270 HKY 272
             Y
Sbjct: 244 DLY 246


>gi|15676763|ref|NP_273908.1| YabO/YceC/SfhB family protein [Neisseria meningitidis MC58]
 gi|7226104|gb|AAF41278.1| YabO/YceC/SfhB family protein [Neisseria meningitidis MC58]
          Length = 307

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|117922144|ref|YP_871336.1| pseudouridine synthase [Shewanella sp. ANA-3]
 gi|117614476|gb|ABK49930.1| pseudouridine synthase [Shewanella sp. ANA-3]
          Length = 305

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 48/169 (28%), Positives = 83/169 (49%), Gaps = 20/169 (11%)

Query: 148 HRLDQETSGILVVARTRAAAQHLT-ESFRMRRIQKIYWSLVWGIPKNKKECIA------- 199
           HRLD+ET+G++++  TR   +H+  + F    I+K Y ++    P+   +  +       
Sbjct: 134 HRLDRETAGVILMT-TRPETRHIYHQLFIDDAIRKDYQAIAKLTPEIMAQYASGELTLPL 192

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +W +K      +    +K  E  AN   +H ++ +     +    E+ P TG+THQLRVH
Sbjct: 193 HWTVKNRMQRSEPSFTMKIVEGEAN---THSEISLVAIHGELGLFELSPITGKTHQLRVH 249

Query: 259 ALHMGCPIVGDHKYCANF-KG--NFTSPIQNKLYLHARYMDLPHPEGGR 304
              +G P++ D  Y   + KG  +F+ P+Q  L    R++D   P  GR
Sbjct: 250 MQSLGMPLLNDRFYPTLYPKGPDDFSKPLQ-LLAQRLRFID---PISGR 294


>gi|254580497|ref|XP_002496234.1| ZYRO0C13684p [Zygosaccharomyces rouxii]
 gi|238939125|emb|CAR27301.1| ZYRO0C13684p [Zygosaccharomyces rouxii]
          Length = 398

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 51/190 (26%), Positives = 81/190 (42%), Gaps = 26/190 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E+  + V NKP+GI +   +G  Y     +   +   G+     +RLD+ TSG+L++
Sbjct: 115 IVHENDNLLVLNKPSGIPIHP-TGQFYQ--NTITEILKRHGKTALPCYRLDKLTSGLLIM 171

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE-------CIANWLLKKSHIGGDY 212
           A+    A  +    R   + K Y + V G  P +  E          + LL        Y
Sbjct: 172 AKNTETAGGIQLKIRDHDMSKYYLARVKGKFPHSSSEDFYEPPIPFQDPLLVTQEESPVY 231

Query: 213 -VHVVKQNEKGAN---------YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            V   KQ   G +         Y + +F   D        +  +P TGRTHQ+R+H   +
Sbjct: 232 TVEPKKQFPSGLSPVKDARTSFYPLKYFPHCDQ-----SLVVCKPLTGRTHQIRIHLARL 286

Query: 263 GCPIVGDHKY 272
           G PIV D  Y
Sbjct: 287 GHPIVNDPFY 296


>gi|161869801|ref|YP_001598969.1| YabO/YceC/SfhB family protein [Neisseria meningitidis 053442]
 gi|161595354|gb|ABX73014.1| YabO/YceC/SfhB family protein [Neisseria meningitidis 053442]
          Length = 307

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|153827526|ref|ZP_01980193.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-2]
 gi|149738545|gb|EDM52900.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-2]
          Length = 172

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 42/170 (24%), Positives = 77/170 (45%), Gaps = 18/170 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVYPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIGGDYVHVVKQ 218
           A +   A  +   F    ++K Y ++V G  +     + ++ LK+    I   +     +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEAN--VLDYPLKEELDKIADKFA----K 117

Query: 219 NEKGANYAISHFKVI---------DCFA-QKFCWLEMQPHTGRTHQLRVH 258
            +K A  A++ ++ +           FA  ++C +EMQP   +T     H
Sbjct: 118 QDKEAQSAVTAYRPLAKVELPISTGKFATTRYCLIEMQPRRAQTSAASPH 167


>gi|21220121|ref|NP_625900.1| ribosomal pseudouridine synthase [Streptomyces coelicolor A3(2)]
 gi|289772662|ref|ZP_06532040.1| ribosomal pseudouridine synthase [Streptomyces lividans TK24]
 gi|6119667|emb|CAB59478.1| putative ribosomal pseudouridine synthase [Streptomyces coelicolor
           A3(2)]
 gi|289702861|gb|EFD70290.1| ribosomal pseudouridine synthase [Streptomyces lividans TK24]
          Length = 324

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 95/219 (43%), Gaps = 35/219 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           ++Y D+ I V +KP  ++     G   H+     + +  +   P L   HRLD+ T+G++
Sbjct: 97  IVYRDAHIVVADKPHFLATTPRGG---HVTQTALARLRRELDIPALGAAHRLDRLTAGLV 153

Query: 159 ---VVARTRAAAQHLTESFRMRRIQKIY-----WSLVWGIPKNKKECIANWLLKKSHIGG 210
              V    R A Q L   F  RR+ K+Y     +     +P+  +  I    LK+  +  
Sbjct: 154 LFTVRPGERGAYQGL---FADRRVHKVYEAVAPYDAALALPRTVRSRI----LKERGV-- 204

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
               +  +   G   A++  +++    +       + P TG+THQLRVH   +G PI+GD
Sbjct: 205 ----LAAREVAGEPNAVTRVELLAHRPEHGLGRYRLVPGTGQTHQLRVHLNALGVPILGD 260

Query: 270 HKY----CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             Y         G+F  P+Q    L AR +    P  GR
Sbjct: 261 PLYPEVAAPVPAGDFRRPLQ----LLARELGFTDPVTGR 295


>gi|254670442|emb|CBA06065.1| pseudouridylate synthase [Neisseria meningitidis alpha153]
 gi|325135925|gb|EGC58535.1| RNA pseudouridine synthase [Neisseria meningitidis M0579]
          Length = 307

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|325133994|gb|EGC56649.1| RNA pseudouridine synthase [Neisseria meningitidis M13399]
          Length = 307

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|256788767|ref|ZP_05527198.1| ribosomal pseudouridine synthase [Streptomyces lividans TK24]
          Length = 304

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 95/219 (43%), Gaps = 35/219 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           ++Y D+ I V +KP  ++     G   H+     + +  +   P L   HRLD+ T+G++
Sbjct: 77  IVYRDAHIVVADKPHFLATTPRGG---HVTQTALARLRRELDIPALGAAHRLDRLTAGLV 133

Query: 159 ---VVARTRAAAQHLTESFRMRRIQKIY-----WSLVWGIPKNKKECIANWLLKKSHIGG 210
              V    R A Q L   F  RR+ K+Y     +     +P+  +  I    LK+  +  
Sbjct: 134 LFTVRPGERGAYQGL---FADRRVHKVYEAVAPYDAALALPRTVRSRI----LKERGV-- 184

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
               +  +   G   A++  +++    +       + P TG+THQLRVH   +G PI+GD
Sbjct: 185 ----LAAREVAGEPNAVTRVELLAHRPEHGLGRYRLVPGTGQTHQLRVHLNALGVPILGD 240

Query: 270 HKY----CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             Y         G+F  P+Q    L AR +    P  GR
Sbjct: 241 PLYPEVAAPVPAGDFRRPLQ----LLARELGFTDPVTGR 275


>gi|294944527|ref|XP_002784300.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239897334|gb|EER16096.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 296

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/215 (25%), Positives = 93/215 (43%), Gaps = 40/215 (18%)

Query: 100 ILLYEDSK--IYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           + + EDS   I   +KPAG+    GG  +   +   L    +    +P   +RLD+ETSG
Sbjct: 114 VFIREDSARGIVAVHKPAGLPTHSGGKYMRTSLVHILARAFNLSTIRP--INRLDRETSG 171

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++++A   +  + L +            SL+  +P   +  IA   + +       +  V
Sbjct: 172 VVLLAADASVHERLKDR-----------SLLSKVPALCRTPIA---VDRHVPNQPLMSRV 217

Query: 217 KQNEKGANYAISHFK-----VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            ++   +    + F+     V+ C          +P TG+THQ+RVH  H+G PI GD  
Sbjct: 218 VEDSTNSTLCTTLFRNLGNGVVAC----------RPVTGKTHQIRVHLSHLGFPIQGDTL 267

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           Y     G  ++P + +L LHA    +  P    LQ
Sbjct: 268 Y-----GGRSTP-EGRLRLHAHCYQVKDPNQATLQ 296


>gi|169633282|ref|YP_001707018.1| putative pseudouridylate synthase [Acinetobacter baumannii SDF]
 gi|169152074|emb|CAP00961.1| putative pseudouridylate synthase [Acinetobacter baumannii]
          Length = 302

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 50/194 (25%), Positives = 88/194 (45%), Gaps = 21/194 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V +KP  +++   G  +   +   LK    +K   P   HRLD+ET+G+++
Sbjct: 94  ILFENDDLLVVDKPHFLTISPTGQYVQETLLVRLKKQTGNKFLTP--IHRLDRETAGVVL 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLV-----WGIPKNKKECIANWLLKKSHIGGDYVH 214
             +   +     + F  R++ KIY ++         P+N K     +L K +      + 
Sbjct: 152 FCKRPQSRGIYQQLFADRQVNKIYHAIAAYKAELKFPQNLKL----YLDKGTPFYT--MQ 205

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+   +      I   +    +A K+C   + P TG+ HQLRVH  H+G PI  D  Y  
Sbjct: 206 VITHTKTNTETKIELIEHNHSWA-KYC---LTPTTGKQHQLRVHLNHLGIPIKNDPFYPI 261

Query: 275 ---NFKGNFTSPIQ 285
                  +F+ P+Q
Sbjct: 262 VQHKADDDFSQPLQ 275


>gi|302836415|ref|XP_002949768.1| pseudouridine synthase [Volvox carteri f. nagariensis]
 gi|300265127|gb|EFJ49320.1| pseudouridine synthase [Volvox carteri f. nagariensis]
          Length = 712

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/157 (28%), Positives = 64/157 (40%), Gaps = 28/157 (17%)

Query: 144 PRL-----THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKK-- 195
           PRL     T+RLD+  SG+L++AR+ A A  +      R   K Y + V G+ P      
Sbjct: 287 PRLWPLYPTYRLDKPVSGVLLLARSSAVAARMRVLLEERGCSKAYVARVQGVFPDTDAAG 346

Query: 196 -----ECIANWLLKKSHIGGDY--------------VHVVKQNEKGANYAISHFKVIDCF 236
                +    W  K +H                     +  +    A  A +HF+ +   
Sbjct: 347 GPLVVDVPLGWEAKTNHATPVPREAVEAAAAGGPLPPGLNPELAASAKPAETHFRRLSVA 406

Query: 237 AQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                 + E  P TGRTHQ+RVH  H+G PI  D +Y
Sbjct: 407 PDGLTSVVEAVPKTGRTHQIRVHLQHLGHPIANDTQY 443


>gi|218767979|ref|YP_002342491.1| hypothetical protein NMA1085 [Neisseria meningitidis Z2491]
 gi|121051987|emb|CAM08296.1| hypothetical protein NMA1085 [Neisseria meningitidis Z2491]
 gi|308389039|gb|ADO31359.1| YabO/YceC/SfhB family protein [Neisseria meningitidis alpha710]
 gi|316985760|gb|EFV64704.1| RNA pseudouridylate synthase family protein [Neisseria meningitidis
           H44/76]
 gi|319410229|emb|CBY90568.1| putative RNA pseudouridine synthase (RNA-uridine isomerase; RNA
           pseudouridylate synthase) [Neisseria meningitidis WUE
           2594]
 gi|325130001|gb|EGC52795.1| RNA pseudouridine synthase [Neisseria meningitidis OX99.30304]
 gi|325139980|gb|EGC62509.1| RNA pseudouridine synthase [Neisseria meningitidis CU385]
 gi|325200448|gb|ADY95903.1| RNA pseudouridine synthase [Neisseria meningitidis H44/76]
 gi|325203940|gb|ADY99393.1| RNA pseudouridine synthase [Neisseria meningitidis M01-240355]
          Length = 307

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|145295560|ref|YP_001138381.1| hypothetical protein cgR_1487 [Corynebacterium glutamicum R]
 gi|140845480|dbj|BAF54479.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 320

 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 100/240 (41%), Gaps = 45/240 (18%)

Query: 35  VNLQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
           V LQK+L        R  ++ +D+ RV+ N+RI + Q VR+ P     N +I+   +   
Sbjct: 80  VRLQKVLAQAGVASRRHAEILIDQGRVEVNDRIVTTQGVRVNPN----NDVIRVDGV--- 132

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
                        I + ED + +V NKP G+       +     G L S   + GQ+   
Sbjct: 133 ------------RIHINEDLEYFVLNKPRGMHSTMSDELGRPCVGDLVSEKTASGQRLFH 180

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD +T G+L++      A  L        + K Y + V G   NK   + + L    
Sbjct: 181 VGRLDADTEGLLLLTNDGELANRLMHP--KYEVSKTYLATVRGEATNK---LVSALR--- 232

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               D V +     K A++A    ++ID F  K   L ++ H GR H +R     +G P+
Sbjct: 233 ----DGVELEDGPAK-ADFA----QIIDVFQGK-SLLRIEIHEGRKHIVRRLFDELGFPV 282


>gi|290986063|ref|XP_002675744.1| predicted protein [Naegleria gruberi]
 gi|284089342|gb|EFC43000.1| predicted protein [Naegleria gruberi]
          Length = 301

 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 56/210 (26%), Positives = 86/210 (40%), Gaps = 57/210 (27%)

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG------IPK 192
           S  +K R  HRLD  TSG+L ++ TR +   L+ SF  +  +K Y +L+ G      +  
Sbjct: 53  SDERKIRFPHRLDMATSGVLCLSMTRESCACLSTSFEDKTSRKFYLALLSGDVNLEELKM 112

Query: 193 NKK---------ECIANWLLKKSHIGGD--------------YVHVVKQNEKGANYAISH 229
           N+K         E   + ++  S IG D                 V+KQ  +     +S 
Sbjct: 113 NEKLRNNVKVVNENDCSKIIITSFIGRDDGGNNENEEYDPTGRGFVMKQTLEKPIEDLSK 172

Query: 230 FKVIDCFAQ-------------KFCWLEMQPHT--------GRTHQLRVHALHMGCPIVG 268
           +K      Q              +  +E +P T        GR HQLR+H+L +G  I+G
Sbjct: 173 YKTKQERQQHQFREGTSEMIILSYGQVENKPVTKVLLRPLSGRKHQLRLHSLLLGHAIIG 232

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           D  Y  N    F+     +L LHA  + +P
Sbjct: 233 DEMYGEN--DGFS-----RLMLHAYSLQIP 255


>gi|254804732|ref|YP_003082953.1| pseudouridylate synthase [Neisseria meningitidis alpha14]
 gi|254668274|emb|CBA05164.1| pseudouridylate synthase [Neisseria meningitidis alpha14]
          Length = 307

 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|330951836|gb|EGH52096.1| pseudouridine synthase [Pseudomonas syringae Cit 7]
          Length = 296

 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 50/177 (28%), Positives = 84/177 (47%), Gaps = 17/177 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + V +KP  + V   G  +   +   L   +D+    P   HR+D+ T+G+++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAGEYVEQTLLRRLIHRLDNPDLVP--LHRIDRHTAGLVL 146

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +   +TR+A Q L   F  RRI K Y ++   +P    E I   L +   + G+    +
Sbjct: 147 FSANRQTRSAYQAL---FPTRRIDKFYQAIAPALP----ELIFPRLHESRLVEGEPFFRM 199

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 200 QEG-VGASNTRTQIEVLE--RQDKLWRYGLYPVTGKKHQLRVHMAALGAAICNDPFY 253


>gi|166714232|ref|ZP_02245439.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 295

 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 55/211 (26%), Positives = 90/211 (42%), Gaps = 18/211 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGI 157
           +++ D+ + V  KP  + V      AY  +  L   V   D+    P   HR+D+ET+G+
Sbjct: 89  VVHADANLVVACKPHFLPVTPAG--AYVRETLLTRLVRRLDNPALVP--LHRIDRETAGL 144

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ +   A        FR RRI+K Y ++   +P+     +    L+     G+    ++
Sbjct: 145 VLFSVNPATRGIYQALFRERRIRKQYLAVAPPLPELSFPYVHRSRLEP----GEPFFRMR 200

Query: 218 QNEKGANYAISHFKVIDCFAQKF-CWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +     N       VID  A     W   ++P TGR HQLRVH   +G PI+ D  Y  +
Sbjct: 201 EGVGEPNSE----TVIDVVAPGADTWTYRLEPVTGRKHQLRVHMAALGAPILHDRFY-PD 255

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
            +       +  L L A  +    P  G L+
Sbjct: 256 LQAQRPDDPERHLQLFAHTLAFDDPITGELR 286


>gi|293399421|ref|ZP_06643574.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae F62]
 gi|291609990|gb|EFF39112.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae F62]
          Length = 307

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAE-GVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|223998226|ref|XP_002288786.1| hypothetical protein THAPSDRAFT_261746 [Thalassiosira pseudonana
           CCMP1335]
 gi|220975894|gb|EED94222.1| hypothetical protein THAPSDRAFT_261746 [Thalassiosira pseudonana
           CCMP1335]
          Length = 383

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 51/201 (25%), Positives = 82/201 (40%), Gaps = 24/201 (11%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I+  +++LTKHS  L       +  +Y  NKPA + V       Y+ +  L      +G 
Sbjct: 81  IVPETISLTKHS--LPDTANCGNGILYCINKPASVPVYPSG--PYYSNSLLMMVEAQEGL 136

Query: 143 KPRL---THRLDQETSGILVVARTRAAAQHLTESFRMRR-------IQKIYWSLVWGIPK 192
            P+     HR+D+ TSG+L+       ++ +      R        I+K+Y + V G   
Sbjct: 137 PPKSLVPCHRIDRATSGVLLCTIDSKVSRAVQGRMASRNEVGTQHPIKKLYLARVQGKFP 196

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGR 251
           +    +        H         +   +    AIS F+++    A     +   P TGR
Sbjct: 197 DPSSSVPVGAASMMH---------RSVSRDGKQAISRFRLLSYDAATDQSLVSCCPITGR 247

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQLRVH   +G PI  D +Y
Sbjct: 248 GHQLRVHLQFIGLPIHNDVEY 268


>gi|167465286|ref|ZP_02330375.1| ribosomal large subunit pseudouridylate synthase D [Paenibacillus
           larvae subsp. larvae BRL-230010]
          Length = 144

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 69/153 (45%), Gaps = 19/153 (12%)

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQ--NEKGANYAISHF 230
            R++ +++ Y +L  G       CI   + +    IG D  H  K+    KG  +A++ +
Sbjct: 1   MRLKTVRREYAALAEG-------CIEPTVGVIDLPIGRDRHHKSKRRVTLKG-QHAVTRY 52

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
            V     Q    L +   TGRTHQ+RVH  H+G P++GD  Y  N      + + ++  L
Sbjct: 53  AVAAQLEQA-ALLHLSLETGRTHQIRVHLSHIGHPLLGDSLYGGN------TALISRQAL 105

Query: 291 HARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           H   +   HP  G  L+I AP P      +  L
Sbjct: 106 HGERISFSHPITGEDLRIEAPWPGDFTALYAKL 138


>gi|320536011|ref|ZP_08036072.1| RNA pseudouridine synthase [Treponema phagedenis F0421]
 gi|320147136|gb|EFW38691.1| RNA pseudouridine synthase [Treponema phagedenis F0421]
          Length = 233

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 46/180 (25%), Positives = 80/180 (44%), Gaps = 15/180 (8%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +RLD+  SG++++A        L+ +F   +I K Y+++     K KK      +L    
Sbjct: 54  NRLDKPVSGLMLIACNSKIHTALSHAFSDGKIVKTYFAIC---EKPKKPTTDIPILVPQT 110

Query: 208 IGGDYVHVVKQ------NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
                +   K+      ++KGA  A   + +     + + +L++ P +GRTHQ+R    H
Sbjct: 111 CNDTLIFSSKKQKAFISDKKGAKEACLSWTLC-ARGENYDFLQVIPISGRTHQIRAQLAH 169

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
           +G PI GD KY     G   S     + LHA  ++  HP   +    +  P +M   W +
Sbjct: 170 IGRPIKGDLKY-----GAKRSEKTGGIRLHAYSLEFLHPVLHKPLHISTYPENMDALWAA 224


>gi|225350851|ref|ZP_03741874.1| hypothetical protein BIFPSEUDO_02425 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225158307|gb|EEG71549.1| hypothetical protein BIFPSEUDO_02425 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 250

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 54/188 (28%), Positives = 79/188 (42%), Gaps = 20/188 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYE+  I V +KP  ++     G+ Y     ++             HRLD+ T+GI+V 
Sbjct: 25  VLYENDAIIVVDKPHFLATTP-RGMWYRETALIRLREQYGEPDIVPAHRLDRLTAGIIVF 83

Query: 161 ART---RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANW-------LLKKSHI 208
            R    R A Q L   F+ R+  K Y  L    P+   +   I           ++ SHI
Sbjct: 84  VRKPELRGAYQML---FQNRKTIKTYECLAPLAPEQHPQYGTIVRIDRHQPFPAIRASHI 140

Query: 209 GGDY--VHVVKQNEK-GANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGC 264
             D   +   +  E   A   I     + C   K +    + P TG+THQLRVH   +G 
Sbjct: 141 CKDRGRLQAYEIPETINAQTLIERGSTVRCLDGKAYVNYVLHPKTGKTHQLRVHMNSLGL 200

Query: 265 PIVGDHKY 272
           PI+GD  Y
Sbjct: 201 PILGDDFY 208


>gi|29833249|ref|NP_827883.1| ribosomal pseudouridine synthase [Streptomyces avermitilis MA-4680]
 gi|29610371|dbj|BAC74418.1| putative ribosomal pseudouridine synthase [Streptomyces avermitilis
           MA-4680]
          Length = 321

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 57/212 (26%), Positives = 96/212 (45%), Gaps = 25/212 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL- 158
           ++Y D  I V +KP  ++    GS +A  +   L+   D    +    HRLD+ T+G++ 
Sbjct: 104 VVYRDEHIVVADKPHFLATTPRGSHVAETVLARLRR--DLGIPELGAAHRLDRLTAGLVL 161

Query: 159 --VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIANWLLKKSHIGGDYVHV 215
             V    R A Q L   FR + + K Y ++    P+      + + +LK+  +      +
Sbjct: 162 FTVRPGERGAYQSL---FRDKLVHKEYEAVATYDPEVALPRTVRSRILKERGL------L 212

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-- 273
             +   G   A+S  ++ +    +  +  + P TG+THQLRVH   +G PI+GD  Y   
Sbjct: 213 AAREVAGEPNAVSRIELTEHRDGRGRY-RLLPRTGQTHQLRVHMNALGLPILGDPLYPVV 271

Query: 274 --ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 G+F  P+Q    L AR ++   P  G
Sbjct: 272 TDPGPAGDFRRPLQ----LLARVLEFTDPVTG 299


>gi|294657495|ref|XP_459803.2| DEHA2E11374p [Debaryomyces hansenii CBS767]
 gi|199432736|emb|CAG88042.2| DEHA2E11374p [Debaryomyces hansenii]
          Length = 582

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 57/244 (23%), Positives = 101/244 (41%), Gaps = 41/244 (16%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +K + +GQV ++KK    ++ +++G ++         +H     +   SS  +       
Sbjct: 124 KKTIAAGQVTLNKKPADLDSIVRNGDLI---------SHRCHRHEPSVSSRGIK------ 168

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ED  I   +KP+GI+V       Y  +   K +    G+     +RLD+ TSG+
Sbjct: 169 ---IVHEDENIIAIDKPSGIAVHPTG--RYRYNTITKIFQHEFGKVVHPCNRLDRLTSGL 223

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--------IPKNKKECIANWLLKKSHIG 209
           + + +    A    +  R R ++K Y + V G        + K  K       L +  + 
Sbjct: 224 MFLGKNAKGADAFVQQIRDRTVKKEYIARVVGKFDIGDVEVDKPLKTVSPKHGLNR--VD 281

Query: 210 GDYVHVVKQNEKGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            D     K   +  +Y   S   ++ CF          P TGRTHQ+RVH  ++G  I  
Sbjct: 282 FDEGKEAKTVFRRISYDPESDTSIVKCF----------PFTGRTHQIRVHLQYIGHAIAN 331

Query: 269 DHKY 272
           D  Y
Sbjct: 332 DPMY 335


>gi|238021958|ref|ZP_04602384.1| hypothetical protein GCWU000324_01863 [Kingella oralis ATCC 51147]
 gi|237866572|gb|EEP67614.1| hypothetical protein GCWU000324_01863 [Kingella oralis ATCC 51147]
          Length = 305

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 60/125 (48%), Gaps = 6/125 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++ +   A        F    IQK Y +L        +  +A  L+ ++ 
Sbjct: 146 HRLDKDTAGVMLFSHNPATRAAYHTLFPSHAIQKTYHALA-----PTRLDLAYPLIVRTR 200

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +       + +   G   A +  ++++   +   + E+QP TG+ HQLRV  + +G P++
Sbjct: 201 LVPSEPFFLMREAAGEANAETRVRLLEPRGEASLY-ELQPVTGKKHQLRVQMMGLGMPLL 259

Query: 268 GDHKY 272
            D  Y
Sbjct: 260 NDALY 264


>gi|153825782|ref|ZP_01978449.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-2]
 gi|149740505|gb|EDM54620.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-2]
          Length = 87

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 2/88 (2%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I   NKP+G+    G  +  H D      VD      ++ HRLD  TSG+++ 
Sbjct: 1   MIYEDEHIIAANKPSGLLSVPGRPVE-HYDSMWARLVDY-CPDVKVVHRLDMSTSGLILF 58

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           A+ +     L + F+ R   KIY++ VW
Sbjct: 59  AKGKHMESALKKQFQYRLTHKIYYARVW 86


>gi|282852229|ref|ZP_06261581.1| ribosomal large subunit pseudouridine synthase D family protein
           [Lactobacillus gasseri 224-1]
 gi|282556648|gb|EFB62258.1| ribosomal large subunit pseudouridine synthase D family protein
           [Lactobacillus gasseri 224-1]
          Length = 107

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 35/105 (33%), Positives = 57/105 (54%), Gaps = 8/105 (7%)

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           N KG   A++HF V++ F + +  ++    TGRTHQ+RVH  ++G P+ GD  Y     G
Sbjct: 4   NPKG-KAAVTHFTVLEQF-KDYSLVKCILETGRTHQIRVHMKYIGHPLAGDPLY-----G 56

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              +   +  +LHA+ +    P   + L+ +APLPA   K  ++L
Sbjct: 57  PKKTLAGHGQFLHAKTLGFYQPSTHKWLEFSAPLPAIFEKQLENL 101


>gi|315445746|ref|YP_004078625.1| 23S RNA-specific pseudouridylate synthase [Mycobacterium sp. Spyr1]
 gi|315264049|gb|ADU00791.1| 23S RNA-specific pseudouridylate synthase [Mycobacterium sp. Spyr1]
          Length = 286

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 63/265 (23%), Positives = 102/265 (38%), Gaps = 29/265 (10%)

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-------LLYEDS 106
           +F  R  +G  V    V  A   +  +  +L    ++  + D    +       +L+ D 
Sbjct: 28  EFQRRWGTGAKVVDGEVFCADGTVADDSTVLPPGAHVYLYRDLPDEVPVPFDMPVLHRDD 87

Query: 107 KIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV-VARTR 164
            I V +KP  ++    GS +       L+  +D     P   HRLD+ T+G+L+  AR  
Sbjct: 88  DIVVVDKPHFLATMPRGSHVVQTALVRLRRELDLPELSP--AHRLDRLTAGVLLFTARRE 145

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
               + T   R    +         I +     + N L+K     G    V +  E  A 
Sbjct: 146 VRGAYQTLFVRGEAAKTYVAHSSHAIDREFPLTVRNRLVKHR---GSLQAVEEPGEPNAE 202

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFT 281
             + +               + P TGRTHQLRVH   +G PI GD  Y        G+F 
Sbjct: 203 TVVEYLGE--------GMYRLTPRTGRTHQLRVHMAGLGIPITGDPLYPDVVDVPPGDFG 254

Query: 282 SPIQNKLYLHARYMDLPHPEGGRLQ 306
           +P++    L A+ ++   P  G L+
Sbjct: 255 APLR----LLAQALEFTDPISGELR 275


>gi|261400179|ref|ZP_05986304.1| RNA pseudouridine synthase [Neisseria lactamica ATCC 23970]
 gi|269210178|gb|EEZ76633.1| RNA pseudouridine synthase [Neisseria lactamica ATCC 23970]
          Length = 307

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 61/125 (48%), Gaps = 6/125 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKY 272
            D  Y
Sbjct: 262 NDALY 266


>gi|325142086|gb|EGC64512.1| RNA pseudouridine synthase [Neisseria meningitidis 961-5945]
          Length = 307

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPIDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|258405801|ref|YP_003198543.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
 gi|257798028|gb|ACV68965.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
          Length = 285

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 65/296 (21%), Positives = 118/296 (39%), Gaps = 38/296 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V  +   +R+D+  +   P       Q+   SG+VR + +  +   R+++G  + 
Sbjct: 7   IERIAVPEEWHGVRIDQGLRLLAPESGLRQRQQWCASGRVRQNGRTERKGGRLEAGATLE 66

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GI 125
           +      L   +  +    S V +    + L ++            KP  +  +  S   
Sbjct: 67  L------LPEPLPSKPQPASGVRVVSVVNALAAVF-----------KPGNVHCEAQSHNP 109

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              ++  L +      Q+PRL +RLD  TSG+++VA ++ A           R++K YW+
Sbjct: 110 EPSVESVLPNLFPR--QRPRLLNRLDYPTSGLVLVALSQGAFDQYQIWQDEGRVRKTYWA 167

Query: 186 LV---WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            +   W  P+  K  I     K+       V VV + +       +H + +   A     
Sbjct: 168 EIHGEWTGPELLKWRIETAKRKR-------VAVVFEPDPDP-LRWTHVRALYRIAPGRTR 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +E+    GR H +R H    G PI GD  Y  +      SP    LYLH   + +P
Sbjct: 220 VEVVIAKGRRHHIRAHLAAAGTPIQGDSLYGED------SP-SAPLYLHHLRVHMP 268


>gi|226941112|ref|YP_002796186.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
 gi|226716039|gb|ACO75177.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 236

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 74/147 (50%), Gaps = 10/147 (6%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD  TSG+L+VAR+  AA  L ++   R+++K Y +L    P+ K+  +    +++
Sbjct: 46  LVHRLDAMTSGLLLVARSADAAAALGQALAARQVEKFYLALSDRSPRKKQGWVIG-DMER 104

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           S      +   +Q+      A++ F        +  +L ++P TGRTHQLRV    +G P
Sbjct: 105 SRRASWKLLPTRQDP-----AVTQFFSAAAGDGRRLFL-LRPRTGRTHQLRVALKSLGAP 158

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHA 292
           I GD  Y     G       ++ YLH+
Sbjct: 159 IWGDPLYHPQEPGREAP---DRGYLHS 182


>gi|309379425|emb|CBX21992.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 307

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 61/125 (48%), Gaps = 6/125 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAE-GVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKY 272
            D  Y
Sbjct: 262 NDALY 266


>gi|325198068|gb|ADY93524.1| RNA pseudouridine synthase [Neisseria meningitidis G2136]
          Length = 307

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPIDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|325132280|gb|EGC54973.1| RNA pseudouridine synthase [Neisseria meningitidis M6190]
 gi|325137749|gb|EGC60324.1| RNA pseudouridine synthase [Neisseria meningitidis ES14902]
          Length = 307

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 61/125 (48%), Gaps = 6/125 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + + +    +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLLYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E G   A +  ++I+     F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAE-GVPNAHTTVELIENRG-GFSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKY 272
            D  Y
Sbjct: 262 NDALY 266


>gi|325144100|gb|EGC66407.1| RNA pseudouridine synthase [Neisseria meningitidis M01-240013]
          Length = 307

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPIDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|328875057|gb|EGG23422.1| hypothetical protein DFA_05554 [Dictyostelium fasciculatum]
          Length = 637

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 41/87 (47%), Gaps = 5/87 (5%)

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           A+ +  +E+  HTGR HQ+RVH    G PIVGD  Y       F  P    L L +  + 
Sbjct: 431 ARNYTLMEITLHTGRQHQIRVHMTSEGLPIVGDPIYSGK-SNQFMVPY---LLLASVALR 486

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSL 322
             HP    +++ T P P H+    D L
Sbjct: 487 FQHPITKQQMEFTIPNPPHLQSFIDQL 513



 Score = 42.0 bits (97), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 62/266 (23%), Positives = 105/266 (39%), Gaps = 84/266 (31%)

Query: 32  INFVNLQKILRSGQVRVDKK-------RVKFNNRI------------------QSGQVVR 66
           +N  ++ K++  GQ+ ++ K       +++ N+RI                  +SGQ   
Sbjct: 41  LNKTSIVKLITQGQISINDKVVQEKNAKIRANDRILITLPTSTTSTTSSSNNSESGQQST 100

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              VI       KE  ++ + ++L          +L+ED  I V NKPAG+ V       
Sbjct: 101 TTTVIG------KEINLVATKIDLN---------ILFEDEYIVVINKPAGMIVHPPPPSP 145

Query: 127 YH-----------IDGFLKSWVDSKG-------QKPRLTHRLDQETSGILVVARTRAAAQ 168
            H           ++  L  +  +KG        +P + HRLD++T+GIL+VA+  +  +
Sbjct: 146 NHPLNEENQTRTLVNALLYRY-GAKGLSIVGGVDRPGIVHRLDKDTAGILIVAKNDSVHE 204

Query: 169 --------HLTESFR-------------MRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
                   H + + +                IQK Y+ LV G PK     I   +   S 
Sbjct: 205 MVKKMLQDHTSTTIKGSMSAKANNNNNKPTTIQKTYYCLVTGKPKESHGIINKAI---SR 261

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVI 233
              D   +V    KG   +I+ +KVI
Sbjct: 262 HPMDRNKMVIDESKGKE-SITEYKVI 286


>gi|215432263|ref|ZP_03430182.1| hypothetical protein MtubE_16739 [Mycobacterium tuberculosis
           EAS054]
 gi|289755423|ref|ZP_06514801.1| conserved hypothetical protein [Mycobacterium tuberculosis EAS054]
 gi|289696010|gb|EFD63439.1| conserved hypothetical protein [Mycobacterium tuberculosis EAS054]
          Length = 304

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 41/141 (29%), Positives = 65/141 (46%), Gaps = 12/141 (8%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ T+G+L+    R         F    ++K Y +     P      +A   L +S 
Sbjct: 132 HRLDRLTAGVLLFTTRREVRGSYQTMFARGLVRKTYLARAPVAPG-----LALPRLVRSR 186

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           I     H+    E G   A +   +++  A+   +  + P TGRTHQLRVH   +G PI+
Sbjct: 187 IVKRRGHLQAVCEPGVPNAET---LVERIARDGLY-RLTPTTGRTHQLRVHMAALGIPIM 242

Query: 268 GDHKY---CANFKGNFTSPIQ 285
           GD  Y    +    +F++P+Q
Sbjct: 243 GDPLYPNVISVAAHDFSTPLQ 263


>gi|164657135|ref|XP_001729694.1| hypothetical protein MGL_3238 [Malassezia globosa CBS 7966]
 gi|159103587|gb|EDP42480.1| hypothetical protein MGL_3238 [Malassezia globosa CBS 7966]
          Length = 937

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 57/127 (44%), Gaps = 6/127 (4%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKK 205
           ++RLD+ TSGI+V + T+ AA  L   F    + K Y   V G  P    +C    L   
Sbjct: 142 SNRLDRLTSGIMVCSTTKEAACELGNDFNAGLVNKAYVCRVVGRFPDGIVDCTEPILSVD 201

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              G + VH   +  +     +S+    D        L  +P TGRTHQ+RVHA  +G  
Sbjct: 202 RQSGLNIVHPKGKECRTLFQRLSYDAATDSSV-----LVCRPITGRTHQIRVHAQWLGHA 256

Query: 266 IVGDHKY 272
           I  D  Y
Sbjct: 257 ISNDPLY 263


>gi|157377205|ref|YP_001475805.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157319579|gb|ABV38677.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 312

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 47/181 (25%), Positives = 81/181 (44%), Gaps = 14/181 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +LY D +I +  KP  +++     +   I+  L + +  K     +   HRLD+ T+G++
Sbjct: 88  VLYRDGQIIIAFKPHFLALHPSGNV---INECLVNRLRIKNGIETIVPAHRLDRATAGLV 144

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHIGGD 211
           ++       Q   E F+   I+K Y +L    P+        +     +W +K   + G+
Sbjct: 145 LLCLYPEHRQQYHELFKHGEIRKEYQALAKLTPELLEQHRTGELTLPVHWTVKNRMVKGE 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               +K  E  AN   S   +I+   +     ++ P TGRTHQLRVH   +G  I+ D  
Sbjct: 205 PSFTMKVVEGEANTH-SEITLIEMRGE-IGVFKLSPITGRTHQLRVHMQSLGMSILNDRC 262

Query: 272 Y 272
           Y
Sbjct: 263 Y 263


>gi|309356679|emb|CAP36772.2| hypothetical protein CBG_19546 [Caenorhabditis briggsae AF16]
          Length = 438

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 79/181 (43%), Gaps = 13/181 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++ E   + V  KP  + V      A H + G L+   +  G   R+ HRLD+ TSG+L+
Sbjct: 156 IISETDDLLVIEKPPSLPVHTCGQYAIHTVLGQLRENEEKTGL--RVLHRLDRATSGVLL 213

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHV-VK 217
            A+          + +     K Y   V G+ P  ++ C       +  IG   + + ++
Sbjct: 214 FAKNYETDLEFKTTLKQGEWSKEYVCKVDGVFPDEEQVC-------EQPIGPLVISMGIQ 266

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A S F+ +         +++   TGRTHQ+RVH+  +G PIVGD  Y +   
Sbjct: 267 CVRPDGKEAKSTFRKLWSDGTHSV-VQVHIETGRTHQIRVHSQFLGYPIVGDQLYNSTVW 325

Query: 278 G 278
           G
Sbjct: 326 G 326


>gi|167622548|ref|YP_001672842.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167352570|gb|ABZ75183.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 312

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 36/161 (22%), Positives = 71/161 (44%), Gaps = 16/161 (9%)

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-------WG 189
           + +  Q+    HRLD+ T+G+++++    +     E F+  +I+K Y ++          
Sbjct: 123 IKTGNQEIVAAHRLDRATAGVMLLSLNSGSRHDYHELFKSGQIRKTYQAIAPLNSEIKTM 182

Query: 190 IPKNKKECIANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           I +        W +K         ++  +   E  ++  I   +V + +       E+ P
Sbjct: 183 IVQGTLTLPMKWTVKNRLQKTVPSFLMCIGDGEANSHSEIRLIEVHNGYG----LFELAP 238

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQ 285
            TGRTHQLRVH + +G P++ D  Y         +F +P++
Sbjct: 239 VTGRTHQLRVHMMSLGMPLLNDRLYPELLDKAADDFAAPLK 279


>gi|288576272|ref|ZP_06394280.1| RNA pseudouridine synthase [Neisseria mucosa ATCC 25996]
 gi|288565855|gb|EFC87415.1| RNA pseudouridine synthase [Neisseria mucosa ATCC 25996]
          Length = 169

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 60/125 (48%), Gaps = 6/125 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A  +     F+ + + K Y +    I   + +      +    
Sbjct: 10  HRLDKDTAGVMLLSHNPATRRDYQTMFQNKTVCKTYEA----IAPTRTDLAYPLNISSRM 65

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+      + E   N A +  ++I+     F    + PHTG+ HQLRVH + +G P++
Sbjct: 66  VRGEKFFTTLEVEGEPN-AHTTVELIENRG-AFSLYRLTPHTGKKHQLRVHMMSLGMPLM 123

Query: 268 GDHKY 272
            D  Y
Sbjct: 124 NDALY 128


>gi|240080333|ref|ZP_04724876.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae FA19]
 gi|268596481|ref|ZP_06130648.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae FA19]
 gi|268550269|gb|EEZ45288.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae FA19]
          Length = 307

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 38/160 (23%), Positives = 73/160 (45%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L    P          ++ +  
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA---PTRTDLPYPIDVVSRLA 204

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            G  +     Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 205 RGEKFF--TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDAFYPVPSEAG-SEDYRKPLKLLAKKIAFTDPLSGRERV 300


>gi|126642162|ref|YP_001085146.1| putative pseudouridylate synthase [Acinetobacter baumannii ATCC
           17978]
          Length = 245

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 49/194 (25%), Positives = 88/194 (45%), Gaps = 21/194 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V +KP  +++   G  +   +   LK    ++   P   HRLD+ET+G+++
Sbjct: 37  ILFENDDLLVVDKPHFLTISPTGQYVQETLLVRLKKQTGNEFLTP--IHRLDRETAGVVL 94

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLV-----WGIPKNKKECIANWLLKKSHIGGDYVH 214
             +   +     + F  R++ KIY ++         P+N K     +L K +      + 
Sbjct: 95  FCKRPQSRGIYQQLFADRQVNKIYHAIAAYKAELKFPQNLKL----YLDKGTPFYT--MQ 148

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+   +      I   +    +A K+C   + P TG+ HQLRVH  H+G PI  D  Y  
Sbjct: 149 VIAHTKTNTETKIELIEHNHSWA-KYC---LTPTTGKQHQLRVHLNHLGIPIKNDPFYPI 204

Query: 275 ---NFKGNFTSPIQ 285
                  +F+ P+Q
Sbjct: 205 VQHKADDDFSQPLQ 218


>gi|304387818|ref|ZP_07369992.1| RNA pseudouridine synthase [Neisseria meningitidis ATCC 13091]
 gi|304338083|gb|EFM04219.1| RNA pseudouridine synthase [Neisseria meningitidis ATCC 13091]
          Length = 307

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAL----TRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEVE-GVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|120600440|ref|YP_965014.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|120560533|gb|ABM26460.1| pseudouridine synthase [Shewanella sp. W3-18-1]
          Length = 305

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 44/151 (29%), Positives = 70/151 (46%), Gaps = 16/151 (10%)

Query: 147 THRLDQETSGILVVARTRAAAQHLT-ESFRMRRIQKIYWSLVWGIP-------KNKKECI 198
            HRLD+ET+G++++   +   +HL  + F    I K Y ++    P       K      
Sbjct: 133 AHRLDRETAGVILMT-IQPETRHLYHQLFVDNAICKDYQAIAKLTPGIIEQYQKGHLTLP 191

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRV 257
            +W +K     GD    ++  E  AN   SH ++ +           + P TG+THQLRV
Sbjct: 192 LHWTVKNRMQPGDPSFTMQVVEGEAN---SHSEISLVAIKDDLGLFHLSPITGKTHQLRV 248

Query: 258 HALHMGCPIVGDHKYCA-NFKG--NFTSPIQ 285
           H L +G P++ D  Y     KG  NF +P++
Sbjct: 249 HMLSLGMPLLNDRFYPKLQPKGPDNFATPLK 279


>gi|261392780|emb|CAX50356.1| putative RNA pseudouridine synthase (RNA-uridine isomerase; RNA
           pseudouridylate synthase) [Neisseria meningitidis 8013]
          Length = 307

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVLSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|254481932|ref|ZP_05095174.1| hypothetical protein GPB2148_3 [marine gamma proteobacterium
           HTCC2148]
 gi|214037622|gb|EEB78287.1| hypothetical protein GPB2148_3 [marine gamma proteobacterium
           HTCC2148]
          Length = 143

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 32/98 (32%), Positives = 47/98 (47%), Gaps = 4/98 (4%)

Query: 232 VIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--NKL 288
            +D + Q ++  + +QP  GR HQLR H  H+G PI+GD K+       F +      +L
Sbjct: 42  AVDRYPQSRYSLVALQPEQGRKHQLRRHMKHLGYPIIGDAKHGKGVHNRFFAEKYGCGRL 101

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            L    MD  HP  G  + I A L A   +   + G+K
Sbjct: 102 LLACTGMDFSHPVNGDTVHIRAGLDAAFQRVLSAFGWK 139


>gi|212716478|ref|ZP_03324606.1| hypothetical protein BIFCAT_01402 [Bifidobacterium catenulatum DSM
           16992]
 gi|212660599|gb|EEB21174.1| hypothetical protein BIFCAT_01402 [Bifidobacterium catenulatum DSM
           16992]
          Length = 250

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 82/204 (40%), Gaps = 23/204 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYE+  I V +KP  ++     G+ Y     ++             HRLD+ T+GI+V 
Sbjct: 25  VLYENDAIIVVDKPHFLATTP-RGMWYRETALIRLREQYGEPDIVPAHRLDRLTAGIVVF 83

Query: 161 ART---RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHV 215
            R    R A Q L   F+ R+  K Y  L    P+   +   I      +        H+
Sbjct: 84  VRKPELRGAYQML---FQNRKTIKTYECLAPLAPEQHPQYGTIVRIDRHQPFPAIRASHI 140

Query: 216 VKQNEKGANYAISHF----------KVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGC 264
            K   +   Y I               + C   K +    + P TG+THQLRVH   +G 
Sbjct: 141 CKDRGRLQAYEIPEIVNAQTLIERGNTVRCIDGKAYVNYVLHPKTGKTHQLRVHMNSLGL 200

Query: 265 PIVGDHKY---CANFKGNFTSPIQ 285
           PI+GD  Y     +   +F+ P++
Sbjct: 201 PILGDDFYPNIVQHSYDDFSQPLE 224


>gi|156095610|ref|XP_001613840.1| hypothetical protein [Plasmodium vivax SaI-1]
 gi|148802714|gb|EDL44113.1| hypothetical protein, conserved [Plasmodium vivax]
          Length = 11429

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 41/71 (57%)

Query: 231  KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
            K ++ + ++F    ++ HTGRTHQ+RVH  H+G P+V D KY      N       +++L
Sbjct: 8228 KEVENYTKEFTLCNVKIHTGRTHQIRVHMRHIGHPLVSDKKYLNPSLSNLDKYWCFRMFL 8287

Query: 291  HARYMDLPHPE 301
            H+  ++  +P+
Sbjct: 8288 HSVILEFNNPD 8298



 Score = 49.3 bits (116), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 32/53 (60%)

Query: 146  LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K KK CI
Sbjct: 7906 LCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYLLLCHGRIKKKKGCI 7958


>gi|297195328|ref|ZP_06912726.1| ribosomal pseudouridine synthase [Streptomyces pristinaespiralis
           ATCC 25486]
 gi|197719590|gb|EDY63498.1| ribosomal pseudouridine synthase [Streptomyces pristinaespiralis
           ATCC 25486]
          Length = 314

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 56/211 (26%), Positives = 94/211 (44%), Gaps = 24/211 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG-IL 158
           +++ D  I + +KP  ++    GS +       ++  +D    +P   HRLD+ T+G +L
Sbjct: 100 VVHRDEHIVIADKPHFLATMPRGSHVRETALARMRRGLDLPSLQP--AHRLDRLTAGLVL 157

Query: 159 VVART--RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIANWLLKKSHIGGDYVHV 215
            V R   R A Q +   FR R ++K Y ++    P       + + ++K+    G    V
Sbjct: 158 FVVRPGDRGAYQTM---FRDRLVRKEYEAVAPYDPAVALPRTVRSRIVKER---GVLTAV 211

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--- 272
            +  E  +   I   +V D   +      + P TGRTHQLRVH   +G PI+ D  Y   
Sbjct: 212 EEPGEPNSESRIELLEVRDGLGR----YRLLPATGRTHQLRVHMNALGLPILHDPLYPVV 267

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +   ++  P+Q    L AR ++   P  G
Sbjct: 268 LPDGPDDYARPLQ----LLARALEFTDPVTG 294


>gi|146291626|ref|YP_001182050.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|145563316|gb|ABP74251.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
          Length = 305

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 42/151 (27%), Positives = 68/151 (45%), Gaps = 18/151 (11%)

Query: 148 HRLDQETSGILVVARTRAAAQHLT-ESFRMRRIQKIYWSLVWGIP-------KNKKECIA 199
           HRLD+ET+G++++   +   +HL  + F    I K Y ++    P       K       
Sbjct: 134 HRLDRETAGVILMT-IQPETRHLYHQLFVDNAICKDYQAIAKLTPGIIEQYQKGHLTLPL 192

Query: 200 NWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +W +K     GD  +   V + E  ++  IS   + D          + P TG+THQLRV
Sbjct: 193 HWTVKNRMQPGDPSFTMQVVEGEANSHSEISLVAIKD----DLGLFHLSPITGKTHQLRV 248

Query: 258 HALHMGCPIVGDHKYC---ANFKGNFTSPIQ 285
           H L +G P++ D  Y         NF +P++
Sbjct: 249 HMLSLGMPLLNDRFYPKLQPKSPDNFATPLK 279


>gi|313668670|ref|YP_004048954.1| pseudouridine synthase (rna-uridine isomerase) (rna pseudouridylat
           synthase) [Neisseria lactamica ST-640]
 gi|313006132|emb|CBN87593.1| pseudouridine synthase (rna-uridine isomerase) (rna pseudouridylat
           synthase) [Neisseria lactamica 020-06]
          Length = 307

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 61/125 (48%), Gaps = 6/125 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPIDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEAE-GVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKY 272
            D  Y
Sbjct: 262 NDALY 266


>gi|308189690|ref|YP_003922621.1| Pseudouridylate synthase [Mycoplasma fermentans JER]
 gi|307624432|gb|ADN68737.1| predicted Pseudouridylate synthase [Mycoplasma fermentans JER]
          Length = 280

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 46/173 (26%), Positives = 73/173 (42%), Gaps = 16/173 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  I + +KP  +SV   +  +   +  +LK +      KP    RLD+ TSG+++
Sbjct: 85  IIYEDDNILIVSKPINLSVHSENNCLDKQVLSYLK-YNQKDSFKPSHVGRLDKATSGLMI 143

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+  A    L  +++    +KIY      +  + KE      +   H    Y  VV  N
Sbjct: 144 YAKNYATLVEL--NYKTSFFEKIY-----KLKSDFKEAKKLVEINIQHDEKLYKMVVTNN 196

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            K              F  K   +     TG+ HQ+R+   H+  PI GD KY
Sbjct: 197 TKDP-------LAKTLFYTKNNKIFASILTGKKHQIRLSMAHLKTPIYGDIKY 242


>gi|262370362|ref|ZP_06063688.1| RNA pseudouridine synthase [Acinetobacter johnsonii SH046]
 gi|262314704|gb|EEY95745.1| RNA pseudouridine synthase [Acinetobacter johnsonii SH046]
          Length = 304

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/193 (24%), Positives = 89/193 (46%), Gaps = 20/193 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+    V +KP  +++   G  +   +   LK     +   P   HRLD+ET+G+++
Sbjct: 97  ILFENDHFLVVDKPHFLTISPTGQYVQQTLLVRLKKQTGIEHLTP--IHRLDRETAGLVM 154

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            ++   +     + F  R++QK Y ++    P N+ E     ++K     G+  + ++  
Sbjct: 155 FSKCIHSRGMYQQMFAERQVQKTYHAIA---PFNR-ELKFPRIVKLHMQKGEPFYTMQVL 210

Query: 220 EKGANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---- 273
           ++  N        I        W   E++P TG+ HQLRVH   +G PI  D  Y     
Sbjct: 211 DEAPNSETE----ILLLEHDETWAKYELKPETGKQHQLRVHLNFLGLPIKNDPFYPKVVH 266

Query: 274 -ANFKGNFTSPIQ 285
            A++  +F+ P+Q
Sbjct: 267 KADY--DFSQPLQ 277


>gi|325127991|gb|EGC50890.1| RNA pseudouridine synthase [Neisseria meningitidis N1568]
          Length = 307

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 32/128 (25%), Positives = 62/128 (48%), Gaps = 12/128 (9%)

Query: 148 HRLDQETSGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           HRLD++T+G+++++    TR A Q + ++       K  W     +   + +      + 
Sbjct: 148 HRLDKDTAGVMLLSHNPDTRGAYQTMFQN-------KTVWKTYEALAPTRTDLPYPLDVV 200

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G 
Sbjct: 201 SRLVRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGM 258

Query: 265 PIVGDHKY 272
           P++ D  Y
Sbjct: 259 PLLNDALY 266


>gi|289675117|ref|ZP_06496007.1| pseudouridine synthase [Pseudomonas syringae pv. syringae FF5]
          Length = 265

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 50/178 (28%), Positives = 80/178 (44%), Gaps = 19/178 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 58  ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGN-PDLVPLHRIDRHTAGLV 114

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  RRI K Y ++   +P+     +    L +S +       
Sbjct: 115 LFSANRQTRSAYQTL---FPTRRIDKFYQAIAPALPE-----LTFPRLHESRLVEGEPFF 166

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 167 RMQEGVGASNTRTQIEVLE--RQDKLWRYGLYPVTGKKHQLRVHMAALGAAICNDPFY 222


>gi|167521497|ref|XP_001745087.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163776701|gb|EDQ90320.1| predicted protein [Monosiga brevicollis MX1]
          Length = 401

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 78/180 (43%), Gaps = 11/180 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++ E   +   +KPA I V       ++ +   L    D     P   HRLD+ TSG+L+
Sbjct: 114 IVGETPDLLAIDKPASIPVHPCGRYRHNTVQAILGHEHDRWRVYP--CHRLDRLTSGLLI 171

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
             +  A A+   +     +++K Y   V G + ++   C A   +    +G   VH    
Sbjct: 172 FCKNPAMAKQFEQWITQHQVEKQYICRVQGRVEQSVLFCDAPLKICDQRLGLCCVH---- 227

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  +++ F+VI    +    L   P TGR HQ+RVH  ++G PIV D  Y +   G
Sbjct: 228 --PEGKASLTRFRVIR-RDKDTTVLHCFPKTGRMHQIRVHVQYLGHPIVNDPVYNSELWG 284


>gi|118464649|ref|YP_883417.1| RNA pseudouridine synthase family protein [Mycobacterium avium 104]
 gi|118165936|gb|ABK66833.1| RNA pseudouridine synthase family protein [Mycobacterium avium 104]
          Length = 287

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 50/234 (21%), Positives = 93/234 (39%), Gaps = 36/234 (15%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSIL-------LYEDSKIYVFNKPAGISVQG- 121
           V+ A   ++ E  +L +  ++  + +    ++       L+ D  I V +KP  ++    
Sbjct: 42  VVTADGAVVDEATVLPAGASVYLYRELPDEVVVPFDLPVLHRDDDIVVVDKPHFLATMPR 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G  +A      L+  +      P   HRLD+ T+G+L+    R         F    + K
Sbjct: 102 GRHVAQTALVRLRRELGLPELSP--AHRLDRLTAGVLLFTARREVRGAYQTLFSRGLVDK 159

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-------EKGANYAISHFKVID 234
            Y +         +  +   L+    + G    +VK         E G   A++  +++ 
Sbjct: 160 TYLA---------RAAVDPALVFPRVLAG---RIVKHRGRMQAVCEPGPPNALTEVELL- 206

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQ 285
                     ++P TGRTHQLR+    +G PI+GD  Y         +F++P+Q
Sbjct: 207 ---SPDGLYRLRPRTGRTHQLRLQMASLGIPIIGDPLYPNMIDVPADDFSTPLQ 257


>gi|322493543|emb|CBZ28831.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 453

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 36/75 (48%), Gaps = 11/75 (14%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-----------NKLYLHAR 293
           + PHTGR HQLRVH   +G PIVGD  YC +       P+             ++YLHA 
Sbjct: 326 LAPHTGRRHQLRVHCRAIGFPIVGDTLYCTDLPWCAALPLGPPTSTWVTAGVRRMYLHAW 385

Query: 294 YMDLPHPEGGRLQIT 308
            + LP     RL  T
Sbjct: 386 RLLLPGTVTPRLGET 400



 Score = 37.4 bits (85), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 26/42 (61%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           H+LD  TSG+L +A T+  A  L   F MR I+K Y +L+ G
Sbjct: 58  HQLDLGTSGVLCLAFTKDMAARLAHCFEMRTIRKYYVALLHG 99


>gi|58580625|ref|YP_199641.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84622566|ref|YP_449938.1| putative pseudouridylate synthase [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
 gi|58425219|gb|AAW74256.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84366506|dbj|BAE67664.1| putative pseudouridylate synthase [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
          Length = 206

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 39/128 (30%), Positives = 60/128 (46%), Gaps = 12/128 (9%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-ANWLLKKS 206
           HR+D+ET+G+++ +   A        FR RRI+K Y  +   +P+     +  +WL    
Sbjct: 85  HRIDRETAGLVLFSANPATRGIYQALFRERRIRKQYLVVAPPLPELSFPYVHRSWLEP-- 142

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWL-EMQPHTGRTHQLRVHALHMGC 264
              G+    +++     N       VID  A     W   ++P TGR HQLRVH   +G 
Sbjct: 143 ---GEPFFRMREGVGEPNSE----TVIDVVAPGADTWTYRLEPVTGRKHQLRVHMAALGA 195

Query: 265 PIVGDHKY 272
           PI+ D  Y
Sbjct: 196 PILHDRFY 203


>gi|17534965|ref|NP_493778.1| hypothetical protein K07E8.7 [Caenorhabditis elegans]
 gi|3915497|sp|O16686|YK27_CAEEL RecName: Full=Uncharacterized protein K07E8.7
 gi|2315726|gb|AAB66153.1| Hypothetical protein K07E8.7 [Caenorhabditis elegans]
          Length = 432

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 47/174 (27%), Positives = 78/174 (44%), Gaps = 11/174 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++ E   ++V  KP  + V      A H + G L+  V+      R+ HRLD+ TSG+L+
Sbjct: 150 VISETDDLFVVEKPPSLPVHTCGQYAIHTVLGQLR--VNEGRTGLRVLHRLDRATSGVLL 207

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            A+          + +     K Y   V G+ P  ++ C          +G   +  V+ 
Sbjct: 208 FAKNYETDLEFKTTLKQGEWSKEYICKVDGVFPDEEQVCEQPIGPLVISMG---IQCVRP 264

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + K A    S F+ +     +   +++   TGRTHQ+RVH+  +G PI GD  Y
Sbjct: 265 DGKDAK---SRFRKLWSDGTQSV-VQVHIETGRTHQIRVHSQFLGHPIAGDQIY 314


>gi|163751188|ref|ZP_02158417.1| YabO/YceC/SfhB family protein [Shewanella benthica KT99]
 gi|161329017|gb|EDQ00090.1| YabO/YceC/SfhB family protein [Shewanella benthica KT99]
          Length = 308

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 37/133 (27%), Positives = 58/133 (43%), Gaps = 9/133 (6%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIA 199
            HRLD+ T+GI+++           + F+  +I K Y +L    P+        +     
Sbjct: 133 AHRLDRATAGIVLMILNPETRTQYHDLFKNHQITKEYQALAKLTPELLASHQVGELALPL 192

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            W +K   + G+    +K  E  +N   S   +ID         ++ P TGRTHQLRVH 
Sbjct: 193 QWTVKNRMVKGEPSFTMKVVEGESNTH-SEISLID-IKDDVGLFKLSPITGRTHQLRVHM 250

Query: 260 LHMGCPIVGDHKY 272
             +G  I+ D  Y
Sbjct: 251 QSLGMSIINDRCY 263


>gi|149247844|ref|XP_001528310.1| hypothetical protein LELG_00830 [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|146448264|gb|EDK42652.1| hypothetical protein LELG_00830 [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 430

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 47/190 (24%), Positives = 81/190 (42%), Gaps = 37/190 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG--------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +++ED  I V +KP+GI V           S I   +  F   W           HRLD+
Sbjct: 109 VVFEDDDIIVIDKPSGIPVHPTGSYMFNSLSEIVKEMFNFDNIWT---------CHRLDK 159

Query: 153 ETSGILVVARTRAAAQHLTESF--RMRRIQKIYWSLVWG-IPKN--KKECI-----ANWL 202
            TSG++++ + R AA         +  +++KIY + V G  P    +  C       N  
Sbjct: 160 VTSGVVILCKNRDAAVKFLNILLEKSDKVKKIYLARVNGKFPDGVYRYTCPILAVNMNGY 219

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           ++ S++           E+    ++S+  ++ C          QP +G+ HQ+R+H  ++
Sbjct: 220 IQPSNLESLLTLTSTIFERVNFDSLSNTSIVRC----------QPISGKFHQIRIHLRNL 269

Query: 263 GCPIVGDHKY 272
           G PI  D  Y
Sbjct: 270 GFPISNDLFY 279


>gi|257453802|ref|ZP_05619080.1| YabO/YceC/SfhB family protein [Enhydrobacter aerosaccus SK60]
 gi|257448729|gb|EEV23694.1| YabO/YceC/SfhB family protein [Enhydrobacter aerosaccus SK60]
          Length = 285

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 57/277 (20%), Positives = 117/277 (42%), Gaps = 35/277 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL  +   H+ HI+  + Q+   SG + +++ + +K ++   +GQ +            +
Sbjct: 4   RLIDYLAAHFSHISLASWQRRFDSGLISLERGEPLKQDSPYLAGQTI-------LYYRQV 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWV 137
           + + I+    N+           L+ D  + V +KP  + V   G  ++  +   L++  
Sbjct: 57  ENEPIIPFEPNI-----------LHLDGHLLVVDKPHFLPVTPSGRYVSQTLLAKLRNHP 105

Query: 138 DSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           D +          HRLD++T+G+++++   ++       F  R I K Y ++    P   
Sbjct: 106 DLQQLAVNDISPLHRLDKDTAGVMLLSVNPSSRACYHALFADRHIHKTYHAIA---PTRS 162

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             C    +  +   G  +   + +  +G   A +  ++I+     F    + P TG+ HQ
Sbjct: 163 DLCYPFHIHSRLERGEPFF--LTKTTQGEPNAHTTIELIENNG-AFSLYRLTPVTGKKHQ 219

Query: 255 LRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQ 285
           LRVH   +G P++ D+ Y            +FT P+Q
Sbjct: 220 LRVHMASLGMPLLHDNFYPTVKTVKPQCSSDFTKPLQ 256


>gi|38233570|ref|NP_939337.1| putative RNA pseudouridylate synthase family protein
           [Corynebacterium diphtheriae NCTC 13129]
 gi|38199830|emb|CAE49493.1| Putative RNA pseudouridylate synthase family protein
           [Corynebacterium diphtheriae]
          Length = 243

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 50/164 (30%), Positives = 71/164 (43%), Gaps = 34/164 (20%)

Query: 148 HRLDQETSGILVVA---RTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLL 203
           HRLD+ T+GIL+ +    TRA  Q L   F+ R I K Y + V G IP   +       +
Sbjct: 92  HRLDRLTTGILLCSTNPETRATYQQL---FQHRAITKRYIAHVAGPIPFGPQWTEIALGM 148

Query: 204 KK-------SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           +K          G      V++ E+G                    +E+QP TG THQLR
Sbjct: 149 RKMGPRVVVDPTGTLTRTRVRRLEEGV-------------------VELQPATGHTHQLR 189

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           V    +GCPI+GD  Y  + +         KL L+A  ++   P
Sbjct: 190 VLLAWVGCPIIGDDTYPVDRRRRIYD-FSKKLELYATSLEFVDP 232


>gi|320324274|gb|EFW80353.1| pseudouridine synthase [Pseudomonas syringae pv. glycinea str.
           B076]
 gi|320328603|gb|EFW84605.1| pseudouridine synthase [Pseudomonas syringae pv. glycinea str. race
           4]
          Length = 324

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 91/210 (43%), Gaps = 20/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 117 ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 173

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  R+I K Y ++   +P      +    L +S +       
Sbjct: 174 LFSANRQTRSAYQAL---FPTRQIDKFYEAIAPALPG-----LEFPRLHESRLVEGEPFF 225

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y  
Sbjct: 226 RMQEGAGASNTRTQIEVLE--RQDQLWRYGLYPVTGKKHQLRVHMAALGAGICNDPFYPD 283

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             K N     QN L L A+ +    P  G+
Sbjct: 284 VVK-NPVDDYQNPLKLLAKGLRFIDPLSGK 312


>gi|71737653|ref|YP_274327.1| RNA pseudouridine synthase family protein [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71558206|gb|AAZ37417.1| RNA pseudouridine synthase family protein [Pseudomonas syringae pv.
           phaseolicola 1448A]
          Length = 296

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 91/210 (43%), Gaps = 20/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 145

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  R+I K Y ++   +P      +    L +S +       
Sbjct: 146 LFSANRQTRSAYQAL---FPTRQIDKFYEAIAPALPG-----LEFPRLHESRLVEGEPFF 197

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y  
Sbjct: 198 RMQEGAGASNTRTQIEVLE--RQDQLWRYGLYPVTGKKHQLRVHMAALGAGICNDPFYPD 255

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             K N     QN L L A+ +    P  G+
Sbjct: 256 VVK-NPVDDYQNPLKLLAKGLRFIDPLSGK 284


>gi|54022716|ref|YP_116958.1| putative RNA pseudouridylate synthase [Nocardia farcinica IFM
           10152]
 gi|54014224|dbj|BAD55594.1| putative RNA pseudouridylate synthase [Nocardia farcinica IFM
           10152]
          Length = 309

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 38/143 (26%), Positives = 63/143 (44%), Gaps = 11/143 (7%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKK 205
            HRLD+ T+G+++     A        F  R ++K Y ++    P+      + + ++K+
Sbjct: 138 AHRLDRVTAGLILFVVDPARRGAYQTMFHRRTVRKQYEAIAPFDPELALPRVVRSRIVKE 197

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            H+         + E  A   +   +  D   +      + PHTGRTHQLR+H   +G P
Sbjct: 198 KHV---LAAREVEGEPNAETLVELLEHRDGLGR----YRLTPHTGRTHQLRLHMNSLGVP 250

Query: 266 IVGDHKYCANFKG---NFTSPIQ 285
           I+GD  Y          FT P+Q
Sbjct: 251 ILGDDFYPVLTDKPVHEFTRPLQ 273


>gi|154486935|ref|ZP_02028342.1| hypothetical protein BIFADO_00768 [Bifidobacterium adolescentis
           L2-32]
 gi|154084798|gb|EDN83843.1| hypothetical protein BIFADO_00768 [Bifidobacterium adolescentis
           L2-32]
          Length = 241

 Score = 50.1 bits (118), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 49/203 (24%), Positives = 84/203 (41%), Gaps = 21/203 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +LYED +I V +KP  ++     G+ Y     ++  +  +  +P +   HRLD+ T+G++
Sbjct: 13  VLYEDERIIVIDKPHFLATTP-RGMWYRETALIR--LRERCGEPDIVPAHRLDRPTAGVV 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----ECIAN----WLLKKSHIG 209
           V  R  A        F+     K Y  +    P  +      E +        +++S I 
Sbjct: 70  VFVRDPAVRGAYQMLFQNHMAVKTYECMAPLAPPQRPRYGTVEQVDRHRPFPTVRRSRIN 129

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCF----AQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            D   +          A +  +  D       + F    + P TG+THQLRVH   +G P
Sbjct: 130 KDRGRLQAYESADMPNAETLIERGDDVWHIDGKPFVNYTLHPRTGKTHQLRVHMNSLGLP 189

Query: 266 IVGDHKY---CANFKGNFTSPIQ 285
           I+GD  Y         +F+ P++
Sbjct: 190 ILGDDFYPDIVQRAYDDFSQPLE 212


>gi|260554620|ref|ZP_05826841.1| pseudouridylate synthase [Acinetobacter baumannii ATCC 19606]
 gi|260411162|gb|EEX04459.1| pseudouridylate synthase [Acinetobacter baumannii ATCC 19606]
          Length = 302

 Score = 50.1 bits (118), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 49/194 (25%), Positives = 88/194 (45%), Gaps = 21/194 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V +KP  +++   G  +   +   LK    ++   P   HRLD+ET+G+++
Sbjct: 94  ILFENDDLLVVDKPHFLTISPTGQYVQETLLVRLKKQTGNEFLTP--IHRLDRETAGVVL 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLV-----WGIPKNKKECIANWLLKKSHIGGDYVH 214
             +   +     + F  R++ KIY ++         P+N K     +L K +      + 
Sbjct: 152 FCKRPQSRGIYQQLFADRQVNKIYHAIAAYKAELKFPQNLKL----YLDKGTPFYT--MQ 205

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+   +      I   +    +A K+C   + P TG+ HQLRVH  H+G PI  D  Y  
Sbjct: 206 VITHTKTNTETKIELIEHNHSWA-KYC---LTPTTGKQHQLRVHLNHLGIPIKNDPFYPI 261

Query: 275 ---NFKGNFTSPIQ 285
                  +F+ P+Q
Sbjct: 262 VQHKADDDFSQPLQ 275


>gi|257486202|ref|ZP_05640243.1| RNA pseudouridine synthase family protein [Pseudomonas syringae pv.
           tabaci ATCC 11528]
 gi|330989270|gb|EGH87373.1| pseudouridine synthase [Pseudomonas syringae pv. lachrymans str.
           M301315]
 gi|331010530|gb|EGH90586.1| pseudouridine synthase [Pseudomonas syringae pv. tabaci ATCC 11528]
          Length = 324

 Score = 50.1 bits (118), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 91/210 (43%), Gaps = 20/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 117 ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 173

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  R+I K Y ++   +P      +    L +S +       
Sbjct: 174 LFSANRQTRSAYQAL---FPTRQIDKFYEAIAPALPG-----LEFPRLHESRLVEGEPFF 225

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y  
Sbjct: 226 RMQEGAGASNTRTQIEVLE--RQDQLWRYGLYPVTGKKHQLRVHMAALGAGICNDPFYPD 283

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             K N     QN L L A+ +    P  G+
Sbjct: 284 VVK-NPVDDYQNPLKLLAKGLRFIDPLNGK 312


>gi|330898112|gb|EGH29531.1| pseudouridine synthase [Pseudomonas syringae pv. japonica str.
           M301072PT]
          Length = 296

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/178 (28%), Positives = 80/178 (44%), Gaps = 19/178 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 145

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  RRI K Y ++   +P+     +    L +S +       
Sbjct: 146 LFSANRQTRSAYQTL---FPTRRIDKFYQAIAPALPE-----LTFPRLHESRLVEGEPFF 197

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 198 RMQEGVGASNTRTQIEVLE--RQDKLWRYGLYPVTGKKHQLRVHMAALGAAICNDPFY 253


>gi|171059970|ref|YP_001792319.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170777415|gb|ACB35554.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
          Length = 258

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 54/208 (25%), Positives = 86/208 (41%), Gaps = 7/208 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILV 159
           +L+ D  +   +KPA   V      A      +++  D   GQ     HRLD+ T G+L+
Sbjct: 6   VLWRDEHLIAIHKPARWLVHRTGLDAGETRFIVQTLRDQLGGQHVYPAHRLDKGTCGVLL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A    AA+ L  SF    ++K Y +LV G      E   +  L+      D        
Sbjct: 66  LALHPEAARGLAMSFARHEVKKRYLALVRGW--MPAEVEVDHPLRPDDTPPDSPAQSAHT 123

Query: 220 EKGANYAISHFKVIDC--FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                 A+   +  D      +   +E +P TGR HQ+R H  H+  PI+GD  +     
Sbjct: 124 RLRRLAALDWPEAADPGFTTTRASLVEARPTTGRRHQIRRHLKHIAHPILGDATHGKGPL 183

Query: 278 GNFTSPIQN--KLYLHARYMDLPHPEGG 303
             + +      +L+LHA  + + HP  G
Sbjct: 184 NRWWAERLGLQRLWLHAWRLQIAHPITG 211


>gi|302840927|ref|XP_002952009.1| pseudouridine synthase [Volvox carteri f. nagariensis]
 gi|300262595|gb|EFJ46800.1| pseudouridine synthase [Volvox carteri f. nagariensis]
          Length = 367

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 62/247 (25%), Positives = 98/247 (39%), Gaps = 34/247 (13%)

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFN 112
           ++ +RI  GQV      +   +H+++   ++  +    +       + +LYED  +    
Sbjct: 50  EWTSRIVGGQVAINGSTVLEPDHVLRVGDVVSYTRRPWREPPSPSYVDVLYEDDDVVALC 109

Query: 113 KPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--------THRLDQETSGILVVARTR 164
           KPAG+ V   +    H    L       G  P           HRL + TSG+L+ ART 
Sbjct: 110 KPAGLQVLPAA--MLHQRTVLTLLQHHYGNPPGTRACVAVAPVHRLGRGTSGLLLCARTT 167

Query: 165 AAAQHLTESFRMRRIQK----------------IYWSLVWGIPKNKKECIANWLLKKSHI 208
            A Q LTE    +                    IY SLV GI    +  +   +    + 
Sbjct: 168 HARQRLTELMSGKTAAAAAAAAAATAGTEARGLIYRSLVQGIVAEDEGRVDVPIGPVQYP 227

Query: 209 GGDYVHVVKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           G D    +     G   A S ++V++      +    +E+   TGR HQ+R+H   MG P
Sbjct: 228 GVD--GGLFAATPGGKPAASIWRVLERRPGGGRSRQAVEIL--TGRPHQIRIHMAAMGHP 283

Query: 266 IVGDHKY 272
           +VGD  Y
Sbjct: 284 LVGDPLY 290


>gi|269214112|ref|ZP_06158361.1| RNA pseudouridine synthase [Neisseria cinerea ATCC 14685]
 gi|269144501|gb|EEZ70919.1| RNA pseudouridine synthase [Neisseria cinerea ATCC 14685]
          Length = 169

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 61/125 (48%), Gaps = 6/125 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 10  HRLDKDTAGVMLLSHNPATRGTYQTMFQNKTVWKTYEALA----PTRTDLPYPIDVVSRL 65

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E   N A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 66  VRGEKFFTTQEAEGEPN-AHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 123

Query: 268 GDHKY 272
            D  Y
Sbjct: 124 NDALY 128


>gi|330945840|gb|EGH47230.1| pseudouridine synthase [Pseudomonas syringae pv. pisi str. 1704B]
          Length = 264

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/178 (28%), Positives = 80/178 (44%), Gaps = 19/178 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 78  ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGN-PDLVPLHRIDRHTAGLV 134

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  RRI K Y ++   +P+     +    L +S +       
Sbjct: 135 LFSANRQTRSAYQTL---FPTRRIDKFYQAIAPALPE-----LTFPRLHESRLVEGEPFF 186

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 187 RMQEGVGASNTRTQIEVLE--RQDKLWRYGLYPVTGKKHQLRVHMAALGAAICNDPFY 242


>gi|330882959|gb|EGH17108.1| pseudouridine synthase [Pseudomonas syringae pv. glycinea str. race
           4]
          Length = 328

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 91/210 (43%), Gaps = 20/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 121 ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 177

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  R+I K Y ++   +P      +    L +S +       
Sbjct: 178 LFSANRQTRSAYQAL---FPTRQIDKFYEAIAPALPG-----LEFPRLHESRLVEGEPFF 229

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y  
Sbjct: 230 RMQEGAGASNTRTQIEVLE--RQDQLWRYGLYPVTGKKHQLRVHMAALGAGICNDPFYPD 287

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             K N     QN L L A+ +    P  G+
Sbjct: 288 VVK-NPVDDYQNPLKLLAKGLRFIDPLSGK 316


>gi|121634642|ref|YP_974887.1| hypothetical protein NMC0808 [Neisseria meningitidis FAM18]
 gi|120866348|emb|CAM10091.1| hypothetical protein NMC0808 [Neisseria meningitidis FAM18]
          Length = 307

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 37/160 (23%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAL----TRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEVE-GVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            D  Y    +   +   +  L L A+ +    P  GR ++
Sbjct: 262 NDALYPVLSEAG-SEDYRKPLKLLAKKIAFADPLSGRERV 300


>gi|41409520|ref|NP_962356.1| hypothetical protein MAP3422c [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41398351|gb|AAS05972.1| hypothetical protein MAP_3422c [Mycobacterium avium subsp.
           paratuberculosis K-10]
          Length = 290

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 54/264 (20%), Positives = 103/264 (39%), Gaps = 51/264 (19%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSIL-------LYEDSKIYVFNKPAGISVQG- 121
           V+ A   ++ E  +L +  ++  + +    ++       L+ D  I V +KP  ++    
Sbjct: 45  VVTADGAVVDEATVLPAGASVYLYRELPDEVVVPFDLPVLHRDDDIVVVDKPHFLATMPR 104

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G  +A      L+  +      P   HRLD+ T+G+L+    R         F    + K
Sbjct: 105 GRHVAQTALVRLRRELGLPELSP--AHRLDRLTAGVLLFTARREVRGAYQTLFSRGLVDK 162

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-------EKGANYAISHFKVID 234
            Y +         +  +   L+    + G    +VK         E G   A++  +++ 
Sbjct: 163 TYLA---------RAAVDPALVFPRVLAG---RIVKHRGRMQAVCEPGPPNALTEVELL- 209

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQ------ 285
                     ++P TGRTHQLR+    +G PI+GD  Y         +F++P+Q      
Sbjct: 210 ---SPDGLYRLRPRTGRTHQLRLQMASLGIPIIGDPLYPNIIDVPADDFSTPLQLLAQRI 266

Query: 286 ---------NKLYLHARYMDLPHP 300
                     +++++ R +D P P
Sbjct: 267 EFDDPRTGARRVFVNRRTLDDPGP 290


>gi|193077696|gb|ABO12544.2| putative pseudouridylate synthase [Acinetobacter baumannii ATCC
           17978]
          Length = 302

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 49/194 (25%), Positives = 88/194 (45%), Gaps = 21/194 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V +KP  +++   G  +   +   LK    ++   P   HRLD+ET+G+++
Sbjct: 94  ILFENDDLLVVDKPHFLTISPTGQYVQETLLVRLKKQTGNEFLTP--IHRLDRETAGVVL 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLV-----WGIPKNKKECIANWLLKKSHIGGDYVH 214
             +   +     + F  R++ KIY ++         P+N K     +L K +      + 
Sbjct: 152 FCKRPQSRGIYQQLFADRQVNKIYHAIAAYKAELKFPQNLKL----YLDKGTPFYT--MQ 205

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+   +      I   +    +A K+C   + P TG+ HQLRVH  H+G PI  D  Y  
Sbjct: 206 VIAHTKTNTETKIELIEHNHSWA-KYC---LTPTTGKQHQLRVHLNHLGIPIKNDPFYPI 261

Query: 275 ---NFKGNFTSPIQ 285
                  +F+ P+Q
Sbjct: 262 VQHKADDDFSQPLQ 275


>gi|184158634|ref|YP_001846973.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|332874330|ref|ZP_08442242.1| pseudouridine synthase, RluA family [Acinetobacter baumannii
           6014059]
 gi|183210228|gb|ACC57626.1| Pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|322507602|gb|ADX03056.1| Pseudouridine synthase [Acinetobacter baumannii 1656-2]
 gi|323518552|gb|ADX92933.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332737458|gb|EGJ68373.1| pseudouridine synthase, RluA family [Acinetobacter baumannii
           6014059]
          Length = 302

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 49/194 (25%), Positives = 88/194 (45%), Gaps = 21/194 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V +KP  +++   G  +   +   LK    ++   P   HRLD+ET+G+++
Sbjct: 94  ILFENDDLLVVDKPHFLTISPTGQYVQETLLVRLKKQTGNEFLTP--IHRLDRETAGVVL 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLV-----WGIPKNKKECIANWLLKKSHIGGDYVH 214
             +   +     + F  R++ KIY ++         P+N K     +L K +      + 
Sbjct: 152 FCKRPQSRGIYQQLFADRQVNKIYHAIAAYKAELKFPQNLKL----YLDKGTPFYT--MQ 205

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+   +      I   +    +A K+C   + P TG+ HQLRVH  H+G PI  D  Y  
Sbjct: 206 VIAHTKTNTETKIELIEHNHSWA-KYC---LTPTTGKQHQLRVHLNHLGIPIKNDPFYPI 261

Query: 275 ---NFKGNFTSPIQ 285
                  +F+ P+Q
Sbjct: 262 VQHKADDDFSQPLQ 275


>gi|317124662|ref|YP_004098774.1| pseudouridine synthase [Intrasporangium calvum DSM 43043]
 gi|315588750|gb|ADU48047.1| pseudouridine synthase [Intrasporangium calvum DSM 43043]
          Length = 321

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 47/195 (24%), Positives = 84/195 (43%), Gaps = 23/195 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D ++ V +KP  +S     G         ++ V +   +    HRLD+ T+G+L+ 
Sbjct: 96  VLHRDERLVVIDKPHFLSTMP-RGRHVVQSALARTRVLTGLDRLTPAHRLDRPTAGVLMF 154

Query: 161 A---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI----GGDYV 213
               R R A Q +   F   R+ K Y ++        ++ +   L++++H+    G    
Sbjct: 155 TTEQRWRGAYQRV---FAEGRVHKEYLAVA-----PVRDGLGLPLVRRTHLVKEHGSHQA 206

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V   E  A   +     ++  +       + P TGRTHQLR     +G PI+GD  Y 
Sbjct: 207 REVHGREPNAETLVE----LEVESGGVGGYRLTPRTGRTHQLRCQLCGLGIPIIGDPLYP 262

Query: 274 ANFK---GNFTSPIQ 285
              +    +F+ P+Q
Sbjct: 263 VEREVADDDFSEPLQ 277


>gi|325122666|gb|ADY82189.1| putative pseudouridylate synthase [Acinetobacter calcoaceticus
           PHEA-2]
          Length = 292

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/194 (25%), Positives = 85/194 (43%), Gaps = 21/194 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V +KP  +++   G  +   +   LK    ++   P   HRLD+ET+G+++
Sbjct: 84  ILFENDDLLVVDKPHFLTISPTGQYVQETLLVRLKKQTGNEFLTP--IHRLDRETAGVVL 141

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL---LKKSH--IGGDYVH 214
             +   +     + F  R++ KIY ++    P  K       L   L K H       + 
Sbjct: 142 FCKRVESRGIYQQLFAERQVNKIYHAIA---PYKKDLNFPQTLHLHLDKGHPFYTMQVIE 198

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            VK N + A   I H        Q +    + P TG+ HQLRVH  ++  PI  D  Y  
Sbjct: 199 NVKANTQTAIELIEH-------NQIWAKYRLTPTTGKQHQLRVHLNYLEIPIKNDPFYPV 251

Query: 275 ---NFKGNFTSPIQ 285
                + +F+ P+Q
Sbjct: 252 VQHKAEDDFSEPLQ 265


>gi|183221495|ref|YP_001839491.1| putative RNA pseudouridine synthase [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
 gi|167779917|gb|ABZ98215.1| Putative RNA pseudouridine synthase (RNA-uridine isomerase; RNA
           pseudouridylate synthase) [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
          Length = 231

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 53/198 (26%), Positives = 88/198 (44%), Gaps = 27/198 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           + YE     +  KP GI V      +  +D      + +  Q P  R  +RLD  TSGI+
Sbjct: 18  IFYECDDFLLAEKPEGIPVHETKDPS-RMD--FTRLLSNHLQIPELRTVNRLDLGTSGIV 74

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP---KNKKECIANWLLKKSHIGGDYVHV 215
           ++ + +     L     ++  +K Y  L  GIP   +++ EC     LK+   G   V++
Sbjct: 75  LLGKNKNKNVEL--DLLLKEAEKTYIFLCDGIPSWREHRMEC----FLKE---GNKQVNL 125

Query: 216 VKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+    G   AI+ F ++     +   +   +  TGR HQ+RV    +G PI+GD  Y  
Sbjct: 126 VRS---GGKKAITEFSILHSDPNESISFGFAKILTGRRHQIRVMLSSLGFPILGDTVYGK 182

Query: 275 NFKGNFTSPIQNKLYLHA 292
             K       + ++YLH+
Sbjct: 183 KEK------TETRMYLHS 194


>gi|325206298|gb|ADZ01751.1| RNA pseudouridine synthase [Neisseria meningitidis M04-240196]
          Length = 307

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 61/125 (48%), Gaps = 6/125 (4%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G+++++   A        F+ + + K Y +L       + +      +    
Sbjct: 148 HRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAL----TRTDLPYPLDVVSRL 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + G+     ++ E G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P++
Sbjct: 204 VRGEKFFTTQEVE-GVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPLL 261

Query: 268 GDHKY 272
            D  Y
Sbjct: 262 NDALY 266


>gi|227547691|ref|ZP_03977740.1| ribosomal pseudouridine synthase [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227080217|gb|EEI18180.1| ribosomal pseudouridine synthase [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 323

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 57/207 (27%), Positives = 87/207 (42%), Gaps = 21/207 (10%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +YED  I V +KP  ++    +  I       L+    ++   P   HRLD+ TSG+L++
Sbjct: 104 VYEDDTILVVDKPPFLATMPRAAHITESATVRLRRATGNEDLTP--AHRLDRMTSGLLLL 161

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL--LKKSHIGGDYVHVVKQ 218
            + +       E F   ++ K Y ++   I     E    W   + K H G     V++ 
Sbjct: 162 TKQKQHRSAYQELFAAHQVHKRYEAIAEDI---GIESPTWWRHHIDKQH-GEIASTVIEG 217

Query: 219 NEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            E  A   +     ID    +             ++P TGRTHQLRV     G PI+GD 
Sbjct: 218 REPNALTHVLEALRIDAPTMQSLHSVTFPLARYLLEPVTGRTHQLRVQMNEAGAPILGDP 277

Query: 271 KY-CANFKG--NFTSPIQNK-LYLHAR 293
            Y   N  G  +F  P++ K +YL  R
Sbjct: 278 VYPTVNPFGEEDFAVPMRLKSVYLGFR 304


>gi|169795560|ref|YP_001713353.1| putative pseudouridylate synthase [Acinetobacter baumannii AYE]
 gi|213158499|ref|YP_002319797.1| RNA pseudouridine synthase family protein [Acinetobacter baumannii
           AB0057]
 gi|215483047|ref|YP_002325252.1| RNA pseudouridylate synthase family protein [Acinetobacter
           baumannii AB307-0294]
 gi|239501495|ref|ZP_04660805.1| RNA pseudouridylate synthase family protein [Acinetobacter
           baumannii AB900]
 gi|301347863|ref|ZP_07228604.1| putative pseudouridylate synthase [Acinetobacter baumannii AB056]
 gi|301510578|ref|ZP_07235815.1| putative pseudouridylate synthase [Acinetobacter baumannii AB058]
 gi|301596370|ref|ZP_07241378.1| putative pseudouridylate synthase [Acinetobacter baumannii AB059]
 gi|332850622|ref|ZP_08432869.1| pseudouridine synthase, RluA family [Acinetobacter baumannii
           6013150]
 gi|332867097|ref|ZP_08437394.1| pseudouridine synthase, RluA family [Acinetobacter baumannii
           6013113]
 gi|169148487|emb|CAM86353.1| putative pseudouridylate synthase [Acinetobacter baumannii AYE]
 gi|213057659|gb|ACJ42561.1| RNA pseudouridine synthase family protein [Acinetobacter baumannii
           AB0057]
 gi|213989079|gb|ACJ59378.1| RNA pseudouridylate synthase family protein [Acinetobacter
           baumannii AB307-0294]
 gi|332730459|gb|EGJ61775.1| pseudouridine synthase, RluA family [Acinetobacter baumannii
           6013150]
 gi|332734290|gb|EGJ65419.1| pseudouridine synthase, RluA family [Acinetobacter baumannii
           6013113]
          Length = 302

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 50/196 (25%), Positives = 85/196 (43%), Gaps = 25/196 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V +KP  +++   G  +   +   LK    ++   P   HRLD+ET+G+++
Sbjct: 94  ILFENDDLLVVDKPHFLTISPTGQYVQETLLVRLKKQTGNEFLTP--IHRLDRETAGVVL 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             +   +     + F  R++ KIY +    I   K E      LK     G   + ++  
Sbjct: 152 FCKRPQSRGIYQQLFADRQVNKIYHA----IAPYKAELKFPQSLKLYLDKGTPFYTMQ-- 205

Query: 220 EKGANYAISHFKV-----IDCFAQKFCWLE--MQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                  I+H K      I+       W +  + P TG+ HQLRVH  H+G PI  D  Y
Sbjct: 206 ------VIAHTKTNTETKIELIEHNHSWAKYCLTPTTGKQHQLRVHLNHLGIPIKNDPFY 259

Query: 273 CA---NFKGNFTSPIQ 285
                    +F+ P+Q
Sbjct: 260 PIVQHKADDDFSQPLQ 275


>gi|296274039|ref|YP_003656670.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
 gi|296098213|gb|ADG94163.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
          Length = 249

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 45/200 (22%), Positives = 92/200 (46%), Gaps = 24/200 (12%)

Query: 78  IKEQKILDSSVNLTKHSDFL-KSI----LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           + ++K+L +  ++++++ F+ K +    ++++D  I   +KPA ++      ++     +
Sbjct: 32  VGDKKVLIARGDISENTKFIVKEVAPIKVIFQDDDILAVDKPAFLT---ADEVSRKFPNY 88

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L            L +RLD+ETSG+++ A+           F+   + K Y ++V G   
Sbjct: 89  L------------LLNRLDKETSGVMLFAKNEEFQTKAIREFKNNNVYKEYVAVVEGKVI 136

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           ++       L  K++ G     V  +  K A   +    V          +++   TGRT
Sbjct: 137 DEIVVDKPILTIKNNKGVARSKVDMKKGKSAKTTVYPMLV----EGNKSKIKVVIDTGRT 192

Query: 253 HQLRVHALHMGCPIVGDHKY 272
           HQ+RVH  ++  PI+GD+ Y
Sbjct: 193 HQIRVHLNYIDYPIIGDNVY 212


>gi|5420076|emb|CAB46588.1| hypothetical protein [Yersinia enterocolitica]
          Length = 125

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 44/88 (50%), Gaps = 2/88 (2%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+    G     ++D      V        L HRLD  TSG++V+A
Sbjct: 21  LYQDDHLVLINKPTGLLSLSGEN-PQNLDSVHHRLV-QIFPGCTLVHRLDFGTSGLMVIA 78

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           R +A    L + F  R + K+Y +L+ G
Sbjct: 79  RNKAINAALCQQFSQRTVTKVYSALLCG 106


>gi|320011705|gb|ADW06555.1| pseudouridine synthase [Streptomyces flavogriseus ATCC 33331]
          Length = 312

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 54/212 (25%), Positives = 96/212 (45%), Gaps = 25/212 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL- 158
           +++ D  + + +KP  ++    G  I   +   L+  +   G +P   HRLD+ T+G++ 
Sbjct: 100 VVHRDDHLVIADKPHFLATTPRGRHITETLVARLRDTLGLPGLQP--AHRLDRLTAGLVL 157

Query: 159 --VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHV 215
             V A  R A Q L   FR R ++K Y ++    P   +   + + ++K+  +      +
Sbjct: 158 CVVRAGDRGAYQTL---FRDRLVRKEYEAVAPYDPGLVRPRTVRSRIVKERGV------I 208

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
             + E G   + S  ++++          + P TGRTHQLRVH   +G P+V D  Y   
Sbjct: 209 AAREEPGPANSESRIELLE-HRGALGRYRLLPATGRTHQLRVHMNALGLPLVNDPVYPVV 267

Query: 275 ---NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                + +F  P+Q    L AR ++   P  G
Sbjct: 268 EPDPEREDFGRPLQ----LLARVLEFTDPVTG 295


>gi|120554606|ref|YP_958957.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120324455|gb|ABM18770.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
          Length = 267

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 38/128 (29%), Positives = 59/128 (46%), Gaps = 20/128 (15%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD + +G++++A    AA  L+E F  R + KIY + V G        +A+ L   
Sbjct: 124 LVHRLDADAAGLMLIAHDGKAAAALSELFAGRAMTKIYRARVAG------NLMADDLRLD 177

Query: 206 SHIGG-DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           + + G D +  V    +  +   +  +V             +  TGR HQ+R H   +G 
Sbjct: 178 TPLDGKDSISRVTTLSRDEDSDTTDVQV-------------RIETGRKHQIRRHLAGIGH 224

Query: 265 PIVGDHKY 272
           PIVGD  Y
Sbjct: 225 PIVGDRLY 232


>gi|325919058|ref|ZP_08181118.1| 23S RNA-specific pseudouridylate synthase [Xanthomonas gardneri
           ATCC 19865]
 gi|325550442|gb|EGD21236.1| 23S RNA-specific pseudouridylate synthase [Xanthomonas gardneri
           ATCC 19865]
          Length = 292

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 41/130 (31%), Positives = 64/130 (49%), Gaps = 16/130 (12%)

Query: 148 HRLDQETSGILVV---ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           HR+D++T+G+++    A TR   Q L   FR RRI+K Y ++   +P      + +  L+
Sbjct: 129 HRIDRDTAGLVLFSANAATRGIYQAL---FRERRIRKHYLAIAPPLPGLTFPYVHHSRLE 185

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWL-EMQPHTGRTHQLRVHALHM 262
                G+    +++     N       VID  A+    W   ++P TGR HQLRVH   +
Sbjct: 186 P----GEPFFRMREGVGEPNSE----TVIDVVARGADTWTYRLEPVTGRKHQLRVHMATL 237

Query: 263 GCPIVGDHKY 272
           G PI+ D  Y
Sbjct: 238 GAPILHDRFY 247


>gi|330977680|gb|EGH77583.1| pseudouridine synthase [Pseudomonas syringae pv. aptata str. DSM
           50252]
          Length = 296

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 50/178 (28%), Positives = 80/178 (44%), Gaps = 19/178 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 145

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  RRI K Y ++   +P+     +    L +S +       
Sbjct: 146 LFSANRQTRSAYQTL---FPTRRIDKFYQAIAPALPE-----LTFPRLHESRLVEGEPFF 197

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 198 RMQEGFGASNTRTQIEVLE--RQDKLWRYGLYPVTGKKHQLRVHMAALGAAICNDPFY 253


>gi|254776711|ref|ZP_05218227.1| RNA pseudouridine synthase family protein [Mycobacterium avium
           subsp. avium ATCC 25291]
          Length = 287

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 50/234 (21%), Positives = 93/234 (39%), Gaps = 36/234 (15%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSIL-------LYEDSKIYVFNKPAGISVQG- 121
           V+ A   ++ E  +L +  ++  + +    ++       L+ D  I V +KP  ++    
Sbjct: 42  VVTADGAVVDEATVLPAGASVYLYRELPDEVVVPFDLPVLHRDDDIVVVDKPHFLATMPR 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G  +A      L+  +      P   HRLD+ T+G+L+    R         F    + K
Sbjct: 102 GRHVAQTALVRLRRELGLPELSP--AHRLDRLTAGVLLFTAQREVRGAYQTLFSRGLVDK 159

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-------EKGANYAISHFKVID 234
            Y +         +  +   L+    + G    +VK         E G   A++  +++ 
Sbjct: 160 TYLA---------RAAVDPALVFPRVLAG---RIVKHRGRMQAVCEPGPPNALTEVELL- 206

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQ 285
                     ++P TGRTHQLR+    +G PI+GD  Y         +F++P+Q
Sbjct: 207 ---SPDGLYRLRPRTGRTHQLRLQMASLGIPIIGDPLYPNIIDVPADDFSTPLQ 257


>gi|42523804|ref|NP_969184.1| putative RNA pseudouridylate synthase [Bdellovibrio bacteriovorus
           HD100]
 gi|39576011|emb|CAE80177.1| putative RNA pseudouridylate synthase [Bdellovibrio bacteriovorus
           HD100]
          Length = 283

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 44/180 (24%), Positives = 78/180 (43%), Gaps = 12/180 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +S +++E+    V NK +G+ V      +  ++  +L+  +    Q   +THRLD  T G
Sbjct: 82  RSRIVFENEHFVVTNKISGLPVHASVDNLHENLQSYLQQTLH---QNVYVTHRLDVPTRG 138

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V A++        +    R + KIY + V G        ++  LL+           V
Sbjct: 139 LIVYAKSPEFQTEFNKLLIAREMNKIYRARVQG------HSLSTGLLQHYMEPSPRAPKV 192

Query: 217 KQNEKGANYAISHFKVIDC--FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              E    +     ++++      +   + ++ HTGRTHQ+R      G PIVGD  Y A
Sbjct: 193 VSKELQPKWQECLLEILEFSKLENEMSEVRIKLHTGRTHQIRAQLSAEGHPIVGDVAYGA 252


>gi|221067233|ref|ZP_03543338.1| pseudouridine synthase [Comamonas testosteroni KF-1]
 gi|220712256|gb|EED67624.1| pseudouridine synthase [Comamonas testosteroni KF-1]
          Length = 305

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 53/223 (23%), Positives = 93/223 (41%), Gaps = 35/223 (15%)

Query: 101 LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ D  + + +KP  + V   G  +   +   LK   D     P   HR+D++T+G++V
Sbjct: 94  VIHRDEHLLIADKPHFLPVVPAGQYLQNTLLVRLKREFDLPELSP--IHRIDRDTAGLVV 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            +  RA        FR R I K+Y            E +A +   ++ +     HV +  
Sbjct: 152 FSLQRATRGIYQGMFRDRAIHKVY------------EAVAPY---RAELSFPREHVSRME 196

Query: 220 EKGANYAISHFK-------VIDCFAQKFCWLE--MQPHTGRTHQLRVHALHMGCPIVGDH 270
           E G  + +           +++       W    + P +G+ HQLRVH   +G P+ GD 
Sbjct: 197 ESGHFFRMHEVAGEPNSRTLMEIIEHNNAWARYRLSPVSGKRHQLRVHMAALGLPLRGDA 256

Query: 271 KYCA---NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
            Y        G+++ P+Q    L AR +    P  G R + T+
Sbjct: 257 FYPVVDDPEPGDYSRPLQ----LLARSLAFDDPLTGQRREFTS 295


>gi|226307709|ref|YP_002767669.1| pseudouridine synthase [Rhodococcus erythropolis PR4]
 gi|226186826|dbj|BAH34930.1| putative pseudouridine synthase [Rhodococcus erythropolis PR4]
          Length = 360

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 98/219 (44%), Gaps = 25/219 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +L+ D  + V +KP  +     SG        ++  V  +   P LT  HRLD+ T+G++
Sbjct: 96  ILHLDDDLVVIDKPHFLPTTP-SGRYLRESALVRLRV--RLDNPDLTPIHRLDRGTAGVV 152

Query: 159 VVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWLLKKSHI----G 209
           + +    TR A Q L   F  R++ K+Y ++     +  ++  A    L+ ++HI    G
Sbjct: 153 MFSARPATRGAYQSL---FEKRQVTKVYEAVSARPSRWDQDAPALDVPLVYRNHIEARRG 209

Query: 210 GDYVHVVKQNEKGANYAI-SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              V V    E  +   I +    +    +      ++P +GR HQLRVH   +G  I+G
Sbjct: 210 ELRVVVDDSREPNSETTIEARGTGVSASGRAVLHTVLRPQSGRMHQLRVHLAALGAGILG 269

Query: 269 DHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           D +Y     +   + + P+Q    L AR ++   P  GR
Sbjct: 270 DRRYPDLLPDAPDDHSLPLQ----LLARELEFTDPLSGR 304


>gi|42522940|ref|NP_968320.1| putative pseudouridine synthase [Bdellovibrio bacteriovorus HD100]
 gi|39574136|emb|CAE79313.1| putative pseudouridine synthase [Bdellovibrio bacteriovorus HD100]
          Length = 225

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 90/218 (41%), Gaps = 25/218 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILV 159
           +++E++   + +KPAG+               L + +   KG +    +RLD E SG++V
Sbjct: 4   IVFENTHFIICDKPAGVLSTPSRFEEDDARLCLGTALQKEKGFQIFPVNRLDFEVSGLVV 63

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-----IPKNKKECIANWLLKKSHIGGDYVH 214
            A+T  A +     F  + ++K Y +L  G     IP N    + N  LK +   G+   
Sbjct: 64  YAKTAEAHRKANAWFEHKTVKKTYRALTTGQSYAHIPAN----VPNEKLKLTPEVGNTFE 119

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKF---------CWLEMQPHTGRTHQLRVHALHMGCP 265
              +  +G   A    +  +C               W ++ P TGR+HQLR      G P
Sbjct: 120 WRCRLLRGKRRAYESPQGKECLTVAVFRGMQGDYQVW-DLNPVTGRSHQLRFDLSRHGFP 178

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           IVGD  Y     G+      N++ L +  +D  +  G 
Sbjct: 179 IVGDKLY-----GSTVELADNRIALRSYRIDFANANGA 211


>gi|229817223|ref|ZP_04447505.1| hypothetical protein BIFANG_02483 [Bifidobacterium angulatum DSM
           20098]
 gi|229785012|gb|EEP21126.1| hypothetical protein BIFANG_02483 [Bifidobacterium angulatum DSM
           20098]
          Length = 264

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 88/226 (38%), Gaps = 25/226 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED +I V +KP  ++     G+ Y     ++             HRLD+ T+GI+V 
Sbjct: 22  VLYEDERIIVVDKPHFLATTP-RGMWYRETALIRLRQTYGEPDIIPAHRLDRLTAGIVVF 80

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKSHIGGD 211
            R RA+       F+     K Y  L          +G  +  +      L ++S I   
Sbjct: 81  VRDRASRGAYQLLFQNHLAVKTYECLAPLRPIGRPCFGTIRKLEPPRPFPLERRSRIVKQ 140

Query: 212 YVHVVKQNEKGANYAISHFKVI-----DCFAQKFCWLE---------MQPHTGRTHQLRV 257
              +    E G   A +  + +     D        ++         + P TG+THQLRV
Sbjct: 141 RGILQAYEEPGTPNAETLIERVGLGHMDRTGYPLSGMDGRHMVARYVLHPRTGKTHQLRV 200

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           H   +G PIVGD  Y    +  +     N L L AR ++   P  G
Sbjct: 201 HMNSLGLPIVGDDFYPRIIEHAYDD-FSNPLELVARELEFDDPLTG 245


>gi|66813276|ref|XP_640817.1| pseudouridine synthase family protein [Dictyostelium discoideum
           AX4]
 gi|60468845|gb|EAL66845.1| pseudouridine synthase family protein [Dictyostelium discoideum
           AX4]
          Length = 578

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 46/154 (29%), Positives = 69/154 (44%), Gaps = 19/154 (12%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPK----NKKECIANWL 202
           HRLD+ TSG+L++ART  +A       +   + K Y + V G  P     N      N  
Sbjct: 288 HRLDRLTSGLLLLARTPDSANKKANQIQSGLVSKQYLAKVIGKFPGSDTINSSSSSFNEQ 347

Query: 203 LK--KSHIGGDYV---HVVKQNEK--------GANYAISHFKVIDCFAQKFCWLEM-QPH 248
           +K  K    G ++    +V Q+ +        G   +I+H K+          + +  P 
Sbjct: 348 IKLCKHLEDGTFIIDQPIVIQSMRLGINHVGVGGKPSITHIKLFSYDQSTNTSIVLCTPK 407

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
           TGRTHQ+RVH   +G PI  D  Y   FK +F +
Sbjct: 408 TGRTHQIRVHLKWLGFPIANDPLYNNEFKESFKA 441


>gi|189911582|ref|YP_001963137.1| pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167776258|gb|ABZ94559.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
          Length = 222

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 53/198 (26%), Positives = 88/198 (44%), Gaps = 27/198 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           + YE     +  KP GI V      +  +D      + +  Q P  R  +RLD  TSGI+
Sbjct: 9   IFYECDDFLLAEKPEGIPVHETKDPS-RMD--FTRLLSNHLQIPELRTVNRLDLGTSGIV 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP---KNKKECIANWLLKKSHIGGDYVHV 215
           ++ + +     L     ++  +K Y  L  GIP   +++ EC     LK+   G   V++
Sbjct: 66  LLGKNKNKNVEL--DLLLKEAEKTYIFLCDGIPSWREHRMEC----FLKE---GNKQVNL 116

Query: 216 VKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V+    G   AI+ F ++     +   +   +  TGR HQ+RV    +G PI+GD  Y  
Sbjct: 117 VRS---GGKKAITEFSILHSDPNESISFGFAKILTGRRHQIRVMLSSLGFPILGDTVYGK 173

Query: 275 NFKGNFTSPIQNKLYLHA 292
             K       + ++YLH+
Sbjct: 174 KEK------TETRMYLHS 185


>gi|302187564|ref|ZP_07264237.1| pseudouridine synthase [Pseudomonas syringae pv. syringae 642]
          Length = 296

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 50/178 (28%), Positives = 79/178 (44%), Gaps = 19/178 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  + V +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 145

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  RRI K Y ++   +P      +    L +S +       
Sbjct: 146 LFSANRQTRSAYQAL---FPTRRIDKFYQAIAPALPG-----LTFPRLHESRLVEGEPFF 197

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 198 RMQEGAGASNTRTQIEVLE--RQDKLWRYGLYPVTGKKHQLRVHMAALGAAICNDPFY 253


>gi|299115647|emb|CBN75848.1| 23S RNA-specific pseudouridylate synthase [Ectocarpus siliculosus]
          Length = 245

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 46/193 (23%), Positives = 76/193 (39%), Gaps = 50/193 (25%)

Query: 158 LVVARTRAAAQHLTESFRMRR-IQKIYWSLVWG------------IPKNKKECIA----- 199
           + VART  AA  L+ SFR R  ++KIY ++V G            +  +    +A     
Sbjct: 1   MCVARTSKAAARLSASFRARDDVEKIYHAVVAGSLAGRGIRQDLLVSPDASGAVARRGRG 60

Query: 200 -----NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF----CWLEMQPHT- 249
                + +  +   GG  +     +      A   ++ I+  +       C     P T 
Sbjct: 61  PRAGLSSVPARGGAGGRLLAAGPTSSPDGKLAQLEWEAINVSSSSAVRLRCPRTGNPRTL 120

Query: 250 -------GRTHQLRVHALHMGCPIVGDHKYCANFKGNFT--------------SPIQNK- 287
                  GR HQ+RV    MG P+VGD +Y  +  G+ T               P++++ 
Sbjct: 121 VRVRLITGRKHQIRVQLAEMGHPVVGDTRYGRSRGGDATDESAVPPPRRAGRIEPLEDRS 180

Query: 288 LYLHARYMDLPHP 300
           + LHA  + +PHP
Sbjct: 181 ILLHASELIVPHP 193


>gi|329908268|ref|ZP_08274842.1| ribosomal large subunit pseudouridine synthase A-like protein
           [Oxalobacteraceae bacterium IMCC9480]
 gi|327546746|gb|EGF31689.1| ribosomal large subunit pseudouridine synthase A-like protein
           [Oxalobacteraceae bacterium IMCC9480]
          Length = 302

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 58/222 (26%), Positives = 94/222 (42%), Gaps = 40/222 (18%)

Query: 100 ILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++L+ D  + V +KP  + V   G  +   +   LK  +  + Q P   HR+D+ET+G++
Sbjct: 82  VVLFRDDTLLVVDKPHFLPVTPAGRYLQQTLLVRLKRKLGIETQAP--MHRIDRETAGLV 139

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL------LKKSHIG 209
           +      TRA  Q L   FR R + K Y            E IA WL      ++ S   
Sbjct: 140 LFTIQPATRAVYQGL---FRDRAVTKHY------------EAIAPWLPALQFPMQVSSRL 184

Query: 210 GDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            D  H +K  E  G   A +  ++++          + P TG+ HQLRV    +G PI  
Sbjct: 185 VDAEHFMKMREVDGEPNAETRIELLEV-QGNLARYALHPSTGQRHQLRVQMEALGIPIRH 243

Query: 269 DHKY-------CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           D  Y        +    +++ P+Q    L A+ ++   P  G
Sbjct: 244 DRIYPQLLPEAPSGMPPDYSKPLQ----LLAKSLEFTDPLSG 281


>gi|406952|gb|AAA03374.1| unknown [Mycoplasma genitalium]
          Length = 119

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 29/97 (29%), Positives = 49/97 (50%), Gaps = 8/97 (8%)

Query: 101 LLYEDSKIYVFNKPAGI--------SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +++ED  I V +KP GI        S+   S +     G+ +   +     P+  HR+D+
Sbjct: 10  IIFEDENIIVVDKPTGIVCQPDKKHSIINLSNMLLKHCGYRQFDSNKLNFYPQFAHRIDR 69

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            TSGI++ A+T  A + L + F+   + K Y  LV+G
Sbjct: 70  NTSGIVIGAKTNKALKELNKVFKNNHLTKRYKGLVFG 106


>gi|76799617|ref|ZP_00781735.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
 gi|76585032|gb|EAO61672.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
          Length = 157

 Score = 49.3 bits (116), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 59/131 (45%), Gaps = 12/131 (9%)

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           + +    + I + YW+LV G    K + + + + +  H     + +  +N + A   I  
Sbjct: 12  INQRLERKEIWREYWALVEGKFSPKHQVLRDKIGRNRHDRRKRI-IDSKNGQHAMTIIDV 70

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
            K I   +   C LE    TGRTHQ+RVH  H G P++GD  Y         S    +L 
Sbjct: 71  LKYIQNSSLIKCRLE----TGRTHQIRVHLSHHGHPLIGDPLYNP-------SSNNERLM 119

Query: 290 LHARYMDLPHP 300
           LHA  + L HP
Sbjct: 120 LHAHRLTLSHP 130


>gi|317153563|ref|YP_004121611.1| pseudouridine synthase [Desulfovibrio aespoeensis Aspo-2]
 gi|316943814|gb|ADU62865.1| pseudouridine synthase [Desulfovibrio aespoeensis Aspo-2]
          Length = 289

 Score = 49.3 bits (116), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 70/314 (22%), Positives = 122/314 (38%), Gaps = 54/314 (17%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +  +V      +RLDR      P       +++  +GQV VD +      +++SGQ
Sbjct: 1   MPQRETCIVAPGLAGVRLDRAMTGLIPGSGLRLRRRLCEAGQVTVDGRARGPGYKVRSGQ 60

Query: 64  VVRI--PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI---S 118
           V+ +  PP     +  +  Q I    + + + +D   ++            KP G+   +
Sbjct: 61  VLALLAPPTDRMAD--LMPQDI--PELRVVERTDLFAAVY-----------KPGGVHSAA 105

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           + G  G++  ++  L +        P L +RLD  TSG+L+VA     A+    S     
Sbjct: 106 IAGKDGLS--VEAALPALFPDA--APVLLNRLDFPTSGLLLVALGPDGAETYRASEEAGG 161

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-------AISH-- 229
           ++K Y ++V G   +    + N L        D        E+ A+        A++H  
Sbjct: 162 VRKFYLAVVHGR-LDGMISVRNRLDTD-----DRPRTRALAEEDADARRWTSVNALAHDH 215

Query: 230 ---FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
                ++ C   K          G  HQ+R H   +  PIVGD  Y           I +
Sbjct: 216 DRDTTLVRCLIMK----------GARHQIRAHLASLDHPIVGDTLYGVPDAATGGEEIGS 265

Query: 287 K--LYLHARYMDLP 298
              L+LH + ++LP
Sbjct: 266 GPLLHLHHQRIELP 279


>gi|157374654|ref|YP_001473254.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157317028|gb|ABV36126.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 282

 Score = 49.3 bits (116), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 47/205 (22%), Positives = 91/205 (44%), Gaps = 24/205 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           L+ ++ +  ++ KP G+  QG   G    I+ + ++ + +  +   + HRLD+  +G+++
Sbjct: 85  LIADEGQYSLWYKPYGMLCQGSKWGDHTTINRYAETHL-APDRPAFIIHRLDRAATGLVL 143

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +  ++     L + F +R + K Y  +V G   N               G D + V   +
Sbjct: 144 IGHSKKTTAALAKLFELRLLDKYYQVIVEGHFSNH--------------GVDEL-VTIDS 188

Query: 220 EKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           E     A SH K +     Q    ++++  +GR HQ+R+H   +G P+VGD ++      
Sbjct: 189 EVDGKPARSHAKQLKYDPEQNRSLVQVKIESGRKHQIRIHMASIGYPVVGDRQH------ 242

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
                 +  L L + Y+  P P  G
Sbjct: 243 GIADESEVNLQLTSCYLKFPCPITG 267


>gi|330967328|gb|EGH67588.1| pseudouridine synthase [Pseudomonas syringae pv. actinidiae str.
           M302091]
          Length = 296

 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 53/207 (25%), Positives = 90/207 (43%), Gaps = 16/207 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + V +KP  + V   G  +   +   L   +D+    P   HR+D+ T+G+++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAGEYVEQTLLRRLIHRLDNPDLVP--LHRIDRHTAGLVL 146

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +   +TR+A Q L   F  RRI K Y ++   +P+     +    L +S +        
Sbjct: 147 FSANRQTRSAYQTL---FPTRRIDKCYEAIAPALPE-----LEFPRLHESRLVEGEPFFR 198

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            Q   G +   +  +V++     + +  + P TG+ HQLRVH   +G  I  D  Y    
Sbjct: 199 MQEGPGVSNTQTRIEVLERHGPLWRY-GLHPVTGKKHQLRVHMAALGAAICNDPFYPDAL 257

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           K       Q+ L L A+ +    P  G
Sbjct: 258 KDPLDD-YQHPLKLLAKSLRFTDPLSG 283


>gi|15828588|ref|NP_325948.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [Mycoplasma pulmonis UAB
           CTIP]
 gi|14089530|emb|CAC13290.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE C (PSEUDOURIDYLATE
           SYNTHASE) (URACIL HYDROLYASE) [Mycoplasma pulmonis]
          Length = 282

 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 61/250 (24%), Positives = 107/250 (42%), Gaps = 50/250 (20%)

Query: 37  LQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +QK+ R   ++V+ KR +  N  +    +++I  + N       +QK++   +       
Sbjct: 31  IQKLFREKDIKVNGKRNIDKNFIVSKDDLIQIYGLTNV------KQKLVFKKIEQ----- 79

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK---PRLTHRLDQ 152
             K  +++ED  I V NK AG+S+         +D  + S+++ K      P    RLD+
Sbjct: 80  --KFNVIFEDQNILVINKQAGVSMHSDEN---SLDKQVLSYLNFKQVDSFVPSSIGRLDK 134

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA----NWLLKKSHI 208
            TSG++V A+  +  + L  +  +R+   ++ S +   P  K E +     N + KK+ +
Sbjct: 135 VTSGVVVYAKNYSILKTLKSNEHLRKTY-VFMSNITLEPNQKIEHVFYHKYNPIKKKAEL 193

Query: 209 GGDYVHVVKQNE------KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             + V   K  +      K  NYA                   +  TGR HQ+R     +
Sbjct: 194 FKENVEESKITKTLLYKVKNNNYA-------------------ELITGRKHQIRATLSKL 234

Query: 263 GCPIVGDHKY 272
           G PI GD KY
Sbjct: 235 GFPIFGDVKY 244


>gi|303325510|ref|ZP_07355953.1| RNA pseudouridine synthase family protein [Desulfovibrio sp.
           3_1_syn3]
 gi|302863426|gb|EFL86357.1| RNA pseudouridine synthase family protein [Desulfovibrio sp.
           3_1_syn3]
          Length = 352

 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 64/319 (20%), Positives = 121/319 (37%), Gaps = 52/319 (16%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+      RLD+      P +     ++++  G V V+ +      R++ G V+ +    
Sbjct: 8   VDAALAGQRLDQALAALTPELGLRGRRRLIARGAVLVNGRVGDAGCRLRPGDVLAL---- 63

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI---SVQGGSGIAYH 128
                     +  +     T  S  +  +L  +    +++ KPAG+   ++ G +G++  
Sbjct: 64  ----------RGTEDGTGATPCSADMPRLLSRQGDYCFLY-KPAGLHSAALAGDNGLS-- 110

Query: 129 IDGFLKSWV--DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           ++  L   +  +S+G+ PRL  RLD  TSGI+  A    AAQ    + R  R +K Y +L
Sbjct: 111 LEALLPVLLSEESEGRAPRLMQRLDYGTSGIVCAALGAKAAQAFRVAERAGRCEKRYLAL 170

Query: 187 VWGI---PKNKKECIANWLLKKSHI------------------------GGDYVHVVKQN 219
           + G    P   +  +     ++S +                         G    +V+  
Sbjct: 171 LRGTLAGPSTVRLALDTADRRQSRVLADTDDRLRWTEFLPLHVWGGAAATGPLAGLVRDT 230

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
             G + + +                 +   G  HQ+R HA  +G P+ GD  Y    + +
Sbjct: 231 AHGESTSSASGAGEGEDPGGLTLAACRIRCGARHQIRAHAAALGHPLWGDGLY---GRSD 287

Query: 280 FTSPIQNKLYLHARYMDLP 298
            + P     +LH   + LP
Sbjct: 288 QSGPAGTGFFLHHGALLLP 306


>gi|325918250|ref|ZP_08180393.1| 23S RNA-specific pseudouridylate synthase [Xanthomonas vesicatoria
           ATCC 35937]
 gi|325535530|gb|EGD07383.1| 23S RNA-specific pseudouridylate synthase [Xanthomonas vesicatoria
           ATCC 35937]
          Length = 306

 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 37/127 (29%), Positives = 60/127 (47%), Gaps = 10/127 (7%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HR+D+ T+G+++ +   A        FR RRI+K Y ++   +P+     +    L+   
Sbjct: 143 HRIDRNTAGLVLFSANPATRGIYQALFRERRIRKHYLAVAPPLPRLTFPYVYRSRLEP-- 200

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWL-EMQPHTGRTHQLRVHALHMGCP 265
             G+    +++     N       VID  A+    W   ++P TGR HQLRVH   +G P
Sbjct: 201 --GEPFFRMREGVGEPNSE----TVIDVVARGADTWTYRLEPVTGRKHQLRVHMAALGAP 254

Query: 266 IVGDHKY 272
           I+ D  Y
Sbjct: 255 ILHDRFY 261


>gi|213420025|ref|ZP_03353091.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 183

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 48/84 (57%), Gaps = 7/84 (8%)

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYM 295
           ++  +E++P TGR HQLR H  H+  PI+GD K+  + + N ++       +L LHA  +
Sbjct: 71  RYGLVELEPKTGRKHQLRRHLAHLRHPIIGDSKH-GDLRQNRSAAEHFACRRLMLHASRL 129

Query: 296 DLPHPEGGRLQITAPLPAHMVKTW 319
           +L HP  G+  I   + A + +TW
Sbjct: 130 ELTHPFTGQPLI---IQAGLDETW 150


>gi|163838844|ref|YP_001623249.1| ribosomal pseudouridine synthase [Renibacterium salmoninarum ATCC
           33209]
 gi|162952320|gb|ABY21835.1| ribosomal pseudouridine synthase [Renibacterium salmoninarum ATCC
           33209]
          Length = 304

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 56/210 (26%), Positives = 93/210 (44%), Gaps = 18/210 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D  + V +KP  + +  GG  +A      L+  +D     P   HRLD+ T+GIL+
Sbjct: 91  VLHQDDHLVVIDKPHFLPTTPGGMYVAESALVRLRVLLDLPDLVP--IHRLDRMTAGILL 148

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            A   +TR   Q L   F  R+++K Y ++      + +E +   L  +S +     +++
Sbjct: 149 FAVNPQTRGKYQLL---FECRQVRKHYEAVA-----SVREDLQLPLTIRSRLYKSRSYLL 200

Query: 217 KQN---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            Q    E  A   +S  +             ++PH+G+THQLRVH   +G  I+ D  Y 
Sbjct: 201 TQELAGEPNAETRVSLERSWPSADGPRGLYRLEPHSGKTHQLRVHMAALGMGILNDPFYP 260

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                      Q  L L AR ++   P  G
Sbjct: 261 V-LSEQAPDDYQKPLQLLARSLEFTDPISG 289


>gi|332017005|gb|EGI57804.1| RNA pseudouridylate synthase domain-containing protein 1
           [Acromyrmex echinatior]
          Length = 295

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 44/165 (26%), Positives = 71/165 (43%), Gaps = 35/165 (21%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD  TSG++ +A  + AA+  + +F   ++QK Y +LV G             + +
Sbjct: 98  FVHRLDYPTSGVMCIALNKRAARAASSAFENHKVQKFYLALVHG------------HIHE 145

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------------------LEMQP 247
            HI  D        EK  N+ +     I C   +  +                  + + P
Sbjct: 146 PHIVIDKPIGADIREKTGNHKMCISDSIFCDKPRRSYTTLVVLEHGFWKGKPATKILLAP 205

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            TGR HQLRVH  ++G  ++GD+ Y    +G    P  ++ YLH+
Sbjct: 206 GTGRRHQLRVHCHYIGHTVIGDYTYS---EGKDIEP--HRTYLHS 245


>gi|237843373|ref|XP_002370984.1| RNA pseudouridylate synthase domain-containing protein [Toxoplasma
           gondii ME49]
 gi|211968648|gb|EEB03844.1| RNA pseudouridylate synthase domain-containing protein [Toxoplasma
           gondii ME49]
 gi|221502314|gb|EEE28047.1| RNA pseudouridylate synthase domain-containing protein, putative
           [Toxoplasma gondii VEG]
          Length = 685

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/153 (25%), Positives = 74/153 (48%), Gaps = 22/153 (14%)

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI-YWSLVWG-IPKNKKE 196
           S  + P+L HRL +E +G+L++ RT+  AQ   +  R      + +++L+ G  P  ++E
Sbjct: 296 SMDETPKLLHRLGKEVTGVLLLGRTKQTAQVAVDRLRGGTFGVLTFFALLHGRPPGGRRE 355

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---------------FC 241
            +    L ++  G   V V    ++G + +++ +K++   + +               F 
Sbjct: 356 GVIRIPLAENEAG---VMVPTAVQRGGSVSVTRWKLLKVASPQTRDVKGDAEQSHACGFS 412

Query: 242 WLEMQ-PHTGRTHQLRVHALH-MGCPIVGDHKY 272
            +E++  H    HQ R H L+ + CPIVGD  Y
Sbjct: 413 LVELEIRHQQCRHQARAHCLYGLSCPIVGDRVY 445


>gi|256379338|ref|YP_003102998.1| pseudouridine synthase [Actinosynnema mirum DSM 43827]
 gi|255923641|gb|ACU39152.1| pseudouridine synthase [Actinosynnema mirum DSM 43827]
          Length = 302

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 51/207 (24%), Positives = 89/207 (42%), Gaps = 16/207 (7%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ D  I V +KP  + ++  G  +       L+  +D     P   HRLD+ T+G+++
Sbjct: 93  VVHRDDAILVVDKPHFLATIPRGKHVVETALVRLRRDLDLPALSP--AHRLDRVTAGLVM 150

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
                A        F  R ++K Y ++        ++ +    + +S I  +   +  Q 
Sbjct: 151 FVVDPALRGRYQTMFADRLVRKEYEAIA-----PVRDDLELPRVVRSRIVKEKGVITAQE 205

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-- 277
             G   A +  ++ +          + P TGRTHQLRVH   +G PIVGD  Y    +  
Sbjct: 206 VPGPVNAETRVELAERRGD-LGRYRLLPTTGRTHQLRVHLSGLGVPIVGDDFYPVLREKP 264

Query: 278 -GNFTSPIQNKLYLHARYMDLPHPEGG 303
             +FT P+Q    L A+ ++   P  G
Sbjct: 265 LDDFTDPLQ----LLAKVLEFTDPVTG 287


>gi|221481814|gb|EEE20184.1| conserved hypothetical protein [Toxoplasma gondii GT1]
          Length = 713

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/153 (25%), Positives = 74/153 (48%), Gaps = 22/153 (14%)

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI-YWSLVWG-IPKNKKE 196
           S  + P+L HRL +E +G+L++ RT+  AQ   +  R      + +++L+ G  P  ++E
Sbjct: 275 SMDETPKLLHRLGKEVTGVLLLGRTKQTAQVAVDRLRGGTFGVLTFFALLHGRPPGGRRE 334

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---------------FC 241
            +    L ++  G   V V    ++G + +++ +K++   + +               F 
Sbjct: 335 GVIRIPLAENEAG---VMVPTAVQRGGSVSVTRWKLLKVASPQTRDVKGDAEQSHACGFS 391

Query: 242 WLEMQ-PHTGRTHQLRVHALH-MGCPIVGDHKY 272
            +E++  H    HQ R H L+ + CPIVGD  Y
Sbjct: 392 LVELEIRHQQCRHQARAHCLYGLSCPIVGDRVY 424


>gi|256090913|ref|XP_002581414.1| ribosomal pseudouridine synthase [Schistosoma mansoni]
 gi|238667306|emb|CAZ37653.1| ribosomal pseudouridine synthase, putative [Schistosoma mansoni]
          Length = 165

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 28/97 (28%), Positives = 52/97 (53%), Gaps = 14/97 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQ-KPRLTHRL 150
           ++Y+D  + + NKP G+ V   +G         + YH+    K      G  +P + HR+
Sbjct: 72  IVYQDDVLAIINKPQGMVVHPSAGHSTGTLVNALLYHV----KDLSSINGVIRPGIVHRI 127

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           D++TSG+L+VA+T  A Q L +  + ++  + Y ++V
Sbjct: 128 DKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIV 164


>gi|167375438|ref|XP_001733644.1| ribosomal pseudouridine synthase [Entamoeba dispar SAW760]
 gi|165905188|gb|EDR30257.1| ribosomal pseudouridine synthase, putative [Entamoeba dispar
           SAW760]
          Length = 402

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 51/181 (28%), Positives = 83/181 (45%), Gaps = 9/181 (4%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  ++ E +     +KP+ + V       ++   F+ S       +P   HRLD+ TSGI
Sbjct: 145 KLTIVKETNDFIAIDKPSSVPVHPCGRYRHNTVIFILSHEGYPNLRP--VHRLDRMTSGI 202

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-V 216
           L++A+T  AA+       +++  K Y   V G  K +K  + + + +K  I    +HV V
Sbjct: 203 LLLAKTIQAAREFQNHMVIKK--KEYICRVRG--KLEKTVVTSKIGRKR-IDDKKIHVSV 257

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQP-HTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            + E+      S F  +    +    + +    +GRTHQLRVH   +  PIV D  Y A 
Sbjct: 258 NKIEEDGKECCSEFNPLFYDEKTNTTVAVALLGSGRTHQLRVHLQSIHHPIVNDPIYAAQ 317

Query: 276 F 276
           F
Sbjct: 318 F 318


>gi|219123231|ref|XP_002181932.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406533|gb|EEC46472.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 418

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 37/131 (28%), Positives = 56/131 (42%), Gaps = 32/131 (24%)

Query: 94  SDFLKS-----ILLYEDSKIYVFNKPAGISVQG-----------------------GSGI 125
           SD L+      +++YE       NKP  + + G                         G+
Sbjct: 43  SDLLRCFEKDKVVVYETDHFLALNKPPDLRMDGHHPSTVLKLLTYWYPPPAFQNLQSKGL 102

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +  F +++ + +G + R  H+LD  TSGIL+VAR R AA     SF  R  +K Y +
Sbjct: 103 LEKVSEF-ENYRNIEGNELRPCHQLDYATSGILLVARNRQAADQARVSFEERSTRKTYLA 161

Query: 186 LVWG---IPKN 193
           LV G   +P N
Sbjct: 162 LVHGHLSVPSN 172



 Score = 46.2 bits (108), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 5/76 (6%)

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q    + ++P TGR HQLRVH+  +G  IVGD  Y A    + T    +++ LH++ ++
Sbjct: 335 GQPVTKVRLEPRTGRRHQLRVHSALLGHAIVGDQTYKAPGSPDLT----DRMCLHSQCLE 390

Query: 297 LPHPEGGRLQITAPLP 312
           +P  E   +++ AP P
Sbjct: 391 IPLFE-ELIKVEAPDP 405


>gi|157821169|ref|NP_001102111.1| RNA pseudouridylate synthase domain-containing protein 3 [Rattus
           norvegicus]
 gi|149036916|gb|EDL91534.1| RNA pseudouridylate synthase domain containing 3 (predicted),
           isoform CRA_c [Rattus norvegicus]
          Length = 320

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/134 (29%), Positives = 60/134 (44%), Gaps = 12/134 (8%)

Query: 152 QETSGILVVARTRAAAQHL----TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +E SG+++++       HL    T S R +R    Y ++  G+P+  +  +   L  +  
Sbjct: 105 KEASGLVLLSSCPQTTSHLQKFFTHSRRAQRPTATYCAITDGVPEPSEGTVHIALRLERM 164

Query: 208 IGGDYVHVV-----KQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALH 261
            G D    V     K  ++G    +SHF V        C L ++QP T    QL+VH   
Sbjct: 165 DGIDLAVPVTSPSRKDIQEGVKRTLSHFHVTATGCG--CALVQLQPLTVFPSQLQVHMAL 222

Query: 262 MGCPIVGDHKYCAN 275
             CPI+GDH Y A 
Sbjct: 223 QLCPILGDHTYAAR 236


>gi|330876755|gb|EGH10904.1| pseudouridine synthase [Pseudomonas syringae pv. morsprunorum str.
           M302280PT]
          Length = 296

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 53/207 (25%), Positives = 90/207 (43%), Gaps = 16/207 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + V +KP  + V   G  +   +   L   +D+    P   HR+D+ T+G+++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAGEYVEQTLLRRLIHRLDNPNLVP--LHRIDRHTAGLVL 146

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +   +TR+A Q L   F  RRI K Y ++   +P+     +    L +S +        
Sbjct: 147 FSANRQTRSAYQTL---FPTRRIDKCYEAIAPALPE-----LEFPRLHESRLVEGEPFFR 198

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            Q   G +   +  +V++     + +  + P TG+ HQLRVH   +G  I  D  Y    
Sbjct: 199 MQEGPGVSNTQTRIEVLERHGPLWRY-GLHPVTGKKHQLRVHMAALGAAICNDPFYPDAL 257

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           K       Q+ L L A+ +    P  G
Sbjct: 258 KDPLDD-YQHPLKLLAKSLRFIDPLSG 283


>gi|160943889|ref|ZP_02091119.1| hypothetical protein FAEPRAM212_01390 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444565|gb|EDP21569.1| hypothetical protein FAEPRAM212_01390 [Faecalibacterium prausnitzii
           M21/2]
          Length = 303

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 80/181 (44%), Gaps = 26/181 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQ 152
           ++YED+   V  KP  ++V       GG+      +G+      + G  P  R  +R+D+
Sbjct: 83  VVYEDAFAVVLEKPPQLAVHPTLNYPGGT----LANGYAAWAA-AHGHSPVFRPVNRIDK 137

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGD 211
           +TSG+++ A+   AA  L        + K+Y+++  G +P  +    A    +   I G 
Sbjct: 138 DTSGLVLAAKNAYAAPLLAGG-----VTKLYYAIAQGALPLGEGAIDAPIGRRGDSIIG- 191

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V    K +    +  K  +  +   C     P TGRTHQ+RVH   +G P+ GD  
Sbjct: 192 --RCVTPEGKPSRTEYTIIKEENGLSLAACV----PVTGRTHQIRVHFASIGHPLAGDDL 245

Query: 272 Y 272
           Y
Sbjct: 246 Y 246


>gi|224438079|ref|ZP_03659018.1| hypothetical protein HcinC1_08895 [Helicobacter cinaedi CCUG 18818]
 gi|313144523|ref|ZP_07806716.1| conserved hypothetical protein [Helicobacter cinaedi CCUG 18818]
 gi|313129554|gb|EFR47171.1| conserved hypothetical protein [Helicobacter cinaedi CCUG 18818]
          Length = 310

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 43/174 (24%), Positives = 77/174 (44%), Gaps = 12/174 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+ +    +++KP  +     G    Y ++  LKS     G +    HRLD++T G+++ 
Sbjct: 76  LFYNDDFAIYDKPHNLLTHPKGRFFHYSLNDILKSRF---GIQANALHRLDKQTGGLVLC 132

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV--HVVKQ 218
           +    + + L    + R I K Y ++V G  + K E + N  +      GD     +V +
Sbjct: 133 SINPKSKKALESLMQSRSIAKSYCAIVEG--RVKAEILINEPIMTQKHKGDLAIKSIVSE 190

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             K +   I        + +    +     TGRTHQ+R+H  ++G  I+GD  Y
Sbjct: 191 KGKESRTLIRPL----AYYKDSTLIHALALTGRTHQIRLHCSYIGHRILGDPLY 240


>gi|330720018|gb|EGG98456.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC2047]
          Length = 179

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 43/157 (27%), Positives = 69/157 (43%), Gaps = 21/157 (13%)

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGDYVH 214
           +VVA+T  A   L +  + R + + Y ++V G+        E I    + +  +G     
Sbjct: 1   MVVAKTLLAHADLVDQLQTREMGREYEAVVQGVMTGGGRVDEPIGRHPVHRKKMGV---- 56

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V    E   NY+++  +   C       LE    TGRTHQ+RVH  H+  P++GD  Y  
Sbjct: 57  VPSGKEAATNYSVA--ERFRCHTHVRLKLE----TGRTHQIRVHMTHINYPLIGDQFYGG 110

Query: 275 NFK------GNFTSPIQN--KLYLHARYMDLPHPEGG 303
             +          + +Q+  +  LHAR + L HP  G
Sbjct: 111 RPRLPPAATEELIAFLQSFKRQALHARRLQLVHPLTG 147


>gi|300121551|emb|CBK22070.2| unnamed protein product [Blastocystis hominis]
          Length = 260

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 53/214 (24%), Positives = 87/214 (40%), Gaps = 31/214 (14%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +K  +LY D  I V +  +  SV             LKS   +    P   HRLD++T+G
Sbjct: 41  MKDRILYCDDHIIVTDLDSARSVISA----------LKSMFSTSLLYP--VHRLDKDTTG 88

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVH 214
           +L+VAR R  A+ L   F    + K+Y +  + +  +        ++        G + H
Sbjct: 89  VLLVARDRETARALGHEFACHEVSKMYLAAGYDVSFSSSHFPRVGIVYSDFEQNAGHFYH 148

Query: 215 VVKQNEKG--------------ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +    K               A  A + ++V+     +   L  + ++G+THQ+RVH  
Sbjct: 149 AINSKVKPLPTNIFPAHIETSVATPAATGYEVVKQ-KDEIVLLRCRLYSGKTHQIRVHLK 207

Query: 261 H-MGCPIVGDHKYCANFKGNFTSPIQNK-LYLHA 292
             +G  ++ D KY    K N    I  K  YLH 
Sbjct: 208 DVLGIELLNDSKYGKRRKMNRNQLIDPKAFYLHC 241


>gi|256822239|ref|YP_003146202.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
 gi|256795778|gb|ACV26434.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
          Length = 305

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/153 (25%), Positives = 64/153 (41%), Gaps = 19/153 (12%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV------------WGIPKNKK 195
           HRLD++T+G+++ +          + F  + I+K Y ++             W I     
Sbjct: 130 HRLDRDTAGLVMFSTNPHTRSDYHQLFAQQNIKKHYQAIAKTQAGESLSGKSWHIKNYLA 189

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                ++ +      D       ++K A YA S     D   Q      + P TGRTHQL
Sbjct: 190 RSEPQFIFQNLDTSPD---DTSPHDKDAQYAESLIHCEDDNLQ-LGLFTLSPITGRTHQL 245

Query: 256 RVHALHMGCPIVGDHKYCA---NFKGNFTSPIQ 285
           R+H + +G PI+ D  Y +       NF+ P+Q
Sbjct: 246 RLHMMSLGFPILNDRFYPSLQPKQADNFSQPLQ 278


>gi|319424856|gb|ADV52930.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 305

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 40/151 (26%), Positives = 69/151 (45%), Gaps = 16/151 (10%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRM--------RRIQKIYWSLVWGIPKNKKECI 198
            HRLD+ET+G++++   +   +HL     +        + I K+   ++    K      
Sbjct: 133 AHRLDRETAGVILMT-IQPETRHLYHQLFVDNAICKDYQAIAKLTPGIIEQYQKGHLTLP 191

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRV 257
            +W +K     GD    ++  E  AN   SH ++ +           + P TG+THQLRV
Sbjct: 192 LHWTVKNRMQPGDPSFTMQVVEGEAN---SHSEISLVAIKDDLGLFHLSPITGKTHQLRV 248

Query: 258 HALHMGCPIVGDHKYCA-NFKG--NFTSPIQ 285
           H L +G P++ D  Y     KG  +F +P++
Sbjct: 249 HMLSLGMPLLNDRFYPKLQPKGPDDFATPLK 279


>gi|254796538|ref|YP_003081374.1| ribosomal large subunit pseudouridine synthase D [Neorickettsia
           risticii str. Illinois]
 gi|254589775|gb|ACT69137.1| ribosomal large subunit pseudouridine synthase D [Neorickettsia
           risticii str. Illinois]
          Length = 126

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 44/82 (53%), Gaps = 11/82 (13%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           YED  + V +KPAG+ V  G G         + +H      S +DS   +P + HRLD++
Sbjct: 36  YEDDSLLVIHKPAGLVVHPGIGNKEQTLVNILEHHYPTEQLSNLDSS--RPGIVHRLDKD 93

Query: 154 TSGILVVARTRAAAQHLTESFR 175
           T+G L+VA+T  +   L+E  +
Sbjct: 94  TAGFLIVAKTNPSHVRLSEMIK 115


>gi|224129476|ref|XP_002328726.1| predicted protein [Populus trichocarpa]
 gi|222839024|gb|EEE77375.1| predicted protein [Populus trichocarpa]
          Length = 177

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 32/48 (66%), Gaps = 1/48 (2%)

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
           A++ ++V+        W+E++P T R HQLRVH A  +G PIVGD+KY
Sbjct: 25  AVTEYRVLGPTINGCSWIELRPLTSRKHQLRVHCAEALGTPIVGDYKY 72


>gi|282864375|ref|ZP_06273431.1| pseudouridine synthase [Streptomyces sp. ACTE]
 gi|282560862|gb|EFB66408.1| pseudouridine synthase [Streptomyces sp. ACTE]
          Length = 314

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 50/168 (29%), Positives = 78/168 (46%), Gaps = 24/168 (14%)

Query: 147 THRLDQETSG-ILVVART--RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIANWL 202
            HRLD+ T+G +L V R   R A Q L   FR R ++K Y ++    P+      +   +
Sbjct: 145 AHRLDRLTAGLVLFVVRPEERGAYQTL---FRDRLVRKEYEAVAPYDPEVALPRTVRGRI 201

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           +K+  +      +  + E G   + S  ++++  A       + P TGRTHQLRVH   +
Sbjct: 202 VKERGV------MAARVEPGEANSESRIELLEHRA-GLGRYRLLPATGRTHQLRVHMNAL 254

Query: 263 GCPIVGDHKYCANFK------GNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G P+V D  Y A          ++T P+Q    L AR ++   P  GR
Sbjct: 255 GLPLVHDPVYPAVLPEPEPGGEDYTRPLQ----LLARVLEFTDPVTGR 298


>gi|297171011|gb|ADI22025.1| pseudouridylate synthases, 23S RNA-specific [uncultured
           myxobacterium HF0200_05J13]
          Length = 154

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 37/142 (26%), Positives = 63/142 (44%), Gaps = 13/142 (9%)

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y ++V+G+P+  +  I     +       +   V + +K    A++ + V+     
Sbjct: 2   VHKRYLAMVFGLPEPSRGIIETLYGRHPTDRKKFSGKVARGKK----AVTSYGVMVSVG- 56

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YLH 291
               +++   TGRTHQ+RVH    G PIVGD  Y        +     ++        LH
Sbjct: 57  GLSQVDLLLGTGRTHQIRVHLSERGHPIVGDPVYSGRQYARISDEGLRRIATEFDYQALH 116

Query: 292 ARYMDLPHP-EGGRLQITAPLP 312
           A  +   HP  G +L +TAP+P
Sbjct: 117 AWEIGFTHPVTGEKLSLTAPMP 138


>gi|119773646|ref|YP_926386.1| pseudouridine synthase [Shewanella amazonensis SB2B]
 gi|119766146|gb|ABL98716.1| pseudouridine synthase [Shewanella amazonensis SB2B]
          Length = 309

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 38/150 (25%), Positives = 66/150 (44%), Gaps = 15/150 (10%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK------NKKECIAN 200
            HRLD+ET+G+++++          + F    I+K Y ++    P+      + +     
Sbjct: 135 AHRLDRETAGVILMSLNPETRHQYHQLFLNGGIRKDYEAIARLTPELMALHGDGQSLPQR 194

Query: 201 WLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           W +K      D  ++  V   E  ++  I+   V D         E+ P TGRTHQLRVH
Sbjct: 195 WTVKNRMQPADPSFLMQVVPGEANSHSEIALLMVKDGRG----LFELSPITGRTHQLRVH 250

Query: 259 ALHMGCPIVGDHKYCA---NFKGNFTSPIQ 285
              +G P+  D  Y +       +F +P++
Sbjct: 251 MQSLGMPLENDRFYPSLQPQSADDFNAPLK 280


>gi|308495566|ref|XP_003109971.1| hypothetical protein CRE_06376 [Caenorhabditis remanei]
 gi|308244808|gb|EFO88760.1| hypothetical protein CRE_06376 [Caenorhabditis remanei]
          Length = 426

 Score = 48.5 bits (114), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 49/181 (27%), Positives = 80/181 (44%), Gaps = 11/181 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++ +   + V  KP  + V      A H + G L+  V+      R+ HRLD+ TSG+L+
Sbjct: 127 IISDTDDLLVIEKPPSLPVHTCGQYAIHTVLGQLR--VNEGITGLRVLHRLDRATSGVLL 184

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            A+          + +     K Y   V G+ P  ++ C          +G   +  V+ 
Sbjct: 185 FAKNYETDLEFKTTLKQGEWSKEYICKVDGVFPDEEQLCDQPIGPLVISMG---IQCVRP 241

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + K A    S FK +         +++   TGRTHQ+RVH+  +G PIVGD  Y +   G
Sbjct: 242 DGKEAK---SRFKKLWSDGTHSV-VQVHIETGRTHQIRVHSQFLGHPIVGDQLYNSTVWG 297

Query: 279 N 279
           +
Sbjct: 298 S 298


>gi|264678344|ref|YP_003278251.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
 gi|262208857|gb|ACY32955.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
          Length = 305

 Score = 48.5 bits (114), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 44/199 (22%), Positives = 85/199 (42%), Gaps = 32/199 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +++ D+ + V +KP  + V       +++   L   +  +   P L+  HR+D++T+G++
Sbjct: 94  VIHRDADLLVADKPHFLPVVPA---GHYLQNTLLVRLRREFDLPELSPIHRIDRDTAGLV 150

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V +  RA        FR R I K+Y            E +A +   ++ +     H  + 
Sbjct: 151 VFSVQRATRGIYQGLFRDRAIHKVY------------EAVAAY---RAELSFPREHASRM 195

Query: 219 NEKGANYAISHFK-------VIDCFAQKFCWLE--MQPHTGRTHQLRVHALHMGCPIVGD 269
            E G  + +           +++       W    + P +G+ HQLRVH   +G P+ GD
Sbjct: 196 EESGHFFRMHEVAGEPNSRTLMEIIEHNKAWARYRLSPVSGKRHQLRVHMAALGLPLRGD 255

Query: 270 HKYCA---NFKGNFTSPIQ 285
             Y        G+++ P+Q
Sbjct: 256 AFYPVVNDPEPGDYSRPLQ 274


>gi|325116689|emb|CBZ52242.1| YDL036Cp-like protein, related [Neospora caninum Liverpool]
          Length = 430

 Score = 48.5 bits (114), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 52/194 (26%), Positives = 80/194 (41%), Gaps = 33/194 (17%)

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           ++  + V   PA  S+ G S +   +     +  +   +   + HRLD  TSG LV A+T
Sbjct: 211 DEEPVEVPTDPAADSIGGPSSM--RVSSVQLALPEEISRPASIVHRLDIGTSGALVAAKT 268

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA------------NWLLKKSHIGGD 211
            AAA++L   +  R++ K Y  L        +E  A              L+  S  G  
Sbjct: 269 IAAAENLKYQWAERKVLKGYIGLCAPEIHKLQEVDAAIRRHPVQRGRMEALINDSRSG-- 326

Query: 212 YVHVVKQNEK-----------GANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVH 258
             H    +EK           GA   +S F  +  +     F  L +   TGRTHQ+R H
Sbjct: 327 -FHETVCDEKVAQNCQSNSRLGAKPGVSVFAPLGGNGVYGMFAALAL---TGRTHQIRAH 382

Query: 259 ALHMGCPIVGDHKY 272
             ++G P++GD  Y
Sbjct: 383 LEYIGHPLLGDPVY 396


>gi|224015040|ref|XP_002297181.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220968156|gb|EED86506.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 590

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 45/149 (30%), Positives = 65/149 (43%), Gaps = 35/149 (23%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+ TSG +V+A+       L  SF +R+  K+Y +LV G       C+ N     
Sbjct: 366 IVHRLDRGTSGAIVLAKNDETHLRLVASFFLRKATKVYSALVPG------SCLQN----- 414

Query: 206 SHIGGDY-VHVVKQNEKGANYAI----------SHFKVIDCFAQ----------KFCWLE 244
             I GD   +V      G+   I          S ++V+  +            +   LE
Sbjct: 415 --IDGDEDANVSAMLTIGSEGEIDLPVDRRPAKSKYRVVKMYGHQEEQTQQPTPEAILLE 472

Query: 245 MQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
           +Q  TGR HQ+RVH A  +G PI  D  Y
Sbjct: 473 VQTLTGRKHQVRVHCASGLGRPIFLDPLY 501


>gi|226327068|ref|ZP_03802586.1| hypothetical protein PROPEN_00929 [Proteus penneri ATCC 35198]
 gi|225204286|gb|EEG86640.1| hypothetical protein PROPEN_00929 [Proteus penneri ATCC 35198]
          Length = 193

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 44/86 (51%), Gaps = 9/86 (10%)

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD--HKYCANFKGNFTSPIQNKLYLHARY 294
             +F  LE++P TGR HQLR H  H+  PI+GD  H      +G       ++L LHA +
Sbjct: 79  TSRFSLLELRPETGRKHQLRRHMSHIRHPIIGDTAHGDLRQNRGVVNYFQSHRLMLHASH 138

Query: 295 MDLPHPEGGRLQITAPLPAHMVKTWD 320
           ++L HP      IT   P ++   WD
Sbjct: 139 LNLIHP------ITLQ-PLNLTAKWD 157


>gi|71033777|ref|XP_766530.1| hypothetical protein [Theileria parva strain Muguga]
 gi|68353487|gb|EAN34247.1| hypothetical protein, conserved [Theileria parva]
          Length = 436

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 102/232 (43%), Gaps = 39/232 (16%)

Query: 72  NALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-- 128
           N L+HI+K  ++I+  ++     +      +++E+ +  V +KP  I V       Y+  
Sbjct: 108 NVLDHILKPNERIIHEAIVHEPVALNSNIPVVWENEEYIVVSKPTSIPVYQTGTYKYNSL 167

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           ++   +     +G K    HR+D+  SG++  A++  +A  L+++ R   ++K+Y + V 
Sbjct: 168 MEIMRRELPSCRGIKLFTIHRIDKLVSGLVAFAKSANSASELSQAIRDNEVKKVYIARVN 227

Query: 189 GIPKNKKECIANWLLKKSH-IGGD--------------YVHV----------VKQNEKGA 223
           G          + LL  SH   GD              Y+ V          V +N +  
Sbjct: 228 G--------DFSHLLNNSHRDSGDKSDDSLENVFESVGYMRVISKKEGRYEFVGENAEDE 279

Query: 224 NY--AISHFKVIDCFAQKFCWLEM-QPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +Y  +++ FK I         L +  P TGRTHQ+R +  ++G PI  D  Y
Sbjct: 280 SYKPSVTRFKFIKYNKDLDESLVLCSPITGRTHQIRANLRYLGHPISNDPWY 331


>gi|70726951|ref|YP_253865.1| ibosomal large subunit pseudouridine synthase RluD subfamily
           protein [Staphylococcus haemolyticus JCSC1435]
 gi|68447675|dbj|BAE05259.1| hypothetical protein, ribosomal large subunit pseudouridine
           synthase, RluD subfamily [Staphylococcus haemolyticus
           JCSC1435]
          Length = 287

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 42/194 (21%), Positives = 87/194 (44%), Gaps = 23/194 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  + + +KP  ++               + Y+++  +   +D+    P +  RLD
Sbjct: 77  ILYEDDYLIIVSKPNYLNSTPSREHPHDSLIERVLYYLN--VGQLIDT-SIVPHIVTRLD 133

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + T GI++ A+      H+        I K Y  + +G      +   + ++++      
Sbjct: 134 RNTKGIVIFAK----HGHIHHLMTTSAIDKRYMCVCYG------QMQLSGVIEEPIARDS 183

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              + ++ +    YA + ++ +    +     E++ HTGRTHQ+RVH  ++G P+VGD  
Sbjct: 184 QSIITRKVDASGKYAKTSYETVMTKPEA-SLCEIKLHTGRTHQIRVHFNYVGHPLVGDDL 242

Query: 272 YCANFKGNFTSPIQ 285
           Y  +    +T  +Q
Sbjct: 243 YEGSHPEIYTQSLQ 256


>gi|328857444|gb|EGG06560.1| hypothetical protein MELLADRAFT_116466 [Melampsora larici-populina
           98AG31]
          Length = 486

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 41/151 (27%), Positives = 65/151 (43%), Gaps = 32/151 (21%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWG-IPKNKKECIANWLLK 204
           ++RLD+ TSG+++ A T  A++ L+  F     ++K Y +   G  P  +  C    L  
Sbjct: 160 SNRLDRLTSGVMICALTIEASRGLSAYFGQEGAVKKEYIARCRGNFPDEEIVCEEPLLTI 219

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              +G + VH                       +    L  +P TGR+HQ+RVH   +G 
Sbjct: 220 DRQVGLNVVH----------------------PEGKLPLLGRPITGRSHQIRVHLQFLGH 257

Query: 265 PIVGDHKYCANFK--------GNFTSPIQNK 287
           PI+ D  YC+N          G F+SP   +
Sbjct: 258 PILNDVIYCSNVAWGPEGGKGGIFSSPTDQR 288


>gi|299532184|ref|ZP_07045578.1| pseudouridine synthase [Comamonas testosteroni S44]
 gi|298719846|gb|EFI60809.1| pseudouridine synthase [Comamonas testosteroni S44]
          Length = 305

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 44/199 (22%), Positives = 85/199 (42%), Gaps = 32/199 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +++ D+ + V +KP  + V       +++   L   +  +   P L+  HR+D++T+G++
Sbjct: 94  VIHRDAHLLVADKPHFLPVVPA---GHYLQNTLLVRLRREFDLPELSPIHRIDRDTAGLV 150

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V +  RA        FR R I K+Y            E +A +   ++ +     H  + 
Sbjct: 151 VFSVQRATRGIYQGLFRDRAIHKVY------------EAVAAY---RAELSFPREHASRM 195

Query: 219 NEKGANYAISHFK-------VIDCFAQKFCWLE--MQPHTGRTHQLRVHALHMGCPIVGD 269
            E G  + +           +++       W    + P +G+ HQLRVH   +G P+ GD
Sbjct: 196 EESGHFFRMHEVAGEPNSRTLMEIIEHNSAWARYRLSPVSGKRHQLRVHMAALGLPLRGD 255

Query: 270 HKYCA---NFKGNFTSPIQ 285
             Y        G+++ P+Q
Sbjct: 256 AFYPMVNDPEPGDYSRPLQ 274


>gi|71279408|ref|YP_270347.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
 gi|71145148|gb|AAZ25621.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
          Length = 318

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 51/198 (25%), Positives = 94/198 (47%), Gaps = 23/198 (11%)

Query: 78  IKEQKILDSSVNLTKHSDFLKS----ILLYEDSKIY-VFNKPAGISVQGGSGIAYHIDGF 132
           IK+Q +    ++   +S+ L S     LL  D   Y V+ KP G+  QG S  + H    
Sbjct: 82  IKKQLVKGDELHFYFNSEVLSSPVPQALLIADLIDYSVWYKPYGMLSQG-SKWSDHCTIA 140

Query: 133 LKSWVDSKGQKPR-LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             +  +   ++P  + HRLD+  +G+++VA +++AA+ L+  F   +++K Y  +V G  
Sbjct: 141 RFAQQNLPNERPAFIVHRLDRAATGLIIVAHSKSAARALSHMFEHHQLEKHYQIIVHGDH 200

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           + +    A   +  S + G          K A    +     +   Q    ++++  +GR
Sbjct: 201 RKR----AQPDIIDSDVDG----------KKARSTFTCLAYDEMTDQSL--IKVKIDSGR 244

Query: 252 THQLRVHALHMGCPIVGD 269
            HQ+R+HA  +  P+VGD
Sbjct: 245 KHQIRLHAASIAMPVVGD 262


>gi|325181219|emb|CCA15633.1| RNA pseudouridylate synthase putative [Albugo laibachii Nc14]
          Length = 440

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 71/302 (23%), Positives = 113/302 (37%), Gaps = 97/302 (32%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVV------RIPPVINALNHIIKEQKILDSSVNLTKHS 94
           +RSG+V V+   V    RIQ+G  +        PPV  + +HI                 
Sbjct: 100 VRSGRVTVNHSIVSQTYRIQNGDFIVHRTHRHEPPV--SSDHIP---------------- 141

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-----------IDGFLKSWVDSKGQK 143
                 ++YED ++ V +KP  I         ++           ++ FL          
Sbjct: 142 ------IVYEDDELLVVSKPCSIPTHPCGAYRHNSLHSILLHQIPVESFL---------- 185

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWL 202
             + HRLD+ TSGI++ A+T AAA+ L+     R++ K Y + V G IP       + W 
Sbjct: 186 -HVVHRLDRLTSGIVIFAKTAAAAKKLSTEMTKRQVHKTYLAGVKGFIP-------SQWD 237

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKV-----IDCFAQK------------------ 239
            +      +     KQ  + +  + S  ++     + C + K                  
Sbjct: 238 EESKKQQNEIKERAKQICEASEISFSKKQIRVKCPLKCLSHKNGVWECHKDGKESETIFE 297

Query: 240 -------------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ 285
                         C L   P TGRTHQ+R+H   +G PI  D  Y      G+ T+P+ 
Sbjct: 298 RDQLTVPVENRDVSCVLRCFPVTGRTHQIRLHLQLIGLPIANDPCYGGELHFGSKTTPLD 357

Query: 286 NK 287
            K
Sbjct: 358 TK 359


>gi|47459310|ref|YP_016172.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma mobile
           163K]
 gi|47458640|gb|AAT27961.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma mobile
           163K]
          Length = 314

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 63/265 (23%), Positives = 115/265 (43%), Gaps = 38/265 (14%)

Query: 37  LQKILRSGQVRVDKKRV-------KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
           L+K+ R+  ++++ KR+       +FN+ I+   +     + N      K+Q        
Sbjct: 50  LEKLFRNKDIKINGKRISSKTYVLQFNDEIEVFGIFDEDSIENFTRSKQKKQT------- 102

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTH 148
            TK  D  K  +++E+  I + NKP  + +    + +   +  +L ++V      P    
Sbjct: 103 -TKTFD-KKLEIIFENLDILIINKPNNLIMHSSKNSLDEQVLNYL-NYVKIDSFVPTHIG 159

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ETSG++V A+       L +  +    +KIY  + +     K   +        +I
Sbjct: 160 RLDKETSGLVVYAKNYKTLIELLD--KQSDFEKIYTFIPFCNLSEKDVLVT------VNI 211

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR-VHALHMGCPIV 267
             D ++   Q       +I+     D  +Q++     Q  TGR HQ+R V A  + CPI+
Sbjct: 212 SEDEINKKMQISNEGKKSITRI-FYDGNSQRYY---AQILTGRKHQIRLVLADFLKCPIL 267

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHA 292
           G+ KY      N T     +L+LH+
Sbjct: 268 GERKY-----ANLTK--DKRLFLHS 285


>gi|262279505|ref|ZP_06057290.1| RNA pseudouridine synthase [Acinetobacter calcoaceticus RUH2202]
 gi|262259856|gb|EEY78589.1| RNA pseudouridine synthase [Acinetobacter calcoaceticus RUH2202]
          Length = 302

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 45/191 (23%), Positives = 85/191 (44%), Gaps = 15/191 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V +KP  +++   G  +   +   LK    ++   P   HRLD+ET+G+++
Sbjct: 94  ILFENDDLLVVDKPHFLTISPTGQYVQETLLVRLKKQTGNEFLTP--IHRLDRETAGVVL 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             +   +     + F  R++ KIY ++    P  K+  +   L    + G  +  +    
Sbjct: 152 FCKRVESRGIYQQLFAERQVNKIYHAVA---PYKKELKLPQTLCLHLNKGTPFYTM---- 204

Query: 220 EKGANYAISHFKVIDCFAQKFCWLE--MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--- 274
           +  AN   +    I+       W +  + P TG+ HQLRVH  ++  PI  D  Y     
Sbjct: 205 QVVANAKANTQTYIELIEHNQIWAKYRLTPTTGKQHQLRVHLNYLDIPIKNDPFYPTVQH 264

Query: 275 NFKGNFTSPIQ 285
               +F+ P+Q
Sbjct: 265 KADNDFSEPLQ 275


>gi|225166280|ref|ZP_03727976.1| pseudouridine synthase [Opitutaceae bacterium TAV2]
 gi|224799481|gb|EEG18014.1| pseudouridine synthase [Opitutaceae bacterium TAV2]
          Length = 98

 Score = 47.8 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 28/96 (29%), Positives = 52/96 (54%), Gaps = 3/96 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQETSGILV 159
           ++YED  +  F+KP+G+ V            +L  +V  + G      HR+D +TSG+L+
Sbjct: 5   IVYEDETMLAFDKPSGLLVAPDRWDKNR--PYLMRYVHERYGHDTANVHRIDADTSGLLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +RT+ A  +L+  F+ +   KIY ++V  +P  ++
Sbjct: 63  CSRTKPALDYLSGQFQSKTPTKIYHAIVVILPPGRE 98


>gi|152998983|ref|YP_001364664.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151363601|gb|ABS06601.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 305

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 67/150 (44%), Gaps = 14/150 (9%)

Query: 147 THRLDQETSGIL---VVARTRAAAQHLTESFRMRR----IQKIYWSLVWGIPKNKKECIA 199
            HRLD+ET+G++   V   TRA    L     +R+    I K+   ++    +       
Sbjct: 133 AHRLDRETAGVILMTVAPETRALYHQLFIDDAIRKDYQAIAKLTPEIIQQYQQGSLTLPL 192

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +W +K      D    +K  E  AN   +H ++ +           + P TG+THQLRVH
Sbjct: 193 HWTVKNRMQPSDPSFTMKIVEGEAN---THSEISLVAIKGDLGLFHLSPITGKTHQLRVH 249

Query: 259 ALHMGCPIVGDHKYCANF-KG--NFTSPIQ 285
              +G P++ D  Y +   KG   F +P++
Sbjct: 250 MQSLGMPLLNDRFYPSLLPKGPDKFATPLK 279


>gi|315185198|gb|EFU18998.1| pseudouridine synthase [Spirochaeta thermophila DSM 6578]
          Length = 86

 Score = 47.8 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 23/51 (45%), Positives = 33/51 (64%), Gaps = 2/51 (3%)

Query: 138 DSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           D  G  PRL   +RLD+ TSGI++ AR R AA   ++ FR R + K+YW++
Sbjct: 36  DGAGAPPRLHLVNRLDRPTSGIVLFARHRKAAGKFSDLFRRRGVYKLYWAV 86


>gi|300717274|ref|YP_003742077.1| Pseudouridine synthase [Erwinia billingiae Eb661]
 gi|299063110|emb|CAX60230.1| Pseudouridine synthase [Erwinia billingiae Eb661]
          Length = 205

 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 33/109 (30%), Positives = 52/109 (47%), Gaps = 5/109 (4%)

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            KI+D+ +    H       +LY+D+ + + NKP G+    G     ++D      V   
Sbjct: 2   SKIIDTFIAPPCHEQIE---ILYQDAYLVLINKPTGLLSLSGKN-PQNLDSVHHRLVQ-L 56

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                L HRLD  TSG++V+AR +A    L   F  R + K+Y +L+ G
Sbjct: 57  FPGCTLIHRLDFGTSGLMVIARNKAINAALCHQFSQRTVTKVYSALLCG 105


>gi|126176071|ref|YP_001052220.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125999276|gb|ABN63351.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 305

 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 67/150 (44%), Gaps = 14/150 (9%)

Query: 147 THRLDQETSGIL---VVARTRAAAQHLTESFRMRR----IQKIYWSLVWGIPKNKKECIA 199
            HRLD+ET+G++   V   TRA    L     +R+    I K+   ++    +       
Sbjct: 133 AHRLDRETAGVILMTVAPETRALYHQLFIDDAIRKDYQAIAKLTPDIIEQYQQESLTLPL 192

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +W +K      D    +K  E  AN   +H ++ +           + P TG+THQLRVH
Sbjct: 193 HWTVKNRMQPSDPSFTMKIVEGEAN---THSEISLVAIKGDLGLFHLSPITGKTHQLRVH 249

Query: 259 ALHMGCPIVGDHKYCANF-KG--NFTSPIQ 285
              +G P++ D  Y +   KG   F +P++
Sbjct: 250 MQSLGMPLLNDRFYPSLLPKGPDKFATPLK 279


>gi|229493866|ref|ZP_04387638.1| ribosomal pseudouridine synthase [Rhodococcus erythropolis SK121]
 gi|229319143|gb|EEN84992.1| ribosomal pseudouridine synthase [Rhodococcus erythropolis SK121]
          Length = 319

 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 97/223 (43%), Gaps = 30/223 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +L+ D  + V +KP  +     SG        ++  V  +   P LT  HRLD+ T+G++
Sbjct: 92  ILHTDDDLVVIDKPHFLPTTP-SGRYLRESALVRLRV--RLDNPDLTPIHRLDRGTAGVV 148

Query: 159 VVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW------LLKKSHI- 208
           + +    TR A Q L   F  R++ K+Y + V   P    +    +      L+ ++HI 
Sbjct: 149 MFSARPATRGAYQSL---FEKRQVTKVYEA-VSARPTRWDQDAPGFAESDGPLVYRNHIE 204

Query: 209 ---GGDYVHVVKQNEKGANYAI-SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              G   V V    E  +   I +    +    +      ++P +GR HQLRVH   +G 
Sbjct: 205 ARRGELRVLVDDSREPNSETMIEARGTGVSASGRAVLHTVLRPQSGRMHQLRVHLAALGA 264

Query: 265 PIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            I+GD +Y     +   + + P+Q    L AR ++   P  G+
Sbjct: 265 GILGDRRYPDLLPDAPDDHSLPLQ----LLARELEFTDPLSGK 303


>gi|224066344|ref|XP_002187027.1| PREDICTED: similar to RNA pseudouridylate synthase
           domain-containing protein 3 [Taeniopygia guttata]
          Length = 270

 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 41/201 (20%), Positives = 87/201 (43%), Gaps = 22/201 (10%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           ++EQ  +++++   +    L+  +++ +  +   +KP G+ + G  G    +D  L +  
Sbjct: 6   MREQ--VEAALGPKETVRLLEGFVVHREGALLALSKPPGLPILGRPG-DLSLDSLLPALR 62

Query: 138 DSKGQKPRL--THRLDQETSGILVVAR----TRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
              G    L       +E SG+++++     T+   Q  T + R  +    Y ++  G+P
Sbjct: 63  RRLGLAAELHVVKAPAREYSGLVLLSSCYHTTKKLHQFFTSARRRGQYPATYRAVTVGVP 122

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
              +  ++  L              +Q    A   ++H++V+         L++QP T  
Sbjct: 123 AEVEGEVSTGL------------CWQQQGDRAMSTLTHYRVLSTTG-GCALLQLQPRTAF 169

Query: 252 THQLRVHALHMGCPIVGDHKY 272
             QL+VH   + CP +GDHK+
Sbjct: 170 PEQLQVHLTLLLCPALGDHKH 190


>gi|328868525|gb|EGG16903.1| hypothetical protein DFA_07884 [Dictyostelium fasciculatum]
          Length = 595

 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 39/135 (28%), Positives = 57/135 (42%), Gaps = 30/135 (22%)

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           ++++L+  S IG         N+ G  YA S F+ +  F       E+  HTGRTHQ+RV
Sbjct: 451 LSHYLVHGSSIGKGI------NKFGPRYAKSEFE-LKGFGAGKALFEVALHTGRTHQIRV 503

Query: 258 HALHMGCPIVGDHKYCANFKGN-FTSPIQN----------------------KLYLHARY 294
           H    G PIVGD  Y   F      S I+N                      +LYL + Y
Sbjct: 504 HMSESGFPIVGDPYYNPYFIDRVIQSNIKNIKDKEKESQQLNNDEDDDSEISRLYLQSYY 563

Query: 295 MDLPHPEGGRLQITA 309
           ++  HP   + ++  
Sbjct: 564 LEFIHPTSQQPEVVT 578


>gi|261867974|ref|YP_003255896.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413306|gb|ACX82677.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 155

 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 37/123 (30%), Positives = 57/123 (46%), Gaps = 15/123 (12%)

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           +++ F   +IQK Y +L    PK K+  I+   ++K+  G       K  +   N A++ 
Sbjct: 1   MSQKFAYHQIQKTYLALATHKPKKKQGRISG-DMQKARRG-----AWKLTQSKENPAVTD 54

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           F V    A       +QP T +THQLRV    +G PI+GD  Y  +          ++ Y
Sbjct: 55  F-VSHSLAPNLRLFILQPKTDKTHQLRVAMKSLGSPILGDALYGGD--------SADRTY 105

Query: 290 LHA 292
           LHA
Sbjct: 106 LHA 108


>gi|255022733|ref|ZP_05294719.1| pseudouridine synthase, RluA family protein [Listeria monocytogenes
           FSL J1-208]
          Length = 124

 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 51/94 (54%), Gaps = 8/94 (8%)

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             YA ++++V++ +   F  + +Q  TGRTHQ+RVH  ++G P++GD  Y  +      +
Sbjct: 30  GKYAKTNYEVLERYT-AFDHVAIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------T 82

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            +  +  LH+ ++ L HP     +    PLPA M
Sbjct: 83  TLLKRQALHSCHLHLVHPVTEEYMAFDLPLPADM 116


>gi|68481156|ref|XP_715493.1| potential pseudouridine synthase [Candida albicans SC5314]
 gi|68481297|ref|XP_715423.1| potential pseudouridine synthase [Candida albicans SC5314]
 gi|74585553|sp|Q5A0Y2|PUS5_CANAL RecName: Full=Pseudouridylate synthase PUS5; AltName:
           Full=Pseudouridine synthase 5; AltName: Full=Uracil
           hydrolyase PUS5
 gi|46437045|gb|EAK96398.1| potential pseudouridine synthase [Candida albicans SC5314]
 gi|46437117|gb|EAK96469.1| potential pseudouridine synthase [Candida albicans SC5314]
          Length = 247

 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 54/203 (26%), Positives = 87/203 (42%), Gaps = 27/203 (13%)

Query: 110 VFNKPAGISVQGG---SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           V NKP+G+        + I    + F K        + RL  RLD+  +G LVVAR +  
Sbjct: 14  VVNKPSGMVCDASHTNNIITALTNEFTKILPSVNSSQFRLVQRLDRFVTGGLVVARNKKW 73

Query: 167 AQHLTESFRMR---RIQKIYWSLVW--GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           A  + +SF      R+ + Y  L+    IP++ +  I         +  DY    K  E 
Sbjct: 74  ADKVRKSFFQEGTLRLTRRYVGLIALDQIPESTQGTID---FPIQALEKDYRGKNKSREL 130

Query: 222 GANYAISHFKVIDCFAQK----FCWLEMQP--------HTGRTHQLRVHALH-MGCPIVG 268
               A++H+K+I    +     F   +  P         TGR +Q+R H +   G P++ 
Sbjct: 131 FTYSAVTHYKLIPSARRTIKGVFPVFQQGPILPIILELETGRKNQIRDHIIQKFGVPLLN 190

Query: 269 DHKYCANFKGNFTSP--IQNKLY 289
           D  + ++FK N   P  + +KLY
Sbjct: 191 DDNF-SDFKLNSEIPKDVNSKLY 212


>gi|255528213|ref|ZP_05395034.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255508086|gb|EET84505.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 148

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 46/139 (33%), Positives = 70/139 (50%), Gaps = 23/139 (16%)

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++V G  K +KE I N  + ++   G+   VV  +E+G   +I+ + V + F  K
Sbjct: 13  EKSYLAVVHGNLK-EKEGIINLPIYRTD-DGNIRRVV--DERGQE-SITCYSVQESF-NK 66

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY-----LHARY 294
              +++   TGRTHQ+RVH  H+G P+ GD  Y           I++K Y     LHA  
Sbjct: 67  GDLVKLTLKTGRTHQIRVHMTHIGHPLYGDTLY---------GQIEDKEYIERQALHAYR 117

Query: 295 MDLPHP---EGGRLQITAP 310
           +  PHP   E   L+I  P
Sbjct: 118 LVFPHPRTREMLELEIGLP 136


>gi|183981253|ref|YP_001849544.1| pseudouridine synthase [Mycobacterium marinum M]
 gi|183174579|gb|ACC39689.1| pseudouridine synthase [Mycobacterium marinum M]
          Length = 288

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 59/261 (22%), Positives = 106/261 (40%), Gaps = 40/261 (15%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-------LLYEDSKIYVFNKPAGISVQG- 121
           V++A   I+    + +    +  + D  + +       +L++D  I V +KP  ++    
Sbjct: 45  VVDAAGAIVDTATVAEPGSYVYLYRDLPEEVPVPFEMPVLHQDEDIVVADKPHFLATMPR 104

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G  +A      L+  +      P   HRLD+ T+G+L+    R         F    ++K
Sbjct: 105 GRHVAQTALVRLRCELGLPELSP--AHRLDRLTAGVLLFTTRRELRGRYQTLFARGAVRK 162

Query: 182 IYWSLV-----WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            Y +          P+     I + ++K+    G    V +  E  A        +++  
Sbjct: 163 TYLARAAVDADLAFPR----VIRSRIVKRR---GHLQAVCEPGEPNAE------TLVELI 209

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYL 290
           + +  +  + P TGRTHQLRVH   +G PI GD  Y        +   +F+SP    L L
Sbjct: 210 SPEGLY-RLTPRTGRTHQLRVHMASLGLPIFGDPLYPNVIPESPHDLSDFSSP----LSL 264

Query: 291 HARYMDLPHP-EGGRLQITAP 310
            A+ ++   P  G R +  +P
Sbjct: 265 LAQRIEFEDPLSGSRREFVSP 285


>gi|306836036|ref|ZP_07469026.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           accolens ATCC 49726]
 gi|304568063|gb|EFM43638.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           accolens ATCC 49726]
          Length = 303

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 53/240 (22%), Positives = 92/240 (38%), Gaps = 49/240 (20%)

Query: 37  LQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           LQK+L        R  ++ +D  RV+ N  +   Q V++ P ++ +       ++    V
Sbjct: 65  LQKVLAKAGVASRRHAEILIDGGRVEVNGNVVLKQGVKVNPAVDVI-------RVDGVRV 117

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           N+             ED + ++ NKP G+       +     G + S   + GQ+     
Sbjct: 118 NVN------------EDQEYFILNKPRGMQSTMSDDLGRPCVGDVVSEKVASGQRLFHVG 165

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKS 206
           RLD +T G+L++      A  L        ++K Y + V G   NK  ++      L+  
Sbjct: 166 RLDADTEGLLILTNDGELANRLMHP--KYEVKKTYLATVLGEADNKLVRQLKEGIELEDG 223

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               D+V VV +N                  Q F  + ++ H GR H +R      G P+
Sbjct: 224 LAKADFVQVVDKN------------------QGFSLVRVELHEGRKHIVRRLLKEAGYPV 265


>gi|301167892|emb|CBW27477.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteriovorax marinus SJ]
          Length = 291

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 40/162 (24%), Positives = 79/162 (48%), Gaps = 15/162 (9%)

Query: 133 LKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L +++D SK  +  L +R+D+ETSG+++ A+  +  + + ++F     +K+Y ++V G  
Sbjct: 111 LSAFLDESKRGESNLLYRIDRETSGLMIFAKKNSIYESIRQNFNHMVKEKVYLAVVEG-- 168

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTG 250
           +  +E + +  L+     G  +      E+  +   S   +++   Q+    + ++   G
Sbjct: 169 EFNQEGVHSHYLESFGKKGAQMRAASSGEERVSIKTS---LVEYNEQRGLSLIRIELGQG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
             HQ+R     +G PIVGD  Y     G   S    +L+LHA
Sbjct: 226 VRHQIRCQLSEIGFPIVGDTLY-----GGCESS---RLFLHA 259


>gi|323446696|gb|EGB02765.1| hypothetical protein AURANDRAFT_34908 [Aureococcus anophagefferens]
          Length = 237

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 57/221 (25%), Positives = 90/221 (40%), Gaps = 34/221 (15%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-------PRLTHRLDQETSGILVVAR 162
             NKPAGISV        + D   +  V ++ Q+       P   HRLD  TSG L+   
Sbjct: 2   AVNKPAGISVH------RNKDTGRRRVVTTQLQRQFRRKVFP--AHRLDHRTSGALLFGF 53

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV--HVVKQNE 220
               A    ++       K Y  L+ G          +W       G D V    VK ++
Sbjct: 54  DGPTAGKAHDALAA--GTKEYLCLLRG---------GDW---PGEGGADVVVEKPVKGDD 99

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQ-PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                A + F+ +    +  C L +  P TGR HQ+R HA H+  P++GD K+  +    
Sbjct: 100 GAPRDARTVFRYLASQEEPRCTLCIAAPATGRPHQIRRHAQHLSMPVIGDSKHGDSRVNR 159

Query: 280 FTSPIQ--NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
           +    +  ++L LH   + L   +G  + + APL   + + 
Sbjct: 160 WWREERGLDRLALHCLAISLDDVDGEAVSLLAPLEGELARA 200


>gi|227503690|ref|ZP_03933739.1| pseudouridine synthase B [Corynebacterium accolens ATCC 49725]
 gi|227075726|gb|EEI13689.1| pseudouridine synthase B [Corynebacterium accolens ATCC 49725]
          Length = 303

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 53/240 (22%), Positives = 92/240 (38%), Gaps = 49/240 (20%)

Query: 37  LQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           LQK+L        R  ++ +D  RV+ N  +   Q V++ P ++ +       ++    V
Sbjct: 65  LQKVLAKAGVASRRHAEILIDAGRVEVNGNVILKQGVKVNPAVDVI-------RVDGVRV 117

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           N+             ED + ++ NKP G+       +     G + S   + GQ+     
Sbjct: 118 NVN------------EDQEYFILNKPRGMQSTMSDDLGRPCVGDVVSEKVASGQRLFHVG 165

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKS 206
           RLD +T G+L++      A  L        ++K Y + V G   NK  ++      L+  
Sbjct: 166 RLDADTEGLLILTNDGELANRLMHP--KYEVKKTYLATVLGEADNKLVRQLKEGIELEDG 223

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               D+V VV +N                  Q F  + ++ H GR H +R      G P+
Sbjct: 224 LAKADFVQVVDKN------------------QGFSLVRVELHEGRKHIVRRLLKEAGYPV 265


>gi|66358534|ref|XP_626445.1| Yd1036cp-like RluD, S4+type 1 pseudouridine synthase
           [Cryptosporidium parvum Iowa II]
 gi|46227837|gb|EAK88757.1| Yd1036cp-like RluD, S4+type 1 pseudouridine synthase
           [Cryptosporidium parvum Iowa II]
          Length = 481

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 59/270 (21%), Positives = 113/270 (41%), Gaps = 56/270 (20%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE-QKILDSSVNLTKHSDFLKSILLYEDS 106
           +D++R+  N+           PV N+L++I++   KI   S+ +       K  +LY+ S
Sbjct: 84  IDQRRLSVNDT----------PV-NSLDYIVRNGDKIKHRSLFIELPVAIDKVKILYDSS 132

Query: 107 KIYVFNKPAGISV--QG---GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
            +    KP GI    QG      +   I     S +++        +RLD+ TSG+++++
Sbjct: 133 TLLAVFKPCGIPCHPQGRFNKLSLTKLIQSEYLSKLNTNSTYIHPINRLDRVTSGLVLLS 192

Query: 162 RTRAAAQHLTES------FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +  +  ++L+        + +  I +   + +  I ++  E ++   L      G   HV
Sbjct: 193 KDSSTTKNLSSKVQFAHKYYLAMINESTSNFISHISQSSIEGVSIRELSLDESHGITSHV 252

Query: 216 VK--------------------QNEKGANYAISHF-KVIDCF------------AQKFCW 242
           +K                     + + + Y++++F  +I C               K+  
Sbjct: 253 IKCEIGLKTLKDREGESLITRIDSSENSKYSLTYFFPLISCLDINEAKKQKINETDKYSI 312

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           L  +P TGRTHQ+R H  ++G PIV D  Y
Sbjct: 313 LLCKPITGRTHQIRAHLKYIGFPIVRDILY 342


>gi|270719457|ref|ZP_06223312.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           influenzae HK1212]
 gi|270315435|gb|EFA27693.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           influenzae HK1212]
          Length = 162

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 45/90 (50%), Gaps = 19/90 (21%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPR--LTHR 149
           ++YED  I V NKP  + V  G+G         + YH    +        + PR  + HR
Sbjct: 81  IVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIV--------EVPRAGIVHR 132

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRI 179
           LD++T+G++VVA+T  A   L    + R+I
Sbjct: 133 LDKDTTGLMVVAKTIPAQTKLVRDLQKRKI 162


>gi|313499768|gb|ADR61134.1| Pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 294

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 50/197 (25%), Positives = 100/197 (50%), Gaps = 21/197 (10%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQET 154
           ++ ++L+ D  + V +KP  + V   +    +++  L   +  +   P L   HR+D+ T
Sbjct: 84  VQEVVLHVDEHLVVADKPHFLPV---TPTGEYVEQTLLRRLIRRLDNPHLVPLHRIDRHT 140

Query: 155 SGILVVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGG 210
           +G+++ +    +R+A Q L   F  RRI K Y ++   +P++     A  L+ KS  + G
Sbjct: 141 AGLVLFSANPHSRSAYQRL---FPERRIDKRYQAIAAAMPQH-----AFPLVHKSRLVHG 192

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +    + + E  AN + +  +V++   +++ +  + P TG+THQLRVH   +G  I  D 
Sbjct: 193 EPFFRMHEVEGEAN-SETLAEVLEKNGERWRY-GLSPVTGKTHQLRVHMAALGAGISNDP 250

Query: 271 KY--CANFKGNFTSPIQ 285
            Y    N + ++  P++
Sbjct: 251 FYPQLLNEEDDYQRPLK 267


>gi|302682125|ref|XP_003030744.1| hypothetical protein SCHCODRAFT_16635 [Schizophyllum commune H4-8]
 gi|300104435|gb|EFI95841.1| hypothetical protein SCHCODRAFT_16635 [Schizophyllum commune H4-8]
          Length = 506

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 49/190 (25%), Positives = 75/190 (39%), Gaps = 39/190 (20%)

Query: 100 ILLYEDSKIY-VFNKPAGISVQGGSG--------IAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +LL++  + + V NKP  I V             I  H  GF K +           +RL
Sbjct: 104 VLLHDTERGFIVVNKPGSIPVHAAGRYNRNSLIHILMHEMGFKKVYT---------VNRL 154

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIG 209
           D+ TSG++++      A+ LT+ F    ++K Y + V G  P  +  C    L     +G
Sbjct: 155 DRLTSGLMIIPLNADLARSLTKEFIEGSVRKEYVARVKGKFPDGEVICEEPLLTVDRQMG 214

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR----THQLRVHALHMGCP 265
            + VH   +  K                  F  +   PHT      +HQLRVH  ++G P
Sbjct: 215 LNIVHPEGRPAKTV----------------FNKIRYDPHTNSSVIHSHQLRVHLQYLGYP 258

Query: 266 IVGDHKYCAN 275
           I  D  Y + 
Sbjct: 259 IANDPVYSSE 268


>gi|15618318|ref|NP_224603.1| pseudouridine synthetase family protein [Chlamydophila pneumoniae
           CWL029]
 gi|15835936|ref|NP_300460.1| pseudouridine synthetase family protein [Chlamydophila pneumoniae
           J138]
 gi|33241749|ref|NP_876690.1| pseudouridine synthetase [Chlamydophila pneumoniae TW-183]
 gi|4376683|gb|AAD18547.1| predicted pseudouridine synthetase family [Chlamydophila pneumoniae
           CWL029]
 gi|8978775|dbj|BAA98611.1| pseudouridine synthetase family [Chlamydophila pneumoniae J138]
 gi|33236258|gb|AAP98347.1| pseudouridine synthetase [Chlamydophila pneumoniae TW-183]
          Length = 232

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 48/94 (51%), Gaps = 16/94 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED    ++ KP  ++ +  +    H+  F               HRLD+ TSG L++
Sbjct: 87  ILWEDDYSIIYEKPPHLTTEQMA----HMTRFFT------------VHRLDKGTSGCLLM 130

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +++ AA  L + F+ R+I K Y + V+G PK K
Sbjct: 131 GKSKQAATELMKLFKQRKIHKQYIAFVFGHPKKK 164


>gi|255071535|ref|XP_002499442.1| predicted protein [Micromonas sp. RCC299]
 gi|226514704|gb|ACO60700.1| predicted protein [Micromonas sp. RCC299]
          Length = 474

 Score = 47.4 bits (111), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 54/221 (24%), Positives = 83/221 (37%), Gaps = 63/221 (28%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIP-----------KNKK 195
           HRLD  TSG+LV+AR  + A    ++ R RR+ K Y  +    +P              +
Sbjct: 249 HRLDVATSGVLVLARRSSFAAEFNDALRRRRVTKTYECVTARAVPVGVLEHWTEESSGAR 308

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE----------- 244
           E  A + +++   G      V  + K   Y+   F   D   +K C L            
Sbjct: 309 EGPARFEMRELEPGDPRWRDVAADGK---YSDDAFVTPD--GRKLCVLRVLGCEETEGLT 363

Query: 245 ------------------------MQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFK 277
                                   ++  TGRTHQ+R     +GCPI+GD  Y     + +
Sbjct: 364 KRLTKRLAGEAGEAGEASRAYVSTIELVTGRTHQIRAQLSAIGCPILGDVLYGGVDLSRE 423

Query: 278 GNFTSPI---QNKLYLHARYMDLPH-----PEGGRLQITAP 310
           G  T  +    ++L LHA  M +       P+G  L+   P
Sbjct: 424 GGATPRVLRDDDRLCLHAAEMRMDADSALGPKGTTLRAGPP 464


>gi|160873570|ref|YP_001552886.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160859092|gb|ABX47626.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315265800|gb|ADT92653.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 303

 Score = 47.4 bits (111), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 67/150 (44%), Gaps = 14/150 (9%)

Query: 147 THRLDQETSGIL---VVARTRAAAQHLTESFRMRR----IQKIYWSLVWGIPKNKKECIA 199
            HRLD+ET+G++   V   TRA    L     +R+    I K+   ++    +       
Sbjct: 133 AHRLDRETAGVILMTVAPETRALYHQLFIDDAIRKDYQAIAKLKPDIIEQYQQGNLTLPL 192

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +W +K      D    +K  E  AN   +H ++ +           + P TG+THQLRVH
Sbjct: 193 HWTVKNRMQPSDPSFTMKIVEGEAN---THSEISLVAIKGDLGLFHLSPITGKTHQLRVH 249

Query: 259 ALHMGCPIVGDHKYCANF-KG--NFTSPIQ 285
              +G P++ D  Y +   KG   F +P++
Sbjct: 250 MQSLGMPLLNDRFYPSLLPKGPDKFATPLK 279


>gi|296119226|ref|ZP_06837795.1| RNA pseudouridine synthase [Corynebacterium ammoniagenes DSM 20306]
 gi|295967747|gb|EFG81003.1| RNA pseudouridine synthase [Corynebacterium ammoniagenes DSM 20306]
          Length = 326

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 47/191 (24%), Positives = 76/191 (39%), Gaps = 31/191 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++YED+ I V +KP  ++       A HI     +K    +        HRLD+ TSG+L
Sbjct: 107 IVYEDADILVADKPPFMATMPR---ARHIVETATVKLRRSTGIDDLAPAHRLDRLTSGLL 163

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLV----WGIPKNKKECIANWLLKKSHIGGDYVH 214
           +  + R         F  R + K Y ++     +  P         W  +     G+   
Sbjct: 164 LFTKHREVRGAYQTLFARREVHKTYSAIADYADFSTP-------LTWQSRMEKTPGEIQG 216

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLE-------------MQPHTGRTHQLRVHALH 261
            +++ E   N   +   V+    ++   LE             + P TG+THQLR+H   
Sbjct: 217 RIEEGE--INAITTLVGVVPLTGEEQKALEKIHGEQSALARYTLAPETGKTHQLRLHMWA 274

Query: 262 MGCPIVGDHKY 272
            G PI+GD  Y
Sbjct: 275 AGVPILGDPVY 285


>gi|330888288|gb|EGH20949.1| pseudouridine synthase [Pseudomonas syringae pv. mori str. 301020]
          Length = 324

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 90/210 (42%), Gaps = 20/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +LY D  +   +KP  + V       Y     L+  +   G  P L   HR+D+ T+G++
Sbjct: 117 ILYADEHLVGADKPHFLPVTPAG--EYVEQTLLRRLIHRLG-NPDLVPLHRIDRHTAGLV 173

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           + +   +TR+A Q L   F  R+I K Y ++   +P      +    L +S +       
Sbjct: 174 LFSANRQTRSAYQAL---FPTRQIDKFYEAIAPALPG-----LEFPRLHESRLVEGEPFF 225

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             Q   GA+   +  +V++   Q   W   + P TG+ HQLRVH   +G  I  D  Y  
Sbjct: 226 RMQEGAGASNTRTQIEVLE--RQDQLWRYGLYPVTGKKHQLRVHMAALGAGICNDPFYPD 283

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             K N     QN L L A+ +    P  G+
Sbjct: 284 VVK-NPVDDYQNPLKLLAKGLRFIDPLSGK 312


>gi|322788452|gb|EFZ14121.1| hypothetical protein SINV_06605 [Solenopsis invicta]
          Length = 299

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 44/165 (26%), Positives = 70/165 (42%), Gaps = 35/165 (21%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD  TSG++ +A  + AA+  + +F   ++QK Y +LV G             + +
Sbjct: 102 FVHRLDYPTSGVMCIALNKRAARAASFAFENHKVQKFYLALVHG------------HIHE 149

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------------------LEMQP 247
            HI  D        EK  N+ +       C   +  +                  + + P
Sbjct: 150 PHIVIDRPIGADIREKTGNHKMCTSDSAFCDKPRKSYTTLVVLEHGYWKGKPATKILLAP 209

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            TGR HQLRVH  H+G  ++GD+ Y    +G    P  ++ YLH+
Sbjct: 210 GTGRRHQLRVHCHHIGHTVIGDYTYS---EGKDVEP--HRTYLHS 249


>gi|322488012|emb|CBZ23257.1| RNA pseudouridylate synthase-like protein [Leishmania mexicana
            MHOM/GT/2001/U1103]
          Length = 1455

 Score = 47.0 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 35/127 (27%), Positives = 63/127 (49%), Gaps = 21/127 (16%)

Query: 206  SHIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHM 262
            +H+   Y  +H   Q+++ A   I+ ++V++ FA     +++++  +GR HQ+R H   +
Sbjct: 1307 AHVHQQYATLHAALQDQRNA---ITRYRVLEYFASAGVAYVQVELRSGRRHQIRQHFAQL 1363

Query: 263  GCPIVGDHKYCANF---KGNFTSPIQNKLYLHARYMDLPHPEGG-----------RLQIT 308
            G P+VGD +Y A     +   T  +Q +  LHA  +D+     G           R+ + 
Sbjct: 1364 GFPLVGDARYHAGVVAGRAGTTFGMQ-RAALHAYTIDILATTDGDGLASGEEVPDRVVVQ 1422

Query: 309  APLPAHM 315
            A LPA M
Sbjct: 1423 AALPADM 1429


>gi|255019167|ref|ZP_05291293.1| hypothetical protein LmonF_18021 [Listeria monocytogenes FSL
           F2-515]
          Length = 163

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 41/173 (23%), Positives = 80/173 (46%), Gaps = 24/173 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE +E+ + L  + K+ +     +   K    G++ V+ +       ++ G  VR+    
Sbjct: 7   VETEEDGLLLRTFLKSKHISKQLLTAVKFGADGKIEVNSEEQNVLXHVKVGDKVRLTFPT 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              N     +++L    NL          +++ED  + + NKPAG++        YH +G
Sbjct: 67  EQQN-----ERLLAEYTNLD---------IVFEDDFLLIINKPAGMASIPSQ---YHPNG 109

Query: 132 FLKSWVDSKGQKPRLTH------RLDQETSGILVVARTRAAAQHLTESFRMRR 178
            + ++V    +   LT+      RLD+ETSG++++A+ R A   L+ +F  +R
Sbjct: 110 SVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLS-TFLXKR 161


>gi|213970524|ref|ZP_03398651.1| Pseudouridine synthase [Pseudomonas syringae pv. tomato T1]
 gi|301384145|ref|ZP_07232563.1| pseudouridine synthase [Pseudomonas syringae pv. tomato Max13]
 gi|302064014|ref|ZP_07255555.1| pseudouridine synthase [Pseudomonas syringae pv. tomato K40]
 gi|302132672|ref|ZP_07258662.1| pseudouridine synthase [Pseudomonas syringae pv. tomato NCPPB 1108]
 gi|213924695|gb|EEB58263.1| Pseudouridine synthase [Pseudomonas syringae pv. tomato T1]
          Length = 296

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 47/181 (25%), Positives = 80/181 (44%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + V +KP  + V   G  +   +   L   +D+    P   HR+D+ T+G+++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAGEYVEQTLLRRLIHRLDNPDLVP--LHRIDRHTAGLVL 146

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +   +TR+A Q L   F  RRI K Y ++   +P      +    L +S +        
Sbjct: 147 FSANRQTRSAYQTL---FPTRRIDKCYEAIAPALPG-----LEFPRLHESRLVEGEPFFR 198

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            Q   G +   +  +V++     + +  + P TG+ HQLRVH   +G  I  D  Y    
Sbjct: 199 MQEGPGVSNTQTRIEVLERHGPLWRY-RLHPVTGKKHQLRVHMAALGAAICNDPFYPDAL 257

Query: 277 K 277
           K
Sbjct: 258 K 258


>gi|315930491|gb|EFV09543.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 144

 Score = 47.0 bits (110), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 57/111 (51%), Gaps = 7/111 (6%)

Query: 82  KILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGI-SVQGGSGIAYHI-DGFLKSWVD 138
           KIL+  V L  + +  K + +++E+    +  K +GI S   G    Y + D     W  
Sbjct: 32  KILNGLVELIVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHLW-- 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             G++  + HRLD+ETSG++++A+ + A   L   F  + +QK Y +L  G
Sbjct: 90  --GKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALAHG 138


>gi|148548835|ref|YP_001268937.1| pseudouridine synthase [Pseudomonas putida F1]
 gi|148512893|gb|ABQ79753.1| pseudouridine synthase [Pseudomonas putida F1]
          Length = 301

 Score = 47.0 bits (110), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 47/196 (23%), Positives = 97/196 (49%), Gaps = 19/196 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQET 154
           ++ ++L+ D  + V +KP  + V   +    +++  L   +  +   P L   HR+D+ T
Sbjct: 91  VQEVVLHVDEHLVVADKPHFLPV---TPTGEYVEQTLLRRLIRRLDNPHLVPLHRIDRHT 147

Query: 155 SGILVVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +G+++ +    +R+A Q L   F  RRI K Y ++   +P++    +     K   + G+
Sbjct: 148 AGLVLFSANPHSRSAYQRL---FPERRIDKRYQAIAAAMPQHTFPLVH----KSRLVHGE 200

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               + + E  AN + +  +V++   +++ +  + P TG+THQLRVH   +G  I  D  
Sbjct: 201 PFFRMHEVEGEAN-SETLAEVLEKNGERWRY-GLSPVTGKTHQLRVHMAALGAGISNDPF 258

Query: 272 Y--CANFKGNFTSPIQ 285
           Y    N + ++  P++
Sbjct: 259 YPQLLNEEDDYQRPLK 274


>gi|183234131|ref|XP_648993.2| hypothetical protein [Entamoeba histolytica HM-1:IMSS]
 gi|169801245|gb|EAL43600.2| hypothetical protein, conserved [Entamoeba histolytica HM-1:IMSS]
          Length = 402

 Score = 47.0 bits (110), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 50/182 (27%), Positives = 83/182 (45%), Gaps = 11/182 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  ++ E +     +KP+ I V       ++   F+ +       +P   HRLD+ TSGI
Sbjct: 145 KLTIVKETNDFIAIDKPSSIPVHPCGRYRHNTVIFILAHEGYTNLRP--VHRLDRMTSGI 202

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-V 216
           L++A+T  AA+       +++  K Y   V G  + +K  + + + +K  I    +HV V
Sbjct: 203 LLLAKTIQAAREFQSYMTIKK--KEYLCRVRG--RLEKTTVTSKIGRKR-IDDKKIHVSV 257

Query: 217 KQNEKGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + E+      S F  +  D        + +   +GRTHQ+RVH   +  PIV D  Y A
Sbjct: 258 NEIEEDGKECHSEFNPLFYDEKTNTTVAVALLG-SGRTHQIRVHLQSIHHPIVNDPIYAA 316

Query: 275 NF 276
            F
Sbjct: 317 QF 318


>gi|304411496|ref|ZP_07393109.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307306728|ref|ZP_07586470.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304350023|gb|EFM14428.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306910696|gb|EFN41125.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 305

 Score = 47.0 bits (110), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 40/150 (26%), Positives = 67/150 (44%), Gaps = 14/150 (9%)

Query: 147 THRLDQETSGIL---VVARTRAAAQHLTESFRMRR----IQKIYWSLVWGIPKNKKECIA 199
            HRLD+ET+G++   V   TRA    L     +R+    I K+   ++    +       
Sbjct: 133 AHRLDRETAGVILMTVAPETRALYHQLFIDDAIRKDYQAIAKLTPEIIQQYQQGSLTLPL 192

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +W ++      D    +K  E  AN   +H ++ +           + P TG+THQLRVH
Sbjct: 193 HWTVRNRMQPSDPSFTMKIVEGEAN---THSEISLVAIKGDLGLFHLSPITGKTHQLRVH 249

Query: 259 ALHMGCPIVGDHKYCANF-KG--NFTSPIQ 285
              +G P++ D  Y +   KG   F +P++
Sbjct: 250 MQSLGMPLLNDRFYPSLLPKGPDKFATPLK 279


>gi|157871141|ref|XP_001684120.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|68127188|emb|CAJ05143.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 977

 Score = 47.0 bits (110), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 5/47 (10%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKL 288
           P+TGR HQ+R+H   +GCPIVGD  Y      A+  G  ++P+Q  L
Sbjct: 643 PYTGRLHQIRMHLSSLGCPIVGDVVYAPTSGSADVPGTPSTPVQPPL 689


>gi|296168884|ref|ZP_06850555.1| RNA pseudouridine synthase [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295896450|gb|EFG76101.1| RNA pseudouridine synthase [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 279

 Score = 47.0 bits (110), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 46/212 (21%), Positives = 84/212 (39%), Gaps = 21/212 (9%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-------LLYEDSKIYVFNKPAGISVQG- 121
           V++A    + E   L +  ++  + +  + +       +L+ D+ I V +KP  ++    
Sbjct: 38  VVDADGSPVDEATALPAGASVYLYRELPEEVPVPFDIPVLHRDADIVVVDKPHFLATMPR 97

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G  +A      L+  +      P   HRLD+ T+G+L+    R         F    ++K
Sbjct: 98  GRHVAQTALVRLRRELGLPELSP--AHRLDRLTAGVLLFTARREVRGAYQTLFSRGLVRK 155

Query: 182 IYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y +     P       + + ++K+  +           + G      + + +   A   
Sbjct: 156 TYLARAAVDPALVLPRVVRSRIIKRRGV----------LQAGCEPGTPNAETLVELASPD 205

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               + P TGRTHQLRVH   +G PI GD  Y
Sbjct: 206 GLYRLTPRTGRTHQLRVHMAALGVPIDGDPLY 237


>gi|118618124|ref|YP_906456.1| pseudouridine synthase [Mycobacterium ulcerans Agy99]
 gi|118570234|gb|ABL04985.1| pseudouridine synthase [Mycobacterium ulcerans Agy99]
          Length = 288

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 59/261 (22%), Positives = 106/261 (40%), Gaps = 40/261 (15%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-------LLYEDSKIYVFNKPAGISVQG- 121
           V++A   I+    +     ++  + D  + +       +L++D  I V +KP  ++    
Sbjct: 45  VVDAAGAIVGTATVAGPGSHVYLYRDLPEEVPVPFEMPVLHQDEDIVVADKPHFLATMPR 104

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G  +A      L+  +      P   HRLD+ T+G+L+    R         F    ++K
Sbjct: 105 GRHVAQTALVRLRCELGLPELSP--AHRLDRLTAGVLLFTTRRELRGRYQTLFARGAVRK 162

Query: 182 IYWSLV-----WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            Y +          P+     I + ++K+    G    V +  E  A        +++  
Sbjct: 163 TYLARAAVDADLAFPR----VIRSRIVKRR---GHLQAVCEPGEPNAE------TLVELI 209

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYL 290
           + +  +  + P TGRTHQLRVH   +G PI GD  Y        +   +F+SP    L L
Sbjct: 210 SPEGLY-RLTPRTGRTHQLRVHMASLGLPIFGDPLYPNVIPESPHDLSDFSSP----LSL 264

Query: 291 HARYMDLPHP-EGGRLQITAP 310
            A+ ++   P  G R +  +P
Sbjct: 265 LAQRIEFEDPLSGSRREFVSP 285


>gi|217971665|ref|YP_002356416.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217496800|gb|ACK44993.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 305

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 40/150 (26%), Positives = 67/150 (44%), Gaps = 14/150 (9%)

Query: 147 THRLDQETSGIL---VVARTRAAAQHLTESFRMRR----IQKIYWSLVWGIPKNKKECIA 199
            HRLD+ET+G++   V   TRA    L     +R+    I K+   ++    +       
Sbjct: 133 AHRLDRETAGVILMTVAPETRALYHQLFIDDAIRKDYQAIAKLTPDIIEQYQQGSLTLPL 192

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +W ++      D    +K  E  AN   +H ++ +           + P TG+THQLRVH
Sbjct: 193 HWTVRNRMQPSDPSFTMKIVEGEAN---THSEISLVAIKGDLGLFHLSPITGKTHQLRVH 249

Query: 259 ALHMGCPIVGDHKYCANF-KG--NFTSPIQ 285
              +G P++ D  Y +   KG   F +P++
Sbjct: 250 MQSLGMPLLNDRFYPSLLPKGPDKFATPLK 279


>gi|294877459|ref|XP_002767995.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239870127|gb|EER00713.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 439

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 49/169 (28%), Positives = 76/169 (44%), Gaps = 51/169 (30%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD  TSG L++A       H  + F M R       LV+   +  KE +A   L K
Sbjct: 203 ILHRLDVGTSGPLLLA-------HSYKGFYMGR-------LVFCSHQIDKEYVA---LVK 245

Query: 206 SHIG--------GDYVHVVKQN-EKGANYA------------------ISHFKVIDCFAQ 238
            H+G         D + ++K   + G +Y+                  ++H+   D   +
Sbjct: 246 GHMGTVGKNIVISDRIKILKSTLDNGQSYSTTCVVAPDGKPSLTEVVPVAHYN--DGSGE 303

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           ++  + ++ HTGRTHQ+RVH  ++G P+V D KY     GN T P   K
Sbjct: 304 EYSLVLVKLHTGRTHQIRVHMAYIGHPLVCDPKY-----GNPTDPEAAK 347


>gi|256089816|ref|XP_002580951.1| ribosomal pseudouridine synthase [Schistosoma mansoni]
 gi|238666672|emb|CAZ37190.1| ribosomal pseudouridine synthase, putative [Schistosoma mansoni]
          Length = 370

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 40/157 (25%), Positives = 65/157 (41%), Gaps = 33/157 (21%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLK 204
             HRLD  TSG++ +A    AA  +  +F  + ++K Y ++VWG +       +++  +K
Sbjct: 99  FVHRLDCPTSGLICIAYDTKAASMIRRAFENKEVKKYYLAIVWGYVGSFCDSGLSSSFVK 158

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHF----KVIDCFAQKFCW------------------ 242
                   VH ++ +     Y   +     K+I       C+                  
Sbjct: 159 HE---SKLVHHIQMSIGSFRYLWPNTGRKQKIIVPITHPECYRPRESLTTVIVLDYGKLM 215

Query: 243 ------LEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
                 + + P TGR HQLRVH A+ +G PI GD  Y
Sbjct: 216 GEPATHILLIPETGRRHQLRVHCAIGLGHPIAGDTTY 252


>gi|257124830|ref|YP_003162944.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
 gi|257048769|gb|ACV37953.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
          Length = 380

 Score = 46.6 bits (109), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 225 YAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
           YA +  KV+  + +K   L E +  TGRTHQ+RVH   +G  IVGD  Y           
Sbjct: 284 YAKTAIKVLKVYPEKNVTLVECELFTGRTHQIRVHLKSIGHTIVGDELYGNGLNKELGI- 342

Query: 284 IQNKLYLHARYMDLPHP 300
             N+ +LHA  +   HP
Sbjct: 343 --NRQFLHAYKVKFIHP 357


>gi|91791846|ref|YP_561497.1| pseudouridine synthase [Shewanella denitrificans OS217]
 gi|91713848|gb|ABE53774.1| pseudouridine synthase [Shewanella denitrificans OS217]
          Length = 312

 Score = 46.6 bits (109), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 40/149 (26%), Positives = 64/149 (42%), Gaps = 12/149 (8%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIA 199
            HRLD++T+GI+++             F   +I K Y +L    P+              
Sbjct: 139 AHRLDKDTAGIVLLTLNPEVRHQYHNLFTQGQISKHYHALAKLTPEIHAAHQGGGLRLPL 198

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            W +K + +G      + Q  +G   + S  ++I    +      + P TG+THQLRVH 
Sbjct: 199 TWTVK-NRLGPATPSFLMQLVEGEANSHSEIQLI-AIKEDMGLFALSPITGKTHQLRVHM 256

Query: 260 LHMGCPIVGDHKYCA-NFKG--NFTSPIQ 285
             +G PI+ D  Y     KG  NF  P++
Sbjct: 257 QSLGVPILNDRFYPQLQPKGVDNFDKPLK 285


>gi|307109346|gb|EFN57584.1| hypothetical protein CHLNCDRAFT_16942 [Chlorella variabilis]
          Length = 275

 Score = 46.6 bits (109), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 70/277 (25%), Positives = 112/277 (40%), Gaps = 34/277 (12%)

Query: 18  NMRLDRWF--------KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           NMR  RWF           +P  +    Q+ L  G++RV+  +V     ++ GQ +R   
Sbjct: 11  NMR-QRWFGQNIIDIFTREFPARDRQYYQQALADGRLRVEGCQVTAETPLKDGQCIR--- 66

Query: 70  VINALNHIIK--EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                 H I   E  +   S+ +   S+   ++       ++V  +    +V G    A 
Sbjct: 67  ------HFIHRHEAPVPAGSIQVVGQSEDAVAVCKPHGMPVHVAGQYRKNTVLG-ILTAE 119

Query: 128 HI-----DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           H         ++S        P    RLD+  SG+L+ AR+ AAA  L        ++K+
Sbjct: 120 HTRLPVSPCLIRSDCSHHAPAPLPVCRLDKPVSGLLLFARSAAAAAALCGRIEGHAVEKV 179

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN------EKG-ANYAISHFKVIDC 235
           Y + V G       C A  L K++                    KG A  A + F+++  
Sbjct: 180 YVARVLGRFPATGVCTACKLRKQAKAERAAAAAAAAAAAAKKPSKGPAKPARTEFRLLA- 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            A+      ++P TGRTHQ+RVH  H+G PI  D +Y
Sbjct: 239 VAEDGLTSVVEPRTGRTHQIRVHLQHLGHPIANDTQY 275


>gi|260434982|ref|ZP_05788952.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp. WH
           8109]
 gi|260412856|gb|EEX06152.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp. WH
           8109]
          Length = 248

 Score = 46.6 bits (109), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 39/166 (23%), Positives = 69/166 (41%), Gaps = 27/166 (16%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPP 69
           V   +  + +  W  + Y H +    Q+ + +G++  +   +  +  +  G+ +  R PP
Sbjct: 20  VPRADAGLLVSEWLADRYRHSDRAVWQQRIAAGELDWNGALLTGDRALHGGETLFWRRPP 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +        EQ I D    +            ++D  + V NKP+G+ V  G G   H 
Sbjct: 80  WL--------EQAIPDQWETI------------HDDGDLLVINKPSGLPVMPGGGFLRHT 119

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
              L + ++  G  P   HRL + TSG+ V ART       ++ FR
Sbjct: 120 ---LTALLEHAGALP--VHRLGRFTSGLQVCARTPQTRALWSKQFR 160


>gi|86739288|ref|YP_479688.1| pseudouridine synthase [Frankia sp. CcI3]
 gi|86566150|gb|ABD09959.1| pseudouridine synthase [Frankia sp. CcI3]
          Length = 304

 Score = 46.6 bits (109), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 34/110 (30%), Positives = 53/110 (48%), Gaps = 7/110 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I V +KP GISV G        D  L +     G++    HR+D+ TSG+++ 
Sbjct: 1   MIYEDEAILVLDKPVGISVMG-----ERHDTDLVTLAGDDGEELFPVHRIDKVTSGLVLF 55

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSL--VWGIPKNKKECIANWLLKKSHI 208
           AR       LT  F+ R + K Y  L    G+P +    +   + +KS +
Sbjct: 56  ARQLRFHGDLTRQFQRRTVDKRYLVLTRTRGLPASGTVDLPLSVGRKSRV 105


>gi|71404491|ref|XP_804947.1| RNA pseudouridylate synthase [Trypanosoma cruzi strain CL Brener]
 gi|70868160|gb|EAN83096.1| RNA pseudouridylate synthase, putative [Trypanosoma cruzi]
          Length = 588

 Score = 46.6 bits (109), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 53/194 (27%), Positives = 88/194 (45%), Gaps = 38/194 (19%)

Query: 112 NKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTR 164
           NKPAG+S      +AY H+  +L   V  KG       +  L +R+D  TSG+++V  T 
Sbjct: 319 NKPAGMSTT--LHVAYPHLIQYLSRCVPWKGVDIPVLFQHGLVNRIDVGTSGLVLVTDT- 375

Query: 165 AAAQHLTESFRM----RRIQKIYWSLVWGIPKNKKECIAN--WLLKKSHI--------GG 210
                L  + R     RR++KIY +LV   P  +    +   W L    +        G 
Sbjct: 376 --GNSLVATRRASVVDRRVEKIYRALVLHCPPPESRAGSEEFWYLNPKGVINWNVFANGA 433

Query: 211 DYVHVVK----QNEKGA-------NYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVH 258
           DY   +     + ++G          A + ++V++ + +    +LE+Q  +GR HQ+R H
Sbjct: 434 DYSLQLAAHDPERKRGLPPAFMDRRPATTMYRVLNYYPSSGVYYLEVQLRSGRRHQIRQH 493

Query: 259 ALHMGCPIVGDHKY 272
              +  P+VGD +Y
Sbjct: 494 FAQICHPLVGDGRY 507


>gi|293609404|ref|ZP_06691706.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292827856|gb|EFF86219.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 302

 Score = 46.6 bits (109), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 45/206 (21%), Positives = 85/206 (41%), Gaps = 45/206 (21%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+E+  + V +KP  +++   G  +   +   LK    ++   P   HRLD+ET+G+++
Sbjct: 94  ILFENDDLLVVDKPHFLTISPTGQYVQETLLVRLKKQTGNEFLTP--IHRLDRETAGVVL 151

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVW-----------------GIPKNKKECIANWL 202
             +   +     + F  R++ KIY ++                   G+P    + I N  
Sbjct: 152 FCKQVESRGIYQQLFAERQVNKIYHAIAPYKKDLNFPQTLHLHLDKGLPFYTMQVIENAK 211

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                    Y+ +++ N+  A Y ++                  P TG+ HQLRVH  ++
Sbjct: 212 ANTQ----TYIELIEHNQIWAKYRLT------------------PTTGKQHQLRVHLNYL 249

Query: 263 GCPIVGDHKYCA---NFKGNFTSPIQ 285
             PI  D  Y       + +F+ P+Q
Sbjct: 250 EIPIKNDPFYPVVQHKAEDDFSEPLQ 275


>gi|146320633|ref|YP_001200344.1| YlyB [Streptococcus suis 98HAH33]
 gi|145691439|gb|ABP91944.1| YlyB [Streptococcus suis 98HAH33]
          Length = 86

 Score = 46.6 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 6/71 (8%)

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E+   T RTHQ+RVH  ++G P+ GD  Y     G   +   +  +LHAR +   HP  G
Sbjct: 8   ELTWETERTHQIRVHMAYIGHPVAGDEAY-----GPRKTLKGHGQFLHARTLGFTHPRTG 62

Query: 304 R-LQITAPLPA 313
             ++ TA  PA
Sbjct: 63  EVVEFTAEAPA 73


>gi|95930635|ref|ZP_01313369.1| pseudouridine synthase [Desulfuromonas acetoxidans DSM 684]
 gi|95133287|gb|EAT14952.1| pseudouridine synthase [Desulfuromonas acetoxidans DSM 684]
          Length = 294

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 50/194 (25%), Positives = 86/194 (44%), Gaps = 13/194 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
               +LY+D  + V  KP  + V  GG  +  ++   L+    +    P   HR+D+ T+
Sbjct: 80  FAETILYQDDALLVACKPHFLPVHPGGRYVTENLVYRLRLATGNDQLAP--VHRIDRFTA 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+           F    I+K Y   V   P+  ++   +W +      GD    
Sbjct: 138 GLVLFAQRSEDRARYNALFSQGNIKKRY-DAVAHCPEEPQQ--RHWQVANRIEQGD-PWF 193

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             Q   G   A S  +++D   Q +    +QP TG+THQLR+H   +G  +V D +Y  N
Sbjct: 194 RWQVVAGDVNARSSIELLD-LRQGYGLFSLQPITGKTHQLRLHMSGLGFGLVND-RYYPN 251

Query: 276 F----KGNFTSPIQ 285
                  +F++P+Q
Sbjct: 252 LLPEQPDDFSTPLQ 265


>gi|303389291|ref|XP_003072878.1| pseudouridylate synthase [Encephalitozoon intestinalis ATCC 50506]
 gi|303302021|gb|ADM11518.1| pseudouridylate synthase [Encephalitozoon intestinalis ATCC 50506]
          Length = 317

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 60/233 (25%), Positives = 96/233 (41%), Gaps = 39/233 (16%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L  G V V+++ V      + G+++RI  VI    HI               H      I
Sbjct: 45  LECGAVTVNEEIV------EPGRILRIGDVIRHTVHI---------------HEPAHPEI 83

Query: 101 -LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++ E+    V NKP G+      G  Y      ++    K  K    +RLD   SG+L+
Sbjct: 84  DIIREEQDYVVVNKPPGMPCHPTGG--YREYSVTRALFGDK--KVACINRLDMPVSGVLI 139

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA       H      +R  +KIY + V G+  +  +       K S   G + +V  + 
Sbjct: 140 VA----VKNHSKCLEAIREARKIYLAKVQGLFPDSIDVDK----KISCAEGKHRYVSDEG 191

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +      ++ F+ +  +      +E +P TGRTHQ+R+H   +G PIV D  Y
Sbjct: 192 KA----CLTLFRRL-AYKDGHSLVECRPITGRTHQIRIHLQSIGFPIVNDIMY 239


>gi|149372534|ref|ZP_01891646.1| ribosomal large subunit pseudouridine synthase D [unidentified
           eubacterium SCB49]
 gi|149354577|gb|EDM43141.1| ribosomal large subunit pseudouridine synthase D [unidentified
           eubacterium SCB49]
          Length = 130

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 59/132 (44%), Gaps = 9/132 (6%)

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V   P   K+ + ++L +       Y +  K  +  +  AI H++VI      +  L +
Sbjct: 1   MVKEKPPKDKDTLVHFLKRNPKQNKSYAYPKKVPD--SKQAILHYEVIKKL-DNYYLLSI 57

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
              TGR HQ+R     + CPI GD KY     G   S     ++LHAR +   HP +   
Sbjct: 58  DLETGRHHQIRSQLAAIKCPIKGDLKY-----GFDRSNKDGSIHLHARKITFTHPVKKEE 112

Query: 305 LQITAPLPAHMV 316
           + I AP P  ++
Sbjct: 113 MTILAPTPDEVI 124


>gi|167032660|ref|YP_001667891.1| pseudouridine synthase [Pseudomonas putida GB-1]
 gi|166859148|gb|ABY97555.1| pseudouridine synthase [Pseudomonas putida GB-1]
          Length = 294

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 55/209 (26%), Positives = 106/209 (50%), Gaps = 24/209 (11%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQET 154
           ++ ++L+ D  + V +KP  + V   +    +++  L   +  +   P L   HR+D+ T
Sbjct: 84  VQEVVLHVDEHLVVADKPHFLPV---TPTGEYVEQTLLRRLIRRLGNPHLVPLHRIDRHT 140

Query: 155 SGILVVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGG 210
           +G+++ +   ++R+A Q L   F  RRI K Y ++   +P++     A  L+ KS  + G
Sbjct: 141 AGLVLFSANPQSRSAYQRL---FPERRIDKRYQAIAAALPQH-----AFPLVHKSRLVHG 192

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +    + + E  AN + +  +V++   + + +  + P TG+THQLRVH   +G  I  D 
Sbjct: 193 EPFFRMHEVEGEAN-SETLAQVLEKNGELWRY-GLSPVTGKTHQLRVHMAALGAGISNDP 250

Query: 271 KY--CANFKGNFTSPIQNKLYLHA-RYMD 296
            Y    N + ++  P+  KL  H+ R+ D
Sbjct: 251 FYPQLRNEEDDYQRPL--KLLAHSLRFED 277


>gi|24215596|ref|NP_713077.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
 gi|24196749|gb|AAN50095.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
          Length = 292

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 51/198 (25%), Positives = 80/198 (40%), Gaps = 36/198 (18%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP----- 144
           + KHS+     + YE        KP GI V          D   +++ D   ++      
Sbjct: 1   MKKHSNIR---IFYESESFLFAEKPPGIPVHATK------DSKRENFTDQLQKQLSLEYL 51

Query: 145 RLTHRLDQETSGILVVART----RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           R  +RLD +TSG++   +     + A Q L  S       KIY  +  G        +  
Sbjct: 52  RTVNRLDLDTSGLVFFCKNPDKNKEADQILKNSL------KIYLCVTSGT------ILEK 99

Query: 201 WLLKKSHI--GGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRV 257
              +  +I  G   VH V     G + A++ F  +   +++ +  L  + HTGR HQ+R 
Sbjct: 100 HFTETCYIKDGNKKVHKVFS---GGDKAVTEFLTLKQNSKENYSVLLAKLHTGRRHQIRF 156

Query: 258 HALHMGCPIVGDHKYCAN 275
           H    G PI+GD  Y  N
Sbjct: 157 HLSEKGYPILGDRVYGKN 174


>gi|331016169|gb|EGH96225.1| pseudouridine synthase [Pseudomonas syringae pv. lachrymans str.
           M302278PT]
          Length = 296

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 47/181 (25%), Positives = 80/181 (44%), Gaps = 15/181 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + V +KP  + V   G  +   +   L   +D+    P   HR+D+ T+G+++
Sbjct: 89  ILYADEHLVVADKPHFLPVTPAGEYVEQTLLRRLIHRLDNPDLVP--LHRIDRHTAGLVL 146

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +   +TR+A Q L   F  RRI K Y ++   +P      +    L +S +        
Sbjct: 147 FSANRQTRSAYQTL---FPTRRIDKCYEAIAPALPG-----LEFPRLHESRLVEGEPFFR 198

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            Q   G +   +  +V++     + +  + P TG+ HQLRVH   +G  I  D  Y    
Sbjct: 199 MQEGPGVSNTQTRIEVLERHGSLWRY-GLHPVTGKKHQLRVHMAALGAAICNDPFYPDAL 257

Query: 277 K 277
           K
Sbjct: 258 K 258


>gi|194374167|dbj|BAG62396.1| unnamed protein product [Homo sapiens]
          Length = 184

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 33/53 (62%), Gaps = 2/53 (3%)

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
           + A  A++ ++V+         +E+QP TG  HQLRVH +  + CPI+GDHKY
Sbjct: 45  RNAQVAVTQYQVLSSTLSS-ALVELQPITGIKHQLRVHLSFGLDCPILGDHKY 96


>gi|134099890|ref|YP_001105551.1| ribosomal pseudouridine synthase [Saccharopolyspora erythraea NRRL
           2338]
 gi|291006074|ref|ZP_06564047.1| ribosomal pseudouridine synthase [Saccharopolyspora erythraea NRRL
           2338]
 gi|133912513|emb|CAM02626.1| ribosomal pseudouridine synthase [Saccharopolyspora erythraea NRRL
           2338]
          Length = 312

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 40/161 (24%), Positives = 71/161 (44%), Gaps = 15/161 (9%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIANWLLKK 205
            HRLD+ T+G+++        +   E F+ R + K Y ++    P  +    + + ++K+
Sbjct: 137 AHRLDRTTAGLVMFVIRPELRKSYQEMFQNRLVHKEYEAVAPFDPGLELPRTVRSRIVKE 196

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
             +      +  Q   G   A +  ++++          + P TGRTHQLRVH   +G P
Sbjct: 197 RGV------LAAQEVPGPPNAETLVELLE-HRDGLGRYRLLPKTGRTHQLRVHLNSIGIP 249

Query: 266 IVGDHKYCA---NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           I+GD  Y         +F  P+Q    L A+ ++   P  G
Sbjct: 250 ILGDDTYPVVNDPAPDDFGRPLQ----LLAKALEFTDPVSG 286


>gi|237747521|ref|ZP_04578001.1| RNA pseudouridylate synthase [Oxalobacter formigenes OXCC13]
 gi|229378883|gb|EEO28974.1| RNA pseudouridylate synthase [Oxalobacter formigenes OXCC13]
          Length = 319

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 46/198 (23%), Positives = 84/198 (42%), Gaps = 16/198 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +  +LY+D  + V +KP  + V   G  ++  +   L+  +      P   HR+D+ET+
Sbjct: 93  FQETVLYQDDWLVVADKPHFLPVTPSGKYVSETLLVRLRKKLGIDTLTP--IHRIDRETA 150

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDY-- 212
           G+++ +            FR   + K Y ++        ++ IA  +  +S I  GD   
Sbjct: 151 GLVLFSVKPEGRNLYQRLFRENFVSKHYEAIA-----PYRDDIAFPMRYRSRIEEGDSFM 205

Query: 213 -VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            + V+      A   IS    I   +  F    ++P TGR HQLR+    +G P++ D  
Sbjct: 206 RMRVIPDGTPNAETEIS----IQQKSNAFAHYHLKPVTGRKHQLRIQMCSLGIPLLNDRI 261

Query: 272 YCANFKGNFTSPIQNKLY 289
           Y  +     T  +Q + +
Sbjct: 262 YPVHLPEAVTDEMQAEEF 279


>gi|229589269|ref|YP_002871388.1| putative ribosomal subunit pseudouridine synthase [Pseudomonas
           fluorescens SBW25]
 gi|229361135|emb|CAY47998.1| putative ribosomal subunit pseudouridine synthase [Pseudomonas
           fluorescens SBW25]
          Length = 296

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 43/177 (24%), Positives = 78/177 (44%), Gaps = 9/177 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++  +LY D  + V +KP  + V   G  +   +   L   +D+    P   HR+D+ T+
Sbjct: 85  VQETILYADEHLVVADKPHFLPVTPAGEYVEQTLLRRLIRCLDNPALVP--LHRIDRHTA 142

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ +   A+     + F  R+I K Y ++   +P      +    + KS +       
Sbjct: 143 GLVLFSANPASRSAYQQLFPTRQIDKFYEAIAPALPN-----LTFPRVHKSRLVEGEPFF 197

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             Q   GA+   +  +V +  A  + +  + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 198 RMQEGPGASNTETAVEVREKKADLWRY-GLFPVTGKKHQLRVHMTALGASICNDPFY 253


>gi|332231641|ref|XP_003265002.1| PREDICTED: LOW QUALITY PROTEIN: RNA pseudouridylate synthase
           domain-containing protein 3-like [Nomascus leucogenys]
          Length = 344

 Score = 46.2 bits (108), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 46/192 (23%), Positives = 83/192 (43%), Gaps = 16/192 (8%)

Query: 89  NLTKHS--DFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKP 144
           NL++    D L++ ++     +   NKP G+ V G  G    + +   L   +  + Q+ 
Sbjct: 69  NLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLREQEL 128

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIAN 200
           ++     +E+SG+++++     A  L + F    R +R    Y ++  GIP   +  I  
Sbjct: 129 QVVRASGKESSGLVLLSSCPQTASRLQKFFTHARRAQRPTATYCAVTNGIPAASEGKI-Q 187

Query: 201 WLLKKSHIGGDYVHV-VKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             LK  HI G  + V VK   +     G    +SHF+V+         +++QP T  + Q
Sbjct: 188 AALKVEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFRVV-ATGSGCALVQLQPLTVFSSQ 246

Query: 255 LRVHALHMGCPI 266
           L+        PI
Sbjct: 247 LQXXXXXXXTPI 258


>gi|330805411|ref|XP_003290676.1| hypothetical protein DICPUDRAFT_81402 [Dictyostelium purpureum]
 gi|325079175|gb|EGC32788.1| hypothetical protein DICPUDRAFT_81402 [Dictyostelium purpureum]
          Length = 731

 Score = 46.2 bits (108), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 42/87 (48%), Gaps = 5/87 (5%)

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           +  F  LE+  HTGR+HQ+RVH      PIVGD  Y +  K    S     L L +  + 
Sbjct: 534 SNTFSLLEITLHTGRSHQIRVHMASENLPIVGDPIYSSKSKQFLVS----HLLLASVSLK 589

Query: 297 LPHPEGGRL-QITAPLPAHMVKTWDSL 322
             HP   ++ + T   P+H  +  DS+
Sbjct: 590 FVHPILNQVKEFTIEHPSHFKQFIDSI 616



 Score = 42.0 bits (97), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 41/93 (44%), Gaps = 18/93 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS------------------GIAYHIDGFLKSWVDSKGQ 142
           +LYED  + V NKPAG+ V   +                   + +   G  K       +
Sbjct: 146 VLYEDDNLAVINKPAGMLVHPSNTTHTVVLNKEDQTHTLVNALIHRYGGISKLSNLGGNE 205

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +P + HRLD++T+GI+++AR     + L   F 
Sbjct: 206 RPGIVHRLDKDTAGIIIIARNNNTHKQLQALFE 238


>gi|45657036|ref|YP_001122.1| pseudouridylate synthase, 23S RNA-specific [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
 gi|45600273|gb|AAS69759.1| pseudouridylate synthase, 23S RNA-specific [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
          Length = 292

 Score = 46.2 bits (108), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 51/198 (25%), Positives = 80/198 (40%), Gaps = 36/198 (18%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP----- 144
           + KHS+     + YE        KP GI V          D   +++ D   ++      
Sbjct: 1   MKKHSNIR---IFYESESFLFAEKPPGIPVHATK------DSKRENFTDQLQKQLSLEYL 51

Query: 145 RLTHRLDQETSGILVVART----RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           R  +RLD +TSG++   +     + A Q L  S       KIY  +  G        +  
Sbjct: 52  RTVNRLDLDTSGLVFFCKNPDKNKEADQILKNSL------KIYLCVTSGT------ILEK 99

Query: 201 WLLKKSHI--GGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRV 257
              +  +I  G   VH V     G + A++ F  +   +++ +  L  + HTGR HQ+R 
Sbjct: 100 HFTETCYIKDGNKKVHKVFS---GGDKAVTEFLTLKQNSKENYSVLLAKLHTGRRHQIRF 156

Query: 258 HALHMGCPIVGDHKYCAN 275
           H    G PI+GD  Y  N
Sbjct: 157 HLSEKGYPILGDRVYGKN 174


>gi|325119935|emb|CBZ55488.1| putative RNA pseudouridylate synthase domain-containing protein
            [Neospora caninum Liverpool]
          Length = 2761

 Score = 46.2 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 44/147 (29%), Positives = 63/147 (42%), Gaps = 26/147 (17%)

Query: 146  LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
            L HRLD +TSG +++A+T  A Q + +    R I K Y  L  G        I + ++  
Sbjct: 1965 LGHRLDVDTSGPIIIAQTLEAWQWIRDQMHKRNISKEYICLCHGTLAEGFHVIDSPIITS 2024

Query: 206  S----------HIGGDYVHVVKQ----NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +          H G   + VVK       K   Y  S   +      +F    ++ HTGR
Sbjct: 2025 TDGRRLQSYIHHAGQPSLTVVKPLAHLEHKELRYPASSVPL------QFTLNWVKIHTGR 2078

Query: 252  THQLRVHALHM----GCP--IVGDHKY 272
            THQ+RVH   +    G P  +V D KY
Sbjct: 2079 THQIRVHLQSLLDSHGRPHCLVSDDKY 2105


>gi|290995478|ref|XP_002680322.1| predicted protein [Naegleria gruberi]
 gi|284093942|gb|EFC47578.1| predicted protein [Naegleria gruberi]
          Length = 279

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 38/147 (25%), Positives = 65/147 (44%), Gaps = 23/147 (15%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK--PR 145
           KH D L+  ++ E++   V  KP GI V       YH +         +    G     +
Sbjct: 127 KHFDKLE--IIKEENDFVVVTKPPGICVHPIK--RYHKNSLFYMLEHEYAHHFGNDLHCK 182

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--------C 197
             HRLD+ET G+L+V +T   A++  +  + ++++K Y + V GI K K +        C
Sbjct: 183 TIHRLDKETCGVLIVGKTSEGAKYFQKLLKEKQVEKQYIARVDGIVKGKPQFEINDPLVC 242

Query: 198 IANW-----LLKKSHIGGDYVHVVKQN 219
           I  W      +    +  +Y  + K+N
Sbjct: 243 IQRWDNIFKSISNKEVEKEYREICKKN 269


>gi|319949614|ref|ZP_08023655.1| pseudouridine synthase [Dietzia cinnamea P4]
 gi|319436720|gb|EFV91799.1| pseudouridine synthase [Dietzia cinnamea P4]
          Length = 329

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 38/146 (26%), Positives = 63/146 (43%), Gaps = 32/146 (21%)

Query: 148 HRLDQETSGILVV---ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           HRLD+ET+G+++    A TR A Q +   F  R + K+Y ++            + W   
Sbjct: 140 HRLDRETAGVVMFSARADTRGAYQSM---FERREVTKVYEAV--------SARPSGWDPA 188

Query: 205 KSHIGGDYVHVVKQ----NEKG-------ANYAISHFKVIDCF-------AQKFCWLEMQ 246
              +GG  V V  +    + +G        +   +   ++D          +      ++
Sbjct: 189 APTLGGHPVPVTHRAHIRSRRGELRVTLHPDLPPNSETLVDVLRTGHSASGRLVVQTLLR 248

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
           P TGR HQLRVH   +G  I+GD +Y
Sbjct: 249 PRTGRLHQLRVHLAALGIGILGDRRY 274


>gi|88607964|ref|YP_506037.1| putative RNA pseudouridylate synthase, truncation [Neorickettsia
           sennetsu str. Miyayama]
 gi|88600133|gb|ABD45601.1| putative RNA pseudouridylate synthase, truncation [Neorickettsia
           sennetsu str. Miyayama]
          Length = 119

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 43/82 (52%), Gaps = 11/82 (13%)

Query: 103 YEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           YED  + V  KPAG+ V  G G         + +H      S +DS   +P + HRLD++
Sbjct: 29  YEDDCLLVIYKPAGLVVHPGIGNREQTLVNILEHHYPTEKLSSLDSS--RPGIVHRLDKD 86

Query: 154 TSGILVVARTRAAAQHLTESFR 175
           T+G L+VA+T  A   L++  +
Sbjct: 87  TAGFLIVAKTNPAHLSLSQMIK 108


>gi|319649950|ref|ZP_08004100.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317398388|gb|EFV79076.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 212

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 33/118 (27%), Positives = 56/118 (47%), Gaps = 17/118 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV----QGGSG------IAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +LYED+ + + NKPAG+S     +  SG      I Y+    LKS          +  RL
Sbjct: 84  ILYEDAYLLIVNKPAGVSTIPSREHPSGSLANRLIGYYQRIGLKSAA-------HIVTRL 136

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           D++TSG++++A+ R      ++  R R+IQ+ Y +   G        I   + +K  +
Sbjct: 137 DRDTSGLVLIAKHRHVHHLFSQQQRFRKIQRTYEAFAEGTISRDAGTIEQPIARKKTV 194


>gi|312959799|ref|ZP_07774315.1| pseudouridine synthase [Pseudomonas fluorescens WH6]
 gi|311285965|gb|EFQ64530.1| pseudouridine synthase [Pseudomonas fluorescens WH6]
          Length = 296

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 42/178 (23%), Positives = 80/178 (44%), Gaps = 11/178 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQET 154
           ++  +LY D  + V +KP  + V   +    +++  L   +  +   P L   HR+D+ T
Sbjct: 85  VQETILYADEHLVVADKPHFLPV---TPAGEYVEQTLLRRLIRRLDNPSLVPLHRIDRHT 141

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G+++ +   A+     + F  R+I K Y ++   +P      +   L+ KS +      
Sbjct: 142 AGLVLFSANPASRAAYQQLFPTRQIDKFYEAIAPALPG-----LTFPLVHKSRLVDSEPF 196

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              Q  +GA+   +  +V +     + +  + P TG+ HQLRVH   +G  I  D  Y
Sbjct: 197 FRMQEGEGASNTETGVQVREKNGDLWRY-GLFPVTGKKHQLRVHMTALGASICNDPFY 253


>gi|223998336|ref|XP_002288841.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220975949|gb|EED94277.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 438

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 31/103 (30%), Positives = 47/103 (45%), Gaps = 19/103 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL-------------- 146
           ++Y ++ + V NKPAG   Q G G      G + + VD K     L              
Sbjct: 132 IIYSNNHLLVVNKPAGWKSQPGDGGG---TGSMSNAVDPKCLLTHLQNQSLGGGSQKNFI 188

Query: 147 --THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             THRLDQ  +G L+ A+   AA  +  ++  R ++K YW +V
Sbjct: 189 SPTHRLDQPCTGALIFAKNGKAASRVQVAWAKRNVKKCYWVVV 231


>gi|148667045|gb|EDK99461.1| mCG132976, isoform CRA_a [Mus musculus]
          Length = 320

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 35/133 (26%), Positives = 60/133 (45%), Gaps = 10/133 (7%)

Query: 152 QETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +E SG+++++     A  L + F    R +R    Y ++  GIP+  +  +   L  +  
Sbjct: 105 KEASGLVLLSSCPQTASRLQKFFIHSRRAQRPTATYCAVTDGIPEPSEGTVCMPLKMEQM 164

Query: 208 IGGDYVHVV-----KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
              D    V     K  ++G    +S F V+    +    +++QP T   +QL+VH    
Sbjct: 165 NDVDLAVPVMSPSRKDIQEGVKRTLSRFHVM-ATGRGCALVQLQPLTVFPNQLQVHMALQ 223

Query: 263 GCPIVGDHKYCAN 275
            CPI+GDH Y A 
Sbjct: 224 LCPILGDHTYAAR 236


>gi|116327749|ref|YP_797469.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116120493|gb|ABJ78536.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
          Length = 277

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 46/195 (23%), Positives = 83/195 (42%), Gaps = 35/195 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQETS 155
           + YE        KP GI V          D   +++ D   ++      R  +RLD +TS
Sbjct: 10  IFYETESFLFAEKPPGIPVHATK------DSKRENFADRLQEQLSLEYLRTVNRLDLDTS 63

Query: 156 GILVVARTRAAAQHLTESFR-MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           G++ + +     +   E+ R ++   KIY             C+A+ ++++ H   +  +
Sbjct: 64  GLVFLCKNPDKNK---EADRILKSSSKIYL------------CVADGIVEEEHFT-ETCY 107

Query: 215 VVKQNEK------GANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +   N+K      G + A++ F  +       +  L  + HTGR HQ+R+H    G  IV
Sbjct: 108 IKDGNKKVRKVFSGGDKAVTEFLTLKRNLKDHYSVLLAKLHTGRRHQIRLHLSEKGHSIV 167

Query: 268 GDHKYCANFKGNFTS 282
           GD+ Y  +   N T+
Sbjct: 168 GDYVYGKSLDLNSTT 182


>gi|170720815|ref|YP_001748503.1| pseudouridine synthase [Pseudomonas putida W619]
 gi|169758818|gb|ACA72134.1| pseudouridine synthase [Pseudomonas putida W619]
          Length = 294

 Score = 45.8 bits (107), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 57/213 (26%), Positives = 101/213 (47%), Gaps = 32/213 (15%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQET 154
           ++  +L+ D  + V +KP  + V   +    +++  L   +  +   P L   HR+D+ T
Sbjct: 84  VEEAILHVDEHLVVADKPHFLPV---TPTGEYVEQTLLRRLIRRLDNPHLVPLHRIDRHT 140

Query: 155 SGILVVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI--G 209
           +G+++ +   +TR+A Q L   F  RRI K Y ++   +P+         L+ KS +  G
Sbjct: 141 AGLVLFSANPQTRSAYQRL---FPERRIDKRYHAIAPALPQRDFP-----LVHKSRLVHG 192

Query: 210 GDY--VHVVKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPI 266
             +  +H V+ ++     A    +V++   Q   W   + P TG+THQLRVH   +G  I
Sbjct: 193 EPFFRMHEVQGDDNSETLA----EVLE--KQGELWRYGLSPVTGKTHQLRVHMAALGAAI 246

Query: 267 VGDHKYCANFK--GNFTSPIQNKLYLHA-RYMD 296
             D  Y    K   ++  P+  KL  H+ R+ D
Sbjct: 247 CNDPFYPELLKVEDDYQRPL--KLLAHSLRFAD 277


>gi|116331588|ref|YP_801306.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116125277|gb|ABJ76548.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 277

 Score = 45.8 bits (107), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 46/195 (23%), Positives = 83/195 (42%), Gaps = 35/195 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQETS 155
           + YE        KP GI V          D   +++ D   ++      R  +RLD +TS
Sbjct: 10  IFYETESFLFAEKPPGIPVHATK------DSKRENFADRLQEQLSLEYLRTVNRLDLDTS 63

Query: 156 GILVVARTRAAAQHLTESFR-MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           G++ + +     +   E+ R ++   KIY             C+A+ ++++ H   +  +
Sbjct: 64  GLVFLCKNPDKNK---EADRILKSSSKIYL------------CVADGIVEEEHFT-ETCY 107

Query: 215 VVKQNEK------GANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +   N+K      G + A++ F  +       +  L  + HTGR HQ+R+H    G  IV
Sbjct: 108 IKDGNKKVRKVFSGGDKAVTEFLTLKRNLKDHYSVLLAKLHTGRRHQIRLHLSEKGHSIV 167

Query: 268 GDHKYCANFKGNFTS 282
           GD+ Y  +   N T+
Sbjct: 168 GDYVYGKSLDLNSTT 182


>gi|328479571|gb|EGF48794.1| ribosomal large subunit 23S pseudouridine synthase D [Lactobacillus
           rhamnosus MTCC 5462]
          Length = 100

 Score = 45.4 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 30/89 (33%), Positives = 45/89 (50%), Gaps = 9/89 (10%)

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           +A++H+  I   A     +E+   TGRTHQ+RVH   +G PI+GD  Y A       +  
Sbjct: 17  FAVTHYHRIAETADT-ATIELNLETGRTHQIRVHLASIGFPIIGDPLYAA-------TET 68

Query: 285 QNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             ++ LHA  + L  P     L +T+P P
Sbjct: 69  ATRMQLHAFRVRLIRPLTIEPLTVTSPSP 97


>gi|193216441|ref|YP_001999683.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           arthritidis 158L3-1]
 gi|193001764|gb|ACF06979.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           arthritidis 158L3-1]
          Length = 277

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 54/241 (22%), Positives = 104/241 (43%), Gaps = 44/241 (18%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           QK ++   VR + K+ K    +Q G VV +  + +A    ++ +    S +N        
Sbjct: 37  QKDIKVNGVRTNDKQYK----MQLGDVVEVYGISDATKAFVQNE----SKINFK------ 82

Query: 98  KSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
              +++ED  + + +K   I++    + +   I  +L   + S   +P    R+D++TSG
Sbjct: 83  ---VIFEDKNLLIVDKAINIAMHSEENSLDDQILKYLNYRLTS-SFRPASIGRIDKKTSG 138

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V A+  AA   L E  + ++     +  V    ++K +   N    K  IG + + V 
Sbjct: 139 LVVYAKNYAA---LVEFEKQQKYFDKVYQFVSDFNEDKLDITVNL---KKDIGNEKMIV- 191

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLE-----MQPHTGRTHQLRVHALHMGCPIVGDHK 271
                   + +         A+   W++      Q  TG+THQ+R    ++  PI+GD K
Sbjct: 192 -----DPKFGVK--------ARTIFWVDGKHKFAQILTGKTHQIRATLSYLKYPILGDSK 238

Query: 272 Y 272
           Y
Sbjct: 239 Y 239


>gi|242208602|ref|XP_002470151.1| predicted protein [Postia placenta Mad-698-R]
 gi|220730753|gb|EED84605.1| predicted protein [Postia placenta Mad-698-R]
          Length = 348

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 51/184 (27%), Positives = 71/184 (38%), Gaps = 17/184 (9%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ----GGSGIAYHIDGFLKSWVDSKGQK 143
           V   + S   K  LLY D  + + NKP+G+  Q           H D     + D   ++
Sbjct: 46  VGTRRLSTLAKHALLYVDRGLLLVNKPSGLVCQYNRKDDREQNAHSD--FNDFTDDLKRQ 103

Query: 144 PRLT------HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NK 194
             L       HRLD+ T+G L  A T + AQ L E F    ++K Y ++V G      N+
Sbjct: 104 LSLDADLLPLHRLDKATTGALAFALTHSHAQDLAEQFNAHTVKKSYLAIVRGGTASFPNR 163

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I   L   +  G        Q EK A        +          + + P TG  HQ
Sbjct: 164 TGNIRGVLYTTN--GRVSSEAQGQWEKRAITETDWEVLASSPVAPLSLVRLSPFTGHKHQ 221

Query: 255 LRVH 258
           LRVH
Sbjct: 222 LRVH 225


>gi|158317482|ref|YP_001509990.1| pseudouridine synthase [Frankia sp. EAN1pec]
 gi|158112887|gb|ABW15084.1| pseudouridine synthase [Frankia sp. EAN1pec]
          Length = 285

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 52/223 (23%), Positives = 83/223 (37%), Gaps = 48/223 (21%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           +T+ +   +S  ++ED  +   +KP G+SV G        D  L S     G++    HR
Sbjct: 1   MTEWTTIRESRKIFEDEAVLALDKPVGVSVMG-----ERHDTDLVSMARDAGEELFPAHR 55

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL--VWGIP-------------KNK 194
           +D+ TSG+++ A+       LT  F  R ++K Y +L    G+P             KN+
Sbjct: 56  IDKVTSGVVLFAKELRFHGDLTRQFNRRTVEKTYLALTRTRGLPALATIDLPLSVGRKNR 115

Query: 195 KECIAN------WLLKKSHIGGDYVHVVKQNEKGANY-----------AISHFKVIDCF- 236
               AN      W         D       ++  A             A   F  +  + 
Sbjct: 116 VRIAANRADIVAWPGPAGTPTPDGPAGTPGSDGPAGSGARSPASWTVPAARTFPNVRSYP 175

Query: 237 ----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                       +   +   P +GR HQ+RVH   +G PI GD
Sbjct: 176 SVTRIARVWEGAEHTLVAAYPISGRRHQIRVHLAWVGHPIEGD 218


>gi|34189548|gb|AAH12951.2| RPUSD1 protein [Homo sapiens]
          Length = 190

 Score = 45.4 bits (106), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 32/54 (59%), Gaps = 3/54 (5%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           ++P TGRTHQLRVH   +G P+VGD  Y     G    P   ++ LHA Y+ +P
Sbjct: 44  LKPLTGRTHQLRVHCSALGHPVVGDLTY-GEVSGREDRPF--RMMLHAFYLRIP 94


>gi|70938677|ref|XP_739983.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56517373|emb|CAH87667.1| hypothetical protein PC302577.00.0 [Plasmodium chabaudi chabaudi]
          Length = 310

 Score = 45.4 bits (106), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 30/50 (60%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K KK
Sbjct: 188 LCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYILLCHGRIKKKK 237


>gi|111220539|ref|YP_711333.1| hypothetical protein FRAAL1074 [Frankia alni ACN14a]
 gi|111148071|emb|CAJ59739.1| hypothetical protein FRAAL1074 [Frankia alni ACN14a]
          Length = 303

 Score = 45.4 bits (106), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 44/86 (51%), Gaps = 5/86 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +YED  +   +KP GISV G      H    ++   D+ G++    HR+D+ TSGI++ A
Sbjct: 18  IYEDEAVLALDKPVGISVMG----ERHDTDLVRLAADA-GEELFPVHRIDKVTSGIVLFA 72

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLV 187
           R       LT  F+ R + K Y +L 
Sbjct: 73  RELRYHGDLTRQFQRRTVGKCYLALT 98



 Score = 38.5 bits (88), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 10/70 (14%)

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM--DLPHP 300
           L   P TGR HQ+RVH   +G PI GD          F    Q + +LH+  +  D    
Sbjct: 218 LAATPQTGRRHQIRVHLAWIGHPIAGDPL--------FVKAPQTRAFLHSWRLAFDAAWA 269

Query: 301 EGGRLQITAP 310
            G R+++ AP
Sbjct: 270 GGARVEVEAP 279


>gi|76363649|ref|XP_888536.1| RNA pseudouridylate synthase [Leishmania major strain Friedlin]
 gi|12311860|emb|CAC22676.1| RNA pseudouridylate synthase-like protein [Leishmania major strain
            Friedlin]
          Length = 1469

 Score = 45.4 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 34/125 (27%), Positives = 60/125 (48%), Gaps = 19/125 (15%)

Query: 207  HIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMG 263
            H+   Y  +H   Q+++ A   I+ ++V++ FA     +++++  +GR HQ+R H   +G
Sbjct: 1318 HVHQQYATLHAALQDQRNA---ITRYRVLEYFASAGVAYVQVELCSGRRHQIRQHFAQLG 1374

Query: 264  CPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-----------RLQITAP 310
             P+VGD +Y A        T+    +  LHA  +D+     G           R+ + A 
Sbjct: 1375 FPLVGDARYHAGVVAGHAGTTLGMRRAALHAYTVDILATTDGDDLASSEEVPDRVVVQAA 1434

Query: 311  LPAHM 315
            LPA M
Sbjct: 1435 LPADM 1439


>gi|119606120|gb|EAW85714.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_b
           [Homo sapiens]
          Length = 183

 Score = 45.4 bits (106), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 32/54 (59%), Gaps = 3/54 (5%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           ++P TGRTHQLRVH   +G P+VGD  Y     G    P   ++ LHA Y+ +P
Sbjct: 37  LKPLTGRTHQLRVHCSALGHPVVGDLTY-GEVSGREDRPF--RMMLHAFYLRIP 87


>gi|70925735|ref|XP_735515.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56509243|emb|CAH81272.1| hypothetical protein PC000519.04.0 [Plasmodium chabaudi chabaudi]
          Length = 248

 Score = 45.4 bits (106), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 30/50 (60%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K KK
Sbjct: 157 LCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYILLCHGRIKKKK 206


>gi|67595791|ref|XP_666024.1| N-terminal part related to RNA:pseudouridine (psi)-synthases
           C-terminal portion contains the deaminase domain
           implicated in Riboflavin synthesis; Rib2p
           [Cryptosporidium hominis TU502]
 gi|54656925|gb|EAL35796.1| N-terminal part related to RNA:pseudouridine (psi)-synthases
           C-terminal portion contains the deaminase domain
           implicated in Riboflavin synthesis; Rib2p
           [Cryptosporidium hominis]
          Length = 481

 Score = 45.4 bits (106), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 55/248 (22%), Positives = 106/248 (42%), Gaps = 49/248 (19%)

Query: 72  NALNHIIKE-QKILDSS--VNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QG---GS 123
           N+L++I++   KI   S  + L   +D +K  +LY+ S +    KP GI    QG     
Sbjct: 97  NSLDYIVRNGDKIKHRSLFIELPVATDKVK--ILYDSSTLLAVFKPCGIPCHPQGRFNKL 154

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES------FRMR 177
            +   I     S +++        +RLD+ TSG++++++  +  ++L+        + + 
Sbjct: 155 SLTKLIQSEYLSKLNTNSTYIHPINRLDRVTSGLVLLSKDSSTTKNLSSKVQFAHKYYLA 214

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK-------------------- 217
            I +   + +  + ++  E ++   L      G   HV+K                    
Sbjct: 215 MINESASNFISHVSQSSIEGVSIRELSLDESHGITSHVIKCEIGLKTLKDREGESLITRI 274

Query: 218 QNEKGANYAISHF-KVIDCF------------AQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            + + + Y++++F  +I C               K+  L  +P TGRTHQ+R H  ++G 
Sbjct: 275 DSSENSKYSLTYFFPLISCLDINEGKKQKINETDKYSILLCKPITGRTHQIRAHLKYIGF 334

Query: 265 PIVGDHKY 272
           PIV D  Y
Sbjct: 335 PIVRDILY 342


>gi|325119615|emb|CBZ55168.1| putative RNA pseudouridylate synthase family protein [Neospora
           caninum Liverpool]
          Length = 1215

 Score = 45.1 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 23/55 (41%), Positives = 34/55 (61%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           D +  K RL H+LD  TSG+L+VA  +  A+ +    + R IQK Y +LV+G P+
Sbjct: 808 DKEPCKVRLCHQLDYATSGLLMVAHNQKTARIVQTLLQRREIQKEYLALVYGHPQ 862



 Score = 43.1 bits (100), Expect = 0.064,   Method: Composition-based stats.
 Identities = 21/44 (47%), Positives = 26/44 (59%), Gaps = 6/44 (13%)

Query: 249  TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            TGR HQLRVH  H+G PIVGD  Y    +  F      +++LHA
Sbjct: 1069 TGRRHQLRVHCEHLGHPIVGDATYGTGDQTPF------RMFLHA 1106


>gi|322504203|emb|CAM41506.2| RNA pseudouridylate synthase-like protein [Leishmania braziliensis
            MHOM/BR/75/M2904]
          Length = 1340

 Score = 45.1 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 32/126 (25%), Positives = 60/126 (47%), Gaps = 19/126 (15%)

Query: 206  SHIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHM 262
            +H+   Y  +H   Q+++ A   I+ ++V++ FA     +++++  +GR HQ+R H   +
Sbjct: 1189 AHVHQQYATLHAALQDQRNA---ITCYRVLEYFASTGVAYVQVELRSGRRHQIRQHFAQL 1245

Query: 263  GCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGG-----------RLQITA 309
            G P+VGD +Y A      +       +  LHA  +++     G           R+ + A
Sbjct: 1246 GFPLVGDARYHAGVAAGHSGTTFGMQRAALHAYAVNILATTSGDGQASNEEGPNRVVVQA 1305

Query: 310  PLPAHM 315
             LPA M
Sbjct: 1306 ALPADM 1311


>gi|154331794|ref|XP_001561714.1| RNA pseudouridylate synthase-like protein [Leishmania braziliensis
            MHOM/BR/75/M2904]
          Length = 1340

 Score = 45.1 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 32/126 (25%), Positives = 60/126 (47%), Gaps = 19/126 (15%)

Query: 206  SHIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHM 262
            +H+   Y  +H   Q+++ A   I+ ++V++ FA     +++++  +GR HQ+R H   +
Sbjct: 1189 AHVHQQYATLHAALQDQRNA---ITCYRVLEYFASTGVAYVQVELRSGRRHQIRQHFAQL 1245

Query: 263  GCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGG-----------RLQITA 309
            G P+VGD +Y A      +       +  LHA  +++     G           R+ + A
Sbjct: 1246 GFPLVGDARYHAGVAAGHSGTTFGMQRAALHAYAVNILATTSGDGQASNEEGPNRVVVQA 1305

Query: 310  PLPAHM 315
             LPA M
Sbjct: 1306 ALPADM 1311


>gi|83645042|ref|YP_433477.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83633085|gb|ABC29052.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 297

 Score = 45.1 bits (105), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 47/178 (26%), Positives = 78/178 (43%), Gaps = 21/178 (11%)

Query: 102 LYEDSKIY-VFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           L  D   Y ++ KPAG+  QG   G    +    +    SK Q   L HRLD+E  G+++
Sbjct: 100 LVADHDAYSIWCKPAGLLTQGSEWGDHCSLLRMAELHFQSKRQV-FLLHRLDREAMGLVI 158

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  +AAA       +   + K Y + V G    ++  I   +  KS +     + V+  
Sbjct: 159 IAHNKAAAGRFGALLQDNALDKFYLARVKGRLAQEQGEIDFPVDGKSALS---YYQVQHY 215

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +   + ++   K+I               TGR HQ+R H   +G P++GD +Y +  K
Sbjct: 216 DDATDSSLVRVKLI---------------TGRKHQIRRHFADLGYPLLGDPRYGSGNK 258


>gi|257068055|ref|YP_003154310.1| 23S RNA-specific pseudouridylate synthase [Brachybacterium faecium
           DSM 4810]
 gi|256558873|gb|ACU84720.1| 23S RNA-specific pseudouridylate synthase [Brachybacterium faecium
           DSM 4810]
          Length = 305

 Score = 45.1 bits (105), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 35/132 (26%), Positives = 56/132 (42%), Gaps = 14/132 (10%)

Query: 148 HRLDQETSGIL---VVARTRAAAQHLTESFRMRRIQKIYWSL-VWGIPKNKKECIANWLL 203
           HRLD+ T+G+L   +    R+A Q L   F  + + K Y +L V G   +    +    +
Sbjct: 127 HRLDRRTAGVLAFGIRPEERSAYQQL---FARQEVDKEYEALLVLGPGTSLPTAVGERAV 183

Query: 204 KKSHIG---GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +  +    G+    V      A  A+     +    +    + + P TGRTHQLR    
Sbjct: 184 LRDRLDKRRGELTTRVLDGPPNAETALE----VRAAGEGLLQVRLHPRTGRTHQLRAQLA 239

Query: 261 HMGCPIVGDHKY 272
             G PI+G+  Y
Sbjct: 240 ARGAPILGEDLY 251


>gi|320581259|gb|EFW95480.1| dolichyl-phosphate beta-glucosyltransferase [Pichia angusta DL-1]
          Length = 898

 Score = 45.1 bits (105), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 41/179 (22%), Positives = 70/179 (39%), Gaps = 54/179 (30%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +YED  + V NKPAG+ +       Y+                                 
Sbjct: 685 VYEDDDVLVVNKPAGMPIHPVQNFYYN--------------------------------T 712

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            + A A+ +  + + ++++K+Y + V G IP+             S +  D V V+ + +
Sbjct: 713 MSVAKAKEIQAAIKNKQVRKVYVARVAGKIPE-------------SLVCEDDV-VIVETK 758

Query: 221 KGANYAISHFKVIDCFAQ-------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +G    I        F +           +E +P TGRTHQ+R+H  ++G PIV D  Y
Sbjct: 759 RGLKDGIDRKSATTVFKRLNYSSVLDESIVECRPLTGRTHQIRIHLRNLGFPIVNDQLY 817


>gi|220915408|ref|YP_002490712.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219953262|gb|ACL63646.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 312

 Score = 45.1 bits (105), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 59/239 (24%), Positives = 94/239 (39%), Gaps = 23/239 (9%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKP 144
              D   S+LL E  +  V  KPAG++V     +A    G L + V ++         +P
Sbjct: 71  PEPDAPLSVLL-ERPRYLVVEKPAGVAVHP---LAPGEGGTLANAVAARHPECAEASPEP 126

Query: 145 R---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           R      RLD ETSG ++ AR   A + L        + K+Y +L  G       C    
Sbjct: 127 REGGAVQRLDLETSGCVLFARDPEAWEALHAQLGAHTVDKVYLALAVGRLPAGGVCSVPL 186

Query: 202 LLKKSHI--GGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             +   +    D     +   +G     A +H++    FA     L ++  TG  HQ+R 
Sbjct: 187 AQRGGRVVPAPDVEAEERLQARGLRPRPAETHYEPERRFAD-HTLLRVRIVTGVMHQIRA 245

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           H   +G P+                P   + +LHA  +    P+G GR+ + +PLP  +
Sbjct: 246 HLALLGHPVA---GDALYGGAAAALPGLERQFLHAWRLAFDDPDGAGRVAVESPLPPEL 301


>gi|327479400|gb|AEA82710.1| pseudouridylate synthase, 23S RNA-specific [Pseudomonas stutzeri
           DSM 4166]
          Length = 274

 Score = 45.1 bits (105), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 42/179 (23%), Positives = 81/179 (45%), Gaps = 21/179 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  +SV   G  +   +   L   + +    P   HR+D+ T+G+++
Sbjct: 64  ILHVDEHLVVADKPHFLSVMPAGEYVNETLLARLSKRLGNADLVP--IHRIDRLTAGLVL 121

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-----NKKECIANWLLKKSHIGGDYVH 214
            +  R +       FR RRI K Y ++   +P       ++ C+         + G+   
Sbjct: 122 FSANRESRDAYQALFRERRIAKRYEAICPALPGLEFPLRRQLCM---------VPGEPFF 172

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++++ +   N + +  +V++   +   W   + P TGR HQLR+H   +G  I  D  Y
Sbjct: 173 LMREGDGEPN-SETLIEVLE--RRDHLWRYALTPITGRKHQLRLHMATLGAGICNDPFY 228


>gi|23003940|ref|ZP_00047527.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 114

 Score = 45.1 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 7/63 (11%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKLYLHARYMDLPHPE 301
           ++PH+GRTHQLR+H   +G PIV D+ Y   +     +++ P+Q    L +R +    P 
Sbjct: 43  LEPHSGRTHQLRLHMARLGVPIVHDNFYPEPYDVSPEDYSRPLQ----LVSRSLAFTDPF 98

Query: 302 GGR 304
            GR
Sbjct: 99  TGR 101


>gi|68535163|ref|YP_249868.1| putative pseudouridylate synthase [Corynebacterium jeikeium K411]
 gi|68262762|emb|CAI36250.1| putative pseudouridylate synthase [Corynebacterium jeikeium K411]
          Length = 338

 Score = 45.1 bits (105), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D+ I V +KP  + ++  G  I       +K+ V     +   +HRLD+ T G+L+
Sbjct: 97  VLHQDADIVVVDKPPFLATLPRGQHITE--TALVKARVQLGIPELSPSHRLDRLTRGVLL 154

Query: 160 VA---RTRAAAQHLTESFRMRRIQKIYWSLV-------------------WGIPKNKKEC 197
           +      R A Q +   F  R   K+Y +L                    W  P  ++  
Sbjct: 155 MTARPEIRGAYQTM---FERRVPHKVYEALTPLPEEAPFAPIAPLADWRSWDPPTPERP- 210

Query: 198 IANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
              W L+   S   G    ++      A   ++  +      +K     ++PHTG+THQL
Sbjct: 211 ---WRLEHSMSKTRGHLSTILTDGSPNALTLVTGLRTEWRGGRKILVWRLEPHTGKTHQL 267

Query: 256 RVHALHMGCPIVGDHKYC 273
           RV    +G PI+ D  Y 
Sbjct: 268 RVVLRSLGLPILNDPLYT 285


>gi|70731574|ref|YP_261315.1| RNA pseudouridine synthase family protein [Pseudomonas fluorescens
           Pf-5]
 gi|68345873|gb|AAY93479.1| RNA pseudouridine synthase family protein [Pseudomonas fluorescens
           Pf-5]
          Length = 296

 Score = 45.1 bits (105), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 92/197 (46%), Gaps = 20/197 (10%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQET 154
           ++  +LY D  + V +KP  + V   +    +++  L   +  +   P L   HR+D+ T
Sbjct: 85  VEETILYADEHLVVADKPHFLPV---TPAGEYVEQTLLRRLIRRLGNPHLVPLHRIDRHT 141

Query: 155 SGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +G+++ +    +R+A Q L   F  R+I+K Y ++   +P+     +   LL KS +   
Sbjct: 142 AGLVLFSANPDSRSAYQAL---FPTRKIEKRYEAIAAALPQ-----LNFPLLHKSRLVDG 193

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                 Q  +G +   +  +V +   + + +  + P TG+ HQLRVH   +G  I  D  
Sbjct: 194 EPFFRMQEAQGPSNTETAIEVREKHGELWRY-ALYPVTGKKHQLRVHMNALGAAICNDPF 252

Query: 272 Y---CANFKGNFTSPIQ 285
           Y     + + ++  P++
Sbjct: 253 YPEVLKDIEDDYARPLK 269


>gi|146281243|ref|YP_001171396.1| pseudouridylate synthase, 23S RNA-specific [Pseudomonas stutzeri
           A1501]
 gi|145569448|gb|ABP78554.1| pseudouridylate synthase, 23S RNA-specific [Pseudomonas stutzeri
           A1501]
          Length = 294

 Score = 45.1 bits (105), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 42/180 (23%), Positives = 79/180 (43%), Gaps = 23/180 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  + V +KP  +SV   G  +   +   L   + +    P   HR+D+ T+G+++
Sbjct: 84  ILHVDEHLVVADKPHFLSVMPAGEYVNETLLARLSKRLGNADLVP--IHRIDRLTAGLVL 141

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-----NKKECIANWLLKKSHIGGDYVH 214
            +  R +       FR RRI K Y ++   +P       ++ C+         + G+   
Sbjct: 142 FSANRESRDAYQALFRERRIAKRYEAICPALPGLEFPLRRQLCM---------VPGEPFF 192

Query: 215 VVKQNEKGANYAISHFKVIDCFAQK-FCW-LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++++ +   N       +I+   ++   W   + P TGR HQLR+H   +G  I  D  Y
Sbjct: 193 LMREGDGEPNSET----LIEVLERRDHLWRYALTPITGRKHQLRLHMATLGAGICNDPFY 248


>gi|46581082|ref|YP_011890.1| RNA pseudouridine synthase family protein [Desulfovibrio vulgaris
           str. Hildenborough]
 gi|46450503|gb|AAS97150.1| RNA pseudouridine synthase family protein [Desulfovibrio vulgaris
           str. Hildenborough]
 gi|311234759|gb|ADP87613.1| pseudouridine synthase [Desulfovibrio vulgaris RCH1]
          Length = 400

 Score = 45.1 bits (105), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 55/266 (20%), Positives = 96/266 (36%), Gaps = 57/266 (21%)

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS-----------KIYVFNKPAGI 117
           PV +   H   E  +         H+  L+ IL  + +           ++    KP G+
Sbjct: 124 PVADPTGHPKGEDPLAPLRPGGEAHAAGLRLILPLDGATDSPPPTGGVPRLVAVYKPGGL 183

Query: 118 -SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            S     G A + +  L +         +L +RLD  TSGIL++A   A  +   ++   
Sbjct: 184 HSAALAGGRAPNAENLLPAL--------KLLNRLDGPTSGILMLAGDTAGERQWRKAEDE 235

Query: 177 RRIQKIYWSLVWG-----------------IPKNKKECIANWLLKKSHIG-------GDY 212
              +K Y ++  G                      + C  +  L+ + +        GD 
Sbjct: 236 GGTRKTYLAVCTGRLERGTVVRAALDTARRTVTRVRPCDTDDRLRHTEVVPLAHFRLGDL 295

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +++  +  GA        ++ C  +K          G  HQ+R H  H+G P++GD  Y
Sbjct: 296 ANLITDDTAGAPACDETVTLVCCRIRK----------GARHQIRAHMAHIGHPLLGDDVY 345

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLP 298
            A        P +  L+LH   + LP
Sbjct: 346 AAPAS---PPPGRMPLFLHHSRITLP 368


>gi|260578643|ref|ZP_05846552.1| pseudouridylate synthase [Corynebacterium jeikeium ATCC 43734]
 gi|258603271|gb|EEW16539.1| pseudouridylate synthase [Corynebacterium jeikeium ATCC 43734]
          Length = 313

 Score = 45.1 bits (105), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 50/199 (25%), Positives = 83/199 (41%), Gaps = 36/199 (18%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L++D+ I V +KP  + ++  G  I       +K+ V     +   +HRLD+ T G+L+
Sbjct: 72  VLHQDADIVVVDKPPFLATLPRGQHITE--TALVKARVQLGIPELSPSHRLDRLTRGVLL 129

Query: 160 VA---RTRAAAQHLTESFRMRRIQ-KIYWSLV-------------------WGIPKNKKE 196
           +      R A Q + E    RRI  K+Y +L                    W  P  ++ 
Sbjct: 130 MTARPEIRGAYQTMFE----RRIPHKVYEALTPLPEEAPFAPIAPLADWRSWDPPTPERP 185

Query: 197 CIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
               W L+   S   G    ++      A   ++  +      +K     ++PHTG+THQ
Sbjct: 186 ----WRLEHSMSKTRGHLSTILTDGSPNALTLVTGLRTEWREGRKILVWRLEPHTGKTHQ 241

Query: 255 LRVHALHMGCPIVGDHKYC 273
           LRV    +G PI+ D  Y 
Sbjct: 242 LRVVLRSLGLPILNDPLYT 260


>gi|121605828|ref|YP_983157.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120594797|gb|ABM38236.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
          Length = 302

 Score = 45.1 bits (105), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 43/184 (23%), Positives = 77/184 (41%), Gaps = 23/184 (12%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            ++ +L++D  + V +KP  + V   G  +   +   LK+ +      P   HR+D+ET+
Sbjct: 90  FEAAVLFQDEHLVVADKPHFLPVTPSGHYLQETLLVRLKNQLGLDSLIP--IHRIDRETA 147

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-------LLKKSHI 208
           G+++              FR   + K Y            E +A W       L +K+ I
Sbjct: 148 GLVLFCVQPGERDAYQALFRRHEVVKHY------------EAVARWRPDLRFPLQRKTRI 195

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             D     ++   G   + +   +++   Q+  +  + P TG+ HQLRVH   +G PI  
Sbjct: 196 VEDEPFFRQREVPGEPNSETLIDLLEIRGQRALY-ALSPVTGKKHQLRVHMNALGMPICN 254

Query: 269 DHKY 272
           D  Y
Sbjct: 255 DRMY 258


>gi|25028115|ref|NP_738169.1| hypothetical protein CE1559 [Corynebacterium efficiens YS-314]
 gi|259507172|ref|ZP_05750072.1| RNA pseudouridine synthase [Corynebacterium efficiens YS-314]
 gi|23493399|dbj|BAC18369.1| conserved hypothetical protein [Corynebacterium efficiens YS-314]
 gi|259165253|gb|EEW49807.1| RNA pseudouridine synthase [Corynebacterium efficiens YS-314]
          Length = 329

 Score = 45.1 bits (105), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 57/247 (23%), Positives = 94/247 (38%), Gaps = 59/247 (23%)

Query: 35  VNLQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
           + LQK+L        R  ++ +D  RV+ N RI + Q  R+ P                 
Sbjct: 89  IRLQKVLAQAGVASRRHAEILIDNGRVEVNGRIVTTQGTRVNP----------------- 131

Query: 87  SVNLTKHSDFLK----SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                 +SD ++     I + ED + +V NKP G+       +     G L S   + GQ
Sbjct: 132 ------NSDVIRVDGVRININEDLEYFVLNKPRGMHSTMSDDLGRPCVGDLVSEKTASGQ 185

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +     RLD +T G+L++      A  L        ++K Y + V G             
Sbjct: 186 RLFHVGRLDADTEGLLLLTNDGELANRLMHP--KYEVRKTYLATVRG------------- 230

Query: 203 LKKSHIGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
                 G + V  +++    E G   A  + ++ID F  K   + ++ H GR H +R   
Sbjct: 231 ----EAGPNLVTTLRKGIELEDGPAKA-DYVQIIDTFQGK-SLIRLEIHEGRKHIVRRML 284

Query: 260 LHMGCPI 266
              G P+
Sbjct: 285 DEAGFPV 291


>gi|302336155|ref|YP_003801362.1| pseudouridine synthase [Olsenella uli DSM 7084]
 gi|301319995|gb|ADK68482.1| pseudouridine synthase [Olsenella uli DSM 7084]
          Length = 355

 Score = 45.1 bits (105), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 63/300 (21%), Positives = 105/300 (35%), Gaps = 57/300 (19%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           ++L  G++ +D   +   +R+  G VV +     A  H            ++   +   +
Sbjct: 46  RVLARGRLSLDGAGLAPASRLAPGDVVGL-----AFAH-----------THVPGPASEAE 89

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--------------- 143
            ++++ D      +KPAGI V    G+   +   ++  +D +G+                
Sbjct: 90  PVVVWRDRFALAVDKPAGILVHADGGVGETLTARVQGLLDREGRPDHEGRPDGQGPPGRM 149

Query: 144 ------------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                       P+   RLD ETSG+++ +               R  +K Y ++V G  
Sbjct: 150 PDGGRDSVARLVPQALQRLDVETSGLVLFSLAEETQPAFDALMAGRVTEKRYLAVVRG-- 207

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                  +  +L    IG D     +        +   +            L ++  TGR
Sbjct: 208 ----PWPSGTMLIDRPIGRDRHDARRMRVSAGGKSSRTWARPLATRGDHTLLLVRIGTGR 263

Query: 252 THQLRVHALHMGCPIVGDHKYCA--------NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            HQ+RVH    G PIVGD  Y A          +G   S     L LHA    L HP  G
Sbjct: 264 RHQIRVHLASTGHPIVGDRLYGALPAGCGGRAGRGGHGSRATGGLMLHAIEERLVHPVTG 323


>gi|162450819|ref|YP_001613186.1| RNA methyltransferase [Sorangium cellulosum 'So ce 56']
 gi|161161401|emb|CAN92706.1| RNA methyltransferase [Sorangium cellulosum 'So ce 56']
          Length = 765

 Score = 45.1 bits (105), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 33/129 (25%), Positives = 56/129 (43%), Gaps = 18/129 (13%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + H LD  TSG++++AR+  AA    E+   +  + IY +   G+   K         
Sbjct: 518 PIIVHPLDPGTSGLVMLARSEEAAARWGEAL-AKTGRLIYLAAAKGVTPGK--------- 567

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                 G     +++  +       + ++    A     L + P  GRTHQ+R H   +G
Sbjct: 568 ------GAITRDLREGTRTYTARTRYRRL--AVASGHSILRVIPDGGRTHQIRRHLAAIG 619

Query: 264 CPIVGDHKY 272
            PI+GD +Y
Sbjct: 620 HPILGDERY 628


>gi|227832810|ref|YP_002834517.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
 gi|262182701|ref|ZP_06042122.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
 gi|227453826|gb|ACP32579.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
          Length = 268

 Score = 45.1 bits (105), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 51/193 (26%), Positives = 87/193 (45%), Gaps = 29/193 (15%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ED  + V +KP  + +   G  +   +   L+  ++     P   HRLD+ TSG+++
Sbjct: 74  VVFEDGDLIVADKPHFLPTTSNGRIVRETLQTRLRVDLNEDSIVP--LHRLDRLTSGLVL 131

Query: 160 VAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS-HIGGDYVHV 215
            +R   TRAA Q L   F+ R + K Y          + +  A +    +  +G   V  
Sbjct: 132 CSRNPRTRAAYQQL---FQKRVVVKHY----------RAQVAAPFSFDGTVRLGMRRVRG 178

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +Q    +    +  +V         W    P TG THQ+RV   H+G PIVGD  Y  +
Sbjct: 179 ERQVRVDSTGTPTVTRVRASGTTADVW----PLTGHTHQIRVVLNHLGHPIVGDDTYPVD 234

Query: 276 FKG----NFTSPI 284
            +G    +F++P+
Sbjct: 235 -RGLDLYDFSTPL 246


>gi|145641816|ref|ZP_01797391.1| hypothetical protein CGSHiR3021_01062 [Haemophilus influenzae
           R3021]
 gi|145273438|gb|EDK13309.1| hypothetical protein CGSHiR3021_01062 [Haemophilus influenzae
           22.4-21]
          Length = 128

 Score = 45.1 bits (105), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 7/74 (9%)

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
           N AI+ F+ + C      ++ ++P TG+THQLRV    +G PI+GD  Y     G  T  
Sbjct: 23  NPAITRFESVSCEPNLRLFI-LKPQTGKTHQLRVAMKSLGSPILGDGLY-----GKNTEK 76

Query: 284 IQNKLYLHARYMDL 297
           I ++ YLHA  ++ 
Sbjct: 77  I-DRTYLHATQLEF 89


>gi|319776874|ref|YP_004136525.1| ribosomal large subunit pseudouridine synthase c [Mycoplasma
           fermentans M64]
 gi|318037949|gb|ADV34148.1| Ribosomal large subunit pseudouridine synthase C [Mycoplasma
           fermentans M64]
          Length = 280

 Score = 44.7 bits (104), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 47/174 (27%), Positives = 76/174 (43%), Gaps = 18/174 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  I + +KP  ++V   +  +   +  +LK +      KP    RLD+ TSG+++
Sbjct: 85  IIYEDDNILIVSKPINLAVHSENNCLDKQVLSYLK-YNQKDSFKPSHVGRLDKVTSGLMI 143

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+  A    L  +++    +KIY  L     + KK    N      H    +  VV  N
Sbjct: 144 YAKNYATLVEL--NYKTGFFEKIY-KLKSDFNEVKKLVEINI----QHDEKLHKMVVTNN 196

Query: 220 EKGA-NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            K      + + K  + FA           TG+ HQ+R+   H+  PI GD KY
Sbjct: 197 AKDPLAKTLFYTKNNEIFASIL--------TGKKHQIRLSMSHLKTPIYGDIKY 242


>gi|320093560|ref|ZP_08025451.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 178 str. F0338]
 gi|319979487|gb|EFW10958.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 178 str. F0338]
          Length = 249

 Score = 44.7 bits (104), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 61/250 (24%), Positives = 99/250 (39%), Gaps = 67/250 (26%)

Query: 35  VNLQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
           V LQK+L        R+ +  +   RV  + ++  GQ +R+ P    + H+  E+ ILD 
Sbjct: 11  VRLQKVLAQAGVASRRAAEQMIADGRVSVDGQVVRGQGMRVDPTAQVI-HVDGERLILDE 69

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-----SVQGGSGIAYHIDGFLKSWVDSKG 141
               TKH              +   NKP G+       +G   +A  + G+ +       
Sbjct: 70  ----TKHV-------------VLAINKPVGVVSTMSDPEGRPTVADIVAGYPE------- 105

Query: 142 QKPRLTH--RLDQETSGILVVARTRAAAQHLT-ESFRMRRIQKIYWSLVWGI--PKNKKE 196
              RL H  RLD +TSG+L++      A  LT  S+    I K Y + + G   P  K+ 
Sbjct: 106 ---RLYHVGRLDIDTSGLLLLTNDGELANRLTHPSY---EISKTYVARLHGEVRPGVKRR 159

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +A   L+   I                 A+  F+V+D +      +E+  H GR   +R
Sbjct: 160 LMAGIELEDGPI-----------------AVDGFRVVDTYGD-ITTVEIVVHEGRNRLVR 201

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 202 RMMDAVGFPV 211


>gi|332240387|ref|XP_003269368.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like, partial [Nomascus leucogenys]
          Length = 182

 Score = 44.7 bits (104), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 32/54 (59%), Gaps = 3/54 (5%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           ++P TGRTHQLRVH   +G P+VGD  Y     G    P   ++ LHA Y+ +P
Sbjct: 36  LKPLTGRTHQLRVHCSALGHPVVGDLTY-GEASGREDRPF--RMMLHAFYLRIP 86


>gi|238809659|dbj|BAH69449.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 296

 Score = 44.7 bits (104), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 47/174 (27%), Positives = 76/174 (43%), Gaps = 18/174 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++YED  I + +KP  ++V   +  +   +  +LK +      KP    RLD+ TSG+++
Sbjct: 101 IIYEDDNILIVSKPINLAVHSENNCLDKQVLSYLK-YNQKDSFKPSHVGRLDKVTSGLMI 159

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+  A    L  +++    +KIY  L     + KK    N      H    +  VV  N
Sbjct: 160 YAKNYATLVEL--NYKTGFFEKIY-KLKSDFNEVKKLVEINI----QHDEKLHKMVVTNN 212

Query: 220 EKGA-NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            K      + + K  + FA           TG+ HQ+R+   H+  PI GD KY
Sbjct: 213 AKDPLAKTLFYTKNNEIFASIL--------TGKKHQIRLSMSHLKTPIYGDIKY 258


>gi|238881201|gb|EEQ44839.1| conserved hypothetical protein [Candida albicans WO-1]
          Length = 274

 Score = 44.7 bits (104), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 51/195 (26%), Positives = 82/195 (42%), Gaps = 25/195 (12%)

Query: 110 VFNKPAGISVQGG---SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           V NKP+G+        + I    + F K        + RL  RLD+  +G LVVAR +  
Sbjct: 14  VVNKPSGMVCDASHTNNIITALTNEFTKILPSVNSSQFRLVQRLDRFVTGGLVVARNKKW 73

Query: 167 AQHLTESFRMR---RIQKIYWSLVW--GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           A  + +SF      R+ + Y  L+    IP++ +  I         +  DY    K  E 
Sbjct: 74  ADKVRKSFFQEGTLRLTRRYVGLIALDQIPESTQGTID---FPIQALEKDYRGKNKSREL 130

Query: 222 GANYAISHFKVIDCFAQK----FCWLEMQP--------HTGRTHQLRVHALH-MGCPIVG 268
               A++H+K+I    +     F   +  P         TGR +Q+R H +   G P++ 
Sbjct: 131 FTYSAVTHYKLIPSARRTIKGVFPVFQQGPILPIILELETGRKNQIRDHIIQKFGVPLLN 190

Query: 269 DHKYCANFKGNFTSP 283
           D  + ++FK N   P
Sbjct: 191 DDNF-SDFKLNPEIP 204


>gi|226327069|ref|ZP_03802587.1| hypothetical protein PROPEN_00930 [Proteus penneri ATCC 35198]
 gi|225204287|gb|EEG86641.1| hypothetical protein PROPEN_00930 [Proteus penneri ATCC 35198]
          Length = 94

 Score = 44.7 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 28/82 (34%), Positives = 46/82 (56%), Gaps = 2/82 (2%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++Y+D  +   NKPAG  V   S +  H   F +++  D  GQ     HRLD+ TSG+L+
Sbjct: 4   IIYQDEYLVAVNKPAGWLVHR-SWLDRHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLL 62

Query: 160 VARTRAAAQHLTESFRMRRIQK 181
           +A +   A+ L++SF   + +K
Sbjct: 63  MALSSDVARALSQSFEQHKTEK 84


>gi|148690494|gb|EDL22441.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_c
           [Mus musculus]
          Length = 177

 Score = 44.7 bits (104), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 27/68 (39%), Positives = 38/68 (55%), Gaps = 4/68 (5%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++P TGRTHQLRVH   +G PIVGD  Y    +     P   ++ LHA Y+ +P  +  R
Sbjct: 37  LKPLTGRTHQLRVHCSALGHPIVGDLTY-GQAEDQEDQPF--RMMLHAFYLRIPT-QAER 92

Query: 305 LQITAPLP 312
           ++   P P
Sbjct: 93  VEACTPDP 100


>gi|114672841|ref|XP_001135109.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           3-like [Pan troglodytes]
          Length = 260

 Score = 44.7 bits (104), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 43/178 (24%), Positives = 79/178 (44%), Gaps = 20/178 (11%)

Query: 89  NLTKHS--DFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQKP 144
           NL++    D L++ ++     +   NKP G+ V G  G    + +   L   +  + Q+ 
Sbjct: 61  NLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLREQEL 120

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIAN 200
           ++     +E+SG+++++     A  L + F    R +R   IY ++  GIP   +  I  
Sbjct: 121 QVVRASGKESSGLVLLSSCPQTASRLQKYFIHARRAQRPTAIYCAVTDGIPAASEGKI-Q 179

Query: 201 WLLKKSHIGGDYVHVV--------KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             LK  HI  D V++         K   +G    +SHF+V+         +++QP TG
Sbjct: 180 AALKLEHI--DAVNLTVPVKAPSRKDILEGVKKTLSHFRVV-ATGSGCALVQLQPLTG 234


>gi|218283677|ref|ZP_03489638.1| hypothetical protein EUBIFOR_02232 [Eubacterium biforme DSM 3989]
 gi|218215666|gb|EEC89204.1| hypothetical protein EUBIFOR_02232 [Eubacterium biforme DSM 3989]
          Length = 253

 Score = 44.3 bits (103), Expect = 0.025,   Method: Compositional matrix adjust.
 Identities = 43/177 (24%), Positives = 81/177 (45%), Gaps = 14/177 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +LYE++ + V  KP  + V         +   ++G+L+  ++      +  HR+D ETSG
Sbjct: 51  ILYENTFLIVAFKPPFLLVHDDGNNQDTLQARVNGYLQ--LNQNKYPAQAIHRIDYETSG 108

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++  +      +  ++     I+K Y +LV G    K + I + + +  H       ++
Sbjct: 109 LVLFCKHPFFQAYCDKNMEEHHIKKEYIALVQGHTNYKNKKIISNIARDRHNAKKM--II 166

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             N K    ++S F  +  +  K C L ++   TGR HQ+RV    +  PI+ D  Y
Sbjct: 167 HPNGKE---SVSIFNTLKNY--KDCSLIQVTILTGRKHQIRVQCASLNHPILNDSLY 218


>gi|303272809|ref|XP_003055766.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226463740|gb|EEH61018.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 483

 Score = 44.3 bits (103), Expect = 0.025,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 4/78 (5%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLK 204
           +THRLD  TSG+LV+AR    A+H  ++ R R++QK Y  +    +P    E   +W   
Sbjct: 231 VTHRLDAATSGVLVLARDVEFARHFNDALRERKVQKTYACVSEARVPVGVME---HWTDP 287

Query: 205 KSHIGGDYVHVVKQNEKG 222
           +    G   HV++   +G
Sbjct: 288 EDATRGPRRHVMRPPREG 305


>gi|294946256|ref|XP_002784994.1| hypothetical protein Pmar_PMAR020318 [Perkinsus marinus ATCC 50983]
 gi|239898369|gb|EER16790.1| hypothetical protein Pmar_PMAR020318 [Perkinsus marinus ATCC 50983]
          Length = 262

 Score = 44.3 bits (103), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 12/71 (16%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L+  +LY D+     NKP G+SV  G  I Y              + P L HRLD  T+G
Sbjct: 194 LEDAVLYRDADFIAINKPWGLSVTDGPKIKY------------SSEVPILIHRLDTATAG 241

Query: 157 ILVVARTRAAA 167
           + ++AR ++AA
Sbjct: 242 VQLLARHKSAA 252


>gi|139436953|ref|ZP_01771113.1| Hypothetical protein COLAER_00086 [Collinsella aerofaciens ATCC
           25986]
 gi|133776600|gb|EBA40420.1| Hypothetical protein COLAER_00086 [Collinsella aerofaciens ATCC
           25986]
          Length = 154

 Score = 44.3 bits (103), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 36/122 (29%), Positives = 53/122 (43%), Gaps = 14/122 (11%)

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCP 265
           D V +   ++  A  AI+ FKV++ F        +  +E    TGRTHQ+RVH  H+   
Sbjct: 16  DRVKMAVSDDPFARQAITTFKVLERFDSTRFDDGYTLVECHLFTGRTHQIRVHMRHINHA 75

Query: 266 IVGDHKYCANFKGNFTSPIQNKL---YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
            VGD  Y     G   +     L   +LH+  +   HP  G R++    LP  +    D 
Sbjct: 76  CVGDPLY-----GKCDARADQGLTRQFLHSWRVAFEHPVTGERIECRDELPWDLAAVLDD 130

Query: 322 LG 323
           L 
Sbjct: 131 LA 132


>gi|327266342|ref|XP_003217965.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           3-like [Anolis carolinensis]
          Length = 312

 Score = 44.3 bits (103), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 35/142 (24%), Positives = 61/142 (42%), Gaps = 11/142 (7%)

Query: 152 QETSGILVVA----RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +E+SG+++++      R        S R +R    Y ++   IP+  +  I+  L     
Sbjct: 78  KESSGLVLLSGCADTVRRVHDFYIRSQRAKRPTATYCAITTRIPEASEGEISTGLKLMQI 137

Query: 208 IGGDYVHVVKQNEKGA------NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
              D V  V    +G+         ++H+KV+D   +    L++QP T    QL VH+  
Sbjct: 138 EDFDLVVPVASPSRGSIERREVKKTLTHYKVLDS-NEDCALLQLQPLTAFPSQLLVHSTL 196

Query: 262 MGCPIVGDHKYCANFKGNFTSP 283
           +  PI+GDH Y +        P
Sbjct: 197 ILSPILGDHMYSSRVGAVLGEP 218


>gi|306835774|ref|ZP_07468775.1| RNA pseudouridine synthase [Corynebacterium accolens ATCC 49726]
 gi|304568348|gb|EFM43912.1| RNA pseudouridine synthase [Corynebacterium accolens ATCC 49726]
          Length = 262

 Score = 44.3 bits (103), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 47/156 (30%), Positives = 64/156 (41%), Gaps = 29/156 (18%)

Query: 148 HRLDQETSGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           HRLD+ T+G+++ +R   TRAA Q +   F   R  K Y     GI K    C     L 
Sbjct: 105 HRLDRLTAGLVICSRNPATRAAYQRI---FLEGRAVKRYR----GIVKQPLFCDEEIQLP 157

Query: 205 KSHI-GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                G   V V       + Y  +  + +           M P TG THQLRV   H+G
Sbjct: 158 MHKPRGSRQVLVADNGTPTSTYVRAAGREV----------TMWPRTGHTHQLRVLLNHLG 207

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
            P++GD  Y         +P    LY  +R + L H
Sbjct: 208 SPLIGDDTY--------PTPRPLDLYDFSRPLSLLH 235


>gi|66814022|ref|XP_641190.1| hypothetical protein DDB_G0280463 [Dictyostelium discoideum AX4]
 gi|60469215|gb|EAL67210.1| hypothetical protein DDB_G0280463 [Dictyostelium discoideum AX4]
          Length = 746

 Score = 44.3 bits (103), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 23/38 (60%)

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           F  LE+  HTGR+HQ+RVH      PIVGD  Y +  K
Sbjct: 547 FSLLEVTLHTGRSHQIRVHMASENIPIVGDPIYSSKSK 584


>gi|242005446|ref|XP_002423576.1| Ribosomal large subunit pseudouridine synthase C, putative
           [Pediculus humanus corporis]
 gi|212506724|gb|EEB10838.1| Ribosomal large subunit pseudouridine synthase C, putative
           [Pediculus humanus corporis]
          Length = 291

 Score = 44.3 bits (103), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 32/100 (32%), Positives = 47/100 (47%), Gaps = 6/100 (6%)

Query: 174 FRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            R R +QK Y   V G  P  + EC     +    IG     V K + KG + + +  K+
Sbjct: 5   IRNRLVQKEYVCRVEGEFPSGQIECSEPIEVVSYKIG-----VCKVSSKGKSCSTTFEKL 59

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               +     +  +PHTGR HQ+RVH  ++G P+V D  Y
Sbjct: 60  GYSSSTNTSIVLCKPHTGRMHQIRVHLQYLGYPVVNDPLY 99


>gi|224083169|ref|XP_002306957.1| predicted protein [Populus trichocarpa]
 gi|222856406|gb|EEE93953.1| predicted protein [Populus trichocarpa]
          Length = 192

 Score = 43.9 bits (102), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 77/185 (41%), Gaps = 51/185 (27%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV--KFNNRIQSGQVVRIPP 69
           V++    +RLD W       I+   +Q I++SG V V+ K     F++ +++G       
Sbjct: 17  VDSKSGKLRLDSWISCRISGISRARVQSIIKSGIVSVNGKITYKVFSHNVKAG------- 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
             + ++ II E K       L    + L   ++YED  + V NKPA + V    G A   
Sbjct: 70  --DEMDCIILEWK------PLRVEPENLPLDIVYEDENVLVVNKPAQMVVHPAPGNATGT 121

Query: 129 -IDGFL------------------------------KSWVDSKGQKPRLTHRLDQETSGI 157
            ++G L                               S+V S   +P + H LD+ TSG+
Sbjct: 122 LVNGILHHSSPTVSNQEVLSDAEDISDDGDGEGLCSSSYVAS--VRPGIVHWLDKGTSGL 179

Query: 158 LVVAR 162
           LVVA+
Sbjct: 180 LVVAK 184


>gi|322496292|emb|CBZ31363.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 1468

 Score = 43.9 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 58/117 (49%), Gaps = 17/117 (14%)

Query: 213  VHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +H   Q+++ A   I+ ++V++ FA     +++++  +GR HQ+R H   +G P+VGD +
Sbjct: 1326 LHAALQDQRNA---ITRYRVLEYFASAGVAYVQVELRSGRRHQIRQHFAQLGFPLVGDAR 1382

Query: 272  YCANFKGNF--TSPIQNKLYLHARYMDL---PHPEG--------GRLQITAPLPAHM 315
            Y A        T+    +  LHA  +D+      +G         R+ + A LPA M
Sbjct: 1383 YHAGVVAGHAGTTFGMQRAALHAYTVDILATTDSDGLASGEEVPDRVVVQAALPADM 1439


>gi|146076176|ref|XP_001462862.1| RNA pseudouridylate synthase-like protein [Leishmania infantum]
 gi|134066943|emb|CAM65048.1| RNA pseudouridylate synthase-like protein [Leishmania infantum JPCM5]
          Length = 1468

 Score = 43.9 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 58/117 (49%), Gaps = 17/117 (14%)

Query: 213  VHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +H   Q+++ A   I+ ++V++ FA     +++++  +GR HQ+R H   +G P+VGD +
Sbjct: 1326 LHAALQDQRNA---ITRYRVLEYFASAGVAYVQVELRSGRRHQIRQHFAQLGFPLVGDAR 1382

Query: 272  YCANFKGNF--TSPIQNKLYLHARYMDL---PHPEG--------GRLQITAPLPAHM 315
            Y A        T+    +  LHA  +D+      +G         R+ + A LPA M
Sbjct: 1383 YHAGVVAGHAGTTFGMQRAALHAYTVDILATTDSDGLASGEEVPDRVVVQAALPADM 1439


>gi|294943238|ref|XP_002783805.1| Ribosomal large subunit pseudouridine synthase A, putative
           [Perkinsus marinus ATCC 50983]
 gi|239896540|gb|EER15601.1| Ribosomal large subunit pseudouridine synthase A, putative
           [Perkinsus marinus ATCC 50983]
          Length = 142

 Score = 43.9 bits (102), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 42/129 (32%), Positives = 56/129 (43%), Gaps = 21/129 (16%)

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--------IPKNKKECIANW 201
           LD  TSGI++VA T AA   L   F+ R I K Y  LV G        I  N +   ++ 
Sbjct: 27  LDIFTSGIIMVAHTYAAYYQLRHQFKKRAILKKYICLVHGHMDEDSGIIDTNIQTYSSSS 86

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
             +  HI               N             +K   LE++  TGRTHQ+R+H  H
Sbjct: 87  NSRSKHIPISSSSSSYSTIINNN-------------KKVSLLEVEIPTGRTHQIRLHMYH 133

Query: 262 MGCPIVGDH 270
           +G PIV D+
Sbjct: 134 IGHPIVSDY 142


>gi|221487535|gb|EEE25767.1| ribosomal pseudouridine synthase, putative [Toxoplasma gondii GT1]
          Length = 254

 Score = 43.9 bits (102), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 35/56 (62%)

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            D+   K RL H+LD  TSG+L++A  + AA+ +    + R IQK Y +LV+G P+
Sbjct: 143 TDADACKVRLCHQLDYATSGLLMLAHNQKAARIVQTLLQRREIQKEYLALVYGHPR 198


>gi|237830323|ref|XP_002364459.1| RNA pseudouridylate synthase family protein [Toxoplasma gondii
           ME49]
 gi|211962123|gb|EEA97318.1| RNA pseudouridylate synthase family protein [Toxoplasma gondii
           ME49]
 gi|221507328|gb|EEE32932.1| ribosomal pseudouridine synthase, putative [Toxoplasma gondii VEG]
          Length = 254

 Score = 43.9 bits (102), Expect = 0.037,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 35/56 (62%)

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            D+   K RL H+LD  TSG+L++A  + AA+ +    + R IQK Y +LV+G P+
Sbjct: 143 TDADACKVRLCHQLDYATSGLLMLAHNQKAARIVQTLLQRREIQKEYLALVYGHPR 198


>gi|311893844|dbj|BAJ26252.1| putative pseudouridine synthase [Kitasatospora setae KM-6054]
          Length = 318

 Score = 43.9 bits (102), Expect = 0.038,   Method: Compositional matrix adjust.
 Identities = 53/203 (26%), Positives = 84/203 (41%), Gaps = 13/203 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           L+ D +I V +KP  ++    GS         L+  +D     PRL+  HRLD+ T+G++
Sbjct: 99  LHRDERIVVADKPHFLATTPRGSHATETALARLRRDLD----LPRLSPAHRLDRLTAGVV 154

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-LLKKSHIGGDYVHVVK 217
           +     A        F  R   K Y ++     +++ +  A   ++  S I  D   +  
Sbjct: 155 LFVADPALRGAYQGLFERREAVKEYEAVA----RHEPDAAARLPVVVCSRIVKDRGRLDA 210

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
               G   A S  ++ +          + P TGRTHQLRVH   +G PI+GD  Y     
Sbjct: 211 YEVPGEPNAESLVELAEERG-GLGRYRLAPRTGRTHQLRVHMNGLGLPILGDPLYPEVLG 269

Query: 278 GNFTSPIQNKLYLHARYMDLPHP 300
                  +  L L AR ++   P
Sbjct: 270 EGDPEDYRRPLQLLARSLEFTDP 292


>gi|260494555|ref|ZP_05814685.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_33]
 gi|260197717|gb|EEW95234.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_33]
          Length = 95

 Score = 43.9 bits (102), Expect = 0.040,   Method: Composition-based stats.
 Identities = 28/94 (29%), Positives = 48/94 (51%), Gaps = 10/94 (10%)

Query: 222 GANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           G   A +H KV++  + +   +LE + +TGRTHQ+R H   +G  +VGD  Y  N     
Sbjct: 1   GGKSAKTHIKVLERNYEKNITFLEARLYTGRTHQIRAHLSLIGHSLVGDELYGGNMN--- 57

Query: 281 TSPIQNKLYLHARYMDLPHP---EGGRLQITAPL 311
              +  +  LHA  ++  +P   E  +++I  P+
Sbjct: 58  ---LAKRQMLHAYKLEFQNPKTLENLKIEIDIPI 88


>gi|254445393|ref|ZP_05058869.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198259701|gb|EDY84009.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 270

 Score = 43.9 bits (102), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 57/241 (23%), Positives = 98/241 (40%), Gaps = 35/241 (14%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQ-----GGSGIAYHIDGFLKSWVDSKGQKPRL-------T 147
           L+  D  ++  NKPAG+ S Q     G   I+  +    +  ++ K Q  +L        
Sbjct: 24  LIANDEGLFAINKPAGLASFQHEWSLGKPDISMALR---RELLNEKPQLKKLGIEGLYRA 80

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           + LD E SG LV A+     + L  +    ++   +  LV    +++ E + +  L   H
Sbjct: 81  YNLDSELSGALVFAKNEEFEKILKNAVGSSQLVFRFHLLVKAETEDR-EFVCDLPLMNHH 139

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                +   +  +K      + F+ +  F Q   W E +  + R HQ+RVHA   G  IV
Sbjct: 140 QAKRMIVSHRSGKK----CETRFRFLRGFGQYQLW-EAETTSLRVHQVRVHAAERGLNIV 194

Query: 268 -------GDHKYCANFKGNFTS------PIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
                  G+  Y +  K ++ S      P+   L +H   ++   P+     I APLP+ 
Sbjct: 195 GEDFYSDGEEIYLSRIKRDYMSGRGREKPLYGSLCVHLVEVEFRIPDLKLESILAPLPSR 254

Query: 315 M 315
            
Sbjct: 255 F 255


>gi|325274510|ref|ZP_08140575.1| pseudouridine synthase [Pseudomonas sp. TJI-51]
 gi|324100350|gb|EGB98131.1| pseudouridine synthase [Pseudomonas sp. TJI-51]
          Length = 294

 Score = 43.5 bits (101), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 51/183 (27%), Positives = 90/183 (49%), Gaps = 21/183 (11%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQET 154
           L+  +L+ D  + V +KP  + V   +    +++  L   +  +   P L   HR+D+ T
Sbjct: 84  LQEHVLHVDEHLVVADKPHFLPV---TPTGEYVEHTLLRRLIRRLDNPHLVPLHRIDRHT 140

Query: 155 SGILVVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-IGG 210
           +G+++ +    TR+A Q L   F  RRI K Y ++   +P++     A  L+ KS  + G
Sbjct: 141 AGLVLFSANPHTRSAYQRL---FPERRIDKRYQAIAAALPQH-----AFPLVHKSRLVHG 192

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +    + + E  AN + +  +V++   +   W   + P TG+THQLRVH   +G  I  D
Sbjct: 193 EPFFRMHEVEGEAN-SETLAEVLE--KRGALWRYGLSPVTGKTHQLRVHMAALGAGISND 249

Query: 270 HKY 272
             Y
Sbjct: 250 PFY 252


>gi|146089719|ref|XP_001470456.1| hypothetical protein [Leishmania infantum JPCM5]
 gi|134070489|emb|CAM68832.1| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 757

 Score = 43.5 bits (101), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 29/47 (61%), Gaps = 5/47 (10%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKL 288
           P+TGR HQ+R+H   +GCPIVGD  Y      A+  G  ++ +Q +L
Sbjct: 424 PYTGRLHQIRMHLSSLGCPIVGDVVYAHTSGNADVPGTSSTQVQPQL 470


>gi|322499928|emb|CBZ35002.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 757

 Score = 43.5 bits (101), Expect = 0.043,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 29/47 (61%), Gaps = 5/47 (10%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKL 288
           P+TGR HQ+R+H   +GCPIVGD  Y      A+  G  ++ +Q +L
Sbjct: 424 PYTGRLHQIRMHLSSLGCPIVGDVVYAHTSGNADVPGTSSTQVQPQL 470


>gi|255325636|ref|ZP_05366733.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           tuberculostearicum SK141]
 gi|255297246|gb|EET76566.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           tuberculostearicum SK141]
          Length = 303

 Score = 43.5 bits (101), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 51/240 (21%), Positives = 90/240 (37%), Gaps = 49/240 (20%)

Query: 37  LQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           LQK+L        R  ++ +D  RV+ N +I S Q V++ P ++ +       ++    V
Sbjct: 65  LQKVLAKAGVASRRHAEILIDAGRVEVNGKIISKQGVKVNPSVDVI-------RVDGVRV 117

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           N+ +  ++            +V NKP G+       +     G + S   + GQ+     
Sbjct: 118 NVNEEHEY------------FVLNKPRGMQSTMSDDLGRPCVGDVVSEKVAAGQRLFHVG 165

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKS 206
           RLD +T G+L++      A  L        + K Y + V G    K  ++      L+  
Sbjct: 166 RLDADTEGLLILTNDGELANRLMHP--KYEVTKTYLATVLGEADRKLVRQLKEGIELEDG 223

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               D+  VV  N                  Q +  + ++ H GR H +R      G P+
Sbjct: 224 LAKADFAQVVDTN------------------QGYSLVRLELHEGRKHIVRRMLKEAGFPV 265


>gi|255024923|ref|ZP_05296909.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Listeria monocytogenes FSL J1-208]
          Length = 180

 Score = 43.5 bits (101), Expect = 0.047,   Method: Compositional matrix adjust.
 Identities = 28/98 (28%), Positives = 47/98 (47%), Gaps = 10/98 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP  +        +Y  D     ++ +++  GQ       HRLDQ TS
Sbjct: 55  IIYEDDFLLVVNKPVDMKTHAND--SYETDTCANAVQYYLEKTGQDANALAVHRLDQTTS 112

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLV---WGI 190
           G+++ A+ + A   L+     R I + Y + V   WG+
Sbjct: 113 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGL 150


>gi|134096436|ref|YP_001101511.1| putative pseudouridylate synthase [Herminiimonas arsenicoxydans]
          Length = 281

 Score = 43.5 bits (101), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 45/181 (24%), Positives = 80/181 (44%), Gaps = 21/181 (11%)

Query: 99  SILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
            ++LY+D  +   +KP  + V   G  +   +   LK  ++     P   HR+D++T+G+
Sbjct: 70  EVVLYQDDYLVAVDKPHFLPVTPAGRYLQETLLVRLKRSLNIDTLAP--MHRIDRDTAGL 127

Query: 158 LVVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           ++      TR   Q L   FR R + K Y ++        +  +A   + +S +      
Sbjct: 128 VLFTIQPHTRNLYQTL---FRERSVSKQYEAIA-----PYRADLALPTVYRSRLLESAAF 179

Query: 215 VVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +  +  +G   A  AI   +V    A+      ++P +G+ HQLR H   +G PIV D  
Sbjct: 180 MKMEEVEGVPNAETAIDLMEVQGALAR----YRLEPVSGQKHQLRAHMAALGMPIVNDRI 235

Query: 272 Y 272
           Y
Sbjct: 236 Y 236


>gi|227501609|ref|ZP_03931658.1| RNA pseudouridylate synthase family protein [Corynebacterium
           accolens ATCC 49725]
 gi|227077634|gb|EEI15597.1| RNA pseudouridylate synthase family protein [Corynebacterium
           accolens ATCC 49725]
          Length = 262

 Score = 43.5 bits (101), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 37/126 (29%), Positives = 50/126 (39%), Gaps = 15/126 (11%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ T+G+++ +R  A        F   R  K Y     GI K    C     L    
Sbjct: 105 HRLDRLTAGLVICSRNPATRADYQRIFLEGRAVKRYR----GIVKQPLFCDEEIRLPMHK 160

Query: 208 I-GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             G   V V       + Y  +  + +           M P TG THQLRV   H+G P+
Sbjct: 161 PRGSRQVLVADNGTPTSTYVRAAGREV----------TMWPRTGHTHQLRVLLNHLGSPL 210

Query: 267 VGDHKY 272
           +GD  Y
Sbjct: 211 IGDDTY 216


>gi|123445956|ref|XP_001311733.1| RNA pseudouridylate synthase family protein [Trichomonas vaginalis
           G3]
 gi|121893554|gb|EAX98803.1| RNA pseudouridylate synthase family protein [Trichomonas vaginalis
           G3]
          Length = 173

 Score = 43.5 bits (101), Expect = 0.053,   Method: Compositional matrix adjust.
 Identities = 29/113 (25%), Positives = 57/113 (50%), Gaps = 6/113 (5%)

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A++ +AA+  TE     +I+K Y + V G    +K+ +   +++ +      V      
Sbjct: 1   MAKSDSAAKRFTEMLNNNKIEKTYIARVLGQFPPEKKIVDLPIIESAESRAKMV-----C 55

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++G   + + F+++    ++   ++  P TGRTHQ+RVH   +G PI  D  Y
Sbjct: 56  KEGGKPSQTEFELVTTNGKE-SIVKCHPITGRTHQIRVHLASIGFPISNDVFY 107


>gi|145641802|ref|ZP_01797377.1| conserved hypothetical pseudouridine synthase [Haemophilus
           influenzae R3021]
 gi|145273424|gb|EDK13295.1| conserved hypothetical pseudouridine synthase [Haemophilus
           influenzae 22.4-21]
          Length = 123

 Score = 43.1 bits (100), Expect = 0.055,   Method: Compositional matrix adjust.
 Identities = 32/104 (30%), Positives = 47/104 (45%), Gaps = 15/104 (14%)

Query: 101 LLYEDSKIYVFNKPAGISV------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++Y+ S   + NK  GISV      QG + +        K W         L HRLD+ T
Sbjct: 5   VVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQLNVPKVW---------LVHRLDKVT 55

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SG+L++A    +A   +  F   +I K Y +L    PK K+  I
Sbjct: 56  SGLLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLI 99


>gi|193222440|emb|CAL63390.2| Putative pseudouridylate synthase 23S RNA-specific [Herminiimonas
           arsenicoxydans]
          Length = 300

 Score = 43.1 bits (100), Expect = 0.055,   Method: Compositional matrix adjust.
 Identities = 45/180 (25%), Positives = 80/180 (44%), Gaps = 21/180 (11%)

Query: 100 ILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           ++LY+D  +   +KP  + V   G  +   +   LK  ++     P   HR+D++T+G++
Sbjct: 90  VVLYQDDYLVAVDKPHFLPVTPAGRYLQETLLVRLKRSLNIDTLAP--MHRIDRDTAGLV 147

Query: 159 VVA---RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +      TR   Q L   FR R + K Y ++        +  +A   + +S +      +
Sbjct: 148 LFTIQPHTRNLYQTL---FRERSVSKQYEAIA-----PYRADLALPTVYRSRLLESAAFM 199

Query: 216 VKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +  +G   A  AI   +V    A+      ++P +G+ HQLR H   +G PIV D  Y
Sbjct: 200 KMEEVEGVPNAETAIDLMEVQGALAR----YRLEPVSGQKHQLRAHMAALGMPIVNDRIY 255


>gi|315635284|ref|ZP_07890561.1| pseudouridylate synthase [Aggregatibacter segnis ATCC 33393]
 gi|315476030|gb|EFU66785.1| pseudouridylate synthase [Aggregatibacter segnis ATCC 33393]
          Length = 233

 Score = 43.1 bits (100), Expect = 0.056,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 71/184 (38%), Gaps = 32/184 (17%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           F +S + +  +++ +FNKP  +  Q            LK ++D     P    RLD+++ 
Sbjct: 31  FSRSKIAFSQTQVILFNKPFDVLCQFSDENGRST---LKDFIDIAEVYP--VGRLDRDSE 85

Query: 156 GILVVARTRAAAQHLTES-FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           G+L++         L E  F+M   +K YW  V G+P    E     L +   +      
Sbjct: 86  GLLLLTNNGEIQHRLAEPKFKM---EKTYWMQVEGVP---DETALEQLRRGVQLKDGMTK 139

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKF-----------CWLEMQPHTGRTHQLRVHALHMG 263
             K         +      DC  Q+             WLE++ + GR  Q+R    H+G
Sbjct: 140 PAK---------VRLISEPDCLWQRVPPIRERKNIPTSWLEIKIYEGRNRQVRRMTAHIG 190

Query: 264 CPIV 267
            P +
Sbjct: 191 FPTL 194


>gi|207109585|ref|ZP_03243747.1| hypothetical protein HpylH_10299 [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 144

 Score = 43.1 bits (100), Expect = 0.057,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 60/130 (46%), Gaps = 12/130 (9%)

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------GQKPR--LTHRLDQETSGILVV 160
           V NKP  + V     +    +  L  W+ SK       G K R  + HRLD++TSG +V+
Sbjct: 2   VLNKPPNLVVHKAPSVK---EPTLVDWLKSKNYELSNLGLKERYGIVHRLDKDTSGGIVI 58

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+      HL+E  + + + + Y +L+    K +K  +  +L +  +     + +    +
Sbjct: 59  AKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKK 118

Query: 221 KGANYAISHF 230
           + + Y+ S F
Sbjct: 119 EKSRYSKSEF 128


>gi|115744559|ref|XP_794566.2| PREDICTED: hypothetical protein, partial [Strongylocentrotus
           purpuratus]
 gi|115963314|ref|XP_001191250.1| PREDICTED: hypothetical protein, partial [Strongylocentrotus
           purpuratus]
          Length = 143

 Score = 43.1 bits (100), Expect = 0.064,   Method: Compositional matrix adjust.
 Identities = 26/67 (38%), Positives = 36/67 (53%), Gaps = 6/67 (8%)

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L +Q HTGR HQLR+H   +G PIVGD+ Y         SP +  L  H  ++ +P   G
Sbjct: 64  LLLQLHTGRRHQLRIHCQSIGHPIVGDYTYSMR---KDVSPYRMMLLAHTLHIPIP---G 117

Query: 303 GRLQITA 309
             + +TA
Sbjct: 118 EGIDVTA 124


>gi|149052130|gb|EDM03947.1| RNA pseudouridylate synthase domain containing 1 (predicted),
           isoform CRA_c [Rattus norvegicus]
          Length = 177

 Score = 43.1 bits (100), Expect = 0.068,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 31/54 (57%), Gaps = 3/54 (5%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           ++P TGRTHQLRVH   +G PIVGD  Y          P   ++ LHA Y+ +P
Sbjct: 37  LKPLTGRTHQLRVHCSALGHPIVGDLTY-GQADDQEDQPF--RMMLHAFYLRIP 87


>gi|322823471|gb|EFZ29216.1| hypothetical protein TCSYLVIO_4532 [Trypanosoma cruzi]
          Length = 346

 Score = 43.1 bits (100), Expect = 0.070,   Method: Compositional matrix adjust.
 Identities = 40/139 (28%), Positives = 64/139 (46%), Gaps = 26/139 (18%)

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            G G+    D   ++ V  +G+K   +  H+LD  TSG+L VA +R  A  L   F MR 
Sbjct: 23  AGGGVEKE-DDTTRTAVRGRGEKKMVKFVHQLDYATSGVLCVAFSREMAARLAHCFEMRT 81

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVID-- 234
            +K Y +++ G+         + + KK  +  G D++       +G+ YA SH + I   
Sbjct: 82  TRKAYLAVLLGMMPT-----TSAMEKKLDTDTGVDFL-------RGSPYA-SHVRRISMD 128

Query: 235 -----CFAQKFCWLEMQPH 248
                CF +K C +E   H
Sbjct: 129 DVPGVCFIRK-CVIEASGH 146



 Score = 36.6 bits (83), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 16/26 (61%), Positives = 18/26 (69%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
           P TGR HQLRVH   +G PI+GD  Y
Sbjct: 217 PRTGRRHQLRVHCHAIGFPILGDVTY 242


>gi|301606985|ref|XP_002933094.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 3
           [Xenopus (Silurana) tropicalis]
          Length = 368

 Score = 43.1 bits (100), Expect = 0.070,   Method: Compositional matrix adjust.
 Identities = 58/278 (20%), Positives = 103/278 (37%), Gaps = 46/278 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD--SKGQKPRLTHRLDQETSGIL 158
           ++Y    +   NKP G+S+ G       +   L         G    +     +E+SG++
Sbjct: 87  VVYLKGPLVAINKPQGLSITGKEQ-EVSVSSLLADLQQHLGLGSDLHIVKAAPKESSGLV 145

Query: 159 VVARTRAAAQHLTESFRM-RRIQKI---YWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +++      + L + + + R+ QK    Y +++ G+P   +  I   L  +       V 
Sbjct: 146 LLSTCHMTTKRLEDYYALCRKAQKPTASYCAVMAGVPHPAEGEIKAALKLERIEDWQLVV 205

Query: 215 VVKQNEKG------ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            V    KG          ++ +KV+D  A     +++QP +    QL VH+  M C I+G
Sbjct: 206 PVTDPSKGRLERREIKRTLTRYKVLDS-ADGCALVQLQPMSVFQAQLLVHSTLMFCRILG 264

Query: 269 DHKYCANF----------------------------KGNFTSPIQNKLYLHARYMDL--- 297
           DH Y A                              + +FT    +++ LH  +  L   
Sbjct: 265 DHTYSARVGKVLGENIFVPMDIALPRTQVLEENVLRRMHFTQQQMHRMPLHLHFQQLMIP 324

Query: 298 -PHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
              P  G   + AP P    +T   LG   ++ L   R
Sbjct: 325 GESPAEGDTFLDAPPPPFFQRTLQLLGLYANKQLCSDR 362


>gi|228469440|ref|ZP_04054448.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           uenonis 60-3]
 gi|228309015|gb|EEK17658.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           uenonis 60-3]
          Length = 133

 Score = 42.7 bits (99), Expect = 0.073,   Method: Compositional matrix adjust.
 Identities = 31/95 (32%), Positives = 44/95 (46%), Gaps = 20/95 (21%)

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KL 288
           C LE    TGRTHQ+R H   +  P+ GD +Y  +    G  TS  Q           + 
Sbjct: 32  CELE----TGRTHQIRAHMKSIDHPLFGDERYGGDQILWGQRTSSYQQFVNNCLKICPRQ 87

Query: 289 YLHARYMDLPHPEGG-RLQITAPLP---AHMVKTW 319
            LHA  +   HP  G R+  +APLP   + +++ W
Sbjct: 88  ALHAETLAFDHPTTGERMHFSAPLPDDMSQLIEKW 122


>gi|261328132|emb|CBH11109.1| hypothetical protein, conserved [Trypanosoma brucei gambiense
           DAL972]
          Length = 727

 Score = 42.7 bits (99), Expect = 0.076,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 28/46 (60%), Gaps = 6/46 (13%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKL 288
           TGRTHQ+RVH   +G PIV DHKY         F GN+   ++++L
Sbjct: 621 TGRTHQVRVHLASVGHPIVDDHKYIYHLSRNTPFTGNYRKEVKSRL 666


>gi|296117982|ref|ZP_06836565.1| RNA pseudouridylate synthase [Corynebacterium ammoniagenes DSM
           20306]
 gi|295969213|gb|EFG82455.1| RNA pseudouridylate synthase [Corynebacterium ammoniagenes DSM
           20306]
          Length = 308

 Score = 42.7 bits (99), Expect = 0.077,   Method: Compositional matrix adjust.
 Identities = 54/250 (21%), Positives = 92/250 (36%), Gaps = 55/250 (22%)

Query: 30  PHINFVNLQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           P+     LQK+L        R  +V +D  RV+ N +I   Q VR+ P  + +       
Sbjct: 63  PNTEGERLQKVLAKAGVASRRHAEVLIDAGRVEVNGKIIKRQGVRVNPNADVI------- 115

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           ++    VN+             ED + ++ NKP G+       +     G + +   + G
Sbjct: 116 RVDGVRVNVN------------EDHEYFILNKPRGVQSTMQDDMGRPCVGDMVAEKTASG 163

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-----IPKNKKE 196
           Q+     RLD +T G+L++      A  L        + K Y + V G     + +  K+
Sbjct: 164 QRLFHVGRLDADTEGLLILTNDGELANRLMHP--KYEVSKTYLATVLGEADKSLVRTLKD 221

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I    L       D+V +V +N                  Q    + ++ H GR H +R
Sbjct: 222 GIE---LDDGMANADFVQIVDKN------------------QGMSLIRLELHEGRKHIVR 260

Query: 257 VHALHMGCPI 266
                 G P+
Sbjct: 261 RMLKAAGYPV 270


>gi|213027168|ref|ZP_03341615.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 119

 Score = 42.7 bits (99), Expect = 0.081,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 44/89 (49%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             +  A + L + F    I+K Y ++V G
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRG 92


>gi|303281636|ref|XP_003060110.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226458765|gb|EEH56062.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 334

 Score = 42.7 bits (99), Expect = 0.082,   Method: Compositional matrix adjust.
 Identities = 55/209 (26%), Positives = 88/209 (42%), Gaps = 21/209 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGS------GIAYHIDGFLKSWV--DSKGQKP-RLTHRL 150
            +++E+  +   +KPAG S  G        G+   I     S     S    P    HRL
Sbjct: 54  FVVFENDDVLCVHKPAGASFHGDDLATRRPGVLARIRQLQASGTLRGSDYDGPLHSVHRL 113

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSG L+ A+    A  L  +F  RR+ K Y +L    P +KK      ++ +S  G 
Sbjct: 114 DKVTSGALLFAKRPDVAAALGAAFASRRVHKYYVALSARRP-SKKMGTVRGVMARSRRGT 172

Query: 211 DYVHVVKQNEKGANYAISHFKVIDC-------FAQKFCWLEMQPHTGRTHQLRVHALHMG 263
             +   ++   G   A +  + +           +    +  +P TG+THQLRV A  +G
Sbjct: 173 WKLTRDERRGGGGAAAAAETRFVGRGIVGHGESKRPLRLIVFRPLTGKTHQLRVAAKSLG 232

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            P++GD  Y            +++ YLHA
Sbjct: 233 SPVLGDAAYAGKDAAA----SEDRAYLHA 257


>gi|299115628|emb|CBN75829.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 505

 Score = 42.7 bits (99), Expect = 0.084,   Method: Compositional matrix adjust.
 Identities = 36/123 (29%), Positives = 57/123 (46%), Gaps = 20/123 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV------------DSKGQKPRL-- 146
           +++++    V +KPAG+           ID  +++ V             S+   P L  
Sbjct: 175 IVHKNEDFVVVDKPAGVPT------VPTIDNGVQNCVFQASLAVAGMPPGSRSLPPPLHA 228

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD  TSGI+V AR + AA+ L E FR RR++K Y +L+   P      +A+    K+
Sbjct: 229 VSRLDVCTSGIVVFARHKEAAKQLNELFRARRVKKRYLALLTPGPAVPTGSMAHCCRSKA 288

Query: 207 HIG 209
             G
Sbjct: 289 FDG 291



 Score = 38.5 bits (88), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 18/36 (50%), Positives = 23/36 (63%), Gaps = 2/36 (5%)

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           A   C +E++  TGRTHQLR+    MG  IVGD +Y
Sbjct: 418 APHLCAMELE--TGRTHQLRLQLAAMGSAIVGDTRY 451


>gi|255520401|ref|ZP_05387638.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J1-175]
          Length = 202

 Score = 42.7 bits (99), Expect = 0.088,   Method: Compositional matrix adjust.
 Identities = 28/98 (28%), Positives = 47/98 (47%), Gaps = 10/98 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRL--THRLDQETS 155
           ++YED  + V NKP  +        +Y  D     ++ +++  GQ       HRLDQ TS
Sbjct: 80  IIYEDDFLLVVNKPVDMKTHPND--SYETDTCANAVQYYLEKTGQDANALAVHRLDQTTS 137

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLV---WGI 190
           G+++ A+ + A   L+     R I + Y + V   WG+
Sbjct: 138 GLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGL 175


>gi|311739374|ref|ZP_07713209.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           pseudogenitalium ATCC 33035]
 gi|311305190|gb|EFQ81258.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           pseudogenitalium ATCC 33035]
          Length = 303

 Score = 42.7 bits (99), Expect = 0.088,   Method: Compositional matrix adjust.
 Identities = 50/240 (20%), Positives = 90/240 (37%), Gaps = 49/240 (20%)

Query: 37  LQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           LQK+L        R  ++ +D  RV+ N +I + Q V++ P ++ +       ++    V
Sbjct: 65  LQKVLAKAGVASRRHAEILIDAGRVEVNGKIIAKQGVKVNPSVDVI-------RVDGVRV 117

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           N+ +  ++            +V NKP G+       +     G + S   + GQ+     
Sbjct: 118 NVNEEHEY------------FVLNKPRGMQSTMSDDLGRPCVGDVVSEKVAAGQRLFHVG 165

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKS 206
           RLD +T G+L++      A  L        + K Y + V G    K  ++      L+  
Sbjct: 166 RLDADTEGLLILTNDGELANRLMHP--KYEVTKTYLATVLGEADRKLVRQLKEGIELEDG 223

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               D+  VV  N                  Q +  + ++ H GR H +R      G P+
Sbjct: 224 LAKADFAQVVDTN------------------QGYSLVRLELHEGRKHIVRRMLKEAGFPV 265


>gi|213419310|ref|ZP_03352376.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 95

 Score = 42.7 bits (99), Expect = 0.090,   Method: Composition-based stats.
 Identities = 24/60 (40%), Positives = 30/60 (50%), Gaps = 3/60 (5%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHPEGG 303
           P TGRTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  +   HP  G
Sbjct: 24  PVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGTG 83


>gi|296225812|ref|XP_002758673.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           3-like [Callithrix jacchus]
          Length = 399

 Score = 42.4 bits (98), Expect = 0.098,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +G    +SHF+V+         +++QP T  + QL+VH +   CP++GDH Y A
Sbjct: 262 EGVKKTLSHFRVL-ATGSGCALVQLQPLTVFSSQLQVHMVLQLCPVLGDHTYSA 314


>gi|313815672|gb|EFS53386.1| conserved domain protein [Propionibacterium acnes HL059PA1]
 gi|315099394|gb|EFT71370.1| conserved domain protein [Propionibacterium acnes HL059PA2]
          Length = 113

 Score = 42.4 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 25/63 (39%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKLYLHARYMDLPHP 300
           E  P TGRTHQ+R+H   +G PIV D  Y         +FT P+Q    L A  M    P
Sbjct: 40  EASPRTGRTHQIRLHMQRLGAPIVNDPFYPVVLDTPVDDFTHPLQ----LQAWRMGFTDP 95

Query: 301 EGG 303
             G
Sbjct: 96  VTG 98


>gi|310828101|ref|YP_003960458.1| pseudouridine synthase [Eubacterium limosum KIST612]
 gi|308739835|gb|ADO37495.1| pseudouridine synthase [Eubacterium limosum KIST612]
          Length = 241

 Score = 42.4 bits (98), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 71/169 (42%), Gaps = 22/169 (13%)

Query: 102 LYEDSKIYVF-NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           + ED KIYV  NKP G+     +    H D   ++ +D    K RL    RLD++T G+L
Sbjct: 55  IAEDKKIYVLLNKPKGVV---STSADRHAD---QTVMDRLPIKERLFTVGRLDKDTEGLL 108

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++         LT         KIY  LV GIP       A  L     +  + V +   
Sbjct: 109 ILTNDGDLTFRLTHPSH--EFNKIYEGLVKGIPS------AGEL----RLFAEGVQIEDD 156

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +      A +  +V+  + +    LEM  H GR  Q+R     +G P++
Sbjct: 157 DHTLHTTAPASVQVLKTY-RSTALLEMTIHEGRKRQIRKMCAAIGHPVI 204


>gi|153825805|ref|ZP_01978472.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-2]
 gi|149740528|gb|EDM54643.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-2]
          Length = 145

 Score = 42.4 bits (98), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 29/54 (53%), Gaps = 4/54 (7%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           P TGR+HQLRVH   +G PIVGD  Y       F     ++L LHA  +   HP
Sbjct: 55  PITGRSHQLRVHMQSLGHPIVGDDLYAPPEAVEFA----DRLQLHAAELCFYHP 104


>gi|47210854|emb|CAF89720.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 220

 Score = 42.4 bits (98), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 24/37 (64%), Gaps = 1/37 (2%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNF 280
           +QP TGRTHQLRVH   +G PIVGD  Y C    G +
Sbjct: 134 LQPLTGRTHQLRVHCSAIGHPIVGDVTYSCGADAGPY 170


>gi|288921576|ref|ZP_06415849.1| pseudouridine synthase [Frankia sp. EUN1f]
 gi|288347046|gb|EFC81350.1| pseudouridine synthase [Frankia sp. EUN1f]
          Length = 279

 Score = 42.4 bits (98), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 44/94 (46%), Gaps = 7/94 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ED  +   +KP G++V G        D  L S     G++    HR+D+ TSG+++ A
Sbjct: 13  IFEDEAVLALDKPVGVAVMG-----ERHDTDLVSMAREAGEELFPAHRIDKVTSGVVLFA 67

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVW--GIPKN 193
           +       LT  F  R + K Y +L    GIP  
Sbjct: 68  KQLRHHGDLTRQFNRRTVDKTYLALTRTHGIPAT 101


>gi|255088607|ref|XP_002506226.1| RNA pseudouridylate synthase [Micromonas sp. RCC299]
 gi|226521497|gb|ACO67484.1| RNA pseudouridylate synthase [Micromonas sp. RCC299]
          Length = 481

 Score = 42.4 bits (98), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 32/100 (32%), Positives = 50/100 (50%), Gaps = 5/100 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +D  +  +++ED  I V NKP  + S+   S    H  G L+  +       R+THRLD 
Sbjct: 178 ADAWRHRVVHEDDAILVVNKPHRLPSMAHESNGVEHCAGCLERSLGLSPSTLRVTHRLDS 237

Query: 153 ETSGILVVARTRAAAQHLTESFR----MRRIQKIYWSLVW 188
            TSG+LV+ +T  A +   +S       + I K Y +LV+
Sbjct: 238 STSGVLVLGKTATAVREFNDSVAKTPGSKEIVKSYAALVY 277


>gi|294879761|ref|XP_002768778.1| hypothetical protein Pmar_PMAR026919 [Perkinsus marinus ATCC 50983]
 gi|239871649|gb|EER01496.1| hypothetical protein Pmar_PMAR026919 [Perkinsus marinus ATCC 50983]
          Length = 302

 Score = 42.4 bits (98), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 37/122 (30%), Positives = 50/122 (40%), Gaps = 50/122 (40%)

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSGI++VA T AA   L   F+ R I                       LKK    
Sbjct: 178 LDIFTSGIIMVAHTYAAYYQLRHQFKNRAI-----------------------LKK---- 210

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                          Y+I+         +K   LE++  TGRTHQ+R+H  H+G PIV D
Sbjct: 211 ---------------YSIAQ--------EKVSLLEVEIPTGRTHQIRLHMYHIGHPIVSD 247

Query: 270 HK 271
           ++
Sbjct: 248 YR 249


>gi|294668516|ref|ZP_06733613.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           elongata subsp. glycolytica ATCC 29315]
 gi|291309479|gb|EFE50722.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           elongata subsp. glycolytica ATCC 29315]
          Length = 186

 Score = 42.4 bits (98), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 40/170 (23%), Positives = 72/170 (42%), Gaps = 26/170 (15%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + +FNKP G+  Q      +     LK  +D+ G  P    RLD ++ G+L++       
Sbjct: 4   LIIFNKPCGVICQFS---PHEKHPSLKDHIDAPGFYP--AGRLDTDSEGLLLLTDDGQLQ 58

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY------VHVVKQNEK 221
             +T+     +++K YW+ + GIP   K      LL++    GD+      + ++ + E 
Sbjct: 59  ARITQP--RFKVEKTYWAQLEGIPDTDK----LQLLQRPMDLGDFTTRPAKIRLLSEEET 112

Query: 222 GA----NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                 N  +   K +  F     WLE++   G+  Q+R      G P +
Sbjct: 113 DGLWPRNPPVRVRKTVPDF-----WLEIKISEGKNRQVRRMTAKAGYPCL 157


>gi|255729054|ref|XP_002549452.1| hypothetical protein CTRG_03749 [Candida tropicalis MYA-3404]
 gi|240132521|gb|EER32078.1| hypothetical protein CTRG_03749 [Candida tropicalis MYA-3404]
          Length = 271

 Score = 42.4 bits (98), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 51/199 (25%), Positives = 94/199 (47%), Gaps = 33/199 (16%)

Query: 110 VFNKPAGI--SVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAA 166
           V NKP+G+  + +G + I   +    K ++ +    + R+  RLD+  +G L++AR +  
Sbjct: 14  VINKPSGLICAARGPNNIVDAVSEEFKQFLPTVSSSQFRIVQRLDRFVTGGLLIARNKKW 73

Query: 167 AQHLTESF----RMRRIQKIYWSLV--WGIPKNKKECIANWL--LKKSHIGG-DYVHVVK 217
           A  + +SF     ++ I++ Y  L+    IPK  K  I + +  L+K + G  +   V+K
Sbjct: 74  ADKVRKSFYGGGNLKLIRR-YVGLIPLTNIPKKTKGVIEHEIEALEKDYRGKHEPRKVLK 132

Query: 218 QNEKGANYAISHFKVIDCFAQK-------FCWLEMQP-----HTGRTHQLRVHALH-MGC 264
              K      +H++++   A+K       F   ++ P      TGR +Q+R H L   G 
Sbjct: 133 YTAK------THYQLLPALARKLEGDYPVFQQSQVVPAIFQLETGRKNQIRDHVLQEFGV 186

Query: 265 PIVGDHKYCANFKGNFTSP 283
            ++ D  +  +FK N   P
Sbjct: 187 TLLNDDNFV-DFKFNSEEP 204


>gi|192361858|ref|YP_001982092.1| putative pseudouridylate synthase [Cellvibrio japonicus Ueda107]
 gi|190688023|gb|ACE85701.1| putative pseudouridylate synthase [Cellvibrio japonicus Ueda107]
          Length = 291

 Score = 42.4 bits (98), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 56/172 (32%), Positives = 83/172 (48%), Gaps = 25/172 (14%)

Query: 104 EDSKIY-VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILVVA 161
           ED   Y V+ KP G+  QG S    H    L  WV+   Q+   L HRLD + +G++++A
Sbjct: 104 EDVGRYSVWYKPHGLLAQG-SQWGDHCS--LLRWVEVVRQRECFLVHRLDADAAGLILIA 160

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNE 220
               AA  L++ F+ R ++K Y + V G      E  A  L L++   G D +  V    
Sbjct: 161 HDAQAAAALSQLFQGRSLRKHYQAWVSG------ELQATGLRLEQPLDGKDALTWV---- 210

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              N A     VID    +   ++++  TGR HQ+R H   +G PI+GD  Y
Sbjct: 211 ---NTA-----VIDQPNNRSL-VDVRIETGRKHQIRRHLAAIGHPIMGDKLY 253


>gi|303277319|ref|XP_003057953.1| RNA pseudouridylate synthase [Micromonas pusilla CCMP1545]
 gi|226460610|gb|EEH57904.1| RNA pseudouridylate synthase [Micromonas pusilla CCMP1545]
          Length = 348

 Score = 42.4 bits (98), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 17/35 (48%), Positives = 22/35 (62%)

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  ++   P TGRTHQ+R+H  H G  IVGD KY
Sbjct: 242 SRCAYVRATPTTGRTHQIRLHCAHAGAAIVGDVKY 276



 Score = 37.0 bits (84), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 18/40 (45%), Positives = 26/40 (65%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           L HRLD++TSG LVVA +  A   LT +F   +++K Y +
Sbjct: 111 LAHRLDRDTSGCLVVATSTRACAALTRAFADGKVRKEYLA 150


>gi|294873272|ref|XP_002766565.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Perkinsus marinus ATCC 50983]
 gi|239867556|gb|EEQ99282.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Perkinsus marinus ATCC 50983]
          Length = 350

 Score = 42.0 bits (97), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 40/146 (27%), Positives = 60/146 (41%), Gaps = 32/146 (21%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI----QKIYWSLVWGIPKNKKECIANW 201
           + HRLD  TSG L++A       H  + F M R+     +I  S +         C+   
Sbjct: 151 ILHRLDVGTSGPLLLA-------HSYKGFYMGRLVFCSHQILKSTLDNGQSYSTTCV--- 200

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
                        V    +     A+      D   +++  + ++ HTGRTHQ+RVH  +
Sbjct: 201 -------------VAPDGKPSLTEAVPVAHYNDGSGEEYSLVLVKLHTGRTHQIRVHMAY 247

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNK 287
           +G P+V D KY     GN T P   K
Sbjct: 248 IGHPLVCDPKY-----GNPTDPEAAK 268


>gi|222150872|ref|YP_002560025.1| truncated ribosomal large subunit pseudouridine synthase
           [Macrococcus caseolyticus JCSC5402]
 gi|222119994|dbj|BAH17329.1| truncated ribosomal large subunit pseudouridine synthase
           [Macrococcus caseolyticus JCSC5402]
          Length = 235

 Score = 42.0 bits (97), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 43/180 (23%), Positives = 79/180 (43%), Gaps = 40/180 (22%)

Query: 100 ILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           ++ Y+D  + + +KP  ++           +   + G L++  D     P    RLD++T
Sbjct: 70  LIHYDDEYLIIVSKPPFMNTIPSKQHPHDSLIEAVYGHLETHDDKSVLHP--VSRLDRDT 127

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V ++ +     LT      +I+K Y  +  G  K+                G+YV+
Sbjct: 128 SGLVVFSKHQ-----LTHHLLTGKIEKFYLLIAAGHVKDH---------------GNYVY 167

Query: 215 VVKQNEKG---------ANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVH---ALH 261
            + + E             +A + + +ID  A+     + ++ HTGRTHQ+RVH   ALH
Sbjct: 168 PIDRREDSIITRTVNVHGQHARTEYHLIDYDAEFDVSLVHVKLHTGRTHQIRVHFSAALH 227


>gi|255084041|ref|XP_002508595.1| rRNA/tRNA pseudouridine synthase [Micromonas sp. RCC299]
 gi|226523872|gb|ACO69853.1| rRNA/tRNA pseudouridine synthase [Micromonas sp. RCC299]
          Length = 730

 Score = 42.0 bits (97), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G+ +      F  +W  S+  +P   HRLD ETSG+L++A+ +  A  L   F  R ++K
Sbjct: 317 GTPVGTPGGSFAGAWTSSQ-VEPIAVHRLDLETSGVLLLAKDKRVASELQAKFEARGVRK 375

Query: 182 IYWSL 186
            Y ++
Sbjct: 376 TYLAV 380



 Score = 40.8 bits (94), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 17/31 (54%), Positives = 22/31 (70%)

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +P TGRTHQ+R+H  H G PIVGD  Y  ++
Sbjct: 534 RPLTGRTHQVRLHLAHAGFPIVGDGLYGVDY 564


>gi|270643349|ref|ZP_06222148.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae HK1212]
 gi|270317303|gb|EFA28858.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae HK1212]
          Length = 99

 Score = 42.0 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 22/51 (43%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHA 292
           ++  P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA
Sbjct: 33  VKASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHA 83


>gi|226505766|ref|NP_001140548.1| hypothetical protein LOC100272613 [Zea mays]
 gi|194699944|gb|ACF84056.1| unknown [Zea mays]
          Length = 205

 Score = 42.0 bits (97), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 3/67 (4%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           P +GRTHQ+R+H  ++G PI GD KY    + +          LHA  +   HP  G  +
Sbjct: 130 PQSGRTHQIRLHCQYLGLPIRGDVKYGGVIEWDGVE--CEGHALHAESLSFVHPITGLPI 187

Query: 306 QITAPLP 312
            + +PLP
Sbjct: 188 TLRSPLP 194


>gi|307243831|ref|ZP_07525961.1| pseudouridine synthase, RluA family [Peptostreptococcus stomatis
           DSM 17678]
 gi|306492794|gb|EFM64817.1| pseudouridine synthase, RluA family [Peptostreptococcus stomatis
           DSM 17678]
          Length = 226

 Score = 42.0 bits (97), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 28/96 (29%), Positives = 46/96 (47%), Gaps = 9/96 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD------SKGQKPRLTHRLDQET 154
           ++YED  + V +KP  + V        H DG L + +        +  + R  +RLD  T
Sbjct: 88  IVYEDQDLIVADKPPFMVVHPTKS---HFDGTLANAITYHIGRIGEDCRIRFVNRLDMNT 144

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           SG++V+A+   A   L+      R+ K Y ++V GI
Sbjct: 145 SGLVVIAKNSYAHHKLSLDMGQDRVHKEYLAIVEGI 180


>gi|300933182|ref|ZP_07148438.1| putative pseudouridylate synthase [Corynebacterium resistens DSM
           45100]
          Length = 402

 Score = 42.0 bits (97), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 9/80 (11%)

Query: 201 WLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVI------DCFAQKFCWLEMQPHTGRT 252
           W+L+     + G     +  +E  A  AI+  +           A +  W  ++PH+GRT
Sbjct: 270 WVLRHHMVKVRGRLATYLTGDEPNAETAITGVRAFLDTSSGPAPATRLAW-RLEPHSGRT 328

Query: 253 HQLRVHALHMGCPIVGDHKY 272
           HQLRV    +G PIV D  Y
Sbjct: 329 HQLRVVMRSLGMPIVNDSLY 348


>gi|148910624|gb|ABR18382.1| unknown [Picea sitchensis]
          Length = 358

 Score = 42.0 bits (97), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 27/93 (29%), Positives = 47/93 (50%), Gaps = 4/93 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSG 156
            +YED  +   NKP+G+  +   S I   +     S   +    P    L +RLD++TSG
Sbjct: 64  FIYEDEWMIAVNKPSGVYCEHVLSSIPELLASSPSSAGAANDVNPLELHLANRLDRDTSG 123

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           ++V+ +    A  L ++F  R+++K Y +L  G
Sbjct: 124 VMVITKLHKIAGQLVKAFTDRKVRKTYLALCIG 156



 Score = 40.4 bits (93), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 41/80 (51%), Gaps = 7/80 (8%)

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQNKLYLHARYMDLPHP 300
           +   P +GRTHQ+R+H  +MG PI GD KY     +KG   +       LHA  +   HP
Sbjct: 283 IRASPLSGRTHQIRLHCQYMGLPIRGDVKYEGPHIWKGITYA----NHALHAESLCFEHP 338

Query: 301 -EGGRLQITAPLPAHMVKTW 319
                ++  APLP  +++ +
Sbjct: 339 VTNNMVKFHAPLPQWVMEAY 358


>gi|321445061|gb|EFX60583.1| hypothetical protein DAPPUDRAFT_9799 [Daphnia pulex]
          Length = 107

 Score = 42.0 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 5/54 (9%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           M+P TGR HQLR+H   +G  IVGD  Y      N    +  +++LH+  + LP
Sbjct: 44  MKPVTGRRHQLRIHCSSLGHTIVGDFTY-----SNGKDVLPYRMFLHSHRLILP 92


>gi|300119373|ref|ZP_07057027.1| RluA family pseudouridine synthase [Bacillus cereus SJ1]
 gi|298723245|gb|EFI64033.1| RluA family pseudouridine synthase [Bacillus cereus SJ1]
          Length = 162

 Score = 41.6 bits (96), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 18/55 (32%), Positives = 33/55 (60%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           + V V+ D    RLD +   H   +   ++ +I+RSG+VR++K RV  + R+++G
Sbjct: 107 RLVEVDQDSAGQRLDNFLIRHLKGVPKTHVYRIIRSGEVRINKGRVSADTRVEAG 161


>gi|217031566|ref|ZP_03437071.1| hypothetical protein HPB128_21g124 [Helicobacter pylori B128]
 gi|216946766|gb|EEC25362.1| hypothetical protein HPB128_21g124 [Helicobacter pylori B128]
          Length = 159

 Score = 41.6 bits (96), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 36/141 (25%), Positives = 62/141 (43%), Gaps = 19/141 (13%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K     Q+ Q VR   +I  +  +I  +    +              
Sbjct: 28  LKEAQRHLDKQRLK-----QNQQAVRKSQMIQGVVSLIHFKPNEKTQA------------ 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQK 181
            +T  +A+ L   F  ++++K
Sbjct: 129 GKTLQSAKDLKALFMQKKVEK 149


>gi|323447392|gb|EGB03315.1| hypothetical protein AURANDRAFT_68127 [Aureococcus anophagefferens]
          Length = 612

 Score = 41.6 bits (96), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 42/85 (49%), Gaps = 2/85 (2%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           ++HRLD +TSG L+VAR+      L   FR +R+ K Y  L  G+ K     + +W L +
Sbjct: 369 VSHRLDAQTSGPLIVARSYWGWAWLQLLFRTKRVAKHYVCLCDGLVKLAPGTLISWPLIR 428

Query: 206 SHIGG--DYVHVVKQNEKGANYAIS 228
             I G      +V  N  GA   I+
Sbjct: 429 EAIPGRVSMRSIVSCNGMGAVTEIA 453


>gi|297715439|ref|XP_002834085.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like, partial [Pongo abelii]
          Length = 142

 Score = 41.6 bits (96), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 41/80 (51%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  +AAA      F+ RR+ K Y +L+ G  +  +  I++ + +
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYRCFKERRVTKAYLALLRGHIQESRVTISHAIGR 120

Query: 205 KSHIGGDYVHVVKQNEKGAN 224
            S  G  +   ++ ++   N
Sbjct: 121 NSTEGRAHTMCIEGSQGCEN 140


>gi|329119600|ref|ZP_08248281.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327464197|gb|EGF10501.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 186

 Score = 41.6 bits (96), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 44/171 (25%), Positives = 75/171 (43%), Gaps = 28/171 (16%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV-ARTRAA 166
           + VFNKP G+  Q G   A+     LK ++D+ G  P    RLD ++ G+L++    R  
Sbjct: 4   LIVFNKPCGVVCQFG---AHEKHRSLKDFIDAPGFYP--AGRLDTDSEGLLLLTCNGRMQ 58

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV---HVVKQNEKGA 223
           A+     F++   +K YW+ + G P+  K       L++    GD+V     ++  + G 
Sbjct: 59  ARIAHPKFKL---EKTYWAQLEGSPQADKLAA----LQRPMDLGDFVARPAKIRLPDAGE 111

Query: 224 NYA-------ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             A       +   K +  F     WLE++   G+  Q+R      G P +
Sbjct: 112 TDALWPRVPPVRLRKTVPDF-----WLEIKIAEGKNRQVRRMTAKAGYPCL 157


>gi|297250655|ref|ZP_06934184.1| ribosomal large subunit pseudouridine synthase [Neisseria
           polysaccharea ATCC 43768]
 gi|296838354|gb|EFH22292.1| ribosomal large subunit pseudouridine synthase [Neisseria
           polysaccharea ATCC 43768]
          Length = 147

 Score = 41.6 bits (96), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 39/132 (29%), Positives = 59/132 (44%), Gaps = 9/132 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV    G    +   L + +    +K  L HRLD++T GIL+ 
Sbjct: 4   ILFRHQDFVAINKPQGISVHRSDG-EVSLTATLAAQLGV--EKVWLLHRLDKQTGGILLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I    ++KS  G     + K   
Sbjct: 61  ALNPQSAAVLAAQFAERKMKKTYLALSDRKPSKKQGWIKGG-MEKSRRG-----MWKLTR 114

Query: 221 KGANYAISHFKV 232
              N A++ F V
Sbjct: 115 NMENIAVTRFSV 126


>gi|183237397|ref|XP_001914609.1| hypothetical protein [Entamoeba histolytica HM-1:IMSS]
 gi|169799122|gb|EDS88615.1| hypothetical protein, conserved [Entamoeba histolytica HM-1:IMSS]
          Length = 220

 Score = 41.6 bits (96), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 39/142 (27%), Positives = 59/142 (41%), Gaps = 28/142 (19%)

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMR--------RIQKIYWSLVWGIPKNKKECIANW 201
           +++ TSGIL+ A+T+  A       + +         +QKIY + V G   +  E   N 
Sbjct: 1   MNKNTSGILLFAKTKTFASSFQSILKEKSSVISSTSSLQKIYLARVVGYFPDTIE--VNL 58

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAI--------SHFKVIDCFAQKFCWLEMQPHTGRTH 253
            L     G +    + ++   A  +         S+  VI+C           PHTGRTH
Sbjct: 59  PLHLVRFGTESQSCICEDGIEARSSFKRLFFDKDSNTSVIECV----------PHTGRTH 108

Query: 254 QLRVHALHMGCPIVGDHKYCAN 275
           QLR+H   +  PI  D  Y  N
Sbjct: 109 QLRLHLKAIHHPIANDSAYLLN 130


>gi|297250654|ref|ZP_06934183.1| ribosomal large subunit pseudouridine synthase [Neisseria
           polysaccharea ATCC 43768]
 gi|296838353|gb|EFH22291.1| ribosomal large subunit pseudouridine synthase [Neisseria
           polysaccharea ATCC 43768]
          Length = 108

 Score = 41.6 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 25/67 (37%), Positives = 37/67 (55%), Gaps = 9/67 (13%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++PHTG+THQLRV    +G PI+GD  Y     G   S      +L+A  +   + +   
Sbjct: 29  LEPHTGKTHQLRVAMKSLGSPILGDRLY-----GGTES---ETTFLYAWKIQFTYQQ-QE 79

Query: 305 LQITAPL 311
           ++ITAPL
Sbjct: 80  IEITAPL 86


>gi|325090610|gb|EGC43920.1| DRAP deaminase [Ajellomyces capsulatus H88]
          Length = 209

 Score = 41.6 bits (96), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 35/141 (24%), Positives = 60/141 (42%), Gaps = 28/141 (19%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           QK +  G V ++ K V  + +IQ+G V+                     S  L +H   +
Sbjct: 82  QKAVEDGAVCINGKAVSIDTKIQNGDVI---------------------SHTLHRHEPPV 120

Query: 98  KSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQ 152
            S    +++ED  + V +KPAG+ V       Y+ +  L+     +G    P   +RLD+
Sbjct: 121 TSQPIGIIHEDDDMIVIDKPAGVPVHPAG--RYNYNSILEIMKAERGNGWVPYPCNRLDR 178

Query: 153 ETSGILVVARTRAAAQHLTES 173
            TSG++ +  T      L +S
Sbjct: 179 LTSGVMFIGSTPRVLSKLAKS 199


>gi|313886695|ref|ZP_07820405.1| RNA pseudouridine synthase [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|312923857|gb|EFR34656.1| RNA pseudouridine synthase [Porphyromonas asaccharolytica
           PR426713P-I]
          Length = 337

 Score = 41.6 bits (96), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 48/216 (22%), Positives = 83/216 (38%), Gaps = 35/216 (16%)

Query: 102 LYEDSKIYVFNKPAGI---SVQGGSG------IAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           LY D +  V +K  GI   SV G S       + +H+       VD   +K  L +RLD+
Sbjct: 93  LYRDEQFIVLHKRPGIPTISVGGASKSSLFQVVTHHLKK-----VDP-NEKIFLLNRLDR 146

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +T GI++VAR R   Q L   +R   +   + +++ G        +     K    G + 
Sbjct: 147 DTEGIIIVARDRQLQQDLLAEWRSFVLSNSFEAVILGALDTSSGELTTLPTKDKKRGPNK 206

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--------HQLRVHALHMGC 264
               + + + +  A         F   +  L   P+  R         + +R     +G 
Sbjct: 207 RRTARSSTRDSKPA--------TFRASYEVLTTGPYITRVKLSLLTRNNSIRSTLASIGH 258

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           P++GDH+   +     +      L L A  + + HP
Sbjct: 259 PLLGDHRASESIAPELS----KYLALRATELTIFHP 290


>gi|261885552|ref|ZP_06009591.1| pseudouridine synthase [Campylobacter fetus subsp. venerealis str.
           Azul-94]
          Length = 155

 Score = 41.2 bits (95), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 26/99 (26%), Positives = 47/99 (47%), Gaps = 16/99 (16%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K +   K +++YED  I   NKP  I+ +  + I                 K  L +RLD
Sbjct: 51  KVTKLAKPVMIYEDDNIVAVNKPPFITSEKVAEIF----------------KFPLLNRLD 94

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           +ETSG++++ +     +   + F   +++K Y ++V GI
Sbjct: 95  KETSGVILLYKNEEFQKAAIKEFANTKVKKTYLAIVRGI 133


>gi|83314457|ref|XP_730367.1| RNA pseudouridylate synthase [Plasmodium yoelii yoelii str. 17XNL]
 gi|23490071|gb|EAA21932.1| RNA pseudouridylate synthase, putative [Plasmodium yoelii yoelii]
          Length = 745

 Score = 41.2 bits (95), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 32/73 (43%), Gaps = 11/73 (15%)

Query: 224 NYAISHFKVIDCFAQKFCWLEM-----------QPHTGRTHQLRVHALHMGCPIVGDHKY 272
           NY IS+   I     KF +L             QP TGRTHQ+R H   +  PI  D  Y
Sbjct: 558 NYQISNQYSIKPSVTKFMFLSYNYKLNESLLLCQPMTGRTHQIRTHLKSLSFPISNDSHY 617

Query: 273 CANFKGNFTSPIQ 285
             NF+  + +  +
Sbjct: 618 NPNFEKEYMTKTE 630


>gi|332300035|ref|YP_004441956.1| pseudouridine synthase [Porphyromonas asaccharolytica DSM 20707]
 gi|332177098|gb|AEE12788.1| pseudouridine synthase [Porphyromonas asaccharolytica DSM 20707]
          Length = 337

 Score = 41.2 bits (95), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 48/216 (22%), Positives = 83/216 (38%), Gaps = 35/216 (16%)

Query: 102 LYEDSKIYVFNKPAGI---SVQGGSG------IAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           LY D +  V +K  GI   SV G S       + +H+       VD   +K  L +RLD+
Sbjct: 93  LYRDEQFIVLHKRPGIPTISVGGASKSSLFQVVTHHL-----KKVDP-NEKIFLLNRLDR 146

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +T GI++VAR R   Q L   +R   +   + +++ G        +     K    G + 
Sbjct: 147 DTEGIIIVARDRQLQQDLLAEWRSFVLSNSFEAVILGALDTSSGELTTRPTKDKKRGPNK 206

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--------HQLRVHALHMGC 264
               + + + +  A         F   +  L   P+  R         + +R     +G 
Sbjct: 207 RRTARSSTRDSKPA--------TFRASYEVLTTGPYITRVKLSLLTRNNSIRSTLASIGH 258

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           P++GDH+   +     +      L L A  + + HP
Sbjct: 259 PLLGDHRASESIAPELS----KYLALRATELTIFHP 290


>gi|72389112|ref|XP_844851.1| hypothetical protein [Trypanosoma brucei TREU927]
 gi|62358662|gb|AAX79120.1| hypothetical protein, conserved [Trypanosoma brucei]
 gi|70801385|gb|AAZ11292.1| hypothetical protein, conserved [Trypanosoma brucei brucei strain
           927/4 GUTat10.1]
          Length = 700

 Score = 41.2 bits (95), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 6/45 (13%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNK 287
           TGRTHQ+RVH   +G PIV DHKY         F GN+   ++++
Sbjct: 594 TGRTHQVRVHLASVGHPIVDDHKYIHHLSRNTPFTGNYRKEVKSR 638


>gi|254967063|gb|ACT97569.1| ribosomal large subunit pseudouridine synthase D [uncultured
           organism]
          Length = 133

 Score = 41.2 bits (95), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 49/108 (45%), Gaps = 14/108 (12%)

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNF 280
             +A++H++V++        +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG  
Sbjct: 12  GKHAVTHYRVLERLGY-VTLVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTH 70

Query: 281 TSPIQN----------KLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            S  +           +  LHA  +   HP  G  +  T+ LP  M +
Sbjct: 71  FSKYKQFVNNCFDTCPRQALHAMTLGFVHPVTGEEMYFTSELPDDMTR 118


>gi|71663022|ref|XP_818509.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70883765|gb|EAN96658.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 378

 Score = 40.8 bits (94), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 28/46 (60%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           +  H+LD  TSG+L VA +R  A  L   F MR  +K Y ++++G+
Sbjct: 80  KFVHQLDYATSGVLCVAFSREMAARLAHCFEMRTTRKAYLAVLFGM 125



 Score = 36.6 bits (83), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 16/26 (61%), Positives = 18/26 (69%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
           P TGR HQLRVH   +G PI+GD  Y
Sbjct: 249 PRTGRRHQLRVHCHAIGFPILGDVTY 274


>gi|332288598|ref|YP_004419450.1| 23S rRNA pseudouridine synthase E [Gallibacterium anatis UMN179]
 gi|330431494|gb|AEC16553.1| 23S rRNA pseudouridine synthase E [Gallibacterium anatis UMN179]
          Length = 223

 Score = 40.8 bits (94), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 47/177 (26%), Positives = 73/177 (41%), Gaps = 22/177 (12%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  L  E  K+ +FNKP  +  Q            LK+++      P    RLD+++ G+
Sbjct: 18  KPKLQLEQIKVVLFNKPYDVLTQFTDEQGRKT---LKNFIHIPDIYP--CGRLDRDSEGL 72

Query: 158 LVVARTRAAAQHLT-ESFRMRRIQKIYWSLVWGIPKNKK-ECIANWLLKKSHIGGDYVHV 215
           L++         LT  +F+ +   K YW  V G+P  +  E +   ++ K   G     +
Sbjct: 73  LLLTNCGEIQHRLTTPAFKSK---KTYWVQVEGVPSEQDLEALRQGVILKD--GKTLPAL 127

Query: 216 VK-----QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           VK     QN    +  I   K I        WLE+  H GR  Q+R    H+G P +
Sbjct: 128 VKFIPPPQNLWQRDPPIRERKTIPT-----SWLEIAIHEGRNRQVRRMTAHIGYPTL 179


>gi|307106309|gb|EFN54555.1| hypothetical protein CHLNCDRAFT_53041 [Chlorella variabilis]
          Length = 362

 Score = 40.8 bits (94), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Q+RVH  H G  I+GD  Y A      T P   +  LHA  + + HP  G  L + APLP
Sbjct: 275 QIRVHLAHAGHAILGDDLYGA------TGPWIARHALHAAAVTIRHPRSGELLTVRAPLP 328

Query: 313 AHMVKTWDSLGFK 325
           A  +   + LG +
Sbjct: 329 ADFLAAMEQLGLQ 341


>gi|322489796|emb|CBZ25056.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 1047

 Score = 40.8 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 18/26 (69%), Positives = 19/26 (73%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA 274
           TGRTHQLRVH   +G PIV D KY A
Sbjct: 905 TGRTHQLRVHLASLGHPIVHDSKYIA 930


>gi|157866798|ref|XP_001681954.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|68125405|emb|CAJ03264.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 1067

 Score = 40.8 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 18/26 (69%), Positives = 19/26 (73%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA 274
           TGRTHQLRVH   +G PIV D KY A
Sbjct: 925 TGRTHQLRVHLASLGHPIVHDSKYIA 950


>gi|109127127|ref|XP_001118548.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Macaca mulatta]
          Length = 213

 Score = 40.8 bits (94), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 26/45 (57%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           R  H+LD  TSG L VA  +AAA      F+ RR+ K Y +L+ G
Sbjct: 61  RFCHQLDFSTSGALCVALNKAAAGSAYRCFKERRVTKAYLALLRG 105


>gi|68064484|ref|XP_674226.1| pseudouridylate synthase [Plasmodium berghei strain ANKA]
 gi|56492648|emb|CAH96681.1| pseudouridylate synthase, putative [Plasmodium berghei]
          Length = 490

 Score = 40.4 bits (93), Expect = 0.36,   Method: Compositional matrix adjust.
 Identities = 16/40 (40%), Positives = 22/40 (55%)

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           QP TGRTHQ+R H   +  PI  D  Y  NF+  + +  +
Sbjct: 336 QPMTGRTHQIRTHLKSLSFPISNDSHYNPNFEKKYMTKTE 375


>gi|6446386|gb|AAF08596.1|U38836_1 the hypothetical protein;similar to orfW-gene of P. aeruginosa
           [Streptococcus pyogenes]
          Length = 69

 Score = 40.4 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 16/45 (35%), Positives = 31/45 (68%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +P + HR+D++TSG+L+VA+T  A Q L E  + ++  + Y +++
Sbjct: 23  RPGIVHRIDKDTSGLLMVAKTDTAHQALAEELKAKKSLRKYLAVI 67


>gi|290983884|ref|XP_002674658.1| predicted protein [Naegleria gruberi]
 gi|284088249|gb|EFC41914.1| predicted protein [Naegleria gruberi]
          Length = 314

 Score = 40.4 bits (93), Expect = 0.36,   Method: Compositional matrix adjust.
 Identities = 39/160 (24%), Positives = 68/160 (42%), Gaps = 25/160 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-------------SGIAYHIDGFLKSWVDSKGQ-KPRL 146
           +L+ED  + V +KP  ++V                + + +H +G L +    +   +P +
Sbjct: 128 ILFEDDFLIVLDKPKFMTVHPSLKPKPRNTTGTLVNALLFHTNGKLSTCGSCEEHYRPGI 187

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMR---------RIQKIYWSLVWGIPKNKKEC 197
            HRLD++TSGI+VVA+       L + F  +         +I + Y +LV     N+ E 
Sbjct: 188 VHRLDRDTSGIMVVAKDDETHLALKKLFENKNVGDENNEDKITRYYQALVEN-ELNQSEG 246

Query: 198 IANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCF 236
                +K+ H       V     E GA  +I+ +K    F
Sbjct: 247 RIEIYIKRHHSMPSKREVTNNALETGAKLSITEYKEQKTF 286


>gi|303242311|ref|ZP_07328797.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
 gi|302590150|gb|EFL59912.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
          Length = 237

 Score = 40.4 bits (93), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 43/176 (24%), Positives = 71/176 (40%), Gaps = 32/176 (18%)

Query: 99  SILLYEDSKIYVF-NKPAGISVQGGSGIAYHIDGFLKSWVDS--KGQKPRL--THRLDQE 153
           S++  E  K+Y+  NKP+G        +    D F +  V    KG   R+    RLD E
Sbjct: 55  SVIKPESKKVYILLNKPSGY-------VTTVKDQFRRPTVIDLLKGVDERVFPVGRLDYE 107

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G+LV+         +T       I+K Y + + G P                   D +
Sbjct: 108 TTGLLVLTNDGDFTHKMTHP--RHEIEKTYQATIAGTPTK-----------------DEI 148

Query: 214 HVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           H  +   +  +Y  S  K+ I    ++ C +E+  H GR  Q+R     +G P++ 
Sbjct: 149 HSFESGLEIEDYVTSPAKLKIISTKERTCVIEVTIHEGRNRQVRKMCEAIGHPVLA 204


>gi|297697698|ref|XP_002825984.1| PREDICTED: hypothetical protein LOC100448251 [Pongo abelii]
          Length = 295

 Score = 40.4 bits (93), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 28/49 (57%), Gaps = 3/49 (6%)

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           GRTHQLRVH   +G P+VGD  Y     G    P   ++ LHA Y+ +P
Sbjct: 154 GRTHQLRVHCSALGHPVVGDLTY-GEASGREDRPF--RMMLHAFYLRIP 199


>gi|207110740|ref|ZP_03244902.1| hypothetical protein HpylH_16920 [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 85

 Score = 40.4 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 29/91 (31%), Positives = 50/91 (54%), Gaps = 7/91 (7%)

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y +L+ GI + ++E  A  L  K+     +  + K+ ++     I+  K+I+    
Sbjct: 2   VKKEYLALIQGIIEEEREINAPILTIKTTKA--FSKISKKGQEAVTI-ITPLKIIN---- 54

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           K   L++   TGRTHQ+RVH  H+  PI+GD
Sbjct: 55  KKTLLKVGIKTGRTHQIRVHLKHINHPIIGD 85


>gi|116333418|ref|YP_794945.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus brevis ATCC 367]
 gi|116098765|gb|ABJ63914.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           brevis ATCC 367]
          Length = 240

 Score = 40.4 bits (93), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 37/155 (23%), Positives = 62/155 (40%), Gaps = 34/155 (21%)

Query: 127 YHIDGFLKSWVDSKGQKPRL------------THRLDQETSGILVVARTRAAAQHLTESF 174
           Y   G + +  D KG+K  +              RLD +TSG+L++      A  LT   
Sbjct: 66  YKPRGVVSTANDDKGRKTVVDLVENVSQRVYPVGRLDYDTSGLLLLTNDGELANRLTHP- 124

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKV 232
               ++K Y + V G+P N                 D +  ++Q     G  YA +  KV
Sbjct: 125 -RYEVEKTYIARVTGVPTN-----------------DAMKQLRQGITVDGETYAPAKSKV 166

Query: 233 IDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           +     +K   + +  H G+ HQ++     +GCP+
Sbjct: 167 LSAADDRKTAIISLTIHEGKNHQVKKMLAAVGCPV 201


>gi|209882431|ref|XP_002142652.1| hypothetical protein [Cryptosporidium muris RN66]
 gi|209558258|gb|EEA08303.1| hypothetical protein, conserved [Cryptosporidium muris RN66]
          Length = 2982

 Score = 40.4 bits (93), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 38/187 (20%), Positives = 72/187 (38%), Gaps = 15/187 (8%)

Query: 143  KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---------IPKN 193
            K  L    D E SG ++++++  + Q+L   +  + I   Y  L  G           +N
Sbjct: 2430 KEELIVTFDDEISGPVLISKSDDSYQNLLNQYNEKEIMAEYVFLCHGQLEKHDGYISFEN 2489

Query: 194  KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                + N +  KS   G    + K    G    ++  +  D      C        G  +
Sbjct: 2490 LATIVCNRIFAKSVTVGSSNCIAKYKVCGIYKHVNSTR--DSLLYSLC--RCHSTAGSVN 2545

Query: 254  QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL--PHPEGGRLQITAPL 311
            ++R     +G PIV D K+  N + N    +   ++ H  Y++   P  +  + Q+   L
Sbjct: 2546 KIRAFMSEIGHPIVCDSKFLNNKQLNADRRLFPHIFFHCWYLEFLKPDKDASKFQVKYSL 2605

Query: 312  PAHMVKT 318
            P+++  T
Sbjct: 2606 PSNLTDT 2612


>gi|291412474|ref|XP_002722515.1| PREDICTED: RNA pseudouridylate synthase domain containing 3-like
           [Oryctolagus cuniculus]
          Length = 306

 Score = 40.4 bits (93), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 40/167 (23%), Positives = 67/167 (40%), Gaps = 14/167 (8%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---QKPRLTHRLD 151
           D L++ ++     +   NKP G+ V G  G    +   L     S G    + ++     
Sbjct: 59  DVLRAAVVDRKGPLVTLNKPQGLPVTGKPG-ELTLHSVLPELSRSLGLGESEFQVVQAPG 117

Query: 152 QETSGILVVARTRAAAQHLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +E SG+++++     A  L E F    R  R    YW++  GIP   +  I   L  +  
Sbjct: 118 KEISGLVLLSSCAQTASRLHEFFTHSRRAHRPTATYWAVTDGIPATPEGEIQAALKLERV 177

Query: 208 IGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHT 249
            G D V  VK   +          +SHF+V+         +++QP T
Sbjct: 178 DGVDLVLPVKPPSRRDVLASVKRTLSHFRVV-ATGSGCALVQLQPLT 223


>gi|328786669|ref|XP_003250827.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Apis mellifera]
          Length = 138

 Score = 40.4 bits (93), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 17/44 (38%), Positives = 26/44 (59%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             HRLD  TSG++ +A  + AAQ  + +F  R  +K Y +L+ G
Sbjct: 45  FVHRLDYVTSGVICIALNKKAAQIASNAFEARTAKKFYLALLHG 88


>gi|156097284|ref|XP_001614675.1| pseudouridylate synthase [Plasmodium vivax SaI-1]
 gi|148803549|gb|EDL44948.1| pseudouridylate synthase, putative [Plasmodium vivax]
          Length = 805

 Score = 40.4 bits (93), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 33/69 (47%), Gaps = 4/69 (5%)

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QP TGRTHQ+R H   +  PI  D +Y  NF   +   ++  +YLH    D    + G  
Sbjct: 623 QPITGRTHQIRAHLKSLSFPISNDAQYNDNFAKEY---MEKSVYLHFHEGDHSGEQSGE- 678

Query: 306 QITAPLPAH 314
           Q+   L  H
Sbjct: 679 QLGEQLGEH 687


>gi|322492659|emb|CBZ27936.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 969

 Score = 40.4 bits (93), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 19/33 (57%), Positives = 23/33 (69%), Gaps = 1/33 (3%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           P+TGR HQ+R H   +GCPIVGD  Y A+  GN
Sbjct: 636 PYTGRLHQIRRHLGSLGCPIVGDVVY-AHTSGN 667


>gi|255324437|ref|ZP_05365554.1| RNA pseudouridine synthase family protein [Corynebacterium
           tuberculostearicum SK141]
 gi|255298343|gb|EET77643.1| RNA pseudouridine synthase family protein [Corynebacterium
           tuberculostearicum SK141]
          Length = 279

 Score = 40.0 bits (92), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 38/134 (28%), Positives = 61/134 (45%), Gaps = 21/134 (15%)

Query: 148 HRLDQETSGILVVAR---TRAAAQHL-TESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           HRLD+ T+G+++ +R   TRAA Q +  E   ++R + +    ++       + IA  + 
Sbjct: 122 HRLDRLTAGLVICSRNPETRAAYQRIFLEGSAVKRYRGVVKQPLF-----VDQEIALRMH 176

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           K    G   V V  +    + Y  +  + +           M P TG THQLRV   H+G
Sbjct: 177 KPR--GSRQVFVAPEGTLTSTYVRAAGREV----------TMWPRTGHTHQLRVLLNHLG 224

Query: 264 CPIVGDHKYCANFK 277
            P++GD  Y    K
Sbjct: 225 HPLLGDDTYPTPRK 238


>gi|213964760|ref|ZP_03392960.1| RNA pseudouridine synthase family protein [Corynebacterium
           amycolatum SK46]
 gi|213952953|gb|EEB64335.1| RNA pseudouridine synthase family protein [Corynebacterium
           amycolatum SK46]
          Length = 317

 Score = 40.0 bits (92), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 17/28 (60%), Positives = 21/28 (75%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +QPHTGRTHQLRV    +G PI+G+  Y
Sbjct: 231 LQPHTGRTHQLRVTMDWLGYPILGEDTY 258


>gi|255079804|ref|XP_002503482.1| predicted protein [Micromonas sp. RCC299]
 gi|226518749|gb|ACO64740.1| predicted protein [Micromonas sp. RCC299]
          Length = 545

 Score = 40.0 bits (92), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 30/104 (28%), Positives = 40/104 (38%), Gaps = 24/104 (23%)

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--------------------- 286
           HTGRTHQ+RVH  H   PI+ D  Y  + + +  SP  +                     
Sbjct: 440 HTGRTHQIRVHMAHADLPILSDPLYGPHIRWDGASPCADASTSAILPPGVDADVWGGPRW 499

Query: 287 --KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
             +  LHA  + L HPE    +   A  P  M     +LG   D
Sbjct: 500 LGRQALHAARLTLRHPETNEEMTFEARAPEDMRGACVALGLDPD 543


>gi|72390299|ref|XP_845444.1| RNA pseudouridylate synthase [Trypanosoma brucei TREU927]
 gi|62359520|gb|AAX79956.1| RNA pseudouridylate synthase, putative [Trypanosoma brucei]
 gi|70801979|gb|AAZ11885.1| RNA pseudouridylate synthase, putative [Trypanosoma brucei brucei
           strain 927/4 GUTat10.1]
          Length = 462

 Score = 40.0 bits (92), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 42/200 (21%), Positives = 78/200 (39%), Gaps = 56/200 (28%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRM------------------------------- 176
           HRLD+ETSG++V+A++  AA+ L+  F                                 
Sbjct: 166 HRLDKETSGLVVLAKSADAARILSGQFERQSQVLNAQLTKYTGGESLTVVTSSQFDELIT 225

Query: 177 --RRIQKIYWSLVWG-IPKNKKECIANWL-------------------LKKSHIGGDYVH 214
             + + K Y +++ G +P+  +  + N +                   LKK  +   +  
Sbjct: 226 MDKSVSKSYIAVLDGSVPEGNEFIVCNRVGLLWEELKDSMKDAEKHTKLKKLKMACYHAS 285

Query: 215 VVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           V K  +     A S  +++      +     +   TGRTHQ+R+H   +G P++GD  Y 
Sbjct: 286 VGKNQQLYGRPACSRIRILSSSDTLRVSVARVDILTGRTHQIRLHCAQIGFPVLGDKLYE 345

Query: 274 ANFKGNFTS--PIQNKLYLH 291
            +  G       + + +YL+
Sbjct: 346 TSTPGRVGGLHAVADDIYLY 365


>gi|71420763|ref|XP_811602.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70876281|gb|EAN89751.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 378

 Score = 40.0 bits (92), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 45/184 (24%), Positives = 76/184 (41%), Gaps = 51/184 (27%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-------------------------GSGIAYHIDGFLKS 135
           ++Y + ++ V NKP  + + G                         G G+    D   ++
Sbjct: 10  VIYGNEELVVVNKPHDVPMDGEACPVTVEKWAWAYLAKGGCADNSAGGGVEKEED-TTRT 68

Query: 136 WVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
               +G+K   +  H+LD  TSG+L VA +R  A  L   F MR  +K Y +++ G+   
Sbjct: 69  AGRGRGEKKMVKFVHQLDYATSGVLCVAFSREMAARLAHCFEMRTTRKAYLAVLLGMMPT 128

Query: 194 KKECIANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVID-------CFAQKFCWLE 244
                 + + KK  +  G D++       +G+ YA SH + I        CF +K C +E
Sbjct: 129 -----TSAMQKKLDTDTGVDFL-------RGSPYA-SHVRRISMDDVPGVCFIRK-CVIE 174

Query: 245 MQPH 248
              H
Sbjct: 175 ASGH 178



 Score = 36.6 bits (83), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 16/26 (61%), Positives = 18/26 (69%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
           P TGR HQLRVH   +G PI+GD  Y
Sbjct: 249 PRTGRRHQLRVHCHAIGFPILGDVTY 274


>gi|209880932|ref|XP_002141905.1| RNA pseudouridylate synthase family protein [Cryptosporidium muris
           RN66]
 gi|209557511|gb|EEA07556.1| RNA pseudouridylate synthase family protein [Cryptosporidium muris
           RN66]
          Length = 527

 Score = 40.0 bits (92), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 29/49 (59%)

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +F+ I+   +   ++  +P TGRTHQ+R H  ++G P+  DH Y  N K
Sbjct: 335 NFESINICHKPNSYVLCKPVTGRTHQIRAHLQYLGFPVTLDHLYSLNRK 383


>gi|224014186|ref|XP_002296756.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220968611|gb|EED86957.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 332

 Score = 40.0 bits (92), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 38/87 (43%), Gaps = 21/87 (24%)

Query: 247 PHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG 303
           P TGRTHQ+R HA      P+VGD ++  +    F       ++L LH  Y+DLP  E  
Sbjct: 199 PITGRTHQIRRHARKAFSSPVVGDREHGDSRVNRFWREKVGLDRLTLHCWYLDLPQAEED 258

Query: 304 ------------------RLQITAPLP 312
                             R+Q  APLP
Sbjct: 259 CVEDRRGVDAVMEEVSKTRIQCMAPLP 285


>gi|311740710|ref|ZP_07714537.1| RNA pseudouridylate synthase [Corynebacterium pseudogenitalium ATCC
           33035]
 gi|311304230|gb|EFQ80306.1| RNA pseudouridylate synthase [Corynebacterium pseudogenitalium ATCC
           33035]
          Length = 287

 Score = 40.0 bits (92), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 41/133 (30%), Positives = 59/133 (44%), Gaps = 19/133 (14%)

Query: 148 HRLDQETSGILVVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           HRLD+ T+G+++ +R   TRAA Q +   F      K Y  +V   P    + IA  + K
Sbjct: 130 HRLDRLTAGLVICSRNPATRAAYQRI---FLEGSAVKKYRGVVKQ-PLFVDQEIALRMHK 185

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               G   V V  +    + Y  +  + +           M P TG THQLRV   H+G 
Sbjct: 186 PR--GSRQVFVAPEGTLTSTYVRAAGREV----------TMWPRTGHTHQLRVLLNHLGH 233

Query: 265 PIVGDHKYCANFK 277
           P++GD  Y    K
Sbjct: 234 PLLGDDTYPTPRK 246


>gi|261328846|emb|CBH11824.1| RNA pseudouridylate synthase, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 462

 Score = 40.0 bits (92), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 42/200 (21%), Positives = 78/200 (39%), Gaps = 56/200 (28%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRM------------------------------- 176
           HRLD+ETSG++V+A++  AA+ L+  F                                 
Sbjct: 166 HRLDKETSGLVVLAKSADAARILSGQFERQSQVLNAQLTKYTGGESLTVVTSSQFDELIT 225

Query: 177 --RRIQKIYWSLVWG-IPKNKKECIANWL-------------------LKKSHIGGDYVH 214
             + + K Y +++ G +P+  +  + N +                   LKK  +   +  
Sbjct: 226 MDKSVSKSYIAVLDGSVPEGNEFIVCNRVGLLWEELKDSMKDAEKHTKLKKLKMACYHAS 285

Query: 215 VVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           V K  +     A S  +++      +     +   TGRTHQ+R+H   +G P++GD  Y 
Sbjct: 286 VEKNQQLYGRPACSRIRILSSSDTLRVSVARVDILTGRTHQIRLHCAQIGFPVLGDKLYE 345

Query: 274 ANFKGNFTS--PIQNKLYLH 291
            +  G       + + +YL+
Sbjct: 346 TSTPGAVGGLHAVADDIYLY 365


>gi|312075546|ref|XP_003140465.1| hypothetical protein LOAG_04880 [Loa loa]
 gi|307764370|gb|EFO23604.1| hypothetical protein LOAG_04880 [Loa loa]
          Length = 479

 Score = 40.0 bits (92), Expect = 0.59,   Method: Compositional matrix adjust.
 Identities = 50/267 (18%), Positives = 101/267 (37%), Gaps = 47/267 (17%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGIS---VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           + + S ++YED ++  F+KP  ++             I   L S +       R+   + 
Sbjct: 216 NVMTSRIIYEDEELIAFDKPYQVAYSNAPSNQAELLRILPKLSSRIAPNMDCLRIVKSIG 275

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +  +G+++ A+ + A + +   +    +++ Y  +    P +++  I   L+K +    +
Sbjct: 276 KSVTGVILFAKNQNAQEKIKVLYDNGLMEQCYHVITNMAPAHQEAAINIPLVKCTRKNNN 335

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH--------------QLRV 257
           Y+ +      GAN +    K I  F +      +  H  + H              Q+R 
Sbjct: 336 YMML----PLGANNS----KEIPPFLEASTHYRLLKHDPKNHTSYMECFVNRDVPEQIRA 387

Query: 258 H-ALHMGCPIVGDHKYC---------------------ANFKGNFTSPIQNKLYLHARYM 295
           H  + + CPI+GD KY                       N  GN    +   ++L    +
Sbjct: 388 HLGIGIACPIIGDVKYNYSRREAGRGIPPRLSDSALQDLNIAGNSFRRLPMYIHLKEMVI 447

Query: 296 DLPHPEGGRLQITAPLPAHMVKTWDSL 322
            L      ++ I APLP+  + T + L
Sbjct: 448 SLSKRSSQKIHICAPLPSFFMYTLNKL 474


>gi|332686546|ref|YP_004456320.1| ribosomal large subunit pseudouridine synthase B [Melissococcus
           plutonius ATCC 35311]
 gi|332370555|dbj|BAK21511.1| ribosomal large subunit pseudouridine synthase B [Melissococcus
           plutonius ATCC 35311]
          Length = 236

 Score = 39.7 bits (91), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 57/234 (24%), Positives = 96/234 (41%), Gaps = 40/234 (17%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           LQK+L    +     R K    I  G+V     +IN L   + +Q  ++           
Sbjct: 4   LQKVLAHAGI---ASRRKAEQIILEGRVKVNGEIINELGRQVSKQDKIE----------- 49

Query: 97  LKSILLYEDSKIY-VFNKPAGI--SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           + ++ +Y+++ +Y +F KP GI  SV          D FL S      ++     RLD +
Sbjct: 50  VDNVPIYQEAPVYYLFYKPRGIITSVSDDKKRKTVADYFLHS-----NERVYPVGRLDYD 104

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G+L+V    +  Q LT       I K+Y + V GI   K        +K         
Sbjct: 105 TTGLLIVTNDGSLTQQLTHP--SHEIDKVYVAKVKGIALRKTLLPLTKGIKI-------- 154

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPI 266
                  KG   A ++F+++    +K   L ++  H GR HQ++     +G P+
Sbjct: 155 -------KGRKTAPANFQILSVDTKKQTSLVQLTIHEGRNHQVKDMLDTVGYPV 201


>gi|108798222|ref|YP_638419.1| pseudouridine synthase [Mycobacterium sp. MCS]
 gi|119867318|ref|YP_937270.1| pseudouridine synthase [Mycobacterium sp. KMS]
 gi|108768641|gb|ABG07363.1| pseudouridine synthase [Mycobacterium sp. MCS]
 gi|119693407|gb|ABL90480.1| pseudouridine synthase [Mycobacterium sp. KMS]
          Length = 287

 Score = 39.7 bits (91), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 45/198 (22%), Positives = 77/198 (38%), Gaps = 22/198 (11%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-------LLYEDSKIYVFNKPAGISVQG- 121
           V+ A   +++   +L    ++  + D    +       +LY D  I V +KP  ++    
Sbjct: 48  VVCADGTVVRPGTVLPPGTHVYLYRDLPVEVPVPFAMPVLYRDDNIVVVDKPHFLATMPR 107

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G  +A      L+  +D     P   HRLD+ T+G+L+    R         F    + K
Sbjct: 108 GRHVAETAVVRLRRALDLPELSP--AHRLDRLTAGVLLFTTRREIRGAYQTMFSDGAVAK 165

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           +Y +   G    +    + + ++K+    G         E  A   + H    D +    
Sbjct: 166 VYLARSAGHAAVDLPTVVRSRIIKER---GRLQAFEAPGEPNAETLVEHLG-DDVY---- 217

Query: 241 CWLEMQPHTGRTHQLRVH 258
               + P TGRTHQLRVH
Sbjct: 218 ---RLTPRTGRTHQLRVH 232


>gi|290993466|ref|XP_002679354.1| predicted protein [Naegleria gruberi]
 gi|284092970|gb|EFC46610.1| predicted protein [Naegleria gruberi]
          Length = 579

 Score = 39.7 bits (91), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 44/202 (21%), Positives = 84/202 (41%), Gaps = 34/202 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN- 75
           E +R+D+      P I+    Q +L +G V+ + K++  +N+      ++   ++  L  
Sbjct: 108 EKIRVDKLLSQTVP-ISREYAQFLLSNGYVKANNKKLNEDNKF-----IKFTDILKGLQI 161

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSIL-----LYEDSKIYVFNKPAGISVQGGSG------ 124
            I  E +   +++   KH +     +     LYED  + V NKP G +V           
Sbjct: 162 EIYLENRPFSANLTPMKHVEMYDGPIAPIHVLYEDKDVIVVNKPVGYAVHSSKSKPESET 221

Query: 125 IAYHIDGFL--------------KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           + Y I  ++              K   ++      L HR++ + SG+L+  +   + Q L
Sbjct: 222 MIYAIRNYVLSKEKEKEKSKKKSKQTTNTLPLNINLAHRMESQMSGVLICGKNSHSIQKL 281

Query: 171 TESFRMR-RIQKIYWSLVWGIP 191
           +E F     +QK Y + V  +P
Sbjct: 282 SEQFLPNTNLQKQYIT-VCAVP 302


>gi|226324970|ref|ZP_03800488.1| hypothetical protein COPCOM_02762 [Coprococcus comes ATCC 27758]
 gi|225206318|gb|EEG88672.1| hypothetical protein COPCOM_02762 [Coprococcus comes ATCC 27758]
          Length = 95

 Score = 39.7 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 11/71 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +LYED  I V NKP G+ V   +G         I YH    L     +   +P + HR+D
Sbjct: 15  ILYEDDDILVVNKPKGMVVHPAAGHYTGTLVNAIMYHCKDRLSGI--NGVMRPGIVHRID 72

Query: 152 QETSGILVVAR 162
            +T+G L+V +
Sbjct: 73  MDTTGSLLVCK 83


>gi|221054544|ref|XP_002258411.1| pseudouridylate synthase [Plasmodium knowlesi strain H]
 gi|193808480|emb|CAQ39183.1| pseudouridylate synthase, putative [Plasmodium knowlesi strain H]
          Length = 795

 Score = 39.7 bits (91), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 3/46 (6%)

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           QP TGRTHQ+R H   +  PI  D +Y  NF   +   +   +YLH
Sbjct: 614 QPITGRTHQIRAHLKSLSFPISNDPQYNDNFAKEY---MDKSVYLH 656


>gi|213621035|ref|ZP_03373818.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 80

 Score = 39.7 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 4/76 (5%)

Query: 251 RTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQ--NKLYLHARYMDLPHP-EGGRLQ 306
           RTHQ+RVH  + G PI  D +Y    F    T       +L+LHA  +   HP  G  ++
Sbjct: 1   RTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGTGDVMR 60

Query: 307 ITAPLPAHMVKTWDSL 322
           I AP+   + +  + L
Sbjct: 61  IEAPMDKQLKRCLEVL 76


>gi|260890825|ref|ZP_05902088.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           hofstadii F0254]
 gi|260859378|gb|EEX73878.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           hofstadii F0254]
          Length = 302

 Score = 39.7 bits (91), Expect = 0.73,   Method: Compositional matrix adjust.
 Identities = 32/115 (27%), Positives = 56/115 (48%), Gaps = 17/115 (14%)

Query: 101 LLYEDSKIYVFNKPAGI---------SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +++ED  I V NK   +              +GI  H   FL+ + + +   PR  +RLD
Sbjct: 74  IIFEDEDILVVNKEPFLLTHPTQKKADFTLANGIVNH---FLEKYGEVRV--PRFYNRLD 128

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             TSG++++A+  + AQ   ++F +   +K Y ++V GI  +K+    N  L K 
Sbjct: 129 MNTSGLIIIAKN-SFAQAFLQNFSI--FEKKYLAIVNGIIDDKEIARINEELAKD 180


>gi|260890826|ref|ZP_05902089.1| ribosomal large subunit pseudouridine synthase C [Leptotrichia
           hofstadii F0254]
 gi|260859379|gb|EEX73879.1| ribosomal large subunit pseudouridine synthase C [Leptotrichia
           hofstadii F0254]
          Length = 78

 Score = 39.3 bits (90), Expect = 0.80,   Method: Composition-based stats.
 Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 3/58 (5%)

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +E +  TGRTHQ+RVH   +G  IVGD  Y             N+ +LHA  +   HP
Sbjct: 2   VECELFTGRTHQIRVHLKSIGHTIVGDELYGNGLNKELGI---NRQFLHAYKVKFTHP 56


>gi|301103159|ref|XP_002900666.1| RNA pseudouridylate synthase-like protein [Phytophthora infestans
           T30-4]
 gi|262101929|gb|EEY59981.1| RNA pseudouridylate synthase-like protein [Phytophthora infestans
           T30-4]
          Length = 458

 Score = 39.3 bits (90), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 38/149 (25%), Positives = 61/149 (40%), Gaps = 7/149 (4%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           N  I +G +    P +  +N         D+     K  D L   +L  D    V NK  
Sbjct: 25  NASISAGHLPEDQPPLVPVNSATNSG---DNERGGPKTQDQLHLRVLSRDEHFVVLNKGP 81

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            + + G   +        + +   + +K R  H+LD  TSG+LVV   + A       FR
Sbjct: 82  DVRMDGAFDVTLE-KALARDF--PQVEKFRWIHQLDFATSGVLVVGVNKDATATGCRLFR 138

Query: 176 MRRIQKIYWSLVWG-IPKNKKECIANWLL 203
            +++QK Y ++V G +P N  E +    L
Sbjct: 139 EKQVQKEYLAVVRGHLPFNPAESVDTAAL 167



 Score = 36.2 bits (82), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 15/28 (53%), Positives = 18/28 (64%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++P  GR HQLR+H  H G PI GD  Y
Sbjct: 356 LRPLNGRRHQLRLHMAHHGFPIAGDVTY 383


>gi|323445870|gb|EGB02271.1| hypothetical protein AURANDRAFT_69035 [Aureococcus anophagefferens]
          Length = 542

 Score = 39.3 bits (90), Expect = 0.85,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 47/93 (50%), Gaps = 4/93 (4%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
            L++   +    +KP  + + GG      A  ID  L++ V +  ++ R  H+LD  TSG
Sbjct: 428 TLIHVCDRYVAVDKPFDMRIDGGREGRDEATLID-VLRARVPAHARELRHCHQLDYATSG 486

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +++ A +R AA   +  F  R  +K Y +LV G
Sbjct: 487 VMLYALSRKAAGEASVCFERRTARKTYVALVVG 519


>gi|294874650|ref|XP_002767032.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239868459|gb|EEQ99749.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 64

 Score = 39.3 bits (90), Expect = 0.87,   Method: Composition-based stats.
 Identities = 20/52 (38%), Positives = 33/52 (63%), Gaps = 1/52 (1%)

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
            ++ A S ++V++ + +    + ++  TG THQ+RVH A  +G PIVGD KY
Sbjct: 10  ASSSAHSEYRVLERYEEGCTLMSVRITTGVTHQIRVHMAQGLGHPIVGDKKY 61


>gi|149020773|ref|ZP_01835302.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP23-BS72]
 gi|147930414|gb|EDK81397.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP23-BS72]
          Length = 131

 Score = 39.3 bits (90), Expect = 0.90,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 3/61 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 51  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 107

Query: 162 R 162
           +
Sbjct: 108 K 108


>gi|302546514|ref|ZP_07298856.1| pseudouridine synthase RluB [Streptomyces hygroscopicus ATCC 53653]
 gi|302464132|gb|EFL27225.1| pseudouridine synthase RluB [Streptomyces himastatinicus ATCC
           53653]
          Length = 226

 Score = 39.3 bits (90), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 54/224 (24%), Positives = 92/224 (41%), Gaps = 51/224 (22%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           +D+ RV+ N +I + Q +R+ P         K++  +D     T+   F           
Sbjct: 11  IDQARVEVNGKIVTEQGLRVDPE--------KDEIKVDGLTVATQSYLF----------- 51

Query: 108 IYVFNKPAGISVQGGSGIAYHIDG--FLKSWVDSKGQKPRLTH--RLDQETSGILVVART 163
            +  NKPAG+            DG   L  +V ++  + RL H  RLD ET GI+++   
Sbjct: 52  -FALNKPAGVV-----STMEDPDGRQCLGDYVTNR--ETRLFHVGRLDTETEGIILLTNH 103

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
              A  LT       ++K Y + + G +P++  + + N +               + E G
Sbjct: 104 GELAHRLTHP--RYGVKKTYLAAIQGPLPRDLGKQLKNGI---------------ELEDG 146

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              A  HFKV+    + +  +E+  H GR H +R      G P+
Sbjct: 147 YARA-DHFKVVQNTGKNY-LVEVSLHEGRKHIVRRMLSEAGFPV 188


>gi|139438597|ref|ZP_01772113.1| Hypothetical protein COLAER_01111 [Collinsella aerofaciens ATCC
           25986]
 gi|133776136|gb|EBA39956.1| Hypothetical protein COLAER_01111 [Collinsella aerofaciens ATCC
           25986]
          Length = 205

 Score = 39.3 bits (90), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 52/216 (24%), Positives = 85/216 (39%), Gaps = 28/216 (12%)

Query: 110 VFNKPAGISVQG-GSG----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
             +KPAG+ V G G+G      Y  D  L           +  +RLD+ T+G+++ +  +
Sbjct: 2   AIDKPAGMIVHGDGTGERTLTDYASDLLLAMGDGFAATDMQPLNRLDRNTTGVVLFSLDK 61

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
                  +       +K Y +L  G     ++ I   + +  H         ++   GA+
Sbjct: 62  QTQPAFDQMVNDHAFEKHYLALAEGKIDWNEKLIDKPIARDRHDS-------RKMRVGAS 114

Query: 225 YAISH--FKVIDCFAQKF-----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              S    KV+     +       +++++  TGR HQ+RVH      P+VGD  Y     
Sbjct: 115 GKPSQTRVKVLKRLKSRRGLPTRSYIDVELLTGRKHQIRVHLASEHHPLVGDDLY----- 169

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                P    L LHA  +   HP  G  + I AP P
Sbjct: 170 -GTARPC--GLMLHAHSVSFTHPVTGEHIHIEAPCP 202


>gi|237750207|ref|ZP_04580687.1| predicted protein [Helicobacter bilis ATCC 43879]
 gi|229374101|gb|EEO24492.1| predicted protein [Helicobacter bilis ATCC 43879]
          Length = 671

 Score = 39.3 bits (90), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 77/169 (45%), Gaps = 32/169 (18%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQV---VRIPPVINAL--------NHIIKEQKIL 84
           + QK+L   +++ D + +   + ++ G V     +P  IN +        NH I +Q I 
Sbjct: 29  DTQKLLDKNRIKQDSRIIHKKDFLEKGYVEILSFMPDDINLIPFFACVPPNHAILQQDIA 88

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK---- 140
           +  + ++++  +             VFNKP+ + +     +A   D   KS +DS     
Sbjct: 89  NLEIKISQNPPYF-----------CVFNKPSKL-LTHPKNLA---DS--KSILDSLRYYF 131

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           G+     HRLD ETSG+LV +  + +   L   F  + ++K Y +++ G
Sbjct: 132 GKHANPCHRLDYETSGLLVCSIDKQSEVMLKNLFLQKGVEKSYMAILHG 180


>gi|308496136|ref|XP_003110256.1| hypothetical protein CRE_06624 [Caenorhabditis remanei]
 gi|308245093|gb|EFO89045.1| hypothetical protein CRE_06624 [Caenorhabditis remanei]
          Length = 787

 Score = 39.3 bits (90), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 17/31 (54%), Positives = 22/31 (70%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           TGRTHQ+RVH+  +G PIVGD  Y +   G+
Sbjct: 646 TGRTHQIRVHSQFLGHPIVGDQLYNSTVWGS 676


>gi|149003851|ref|ZP_01828679.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS69]
 gi|147758185|gb|EDK65188.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS69]
          Length = 119

 Score = 39.3 bits (90), Expect = 0.96,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 3/61 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A
Sbjct: 44  VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFA 100

Query: 162 R 162
           +
Sbjct: 101 K 101


>gi|298715322|emb|CBJ27950.1| ribosomal large subunit pseudouridine synthase D [Ectocarpus
           siliculosus]
          Length = 237

 Score = 39.3 bits (90), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 30/54 (55%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            RLD  TSG++V AR + A + L E FR RR++K Y +L+   P      +  W
Sbjct: 97  SRLDVCTSGVVVFARHKDATKQLNELFRARRVKKRYLALLTPGPPVSTGSMVRW 150


>gi|149200710|ref|ZP_01877696.1| Pseudouridylate synthase, 23S RNA-specific [Lentisphaera araneosa
           HTCC2155]
 gi|149136200|gb|EDM24667.1| Pseudouridylate synthase, 23S RNA-specific [Lentisphaera araneosa
           HTCC2155]
          Length = 134

 Score = 39.3 bits (90), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K  E   N A++ F        K  +L ++P TG+THQLRV    +G PI GD  Y    
Sbjct: 15  KLCESRKNPAVTQFFSYSIGQGKRVYL-LRPRTGKTHQLRVAMKAIGAPICGDPNYYPGL 73

Query: 277 -KGNFTSPIQNKLYLHA 292
            KG+     + + YLHA
Sbjct: 74  IKGH-----EERCYLHA 85


>gi|325187007|emb|CCA21551.1| RNA pseudouridylate synthaselike protein putative [Albugo laibachii
           Nc14]
          Length = 639

 Score = 39.3 bits (90), Expect = 1.00,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 3/48 (6%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++P +GR HQLR+H  H+G PI+GD  Y  +    F  P  +++ LHA
Sbjct: 384 LRPLSGRRHQLRLHLKHIGFPILGDATY-GSANPLFRPP--SRMMLHA 428


>gi|149583335|ref|XP_001512490.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 1, partial [Ornithorhynchus anatinus]
          Length = 140

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 21/45 (46%), Positives = 25/45 (55%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           R  H+LD  TSG L VA  RAAA      F+ R + K Y +LV G
Sbjct: 61  RFCHQLDFSTSGALCVALNRAAAGRAYRCFKERIVTKAYVALVRG 105


>gi|328792457|ref|XP_003251726.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like, partial [Apis mellifera]
          Length = 312

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 68/292 (23%), Positives = 115/292 (39%), Gaps = 60/292 (20%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGI------SVQG-----GSGIAYHIDGFLKSWVD 138
           L + S  L + L+Y +  + + NKP GI      S Q       +G+ Y ++  L  ++ 
Sbjct: 13  LLEFSSDLVNNLIYNEDGLIILNKPYGIRSRKSNSFQSLKNNVSNGVNYTLEDAL-PYIA 71

Query: 139 SKGQKPRLTHRLDQE--TSGILVVARTRAAAQHLTESFRMRRIQ-----KIYWSLVWGIP 191
            +   P L      E   SGI ++    AA  ++  +  +  I        YW +  GIP
Sbjct: 72  KELNYPNLNIIKSPEMYMSGITLL----AANSNIQNAIELAYIHGQYFINTYWIVTVGIP 127

Query: 192 K--NKKECIANWLLKKSHIGGDYVHVV----KQNEKGANYAISHFKVIDCFAQKFCWL-E 244
           K  N    +   L+           ++    K  EK      + +K++       C L +
Sbjct: 128 KQSNNYSRLGIKLVSHPQFKNKKQILITSWSKNEEKKIKILKTEYKILSNSILNLCSLIQ 187

Query: 245 MQPHTGRTHQLRVHA-LHMGCPIVGDHKYCANFK--GN--------FTSP---IQNKLY- 289
           +   T   H +R+ A   + CPI+GD+ Y +  +  GN        FT     + +KL+ 
Sbjct: 188 LVSSTHHKHAIRLFASTFLYCPILGDNIYASQIQKIGNTYVRVHPFFTCSAPKLDDKLFK 247

Query: 290 ---------------LHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                          +H R + L +  G  L+I APLP +   T + L FK+
Sbjct: 248 LLGVKPNNENIIPTHIHLRSIVLRNFLGKTLKIEAPLPPYFDWTCNQLEFKH 299


>gi|305680918|ref|ZP_07403725.1| putative pseudouridine synthase B, ribosomal large subunit
           [Corynebacterium matruchotii ATCC 14266]
 gi|305659123|gb|EFM48623.1| putative pseudouridine synthase B, ribosomal large subunit
           [Corynebacterium matruchotii ATCC 14266]
          Length = 285

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 55/246 (22%), Positives = 91/246 (36%), Gaps = 49/246 (19%)

Query: 31  HINFVNLQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + + V LQK+L        R+ ++ +D  RV+ N  +   Q VR+ P ++ +       +
Sbjct: 41  YTDGVRLQKVLAQAGVASRRNAEIMIDSGRVEVNGAVVMQQGVRVNPKVDVI-------R 93

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +    VN+  +  +            +V NKP GI       +     G L S   S GQ
Sbjct: 94  VDGVRVNVNNNHQY------------FVLNKPRGIHSTMSDDLGRPCIGDLVSERISAGQ 141

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANW 201
                 RLD +T G++++      A  L  S     + K Y + V G   ++    + N 
Sbjct: 142 GLFHVGRLDADTEGLILLTNDGELANRL--SHPKYEVSKTYIAEVLGEADRSLVTTLKNG 199

Query: 202 L-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           + L       DYV +V                     Q    + +Q H GR H +R    
Sbjct: 200 VELDDGPAAADYVQIVD------------------VHQGRSLVRVQLHEGRKHIVRRMLK 241

Query: 261 HMGCPI 266
             G P+
Sbjct: 242 AAGYPV 247


>gi|320011602|gb|ADW06452.1| pseudouridine synthase [Streptomyces flavogriseus ATCC 33331]
          Length = 389

 Score = 38.9 bits (89), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 48/192 (25%), Positives = 85/192 (44%), Gaps = 34/192 (17%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVF---NKPAGISVQGGSGIAYHIDGF--LKSWV 137
           +L+  + +    D +K   L   ++ Y+F   NKPAG+    G       DG   L  +V
Sbjct: 186 VLEQGMRVDPQKDEIKVDGLTVATQSYLFFALNKPAGVVSTMGD-----PDGRQNLGDYV 240

Query: 138 DSKGQKPRLTH--RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
           +++  + RL H  RLD ET GI+++      A  LT       ++K Y + + G +P++ 
Sbjct: 241 NNR--ETRLFHVGRLDTETEGIILLTNHGELAHRLTHP--KYGVKKTYLAAIQGPLPRDL 296

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + + + +               Q E G   A  HF+V++   + +  +E+  H GR H 
Sbjct: 297 GKRLKDGI---------------QLEDGYARA-DHFRVVENTGKNYL-VEVTLHEGRKHI 339

Query: 255 LRVHALHMGCPI 266
           +R      G P+
Sbjct: 340 VRRMLAEAGFPV 351


>gi|322504491|emb|CAM42057.2| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 1015

 Score = 38.5 bits (88), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 18/26 (69%), Positives = 19/26 (73%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA 274
           TGRTHQLRVH   +G PIV D KY A
Sbjct: 876 TGRTHQLRVHLASLGHPIVRDRKYIA 901


>gi|154334484|ref|XP_001563489.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
          Length = 1015

 Score = 38.5 bits (88), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 18/26 (69%), Positives = 19/26 (73%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA 274
           TGRTHQLRVH   +G PIV D KY A
Sbjct: 876 TGRTHQLRVHLASLGHPIVRDRKYIA 901


>gi|72390235|ref|XP_845412.1| hypothetical protein [Trypanosoma brucei TREU927]
 gi|62360582|gb|AAX80994.1| hypothetical protein, conserved [Trypanosoma brucei]
 gi|70801947|gb|AAZ11853.1| hypothetical protein, conserved [Trypanosoma brucei brucei strain
           927/4 GUTat10.1]
          Length = 377

 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 28/49 (57%), Gaps = 5/49 (10%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHAR 293
           P TGR HQLR+H   +G PIVGD  Y  +   +F S +  QN+  +  R
Sbjct: 250 PQTGRRHQLRLHCNALGFPIVGDVTYGIS---SFPSTVLHQNEALMEGR 295



 Score = 36.2 bits (82), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 35/145 (24%), Positives = 58/145 (40%), Gaps = 35/145 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS--------GIAYHI---DG-------FLKSWVDSKGQ 142
           ++YE+ ++ V NKP  + + G           +AY     DG       F +  +    Q
Sbjct: 10  VIYENDELVVVNKPNDVPMDGVGCELTVERWALAYRSRRNDGDKVDSERFNEEVMKDASQ 69

Query: 143 KP--------------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            P              +  H+LD  TSG+L +A ++  A  L   F MR  +K Y +++ 
Sbjct: 70  LPDFVTEKPKGKKKMVKFVHQLDYATSGVLCIAFSKEMAARLAHCFEMRTAKKAYVAVLH 129

Query: 189 GIPKNKKECIAN---WLLKKSHIGG 210
           G        I N   +L + +  GG
Sbjct: 130 GSVSPLSSTIPNSTSFLSRNATQGG 154


>gi|261328814|emb|CBH11792.1| hypothetical protein, conserved [Trypanosoma brucei gambiense
           DAL972]
          Length = 377

 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 28/49 (57%), Gaps = 5/49 (10%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHAR 293
           P TGR HQLR+H   +G PIVGD  Y  +   +F S +  QN+  +  R
Sbjct: 250 PQTGRRHQLRLHCNALGFPIVGDVTYGIS---SFPSTVLHQNEALMEGR 295



 Score = 36.2 bits (82), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 35/145 (24%), Positives = 58/145 (40%), Gaps = 35/145 (24%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS--------GIAYHI---DG-------FLKSWVDSKGQ 142
           ++YE+ ++ V NKP  + + G           +AY     DG       F +  +    Q
Sbjct: 10  VIYENDELVVVNKPNDVPMDGVGCELTVERWALAYRSRRNDGDKVDSERFNEEVMKDASQ 69

Query: 143 KP--------------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            P              +  H+LD  TSG+L +A ++  A  L   F MR  +K Y +++ 
Sbjct: 70  LPDFVTEKPKGKKKMVKFVHQLDYATSGVLCIAFSKEMAARLAHCFEMRTAKKAYVAVLH 129

Query: 189 GIPKNKKECIAN---WLLKKSHIGG 210
           G        I N   +L + +  GG
Sbjct: 130 GSVSPLSSTIPNSTSFLSRNATQGG 154


>gi|120554678|ref|YP_959029.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120324527|gb|ABM18842.1| ribosomal large subunit pseudouridine synthase E [Marinobacter
           aquaeolei VT8]
          Length = 202

 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 41/164 (25%), Positives = 67/164 (40%), Gaps = 10/164 (6%)

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
           +K+ +FNKP  +  Q     A H    L  W+D  G  P    RLD ++ G+L++   + 
Sbjct: 2   AKLILFNKPFHVLSQFTDERASHPRATLADWIDQPGVYP--AGRLDYDSEGLLLLT-DQG 58

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           A QH   S    ++ K YW  V G  +   E +    L+K  +  D +    + E+    
Sbjct: 59  ALQHRIASP-TNKMPKTYWVQVEG--ELTDEALHK--LRKGVVLKDGITRPARAERLETP 113

Query: 226 AISHFKVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +        F Q     WL +    G+  Q+R     +G P +
Sbjct: 114 DLWPRNPPVRFRQNVPTTWLALTITEGKNRQVRRMTAAVGYPTL 157


>gi|239940238|ref|ZP_04692175.1| putative pseudouridine synthase [Streptomyces roseosporus NRRL
           15998]
 gi|239986727|ref|ZP_04707391.1| putative pseudouridine synthase [Streptomyces roseosporus NRRL
           11379]
 gi|291443668|ref|ZP_06583058.1| pseudouridine synthase [Streptomyces roseosporus NRRL 15998]
 gi|291346615|gb|EFE73519.1| pseudouridine synthase [Streptomyces roseosporus NRRL 15998]
          Length = 427

 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 47/192 (24%), Positives = 87/192 (45%), Gaps = 34/192 (17%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVF---NKPAGI--SVQGGSGIAYHIDGFLKSWV 137
           +++  + +  H D +K   L   ++ Y+F   NKPAG+  S++   G        L  +V
Sbjct: 224 VVEQGMRVDVHKDEIKVDGLTVAAQSYLFFALNKPAGVVSSMEDPDGRQ-----CLGDYV 278

Query: 138 DSKGQKPRLTH--RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
           +++  + RL H  RLD ET GI+++      A  LT       ++K Y + + G +P++ 
Sbjct: 279 NNR--ETRLFHVGRLDTETEGIIMLTNHGELAHRLTHP--KYGVKKTYLAAIQGPLPRDL 334

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + + + +               Q E G   A  HF+V++   + +  +E+  H GR H 
Sbjct: 335 GKRLKDGI---------------QLEDGYARA-DHFRVVENTGKNY-LVEVTLHEGRKHI 377

Query: 255 LRVHALHMGCPI 266
           +R      G P+
Sbjct: 378 VRRMLAEAGFPV 389


>gi|225021516|ref|ZP_03710708.1| hypothetical protein CORMATOL_01537 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945898|gb|EEG27107.1| hypothetical protein CORMATOL_01537 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 241

 Score = 38.5 bits (88), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 54/240 (22%), Positives = 88/240 (36%), Gaps = 49/240 (20%)

Query: 37  LQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           LQK+L        R+ ++ +D  RV+ N  +   Q VR+ P ++ +       ++    V
Sbjct: 3   LQKVLAQAGVASRRNAEIMIDSGRVEVNGAVVMQQGVRVNPEVDVI-------RVDGVRV 55

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           N+  +  +            +V NKP GI       +     G L S   S GQ      
Sbjct: 56  NVNNNHQY------------FVLNKPRGIHSTMSDDLGRPCIGDLVSERISAGQGLFHVG 103

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWL-LKKS 206
           RLD +T G++++      A  L  S     + K Y + V G   ++    + N + L   
Sbjct: 104 RLDADTEGLILLTNDGELANRL--SHPKYEVSKTYIAEVLGEADRSLVTTLKNGVELDDG 161

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               DYV +V                     Q    + +Q H GR H +R      G P+
Sbjct: 162 PAAADYVQIVD------------------VHQGRSLVRVQLHEGRKHIVRRMLKAAGYPV 203


>gi|226486578|emb|CAX74366.1| pseudouridylate synthase [Schistosoma japonicum]
          Length = 258

 Score = 38.5 bits (88), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 3/90 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILV 159
            +++   + V NKP  I +       Y ++          G +P R THRLD+ TSG+L+
Sbjct: 157 FIHDSHDMLVINKPPSIPIHPCG--RYTLNSITHILAKDYGLRPLRFTHRLDRMTSGLLL 214

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +A+    +  L      + + K Y   V G
Sbjct: 215 IAKDYDTSVRLQSQIASKEVTKHYICHVDG 244


>gi|118592945|ref|ZP_01550333.1| V-type ATP synthase subunit B [Stappia aggregata IAM 12614]
 gi|118434479|gb|EAV41132.1| V-type ATP synthase subunit B [Stappia aggregata IAM 12614]
          Length = 455

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 28/126 (22%), Positives = 58/126 (46%), Gaps = 10/126 (7%)

Query: 58  RIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           R+ + +++R   P+I+  N +++ QKI   SV+   ++ FL  I +  D+ I VF     
Sbjct: 127 RVLASRMIRTDVPMIDIFNCLVESQKIPIFSVSGEPYNPFLARIGIQADADIVVF----- 181

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               GG G+ +    F +   +  G  PR    ++Q +  ++   +    A  + E F +
Sbjct: 182 ----GGLGLIFDDYAFFRQQFEDAGVFPRTVMFINQASDPVVERLQVPDMALAVAEKFAV 237

Query: 177 RRIQKI 182
              +++
Sbjct: 238 EEGKRV 243


>gi|322497782|emb|CBZ32858.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 516

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 18/26 (69%), Positives = 19/26 (73%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA 274
           TGRTHQLRVH   +G PIV D KY A
Sbjct: 374 TGRTHQLRVHLASLGHPIVHDSKYIA 399


>gi|270659692|ref|ZP_06222356.1| tRNA pseudouridine synthase C [Haemophilus influenzae HK1212]
 gi|270316970|gb|EFA28650.1| tRNA pseudouridine synthase C [Haemophilus influenzae HK1212]
          Length = 97

 Score = 38.1 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 22/67 (32%), Positives = 34/67 (50%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAA 167
           A +   A
Sbjct: 64  ALSSEIA 70


>gi|146081861|ref|XP_001464379.1| hypothetical protein [Leishmania infantum JPCM5]
 gi|134068471|emb|CAM66761.1| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 516

 Score = 38.1 bits (87), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 18/26 (69%), Positives = 19/26 (73%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA 274
           TGRTHQLRVH   +G PIV D KY A
Sbjct: 374 TGRTHQLRVHLASLGHPIVHDSKYIA 399


>gi|90961422|ref|YP_535338.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           salivarius UCC118]
 gi|90820616|gb|ABD99255.1| Ribosomal small subunit pseudouridine synthase A [Lactobacillus
           salivarius UCC118]
          Length = 240

 Score = 38.1 bits (87), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 37/138 (26%), Positives = 64/138 (46%), Gaps = 14/138 (10%)

Query: 60  QSGQVVRIPP--VINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSK--IYVFNK 113
           Q+G+  R     VI A    + ++ + D  + + + SD  FL   LL  ++K   Y+ NK
Sbjct: 11  QTGKFTRAEAKKVIKAKRVRLNDEVVKDGKIKINEESDKIFLDGELLALNNKEVYYMLNK 70

Query: 114 PAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLT 171
           PAG+     S      D  +   ++  G+K  L    RLD+ET+G+L++      A  + 
Sbjct: 71  PAGVV----SATRDDKDKTVIDLINFPGRKEDLFPVGRLDKETTGLLIITNDGKFAHDII 126

Query: 172 ESFRMRRIQKIYWSLVWG 189
                + + K Y ++V G
Sbjct: 127 SP--KKHVSKTYEAVVTG 142


>gi|213027661|ref|ZP_03342108.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 37

 Score = 38.1 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 17/35 (48%), Positives = 26/35 (74%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           HRLD++TSG+L+VA+ R+A + L E  R +R  +I
Sbjct: 2   HRLDRDTSGVLLVAKKRSALRSLHEQLRRKRDAEI 36


>gi|66824235|ref|XP_645472.1| pseudouridine synthase family protein [Dictyostelium discoideum
           AX4]
 gi|60473647|gb|EAL71588.1| pseudouridine synthase family protein [Dictyostelium discoideum
           AX4]
          Length = 316

 Score = 38.1 bits (87), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 17/26 (65%), Positives = 18/26 (69%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY 272
           P TGR HQLRVH L +G  IVGD  Y
Sbjct: 242 PKTGRRHQLRVHLLSIGHVIVGDETY 267



 Score = 37.7 bits (86), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 22/89 (24%), Positives = 43/89 (48%), Gaps = 1/89 (1%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +Y D +  V NKP  +++   +G     +  ++++         R  +R+D  TSG++VV
Sbjct: 24  IYLDKEYIVVNKPFDVNIDDETGERLTTVVKYIETEYPEHFGNVRFVNRIDYATSGLVVV 83

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +  + +     E F+ R   K Y ++V G
Sbjct: 84  SFNKKSTTVAMELFQSRETSKTYLAIVHG 112


>gi|254504650|ref|ZP_05116801.1| ATP synthase alpha/beta family, nucleotide-binding domain protein
           [Labrenzia alexandrii DFL-11]
 gi|222440721|gb|EEE47400.1| ATP synthase alpha/beta family, nucleotide-binding domain protein
           [Labrenzia alexandrii DFL-11]
          Length = 460

 Score = 38.1 bits (87), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 28/126 (22%), Positives = 58/126 (46%), Gaps = 10/126 (7%)

Query: 58  RIQSGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           R+ + +++R   P+I+  N +++ QKI   SV+   ++ FL  I +  D+ I VF     
Sbjct: 127 RVLASRMIRTDVPMIDIFNCLVESQKIPIFSVSGEPYNAFLARIGIQADADIVVF----- 181

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               GG G+ +    F +   +  G  PR    ++Q +  ++   +    A  + E F +
Sbjct: 182 ----GGLGLIFDDYAFFRKQFEDAGVFPRTVMFINQASDPVVERLQVPDMALAVAEKFAV 237

Query: 177 RRIQKI 182
              +++
Sbjct: 238 EEGKRV 243


>gi|154339315|ref|XP_001562349.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134062932|emb|CAM39380.1| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 957

 Score = 38.1 bits (87), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 18/37 (48%), Positives = 23/37 (62%), Gaps = 1/37 (2%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
           P+TGR HQ+R+H   + CPIVGD  Y A   G+   P
Sbjct: 641 PYTGRLHQIRMHLSSLDCPIVGDVVY-ARTTGSADVP 676


>gi|57158194|dbj|BAD84160.1| putative ribosomal pseudouridine synthase [Corynebacterium
           glutamicum]
          Length = 74

 Score = 38.1 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 7/60 (11%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           + P TG+THQLR+H      PI+GD  Y    A    ++T+P    ++L AR +    P+
Sbjct: 3   LAPSTGKTHQLRIHMRDFAAPILGDPLYPVLHAVDDEDYTTP----MHLIARTLTFVDPQ 58


>gi|147833193|emb|CAN68642.1| hypothetical protein VITISV_030809 [Vitis vinifera]
          Length = 400

 Score = 37.7 bits (86), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 18/40 (45%), Positives = 19/40 (47%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
           TGRTHQ+R      G PIVGD  Y        TSP  N  
Sbjct: 305 TGRTHQIRAQLAACGAPIVGDSMYMPAAIAEITSPGLNPF 344


>gi|71418712|ref|XP_810945.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70875553|gb|EAN89094.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 682

 Score = 37.7 bits (86), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 18/40 (45%), Positives = 24/40 (60%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
           TGRTHQ+RVH   +G PI GD KY      + + P++  L
Sbjct: 573 TGRTHQVRVHLASLGHPIRGDKKYIRLAADSPSIPLRTDL 612


>gi|60599504|gb|AAX26297.1| unknown [Schistosoma japonicum]
          Length = 148

 Score = 37.7 bits (86), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 9/92 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILVV 160
           +++   + V NKP  I +       Y ++          G +P R THRLD+ TSG+L++
Sbjct: 53  IHDSHDMLVINKPPSIPIHPCG--RYTLNSITHILAKDYGLRPLRFTHRLDRMTSGLLLI 110

Query: 161 ARTRAAAQHLT------ESFRMRRIQKIYWSL 186
           A+    +  L       E  ++ R+ KI +++
Sbjct: 111 AKDYDTSVRLQSQIASKEVTKVTRLSKILYTI 142


>gi|303274711|ref|XP_003056671.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226461023|gb|EEH58316.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 548

 Score = 37.7 bits (86), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 28/96 (29%), Positives = 41/96 (42%), Gaps = 10/96 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGS--------GIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           ++YED +    NKP  +  Q           G      GF     D       +THRLD 
Sbjct: 210 VVYEDEETLAVNKPHALPTQAHESNAAECVPGCVARALGFTGGVTDGDDAL-LVTHRLDA 268

Query: 153 ETSGILVVARTRAAAQHLTESFR-MRRIQKIYWSLV 187
            TSG++V+ +T  A +    S    +R+ K Y +LV
Sbjct: 269 STSGVVVLGKTLGAVRAFNASIAGGKRVTKTYVALV 304


>gi|149036914|gb|EDL91532.1| RNA pseudouridylate synthase domain containing 3 (predicted),
           isoform CRA_a [Rattus norvegicus]
          Length = 157

 Score = 37.7 bits (86), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 30/60 (50%), Gaps = 3/60 (5%)

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           K  ++G    +SHF V        C L ++QP T    QL+VH     CPI+GDH Y A 
Sbjct: 16  KDIQEGVKRTLSHFHVTATGCG--CALVQLQPLTVFPSQLQVHMALQLCPILGDHTYAAR 73


>gi|46200774|ref|ZP_00207837.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 66

 Score = 37.7 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 29/50 (58%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           D + S +LY+D  + V +KPAG++V  G     H++ +L  W  +  ++P
Sbjct: 4   DEILSRVLYKDQDVIVLDKPAGLAVHAGPNSPDHLELYLGPWPSAGPRRP 53


>gi|301107450|ref|XP_002902807.1| conserved hypothetical protein [Phytophthora infestans T30-4]
 gi|262097925|gb|EEY55977.1| conserved hypothetical protein [Phytophthora infestans T30-4]
          Length = 263

 Score = 37.7 bits (86), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 45/95 (47%), Gaps = 6/95 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFL--KSWVDSKGQK---PRLTHRLDQET 154
           ++YE S + +  KP GI V+G G          L  K  VD+   +   P   HRLD   
Sbjct: 113 VVYECSILALVVKPVGIHVKGRGKRTVEQALPLLLRKQHVDAGDFELPLPHAVHRLDYRV 172

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G+L+VA+TR     L+  F    + K Y +++ G
Sbjct: 173 GGLLLVAKTRKMEVKLSAQFERHSVAKQYRAILVG 207


>gi|213865434|ref|ZP_03387553.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
          enterica serovar Typhi str. M223]
          Length = 56

 Score = 37.7 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 28/48 (58%)

Query: 7  VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK 54
          V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K
Sbjct: 8  VKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIK 55


>gi|182439522|ref|YP_001827241.1| putative pseudouridine synthase [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178468038|dbj|BAG22558.1| putative pseudouridine synthase [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 434

 Score = 37.7 bits (86), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 47/192 (24%), Positives = 86/192 (44%), Gaps = 34/192 (17%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVF---NKPAGI--SVQGGSGIAYHIDGFLKSWV 137
           +++  + +  H D +K   L   ++ Y+F   NKPAG+  S++   G        L  +V
Sbjct: 231 VVEQGMRVDVHKDEIKVDGLTVAAQSYLFFALNKPAGVVSSMEDPDGRQ-----CLGDYV 285

Query: 138 DSKGQKPRLTH--RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
            ++  + RL H  RLD ET GI+++      A  LT       ++K Y + + G +P++ 
Sbjct: 286 TNR--ETRLFHVGRLDTETEGIIMLTNHGELAHRLTHP--KYGVKKTYLAAIQGPLPRDL 341

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + + + +               Q E G   A  HF+V++   + +  +E+  H GR H 
Sbjct: 342 GKRLKDGI---------------QLEDGYARA-DHFRVVENTGKNY-LVEVTLHEGRKHI 384

Query: 255 LRVHALHMGCPI 266
           +R      G P+
Sbjct: 385 VRRMLAEAGFPV 396


>gi|326780186|ref|ZP_08239451.1| pseudouridine synthase Rsu [Streptomyces cf. griseus XylebKG-1]
 gi|326660519|gb|EGE45365.1| pseudouridine synthase Rsu [Streptomyces cf. griseus XylebKG-1]
          Length = 433

 Score = 37.4 bits (85), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 47/192 (24%), Positives = 86/192 (44%), Gaps = 34/192 (17%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVF---NKPAGI--SVQGGSGIAYHIDGFLKSWV 137
           +++  + +  H D +K   L   ++ Y+F   NKPAG+  S++   G        L  +V
Sbjct: 230 VVEQGMRVDVHKDEIKVDGLTVAAQSYLFFALNKPAGVVSSMEDPDGRQ-----CLGDYV 284

Query: 138 DSKGQKPRLTH--RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
            ++  + RL H  RLD ET GI+++      A  LT       ++K Y + + G +P++ 
Sbjct: 285 TNR--ETRLFHVGRLDTETEGIIMLTNHGELAHRLTHP--KYGVKKTYLAAIQGPLPRDL 340

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + + + +               Q E G   A  HF+V++   + +  +E+  H GR H 
Sbjct: 341 GKRLKDGI---------------QLEDGYARA-DHFRVVENTGKNY-LVEVTLHEGRKHI 383

Query: 255 LRVHALHMGCPI 266
           +R      G P+
Sbjct: 384 VRRMLAEAGFPV 395


>gi|328467386|gb|EGF38463.1| pseudouridine synthase [Lactobacillus rhamnosus MTCC 5462]
          Length = 159

 Score = 37.4 bits (85), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 40/87 (45%), Gaps = 11/87 (12%)

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           HTGRTHQ+RVH   +G P+ GD  Y      N  +    +  LH  ++    P    LQ 
Sbjct: 57  HTGRTHQIRVHFAAIGHPLFGDDLY------NRQADDFKRQALHCAHLRFWQP----LQK 106

Query: 308 TAPLPAHMVK-TWDSLGFKYDRNLYIK 333
           +  +  H  + TW SL       L+I+
Sbjct: 107 SGSICMHRYQLTWQSLATTCIYQLFIR 133


>gi|330793622|ref|XP_003284882.1| hypothetical protein DICPUDRAFT_28377 [Dictyostelium purpureum]
 gi|325085191|gb|EGC38603.1| hypothetical protein DICPUDRAFT_28377 [Dictyostelium purpureum]
          Length = 315

 Score = 37.4 bits (85), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 6/68 (8%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           + P +GR HQLRVH   +G  IVGD  Y          P   ++ LH+  + LP     +
Sbjct: 247 LTPKSGRRHQLRVHLQSIGHIIVGDETYGP------KDPQSERMMLHSWKLILPFKNEPQ 300

Query: 305 LQITAPLP 312
           + +    P
Sbjct: 301 INVETDDP 308


>gi|223999175|ref|XP_002289260.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220974468|gb|EED92797.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 571

 Score = 37.4 bits (85), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLL 203
           R+ H+LD  TSG+L+ A+ R AA     SF+ R+  K Y ++V    P   +  ++   L
Sbjct: 162 RIVHQLDYATSGVLLYAKNRKAAGKACISFQERKTDKQYVAIVTNQDPAASETPLSQDFL 221

Query: 204 KK 205
           KK
Sbjct: 222 KK 223



 Score = 37.0 bits (84), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 30/55 (54%), Gaps = 2/55 (3%)

Query: 245 MQPHTGRTHQLRVH-ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           ++P TGR HQLRVH AL  G PI+GD  Y            + ++ LHA  + +P
Sbjct: 482 LKPWTGRRHQLRVHLALVAGFPILGDVAYSKEETKQRVMTCE-RMCLHAHMLSIP 535


>gi|218886233|ref|YP_002435554.1| pseudouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|218757187|gb|ACL08086.1| pseudouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
          Length = 463

 Score = 37.4 bits (85), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 49/205 (23%), Positives = 74/205 (36%), Gaps = 54/205 (26%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI------------- 190
           PRL +RLD  TSGIL+ AR   AAQ    +    +  K Y +LV G+             
Sbjct: 233 PRLLNRLDGPTSGILLAARAPQAAQRFHAAENSGQATKTYIALVHGVLAQPMKVRRGLDT 292

Query: 191 ---------PKNKKECIANWLLKK----------------SHIGGDYVHVVKQNEKGANY 225
                    P++  + + + ++                    + GD      Q+   A+ 
Sbjct: 293 ANRATTRVLPQDTPDALRHTMVTPLGIMQTTDIPDAAPCTPTLAGD----AGQDSAPASA 348

Query: 226 AISHFKVIDCFAQKFCWL-EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-- 282
             +H     C +   C L       G  HQ+R H   +G PIVGD +Y        T+  
Sbjct: 349 CTTHAPGPACTSGTPCTLVRCVIRKGARHQIRAHLAVLGHPIVGDTRYGTPDGAGATTMP 408

Query: 283 ---------PIQNKLYLHARYMDLP 298
                    P    L+LH   ++LP
Sbjct: 409 QGAPHSARLPAPATLFLHHARIELP 433


>gi|325181852|emb|CCA16307.1| RNA pseudouridylate synthase putative [Albugo laibachii Nc14]
          Length = 226

 Score = 37.4 bits (85), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNK 287
           C L   P TGRTHQ+R+H   +G PI  D  Y      G+ T+P+  K
Sbjct: 98  CVLRCFPVTGRTHQIRLHLQLIGLPIANDPCYGGELHFGSKTTPLDTK 145


>gi|303284197|ref|XP_003061389.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226456719|gb|EEH54019.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 497

 Score = 37.4 bits (85), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 16/37 (43%), Positives = 22/37 (59%)

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             ++   +  +P TGRTHQ+R H   +G PIV D KY
Sbjct: 310 LPRRALLVRCRPTTGRTHQIRAHLSRLGWPIVNDVKY 346


>gi|213419331|ref|ZP_03352397.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 78

 Score = 37.0 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 25/87 (28%), Positives = 37/87 (42%), Gaps = 26/87 (29%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
           +LY+D  +   NKPAG  V              +SW+D               GQ     
Sbjct: 4   ILYQDPWLVAVNKPAGWLVH-------------RSWLDRDEKVVVMQTVRDQIGQHVFTA 50

Query: 148 HRLDQETSGILVVARTRAAAQHLTESF 174
           HRLD+ TSG+L++  +  A + L + F
Sbjct: 51  HRLDRPTSGVLLMGLSSEAGRRLAQQF 77


>gi|71417514|ref|XP_810586.1| RNA pseudouridylate synthase [Trypanosoma cruzi strain CL Brener]
 gi|70875140|gb|EAN88735.1| RNA pseudouridylate synthase, putative [Trypanosoma cruzi]
          Length = 474

 Score = 37.0 bits (84), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 14/30 (46%), Positives = 19/30 (63%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           TGRTHQ+R+H   +G P++GD  Y     G
Sbjct: 339 TGRTHQIRIHCAQLGYPVLGDKLYETTTPG 368


>gi|221110365|ref|XP_002168193.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 153

 Score = 37.0 bits (84), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 1/85 (1%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           + ++ V NKPA I V       ++   F+    D         HR+D+ TSG+L+ A+T 
Sbjct: 57  NEEVVVINKPASIPVHPCGRFRHNTIVFILGK-DYGLYNLHTIHRIDRLTSGVLMFAKTS 115

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWG 189
             A+ L    R R + K Y + V G
Sbjct: 116 KKARELEGLVRGRLVIKEYLARVIG 140


>gi|149592489|ref|XP_001521009.1| PREDICTED: hypothetical protein, partial [Ornithorhynchus anatinus]
          Length = 152

 Score = 37.0 bits (84), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 25/45 (55%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           + R  H+LD  TSG L VA  RAAA      F+ R + K Y +LV
Sbjct: 39  RSRFCHQLDFSTSGALCVALNRAAAGRAYRCFKERIVTKAYVALV 83


>gi|126433880|ref|YP_001069571.1| pseudouridine synthase [Mycobacterium sp. JLS]
 gi|126233680|gb|ABN97080.1| pseudouridine synthase [Mycobacterium sp. JLS]
          Length = 287

 Score = 37.0 bits (84), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 40/160 (25%), Positives = 64/160 (40%), Gaps = 15/160 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ D  I V +KP  ++    G  +A      L+  +D     P   HRLD+ T+G+L+
Sbjct: 86  VLHRDDNIVVVDKPHFLATMPRGRHVAETAVVRLRRALDLPELSP--AHRLDRLTAGVLL 143

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
               R         F    + K+Y +   G    +    + + ++K+    G        
Sbjct: 144 FTTRREIRGAYQTMFSDGAVAKVYLARSAGHATVDLPTVVRSRIIKER---GRLQAFEAP 200

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            E  A   + H    D +        + P TGRTHQLRVH
Sbjct: 201 GEPNAETLVEHLG-DDVY-------RLTPRTGRTHQLRVH 232


>gi|71403307|ref|XP_804468.1| RNA pseudouridylate synthase [Trypanosoma cruzi strain CL Brener]
 gi|70867455|gb|EAN82617.1| RNA pseudouridylate synthase, putative [Trypanosoma cruzi]
          Length = 474

 Score = 37.0 bits (84), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 14/30 (46%), Positives = 19/30 (63%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           TGRTHQ+R+H   +G P++GD  Y     G
Sbjct: 339 TGRTHQIRIHCAQLGYPVLGDKLYETTTPG 368


>gi|281211738|gb|EFA85900.1| Mrp/NBP35 family protein [Polysphondylium pallidum PN500]
          Length = 687

 Score = 37.0 bits (84), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 16/24 (66%), Positives = 17/24 (70%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGRTHQLR+H    G PIVGD  Y
Sbjct: 584 TGRTHQLRIHFSESGFPIVGDPYY 607


>gi|322824625|gb|EFZ29968.1| hypothetical protein TCSYLVIO_3750 [Trypanosoma cruzi]
          Length = 681

 Score = 37.0 bits (84), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 16/24 (66%), Positives = 18/24 (75%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGRTHQ+RVH   +G PI GD KY
Sbjct: 573 TGRTHQVRVHLASLGHPIRGDKKY 596


>gi|159489452|ref|XP_001702711.1| pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158280733|gb|EDP06490.1| pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 301

 Score = 37.0 bits (84), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 33/108 (30%), Positives = 51/108 (47%), Gaps = 13/108 (12%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----IAYHIDGFLKSWVDSK 140
           D  V L       + +L  +   +++ NKPAG+ V G +      A   DG   +     
Sbjct: 119 DKVVRLLTPERVRRWVLGVQPGLVFI-NKPAGVRVHGRAAGDVDSAGGRDGGGPTLDSVM 177

Query: 141 GQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G+        +P+L HRLD + SG++VVAR   AA  L+ +FR +  Q
Sbjct: 178 GEALRFGEQDEPKLVHRLDAQASGVMVVARNADAAAWLSAAFRGKSRQ 225


>gi|217031565|ref|ZP_03437070.1| hypothetical protein HPB128_21g123 [Helicobacter pylori B128]
 gi|216946765|gb|EEC25361.1| hypothetical protein HPB128_21g123 [Helicobacter pylori B128]
          Length = 147

 Score = 36.6 bits (83), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 27/95 (28%), Positives = 42/95 (44%), Gaps = 13/95 (13%)

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---------NFKGNFTSPIQNKLYLH 291
             L++ P TGRTHQ+R+H   +G  IVG+  Y             K    +P+   L LH
Sbjct: 57  SLLKITPITGRTHQIRLHLSSVGHRIVGEGLYGVIDENAREYLQLKRENNAPL---LMLH 113

Query: 292 ARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
           A  ++    +    +IT+P+P   +     L   Y
Sbjct: 114 ASSLEFEF-KKAFYEITSPMPKRFMPFLKDLALFY 147


>gi|121591505|ref|ZP_01678772.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 2740-80]
 gi|121546635|gb|EAX56823.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 2740-80]
          Length = 134

 Score = 36.6 bits (83), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 7/47 (14%)

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           +PHTG+THQ+RV    +G  IVGD  Y        T+   ++ YLHA
Sbjct: 38  KPHTGKTHQIRVALKSIGSAIVGDPIYN-------TADESDRGYLHA 77


>gi|298713714|emb|CBJ48905.1| putative RNA pseudouridylate synthase [Ectocarpus siliculosus]
          Length = 555

 Score = 36.6 bits (83), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 16/30 (53%), Positives = 20/30 (66%)

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +E+Q  TGRTHQ+R      GCPI GD+ Y
Sbjct: 449 VEVQLLTGRTHQIRGQLAAEGCPIYGDYLY 478


>gi|255527012|ref|ZP_05393904.1| RNA-binding S4 domain protein [Clostridium carboxidivorans P7]
 gi|255509322|gb|EET85670.1| RNA-binding S4 domain protein [Clostridium carboxidivorans P7]
          Length = 173

 Score = 36.6 bits (83), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 39/161 (24%), Positives = 73/161 (45%), Gaps = 25/161 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ +EE M+L  + K+    ++   ++     G++ V+  RVK N  I+    +      
Sbjct: 32  VKGNEEGMKLRAYLKD-VQKLSSRLIKGAALDGRISVNNNRVKLNYVIKLDDEIAFDVEK 90

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
               +I  E+  +D               ++YEDS + V NK  G+ V        + +G
Sbjct: 91  KESQNIEPEKMDID---------------VVYEDSDLIVVNKQPGMVVHPTKS---YPNG 132

Query: 132 FLKS----WVDSKGQK--PRLTHRLDQETSGILVVARTRAA 166
            L +    +   KG++   RL  RLD +TSG++++A+ + A
Sbjct: 133 TLANGLLYYFKEKGEQCIVRLVSRLDMDTSGLIIIAKNQFA 173


>gi|194467810|ref|ZP_03073796.1| pseudouridine synthase [Lactobacillus reuteri 100-23]
 gi|194452663|gb|EDX41561.1| pseudouridine synthase [Lactobacillus reuteri 100-23]
          Length = 238

 Score = 36.6 bits (83), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 72/165 (43%), Gaps = 21/165 (12%)

Query: 109 YVFNKPAGI--SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           Y+ NKP G+  S     G    +D    + +D   ++     RLD +T+GIL++    A 
Sbjct: 63  YLLNKPRGVISSAHDDKGRRTVVDIIHDADID---ERIYPVGRLDYDTTGILLLTNDGAL 119

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           A  L        ++K Y + V GI KN +       LK+  +G     VV    K    A
Sbjct: 120 ANKLMHP--KYEVEKTYVAKVEGIVKNDE-------LKQLRLG-----VVIDGRK-TKPA 164

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            S    +D  A+K   +++  H GR HQ++     +G P+   H+
Sbjct: 165 KSKLLNVDR-AKKTSLVQLTIHEGRNHQVKNMFKAVGHPVTKLHR 208


>gi|162454763|ref|YP_001617130.1| hypothetical protein sce6481 [Sorangium cellulosum 'So ce 56']
 gi|161165345|emb|CAN96650.1| hypothetical protein predicted by Glimmer/Critica [Sorangium
           cellulosum 'So ce 56']
          Length = 368

 Score = 36.6 bits (83), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 33/166 (19%), Positives = 66/166 (39%), Gaps = 31/166 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-------DKKRVKFNNRIQSG 62
           + +   +   RLD+      P +     +++   G+VRV         +R    +   +G
Sbjct: 57  ITITELDAGTRLDKLLVQLLPGLGRAGAKRLFSEGRVRVLGVGKSGAGRRASKGDVAAAG 116

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-- 120
           +V+ +            + +  ++S   T        ++L  D  + V NKPAG+     
Sbjct: 117 EVLEV------------DVEPTEASGAATPDPSAPLDVVLERDD-LVVVNKPAGVPTAPL 163

Query: 121 --GGSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILV 159
             G  G     +  +  + +  G     ++P L HRLD +TSG+++
Sbjct: 164 HPGERGTVA--NALVARYPEMAGIGFSPREPGLCHRLDTDTSGLVL 207


>gi|307328933|ref|ZP_07608102.1| pseudouridine synthase [Streptomyces violaceusniger Tu 4113]
 gi|306885443|gb|EFN16460.1| pseudouridine synthase [Streptomyces violaceusniger Tu 4113]
          Length = 366

 Score = 36.2 bits (82), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 59/252 (23%), Positives = 100/252 (39%), Gaps = 61/252 (24%)

Query: 29  YPHINFVNLQKIL--------RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +  +    LQK+L        R+ +  +D+ RV+ N +I + Q +R+ P         K+
Sbjct: 124 FGEVEGERLQKVLARAGMGSRRACEELIDQARVEVNGKIVTEQGLRVDPE--------KD 175

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG--FLKSWVD 138
           +  +D     T+   F            +  NKPAG+            DG   L  +V 
Sbjct: 176 EIKVDGLTVATQSYLF------------FALNKPAGVV-----STMEDPDGRQCLGDYVT 218

Query: 139 SKGQKPRLTH--RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKN-K 194
           ++  + RL H  RLD ET GI+++      A  LT       ++K Y + + G +P++  
Sbjct: 219 NR--ETRLFHVGRLDTETEGIILLTNHGELAHRLTHPRYG--VKKTYLAAIQGPLPRDLG 274

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K   +   L+  +   D+  VV+    G NY +                E+  H GR H 
Sbjct: 275 KRLKSGIELEDGYARADHFRVVQNT--GKNYLV----------------EVTLHEGRKHI 316

Query: 255 LRVHALHMGCPI 266
           +R      G P+
Sbjct: 317 VRRMLAEAGFPV 328


>gi|227544893|ref|ZP_03974942.1| pseudouridylate synthase [Lactobacillus reuteri CF48-3A]
 gi|300910080|ref|ZP_07127540.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri SD2112]
 gi|227185105|gb|EEI65176.1| pseudouridylate synthase [Lactobacillus reuteri CF48-3A]
 gi|300892728|gb|EFK86088.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri SD2112]
          Length = 238

 Score = 35.8 bits (81), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 44/165 (26%), Positives = 72/165 (43%), Gaps = 21/165 (12%)

Query: 109 YVFNKPAGI--SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           Y+ NKP G+  S     G    +D    + +D   ++     RLD +T+GIL++    A 
Sbjct: 63  YLLNKPRGVISSAHDDKGRRTVVDIIHDAEID---ERIYPVGRLDYDTTGILLLTNDGAL 119

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           A  +        ++K Y + V GI KN +       LK+  +G     VV    K    A
Sbjct: 120 ANKMMHP--KYEVEKTYVAKVEGIVKNDE-------LKQLRLG-----VVIDGRK-TKPA 164

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            S    +D  A+K   +++  H GR HQ++     +G P+   H+
Sbjct: 165 KSKLLNVDR-AKKTSLVQLTIHEGRNHQVKNMFKAVGHPVTKLHR 208


>gi|435099|gb|AAA16215.1| ORFX homologue [Mycoplasma capricolum subsp. capricolum ATCC 27343]
          Length = 145

 Score = 35.8 bits (81), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 38/154 (24%), Positives = 73/154 (47%), Gaps = 22/154 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  +++N  L ++ K  +       + K +R+  ++++ KRV  N++    ++  +  V
Sbjct: 5   IVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRV--NDKNYLLKINDVVEV 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            ++   II++Q    S+VNL          ++YED+ I + NKP  + +     +   +D
Sbjct: 63  YDSNKPIIRDQFNYISNVNLD---------IVYEDNNILIVNKPNNLEMHSIYNLC--LD 111

Query: 131 GFLKSW-VDSKGQKPRL--------THRLDQETS 155
             +KS+ VD K     L         HRLD+ TS
Sbjct: 112 DMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTS 145


>gi|261329116|emb|CBH12095.1| hypothetical protein, conserved [Trypanosoma brucei gambiense
           DAL972]
          Length = 638

 Score = 35.8 bits (81), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 21/33 (63%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           P +GR HQ+R+H    G PIVGD  Y  N +G+
Sbjct: 483 PFSGRMHQIRIHLSDWGHPIVGDVTYNTNERGH 515


>gi|72390816|ref|XP_845702.1| hypothetical protein [Trypanosoma brucei TREU927]
 gi|62176177|gb|AAX70294.1| hypothetical protein, conserved [Trypanosoma brucei]
 gi|70802238|gb|AAZ12143.1| hypothetical protein, conserved [Trypanosoma brucei brucei strain
           927/4 GUTat10.1]
          Length = 638

 Score = 35.8 bits (81), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 21/33 (63%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           P +GR HQ+R+H    G PIVGD  Y  N +G+
Sbjct: 483 PFSGRMHQIRIHLSDWGHPIVGDVTYNTNERGH 515


>gi|313815673|gb|EFS53387.1| RNA pseudouridine synthase [Propionibacterium acnes HL059PA1]
 gi|315099393|gb|EFT71369.1| RNA pseudouridine synthase [Propionibacterium acnes HL059PA2]
          Length = 168

 Score = 35.8 bits (81), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 32/105 (30%), Positives = 51/105 (48%), Gaps = 15/105 (14%)

Query: 101 LLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGI 157
           +LY D +I V +KP  +S +  G  +   +   L++ +      P LT  HRLD+ T+G+
Sbjct: 64  ILYSDERILVVDKPHFLSSIPRGRHVLESVVVRLRTQLGL----PELTVAHRLDRVTAGV 119

Query: 158 LVVARTRAAAQHLTESFRMRRIQK-IYWSLVW-------GIPKNK 194
           L++ R R   +   E F  R + K I W   W       G+P+ K
Sbjct: 120 LLLTRERKWRRPYQEIFERREVVKSIGWWHPWCTIQLGRGLPRQK 164


>gi|256828202|ref|YP_003156930.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256577378|gb|ACU88514.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 281

 Score = 35.8 bits (81), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 64/282 (22%), Positives = 102/282 (36%), Gaps = 44/282 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLDR              + ++ +G+V VD +       I+ GQ +R+           
Sbjct: 14  IRLDRVLALQL-GFGVRRCRALIEAGRVLVDDRPCAKGALIRPGQHIRV----------- 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                   S+      D     L+  +       KP G+    G   A      L+S + 
Sbjct: 62  --------SLPEDAAPDCHDVRLVDRNESFAALAKPDGLHTVAGQEAAC-----LESCLP 108

Query: 139 SKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             G +   L +RLD  TSG+++ A  +  A          ++ K Y +L  G      EC
Sbjct: 109 GLGLEGWELLNRLDCLTSGLVLAAAEKRDAAAYKVWQDAGQVSKWYLALARG-EVATLEC 167

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYA-ISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
               L  K  +    V V    ++   +  +   + ID        L ++   GR HQ+R
Sbjct: 168 RGRILDDKRSV----VRVTADEDEPLRWTRVRALRQID----GNTLLLVKIFKGRRHQIR 219

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            H  H G P++GD  Y     G         LYLH   +D+P
Sbjct: 220 AHLAHAGHPLIGDPVYGVCEPGG--------LYLHHWRLDMP 253


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


Results from round 2




>gi|254780608|ref|YP_003065021.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Liberibacter asiaticus str. psy62]
 gi|254040285|gb|ACT57081.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Liberibacter asiaticus str. psy62]
          Length = 346

 Score =  496 bits (1277), Expect = e-138,   Method: Composition-based stats.
 Identities = 346/346 (100%), Positives = 346/346 (100%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ
Sbjct: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ
Sbjct: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ
Sbjct: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF
Sbjct: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP
Sbjct: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL 346
           EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL
Sbjct: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL 346


>gi|315121808|ref|YP_004062297.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Liberibacter solanacearum CLso-ZC1]
 gi|313495210|gb|ADR51809.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Liberibacter solanacearum CLso-ZC1]
          Length = 336

 Score =  397 bits (1019), Expect = e-108,   Method: Composition-based stats.
 Identities = 251/336 (74%), Positives = 292/336 (86%), Gaps = 1/336 (0%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  MT V+++++END ENMR DRWFK HYPHINF NLQK+LRSGQ+R+DK+RVK N+R+Q
Sbjct: 1   MLFMTCVKHIIIENDVENMRFDRWFKLHYPHINFGNLQKLLRSGQIRLDKRRVKSNDRVQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SGQVVRIPP+I+ L+H  +++  LDSSV+  K+S FLK+ILLYED+K+Y+FNKP GISVQ
Sbjct: 61  SGQVVRIPPIIDVLDHATEKRYSLDSSVDFLKNSAFLKNILLYEDNKLYIFNKPPGISVQ 120

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+ YHIDGFLKSW DSKGQKPRL HRLD+ETSGILVVARTRAAAQ LTESFRMRRI+
Sbjct: 121 GGSGVTYHIDGFLKSWSDSKGQKPRLIHRLDRETSGILVVARTRAAAQSLTESFRMRRIR 180

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIYWSLV G+P+NKKECI+ WL KK+ IGGDYV VV QNEKGA+YAISHFKVID F  KF
Sbjct: 181 KIYWSLVRGVPQNKKECISGWLFKKAKIGGDYVQVVDQNEKGAHYAISHFKVIDRFEYKF 240

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPH 299
           CWLEMQP+TGRTHQLRVHALH+G PIVGD KY   + K  F++ IQNKLYLHARY+D PH
Sbjct: 241 CWLEMQPYTGRTHQLRVHALHVGHPIVGDKKYRINDSKEIFSNHIQNKLYLHARYIDFPH 300

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
           PEGGRLQITAPLP HM KTWDS GFKY++++ IKRL
Sbjct: 301 PEGGRLQITAPLPVHMAKTWDSFGFKYNQDIDIKRL 336


>gi|163760834|ref|ZP_02167913.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE C [Hoeflea
           phototrophica DFL-43]
 gi|162281878|gb|EDQ32170.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE C [Hoeflea
           phototrophica DFL-43]
          Length = 329

 Score =  351 bits (902), Expect = 6e-95,   Method: Composition-based stats.
 Identities = 164/323 (50%), Positives = 229/323 (70%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  VQ   V+ DE  MRLDRWFK H+P + F  LQK+LRSGQ+RVD  RVK + R+Q GQ
Sbjct: 1   MAGVQLKQVDPDETGMRLDRWFKTHFPGLGFGQLQKLLRSGQIRVDGGRVKSDARLQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++      D L  +LL+EDSK+ VFNKPAG++VQGGS
Sbjct: 61  TVRIPPMGVDEKGSAP---LTAKTIRNRDDGDVLSQMLLHEDSKVLVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  ++D  L++W + KG+KPRL HRLD++T+G+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 118 GVTRNVDDMLEAWRNKKGEKPRLVHRLDRDTAGVLVVARTRGAAQALTAAFRERTTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P++++  I+ WL+K++   GD + V K  E GA++A+S++++I+  AQ  CWL
Sbjct: 178 WALVTGVPRDREGKISTWLVKEATDDGDRMRVAKHGEPGADHAVSYYRIIEKAAQNLCWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEG 302
           E++P+TGRTHQLRVH LH+G PI+GD KY  + K   F   +Q +L+L AR++ +PHP+G
Sbjct: 238 ELEPYTGRTHQLRVHCLHLGHPILGDPKYYDHDKNREFPGGMQKRLHLLARHISVPHPDG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           GRL +TAPLP HMV++W+ LGF 
Sbjct: 298 GRLSVTAPLPPHMVQSWNLLGFD 320


>gi|15965142|ref|NP_385495.1| ribosomal large subunit pseudouridine synthase C protein
           [Sinorhizobium meliloti 1021]
 gi|307314392|ref|ZP_07593998.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti BL225C]
 gi|307322745|ref|ZP_07602066.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti AK83]
 gi|15074322|emb|CAC45968.1| Probable ribosomal large subunit pseudouridine synthase C
           [Sinorhizobium meliloti 1021]
 gi|306891605|gb|EFN22470.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti AK83]
 gi|306899090|gb|EFN29732.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti BL225C]
          Length = 330

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 165/325 (50%), Positives = 230/325 (70%), Gaps = 2/325 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +++  V++DE  MRLDRWFK H+P + F  LQK+LRSGQ+RVD  R K + RIQ GQ
Sbjct: 1   MAGIEHRQVDSDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQIRVDGARAKSDTRIQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+        K   I    +  +   + L  ++L+ED+K+ V NKPAG++VQGGS
Sbjct: 61  TIRIPPLGVDPKE-AKSGPIGGRDLRQSPDGELLSRMVLHEDAKVIVLNKPAGLAVQGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HID  L++W   KG+KPRL HRLD++TSG+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 120 GVNRHIDKMLEAWTSQKGEKPRLVHRLDRDTSGVLVVARTRGAAQQLTAAFRERDTKKTY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD V + K  E GA++AIS++++++   Q   WL
Sbjct: 180 WALVRGVPRKREDKISTWLVKEPTPDGDRVRIAKHGEDGADHAISYYRIVEQAGQNLAWL 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA H+G PI+GD KY  A+    F   +QN+L+LHAR++D+PHP G
Sbjct: 240 EMEPYTGRTHQLRVHAAHIGHPIIGDPKYFEADVNWTFPGGMQNRLHLHARHIDIPHPNG 299

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           GRL+ITAPLP HMV++W+ LGF  +
Sbjct: 300 GRLKITAPLPQHMVQSWNLLGFDEN 324


>gi|260468522|ref|ZP_05813689.1| pseudouridine synthase, RluA family [Mesorhizobium opportunistum
           WSM2075]
 gi|259028678|gb|EEW29987.1| pseudouridine synthase, RluA family [Mesorhizobium opportunistum
           WSM2075]
          Length = 326

 Score =  350 bits (899), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 159/323 (49%), Positives = 231/323 (71%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + VE  E  MRLDRWFK H+P + F +LQK+LRSGQ+RVD  RVK ++R++ GQ
Sbjct: 1   MAGVEQITVEAGEAGMRLDRWFKTHFPGLGFGHLQKLLRSGQIRVDGGRVKADSRVEPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+         E  +   S+     +D L  +L++ED K++VFNKPAG++VQGGS
Sbjct: 61  VVRVPPLEVDKKG---ESPLTGHSIRNQGDADVLAKMLIHEDPKVFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  ++D  L++W + KG+KPRL HRLD++TSG+LVVARTR AA  L+E+FR R  +K Y
Sbjct: 118 GVTRNVDDMLEAWRNQKGEKPRLVHRLDRDTSGVLVVARTRLAAMKLSEAFRARETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P  +++ I+ WL+K+    GD V +    EKGA++A+S++++I+  AQ   WL
Sbjct: 178 WALVKGVPPKREDKISTWLIKEPTPDGDRVRIAAHGEKGADHAVSYYRIIEQAAQTMTWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++GCPI+GD KY  A+   +F   IQN+L+LHAR + +PHP+ 
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGCPIIGDPKYFEADTNWDFPGGIQNRLHLHARRIVIPHPDK 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G + +TAP+P HM ++W+ +GF 
Sbjct: 298 GFIDVTAPMPPHMRQSWNLIGFD 320


>gi|319783351|ref|YP_004142827.1| pseudouridine synthase, RluA family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317169239|gb|ADV12777.1| pseudouridine synthase, RluA family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 326

 Score =  350 bits (899), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 160/323 (49%), Positives = 229/323 (70%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + VE  E  MRLDRWFK H+P + F +LQK+LRSGQ+RVD  RVK + R++ GQ
Sbjct: 1   MAGVEQITVEAGEAGMRLDRWFKTHFPGLGFGHLQKLLRSGQIRVDGGRVKADTRVEPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP+         E  +   S+     +D L  +L++ED K++VFNKPAG++VQGGS
Sbjct: 61  MVRVPPLEVDKKG---ESALTGHSIRNQGDADVLSKMLIHEDPKVFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  ++D  L++W   KG+KPRL HRLD++TSG+LVVARTR AA  L+E+FR R  +K Y
Sbjct: 118 GVTRNVDDMLEAWRSPKGEKPRLVHRLDRDTSGVLVVARTRLAAMKLSEAFRARETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P  +++ I+ WL+K+    GD V V    EKGA++A+S+++VI+  AQ   WL
Sbjct: 178 WALVKGVPPKREDKISTWLIKEPTPDGDRVRVAAHGEKGADHAVSYYRVIEQAAQTMTWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++GCPI+GD KY  A+   +F   IQN+L+LHAR + +PHP+ 
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGCPILGDPKYFEADTNWDFPGGIQNRLHLHARRIIIPHPDK 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G + +TAP+P HM ++W+ +GF 
Sbjct: 298 GVIDVTAPMPPHMRQSWNLIGFD 320


>gi|222086089|ref|YP_002544621.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221723537|gb|ACM26693.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 332

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 169/323 (52%), Positives = 235/323 (72%), Gaps = 2/323 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK++RSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIEVEPDEAGMRLDRWFKVHFPGLGFGQLQKLMRSGQVRVDGGRVKTDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP ++      K   I +  +  +  +D L  +LL+ED K++V NKPAG++VQGGS
Sbjct: 61  IVRVPP-LDVDAKGPKSGPIGNKDMKHSSDADLLARMLLHEDEKVFVLNKPAGLAVQGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+D  L++W   KG+KPRL HRLD++TSG+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 120 GLTRHLDKMLEAWTSKKGEKPRLVHRLDRDTSGVLVVARTRGAAQKLTAAFRERDTKKTY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           WSLV G+P+  ++ I+ WL+K++   GD + + K  E GA++AI++++V++  AQ   WL
Sbjct: 180 WSLVKGVPRKHEDKISTWLVKEATADGDRMRIAKHGEDGADHAITYYRVLETAAQSLAWL 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALHMG PI+GD KY   +   +F   +QN+L+LHAR++D+PHP G
Sbjct: 240 EMEPYTGRTHQLRVHALHMGHPIIGDPKYFDDDHNWDFPGGVQNRLHLHARHIDIPHPNG 299

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           GRL+ITAPLP HMV+TW+ LG  
Sbjct: 300 GRLRITAPLPPHMVQTWNLLGLD 322


>gi|153009413|ref|YP_001370628.1| RluA family pseudouridine synthase [Ochrobactrum anthropi ATCC
           49188]
 gi|151561301|gb|ABS14799.1| pseudouridine synthase, RluA family [Ochrobactrum anthropi ATCC
           49188]
          Length = 326

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 158/325 (48%), Positives = 228/325 (70%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LRSGQVR+D  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDTGEAGMRLDRWFKVHYPGLGFGHLQKLLRSGQVRIDGSRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+      +     +   ++   +  D L  +LLYED K+YVFNKPAG++VQGGS
Sbjct: 61  TVRIPPLGVDEKAV---GPVTARTIRSQQDGDVLSQMLLYEDPKVYVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G++ H+DG L++W + KG+KPRL HR+D++TSG+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 118 GVSRHVDGMLEAWRNKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTTAFRERDTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+++    GD + V +  E  +++A+S++++I+       WL
Sbjct: 178 WALVKGVPRKREDKISTWLVREQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLTWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 298 GTIDVTAPLPPHMVQSWNLLGFDEE 322


>gi|13470583|ref|NP_102152.1| ribosomal large subunit pseudouridine synthase C [Mesorhizobium
           loti MAFF303099]
 gi|14021325|dbj|BAB47938.1| ribosomal large subunit pseudouridine synthase C [Mesorhizobium
           loti MAFF303099]
          Length = 326

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 161/323 (49%), Positives = 231/323 (71%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + VE  E  MRLDRWFK H+P + F +LQK+LRSGQ+RVD  RVK ++R++ GQ
Sbjct: 1   MAGVEQITVEAGEAGMRLDRWFKTHFPGLGFGHLQKLLRSGQIRVDGGRVKADSRVEPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVRIPP+         E  +   S+     +D L  +L++ED K++VFNKPAG++VQGGS
Sbjct: 61  VVRIPPLEVDKKG---ESALTGHSIRNQGDADVLAKMLIHEDPKVFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  ++D  L++W + KG+KPRL HRLD++TSG+LVVARTR AA  L+E+FR R  +K Y
Sbjct: 118 GVTRNVDDMLEAWRNQKGEKPRLVHRLDRDTSGVLVVARTRLAAMKLSEAFRARETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P  +++ I+ WL+K+    GD V V    EKGA++A+S++++I+  AQ   WL
Sbjct: 178 WALVKGVPPKREDKISTWLIKEPTEDGDRVRVAAHGEKGADHAVSYYRIIEQAAQTMTWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++GCPI+GD KY  A+   +F   IQN+L+LHAR + +PHP+ 
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGCPIIGDPKYFEADTNWDFPGGIQNRLHLHARRIIIPHPDK 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G + +TAP+P HM ++W+ +GF 
Sbjct: 298 GLIDVTAPMPPHMRQSWNLIGFD 320


>gi|325292801|ref|YP_004278665.1| ribosomal large subunit pseudouridine synthase C [Agrobacterium sp.
           H13-3]
 gi|325060654|gb|ADY64345.1| ribosomal large subunit pseudouridine synthase C [Agrobacterium sp.
           H13-3]
          Length = 329

 Score =  349 bits (896), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 175/323 (54%), Positives = 235/323 (72%), Gaps = 3/323 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK HYP + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEADEAGMRLDRWFKIHYPGLGFGQLQKLLRSGQVRVDGGRVKTDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PPV + L   +K   I    +  +   + L  +LL+ED K+ VFNKPAGI+VQGGS
Sbjct: 61  MVRVPPVDSDLK--VKSGPIGSRDLKHSADGELLARMLLHEDDKVLVFNKPAGIAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HRLD++TSG+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 119 GVNRHIDGLLEAWTSPKGEKPRLVHRLDRDTSGVLVVARTRGAAQKLTAAFRERDTKKTY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+  ++ I+ WL+K+    GD + + K  E+GA++AIS+++VID  AQ   WL
Sbjct: 179 WALVRGVPRKHQDKISTWLVKEQTPDGDRMRIAKHGEEGADHAISYYRVIDTAAQNLAWL 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALHMG PI+GD KY   +   +F   +Q +L+LHAR++D+PHP G
Sbjct: 239 EMEPYTGRTHQLRVHALHMGHPIIGDPKYYIDDPNWDFPGGVQKRLHLHARHIDIPHPNG 298

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           GRL+++APLP HMV+TW+ LG  
Sbjct: 299 GRLRVSAPLPPHMVQTWNLLGLD 321


>gi|326409020|gb|ADZ66085.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           M28]
 gi|326538730|gb|ADZ86945.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           M5-90]
          Length = 331

 Score =  348 bits (894), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 161/325 (49%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 6   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 65

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 66  AVRIPPLGVDEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 122

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K Y
Sbjct: 123 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTY 182

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WL
Sbjct: 183 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWL 242

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 243 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 302

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 303 GIIDVTAPLPPHMVQSWNLLGFDEE 327


>gi|239831992|ref|ZP_04680321.1| pseudouridine synthase, RluA family [Ochrobactrum intermedium LMG
           3301]
 gi|239824259|gb|EEQ95827.1| pseudouridine synthase, RluA family [Ochrobactrum intermedium LMG
           3301]
          Length = 326

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 158/325 (48%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LRSGQ+R+D  R K + R+Q+GQ
Sbjct: 1   MAVVEQKIVDTGEAGMRLDRWFKVHYPGLGFGHLQKLLRSGQIRIDGSRAKADTRVQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED K+YVFNKPAG++VQGGS
Sbjct: 61  TVRIPPLGVDEKAT---GPVTARTIRSQQDGDVLSQMLLYEDPKVYVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W + KG+KPRL HR+D++TSG+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 118 GVTRHIDGMLEAWRNKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTAAFRERDTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K     GD + V +  E  +++A+S++++I+       WL
Sbjct: 178 WALVKGVPRKREDKISTWLVKDQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLTWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 298 GIIDVTAPLPPHMVQSWNLLGFDEE 322


>gi|256061091|ref|ZP_05451246.1| pseudouridine synthase, RluA family protein [Brucella neotomae
           5K33]
 gi|261325093|ref|ZP_05964290.1| pseudouridine synthase [Brucella neotomae 5K33]
 gi|261301073|gb|EEY04570.1| pseudouridine synthase [Brucella neotomae 5K33]
          Length = 326

 Score =  348 bits (892), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 162/325 (49%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDASEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 61  AVRIPPLGVDEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K Y
Sbjct: 118 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +N+A+S++++I+       WL
Sbjct: 178 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSNHAVSYYRIIEKAGNNLAWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFLGGIQKRLHLHARRIRIPNPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 298 GIIDVTAPLPPHMVQSWNLLGFDEE 322


>gi|17987266|ref|NP_539900.1| ribosomal large subunit pseudouridine synthase C [Brucella
           melitensis bv. 1 str. 16M]
 gi|225627477|ref|ZP_03785514.1| pseudouridine synthase, RluA family protein [Brucella ceti str.
           Cudo]
 gi|17982942|gb|AAL52164.1| ribosomal large subunit pseudouridine synthase c [Brucella
           melitensis bv. 1 str. 16M]
 gi|225617482|gb|EEH14527.1| pseudouridine synthase, RluA family protein [Brucella ceti str.
           Cudo]
          Length = 343

 Score =  348 bits (892), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 161/325 (49%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 18  MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 77

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 78  AVRIPPLGVDEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 134

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K Y
Sbjct: 135 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTY 194

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WL
Sbjct: 195 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWL 254

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 255 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 314

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 315 GIIDVTAPLPPHMVQSWNLLGFDEE 339


>gi|116252313|ref|YP_768151.1| ribosomal large subunit pseudouridine synthase C [Rhizobium
           leguminosarum bv. viciae 3841]
 gi|115256961|emb|CAK08055.1| putative ribosomal large subunit pseudouridine synthase C
           [Rhizobium leguminosarum bv. viciae 3841]
          Length = 330

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 165/323 (51%), Positives = 231/323 (71%), Gaps = 3/323 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEPDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+   ++  +K   I    +  +   + L  ++L+ED K+ V NKP G++VQGGS
Sbjct: 61  TVRVPPM--DVDAKLKSGPIAGKDLKHSTDFELLSRMVLHEDEKVIVLNKPPGLAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K Y
Sbjct: 119 GVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRERDTKKTY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+  ++ I+ WL+K+    GD + + K  E GA++AIS ++V++  AQ   WL
Sbjct: 179 WALVKGVPRKHEDKISTWLVKEPTADGDRMRIAKHGEDGADHAISFYRVLETAAQNLAWL 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALH+G PI+GD KY   +   +F   +Q KL+LHAR++D+PHP G
Sbjct: 239 EMEPYTGRTHQLRVHALHIGHPIIGDPKYFDDDPNWDFPGGVQKKLHLHARHIDIPHPSG 298

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           GRL+++APLP+HMV+TW+ LG  
Sbjct: 299 GRLRVSAPLPSHMVQTWNLLGLD 321


>gi|254719077|ref|ZP_05180888.1| ribosomal large subunit pseudouridine synthase C [Brucella sp.
           83/13]
 gi|265984067|ref|ZP_06096802.1| pseudouridine synthase [Brucella sp. 83/13]
 gi|306838360|ref|ZP_07471205.1| pseudouridine synthase, RluA family [Brucella sp. NF 2653]
 gi|306843875|ref|ZP_07476470.1| pseudouridine synthase, RluA family [Brucella sp. BO1]
 gi|264662659|gb|EEZ32920.1| pseudouridine synthase [Brucella sp. 83/13]
 gi|306275630|gb|EFM57354.1| pseudouridine synthase, RluA family [Brucella sp. BO1]
 gi|306406500|gb|EFM62734.1| pseudouridine synthase, RluA family [Brucella sp. NF 2653]
          Length = 326

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 162/325 (49%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LRSGQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRSGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 61  AVRIPPLGVDEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K Y
Sbjct: 118 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WL
Sbjct: 178 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 298 GIIDVTAPLPPHMVQSWNLLGFDEE 322


>gi|159184771|ref|NP_354476.2| ribosomal large subunit pseudouridine synthase C [Agrobacterium
           tumefaciens str. C58]
 gi|159140059|gb|AAK87261.2| ribosomal large subunit pseudouridine synthase C [Agrobacterium
           tumefaciens str. C58]
          Length = 329

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 174/323 (53%), Positives = 234/323 (72%), Gaps = 3/323 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK HYP + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEADEAGMRLDRWFKIHYPGLGFGQLQKLLRSGQVRVDGGRVKTDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PPV + +    K   I    +  +   + L  +LL+ED K+ VFNKPAGI+VQGGS
Sbjct: 61  MVRVPPVDSDMKT--KTGPIGSKDLKHSADGELLARMLLHEDDKVLVFNKPAGIAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HRLD++TSG+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 119 GVNRHIDGLLEAWTSPKGEKPRLVHRLDRDTSGVLVVARTRGAAQKLTAAFRERDTKKTY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+  ++ I+ WL+K+    GD + + K  E+GA++AIS+++VID  AQ   WL
Sbjct: 179 WALVRGVPRKHQDKISTWLVKEQTPDGDRMRIAKHGEEGADHAISYYRVIDTAAQNLAWL 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALHMG PI+GD KY   +   +F   +Q +L+LHAR++D+PHP G
Sbjct: 239 EMEPYTGRTHQLRVHALHMGHPIIGDPKYYIDDPNWDFPGGVQKRLHLHARHIDIPHPNG 298

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           GRL+++APLP HMV+TW+ LG  
Sbjct: 299 GRLRVSAPLPPHMVQTWNLLGLD 321


>gi|241204807|ref|YP_002975903.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240858697|gb|ACS56364.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 330

 Score =  347 bits (890), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 167/323 (51%), Positives = 230/323 (71%), Gaps = 3/323 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEPDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+   ++  +K   I    +  +     L  ++L+ED K+ V NKP G++VQGGS
Sbjct: 61  TVRVPPM--DVDAKLKSGPIAGKDLKHSSDFQLLSRMVLHEDDKVIVLNKPPGLAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K Y
Sbjct: 119 GVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRERDTKKTY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+  ++ I+ WL+K+    GD + + K  E GA++AIS ++V++  AQ   WL
Sbjct: 179 WALVKGVPRKHEDKISTWLVKEPTADGDRMRIAKHGEDGADHAISFYRVLETAAQNLAWL 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALH+G PI+GD KY   +   +F   +Q KL+LHAR++D+PHP G
Sbjct: 239 EMEPYTGRTHQLRVHALHIGHPIIGDPKYFDDDPNWDFPGGVQKKLHLHARHIDIPHPSG 298

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           GRL+I+APLPAHMV+TW+ LG  
Sbjct: 299 GRLRISAPLPAHMVQTWNLLGLD 321


>gi|260754735|ref|ZP_05867083.1| pseudouridine synthase [Brucella abortus bv. 6 str. 870]
 gi|260757958|ref|ZP_05870306.1| pseudouridine synthase [Brucella abortus bv. 4 str. 292]
 gi|260761781|ref|ZP_05874124.1| pseudouridine synthase [Brucella abortus bv. 2 str. 86/8/59]
 gi|260883756|ref|ZP_05895370.1| pseudouridine synthase [Brucella abortus bv. 9 str. C68]
 gi|297248324|ref|ZP_06932042.1| ribosomal large subunit pseudouridine synthase C [Brucella abortus
           bv. 5 str. B3196]
 gi|260668276|gb|EEX55216.1| pseudouridine synthase [Brucella abortus bv. 4 str. 292]
 gi|260672213|gb|EEX59034.1| pseudouridine synthase [Brucella abortus bv. 2 str. 86/8/59]
 gi|260674843|gb|EEX61664.1| pseudouridine synthase [Brucella abortus bv. 6 str. 870]
 gi|260873284|gb|EEX80353.1| pseudouridine synthase [Brucella abortus bv. 9 str. C68]
 gi|297175493|gb|EFH34840.1| ribosomal large subunit pseudouridine synthase C [Brucella abortus
           bv. 5 str. B3196]
          Length = 331

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 161/325 (49%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 6   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 65

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 66  AVRIPPLGVDEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 122

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K Y
Sbjct: 123 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTY 182

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WL
Sbjct: 183 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWL 242

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 243 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 302

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 303 GIIDVTAPLPLHMVQSWNLLGFDEE 327


>gi|52430461|ref|YP_089633.1| ribosomal large subunit pseudouridine synthase C [Brucella suis
           1330]
 gi|47524242|gb|AAT34905.1| ribosomal large subunit pseudouridine synthase C [Brucella suis
           1330]
          Length = 326

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 161/325 (49%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 61  AVRIPPLGVDEK---AADPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K Y
Sbjct: 118 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WL
Sbjct: 178 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 298 GIIDVTAPLPPHMVQSWNLLGFDEE 322


>gi|225852505|ref|YP_002732738.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           ATCC 23457]
 gi|254693715|ref|ZP_05155543.1| ribosomal large subunit pseudouridine synthase C [Brucella abortus
           bv. 3 str. Tulya]
 gi|254706805|ref|ZP_05168633.1| ribosomal large subunit pseudouridine synthase C [Brucella
           pinnipedialis M163/99/10]
 gi|254710085|ref|ZP_05171896.1| ribosomal large subunit pseudouridine synthase C [Brucella
           pinnipedialis B2/94]
 gi|254714086|ref|ZP_05175897.1| ribosomal large subunit pseudouridine synthase C [Brucella ceti
           M644/93/1]
 gi|254716858|ref|ZP_05178669.1| ribosomal large subunit pseudouridine synthase C [Brucella ceti
           M13/05/1]
 gi|256031581|ref|ZP_05445195.1| ribosomal large subunit pseudouridine synthase C [Brucella
           pinnipedialis M292/94/1]
 gi|256044659|ref|ZP_05447563.1| ribosomal large subunit pseudouridine synthase C [Brucella
           melitensis bv. 1 str. Rev.1]
 gi|256113553|ref|ZP_05454373.1| ribosomal large subunit pseudouridine synthase C [Brucella
           melitensis bv. 3 str. Ether]
 gi|256159719|ref|ZP_05457466.1| ribosomal large subunit pseudouridine synthase C [Brucella ceti
           M490/95/1]
 gi|256254981|ref|ZP_05460517.1| ribosomal large subunit pseudouridine synthase C [Brucella ceti
           B1/94]
 gi|256264005|ref|ZP_05466537.1| pseudouridine synthase [Brucella melitensis bv. 2 str. 63/9]
 gi|256369422|ref|YP_003106930.1| ribosomal large subunit pseudouridine synthase C [Brucella microti
           CCM 4915]
 gi|260168711|ref|ZP_05755522.1| ribosomal large subunit pseudouridine synthase C [Brucella sp.
           F5/99]
 gi|260564005|ref|ZP_05834491.1| pseudouridine synthase [Brucella melitensis bv. 1 str. 16M]
 gi|261213987|ref|ZP_05928268.1| pseudouridine synthase [Brucella abortus bv. 3 str. Tulya]
 gi|261218659|ref|ZP_05932940.1| pseudouridine synthase [Brucella ceti M13/05/1]
 gi|261222167|ref|ZP_05936448.1| pseudouridine synthase [Brucella ceti B1/94]
 gi|261314272|ref|ZP_05953469.1| pseudouridine synthase [Brucella pinnipedialis M163/99/10]
 gi|261317634|ref|ZP_05956831.1| pseudouridine synthase [Brucella pinnipedialis B2/94]
 gi|261321843|ref|ZP_05961040.1| pseudouridine synthase [Brucella ceti M644/93/1]
 gi|261758188|ref|ZP_06001897.1| pseudouridine synthase [Brucella sp. F5/99]
 gi|265988669|ref|ZP_06101226.1| pseudouridine synthase [Brucella pinnipedialis M292/94/1]
 gi|265991083|ref|ZP_06103640.1| pseudouridine synthase [Brucella melitensis bv. 1 str. Rev.1]
 gi|265994920|ref|ZP_06107477.1| pseudouridine synthase [Brucella melitensis bv. 3 str. Ether]
 gi|265998132|ref|ZP_06110689.1| pseudouridine synthase [Brucella ceti M490/95/1]
 gi|225640870|gb|ACO00784.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           ATCC 23457]
 gi|255999582|gb|ACU47981.1| ribosomal large subunit pseudouridine synthase C [Brucella microti
           CCM 4915]
 gi|260154021|gb|EEW89113.1| pseudouridine synthase [Brucella melitensis bv. 1 str. 16M]
 gi|260915594|gb|EEX82455.1| pseudouridine synthase [Brucella abortus bv. 3 str. Tulya]
 gi|260920751|gb|EEX87404.1| pseudouridine synthase [Brucella ceti B1/94]
 gi|260923748|gb|EEX90316.1| pseudouridine synthase [Brucella ceti M13/05/1]
 gi|261294533|gb|EEX98029.1| pseudouridine synthase [Brucella ceti M644/93/1]
 gi|261296857|gb|EEY00354.1| pseudouridine synthase [Brucella pinnipedialis B2/94]
 gi|261303298|gb|EEY06795.1| pseudouridine synthase [Brucella pinnipedialis M163/99/10]
 gi|261738172|gb|EEY26168.1| pseudouridine synthase [Brucella sp. F5/99]
 gi|262552600|gb|EEZ08590.1| pseudouridine synthase [Brucella ceti M490/95/1]
 gi|262766033|gb|EEZ11822.1| pseudouridine synthase [Brucella melitensis bv. 3 str. Ether]
 gi|263001867|gb|EEZ14442.1| pseudouridine synthase [Brucella melitensis bv. 1 str. Rev.1]
 gi|263094149|gb|EEZ18071.1| pseudouridine synthase [Brucella melitensis bv. 2 str. 63/9]
 gi|264660866|gb|EEZ31127.1| pseudouridine synthase [Brucella pinnipedialis M292/94/1]
          Length = 326

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 161/325 (49%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 61  AVRIPPLGVDEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K Y
Sbjct: 118 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WL
Sbjct: 178 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 298 GIIDVTAPLPPHMVQSWNLLGFDEE 322


>gi|254701751|ref|ZP_05163579.1| ribosomal large subunit pseudouridine synthase C [Brucella suis bv.
           5 str. 513]
 gi|261752304|ref|ZP_05996013.1| pseudouridine synthase [Brucella suis bv. 5 str. 513]
 gi|261742057|gb|EEY29983.1| pseudouridine synthase [Brucella suis bv. 5 str. 513]
          Length = 326

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 161/325 (49%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 61  AVRIPPLGVDEKAASP---MTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K Y
Sbjct: 118 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WL
Sbjct: 178 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 298 GIIDVTAPLPPHMVQSWNLLGFDEE 322


>gi|163843268|ref|YP_001627672.1| RluA family pseudouridine synthase [Brucella suis ATCC 23445]
 gi|163673991|gb|ABY38102.1| pseudouridine synthase, RluA family [Brucella suis ATCC 23445]
          Length = 326

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 160/325 (49%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 61  AVRIPPLGVDEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LV+ARTR AAQ LT SFR R  +K Y
Sbjct: 118 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVLARTRGAAQALTASFRERDTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WL
Sbjct: 178 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 298 GIIDVTAPLPPHMVQSWNLLGFDEE 322


>gi|190891935|ref|YP_001978477.1| RNA-pseudouridine synthase, ribosomal large subunit C [Rhizobium
           etli CIAT 652]
 gi|190697214|gb|ACE91299.1| RNA-pseudouridine synthase protein, ribosomal large subunit C
           [Rhizobium etli CIAT 652]
          Length = 330

 Score =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 168/323 (52%), Positives = 231/323 (71%), Gaps = 3/323 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEPDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+   ++  +K   I    +  +   D L  ++L+ED K+ V NKP GI+VQGGS
Sbjct: 61  TVRVPPL--DVDAKLKSGPIAGKDLKHSSDFDLLSRMVLHEDEKVIVLNKPPGIAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K Y
Sbjct: 119 GVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRERDTKKTY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+  ++ I+ WL+K++   GD + + K  E GA++AIS ++V++  AQ   WL
Sbjct: 179 WALVKGVPRKHEDKISTWLVKEATADGDRMRIAKHGEDGADHAISFYRVLETAAQNLAWL 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALH+G PI+GD KY   +   +F   IQ KL+LHAR++D+PHP G
Sbjct: 239 EMEPYTGRTHQLRVHALHIGHPIIGDPKYFDDDPNWDFPGGIQKKLHLHARHIDIPHPSG 298

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           GRL+++APLP HMV+TW+ LG  
Sbjct: 299 GRLRVSAPLPPHMVQTWNLLGLD 321


>gi|237815424|ref|ZP_04594422.1| pseudouridine synthase, RluA family [Brucella abortus str. 2308 A]
 gi|237790261|gb|EEP64471.1| pseudouridine synthase, RluA family [Brucella abortus str. 2308 A]
          Length = 343

 Score =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 161/325 (49%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 18  MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 77

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 78  AVRIPPLGVDEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 134

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K Y
Sbjct: 135 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTY 194

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WL
Sbjct: 195 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWL 254

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 255 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 314

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 315 GIIDVTAPLPLHMVQSWNLLGFDEE 339


>gi|161618953|ref|YP_001592840.1| RluA family pseudouridine synthase [Brucella canis ATCC 23365]
 gi|254704293|ref|ZP_05166121.1| RluA family pseudouridine synthase [Brucella suis bv. 3 str. 686]
 gi|260566460|ref|ZP_05836930.1| pseudouridine synthase [Brucella suis bv. 4 str. 40]
 gi|261754961|ref|ZP_05998670.1| pseudouridine synthase [Brucella suis bv. 3 str. 686]
 gi|161335764|gb|ABX62069.1| pseudouridine synthase, RluA family [Brucella canis ATCC 23365]
 gi|260155978|gb|EEW91058.1| pseudouridine synthase [Brucella suis bv. 4 str. 40]
 gi|261744714|gb|EEY32640.1| pseudouridine synthase [Brucella suis bv. 3 str. 686]
          Length = 326

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 160/325 (49%), Positives = 224/325 (68%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 61  AVRIPPLGVDEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K Y
Sbjct: 118 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WL
Sbjct: 178 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY   +    F   IQ +L+LHAR + +P+P G
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEVDQNWEFPGGIQKRLHLHARRIRIPNPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 298 GIIDVTAPLPPHMVQSWNLLGFDEE 322


>gi|327191042|gb|EGE58095.1| RNA-pseudouridine synthase protein, ribosomal large subunit C
           [Rhizobium etli CNPAF512]
          Length = 330

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 166/323 (51%), Positives = 231/323 (71%), Gaps = 3/323 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEPDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+   ++  +K   I    +  +   + L  ++L+ED K+ V NKP GI+VQGGS
Sbjct: 61  TVRVPPL--DVDAKLKSGPIAGKDLKHSSDFELLSRMVLHEDDKVIVLNKPPGIAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K Y
Sbjct: 119 GVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRERDTKKTY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+  ++ I+ WL+K++   GD + + K  E GA++AIS ++V++  AQ   W+
Sbjct: 179 WALVKGVPRKHEDKISTWLVKEATADGDRMRIAKHGEDGADHAISFYRVLETAAQNLAWI 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALH+G PI+GD KY   +   +F   IQ KL+LHAR++D+PHP G
Sbjct: 239 EMEPYTGRTHQLRVHALHIGHPIIGDPKYFDDDPNWDFPGGIQKKLHLHARHIDIPHPSG 298

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           GRL+++APLP HMV+TW+ LG  
Sbjct: 299 GRLRVSAPLPPHMVQTWNLLGLD 321


>gi|294852409|ref|ZP_06793082.1| ribosomal large subunit pseudouridine synthase C [Brucella sp. NVSL
           07-0026]
 gi|294820998|gb|EFG37997.1| ribosomal large subunit pseudouridine synthase C [Brucella sp. NVSL
           07-0026]
          Length = 331

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 159/325 (48%), Positives = 224/325 (68%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 6   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 65

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 66  AVRIPPLGVDEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 122

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K Y
Sbjct: 123 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTY 182

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++++       WL
Sbjct: 183 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRILEKAGNNLAWL 242

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 243 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 302

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + + APLP HMV++W+ LGF  +
Sbjct: 303 GIIDVMAPLPPHMVQSWNLLGFDEE 327


>gi|62289923|ref|YP_221716.1| ribosomal large subunit pseudouridine synthase C [Brucella abortus
           bv. 1 str. 9-941]
 gi|82699851|ref|YP_414425.1| RNA-binding protein S4 [Brucella melitensis biovar Abortus 2308]
 gi|189024165|ref|YP_001934933.1| Pseudouridine synthase [Brucella abortus S19]
 gi|254689230|ref|ZP_05152484.1| Pseudouridine synthase [Brucella abortus bv. 6 str. 870]
 gi|254697365|ref|ZP_05159193.1| Pseudouridine synthase [Brucella abortus bv. 2 str. 86/8/59]
 gi|254730263|ref|ZP_05188841.1| Pseudouridine synthase [Brucella abortus bv. 4 str. 292]
 gi|256257480|ref|ZP_05463016.1| Pseudouridine synthase [Brucella abortus bv. 9 str. C68]
 gi|260545328|ref|ZP_05821069.1| pseudouridine synthase [Brucella abortus NCTC 8038]
 gi|62196055|gb|AAX74355.1| ribosomal large subunit pseudouridine synthase C [Brucella abortus
           bv. 1 str. 9-941]
 gi|82615952|emb|CAJ10975.1| RNA-binding S4:Pseudouridine synthase:Pseudouridine synthase,
           Rlu:Pseudouridine synthase, RluD [Brucella melitensis
           biovar Abortus 2308]
 gi|189019737|gb|ACD72459.1| Pseudouridine synthase [Brucella abortus S19]
 gi|260096735|gb|EEW80610.1| pseudouridine synthase [Brucella abortus NCTC 8038]
          Length = 326

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 161/325 (49%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V+  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ
Sbjct: 1   MAGVEQKIVDAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+            +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGS
Sbjct: 61  AVRIPPLGVDEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K Y
Sbjct: 118 GVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WL
Sbjct: 178 WALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P G
Sbjct: 238 EMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G + +TAPLP HMV++W+ LGF  +
Sbjct: 298 GIIDVTAPLPLHMVQSWNLLGFDEE 322


>gi|150396240|ref|YP_001326707.1| RluA family pseudouridine synthase [Sinorhizobium medicae WSM419]
 gi|150027755|gb|ABR59872.1| pseudouridine synthase, RluA family [Sinorhizobium medicae WSM419]
          Length = 330

 Score =  345 bits (884), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 160/325 (49%), Positives = 229/325 (70%), Gaps = 2/325 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +++  V++DE  MRLDRWFK H+P + F  LQK+LRSGQ+RVD  R K + RIQ GQ
Sbjct: 1   MAGIEHRQVDSDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQIRVDGARAKSDTRIQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+        K   I    +  +   + L  ++L+ED+K+ V NKP G++VQGGS
Sbjct: 61  TIRIPPLGVDPKE-KKTGPIGGRDLRQSPDGELLSRMVLHEDAKVIVLNKPPGLAVQGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K Y
Sbjct: 120 GVNRHIDKMLEAWTSQKGEKPRLVHRLDRDTSGVLVIARTRGAAQQLTAAFRERDTKKTY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ +++ I+ W++K+    GD V + K  E GA++AIS +++++   Q   WL
Sbjct: 180 WALVRGVPRKREDKISTWVVKEQTPDGDRVRIAKHGEDGADHAISFYRIVEQAGQNLAWL 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA H+G PI+GD KY  A+    F   +QN+L+LHAR++D+PHP G
Sbjct: 240 EMEPYTGRTHQLRVHAAHIGHPIIGDPKYFEADVNWTFPGGMQNRLHLHARHIDIPHPNG 299

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           GRL++TAPLP HM+++W+ LGF+ +
Sbjct: 300 GRLKVTAPLPQHMMQSWNLLGFEEN 324


>gi|209549478|ref|YP_002281395.1| pseudouridine synthase [Rhizobium leguminosarum bv. trifolii
           WSM2304]
 gi|209535234|gb|ACI55169.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 329

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 167/323 (51%), Positives = 227/323 (70%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEADEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+        K   I    +  +   + L  ++L+ED K+ V NKP GI+VQGGS
Sbjct: 61  TVRVPPLDVDAK---KSGPIAGKDLKHSSDFELLSRMVLHEDDKVIVLNKPPGIAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K Y
Sbjct: 118 GVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRERDTKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+  ++ I+ WL+K+    GD + + K  E GA++AIS ++VI+  AQ   WL
Sbjct: 178 WALVKGVPRKHEDKISTWLVKEPTADGDRMRIAKHGEDGADHAISFYRVIETAAQNLAWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALH+G PI+GD KY   +   +F   +Q KL+LHAR++D+PHP G
Sbjct: 238 EMEPYTGRTHQLRVHALHIGHPIIGDPKYFDDDPNWDFPGGVQKKLHLHARHIDIPHPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           GRL+++APLP HMV+TW+ LG  
Sbjct: 298 GRLRVSAPLPPHMVQTWNLLGLD 320


>gi|227821788|ref|YP_002825758.1| ribosomal large subunit pseudouridine synthase C [Sinorhizobium
           fredii NGR234]
 gi|227340787|gb|ACP25005.1| ribosomal large subunit pseudouridine synthase C [Sinorhizobium
           fredii NGR234]
          Length = 330

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 163/325 (50%), Positives = 228/325 (70%), Gaps = 2/325 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +++  V+ DE  MRLDRWFK HYP + F  LQK+LRSGQ+RVD  R K + R+Q GQ
Sbjct: 1   MAGIEHRQVDGDEAGMRLDRWFKVHYPGLGFGPLQKLLRSGQIRVDGARAKSDTRVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP+        K   I    +  +   D L  ++L+ED+K+ V NKPAG++VQGGS
Sbjct: 61  TIRVPPLGVDAKDT-KTGPIGGRDLRHSSDGDLLSRMVLHEDAKVIVLNKPAGLAVQGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G++ HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +KIY
Sbjct: 120 GVSRHIDKMLEAWTSQKGEKPRLVHRLDRDTSGVLVIARTRGAAQQLTAAFRERDTRKIY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           WSLV G+P+ +++ I+ WL+K+    GD + + K  + GA++AIS++++++   Q   WL
Sbjct: 180 WSLVKGVPRKREDRISTWLVKEQTPDGDRMRIAKHGDDGADHAISYYRIVEQAGQNLAWL 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA H+G PI+GD KY  A+    F   IQN+L+LHAR +D+PHP G
Sbjct: 240 EMEPYTGRTHQLRVHAAHIGHPIIGDPKYFEADVNWTFPGGIQNRLHLHARCIDIPHPNG 299

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           GRL++TAPLP HMV++W+ LG    
Sbjct: 300 GRLKVTAPLPPHMVQSWNLLGLDES 324


>gi|222148667|ref|YP_002549624.1| ribosomal large subunit pseudouridine synthase C [Agrobacterium
           vitis S4]
 gi|221735653|gb|ACM36616.1| ribosomal large subunit pseudouridine synthase C [Agrobacterium
           vitis S4]
          Length = 330

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 164/325 (50%), Positives = 230/325 (70%), Gaps = 2/325 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ V  DE  MRLDRWFK HYP + F  LQK++RSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHITVGPDEAGMRLDRWFKIHYPGLGFGPLQKLMRSGQVRVDGGRVKTDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+ +      K   I    +      + L  +LL+ED K++V NKPAG++VQGGS
Sbjct: 61  VVRVPPM-DVDAKTPKSGPIASHDLKHAGDGELLARMLLHEDEKVFVLNKPAGLAVQGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HID  L++W   KG+KPRL HRLD++TSG+LVVARTR AAQ LT +FR R  +K Y
Sbjct: 120 GLNRHIDQMLEAWTSKKGEKPRLVHRLDRDTSGVLVVARTRGAAQKLTAAFRERDTKKTY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+   + I+ W++K+    GD + + +  E GA++A+S+++V++  AQ   WL
Sbjct: 180 WALVKGVPRKHDDKISTWVVKEQTEDGDRMRIARHGEDGADHAVSYYRVLETAAQSLAWL 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLR+HALH+G PI+GD KY   +   +F   +Q +L+LHAR++D+PHP+G
Sbjct: 240 EMEPYTGRTHQLRLHALHIGHPIIGDPKYYIDDPNWDFPGGVQKRLHLHARHIDIPHPDG 299

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           GRL+ITAPLP HMV+TW+ LG   +
Sbjct: 300 GRLRITAPLPPHMVQTWNLLGLDME 324


>gi|114704677|ref|ZP_01437585.1| ribosomal large subunit pseudouridine synthase C [Fulvimarina
           pelagi HTCC2506]
 gi|114539462|gb|EAU42582.1| ribosomal large subunit pseudouridine synthase C [Fulvimarina
           pelagi HTCC2506]
          Length = 328

 Score =  339 bits (870), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 156/326 (47%), Positives = 222/326 (68%), Gaps = 2/326 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   V++DE  +RLDRWFK HYP + F  LQK+LRSGQ+RVD  R K + R+  GQ
Sbjct: 1   MAAVEQRRVDDDEAGLRLDRWFKLHYPGLAFGQLQKLLRSGQIRVDGGRAKSDTRVAPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP +   +       +  +++      D L  +++YED K+ VFNKPAG++VQGGS
Sbjct: 61  MVRVPP-LATDSKTSTNHPLTANTIKGRPDGDVLSQMVIYEDEKVIVFNKPAGLAVQGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+A H+D  L++W + KG+KPRL HRLD++TSGILVVARTR AA  LT++FR R  +K+Y
Sbjct: 120 GVARHVDDMLEAWRNKKGEKPRLVHRLDRDTSGILVVARTRGAATALTKAFRERDTKKLY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++V G+P  K+  I+ +L K+    GD + + +  ++GA++A+SH++VID  AQ F WL
Sbjct: 180 WAVVKGVPAKKEGRISTYLKKEQTPDGDRMRIARHGDEGADHALSHYRVIDQVAQNFAWL 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           E++PHTGRTHQLRVHA H+G PI+GD KY   +    F   +Q +L+LHAR + +PHP G
Sbjct: 240 ELEPHTGRTHQLRVHAAHIGHPILGDPKYFEHDTNWEFPGGVQMRLHLHARRLVIPHPSG 299

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDR 328
           G +   APLP HM +T++  GF    
Sbjct: 300 GMIDQIAPLPQHMRQTFNLFGFDEAE 325


>gi|121602476|ref|YP_989029.1| RluA family pseudouridine synthase [Bartonella bacilliformis KC583]
 gi|120614653|gb|ABM45254.1| pseudouridine synthase, RluA family [Bartonella bacilliformis
           KC583]
          Length = 327

 Score =  339 bits (869), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 168/325 (51%), Positives = 227/325 (69%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++   VE DE  MRLDRWFK HYP + F  LQKILRSGQVRVD  RVK N R+ +GQ
Sbjct: 1   MVNIKIKNVEEDENGMRLDRWFKVHYPGLGFGYLQKILRSGQVRVDGGRVKANMRLVTGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+P         I    I    ++     D LK +LLYED KI+VFNKPAG++VQGGS
Sbjct: 61  SIRVPSFFIESKRNIS---ITSKVISQQDDGDLLKKMLLYEDPKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+DG L++W + KG+KPRL HRLD+ETSG+LVVAR+R+AAQ LT +FR R ++KIY
Sbjct: 118 GLTRHVDGMLEAWRNKKGEKPRLVHRLDRETSGLLVVARSRSAAQALTAAFRTREMKKIY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ K+E I+ W+ K++   GD + V +  E  AN+A+S+++++D  A+   WL
Sbjct: 178 WALVRGVPRKKQEKISTWMAKETTAQGDKMRVCEHGELDANHAVSYYRILDTRARALSWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA H+G PI+GD KY  ++        +QN+L+LHAR + +PHP G
Sbjct: 238 EMEPYTGRTHQLRVHASHIGHPIIGDSKYFFSDSNWELPGGMQNRLHLHARRIRIPHPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G L ITAPLP HMV++++ L F   
Sbjct: 298 GILDITAPLPPHMVQSFNLLAFNES 322


>gi|148560154|ref|YP_001258940.1| ribosomal large subunit pseudouridine synthase C [Brucella ovis
           ATCC 25840]
 gi|148371411|gb|ABQ61390.1| ribosomal large subunit pseudouridine synthase C [Brucella ovis
           ATCC 25840]
          Length = 318

 Score =  338 bits (867), Expect = 8e-91,   Method: Composition-based stats.
 Identities = 158/316 (50%), Positives = 221/316 (69%), Gaps = 4/316 (1%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           +  E  MRLDRWFK HYP + F +LQK+LR+GQVRVD  R K + RIQ+GQ VRIPP+  
Sbjct: 2   DAGEAGMRLDRWFKIHYPGLGFGHLQKLLRAGQVRVDGGRAKADTRIQAGQAVRIPPLGV 61

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                     +   ++   +  D L  +LLYED KI+VFNKPAG++VQGGSG+  HIDG 
Sbjct: 62  DEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAVQGGSGVTRHIDGM 118

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L++W  +KG+KPRL HR+D++TSG+LVVARTR AAQ LT SFR R  +K YW+LV G+P+
Sbjct: 119 LEAWRSTKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERDTKKTYWALVKGVPR 178

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +++ I+ WL+K+    GD + V +  E  +++A+S++++I+       WLEM+P+TGRT
Sbjct: 179 KREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHAVSYYRIIEKAGNNLAWLEMEPYTGRT 238

Query: 253 HQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           HQLRVHA ++G PI+GD KY  A+    F   IQ +L+LHAR + +P+P GG + +TAPL
Sbjct: 239 HQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQKRLHLHARRIRIPNPSGGIIDVTAPL 298

Query: 312 PAHMVKTWDSLGFKYD 327
           P HMV++W+ LGF  +
Sbjct: 299 PPHMVQSWNLLGFDEE 314


>gi|110634000|ref|YP_674208.1| ribosomal large subunit pseudouridine synthase C [Mesorhizobium sp.
           BNC1]
 gi|110284984|gb|ABG63043.1| ribosomal large subunit pseudouridine synthase C [Chelativorans sp.
           BNC1]
          Length = 327

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 153/323 (47%), Positives = 223/323 (69%), Gaps = 5/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V++ E  MRLDRWFK HYP + F  LQK+LR+GQVRVD  R K + R+Q+GQ
Sbjct: 1   MAGVEQIEVDSGEAGMRLDRWFKTHYPGLGFGQLQKLLRTGQVRVDGGRAKADTRVQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++R+PP+        K       ++     ++ L  +L++ED K++VFNKPAG++VQGGS
Sbjct: 61  MIRVPPLAVDH----KGAPATIRTMRDRGDAEVLSQMLIHEDEKVFVFNKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+DG L++W + +G+KPRL HRLD++TSG+LVVARTR AA  LTESFR R  +KIY
Sbjct: 117 GVNRHVDGMLEAWRNKRGEKPRLVHRLDRDTSGVLVVARTRLAAVKLTESFRARETKKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+L+ G+PK  +  I+ WL++++   GD + + K  E GA++A+S +++++       WL
Sbjct: 177 WALIKGVPKKAEGRISTWLVRETTPDGDRMRIAKHGEPGADHAVSTYRLVEQAGTALSWL 236

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            M+P TGR HQLRVHA H+GCPI+GD KY  A+        IQN+L+LHAR + +PHP+G
Sbjct: 237 VMEPFTGRMHQLRVHAAHIGCPIIGDPKYFEADQNWELPGGIQNRLHLHARRIIIPHPDG 296

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G + +TA +P HM ++W+ LGF 
Sbjct: 297 GSIDVTAEMPPHMQQSWNLLGFN 319


>gi|304391488|ref|ZP_07373430.1| rRNA pseudouridylate synthase C [Ahrensia sp. R2A130]
 gi|303295717|gb|EFL90075.1| rRNA pseudouridylate synthase C [Ahrensia sp. R2A130]
          Length = 338

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 162/333 (48%), Positives = 226/333 (67%), Gaps = 4/333 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +T V    V+ DE  MRLDRWFK HYP + F  LQK+LRSGQVRVD  RVK  +R+++GQ
Sbjct: 3   LTGVSQKTVDEDEGGMRLDRWFKLHYPGVGFGKLQKLLRSGQVRVDGGRVKTASRLEAGQ 62

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVRIPP+ +A +   K   +  +++      D L+ ++LYED K+ VFNKP+G++VQGGS
Sbjct: 63  VVRIPPLDSAASD--KPLHMTSNTIRDRHDEDVLRDMILYEDKKVLVFNKPSGLAVQGGS 120

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           GI+  +D  L+S  D  GQKPRL HRLD++TSG+LVVA+TR AA  LT+SFR R  QK Y
Sbjct: 121 GISRSVDSMLESLRDKAGQKPRLCHRLDRDTSGVLVVAKTRGAAAALTKSFRQRTTQKTY 180

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV GIP+ K+  I+ +L+K+    GD + V K  E+ A++A+S ++VID   +   W+
Sbjct: 181 WALVRGIPRQKEGRISTYLVKEQTEDGDRMRVAKHGERHADHAVSFYRVIDSNPRTVSWV 240

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E+ PHTGRTHQLRVHA H+G PI+GD+KY +         IQ +L+LHAR + +PHP+  
Sbjct: 241 ELSPHTGRTHQLRVHADHIGHPIIGDNKYFSTENWEMPGGIQKRLHLHARRIRIPHPDEN 300

Query: 304 R--LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           +  L +TAPLP HMV++W+   F+    + +  
Sbjct: 301 QPTLDVTAPLPPHMVQSWNLFAFEEADGVEVDE 333


>gi|209884846|ref|YP_002288703.1| pseudouridine synthase, RluD [Oligotropha carboxidovorans OM5]
 gi|209873042|gb|ACI92838.1| pseudouridine synthase, RluD [Oligotropha carboxidovorans OM5]
          Length = 412

 Score =  336 bits (861), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 145/336 (43%), Positives = 219/336 (65%), Gaps = 5/336 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ VVV  DE NMR+DR+ + H+P ++F ++Q+I+R G++RV+ KR    +R+  G
Sbjct: 82  LPTKVQTVVVTADENNMRVDRFLEAHFPGLSFSHIQRIVRKGELRVNGKRADSKDRLNEG 141

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             VRIPP+      +   +   + S   +K  D L+ ++L+ED+ + V NKPAG++VQGG
Sbjct: 142 DNVRIPPL-----KLDAPKTGGNLSEAGSKVLDELRKMVLFEDADVMVLNKPAGLAVQGG 196

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+  H+DG L+   D+KGQ+PRL HRLD+ETSG L++A+TR AA  LT SFR R  +KI
Sbjct: 197 SGLTRHVDGMLEVMRDAKGQRPRLVHRLDRETSGCLLIAKTRFAASTLTGSFRHRSARKI 256

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K+ +     + +    ++GA +A++++ V++  AQK  W
Sbjct: 257 YWALVAGVPKPKQGRISTYLAKEENEEDSIMRIAAHGDEGAAHAVTYYAVVEASAQKLAW 316

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+G  IVGD KY           +QN+L+L AR + +PHP G
Sbjct: 317 VSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNKENWQLPGGLQNRLHLLARRIVIPHPRG 376

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           G + +TAPLP HM+++W+ LG + DR   I+    +
Sbjct: 377 GVIDVTAPLPPHMLQSWNLLGLEADRFDPIENAPEE 412


>gi|146341534|ref|YP_001206582.1| putative ribosomal large subunit pseudouridine synthase RluC-like
           protein [Bradyrhizobium sp. ORS278]
 gi|146194340|emb|CAL78364.1| putative ribosomal large subunit pseudouridine synthase RluC-like
           (23S RNA pseudouridylate synthase) (RNA-uridine
           isomerase) [Bradyrhizobium sp. ORS278]
          Length = 458

 Score =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 148/336 (44%), Positives = 218/336 (64%), Gaps = 5/336 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ VVV  DE NMR+DR+ +  +P ++F ++Q+I+R G++RVD KR    +R++ G
Sbjct: 128 LPTKVQTVVVTADENNMRVDRFLEARFPGLSFSHIQRIVRKGELRVDGKRADSKDRLEEG 187

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP+      +   ++    S    K  D LK++ LYED  + V NKPAG++VQGG
Sbjct: 188 QSVRIPPL-----KLDAPKERAGLSEGERKTLDSLKAMTLYEDDDVLVLNKPAGLAVQGG 242

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+  HID  L+   D+KGQKPRL HR+D+ETSG L++A+TR AA HLT +FR R  +K+
Sbjct: 243 SGMTRHIDQMLEVMRDAKGQKPRLVHRIDRETSGCLLIAKTRFAATHLTGAFRHRSARKV 302

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K        + V    ++GA++A++++ V++  A K  W
Sbjct: 303 YWALVAGVPKPKQGRISTYLAKDEGEDDTIMRVAAHGDEGASHAVTYYAVVEASANKLAW 362

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+G PIVGD KY      +    +QN+L+L AR + +PHP G
Sbjct: 363 VSLKPVTGRTHQLRAHMAHIGHPIVGDPKYFNIENWSLPGGLQNRLHLLARRIVIPHPRG 422

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           G +  TAPLP HM+++W+ LG ++DR   I+    +
Sbjct: 423 GVIDATAPLPPHMLQSWNLLGLEHDRFDPIENAPEE 458


>gi|115525546|ref|YP_782457.1| RluA family pseudouridine synthase [Rhodopseudomonas palustris
           BisA53]
 gi|115519493|gb|ABJ07477.1| ribosomal large subunit pseudouridine synthase C [Rhodopseudomonas
           palustris BisA53]
          Length = 458

 Score =  335 bits (858), Expect = 8e-90,   Method: Composition-based stats.
 Identities = 144/336 (42%), Positives = 215/336 (63%), Gaps = 5/336 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ VVV  DE  MR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 128 LPTKVQTVVVTADENAMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 187

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP+      +   +   + S    K    LK+++LYED+ + V NKPAG++VQGG
Sbjct: 188 QSVRIPPL-----QLDAPKGGGNLSEAEQKTLAALKAMILYEDADVMVLNKPAGLAVQGG 242

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   H+D  L+   DSKGQKPRL HRLD+ET+G L+VA+TR AA  LT SFR R  +K+
Sbjct: 243 SGTTRHVDLMLEVMRDSKGQKPRLVHRLDKETAGCLLVAKTRFAATALTGSFRSRSARKV 302

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K        + V    ++GA++A++++ V++  AQK  W
Sbjct: 303 YWALVAGVPKPKQGRISTYLAKDESEDDSIMRVAAHGDEGASHAVTYYAVVETSAQKLAW 362

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+G  I+GD KY           +Q +L+L AR + +PHP G
Sbjct: 363 VSLKPVTGRTHQLRAHMAHIGHAIIGDPKYFNIENWELPGGLQKRLHLLARRIAIPHPRG 422

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           G + +TAPLP HM+++W+ LG ++DR   I+    +
Sbjct: 423 GVIDVTAPLPPHMLQSWNLLGLEHDRFDPIENAPEE 458


>gi|90417736|ref|ZP_01225648.1| ribosomal large subunit pseudouridine synthase C [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90337408|gb|EAS51059.1| ribosomal large subunit pseudouridine synthase C [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 328

 Score =  333 bits (854), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 156/323 (48%), Positives = 223/323 (69%), Gaps = 2/323 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   +E+DE  +RLDRWFK HYP + F +LQK+LRSGQVRVD  R K + R+Q GQ
Sbjct: 1   MASVEQRRIEDDEAGLRLDRWFKLHYPGLGFGHLQKLLRSGQVRVDGGRAKTDTRVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VRIPP+        K   +  +++      + L  +L+YED K++VFNKPAG++VQGGS
Sbjct: 61  MVRIPPMSGDAGRP-KIGPLTANTMRDKHDDEVLSQMLIYEDEKVFVFNKPAGLAVQGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+D  L++W   KG+KPRL HRLD++TSG+LVVARTR AA  LT++FR R  +K Y
Sbjct: 120 GLNRHVDKMLEAWRSRKGEKPRLVHRLDRDTSGVLVVARTRGAATALTKAFRERDTKKTY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+++ G+P   +  I+ +L+K+    GD +   K  E+GA++A++H++VI+  AQ F W+
Sbjct: 180 WAILKGVPVPHEGRISTFLVKEQTPDGDRMRTAKHGEEGADHALTHYRVIENLAQNFSWV 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHALH+G PI+GD KY   +    F   +Q +L+LHAR + +PHP G
Sbjct: 240 EMEPYTGRTHQLRVHALHIGNPILGDPKYFEHDTNWEFPGGVQKRLHLHARRIVIPHPSG 299

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G +   APLP HM++T++  GF 
Sbjct: 300 GFIDQIAPLPPHMIQTFNLFGFD 322


>gi|75675586|ref|YP_318007.1| pseudouridine synthase, RluD [Nitrobacter winogradskyi Nb-255]
 gi|74420456|gb|ABA04655.1| ribosomal large subunit pseudouridine synthase C [Nitrobacter
           winogradskyi Nb-255]
          Length = 412

 Score =  333 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 138/334 (41%), Positives = 218/334 (65%), Gaps = 5/334 (1%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T VQ V V  DE NMR+DR+ +  +P ++F ++Q+++R G++RV+ +R    +R+  G  
Sbjct: 84  TKVQTVAVTADEANMRVDRFLEARFPGLSFSHIQRVVRKGELRVNGRRADSKDRVSEGDK 143

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+      +   +  +  S   TK  D L+ ++L+ED+ + V NKPAG++VQGGSG
Sbjct: 144 VRIPPL-----KLDTPKAAVGLSDAETKIRDELRKMVLFEDADVMVLNKPAGLAVQGGSG 198

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++ HIDG L++  D+KGQ+PRL HRLD+ET+G L++A+TR AA  LT +FR R  +KIYW
Sbjct: 199 LSRHIDGMLETMRDAKGQRPRLVHRLDRETAGCLLIAKTRFAATALTGAFRHRSARKIYW 258

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+PK K+  I+ +L K+ +     + +    ++GA++A++++ V++  AQK  W+ 
Sbjct: 259 ALVAGVPKPKQGRISTYLAKEENEEESIMRIAAHGDEGASHAVTYYAVVETSAQKLAWVS 318

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++P TGRTHQLR H  H+G  I+GD KY           +QN+L+L AR + +PHP GG 
Sbjct: 319 LKPVTGRTHQLRAHMAHIGHAIIGDPKYFNKENWQLPGGLQNRLHLLARRIVIPHPRGGV 378

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           +  +APLP HM+++W+ LG + DR   I+    +
Sbjct: 379 IDASAPLPPHMLQSWNLLGLEADRFDPIENAPEE 412


>gi|163849730|ref|YP_001637773.1| RluA family pseudouridine synthase [Methylobacterium extorquens
           PA1]
 gi|163661335|gb|ABY28702.1| pseudouridine synthase, RluA family [Methylobacterium extorquens
           PA1]
          Length = 468

 Score =  331 bits (850), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 138/329 (41%), Positives = 213/329 (64%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + V+ DE  MR+DR+    +P + F  +Q I+R G++RVD KR K N+R++ 
Sbjct: 135 TLASGVQTLTVDPDEAGMRIDRFLGARFPQLPFTRVQSIVRKGELRVDGKRAKPNDRLEP 194

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+      + +  +   S+  +   ++FL+S++LYED+ + + NKP G++VQG
Sbjct: 195 GSSVRVPPL-----KLDQPTERPRSAAKIDGDAEFLRSLILYEDADMMILNKPFGLAVQG 249

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L++     GQ+PRL HRLD++T+G L+VA+TR AA  L +SFR R  +K
Sbjct: 250 GSGTVRHVDGLLEALTGPDGQRPRLVHRLDKDTAGCLIVAKTRLAASTLAKSFRSRAARK 309

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+LV G+P+ ++  ++ +L+K      D  + V K  + GA++A++++  +D  AQK 
Sbjct: 310 IYWALVAGVPRTRQGRVSTYLVKDEPTDADARMRVAKHGDDGASHALTYYATVDQAAQKL 369

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP
Sbjct: 370 AWLSLKPVTGRTHQLRAHAAHIGHPIVGDPKYFDVENWELPGGIQNRLHLLARRIVIPHP 429

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 430 RTGQPVDVSAPLPPHMAQSWNLLGFDAAR 458


>gi|148256356|ref|YP_001240941.1| ribosomal large subunit pseudouridine synthase C [Bradyrhizobium
           sp. BTAi1]
 gi|146408529|gb|ABQ37035.1| ribosomal large subunit pseudouridine synthase C [Bradyrhizobium
           sp. BTAi1]
          Length = 458

 Score =  331 bits (850), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 149/336 (44%), Positives = 217/336 (64%), Gaps = 5/336 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ VVV  DE NMR+DR+ +  +P ++F ++Q+I+R G++RVD KR    +R++ G
Sbjct: 128 LPTKVQTVVVTADENNMRVDRFLEARFPGLSFSHIQRIVRKGELRVDGKRADSKDRLEEG 187

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP+        KE+  L  +    K  + LK++ LYED  + V NKP G++VQGG
Sbjct: 188 QTVRIPPLKL---DAPKERAGLSEAER--KTLESLKAMTLYEDDDVLVLNKPVGLAVQGG 242

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+  HID  L+   D+KGQKPRL HR+D+ETSG L++A+TR AA HLT +FR R  +KI
Sbjct: 243 SGMTRHIDQMLEVMRDAKGQKPRLVHRIDRETSGCLLIAKTRFAATHLTGAFRSRSARKI 302

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K        + V    ++GA++A++++ V++  A K  W
Sbjct: 303 YWALVAGVPKPKQGRISTYLAKDEGEDDTIMRVAAHGDEGASHAVTYYAVVEASANKLAW 362

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+G PIVGD KY           +QN+L+L AR + +PHP G
Sbjct: 363 VSLKPVTGRTHQLRAHMAHIGHPIVGDPKYFNIENWALPGGLQNRLHLLARRIVIPHPRG 422

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           G +  TAPLP HM+++W+ LG ++DR   I+    +
Sbjct: 423 GVIDATAPLPPHMLQSWNLLGLEHDRFDPIENAPEE 458


>gi|85715100|ref|ZP_01046084.1| pseudouridine synthase, RluD [Nitrobacter sp. Nb-311A]
 gi|85698015|gb|EAQ35888.1| pseudouridine synthase, RluD [Nitrobacter sp. Nb-311A]
          Length = 380

 Score =  331 bits (849), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 140/334 (41%), Positives = 219/334 (65%), Gaps = 5/334 (1%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T VQ V V  DE NMR+DR+ +  +P ++F ++Q+I+R G++RV+ +R    +R+  G  
Sbjct: 52  TRVQTVAVTADEANMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGRRADSKDRVSEGDK 111

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+      +   +  +  S   TK  D L+ ++L+ED+ + V NKPAG++VQGGSG
Sbjct: 112 VRIPPL-----RLDTPKAAVGLSDAETKIRDELRKMVLFEDADVMVLNKPAGLAVQGGSG 166

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++ HIDG L++  D+KGQ+PRL HRLD+ET+G L++ARTR AA  LT +FR R  +KIYW
Sbjct: 167 LSRHIDGMLETMRDAKGQRPRLVHRLDRETAGCLLIARTRFAATALTGAFRHRSARKIYW 226

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+PK K+  I+ +L K+ +     + V    ++GA++A++++ V++  AQK  W+ 
Sbjct: 227 ALVAGVPKPKQGRISTYLAKEENEEESIMRVAAHGDEGASHAVTYYAVVETSAQKLAWVS 286

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++P TGRTHQLR H  H+G  I+GD KY           +QN+L+L AR + +PHP GG 
Sbjct: 287 LKPVTGRTHQLRAHMAHVGHAIIGDPKYFNKENWQLPGGLQNRLHLLARRIVIPHPRGGV 346

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           + ++APLP HM+++W+ LG + +R   I+    +
Sbjct: 347 IDVSAPLPPHMLQSWNLLGLEANRFDPIENAPEE 380


>gi|92117127|ref|YP_576856.1| pseudouridine synthase, RluD [Nitrobacter hamburgensis X14]
 gi|91800021|gb|ABE62396.1| ribosomal large subunit pseudouridine synthase C [Nitrobacter
           hamburgensis X14]
          Length = 411

 Score =  331 bits (849), Expect = 9e-89,   Method: Composition-based stats.
 Identities = 140/334 (41%), Positives = 213/334 (63%), Gaps = 5/334 (1%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T VQ V V  DE NMR+DR+ +  +P ++F ++Q+++R G++RV+ KR    +R+  G  
Sbjct: 83  TKVQTVAVTADEANMRVDRFLEARFPGLSFSHIQRVVRKGELRVNGKRADSKDRLGEGDK 142

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+      +       +     TK  D L+ ++L+ED+ + V NKPAG++VQGGSG
Sbjct: 143 VRIPPLKLDTPKVAAGLSEAE-----TKIRDELQKMVLFEDADVMVLNKPAGLAVQGGSG 197

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++ HIDG L+   D+KGQ+PRL HRLD+ET+G L+VA+TR AA  LT SFR R  +KIYW
Sbjct: 198 LSRHIDGMLEVMCDAKGQRPRLVHRLDRETAGCLLVAKTRFAATALTGSFRHRSARKIYW 257

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+PK K+  I+ +L K+       + +    ++GA++A++++ V++  AQK  W+ 
Sbjct: 258 ALVAGVPKPKQGRISTYLAKEESEEDSIMRIAAHGDEGASHAVTYYAVVETSAQKLAWVS 317

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++P TGRTHQLR H  H+   IVGD KY           +Q +L+L AR + +PHP GG 
Sbjct: 318 LKPVTGRTHQLRAHMAHIDHAIVGDPKYFNKENWQLPGGLQKRLHLLARRIVIPHPRGGV 377

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           + +TAPLP HM+++W+ LG + DR   I+    +
Sbjct: 378 IDVTAPLPPHMLQSWNLLGLEADRFDPIENAPEE 411


>gi|27380477|ref|NP_772006.1| ribosomal large subunit pseudouridine synthase C [Bradyrhizobium
           japonicum USDA 110]
 gi|27353641|dbj|BAC50631.1| bll5366 [Bradyrhizobium japonicum USDA 110]
          Length = 405

 Score =  331 bits (848), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 141/336 (41%), Positives = 211/336 (62%), Gaps = 5/336 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ V V  DE NMR+DR+ +  +P ++F ++Q+++R G++RVD KRV   +R++ G
Sbjct: 75  LPTKVQTVTVTADENNMRVDRFLEARFPGLSFSHIQRVVRKGELRVDGKRVDSKDRLEEG 134

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP+      +   + + + S    K    LK + +YED  + V NKP G++VQGG
Sbjct: 135 QSVRIPPL-----KLDAPKAVGELSEAAQKTLKALKEMTIYEDDDVLVLNKPFGLAVQGG 189

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   HID  L+   DSKGQKPRL HR+D++TSG L++A+TR AA HLT +FR R  +K+
Sbjct: 190 SGTTRHIDQMLEVMRDSKGQKPRLVHRIDKDTSGCLLIAKTRFAASHLTGAFRSRSARKV 249

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K+       + + +  ++GA++A++++ V++    K  W
Sbjct: 250 YWALVPGLPKPKQGRISTFLAKEESEDDTIMRIAQHGDEGASHAVTYYAVVETAGNKLTW 309

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+G PIVGD KY           +QN+L+L AR + +PHP G
Sbjct: 310 VSLKPVTGRTHQLRAHMEHIGHPIVGDPKYFNIENWQLPGGLQNRLHLLARRIVIPHPRG 369

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           G +  TAPLP HM ++W+ LG    R   I+    +
Sbjct: 370 GVIDATAPLPPHMQQSWNLLGLDASRFDPIENAPEE 405


>gi|218528371|ref|YP_002419187.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
 gi|218520674|gb|ACK81259.1| pseudouridine synthase, RluA family [Methylobacterium
           chloromethanicum CM4]
          Length = 468

 Score =  331 bits (848), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 138/329 (41%), Positives = 213/329 (64%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + V+ DE  MR+DR+    +P + F  +Q I+R G++RVD KR K N+R++ 
Sbjct: 135 TLASGVQTLTVDPDEAGMRIDRFLGARFPQLPFTRVQSIVRKGELRVDGKRAKPNDRLEP 194

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+      + +  +   S+  +   ++FL+S++LYED+ + + NKP G++VQG
Sbjct: 195 GSSVRVPPL-----KLDQPTERPRSAAKIDGDAEFLRSLILYEDADMMILNKPFGLAVQG 249

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L++     GQ+PRL HRLD++T+G L+VA+TR AA  L +SFR R  +K
Sbjct: 250 GSGTVRHVDGLLEALTGPDGQRPRLVHRLDKDTAGCLIVAKTRLAASTLAKSFRSRAARK 309

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+LV G+P+ ++  ++ +L+K      D  + V K  + GA++A++++  +D  AQK 
Sbjct: 310 IYWALVAGVPRTRQGRVSTYLVKDEPTDADARMRVAKHGDDGASHALTYYATVDQAAQKL 369

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP
Sbjct: 370 AWLSLKPVTGRTHQLRAHAAHIGHPIVGDPKYFDVENWELPGGIQNRLHLLARRIVIPHP 429

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 430 RTGQPVDVSAPLPPHMAQSWNLLGFDAAR 458


>gi|192291994|ref|YP_001992599.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           TIE-1]
 gi|192285743|gb|ACF02124.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           TIE-1]
          Length = 455

 Score =  331 bits (848), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 141/331 (42%), Positives = 211/331 (63%), Gaps = 5/331 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T V+ V V  DE  MR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 125 LPTKVETVTVTADENGMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 184

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP+      +       +      K    LK++ L+ED+ + V NKPAG++VQGG
Sbjct: 185 QSVRIPPLKLDTPKLPGHLSEAEQ-----KTLQTLKAMTLFEDADVLVLNKPAGLAVQGG 239

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   HID  L+   D+KGQKPRL HR+D+ET+G L+VA+TR AA  LT SFR R  +KI
Sbjct: 240 SGTTRHIDQMLEVLRDAKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRHRSARKI 299

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K+       + V K  + GA++A++++ V++   QK  W
Sbjct: 300 YWALVAGVPKPKQGRISTYLAKEESEDDSIMRVAKHGDDGASHAVTYYAVVETSGQKLAW 359

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+G  IVGD KY           +QN+L+L AR + +PHP G
Sbjct: 360 VSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNIENWQLPGGLQNRLHLLARRIVIPHPRG 419

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
           G + ++APLP HM+++W+ LG ++DR   I+
Sbjct: 420 GVIDVSAPLPPHMLQSWNLLGLEHDRFDPIE 450


>gi|39936271|ref|NP_948547.1| pseudouridine synthase RluD [Rhodopseudomonas palustris CGA009]
 gi|39650126|emb|CAE28649.1| possible ribosomal large subunit pseudouridine synthase C
           [Rhodopseudomonas palustris CGA009]
          Length = 455

 Score =  331 bits (848), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 142/331 (42%), Positives = 210/331 (63%), Gaps = 5/331 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T V+ V V  DE  MR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 125 LPTKVETVTVTADENGMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 184

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP+      +       +      K    LK++ L+ED+ + V NKPAG++VQGG
Sbjct: 185 QSVRIPPLKLDTPKLPGHLSEAEQ-----KTLQTLKAMTLFEDADVLVLNKPAGLAVQGG 239

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   HID  L+   DSKGQKPRL HR+D+ET+G L+VA+TR AA  LT SFR R  +KI
Sbjct: 240 SGTTRHIDQMLEVLRDSKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRHRSARKI 299

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K        + V K  + GA++A++++ V++   QK  W
Sbjct: 300 YWALVAGVPKPKQGRISTYLAKDESEEDSIMRVAKHGDDGASHAVTYYAVVETSGQKLAW 359

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+G  IVGD KY           +QN+L+L AR + +PHP G
Sbjct: 360 VSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNIENWQLPGGLQNRLHLLARRIVIPHPRG 419

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
           G + ++APLP HM+++W+ LG ++DR   I+
Sbjct: 420 GVIDVSAPLPPHMLQSWNLLGLEHDRFDPIE 450


>gi|254558792|ref|YP_003065887.1| pseudouridylate synthase [Methylobacterium extorquens DM4]
 gi|254266070|emb|CAX21822.1| pseudouridylate synthase [Methylobacterium extorquens DM4]
          Length = 468

 Score =  330 bits (847), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 138/329 (41%), Positives = 213/329 (64%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + V+ DE  MR+DR+    +P + F  +Q I+R G++RVD KR K N+R++ 
Sbjct: 135 TLASGVQTLTVDPDEAGMRIDRFLGARFPQLPFTRVQSIVRKGELRVDGKRAKPNDRLEP 194

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+      + +  +   S+  +   ++FL+S++LYED+ + + NKP G++VQG
Sbjct: 195 GSSVRVPPL-----KLDQPTERPRSAAKIDGDAEFLRSLILYEDADMMILNKPFGLAVQG 249

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L++     GQ+PRL HRLD++T+G L+VA+TR AA  L +SFR R  +K
Sbjct: 250 GSGTVRHVDGLLEALTGPDGQRPRLVHRLDKDTAGCLIVAKTRLAASTLAKSFRSRAARK 309

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+LV G+P+ ++  ++ +L+K      D  + V K  + GA++A++++  +D  AQK 
Sbjct: 310 IYWALVAGVPRTRQGRVSTYLVKDEPTDADARMRVAKHGDDGASHALTYYATVDQAAQKL 369

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP
Sbjct: 370 AWLSLKPVTGRTHQLRAHAAHIGHPIVGDPKYFDVENWELPGGIQNRLHLLARRIVIPHP 429

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 430 RTGQPVDVSAPLPPHMAQSWNLLGFDAAR 458


>gi|240136939|ref|YP_002961408.1| Pseudouridine synthase, RluD [Methylobacterium extorquens AM1]
 gi|240006905|gb|ACS38131.1| Pseudouridine synthase, RluD [Methylobacterium extorquens AM1]
          Length = 463

 Score =  330 bits (847), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 138/329 (41%), Positives = 213/329 (64%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + V+ DE  MR+DR+    +P + F  +Q I+R G++RVD KR K N+R++ 
Sbjct: 130 TLASGVQTLTVDPDEAGMRIDRFLGARFPQLPFTRVQSIVRKGELRVDGKRAKPNDRLEP 189

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+      + +  +   S+  +   ++FL+S++LYED+ + + NKP G++VQG
Sbjct: 190 GSSVRVPPL-----KLDQPTERPRSAAKIDGDAEFLRSLILYEDADMMILNKPFGLAVQG 244

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L++     GQ+PRL HRLD++T+G L+VA+TR AA  L +SFR R  +K
Sbjct: 245 GSGTVRHVDGLLEALTGPDGQRPRLVHRLDKDTAGCLIVAKTRLAASTLAKSFRSRAARK 304

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+LV G+P+ ++  ++ +L+K      D  + V K  + GA++A++++  +D  AQK 
Sbjct: 305 IYWALVAGVPRTRQGRVSTYLVKDEPTDADARMRVAKHGDDGASHALTYYATVDQAAQKL 364

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP
Sbjct: 365 AWLSLKPVTGRTHQLRAHAAHIGHPIVGDPKYFDVENWELPGGIQNRLHLLARRIVIPHP 424

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 425 RTGQPVDVSAPLPPHMAQSWNLLGFDAAR 453


>gi|316933564|ref|YP_004108546.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           DX-1]
 gi|315601278|gb|ADU43813.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           DX-1]
          Length = 455

 Score =  330 bits (847), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 141/331 (42%), Positives = 209/331 (63%), Gaps = 5/331 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T V+ V V  DE  MR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 125 LPTKVETVTVTADENGMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 184

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP+      +       +      K    L+ + L+ED+ + V NKPAG++VQGG
Sbjct: 185 QSVRIPPLKLDTPKLPGHLSEAEQ-----KTLQALRDMTLFEDADVLVLNKPAGLAVQGG 239

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   HID  L+   DSKGQKPRL HR+D+ET+G L+VA+TR AA  LT SFR R  +KI
Sbjct: 240 SGTTRHIDQMLEVLRDSKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRHRSARKI 299

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K        + V K  + GA++A++++ V++   QK  W
Sbjct: 300 YWALVAGVPKPKQGRISTYLAKDESEEDSIMRVAKHGDDGASHAVTYYAVVETSGQKLAW 359

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+G  IVGD KY           +QN+L+L AR + +PHP G
Sbjct: 360 VSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNIENWQLPGGLQNRLHLLARRIVIPHPRG 419

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
           G + ++APLP HM+++W+ LG ++DR   I+
Sbjct: 420 GVIDVSAPLPPHMLQSWNLLGLEHDRFDPIE 450


>gi|86357851|ref|YP_469743.1| pseudouridylate synthase, ribosomal large subunit C protein
           [Rhizobium etli CFN 42]
 gi|86281953|gb|ABC91016.1| pseudouridylate synthase, ribosomal large subunit C protein
           [Rhizobium etli CFN 42]
          Length = 317

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 161/310 (51%), Positives = 227/310 (73%), Gaps = 3/310 (0%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ+VR+PP+   ++  +
Sbjct: 1   MRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQMVRVPPL--DVDAKL 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K   I    +  +   + L  ++L+ED K+ V NKP G++VQGGSG+A HID  L++W+ 
Sbjct: 59  KSGPIAGKDLKHSSDFELLSRMVLHEDEKVIVLNKPPGLAVQGGSGVARHIDQMLEAWIS 118

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +K YWSLV G+P+  ++ I
Sbjct: 119 PKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRERDTKKTYWSLVKGVPRKHEDKI 178

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           + WL+K+    GD + + K  E GA++A+S+++V++  AQ+  WLEM+P+TGRTHQLRVH
Sbjct: 179 STWLVKEPTADGDRMRIAKHGEDGADHAVSYYRVVETAAQRLAWLEMEPYTGRTHQLRVH 238

Query: 259 ALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
           ALH+G PI+GD KY   +   +F   IQ +L+LHAR++D+PHP GGRL++TAPLP HMV+
Sbjct: 239 ALHIGHPIIGDPKYFDDDPNWDFPGGIQKRLHLHARHIDIPHPSGGRLRVTAPLPPHMVQ 298

Query: 318 TWDSLGFKYD 327
           +W+ LGF  +
Sbjct: 299 SWNLLGFDEN 308


>gi|188579622|ref|YP_001923067.1| pseudouridine synthase [Methylobacterium populi BJ001]
 gi|179343120|gb|ACB78532.1| pseudouridine synthase, RluA family [Methylobacterium populi BJ001]
          Length = 446

 Score =  330 bits (845), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 138/329 (41%), Positives = 212/329 (64%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + V  DE  MR+DR+    +P + F  +Q I+R G++RVD KR K N+R++ 
Sbjct: 113 TLASGVQTLTVAPDEAGMRIDRFLGARFPQLPFTRVQSIVRKGELRVDGKRAKPNDRLEP 172

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+      + +      S+  +   ++FL+S++LYED+ + + NKP G++VQG
Sbjct: 173 GSSVRVPPL-----KLEQPTDRPRSAAKVVGDAEFLRSLILYEDADMMILNKPFGLAVQG 227

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L++     GQ+PRL HRLD++T+G L+VA+TR AA  L +SFR R  +K
Sbjct: 228 GSGTVRHVDGLLEALTGPDGQRPRLVHRLDKDTAGCLIVAKTRLAAATLAKSFRSRAARK 287

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+LV G+P+ ++  ++ +L+K      D  + V K  ++GA++A++++  +D  AQK 
Sbjct: 288 IYWALVAGVPRTRQGRVSTYLVKDEPTDADARMRVAKHGDEGASHALTYYATVDQAAQKL 347

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP
Sbjct: 348 AWLSLKPVTGRTHQLRAHAAHIGHPIVGDPKYFDVENWELPGGIQNRLHLLARRIVIPHP 407

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 408 RTGQPVDVSAPLPPHMAQSWNLLGFDAAR 436


>gi|299135225|ref|ZP_07028416.1| pseudouridine synthase, RluA family [Afipia sp. 1NLS2]
 gi|298590202|gb|EFI50406.1| pseudouridine synthase, RluA family [Afipia sp. 1NLS2]
          Length = 413

 Score =  330 bits (845), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 142/336 (42%), Positives = 219/336 (65%), Gaps = 5/336 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ VVV  DE NMR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 83  LPTKVQTVVVTADENNMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 142

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP+      +   +   + S   TK  + L+ ++L+ED+ + V NKPAG++VQGG
Sbjct: 143 QSVRIPPL-----KLDAPKTGGNLSEAATKTLEELRKMILFEDADVMVLNKPAGLAVQGG 197

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG++ H+D  L+   D+KGQ+PRL HRLD+ETSG L++A+TR AA  LT SFR R  +KI
Sbjct: 198 SGLSRHVDQMLEVMRDAKGQRPRLVHRLDRETSGCLLIAKTRFAASVLTGSFRHRSARKI 257

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K+ +     + + +  ++GA +A++++ V++  AQK  W
Sbjct: 258 YWALVAGVPKPKQGRISTYLAKEENEEDSIMRIAEHGDEGAAHAVTYYAVVEASAQKLAW 317

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+   IVGD KY           +Q +L+L AR + +PHP G
Sbjct: 318 VSLKPVTGRTHQLRAHMAHIDHAIVGDPKYFNKENWQLPGGLQKRLHLLARRIVIPHPRG 377

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           G + +TAPLP HM+++W+ LG + DR   I+    +
Sbjct: 378 GVIDVTAPLPPHMLQSWNLLGLEADRFDPIEDAPEE 413


>gi|49474373|ref|YP_032415.1| ribosomal large subunit pseudouridine synthase c [Bartonella
           quintana str. Toulouse]
 gi|49239877|emb|CAF26275.1| Ribosomal large subunit pseudouridine synthase c [Bartonella
           quintana str. Toulouse]
          Length = 327

 Score =  330 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 163/323 (50%), Positives = 221/323 (68%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   VE DE  MRLDRWFK +YP + F  LQK+LRSGQ+RVD  RVK + R+  GQ
Sbjct: 1   MAGVEIKKVEADESGMRLDRWFKVYYPGLGFGYLQKLLRSGQIRVDGGRVKADTRLLIGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP++      +    + D  +        LK +LLYEDSKI+VFNKPAG++VQGGS
Sbjct: 61  VVRVPPLLVDEKESLP---VTDKIIREQDDRVILKKMLLYEDSKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H D  L+ W + KG+KPRL HRLD+ETSG+L+VAR+R AAQ LT +FR R  +K Y
Sbjct: 118 GLTRHFDSMLEVWRNKKGEKPRLVHRLDRETSGVLIVARSRGAAQTLTAAFRARETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+PK K++ I+ W++K     GD + V +  E  +N+A+S+++V+D   +   WL
Sbjct: 178 WALVRGVPKKKQDKISTWVVKDITAQGDKMCVCEHGEPDSNHAVSYYRVLDTRGRALSWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA +M  PI+GD KY  ++        IQN+L+LHAR + +PHP G
Sbjct: 238 EMEPYTGRTHQLRVHAAYMDNPIIGDSKYFFSDSNWKLPRGIQNRLHLHARRIRIPHPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G L ITAPLP HMV++++ L F 
Sbjct: 298 GILDITAPLPPHMVQSFNLLAFN 320


>gi|328543393|ref|YP_004303502.1| Pseudouridine synthase [polymorphum gilvum SL003B-26A1]
 gi|326413138|gb|ADZ70201.1| Pseudouridine synthase [Polymorphum gilvum SL003B-26A1]
          Length = 334

 Score =  328 bits (842), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 150/338 (44%), Positives = 219/338 (64%), Gaps = 5/338 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++   V  DE  MRLDRWFK+HYP + F +LQK+LR+GQVRVD KR     R+ +GQ
Sbjct: 1   MAAIELKTVTADEAGMRLDRWFKSHYPGLGFGHLQKLLRTGQVRVDGKRADSATRLATGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+   +     +     SS  +      ++ ++LYED ++ V NKPAG++VQGGS
Sbjct: 61  SVRVPPLGVVVAADDTKNARPKSSRLIADDRKAVEDMILYEDDQVMVLNKPAGLAVQGGS 120

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G++ H+DG L ++ + KG+KPRL HRLD+ETSG+L+VA+TR AAQ LT +FR R  +KIY
Sbjct: 121 GLSRHLDGMLDAFTNKKGEKPRLVHRLDRETSGVLLVAKTRKAAQELTRAFRQRSTRKIY 180

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+L+ G+PK ++  I+ +L +    G + + V +  +  A +A+S + V++  AQK  W+
Sbjct: 181 WALLAGVPKPRQGRISTYLARDE--GSEKMKVARHGDDEAQHAVSLYSVVEQSAQKLAWV 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
            ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP G 
Sbjct: 239 SLRPVTGRTHQLRAHAAHIGHPIVGDDKYFNIENWELPGGIQNRLHLLARRIVIPHPSGH 298

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           G + ++APLP HM ++W+ LGF  D + Y   +   +E
Sbjct: 299 GTIDVSAPLPPHMQQSWNLLGF--DASDYDPDVSDPEE 334


>gi|118591144|ref|ZP_01548543.1| ribosomal large subunit pseudouridine synthase C [Stappia aggregata
           IAM 12614]
 gi|118436220|gb|EAV42862.1| ribosomal large subunit pseudouridine synthase C [Stappia aggregata
           IAM 12614]
          Length = 355

 Score =  328 bits (840), Expect = 9e-88,   Method: Composition-based stats.
 Identities = 158/338 (46%), Positives = 221/338 (65%), Gaps = 5/338 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ ++   V  DE  MRLDRWFK+HYP + F +LQK+LR+GQVRVD KR + N RI  GQ
Sbjct: 17  MSAIEQKQVTADEAGMRLDRWFKSHYPGLGFGHLQKLLRTGQVRVDGKRAETNTRIAKGQ 76

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++RIPP+   L    K+     S+  +      ++ +LL+EDS++ V NKPAG++VQGGS
Sbjct: 77  MIRIPPLGVELPADDKKNAKPKSTKLIADDRKAIEDMLLFEDSQVMVLNKPAGLAVQGGS 136

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+DG L ++ D KG KPRL HRLD+ETSGI++VARTR AAQ LT++FR R  +KIY
Sbjct: 137 GLKRHLDGMLDAYTDRKGNKPRLVHRLDRETSGIILVARTRQAAQELTKAFRHRNTRKIY 196

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+++ G+PK  +  I+ +L +    G + + VV+Q E  A +A+S + V +   QK  W+
Sbjct: 197 WAILAGVPKPFQGRISTFLARND--GEERMQVVRQGEDEAQHAVSLYSVFEKSGQKLSWV 254

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
            M+P TGRTHQLR HA H+G PI+GD KY           IQN+L+L AR + +PHP G 
Sbjct: 255 TMKPVTGRTHQLRAHAAHIGHPIIGDDKYFNIENWELPGGIQNRLHLLARRIVIPHPSGH 314

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           G + ++APLP HM +TW+ LGF  D   Y   +   D+
Sbjct: 315 GTIDVSAPLPPHMQQTWNLLGF--DATDYDPEVDDPDD 350


>gi|307946319|ref|ZP_07661654.1| rRNA pseudouridylate synthase C [Roseibium sp. TrichSKD4]
 gi|307769983|gb|EFO29209.1| rRNA pseudouridylate synthase C [Roseibium sp. TrichSKD4]
          Length = 333

 Score =  328 bits (840), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 148/323 (45%), Positives = 213/323 (65%), Gaps = 3/323 (0%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ ++   V  DE  MRLDRWFK HYP + F  LQK+LR+GQVRVD KR + N RI  GQ
Sbjct: 1   MSAIEQKTVTADEAGMRLDRWFKAHYPGMGFGRLQKLLRTGQVRVDGKRAESNTRIAKGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+   L    K+     SS  +      ++ ++L+ED+ + V NKPAG++VQGGS
Sbjct: 61  TVRIPPLGVELPANDKKNAKPKSSKLMADDKAAIEDMMLFEDNHVMVLNKPAGLAVQGGS 120

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+DG L+++ + KG+KP+L HRLD+ETSGI++VA+TR AAQ LT++FR R  +KIY
Sbjct: 121 GLKRHLDGMLEAYTNKKGEKPKLVHRLDRETSGIILVAKTRKAAQELTKAFRHRNTRKIY 180

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+++ G+PK  +  I+ +L +   +  + + V +  +  A +A+S + V +  AQK  W+
Sbjct: 181 WAMLAGVPKPHQGRISTYLARSEEM--ERMRVARHGDDEAQHAVSLYSVFEKSAQKLSWV 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
            ++P TGRTHQLR HA H+G PI+GD KY           IQN+L+L AR + +PHP G 
Sbjct: 239 TLKPVTGRTHQLRAHAAHIGHPIIGDDKYFNIENWELPGGIQNRLHLLARRIVIPHPSGN 298

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G + ++APLP HM +TW+ LGF 
Sbjct: 299 GMIDVSAPLPPHMQQTWNLLGFD 321


>gi|23012328|ref|ZP_00052441.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 456

 Score =  327 bits (839), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 136/329 (41%), Positives = 210/329 (63%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + V  DE  MR+DR+    +P + F  +Q I+R G++RVD KR K ++R++ 
Sbjct: 123 TLASGVQTLTVSPDEAGMRIDRFLGARFPQLPFTRVQSIVRKGELRVDGKRAKPSDRLEP 182

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+      + +      S   +   ++FL+S++LYED+ + + NKP G++VQG
Sbjct: 183 GSSVRVPPL-----KLDQPTDRPRSPNKVAGDAEFLRSLILYEDADMMILNKPFGLAVQG 237

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L++     GQ+PRL HRLD++T+G L++A+TR AA  L +SFR R  +K
Sbjct: 238 GSGTVRHVDGLLEALTGPDGQRPRLVHRLDKDTAGCLIIAKTRLAAATLAKSFRSRAARK 297

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+LV G+P+ ++  ++ +L+K      D  + V K  + GA++A++++  +D  AQK 
Sbjct: 298 IYWALVAGVPRTRQGRVSTYLVKDEPTDADARMRVAKHGDDGASHALTYYATVDQAAQKL 357

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL ++P TGRTHQLR HA H+G PIVGD KY           IQN+L+L AR + +PHP
Sbjct: 358 AWLSLKPVTGRTHQLRAHAAHIGHPIVGDPKYFDVENWELPGGIQNRLHLLARRIVIPHP 417

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 418 RTGQPVDVSAPLPPHMAQSWNLLGFDAAR 446


>gi|86749455|ref|YP_485951.1| pseudouridine synthase RluD [Rhodopseudomonas palustris HaA2]
 gi|86572483|gb|ABD07040.1| ribosomal large subunit pseudouridine synthase C [Rhodopseudomonas
           palustris HaA2]
          Length = 453

 Score =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 143/331 (43%), Positives = 214/331 (64%), Gaps = 5/331 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T V+ VVV  DE  MR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 123 LPTKVETVVVTADENGMRVDRFLEGRFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 182

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP+      +   +     S    K    LK++ LYED+ + V NKPAG++VQGG
Sbjct: 183 QSVRIPPL-----KLDTPKAPGHLSEAEQKTLAALKAMTLYEDADVLVLNKPAGLAVQGG 237

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   HID  L+   DSKGQKPRL HR+D+ET+G L+VA+TR AA  LT SFR R  +KI
Sbjct: 238 SGTTKHIDLMLEVMRDSKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRHRSARKI 297

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K+       + + +  ++GA++A++++ V++  AQK  W
Sbjct: 298 YWALVAGVPKPKQGRISTYLAKEESEDDSIMRIAEHGDEGASHAVTYYAVVETSAQKLAW 357

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+G  IVGD KY           +Q +L+L AR + +PHP G
Sbjct: 358 VSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNIENWQLPGGLQKRLHLLARRIVIPHPRG 417

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
           G + ++APLP HM+++W+ LG ++DR   I+
Sbjct: 418 GTIDVSAPLPPHMLQSWNLLGLEHDRFDPIE 448


>gi|163868619|ref|YP_001609828.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           tribocorum CIP 105476]
 gi|161018275|emb|CAK01833.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           tribocorum CIP 105476]
          Length = 327

 Score =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 161/323 (49%), Positives = 219/323 (67%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   VE DE  MRLDRWFK HYP + F  LQK+LRSGQ+RVD  RVK + R+  GQ
Sbjct: 1   MAGVEIKKVETDENGMRLDRWFKVHYPGLGFGALQKLLRSGQIRVDGGRVKADTRLCMGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+       +    I D ++        LK +LLYED K++VFNKPAG++VQGGS
Sbjct: 61  SVRVPPLPLDNMISLP---ITDKTLRGQDDGTILKKMLLYEDPKVFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HID  L+ W + KG+KPRL HRLD+ETSG+L+VAR+R AAQ LT +FR R  +K Y
Sbjct: 118 GLTRHIDSMLEVWRNKKGEKPRLVHRLDRETSGVLIVARSRGAAQALTAAFRERETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+PK K++ I+ W++K+    GD + V    E  +++A+S+++V+D   +   WL
Sbjct: 178 WALVRGVPKKKQDKISTWMVKEMTAQGDKMRVCDHGEPDSHHAVSYYRVLDTRGRTLSWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA +M  PI+GD KY  ++        IQN+L+LHAR + +PHP G
Sbjct: 238 EMEPYTGRTHQLRVHAAYMDHPIIGDSKYFFSDSNWTLPGGIQNRLHLHARRIRIPHPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G L I APLP HMV++++ L F 
Sbjct: 298 GILDIIAPLPPHMVQSFNLLSFN 320


>gi|170747290|ref|YP_001753550.1| RluA family pseudouridine synthase [Methylobacterium radiotolerans
           JCM 2831]
 gi|170653812|gb|ACB22867.1| pseudouridine synthase, RluA family [Methylobacterium radiotolerans
           JCM 2831]
          Length = 471

 Score =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 137/329 (41%), Positives = 211/329 (64%), Gaps = 7/329 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +L + VQ + VE DE  MR+DR+    +P + F  +Q I+R G++RVD KR K N+R++ 
Sbjct: 138 TLASGVQTLTVEPDEAGMRIDRFLTARFPLLPFTRVQTIVRKGELRVDGKRAKPNDRLEP 197

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+      + +  +   S+      + F++S++LYED+ + + NKP G++VQG
Sbjct: 198 GMSVRVPPL-----RLDQPTERPRSAAREQDDAAFIRSLILYEDADMMILNKPFGLAVQG 252

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG   H+DG L +     GQKPRL HRLD++T+G L++A+TR AA  L +SFR R  +K
Sbjct: 253 GSGTVRHVDGLLAALTGPDGQKPRLVHRLDKDTAGCLIIAKTRLAAATLAKSFRSRAARK 312

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IYW+L  G+P+ ++  ++ +L K+     D  + V K  ++GA++A++++ ++D  AQK 
Sbjct: 313 IYWALTAGVPRVRQGRVSTYLAKEEPTDADARMRVAKHGDEGASHALTYYAMVDQAAQKL 372

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            WL  +P TGRTHQLR HA H+G PIVGD KY +         IQN+L+L AR + +PHP
Sbjct: 373 SWLSFKPVTGRTHQLRAHAAHIGHPIVGDPKYFSVENWELPGGIQNRLHLLARRIVIPHP 432

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G+ + ++APLP HM ++W+ LGF   R
Sbjct: 433 RTGKPVDVSAPLPPHMAQSWNLLGFDAAR 461


>gi|170744410|ref|YP_001773065.1| RluA family pseudouridine synthase [Methylobacterium sp. 4-46]
 gi|168198684|gb|ACA20631.1| pseudouridine synthase, RluA family [Methylobacterium sp. 4-46]
          Length = 469

 Score =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 134/328 (40%), Positives = 203/328 (61%), Gaps = 8/328 (2%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ + V  DE  MR+DR+    +P + F  +Q ++R G++RV+ KR K  +R++ G
Sbjct: 138 LATGVQTLEVTPDEAGMRIDRFLSARFPQLPFTRIQSLVRKGELRVNGKRAKAADRVEPG 197

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             VR+PP+       +   K   S         +L+S++LYED  + V NKP G++VQGG
Sbjct: 198 ASVRVPPLK------LDAAKPGPSPARAESDLAYLRSLVLYEDQDMMVLNKPYGLAVQGG 251

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   H+DG L++     GQKPRL HRLD++T+G LV+A+TR AA  L ++FR R  +KI
Sbjct: 252 SGTKRHVDGLLEALRAPDGQKPRLVHRLDKDTAGCLVIAKTRLAAATLAKTFRSRAARKI 311

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           YW+L  G+PK ++  ++ +L K+     D  + V +  ++GA++A++++ V+D   QK  
Sbjct: 312 YWALAAGVPKVRQGRVSTYLAKEEVGEADARMRVAQHGDEGASHALTYYAVVDQAGQKLS 371

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           WL ++P TGRTHQLR HA H+G P+VGD KY           +QN+L+L AR + +PHP 
Sbjct: 372 WLSLKPVTGRTHQLRAHAAHIGHPLVGDPKYFDIENWELPGGLQNRLHLLARRIVIPHPR 431

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             + + +TAPLP HM ++W+ LGF   R
Sbjct: 432 TNKPVDVTAPLPPHMAQSWNLLGFDAGR 459


>gi|90424892|ref|YP_533262.1| pseudouridine synthase RluD [Rhodopseudomonas palustris BisB18]
 gi|90106906|gb|ABD88943.1| ribosomal large subunit pseudouridine synthase C [Rhodopseudomonas
           palustris BisB18]
          Length = 501

 Score =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 141/338 (41%), Positives = 217/338 (64%), Gaps = 4/338 (1%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           + L T V+ VVV  DE NMR+DR+ +  YP ++F ++Q+I+R G++RVD KR    +R++
Sbjct: 168 VPLPTKVETVVVSADENNMRVDRFLEARYPGLSFSHIQRIVRKGELRVDGKRADSKDRLE 227

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            GQ VRIPP+      +         S    K    L++++LYED+ + V NKPAG++VQ
Sbjct: 228 EGQTVRIPPLKLDAPKVGTGN----LSEAEQKTMAALRAMILYEDADVMVLNKPAGLAVQ 283

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG   H+D  L+   D+KGQKPRL HRLD+ET+G L++A+TR AA  LT +FR R  +
Sbjct: 284 GGSGTTRHVDLMLEVMRDAKGQKPRLVHRLDKETAGCLLIAKTRFAATALTGAFRERSAR 343

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+YW+LV G+PK K+  I+ +L K+       + + +  ++GA++A++++ V++  A K 
Sbjct: 344 KVYWALVAGVPKPKQGRISTYLAKEESEDDTIMRIAEHGDEGASHAVTYYAVVETSASKL 403

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            W+ ++P TGRTHQLR H  H+G  IVGD KY           +QN+L+L AR + +PHP
Sbjct: 404 AWVSLKPVTGRTHQLRAHMAHIGHAIVGDPKYFNIENWQLPGGLQNRLHLLARRIVIPHP 463

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
            GG + ++APLP HM+++W+ LG ++DR   I+    +
Sbjct: 464 RGGTIDVSAPLPPHMLQSWNLLGLEHDRFDPIENAPEE 501


>gi|240850791|ref|YP_002972191.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           grahamii as4aup]
 gi|240267914|gb|ACS51502.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           grahamii as4aup]
          Length = 327

 Score =  326 bits (835), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 161/325 (49%), Positives = 220/325 (67%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   VE DE  MRLDRWFK HYP + F  LQK+LRSGQ+R+D  RVK + R+  GQ
Sbjct: 1   MVGVEIKKVEVDENGMRLDRWFKVHYPGLGFGALQKLLRSGQIRLDGGRVKADTRLCMGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+       +    I D ++        LK +LLYED K++VFNKPAG++VQGGS
Sbjct: 61  AVRIPPLPINDKANLS---ITDKTLRGQDDETVLKKMLLYEDPKVFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+D  L+ W + KG+KPRL HRLD+ETSG+L+VAR+R AAQ LT +FR R  +K Y
Sbjct: 118 GLTRHMDSMLEVWRNKKGEKPRLVHRLDRETSGVLIVARSRGAAQSLTAAFRARETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+PK K++ I+ W++K+    GD + V +  E  A++A+S+++V+D   +   WL
Sbjct: 178 WALVRGVPKKKQDKISTWMVKEMTAQGDKMRVCEHGEPDAHHAVSYYRVLDTRGRALSWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA +M  PI+GD KY  ++        IQN+L+LHAR + +PHP G
Sbjct: 238 EMEPYTGRTHQLRVHAAYMDHPIIGDTKYFFSDSNWTLPGGIQNRLHLHARRIRIPHPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G L I APLP HMV++++ L F   
Sbjct: 298 GILDIVAPLPPHMVQSFNLLSFNES 322


>gi|49475763|ref|YP_033804.1| ribosomal large subunit pseudouridine synthase c [Bartonella
           henselae str. Houston-1]
 gi|49238570|emb|CAF27811.1| Ribosomal large subunit pseudouridine synthase c [Bartonella
           henselae str. Houston-1]
          Length = 327

 Score =  324 bits (831), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 161/323 (49%), Positives = 220/323 (68%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   VE DE  MRLDRWFK HYP + F +LQK+LRSGQ+R+D +RVK + R+  GQ
Sbjct: 1   MAGVEIKKVEVDESGMRLDRWFKAHYPGLGFGHLQKLLRSGQIRIDGRRVKADTRLLMGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVRIPP+       +    + D ++        LK +LLYED KI+VFNKPAG++VQGGS
Sbjct: 61  VVRIPPLPVNDMGSLP---VTDKTLRGQDDEVILKKMLLYEDPKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+D  L+ W + KG+KPRL HRLD+ETSG+L+VAR+R AAQ LT +FR R  +K Y
Sbjct: 118 GLTRHVDSMLRVWRNKKGEKPRLVHRLDRETSGVLIVARSRGAAQALTTAFRTRETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+PK K++ I+ W++K      D + V +  E  + +A+S+++V+D   +   WL
Sbjct: 178 WALVRGVPKKKQDKISTWMVKDISTQVDKMRVCEHGEPDSYHAVSYYRVVDTRGRALSWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA HM  PI+GD KY  ++        IQN+L+LHAR + +PHP G
Sbjct: 238 EMEPYTGRTHQLRVHAAHMDHPIIGDAKYFFSDSNWTLPGGIQNRLHLHARRIRIPHPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G L I APLP HMV++++ L F 
Sbjct: 298 GILDIVAPLPPHMVQSFNLLAFD 320


>gi|220926865|ref|YP_002502167.1| RluA family pseudouridine synthase [Methylobacterium nodulans ORS
           2060]
 gi|219951472|gb|ACL61864.1| pseudouridine synthase, RluA family [Methylobacterium nodulans ORS
           2060]
          Length = 457

 Score =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 134/328 (40%), Positives = 202/328 (61%), Gaps = 8/328 (2%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T VQ + V  DE  MR+DR+    +P + F  +Q ++R G++RV+ KR K  +R++ G
Sbjct: 126 LATGVQMLEVTPDEAGMRIDRFLSARFPQLPFTRIQSLVRKGELRVNGKRAKAADRVEPG 185

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             VR+PP+       +       S         FL+S++LYED  + V NKP G++VQGG
Sbjct: 186 ASVRVPPLK------LDAPPSSPSPARAESDLAFLRSLVLYEDQDMMVLNKPFGLAVQGG 239

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   H+DG L++     GQKPRL HRLD++T+G LVVA++R AA  L ++FR R  +KI
Sbjct: 240 SGTKRHVDGLLEALRTPDGQKPRLVHRLDKDTAGCLVVAKSRLAAATLAKTFRSRAARKI 299

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           YW+L  G+P+ ++  I+ +L K+     D  + V +  ++GA++A++++ V+D   QK  
Sbjct: 300 YWALAAGVPRVRQGRISTYLAKEEMGDADARMRVAQHGDEGASHALTYYAVVDQAGQKLS 359

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           WL ++P TGRTHQLR HA H+G P+VGD KY           +QN+L+L AR + +PHP 
Sbjct: 360 WLSLKPVTGRTHQLRAHAAHIGHPLVGDPKYFDIENWELPGGLQNRLHLLARRIVIPHPR 419

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             + + +TAPLP HM ++W+ LGF   R
Sbjct: 420 TNKPVDVTAPLPPHMAQSWNLLGFDASR 447


>gi|319404393|emb|CBI77996.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           rochalimae ATCC BAA-1498]
          Length = 327

 Score =  323 bits (828), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 154/323 (47%), Positives = 224/323 (69%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   VE DE  MRLDRWFK +YP + F  LQK+LRSGQ+RVD  RVK + R+  GQ
Sbjct: 1   MVGVKIKKVEADENGMRLDRWFKVYYPDVGFGYLQKLLRSGQIRVDGGRVKNDVRLVMGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP++           +++  V    +   LK +LLYEDSKI+VFNKPAG++VQGGS
Sbjct: 61  SIRVPPLLIDKEDSFP---VINKIVCGQDNDIILKDMLLYEDSKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+D  L+ W + KG+KPRL HR+D+ETSG+LVVAR+R AAQ LT +FR R  +K Y
Sbjct: 118 GLTRHVDSMLEVWRNKKGEKPRLVHRIDRETSGVLVVARSRGAAQALTAAFRTRETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ K++ I+ W++++    GD + V ++ +  +N+A+S+++V+D   +   WL
Sbjct: 178 WALVRGVPRKKQDKISTWMVREITAQGDKMRVCERRQPDSNHAVSYYRVLDTRGKALSWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++  PI+GD KY  ++   +    +QN+L+LHAR + +PHP G
Sbjct: 238 EMEPYTGRTHQLRVHAAYINHPIIGDSKYFFSDSNWDLPGGMQNRLHLHARRIRIPHPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G L +TAPLP HMV++++   F 
Sbjct: 298 GILDVTAPLPPHMVQSFNLFAFN 320


>gi|254500715|ref|ZP_05112866.1| pseudouridine synthase, RluA family [Labrenzia alexandrii DFL-11]
 gi|222436786|gb|EEE43465.1| pseudouridine synthase, RluA family [Labrenzia alexandrii DFL-11]
          Length = 340

 Score =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 156/339 (46%), Positives = 217/339 (64%), Gaps = 6/339 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ ++   V  DE  MRLDRWFK HYP + F  LQK+LR+GQVRVD KR + N RI  GQ
Sbjct: 1   MSAIEQKKVTADEAGMRLDRWFKAHYPGLGFGRLQKLLRTGQVRVDGKRAESNTRIAKGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++RIPP+   L    K+     S+  +      ++ +LLYED+++ V NKPAG++VQGGS
Sbjct: 61  IIRIPPLGVELPADDKKNARPKSTKLIADDKKAIEDMLLYEDNQVMVLNKPAGLAVQGGS 120

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+DG L ++ D KG KPRL HRLD+ETSGI++VARTR AAQ LT++FR R  +K+Y
Sbjct: 121 GLKRHLDGMLDAFTDQKGNKPRLVHRLDRETSGIILVARTRQAAQELTKAFRHRNTRKVY 180

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCW 242
           W+++ G+PK  +  I+ +L +      + + VV+Q     A +A+S + V +   QK  W
Sbjct: 181 WTILAGVPKPHQGRISTFLARDEEE--ERMQVVRQGGADDAQHAVSLYSVFEKSGQKLSW 238

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + M+P TGRTHQLR HA H+G PI+GD KY           IQN+L+L AR + +PHP G
Sbjct: 239 VTMKPVTGRTHQLRAHAAHIGHPIIGDDKYFNIENWELPGGIQNRLHLLARRIVIPHPSG 298

Query: 303 -GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
            G++ ++APLP HM +TW+ LGF  D   Y       DE
Sbjct: 299 HGKIDVSAPLPPHMQQTWNLLGF--DATDYDPETDDPDE 335


>gi|319899068|ref|YP_004159161.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           clarridgeiae 73]
 gi|319403032|emb|CBI76587.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           clarridgeiae 73]
          Length = 327

 Score =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 156/325 (48%), Positives = 223/325 (68%), Gaps = 4/325 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++   VE DE  MRLDRWFK +YP++ F  LQK+LRSGQ+R+D  RVK + R+  GQ
Sbjct: 1   MVGIKIRKVEADESGMRLDRWFKIYYPNVGFGYLQKLLRSGQIRIDGGRVKNDMRLVVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP+            +++ ++        LK+ILLYEDSKI+VFNKPAG++VQGGS
Sbjct: 61  SIRVPPLFTDKKDGFP---VINKTICGQDDRITLKNILLYEDSKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+D  L++W + KG+KPRL HRLD+ETSGILVVAR+R AAQ LT +FR R  +K Y
Sbjct: 118 GLTRHVDSMLEAWRNKKGEKPRLVHRLDRETSGILVVARSRGAAQVLTAAFRARETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ K++ I+ W+ ++     D + V +  +  +N+AIS+++V+D   +   WL
Sbjct: 178 WALVRGVPRKKQDKISTWMAREITTQADKMRVCEHRQPDSNHAISYYRVLDTRGKSLSWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA H+  PI+GD KY  ++        +QN+L+LHAR + +PHP G
Sbjct: 238 EMEPYTGRTHQLRVHAAHINHPIIGDSKYFFSDSNWELPRGVQNRLHLHARRIRIPHPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYD 327
           G L ITAPLP HMV++++   F  +
Sbjct: 298 GILDITAPLPPHMVQSFNIFAFNEN 322


>gi|319408734|emb|CBI82391.1| ribosomal large subunit pseudouridine synthase C [Bartonella
           schoenbuchensis R1]
          Length = 326

 Score =  323 bits (827), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 155/322 (48%), Positives = 221/322 (68%), Gaps = 4/322 (1%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   VE  E  MRLDRWFK HYP + F  LQK+LRSGQ+RVD +RVK + R+  GQ +R
Sbjct: 3   VEIKKVEEGESGMRLDRWFKVHYPGLAFGYLQKLLRSGQIRVDGRRVKTDIRLIVGQSIR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P +        K   + D +++       L+ +LLY+D KI+V NKPAG++VQGGSG+ 
Sbjct: 63  VPFLSVDNK---KNLSVTDKTIHDQAKLAILEKMLLYKDPKIFVLNKPAGLAVQGGSGLT 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            HIDG L+ W + KG+KPRL HRLD+ETSG+L++AR+R AAQ LT +FR R  +K YW+L
Sbjct: 120 CHIDGMLEVWRNKKGEKPRLVHRLDRETSGVLIIARSRGAAQALTAAFRARETKKTYWAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+P+ K++ I+ W++K++   GD + V +  E  +N+A+S+++V+D   +   WLEM+
Sbjct: 180 VRGVPRKKQDKISTWMVKETTAQGDKMRVCEHGEPDSNHAVSYYRVLDTRGRALSWLEME 239

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           P+TGRTHQLRVHA +M  PI+GD KY  ++        IQN+L+LHAR + +PHP GG L
Sbjct: 240 PYTGRTHQLRVHAAYMDHPIIGDSKYFFSDNNWELPGGIQNRLHLHARRIRIPHPSGGIL 299

Query: 306 QITAPLPAHMVKTWDSLGFKYD 327
            I APLP HMV++++ L F  +
Sbjct: 300 DIIAPLPPHMVQSFNLLAFNEN 321


>gi|319407393|emb|CBI81044.1| ribosomal large subunit pseudouridine synthase C [Bartonella sp.
           1-1C]
          Length = 327

 Score =  322 bits (825), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 156/323 (48%), Positives = 223/323 (69%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   VE DE  MRLDRWFK +YP + F  LQK+LRSGQ+RVD  RVK + R+  GQ
Sbjct: 1   MVSVKIKKVEADESGMRLDRWFKVYYPDVGFGYLQKLLRSGQIRVDGGRVKNDMRLVVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP++           +++  V        LK +LLYEDSKI+VFNKPAG++VQGGS
Sbjct: 61  SIRVPPLLIDKEDSFS---VINKIVCGRDDDIILKDMLLYEDSKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  HID  L+ W + KG+KPRL HR+D+ETSGILVVAR+R AAQ LT +FR R  +K Y
Sbjct: 118 GLTRHIDNMLEVWRNKKGEKPRLVHRIDRETSGILVVARSRGAAQALTAAFRTRETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ K++ I+ W++++    GD + V ++ +  +N+A+S+++V+D   +   WL
Sbjct: 178 WALVRGVPRKKQDKISTWMVREITAQGDKMRVCERRQPDSNHAVSYYRVLDTRGKALSWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA ++  PI+GD KY  ++   +    +QN+L+LHAR + +PHP G
Sbjct: 238 EMEPYTGRTHQLRVHAAYINHPIIGDSKYFFSDSNWDLPRGMQNRLHLHARRIRIPHPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G L +TAPLP HMV++++   F 
Sbjct: 298 GVLDVTAPLPPHMVQSFNLFAFN 320


>gi|319405867|emb|CBI79499.1| ribosomal large subunit pseudouridine synthase C [Bartonella sp. AR
           15-3]
          Length = 327

 Score =  321 bits (823), Expect = 8e-86,   Method: Composition-based stats.
 Identities = 154/323 (47%), Positives = 221/323 (68%), Gaps = 4/323 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   V+ DE  MRLDRWFK +YP + F  LQK+LRSGQ+RVD +RVK + R+  GQ
Sbjct: 1   MVGVKIKKVKADESGMRLDRWFKVYYPDVGFGYLQKLLRSGQIRVDGRRVKNDVRLVVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP +           + +  +   +    LK +LLYEDSKI+VFNKPAG++VQGGS
Sbjct: 61  SIRVPPFLIDKEDSAP---VFNKIIFGQEDEVILKDMLLYEDSKIFVFNKPAGLAVQGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+  H+D  L+ W + KG+KPRL HR+D+ETSG+LVVAR+R AAQ LT +FR R  +K Y
Sbjct: 118 GLTRHVDSMLEVWRNKKGEKPRLVHRIDRETSGVLVVARSRGAAQALTAAFRTRETKKTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P+ K++ I+ W++++    GD V V ++ +  +N+A+S+++V+D   +   WL
Sbjct: 178 WALVRGVPRKKQDKISTWMVREITEQGDKVRVCERRQADSNHAVSYYRVLDTRGKALSWL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           EM+P+TGRTHQLRVHA +M  PI+GD KY   +        +QN+L+LHAR + +PHP G
Sbjct: 238 EMEPYTGRTHQLRVHAAYMKHPIIGDSKYFFPDSNWALPGGMQNRLHLHARRIRIPHPSG 297

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G L ITAPLP HM+++++   F 
Sbjct: 298 GILDITAPLPPHMLQSFNLFAFN 320


>gi|91977597|ref|YP_570256.1| pseudouridine synthase RluD [Rhodopseudomonas palustris BisB5]
 gi|91684053|gb|ABE40355.1| ribosomal large subunit pseudouridine synthase C [Rhodopseudomonas
           palustris BisB5]
          Length = 444

 Score =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 142/331 (42%), Positives = 209/331 (63%), Gaps = 5/331 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L T V+ VVV  DE NMR+DR+ +  +P ++F ++Q+I+R G++RV+ KR    +R++ G
Sbjct: 114 LPTKVETVVVTADENNMRVDRFLEARFPGLSFSHIQRIVRKGELRVNGKRADSKDRLEEG 173

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP+      +       +      K    LK + LYED+ + V NKP G++VQGG
Sbjct: 174 QSVRIPPLKLDTPKLPGHLSEAEQ-----KTLQALKEMTLYEDADVLVLNKPLGLAVQGG 228

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   HID  L+   DSKGQKPRL HR+D+ET+G L+VA+TR AA  LT SFR R  +KI
Sbjct: 229 SGTTRHIDLMLEVMRDSKGQKPRLVHRIDKETAGCLLVAKTRFAATALTGSFRSRSARKI 288

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK K+  I+ +L K        + V    + GA++A++++ V++  A K  W
Sbjct: 289 YWALVAGVPKPKQGRISTYLAKDESEDDSIMRVAAHGDDGASHAVTYYAVVETSATKLAW 348

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H  H+G  I+GD KY           +QN+L+L AR + +PHP G
Sbjct: 349 VSLKPVTGRTHQLRAHMAHIGHAIIGDPKYFNIENWKLPGGLQNRLHLLARRIVIPHPRG 408

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
           G + ++APLP HM+++W+ LG ++DR   I+
Sbjct: 409 GVIDVSAPLPPHMLQSWNLLGLEHDRFDPIE 439


>gi|99080132|ref|YP_612286.1| ribosomal large subunit pseudouridine synthase C [Ruegeria sp.
           TM1040]
 gi|99036412|gb|ABF63024.1| ribosomal large subunit pseudouridine synthase C [Ruegeria sp.
           TM1040]
          Length = 348

 Score =  316 bits (811), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 129/341 (37%), Positives = 196/341 (57%), Gaps = 21/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  D+   R+DRW +  +PH+N   ++K+ R G++R+D  RVK N R+++GQ
Sbjct: 1   MSGVQMITVTEDDGGQRIDRWLRRLFPHVNQGRIEKMCRKGELRLDGGRVKANTRVEAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+  +     + + +  S  +    +  ++  ++Y+D  + V NKPAG++VQGGS
Sbjct: 61  VVRVPPLAESDMKPAEARPVKISDAD----AKMIRDCVIYKDDDVLVINKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG  ++       KPRL HRLD++TSG+LV+AR R AAQ LT +FR +  +KIY
Sbjct: 117 GTTKHVDGLSEALRFDAEDKPRLVHRLDKDTSGLLVLARNRKAAQGLTAAFRHKNTRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+LV G+P      I   L+K    G    G+ +  V   +     GA  A +++  +  
Sbjct: 177 WALVAGVPTPYLGEIKTGLVKAPGHGKSGEGEKMIPVDPRDVDATPGAKRAHTYYATLYR 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ M+P TGRTHQLR H   MG PI+GD KY  + + N            I  K
Sbjct: 237 VASRASWVAMEPVTGRTHQLRAHMAGMGHPIIGDGKYGGSGQENLGDGWGAQIGGLISKK 296

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR +   HP  G+ + +TA LP HM ++WD+ G+  D
Sbjct: 297 LHLHARRLQFEHPVTGKVVTVTAALPDHMKESWDTFGWTED 337


>gi|254476979|ref|ZP_05090365.1| pseudouridine synthase, RluD [Ruegeria sp. R11]
 gi|214031222|gb|EEB72057.1| pseudouridine synthase, RluD [Ruegeria sp. R11]
          Length = 348

 Score =  316 bits (810), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 128/341 (37%), Positives = 192/341 (56%), Gaps = 21/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  D+   R+DRW +  +PH++   ++K+ R G++R+D  RVK ++R+++GQ
Sbjct: 1   MSGVQMITVTEDDAGQRIDRWLRRLFPHVSQGRIEKMCRKGELRLDGGRVKASSRVEAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+  +     +      S       +  ++  ++Y+D  + V NKPAG++VQGGS
Sbjct: 61  TVRVPPLPASDLKPAE----APSRRISDADAKMIRGCVIYKDDAVIVLNKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG  ++      +KPRL HRLD++TSG+LV+ARTR AAQ LT +FR    +KIY
Sbjct: 117 GTTKHVDGLSEALKFDAEEKPRLVHRLDKDTSGVLVLARTRQAAQALTAAFRHHATRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+LV G+P      I   L+K    G    G+ +  +  NE     GA  + + +  +  
Sbjct: 177 WALVAGVPTPYLGEIKCGLVKAPGHGKSGEGEKMIAIHSNEVDSTPGAKRSHTQYATLYR 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ M+P TGRTHQLR H   +G PI GD KY  + + N            I  K
Sbjct: 237 VASRAAWVAMEPITGRTHQLRAHMAEIGHPIAGDGKYGGSGQENLGDGWGAQLGGIISKK 296

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LH R M   HP   + L ITAPLP HM ++WD+ G+  D
Sbjct: 297 LHLHCRRMAFEHPTTKKPLSITAPLPEHMKESWDTFGWSED 337


>gi|259416795|ref|ZP_05740715.1| ribosomal large subunit pseudouridine synthase C [Silicibacter sp.
           TrichCH4B]
 gi|259348234|gb|EEW60011.1| ribosomal large subunit pseudouridine synthase C [Silicibacter sp.
           TrichCH4B]
          Length = 348

 Score =  316 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 129/341 (37%), Positives = 196/341 (57%), Gaps = 21/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  D+   R+DRW +  +PH+N   ++K+ R G++R+D  RVK N R+++GQ
Sbjct: 1   MSGVQMITVTEDDGGQRIDRWLRRLFPHVNQGRIEKMCRKGELRLDGGRVKANTRVEAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+  +     + + +  S  +    +  ++  ++Y+D  + V NKPAG++VQGGS
Sbjct: 61  VVRVPPLAKSDMKPAEARPVKISDAD----AKMIRDCVVYKDDDVLVINKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG  ++       KPRL HRLD++TSG+LV+AR R AAQ LT +FR +  +KIY
Sbjct: 117 GTTKHVDGLSEALRFDAEDKPRLVHRLDKDTSGLLVLARNRKAAQGLTAAFRHKNTRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+LV G+P      I   L+K    G    G+ +  V   +     GA  A +++  +  
Sbjct: 177 WALVAGVPTPYLGEIKTGLVKAPGHGKSGEGEKMIPVDPRDVDATPGAKRAHTYYATLYR 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ M+P TGRTHQLR H   MG PI+GD KY  + + N            I  K
Sbjct: 237 VASRASWVAMEPVTGRTHQLRAHMAGMGHPIIGDGKYGGSGQENLGDGWGAQIGGLISKK 296

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR +   HP  G+ + +TA LP HM ++WD+ G+  D
Sbjct: 297 LHLHARRLQFEHPVTGKVVTVTAALPDHMKESWDTFGWTED 337


>gi|254470362|ref|ZP_05083766.1| ribosomal large subunit pseudouridine synthase C [Pseudovibrio sp.
           JE062]
 gi|211960673|gb|EEA95869.1| ribosomal large subunit pseudouridine synthase C [Pseudovibrio sp.
           JE062]
          Length = 349

 Score =  316 bits (809), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 139/321 (43%), Positives = 211/321 (65%), Gaps = 3/321 (0%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++   V+ D+  +RLDRWFK ++P + F  LQK+LR+ QVRVD KR + + R+++GQ +
Sbjct: 19  KIEMRRVDEDDAGIRLDRWFKENFPELGFGRLQKLLRTKQVRVDGKRAEASTRLEAGQEI 78

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP+   L    ++     +   +    + ++ ++L+EDS + V NKPAG++VQGGSG+
Sbjct: 79  RIPPLGVELAADDRKNAKPRARKLVDSDREAIEQMMLFEDSHVMVLNKPAGLAVQGGSGL 138

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG L ++ + KG KPRL HRLD+ETSGIL+VA+TR AAQ LT++FR R  +KIYW+
Sbjct: 139 KRHVDGMLDAFTNQKGDKPRLVHRLDRETSGILLVAKTRRAAQELTKAFRHRNTRKIYWA 198

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+PK ++  I+ +L +    G + + V +  +  A +A+S + V++   QK  W+ +
Sbjct: 199 MVAGVPKPRQGRISTYLARDE--GEERMRVARHGDDEAQHAVSLYNVVEQSGQKLAWVTL 256

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
           +P TGRTHQLR H+ H+G PI+GD KY           IQNKL+L AR + +PHP G G 
Sbjct: 257 KPVTGRTHQLRAHSAHIGHPIIGDPKYFNIQNWELPGGIQNKLHLLARRIVIPHPSGNGV 316

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           + ++APLP HM +TW+ LG  
Sbjct: 317 IDVSAPLPPHMQQTWNLLGMD 337


>gi|163739478|ref|ZP_02146888.1| Pseudouridine synthase, RluD [Phaeobacter gallaeciensis BS107]
 gi|163740271|ref|ZP_02147665.1| ribosomal large subunit pseudouridine synthase C [Phaeobacter
           gallaeciensis 2.10]
 gi|161386129|gb|EDQ10504.1| ribosomal large subunit pseudouridine synthase C [Phaeobacter
           gallaeciensis 2.10]
 gi|161387231|gb|EDQ11590.1| Pseudouridine synthase, RluD [Phaeobacter gallaeciensis BS107]
          Length = 348

 Score =  315 bits (807), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 132/341 (38%), Positives = 194/341 (56%), Gaps = 21/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  D+ + R+DRW +  +PH++   ++K+ R G++R+D  RVK N+R+ +GQ
Sbjct: 1   MSGVQMITVSEDDADQRIDRWLRRLFPHVSQGRIEKMCRKGELRLDGGRVKANSRVAAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+  +     +      S  +    +  ++  ++Y+D  + V NKPAG++VQGGS
Sbjct: 61  VVRVPPLGASDLKPAEAPSYRISEAD----AKMIRGCVIYKDDAVIVLNKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG   +      +KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R  +KIY
Sbjct: 117 GTTKHVDGLSAALQFDAEEKPRLVHRLDKDTSGVLVLARTRLAAQSLTAAFRHRATRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+LV G+P      I   L+K    G    G+ +  +  NE     GA  + +H+  +  
Sbjct: 177 WALVAGVPTPYLGEIKCGLVKAPGHGKSGEGEKMIAIHSNEVDSTPGAKRSHTHYATLYR 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ M+P TGRTHQLR H   +G PI GD KY  + + N            I  K
Sbjct: 237 VASRAAWVAMEPITGRTHQLRAHMAEIGHPIAGDGKYGGSSQENLGDGWGAQLGGIISKK 296

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LH R M   HP   + L ITAPLP HM  +WD+ G+  D
Sbjct: 297 LHLHCRRMAFEHPTTKKPLSITAPLPDHMKDSWDTFGWSED 337


>gi|154248685|ref|YP_001419643.1| RluA family pseudouridine synthase [Xanthobacter autotrophicus Py2]
 gi|154162770|gb|ABS69986.1| pseudouridine synthase, RluA family [Xanthobacter autotrophicus
           Py2]
          Length = 364

 Score =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 145/350 (41%), Positives = 205/350 (58%), Gaps = 34/350 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V  DE  MRLDRWFK H+P ++F +LQK++R+GQVRVD  RVK ++R++ GQ VRIPP+
Sbjct: 7   TVAEDEAGMRLDRWFKVHFPDLSFGHLQKLVRTGQVRVDGGRVKTSSRVEPGQSVRIPPL 66

Query: 71  INALNHII-------------------------------KEQKILDSSVNLTKHSDFLKS 99
            +                                       Q    +     +   FLKS
Sbjct: 67  GDEPQDEPAGKPGAAGKASEAGRVSAGGEASGTTEAPAKPRQSASAAKRKEDEDRAFLKS 126

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           I L+ED  + V NKP G++VQGGSG   H+DG L+   D  GQKPRL HR+D++TSG L+
Sbjct: 127 ITLFEDKDVMVLNKPYGLAVQGGSGTYRHMDGILEVLRDKDGQKPRLVHRIDKDTSGCLL 186

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+TR AA  L +SFR R  +K+YW++V G+PK K+  I+ +L +      + + V +  
Sbjct: 187 VAKTRFAASVLAKSFRSREARKVYWAVVPGVPKPKQGRISTYLARDE--DEEKMRVARHG 244

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E  A++AI+++ V+D  AQK  WL ++P TGRTHQLR H  H+G PIVGD KY       
Sbjct: 245 EDEASHAITYYAVVDQAAQKMSWLSLKPVTGRTHQLRAHLAHIGHPIVGDPKYFDIENWE 304

Query: 280 FTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDR 328
               +QN+L+L AR + +PHP G G + ++APLP HM +++  LGF   +
Sbjct: 305 LPGGLQNRLHLLARRLVIPHPRGQGLIDVSAPLPHHMAQSFAVLGFDASQ 354


>gi|83593991|ref|YP_427743.1| ribosomal large subunit pseudouridine synthase C [Rhodospirillum
           rubrum ATCC 11170]
 gi|83576905|gb|ABC23456.1| ribosomal large subunit pseudouridine synthase C [Rhodospirillum
           rubrum ATCC 11170]
          Length = 330

 Score =  313 bits (801), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 197/318 (61%), Gaps = 5/318 (1%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V V  DE+  RLDRWFK  YP +    L+K+LR+GQ+RVD KRVK   R+++GQ VR
Sbjct: 3   VETVAVTQDEDGSRLDRWFKRRYPALTHGRLEKLLRTGQIRVDGKRVKSGERLEAGQQVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+ +           +            L+  +L+ED+ + V NK AG++VQGG+G  
Sbjct: 63  VPPLGDEAPSPSSSGHAVPRPAA-EGEIRALRRAILHEDAHLIVINKEAGLAVQGGTGTP 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +H+DG L+S  D  G+ PRL HRLD++TSG+LV+ART+AAA+ LT +FR R   K+YW++
Sbjct: 122 HHLDGMLESLADG-GETPRLVHRLDKDTSGVLVLARTQAAARALTSAFRSREALKVYWAI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G P   +  I   L K +   G+ + +   NE+    A++ F+V+D  A+   W+E+ 
Sbjct: 181 VVGRPPMLQGTIKGALAKVAGGRGERMEI---NEEEGKRAVTDFRVVDQAAKACAWVELH 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P TGRTHQLRVH L MG PI+GD KY         + +  +++LHAR + LPHP GG L+
Sbjct: 238 PRTGRTHQLRVHCLEMGTPILGDGKYGGPGAFLEGTELPKRMHLHARALALPHPAGGVLE 297

Query: 307 ITAPLPAHMVKTWDSLGF 324
           I AP P H V++  +LGF
Sbjct: 298 IIAPPPPHFVESLKTLGF 315


>gi|260432477|ref|ZP_05786448.1| ribosomal large subunit pseudouridine synthase C [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260416305|gb|EEX09564.1| ribosomal large subunit pseudouridine synthase C [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 347

 Score =  310 bits (795), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 131/341 (38%), Positives = 193/341 (56%), Gaps = 22/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + VE  + + RLDRW +  +PH++   ++K+ R G++RVD  RVK + R+Q+GQ
Sbjct: 1   MSGVQMITVEPGDGDQRLDRWLRRLFPHVSQGRIEKMCRKGELRVDGGRVKGSTRLQAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+ +  +     +  +         +  ++S ++Y D  +   NKP G+ VQGGS
Sbjct: 61  VVRVPPLPDPDHKPAPTRPRV-----TDADAKMIQSCVIYRDDHVLALNKPHGLPVQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G A H+DG  ++      + PRL HRLD++TSG+L++ARTR AA+ LT +FR R  +KIY
Sbjct: 116 GQARHVDGLAEALRFGYDENPRLVHRLDKDTSGVLLMARTREAAKGLTAAFRHRNTRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+LV G+P      I   L+K    G    G+ +  V  NE     GA  A + +  +  
Sbjct: 176 WALVAGVPTPYLGEIKTGLVKAPGHGKQGEGEKMIAVHLNEIDSTPGAKRAHTLYATLFR 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ M+P TGRTHQLR H   +G PI+GD KY  + + N            I  K
Sbjct: 236 VASRASWVAMEPVTGRTHQLRAHMAAIGHPIIGDGKYGGSGQENLGDGWGAQLGGVISKK 295

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR     HP  G+ + I APLP HM  +WD+LG+  D
Sbjct: 296 LHLHARTASFKHPMTGKQVTINAPLPPHMKDSWDTLGWTED 336


>gi|158424148|ref|YP_001525440.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
 gi|158331037|dbj|BAF88522.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
          Length = 384

 Score =  310 bits (795), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 137/352 (38%), Positives = 210/352 (59%), Gaps = 32/352 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V  DE +MRLDRWFK H+P ++F +LQK++R+GQVRVD  RVK + R+  GQ VR
Sbjct: 25  VELKQVTEDEADMRLDRWFKTHFPDLSFGHLQKLVRTGQVRVDGGRVKTSTRLSPGQSVR 84

Query: 67  IPPVINALNHI-----------------------------IKEQKILDSSVNLTKHSDFL 97
           +PP+ +                                      ++  ++      ++FL
Sbjct: 85  VPPLGDDAAPAASPAQSKTKGEGAVAGEEGGFAGSGSPFAPAAHQVRAAARREQTDAEFL 144

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +SI+L+ED  + V NKP+GI+VQGGSG   HIDG L +     GQKPRL HR+D++T+G 
Sbjct: 145 RSIILFEDKDVLVLNKPSGIAVQGGSGTFRHIDGMLDALRAKDGQKPRLVHRIDKDTAGC 204

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+ R +A  L ++FR R  +KIYW+LV G+PK ++  I+ +L ++     + + V +
Sbjct: 205 LLIAKNRLSAAQLAKNFRSREARKIYWALVPGVPKPRQGRISTYLAREE--AEERMRVAR 262

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             E+ A++A++++ V++  AQK  WL ++P TGRTHQ+R H  H+  PIVGD KY     
Sbjct: 263 HGEEDASHAVTYYAVVEHAAQKMSWLSLKPVTGRTHQIRAHLAHIHHPIVGDPKYFNIEN 322

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDR 328
                 +QN+L+L AR + +PHP G G + ++APLP HM ++W  LGF   +
Sbjct: 323 WELPGGLQNRLHLLARRLVIPHPRGEGMIDVSAPLPPHMAQSWAVLGFDATQ 374


>gi|56695430|ref|YP_165778.1| ribosomal large subunit pseudouridine synthase C [Ruegeria pomeroyi
           DSS-3]
 gi|56677167|gb|AAV93833.1| ribosomal large subunit pseudouridine synthase C [Ruegeria pomeroyi
           DSS-3]
          Length = 347

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 132/342 (38%), Positives = 193/342 (56%), Gaps = 24/342 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRWF+  +PH+    ++K+ R G++RVD  R K   R++ GQ
Sbjct: 1   MSGVQMITVGEGDGDQRLDRWFRRMFPHVGQGRIEKMCRKGELRVDGARAKPATRLEVGQ 60

Query: 64  VVRIPPVINALNHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VRIPP+          + ++ DS   L      +++ +L+ D  I V NKPAG++VQGG
Sbjct: 61  QVRIPPLPAPGERPEPVKSRVSDSDAKL------IRACVLHRDDDIIVLNKPAGLAVQGG 114

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   H+DG  ++      + PRL HRLD++TSG+LV+ARTR AA  LT +FR R  +KI
Sbjct: 115 SGQTRHVDGLSEALRFGNDENPRLVHRLDKDTSGVLVLARTREAAARLTAAFRHRNTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVID 234
           YW+LV G+P      I   L+K    G    G+ ++VV  +E     GA  A +++  + 
Sbjct: 175 YWALVAGVPTPYLGEIKTGLVKAGGHGARGEGEKMNVVHLSELDATPGAKRAHTYYATLY 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQN 286
             A +  W+ M+P TGRTHQLR H   +G PI+GD KY  + + N            I  
Sbjct: 235 RVAGRASWVAMEPVTGRTHQLRAHMAGIGHPIIGDGKYGGSGQENLGDGWGAQLGGIISK 294

Query: 287 KLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
           KL+LHAR +   HP    ++  TAPLP HM ++WD+ G+  D
Sbjct: 295 KLHLHARSLSFEHPSTRKKVTFTAPLPEHMRESWDTFGWTED 336


>gi|332187840|ref|ZP_08389574.1| pseudouridine synthase, RluA family protein [Sphingomonas sp. S17]
 gi|332012190|gb|EGI54261.1| pseudouridine synthase, RluA family protein [Sphingomonas sp. S17]
          Length = 363

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 127/344 (36%), Positives = 196/344 (56%), Gaps = 7/344 (2%)

Query: 4   MT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           MT +V+   V  D++ +RLDRWFK H P  +F  + K  R+GQ+RVD  R    +RI +G
Sbjct: 1   MTDFVRQFTVGYDDDGIRLDRWFKRHLPDTSFTTVAKWARTGQLRVDGARATPGDRITAG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           QV+R+PP   A     K  +    ++     + F + +++++D    V NKP G++ QGG
Sbjct: 61  QVLRVPPAEPAPAESAKPSR--PRNILSEDEAAFAREMVIHKDRDALVLNKPPGLATQGG 118

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +    H+DG L +       +P+L HRLD++TSG L+VAR   +A    ++F  R  +KI
Sbjct: 119 TKTTTHVDGLLDALQFEAEGRPKLVHRLDKDTSGALLVARNARSAAFFAKAFSGRTAKKI 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+P  +   I   + K+   GG+ +HV   +E+    A S ++VI+    + CW
Sbjct: 179 YWALVVGVPSIEDGTIELPIAKQPGTGGEKMHV---DEENGQAARSRYRVIERAGNRCCW 235

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+QP TGRTHQLRVH   +G PIVGD KY        T  I  K++LHAR + + HP+G
Sbjct: 236 VELQPFTGRTHQLRVHMAAIGHPIVGDGKYGG-AAAFLTGGISRKMHLHARRIRVDHPDG 294

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL 346
           GR+  TA LP+H  ++ + LGF   R   + +   +    +++L
Sbjct: 295 GRIDQTAELPSHFAESMNQLGFDEIRGDVLPQEEDRGPPPKDVL 338


>gi|126737039|ref|ZP_01752774.1| ribosomal large subunit pseudouridine synthase C [Roseobacter sp.
           SK209-2-6]
 gi|126721624|gb|EBA18327.1| ribosomal large subunit pseudouridine synthase C [Roseobacter sp.
           SK209-2-6]
          Length = 348

 Score =  309 bits (792), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 127/341 (37%), Positives = 194/341 (56%), Gaps = 21/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  ++++ R+DRW +  +PH+N   ++K+ R G++R+D  RVK + R+ +GQ
Sbjct: 1   MSGVQMITVTEEDDDQRIDRWLRRLFPHVNQGRIEKMCRKGELRLDGGRVKASTRVATGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP + A +    E +    S      +  ++  ++Y+D  + V NKPAG++VQGGS
Sbjct: 61  VVRVPP-LPASDLKPAEPRATKIS---DADAKMIRGCVIYKDDDVIVLNKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG  ++      +KPRL HRLD++TSG+LV+AR R AAQ LT +FR +  +KIY
Sbjct: 117 GTTRHVDGLSEALRLEAEEKPRLVHRLDKDTSGVLVLARNRKAAQALTAAFRHKNTRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQ----NEKGANYAISHFKVIDC 235
           W+LV G+P      I   L+K    G     + +  V      +  GA  A +H+  +  
Sbjct: 177 WALVAGVPTPYLGEIKTGLVKAPGHGRSGEGEKMIPVHPRDIDDTPGAKRAHTHYATLYR 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ M+P TGRTHQLR H   +G PI GD KY  + + N            I  K
Sbjct: 237 VASRASWVAMEPITGRTHQLRAHMAAIGHPIAGDGKYGGSGQENLGDGWGAQLGGIISKK 296

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR +   HP   + + + A LP HM ++WD+LG+  D
Sbjct: 297 LHLHARRLVFEHPVSHKPISVEAELPEHMKESWDTLGWTED 337


>gi|298291467|ref|YP_003693406.1| pseudouridine synthase [Starkeya novella DSM 506]
 gi|296927978|gb|ADH88787.1| pseudouridine synthase, RluA family [Starkeya novella DSM 506]
          Length = 363

 Score =  309 bits (791), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 152/352 (43%), Positives = 213/352 (60%), Gaps = 33/352 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V+ DEE MRLDRWFK H+P ++F +LQK+LRSGQVRVD  RVK N R+ SGQ VR
Sbjct: 3   VETRRVDRDEEGMRLDRWFKTHFPELSFGHLQKLLRSGQVRVDGGRVKTNTRLSSGQSVR 62

Query: 67  IPP-----VINALNHIIKEQKILDSSVNL-------------------------TKHSDF 96
           IPP      ++A +HI  E+ I                                 K +  
Sbjct: 63  IPPLEEKPQLSAADHIEAEEAIARGEAPPRPPRNGEGARRSDLAAPAVKRASVDDKDAAA 122

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           LK++ L+ED  + V NKP G++VQGGSG   H+DG L++     GQKPRL HR+D++TSG
Sbjct: 123 LKAMTLFEDRDVLVLNKPYGLAVQGGSGTYRHVDGMLEALRGDDGQKPRLVHRIDKDTSG 182

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           IL+VA++R AA  L ++FR R  +K+YW+LV G+P+  +  I+ +L K      + + V 
Sbjct: 183 ILLVAKSRLAASTLAKTFRSRSARKVYWALVPGVPRPAQGRISTYLAKDE--AAERMRVA 240

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +  +  A++AIS++ V+D  AQK  WL M+P TGRTHQLR HA H+G PIVGD KY    
Sbjct: 241 RHGDDEASHAISYYAVVDHAAQKLSWLSMKPVTGRTHQLRAHAAHIGHPIVGDPKYFNVE 300

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
                  +QN+L+L AR + +PHP   + + ++APLP HM ++W+ LGF   
Sbjct: 301 NWPLPGGLQNRLHLLARRLVIPHPRADKLIDVSAPLPPHMQQSWNVLGFDTS 352


>gi|89053115|ref|YP_508566.1| ribosomal large subunit pseudouridine synthase C [Jannaschia sp.
           CCS1]
 gi|88862664|gb|ABD53541.1| ribosomal large subunit pseudouridine synthase C [Jannaschia sp.
           CCS1]
          Length = 354

 Score =  308 bits (790), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 126/340 (37%), Positives = 196/340 (57%), Gaps = 18/340 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + +  D+ + RLDRWF+  +PH+    ++K+ R G++RVD  RVK N R++ GQ
Sbjct: 1   MSGVQTLEIGPDDGDQRLDRWFRRIFPHVPQGRIEKMCRKGEIRVDGGRVKSNTRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAGISVQGG 122
           +VR+PP+ +A +        ++++  ++   +  +++ ++Y D  I   NKPAG+  QGG
Sbjct: 61  MVRVPPLPDAADPKADPANWVNNASRISDADEKMIRAAVIYRDDHIIAINKPAGLPTQGG 120

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +G + H+DG  ++       KPRL HRLD++TSG+L++ARTR  A+ LT++FR+R  +KI
Sbjct: 121 TGQSRHVDGLAEALKFGLEDKPRLVHRLDKDTSGVLLMARTRMGAKALTDAFRLRSTRKI 180

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNE----KGANYAISHFKVID 234
           YW+ V G P  +   I   L+K    G     + +  V  +E     GA  A + + V+ 
Sbjct: 181 YWAAVAGSPLPRMGTIKLGLVKAPGHGRGGENEKMRAVPVDEIAQVDGAKRAETDYAVMS 240

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQN 286
               + CW  + P TGRTHQLR H   +G PI+GD KY  + + N            I  
Sbjct: 241 NLGGRVCWCALVPITGRTHQLRAHMAEIGHPIIGDGKYGGSGQENLGDGWGAQLGGEISR 300

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           KL+LHAR +   HP  G ++ + APLP HM KTWD+LG+ 
Sbjct: 301 KLHLHARSLSFRHPMTGAQVNLVAPLPEHMAKTWDTLGWD 340


>gi|89070524|ref|ZP_01157813.1| ribosomal large subunit pseudouridine synthase C [Oceanicola
           granulosus HTCC2516]
 gi|89043831|gb|EAR50029.1| ribosomal large subunit pseudouridine synthase C [Oceanicola
           granulosus HTCC2516]
          Length = 348

 Score =  308 bits (789), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 129/339 (38%), Positives = 191/339 (56%), Gaps = 22/339 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + VE DE +MRLDRW +  +P +    ++K+ R G++R+D  RVK N RI  GQ
Sbjct: 1   MSGVQTITVEADEADMRLDRWLRARFPQLTQGRIEKMCRKGELRIDGGRVKSNTRIAPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+         E +         + ++ +++ +LY D  + V NKP G+  QGGS
Sbjct: 61  QVRVPPLPPPG-----EVRPAGRDEPSAQDAEMMRAAVLYRDDHLIVLNKPPGLPTQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG   +      +KPRL HRLD++TSGIL++ARTRAAA+ LT++FR R  +KIY
Sbjct: 116 RQTRHVDGLSAALTFGLEEKPRLVHRLDKDTSGILLLARTRAAAKGLTDAFRSRETRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+ V G+P  +   +   L+K+   G     + +  +  +E      A  A++ + VI+ 
Sbjct: 176 WAAVAGVPHPRMGTVKYGLVKQPGHGARGENEKMRCIHPDEVLRTPDAKRAVTDYAVIET 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNK 287
            A++  W+ + P TGRTHQLR H   +G PI GD KY  + + N            I  K
Sbjct: 236 LARRAAWVALVPVTGRTHQLRAHMAELGHPIAGDGKYGGSGQENLGDGWGAGLGGDISRK 295

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           L LHAR + L HP  G R+  TAPLP HM +TW+ +G+ 
Sbjct: 296 LQLHARSLSLTHPVSGARMTFTAPLPDHMARTWEYVGWD 334


>gi|300023017|ref|YP_003755628.1| pseudouridine synthase [Hyphomicrobium denitrificans ATCC 51888]
 gi|299524838|gb|ADJ23307.1| pseudouridine synthase, RluA family [Hyphomicrobium denitrificans
           ATCC 51888]
          Length = 327

 Score =  307 bits (786), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 135/324 (41%), Positives = 205/324 (63%), Gaps = 6/324 (1%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V + E +MRLDRWF+ H+P + +  LQK+LRSGQVRV+ KR + N+R+ +G  +R
Sbjct: 3   VETITVADGEADMRLDRWFRVHFPEVGYTYLQKLLRSGQVRVNSKRAQANDRLSAGAEIR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P ++     +    +         +  D ++ ++L+ED  + V NKP G++VQGG+G  
Sbjct: 63  VPAIVREPKKLSPTGRPALGVSKGDR--DAIEKMILFEDDHVLVLNKPFGLAVQGGTGTK 120

Query: 127 YHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            HIDG L+   D   G++PRL HRLD++T+G+L+VA+TR AA  L  +F+ R   K YW+
Sbjct: 121 KHIDGMLEGMADRFGGERPRLVHRLDRDTTGVLLVAKTREAAAKLGRTFQTRSAAKTYWA 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFCWLE 244
           LV G+PK  +  +   L+K S   GD V   +  E+  A +A +H+ V+D  A K  W+ 
Sbjct: 181 LVKGVPKPPQGKVEAALVKASGPDGDRVRKARPGEQDAAMHATTHYSVVDRAAHKAAWVS 240

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++P TGR HQLR H   +G PIVGD+KY  +      + I+ KL+LHAR + +PHP+GG+
Sbjct: 241 LKPVTGRQHQLRAHMHLIGHPIVGDNKYEGDVHMPAEN-IEKKLHLHARRLVIPHPKGGK 299

Query: 305 -LQITAPLPAHMVKTWDSLGFKYD 327
            + +TAPLPAHM+ +WD LGF  +
Sbjct: 300 TIDVTAPLPAHMLASWDLLGFDVN 323


>gi|254466117|ref|ZP_05079528.1| pseudouridine synthase, RluD [Rhodobacterales bacterium Y4I]
 gi|206687025|gb|EDZ47507.1| pseudouridine synthase, RluD [Rhodobacterales bacterium Y4I]
          Length = 348

 Score =  306 bits (785), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 127/341 (37%), Positives = 197/341 (57%), Gaps = 21/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  D+   R+DRW +  +PH+N   ++K+ R G++R+D  RVK ++R+++GQ
Sbjct: 1   MSGVQMITVSEDDGGQRIDRWLRRLFPHVNQGRIEKMCRKGELRLDGARVKASSRVEAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+ ++     + + +  S  +    +  ++S ++Y D  + V NKPAG++VQGGS
Sbjct: 61  VVRVPPLADSDLKPAEPRAMKISDAD----AKMIQSCVIYRDDDVIVLNKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG  ++      +KP+L HR+D++TSG+LV+AR R AAQ LT +FR +  +KIY
Sbjct: 117 GTTKHVDGLAEALKFGLEEKPKLVHRIDKDTSGVLVLARNRKAAQGLTAAFRHKNTRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQ----NEKGANYAISHFKVIDC 235
           W+LV G+P      I N L+K    G    G+ +  V      +  GA  A + +  +  
Sbjct: 177 WALVAGVPTPYLGEIKNGLVKAPGHGKSGEGEKMINVHPRDIDDTPGAKRAHTLYATLYR 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ M+P TGRTHQLR H   MG PI GD KY  + + N            I  K
Sbjct: 237 VASRAAWVAMEPITGRTHQLRAHMSGMGHPIAGDGKYGGSGQENMGDGWGAQIGGVISKK 296

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR M   HP   + + + APLP HM ++W++ G+  D
Sbjct: 297 LHLHARRMVFEHPVTRKPVSVVAPLPEHMKESWETFGWSED 337


>gi|84499811|ref|ZP_00998099.1| ribosomal large subunit pseudouridine synthase C [Oceanicola
           batsensis HTCC2597]
 gi|84392955|gb|EAQ05166.1| ribosomal large subunit pseudouridine synthase C [Oceanicola
           batsensis HTCC2597]
          Length = 347

 Score =  304 bits (780), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 124/341 (36%), Positives = 189/341 (55%), Gaps = 22/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  ++   RLDRW +  +P +    ++K+ R G +RVDK RVK + R+++GQ
Sbjct: 1   MSGVQMLTVAPEDAGQRLDRWLRRLFPQVTQGRIEKMCRKGDLRVDKGRVKSSTRLEAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+  +       +  +  +      +  ++  +L+ D  I   NKPAG+  QGGS
Sbjct: 61  VVRVPPLPESAAPEPAPRDAVSEA-----DARLIRDCVLWSDDHIVALNKPAGLPTQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             + H+DG  ++ V +  +KPRL HRLD++TSG+L++ARTR AAQ LT + R ++ +KIY
Sbjct: 116 KQSRHVDGLSQALVPAGAEKPRLVHRLDKDTSGVLLLARTRVAAQGLTAALRHKQTRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK--------QNEKGANYAISHFKVIDC 235
           W+LV G+P      I   L+K    G                +   GA  A + +  +  
Sbjct: 176 WALVAGVPTPYLGEIRYGLVKAPGHGKGGEGEKMIAVHPAEVEGTPGAKRAHTLYATLYR 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ ++P TGRTHQLR H   +G PI+GD KY  + + N            I  K
Sbjct: 236 VASRASWVALEPLTGRTHQLRAHLAEIGHPIIGDGKYGGSGQENLGDGWGAQLGGIISRK 295

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR M   HP  G+ + +TAPLP HM ++WD+LG+  D
Sbjct: 296 LHLHARSMTFEHPVTGKPVTVTAPLPDHMAESWDTLGWAED 336


>gi|84685385|ref|ZP_01013283.1| ribosomal large subunit pseudouridine synthase C [Maritimibacter
           alkaliphilus HTCC2654]
 gi|84666542|gb|EAQ13014.1| ribosomal large subunit pseudouridine synthase C [Rhodobacterales
           bacterium HTCC2654]
          Length = 350

 Score =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 131/354 (37%), Positives = 196/354 (55%), Gaps = 24/354 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRWFK  +PH+    ++K+ R G++RVD  RVK + R++ GQ
Sbjct: 1   MSRVQTITVAEGDGDQRLDRWFKRQFPHVPQGRVEKMCRKGEIRVDGGRVKASTRVEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+ +       E+          K +  ++  ++Y D  I   NKP G+  QGGS
Sbjct: 61  EVRIPPLPDPG-----ERPAAPRPSVTDKDAQMIRDCVIYRDDHIIALNKPPGLPTQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  +        KPRL HRLD++TSG+L++ARTR  A+ LT++FR R  +KIY
Sbjct: 116 KQTRHVDGLAEVLTFGYDDKPRLVHRLDKDTSGVLLLARTRQVAKDLTDAFRHRNTRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W++V G+P  +K  +   L+K    G    G+ +  +  +E    +GA  A + + VI+ 
Sbjct: 176 WAVVAGVPLPRKGTVKWGLVKAPGHGGQGEGEKMLCIHPSEVAKVEGAKRAETDYVVIEN 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNK 287
            AQ+  W+ + P TGRTHQLR H   MG PIVGD KY  + + N            I  K
Sbjct: 236 LAQRAAWVGLTPITGRTHQLRAHMAEMGHPIVGDGKYGGSGQENLGDGWGAMLGGEISKK 295

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           L+LHAR +++ HP   + + I A LP HM +TW+ LGF+ D        + ++E
Sbjct: 296 LHLHARSIEIEHPVTKKPIFIEAALPEHMARTWEQLGFRVDDA--PDDPFEEEE 347


>gi|329114604|ref|ZP_08243363.1| Ribosomal large subunit pseudouridine synthase C [Acetobacter
           pomorum DM001]
 gi|326696084|gb|EGE47766.1| Ribosomal large subunit pseudouridine synthase C [Acetobacter
           pomorum DM001]
          Length = 328

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 134/321 (41%), Positives = 194/321 (60%), Gaps = 8/321 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V    V  DE+ +RLDR+F+ HYPH+    LQK+ R+GQ+RV+ KRV+ + R++ GQ
Sbjct: 1   MSVVNR-TVSEDEDGIRLDRYFRRHYPHLTQGALQKLCRTGQIRVEGKRVEASTRLEPGQ 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+  A        + LD  +        ++ +++Y+D  + V NKPAG++VQGG 
Sbjct: 60  TVRVPPIPMAAKPARDVPRPLDEKLARE-----IRKMVVYQDKHVIVLNKPAGLAVQGGP 114

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           GI  HID  L    +    +PRL HR+D++TSG+L++ART   A  L  SFR R ++KIY
Sbjct: 115 GITKHIDMMLDGLREEDDPRPRLVHRIDKDTSGLLLLARTPGVAAKLAASFRGRDVKKIY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++V G P      I   L +     G       + +  A +A S ++V+D  A+KF WL
Sbjct: 175 WAVVVGRPDPLSGEIDQPLARLGAGPGSITVAADRKDADAQFARSVYEVLDSAARKFSWL 234

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E+ P TGRTHQLRVH   +G PI+GD KY         S   ++L+LHAR +D+PHP GG
Sbjct: 235 ELSPLTGRTHQLRVHCESLGTPILGDPKYGG--AAAHPSGFTDRLHLHARMLDMPHPAGG 292

Query: 304 RLQITAPLPAHMVKTWDSLGF 324
           RL ++A LP HM +T+ +LGF
Sbjct: 293 RLTVSAELPPHMRETFRTLGF 313


>gi|258542797|ref|YP_003188230.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256633875|dbj|BAH99850.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256636934|dbj|BAI02903.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-03]
 gi|256639987|dbj|BAI05949.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-07]
 gi|256643043|dbj|BAI08998.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-22]
 gi|256646098|dbj|BAI12046.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-26]
 gi|256649151|dbj|BAI15092.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-32]
 gi|256652138|dbj|BAI18072.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-01-42C]
 gi|256655195|dbj|BAI21122.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase C
           [Acetobacter pasteurianus IFO 3283-12]
          Length = 328

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 133/321 (41%), Positives = 192/321 (59%), Gaps = 8/321 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V    V  DE  +RLDR+F+ HYPH+    LQK+ R+GQ+RV+ KRV+ + R++ GQ
Sbjct: 1   MSVVNR-TVSEDEAGIRLDRYFRRHYPHLTQGALQKLCRTGQIRVEGKRVEASTRLEPGQ 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+  A        + LD      K +  ++ +++Y+D  +   NKPAG++VQGG 
Sbjct: 60  TVRVPPIPMAAKPARDVPRPLDE-----KLAREIRKMVVYQDKHVIALNKPAGLAVQGGP 114

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           GI  H+D  L    +    +PRL HR+D++TSG+L++ART   A  L  SFR R ++KIY
Sbjct: 115 GITKHVDMMLDGLREEDDPRPRLVHRIDKDTSGLLLLARTPGVAAKLAASFRGRDVKKIY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++V G P      I   L +     G       + +  A  A S ++V+D  A+KF WL
Sbjct: 175 WAVVVGRPDPLSGEIDQPLARLGAGPGSITVAADRKDADAQSARSVYEVLDSAARKFSWL 234

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E+ P TGRTHQLRVH   +G PI+GD KY         S   ++L+LHAR +D+PHP GG
Sbjct: 235 ELSPLTGRTHQLRVHCESLGTPILGDPKYGG--AAAHPSGFTDRLHLHARMLDMPHPAGG 292

Query: 304 RLQITAPLPAHMVKTWDSLGF 324
           RL ++A LP HM +T+ +LGF
Sbjct: 293 RLTVSAELPPHMRETFRTLGF 313


>gi|326388341|ref|ZP_08209937.1| ribosomal large subunit pseudouridine synthase C [Novosphingobium
           nitrogenifigens DSM 19370]
 gi|326207073|gb|EGD57894.1| ribosomal large subunit pseudouridine synthase C [Novosphingobium
           nitrogenifigens DSM 19370]
          Length = 436

 Score =  303 bits (775), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 130/344 (37%), Positives = 193/344 (56%), Gaps = 12/344 (3%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+  VV  D++ +RLDRWFK H P + F  + +  R+GQ+RVD KR   + R+  GQ +R
Sbjct: 10  VRQFVVGRDDDGVRLDRWFKRHLPQVGFATVSRWARTGQIRVDGKRADVDTRLVPGQTLR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFL-KSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +PP            +   +   LT+    L + I+L +D    V NKP G++ QGGSG 
Sbjct: 70  VPPGGTQ----APGSRGPRTRKPLTEEEMALAERIVLTQDRAAIVLNKPPGLATQGGSGT 125

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG L ++      +PRL HRLD++TSG+L++ART  +A + +  F  R  +KIYW+
Sbjct: 126 HSHVDGLLDAYAGDNDPRPRLVHRLDKDTSGVLLIARTPGSAAYFSRHFSGRSAKKIYWA 185

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV GIP+     I   L K+   GG+ + V +  E     A + ++VID    +  W+E+
Sbjct: 186 LVMGIPEINDGYIDLPLAKQPGTGGEKMMVDESGE--GQTARTRYRVIDRAGNRAAWVEL 243

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QP TGRTHQLRVH   +G PIVGD KY        +  I  KL+LHAR + +PHPEG  +
Sbjct: 244 QPLTGRTHQLRVHMAAIGHPIVGDGKYGGQ-AAFLSGSISRKLHLHARRLLIPHPEGDTI 302

Query: 306 QITAPLPAHMVKTWDSLGF-KYDRNLYIKR---LYSQDECKQNI 345
            + APLP H   +   LGF + + +L +++   +  +D  K+  
Sbjct: 303 DVVAPLPEHFAASLAQLGFTESEGDLPLEKPQVIDPRDAQKRAA 346


>gi|288958958|ref|YP_003449299.1| ribosomal large subunit pseudouridine synthase C [Azospirillum sp.
           B510]
 gi|288911266|dbj|BAI72755.1| ribosomal large subunit pseudouridine synthase C [Azospirillum sp.
           B510]
          Length = 354

 Score =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 131/330 (39%), Positives = 197/330 (59%), Gaps = 11/330 (3%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+   V  DE +MRLDRWFK H+P +N   LQK+LR+GQVR+D KR + ++R+ +GQ 
Sbjct: 19  SKVEIRTVTADEADMRLDRWFKRHFPDVNHSYLQKLLRTGQVRIDGKRAETSSRLAAGQG 78

Query: 65  VRIPP------VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           VRIPP       +   NH   +       ++  K    L++++LY D+ +   NKPAG++
Sbjct: 79  VRIPPLAAWAAPVKGPNHGSNQGAGKPKGMS-DKQIAELQALVLYRDADVIAINKPAGLA 137

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           VQGG+G + H+D  L +      ++P+L HRLD++TSG+L++ART  AA  LTE FR   
Sbjct: 138 VQGGTGTSKHLDAMLDALRFDGNERPKLVHRLDKDTSGVLLLARTTFAASKLTELFRGSA 197

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++KIYW++  G+P   +  I   L K+    G+    V +N++    A++ + V +   +
Sbjct: 198 VRKIYWAVTVGVPTPYQGKIDLALAKEGGPHGER---VAENKEEGKRAVTVYSVQENVGK 254

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +  ++ M P TGRTHQLRVH   +G PI+GD KY         + +  KL+LHAR + LP
Sbjct: 255 QAAFVAMWPLTGRTHQLRVHMAAVGTPILGDGKYAGQGAFLAGAEVAKKLHLHARRLILP 314

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           HP GG+ + +TAPLP HM  TW   GF  +
Sbjct: 315 HPRGGKTIDVTAPLPDHMQATWKYFGFSPN 344


>gi|163733779|ref|ZP_02141221.1| ribosomal large subunit pseudouridine synthase C [Roseobacter
           litoralis Och 149]
 gi|161392890|gb|EDQ17217.1| ribosomal large subunit pseudouridine synthase C [Roseobacter
           litoralis Och 149]
          Length = 346

 Score =  302 bits (773), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 129/341 (37%), Positives = 182/341 (53%), Gaps = 22/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE + RLDRWFK  +P I+   ++K+ R G++RVD  RVK   R++ GQ
Sbjct: 1   MSAVQTLTVGEDEGDQRLDRWFKKQFPLISQGRVEKMCRKGEIRVDGGRVKAATRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+ +           +  S      +  ++S ++Y D  I   NKPAG+  QGGS
Sbjct: 61  QVRIPPLPDT-----AAPAPVARSAVSAADAKLIQSCVIYRDDHIIAINKPAGLPTQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG  ++       KPRL HRLD++TSG+L++ARTR AA+ LT + R +  +KIY
Sbjct: 116 GQTRHVDGLSEALKFGFEDKPRLVHRLDKDTSGVLLLARTRMAAKALTTAMRHKETRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD--------YVHVVKQNEKGANYAISHFKVIDC 235
           W+LV G+P      I   L+K    G                    GA  A + +  +  
Sbjct: 176 WALVAGVPTPYLGEIRYALVKAPGHGRRGEGEKMIALPPREVDETPGAKRAHTLYATLYR 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
              +  W+ M+P TGRTHQLRVH   +G PIVGD KY  + + N            I  K
Sbjct: 236 VGSRASWVAMEPITGRTHQLRVHMAEIGHPIVGDGKYGGSGQENMGDGWGAQLGGVISKK 295

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR M   HPE  + + ITA +P HM ++WD+ G+  D
Sbjct: 296 LHLHARMMRFEHPETRKPVTITADMPDHMKQSWDTFGWTED 336


>gi|260428027|ref|ZP_05782006.1| ribosomal large subunit pseudouridine synthase C [Citreicella sp.
           SE45]
 gi|260422519|gb|EEX15770.1| ribosomal large subunit pseudouridine synthase C [Citreicella sp.
           SE45]
          Length = 351

 Score =  301 bits (772), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 125/341 (36%), Positives = 188/341 (55%), Gaps = 18/341 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + +   + + RLDRW K H+PH+    ++K+ R G++RVD  RVK + R++ GQ
Sbjct: 1   MSRVQTITIGPGDGDQRLDRWLKRHFPHLAQGRIEKMCRKGEIRVDGGRVKASTRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+                 V+    +  ++  ++++D  I   NKP G+ VQGGS
Sbjct: 61  QVRIPPLPEPDAVNAAPAAAPKPRVS-DADTKLIQDAVIWKDDHIIALNKPPGLPVQGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  ++      +KPRL HRLD++TSG+L++ARTRA AQ LT + R ++ +KIY
Sbjct: 120 KTTRHVDGLSEALRFGLDEKPRLVHRLDKDTSGVLLLARTRAVAQALTAAIRHKQTRKIY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W++V G+P      I   L+K    G    G+ +  V   +    +GA  A + +  +  
Sbjct: 180 WAVVAGVPTPYLGEIRYALVKAPGHGSSGEGEKMICVHPRDVDRTEGAKRAHTLYATLYR 239

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ ++P TGRTHQLR H   +G PI+GD KY  + + N            I  K
Sbjct: 240 VAGRASWVALEPITGRTHQLRAHMAEIGHPIIGDGKYGGSGQENLGDGWGAQLGGVISKK 299

Query: 288 LYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR M   HP    R+ +TAPLP HM  TW++LG+  D
Sbjct: 300 LHLHARSMTFEHPVTHKRVTVTAPLPEHMKHTWETLGWTED 340


>gi|126728208|ref|ZP_01744024.1| ribosomal large subunit pseudouridine synthase C [Sagittula
           stellata E-37]
 gi|126711173|gb|EBA10223.1| ribosomal large subunit pseudouridine synthase C [Sagittula
           stellata E-37]
          Length = 347

 Score =  301 bits (771), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 128/344 (37%), Positives = 193/344 (56%), Gaps = 28/344 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRW K  +PH+    ++K+ R G++R+D  R K ++R+++G 
Sbjct: 1   MSRVQTITVGPGDGDQRLDRWLKRLFPHVAQSRIEKMCRKGELRLDGGRCKASSRVETGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNL---TKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            VRIPP        + E   +DS+       K ++ +++ +L++D  I   NKP G++ Q
Sbjct: 61  QVRIPP--------LPEPGQVDSAPKPSFNEKDAEMIRACVLWKDDHIIALNKPPGLATQ 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG   H+DG  ++      +KPRL HRLD++TSG+L++ARTRA A+ LTE+ R R  +
Sbjct: 113 GGSGQTRHVDGLSEALTFGMDEKPRLVHRLDKDTSGVLLLARTRAVAKALTEAIRHREAR 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNE----KGANYAISHFKV 232
           KIYW+LV G+P      I   L+K    G     + +  V   E    +GA  A + +  
Sbjct: 173 KIYWALVAGVPTPYLGEIKYGLVKAPGHGKGGEAEKMRCVHPKEIATTEGAKRAHTLYAT 232

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------I 284
           +   A +  W+ M+P TGRTHQLR H   +G PI+GD KY  + + N            I
Sbjct: 233 LYRVAGRASWVAMEPVTGRTHQLRAHMAEIGHPIIGDGKYGGSGQENLGDGWGAQLGGII 292

Query: 285 QNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
             KL+LHAR + L HP        TAPLP HM ++WD+LG++ D
Sbjct: 293 SKKLHLHARSLTLLHPVTKTPFTATAPLPEHMKQSWDTLGWEED 336


>gi|254459621|ref|ZP_05073037.1| pseudouridine synthase, RluA family [Rhodobacterales bacterium
           HTCC2083]
 gi|206676210|gb|EDZ40697.1| pseudouridine synthase, RluA family [Rhodobacteraceae bacterium
           HTCC2083]
          Length = 347

 Score =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 124/339 (36%), Positives = 194/339 (57%), Gaps = 22/339 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ +++E D+ + RLDR+ K  +P +    ++K+ R G++R+D  RVK N+R+++G 
Sbjct: 1   MSRVQTIIIEEDDGDQRLDRFLKRKFPQVTQGMIEKMCRKGELRLDGGRVKANSRVETGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+ ++        K    S      + F++S ++Y+D  +   NKPAG+ VQGG+
Sbjct: 61  QLRIPPLPDS-----AAPKHAAPSKVSAADTKFIRSCVIYKDDHVIALNKPAGLPVQGGT 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G A H+DG L + +    ++P+L HRLD++TSG+L++ RTR A   LT SFR R  +KIY
Sbjct: 116 GHARHVDGLLDALMYDFEERPKLVHRLDKDTSGVLILGRTRRATADLTASFRHRNTRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+ + G+P  +   I   L+K    G    G+ +  +   E    +GA  A++ + V++ 
Sbjct: 176 WAAIAGVPNPRMGTIKYGLMKAPGHGARGEGEKMICIHPREVDQTEGAKRALTDYAVLET 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
             Q+  W  + P TGRTHQLR H   MG P+VGD KY  + + N            +  K
Sbjct: 236 AGQRTSWCALIPITGRTHQLRAHMSEMGHPVVGDGKYGGSGQENLGDGWGSQLGGDLSKK 295

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           L+LHAR + + HP     L ITAPLP HM +TWD+  + 
Sbjct: 296 LHLHARSLQIEHPSTKATLHITAPLPDHMQRTWDTFAWD 334


>gi|86135800|ref|ZP_01054379.1| ribosomal large subunit pseudouridine synthase C [Roseobacter sp.
           MED193]
 gi|85826674|gb|EAQ46870.1| ribosomal large subunit pseudouridine synthase C [Roseobacter sp.
           MED193]
          Length = 348

 Score =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 125/341 (36%), Positives = 193/341 (56%), Gaps = 21/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   +++ R+DRW +  +PH+N   ++K+ R G++R+D  RVK N R+ +GQ
Sbjct: 1   MSGVQMITVAEADDDQRIDRWLRRLFPHVNQGRIEKMCRKGELRLDGGRVKANTRVAAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+  +       +    S  +    +  ++  ++Y+D  + V NKPAG++VQGGS
Sbjct: 61  VVRVPPLAESDLKPAAPRVARISETD----AKMIRGCVIYKDDDVIVLNKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG   +      +KPRL HRLD++TSG+LV+AR R AA+ LT +FR R  +KIY
Sbjct: 117 GTTKHVDGLADALRFDAEEKPRLVHRLDKDTSGVLVLARNRLAAKSLTAAFRHRNTRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLK----KSHIGGDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+LV G+P      I   L+K     +   G+ +  V  NE     GA  A +++  +  
Sbjct: 177 WALVAGVPTPYLGEIKAGLVKAGGHGAGGEGEKMIAVHPNEIDRTPGAKRAHTYYATLYR 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ M+P TGRTHQLR H   +G PI+GD KY  + + N            I  K
Sbjct: 237 VAGRASWVAMEPVTGRTHQLRAHMAEIGHPIIGDGKYGGSGQENLGDGWGAQLGGVISKK 296

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR +   HP   + + + A LP+HM  +W++ G+  D
Sbjct: 297 LHLHARRLVFEHPTTKKDIVMMAELPSHMKDSWETFGWTED 337


>gi|114766871|ref|ZP_01445793.1| ribosomal large subunit pseudouridine synthase C [Pelagibaca
           bermudensis HTCC2601]
 gi|114540917|gb|EAU43977.1| ribosomal large subunit pseudouridine synthase C [Roseovarius sp.
           HTCC2601]
          Length = 350

 Score =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 123/341 (36%), Positives = 182/341 (53%), Gaps = 19/341 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRW K  +PH+    ++K+ R G++RVD  R K   R++ GQ
Sbjct: 1   MSRVQTITVGPGDGDQRLDRWLKRQFPHLQQGRIEKMCRKGELRVDGGRCKAATRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+           K    +      +  ++  ++Y D  I   NKP G+ VQGGS
Sbjct: 61  QVRVPPLPEPGETPAPAAK--PKATVSDADAKMIRDAVIYRDDHIIALNKPPGLPVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  ++      +KPRL HRLD++TSG+L++ARTR  AQ LT + R ++ +KIY
Sbjct: 119 KQERHVDGLAEALRFDYDEKPRLVHRLDKDTSGVLLLARTREIAQALTGAIRHKQTRKIY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W++V G+P      I   L+K    G    G+ +  V   E     GA  A + +  +  
Sbjct: 179 WAVVAGVPTPYLGEIRFGLVKAPGHGKSGEGEKMICVHPREMDRTPGAKRAHTLYATLYR 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
            A +  W+ ++P TGRTHQLR H   +G PI+GD KY  + + N            I  K
Sbjct: 239 VAGRASWVALEPITGRTHQLRAHMAEIGHPIIGDGKYGGSGQENLGDGWGAQLGGVISKK 298

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR M   HP   + + +TA LPAHM  TW++LG+  D
Sbjct: 299 LHLHARSMTFLHPVTKKPVTVTASLPAHMANTWETLGWAED 339


>gi|149913096|ref|ZP_01901630.1| hypothetical protein RAZWK3B_03870 [Roseobacter sp. AzwK-3b]
 gi|149813502|gb|EDM73328.1| hypothetical protein RAZWK3B_03870 [Roseobacter sp. AzwK-3b]
          Length = 348

 Score =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 128/342 (37%), Positives = 184/342 (53%), Gaps = 21/342 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRW + H+PH++   ++K+ R G++RVD  RVK + R++ GQ
Sbjct: 1   MSGVQTLTVTEGDADQRLDRWLRRHFPHVSQGRIEKLCRKGELRVDGGRVKASTRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+ +              S      +  ++S ++Y D  I   NKP G+ VQGGS
Sbjct: 61  QVRIPPLPDPGQI----DSASPHSRISDADARMIQSAVIYRDDHIIALNKPPGLPVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG   +      +KPRL HRLD++TSG+L++AR+RA A+ LT  FR R  +KIY
Sbjct: 117 KQTRHVDGLADALRFGAEEKPRLVHRLDKDTSGVLILARSRAVAKTLTAGFRHRDTRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQN----EKGANYAISHFKVIDC 235
           W+ V G+P  +   I   L+K    G    G+ +  +         GA  A + F VI+ 
Sbjct: 177 WAAVAGVPSPRMGTIRFGLVKAPGHGAQGEGEKMLCLHPEAVDSTPGAKRATTDFAVIES 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNK 287
              +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            I  K
Sbjct: 237 AGARCAWVALVPVTGRTHQLRAHMAEIGHPIVGDGKYGGSGQENMGDGWGAQLGGEISRK 296

Query: 288 LYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDR 328
           L+LHAR + L HP    RL +TAPLP HM +TWD   ++   
Sbjct: 297 LHLHARSLTLEHPVSRARLHLTAPLPDHMKRTWDMFQWQTSE 338


>gi|296284584|ref|ZP_06862582.1| pseudouridylate synthase [Citromicrobium bathyomarinum JL354]
          Length = 388

 Score =  299 bits (767), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 125/338 (36%), Positives = 192/338 (56%), Gaps = 11/338 (3%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V+   V  D+E +RLDRWFK H P + F  + +  R+GQ+RVD  R K ++R+  GQV+
Sbjct: 12  EVRQYTVAEDDEGVRLDRWFKRHLPEVGFATVARWARTGQIRVDGARAKPDDRLTQGQVL 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP   A       ++ L             +++++ E     V NKP G++ QGGS  
Sbjct: 72  RIPPGNPARAKTPPRRRELTEDQKAQ-----ARAMVIKETPNAIVLNKPPGLATQGGSKT 126

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG L ++V+  G +PRL HRLD++TSG+L++ART  +A   ++ F  R  +K+YW+
Sbjct: 127 FSHVDGLLDAFVEGDGPRPRLVHRLDKDTSGVLLIARTPGSAAAFSKRFAGRSAKKVYWA 186

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G+P+     I   L K+   GG+ +HV   + +G   A + ++V++    +  WLE+
Sbjct: 187 LVVGVPEQHVGEIDAPLAKQPGTGGEKMHV---DTEGGQPAKTRYRVVERAGNRAAWLEL 243

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +P TGRTHQLRVH   MG PIVGD KY    +   T  +  K++LHAR + +  P GG+L
Sbjct: 244 EPLTGRTHQLRVHCAAMGHPIVGDGKYGGQ-EAFLTGSVSRKMHLHARRLIISQPGGGQL 302

Query: 306 QITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQ 343
            +TA LP H   T + +GF  D +L   +   ++   +
Sbjct: 303 DVTAELPEHFAATMEQMGF--DLSLSDAQPLREEAPPK 338


>gi|87200850|ref|YP_498107.1| ribosomal large subunit pseudouridine synthase C [Novosphingobium
           aromaticivorans DSM 12444]
 gi|87136531|gb|ABD27273.1| ribosomal large subunit pseudouridine synthase C [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 436

 Score =  299 bits (767), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 126/336 (37%), Positives = 190/336 (56%), Gaps = 5/336 (1%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V+   +  D+   RLDRWFK H P + F  + +  R+GQ+R+D KR   + R+++GQ++
Sbjct: 10  QVRQFTIGKDDAGARLDRWFKRHLPQVGFATVSRWARTGQIRIDGKRADVDTRLEAGQIL 69

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP          + +     +   +     +S++L +D    V NKP G++ QGGSG 
Sbjct: 70  RVPPGNATPVGTPGKGERARKPLT-EEQIQLAESMVLEKDRAAIVLNKPPGLATQGGSGT 128

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG L ++V+    +PRL HRLD++TSG+L++ART  +A   ++ F  R  +KIYW+
Sbjct: 129 HEHVDGLLDAYVNEGEARPRLVHRLDKDTSGVLLIARTPGSAAFFSKRFSCRSARKIYWA 188

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G+P  K   I   L K+   GG+ + V +  +     A S ++VI        W+E+
Sbjct: 189 LVVGVPDVKDGLIELPLAKQPGTGGEKMMVDESGQ--GQSARSRYRVISRAGNAAAWVEL 246

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QP TGRTHQLRVH   +G PIVGD KY        T  I  K++LHAR + + HPEG  +
Sbjct: 247 QPLTGRTHQLRVHMAAIGHPIVGDGKYGGQ-AAFLTGSISRKMHLHARRLRIEHPEGDMI 305

Query: 306 QITAPLPAHMVKTWDSLGFKYDR-NLYIKRLYSQDE 340
            +TAPLPAH   +  SLGF  +  +L ++ +   DE
Sbjct: 306 DVTAPLPAHFAASMASLGFHEEEGDLPLEPVKLVDE 341


>gi|310816979|ref|YP_003964943.1| RluA family pseudouridine synthase [Ketogulonicigenium vulgare Y25]
 gi|308755714|gb|ADO43643.1| RluA family pseudouridine synthase [Ketogulonicigenium vulgare Y25]
          Length = 347

 Score =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 128/337 (37%), Positives = 194/337 (57%), Gaps = 19/337 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   E ++RLDRW +  +P++    ++K+ R G++RVD  RVK N R++ GQ
Sbjct: 1   MSGVQTITVAEGEGDLRLDRWLRKKFPNLTQGQIEKMCRKGELRVDGGRVKSNARLEDGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VRIPP    L   I++Q  +     +T+  ++ +++ +L++D  I V NKP G+  QGG
Sbjct: 61  NVRIPP----LGAEIEQQAPMAVRTRVTRSDAEMIQAAVLWKDEHIIVLNKPPGLPSQGG 116

Query: 123 SGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           SG+   H+DG  ++ +     +P+L HRLD++TSG+L++ART   A+ L+E+ R R ++K
Sbjct: 117 SGLGDRHVDGLTEALMFGYKDRPKLVHRLDKDTSGLLLLARTDRVARALSEALRHRNVRK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ----NEKGANYAISHFKVIDCFA 237
           IYW+ V GIP      +   L+K    G + +H V        +GA  A + + V D   
Sbjct: 177 IYWAAVAGIPTPWAGSVKYGLVKMGRRGDEKMHCVHPAAVATTEGAKRAHTDYAVQDQAG 236

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLY 289
           Q+  W+ + P TGRTHQLR H   +G PI+GD KY  +   N            +QNKL+
Sbjct: 237 QRMAWMALVPITGRTHQLRAHMAEIGHPIIGDGKYGGSNAENAGDGWGAGIGGGVQNKLH 296

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           LHAR + + HP     L + APLPAHM  TWD LG+ 
Sbjct: 297 LHARTLIIEHPITKETLTLQAPLPAHMQSTWDYLGWN 333


>gi|254512315|ref|ZP_05124382.1| ribosomal large subunit pseudouridine synthase C [Rhodobacteraceae
           bacterium KLH11]
 gi|221536026|gb|EEE39014.1| ribosomal large subunit pseudouridine synthase C [Rhodobacteraceae
           bacterium KLH11]
          Length = 347

 Score =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 126/342 (36%), Positives = 195/342 (57%), Gaps = 24/342 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRW +  +PH++   ++K+ R G++RVD  RVK + R++ GQ
Sbjct: 1   MSGVQMITVAEGDGDQRLDRWLRRLFPHVSQGRIEKMCRKGELRVDGGRVKASTRLEVGQ 60

Query: 64  VVRIPPVINALNHI-IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           VVR+PP+ +A +   +   ++ D+          ++S ++Y+D ++   NKP G+ VQGG
Sbjct: 61  VVRVPPLPDADHKPAVVRHRVSDADAK------MIQSCVIYKDDQVLALNKPHGLPVQGG 114

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   H+D   ++      + PRL HRLD++TSG+L++ARTR AA+ LT +FR R  +KI
Sbjct: 115 SGQTRHVDSLSEALRFGYDENPRLVHRLDKDTSGVLLMARTRDAAKALTAAFRHRNTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVID 234
           YW+LV G+P      I   L+K S  G    G+ +  +  +E     GA  A + +  + 
Sbjct: 175 YWALVAGVPTPYLGEIKTGLVKASGHGKQGEGEKMIALHPSEVNDTPGAKRAHTLYATLY 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQN 286
             A +  W+ M+P TGRTHQLR H   +G PI+GD KY  + + N            I  
Sbjct: 235 RVAGRAAWVAMEPVTGRTHQLRAHMAAIGHPIIGDGKYGGSGQENLGDGWGAQLGGIISK 294

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           KL+LHAR +   HP   + + + APLP HM  +WD+LG+  D
Sbjct: 295 KLHLHARSLSFEHPITRKPVSLAAPLPDHMKHSWDTLGWTED 336


>gi|58040098|ref|YP_192062.1| ribosomal large subunit pseudouridine synthase C [Gluconobacter
           oxydans 621H]
 gi|58002512|gb|AAW61406.1| Ribosomal large subunit pseudouridine synthase C [Gluconobacter
           oxydans 621H]
          Length = 335

 Score =  299 bits (765), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 133/339 (39%), Positives = 193/339 (56%), Gaps = 10/339 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT V   +V  DE ++RLDRWF+ HYP++    LQK+ R GQ+RV+  RV+ N R+  GQ
Sbjct: 1   MT-VTNRIVTEDEADIRLDRWFRRHYPNLTQGALQKLCRKGQIRVEGGRVQTNTRLIPGQ 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+ +         K           +  ++ +++YED  + V +KP+G++ QGG 
Sbjct: 60  SVRIPPLPDV-------DKPAPLPPPDPMLAREIRKMVIYEDEHLLVLDKPSGLATQGGP 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           GI  H+D  L       G +PRL HR+D++TSGIL++ART   A  L  +FR R ++K Y
Sbjct: 113 GITKHVDMMLDGLRTEGGDRPRLVHRIDRDTSGILLIARTPGVAAKLAAAFRGRDVEKTY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++V G P  +   I   L K    G   V    ++E+ A  A + ++ +D   +K  WL
Sbjct: 173 WAVVVGRPSPESGIIDQPLAKIGAGGAALVIAASRDEEDAASAKTEYETLDAAGKKLSWL 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++ P TGRTHQLRVH   +G PI+GD +Y    K        ++L+LHAR +D+PHP GG
Sbjct: 233 KLSPLTGRTHQLRVHTESIGTPILGDPRYGG--KAAHPEGFIDRLHLHARQLDIPHPAGG 290

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECK 342
           RL +TAPLP HM +T+ +LGF        KR+      K
Sbjct: 291 RLIVTAPLPPHMRETFRTLGFVPGETPAPKRVRGGSSSK 329


>gi|126736635|ref|ZP_01752375.1| Pseudouridine synthase, RluD [Roseobacter sp. CCS2]
 gi|126713948|gb|EBA10819.1| Pseudouridine synthase, RluD [Roseobacter sp. CCS2]
          Length = 351

 Score =  298 bits (764), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 127/338 (37%), Positives = 188/338 (55%), Gaps = 19/338 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ  V+  D+ + RLDR+ +  +PH+    ++K+ R G+VRVD  RVK N+R++ GQ
Sbjct: 1   MSGVQTRVIGPDDGDQRLDRYLRRLFPHLTQGRIEKMCRKGEVRVDGGRVKSNSRVEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+             L         +  ++S ++Y+D  I   NKP G++ QGG+
Sbjct: 61  KIRIPPLPTEEEAAAAAS--LAKHGVTKADAKLIQSCVIYKDDHIIAINKPHGLATQGGT 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  ++ +    +KPRL HRLD++TSG+L++ARTR  A+ LTE+ + R  +KIY
Sbjct: 119 NTTRHVDGLSEALMFDYDEKPRLVHRLDKDTSGVLLLARTRMMAKQLTENLKHRETRKIY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNE----KGANYAISHFKVIDC 235
           W+ V G+P  +   I   L+K    G     + +  V   +    +GA  A S + V+D 
Sbjct: 179 WAAVAGVPHPRAGTIKYGLVKAPGHGRGGENEKMRCVHPRDLDSVEGAKRATSDYAVMDT 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNK 287
            A +  W  + P TGRTHQLR H   +G PIVGD KY  + + N          S I  K
Sbjct: 239 LASRAAWCALVPITGRTHQLRAHMAEIGHPIVGDGKYGGSGQENLGDGWGAGMGSEIGRK 298

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
           L+LHAR + + HP  G  L +TAPLP HM  TWD +G+
Sbjct: 299 LHLHARSLTIEHPATGATLHLTAPLPEHMQNTWDFVGW 336


>gi|83854943|ref|ZP_00948473.1| ribosomal large subunit pseudouridine synthase C [Sulfitobacter sp.
           NAS-14.1]
 gi|83941466|ref|ZP_00953928.1| ribosomal large subunit pseudouridine synthase C [Sulfitobacter sp.
           EE-36]
 gi|83842786|gb|EAP81953.1| ribosomal large subunit pseudouridine synthase C [Sulfitobacter sp.
           NAS-14.1]
 gi|83847286|gb|EAP85161.1| ribosomal large subunit pseudouridine synthase C [Sulfitobacter sp.
           EE-36]
          Length = 349

 Score =  298 bits (763), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 130/339 (38%), Positives = 192/339 (56%), Gaps = 23/339 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ++VVE  + + RLDRWFK  +P I    ++K+ R G +RVD  RVK + R++ GQ
Sbjct: 1   MSRVQHLVVEEGDGDQRLDRWFKRTFPLIGQGLIEKMCRKGDIRVDGGRVKASTRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+ +       ++  +  +      + F++S ++Y D  I   NKP G+ VQGGS
Sbjct: 61  TVRIPPLPDEKAPPPPKRTRISEA-----DTKFIRSCVIYRDDHIIALNKPPGLPVQGGS 115

Query: 124 G-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    H+D    + +    +KPRL HRLD++TSG+L++ARTR+ A  LT SFR R  +KI
Sbjct: 116 GQSDRHVDALADALMFELDEKPRLVHRLDKDTSGVLIMARTRSIAAALTASFRHRETRKI 175

Query: 183 YWSLVWGIPKNKKECIANWLLKK----SHIGGDYVHVVKQNE----KGANYAISHFKVID 234
           YW+ V G+P  +   I   L+K     +   G+ ++ V   +    +GA  A + +  + 
Sbjct: 176 YWAAVAGVPHPRNGTIKFGLVKAFGHGARGEGEKMYCVHPKDMETTEGAKRATTDYATLA 235

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQN 286
              ++ CW+ + P TGRTHQLR H   +G PIVGD KY  + + N            I  
Sbjct: 236 QAGKRTCWMALIPVTGRTHQLRAHMAEIGHPIVGDGKYGGSGQENMGDGWGAQLGGDISK 295

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
           KL+LHAR + L HP    RL +TAPLP HM +TWD+  +
Sbjct: 296 KLHLHARSLTLEHPVTKARLNLTAPLPDHMARTWDTFQW 334


>gi|255263430|ref|ZP_05342772.1| ribosomal large subunit pseudouridine synthase C [Thalassiobium sp.
           R2A62]
 gi|255105765|gb|EET48439.1| ribosomal large subunit pseudouridine synthase C [Thalassiobium sp.
           R2A62]
          Length = 347

 Score =  298 bits (763), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 119/339 (35%), Positives = 189/339 (55%), Gaps = 22/339 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ ++V   + + R+DRW +  +PH++   ++K+ R G +RVD  RVK N R++ GQ
Sbjct: 1   MSGVQKIIVAEGDGDQRVDRWLRRLFPHVSQGRIEKMCRKGDLRVDGGRVKSNTRVEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+ +A      E      +   +  ++ ++S+++Y+D  I   NKP+GI+ QGGS
Sbjct: 61  EVRVPPLPDAD-----EITAGPVTKITSADAEMMRSLVIYKDDHIIALNKPSGIASQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  ++      +KPRL HRLD++TSG+ ++ARTR  A+ ++++F+ R  +KIY
Sbjct: 116 KQVRHLDGLAEALKFDYFEKPRLVHRLDRDTSGVFIMARTREIAKAMSDAFKERETRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNE----KGANYAISHFKVIDC 235
           W+ V G+P      +   L+K    G     + +  +   E     GA  A + + ++D 
Sbjct: 176 WAAVGGVPHPAMGTVRWGLIKSGGHGRGGENEKMRCIHPREVEHTPGAKRATTDYALLDR 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNK 287
              +  W+ + P TGRTHQLR H   MG PI+GD KY  + + N            I  K
Sbjct: 236 LGSRAAWIALVPVTGRTHQLRAHMAEMGHPIIGDGKYGGSGQENLGDGWGAGMGEEIGRK 295

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           L+LHAR +   HP  G R+ +TA LP HM  TWD +G+ 
Sbjct: 296 LHLHARSLSFTHPATGKRVNLTASLPEHMKHTWDFVGWN 334


>gi|110678758|ref|YP_681765.1| ribosomal large subunit pseudouridine synthase C [Roseobacter
           denitrificans OCh 114]
 gi|109454874|gb|ABG31079.1| ribosomal large subunit pseudouridine synthase C [Roseobacter
           denitrificans OCh 114]
          Length = 346

 Score =  298 bits (763), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 126/341 (36%), Positives = 181/341 (53%), Gaps = 22/341 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE + RLDRWFK  +P I+   ++K+ R G++RVD  RVK   R++ GQ
Sbjct: 1   MSAVQTLTVGEDEGDQRLDRWFKKQFPLISQGRVEKMCRKGEIRVDGGRVKAATRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+ +           +  S      +  ++S ++Y D  I   NKPAG+  QGGS
Sbjct: 61  QVRIPPLPDT-----AAPAPVARSAVSAADARMIQSCVIYRDDHIIAINKPAGLPTQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG  ++       KPRL HRLD++TSG+L++ARTR AA+ LT + R +  +KIY
Sbjct: 116 GQTRHVDGLAEALKFGFEDKPRLVHRLDKDTSGVLLLARTRMAAKALTTAMRHKETRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVH--------VVKQNEKGANYAISHFKVIDC 235
           W+LV G+P      I   L+K    G                    GA  A + +  +  
Sbjct: 176 WALVAGVPTPYLGEIRYALVKAQGRGRGGEGEKMIALPPREVDETPGAKRAHTLYATLYR 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
              +  W+ M+P TGRTHQLR H   +G PI+GD KY  + + N            I  K
Sbjct: 236 VGSRASWVAMEPITGRTHQLRAHMAEIGHPIIGDGKYGGSGQENMGDGWGAQLGGVISKK 295

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L+LHAR M   HPE  + + ITA +P HM ++W++ G+  D
Sbjct: 296 LHLHARMMRFEHPETRKPVTITADMPDHMKQSWETFGWTED 336


>gi|182678295|ref|YP_001832441.1| RluA family pseudouridine synthase [Beijerinckia indica subsp.
           indica ATCC 9039]
 gi|182634178|gb|ACB94952.1| pseudouridine synthase, RluA family [Beijerinckia indica subsp.
           indica ATCC 9039]
          Length = 350

 Score =  298 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 138/342 (40%), Positives = 204/342 (59%), Gaps = 31/342 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V+ DEE MRLDRWFK   P ++  +L KI+R+GQVRVD  RVK   R+ +GQ VR+
Sbjct: 4   KTLTVDTDEEGMRLDRWFKRRLPDLSLSHLNKIVRTGQVRVDGARVKTATRLAAGQSVRV 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP+          ++ L+    ++  +  L+ ++L+ED  + V NKP G++VQGGSG+ +
Sbjct: 64  PPLDLP-------ERPLEKPAIVSADAQALREMILFEDRDLMVLNKPFGLAVQGGSGMTH 116

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           HID  L S  + +G +P L HRLD++TSG+L+VA+TR  A  L E FR R+ +KIYW++V
Sbjct: 117 HIDKMLASLPNERGDRPVLVHRLDRDTSGVLLVAKTRRMAAELGEIFRSRQARKIYWAVV 176

Query: 188 WGIPKNKKECIANWLLK---------------KSHIGGDYVHVVKQNEKGANYAISHFKV 232
            G+PK  +  I+ +L K               ++  G + + V K  E+ A ++++++ +
Sbjct: 177 EGVPKPAQGRISLYLAKGEGMEDKRGPHGRDAEARAGLEKMRVAKHGEEDARHSVTYYAI 236

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK----- 287
           +D    +  WL M+P TGRTHQLR HA  +G PI+GD KY    K +      N+     
Sbjct: 237 VDKVPSRLAWLSMKPITGRTHQLRAHAEAIGHPIIGDPKYGLKPKDDPRRNDPNRAIPEG 296

Query: 288 ----LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
               L+L AR + LPHP GG L +TAPLP HM KT+D  GF 
Sbjct: 297 VERKLHLLARRLILPHPRGGILDVTAPLPPHMQKTFDLFGFD 338


>gi|162148058|ref|YP_001602519.1| ribosomal large subunit pseudouridine synthase A [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209542674|ref|YP_002274903.1| RluA family pseudouridine synthase [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|161786635|emb|CAP56217.1| putative ribosomal large subunit pseudouridine synthase A
           [Gluconacetobacter diazotrophicus PAl 5]
 gi|209530351|gb|ACI50288.1| pseudouridine synthase, RluA family [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 325

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 134/332 (40%), Positives = 194/332 (58%), Gaps = 9/332 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  + V  DE ++RLDRWF+ HYPH+    LQK+ R+GQVRVD KR + + R+  GQ
Sbjct: 1   MSVV-TLTVSEDEADIRLDRWFRRHYPHLTQGALQKLCRTGQVRVDGKRAETSTRLLPGQ 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+  A       + +LD  +        ++ +++Y D ++ V NKPAG+ VQGG 
Sbjct: 60  AVRVPPIPGASRPAPPPRPVLDERLVRE-----IRGMVIYSDDQVIVLNKPAGLPVQGGP 114

Query: 124 GIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           GI +H+D  L    D     +PRL HR+D++TSG+L++ART   A  L  SFR R ++K 
Sbjct: 115 GIIHHVDAMLDGLKDQDDDPRPRLVHRIDRDTSGLLLLARTPGVAAKLAASFRGRDVRKT 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G P      I   L +     G    V  + +  A +A+S ++V+D   +K  W
Sbjct: 175 YWAIVVGRPSPASGVIDQPLARLGAGPGALTVVASRKDADAAHALSEYEVLDAAGRKLSW 234

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L + P TGRTHQLRVH   +G PI+GD KY  +          ++L+LHAR +DLPHP G
Sbjct: 235 LALSPLTGRTHQLRVHCEALGTPILGDPKYGGD--TAHPEGFVDRLHLHARTLDLPHPAG 292

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           GRL ++A LP+HM +T+  LGF        +R
Sbjct: 293 GRLVVSADLPSHMRETFRQLGFSAGATQPPRR 324


>gi|149187024|ref|ZP_01865331.1| pseudouridylate synthase [Erythrobacter sp. SD-21]
 gi|148829313|gb|EDL47757.1| pseudouridylate synthase [Erythrobacter sp. SD-21]
          Length = 376

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 127/326 (38%), Positives = 196/326 (60%), Gaps = 10/326 (3%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     V+   VE D++ +RLDRWFK H P I F  + K  R+GQ+RVD  R K ++R+ 
Sbjct: 1   MKTSDEVRNFTVEADDDGIRLDRWFKRHLPQIGFGTVSKWARTGQIRVDGSRAKPDDRLA 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            GQ +R+PP  +A +   K+++ L  +       +  +++L+ +     V NKP G++ Q
Sbjct: 61  QGQQIRVPPGGDAPHKKPKQKRELTKA-----EIEQAEAMLIEQTKSALVINKPPGLATQ 115

Query: 121 GGSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           GG+    H+DG L ++++  + Q+PRL HRLD++TSGIL+VART  +A   ++ F  R  
Sbjct: 116 GGTNTFNHVDGLLDAYMEEGEEQRPRLVHRLDKDTSGILLVARTPGSAAFFSKRFSGRSA 175

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +KIYW+LV G+P  ++  I   L K+   GG+ +HV   + +G   A + ++V++   +K
Sbjct: 176 KKIYWALVVGVPDIRQGVIEAPLAKQPGSGGEKMHV---DHEGGAPAKTKYRVVESAGKK 232

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
             WLE+QP TGRTHQLRVH   MG PIVGD KY    +   T  +  K++LHAR + +  
Sbjct: 233 VAWLELQPMTGRTHQLRVHCAAMGHPIVGDGKYGGK-EAFLTGSVSRKMHLHARRLIIDS 291

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFK 325
           P+GG+L +TA LP H   + + +GF 
Sbjct: 292 PDGGKLDVTAELPEHFAASMEQIGFD 317


>gi|114771239|ref|ZP_01448659.1| ribosomal large subunit pseudouridine synthase C [alpha
           proteobacterium HTCC2255]
 gi|114548164|gb|EAU51051.1| ribosomal large subunit pseudouridine synthase C [alpha
           proteobacterium HTCC2255]
          Length = 348

 Score =  296 bits (759), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 121/339 (35%), Positives = 187/339 (55%), Gaps = 21/339 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V++D ++ RLDR+ +  +P +    ++K+ R G+ RVD  RVK + R+  GQ
Sbjct: 1   MSGVQIIEVDDDGQDQRLDRFLRRTFPELGQGRIEKMCRKGECRVDGSRVKASTRLSVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+ +  +      +   ++      +  ++  +LY+D  I   NKPAG++VQGGS
Sbjct: 61  TVRVPPLPDTKDM----PRDTATAKITKADAQMIRDAVLYKDDYIIAINKPAGLAVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+DG   +       KP+L HRLD++TSG+L++ART  AA  LT++F+ R  +KIY
Sbjct: 117 GQMRHVDGLSAALKFDLENKPKLVHRLDKDTSGVLLLARTGLAASGLTKAFQSRETRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+ V G P  K   I   L+K    G    G+ +  +  +E      A +A + + V++ 
Sbjct: 177 WAAVAGCPHPKIGTIKYGLIKAGGHGPNGSGEKMQCIHPSEVTDMPDAKHATTDYTVLED 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNK 287
             ++  W+ + P TGRTHQLR H   +G PIVGD KY  N + N            I  K
Sbjct: 237 VGKRASWVALVPITGRTHQLRAHMAELGNPIVGDGKYGTNTQTNDGDGWGAQLGGDISRK 296

Query: 288 LYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
           ++LHAR +   HP     + ITA LP HM KTW + G++
Sbjct: 297 MHLHARSITFTHPITKKEIHITAELPDHMEKTWTTFGWE 335


>gi|148555622|ref|YP_001263204.1| ribosomal large subunit pseudouridine synthase C [Sphingomonas
           wittichii RW1]
 gi|148500812|gb|ABQ69066.1| ribosomal large subunit pseudouridine synthase C [Sphingomonas
           wittichii RW1]
          Length = 368

 Score =  296 bits (757), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 125/342 (36%), Positives = 195/342 (57%), Gaps = 7/342 (2%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS     +   V  D+  +RLDRWFK H P  +F  + +  R+GQ+RVD KR    +RI+
Sbjct: 1   MSGADDSRQFTVGEDDHGIRLDRWFKRHMPDTSFNIVSRWARTGQLRVDGKRAAPGDRIE 60

Query: 61  SGQVVRIPPVINALNHIIKE-QKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGIS 118
           +GQV+R+PP   A      + Q+       LT+    F +S+++++D +  V NKP G++
Sbjct: 61  AGQVIRLPPAEIAAAATAAKAQRPARPRAPLTEEEIAFARSLVIHQDRQAIVINKPPGLA 120

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            QGG+    H+D  L +       +P+L HRLD++TSG+L++ART  AA H  ++F  R 
Sbjct: 121 TQGGTKTDIHVDRLLDALQFDAESRPKLVHRLDKDTSGVLLLARTSRAAAHFAKAFSSRT 180

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            +K+YW++  G+P      I   + K+   GG+ +HV   +EK  + A + ++VI+    
Sbjct: 181 ARKVYWAIATGVPSIDDGMIELPIAKQPGTGGEKMHV---DEKEGSPARTRYRVIERAGN 237

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           + CW+E+QPHTGRTHQLRVH   +G PIVGD KY    +   +  I  K++LHAR + + 
Sbjct: 238 RACWVELQPHTGRTHQLRVHLAAIGHPIVGDGKYGG-AEAFLSGTISRKMHLHARRLRVD 296

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGFKYDR-NLYIKRLYSQD 339
           HP+GG L + A  P H+  +  +LGF     +L I  +   +
Sbjct: 297 HPDGGTLDVIAEPPEHITDSLRNLGFDEAEGDLPIDEVKFSE 338


>gi|296114939|ref|ZP_06833585.1| pseudouridine synthase, RluA family protein [Gluconacetobacter
           hansenii ATCC 23769]
 gi|295978497|gb|EFG85229.1| pseudouridine synthase, RluA family protein [Gluconacetobacter
           hansenii ATCC 23769]
          Length = 325

 Score =  296 bits (757), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 135/322 (41%), Positives = 195/322 (60%), Gaps = 9/322 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  + V +DE ++RLDRWF+ HYPH+    LQK+ R+GQ+RVD  RV  + R+  GQ
Sbjct: 1   MSVV-TLTVSDDEADIRLDRWFRRHYPHLTQGALQKLCRTGQIRVDGGRVTTSTRLAPGQ 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+  A        + LD      +    ++ +++Y D ++ V NKPAGI+VQGG 
Sbjct: 60  AVRVPPIPQASRPAPVTHRTLD-----DRQVREIRKMVIYSDDQVIVLNKPAGIAVQGGP 114

Query: 124 GIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           GI +HIDG L          +PRL HR+D++TSG+L++ART   A  L  SFR R ++K+
Sbjct: 115 GITHHIDGLLDGLREQPDDPRPRLVHRIDRDTSGLLLLARTPGVAAKLAASFRSRDVRKV 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++  G P      +   L +     G  + V  + +K A +A+S ++V+D   +K  W
Sbjct: 175 YWAVTVGRPTPASGIVDQPLTRLGAGAGAIMVVAGRRDKDAVHALSEYEVLDAAGRKLSW 234

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L + P TGRTHQLRVH   +G PI+GD KY  +       P  ++L+LHAR +DLPHP G
Sbjct: 235 LALSPLTGRTHQLRVHCEALGTPILGDPKYGDDRAHVEGFP--DQLHLHARMLDLPHPAG 292

Query: 303 GRLQITAPLPAHMVKTWDSLGF 324
           GRL ++A LPAHM +T+  LGF
Sbjct: 293 GRLVVSADLPAHMKETFRQLGF 314


>gi|330993253|ref|ZP_08317189.1| Ribosomal large subunit pseudouridine synthase C [Gluconacetobacter
           sp. SXCC-1]
 gi|329759655|gb|EGG76163.1| Ribosomal large subunit pseudouridine synthase C [Gluconacetobacter
           sp. SXCC-1]
          Length = 322

 Score =  295 bits (756), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 134/327 (40%), Positives = 192/327 (58%), Gaps = 8/327 (2%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V +DE ++RLDRWF+ HYPH+    LQK+ R+GQVRVD +R     R++ GQ VR+P
Sbjct: 2   TLTVSDDEADIRLDRWFRRHYPHLTQGALQKLCRTGQVRVDGRRATAATRLEPGQAVRVP 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P+ NA        K LD+     +    +  +++Y D  + V NKPAGI+VQGG GI +H
Sbjct: 62  PIPNASRPPPLAVKPLDA-----RQVREINQMVIYRDDHVIVLNKPAGIAVQGGPGITHH 116

Query: 129 IDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ID  L    DS    +PRL HR+D++TSG+L+VART   A  L  +FR R + K+YW++V
Sbjct: 117 IDALLDGLRDSPDDPRPRLVHRIDRDTSGLLLVARTPGVAAKLAAAFRGRDVHKVYWAVV 176

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G P      I   L +     G    V ++ +  A +A+S ++V+D  A+K  WL + P
Sbjct: 177 VGRPSPATGIIDQPLTRLGAGAGAISVVAERGDADAVHALSEYEVLDAAARKMSWLALSP 236

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQLRVH   +G PI+GD KY  +      +   ++L+LHAR ++LPHP GG L +
Sbjct: 237 LTGRTHQLRVHCEALGNPILGDPKYGGDVA--HVAGFADRLHLHARRLELPHPAGGTLVV 294

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            A LP HM +T+  +GF        +R
Sbjct: 295 EADLPPHMRETFRQIGFDTPAARPPRR 321


>gi|85703848|ref|ZP_01034951.1| ribosomal large subunit pseudouridine synthase C [Roseovarius sp.
           217]
 gi|85671168|gb|EAQ26026.1| ribosomal large subunit pseudouridine synthase C [Roseovarius sp.
           217]
          Length = 347

 Score =  295 bits (755), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 126/338 (37%), Positives = 185/338 (54%), Gaps = 22/338 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ  VV  D+ + RLDRW +  +PH+  V ++K+ R G+VRVD  RVK   R++ GQ
Sbjct: 1   MSGVQTRVVGPDDGDQRLDRWIRRLFPHVGQVQIEKMCRKGEVRVDGGRVKPATRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+ +           +  +      +  ++S ++Y D  +   NKP G+ VQGGS
Sbjct: 61  SVRIPPLPDTDERPTGALARISPA-----DAKMIQSCVIYRDDHVIALNKPPGLPVQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  ++      +KPRL HRLD++TSG+L++ARTR AA+ LT +FR R  +KIY
Sbjct: 116 KQTRHVDGLAEALRFGAEEKPRLVHRLDKDTSGVLLLARTREAAKGLTAAFRHRNTRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+ V G+P  +   +   L+K    G    G+ +  V   E     GA  A + + VI+ 
Sbjct: 176 WAAVAGVPTPRMGTVRYGLVKAPGHGAKGEGEKMICVHPREVESTPGAKPATTDYAVIEA 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
              +  W+ + P TGRTHQLR H   +G P+VGD KY  + + N            +  K
Sbjct: 236 AGARTSWMALIPVTGRTHQLRAHMAEIGHPVVGDGKYGGSGQENLGDGWGAQLGGDVSRK 295

Query: 288 LYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
           L+LHAR + + HP    +  ITAPLP HM +TWD   +
Sbjct: 296 LHLHARSLKIEHPVSRAILHITAPLPEHMQRTWDLFQW 333


>gi|254486362|ref|ZP_05099567.1| 23S rRNA pseudouridylate synthase [Roseobacter sp. GAI101]
 gi|214043231|gb|EEB83869.1| 23S rRNA pseudouridylate synthase [Roseobacter sp. GAI101]
          Length = 349

 Score =  295 bits (755), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 125/342 (36%), Positives = 190/342 (55%), Gaps = 23/342 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ +++E  + + RLDRWFK  +P I+   ++K+ R G +RV+  RVK + R++ GQ
Sbjct: 1   MSRVQNLIIEQGDGDQRLDRWFKRMFPLISQGRIEKMCRKGDIRVNGGRVKASTRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+ +       ++  +         + F++S ++Y D  I   NKP G+ VQGGS
Sbjct: 61  EIRIPPLPDTEAPPPPKRTRIS-----DADAKFIRSCVIYRDDYIIALNKPPGLPVQGGS 115

Query: 124 G-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    H+D    + +    +KPRL HRLD++TSG+L++ARTR+ A  LT SFR R+ +KI
Sbjct: 116 GQSDRHVDALADALMFDLDEKPRLVHRLDKDTSGVLIMARTRSIAADLTSSFRHRQTRKI 175

Query: 183 YWSLVWGIPKNKKECIANWLLKK----SHIGGDYVHVVKQNE----KGANYAISHFKVID 234
           YW+ V G+P  K   I   L+K     +   G+ ++ V   +    +GA  A + +  + 
Sbjct: 176 YWAAVAGVPHPKNGTIKFGLVKAFGHGARGEGEKMYCVHPKDMDTTEGAKRATTDYATLA 235

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQN 286
               + CW+ + P TGRTHQLR H   +G PIVGD KY  + + N            I  
Sbjct: 236 QAGTRTCWVALIPVTGRTHQLRAHMAEIGHPIVGDGKYGGSGQENMGDGWGAQLGGDISK 295

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
           KL+LHAR + L HP     L + AP+P HMV+TWD+  +   
Sbjct: 296 KLHLHARSLTLEHPVTKATLNLIAPMPDHMVRTWDTFQWSPS 337


>gi|296535679|ref|ZP_06897854.1| ribosomal large subunit pseudouridine synthase C [Roseomonas
           cervicalis ATCC 49957]
 gi|296264003|gb|EFH10453.1| ribosomal large subunit pseudouridine synthase C [Roseomonas
           cervicalis ATCC 49957]
          Length = 331

 Score =  294 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 135/336 (40%), Positives = 201/336 (59%), Gaps = 13/336 (3%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           + MT +Q+  V   + + RLDRWF+ H+P +    LQK+LR+GQ+RVD KR + N R+  
Sbjct: 4   TAMT-IQHRTVHAADADSRLDRWFRRHFPQLTQGALQKMLRTGQIRVDGKRAEANTRLAR 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           GQ +RIPP+         E    D  V+  + +  L++++LY D  I   NKP G+ VQG
Sbjct: 63  GQEIRIPPLPEGP---APEPVARDRQVS-AEDAKALEAMILYRDDYIIALNKPHGLPVQG 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G  I  H+DG L +    K ++PRL HRLD++TSG++++AR  +AA  L ++FR R  +K
Sbjct: 119 GPNIKKHLDGMLDALTFEKEERPRLVHRLDRDTSGVILLARDASAAGFLAKAFRGRDAEK 178

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYV--HVVKQNEKGANYAISHFKVIDCFAQK 239
            YW++V G P+ +   I    ++ +  GG  +   VV    +   +AI+ F  +D   + 
Sbjct: 179 TYWAIVVGQPQYQGGRID---MRLAKQGGGPMGERVVPAEGRDGAHAITEFDTVDVARRH 235

Query: 240 FCWLEMQPHTGRTHQLRVHA-LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             WLE++P TGRTHQLRVH    + CPI+GD KY    +      + N L+LHAR + +P
Sbjct: 236 ATWLELRPLTGRTHQLRVHCAAALSCPILGDGKYGG--QAAHLEGMSNALHLHARRIVVP 293

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           HPEGG L++TAPLP HM++++ +LGF   RN   KR
Sbjct: 294 HPEGGTLEVTAPLPPHMLESFATLGFDKPRNTAPKR 329


>gi|84515664|ref|ZP_01003025.1| ribosomal large subunit pseudouridine synthase C [Loktanella
           vestfoldensis SKA53]
 gi|84510106|gb|EAQ06562.1| ribosomal large subunit pseudouridine synthase C [Loktanella
           vestfoldensis SKA53]
          Length = 351

 Score =  294 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 123/338 (36%), Positives = 185/338 (54%), Gaps = 19/338 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V    +  D+ + RLDR+ +  +PH+    ++K+ R G++RVD  RVK + R++ GQ
Sbjct: 1   MSGVHTRTIGPDDGDQRLDRYLRRLFPHLTQGRIEKLCRKGELRVDGGRVKTSTRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+             L         +  ++S ++Y D  I   NKP G++ QGG+
Sbjct: 61  KVRIPPLPTEQEAAAA--ATLARHGVTKADAKLIQSCVIYRDDHIIAINKPHGLATQGGT 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  ++ +    +KPRL HRLD++TSG+L++ARTR  A+ LTE+ + R  +KIY
Sbjct: 119 NTTRHVDGMAEALMFGYDEKPRLVHRLDRDTSGVLLLARTRMMAKQLTENLKHRETRKIY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNE----KGANYAISHFKVIDC 235
           W+ V G+P  +   I   L+K    G     + +  V  NE    +GA  A S + V+D 
Sbjct: 179 WAAVAGVPHPRAGTIKYGLVKAPGHGKGGENEKMRCVHPNEIASTEGAKRATSDYAVMDT 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNK 287
            A +  W  + P TGRTHQLR H   +G PI+GD KY  + + N          S I  K
Sbjct: 239 LASRAAWCALVPITGRTHQLRAHMAEIGHPIIGDGKYGGSGQENLGDGWGASMGSEIGRK 298

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           ++LHAR + + HP  G+ L +TA LP HM  TWD +G+
Sbjct: 299 MHLHARSLTIEHPATGKTLHLTADLPEHMQNTWDFVGW 336


>gi|146278539|ref|YP_001168698.1| RluA family pseudouridine synthase [Rhodobacter sphaeroides ATCC
           17025]
 gi|145556780|gb|ABP71393.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides ATCC 17025]
          Length = 346

 Score =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 126/340 (37%), Positives = 185/340 (54%), Gaps = 24/340 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  VQ + V  DE   RLDRWFK  +PH+    ++K+ R+GQVRVD  R K ++R+  G 
Sbjct: 1   MKSVQLLTVTADEGEQRLDRWFKRRFPHVTQGAVEKMCRTGQVRVDGARAKASDRVAEGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP+ +      +  ++  S          ++  ++Y+D+ I V NKPAG+  QGGS
Sbjct: 61  EIRVPPLPDPDAPRPQASRVTKSD------EQMIQDCVIYKDNDIIVLNKPAGLPSQGGS 114

Query: 124 G-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    H+DG  ++      ++P+L HRLD++TSG+LV+ART   A+ L+ESFR R  +KI
Sbjct: 115 GQGERHVDGLTEALKFGYKERPKLVHRLDKDTSGVLVLARTDRVARALSESFRHRNTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNE----KGANYAISHFKVID 234
           YW+LV G+P  K+  I   L+K +  G     + +  +   +      A  A + F  + 
Sbjct: 175 YWALVAGVPSPKQGSIKYALMKAAGHGRGGEGEKMLCIHPAKVGDYPEAKRAQTDFFTLW 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQN 286
               +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            +  
Sbjct: 235 FLGTRCAWMALSPITGRTHQLRAHMAELGHPIVGDGKYGGSSQENAGDGWGAQIGGEVSR 294

Query: 287 KLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
           KL+LHAR + + HP    L   TAPLP HM KTW  L +K
Sbjct: 295 KLHLHARSLTIEHPIRKELVTFTAPLPPHMAKTWKLLDWK 334


>gi|56551335|ref|YP_162174.1| RluA family pseudouridine synthase [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241760988|ref|ZP_04759077.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|260753046|ref|YP_003225939.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis NCIMB
           11163]
 gi|56542909|gb|AAV89063.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241374607|gb|EER64068.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|258552409|gb|ACV75355.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
          Length = 374

 Score =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 122/344 (35%), Positives = 197/344 (57%), Gaps = 11/344 (3%)

Query: 4   MTY-VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M+  V+  VV++D++ +RLDRWF+ H P   F  + +  R+GQ+R+D +R    +R+ +G
Sbjct: 1   MSDNVRNFVVDDDDDGIRLDRWFQRHLPDTGFARIARWTRTGQIRLDGRRATPGSRVMAG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q +R+PP    L      +             +F +S++++ D    V NKPAG++ QGG
Sbjct: 61  QSIRVPPAEPNLQDNRPTKPSRPELTEAEI--EFAQSLVIHRDKAAIVVNKPAGLATQGG 118

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   YH+DG L +       +P+L HRLD++TSG+L++AR+   A + +++F  R   K+
Sbjct: 119 TKTHYHLDGLLDALQFEAPSRPKLVHRLDKDTSGVLLLARSANNAGYFSKAFSGRTAHKV 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+P   +  I   L ++   GG+ +HV   +E+    A + ++VI+      CW
Sbjct: 179 YWALVVGVPSITEGLIDLPLARQPGSGGEKMHV---DEENGATAKTLYRVIERAGNAACW 235

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           LE+QP TGRTHQLR H   +G PIVGD KY    +   T  +  K++LHAR + +PHP+G
Sbjct: 236 LELQPLTGRTHQLRAHLSAIGFPIVGDGKYGGK-EAFLTGGVSRKMHLHARRLVIPHPDG 294

Query: 303 GRLQITAPLPAHMVKTWDSLGFK----YDRNLYIKRLYSQDECK 342
             L + A LP H +++   LGF     YDR L  +++  ++  K
Sbjct: 295 SNLDVHADLPEHFLESMSLLGFDLENGYDRPLGGEKVIDKEAEK 338


>gi|187923831|ref|YP_001895473.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187715025|gb|ACD16249.1| pseudouridine synthase, RluA family [Burkholderia phytofirmans
           PsJN]
          Length = 431

 Score =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 94/350 (26%), Positives = 159/350 (45%), Gaps = 30/350 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV ++    RLD+     +P  +   LQ  + + +VR+D K  K    +  G  + +
Sbjct: 66  RSVVVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAKIRQPVPLGATIEL 125

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 126 VP------DLLPEQ--------LAFTPEPVPLEIVYEDDTLVVINKPAGMVVHPAAGNWS 171

Query: 126 AYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + D+     +  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 172 GTVLNGLLYRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 231

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKF 240
            +LVWG    ++  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 232 LALVWGNMP-EEGTIDAPIGRDP---RERTRMAVVTSASGKPARTHFRRVDSAIWQRQPV 287

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             +     TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 288 TAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGL 347

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF-KYDRNLYIKRLYSQDECKQNI 345
            HP+ GR +Q  A  PA M     +LG  + D   + +  Y +D+   ++
Sbjct: 348 IHPQTGRTMQWRADAPADMEALSAALGLGRDDAGEFDETYYEEDDYDASL 397


>gi|296157780|ref|ZP_06840614.1| pseudouridine synthase, RluA family [Burkholderia sp. Ch1-1]
 gi|295892026|gb|EFG71810.1| pseudouridine synthase, RluA family [Burkholderia sp. Ch1-1]
          Length = 431

 Score =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 93/350 (26%), Positives = 159/350 (45%), Gaps = 30/350 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV ++    RLD+     +P  +   LQ  + + +VR+D K  K    +  G  + +
Sbjct: 66  RSVVVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAKIRQPVPLGATIEL 125

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 126 VP------DLLPEQ--------LAFTPEPVPLAIVYEDDTLVVINKPAGMVVHPAAGNWS 171

Query: 126 AYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + D+     +  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 172 GTLLNGLLYRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 231

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKF 240
            +LVWG    ++  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 232 LALVWGNMP-EEGTIDAPIGRDP---RERTRMAVVTSASGKPARTHFRRVDSAIWERQPV 287

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L
Sbjct: 288 TAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGGFARQALHAWRLGL 347

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF-KYDRNLYIKRLYSQDECKQNI 345
            HP+ GR +Q  A +P  M     +LG  + D   + +  Y +D+ + ++
Sbjct: 348 IHPKTGRTMQWRADVPEDMEALSAALGLGRDDAGEFDETYYEEDDYEASL 397


>gi|254294409|ref|YP_003060432.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254042940|gb|ACT59735.1| pseudouridine synthase, RluA family [Hirschia baltica ATCC 49814]
          Length = 343

 Score =  293 bits (749), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 124/325 (38%), Positives = 193/325 (59%), Gaps = 5/325 (1%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + V + E ++RLDRW K  +P +    ++K+LR G+VRVD  R K + R++ GQVV
Sbjct: 7   QVLQIPVGDTEGDVRLDRWLKRRFPGLTQGQVEKLLRKGEVRVDGSRAKSSTRLEPGQVV 66

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP+ +        QK  +  V+  + ++ ++S++LYED  +YV NKP+G++VQGG+  
Sbjct: 67  RVPPMPSTDQGKKHPQKEEEVYVS-PRDAELIQSLILYEDEDVYVLNKPSGLAVQGGTKT 125

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG   +       KPRL HRLD++TSG+LV+A+T  +A  +++ FR R + KIYW+
Sbjct: 126 LRHVDGMANALTRPGQDKPRLVHRLDKDTSGLLVLAKTAQSAAEMSKHFRSRELDKIYWA 185

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +V G+P   +  +  W++K    G D   +      +KGA +AI+ FKV+    Q+  W+
Sbjct: 186 VVKGVPNPNEGELRGWMMKAHGPGQDKELMTAGVHGQKGAVFAITDFKVVSTAGQRASWV 245

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++P TGR HQLR H   +G  I+GD KY  + +     P    L+LHAR + +P   G 
Sbjct: 246 ALKPSTGRKHQLRYHMSEIGNSILGDAKYTCDRETPAGLP--PGLHLHARALRMPRRRGS 303

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDR 328
            +++ APLP HM KT+D  GF  D 
Sbjct: 304 DVEVIAPLPEHMKKTFDFFGFSEDE 328


>gi|83719070|ref|YP_442774.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis E264]
 gi|83652895|gb|ABC36958.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis E264]
          Length = 391

 Score =  293 bits (749), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 98/343 (28%), Positives = 154/343 (44%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRVD    K    +  G  + +
Sbjct: 53  RVVDVPPALAGERLDKALAQLFPEFSRSRLQQWIESERVRVDGAPAKIRQAVPLGATIEL 112

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                 L  ++ EQ        L    + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 113 ------LPDLLPEQ--------LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 158

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 159 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYF 218

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFC 241
           +LVWG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 219 ALVWGQMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTPWERQPVS 274

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 275 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 334

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 335 HPATGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 377


>gi|159042871|ref|YP_001531665.1| ribosomal large subunit pseudouridine synthase C [Dinoroseobacter
           shibae DFL 12]
 gi|157910631|gb|ABV92064.1| ribosomal large subunit pseudouridine synthase C [Dinoroseobacter
           shibae DFL 12]
          Length = 348

 Score =  293 bits (749), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 126/340 (37%), Positives = 190/340 (55%), Gaps = 21/340 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE + RLDRW +  +PH+    ++K+ R G++RVD  RVK   R+Q+GQ
Sbjct: 1   MSGVQTLTVGVDEGDQRLDRWLRRRFPHLGQGRIEKMCRKGELRVDGGRVKPATRLQTGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+        +  +   S  +     + L+  ++Y D+ I   NKPAG+ VQGGS
Sbjct: 61  AVRVPPLPAPGEITARPARARISDADR----EMLQGTVIYRDADILALNKPAGLPVQGGS 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   HIDG  ++      + PRL HRLD++TSG+L++ARTR +A  LT +FR R+ +KIY
Sbjct: 117 GQERHIDGMAEALQFELDEPPRLVHRLDKDTSGVLLMARTRRSAAALTAAFRARQTRKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYV----HVVKQNEKGANYAISHFKVIDC 235
           W+ V G+P+ +   +   L+K    G    G+ +             A  A + + V+  
Sbjct: 177 WAAVAGVPQPQLGTVRYALMKAPGHGKRGEGEKMLCIDPRQMDAHPDAKRATTDYAVLSA 236

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNK 287
             ++  W  + P TGRTHQLR H   +G PI+GD KY  + + N            +  K
Sbjct: 237 LGRRVAWCVLVPITGRTHQLRAHMAELGHPIIGDGKYGGSGQENLGDGWGAQLGGEMSKK 296

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
           L+LHAR++ L HP  G +L +TAPLP HM +TW++LG+  
Sbjct: 297 LHLHARHLSLTHPVTGAQLSLTAPLPPHMARTWEALGWDA 336


>gi|78044742|ref|YP_360337.1| ribosomal large subunit pseudouridine synthase A [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77996857|gb|ABB15756.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Carboxydothermus hydrogenoformans Z-2901]
          Length = 305

 Score =  293 bits (749), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 86/329 (26%), Positives = 154/329 (46%), Gaps = 33/329 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           + T ++ VVV ++   +RLD++        ++   ++K++  G+V V+    K + +++ 
Sbjct: 1   MDTEIK-VVVNSEYSGLRLDKFLAEQEELELSRSFIKKLIEEGKVTVNGLHRKASYKVRG 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G+++ +               +L     L+   + +   ++YED  + V NK AG+ V  
Sbjct: 60  GEIIAV---------------LLPPPRELSVKPEEIPLDIVYEDEDLVVVNKKAGMVVHP 104

Query: 122 GSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++  L    +  G     +P + HRLD++TSG+LVVA+   A Q L E  +
Sbjct: 105 AEGNWDGTLVNALLYHCQNLSGIGGVLRPGIVHRLDKDTSGLLVVAKNDLAHQSLAEQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            ++  + YW++V G  KNK+  I   + +        + VV         A + +KV++ 
Sbjct: 165 EKKAVREYWTIVHGYLKNKEGIIDLPIGRHPR-DRQKMAVVS----NGKTAQTVYKVLEE 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F + F  ++ +  TGRTHQ+RVH  ++G P++GD KY              +  LHA  +
Sbjct: 220 FNKGFTLIQAKLLTGRTHQIRVHFSYLGHPVLGDPKYGHQNNP----FGVKRQMLHAIKL 275

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              HP  G  L+ TAPLP    +    L 
Sbjct: 276 SFIHPRSGELLEFTAPLPEDFQRVLAKLR 304


>gi|217976287|ref|YP_002360434.1| pseudouridine synthase, RluA family [Methylocella silvestris BL2]
 gi|217501663|gb|ACK49072.1| pseudouridine synthase, RluA family [Methylocella silvestris BL2]
          Length = 349

 Score =  292 bits (748), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 137/341 (40%), Positives = 198/341 (58%), Gaps = 28/341 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ   V  DE+ +RLDRWFK   P ++  +L KI+R+GQVRVD  RVK   R+  GQ VR
Sbjct: 3   VQTYEVAEDEDGLRLDRWFKRRIPALSLSHLNKIVRTGQVRVDGARVKTATRLAQGQNVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+           +I +           L+ ++L+ED  + V NKP G++VQGGSG+ 
Sbjct: 63  VPPLNLEAAPEAPVFRISEED------QRDLRQMILFEDKDLMVLNKPYGLAVQGGSGMR 116

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            HIDG L S  + +G +P L HRLD++TSG+L++A+TR  A  L E FR R+ QKIYW+L
Sbjct: 117 RHIDGMLASLPNERGDRPVLVHRLDRDTSGVLLIAKTRKMAADLGEIFRSRQAQKIYWAL 176

Query: 187 VWGIPKNKKECIANWLLK-------------KSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           V G+PK  +  I+ +L K             +     + + V K  ++ A ++++++  +
Sbjct: 177 VEGVPKPAQGKISLFLAKGEGMDARGPRRSDEERASMEKMRVAKHGDEDAQHSVTYYATV 236

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN---------FTSPI 284
           D F+ +  WL M+P TGRTHQLR HA  +G PI+GD KY    K +             I
Sbjct: 237 DTFSPRAAWLSMKPITGRTHQLRAHAEAIGHPIIGDPKYGLRPKTDPRRNDPLRAIPETI 296

Query: 285 QNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           + KL+L AR + LPHP GG L +TAPLP HM  ++++ GF 
Sbjct: 297 ERKLHLLARRLVLPHPRGGVLDVTAPLPPHMANSFETFGFD 337


>gi|85373096|ref|YP_457158.1| pseudouridylate synthase [Erythrobacter litoralis HTCC2594]
 gi|84786179|gb|ABC62361.1| pseudouridylate synthase [Erythrobacter litoralis HTCC2594]
          Length = 399

 Score =  292 bits (748), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 126/339 (37%), Positives = 193/339 (56%), Gaps = 17/339 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   VE D+E +RLDRWFK + P + F  + +  R+GQ+RVD KR +  +R+ +GQV+R
Sbjct: 10  VRQFTVEADDEGVRLDRWFKRNLPQVGFGTISRWARTGQLRVDGKRARPEDRLAAGQVLR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP         + +K L       +     + +++ E     V NKP G++ QGG+   
Sbjct: 70  IPPGGEDPERNPRARKPLSP-----EQVRMAQDMVIKETKSAIVLNKPPGLATQGGTKTT 124

Query: 127 YHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            H+DG L ++VD +   +PRL HRLD++TSG+L++ART  +A   ++ F  R  +K+YW+
Sbjct: 125 KHVDGLLDAFVDGEDDPRPRLVHRLDKDTSGVLLIARTPGSAAAYSKRFAGRSAKKVYWA 184

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G+P   +  I   L K+   GG+ +HV   +E+    A + ++V++    + CW+E+
Sbjct: 185 LVVGVPDLHEGEIDAPLAKQPGTGGEKMHV---DEENGQPAKTRYRVVERAGNRACWVEL 241

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP----- 300
           +P TGRTHQLRVH   MG PIVGD KY        T  +  K++LHAR + +  P     
Sbjct: 242 EPMTGRTHQLRVHMAAMGHPIVGDGKYGGQ-DAFLTGSVSRKMHLHARRLIIAQPAENGK 300

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQD 339
            GG+L +TA LP H   + + LGF  D +L   R   +D
Sbjct: 301 SGGKLDVTADLPEHFAASMEQLGF--DISLSKARPLRED 337


>gi|307294362|ref|ZP_07574206.1| pseudouridine synthase, RluA family [Sphingobium chlorophenolicum
           L-1]
 gi|306880513|gb|EFN11730.1| pseudouridine synthase, RluA family [Sphingobium chlorophenolicum
           L-1]
          Length = 432

 Score =  292 bits (748), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 118/345 (34%), Positives = 193/345 (55%), Gaps = 11/345 (3%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V+   V  D++ +RLDRWF+ H P + F  + +  R+GQ+RVD  R    +RI  GQ +
Sbjct: 66  DVRQFRVGADDDGIRLDRWFQRHLPDVGFNTVSRWARTGQLRVDGARAAPGDRIAEGQSI 125

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP         K +++     +      F + I+++ D++  V NKP G++ QGG+  
Sbjct: 126 RVPPAEPKAAETAKPKRVRPQLTD--DQIAFAQGIVIHRDAQAIVINKPPGLATQGGTKT 183

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG L +      Q+P+L HRLD++TSG L++ART  +A    ++F  R  +K+YW+
Sbjct: 184 DDHVDGLLDALEYELDQRPKLVHRLDKDTSGALLIARTARSAAFFAKAFSSRTARKVYWA 243

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+P  +   +   + K+   GG+ +HV   +E+    + S ++VI+    +  W+E+
Sbjct: 244 IVMGVPSIEDGMVELPIAKQPGTGGEKMHV---DEEEGLPSRSRYRVIERAGNRAAWVEL 300

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QP+TGRTHQLRVH   +G PIVGD KY    +   +  I  K++LHAR + + HP+GGR+
Sbjct: 301 QPYTGRTHQLRVHMAAIGHPIVGDGKYGGK-EAFLSGTISRKMHLHARRIRVDHPDGGRV 359

Query: 306 QITAPLPAHMVKTWDSLGFKYDR-----NLYIKRLYSQDECKQNI 345
            + A LP H   +  SLGF         +  I R  ++++ K+  
Sbjct: 360 DVRAELPEHFAASLASLGFDLSTGDLPLDEEIARAPTREDEKKAA 404


>gi|91783470|ref|YP_558676.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           xenovorans LB400]
 gi|91687424|gb|ABE30624.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           xenovorans LB400]
          Length = 438

 Score =  292 bits (748), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 92/350 (26%), Positives = 156/350 (44%), Gaps = 29/350 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +VV ++    RLD+     +P  +   LQ  + + +VR+D K  K    +  G  + +
Sbjct: 66  RSIVVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAKIRQPVPLGATIEL 125

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 126 VP------DLLPEQ--------LAFTPEPVPLEIIYEDDTLVVINKPAGMVVHPAAGNWS 171

Query: 126 AYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + D+     +  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 172 GTLLNGLLYRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 231

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKF 240
            +LVWG    ++  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 232 LALVWGNMP-EEGTIDAPIGRDP---RERTRMAVVTSAAGKPARTHFRRVDSAIWERQPV 287

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L
Sbjct: 288 TAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGGFARQALHAWRLGL 347

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL 346
            HP+ GR +Q  A +P  M     +LG   D        Y +++  + +L
Sbjct: 348 IHPKTGRTMQWRADVPEDMEALSAALGLGRDDAGEFDETYYEEDDYEALL 397


>gi|257138984|ref|ZP_05587246.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis E264]
          Length = 385

 Score =  292 bits (747), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 98/343 (28%), Positives = 154/343 (44%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRVD    K    +  G  + +
Sbjct: 47  RVVDVPPALAGERLDKALAQLFPEFSRSRLQQWIESERVRVDGAPAKIRQAVPLGATIEL 106

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                 L  ++ EQ        L    + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 107 ------LPDLLPEQ--------LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 152

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 153 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYF 212

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFC 241
           +LVWG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 213 ALVWGQMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTPWERQPVS 268

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 269 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 328

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 329 HPATGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 371


>gi|332981610|ref|YP_004463051.1| ribosomal large subunit pseudouridine synthase D [Mahella
           australiensis 50-1 BON]
 gi|332699288|gb|AEE96229.1| ribosomal large subunit pseudouridine synthase D [Mahella
           australiensis 50-1 BON]
          Length = 304

 Score =  291 bits (746), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 84/322 (26%), Positives = 151/322 (46%), Gaps = 32/322 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V +D+ + RLD +    +      ++Q ++++G + V+ + +K   +++ G ++++ 
Sbjct: 5   TLCVTSDKADQRLDTFLAESFEQWTRSHIQNLIKNGNITVNGQHIKSGYKLKDGDIIKVE 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                          +     +    + +   +LYED  I V NKP G+ V   +G   A
Sbjct: 65  ---------------VPELRPIDIQPEDIPLNILYEDEDIIVINKPQGMVVHPAAGNYSA 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D  G     +P + HR+D++TSG+LVVA+   A   L +  + +   + 
Sbjct: 110 TLVNALLAHCKDLSGINGEIRPGIVHRIDKDTSGVLVVAKNDMAHVALAQQIKEKTAIRK 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L+ G  K     I   + +        + VV     G   A++HFKV++ F + +  
Sbjct: 170 YVALLEGDIKEDTGVINAPIARH-PTDRKKMAVVS----GGRSAVTHFKVLERFGR-YTL 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+RVH  ++G P+VGD  Y    +    +       LHA+Y+   HP  
Sbjct: 224 IEARLETGRTHQIRVHMAYIGHPVVGDPVYGYRKQ----AFALKGQLLHAQYLGFVHPRT 279

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           GR ++  APLP + V   D L 
Sbjct: 280 GRYMEFCAPLPDYFVDIIDKLR 301


>gi|294675889|ref|YP_003576504.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           capsulatus SB 1003]
 gi|294474709|gb|ADE84097.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           capsulatus SB 1003]
          Length = 355

 Score =  291 bits (746), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 128/341 (37%), Positives = 189/341 (55%), Gaps = 20/341 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE   RLDRW K  +P +    ++K+ R+GQ+RVD  RVK ++RI  G 
Sbjct: 1   MSSVQLIKVTEDEGESRLDRWLKKKFPVLTQGAVEKMCRTGQLRVDGGRVKASDRIGPGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKIYVFNKPAGISVQG 121
            VR+PP+  A     + +            +D   +++ +L++D  I   NKPAG+  QG
Sbjct: 61  EVRVPPLPEAGAKAPESRSEARRDATQISPADEKMIQAAVLWKDEHIIALNKPAGLPSQG 120

Query: 122 GSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GSG    H+DG L++       +P++ HRLD++TSG+L++ART   A+ L+ESFR++  +
Sbjct: 121 GSGQGDRHVDGLLEALKFGYKDRPKMVHRLDKDTSGVLLIARTDRVARALSESFRLKTTR 180

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNE----KGANYAISHFKV 232
           KIYW+ V G+P  KK  I   L+K    G     + +  +  ++      A  A + F V
Sbjct: 181 KIYWAAVAGVPSPKKGTIRYGLVKAPGHGRGGEGEKMLCIHPSKVDATPDAKRATTDFAV 240

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PI 284
           ID    +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            I
Sbjct: 241 IDGLGSRVSWVGLVPITGRTHQLRAHMAELGHPIVGDGKYGGSGQENLGDGWGSQLGGEI 300

Query: 285 QNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF 324
             KL+LHAR +   HP    R+ +TAPLP HMV+TW +LG+
Sbjct: 301 SRKLHLHARTISFDHPITKKRITLTAPLPDHMVRTWKTLGW 341


>gi|306840487|ref|ZP_07473246.1| pseudouridine synthase, RluA family [Brucella sp. BO2]
 gi|306289502|gb|EFM60720.1| pseudouridine synthase, RluA family [Brucella sp. BO2]
          Length = 284

 Score =  291 bits (746), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 136/282 (48%), Positives = 195/282 (69%), Gaps = 4/282 (1%)

Query: 47  RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
           RVD  R K + RIQ+GQ VRIPP+            +   ++   +  D L  +LLYED 
Sbjct: 2   RVDGGRAKADTRIQAGQAVRIPPLGVDEK---AAGPMTAKTIRNQQDGDVLSQMLLYEDP 58

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           K++VFNKPAG++VQGGSG+  HIDG L++W   KG+KPRL HR+D++TSG+LVVARTR A
Sbjct: 59  KVFVFNKPAGLAVQGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGA 118

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           AQ LT SFR R  +K YW+LV G+P+ +++ I+ WL+K+    GD + V +  E  +++A
Sbjct: 119 AQALTASFRERDTKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEPDSDHA 178

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQ 285
           +S++++I+       WLEM+P+TGRTHQLRVHA ++G PI+GD KY  A+    F   IQ
Sbjct: 179 VSYYRIIEKAGNNLAWLEMEPYTGRTHQLRVHAAYIGHPIIGDPKYFEADQNWEFPGGIQ 238

Query: 286 NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            +L+LHAR++ +P+P GG + +TAPLP HMV++W+ LGF  +
Sbjct: 239 KRLHLHARHIRIPNPSGGIIDVTAPLPPHMVQSWNLLGFDEE 280


>gi|83950496|ref|ZP_00959229.1| ribosomal large subunit pseudouridine synthase C [Roseovarius
           nubinhibens ISM]
 gi|83838395|gb|EAP77691.1| ribosomal large subunit pseudouridine synthase C [Roseovarius
           nubinhibens ISM]
          Length = 346

 Score =  291 bits (746), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 122/332 (36%), Positives = 180/332 (54%), Gaps = 17/332 (5%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +   + + RLDRW +  +PH+    ++K+ R G++RVD  RVK ++R+Q GQ VRIPP+ 
Sbjct: 3   ITPADADQRLDRWLRRLFPHLGQGRIEKMCRKGELRVDGGRVKSSHRLQVGQSVRIPPIP 62

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              +   K       S    + +  +++ ++Y D  I   NKP G+ VQGGS    H+DG
Sbjct: 63  APDDSEDKAAPPRPRSRVSDEDAAMIRAAVIYRDDHIIALNKPPGLPVQGGSKQTRHVDG 122

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             ++      +KPRL HRLD++TSG+L++ARTR  A  LT +FR R  +KIYW+ V G+P
Sbjct: 123 LAEALRFDLDEKPRLVHRLDKDTSGVLILARTRQMAADLTAAFRHRNTRKIYWAAVAGVP 182

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVK--------QNEKGANYAISHFKVIDCFAQKFCWL 243
             +   +   L+K    G                 N  GA +A S + V++   Q+  W+
Sbjct: 183 LPRMGTVKYGLVKAPGHGKGGEGEKMLCIHPREVDNTPGAKHATSDYAVLENAGQRTAWM 242

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNKLYLHARYM 295
            + P TGRTHQLR H   +G PIVGD KY  + + N            +  KL+LHAR +
Sbjct: 243 ALVPVTGRTHQLRAHMAELGHPIVGDGKYGGSGQENLGDGWGAQLGGDVSRKLHLHARSL 302

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
            + HP  G RL +TAPLP HM +TWD   ++ 
Sbjct: 303 TIRHPATGARLHLTAPLPDHMARTWDLFQWRA 334


>gi|167619842|ref|ZP_02388473.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis Bt4]
          Length = 385

 Score =  291 bits (745), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 98/343 (28%), Positives = 154/343 (44%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRVD    K    +  G  + +
Sbjct: 47  RVVDVPPALAGERLDKALAQLFPEFSRSRLQQWIESERVRVDGAPAKIRQAVPLGATIEL 106

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                 L  ++ EQ        L    + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 107 ------LPDLLPEQ--------LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 152

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 153 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYF 212

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +LVWG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 213 ALVWGQMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVS 268

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 269 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 328

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 329 HPATGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 371


>gi|77462289|ref|YP_351793.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides 2.4.1]
 gi|332560170|ref|ZP_08414492.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides WS8N]
 gi|77386707|gb|ABA77892.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides 2.4.1]
 gi|332277882|gb|EGJ23197.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides WS8N]
          Length = 346

 Score =  291 bits (745), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 126/340 (37%), Positives = 184/340 (54%), Gaps = 24/340 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE   RLDRWFK  +PH+    ++K+ R+GQVRVD  R K ++R+  G 
Sbjct: 1   MSSVQLLKVTADEGEQRLDRWFKRRFPHVTQGAVEKMCRTGQVRVDGARAKASDRVAEGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP+ +      +  ++  S          ++  ++Y D+ I V NKPAG+  QGGS
Sbjct: 61  EIRVPPLPDPDAPRPQASRVTKSD------EQMIQDCVIYRDNDIIVLNKPAGLPSQGGS 114

Query: 124 G-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    H+DG  ++      ++P+L HRLD++TSG+LV+ART   A+ L+ESFR R  +KI
Sbjct: 115 GQGERHVDGLTEALKFGYKERPKLVHRLDKDTSGVLVLARTDRVARALSESFRHRNTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNE----KGANYAISHFKVID 234
           YW+LV G+P  K+  I   L+K    G     + +  +   +      A  A + F  + 
Sbjct: 175 YWALVAGVPSPKQGSIKYALMKAPGHGRGGEGEKMLCIHPAKVGDYPEAKRAQTDFFTLW 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQN 286
               +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            +  
Sbjct: 235 FLGSRCAWMALSPITGRTHQLRAHMAELGHPIVGDGKYGGSGQENLGDGWGAQIGGEMSR 294

Query: 287 KLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
           KL+LHAR + + HP    L   TAPLP HM KTW  L +K
Sbjct: 295 KLHLHARSLTIEHPIKKDLVTFTAPLPGHMAKTWKLLDWK 334


>gi|83858519|ref|ZP_00952041.1| ribosomal large subunit pseudouridine synthase C [Oceanicaulis
           alexandrii HTCC2633]
 gi|83853342|gb|EAP91194.1| ribosomal large subunit pseudouridine synthase C [Oceanicaulis
           alexandrii HTCC2633]
          Length = 325

 Score =  291 bits (745), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 126/329 (38%), Positives = 197/329 (59%), Gaps = 10/329 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ V V  DE+ MR+DRWFK H+PH++   ++K+LR+GQ+RVD  R K N R+ +GQ
Sbjct: 1   MSGVQTVEVTRDEDEMRVDRWFKKHFPHVSHGMIEKLLRTGQIRVDGGRAKGNQRLSAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+ +A        +  +      + + F +S+++YED ++   NKP G++VQGGS
Sbjct: 61  SVRVPPMPDA-------GEPREQGSITRQDAQFARSLVIYEDKQMIALNKPPGLAVQGGS 113

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            +  H+D  L+++     QKPRL HRLD++TSG+LVVA+T  +A+ L   F+ R ++K Y
Sbjct: 114 KVTMHLDHLLQAF-GKGDQKPRLVHRLDKDTSGVLVVAKTAQSAKRLARLFQTRDVKKTY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++  G+P  +   I  ++ K      + +   +  E+GA +A++ + V D    +  W+
Sbjct: 173 WAICLGLPAPRAGEIKGFMKKSMEGDRELMVGARHGEEGAQHALTRYAVADNAGARASWV 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++P TGRTHQLRVH   MG  I GD KY  ++       +  KL+LHAR +++P     
Sbjct: 233 VLRPETGRTHQLRVHMQAMGHSIYGDGKYTCDYPD--PEGLSRKLHLHARKIEIPREGQK 290

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            L I A LP HM  ++D+LGF    NL +
Sbjct: 291 PLVIEADLPKHMADSFDALGFNPGDNLML 319


>gi|16126223|ref|NP_420787.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus CB15]
 gi|221234996|ref|YP_002517432.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus NA1000]
 gi|13423445|gb|AAK23955.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus CB15]
 gi|220964168|gb|ACL95524.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus NA1000]
          Length = 331

 Score =  291 bits (745), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 124/328 (37%), Positives = 182/328 (55%), Gaps = 11/328 (3%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    V+ + V+  E+ +RLDRWFK  +PH+N + L K+ RSGQVRVD  R K + ++ 
Sbjct: 1   MST-KEVRTLYVDAGEDGVRLDRWFKRRWPHLNHIQLNKLFRSGQVRVDGSRAKADTKLA 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  +R+PP+ +A           D +    +   + KS++LYED ++   NKPAG++VQ
Sbjct: 60  AGSQIRVPPLPDA-------PDPSDKNKLSARDVAYAKSLVLYEDEEVLALNKPAGLAVQ 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GG+    HID  L +W      +PRL HRLD++TSG+L++ +T +AA  L+ +F  R+ Q
Sbjct: 113 GGTKTTKHIDKLLSAW-GEGVDRPRLVHRLDRDTSGVLLLGKTPSAAARLSGAFAKRKAQ 171

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW++V G P   +  +   L K+     + V   +  +  A  A + F  I     + 
Sbjct: 172 KTYWAIVAGNPHPTEGVMELHLAKRGVGDRELVVPAQPKDPDAQPAETEFVTISRAGPRV 231

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            W+ ++PHTGRTHQLR H   MG PI+GD KY        +  +  KL LHAR + LPHP
Sbjct: 232 TWMALRPHTGRTHQLRAHMKAMGHPILGDPKYGDEKSAPLSEGL--KLQLHARSILLPHP 289

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
             G L I APL   M + +   GF  D 
Sbjct: 290 SAGMLHIEAPLSPEMKEGFRKFGFSEDE 317


>gi|323138142|ref|ZP_08073215.1| pseudouridine synthase, RluA family [Methylocystis sp. ATCC 49242]
 gi|322396604|gb|EFX99132.1| pseudouridine synthase, RluA family [Methylocystis sp. ATCC 49242]
          Length = 351

 Score =  291 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 134/338 (39%), Positives = 195/338 (57%), Gaps = 24/338 (7%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V    V  DE  MR+DRWFK  YP +   +L KI R G+VRVD KRV+ + R++ GQ 
Sbjct: 8   SGVSTTTVTEDEAGMRVDRWFKRRYPTLALSHLAKICRKGEVRVDGKRVETSTRLEEGQK 67

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP+       I+  +         + +  LK++ L+ED  + V NKP G++ QGGSG
Sbjct: 68  VRVPPLR------IEAPEAPAVKRASPEDAQALKAMTLFEDKDVLVLNKPWGLATQGGSG 121

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              H+DG L+S       +P L HRLD++TSG+L+VA+TR  A  L E FR R+ +KIYW
Sbjct: 122 QKRHVDGMLESLARGDS-RPVLVHRLDRDTSGVLLVAKTRRMAADLGEIFRSRQAKKIYW 180

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGG--------DYVHVVKQNEKGANYAISHFKVIDCF 236
           +LV G+PK  +  ++ +L K + +          + + V K  E  A ++++++ ++D  
Sbjct: 181 ALVEGVPKPAQGRVSLYLAKGAGMEKARGGGRDLEKMRVAKHGEADAQHSLTYYAIVDKV 240

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN---------FTSPIQNK 287
           A +  WL M+P TGRTHQLR HA  +G PI GD KY    + +             ++ K
Sbjct: 241 APRCAWLSMKPLTGRTHQLRAHAEAIGHPIFGDPKYGRRPEDDVRRRDPLRAMPDGLERK 300

Query: 288 LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           L+L AR + LPHP GG L +TAPLP HM K+W+  GF 
Sbjct: 301 LHLLARRLVLPHPRGGTLDVTAPLPPHMQKSWELFGFD 338


>gi|85707668|ref|ZP_01038734.1| pseudouridylate synthase [Erythrobacter sp. NAP1]
 gi|85689202|gb|EAQ29205.1| pseudouridylate synthase [Erythrobacter sp. NAP1]
          Length = 395

 Score =  291 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 125/330 (37%), Positives = 191/330 (57%), Gaps = 16/330 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V+   V +D++ +RLDRWFK + P I F  + +  R+GQVRVD  RVK  +R+++GQV
Sbjct: 6   NEVRQFTVSDDDDGIRLDRWFKRNLPKIGFATISRWARTGQVRVDGGRVKPEDRLEAGQV 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+PP         K ++ L       +     +++++ E     V NKP G++ QGGS 
Sbjct: 66  LRVPPGGEDQKRGPKPRRPLTE-----EEIAEARAMVIRETPSAIVLNKPPGLATQGGSK 120

Query: 125 IAYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              H+DG L ++VD       +PRL HRLD++TSG+L++ART  +A   +  F  R  +K
Sbjct: 121 TTKHVDGLLDAFVDDQEEDAPRPRLVHRLDKDTSGVLLIARTPGSAATYSRKFSGRSARK 180

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +YW+LV G+P+ ++  I   L K+   GG+ +HV   +E+G   A + ++V++    +  
Sbjct: 181 VYWALVVGVPEVREGTIDAPLAKQPGTGGEKMHV---DEEGGQIAKTRYRVVERAGTRAA 237

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           W+E++P TGRTHQLRVH   +G PIVGD KY        T  I  K++LHAR + +  PE
Sbjct: 238 WVELEPLTGRTHQLRVHLAAIGHPIVGDGKYGGQ-DAFLTGAISRKMHLHARRLIIGTPE 296

Query: 302 ----GGRLQITAPLPAHMVKTWDSLGFKYD 327
               GG+L +TA LP H   + +SLGF   
Sbjct: 297 SKGAGGKLDVTADLPEHFATSMESLGFDLS 326


>gi|167581726|ref|ZP_02374600.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis TXDOH]
          Length = 389

 Score =  291 bits (744), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 98/343 (28%), Positives = 154/343 (44%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRVD    K    +  G  + +
Sbjct: 51  RVVDVPPALAGERLDKALAQLFPEFSRSRLQQWIESERVRVDGAPAKIRQAVPLGATIEL 110

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                 L  ++ EQ        L    + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 111 ------LPDLLPEQ--------LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 156

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 157 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYF 216

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +LVWG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 217 ALVWGQMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVS 272

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 273 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 332

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 333 HPATGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 375


>gi|260893452|ref|YP_003239549.1| pseudouridine synthase, RluA family [Ammonifex degensii KC4]
 gi|260865593|gb|ACX52699.1| pseudouridine synthase, RluA family [Ammonifex degensii KC4]
          Length = 331

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 91/323 (28%), Positives = 153/323 (47%), Gaps = 32/323 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + VE +E  +RLD +   + P  +   LQ+++  G V+V  ++VK + +++ G+ + +  
Sbjct: 7   LQVEEEEAGVRLDVYLARNLPENSRSYLQRLINEGYVQVGGRKVKPSYKVKPGEEILV-- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                         L  +  L    + +   ++YED  + V NKP G+ V  G+G     
Sbjct: 65  -------------FLPPAETLEVEPEPIPLEIIYEDEDLLVVNKPRGMVVHPGAGHKRGT 111

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L       G     +P + HRLD++TSG+L+VA+  AA   L+   + RR+ K Y
Sbjct: 112 LVNALLYHCRSLSGINGVLRPGIVHRLDKDTSGLLMVAKNDAAHLSLSAQLKERRVLKEY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV+G  K  +  I   + +          V      G   A++H++V++ F   +  L
Sbjct: 172 WALVYGEVKPAQGRIEAPIGRHPRYRQKMAVVA-----GGRPAVTHYEVVEYFP-GYTLL 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++P TGRTHQ+RVH  ++G PIVGD KY                +LHA  +   HP  G
Sbjct: 226 RVRPETGRTHQIRVHLHYLGHPIVGDLKYGPARP----HLGLEGQFLHAGVLGFTHPRTG 281

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
             L+  APLP  + +    L  +
Sbjct: 282 EFLRFEAPLPPELERVLAELRAR 304


>gi|148259184|ref|YP_001233311.1| RluA family pseudouridine synthase [Acidiphilium cryptum JF-5]
 gi|326402337|ref|YP_004282418.1| pseudouridine synthase [Acidiphilium multivorum AIU301]
 gi|146400865|gb|ABQ29392.1| ribosomal large subunit pseudouridine synthase C [Acidiphilium
           cryptum JF-5]
 gi|325049198|dbj|BAJ79536.1| pseudouridine synthase [Acidiphilium multivorum AIU301]
          Length = 324

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 128/328 (39%), Positives = 187/328 (57%), Gaps = 7/328 (2%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V V  D+ +MRLDR+ ++ +P +    +QK  R+GQVRVD KR + +  + +GQ VR
Sbjct: 3   VRIVTVGPDQADMRLDRFLRSLHPGLTQGAIQKFCRTGQVRVDGKRAEASTHLAAGQAVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV           K   + V        L + +L+ D+ + V +KPAG++ QGG GIA
Sbjct: 63  IPPVPET-----PAPKPRQTVVANEWDVKELNARILHRDADVLVIDKPAGLATQGGKGIA 117

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            H+DG L +      ++PRL HRLD++TSG+LV+AR   AA  L  +FR R ++K YW++
Sbjct: 118 RHLDGMLDALRFDAAERPRLVHRLDRDTSGVLVLARNAFAANRLAAAFRGRDMEKTYWAI 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+P   +  I   L +     G       ++++ A  AI+ ++ +D   +KF WLE+ 
Sbjct: 178 VVGLPIPMEGQIDLPLARIGGAQGARTRPADRDDEDAAKAITDYRTLDHAGRKFSWLELH 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P TGRTHQLR H   +G PI+GD  Y  +    F      +L+LHAR + LPHP GGRL 
Sbjct: 238 PLTGRTHQLRAHCAAIGTPILGDAPYGEHLA--FAEGFPRQLHLHARRLVLPHPRGGRLS 295

Query: 307 ITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           + A LPAHM  T+ +LGF        +R
Sbjct: 296 VEAELPAHMKTTFATLGFTAPHATPARR 323


>gi|294011526|ref|YP_003544986.1| ribosomal large subunit pseudouridine synthase C [Sphingobium
           japonicum UT26S]
 gi|292674856|dbj|BAI96374.1| ribosomal large subunit pseudouridine synthase C [Sphingobium
           japonicum UT26S]
          Length = 436

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 115/340 (33%), Positives = 191/340 (56%), Gaps = 7/340 (2%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V+   V  D++ +RLDRWF+ H P + F  + +  R+GQ+RVD  R    +RI  GQ +
Sbjct: 70  DVRQFRVGADDDGIRLDRWFQRHLPDVGFNTVSRWARTGQLRVDGARAAPGDRIAEGQSI 129

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP         K +++     +      F + ++++ D++  V NKP G++ QGG+  
Sbjct: 130 RVPPAEPKAPETAKPRRVRPQLTD--DQMAFAQGLVIHRDAQAIVINKPPGLATQGGTKT 187

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG L +      Q+P+L HRLD++TSG L++ART  +A +  ++F  R  +K+YW+
Sbjct: 188 DDHVDGLLDALEFDLDQRPKLVHRLDKDTSGALLIARTARSAAYFAKAFSSRTARKVYWA 247

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+P  +   I   + K+   GG+ +HV   +E+    + S ++VI+    +  W+E+
Sbjct: 248 IVMGVPSIEDGMIELPIAKQPGTGGEKMHV---DEEEGLPSRSRYRVIERAGNRAAWVEL 304

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QP+TGRTHQLRVH   +G PIVGD KY        +  I  K++LHAR + + HP+GG +
Sbjct: 305 QPYTGRTHQLRVHMAAIGHPIVGDGKYGGK-DAFLSGTISRKMHLHARRIRVDHPDGGPV 363

Query: 306 QITAPLPAHMVKTWDSLGFKYDR-NLYIKRLYSQDECKQN 344
            + A LP H   +  SLGF     +L +    ++   +++
Sbjct: 364 DVRAELPEHFAASLASLGFDLSAGDLPLDEEIARPPTRED 403


>gi|323526134|ref|YP_004228287.1| RluA family pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323383136|gb|ADX55227.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1001]
          Length = 426

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 92/349 (26%), Positives = 157/349 (44%), Gaps = 30/349 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV ++    RLD+     +P  +   LQ  + + +VR+D K  K    +  G  + +
Sbjct: 66  RSVVVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAKIRQPVPLGATIEL 125

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 126 VP------DLLPEQ--------LAFTPEPVPLDIVYEDDTLVVINKPAGMVVHPAAGNWS 171

Query: 126 AYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + D+     +  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 172 GTVLNGLLYRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 231

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKF 240
            +LVWG    ++  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 232 LALVWGNMP-EEGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRRVDTALWQRQPV 287

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L
Sbjct: 288 TAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVAPLPGDFARQALHAWRLGL 347

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF-KYDRNLYIKRLYSQDECKQN 344
            HP+ GR +Q  A +P  +     +LG  + D   + +  Y +D  + +
Sbjct: 348 IHPKTGRTMQWRADVPEDIAALSAALGLGRDDAGEFDETYYEEDGYEAS 396


>gi|254478536|ref|ZP_05091911.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
 gi|214035544|gb|EEB76243.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
          Length = 309

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 87/335 (25%), Positives = 154/335 (45%), Gaps = 35/335 (10%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  +V+  E ++E  R+D +  +     +   ++K++  G V V+ K VK + +++ 
Sbjct: 1   MNIVDRIVLQGEKEDEGKRIDVFLASEL-DYSRSYIKKLIEEGLVLVNGKNVKPSYKVKE 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V +         ++ E   LD               +LYED  I V NKP G+ V  
Sbjct: 60  DDEVVVNIPEAEKIEVVPENIPLD---------------ILYEDEDIIVINKPQGMVVHP 104

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++  L    +  G     +P + HRLD++TSG++VVA+   A   L+   +
Sbjct: 105 APGNYSGTLVNALLYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHMSLSNQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y ++V G+ K ++  I   + +   +    + VV    +   YA++ +KV++ 
Sbjct: 165 ERSVLKKYVAIVEGVIKEEEGKIEAPIGRH-PVDRKRMAVV----QDGRYALTLYKVLER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F     ++E    TGRTHQ+RVH  ++G P+VGD  Y    +            LH++ +
Sbjct: 220 FKNN-TFVEATIKTGRTHQIRVHFSYIGHPVVGDPVYGYKKQ----KFKLEGQALHSKVL 274

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
              HP  G  ++  APLP +  +  + L  + DR+
Sbjct: 275 GFIHPTKGVYMEFEAPLPDYFTRLLEILRAEKDRD 309


>gi|126461165|ref|YP_001042279.1| RluA family pseudouridine synthase [Rhodobacter sphaeroides ATCC
           17029]
 gi|126102829|gb|ABN75507.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides ATCC 17029]
          Length = 346

 Score =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 125/340 (36%), Positives = 183/340 (53%), Gaps = 24/340 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE   RLDRWFK  +PH+    ++K+ R+GQVRVD  R K ++R+  G 
Sbjct: 1   MSSVQLLKVTADEGEQRLDRWFKRRFPHVTQGAVEKMCRTGQVRVDGARAKASDRVAEGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP+ +      +  ++  S          ++  ++Y D+ I V NKP G+  QGGS
Sbjct: 61  EIRVPPLPDPDAPRPQASRVTKSD------EQMIQDCVIYRDNDIIVLNKPPGLPSQGGS 114

Query: 124 G-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    H+DG  ++      ++P+L HRLD++TSG+LV+ART   A+ L+ESFR R  +KI
Sbjct: 115 GQGERHVDGLTEALKFGYKERPKLVHRLDKDTSGVLVLARTDRVARALSESFRHRNTRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNE----KGANYAISHFKVID 234
           YW+LV G+P  K+  I   L+K    G     + +  +   +      A  A + F  + 
Sbjct: 175 YWALVAGVPSPKQGSIKYALMKAPGHGRGGEGEKMLCIHPAKVGDYPEAKRAQTDFFTLW 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQN 286
               +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            +  
Sbjct: 235 FLGSRCAWMALSPITGRTHQLRAHMAELGHPIVGDGKYGGSGQENLGDGWGAQIGGEMSR 294

Query: 287 KLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
           KL+LHAR + + HP    L   TAPLP HM KTW  L +K
Sbjct: 295 KLHLHARSLTIEHPIKKDLVTFTAPLPGHMAKTWKLLDWK 334


>gi|254478004|ref|ZP_05091388.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
 gi|214036008|gb|EEB76698.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
          Length = 309

 Score =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 85/335 (25%), Positives = 156/335 (46%), Gaps = 35/335 (10%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  +V+  E ++E  R+D +  +     +   ++K++  G V V+ K VK + +++ 
Sbjct: 1   MNIVDRIVLQGEKEDEGKRIDVFLASEL-DYSRSYIKKLIEEGLVLVNGKNVKPSYKVKE 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              + +         ++ E   LD               +LYED  I V NKP G+ V  
Sbjct: 60  DDEIVVNIKEAEKIEVVPENIPLD---------------ILYEDEDIIVINKPQGMVVHP 104

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +G      ++  L    +  G     +P + HRLD++TSG++VVA+   A   L+   +
Sbjct: 105 AAGNYSGTLVNALLYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHMSLSNQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y ++V G+ K ++  +   + +   +    + VV++      YA++ +KV++ 
Sbjct: 165 ERSVLKKYIAIVEGVIKEEEGKVEAPIGRH-PVDRKRMAVVQE----GRYALTLYKVLER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F     ++E    TGRTHQ+RVH  ++G P+VGD  Y    +            LH++ +
Sbjct: 220 FKNN-TFVEATIKTGRTHQIRVHFSYIGHPVVGDPVYGYKKQ----RFKLEGQALHSKVL 274

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
              HP  G  ++  APLP +  +  + L  + DR+
Sbjct: 275 GFIHPTKGVYMEFEAPLPDYFTRLLEILRAEKDRD 309


>gi|194015066|ref|ZP_03053683.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus pumilus ATCC 7061]
 gi|194014092|gb|EDW23657.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus pumilus ATCC 7061]
          Length = 304

 Score =  290 bits (742), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 92/327 (28%), Positives = 159/327 (48%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V  + V  ++ + RLD++     P  +   +Q+ ++ G + V+ K+VK N ++Q+G 
Sbjct: 1   MNQVN-IAVSEEQTSERLDKFLSTTEPEWSRTQVQQWVKDGLIEVNGKQVKANYKVQAGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +++          I E ++LD        ++ +   + YED+ + V NKP G+ V    
Sbjct: 60  QIKVE---------IPEPEVLDV------EAEPMDLDIYYEDADVLVVNKPRGMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHVSGTLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V GI ++    I   + +           +   ++ A  A++HF VI+ F 
Sbjct: 165 TVTRKYTAVVHGIIQHDTGTIDAPIGRDKKD----RQSMTVTKESAKQAVTHFDVIERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +  
Sbjct: 220 QDFTVVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPRKTVDF-----NGQLLHAGVLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++ TAP+PA M    DSL 
Sbjct: 275 DHPRTGEYIEFTAPIPADMQAFIDSLR 301


>gi|167645622|ref|YP_001683285.1| RluA family pseudouridine synthase [Caulobacter sp. K31]
 gi|167348052|gb|ABZ70787.1| pseudouridine synthase, RluA family [Caulobacter sp. K31]
          Length = 329

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 124/328 (37%), Positives = 182/328 (55%), Gaps = 10/328 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V+  E+ +RLDRWFK  +PH+N + L K+ RSGQVRVD  R K + ++ +G 
Sbjct: 1   MREVRTLFVDAGEDGVRLDRWFKRRWPHLNHIQLNKLFRSGQVRVDGSRAKADTKLAAGS 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+ P +       ++QK+    +       F KS++LYED ++   NKPAG++VQGG+
Sbjct: 61  QIRV-PPLPDAPDPDEKQKLSPRDIA------FAKSLVLYEDEEVLALNKPAGLAVQGGT 113

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              +HID  L +W      +P+L HRLD++TSG+L++ +T AAA  L+ SF  R+ QK Y
Sbjct: 114 KTTHHIDKLLSAW-GEGVNRPKLVHRLDRDTSGVLLLGKTPAAAARLSGSFAKRKAQKTY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W++V G P   +  I   L K+     + V   +  +     A + F  I     +  W+
Sbjct: 173 WAIVAGNPHPTEGVIELHLAKRGVGDRELVVPAEPKDPDGQPAETEFVSISRAGPRVTWM 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++PHTGRTHQLR H   +G PI+GD KY  +     +  +  KL LHAR + LPHP  G
Sbjct: 233 ALRPHTGRTHQLRAHMKAIGHPILGDPKYSDDKALQLSEGL--KLQLHARSIVLPHPSVG 290

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNLY 331
            L I APL   M   +   GF  D   Y
Sbjct: 291 TLAIQAPLSPEMKAGFAKFGFSEDEAEY 318


>gi|20807974|ref|NP_623145.1| pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter
           tengcongensis MB4]
 gi|20516547|gb|AAM24749.1| Pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter
           tengcongensis MB4]
          Length = 309

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 87/335 (25%), Positives = 154/335 (45%), Gaps = 35/335 (10%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  +V+  E ++E  R+D +  +     +   ++K++  G V V+ K VK + +++ 
Sbjct: 1   MNIVDRIVLQGEKEDEGKRIDVFLASEL-DYSRSYIKKLIEEGLVLVNGKNVKPSYKVKE 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V +         ++ E   LD               +LYED  I V NKP G+ V  
Sbjct: 60  DDEVIVNIKEAEKIEVVPENIPLD---------------ILYEDEDIIVINKPQGMVVHP 104

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++  L    +  G     +P + HRLD++TSG++VVA+   A   L+   +
Sbjct: 105 APGNYSGTLVNALLYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHMSLSNQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y ++V G+ K ++  I   + +   +    + VV    +   YA++ +KV++ 
Sbjct: 165 ERSVLKKYVAIVEGVIKEEEGKIEAPIGRH-PVDRKRMAVV----QDGRYALTLYKVLER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F     ++E    TGRTHQ+RVH  ++G P+VGD  Y    +            LH++ +
Sbjct: 220 FKNN-TFVEATIKTGRTHQIRVHLSYIGHPVVGDPVYGYKKQ----KFKLEGQALHSKVL 274

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
              HP  G  ++  APLP +  +  + L  + DR+
Sbjct: 275 GFIHPTKGVYMEFEAPLPDYFTRLLEILRAEKDRD 309


>gi|254449547|ref|ZP_05062984.1| ribosomal large subunit pseudouridine synthase C [Octadecabacter
           antarcticus 238]
 gi|198263953|gb|EDY88223.1| ribosomal large subunit pseudouridine synthase C [Octadecabacter
           antarcticus 238]
          Length = 347

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 133/340 (39%), Positives = 193/340 (56%), Gaps = 24/340 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE + RLDRW K  +  +    ++K+ R G++RVD  RVK N R++ GQ
Sbjct: 1   MSRVQNLTVGPDEGDQRLDRWIKRRFAQLQQGGIEKMCRKGEIRVDGGRVKSNTRVEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+ +A     + + +  + + L      ++  ++Y+D  + V NKPAG+  QGGS
Sbjct: 61  TVRIPPLPDADEVDDRPRDMTKADIQL------IQGCVIYKDDHVIVLNKPAGLPTQGGS 114

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  ++      ++PRL HRLD++TSG+LV+ARTR AA+ LTE+FR R  +KIY
Sbjct: 115 KQLRHVDGMAEALRFGYDERPRLVHRLDKDTSGVLVLARTRMAAKSLTEAFRHRNTEKIY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNEK----GANYAISHFKVIDC 235
           W+LV G+P  K   I   L+K+   GG    + +  V   +     GA  A++++ V+  
Sbjct: 175 WALVAGVPIPKLGSIKYGLVKQGGHGGKGDNERMKCVHPKDVDKTFGAKRALTNYTVLTS 234

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---------NFKGNFTSPIQN 286
            A +  W+ + P TGRTHQLR H   +G PIVGD KY A          +       I  
Sbjct: 235 LADRTAWVALTPVTGRTHQLRAHIAEIGHPIVGDGKYGAAAVQDNPGDGWGAGMGEEIGR 294

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           KL+LHAR + + HPE G  L I A LP HM KTW   G++
Sbjct: 295 KLHLHARSLRIEHPETGKELWIKASLPQHMEKTWGFFGWE 334


>gi|308173508|ref|YP_003920213.1| pseudouridylate synthase [Bacillus amyloliquefaciens DSM 7]
 gi|307606372|emb|CBI42743.1| pseudouridylate synthase [Bacillus amyloliquefaciens DSM 7]
 gi|328553560|gb|AEB24052.1| pseudouridylate synthase [Bacillus amyloliquefaciens TA208]
 gi|328911647|gb|AEB63243.1| pseudouridylate synthase [Bacillus amyloliquefaciens LL3]
          Length = 304

 Score =  289 bits (740), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 83/322 (25%), Positives = 149/322 (46%), Gaps = 32/322 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V+ ++++ R+D++  +   + +   +Q+ ++ G V V+ K VK N ++Q G  V + 
Sbjct: 5   EITVQPEQKSERIDKFLASTGENWSRTQVQQWVKEGLVSVNGKSVKANYKMQPGDQVNVT 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                          +     L   ++ +   + YED  + V NKP G+ V    G    
Sbjct: 65  ---------------IPEPEELDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHVTG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + 
Sbjct: 110 TLVNGLMAHCNDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRK 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G+  +    I   + +           +    +G+  A++HF V++ F Q F  
Sbjct: 170 YTAVVHGVISHDDGTIDAPIGRDKKD----RQSMTVTREGSKNAVTHFHVLERF-QDFTL 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   HP  
Sbjct: 225 VECRLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTVDF-----NGQALHAGILGFDHPRT 279

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  ++  APLP  M K  + L 
Sbjct: 280 GEYMEFEAPLPEDMKKLIELLR 301


>gi|56419681|ref|YP_146999.1| hypothetical protein GK1146 [Geobacillus kaustophilus HTA426]
 gi|261419335|ref|YP_003253017.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|297530695|ref|YP_003671970.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|319766151|ref|YP_004131652.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
 gi|56379523|dbj|BAD75431.1| hypothetical conserved protein [Geobacillus kaustophilus HTA426]
 gi|261375792|gb|ACX78535.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC61]
 gi|297253947|gb|ADI27393.1| pseudouridine synthase, RluA family [Geobacillus sp. C56-T3]
 gi|317111017|gb|ADU93509.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC52]
          Length = 304

 Score =  289 bits (740), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 84/327 (25%), Positives = 149/327 (45%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  + +  +E++ +  R+D+         +   +Q+ +++G V V+ + VK N + ++G 
Sbjct: 1   MDTITFH-IEDEYDGERIDKVIAALNEEWSRSQVQQWIKNGLVTVNGQTVKANYKCEAGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V + P      H+  E   LD               + YED  + V NKP G+ V    
Sbjct: 60  SVAVSPPEPEPLHVEPEPIPLD---------------IYYEDEDVLVVNKPRGMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HR+D++TSG+L+VA+  AA + L E    +
Sbjct: 105 GHMRGTLVNALLAHCRDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDAAHRSLVEQLVNK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  +    I   + +           +   E+    A++HF+V++ F 
Sbjct: 165 TVTRRYKAIVHGVIPHDYGTIDAPIGRDKRDRKK----MAVTEENGKEAVTHFRVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + + ++E Q  TGRTHQ+RVH  ++G P+ GD +Y         +   +   LHA  +  
Sbjct: 220 RHYTYVECQLETGRTHQIRVHMKYIGYPLAGDPQYGPK-----KTLAIDGQALHAGVLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  L+  APLP    +  D L 
Sbjct: 275 RHPRSGEYLEFEAPLPPEFAELLDWLR 301


>gi|126724897|ref|ZP_01740740.1| Pseudouridine synthase, RluD [Rhodobacterales bacterium HTCC2150]
 gi|126706061|gb|EBA05151.1| Pseudouridine synthase, RluD [Rhodobacterales bacterium HTCC2150]
          Length = 347

 Score =  289 bits (740), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 129/342 (37%), Positives = 189/342 (55%), Gaps = 24/342 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  +E   RLDRW + H+P ++   ++K+ R G++RVD  RVK N R+  GQ
Sbjct: 1   MSAVQTIAVGENEAEQRLDRWMRRHFPDLSQGQVEKMCRKGEIRVDGGRVKANTRVTQGQ 60

Query: 64  VVRIPPVINALNHII-KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           ++RIPP+ +    +   E KI D+   L      +  +++Y+D  I   NKP GI VQGG
Sbjct: 61  LIRIPPLKDGPKKVYYDEPKISDADRKL------MMDMVIYKDDYIIALNKPPGIPVQGG 114

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG   HIDG  ++      +KPRL HRLD++TSG+L++AR + +A  LT  FR R  +KI
Sbjct: 115 SGQKRHIDGLSEALRFDSDEKPRLVHRLDKDTSGVLLLARNQRSASELTAVFRSRESRKI 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHI----GGDYVHVVKQNE----KGANYAISHFKVID 234
           YW+ V G+P  K   I   L+K        GG+ +  +   +     GA  A + + V+ 
Sbjct: 175 YWAAVGGVPHPKMGTIRFGLVKAPGHGPSGGGEKMICIHPRDIDKTDGAKRATTDYAVMT 234

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQN 286
             A++  W+ + P TGRTHQLR H   +G PI+GD KY  + + N            I  
Sbjct: 235 TLARRSAWMALVPVTGRTHQLRAHMAELGHPIIGDGKYGGSGQENLGDGWGAQLGGDISK 294

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            L+LHAR + L HP  G RL + A LP HM  TW ++G+  +
Sbjct: 295 NLHLHARSLTLKHPVTGARLHLVAELPRHMAATWKTVGWHEN 336


>gi|149203330|ref|ZP_01880300.1| Pseudouridine synthase, RluD [Roseovarius sp. TM1035]
 gi|149143163|gb|EDM31202.1| Pseudouridine synthase, RluD [Roseovarius sp. TM1035]
          Length = 347

 Score =  289 bits (739), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 125/338 (36%), Positives = 184/338 (54%), Gaps = 22/338 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ  +V  D+ + RLDRW +  +PH+  V ++K+ R G++RVD  RVK   R++ GQ
Sbjct: 1   MSGVQTRIVGPDDGDQRLDRWVRRLFPHVGQVQIEKMCRKGELRVDGGRVKPATRLEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPP+ +           +  +      +  ++S ++Y D  I   NKP G+ VQGGS
Sbjct: 61  SVRIPPLPDTDERPTGALARISPA-----DAKMIQSCVIYRDDHIIALNKPPGLPVQGGS 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  ++       KPRL HRLD++TSG+L++ARTR AA+ LT +FR R  +KIY
Sbjct: 116 KQLRHVDGLAEALRFGAEDKPRLVHRLDKDTSGVLLLARTREAAKGLTAAFRHRNTRKIY 175

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNE----KGANYAISHFKVIDC 235
           W+ V G+P  +   I   L+K    G    G+ +  +   +     GA  A + + VI+ 
Sbjct: 176 WAAVAGVPTPRMGTIRFGLVKAPGHGAKGEGEKMLCLHPRDIDATPGAKPATTDYAVIEA 235

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNK 287
              +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            +  K
Sbjct: 236 AGARTAWMALIPVTGRTHQLRAHMAEIGHPIVGDGKYGGSGQENLGDGWGAQLGGDVSRK 295

Query: 288 LYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
           L+LHAR + + HP    +  ITAPLP HM +TWD   +
Sbjct: 296 LHLHARSLKIEHPVSRAILHITAPLPEHMARTWDLFQW 333


>gi|167562573|ref|ZP_02355489.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           oklahomensis EO147]
 gi|167569756|ref|ZP_02362630.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           oklahomensis C6786]
          Length = 395

 Score =  288 bits (738), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 94/343 (27%), Positives = 152/343 (44%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V       RLD+     +P  +   LQ+ + S +VRVD    K    +  G  + +
Sbjct: 57  RVIEVPPALAGERLDKALAQLFPEFSRSRLQQWIESERVRVDGALAKIRQPVPLGATIEL 116

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                 L  ++ EQ        L    + +   ++YED  + V +KPAG+ V   +G   
Sbjct: 117 ------LPDLLPEQ--------LAFAPEPVPLSVVYEDDTLVVIDKPAGLVVHPAAGNWS 162

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 163 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYF 222

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFC 241
           +L WG    +   I   + +      +   +          A +HF+ +D      Q   
Sbjct: 223 ALAWGQMPAE-GTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTAMWARQPVS 278

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 279 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 338

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLP  +    D+LGF  D   +       D+
Sbjct: 339 HPATGRTMQWRAPLPDDLAALVDALGFGSDDAEFGDDDAVYDD 381


>gi|307729591|ref|YP_003906815.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1003]
 gi|307584126|gb|ADN57524.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1003]
          Length = 430

 Score =  288 bits (738), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 92/344 (26%), Positives = 153/344 (44%), Gaps = 29/344 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV ++    RLD+     +P  +   LQ  + + +VR+D K  K    +  G  + +
Sbjct: 66  RTVVVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAKIRQPVPLGASIEL 125

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P       ++ EQ        L    + +   +++ED  + V NKPAG+ V   +G   
Sbjct: 126 VP------DLLPEQ--------LAFTPEPVPLEIVFEDDTLVVINKPAGMVVHPAAGNWS 171

Query: 126 AYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + D+     +  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 172 GTVLNGLLYRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 231

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKF 240
            +LVWG    ++  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 232 LALVWGNMP-EEGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRRVDTAIWQRQPV 287

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L
Sbjct: 288 TAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGEFARQALHAWRLGL 347

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
            HP+ GR +Q  A +P  M     +LG   D        Y +D+
Sbjct: 348 IHPKTGRSMQWRADVPEDMAALSAALGLGRDDAGEFDDTYYEDD 391


>gi|154253208|ref|YP_001414032.1| RluA family pseudouridine synthase [Parvibaculum lavamentivorans
           DS-1]
 gi|154157158|gb|ABS64375.1| pseudouridine synthase, RluA family [Parvibaculum lavamentivorans
           DS-1]
          Length = 330

 Score =  288 bits (738), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 130/322 (40%), Positives = 191/322 (59%), Gaps = 5/322 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V  + V  +E+ +RLDRWFK  +P +    L+K+LR+GQVRVD  R K N R+ +GQ
Sbjct: 1   MNQVSQLDVTEEEDGVRLDRWFKRRFPMLTHGRLEKLLRTGQVRVDGARAKANARLATGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP+    +    +Q            ++ L++ ++Y+D  + V NKP G++VQGG+
Sbjct: 61  VVRVPPLGEDAD----KQAPKAVHAPSVDDAEMLRANVIYKDKSVLVLNKPVGLAVQGGT 116

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG L + +    ++PRL HRLD++TSG+LV+ART  AA  L ++F+ +  QKIY
Sbjct: 117 KTERHLDGMLDALIFDAKERPRLVHRLDRDTSGVLVLARTAKAAAALAQAFKQKDAQKIY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+P  ++  I   L K+     + V   K+ ++GA  A++HF  +   A    W+
Sbjct: 177 WALVVGVPVPRQGTIDLALSKQGGPRAERVFAAKRGDEGARDAVTHFSTVSTAAHTLAWV 236

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              P TGRTHQ+R HA  +  PIVGD KY      +    I  KL+LHAR +D+ HP+GG
Sbjct: 237 AFMPLTGRTHQIRAHAAAIETPIVGDGKYGG-VNAHPGGEIPRKLHLHARSIDIAHPDGG 295

Query: 304 RLQITAPLPAHMVKTWDSLGFK 325
           RL + A LP HM  +W  LGF 
Sbjct: 296 RLHVEADLPPHMKTSWKLLGFD 317


>gi|167836421|ref|ZP_02463304.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis MSMB43]
          Length = 344

 Score =  288 bits (737), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 97/339 (28%), Positives = 152/339 (44%), Gaps = 28/339 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V       RLD+     +P  +   LQ+ + S +VRVD    K    +  G  + +    
Sbjct: 10  VPPALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVDGAPAKIRQPVPLGATIEL---- 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
             L  ++ EQ        L    + +   ++YED  I V +KPAG+ V   +G      +
Sbjct: 66  --LPDLLPEQ--------LAFTPEPVPLSIVYEDEAIVVVDKPAGLVVHPAAGNWSGTLL 115

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y++LVW
Sbjct: 116 NGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVW 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEM 245
           G     K  I   + +      +   +          A +HF+ +D      Q    +  
Sbjct: 176 GQMP-DKGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRAVDTTLWERQPVSAIHC 231

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEG 302
              TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L HP  
Sbjct: 232 DLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVTPLPGGFARQALHAWRLGLVHPAT 291

Query: 303 GR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           GR +Q  APLPA +    ++LGF  D   +       D+
Sbjct: 292 GRTMQWRAPLPADLAALVEALGFGADDAEFGDDDAVYDD 330


>gi|163796887|ref|ZP_02190844.1| Pseudouridine synthase, RluD [alpha proteobacterium BAL199]
 gi|159177876|gb|EDP62425.1| Pseudouridine synthase, RluD [alpha proteobacterium BAL199]
          Length = 331

 Score =  288 bits (737), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 121/322 (37%), Positives = 186/322 (57%), Gaps = 4/322 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V  D+ + RLDRWFK ++P +  V+L K+LR+GQVRVD +RVK   R+++GQ
Sbjct: 1   MKAVETRIVAQDDGDQRLDRWFKRYFPTLGHVHLTKLLRTGQVRVDGRRVKAGERLEAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+ +      +  K         + ++ L+ ++L+ D  +   NKPAG++VQGGS
Sbjct: 61  TIRIPPM-DVPAASAEAVKAKPGGKGDAETAEQLRRLILHTDRDVLAINKPAGLAVQGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           GI  H+DG L   +    ++PRL HRLD++TSG+L+V R+  AA+ LTE+FR +   KIY
Sbjct: 120 GITKHVDGALDGLMFDAKERPRLVHRLDKDTSGVLLVGRSYQAARRLTEAFRAKSAMKIY 179

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G PK     I   + K     G+ + +   + +    A + +  ++    K  W+
Sbjct: 180 WALVVGEPKPNAGSIEGAIGKLPGRAGEKMAI---DLENGKRAFTRYVTVERLGGKVTWV 236

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            + P TGRTHQLRVH   +G PI+GD KY           +  KL+LHAR + +P  +G 
Sbjct: 237 ALFPVTGRTHQLRVHMAELGTPILGDGKYGGAEAFLQGEGVSRKLHLHARAIRIPDAKGR 296

Query: 304 RLQITAPLPAHMVKTWDSLGFK 325
            +++ APL  HM ++W   G  
Sbjct: 297 PVEVIAPLADHMARSWAFFGLD 318


>gi|254436973|ref|ZP_05050467.1| pseudouridine synthase, RluA family [Octadecabacter antarcticus
           307]
 gi|198252419|gb|EDY76733.1| pseudouridine synthase, RluA family [Octadecabacter antarcticus
           307]
          Length = 347

 Score =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 130/340 (38%), Positives = 192/340 (56%), Gaps = 24/340 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE + RLDRW K  + H+    ++K+ R G++RVD  RVK N R++ GQ
Sbjct: 1   MSRVQNLTVGLDEGDQRLDRWIKRRFAHLQQGGIEKMCRKGEIRVDGGRVKTNTRVEVGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+ +A     + + +  + + L      ++  ++Y+D  +   NKPAG+  QGGS
Sbjct: 61  KIRIPPLPDANEVDERPRDMTKADIQL------IQGCVIYKDDHVIALNKPAGLPTQGGS 114

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG  ++      +KPRL HRLD++TSG+L++ARTR AA+ LT++FR R  +KIY
Sbjct: 115 KQLRHVDGMAEALRFGYDEKPRLVHRLDKDTSGVLILARTRMAAKSLTDAFRHRNTEKIY 174

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNEK----GANYAISHFKVIDC 235
           W+LV G+P  K   +   L+K+   GG    + +  V   +     GA  A++++ V+  
Sbjct: 175 WALVAGVPIPKLGSVKYGLVKQGGHGGKGDNERMKCVHPKDVDKTFGAKRALTNYTVLTS 234

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---------KGNFTSPIQN 286
            A +  W+ + P TGRTHQLR H   +G PIVGD KY A                  I  
Sbjct: 235 LADRTAWVALTPVTGRTHQLRAHMAEIGHPIVGDGKYGAQAVQDNPGDGWGAGMGEEIGR 294

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           KL+LHAR + + HPE G  L I A LP HM KTW   G++
Sbjct: 295 KLHLHARSLRIEHPETGKELWIKASLPPHMGKTWSFFGWE 334


>gi|221212790|ref|ZP_03585766.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Burkholderia multivorans CGD1]
 gi|221167003|gb|EED99473.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Burkholderia multivorans CGD1]
          Length = 400

 Score =  288 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 145/328 (44%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +VRVD    K    +  G  + +
Sbjct: 58  RVVEVPASLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRVDGAPAKIRQPVPLGATIEL 117

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 118 VP------DLLPEQ--------LAFTPEPVPLDIVYEDDALVVINKPAGLVVHPAAGNWS 163

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 164 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 223

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG     +  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 224 FALVWGAMP-DEGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCLWQRQPV 279

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L
Sbjct: 280 SAIQCDLETGRTHQIRVHCSHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGL 339

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G  +Q   PLP  M    D+LGF
Sbjct: 340 VHPVTGSAMQWRCPLPDDMTALVDALGF 367


>gi|154685962|ref|YP_001421123.1| YlyB [Bacillus amyloliquefaciens FZB42]
 gi|154351813|gb|ABS73892.1| YlyB [Bacillus amyloliquefaciens FZB42]
          Length = 304

 Score =  288 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 84/322 (26%), Positives = 151/322 (46%), Gaps = 32/322 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V+ ++++ R+D++  +   + +   +Q+ ++ G V V+ K VK N ++Q G  V + 
Sbjct: 5   EITVQPEQKSERIDKFLASTGENWSRTQVQQWVKEGLVSVNGKSVKANYKMQPGDQVNVT 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                          +     L   ++ +   + YED  + V NKP G+ V    G    
Sbjct: 65  ---------------IPEPEELDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHVTG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + 
Sbjct: 110 TLVNGLMAHCNDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRK 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G+  +    I   + +        + V +++ K    A++HF V++ F Q F  
Sbjct: 170 YTAVVHGVISHDDGTIDAPIGRDKK-DRQSMTVTRESSKN---AVTHFHVLERF-QDFTL 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   HP  
Sbjct: 225 VECRLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDF-----NGQALHAGILGFDHPRT 279

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  ++  APLP  M K  + L 
Sbjct: 280 GEYMEFEAPLPEDMKKLIEDLR 301


>gi|295688947|ref|YP_003592640.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
 gi|295430850|gb|ADG10022.1| pseudouridine synthase, RluA family [Caulobacter segnis ATCC 21756]
          Length = 332

 Score =  288 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 124/328 (37%), Positives = 183/328 (55%), Gaps = 10/328 (3%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    V+ + V+  E+ +RLDRWFK  +PH+N + L K+ RSGQVRVD  R K + ++ 
Sbjct: 1   MSTTKEVRTLYVDAGEDGVRLDRWFKRRWPHLNHIQLNKLFRSGQVRVDGSRAKADTKLA 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  +R+PP+ +A +   K +          +   + KS++LYED ++   NKPAG++VQ
Sbjct: 61  AGSQIRVPPLPDAPDPADKNK-------LSARDVAYAKSLVLYEDEEVLALNKPAGLAVQ 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GG+    HID  L +W      +PRL HRLD++TSG+L++ +T +AA  L+ +F  R+ Q
Sbjct: 114 GGTKTTKHIDKLLSAW-GEGVDRPRLVHRLDRDTSGVLLLGKTPSAAARLSGAFAKRKAQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW++V G P   +  +   L K+     + V   +  +  A  A + F  I     + 
Sbjct: 173 KTYWAIVAGNPHPTEGVMELHLAKRGVGDRELVVPAQPKDADAQPAETEFVTISRAGPRV 232

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            W+ ++PHTGRTHQLR H   MG PI+GD KY        +  +  KL LHAR + LPHP
Sbjct: 233 TWMALRPHTGRTHQLRAHMKAMGHPILGDPKYGDEKSAPLSEGL--KLQLHARSILLPHP 290

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
             G L I APL   M + +   GF  D 
Sbjct: 291 SAGMLHIEAPLSPEMKEGFRKFGFSEDE 318


>gi|253577879|ref|ZP_04855151.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850197|gb|EES78155.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 304

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 87/331 (26%), Positives = 155/331 (46%), Gaps = 36/331 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M ++ Y     V + +  +R+DR+       ++   +QK+L+  ++ V+   VK N ++Q
Sbjct: 1   MEILNY----QVSDGQSGIRIDRYLSEMNEELSRSYIQKLLKEQKITVNGSAVKANYKVQ 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +          IKE  IL   + L          +LYED  + + NKP G+ V 
Sbjct: 57  EGDEISV------AVPDIKEPDILPEDIPLD---------ILYEDDDVLIVNKPKGMVVH 101

Query: 121 GGSGIA--YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
             +G      ++  +    D+        +P + HR+D++T+G L+V +   A ++L E 
Sbjct: 102 PSAGHTSGTLVNAIMFHCKDNLSGINGVLRPGIVHRIDKDTTGALLVCKNDNAHRNLAEQ 161

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            +   I++ Y ++V G+ K  +  I   + +   I    + V   N K    A++H+KV+
Sbjct: 162 LKEHSIRRRYRAIVAGVLKEDEGTIEGPIGRH-PIDRKKMAV---NYKNGKDAVTHYKVL 217

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +   ++E +  TGRTHQ+RVH   +G P++GD  Y +               LHA 
Sbjct: 218 ERF-KNATYVECRLETGRTHQIRVHMTSIGHPLLGDEVYGSGKNPYH----LQGQTLHAM 272

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            +   HP  G  ++ TAPLP + VK  + L 
Sbjct: 273 ILGFVHPSTGEYMEFTAPLPEYFVKLLEKLR 303


>gi|295676473|ref|YP_003604997.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1002]
 gi|295436316|gb|ADG15486.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1002]
          Length = 416

 Score =  287 bits (735), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 91/331 (27%), Positives = 149/331 (45%), Gaps = 29/331 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV N+    RLD+     +P  +   LQ  + + +VRVD K  K    +  G  + +
Sbjct: 68  RRVVVPNELAGERLDKVLAKVFPEFSRSRLQSWIEAQRVRVDGKPAKIRQPVPLGATIEL 127

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 128 VP------DLLPEQ--------LAFTPEPVPLEIVYEDDTLVVINKPAGMVVHPAAGNWS 173

Query: 126 AYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + ++     +  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 174 GTVLNGLLHRYGETAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 233

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKF 240
            +LVWG     +  I   + +      +   +          A +HF+ +       Q  
Sbjct: 234 LALVWGNMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRRVASAIWQRQPV 289

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             +     TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 290 TAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGL 349

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            HP+ GR +Q  A +PA +     +LG   D
Sbjct: 350 IHPKTGRSMQWRADVPADIEALSAALGLGRD 380


>gi|315179570|gb|ADT86484.1| ribosomal large subunit pseudouridine synthase C [Vibrio furnissii
           NCTC 11218]
          Length = 316

 Score =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 109/326 (33%), Positives = 184/326 (56%), Gaps = 16/326 (4%)

Query: 1   MSLM-TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS M T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++
Sbjct: 1   MSEMRTQVQFIDIDEDMAGQRIDNFLRNQLKSIPKSVVYRILRKGEVRVNKKRVKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VR+PPV       +KE ++   S  L K ++ L+  +LYED  + V NKP+G +V
Sbjct: 61  EAGDIVRVPPVTID----VKEDEVAAPSTKLNKVAE-LEHCILYEDDHMLVLNKPSGTAV 115

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL++A+ R+A + L   FR + +
Sbjct: 116 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLIAKKRSALRQLQSQFREKTV 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y++LV G  K++ + +   LLK        V+ + +       + + FK+++ FA  
Sbjct: 175 QKYYFALVMGEWKSQCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKILEKFAD- 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  ++G PI  D +Y       +T+    ++L+LHA  +   
Sbjct: 228 ATLVQASPITGRTHQIRVHTQYVGHPIAWDDRYGDRRFDAYTAQFGIDRLFLHAANIQFT 287

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLG 323
           HP  G +++I APL A + K    + 
Sbjct: 288 HPASGEKMEINAPLDAKLEKALAKMR 313


>gi|119383542|ref|YP_914598.1| RluA family pseudouridine synthase [Paracoccus denitrificans
           PD1222]
 gi|119373309|gb|ABL68902.1| ribosomal large subunit pseudouridine synthase C [Paracoccus
           denitrificans PD1222]
          Length = 348

 Score =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 125/342 (36%), Positives = 186/342 (54%), Gaps = 23/342 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V  DE   R+DRW K  +P +    ++K+ R+GQ+RVD  RVK N RI+ GQ
Sbjct: 1   MSGVQTIRVGEDEGEQRIDRWLKKRFPQLTQGAVEKMCRTGQLRVDGGRVKANTRIEPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+          +  +  S      ++ ++S +L+ D  I   NKP G+  QGGS
Sbjct: 61  EVRVPPLPEGAPPPAAPKASVKQS-----DAEMIQSCVLWRDEHIIALNKPPGLPSQGGS 115

Query: 124 G-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    H+DG   + +     +P+L HRLD++TSG+L++ART   A+ L+E+FR R  +KI
Sbjct: 116 GQGDRHVDGLTTALMFGYKDRPKLVHRLDKDTSGVLLLARTDRIARALSEAFRHRLTRKI 175

Query: 183 YWSLVWGIPKNKKECIANWLLKKS----HIGGDYVHVVKQN----EKGANYAISHFKVID 234
           YW+ V G+P  +   I   L+K         G+ +  V  +     +GA  A + + V+D
Sbjct: 176 YWAAVAGVPHPRMGSIKYGLVKAPGRGRGGEGEKMMAVHPSAVAATEGAKRAHTDYAVLD 235

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQN 286
               +  W+ M P TGRTHQLR H   +G PIVGD KY  + + N            I  
Sbjct: 236 ALGGRVSWVAMVPVTGRTHQLRAHMAEIGHPIVGDGKYGGSGQENLGDGWGAQLGGEISR 295

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           KL+LHAR +   HP   + + +TAPLP HM +TW +LG+  +
Sbjct: 296 KLHLHARMIRFEHPITKKLITVTAPLPEHMSRTWKTLGWSEN 337


>gi|321315311|ref|YP_004207598.1| pseudouridylate synthase [Bacillus subtilis BSn5]
 gi|320021585|gb|ADV96571.1| pseudouridylate synthase [Bacillus subtilis BSn5]
          Length = 303

 Score =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 84/327 (25%), Positives = 146/327 (44%), Gaps = 34/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  +    ++++ R+D++  +     +   +Q+ ++ GQV V+   VK N +IQ G 
Sbjct: 1   MNQID-ITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSAVKANYKIQPGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +                +     L   ++ L   + YED  + V NKP G+ V    
Sbjct: 60  QVTVT---------------VPEPEALDVLAEPLDLDIYYEDQDVLVVNKPRGMVVHPAP 104

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHLTGTLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  +    I   + +                +    A++HF V++ F 
Sbjct: 165 TVTRKYTAVVHGLISHDDGTIDAPIGRDKKD-----RQSMTVTRDGKNAVTHFHVLERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q F  +E Q  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +  
Sbjct: 219 QDFTLVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDF-----NGQALHAGVLGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  APLP  M +  ++L 
Sbjct: 274 DHPRTGEYVEFEAPLPEDMAELIENLR 300


>gi|161524654|ref|YP_001579666.1| RluA family pseudouridine synthase [Burkholderia multivorans ATCC
           17616]
 gi|189350589|ref|YP_001946217.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans ATCC 17616]
 gi|160342083|gb|ABX15169.1| pseudouridine synthase, RluA family [Burkholderia multivorans ATCC
           17616]
 gi|189334611|dbj|BAG43681.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans ATCC 17616]
          Length = 400

 Score =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 145/328 (44%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +VRVD    K    +  G  + +
Sbjct: 58  RVVEVPASLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRVDGAPAKIRQPVPLGATIEL 117

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 118 VP------DLLPEQ--------LAFTPEPVPLDIVYEDDALVVINKPAGLVVHPAAGNWS 163

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 164 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 223

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG     +  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 224 FALVWGAMP-DEGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCLWQRQPV 279

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L
Sbjct: 280 SAIQCDLETGRTHQIRVHCSHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGL 339

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G  +Q   PLP  M    ++LGF
Sbjct: 340 VHPVTGSAMQWRCPLPDDMTALVEALGF 367


>gi|296133340|ref|YP_003640587.1| pseudouridine synthase, RluA family [Thermincola sp. JR]
 gi|296031918|gb|ADG82686.1| pseudouridine synthase, RluA family [Thermincola potens JR]
          Length = 321

 Score =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 79/314 (25%), Positives = 141/314 (44%), Gaps = 31/314 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              R+D +    + H++   +QK++  G + V+  RVK N ++++G++VR+         
Sbjct: 31  AGTRIDVYLAGIFDHLSRSFIQKLIGDGYITVNGTRVKANYKLKAGELVRVE-------- 82

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
                  +  +  L   ++ +   +LYED  + V NKP G+ V    G      ++  L 
Sbjct: 83  -------IPYTEELEVSAEPIPLEILYEDRDVIVINKPQGMVVHPAPGNYSGTLVNALLW 135

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++TSG+++ A+       L +  + R + + Y +L+ G+
Sbjct: 136 HCKDLSGINGVMRPGIVHRLDKDTSGVIMAAKNDETHASLAKQIKDRTVTRRYLALIHGV 195

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                  I   + +           +    K +  A++H+KV++ F  K+ ++E +  TG
Sbjct: 196 IPEPAGIIEAPIGRDPKDRKK----MAVTTKNSKPAVTHYKVLERF-NKYTFVECKLETG 250

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++  P+VGD  Y            Q    LHA  +   HP  G  L+  A
Sbjct: 251 RTHQIRVHMAYLKYPVVGDPVYGP----AKNEFGQTGQLLHAHILGFHHPRTGEYLEFKA 306

Query: 310 PLPAHMVKTWDSLG 323
           PLP +       L 
Sbjct: 307 PLPEYFNNILSKLR 320


>gi|229162828|ref|ZP_04290785.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           R309803]
 gi|228620710|gb|EEK77579.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           R309803]
          Length = 302

 Score =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 145/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N ++++  
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKVVKGNYKVKAND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIGRD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|296444792|ref|ZP_06886755.1| pseudouridine synthase, RluA family [Methylosinus trichosporium
           OB3b]
 gi|296257740|gb|EFH04804.1| pseudouridine synthase, RluA family [Methylosinus trichosporium
           OB3b]
          Length = 365

 Score =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 137/354 (38%), Positives = 201/354 (56%), Gaps = 32/354 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + VQ + V  DE  +RLDRWFK  +P +   +L KI R G+VRVD KRV    R++  Q 
Sbjct: 12  SPVQTLTVTEDEAGLRLDRWFKRRFPALALSHLAKICRKGEVRVDGKRVDTATRLEQDQK 71

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+PP+   L        IL +S    + +  L  + LYED+ + V NKP G++VQGGSG
Sbjct: 72  IRVPPL--KLEAAAAAPTILRAS---PEDARALADMTLYEDASLLVLNKPYGLAVQGGSG 126

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +  HIDG L+S       +P L HRLD++TSG+L++A+ R  A  L E FR R+ +KIYW
Sbjct: 127 MTRHIDGMLESLAKGDT-RPVLVHRLDRDTSGVLLIAKNRRTAADLGEIFRSRQAKKIYW 185

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDY-----------------VHVVKQNEKGANYAI 227
           +LV G+PK  +  ++ +L K + +G D                  + V +  ++GA +++
Sbjct: 186 ALVEGVPKPAQGRVSLYLAKGAAMGDDRPPRPGSERREAADAREKMRVARHGDEGAQHSL 245

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-------- 279
           +++ +++  A +  WL M+P TGRTHQLR HA  + CPI GD KY    +          
Sbjct: 246 TYYAIVEKAAPRCAWLSMKPLTGRTHQLRAHAEAIACPIFGDPKYGHRPEDEVRRRDPMR 305

Query: 280 -FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
                ++ KL+L AR + LP+P+GG L +TAPLPAHM  +WD  GF   R   I
Sbjct: 306 AMPEGLERKLHLLARRLILPNPKGGTLDVTAPLPAHMQTSWDVFGFDASRQDPI 359


>gi|323702053|ref|ZP_08113721.1| pseudouridine synthase, RluA family [Desulfotomaculum nigrificans
           DSM 574]
 gi|323532935|gb|EGB22806.1| pseudouridine synthase, RluA family [Desulfotomaculum nigrificans
           DSM 574]
          Length = 307

 Score =  286 bits (732), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 83/318 (26%), Positives = 145/318 (45%), Gaps = 31/318 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ +    RLD +       ++   +Q+++  GQV V+    K N +++ G  V +    
Sbjct: 8   VDQENAKSRLDVFLSGQCHDLSRSYIQRLIEEGQVTVNDLPTKANYKLRVGDRVAVEVPP 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHI 129
                ++ E   LD               + YED+ + V NKP G+ V    G+     +
Sbjct: 68  AEELQVVPEPIPLD---------------IYYEDNDVIVVNKPRGMVVHPAEGNTSGTLV 112

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HRLD++TSG+++VA+   A   L +  + R + + Y +
Sbjct: 113 NALLYHCRDLSGINGVLRPGIVHRLDKDTSGLIMVAKNDLAHNSLAQQLKDRTVTRRYRA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV    + +   +   + +        + VV   E+ +  A++H++V++ F Q +  +E 
Sbjct: 173 LVHNNIREEVGTVNAPIGRDPR-DRQRMAVV---ERNSKPAVTHYRVLERFGQ-YTLVEC 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +  TGRTHQ+RVH  ++G P+VGD KY             +   LHA  +   HP  G+ 
Sbjct: 228 RLETGRTHQIRVHMAYIGHPVVGDPKYGP----TKPHFDLDGQLLHAGVLGFKHPTTGQY 283

Query: 305 LQITAPLPAHMVKTWDSL 322
           L+ TAPLP    +    L
Sbjct: 284 LEFTAPLPDIFEQVLHKL 301


>gi|114327246|ref|YP_744403.1| ribosomal large subunit pseudouridine synthase C [Granulibacter
           bethesdensis CGDNIH1]
 gi|114315420|gb|ABI61480.1| ribosomal large subunit pseudouridine synthase C [Granulibacter
           bethesdensis CGDNIH1]
          Length = 366

 Score =  286 bits (732), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 126/335 (37%), Positives = 188/335 (56%), Gaps = 13/335 (3%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           ++M+ V    V +DE ++RLDRWF+ HYP +  V +QK+ R+GQ+RVD  R +   R+Q 
Sbjct: 30  TIMS-VTTRQVTDDEADIRLDRWFRRHYPSLTQVAIQKMCRTGQIRVDGARAEAATRLQP 88

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           GQ VRIPP+         EQ+              L+S +LY+D  + V NKP+G+  QG
Sbjct: 89  GQSVRIPPLKVPS---AAEQEGEGPRALDPIQQKELESWILYKDDHLIVLNKPSGLPSQG 145

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G GI  H+DG L      +  +PRL HRLD++TSG++V+AR+   A  L   FR R  +K
Sbjct: 146 GPGITRHLDGLLDGLRFGRDDRPRLVHRLDRDTSGVIVIARSPGVAAKLAALFRTRETEK 205

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +YW++V G P   +  I   LL+  +   + V +  + ++    AI+ ++ +D  A+K  
Sbjct: 206 VYWAVVAGRPVPVEGRIDRPLLR-QNDRNEPVVLADRKDRDKVTAITDYRTLDHAARKLA 264

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--------ANFKGNFTSPIQNKLYLHAR 293
           WLE++P TGR HQLRVH   M  PI+GD +Y                   +  +L+LHAR
Sbjct: 265 WLELRPLTGRMHQLRVHCAAMDAPILGDERYGSWRNTDERGVRNTALVEGLSRRLHLHAR 324

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
            + LPHP GG L + A L  HM +T+++LGF   +
Sbjct: 325 RLSLPHPAGGMLSVEADLSPHMAETFETLGFTAPK 359


>gi|221309420|ref|ZP_03591267.1| hypothetical protein Bsubs1_08546 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221313745|ref|ZP_03595550.1| hypothetical protein BsubsN3_08482 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221318669|ref|ZP_03599963.1| hypothetical protein BsubsJ_08416 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221322942|ref|ZP_03604236.1| hypothetical protein BsubsS_08522 [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|255767360|ref|NP_389429.3| pseudouridylate synthase [Bacillus subtilis subsp. subtilis str.
           168]
 gi|254763395|sp|Q45480|YLYB_BACSU RecName: Full=Uncharacterized RNA pseudouridine synthase ylyB;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|1373157|gb|AAB57767.1| orf-X; hypothetical protein; Method: conceptual translation
           supplied by author [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|225184987|emb|CAB13420.3| pseudouridylate synthase [Bacillus subtilis subsp. subtilis str.
           168]
          Length = 303

 Score =  286 bits (732), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 146/327 (44%), Gaps = 34/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  +    ++++ R+D++  +     +   +Q+ ++ GQV V+   VK N +IQ G 
Sbjct: 1   MNQID-ITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSAVKANYKIQPGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +                +     L   ++ +   + YED  + V NKP G+ V    
Sbjct: 60  QVTVT---------------VPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAP 104

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHLTGTLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  +    I   + +                +    A++HF V++ F 
Sbjct: 165 TVTRKYTAVVHGLISHDDGTIDAPIGRDKKD-----RQSMTVTRDGKNAVTHFHVLERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q F  +E Q  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +  
Sbjct: 219 QDFTLVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDF-----NGQALHAGVLGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  APLP  M +  ++L 
Sbjct: 274 DHPRTGEYVEFEAPLPEDMAELIENLR 300


>gi|229168633|ref|ZP_04296355.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH621]
 gi|228614789|gb|EEK71892.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH621]
          Length = 302

 Score =  286 bits (732), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 145/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVKGNYKVKGND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTKGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGIIDAPIGRD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  AP+P    +  + L 
Sbjct: 275 NHPRTGEYIEFEAPIPEVFEEALNILR 301


>gi|254419979|ref|ZP_05033703.1| pseudouridine synthase, RluA family [Brevundimonas sp. BAL3]
 gi|196186156|gb|EDX81132.1| pseudouridine synthase, RluA family [Brevundimonas sp. BAL3]
          Length = 341

 Score =  286 bits (732), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 118/323 (36%), Positives = 180/323 (55%), Gaps = 8/323 (2%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + V  DE+ +RLDRWF+  +PH++ + +QK+ RSGQ+RVD  R+K   R+ +G  V
Sbjct: 14  EVLTIYVAEDEDGIRLDRWFRRRWPHLSNIQVQKMARSGQIRVDGARIKPEGRLTAGAAV 73

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP+ +  +    +   L       +   F KS++LYED  +   NKP G++VQGG+  
Sbjct: 74  RVPPIPDDTSRQAGDLHTLSE-----RDIAFAKSLVLYEDDMVIAINKPHGLAVQGGTKT 128

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           + H+D  L +W +    +PRL HRLD++TSG+L++ +   AA+ L  +F  R+ +K YW+
Sbjct: 129 SRHVDRLLSAWGEGMD-RPRLVHRLDRDTSGVLLLGKGPEAAKRLAGAFARRQAKKTYWA 187

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G PK     I   L K      + +    + +  A  A + F  I   + +  W+ +
Sbjct: 188 IVIGNPKPYSGQIDMPLKKTGINDFEMMRPADRKDPKAEPAETAFSTISRASHRAAWMAL 247

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +P TGRTHQLR H   +G PI+GD KY        + P+  KL LHAR ++L HP GG L
Sbjct: 248 RPFTGRTHQLRAHMAGIGHPILGDPKYGDEKSRELSGPL--KLQLHARSIELDHPRGGLL 305

Query: 306 QITAPLPAHMVKTWDSLGFKYDR 328
           ++TAPL   M   +   GF  D 
Sbjct: 306 KVTAPLSPEMKAGFAHFGFSEDE 328


>gi|157692226|ref|YP_001486688.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
 gi|157680984|gb|ABV62128.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
          Length = 304

 Score =  286 bits (732), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 87/327 (26%), Positives = 154/327 (47%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V  + V  ++ + RLD++     P  +   +Q+ ++ G + V+ K+VK N ++Q+G 
Sbjct: 1   MNQVN-IAVSEEQTSERLDKFLSTSEPEWSRTQVQQWVKDGLIEVNGKQVKANYKVQAGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +++                +     L   ++ +   + YED+ + V NKP G+ V    
Sbjct: 60  QIKVE---------------IPEPEALDVEAEAMDLDIYYEDADVLVVNKPRGMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHVSGTLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V GI ++    I   + +           +   ++ +  A++HF VI+ F 
Sbjct: 165 TVTRKYTAVVHGIIQHDTGTIDAPIGRDKKD----RQSMTVTKESSKQAVTHFDVIERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +  
Sbjct: 220 DDFTVVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPRKTVDF-----NGQLLHAGVLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++ TAP+PA M    DSL 
Sbjct: 275 DHPRTGEYIEFTAPVPADMRGFIDSLR 301


>gi|291484098|dbj|BAI85173.1| hypothetical protein BSNT_02552 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 303

 Score =  286 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 146/327 (44%), Gaps = 34/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  +    ++++ R+D++  +     +   +Q+ ++ GQV V+   VK N +IQ G 
Sbjct: 1   MNQID-ITASEEQKSERIDKFLASSENDWSRTQVQQWVKDGQVVVNGSAVKANYKIQPGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +                +     L   ++ +   + YED  + V NKP G+ V    
Sbjct: 60  QVTVT---------------VPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAP 104

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHLTGTLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  +    I   + +                +    A++HF V++ F 
Sbjct: 165 TVTRKYTAVVHGLISHDDGTIDAPIGRDKKD-----RQSMTVTRDGKSAVTHFHVLERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q F  +E Q  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +  
Sbjct: 219 QDFTLVECQLETGRTHQIRVHMRYIGFPLAGDPKYGPRKTIDF-----NGQALHAGVLGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  APLP  M +  ++L 
Sbjct: 274 DHPRTGEYVEFEAPLPEDMAELIENLR 300


>gi|296331122|ref|ZP_06873596.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305674277|ref|YP_003865949.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
 gi|296151766|gb|EFG92641.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305412521|gb|ADM37640.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
          Length = 303

 Score =  286 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 146/327 (44%), Gaps = 34/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  +    ++++ R+D++  +     +   +Q+ ++ GQV V+   VK N +IQ G 
Sbjct: 1   MNQID-ITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSPVKSNYKIQPGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +                +     L   ++ +   + YED  + V NKP G+ V    
Sbjct: 60  QVTVT---------------VPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAP 104

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHLTGTLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  +    I   + +                +    A++HF V++ F 
Sbjct: 165 TVTRKYTAVVHGLISHDDGTIDAPIGRDKKD-----RQSMTVTRDGKNAVTHFHVLERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q F  +E Q  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +  
Sbjct: 219 QDFTLVECQLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDF-----NGQALHAGILGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  APLP  M +  ++L 
Sbjct: 274 DHPRTGEYVEFEAPLPEDMAELIENLR 300


>gi|119775123|ref|YP_927863.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119767623|gb|ABM00194.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           amazonensis SB2B]
          Length = 330

 Score =  286 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 103/323 (31%), Positives = 171/323 (52%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           ++ T VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++ +
Sbjct: 15  TVPTQVQLISIDEDGAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLAA 74

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP       + ++      S NL + +  L+  +L+ED +I V NKPAGI+V G
Sbjct: 75  GDEVRVPP-----VRVAEKDYRTAPSANLNRVAQ-LEDRILFEDKQIIVLNKPAGIAVHG 128

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ Y +   L+S   +  +   L HRLD++TSG+L++A+ R A +HL +  R +++QK
Sbjct: 129 GSGVDYGVIESLRSLRPT-CKFLELVHRLDRDTSGVLLIAKKRMALRHLHDQLRNKQMQK 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y +LV G  +     +   LLK +   G+ +  V         + + F+V+  F  +  
Sbjct: 188 VYQALVRGQWQEHDRVVKAPLLKITLKSGERIVRVNSE---GKPSETRFRVLRRF-DEAS 243

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
            +E  P TGRTHQ+RVH  + G PI  D KY    F     +    +L+LHA  +   HP
Sbjct: 244 LVEASPVTGRTHQIRVHCQYQGHPIACDDKYSEQKFDDAMRAKGLQRLFLHAAQLTFTHP 303

Query: 301 EGG-RLQITAPLPAHMVKTWDSL 322
           E   ++ + APL   +    D+L
Sbjct: 304 ESETQMTVQAPLDGDLTAVLDAL 326


>gi|221198059|ref|ZP_03571105.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans CGD2M]
 gi|221204383|ref|ZP_03577400.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans CGD2]
 gi|221175240|gb|EEE07670.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans CGD2]
 gi|221181991|gb|EEE14392.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans CGD2M]
          Length = 399

 Score =  286 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 145/328 (44%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +VRVD    K    +  G  + +
Sbjct: 58  RVVEVPASLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRVDGAPAKIRQPVPLGATIEL 117

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 118 VP------DLLPEQ--------LAFTPEPVPLDIVYEDDALVVINKPAGLVVHPAAGNWS 163

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 164 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 223

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG     +  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 224 FALVWGAMP-DEGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCLWQRQPV 279

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L
Sbjct: 280 SAIQCDLETGRTHQIRVHCSHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGL 339

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G  +Q   PLP  M    ++LGF
Sbjct: 340 VHPVTGSAMQWRCPLPDDMTALVEALGF 367


>gi|163745572|ref|ZP_02152932.1| ribosomal large subunit pseudouridine synthase C [Oceanibulbus
           indolifex HEL-45]
 gi|161382390|gb|EDQ06799.1| ribosomal large subunit pseudouridine synthase C [Oceanibulbus
           indolifex HEL-45]
          Length = 348

 Score =  286 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 125/342 (36%), Positives = 191/342 (55%), Gaps = 23/342 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + V   + + RLDRWFK  +P IN   ++K+ R G++RVD  RVK N R+++GQ
Sbjct: 1   MSRVQTITVAVGDGDQRLDRWFKRMFPQINQGLIEKMCRKGEIRVDGGRVKANTRLEAGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+ ++      ++  +         +  +++ ++Y D  +   NKP G++VQGGS
Sbjct: 61  EVRVPPLPDSAPPPPPKRTRI-----TDADAKMIRNCVIYRDEHVIALNKPPGLAVQGGS 115

Query: 124 GIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G A  H+D   ++ +    +KPRL HRLD++TSG+L++ARTR AA+ LT + R R  +KI
Sbjct: 116 GQADRHVDALSEALIFDAEEKPRLVHRLDRDTSGVLLLARTRLAAKALTAAMRHRETRKI 175

Query: 183 YWSLVWGIPKNKKECIANWLLK-----KSHIGGDYVHVVKQN---EKGANYAISHFKVID 234
           YW++V G+P      +   L+K     +S  G   + V  ++     GA  A + +  + 
Sbjct: 176 YWAIVAGVPTPYLGEVKYGLVKAGGHGRSGEGEKMIAVHPRDMDATPGAKRAHTLYATLF 235

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQN 286
               +  W+ M+P TGRTHQLR H   +G PIVGD KY  + + N            I  
Sbjct: 236 RVGSRASWVAMEPVTGRTHQLRAHMAEIGHPIVGDGKYGGSGQENLGDGWGAQLGGIISK 295

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           KL+LHAR M   HP   + + ITA LP HM  +WD+ G+  D
Sbjct: 296 KLHLHARMMRFEHPHTRKPVTITAELPEHMAHSWDTFGWTED 337


>gi|237731018|ref|ZP_04561499.1| 23S rRNA pseudouridylate synthase [Citrobacter sp. 30_2]
 gi|226906557|gb|EEH92475.1| 23S rRNA pseudouridylate synthase [Citrobacter sp. 30_2]
          Length = 331

 Score =  286 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 109/329 (33%), Positives = 174/329 (52%), Gaps = 15/329 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 15  MKTETPAVKTVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 74

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G +VRIPPV       + E++    S NL K +  L  ++LYED  I V NKP+G +V
Sbjct: 75  EDGDIVRIPPVR------VAEREEEAISPNLQKVA-ALTDVILYEDDHILVLNKPSGTAV 127

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 128 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 186

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 187 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVNQE---GKPSETRFKVEERYA-F 242

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +   
Sbjct: 243 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLADTGLNRLFLHAAALKFT 302

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HP  G  ++I AP+   + +  + L  K 
Sbjct: 303 HPGTGEVMRIEAPMDKQLKRCLEVLRSKA 331


>gi|167587072|ref|ZP_02379460.1| pseudouridine synthase, RluA family protein [Burkholderia ubonensis
           Bu]
          Length = 401

 Score =  286 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 145/328 (44%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +VRVD    K    +  G  + +
Sbjct: 58  RVVEVPPSLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRVDGAPAKIRQPVPLGATIEL 117

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 118 AP------DLLPEQ--------LAFTPEPVPLDIVYEDDALVVINKPAGLVVHPAAGNWS 163

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 164 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 223

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG     +  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 224 FALVWGTMP-DEGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCLWQRQPV 279

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 280 SAIQCDLETGRTHQIRVHCAHAGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGL 339

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G+ +Q   PLP  M     +LGF
Sbjct: 340 VHPVSGKTMQWRCPLPDDMTALVAALGF 367


>gi|121533717|ref|ZP_01665544.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
 gi|121307708|gb|EAX48623.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
          Length = 309

 Score =  286 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 89/331 (26%), Positives = 148/331 (44%), Gaps = 32/331 (9%)

Query: 1   MSLMTYVQYVVVEND-EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M+ +T   +  +  D ++  RLD +     P ++  ++Q+I+ +G+V V+ K  K N ++
Sbjct: 1   MTALTNKTFSFIAEDVDKGKRLDLFLVERLPELSRTHIQRIIAAGEVTVNGKAGKANYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
                V I                L         ++ +   +LYED  I V NKP G+ V
Sbjct: 61  APADYVTIR---------------LPEPKPAEIKAEAISLDILYEDEDIIVINKPRGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              +G      ++  L+      G     +P + HRLD++TSG+++VA+T  A   L   
Sbjct: 106 HPAAGNYEGTLVNALLRHCDRLSGINGVSRPGIVHRLDKDTSGVMMVAKTDRAHLDLARQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + R   + Y ++V G  K  +  I   + +        + VV  N   +  AI+ F+V+
Sbjct: 166 IKERTAGRKYVAIVHGNIKENQGIINAPIGRH-PTDRKKMAVVFTN---SKEAITTFQVL 221

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F   +  +E +  TGRTHQ+RVH  ++G P+VGD KY    +            LHA 
Sbjct: 222 ERFGD-YTLVECRLFTGRTHQIRVHMAYIGHPVVGDPKYGPGRQRFAIM----GQALHAA 276

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            +   HP  G R+  T PLP  M    + L 
Sbjct: 277 ELTFQHPVTGERMSFTVPLPDDMRAILEELR 307


>gi|260767405|ref|ZP_05876343.1| ribosomal large subunit pseudouridine synthase C [Vibrio furnissii
           CIP 102972]
 gi|260617640|gb|EEX42821.1| ribosomal large subunit pseudouridine synthase C [Vibrio furnissii
           CIP 102972]
          Length = 316

 Score =  285 bits (730), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 109/326 (33%), Positives = 184/326 (56%), Gaps = 16/326 (4%)

Query: 1   MSLM-TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS M T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++
Sbjct: 1   MSEMRTQVQFIDIDEDMAGQRIDNFLRNQLKSIPKSVVYRILRKGEVRVNKKRVKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VR+PPV       +KE ++   S  L K ++ L+  +LYED  + V NKP+G +V
Sbjct: 61  EAGDIVRVPPVTID----VKEDEVAAPSTKLNKVAE-LEHCILYEDDHMLVLNKPSGTAV 115

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL++A+ R+A + L   FR + +
Sbjct: 116 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLIAKKRSALRQLQSQFREKTV 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y++LV G  K++ + +   LLK        V+ + +       + + FK+++ FA  
Sbjct: 175 QKYYFALVMGEWKSQCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKILEKFAD- 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  ++G PI  D +Y       +T+    ++L+LHA  +   
Sbjct: 228 ATLVQASPITGRTHQIRVHTQYVGHPIAWDDRYGDRRFDAYTAQFGIDRLFLHAANIQFA 287

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLG 323
           HP  G +++I APL A + K    + 
Sbjct: 288 HPASGEKMEINAPLDAKLEKALAKMR 313


>gi|269962047|ref|ZP_06176401.1| ribosomal large subunit pseudouridine synthase C [Vibrio harveyi
           1DA3]
 gi|269833131|gb|EEZ87236.1| ribosomal large subunit pseudouridine synthase C [Vibrio harveyi
           1DA3]
          Length = 355

 Score =  285 bits (730), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 107/326 (32%), Positives = 179/326 (54%), Gaps = 17/326 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++
Sbjct: 43  MSEIRTQVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKL 102

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VRIPP       + K++  +  S  L K ++ L+  +++ED  + V NKP+G +V
Sbjct: 103 KAGDLVRIPP-----VTVEKKEDDVAPSTKLNKVAE-LEDKIIFEDDHLLVLNKPSGTAV 156

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 157 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFRGKTV 215

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y++LV G  KN  + +   LLK        V+ + +       + + FKV++ F Q 
Sbjct: 216 KKFYFALVMGEWKNSCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKVLEKFEQ- 268

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T     N+L+LHA  +   
Sbjct: 269 ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGLNRLFLHAANIKFQ 328

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP     ++I AP+ A + K    L 
Sbjct: 329 HPSNDEWMEINAPMEAKLEKVLAGLR 354


>gi|221638143|ref|YP_002524405.1| Ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides KD131]
 gi|221158924|gb|ACL99903.1| Ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides KD131]
          Length = 343

 Score =  285 bits (730), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 124/337 (36%), Positives = 182/337 (54%), Gaps = 24/337 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V  DE   RLDRWFK  +PH+    ++K+ R+GQVRVD  R K ++R+  G  +R
Sbjct: 1   MQLLKVTADEGEQRLDRWFKRRFPHVTQGAVEKMCRTGQVRVDGARAKASDRVAEGMEIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-I 125
           +PP+ +      +  ++  S          ++  ++Y D+ I V NKPAG+  QGGSG  
Sbjct: 61  VPPLPDPDAPRPQASRVTKSD------EQMIQDCVIYRDNDIIVLNKPAGLPSQGGSGQG 114

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG  ++      ++P+L HRLD++TSG+LV+ART   A+ L+ESFR R  +KIYW+
Sbjct: 115 ERHVDGLTEALKFGYKERPKLVHRLDKDTSGVLVLARTDRVARALSESFRHRNTRKIYWA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNE----KGANYAISHFKVIDCFA 237
           LV G+P  K+  I   L+K    G     + +  +   +      A  A + F  +    
Sbjct: 175 LVAGVPSPKQGSIKYALMKAPGHGRGGEGEKMLCIHPAKVGDYPEAKRAQTDFFTLWFLG 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLY 289
            +  W+ + P TGRTHQLR H   +G PIVGD KY  + + N            +  KL+
Sbjct: 235 SRCAWMALSPITGRTHQLRAHMAELGHPIVGDGKYGGSGQENLGDGWGAQIGGEMSRKLH 294

Query: 290 LHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
           LHAR + + HP    L   TAPLP HM KTW  L +K
Sbjct: 295 LHARSLTIEHPIKKDLVTFTAPLPGHMAKTWKLLDWK 331


>gi|170692348|ref|ZP_02883511.1| pseudouridine synthase, RluA family [Burkholderia graminis C4D1M]
 gi|170142778|gb|EDT10943.1| pseudouridine synthase, RluA family [Burkholderia graminis C4D1M]
          Length = 450

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 93/347 (26%), Positives = 157/347 (45%), Gaps = 30/347 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV ++    RLD+     +P  +   LQ  + + +VR+D K  K    +  G  + +
Sbjct: 66  RSVVVPDELAGERLDKVLARLFPEFSRNRLQSWIEAERVRIDGKPAKIRQPVPLGATIEL 125

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 126 VP------DLLPEQ--------LAFTPEPVPLEIVYEDDTLVVINKPAGMVVHPAAGNWS 171

Query: 126 AYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + D+     +  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 172 GTVLNGLLYRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 231

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKF 240
            +LVWG    ++  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 232 LALVWGNMP-EEGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRRVDTAIWQRQPV 287

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L
Sbjct: 288 TAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGEFARQALHAWRLGL 347

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF-KYDRNLYIKRLYSQDECK 342
            HP+ GR +Q  A +PA +     +LG  + D   + +  Y +D  +
Sbjct: 348 IHPKTGRTMQWRADVPADIAALSAALGLGRDDAGEFDETYYEEDGYE 394


>gi|163941632|ref|YP_001646516.1| RluA family pseudouridine synthase [Bacillus weihenstephanensis
           KBAB4]
 gi|229013077|ref|ZP_04170242.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus mycoides
           DSM 2048]
 gi|163863829|gb|ABY44888.1| pseudouridine synthase, RluA family [Bacillus weihenstephanensis
           KBAB4]
 gi|228748331|gb|EEL98191.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus mycoides
           DSM 2048]
          Length = 302

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 145/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVKGNYKVKGND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTKGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGIIDAPIGRD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  AP+P    +  + L 
Sbjct: 275 DHPRTGEYIEFEAPIPEVFEEALNVLR 301


>gi|229134702|ref|ZP_04263511.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-ST196]
 gi|228648748|gb|EEL04774.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-ST196]
          Length = 302

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 145/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVKGNYKVKGND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTKGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGIIDAPIGRD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  AP+P    +  + L 
Sbjct: 275 DHPRTGEYIEFEAPIPEVFEEALNILR 301


>gi|256822394|ref|YP_003146357.1| RluA family pseudouridine synthase [Kangiella koreensis DSM 16069]
 gi|256795933|gb|ACV26589.1| pseudouridine synthase, RluA family [Kangiella koreensis DSM 16069]
          Length = 316

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 106/322 (32%), Positives = 171/322 (53%), Gaps = 16/322 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ+V V  +E   R+D +       +   ++ K+LR G+VRV+K R+K   +I+ G  
Sbjct: 7   PKVQFVEVHAEEAGQRIDNFLLKKLKGVPKSHIYKMLRKGEVRVNKGRIKAEYKIKEGDS 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PPV              +  V L    + L+S +LYED ++ V NKP G++V GGSG
Sbjct: 67  VRLPPVKTT-------NTATEVPVKLNIVQE-LESAILYEDKRLIVLNKPHGMAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  +     L HRLD++TSG L++A+ R+  + L E  + + + K YW
Sbjct: 119 MSFGVIEALRA-LRPEAPFLELVHRLDRDTSGCLLIAKKRSTLRFLHEQLQKKLMSKQYW 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G    K + I   L K     G+ V  V +N      +++ F V++ F + F  + 
Sbjct: 178 ALVEGKWPAKLKHIDFPLAKNHLKSGERVVRVTEN---GKPSLTSFNVVEVF-KNFSLVS 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP-HPE 301
            +P TGRTHQ+RVHA   G P+VGD KY  +   +      +  +L+LHA  +     PE
Sbjct: 234 AEPVTGRTHQIRVHAQQAGHPLVGDPKYGNDDVTEQFKRQGLSGRLFLHAYSLTFKVTPE 293

Query: 302 GGRLQITAPLPAHMVKTWDSLG 323
              +++ APLPA + KT + L 
Sbjct: 294 DKAIRVEAPLPADLQKTLEYLR 315


>gi|269102256|ref|ZP_06154953.1| ribosomal large subunit pseudouridine synthase C [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268162154|gb|EEZ40650.1| ribosomal large subunit pseudouridine synthase C [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 344

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 106/329 (32%), Positives = 177/329 (53%), Gaps = 20/329 (6%)

Query: 1   MSLMTYV----QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN 56
           ++LMT V    Q++ + +D    R+D + +    ++    + +ILR G+VRV+KKR+K  
Sbjct: 27  ITLMTEVKPKVQFIEISDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPE 86

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
            ++Q G +VR+PP       I +++     S NL K ++ L+S ++YED  + V NKP+G
Sbjct: 87  YKLQDGDLVRVPP-----VSIPEKEDQAPISTNLNKVAE-LESCIIYEDDHLLVLNKPSG 140

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            +V GGSG+ +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR 
Sbjct: 141 TAVHGGSGLKFGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRRLQEQFRN 199

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + +QK Y++LV G  K   + +   LLK        V+ + +       + + FKV++ F
Sbjct: 200 KTVQKYYFALVMGEWKASCKKVTAPLLKNE------VNSIVRVNPNGKPSDTRFKVLERF 253

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYM 295
            Q    ++  P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +
Sbjct: 254 HQ-ATLVQASPVTGRTHQIRVHCQYTGHPIAWDDRYGDPRFDAYTKKTGLNRLFLHAANI 312

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              HP     ++I AP+   + +  + L 
Sbjct: 313 QFTHPSTDEAMEINAPMEPKLERCLEKLR 341


>gi|315607390|ref|ZP_07882389.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
 gi|315250947|gb|EFU30937.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
          Length = 367

 Score =  285 bits (730), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 88/332 (26%), Positives = 151/332 (45%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +  +R+D++     PH +   +Q    +G +RV+ + VK N +++ G VV +  
Sbjct: 37  IEVDAGQAPVRIDKFLTEKNPHQSRNRIQSAADAGFIRVNGRPVKSNYKVRPGDVVTLM- 95

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I+   + L          ++YED  + V NKPAG+ V  G+G     
Sbjct: 96  ----LDRPKHDTSIVPEDIPLA---------VVYEDDGLMVINKPAGMVVHPGAGNFTGT 142

Query: 125 IAYHIDGFLKSW--VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   +  +LK     D+   +  L HR+D++TSG+LVVA+T  A   L + F  +   + 
Sbjct: 143 LINAVAYYLKDLPTFDANSPEVGLVHRIDKDTSGLLVVAKTPEAKTCLGKQFFNKTTHRS 202

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG   + +  I   + +        + V          A++H++V++ F      
Sbjct: 203 YNALVWGNIVDDEGRIEGNIARDPR-NRLRMKVFAPGSGIGKSAVTHYRVLERFG-YTTL 260

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQN------KLYL 290
           +E +  TGRTHQ+R H  H+G P+ GD  Y             + + IQN      +  L
Sbjct: 261 VECRLETGRTHQIRAHMKHIGHPLFGDETYGGTEILRGQRSSTYKAFIQNCFKLCPRQAL 320

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HAR +   HP  GR +  ++  PA      D 
Sbjct: 321 HARTLGFVHPVSGRQMDFSSEWPADFAALIDK 352


>gi|312869892|ref|ZP_07730031.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
 gi|311094477|gb|EFQ52782.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
          Length = 304

 Score =  285 bits (729), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 89/325 (27%), Positives = 142/325 (43%), Gaps = 33/325 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     + V++     R+D+   + +   +  +LQK +  G VRV+ + VK   ++  G 
Sbjct: 1   MADTLKLTVDDTLTG-RIDKVLAHQFNQFSRSHLQKWIVDGNVRVNGQPVKPKYKLAVGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V I P       +  E+  LD               ++YED  + V NKP G+ V    
Sbjct: 60  QVVIEPEAPQKVDLTPEKIPLD---------------IVYEDDDVIVVNKPQGMVVHPAP 104

Query: 124 GIAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G   H   +  L     S      +P + HR+D++TSG+L+VA+   A + L    + + 
Sbjct: 105 GHPDHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDLAHRSLAAQLKAKT 164

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            Q+ Y +LV G+ K     I   + +          V         +A++HFKV+  F +
Sbjct: 165 NQREYVALVHGVIKQDAGTIDAPIGRSKKDRKKQAVVS-----DGRHAVTHFKVLRRF-R 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +  +  TGRTHQ+RVH   +G P+ GD  Y         +      YLHAR +   
Sbjct: 219 HYTLVSCRLETGRTHQIRVHMKSIGHPLAGDPLYGPR-----KTLPGRGQYLHARLLGFK 273

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  G+ L  TAPLP +  +  D L
Sbjct: 274 HPRTGKDLVFTAPLPEYFQQMLDKL 298


>gi|46201801|ref|ZP_00054336.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 324

 Score =  285 bits (729), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 126/332 (37%), Positives = 199/332 (59%), Gaps = 10/332 (3%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +E  +RLDRWFK H+P +    L+K LR+G VRVD KR K N R+++GQ +R+PP
Sbjct: 1   MTVAEEESEIRLDRWFKRHFPTVGHGLLEKWLRAGNVRVDGKRAKSNQRLEAGQAIRVPP 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            + A    ++E K +     + +    L+  +LY D  +   NKP G++VQGG+G+A  H
Sbjct: 61  -LPADEAPVREAKPVVVDEKIAR---MLRDAVLYMDDDVIALNKPPGLAVQGGTGMADKH 116

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +D +L +     G +P+L HRLD++TSG+L++ RT  AA  L  +F+ R  +K YW+LV 
Sbjct: 117 LDAWLDALCFGAG-RPKLVHRLDKDTSGVLLLGRTANAASKLAAAFKSRSARKCYWALVA 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+P+  +  I   L K     G+ + V   +++   +A+++++V+D   ++  WLEM+P 
Sbjct: 176 GVPRYPQGRIDAPLAKLPGKAGEKMAV---DKEEGKHAVTYYRVVDSTLKRAAWLEMEPR 232

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QI 307
           TGRTHQLR H L +G PI+GD KY         + +  KL+LHAR + LPHP  G++ ++
Sbjct: 233 TGRTHQLRAHCLLLGTPIMGDGKYGGQDALIEGTGVSRKLHLHARAVRLPHPRTGKMLEV 292

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQD 339
            APLP H+  ++D  GF   R+      + +D
Sbjct: 293 AAPLPPHIKASFDFFGFTESRSGPPFVSFDED 324


>gi|332141130|ref|YP_004426868.1| ribosomal large subunit pseudouridine synthase C [Alteromonas
           macleodii str. 'Deep ecotype']
 gi|327551152|gb|AEA97870.1| ribosomal large subunit pseudouridine synthase C [Alteromonas
           macleodii str. 'Deep ecotype']
          Length = 313

 Score =  285 bits (729), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 102/319 (31%), Positives = 172/319 (53%), Gaps = 15/319 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V++V V+ D    R+D + +     +    + +ILR G+VRV+K RVK   ++Q+  +V
Sbjct: 8   KVRFVTVDADLAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKGRVKPEYKLQADDIV 67

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPPV  +        K+   +         L+S +L+ED +I V NKP+G++V GGSG+
Sbjct: 68  RIPPVRVSEGAPAPSPKLDKIAA--------LESHILFEDDRILVMNKPSGMAVHGGSGL 119

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L++ +    +   L HRLD++TSG +++A+ R+A +H+ E  R  ++ K Y +
Sbjct: 120 SFGLIEGLRA-LRPDAKFMELVHRLDRDTSGCILIAKKRSALRHMHEQLRTGKMDKRYNA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     +  +   L K     G+ +  V  +      + + +++++ +A     +E 
Sbjct: 179 LVAGEWPKNRFKVKAPLRKNVLQSGERMVSVSDD---GKPSETRYRILEEYA-GATLVEA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
            P TGRTHQ+RVH LH G PI  D KY  A+F  +      N+L+LHAR + L HP    
Sbjct: 235 SPITGRTHQIRVHCLHAGHPIACDPKYGDADFDASMRQKGLNRLFLHARSISLLHPATEE 294

Query: 304 RLQITAPLPAHMVKTWDSL 322
           R+  +APL   +  T ++L
Sbjct: 295 RVTFSAPLDPILSNTLNAL 313


>gi|302382665|ref|YP_003818488.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
 gi|302193293|gb|ADL00865.1| pseudouridine synthase, RluA family [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 350

 Score =  285 bits (729), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 116/326 (35%), Positives = 183/326 (56%), Gaps = 8/326 (2%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
             Q + V   E+ +RLDRWF+  +PH++ + +QK+ R GQ+RVD  R+K   R+ +G  V
Sbjct: 23  EAQILYVAEAEDGIRLDRWFRRRWPHLSNIQVQKMARGGQIRVDGARIKPEGRLTAGAAV 82

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP+   +     E   L  +        F KS+++YED  +   NKP G++VQGG+  
Sbjct: 83  RVPPIPEPIVRAPGEHMALTPA-----DIAFAKSMVIYEDDLVIALNKPWGLAVQGGTKT 137

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+D  L +W     ++PRL HRLD++TSG+L++ +   AA+ L  +F  R+ +K YW+
Sbjct: 138 TRHVDRLLSAW-GEGMERPRLVHRLDRDTSGVLLLGKGPEAAKRLAGAFARRQAKKTYWA 196

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+PK     I+  L K      + +      + GA  A + + VI   AQ+  W+ +
Sbjct: 197 IVMGLPKPADGQISVHLKKSGINDYEIMRPADPKDPGAEPAETAYAVISHAAQRASWMAL 256

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +P TGRTHQLR H   +G PI+GD KY  +     + P+  KL LHAR ++L HP GG L
Sbjct: 257 RPFTGRTHQLRAHMKAIGHPILGDPKYGDDASTQLSGPL--KLQLHARRIELDHPAGGTL 314

Query: 306 QITAPLPAHMVKTWDSLGFKYDRNLY 331
            + AP+ A +   ++  GF  + + +
Sbjct: 315 VVEAPISAELRAGFEHFGFDENESDH 340


>gi|229104455|ref|ZP_04235123.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-28]
 gi|229117388|ref|ZP_04246765.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock1-3]
 gi|228666088|gb|EEL21553.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock1-3]
 gi|228678977|gb|EEL33186.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-28]
          Length = 302

 Score =  284 bits (728), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 148/327 (45%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKEND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L   ++ +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P    +T + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEETLNILR 301


>gi|229075650|ref|ZP_04208632.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock4-18]
 gi|228707426|gb|EEL59617.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock4-18]
          Length = 302

 Score =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 148/327 (45%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKEND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L   ++ +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P    +T + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEETLNVLR 301


>gi|288925171|ref|ZP_06419106.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           D17]
 gi|288337936|gb|EFC76287.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           D17]
          Length = 358

 Score =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 88/332 (26%), Positives = 151/332 (45%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +  +R+D++     PH +   +Q    +G +RV+ + VK N +++ G VV +  
Sbjct: 28  IEVDAGQAPVRIDKFLTEKNPHQSRNRIQSAADAGFIRVNGRPVKSNYKVRPGDVVTLM- 86

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    +  I+   + L          ++YED  + V NKPAG+ V  G+G     
Sbjct: 87  ----LDRPKHDTSIVPEDIPLA---------VVYEDDGLMVINKPAGMVVHPGAGNFTGT 133

Query: 125 IAYHIDGFLKSW--VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   +  +LK     D+   +  L HR+D++TSG+LVVA+T  A   L + F  +   + 
Sbjct: 134 LINAVAYYLKDLPTFDANSPEVGLVHRIDKDTSGLLVVAKTPEAKTCLGKQFFNKTTHRS 193

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG   + +  I   + +        + V          A++H++V++ F      
Sbjct: 194 YNALVWGNIVDDEGRIEGNIARDPR-NRLRMKVFAPGSGIGKSAVTHYRVLERFG-YTTL 251

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQN------KLYL 290
           +E +  TGRTHQ+R H  H+G P+ GD  Y             + + IQN      +  L
Sbjct: 252 VECRLETGRTHQIRAHMKHIGHPLFGDETYGGTEILRGQRSSTYKAFIQNCFKLCPRQAL 311

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HAR +   HP  GR +  ++  PA      D 
Sbjct: 312 HARTLGFVHPVSGRQMDFSSEWPADFAALIDK 343


>gi|229061498|ref|ZP_04198842.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH603]
 gi|228717732|gb|EEL69382.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH603]
          Length = 302

 Score =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 145/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDAVVTVNGKSVKGNYKVKVND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTKGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V+D F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIGRD-----KKERQSMTVDENGKNAVTHFQVLDRF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  AP+P    +  + L 
Sbjct: 275 DHPRTGEYIEFEAPIPEVFEEALNILR 301


>gi|153216570|ref|ZP_01950521.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           1587]
 gi|229513684|ref|ZP_04403146.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           TMA 21]
 gi|229521940|ref|ZP_04411357.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           TM 11079-80]
 gi|229524038|ref|ZP_04413443.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           bv. albensis VL426]
 gi|254226963|ref|ZP_04920527.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           V51]
 gi|254286849|ref|ZP_04961802.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           AM-19226]
 gi|124114199|gb|EAY33019.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           1587]
 gi|125620503|gb|EAZ48873.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           V51]
 gi|150423140|gb|EDN15088.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           AM-19226]
 gi|229337619|gb|EEO02636.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           bv. albensis VL426]
 gi|229340865|gb|EEO05870.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           TM 11079-80]
 gi|229348865|gb|EEO13822.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           TMA 21]
          Length = 315

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 106/324 (32%), Positives = 182/324 (56%), Gaps = 15/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G    + + +   LLK        V+ + +       + + F++++ FA+   
Sbjct: 177 YYYALVMGHWDAECKVVNAPLLKNE------VNSIVRVNPNGKPSETRFRILEKFAE-AT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP
Sbjct: 230 LVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVHP 289

Query: 301 EGG-RLQITAPLPAHMVKTWDSLG 323
               +L+I APL AH+ +    + 
Sbjct: 290 ASEKKLEIHAPLEAHLEQALAKMR 313


>gi|115351782|ref|YP_773621.1| RluA family pseudouridine synthase [Burkholderia ambifaria AMMD]
 gi|115281770|gb|ABI87287.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           ambifaria AMMD]
          Length = 405

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 89/328 (27%), Positives = 144/328 (43%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +V +D    K    +  G  + +
Sbjct: 58  RVVEVPLSLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAKIRQPVPLGARIEL 117

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 118 VP------DLLPEQ--------LAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWS 163

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 164 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 223

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG        I   + +      +   +          A +HF+ +D      Q  
Sbjct: 224 FALVWGTMPED-GTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCLWQRQPV 279

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 280 SAIQCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPDGFARQALHAWRLGL 339

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G+ +Q   PLP  M     +LGF
Sbjct: 340 VHPLTGKTMQWRCPLPDDMNALIAALGF 367


>gi|144899540|emb|CAM76404.1| ribosomal large subunit pseudouridine synthase C [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 333

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 134/338 (39%), Positives = 190/338 (56%), Gaps = 7/338 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  VQ + V  D+ ++RLDRWFK HYP +    L+K LR+GQVRVD KR K N R+  G 
Sbjct: 1   MNSVQILAVAEDDADIRLDRWFKRHYPTVGHGLLEKWLRTGQVRVDGKRAKANQRLSPGL 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PPV        K            K +  L+  +LY D  +   NKPAGI+VQGG+
Sbjct: 61  HIRVPPVPE--GEAPKANPENRRPAVDEKIARMLRDAVLYMDDDVIALNKPAGIAVQGGT 118

Query: 124 GIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    HID +L + +  +  +PRL HRLD++TSG+L++ R+  AA  L  +F+ R  +K 
Sbjct: 119 GTGDKHIDAWLDALMFDRDDRPRLVHRLDKDTSGVLLLGRSANAAAKLAAAFKSRAARKC 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G+PK ++  I   L K     G+ + V   +E     A++ ++V+D   +K  W
Sbjct: 179 YWALVVGVPKLRQGRIDAALAKLPGRAGEKMAV---DEDEGKRAVTWYRVVDNALRKAAW 235

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           LEM+P TGRTHQLR H   MG PI+GD KY         + +  K++LHAR + +PHP  
Sbjct: 236 LEMEPRTGRTHQLRAHTALMGTPIMGDGKYGGTEAFISGTGVSRKMHLHARAVRIPHPRT 295

Query: 303 G-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQD 339
           G  L + APLP HM K+++  GF           + QD
Sbjct: 296 GKELVVVAPLPEHMEKSFEFFGFDLSSAGKPFDAFEQD 333


>gi|297579532|ref|ZP_06941460.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC385]
 gi|297537126|gb|EFH75959.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC385]
          Length = 315

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 105/324 (32%), Positives = 182/324 (56%), Gaps = 15/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G    + + +   LLK        V+ + +       + + F++++ FA+   
Sbjct: 177 YYYALVMGHWDAECKVVNAPLLKNE------VNSIVRVNPNGKPSETRFRILEKFAE-AT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP
Sbjct: 230 LVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIQRLFLHAANIQFVHP 289

Query: 301 EGG-RLQITAPLPAHMVKTWDSLG 323
               +L+I APL +H+ +    + 
Sbjct: 290 ASEKKLEIHAPLESHLEQALAKMR 313


>gi|239994407|ref|ZP_04714931.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase [Alteromonas macleodii ATCC
           27126]
          Length = 313

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 103/319 (32%), Positives = 170/319 (53%), Gaps = 15/319 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V++V VE D    R+D + +     +    + +ILR G+VRV+K RVK   ++Q+  ++
Sbjct: 8   KVRFVTVEADLAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKGRVKPEYKLQADDLI 67

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPPV  +        K+   +         L+S +L+ED +I V NKP+G++V GGSG+
Sbjct: 68  RIPPVRVSEGAPAPSPKLDKIA--------SLESHILFEDDRILVINKPSGMAVHGGSGL 119

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L++ +    +   L HRLD++TSG +++A+ R+A +H+ E  R  ++ K Y +
Sbjct: 120 SFGLIEGLRA-LRPDAKFMELVHRLDRDTSGCILIAKKRSALRHMHEQLRTGKMDKRYNA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     +  +   L K     G+ +  V  +      + + +++++ +A     +E 
Sbjct: 179 LVAGEWPKTRFKVKAALRKNVLQSGERMVSVSDD---GKPSETRYRILEEYA-GATLVEA 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
            P TGRTHQ+RVH LH G PI  D KY  A+F         N+L+LHAR + L HP    
Sbjct: 235 SPITGRTHQIRVHCLHAGHPIACDPKYGDADFDAAMRQKGLNRLFLHARSISLLHPATEE 294

Query: 304 RLQITAPLPAHMVKTWDSL 322
           R+  TAPL   +  T  +L
Sbjct: 295 RVTFTAPLDDTLSNTLKAL 313


>gi|304319748|ref|YP_003853391.1| Ribosomal large subunit pseudouridine synthase C [Parvularcula
           bermudensis HTCC2503]
 gi|303298651|gb|ADM08250.1| Ribosomal large subunit pseudouridine synthase C [Parvularcula
           bermudensis HTCC2503]
          Length = 324

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 114/327 (34%), Positives = 182/327 (55%), Gaps = 12/327 (3%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + VQ V V + E   RLDRW K  +P +    +QK LR GQVR++  RVK ++R++SG+V
Sbjct: 6   SGVQEVTVTSAEAGQRLDRWMKRRFPGVTQGQVQKWLRKGQVRLNGGRVKADHRVESGEV 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP+          + ++  +      ++ ++ +++YED  I   NKPAG++VQGG+ 
Sbjct: 66  VRVPPIDPEAAAPPPSRPVVGPA-----EAEMMRGLVIYEDDDILALNKPAGLAVQGGAK 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              HIDG L  + + +  +PRL HRLD++T G+L++A++RA A  L+ +F+  RI K YW
Sbjct: 121 TLIHIDGMLDVFGEGEA-RPRLVHRLDRDTGGVLLLAKSRAVAATLSLAFQQHRIGKTYW 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G+P      I   + K    G + +   +Q       A++ ++ ++   QK  +L 
Sbjct: 180 AITKGVPHPLFGRIDMRIEKAGEPGREKMRGTEQ----GQSALTDYQTVETAGQKAAFLA 235

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++PHTGRTHQ+RVH   +G PIVGD KY     G     + N+++L  R M +P      
Sbjct: 236 LRPHTGRTHQIRVHLSAIGTPIVGDRKYGG--AGAVLEGLPNQMHLFCRQMHVPRRGRPP 293

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNLY 331
           L +TA L   M  +W   GF    +L 
Sbjct: 294 LVVTADLTGGMATSWSIFGFSRPDDLE 320


>gi|228998673|ref|ZP_04158260.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus mycoides
           Rock3-17]
 gi|228761141|gb|EEM10100.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus mycoides
           Rock3-17]
          Length = 302

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 147/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++ G V V+   +K N +++   
Sbjct: 1   MSEVVQVTVTEEQKSERIDKFLAGVNNEWSRSQVQQWIKDGVVTVNGNAIKGNYKVKVND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EIAV---------------AIPDPEELDILPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIGRDKKD-----RQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLD-----INGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  AP+PA   +  + L 
Sbjct: 275 DHPRTGEYIEFEAPVPAVFEEVLNVLR 301


>gi|229098363|ref|ZP_04229309.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-29]
 gi|228685068|gb|EEL39000.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-29]
          Length = 302

 Score =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 148/327 (45%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKEND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L   ++ +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V+D F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLDRF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P    +T + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEETLNILR 301


>gi|15642030|ref|NP_231662.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|121729883|ref|ZP_01682310.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           V52]
 gi|147673109|ref|YP_001217555.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O395]
 gi|227082155|ref|YP_002810706.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           M66-2]
 gi|229507883|ref|ZP_04397388.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           BX 330286]
 gi|229511882|ref|ZP_04401361.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
 gi|229519018|ref|ZP_04408461.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC9]
 gi|229607428|ref|YP_002878076.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MJ-1236]
 gi|254849115|ref|ZP_05238465.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MO10]
 gi|255745223|ref|ZP_05419172.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholera
           CIRS 101]
 gi|262167652|ref|ZP_06035355.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC27]
 gi|298497942|ref|ZP_07007749.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MAK 757]
 gi|14423896|sp|Q9KQH0|RLUC_VIBCH RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|9656573|gb|AAF95176.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|121628373|gb|EAX60874.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           V52]
 gi|146314992|gb|ABQ19531.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O395]
 gi|227010043|gb|ACP06255.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           M66-2]
 gi|227013925|gb|ACP10135.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O395]
 gi|229343707|gb|EEO08682.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC9]
 gi|229351847|gb|EEO16788.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
 gi|229355388|gb|EEO20309.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           BX 330286]
 gi|229370083|gb|ACQ60506.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MJ-1236]
 gi|254844820|gb|EET23234.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MO10]
 gi|255737053|gb|EET92449.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholera
           CIRS 101]
 gi|262023857|gb|EEY42555.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC27]
 gi|297542275|gb|EFH78325.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MAK 757]
          Length = 315

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 106/324 (32%), Positives = 182/324 (56%), Gaps = 15/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G    + + +   LLK        V+ + +       + + F++++ FA+   
Sbjct: 177 YYYALVMGHWDAECKVVNAPLLKNE------VNSIVRVNPNGKPSETRFRILEKFAE-AT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP
Sbjct: 230 LVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVHP 289

Query: 301 EGG-RLQITAPLPAHMVKTWDSLG 323
               +L+I APL AH+ +    + 
Sbjct: 290 ASEKKLEIHAPLEAHLEQALTKMR 313


>gi|153827554|ref|ZP_01980221.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MZO-2]
 gi|149738478|gb|EDM52874.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MZO-2]
          Length = 315

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 106/324 (32%), Positives = 182/324 (56%), Gaps = 15/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G    + + +   LLK        V+ + +       + + F++++ FA+   
Sbjct: 177 YYYALVMGHWDAECKVVNAPLLKNE------VNSIVRVNPNGKSSETRFRILEKFAE-AT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP
Sbjct: 230 LVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVHP 289

Query: 301 EGG-RLQITAPLPAHMVKTWDSLG 323
               +L+I APL AH+ +    + 
Sbjct: 290 ASEKKLEIHAPLEAHLEQALAKMR 313


>gi|238920268|ref|YP_002933783.1| 23S rRNA pseudouridylate synthase C [Edwardsiella ictaluri 93-146]
 gi|238869837|gb|ACR69548.1| ribosomal large subunit pseudouridine synthase C [Edwardsiella
           ictaluri 93-146]
          Length = 320

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 111/323 (34%), Positives = 175/323 (54%), Gaps = 14/323 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V+ V +  DE   R+D + +N    +    + +I+R G+VRV+KKR+K   ++++G  
Sbjct: 6   TSVKLVTIAADEAGQRIDNFLRNQLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLEAGDQ 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S  L K +  L   +LYED  + V NKP+G +V GGSG
Sbjct: 66  VRIPPVR------VAERDEAPVSARLDKVA-ALNGCILYEDDYLLVLNKPSGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD+ETSG+L+VA+ R+A + L E  R + +QK Y 
Sbjct: 119 LSFGVIEGLRA-LRPEARFLELVHRLDRETSGVLLVAKKRSALRSLHEQLREKGMQKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + +   LLK +   G+ V  V         + + FKV + FA     ++
Sbjct: 178 ALVRGQWQSHCKVVQAPLLKNTLQSGERVVRVNAE---GKPSETRFKVEERFA-NATLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D +Y   +F         N+L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHTLHAGHPIAFDDRYGDRDFDRELADTGLNRLFLHAAALRFVHPHSG 293

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
             L++ APL A +    ++L  +
Sbjct: 294 ETLRVEAPLDAALRHCLNALRAR 316


>gi|229019095|ref|ZP_04175930.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH1273]
 gi|229025339|ref|ZP_04181757.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH1272]
 gi|228735924|gb|EEL86501.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH1272]
 gi|228742195|gb|EEL92360.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH1273]
          Length = 302

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 144/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKGND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPDPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIGRD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|172060753|ref|YP_001808405.1| RluA family pseudouridine synthase [Burkholderia ambifaria MC40-6]
 gi|171993270|gb|ACB64189.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MC40-6]
          Length = 407

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 89/328 (27%), Positives = 144/328 (43%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +V +D    K    +  G  + +
Sbjct: 58  RVVEVPLSLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAKIRQPVPLGARIEL 117

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 118 VP------DLLPEQ--------LAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWS 163

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 164 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 223

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG        I   + +      +   +          A +HF+ +D      Q  
Sbjct: 224 FALVWGTMPED-GTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCLWQRQPV 279

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 280 SAIQCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPDGFARQALHAWRLGL 339

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G+ +Q   PLP  M     +LGF
Sbjct: 340 VHPLTGKTMQWRCPLPDDMNALIAALGF 367


>gi|153820359|ref|ZP_01973026.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           NCTC 8457]
 gi|126509095|gb|EAZ71689.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           NCTC 8457]
          Length = 310

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 106/321 (33%), Positives = 181/321 (56%), Gaps = 15/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++G V
Sbjct: 1   TQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEAGDV 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V GGSG
Sbjct: 61  VRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHGGSG 115

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK Y+
Sbjct: 116 LHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYY 174

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G    + + +   LLK        V+ + +       + + F++++ FA+    ++
Sbjct: 175 ALVMGHWDAECKVVNAPLLKNE------VNSIVRVNPNGKPSETRFRILEKFAE-ATLVQ 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP   
Sbjct: 228 ASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVHPASE 287

Query: 304 -RLQITAPLPAHMVKTWDSLG 323
            +L+I APL AH+ +    + 
Sbjct: 288 KKLEIHAPLEAHLEQALTKMR 308


>gi|229528953|ref|ZP_04418343.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           12129(1)]
 gi|229332727|gb|EEN98213.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           12129(1)]
          Length = 315

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 106/324 (32%), Positives = 182/324 (56%), Gaps = 15/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G    + + +   LLK        V+ + +       + + F++++ FA+   
Sbjct: 177 YYYALVMGHWDAECKVVNAPLLKNE------VNSIVRVNSNGKPSETRFRILEKFAE-AT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP
Sbjct: 230 LVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVHP 289

Query: 301 EGG-RLQITAPLPAHMVKTWDSLG 323
               +L+I APL AH+ +    + 
Sbjct: 290 ASEKKLEIHAPLEAHLEQALAKMR 313


>gi|163814069|ref|ZP_02205461.1| hypothetical protein COPEUT_00222 [Coprococcus eutactus ATCC 27759]
 gi|158450518|gb|EDP27513.1| hypothetical protein COPEUT_00222 [Coprococcus eutactus ATCC 27759]
          Length = 304

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 71/318 (22%), Positives = 142/318 (44%), Gaps = 31/318 (9%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             +  + RLD+    ++   +   ++K+   G + V+ K VK + ++++G ++ I     
Sbjct: 9   SEEWTDRRLDKVLSEYFDGYSRSFIKKLFDDGLILVNSKAVKPSYKVRAGDMIDIS---- 64

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHID 130
                      +   V++    + +   ++YED  + + NKP G+ V    G      ++
Sbjct: 65  -----------VPDPVSIDIVPEDIPLDIIYEDDDVILVNKPKGMVVHPAPGHYSGTLVN 113

Query: 131 GFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           G +  +  S        +P + HR+D +T+G+LVV +   A + L+E      I + Y++
Sbjct: 114 GLMYHFGSSLSGINGEFRPGIVHRIDMDTTGVLVVCKNDNAHRALSEQLHEHSITRKYYA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V+G   + +  +   + +           +  N +    A++H++V++ F  ++ ++E 
Sbjct: 174 IVYGNISSDEGTVDAPIGRSPKDRKK----MAINNRNGRRAVTHYRVLERFGGRYTYIEC 229

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH   +G PI+GD  Y                 LHA  +   HP  G  
Sbjct: 230 QLETGRTHQIRVHMASIGHPILGDEVYGPKK----CPFKLQGQTLHAGVLGFIHPSTGEY 285

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++  A LP +     + L
Sbjct: 286 VEFKAELPEYFKAVLEKL 303


>gi|223984556|ref|ZP_03634687.1| hypothetical protein HOLDEFILI_01982 [Holdemania filiformis DSM
           12042]
 gi|223963484|gb|EEF67865.1| hypothetical protein HOLDEFILI_01982 [Holdemania filiformis DSM
           12042]
          Length = 307

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 87/325 (26%), Positives = 144/325 (44%), Gaps = 32/325 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
             + ++VE  ++ +RLD++        +    Q+++    VR+D   VK + ++++G  +
Sbjct: 2   ETRILIVEEQDQGVRLDKYLSTAMDDCSRSRAQQLIDEEAVRIDDLPVKNSYKVKAGDEI 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                L     L      +   ++YED  + V NKP G+ V  G G 
Sbjct: 62  EVT---------------LPEEEALEAQPQEMALNVVYEDHDVIVINKPKGLVVHPGPGN 106

Query: 126 AYHI--DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             H   +G L    D  G     +P + HR+D++TSG++V  +   A Q L +    +  
Sbjct: 107 PDHTLVNGLLWHCHDLSGINGVLRPGIVHRIDKDTSGLIVACKNDNAHQSLAKQLAEKTA 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y++LV G+  ++   I   + +           +   EK +  AI+HFKV++ F   
Sbjct: 167 GRQYYALVHGVINHEYGTIDAPIGRDEKDRQK----MAVTEKNSRPAITHFKVVERF-DN 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +  +  TGRTHQ+RVH  ++G PIVGD KY        T P Q    LHA  +   H
Sbjct: 222 YTLVSCRLETGRTHQIRVHMQYIGFPIVGDPKYSLRK----TLPTQG-QMLHAYQLSFTH 276

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLG 323
           P  G R+   APLP         L 
Sbjct: 277 PSTGERMTFEAPLPPEFEALLTQLR 301


>gi|209522216|ref|ZP_03270853.1| pseudouridine synthase, RluA family [Burkholderia sp. H160]
 gi|209497345|gb|EDZ97563.1| pseudouridine synthase, RluA family [Burkholderia sp. H160]
          Length = 419

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 90/331 (27%), Positives = 149/331 (45%), Gaps = 29/331 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV ++    RLD+     +P  +   LQ  + + +VRVD K  K    +  G  + +
Sbjct: 68  RRVVVPDELAGERLDKVVAKVFPEFSRSRLQSWIEAERVRVDGKPAKIRQPVPLGATIEL 127

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 128 EP------DLLPEQ--------LAFTPEPVPLDIVYEDDTLVVINKPAGMVVHPAAGNWS 173

Query: 126 AYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + ++     +  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 174 GTVLNGLLYRYGEAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 233

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKF 240
            +LVWG     +  I   + +      +   +          A +HF+ +       Q  
Sbjct: 234 LALVWGNMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRRVTSAIWQRQPV 289

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             +     TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 290 TAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGL 349

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            HP+ GR +Q  A +PA +     +LG   D
Sbjct: 350 IHPKTGRSMQWRADVPADIEALSAALGLGRD 380


>gi|217961313|ref|YP_002339881.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|222097338|ref|YP_002531395.1| ribosomal large subunit pseudouridine synthase, rlud subfamily
           [Bacillus cereus Q1]
 gi|229140541|ref|ZP_04269096.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-ST26]
 gi|217063169|gb|ACJ77419.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|221241396|gb|ACM14106.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus Q1]
 gi|228643102|gb|EEK99378.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-ST26]
          Length = 302

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 145/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDNVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|52141596|ref|YP_085233.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
 gi|228987037|ref|ZP_04147162.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar tochigiensis BGSC 4Y1]
 gi|229157471|ref|ZP_04285548.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           ATCC 4342]
 gi|51975065|gb|AAU16615.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
 gi|228625921|gb|EEK82671.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           ATCC 4342]
 gi|228772631|gb|EEM21072.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar tochigiensis BGSC 4Y1]
          Length = 302

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 145/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVKEND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|261346051|ref|ZP_05973695.1| ribosomal large subunit pseudouridine synthase [Providencia
           rustigianii DSM 4541]
 gi|282565938|gb|EFB71473.1| ribosomal large subunit pseudouridine synthase [Providencia
           rustigianii DSM 4541]
          Length = 318

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 107/330 (32%), Positives = 173/330 (52%), Gaps = 14/330 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     VQ++ + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q
Sbjct: 1   MKTENQVQFIDISDDEAGQRIDNFLLGKLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +   VR+PPV       + E++    S  L K +  L   +LYED  I V NKP+G +V 
Sbjct: 61  ANDQVRVPPVR------VAERENAPISAKLDKVA-ALADCILYEDESILVINKPSGTAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R++++Q
Sbjct: 114 GGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRALHEQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + +   LLK     G+ +  V         + + FKV + F    
Sbjct: 173 KDYLALVRGNWQSHMKVVQAPLLKNILQSGERIVRVNSE---GKPSETRFKVEERF-DNA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH LH G PI  D +Y    F    T     +L+LHA  +   H
Sbjct: 229 TLVKASPVTGRTHQIRVHTLHAGHPIAFDDRYGDKQFDSQLTGTGLKRLFLHANALTFTH 288

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           P+ G  +++ APL   + K    L  K  +
Sbjct: 289 PKTGEEMRVVAPLHEDLNKCLKILRAKKSQ 318


>gi|183599498|ref|ZP_02960991.1| hypothetical protein PROSTU_02977 [Providencia stuartii ATCC 25827]
 gi|188021745|gb|EDU59785.1| hypothetical protein PROSTU_02977 [Providencia stuartii ATCC 25827]
          Length = 317

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 107/327 (32%), Positives = 172/327 (52%), Gaps = 14/327 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     VQ++ + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++ 
Sbjct: 1   MKTQNQVQFIDISDDEAGQRIDNFLLAKLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLI 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  VR+PPV       + E++    S  L K S  L   +LYED  I V NKP+G +V 
Sbjct: 61  AGDQVRVPPVR------VAEREEAPVSAKLDKVS-ALADCILYEDDAILVINKPSGTAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R++++Q
Sbjct: 114 GGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRALHEQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + I   LLK     G+ V  V         + + FKV + F    
Sbjct: 173 KDYLALVRGHWQSHTKVIQAPLLKNILQSGERVVRV---SPEGKPSETRFKVEERF-DNA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH LH G PI  D++Y    F          +L+LHA  +   H
Sbjct: 229 TLVKASPVTGRTHQIRVHTLHAGHPIAFDNRYGDKQFDSQLADTGLKRLFLHASALKFTH 288

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLGFK 325
           P+ G  +++ APL   + +    L  +
Sbjct: 289 PKTGEEMRLQAPLDKELNQCLKVLRSR 315


>gi|206976765|ref|ZP_03237669.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
 gi|206745075|gb|EDZ56478.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
          Length = 302

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 146/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDNVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G+ +Q  AP+P       + L 
Sbjct: 275 DHPRTGKYIQFEAPIPEVFEDALNILR 301


>gi|291528977|emb|CBK94563.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale M104/1]
          Length = 312

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 82/322 (25%), Positives = 148/322 (45%), Gaps = 28/322 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
              V++++E  RLD++  + YP I+    Q+IL+  Q+ V+ K  K N R+++  +V + 
Sbjct: 5   TFEVQSEQEGERLDKYLSSIYPDISRSFFQRILKENQILVNDKPQKANYRLKTDDIVDVT 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                   I+ +   LD               +LYED  + V NKP G+ V   +G    
Sbjct: 65  IPDAVQTPILPQDIPLD---------------ILYEDDDVLVVNKPKGMVVHPSAGHYSD 109

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             ++  +    DS        +P + HR+D +T+G L+V +   +   ++E  +     +
Sbjct: 110 TLVNAIMYHCKDSLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHIKISEQIKHHSCNR 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY  +V G  KN +  I   + +  +        +  NEK    A++H+KV++ F   + 
Sbjct: 170 IYVGIVCGNVKNDEGTIEGAIGRNPNDRKK----MAINEKNGKPAVTHYKVLERFGD-YT 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +++ +  TGRTHQ+RVH   +  P++GD  Y +               LHA+ +   HP+
Sbjct: 225 YMQFKLETGRTHQIRVHMASINHPLLGDMLYSSYSPTKNRFKGLEGQCLHAKTIGFVHPK 284

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++  APLP +     + L
Sbjct: 285 TGEYMEFDAPLPKYFANLLEVL 306


>gi|229174558|ref|ZP_04302089.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           MM3]
 gi|228608927|gb|EEK66218.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           MM3]
          Length = 302

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 145/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKEND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L   ++ +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPDPEELDIQAEDMGLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIGRD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|138894673|ref|YP_001125126.1| ribosomal large subunit pseudouridine synthase D-like protein
           [Geobacillus thermodenitrificans NG80-2]
 gi|196247711|ref|ZP_03146413.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
 gi|134266186|gb|ABO66381.1| ribosomal large subunit pseudouridine synthase D-like protein
           [Geobacillus thermodenitrificans NG80-2]
 gi|196212495|gb|EDY07252.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
          Length = 304

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 147/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  + +  +E + +  R+D+         +   +Q+ +++G V V+ + VK N + + G 
Sbjct: 1   MDTITFH-IEEEYDGERIDKVIAALNDEWSRSQVQQWIKNGLVTVNGRTVKANYKSELGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V I P      H+  E   LD               + YED  + V NKP G+ V    
Sbjct: 60  TVAISPPEPEPLHVEPEPIPLD---------------IYYEDEDVLVVNKPRGMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HR+D++TSG+L+VA+  AA + L E    +
Sbjct: 105 GHMRGTLVNALLAHCRDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDAAHRSLVEQLVNK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  +    I   + +           +   ++    A++HF+V++ F 
Sbjct: 165 TVTRRYKAIVHGVIPHDYGTIDAPIGRDKRDRKK----MAVTDENGKEAVTHFRVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +++ ++E Q  TGRTHQ+RVH  ++G P+ GD +Y         +       LHA  +  
Sbjct: 220 RQYTYVECQLETGRTHQIRVHMKYIGYPLAGDPQYGPK-----KTLSIEGQALHAGVLGF 274

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLG 323
            HP  G  L+  APLP    +  + L 
Sbjct: 275 RHPRSGDYLEFEAPLPPEFAELLEWLR 301


>gi|238924093|ref|YP_002937609.1| pseudouridine synthase, RluA family [Eubacterium rectale ATCC
           33656]
 gi|238875768|gb|ACR75475.1| pseudouridine synthase, RluA family [Eubacterium rectale ATCC
           33656]
 gi|291524836|emb|CBK90423.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale DSM 17629]
          Length = 312

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 81/322 (25%), Positives = 148/322 (45%), Gaps = 28/322 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
              V++++E  RLD++  + YP I+    Q+IL+  Q+ V+ K  K N R+++  +V + 
Sbjct: 5   TFEVQSEQEGERLDKYLSSIYPDISRSFFQRILKENQILVNDKPQKANYRLKTDDIVDVT 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                   I+ +   LD               +LYED  + V NKP G+ V   +G    
Sbjct: 65  IPDAVQTPILPQDIPLD---------------ILYEDDDVLVVNKPKGMVVHPSAGHYSD 109

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             ++  +    DS        +P + HR+D +T+G L+V +   +   ++E  +     +
Sbjct: 110 TLVNAIMYHCKDSLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHIKISEQIKDHSCNR 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY  +V G  K+ +  I   + +  +        +  NEK    A++H+KV++ F   + 
Sbjct: 170 IYVGIVCGNVKDDEGTIEGAIGRNPNDRKK----MAINEKNGKPAVTHYKVLERFGD-YT 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +++ +  TGRTHQ+RVH   +  P++GD  Y +               LHA+ +   HP+
Sbjct: 225 YMQFKLETGRTHQIRVHMASINHPLLGDMLYSSYSPTKNRFKGLEGQCLHAKTIGFVHPK 284

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++  APLP +     + L
Sbjct: 285 TGEYMEFDAPLPKYFANLLEVL 306


>gi|262404383|ref|ZP_06080938.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. RC586]
 gi|262349415|gb|EEY98553.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. RC586]
          Length = 315

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 103/324 (31%), Positives = 177/324 (54%), Gaps = 15/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKTIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEATPPSTKLNKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G    + + +   LLK        V+ + +       + + F++++ F +   
Sbjct: 177 YYYALVMGHWDAECKVVNAPLLKNE------VNSIVRVNPNGKPSETRFRILEKFTE-AT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP
Sbjct: 230 LVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAKFGIERLFLHAANIQFVHP 289

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
                ++I APL  H+ +    + 
Sbjct: 290 ASEEKMEIHAPLEEHLEQALAKMR 313


>gi|169827034|ref|YP_001697192.1| putative RNA pseudouridine synthase ylyB [Lysinibacillus sphaericus
           C3-41]
 gi|168991522|gb|ACA39062.1| Hypothetical RNA pseudouridine synthase ylyB [Lysinibacillus
           sphaericus C3-41]
          Length = 303

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 148/330 (44%), Gaps = 34/330 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT V Y  +E  ++  R+D+   +     +   +   +  G ++V+   VK   ++++G 
Sbjct: 1   MTEVTY-TIEEQQQGERIDKALSSLQSEWSRTQIGNWISDGNIKVNGDAVKAKYKVKAGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ I                +  +  L   ++ L   ++YED+ + V NKP G+ V    
Sbjct: 60  VIAID---------------VPEAEPLDVIAENLALDIVYEDADVLVVNKPKGMVVHPAP 104

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L +    +
Sbjct: 105 GHMTGTLVNGLMYQCKDLSGINGIMRPGIVHRIDKDTSGLLMVAKNDVAHESLVDQLVNK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G   + K  I   + +          V         +A++HF V++ F 
Sbjct: 165 TVTRKYIALVHGHIAHDKGTIDAPIGRDQKDRQKQAIV-----DNGKHAVTHFHVVERFG 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +F         LHA  +  
Sbjct: 220 D-YTLVECRLETGRTHQIRVHMNYIGFPLVGDPKYGPKKTIDF-----GGQVLHAATLGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            HP  G  L+   PLPA   +  + L  ++
Sbjct: 274 NHPSSGEYLEFETPLPADYEQLLNELRNRH 303


>gi|229031524|ref|ZP_04187524.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH1271]
 gi|228729813|gb|EEL80793.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH1271]
          Length = 302

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 146/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINSEWSRSQVQQWIKEDVVTVNGKSVKVNYKVKEND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L   ++ +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+VI+ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVIERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|289578538|ref|YP_003477165.1| pseudouridine synthase [Thermoanaerobacter italicus Ab9]
 gi|289528251|gb|ADD02603.1| pseudouridine synthase, RluA family [Thermoanaerobacter italicus
           Ab9]
          Length = 305

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 86/331 (25%), Positives = 149/331 (45%), Gaps = 35/331 (10%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  +V+  E ++E  R+D +            ++K++  G V V+ K VK + +++ 
Sbjct: 1   MNIVDKIVLQGEKEDEGKRIDVFLAAEL-DYTRSYIKKLIVDGLVFVNGKTVKPSYKVKE 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V +         ++ E   LD               +LYED  I V NKP G+ V  
Sbjct: 60  NDEVVVNIPEAEKIDVLPENIPLD---------------ILYEDDDIIVINKPQGMVVHP 104

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++  L    +  G     +P + HRLD++TSG++VVA+   A   L+   +
Sbjct: 105 APGNYSGTLVNALLYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y ++V G+ K+++  I   + +   +    + V+    +   YA++ +KV++ 
Sbjct: 165 ERSVFKKYVAIVEGVIKDEEGKIEAPIGRH-PVDRKKMAVI----EDGRYALTLYKVLER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F +    +E    TGRTHQ+RVH   +G P+VGD  Y    +            LH+  +
Sbjct: 220 FKEN-TLVEAVIKTGRTHQIRVHMAFIGHPVVGDPVYGFKKQ----KFKLEGQALHSSIL 274

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
              HP  G  ++  APLP + V+  + L  K
Sbjct: 275 GFIHPTKGVYMEFEAPLPEYFVRLIEILRNK 305


>gi|89094316|ref|ZP_01167257.1| ribosomal large subunit pseudouridine synthase C [Oceanospirillum
           sp. MED92]
 gi|89081375|gb|EAR60606.1| ribosomal large subunit pseudouridine synthase C [Oceanospirillum
           sp. MED92]
          Length = 321

 Score =  283 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 106/322 (32%), Positives = 164/322 (50%), Gaps = 13/322 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  T V++V + ++    R+D +            + +I+R G+VRV+KKR+K   R+  
Sbjct: 7   SPNTQVRFVEITDNNAGQRIDNFLITALKGAPKSLVYRIVRKGEVRVNKKRIKPEYRLAL 66

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV  A        +    +   ++ SD L+  +LYED  + V NKP+GI+V G
Sbjct: 67  GDLVRIPPVRLA--------EKAPPAKVSSRLSDQLEQAVLYEDDDLIVVNKPSGIAVHG 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSGI+  +    +       +   L HRLD++TSG +++A+ R+  + + +S +   I K
Sbjct: 119 GSGISLGLIESFRQMRPQ-CKFLELVHRLDRDTSGCILIAKKRSTLKLMHDSLKKSTITK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY +LV G    +K  I   L K     G+ V  V  +       ++ +KV+  F ++  
Sbjct: 178 IYHALVVGSWSERKRRIDAPLKKNELKSGERVVKVTAD---GKECLTEYKVLQRFGREAT 234

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            +E +P TGRTHQ+RVH    G PIVGD KY  +            +L+LHA  +  P P
Sbjct: 235 LVEARPITGRTHQIRVHCQFAGHPIVGDEKYGVDEVNAEMREKGFKRLFLHAAELRFPLP 294

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
            GGR  + APL   + K   SL
Sbjct: 295 SGGRQVVKAPLEMPLQKAIKSL 316


>gi|262043217|ref|ZP_06016352.1| ribosomal large subunit pseudouridine synthase C [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|259039444|gb|EEW40580.1| ribosomal large subunit pseudouridine synthase C [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
          Length = 331

 Score =  283 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 108/326 (33%), Positives = 172/326 (52%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V    DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++
Sbjct: 15  MKTETPTVKMVATAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKL 74

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 75  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALSEVILYEDDHILVLNKPSGTAV 127

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG++Y +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 128 HGGSGLSYGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGM 186

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + + + 
Sbjct: 187 QKDYLALVRGQWQSHTKVVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERY-EF 242

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F    ++   N+L+LHA  +   
Sbjct: 243 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLSATGLNRLFLHAAALKFT 302

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  +++ APL   +      L 
Sbjct: 303 HPGSGEVMRVEAPLDNQLKHCLQVLR 328


>gi|167037761|ref|YP_001665339.1| RluA family pseudouridine synthase [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|320116174|ref|YP_004186333.1| RluA family pseudouridine synthase [Thermoanaerobacter brockii
           subsp. finnii Ako-1]
 gi|166856595|gb|ABY95003.1| pseudouridine synthase, RluA family [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|319929265|gb|ADV79950.1| pseudouridine synthase, RluA family [Thermoanaerobacter brockii
           subsp. finnii Ako-1]
          Length = 305

 Score =  283 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 85/331 (25%), Positives = 151/331 (45%), Gaps = 35/331 (10%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  +V+  E ++E  R+D +            ++K++  G V V+ K VK + +++ 
Sbjct: 1   MNIVDKIVLQGEKEDEGKRIDVFLAAEL-DYTRSYIKKLIVDGLVFVNGKTVKPSYKVKE 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V +                +  +  +    + +   +LYED  I V NKP G+ V  
Sbjct: 60  NDEVVLN---------------VPEAEKIDVLPEDIPLDILYEDDDIIVINKPQGMVVHP 104

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++  L    +  G     +P + HRLD++TSG++VVA+   A   L+   +
Sbjct: 105 APGNYSGTLVNALLYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y ++V G+ K+++  I   + +   +    + V+    +   YA++ +KV++ 
Sbjct: 165 ERSVFKKYVAIVEGVIKDEEGKIEAPIGRH-PVDRKKMAVI----EDGRYALTLYKVLER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F +    +E    TGRTHQ+RVH  ++G PIVGDH Y    +            LH+  +
Sbjct: 220 FKEN-TLVEAVIKTGRTHQIRVHMAYIGHPIVGDHVYGFKRQ----KFKLEGQALHSSVL 274

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
              HP  G  ++  APLP + V+  + L  K
Sbjct: 275 GFMHPTKGVYMEFEAPLPEYFVRLIEILRNK 305


>gi|153830613|ref|ZP_01983280.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           623-39]
 gi|148873911|gb|EDL72046.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           623-39]
          Length = 315

 Score =  283 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 106/324 (32%), Positives = 182/324 (56%), Gaps = 15/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQXKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G    + + +   LLK        V+ + +       + + F++++ FA+   
Sbjct: 177 YYYALVMGHWDAECKVVNAPLLKNE------VNSIVRVNPNGKPSETRFRILEKFAE-AT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP
Sbjct: 230 LVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFVHP 289

Query: 301 EGG-RLQITAPLPAHMVKTWDSLG 323
               +L+I APL AH+ +    + 
Sbjct: 290 ASEKKLEIHAPLEAHLEQALAKMR 313


>gi|152969638|ref|YP_001334747.1| 23S rRNA pseudouridylate synthase C [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|329999760|ref|ZP_08303517.1| rRNA pseudouridylate synthase [Klebsiella sp. MS 92-3]
 gi|150954487|gb|ABR76517.1| 23S rRNA pseudouridylate synthase [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|328538217|gb|EGF64365.1| rRNA pseudouridylate synthase [Klebsiella sp. MS 92-3]
          Length = 331

 Score =  283 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 107/326 (32%), Positives = 173/326 (53%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++
Sbjct: 15  MKTETPTVKMVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKL 74

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 75  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALSEVILYEDDHILVLNKPSGTAV 127

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 128 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGM 186

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + + + 
Sbjct: 187 QKDYLALVRGQWQSHTKVVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERY-EF 242

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F    ++   N+L+LHA  +   
Sbjct: 243 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLSATGLNRLFLHAAALKFT 302

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  +++ APL   +      L 
Sbjct: 303 HPGSGEVMRVEAPLDNQLKHCLQVLR 328


>gi|297583963|ref|YP_003699743.1| RluA family pseudouridine synthase [Bacillus selenitireducens
           MLS10]
 gi|297142420|gb|ADH99177.1| pseudouridine synthase, RluA family [Bacillus selenitireducens
           MLS10]
          Length = 307

 Score =  283 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 88/331 (26%), Positives = 152/331 (45%), Gaps = 33/331 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ V   DE+  RLD+W  +     +    Q  ++ G V V+ +  K N +++ G 
Sbjct: 1   MNTFEFTV---DEQGKRLDKWLTDQSDDWSRSLTQSWIQEGYVTVNDETSKANYKLKIGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+                +     L   ++ L   ++YED  + V NKPAG+ V    
Sbjct: 58  VVRVK---------------VPEVEELEITAEDLDLDIVYEDQDVIVVNKPAGMVVHPAP 102

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 103 GHPSGTLVNGLMYHCQDLSGINGVARPGIVHRIDKDTSGLLMVAKHDKAHESLVDQLKNK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G   ++K  +   + +           +   E+ A  A++HF+VI+   
Sbjct: 163 TTIRQYEALVVGTIPHEKGTVDAPIGRDPQDRQK----MTVTEENARDAVTHFQVIERM- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +  +  TGRTHQ+RVH  ++G PIVGD KY    K +F+        LHAR +  
Sbjct: 218 NGYTHVLCELETGRTHQIRVHMKYIGYPIVGDPKYGPRKKHDFS---IEGQALHARTLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            HP  G  +   A +P    +T D +  ++ 
Sbjct: 275 VHPVTGEQMTFEAEVPERFKETLDQMKREFP 305


>gi|42782985|ref|NP_980232.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 10987]
 gi|49186742|ref|YP_029994.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|118479113|ref|YP_896264.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|165872288|ref|ZP_02216925.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|167636442|ref|ZP_02394741.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|167641146|ref|ZP_02399401.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|170688858|ref|ZP_02880061.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|170708814|ref|ZP_02899250.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|177654900|ref|ZP_02936617.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|190565878|ref|ZP_03018797.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|196035788|ref|ZP_03103190.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
 gi|196045901|ref|ZP_03113130.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|218905022|ref|YP_002452856.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|225865874|ref|YP_002751252.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|228916530|ref|ZP_04080096.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar pulsiensis BGSC 4CC1]
 gi|228928941|ref|ZP_04091973.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar pondicheriensis BGSC 4BA1]
 gi|228935208|ref|ZP_04098034.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar andalousiensis BGSC 4AW1]
 gi|228947612|ref|ZP_04109902.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar monterrey BGSC 4AJ1]
 gi|229092938|ref|ZP_04224071.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-42]
 gi|229123406|ref|ZP_04252610.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           95/8201]
 gi|229186133|ref|ZP_04313302.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BGSC 6E1]
 gi|254683398|ref|ZP_05147258.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. CNEVA-9066]
 gi|254735932|ref|ZP_05193638.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Western North America USA6153]
 gi|254739820|ref|ZP_05197513.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Kruger B]
 gi|254751010|ref|ZP_05203049.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Vollum]
 gi|301055383|ref|YP_003793594.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           anthracis CI]
 gi|42738912|gb|AAS42840.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus ATCC 10987]
 gi|49180669|gb|AAT56045.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|118418338|gb|ABK86757.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|164711964|gb|EDR17504.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|167510926|gb|EDR86317.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|167528184|gb|EDR90971.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|170126299|gb|EDS95190.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|170667213|gb|EDT17973.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|172080411|gb|EDT65498.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|190562797|gb|EDV16763.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|195991437|gb|EDX55403.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
 gi|196023341|gb|EDX62019.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|218538740|gb|ACK91138.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|225786554|gb|ACO26771.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|228597309|gb|EEK54960.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BGSC 6E1]
 gi|228660182|gb|EEL15818.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           95/8201]
 gi|228690442|gb|EEL44226.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-42]
 gi|228812132|gb|EEM58463.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar monterrey BGSC 4AJ1]
 gi|228824373|gb|EEM70179.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar andalousiensis BGSC 4AW1]
 gi|228830748|gb|EEM76353.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar pondicheriensis BGSC 4BA1]
 gi|228843109|gb|EEM88191.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar pulsiensis BGSC 4CC1]
 gi|300377552|gb|ADK06456.1| ribosomal large subunit pseudouridylate synthase D [Bacillus cereus
           biovar anthracis str. CI]
 gi|324327791|gb|ADY23051.1| 23S rRNA pseudouridine synthase D [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 302

 Score =  282 bits (722), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 145/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|327481320|gb|AEA84630.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           stutzeri DSM 4166]
          Length = 317

 Score =  282 bits (722), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 108/323 (33%), Positives = 177/323 (54%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  + VQ + V  +    R+D + +     +    + +ILR G+VRV+K R+K   ++Q+
Sbjct: 6   SQTSGVQILEVAPELAGQRIDNFLRTQLRGVPKTLIYRILRKGEVRVNKGRIKPEYKLQA 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VR+PP+  A      E + L   +      + L+S ++YED  + V NKPAGI+V G
Sbjct: 66  GDLVRVPPLRLAERD---EPEPLAQGL-----LERLESAIVYEDKALIVLNKPAGIAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG++Y +   L+  +    ++  L HRLD++TSG+L+VA+ R+  +HL ++ R   + K
Sbjct: 118 GSGLSYGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMVAKKRSMLRHLHQALRGDGVDK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G     K+ ++  LLK +   G+ +  V ++      A++ F+V+  F     
Sbjct: 177 RYMALVRGRWDTSKKQVSAPLLKNTLRSGERMVEVTED---GKEALTLFRVLRRFGDFAT 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
            +E +P TGRTHQ+RVHA H G  I GD KY   +F          +L+LHA  + +P P
Sbjct: 234 LVEAKPVTGRTHQIRVHARHAGHSIAGDSKYGDEDFTREVRELGGKRLFLHAYALKVPLP 293

Query: 301 EGGRLQITAPLPAHMVKTWDSLG 323
           +GG L + AP+     +T + LG
Sbjct: 294 DGGELSLEAPVDEVWARTLERLG 316


>gi|258621208|ref|ZP_05716242.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM573]
 gi|258586596|gb|EEW11311.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM573]
          Length = 316

 Score =  282 bits (722), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 106/324 (32%), Positives = 180/324 (55%), Gaps = 15/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKTIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEAPPPSTKLNKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G   ++ + +   LLK        V+ + +       + + F++++ FA+   
Sbjct: 177 YYYALVMGHWDSECKVVNAPLLKNE------VNSIVRVNPNGKPSETRFRILEKFAE-AT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP
Sbjct: 230 LVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAKFGIERLFLHAANIQFVHP 289

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
                L+I APL AH+ +    + 
Sbjct: 290 ASEEKLEIHAPLEAHLEQALTKMR 313


>gi|258625453|ref|ZP_05720346.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM603]
 gi|258582257|gb|EEW07113.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM603]
          Length = 316

 Score =  282 bits (722), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 105/324 (32%), Positives = 178/324 (54%), Gaps = 15/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKTIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEATPPSTKLNKVAE-LEHCIVYEDEHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G    + + +   LLK        V+ + +       + + F++++ F +   
Sbjct: 177 YYYALVMGHWDPECKVVNAPLLKNE------VNSIVRVNPNGKPSETRFRILEKFTE-AT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP
Sbjct: 230 LVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAKFGIERLFLHAANIQFVHP 289

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
                L+I APL AH+ +    + 
Sbjct: 290 ASEEKLEIHAPLEAHLEQALTKMR 313


>gi|212712798|ref|ZP_03320926.1| hypothetical protein PROVALCAL_03895 [Providencia alcalifaciens DSM
           30120]
 gi|212684490|gb|EEB44018.1| hypothetical protein PROVALCAL_03895 [Providencia alcalifaciens DSM
           30120]
          Length = 318

 Score =  282 bits (722), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 105/327 (32%), Positives = 171/327 (52%), Gaps = 14/327 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     VQ++ + +DE   R+D +  +    +    + +I+R G+VRV+K R+K   ++ 
Sbjct: 1   MKTENQVQFIDISDDEAGQRIDNFLLSKLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLL 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  VR+PPV       + E++    S  L K +  L   +LYED  I V NKP+G +V 
Sbjct: 61  EGDQVRVPPVR------VAERETAPVSAKLDKVA-ALADCILYEDESILVINKPSGTAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R++++Q
Sbjct: 114 GGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRALHEQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + +   LLK     G+ +  V         + + FKV + F +  
Sbjct: 173 KDYLALVRGNWQSHTKVVQAPLLKNILQSGERIVRVSSE---GKPSETRFKVEERF-ENA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH LH G PI  D +Y    F          +L+LHA  +   H
Sbjct: 229 TLVKASPVTGRTHQIRVHTLHAGHPIAFDDRYGDKQFDSQLADTGLKRLFLHAYALKFTH 288

Query: 300 P-EGGRLQITAPLPAHMVKTWDSLGFK 325
           P  G  +++ APL   + +    L  K
Sbjct: 289 PKSGEEMRVVAPLHNDLNQCLKVLRAK 315


>gi|330829706|ref|YP_004392658.1| 23S rRNA pseudouridylate synthase C [Aeromonas veronii B565]
 gi|328804842|gb|AEB50041.1| 23S rRNA pseudouridylate synthase C [Aeromonas veronii B565]
          Length = 327

 Score =  282 bits (722), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 102/319 (31%), Positives = 176/319 (55%), Gaps = 15/319 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            VQ + +E + +  R+D + K     +    + +ILR G+VRV+KKR+K   ++ +G  V
Sbjct: 20  QVQLLTIEAEHDGQRIDNFLKTQLKGVPKSLIYRILRKGEVRVNKKRIKPEYKLCAGDEV 79

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP       + ++ ++  +++ + +    L+S +L+ED  + V NKP+G++V GGSG+
Sbjct: 80  RVPP-----VRVAEKNELPSANLGVIQR---LESQILFEDDAMIVLNKPSGMAVHGGSGL 131

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ ++K Y +
Sbjct: 132 SFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRVKTMRKQYLA 190

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  +   + +   L K     G+ V  V  +      + + F+++  FA+    +E 
Sbjct: 191 LVRGKWQAHVKVVNAPLRKNDLQSGERVVRVSAD---GKPSETRFRIVRQFAE-ATLVEC 246

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH LH G PI  D KY  A F     S    +L+LHA  +   HP  GR
Sbjct: 247 SPITGRTHQIRVHTLHAGHPIACDDKYGEAAFDEKMRSQGLKRLFLHAWKLSFTHPADGR 306

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +Q+ APL   +    + L
Sbjct: 307 EMQVEAPLAPELDNFLNGL 325


>gi|288936150|ref|YP_003440209.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|290510796|ref|ZP_06550166.1| ribosomal large subunit pseudouridine synthase C [Klebsiella sp.
           1_1_55]
 gi|288890859|gb|ADC59177.1| pseudouridine synthase, RluA family [Klebsiella variicola At-22]
 gi|289777512|gb|EFD85510.1| ribosomal large subunit pseudouridine synthase C [Klebsiella sp.
           1_1_55]
          Length = 331

 Score =  282 bits (722), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 107/326 (32%), Positives = 172/326 (52%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++
Sbjct: 15  MKTETPTVKMVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKL 74

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 75  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALSEVILYEDDHILVLNKPSGTAV 127

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 128 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGM 186

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + + + 
Sbjct: 187 QKDYLALVRGQWQSHTKVVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERY-EF 242

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F    +    N+L+LHA  +   
Sbjct: 243 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLSGTGLNRLFLHAAALKFT 302

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  +++ APL   +      L 
Sbjct: 303 HPGSGEVMRVEAPLDNQLKHCLQVLR 328


>gi|30021981|ref|NP_833612.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|229129170|ref|ZP_04258143.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-Cer4]
 gi|296504387|ref|YP_003666087.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
 gi|29897537|gb|AAP10813.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|228654407|gb|EEL10272.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-Cer4]
 gi|296325439|gb|ADH08367.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
          Length = 302

 Score =  282 bits (722), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 144/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAAEQKNERIDKFVAGINNEWSRTQVQQWIKDNVVTVNGKAVKGNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|47570307|ref|ZP_00240954.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           G9241]
 gi|47553016|gb|EAL11420.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           G9241]
          Length = 302

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 146/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKSERIDKFVAEINGEWSRSQVQQWIKDDVVTVNGKSVKVNYKVKEND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L   ++ +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|260597456|ref|YP_003210027.1| 23S rRNA pseudouridylate synthase C [Cronobacter turicensis z3032]
 gi|260216633|emb|CBA29938.1| Ribosomal large subunit pseudouridine synthase C [Cronobacter
           turicensis z3032]
          Length = 333

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 107/326 (32%), Positives = 171/326 (52%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  D+   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 17  MKTETPSVKIVAISADQAGQRIDNFLRTQLKGVPKSLIYRILRKGEVRVNKKRIKPEYKL 76

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 77  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALSDVILYEDDHILVLNKPSGTAV 129

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 130 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGM 188

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + FA  
Sbjct: 189 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVNQE---GKPSETRFKVEERFAS- 244

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH    G PI  D +Y    F     S   N+L+LHA  +   
Sbjct: 245 ATLVRCSPVTGRTHQIRVHTQFAGHPIAFDDRYGDRTFDAQLASTGLNRLFLHAAALRFE 304

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  +++ AP+   +      L 
Sbjct: 305 HPGTGETMRVEAPMDEELKHCLKVLR 330


>gi|262166132|ref|ZP_06033869.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM223]
 gi|262025848|gb|EEY44516.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM223]
          Length = 316

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 104/324 (32%), Positives = 178/324 (54%), Gaps = 15/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKTIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEATPPSTKLNKVAE-LEHCIVYEDEHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G    + + +   LLK        V+ + +       + + F++++ F +   
Sbjct: 177 YYYALVMGHWDPECKVVNAPLLKNE------VNSIVRVNPNGKPSETRFRILEKFTE-AT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP
Sbjct: 230 LVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAKFGIERLFLHAANIQFVHP 289

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
                L+I APL A++ +    + 
Sbjct: 290 ASEEKLEIHAPLEAYLEQALTKMR 313


>gi|227529323|ref|ZP_03959372.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           vaginalis ATCC 49540]
 gi|227350751|gb|EEJ41042.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           vaginalis ATCC 49540]
          Length = 305

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 89/325 (27%), Positives = 148/325 (45%), Gaps = 33/325 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    + +++     R+D+   +H   I+   LQK +  G V V+ ++VK   ++  G 
Sbjct: 1   MTDELKLTIDSAMTG-RIDKELAHHLTDISRSQLQKWIEDGNVTVNGEKVKPKYKLVVGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V + P       +  E   LD               ++YED  + V NKP G+ V    
Sbjct: 60  RVVVQPKKPQKIDLEPENIPLD---------------IVYEDDDVIVVNKPQGMVVHPAP 104

Query: 124 GIAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G   H   +  L     S      +P + HR+D++TSG+L++A+   A + L    + + 
Sbjct: 105 GHPNHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTSGLLMIAKNDLAHRSLAAQLKAKT 164

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LV G+ K ++  I   L +          V     +   +A++HFKV++ F Q
Sbjct: 165 NEREYVALVHGVIKEERGTIDAPLGRSKKDRKKQAVV-----EDGRHAVTHFKVLELF-Q 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +  +  TGRTHQ+RVH  ++G P+ GD  Y         +   N  YLHAR +   
Sbjct: 219 HYTLVSCRLETGRTHQIRVHMKYIGHPLAGDPLYGPR-----KTLPGNGQYLHARLLGFK 273

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  G+ +  T+PLP +  K  D L
Sbjct: 274 HPRTGKQMTFTSPLPEYFQKMIDHL 298


>gi|254252275|ref|ZP_04945593.1| Pseudouridine synthase RluD [Burkholderia dolosa AUO158]
 gi|124894884|gb|EAY68764.1| Pseudouridine synthase RluD [Burkholderia dolosa AUO158]
          Length = 400

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 146/328 (44%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +VR+D    K    +  G  + +
Sbjct: 57  RIVAVPASLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRIDGAPAKIRQPVPLGATIEL 116

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 117 VP------DLLPEQ--------LAFTPEPVPLDVVYEDDALVVINKPAGVVVHPAAGNWS 162

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 163 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 222

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG    +   I   + +      +   +          A +HF+ +D      Q  
Sbjct: 223 FALVWGTMP-EAGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCVWQRQPV 278

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 279 SAIQCDLETGRTHQIRVHCSHVGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGL 338

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G+ +Q   PLP  M     +LGF
Sbjct: 339 VHPVTGKAMQWRCPLPDDMNALVAALGF 366


>gi|228992627|ref|ZP_04152553.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           pseudomycoides DSM 12442]
 gi|229006175|ref|ZP_04163861.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus mycoides
           Rock1-4]
 gi|228755016|gb|EEM04375.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus mycoides
           Rock1-4]
 gi|228766959|gb|EEM15596.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           pseudomycoides DSM 12442]
          Length = 302

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 147/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  ++++ R+D++        +   +Q+ ++ G V V+   +K N +++   
Sbjct: 1   MSEVVQVTVTEEQKSERIDKFLAGVNNEWSRSQVQQWIKDGVVTVNGNDIKGNYKVKVND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EIAV---------------AIPDPEELDILPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIGRDKKD-----RQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLD-----INGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  AP+PA   +  + L 
Sbjct: 275 DHPRTGEYIEFEAPVPAVFEEVLNVLR 301


>gi|291085563|ref|ZP_06353360.2| ribosomal large subunit pseudouridine synthase [Citrobacter youngae
           ATCC 29220]
 gi|291071302|gb|EFE09411.1| ribosomal large subunit pseudouridine synthase [Citrobacter youngae
           ATCC 29220]
          Length = 331

 Score =  282 bits (721), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 106/329 (32%), Positives = 175/329 (53%), Gaps = 15/329 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 15  MKTETPAVKTVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 74

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G +VRIPPV  A     +E++ +  ++   +    L  ++LYED  I V NKP+G +V
Sbjct: 75  EDGDIVRIPPVRVAD----REEEAISPNL---QKVAALTDVILYEDDHILVLNKPSGTAV 127

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 128 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 186

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 187 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVNQE---GKPSETRFKVEERYA-F 242

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +   
Sbjct: 243 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLADTGLNRLFLHAAALKFT 302

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HP  G  ++I AP+   + ++ + L  K 
Sbjct: 303 HPGTGEVMRIEAPMDKQLKRSLEVLRSKA 331


>gi|171320446|ref|ZP_02909479.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MEX-5]
 gi|171094306|gb|EDT39380.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MEX-5]
          Length = 369

 Score =  282 bits (721), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 90/335 (26%), Positives = 146/335 (43%), Gaps = 30/335 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +V +D    K    +  G  + +
Sbjct: 16  RVVEVPLSLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAKIRQPVPLGARIEL 75

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 76  VP------DLLPEQ--------LAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWS 121

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 122 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 181

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG        I   + +      +   +          A +HF+ +D      Q  
Sbjct: 182 FALVWGTMPED-GTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCLWQRQPV 237

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 238 SAIQCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPDGFARQALHAWRLGL 297

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF-KYDRNL 330
            HP  G+ +Q   PLP  M     +LGF + D   
Sbjct: 298 VHPLTGKTMQWRCPLPDDMNALIAALGFGQADEEF 332


>gi|114570313|ref|YP_756993.1| ribosomal large subunit pseudouridine synthase C [Maricaulis maris
           MCS10]
 gi|114340775|gb|ABI66055.1| ribosomal large subunit pseudouridine synthase C [Maricaulis maris
           MCS10]
          Length = 330

 Score =  282 bits (721), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 122/346 (35%), Positives = 201/346 (58%), Gaps = 21/346 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ VQ + VE  E+  R+DRWFK  +PH++ + +QK+ R GQ+RVD  RVK ++R+  GQ
Sbjct: 1   MSGVQTIKVEATEDGSRVDRWFKRRFPHVSAIMVQKLCRKGQIRVDGGRVKGDSRVHEGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP       + +  +    +    +   ++KS+++Y+D ++  FNKPAG++VQGGS
Sbjct: 61  EIRIPP-------LPEPGERPPVNRMSDEDIAYVKSLVIYQDDELIAFNKPAGLAVQGGS 113

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               H+DG L ++ +    +PRL HRLD++TSGIL+V +   A   L ++F+  + +K Y
Sbjct: 114 KTTRHLDGMLDAFGEGLD-RPRLVHRLDKDTSGILIVGKGPKATARLAKAFQSHKTRKTY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           W++  G+PK K   I  ++ K +  G     + +      ++GA +A++ + VI    QK
Sbjct: 173 WAIAIGVPKPKMGEIKGFMRKAAASGVDSERETMVAAGHGDEGAQHALTRYVVIGEAGQK 232

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
             W+ ++P TGRTHQLRVH   MG  I+GD KY  +        +  +L LHAR +++P 
Sbjct: 233 ASWVALRPVTGRTHQLRVHLAAMGTAILGDKKYTCHRPA--PEDLGRRLCLHARRLEIPR 290

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNI 345
           P G  L +TA LP  + K +D+LGF         +  S+ + ++++
Sbjct: 291 PGGKPLVLTADLPPALKKIYDTLGFSV-------KEISETDIEEDL 329


>gi|291546177|emb|CBL19285.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus sp.
           SR1/5]
          Length = 304

 Score =  282 bits (721), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 86/326 (26%), Positives = 149/326 (45%), Gaps = 32/326 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            +    VE +E  +R+DR+       ++   LQK+L+ GQ+ V +K  K N +++    +
Sbjct: 2   EIYDYTVEKEESGIRIDRYLAEKDSGLSRSFLQKLLKEGQITVGEKAAKSNYKVRENDRI 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +    ++   I+ E   LD               +LYED  + + NKP G+ V   +G 
Sbjct: 62  HLEIPDSSEPDIVPEDIPLD---------------ILYEDEDVLIVNKPKGMVVHPAAGH 106

Query: 126 --AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  +    DS        +P + HR+D++T+G L+V +   A + L E  +   
Sbjct: 107 YQGTLVNAVMAHCGDSLSGINGVMRPGIVHRIDKDTTGALLVCKNDIAHRDLAEQLKCHS 166

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I++ Y ++V G  K  +  I   + +           +  N K    AI+H+KV++ F +
Sbjct: 167 IRRRYRAVVQGNLKEDEGTIEGPIGRHPTDRKK----MAINHKNGKDAITHYKVLERFGE 222

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              ++E +  TGRTHQ+RVH   +G P++GD  Y ++              LHA  +   
Sbjct: 223 -ATYVECRLETGRTHQIRVHMASIGHPLLGDTVYGSSRNPYHLE----GQALHAMILGFV 277

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  ++ TAPLP + VK    L 
Sbjct: 278 HPRTGEYMEFTAPLPEYFVKLLTKLR 303


>gi|326389927|ref|ZP_08211490.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           JW 200]
 gi|325993987|gb|EGD52416.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           JW 200]
          Length = 305

 Score =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 87/331 (26%), Positives = 152/331 (45%), Gaps = 35/331 (10%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  +V+  E ++E  R+D +            ++K++  G V V+ K VK + +++ 
Sbjct: 1   MNIVDKIVLQGEKEDEGKRIDVFLAAEL-DYTRSYIKKLIVDGLVFVNGKTVKPSYKVKE 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V +         ++ E   LD               +LYED  I V NKP G+ V  
Sbjct: 60  NDEVVVNIPEAEKIDVLPENIPLD---------------ILYEDDDIIVINKPQGMVVHP 104

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++  L    +  G     +P + HRLD++TSG++VVA+   A   L+   +
Sbjct: 105 APGNYSGTLVNALLYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y ++V G+ K+++  I   L+ +  +    + V+    +   YA++ +KV++ 
Sbjct: 165 ERSVFKKYVAIVEGVIKHEEGKIEA-LIGRHPVDRKKMAVI----EDGRYALTLYKVLER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F +    +E    TGRTHQ+RVH  ++G P+VGD  Y    +            LH+R +
Sbjct: 220 FKEN-TLIEAVIKTGRTHQIRVHMAYIGHPVVGDPVYGFKKQ----KFKLEGQALHSRVL 274

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
              HP  G  ++  APLP + V+  + L  +
Sbjct: 275 GFMHPTKGVYMEFEAPLPEYFVRLIEILRNR 305


>gi|196038675|ref|ZP_03105983.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
 gi|196030398|gb|EDX68997.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
          Length = 302

 Score =  281 bits (720), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 145/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVIRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|226330541|ref|ZP_03806059.1| hypothetical protein PROPEN_04459 [Proteus penneri ATCC 35198]
 gi|225201336|gb|EEG83690.1| hypothetical protein PROPEN_04459 [Proteus penneri ATCC 35198]
          Length = 317

 Score =  281 bits (720), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 104/325 (32%), Positives = 174/325 (53%), Gaps = 14/325 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     VQ+V ++ DE   R+D +       +    + +I+R G+VRV+K R+K   ++ 
Sbjct: 1   MKSFNQVQFVTIDGDEAGQRIDNFLLARLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLN 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  +RIPPV       + E++ +  S  L K S  L + +LYED  + + NKP+G +V 
Sbjct: 61  AGDSIRIPPVR------VSEKEEVAVSPKLDKVS-ALANCILYEDDHLMLINKPSGTAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HRLD++TSG+L++A+ R+A + L E  R++++Q
Sbjct: 114 GGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLIAKKRSALRALHEQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + +   LLK     G+ V  V         + + FKV + F +  
Sbjct: 173 KDYLALVRGQWQSHTKVVQAPLLKNILQSGERVVKV---SNEGKPSETRFKVEERF-EFA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH LH G PI  D +Y   +F         N+L+LHA  +   H
Sbjct: 229 TLVKASPVTGRTHQIRVHTLHAGHPIAFDDRYGDRDFDSQLVGTKLNRLFLHASSLTFTH 288

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLG 323
           P  G +++I AP+   +      L 
Sbjct: 289 PSTGDQMRIEAPMDNQLRYCLQVLR 313


>gi|156934429|ref|YP_001438345.1| 23S rRNA pseudouridylate synthase C [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156532683|gb|ABU77509.1| hypothetical protein ESA_02260 [Cronobacter sakazakii ATCC BAA-894]
          Length = 317

 Score =  281 bits (720), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 110/326 (33%), Positives = 173/326 (53%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V V  D+   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAVSADQAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALSDVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A ++L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRYLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + FA  
Sbjct: 173 QKDYLALVRGQWQSHVKNVQAPLLKNILQSGERIVRVNQE---GKPSETRFKVEERFA-I 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F     S   N+L+LHA  +   
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDRAFDAQLASTGLNRLFLHAAALRFE 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  ++I APL   +      L 
Sbjct: 289 HPGTGETMRIEAPLDDELKHCLKVLR 314


>gi|319649641|ref|ZP_08003797.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317398803|gb|EFV79485.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 300

 Score =  281 bits (720), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 76/320 (23%), Positives = 141/320 (44%), Gaps = 33/320 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ +++   R+D+         +   +Q+ ++ G V V+ ++ K N +  +   + I   
Sbjct: 4   IIPDEQAGERIDKVLSTLNADWSRTQVQQWIKDGNVLVNGQKPKTNYKCTANDKIEIS-- 61

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYH 128
                        +     L    + +   + YED  + V NKP G+ V    G G    
Sbjct: 62  -------------IPEPEELDVVPEKMDLDIYYEDKDVLVVNKPKGMVVHPAAGHGTGTL 108

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y 
Sbjct: 109 VNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLMNKTVTRKYR 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G+  +    I   + +      D   +   +     +A++HF+V++ F + F  +E
Sbjct: 169 AVVHGVIPHDYGTIDAPIARDPK---DRQSMTVVD--NGKHAVTHFQVLERF-RDFTLVE 222

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            Q  TGRTHQ+RVH  ++G P+ GD KY      +          LHA  +   HP  G 
Sbjct: 223 CQLETGRTHQIRVHMKYIGYPLAGDPKYGPRKTLD-----IGGQALHAGVLGFEHPRTGE 277

Query: 305 -LQITAPLPAHMVKTWDSLG 323
            L+  A +PA+  +  D L 
Sbjct: 278 YLEFEASIPAYFEELLDKLA 297


>gi|254719684|ref|ZP_05181495.1| RluA family pseudouridine synthase [Brucella sp. 83/13]
 gi|265984699|ref|ZP_06097434.1| pseudouridine synthase [Brucella sp. 83/13]
 gi|306840039|ref|ZP_07472826.1| pseudouridine synthase, RluA family [Brucella sp. NF 2653]
 gi|264663291|gb|EEZ33552.1| pseudouridine synthase [Brucella sp. 83/13]
 gi|306404853|gb|EFM61145.1| pseudouridine synthase, RluA family [Brucella sp. NF 2653]
          Length = 334

 Score =  281 bits (720), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 88/346 (25%), Positives = 163/346 (47%), Gaps = 45/346 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMN 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L          + +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +    DS       ++P + HRLD++TSG++VVA+   A +HL+E F   
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADH 165

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                +++ Y +LVWG+ +  +  +  +L + SH       VV++  + A +AI+H+  +
Sbjct: 166 GRTGDLERAYLALVWGMTERPQGTVDAYLGR-SHRDRTKQAVVREEREDARHAITHYATV 224

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPI 284
           + F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        P+
Sbjct: 225 EKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPEPL 284

Query: 285 Q------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +      ++  LHA  +   HP     ++  APLP  M +  ++  
Sbjct: 285 KQAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPDDMEQLLENFR 330


>gi|228960110|ref|ZP_04121774.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar pakistani str. T13001]
 gi|229047577|ref|ZP_04193167.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH676]
 gi|229111362|ref|ZP_04240915.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock1-15]
 gi|228672138|gb|EEL27429.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock1-15]
 gi|228723824|gb|EEL75179.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           AH676]
 gi|228799626|gb|EEM46579.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar pakistani str. T13001]
          Length = 302

 Score =  281 bits (720), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 144/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAAEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|229198004|ref|ZP_04324718.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           m1293]
 gi|228585483|gb|EEK43587.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           m1293]
          Length = 302

 Score =  281 bits (720), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 145/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPKVFEDALNILR 301


>gi|322616557|gb|EFY13466.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322620502|gb|EFY17366.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322622496|gb|EFY19341.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322629647|gb|EFY26422.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322632633|gb|EFY29379.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322636872|gb|EFY33575.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322646483|gb|EFY42993.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322650020|gb|EFY46438.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322653945|gb|EFY50268.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322658477|gb|EFY54739.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322663335|gb|EFY59537.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322670069|gb|EFY66209.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322674867|gb|EFY70958.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322676663|gb|EFY72730.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322682585|gb|EFY78604.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322686662|gb|EFY82641.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323195776|gb|EFZ80952.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323198332|gb|EFZ83436.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323204846|gb|EFZ89840.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323209187|gb|EFZ94124.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323213429|gb|EFZ98225.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323217853|gb|EGA02568.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323222141|gb|EGA06525.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323224914|gb|EGA09172.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323229655|gb|EGA13778.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323232880|gb|EGA16976.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323240615|gb|EGA24657.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323242929|gb|EGA26950.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323247713|gb|EGA31657.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323252621|gb|EGA36459.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323258851|gb|EGA42504.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323266949|gb|EGA50434.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323269990|gb|EGA53439.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
          Length = 317

 Score =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 108/329 (32%), Positives = 174/329 (52%), Gaps = 15/329 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +   
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLADTGLNRLFLHAAALKFT 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HP  G  ++I AP+   + +  + L  K 
Sbjct: 289 HPGTGEVMRIEAPMDKQLKRCLEVLRSKA 317


>gi|257884651|ref|ZP_05664304.1| pseudouridylate synthase [Enterococcus faecium 1,231,501]
 gi|261207803|ref|ZP_05922488.1| pseudouridylate synthase [Enterococcus faecium TC 6]
 gi|289566255|ref|ZP_06446687.1| RNA pseudouridine synthase ylyB [Enterococcus faecium D344SRF]
 gi|294616594|ref|ZP_06696370.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1636]
 gi|257820489|gb|EEV47637.1| pseudouridylate synthase [Enterococcus faecium 1,231,501]
 gi|260078186|gb|EEW65892.1| pseudouridylate synthase [Enterococcus faecium TC 6]
 gi|289161962|gb|EFD09830.1| RNA pseudouridine synthase ylyB [Enterococcus faecium D344SRF]
 gi|291590544|gb|EFF22277.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1636]
          Length = 303

 Score =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 149/327 (45%), Gaps = 36/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT ++  +     E+ R+D+   N +   +   +Q  L++G V V+ + VK N +++ G 
Sbjct: 1   MTELKTTI---HHESGRIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVKANYKVKQGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +               ++     L    + +   ++YED  + V NKP G+ V   +
Sbjct: 58  EITV---------------LIPEPETLDVVPENIPLTIVYEDEDVAVINKPQGMVVHPSA 102

Query: 124 GIAY-HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G  +  +   L   +          +P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 103 GHTHGTMVNALMYHIKDLSTINGVIRPGIVHRIDKDTSGLLMVAKNDQAHESLAQQLKDK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G   ++K  I   + + S        +     +    A++HF V++ F 
Sbjct: 163 TSLRKYVALVHGEIPHEKGTINAPIGR-SKENRKMQAIR----EDGKPAVTHFTVLERF- 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E++  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +  
Sbjct: 217 EGFTLVELKLETGRTHQIRVHMKYIGYPLAGDPVYGPK-----KTLKGNGQFLHAQMLGF 271

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLG 323
            HP    ++   APLP    KT + L 
Sbjct: 272 THPTTNEKMIFEAPLPEVFEKTLEKLR 298


>gi|228922645|ref|ZP_04085945.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar huazhongensis BGSC 4BD1]
 gi|228837074|gb|EEM82415.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar huazhongensis BGSC 4BD1]
          Length = 302

 Score =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 144/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAAEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGIMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|261339387|ref|ZP_05967245.1| ribosomal large subunit pseudouridine synthase [Enterobacter
           cancerogenus ATCC 35316]
 gi|288318188|gb|EFC57126.1| ribosomal large subunit pseudouridine synthase [Enterobacter
           cancerogenus ATCC 35316]
          Length = 315

 Score =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 103/326 (31%), Positives = 172/326 (52%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  D+   R+D + +     +    + +ILR G+VRV+KKRVK   ++
Sbjct: 1   MKTETPAVKMVAIAEDDAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  +RIPPV  A     +E++++   +   +    L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEIRIPPVRVAE----REEEVVSPKL---QKVAALSDVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + + + 
Sbjct: 173 QKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVRVNQE---GKPSETRFKVEERY-EF 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F         ++L+LHA  +   
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLAGTGLSRLFLHAAALKFT 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  ++I APL   + +    L 
Sbjct: 289 HPNTGEVIRIEAPLDEQLKRCLKVLR 314


>gi|170703044|ref|ZP_02893871.1| pseudouridine synthase, RluA family [Burkholderia ambifaria
           IOP40-10]
 gi|170132052|gb|EDT00553.1| pseudouridine synthase, RluA family [Burkholderia ambifaria
           IOP40-10]
          Length = 365

 Score =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 90/335 (26%), Positives = 146/335 (43%), Gaps = 30/335 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +V +D    K    +  G  + +
Sbjct: 16  RVVEVPLSLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAKIRQPVPLGARIEL 75

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 76  VP------DLLPEQ--------LAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWS 121

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 122 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 181

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG        I   + +      +   +          A +HF+ +D      Q  
Sbjct: 182 FALVWGTMPED-GTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCLWQRQPV 237

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H+G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 238 SAIQCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPDGFARQALHAWRLGL 297

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF-KYDRNL 330
            HP  G+ +Q   PLP  M     +LGF + D   
Sbjct: 298 VHPLTGKTMQWRCPLPEDMNALIAALGFGQADEEF 332


>gi|228940981|ref|ZP_04103539.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar berliner ATCC 10792]
 gi|228973912|ref|ZP_04134487.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar thuringiensis str. T01001]
 gi|228980501|ref|ZP_04140811.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis Bt407]
 gi|228779321|gb|EEM27578.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis Bt407]
 gi|228785778|gb|EEM33782.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar thuringiensis str. T01001]
 gi|228818660|gb|EEM64727.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar berliner ATCC 10792]
 gi|326941662|gb|AEA17558.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar chinensis CT-43]
          Length = 302

 Score =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 144/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAAEQKNERIDKFVTGINNEWSRSQVQQWIKDDVVTVNGKAVKVNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEALDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIGRD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|310828904|ref|YP_003961261.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           limosum KIST612]
 gi|308740638|gb|ADO38298.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           limosum KIST612]
          Length = 307

 Score =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 86/326 (26%), Positives = 152/326 (46%), Gaps = 33/326 (10%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++   V  ++  +RLD +     P  +   ++ +L  G V+VD  + K + +++  +++
Sbjct: 2   EIKEYHVSEEKAGVRLDAYCAEQEPDFSRGYIKNLLNEGAVKVDGGQKKASYKLKGKEII 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                +      T   + +   ++YED  + V NKP G+ V    G 
Sbjct: 62  TME---------------IPEPAESTIEPENIPLEIIYEDEDVIVVNKPKGMVVHPAPGS 106

Query: 126 A--------YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                     H  G L +   +   +P + HR+D++TSG+L+VA+  AA Q+LTE  +  
Sbjct: 107 PSGTLVNALMHHTGALSNI--NGVYRPGIIHRIDKDTSGLLMVAKNNAAHQNLTEQLKAH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I + Y +LV GI +N +  I   + +        + VVK+N   +  A++HF+ +  +A
Sbjct: 165 TITRQYKALVKGIMENNRGTIDMPIGRHPK-DRVRMAVVKEN---SKEAVTHFETLKRYA 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  ++ +  TGRTHQ+RVH   +G PI GD  Y  + K  F +       LHA  +  
Sbjct: 221 EGYTLMQFRLETGRTHQIRVHMQAIGYPIAGDPLYKGDKKNPFKTEG---QCLHAELLGF 277

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  ++ +APLP       D L
Sbjct: 278 KHPRTGEYMEFSAPLPEAFQAILDGL 303


>gi|218549187|ref|YP_002382978.1| 23S rRNA pseudouridylate synthase C [Escherichia fergusonii ATCC
           35469]
 gi|218356728|emb|CAQ89356.1| 23S rRNA pseudouridylate synthase [Escherichia fergusonii ATCC
           35469]
 gi|324113880|gb|EGC07854.1| RluA family protein pseudouridine synthase [Escherichia fergusonii
           B253]
          Length = 331

 Score =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 106/326 (32%), Positives = 172/326 (52%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 15  MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 74

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            +G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 75  AAGDEVRIPPVR------VAEREEDAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 127

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 128 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 186

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 187 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-I 242

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F     +   ++L+LHA  +   
Sbjct: 243 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLANTGLSRLFLHAAALKFT 302

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  ++I AP+   + +    L 
Sbjct: 303 HPGTGEVMRIEAPMDDGLKRCLQKLR 328


>gi|210612741|ref|ZP_03289456.1| hypothetical protein CLONEX_01658 [Clostridium nexile DSM 1787]
 gi|210151434|gb|EEA82442.1| hypothetical protein CLONEX_01658 [Clostridium nexile DSM 1787]
          Length = 305

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 83/324 (25%), Positives = 150/324 (46%), Gaps = 32/324 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q V VE +    R+D++    +P ++   +QK+++ G V  + K VK N ++ +   + 
Sbjct: 2   IQTVTVEKEFSGNRVDKFLSEQFPDLSRSYIQKLIKDGHVTANGKIVKANYKLNALDTLA 61

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +         I+ E   +D               +LYED  I + NKP G+ V   +G  
Sbjct: 62  LDKPELQEPDIVPENIPID---------------ILYEDEDILIVNKPKGMVVHPSAGHY 106

Query: 126 -AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  +    D         +P + HR+D +T+G L+V +     Q L E  +   I
Sbjct: 107 SGTLVNALMYHCKDQLSGINGIMRPGIVHRIDMDTTGSLLVCKNDFVHQDLAEQLKEHSI 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Q+IY ++V G+ K  +  I   + +   I    + V   N K   +A++H+KVI+ F + 
Sbjct: 167 QRIYHAIVHGVIKEDEGTIDAPIGRH-PIERKKMSV---NYKNGKHAVTHYKVIERF-KN 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           + +++ +  TGRTHQ+RVH  H+  P++GD  Y                 LHA+ + + H
Sbjct: 222 YTYIKCRLETGRTHQIRVHMAHIRHPLLGDAVYGP----AKCPFKLQGQTLHAKTLGIVH 277

Query: 300 PEG-GRLQITAPLPAHMVKTWDSL 322
           P     +++ APLP + +   + L
Sbjct: 278 PRTHEYIEVDAPLPDYFISLLNKL 301


>gi|134295824|ref|YP_001119559.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           vietnamiensis G4]
 gi|134138981|gb|ABO54724.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           vietnamiensis G4]
          Length = 401

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 148/328 (45%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +V +D    K    +  G  + +
Sbjct: 58  RVVEVPLSLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAKIRQPVPLGAKIEL 117

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P       ++ EQ        L   ++ +   ++YED  + V NKPAG+ V   +G   
Sbjct: 118 VP------DLLPEQ--------LAFAAEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWS 163

Query: 126 AYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 164 GTLLNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 223

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG    ++  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 224 FALVWGTMP-EEGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCVWQRQPV 279

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H G P++GD  Y         +P+ N   +  LHA  + L
Sbjct: 280 SAIQCDLETGRTHQIRVHCSHAGHPLLGDPVYGRARGKRSVTPLPNGFARQALHAWRLGL 339

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G+ +Q   PLP  M +   +LGF
Sbjct: 340 VHPVTGKTMQWRCPLPDDMNELVAALGF 367


>gi|53723511|ref|YP_102984.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           mallei ATCC 23344]
 gi|76810454|ref|YP_333728.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei 1710b]
 gi|52426934|gb|AAU47527.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           mallei ATCC 23344]
 gi|76579907|gb|ABA49382.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei 1710b]
          Length = 395

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 148/343 (43%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRV     K    +  G  + +
Sbjct: 57  RTVDVPLALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIEL 116

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P +                       + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 117 LPELLPEQL--------------AFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 162

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 163 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYF 222

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +L WG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 223 ALAWGRMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVS 278

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 279 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 338

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 339 HPASGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 381


>gi|330817148|ref|YP_004360853.1| Pseudouridine synthase RluD [Burkholderia gladioli BSR3]
 gi|327369541|gb|AEA60897.1| Pseudouridine synthase RluD [Burkholderia gladioli BSR3]
          Length = 398

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 88/328 (26%), Positives = 145/328 (44%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV +     RLD+     +P  +   LQ  +   +VRVD    K    +  G  + +
Sbjct: 57  RVVVVPDSLAGERLDKALAQLFPEFSRSRLQGWIDEQRVRVDGAPAKVRQPVPLGATIEL 116

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P       ++ EQ        L    + +   ++YED  + V +KPAG+ V   +G   
Sbjct: 117 VP------DLLPEQ--------LAFAPEPVPLSIVYEDEALVVIDKPAGLVVHPAAGNWS 162

Query: 126 AYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + ++     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 163 GTLLNGLLHRYGEAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 222

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKF 240
           ++LVWG    +   I   + +      +   +          A +HF+ +D      Q  
Sbjct: 223 FALVWGRMP-ESGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRCVDTVLWQNQPV 278

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             +     TGRTHQ+RVH  H G P++GD  Y         + +     +  LHA  + L
Sbjct: 279 SAIHCDLETGRTHQIRVHCAHTGHPLLGDPVYGRARGKRSVAALPGGFARQALHAWRLGL 338

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  GR +Q   P+P  + +   +LGF
Sbjct: 339 VHPLTGRSMQWRCPVPDDIAELAAALGF 366


>gi|49478436|ref|YP_037954.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|49329992|gb|AAT60638.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
          Length = 302

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 145/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREDD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|256045267|ref|ZP_05448161.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           bv. 1 str. Rev.1]
 gi|256114226|ref|ZP_05454971.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           bv. 3 str. Ether]
 gi|256263395|ref|ZP_05465927.1| ribosomal large subunit pseudouridine synthase [Brucella melitensis
           bv. 2 str. 63/9]
 gi|260565840|ref|ZP_05836323.1| ribosomal large subunit pseudouridine synthase [Brucella melitensis
           bv. 1 str. 16M]
 gi|265991692|ref|ZP_06104249.1| pseudouridine synthase [Brucella melitensis bv. 1 str. Rev.1]
 gi|265995529|ref|ZP_06108086.1| pseudouridine synthase [Brucella melitensis bv. 3 str. Ether]
 gi|260151213|gb|EEW86308.1| ribosomal large subunit pseudouridine synthase [Brucella melitensis
           bv. 1 str. 16M]
 gi|262766813|gb|EEZ12431.1| pseudouridine synthase [Brucella melitensis bv. 3 str. Ether]
 gi|263002648|gb|EEZ15051.1| pseudouridine synthase [Brucella melitensis bv. 1 str. Rev.1]
 gi|263093392|gb|EEZ17461.1| ribosomal large subunit pseudouridine synthase [Brucella melitensis
           bv. 2 str. 63/9]
 gi|326409663|gb|ADZ66728.1| pseudouridine synthase [Brucella melitensis M28]
 gi|326539370|gb|ADZ87585.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           M5-90]
          Length = 334

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 88/346 (25%), Positives = 162/346 (46%), Gaps = 45/346 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMN 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L          + +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +    DS       ++P + HRLD++TSG++VVA+   A +HL+E F   
Sbjct: 106 NWTGTLVNALIYQCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADH 165

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                +++ Y +LVWG+ +  +  +  +L + SH       VV +  + A +AI+H+  +
Sbjct: 166 GRTGDLERAYLALVWGMTERPQGTVDAYLGR-SHRDRTKQAVVHEEREDARHAITHYATV 224

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPI 284
           + F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        P+
Sbjct: 225 EKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPEPL 284

Query: 285 Q------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +      ++  LHA  +   HP     ++  APLP  M +  ++  
Sbjct: 285 KEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDMEQLLENFR 330


>gi|255528132|ref|ZP_05394960.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
 gi|296186658|ref|ZP_06855060.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
 gi|255508173|gb|EET84585.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
 gi|296048695|gb|EFG88127.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
          Length = 305

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 82/324 (25%), Positives = 141/324 (43%), Gaps = 32/324 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
             +  +++ +  N RLD +        +   +Q ++   QV+V+    K N +++    +
Sbjct: 2   ETREFIIDENSVNTRLDLFLSERMEDKSRSYIQGLIEKSQVKVNGILKKSNYKLKIKDKI 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I                +   V L    + +   ++YEDS + V NKP G+ V   SG+
Sbjct: 62  LIT---------------IPDPVGLDIEPEDIPLDIVYEDSDVIVVNKPQGMVVHPASGV 106

Query: 126 --AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++  L    D  G     +P + HR+D++TSGILVVA+   +   L E  +   +
Sbjct: 107 YTGTLVNALLNHCSDLSGINGVTRPGIVHRIDKDTSGILVVAKNDKSHNKLAEQLKDHSM 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y +LV GI K  +  I   L +          +     K    A++H++V++ F   
Sbjct: 167 TRAYTALVEGILKEDEGTIDKPLGRHPVERIKISVI-----KDGKRAVTHYRVLERFKSN 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E    TGRTHQ+RVH  ++G P+VGD  Y    +        N   LHA+ +   H
Sbjct: 222 -TLVECVLETGRTHQIRVHMAYIGHPLVGDPVYGYKKQ----KFNLNGQMLHAKKLGFIH 276

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P     ++ T+ LP +  K  + L
Sbjct: 277 PSTNEYIEFTSDLPDYFKKVLNVL 300


>gi|325528651|gb|EGD05737.1| RluA family pseudouridine synthase [Burkholderia sp. TJI49]
          Length = 359

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 146/328 (44%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +VR+D    K    +  G  + +
Sbjct: 16  RIVEVPASLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRIDGAPAKIRQPVPLGATIEL 75

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 76  VP------DLLPEQ--------LAFTPEPVPLDVVYEDDALVVINKPAGLVVHPAAGNWS 121

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 122 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 181

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG+       I   + +      +   +          A +HF+ +D      Q  
Sbjct: 182 FALVWGMMPED-GTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCVWQRQPV 237

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H+G P++GD  Y         + + N   +  LHA  + L
Sbjct: 238 SAIQCDLETGRTHQIRVHCSHVGHPLLGDPVYGRARGKRSVAALPNGFARQALHAWRLGL 297

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G+ +Q   PLP  M    ++LGF
Sbjct: 298 IHPVTGKAMQWRCPLPDDMNALVEALGF 325


>gi|229086457|ref|ZP_04218629.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-44]
 gi|228696774|gb|EEL49587.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock3-44]
          Length = 302

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 75/327 (22%), Positives = 146/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V+ ++++ R+D++        +   +Q+ ++ G V V+   +K N +++   
Sbjct: 1   MSEVVQVTVKEEQKSERIDKFLAGINNEWSRSQVQQWIKDGVVTVNGNDIKGNYKVKEND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L   ++ +   + YED+ + V NKP G+ V    
Sbjct: 61  EIAV---------------AIPEPEELDIRAEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMYHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIGRD-----KKERQSMAVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLD-----INGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP     ++  AP+P    +  + L 
Sbjct: 275 DHPRTDEYIEFEAPIPEVFEEVLNILR 301


>gi|206971264|ref|ZP_03232215.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
 gi|228954169|ref|ZP_04116197.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar kurstaki str. T03a001]
 gi|229071392|ref|ZP_04204614.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           F65185]
 gi|229081145|ref|ZP_04213655.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock4-2]
 gi|229180168|ref|ZP_04307512.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           172560W]
 gi|229192062|ref|ZP_04319031.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           ATCC 10876]
 gi|206734036|gb|EDZ51207.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
 gi|228591388|gb|EEK49238.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           ATCC 10876]
 gi|228603377|gb|EEK60854.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           172560W]
 gi|228702189|gb|EEL54665.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           Rock4-2]
 gi|228711683|gb|EEL63636.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           F65185]
 gi|228805489|gb|EEM52080.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar kurstaki str. T03a001]
          Length = 302

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 144/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAAEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDVLNILR 301


>gi|312114370|ref|YP_004011966.1| pseudouridine synthase [Rhodomicrobium vannielii ATCC 17100]
 gi|311219499|gb|ADP70867.1| pseudouridine synthase, RluA family [Rhodomicrobium vannielii ATCC
           17100]
          Length = 326

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 131/328 (39%), Positives = 197/328 (60%), Gaps = 8/328 (2%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT ++   V  D++ +RLDRW K +YP +    +QK++R+GQVRVD  RVK ++R+ +GQ
Sbjct: 1   MT-IEKRAVRTDDDGLRLDRWLKKNYPTLPHTLVQKLVRTGQVRVDGGRVKADSRLSTGQ 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VR+P       +    Q  L     L+K   DF++ ++++E+ ++++ NKP GI+VQGG
Sbjct: 60  EVRVPTHFAEPEN--APQPSLKPPPGLSKADRDFIERMIVFENDEMFILNKPFGIAVQGG 117

Query: 123 SGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           +    HIDG L    D   G++PRL HRLD++T+GIL VA+ R  A  L   F+ R +QK
Sbjct: 118 TKTTRHIDGLLAGMADRFGGERPRLVHRLDRDTTGILAVAKDRQTAARLGRLFQTRSVQK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKF 240
           IYW++  GIPK  +  +   L+K S   GD V   +  E+  A +A + + VID  A   
Sbjct: 178 IYWAITRGIPKPTQGKVEAALVKASGPDGDRVRKARPGEQELAQHATTFYSVIDRAA-NM 236

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            W+ ++P TGR HQLR H   +G PI+GD KY  +        I+ KL+LHAR + L  P
Sbjct: 237 AWVSLKPVTGRQHQLRAHMDILGTPILGDQKYG-DGTEIPIENIERKLHLHARRLTLKDP 295

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           + G + I+APLP+H+ +T++ LGF   R
Sbjct: 296 KLGEIDISAPLPSHIAQTFELLGFDAGR 323


>gi|126649705|ref|ZP_01721941.1| YlyB [Bacillus sp. B14905]
 gi|126593424|gb|EAZ87369.1| YlyB [Bacillus sp. B14905]
          Length = 303

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 84/330 (25%), Positives = 148/330 (44%), Gaps = 34/330 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT V Y  +E  ++  R+D+   +     +   +   +  G ++V+   VK   ++++G 
Sbjct: 1   MTQVTY-TIEEQQQGERIDKALSSLQSEWSRTQIGNWVSDGNIKVNGDAVKPKYKVKAGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ I                +  +  L   ++ L   ++YED+ + V NKP G+ V    
Sbjct: 60  VIAID---------------VPEAEPLDVIAENLALDIVYEDADVLVVNKPKGMVVHPAP 104

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L +    +
Sbjct: 105 GHLTGTLVNGLMYQCKDLSGINGIMRPGIVHRIDKDTSGLLMVAKNDVAHESLVDQLVNK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G   + K  I   + +          V         +A++HF V++ F 
Sbjct: 165 TVTRKYIALVHGHIAHDKGTIDAPIGRDQKDRQKQAIV-----DNGKHAVTHFHVVERFG 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +F         LHA  +  
Sbjct: 220 D-YTLVECRLETGRTHQIRVHMNYIGFPLVGDPKYGPKKTIDF-----GGQVLHAATLGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            HP  G  L+   PLPA   +  + L  K+
Sbjct: 274 NHPSSGEYLEFETPLPADYEQLLNELRNKH 303


>gi|323486916|ref|ZP_08092232.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323399779|gb|EGA92161.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 305

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 78/324 (24%), Positives = 144/324 (44%), Gaps = 32/324 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q  +V      +R+D++     P      LQK+L+S  V V+ K VK + +  +G  V  
Sbjct: 3   QEYIVPEKSSGLRIDKFLTESCPDYTRSFLQKLLKSELVEVNGKPVKSSYKTAAGDTVTF 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                           +  +V     +  +   +LYED  + + NKP G+ V   +G   
Sbjct: 63  E---------------VPEAVEAEITAQEMPLDILYEDEDVILINKPKGMVVHPAAGHYE 107

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++G +    +         +P + HR+D +T+G+L+V +   A   + E  ++  I 
Sbjct: 108 GTLVNGLMHHCREQLSGINGVMRPGIVHRIDMDTTGVLIVCKNDLAHNSIAEQLKVHSIT 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y+++V+G  K+ +  I   + +  +        +  N K    A++H+KV++ F   +
Sbjct: 168 RKYYAVVFGSLKDDEGTIHAPIGRHPNDRKK----MSINSKNGKDAVTHYKVLERF-HGY 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E +  TGRTHQ+RVH   +G P++GD  Y    +            LHA  +   HP
Sbjct: 223 TLVECRLETGRTHQIRVHMASIGHPLLGDQVYGPAKQP----FRLQGQTLHAGVLGFLHP 278

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  ++ +APLP +  +  + L 
Sbjct: 279 RTGEYMEFSAPLPKYFEELLEKLR 302


>gi|62290527|ref|YP_222320.1| ribosomal large subunit pseudouridine synthase D [Brucella abortus
           bv. 1 str. 9-941]
 gi|82700443|ref|YP_415017.1| ribosomal large subunit pseudouridine synthase [Brucella melitensis
           biovar Abortus 2308]
 gi|148558837|ref|YP_001259509.1| ribosomal large subunit pseudouridine synthase D [Brucella ovis
           ATCC 25840]
 gi|189024749|ref|YP_001935517.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella abortus S19]
 gi|254689825|ref|ZP_05153079.1| RluA family pseudouridine synthase [Brucella abortus bv. 6 str.
           870]
 gi|254694317|ref|ZP_05156145.1| RluA family pseudouridine synthase [Brucella abortus bv. 3 str.
           Tulya]
 gi|254697973|ref|ZP_05159801.1| RluA family pseudouridine synthase [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254700318|ref|ZP_05162146.1| RluA family pseudouridine synthase [Brucella suis bv. 5 str. 513]
 gi|254703437|ref|ZP_05165265.1| RluA family pseudouridine synthase [Brucella suis bv. 3 str. 686]
 gi|254708478|ref|ZP_05170306.1| RluA family pseudouridine synthase [Brucella pinnipedialis
           M163/99/10]
 gi|254730859|ref|ZP_05189437.1| RluA family pseudouridine synthase [Brucella abortus bv. 4 str.
           292]
 gi|256061695|ref|ZP_05451832.1| RluA family pseudouridine synthase [Brucella neotomae 5K33]
 gi|256258078|ref|ZP_05463614.1| RluA family pseudouridine synthase [Brucella abortus bv. 9 str.
           C68]
 gi|260547225|ref|ZP_05822963.1| ribosomal large subunit pseudouridine synthase [Brucella abortus
           NCTC 8038]
 gi|260568746|ref|ZP_05839214.1| ribosomal large subunit pseudouridine synthase [Brucella suis bv. 4
           str. 40]
 gi|260755356|ref|ZP_05867704.1| pseudouridine synthase [Brucella abortus bv. 6 str. 870]
 gi|260758578|ref|ZP_05870926.1| pseudouridine synthase [Brucella abortus bv. 4 str. 292]
 gi|260762410|ref|ZP_05874747.1| pseudouridine synthase [Brucella abortus bv. 2 str. 86/8/59]
 gi|260884372|ref|ZP_05895986.1| pseudouridine synthase [Brucella abortus bv. 9 str. C68]
 gi|261214623|ref|ZP_05928904.1| pseudouridine synthase [Brucella abortus bv. 3 str. Tulya]
 gi|261315976|ref|ZP_05955173.1| pseudouridine synthase [Brucella pinnipedialis M163/99/10]
 gi|261325700|ref|ZP_05964897.1| pseudouridine synthase [Brucella neotomae 5K33]
 gi|261750812|ref|ZP_05994521.1| pseudouridine synthase [Brucella suis bv. 5 str. 513]
 gi|261754066|ref|ZP_05997775.1| pseudouridine synthase [Brucella suis bv. 3 str. 686]
 gi|62196659|gb|AAX74959.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella abortus bv. 1 str. 9-941]
 gi|82616544|emb|CAJ11622.1| Prenyl group binding site (CAAX box):RNA-binding S4:Pseudouridine
           synthase:Pseudouridine synthase, Rlu:Pseudouridine
           synthase [Brucella melitensis biovar Abortus 2308]
 gi|148370094|gb|ABQ60073.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella ovis ATCC 25840]
 gi|189020321|gb|ACD73043.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella abortus S19]
 gi|260095590|gb|EEW79468.1| ribosomal large subunit pseudouridine synthase [Brucella abortus
           NCTC 8038]
 gi|260154130|gb|EEW89212.1| ribosomal large subunit pseudouridine synthase [Brucella suis bv. 4
           str. 40]
 gi|260668896|gb|EEX55836.1| pseudouridine synthase [Brucella abortus bv. 4 str. 292]
 gi|260672836|gb|EEX59657.1| pseudouridine synthase [Brucella abortus bv. 2 str. 86/8/59]
 gi|260675464|gb|EEX62285.1| pseudouridine synthase [Brucella abortus bv. 6 str. 870]
 gi|260873900|gb|EEX80969.1| pseudouridine synthase [Brucella abortus bv. 9 str. C68]
 gi|260916230|gb|EEX83091.1| pseudouridine synthase [Brucella abortus bv. 3 str. Tulya]
 gi|261301680|gb|EEY05177.1| pseudouridine synthase [Brucella neotomae 5K33]
 gi|261305002|gb|EEY08499.1| pseudouridine synthase [Brucella pinnipedialis M163/99/10]
 gi|261740565|gb|EEY28491.1| pseudouridine synthase [Brucella suis bv. 5 str. 513]
 gi|261743819|gb|EEY31745.1| pseudouridine synthase [Brucella suis bv. 3 str. 686]
          Length = 334

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 88/346 (25%), Positives = 162/346 (46%), Gaps = 45/346 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMN 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L          + +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +    DS       ++P + HRLD++TSG++VVA+   A +HL+E F   
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADH 165

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                +++ Y +LVWG+ +  +  +  +L + SH       VV +  + A +AI+H+  +
Sbjct: 166 GRTGDLERAYLALVWGMTERPQGTVDAYLGR-SHRDRTKQAVVHEEREDARHAITHYATV 224

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPI 284
           + F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        P+
Sbjct: 225 EKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPEPL 284

Query: 285 Q------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +      ++  LHA  +   HP     ++  APLP  M +  ++  
Sbjct: 285 KEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDMEQLLENFR 330


>gi|217421724|ref|ZP_03453228.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 576]
 gi|217395466|gb|EEC35484.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 576]
          Length = 395

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 148/343 (43%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRV     K    +  G  + +
Sbjct: 57  RTVDVPLALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIEL 116

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P +                       + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 117 LPELLPEQL--------------AFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 162

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 163 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYF 222

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +L WG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 223 ALAWGRMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVS 278

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 279 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 338

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 339 HPASGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 381


>gi|78066563|ref|YP_369332.1| ribosomal large subunit pseudouridine synthase D [Burkholderia sp.
           383]
 gi|77967308|gb|ABB08688.1| ribosomal large subunit pseudouridine synthase D [Burkholderia sp.
           383]
          Length = 402

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 146/328 (44%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +V VD    K    +  G  +++
Sbjct: 58  RVVEVPLSLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAPAKIRQPVPLGAKIQL 117

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 118 VP------DLLPEQ--------LAFTPEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWS 163

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 164 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 223

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG    ++  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 224 FALVWGTMP-EEGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCLWQRQPV 279

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 280 SAIQCDLETGRTHQIRVHCAHAGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGL 339

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G+ +Q   PLP  M     +LGF
Sbjct: 340 VHPVTGKAMQWRCPLPDDMNTLVAALGF 367


>gi|53719166|ref|YP_108152.1| putative ribosomal large subunit pseudouridine synthase D
           [Burkholderia pseudomallei K96243]
 gi|126454439|ref|YP_001066469.1| RluA family pseudouridine synthase [Burkholderia pseudomallei
           1106a]
 gi|242316335|ref|ZP_04815351.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106b]
 gi|52209580|emb|CAH35533.1| putative ribosomal large subunit pseudouridine synthase D
           [Burkholderia pseudomallei K96243]
 gi|126228081|gb|ABN91621.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106a]
 gi|242139574|gb|EES25976.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106b]
          Length = 395

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 148/343 (43%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRV     K    +  G  + +
Sbjct: 57  RTVDVPLALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIEL 116

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P +                       + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 117 LPELLPEQL--------------AFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 162

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 163 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYF 222

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +L WG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 223 ALAWGRMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVS 278

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 279 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 338

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 339 HPASGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 381


>gi|294617890|ref|ZP_06697499.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1679]
 gi|291595835|gb|EFF27119.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1679]
          Length = 303

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 149/327 (45%), Gaps = 36/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT ++  +     E+ R+D+   N +   +   +Q  L++G V V+ + VK N +++ G 
Sbjct: 1   MTELKTTI---HHESGRIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVKANYKVKQGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +               ++     L    + +   ++YED  + V NKP G+ V   +
Sbjct: 58  EITV---------------LIPEPETLDVVPENIPLTIVYEDEDVAVINKPQGMVVHPSA 102

Query: 124 GIAY-HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G  +  +   L   +          +P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 103 GHTHGTMVNALIYHIKDLSTINGVIRPGIVHRIDKDTSGLLMVAKNDQAHESLAQQLKDK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G   ++K  I   + + S        +     +    A++HF V++ F 
Sbjct: 163 TSLRKYVALVHGEIPHEKGTINAPIGR-SKENRKMQAIR----EDGKPAVTHFTVLERF- 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E++  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +  
Sbjct: 217 EGFTLVELKLETGRTHQIRVHMKYIGYPLAGDPVYGPK-----KTLKGNGQFLHAQMLGF 271

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLG 323
            HP    ++   APLP    KT + L 
Sbjct: 272 THPTTNEKMIFEAPLPEVFEKTLEKLR 298


>gi|147678153|ref|YP_001212368.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI]
 gi|146274250|dbj|BAF59999.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI]
          Length = 312

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 84/335 (25%), Positives = 148/335 (44%), Gaps = 31/335 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V    V  ++   RLD +       +    +QK++  G   V+ +R + + R++ G 
Sbjct: 1   MLTVNSFQVGEEDAGKRLDLFLAGEMEGLTRTYVQKLIAEGMASVNGQRGRASYRVKPGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VV +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  VVVLQ---------------VPEPEGLEIKKEPIPLEVYYEDADVIVINKPRGMVVHPAD 105

Query: 124 GI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HRLD++TSG+++VA+   A   L    + R
Sbjct: 106 GNYSGTLVNALLYHCSDLSGINGVMRPGIVHRLDKDTSGLIMVAKNDTAHLSLARQLKER 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +I + Y +LV G+ K +   +   + +          +    +K A  A++ ++V++ F 
Sbjct: 166 QITRRYLALVHGLLKEQSGMVDAPIGRDPRDRKKMAVL----QKNAKQAVTRYRVLERF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + + ++E+   TGRTHQ+RVH  ++G P+VGD KY  +             +LHA  +  
Sbjct: 221 KGYTYIELMLETGRTHQIRVHMSYIGHPVVGDLKYGPSRP----HFGLEGQFLHAAVLGF 276

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLY 331
            HP  G  LQ  APLP  +    + L  +    L+
Sbjct: 277 HHPRTGEYLQFEAPLPDVLKAVLEKLRLENPGKLH 311


>gi|323691964|ref|ZP_08106213.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
 gi|323503973|gb|EGB19786.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
          Length = 305

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 78/324 (24%), Positives = 144/324 (44%), Gaps = 32/324 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q  +V      +R+D++     P      LQK+L+S  V V+ K VK + +  +G  V  
Sbjct: 3   QEYIVPEKSSGLRIDKFLTEICPDYTRSFLQKLLKSELVEVNGKPVKSSYKTAAGDTVTF 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                           +  +V     +  +   +LYED  + + NKP G+ V   +G   
Sbjct: 63  E---------------VPEAVEAEITAQEMPLDILYEDEDVILINKPKGMVVHPAAGHYE 107

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++G +    +         +P + HR+D +T+G+L+V +   A   + E  ++  I 
Sbjct: 108 GTLVNGLMHHCREQLSGINGVMRPGIVHRIDMDTTGVLIVCKNDLAHNSIAEQLKVHSIT 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y+++V+G  K+ +  I   + +  +        +  N K    A++H+KV++ F   +
Sbjct: 168 RKYYAVVFGSLKDDEGTIHAPIGRHPNDRKK----MSINSKNGKDAVTHYKVLERF-HGY 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E +  TGRTHQ+RVH   +G P++GD  Y    +            LHA  +   HP
Sbjct: 223 TLVECRLETGRTHQIRVHMASIGHPLLGDQVYGPAKQP----FRLQGQTLHAGVLGFLHP 278

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  ++ +APLP +  +  + L 
Sbjct: 279 RTGEYMEFSAPLPKYFEELLEKLR 302


>gi|257878226|ref|ZP_05657879.1| pseudouridylate synthase [Enterococcus faecium 1,230,933]
 gi|257880994|ref|ZP_05660647.1| pseudouridylate synthase [Enterococcus faecium 1,231,502]
 gi|257889576|ref|ZP_05669229.1| pseudouridylate synthase [Enterococcus faecium 1,231,410]
 gi|257892484|ref|ZP_05672137.1| pseudouridylate synthase [Enterococcus faecium 1,231,408]
 gi|258616265|ref|ZP_05714035.1| hypothetical protein EfaeD_11195 [Enterococcus faecium DO]
 gi|260559776|ref|ZP_05831955.1| pseudouridylate synthase [Enterococcus faecium C68]
 gi|293559348|ref|ZP_06675890.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1162]
 gi|293569846|ref|ZP_06680933.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1071]
 gi|294621730|ref|ZP_06700894.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium U0317]
 gi|314939741|ref|ZP_07846963.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|314941758|ref|ZP_07848635.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|314948303|ref|ZP_07851695.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
 gi|314952391|ref|ZP_07855398.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|314991990|ref|ZP_07857443.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|314995712|ref|ZP_07860802.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|257812454|gb|EEV41212.1| pseudouridylate synthase [Enterococcus faecium 1,230,933]
 gi|257816652|gb|EEV43980.1| pseudouridylate synthase [Enterococcus faecium 1,231,502]
 gi|257825936|gb|EEV52562.1| pseudouridylate synthase [Enterococcus faecium 1,231,410]
 gi|257828863|gb|EEV55470.1| pseudouridylate synthase [Enterococcus faecium 1,231,408]
 gi|260074000|gb|EEW62323.1| pseudouridylate synthase [Enterococcus faecium C68]
 gi|291587594|gb|EFF19471.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1071]
 gi|291598739|gb|EFF29792.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium U0317]
 gi|291606712|gb|EFF36104.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1162]
 gi|313590103|gb|EFR68948.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313593425|gb|EFR72270.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|313595508|gb|EFR74353.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|313599436|gb|EFR78279.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|313640970|gb|EFS05550.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|313645284|gb|EFS09864.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
          Length = 303

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 149/327 (45%), Gaps = 36/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT ++  +     E+ R+D+   N +   +   +Q  L++G V V+ + VK N +++ G 
Sbjct: 1   MTELKTTI---HHESGRIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVKANYKVKQGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +               ++     L    + +   ++YED  + V NKP G+ V   +
Sbjct: 58  EITV---------------LIPEPETLDVVPENIPLTIVYEDEDVAVINKPQGMVVHPSA 102

Query: 124 GIAY-HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G  +  +   L   +          +P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 103 GHTHGTMVNALMYHIKDLSTINGVIRPGIVHRIDKDTSGLLMVAKNDQAHESLAQQLKDK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G   ++K  I   + + S        +     +    A++HF V++ F 
Sbjct: 163 TSLRKYVALVHGEIPHEKGTINAPIGR-SKENRKMQAIR----EDGKSAVTHFTVLERF- 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E++  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +  
Sbjct: 217 EGFTLVELKLETGRTHQIRVHMKYIGYPLAGDPVYGPK-----KTLKGNGQFLHAQMLGF 271

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLG 323
            HP    ++   APLP    KT + L 
Sbjct: 272 THPTTNEKMIFEAPLPEVFEKTLEKLR 298


>gi|167910661|ref|ZP_02497752.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei 112]
          Length = 389

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 148/343 (43%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRV     K    +  G  + +
Sbjct: 51  RTVDVPLALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIEL 110

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P +                       + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 111 LPELLPEQL--------------AFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 156

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 157 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYF 216

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +L WG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 217 ALAWGRMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVS 272

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 273 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 332

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 333 HPASGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 375


>gi|254189036|ref|ZP_04895547.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pasteur 52237]
 gi|157936715|gb|EDO92385.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pasteur 52237]
          Length = 395

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 148/343 (43%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRV     K    +  G  + +
Sbjct: 57  RTVDVPLALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIEL 116

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P +                       + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 117 LPELLPEQL--------------AFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 162

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 163 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYF 222

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +L WG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 223 ALAWGRMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVS 278

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 279 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 338

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 339 HPASGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 381


>gi|317492376|ref|ZP_07950805.1| RluA family pseudouridine synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316919715|gb|EFV41045.1| RluA family pseudouridine synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 318

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 109/321 (33%), Positives = 171/321 (53%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V+ V +  DE   R+D + +N    +    + +I+R G+VRV+KKR+K   ++QSG  
Sbjct: 6   TSVKLVTIAADEAGQRIDNFLRNQLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQSGDE 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       I E+     S  L K +  L   +++ED  + V NKP+G +V GGSG
Sbjct: 66  VRIPPVR------IAERDEAPVSAKLDKVA-ALNDCIIFEDDYLLVLNKPSGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD+ETSG+L+VA+ R+A + L E  RM+ +QK Y 
Sbjct: 119 LSFGVIEGLRA-LRPEARFLELVHRLDRETSGVLLVAKKRSALRALHEQLRMKGMQKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + +   LLK     G+ +  V         + + FKV + F +    ++
Sbjct: 178 ALVRGQWQSHCKVVQAPLLKNILQSGERIVRVNAE---GKPSETRFKVEERF-ENATLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D +Y    F         ++L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHTLHAGHPIAFDDRYGDREFDSELKGTGLDRLFLHAAALRFEHPNTG 293

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             +++ APL   +    D L 
Sbjct: 294 ETMRVEAPLDKKLRHCLDVLR 314


>gi|329889168|ref|ZP_08267511.1| pseudouridine synthase, RluA family protein [Brevundimonas diminuta
           ATCC 11568]
 gi|328844469|gb|EGF94033.1| pseudouridine synthase, RluA family protein [Brevundimonas diminuta
           ATCC 11568]
          Length = 331

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 121/326 (37%), Positives = 182/326 (55%), Gaps = 8/326 (2%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   VQ + V  DE+++RLDRWFK  +PH+  + ++K+ RSGQ+RVD  RVK  +R+ +G
Sbjct: 1   MSREVQTLYVAEDEDDIRLDRWFKRRWPHLTHIQVEKMARSGQIRVDGSRVKPQDRLTAG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             VR+PP+ +A        K  D      +   + KS++LYED  +   NKP G++VQGG
Sbjct: 61  AAVRVPPLPDANPR-----KPGDLHELSERDIAYAKSLVLYEDHMVIALNKPHGLAVQGG 115

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +    HID  L +W +    +PRL HRLD++TSG+L++ +   AA+ L  +F  R+ +K 
Sbjct: 116 TKTTKHIDRLLSAWGEGMD-RPRLVHRLDRDTSGVLLLGKGPEAAKRLAGAFARRQAKKT 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G PK     I   L K      + +   +  +     A + F  I   A +  W
Sbjct: 175 YWAIVIGNPKPSAGQIDMALKKTGINDFEMMRPAEPKDPKGEPAETAFATISRAAHRAAW 234

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P TGRTHQLR H   +G PI+GD KY  +     + P+  KL LHAR ++L HP G
Sbjct: 235 MALRPFTGRTHQLRAHMAAIGHPILGDPKYGDDKSRELSGPL--KLQLHARRIELDHPGG 292

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDR 328
           G+L + APL   M   ++  GF  D 
Sbjct: 293 GKLIVEAPLSPEMKAGFNHFGFSEDE 318


>gi|329851361|ref|ZP_08266118.1| pseudouridine synthase, RluA family protein [Asticcacaulis
           biprosthecum C19]
 gi|328840207|gb|EGF89779.1| pseudouridine synthase, RluA family protein [Asticcacaulis
           biprosthecum C19]
          Length = 334

 Score =  281 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 120/323 (37%), Positives = 188/323 (58%), Gaps = 6/323 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   V+ + V   E+ +R+DR+FK  +PH+N V L K+LRSGQVRVD  RVK + R+ +G
Sbjct: 1   MSNEVKTLYVAEGEDGIRVDRFFKRRWPHVNHVQLNKLLRSGQVRVDGGRVKADTRLATG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VR+PP+    +   ++++  + S    +   + +S++LYED  +   NKP+G++VQGG
Sbjct: 61  QTVRVPPLPAVPDQDQQKRERAELS---PQEIRYARSLVLYEDEDVIAINKPSGLAVQGG 117

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +    H+D  L +W +   ++PRL HRLD++TSG+L++ ++ +AA  L  +F  RR  K 
Sbjct: 118 TKTKNHVDRLLSAWGEGL-ERPRLVHRLDRDTSGVLLLGKSPSAAARLAGAFAKRRANKT 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G PK ++  I   L+KK     + V      E GA  A + +  I     +  W
Sbjct: 177 YWALVVGNPKPEEGYIDTPLIKKGFHDREIVQPADPKEPGAEPAETEYVTIGRAGPRVAW 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++PHTGRTHQLR H   +G  I+GD KY  +   + +  +   L LH R ++LPHP  
Sbjct: 237 MGLRPHTGRTHQLRAHMQAIGHSILGDPKYGNDESRSLSEGL--GLQLHHRRIELPHPTQ 294

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G L + APL   +   +D  GF+
Sbjct: 295 GTLIVEAPLDPVIKAGFDRFGFE 317


>gi|229146464|ref|ZP_04274835.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-ST24]
 gi|228637097|gb|EEK93556.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           BDRD-ST24]
          Length = 302

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 144/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVVAEQKNERIDKFVAGINNEWSRTQVQQWIKDNVVTVNGKAVKGNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|67641328|ref|ZP_00440109.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           mallei GB8 horse 4]
 gi|121600453|ref|YP_993132.1| RluA family pseudouridine synthase [Burkholderia mallei SAVP1]
 gi|124385530|ref|YP_001026092.1| RluA family pseudouridine synthase [Burkholderia mallei NCTC 10229]
 gi|126448439|ref|YP_001080638.1| RluA family pseudouridine synthase [Burkholderia mallei NCTC 10247]
 gi|134277051|ref|ZP_01763766.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 305]
 gi|167902420|ref|ZP_02489625.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei NCTC 13177]
 gi|254177619|ref|ZP_04884274.1| pseudouridine synthase, RluA family [Burkholderia mallei ATCC
           10399]
 gi|254199929|ref|ZP_04906295.1| pseudouridine synthase, RluA family [Burkholderia mallei FMH]
 gi|254206262|ref|ZP_04912614.1| pseudouridine synthase, RluA family [Burkholderia mallei JHU]
 gi|254260754|ref|ZP_04951808.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1710a]
 gi|254358323|ref|ZP_04974596.1| pseudouridine synthase, RluA family [Burkholderia mallei
           2002721280]
 gi|121229263|gb|ABM51781.1| pseudouridine synthase, RluA family [Burkholderia mallei SAVP1]
 gi|124293550|gb|ABN02819.1| pseudouridine synthase, RluA family [Burkholderia mallei NCTC
           10229]
 gi|126241309|gb|ABO04402.1| pseudouridine synthase, RluA family [Burkholderia mallei NCTC
           10247]
 gi|134250701|gb|EBA50780.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 305]
 gi|147749525|gb|EDK56599.1| pseudouridine synthase, RluA family [Burkholderia mallei FMH]
 gi|147753705|gb|EDK60770.1| pseudouridine synthase, RluA family [Burkholderia mallei JHU]
 gi|148027450|gb|EDK85471.1| pseudouridine synthase, RluA family [Burkholderia mallei
           2002721280]
 gi|160698658|gb|EDP88628.1| pseudouridine synthase, RluA family [Burkholderia mallei ATCC
           10399]
 gi|238522242|gb|EEP85688.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           mallei GB8 horse 4]
 gi|254219443|gb|EET08827.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1710a]
          Length = 389

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 148/343 (43%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRV     K    +  G  + +
Sbjct: 51  RTVDVPLALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIEL 110

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P +                       + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 111 LPELLPEQL--------------AFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 156

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 157 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYF 216

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +L WG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 217 ALAWGRMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVS 272

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 273 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 332

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 333 HPASGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 375


>gi|293553487|ref|ZP_06674115.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1039]
 gi|291602364|gb|EFF32588.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E1039]
          Length = 303

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 149/327 (45%), Gaps = 36/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT ++  +     E+ R+D+   N +   +   +Q  L++G V V+ + VK N +++ G 
Sbjct: 1   MTELKTTI---HHESGRIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVKANYKVKQGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +               ++     L    + +   ++YED  + V NKP G+ V   +
Sbjct: 58  DITV---------------LIPEPETLDVVPENIPLTIVYEDEDVAVINKPQGMVVHPSA 102

Query: 124 GIAY-HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G  +  +   L   +          +P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 103 GHTHGTMVNALMYHIKDLSTINGVIRPGIVHRIDKDTSGLLMVAKNDQAHESLAQQLKDK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G   ++K  I   + + S        +     +    A++HF V++ F 
Sbjct: 163 TSLRKYVALVHGEIPHEKGTINAPIGR-SKENRKMQAIR----EDGKPAVTHFTVLERF- 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E++  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +  
Sbjct: 217 EGFTLVELKLETGRTHQIRVHMKYIGYPLAGDPVYGPK-----KTLKGNGQFLHAQMLGF 271

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLG 323
            HP    ++   APLP    KT + L 
Sbjct: 272 THPTTNEKMFFEAPLPEVFEKTLEKLR 298


>gi|284007272|emb|CBA72588.1| 23S rRNA pseudouridylate synthase C [Arsenophonus nasoniae]
          Length = 315

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 107/325 (32%), Positives = 172/325 (52%), Gaps = 14/325 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M +   VQ+V ++NDE   R+D +       +    + +I+R G+VR++  R+K   +IQ
Sbjct: 1   MKIQNQVQFVTIDNDEAGQRIDNFLLTRLKGVPKSMIYRIIRKGEVRINSGRIKPEYKIQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G ++RIPPV  A      E++    S  L K +  L   +LYED  + V NKP+G++V 
Sbjct: 61  AGDLIRIPPVRQA------EKQQTVISAKLDKVA-ALSDCILYEDDHLLVLNKPSGMAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+ + I   L+  +  + +   L HRLD+ETSG+L++A+ R+A + L +  R++++Q
Sbjct: 114 GGSGVNFGIIEALR-ILRPEARFLELVHRLDRETSGVLLIAKKRSALRVLHQQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G   +  + I   LLK     G+ +  V        Y+ +HFK+ + F+   
Sbjct: 173 KQYLALVKGQWPSHIKVIQAPLLKNILQSGERIVKV---GTDGKYSETHFKIEERFS-NA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVHA +   PI  D++Y   +F          +L+LHA  + L H
Sbjct: 229 TLVKASPITGRTHQIRVHAQYAKHPIACDNRYGDLDFDQQLAITGLKRLFLHASSLILIH 288

Query: 300 PEG-GRLQITAPLPAHMVKTWDSLG 323
           P    RL   APL   +      L 
Sbjct: 289 PSSEERLTFNAPLDQQLKSCLAILR 313


>gi|125973425|ref|YP_001037335.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           thermocellum ATCC 27405]
 gi|256004403|ref|ZP_05429384.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281417627|ref|ZP_06248647.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|125713650|gb|ABN52142.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           thermocellum ATCC 27405]
 gi|255991687|gb|EEU01788.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281409029|gb|EFB39287.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|316940339|gb|ADU74373.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           1313]
          Length = 303

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 86/325 (26%), Positives = 156/325 (48%), Gaps = 32/325 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +++ ++E  +R+D W        +   +QK++  G + V+ K VK N +I+    + 
Sbjct: 1   MEEIILVSNESGIRIDAWLCGKVKDYSRSYIQKLINDGMILVNGKPVKSNYKIKQNDEI- 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
                      I E ++LD        ++ +   +LYED  I V +KP G+ V   +G  
Sbjct: 60  --------LARIPEPQVLDV------VAEDIDVPILYEDEHIIVVDKPKGMVVHPAAGNY 105

Query: 126 -AYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  LK    +        +P + HR+D++TSG+LVVA++ AA + L+E  +   I
Sbjct: 106 SGTLVNALLKHCGTNLSNINGIIRPGIVHRIDKDTSGVLVVAKSNAAHEGLSEKLKDHDI 165

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +++Y ++V GI +     I   + +   +    + V   N K    A++ FKV++ F + 
Sbjct: 166 ERVYIAVVHGIIREDYGKIDAPIGRH-PVDRKKMAV---NTKNGRRAVTRFKVLERF-KD 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
             ++E    TGRTHQ+RVH  ++G PI+GD  Y             N   LHA+ +   H
Sbjct: 221 ATYIEATLETGRTHQIRVHMSYIGFPIIGDTVYGRKND----IYNINGQALHAKKLGFVH 276

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  G  ++  +PLP +  +  + L 
Sbjct: 277 PIKGEYMEFESPLPEYFKELLEKLR 301


>gi|260773154|ref|ZP_05882070.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           metschnikovii CIP 69.14]
 gi|260612293|gb|EEX37496.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           metschnikovii CIP 69.14]
          Length = 318

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 106/325 (32%), Positives = 181/325 (55%), Gaps = 19/325 (5%)

Query: 1   MSLMTY----VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN 56
           M++M+     VQ+V ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK  
Sbjct: 1   MAVMSEIKTQVQFVDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAE 60

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
            ++ +G  +RIPPV   +N    + +    S+ L + ++ L++ ++YED  + + NKP+G
Sbjct: 61  YKLAAGDSIRIPPVTMEVN----DSEPAAPSIKLNRVAE-LEACIVYEDDHLLILNKPSG 115

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            +V GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR 
Sbjct: 116 TAVHGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFRE 174

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + +QK Y++LV G      + +   LLK        ++ + +       + + F+V++ F
Sbjct: 175 KTVQKYYFALVMGRWPANVKVVNAPLLKNE------INSIVRVNPNGKPSETRFRVLEQF 228

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYM 295
           AQ    L+  P TGRTHQ+RVH  + G PI  D +Y       + S    N+L+LHA  +
Sbjct: 229 AQ-ATLLQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYVSQFSINRLFLHAANI 287

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTW 319
              HP  G ++ I+APL A + +  
Sbjct: 288 QFMHPATGDKMDISAPLDASLERAL 312


>gi|226197455|ref|ZP_03793032.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pakistan 9]
 gi|225930834|gb|EEH26844.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pakistan 9]
          Length = 389

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 148/343 (43%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRV     K    +  G  + +
Sbjct: 51  RTVDVPLALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIEL 110

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P +                       + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 111 LPELLPEQL--------------AFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 156

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 157 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYF 216

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +L WG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 217 ALAWGRMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVS 272

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 273 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 332

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 333 HPASGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 375


>gi|229541180|ref|ZP_04430240.1| pseudouridine synthase, RluA family [Bacillus coagulans 36D1]
 gi|229325600|gb|EEN91275.1| pseudouridine synthase, RluA family [Bacillus coagulans 36D1]
          Length = 303

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 86/327 (26%), Positives = 152/327 (46%), Gaps = 34/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  + + ++E  E N RLD+   +     +   +Q+ ++ G + V+ K+ K N R+Q+G 
Sbjct: 1   MEKMDHTILE-HEANERLDKMVSSIREEWSRSQVQQWIKDGDITVNGKKEKANYRLQTGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V I          + E ++ D         + L   + YED+ + V NKP G+ V   +
Sbjct: 60  LVEIE---------VPEPELPD------IEPEDLHLDIYYEDADVLVVNKPKGMVVHPSN 104

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHFTGTLVNGLMYHCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDYAHEKLAAQLSEK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y++LV G   ++   I   + +        + VV         A++HF V++ F 
Sbjct: 165 TVTRKYFALVHGNIPHEAGTIDAPIGRD-PADRQRMAVVD----NGKDAVTHFHVLERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            ++ ++E +  TGRTHQ+RVH  ++G P+ GD KY      +F         LHA  +  
Sbjct: 219 DRYTFIECRLETGRTHQIRVHMKYIGHPLAGDPKYGPKKTIDF-----GGQALHAGVLGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  L   APLP       +++ 
Sbjct: 274 CHPRTGETLTFEAPLPDDFAHLLNTMR 300


>gi|262170983|ref|ZP_06038661.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           MB-451]
 gi|261892059|gb|EEY38045.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           MB-451]
          Length = 316

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 104/324 (32%), Positives = 177/324 (54%), Gaps = 15/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKTIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEATPPSTKLNKVAE-LEHCIVYEDEHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G    + + +   LLK        V+ + +       + + F++++ F +   
Sbjct: 177 YYYALVMGHWDPECKVVNAPLLKNE------VNSIVRVNPNGKPSETRFRILEKFTE-AT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   HP
Sbjct: 230 LVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAKFGIERLFLHAANIQFVHP 289

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
                L+I APL  H+ +    + 
Sbjct: 290 ASEEKLEIHAPLEVHLEQALTKMR 313


>gi|148544158|ref|YP_001271528.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri DSM 20016]
 gi|184153530|ref|YP_001841871.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227364587|ref|ZP_03848648.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM2-3]
 gi|325682298|ref|ZP_08161815.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
 gi|148531192|gb|ABQ83191.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri DSM 20016]
 gi|183224874|dbj|BAG25391.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227070424|gb|EEI08786.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM2-3]
 gi|324978137|gb|EGC15087.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
          Length = 303

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 89/326 (27%), Positives = 148/326 (45%), Gaps = 33/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+    + ++ +    R+D+   +H+   +   +Q  +  G V V+ K+VK   ++  G 
Sbjct: 1   MSEELELTIDGEMVG-RIDKQLGHHFDQFSRSQIQHWIEDGHVLVNGKQVKPKYKLLVGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V+I               I +    +    + +   ++YED  + V NKP G+ V    
Sbjct: 60  HVQI---------------IPEEPQKIDLAPEDIPLDIVYEDDDVIVVNKPQGMVVHPAP 104

Query: 124 GIAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G   H   +  L     S      +P + HR+D++TSG+L+VA+   A + LT   + + 
Sbjct: 105 GHPDHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKT 164

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LV G+ K  K  I   L +          VV        +A++HF V++ F +
Sbjct: 165 NKREYVALVHGVIKEDKGTIDAPLGRSLKDRKKQAVVV-----DGRHAVTHFNVLERF-K 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +  Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  YLHAR +   
Sbjct: 219 NYTLVACQLETGRTHQIRVHMKYIGHPLAGDPLYGPR-----KTLAGNGQYLHARLLGFK 273

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +  TAPLPA+ VK  + L 
Sbjct: 274 HPRTGKEMVFTAPLPAYFVKMLEHLR 299


>gi|254482018|ref|ZP_05095260.1| pseudouridine synthase, RluA family [marine gamma proteobacterium
           HTCC2148]
 gi|214037708|gb|EEB78373.1| pseudouridine synthase, RluA family [marine gamma proteobacterium
           HTCC2148]
          Length = 318

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 103/318 (32%), Positives = 164/318 (51%), Gaps = 14/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+++ V+ +    RLD +       +    L + LR G++RV+K RVK + R+ +G +VR
Sbjct: 11  VRHLTVDENSSGQRLDNFLTRELKGVPRTRLYRALRKGEIRVNKGRVKADYRLVTGDLVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++     D        S+ LK  ++YED  + V +KP+G++V GGSG+ 
Sbjct: 71  IPP--------LRTPAPSDPPTIPRYWSEQLKQRVIYEDGGLLVVDKPSGLAVHGGSGLN 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+  + S+ +   L HRLD++TSG+++VAR  A  + L    R   + K Y +L
Sbjct: 123 FGMIESLRQ-IRSEDRYLELVHRLDRDTSGLIMVARKPAILRELHRQLREDHVDKRYLAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     K  +   L K     G+ +  V    K    +I+ F V++ F +    +E +
Sbjct: 182 VAGKWPRSKVRVDAPLQKNVLQSGERMVRV---AKEGKRSITDFTVVERF-KGATLVEAK 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-QNKLYLHARYMDLPHPEGGRL 305
           P TGRTHQ+RVHALH G P++GD KY +         I   +L+LHAR +    P  GR+
Sbjct: 238 PVTGRTHQIRVHALHAGFPLLGDSKYGSPKGEALCEQIGLKRLFLHARALRFKLPGVGRM 297

Query: 306 QITAPLPAHMVKTWDSLG 323
           ++ APL   +    D L 
Sbjct: 298 ELEAPLDKDLEMALDKLR 315


>gi|197284738|ref|YP_002150610.1| 23S rRNA pseudouridylate synthase C [Proteus mirabilis HI4320]
 gi|227357743|ref|ZP_03842092.1| ribosomal large subunit pseudouridine synthase C [Proteus mirabilis
           ATCC 29906]
 gi|194682225|emb|CAR41940.1| ribosomal large subunit pseudouridine synthase C [Proteus mirabilis
           HI4320]
 gi|227162072|gb|EEI47086.1| ribosomal large subunit pseudouridine synthase C [Proteus mirabilis
           ATCC 29906]
          Length = 317

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 105/325 (32%), Positives = 172/325 (52%), Gaps = 14/325 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     VQ+V ++ DE   R+D +       +    + +I+R G+VRV+K R+K   ++ 
Sbjct: 1   MKSFNQVQFVTIDGDEAGQRIDNFLLARLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLA 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  +RIPPV       + E++    S  L K S  L   +LYED  + + NKP+G +V 
Sbjct: 61  AGDSIRIPPVR------VAEKEEHAVSPKLEKVS-ALAECILYEDEHVMLINKPSGTAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HRLD++TSG+L++A+ R+A + L E  R++++Q
Sbjct: 114 GGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLIAKKRSALRSLHEQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + +   LLK     G+ V  V         + + FKV + F +  
Sbjct: 173 KDYLALVRGQWQSHTKVVQAPLLKNILQSGERVVKVSSE---GKPSETRFKVEERF-EFA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH LH G PI  D +Y   +F     S   N+L+LHA  +   H
Sbjct: 229 TLVKASPVTGRTHQIRVHTLHAGHPIAFDDRYGDRDFDTQLASTKLNRLFLHASSLTFIH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  G  ++I AP+   +      L 
Sbjct: 289 PSTGEKMRIEAPMDKTLRYCLQVLR 313


>gi|255659722|ref|ZP_05405131.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
 gi|260848296|gb|EEX68303.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
          Length = 308

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 98/335 (29%), Positives = 154/335 (45%), Gaps = 34/335 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS  T V       D++  RLDR+     P ++  ++QK++  GQ  V  +  K N ++Q
Sbjct: 1   MSDSTKVYT----ADQDGERLDRFLTRMEPTLSRAHVQKVIAEGQALVSGRVRKANYKLQ 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ V           I+ E   LD               +LYEDS I V NK  G+ V 
Sbjct: 57  AGEKVTFHLPEAKPVEILPEDIPLD---------------ILYEDSDIIVINKARGMVVH 101

Query: 121 GGSGI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             +GI     ++  L    D  G     +P + HRLD++TSG++V A+  AA   L E  
Sbjct: 102 PATGIYTGTLVNALLYHCKDLSGINGEIRPGIVHRLDKDTSGVMVAAKNDAAHLDLAEQI 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R +   +IY ++V G  + +   I   + +        + +V ++      A++HF+V++
Sbjct: 162 RTKAAHRIYRAIVCGNIREEAGVIKGDIGRH-PTDRKKMAIVHEH---GKPAVTHFRVLE 217

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F   +  +E +  TGRTHQ+RVH   +G P++GD KY       F         LH+  
Sbjct: 218 RFG-AYTLVECRLETGRTHQIRVHMASIGHPVLGDPKYGPRKACPF---AIKGQALHSLQ 273

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           + L HP     +  TAPLP  M K   +L  K+ R
Sbjct: 274 LTLTHPRTREVMTFTAPLPEDMEKILKALRAKFQR 308


>gi|17986660|ref|NP_539294.1| ribosomal large subunit pseudouridine synthase D [Brucella
           melitensis bv. 1 str. 16M]
 gi|225853117|ref|YP_002733350.1| pseudouridine synthase [Brucella melitensis ATCC 23457]
 gi|17982277|gb|AAL51558.1| ribosomal large subunit pseudouridine synthase d [Brucella
           melitensis bv. 1 str. 16M]
 gi|225641482|gb|ACO01396.1| pseudouridine synthase, RluA family protein [Brucella melitensis
           ATCC 23457]
          Length = 347

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 89/348 (25%), Positives = 163/348 (46%), Gaps = 45/348 (12%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           T ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G
Sbjct: 12  TRLKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREG 71

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I               +L          + +   +LYED  + V NKPAG+ V  G
Sbjct: 72  MNIAI---------------VLPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPG 116

Query: 123 SG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +G      ++  +    DS       ++P + HRLD++TSG++VVA+   A +HL+E F 
Sbjct: 117 NGNWTGTLVNALIYQCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFA 176

Query: 176 MR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
                  +++ Y +LVWG+ +  +  +  +L + SH       VV +  + A +AI+H+ 
Sbjct: 177 DHGRTGDLERAYLALVWGMTERPQGTVDAYLGR-SHRDRTKQAVVHEEREDARHAITHYA 235

Query: 232 VIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTS 282
            ++ F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        
Sbjct: 236 TVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPE 295

Query: 283 PIQ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           P++      ++  LHA  +   HP     ++  APLP  M +  ++  
Sbjct: 296 PLKEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDMEQLLENFR 343


>gi|126438505|ref|YP_001059203.1| RluA family pseudouridine synthase [Burkholderia pseudomallei 668]
 gi|167738292|ref|ZP_02411066.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei 14]
 gi|167815478|ref|ZP_02447158.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei 91]
 gi|167845428|ref|ZP_02470936.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei B7210]
 gi|126217998|gb|ABN81504.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 668]
          Length = 389

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 148/343 (43%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRV     K    +  G  + +
Sbjct: 51  RTVDVPLALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIEL 110

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P +                       + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 111 LPELLPEQL--------------AFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 156

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 157 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYF 216

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +L WG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 217 ALAWGRMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVS 272

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 273 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 332

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 333 HPASGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 375


>gi|254708671|ref|ZP_05170482.1| RluA family pseudouridine synthase [Brucella pinnipedialis B2/94]
 gi|254714518|ref|ZP_05176329.1| RluA family pseudouridine synthase [Brucella ceti M644/93/1]
 gi|254717416|ref|ZP_05179227.1| RluA family pseudouridine synthase [Brucella ceti M13/05/1]
 gi|256030197|ref|ZP_05443811.1| RluA family pseudouridine synthase [Brucella pinnipedialis
           M292/94/1]
 gi|256160371|ref|ZP_05458061.1| RluA family pseudouridine synthase [Brucella ceti M490/95/1]
 gi|256255579|ref|ZP_05461115.1| RluA family pseudouridine synthase [Brucella ceti B1/94]
 gi|261219246|ref|ZP_05933527.1| pseudouridine synthase [Brucella ceti M13/05/1]
 gi|261316161|ref|ZP_05955358.1| pseudouridine synthase [Brucella pinnipedialis B2/94]
 gi|261322307|ref|ZP_05961504.1| pseudouridine synthase [Brucella ceti M644/93/1]
 gi|265987225|ref|ZP_06099782.1| pseudouridine synthase [Brucella pinnipedialis M292/94/1]
 gi|265998740|ref|ZP_06111297.1| pseudouridine synthase [Brucella ceti M490/95/1]
 gi|260924335|gb|EEX90903.1| pseudouridine synthase [Brucella ceti M13/05/1]
 gi|261294997|gb|EEX98493.1| pseudouridine synthase [Brucella ceti M644/93/1]
 gi|261295384|gb|EEX98880.1| pseudouridine synthase [Brucella pinnipedialis B2/94]
 gi|262553429|gb|EEZ09198.1| pseudouridine synthase [Brucella ceti M490/95/1]
 gi|264659422|gb|EEZ29683.1| pseudouridine synthase [Brucella pinnipedialis M292/94/1]
          Length = 334

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 88/346 (25%), Positives = 162/346 (46%), Gaps = 45/346 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMN 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L          + +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLSEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +    DS       ++P + HRLD++TSG++VVA+   A +HL+E F   
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADH 165

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                +++ Y +LVWG+ +  +  +  +L + SH       VV +  + A +AI+H+  +
Sbjct: 166 GRTGDLERAYLALVWGMTERPQGTVDAYLGR-SHRDRTKQAVVHEEREDARHAITHYATV 224

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPI 284
           + F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        P+
Sbjct: 225 EKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPEPL 284

Query: 285 Q------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +      ++  LHA  +   HP     ++  APLP  M +  ++  
Sbjct: 285 KEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDMEQLLENFR 330


>gi|302386409|ref|YP_003822231.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
 gi|302197037|gb|ADL04608.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
          Length = 304

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 83/324 (25%), Positives = 148/324 (45%), Gaps = 32/324 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q  VV  +E  +R+DR+  +    I+   LQK+L+   V V++K VK N ++ +G  + +
Sbjct: 3   QEYVVAPEEAGVRIDRYLSDRCQDISRSYLQKLLKEQSVLVEEKPVKSNYKVNAGDRISV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                              S       + +   ++YED  I + NKP G+ V   +G   
Sbjct: 63  FF---------------PESKEPEIQPEDIPLNIIYEDKDIILINKPKGMVVHPAAGHYS 107

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++G +              +P + HR+D +T+G+L+V +   A   ++E  +   I 
Sbjct: 108 GTLVNGLMSHCRSELSGINGVMRPGIVHRIDMDTTGVLIVCKNDMAHSSISEQLKEHSIT 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G+ K  +  +   + +   +    + +   NEK    A++H++V++ F Q F
Sbjct: 168 RKYAAIVHGVLKEDEGTVNAPIGRH-PVDRKKMSI---NEKNGREAVTHYRVLERFKQ-F 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++E Q  TGRTHQ+RVH   +G P++GD  Y  +              LHA  + + HP
Sbjct: 223 TYIECQLETGRTHQIRVHMASIGHPLLGDSVYGPSK----CPFRLTGQTLHAGILGIIHP 278

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  ++ TAPLP +       L 
Sbjct: 279 RTGEYMEFTAPLPDYFEDLLRILR 302


>gi|167893970|ref|ZP_02481372.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei 7894]
 gi|167918689|ref|ZP_02505780.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei BCC215]
 gi|237812527|ref|YP_002896978.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei MSHR346]
 gi|254179573|ref|ZP_04886172.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1655]
 gi|184210113|gb|EDU07156.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1655]
 gi|237504431|gb|ACQ96749.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei MSHR346]
          Length = 389

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 148/343 (43%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRV     K    +  G  + +
Sbjct: 51  RTVDVPLALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIEL 110

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P +                       + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 111 LPELLPEQL--------------AFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 156

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 157 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYF 216

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +L WG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 217 ALAWGRMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVS 272

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 273 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 332

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 333 HPASGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 375


>gi|167040454|ref|YP_001663439.1| RluA family pseudouridine synthase [Thermoanaerobacter sp. X514]
 gi|300914505|ref|ZP_07131821.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X561]
 gi|307724259|ref|YP_003904010.1| RluA family pseudouridine synthase [Thermoanaerobacter sp. X513]
 gi|166854694|gb|ABY93103.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X514]
 gi|300889440|gb|EFK84586.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X561]
 gi|307581320|gb|ADN54719.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X513]
          Length = 305

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 87/331 (26%), Positives = 149/331 (45%), Gaps = 35/331 (10%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  +V+  E ++E  R+D +            ++K++    V V+ K VK + +++ 
Sbjct: 1   MNIVDKIVLQGEKEDEGKRIDVFLAAEL-DYTRSYIKKLIVDELVFVNGKTVKPSYKVKE 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V +         ++ E   LD               +LYED  I V NKP G+ V  
Sbjct: 60  NDEVVVNIPEAEKIDVLPENIPLD---------------ILYEDDDIIVINKPQGMVVHP 104

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++  L    +  G     +P + HRLD++TSG++VVA+   A   L+   +
Sbjct: 105 APGNYSGTLVNALLYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y ++V G+ K+++  I   + +   +    + V+    +   YA++ +KV++ 
Sbjct: 165 ERSVFKKYVAIVEGVIKDEEGKIEAPIGRH-PVDRKKMAVI----EDGRYALTLYKVLER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F +    +E    TGRTHQ+RVH  ++G PIVGDH Y    +            LH+  +
Sbjct: 220 FKEN-TLVEAVIKTGRTHQIRVHMAYIGHPIVGDHVYGFKRQ----KFKLEGQALHSSVL 274

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
              HP  G  ++  APLP +  K  + L  K
Sbjct: 275 GFMHPTKGVYMEFEAPLPEYFKKLIEILRNK 305


>gi|237808945|ref|YP_002893385.1| pseudouridine synthase, RluA family [Tolumonas auensis DSM 9187]
 gi|237501206|gb|ACQ93799.1| pseudouridine synthase, RluA family [Tolumonas auensis DSM 9187]
          Length = 314

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 99/320 (30%), Positives = 170/320 (53%), Gaps = 15/320 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ++ ++ +++  R+D + K     +    + +ILR G+VRV+KKR+K   ++  G  
Sbjct: 6   PGVQFITIDAEQDGQRIDNFLKTQLKGVPKSLIYRILRKGEVRVNKKRIKPEYKLCVGDE 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+PP       + +E ++  S +   +    L   ++YED  I V NKP+G++V GGSG
Sbjct: 66  IRVPP-----VRVAEENELPSSKLGSVQ---ALAHQIIYEDEAIIVLNKPSGLAVHGGSG 117

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A +HL E  R++ ++K Y 
Sbjct: 118 LSFGVIEGLRA-LRPESRFLELVHRLDRDTSGLLLVAKKRSALKHLHEQLRVKTMRKQYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  +   + +   LLK     G+ +  V         + + F+++  FA     + 
Sbjct: 177 ALVRGQWQPHVKAVNAPLLKNILQSGERIVRVNSE---GKPSETRFQIMQKFAH-ATLVM 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D KY   +F         ++L+LHA  +   HP  G
Sbjct: 233 ASPITGRTHQIRVHTLHAGHPIACDDKYGERDFDEQVKKAGLHRLFLHAYRLTFTHPVTG 292

Query: 304 -RLQITAPLPAHMVKTWDSL 322
             + + APL   +    D L
Sbjct: 293 KEMSVEAPLDKELQSALDRL 312


>gi|86605450|ref|YP_474213.1| RluA family pseudouridine synthase [Synechococcus sp. JA-3-3Ab]
 gi|86553992|gb|ABC98950.1| pseudouridine synthase, RluA family [Synechococcus sp. JA-3-3Ab]
          Length = 310

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 88/328 (26%), Positives = 153/328 (46%), Gaps = 30/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSG 62
           M  ++ V V   ++ +RLDR      P ++   LQ+++R GQV ++ +     +R +Q+G
Sbjct: 1   MAEIRRVTVTEKQQGLRLDRGLAEQLPELSRSRLQQLIRQGQVWLNGQPCLDKDRPLQAG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +                +  +       + +   +LYED  + V NKP G+ V   
Sbjct: 61  DQIEVR---------------IPPATPTPLQPERIPLDILYEDEDLLVINKPRGLVVHPA 105

Query: 123 SGIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G A    +   L       G    Q+P + HRLD++T+G LV+A+   A QHL    + 
Sbjct: 106 PGHASGTLVHALLAHCPRLSGINGEQRPGIVHRLDKDTTGALVIAKHDQAHQHLQAQIQA 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           +  ++IY  +V+G P   +  I+  + +   +    + VV   +     A++H++V++  
Sbjct: 166 KTARRIYLGVVFGRPAQSQGTISAPIGRH-PVDRQKMAVVPPGQ--GRAAVTHWQVLERL 222

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  ++ +  TGRTHQ+RVHA H+  PIVGD  Y    +   +    +   LHA  + 
Sbjct: 223 G-NYTLMQFELETGRTHQIRVHAAHLRLPIVGDPLY---TQSKTSPVKLSGQALHAWKLS 278

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G+ LQ+TAPLP    +    L 
Sbjct: 279 FVHPRTGQPLQVTAPLPEEFERLLRQLR 306


>gi|27366288|ref|NP_761816.1| ribosomal large subunit pseudouridine synthase C [Vibrio vulnificus
           CMCP6]
 gi|320156795|ref|YP_004189174.1| ribosomal large subunit pseudouridine synthase C [Vibrio vulnificus
           MO6-24/O]
 gi|34395774|sp|Q8D8G1|RLUC_VIBVU RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|27362489|gb|AAO11343.1| Ribosomal large subunit pseudouridine synthase C [Vibrio vulnificus
           CMCP6]
 gi|319932107|gb|ADV86971.1| ribosomal large subunit pseudouridine synthase C [Vibrio vulnificus
           MO6-24/O]
          Length = 315

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 109/324 (33%), Positives = 176/324 (54%), Gaps = 16/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ V ++ D    R+D + +N    +    + +I+R G+VRV+KKRVK   ++ +
Sbjct: 3   EIRTKVQIVDIDEDMAGQRIDNFLRNQLKDVPKSMIYRIVRKGEVRVNKKRVKAEYKLAA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVRIPP       + K+      S  L K ++ L+ +++YED  + V NKP+G +V G
Sbjct: 63  GDVVRIPP-----VTLEKKDPETAPSTKLNKVAE-LQDLIIYEDDHLLVLNKPSGTAVHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 117 GSGLKFGAIEALRA-LRPEARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  KN  + +   LLK        V+ + +       + + FKVI+ F Q   
Sbjct: 176 YYFALVMGEWKNSCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKVIEKFPQ-AT 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T+    N+L+LHA  +   HP
Sbjct: 229 LVQASPITGRTHQIRVHTQYSGHPIAWDDRYGDRRFDAYTAQHGLNRLFLHAANIRFTHP 288

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
              + ++I AP+   + K   SL 
Sbjct: 289 ATEQPMEINAPMGEQLEKVVQSLR 312


>gi|254297450|ref|ZP_04964903.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           406e]
 gi|157806772|gb|EDO83942.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           406e]
          Length = 389

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 148/343 (43%), Gaps = 28/343 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRV     K    +  G  + +
Sbjct: 51  RTVDVPLALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIEL 110

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P +                       + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 111 LPELLPEQL--------------AFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 156

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 157 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYF 216

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +L WG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 217 ALAWGRMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVS 272

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLP 298
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L 
Sbjct: 273 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPGGFARQALHAWRLGLV 332

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 333 HPASGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 375


>gi|238894120|ref|YP_002918854.1| 23S rRNA pseudouridylate synthase C [Klebsiella pneumoniae
           NTUH-K2044]
 gi|238546436|dbj|BAH62787.1| 23S rRNA pseudouridylate synthase [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 317

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 107/326 (32%), Positives = 173/326 (53%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++
Sbjct: 1   MKTETPTVKMVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALSEVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + + + 
Sbjct: 173 QKDYLALVRGQWQSHTKVVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERY-EF 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F    ++   N+L+LHA  +   
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLSATGLNRLFLHAAALKFT 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  +++ APL   +      L 
Sbjct: 289 HPGSGEVMRVEAPLDNQLKHCLQVLR 314


>gi|52430462|ref|YP_089634.1| ribosomal large subunit pseudouridine synthase D [Brucella suis
           1330]
 gi|161619586|ref|YP_001593473.1| RluA family pseudouridine synthase [Brucella canis ATCC 23365]
 gi|163845235|ref|YP_001622890.1| RluA family pseudouridine synthase [Brucella suis ATCC 23445]
 gi|237816033|ref|ZP_04595029.1| pseudouridine synthase, RluA family [Brucella abortus str. 2308 A]
 gi|256370063|ref|YP_003107574.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella microti CCM 4915]
 gi|294850907|ref|ZP_06791583.1| ribosomal large subunit pseudouridine synthase D [Brucella sp. NVSL
           07-0026]
 gi|297248929|ref|ZP_06932637.1| ribosomal large subunit pseudouridine synthase D [Brucella abortus
           bv. 5 str. B3196]
 gi|47524301|gb|AAT34906.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella suis 1330]
 gi|161336397|gb|ABX62702.1| pseudouridine synthase, RluA family [Brucella canis ATCC 23365]
 gi|163675958|gb|ABY40068.1| pseudouridine synthase, RluA family [Brucella suis ATCC 23445]
 gi|237788696|gb|EEP62908.1| pseudouridine synthase, RluA family [Brucella abortus str. 2308 A]
 gi|256000226|gb|ACU48625.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Brucella microti CCM 4915]
 gi|294821550|gb|EFG38546.1| ribosomal large subunit pseudouridine synthase D [Brucella sp. NVSL
           07-0026]
 gi|297174062|gb|EFH33419.1| ribosomal large subunit pseudouridine synthase D [Brucella abortus
           bv. 5 str. B3196]
          Length = 347

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 89/348 (25%), Positives = 163/348 (46%), Gaps = 45/348 (12%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           T ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G
Sbjct: 12  TRLKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREG 71

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I               +L          + +   +LYED  + V NKPAG+ V  G
Sbjct: 72  MNIAI---------------VLPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPG 116

Query: 123 SG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +G      ++  +    DS       ++P + HRLD++TSG++VVA+   A +HL+E F 
Sbjct: 117 NGNWTGTLVNALIYHCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFA 176

Query: 176 MR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
                  +++ Y +LVWG+ +  +  +  +L + SH       VV +  + A +AI+H+ 
Sbjct: 177 DHGRTGDLERAYLALVWGMTERPQGTVDAYLGR-SHRDRTKQAVVHEEREDARHAITHYA 235

Query: 232 VIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTS 282
            ++ F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        
Sbjct: 236 TVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPE 295

Query: 283 PIQ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           P++      ++  LHA  +   HP     ++  APLP  M +  ++  
Sbjct: 296 PLKEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDMEQLLENFR 343


>gi|299535889|ref|ZP_07049209.1| putative RNA pseudouridine synthase ylyB [Lysinibacillus fusiformis
           ZC1]
 gi|298728641|gb|EFI69196.1| putative RNA pseudouridine synthase ylyB [Lysinibacillus fusiformis
           ZC1]
          Length = 303

 Score =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 146/330 (44%), Gaps = 34/330 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT V Y  +E  ++  R+D+   +     +   +   +  G ++V+   VK   ++++G 
Sbjct: 1   MTQVTY-TIEEQQQGERIDKALSSLQSEWSRTQIGNWISDGVIKVNGDAVKAKYKVKAGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I                +     L    + L   ++YED+ + V NKP G+ V    
Sbjct: 60  IIAID---------------VPEVEELDVVPENLDLDIVYEDADVLVVNKPKGMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHMGGTLVNGLMYHCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDTAHESLVNQLVNK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G   + K  I   + +          V         +A++HF+V++ F 
Sbjct: 165 TVTRKYIALVHGHIAHDKGTIDAPIGRDQKDRQKQAVV-----DNGKHAVTHFQVVERFG 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +F         LHA  +  
Sbjct: 220 D-YTLVECRLETGRTHQIRVHMNYIGFPLVGDPKYGPKKTIDF-----GGQVLHAATLGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            HP  G  L+   PLPA   +  + L  ++
Sbjct: 274 DHPSSGEYLEFETPLPADYEQLLNDLRNRH 303


>gi|218233909|ref|YP_002368692.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
 gi|229152090|ref|ZP_04280285.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           m1550]
 gi|218161866|gb|ACK61858.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
 gi|228631439|gb|EEK88073.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus cereus
           m1550]
          Length = 302

 Score =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 144/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAAEQKNERIDKFVTGINNEWSRTQVQQWIKDEVVTVNGKAVKGNYKVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + L   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++    A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKNAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|194468025|ref|ZP_03074011.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
 gi|194452878|gb|EDX41776.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
          Length = 303

 Score =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 89/326 (27%), Positives = 148/326 (45%), Gaps = 33/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+    + ++ +    R+D+   +H+   +   +Q  +  G V V+ K+VK   ++  G 
Sbjct: 1   MSEELELTIDGEMVG-RIDKQLGHHFDQFSRSQIQHWIEDGHVLVNGKQVKPKYKLLVGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V+I               I +    +    + +   ++YED  + V NKP G+ V    
Sbjct: 60  HVQI---------------IPEEPQKIDLAPEDIPLDIVYEDDDVIVVNKPQGMVVHPAP 104

Query: 124 GIAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G   H   +  L     S      +P + HR+D++TSG+L+VA+   A + LT   + + 
Sbjct: 105 GHPDHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKT 164

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LV G+ K  K  I   L +          VV        +A++HF V++ F +
Sbjct: 165 NKREYVALVHGVIKEDKGTIDAPLGRSLKDRKKQGVVV-----DGRHAVTHFNVLERF-K 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +  Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  YLHAR +   
Sbjct: 219 NYTLVACQLETGRTHQIRVHMKYIGHPLAGDPLYGPR-----KTLAGNGQYLHARLLGFK 273

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +  TAPLPA+ VK  + L 
Sbjct: 274 HPRTGKEMVFTAPLPAYFVKMLEHLR 299


>gi|328542559|ref|YP_004302668.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [polymorphum gilvum SL003B-26A1]
 gi|326412305|gb|ADZ69368.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Polymorphum gilvum SL003B-26A1]
          Length = 346

 Score =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 96/342 (28%), Positives = 159/342 (46%), Gaps = 46/342 (13%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRI 67
            + V  ++   RLD     H   ++   +Q ++RSG+V VD  K V+   R+  G  + +
Sbjct: 22  TLQVGAEDAGKRLDAVLAAHLADLSRTRVQALIRSGEVTVDGGKIVEPKYRVNEGATLAL 81

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           L          + +  +++YED  + V +KPAG+ V  G+G   
Sbjct: 82  G---------------LPEPEEAEPKGEDIPLVVVYEDDDLIVIDKPAGLVVHPGAGNWT 126

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-- 178
              ++  ++   DS       ++P + HRLD+ETSG+LVVA+T AA + L+E F      
Sbjct: 127 GTLVNALIRHCGDSLSGIGGVRRPGIVHRLDKETSGLLVVAKTDAAHKGLSEQFADHGRS 186

Query: 179 --IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             +++ Y +LVWG P   +  +   L + S      + VV+    G  +A++H++V++ F
Sbjct: 187 GPLERAYAALVWGAPATLRGTVDANLAR-SDANRQKISVVR---NGGRHAVTHWQVLERF 242

Query: 237 AQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQ--- 285
                      LE +  TGRTHQ+RVH  H+G P++GD  Y A F+     F  PI+   
Sbjct: 243 GPADQPAVASLLECRLETGRTHQIRVHMAHIGHPLIGDQIYGAGFRTKANRFPEPIRTHV 302

Query: 286 ---NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
               +  LHA  +   HP  G  L+  +P P    +   +L 
Sbjct: 303 GGFPRQALHAGLLAFAHPRTGETLRFESPYPDDFQQLLGALR 344


>gi|206577057|ref|YP_002239295.1| ribosomal large subunit pseudouridine synthase C [Klebsiella
           pneumoniae 342]
 gi|206566115|gb|ACI07891.1| ribosomal large subunit pseudouridine synthase C [Klebsiella
           pneumoniae 342]
          Length = 317

 Score =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 107/326 (32%), Positives = 172/326 (52%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++
Sbjct: 1   MKTETPTVKMVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALSEVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + + + 
Sbjct: 173 QKDYLALVRGQWQSHTKVVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERY-EF 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F    +    N+L+LHA  +   
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLSGTGLNRLFLHAAALKFT 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  +++ APL   +      L 
Sbjct: 289 HPGSGEVMRVEAPLDNQLKHCLQVLR 314


>gi|256752464|ref|ZP_05493322.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           CCSD1]
 gi|256748666|gb|EEU61712.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           CCSD1]
          Length = 305

 Score =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 88/331 (26%), Positives = 149/331 (45%), Gaps = 35/331 (10%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  VV+  E ++E  R+D +            ++K++    V V+ K VK + +++ 
Sbjct: 1   MNIVDKVVLQGEKEDEGKRIDVFLAAEL-DYTRSYIKKLIVDELVFVNGKTVKPSYKVKE 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V +         ++ E   LD               +LYED  I V NKP G+ V  
Sbjct: 60  NDEVVVNIPEAEKIDVLPENIPLD---------------ILYEDDDIIVINKPQGMVVHP 104

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++  L    +  G     +P + HRLD++TSG++VVA+   A   L+   +
Sbjct: 105 APGNYSGTLVNALLYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y ++V G+ K+++  I   + +   +    + V+    +   YA++ +KV++ 
Sbjct: 165 ERSVFKKYVAIVEGVIKDEEGKIEAPIGRH-PVDRKKMAVI----EDGRYALTLYKVLER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F +    +E    TGRTHQ+RVH  ++G PIVGDH Y    +            LH+  +
Sbjct: 220 FKEN-TLVEAVIKTGRTHQIRVHMAYIGHPIVGDHVYGFKRQ----KFKLEGQALHSSVL 274

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
              HP  G  ++  APLP +  K  + L  K
Sbjct: 275 GFMHPTKGVYMEFEAPLPEYFKKLIEILRNK 305


>gi|107029027|ref|YP_626122.1| pseudouridine synthase, RluD [Burkholderia cenocepacia AU 1054]
 gi|116689814|ref|YP_835437.1| RluA family pseudouridine synthase [Burkholderia cenocepacia
           HI2424]
 gi|254248088|ref|ZP_04941409.1| Pseudouridine synthase, RluD [Burkholderia cenocepacia PC184]
 gi|105898191|gb|ABF81149.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           cenocepacia AU 1054]
 gi|116647903|gb|ABK08544.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           cenocepacia HI2424]
 gi|124872864|gb|EAY64580.1| Pseudouridine synthase, RluD [Burkholderia cenocepacia PC184]
          Length = 402

 Score =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 145/328 (44%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +V VD    K    +  G  + +
Sbjct: 58  RVVEVPLSLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAPAKIRQPVPLGAKIAL 117

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 118 VP------DLLPEQ--------LAFTPEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWS 163

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 164 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 223

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG    ++  I   + +      +   +          A +HF+ +D      Q  
Sbjct: 224 FALVWGTMP-EEGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCLWQRQPV 279

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 280 SAIQCDLETGRTHQIRVHCAHAGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGL 339

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G+ +Q   PLP  M     +LGF
Sbjct: 340 VHPVTGKAMQWRCPLPDDMNTLVAALGF 367


>gi|297544813|ref|YP_003677115.1| RluA family pseudouridine synthase [Thermoanaerobacter mathranii
           subsp. mathranii str. A3]
 gi|296842588|gb|ADH61104.1| pseudouridine synthase, RluA family [Thermoanaerobacter mathranii
           subsp. mathranii str. A3]
          Length = 305

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 89/331 (26%), Positives = 149/331 (45%), Gaps = 35/331 (10%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  VV+  E ++E  R+D +            ++K++  G   V+ K VK + +++ 
Sbjct: 1   MNIVDKVVLQGEKEDEGKRIDVFLAAEL-DYTRSYIKKLIVDGLAFVNGKTVKPSYKVKE 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V +         ++ E   LD               +LYED  I V NKP G+ V  
Sbjct: 60  NDKVVVNIPEAEKIDVLPENIPLD---------------ILYEDDDIIVINKPQGMVVHP 104

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++  L    +  G     +P + HRLD++TSG++VVA+   A   L+   +
Sbjct: 105 APGNYSGTLVNALLYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y ++V G+ KN++E I   + +   +    + V+    +   YA++ +KV++ 
Sbjct: 165 ERSVFKKYVAIVEGVIKNEEEKIEAPIGRH-PVDRKKMAVI----EDGRYALTLYKVLER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F +    +E    TGRTHQ+RVH   +G P+VGD  Y    +            LH+R +
Sbjct: 220 FKEN-TLIEAVIKTGRTHQIRVHMAFIGHPVVGDPVYGFKKQ----KFKLEGQALHSRVL 274

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
              HP  G  ++  APLP +  K  + L  K
Sbjct: 275 GFMHPTKGVYMEFEAPLPEYFKKLIEILRNK 305


>gi|221135371|ref|ZP_03561674.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase [Glaciecola sp. HTCC2999]
          Length = 316

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 102/319 (31%), Positives = 170/319 (53%), Gaps = 15/319 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V +V ++ +    R+D + K H   +    + +ILR G+VRV+KKR+K   ++Q+  V+
Sbjct: 9   QVSFVEIDPELAGQRIDNFLKTHLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLQAHDVI 68

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP+  +             +V L K +  ++  ++YED +I V NKP+G++V GGSG+
Sbjct: 69  RVPPIRVS-------DAPEPVNVKLDKVA-VMQDYIIYEDDRIMVINKPSGLAVHGGSGL 120

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L++ +    +   L HR+D++TSGIL+VA+ R+A +HL E  R +++QK Y +
Sbjct: 121 SFGLIEGLRA-LRPDAKFMELVHRIDRDTSGILLVAKRRSALRHLHEQLRDKKMQKRYHA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LVWG     +  +   LLK     G+ +  V         + + ++V+  FAQ    +E 
Sbjct: 180 LVWGQWPENRFKVKAPLLKNVLKSGERIVNVN---PEGKPSETRYRVLQAFAQ-TTLVEA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
            P TGRTHQ+RVH LH G PI GD KY   +      +    +L+LHA  +   HP+   
Sbjct: 236 SPITGRTHQIRVHCLHAGFPIGGDPKYNDIDGNAQLATQGLKRLFLHAHSLSFIHPKTLE 295

Query: 304 RLQITAPLPAHMVKTWDSL 322
           ++   AP    +      L
Sbjct: 296 QVTFKAPYDEQLTNIIAKL 314


>gi|254518704|ref|ZP_05130760.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
 gi|226912453|gb|EEH97654.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
          Length = 305

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 76/327 (23%), Positives = 148/327 (45%), Gaps = 30/327 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  + + + E +   +R+D++  N     +   +Q ++ SG + V+ K VK N ++++  
Sbjct: 1   MDELVFKITEEENIGIRIDKYLSNIIEGKSRSFIQGLIDSGAILVNNKEVKSNYKLRNHD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +   + L    + +   ++YED  + V NKP G+ V    
Sbjct: 61  EIIVS---------------MPEPIELDVEPEDIDLNIVYEDEDVIVLNKPQGVVVHPAP 105

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G L    D  G     +P + HR+D++TSGILV+A+   A  HL + F+  
Sbjct: 106 GNYSGTLVNGLLYHCKDLSGINGVIRPGIVHRIDKDTSGILVIAKNDDAHNHLAKQFKNH 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I++ Y++LV G     +  +   + +          +     +    A++H+ V++ + 
Sbjct: 166 SIKREYYALVEGKFSKIEGTVDKPIGRNKKDRLKMAIM-----EDGKRAVTHYNVLEQYN 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                ++    TGRTHQ+RVH   +G P+VGD  Y +N K  F         LHA+ +  
Sbjct: 221 NGTALVKCTLETGRTHQIRVHMASIGHPLVGDPLYNSNKKQKFK---LQGQVLHAKTLGF 277

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP     ++  + LP + ++  +++ 
Sbjct: 278 IHPRSNEYIEFDSELPKYYLELLENIR 304


>gi|127512523|ref|YP_001093720.1| RluA family pseudouridine synthase [Shewanella loihica PV-4]
 gi|126637818|gb|ABO23461.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           loihica PV-4]
          Length = 329

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 107/321 (33%), Positives = 167/321 (52%), Gaps = 13/321 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +  V+ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G 
Sbjct: 17  LNKVELVTIDEDNLGQRIDNFLVTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQDGD 76

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VRIPP       +   +     S  LTK S  L+  +L+ED  I V NKPAGI+V GGS
Sbjct: 77  IVRIPP-----VRVSASEDKPGPSAKLTKVSQ-LEGRILFEDKAIIVLNKPAGIAVHGGS 130

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+ + +   ++S    +     L HRLD+ETSG+L++A+ R A +HL +  R +++QK Y
Sbjct: 131 GVDFGVIEAMRSLRPQQKF-LELVHRLDKETSGVLLIAKKRRALKHLHDQLRYKKMQKDY 189

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G  +N  + I   LLK +   G+ +  V Q       + + FK++  + Q    +
Sbjct: 190 MALVRGEWQNHDKVINAPLLKLTLKSGERIVRVNQE---GKPSETRFKIMQRY-QGATLV 245

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +  P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP  
Sbjct: 246 QASPVTGRTHQIRVHCQYAGHPIACDEKYSEQKFDDAMRELGLNRLFLHAAQLKFTHPVS 305

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
              +Q+ APL   +    + L
Sbjct: 306 EEVMQVKAPLDKALQDLLNKL 326


>gi|260663035|ref|ZP_05863928.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
 gi|260552656|gb|EEX25656.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
          Length = 304

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 87/326 (26%), Positives = 148/326 (45%), Gaps = 33/326 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +    Q + V +     R+D+   +H+P  +   L++ +  G V V+ + VK   ++Q+G
Sbjct: 1   MDQTTQTLTVTDGMTG-RIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V I P               ++ V +    + +   ++YED  + V NKP G+ V   
Sbjct: 60  DRVVIEP---------------ETPVEIDLEPENIPLDIVYEDDDVLVVNKPQGMVVHPA 104

Query: 123 SGIAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G   H   +  +     S      +P + HR+D++TSG+L+VA+T  A + LT   + +
Sbjct: 105 PGHPNHTLVNALMYHAPLSSINGELRPGIVHRIDKDTSGLLMVAKTDRAHRSLTAQLKEK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G+ K  +  I   L +          VV     G  +AI+HF+V+  + 
Sbjct: 165 SNLREYVALVHGVIKENEGTIDAPLARSPKDRKKQAVVV-----GGRHAITHFRVLKRY- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q +  +  +  TGRTHQ+RVH  ++  P+ GD  Y         +   +  YLHAR +  
Sbjct: 219 QHYTLVACRLETGRTHQIRVHMKYINHPLAGDPLYGPR-----KTLPGHGQYLHARLLGF 273

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL 322
            HP  G  +  TAPLP +  +    L
Sbjct: 274 EHPVTGEEMVFTAPLPDYFEQMLSYL 299


>gi|323937826|gb|EGB34090.1| RluA family protein pseudouridine synthase [Escherichia coli E1520]
          Length = 319

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDSEFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|312172072|emb|CBX80329.1| pseudouridylate synthase [Erwinia amylovora ATCC BAA-2158]
          Length = 320

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 104/319 (32%), Positives = 172/319 (53%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  +R
Sbjct: 8   VHFIAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++  + S  L K +  L++ ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVR------VAEREEENVSPKLAKVA-ALEAAIIYEDDYLLVMNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+ V  V         + + FKV + +A     ++  
Sbjct: 180 VRGQWPSHVKAVRAPLLKNILQSGERVVKVSSE---GKPSETLFKVEERYA-IATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y  A F    +     +L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTLHAGHPIAFDDRYGEAGFDQQLSGTGLKRLFLHAAALRFTHPNTGEI 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           +++ APL   + +    L 
Sbjct: 296 MRVEAPLDEQLKRCLAVLR 314


>gi|304404034|ref|ZP_07385696.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
 gi|304347012|gb|EFM12844.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
          Length = 324

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 84/322 (26%), Positives = 142/322 (44%), Gaps = 34/322 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           VVE DE   RLD++    +    ++   +Q+ ++SG V V+    K  +R+++G V+ + 
Sbjct: 26  VVEVDEAGERLDKYVTESFADSAVSRTQIQEWIKSGAVLVNGTEAKAKHRLEAGDVITVE 85

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                   II E                +   ++YED  + V NK  G+ V    G    
Sbjct: 86  VPEPEPAEIIAEP---------------IPLNIVYEDEDVIVINKQRGLVVHPAPGHHSG 130

Query: 129 I--DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +  +    D  G     +P + HR+D++TSG+L+ A+  AA   L+   +   + + 
Sbjct: 131 TVVNALMYHCQDLSGINGSIRPGIVHRIDKDTSGLLMAAKNDAAHASLSAQLKEHTVTRK 190

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G   + +  +   + + S        +    +K + +A++HF VI+     +  
Sbjct: 191 YIALVHGNLPHDRGTVDAPIGRDSRDRK----MFAVTDKNSKHAVTHFSVIERL-DDYTV 245

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           LE+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N   LHA  +   HP  
Sbjct: 246 LELQLETGRTHQIRVHMKYIGHPLAGDPMYG-----RSKTVALNGQALHAAILGFNHPRT 300

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
              L+  AP+P  M     SL 
Sbjct: 301 NEYLEFEAPIPEDMENVLHSLR 322


>gi|218689038|ref|YP_002397250.1| 23S rRNA pseudouridylate synthase C [Escherichia coli ED1a]
 gi|306814065|ref|ZP_07448238.1| 23S rRNA pseudouridylate synthase C [Escherichia coli NC101]
 gi|218426602|emb|CAR07430.1| 23S rRNA pseudouridylate synthase [Escherichia coli ED1a]
 gi|305852702|gb|EFM53150.1| 23S rRNA pseudouridylate synthase C [Escherichia coli NC101]
          Length = 319

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDGEFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|117620828|ref|YP_856764.1| ribosomal large subunit pseudouridine synthase C [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117562235|gb|ABK39183.1| ribosomal large subunit pseudouridine synthase C [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 327

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 107/320 (33%), Positives = 171/320 (53%), Gaps = 15/320 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            VQ + +E + E  R+D + K     +    + +ILR G+VRV+KKR+K   ++ +G  V
Sbjct: 20  QVQLLTIEAEHEGQRIDNFLKTQLKGVPKSLIYRILRKGEVRVNKKRIKPEYKLCTGDEV 79

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A  + +        S NL      L+S +L+ED  + V NKP+G++V GGSG+
Sbjct: 80  RVPPVRVAEKNELP-------SANLGSIQR-LESQILFEDDAMIVLNKPSGMAVHGGSGL 131

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ ++K Y +
Sbjct: 132 SFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRVKTMRKQYLA 190

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  +   + +   L K     G+ V  V  +      + + F++   FA+    +E 
Sbjct: 191 LVRGQWQPHVKVVNAPLRKNDLQSGERVVRVSSD---GKPSETRFRIARQFAE-ATLVEC 246

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  H G PI  D KY  A F     S    +L+LHA  +   HP  GR
Sbjct: 247 SPITGRTHQIRVHTQHAGHPIACDDKYGEAAFDDKMRSHGLKRLFLHAWKLSFIHPADGR 306

Query: 305 -LQITAPLPAHMVKTWDSLG 323
            +Q+ APL   +    + L 
Sbjct: 307 EMQVEAPLAPELDDFLNKLA 326


>gi|146311257|ref|YP_001176331.1| 23S rRNA pseudouridylate synthase C [Enterobacter sp. 638]
 gi|145318133|gb|ABP60280.1| ribosomal large subunit pseudouridine synthase C [Enterobacter sp.
           638]
          Length = 315

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 107/326 (32%), Positives = 173/326 (53%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V + +DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++
Sbjct: 1   MKTETPSVKMVAIADDEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L + +LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLNKVA-ALTNAILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V         + + FKV + + + 
Sbjct: 173 QKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVRVNSE---GKPSETRFKVEERY-EF 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH LH G PI  D +Y    F         ++L+LHA  +   
Sbjct: 229 CTLVRCSPVTGRTHQIRVHTLHAGHPIAFDDRYGDREFDKQLAGTGLSRLFLHAAALKFT 288

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLG 323
           HP  G  +++ APL   + +    L 
Sbjct: 289 HPGTGEEMRVEAPLDNQLKRCLKILR 314


>gi|94497617|ref|ZP_01304185.1| pseudouridylate synthase [Sphingomonas sp. SKA58]
 gi|94422834|gb|EAT07867.1| pseudouridylate synthase [Sphingomonas sp. SKA58]
          Length = 394

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 113/314 (35%), Positives = 183/314 (58%), Gaps = 5/314 (1%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V+   V  D++ +RLDRWF+ H P + F  + +  R+GQ+RVD  R    +RI  GQ++
Sbjct: 86  DVRQYRVAADDDGIRLDRWFQRHLPDVGFNLVSRWSRTGQLRVDGARAAPGDRISEGQMI 145

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP     +   + ++     +   + S + + ++++ D++  V NKP G++ QGG+  
Sbjct: 146 RVPPAEQKPDAADRPKRARIVDLTPDEIS-YAQDMVIHRDAQAIVINKPPGLATQGGTKT 204

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+D  L + +     +P+L HRLD++TSG L++ART  AA H  ++F  R  +K+YW+
Sbjct: 205 DEHVDKLLDALLFDAESRPKLVHRLDKDTSGALLLARTSRAAAHFAKAFSSRTARKVYWA 264

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G+P  +   I   + K+   GG+ +HV   +E+    A S ++VI+    +  W+E+
Sbjct: 265 LVMGVPSIEDGMIELPIAKQPGTGGEKMHV---DEEEGLPARSRYRVIERAGNRAAWIEL 321

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QP+TGRTHQLRVH   +G PIVGD KY        +  I  K++LHAR + + HP+GGR+
Sbjct: 322 QPYTGRTHQLRVHMAAIGHPIVGDGKYGGK-DAFLSGTISRKMHLHARRIRVDHPDGGRV 380

Query: 306 QITAPLPAHMVKTW 319
            +TA LP H   + 
Sbjct: 381 DMTAELPTHFANSL 394


>gi|311280008|ref|YP_003942239.1| pseudouridine synthase, RluA family [Enterobacter cloacae SCF1]
 gi|308749203|gb|ADO48955.1| pseudouridine synthase, RluA family [Enterobacter cloacae SCF1]
          Length = 341

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 109/326 (33%), Positives = 171/326 (52%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++
Sbjct: 27  MKTETPTVKMVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKL 86

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 87  EAGDEVRIPPVR------VAEREEDAVSPHLQKVA-ALSDVILYEDDHILVLNKPSGTAV 139

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 140 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRDKGM 198

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V         + + FKV + FA  
Sbjct: 199 QKDYLALVRGQWQSHTKVVQAPLLKNILQSGERIVRVSSE---GKPSETRFKVEERFA-F 254

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  H G PI  D +Y    F         N+L+LHA  +   
Sbjct: 255 ATLVRCSPVTGRTHQIRVHTQHAGHPIAFDDRYGDREFDKQLAGTGLNRLFLHAAALKFT 314

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  +++ AP+ A +      L 
Sbjct: 315 HPGTGETMRVEAPMDAQLKHCLKVLR 340


>gi|303238885|ref|ZP_07325416.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
 gi|302593518|gb|EFL63235.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
          Length = 308

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 87/330 (26%), Positives = 154/330 (46%), Gaps = 35/330 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++ V   ++E  +R+D W  +     +   +QK+L  G V V+   VK N +I+S  
Sbjct: 5   MEEIKLV---SEESGVRIDAWISSRLKEYSRSYIQKLLNDGHVLVNGSLVKSNYKIKSSD 61

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          I E ++LD         + ++  +LYED  + V NKP G+ V   +
Sbjct: 62  EITVQ---------IPEPEVLD------IVPENIEIPVLYEDEHVLVVNKPKGMVVHPAA 106

Query: 124 GI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  +    DS        +P + HR+D++TSG+LVVA++  A + L+   + 
Sbjct: 107 GNYSGTLVNALMDYCGDSLSSINGVIRPGIVHRIDKDTSGVLVVAKSNEAHEKLSLKLKD 166

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I ++Y +LV GI + +   I   + +   +    + V   N      A+++FKV++ F
Sbjct: 167 HDINRVYVALVHGIIREESGKIDAPIGRH-PVDRKKMAV---NTNNGRRAVTYFKVLERF 222

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    +E++  TGRTHQ+RVH  ++G PI+GD  Y                 LHA+ + 
Sbjct: 223 -KDATLVEVKLETGRTHQIRVHMSYIGYPIIGDTVYGKKKD----KYDIGGQALHAKTLG 277

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
             HP     ++  A LP +  K  + L + 
Sbjct: 278 FVHPVKNEYMEFEAELPEYFKKLLEELRWD 307


>gi|269139453|ref|YP_003296154.1| 23S rRNA pseudouridylate synthase [Edwardsiella tarda EIB202]
 gi|267985114|gb|ACY84943.1| 23S rRNA pseudouridylate synthase [Edwardsiella tarda EIB202]
 gi|304559348|gb|ADM42012.1| Ribosomal large subunit pseudouridine synthase C [Edwardsiella
           tarda FL6-60]
          Length = 320

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 110/321 (34%), Positives = 172/321 (53%), Gaps = 14/321 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +N    +    + +I+R G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VKLVTIAADEAGQRIDNFLRNQLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLEAGDQVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+     S  L K +  L   +LYED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVR------VAERDEAPVSARLDKVA-ALNDCILYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD+ETSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRETSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK +   G+ V  V         + + FKV + FA     ++  
Sbjct: 180 VRGQWQSHCKVVQAPLLKNTLQSGERVVRVNAE---GKPSETRFKVEERFA-NATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y   +F         N+L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTLHAGHPIAFDDRYGDRDFDRELADTGLNRLFLHAAALRFVHPHSGET 295

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L++ APL A +      L  +
Sbjct: 296 LRVEAPLDAALRHCLSVLRAR 316


>gi|294636835|ref|ZP_06715170.1| ribosomal large subunit pseudouridine synthase [Edwardsiella tarda
           ATCC 23685]
 gi|291089978|gb|EFE22539.1| ribosomal large subunit pseudouridine synthase [Edwardsiella tarda
           ATCC 23685]
          Length = 320

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 109/321 (33%), Positives = 172/321 (53%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V+ V +  DE   R+D + +N    +    + +I+R G+VRV+KKR+K   ++++G  
Sbjct: 6   TSVKLVTIAADEAGQRIDNFLRNQLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLEAGDE 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S  L K +  L   +LYED  + V NKP+G +V GGSG
Sbjct: 66  VRIPPVR------VAERDEAPVSARLDKVA-ALNDCVLYEDDYLMVLNKPSGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD+ETSG+L+VA+ R+A + L E  R + +QK Y 
Sbjct: 119 LSFGVIEGLRA-LRPEARFLELVHRLDRETSGVLLVAKKRSALRSLHEQLREKGMQKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + +   LLK     G+ +  V         + + FKV + FA     ++
Sbjct: 178 ALVRGHWQSHCKVVQAPLLKNILQSGERIVRVNAE---GKPSETRFKVEERFA-NATLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D +Y   +F         N+L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHTLHAGHPIAFDDRYGDRDFDRELAETGLNRLFLHAAALRFVHPHSG 293

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             +++ APL A + +    L 
Sbjct: 294 ETMRVEAPLDAALRRCLAVLR 314


>gi|224541418|ref|ZP_03681957.1| hypothetical protein CATMIT_00580 [Catenibacterium mitsuokai DSM
           15897]
 gi|224525664|gb|EEF94769.1| hypothetical protein CATMIT_00580 [Catenibacterium mitsuokai DSM
           15897]
          Length = 306

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 92/329 (27%), Positives = 152/329 (46%), Gaps = 32/329 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            +Q +  E +E+ +RLD+   NH P  +   +QK +++GQV V+    K N +++   V+
Sbjct: 2   EIQSITPELEEKGLRLDKVILNHMPDRSRTEIQKWIKAGQVIVNDNVEKANYKVEEEDVI 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           ++         I  E   LD               ++YED  + V NKP G+ V   +GI
Sbjct: 62  QVTLPDPQSTEIRPEDIPLD---------------IIYEDEDVIVVNKPTGMIVHPSAGI 106

Query: 126 --AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++  L    D        +P + HR+D+ETSG+L+VA+   A + L++      +
Sbjct: 107 YSGTLVNALLYHCHDLSAINGITRPGIVHRIDKETSGLLMVAKNDNAHRSLSKQLEEHSV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y +LV G+  +    I   + + S         +    K A  AI++FKV++ +   
Sbjct: 167 VRRYVALVHGVINHNVGRIEAPIGRDSKDRKK----MAVTSKNAKDAITNFKVLERY-DD 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E +  TGRTHQ+RVH  ++G P+ GD +Y      N      N  YLHAR +   H
Sbjct: 222 MTLIECRLETGRTHQIRVHMQYIGHPVYGDPQYGFRNDDNT-----NGQYLHARVLGFVH 276

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           P     +   APLP    +    LG +Y+
Sbjct: 277 PRTNEHMYFEAPLPDFFEEKIKELGGEYN 305


>gi|292487948|ref|YP_003530825.1| pseudouridylate synthase [Erwinia amylovora CFBP1430]
 gi|292899167|ref|YP_003538536.1| ribosomal large subunit pseudouridine synthase C [Erwinia amylovora
           ATCC 49946]
 gi|291199015|emb|CBJ46126.1| ribosomal large subunit pseudouridine synthase C [Erwinia amylovora
           ATCC 49946]
 gi|291553372|emb|CBA20417.1| pseudouridylate synthase [Erwinia amylovora CFBP1430]
          Length = 320

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 104/319 (32%), Positives = 172/319 (53%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  +R
Sbjct: 8   VHFIAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++  + S  L K +  L++ ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVR------VAEREEENVSPKLAKVA-ALEAAIIYEDDYLLVMNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+ V  V         + + FKV + +A     ++  
Sbjct: 180 VRGQWPSHVKAVRAPLLKNILQSGERVVKVSSE---GKPSETLFKVEERYA-IATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y  A F    +     +L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTLHAGHPIAFDDRYGEAGFDQQLSGTGLKRLFLHAAALRFTHPNTGEI 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           +++ APL   + +    L 
Sbjct: 296 MRVEAPLDEQLKRCLAVLR 314


>gi|65321221|ref|ZP_00394180.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Bacillus
           anthracis str. A2012]
 gi|229600532|ref|YP_002868128.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|270000606|ref|YP_003329045.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. Ames]
 gi|291612221|ref|YP_003541035.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. 'Ames Ancestor']
 gi|224552855|gb|ACN55066.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. 'Ames Ancestor']
 gi|229264940|gb|ACQ46577.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|269850243|gb|ACZ49983.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. Ames]
          Length = 302

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 144/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP  + V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEIYYEDADVLVVNKPRSMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +      N   LHA  +  
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +Q  AP+P       + L 
Sbjct: 275 DHPRTGEYIQFEAPIPEVFEDALNILR 301


>gi|261222782|ref|ZP_05937063.1| ribosomal large subunit pseudouridine synthase D [Brucella ceti
           B1/94]
 gi|260921366|gb|EEX88019.1| ribosomal large subunit pseudouridine synthase D [Brucella ceti
           B1/94]
          Length = 347

 Score =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 89/348 (25%), Positives = 163/348 (46%), Gaps = 45/348 (12%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           T ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G
Sbjct: 12  TRLKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREG 71

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I               +L          + +   +LYED  + V NKPAG+ V  G
Sbjct: 72  MNIAI---------------VLSEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPG 116

Query: 123 SG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +G      ++  +    DS       ++P + HRLD++TSG++VVA+   A +HL+E F 
Sbjct: 117 NGNWTGTLVNALIYHCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFA 176

Query: 176 MR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
                  +++ Y +LVWG+ +  +  +  +L + SH       VV +  + A +AI+H+ 
Sbjct: 177 DHGRTGDLERAYLALVWGMTERPQGTVDAYLGR-SHRDRTKQAVVHEEREDARHAITHYA 235

Query: 232 VIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTS 282
            ++ F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        
Sbjct: 236 TVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPE 295

Query: 283 PIQ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           P++      ++  LHA  +   HP     ++  APLP  M +  ++  
Sbjct: 296 PLKEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDMEQLLENFR 343


>gi|154504404|ref|ZP_02041142.1| hypothetical protein RUMGNA_01908 [Ruminococcus gnavus ATCC 29149]
 gi|153795333|gb|EDN77753.1| hypothetical protein RUMGNA_01908 [Ruminococcus gnavus ATCC 29149]
          Length = 309

 Score =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 142/328 (43%), Gaps = 32/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++   E    N R+D++     P  +   +QK+++ G V V+ K+VK N ++ S  
Sbjct: 1   MREERFFTAEETVTNERIDKFLSAQMPDRSRSYIQKLIKDGLVEVNGKQVKTNYKLGSED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++      +  I+ E+  LD               +LYED+ + V NKP G+ V    
Sbjct: 61  EVKLQIPELEVPDILPEEIPLD---------------ILYEDTDLLVVNKPKGMVVHPAP 105

Query: 124 G--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  +    ++        +P + HR+D +T+G L+V +   A Q L E  + 
Sbjct: 106 GHYTGTLVNALMYHCRENLSGINGVMRPGIVHRIDMDTTGSLLVCKNDRAHQILAEQLKD 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y ++V G  K     +   + +           +  +      A++H++V++ F
Sbjct: 166 HSITRRYEAIVHGNLKEDSGTVNAPIGRHPTDRKK----MSVHAPHGREAVTHYRVLERF 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  +E +  TGRTHQ+RVH   +G PI+GD  Y                 LHAR + 
Sbjct: 222 G-NYTHIECELETGRTHQIRVHMASIGHPILGDLVYGP----TKCPFRLQGQTLHARILG 276

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLG 323
             HP  G  +Q  APLP +  +    L 
Sbjct: 277 FVHPSTGAYVQFDAPLPEYFEELLKKLR 304


>gi|156975190|ref|YP_001446096.1| rRNA ribosomal pseudouridine synthase [Vibrio harveyi ATCC
           BAA-1116]
 gi|156526784|gb|ABU71870.1| hypothetical protein VIBHAR_02917 [Vibrio harveyi ATCC BAA-1116]
          Length = 339

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 107/328 (32%), Positives = 181/328 (55%), Gaps = 17/328 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++
Sbjct: 26  MSEIRTKVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKL 85

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VRIPP       + K++  +  S  L K ++ L+ ++++ED  + V NKP+G +V
Sbjct: 86  KAGDLVRIPP-----VTVEKKEDDVAPSTKLNKVAE-LEHMIIFEDDHMLVLNKPSGTAV 139

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 140 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 198

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y++LV G  KN  + +   LLK        V+ + +       + + FKV++ F Q 
Sbjct: 199 KKFYFALVMGEWKNSCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKVLERFEQ- 251

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  +   
Sbjct: 252 ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGLDRLFLHAANIKFQ 311

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           HP     ++I AP+ A + K    L  K
Sbjct: 312 HPSNDEWMEINAPMEAKLEKVLVGLRKK 339


>gi|290475862|ref|YP_003468754.1| 23S rRNA pseudouridylate synthase [Xenorhabdus bovienii SS-2004]
 gi|289175187|emb|CBJ81990.1| 23S rRNA pseudouridylate synthase [Xenorhabdus bovienii SS-2004]
          Length = 318

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 104/319 (32%), Positives = 170/319 (53%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +++DE   R+D +       +    + +ILR G+VRV+K R+K   ++ +  V+R
Sbjct: 8   VQFVTIDDDEAGQRIDNFLLARLKGVPKSMIYRILRKGEVRVNKGRIKPEYKLAAADVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       I E++    S  L K    L   +LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPVR------IAEKQQPPVSAKLGKVV-ALAECILYEDDYILVINKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L++A+ R+A + L E  R++++QK Y++L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLIAKKRSALRTLHEQLRLKQMQKDYFAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FKV + + +    +   
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILQSGERIVKVSSE---GKPSETRFKVEERY-EFATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y    F    T    N+L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHTLHAGHPIAFDDRYGDRAFDAQLTETGLNRLFLHASSLKFTHPSTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+  A +   + +   +L 
Sbjct: 296 LRFEAQMDDELRQCLTTLR 314


>gi|288871585|ref|ZP_06410236.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           hathewayi DSM 13479]
 gi|288862917|gb|EFC95215.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           hathewayi DSM 13479]
          Length = 304

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 82/324 (25%), Positives = 155/324 (47%), Gaps = 32/324 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q  VVE +++ +R+D++     P ++   LQK+L++  V V  K VK N +  +G ++ +
Sbjct: 3   QQFVVEEEDKAIRIDKYLSERCPELSRSYLQKLLKAEAVFVGGKPVKSNYKTAAGDLIEL 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                           +  +V      + +   +LYEDS I + NKP G+ V   +G   
Sbjct: 63  E---------------VPEAVEPKIVPEEMDLDILYEDSDIILINKPKGMVVHPAAGHYS 107

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++G +              +P + HR+D +T+G+L+V +   A   + E  ++  I 
Sbjct: 108 GTLVNGLMAHCRADLSGINGVMRPGIVHRIDMDTTGVLIVCKNDMAHNSIAEQLKVHSIT 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y+++V G+ K  +  ++  + +   +    + +   NEK    A++H++V++ F ++F
Sbjct: 168 RKYYAVVHGVMKEDEGTVSGPIGRH-PVDRKKMCI---NEKNGRDAVTHYRVLERF-RQF 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++E +  TGRTHQ+RVH   +G P++GD  Y                 LHA  + + HP
Sbjct: 223 TYVECRLETGRTHQIRVHMASIGHPLLGDAVYGP----AKCPYKLTGQTLHAGVLGIVHP 278

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  ++ TAPLP +  +    L 
Sbjct: 279 RTGEYMEFTAPLPEYFEELLRKLR 302


>gi|323967027|gb|EGB62453.1| RluA family protein pseudouridine synthase [Escherichia coli M863]
 gi|323976541|gb|EGB71629.1| RluA family protein pseudouridine synthase [Escherichia coli
           TW10509]
 gi|327253484|gb|EGE65122.1| pseudouridine synthase, RluA family protein [Escherichia coli
           STEC_7v]
          Length = 319

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDEHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|215486297|ref|YP_002328728.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O127:H6 str.
           E2348/69]
 gi|312968838|ref|ZP_07783045.1| pseudouridine synthase, RluA family protein [Escherichia coli
           2362-75]
 gi|331682589|ref|ZP_08383208.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli H299]
 gi|215264369|emb|CAS08726.1| 23S rRNA pseudouridy late synthase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|312286240|gb|EFR14153.1| pseudouridine synthase, RluA family protein [Escherichia coli
           2362-75]
 gi|331080220|gb|EGI51399.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli H299]
          Length = 319

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 107/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       I E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------IAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|212639635|ref|YP_002316155.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
 gi|212561115|gb|ACJ34170.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
          Length = 303

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 142/327 (43%), Gaps = 34/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +Q + +E   +  R+D+         +   +Q+ L+ G V V+ K VK N +     
Sbjct: 1   MEQIQ-LTIEEQHDGERIDKVIAELNEQWSRSQVQQWLKEGHVLVNGKAVKPNYKCHVDD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V I                + S   L    + +   + YED+ + V NKP G+ V    
Sbjct: 60  EVVIS---------------IPSPEPLDVAPEPIPLDIYYEDADVLVVNKPRGMVVHPAP 104

Query: 124 GIAY--HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G  +   ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHMHGTLVNALLAHCQDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDLAHESLVNQLVNK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  +    I   + +          V     +    A++HF+V++ F 
Sbjct: 165 TVTRKYVAIVHGVIPHDYGTIDAPIGRDPRDRQSMAVV-----ENGKEAVTHFRVLERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + + ++E Q  TGRTHQ+RVH  ++G P+ GD KY         +   +   LHA  +  
Sbjct: 219 EHYTFVECQLETGRTHQIRVHMKYIGYPLAGDPKYGPR-----KTLPIDGQALHAGVLGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  LQ  AP+P    +  D L 
Sbjct: 274 QHPRTGEYLQFEAPIPHEFERLLDMLR 300


>gi|16129049|ref|NP_415604.1| 23S rRNA pseudouridine synthase; specific to U955, U2504, and U2580
           [Escherichia coli str. K-12 substr. MG1655]
 gi|24112492|ref|NP_707002.1| 23S rRNA pseudouridylate synthase C [Shigella flexneri 2a str. 301]
 gi|30062620|ref|NP_836791.1| 23S rRNA pseudouridylate synthase C [Shigella flexneri 2a str.
           2457T]
 gi|89107932|ref|AP_001712.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12
           substr. W3110]
 gi|91210238|ref|YP_540224.1| 23S rRNA pseudouridylate synthase C [Escherichia coli UTI89]
 gi|110641262|ref|YP_668992.1| 23S rRNA pseudouridylate synthase C [Escherichia coli 536]
 gi|117623272|ref|YP_852185.1| 23S rRNA pseudouridylate synthase C [Escherichia coli APEC O1]
 gi|157156049|ref|YP_001462319.1| 23S rRNA pseudouridylate synthase C [Escherichia coli E24377A]
 gi|157160612|ref|YP_001457930.1| 23S rRNA pseudouridylate synthase C [Escherichia coli HS]
 gi|170020519|ref|YP_001725473.1| 23S rRNA pseudouridylate synthase C [Escherichia coli ATCC 8739]
 gi|170080737|ref|YP_001730057.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           str. K-12 substr. DH10B]
 gi|188495899|ref|ZP_03003169.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           53638]
 gi|209918340|ref|YP_002292424.1| 23S rRNA pseudouridylate synthase C [Escherichia coli SE11]
 gi|218553663|ref|YP_002386576.1| 23S rRNA pseudouridylate synthase C [Escherichia coli IAI1]
 gi|218557967|ref|YP_002390880.1| 23S rRNA pseudouridylate synthase C [Escherichia coli S88]
 gi|218694619|ref|YP_002402286.1| 23S rRNA pseudouridylate synthase C [Escherichia coli 55989]
 gi|218700411|ref|YP_002408040.1| 23S rRNA pseudouridylate synthase C [Escherichia coli IAI39]
 gi|237706929|ref|ZP_04537410.1| ribosomal large subunit pseudouridine synthase C [Escherichia sp.
           3_2_53FAA]
 gi|238900340|ref|YP_002926136.1| 23S rRNA pseudouridylate synthase [Escherichia coli BW2952]
 gi|253773891|ref|YP_003036722.1| 23S rRNA pseudouridylate synthase C [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254161192|ref|YP_003044300.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B str.
           REL606]
 gi|256018658|ref|ZP_05432523.1| 23S rRNA pseudouridylate synthase C [Shigella sp. D9]
 gi|256023217|ref|ZP_05437082.1| 23S rRNA pseudouridylate synthase C [Escherichia sp. 4_1_40B]
 gi|260843326|ref|YP_003221104.1| 23S rRNA pseudouridylate synthase rluC [Escherichia coli O103:H2
           str. 12009]
 gi|260854569|ref|YP_003228460.1| 23S rRNA pseudouridylate synthase rluC [Escherichia coli O26:H11
           str. 11368]
 gi|260867449|ref|YP_003233851.1| 23S rRNA pseudouridylate synthase rluC [Escherichia coli O111:H-
           str. 11128]
 gi|293409451|ref|ZP_06653027.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B354]
 gi|293414379|ref|ZP_06657028.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B185]
 gi|293433375|ref|ZP_06661803.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B088]
 gi|300816787|ref|ZP_07097007.1| pseudouridine synthase, RluA family [Escherichia coli MS 107-1]
 gi|300821134|ref|ZP_07101283.1| pseudouridine synthase, RluA family [Escherichia coli MS 119-7]
 gi|300902476|ref|ZP_07120458.1| pseudouridine synthase, RluA family [Escherichia coli MS 84-1]
 gi|300928363|ref|ZP_07143897.1| pseudouridine synthase, RluA family [Escherichia coli MS 187-1]
 gi|300938652|ref|ZP_07153381.1| pseudouridine synthase, RluA family [Escherichia coli MS 21-1]
 gi|300948672|ref|ZP_07162753.1| pseudouridine synthase, RluA family [Escherichia coli MS 116-1]
 gi|300956251|ref|ZP_07168560.1| pseudouridine synthase, RluA family [Escherichia coli MS 175-1]
 gi|300982570|ref|ZP_07176192.1| pseudouridine synthase, RluA family [Escherichia coli MS 200-1]
 gi|301023272|ref|ZP_07187069.1| pseudouridine synthase, RluA family [Escherichia coli MS 69-1]
 gi|301029700|ref|ZP_07192754.1| pseudouridine synthase, RluA family [Escherichia coli MS 196-1]
 gi|301304976|ref|ZP_07211078.1| pseudouridine synthase, RluA family [Escherichia coli MS 124-1]
 gi|301644499|ref|ZP_07244494.1| pseudouridine synthase, RluA family [Escherichia coli MS 146-1]
 gi|307137721|ref|ZP_07497077.1| 23S rRNA pseudouridylate synthase C [Escherichia coli H736]
 gi|307310137|ref|ZP_07589787.1| pseudouridine synthase, RluA family [Escherichia coli W]
 gi|312971222|ref|ZP_07785400.1| pseudouridine synthase, RluA family protein [Escherichia coli
           1827-70]
 gi|331641629|ref|ZP_08342764.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli H736]
 gi|331667486|ref|ZP_08368350.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli TA271]
 gi|331676876|ref|ZP_08377572.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli H591]
 gi|332279727|ref|ZP_08392140.1| ribosomal large subunit pseudouridine synthase C [Shigella sp. D9]
 gi|76363884|sp|P0AA39|RLUC_ECOLI RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|92090792|sp|P0AA40|RLUC_SHIFL RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|1787327|gb|AAC74170.1| 23S rRNA pseudouridine synthase; specific to U955, U2504, and U2580
           [Escherichia coli str. K-12 substr. MG1655]
 gi|4062660|dbj|BAA35894.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K12
           substr. W3110]
 gi|24051379|gb|AAN42709.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
 gi|30040866|gb|AAP16597.1| hypothetical protein S1170 [Shigella flexneri 2a str. 2457T]
 gi|91071812|gb|ABE06693.1| hypothetical protein UTI89_C1211 [Escherichia coli UTI89]
 gi|110342854|gb|ABG69091.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           536]
 gi|115512396|gb|ABJ00471.1| conserved hypothetical protein [Escherichia coli APEC O1]
 gi|157066292|gb|ABV05547.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           HS]
 gi|157078079|gb|ABV17787.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           E24377A]
 gi|169755447|gb|ACA78146.1| pseudouridine synthase, RluA family [Escherichia coli ATCC 8739]
 gi|169888572|gb|ACB02279.1| Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           str. K-12 substr. DH10B]
 gi|188491098|gb|EDU66201.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           53638]
 gi|209911599|dbj|BAG76673.1| 23S rRNA pseudouridylate synthase [Escherichia coli SE11]
 gi|218351351|emb|CAU97057.1| 23S rRNA pseudouridylate synthase [Escherichia coli 55989]
 gi|218360431|emb|CAQ97985.1| 23S rRNA pseudouridylate synthase [Escherichia coli IAI1]
 gi|218364736|emb|CAR02426.1| 23S rRNA pseudouridylate synthase [Escherichia coli S88]
 gi|218370397|emb|CAR18202.1| 23S rRNA pseudouridylate synthase [Escherichia coli IAI39]
 gi|226898139|gb|EEH84398.1| ribosomal large subunit pseudouridine synthase C [Escherichia sp.
           3_2_53FAA]
 gi|238859760|gb|ACR61758.1| 23S rRNA pseudouridylate synthase [Escherichia coli BW2952]
 gi|242376889|emb|CAQ31607.1| 23S rRNA pseudouridine synthase [Escherichia coli BL21(DE3)]
 gi|253324935|gb|ACT29537.1| pseudouridine synthase, RluA family [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253973093|gb|ACT38764.1| 23S rRNA pseudouridylate synthase [Escherichia coli B str. REL606]
 gi|253977307|gb|ACT42977.1| 23S rRNA pseudouridylate synthase [Escherichia coli BL21(DE3)]
 gi|257753218|dbj|BAI24720.1| 23S rRNA pseudouridylate synthase rluC [Escherichia coli O26:H11
           str. 11368]
 gi|257758473|dbj|BAI29970.1| 23S rRNA pseudouridylate synthase rluC [Escherichia coli O103:H2
           str. 12009]
 gi|257763805|dbj|BAI35300.1| 23S rRNA pseudouridylate synthase rluC [Escherichia coli O111:H-
           str. 11128]
 gi|260449775|gb|ACX40197.1| pseudouridine synthase, RluA family [Escherichia coli DH1]
 gi|281600502|gb|ADA73486.1| Ribosomal large subunit pseudouridine synthase C [Shigella flexneri
           2002017]
 gi|291324194|gb|EFE63616.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B088]
 gi|291434437|gb|EFF07410.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B185]
 gi|291469919|gb|EFF12403.1| 23S rRNA pseudouridylate synthase C [Escherichia coli B354]
 gi|294492107|gb|ADE90863.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           IHE3034]
 gi|299877388|gb|EFI85599.1| pseudouridine synthase, RluA family [Escherichia coli MS 196-1]
 gi|300307151|gb|EFJ61671.1| pseudouridine synthase, RluA family [Escherichia coli MS 200-1]
 gi|300316920|gb|EFJ66704.1| pseudouridine synthase, RluA family [Escherichia coli MS 175-1]
 gi|300397117|gb|EFJ80655.1| pseudouridine synthase, RluA family [Escherichia coli MS 69-1]
 gi|300405508|gb|EFJ89046.1| pseudouridine synthase, RluA family [Escherichia coli MS 84-1]
 gi|300451827|gb|EFK15447.1| pseudouridine synthase, RluA family [Escherichia coli MS 116-1]
 gi|300456437|gb|EFK19930.1| pseudouridine synthase, RluA family [Escherichia coli MS 21-1]
 gi|300463621|gb|EFK27114.1| pseudouridine synthase, RluA family [Escherichia coli MS 187-1]
 gi|300526433|gb|EFK47502.1| pseudouridine synthase, RluA family [Escherichia coli MS 119-7]
 gi|300530561|gb|EFK51623.1| pseudouridine synthase, RluA family [Escherichia coli MS 107-1]
 gi|300839694|gb|EFK67454.1| pseudouridine synthase, RluA family [Escherichia coli MS 124-1]
 gi|301077163|gb|EFK91969.1| pseudouridine synthase, RluA family [Escherichia coli MS 146-1]
 gi|306909855|gb|EFN40349.1| pseudouridine synthase, RluA family [Escherichia coli W]
 gi|307627444|gb|ADN71748.1| 23S rRNA pseudouridylate synthase C [Escherichia coli UM146]
 gi|309701358|emb|CBJ00659.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           ETEC H10407]
 gi|310336424|gb|EFQ01610.1| pseudouridine synthase, RluA family protein [Escherichia coli
           1827-70]
 gi|313650461|gb|EFS14868.1| pseudouridine synthase, RluA family protein [Shigella flexneri 2a
           str. 2457T]
 gi|315060363|gb|ADT74690.1| 23S rRNA pseudouridylate synthase [Escherichia coli W]
 gi|315135718|dbj|BAJ42877.1| 23S rRNA pseudouridylate synthase C [Escherichia coli DH1]
 gi|315253886|gb|EFU33854.1| pseudouridine synthase, RluA family [Escherichia coli MS 85-1]
 gi|315287423|gb|EFU46834.1| pseudouridine synthase, RluA family [Escherichia coli MS 110-3]
 gi|323156893|gb|EFZ43027.1| pseudouridine synthase, RluA family protein [Escherichia coli
           EPECa14]
 gi|323163696|gb|EFZ49517.1| pseudouridine synthase, RluA family protein [Escherichia coli
           E128010]
 gi|323175240|gb|EFZ60853.1| pseudouridine synthase, RluA family protein [Escherichia coli
           LT-68]
 gi|323175683|gb|EFZ61277.1| pseudouridine synthase, RluA family protein [Escherichia coli 1180]
 gi|323185792|gb|EFZ71153.1| pseudouridine synthase, RluA family protein [Escherichia coli 1357]
 gi|323379076|gb|ADX51344.1| pseudouridine synthase, RluA family [Escherichia coli KO11]
 gi|323942555|gb|EGB38722.1| RluA family protein pseudouridine synthase [Escherichia coli E482]
 gi|323947612|gb|EGB43616.1| RluA family protein pseudouridine synthase [Escherichia coli H120]
 gi|323953228|gb|EGB49094.1| RluA family protein pseudouridine synthase [Escherichia coli H252]
 gi|323957910|gb|EGB53622.1| RluA family protein pseudouridine synthase [Escherichia coli H263]
 gi|323962685|gb|EGB58263.1| RluA family protein pseudouridine synthase [Escherichia coli H489]
 gi|323973325|gb|EGB68514.1| RluA family protein pseudouridine synthase [Escherichia coli TA007]
 gi|324007925|gb|EGB77144.1| pseudouridine synthase, RluA family [Escherichia coli MS 57-2]
 gi|324013284|gb|EGB82503.1| pseudouridine synthase, RluA family [Escherichia coli MS 60-1]
 gi|324117343|gb|EGC11250.1| RluA family protein pseudouridine synthase [Escherichia coli E1167]
 gi|331038427|gb|EGI10647.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli H736]
 gi|331065071|gb|EGI36966.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli TA271]
 gi|331075565|gb|EGI46863.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli H591]
 gi|332102079|gb|EGJ05425.1| ribosomal large subunit pseudouridine synthase C [Shigella sp. D9]
 gi|332342633|gb|AEE55967.1| pseudouridine synthase RluC [Escherichia coli UMNK88]
 gi|332758246|gb|EGJ88569.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           4343-70]
 gi|332759613|gb|EGJ89918.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           2747-71]
 gi|332761433|gb|EGJ91717.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           K-671]
 gi|332767695|gb|EGJ97888.1| 23S rRNA pseudouridine synthase [Shigella flexneri 2930-71]
 gi|333004896|gb|EGK24416.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           VA-6]
 gi|333005699|gb|EGK25217.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           K-218]
 gi|333008291|gb|EGK27765.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           K-272]
 gi|333019472|gb|EGK38755.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           K-304]
 gi|333019781|gb|EGK39053.1| pseudouridine synthase, RluA family protein [Shigella flexneri
           K-227]
          Length = 319

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|37526730|ref|NP_930074.1| 23S rRNA pseudouridylate synthase C [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|36786162|emb|CAE15214.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 319

 Score =  279 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 108/323 (33%), Positives = 179/323 (55%), Gaps = 14/323 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +++DE   R+D +       +    + +I+R G+VR++K R+K   ++ +G VVR
Sbjct: 8   VQFVTIDDDEAGQRVDNFLLARLKGVPKSMIYRIVRKGEVRINKGRIKPEYKLSAGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++ +  S  L K +  L   +LYED  I V NKPAG +V GGSG++
Sbjct: 68  IPPVR------VAERQAVPVSAKLDKVA-ALDDCILYEDDHILVLNKPAGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+  +  + +   L HRLD++TSGIL++A+ R+A + L E  R++++QK Y +L
Sbjct: 121 FGVIEGLR-VLRPEAKFLELVHRLDRDTSGILLIAKKRSALRALHEQLRLKQMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+   +VK N +G   + + FKV + FA     ++  
Sbjct: 180 VRGQWPSHCKVVQAPLLKNILQSGER--IVKVNSEG-KPSETRFKVEERFA-NATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D++Y    F    ++   N+L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTQYAGHPIAFDNRYGDKVFDSQLSATGLNRLFLHASVIKFTHPSTGET 295

Query: 305 LQITAPLPAHMVKTWDSLGFKYD 327
           L++ AP+   +    ++L   + 
Sbjct: 296 LRLEAPMDEQLRYCINTLRQNHS 318


>gi|325497607|gb|EGC95466.1| 23S rRNA pseudouridylate synthase C [Escherichia fergusonii ECD227]
          Length = 317

 Score =  279 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 106/326 (32%), Positives = 172/326 (52%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            +G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  AAGDEVRIPPVR------VAEREEDAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-I 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F     +   ++L+LHA  +   
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLANTGLSRLFLHAAALKFT 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  ++I AP+   + +    L 
Sbjct: 289 HPGTGEVMRIEAPMDDGLKRCLQKLR 314


>gi|330502588|ref|YP_004379457.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           mendocina NK-01]
 gi|328916874|gb|AEB57705.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           mendocina NK-01]
          Length = 317

 Score =  279 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 107/322 (33%), Positives = 171/322 (53%), Gaps = 13/322 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  + VQ + V  +    R+D + +     +    + +ILR G+VRV+K R+K   ++Q+
Sbjct: 6   SPTSGVQLIEVAPELAGQRIDNFLRAQLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQA 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PP+  A      E + L   +      + L++ ++YED  + V NKPAGI+V G
Sbjct: 66  GDVVRVPPLRLAERD---EPEPLAQGL-----LERLEAAIVYEDKALIVLNKPAGIAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ Y +    +  +    +   L HRLD++TSG+L++A+ R+  +HL E  R   + K
Sbjct: 118 GSGLNYGVIEAFRQ-LRPDAKDLELVHRLDRDTSGLLMIAKKRSMLRHLHEQLRGDGVDK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G     K+ +   L K +   G+ +  V   +     A++ F+V+  F +   
Sbjct: 177 RYMALVRGHWATAKKQVNAPLQKSNLRSGERMVEV---DGEGKEALTLFRVLRRFGEFAT 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            +E +P TGRTHQ+RVHA H G  I GD KY  + F          +L+LHA  + +P P
Sbjct: 234 LVEAKPVTGRTHQIRVHAKHAGHSIAGDSKYGDDGFTREIRELGGKRLFLHAYELHVPLP 293

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
           EGG L++ AP+     KT + L
Sbjct: 294 EGGVLKLEAPVDEMWAKTLERL 315


>gi|282859073|ref|ZP_06268205.1| pseudouridine synthase, RluA family [Prevotella bivia JCVIHMP010]
 gi|282588153|gb|EFB93326.1| pseudouridine synthase, RluA family [Prevotella bivia JCVIHMP010]
          Length = 364

 Score =  279 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 149/334 (44%), Gaps = 40/334 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +E  R+D++      H +   +QK   SG + V+ + VK N +++   V+ +  
Sbjct: 34  IEVDKGQEKERIDKFLFERMQHSSRNRIQKAADSGFIHVNGQPVKSNYKVRPLDVITLML 93

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                ++ I+ + I                 ++YED  + V  KPAG+ V  G+G     
Sbjct: 94  DRPKHDNTIEPEDI--------------PLDVIYEDDDLMVIMKPAGLVVHPGAGNFHGT 139

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+     +  D+   +  L HR+D++TSG+L++A+T  A   L + F  +   
Sbjct: 140 LINAIAWHLKDL--ASFDANDPEVGLVHRIDKDTSGLLLIAKTPEAKTKLGKQFFNKTTH 197

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG     +  I   + +        + V   + +   +A++H+KVI+ F    
Sbjct: 198 RSYIALVWGNFVEDEGRIEGNIARDPK-DRLRMTVFPPDSEIGKHAVTHYKVIERFG-YT 255

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------------PIQNKL 288
             +E    TGRTHQ+R H  ++G P+ GD +Y        T              +  + 
Sbjct: 256 TLIECILETGRTHQIRAHMKYIGHPLFGDERYGGKEVLRGTRSSTYNAFVKNGFKLCPRQ 315

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            LHA+ +   HP  G+ +  T+ LPA +    + 
Sbjct: 316 ALHAKTLGFVHPTTGKQMDFTSKLPADLEALIEK 349


>gi|74311647|ref|YP_310066.1| 23S rRNA pseudouridylate synthase C [Shigella sonnei Ss046]
 gi|73855124|gb|AAZ87831.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|323165595|gb|EFZ51382.1| pseudouridine synthase, RluA family protein [Shigella sonnei 53G]
          Length = 319

 Score =  279 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 105/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L++A+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLIAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|225567968|ref|ZP_03776993.1| hypothetical protein CLOHYLEM_04041 [Clostridium hylemonae DSM
           15053]
 gi|225163256|gb|EEG75875.1| hypothetical protein CLOHYLEM_04041 [Clostridium hylemonae DSM
           15053]
          Length = 304

 Score =  278 bits (712), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 89/327 (27%), Positives = 154/327 (47%), Gaps = 38/327 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++  VEN+E   R+DR+        +   +QK+++   + V+ K VK N R+  G ++ +
Sbjct: 3   EFFTVENEE-GERIDRYLAEMLSDRSRSYIQKLIKDSHILVNNKPVKANYRLSCGDMLEV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                      KE  IL   + L          +LYED+ I + NKP  + V    G   
Sbjct: 62  TIPS------AKEPDILPEDIPLH---------ILYEDADIIIVNKPKQMVVHPAPG--- 103

Query: 128 HIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           H  G L + +               +P + HR+D +T+G L+V +   A Q L+E  +  
Sbjct: 104 HYSGTLVNALMFHCGRELSGINGMMRPGIVHRIDMDTTGSLIVCKNDMAHQALSEQLKKH 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I++IY ++V G  K ++  ++  + +           +  + K A  A++H+KV++ F 
Sbjct: 164 SIRRIYEAVVHGGFKEEEGTVSAPIGRHPTDRK----RMSTHAKNAREAVTHYKVLERFG 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + + +++ +  TGRTHQ+RVH   +G PIVGD  Y          P      LHA+ + +
Sbjct: 220 E-YSYIQCELETGRTHQIRVHMSSIGHPIVGDMVYGPR---RCPFPGLQGQTLHAKTLGI 275

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  L++ APLP + V+  + L 
Sbjct: 276 IHPRTGEYLEVEAPLPQYFVELLEKLR 302


>gi|145299036|ref|YP_001141877.1| ribosomal large subunit pseudouridine synthase C [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142851808|gb|ABO90129.1| ribosomal large subunit pseudouridine synthase C [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 327

 Score =  278 bits (712), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 107/320 (33%), Positives = 168/320 (52%), Gaps = 15/320 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            VQ + +E + E  R+D + K     +    + +ILR G+VRV+KKR+K   ++  G  V
Sbjct: 20  QVQLLTIEAEHEGQRIDNFLKTQLKGVPKSLIYRILRKGEVRVNKKRIKPEYKLCPGDEV 79

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A  + +        S NL      L+S +L+ED  + V NKP+G++V GGSG+
Sbjct: 80  RVPPVRVAEKNELP-------SANLGSIQR-LESQILFEDDAMIVLNKPSGMAVHGGSGL 131

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L++ +    +   L HRLD++TSG+L+VA+ R+A + L E  R++ ++K Y +
Sbjct: 132 SFGVIEGLRA-LRPDARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRVKTMRKQYLA 190

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  +   + +   L K     G+ V  V  +      + + F++   FA+    +E 
Sbjct: 191 LVRGQWQPHVKVVNAPLRKNDLQSGERVVRVSSD---GKPSETRFRIARQFAE-ATLVEC 246

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  H G PI  D KY  A F     S    +L+LHA  +   HP  GR
Sbjct: 247 SPITGRTHQIRVHTQHAGHPIACDDKYGEAAFDEKMRSQGLKRLFLHAWKLTFTHPVDGR 306

Query: 305 -LQITAPLPAHMVKTWDSLG 323
            + I APL   +    + L 
Sbjct: 307 EVLIEAPLAPELDNFLNKLA 326


>gi|296102896|ref|YP_003613042.1| 23S rRNA pseudouridylate synthase C [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295057355|gb|ADF62093.1| 23S rRNA pseudouridylate synthase C [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 306

 Score =  278 bits (712), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 102/316 (32%), Positives = 168/316 (53%), Gaps = 14/316 (4%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V + +DE   R+D + +     +    + +ILR G+VRV+KKRVK   ++++G  VRIPP
Sbjct: 2   VAIADDEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLEAGDEVRIPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A     +E++++   +   +    L  ++LYED  I V NKP+G +V GGSG+++ +
Sbjct: 62  VRVAE----REEEVVSPKL---QKVAALSDVILYEDDHILVLNKPSGTAVHGGSGLSFGV 114

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +LV G
Sbjct: 115 IEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRG 173

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             ++  + +   LLK     G+ +  V Q       + + FKV + + +    +   P T
Sbjct: 174 QWQSHVKVVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERY-EFATLVRCSPVT 229

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           GRTHQ+RVH    G PI  D +Y    F         ++L+LHA  +   HP  G  ++I
Sbjct: 230 GRTHQIRVHTQFAGHPIAFDDRYGDREFDKQLAGTGLSRLFLHAAALKFTHPNTGETIRI 289

Query: 308 TAPLPAHMVKTWDSLG 323
            APL   + +    L 
Sbjct: 290 EAPLDEQLKRCLKVLR 305


>gi|331646343|ref|ZP_08347446.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli M605]
 gi|330910900|gb|EGH39410.1| pseudouridylate synthase, 23S RNA-specific [Escherichia coli AA86]
 gi|331045095|gb|EGI17222.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli M605]
          Length = 319

 Score =  278 bits (712), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|82777302|ref|YP_403651.1| 23S rRNA pseudouridylate synthase C [Shigella dysenteriae Sd197]
 gi|309788155|ref|ZP_07682761.1| pseudouridine synthase, RluA family protein [Shigella dysenteriae
           1617]
 gi|81241450|gb|ABB62160.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
 gi|308924007|gb|EFP69508.1| pseudouridine synthase, RluA family protein [Shigella dysenteriae
           1617]
 gi|323190599|gb|EFZ75871.1| pseudouridine synthase, RluA family protein [Escherichia coli
           RN587/1]
          Length = 319

 Score =  278 bits (712), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDYILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|306844672|ref|ZP_07477257.1| pseudouridine synthase, RluA family [Brucella sp. BO1]
 gi|306274844|gb|EFM56614.1| pseudouridine synthase, RluA family [Brucella sp. BO1]
          Length = 334

 Score =  278 bits (712), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 87/346 (25%), Positives = 162/346 (46%), Gaps = 45/346 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMN 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L          + +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +    DS       ++P + HRLD++TSG++VVA+   A +HL+E F   
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADH 165

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                +++ Y +LVWG+ +  +  +  +L + SH       VV++  + A +AI+H+  +
Sbjct: 166 GRTGDLERAYLALVWGMTERPQGTVDAYLGR-SHRDRTKQAVVREEREDARHAITHYATV 224

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPI 284
           + F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        P+
Sbjct: 225 EKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPEPL 284

Query: 285 QN------KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +       +  LHA  +   HP     ++  APLP  + +  ++  
Sbjct: 285 KKAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPDDIEQLLENFR 330


>gi|146306651|ref|YP_001187116.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           mendocina ymp]
 gi|145574852|gb|ABP84384.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           mendocina ymp]
          Length = 332

 Score =  278 bits (712), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 106/322 (32%), Positives = 171/322 (53%), Gaps = 13/322 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  + VQ + V  D    R+D + +     +    + +ILR G+VRV+K R+K   ++Q+
Sbjct: 21  SPTSGVQLIEVAPDFAGQRIDNFLRTQLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQA 80

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VR+PP+  A      E + +   +      + L++ ++YED  + V NKPAGI+V G
Sbjct: 81  GDIVRVPPLRLAERD---EPEPVAQGL-----LERLEAAIVYEDKALIVLNKPAGIAVHG 132

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ Y +    +  +    +   L HRLD++TSG+L++A+ R+  +HL E+ R   + K
Sbjct: 133 GSGLNYGVIEAFRQ-LRPDAKDLELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDK 191

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G     K+ +   L K +   G+ +  V   +     A++ F+V+  F     
Sbjct: 192 RYMALVRGHWATAKKQVNAPLQKSNLRSGERMVEV---DGEGKEALTLFRVLRRFGDFAT 248

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            +E +P TGRTHQ+RVHA H G  I GD KY   +F          +L+LHA  + +P P
Sbjct: 249 LVEAKPVTGRTHQIRVHAKHAGHCIAGDSKYGDDDFTREIRELGGKRLFLHAYELHVPLP 308

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
           EGG L++ AP+     KT + L
Sbjct: 309 EGGVLKLEAPVDDMWAKTLERL 330


>gi|256847299|ref|ZP_05552745.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           coleohominis 101-4-CHN]
 gi|256715963|gb|EEU30938.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           coleohominis 101-4-CHN]
          Length = 308

 Score =  278 bits (712), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 80/313 (25%), Positives = 137/313 (43%), Gaps = 32/313 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E  R+D+        ++   ++K +  G V V+K+ VK    +Q+G +V++        
Sbjct: 13  QETGRIDKQLATLLSDVSRSQIKKWIEDGNVTVNKQSVKPKYHLQAGDIVQV-------- 64

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFL 133
                  I +    +    + +   ++YED  + V NKP G+ V   +G   H   +  L
Sbjct: 65  -------IPEQPQKIDLEPENIPLEIVYEDDDVLVVNKPQGMVVHPSAGHPNHTLVNALL 117

Query: 134 KSWVDSK---GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                S      +P + HR+D++TSG+L+VA+   A + L    + +  Q+ Y +LV G+
Sbjct: 118 YHCPLSHINGEYRPGIVHRIDKDTSGLLMVAKNDRAHRSLAAQLKAKTNQREYVALVHGV 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K  +  I   L +          V          A++HF+V+  +   +  +  +  TG
Sbjct: 178 IKEDQGTIDAPLGRSPKDRKKQAVVA-----DGRPAVTHFRVLKRY-LHYTLVACKLETG 231

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +   N  YLHAR +   HP  G  +   A
Sbjct: 232 RTHQIRVHMKYIGHPLAGDPLYGPR-----KTLKGNGQYLHARLLGFKHPVTGKEMVFEA 286

Query: 310 PLPAHMVKTWDSL 322
           PLP    +    L
Sbjct: 287 PLPTWFAQMLKHL 299


>gi|26247226|ref|NP_753266.1| 23S rRNA pseudouridylate synthase C [Escherichia coli CFT073]
 gi|227886557|ref|ZP_04004362.1| 23S rRNA pseudouridylate synthase C [Escherichia coli 83972]
 gi|300974389|ref|ZP_07172601.1| pseudouridine synthase, RluA family [Escherichia coli MS 45-1]
 gi|301051128|ref|ZP_07197959.1| pseudouridine synthase, RluA family [Escherichia coli MS 185-1]
 gi|331657147|ref|ZP_08358109.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli TA206]
 gi|34395779|sp|Q8FIP7|RLUC_ECOL6 RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|26107627|gb|AAN79826.1|AE016759_100 Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           CFT073]
 gi|227836761|gb|EEJ47227.1| 23S rRNA pseudouridylate synthase C [Escherichia coli 83972]
 gi|300297212|gb|EFJ53597.1| pseudouridine synthase, RluA family [Escherichia coli MS 185-1]
 gi|300410632|gb|EFJ94170.1| pseudouridine synthase, RluA family [Escherichia coli MS 45-1]
 gi|307553087|gb|ADN45862.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           ABU 83972]
 gi|315291063|gb|EFU50426.1| pseudouridine synthase, RluA family [Escherichia coli MS 153-1]
 gi|315296716|gb|EFU56011.1| pseudouridine synthase, RluA family [Escherichia coli MS 16-3]
 gi|331055395|gb|EGI27404.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli TA206]
          Length = 319

 Score =  278 bits (712), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSYVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|227544604|ref|ZP_03974653.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri CF48-3A]
 gi|300910266|ref|ZP_07127726.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
 gi|227185411|gb|EEI65482.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri CF48-3A]
 gi|300892914|gb|EFK86274.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
          Length = 303

 Score =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 88/326 (26%), Positives = 146/326 (44%), Gaps = 33/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     + ++ +    R+D+   +H+   +   +Q  +  G V V+ ++VK   ++  G 
Sbjct: 1   MPEELELTIDGEMVG-RIDKQLGHHFDQFSRSQIQHWIEDGHVLVNGEQVKPKYKLLVGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V+I               I +    +    + +   ++YED  + V NKP G+ V    
Sbjct: 60  HVQI---------------IPEEPQKIDLTPEDIPLDIVYEDDDVIVVNKPQGMVVHPAP 104

Query: 124 GIAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G   H   +  L     S      +P + HR+D++TSG+L+VA+   A + LT   + + 
Sbjct: 105 GHPNHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKT 164

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LV G+ K  K  I   L +          VV        +AI+HF V++ F +
Sbjct: 165 NKREYVALVHGVIKEDKGTIDAPLGRSLKDRKKQAVVV-----DGRHAITHFNVLERF-K 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +  Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  YLHAR +   
Sbjct: 219 NYTLVACQLETGRTHQIRVHMKYIGHPLAGDPLYGPR-----KTLAGNGQYLHARLLGFK 273

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +  TAPLPA+  K  + L 
Sbjct: 274 HPRTGKEMVFTAPLPAYFTKMLEHLR 299


>gi|332993476|gb|AEF03531.1| ribosomal large subunit pseudouridine synthase C [Alteromonas sp.
           SN2]
          Length = 314

 Score =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 104/318 (32%), Positives = 168/318 (52%), Gaps = 15/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++V VE D    R+D + +     +    + +ILR G+VRV+K RVK   ++ +  VVR
Sbjct: 9   VRFVTVEPDLAGQRVDNFLRTQLKGVPKSMIYRILRKGEVRVNKGRVKPEYKLVADDVVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +        K+   +         L+S +L+ED +I V NKP+GI+V GGSG++
Sbjct: 69  IPPVRVSEGTPGPSPKLDKIAA--------LESQILFEDERIIVINKPSGIAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +        L HRLD++TSG +++A+ R+A +H+ E  R  ++ K Y +L
Sbjct: 121 FGLIEGLRA-LRPDANFMELVHRLDRDTSGCILIAKKRSALRHMHEQLRTGKMDKRYQAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   + +  +   L K     G+ +  V ++      + + ++++  F      +E  
Sbjct: 180 VAGQWPDNRFKVKAPLRKNVLQSGERMVSVSED---GKPSETRYRILQKF-DTATLVEAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
           P TGRTHQ+RVH LH   PI  D KY  A F  +      N+L+LHA  + L HP    R
Sbjct: 236 PITGRTHQIRVHCLHAEHPIACDPKYGDAEFDESMRQKGLNRLFLHAHSISLIHPGTEER 295

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++ TAPL A +  T  +L
Sbjct: 296 VKFTAPLDATLTNTLKAL 313


>gi|293376242|ref|ZP_06622485.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|325845167|ref|ZP_08168476.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
 gi|292645134|gb|EFF63201.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|325488832|gb|EGC91232.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
          Length = 302

 Score =  278 bits (711), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 150/322 (46%), Gaps = 32/322 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + ++V  +   +RLD+     +   +   LQ++++ G+V ++ +  K N + +    + I
Sbjct: 4   ENMIVTEELVGVRLDKVLNESFEDYSRSYLQQLIKEGRVLINGQVAKANYKCRLNDQIEI 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                     I E ++LD         + +   ++Y+D  + V NKP  + V    G   
Sbjct: 64  N---------IPEPEVLDV------IPEEMDLDIVYQDDYVIVVNKPENMVVHPAPGSMS 108

Query: 126 AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + +
Sbjct: 109 GTLVNGLMAQVTDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVEKTVTR 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G+  +    I   + +          V     +   +A++HFKV+  F + F 
Sbjct: 169 RYVALVHGVIPHDNGTIDAPIGRDPKDRKKMAVV-----ESGKHAVTHFKVLQRFKE-FT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E +  TGRTHQ+RVH  ++G P+ GD +Y        T   ++  +LHA+ +   HP+
Sbjct: 223 LIECRLETGRTHQIRVHMRYIGYPLAGDPQYGPRK----TIGAEHGQFLHAKVLGFVHPK 278

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
               ++ +AP+P +  +   +L
Sbjct: 279 TEEYMEFSAPIPTYFEEALANL 300


>gi|315618256|gb|EFU98846.1| pseudouridine synthase, RluA family protein [Escherichia coli 3431]
          Length = 319

 Score =  278 bits (711), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEVGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|300922611|ref|ZP_07138711.1| pseudouridine synthase, RluA family [Escherichia coli MS 182-1]
 gi|300421088|gb|EFK04399.1| pseudouridine synthase, RluA family [Escherichia coli MS 182-1]
          Length = 319

 Score =  278 bits (711), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARVLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|239826543|ref|YP_002949167.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239806836|gb|ACS23901.1| pseudouridine synthase, RluA family [Geobacillus sp. WCH70]
          Length = 304

 Score =  278 bits (711), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 147/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +Q+  ++ + +N R+D+         +   +Q+ ++ G V V+ + VK N +  +G 
Sbjct: 1   MDVIQFH-IDAEYDNERIDKVIAALNEEWSRSKVQQWIKDGLVTVNDQHVKANYKSSAGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VV +        H++ E   LD               + YED+ + V NKP G+ V    
Sbjct: 60  VVVVRLPEPEPLHVVPENIPLD---------------IYYEDADVLVVNKPRGMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HR+D++TSG+L+VA+   A Q L +    +
Sbjct: 105 GHMRGTLVNALLAHCTDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDMAHQSLVDQLVKK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  +    I   + +           +   E+    A++HF+V++ F 
Sbjct: 165 TVTRKYKAIVHGVIPHDYGTIDAPIGRDKRDRKK----MTVTEENGKEAVTHFRVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + + ++E Q  TGRTHQ+RVH  ++G P+ GD +Y         +   +   LHA  +  
Sbjct: 220 RHYTFVECQLETGRTHQIRVHMKYIGYPLAGDPQYGPK-----KTLPIDGQALHAGVLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  L+  APLP         L 
Sbjct: 275 THPRTGEYLEFEAPLPPEFEHLLQLLR 301


>gi|15801203|ref|NP_287220.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7
           EDL933]
 gi|15830718|ref|NP_309491.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           Sakai]
 gi|195935476|ref|ZP_03080858.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           EC4024]
 gi|208807624|ref|ZP_03249961.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4206]
 gi|208816352|ref|ZP_03257531.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4045]
 gi|209400210|ref|YP_002269931.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4115]
 gi|217328324|ref|ZP_03444406.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. TW14588]
 gi|218704495|ref|YP_002412014.1| 23S rRNA pseudouridylate synthase C [Escherichia coli UMN026]
 gi|254792468|ref|YP_003077305.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           TW14359]
 gi|261227010|ref|ZP_05941291.1| Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. FRIK2000]
 gi|261256244|ref|ZP_05948777.1| Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. FRIK966]
 gi|293404372|ref|ZP_06648366.1| 23S rRNA pseudouridylate synthase C [Escherichia coli FVEC1412]
 gi|298380151|ref|ZP_06989756.1| 23S rRNA pseudouridylate synthase C [Escherichia coli FVEC1302]
 gi|300899606|ref|ZP_07117845.1| pseudouridine synthase, RluA family [Escherichia coli MS 198-1]
 gi|331662494|ref|ZP_08363417.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli TA143]
 gi|34395798|sp|Q8X8J3|RLUC_ECO57 RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|12514630|gb|AAG55832.1|AE005319_1 orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]
 gi|13360928|dbj|BAB34887.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|208727425|gb|EDZ77026.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4206]
 gi|208733000|gb|EDZ81688.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4045]
 gi|209161610|gb|ACI39043.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4115]
 gi|209773278|gb|ACI84951.1| hypothetical protein ECs1464 [Escherichia coli]
 gi|209773280|gb|ACI84952.1| hypothetical protein ECs1464 [Escherichia coli]
 gi|209773282|gb|ACI84953.1| hypothetical protein ECs1464 [Escherichia coli]
 gi|209773284|gb|ACI84954.1| hypothetical protein ECs1464 [Escherichia coli]
 gi|209773286|gb|ACI84955.1| hypothetical protein ECs1464 [Escherichia coli]
 gi|217318751|gb|EEC27177.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. TW14588]
 gi|218431592|emb|CAR12471.1| 23S rRNA pseudouridylate synthase [Escherichia coli UMN026]
 gi|254591868|gb|ACT71229.1| Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. TW14359]
 gi|281178195|dbj|BAI54525.1| 23S rRNA pseudouridylate synthase [Escherichia coli SE15]
 gi|291428958|gb|EFF01983.1| 23S rRNA pseudouridylate synthase C [Escherichia coli FVEC1412]
 gi|298279849|gb|EFI21357.1| 23S rRNA pseudouridylate synthase C [Escherichia coli FVEC1302]
 gi|300356877|gb|EFJ72747.1| pseudouridine synthase, RluA family [Escherichia coli MS 198-1]
 gi|320189769|gb|EFW64425.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           EC1212]
 gi|320637537|gb|EFX07337.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           G5101]
 gi|320643098|gb|EFX12299.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H- str.
           493-89]
 gi|320648556|gb|EFX17211.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H- str.
           H 2687]
 gi|320653870|gb|EFX21944.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320659350|gb|EFX26919.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|320664485|gb|EFX31636.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           LSU-61]
 gi|326339308|gb|EGD63122.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           1125]
 gi|326344731|gb|EGD68479.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O157:H7 str.
           1044]
 gi|331060916|gb|EGI32880.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli TA143]
          Length = 319

 Score =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDDGLKRCLQKLR 316


>gi|89900510|ref|YP_522981.1| pseudouridine synthase RluD [Rhodoferax ferrireducens T118]
 gi|89345247|gb|ABD69450.1| Pseudouridine synthase, RluD [Rhodoferax ferrireducens T118]
          Length = 346

 Score =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 102/327 (31%), Positives = 164/327 (50%), Gaps = 18/327 (5%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
             + V+ D    RLD +   H   +   ++ +I+RSG+VRV+K R   + R+ +G  VR+
Sbjct: 17  TTIRVDEDAAGQRLDNFLMRHLKGVPKTHVYRIIRSGEVRVNKGRASADARLAAGDTVRL 76

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP+  +     K + +  +  +     DF    +L+ED ++ V +KPAG++V GGSG+++
Sbjct: 77  PPLRISERVAEKAEAMTQAMAHGAPARDF---PILFEDEQLLVIDKPAGVAVHGGSGVSF 133

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L+     + +   L HRLD++TSGIL++A+ R+A   L   FR R   K Y +LV
Sbjct: 134 GVIEQLR-MARPEAKFLELVHRLDRDTSGILLIAKKRSALTRLQSQFRERETGKTYLALV 192

Query: 188 WGIPKNKKECIANWLLKKSHIGGD--------YVHVVKQNEKGANYAISHFKVIDCFAQK 239
            G     ++ +   L K    G D         V VV +++     +++  KV +  A  
Sbjct: 193 AGHWPANRKVLDKPLYKYLLPGKDGSAGEGERRVKVVSRDDPNGMPSVTLVKVRETTATS 252

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARY 294
           F  LE+   TGRTHQ+RVH    G PI GD KY           +   P   +++LHA  
Sbjct: 253 FTLLEVTIKTGRTHQIRVHLASEGYPIAGDDKYGDFGLNKKLLQSGPRPGLKRMFLHAWR 312

Query: 295 MDLPHP-EGGRLQITAPLPAHMVKTWD 320
           +   HP  G R+++ APLP  +    D
Sbjct: 313 LQFNHPASGERMELLAPLPTELEAFSD 339


>gi|302345911|ref|YP_003814264.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
 gi|302150113|gb|ADK96375.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
          Length = 365

 Score =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 83/332 (25%), Positives = 149/332 (44%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V+V+  +E  R+D++      H +   +QK   +G + V+   VK N +++   V+ +  
Sbjct: 36  VIVDKGQEPARIDKFLFERMQHSSRNRIQKAADAGYIHVNNAPVKSNYKVRPEDVITLML 95

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                ++ I+              ++ +   ++YED  + V NKPAG+ V  G+G  +  
Sbjct: 96  DRPKHDNTIE--------------AEDIPLDVVYEDDVLMVVNKPAGLVVHPGAGNFHGT 141

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+LV+A+T  A   L + F  +   + 
Sbjct: 142 LINAIAWHLKDMPSFDPNDPEVGLVHRIDKDTSGLLVIAKTPDAKTALGKQFFNKTTHRS 201

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++VWG     +  I   + +        + V   + +    A++H++VI+ F      
Sbjct: 202 YNAIVWGNMTEDEGRIEGNIARDPK-DRLRMTVFPPDSEVGKPAVTHYRVIERFG-YTTL 259

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----------IQNKLYL 290
           +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S           + N+  L
Sbjct: 260 IECILETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSTYKAFIRNCLALCNRQAL 319

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HAR +   HP  G  +  T+ LPA +    + 
Sbjct: 320 HARTLGFVHPVTGEQMDFTSELPADLSALIEK 351


>gi|288803980|ref|ZP_06409402.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           melaninogenica D18]
 gi|288333550|gb|EFC72003.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           melaninogenica D18]
          Length = 365

 Score =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 83/332 (25%), Positives = 150/332 (45%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V+V+  +E +R+D++      H +   +QK   +G + V+   VK N +++   V+ +  
Sbjct: 36  VIVDKGQEPVRIDKFLFERMQHSSRNRIQKAADAGYIHVNNAPVKSNYKVRPEDVITLML 95

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                ++ I+              ++ +   ++YED  + V NKPAG+ V  G+G  +  
Sbjct: 96  DRPKHDNTIE--------------AEDIPLDVVYEDDILMVVNKPAGLVVHPGAGNFHGT 141

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+LV+A+T  A   L + F  +   + 
Sbjct: 142 LINAIAWHLKDMPSFDPNDPEVGLVHRIDKDTSGLLVIAKTPDAKTALGKQFFNKTTHRS 201

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++VWG     +  I   + +        + V   + +    A++H++VI+ F      
Sbjct: 202 YNAIVWGNMTEDEGRIEGNIARDPK-DRLRMTVFPPDSEVGKPAVTHYRVIERFG-YTTL 259

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----------IQNKLYL 290
           +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S           + N+  L
Sbjct: 260 IECILETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSTYKAFIRNCLALCNRQAL 319

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HAR +   HP  G  +  T+ LPA +    + 
Sbjct: 320 HARTLGFVHPVTGEQMDFTSELPADLSALIEK 351


>gi|310767299|gb|ADP12249.1| 23S rRNA pseudouridylate synthase C [Erwinia sp. Ejp617]
          Length = 320

 Score =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 105/319 (32%), Positives = 172/319 (53%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VHFIAISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++  + S  L K +  L++ ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVR------VAEREEENVSPKLAKVA-ALEAAIIYEDDYLLVMNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +    +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPDARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+ V  V         + + FKV + +A     ++  
Sbjct: 180 VRGQWPSHVKAVRAPLLKNILQSGERVVKVSSE---GKPSETLFKVEERYA-IATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y    F    +S    +L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTLHAGHPIAFDDRYGETEFDQQLSSTGLKRLFLHAAALRFTHPNTGEI 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           +++ APL   + +   +L 
Sbjct: 296 MRVEAPLDEQLKRCLVALR 314


>gi|15615105|ref|NP_243408.1| hypothetical protein BH2542 [Bacillus halodurans C-125]
 gi|10175162|dbj|BAB06261.1| BH2542 [Bacillus halodurans C-125]
          Length = 305

 Score =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 147/326 (45%), Gaps = 32/326 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+      +   ++  R+D++        +   +Q+ ++ G V ++ + +K N ++++G 
Sbjct: 1   MSEQLTWTISEQQQGERIDKFLTAQGEEWSRTQVQQWIKDGHVLINGRTIKSNYKVETGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +      +  ++ E   ++               ++YED  + V NKP G+ V    
Sbjct: 61  TLELFVPEPEVLEVVPENIPIE---------------IIYEDEDVAVVNKPRGMVVHPAP 105

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  +    D        +P + HR+D++TSG+L++A+   A + L    + +
Sbjct: 106 GHTTGTLVNALMYHCNDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDRAHESLVNQLKAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +++Y ++V G   +    I   + +   +    + V ++N +    A++HF V++ F 
Sbjct: 166 TTERVYQAIVHGNIPHDHGTIDAPIGRD-KVDRQSMTVTEENSRD---AVTHFTVLERFG 221

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F ++E Q  TGRTHQ+RVH  ++G P+ GD KY         +   +   LHA+ +  
Sbjct: 222 D-FTFVECQLETGRTHQIRVHFKYIGFPLAGDPKYGPK-----KTLSIDGQALHAQKLGF 275

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  ++    +P  M K    L
Sbjct: 276 EHPRTGEFMRFKVEMPEEMKKLIRQL 301


>gi|257898611|ref|ZP_05678264.1| pseudouridylate synthase [Enterococcus faecium Com15]
 gi|257836523|gb|EEV61597.1| pseudouridylate synthase [Enterococcus faecium Com15]
          Length = 303

 Score =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 147/327 (44%), Gaps = 36/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT ++  +     E+ R+D+   N +   +   +Q  L+   V V+ + VK N +++ G 
Sbjct: 1   MTELKTTI---RHESGRIDKVLTNLFSDYSRSQIQLWLKERAVSVNGQPVKANYKVKQGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +               ++     L    + +   ++YED  + V NKP G+ V   +
Sbjct: 58  EITV---------------LIPEPETLDVVPENIPLTIVYEDEDVAVINKPQGMVVHPSA 102

Query: 124 GIAY-HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G  +  +   L   +          +P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 103 GHTHGTMVNALMYHIKDLSTINGVIRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKDK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G   ++K  I   + + S        +     +    A++HF V++ F 
Sbjct: 163 TSLRKYVALVHGEIPHEKGTINAPIGR-SKENRKMQAIR----EDGKPAVTHFTVLERF- 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E++  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +  
Sbjct: 217 EGFTLVELKLETGRTHQIRVHMKYIGYPLAGDPVYGPK-----KTLKGNGQFLHAQMLGF 271

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLG 323
            HP    ++   APLP    KT + L 
Sbjct: 272 THPTTNEKMVFEAPLPEVFEKTLEKLR 298


>gi|251789227|ref|YP_003003948.1| pseudouridine synthase, RluA family [Dickeya zeae Ech1591]
 gi|247537848|gb|ACT06469.1| pseudouridine synthase, RluA family [Dickeya zeae Ech1591]
          Length = 320

 Score =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 104/319 (32%), Positives = 167/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ +  +E   R+D + +     +    + +ILR G+VRV+KKR+K   ++Q G  VR
Sbjct: 8   VQFLTISAEEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +      E++    S +L K S  L   +LYED  + + NKP+G +V GGSG++
Sbjct: 68  IPPVRQS------EREEAAVSASLDKVS-ALADCILYEDDHLLLLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +    +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPDARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRGKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FKV + F      +   
Sbjct: 180 VRGQWQSHCKSVQAPLLKNVLQSGERIVRVNSE---GKPSETLFKVEERF-DCATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           P TGRTHQ+RVH  + G PI  D +Y   +F    T     +L+LHA+ +   HP  G +
Sbjct: 236 PVTGRTHQIRVHTQYAGHPIAFDDRYGDRDFDAQLTGTGLKRLFLHAQALRFEHPHTGEM 295

Query: 306 -QITAPLPAHMVKTWDSLG 323
            +I APL   +      L 
Sbjct: 296 LRIEAPLDEALRHCLQVLR 314


>gi|225628223|ref|ZP_03786257.1| pseudouridine synthase, RluA family protein [Brucella ceti str.
           Cudo]
 gi|260167874|ref|ZP_05754685.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Brucella sp. F5/99]
 gi|261757311|ref|ZP_06001020.1| ribosomal large subunit pseudouridine synthase [Brucella sp. F5/99]
 gi|225616069|gb|EEH13117.1| pseudouridine synthase, RluA family protein [Brucella ceti str.
           Cudo]
 gi|261737295|gb|EEY25291.1| ribosomal large subunit pseudouridine synthase [Brucella sp. F5/99]
          Length = 334

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 88/346 (25%), Positives = 162/346 (46%), Gaps = 45/346 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ ++ ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELIADSDAAGKRLDQWLAAALGPELSRSRVQSLIAYGHVTIDGAPARETKQKLREGMN 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L          + +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLSEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +    DS       ++P + HRLD++TSG++VVA+   A +HL+E F   
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADH 165

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                +++ Y +LVWG+ +  +  +  +L + SH       VV +  + A +AI+H+  +
Sbjct: 166 GRTGDLERAYLALVWGMTERPQGTVDAYLGR-SHRDRTKQAVVHEEREDARHAITHYATV 224

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPI 284
           + F+ +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        P+
Sbjct: 225 EKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPEPL 284

Query: 285 Q------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +      ++  LHA  +   HP     ++  APLP  M +  ++  
Sbjct: 285 KEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDMEQLLENFR 330


>gi|161503726|ref|YP_001570838.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160865073|gb|ABX21696.1| hypothetical protein SARI_01811 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 317

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 107/326 (32%), Positives = 173/326 (53%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  + V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDYLLVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + FA  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERFA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  ++G PI  D +Y    F         ++L+LHA  +   
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYVGHPIAFDDRYGDREFDKQLAGTGLSRLFLHAAALKFT 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  L+I AP+   + +    L 
Sbjct: 289 HPGTGDVLRIEAPMDDQLKRCLQVLR 314


>gi|170684091|ref|YP_001744093.1| 23S rRNA pseudouridylate synthase C [Escherichia coli SMS-3-5]
 gi|170521809|gb|ACB19987.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           SMS-3-5]
 gi|222032839|emb|CAP75578.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           LF82]
 gi|312945648|gb|ADR26475.1| 23S rRNA pseudouridylate synthase C [Escherichia coli O83:H1 str.
           NRG 857C]
          Length = 319

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 172/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP---IQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y         +      N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRHLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|304409811|ref|ZP_07391431.1| pseudouridine synthase, RluA family [Shewanella baltica OS183]
 gi|307304167|ref|ZP_07583920.1| pseudouridine synthase, RluA family [Shewanella baltica BA175]
 gi|304352329|gb|EFM16727.1| pseudouridine synthase, RluA family [Shewanella baltica OS183]
 gi|306913065|gb|EFN43488.1| pseudouridine synthase, RluA family [Shewanella baltica BA175]
          Length = 319

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 108/323 (33%), Positives = 173/323 (53%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q 
Sbjct: 5   STPQQVQLITIDEDHFEQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQI 64

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPP       + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V G
Sbjct: 65  GDIVRIPP-----VRVAEPDNRTAPSPNLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHG 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ Y +   L+S    +     L HRLD++TSG+L+VA+ R+A +HL +  R +++QK
Sbjct: 119 GSGVDYGVIEALRSLRPQQKF-LELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G    + + +   LLK +   G+ +  V         + + FK++  + Q   
Sbjct: 178 DYLALVKGEWSAQDKAVKQPLLKITLKSGERIVRVNAE---GKPSETRFKIMQRY-QGCT 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH    G PI  D KY    F G+  S    +L+LHA  +   HP
Sbjct: 234 LVKASPVTGRTHQIRVHCQFAGHPIACDDKYSEQGFDGSMRSLGLARLFLHAAELMFIHP 293

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E    ++++APL  ++ +  D L
Sbjct: 294 ENDEVMRVSAPLDENLSQLLDKL 316


>gi|288553139|ref|YP_003425074.1| large ribosomal pseudouridine synthesis protein [Bacillus
           pseudofirmus OF4]
 gi|288544299|gb|ADC48182.1| large ribosomal pseudouridine synthesis protein [Bacillus
           pseudofirmus OF4]
          Length = 304

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 83/329 (25%), Positives = 153/329 (46%), Gaps = 32/329 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +Q+ ++E + +N R+D++        +   +Q+ ++ GQV+V+ K  K N ++Q   
Sbjct: 1   MEEIQWTILEEN-KNERIDKFLTAQNGEWSRSQVQQWIKDGQVQVNGKATKSNYKMQVED 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +                +     L   ++ +   ++YED+ + V NKP G+ V    
Sbjct: 60  QVTLS---------------IPEPEELDVIAEDIPLDVVYEDADVIVVNKPRGMVVHPAP 104

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L    + +
Sbjct: 105 GHYTGTLVNALLYHCKDLSGINGVIRPGIVHRIDKDTSGLLMVAKNDHAHESLVSQLKAK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++ Y ++V G+  ++   I   + +           +   E  +  A++HF V++CF 
Sbjct: 165 TTKRHYKAIVHGVIPHQHGTIEAPIGRDKKD----RQSMTVTEDNSRDAVTHFTVLECF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F +++ +  TGRTHQ+RVH  ++G P+ GD KY    K    +       LHA  +  
Sbjct: 220 KDFTYVQCELETGRTHQIRVHMKYIGYPLAGDPKYGPKKK----TLEIEGQALHAATLGF 275

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
            HP  G  L+ +AP+P  M      L  K
Sbjct: 276 THPRTGEELEFSAPIPEDMEHLLHYLRKK 304


>gi|331652138|ref|ZP_08353157.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli M718]
 gi|320200981|gb|EFW75565.1| 23S rRNA pseudouridylate synthase C [Escherichia coli EC4100B]
 gi|331050416|gb|EGI22474.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Escherichia coli M718]
 gi|332089150|gb|EGI94259.1| pseudouridine synthase, RluA family protein [Shigella boydii
           5216-82]
 gi|332092815|gb|EGI97883.1| pseudouridine synthase, RluA family protein [Shigella dysenteriae
           155-74]
          Length = 319

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDDGLKRCLQKLR 316


>gi|37679452|ref|NP_934061.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio vulnificus YJ016]
 gi|37198196|dbj|BAC94032.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio vulnificus YJ016]
          Length = 315

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 107/324 (33%), Positives = 176/324 (54%), Gaps = 16/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ V ++ D    R+D + +N    +    + +I+R G+VRV+KKRVK   ++ +
Sbjct: 3   EIRTKVQIVDIDEDMAGQRIDNFLRNQLKDVPKSMIYRIVRKGEVRVNKKRVKAEYKLAA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPP       + K+      S  L K ++ L+ +++YED  + V NKP+G +V G
Sbjct: 63  GDIVRIPP-----VTLEKKDPETAPSTKLNKVAE-LQDLIIYEDDHLLVLNKPSGTAVHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 117 GSGLKFGAIEALRA-LRPEARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G  +N  + +   LLK        V+ + +       + + FKVI+ F Q   
Sbjct: 176 YYFALVMGEWENSCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKVIEKFPQ-AT 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T+    N+L+LHA  +   HP
Sbjct: 229 LVQASPITGRTHQIRVHTQYSGHPIAWDDRYGDRRFDAYTAQHGLNRLFLHAANIRFTHP 288

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
              + ++I AP+   + K   SL 
Sbjct: 289 ATEQIMEINAPMGELLEKVVQSLR 312


>gi|261493033|ref|ZP_05989574.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261496687|ref|ZP_05993066.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261307656|gb|EEY08980.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261311310|gb|EEY12472.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 320

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 105/322 (32%), Positives = 167/322 (51%), Gaps = 14/322 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q   +VR
Sbjct: 11  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQPDDLVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E+     S  L K ++ L+S +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPVR------VAEKNEAPISTKLNKVAE-LESQILYEDDSMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+ +  V    +    + + F + + +A     ++  
Sbjct: 183 VRGQWQAHTKVIKAPLLKNELASGERIVRV---SEEGKPSETRFSIEERYA-NATLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY    F          +L+LHA  +   HP+ G  
Sbjct: 239 PITGRTHQIRVHTQYAGHPIALDDKYGDVEFDSKMKEVGLQRLFLHAHAIRFEHPKTGEE 298

Query: 305 LQITAPLPAHMVKTWDSLGFKY 326
           + ITAPL   +      L   Y
Sbjct: 299 MVITAPLDKTLKGVLAKLRANY 320


>gi|288929438|ref|ZP_06423283.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 317 str. F0108]
 gi|288329540|gb|EFC68126.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 317 str. F0108]
          Length = 349

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 86/332 (25%), Positives = 153/332 (46%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+DR+      H +   +QK   +G V V+++ VK N +++ G V+ +  
Sbjct: 24  IVVDRGQVPVRIDRFMTERLQHSSRNRIQKAADAGFVHVNERPVKSNYKVRPGDVITLML 83

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +  I+              ++ +   ++YED  + V NKPAG+ V  G+G  +  
Sbjct: 84  DRPHHDTTIE--------------AEDIPLDVVYEDDALMVINKPAGMVVHPGAGNFHGT 129

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+   +  L HR+D++TSG+LVVA+T  A + L   F  +   + 
Sbjct: 130 LINAVAWHLRNMPSFDANDPEVGLVHRIDKDTSGLLVVAKTPEAKRKLGLQFFNKTTHRS 189

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVW      +  I   + +        + V   + +    A++H++V++ F     +
Sbjct: 190 YNALVWANFAEDEGRIEGNIGRDPR-DRLRMAVFPPDSETGKPAVTHYRVLERFG-YVTF 247

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----------IQNKLYL 290
           +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S           +  +  L
Sbjct: 248 VECILETGRTHQIRAHMKHIGHPMFGDERYGGTEILRGERSSTYKAYIQNCFKLCPRQAL 307

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HAR +   HP  G ++  T+PLP  M +  D 
Sbjct: 308 HARTLGFVHPTTGQQMDFTSPLPQDMEQLLDK 339


>gi|304383942|ref|ZP_07366399.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
 gi|304335020|gb|EFM01293.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
          Length = 357

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 83/332 (25%), Positives = 152/332 (45%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV++ +  +R+D++      H +   +Q    +G + V+ K VK N +++   VV +  
Sbjct: 28  TVVDSGQMPVRIDKYLFEKMQHSSRNRIQNAADAGFIHVNGKPVKSNYKVRPSDVVTLML 87

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +  I+ ++              +   ++YED+ + V NKPAG+ V  G+G  +  
Sbjct: 88  DRPQHDTTIEPEE--------------MPLEVVYEDNDLMVINKPAGLVVHPGAGNFHGT 133

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+L++A+T  A   L   F  +   + 
Sbjct: 134 LVNALAWYLKDLDTYDPNDPEVGLVHRIDKDTSGLLLIAKTPEAKSKLGVQFLNKTTHRS 193

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG   +++  I   + +        + V+  + +    A++H+KV++ F     W
Sbjct: 194 YVALVWGNFTDEEGRIEGNIARDPK-DRLRMTVLPSDSEMGKPAVTHYKVLERFG-YTTW 251

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ----------NKLYL 290
           +E    TGRTHQ+R H  ++G P+ GD +Y      +GN +S  +           +  L
Sbjct: 252 IECVLETGRTHQIRAHMKYIGHPLFGDERYGGTEILRGNRSSTYKAFVQNGLKICPRQAL 311

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA+ +   HP  GR +  T+PLP  +      
Sbjct: 312 HAQTLGFIHPTTGRQMDFTSPLPEDLSALLKR 343


>gi|170720703|ref|YP_001748391.1| RluA family pseudouridine synthase [Pseudomonas putida W619]
 gi|169758706|gb|ACA72022.1| pseudouridine synthase, RluA family [Pseudomonas putida W619]
          Length = 333

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 105/320 (32%), Positives = 172/320 (53%), Gaps = 13/320 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + VQ + V  +    R+D +       +    + +ILR G+VRV+K RVK   +IQ+G +
Sbjct: 24  SGVQLIEVAPELAGQRIDNFLITALKGVPRTLVYRILRKGEVRVNKGRVKPEYKIQAGDI 83

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP       + +  +    +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 84  VRVPP-----VRLPERDEPAPVAQGLLQR---LEAAIVYEDKALIVMNKPAGIAVHGGSG 135

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L+  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y 
Sbjct: 136 LSFGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYM 194

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     K+ +   LLK +   G+ +  V         A++ F+V+  F +    +E
Sbjct: 195 ALVRGHWPTSKKQVNAPLLKSNLRSGERMVEVNDE---GKEALTLFRVLRRFGEFATIVE 251

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   +F          +L+LHA  + +P P+GG
Sbjct: 252 ARPITGRTHQIRVHTLHAGHMIAGDSKYGDEDFSREIRDLGGKRLFLHAYALTVPLPDGG 311

Query: 304 RLQITAPLPAHMVKTWDSLG 323
            L++ AP+     KT + LG
Sbjct: 312 ELKLEAPVDEVWAKTVERLG 331


>gi|260912693|ref|ZP_05919179.1| ribosomal large subunit pseudouridine synthase C [Pasteurella
           dagmatis ATCC 43325]
 gi|260633071|gb|EEX51236.1| ribosomal large subunit pseudouridine synthase C [Pasteurella
           dagmatis ATCC 43325]
          Length = 381

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 169/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  +E   R+D +       +    + +ILR G+VRV+K R+K   ++Q+  +VR
Sbjct: 74  VKMLTISEEEAGQRIDNYLLAKLKGVPKSLIYRILRKGEVRVNKGRIKPEYKLQASDIVR 133

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E++    S  L K +  L++ +L+ED  + V NKP+GI+V GGSG+ 
Sbjct: 134 VPPVR------VSEKEQAPVSTKLNKVNQ-LENQILFEDDCLLVLNKPSGIAVHGGSGLN 186

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A ++L E  R + +QK Y +L
Sbjct: 187 FGVIEALRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRNLHEQLREKTVQKDYLAL 245

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V +       + + F + + + +    ++  
Sbjct: 246 VRGQWQSHCKVVKAPLLKNELSSGERIVRVSEQ---GKPSETRFSIEERY-ENATLVKAS 301

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F    +     +L+LHA  +   HP+ G  
Sbjct: 302 PVTGRTHQIRVHTQYAGHPIAFDDKYGDKQFDEQMSEIGLKRLFLHAFSIRFEHPKSGET 361

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+I APL   M      L 
Sbjct: 362 LRINAPLDDEMKGILKKLR 380


>gi|184155639|ref|YP_001843979.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
 gi|183226983|dbj|BAG27499.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
          Length = 304

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 85/326 (26%), Positives = 147/326 (45%), Gaps = 33/326 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +    Q + V +     R+D+   +H+P  +   L++ +  G V V+ + VK   ++Q+G
Sbjct: 1   MDQTTQTLTVTDGMTG-RIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V I P               ++ V +    + +   ++YED  + V NKP G+ V   
Sbjct: 60  DRVVIEP---------------ETPVEIDLEPENIPLDIVYEDDDVLVVNKPQGMVVHPA 104

Query: 123 SGIAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G   H   +  +     S      +P + HR+D++TSG+L+VA+T  A + LT   + +
Sbjct: 105 PGHPNHTLVNALMYHAPLSSINGELRPGIVHRIDKDTSGLLMVAKTDRAHRSLTAQLKEK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G+ K  +  I   L +          VV     G  +A++HF+V+  + 
Sbjct: 165 SNLREYVALVHGVIKENEGTIDAPLARSPKDRKKQAVVV-----GGRHAVTHFRVLKRY- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q +  +  +  TGRTHQ+RVH  ++  P+ GD  Y         +   +  YLHAR +  
Sbjct: 219 QHYTLVACRLETGRTHQIRVHMKYINHPLAGDPLYGPR-----KTLPGHGQYLHARLLGF 273

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL 322
            HP  G  +  TAP P +  +    L
Sbjct: 274 EHPVTGEEMVFTAPWPDYFEQMLSYL 299


>gi|225027663|ref|ZP_03716855.1| hypothetical protein EUBHAL_01922 [Eubacterium hallii DSM 3353]
 gi|224954977|gb|EEG36186.1| hypothetical protein EUBHAL_01922 [Eubacterium hallii DSM 3353]
          Length = 319

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 83/321 (25%), Positives = 144/321 (44%), Gaps = 32/321 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           Y  V  ++E MRLD++        +   +QK+++ G+V V  K+ K   R++    V I 
Sbjct: 21  YYTVMEEQEGMRLDQFLAGELKEHSRSYIQKLIKEGRVTVGDKKEKPGCRLKVEDNVVIC 80

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                    +KE ++L   ++L          ++YED  + + NKP  + V    G    
Sbjct: 81  ------VPPLKELEVLPEKMDLD---------IIYEDEDVILINKPKDMVVHPCPGRYTG 125

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             ++G L    D+        +P + HR+D++T+G+LVV +   A + L E  +   I +
Sbjct: 126 TLVNGLLYHCRDNLSGINGVLRPGIVHRIDKDTTGVLVVCKNDMAHKSLAEQLKEHSITR 185

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V+     ++  +   + + S      + V     K    A++H+KV+     +F 
Sbjct: 186 KYEAIVYNNFTQEEGTVDAPIGR-SPADRKKMAV---EPKNGKRAVTHYKVLSHLNHQFN 241

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E Q  TGRTHQ+RVH   +  P++GD  Y        T        LHAR +   HP 
Sbjct: 242 HIECQLETGRTHQIRVHMASIRHPLLGDTTYGPKNAMGLT-----GQCLHARVLGFIHPR 296

Query: 302 GGR-LQITAPLPAHMVKTWDS 321
            G  ++  APLP +  K  + 
Sbjct: 297 TGEYVEFEAPLPEYFQKLLEK 317


>gi|300723637|ref|YP_003712942.1| 23S rRNA pseudouridylate synthase [Xenorhabdus nematophila ATCC
           19061]
 gi|297630159|emb|CBJ90796.1| 23S rRNA pseudouridylate synthase [Xenorhabdus nematophila ATCC
           19061]
          Length = 318

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 105/319 (32%), Positives = 167/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +++DE   R+D +       +    + +ILR G+VR++K RVK   ++  G  +R
Sbjct: 8   VQFVTIDDDEAGQRIDNFLLARLKGVPKSMIYRILRKGEVRINKGRVKPEYKLTVGDTIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+       + E++    S  L K +  L   +LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPIR------VSEKQEPPVSAKLDKVA-ALAECILYEDDHILVINKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL++A+ R+A + L E  R++++QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRALHEQLRLKQMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ V  V         + + FKV + +A     +   
Sbjct: 180 VRGQWQSHCKVVEAPLLKNILQSGERVVKVSSE---GKPSETRFKVEERYA-FATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPE-GGR 304
           P TGRTHQ+RVH LH G PI  D +Y    F         N+L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTLHAGHPIAFDDRYGDRAFDAQLAETNLNRLFLHASSLKFTHPSMGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+  AP+   +      L 
Sbjct: 296 LRFEAPMDDRLRNCLRMLR 314


>gi|167855918|ref|ZP_02478667.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parasuis 29755]
 gi|219871480|ref|YP_002475855.1| 23S rRNA pseudouridylate synthase C [Haemophilus parasuis SH0165]
 gi|167852955|gb|EDS24220.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parasuis 29755]
 gi|219691684|gb|ACL32907.1| 23S rRNA pseudouridylate synthase C [Haemophilus parasuis SH0165]
          Length = 319

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 104/321 (32%), Positives = 169/321 (52%), Gaps = 14/321 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  + +DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q+  +VR
Sbjct: 11  VQFFTISDDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQADDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPVR------VAEKNEAPISTKLNKVAE-LEHQILYEDEVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGLLLVAKKRSALRSLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+ +  V    +    + + F VI+        ++  
Sbjct: 183 VRGQWQSHVKVIKAPLLKNELASGERIVRV---SEEGKPSETRF-VIEERYPIATLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGDREFDQKMQQAGLNRLFLHAHSIRFVHPKTGEE 298

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           + +TAPL   +      L  K
Sbjct: 299 MVVTAPLDKQLKAVLAKLRVK 319


>gi|320179214|gb|EFW54172.1| 23S rRNA pseudouridylate synthase C [Shigella boydii ATCC 9905]
          Length = 319

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 107/328 (32%), Positives = 174/328 (53%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSLG 323
             HP  GG ++I AP+   + +    L 
Sbjct: 289 FTHPGTGGVMRIEAPMDDGLKRCLQKLR 316


>gi|206560228|ref|YP_002230992.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           cenocepacia J2315]
 gi|198036269|emb|CAR52165.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           cenocepacia J2315]
          Length = 361

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 144/328 (43%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +V VD    K    +  G  + +
Sbjct: 16  RIVEVPLSLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAPAKIRQPVPLGAKIAL 75

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 76  VP------DLLPEQ--------LAFTPEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWS 121

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 122 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 181

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG    +   I   + +      +   +          A +HF+ +D      Q  
Sbjct: 182 FALVWGTMP-EAGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCLWQRQPV 237

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 238 SAIQCDLETGRTHQIRVHCAHAGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGL 297

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G+ +Q   PLP  M     +LGF
Sbjct: 298 VHPVTGKAMQWRCPLPDDMNALVAALGF 325


>gi|309796571|ref|ZP_07690978.1| pseudouridine synthase, RluA family [Escherichia coli MS 145-7]
 gi|308119883|gb|EFO57145.1| pseudouridine synthase, RluA family [Escherichia coli MS 145-7]
          Length = 319

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPAYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDDGLKRCLQKLR 316


>gi|294669553|ref|ZP_06734620.1| hypothetical protein NEIELOOT_01452 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291308466|gb|EFE49709.1| hypothetical protein NEIELOOT_01452 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 372

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 85/337 (25%), Positives = 145/337 (43%), Gaps = 29/337 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +   +RLD       P  +   L   ++ G V V+ K  K  +++  G+ + +  
Sbjct: 30  LTIPLEYAGLRLDAALAKLLPDYSRSRLADWIKEGAVSVNGKPAKPKDKLIGGEKLAV-- 87

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                       +I +S+  L    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 88  ------------QIRESNETLAFTPEAMDLDIIYEDDSVIVLNKPAGLVVHPAAGNWSGT 135

Query: 128 HIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L      +   +  + HRLD++TSG++VVA+T  A  HL +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPALQNIPRAGIVHRLDKDTSGLMVVAKTLPAQNHLVQQLQTRTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ + Q   ++E  
Sbjct: 196 ADGIVP-FDGKIETQIGRDPH-NRVKMAVVKF---GGKEAVTHVKVLERY-QAHSYIECA 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-----NFTSPIQNKLYLHARYMDLPHP- 300
             TGRTHQ+RVH      P+ GD  Y                   +  LHA  +   HP 
Sbjct: 250 LETGRTHQIRVHMREAKHPLAGDPVYGNPRHPCSDTVKTEIKALARQALHAYRLSFIHPQ 309

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            GG +Q  APLP  +      L  +   +  + R   
Sbjct: 310 NGGEMQFEAPLPQDIYHLLSVLRLESGLDSPLSREEE 346


>gi|118443119|ref|YP_878025.1| ribosomal large subunit pseudouridine synthase D [Clostridium novyi
           NT]
 gi|118133575|gb|ABK60619.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium novyi NT]
          Length = 304

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 82/324 (25%), Positives = 141/324 (43%), Gaps = 32/324 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
             +  ++  DE N RLD +    +   +    QK++    V V+    K N ++++G  V
Sbjct: 2   KTENFLINEDEANSRLDVFISKCFEEKSRSYAQKLIEDKNVLVNGSIKKSNYKLKTGDNV 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                +     +    + +K  +LYED  + V +KP G+ V  G+G 
Sbjct: 62  EVT---------------IKEDETINIEPEDIKLNILYEDEDVIVIDKPQGMVVHPGNGN 106

Query: 126 --AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++G L             +P + HR+D++TSG+LVVA+   A   L+E  +   +
Sbjct: 107 YSGTLVNGLLYHCDSLSSINGDVRPGIVHRIDKDTSGVLVVAKNDNAHIILSEQLKEHSM 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +LV GI K+ +  I   L +          V     +    AI+H++VI  F + 
Sbjct: 167 KREYVALVEGIIKDDEGTIDEPLGRNPKDRIKRAVV-----RNGKNAITHYEVIRRFNKN 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              ++    TGRTHQ+RVH  H+  P+VGD  Y    +        N   LHAR +   H
Sbjct: 222 -TLVKCILETGRTHQIRVHMAHINHPLVGDPMYGFKKQ----RFKLNGQMLHARKLGFIH 276

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P   + ++  + LP +  +    L
Sbjct: 277 PSSKKYMEFQSELPNYYKEILFKL 300


>gi|170726386|ref|YP_001760412.1| RluA family pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169811733|gb|ACA86317.1| pseudouridine synthase, RluA family [Shewanella woodyi ATCC 51908]
          Length = 319

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 105/323 (32%), Positives = 174/323 (53%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    VQ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q 
Sbjct: 5   SPKIKVQLVTIDEDHVGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQD 64

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VR+PP       + ++ +    S NL+K S  L+  +L+ED  + V NKPAG++V G
Sbjct: 65  GDIVRVPP-----VRVSEKDERPGPSANLSKVSQ-LEERILFEDKHLIVLNKPAGLAVHG 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ + I   ++S   ++     L HRLD++TSG+L++A+ R+A +HL +  R +++QK
Sbjct: 119 GSGVDFGIIEAMRSLRPTQKF-LELAHRLDKDTSGVLLIAKKRSALRHLHDQLRFKKMQK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  + + + I   LLK +   G+ +  V Q         + FK++  + Q   
Sbjct: 178 DYQALVKGTWQARDKAIKAPLLKLTLKSGERIVRVNQE---GKECETRFKILQRY-QGST 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D KY    +  +  +   N+L+LHA  +   HP
Sbjct: 234 LVQASPVTGRTHQIRVHCQYTGHPIACDEKYSEQKYDDSMRALGLNRLFLHAAQLRFTHP 293

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                + + APL   + +T D L
Sbjct: 294 GNEEVMIVKAPLDPVLTQTLDKL 316


>gi|259908803|ref|YP_002649159.1| 23S rRNA pseudouridylate synthase C [Erwinia pyrifoliae Ep1/96]
 gi|224964425|emb|CAX55934.1| 23S rRNA pseudouridylate synthase [Erwinia pyrifoliae Ep1/96]
 gi|283478783|emb|CAY74699.1| pseudouridylate synthase [Erwinia pyrifoliae DSM 12163]
          Length = 320

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 104/319 (32%), Positives = 172/319 (53%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  VR
Sbjct: 8   VHFIAISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++  + S  L K +  L++ +++ED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVR------VAEREEENVSPKLAKVA-ALEAAIIFEDDYLLVMNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +    +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPDARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+ V  V         + + FKV + +A     ++  
Sbjct: 180 VRGQWPSHVKAVRAPLLKNILQSGERVVKVSSE---GKPSETLFKVEERYA-IATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y    F    +S    +L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTLHAGHPIALDDRYGETEFDQQLSSTGLKRLFLHAAALRFTHPNTGEI 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           +++ APL   + +   +L 
Sbjct: 296 MRVEAPLDEQLKRCLAALR 314


>gi|308049100|ref|YP_003912666.1| ribosomal large subunit pseudouridine synthase C [Ferrimonas
           balearica DSM 9799]
 gi|307631290|gb|ADN75592.1| ribosomal large subunit pseudouridine synthase C [Ferrimonas
           balearica DSM 9799]
          Length = 320

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 100/321 (31%), Positives = 169/321 (52%), Gaps = 13/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ+V +  D    R+D + +     +    + ++LR G+VRV+KKR+K   ++  G  
Sbjct: 10  PQVQWVDITEDHAGQRIDNFLRTFLKGVPKSLIYRLLRKGEVRVNKKRIKPEYKLADGDQ 69

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RI P+      + +  + +  S  L K +  L+S ++YED  + V NKP+GI+V GGSG
Sbjct: 70  IRIAPI-----RVSERDETVAPSAKLEKVAQ-LESQIVYEDKVMLVINKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           I + +   L++   ++ Q   L HRLD+ TSG+L+VA+ R+A +HL +  R + ++K Y 
Sbjct: 124 INFGVIEALRALRPNERQ-LELVHRLDRATSGLLMVAKRRSALKHLQDQLREKTMRKQYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G    K   +   LLK +   G+ +  V   +     + + F++++ FA+    +E
Sbjct: 183 ALVKGQWNPKTRAVQAPLLKNTLGTGERLVRV---DAAGKPSETRFRIVENFAEG-TLVE 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  H G PI  D +Y  + F         ++L+LHA  +   HP   
Sbjct: 239 CSPITGRTHQIRVHTQHAGHPIACDERYGDDEFDVLMRKKGLDRLFLHAFRLSFTHPVEE 298

Query: 304 -RLQITAPLPAHMVKTWDSLG 323
             + + APL   +    ++L 
Sbjct: 299 VTMTVEAPLDNKLEAALEALR 319


>gi|157146217|ref|YP_001453536.1| 23S rRNA pseudouridylate synthase C [Citrobacter koseri ATCC
           BAA-895]
 gi|157083422|gb|ABV13100.1| hypothetical protein CKO_01974 [Citrobacter koseri ATCC BAA-895]
          Length = 317

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 109/329 (33%), Positives = 173/329 (52%), Gaps = 15/329 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH LH G PI  D +Y    F         ++L+LHA  +   
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTLHAGHPIAFDDRYGDREFDKQLAGTGLSRLFLHAAALKFT 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HP  G  ++I AP+   +      L  K 
Sbjct: 289 HPGTGEVMRIEAPMDNQLKHCLQVLRNKA 317


>gi|324017411|gb|EGB86630.1| pseudouridine synthase, RluA family [Escherichia coli MS 117-3]
          Length = 319

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQVPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|297519884|ref|ZP_06938270.1| 23S rRNA pseudouridylate synthase C [Escherichia coli OP50]
          Length = 319

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 105/328 (32%), Positives = 172/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+V + R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVTKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|319425978|gb|ADV54052.1| pseudouridine synthase, RluA family [Shewanella putrefaciens 200]
          Length = 330

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 107/319 (33%), Positives = 171/319 (53%), Gaps = 13/319 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +V
Sbjct: 20  QVQLITIDEDHFEQRIDNFLMTALKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQMGDIV 79

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP       + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V GGSG+
Sbjct: 80  RIPP-----VRVAESDNRTAPSANLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHGGSGV 133

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            Y +   L+S    +     L HRLD++TSG+L+VA+ R+A +HL +  R +++QK Y +
Sbjct: 134 DYGVIEALRSLRPQQKF-LELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQKDYLA 192

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G    + + +   LLK +   G+ +  V         + + FK++  + Q    ++ 
Sbjct: 193 LVKGEWSAQDKVVKQPLLKITLKSGERIVRVNAE---GKPSETRFKIMQRY-QGCTLVKA 248

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HPE   
Sbjct: 249 SPVTGRTHQIRVHCQFAGHPIACDDKYSEQGFDDSMRSLGLTRLFLHAAELMFIHPENDE 308

Query: 305 -LQITAPLPAHMVKTWDSL 322
            ++I+APL  ++ +  D L
Sbjct: 309 VMRISAPLDENLSQLLDKL 327


>gi|227551404|ref|ZP_03981453.1| pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|257887487|ref|ZP_05667140.1| pseudouridylate synthase [Enterococcus faecium 1,141,733]
 gi|257895982|ref|ZP_05675635.1| pseudouridylate synthase [Enterococcus faecium Com12]
 gi|293570492|ref|ZP_06681547.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E980]
 gi|227179523|gb|EEI60495.1| pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|257823541|gb|EEV50473.1| pseudouridylate synthase [Enterococcus faecium 1,141,733]
 gi|257832547|gb|EEV58968.1| pseudouridylate synthase [Enterococcus faecium Com12]
 gi|291609438|gb|EFF38705.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecium E980]
          Length = 303

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 148/327 (45%), Gaps = 36/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT ++  +     E+ R+D+   N + + +   +Q  L+   V V+ + VK N +++ G 
Sbjct: 1   MTELKTTI---YHESGRIDKVLTNLFSNYSRSQIQLWLKERAVSVNGEPVKANYKVKQGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +               ++     L    + +   ++YED  + V NKP G+ V   +
Sbjct: 58  EITV---------------LIPEPETLDVVPENIPLTIVYEDEDVAVINKPQGMVVHPSA 102

Query: 124 GIAY-HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G  +  +   L   V          +P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 103 GHTHGTMVNALMYHVKDLSTINGVIRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKDK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G   ++K  I   + + S        +     +    A++HF V++ F 
Sbjct: 163 TSLRKYVALVHGEIPHEKGTINAPIGR-SKENRKMQAIR----EDGKPAVTHFTVLERF- 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E++  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +  
Sbjct: 217 EGFTLVELKLETGRTHQIRVHMKYIGYPLAGDPVYGPK-----KTLKGNGQFLHAQMLGF 271

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLG 323
            HP    ++   APLP    KT + L 
Sbjct: 272 THPTTNEKMIFEAPLPEVFEKTLEKLR 298


>gi|117925074|ref|YP_865691.1| ribosomal large subunit pseudouridine synthase C [Magnetococcus sp.
           MC-1]
 gi|117608830|gb|ABK44285.1| ribosomal large subunit pseudouridine synthase C [Magnetococcus sp.
           MC-1]
          Length = 328

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 109/325 (33%), Positives = 175/325 (53%), Gaps = 12/325 (3%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  T V+ V V+ +    RLD++ K+ +P + F  +Q+++R+GQVRV+K R + + R+  
Sbjct: 5   SKPTAVRTVQVDEEYAGSRLDKFLKSQFPSVPFSLIQRLMRTGQVRVNKGRARGDRRLAF 64

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PPV         E+    +   +   S  +++  L+ D  I V NKPAGI V G
Sbjct: 65  GDWVRLPPVTP----PTAEELEHPNKEKILHQSADVEARTLHRDGWILVLNKPAGIPVHG 120

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           GSG  + +   +++ ++  G + +  L HRLD+ETSG+L+      A + LTE+ R  ++
Sbjct: 121 GSGHQWGVVDAVRASLEKLGIEAQAELCHRLDKETSGLLLFGLRPRAVRLLTEAMRENQV 180

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G+P  ++  I   L K +  GG+ + VV   E+G   A++H++V+  +   
Sbjct: 181 TKTYLTLVQGVPAARQGVINQPLSKGNVRGGERMVVV---EQGGQRAVTHYRVLRSYG-V 236

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              LE+Q  TGRTHQ+RVH   +G P+ GD KY    F          +L+LHA  +   
Sbjct: 237 ASLLEVQLETGRTHQIRVHMQWLGHPVAGDGKYGDKAFNKWMRERGLKRLFLHASELAFR 296

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSL 322
           HPE   +L   APL   + +  + L
Sbjct: 297 HPENEQKLAYQAPLDDELTRVLEGL 321


>gi|157375768|ref|YP_001474368.1| lysozyme [Shewanella sediminis HAW-EB3]
 gi|157318142|gb|ABV37240.1| Lysozyme [Shewanella sediminis HAW-EB3]
          Length = 325

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 105/320 (32%), Positives = 174/320 (54%), Gaps = 13/320 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + VQ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +
Sbjct: 14  SKVQLVTIDEDNVGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQDGDI 73

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP       +  +++    S  L+K S  L+  +L+ED  + V NKPAG++V GGSG
Sbjct: 74  VRVPP-----VRMADKEERPGPSAKLSKVSQ-LEDRILFEDKHLIVLNKPAGLAVHGGSG 127

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + I   ++S   ++     L HRLD++TSG+L++A+ R+A +HL +  R +++QK Y 
Sbjct: 128 VDFGIIEAMRSLRPTQKF-LELAHRLDKDTSGVLLIAKKRSALRHLHDQLRFKKMQKDYQ 186

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  + + + I   LLK +   G+ +  V Q         + FK+I  + Q    ++
Sbjct: 187 ALVKGTWQARDKAIKAPLLKLTLKSGERIVRVNQE---GKECETRFKIIQRY-QGSTLVQ 242

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY    +  +  +   N+L+LHA  +   HP   
Sbjct: 243 ASPVTGRTHQIRVHCQYTGHPIACDEKYSEQKYDDSIRALGLNRLFLHAAQLRFTHPGTE 302

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             + + APL   ++KT D L
Sbjct: 303 EVMIVKAPLDPVLIKTLDKL 322


>gi|163751081|ref|ZP_02158312.1| RluC [Shewanella benthica KT99]
 gi|161329242|gb|EDQ00241.1| RluC [Shewanella benthica KT99]
          Length = 319

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 105/320 (32%), Positives = 168/320 (52%), Gaps = 13/320 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +
Sbjct: 8   PKVQLVTIDEDHLGQRIDNYLMTKLKGVPKSRIYRIVRKGEVRVNKKRIKPEYKLQDGDI 67

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       +  +      S  LTK S  L+  +++ED  I V NKP+GI+V GGSG
Sbjct: 68  VRIPP-----VRVSDKSDRPGPSAKLTKVSQ-LEDRIVFEDKFIIVLNKPSGIAVHGGSG 121

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   +++   ++     L HRLD++TSG+L++A+ R+A +HL +  R +++QK Y 
Sbjct: 122 VDFGVIEAMRALRPTQKF-LELVHRLDKDTSGVLLIAKKRSALRHLHDQLRFKKMQKDYQ 180

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  + + + I   LLK +   G+ +  V Q         + FK++  + Q    ++
Sbjct: 181 ALVKGTWQARDKVIKAPLLKLTLKSGERIVRVNQE---GKECETRFKILQRY-QGATLVQ 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP   
Sbjct: 237 ASPVTGRTHQIRVHCQYAGHPIACDDKYSEQRFDDTMRVHGLNRLFLHAAQLRFTHPGTE 296

Query: 304 RLQI-TAPLPAHMVKTWDSL 322
            + I  APL   + +T D L
Sbjct: 297 EIMIVQAPLDPVLTETLDKL 316


>gi|317129279|ref|YP_004095561.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
 gi|315474227|gb|ADU30830.1| pseudouridine synthase, RluA family [Bacillus cellulosilyticus DSM
           2522]
          Length = 305

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 146/320 (45%), Gaps = 30/320 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   + ++E  +R+D++  +H+P  +   +Q+ +    ++V+   +K   ++++G  + 
Sbjct: 1   MELYEITSEENGVRIDKFISDHFPQWSRTIIQQWIVDNHIQVNGTPIKSKYKVKAGDHIE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           I                    + L   ++ L   ++YED  + V NKP G+ V    G  
Sbjct: 61  IR---------------EPDPIPLEIPAENLNLDIIYEDGDVLVVNKPRGMVVHPAPGHY 105

Query: 125 IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L    + +  +
Sbjct: 106 TGTLVNGLMYHCHDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDRAHESLVNQLKNKETK 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y+++V GI  + K  I   + +        +      EK +  A++HF+V++ F +  
Sbjct: 166 RRYYAIVSGIIPHDKGTIDAPIGRNPEDRQSMM----VTEKNSRDAVTHFQVVERFYR-H 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +  +  TGRTHQ+RVH  ++G PIVGD KY    K  F         LHA  +   HP
Sbjct: 221 TLVSCELETGRTHQIRVHLKYIGFPIVGDPKYGPRKKQKFP---IEGQALHAELLGFQHP 277

Query: 301 EGGRL-QITAPLPAHMVKTW 319
               L     P+P  M    
Sbjct: 278 STNELKTFQVPMPHDMETVL 297


>gi|251797854|ref|YP_003012585.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247545480|gb|ACT02499.1| pseudouridine synthase, RluA family [Paenibacillus sp. JDR-2]
          Length = 315

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 84/321 (26%), Positives = 147/321 (45%), Gaps = 33/321 (10%)

Query: 14  NDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
            ++   R+D++  +      I+   +Q+ ++SG V V++  VK N ++ SG  V I    
Sbjct: 19  PEQAGERIDKFVTDSLNEDSISRTQVQEWIKSGAVLVNQNTVKPNYKLSSGDHVGIRVPE 78

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
                I+ E   LD               ++YED+ + V NKP G+ V    G +     
Sbjct: 79  PEDAAIVAEDIPLD---------------IVYEDADVIVINKPRGMVVHPAPGHSSGTVV 123

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L+ A+   A   L E  +   + + Y +
Sbjct: 124 NALMYHCKDLSGINGVLRPGIVHRIDKDTSGLLMAAKNDLAHVSLAEQLKDHSVSRKYIA 183

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   + +  I   + +  +       +    ++ + +A++HF V++  A  +  +E+
Sbjct: 184 LVHGNLPHDQGTIDAPIGRDQNDRK----LFTVTDRNSKHAVTHFAVLERIADDYTIVEL 239

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y  N      +       LHA  +   HP  G  
Sbjct: 240 QLETGRTHQIRVHMKYIGYPLAGDPMYGRN-----KTVALKGQALHAAVLGFKHPRTGEF 294

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L+  AP+PA M    +SL  +
Sbjct: 295 LEFEAPIPADMEHVINSLRLR 315


>gi|109898450|ref|YP_661705.1| RluA family pseudouridine synthase [Pseudoalteromonas atlantica
           T6c]
 gi|109700731|gb|ABG40651.1| ribosomal large subunit pseudouridine synthase C [Pseudoalteromonas
           atlantica T6c]
          Length = 318

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 103/322 (31%), Positives = 172/322 (53%), Gaps = 15/322 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            VQ++ +E D E  R+D + +     +    + +I+R G++RV+KKRVK   ++Q+   +
Sbjct: 9   KVQFIDIEPDLEGQRIDNFLRTLLKGVPKSLIYRIVRKGEIRVNKKRVKPEYKLQAHDQL 68

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP+  +       +     S  L K +  L+S +L+ED  + V NKP+G++V GGSG+
Sbjct: 69  RIPPIRVS-------EPNEAPSTKLDKVA-SLESHILFEDDLLIVLNKPSGMAVHGGSGL 120

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L++ +  + +   L HRLD++TSG LV+A+ R+A ++L E  R +++ K Y +
Sbjct: 121 SFGVIEALRA-LRPQARFLELVHRLDRDTSGCLVIAKKRSALKNLHEQLRDKKMDKRYQA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     +  +   LLK     G+ +  V   +     + + F+V+D F+     +E 
Sbjct: 180 LVVGEWPENRYKVNAPLLKNILKSGERLVSV---DTEGKPSETRFRVLDRFS-GATLVEA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
            P TGRTHQ+RVH LH G PI  D KY  + F G        +L+LHA  +   HP+   
Sbjct: 236 SPITGRTHQIRVHCLHAGHPIACDDKYGDSEFTGLMNQKGLKRLFLHAYSLAFIHPKTED 295

Query: 304 RLQITAPLPAHMVKTWDSLGFK 325
           R+   APL   + +    L  +
Sbjct: 296 RVSFQAPLDKQLNRALSVLEIR 317


>gi|268589209|ref|ZP_06123430.1| ribosomal large subunit pseudouridine synthase [Providencia
           rettgeri DSM 1131]
 gi|291315465|gb|EFE55918.1| ribosomal large subunit pseudouridine synthase [Providencia
           rettgeri DSM 1131]
          Length = 319

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 103/327 (31%), Positives = 172/327 (52%), Gaps = 14/327 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+    VQ++ + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++ 
Sbjct: 1   MNTQNQVQFIDISDDEAGQRIDNFLLTKLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLV 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  VR+PPV       + E++    S  L K +  L + +L+ED  + V NKP+G +V 
Sbjct: 61  EGDQVRVPPVR------VAERETAPVSAKLDKVA-ALANCILFEDDVLLVLNKPSGTAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+++ +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R++++Q
Sbjct: 114 GGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRALHEQLRLKQMQ 172

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  ++  + +   LLK     G+ V  V         + + FKV + F    
Sbjct: 173 KDYLALVRGNWQSHMKVVQAPLLKNILQSGERVVKVSSE---GKPSETRFKVEERF-DNA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPH 299
             ++  P TGRTHQ+RVH L+ G PI  D +Y    F         N+L+LHA  +   H
Sbjct: 229 TLIKASPVTGRTHQIRVHTLYAGHPIAFDDRYGDKQFDSQLAGTGLNRLFLHASALKFTH 288

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLGFK 325
           P+ G  +++ APL   +      L  +
Sbjct: 289 PKTGDEMRLQAPLDNQLNHCLKILRSR 315


>gi|170768204|ref|ZP_02902657.1| ribosomal large subunit pseudouridine synthase C [Escherichia
           albertii TW07627]
 gi|170122970|gb|EDS91901.1| ribosomal large subunit pseudouridine synthase C [Escherichia
           albertii TW07627]
          Length = 319

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 109/328 (33%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            +G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  DAGDEVRIPPVR------VAEREEDAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTS--PIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y    F   FT      N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQFTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|300854258|ref|YP_003779242.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           ljungdahlii DSM 13528]
 gi|300434373|gb|ADK14140.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           ljungdahlii DSM 13528]
          Length = 302

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 86/326 (26%), Positives = 141/326 (43%), Gaps = 33/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +++V   +E NMRLD +    +   +   +Q ++    V V+ K  K N +I+SG 
Sbjct: 1   MESKKFLVCSEEE-NMRLDVFLSKCFQDKSRSYIQNVIEYKLVEVNGKAKKSNYKIKSGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I                +   VNL   S+ +   +LYED  + V NKP G+ V    
Sbjct: 60  NIEIT---------------IPDPVNLNIQSEDIPLDILYEDKDVIVVNKPQGMIVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G+     ++  L    D  G     +P + HR+D++TSGILVVA+   +   L +  +  
Sbjct: 105 GVYEGTLVNALLNHCRDLSGINGVTRPGIVHRIDKDTSGILVVAKNDNSHNKLAKQLKDH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G+ K  +  +   + +           V         AI+H+KVI  F 
Sbjct: 165 SMTREYIALVEGVVKLDEGTVDEPIARHPKDKIKMAVCV-----NGKRAITHYKVIKRFK 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                ++    TGRTHQ+RVH  ++G P+VGD  Y    +            LHA  +  
Sbjct: 220 NN-TLIKCILETGRTHQIRVHMAYIGHPLVGDPVYGYKKQ----RFKLGGQLLHAEKLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G+ ++    +P +  K    L
Sbjct: 275 IHPATGKYIEFETEIPDYFKKVIKVL 300


>gi|160880488|ref|YP_001559456.1| RluA family pseudouridine synthase [Clostridium phytofermentans
           ISDg]
 gi|160429154|gb|ABX42717.1| pseudouridine synthase, RluA family [Clostridium phytofermentans
           ISDg]
          Length = 313

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 74/334 (22%), Positives = 145/334 (43%), Gaps = 37/334 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++   ++++ E+ R+D +       I+   +QK+++   V+++   +K N R++ G 
Sbjct: 1   MENIKTCCIDSEYEDERIDSFLAEFEEGISRSYIQKLIKDSLVKINGNVIKANYRLKEGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++                  +   V+L   ++ +   +LYED  I V NKP G+ V   +
Sbjct: 61  ILTYE---------------VPQPVSLEIAAENIPLDILYEDEDIIVINKPKGLVVHPAA 105

Query: 124 GI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  L    D         +P + HR+D  T+G+LVV +   + Q + E  ++
Sbjct: 106 GHYSGTLVNALLYHCKDRLSGINGVMRPGIVHRIDMNTTGVLVVCKNDKSHQSIAEQLKV 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC- 235
             I + Y +LV+   K  +  +   + +   +    + +   N K    A+++++V++  
Sbjct: 166 HSITRKYEALVYNSFKQTEGTVDAPIGRH-PVDRKKMAI---NHKNGKNAVTNYRVLENF 221

Query: 236 -----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
                  Q +  +E    TGRTHQ+RVH   +  P++GD  Y                 L
Sbjct: 222 NLGYVHNQGYAHIECTLKTGRTHQIRVHMASLHHPLLGDDVYGPEKD----KFHLEGQAL 277

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           HAR +   HP     ++  APLP +  +  + L 
Sbjct: 278 HARVLGFLHPTTQEYMEFEAPLPEYFQQLIEKLR 311


>gi|311068067|ref|YP_003972990.1| pseudouridylate synthase [Bacillus atrophaeus 1942]
 gi|310868584|gb|ADP32059.1| pseudouridylate synthase [Bacillus atrophaeus 1942]
          Length = 303

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 82/322 (25%), Positives = 148/322 (45%), Gaps = 33/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            +    ++++ R+D++  +     +   +Q+ ++ G + V+   VK N ++Q G  V++ 
Sbjct: 5   EITALPEQKSERIDKFLASAEKDWSRTQVQQWVKDGHIEVNGSPVKANYKMQPGDQVKVT 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                          +     L   ++ +   + YED  + V NKP G+ V    G    
Sbjct: 65  ---------------VPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHVTG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + 
Sbjct: 110 TLVNGLMAHCKDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVHKTVTRK 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V GI  +    I   + +        + VV++       A++HF V++ F Q F  
Sbjct: 170 YMAVVHGIISHDDGTIDAPIGRDKK-DRQSMTVVRE----GKNAVTHFHVLERF-QDFTL 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E Q  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   HP  
Sbjct: 224 VECQLETGRTHQIRVHMKYIGFPLAGDPKYGPRKTIDF-----NGQALHAGILGFQHPRT 278

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
            + ++  APLP  M K  ++L 
Sbjct: 279 DKYIEFEAPLPGDMTKLIENLR 300


>gi|315500130|ref|YP_004088933.1| pseudouridine synthase, rlua family [Asticcacaulis excentricus CB
           48]
 gi|315418142|gb|ADU14782.1| pseudouridine synthase, RluA family [Asticcacaulis excentricus CB
           48]
          Length = 335

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 120/323 (37%), Positives = 186/323 (57%), Gaps = 6/323 (1%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   V+ + V   E+ +R+D++FK  +PH+N + L K+LRSGQVRVD  R K + R+ +G
Sbjct: 1   MSREVKILYVAEGEDGVRIDKFFKRRWPHLNHIQLNKLLRSGQVRVDGARAKADTRLSTG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VR+PP+ +A +   +EQ+  + +    +   + KS++LYED  +   NKP+G++VQGG
Sbjct: 61  QSVRVPPLPDAPS---EEQQKRERAELSPQEVRYAKSLVLYEDEDVIAINKPSGLAVQGG 117

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +    HID  L +W +   ++PRL HRLD++TSG+L++ ++ +AA  L  +F  R+  K 
Sbjct: 118 TKTKNHIDRLLSAWGEGL-ERPRLVHRLDRDTSGVLLLGKSPSAAARLAGAFAKRKAYKT 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+LV G P  K+  I   L+KK     + V      E GA  A + +  I   A +  W
Sbjct: 177 YWALVAGTPDPKEGVIDVPLVKKGINDREMVMPADPKEPGAEAAETEYVTISRAAHRLAW 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++PHTGRTHQLR H   +G  I+GD KY        +  +   L LH R +++PHP  
Sbjct: 237 MALRPHTGRTHQLRAHMQAIGHCILGDPKYKDEKSIALSEGL--GLQLHHRRIEIPHPTH 294

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
           G L + APL   +   +D  GF 
Sbjct: 295 GTLIVEAPLDPVIQAGFDRYGFD 317


>gi|78485049|ref|YP_390974.1| pseudouridine synthase, RluD [Thiomicrospira crunogena XCL-2]
 gi|78363335|gb|ABB41300.1| ribosomal large subunit pseudouridine synthase C [Thiomicrospira
           crunogena XCL-2]
          Length = 312

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 101/324 (31%), Positives = 171/324 (52%), Gaps = 16/324 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+++ V +++   R+D +   HY ++    + +I+R G+VRV+K RVK N R+  G  VR
Sbjct: 3   VRFIEVTSEDAGQRVDNFLMRHYRNVPKTLIYRIIRKGEVRVNKGRVKQNTRLNDGDTVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+       +            T     ++  +LYED+ + V NKP+GI+V GGSGI 
Sbjct: 63  VPPIRVPEKTEVTVP---------TNQMQRIEDSILYEDNDLLVINKPSGIAVHGGSGIQ 113

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   +++ +    ++  L HR+D++TSG +++A+  +  + L E  R  ++ K Y +L
Sbjct: 114 WGLIEIVRA-LRPLAKRLELVHRIDRDTSGCILLAKKASVLKALHEQIRENKMTKEYLAL 172

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V        E I   LLK +   G+ V  V         ++S+F+V++ + Q+   + ++
Sbjct: 173 VAHHWPKGLEKIDLPLLKNTLKSGERVVKVSDE---GKPSVSYFRVVERY-QECDLVAVR 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGGR- 304
             TGRTHQ+RVHAL  GCP+VGD KY        F +    +L LHA+Y+   HP     
Sbjct: 229 LKTGRTHQIRVHALSQGCPLVGDDKYGEKETNKIFRAKGMKRLALHAQYLGFEHPVTEEW 288

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           L+I APL     +T  +L  + + 
Sbjct: 289 LKIEAPLHDDFKQTIANLKREKNE 312


>gi|269967347|ref|ZP_06181408.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           alginolyticus 40B]
 gi|269828055|gb|EEZ82328.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           alginolyticus 40B]
          Length = 368

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 100/324 (30%), Positives = 176/324 (54%), Gaps = 16/324 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++++
Sbjct: 57  EIRTKVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKLKA 116

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPP       + K+   +  S  L K ++ L++++++ED  + + NKP+G +V G
Sbjct: 117 GDLVRIPP-----VTVEKKDDDVAPSTKLNKVAE-LENMIIFEDDHMLILNKPSGTAVHG 170

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K
Sbjct: 171 GSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKK 229

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  K+  + +   LLK        V+ + +       + + FK+++ F Q   
Sbjct: 230 FYLALVMGQWKSSCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKILEKFEQ-AT 282

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  +   HP
Sbjct: 283 LIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGLDRLFLHAANIKFQHP 342

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
                ++I AP+   + K    L 
Sbjct: 343 SNDEWMEINAPMEPKLEKVLAGLR 366


>gi|167464425|ref|ZP_02329514.1| YlyB [Paenibacillus larvae subsp. larvae BRL-230010]
 gi|322384100|ref|ZP_08057818.1| pseudouridylate synthase-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
 gi|321151180|gb|EFX44489.1| pseudouridylate synthase-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
          Length = 311

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 140/322 (43%), Gaps = 32/322 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   +    R+D++       ++   +Q+ ++ G + V++K+VK N ++  G  +++   
Sbjct: 15  IAGEEHAGERIDKFVSECLDGVSRTQIQQWIKEGHISVNEKQVKPNYKLAEGDRIKLNIP 74

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                 I  E   LD               + YED  + V NKP G+ V    G      
Sbjct: 75  DPEQVDIRPEPIPLD---------------IYYEDKDVIVVNKPRGMVVHPAPGHSSGTL 119

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  +    D  G     +P + HR+D++TSG+++ A+   A   L +  +   + + Y 
Sbjct: 120 VNALMYHCKDLSGINGEMRPGIVHRIDKDTSGLIMAAKHDKAHASLADQLKEHSVTRKYL 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   +++  +   + +       Y       EK +  A++HF V++ F   +   E
Sbjct: 180 ALVQGNLAHEQGTVEAPIGRDPKDRKLY----TVTEKNSKEAVTHFVVMERFGD-YTLTE 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++  TGRTHQ+RVH   +G P+VGD  Y  + K            LHA  +   HP    
Sbjct: 235 LKLETGRTHQIRVHMKFIGHPLVGDPAYGKSKK-----EWIRGQALHAAVLGFKHPMTRE 289

Query: 305 -LQITAPLPAHMVKTWDSLGFK 325
            L+  APLP  M +   SL  +
Sbjct: 290 YLEFEAPLPEDMKQLIHSLRNR 311


>gi|227111672|ref|ZP_03825328.1| 23S rRNA pseudouridylate synthase C [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 318

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 106/319 (33%), Positives = 171/319 (53%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  DE   R+D +   H   +    + +ILR G+VR++KKRVK   ++  G V+R
Sbjct: 8   VQFVTISADEAGQRIDNFLHTHLKGVPKSMVYRILRKGEVRINKKRVKPEYKLLDGDVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A      E+     S +L K +  L   ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRQA------ERDETPVSASLGKVA-ALAECIIYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V  +      + + FK+ + F +    +   
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILQSGERIVRVNSD---GKPSETRFKIEERF-EHATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA H G PI  D +Y    F          +L+LHA+ +   HP  G  
Sbjct: 236 PVTGRTHQIRVHAQHAGHPIAFDDRYGDREFDQQLADTGLKRLFLHAQALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L++ APL + + +    L 
Sbjct: 296 LRVEAPLDSGLRRCLQVLR 314


>gi|325680269|ref|ZP_08159829.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
 gi|324107978|gb|EGC02234.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
          Length = 304

 Score =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 142/330 (43%), Gaps = 38/330 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      +   ++   R+D+        ++   LQK+   G V V  K V  N ++++G 
Sbjct: 1   MGERFEFIAAPEDAGTRIDKLLSAQLSDMSRSALQKLTEDGSVLVGGKAVSKNYKLKNGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +                +     L      +   ++YED  + V NKP G+ V   +
Sbjct: 61  VITVD---------------IPEPQELKAEPQDIPIDIVYEDDALLVVNKPKGMVVHPAA 105

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + YH  G L S   +   +P + HR+D+ TSG+L+VA+T  A   L    
Sbjct: 106 GNPDGTLVNALLYHCKGRLSSI--NGVIRPGIVHRIDKFTSGLLMVAKTDKAHNSLAAQI 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +     + Y ++  G  K     I   + + S      + V  QN   +  A++H++VI+
Sbjct: 164 KEHSFTREYNAVCVGRFKEPTGTINEPIGR-SKFDRKKMCVTYQN---SKEAVTHYEVIE 219

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              Q +  +  +  TGRTHQ+RVH+  +G P++GD  Y   +KG           LHA+ 
Sbjct: 220 ELGQ-YSLVRFRLETGRTHQIRVHSAFIGHPVLGDDVYGRPYKG------IEGQCLHAKK 272

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +   HPE G  ++  + LP +  +  D L 
Sbjct: 273 LGFVHPETGEYMEFDSQLPDYFTRILDKLR 302


>gi|170733153|ref|YP_001765100.1| RluA family pseudouridine synthase [Burkholderia cenocepacia MC0-3]
 gi|169816395|gb|ACA90978.1| pseudouridine synthase, RluA family [Burkholderia cenocepacia
           MC0-3]
          Length = 360

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 144/328 (43%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +V VD    K    +  G  + +
Sbjct: 16  RVVEVPLSLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAPAKIRQPVPLGAKIAL 75

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V NKPAG+ V   +G   
Sbjct: 76  VP------DLLPEQ--------LAFTPEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWS 121

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + D+     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 122 GTILNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 181

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
           ++LVWG    +   I   + +      +   +          A +HF+ +D      Q  
Sbjct: 182 FALVWGTMP-EAGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDTCLWQRQPV 237

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H G P++GD  Y         +P+ +   +  LHA  + L
Sbjct: 238 SAIQCDLETGRTHQIRVHCAHAGHPLLGDPVYGRARGKRSVTPLPDGFARQALHAWRLGL 297

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP  G+ +Q   PLP  M     +LGF
Sbjct: 298 VHPVTGKAMQWRCPLPDDMNTLVAALGF 325


>gi|149192304|ref|ZP_01870513.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio shilonii AK1]
 gi|148833857|gb|EDL50885.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio shilonii AK1]
          Length = 315

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 108/325 (33%), Positives = 180/325 (55%), Gaps = 17/325 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V +++D    R+D + +N   +I    + +I+R G+VRV+KKRVK   ++
Sbjct: 1   MSEIRTKVQFVDIDDDMAGQRIDNFLRNQLKNIPKSVVYRIVRKGEVRVNKKRVKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G  VRIPP       I ++Q+    S  L K ++ L+S ++YED  + + NKP+GI+V
Sbjct: 61  QAGDSVRIPP-----VTIEEKQEEAPISTKLNKVAE-LESQIIYEDDHMLILNKPSGIAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y++LV G  K     +   LLK        V+ + +       + + FKV++ F Q 
Sbjct: 174 QKYYFALVMGKWKPSCRVVKAPLLKNE------VNSIVRVNPNGKPSETRFKVLESFEQ- 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T+    ++L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTAKVGLDRLFLHAANIVFM 286

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSL 322
           HP    +++I A +   + +    L
Sbjct: 287 HPANDEKMEIHAEMEPKLQQAIKKL 311


>gi|153810897|ref|ZP_01963565.1| hypothetical protein RUMOBE_01281 [Ruminococcus obeum ATCC 29174]
 gi|149833293|gb|EDM88375.1| hypothetical protein RUMOBE_01281 [Ruminococcus obeum ATCC 29174]
          Length = 304

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 87/331 (26%), Positives = 155/331 (46%), Gaps = 39/331 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +++  +++ E+N+R+D++     P ++   LQK+L+ G V V+ + VK N + Q G 
Sbjct: 1   MEKLEF-NIDSSEKNVRIDKYLAECCPDLSRSYLQKLLKDGAVSVNTRIVKANYKTQPGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +         I  E   LD               +LYED  + V NKP  + V   +
Sbjct: 60  HVILNIPDLQTPDIKPENIPLD---------------ILYEDQWLMVVNKPKDMVVHPSA 104

Query: 124 GIAYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           G   H++G L + V +             +P + HR+D++T+G L++ +     ++L E 
Sbjct: 105 G---HMEGTLVNAVMAHCGDNLSGINGVMRPGIVHRIDKDTTGALLICKDDMVHRNLAEQ 161

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            +   I++ Y ++V G  K  +  +   + +   I    + +   N K    A++H+KV+
Sbjct: 162 LKEHSIKRRYRAIVQGNIKEDEGTVDAPIGRH-PIDRKKMAI---NHKNGKEAVTHYKVL 217

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F Q   ++E +  TGRTHQ+RVH   +G P++GD  Y ++              LHA 
Sbjct: 218 ERFGQ-TTYIECRLETGRTHQIRVHMASLGHPLLGDTVYGSSKNPYH----LQGQALHAM 272

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            +   HP  G  ++  AP+P +  K  D L 
Sbjct: 273 ILGFIHPVTGEYMEFEAPIPEYFSKLLDKLR 303


>gi|307267026|ref|ZP_07548541.1| pseudouridine synthase, RluA family [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|306917951|gb|EFN48210.1| pseudouridine synthase, RluA family [Thermoanaerobacter wiegelii
           Rt8.B1]
          Length = 305

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 86/331 (25%), Positives = 150/331 (45%), Gaps = 35/331 (10%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M  V  +V+  E ++E  R+D +            ++K++    V V+ K VK + +++ 
Sbjct: 1   MNVVDKIVLQGEKEDEGKRIDVFLAAEL-DYTRSYIKKLIVDELVFVNGKTVKPSYKVKE 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              V +         ++ E   LD               +LYED  I V NKP G+ V  
Sbjct: 60  NDEVVVNIPEAEKIDVLPENIPLD---------------ILYEDDDIIVINKPQGMVVHP 104

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++  L    +  G     +P + HRLD++TSG++VVA+   A   L+   +
Sbjct: 105 APGNYSGTLVNALLYHCKNLSGINGILRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y ++V G+ K+++  I   L+ +  +    + V+    +   YA++ +KV++ 
Sbjct: 165 ERSVFKKYVAIVEGVIKHEEGKIEA-LIGRHPVDRKKMAVI----EDGRYALTLYKVLER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F +    +E    TGRTHQ+RVH  ++G P+VGD  Y    +            LH+  +
Sbjct: 220 FKEN-TLVEAVIKTGRTHQIRVHMAYIGHPVVGDPVYGFKKQ----KFKLEGQALHSHVL 274

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
              HP  G  ++  APLP + V+  + L  K
Sbjct: 275 GFMHPTKGVYMEFEAPLPEYFVRLIEILRNK 305


>gi|256964973|ref|ZP_05569144.1| pseudouridylate synthase [Enterococcus faecalis HIP11704]
 gi|256955469|gb|EEU72101.1| pseudouridylate synthase [Enterococcus faecalis HIP11704]
 gi|295113102|emb|CBL31739.1| ribosomal large subunit pseudouridine synthase D [Enterococcus sp.
           7L76]
          Length = 301

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 88/327 (26%), Positives = 154/327 (47%), Gaps = 39/327 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  + 
Sbjct: 1   MEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          I E ++LD        ++ +   ++YED+ + V NKP G+ V   +G  
Sbjct: 61  VT---------IPEPEVLD------MVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAG-- 103

Query: 127 YHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            H +G L + +               P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 104 -HPNGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ F 
Sbjct: 163 TSLRKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLERF- 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +  
Sbjct: 217 DAFTLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLLGF 271

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  L   APLP    KT   L 
Sbjct: 272 THPTTGEQLVFEAPLPEVFEKTLHQLR 298


>gi|260909666|ref|ZP_05916361.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 472 str. F0295]
 gi|260636225|gb|EEX54220.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 472 str. F0295]
          Length = 349

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 89/335 (26%), Positives = 156/335 (46%), Gaps = 42/335 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+DR+      H +   +QK   SG V V+++ VK N +++ G V+ +  
Sbjct: 24  IVVDKGQVPVRIDRFMTERLQHSSRNRIQKAADSGFVHVNERPVKSNYKVRPGDVITLML 83

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +  I+ ++I                 ++YED  + V NKPAG+ V  G+G   + 
Sbjct: 84  DRPHHDTTIEAEEI--------------PLDVVYEDEALMVINKPAGMVVHPGAG---NF 126

Query: 130 DGFLKSWV----------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +G L + V          D+   +  L HR+D++TSG+LVVA+T  A + L   F  +  
Sbjct: 127 NGTLINAVAWHLRNMPSFDANDPEVGLVHRIDKDTSGLLVVAKTPEAKRKLGLQFFNKTT 186

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y +LVW      +  I   + +        + V   + +    A++H++V++ F   
Sbjct: 187 HRSYNALVWANFAENEGRIEGNIGRDPR-DRLRMAVFPPDSEMGKPAVTHYRVLERFG-Y 244

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----------IQNK 287
             ++E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S           +  +
Sbjct: 245 VTFVECILETGRTHQIRAHMKHIGHPMFGDERYGGTEILRGERSSTYKAYIQNCFKLCPR 304

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
             LHAR +   HP  G ++  T+P+P  M +  D 
Sbjct: 305 QALHARTLGFVHPNTGQQMDFTSPMPQDMEQLLDK 339


>gi|312111747|ref|YP_003990063.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
 gi|311216848|gb|ADP75452.1| pseudouridine synthase, RluA family [Geobacillus sp. Y4.1MC1]
          Length = 304

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 147/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V++  ++ + +N R+D+         +   +Q+ +++  V V+ + VK N +  +G 
Sbjct: 1   MDIVRFH-IDEEYDNERIDKVIAALNEDWSRSKVQQWIKNQLVTVNDQHVKANYKCSAGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V +                L     L    + +   + YED+ + V NKP G+ V    
Sbjct: 60  IVVVR---------------LPEPEPLYVEPENIPLDIYYEDADVLVVNKPRGMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HR+D++TSG+L+VA+   A Q L +    +
Sbjct: 105 GHMRGTLVNALLAHCHDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDMAHQALVDQLVKK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  +    I   + +           +   E+    A++HF+V++ F 
Sbjct: 165 TVTRKYKAIVHGVIPHDYGTIDAPIGRDKRDRKK----MAVTEENGKEAVTHFRVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +++ ++E Q  TGRTHQ+RVH  ++G P+ GD +Y         +   +   LHA  +  
Sbjct: 220 RQYTFIECQLETGRTHQIRVHMKYIGYPLAGDPQYGPK-----KTLPIDGQALHAGVLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  L+  APLP    +    L 
Sbjct: 275 SHPRTGEYLEFEAPLPPEFEQLLQLLR 301


>gi|254361221|ref|ZP_04977365.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|153092712|gb|EDN73761.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
          Length = 320

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 106/322 (32%), Positives = 167/322 (51%), Gaps = 14/322 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R K   ++Q   +VR
Sbjct: 11  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRNKPEYKLQPDDLVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E+     S  L K ++ L+S +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPVR------VAEKNEAPISTKLNKVAE-LESQILYEDESMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+ +  V    +    + + F + + +A     ++  
Sbjct: 183 VRGQWQAHTKVIKAPLLKNELASGERIVRV---SEEGKPSETRFSIEERYA-NATLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F          +L+LHA  +   HP+ G  
Sbjct: 239 PITGRTHQIRVHTQYAGHPIALDDKYGDAEFDSKMKEVGLQRLFLHAHAIRFEHPKTGEE 298

Query: 305 LQITAPLPAHMVKTWDSLGFKY 326
           + ITAPL   +      L   Y
Sbjct: 299 MVITAPLDKTLKGVLAKLRANY 320


>gi|308186402|ref|YP_003930533.1| pseudouridylate synthase [Pantoea vagans C9-1]
 gi|308056912|gb|ADO09084.1| putative pseudouridylate synthase [Pantoea vagans C9-1]
          Length = 318

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 104/321 (32%), Positives = 167/321 (52%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V +V +  +    R+D + +     +    + +I+R G+VRV+KKRVK   +++ G  
Sbjct: 6   PGVHFVAITAENAGQRIDNFLRTQLKGVPKSMIYRIVRKGEVRVNKKRVKPEYKLEEGDE 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S  L K +  L   +L+ED  + V NKP+G +V GGSG
Sbjct: 66  VRIPPVR------VAERDEDAVSPKLAKVA-SLADAILFEDESLLVMNKPSGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y 
Sbjct: 119 LSFGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   +  + +   LLK     G+ V  V         + + FKV + F +    ++
Sbjct: 178 ALVRGNWPSHLKVVQAPLLKNILQSGERVVRVSSE---GKASETRFKVEERF-EFATLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D +Y   +F     S    +L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHTLHAGHPIAFDDRYGERDFDSQLASTGLKRLFLHAAALTFTHPATG 293

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             +++ APL   + +  + L 
Sbjct: 294 EVMRVEAPLDEGLKQCLNKLR 314


>gi|16764542|ref|NP_460157.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|168237272|ref|ZP_02662330.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|168244787|ref|ZP_02669719.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|168822633|ref|ZP_02834633.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|194444187|ref|YP_002040440.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194448791|ref|YP_002045185.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194738103|ref|YP_002114185.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197263790|ref|ZP_03163864.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|198244450|ref|YP_002215951.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|204930731|ref|ZP_03221604.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|207857306|ref|YP_002243957.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|238910994|ref|ZP_04654831.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|34395808|sp|Q8ZQ16|RLUC_SALTY RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|16419703|gb|AAL20116.1| 23S rRNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|194402850|gb|ACF63072.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194407095|gb|ACF67314.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|194713605|gb|ACF92826.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|197242045|gb|EDY24665.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197289855|gb|EDY29216.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|197938966|gb|ACH76299.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|204320190|gb|EDZ05394.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205336408|gb|EDZ23172.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|205340990|gb|EDZ27754.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|206709109|emb|CAR33442.1| ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70)
           [Salmonella enterica subsp. enterica serovar Enteritidis
           str. P125109]
 gi|261246398|emb|CBG24207.1| ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70)
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. D23580]
 gi|301157727|emb|CBW17219.1| ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70)
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. SL1344]
 gi|312912174|dbj|BAJ36148.1| 23S rRNA pseudouridine synthase C [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|321223804|gb|EFX48867.1| Ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|323129456|gb|ADX16886.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|326623699|gb|EGE30044.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332988077|gb|AEF07060.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 319

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 105/328 (32%), Positives = 172/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +         +L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDNALKRCLQVLR 316


>gi|54308380|ref|YP_129400.1| putative 23S rRNA ribosomal pseudouridinesynthase [Photobacterium
           profundum SS9]
 gi|46912808|emb|CAG19598.1| putative 23S rRNA ribosomal pseudouridinesynthase [Photobacterium
           profundum SS9]
          Length = 307

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 176/319 (55%), Gaps = 16/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q++ + +D    R+D + +    ++    + +ILR G+VRV+KKR+K   ++Q G ++R
Sbjct: 1   MQFIDITDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDLIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      + +++     S  L+K ++ L+S ++YED  + V NKP+G +V GGSG+ 
Sbjct: 61  VPPIF-----MPEQENQAPISTKLSKVAE-LESCVIYEDDHLLVLNKPSGTAVHGGSGLK 114

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + ++K Y++L
Sbjct: 115 FGAIEALRA-LRPDARYLELVHRIDRDTSGILLVAKKRSALRKLQEQFREKTVKKYYFAL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K   + +   LLK        V+ + +       + + FKV++ F +    ++  
Sbjct: 174 VMGEWKASSKKVTAPLLKNE------VNSIVRVNPNGKASDTRFKVLERF-EHATLVQAS 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +   HP     
Sbjct: 227 PVTGRTHQIRVHCQYEGHPIAWDDRYGDPRFDAYTKKTGLNRLFLHAANIKFTHPSTDEP 286

Query: 305 LQITAPLPAHMVKTWDSLG 323
           + I+APL A + ++ D+L 
Sbjct: 287 VDISAPLDALLTRSLDNLR 305


>gi|253688887|ref|YP_003018077.1| pseudouridine synthase, RluA family [Pectobacterium carotovorum
           subsp. carotovorum PC1]
 gi|251755465|gb|ACT13541.1| pseudouridine synthase, RluA family [Pectobacterium carotovorum
           subsp. carotovorum PC1]
          Length = 318

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 107/319 (33%), Positives = 169/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  DE   R+D +   H   +    + +ILR G+VR++KKRVK   ++  G V+R
Sbjct: 8   VQFVTISADEAGQRVDNFLHTHLKGVPKSMVYRILRKGEVRINKKRVKPEYKLLDGDVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A      E+     S +L K +  L   ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRQA------ERDETPVSASLGKVA-ALAECIIYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ V  V         + + FKV + F +    +   
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILQSGERVVRVNSE---GKPSETRFKVEERF-EHATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D +Y    F          +L+LHA+ +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDEQLADTGLKRLFLHAQALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+I APL   + +   +L 
Sbjct: 296 LRIEAPLDNGLRRCLQALR 314


>gi|323339837|ref|ZP_08080106.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           ruminis ATCC 25644]
 gi|323092710|gb|EFZ35313.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           ruminis ATCC 25644]
          Length = 301

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 81/322 (25%), Positives = 143/322 (44%), Gaps = 34/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  VVE   +N RLD+     +   +   ++++L  G + V+ K  K   +++SG V+R
Sbjct: 1   MKETVVE--MQNGRLDKVCSEIFSDYSRSQIKQLLDGGNITVNGKTEKAKYKVKSGDVIR 58

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +                   +  L    + +   ++YED  + V NKP G+ V    G  
Sbjct: 59  LE---------------EPETKTLELRPENIPLDIVYEDDDVIVINKPQGMVVHPAPGHD 103

Query: 127 YHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            H   +  L     S      +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 104 EHTLVNALLYHCPLSTINGTFRPGIVHRIDKDTSGLLMVAKNDKAHRSLAKQLKDKTNIR 163

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G     +  I   + +          V     K    A++HF+V+  + + + 
Sbjct: 164 EYVALVHGRIAEDEGTINAPIGRSLKDRKKQAVV-----KDGRNAVTHFEVLKKY-RDYT 217

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +++    TGRTHQ+RVH  ++G P+VGD  Y         +   N  +LHA  +   HP 
Sbjct: 218 FVKCILETGRTHQIRVHMKYIGHPLVGDPLYGPK-----KTIKGNGQFLHAGKLGFVHPT 272

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G+ L   APLP    +  + L
Sbjct: 273 TGKLLIFEAPLPKIFQECLEKL 294


>gi|283784875|ref|YP_003364740.1| ribosomal large subunit pseudouridine synthase C [Citrobacter
           rodentium ICC168]
 gi|282948329|emb|CBG87914.1| ribosomal large subunit pseudouridine synthase C [Citrobacter
           rodentium ICC168]
          Length = 317

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 106/326 (32%), Positives = 172/326 (52%), Gaps = 15/326 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  +RIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEIRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKNVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F     +   ++L+LHA  +   
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLAATGLSRLFLHAAALKFT 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  L+I AP+   +      L 
Sbjct: 289 HPGTGEVLRIEAPMDGQLKHCLQVLR 314


>gi|267992961|gb|ACY87846.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|320086374|emb|CBY96147.1| pseudouridylate synthase [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
          Length = 347

 Score =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 105/328 (32%), Positives = 172/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 29  MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 88

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 89  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 141

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 142 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 200

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 201 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 256

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +         +L+LHA  + 
Sbjct: 257 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALK 316

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 317 FTHPGTGEVMRIEAPMDNALKRCLQVLR 344


>gi|295399734|ref|ZP_06809715.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294978137|gb|EFG53734.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 304

 Score =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 146/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V++  ++ + +N R+D+         +   +Q+ ++   V V+ + VK N +  +G 
Sbjct: 1   MDIVRFH-IDEEYDNERIDKVIAALNEDWSRSKVQQWIKKQLVTVNDQHVKANYKCSAGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V +                L     L    + +   + YED+ + V NKP G+ V    
Sbjct: 60  IVVVR---------------LPEPEPLYVEPENIPLDIYYEDADVLVVNKPRGMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HR+D++TSG+L+VA+   A Q L +    +
Sbjct: 105 GHMRGTLVNALLAHCHDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDMAHQALVDQLVKK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  +    I   + +           +   E+    A++HF+V++ F 
Sbjct: 165 TVTRKYKAIVHGVIPHDYGTIDAPIGRDKRDRKK----MAVTEENGKEAVTHFRVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +++ ++E Q  TGRTHQ+RVH  ++G P+ GD +Y         +   +   LHA  +  
Sbjct: 220 RQYTFIECQLETGRTHQIRVHMKYIGYPLAGDPQYGPK-----KTLPIDGQALHAGVLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  L+  APLP    +    L 
Sbjct: 275 SHPRTGEYLEFEAPLPPEFEQLLQLLR 301


>gi|186475732|ref|YP_001857202.1| RluA family pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184192191|gb|ACC70156.1| pseudouridine synthase, RluA family [Burkholderia phymatum STM815]
          Length = 436

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 88/328 (26%), Positives = 146/328 (44%), Gaps = 29/328 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +V VD +  K    +  G  + +
Sbjct: 81  RVVTVPPGLAGERLDKVLAKVFPEFSRSRLQSWIEAQRVHVDGQPAKIRQPVPLGASIEL 140

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P       ++ EQ        L   ++ +   ++YED  + V NKPAG+ V   +G   
Sbjct: 141 VP------DLLPEQ--------LAFTAEPVPLDVVYEDDTLVVINKPAGLVVHPAAGNWS 186

Query: 126 AYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G L  + D+     +  + HRLD+ETSG++VVART  A   L    + R +++ Y
Sbjct: 187 GTVLNGLLHRYGDAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRY 246

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKF 240
            +LVWG   +    I   + +      +   +          A +HF+ ID      Q  
Sbjct: 247 LALVWGNMPDD-GTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRRIDSTVWERQPV 302

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             +     TGRTHQ+RVH  H+G P++GD  Y         +P+     +  LHA  + L
Sbjct: 303 SAIHCDLETGRTHQIRVHCAHIGHPLLGDPVYGRARGKRSVTPLPGGFARQALHAWRLAL 362

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            HP+ GR +Q  A +P  + +  ++LG 
Sbjct: 363 VHPKTGRTMQWRADVPGDIAELSEALGL 390


>gi|197249745|ref|YP_002146857.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197213448|gb|ACH50845.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
          Length = 319

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLKK    G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKKILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +         +L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDNALKRCLQVLR 316


>gi|240948340|ref|ZP_04752726.1| 23S rRNA pseudouridylate synthase C [Actinobacillus minor NM305]
 gi|240297379|gb|EER47920.1| 23S rRNA pseudouridylate synthase C [Actinobacillus minor NM305]
          Length = 320

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 102/321 (31%), Positives = 169/321 (52%), Gaps = 14/321 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  + +DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q+  +VR
Sbjct: 11  VQFFTISDDEAGQRLDNFLLTKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQADDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  VPPVR------VAEKNEAPISTKLNKVAE-LEHQILYEDDVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSG+L+VA+ R+  ++L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGLLLVAKKRSVLRNLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+ +  V    +    + + F VI+        ++  
Sbjct: 183 VRGQWQSHVKVIKAPLLKNELASGERIVRV---SEEGKPSETRF-VIEERYPTATLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGDREFDQKMQQAGLNRLFLHAHSIRFVHPKTGEE 298

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           + +TAPL   +      L  +
Sbjct: 299 MVVTAPLDKQLKAVLAKLRAE 319


>gi|167753888|ref|ZP_02426015.1| hypothetical protein ALIPUT_02173 [Alistipes putredinis DSM 17216]
 gi|167658513|gb|EDS02643.1| hypothetical protein ALIPUT_02173 [Alistipes putredinis DSM 17216]
          Length = 356

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 73/332 (21%), Positives = 139/332 (41%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +  +  +  +RLD++   H    +   +Q    +G + V+ K  K + +++ G  + +  
Sbjct: 30  ITADRGQSPLRLDKFLTIHMERCSRNRIQTAADAGNILVNGKPAKSSYKVKPGDRISL-- 87

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               + +  +E +I+  ++ L          + YED  + + NKPAG+ V  G G     
Sbjct: 88  ---VMPYPKREIEIIPENIPLE---------IPYEDDDLLLVNKPAGMVVHPGHGNYSAT 135

Query: 125 IAYHIDGFLKS--WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   +  +L++         +  L HR+D+ TSG+LV+A+   A   L + F    I + 
Sbjct: 136 LVNALTYYLQNLPLFQEGDMRAGLVHRIDKNTSGLLVIAKNERAHARLAKQFFDHTITRR 195

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +  +  I   + +           V ++     +A++H++V+  +      
Sbjct: 196 YVALVWGNFEEDEGTITGNIGRSPKDRQK--MWVFEDGSDGKHAVTHYRVLKRYG-YVTL 252

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYL 290
           +E +  TGRTHQ+RVH    G P+ GD +Y  +     T+                +  L
Sbjct: 253 IECRLETGRTHQIRVHMQWKGHPLFGDERYGGDRILKGTTFNKYKQFIENCFAAMPRQAL 312

Query: 291 HARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDS 321
           HA+ +   HP  G      + LP         
Sbjct: 313 HAKSLGFQHPTTGEQVYFESELPEDFRTVLAK 344


>gi|315267102|gb|ADT93955.1| pseudouridine synthase, RluA family [Shewanella baltica OS678]
          Length = 319

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 107/323 (33%), Positives = 172/323 (53%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q 
Sbjct: 5   STPQQVQLITIDEDHFEQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQI 64

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPP       + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V G
Sbjct: 65  GDIVRIPP-----VRVAEPDNRTAPSPNLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHG 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ Y +   L+S    +     L HRLD++TSG+L+VA+ R+A +HL +  R +++QK
Sbjct: 119 GSGVDYGVIEALRSLRPQQKF-LELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G    + + +   LLK +   G+ +  V         + + FK++  + Q   
Sbjct: 178 DYLALVKGEWSAQDKAVKQPLLKITLKSGERIVRVNAE---GKPSETRFKIMQRY-QGCT 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HP
Sbjct: 234 LVKASPVTGRTHQIRVHCQFAGHPIACDDKYSEQAFDDSMRSLGLTRLFLHAAELMFIHP 293

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E    ++++APL  ++ +  D L
Sbjct: 294 ENDEVMRVSAPLDENLSQLLDKL 316


>gi|217973818|ref|YP_002358569.1| RluA family pseudouridine synthase [Shewanella baltica OS223]
 gi|217498953|gb|ACK47146.1| pseudouridine synthase, RluA family [Shewanella baltica OS223]
          Length = 319

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 107/323 (33%), Positives = 172/323 (53%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q 
Sbjct: 5   STPQQVQLITIDEDHFEQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQI 64

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPP       + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V G
Sbjct: 65  GDIVRIPP-----VRVAEPDNRTAPSPNLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHG 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ Y +   L+S    +     L HRLD++TSG+L+VA+ R+A +HL +  R +++QK
Sbjct: 119 GSGVDYGVIEALRSLRPQQKF-LELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G    + + +   LLK +   G+ +  V         + + FK++  + Q   
Sbjct: 178 DYLALVKGEWSAQDKAVKQPLLKITLKSGERIVRVNAE---GKPSETRFKIMQRY-QGCT 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HP
Sbjct: 234 LVKASPVTGRTHQIRVHCQFAGHPIACDDKYSEQGFDDSMRSLGLARLFLHAAELMFIHP 293

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E    ++++APL  ++ +  D L
Sbjct: 294 ENDEVMRVSAPLDENLSQLLDKL 316


>gi|291617029|ref|YP_003519771.1| RluC [Pantoea ananatis LMG 20103]
 gi|291152059|gb|ADD76643.1| RluC [Pantoea ananatis LMG 20103]
          Length = 318

 Score =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 103/321 (32%), Positives = 167/321 (52%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V +V +  +    R+D + +     +    + +I+R G+VRV+KKR+K   +++ G  
Sbjct: 6   PGVHFVAITAENAGQRIDNFLRTQLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLEEGDE 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S  L K +  L + +L+ED  + V NKP+G +V GGSG
Sbjct: 66  VRIPPVR------VAERDEEAVSPKLAKVA-SLANAILFEDDHLLVLNKPSGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y 
Sbjct: 119 LSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   +  + +   LLK     G+ +  V  +      + + FKV + F      ++
Sbjct: 178 ALVQGNWPSHLKVVQAPLLKNILQSGERMVRVSSD---GKPSETRFKVEERF-DFATLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D +Y    F    +S   N+L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHTLHAGHPIAFDDRYGDRAFDSQLSSTGLNRLFLHAAALTFTHPNTG 293

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L++ APL   +      L 
Sbjct: 294 ETLRMEAPLDDKLQHCLTMLR 314


>gi|300812431|ref|ZP_07092861.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
 gi|300496598|gb|EFK31690.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
          Length = 304

 Score =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 151/325 (46%), Gaps = 33/325 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   +  +E   RLD++      +++   +++++++G+V V+ K+ K + ++Q G ++++
Sbjct: 3   REYELTAEESGQRLDKYLAGEMTNLSRSRIKELVQAGEVLVNGKKSKVSYKVQKGDLIQV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +      +  E   LD               ++YED  + V NKP G+ V   +G   
Sbjct: 63  TVLPLEPLKLEAENIPLD---------------IVYEDEDVIVVNKPQGMVVHPAAGHPS 107

Query: 128 HI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H   +  L    D     +G +P + HR+D++TSG+L+VA+  AA + L +    +  ++
Sbjct: 108 HTLVNALLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G    ++  I   + +          V K        A++HFKV++ + Q + 
Sbjct: 168 QYLAIVHGNFAEEEGTIDAPIGRNPKDRKQMAVVEK-----GKSAVTHFKVLEQY-QGYS 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +    P 
Sbjct: 222 LVECQLETGRTHQIRVHMAYIGHPLAGDPLYGPR-----KTLPGHGQFLHAKTLGFEQPS 276

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            G  L+ +   P    +T   L  K
Sbjct: 277 TGEWLEFSVQPPEIFQQTVADLRKK 301


>gi|313123676|ref|YP_004033935.1| pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
 gi|312280239|gb|ADQ60958.1| Pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
          Length = 304

 Score =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 150/325 (46%), Gaps = 33/325 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   +  +E   RLD++       ++   +++++++G+V V+ K+ K + ++Q G ++++
Sbjct: 3   REYELTAEESGQRLDKYLAGEMTDLSRSRIKELVQAGEVLVNGKKSKVSYKVQKGDLIQV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +      +  E   LD               ++YED  I V NKP G+ V   +G   
Sbjct: 63  TVLPLEPLKLEAENIPLD---------------IVYEDEDIIVVNKPQGMVVHPAAGHPS 107

Query: 128 HI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H   +  L    D     +G +P + HR+D++TSG+L+VA+  AA + L +    +  ++
Sbjct: 108 HTLVNALLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G    ++  I   + +          V K        A++HFKV++ + Q + 
Sbjct: 168 QYLAIVHGNFAEEEGTIDAPIGRNPKDRKQMAVVEK-----GKSAVTHFKVLEQY-QGYS 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +    P 
Sbjct: 222 LVECQLETGRTHQIRVHMAYIGHPLAGDPLYGPR-----KTLPGHGQFLHAKTLGFEQPS 276

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            G  L+ +   P    +T   L  K
Sbjct: 277 TGEWLEFSVQPPEIFQQTVADLRKK 301


>gi|126173940|ref|YP_001050089.1| RluA family pseudouridine synthase [Shewanella baltica OS155]
 gi|125997145|gb|ABN61220.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           baltica OS155]
          Length = 329

 Score =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 107/323 (33%), Positives = 172/323 (53%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q 
Sbjct: 15  STPQQVQLITIDEDHFEQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQI 74

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPP       + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V G
Sbjct: 75  GDIVRIPP-----VRVAEPDNRTAPSPNLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHG 128

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ Y +   L+S    +     L HRLD++TSG+L+VA+ R+A +HL +  R +++QK
Sbjct: 129 GSGVDYGVIEALRSLRPQQKF-LELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQK 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G    + + +   LLK +   G+ +  V         + + FK++  + Q   
Sbjct: 188 DYLALVKGEWSAQDKAVKQPLLKITLKSGERIVRVNAE---GKPSETRFKIMQRY-QGCT 243

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HP
Sbjct: 244 LVKASPVTGRTHQIRVHCQFAGHPIACDDKYSEQGFDDSMRSLGLTRLFLHAAELMFIHP 303

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E    ++++APL  ++ +  D L
Sbjct: 304 ENDEVMRVSAPLDENLSQLLDKL 326


>gi|169634491|ref|YP_001708227.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii SDF]
 gi|169153283|emb|CAP02389.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii]
          Length = 310

 Score =  276 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 98/317 (30%), Positives = 163/317 (51%), Gaps = 19/317 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   ++  G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLAIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAAPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y ++
Sbjct: 123 YGLIEALRAATGKKY--LELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     K+ I   L +     G+    V    K    + + + V + F +    +   
Sbjct: 181 VKGQVSLDKQLIDAPLFRYELANGERRVRV---SKEGKPSKTEWVVAERF-KNATLVHAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P+VGD KY  N    +T P   +L LHA  +D+P    G   
Sbjct: 237 PLSGRTHQIRVHGLSIGHPLVGDDKYGHN--TAYTGPEARRLCLHAMRLDIP----GYPT 290

Query: 307 ITAPLPAHMVKTWDSLG 323
           I APLP  M +  ++L 
Sbjct: 291 IEAPLPEDMTQLLEALR 307


>gi|82544448|ref|YP_408395.1| 23S rRNA pseudouridylate synthase C [Shigella boydii Sb227]
 gi|110805101|ref|YP_688621.1| 23S rRNA pseudouridylate synthase C [Shigella flexneri 5 str. 8401]
 gi|187732109|ref|YP_001880745.1| 23S rRNA pseudouridylate synthase C [Shigella boydii CDC 3083-94]
 gi|300918689|ref|ZP_07135269.1| pseudouridine synthase, RluA family [Escherichia coli MS 115-1]
 gi|81245859|gb|ABB66567.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|110614649|gb|ABF03316.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|187429101|gb|ACD08375.1| ribosomal large subunit pseudouridine synthase C [Shigella boydii
           CDC 3083-94]
 gi|300414163|gb|EFJ97473.1| pseudouridine synthase, RluA family [Escherichia coli MS 115-1]
 gi|320186966|gb|EFW61679.1| 23S rRNA pseudouridylate synthase C [Shigella flexneri CDC 796-83]
 gi|332094085|gb|EGI99137.1| pseudouridine synthase, RluA family protein [Shigella boydii
           3594-74]
          Length = 319

 Score =  276 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 105/328 (32%), Positives = 172/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV    ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRSQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDEGLKRCLQKLR 316


>gi|327441137|dbj|BAK17502.1| pseudouridylate synthase, 23S RNA-specific [Solibacillus silvestris
           StLB046]
          Length = 300

 Score =  276 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 141/327 (43%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT V   +   +    R+D+         +   +   L   ++ V+   VK   +++ G 
Sbjct: 1   MTVVTLTI--EEFAGERIDKALSQMEESWSRSQISNWLDEERILVNGAAVKAKYKVKQGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +                +    +L    + L   ++YED+ + V NKP G+ V    
Sbjct: 59  VIEVT---------------VPEVEDLEIIPEDLNLEIVYEDADVLVVNKPRGMVVHPAP 103

Query: 124 GIA--YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G A    ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 104 GHATGTLVNGLMHHCKDLSGINGVARPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVEK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G   ++K  I   + +          V K       +A++HF+VI+ F 
Sbjct: 164 SVTRKYTALVHGHIAHEKGTIDAPIGRDQKDRQKQAVVDK-----GKHAVTHFQVIERFG 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +F         LHA  +  
Sbjct: 219 E-FTLVECRLETGRTHQIRVHMNYIGFPLAGDPKYGPRKTIDF-----GGQVLHAGVLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP     L+  +PLP    +  + L 
Sbjct: 273 IHPVTKEYLEFESPLPEDFKQLIEELR 299


>gi|160874866|ref|YP_001554182.1| RluA family pseudouridine synthase [Shewanella baltica OS195]
 gi|160860388|gb|ABX48922.1| pseudouridine synthase, RluA family [Shewanella baltica OS195]
          Length = 329

 Score =  276 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 107/323 (33%), Positives = 172/323 (53%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q 
Sbjct: 15  STPQQVQLITIDEDHFEQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQI 74

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPP       + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V G
Sbjct: 75  GDIVRIPP-----VRVAEPDNRTAPSPNLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHG 128

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ Y +   L+S    +     L HRLD++TSG+L+VA+ R+A +HL +  R +++QK
Sbjct: 129 GSGVDYGVIEALRSLRPQQKF-LELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQK 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G    + + +   LLK +   G+ +  V         + + FK++  + Q   
Sbjct: 188 DYLALVKGEWSAQDKAVKQPLLKITLKSGERIVRVNAE---GKPSETRFKIMQRY-QGCT 243

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HP
Sbjct: 244 LVKASPVTGRTHQIRVHCQFAGHPIACDDKYSEQAFDDSMRSLGLTRLFLHAAELMFIHP 303

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E    ++++APL  ++ +  D L
Sbjct: 304 ENDEVMRVSAPLDENLSQLLDKL 326


>gi|197104733|ref|YP_002130110.1| ribosomal large subunit pseudouridine synthase C [Phenylobacterium
           zucineum HLK1]
 gi|196478153|gb|ACG77681.1| ribosomal large subunit pseudouridine synthase C [Phenylobacterium
           zucineum HLK1]
          Length = 325

 Score =  276 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 131/334 (39%), Positives = 192/334 (57%), Gaps = 13/334 (3%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V+  EE +RLDRWFK  +PH+N + +QK+ RSGQ+RVD  R K + R+ +G 
Sbjct: 1   MREVRTLYVDKGEEGVRLDRWFKRRWPHLNHIQIQKLTRSGQIRVDGARAKPDTRLSAGS 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+ +A     K +  LD      + + + +S+++YED  +   NKP+G++VQGG+
Sbjct: 61  QVRVPPLPDAPPPRAKGE--LDP-----REAAYARSLVIYEDEDVLALNKPSGLAVQGGT 113

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               HIDG L +W +   ++PRL HRLD++TSG+LV+ +T  AA  L  +F  RR QKIY
Sbjct: 114 KTTRHIDGLLSAWGEGL-ERPRLVHRLDRDTSGVLVLGKTPGAAAKLAGAFAKRRTQKIY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G+PK  +  +   L KK     + +      +  A  A + F  +   A K  W+
Sbjct: 173 WALVAGLPKPGQGVLELPLAKKGVGDREMMVPADPKDPRAETAETEFVTLARAADKVAWM 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            + PHTGRTHQLR H L MG PI+GD KY        +  +  KL LHAR + LPHP  G
Sbjct: 233 ALWPHTGRTHQLRAHMLAMGHPILGDPKYKTEASEALSGGL--KLQLHARRLVLPHPSRG 290

Query: 304 RLQITAPLPAHMVKTWDSLGF---KYDRNLYIKR 334
            L + AP+   M   ++  GF   + D   + +R
Sbjct: 291 TLMLEAPIGKEMKAGFERFGFDEHEADPEPFSRR 324


>gi|327393480|dbj|BAK10902.1| ribosomal large subunit pseudouridine synthase C RluC [Pantoea
           ananatis AJ13355]
          Length = 318

 Score =  276 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 103/321 (32%), Positives = 167/321 (52%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V +V +  +    R+D + +     +    + +I+R G+VRV+KKR+K   +++ G  
Sbjct: 6   PGVHFVAITAENAGQRIDNFLRTQLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLEEGDE 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S  L K +  L + +L+ED  + V NKP+G +V GGSG
Sbjct: 66  VRIPPVR------VAERDEEAVSPKLAKVA-SLANAILFEDDHLLVLNKPSGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y 
Sbjct: 119 LSFGVIEGLRA-LRPESRFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   +  + +   LLK     G+ +  V  +      + + FKV + F      ++
Sbjct: 178 ALVQGNWPSHLKVVQAPLLKNILQSGERMVRVSSD---GKPSETRFKVEERF-DFATLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D +Y    F    +S   N+L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHTLHAGHPIAFDDRYGDRAFDSQLSSTGLNRLFLHAAALTFTHPNTG 293

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L++ APL   +      L 
Sbjct: 294 ETLRMEAPLDDKLQHCLTMLR 314


>gi|167032492|ref|YP_001667723.1| RluA family pseudouridine synthase [Pseudomonas putida GB-1]
 gi|166858980|gb|ABY97387.1| pseudouridine synthase, RluA family [Pseudomonas putida GB-1]
          Length = 333

 Score =  276 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 104/319 (32%), Positives = 171/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + VQ + V  +    R+D +       +    + +ILR G+VRV+K RVK   +IQ+G +
Sbjct: 24  SGVQLIEVAPELAGQRIDNFLITALKGVPKTLVYRILRKGEVRVNKGRVKPEYKIQAGDI 83

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP       + +  +    +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 84  VRVPP-----VRLPERDEPAPVAQGLLQR---LEAAIVYEDKALIVMNKPAGIAVHGGSG 135

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L+  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y 
Sbjct: 136 LSFGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYM 194

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     K+ +   LLK +   G+ +  V         A++ F+V+  F +    +E
Sbjct: 195 ALVRGHWPTSKKQVNAPLLKSNLRSGERMVEVSDE---GKEALTLFRVLRRFGEFATIVE 251

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   +F          +L+LHA  + +P P+GG
Sbjct: 252 ARPITGRTHQIRVHTLHAGHMIAGDSKYGDEDFSREIRELGGKRLFLHAYALTVPLPDGG 311

Query: 304 RLQITAPLPAHMVKTWDSL 322
            L++ AP+     KT + L
Sbjct: 312 ELKLEAPVDEVWAKTIERL 330


>gi|16760064|ref|NP_455681.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|29142165|ref|NP_805507.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|213163779|ref|ZP_03349489.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213425012|ref|ZP_03357762.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
 gi|213580589|ref|ZP_03362415.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213646390|ref|ZP_03376443.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|289829597|ref|ZP_06547152.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|34395803|sp|Q8Z7J7|RLUC_SALTI RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|25322405|pir||AE0641 pseudouridylate synthase (EC 4.2.1.70) - Salmonella enterica subsp.
           enterica serovar Typhi (strain CT18)
 gi|16502358|emb|CAD08312.1| ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70)
           [Salmonella enterica subsp. enterica serovar Typhi]
 gi|29137794|gb|AAO69356.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Typhi str. Ty2]
          Length = 319

 Score =  276 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 107/331 (32%), Positives = 174/331 (52%), Gaps = 17/331 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +SG  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  ESGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +         +L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
             HP  G  ++I AP+   + +  + L  K 
Sbjct: 289 FTHPGTGDVMRIEAPMDKQLKRCLEVLRSKA 319


>gi|307273068|ref|ZP_07554314.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|306510053|gb|EFM79077.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|315147417|gb|EFT91433.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4244]
 gi|315150758|gb|EFT94774.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0012]
          Length = 310

 Score =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 88/329 (26%), Positives = 154/329 (46%), Gaps = 39/329 (11%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  
Sbjct: 8   AKMEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDE 67

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +          I E ++LD        ++ +   ++YED+ + V NKP G+ V   +G
Sbjct: 68  IVVT---------IPEPEVLD------MVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAG 112

Query: 125 IAYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
              H +G L + +               P + HR+D++TSG+L+VA+   A + L +  +
Sbjct: 113 ---HPNGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLK 169

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +   + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ 
Sbjct: 170 EKTSLRKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLER 224

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F   F  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +
Sbjct: 225 F-DAFTLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLL 278

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              HP  G  L   APLP    KT   L 
Sbjct: 279 GFTHPTTGEQLVFEAPLPEVFEKTLHQLR 307


>gi|317056645|ref|YP_004105112.1| RluA family pseudouridine synthase [Ruminococcus albus 7]
 gi|315448914|gb|ADU22478.1| pseudouridine synthase, RluA family [Ruminococcus albus 7]
          Length = 304

 Score =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 80/330 (24%), Positives = 145/330 (43%), Gaps = 38/330 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+      V  +    R+D+      P ++  +LQK++  G V V+   V  N +I++  
Sbjct: 1   MSDHYNFTVSEENIGDRIDKVLSKQLPEMSRSSLQKLVNDGCVLVNGNIVSKNYKIKNSD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +  +  L      +   ++YED  + V NKP G+ V   +
Sbjct: 61  TISVE---------------IPEAEELKAEPQDIPIDIVYEDDSLLVVNKPQGMVVHPAA 105

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + +H  G L S   +   +P + HR+D+ TSG+L+VA+T  A   L +  
Sbjct: 106 GNPDGTLVNALLFHCKGRLSSI--NGVIRPGIVHRIDKFTSGLLMVAKTDKAHNFLAQQI 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +     + Y ++  G  K     +   + + S      + V  QN      A++H++V++
Sbjct: 164 KDHNFTREYNAICIGRFKEPTGTVNEPIGR-SKFDRKKMCVTYQN---CKEAVTHYEVLE 219

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              Q +  ++ +  TGRTHQ+RVH+  +G P++GD  Y   +KG           LHA+ 
Sbjct: 220 DLGQ-YSLVKFRLETGRTHQIRVHSAFIGHPVLGDDVYGKAYKG------LEGQCLHAKK 272

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +   HPE    ++  + LP + VK  + L 
Sbjct: 273 LGFIHPETKEYMEFDSELPVYFVKVLEKLR 302


>gi|153000233|ref|YP_001365914.1| RluA family pseudouridine synthase [Shewanella baltica OS185]
 gi|151364851|gb|ABS07851.1| pseudouridine synthase, RluA family [Shewanella baltica OS185]
          Length = 329

 Score =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 106/323 (32%), Positives = 172/323 (53%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q 
Sbjct: 15  STPQQVQLITIDEDHFEQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQI 74

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPP       + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V G
Sbjct: 75  GDIVRIPP-----VRVAEPDNRTAPSPNLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHG 128

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ Y +   L+S    +     L HRLD++TSG+L+VA+ R+A +HL +  R +++QK
Sbjct: 129 GSGVDYGVIEALRSLRPQQKF-LELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQK 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G    + + +   LLK +   G+ +  V         + + FK++  + Q   
Sbjct: 188 DYLALVKGEWSAQDKAVKQPLLKITLKSGERIVRVNAE---GKPSETRFKIMQRY-QGCT 243

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HP
Sbjct: 244 LVKASPVTGRTHQIRVHCQFAGHPIACDDKYSEQGFDDSMRSLGLTRLFLHAAELMFIHP 303

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E    ++++APL  ++ +  + L
Sbjct: 304 ENDEVMRVSAPLDENLSQLLNKL 326


>gi|205353078|ref|YP_002226879.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205272859|emb|CAR37786.1| ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70)
           [Salmonella enterica subsp. enterica serovar Gallinarum
           str. 287/91]
 gi|326628157|gb|EGE34500.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 319

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 105/328 (32%), Positives = 172/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARLLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +         +L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDNALKRCLQVLR 316


>gi|90415859|ref|ZP_01223792.1| Predicted pseudouridylate synthase, Rlu family protein [marine
           gamma proteobacterium HTCC2207]
 gi|90332233|gb|EAS47430.1| Predicted pseudouridylate synthase, Rlu family protein [marine
           gamma proteobacterium HTCC2207]
          Length = 324

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 98/323 (30%), Positives = 161/323 (49%), Gaps = 15/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  + V YV +  ++   RLD +       +    + ++LR G+VRV+K RVK  +R++ 
Sbjct: 15  SQFSQVSYVDIGPEQAGQRLDNFLIKILKGVPKSRIYRLLRKGEVRVNKGRVKAESRLKE 74

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VR+PP+  A           +      +   +L   +L+ED  + + NKP+G++V G
Sbjct: 75  GDIVRLPPIRVAERG--------EMPAVGRQLKQYLADNILFEDDGLLIINKPSGLAVHG 126

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG++      L++    + +   L HRLD++TSG L++A+ RA    L +  +   I+K
Sbjct: 127 GSGVSLGAIEALRAE-HPELRFLELVHRLDRDTSGCLMLAKKRAVLLALQQDMQRNYIEK 185

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L  G     K  I   L K +   G+ +  V   +     +++HFK +  +     
Sbjct: 186 RYTALSKGRWPKGKNTINAPLRKNTLQSGERMVRV---DASGKASVTHFKSLQQYPS-AT 241

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-QNKLYLHARYMDLPHP 300
            L+++  TGRTHQ+RVH      PI GD KY          P+   +L+LHARY+   HP
Sbjct: 242 LLDIKLETGRTHQIRVHCQFAEQPIAGDPKYGDEHFNESLKPLGLKRLFLHARYLRFKHP 301

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  +++ APLPA + K    L
Sbjct: 302 LSGDWVEVEAPLPADLEKVLTKL 324


>gi|168767745|ref|ZP_02792752.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4486]
 gi|189363263|gb|EDU81682.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O157:H7 str. EC4486]
          Length = 319

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 173/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKREYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDDGLKRCLQKLR 316


>gi|182417977|ref|ZP_02949285.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum 5521]
 gi|237667420|ref|ZP_04527404.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum E4 str. BoNT E BL5262]
 gi|182378148|gb|EDT75683.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum 5521]
 gi|237655768|gb|EEP53324.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum E4 str. BoNT E BL5262]
          Length = 304

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 146/320 (45%), Gaps = 32/320 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +E +R+D++  N +   +   +Q ++    V+V+ K +K N +++    + I  
Sbjct: 6   IKVDEQDEGLRIDKYLSNIFKDKSRSFIQGLIEKENVKVNSKTLKSNYKLKKADEIEI-- 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                  +I E +I      L+  ++ +   ++YED  + V NK  G+ V    G     
Sbjct: 64  -------MIPEPEI------LSVEAENIPIDIVYEDEDVIVVNKAQGMVVHPAPGNYNGT 110

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D        +P + HR+D++TSGILV+A+   A   L+E  +   +++ Y
Sbjct: 111 LVNALLYHCKDLSSINGVIRPGIVHRIDKDTSGILVIAKNDDAHNKLSEQLKDHSMKREY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++L+ G  KN    I   L +          +     +    A++H++V++ +   +  +
Sbjct: 171 YALIEGRLKNNDGTIDKPLGRCKKDRLKIGII-----EDGKRAVTHYEVVERY-NGYTLV 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    TGRTHQ+RVH   +G P+VGD  Y    +            LHAR +   HP  G
Sbjct: 225 KCVLETGRTHQIRVHMASIGFPLVGDPLYGFKRQ----KFKLEGQVLHARTLGFIHPRTG 280

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             ++ T+ LP +     + L
Sbjct: 281 EYMEFTSELPQYFCDLINKL 300


>gi|239832765|ref|ZP_04681094.1| pseudouridine synthase, RluA family [Ochrobactrum intermedium LMG
           3301]
 gi|239825032|gb|EEQ96600.1| pseudouridine synthase, RluA family [Ochrobactrum intermedium LMG
           3301]
          Length = 402

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 89/348 (25%), Positives = 160/348 (45%), Gaps = 45/348 (12%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           T V+ +  ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G
Sbjct: 67  TRVKELTTDSDATGKRLDQWLAAALGPDLSRSRVQSLIAEGHVTIDGVPARETKQKLREG 126

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +               +L         ++ +   +LYED  + V NKPAG+ V  G
Sbjct: 127 MTIAV---------------VLPEPEPAEPIAENIPLDILYEDDDLIVINKPAGLVVHPG 171

Query: 123 SG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +G      ++  +    DS       ++P + HRLD++TSG++VVA+   + +HL+E F 
Sbjct: 172 NGNWTGTLVNALIYHCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDLSHRHLSEQFA 231

Query: 176 MR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
                  +++ Y +LVWG+ +  +  I   L + SH       VV +    A +AI+H+ 
Sbjct: 232 DHGRTGDLERAYLALVWGMTERPQGYIDAHLGR-SHRDRTKQAVVNEERDDARHAITHYA 290

Query: 232 VIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTS 282
            ++ F  +         +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        
Sbjct: 291 TVEKFGPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPE 350

Query: 283 PIQ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           P++      ++  LHA  +   HP  G  ++  AP+P  M    ++  
Sbjct: 351 PLKEAVRGFHRQALHAFLLAFTHPSSGELMRFEAPVPEDMKHLLENFR 398


>gi|299821727|ref|ZP_07053615.1| ribosomal large subunit pseudouridine synthase [Listeria grayi DSM
           20601]
 gi|299817392|gb|EFI84628.1| ribosomal large subunit pseudouridine synthase [Listeria grayi DSM
           20601]
          Length = 302

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 93/323 (28%), Positives = 149/323 (46%), Gaps = 34/323 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  E+ MR+D++        +  ++Q++L+ GQV VD + VK N + Q G +V +  
Sbjct: 6   VEVKETEKGMRIDKFLAEKASK-SRSSVQQLLKDGQVTVDGEVVKPNYKCQLGDIVEMEE 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
               +  I  E   LD               + YED  + V NKP G+ V   +G     
Sbjct: 65  RAPEVIEIEAEDIPLD---------------IYYEDEDLLVVNKPEGMVVHPSAGHYTGT 109

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HR+D++TSG+L+VA+  AA + L    + +   + Y
Sbjct: 110 LVNALLYHCKDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDAAHESLASQLKAKTSHREY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G   ++K  I   + + +      + VV         A +HF+V++ F   F  +
Sbjct: 170 VALVHGDIAHQKGTIEAPIGR-AKDDRQKMAVV----GDGKEARTHFEVLERFGD-FTLI 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
             Q  TGRTHQ+RVH  ++G P+ GD KY         +   N  YLHA+ +   HP   
Sbjct: 224 TCQLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTLPGNGQYLHAKKLGFVHPRTK 278

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
             L   +PLPA   +  + L  K
Sbjct: 279 EELSFESPLPADFEEVLEKLRTK 301


>gi|284920910|emb|CBG33973.1| ribosomal large subunit pseudouridine synthase C [Escherichia coli
           042]
          Length = 319

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 172/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y  LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLVLVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDDGLKRCLQKLR 316


>gi|304397213|ref|ZP_07379092.1| pseudouridine synthase, RluA family [Pantoea sp. aB]
 gi|304355362|gb|EFM19730.1| pseudouridine synthase, RluA family [Pantoea sp. aB]
          Length = 318

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 104/321 (32%), Positives = 166/321 (51%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V +V +  +    R+D + +     +    + +I+R G+VRV+KKRVK   +++ G  
Sbjct: 6   PGVHFVAITAENAGQRIDNFLRTQLKGVPKSMIYRIVRKGEVRVNKKRVKPEYKLEEGDE 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S  L K +  L   +L+ED  + V NKP+G +V GGSG
Sbjct: 66  VRIPPVR------VAERDEDAVSPKLAKVA-SLADAILFEDESLLVMNKPSGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y 
Sbjct: 119 LSFGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   +  + +   LLK     G+ V  V         + + FKV + F      ++
Sbjct: 178 ALVRGNWPSHLKVVQAPLLKNILQSGERVVRVSSE---GKASETRFKVEERF-DFATLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D +Y   +F     S    +L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHTLHAGHPIAFDDRYGERDFDSQLASTGLKRLFLHAAALTFTHPGTG 293

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             +++ APL   + +  + L 
Sbjct: 294 EVMRVEAPLDDGLKQCLNKLR 314


>gi|145628779|ref|ZP_01784579.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 22.1-21]
 gi|145640373|ref|ZP_01795957.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae R3021]
 gi|144979249|gb|EDJ88935.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 22.1-21]
 gi|145274959|gb|EDK14821.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 22.4-21]
          Length = 322

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 104/321 (32%), Positives = 172/321 (53%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+  +  S NL K +  L++ +L+ED  + V NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDVPISKNLNKVT-ALENQILFEDDCLIVLNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+ +  V +       + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGERIVRVSEQ---GKPSETRFSIEERYT-NATLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L+  APL   M      L 
Sbjct: 299 ETLRFNAPLDHQMKAILQKLR 319


>gi|238917079|ref|YP_002930596.1| lysozyme [Eubacterium eligens ATCC 27750]
 gi|238872439|gb|ACR72149.1| lysozyme [Eubacterium eligens ATCC 27750]
          Length = 310

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 77/329 (23%), Positives = 146/329 (44%), Gaps = 33/329 (10%)

Query: 4   MTY-VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M+  VQ ++ E +++  R+D++       ++   +QK+L  G + VD K VK N ++   
Sbjct: 1   MSDSVQNLIAEPEDKGTRIDKYLSQELEDVSRSRIQKLLDDGDITVDDKCVKSNYKLNGT 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + + I      +  I+ E                +   ++YED  + + +KP G+ V   
Sbjct: 61  EHITITIPELIVPQILPEN---------------IPLNIIYEDDDVILIDKPKGMVVHPA 105

Query: 123 SG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +G      ++  +    D+        +P + HR+D  T+G++V  +   A   +     
Sbjct: 106 AGHYTGTVVNALMYHCRDNLSGINGVMRPGIVHRIDMNTTGVIVACKNDKAHNDIAAQLA 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           +  I + Y+ +V    K ++  +   + +          ++  + K   +A++H++V++ 
Sbjct: 166 VHSITRKYYCIVHNRFKEEEGTVDAPIGRNPKDRK----MMAVDRKNGKHAVTHYRVLEN 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F  K+ ++E Q  TGRTHQ+RVH   +G PI+GD  YC    G           LHA  +
Sbjct: 222 F-DKYSFIECQLETGRTHQIRVHMASIGHPILGDDVYCHARSGYK----LQGQTLHAGVL 276

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              HP  G  ++  APLP +  K    L 
Sbjct: 277 GFIHPSTGEYMEFKAPLPGYFEKLLKDLR 305


>gi|90413248|ref|ZP_01221243.1| putative 23S rRNA ribosomal pseudouridinesynthase [Photobacterium
           profundum 3TCK]
 gi|90325800|gb|EAS42258.1| putative 23S rRNA ribosomal pseudouridinesynthase [Photobacterium
           profundum 3TCK]
          Length = 314

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 102/321 (31%), Positives = 176/321 (54%), Gaps = 16/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ++ + +D    R+D + +    ++    + +ILR G+VRV+KKR+K   ++Q G +
Sbjct: 6   PKVQFIDITDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDL 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+PP+      + ++      S  L+K ++ L+S ++YED  + V NKP+G +V GGSG
Sbjct: 66  IRVPPIF-----LPEQADQAPISTKLSKVAE-LESCVIYEDDHLLVLNKPSGTAVHGGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + +QK Y+
Sbjct: 120 LKFGAIEALRA-LRPDARYLELVHRIDRDTSGILLVAKKRSALRKLQEQFREKTVQKYYF 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  K   + +   LLK        V+ + +  +    + + FKV++ F +    ++
Sbjct: 179 ALVMGEWKASCKKVTAPLLKNE------VNSIVRVNQNGKASDTRFKVLERF-EHATLVQ 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +   HP   
Sbjct: 232 ASPVTGRTHQIRVHCQYEGHPIAWDDRYGDPRFDAYTKKTGLNRLFLHAANIKFTHPSTD 291

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             + I+APL A + ++ D+L 
Sbjct: 292 EPVDISAPLDALLTRSLDNLR 312


>gi|56413826|ref|YP_150901.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197362749|ref|YP_002142386.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|56128083|gb|AAV77589.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Paratyphi A str. ATCC
           9150]
 gi|197094226|emb|CAR59731.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Paratyphi A str.
           AKU_12601]
          Length = 319

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 107/331 (32%), Positives = 174/331 (52%), Gaps = 17/331 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +SG  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  ESGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LHPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +         +L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
             HP  G  ++I AP+   + +  + L  K 
Sbjct: 289 FTHPGTGDVMRIEAPMDKQLKRCLEVLRSKA 319


>gi|295109999|emb|CBL23952.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           obeum A2-162]
          Length = 304

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 87/323 (26%), Positives = 147/323 (45%), Gaps = 38/323 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+    N+R+DR+  +  P  +   +QK+L+  QV V+ + +K N + QSG  +      
Sbjct: 8   VDASANNIRIDRYLADQCPEHSRSYIQKLLKEEQVLVNGRVIKANYKTQSGDYIEFHIPD 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
             +  I+ E   LD               +LYED  + V NKP  + V   +G   H  G
Sbjct: 68  PEVPDILPENIPLD---------------ILYEDDYVLVVNKPKDMVVHPSAG---HTSG 109

Query: 132 FLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            L + V +             +P + HR+D++T+G L++ +     + L E  +   I++
Sbjct: 110 TLVNAVMAHCGEHLSGINGVLRPGIVHRIDKDTTGALLICKDDVVHRDLAEQLKEHSIKR 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G  K  +  + N  + +       + +   N K    AI+H+KV++ F Q   
Sbjct: 170 RYRAVVQGNLKEDEGTV-NAPVGRHPTDRKKMAI---NHKNGKEAITHYKVLERFGQ-AT 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           ++E +  TGRTHQ+RVH   +G P++GD  Y ++              LHA  +   HP 
Sbjct: 225 YIECRLETGRTHQIRVHMASLGHPLLGDTVYGSSKNPYH----LQGQALHAMILGFVHPI 280

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            G  L+  APLP +  K  + L 
Sbjct: 281 TGEYLEFEAPLPEYFSKLLEKLR 303


>gi|168264021|ref|ZP_02685994.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|205347383|gb|EDZ34014.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
          Length = 319

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 105/328 (32%), Positives = 171/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EVGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +         +L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDNALKRCLQVLR 316


>gi|259503429|ref|ZP_05746331.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           antri DSM 16041]
 gi|259168507|gb|EEW53002.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           antri DSM 16041]
          Length = 303

 Score =  275 bits (704), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 86/319 (26%), Positives = 141/319 (44%), Gaps = 33/319 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V++     R+D+   +H+   +   LQK +  G V+V+ + VK   ++  G  V I P
Sbjct: 6   LTVDDTLTG-RVDKALAHHFRQFSRSQLQKWIADGNVQVNGEAVKAKAKLAVGDQVVIKP 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  ++ E+  LD               ++YED  + V NKP G+ V    G   H 
Sbjct: 65  EAPQKIDLVPEKIPLD---------------IVYEDDDVIVVNKPQGMVVHPAPGHPDHT 109

Query: 130 --DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +  L     S      +P + HR+D++TSG+L+VA+   A + L    + +  Q+ Y 
Sbjct: 110 LVNALLYHCPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDLAHRSLAAQLKAKTNQREYV 169

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+ K     +   + +          V         +A++HFKV++ F + +  + 
Sbjct: 170 ALVHGVIKQDAGTVDAPIGRSKKDRKKQAIVS-----DGRHAVTHFKVLERF-RHYTLVS 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
            +  TGRTHQ+RVH   +G P+ GD  Y         +      YLHAR +   HP  G 
Sbjct: 224 CRLETGRTHQIRVHMKSIGHPLAGDPLYGPR-----KTLPGRGQYLHARLLGFKHPRTGQ 278

Query: 304 RLQITAPLPAHMVKTWDSL 322
            L  T PLP +  +  D L
Sbjct: 279 ELVFTVPLPDYFQQMVDKL 297


>gi|256619215|ref|ZP_05476061.1| pseudouridylate synthase [Enterococcus faecalis ATCC 4200]
 gi|256853277|ref|ZP_05558647.1| pseudouridylate synthase [Enterococcus faecalis T8]
 gi|300860210|ref|ZP_07106297.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|256598742|gb|EEU17918.1| pseudouridylate synthase [Enterococcus faecalis ATCC 4200]
 gi|256711736|gb|EEU26774.1| pseudouridylate synthase [Enterococcus faecalis T8]
 gi|300849249|gb|EFK76999.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
          Length = 301

 Score =  275 bits (704), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 83/324 (25%), Positives = 148/324 (45%), Gaps = 33/324 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  + 
Sbjct: 1   MEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +                +     L   ++ +   ++YED+ + V NKP G+ V   +G  
Sbjct: 61  VT---------------IPEPEALDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHP 105

Query: 126 -AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L             +P + HR+D++TSG+L+VA+   A + L +  + +   
Sbjct: 106 KGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSL 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ F   F
Sbjct: 166 RKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLERF-DAF 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   HP
Sbjct: 220 TLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLLGFTHP 274

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  L   APLP    KT   L 
Sbjct: 275 TTGEQLVFEAPLPEVFEKTLHQLR 298


>gi|170717346|ref|YP_001784455.1| 23S rRNA pseudouridylate synthase C [Haemophilus somnus 2336]
 gi|168825475|gb|ACA30846.1| pseudouridine synthase, RluA family [Haemophilus somnus 2336]
          Length = 326

 Score =  275 bits (704), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 109/326 (33%), Positives = 175/326 (53%), Gaps = 14/326 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  DE   R+D +       +    + +ILR G+VRV+K R+K   ++QSG +VR
Sbjct: 13  VKILTINEDESGQRIDNFLLAKLKSVPKSLIYRILRKGEVRVNKGRIKPEYKLQSGDIVR 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       I E++    S  L K +  L+  +++ED+ + V NKP+G++V GGSG+ 
Sbjct: 73  IPPVR------IAEKEHTPISKKLNKVAQ-LEQQIIFEDNYLLVLNKPSGLAVHGGSGLN 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +     L++ +  + +   L HRLD++TSGIL++A+ R+A + L E  R + IQK Y +L
Sbjct: 126 FGAIEALRT-LRPEARFLELVHRLDRDTSGILLIAKKRSALRSLHEQLREKTIQKEYLAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+ +  V +       + + F V + +      ++  
Sbjct: 185 VRGHWQSHCKMIQAPLLKSELTSGERIVKVSEQ---GKPSETKFSVEERY-NNATLVKAS 240

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY   NF    T+   N+L+LHA  +   HP+ G R
Sbjct: 241 PITGRTHQIRVHTQYAGHPIALDDKYGDKNFNQQMTALGLNRLFLHAFAICFEHPKTGER 300

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNL 330
           L++ APL   M     +L    ++ L
Sbjct: 301 LRLVAPLDLAMKNILQALRETKNKTL 326


>gi|84394338|ref|ZP_00993060.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio splendidus 12B01]
 gi|84375031|gb|EAP91956.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio splendidus 12B01]
          Length = 314

 Score =  275 bits (704), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 108/326 (33%), Positives = 178/326 (54%), Gaps = 17/326 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V ++ D    R+D + +N   +I    + +I+R G+VRV+KKR+K   ++
Sbjct: 1   MSEIRTQVQFVDIDEDMAGQRIDNFLRNQLKNIPKSMIYRIVRKGEVRVNKKRIKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VRIPP       I ++ +    S  L K S+ L+  ++YED  + + NKP+G +V
Sbjct: 61  KAGDLVRIPP-----VTIEEKTEENVPSTKLNKVSE-LEQCIIYEDDHMLILNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +    +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPDSRFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y++LV G  KN  + +   LLK        V+ + +       + + FKV++ F Q 
Sbjct: 174 QKYYFALVMGEWKNSCKVVNAPLLKNE------VNSIVRVNPNGKASETRFKVLEKF-QD 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVHA + G PI  D +Y       +T     N+L+LHA  +   
Sbjct: 227 ATLVQASPITGRTHQIRVHAQYTGHPIAWDDRYGDRRFDAYTGKVGLNRLFLHAANIKFT 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP     + I+AP+   + +    L 
Sbjct: 287 HPGSEEKIDISAPMEKRLERALTGLR 312


>gi|295425512|ref|ZP_06818204.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           amylolyticus DSM 11664]
 gi|295064803|gb|EFG55719.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           amylolyticus DSM 11664]
          Length = 302

 Score =  275 bits (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 155/327 (47%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    + VEN++   RLD++  +    ++   +++++  G + V++K  K + +++ G 
Sbjct: 1   MTKKYELTVENEKG--RLDKYLADKIDDLSRTRVKELIDDGLILVNQKVEKASYKVKDGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         +I E   LD               ++YED+ + V NKP G+ V   +
Sbjct: 59  AIEVTVPAVKPLDVIPENIPLD---------------IIYEDNDVIVVNKPQGMVVHPAA 103

Query: 124 GIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +  L    D     +G +P + HR+D++TSG+L++A+     + L +    +
Sbjct: 104 GHPDHTLVNALLYHTKDLASSPEGFRPGIVHRIDKDTSGLLMIAKNSQVRESLEDQLAHK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +++Y ++V G    ++  I   + +  H       V      G  +A++HFKVI+ F 
Sbjct: 164 TNKRLYLAIVHGNFAEEEGTIDAPIARNPHDRKKMGVVA-----GGKHAVTHFKVIEQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  ++ +  TGRTHQ+RVH  ++G P+ GD  Y +       +   N  +LHA+ +  
Sbjct: 218 KGYSLIQCKLETGRTHQIRVHLSYIGHPVAGDPLYGSR-----KTLKGNGQFLHAQVLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP+ G+ L+     P    +T + L 
Sbjct: 273 KHPKTGKWLEFKVDPPKIFQETLNKLR 299


>gi|167623698|ref|YP_001673992.1| RluA family pseudouridine synthase [Shewanella halifaxensis
           HAW-EB4]
 gi|167353720|gb|ABZ76333.1| pseudouridine synthase, RluA family [Shewanella halifaxensis
           HAW-EB4]
          Length = 319

 Score =  275 bits (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 106/323 (32%), Positives = 173/323 (53%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    VQ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++  
Sbjct: 5   SQKAQVQMVTIDEDHVGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLAD 64

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPP       + + +     S  LTK S  L+  +L+ED  + V NKP+GI+V G
Sbjct: 65  GDIVRIPP-----VRVSESEGRPGPSAKLTKVSQ-LEERILFEDKYLIVLNKPSGIAVHG 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ + +   ++S + ++ +   L HRLD+ETSG+L++A+ R+A +HL +  R +++QK
Sbjct: 119 GSGVEFGVIEAMRS-LRTQQKFLELVHRLDKETSGVLLIAKKRSALRHLHDQLRYKKMQK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  ++  + I   LLK +   G+ +  V    K    + + FK++  ++    
Sbjct: 178 DYVALVRGEWQSHDKVIKAPLLKLTLKSGERIVRVN---KEGKESETRFKILQRYSDS-T 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH    G PI  D KY    F  +  +   N+L+LHA  +   HP
Sbjct: 234 LVQASPVTGRTHQIRVHCQFAGHPIACDEKYSEQKFDDSMRAQGLNRLFLHAAQLKFTHP 293

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E    +Q+ APL   +  T   L
Sbjct: 294 ETEEVMQVKAPLDTILESTLKKL 316


>gi|254229869|ref|ZP_04923274.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. Ex25]
 gi|151937638|gb|EDN56491.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. Ex25]
          Length = 345

 Score =  275 bits (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 102/326 (31%), Positives = 177/326 (54%), Gaps = 17/326 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++
Sbjct: 32  MSEIRTKVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKL 91

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VRIPP       + K+   +  S  L K ++ L+ ++++ED  + + NKP+G +V
Sbjct: 92  KAGDLVRIPP-----VTVEKKDDDVAPSTKLNKVAE-LEDMIIFEDDHMLILNKPSGTAV 145

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 146 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 204

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G  K+  + +   LLK        V+ + +       + + FK+++ F Q 
Sbjct: 205 KKFYLALVMGQWKSSCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKILEKFEQ- 257

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  +   
Sbjct: 258 ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGLDRLFLHAANIKFQ 317

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP     ++I AP+   + K    L 
Sbjct: 318 HPSNDEWMEINAPMEPKLEKVLAGLR 343


>gi|113970739|ref|YP_734532.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           MR-4]
 gi|114047966|ref|YP_738516.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           MR-7]
 gi|113885423|gb|ABI39475.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           MR-4]
 gi|113889408|gb|ABI43459.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           MR-7]
          Length = 329

 Score =  275 bits (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 106/323 (32%), Positives = 176/323 (54%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    VQ + ++ D  + R+D +       +    + +I+R G+VRV+KKR+K   ++Q 
Sbjct: 15  SPQLQVQLITIDEDHLDQRIDNFLITVLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQI 74

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PP       + ++      S NL+K S  L+  +L+ED+ + V NKPAGI+V G
Sbjct: 75  GDVVRVPP-----VRMAEQDNRTAPSANLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHG 128

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ Y +   L+S    +     L HRLD++TSG+L+VA+ R+A +HL +  R +++QK
Sbjct: 129 GSGVDYGVIEALRSLRPQQKF-LELVHRLDKDTSGVLLVAKKRSALKHLHDQLRQKKMQK 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G    + + +   LLK +   G+ +  V         + + FK++  + Q   
Sbjct: 188 DYLALVKGEWSAQDKVVKQPLLKLTLKSGERIVRVNGE---GKPSETRFKIVQRY-QGCT 243

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D KY    F  +  +   ++L+LHA  +   HP
Sbjct: 244 LVQASPVTGRTHQIRVHCQYMGHPIACDEKYSEQTFDDSMRALGLSRLFLHAAELMFIHP 303

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E    ++++APL  ++ +    L
Sbjct: 304 ENDEVMRVSAPLDDNLQQLLSKL 326


>gi|257087008|ref|ZP_05581369.1| pseudouridylate synthase [Enterococcus faecalis D6]
 gi|256995038|gb|EEU82340.1| pseudouridylate synthase [Enterococcus faecalis D6]
          Length = 301

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 88/327 (26%), Positives = 153/327 (46%), Gaps = 39/327 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  + 
Sbjct: 1   MEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          I E ++LD        ++ +   ++YED+ + V NKP G+ V    G  
Sbjct: 61  VT---------IPEPEVLD------MVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSVG-- 103

Query: 127 YHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            H +G L + +               P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 104 -HPNGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ F 
Sbjct: 163 TSLRKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLERF- 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +  
Sbjct: 217 DAFTLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLLGF 271

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  L   APLP    KT   L 
Sbjct: 272 THPTTGEQLVFEAPLPEVFEKTLHQLR 298


>gi|325265702|ref|ZP_08132391.1| ribosomal large subunit pseudouridine synthase D [Kingella
           denitrificans ATCC 33394]
 gi|324982833|gb|EGC18456.1| ribosomal large subunit pseudouridine synthase D [Kingella
           denitrificans ATCC 33394]
          Length = 367

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 83/325 (25%), Positives = 143/325 (44%), Gaps = 29/325 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V N+    RLD       P  +   +   ++ G V+ + +     +++  G+++R+  
Sbjct: 25  LTVPNELAGTRLDAALAKLLPDYSRSRITSWIKDGLVQCNGQTASPKHKLIGGELLRV-- 82

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                       +I  S  N     + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 83  ------------QIQPSDENQAFEPEAMDLDIVYEDDSVIVLNKPAGLVVHPAAGNWTGT 130

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    +  +  +  + HRLD++TSG++VVA+T  A  HL +  + R +++IY ++
Sbjct: 131 LLNGLLAHCPELGQVPRAGIVHRLDKDTSGLMVVAKTLPAQNHLVQQLQNRSVKRIYRAV 190

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H  V++ + Q   ++E +
Sbjct: 191 ADGIVP-FDGKIETLIGRDPH-NRLKMAVVKF---GGKEAVTHVSVLERY-QAHSYIECR 244

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-----NFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH      P+ GD  Y             T     +  LHA  +   HP+
Sbjct: 245 LETGRTHQIRVHMREARHPLAGDPVYGNPRHACSPAVKETVKQLARQALHAHRLSFIHPK 304

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            G  L   AP+PA M      L  +
Sbjct: 305 SGEWLSFEAPIPADMYHLLSVLRLE 329


>gi|302389579|ref|YP_003825400.1| ribosomal large subunit pseudouridine synthase D
           [Thermosediminibacter oceani DSM 16646]
 gi|302200207|gb|ADL07777.1| ribosomal large subunit pseudouridine synthase D
           [Thermosediminibacter oceani DSM 16646]
          Length = 307

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 86/323 (26%), Positives = 151/323 (46%), Gaps = 31/323 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V+ D+   RLD +       ++   +QK +  G V+V+++ VK + +++ G V+    
Sbjct: 7   ILVQEDDAKKRLDVFLSGVINDLSRSYIQKGIEEGWVKVNERIVKPHYKLKKGDVIV--- 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                         + S   L+   + +   +++ED  I V NKP G+ V    G     
Sbjct: 64  ------------ADIPSPKPLSLEPENIPLDIIHEDRDIIVVNKPRGMVVYPAPGNYSGT 111

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HRLD++TSG++VVA+   A + L   F+ + ++K Y
Sbjct: 112 LVNALLYHTKDLSGINGVMRPGIVHRLDKDTSGVIVVAKNDMAHRELAMQFKNKLVKKTY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++VWG     +  I   + +           +    K    AI+HFKV++ F + F ++
Sbjct: 172 LAVVWGNIPEDRATIEAPIGRHPA----KRVEMAVTAKNGKEAITHFKVLERF-EDFTFI 226

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E+   TGRTHQ+RVH   +G P+VGD  Y        +    N   LHA  + L HP  G
Sbjct: 227 EVNIETGRTHQIRVHMSFIGHPVVGDPLYSRKK----SPFNINGQALHAYRLGLNHPRTG 282

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
             +   AP+P  + +  ++L  +
Sbjct: 283 EFMTFEAPIPQDITEILNTLRKR 305


>gi|223041614|ref|ZP_03611813.1| ribosomal large subunit pseudouridine synthase [Actinobacillus
           minor 202]
 gi|223017589|gb|EEF16001.1| ribosomal large subunit pseudouridine synthase [Actinobacillus
           minor 202]
          Length = 320

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 103/325 (31%), Positives = 170/325 (52%), Gaps = 14/325 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q+ 
Sbjct: 7   ISAQVQFFSISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQAD 66

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +VR+PPV       + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GG
Sbjct: 67  DIVRVPPVR------VAEKNEAPISTKLNKVAE-LEHQILYEDDVMLVINKPSGIAVHGG 119

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+++ +   L++ +  + +   L HR+D++TSG+L+VA+ R+A ++L E  R + +QK 
Sbjct: 120 SGLSFGVIEALRA-LRPQARFLELVHRIDRDTSGLLLVAKKRSALRNLHEQLREKVVQKD 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G  ++  + I   LLK     G+ +  V    +    + + F VI+        
Sbjct: 179 YLALVRGQWQSHVKVIKAPLLKNELASGERIVRV---SEEGKPSETRF-VIEERYPTATL 234

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPE 301
           ++  P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP+
Sbjct: 235 VKASPVTGRTHQIRVHTQYAGHPIALDDKYGDREFDQKMQQAGLNRLFLHAHSIRFVHPK 294

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFK 325
            G  + +TAPL   +      L  +
Sbjct: 295 TGEEMIVTAPLDKQLKAVLAKLRAE 319


>gi|120599252|ref|YP_963826.1| RluA family pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|146292674|ref|YP_001183098.1| RluA family pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|120559345|gb|ABM25272.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           W3-18-1]
 gi|145564364|gb|ABP75299.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           putrefaciens CN-32]
          Length = 330

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 107/319 (33%), Positives = 171/319 (53%), Gaps = 13/319 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +V
Sbjct: 20  QVQLITIDEDHFEQRIDNFLMTALKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQMGDIV 79

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP       + +       S NL+K S  L+  +L+ED+ + V NKPAGI+V GGSG+
Sbjct: 80  RIPP-----VRVAESDNRTAPSANLSKVSQ-LEDRILHEDNHLIVLNKPAGIAVHGGSGV 133

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            Y +   L+S    +     L HRLD++TSG+L+VA+ R+A +HL +  R +++QK Y +
Sbjct: 134 DYGVIEALRSLRPQQKF-LELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQKDYLA 192

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G    + + +   LLK +   G+ +  V         + + FK++  + Q    ++ 
Sbjct: 193 LVKGEWSAQDKVVKQPLLKITLKSGERIVRVNAE---GKPSETRFKIMQRY-QGCTLVKA 248

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH    G PI  D KY    F  +  S    +L+LHA  +   HPE   
Sbjct: 249 SPVTGRTHQIRVHCQFAGHPIACDDKYSEQGFDDSMRSLGLTRLFLHAAELMFIHPENDD 308

Query: 305 -LQITAPLPAHMVKTWDSL 322
            ++I+APL  ++ +  D L
Sbjct: 309 VMRISAPLDENLSQLLDKL 327


>gi|200389528|ref|ZP_03216139.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|199601973|gb|EDZ00519.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
          Length = 319

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 105/328 (32%), Positives = 172/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +         +L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FMHPGTGEVMRIEAPMDNALKRCLQVLR 316


>gi|52080148|ref|YP_078939.1| pseudouridine synthase [Bacillus licheniformis ATCC 14580]
 gi|52785525|ref|YP_091354.1| YlyB [Bacillus licheniformis ATCC 14580]
 gi|319646073|ref|ZP_08000303.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
 gi|52003359|gb|AAU23301.1| Pseudouridine synthase [Bacillus licheniformis ATCC 14580]
 gi|52348027|gb|AAU40661.1| YlyB [Bacillus licheniformis ATCC 14580]
 gi|317391823|gb|EFV72620.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
          Length = 304

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 84/323 (26%), Positives = 145/323 (44%), Gaps = 32/323 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  + +  R+D++        +   +Q+ ++  +V V+   VK N ++Q G  V +  
Sbjct: 6   MTVHEEHKGERIDKYLTAVEADWSRTQVQQWIKEDRVLVNGNAVKANYKVQEGDAVSVQ- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                         +     L   ++ +   + YED  + V NKP G+ V    G     
Sbjct: 65  --------------VPEPEPLDVTAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGT 110

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y
Sbjct: 111 LVNGLMAHCDDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G+  +    I   + +        + V ++N     +A++HF+VI+ F   F  +
Sbjct: 171 TALVHGVIPHDHGTIDAPIGRDKK-DRQSMTVTREN---GKHAVTHFEVIERF-DDFTVV 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E Q  TGRTHQ+RVH  ++G P+ GD KY      +F     N   LHA  +   HP  G
Sbjct: 226 ECQLETGRTHQIRVHMKYIGFPLAGDPKYGPKKTVDF-----NGQVLHAGVLGFDHPRTG 280

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
             ++  APLP  M    D +  K
Sbjct: 281 EYVEFEAPLPDDMKNLLDKIRNK 303


>gi|169797345|ref|YP_001715138.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii AYE]
 gi|184156731|ref|YP_001845070.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|213155841|ref|YP_002317886.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           baumannii AB0057]
 gi|215484783|ref|YP_002327018.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB307-0294]
 gi|260556236|ref|ZP_05828455.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           baumannii ATCC 19606]
 gi|301345638|ref|ZP_07226379.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB056]
 gi|301511837|ref|ZP_07237074.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB058]
 gi|301597322|ref|ZP_07242330.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB059]
 gi|332852954|ref|ZP_08434464.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6013150]
 gi|332867958|ref|ZP_08437946.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6013113]
 gi|332873142|ref|ZP_08441099.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6014059]
 gi|169150272|emb|CAM88169.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii AYE]
 gi|183208325|gb|ACC55723.1| Pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|213055001|gb|ACJ39903.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           baumannii AB0057]
 gi|213987620|gb|ACJ57919.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB307-0294]
 gi|260410291|gb|EEX03590.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           baumannii ATCC 19606]
 gi|322506621|gb|ADX02075.1| rluC [Acinetobacter baumannii 1656-2]
 gi|323516497|gb|ADX90878.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332728890|gb|EGJ60245.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6013150]
 gi|332733659|gb|EGJ64818.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6013113]
 gi|332738654|gb|EGJ69524.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6014059]
          Length = 310

 Score =  275 bits (703), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 98/317 (30%), Positives = 162/317 (51%), Gaps = 19/317 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   ++  G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLAIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   +       +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAVPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y ++
Sbjct: 123 YGLIEALRAATGKKY--LELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     K+ I   L +     G+    V    K    + + + V + F +    +   
Sbjct: 181 VKGQVSLDKQLIDAPLFRYELANGERRVRV---SKEGKPSKTEWVVAERF-KNATLVHAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P+VGD KY  N    +T P   +L LHA  +D+P    G   
Sbjct: 237 PLSGRTHQIRVHGLSIGHPLVGDDKYGHN--TAYTGPEARRLCLHAMRLDIP----GYPT 290

Query: 307 ITAPLPAHMVKTWDSLG 323
           I APLP  M +  ++L 
Sbjct: 291 IEAPLPEDMTQLLEALR 307


>gi|166031852|ref|ZP_02234681.1| hypothetical protein DORFOR_01553 [Dorea formicigenerans ATCC
           27755]
 gi|166028305|gb|EDR47062.1| hypothetical protein DORFOR_01553 [Dorea formicigenerans ATCC
           27755]
          Length = 302

 Score =  275 bits (703), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 84/327 (25%), Positives = 145/327 (44%), Gaps = 38/327 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            +Y  VEN+E   R+DR+     P  +   LQK+++   ++V+ K VK N R+  G  V 
Sbjct: 2   TEYFTVENEE-GDRIDRYLAEEMPERSRSYLQKLIKEQYIKVNNKPVKANYRLVLGDRVE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +                +  +       + +   +LYED  + V NKP  + V    G  
Sbjct: 61  VC---------------IPEAKEPDIEPENIPLDILYEDEDVIVVNKPKQMVVHPAPG-- 103

Query: 127 YHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            H  G L + +               +P + HR+D +T+G L++ +   A Q L      
Sbjct: 104 -HYSGTLVNALMYHCGNELSGINGTSRPGIVHRIDMDTTGSLIICKNDMAHQSLAVQLEE 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I +IY ++V G  K ++  +   + +           +  + K A  AI+H+KV+  F
Sbjct: 163 HSINRIYEAIVHGNIKEEEGTVNAPIGRHPTDRKK----MSIHAKNARNAITHYKVLKRF 218

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              + +++ +  TGRTHQ+RVH   +G P++GD  Y    K  F+  +   L  HAR + 
Sbjct: 219 GD-YTYIQCKLETGRTHQIRVHMASIGHPLLGDQVYGPK-KCPFSKLVGQTL--HARTLG 274

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP     +++ APLP + +   + L
Sbjct: 275 FIHPRTNEYIEVNAPLPDYFLNLLEKL 301


>gi|148977658|ref|ZP_01814234.1| 23S rRNA ribosomal pseudouridine synthase [Vibrionales bacterium
           SWAT-3]
 gi|145963173|gb|EDK28441.1| 23S rRNA ribosomal pseudouridine synthase [Vibrionales bacterium
           SWAT-3]
          Length = 314

 Score =  275 bits (703), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 108/328 (32%), Positives = 181/328 (55%), Gaps = 21/328 (6%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V ++ D    R+D + +N   +I    + +I+R G+VRV+KKR+K   ++
Sbjct: 1   MSEIRTQVQFVDIDEDMAGQRIDNFLRNQLKNIPKSMIYRIVRKGEVRVNKKRIKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILD--SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           ++G +VRIPP       +  E+K+ +   S  L K S+ L+  ++YED  + + NKP+G 
Sbjct: 61  KAGDLVRIPP-------VTIEEKVEENVPSTKLNKVSE-LEQCIIYEDDHMLILNKPSGT 112

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +V GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR +
Sbjct: 113 AVHGGSGLKFGAIEALRA-LRPEARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREK 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +QK Y++LV G  KN  + +   LLK        V+ + +       + + FKV++ F 
Sbjct: 172 TVQKYYFALVMGEWKNSCKVVNAPLLKNE------VNSIVRVNPNGKASETRFKVLEKF- 224

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMD 296
           +    ++  P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  + 
Sbjct: 225 KDATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIK 284

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP     + I+AP+ A + K    L 
Sbjct: 285 FTHPGSEEKMDISAPIEARLEKALTGLR 312


>gi|300716227|ref|YP_003741030.1| 23S rRNA pseudouridylate synthase [Erwinia billingiae Eb661]
 gi|299062063|emb|CAX59179.1| 23S rRNA pseudouridylate synthase [Erwinia billingiae Eb661]
          Length = 320

 Score =  275 bits (703), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 103/319 (32%), Positives = 166/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V +  DE   R+D + +     +    + +ILR G+VRV+K R+K   ++ +G  +R
Sbjct: 8   VRMVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKGRIKPEYKLVAGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++    S  L K +  L   ++YED  I V NKP+G +V GGSG++
Sbjct: 68  IPPVR------VAEREEEAISPKLDKVA-ALAHAIVYEDDYILVMNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+ +  V         + + FKV + +A     ++  
Sbjct: 180 VRGSWPSHIKAVQAPLLKNILQSGERIVRVNSE---GKPSETRFKVEERYAH-ATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y   +F          +L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHTLHAGHPIAFDDRYGERDFDAQLAGTGLKRLFLHAAALKFTHPNTGEV 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           +++ APL   +    + L 
Sbjct: 296 MRVEAPLDNELKHCLEVLR 314


>gi|257416242|ref|ZP_05593236.1| pseudouridylate synthase [Enterococcus faecalis AR01/DG]
 gi|257158070|gb|EEU88030.1| pseudouridylate synthase [Enterococcus faecalis ARO1/DG]
          Length = 301

 Score =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 88/327 (26%), Positives = 155/327 (47%), Gaps = 39/327 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  + 
Sbjct: 1   MEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          I E ++LD        ++ +   ++YED+ + V NKP G+ V   +G  
Sbjct: 61  VT---------IPEPEVLD------MVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAG-- 103

Query: 127 YHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            H +G L + +               P + HR+D++TSG+L+VA++  A + L +  + +
Sbjct: 104 -HPNGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKSDQAHESLAKQLKEK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ F 
Sbjct: 163 TSLRKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLERF- 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +  
Sbjct: 217 DTFTLVELQLETGRTHQIRVHMKYIGYPLAGDTLYGPK-----KTLPGNGQFLHAKLLGF 271

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  L   APLP    KT   L 
Sbjct: 272 THPTTGEQLVFEAPLPEVFEKTLHQLR 298


>gi|261822069|ref|YP_003260175.1| 23S rRNA pseudouridylate synthase C [Pectobacterium wasabiae
           WPP163]
 gi|261606082|gb|ACX88568.1| pseudouridine synthase, RluA family [Pectobacterium wasabiae
           WPP163]
          Length = 318

 Score =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 105/319 (32%), Positives = 170/319 (53%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  DE   R+D +   H   +    + +ILR G+VR++KKRVK   ++  G V+R
Sbjct: 8   VQFVTISADEAGQRIDNFLHTHLKGVPKSLVYRILRKGEVRINKKRVKPEYKLLDGDVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A      E+     S +L K +  L   ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRQA------ERDETPVSASLGKVA-ALTECIIYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FK+ + F +    +   
Sbjct: 180 VRGQWQSHCKAVQAPLLKNILQSGERIVRVNSE---GKPSETRFKIEERF-EHATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA + G PI  D +Y    F          +L+LHA+ +   HP  G  
Sbjct: 236 PVTGRTHQIRVHAQYAGHPIAFDDRYGDREFDQQLADTGLKRLFLHAQALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L++ APL + + +    L 
Sbjct: 296 LRVEAPLDSGLRRCLQVLR 314


>gi|262276054|ref|ZP_06053863.1| ribosomal large subunit pseudouridine synthase C [Grimontia
           hollisae CIP 101886]
 gi|262219862|gb|EEY71178.1| ribosomal large subunit pseudouridine synthase C [Grimontia
           hollisae CIP 101886]
          Length = 318

 Score =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 100/321 (31%), Positives = 171/321 (53%), Gaps = 16/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ++ + +D    R+D + +N   ++    + ++LR G+VRV+KKR+K   ++Q+G V
Sbjct: 6   PKVQFIDISDDIAGQRIDNFLRNRLKNVPKSMIYRVLRKGEVRVNKKRIKPEYKLQAGDV 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+PP+       I E    ++          L+  ++YED  + V NKP+G +V GGSG
Sbjct: 66  IRVPPIK------IPETAQAEAPSTKLNRVAELEKCVIYEDDHMLVLNKPSGTAVHGGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +     ++S +    +   L HR+D++TSGIL++A+ R+A +HL   FR + +QK Y+
Sbjct: 120 LHFGAIEAMRS-LRPDARFLELVHRIDRDTSGILLIAKKRSALRHLQAQFREKTVQKYYF 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L  G  K   + +   LLK        V+ + +       + + FKV++ F Q    ++
Sbjct: 179 ALTMGNWKPSMKKVTAPLLKNE------VNSIVRVNPDGKPSETRFKVLEQFDQ-ATLVQ 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVHA ++G P+  D +Y    F         N+L+LHA  +   HP  G
Sbjct: 232 ASPITGRTHQIRVHAQYVGHPLAWDDRYGDPRFDAYTKKFGLNRLFLHAANIKFTHPGSG 291

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             + I+AP+   + KT + L 
Sbjct: 292 EMMDISAPMDKQLEKTLEGLR 312


>gi|168215478|ref|ZP_02641103.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
 gi|182382386|gb|EDT79865.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
          Length = 306

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 145/330 (43%), Gaps = 33/330 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSL   V  + +  +E+ +R D++       ++   +Q +   G++ ++ K  K   ++ 
Sbjct: 1   MSLSKEV--IKITEEEKGIRADKFLALKIEGVSRNFIQGLFDDGKILINGKAEKGKYKLS 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G                  +  +     L   ++ +   ++YED  + V NKP G+ V 
Sbjct: 59  VGDC---------------VEVEIPEPEELKVEAEDIPLNIVYEDEDVIVVNKPKGMVVH 103

Query: 121 GGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++  L    D  G     +P + HR+D++TSGILVVA+   A Q L E F
Sbjct: 104 PAPGNYTGTLVNALLYHCDDLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQF 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +   I++ Y+++V G  K +   I   L +       Y  V     K    A++H++V+ 
Sbjct: 164 KDHSIKREYYAIVEGRFKKEGGTIDAPLGRHHRDRLKYAVV-----KDGKRAVTHYEVLK 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F      ++    TGRTHQ+RVH   +G P++GD  Y    +   +   Q    LHA+ 
Sbjct: 219 VF-NSCSLVKCTLETGRTHQIRVHMAFIGHPLLGDTVYGLKKQKKLS---QEGQVLHAKT 274

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +   HP  G  ++  + LP +  K  + LG
Sbjct: 275 LGFIHPTTGEYVEFDSELPEYFEKIVEKLG 304


>gi|150020881|ref|YP_001306235.1| RluA family pseudouridine synthase [Thermosipho melanesiensis
           BI429]
 gi|149793402|gb|ABR30850.1| pseudouridine synthase, RluA family [Thermosipho melanesiensis
           BI429]
          Length = 306

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 85/325 (26%), Positives = 144/325 (44%), Gaps = 30/325 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +  + V   E+  RLD++ +   P  I+   +Q+ ++SG V V+ +  K + ++++G VV
Sbjct: 1   MLEIQVTAREKGWRLDKFIQEKAPDWISRTYIQRAIKSGMVTVNNEEKKPSYKLKNGDVV 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                           ++ +    +    + L   ++YED  I V NK  G+        
Sbjct: 61  SF--------------ELPEEPKKVEILPENLPLKIIYEDKDIIVVNKDPGVVTHPTPTF 106

Query: 126 --AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++  +    D +G     +P + HRLD++TSG++VVA+   A Q L+  F+ R+ 
Sbjct: 107 LSGTLVNALMYHCNDFQGIGGELRPGIVHRLDKDTSGVIVVAKNDKAHQSLSMQFKERKT 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++V G  K     I   L +   +      V          AI++FKVI  F + 
Sbjct: 167 EKTYIAIVSGEVKKNYGTIDVPLGRNPVVRTKIAPVDW-----GKNAITYFKVIKRF-KN 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L   P TGRTHQ+RVH  ++G P++GD  Y    K         +  LHA  +   H
Sbjct: 221 ATLLLAFPKTGRTHQIRVHMKYIGHPLLGDELYGRGKKDEI--FGVKRQMLHALKLSFYH 278

Query: 300 PEG-GRLQITAPLPAHMVKTWDSLG 323
           P    ++   APLP    +   +L 
Sbjct: 279 PSTNEKMIFVAPLPEDFKQVIRNLA 303


>gi|227553528|ref|ZP_03983577.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|255972642|ref|ZP_05423228.1| pseudouridylate synthase [Enterococcus faecalis T1]
 gi|255975694|ref|ZP_05426280.1| pseudouridylate synthase [Enterococcus faecalis T2]
 gi|256762651|ref|ZP_05503231.1| pseudouridylate synthase [Enterococcus faecalis T3]
 gi|256961775|ref|ZP_05565946.1| pseudouridylate synthase [Enterococcus faecalis Merz96]
 gi|257079163|ref|ZP_05573524.1| pseudouridylate synthase [Enterococcus faecalis JH1]
 gi|257085033|ref|ZP_05579394.1| pseudouridylate synthase [Enterococcus faecalis Fly1]
 gi|257419447|ref|ZP_05596441.1| pseudouridylate synthase [Enterococcus faecalis T11]
 gi|257422461|ref|ZP_05599451.1| pseudouridylate synthase [Enterococcus faecalis X98]
 gi|294779380|ref|ZP_06744781.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|227177333|gb|EEI58305.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|255963660|gb|EET96136.1| pseudouridylate synthase [Enterococcus faecalis T1]
 gi|255968566|gb|EET99188.1| pseudouridylate synthase [Enterococcus faecalis T2]
 gi|256683902|gb|EEU23597.1| pseudouridylate synthase [Enterococcus faecalis T3]
 gi|256952271|gb|EEU68903.1| pseudouridylate synthase [Enterococcus faecalis Merz96]
 gi|256987193|gb|EEU74495.1| pseudouridylate synthase [Enterococcus faecalis JH1]
 gi|256993063|gb|EEU80365.1| pseudouridylate synthase [Enterococcus faecalis Fly1]
 gi|257161275|gb|EEU91235.1| pseudouridylate synthase [Enterococcus faecalis T11]
 gi|257164285|gb|EEU94245.1| pseudouridylate synthase [Enterococcus faecalis X98]
 gi|294453509|gb|EFG21910.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|323480881|gb|ADX80320.1| pseudouridine synthase, RluA family protein [Enterococcus faecalis
           62]
          Length = 301

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 86/324 (26%), Positives = 152/324 (46%), Gaps = 33/324 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  + 
Sbjct: 1   MEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +          I E ++LD        ++ +   ++YED+ + V NKP G+ V   +G  
Sbjct: 61  VT---------IPEPEVLD------MVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHP 105

Query: 126 -AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L             +P + HR+D++TSG+L+VA+   A + L +  + +   
Sbjct: 106 KGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSL 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ F   F
Sbjct: 166 RKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLERF-DAF 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   HP
Sbjct: 220 TLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLLGFTHP 274

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  L   APLP    KT   L 
Sbjct: 275 TTGEQLVFEAPLPEVFEKTLHQLR 298


>gi|15602857|ref|NP_245929.1| 23S rRNA pseudouridylate synthase C [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|20139710|sp|Q9CM51|RLUC_PASMU RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|12721319|gb|AAK03076.1| RluC [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 326

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 105/325 (32%), Positives = 171/325 (52%), Gaps = 14/325 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  DE   R+D +       +    + +ILR G+VRV+K R+K   ++Q+  +VR
Sbjct: 14  VKMLTISEDEAGQRIDNYLLAKLKGVPKSLIYRILRKGEVRVNKGRIKPEYKLQANDIVR 73

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E++    S  L K S  L+  +L+ED  + V NKP+GI+V GGSG++
Sbjct: 74  VPPVR------VSEKEHAPISTKLNKVSQ-LEKQILFEDECLLVLNKPSGIAVHGGSGLS 126

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +    +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 127 FGVIEALRT-LRPDARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKTVQKDYLAL 185

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V +       + + F + + + +    ++  
Sbjct: 186 VRGQWQSHCKVVKAPLLKNELSSGERIVRVSEQ---GKPSETRFSIEERY-EYATLVKAS 241

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F    T     +L+LHA  +   HP+ G  
Sbjct: 242 PVTGRTHQIRVHTQYAGHPIALDDKYGDKHFDEQMTQLGLTRLFLHAFSIRFEHPKTGET 301

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRN 329
           L+I APL   M K   +L  +   N
Sbjct: 302 LRINAPLDPEMKKILGALREQKSSN 326


>gi|325954148|ref|YP_004237808.1| pseudouridine synthase [Weeksella virosa DSM 16922]
 gi|323436766|gb|ADX67230.1| pseudouridine synthase, RluA family [Weeksella virosa DSM 16922]
          Length = 362

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 84/334 (25%), Positives = 153/334 (45%), Gaps = 41/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +  +R+D++      +     +Q+   +G + V+   VK N +++ G  ++I  
Sbjct: 22  ITVDKGQSLLRIDKFLMIRIENATRNKIQQAAENGNILVNNLPVKSNYKVKPGDFIQIM- 80

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L +  +E KI+   + L          +++ED ++ V +KPAG+ V  G G     
Sbjct: 81  ----LENPPREHKIIAEDLPLN---------IVFEDDQVLVIDKPAGMVVHPGHGNYSGT 127

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + +H D      + ++ ++P L HR+D++TSG+LV+A+T  A  HL   F      
Sbjct: 128 LVNALKFHFDNLPS--MSAELERPGLVHRIDKDTSGLLVIAKTEQAMNHLALQFANHTTT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG     +  I   + +  H+       V ++     +A++H+KV++  +   
Sbjct: 186 RKYNALVWGNVTEDEGTITGHIGR--HLKDRMQMAVFEDGSQGKHAVTHYKVLERLS-YV 242

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKL 288
             +E Q  TGRTHQ+R H  ++G P+  D +Y  N     T+             I  + 
Sbjct: 243 TLVECQLETGRTHQIRTHFKYIGHPLFNDERYGGNKILKGTTFTKYKQFVENCFNICPRQ 302

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            LHAR +   HP  G  ++  A LP  M    + 
Sbjct: 303 ALHARTLGFTHPTTGEFMEFEATLPNDMQSLIEK 336


>gi|282879373|ref|ZP_06288116.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
 gi|281298486|gb|EFA90912.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
          Length = 355

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 84/332 (25%), Positives = 152/332 (45%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +E +R+D++      H +   +QK   +G V V+ + VK N +++   V+ +  
Sbjct: 25  IVVDKGQEPLRVDKYMFERLKHSSRNRIQKAADAGFVHVNDQPVKSNYKVRPLDVITLML 84

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +H I+              ++ +   ++YEDS + V NK  G+ V  G+G  +  
Sbjct: 85  DAPQHDHTIE--------------AEDIPLDIVYEDSDLMVVNKAPGMVVHPGAGNFHGT 130

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A   L   F  +   + 
Sbjct: 131 LINAVAWHLKDLTSFDANDPAVGLVHRIDKDTSGLLVIAKTPVAKTKLGLQFFNKTTHRS 190

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG    ++  I   + +        ++V   + +    A++H+++++ F      
Sbjct: 191 YNALVWGNFNEEEGRIEGNIGRDPR-DRLRMNVFPPDSEIGKSAVTHYRILERFG-YVTL 248

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ----------NKLYL 290
           +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S  +          N+  L
Sbjct: 249 VECILETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSTYKAFIQNCFKVCNRQAL 308

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA+ +   HP  GR +  T+ LP  M +  D 
Sbjct: 309 HAKTLGFVHPTTGRQMDFTSDLPNDMQQLLDK 340


>gi|323489511|ref|ZP_08094738.1| putative RNA pseudouridine synthase ylyB [Planococcus donghaensis
           MPA1U2]
 gi|323396642|gb|EGA89461.1| putative RNA pseudouridine synthase ylyB [Planococcus donghaensis
           MPA1U2]
          Length = 303

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 80/322 (24%), Positives = 147/322 (45%), Gaps = 33/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + +  +    R+D+   +     +   +   ++ G V+V+ + VK N +++   ++ + 
Sbjct: 5   TIEITKEMAGERVDKAVSSIDGDWSRSQISNWVKEGAVKVNGETVKPNYKVRLQDIIIVT 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
           P        ++E  ++   +NL          ++YED  + V NKP G+ V    G A  
Sbjct: 65  PPE------LEELDVVPEDLNLE---------IVYEDEDVLVVNKPKGMVVHPAPGHAKG 109

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +    D  G     +P + HR+D++TSG+L+VA+  AA   L +    + + + 
Sbjct: 110 TLVNGLMHHCTDLSGINGVVRPGIVHRIDKDTSGLLMVAKNDAAHTSLVDQLVKKTVTRK 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G   + K  I   + +      +   V K       +A++HF+V++ F   F  
Sbjct: 170 YVALVHGHIPHDKGTIQAPIARDPKERQNMAIVDK-----GKHAVTHFRVLERFG-NFTL 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +   HP  
Sbjct: 224 VECRLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTMD-----IGGQALHAEVIGFNHPRT 278

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
              ++ +A  PA   +  +SL 
Sbjct: 279 NEYMEFSAEPPAEFAELLESLR 300


>gi|242239020|ref|YP_002987201.1| pseudouridine synthase [Dickeya dadantii Ech703]
 gi|242131077|gb|ACS85379.1| pseudouridine synthase, RluA family [Dickeya dadantii Ech703]
          Length = 319

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 105/319 (32%), Positives = 169/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ + ++E   R+D + +     +    + +ILR G+VR++KKRVK   ++  G  VR
Sbjct: 8   VQFMTISSEEAGQRIDNFLRVRLKGVPKSMIYRILRKGEVRINKKRVKPEYKLLDGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +      E+ + + S +L K S  L   +LYED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRQS------ERDVPEVSASLDKVS-SLTHCILYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRALHEQLRSKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FKV + F      ++  
Sbjct: 180 VRGQWQSHCKSVQAPLLKNILKSGERIVRVNGE---GKPSETLFKVEERF-DCATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA + G PI  D +Y    F          +L+LHA  + L HP  G  
Sbjct: 236 PVTGRTHQIRVHAQYAGHPIAFDDRYGDRAFDQQLADTGLKRLFLHAHALRLEHPHTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+  APL   + +    L 
Sbjct: 296 LRFEAPLDDALRRCLQLLR 314


>gi|157962324|ref|YP_001502358.1| RluA family pseudouridine synthase [Shewanella pealeana ATCC
           700345]
 gi|157847324|gb|ABV87823.1| pseudouridine synthase, RluA family [Shewanella pealeana ATCC
           700345]
          Length = 319

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 106/323 (32%), Positives = 172/323 (53%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    VQ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++  
Sbjct: 5   SQKAQVQLVTIDEDHVGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLAD 64

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPP       + + +     S  LTK S  L+  +L+ED  + V NKP+GI+V G
Sbjct: 65  GDIVRIPP-----VRVSESEGRPGPSAKLTKVSQ-LEERILFEDKYLIVLNKPSGIAVHG 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ + +   ++S + ++ +   L HRLD+ETSG+L++A+ R+A +HL +  R +++QK
Sbjct: 119 GSGVEFGVIEAMRS-LRTQQKFLELVHRLDKETSGVLLIAKKRSALRHLHDQLRYKKMQK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  ++  + I   LLK +   G+ +  V    K    + + FK++  +     
Sbjct: 178 DYVALVRGEWQSHDKVIKAPLLKLTLKSGERIVRVN---KEGKESETRFKILQRYEDS-T 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH    G PI  D KY    F  +  +   N+L+LHA  +   HP
Sbjct: 234 LVQASPVTGRTHQIRVHCQFAGHPIACDEKYSEQKFDDSMRAQGLNRLFLHAAQLKFTHP 293

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E    +Q+ APL   +  T   L
Sbjct: 294 ETEEVMQVKAPLDTILESTLKKL 316


>gi|227326844|ref|ZP_03830868.1| 23S rRNA pseudouridylate synthase C [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 318

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 106/319 (33%), Positives = 171/319 (53%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  DE   R+D +   H   +    + +ILR G+VR++KKRVK   ++  G V+R
Sbjct: 8   VQFVTISADEAGQRVDNFLHTHLKGVPKSMVYRILRKGEVRINKKRVKPEYKLLDGDVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A      E+     S +L K +  L   ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRQA------ERDETPVSASLGKVA-ALAECIIYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V  +      + + FK+ + F +    +   
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILQSGERIVRVNSD---GKQSETRFKIEERF-EHATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA H G PI  D +Y    F          +L+LHA+ +   HP  G  
Sbjct: 236 PVTGRTHQIRVHAQHAGHPIAFDDRYGDREFDQQLADTGLKRLFLHAQALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L++ APL + + +    L 
Sbjct: 296 LRVEAPLDSGLRRCLQVLR 314


>gi|293390568|ref|ZP_06634902.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951102|gb|EFE01221.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 319

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 107/319 (33%), Positives = 169/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ V +DE   RLD +       +    + +I+R G+VRV+K R K   ++++  VVR
Sbjct: 10  VQFLTVSDDEAGQRLDNFLLARLKGVPKSLIYRIVRKGEVRVNKGRSKPEYKLRADDVVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+     S  LTK +  L+  +++ED+ + V NKP+GI+V GGSG+ 
Sbjct: 70  IPPVR------VAEKAQATISNKLTKVAQ-LEQHIIFEDNYLLVLNKPSGIAVHGGSGLD 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++   +      L HRLD++TSGIL+VA+ R+A ++L E  R + +QK Y +L
Sbjct: 123 FGVIEALRALRPAACF-LELVHRLDRDTSGILLVAKKRSALRNLHEQLREKTVQKDYLAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK    GG+ +  V +       + + F V + +      ++  
Sbjct: 182 VRGQWQSHCKVVQAPLLKNELAGGERIVKVSEQ---GKPSETRFSVEERYT-NATLIKAS 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F  +      N+L+LHA  +   HP  G  
Sbjct: 238 PVTGRTHQIRVHTQYAGHPIAFDSKYGDKEFDQHMVELGLNRLFLHAYAIRFEHPHSGET 297

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L++TAPL   M      L 
Sbjct: 298 LRLTAPLEEKMKGILKRLR 316


>gi|257082401|ref|ZP_05576762.1| pseudouridylate synthase [Enterococcus faecalis E1Sol]
 gi|256990431|gb|EEU77733.1| pseudouridylate synthase [Enterococcus faecalis E1Sol]
          Length = 301

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 86/324 (26%), Positives = 152/324 (46%), Gaps = 33/324 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  + 
Sbjct: 1   MEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +          I E ++LD        ++ +   ++YED+ + V NKP G+ V   +G  
Sbjct: 61  VT---------IPEPEVLD------MVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHP 105

Query: 126 -AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L             +P + HR+D++TSG+L+VA+   A + L +  + +   
Sbjct: 106 KGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSL 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ F   F
Sbjct: 166 RKYVALVHGVIPHDKGEINTPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLERF-DAF 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   HP
Sbjct: 220 TLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLLGFTHP 274

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  L   APLP    KT   L 
Sbjct: 275 TTGEQLVFEAPLPEVFEKTLHQLR 298


>gi|218709011|ref|YP_002416632.1| ribosomal large subunit pseudouridine synthase C [Vibrio splendidus
           LGP32]
 gi|218322030|emb|CAV18069.1| Ribosomal large subunit pseudouridine synthase C [Vibrio splendidus
           LGP32]
          Length = 314

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 109/326 (33%), Positives = 179/326 (54%), Gaps = 17/326 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V ++ D    R+D + +N   +I    + +I+R G+VRV+KKR+K   ++
Sbjct: 1   MSEIRTQVQFVDIDEDMAGQRIDNFLRNQLKNIPKSMIYRIVRKGEVRVNKKRIKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VRIPP       I ++ +    S  L K S+ L+  ++YED  + + NKP+G +V
Sbjct: 61  KAGDLVRIPP-----VTIEEKTEENVPSTKLNKVSE-LEQCIIYEDDHMLILNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +    +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y++LV G  KN  + +   LLK        V+ + +       + + FKV++ F Q+
Sbjct: 174 QKYYFALVMGEWKNSCKVVNAPLLKNE------VNSIVRVNPNGKASETRFKVLEKF-QE 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVHA + G PI  D +Y       +T     N+L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHAQYTGHPIAWDDRYGDRRFDAYTGKVGLNRLFLHAANIKFI 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP     + I+AP+   + K    L 
Sbjct: 287 HPGSEEKMDISAPMERRLEKALTGLR 312


>gi|113460859|ref|YP_718926.1| 23S rRNA pseudouridylate synthase C [Haemophilus somnus 129PT]
 gi|112822902|gb|ABI24991.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           somnus 129PT]
          Length = 326

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 112/326 (34%), Positives = 178/326 (54%), Gaps = 14/326 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  DE   R+D +       +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 13  VKILTINEDESGQRIDNFLLAKLKSVPKSLIYRILRKGEVRVNKGRIKPEYKLQNGDIVR 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       I E++    S  L K +  L+  +++ED+ + V NKP+G++V GGSG+ 
Sbjct: 73  IPPVR------IAEKEHTPISKKLNKVAQ-LEQQIIFEDNYLLVLNKPSGLAVHGGSGLN 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +     L++ +  + +   L HRLD++TSGIL++A+ R+A + L E  R + IQK Y +L
Sbjct: 126 FGAIEALRT-LRPEARFLELVHRLDRDTSGILLIAKKRSALRSLHEQLREKTIQKEYLAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+   +VK NE+G   + + F V + +      ++  
Sbjct: 185 VRGHWQSHCKMIQAPLLKNELTSGER--IVKVNEQG-KPSETKFSVEERY-NNATLVKAS 240

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY   NF    T+   N+L+LHA  +   HP+ G R
Sbjct: 241 PITGRTHQIRVHTQYAGHPIALDDKYGDKNFDQQMTALGLNRLFLHAFAICFEHPKTGER 300

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNL 330
           L++ APL   M      L    ++ L
Sbjct: 301 LRLVAPLDLAMKNILQVLREIKNKTL 326


>gi|227514877|ref|ZP_03944926.1| pseudouridylate synthase [Lactobacillus fermentum ATCC 14931]
 gi|227086724|gb|EEI22036.1| pseudouridylate synthase [Lactobacillus fermentum ATCC 14931]
          Length = 291

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 83/309 (26%), Positives = 141/309 (45%), Gaps = 32/309 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+   +H+P  +   L++ +  G V V+ + VK   ++Q+G  V I P          
Sbjct: 4   RIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAGDRVVIKP---------- 53

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                ++ V +    + +   ++YED  + V NKP G+ V    G   H       +   
Sbjct: 54  -----ETPVEIDLEPENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALMYYAP 108

Query: 140 KG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                   +P + HR+D++TSG+L+VA+T  A + LT   + +   + Y +LV G+ K  
Sbjct: 109 LSSINGELRPGIVHRIDKDTSGLLMVAKTDRAHRSLTAQLKEKSNLREYVALVHGVIKEN 168

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I   L +          VV     G  +A++HF+V+  + Q +  +  +  TGRTHQ
Sbjct: 169 EGTIDAPLARSPKDRKKQAVVV-----GGRHAVTHFRVLKRY-QHYTLVACRLETGRTHQ 222

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPA 313
           +RVH  ++  P+ GD  Y         +   +  YLHAR +   HP  G  +  TAPLP 
Sbjct: 223 IRVHMKYINHPLAGDPLYGPR-----KTLPGHGQYLHARLLGFEHPVTGEEMVFTAPLPD 277

Query: 314 HMVKTWDSL 322
           +  +    L
Sbjct: 278 YFEQMLSYL 286


>gi|49066398|gb|AAT49291.1| putative bacteriocin [Prevotella nigrescens]
 gi|242332477|tpg|DAA06525.1| TPA_exp: NigA [Prevotella nigrescens]
          Length = 363

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 86/332 (25%), Positives = 149/332 (44%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +E +R+D++      H +   +QK   +G + V+   VK N +++   V+ +  
Sbjct: 36  VEVDKGQEAVRIDKFLFERMQHSSRNRIQKAADAGSIYVNGTPVKSNYKVRPNDVITLML 95

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                ++ I               ++ +   ++YED++I V NKPAG+ V  G+G     
Sbjct: 96  DRPKHDNTI--------------VAEDMPLNVVYEDNEIMVINKPAGLVVHPGAGNFRGT 141

Query: 128 HIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            I+       D K   P      L HR+D++TSG+L++A+T  A   L + F  +   + 
Sbjct: 142 LINAIAWHLRDLKNFDPNDPAVGLVHRIDKDTSGLLLIAKTPDAKTFLGKQFFNKTTHRS 201

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + + S      + V   +      A++H+KV++ F      
Sbjct: 202 YVALVWGNFTEDEGRIEGNIGRDSK-DRLRMKVFDTDSGIGKPAVTHYKVLERFG-YTTL 259

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKLYL 290
           +E    TGRTHQ+R H  H+G P+ GD +Y      +G  TS           + N+  L
Sbjct: 260 IECILETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRTSAYRAYIQNCFKLCNRQAL 319

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA+ +   HP  G  +  T+ LP  +    + 
Sbjct: 320 HAKTLGFVHPRTGEQMDFTSELPDDLSSVIEK 351


>gi|332288916|ref|YP_004419768.1| 23S rRNA pseudouridylate synthase C [Gallibacterium anatis UMN179]
 gi|330431812|gb|AEC16871.1| 23S rRNA pseudouridylate synthase C [Gallibacterium anatis UMN179]
          Length = 321

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 105/319 (32%), Positives = 172/319 (53%), Gaps = 13/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +E DEE  R+D +       +    + +I+R G+VRV+K R+K   ++Q G VVR
Sbjct: 13  VQLLTIEPDEELQRIDNYLLTKLKGVPKSLIYRIIRKGEVRVNKGRIKPEYKLQVGDVVR 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP       I ++      S  L K +  L+  +L+ED ++ + NKP+GI+V GGSG++
Sbjct: 73  IPP-----VRISEKSNTAPLSTKLNKVN-ALEQQILFEDDQLLILNKPSGIAVHGGSGLS 126

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A ++L +  R + IQK Y +L
Sbjct: 127 FGVIEALRA-LRPQAKFLELVHRLDRDTSGILLVAKKRSALRNLHQQLREKTIQKDYLAL 185

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FKV + F +    ++  
Sbjct: 186 VRGEWQSHCKVVKAPLLKNELSSGERIVKVSDQ---GKPSETRFKVEERF-KIATLVKAS 241

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-QNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY +       +P+   +L+LHA  +   HP+ G  
Sbjct: 242 PVTGRTHQIRVHTQYAGHPIAFDSKYGSKEFDQLLAPLGLQRLFLHAASIRFTHPKSGEQ 301

Query: 305 LQITAPLPAHMVKTWDSLG 323
           + I+APL     +    L 
Sbjct: 302 MVISAPLDQQCKQLLAKLR 320


>gi|257090036|ref|ZP_05584397.1| pseudouridylate synthase [Enterococcus faecalis CH188]
 gi|256998848|gb|EEU85368.1| pseudouridylate synthase [Enterococcus faecalis CH188]
          Length = 301

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 86/324 (26%), Positives = 152/324 (46%), Gaps = 33/324 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  + 
Sbjct: 1   MEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +          I E ++LD        ++ +   ++YED+ + V NKP G+ V   +G  
Sbjct: 61  VT---------IPEPEVLD------MIAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHP 105

Query: 126 -AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L             +P + HR+D++TSG+L+VA+   A + L +  + +   
Sbjct: 106 KGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSL 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ F   F
Sbjct: 166 RKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLERF-DAF 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   HP
Sbjct: 220 TLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLLGFTHP 274

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  L   APLP    KT   L 
Sbjct: 275 TTGEQLVFEAPLPEVFEKTLHQLR 298


>gi|229545666|ref|ZP_04434391.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|307275817|ref|ZP_07556956.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|307291840|ref|ZP_07571711.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|229309234|gb|EEN75221.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|306497106|gb|EFM66652.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|306507509|gb|EFM76640.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|315029545|gb|EFT41477.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4000]
 gi|315032018|gb|EFT43950.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0017]
 gi|315144961|gb|EFT88977.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2141]
 gi|315168880|gb|EFU12897.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1341]
          Length = 310

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 83/326 (25%), Positives = 148/326 (45%), Gaps = 33/326 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  
Sbjct: 8   AKMEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDE 67

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +                +     L   ++ +   ++YED+ + V NKP G+ V   +G
Sbjct: 68  IVVT---------------IPEPEALDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAG 112

Query: 125 I--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 ++  L             +P + HR+D++TSG+L+VA+   A + L +  + + 
Sbjct: 113 HPKGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKT 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ F  
Sbjct: 173 SLRKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLERF-D 226

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   
Sbjct: 227 AFTLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLLGFT 281

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  L   APLP    KT   L 
Sbjct: 282 HPTTGEQLVFEAPLPEVFEKTLHQLR 307


>gi|253989177|ref|YP_003040533.1| 23S rRNA pseudouridylate synthase C [Photorhabdus asymbiotica
           subsp. asymbiotica ATCC 43949]
 gi|253780627|emb|CAQ83789.1| 23S rRNA pseudouridine synthase [Photorhabdus asymbiotica]
          Length = 319

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 104/319 (32%), Positives = 170/319 (53%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +++DE   R+D +       +    + +I+R G+VRV+K RVK   ++ +G VVR
Sbjct: 8   VQFVTIDDDEAGQRVDNFLLARLKGVPKSMIYRIVRKGEVRVNKGRVKPEYKLSAGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++ +  S  L K +  L   +LYED  I V NKP+G +V GGSG++
Sbjct: 68  IPPVR------VAERQEIAVSAKLHKVA-ALDGCILYEDDYILVINKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+  +  + +   L HRLD++TSGIL++A+ R+  + L E  R++++QK Y +L
Sbjct: 121 FGVIEGLR-VLRPEAKFLELVHRLDRDTSGILLIAKKRSVLRALHEQLRLKQMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FK+ + F      +   
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILQSGERIVKV---SGEGKPSETRFKIEERFT-NATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA ++G PI  D +Y    F    +    N+L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHAQYVGHPIAFDDRYGDKTFDSQLSDTGLNRLFLHASALKFTHPSTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L++ AP+   +      L 
Sbjct: 296 LRLEAPMDGQLYSCIKMLR 314


>gi|239500866|ref|ZP_04660176.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB900]
          Length = 310

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 96/317 (30%), Positives = 161/317 (50%), Gaps = 19/317 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   ++  G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLAIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   +       +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAVPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y ++
Sbjct: 123 YGLIEALRAATGKKY--LELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     K+ I   L +     G+    V    K    + + + V + F +    +   
Sbjct: 181 VKGQVSLDKQLIDAPLFRYELANGERRVRV---SKEGKPSKTEWVVAERF-KNATLVHAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P++GD KY  N    +  P   +L LHA  +D+P    G   
Sbjct: 237 PLSGRTHQIRVHGLSIGHPLLGDDKYGHN--TAYAGPEARRLCLHAMRLDIP----GYPT 290

Query: 307 ITAPLPAHMVKTWDSLG 323
           I APLP  M +  ++L 
Sbjct: 291 IEAPLPEDMTQLLEALR 307


>gi|330824017|ref|YP_004387320.1| RluA family pseudouridine synthase [Alicycliphilus denitrificans
           K601]
 gi|329309389|gb|AEB83804.1| pseudouridine synthase, RluA family [Alicycliphilus denitrificans
           K601]
          Length = 336

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 82/331 (24%), Positives = 143/331 (43%), Gaps = 31/331 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
             ++ V+V   +   RLD+      P  +   LQ++L  G VR++ +   K  +++++G 
Sbjct: 29  AELREVMVPAAQHQARLDKALAELVPEFSRSYLQQLLAQGDVRLNGQPAAKPAHKVRAGD 88

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +       +   K               + L   +++ED  + V +KPAG+ V    
Sbjct: 89  QVAVRMRPTQQSQAFK--------------PESLPLDVVHEDEHLLVIDKPAGLVVHPAP 134

Query: 124 GIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +  G L + +  +        +  + HRLD++TSG++VVAR RAA   L      R
Sbjct: 135 G---NWSGTLLNALLGRDAQAMQVPRAGIVHRLDKDTSGLMVVARNRAAMDALVRMIAAR 191

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L WG     ++      + +       + VV   +     A + F ++    
Sbjct: 192 EVSRQYLALAWGAWSGSEQRRIRAPIGRDPRNRLRMAVVDLGQHAGKEACTDFDLLAS-G 250

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++ C +    HTGRTHQ+RVH   +  P+V D  Y     G        +  LHA  +  
Sbjct: 251 EEVCLVRCTLHTGRTHQIRVHMASIRHPLVADALYGGAVGGPM-----RRQALHAFRLAF 305

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            HP  G+ ++  APLP  M +  D  G +Y+
Sbjct: 306 THPVTGKPMEFHAPLPEDMRQALDFWGLRYN 336


>gi|322833656|ref|YP_004213683.1| pseudouridine synthase, RluA family [Rahnella sp. Y9602]
 gi|321168857|gb|ADW74556.1| pseudouridine synthase, RluA family [Rahnella sp. Y9602]
          Length = 320

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 103/321 (32%), Positives = 170/321 (52%), Gaps = 14/321 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + + +DE   R+D +       +    + +I+R G+VRV+KKR+K   ++ +G  VR
Sbjct: 8   VQLIPISDDEAGQRIDNFLLKILKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLIAGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       + E+     S  L K +  L   +LYED  + + NKP+G +V GGSG++
Sbjct: 68  VPPVR------VAERDEAPVSAKLDKVA-ALADCILYEDDHLLILNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +    +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPDARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRVKSMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+ +  V         + + FK+ + + +    ++  
Sbjct: 180 VRGEWPSHCKVVQAPLLKNILQSGERIVRVNAE---GKPSETRFKIEERY-EFATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y   +F    +    N+L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHALHAGHPIAFDDRYGERDFDAKLSGTGLNRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           ++I AP+ A +      L  K
Sbjct: 296 MRIEAPMDAKLRNCLKVLRGK 316


>gi|187734524|ref|YP_001876636.1| pseudouridine synthase, RluA family [Akkermansia muciniphila ATCC
           BAA-835]
 gi|187424576|gb|ACD03855.1| pseudouridine synthase, RluA family [Akkermansia muciniphila ATCC
           BAA-835]
          Length = 323

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 136/313 (43%), Gaps = 29/313 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +  ++ +  +RLD++   H P ++   +Q +++SG V V+    K  N +  G  + +  
Sbjct: 3   LTTDDADGKIRLDQYLAAHLPELSRSRIQSLIKSGDVLVNGSPAKPKNPVSRGDSITVR- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                         +            +   +LYED  + V NK +G+ V   +G     
Sbjct: 62  --------------IPEPEPAEAQPQDIPLDILYEDEDVVVINKESGMVVHPAAGNPDGT 107

Query: 130 --DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             +  L    D  G    ++P + HRLD++TSG LV+A+   A Q LT  F  R  +K Y
Sbjct: 108 IVNALLHHCGDLSGIGGVERPGIVHRLDKDTSGCLVIAKNDGAHQSLTAQFAARSTEKRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCW 242
            ++V GIP      +   + +      + + +   N      AI+ + ++    +     
Sbjct: 168 LAVVQGIPSQSSGTVFTHIGRHP---VNRLKMAVVNPGSGKAAITDYDLLCADPSTDSSL 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +    HTGRTHQ+RVH L++G P++GD  Y    +         +L LHA  +   HP  
Sbjct: 225 VLCTLHTGRTHQIRVHMLYLGHPLIGDPIYAKPARQKAKP---GRLMLHAWRLGFDHPRT 281

Query: 303 G-RLQITAPLPAH 314
           G R+   AP+P  
Sbjct: 282 GKRMDFEAPVPPE 294


>gi|317504079|ref|ZP_07962082.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           salivae DSM 15606]
 gi|315664821|gb|EFV04485.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           salivae DSM 15606]
          Length = 355

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 81/332 (24%), Positives = 145/332 (43%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +  +R+D++     P+ +   +Q+   SG +RV+ + VK N +++ G V+ +  
Sbjct: 25  IEVDKGQTPVRIDKFLAEKNPYQSRNRIQQAADSGCIRVNNQPVKSNYKVRPGDVITLML 84

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                +  I               ++ +   ++YED  + V NKPAG+ V  G+G     
Sbjct: 85  DRPKHDTSI--------------IAEDIPLDIVYEDDVLMVVNKPAGMVVHPGAGNFTGT 130

Query: 128 HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            I+       D KG      +  L HR+D++TSG+LVVA+T  A   L + F  +   + 
Sbjct: 131 LINAVAWHLKDLKGFDANDPEVGLVHRIDKDTSGLLVVAKTPEAKTVLGKQFFNKTTHRS 190

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + +        + V          A++H++VI+ +      
Sbjct: 191 YNALVWGNLVEDEGTIEGNVARDPK-NRLRMKVFSPESGIGKNAVTHYRVIERYG-YTTL 248

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ----------NKLYL 290
           +E    TGRTHQ+RVH  H+G P+  D  Y      +G  +S  +           +  L
Sbjct: 249 VECILETGRTHQIRVHMKHIGHPLFADATYGGEEVLRGQRSSTYKAFINNCFKCCPRQAL 308

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA+ +   HP  G ++   +  P    +  + 
Sbjct: 309 HAKTLGFIHPITGVQMDFDSEWPDDFRQLIEK 340


>gi|161614588|ref|YP_001588553.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|162139595|ref|YP_216121.2| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|168467142|ref|ZP_02700984.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|224584309|ref|YP_002638107.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|161363952|gb|ABX67720.1| hypothetical protein SPAB_02338 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|195630420|gb|EDX49046.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|224468836|gb|ACN46666.1| ribosomal large subunit pseudouridine synthase C [Salmonella
           enterica subsp. enterica serovar Paratyphi C strain
           RKS4594]
 gi|322714174|gb|EFZ05745.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 319

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 105/328 (32%), Positives = 172/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +         +L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGDVMRIEAPMDNALKRCLQVLR 316


>gi|77460386|ref|YP_349893.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens Pf0-1]
 gi|77384389|gb|ABA75902.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens Pf0-1]
          Length = 320

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 101/319 (31%), Positives = 170/319 (53%), Gaps = 12/319 (3%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ + V  +    R+D +       +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 9   PGVQLLEVSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRVPP-----VRVPERDEPVPLAQGLLQR---LEASIVYEDKALIVINKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + Y +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y 
Sbjct: 121 LNYGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G      + +   L K +   G+ +  V+ +E+    +++ FKV+  F      +E
Sbjct: 180 ALVRGNWATSIKQVRAALGKSNLRSGERM--VEVDEEEGKESVTVFKVLRRFGDFATLIE 237

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY  + F          +L+LHA  + +P P+GG
Sbjct: 238 AKPITGRTHQIRVHTLHAGHCIAGDTKYGDDNFSKEIRDLGGKRLFLHAYMLTVPLPDGG 297

Query: 304 RLQITAPLPAHMVKTWDSL 322
            L++ AP+     KT + L
Sbjct: 298 ELKLQAPVDEMWAKTVERL 316


>gi|315027878|gb|EFT39810.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2137]
          Length = 310

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 88/329 (26%), Positives = 153/329 (46%), Gaps = 39/329 (11%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  
Sbjct: 8   AKMEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDE 67

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +          I E ++LD        ++ +   ++YED+ + V NKP G+ V    G
Sbjct: 68  IVVT---------IPEPEVLD------MVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSVG 112

Query: 125 IAYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
              H +G L + +               P + HR+D++TSG+L+VA+   A + L +  +
Sbjct: 113 ---HPNGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLK 169

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +   + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ 
Sbjct: 170 EKTSLRKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLER 224

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F   F  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +
Sbjct: 225 F-DAFTLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLL 278

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              HP  G  L   APLP    KT   L 
Sbjct: 279 GFTHPTTGEQLVFEAPLPEVFEKTLHQLR 307


>gi|319763720|ref|YP_004127657.1| pseudouridine synthase, rlua family [Alicycliphilus denitrificans
           BC]
 gi|317118281|gb|ADV00770.1| pseudouridine synthase, RluA family [Alicycliphilus denitrificans
           BC]
          Length = 332

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 82/331 (24%), Positives = 143/331 (43%), Gaps = 31/331 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
             ++ V+V   +   RLD+      P  +   LQ++L  G VR++ +   K  +++++G 
Sbjct: 25  AELREVMVPAAQHQARLDKALAELVPEFSRSYLQQLLAQGDVRLNGQPAAKPAHKVRAGD 84

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +       +   K               + L   +++ED  + V +KPAG+ V    
Sbjct: 85  QVAVRMRPTQQSQAFK--------------PESLPLDVVHEDEHLLVIDKPAGLVVHPAP 130

Query: 124 GIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +  G L + +  +        +  + HRLD++TSG++VVAR RAA   L      R
Sbjct: 131 G---NWSGTLLNALLGRDAQAMQVPRAGIVHRLDKDTSGLMVVARNRAAMDALVRMIAAR 187

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L WG     ++      + +       + VV   +     A + F ++    
Sbjct: 188 EVSRQYLALAWGAWSGSEQRRIRAPIGRDPRNRLRMAVVDLGQHAGKEACTDFDLLAS-G 246

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++ C +    HTGRTHQ+RVH   +  P+V D  Y     G        +  LHA  +  
Sbjct: 247 EEVCLVRCTLHTGRTHQIRVHMASIRHPLVADALYGGAVGGPM-----RRQALHAFRLAF 301

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            HP  G+ ++  APLP  M +  D  G +Y+
Sbjct: 302 THPVTGKPMEFHAPLPEDMRQALDFWGLRYN 332


>gi|62127337|gb|AAX65040.1| 23S rRNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
          Length = 347

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 105/328 (32%), Positives = 172/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 29  MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 88

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 89  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 141

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 142 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 200

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 201 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 256

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  + G PI  D +Y     + +         +L+LHA  + 
Sbjct: 257 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALK 316

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 317 FTHPGTGDVMRIEAPMDNALKRCLQVLR 344


>gi|260887804|ref|ZP_05899067.1| ribosomal large subunit pseudouridine synthase D [Selenomonas
           sputigena ATCC 35185]
 gi|330838700|ref|YP_004413280.1| pseudouridine synthase, RluA family [Selenomonas sputigena ATCC
           35185]
 gi|260862480|gb|EEX76980.1| ribosomal large subunit pseudouridine synthase D [Selenomonas
           sputigena ATCC 35185]
 gi|329746464|gb|AEB99820.1| pseudouridine synthase, RluA family [Selenomonas sputigena ATCC
           35185]
          Length = 301

 Score =  274 bits (701), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 82/323 (25%), Positives = 139/323 (43%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + ++V+      RLDR+       ++  ++QK++ SG V V+ +  K N +++ G  V  
Sbjct: 3   ERLIVDEGAAGERLDRFLAGRELEVSRSHIQKLIESGCVLVNGRTAKANAKLREGDAV-- 60

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                        +  L  +  L    + +   +LYEDS + V NK  G+ V   +G   
Sbjct: 61  -------------ETELPEARELEILPEDIPLDILYEDSDVIVINKARGMVVHPAAGAAD 107

Query: 126 AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HRLD++TSG++V A+   A   L E  R +  Q+
Sbjct: 108 GTLVNALLHHCEDLSGINGVIRPGIVHRLDKDTSGVMVAAKNDRAHVDLAEQIREKTAQR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY ++V G     +  I   + +          V      G   A + F+V++ F     
Sbjct: 168 IYRAIVCGTIAEDRGEIRAPIGRHPTERKKMAVV-----PGGKEATTLFRVVERFP-AHT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E +  TGRTHQ+RVH  ++  P++GD KY         +P      LH+  +   HP 
Sbjct: 222 LVECRLKTGRTHQIRVHMAYIDHPLLGDPKYGRK------TPDIAGQALHSCELSFAHPR 275

Query: 302 G-GRLQITAPLPAHMVKTWDSLG 323
              R+   A +P  M     +L 
Sbjct: 276 TKERMTFAAEMPEDMKAILHALR 298


>gi|317047700|ref|YP_004115348.1| RluA family pseudouridine synthase [Pantoea sp. At-9b]
 gi|316949317|gb|ADU68792.1| pseudouridine synthase, RluA family [Pantoea sp. At-9b]
          Length = 318

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 105/321 (32%), Positives = 167/321 (52%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ+V +  +    R+D + +     +    + +ILR G+VRV+KKR+K   +++ G  
Sbjct: 6   PGVQFVAITAENAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEEGDE 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RIPPV       + E++    S  L K +  L   +LYED  + V NKP+G +V GGSG
Sbjct: 66  IRIPPVR------VAEREEQAVSPKLEKVA-SLADAILYEDDYLLVLNKPSGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y 
Sbjct: 119 LSFGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   +  + +   LLK     G+ V  V         + + FKV + F      ++
Sbjct: 178 ALVRGDWPSHLKVVQAPLLKNILQSGERVVRV---SAEGKPSETRFKVEERFG-FATLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D +Y    F+    +   ++L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHTLHAGHPIAFDDRYGDREFERQLAATGLSRLFLHAAALTFTHPNTG 293

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L++ APL   +      L 
Sbjct: 294 ETLRMEAPLDGALKHCLTQLR 314


>gi|86147922|ref|ZP_01066226.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio sp. MED222]
 gi|85834247|gb|EAQ52401.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio sp. MED222]
          Length = 314

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 109/326 (33%), Positives = 179/326 (54%), Gaps = 17/326 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V ++ D    R+D + +N   +I    + +I+R G+VRV+KKR+K   ++
Sbjct: 1   MSEIRTQVQFVDIDEDMAGQRIDNFLRNQLKNIPKSMIYRIVRKGEVRVNKKRIKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VRIPP       I ++ +    S  L K S+ L+  ++YED  + + NKP+G +V
Sbjct: 61  KAGDLVRIPP-----VTIEEKTEENVPSTKLNKVSE-LEQCIIYEDDHMLILNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +    +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y++LV G  KN  + +   LLK        V+ + +       + + FKV++ F Q+
Sbjct: 174 QKYYFALVMGEWKNSCKVVNAPLLKNE------VNSIVRVNPNGKASETRFKVLEKF-QE 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVHA + G PI  D +Y       +T     N+L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHAQYTGHPIAWDDRYGDRRFDAYTGKVGLNRLFLHAANIKFI 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP     + I+AP+   + K    L 
Sbjct: 287 HPGSEEKIDISAPMERRLEKALTGLR 312


>gi|291087665|ref|ZP_06572048.1| ribosomal large subunit pseudouridine synthase D [Clostridium sp.
           M62/1]
 gi|291074400|gb|EFE11764.1| ribosomal large subunit pseudouridine synthase D [Clostridium sp.
           M62/1]
          Length = 300

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 153/320 (47%), Gaps = 32/320 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  + + +R+D++       ++   LQK+L+S  V VDK+ VK + ++ +G+ +      
Sbjct: 2   VPAEAQGVRIDKFLSEACDGLSRSYLQKLLKSELVEVDKRTVKNSYKLSAGEKIEFE--- 58

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                       +  +      ++ +   ++YEDS I + NKP G+ V   +G      +
Sbjct: 59  ------------VPEAAEPEIKAEDIPLDIIYEDSDIILVNKPKGMVVHPAAGHYSQTLV 106

Query: 130 DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +G +    D         +P + HR+D +T+G+L+V +   A   + E  ++  I + Y+
Sbjct: 107 NGLMYHCRDGLSGINGVLRPGIVHRIDMDTTGVLIVCKNDFAHNAIAEQLKVHSITRKYF 166

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G+ +  +  +   + +   +    + +   N K    A++H++V++ F ++F ++E
Sbjct: 167 AIVHGVIQEDEGTVDAPIGRH-PVDRKKMSI---NRKNGKEAVTHYRVLERF-RQFTYVE 221

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
            Q  TGRTHQ+RVH   +G P++GD  Y  +              LHA  + + HP  G 
Sbjct: 222 CQLETGRTHQIRVHMASIGHPLLGDSVYGPSK----IPFKLQGQTLHAGVLGIVHPRTGN 277

Query: 304 RLQITAPLPAHMVKTWDSLG 323
            ++ +APLP +  +  D L 
Sbjct: 278 YMEFSAPLPEYFSELLDKLR 297


>gi|110803816|ref|YP_699133.1| pseudouridine synthase [Clostridium perfringens SM101]
 gi|110684317|gb|ABG87687.1| pseudouridine synthase, RluA family [Clostridium perfringens SM101]
          Length = 306

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 146/330 (44%), Gaps = 33/330 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSL   V  + +  +E+ +R D++       ++   +Q +   G++ ++ K  K   ++ 
Sbjct: 1   MSLSKEV--IKITEEEKGIRADKFLALKIDGVSRNFIQGLFDDGKILINGKAEKGKYKLS 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G                  +  +     L   ++ +   ++YED  + V NKP G+ V 
Sbjct: 59  VGDC---------------VEVEIPEPEELKVEAEDIPLNIIYEDEDVIVVNKPKGMVVH 103

Query: 121 GGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++  L    D  G     +P + HR+D++TSGILVVA+   A Q L E F
Sbjct: 104 PAPGNYTGTLVNALLYHCDDLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQF 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +   I++ Y+++V G  K +   I   L +       Y  V     K    A++H++V+ 
Sbjct: 164 KDHSIKREYYAIVEGRFKKEGGTIDAPLGRHHRDRLKYAVV-----KDGKRAVTHYEVLK 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F      ++    TGRTHQ+RVH   +G P++GD  Y    +   +   Q    LHA+ 
Sbjct: 219 VF-NSCSLVKCTLETGRTHQIRVHMAFIGHPLLGDTVYGLKKQKKLS---QEGQVLHAKT 274

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +   HP  G+ ++  + LP +  K  + LG
Sbjct: 275 LGFIHPTTGKYVEFDSELPEYFEKIVEKLG 304


>gi|148549014|ref|YP_001269116.1| RluA family pseudouridine synthase [Pseudomonas putida F1]
 gi|148513072|gb|ABQ79932.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           putida F1]
          Length = 333

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 105/319 (32%), Positives = 170/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + VQ + V  +    R+D +       +    + +ILR G+VRV+K RVK   +IQ+G +
Sbjct: 24  SGVQLIEVAPELAGQRIDNFLITALKGVPKTLVYRILRKGEVRVNKGRVKPEYKIQAGDI 83

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP       + +  +    +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 84  VRVPP-----VRLPERDEPAPVAQGLLQR---LEAAIVYEDKALIVMNKPAGIAVHGGSG 135

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L+  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y 
Sbjct: 136 LSFGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYM 194

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     K+ +   LLK +   G+ +  V         A++ F+V+  F      +E
Sbjct: 195 ALVRGHWPTSKKQVNAPLLKSNLRSGERMVEVNDE---GKEALTLFRVLRRFGDFATIVE 251

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   +F          +L+LHA  + +P P+GG
Sbjct: 252 ARPITGRTHQIRVHTLHAGHMIAGDSKYGDEDFSREIRELGGKRLFLHAYALTVPLPDGG 311

Query: 304 RLQITAPLPAHMVKTWDSL 322
            L++ AP+     KT D L
Sbjct: 312 ELKLEAPVDEVWAKTVDRL 330


>gi|194472684|ref|ZP_03078668.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194459048|gb|EDX47887.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
          Length = 319

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 104/328 (31%), Positives = 171/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P TGRTHQ+RVH  +   PI  D +Y     + +         +L+LHA  + 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYASHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDNALKRCLQVLR 316


>gi|237748406|ref|ZP_04578886.1| ribosomal large subunit pseudouridine synthase C [Oxalobacter
           formigenes OXCC13]
 gi|229379768|gb|EEO29859.1| ribosomal large subunit pseudouridine synthase C [Oxalobacter
           formigenes OXCC13]
          Length = 339

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 114/337 (33%), Positives = 168/337 (49%), Gaps = 26/337 (7%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           +S    V+ V V  +++  R+D +       +   ++ +ILRSG+VRV+KKR+    R+Q
Sbjct: 22  ISSFQQVRQVTVTENDDGQRIDNFLFRTCKGVPKSHIYRILRSGEVRVNKKRIDQTYRLQ 81

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  +RIPP+  A                  KH       +LYED  I V NKPAG++V 
Sbjct: 82  EGDTIRIPPIKVAERE--------------EKHVPGASFDILYEDDSILVINKPAGVAVH 127

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG++Y +   L++      +   L HRLD+ETSGILV+A+ R+A   L E  R   I 
Sbjct: 128 GGSGVSYGVIEQLRAAR-PNARFLELVHRLDKETSGILVLAKKRSALVKLHEQIREGSID 186

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  KN+++ +   LLK     G+    V   + G   + + F V+  F + F
Sbjct: 187 KRYQALVKGDWKNQRQHVKLPLLKYHTADGERRVRV---DAGGLASHTIFNVLKRFPE-F 242

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQNKLYLHARY 294
             LE +  TGRTHQ+RVH    G  I GD KY          KG        +++LHA  
Sbjct: 243 TLLEAELKTGRTHQIRVHLASSGHVIAGDDKYGDFELNREIQKGKKGEDALKRMFLHAYK 302

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           +   HPE G+ L ++APLP         L  + D+++
Sbjct: 303 ITFIHPETGKPLTVSAPLPDECSGYLKGLDAENDKDV 339


>gi|90579091|ref|ZP_01234901.1| putative 23S rRNA ribosomal pseudouridinesynthase [Vibrio angustum
           S14]
 gi|90439924|gb|EAS65105.1| putative 23S rRNA ribosomal pseudouridinesynthase [Vibrio angustum
           S14]
          Length = 314

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 99/321 (30%), Positives = 170/321 (52%), Gaps = 16/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ++ + +D    R+D + +    ++    + +ILR G+VRV+KKR+K   ++Q G +
Sbjct: 6   PKVQFIEISDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDL 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PPV      + ++++    S  L K ++ L+  ++YED  + + NKP+G +V GGSG
Sbjct: 66  VRVPPVF-----VPEKEEQAPVSTKLNKVAE-LEHCIIYEDDHMLILNKPSGTAVHGGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + +QK Y+
Sbjct: 120 LKFGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRQLQEQFRNKTVQKYYF 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  K     +   LLK        V+ + +       + + FKV++ F Q    ++
Sbjct: 179 ALVMGEWKANCRKVTAPLLKNE------VNSIVRVNPQGKASDTRFKVLERFPQ-ATLVQ 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D +Y    F          +L+LHA  +   HP   
Sbjct: 232 ASPVTGRTHQIRVHCQYEGHPIAWDDRYGDPRFDAYTKKTGLGRLFLHAANIKFTHPSTD 291

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             + I+AP+   + +  + L 
Sbjct: 292 EGMDISAPMEPVLERCLEKLR 312


>gi|227518911|ref|ZP_03948960.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|229549858|ref|ZP_04438583.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|293383481|ref|ZP_06629394.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecalis R712]
 gi|293388864|ref|ZP_06633350.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecalis S613]
 gi|307269533|ref|ZP_07550872.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|307277912|ref|ZP_07558996.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
 gi|307289260|ref|ZP_07569216.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|312901873|ref|ZP_07761138.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
 gi|312907690|ref|ZP_07766681.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|312910308|ref|ZP_07769155.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
 gi|312951652|ref|ZP_07770547.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|227073600|gb|EEI11563.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|229305127|gb|EEN71123.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|291079272|gb|EFE16636.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecalis R712]
 gi|291081789|gb|EFE18752.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecalis S613]
 gi|306499969|gb|EFM69330.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|306505309|gb|EFM74495.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
 gi|306514153|gb|EFM82729.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|310626718|gb|EFQ10001.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|310630369|gb|EFQ13652.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|311289581|gb|EFQ68137.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
 gi|311291066|gb|EFQ69622.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
 gi|315152327|gb|EFT96343.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0031]
 gi|315156128|gb|EFU00145.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0043]
 gi|315158230|gb|EFU02247.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0312]
 gi|315162361|gb|EFU06378.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0645]
 gi|315163874|gb|EFU07891.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1302]
 gi|315169613|gb|EFU13630.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1342]
 gi|315172438|gb|EFU16455.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1346]
 gi|315576067|gb|EFU88258.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309B]
 gi|315580642|gb|EFU92833.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309A]
 gi|327535286|gb|AEA94120.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           faecalis OG1RF]
 gi|329571882|gb|EGG53560.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1467]
          Length = 310

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 86/326 (26%), Positives = 152/326 (46%), Gaps = 33/326 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  
Sbjct: 8   AKMEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDE 67

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +          I E ++LD        ++ +   ++YED+ + V NKP G+ V   +G
Sbjct: 68  IVVT---------IPEPEVLD------MVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAG 112

Query: 125 I--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 ++  L             +P + HR+D++TSG+L+VA+   A + L +  + + 
Sbjct: 113 HPKGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKT 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ F  
Sbjct: 173 SLRKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLERF-D 226

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   
Sbjct: 227 AFTLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLLGFT 281

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  L   APLP    KT   L 
Sbjct: 282 HPTTGEQLVFEAPLPEVFEKTLHQLR 307


>gi|50120723|ref|YP_049890.1| 23S rRNA pseudouridylate synthase C [Pectobacterium atrosepticum
           SCRI1043]
 gi|49611249|emb|CAG74695.1| ribosomal large subunit pseudouridine synthase C [Pectobacterium
           atrosepticum SCRI1043]
          Length = 318

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 105/319 (32%), Positives = 169/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V +  DE   R+D +   H   +    + +ILR G+VR++KKRVK   ++  G V+R
Sbjct: 8   VQFVTISADEAGQRIDNFLHTHLKGVPKSMVYRILRKGEVRINKKRVKPEYKLLDGDVIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A      E+     S +L K +  L   ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVRQA------ERDETPVSASLGKVA-ALAECIIYEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FK+ + F +    +   
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILQSGERIVRVNSE---GKASETRFKIEERF-EHATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA + G PI  D +Y    F          +L+LHA+ +   HP  G  
Sbjct: 236 PVTGRTHQIRVHAQYAGHPIAFDDRYGDREFDRQLAGSGLKRLFLHAQALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L++ APL   + +    L 
Sbjct: 296 LRVEAPLDNGLRRCLQVLR 314


>gi|332970080|gb|EGK09077.1| ribosomal large subunit pseudouridine synthase D [Kingella kingae
           ATCC 23330]
          Length = 371

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 84/326 (25%), Positives = 147/326 (45%), Gaps = 31/326 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V ND   MRLD       P  +   +   ++ G V+ + K      ++  G+ + +  
Sbjct: 30  LIVPNDLAGMRLDAALAKLLPDYSRSRITTWIKDGFVQCNGKTASPKEKLIGGEELSV-- 87

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                       +I  S  N     + +   +++ED  + V NKPAG+ V   +G     
Sbjct: 88  ------------QIQQSDENQAYEPEHMDLNIVFEDDTVIVLNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD++TSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKDTSGLMVVAKTLPAQNSLVQQLQNRTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ADGIVP-FDGKIETLIGRDPH-NRLKMAVVKF---GGKEAVTHVKVLERY-HAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------KLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y  N +   + P+++      +  LHA ++   HP
Sbjct: 250 LETGRTHQIRVHMKEARHPLAGDPVYG-NPRHVCSQPVKDVVKSLARQALHAYHLSFVHP 308

Query: 301 EGGRL-QITAPLPAHMVKTWDSLGFK 325
           + G L    AP+P  M      L  +
Sbjct: 309 KSGELVSFEAPMPDDMYHLLSVLRLE 334


>gi|294141325|ref|YP_003557303.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           violacea DSS12]
 gi|293327794|dbj|BAJ02525.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           violacea DSS12]
          Length = 319

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 105/319 (32%), Positives = 168/319 (52%), Gaps = 13/319 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            VQ + ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G +V
Sbjct: 9   KVQLITIDEDHLGQRIDNYLMTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQDGDIV 68

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP       I         S  LTK S  L+  +++ED  I V NKP+GI+V GGSG+
Sbjct: 69  RIPP-----VRISDRSDRPGPSAKLTKVSQ-LEDRIVFEDKSIIVLNKPSGIAVHGGSGV 122

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + +   ++S   ++     L HRLD++TSG+L++A+ R+A +HL +  R +++QK Y +
Sbjct: 123 DFGVIEAMRSLRPTQKF-LELVHRLDKDTSGVLLIAKKRSALRHLHDQLRFKKMQKDYQA 181

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  + + + I   LLK +   G+ +  V Q         + FK++  + Q    ++ 
Sbjct: 182 LVKGTWQARDKVIKAPLLKLTLKSGERIVRVNQE---GKECETRFKILQRY-QGATLVQA 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQ+RVH  + G PI  D KY    F  +      N+L+LHA  +   HP    
Sbjct: 238 SPVTGRTHQIRVHCQYAGHPIACDDKYSEQRFDDSMRVHGLNRLFLHAAQLRFIHPGTEE 297

Query: 305 -LQITAPLPAHMVKTWDSL 322
            + + APL   + +T D L
Sbjct: 298 VMVVQAPLDPVLTETLDKL 316


>gi|188590369|ref|YP_001921578.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum E3 str. Alaska E43]
 gi|188500650|gb|ACD53786.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum E3 str. Alaska E43]
          Length = 302

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 133/319 (41%), Gaps = 31/319 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  + E +R+D++        +   +Q ++    ++V+ K +K N ++++   + I    
Sbjct: 8   VSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNNKLIKSNYKLKACDEIVIT--- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                       +  +  L   S+ +   +LYED  + V NK  G+ V    G      +
Sbjct: 65  ------------MPEAEILKVESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLV 112

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D        +P + HR+D++TSG+LV+A+   +   L    +   + + Y++
Sbjct: 113 NALLFHCTDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  KN    I   L +                +    AI+H++V++ +      ++ 
Sbjct: 173 LVEGRFKNDSGVIDKPLGRDKKNRLKIAI-----TEDGRRAITHYEVLERYDTGCTLIKC 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +  TGRTHQ+RVH   +G P+VGD  Y    +            LHA+ +   HP     
Sbjct: 228 KLETGRTHQIRVHMASLGHPLVGDPLYGFKKQ----RFKLKGQMLHAKKLGFIHPTKNEY 283

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++    LP +  +  + L 
Sbjct: 284 MEFETNLPEYFEEIIEKLR 302


>gi|18310832|ref|NP_562766.1| hypothetical protein CPE1850 [Clostridium perfringens str. 13]
 gi|110801362|ref|YP_696533.1| RluA family pseudouridine synthase [Clostridium perfringens ATCC
           13124]
 gi|168206096|ref|ZP_02632101.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
 gi|168210787|ref|ZP_02636412.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
 gi|18145514|dbj|BAB81556.1| conserved hypothetical protein [Clostridium perfringens str. 13]
 gi|110676009|gb|ABG84996.1| pseudouridine synthase, RluA family [Clostridium perfringens ATCC
           13124]
 gi|170662443|gb|EDT15126.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
 gi|170711120|gb|EDT23302.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
          Length = 306

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 145/330 (43%), Gaps = 33/330 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSL   V  + +  +E+ +R D++       ++   +Q +   G++ ++ K  K   ++ 
Sbjct: 1   MSLSKEV--IKITEEEKGIRADKFLALKIDGVSRNFIQGLFDDGKILINGKAEKGKYKLS 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G                  +  +     L   ++ +   ++YED  + V NKP G+ V 
Sbjct: 59  VGDC---------------VEVEIPEPEELKVEAEDIPLNIVYEDEDVIVVNKPKGMVVH 103

Query: 121 GGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++  L    D  G     +P + HR+D++TSGILVVA+   A Q L E F
Sbjct: 104 PAPGNYTGTLVNALLHHCDDLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQF 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +   I++ Y+++V G  K +   I   L +       Y  V     K    A++H++V+ 
Sbjct: 164 KDHSIKREYYAIVEGRFKKEGGTIDAPLGRHHRDRLKYAVV-----KDGKRAVTHYEVLK 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F      ++    TGRTHQ+RVH   +G P++GD  Y    +   +   Q    LHA+ 
Sbjct: 219 VF-NSCSLVKCTLETGRTHQIRVHMAFIGHPLLGDTVYGLKKQKKLS---QEGQVLHAKT 274

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +   HP  G  ++  + LP +  K  + LG
Sbjct: 275 LGFIHPTTGEYVEFDSELPEYFEKIVEKLG 304


>gi|169343529|ref|ZP_02864528.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
 gi|169298089|gb|EDS80179.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
          Length = 306

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 145/330 (43%), Gaps = 33/330 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSL   V  + +  +E+ +R D++       ++   +Q +   G++ ++ K  K   ++ 
Sbjct: 1   MSLSKEV--IKITEEEKGIRADKFLALKIDGVSRNFIQGLFDDGKILINGKAEKGKYKLS 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G                  +  +     L   ++ +   ++YED  + V NKP G+ V 
Sbjct: 59  VGDC---------------VEVEIPEPEELKVEAEDIPLNIVYEDEDVIVVNKPKGMVVH 103

Query: 121 GGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++  L    D  G     +P + HR+D++TSGILVVA+   A Q L E F
Sbjct: 104 PAPGNYTGTLVNALLHHCDDLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQF 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +   I++ Y+++V G  K +   I   L +       Y  V     K    A++H++V+ 
Sbjct: 164 KDHSIKREYYAIVEGRFKKEGGTIDAPLGRHHRDRLKYAVV-----KDGKRAVTHYEVLK 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F      ++    TGRTHQ+RVH   +G P++GD  Y    +   +   Q    LHA+ 
Sbjct: 219 VF-NSCSLVKCNLETGRTHQIRVHMAFIGHPLLGDTVYGLKKQKKLS---QEGQVLHAKT 274

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +   HP  G  ++  + LP +  K  + LG
Sbjct: 275 LGFIHPTTGEYVEFDSELPEYFEKIVEKLG 304


>gi|260549179|ref|ZP_05823400.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter sp.
           RUH2624]
 gi|260407907|gb|EEX01379.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter sp.
           RUH2624]
          Length = 310

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 96/317 (30%), Positives = 162/317 (51%), Gaps = 19/317 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   ++  G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLAIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   +       +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAVPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y ++
Sbjct: 123 YGLIEALRAATGKKY--LELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     K+ I   L +     G+    V    K    + + + V + F +    +   
Sbjct: 181 VKGQVSLDKQLIDAPLFRYELANGERRVRV---SKEGKPSKTEWVVAERF-KNATLVHAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P++GD KY  N    +  P   +L LHA  +D+P    G   
Sbjct: 237 PLSGRTHQIRVHGLSIGHPLLGDDKYGHN--TAYAGPEARRLCLHAMRLDIP----GYPT 290

Query: 307 ITAPLPAHMVKTWDSLG 323
           I APLP  M++  ++L 
Sbjct: 291 IEAPLPEDMIQLLEALR 307


>gi|197301721|ref|ZP_03166791.1| hypothetical protein RUMLAC_00447 [Ruminococcus lactaris ATCC
           29176]
 gi|197299161|gb|EDY33691.1| hypothetical protein RUMLAC_00447 [Ruminococcus lactaris ATCC
           29176]
          Length = 304

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 75/331 (22%), Positives = 142/331 (42%), Gaps = 38/331 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  M+ +      + ++  R+D++   +   ++   +QK+L+ G + V+ K+VK N ++ 
Sbjct: 1   MEQMSLI------SKKKGERIDKFLGENLDDLSRSYIQKLLKDGLILVNGKKVKANYKLN 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +                +     L   ++ +   +LYED  I + NKP G+ V 
Sbjct: 55  EGDQIDVE---------------VPDPEPLDIAAENIPLDILYEDEDILIVNKPKGMVVH 99

Query: 121 GGSGIAYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              G   H   +  L    +         +P + HR+D  T+G L++ +   A Q L E 
Sbjct: 100 PSPGHPDHTLVNAILYHCGEHLSGINGVIRPGIVHRIDMNTTGSLLICKNDHAHQILAEQ 159

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            +   I + Y ++V G  K     +   + +           +        +A++H++V+
Sbjct: 160 LKEHSITRRYHAIVHGSLKADTGTVNASIGRHPTDRKK----MSTKALNGRHAVTHYRVL 215

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           +     + ++E +  TGRTHQ+RVH   +G PI+GD  Y                 LHA+
Sbjct: 216 ERLG-NYTYIECELETGRTHQIRVHMASIGHPILGDDVYGP----AKCPFHLEGQTLHAK 270

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            + + HP  G  ++  APLP + +K   +L 
Sbjct: 271 ILGITHPATGEYMEFDAPLPEYFMKLLSTLR 301


>gi|182625703|ref|ZP_02953472.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
 gi|177909105|gb|EDT71580.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
          Length = 306

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 145/330 (43%), Gaps = 33/330 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSL   V  + +  +E+ +R D++       ++   +Q +   G++ ++ K  K   ++ 
Sbjct: 1   MSLSKEV--IKITEEEKGIRADKFLALKIDGVSRNFIQGLFDDGKILINGKAEKGKYKLS 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G                  +  +     L   ++ +   ++YED  + V NKP G+ V 
Sbjct: 59  VGDC---------------VEVEIPEPEELKVEAEDIPLNIVYEDEDVIVVNKPKGMVVH 103

Query: 121 GGSG--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++  L    D  G     +P + HR+D++TSGILVVA+   A Q L E F
Sbjct: 104 PAPGNYTGTLVNALLHHCDDLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQF 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +   I++ Y+++V G  K +   I   L +       Y  V     K    A++H++V+ 
Sbjct: 164 KDHSIKREYYAIVEGRFKKEGGTIDAPLGRHHRDRLKYAVV-----KDGKRAVTHYEVLK 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F      ++    TGRTHQ+RVH   +G P++GD  Y    +   +   Q    LHA+ 
Sbjct: 219 VF-NSCSLVKCTLETGRTHQIRVHMAFIGHPLLGDTVYGLKKQKKLS---QEGQVLHAKT 274

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +   HP  G  ++  + LP +  K  + LG
Sbjct: 275 LGFIHPTTGEYVEFDSELPEYFKKIVEKLG 304


>gi|88798806|ref|ZP_01114389.1| ribosomal large subunit pseudouridine synthase C [Reinekea sp.
           MED297]
 gi|88778569|gb|EAR09761.1| ribosomal large subunit pseudouridine synthase C [Reinekea sp.
           MED297]
          Length = 313

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 103/313 (32%), Positives = 167/313 (53%), Gaps = 14/313 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  VQ++ V  D    RLD + + +  ++    + +I+R G+VRV+KKR K + ++  G 
Sbjct: 1   MAKVQFIEVSADRAEQRLDNFLRYYLNNVPKSRIYRIIRKGEVRVNKKRAKPDTKLSEGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PPV  A       +K +++          L   +++EDS +   NKP+G++V GGS
Sbjct: 61  VVRVPPVTMA-------EKTIENPQPSAGLRKALDHAIVFEDSALLAVNKPSGLAVHGGS 113

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKI 182
           G+   +   L++  +S+     L HRLD++TSG+++VA+ R +   L + FR +  ++K 
Sbjct: 114 GLKLGLIEALRAQRESE-PFLELVHRLDRDTSGVVLVAKKRKSLTLLQDEFRQKTRVRKT 172

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW LV G   +    +   LL+          V  Q       + +HF+V+  + Q   W
Sbjct: 173 YWCLVKGHWPDGCSVVDAPLLRHEESASGERRVSVQ--ANGKPSRTHFRVLKQY-QDCAW 229

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-QNKLYLHARYMDLPHPE 301
           +E  P TGRTHQ+RVH  ++GCPI+GD KY  +   +  S +  N+L+LHA  + LPHPE
Sbjct: 230 VEALPITGRTHQIRVHCQYVGCPILGDDKYQDSEAESLASKLGLNRLFLHAAQLTLPHPE 289

Query: 302 G-GRLQITAPLPA 313
               +   A L  
Sbjct: 290 TREEMTFVADLDE 302


>gi|89098727|ref|ZP_01171609.1| ribosomal large subunit pseudouridine synthase D [Bacillus sp. NRRL
           B-14911]
 gi|89086689|gb|EAR65808.1| ribosomal large subunit pseudouridine synthase D [Bacillus sp. NRRL
           B-14911]
          Length = 301

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 143/327 (43%), Gaps = 34/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++Y+ +  +    RLD+        ++    Q++++ G + V+ +  K N +     
Sbjct: 1   MEKMEYI-INEEVAGERLDKAVSLLNEELSRSQAQQMIKDGHILVNGQGTKTNYKCSIDD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I         ++ E+               +   + YED  + V NKP G+ V    
Sbjct: 60  KIEISFPEPEELDVLPEE---------------MDLDIYYEDGDVLVVNKPKGMVVHPAP 104

Query: 124 GIA--YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G A    ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHASGTLVNGLMAHCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G   +    +   L +      D   +   +  G  +A++HF VI  + 
Sbjct: 165 TVTRKYQAIVHGTIPHDYGTVDAPLGRDPK---DRQSMTVVD--GGKHAVTHFHVIHRY- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E Q  TGRTHQ+RVH  ++G P+ GD KY         +       LHA  +  
Sbjct: 219 KDFTHVECQLETGRTHQIRVHMKYIGYPLAGDPKYGPR-----KTLEIGGQALHAGVLGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  APLPA+  +  + LG
Sbjct: 274 VHPRTGEYMEFEAPLPAYFSELLEKLG 300


>gi|188534161|ref|YP_001907958.1| 23S rRNA pseudouridylate synthase C [Erwinia tasmaniensis Et1/99]
 gi|188029203|emb|CAO97075.1| 23S rRNA pseudouridylate synthase [Erwinia tasmaniensis Et1/99]
          Length = 320

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 103/314 (32%), Positives = 170/314 (54%), Gaps = 14/314 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++++G  +R
Sbjct: 8   VHFIAISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E++  + S  L K +  L++ ++YED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVR------VAEREDDNVSPKLAKVA-ALEAAIIYEDDYLLVMNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +    +   L HRLD++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPDARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   LLK     G+ V  V         + + FKV + +A     ++  
Sbjct: 180 VRGQWPSHVKAVRAPLLKNILQSGERVVKVSSE---GKPSETLFKVEERYA-IATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y  A F    +     +L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHTLHAGHPIAFDDRYGEAEFDQQLSGTGLKRLFLHAAALRFTHPNTGEV 295

Query: 305 LQITAPLPAHMVKT 318
           +++ APL   + + 
Sbjct: 296 MRVEAPLDEQLKRC 309


>gi|329922661|ref|ZP_08278213.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
 gi|328942003|gb|EGG38286.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
          Length = 322

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 77/329 (23%), Positives = 143/329 (43%), Gaps = 33/329 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           T      VE D    R+D++   +    ++   +Q  +  G V V+   +K N ++  G 
Sbjct: 19  TEASEWTVEADAAKTRIDKYITENLGEDVSRSQVQLWIADGHVSVNDGPIKSNYKVSQGD 78

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +     +   II E   L+               + +ED  + V NKP G+ V    
Sbjct: 79  RIVLKVPEPSAVEIIPEDIPLE---------------IAFEDGDVIVVNKPRGMVVHPAP 123

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  +    D  G     +P + HR+D++T+G+++ A+   A   L    +  
Sbjct: 124 GHSSGTLVNALMFHCKDLSGINGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKEH 183

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G   + +  I   + + +     Y       ++ + +A++HF V++ F 
Sbjct: 184 SVNRRYLALVHGNISHDQGTIDAPIGRDAQDRKLY----TVTDRNSKHAVTHFTVVERFG 239

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  LE++  TGRTHQ+RVH  ++G P+VGD  Y  +          N   LHA  +  
Sbjct: 240 D-YSLLELKLETGRTHQIRVHMKYIGHPLVGDPVYGKSKGIKL-----NGQALHAAVLGF 293

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  ++ +AP+P+ M +    L  +
Sbjct: 294 VHPSTGEYMEFSAPMPSDMNELLTILRGR 322


>gi|187932847|ref|YP_001886621.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum B str. Eklund 17B]
 gi|187721000|gb|ACD22221.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum B str. Eklund 17B]
          Length = 302

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 133/319 (41%), Gaps = 31/319 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  + E +R+D++        +   +Q ++    ++V+ K +K N ++++   + I    
Sbjct: 8   VSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNDKLIKNNYKLKACDEIVIT--- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                       +  +  L   S+ +   +LYED  + V NK  G+ V    G      +
Sbjct: 65  ------------MPEAETLKVESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLV 112

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D        +P + HR+D++TSG+LV+A+   +   L    +   + + Y++
Sbjct: 113 NALLFHCTDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  KN    I   L +                +    AI+H++V++ +      ++ 
Sbjct: 173 LVEGRFKNDSGIIDKPLGRDKKNRLKIAI-----TEDGRRAITHYEVLERYDTGCTLIKC 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +  TGRTHQ+RVH   +G P+VGD  Y    +            LHA+ +   HP     
Sbjct: 228 KLETGRTHQIRVHMASLGHPLVGDPLYGFKKQ----KFKLKGQMLHAKKLGFIHPTKNEY 283

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++    LP +  +  + L 
Sbjct: 284 MEFETNLPEYFEEIIEKLR 302


>gi|325860234|ref|ZP_08173359.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
 gi|325482321|gb|EGC85329.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
          Length = 361

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 147/330 (44%), Gaps = 36/330 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  +E +R+D++      H +   +QK   +G + V+   VK + +++   V+ +    
Sbjct: 35  VDKGQEPVRIDKFLYERMQHSSRNRIQKAADAGFIHVNGAAVKSSYKVRPEDVITLMLDR 94

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              ++ I+              ++ +   ++YED  + V NKPAG+ V  G+G  +    
Sbjct: 95  PKHDNTIE--------------AEDIPLDIVYEDDVLMVINKPAGLVVHPGAGNFHGTLI 140

Query: 132 FLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              +W        D    +  L HR+D++TSG+LVVA+T  A   L   F  +   + Y 
Sbjct: 141 NAVAWHLKDMPAFDPNDPEVGLVHRIDKDTSGLLVVAKTPDAKTDLGRQFFNKTTHRSYN 200

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG    ++  I   + +        + V     +    A++H++VI+ F      +E
Sbjct: 201 ALVWGNFTEEEGRIEGNIARDPR-DRLRMAVFPPGSETGKPAVTHYRVIERFG-YTTLIE 258

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ----------NKLYLHA 292
               TGRTHQ+R H  H+G P+ GD +Y      +G  +S  +          N+  LHA
Sbjct: 259 CVLETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSTYKAFIRNCLAICNRQALHA 318

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           R +   HP  GR +  T+ LP  +    + 
Sbjct: 319 RTLGFVHPVTGRQMDFTSGLPDDLAALIEK 348


>gi|312903470|ref|ZP_07762650.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
 gi|310633346|gb|EFQ16629.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
 gi|315577834|gb|EFU90025.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0630]
          Length = 310

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 86/326 (26%), Positives = 152/326 (46%), Gaps = 33/326 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  
Sbjct: 8   AKMEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDE 67

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +          I E ++LD        ++ +   ++YED+ + V NKP G+ V   +G
Sbjct: 68  IVVT---------IPEPEVLD------MIAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAG 112

Query: 125 I--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 ++  L             +P + HR+D++TSG+L+VA+   A + L +  + + 
Sbjct: 113 HPKGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKT 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ F  
Sbjct: 173 SLRKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLERF-D 226

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   
Sbjct: 227 AFTLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLLGFT 281

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  L   APLP    KT   L 
Sbjct: 282 HPTTGEQLVFEAPLPEVFEKTLHQLR 307


>gi|332306496|ref|YP_004434347.1| pseudouridine synthase, RluA family [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332173825|gb|AEE23079.1| pseudouridine synthase, RluA family [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 318

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 98/319 (30%), Positives = 166/319 (52%), Gaps = 15/319 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            VQ++ +E D E  R+D + +     +    + +I+R G++RV+KKRVK   ++Q+   +
Sbjct: 9   KVQFIEIEPDLEGQRIDNFLRTLLKGVPKSLIYRIVRKGEIRVNKKRVKPEYKLQAHDQL 68

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP+  +  +     K+             L+S +L+ED  + V NKP+G++V GGSG+
Sbjct: 69  RIPPIRVSEPNAAPSTKL--------DKVASLESHILFEDDLLIVLNKPSGMAVHGGSGL 120

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L++ +  + +   L HRLD++TSG LV+A+ R+A ++L E  R +++ K Y +
Sbjct: 121 SFGVIEALRA-LRPQARFLELVHRLDRDTSGCLVIAKKRSALKNLHEQLRDKKMDKRYHA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     +  +   LLK     G+ +  V   +     + + F+V++ +      +E 
Sbjct: 180 LVVGEWPENRYKVNAPLLKNILKSGERLVSV---DSEGKPSETRFRVLERYV-GATLVEA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
            P TGRTHQ+RVH LH   PI  D KY    F          +L+LHA  +   HP+   
Sbjct: 236 SPITGRTHQIRVHCLHAVHPIACDDKYGDGEFTELMNKKGLKRLFLHAYSLAFIHPKTEE 295

Query: 304 RLQITAPLPAHMVKTWDSL 322
           R+   APL   + K   +L
Sbjct: 296 RVSFQAPLDQQLNKALSAL 314


>gi|292669557|ref|ZP_06602983.1| ribosomal large subunit pseudouridine synthase D [Selenomonas noxia
           ATCC 43541]
 gi|292648766|gb|EFF66738.1| ribosomal large subunit pseudouridine synthase D [Selenomonas noxia
           ATCC 43541]
          Length = 302

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 83/318 (26%), Positives = 146/318 (45%), Gaps = 31/318 (9%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             D    RLD +     P ++    Q+++   +V VD    K N +++ G+ V       
Sbjct: 6   SADCAGERLDVFLVRKMPDLSRSYAQRLIEEKRVTVDGTPRKANYKLRGGECVACD---- 61

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHID 130
                      L     ++  ++ +   +LYED+ I V NKP G+ V   +GI     ++
Sbjct: 62  -----------LPPVEEVSVRAENIPLDILYEDADIIVVNKPRGMVVHPAAGISGGTLVN 110

Query: 131 GFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             L    D  G     +P + HRLD++TSG++  A+  AA + L E  + +  ++ Y ++
Sbjct: 111 ALLYHCRDLSGINGALRPGIVHRLDKDTSGVMAAAKNDAAHRSLAEQIQKKEARREYRAI 170

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G    +   I   + +        + +V++N     +A +HF+V++ F   + ++  +
Sbjct: 171 VYGNIAERAGIITGDIGRH-PTDRKRMAIVREN---GKHATTHFEVLERFG-GYTFVACR 225

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRL 305
             TGRTHQ+RVH   +G P+VGD KY +               LH+  + L HP  G  +
Sbjct: 226 LETGRTHQIRVHMTSIGHPLVGDAKYTSKKNP----FAIAGQALHSLTLTLAHPRSGEEM 281

Query: 306 QITAPLPAHMVKTWDSLG 323
             TAPLPA + +   +L 
Sbjct: 282 AFTAPLPADIEEILCALR 299


>gi|300726252|ref|ZP_07059705.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bryantii B14]
 gi|299776449|gb|EFI73006.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bryantii B14]
          Length = 352

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 82/332 (24%), Positives = 150/332 (45%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++     P+ +   +Q    +G ++V+   VK N +++   V+ +  
Sbjct: 22  VQVDEGQTPVRIDKYLAEKNPYQSRNRIQNAADAGFIQVNGTPVKSNYKVRPNDVITLM- 80

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L++   +  I+  ++ +          ++YED  + V NK AG+ V  G+G     
Sbjct: 81  ----LDYPKHDTSIVAENIPID---------VVYEDDDLMVINKAAGMVVHPGAGNFTGT 127

Query: 125 IAYHIDGFLKSW--VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   I  +L+     D+   +  L HR+D++TSG+LVVA+T  A   L + F  +   + 
Sbjct: 128 LINAIAYYLRDLESFDANNPEVGLVHRIDKDTSGLLVVAKTPEAKSALGKQFFNKTTHRS 187

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + +        + V + +      A++H++V++ F      
Sbjct: 188 YNALVWGNIVEDEGRIEGNIGRDPK-NRLRMKVFEPDSGIGKSAVTHYRVLERFG-YTTL 245

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKLYL 290
           +E    TGRTHQ+R H  H+G P+  D  Y  N   +G  +S           I  +  L
Sbjct: 246 IECILETGRTHQIRAHMKHIGHPLFADETYGGNEVLRGQRSSSYKAYIQNCFKICPRQAL 305

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA+ +   HP  G +L  T+  PA      + 
Sbjct: 306 HAKTLGFIHPRTGQQLDFTSEWPADFSALIEK 337


>gi|325686216|gb|EGD28262.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 304

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 149/325 (45%), Gaps = 33/325 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   +  +E   RLD++       ++   +++++++G+V V+ K+ K + ++Q G ++++
Sbjct: 3   REYELTAEESGQRLDKYLAGEMIDLSRSRIKELVQAGEVLVNGKKSKVSYKVQKGDLIQV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +      +  E   LD               ++YED  I V NKP G+ V    G   
Sbjct: 63  TVLPLEPLKLEAENIPLD---------------IVYEDEDIIVVNKPQGMVVHPAVGHPS 107

Query: 128 HI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H   +  L    D     +G +P + HR+D++TSG+L+VA+  AA + L +    +  ++
Sbjct: 108 HTLVNALLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G    ++  I   + +          V K        A++HFKV++ + Q + 
Sbjct: 168 QYLAIVHGNFAEEEGTIDAPIGRNPKDRKQMAVVEK-----GKSAVTHFKVLEQY-QGYS 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +    P 
Sbjct: 222 LVECQLETGRTHQIRVHMAYIGHPLAGDPLYGPR-----KTLPGHGQFLHAKTLGFEQPS 276

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            G  L+ +   P    +T   L  K
Sbjct: 277 TGEWLEFSVQPPEIFQQTVADLRKK 301


>gi|251778563|ref|ZP_04821483.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum E1 str. 'BoNT E Beluga']
 gi|243082878|gb|EES48768.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum E1 str. 'BoNT E Beluga']
          Length = 302

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 132/319 (41%), Gaps = 31/319 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  + E +R+D++        +   +Q ++    ++V+ K +K N ++++   + I    
Sbjct: 8   VSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNDKLIKSNYKLKACDEIVIT--- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                       +     L   S+ +   +LYED  + V NK  G+ V    G      +
Sbjct: 65  ------------MPEVETLKVESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLV 112

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D        +P + HR+D++TSG+LV+A+   +   L    +   + + Y++
Sbjct: 113 NALLFHCTDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  KN    I   L +                +    AI+H++V++ +      ++ 
Sbjct: 173 LVEGRFKNDSGVIDKPLGRDKKNRLKIAI-----TEDGRRAITHYEVLERYDTGCTLIKC 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +  TGRTHQ+RVH   +G P+VGD  Y    +            LHA+ +   HP     
Sbjct: 228 KLETGRTHQIRVHMASLGHPLVGDPLYGFKKQ----RFKLKGQMLHAKKLGFIHPTKNEY 283

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++    LP +  +  + L 
Sbjct: 284 MEFETNLPEYFEEIIEKLR 302


>gi|302874641|ref|YP_003843274.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
 gi|307690747|ref|ZP_07633193.1| pseudouridine synthase, RluA family protein [Clostridium
           cellulovorans 743B]
 gi|302577498|gb|ADL51510.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
          Length = 313

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 139/322 (43%), Gaps = 32/322 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++ N+  + R+D++        +   +Q I+    V V+ K  K N +++    + +
Sbjct: 3   EIIIIFNELSSKRIDKFLAEQLDGYSRSFIQNIIDGNNVLVNGKPCKSNLKLKMQDEITV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                          I+     +    + +   +LYED  + V NKP G+ V   SG+  
Sbjct: 63  ---------------IIPEPQEMNVVPENISLNILYEDEDLIVINKPQGMVVHPASGVYN 107

Query: 128 HI--DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           +   +  L    D  G     +P + HR+D++TSG++VVA+   +   L    +   +++
Sbjct: 108 NTLVNALLYHCKDLSGINGKLRPGIVHRIDKDTSGVIVVAKNDKSHNFLAAQLKEHSMKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV GI K ++  I   L +          V     KG   AI+H+KVI+ F +   
Sbjct: 168 EYIALVEGIIKEEEGTINQPLARDPKERIKIAVV-----KGGREAITHYKVIERFKEN-T 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +     TGRTHQ+RVH  +   P+VGD  Y    +        N   LHA+ +   HP 
Sbjct: 222 LVRCILETGRTHQIRVHMNYKKHPLVGDPVYGYKKQ----RFSLNGQLLHAQKLGFIHPT 277

Query: 302 G-GRLQITAPLPAHMVKTWDSL 322
               ++ +  +P   +K    L
Sbjct: 278 TMKYMEFSTNIPQEFLKVLKVL 299


>gi|323499352|ref|ZP_08104328.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           sinaloensis DSM 21326]
 gi|323315537|gb|EGA68572.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           sinaloensis DSM 21326]
          Length = 314

 Score =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 107/326 (32%), Positives = 182/326 (55%), Gaps = 17/326 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V +++D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++
Sbjct: 1   MSEIRTKVQFVDIDDDMAGQRIDNFLRNQLKSIPKSMVYRILRKGEVRVNKKRVKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G +VRIPP       I ++ + +  S  L K ++ L+ +++YED  + + NKP+G +V
Sbjct: 61  QAGDLVRIPP-----VTIEEKAEEVAPSTKLNKVAE-LEHMIIYEDEHMLILNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y++LV G  K+  + +   LLK        V+ + +       + + FK+I+ F++ 
Sbjct: 174 KKFYFALVMGQWKSSCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKIIEKFSE- 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKFQ 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP     ++I AP+ A + K    L 
Sbjct: 287 HPSNDEWMEINAPMEAKLEKALAGLR 312


>gi|327312694|ref|YP_004328131.1| RluA family pseudouridine synthase [Prevotella denticola F0289]
 gi|326946223|gb|AEA22108.1| pseudouridine synthase, RluA family [Prevotella denticola F0289]
          Length = 361

 Score =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 147/330 (44%), Gaps = 36/330 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  +E +R+D++      H +   +QK   +G + V+   VK + +++   V+ +    
Sbjct: 35  VDKGQEPVRIDKFLYERMQHSSRNRIQKAADAGFIHVNGTAVKSSYKVRPEDVITLMLDR 94

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              ++ I+              ++ +   ++YED  + V NKPAG+ V  G+G  +    
Sbjct: 95  PKHDNTIE--------------AEDIPLDIVYEDDVLMVINKPAGLVVHPGAGNFHGTLI 140

Query: 132 FLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              +W        D    +  L HR+D++TSG+LVVA+T  A   L   F  +   + Y 
Sbjct: 141 NAVAWHLKDMPAFDPNDPEVGLVHRIDKDTSGLLVVAKTPDAKTDLGRQFFNKTTHRSYN 200

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG    ++  I   + +        + V     +    A++H++VI+ F      +E
Sbjct: 201 ALVWGNFTEEEGRIEGNIARDPR-DRLRMAVFPPGSETGKPAVTHYRVIERFG-YTTLIE 258

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ----------NKLYLHA 292
               TGRTHQ+R H  H+G P+ GD +Y      +G  +S  +          N+  LHA
Sbjct: 259 CILETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSTYKAFIRNCLAICNRQALHA 318

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           R +   HP  GR +  T+ LP  +    + 
Sbjct: 319 RTLGFVHPVTGRQMDFTSGLPDDLAALIEK 348


>gi|257126163|ref|YP_003164277.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
 gi|257050102|gb|ACV39286.1| pseudouridine synthase, RluA family [Leptotrichia buccalis
           C-1013-b]
          Length = 326

 Score =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 150/327 (45%), Gaps = 33/327 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +VV  +E   R+D++       +    +Q++++   + V++K+ K   +I+    +++
Sbjct: 24  ENIVVLKEEAGSRIDKFLSERL-ELTRTRIQQLIKDENILVNEKKTKPAYKIEENDTIKV 82

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                          ++     +    + +   ++YED+ + V NK AGI V   +G   
Sbjct: 83  ---------------VIPELETVEIKPENIDIEIIYEDNDLAVINKKAGIVVHPANGHYS 127

Query: 126 AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HRLD++TSG+L++A+   A   L++ F  + ++K
Sbjct: 128 GTLVNAILYHIKDLSGINGEIRPGIVHRLDKDTSGLLIIAKNDKAHLKLSQMFHDKTVKK 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY +++ G    K   I   + +  +       +   N      AI++++VI    +KF 
Sbjct: 188 IYLAILKGKLNQKSGRIVTQIGRDKNDRKKMTVINDLNS--GKTAITNYEVI-SQTEKFT 244

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++   TGRTHQ+RVH  H+G PI+GD  Y         +  + +  LHA  ++  HP 
Sbjct: 245 LVKVHIETGRTHQIRVHMKHLGYPILGDSVYG-------RTDTEKRQMLHAYKLEFQHPI 297

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFKYD 327
               L+  A LP    K     G +++
Sbjct: 298 TEENLEFIAKLPEDFKKALKKCGLEFE 324


>gi|226313367|ref|YP_002773261.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226096315|dbj|BAH44757.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
          Length = 309

 Score =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 80/320 (25%), Positives = 148/320 (46%), Gaps = 32/320 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V+  ++N R+D++        +   +Q  ++ G+V V+ + +K N ++Q+   V +   
Sbjct: 13  TVDPADKNERIDKFITLQNEDWSRSQVQAWVKEGRVTVNGEPIKNNYKLQAEDEVTLR-- 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                        +     +    + +   ++YEDS + V NKP G+ V    G      
Sbjct: 71  -------------VPPPKEMAIQPEEMSLDIVYEDSDVVVVNKPRGLVVHPAPGHYSGTL 117

Query: 129 IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++G L    D  G     +P + HR+D++TSG+L+VA+   A   L E  +   + + Y 
Sbjct: 118 VNGLLAHCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDKAHMGLAEQLKAHTVNRKYV 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+  ++   I   + +        + VV +N   +  A++HF V++ F + +  +E
Sbjct: 178 ALVHGVIPHEMGTIEAPIGRDPK-NRQQMAVVFEN---SKPAVTHFIVLERFKE-YTMVE 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++  TGRTHQ+RVH  ++  P+ GD KY             +   LHA+ +   HP  G 
Sbjct: 233 LKLETGRTHQIRVHMKYIDYPLAGDPKYGPKNTLEL-----DGQALHAKTLGFIHPRTGE 287

Query: 305 -LQITAPLPAHMVKTWDSLG 323
            L+  AP+P  M+   + L 
Sbjct: 288 QLEFEAPMPKEMLDVIEVLR 307


>gi|325268629|ref|ZP_08135259.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           multiformis DSM 16608]
 gi|324989157|gb|EGC21110.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           multiformis DSM 16608]
          Length = 364

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 81/332 (24%), Positives = 147/332 (44%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++      H +   +QK   +G + V+   VK N +++   V+ +  
Sbjct: 36  VAVDKGQVPVRIDKFLFERMQHSSRNRIQKAADAGFIHVNGSPVKSNYKVRPEDVITLML 95

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                ++ I+              ++ +   ++YED+ + V NKPAG+ V  G+G  +  
Sbjct: 96  DRPKHDNTIE--------------AEDIPLDIVYEDTVLMVINKPAGLVVHPGAGNFHGT 141

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+LVVA+T  A   L + F  +   + 
Sbjct: 142 LINAVAWHLRDMPAFDPNDPEVGLVHRIDKDTSGLLVVAKTPDAKTALGKQFFNKTTHRS 201

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + +        + V     +   +A++H++V++ F      
Sbjct: 202 YNALVWGNFTEDEGRIEGNIARDPR-DRLRMTVFPPGSETGKHAVTHYRVLERFG-YTTL 259

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ----------NKLYL 290
           +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S  +          ++  L
Sbjct: 260 IECILETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSSYKAFIRNCLACCSRQAL 319

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HAR +   HP  G  +  T+ LP  +      
Sbjct: 320 HARTLGFVHPVTGEQMNFTSDLPEDLSSLLAK 351


>gi|134299530|ref|YP_001113026.1| RluA family pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134052230|gb|ABO50201.1| ribosomal large subunit pseudouridine synthase D [Desulfotomaculum
           reducens MI-1]
          Length = 306

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 84/322 (26%), Positives = 144/322 (44%), Gaps = 31/322 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
             +V+ +    RLD +  N    I+   +QK++  G V VD K  + N++++  + + + 
Sbjct: 5   TYIVDGENAKCRLDVFLANQCQDISRSYIQKLIEDGLVTVDGKPARANHKLRVEETIHMQ 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                          +  +  L    + +   + YEDS + V NKP G+ V    G    
Sbjct: 65  ---------------IPPAEELKVEPENIPLDIYYEDSHVIVVNKPRGMVVHPAEGNIAG 109

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D  G     +P + HRLD++TSG+++ A+   A Q L    + R + + 
Sbjct: 110 TLVNALLYHCHDLSGINGIMRPGIVHRLDKDTSGLIMAAKHDQAHQSLARQLKDRTVTRR 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV    K     I   + +        + VV   E+ +  A++HF+V++ F   +  
Sbjct: 170 YQALVHHNIKGDFGTINAPIGRDPR-DRQKMAVV---ERNSKNAVTHFQVLERFGD-YTL 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+RVH  ++G P+VGD KY  +     +    +   LHA+ +   HP  
Sbjct: 225 IECRLETGRTHQIRVHMAYIGFPLVGDPKYGPSK----SHFHLDGQLLHAKVLGFLHPVS 280

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+  APLP         L 
Sbjct: 281 GEYLEFIAPLPDVFENVLVKLR 302


>gi|152976253|ref|YP_001375770.1| RluA family pseudouridine synthase [Bacillus cereus subsp.
           cytotoxis NVH 391-98]
 gi|152025005|gb|ABS22775.1| pseudouridine synthase, RluA family [Bacillus cytotoxicus NVH
           391-98]
          Length = 302

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 142/313 (45%), Gaps = 33/313 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N R+D++  +     +   +Q+ ++ G + V+ K VK N +++    + +          
Sbjct: 15  NERIDKFVASVNHEWSRTQVQQWIKDGVITVNGKTVKGNYKVKENDEITVT--------- 65

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKS 135
                 +     L   ++ +   + YED+ + V NKP G+ V    G      ++G +  
Sbjct: 66  ------VPEPEELDIRAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMYH 119

Query: 136 WVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y ++V G+ 
Sbjct: 120 CTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRRYQAIVHGVI 179

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            + K  I   + +               ++   +A++HF+V++ F + F  +E +  TGR
Sbjct: 180 PHDKGTIDAPIARDKKD-----RQSMAVDENGKHAVTHFQVLERF-KDFTLVECRLETGR 233

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P+ GD KY      N      N   LHA  +   HP  G  LQ  AP
Sbjct: 234 THQIRVHMKYIGYPLAGDPKYGPKKTLNL-----NGQALHAGILGFNHPRTGEYLQFEAP 288

Query: 311 LPAHMVKTWDSLG 323
            PA   +T + L 
Sbjct: 289 APAIFEETLNILR 301


>gi|261868551|ref|YP_003256473.1| 23S rRNA pseudouridylate synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413883|gb|ACX83254.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 319

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 106/319 (33%), Positives = 167/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ V +DE   RLD +       +    + +I+R G+VRV+K R K   ++ +  VVR
Sbjct: 10  VQFLTVSDDEAGQRLDNFLLARLKGVPKSLIYRIVRKGEVRVNKARSKPEYKLLADDVVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A       +K  D+  N       L+  +++ED+ + V NKP+GI+V GGSG+ 
Sbjct: 70  IPPVRVA-------EKAQDTISNKLTKVAQLEQHIIFEDNYLLVLNKPSGIAVHGGSGLD 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++   +  +   L HRLD++TSGIL+VA+ R+A ++L E  R + +QK Y +L
Sbjct: 123 FGVIEALRALRPA-ARFLELVHRLDRDTSGILLVAKKRSALRNLHEQLREKTVQKDYLAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK    GG+ +  V +       + + F V + +      ++  
Sbjct: 182 VRGQWQSHCKVVQAPLLKNELAGGERIVKVSEQ---GKPSETRFSVEERYT-NATLIKAS 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F  +      N+L+LHA  +   HP  G  
Sbjct: 238 PVTGRTHQIRVHTQYAGHPIAFDSKYGDKEFDQHMVELGLNRLFLHAYTIRFEHPHSGET 297

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L++TAPL   M      L 
Sbjct: 298 LRLTAPLEEKMKGILKRLR 316


>gi|193212389|ref|YP_001998342.1| pseudouridine synthase, RluA family [Chlorobaculum parvum NCIB
           8327]
 gi|193085866|gb|ACF11142.1| pseudouridine synthase, RluA family [Chlorobaculum parvum NCIB
           8327]
          Length = 349

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 82/335 (24%), Positives = 146/335 (43%), Gaps = 37/335 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V   +  MR+DR+      ++    +Q  +  G+V V+ K VK N R++S   + + 
Sbjct: 24  TLDVSKVQTPMRIDRYLTQQVENMTRNKVQAAIEEGRVLVNGKPVKSNYRVKSCDHIHLT 83

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIA 126
            +      +  E                +   +LYED  + V +K AG+ V    G+   
Sbjct: 84  FLRPPAPELAPED---------------IPITILYEDDDLMVIDKEAGMVVHPAFGNWTG 128

Query: 127 YHIDGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  L         +D    +P + HRLD++TSG++++A+   A   L   F  R+++
Sbjct: 129 TLANAILHHLGKDADELDKTEMRPGIVHRLDKDTSGLIIIAKNPTALHKLARQFANRQVE 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y ++VWG+PK +   I   + + SH     +           +AI+ ++V++     F
Sbjct: 189 KVYKAIVWGVPKAESGTIKTNIGR-SHKNRKVMANFPYEGAEGKHAITDYQVVEDLG-YF 246

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----------SPIQNKLY 289
             +++  HTGRTHQ+RVH  H+G  I+GD  Y                      + ++  
Sbjct: 247 SLMDVTLHTGRTHQIRVHLQHLGHSILGDETYGGATPRTLPFSKSEPFTRNLLELMSRQA 306

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           LHA+ +    P  G  L  +APLP  M    + + 
Sbjct: 307 LHAQTLRFRQPTTGEPLSFSAPLPEDMELVLEKIR 341


>gi|53804453|ref|YP_113936.1| ribosomal large subunit pseudouridine synthase C [Methylococcus
           capsulatus str. Bath]
 gi|53758214|gb|AAU92505.1| ribosomal large subunit pseudouridine synthase C [Methylococcus
           capsulatus str. Bath]
          Length = 316

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 92/316 (29%), Positives = 163/316 (51%), Gaps = 19/316 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V+ +    R+D +  +    +   ++ +ILR+GQVR++  R K   R+  G VVRI
Sbjct: 13  RLIEVDAETAGQRIDNFLFSRLKGVPKSHVYRILRTGQVRINGGRSKAQQRLNEGDVVRI 72

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP+             L  +      + +L++ +L+ED  + V NKPAG++V GGSG+ +
Sbjct: 73  PPLR------------LAEAPEAGIPTPWLENRILHEDEDLLVVNKPAGMAVHGGSGLRF 120

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L++      +   L HRLD++TSG L++A+ R+A + L E FR   + K Y +L 
Sbjct: 121 GVIEGLRAAR-EDARFLELVHRLDRDTSGCLLIAKRRSALRQLHEQFRGEGVDKTYLALF 179

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+   +++ +   LLK     G+ +  +         AI+ F+ ++  +     +E +P
Sbjct: 180 SGVWARRRQVVDAPLLKNVLQSGERMVKISSE---GKAAITEFRRLEPLS-GATLVEARP 235

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
            TGRTHQ+RVHA  +G P+ GD +Y   +   +F      +++LHA  +   HP  GR +
Sbjct: 236 VTGRTHQIRVHARSLGHPLAGDERYGDPSLNQDFRQRGLKRMFLHAATLAFTHPRNGREI 295

Query: 306 QITAPLPAHMVKTWDS 321
           ++ APL   +     +
Sbjct: 296 RVEAPLEPDLQDFLSA 311


>gi|3915406|sp|O50310|Y723_CHLP8 RecName: Full=Uncharacterized RNA pseudouridine synthase Cpar_0723;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2661852|emb|CAB06297.1| hypothetical protein [Prosthecochloris vibrioformis]
          Length = 327

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 82/335 (24%), Positives = 146/335 (43%), Gaps = 37/335 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V   +  MR+DR+      ++    +Q  +  G+V V+ K VK N R++S   + + 
Sbjct: 2   TLDVSKVQTPMRIDRYLTQQVENMTRNKVQAAIEEGRVLVNGKPVKSNYRVKSCDHIHLT 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIA 126
            +      +  E                +   +LYED  + V +K AG+ V    G+   
Sbjct: 62  FLRPPAPELAPED---------------IPITILYEDDDLMVIDKEAGMVVHPAFGNWTG 106

Query: 127 YHIDGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  L         +D    +P + HRLD++TSG++++A+   A   L   F  R+++
Sbjct: 107 TLANAILHHLGKDADELDKTEMRPGIVHRLDKDTSGLIIIAKNPTALHKLARQFANRQVE 166

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y ++VWG+PK +   I   + + SH     +           +AI+ ++V++     F
Sbjct: 167 KVYKAIVWGVPKAESGTIKTNIGR-SHKNRKVMANFPYEGAEGKHAITDYQVVEDLG-YF 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----------SPIQNKLY 289
             +++  HTGRTHQ+RVH  H+G  I+GD  Y                      + ++  
Sbjct: 225 SLMDVTLHTGRTHQIRVHLQHLGHSILGDETYGGATPRTLPFSKSEPFTRNLLELMSRQA 284

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           LHA+ +    P  G  L  +APLP  M    + + 
Sbjct: 285 LHAQTLRFRQPTTGEPLSFSAPLPEDMELVLEKIR 319


>gi|262393762|ref|YP_003285616.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. Ex25]
 gi|262337356|gb|ACY51151.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. Ex25]
          Length = 314

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 102/326 (31%), Positives = 177/326 (54%), Gaps = 17/326 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++
Sbjct: 1   MSEIRTKVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VRIPP       + K+   +  S  L K ++ L+ ++++ED  + + NKP+G +V
Sbjct: 61  KAGDLVRIPP-----VTVEKKDDDVAPSTKLNKVAE-LEDMIIFEDDHMLILNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G  K+  + +   LLK        V+ + +       + + FK+++ F Q 
Sbjct: 174 KKFYLALVMGQWKSSCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKILEKFEQ- 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGLDRLFLHAANIKFQ 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP     ++I AP+   + K    L 
Sbjct: 287 HPSNDEWMEINAPMEPKLEKVLAGLR 312


>gi|238749676|ref|ZP_04611181.1| Ribosomal large subunit pseudouridine synthase C [Yersinia rohdei
           ATCC 43380]
 gi|238712331|gb|EEQ04544.1| Ribosomal large subunit pseudouridine synthase C [Yersinia rohdei
           ATCC 43380]
          Length = 319

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 103/322 (31%), Positives = 167/322 (51%), Gaps = 14/322 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 8   VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+  +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 68  IPPVR------VAERDEIQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + +   LLK     G+ +  V         + + FK+ + F +    ++  
Sbjct: 180 VRGQWQPHCKAVQAPLLKNIMQSGERMVKVSSE---GKPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDPEFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLGFKY 326
           +++ APL   +      L  K 
Sbjct: 296 MRVEAPLDNQLRHCLAVLRKKA 317


>gi|89073417|ref|ZP_01159941.1| putative 23S rRNA ribosomal pseudouridine synthase [Photobacterium
           sp. SKA34]
 gi|89050904|gb|EAR56378.1| putative 23S rRNA ribosomal pseudouridine synthase [Photobacterium
           sp. SKA34]
          Length = 314

 Score =  273 bits (697), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 98/321 (30%), Positives = 169/321 (52%), Gaps = 16/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ++ + +D    R+D + +    ++    + +ILR G+VRV+KKR+K   ++Q G +
Sbjct: 6   PKVQFIDISDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDL 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PPV      + ++++    S  L K ++ L+  ++YED  + + NKP+G +V GGSG
Sbjct: 66  VRVPPVF-----VPEKEEQAPVSTKLNKVAE-LEHCIIYEDDHLLILNKPSGTAVHGGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + +QK Y+
Sbjct: 120 LKFGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRQLQEQFRNKTVQKYYF 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  K     +   LLK        V+ + +       + + FKV++ F      ++
Sbjct: 179 ALVMGEWKANCRKVTAPLLKNE------VNSIVRVNPQGKASDTRFKVLERFPL-ATLVQ 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D +Y    F          +L+LHA  +   HP   
Sbjct: 232 ASPVTGRTHQIRVHCQYEGHPIAWDDRYGDPRFDAYTKKTGLGRLFLHAANIKFTHPSTD 291

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             + I+AP+   + +  + L 
Sbjct: 292 EAMDISAPMEPALERCLEKLR 312


>gi|261400385|ref|ZP_05986510.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           lactamica ATCC 23970]
 gi|269209820|gb|EEZ76275.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           lactamica ATCC 23970]
          Length = 374

 Score =  273 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 84/327 (25%), Positives = 140/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V       RLD       P  +   L   +R G V V+ K  +  +++  G+ +R+  
Sbjct: 30  LTVPPKLAGGRLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKPSQPKDKMIGGEQIRVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWSGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAGDPVYGNLRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPNDIYHLLSVLRLEA 336


>gi|149911608|ref|ZP_01900220.1| ribosomal large subunit pseudouridine synthase C [Moritella sp.
           PE36]
 gi|149805329|gb|EDM65342.1| ribosomal large subunit pseudouridine synthase C [Moritella sp.
           PE36]
          Length = 317

 Score =  273 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 98/322 (30%), Positives = 167/322 (51%), Gaps = 14/322 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   V +V +  D +  R+D + +     +    + +I+R G+VRV+K R+K   ++Q  
Sbjct: 5   ISPKVAFVTITEDYQGQRIDNFLRTKLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLQPE 64

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +VRIPPV       + E + +  S NL      L+S ++YED  + V NKP+G++V GG
Sbjct: 65  DIVRIPPVR------VSETEAISPSANLDSVR-ALESQIIYEDDYLIVINKPSGMAVHGG 117

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+++ +   L++ +    +   L HRLD++TSG L+VA+ R+  + L E  R++ ++K 
Sbjct: 118 SGLSFGLIEGLRA-IRPDSRFLELVHRLDRDTSGCLLVAKKRSTLKALHEQLRLKTMRKD 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G        +   LLK +   G+ +  V   +     + + F +I  +      
Sbjct: 177 YQALVAGAWPRSSRIVNAPLLKNTVSSGERLVRV---DSEGKESQTRFSIIQRYEHG-TL 232

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           ++  P TGRTHQ+RVHALH G PI  D KY   +F  +       +L+LHA  +   +P 
Sbjct: 233 VQASPITGRTHQIRVHALHAGHPIACDDKYGDKDFTKHMNGLGLKRLFLHAARLQFFNPG 292

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
                ++ APL   +V+  + L
Sbjct: 293 TQETQEVEAPLDMALVRALEKL 314


>gi|28898835|ref|NP_798440.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|153839692|ref|ZP_01992359.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus AQ3810]
 gi|260361710|ref|ZP_05774737.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus K5030]
 gi|260879491|ref|ZP_05891846.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus AN-5034]
 gi|260898210|ref|ZP_05906706.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus Peru-466]
 gi|34395766|sp|Q87N15|RLUC_VIBPA RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|28807054|dbj|BAC60324.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|149746785|gb|EDM57773.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus AQ3810]
 gi|308088378|gb|EFO38073.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus Peru-466]
 gi|308093528|gb|EFO43223.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus AN-5034]
 gi|308111282|gb|EFO48822.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus K5030]
 gi|328474606|gb|EGF45411.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus 10329]
          Length = 315

 Score =  273 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 103/326 (31%), Positives = 182/326 (55%), Gaps = 17/326 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++
Sbjct: 1   MSEIRTQVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VRIPP       + K+++ +  S  L K ++ L+ +++YED  + + NKP+G +V
Sbjct: 61  KAGDLVRIPP-----VTVEKKEEDVAPSTKLNKVAE-LEHMIIYEDDHMLILNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y++LV G  K+  + +   LLK        V+ + +       + + FK+++ F Q 
Sbjct: 174 KKFYFALVMGQWKSSCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKILEKFEQ- 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-QNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T  +  ++L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQLGLDRLFLHAANIKFQ 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP     ++I AP+ + + K    L 
Sbjct: 287 HPSNDEWMEINAPMESKLEKVLVGLR 312


>gi|270261338|ref|ZP_06189611.1| ribosomal large subunit pseudouridine synthase C [Serratia
           odorifera 4Rx13]
 gi|270044822|gb|EFA17913.1| ribosomal large subunit pseudouridine synthase C [Serratia
           odorifera 4Rx13]
          Length = 320

 Score =  273 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 102/322 (31%), Positives = 168/322 (52%), Gaps = 14/322 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +  VQ + + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++ +G 
Sbjct: 5   IPAVQLITISDDEAGQRIDNFLLARLKGVPKSMIYRIVRKGEVRVNKGRIKAEYKLAAGD 64

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVRIPPV       + E++    S  L K +  L   +LYED  + + NKP+G +V GGS
Sbjct: 65  VVRIPPVR------VAEREEAPVSAKLDKVA-ALADCILYEDDHLLLLNKPSGTAVHGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y
Sbjct: 118 GLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G  ++  + +   LLK     G+ +  V         + + FKV + F +    +
Sbjct: 177 LALVRGQWQSHCKAVQAPLLKNILQSGERIVRVNSE---GKPSETRFKVEERF-EHATLV 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +  P TGRTHQ+RVH LH G PI  D +Y    F          +L+LHA  +   HP  
Sbjct: 233 KASPITGRTHQIRVHTLHAGHPIAFDDRYGDREFDRQLAGTGLKRLFLHAAALRFEHPGT 292

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  ++I AP+   +      L 
Sbjct: 293 GETMRIEAPMDEELRHCLQVLR 314


>gi|145636319|ref|ZP_01791988.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittHH]
 gi|145270484|gb|EDK10418.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittHH]
          Length = 322

 Score =  273 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 103/321 (32%), Positives = 171/321 (53%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRIKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+ +  V +       + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGERIVRVSEQ---GKPSETRFSIEERYI-NATLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L+  APL   M      L 
Sbjct: 299 ETLRFNAPLDHQMKAILQKLR 319


>gi|145630415|ref|ZP_01786196.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae R3021]
 gi|145638677|ref|ZP_01794286.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittII]
 gi|229844426|ref|ZP_04464566.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae 6P18H1]
 gi|144984150|gb|EDJ91587.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae R3021]
 gi|145272272|gb|EDK12180.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittII]
 gi|229812675|gb|EEP48364.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae 6P18H1]
 gi|309750170|gb|ADO80154.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae R2866]
          Length = 322

 Score =  273 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 103/321 (32%), Positives = 171/321 (53%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRIKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+ +  V +       + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGERIVRVSEQ---GKPSETRFSIEERYI-NATLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L+  APL   M      L 
Sbjct: 299 ETLRFNAPLDHQMKAILQKLR 319


>gi|260582324|ref|ZP_05850117.1| pseudouridylate synthase [Haemophilus influenzae NT127]
 gi|319898067|ref|YP_004136264.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae F3031]
 gi|260094692|gb|EEW78587.1| pseudouridylate synthase [Haemophilus influenzae NT127]
 gi|309972429|gb|ADO95630.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae R2846]
 gi|317433573|emb|CBY81957.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae F3031]
          Length = 322

 Score =  273 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 103/321 (32%), Positives = 171/321 (53%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+ +  V +       + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGERIVRVSEQ---GKPSETRFSIEERYI-NATLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L+  APL   M      L 
Sbjct: 299 ETLRFNAPLDHQMKAILQKLR 319


>gi|317131689|ref|YP_004091003.1| pseudouridine synthase, RluA family [Ethanoligenens harbinense
           YUAN-3]
 gi|315469668|gb|ADU26272.1| pseudouridine synthase, RluA family [Ethanoligenens harbinense
           YUAN-3]
          Length = 302

 Score =  273 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 84/328 (25%), Positives = 145/328 (44%), Gaps = 35/328 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  Q  V   ++   RLDR      P      LQK+L  G V ++ K    ++R+++G 
Sbjct: 1   MTR-QTFVAGMEQAGERLDRALARLCPDQTRSGLQKLLECGLVTLNGKPAGKHDRMRAGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                    V L   +  +   ++YED  + V NKP G+ V  G+
Sbjct: 60  EIVVEF---------------PDPVPLEAKAQDIPIEVVYEDDDLLVVNKPQGMVVHPGA 104

Query: 124 G--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  L    DS        +P + HR+D++TSG+L+VA+   A Q L    + 
Sbjct: 105 GNPDGTLVNALLFHCGDSLSGIGGVLRPGIVHRIDKDTSGLLMVAKNDRAHQSLAAQIKA 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
               + Y ++V G+ K     +    + +       + V    +K + +A++H+ V+  +
Sbjct: 165 HSFLREYEAVVCGVIKEDSGTVDAP-VGRHPTNRKRMAV---TQKNSRHAVTHYTVLRRY 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  L ++  TGRTHQ+R+H  ++G P+ GD  Y     G           LHAR + 
Sbjct: 221 TH-YTHLRLRLETGRTHQIRLHMAYIGHPVAGDPVYGKPLCG------LRGQCLHARTLG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  GR ++ T+ LPA+  +   +L 
Sbjct: 274 FVHPSTGRYMEFTSELPAYFRQFLTTLA 301


>gi|163803777|ref|ZP_02197632.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio sp. AND4]
 gi|159172418|gb|EDP57289.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio sp. AND4]
          Length = 314

 Score =  273 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 108/328 (32%), Positives = 182/328 (55%), Gaps = 17/328 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++
Sbjct: 1   MSEIRTKVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VRIPPV      +      +  S  L K ++ L+ ++++ED  + V NKP+G +V
Sbjct: 61  KAGDLVRIPPVTVEQKEVD-----VAPSTKLNKVAE-LEHMIIFEDEHMLVLNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A ++L   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRYLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y++LV G  KN  + +   LLK      +   +V+ N KG   + + FK+++ F Q 
Sbjct: 174 KKFYFALVMGEWKNSCKVVNAPLLKN-----EVNSIVRVNPKG-KPSETRFKILEKFEQ- 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKFQ 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           HP     ++I AP+ A + K    L  K
Sbjct: 287 HPSNDEWMEINAPMEAKLEKALAGLRNK 314


>gi|301301197|ref|ZP_07207353.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300851196|gb|EFK78924.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 298

 Score =  272 bits (696), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 82/309 (26%), Positives = 135/309 (43%), Gaps = 32/309 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+   N +       L+K++  G ++V+    K N ++  G  +              
Sbjct: 13  RLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGDVKKANYKVNLGDEITFD----------- 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWV 137
                     L+   + +   ++YED  + V NKP G+ V    G   H   +  L    
Sbjct: 62  ----KPEVKKLSLEPENIPLDIVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNALLYHSP 117

Query: 138 DS---KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            S      +P + HR+D++TSG+L+VA+   A Q L +  + +   + Y +LV G  K  
Sbjct: 118 LSTINGTYRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYIALVHGNIKED 177

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I   L + S +      VV    K    A++HF+V+  +   +  ++    TGRTHQ
Sbjct: 178 SGTIDAPLGR-SKVDRKKQAVV----KDGRNAVTHFEVLKRYGD-YTLVKCVLETGRTHQ 231

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH  ++G P+VGD  Y         +   +  +LHA  +   HP     L+ TAPLP 
Sbjct: 232 IRVHMKYIGHPLVGDQLYGPR-----KTLGNSGQFLHAEKLGFVHPRTNEYLEFTAPLPE 286

Query: 314 HMVKTWDSL 322
           +  K  +SL
Sbjct: 287 NFKKLLESL 295


>gi|59712354|ref|YP_205130.1| 23S rRNA pseudouridylate synthase [Vibrio fischeri ES114]
 gi|59480455|gb|AAW86242.1| 23S rRNA pseudouridylate synthase [Vibrio fischeri ES114]
          Length = 315

 Score =  272 bits (696), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 103/323 (31%), Positives = 168/323 (52%), Gaps = 16/323 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ+V +++D    R+D +      ++    + +I+R G+VRV+KKR+K   ++Q G V
Sbjct: 6   PKVQFVDIDDDFAGQRIDNFLLARLKNVPKSMIYRIVRKGEVRVNKKRIKPEYKLQEGDV 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E    D           L+  ++YED  + + NKP+G +V GGSG
Sbjct: 66  VRIPPVK------VPESTAPDLPNVKLGKVAELEHCIIYEDDHVLILNKPSGTAVHGGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + +QK Y+
Sbjct: 120 LKFGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRRLQEQFRNKTVQKYYF 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  KN  + +   LLK        V+ + +       + + FKV++ F Q    ++
Sbjct: 179 ALVMGQWKNSCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKVLEKFEQ-ATLIQ 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-SPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  +   HP   
Sbjct: 232 ASPITGRTHQIRVHTQYTGHPIGWDDRYGDRRFDAYTGQFGLDRLFLHAANIKFTHPATE 291

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
             + I+AP+ A + +    L  K
Sbjct: 292 ELMDISAPMGAKLERVLKGLRSK 314


>gi|304312939|ref|YP_003812537.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium HdN1]
 gi|301798672|emb|CBL46904.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium HdN1]
          Length = 311

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 103/324 (31%), Positives = 170/324 (52%), Gaps = 14/324 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q++ VE +    R+D +       +    + + LR G+VRV+K R+K + R+Q G ++R
Sbjct: 1   MQWLEVEAEYAGQRIDNFLVARLKGVPKSVIYRCLRKGEVRVNKGRIKPDYRVQGGDLIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  +       ++  D      +  + L+  +LYED  + V NKPAG++V GGSG++
Sbjct: 61  IPPLRRS-------EQSDDEIHVGERIRNLLEGAILYEDEGLIVLNKPAGMAVHGGSGVS 113

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L++ +    +   L HRLD++TSG L+VA+ R+  + L E  +   I+K+YW+L
Sbjct: 114 VGVIEALRA-IRPLSRHLELVHRLDRDTSGCLMVAKKRSRLRVLHEQLQAGEIRKVYWAL 172

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K K   I   L K    GG+ +  V Q       + + F V+    ++   +E  
Sbjct: 173 VEGRWKGKFRRIDAPLQKFGEQGGERIVKVSQQ---GKPSSTEF-VLLRHFEETSLVEAS 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGGRL 305
           P TGRTHQ+RVHA   G PIVGD KY    +   F      +++LHA+ +++P  + G++
Sbjct: 229 PLTGRTHQIRVHAQFAGHPIVGDDKYENKERARYFRDLGAGRMFLHAKSLEIPS-DQGKM 287

Query: 306 QITAPLPAHMVKTWDSLGFKYDRN 329
              APL        D LG +  ++
Sbjct: 288 VFDAPLDTAFQSFIDQLGREGSKS 311


>gi|85713201|ref|ZP_01044230.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
 gi|85692974|gb|EAQ30943.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
          Length = 315

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 95/320 (29%), Positives = 159/320 (49%), Gaps = 15/320 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ+  V  DE   R+D +       +    + +ILR G+VRV+KKR K + +I++G  
Sbjct: 6   NQVQWHDVARDEAGQRIDNFLIARLRGVPKSLVYRILRKGEVRVNKKRTKPDYKIKAGDA 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RIPPV  +    +   K+   +         L+  ++YED    + NKP+G++V GGSG
Sbjct: 66  IRIPPVKVSPKPELPSPKLAKVAE--------LEQAIVYEDDAFMIVNKPSGLAVHGGSG 117

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++          L HRLD++TSG++++A+ R+  + L    R + + K Y 
Sbjct: 118 LNFGLIEGLRALRPQD-NALELVHRLDRDTSGLIMIAKKRSVLKVLHAQLRDKEMNKQYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  +     +   L K +   G+ +  V   +     + + F++   +A+    +E
Sbjct: 177 ALVRGQWQKNVRNVEAPLKKNTLKSGERIVRV---DAEGKPSHTRFRINQRYAE-ATLVE 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVHALH G PI GD KY  A+F          +L+LHA  +   HP   
Sbjct: 233 ASPVTGRTHQIRVHALHAGHPIAGDPKYGDASFNERMQQGGLTRLFLHAWQLSFKHPVTE 292

Query: 304 R-LQITAPLPAHMVKTWDSL 322
           + +   AP+ + +      L
Sbjct: 293 KTVSFEAPMDSSLTAILSEL 312


>gi|163755786|ref|ZP_02162904.1| ribosomal large subunit pseudouridine synthase D [Kordia algicida
           OT-1]
 gi|161324307|gb|EDP95638.1| ribosomal large subunit pseudouridine synthase D [Kordia algicida
           OT-1]
          Length = 346

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 79/334 (23%), Positives = 147/334 (44%), Gaps = 41/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
              E  ++ +R+D++  N         +Q+  + G + V+ K VK N +++   V+++  
Sbjct: 22  FTAEKGQQPLRVDKYLMNFIEGATRNKIQQAAKDGNIFVNGKPVKSNYKVKGNDVIKV-- 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                 H   E  ++   + +          ++YED  + V NKPAG+ V  G G     
Sbjct: 80  ---LFAHPPYENLLVGEDIPID---------IVYEDDDLLVVNKPAGMVVHPGHGNYSGT 127

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH D        +  ++P L HR+D++TSG+LVVA+T  A  HL + F  +  +
Sbjct: 128 LINALIYHFDNL----PKNSNERPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTSE 183

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           +IY++LVWG  +  +  +   + +             ++      A++H+KV++      
Sbjct: 184 RIYYALVWGNVEEDEGTVEGNIGRHPKNRLQNTVFFGEDADKGKPAVTHYKVLERLG-YV 242

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKL 288
             +  Q  TGRTHQ+RVH  H+G  +  D +Y        T+             I  + 
Sbjct: 243 TLVSCQLETGRTHQIRVHMKHIGHTLFNDERYGGERILKGTTFTKYKQFVENCFKILPRQ 302

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            LHA+ +   HP  G  +   + +P+ + +  + 
Sbjct: 303 ALHAKTLGFIHPRTGEKMSFNSEVPSDIAECIEK 336


>gi|196228386|ref|ZP_03127253.1| pseudouridine synthase, RluA family [Chthoniobacter flavus
           Ellin428]
 gi|196227789|gb|EDY22292.1| pseudouridine synthase, RluA family [Chthoniobacter flavus
           Ellin428]
          Length = 302

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 86/314 (27%), Positives = 143/314 (45%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+      RLD++  +    ++   +Q +++ G V ++    K + R+++G  V +    
Sbjct: 8   VDAAAAGPRLDQFLASAAAGLSRARIQDLIKEGHVTLNGGVAKASARLRAGDAVTLHEPP 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                 + E+  LD               +L+ED  + V NKPAG+ V   +G      +
Sbjct: 68  PVPTETVAEEIALD---------------VLFEDDDLIVINKPAGLVVHPAAGNWSGTVV 112

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L       G    Q+P + HRLD++TSG LVVA+  AA Q L + F  R + KIY +
Sbjct: 113 NALLHHCQTLSGIGGEQRPGIVHRLDKDTSGCLVVAKNDAAHQSLAKQFAGREVTKIYLA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L  G    K   I   + +   +    + V+  ++     A + ++V+         +E 
Sbjct: 173 LAAGKWARKSGVIEAPIGRH-PVQRKKMTVLPADK--GRAAKTGYRVLLELPVG-TLVEC 228

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
             HTGRTHQ+RVH  H+G PI+GD  Y    +G+F      +  LHA  +   HP  G+ 
Sbjct: 229 TLHTGRTHQIRVHLKHLGHPILGDEVYG--RRGDFA-----RQMLHAWRLGFVHPGTGKH 281

Query: 305 LQITAPLPAHMVKT 318
           L   +P+P   V+ 
Sbjct: 282 LNFESPIPPDFVEA 295


>gi|86608591|ref|YP_477353.1| RluA family pseudouridine synthase [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86557133|gb|ABD02090.1| pseudouridine synthase, RluA family [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 317

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 86/327 (26%), Positives = 147/327 (44%), Gaps = 30/327 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQ 63
             ++ + V   ++ +RLDR      P ++   LQ+++R GQV ++ +  +  +R +Q+G 
Sbjct: 9   ADIRQIRVTEKQQGLRLDRGLAEQLPELSRSRLQQLIRQGQVWLNGQPCRDKDRPLQAGD 68

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +         +  E   LD               +LYED  + V NKP G+ V    
Sbjct: 69  EVEVRIPPATPTALQPEPIPLD---------------ILYEDDDLLVINKPRGLVVHPAP 113

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G A    +   L       G    Q+P + HRLD++T+G LV+A+   A QHL    + +
Sbjct: 114 GHASGTLVHALLAHCPRLSGINGEQRPGIVHRLDKDTTGALVIAKHDQAHQHLQAQIQAK 173

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +++Y  +V+G P   +  ++  + +      D   +          A++H++V++   
Sbjct: 174 TARRLYLGVVFGRPAQSQGTVSAPIGRHP---VDRQKMAVLTPGQGRVAVTHWQVLERLG 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  ++ +  TGRTHQ+RVHA H+  PIVGD  Y    +   +        LHA  +  
Sbjct: 231 -NYTLMQFELETGRTHQIRVHAAHLRLPIVGDPLY---TQSKTSPVKLGGQALHAWKLSF 286

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
             P  G+ LQ TAPLP    +    L 
Sbjct: 287 VQPRTGQPLQFTAPLPEEFERLLRQLR 313


>gi|15643228|ref|NP_228272.1| hypothetical protein TM0462 [Thermotoga maritima MSB8]
 gi|4980971|gb|AAD35547.1|AE001724_5 conserved hypothetical protein [Thermotoga maritima MSB8]
          Length = 311

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 86/319 (26%), Positives = 147/319 (46%), Gaps = 29/319 (9%)

Query: 12  VENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VE  EE  RLD++ K   P  I+   +QK ++ G+V+V+ +  K + +++ G++V +   
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSMIQKAIKEGKVKVNGQIKKPSYKLKEGEIVEV--- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYH 128
                       + +     T   + ++  +LYED  I V +KP  + V           
Sbjct: 63  -----------DLPEKPQEATVQPEEIELKVLYEDRDIIVIDKPGDMIVHPVPSKLSGTL 111

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D +G     +P + HRLD+ETSG++VVA+   A Q L++ F+ R+++K Y 
Sbjct: 112 VNALLHHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYI 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  KN +  I   L +        + +     +    AI+ ++V+  F      + 
Sbjct: 172 LLVKGKMKNDEGVIDLPLARHP-----VLRIKMAVVETGKEAITEYRVLKRFDDVATLVL 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P TGRTHQ+RVH   +G PI+GD  Y    +         +  LHA  +   HP  G 
Sbjct: 227 AFPKTGRTHQIRVHMKSLGHPIMGDKIYGKPKEDEI--FGIKRQMLHALKLGFFHPRTGE 284

Query: 305 -LQITAPLPAHMVKTWDSL 322
            ++  +PLP    +    +
Sbjct: 285 WMEFVSPLPEDFKEAIRRI 303


>gi|150016471|ref|YP_001308725.1| RluA family pseudouridine synthase [Clostridium beijerinckii NCIMB
           8052]
 gi|149902936|gb|ABR33769.1| pseudouridine synthase, RluA family [Clostridium beijerinckii NCIMB
           8052]
          Length = 305

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 141/323 (43%), Gaps = 32/323 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +V+  +   R+D++    +   +   +Q ++    ++V+ K  K N ++++   + +  
Sbjct: 6   FIVDEKDRGERIDKYLAEIFVDKSRSFIQGLIEKDDIKVNNKTPKSNYKLRALDEIEVTF 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
               +  +  E+               +   +LYED  + V NKP G+ V    G     
Sbjct: 66  SEPEVLRVEAEE---------------IPINILYEDKDVVVVNKPQGMVVHPAPGNYNGT 110

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D        +P + HR+D++TSG+LVVA+   A   L++  +   +++ Y
Sbjct: 111 LVNALLYHCKDLSSINGIIRPGIVHRIDKDTSGVLVVAKNDEAHNKLSDQLKDHSMKREY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++LV G  KN K  I   L +          V     +G   A++H++V++ F   +  +
Sbjct: 171 YALVEGRLKNDKGIIDKPLARNKRDRLKIGIV-----EGGKRAVTHYEVLERF-NGYTLI 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    TGRTHQ+RVH   +G P+VGD  Y    +            LHA+ +   HP   
Sbjct: 225 KCILETGRTHQIRVHMASIGFPLVGDPLYGFKKQ----RFKLKGQVLHAKTLGFVHPSKN 280

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
             ++ T  LP +  +  + L  +
Sbjct: 281 EYMEFTTELPEYFQEIIEKLRNE 303


>gi|117921007|ref|YP_870199.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           ANA-3]
 gi|117613339|gb|ABK48793.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           ANA-3]
          Length = 329

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 104/323 (32%), Positives = 175/323 (54%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    VQ + ++ D  + R+D +       +    + +I+R G+VRV+KKR+K   ++Q 
Sbjct: 15  SPQLQVQLITIDEDHLDQRIDNFLITVLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQI 74

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PP       + ++      S NL++ S  L+  +L+ED+ + V NKPAGI+V G
Sbjct: 75  GDVVRVPP-----VRMAEQDNRTAPSANLSRVSQ-LEDRILHEDNHLIVLNKPAGIAVHG 128

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ Y +   L+S    +     L HRLD++TSG+L+VA+ R+A +H+ +  R +++QK
Sbjct: 129 GSGVDYGVIEALRSLRPQQKF-LELVHRLDKDTSGVLLVAKKRSALKHMHDQLRYKKMQK 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G    + + +   LLK +   G+ +  V         + + FK++  + Q   
Sbjct: 188 DYLALVKGEWSAQDKVVKQPLLKLTLKSGERIVRVNAE---GKPSETRFKIVQRY-QGCT 243

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  +MG PI  D KY    F  +  +    +L+LHA  +   HP
Sbjct: 244 LVQASPVTGRTHQIRVHCQYMGHPIACDEKYSEQAFDDSMRALGLTRLFLHAAELMFIHP 303

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E    ++++APL  ++ +    L
Sbjct: 304 ENDEVMRVSAPLDDNLQQLLSKL 326


>gi|225419732|ref|ZP_03762035.1| hypothetical protein CLOSTASPAR_06070 [Clostridium asparagiforme
           DSM 15981]
 gi|225041622|gb|EEG51868.1| hypothetical protein CLOSTASPAR_06070 [Clostridium asparagiforme
           DSM 15981]
          Length = 303

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 79/324 (24%), Positives = 149/324 (45%), Gaps = 31/324 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   V +++  +R+D++  +    ++   LQK+L+SGQV V  + VK +  +Q G ++ 
Sbjct: 1   MERFRVTDEDGGVRIDKYLTSVCEGLSRSYLQKLLKSGQVLVGGQGVKASYAVQEGDLIE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +                +  +V     ++ +   +LYED  I + NKP G+ V   +G  
Sbjct: 61  LE---------------VPEAVEPEILAEPMDLDVLYEDEDIILINKPKGMVVHPAAGHY 105

Query: 127 YHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            H   +G L              +P + HR+D +T+G+++  +   A   L E  +   I
Sbjct: 106 THTLVNGLLDHCRGQLSGINGVMRPGIVHRIDMDTTGVIIACKNDLAHSCLAEQLKEHSI 165

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G+ K  +  +   + +   +    + +   N      A++H+KV+  F ++
Sbjct: 166 TRRYQAIVHGVVKEDEGTVDAPIGRH-PVERKKMSI---NYNNGREAVTHYKVLRRF-RQ 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +E +  TGRTHQ+RVH   +  P++GD  Y          P      LHA  + + H
Sbjct: 221 YTHVECRLETGRTHQIRVHMASIHHPLLGDAVYGP---ARCPIPGLQGQTLHAGVLGIRH 277

Query: 300 PEGG-RLQITAPLPAHMVKTWDSL 322
           P  G  ++ TAPLP +  K   +L
Sbjct: 278 PRTGAYMEFTAPLPDYFAKLLRTL 301


>gi|261405686|ref|YP_003241927.1| RluA family pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261282149|gb|ACX64120.1| pseudouridine synthase, RluA family [Paenibacillus sp. Y412MC10]
          Length = 324

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 76/329 (23%), Positives = 142/329 (43%), Gaps = 33/329 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           T      V+ D    R+D++   +    ++   +Q  +  G V V+   +K N ++  G 
Sbjct: 21  TEASEWTVDADAAKTRIDKYLTENLGEDVSRSQVQLWIADGHVSVNDGPIKSNYKVSQGD 80

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +     +   II E   L+               + +ED  + V NKP G+ V    
Sbjct: 81  RIVLKVPEPSAVEIIPEDIPLE---------------IAFEDGDVIVVNKPRGMVVHPAP 125

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  +    D  G     +P + HR+D++T+G+++ A+   A   L    +  
Sbjct: 126 GHSSGTLVNALMFHCKDLSGINGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKEH 185

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G   + +  I   + + +     Y       ++ + +A++HF V++ F 
Sbjct: 186 SVNRRYLALVHGNISHDQGTIDAPIGRDAQDRKLY----TVTDRNSKHAVTHFTVVERFG 241

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  LE++  TGRTHQ+RVH  ++G P+VGD  Y  +          N   LHA  +  
Sbjct: 242 D-YSLLELKLETGRTHQIRVHMKYIGHPLVGDPVYGKSKGIKL-----NGQALHAAVLGF 295

Query: 298 PHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
            HP  G   + +AP+P+ M +    L  +
Sbjct: 296 VHPSTGEYKEFSAPMPSDMNELLTILRGR 324


>gi|253576153|ref|ZP_04853485.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251844496|gb|EES72512.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 315

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 78/323 (24%), Positives = 145/323 (44%), Gaps = 33/323 (10%)

Query: 11  VVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V    +   R+D++ K       +   +Q  + +G + V+   VK N ++  G  + +  
Sbjct: 18  VAGPADAKERIDKYAKTQLGEEFSRSQIQLWIEAGNLVVNGAPVKANYKLAEGDRIVL-- 75

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
                        ++  +       + +   + YEDS + V NKP G+ V    G     
Sbjct: 76  -------------VIPEAEPTEIVPEDIPLEIYYEDSDVIVVNKPRGMVVHPAPGHTSGT 122

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  +    D  G     +P + HR+D++TSG+++ A+   A   L    +   + + Y
Sbjct: 123 LVNALMFHCKDLSGINGELRPGIVHRIDKDTSGLIMAAKNDKAHASLAAQLKAHTVTRKY 182

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++LV G   + +  +   + +  H    Y  +    E+ + +A++HF+V++ F   +  L
Sbjct: 183 YALVHGNVSHDQGTVDAPIGRDPHDRKMYTVI----ERNSKHAVTHFQVVERFGD-YTLL 237

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E++  TGRTHQ+RVH   +G P+VGD  Y  +          +   LHA  +   HPE G
Sbjct: 238 ELKLETGRTHQIRVHMKFIGHPLVGDPLYGRSKGIKM-----DGQALHAAVLGFDHPEDG 292

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
           + L+ +AP+PA M     SL  +
Sbjct: 293 QYLEFSAPIPADMENVLQSLRNR 315


>gi|86132824|ref|ZP_01051415.1| pseudouridine synthase, RluA family [Dokdonia donghaensis MED134]
 gi|85816530|gb|EAQ37717.1| pseudouridine synthase, RluA family [Dokdonia donghaensis MED134]
          Length = 347

 Score =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 84/330 (25%), Positives = 147/330 (44%), Gaps = 33/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
                 +E +R+D++  N   +     +QK  ++G ++V+ K VK N ++++G VVR   
Sbjct: 22  FTASKGQEPLRVDKFLMNFVENATRNKIQKAAKNGSIQVNNKVVKQNYKVKAGDVVR--- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                 H   E  +    + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 79  --AMFEHPPHEFLLTPEDIPLD---------IIYEDDDLLVVNKPAGMVVHPGHGNYSGT 127

Query: 128 HIDGFLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            I+  +       ++  ++P L HR+D++TSG+LVVA+T  A  HL++ F  +  ++ Y 
Sbjct: 128 LINALIHHIDNLPNNSSERPGLVHRIDKDTSGLLVVAKTEHAMTHLSKQFFNKTTEREYV 187

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++VWG   + +  I   + +               E+    A++H+KV++        + 
Sbjct: 188 AIVWGNVVDDEGTIEGNIGRHPKNRLQNTVFKDDEEEQGKPAVTHYKVLERLG-YVTQVA 246

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHA 292
            +  TGRTHQ+RVH  ++G  +  D +Y  N     TS             I  +  LHA
Sbjct: 247 CKLETGRTHQIRVHMKYIGHTLFNDERYGGNAILKGTSFTKYKQFVENCFKILPRQALHA 306

Query: 293 RYMDLPHPEGGRL-QITAPLPAHMVKTWDS 321
           + +   HP  G   +   P+P  M    + 
Sbjct: 307 KTLGFVHPTTGEYKRFETPVPEDMAGCIEK 336


>gi|90961803|ref|YP_535719.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|90820997|gb|ABD99636.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|300214544|gb|ADJ78960.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 298

 Score =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 82/309 (26%), Positives = 135/309 (43%), Gaps = 32/309 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+   N +       L+K++  G ++V+    K N ++  G  +              
Sbjct: 13  RLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGDVKKANYKVNLGDEITFD----------- 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWV 137
                     L+   + +   ++YED  + V NKP G+ V    G   H   +  L    
Sbjct: 62  ----KPEVKKLSLEPENIPLDIVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNALLYHSP 117

Query: 138 DS---KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            S      +P + HR+D++TSG+L+VA+   A Q L +  + +   + Y +LV G  K  
Sbjct: 118 LSTINGTYRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYVALVHGNIKED 177

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I   L + S +      VV    K    A++HF+V+  +   +  ++    TGRTHQ
Sbjct: 178 SGTIDAPLGR-SKVDRKKQAVV----KDGRNAVTHFEVLKRYGD-YTLVKCVLETGRTHQ 231

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH  ++G P+VGD  Y         +   +  +LHA  +   HP     L+ TAPLP 
Sbjct: 232 IRVHMKYIGHPLVGDQLYGPR-----KTLGNSGQFLHAEKLGFVHPRTNEYLEFTAPLPE 286

Query: 314 HMVKTWDSL 322
           +  K  +SL
Sbjct: 287 NFKKLLESL 295


>gi|229824765|ref|ZP_04450834.1| hypothetical protein GCWU000182_00113 [Abiotrophia defectiva ATCC
           49176]
 gi|229791094|gb|EEP27208.1| hypothetical protein GCWU000182_00113 [Abiotrophia defectiva ATCC
           49176]
          Length = 326

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 78/330 (23%), Positives = 146/330 (44%), Gaps = 36/330 (10%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + V +++   R+D++        +   L+ ++  G+VRV+ K VK + ++  G  +
Sbjct: 21  EVIELSVVSEDSGERIDKYLSGKLTEYSRSYLKGLIDEGKVRVEGKPVKSSFKVTEGINI 80

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            I         II E   LD               +LYED  + + NKP G+ V   +G 
Sbjct: 81  SISIPPVKEAEIIPENIPLD---------------ILYEDEDVILINKPKGMVVHPAAGH 125

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  +    D+        +P + HR+D +T+G+++  +   + + + E  +   
Sbjct: 126 YTGTLVNALMYHCRDNLSGINGELRPGIVHRIDMDTTGVIIACKNDVSHRIIAEQLKEHS 185

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-- 236
           I++ Y ++V+G+ K+++  I   + + S      + V+         A++H++VI  +  
Sbjct: 186 IKRKYQAIVYGVFKDEEGRIEGSIGR-SKTDRKKMAVI----PDGKPAVTHYRVIRNYTS 240

Query: 237 --AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                F  +E +  TGRTHQ+RVH   +G P++GD  Y A           +   LHA  
Sbjct: 241 PNGNNFAHIECELETGRTHQIRVHMTSIGHPLLGDEIYGA----AKNPFKLDGQALHAEM 296

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +   HP  G  ++  APLP +  K    L 
Sbjct: 297 LGFVHPRTGEYMEFHAPLPEYFSKLLTKLA 326


>gi|78186656|ref|YP_374699.1| pseudouridine synthase, RluD [Chlorobium luteolum DSM 273]
 gi|78166558|gb|ABB23656.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           luteolum DSM 273]
          Length = 354

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 84/338 (24%), Positives = 146/338 (43%), Gaps = 37/338 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V   +  MR+D++      +     +Q+ +  G+V V+ K VK N R++S   + + 
Sbjct: 28  TLQVSRVQCPMRIDQYLTRQVENATRNKVQEAIEDGRVLVNGKSVKSNYRVKSCDSIEMT 87

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIA 126
            +      +  E   +D               ++YEDS + V NK  G+ V    G+   
Sbjct: 88  FLRPPAPELAPEDIPID---------------IVYEDSDLMVVNKAPGMVVHPAFGNWTG 132

Query: 127 YHIDGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  L  +      +++   +P + HRLD++TSG+++VAR   A   L   F  R++ 
Sbjct: 133 TLANAILHHFGTDAEELETDELRPGIVHRLDKDTSGLIIVARNPTALHRLARQFADRKVS 192

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y +++WG+P+ ++  I   + + S      +            AI+ ++V +     F
Sbjct: 193 KLYTAILWGVPEPQEGTIHTNIGR-SRRDRKVMANFPYEGLEGKTAITDYRVTENL-HWF 250

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-----------IQNKLY 289
              E+  HTGRTHQ+R H  H+G  I+GD  Y          P           +  +  
Sbjct: 251 SLAELTLHTGRTHQIRAHMQHLGHQILGDTTYGGASLRTLDFPRSESFVKNLLDLLPRQA 310

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           LHA  +    P  GR L  TAPLP  M +  + +   Y
Sbjct: 311 LHAASLSFHQPTTGRPLSFTAPLPEDMAQALEKIRVIY 348


>gi|209695670|ref|YP_002263599.1| ribosomal large subunit pseudouridine synthase C (rRNA uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Aliivibrio salmonicida LFI1238]
 gi|208009622|emb|CAQ79918.1| ribosomal large subunit pseudouridine synthase C (rRNA uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Aliivibrio salmonicida LFI1238]
          Length = 315

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 103/321 (32%), Positives = 173/321 (53%), Gaps = 16/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ+V +++D    R+D +      ++    + +I+R G+VRV+KKR+K   +IQ G +
Sbjct: 6   PKVQFVEIDDDFAGQRIDNYLLARLKNVPKSMIYRIVRKGEVRVNKKRIKPEYKIQEGDI 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       + +   +   SV L K S+ L+S ++YED  + + NKP+G +V GGSG
Sbjct: 66  VRIPP-----VKLPESTAVELPSVKLAKVSE-LESCIIYEDDHLLILNKPSGTAVHGGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +     L++ +    +   L HR+D++TSGIL++A+ R+A + L E FR + +QK Y+
Sbjct: 120 LKFGAIEALRA-LRPDARYLELVHRIDRDTSGILLIAKKRSALRRLQEQFRNKTVQKYYF 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  K+  + +   LLK        V+ + +       + + FK+++ F Q    ++
Sbjct: 179 ALVMGHWKSTCKVVNVPLLKNE------VNSIVRVNPNGKPSETRFKILEKFEQ-ATLIQ 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-SPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVHA H G PI  D +Y       +T     ++L+LHA  +   HP   
Sbjct: 232 ASPITGRTHQIRVHAQHAGHPIGWDDRYGDRRFDAYTGQFGLDRLFLHAANIKFTHPSTE 291

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             + I+AP+   + +    L 
Sbjct: 292 ELMDISAPMEKRLERVLTGLR 312


>gi|153008568|ref|YP_001369783.1| RluA family pseudouridine synthase [Ochrobactrum anthropi ATCC
           49188]
 gi|151560456|gb|ABS13954.1| pseudouridine synthase, RluA family [Ochrobactrum anthropi ATCC
           49188]
          Length = 334

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 88/346 (25%), Positives = 159/346 (45%), Gaps = 45/346 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ +  ++D    RLD+W      P ++   +Q ++  G V +D    +    +++ G  
Sbjct: 1   MKELTTDSDATGKRLDQWLAAALGPELSRSRVQSLIAEGHVTIDGAPAREAKQKLREGMT 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I               +L         ++ +   +LYED  + V NKPAG+ V  G+G
Sbjct: 61  IAI---------------VLPEPEPAEPIAENIPLDILYEDDDLIVINKPAGLVVHPGNG 105

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +    DS       ++P + HRLD++TSG++VVA+   + +HL+E F   
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGIRRPGIVHRLDKDTSGVMVVAKNDRSHRHLSEQFADH 165

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                +++ Y +LVWG+ +  +  I   L + SH       VV +  + A +AI+H+  +
Sbjct: 166 GRTGDLERAYLALVWGMTERPQGFIDAHLGR-SHRDRTKQAVVNEEREDARHAITHYVTV 224

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPI 284
           + FA           +E +  TGRTHQ+RVH  H+G P+VGD  Y + +K        P+
Sbjct: 225 EKFAPLEDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMDYGSAYKTKANKLPEPL 284

Query: 285 Q------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +      ++  LHA  +   HP     ++  AP+P  M    ++  
Sbjct: 285 KEAVRGFHRQALHAWLLAFTHPATEELMRFEAPVPEDMEHLLENFR 330


>gi|114562667|ref|YP_750180.1| pseudouridine synthase, RluA family protein [Shewanella
           frigidimarina NCIMB 400]
 gi|114333960|gb|ABI71342.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           frigidimarina NCIMB 400]
          Length = 318

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 108/323 (33%), Positives = 173/323 (53%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
                V+YV ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q 
Sbjct: 4   ETTPQVEYVTIDEDHFEQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQI 63

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VR+PPV  A     K       S NL++ S  L+  +++ED+ + V NKPAGI+V G
Sbjct: 64  GDIVRVPPVRVAEKDNRK-----APSPNLSRVSQ-LEDRIIHEDNHLIVLNKPAGIAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ Y +   L+S    +     L HRLD++TSG+L+VA+ R+A +HL E  R + +QK
Sbjct: 118 GSGVDYGVIEGLRSLRPQQKF-LELVHRLDKDTSGVLLVAKKRSALKHLHEQLRSKTMQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  +   + +   LLK +   G+ +  V    K    + + +K++  + Q   
Sbjct: 177 DYLALVRGEWQASDKVVKAPLLKITLKSGERIVRVN---KEGKESETRYKIMQRY-QGCT 232

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G  I  D KY    F  +  +   ++L+LHA  +   HP
Sbjct: 233 LVKASPVTGRTHQIRVHCQYAGHAIACDDKYSEQQFDDSMRALGLDRLFLHAAELKFTHP 292

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E    +Q+ APL   ++ T D L
Sbjct: 293 ENDEIMQVKAPLDPVLLSTLDKL 315


>gi|167758164|ref|ZP_02430291.1| hypothetical protein CLOSCI_00502 [Clostridium scindens ATCC 35704]
 gi|167664061|gb|EDS08191.1| hypothetical protein CLOSCI_00502 [Clostridium scindens ATCC 35704]
          Length = 304

 Score =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 146/326 (44%), Gaps = 36/326 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++  VEN ++  R+DR+        +   +QK+++   V V++K VK N R+  G  V I
Sbjct: 3   EFFTVEN-QDGERIDRYLSEELADRSRSYIQKLIKENYVTVNQKPVKANYRLSLGDRVEI 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           L  +       + +   +LYED  I + NKP  + V    G  +
Sbjct: 62  D---------------LPEAKEPDIRPEDIPLDILYEDKDIIIVNKPKQMVVHPAPG--H 104

Query: 128 HIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           +    + + +   G          +P + HR+D +T+G LV  +   A Q L+   +   
Sbjct: 105 YSQTLVNALMYHCGSDLSGINGTMRPGIVHRIDMDTTGSLVACKNDMAHQSLSRQLKEHS 164

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I++IY ++V G  K +   +   + +           +  + +    A++H++V++ F  
Sbjct: 165 IRRIYVAIVHGNIKEEYGTVNAPIGRHPTERKK----MSIHSRNGREAVTHYQVLERFGD 220

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            + ++  +  TGRTHQ+RVH   +G P++GD  Y          P      LHAR + + 
Sbjct: 221 -YTYIRCELETGRTHQIRVHMASLGHPLLGDGVYGPK---KCPFPPLQGQTLHARTLGII 276

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  L++ APLPA+ ++  D L 
Sbjct: 277 HPRTGEYLEVNAPLPAYFIELLDKLR 302


>gi|237746016|ref|ZP_04576496.1| ribosomal large subunit pseudouridine synthase C [Oxalobacter
           formigenes HOxBLS]
 gi|229377367|gb|EEO27458.1| ribosomal large subunit pseudouridine synthase C [Oxalobacter
           formigenes HOxBLS]
          Length = 340

 Score =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 111/328 (33%), Positives = 165/328 (50%), Gaps = 26/328 (7%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S M  V+ +    +E+  R+D +    +  +   ++ +ILRSG++RV+KKRV    RI++
Sbjct: 23  SQMRQVRLITATENEDGQRIDNYLFRTFKGVPKSHVYRILRSGEIRVNKKRVDQTYRIRT 82

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G ++RIPPV  A                  KH       +LYED  + V NKPAG++V G
Sbjct: 83  GDIIRIPPVKTAEQK--------------EKHIPPAGFDILYEDDSVLVINKPAGVAVHG 128

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG++Y +   L++      +   L HRLD+ETSGILV+A+ R+A   L E  R   + K
Sbjct: 129 GSGVSYGVIEQLRAMRPG-AKFLELVHRLDKETSGILVLAKKRSALTRLHEQIRDGSVDK 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  KN ++ +   LLK     G+    V   ++    + + F V+  +   F 
Sbjct: 188 RYQALVHGDWKNPRQHVRLPLLKYHTAEGERRVRV---DESGQASHTIFNVLKHYPD-FT 243

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQNKLYLHARYM 295
            LE +  TGRTHQ+RVH    G  I GD KY          KG        +++LHA  +
Sbjct: 244 LLEAELKTGRTHQIRVHLASSGFVIAGDDKYGDFELNRQLQKGKKGEDALKRMFLHAYKI 303

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HPE G+ L I+APLP   +    +L
Sbjct: 304 TFIHPETGKPLTISAPLPDECIGYLKTL 331


>gi|37519642|ref|NP_923019.1| pseudouridine synthase [Gloeobacter violaceus PCC 7421]
 gi|35210633|dbj|BAC88014.1| glr0073 [Gloeobacter violaceus PCC 7421]
          Length = 310

 Score =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 90/323 (27%), Positives = 144/323 (44%), Gaps = 34/323 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V+ D+  MRLDRW       ++   +Q ++  G V ++ +  +  + + SG  V + 
Sbjct: 10  TLTVQPDQSAMRLDRWLAEQVADLSRARIQALIDQGLVLLNNRPCRPRDLVHSGDAVALT 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                          + +   L   +  +   ++YED ++ V +KP G+ V    G    
Sbjct: 70  ---------------IPAPEPLAIEARPIALDIVYEDEELIVIDKPRGLVVHPAPGHSDD 114

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    +  G     +P + HRLD++T+G+LVVA+T  A QHL    + +  ++ 
Sbjct: 115 TLVNALLAHCRNLSGINGVLRPGIVHRLDKDTTGLLVVAKTDRAHQHLQTQIQAKTARRD 174

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFC 241
           Y +++ G P      I         IG   VH  K         A +H++V++     F 
Sbjct: 175 YLAIIAGAPAETTGTIDAP------IGRHPVHRQKMAVHPKGRPARTHWRVLERLG-NFT 227

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E    TGRTHQ+RVH LH G PI GD  Y +           N   LHA  +   HP 
Sbjct: 228 LVEFSLQTGRTHQIRVHCLHKGWPIAGDPLYGS----VKVPATLNGQALHAFRLGFEHPV 283

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G RL   +P+PA MVK  D+L 
Sbjct: 284 TGERLTFESPMPAEMVKLLDALR 306


>gi|56460456|ref|YP_155737.1| pseudouridylate synthase Rlu family protein [Idiomarina loihiensis
           L2TR]
 gi|56179466|gb|AAV82188.1| Predicted pseudouridylate synthase, Rlu family [Idiomarina
           loihiensis L2TR]
          Length = 315

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 95/323 (29%), Positives = 168/323 (52%), Gaps = 15/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           ++   V++  V  +E   R+D +       +    + +I+R G+VR +KKR+K + +++ 
Sbjct: 3   TIQQEVRWHTVSAEESGQRIDNFLIAQLRGVPKSLVYRIVRKGEVRANKKRIKPDYKLKE 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G ++RIPP        +K  +  D      +    L+  +LYED  + + NKP+G++V G
Sbjct: 63  GDLIRIPP--------VKVNERPDLPSANLEQVAALEHAILYEDDALMLINKPSGVAVHG 114

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ + +   L++ +  K +   L HR+D++TSG+L+VA+ R+  + L E  R + + K
Sbjct: 115 GSGLQFGLIEGLRA-LRPKEKSLELVHRIDRDTSGLLLVAKKRSVLRSLHEQLRNKEMNK 173

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  + +   +   L K +   G+ +  V   +     +++ F++   + +   
Sbjct: 174 QYLALVRGQWQKRVRSVEAPLKKNTLKSGERIVRV---DAEGKASLTRFRIQQRYKEG-T 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
            +E  P TGRTHQ+RVHALH G PI  D KY   +F    +    N+L+LHA  +   HP
Sbjct: 230 LVEASPVTGRTHQIRVHALHAGHPIAKDPKYGDTDFDNTMSRLGLNRLFLHAWQLRFLHP 289

Query: 301 EGG-RLQITAPLPAHMVKTWDSL 322
             G  +   APL  ++ +T   L
Sbjct: 290 VTGKEVAFEAPLDDNLQQTLKQL 312


>gi|288800657|ref|ZP_06406114.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 299 str. F0039]
 gi|288332118|gb|EFC70599.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 299 str. F0039]
          Length = 358

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 86/332 (25%), Positives = 149/332 (44%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V +  ++ +R+D++      H +   +QK   +G V V+ + VK N +I+   VV +  
Sbjct: 28  IVADEGQKPLRVDKFMFEKLQHSSRNRIQKAAEAGFVHVNDQPVKSNYKIRPNDVVTLML 87

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                ++ I+              ++ +   ++YED+++ V NKPAG+ V  G G  +  
Sbjct: 88  DRPRHDNTIE--------------AENIPLDIVYEDAELLVVNKPAGLVVHPGVGNFHGT 133

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+   +  L HR+D++TSG+LVVA+T  A   L   F  +   + 
Sbjct: 134 LINAVAWHMKDDKNFDANSPEVGLVHRIDKDTSGLLVVAKTPNAKTKLGVQFFNKTTTRS 193

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + +        + V   +      A++H+KVI+ F      
Sbjct: 194 YKALVWGHIAEDEGRIEGNIGRDPK-DRQRMTVFSPDSGIGKPAVTHYKVIERFG-YTTL 251

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKLYL 290
           +E    TGRTHQ+R H  H+G P+ GD +Y      +GN +S           I ++  L
Sbjct: 252 IECILETGRTHQIRAHMKHIGHPLFGDERYGGKEILRGNRSSSYKSFVQNCFNICDRQAL 311

Query: 291 HARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           HA+ +   HP        T+PLP  +    + 
Sbjct: 312 HAQTLGFVHPTTQKECHFTSPLPNDLDTMLNK 343


>gi|282881100|ref|ZP_06289787.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
 gi|281304904|gb|EFA96977.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
          Length = 355

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 86/332 (25%), Positives = 151/332 (45%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+ ++E +R+D++      H +   +QK   +G V V+ + VK N +++   V+ +  
Sbjct: 25  VVVDKNQEPLRIDKYMFERLKHSSRNRIQKAADAGFVHVNDQPVKSNYKVRPLDVITLML 84

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +  I+ ++I                 ++YED+++ V NKPAG+ V  G+G  +  
Sbjct: 85  DAPQHDSTIEAEEI--------------PLNIVYEDTEVMVVNKPAGMVVHPGAGNFHGT 130

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A   L   F  +   + 
Sbjct: 131 LINAVAWHLKDLPTFDANDPAVGLVHRIDKDTSGLLVIAKTPDAKTKLGLQFFNKTTHRS 190

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG    ++  I   + +        + V   +      AI+H++V++ F      
Sbjct: 191 YHALVWGNFNEEEGRIEGNIARDPK-DRLRMCVFPPDSAVGKTAITHYRVLERFG-YVTL 248

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQN------KLYL 290
           +E    TGRTHQ+R H  H+G P+ GD +Y             + + IQN      +  L
Sbjct: 249 IECILETGRTHQIRAHMKHIGHPLFGDERYGGMEILRGQRSSTYKAFIQNCLSLCHRQAL 308

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA+ +   HP+  R +  T+ LP  M +    
Sbjct: 309 HAKTLGFVHPKTNREMNFTSDLPEDMQQLLQK 340


>gi|291282106|ref|YP_003498924.1| Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O55:H7 str. CB9615]
 gi|290761979|gb|ADD55940.1| Ribosomal large subunit pseudouridine synthase C [Escherichia coli
           O55:H7 str. CB9615]
          Length = 319

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 104/328 (31%), Positives = 171/328 (52%), Gaps = 17/328 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMD 296
              +   P  GRTHQ+RVH  + G PI  D +Y     + +        N+ +LHA  + 
Sbjct: 229 ATLVRCSPVAGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRPFLHAAALK 288

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++I AP+   + +    L 
Sbjct: 289 FTHPGTGEVMRIEAPMDDGLKRCLQKLR 316


>gi|227872363|ref|ZP_03990714.1| pseudouridylate synthase [Oribacterium sinus F0268]
 gi|227841792|gb|EEJ52071.1| pseudouridylate synthase [Oribacterium sinus F0268]
          Length = 303

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 142/326 (43%), Gaps = 39/326 (11%)

Query: 12  VENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V  +EE  RLD++      H  +   L K ++ G V V+ ++ K + ++++G  +     
Sbjct: 5   VAKEEEGQRLDKYLSEQKDHDFSRSYLGKCIQEGCVSVNGEKAKASLKVKAGDRIDFDIP 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 ++ E   LD               ++YED  + V NK  G+ V   +G   H  
Sbjct: 65  EQKDPEVLPEAIPLD---------------IVYEDDDLLVVNKERGMVVHPAAG---HYS 106

Query: 131 GFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G L + V +             +P + HR+D++T+G+L++ +   + Q L +      I 
Sbjct: 107 GTLVNAVLAHAGSSLSSINGVNRPGIVHRIDKDTTGLLLICKNDLSHQSLAKQLEEHSIT 166

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV+G  K +   I+  + +            K        A++H+KV++ F+   
Sbjct: 167 RRYHALVFGKIKEEDGIISAPIGRDEKDRKKQAISYKH----GKEALTHYKVLERFSDS- 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E +  TGRTHQ+RVH   +G P++GD  Y    + +      +   LHA  +   HP
Sbjct: 222 TLVECRLETGRTHQIRVHMKSIGHPLLGDPVYGLKNRKD----GISGQALHAMILGFQHP 277

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFK 325
             G  ++ +AP PA      + L  K
Sbjct: 278 RTGEYMEFSAPYPADFQALLEKLRKK 303


>gi|260776340|ref|ZP_05885235.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260607563|gb|EEX33828.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 314

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 107/326 (32%), Positives = 183/326 (56%), Gaps = 17/326 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V ++ D    R+D + +N    I    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MSEIRTKVQFVDIDEDMAGQRIDNFLRNQLKSIPKSMVYRILRKGEVRVNKKRIKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VRIPP       I ++Q  +  S  L K ++ L+ ++++ED  + + NKP+G +V
Sbjct: 61  KAGDLVRIPP-----VTIEEKQDEVAPSTKLNKVAE-LEHMIIHEDEHMLILNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y++LV G  K+  + +   LLK        V+ + +       + + FK+I+ FA+ 
Sbjct: 174 QKYYFALVMGQWKSSCKVVNAPLLKNE------VNSIVRVNPQGKPSETRFKIIEKFAE- 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKFK 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP     ++++AP+ A + K   SL 
Sbjct: 287 HPSNDEWMEVSAPMEAKLEKALASLR 312


>gi|328957532|ref|YP_004374918.1| pseudouridylate synthase [Carnobacterium sp. 17-4]
 gi|328673856|gb|AEB29902.1| pseudouridylate synthase [Carnobacterium sp. 17-4]
          Length = 301

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 83/316 (26%), Positives = 148/316 (46%), Gaps = 33/316 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +EE+ RLD+   +  P I   ++Q+ ++ G V V+ +++K N ++Q G  + I       
Sbjct: 10  NEESGRLDKVLTDLLPSITRSHIQQWIKEGNVSVNGEKMKANYKVQPGDEIAI------- 62

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGF 132
                   +    V+L   ++ +   ++Y+D  + V NK  G+ V   +G      ++  
Sbjct: 63  --------VEPELVSLEVLAEDIPIEIVYQDEDVVVVNKAQGMVVHPSAGHQTGTLVNAL 114

Query: 133 LKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +    D  G     +P + HR+D++TSG+L+VA+  AA + L    + +   + Y +LV 
Sbjct: 115 MHHITDLSGINGTIRPGIVHRIDKDTSGLLMVAKNDAAHEKLAAQLKDKTSLREYIALVH 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+  ++K  I   L + S        ++     G   A++HF V++ F + F  + ++  
Sbjct: 175 GVIPHEKGTIDAPLGR-SKQDRKKQDIID----GGRAAVTHFTVLERF-KDFTLVSLKLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  ++G P+ GD  Y         +      +LHA  +   HP  G  L  
Sbjct: 229 TGRTHQIRVHMKYIGYPLAGDPIYGPR-----KTLEGKGQFLHATTLGFKHPTSGEFLTF 283

Query: 308 TAPLPAHMVKTWDSLG 323
            APLP     T + L 
Sbjct: 284 EAPLPKLFEDTLNDLR 299


>gi|323495017|ref|ZP_08100106.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           brasiliensis LMG 20546]
 gi|323310674|gb|EGA63849.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           brasiliensis LMG 20546]
          Length = 319

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 106/326 (32%), Positives = 181/326 (55%), Gaps = 17/326 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V +++D    R+D + +NH   I    + +ILR G+VRV+KKRVK   ++
Sbjct: 1   MSEIRTKVQFVDIDDDMAGQRIDNFLRNHLKSIPKSMVYRILRKGEVRVNKKRVKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +VRIPP       I ++ + +  S  L K ++ L+ +++YED  + + NKP+G +V
Sbjct: 61  KAGDLVRIPP-----VTIEEKAQEVAPSTKLNKVAE-LEHMIIYEDDHMLILNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPEARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y++LV G  K+  + +   LLK        V+ + +       + + FK+++ FA  
Sbjct: 174 KKFYFALVMGQWKSSCKVVNAPLLKNE------VNSIVRVNPNGKASETRFKILEKFAD- 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKFQ 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP     ++I AP+   + K    L 
Sbjct: 287 HPSNDEWMEINAPMEPKLEKVLKGLR 312


>gi|254785800|ref|YP_003073229.1| ribosomal large subunit pseudouridine synthase C [Teredinibacter
           turnerae T7901]
 gi|237685873|gb|ACR13137.1| ribosomal large subunit pseudouridine synthase C [Teredinibacter
           turnerae T7901]
          Length = 314

 Score =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 101/324 (31%), Positives = 168/324 (51%), Gaps = 17/324 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    VQ+  + +D    R+D +            + +I+R G+VRV+K RVK   ++ 
Sbjct: 1   MSQ--QVQFFTITDDNAGQRIDNFLVARLKGAPKSLIYRIIRRGEVRVNKGRVKPERKLA 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G +VR+PP+      + +      +  +L      L+  +LYE  ++ V NKP+G++V 
Sbjct: 59  VGDLVRVPPI-----RLAEPDAPTPAGKSLLL---ALEDAVLYETDQLLVVNKPSGLAVH 110

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRI 179
           GGSG+   +   ++  + +K     L HRLD+ETSG +++AR R+  ++L + FR  +++
Sbjct: 111 GGSGVNLGLIEAIRQ-LKAKDTALELVHRLDRETSGCILIARKRSMLRYLQDLFRGEKQV 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G   N+   +   LLK     G+ +            + + F V++ F + 
Sbjct: 170 DKRYQALVKGRWPNRAHSVNVPLLKGEVGNGERIVRA---SPEGKPSRTEFDVLERF-ES 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +E +P TGRTHQ+RVHA + G P+VGD KY  + F    +     +L+LHA Y+ +P
Sbjct: 226 ATLIEARPITGRTHQIRVHAQYKGHPLVGDDKYGDDEFNKVMSQFGSRRLFLHAGYLGVP 285

Query: 299 HPEGGRLQITAPLPAHMVKTWDSL 322
            P+G  L+  APLP  +  T   L
Sbjct: 286 MPDGEYLEFRAPLPDDLQATLKQL 309


>gi|313499940|gb|ADR61306.1| RluA family pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 318

 Score =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 104/319 (32%), Positives = 170/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + VQ + V  +    R+D +       +    + +ILR G+VRV+K RVK   +IQ+G +
Sbjct: 9   SGVQLIEVAPELAGQRIDNFLITALKGVPKTLVYRILRKGEVRVNKGRVKPEYKIQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP       + +  +    +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRVPP-----VRLPERDEPAPVAQGLLQR---LEAAIVYEDKALIVMNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L+  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y 
Sbjct: 121 LSFGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     K+ +   LLK +   G+ +  V         A++ F+V+  F      +E
Sbjct: 180 ALVRGHWPTSKKQVNAPLLKSNLRSGERMVEVNDE---GKEALTLFRVLRRFGDFATIVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   +F          +L+LHA  + +P P+GG
Sbjct: 237 ARPITGRTHQIRVHTLHAGHMIAGDSKYGDEDFSREIRELGGKRLFLHAYALTVPLPDGG 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
            L++ AP+     KT + L
Sbjct: 297 ELKLEAPVDEVWAKTVERL 315


>gi|313896045|ref|ZP_07829599.1| pseudouridine synthase, RluA family [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312975470|gb|EFR40931.1| pseudouridine synthase, RluA family [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 301

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 85/317 (26%), Positives = 141/317 (44%), Gaps = 31/317 (9%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            D    RLD +      + +   +Q+++  G VRVD   VK N +++SG+ +        
Sbjct: 6   ADCAGERLDVFLARQIENCSRSYVQRLITDGNVRVDGAPVKPNYKLRSGEEICCT----- 60

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
                     +  +  +   ++ +   +LYED  I V NK  G+ V   +G      ++ 
Sbjct: 61  ----------VPPAEEVVIAAEDIPLDVLYEDEDIIVINKARGMVVHPAAGNLTGTLVNA 110

Query: 132 FLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    D  G     +P + HRLD++TSG++V A+   A   L +  R +  ++ Y +LV
Sbjct: 111 LLFRCRDLSGINGELRPGIVHRLDKDTSGVMVAAKNDMAHHFLAQQIRSKDARREYRALV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    +   I   + +        + +V+    G   A +HF+V++ F   +  +    
Sbjct: 171 HGNIAERAGVITGDIGRH-PTDRKRMAIVRS---GGKSATTHFEVLERFGD-YTLVSCVL 225

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            TGRTHQ+RVH   +G P+VGD KY A           +   LH+  + L HP  G +++
Sbjct: 226 ETGRTHQIRVHMTSIGHPLVGDAKYTA----MKNPFGIHGQALHSHILTLAHPRTGAQMR 281

Query: 307 ITAPLPAHMVKTWDSLG 323
            TAPLPA M      L 
Sbjct: 282 FTAPLPADMEDILHRLR 298


>gi|293610198|ref|ZP_06692499.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292827430|gb|EFF85794.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 310

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 95/317 (29%), Positives = 162/317 (51%), Gaps = 19/317 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   +++ G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLEIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAAPVSDSVAQSLLSRVVYEDEGLLVINKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y ++
Sbjct: 123 YGLIEALRAATGKKY--LELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     K+ I   L +     G+    V    K    + + + V + F +    +   
Sbjct: 181 VKGQVSLDKQLIDAPLFRYELANGERRVRV---SKEGKPSKTEWVVAERF-KNATLVHAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P++GD KY       ++ P   +L LHA  +D+P    G   
Sbjct: 237 PLSGRTHQIRVHGLSIGHPLLGDDKYG--HTTEYSGPQARRLCLHAMRLDIP----GYPP 290

Query: 307 ITAPLPAHMVKTWDSLG 323
           I APLP  M +   +L 
Sbjct: 291 IEAPLPEDMTQLLKALR 307


>gi|258515575|ref|YP_003191797.1| pseudouridine synthase, RluA family [Desulfotomaculum acetoxidans
           DSM 771]
 gi|257779280|gb|ACV63174.1| pseudouridine synthase, RluA family [Desulfotomaculum acetoxidans
           DSM 771]
          Length = 305

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 87/314 (27%), Positives = 147/314 (46%), Gaps = 31/314 (9%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD +  N YP I+   LQ+++  G V ++ K+V    +I+ G  + +        
Sbjct: 11  EIGQRLDVYLSNCYPDISRSQLQRLIAQGLVEINGKKVAAKYKIKPGDYINLT------- 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                   +   V ++  ++ +   + +ED  + V NKP G+ V    G      ++  L
Sbjct: 64  --------IPDPVGVSVEAENIALDIYFEDEDVIVINKPRGMVVHPAEGNYTGTMVNALL 115

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D  G     +P + HRLD++TSG+L+VA+   A  +L      R + + Y +LV G
Sbjct: 116 YHCRDLSGINGVLRPGIVHRLDKDTSGLLMVAKNDLAHNNLAAQLEKRLVNRRYLALVHG 175

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             K     +   + + +      + V  +N   +  A++HFKV+  F + +  LE++  T
Sbjct: 176 NLKQDAGTVDAPIGRDA-CSRQKMAVTDRN---SRSAVTHFKVLKRFGR-YTLLELKLET 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G  +VGD KY  +          +  +LHA  +   HP  G+ L+  
Sbjct: 231 GRTHQIRVHMKYIGYQVVGDPKYGPSKP----HFNLDGQFLHACLLGFAHPRTGKYLEFN 286

Query: 309 APLPAHMVKTWDSL 322
           APLP  +VK    L
Sbjct: 287 APLPDILVKVLAEL 300


>gi|254508499|ref|ZP_05120618.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus 16]
 gi|219548611|gb|EED25617.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus 16]
          Length = 314

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 106/326 (32%), Positives = 180/326 (55%), Gaps = 17/326 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V +++D    R+D + +N    I    + +ILR G+VRV+KKRVK   ++
Sbjct: 1   MSEIRTKVQFVDIDDDMAGQRIDNFLRNQLKSIPKSMVYRILRKGEVRVNKKRVKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G +VRIPP       + ++   +  S  L K ++ L+ +++YED  + + NKP+G +V
Sbjct: 61  QAGDLVRIPP-----VTMEEKTDEIAPSTKLNKVAE-LEHMIIYEDDHMLILNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  K +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPKARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y++LV G  K+  + +   LLK        V+ + +       + + FK+I+ F+  
Sbjct: 174 KKFYFALVMGQWKSSCKVVNAPLLKNE------VNSIVRVNPNGKASETRFKIIEKFSD- 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  +   
Sbjct: 227 ATLVQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKVGLDRLFLHAANIKFQ 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP     ++I AP+ A + +    L 
Sbjct: 287 HPSNDEWMEINAPMEAKLERVLAGLR 312


>gi|110635475|ref|YP_675683.1| ribosomal large subunit pseudouridine synthase D [Mesorhizobium sp.
           BNC1]
 gi|110286459|gb|ABG64518.1| ribosomal large subunit pseudouridine synthase D [Chelativorans sp.
           BNC1]
          Length = 343

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 87/345 (25%), Positives = 152/345 (44%), Gaps = 45/345 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           + ++ +   E  RLD+W      P  +   +Q ++R G V ++ + V +   ++ +G+  
Sbjct: 13  KELLADEKAEGNRLDQWLAARLAPDFSRSRIQALIREGAVTLNGRTVAEPKRKVAAGEFY 72

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            I                L          + +   +LYED  + V +KPAG+ V  G G 
Sbjct: 73  CIT---------------LPEPEAPEPQGEDIPLDILYEDEALIVIDKPAGLVVHPGPGN 117

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR- 177
                ++  +    D+       ++P + HRLD++TSG++VVA+T  A + L E+F    
Sbjct: 118 WTGTLVNALIHHCGDTLSGIGGVRRPGIVHRLDRDTSGVMVVAKTDQAHRVLAEAFADHG 177

Query: 178 ---RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y +LVWG+P+     +   L + +        VV Q    A +A++H+ V++
Sbjct: 178 QDGDLERAYVALVWGVPRRISGLVDAPLGRSAS-DRTLRAVVPQGRADARHAVTHYTVLE 236

Query: 235 CFA------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------ 282
            +       Q    +E +  TGRTHQ+RVH  H+G P+VGD  Y   F+           
Sbjct: 237 RYGTGTPEEQIAALVECRLETGRTHQIRVHMAHIGHPLVGDPAYGRAFRTKANRLPPALA 296

Query: 283 ---PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                  +  LHAR +   HP  G+ ++  A +PA M        
Sbjct: 297 EMVAAFPRQALHARLLAFRHPVSGKIMRFEAAIPADMENLLKGFA 341


>gi|227890823|ref|ZP_04008628.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
 gi|227867232|gb|EEJ74653.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
          Length = 301

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 84/328 (25%), Positives = 141/328 (42%), Gaps = 36/328 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  M+  + +    D+   RLD+   N +       L+K++  G ++V+    K N ++ 
Sbjct: 1   MKKMSDYKVL---ADKTG-RLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGDVKKANYKVN 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  +                        L+   + +   ++YED  + V NKP G+ V 
Sbjct: 57  LGDEITFD---------------KPEVKKLSLEPENIPLDIVYEDDDVIVVNKPQGMVVH 101

Query: 121 GGSGIAYHI--DGFLKSWVDS---KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
              G   H   +  L     S      +P + HR+D++TSG+L+VA+   A Q L +  +
Sbjct: 102 PSPGHFEHTLVNALLYHSPLSTINGTYRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLK 161

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +   + Y +LV G  K     I   L + S +      VV    K    A++HF+V+  
Sbjct: 162 DKTNTREYVALVHGNIKEDSGTIDAPLGR-SKVDRKKQAVV----KDGRNAVTHFEVLKR 216

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           +   +  ++    TGRTHQ+RVH  ++G P+VGD  Y         +   +  +LHA  +
Sbjct: 217 YGD-YTLVKCVLETGRTHQIRVHMKYIGHPLVGDQLYGPR-----KTLGNSGQFLHAEKL 270

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP     L+ TAPLP +  K  + L
Sbjct: 271 GFIHPRTNEYLEFTAPLPENFKKLLELL 298


>gi|308069860|ref|YP_003871465.1| RNA pseudouridine synthase (RNA-uridine isomerase) [Paenibacillus
           polymyxa E681]
 gi|305859139|gb|ADM70927.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Paenibacillus polymyxa E681]
          Length = 334

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 76/317 (23%), Positives = 137/317 (43%), Gaps = 32/317 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +  +R+D++       ++   +Q  + +G+V V+   +K N ++  G  + +        
Sbjct: 43  DAKIRIDKYIAEEMKEVSRSQIQMWIGNGRVLVNGTAIKANYKLAEGDRIVLSVPEPESV 102

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL 133
            I+ E   LD               ++YEDS + V NK  G+ V    G      ++  +
Sbjct: 103 DIVPENIPLD---------------VVYEDSDVIVINKQRGLVVHPAPGHSSGTLVNALM 147

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D  G     +P + HR+D++TSG+L+ A+   A   L    +   + + Y +LV G
Sbjct: 148 YHCHDLSGINGELRPGIVHRIDKDTSGLLMAAKNDQAHASLAAQLKDHSVTRKYIALVHG 207

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              + +  +   + + S        +    E+ + +A++HF VI+     +  LE+Q  T
Sbjct: 208 HLSHDQGTVDAPIGRDSGDRK----LFTVTERNSKHAVTHFLVIERLGD-YTLLELQLET 262

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH   +G P+VGD  Y  +              LHA  +   HP  G  ++ +
Sbjct: 263 GRTHQIRVHMKFIGHPLVGDPMYGRSKGVRME-----GQALHAAVLGFKHPSTGEYMEFS 317

Query: 309 APLPAHMVKTWDSLGFK 325
            P+P  M     SL  +
Sbjct: 318 RPIPPDMEDVLASLRSR 334


>gi|256959131|ref|ZP_05563302.1| pseudouridylate synthase [Enterococcus faecalis DS5]
 gi|256949627|gb|EEU66259.1| pseudouridylate synthase [Enterococcus faecalis DS5]
          Length = 301

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 85/324 (26%), Positives = 151/324 (46%), Gaps = 33/324 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  + 
Sbjct: 1   MEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDEIV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +          I E ++LD        ++ +   ++YED+ + V NKP  + V   +G  
Sbjct: 61  VT---------IPEPEVLD------MVAEDIPLTIVYEDNDVIVVNKPQDMVVHPSAGHP 105

Query: 126 -AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L             +P + HR+D++TSG+L+VA+   A + L +  + +   
Sbjct: 106 KGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSL 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ F   F
Sbjct: 166 RKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLERF-DAF 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   HP
Sbjct: 220 TLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLLGFTHP 274

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  L   APLP    KT   L 
Sbjct: 275 TTGEQLVFEAPLPEVFEKTLHQLR 298


>gi|194098000|ref|YP_002001048.1| RluD [Neisseria gonorrhoeae NCCP11945]
 gi|239998466|ref|ZP_04718390.1| RluD [Neisseria gonorrhoeae 35/02]
 gi|240112385|ref|ZP_04726875.1| RluD [Neisseria gonorrhoeae MS11]
 gi|254493184|ref|ZP_05106355.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae 1291]
 gi|268594325|ref|ZP_06128492.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae 35/02]
 gi|268598444|ref|ZP_06132611.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae MS11]
 gi|193933290|gb|ACF29114.1| RluD [Neisseria gonorrhoeae NCCP11945]
 gi|226512224|gb|EEH61569.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae 1291]
 gi|268547714|gb|EEZ43132.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae 35/02]
 gi|268582575|gb|EEZ47251.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae MS11]
          Length = 374

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 138/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPPELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     +  VK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAAVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 250 LGTGRTHQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|152979496|ref|YP_001345125.1| 23S rRNA pseudouridylate synthase C [Actinobacillus succinogenes
           130Z]
 gi|150841219|gb|ABR75190.1| pseudouridine synthase, RluA family [Actinobacillus succinogenes
           130Z]
          Length = 319

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 102/322 (31%), Positives = 173/322 (53%), Gaps = 15/322 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G ++R
Sbjct: 10  VKMLQISDDEAGQRIDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQAGDIIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +       +K    S  L K +  L+  +++ED  + V NKP+GI+V GGSG++
Sbjct: 70  VPPVRIS-------EKETPVSTKLNKVAQ-LEQQIIFEDDCLLVLNKPSGIAVHGGSGLS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +    +   L HRLD++TSGIL+VA+ R+  ++L E  R++ +QK Y +L
Sbjct: 122 FGVIEGLRA-LRPHARFLELVHRLDRDTSGILLVAKKRSVLRNLHEQLRLKTVQKDYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK    GG+ +  V +       + + F V + +A     ++  
Sbjct: 181 VRGQWQSHVKAVKAPLLKNELSGGERMVRVSEQ---GKPSETRFSVEERYAD-ATLVKAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHA + G PI  D KY    F     +   N+L+LHA  +   HP+ G  
Sbjct: 237 PVTGRTHQIRVHAQYAGHPIAMDDKYGDRNFDAGMAALGLNRLFLHAANIRFEHPKTGEP 296

Query: 305 LQITAPLPAHMVKTWDSLGFKY 326
           L++ APL   M      L  + 
Sbjct: 297 LRLNAPLDDKMKAVLKKLREQA 318


>gi|209963759|ref|YP_002296674.1| RNA pseudouridine synthase [Rhodospirillum centenum SW]
 gi|209957225|gb|ACI97861.1| RNA pseudouridine synthase [Rhodospirillum centenum SW]
          Length = 336

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 129/324 (39%), Positives = 193/324 (59%), Gaps = 6/324 (1%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V+  +V +DE  +RLDRWFK HYP ++ + LQK+LR+GQVRVD KR + + R+  GQ V
Sbjct: 8   QVETRLVGDDEGEVRLDRWFKRHYPLLSHIQLQKLLRTGQVRVDGKRAEASTRLLPGQSV 67

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP+ +A        K         + +  L++ +L+ D  + V +KPAG++ QGG+  
Sbjct: 68  RIPPLPDAPPPDAVRPKARPEVDE--RAAKELRARVLFRDHDVIVLDKPAGLATQGGTNQ 125

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+D  L +       +P+L HRLD++TSG LV+AR+ AAA  LT +FR R  +KIYW+
Sbjct: 126 VKHLDAMLDALKFEAEGRPKLVHRLDKDTSGCLVLARSAAAAAKLTAAFRSREARKIYWA 185

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G+PK  K  I   + K++   G+ + V   +E    +AI+++ V++   ++  ++ +
Sbjct: 186 VTVGVPKPMKGRIDLPVAKEAGTRGERMTV---DEDEGVHAITYYTVLEHAHKQAAFVAL 242

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHPEGGR 304
            P TGRTHQLRVH   +G PI+GD KY         +    + L+LHAR + LPHP GG 
Sbjct: 243 WPRTGRTHQLRVHMAALGTPILGDGKYAGQGAFLEGAGDLPRQLHLHARRIILPHPRGGV 302

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           + +TAPLP HM   WD  GF+  R
Sbjct: 303 IDVTAPLPKHMRPAWDYFGFEDKR 326


>gi|160933118|ref|ZP_02080507.1| hypothetical protein CLOLEP_01961 [Clostridium leptum DSM 753]
 gi|156868192|gb|EDO61564.1| hypothetical protein CLOLEP_01961 [Clostridium leptum DSM 753]
          Length = 306

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 144/327 (44%), Gaps = 32/327 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+    +V+   EE +RLD+      P +    +Q++L   QV ++ K    N + ++G 
Sbjct: 1   MSEPVELVLSEREEGIRLDKVLAERLPDLTRTAIQRLLEEEQVLINGKPAAKNRKGRAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +                +     L   ++ +   ++YED  + V NKP G+ V    
Sbjct: 61  SVALR---------------IPDPEPLCLQAENVPLDIVYEDDDLLVVNKPQGMVVHPAP 105

Query: 124 GI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  L    +S        +P + HR+D++TSG+L+VA+   A Q L    + 
Sbjct: 106 GNYQGTLVNALLAHCGNSLSGINGVIRPGIVHRIDKDTSGLLMVAKNDFAHQGLARQIKE 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
              ++ Y ++V G  K +   +   + +   I    + V    EK +  A+++F+VI  +
Sbjct: 166 HSFRREYEAVVAGRMKQESGVVNAPIGRH-PIDRKKMAV---TEKNSKEAVTYFRVIAEY 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  + ++  TGRTHQ+RVH  ++G P+ GD  Y                 LHAR + 
Sbjct: 222 P-GYTHIRLRLETGRTHQIRVHMAYLGHPVAGDPAYGPRKP----DLGLKGQCLHARLIG 276

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  GR L+  +PLP +  +    L
Sbjct: 277 FVHPRDGRYLEFESPLPDYFTRLLTKL 303


>gi|77920540|ref|YP_358355.1| suppressor of ftsH mutation [Pelobacter carbinolicus DSM 2380]
 gi|77546623|gb|ABA90185.1| ribosomal large subunit pseudouridine synthase D [Pelobacter
           carbinolicus DSM 2380]
          Length = 326

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 80/345 (23%), Positives = 150/345 (43%), Gaps = 35/345 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  +    +    RLDR+     P ++   L+K++  G+V +D    K  ++++ G+
Sbjct: 1   MGQLFTLCFGRERSPERLDRFLVEQLPELSRSQLKKLIDDGRVLLDGAAAKPGSKLKGGE 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +         S+ +  ++LYED  + V +KP G+ V    
Sbjct: 61  TLTVD---------------VPDPSPAEAVSEDIPLVILYEDRHLIVIDKPPGMVVHPAP 105

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HRLD++TSG++V  +T +A Q L   F+  
Sbjct: 106 GHYQGTLVNALLHHCQDLSGIGGELRPGIVHRLDKDTSGVMVATKTDSAHQSLAAQFKAH 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF- 236
            I + Y +L+ G+    +  I   + +            +       +A++H++V+  F 
Sbjct: 166 SITRRYIALIHGVLTGDRGSIDRPIGRHPTHRKKMSTTCR----TGRHAVTHWRVLRRFD 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--------NFKGNFTSPIQNKL 288
             +   +E+   TGRTHQ+RVH      P++GD  Y          + +    +    + 
Sbjct: 222 DDRLTLVELALETGRTHQIRVHFSEQQHPLLGDPVYGGSGRLKTINDPQLLKRAKALGRQ 281

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            LHAR +   HPE G+ L+ ++PLP  +    D L  KY +  ++
Sbjct: 282 ALHARLLGFQHPETGKYLEFSSPLPEDLRSVIDYLTEKYGQPPFV 326


>gi|88859600|ref|ZP_01134240.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas tunicata D2]
 gi|88818617|gb|EAR28432.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas tunicata D2]
          Length = 320

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 97/324 (29%), Positives = 170/324 (52%), Gaps = 14/324 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V +  V  D +  R+D +       +    + +ILR G+VRV+KKR+K   ++  G  
Sbjct: 7   TQVIFHTVTEDHDGQRIDNFLITKLKGVPKSAIYRILRKGEVRVNKKRIKPIYKLNIGDE 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+      + ++++ +  ++++      L+  +L+ED  + V NKPAG++V GGSG
Sbjct: 67  VRIPPI-----KMAEQEEFVPKNLDVISR---LEDAILFEDKYLIVINKPAGMAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++Y +   +++    +     L HRLD++TSG L++++ R+  + L E  R + +QK YW
Sbjct: 119 LSYGLIEAMRTLRPQET-ALELVHRLDRDTSGCLLISKKRSVLKSLHEQLREKTMQKNYW 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   +K + +   L K +   G+   VV+ + +    + + F+V++ F      ++
Sbjct: 178 ALVSGEWLSKDKNVTEPLRKNTLQSGER--VVRVDHEEGKASHTRFRVLERFRDG-TLVQ 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH    G PI  D KY    F         N+L+LHA  +   HP+  
Sbjct: 235 ASPVTGRTHQIRVHTQCKGHPIACDDKYGDTEFDQKMKGFGLNRLFLHAHDLTFYHPKLE 294

Query: 304 R-LQITAPLPAHMVKTWDSLGFKY 326
           + + + APL   + +T   L   +
Sbjct: 295 QDMTVEAPLDETLKRTIVRLRADH 318


>gi|220909998|ref|YP_002485309.1| RluA family pseudouridine synthase [Cyanothece sp. PCC 7425]
 gi|219866609|gb|ACL46948.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7425]
          Length = 313

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 88/325 (27%), Positives = 152/325 (46%), Gaps = 33/325 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVV 65
           ++ +    +E   RLDR+     P ++   +Q+++  GQV V+ +  +     +Q G  +
Sbjct: 1   MEIITTAGNE---RLDRYLAAQLPDLSRSRIQQLIEQGQVYVNGQLCQAKKQIVQVGDRI 57

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           ++                L   V      + +   +LYED ++ + NKPAG+ V    G 
Sbjct: 58  QLE---------------LPPPVAAEPLPEHIPLDILYEDDQLLIVNKPAGLVVHPAPGH 102

Query: 126 --AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++  L    D  G    Q+P + HRLD++TSG + +A+T  A +HL    + +  
Sbjct: 103 SGGTLVNALLAHCGDLPGIGGVQRPGIVHRLDKDTSGAIAIAKTELAHRHLQAQIKAKTA 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y  +V+G+PK     I   + +   +    + VV  ++     A++H+++ +     
Sbjct: 163 RREYLGVVYGVPKTSSGRIDLPIGRH-PVDRKKMAVVASDK--GRSAVTHWQIQERLG-N 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           F  L+ Q  TGRTHQ+RVH   +G PIVGD  Y +   G+ T        LHA  + L H
Sbjct: 219 FTLLQFQLETGRTHQIRVHIAQLGHPIVGDPLYSS---GHATGVNLTGQALHAWKLALQH 275

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLG 323
           P  G  + +TAPLP  + K  + L 
Sbjct: 276 PVTGATIAVTAPLPPELTKLLEVLR 300


>gi|330811001|ref|YP_004355463.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327379109|gb|AEA70459.1| Ribosomal large subunit pseudouridine synthase C [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 322

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 102/319 (31%), Positives = 169/319 (52%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ + V  +    R+D +       +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 13  PGVQLLEVSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDI 72

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 73  VRVPP-----VRVPERDEPVPLAQGLLQR---LEASIIYEDKALIVINKPAGIAVHGGSG 124

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL E  R   + K Y 
Sbjct: 125 LNFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHEQLRGDGVDKRYM 183

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  +   + +   LLK +   G+ +  V +       A++ FKV+  F      +E
Sbjct: 184 ALVRGRWETSIKQVRAPLLKSNLRSGERMVEVNEE---GKEALTVFKVLRRFDDFATLIE 240

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   +F          +L+LHA  + +P P+GG
Sbjct: 241 AKPVTGRTHQIRVHTLHAGHCIAGDSKYGDDDFTKEIRDLGGKRLFLHAYMLTVPLPDGG 300

Query: 304 RLQITAPLPAHMVKTWDSL 322
            L++ AP+     KT + L
Sbjct: 301 ELKLQAPVDDMWAKTVERL 319


>gi|330962632|gb|EGH62892.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. maculicola str. ES4326]
          Length = 318

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 104/319 (32%), Positives = 171/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 9   PGVQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRIPP-----VRVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y 
Sbjct: 121 LSFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     ++ +   LLK +   G+ +  V +       A++ FKV+  F      +E
Sbjct: 180 ALVRGNWATAQKQVRAPLLKSNLRSGERMVEVNEE---GKEALTLFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   NF          +L+LHA  + +P P+G 
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHAIAGDTKYGDENFSREIRDLGGKRLFLHAYMLTVPMPDGS 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L + AP+     KT + L
Sbjct: 297 KLNVQAPVDEMWAKTVERL 315


>gi|325202501|gb|ADY97955.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M01-240149]
 gi|325207748|gb|ADZ03200.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis NZ-05/33]
          Length = 374

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 140/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T +A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|332535383|ref|ZP_08411176.1| ribosomal large subunit pseudouridine synthase C [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332035211|gb|EGI71720.1| ribosomal large subunit pseudouridine synthase C [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 319

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 101/320 (31%), Positives = 166/320 (51%), Gaps = 14/320 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V YV +  D    R+D +   H   +    + K+LR G+VRV+KKR+K   ++Q   V+
Sbjct: 8   QVTYVTINEDHLGQRIDNFLITHLKGVPKSAIYKLLRKGEVRVNKKRIKPVYKLQLDDVL 67

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RI P+      + + ++ + S ++       L++ +L+ED  + V NKP+G++V GGSG+
Sbjct: 68  RIAPI-----RVAEREEFVPSKLDKVTR---LENDILFEDKYLIVINKPSGMAVHGGSGL 119

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +Y +   L++    + +   L HRLD++TSG L++A+ R+    L E  R + ++K YW+
Sbjct: 120 SYGLIEALRALRPEE-RSLELVHRLDRDTSGCLLIAKRRSVLTALHEQLREKTMEKNYWA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   +K + +   L K +   G+ V  V   E     + + FKV++ F      ++ 
Sbjct: 179 LVEGQWDSKTKNVTEGLRKNTLKSGERVVRVDNTE--GKPSHTRFKVLERFND-CSLVQA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
            P TGRTHQ+RVH    G PI  D KY    F  +      N+L+LHA  +   HP+   
Sbjct: 236 SPVTGRTHQIRVHTQCKGHPIACDDKYGDQGFDESMRKVGLNRLFLHAHDLSFYHPKNET 295

Query: 304 RLQITAPLPAHMVKTWDSLG 323
            ++I APL   +  T   L 
Sbjct: 296 TMRIEAPLDKTLKNTLLKLR 315


>gi|330446422|ref|ZP_08310074.1| 23S rRNA pseudouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328490613|dbj|GAA04571.1| 23S rRNA pseudouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 314

 Score =  271 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 98/321 (30%), Positives = 170/321 (52%), Gaps = 16/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ++ + +D    R+D + +    ++    + +ILR G+VRV+KKR+K   ++Q G +
Sbjct: 6   PKVQFIDINDDFAGQRIDNFLRARLKNVPKSMIYRILRKGEVRVNKKRIKPEYKLQDGDL 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP+      + ++++    S  L K ++ L+  ++YED  + + NKP+G +V GGSG
Sbjct: 66  VRVPPIF-----VPEKEEQEQVSTKLNKVAE-LEHCIIYEDDHMLILNKPSGTAVHGGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + +QK Y+
Sbjct: 120 LKFGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRKLQEQFRNKTVQKYYF 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  K   + +   LLK        V+ + +       + + FKV++ F Q    ++
Sbjct: 179 ALVMGEWKASCKKVTAPLLKNE------VNSIVRVNPQGKPSDTRFKVLERFPQ-ATLVQ 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D +Y    F          +L+LHA  +   HP   
Sbjct: 232 ASPVTGRTHQIRVHCQYEGHPIAWDDRYGDPRFDAYTKKTGLGRLFLHAANIKFTHPNTD 291

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             + I+AP+   + +    L 
Sbjct: 292 EMMDISAPMEPVLERCLAKLR 312


>gi|325127790|gb|EGC50698.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis N1568]
          Length = 374

 Score =  271 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 139/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LTHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|52425679|ref|YP_088816.1| 23S rRNA pseudouridylate synthase C [Mannheimia succiniciproducens
           MBEL55E]
 gi|52307731|gb|AAU38231.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 325

 Score =  271 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 104/319 (32%), Positives = 170/319 (53%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G  VR
Sbjct: 15  VKMLQISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDTVR 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A     KEQ  + + +N       L+  +++ED  + V NKP+GI+V GGSG++
Sbjct: 75  IPPVRVAE----KEQAPISNKLN---KVAALEKQIIFEDDCLLVLNKPSGIAVHGGSGLS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+S +  + +   L HR+D++TSGIL+VA+ R+A ++L E  R++ ++K Y +L
Sbjct: 128 FGVIEALRS-LRPEARFLELVHRIDRDTSGILLVAKKRSALRNLHEQLRIKTVKKDYLAL 186

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK    GG+ +  V +       + + F + + +      +   
Sbjct: 187 VRGQWQSHVKVIRAPLLKNELSGGERIVRVNEQ---GKPSETRFAIEERYP-TATLVRAS 242

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP  G  
Sbjct: 243 PVTGRTHQIRVHTQYAGHPIALDDKYGDKEFDQQMQKLGLNRLFLHAYSIKFEHPKSGEE 302

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L++TAPL  +M      L 
Sbjct: 303 LRLTAPLDENMKGILKKLR 321


>gi|312882470|ref|ZP_07742211.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           caribbenthicus ATCC BAA-2122]
 gi|309369870|gb|EFP97381.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           caribbenthicus ATCC BAA-2122]
          Length = 315

 Score =  271 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 102/326 (31%), Positives = 182/326 (55%), Gaps = 17/326 (5%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V +++D    R+D + +N    +    + +ILR G+VRV+KKRVK   ++
Sbjct: 1   MSEIRTKVQFVDIDDDMAGQRIDNFLRNQLKAVPKSMVYRILRKGEVRVNKKRVKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G +VR+PP       + +++  +  S  L K ++ L+ ++++ED  + V NKP+G +V
Sbjct: 61  QAGDIVRVPP-----VTLSEKEDNVALSTKLNKVAE-LEEMIIFEDDHLLVLNKPSGTAV 114

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +
Sbjct: 115 HGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y++LV G  K++ + +   LLK        V+ + +       + + FK+++ FA  
Sbjct: 174 KKYYYALVMGEWKSQCKVVNAPLLKNE------VNSIVRVNPNGKASETRFKILEKFA-N 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-SPIQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  + G PI  D +Y       +T     ++L+LHA  +   
Sbjct: 227 ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGKAGLDRLFLHAANIQFV 286

Query: 299 HPEGGRL-QITAPLPAHMVKTWDSLG 323
           HP    + +++AP+   + K    L 
Sbjct: 287 HPGSDNMIELSAPMGEKLEKVLGLLR 312


>gi|262046428|ref|ZP_06019390.1| pseudouridine synthase [Lactobacillus crispatus MV-3A-US]
 gi|260573299|gb|EEX29857.1| pseudouridine synthase [Lactobacillus crispatus MV-3A-US]
          Length = 303

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 82/326 (25%), Positives = 150/326 (46%), Gaps = 35/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    + V+N++   RLD++     P ++   ++++++   + V+ K  K + +IQ+G 
Sbjct: 1   MTKEYSLEVKNEKG--RLDKFVSEQIPDLSRTRVKELVKDQNILVNGKVEKVSYKIQAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         +I E   LD               ++YED  + V NKP G+ V    
Sbjct: 59  KIEVNIPAVKPLDVIPENIPLD---------------IVYEDDDVIVVNKPQGMVVHPAP 103

Query: 124 GIAYHI--DGFLKS----WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +  L          +G +P + HR+D++TSG+L++A+T  A + L +    +
Sbjct: 104 GHPDHTLVNALLYHSKALAQSPEGFRPGIVHRIDKDTSGLLMIAKTAKARESLEDQLAHK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +++YW++V G    +   I   + +  +       V     +    AI+HFKV++ F 
Sbjct: 164 TNKRLYWAIVHGNFAEENGVIDAPIGRNPYDRKKMAVV-----ETGKKAITHFKVLEQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +  
Sbjct: 218 KDYSLIECQLETGRTHQIRVHLDYIGHPVAGDPLYGPR-----KTLKGHGQFLHAKVLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  L+ +   P    +T   L
Sbjct: 273 KHPSTGEWLEFSVEPPQIFQETLAQL 298


>gi|254670508|emb|CBA06264.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis alpha153]
          Length = 373

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 139/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 48  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 106

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 107 -------------VRPSEENLAFVPEPMALDIIYEDDTVIVVNKPAGLVVHPAAGNWTGT 153

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 154 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAV 213

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 214 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y        +        +  +  LHA  +   HP
Sbjct: 268 LETGRTHQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 327

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 328 ESGETVSFEAPIPDDIYHLLSVLRLEA 354


>gi|229918562|ref|YP_002887208.1| pseudouridine synthase, RluA family [Exiguobacterium sp. AT1b]
 gi|229469991|gb|ACQ71763.1| pseudouridine synthase, RluA family [Exiguobacterium sp. AT1b]
          Length = 303

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 147/321 (45%), Gaps = 35/321 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           Y  V +++   R+D+W  +     +   +Q+ +++G + V+   VK N ++Q G  V + 
Sbjct: 4   YTFVADEKA--RIDKWVSDR-GEWSRSQVQEWIKTGALLVNGSAVKANYKLQVGDEVEVN 60

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                          +  +V L    + +   +++ED  + V NK  G+ V   +G    
Sbjct: 61  ---------------VPEAVELEVLPEDIPLEIVFEDEDVIVVNKARGMVVHPAAGHTSG 105

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D  G    ++P + HR+D++T+G+L+VA+   A + L    + + I++ 
Sbjct: 106 TLVNALLYHCDDLSGINGVKRPGIVHRIDKDTTGLLMVAKNDLAHESLASQLKDKTIKRE 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G   ++   I   + + ++        +   ++ A  A++HF++++ + + F  
Sbjct: 166 YIALVHGELVHELGTIEAPIGRDTND----RQRMTVTDRNAKEAVTHFRLLERY-KDFTL 220

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+RVH  ++G P+ GD KY      +          LHA  +   HP  
Sbjct: 221 VECKLETGRTHQIRVHMRYIGHPLAGDPKYGPRRTIDL-----GGQALHAATLGFHHPRT 275

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
              ++  APLP         L
Sbjct: 276 KEWMEFEAPLPEDFNAELAKL 296


>gi|227878615|ref|ZP_03996537.1| pseudouridylate synthase [Lactobacillus crispatus JV-V01]
 gi|256843219|ref|ZP_05548707.1| pseudouridine synthase [Lactobacillus crispatus 125-2-CHN]
 gi|256850423|ref|ZP_05555851.1| pseudouridine synthase [Lactobacillus crispatus MV-1A-US]
 gi|293380626|ref|ZP_06626679.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
 gi|295692991|ref|YP_003601601.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|312977447|ref|ZP_07789195.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           crispatus CTV-05]
 gi|227861792|gb|EEJ69389.1| pseudouridylate synthase [Lactobacillus crispatus JV-V01]
 gi|256614639|gb|EEU19840.1| pseudouridine synthase [Lactobacillus crispatus 125-2-CHN]
 gi|256712820|gb|EEU27813.1| pseudouridine synthase [Lactobacillus crispatus MV-1A-US]
 gi|290922813|gb|EFD99762.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
 gi|295031097|emb|CBL50576.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|310895878|gb|EFQ44944.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           crispatus CTV-05]
          Length = 303

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 82/326 (25%), Positives = 150/326 (46%), Gaps = 35/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    + V+N++   RLD++     P ++   ++++++   + V+ K  K + +IQ+G 
Sbjct: 1   MTKEYSLEVKNEKG--RLDKFVSEQIPDLSRTRVKELVKDQNILVNGKVEKVSYKIQAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         +I E   LD               ++YED  + V NKP G+ V    
Sbjct: 59  KIEVNIPAVKPLDVIPENIPLD---------------IVYEDDDVIVVNKPQGMVVHPAP 103

Query: 124 GIAYHI--DGFLKS----WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +  L          +G +P + HR+D++TSG+L++A+T  A + L +    +
Sbjct: 104 GHPDHTLVNALLYHTKALAQSPEGFRPGIVHRIDKDTSGLLMIAKTAKARESLEDQLAHK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +++YW++V G    +   I   + +  +       V     +    AI+HFKV++ F 
Sbjct: 164 TNKRLYWAIVHGNFAEENGVIDAPIGRNPYDRKKMAVV-----ETGKKAITHFKVLEQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +  
Sbjct: 218 KDYSLIECQLETGRTHQIRVHLDYIGHPVAGDPLYGPR-----KTLKGHGQFLHAKVLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  L+ +   P    +T   L
Sbjct: 273 KHPSTGEWLEFSVEPPQIFQETLAQL 298


>gi|187779872|ref|ZP_02996345.1| hypothetical protein CLOSPO_03468 [Clostridium sporogenes ATCC
           15579]
 gi|187773497|gb|EDU37299.1| hypothetical protein CLOSPO_03468 [Clostridium sporogenes ATCC
           15579]
          Length = 305

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 88/321 (27%), Positives = 149/321 (46%), Gaps = 32/321 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE + +N+RLD +    +   +   LQ I+  G V V+ K  K N +++ G  +++    
Sbjct: 8   VEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIKVN--- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                       +     L    + +K  ++YED  + V NKP  + V    G+     +
Sbjct: 65  ------------IPEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLV 112

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+   I ++Y +
Sbjct: 113 NALLSHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV GI K+ +  I   + +   +    + VV    K   YA++H+KVI+ F +    +E 
Sbjct: 173 LVEGIIKDGQGTIEAPIGRH-PVDRIKMAVV----KDGRYAVTHYKVIERF-KNHTLVEC 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +  TGRTHQ+RVH  H+  P+VGD  Y    +            LHA+ +   HP  G+ 
Sbjct: 227 KLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQ----RFNLKGQMLHAKLLGFIHPTTGQY 282

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           ++  + LP +  K    L  +
Sbjct: 283 VEFESQLPEYFKKIIKILRNE 303


>gi|307564398|ref|ZP_07626939.1| pseudouridine synthase, RluA family [Prevotella amnii CRIS 21A-A]
 gi|307346758|gb|EFN92054.1| pseudouridine synthase, RluA family [Prevotella amnii CRIS 21A-A]
          Length = 361

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 84/334 (25%), Positives = 152/334 (45%), Gaps = 40/334 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  ++  R+D++      H +   +QK  ++G + V+   VK N +++   V+ +  
Sbjct: 31  IEVDKGQKAERIDKYLFERMQHSSRNRIQKAAQAGFIHVNGSPVKSNYKVRPEDVITLML 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                ++ I+              ++ +   ++YED  + V  KPAG+ V  G+G     
Sbjct: 91  DRPKHDNTIE--------------AEDIPLDVVYEDDSLMVVMKPAGLVVHPGAGNFHGT 136

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+ G   +  D+   +  L HR+D++TSG+L++A+T  A   L + F  +   
Sbjct: 137 LINAIAWHLRGL--ASFDANDPEVGLVHRIDKDTSGLLLIAKTPEAKSSLGKQFFYKTTH 194

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG   +++  I   + +        + V          A++H+KVI+ F    
Sbjct: 195 RSYIALVWGNIVDEQGRIEGNISRDPK-DRLRMTVFPPESDIGKPAVTHYKVIERFG-YT 252

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKL 288
             +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S           I  + 
Sbjct: 253 TLIECVLETGRTHQIRAHMKHIGHPLFGDERYGGREILRGQRSSSYKAFVQNGFKICPRQ 312

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            LHA+ +   HP  G  +  T+PLP  +    D 
Sbjct: 313 ALHAKTLGFVHPVTGEQMDFTSPLPDDLSALIDK 346


>gi|229496851|ref|ZP_04390560.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           endodontalis ATCC 35406]
 gi|229316262|gb|EEN82186.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           endodontalis ATCC 35406]
          Length = 359

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 86/330 (26%), Positives = 152/330 (46%), Gaps = 36/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+D++  +   H +   +Q    +G + V +  +K N +++ G V+ +  
Sbjct: 35  IVVDKGQTPLRIDKFLVDKLEHSSRHRIQLAAEAGYLFVGETPIKSNYKVRPGDVITL-- 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYH 128
               L     E+ I+   + L          ++YED+ + V NKPAG+ V  G+G     
Sbjct: 93  ---RLARPPHERGIVAEDIPLE---------VVYEDNDLLVVNKPAGMVVHPGNGNYTGT 140

Query: 129 IDGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   L  +       D+      L HR+D++TSG+LVVA+   A   L + F  +  ++ 
Sbjct: 141 LVNALAYYFRDDPKYDANDPNVGLVHRIDKDTSGLLVVAKRPEAKTALGKQFFEKTSERS 200

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  K  +  I   + +        + V   N      AI+H++V++ FA    +
Sbjct: 201 YRALVWGAFKESEGRIEGNIGRDPR-DRTRMSVFPPNSDEGKNAITHYRVLETFA-FVSY 258

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKLYL 290
           +E +  TGRTHQ+R H   +  P+ GD KY  +   +G  +S           +  +  L
Sbjct: 259 IECRLETGRTHQIRAHMKSINHPLFGDEKYGGSEILRGRPSSSYLSFARHMLELCPRQAL 318

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           HAR +   HP  G  ++  AP+P  M +  
Sbjct: 319 HARTLGFTHPLTGEFMRFEAPIPRDMEQLI 348


>gi|331084859|ref|ZP_08333947.1| hypothetical protein HMPREF0987_00250 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330410953|gb|EGG90375.1| hypothetical protein HMPREF0987_00250 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 301

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 85/327 (25%), Positives = 147/327 (44%), Gaps = 34/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +Y   +ND   MR+D++     P ++   LQK+++  +V V+ + VK N ++    
Sbjct: 1   MEERRYTTEKNDL--MRIDKFLSEKLPDLSRSYLQKLIKEKEVLVNGQPVKANYKLSLED 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I+ EQ  LD               +LYED  I V NKP G+ V   +
Sbjct: 59  HISVMIPELKEPDILPEQIPLD---------------ILYEDEDILVVNKPKGMVVHPSA 103

Query: 124 GI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  +    D         +P + HR+D +T+G L+V +   A Q L E  + 
Sbjct: 104 GHYSGTLVNALMFHCKDQLSGINGVMRPGIVHRIDMDTTGSLIVCKNDFAHQSLAEQLKD 163

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y ++V G+ K     I   + +   +    + V   N K   +A++H++V+  F
Sbjct: 164 HTITRKYHAIVHGVLKEDNGTIDAPIGRH-PVERKKMSV---NYKNGKHAVTHYRVLKRF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +KF ++E Q  TGRTHQ+RVH   +  P++GD  Y        +        LHA+ + 
Sbjct: 220 -EKFTYVECQLETGRTHQIRVHMASIRHPLLGDAIYGP----AKSPMKLQGQTLHAKILG 274

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + HP   + ++  A LP +     + L
Sbjct: 275 IIHPRTSQYMEFNAELPDYFKHLLEIL 301


>gi|304387998|ref|ZP_07370170.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis ATCC 13091]
 gi|304337997|gb|EFM04135.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis ATCC 13091]
          Length = 374

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 139/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LTHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|320530727|ref|ZP_08031771.1| pseudouridine synthase, RluA family [Selenomonas artemidis F0399]
 gi|320137014|gb|EFW28952.1| pseudouridine synthase, RluA family [Selenomonas artemidis F0399]
          Length = 301

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 86/317 (27%), Positives = 143/317 (45%), Gaps = 31/317 (9%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            D    RLD +      + +   +Q+++  G VRVD  RVK N +++SG+ +        
Sbjct: 6   ADSTGERLDVFLARQMENCSRSYVQRLITDGNVRVDGARVKPNYKLRSGEEICCT----- 60

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
                     +  +  +   ++ +   +LYED  I V NK  G+ V   +G      ++ 
Sbjct: 61  ----------VPPAEEVVIAAEDIPLDVLYEDEDIIVINKERGMVVHPAAGNLTGTLVNA 110

Query: 132 FLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    D  G     +P + HRLD++TSG++V A+   A   L +  R +  ++ Y +LV
Sbjct: 111 LLFRCRDLSGINGELRPGIVHRLDKDTSGVMVAAKNDMAHHFLAQQIRSKAARREYRALV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    +   I   + +        + +V+    G   A +HF+V++ F   + ++    
Sbjct: 171 HGNIAERAGVITGDIGRH-PTDRKRMAIVRS---GGKSATTHFEVLERFGD-YTFVSCVL 225

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            TGRTHQ+RVH   +G P+VGD KY A           +   LH+  + L HP  G +++
Sbjct: 226 ETGRTHQIRVHMTSIGHPLVGDAKYTA----MKNPFGIHGQALHSHILTLVHPRTGAQMR 281

Query: 307 ITAPLPAHMVKTWDSLG 323
            TAPLPA M      L 
Sbjct: 282 FTAPLPADMGDILHRLR 298


>gi|262340910|ref|YP_003283765.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase D) [Blattabacterium sp. (Blattella germanica)
           str. Bge]
 gi|262272247|gb|ACY40155.1| pseudouridylate synthase (ribosomal large subunit pseudouridine
           synthase D) [Blattabacterium sp. (Blattella germanica)
           str. Bge]
          Length = 342

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 91/348 (26%), Positives = 163/348 (46%), Gaps = 43/348 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++   +++ +R+D++ KN+  +I+   +QK   SG++ V+K  VK N +I+    V I  
Sbjct: 12  IITNKNQKEIRIDKFLKNYIQNISRNQIQKWTTSGKILVNKNIVKKNYKIKPLDFVEIEI 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
            I ++   ++ + I    +NL          +LYED  + V NKPAG+ V  G       
Sbjct: 72  SIPSVLDHLEYKNITAEKINLD---------ILYEDEDVLVVNKPAGMVVHPGFGNETGT 122

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              GI YH+     +  +    +  L HRLD++TSG+LV A+   + +HL + F  R IQ
Sbjct: 123 LIHGIKYHLTN--SNLNNFNLYRCGLVHRLDKDTSGLLVFAKNEYSQKHLFQQFYSRTIQ 180

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG---ANYAISHFKVIDCFA 237
           + Y +L+WG    +K  I  ++ +        + ++KQ  +      ++++H+KV++ F 
Sbjct: 181 RKYIALIWGNLIEEKGTITGFIGRDPK-NRKKMTILKQENQEFNKGKFSVTHYKVLERF- 238

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-------------GNFTSPI 284
           +   ++     TG+THQ+R H  H+G P+  D  Y  N                N    I
Sbjct: 239 KYLTYVSCNIKTGKTHQIRAHFKHLGHPLFHDSIYGGNRIFMKKKCSNQNIEFLNTCLKI 298

Query: 285 QNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
             +  LHA  +   HP  G+     P+P       ++      RN+++
Sbjct: 299 LQRQALHAISLSFIHPRNGKCHFLCPIPEDFKTVLENC-----RNMFL 341


>gi|116514036|ref|YP_812942.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|116093351|gb|ABJ58504.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|325125726|gb|ADY85056.1| Pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           2038]
          Length = 304

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 150/325 (46%), Gaps = 33/325 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   +  +E   RLD++       ++   +++++++G++ V+ K+ K + ++Q   ++++
Sbjct: 3   REYELTAEESGQRLDKYLAGEMTDLSRSRIKELVQAGEILVNGKKSKVSYKVQKDDLIQV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                          I+     L   ++ +   ++YED  + V NKP G+ V   +G   
Sbjct: 63  ---------------IVLPLEPLKLEAENIPLDIVYEDKDVIVVNKPQGMVVHPAAGHPS 107

Query: 128 HI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H   +  L    D     +G +P + HR+D++TSG+L+VA+  AA + L +    +  ++
Sbjct: 108 HTLVNALLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G    ++  I   + +          V K        A++HFKV++ + Q + 
Sbjct: 168 QYLAIVHGNFAEEEGTIDAPIGRNPKDRKQMAVVEK-----GKSAVTHFKVLEQY-QGYS 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +    P 
Sbjct: 222 LVECQLETGRTHQIRVHMAYIGHPLAGDPLYGPR-----KTLPGHGQFLHAKTLGFEQPS 276

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            G  L+ +   P    +T   L  K
Sbjct: 277 TGEWLEFSVQPPEIFQQTVADLRKK 301


>gi|325275825|ref|ZP_08141690.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas sp.
           TJI-51]
 gi|324099044|gb|EGB97025.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas sp.
           TJI-51]
          Length = 318

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 104/319 (32%), Positives = 171/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + VQ + V  +    R+D +       +    + +ILR G+VRV+K RVK   +IQ+G +
Sbjct: 9   SGVQLIEVAPELAGQRIDNFLITALKGVPKTLVYRILRKGEVRVNKGRVKPEYKIQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP       + +  +    +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRVPP-----VRLPERDEPAPVAQGLLQR---LEAAIVYEDKALIVMNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L+  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y 
Sbjct: 121 LSFGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     K+ +   LLK +   G+ +  V         A++ F+V+  F      +E
Sbjct: 180 ALVRGHWPTAKKQVNAPLLKSNLRSGERMVEVNDE---GKEALTLFRVLRRFGDFATIVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD+KY   +F          +L+LHA  + +P P+GG
Sbjct: 237 ARPITGRTHQIRVHTLHAGHMIAGDNKYGDEDFSREIRELGGKRLFLHAYALTVPLPDGG 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
            L++ AP+     KT + L
Sbjct: 297 ELKLEAPVDEVWAKTVERL 315


>gi|170660217|ref|YP_001740053.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213969773|ref|ZP_03397908.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato T1]
 gi|301382849|ref|ZP_07231267.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato Max13]
 gi|302062845|ref|ZP_07254386.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato K40]
 gi|302131353|ref|ZP_07257343.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato NCPPB 1108]
 gi|118201620|gb|ABK79683.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213925581|gb|EEB59141.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato T1]
 gi|330878259|gb|EGH12408.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
 gi|331019164|gb|EGH99220.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. lachrymans str. M302278PT]
          Length = 318

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 103/319 (32%), Positives = 170/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 9   PGVQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRIPP-----VRVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y 
Sbjct: 121 LSFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     ++ +   LLK +   G+ +  V +       A++ FKV+  F      +E
Sbjct: 180 ALVRGNWATAQKQVRAPLLKSNLRSGERMVEVNEE---GKEALTLFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY    F          +L+LHA  + +P P+G 
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHAIAGDTKYGDESFSREIRDLGGKRLFLHAYMLTVPMPDGS 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L + AP+     KT + L
Sbjct: 297 KLNVQAPVDEMWAKTVERL 315


>gi|315037134|gb|EFT49066.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0027]
          Length = 310

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 85/326 (26%), Positives = 151/326 (46%), Gaps = 33/326 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             ++ + V    E  R+D+    H P+ +   +Q+ L+   V V+ + V+ N ++ +G  
Sbjct: 8   AKMEQINVTIQTEKGRIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVRANYKVTAGDE 67

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +          I E ++LD        ++ +   ++YED+ + V NKP  + V   +G
Sbjct: 68  IVVT---------IPEPEVLD------MVAEDIPLTIVYEDNDVIVVNKPQDMVVHPSAG 112

Query: 125 I--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 ++  L             +P + HR+D++TSG+L+VA+   A + L +  + + 
Sbjct: 113 HPKGTLVNALLHHADHLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKT 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             + Y +LV G+  + K  I   + + S +      V+    +G   A++HF V++ F  
Sbjct: 173 SLRKYVALVHGVIPHDKGEINAPIGR-SKVDRKMQAVI----EGGKEAVTHFTVLERF-D 226

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   
Sbjct: 227 AFTLVELQLETGRTHQIRVHMKYIGYPLAGDPLYGPK-----KTLPGNGQFLHAKLLGFT 281

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  L   APLP    KT   L 
Sbjct: 282 HPTTGEQLVFEAPLPEVFEKTLHQLR 307


>gi|15895383|ref|NP_348732.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|15025103|gb|AAK80072.1|AE007712_8 Predicted pseudouridylate synthase, YLYB B.subtilis ortholog
           [Clostridium acetobutylicum ATCC 824]
 gi|325509529|gb|ADZ21165.1| pseudouridylate synthase [Clostridium acetobutylicum EA 2018]
          Length = 305

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 83/323 (25%), Positives = 150/323 (46%), Gaps = 32/323 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            ++E + EN R+D +    + +I+  ++Q ++   +V V+ K VK N +++S   V    
Sbjct: 6   FIIEEEYENQRIDVYLAQEFENISRSHIQDLIGKKKVFVNGKAVKSNYKLKSRDNVEFE- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                         +  +  L   ++ +   ++YED  I V NK  G+ V    G     
Sbjct: 65  --------------IPDNEELKIEAENIPLDIVYEDRDIVVVNKAQGMVVHPAPGNYNGT 110

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HR+D++TSGILVVA+  AA ++L    +   + ++Y
Sbjct: 111 LVNALLYHCKDLSGINGVLRPGIVHRIDKDTSGILVVAKNDAAHKNLANQLKEHSMNRVY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V GI K  +  +   L +   +    + VV    KG   A++H+KV++ + +    +
Sbjct: 171 RAVVEGIIKEDEGTVDKPLARH-PVERVKIAVV----KGGRNAVTHYKVLERY-RNSTLI 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E +  TGRTHQ+RVH  ++G  +VGD  Y    +            LHA+ +   HP  G
Sbjct: 225 ECKLETGRTHQIRVHMAYIGHALVGDPLYGYKKQ----RFNLEGQMLHAQKLGFIHPTKG 280

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
           + ++     P+H  K    L  +
Sbjct: 281 KYMEFEREAPSHFQKIITILRNE 303


>gi|320538809|ref|ZP_08038486.1| putative 23S rRNA pseudouridylate synthase [Serratia symbiotica
           str. Tucson]
 gi|320031154|gb|EFW13156.1| putative 23S rRNA pseudouridylate synthase [Serratia symbiotica
           str. Tucson]
          Length = 319

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 102/319 (31%), Positives = 167/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + + +DE   R+D +       +    + +I+R G+VRV+K+R+K   ++ +G +VR
Sbjct: 8   VQVITISDDEAGQRIDNFLLARLKGVPKSMIYRIVRKGEVRVNKRRIKAEYKLAAGDLVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A   ++     LD  V LT         +LYED  + + NKP+G +V GGSG++
Sbjct: 68  VPPVRIAEREVVPVSAKLDKVVALTN-------CILYEDDHLLILNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L + +  + +   L HRLD++TSG+L+VA+ R+A + L E  RM+ +QK Y +L
Sbjct: 121 FGVIEGLHA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRMKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FKV +   +    ++  
Sbjct: 180 VRGQWQSHCKVVQAPLLKNILHSGERIVRVSSE---GKSSETRFKV-EARYEFATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F          +L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDRQLLGTGLKRLFLHAAALHFEHPATGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++I AP+   + +    L 
Sbjct: 296 VRIEAPMDGALRQCLQRLR 314


>gi|315640856|ref|ZP_07895955.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           italicus DSM 15952]
 gi|315483395|gb|EFU73892.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           italicus DSM 15952]
          Length = 302

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 85/326 (26%), Positives = 149/326 (45%), Gaps = 39/326 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + + +   EE  R+D+       + +   +Q  L+   V++D   VK N ++Q G  + 
Sbjct: 2   TEELKISITEEKGRIDKVLAEKLANYSRSQIQLWLKEACVKIDGVVVKANYKVQKGDRIT 61

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I                +     L   ++ L   ++YED+ + V NKP G+ V   +G  
Sbjct: 62  IQ---------------IPEPETLDLIAENLPLEIVYEDADVAVINKPQGMVVHPSAG-- 104

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            H +G L + +              +P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 105 -HPNGTLVNALIYHLNSLSSINGVIRPGIVHRIDKDTSGLLMVAKNDQAHEDLAKQLKDK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G+  + K  I   + + S +      VV         A++HF+V++ + 
Sbjct: 164 TSLRKYVALVHGVIPHDKGVIRAPIGR-STVDRKMQAVVD----NGKDAVTHFQVLERY- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E+Q  TGRTHQ+RVH  ++G P+VGD  Y         +   N  +LHA+ +  
Sbjct: 218 EDYTLVELQLETGRTHQIRVHMQYIGYPLVGDPVYGLK-----RTIKGNGQFLHAKLLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  +   APLP    KT   L
Sbjct: 273 THPSTGEKMVFEAPLPEIFKKTLAKL 298


>gi|238791866|ref|ZP_04635503.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           intermedia ATCC 29909]
 gi|238728970|gb|EEQ20487.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           intermedia ATCC 29909]
          Length = 327

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 106/324 (32%), Positives = 169/324 (52%), Gaps = 14/324 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G VVR
Sbjct: 15  VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGDVVR 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       I E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 75  VPPVR------IAEREEVQISAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 128 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 186

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ V  V         + + FKV + F +    ++  
Sbjct: 187 VRGQWQSHCKAVQAPLLKNILQSGERVVKVSSE---GKPSETRFKVEERF-EHATLVKAS 242

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 243 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNSGET 302

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           ++I APL   +      L  K   
Sbjct: 303 MRIEAPLDNQLRHCLLMLRKKAAE 326


>gi|228909719|ref|ZP_04073542.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis IBL 200]
 gi|228850008|gb|EEM94839.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis IBL 200]
          Length = 302

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 137/313 (43%), Gaps = 33/313 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N R+D++        +   +Q+ ++   V V+ K VK N +++    + +          
Sbjct: 15  NERIDKFVAGINNEWSRSQVQQWIKDDVVTVNGKTVKVNYKVKEEDEITVT--------- 65

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKS 135
                 +     L    + +   + YED+ + V NKP G+ V    G      ++G +  
Sbjct: 66  ------IPEPEALDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHH 119

Query: 136 WVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y ++V G+ 
Sbjct: 120 CTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVI 179

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            + K  I   + +               ++    A++HF+V++ F + F  +E +  TGR
Sbjct: 180 PHDKGTIDAPIGRD-----KKERQSMTVDENGKNAVTHFQVLERF-KDFTLVECRLETGR 233

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P+ GD KY      +      N   LHA  +   HP  G  +Q  AP
Sbjct: 234 THQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGFDHPRTGEYIQFEAP 288

Query: 311 LPAHMVKTWDSLG 323
           +P    +  + L 
Sbjct: 289 IPEVFEEALNILR 301


>gi|310642966|ref|YP_003947724.1| RNA pseudouridine synthase ylyb [Paenibacillus polymyxa SC2]
 gi|309247916|gb|ADO57483.1| Uncharacterized RNA pseudouridine synthase ylyB [Paenibacillus
           polymyxa SC2]
          Length = 323

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 80/322 (24%), Positives = 139/322 (43%), Gaps = 32/322 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
             ++     R+D++       ++   +Q  + +G+V V+   VK N ++  G  + +   
Sbjct: 27  TADSGNVKTRIDKYIAEEMKEVSRSQIQLWIGNGRVLVNGTAVKANYKLAEGDHIVLSVP 86

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                 I+ E   LD               ++YEDS + V NK  G+ V    G      
Sbjct: 87  EPESVDIMPENIPLD---------------VVYEDSDVIVINKQRGLVVHPAPGHSSGTL 131

Query: 129 IDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  +    D  G     +P + HR+D++TSG+L+ A+   A   L    +   + + Y 
Sbjct: 132 VNALMYHCHDLSGINGELRPGIVHRIDKDTSGLLMAAKNDQAHASLAAQLKDHSVTRKYI 191

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   + +  +   + + S  G   +  V   E+ + +A++HF VI+     +  LE
Sbjct: 192 ALVHGHLSHDQGTVDAPIGRDS--GDRKMFTV--TERNSKHAVTHFLVIERLGD-YTLLE 246

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH   +G P+VGD  Y  +              LHA  +   HP  G 
Sbjct: 247 LQLETGRTHQIRVHMKFIGHPLVGDPMYGRSKGVRME-----GQALHAAVLGFKHPTTGE 301

Query: 305 -LQITAPLPAHMVKTWDSLGFK 325
            L+ + P+P  M     SL  +
Sbjct: 302 YLEFSRPIPPDMEDVLTSLRSR 323


>gi|330966256|gb|EGH66516.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 318

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 103/319 (32%), Positives = 170/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 9   PGVQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRIPP-----VRVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y 
Sbjct: 121 LSFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     ++ +   LLK +   G+ +  V +       A++ FKV+  F      +E
Sbjct: 180 ALVRGNWATAQKQVRAPLLKSNLRSGERMVEVNEE---GKEALTLFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY    F          +L+LHA  + +P P+G 
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHAIAGDTKYGDESFSREIRDLGGKRLFLHAYMLTVPMPDGS 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L + AP+     KT + L
Sbjct: 297 KLNVQAPVDEMWAKTVERL 315


>gi|291550385|emb|CBL26647.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           torques L2-14]
          Length = 304

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 76/328 (23%), Positives = 137/328 (41%), Gaps = 35/328 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  + +     D    R+D++       ++   +QK+++  ++ V++  VK N ++ +G 
Sbjct: 1   MEELHF---NADITGERIDKFLDGRIESLSRSYIQKLIKEKKILVNQLPVKANYKLTTGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   +LYED  I V NKP G+ V    
Sbjct: 58  TIILQ---------------IPDPEPLDIQPENIPLDILYEDDDILVVNKPKGMVVHPAP 102

Query: 124 GIAYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G   H   +  L    ++        +P + HR+D  T+G L++ +   A Q L E  + 
Sbjct: 103 GHYSHTLVNAVLYHCGENLSGINGVIRPGIVHRIDMNTTGSLLICKNDKAHQILAEQLKE 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y S+V G  K     +   + +           +        +A++H++V++ F
Sbjct: 163 HSITRKYHSIVHGNLKEDTGTVNAPIGRHPTDRKK----MSTKAPNGRHAVTHYRVLERF 218

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              F ++E Q  TGRTHQ+RVH   +G PI+GD  Y                 LHA+ + 
Sbjct: 219 G-NFTYIECQLETGRTHQIRVHMSSIGHPILGDEIYGP----AKCPYKLQGQTLHAKILG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           + HP  G  ++  APLP +     + L 
Sbjct: 274 ITHPSTGEYIEFDAPLPEYFKDLLNKLR 301


>gi|225378086|ref|ZP_03755307.1| hypothetical protein ROSEINA2194_03746 [Roseburia inulinivorans DSM
           16841]
 gi|225210087|gb|EEG92441.1| hypothetical protein ROSEINA2194_03746 [Roseburia inulinivorans DSM
           16841]
          Length = 303

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 84/324 (25%), Positives = 148/324 (45%), Gaps = 32/324 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   VE + E  RLD++    +P  +    QK+++ G V V+ K  K N R+++  +V +
Sbjct: 4   ETFEVEYEYEGERLDKYVSILFPEQSRSFFQKLIKDGNVSVNDKVQKANYRLKTEDLVTV 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                    I+ E   LD               +LYED  + V NKP G+ V   +G   
Sbjct: 64  EIPDAVETQILPEDIPLD---------------ILYEDDDLLVVNKPKGMVVHPSAGHYS 108

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++  +    DS        +P + HR+D +T+G L+V +   +   + E  +   + 
Sbjct: 109 GTLVNAIMYHCKDSLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHVFIAEQIKEHSVN 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y  +V+G+ ++ +  I   + +   +    + +   NEK    AI+H+KV++ F  K+
Sbjct: 169 RRYRGIVYGVVRDDEGTIHAPIGRH-PVDRKKMAI---NEKNGKDAITHYKVLERF-DKY 223

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++E +  TGRTHQ+RVH   +G P++GD  Y        +        LHA  +   HP
Sbjct: 224 TYMEFKLETGRTHQIRVHMASIGHPLLGDTLYS----NGKSPYKLQGQTLHAMTIGFIHP 279

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
                ++I+APLP +  K    L 
Sbjct: 280 GTREYMEISAPLPEYFEKILRDLR 303


>gi|222110296|ref|YP_002552560.1| RluA family pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221729740|gb|ACM32560.1| pseudouridine synthase, RluA family [Acidovorax ebreus TPSY]
          Length = 334

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 87/332 (26%), Positives = 145/332 (43%), Gaps = 31/332 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
             ++ VVV  ++   RLD+      P  +   LQ++L  G VR++ + V K  +R+++G 
Sbjct: 25  AELREVVVGAEQHAQRLDKALAELVPEFSRSYLQQLLLQGCVRLNGREVQKPASRVKAGD 84

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +       +   +               +     ++YED  I V +KPAG+ V    
Sbjct: 85  RIAVEMRPTQQSQAFR--------------PEQWPLDVVYEDEHILVIHKPAGLVVHPAP 130

Query: 124 GIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +  G L + +  +        +  + HRLD++TSG++VVAR+R+A   L      R
Sbjct: 131 G---NWSGTLLNALLGRDAQAMQVPRAGIVHRLDKDTSGLMVVARSRSAMDALVRMIAAR 187

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L WG          +  + +       + VV   +     A + F +ID   
Sbjct: 188 EVSRQYVALGWGGWTGAAHRSVHAPIGRDPRNRLRMAVVDLAQHPGKEARTDFDLIDANE 247

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +  C +    HTGRTHQ+RVH   +  P+V D  Y     G       ++  LHA  +  
Sbjct: 248 E-VCLVRCTLHTGRTHQIRVHMASIRHPLVADVLYGGAMAGPM-----HRQALHAFRLAF 301

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            HP  G  L+  APLP  M +  D  G +Y+R
Sbjct: 302 VHPVTGAPLEFHAPLPEDMTQALDFWGLRYNR 333


>gi|121593575|ref|YP_985471.1| ribosomal large subunit pseudouridine synthase D [Acidovorax sp.
           JS42]
 gi|120605655|gb|ABM41395.1| ribosomal large subunit pseudouridine synthase D [Acidovorax sp.
           JS42]
          Length = 334

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 87/333 (26%), Positives = 145/333 (43%), Gaps = 31/333 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
             ++ VVV  ++   RLD+      P  +   LQ++L  G VR++ + V K  +R++ G 
Sbjct: 25  AELREVVVGAEQHAQRLDKALAELVPEFSRSYLQQLLLQGCVRLNGREVQKPASRVKVGD 84

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +       +   +               +     ++YED  I V +KPAG+ V    
Sbjct: 85  RIAVEMRPTQQSQAFR--------------PEQWPLDVVYEDEHILVIHKPAGLVVHPAP 130

Query: 124 GIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +  G L + +  +        +  + HRLD++TSG++VVAR+R+A   L      R
Sbjct: 131 G---NWSGTLLNALLGRDAQAMQVPRAGIVHRLDKDTSGLMVVARSRSAMDALVRMIAAR 187

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L WG          +  + +       + VV   +     A + F +ID   
Sbjct: 188 EVSRQYVALGWGGWTGAAHRSVHAPIGRDPRNRLRMAVVDLAQHPGKEARTDFDLIDANE 247

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +  C +    HTGRTHQ+RVH   +  P+V D  Y     G       ++  LHA  +  
Sbjct: 248 E-VCLVRCTLHTGRTHQIRVHMASIRHPLVADALYGGALAGPM-----HRQALHAFRLAF 301

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
            HP  G  L+  APLP  M +  D  G +Y+R+
Sbjct: 302 VHPVTGAALEFHAPLPEDMAQALDFWGLRYNRS 334


>gi|319410076|emb|CBY90410.1| K06180 ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis WUE 2594]
          Length = 392

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 140/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ +R+  
Sbjct: 48  LTVPLELAGGRLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKPSQPKDKMIGGEQIRVT- 106

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 107 -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 153

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 154 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 213

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 214 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 268 LETGRTHQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 327

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 328 ESGETVSFEAPIPDDIYHLLSVLRLEA 354


>gi|13473214|ref|NP_104781.1| pseudouridine synthase [Mesorhizobium loti MAFF303099]
 gi|14023962|dbj|BAB50567.1| pseudouridine synthase [Mesorhizobium loti MAFF303099]
          Length = 329

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 93/338 (27%), Positives = 155/338 (45%), Gaps = 46/338 (13%)

Query: 10  VVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
           +VV  D    RLD+W      P ++   +Q ++R G V VD K       ++ +G+ V I
Sbjct: 2   LVVGADAAGQRLDQWLAASLGPDMSRSRVQMLIRQGAVSVDGKPADETKRKMSAGESVSI 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           +          + +   +LYED  + V NKPAG+ V  G+G   
Sbjct: 62  ---------------AMPEPEPAAPQGEAIALDVLYEDDALIVINKPAGLVVHPGAGNWT 106

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--- 177
              ++  +    DS       ++P + HRLD+ETSG++VVA+T  A + L+E+F      
Sbjct: 107 GTLVNALIHHCGDSLSGIGGVRRPGIVHRLDKETSGVMVVAKTDRAHKALSEAFADHGRT 166

Query: 178 -RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             +++ Y +LVWGIP+     +   L + +        VV +    A +A++HF V + F
Sbjct: 167 GDLERAYLALVWGIPQRPTGTVDAPLGRAA--DRVRRAVVPEGRDDARHAVTHFAVQERF 224

Query: 237 AQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQ-- 285
            +          +E +  TGRTHQ+RVH  H+G P++GD  Y   F+        P++  
Sbjct: 225 GENQQEFATASLVECRLETGRTHQIRVHMAHIGHPVIGDPDYGQAFRTKANRLPEPLKSQ 284

Query: 286 ----NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
               ++  LHA  +   HP+    ++  AP+P  M + 
Sbjct: 285 VKAFSRQALHAWLLAFRHPDTHLTMRFEAPIPRDMEEL 322


>gi|255531126|ref|YP_003091498.1| pseudouridine synthase, RluA family [Pedobacter heparinus DSM 2366]
 gi|255344110|gb|ACU03436.1| pseudouridine synthase, RluA family [Pedobacter heparinus DSM 2366]
          Length = 342

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 74/334 (22%), Positives = 151/334 (45%), Gaps = 42/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+D++  +   + +   +Q  + +G V V++K VK + +++    + I  
Sbjct: 21  IVVDKGQSLLRIDKFLMHRMENASRNRIQNAIEAGNVLVNQKTVKASYKVKPADEISI-- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
                 H  ++ ++    + L          ++YED+ + V NKPAG+ V  G       
Sbjct: 79  ---VFPHPPRDTEVYPEDIPLD---------IVYEDNDLLVVNKPAGMVVHPGYNNYTGT 126

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             + +A+H    L     ++G +P L HR+D++TSG+L++++       L + F    I 
Sbjct: 127 LVNALAFHF-EQLPQLPGNEG-RPGLVHRIDKDTSGLLLISKNEITMTRLAKQFFDHTIT 184

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +L WG  +     +  ++ + +      V  V  +E+   ++++H+ V++      
Sbjct: 185 RKYVALAWGDIEKD-GTVTGYIGRSAK--NRIVMDVYDDEEKGKWSVTHYAVLERLG-YV 240

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------------PIQNKL 288
             +  Q  TGRTHQ+R H  H+G P+  D  Y  +     T+             +  + 
Sbjct: 241 TLISCQLETGRTHQIRAHMQHIGHPLFNDANYGGDKILKGTTFNKYKQFVQNCFELLPRQ 300

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            LHA+ +   HP   + ++  APLP+      + 
Sbjct: 301 ALHAQTLGFIHPGTKKYMEFEAPLPSDFDSALNK 334


>gi|103487583|ref|YP_617144.1| pseudouridine synthase, RluD [Sphingopyxis alaskensis RB2256]
 gi|98977660|gb|ABF53811.1| ribosomal large subunit pseudouridine synthase C [Sphingopyxis
           alaskensis RB2256]
          Length = 405

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 112/316 (35%), Positives = 175/316 (55%), Gaps = 11/316 (3%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-P 69
           V+  +++ +RLDRWFK H P      L +  RSGQ+ +D ++   ++RI  GQ + +P P
Sbjct: 12  VIGEEDDGIRLDRWFKRHRPGTPHALLARWARSGQLTLDGRKADVSDRIAVGQRLVMPVP 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            + A     ++ + L  +          +S+L++ D+   V NK  G++ QGG+   +H+
Sbjct: 72  PVEAEARPARKDRPLTEA-----DVALAESMLIHRDASAIVLNKLPGLATQGGTKTEHHV 126

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           DG L +       +P+L HRLD++TSG L++ART  AA    +SF  R  +K YW++V G
Sbjct: 127 DGLLDALKYDAPVRPKLVHRLDKDTSGALLIARTPRAAAWFAKSFSNRSAKKTYWAIVVG 186

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +P   +  I   L K+   GG+ +HV          + + ++VID       W+E+QP T
Sbjct: 187 VPDIAQGEIDLPLAKQPGSGGEKMHV----HDSGLASKTRYRVIDRAGNSAAWVELQPLT 242

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           GRTHQLRVH   +G PIVGD KY        T  I  KL+LH+R + + HP+GG + ++A
Sbjct: 243 GRTHQLRVHMAAIGHPIVGDGKYGGK-GAFLTGTISRKLHLHSRRLRIDHPDGGVIDVSA 301

Query: 310 PLPAHMVKTWDSLGFK 325
            +P H   + D+LGF 
Sbjct: 302 DVPDHFAASLDALGFD 317


>gi|239623975|ref|ZP_04667006.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239522006|gb|EEQ61872.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 314

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 75/316 (23%), Positives = 143/316 (45%), Gaps = 31/316 (9%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E ++R+DR+     P ++   +QK+L+SGQV V+ + +K +  + +   + +        
Sbjct: 22  ESDVRIDRYLAETCPELSRSYIQKLLKSGQVLVNGRLIKASYVVTADDHIEVD------- 74

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFL 133
                   +  +V     ++ +   +LYED  I + NKP G+ V   +G   H   +G +
Sbjct: 75  --------VPEAVEPEIEAEPMDLDILYEDQDIILVNKPKGMVVHPAAGHYSHTLVNGLM 126

Query: 134 KSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               +         +P + HR+D +T+G+L+V +   A   +    +   I + Y ++V 
Sbjct: 127 YHCKNQLSGINGVMRPGIVHRIDMDTTGVLIVCKNDMAHNSIAAQLKEHSITRRYQAIVH 186

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+ K  +  +   + +           +  N      A++H++V+  F Q + ++E +  
Sbjct: 187 GVIKEDEGTVDAPIGRHQTERKK----MCINYNNGRNAVTHYQVLRRFEQ-YTYVECRLE 241

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH   +  P++GD  Y          P      LHA  + + HP  G  ++ 
Sbjct: 242 TGRTHQIRVHMASLHHPLLGDKVYGP---AKCPVPGLTGQTLHAGVLGIVHPRTGEYMEF 298

Query: 308 TAPLPAHMVKTWDSLG 323
           TAPLP +  +   +L 
Sbjct: 299 TAPLPEYFERLLRNLR 314


>gi|225572138|ref|ZP_03781002.1| hypothetical protein RUMHYD_00432 [Blautia hydrogenotrophica DSM
           10507]
 gi|225040404|gb|EEG50650.1| hypothetical protein RUMHYD_00432 [Blautia hydrogenotrophica DSM
           10507]
          Length = 307

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 87/334 (26%), Positives = 147/334 (44%), Gaps = 39/334 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    V ++  E  +EN R+D++     P I+    QK+L+ G V +D K  K ++R+Q
Sbjct: 1   MSDSENV-WLKAEEQDENQRIDKYLARVMPEISRSYFQKLLKDGGVFIDGKVAKASDRLQ 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  +                  +  S       + L   +LYED  + V NKP G+ V 
Sbjct: 60  CGDEIYFQ---------------MPKSREPDIEPEDLSLDILYEDPYLLVINKPKGMVVH 104

Query: 121 GGSGIAYHIDGFLKS--WVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHL 170
              G   H  G L +      KGQ        +P + HR+D++T+G LVV +     ++L
Sbjct: 105 PCPG---HYSGTLVNGVLFHCKGQLSGINGVLRPGIVHRIDKDTTGALVVCKDDQTHRNL 161

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
                   I + Y ++V G     +  +   + +   +    + +   N K    A++H+
Sbjct: 162 AVQLAEHTITRRYRAIVTGNLSADEGTVEGPIGRH-PVDRKKMSI---NFKNGKDAVTHY 217

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           +V++ F  K  ++E +  TGRTHQ+RVH   +G P++GD  Y ++              L
Sbjct: 218 RVLERFG-KATYIECRLETGRTHQIRVHLSSIGHPLLGDTVYGSSKNPYE----LQGQTL 272

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           HA  +   HP   + ++  APLP +  K  + L 
Sbjct: 273 HAMVLGFTHPYYEKYVEFEAPLPEYFQKMLEKLR 306


>gi|226951907|ref|ZP_03822371.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ATCC 27244]
 gi|294649166|ref|ZP_06726607.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           haemolyticus ATCC 19194]
 gi|226837447|gb|EEH69830.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ATCC 27244]
 gi|292824964|gb|EFF83726.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           haemolyticus ATCC 19194]
          Length = 310

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 99/317 (31%), Positives = 165/317 (52%), Gaps = 19/317 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  ++  R+D +       +    + +++R GQVRV+KKR+K   R+Q G  +R
Sbjct: 10  VTWFDVDEHQDGQRIDNFLFTRLKGVPKSRIYRLIREGQVRVNKKRIKAETRLQIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAAPVSDSVAQSLLSRVVYEDEGLLVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    K     L HR+D++TSG++++++ R+  + L +  R  +IQK Y ++
Sbjct: 123 YGLIEALRAATGKKY--LELIHRIDRDTSGLVMISKKRSTLKLLQDLLREHKIQKTYAAI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     K+ I   LL+     G+    V    K    + + +KV + F +    +   
Sbjct: 181 VKGQVSLDKQLIDAPLLRYELANGERRVRVT---KEGKPSKTEWKVAERF-KTATLVHAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P++GD KY  N    ++ P   +L LHA  +++P+       
Sbjct: 237 PLSGRTHQIRVHGLSIGHPLIGDDKYGHN--TAYSGPEARRLCLHAMRLEIPNYPT---- 290

Query: 307 ITAPLPAHMVKTWDSLG 323
           I AP+P  M +  D L 
Sbjct: 291 IEAPMPEDMQQLIDELR 307


>gi|332974183|gb|EGK11117.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter sp.
           1501(2011)]
          Length = 456

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 144/326 (44%), Gaps = 34/326 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V +D+   R+D+     +   +   LQ+ L+SG + V+ +  K   R++ G  + +   
Sbjct: 149 TVTDDKAGQRIDKLAAELFADHSRSQLQEWLKSGNLTVNGEVEKPKYRVRVGDKLLLQAK 208

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           +                 + T   + +   ++YED  + V NKP G+ V  G+G      
Sbjct: 209 LEQ---------------HGTDEPEDIALDIMYEDDSVLVINKPVGMVVHPGAGNWTGTL 253

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++G L  + +     +  L HR+D+ TSG+LV+ +T+AA   L +  R + + + Y  +V
Sbjct: 254 VNGLLYHYPNQAHLPRAGLVHRIDKNTSGLLVIGKTKAAQMELQDQLRDKTVYRHYQCIV 313

Query: 188 WGIPK--NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            G      ++  I   + +        + V          A++H   I      +  L++
Sbjct: 314 AGDVASLKRQRTIDAPIGRHRTQ-RTKMTVSSV----GKPAVTHIMNITALNDNYSLLDV 368

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--------KLYLHARYMDL 297
           Q  TGRTHQ+RVH  H+G PI+GD  Y    +       +         +  LHA  +  
Sbjct: 369 QLETGRTHQIRVHLSHIGHPIIGDDVYGNRQQLRAGLTPEQREAIQKFPRQALHAYQLGF 428

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HPE G  +++TAPLP  ++K  + L
Sbjct: 429 VHPETGEDIEVTAPLPDDIIKLAEIL 454


>gi|319638102|ref|ZP_07992866.1| ribosomal large subunit pseudouridine synthase D [Neisseria mucosa
           C102]
 gi|317400747|gb|EFV81404.1| ribosomal large subunit pseudouridine synthase D [Neisseria mucosa
           C102]
          Length = 374

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 84/341 (24%), Positives = 144/341 (42%), Gaps = 30/341 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+++ +  
Sbjct: 30  LTVPLEMAGGRLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQPKDKMIGGELIAVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   SG     
Sbjct: 89  -------------VRPSEENLAFTPEPMDLDIIYEDDTVIVINKPAGLVVHPASGNWSGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAI 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   AI+H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAITHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y       ++        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNLRHPCSDAVKEAVKALGARQALHAYRLSFVHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           + G  +   AP+P  M      L  +   +  +       E
Sbjct: 310 KTGETVSFEAPMPDDMYHLLSVLRLEAGLDSSLSNEEEWQE 350


>gi|291044392|ref|ZP_06570101.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae DGI2]
 gi|291011286|gb|EFE03282.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae DGI2]
          Length = 392

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 138/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 48  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 106

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 107 -------------VRPSEENLAFVPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 153

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 154 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 213

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     +  VK    G   A++H KV++ +     ++E  
Sbjct: 214 ANGIVPFD-GKIETQIGRDPH-NRLKMAAVKF---GGKPAVTHVKVLERY-LAHSYIECS 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 268 LGTGRTHQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 327

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 328 ESGETVSFEAPIPDDIYHLLSVLRLEA 354


>gi|222151016|ref|YP_002560170.1| hypothetical protein MCCL_0767 [Macrococcus caseolyticus JCSC5402]
 gi|222120139|dbj|BAH17474.1| conserved hypothetical protein [Macrococcus caseolyticus JCSC5402]
          Length = 301

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 143/319 (44%), Gaps = 33/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  +E  +R+D++  +  P  +   +Q  +++  V V+ K +K N +++    + +    
Sbjct: 8   INEEETGIRIDKFLADANPDWSRSQIQDWIKNEFVLVNGKVIKSNYKLRLNDEISVTEKP 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                ++               +  L   + YED  + +  KP G+ V    G      +
Sbjct: 68  VEEVDLV---------------AQDLGLEIYYEDKDVAIVYKPKGMVVHPAPGHPDGTLV 112

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +G + +  D  G     +P + HR+D++TSG+L++A+   A + L +    + + + Y +
Sbjct: 113 NGLMHAITDLSGINGEIRPGIVHRIDKDTSGLLMIAKNDIAHRGLVDQLVDKSVTRKYTA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G+  ++   I   + +      +   V         +A++HF V++ F  K+  +E 
Sbjct: 173 LVHGVIPHEFGTIDAPIGRNQKDRQEMAIV-----DNGKHAVTHFNVLETF-DKYTLVEC 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
              TGRTHQ+RVH  H+G P+VGD KY      +          LHA  +   HP  G  
Sbjct: 227 VLETGRTHQIRVHMKHIGFPLVGDPKYGPKKTMD-----IGGQALHAGVLGFEHPVTGEY 281

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++ +APLPA+  +    L 
Sbjct: 282 IERSAPLPAYFEELLTKLR 300


>gi|119469426|ref|ZP_01612365.1| 23S rRNA pseudouridylate synthase [Alteromonadales bacterium TW-7]
 gi|119447290|gb|EAW28559.1| 23S rRNA pseudouridylate synthase [Alteromonadales bacterium TW-7]
          Length = 320

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 101/327 (30%), Positives = 167/327 (51%), Gaps = 16/327 (4%)

Query: 1   MSLMTYVQ--YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR 58
           MS  T +Q  +V +  D    R+D +   H   +    + KILR G+VRV+KKR+K   +
Sbjct: 1   MSEKTGLQVSFVTINEDHLGQRIDNFLITHLKGVPKSAIYKILRKGEVRVNKKRIKPVYK 60

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +Q   ++RIPP+      + + ++ + S ++       L+  +L+ED  + V NKP+G++
Sbjct: 61  LQLDDIIRIPPI-----KVAEREEFVPSKLDKVTR---LEDDILFEDKYLIVINKPSGMA 112

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           V GGSG++Y +   L+     + +   L HRLD++TSG L++++ R+    L E  R + 
Sbjct: 113 VHGGSGLSYGLIEALRVLRPEE-RNLELVHRLDRDTSGCLLISKRRSVLTSLHEQLREKT 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K YW+LV G    K + +   L K +   G+ V  V   E     + + FKV++ F +
Sbjct: 172 MEKNYWALVDGQWDGKTKNVTEGLRKNTLKSGERVVRVDNVE--GKPSHTRFKVLERFNE 229

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDL 297
               ++  P TGRTHQ+RVH    G PI  D KY    F         N+L+LHA  +  
Sbjct: 230 -CSLVQASPVTGRTHQIRVHTQCKGHPIACDDKYGDQAFDAGMRKVGLNRLFLHAHDLSF 288

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLG 323
            HP+    +++ APL   +      L 
Sbjct: 289 YHPKNETTMRVEAPLDKALSNCLLKLR 315


>gi|325263923|ref|ZP_08130656.1| ribosomal large subunit pseudouridine synthase D [Clostridium sp.
           D5]
 gi|324030961|gb|EGB92243.1| ribosomal large subunit pseudouridine synthase D [Clostridium sp.
           D5]
          Length = 305

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 142/326 (43%), Gaps = 32/326 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++ +        +R+D++     P +   ++QK++ +G V V +K VK N +      +
Sbjct: 2   QMEELYFTAGTAGIRIDKFLAEAIPDVTRSHIQKLISTGLVTVGQKAVKANYKTALNDEI 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +          I E +I D         + +   +LYED+ I + NKP G+ V    G 
Sbjct: 62  AVR---------IPEPEIPD------IQPEDIPLDILYEDNDILIVNKPKGMVVHPAPGH 106

Query: 126 AYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             +   +  +    D+        +P + HR+D +T+G L++ +   A Q L E  +   
Sbjct: 107 YSNTLVNAVMYHCRDNLSGINGVARPGIVHRIDMDTTGSLIICKNDTAHQALAEQLKEHH 166

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y ++V G  K   + +   + +                     A++H+KV++ F +
Sbjct: 167 ITRKYHAVVHGNLKEDSQTVDAPIGRHPVDRKKMSTRA----PHGRQAVTHYKVLERFGE 222

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            + ++E +  TGRTHQ+RVH   +G PIVGD  Y                 LHA+ + + 
Sbjct: 223 -YTYIECELETGRTHQIRVHMASIGHPIVGDTVYGP----AKCPFKLQGQTLHAKILGIT 277

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  ++  APLP + ++  + L 
Sbjct: 278 HPSTGEYMEFDAPLPEYFLELLNKLR 303


>gi|268611664|ref|ZP_06145391.1| RluA family pseudouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 304

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 147/327 (44%), Gaps = 34/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ +  + V + +   R+D++  ++   +    +Q ++  G++ V  K V  N +++ G 
Sbjct: 1   MSDIITLNVSDSDRGARIDKFISDNVEELTRSAVQGLMEKGKILVSGKSVSKNYKLRDGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +                +     +    + +   ++YEDS + V NKP G+ V    
Sbjct: 61  TVEVE---------------IPEPEPMDALPEDIPLDIVYEDSDLLVVNKPKGMVVHPAH 105

Query: 124 GIA--YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  L    DS        +P + HR+D+ TSG+L+VA+  AA  HL E  ++
Sbjct: 106 GNHSGTLVNALLHHCGDSLSGINGVIRPGIVHRIDKNTSGLLIVAKNDAAHLHLAEQIKV 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
               + Y ++  G  K  +  I   + +        + V  +N +    A++H+ VI  +
Sbjct: 166 HSFTREYEAVASGYFKETEGTIDAPIGRH-KTDRKKMCVTTENSRN---AVTHYSVIRQY 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  + ++  TGRTHQ+RVH  ++G P++GD  Y   +KG           LHAR + 
Sbjct: 222 G-GYAHVRLRLETGRTHQIRVHLAYIGHPVLGDDVYGKAYKG------IEGQCLHARKIG 274

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G  ++ T+ LP + V   + L
Sbjct: 275 FIHPTTGEYMEFTSELPDYFVSILNKL 301


>gi|254500895|ref|ZP_05113046.1| pseudouridine synthase, RluA family [Labrenzia alexandrii DFL-11]
 gi|222436966|gb|EEE43645.1| pseudouridine synthase, RluA family [Labrenzia alexandrii DFL-11]
          Length = 341

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 85/340 (25%), Positives = 154/340 (45%), Gaps = 46/340 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           + V+ ++   R+D    +H   ++   +Q ++++G V +   ++ +   R+  G  + + 
Sbjct: 18  LTVDPEDAGKRIDAVLASHLETLSRNRIQSLIKAGDVSIGGAKIGEPKYRVNEGDEITLH 77

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                          L    +     + +   +++ED+ + V +KPAG+ V  G+G    
Sbjct: 78  ---------------LPEPEDPDPKGEDIPLSVVFEDAHVIVIDKPAGLVVHPGAGNWTG 122

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--- 178
             ++  +    DS       ++P + HR+D++TSG+LVVA+T  A Q L   F       
Sbjct: 123 TLVNALIHHCGDSLSGIGGVKRPGIVHRIDKDTSGLLVVAKTDQAHQGLAAQFADHGRTG 182

Query: 179 -IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LVWG P + K  I   L + S      + VVK +     +AI+H++V + F 
Sbjct: 183 PLERAYSALVWGAPSSLKGTIDANLAR-SQANRQKMAVVKTS---GRHAITHWQVKERFG 238

Query: 238 QK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQN--- 286
                     +E +  TGRTHQ+RVH  H+G P++GD  Y + FK        P+++   
Sbjct: 239 AADQPPLASLMECRLETGRTHQIRVHMAHIGHPLLGDDDYGSGFKTKINRLEEPLKSLVG 298

Query: 287 ---KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              +  LHA  +   HP  G  L+  +P P         L
Sbjct: 299 GFTRQALHAGLLAFEHPVSGETLRFESPYPNDFANLLSGL 338


>gi|325203791|gb|ADY99244.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M01-240355]
          Length = 374

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 140/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T +A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           + G  +   AP+P  +      L  + 
Sbjct: 310 KTGETVSFEAPIPNDIYHLLSVLRLEA 336


>gi|197336060|ref|YP_002156569.1| ribosomal large subunit pseudouridine synthase C [Vibrio fischeri
           MJ11]
 gi|197317550|gb|ACH66997.1| ribosomal large subunit pseudouridine synthase C [Vibrio fischeri
           MJ11]
          Length = 315

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 102/323 (31%), Positives = 167/323 (51%), Gaps = 16/323 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ+V +++D    R+D +      ++    + +I+R G+VRV+KKR+K   ++Q G V
Sbjct: 6   PKVQFVDIDDDFAGQRIDNFLLARLKNVPKSMIYRIVRKGEVRVNKKRIKPEYKLQEGDV 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E    D           L+  ++YED  + + NKP+G +V GGSG
Sbjct: 66  VRIPPVK------VPESTAPDLPNVKLGKVAELEHCIIYEDDHVLILNKPSGTAVHGGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +     L++ +    +   L HR+D++TSGIL+VA+ R+A + L E FR + +QK Y+
Sbjct: 120 LKFGAIEALRA-LRPDARFLELVHRIDRDTSGILLVAKKRSALRRLQEQFRNKTVQKYYF 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  KN  + +   LLK        V+ + +       + + FKV++ F Q    ++
Sbjct: 179 ALVMGQWKNSCKVVNAPLLKNE------VNSIVRVNPNGKPSETRFKVLEKFEQ-ATLIQ 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-SPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G  I  D +Y       +T     ++L+LHA  +   HP   
Sbjct: 232 ASPITGRTHQIRVHTQYTGHSIGWDDRYGDRRFDAYTGQFGLDRLFLHAANIKFTHPATE 291

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
             + I+AP+ A + +    L  K
Sbjct: 292 ELMDISAPMEAKLERVLKGLRSK 314


>gi|261377888|ref|ZP_05982461.1| ribosomal large subunit pseudouridine synthase D [Neisseria cinerea
           ATCC 14685]
 gi|269145743|gb|EEZ72161.1| ribosomal large subunit pseudouridine synthase D [Neisseria cinerea
           ATCC 14685]
          Length = 374

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 140/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   +R G V V+ K  +  +++  G+ +R+  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKPSQPKDKMIGGEQIRVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWSGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLQAQNSLVQQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y       +         +  +  LHA  +   +P
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNLRHPCSESAKEAVKSLGARQALHAYRLSFVYP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           + G  +   AP+P  M      L  + 
Sbjct: 310 KTGETVSFEAPIPDDMYHLLSVLRLEA 336


>gi|104780776|ref|YP_607274.1| 23S rRNA pseudouridylate synthase [Pseudomonas entomophila L48]
 gi|95109763|emb|CAK14468.1| 23S rRNA pseudouridylate synthase [Pseudomonas entomophila L48]
          Length = 318

 Score =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 101/319 (31%), Positives = 170/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + VQ + V  +    R+D +       +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 9   SGVQLIEVAPELAGQRIDNFLITALKGVPKTLVYRILRKGEVRVNKGRIKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP       + +  +    +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRVPP-----VRLPERDEPAPVAQGLLQR---LEAAIVYEDKALIVMNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L+  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y 
Sbjct: 121 LSFGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     K+ +   L K +   G+ +  V         A++ F+V+  F +    +E
Sbjct: 180 ALVRGHWPTSKKQVNAPLQKSNLRSGERMVEVNDE---GKEALTMFRVLRRFGEFATIVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   +F          +L+LHA  + +P P+GG
Sbjct: 237 ARPITGRTHQIRVHTLHAGHMIAGDSKYGDEDFSREIRELGGKRLFLHAYQLTVPLPDGG 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
            L++ AP+     KT + L
Sbjct: 297 ELKLEAPVDEVWAKTVERL 315


>gi|71735436|ref|YP_273876.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|257487558|ref|ZP_05641599.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tabaci ATCC 11528]
 gi|298486212|ref|ZP_07004275.1| Ribosomal large subunit pseudouridine synthase C [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|71555989|gb|AAZ35200.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|298159219|gb|EFI00277.1| Ribosomal large subunit pseudouridine synthase C [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|320325303|gb|EFW81370.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. glycinea str. B076]
 gi|320327712|gb|EFW83720.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330877844|gb|EGH11993.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330891478|gb|EGH24139.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. mori str. 301020]
 gi|330985584|gb|EGH83687.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. lachrymans str. M301315]
          Length = 318

 Score =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 103/319 (32%), Positives = 171/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 9   PGVQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRIPP-----VRVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y 
Sbjct: 121 LSFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     ++ +   L+K +   G+ +  V +       A++ FKV+  F      +E
Sbjct: 180 ALVRGNWATAQKQVRAPLMKSNLRSGERMVEVNEE---GKEALTIFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   NF          +L+LHA  + +P P+G 
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHAIAGDTKYGDENFSREIRDLGGKRLFLHAYMLTVPMPDGS 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L + AP+     KT + L
Sbjct: 297 KLNVQAPVDEMWAKTVERL 315


>gi|251793109|ref|YP_003007835.1| 23S rRNA pseudouridylate synthase C [Aggregatibacter aphrophilus
           NJ8700]
 gi|247534502|gb|ACS97748.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           aphrophilus NJ8700]
          Length = 319

 Score =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 103/319 (32%), Positives = 168/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ + +DE   RLD +       +    + +I+R G+VRV+K R K   ++Q+  VVR
Sbjct: 10  VQFLTINDDEAGQRLDNFLLARLKGVPKSLIYRIVRKGEVRVNKGRSKPEYKLQADDVVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+     S  LTK +  L+  +++ED+ + V NKP+GI+V GGSG+ 
Sbjct: 70  IPPVR------VAEKAQETISNKLTKVAQ-LEQQIIFEDNYLLVLNKPSGIAVHGGSGLD 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A ++L +  R + +QK Y +L
Sbjct: 123 FGVIEALRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRNLHKQLREKTVQKEYLAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V +       + + F V + +      ++  
Sbjct: 182 VRGQWQSHCKVVQAPLLKNELSSGERIVKVSEQ---GKPSETRFSVEERYV-NATLVKAS 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F          +L+LHA  +   HP  G  
Sbjct: 238 PVTGRTHQIRVHTQYAGHPIALDSKYGDKVFNQQMAELGLTRLFLHAYSIRFEHPHTGET 297

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L++TA L  +M      L 
Sbjct: 298 LRLTAQLDNYMKGILKRLR 316


>gi|118588308|ref|ZP_01545717.1| Prenyl group binding site (CAAX box):RNA-binding S4:Pseudouridine
           synthase:Pseudouridine synthase, Rlu:Pseudouridine
           [Stappia aggregata IAM 12614]
 gi|118439014|gb|EAV45646.1| Prenyl group binding site (CAAX box):RNA-binding S4:Pseudouridine
           synthase:Pseudouridine synthase, Rlu:Pseudouridine
           [Stappia aggregata IAM 12614]
          Length = 341

 Score =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 91/340 (26%), Positives = 152/340 (44%), Gaps = 46/340 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIP 68
           + V+  +   RLD     H   ++   +Q +++SG V V   K V+   R+  G  + + 
Sbjct: 18  LTVDAADAGKRLDAVLATHLEALSRNRIQSLIKSGDVTVGGAKIVEPKYRVNEGDALTLT 77

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                          L  + +     + +   +++ED  + V +KPAG+ V  G+G    
Sbjct: 78  ---------------LPQAEDPEPKGEDIPVTVVFEDEHLIVVDKPAGLVVHPGAGNWTG 122

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--- 178
             ++  +    DS       ++P + HR+D++TSG+LVVA+T  A + L   F       
Sbjct: 123 TLVNALIHHCGDSLSGIGGVKRPGIVHRIDKDTSGLLVVAKTDQAHKGLAAQFADHGRTG 182

Query: 179 -IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LVWG P   K  I   L + S      + VVK +      AI+H++V + F 
Sbjct: 183 PLERAYSALVWGAPSGLKGTINANLAR-SQANRQKIAVVKTS---GRQAITHWQVKERFG 238

Query: 238 QK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQ---- 285
                     LE +  TGRTHQ+RVH  H+G P++GD  Y + FK        P++    
Sbjct: 239 NAEQPALASLLECRLETGRTHQIRVHMAHIGHPLIGDDDYGSGFKTKANRLEEPLKSLVN 298

Query: 286 --NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             ++  LHA  +   HP  G+ L+  +P PA        L
Sbjct: 299 GFHRQALHAGLLAFEHPVNGKTLRFESPYPADFANLLSGL 338


>gi|289649339|ref|ZP_06480682.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aesculi str. 2250]
          Length = 318

 Score =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 103/319 (32%), Positives = 171/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 9   PGVQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRIPP-----VRVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y 
Sbjct: 121 LSFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     ++ +   L+K +   G+ +  V +       A++ FKV+  F      +E
Sbjct: 180 ALVRGNWATAQKQVRAPLMKSNLRSGERMVEVNEE---GKEALTIFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   NF          +L+LHA  + +P P+G 
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHAIAGDTKYGDENFSREIRDLGGKRLFLHAYMLTVPMPDGC 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L + AP+     KT + L
Sbjct: 297 KLNVQAPVDEMWAKTVERL 315


>gi|300704630|ref|YP_003746233.1| ribosomal large subunit pseudouridine synthase c [Ralstonia
           solanacearum CFBP2957]
 gi|299072294|emb|CBJ43627.1| Ribosomal large subunit pseudouridine synthase C [Ralstonia
           solanacearum CFBP2957]
          Length = 350

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 102/323 (31%), Positives = 165/323 (51%), Gaps = 19/323 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D +  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 29  VAYVEIGEDAQGQRIDNFLMRLAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 88

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A        +     V   +     +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 89  IPPLRIA--------QPSAEQVEAARAVPAAEFTILHEDTHLLVIDKPAGVAVHGGSGVA 140

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++ 
Sbjct: 141 FGVIEQLRR-SRPDAKFLELVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFAA 199

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  ++++ I   L K +   G+    V+ +      + + F  +  F   +  LE +
Sbjct: 200 VKGVWPHQRQHIKAPLFKYTTPEGERRVRVQAD---GQPSHTIFNKVGVFG-PYTLLEAE 255

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H G PI+GD KY              SP   +++LHA  + L HP+
Sbjct: 256 LKTGRTHQIRVHLAHAGFPILGDDKYGDFALNKALSRANASPRLARMFLHAHTLRLTHPQ 315

Query: 302 GGRL-QITAPLPAHMVKTWDSLG 323
            G +    APLPA      D+L 
Sbjct: 316 SGEIVTFKAPLPAECAAFLDALR 338


>gi|325133782|gb|EGC56438.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M13399]
          Length = 356

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 140/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 12  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 71  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 117

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T +A   L    + R +++IY ++
Sbjct: 118 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAV 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 178 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LTHSYIECS 231

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 232 LETGRTHQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 291

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 292 ESGETVSFEAPIPDDIYHLLSVLRLEA 318


>gi|260593408|ref|ZP_05858866.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           veroralis F0319]
 gi|260534684|gb|EEX17301.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           veroralis F0319]
          Length = 366

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 147/332 (44%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++      H +   +QK   +G + V+   VK N +++    + +  
Sbjct: 37  VEVDKGQVPVRIDKFLFERMQHSSRNRIQKAADAGFIHVNGAPVKSNYKVRPEDTITLML 96

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                ++ I+              ++ +   ++YED+ + V NKPAG+ V  G+G  +  
Sbjct: 97  DRPKHDNTIE--------------AEDIPLDIVYEDNALMVVNKPAGLVVHPGAGNFHGT 142

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+LV+A+T  A   L + F  +   + 
Sbjct: 143 LINAIAWHLKDLPSFDPNDPEVGLVHRIDKDTSGLLVIAKTPDAKTILGKQFFNKTTHRS 202

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + +        + V   + +    A++H++V++ F      
Sbjct: 203 YNALVWGNLTADEGRIEGNIARDPK-DRLRMTVFPPDSEIGKPAVTHYRVLERFG-YTTL 260

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKLYL 290
           +E    TGRTHQ+R H  H+G P+ GD +Y      +G  +S           + N+  L
Sbjct: 261 IECVLETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSSYKAFIRNCLTLCNRQAL 320

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HAR +   HP  G ++  T+ LP  +      
Sbjct: 321 HARTLGFVHPVTGQQMDFTSDLPQDLASLITK 352


>gi|260889966|ref|ZP_05901229.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           hofstadii F0254]
 gi|260860572|gb|EEX75072.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           hofstadii F0254]
          Length = 326

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 75/327 (22%), Positives = 148/327 (45%), Gaps = 33/327 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +VV  +E   R+D++       +    +Q++++   + V++K+ K   +I+    +++
Sbjct: 24  ENIVVLKEEAESRIDKFLSERL-ELTRTRIQQLIKDENILVNEKKTKPAYKIEENDTIKV 82

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                          ++     +    + +   ++YED+ + V NK AGI V   +G   
Sbjct: 83  ---------------VIPELETVEIKPENIDIEIIYEDNDLAVINKKAGIVVHPANGHYS 127

Query: 126 AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HRLD++TSG+L++A+   A   L++ F  + ++K
Sbjct: 128 GTLVNAILYYIKDLSGINGEIRPGIVHRLDKDTSGLLIIAKNDKAHLKLSQMFHDKTVKK 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +++ G    K   I   + +           V  +      AI++++VI    +KF 
Sbjct: 188 TYLAILKGKLSQKSGRIVTQIGRDK--NDRKKMTVTNDLNSGKTAITNYEVI-SQTEKFT 244

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            +++   TGRTHQ+RVH  H+G PI+GD  Y         +  + +  LHA  ++  HP 
Sbjct: 245 LVKVHIETGRTHQIRVHMKHLGYPILGDSVYG-------RTDTEKRQMLHAYKLEFEHPI 297

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYD 327
               ++  A LP    K     G +++
Sbjct: 298 IEKEIEFIAELPEDFEKALKKCGLEFE 324


>gi|194334247|ref|YP_002016107.1| RluA family pseudouridine synthase [Prosthecochloris aestuarii DSM
           271]
 gi|194312065|gb|ACF46460.1| pseudouridine synthase, RluA family [Prosthecochloris aestuarii DSM
           271]
          Length = 347

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 139/334 (41%), Gaps = 37/334 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V   +  MR+D +      +     +Q+ +   +V V+ K +K N RI+S   + + 
Sbjct: 24  TLRVARTQTPMRIDVYLAQQVENATRNKVQEAIAEHRVLVNGKTIKSNYRIKSLDSIEVT 83

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIA 126
            +      +  E   +D               ++YED  + V NK + + V    G+   
Sbjct: 84  FLRPPAPELAPEDIPID---------------IIYEDEDLMVVNKASDMVVHPAFGNWTG 128

Query: 127 YHIDGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  L         +D    +P + HRLD+ TSG++++A+   A   L   F  R+++
Sbjct: 129 TLANAILHHIGKEAGDLDCSDMRPGIVHRLDKNTSGLIIIAKNSTALHRLARQFANRQVE 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++VWG+P+     I   + +        +       K    AI+ ++V       F
Sbjct: 189 KKYQAIVWGVPEPATGLIKTNIGRSVR-NRKVMTSYPFEGKDGKTAITEYRVQQSLC-YF 246

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----------SPIQNKLY 289
             +E+  HTGRTHQ+RVH  H+G PI+GD  Y  +   N                  +  
Sbjct: 247 SLVEVTLHTGRTHQIRVHMQHLGHPILGDETYGGSSIRNLPFSKSESFVKNLLETIPRQA 306

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           LHA  +    P  G RL  TAPLP  M+   + +
Sbjct: 307 LHAESLTFTQPTTGERLSFTAPLPEDMLTALEKI 340


>gi|330720408|gb|EGG98730.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC2047]
          Length = 330

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 91/320 (28%), Positives = 164/320 (51%), Gaps = 15/320 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + VQ++ +  D    R+D +       +    + +I+R G+VRV+K R+K + ++QSG V
Sbjct: 22  SKVQFLEITEDSAGQRIDNFLCARLKGVPRTRIYRIVRKGEVRVNKGRIKADYKLQSGDV 81

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP+      + +  ++  +   L    + L+  +LYED  + + NKP+G++V GGSG
Sbjct: 82  VRVPPI-----RVAEANELPQAGKGL---KEALEQAVLYEDDSLLIINKPSGLAVHGGSG 133

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           I   +   L+  +  + +   L HRLD++TSG ++VA+ R+  ++L +  R   + K Y 
Sbjct: 134 IKLGLIETLRQ-LRPEARFLELVHRLDRDTSGCVMVAKKRSMLRYLHDLLRTNGVTKHYQ 192

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G    +K  +   L K +   G+ + V    +     +++ ++V   F+  +  ++
Sbjct: 193 ALVVGKWPTRKHKVDVPLQKNTLQSGERMVVA---DPDGKPSLTRYEVRQRFS-GYTLVQ 248

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P +GRTHQ+RVH    G  I GD KY   +      +    +L+LHA  +    PE G
Sbjct: 249 AYPVSGRTHQIRVHCQFAGHSIAGDDKYTDEDTNKRLKAMGLRRLFLHAESLAFKLPETG 308

Query: 304 R-LQITAPLPAHMVKTWDSL 322
           + L++ APL   +      L
Sbjct: 309 KLLRVEAPLDEQLQSFLTQL 328


>gi|281411684|ref|YP_003345763.1| pseudouridine synthase, RluA family [Thermotoga naphthophila
           RKU-10]
 gi|281372787|gb|ADA66349.1| pseudouridine synthase, RluA family [Thermotoga naphthophila
           RKU-10]
          Length = 311

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 84/319 (26%), Positives = 146/319 (45%), Gaps = 29/319 (9%)

Query: 12  VENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VE  EE  RLD++ K   P  I+   +QK ++ G+V+V+ +  K + +++ G++V +   
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSMIQKAIKEGKVKVNGQIKKPSYKLKEGEIVEV--- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYH 128
                       + +     T   + ++  +LYED  I V +KP  + V           
Sbjct: 63  -----------DLPEKPQEATVQPEEIELKVLYEDRDIVVIDKPRDMIVHPVPSKLSGTL 111

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D +G     +P + HRLD+ETSG++VVA+   A Q L++ F+ R+++K Y 
Sbjct: 112 VNALLNHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYI 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  K  +  +   L +        + +     +    AI+ ++V+  F      + 
Sbjct: 172 LLVKGRVKKDEGVVDLPLARHP-----VLRIKMAVVETGKEAITEYRVLKRFDDVATLVL 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P TGRTHQ+RVH   +G PI+GD  Y    +         +  LHA  +   HP  G 
Sbjct: 227 AFPKTGRTHQIRVHMKSLGHPIMGDKIYGKPKEDEI--FGIKRQMLHALKLGFFHPRTGE 284

Query: 305 -LQITAPLPAHMVKTWDSL 322
            ++  +PLP    +    +
Sbjct: 285 WMEFVSPLPEDFKEAIRKI 303


>gi|289624528|ref|ZP_06457482.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aesculi str. NCPPB3681]
 gi|330869277|gb|EGH03986.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aesculi str. 0893_23]
          Length = 318

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 106/319 (33%), Positives = 175/319 (54%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 9   PGVQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRIPP-----VRVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y 
Sbjct: 121 LSFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     ++ +   L+K +   G+ +  V+ NE+G   A++ FKV+  F      +E
Sbjct: 180 ALVRGNWATAQKQVRAPLMKSNLRSGERM--VEVNEEGKK-ALTIFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   NF          +L+LHA  + +P P+G 
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHAIAGDTKYGDENFSREIRDLGGKRLFLHAYMLTVPMPDGS 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L + AP+     KT + L
Sbjct: 297 KLNVQAPVDEMWAKTVERL 315


>gi|331012623|gb|EGH92679.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 318

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 103/319 (32%), Positives = 171/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 9   PGVQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRIPP-----VRVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y 
Sbjct: 121 LSFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     ++ +   L+K +   G+ +  V +       A++ FKV+  F      +E
Sbjct: 180 ALVRGNWATAQKQVRAPLMKSNLRSGERMGEVNEE---GKEALTIFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   NF          +L+LHA  + +P P+G 
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHAIAGDTKYGDENFSREIRDLGGKRLFLHAYMLTVPMPDGS 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L + AP+     KT + L
Sbjct: 297 KLNVQAPVDEMWAKTVERL 315


>gi|145634591|ref|ZP_01790300.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittAA]
 gi|148825307|ref|YP_001290060.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittEE]
 gi|148827612|ref|YP_001292365.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittGG]
 gi|229846499|ref|ZP_04466607.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae 7P49H1]
 gi|319775660|ref|YP_004138148.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae F3047]
 gi|329122287|ref|ZP_08250875.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           aegyptius ATCC 11116]
 gi|145268136|gb|EDK08131.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittAA]
 gi|148715467|gb|ABQ97677.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae PittEE]
 gi|148718854|gb|ABQ99981.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae PittGG]
 gi|229810592|gb|EEP46310.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae 7P49H1]
 gi|317450251|emb|CBY86467.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae F3047]
 gi|327473848|gb|EGF19265.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           aegyptius ATCC 11116]
          Length = 322

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 102/321 (31%), Positives = 170/321 (52%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+ +  V +       + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGERIVRVSEQ---GKPSETRFSIEERYI-NATLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L+  A L   M      L 
Sbjct: 299 ETLRFNASLDHQMKAILQKLR 319


>gi|148269598|ref|YP_001244058.1| RluA family pseudouridine synthase [Thermotoga petrophila RKU-1]
 gi|147735142|gb|ABQ46482.1| ribosomal large subunit pseudouridine synthase D [Thermotoga
           petrophila RKU-1]
          Length = 311

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 84/319 (26%), Positives = 147/319 (46%), Gaps = 29/319 (9%)

Query: 12  VENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VE  EE  RLD++ K   P  I+   +QK ++ G+V+V+ +  K + +++ G++V +   
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSLIQKAIKEGKVKVNGQIKKPSYKLKEGEIVEV--- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYH 128
                       + +     T   + ++  +LYED  I V +KP  + V           
Sbjct: 63  -----------DLPEKPQEATVQPEEIELKVLYEDRDIVVIDKPGDMIVHPVPSKLSGTL 111

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D +G     +P + HRLD+ETSG++VVA+   A Q L++ F+ R+++K Y 
Sbjct: 112 VNALLNHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYI 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  K  +  +   L +        + +     +    AI+ ++V+  F      + 
Sbjct: 172 LLVKGRVKKDEGVVDLPLARHP-----VLRIKMAVVETGKEAITEYRVLKRFDDVATLVL 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P TGRTHQ+RVH   +G PI+GD  Y    +         +  LHA  +   HP  G+
Sbjct: 227 AFPKTGRTHQIRVHMKSLGHPIMGDKIYGKPKEDEI--FGIKRQMLHALKLGFFHPRTGK 284

Query: 305 -LQITAPLPAHMVKTWDSL 322
            ++  +PLP    +    +
Sbjct: 285 WMEFVSPLPEDFKEAIRRI 303


>gi|145632659|ref|ZP_01788393.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 3655]
 gi|144986854|gb|EDJ93406.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 3655]
          Length = 322

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 102/321 (31%), Positives = 170/321 (52%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKSRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+ +  V +       + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGERIVRVSEQ---GKPSETRFSIEERYI-NATLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L+  A L   M      L 
Sbjct: 299 ETLRFNASLDHQMKAILQKLR 319


>gi|170288274|ref|YP_001738512.1| RluA family pseudouridine synthase [Thermotoga sp. RQ2]
 gi|170175777|gb|ACB08829.1| pseudouridine synthase, RluA family [Thermotoga sp. RQ2]
          Length = 311

 Score =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 85/319 (26%), Positives = 148/319 (46%), Gaps = 29/319 (9%)

Query: 12  VENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VE  EE  RLD++ K   P  I+   +QK ++ G+V+V+ +  K + +++ G++V +   
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSLIQKAIKEGKVKVNGQIKKPSYKLKEGEIVEV--- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYH 128
                       + +     T   + ++  +LYED  I V +KP  + V           
Sbjct: 63  -----------DLPEKPQEATVQPEEIELKVLYEDRDIVVIDKPGDMIVHPVPSKLSGTL 111

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  L    D +G     +P + HRLD+ETSG++VVA+   A Q L++ F+ R+++K Y 
Sbjct: 112 VNALLHHCKDLQGVGGKLRPGIVHRLDKETSGVIVVAKNDFAHQSLSKQFKDRKVKKTYI 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  K+ +  I   L +        + +     +    AI+ ++V+  F      + 
Sbjct: 172 LLVKGRVKSDEGVIDLPLARHP-----VLRIKMAVVETGKEAITEYRVLKRFDDVATLVL 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P TGRTHQ+RVH   +G PI+GD  Y    +         +  LHA  +   HP  G+
Sbjct: 227 AFPKTGRTHQIRVHMKSLGHPIMGDKIYGKPKEDEI--FGIKRQMLHALKLGFFHPRTGK 284

Query: 305 -LQITAPLPAHMVKTWDSL 322
            ++  +PLP    +    +
Sbjct: 285 WMEFVSPLPEDFKEAIRRI 303


>gi|261364920|ref|ZP_05977803.1| ribosomal large subunit pseudouridine synthase D [Neisseria mucosa
           ATCC 25996]
 gi|288566705|gb|EFC88265.1| ribosomal large subunit pseudouridine synthase D [Neisseria mucosa
           ATCC 25996]
          Length = 374

 Score =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 139/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLMPDYSRSRLTSWIKEGAVIVNDKPAQPKDKMIGGESISVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFKPEAMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y       +         +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNLRHPCSEPVKEAVKSLGARQALHAYRLSFVHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           + G  +   AP+P  M      L  + 
Sbjct: 310 KTGETVSFEAPIPEDMYHLLSVLRLEA 336


>gi|255280911|ref|ZP_05345466.1| ribosomal large subunit pseudouridine synthase D [Bryantella
           formatexigens DSM 14469]
 gi|255268359|gb|EET61564.1| ribosomal large subunit pseudouridine synthase D [Bryantella
           formatexigens DSM 14469]
          Length = 325

 Score =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 86/327 (26%), Positives = 147/327 (44%), Gaps = 33/327 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           +  + ++VE D    R+D++        +   LQK+L+  +V      VK + RI +G V
Sbjct: 22  STQKILIVEPDAVPERIDKYLSERLSG-SRSFLQKLLKENRVSAGGVPVKASYRICAGDV 80

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+     +   I+ E   LD               +LYED  + V NKP G+ V  G+G
Sbjct: 81  IRVDIPAQSEPDILAEDIPLD---------------ILYEDDDLLVVNKPKGMVVHPGAG 125

Query: 125 IAYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
              H   +  +    D+        +P + HR+DQ T+G L+V +   +   +    +  
Sbjct: 126 HYSHTLVNALMYHCRDNLSGINGVLRPGIVHRIDQNTTGSLLVCKNDFSHNFIAGQLKEH 185

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I + Y ++V G   +      N  + +  +    + V   NEK    A++H++V++ F 
Sbjct: 186 SITRRYRAIVHGKISSDGTV--NAPIGRHPVERKKMAV---NEKNGKPAVTHYRVLEQF- 239

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +KF ++E    TGRTHQ+RVH   +  PI+GD  Y          P      LHA+ +  
Sbjct: 240 EKFTYIECVLETGRTHQIRVHMSSIHHPILGDDVYGP---ARCPFPGLQGQTLHAQVLGF 296

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++ +APLP +  +  + L 
Sbjct: 297 IHPRTGEYMEFSAPLPQYFEELLEKLR 323


>gi|77360755|ref|YP_340330.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875666|emb|CAI86887.1| 23S rRNA pseudouridylate synthase, in E. coli modifies positions
           955, 2504, and 2580 in 23 S ribosomal RNA
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 319

 Score =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 98/320 (30%), Positives = 165/320 (51%), Gaps = 14/320 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V YV +  D    R+D +   H   +    + K+LR G+VRV+KKR+K   ++Q   V+
Sbjct: 8   QVTYVTINEDHLGQRIDNFLITHLKGVPKSAIYKLLRKGEVRVNKKRIKPVYKLQLEDVL 67

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RI P+      + + ++ + S ++       L++ +++ED  + V NKP+G++V GGSG+
Sbjct: 68  RIAPI-----RVAEREEFVPSKLDKVTR---LENDIIFEDKYLIVINKPSGMAVHGGSGL 119

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +Y +   L+     + +   L HRLD++TSG L++A+ R+    L E  R + ++K YW+
Sbjct: 120 SYGLIEALRVLRPEE-RSLELVHRLDRDTSGCLLIAKRRSVLTALHEQLREKTMEKNYWA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   +K + +   L K +   G+ V  V   E     + + FKV++ F +    ++ 
Sbjct: 179 LVDGQWDSKTKNVTEGLRKNTLKSGERVVRVDNTE--GKPSHTRFKVLERFNE-CSLVQA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
            P TGRTHQ+RVH    G PI  D KY    F  +      N+L+LHA  +   HP+   
Sbjct: 236 SPVTGRTHQIRVHTQCKGHPIACDDKYGDEEFDNSMRKTGLNRLFLHAHDLTFYHPKNET 295

Query: 304 RLQITAPLPAHMVKTWDSLG 323
            +++ APL   +      L 
Sbjct: 296 TMRVEAPLDKALANCLVKLR 315


>gi|260587704|ref|ZP_05853617.1| ribosomal large subunit pseudouridine synthase D [Blautia hansenii
           DSM 20583]
 gi|331084005|ref|ZP_08333112.1| hypothetical protein HMPREF0992_02036 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260541969|gb|EEX22538.1| ribosomal large subunit pseudouridine synthase D [Blautia hansenii
           DSM 20583]
 gi|330402367|gb|EGG81937.1| hypothetical protein HMPREF0992_02036 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 305

 Score =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 86/322 (26%), Positives = 141/322 (43%), Gaps = 31/322 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V++     R+D++        +   LQK L+ G V V++K  K + ++     VRI  
Sbjct: 6   LQVDSAYAGERIDKYLAEVMNDYSRSFLQKQLKDGNVSVNEKTAKASLKVAEDDEVRIFI 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
             N    I+ E   LD               +LYED ++ V NKP G+ V   +G     
Sbjct: 66  PENKEPDIVPEDIPLD---------------ILYEDQQLLVVNKPKGMVVHPSAGHYSQT 110

Query: 128 HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++  +    D         +P + HR+D +T+G LVV +T  A Q L E  ++  I ++
Sbjct: 111 LVNALMFHCKDQLSGINGVLRPGIVHRIDMDTTGALVVCKTDLAHQSLAEQLKVHSITRL 170

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G  K     I   + +           +  N +    A +H+KV++ F  +F +
Sbjct: 171 YRAIVHGRLKEDFGTIEGTIGRHPTDRKK----MAINVRNGKPATTHYKVLERF-DRFTY 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+RVH   +G P++GD  Y          P      LHA  +   HP  
Sbjct: 226 VECELETGRTHQIRVHMSSIGHPLLGDIVYGPK---KSALPNLQGQTLHAMVLGFLHPVS 282

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
              ++ TAPLP +  K   +  
Sbjct: 283 NEYMEFTAPLPEYFEKLLKNFR 304


>gi|238027090|ref|YP_002911321.1| Pseudouridine synthase RluD [Burkholderia glumae BGR1]
 gi|237876284|gb|ACR28617.1| Pseudouridine synthase RluD [Burkholderia glumae BGR1]
          Length = 400

 Score =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 83/318 (26%), Positives = 139/318 (43%), Gaps = 29/318 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ  + + +VRVD +  K    +  G  + +
Sbjct: 57  RLVAVPPALAGERLDKALAQLFPEFSRSRLQSWIEAQRVRVDGEPAKVRQPVPLGATIEL 116

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P       ++ EQ        L    + +   ++YED  + V +KPAG+ V   +G   
Sbjct: 117 VP------DLLPEQ--------LAFTPEPVPLAIVYEDEALVVIDKPAGLVVHPAAGNWN 162

Query: 128 HI--DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               +G L  + ++     +  + HRLD+ETSG++VVART AA   L    + R +++ Y
Sbjct: 163 GTLLNGLLHRYGEAAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRY 222

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKF 240
           ++LVWG        I   + +      +   +          A +HF+ +D      Q  
Sbjct: 223 FALVWGR-TPASGTIDAPIGRDP---RERTRMAVVTGASGKPARTHFRTVDSVLWQNQPV 278

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDL 297
             ++    TGRTHQ+RVH  H+G P++GD  Y         + + +   +  LHA  + L
Sbjct: 279 SAIQCDLETGRTHQIRVHCAHLGHPLLGDPVYGRARGKRSVAALPDGFARQALHAWRLGL 338

Query: 298 PHPEGGR-LQITAPLPAH 314
            HP  GR +Q    +P  
Sbjct: 339 VHPVTGRSMQWRCAVPDD 356


>gi|168186171|ref|ZP_02620806.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum C str. Eklund]
 gi|169295643|gb|EDS77776.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum C str. Eklund]
          Length = 304

 Score =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 141/327 (43%), Gaps = 38/327 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++  ++   E N RLD +    +   +    QK++    V V+    K N +++ G  V
Sbjct: 2   KIKDFLINESEVNSRLDVFISKCFEEKSRSYAQKLIEEKNVFVNNSSKKSNYKLKIGDYV 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--- 122
            I                +     +    + +K  ++YED  + V +KP G+ V  G   
Sbjct: 62  EIK---------------IKEDEKINIKPEDIKLNIIYEDEDVIVIDKPQGMVVHPGAGN 106

Query: 123 ------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                 +G+ YH D        +   +P + HR+D++TSG+LVVA+  +A   L+E  + 
Sbjct: 107 YSGTLVNGLLYHCDSLSSI---NGDVRPGIVHRIDKDTSGVLVVAKNDSAHIILSEQLKE 163

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             +++ Y +LV GI KN +  I   L +          V     +    A++H+ V+  F
Sbjct: 164 HSMKREYIALVEGIIKNDEGIIDAPLGRNPKDRIKRAVV-----RNGKSAVTHYNVLRRF 218

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    ++    TGRTHQ+RVH  H+  P+VGD  Y    +        N   LHAR + 
Sbjct: 219 NKN-TLVKCILETGRTHQIRVHMAHINHPLVGDPMYGFRKQ----RFKLNGQMLHARKLG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP   + ++  + LP +  +    L
Sbjct: 274 FIHPSSKKYMEFQSELPNYYKEILFKL 300


>gi|313668816|ref|YP_004049100.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           lactamica ST-640]
 gi|313006278|emb|CBN87741.1| putative ribosomal large subunit pseudouridine synthase D
           [Neisseria lactamica 020-06]
          Length = 374

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 139/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   +R G V V+ K  +  +++  G+ +R+  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKPSQPKDKMIGGEQIRVTV 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
             +A                     + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 90  RPSAEYSAFA--------------PEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWSGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAGDPVYGNLRHPCGDTVKEAVKSLGARQALHAYRLSFVHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ETGETVSFEAPIPNDIYHLLSVLRLEA 336


>gi|148379448|ref|YP_001253989.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 3502]
 gi|153934249|ref|YP_001383827.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           ATCC 19397]
 gi|153935171|ref|YP_001387377.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           Hall]
 gi|148288932|emb|CAL83019.1| putative ribosomal large subunit pseudouridine synthase
           [Clostridium botulinum A str. ATCC 3502]
 gi|152930293|gb|ABS35793.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 19397]
 gi|152931085|gb|ABS36584.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           Hall]
 gi|322805794|emb|CBZ03359.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum H04402 065]
          Length = 305

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 87/326 (26%), Positives = 150/326 (46%), Gaps = 33/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  + VE + +N+RLD +    +   +   LQ I+  G V V+ K  K N +++ G 
Sbjct: 1   MEKIN-LQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +K  ++YED  + V NKP  + V    
Sbjct: 60  NIEVN---------------IPEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G+     ++  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+  
Sbjct: 105 GVYSGTLVNALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I ++Y +LV GI K+++  I   + +   +    + VV    K   +A++H+KVI+ F 
Sbjct: 165 SISRVYMALVEGIIKDEQGTIEAPIGRH-PVDRIKMAVV----KDGRHAVTHYKVIERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    +E +  TGRTHQ+RVH  H+  P+VGD  Y    +            LHA+ +  
Sbjct: 219 KNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQ----RFNLKGQMLHAKLLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP   + ++  + LP +  K    L
Sbjct: 275 IHPTTRQYVEFESELPEYFKKIIKIL 300


>gi|153814897|ref|ZP_01967565.1| hypothetical protein RUMTOR_01112 [Ruminococcus torques ATCC 27756]
 gi|317500410|ref|ZP_07958634.1| pseudouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089583|ref|ZP_08338482.1| hypothetical protein HMPREF1025_02065 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145847928|gb|EDK24846.1| hypothetical protein RUMTOR_01112 [Ruminococcus torques ATCC 27756]
 gi|316898165|gb|EFV20212.1| pseudouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330404951|gb|EGG84489.1| hypothetical protein HMPREF1025_02065 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 303

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 146/327 (44%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +++     D    R+DR+   +  +++   +QK+L+ G++ V++  VK N +I    
Sbjct: 1   MEQIKF---TADRSGERIDRFLSENLENLSRSYIQKLLKDGKISVNQSSVKPNYKISEND 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +      +  I+ E   LD               +LYEDS I + NKP  + V    
Sbjct: 58  KIEVFIPDPEVLDILPENIPLD---------------ILYEDSDILIVNKPKNMVVHPAP 102

Query: 124 GIAYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G   H   +  +    D+        +P + HR+D +T+G L++ +   A Q + E  + 
Sbjct: 103 GHYEHTLVNAVMYHCKDNLSGINGILRPGIVHRIDMDTTGSLLICKNDKAHQIIAEQLKE 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y ++V G  K     +   + +   I    +       K   +A++H+ V+  F
Sbjct: 163 HSITRRYHAIVHGKIKEDNGVVNAPIGRH-PIDRKKMST---KAKNGKHAVTHYTVLRRF 218

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + + ++E +  TGRTHQ+RVH   +G PI+GD  Y  +              LHA+ + 
Sbjct: 219 -KDYTYIECELETGRTHQIRVHMASIGHPILGDSMYGPSK----CPFKLQGQTLHAKVLG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + HP  G+ +++ APLP +  K    L
Sbjct: 274 ITHPSTGKYIEVDAPLPEYFNKLLKQL 300


>gi|91793653|ref|YP_563304.1| pseudouridine synthase, RluD [Shewanella denitrificans OS217]
 gi|91715655|gb|ABE55581.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           denitrificans OS217]
          Length = 318

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 107/323 (33%), Positives = 171/323 (52%), Gaps = 13/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
              T VQ V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q 
Sbjct: 4   ETPTQVQLVTIDEDHFEQRIDNYLITALKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQI 63

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVRIPP       + ++      S NL++ S  L++ +++ED  + V NKPAGI+V G
Sbjct: 64  GDVVRIPP-----VRMAEKDYRTAPSANLSRVS-VLETRIIHEDKHLIVLNKPAGIAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSGI + +   L+S    +     L HRLD++TSG+L+VA+ R+A +HL +  R + +QK
Sbjct: 118 GSGIDFGVIEGLRSLRPQQKF-LELVHRLDKDTSGVLLVAKKRSALKHLHDQLRNKTMQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  + K + I   LLK +   G+ +  V         + + F+++  +     
Sbjct: 177 DYLALVRGEWQAKDKSIKAPLLKITLASGERIVRVNAE---GKASETRFRIMQRY-DGCT 232

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH    G  I  D KY    F  +      N+L+LHA  +   HP
Sbjct: 233 LVKASPVTGRTHQIRVHCQFAGHAIACDDKYSEQSFDDSMRVHGLNRLFLHAAELKFIHP 292

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
           E    +Q+ APL  ++ +T + L
Sbjct: 293 ENDEVMQVQAPLDENLSQTLEKL 315


>gi|172057958|ref|YP_001814418.1| RluA family pseudouridine synthase [Exiguobacterium sibiricum
           255-15]
 gi|171990479|gb|ACB61401.1| pseudouridine synthase, RluA family [Exiguobacterium sibiricum
           255-15]
          Length = 307

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 82/326 (25%), Positives = 147/326 (45%), Gaps = 33/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M       V+ +    R+D+W        +   +Q  L++G V VD + VK N ++   +
Sbjct: 1   MNEQNEWAVKANGATGRIDKWLAEQ-QDWSRSQVQDWLKAGHVEVDGRIVKPNYKMSGTE 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +  +V L    + +   ++YEDS + V NKP G+ V   +
Sbjct: 60  EILVR---------------IPEAVELEVLPEDIPLDVVYEDSDVIVINKPKGMVVHPAA 104

Query: 124 GI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G    ++P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 105 GHVSGTLVNALLHHCQDLSGINGVKRPGIVHRIDKDTSGLLMVAKNDLAHESLAQQLKDK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +++Y +LV G   ++   I   + +      +    +   +K +  A++HF+V++ + 
Sbjct: 165 TTERLYIALVHGEIPHELGTIEAPVGRD----KNDRQRMTVTDKNSKAAVTHFRVLERY- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY             N   LHA  +  
Sbjct: 220 EGFTVVECKLETGRTHQIRVHMRYIGFPLAGDPKYGPRKTMKM-----NGQALHAAVLGF 274

Query: 298 PHPEGGRL-QITAPLPAHMVKTWDSL 322
            HP  G +    APLP  M      L
Sbjct: 275 KHPRTGEMLHFEAPLPEEMTFEISQL 300


>gi|107102524|ref|ZP_01366442.1| hypothetical protein PaerPA_01003588 [Pseudomonas aeruginosa PACS2]
          Length = 318

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 102/323 (31%), Positives = 169/323 (52%), Gaps = 14/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S +T VQ + V  +    R+D +            + +ILR G+VRV+K R+K + R+Q+
Sbjct: 6   SPITGVQLLDVPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRIKPDYRLQA 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+  A           + +       + +++ ++YED  + V NKPAGI+V G
Sbjct: 66  GDQVRVPPLRLAERD--------EPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQ 180
           GSG++  +    +  +    +   L HRLD++TSG+L++A+ R+  +HL E+ R  + + 
Sbjct: 118 GSGVSAGVIEVFRQ-LRPDAKDIELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKIVD 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G     K+ +   LLK +   G+ +  V    K    A++ F+V+  F    
Sbjct: 177 KRYHALVRGHWPAGKKNVRAPLLKNNLRSGERMVEVNVEGKD---ALTEFRVLRRFGDFA 233

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPH 299
             +E +P TGRTHQ+RVHA H G  I GD KY   +F          +L+LHA  + +P 
Sbjct: 234 TLVEARPITGRTHQIRVHAKHAGHAIAGDPKYGDEDFSREIRELGGKRLFLHAAQLRVPL 293

Query: 300 PEGGRLQITAPLPAHMVKTWDSL 322
           P+G  L++ AP+     ++ + L
Sbjct: 294 PDGQVLELEAPVDEMWQRSLERL 316


>gi|315634769|ref|ZP_07890051.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           segnis ATCC 33393]
 gi|315476321|gb|EFU67071.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           segnis ATCC 33393]
          Length = 349

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 107/319 (33%), Positives = 168/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ + +DE   RLD +       +    + +I+R G+VRV+K R K   ++Q+  VVR
Sbjct: 40  VQFLTISDDEAGQRLDNFLLARLKGVPKSLIYRIVRKGEVRVNKGRSKPEYKLQAEDVVR 99

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV       + E+     S  LTK +  L+  +++ED+ + V NKP+GI+V GGSG+ 
Sbjct: 100 IPPVR------VAEKAQETVSHKLTKVAQ-LEQHIIFEDNYLLVLNKPSGIAVHGGSGLD 152

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A +HL E  R + IQK Y +L
Sbjct: 153 FGVIEALRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRHLHEQLREKTIQKEYLAL 211

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V +       + + F V + +      ++  
Sbjct: 212 VRGQWQSHCKVVQAPLLKNELSSGERIVKVSEQ---GKPSETRFSVEERYV-NATLVKAS 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP  G  
Sbjct: 268 PVTGRTHQIRVHTQYAGHPIALDSKYGDKVFDQQMAELGLNRLFLHAYSIRFEHPHSGET 327

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L++TA L   M      L 
Sbjct: 328 LRLTAQLDEKMKGILKRLR 346


>gi|260461536|ref|ZP_05809783.1| pseudouridine synthase, RluA family [Mesorhizobium opportunistum
           WSM2075]
 gi|259032606|gb|EEW33870.1| pseudouridine synthase, RluA family [Mesorhizobium opportunistum
           WSM2075]
          Length = 334

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 92/344 (26%), Positives = 156/344 (45%), Gaps = 46/344 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQS 61
           M     +V   D    RLD+W      P ++   +Q ++R G V ++ K V     ++  
Sbjct: 1   MEAPTVLVTGADAAGQRLDQWLAASLGPDMSRSRVQMLIRQGAVSINGKPVDETKRKMLP 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G+ V +                +          + +   +LYED  + V NKPAG+ V  
Sbjct: 61  GESVSV---------------AMPEPEPAEPQGENIALDVLYEDDALIVINKPAGLVVHP 105

Query: 122 GSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G+G      ++  +    DS       ++P + HRLD+ETSG++VVA+T  A + L+E+F
Sbjct: 106 GAGNWTGTLVNALIHHCGDSLSGIGGVRRPGIVHRLDKETSGVMVVAKTDRAHKALSEAF 165

Query: 175 RMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
                   +++ Y +LVWGIP+     +   L + +        VV +    A +A++HF
Sbjct: 166 ADHGLTGDLERAYLALVWGIPQRPTGTVDAPLGRAA--DRVRRAVVPEGRDDARHAVTHF 223

Query: 231 KVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFT 281
            V + F +K         +E +  TGRTHQ+RVH  H+G P++GD  Y   F+       
Sbjct: 224 AVQERFGEKQQEFATASLVECRLETGRTHQIRVHMAHIGHPVIGDPDYGQAFRTKANRLP 283

Query: 282 SPIQ------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
            P++      ++  LHA  +   HP+    ++  AP+P  M + 
Sbjct: 284 EPLKSQVKAFSRQALHAWLLAFRHPDTHLTMRFEAPIPRDMEEL 327


>gi|160914264|ref|ZP_02076485.1| hypothetical protein EUBDOL_00274 [Eubacterium dolichum DSM 3991]
 gi|158433891|gb|EDP12180.1| hypothetical protein EUBDOL_00274 [Eubacterium dolichum DSM 3991]
          Length = 303

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 147/319 (46%), Gaps = 32/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  D ++ R+D++       ++   +  ++  G + V+ + ++   +++    +      
Sbjct: 8   VAEDADSQRIDKYLSMVVEDLSRSRIASLIEEGSILVNGEVIRAKYKVKPADHIT----- 62

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                        +  + L    + ++  + YED  + V NKP GI V   +G      +
Sbjct: 63  ----------AAFEDEMALEAAPEKMELDIRYEDHDVIVINKPKGIVVHPANGNQSGTLV 112

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +G L    D  G     +P + HR+D++T+G+L+VA+   A   L++  + + + ++Y++
Sbjct: 113 NGLLYHCKDLSGINGVLRPGIVHRIDKDTTGLLIVAKNDKAHASLSKQLQNKSVNRLYYA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G+ +++   I   + +        + V+  N   +  A +HF+V++ FA K+  +E 
Sbjct: 173 LVHGVIEHEFGTIDAPIGRDPK-DRQKMAVIATN---SKPARTHFRVVERFA-KYTLVEC 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
           +  TGRTHQ+RVH  ++G P+VGD KY             N   LHA  +   HP    R
Sbjct: 228 RLETGRTHQIRVHMQYIGHPVVGDEKYSYRKTMKT-----NGQLLHAHQLTFLHPTTNER 282

Query: 305 LQITAPLPAHMVKTWDSLG 323
           + + APLP       + L 
Sbjct: 283 ITVEAPLPKQFADILEELR 301


>gi|240146315|ref|ZP_04744916.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis L1-82]
 gi|257201556|gb|EEU99840.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis L1-82]
          Length = 310

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 84/330 (25%), Positives = 147/330 (44%), Gaps = 39/330 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHI-------NFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           +   +E + E  RLD++    +          +    QK++R G V+V+    K N R++
Sbjct: 4   ETFEIEAEYEGERLDKYLSVIFEQSKTSSNAPSRSFFQKLIRDGHVKVNDSIAKANYRLR 63

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
              +V +         I+ E   LD               +LYED  + V NKP G+ V 
Sbjct: 64  MDDLVCVEIPDAVETPILPEDIPLD---------------ILYEDDDLLVVNKPKGMVVH 108

Query: 121 GGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
             +G      ++  +    DS        +P + HR+D +T+G L+V +   +   + E 
Sbjct: 109 PSAGHYSGTLVNAIMFHCKDSLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHIKIAEQ 168

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            +   + + Y  +V+G+ K+ +  I   + +           +  NEK    AI+H+KV+
Sbjct: 169 IKEHSVNRRYRGIVYGVVKDDEGTINAPIGRHPTNRKK----MAINEKNGKPAITHYKVL 224

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F+  + ++E +  TGRTHQ+RVH   +G P++GD  Y +      T        LHA 
Sbjct: 225 ERFS-NYTYMEFKLETGRTHQIRVHMASIGHPLLGDTVYSSGKSPFKT----QGQTLHAM 279

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +   HP     ++I+APLP + +K   SL
Sbjct: 280 TIGFIHPHTNEYMEISAPLPEYFLKILKSL 309


>gi|218767826|ref|YP_002342338.1| putative ribosomal large subunit pseudouridine synthase D
           [Neisseria meningitidis Z2491]
 gi|34395831|sp|Q9JVB6|RLUD_NEIMA RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|121051834|emb|CAM08140.1| putative ribosomal large subunit pseudouridine synthase D
           [Neisseria meningitidis Z2491]
          Length = 374

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 140/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ +R+  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKPSQPKDKMIGGEQIRVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVWQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|169831112|ref|YP_001717094.1| RluA family pseudouridine synthase [Candidatus Desulforudis
           audaxviator MP104C]
 gi|169637956|gb|ACA59462.1| pseudouridine synthase, RluA family [Candidatus Desulforudis
           audaxviator MP104C]
          Length = 309

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 87/326 (26%), Positives = 142/326 (43%), Gaps = 31/326 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +    VE ++E  RLD +     P ++   +QK++    V V+ +  + ++R++ G 
Sbjct: 1   MATLNRYTVEEEDEQTRLDVFLAGQNPELSRARIQKLISLELVTVNGRPARASHRVRGGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +         I  E   L+               + +ED  + V NKP G+ V    
Sbjct: 61  CVELKVPDPETPRIEPEAIPLE---------------VCFEDPDVLVVNKPRGLVVHPAV 105

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HRLD++TSG+L+VA+  AA   L    + R
Sbjct: 106 GHYSGTLVNALLHHCRDLSGINGILRPGIVHRLDRDTSGLLMVAKNDAAHLALAGQLKDR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G P+ +   +   + +           +    +    A +H++V+  F 
Sbjct: 166 AVLRRYTALVHGRPRRETGTVDAPIGRHPRD----RQRMAVTPRSGRAARTHYRVVRRF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            KF  LE+   TGRTHQ+RVH  H+G P+VGD KY                +LHA  +  
Sbjct: 221 DKFSLLELTLDTGRTHQIRVHMAHVGHPLVGDLKYGHARP----ELGLEGQFLHAGTLGF 276

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  L   APLP+ +    + L
Sbjct: 277 RHPRTGEVLVFEAPLPSELAAVLERL 302


>gi|59800728|ref|YP_207440.1| RluD [Neisseria gonorrhoeae FA 1090]
 gi|240016030|ref|ZP_04722570.1| RluD [Neisseria gonorrhoeae FA6140]
 gi|240080171|ref|ZP_04724714.1| RluD [Neisseria gonorrhoeae FA19]
 gi|240115125|ref|ZP_04729187.1| RluD [Neisseria gonorrhoeae PID18]
 gi|240122965|ref|ZP_04735921.1| RluD [Neisseria gonorrhoeae PID332]
 gi|240125216|ref|ZP_04738102.1| RluD [Neisseria gonorrhoeae SK-92-679]
 gi|240127670|ref|ZP_04740331.1| RluD [Neisseria gonorrhoeae SK-93-1035]
 gi|260441058|ref|ZP_05794874.1| RluD [Neisseria gonorrhoeae DGI2]
 gi|268596320|ref|ZP_06130487.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae FA19]
 gi|268600798|ref|ZP_06134965.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae PID18]
 gi|268681584|ref|ZP_06148446.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae PID332]
 gi|268683812|ref|ZP_06150674.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae SK-92-679]
 gi|268686054|ref|ZP_06152916.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae SK-93-1035]
 gi|293399573|ref|ZP_06643726.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae F62]
 gi|59717623|gb|AAW89028.1| putative ribosomal large subunit pseudouridine synthase D
           [Neisseria gonorrhoeae FA 1090]
 gi|268550108|gb|EEZ45127.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae FA19]
 gi|268584929|gb|EEZ49605.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae PID18]
 gi|268621868|gb|EEZ54268.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae PID332]
 gi|268624096|gb|EEZ56496.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae SK-92-679]
 gi|268626338|gb|EEZ58738.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae SK-93-1035]
 gi|291610142|gb|EFF39264.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae F62]
          Length = 374

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 138/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     +  VK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAAVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 250 LGTGRTHQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|331005269|ref|ZP_08328661.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC1989]
 gi|330420946|gb|EGG95220.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC1989]
          Length = 362

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 99/347 (28%), Positives = 175/347 (50%), Gaps = 33/347 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ++ ++      R+D +  +    +    + +ILR G+VRV+K RVK   ++  G V
Sbjct: 26  NSVQFITIDAGNTAQRIDNFLLSRLKGVPKSRIYRILRKGEVRVNKGRVKPEYKLCDGDV 85

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP+  +           +      K S  L+  +L+E+  + V NKP+G++V GGSG
Sbjct: 86  VRVPPIRVSQRD--------EPPQPSQKLSTLLEDSILFENDDLMVVNKPSGLAVHGGSG 137

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           I+  +    +       +   L HRLD++TSG +++A+ R++ +++ +  R  RIQKIY 
Sbjct: 138 ISLGLIESFRQMR-PDNRFLELVHRLDRDTSGCIMIAKKRSSLRYIQQELREGRIQKIYR 196

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFA------ 237
           +LV G   N+++ + + L+K     G+ V  + Q E +GA  + + + VI  +       
Sbjct: 197 ALVDGRWPNRRKNVTSPLVKNQLSSGERVVRIAQPETEGAKASRTEYNVIQRYQYTANSH 256

Query: 238 ---------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFT 281
                          ++   +E +P TGRTHQ+RVH   +GC I+GD KYC       + 
Sbjct: 257 GECNGGQNGGQFDGRRECTLVEAKPITGRTHQIRVHCQSVGCAIIGDDKYCDGEINKYYR 316

Query: 282 SPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
                +L+LHA  +    P+G  + + APL + ++  + ++  K DR
Sbjct: 317 GAGLKRLFLHAFQLTFCLPDGSSVSVEAPLGSDLLPVFKNIQ-KSDR 362


>gi|194290175|ref|YP_002006082.1| ribosomal large subunit pseudouridine synthase c [Cupriavidus
           taiwanensis LMG 19424]
 gi|193224010|emb|CAQ70019.1| Ribosomal large subunit pseudouridine synthase C [Cupriavidus
           taiwanensis LMG 19424]
          Length = 333

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 107/325 (32%), Positives = 165/325 (50%), Gaps = 22/325 (6%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V YV ++   E  R+D +       +   ++ ++LRSG+VRV+K R+    R+QSG V
Sbjct: 19  PQVAYVTIDEGSEGQRIDNFLLKVAKGVPKSHIYRVLRSGEVRVNKGRIDATYRLQSGDV 78

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+           ++  ++ +        +  +L+ED+ + V NKPAG++V GGSG
Sbjct: 79  VRIPPM-----------RVASAAQSGAAPVPAGEFPVLFEDAHLLVINKPAGVAVHGGSG 127

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +A+ +   L+     + +   L HRLD+ETSGILV+A+ R+A  HL E  R   + K Y+
Sbjct: 128 VAFGVIEQLRR-SRPQAKFLELVHRLDRETSGILVLAKKRSALVHLHEQIRGNTMDKRYY 186

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           + V G   N ++ +   L K S   G+    V+ +      + + F  ++ F   F  LE
Sbjct: 187 ACVAGEFLNARQHVKLPLYKYSTPDGERRVRVQAD---GLASHTVFNRVEAFP-GFTLLE 242

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPH 299
            +  TGRTHQ+RVH  H G PIVGD KY       +   +   P   +++LHA  +   H
Sbjct: 243 AELKTGRTHQIRVHLAHSGFPIVGDEKYGDFTLNKSLARSGAKPGIKRMFLHAHRLVFIH 302

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  G  L + APLP   V     L 
Sbjct: 303 PATGEPLSVEAPLPDECVGFLQQLR 327


>gi|331091117|ref|ZP_08339959.1| hypothetical protein HMPREF9477_00602 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330405339|gb|EGG84875.1| hypothetical protein HMPREF9477_00602 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 307

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 78/323 (24%), Positives = 148/323 (45%), Gaps = 32/323 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  ++  +E  MR+D +      +++   +QK+++  ++ V+   VK N ++ +  +V++
Sbjct: 4   EQFIINQEENGMRIDVFLSKKMDNVSRSYIQKLIKEKEISVNGMAVKANYKVSANDIVQL 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                +   I+ E   LD               +LYED+ I + NKP G+ V        
Sbjct: 64  TIPDLSEPDILPENIPLD---------------ILYEDADILIVNKPKGMVVHPSPSHYT 108

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++  +    D         +P + HR+D +T+G L+V +   A Q L E  ++  I+
Sbjct: 109 GTLVNALMYYCKDDLSGINGVMRPGIVHRIDMDTTGSLLVCKNDFAHQKLAEDLKVHNIK 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           +IY ++V G+ K  +  +   + +   I    + +   N K    A++H++V+  F+  +
Sbjct: 169 RIYHAIVHGVIKEDEGTVEGPIGRH-PIDRKKMSI---NYKNGKPAVTHYRVLKRFS-NY 223

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++E Q  TGRTHQ+RVH   +   +VGD  Y        +        LHA+ + + HP
Sbjct: 224 TYIECQLETGRTHQIRVHMASIHHALVGDTVYGP----AKSPFHLQGQTLHAKILGIHHP 279

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                L+I APLP +     + L
Sbjct: 280 RTNEYLEIDAPLPEYFTDLLEKL 302


>gi|330995872|ref|ZP_08319768.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
 gi|329574403|gb|EGG55974.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
          Length = 363

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 82/332 (24%), Positives = 149/332 (44%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +  ++ ++ MR+D++   H  + +   LQ+      + V+ + VK + +++    + I  
Sbjct: 37  LTADSGQKPMRIDKFLMEHLYNTSRNRLQRAAEQEFILVNGRPVKSSYKVKPLDEIVI-- 94

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
               L+    E +I+   + L          ++YED  + V +KPAG+ V  G G     
Sbjct: 95  ---LLDRPKYENEIIPEDIPLD---------IVYEDEDLMVVDKPAGLVVHPGCGNYTGT 142

Query: 128 HIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++       D+    P      L HR+D++TSG+LVVA+   A  HL   F  +  Q++
Sbjct: 143 LVNAIAWHLKDNPDYDPNDPTVGLVHRIDKDTSGLLVVAKNADAKTHLGRQFFNKTTQRL 202

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  ++++  I   + +        + V   +     +A++H++V++ F      
Sbjct: 203 YNALVWGSFQDEEGRIEGNIARHPK-DRMQMAVFPPDSGIGKHAVTHYRVLENF-NYVTL 260

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYL 290
           +E +  TGRTHQ+R H  H+G P+  D +Y  N     T   +             +  L
Sbjct: 261 VECRLETGRTHQIRAHMKHIGHPLFNDERYGGNEILRGTQFSKYKQFIQNCFAVCPRQAL 320

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HAR +   HP  G  +  T+ LPA M    + 
Sbjct: 321 HARTLGFIHPRSGQEMYFTSELPADMTALLER 352


>gi|119897309|ref|YP_932522.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119669722|emb|CAL93635.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 324

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 83/320 (25%), Positives = 144/320 (45%), Gaps = 24/320 (7%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  +    RLD+     +P  +   LQ  L+ G +R+D    +  +++  G+ + +    
Sbjct: 24  VPVELAGARLDQVLARLFPEHSRSRLQAWLKDGLIRLDGMERQAKHKVHGGEELVV---- 79

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                      +      L    + +   ++YED+ I V +KPAG+ V  GSG      +
Sbjct: 80  ---------AGLPPLPEQLAFEPEAIPLDVVYEDASILVIDKPAGLVVHPGSGNWSGTLL 130

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L       G  +  + HRLD++T+G++VVA+T  A   L    + R + + Y++LV+
Sbjct: 131 NALLHHAPALAGLPRAGIVHRLDKDTTGLMVVAKTLEAQTDLVRQLQQRTVARHYYALVY 190

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G   +  E  A+  + +  +    + VV     G   A++ + V          +E +  
Sbjct: 191 GDIASDGEIDAD--IDRHPVQRTRMAVV----PGGRPALTRYAVRQRL-HGLTLVECRLQ 243

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  H+G P+VGD  Y      +      ++  LHA  + L HP  G  +  
Sbjct: 244 TGRTHQIRVHMAHLGHPLVGDPVYGPRRVTDSRVDGFSRQALHAFRLGLLHPASGEDMVW 303

Query: 308 TAPLPAHMVKTWDSLGFKYD 327
           +APLPA      + +G + D
Sbjct: 304 SAPLPADFAALLEKVGGRAD 323


>gi|315646052|ref|ZP_07899173.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
 gi|315278813|gb|EFU42127.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
          Length = 323

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 77/323 (23%), Positives = 145/323 (44%), Gaps = 33/323 (10%)

Query: 11  VVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V+ D    RLD++        ++   +Q  +  G V+V+++ VK N ++  G  + +  
Sbjct: 26  TVDADSSKTRLDKYITESLGEEVSRSQVQLWITDGHVKVNEEPVKSNYKVSQGDHIVLSV 85

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
              ++  II E   L+               + +ED  + V NKP G+ V    G     
Sbjct: 86  PQPSVVEIIPEDIPLE---------------IAFEDRDVIVVNKPRGMVVHPAPGHSSGT 130

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  +    D  G     +P + HR+D++T+G+++ A+   A   L    +   + + Y
Sbjct: 131 LVNALMFHCKDLSGINGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKDHSVNRRY 190

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G   + +  I   + + +     Y       ++ + +A++HF V++ F   +  L
Sbjct: 191 LALVHGNISHDQGTIDAPIGRDAQDRKLY----TVTDRNSKHAVTHFTVVERFGD-YSLL 245

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E++  TGRTHQ+RVH  ++G P+VGD  Y  +          N   LHA  +   HP  G
Sbjct: 246 ELKLETGRTHQIRVHMKYIGHPLVGDPVYGKSKGIKL-----NGQALHAAVLGFVHPSSG 300

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
           + ++ +AP+P  M +    L  +
Sbjct: 301 QYMEFSAPMPKDMEELLAILRGR 323


>gi|83748464|ref|ZP_00945486.1| Ribosomal large subunit pseudouridine synthase C [Ralstonia
           solanacearum UW551]
 gi|83724875|gb|EAP72031.1| Ribosomal large subunit pseudouridine synthase C [Ralstonia
           solanacearum UW551]
          Length = 350

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 101/323 (31%), Positives = 164/323 (50%), Gaps = 19/323 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D +  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 29  VAYVEIGEDAQGQRIDNFLMRLAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 88

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A        +     V   +     +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 89  IPPLRIA--------QPSAEQVEAARAVPAAEFTILHEDTHLLVIDKPAGVAVHGGSGVA 140

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++ 
Sbjct: 141 FGVIEQLRR-SRPDAKFLELVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFAA 199

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  ++++ I   L K +   G+    V+ +      + + F  +  F   +  LE +
Sbjct: 200 VKGVWPHQRQHIKAPLFKYTTPEGERRVRVQAD---GQPSHTIFNRVGVFG-PYTLLEAE 255

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H G PI+GD KY              SP   +++LHA  + L HP+
Sbjct: 256 LKTGRTHQIRVHLAHAGFPILGDDKYGDFALNKALSRANASPRLARMFLHAHTLRLTHPQ 315

Query: 302 GGRL-QITAPLPAHMVKTWDSLG 323
            G +    APLPA      D+  
Sbjct: 316 SGEIVTFKAPLPAECAAFLDAFR 338


>gi|313108160|ref|ZP_07794295.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa 39016]
 gi|310880797|gb|EFQ39391.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa 39016]
          Length = 326

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 102/323 (31%), Positives = 168/323 (52%), Gaps = 14/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  T VQ + V  +    R+D +            + +ILR G+VRV+K R+K + R+Q+
Sbjct: 14  SPTTGVQLLDVPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRIKPDYRLQA 73

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+  A           + +       + +++ ++YED  + V NKPAGI+V G
Sbjct: 74  GDQVRVPPLRLAERD--------EPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVHG 125

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQ 180
           GSG++  +    +  +    +   L HRLD++TSG+L++A+ R+  +HL E+ R  + + 
Sbjct: 126 GSGVSAGVIEVFRQ-LRPDAKDIELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKIVD 184

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G     K+ +   LLK +   G+ +  V    K    A++ F+V+  F    
Sbjct: 185 KRYHALVRGHWPAGKKNVRAPLLKNNLRSGERMVEVNVEGKD---ALTEFRVLRRFGDFA 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPH 299
             +E +P TGRTHQ+RVHA H G  I GD KY   +F          +L+LHA  + +P 
Sbjct: 242 TLVEARPITGRTHQIRVHAKHAGHAIAGDPKYGDEDFSREIRELGGKRLFLHAAQLRVPL 301

Query: 300 PEGGRLQITAPLPAHMVKTWDSL 322
           P+G  L++ AP+     ++ + L
Sbjct: 302 PDGQVLELEAPVDEMWQRSLERL 324


>gi|110597884|ref|ZP_01386166.1| Pseudouridine synthase, RluD [Chlorobium ferrooxidans DSM 13031]
 gi|110340461|gb|EAT58947.1| Pseudouridine synthase, RluD [Chlorobium ferrooxidans DSM 13031]
          Length = 349

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 87/341 (25%), Positives = 139/341 (40%), Gaps = 37/341 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V   +  MR+D++      +     +Q+ +  G+V V++KRVK N RI+S   ++I 
Sbjct: 24  TLQVSRVQTPMRIDQYLTRQVENATRNKVQEAIEEGRVLVNEKRVKSNYRIKSCDTIQIT 83

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
            +      +  E   +D               ++YED  + V NK  G+ V    G    
Sbjct: 84  FLRPPAPELAPEDIPID---------------IIYEDEDLMVINKKPGMVVHPAFGNWTG 128

Query: 128 -------HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                  H  G     +D    +P + HRLD+ TSG+++VA+   A   L   F  R++ 
Sbjct: 129 TLANAILHHIGIGAEELDKSSLRPGIVHRLDKNTSGLIIVAKNPVALHRLARQFADRQVV 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY ++VWG+P  +   I   + + S      +       K    AI+ + V +     F
Sbjct: 189 KIYKAIVWGVPAEQSGTITTNIGR-SKKDRKVMANFPYEGKDGKTAITDYSVTENL-HWF 246

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----------SPIQNKLY 289
             L +  HTGRTHQ+R H  H+G  I+GD  Y                      +  +  
Sbjct: 247 SLLSLTLHTGRTHQIRAHMQHLGHQILGDETYGGAVLRTLPFSRSEGFVRNLLELLPRQA 306

Query: 290 LHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDRN 329
           LHA  +    P     L  TAPLP  M    + +    + N
Sbjct: 307 LHAATLSFHQPTTREPLSFTAPLPEDMQSAIEKIRAVVEAN 347


>gi|237734795|ref|ZP_04565276.1| ribosomal large subunit pseudouridine synthase D [Mollicutes
           bacterium D7]
 gi|229382123|gb|EEO32214.1| ribosomal large subunit pseudouridine synthase D [Coprobacillus sp.
           D7]
          Length = 316

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 151/326 (46%), Gaps = 34/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  ++   ++ N+RLD+        ++   +Q ++  G V V++K+ K + + +   
Sbjct: 11  MEKINLII--EEDNNLRLDKVIAMQLQELSRTQIQDMINQGLVLVNQKKEKASYKTKLND 68

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I  + N               V+L    + +   ++YED  + V +KP G+ V   +
Sbjct: 69  EIEITILDN---------------VDLDIEPEDISLKIVYEDEDVIVVDKPTGMIVHPSA 113

Query: 124 GIAY--HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           GI +   ++  L    D  G     +P + HR+D+ETSG+L+VA+   A + L++  +  
Sbjct: 114 GIMHGTLVNALLFHCKDLSGINGVNRPGIVHRIDKETSGLLMVAKNDNAHRLLSKQLKDH 173

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G+  ++   +   + +        + V + N   +  A+++F V+  + 
Sbjct: 174 TVVRRYVALVHGLIPHEHGKVDAPIGRNPK-DRQSMAVTRTN---SKEAVTNFTVLKRY- 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +E +  TGRTHQ+RVH  ++G P+ GD KY             +  +LHA+ +  
Sbjct: 229 NAMSLIECRLETGRTHQIRVHMSYIGYPVYGDPKYGYRKDD-----FSHGQFLHAKKLGF 283

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP   + ++  +PLP +     D L
Sbjct: 284 IHPTTQKYMEFESPLPDYFQAKLDEL 309


>gi|237653787|ref|YP_002890101.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|237625034|gb|ACR01724.1| pseudouridine synthase, RluA family [Thauera sp. MZ1T]
          Length = 327

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 82/322 (25%), Positives = 136/322 (42%), Gaps = 31/322 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + +  +   +RLD+      P  +   LQ  L+ G +RVD        ++  G+ V I
Sbjct: 25  EALTIPVELGGLRLDQALARLLPQHSRSRLQGWLKEGWIRVDGASPDARRKVCGGECVEI 84

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                                      + +   ++YED  + V +KP G+ V  GSG   
Sbjct: 85  --------------DAPPPPEVTAALPEDIPLAVVYEDEDLLVIDKPVGLVVHPGSG--- 127

Query: 128 HIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           +  G L + +  +        +  + HRLD++TSG++VVA+T AA   L    + R + +
Sbjct: 128 NWSGTLLNALLHRNPALAGVPRAGIVHRLDKDTSGLMVVAKTLAAQTELVRQLQARTVGR 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G        +   + +        + VV         A++H++V + F +   
Sbjct: 188 HYRALVQGAL-TAGGTVDAPIGRHPTQ-RTRMAVV----GNGRPAVTHYRVTERFPR-AT 240

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E +  TGRTHQ+RVH  H+G  +VGD  Y A   G+       +  LHA  + L HP 
Sbjct: 241 LVECRLETGRTHQIRVHMAHIGHALVGDPLYGARRCGDVRLDAFPRQALHAFRLGLTHPR 300

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++   PL A      D L
Sbjct: 301 SGEAMRWEVPLAADFAALLDEL 322


>gi|262280824|ref|ZP_06058607.1| 23S rRNA pseudouridylate synthase [Acinetobacter calcoaceticus
           RUH2202]
 gi|262257724|gb|EEY76459.1| 23S rRNA pseudouridylate synthase [Acinetobacter calcoaceticus
           RUH2202]
          Length = 310

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 97/317 (30%), Positives = 162/317 (51%), Gaps = 19/317 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R  QVRV+KKRVK   +++ G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIRESQVRVNKKRVKAETKLEIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETTAPVSDNVAQSLLSRIVYEDEGLLVVNKPSGIAVHGGSGMA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y ++
Sbjct: 123 YGLIEALRAATGKKY--LELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     K+ I   LL+     G+    V    K    + + + V + F +    +   
Sbjct: 181 VKGQVSLDKQLIDAPLLRYELANGERRVRVT---KDGKPSKTEWVVAERF-KNATLIHAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P++GD KY       +T P   +L LHA  +D+P    G   
Sbjct: 237 PLSGRTHQIRVHGLSIGHPLIGDDKYG--HTTAYTGPEARRLCLHAMRLDIP----GYPP 290

Query: 307 ITAPLPAHMVKTWDSLG 323
           I APLP  M +   +L 
Sbjct: 291 IEAPLPEDMTQLLKALR 307


>gi|212635834|ref|YP_002312359.1| pseudouridine synthase RluD [Shewanella piezotolerans WP3]
 gi|212557318|gb|ACJ29772.1| Pseudouridine synthase, RluD [Shewanella piezotolerans WP3]
          Length = 308

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 103/315 (32%), Positives = 172/315 (54%), Gaps = 13/315 (4%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++ D    R+D +       +    + +I+R G+VRV+KKR+K   ++Q G VVRIPP
Sbjct: 2   VTIDEDHTGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIKPEYKLQDGDVVRIPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  + + +     S  LTK S  L++ ++YED  I V NKP+GI+V GGSG+ + +
Sbjct: 62  -----VRVSESEGRPGPSAKLTKVSQ-LENRIIYEDKFIIVLNKPSGIAVHGGSGVDFGV 115

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++S + ++ +   L HRLD++TSG+L++A+ R+A +HL +  R +++QK Y +LV G
Sbjct: 116 IEAMRS-LRTQQKFLELVHRLDKDTSGLLLIAKKRSALKHLHDQLRYKKMQKDYLALVRG 174

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +   + +   LLK +   G+ +  V    K    + + FK++  ++     ++  P T
Sbjct: 175 EWQKHDKAVKAPLLKLTLKSGERIVRVN---KEGKESETRFKIMQRYSD-ATLVQASPIT 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           GRTHQ+RVH  + G PI  D KY    F  +  +   N+L+LHA  +   HP+    +Q+
Sbjct: 231 GRTHQIRVHCQYAGHPIACDEKYSEQKFDDSMRAHGLNRLFLHAAQLRFIHPDTDEVMQV 290

Query: 308 TAPLPAHMVKTWDSL 322
            APL   +  T   L
Sbjct: 291 KAPLDPILESTLSKL 305


>gi|68249014|ref|YP_248126.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae
           86-028NP]
 gi|68057213|gb|AAX87466.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 86-028NP]
          Length = 331

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 102/321 (31%), Positives = 170/321 (52%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 20  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 79

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 80  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 132

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 133 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 191

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+ +  V +       + + F + + +      ++
Sbjct: 192 ALVRGQWQSHIKVIQAPLLKNELSSGERIVRVSEQ---GKPSETRFSIEERYI-NATLVK 247

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 248 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 307

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L+  A L   M      L 
Sbjct: 308 ETLRFNASLDHQMKAILQKLR 328


>gi|218899046|ref|YP_002447457.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
 gi|228902397|ref|ZP_04066552.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis IBL 4222]
 gi|228966845|ref|ZP_04127889.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar sotto str. T04001]
 gi|218543499|gb|ACK95893.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
 gi|228792944|gb|EEM40502.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis serovar sotto str. T04001]
 gi|228857254|gb|EEN01759.1| Uncharacterized RNA pseudouridine synthase ylyB [Bacillus
           thuringiensis IBL 4222]
          Length = 302

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 137/313 (43%), Gaps = 33/313 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N R+D++        +   +Q+ ++   V V+ K VK N +++    + +          
Sbjct: 15  NERIDKFVAGINNEWSRSQVQQWIKDDVVTVNGKAVKVNYKVKEEDEITVT--------- 65

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKS 135
                 +     L    + +   + YED+ + V NKP G+ V    G      ++G +  
Sbjct: 66  ------IPDPEALDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHH 119

Query: 136 WVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y ++V G+ 
Sbjct: 120 CTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVI 179

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            + K  I   + +               ++    A++HF+V++ F + F  +E +  TGR
Sbjct: 180 PHDKGTIDAPIGRD-----KKERQSMTVDENGKNAVTHFQVLERF-KDFTLVECRLETGR 233

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P+ GD KY      +      N   LHA  +   HP  G  +Q  AP
Sbjct: 234 THQIRVHMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGFDHPRTGEYIQFEAP 288

Query: 311 LPAHMVKTWDSLG 323
           +P    +  + L 
Sbjct: 289 IPEVFEEALNILR 301


>gi|325661581|ref|ZP_08150205.1| hypothetical protein HMPREF0490_00939 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325472108|gb|EGC75322.1| hypothetical protein HMPREF0490_00939 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 310

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 84/327 (25%), Positives = 146/327 (44%), Gaps = 34/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +Y   +ND   MR+D++     P ++   LQK+++  +V V+ + VK N ++    
Sbjct: 1   MEERRYTAEKNDL--MRIDKFLSEKLPDLSRSYLQKLIKEKEVLVNGQPVKANYKLSLED 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I+ EQ  LD               +LYED  I V NKP G+ V   +
Sbjct: 59  HISVTIPELKEPDILPEQIPLD---------------ILYEDEDILVVNKPKGMVVHPSA 103

Query: 124 GI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  +    D         +P + HR+D +T+G L+V +   A Q L E  + 
Sbjct: 104 GHYSGTLVNALMFHCKDQLSGINGVMRPGIVHRIDMDTTGSLIVCKNDFAHQSLAEQLKD 163

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y ++V G+ K     I   + +   +    + V   N K   +A++H++V+  F
Sbjct: 164 HTITRKYHAIVHGVLKEDNGTIDAPIGRH-PVERKKMSV---NYKNGKHAVTHYRVLKRF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +KF ++E Q  TGRTHQ+RVH   +  P++GD  Y        +        LHA+ + 
Sbjct: 220 -EKFTYVECQLETGRTHQIRVHMASIRHPLLGDAVYGP----AKSPMKLQGQTLHAKILG 274

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + HP   + ++  A LP +     +  
Sbjct: 275 IIHPRTSQYMEFNAELPDYFKHLLEIF 301


>gi|49083776|gb|AAT51141.1| PA2975 [synthetic construct]
          Length = 319

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 102/323 (31%), Positives = 168/323 (52%), Gaps = 14/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  T VQ + V  +    R+D +            + +ILR G+VRV+K R+K + R+Q+
Sbjct: 6   SPTTGVQLLDVPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRIKPDYRLQA 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+  A           + +       + +++ ++YED  + V NKPAGI+V G
Sbjct: 66  GDQVRVPPLRLAERD--------EPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQ 180
           GSG++  +    +  +    +   L HRLD++TSG+L++A+ R+  +HL E+ R  + + 
Sbjct: 118 GSGVSAGVIEVFRQ-LRPDAKDIELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKIVD 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G     K+ +   LLK +   G+ +  V    K    A++ F+V+  F    
Sbjct: 177 KRYHALVRGHWPAGKKNVRAPLLKNNLRSGERMVEVNVEGKD---ALTEFRVLRRFGDFA 233

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPH 299
             +E +P TGRTHQ+RVHA H G  I GD KY   +F          +L+LHA  + +P 
Sbjct: 234 TLVEARPITGRTHQIRVHAKHAGHAIAGDPKYGDEDFSREIRELGGKRLFLHAAQLRVPL 293

Query: 300 PEGGRLQITAPLPAHMVKTWDSL 322
           P+G  L++ AP+     ++ + L
Sbjct: 294 PDGQVLELEAPVDEMWQRSLERL 316


>gi|225011533|ref|ZP_03701971.1| pseudouridine synthase, RluA family [Flavobacteria bacterium
           MS024-2A]
 gi|225004036|gb|EEG42008.1| pseudouridine synthase, RluA family [Flavobacteria bacterium
           MS024-2A]
          Length = 346

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 145/330 (43%), Gaps = 35/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
              +  +  +R+D++      ++    +Q+  ++G + VD   VK N +++ G  V++  
Sbjct: 24  FTADPGQSPLRVDKFLMARVENVTRSKIQQAAKAGSIFVDGNEVKSNYKVKGGDKVKV-- 81

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                +H   E  ++   + L          +++ED  + V NKP G+ V  G G     
Sbjct: 82  ---LFSHPPYENLLVPEDMPLD---------IVFEDDILVVVNKPPGMVVHPGHGNYSGT 129

Query: 128 HIDGFLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            ++G L        +  ++P L HR+D++TSG+LV+A+T  A  HL + F  +  ++ Y 
Sbjct: 130 LLNGLLYHFDQLPKNSNERPGLVHRIDKDTSGLLVIAKTEQAMTHLAKQFFDKTSERKYS 189

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG  K ++  I   + +  H        V ++      A +HFKVI+ F      +E
Sbjct: 190 ALVWGDVKEEEGTIEGAIGR--HPKNRLQMAVFEDNSQGKEAKTHFKVIERFG-YVTLIE 246

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHA 292
            Q  TGRTHQ+R H   +G  +  D +Y  +     TS             +  +  LHA
Sbjct: 247 CQLETGRTHQIRAHLKFIGHTLFNDARYGGDKILKGTSFTKYKQFVENCFALLPRQALHA 306

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP  G  +    PLP       + 
Sbjct: 307 QTLGFIHPSSGEKMLFETPLPDDFKAALEK 336


>gi|329297204|ref|ZP_08254540.1| 23S rRNA pseudouridylate synthase C [Plautia stali symbiont]
          Length = 319

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 106/321 (33%), Positives = 168/321 (52%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ+V +  +  + R+D + +     +    + +ILR G+VRV+KKRVK   +++ G  
Sbjct: 6   PGVQFVAITAENADQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLEDGDE 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PPV       + E++    S  L K +  L+S +LYED  + V NKP+G +V GGSG
Sbjct: 66  VRVPPVR------VAEREEQAVSPKLDKVA-ALESCILYEDDYLLVLNKPSGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD++TSGIL+VA+ R+A + L E  R + + K Y 
Sbjct: 119 LSFGVIEGLRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMLKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   +  + +   LLK     G+ V  V         + + FKV + F      ++
Sbjct: 178 ALVRGDWPSHLKVVQAPLLKNILQSGERVVRV---SAEGKPSETRFKVEERFGL-ATLVK 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH LH G PI  D +Y         +P   ++L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHTLHGGHPIAFDDRYGDREFDRQLAPTGLSRLFLHAAALTFTHPNTG 293

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L++ APL   +      L 
Sbjct: 294 ESLRMEAPLDKALKHCLSQLR 314


>gi|154249782|ref|YP_001410607.1| RluA family pseudouridine synthase [Fervidobacterium nodosum
           Rt17-B1]
 gi|154153718|gb|ABS60950.1| pseudouridine synthase, RluA family [Fervidobacterium nodosum
           Rt17-B1]
          Length = 314

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 88/322 (27%), Positives = 150/322 (46%), Gaps = 29/322 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           + V + E   RLD++     P  I+   +Q+ +++G+V V+    K + +++SG ++ + 
Sbjct: 3   IQVTSRENGWRLDKFVMEKTPEWISRTFIQRAIKNGEVLVNGTSKKPSYKVKSGDIITLN 62

Query: 69  -PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGI 125
            P    +  I+ E   LD               ++YED  I V NK  GI          
Sbjct: 63  APEAPEIPEILPEDIPLD---------------IIYEDRDILVINKQPGIITHPIPSHTS 107

Query: 126 AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++G L    D +G     +P + HRLD++TSG++V+A+   A Q LT+ F+ R  +K
Sbjct: 108 GTIVNGVLYHCKDLQGIGGVLRPGIVHRLDKDTSGVMVIAKNDLAHQSLTKQFKDRLTEK 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y  LV G+PK K+  I   + +   +    V +   N +    A++H+KV+  F     
Sbjct: 168 LYICLVKGVPKRKEGDIEINIARNPVL---RVKMTVTNSEYGKPALTHYKVVREFGDIAA 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +   P TGRTHQ+RVH  ++G P++GD  Y    +         +  LHA  +   HP 
Sbjct: 225 LVFAYPKTGRTHQIRVHMKYIGHPLMGDEVYGRAKEDEI--FGIKRQMLHALSLSFYHPR 282

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++  A +P    +    L
Sbjct: 283 TGEKVKFIAKIPQDFKEAIQKL 304


>gi|207725237|ref|YP_002255633.1| ribosomal large subunit pseudouridine synthase c protein [Ralstonia
           solanacearum MolK2]
 gi|207743612|ref|YP_002260004.1| ribosomal large subunit pseudouridine synthase c protein [Ralstonia
           solanacearum IPO1609]
 gi|206590471|emb|CAQ37433.1| ribosomal large subunit pseudouridine synthase c protein [Ralstonia
           solanacearum MolK2]
 gi|206595011|emb|CAQ61938.1| ribosomal large subunit pseudouridine synthase c protein [Ralstonia
           solanacearum IPO1609]
          Length = 352

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 101/323 (31%), Positives = 164/323 (50%), Gaps = 19/323 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D +  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 31  VAYVEIGEDAQGQRIDNFLMRLAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 90

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A        +     V   +     +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 91  IPPLRIA--------QPSAEQVEAARAVPAAEFTILHEDTHLLVIDKPAGVAVHGGSGVA 142

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++ 
Sbjct: 143 FGVIEQLRR-SRPDAKFLELVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFAA 201

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  ++++ I   L K +   G+    V+ +      + + F  +  F   +  LE +
Sbjct: 202 VKGVWPHQRQHIKAPLFKYTTPEGERRVRVQAD---GQPSHTIFNRVGVFG-PYTLLEAE 257

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H G PI+GD KY              SP   +++LHA  + L HP+
Sbjct: 258 LKTGRTHQIRVHLAHAGFPILGDDKYGDFALNKALSRANASPRLARMFLHAHTLRLTHPQ 317

Query: 302 GGRL-QITAPLPAHMVKTWDSLG 323
            G +    APLPA      D+  
Sbjct: 318 SGEIVTFKAPLPAECAAFLDAFR 340


>gi|301169114|emb|CBW28711.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae 10810]
          Length = 322

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 102/321 (31%), Positives = 170/321 (52%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDETGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+ +  V +       + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQAPLLKNELSSGERIVRVSEQ---GKPSETRFSIEERYI-NATLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L+  A L   M      L 
Sbjct: 299 ETLRFNASLDHQMKAILQKLR 319


>gi|225076527|ref|ZP_03719726.1| hypothetical protein NEIFLAOT_01575 [Neisseria flavescens
           NRL30031/H210]
 gi|224952206|gb|EEG33415.1| hypothetical protein NEIFLAOT_01575 [Neisseria flavescens
           NRL30031/H210]
          Length = 374

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 83/341 (24%), Positives = 144/341 (42%), Gaps = 30/341 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+++ +  
Sbjct: 30  LTVPLEMAGGRLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQPKDKMIGGELIAVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFTPEPMDLDIIYEDDTVIVINKPAGLVVHPAAGNWSGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCSELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   AI+H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAITHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y       ++        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNLRHPCSDAVKEAIKALGARQALHAYRLSFVHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           + G  +   AP+P  M      L  +   +  +       E
Sbjct: 310 KTGETVSFEAPMPDDMYHLLSVLRLEAGLDSSLSNEEEWQE 350


>gi|119357434|ref|YP_912078.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           phaeobacteroides DSM 266]
 gi|119354783|gb|ABL65654.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           phaeobacteroides DSM 266]
          Length = 350

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 88/329 (26%), Positives = 148/329 (44%), Gaps = 37/329 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V   +  MR+D++      +     +Q+ +  G+V V+ K VK N +I+S  +++I  
Sbjct: 25  IQVSRVQIPMRIDKYLTQQVENATRNKVQEAITEGRVLVNGKPVKSNYKIKSCDLIQITF 84

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAY 127
           +      +  E   +D               ++YED+ + V NK AG+ V    G+    
Sbjct: 85  LRPPAPEMAPENIPID---------------IIYEDADLMVVNKEAGMVVHPAFGNWTGT 129

Query: 128 HIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             +  L    +  G      Q+P + HRLD++TSG++++A+   A Q L   F  R+++K
Sbjct: 130 LANAILHHIGNDTGELDCSLQRPGIVHRLDKDTSGLIIIAKNPLALQRLARQFAQRQVEK 189

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY +LVWG+P+     I   + + S      +           +AI+ + VI+   + F 
Sbjct: 190 IYHALVWGVPEPASGTIKTNIGR-SKKNRKVMTTYPFEGIDGKHAITDYAVIEDL-RYFS 247

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----------SPIQNKLYL 290
            + ++ HTGRTHQ+RVH  H+G PI+GD  Y                      I  +  L
Sbjct: 248 LVSIKLHTGRTHQIRVHLQHLGHPILGDTVYGGASIRTLPFSKSESFIKNLLEIIPRQAL 307

Query: 291 HARYMDLPHPEG-GRLQITAPLPAHMVKT 318
           HA+ +    P     L  TAPLP  M+  
Sbjct: 308 HAQTLRFTQPLTHEPLSFTAPLPGDMINA 336


>gi|307822685|ref|ZP_07652916.1| pseudouridine synthase, RluA family [Methylobacter tundripaludum
           SV96]
 gi|307736289|gb|EFO07135.1| pseudouridine synthase, RluA family [Methylobacter tundripaludum
           SV96]
          Length = 319

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 107/321 (33%), Positives = 160/321 (49%), Gaps = 15/321 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S+   VQ V +  +  + RLD +       +    + +I+R G+VRV+K RV    R+ +
Sbjct: 7   SVTPKVQLVEITEENCDQRLDNFLIARLKGVPKSRIYRIVRKGEVRVNKGRVDVKYRLVA 66

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +VRIPPV  A           + S         L+  +L+ED    + NKPAG +V G
Sbjct: 67  GDIVRIPPVRVAERS--------EESYVPQGLQAALQQGILFEDEGFLIVNKPAGFAVHG 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG++  I   L+  +  +     L HRLD++TSG L++A+ R+A + L E FR   I K
Sbjct: 119 GSGVSSGIIEGLR-LIRPEAHFLELVHRLDKDTSGCLIIAKKRSALKLLHELFRDNHIHK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L+ G    KK  +   LLK    GG+ + V+ Q+      A + F+ +  F+    
Sbjct: 178 TYLALLAGQWARKKLVVTAPLLKNVAKGGERMVVISQS---GKEAETLFRRVKLFSDS-T 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            +E  P TGRTHQ+RVHA  +G PIVGD +Y   +    F      +++LHA  +   HP
Sbjct: 234 LVEASPKTGRTHQIRVHAASLGHPIVGDERYGRDDINRGFKGRGYKRMFLHAEKLKFQHP 293

Query: 301 EGGR-LQITAPLPAHMVKTWD 320
             G  L I APLP  +     
Sbjct: 294 VTGEPLTILAPLPQPLEDLLK 314


>gi|241760159|ref|ZP_04758257.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           flavescens SK114]
 gi|241319613|gb|EER56043.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           flavescens SK114]
          Length = 374

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 83/341 (24%), Positives = 144/341 (42%), Gaps = 30/341 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+++ +  
Sbjct: 30  LTVPLEMAGGRLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQPKDKMIGGELIAVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFTPEPMDLDIIYEDDAVIVINKPAGLVVHPAAGNWSGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   AI+H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAITHVKVLERY-LSHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y       ++        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNLRHPCSDAVKEAIKALGARQALHAYRLSFVHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           + G  +   AP+P  M      L  +   +  +       E
Sbjct: 310 KTGETVAFEAPMPDDMYHLLSVLRLEAGLDSSLSNEEEWQE 350


>gi|332707717|ref|ZP_08427744.1| ribosomal large subunit pseudouridine synthase D [Lyngbya majuscula
           3L]
 gi|332353420|gb|EGJ32933.1| ribosomal large subunit pseudouridine synthase D [Lyngbya majuscula
           3L]
          Length = 320

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 86/341 (25%), Positives = 150/341 (43%), Gaps = 35/341 (10%)

Query: 1   MSLMTYVQYVVVENDEENM------RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-V 53
           M+    ++++ V+   ++       RLD +     P ++   +QK++  G V+V+    +
Sbjct: 1   MTPQLSIKFLQVQETSKSTGSTPSYRLDSYIAQQTPDLSRSRIQKLIEQGNVQVNDHVCI 60

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
               ++Q G  + +                +     L    + +   +LYED  + + NK
Sbjct: 61  SKKAKVQLGDRISLT---------------IPDPKPLELQPEVIPLDILYEDDVLIIINK 105

Query: 114 PAGISVQGGSGIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAA 167
           PAG+ V    G      ++  L       G    Q+P + HRLD++T+G + +A+T  A 
Sbjct: 106 PAGLVVHPAPGHESGTLVNALLAHCPKLTGIGGVQRPGIVHRLDKDTTGAIAIAKTDQAH 165

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
            HL    + +  Q+ Y  +V+G P  +   I   + +  H        V   EKG   AI
Sbjct: 166 GHLQAQLQAKTAQRQYLGVVYGAPSAESGTINQPIGR--HPVDRKKMAVVPVEKGGRPAI 223

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +H++V +     +  +  Q  TGRTHQ+RVH+ ++G PIVGD  Y +        P    
Sbjct: 224 THWQVRERLG-NYTLMHFQLETGRTHQIRVHSSYIGHPIVGDTVYSSARSVGVNLPG--- 279

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             LHA  + L HP  G  ++  AP P  ++K  D L  ++ 
Sbjct: 280 QALHAWRLQLQHPVSGEWIEFVAPPPLALIKLLDVLRLRFS 320


>gi|325280294|ref|YP_004252836.1| pseudouridine synthase, RluA family [Odoribacter splanchnicus DSM
           20712]
 gi|324312103|gb|ADY32656.1| pseudouridine synthase, RluA family [Odoribacter splanchnicus DSM
           20712]
          Length = 353

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 80/344 (23%), Positives = 153/344 (44%), Gaps = 44/344 (12%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S M     +  +N +  +R+D++  +  P+ +   +Q+   +G + V+ K VK + +++ 
Sbjct: 20  SEMYEHHRIEADNGQNLLRVDKFLMSRLPNASRTKIQEAADAGNILVNGKAVKSSYKVKP 79

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
             +V +      + +  +E +I+  ++ L          ++YED  + V NKPAG+ V  
Sbjct: 80  KDIVSV-----VMAYPRREIEIIPENIPLN---------IVYEDDDLMVVNKPAGMVVHP 125

Query: 122 GSGIAYHIDGFLKSWV-----------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
             G   H  G L + +           D+   +P L HR+D++TSG+LV+A+T  A  HL
Sbjct: 126 SYG---HYTGTLVNALAWHLKGNPLFKDNNDPRPGLVHRIDKDTSGLLVIAKTEKAKTHL 182

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              F  +   + Y ++ WG  +++   I   + +   +    V     +     +A++H+
Sbjct: 183 GLQFFNKTSDRKYVAVCWGNLEDETGTITGHIGRN--LTNRKVMACFPDGSHGKHAVTHY 240

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-------- 282
           +V++        +E    TGRTHQ+R H  ++  P+  D +Y  N     T+        
Sbjct: 241 RVLERLG-YVNVVECILETGRTHQIRAHFKYIKHPLFNDKEYGGNEILKGTTFARYKQFV 299

Query: 283 ----PIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
                I  +  LHA+ +   HP  G RL   + +P  M +    
Sbjct: 300 NNCFEICPRQALHAKTLGFEHPTTGERLSFDSEIPDDMQQLIQK 343


>gi|293377440|ref|ZP_06623642.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
 gi|292643958|gb|EFF62066.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
          Length = 305

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 144/319 (45%), Gaps = 36/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT ++  +     E+ R+D+   N + + +   +Q  L+   V V+ + VK N +++ G 
Sbjct: 1   MTELKTTI---YHESGRIDKVLTNLFSNYSRSQIQLWLKERAVSVNGEPVKANYKVKQGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +               ++     L    + +   ++YED  + V NKP G+ V   +
Sbjct: 58  EITV---------------LIPEPETLDVVPENIPLTIVYEDEDVAVINKPQGMVVHPSA 102

Query: 124 GIAY-HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G  +  +   L   V          +P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 103 GHTHGTMVNALMYHVKDLSTINGVIRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKDK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G   ++K  I   + + S        +     +    A++HF V++ F 
Sbjct: 163 TSLRKYVALVHGEIPHEKGTINAPIGR-SKENRKMQAIR----EDGKPAVTHFTVLERF- 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E++  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +  
Sbjct: 217 EGFTLVELKLETGRTHQIRVHMKYIGYPLAGDPVYGPK-----KTLKGNGQFLHAQMLGF 271

Query: 298 PHPEG-GRLQITAPLPAHM 315
            HP    ++   APLP   
Sbjct: 272 THPTTNEKMIFEAPLPEVF 290


>gi|163790406|ref|ZP_02184837.1| Pseudouridylate synthase, 23S rRNA-specific [Carnobacterium sp.
           AT7]
 gi|159874310|gb|EDP68383.1| Pseudouridylate synthase, 23S rRNA-specific [Carnobacterium sp.
           AT7]
          Length = 301

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 147/327 (44%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      +++ +    RLD+      P I   ++Q+ ++ G V V+ + +K N ++Q   
Sbjct: 1   MPQEHNFIIKEETG--RLDKVLTELLPSITRSHIQQWIKEGNVTVNGENLKANYKVQPSD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I               I    V+L   ++ +   ++Y+D  + V NK  G+ V   +
Sbjct: 59  EIVI---------------IEPELVSLEVLAEDIPIEIVYQDEDVVVVNKAQGMVVHPSA 103

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  +    D  G     +P + HR+D++TSG+L+VA+  +A + L    + +
Sbjct: 104 GHQTGTLVNALMYHIKDLSGINGTIRPGIVHRIDKDTSGLLMVAKNDSAHEKLAAQLKDK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G+  ++K  I   L + S +      ++     G   A++HF V++ F 
Sbjct: 164 TSLREYIALVHGVIPHEKGTIDAPLGR-SKVDRKKQDIID----GGREAVTHFTVLERF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  + ++  TGRTHQ+RVH  ++G P+ GD  Y         +      +LHA+ +  
Sbjct: 218 KDFTLVSLKLETGRTHQIRVHMKYIGYPLAGDPIYGPR-----KTLEGKGQFLHAQTLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +   APLP     T   L 
Sbjct: 273 KHPTTGEFVTFEAPLPQLFEDTLTKLR 299


>gi|261380320|ref|ZP_05984893.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           subflava NJ9703]
 gi|284796836|gb|EFC52183.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           subflava NJ9703]
          Length = 374

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 83/341 (24%), Positives = 145/341 (42%), Gaps = 30/341 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+++ +  
Sbjct: 30  LTVPLEMAGGRLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQPKDKMIGGELIAVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFTPEPMDLDIIYEDDTVIVINKPAGLVVHPAAGNWSGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAI 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   AI+H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAITHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y       ++        +  +  LHA ++   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNLRHPCSDAVKEAIKALGARQALHAYHLSFVHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           + G  +   AP+P  M      L  +   +  +       E
Sbjct: 310 KTGETVSFEAPMPDDMYHLLSVLRLEAGLDSSLSNEEEWQE 350


>gi|121634501|ref|YP_974746.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis FAM18]
 gi|120866207|emb|CAM09947.1| putative ribosomal large subunit pseudouridine synthase D
           [Neisseria meningitidis FAM18]
 gi|325131843|gb|EGC54543.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M6190]
 gi|325137893|gb|EGC60468.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis ES14902]
          Length = 374

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 141/327 (43%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ +R+  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKPSQPKDKMIGGEQIRVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWRGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LTHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y       ++        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAGDPVYGNPRHPCSDPVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|325197923|gb|ADY93379.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis G2136]
          Length = 374

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 141/327 (43%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ +R+  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKPSQPKDKMIGGEQIRVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWRGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LPHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y       ++        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAGDPVYGNPRHPCSDPVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|81428560|ref|YP_395560.1| pseudouridylate synthase, 23S rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610202|emb|CAI55251.1| Pseudouridylate synthase, 23S rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 301

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 147/329 (44%), Gaps = 40/329 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  +   +  +    R+D+      P  +   +Q+ L+   V ++ +  K N+++ + +
Sbjct: 1   MTEKKEFTITTETG--RIDKVLSQLLPDYSRSQIQQWLKKDLVEINGQTSKGNHKVVADE 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +   V+L    + +   ++YED ++ V NKP G+ V    
Sbjct: 59  KISVT---------------IPDPVSLDLVPEDIPLDIVYEDDQVLVVNKPQGMVVHPSP 103

Query: 124 GIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G   H +G L + + +           +P + HR+D++TSG+L+VA+T  A + L+E  +
Sbjct: 104 G---HPNGTLVNALLAHTPLSEINGVFRPGIVHRIDKDTSGLLMVAKTNEAHESLSEQLK 160

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +   + Y +LV G  +  +  I   + + S +      +V         A++HF+V++ 
Sbjct: 161 AKSNLREYLALVHGNIEEDEGTIDAPIGR-SKLDRMKQAIV----PDGRPAVTHFEVVER 215

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F   +  +  +  TGRTHQ+RVH  ++  P+ GD  Y         +      +LHA  +
Sbjct: 216 FTD-YTLIRCRLETGRTHQIRVHLAYINRPVAGDPTYGPR-----KTLPGKGQFLHAAVL 269

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              HP  G  ++  APLPA   KT   L 
Sbjct: 270 GFKHPTTGENMRFEAPLPAIFEKTLQELR 298


>gi|15598171|ref|NP_251665.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PAO1]
 gi|116050977|ref|YP_790198.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|218890827|ref|YP_002439691.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa LESB58]
 gi|254235949|ref|ZP_04929272.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa C3719]
 gi|296388532|ref|ZP_06878007.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PAb1]
 gi|34395830|sp|Q9HZM9|RLUC_PSEAE RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|9949074|gb|AAG06363.1|AE004723_7 ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PAO1]
 gi|115586198|gb|ABJ12213.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|126167880|gb|EAZ53391.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa C3719]
 gi|218771050|emb|CAW26815.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa LESB58]
          Length = 318

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 102/323 (31%), Positives = 168/323 (52%), Gaps = 14/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  T VQ + V  +    R+D +            + +ILR G+VRV+K R+K + R+Q+
Sbjct: 6   SPTTGVQLLDVPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRIKPDYRLQA 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+  A           + +       + +++ ++YED  + V NKPAGI+V G
Sbjct: 66  GDQVRVPPLRLAERD--------EPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQ 180
           GSG++  +    +  +    +   L HRLD++TSG+L++A+ R+  +HL E+ R  + + 
Sbjct: 118 GSGVSAGVIEVFRQ-LRPDAKDIELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKIVD 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G     K+ +   LLK +   G+ +  V    K    A++ F+V+  F    
Sbjct: 177 KRYHALVRGHWPAGKKNVRAPLLKNNLRSGERMVEVNVEGKD---ALTEFRVLRRFGDFA 233

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPH 299
             +E +P TGRTHQ+RVHA H G  I GD KY   +F          +L+LHA  + +P 
Sbjct: 234 TLVEARPITGRTHQIRVHAKHAGHAIAGDPKYGDEDFSREIRELGGKRLFLHAAQLRVPL 293

Query: 300 PEGGRLQITAPLPAHMVKTWDSL 322
           P+G  L++ AP+     ++ + L
Sbjct: 294 PDGQVLELEAPVDEMWQRSLERL 316


>gi|241896496|ref|ZP_04783792.1| pseudouridylate synthase [Weissella paramesenteroides ATCC 33313]
 gi|241870218|gb|EER73969.1| pseudouridylate synthase [Weissella paramesenteroides ATCC 33313]
          Length = 304

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 143/328 (43%), Gaps = 41/328 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  + + +  D+E  RLD+     +       + K +  G + V+ +  K   ++ +G 
Sbjct: 1   MTE-ESLTIT-DQEG-RLDKVVAEAFTDYTRTQMSKWIDDGILTVNGETKKAKYKVHAGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+                 ++   V L    + L   ++YED  + V NKP G+ V   +
Sbjct: 58  VISF---------------VVPEPVVLDIKPENLPLDIVYEDDDLLVVNKPQGMVVHPAA 102

Query: 124 GIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G   H +G L + +    +        +P + HR+D++TSG+L+VA+   A + L+   +
Sbjct: 103 G---HPNGTLVNALMYHTELSSINGVIRPGIVHRIDKDTSGLLMVAKNDQAHEALSADLK 159

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            ++  + Y++LV G     K  I   L +          +      G   A++HF+V+  
Sbjct: 160 DKKNLRQYYALVHGEFSENKGTIKAPLGRSKTDRKKQAVIA-----GGRDAVTHFEVVKR 214

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           +   +  L +   TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA  +
Sbjct: 215 YV-GYTLLRVTLETGRTHQIRVHMAYIGHPVAGDPLYGPK-----KTLAGNGQFLHAATL 268

Query: 296 DLPHPEG-GRLQITAPLPAHMVKTWDSL 322
            L  P     L   APLP + V+T   L
Sbjct: 269 GLTQPTTKKELTFEAPLPQYFVETLAQL 296


>gi|165977322|ref|YP_001652915.1| 23S rRNA pseudouridylate synthase C [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|165877423|gb|ABY70471.1| ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
          Length = 321

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 101/319 (31%), Positives = 163/319 (51%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q      
Sbjct: 11  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQP----- 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 66  -DDVVRVPPVRVAEKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+ +  V +       + +HF + + +A     ++  
Sbjct: 183 VRGQWQAHTKVIKAPLLKNELASGERIVRVSEE---GKPSETHFSIEERYA-NATLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 298

Query: 305 LQITAPLPAHMVKTWDSLG 323
           + ITAPL   +      L 
Sbjct: 299 MLITAPLDKTLKDVLAKLR 317


>gi|78189580|ref|YP_379918.1| pseudouridine synthase, RluD [Chlorobium chlorochromatii CaD3]
 gi|78171779|gb|ABB28875.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           chlorochromatii CaD3]
          Length = 363

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 84/332 (25%), Positives = 143/332 (43%), Gaps = 37/332 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V   +  MR+D +      +     +Q+ +  G+V V+ K VK N R++S  V+ +  + 
Sbjct: 41  VSRTQSPMRIDVYLTQQVENATRNKVQEAIEEGRVVVNGKCVKANYRLKSCDVIEVTFLR 100

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHI 129
                +  E                +   ++YED  + V NK  G+ V    G+      
Sbjct: 101 PPAPELAPE---------------AIPIAIMYEDDDLMVINKEPGMVVHPAFGNWTGTLA 145

Query: 130 DGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +  L         +D+   +P + HRLD++TSG++++A+   A   L   F  R++ KIY
Sbjct: 146 NAILHHLGNSAEALDASEMRPGIVHRLDKDTSGLIIIAKNPIALHKLARQFAERKVGKIY 205

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L WG+PK     I   + + SH     +            AI+ + V +   + F  +
Sbjct: 206 KALTWGVPKQASGTITTNIGR-SHKNRKVMANFPFEGLEGKTAITDYCV-EENLEWFSVM 263

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----------SPIQNKLYLHA 292
            ++ HTGRTHQ+RVH  H+G PIVGD  Y                      +  +  LHA
Sbjct: 264 SLRLHTGRTHQIRVHLQHLGLPIVGDVTYGGATPRALPFSKSEHFVKNLLELLPRQALHA 323

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
             +   HP  G  + ++APLP  M++  + + 
Sbjct: 324 ETLTFHHPTTGEEITLSAPLPEDMLQALEKIR 355


>gi|299771717|ref|YP_003733743.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. DR1]
 gi|298701805|gb|ADI92370.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. DR1]
          Length = 310

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 97/317 (30%), Positives = 162/317 (51%), Gaps = 19/317 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R  QVRV+KKRVK   +++ G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIRESQVRVNKKRVKAETKLEIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAAPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAVHGGSGMA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y ++
Sbjct: 123 YGLIEALRAATGKKY--LELIHRIDRDTSGLVMISKKRSTLKQLQDMLREHKIRKTYAAI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     K+ I   LL+     G+    V    K    + + + V + F +    +   
Sbjct: 181 VKGQVSLDKQLIDAPLLRYELANGERRVRVT---KDGKPSKTEWVVAERF-KNATLVHAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P++GD KY       +T P   +L LHA  +D+P    G   
Sbjct: 237 PLSGRTHQIRVHGLSIGHPLIGDDKYG--HTTEYTGPEARRLCLHAMRLDIP----GYPP 290

Query: 307 ITAPLPAHMVKTWDSLG 323
           I APLP  M +   +L 
Sbjct: 291 IEAPLPEDMTQLLKALR 307


>gi|84779551|dbj|BAE74328.1| ribosomal large subunit pseudouridine synthase C [Sodalis
           glossinidius str. 'morsitans']
          Length = 328

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 106/317 (33%), Positives = 163/317 (51%), Gaps = 14/317 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V ++ +  DE   R+D + + +   +    + +I+R G+VRV+KKRVK   ++Q+   
Sbjct: 16  PGVHFITISADEAGQRIDNFLRTYLKGVPKSMIYRIVRKGEVRVNKKRVKPEYKLQNDDE 75

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV  +          LD    L +        +LYED  + + NKPAG +V GGSG
Sbjct: 76  VRIPPVRRSDEEHAPISTGLDKVAALNE-------AVLYEDDHLLILNKPAGTAVHGGSG 128

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +    +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y 
Sbjct: 129 LSFGVIEGLRA-LRPDARFLELVHRLDRDTSGVLLVAKKRSALRALHEQLRAKGMQKDYL 187

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + IA  LLK     G+ +  V         + + FKV + F      + 
Sbjct: 188 ALVRGQWQSHVKTIAAPLLKNILASGERIVRVNSE---GKPSETCFKVEERFTL-AMLVR 243

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVHA H G PI  D +Y    F         N+L+LHA  +   HP  G
Sbjct: 244 ASPVTGRTHQIRVHAQHAGHPIAFDDRYGDGMFDQQLKGCGLNRLFLHAAALRFDHPGSG 303

Query: 304 R-LQITAPLPAHMVKTW 319
             L+I APL A + +  
Sbjct: 304 ETLRIDAPLDASLRQCL 320


>gi|21674122|ref|NP_662187.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           tepidum TLS]
 gi|21647279|gb|AAM72529.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           tepidum TLS]
          Length = 329

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 88/335 (26%), Positives = 142/335 (42%), Gaps = 37/335 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V   +  MR+DR+      +     +QK +   +V V+ K VK N RI+S   + I 
Sbjct: 2   TLQVSKVQTPMRIDRYLTQQVENATRNKVQKAIEEQRVLVNGKPVKSNYRIKSCDHIHIT 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIA 126
            +      +  E                +   +LYED  + V +K AG+ V    G+   
Sbjct: 62  FLRPPAPELAPED---------------IPISILYEDDDLMVIDKEAGMVVHPAFGNWTG 106

Query: 127 YHIDGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  L         +D    +P + HRLD++TSG+++VA+   A   L   F  R+++
Sbjct: 107 TLANAILHHLGKDADDLDKTEMRPGIVHRLDKDTSGLIIVAKNPVALHKLATQFARRQVE 166

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y ++VWG+P      I   + + SH     +           +AI+ + V++  A  F
Sbjct: 167 KVYKAIVWGVPNPPSGTIKTNIGR-SHKNRKVMANFPFEGAEGKHAITDYLVVEDLA-YF 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----------SPIQNKLY 289
             ++M  HTGRTHQ+RVH  H+G PI+GD  Y                      +  +  
Sbjct: 225 ALMDMTLHTGRTHQIRVHLQHLGHPILGDQTYGGATPRTLPFSKSEPFTHNLLELMGRQA 284

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           LHA  +    P  G  L  TAPLP  M    + + 
Sbjct: 285 LHAETLRFRQPTTGEPLAFTAPLPEDMKTVLEKIR 319


>gi|82702194|ref|YP_411760.1| pseudouridine synthase, RluD [Nitrosospira multiformis ATCC 25196]
 gi|82410259|gb|ABB74368.1| ribosomal large subunit pseudouridine synthase C [Nitrosospira
           multiformis ATCC 25196]
          Length = 328

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 102/317 (32%), Positives = 167/317 (52%), Gaps = 17/317 (5%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++  + +  R+D +      ++   ++ ++LRSGQVR++ KR   +  +QSG +VRIPPV
Sbjct: 4   IIGEESKGQRIDNFLIKRLKNVPKSHVYRLLRSGQVRINSKRAPPDYHLQSGDIVRIPPV 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                  +  +K+            F+   +L+ED  +   NKP G++V GGSGI++ + 
Sbjct: 64  RTVEKSALPPKKLSKPG--------FIAFQVLFEDDALIAVNKPPGVAVHGGSGISFGVI 115

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L++      +   L HRLD+ETSG+L++A+ RAA   L    RM  ++K Y +LV G 
Sbjct: 116 EQLRAQ-HPDWRFLELAHRLDRETSGVLLLAKNRAALVELHRQLRMGEVEKHYLTLVKGR 174

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKFCWLEMQP 247
            +N ++ +   L K    GG+    V+++   +KG   A + F ++    Q F  LE + 
Sbjct: 175 WRNGRQSVRLSLRKYLTPGGERRVAVEKDADEKKGGMSAHTVF-ILRESWQSFSLLEAEL 233

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
            TGRTHQ+RVH  ++G PI GD KY     N       P   +++LHA  ++  HP    
Sbjct: 234 KTGRTHQIRVHLAYLGFPIAGDDKYGDFVLNKDIARRVPGLGRMFLHAWAVEFTHPVTHE 293

Query: 304 RLQITAPLPAHMVKTWD 320
           +L++ APLP  + K  D
Sbjct: 294 KLRLEAPLPDDLQKFLD 310


>gi|291536189|emb|CBL09301.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis M50/1]
          Length = 310

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 147/330 (44%), Gaps = 39/330 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHI-------NFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           +   +E + E  RLD++    +          +    QK++R G V+V+    K N R++
Sbjct: 4   ETFEIEAEYEGERLDKYLSVIFEQSKTSSNAPSRSFFQKLIRDGHVKVNDSIAKANYRLR 63

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
              +V +         I+ E   LD               +LYED  + V NKP G+ V 
Sbjct: 64  MDDLVCVEIPDAVETPILPEDIPLD---------------ILYEDDDLLVVNKPKGMVVH 108

Query: 121 GGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
             +G      ++  +    DS        +P + HR+D +T+G L+V +   +   + E 
Sbjct: 109 PSAGHYSGTLVNAIMFHCKDSLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHVKIAEQ 168

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            +   + + Y  +V+G+ K+ +  I   + +           +  N+K    AI+H+KV+
Sbjct: 169 IKEHSVNRRYRGIVYGVVKDDEGTINAPIGRHPTNRKK----MAINKKNGKPAITHYKVL 224

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F+  + ++E +  TGRTHQ+RVH   +G P++GD  Y +      T        LHA 
Sbjct: 225 ERFS-NYTYMEFKLETGRTHQIRVHMASIGHPLLGDTVYSSGKSPFKT----QGQTLHAM 279

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +   HP     ++I+APLP + +K   SL
Sbjct: 280 TIGFIHPHTNEYMEISAPLPEYFLKILKSL 309


>gi|332292606|ref|YP_004431215.1| pseudouridine synthase, RluA family [Krokinobacter diaphorus
           4H-3-7-5]
 gi|332170692|gb|AEE19947.1| pseudouridine synthase, RluA family [Krokinobacter diaphorus
           4H-3-7-5]
          Length = 347

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/330 (25%), Positives = 148/330 (44%), Gaps = 33/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
                 +E +R+D++  N   +     +QK  ++G ++V+   VK N ++++G VVR   
Sbjct: 22  FTASKGQEPLRVDKFLMNFVENATRNKIQKAAKNGSIQVNNIVVKQNYKVKAGDVVR--- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                 H   E  +    +++          ++YED ++ V NKPAG+ V  G G     
Sbjct: 79  --AMFEHPPHEFLLTPEDIDID---------VVYEDDQLMVVNKPAGMVVHPGHGNYSGT 127

Query: 128 HIDGFLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            I+  +       ++   +P L HR+D++TSG+LVVA+T  A  HL++ F  +  ++ Y 
Sbjct: 128 LINALIHHVDNLPNNSSDRPGLVHRIDKDTSGLLVVAKTEQAMTHLSKQFFNKTTEREYV 187

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++VWG   + +  I   + +             ++E     A++H+KVI+        + 
Sbjct: 188 AIVWGNVVDDEGTIEGNIGRHPKNRLQNTVFYGEDEDQGKPAVTHYKVIERLG-YVTLVS 246

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHA 292
            +  TGRTHQ+RVH  H+G  +  D +Y  N     T+             I  +  LHA
Sbjct: 247 CKLETGRTHQIRVHMKHIGHTLFNDERYGGNAILKGTTFTKYKQFVDNCFKILPRQALHA 306

Query: 293 RYMDLPHPEGGRL-QITAPLPAHMVKTWDS 321
           + +   HP  G   +   P+P  M    D 
Sbjct: 307 KTLGFVHPTTGEYKRFETPVPEDMTGCIDK 336


>gi|33151828|ref|NP_873181.1| 23S rRNA pseudouridylate synthase C [Haemophilus ducreyi 35000HP]
 gi|34395752|sp|P59835|RLUC_HAEDU RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|33148049|gb|AAP95570.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           ducreyi 35000HP]
          Length = 320

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 102/326 (31%), Positives = 168/326 (51%), Gaps = 14/326 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           ++   VQ+  + +DE   RLD +       +    + +I+R G+VRV+K RVK + ++Q 
Sbjct: 6   TISANVQFFTISDDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRVKPDYKLQH 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
             +VRIP     L  +  + +    S  L K ++ L+  +LYED  + V NKP+GI V G
Sbjct: 66  NDIVRIP-----LVRVTPKNE-APISTKLNKVAE-LEQHILYEDDVMLVLNKPSGIGVHG 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+++ +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK
Sbjct: 119 GSGLSFGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRALHEQLREKVVQK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  +     I   LLK     G+ +  V +       + + F + + +     
Sbjct: 178 DYLALVRGQWQAHINVIKAPLLKNELQSGERIVKVSEQ---GKPSETRFSIEERYP-NAT 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  +   HP
Sbjct: 234 LIKASPITGRTHQIRVHTQYAGHPIACDDRYGDQAFDAKLKQAGLNRLFLHAHSIRFEHP 293

Query: 301 EG-GRLQITAPLPAHMVKTWDSLGFK 325
           +   ++ ITAPL  H+      L  +
Sbjct: 294 KTAEQMFITAPLDHHLKTILAKLRAE 319


>gi|95929105|ref|ZP_01311850.1| Pseudouridine synthase, RluD [Desulfuromonas acetoxidans DSM 684]
 gi|95135006|gb|EAT16660.1| Pseudouridine synthase, RluD [Desulfuromonas acetoxidans DSM 684]
          Length = 350

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 93/339 (27%), Positives = 152/339 (44%), Gaps = 35/339 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M       +E  +   RLDR+     P +    L+K++  G VRV+ + VK   +++ G+
Sbjct: 1   MNENLTFYIEPGQAAERLDRFLTRQLPELTRSQLKKLVDDGLVRVNDQTVKAGAKLRGGE 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +                L  + ++    + L   +LYEDS + V NK AG+ V   +
Sbjct: 61  TVCVT---------------LPQAQSVETLPEDLPLTVLYEDSDLIVINKAAGMVVHPAA 105

Query: 124 GI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HRLD++TSG++V  +      HL   F+  
Sbjct: 106 GHSSGTLVNALLYHCHDLSGVGGELRPGIVHRLDKDTSGVMVATKNDVTHNHLAAQFKDH 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF- 236
            IQ+ Y +LV G  +N +  I   + +           +    +G   A++H+KV+  + 
Sbjct: 166 SIQRRYVALVHGQVQNARGTIDAPIGRHPTHRKK----MTSKGRGGRRAVTHWKVLRRYD 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKL 288
           A +   LEM+  TGRTHQ+RVH   M  P+VGD  Y    + N  + ++        ++ 
Sbjct: 222 ADRLSLLEMRLETGRTHQIRVHLSEMNLPLVGDPLYGNRTRANGINDLEVRNRVHALHRQ 281

Query: 289 YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
            LHAR +   HP  G  L+ T+ LP  +      L  KY
Sbjct: 282 ALHARLLGFIHPRTGDYLEFTSDLPGDLASIVAFLDDKY 320


>gi|145219868|ref|YP_001130577.1| ribosomal large subunit pseudouridine synthase D [Prosthecochloris
           vibrioformis DSM 265]
 gi|145206032|gb|ABP37075.1| ribosomal large subunit pseudouridine synthase D [Chlorobium
           phaeovibrioides DSM 265]
          Length = 349

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 83/338 (24%), Positives = 143/338 (42%), Gaps = 37/338 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V   +  MR+D++      +     +Q+ +  G+V V+ K VK N RI+S  ++ + 
Sbjct: 24  TLQVSKVQIPMRIDQYLSRQVENATRNKVQEAIEDGRVLVNDKVVKSNYRIKSCDLIEMT 83

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIA 126
            +      +  E                +   ++YEDS++ V NK  G+ V    G+   
Sbjct: 84  FLRPPAPELAPED---------------IPIAIVYEDSELMVINKEPGMVVHPAFGNWTG 128

Query: 127 YHIDGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  L         +D    +P + HRLD++TSG++++A+   A   L + F  R++ 
Sbjct: 129 TLANAILHHIGENAGSLDESELRPGIVHRLDKDTSGLIIIAKNPTALHRLAKQFADRKVV 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LVWG+P   +  I   + + S      +       +    AI+ ++ ++     F
Sbjct: 189 KTYKALVWGVPATPEGTIRTNIGR-SRKDRKVMANFPYEGEEGKTAITDYR-LEEDLHWF 246

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-----------IQNKLY 289
             L +  HTGRTHQ+R H  H+G  I+ D  Y      N   P           +  +  
Sbjct: 247 SLLSLTLHTGRTHQIRAHMQHLGHQILSDATYGGASIRNLDFPKSESFVRNLLDLLPRQA 306

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           LHA  +   HP  G  +   APLP  M +  D +   Y
Sbjct: 307 LHAESLSFQHPTTGETISFHAPLPLDMAQAIDKIRVIY 344


>gi|315651411|ref|ZP_07904436.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saburreum DSM 3986]
 gi|315486370|gb|EFU76727.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saburreum DSM 3986]
          Length = 303

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 70/323 (21%), Positives = 141/323 (43%), Gaps = 34/323 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            ++ E  + + R+D +   +    +   +Q +++ G+V ++ K +K N R++ G+ V + 
Sbjct: 5   EIIAEESDVDKRIDLFLAKNLESFSRSYIQDLIKKGKVTINNKIIKANYRLKEGECVVLD 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                   I+ E   +D               +LYED  + + NKP G+ V   +G    
Sbjct: 65  IPKPEPLEIVPENIPID---------------ILYEDEDVILVNKPKGMVVHPAAGHYKG 109

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             ++  L     +        +P + HR+D +T+G++++ +   A QH+ +      I +
Sbjct: 110 TLVNALLYHCKSNLSGINGVLRPGIVHRIDMDTTGVIIICKNDIAHQHIAKQLANHSITR 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G  K  +  I   + + S      + V    +K    A++H+KV++     + 
Sbjct: 170 KYVAIVTGNIKEDEGVIDAAIAR-SKSDRKKMAV----DKDGKRAVTHYKVLERL-NGYT 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           ++E    TGRTHQ+RVH  ++  P++GD  Y                 LHA  +   HP+
Sbjct: 224 YIECVLETGRTHQIRVHMAYIHHPLLGDEVYAGKSGMKL-----QGQCLHAMVLGFIHPK 278

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
               ++  AP+P +  +  +   
Sbjct: 279 TKEYMEFEAPIPEYFNEILNKFR 301


>gi|163758760|ref|ZP_02165847.1| putative ribosomal large subunit pseudouridine synthase protein
           [Hoeflea phototrophica DFL-43]
 gi|162284050|gb|EDQ34334.1| putative ribosomal large subunit pseudouridine synthase protein
           [Hoeflea phototrophica DFL-43]
          Length = 339

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 83/340 (24%), Positives = 152/340 (44%), Gaps = 47/340 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           + +VV  D    RLD W      P ++   ++ ++ +G V V+    +   ++I+ G  +
Sbjct: 11  ETLVVGEDAAG-RLDAWLAEALAPGLSRSRVKALIEAGAVSVNGTPARQAKHKIKPGDEI 69

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +               ++    +     + +   +LYED+ + V NK AG+ V  G+G 
Sbjct: 70  SL---------------VVPDPEDPEPEGEDIPLSILYEDADLIVINKQAGLVVHPGAGN 114

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  +    DS       ++P + HRLD++T+G++VVA+   A +HL + F    
Sbjct: 115 WTGTLVNALIHHCGDSLSGIGGVRRPGIVHRLDRDTTGVMVVAKHDQAHRHLADQFADHG 174

Query: 179 I----QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +    ++ Y ++VWG P   K  I   L +          V   +     +A++H+ V +
Sbjct: 175 LTGPLERAYQAVVWGKPAGLKGTIDAGLGRAR--DRIRRAVRTDDAPDVRHAVTHYLVRE 232

Query: 235 CFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQ 285
            + +K         +E +  TGRTHQ+RVH  H+G P++GD  Y A ++        P++
Sbjct: 233 RYGEKPDGTCAATLVECRLETGRTHQIRVHMAHIGHPLIGDEDYGAGYRTKANRLPEPLR 292

Query: 286 ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
                  +  LHA  +   HP  G  ++  APLP  M + 
Sbjct: 293 GIVGDFKRQALHAFLLVFEHPATGETMRFEAPLPDDMEQM 332


>gi|309378792|emb|CBX22618.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 374

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 81/338 (23%), Positives = 140/338 (41%), Gaps = 30/338 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V       RLD       P  +   L   ++ G V V+ K  +  +++  G+ +R+  
Sbjct: 30  LTVPPKLAGGRLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKPSQPKDKMIGGEHIRVSI 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
             +A                     + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 90  RPSAEYSAFA--------------PEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y       +         +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAGDPVYGNLRHPCSEPVKEAVKSLGARQALHAYRLSFVHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           + G  +   AP+P  M      L  +   +  +     
Sbjct: 310 KTGETVSFEAPIPDDMYHLLSVLRLEAGLDSSLDNEEE 347


>gi|332521351|ref|ZP_08397807.1| pseudouridine synthase, RluA family [Lacinutrix algicola 5H-3-7-4]
 gi|332043079|gb|EGI79277.1| pseudouridine synthase, RluA family [Lacinutrix algicola 5H-3-7-4]
          Length = 345

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 80/334 (23%), Positives = 148/334 (44%), Gaps = 41/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            + +  +  +R+D+W  N   +     +Q   + G + V+ + VK N +++   V+++  
Sbjct: 21  FIADKGQAPLRIDKWLMNKVENATRNKIQAAAKEGNIYVNDQPVKSNYKVKPLDVIKVLF 80

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                 +++                + L   ++YED  + V NKPAG+ V  G G     
Sbjct: 81  EHPPFENLL--------------VGEDLPLDIVYEDDTLLVVNKPAGMVVHPGHGNYSGT 126

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH D   K+  D    +P L HR+D++TSG+LVVA+T  A  HL++ F+ +  +
Sbjct: 127 LINALIYHFDNLPKNSSD----RPGLVHRIDKDTSGLLVVAKTEHAMAHLSKQFKDKTSE 182

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++VWG  +  +  I   + +           +  +      A++H+KV++      
Sbjct: 183 REYVAIVWGNMEEDEGTIEGNIGRHPKNRLQNTVYMDDDADKGKPAVTHYKVLERLT-YV 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKL 288
             +  +  TGRTHQ+RVH  H+G  +  D +Y        T+  +             + 
Sbjct: 242 TLVSCKLETGRTHQIRVHMKHIGHTLFNDERYGGERILKGTTFTKYKQFVDNCFKVLPRQ 301

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            LHA+ +   HPE G+ +Q   P+P  M    + 
Sbjct: 302 ALHAKTLGFEHPETGKIMQFNTPVPDDMQACIEK 335


>gi|261392924|emb|CAX50509.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D; rRNA pseudouridylate synthase D) [Neisseria
           meningitidis 8013]
          Length = 374

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 139/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIIYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|170759197|ref|YP_001786899.1| RluA family pseudouridine synthase [Clostridium botulinum A3 str.
           Loch Maree]
 gi|169406186|gb|ACA54597.1| pseudouridine synthase, RluA family [Clostridium botulinum A3 str.
           Loch Maree]
          Length = 305

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 90/326 (27%), Positives = 149/326 (45%), Gaps = 33/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  + VE + +N+RLD      +   +   LQ I+  G V V+ K  K N +++ G 
Sbjct: 1   MEKI-SLQVEKEFDNVRLDLCLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I                +     L    + +K  ++YED  + V NKP  + V    
Sbjct: 60  NIEIN---------------IPEPKLLQIEPEDVKLDVIYEDKDVIVVNKPQEMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G+     ++  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+  
Sbjct: 105 GVYSGTLVNALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I ++Y +LV GI KN++  I   + +   +    + VV    K   +A++H+KVI  F 
Sbjct: 165 SISRVYMALVEGIIKNEQGTIEAPIGRH-PVDRIKMAVV----KDGRHAVTHYKVIKRF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    +E +  TGRTHQ+RVH  H+  P+VGD  Y    +            LHA+ +  
Sbjct: 219 KNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQ----RFNLKGQMLHAKLLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G+ ++  + LP +  K    L
Sbjct: 275 IHPTTGQYVEFESELPEYFKKIIKIL 300


>gi|153940691|ref|YP_001390824.1| RluA family pseudouridine synthase [Clostridium botulinum F str.
           Langeland]
 gi|152936587|gb|ABS42085.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           Langeland]
 gi|295318893|gb|ADF99270.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           230613]
          Length = 305

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 87/326 (26%), Positives = 149/326 (45%), Gaps = 33/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  + VE + +N+RLD +    +   +   LQ I+  G V V+ K  K N +++ G 
Sbjct: 1   MEKIN-LQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +K  ++YED  + V NKP  + V    
Sbjct: 60  NIEVN---------------IPEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G+     ++  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+  
Sbjct: 105 GVYSGTLVNALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I ++Y +LV GI K ++  I   + +   +    + VV    K   +A++H+KVI+ F 
Sbjct: 165 SISRVYMALVEGIIKYEQGTIEAPIGRH-PVDRIKMAVV----KDGRHAVTHYKVIERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    +E +  TGRTHQ+RVH  H+  P+VGD  Y    +            LHA+ +  
Sbjct: 219 KNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQ----RFNLKGQMLHAKLLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP   + ++  + LP +  K    L
Sbjct: 275 IHPTTRQYVEFESELPEYFKKIIKIL 300


>gi|66044884|ref|YP_234725.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           B728a]
 gi|289671959|ref|ZP_06492849.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. syringae FF5]
 gi|63255591|gb|AAY36687.1| Pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           B728a]
 gi|330900159|gb|EGH31578.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. japonica str. M301072PT]
 gi|330952677|gb|EGH52937.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae Cit 7]
 gi|330973866|gb|EGH73932.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aceris str. M302273PT]
 gi|330975220|gb|EGH75286.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aptata str. DSM 50252]
          Length = 318

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 103/319 (32%), Positives = 170/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 9   PGVQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRIPP-----VRVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y 
Sbjct: 121 LSFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G      + +   L+K +   G+ +  V +       A++ FKV+  F      +E
Sbjct: 180 ALVRGNWATALKQVRAPLMKSNLRSGERMVEVNEE---GKEALTIFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   NF          +L+LHA  + +P P+G 
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHAIAGDTKYGDENFSREIRDLGGKRLFLHAYMLTVPMPDGS 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L + AP+     KT + L
Sbjct: 297 KLNVQAPVDDMWAKTVERL 315


>gi|282850533|ref|ZP_06259912.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
 gi|282580026|gb|EFB85430.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
          Length = 307

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 85/321 (26%), Positives = 143/321 (44%), Gaps = 32/321 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   +V  ++E MRLD +        +   +Q +++ G V V  K  K N R+    ++R
Sbjct: 1   MNEYIVSAEQEGMRLDVFLTEQMEG-SRSYIQSLIKGGHVTVGGKVGKANLRLTPDTIIR 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSG 124
           +                +    ++    + +    LYED  I + NKP G+ V    G+ 
Sbjct: 60  VE---------------IPEPESIEVKPEDIPLDYLYEDHDIVIVNKPRGMVVHPAVGNY 104

Query: 125 IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L    D  G     +P + HRLD++TSG+++VA+  AA   L E  +    +
Sbjct: 105 SGTLVNALLFHCKDLSGINGEIRPGIVHRLDKDTSGVMMVAKNDAAHIGLAEQVKTHSAR 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + YW+LV G    +K  I   + +        + VV +N K    A++HFKV++ +  + 
Sbjct: 165 RTYWALVQGNIVEEKGTIKAPIGRHPK-DRMKMAVVFENSKD---AVTHFKVLERYGHQ- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E    TGRTHQ+RVH  H+G P+V D  Y                 LH++ +D+ HP
Sbjct: 220 TLVECNLETGRTHQIRVHFAHIGHPVVNDPFYGYRR----MDFPIEGQALHSKSLDVKHP 275

Query: 301 -EGGRLQITAPLPAHMVKTWD 320
             G  +   AP+PA      +
Sbjct: 276 ITGEEMHFEAPIPADFKACLE 296


>gi|319937281|ref|ZP_08011688.1| pseudouridine synthase [Coprobacillus sp. 29_1]
 gi|319807647|gb|EFW04240.1| pseudouridine synthase [Coprobacillus sp. 29_1]
          Length = 305

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 155/331 (46%), Gaps = 33/331 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++  +VE +++  R+D+         +   +Q ++++G V +D+K +K + ++++G+
Sbjct: 1   MEDIKIRIVE-EQKGQRIDKILAKELADFSRTQIQSLIQNGYVVIDEKPIKASYKVETGE 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +         I+ E   LD               ++YED  + V NKP G+ V    
Sbjct: 60  DVIVYIPKPESTDILPEDIPLD---------------VVYEDQDVIVINKPTGMIVHPSI 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           GI     ++  L    D  G     +P + HR+D+ETSG+L+VA+   A Q L++  +  
Sbjct: 105 GIYSGTLVNALLYHCHDLSGINGVTRPGIVHRIDKETSGLLMVAKNDKAHQSLSKQLQEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G+  ++   I   + +  +        +   +K A  AI++FKVI+ F 
Sbjct: 165 TVTRRYLALVHGLIPHEFGRIEAPIGRDKNDRQK----MTCTDKNAKDAITNFKVIERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    +E +  TGRTHQ+RVH  ++G P+ GD +Y             +  +LHA+ +  
Sbjct: 220 RDMSLVECRLETGRTHQIRVHMQYIGYPVYGDPQYGLRRDDT-----SHGQFLHAKILGF 274

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            HP  G  +   + LP    K    L  + +
Sbjct: 275 VHPRTGEEMYFESELPDFFEKKLQELRNEME 305


>gi|167755826|ref|ZP_02427953.1| hypothetical protein CLORAM_01342 [Clostridium ramosum DSM 1402]
 gi|167704765|gb|EDS19344.1| hypothetical protein CLORAM_01342 [Clostridium ramosum DSM 1402]
          Length = 306

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 151/326 (46%), Gaps = 34/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  ++   ++ N+RLD+        ++   +Q ++  G V V++K+ K + + +   
Sbjct: 1   MEKINLII--EEDNNLRLDKVIAMQLQELSRTQIQDMINQGLVLVNQKKEKASYKTKLND 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I  + N               V+L    + +   ++YED  + V +KP G+ V   +
Sbjct: 59  EIEITILDN---------------VDLDIEPEDISLKIVYEDEDVIVVDKPTGMIVHPSA 103

Query: 124 GIAY--HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           GI +   ++  L    D  G     +P + HR+D+ETSG+L+VA+   A + L++  +  
Sbjct: 104 GIMHGTLVNALLFHCKDLSGINGVNRPGIVHRIDKETSGLLMVAKNDNAHRLLSKQLKDH 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G+  ++   +   + +        + V + N   +  A+++F V+  + 
Sbjct: 164 TVVRRYVALVHGLIPHEHGKVDAPIGRNPK-DRQSMAVTRTN---SKEAVTNFTVLKRY- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +E +  TGRTHQ+RVH  ++G P+ GD KY             +  +LHA+ +  
Sbjct: 219 NAMSLIECRLETGRTHQIRVHMSYIGYPVYGDPKYGYRKDD-----FSHGQFLHAKKLGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP   + ++  +PLP +     D L
Sbjct: 274 IHPTTQKYMEFESPLPDYFQAKLDEL 299


>gi|312864274|ref|ZP_07724508.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
 gi|322517241|ref|ZP_08070120.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           vestibularis ATCC 49124]
 gi|311100275|gb|EFQ58484.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
 gi|322124147|gb|EFX95681.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           vestibularis ATCC 49124]
          Length = 296

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 142/315 (45%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++     + +++G V V+ K  K    ++ G V+          
Sbjct: 7   EAGNRLDKALAD-LTELSRSQANEAIKAGTVLVNGKSAKAKYAVKEGDVIT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFL 133
           +++ E+++L+        ++ +   ++YED+ + V NKP G+ V   +G      ++  +
Sbjct: 57  YVLPEEEVLE------YKAEDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++V G
Sbjct: 111 YHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +            K        A++ F V++ F   +  +E+Q  T
Sbjct: 171 NLPNDRGVIEAPIGRSDKDRKKQAVTAK-----GKPAVTRFTVLERFG-NYTLVELQLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G L + T
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLKGHGQFLHAKTLGFTHPTTGELVEFT 279

Query: 309 APLPAHMVKTWDSLG 323
           A  PA   KT + L 
Sbjct: 280 AEEPAIFKKTLEKLR 294


>gi|317498467|ref|ZP_07956761.1| RluA family pseudouridine synthase [Lachnospiraceae bacterium
           5_1_63FAA]
 gi|316894160|gb|EFV16348.1| RluA family pseudouridine synthase [Lachnospiraceae bacterium
           5_1_63FAA]
          Length = 305

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 136/327 (41%), Gaps = 32/327 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     + V N+    RLD         +    + K+ +  +  ++ K  K N + + G 
Sbjct: 1   MDETIEIKVTNEMAGKRLDVVLSEQCSDLTRSYINKLCKEERAALNGKTSKGNKKCKEGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +                +     L    + +   ++YED  + + NKP G+ V   +
Sbjct: 61  VITLQ---------------VPEPTELEILPEEMNLDIVYEDQDVILINKPKGMVVHPAA 105

Query: 124 GI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++G +    D         +P + HR+D++T+GIL+V +   A Q + +    
Sbjct: 106 GHYSGTLVNGLMAHCKDDLSGINGVLRPGIVHRIDKDTTGILIVCKNDMAHQSIAKQLYD 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y ++V+G  K ++  +   + +          V+        +A++H+KV+   
Sbjct: 166 HSITRKYHAIVYGNIKEEEGTVNAPIGRSLKDRKKMGIVM-----DGKHAVTHYKVLKRL 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F ++E Q  TGRTHQ+RVH   +  P++GD  Y        +        LHA+ + 
Sbjct: 221 KKGFTYIECQLETGRTHQIRVHMASIKHPLLGDDVYGPKK----SKYTLEGQCLHAKVLG 276

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G  ++   PLP +  K  + L
Sbjct: 277 FVHPRTGEYMEFEVPLPEYFEKLLNKL 303


>gi|162382793|ref|YP_454733.2| 23S rRNA pseudouridylate synthase C [Sodalis glossinidius str.
           'morsitans']
          Length = 318

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 106/317 (33%), Positives = 163/317 (51%), Gaps = 14/317 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V ++ +  DE   R+D + + +   +    + +I+R G+VRV+KKRVK   ++Q+   
Sbjct: 6   PGVHFITISADEAGQRIDNFLRTYLKGVPKSMIYRIVRKGEVRVNKKRVKPEYKLQNDDE 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV  +          LD    L +        +LYED  + + NKPAG +V GGSG
Sbjct: 66  VRIPPVRRSDEEHAPISTGLDKVAALNE-------AVLYEDDHLLILNKPAGTAVHGGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +    +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y 
Sbjct: 119 LSFGVIEGLRA-LRPDARFLELVHRLDRDTSGVLLVAKKRSALRALHEQLRAKGMQKDYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + IA  LLK     G+ +  V         + + FKV + F      + 
Sbjct: 178 ALVRGQWQSHVKTIAAPLLKNILASGERIVRVNSE---GKPSETCFKVEERFTL-AMLVR 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVHA H G PI  D +Y    F         N+L+LHA  +   HP  G
Sbjct: 234 ASPVTGRTHQIRVHAQHAGHPIAFDDRYGDGMFDQQLKGCGLNRLFLHAAALRFDHPGSG 293

Query: 304 R-LQITAPLPAHMVKTW 319
             L+I APL A + +  
Sbjct: 294 ETLRIDAPLDASLRQCL 310


>gi|161507611|ref|YP_001577565.1| pseudouridine synthase [Lactobacillus helveticus DPC 4571]
 gi|160348600|gb|ABX27274.1| pseudouridine synthase [Lactobacillus helveticus DPC 4571]
          Length = 303

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/326 (25%), Positives = 148/326 (45%), Gaps = 35/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     + VEN+    RLD++     P ++   ++++++  ++ V+ K  K + +IQ+G 
Sbjct: 1   MPKKYELQVENEYG--RLDKFISEQIPDLSRTRVKELVKEKEILVNHKVEKVSYKIQAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I         ++ E   LD               ++YED  + V NKP G+ V    
Sbjct: 59  KIEINVPAVKPLDVVPENIPLD---------------IVYEDEVVIVVNKPQGMVVHPAP 103

Query: 124 GIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +  L    D     +G +P + HR+D++TSG+L++A+   A + L +    +
Sbjct: 104 GHPDHTLVNALLYHTQDLAQSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++IYW++V G    +   I   + +  +       V     +    A++HFKV+  F 
Sbjct: 164 TNKRIYWAIVHGDFGEENGVIDAPIGRNPYDRKKMAVV-----ENGKKAVTHFKVLKQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G  + GD  Y         +   N  +LHA+ +  
Sbjct: 218 KGYSLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPR-----KTLKGNGQFLHAKVLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G+ L+ TA  P     T   L
Sbjct: 273 KHPRTGKWLEFTAEPPKIFQDTLAQL 298


>gi|304437216|ref|ZP_07397176.1| ribosomal large subunit pseudouridine synthase D [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369708|gb|EFM23373.1| ribosomal large subunit pseudouridine synthase D [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 300

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 83/317 (26%), Positives = 144/317 (45%), Gaps = 31/317 (9%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +D+   RLD +     P ++    Q+++  G V VD +R K N ++  G+ V        
Sbjct: 6   SDQAGERLDVFLVRQLPTLSRSYAQRLVAEGHVTVDGERRKANFKLSGGESVACT----- 60

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDG 131
                     +  +  +   ++ +   +LYED+ I V NKP G+ V   +G+     ++ 
Sbjct: 61  ----------IPPAEAVEIRAENIPLNVLYEDADIIVINKPRGMVVHPAAGVYTGTLVNA 110

Query: 132 FLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    D  G     +P + HRLD++TSG++V A+   A   L    R +  ++ Y ++V
Sbjct: 111 LLHHCSDLSGINGDLRPGIVHRLDKDTSGVMVAAKNDMAHHFLARQIRDKEARREYRAIV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G    +   I   + +        + +V++N      A +HF+V++ F   + ++  + 
Sbjct: 171 YGNIVERAGVITGDIGRH-PTDRKKMAIVREN---GKPATTHFEVLERFGD-YTFVACRL 225

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            TGRTHQ+RVH   +G P+VGD KY A               LH+  + L HP     + 
Sbjct: 226 ETGRTHQIRVHMTSIGHPLVGDTKYTAKKNP----FAIAGQALHSLTLTLTHPRTQAEMT 281

Query: 307 ITAPLPAHMVKTWDSLG 323
            TAPL A M +   +L 
Sbjct: 282 FTAPLSADMDEILHTLR 298


>gi|281425096|ref|ZP_06256009.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           F0302]
 gi|281400940|gb|EFB31771.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           F0302]
          Length = 377

 Score =  268 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 142/332 (42%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++     P+ +   +Q+   SG + V+ K VK N +++ G V+ +  
Sbjct: 47  VEVDMGQTPVRIDKFLAEKNPYQSRNRIQQAADSGFIYVNDKPVKSNYKVRPGDVITLML 106

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                +  I               ++ +   ++YED  + V NK AG+ V  G+G     
Sbjct: 107 DRPKHDTSI--------------VAEDIPLDIVYEDDALMVINKQAGMVVHPGAGNFTGT 152

Query: 128 HIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            I+            D+   +  L HR+D++TSG+LVVA+T  A   L + F  +   + 
Sbjct: 153 LINAVAWHLKDLESFDANDPEVGLVHRIDKDTSGLLVVAKTADAKSALGKQFFNKSTHRS 212

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG   + +  I   + +        + V   +      A++H++VI+ F      
Sbjct: 213 YNALVWGNLIDDEGTIEGNIARDPK-NRLRMKVFSPDSGIGKNAVTHYRVIERFG-YTTL 270

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----------IQNKLYL 290
           +E    TGRTHQ+R H  H+G P+  D  Y      +G  +S           +  +  L
Sbjct: 271 VECILETGRTHQIRAHMKHIGHPLFADATYGGEQVLRGQRSSTYKAFIQNCFKLCPRQAL 330

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA+ +   HP  GR +   +  P    +    
Sbjct: 331 HAKTLGFVHPSTGRQMDFDSEWPDDFSQLIAK 362


>gi|94311375|ref|YP_584585.1| ribosomal large subunit pseudouridine synthase C [Cupriavidus
           metallidurans CH34]
 gi|93355227|gb|ABF09316.1| 23S rRNA pseudouridylate synthase [Cupriavidus metallidurans CH34]
          Length = 338

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 106/324 (32%), Positives = 167/324 (51%), Gaps = 22/324 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V YV V+   E  R+D +       +   ++ ++LRSG+VRV+K RV    R+Q+G VV
Sbjct: 22  QVAYVTVDESSEGQRIDNFLLKVAKGVPKSHIYRVLRSGEVRVNKGRVDATYRLQNGDVV 81

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP+           ++ + +          +  +L+ED+ + V +KPAG++V GGSG+
Sbjct: 82  RIPPM-----------RVAEKAAPTGGFVPAGEFPVLFEDAALLVIDKPAGVAVHGGSGV 130

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   L+     + +   L HRLD+ETSGILV+A+ R+   HL E  R   + K Y++
Sbjct: 131 AFGVIEQLRRAR-PEAKFLELVHRLDRETSGILVLAKKRSVLVHLHEQIRGNGMDKRYFA 189

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G   N ++ +   L K S   G+    V+ +      + + F  ++ F   +  LE 
Sbjct: 190 CVAGEFPNTRQHVKLPLYKYSTPDGERRVRVQAD---GLASHTVFNRMEAF-DGYTLLEA 245

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +  TGRTHQ+RVH   +G PIVGD KY           + T P   +++LHA  + L HP
Sbjct: 246 ELKTGRTHQIRVHLQSIGFPIVGDDKYGDFALNKALSRSGTKPGLKRMFLHAHRLTLTHP 305

Query: 301 EGG-RLQITAPLPAHMVKTWDSLG 323
             G  + ++APLPA  V+    L 
Sbjct: 306 VTGAPMTVSAPLPAECVEFLQQLR 329


>gi|191638454|ref|YP_001987620.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|190712756|emb|CAQ66762.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|327382486|gb|AEA53962.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Lactobacillus casei LC2W]
          Length = 307

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 85/335 (25%), Positives = 144/335 (42%), Gaps = 42/335 (12%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +MT    +  E      R+D+    H        +QK L+ G V V+ +  K N ++ SG
Sbjct: 1   MMTSTFTITTEQG----RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQPTKANYKVASG 56

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V+ I                +  +  L    + +   ++YED ++ V +KP G+ V   
Sbjct: 57  DVIAIS---------------IPEAKPLEAIPEPIPLDIVYEDDQVIVVDKPQGMVVHPA 101

Query: 123 SGIAYHIDGFLKSWVDSKG--------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            G   H DG L + +             +P + HR+D++TSG+L+VA+T  A   L+   
Sbjct: 102 PG---HPDGTLVNGLLYHTDLPGINGVIRPGIVHRIDKDTSGLLMVAKTEKAQLSLSAQL 158

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + +   + Y +LV G  K  +  I   L +          V         +A++HF+V++
Sbjct: 159 KAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRDRKRQAVVA-----AGRHAVTHFQVLE 213

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F + + +++    TGRTHQ+RVH  ++  P+ GD  Y         +      +LHA  
Sbjct: 214 RF-EHYTFIKCILETGRTHQIRVHMAYIHHPVAGDPLYGPK-----RTLPGKGQFLHAAK 267

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           +   HP  G+ L   AP+P    KT   L    D+
Sbjct: 268 LGFVHPTTGQLLVFEAPVPPIFEKTLADLRAGIDK 302


>gi|152986000|ref|YP_001347558.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PA7]
 gi|150961158|gb|ABR83183.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PA7]
          Length = 318

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 103/323 (31%), Positives = 169/323 (52%), Gaps = 14/323 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  T VQ + V  +    R+D +            + +ILR G+VRV+K R+K + R+Q+
Sbjct: 6   SPTTGVQLLDVPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRIKPDYRLQA 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VR+PP+  A           + +       + +++ ++YED  + V NKPAGI+V G
Sbjct: 66  GDQVRVPPLRLAERD--------EPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQ 180
           GSG++  +    +  +  + +   L HRLD++TSG+L++A+ R+  +HL E+ R  + + 
Sbjct: 118 GSGVSAGVIEVFRQ-LRPEARDIELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKIVD 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G     K+ I   LLK +   G+ +  V    K    A++ F+V+  F    
Sbjct: 177 KRYHALVRGHWPAGKKNIRAPLLKNNLRSGERMVEVNVEGKD---ALTEFRVLRRFGDFA 233

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPH 299
             +E +P TGRTHQ+RVHA H G  I GD KY   +F          +L+LHA  + +P 
Sbjct: 234 TLVEARPITGRTHQIRVHAKHAGHAIAGDPKYGDEDFSREIRELGGKRLFLHAAQLRVPL 293

Query: 300 PEGGRLQITAPLPAHMVKTWDSL 322
           P+G  L++ AP+     ++ + L
Sbjct: 294 PDGQVLELEAPVDEVWRRSLERL 316


>gi|300703940|ref|YP_003745542.1| ribosomal large subunit pseudouridine synthase d [Ralstonia
           solanacearum CFBP2957]
 gi|299071603|emb|CBJ42927.1| Ribosomal large subunit pseudouridine synthase D [Ralstonia
           solanacearum CFBP2957]
          Length = 370

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 89/335 (26%), Positives = 144/335 (42%), Gaps = 32/335 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V +       RLD+      P  +   LQ+ + +G VRV    V+    +  G  + + P
Sbjct: 53  VQIPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVRPRAAVCGGDRIEVVP 112

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
              A      E   +   ++L          ++YED  + V NKPAG+ V   +G     
Sbjct: 113 QRAAD-----ENAFVAEPIDLD---------VVYEDDTLLVINKPAGLVVHPAAGNWSGT 158

Query: 128 HIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  +  + G  +  + HRLD+ETSG++VVART  A   L    + R +++ Y +L
Sbjct: 159 VLNGLLHRYPQAAGLPRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLAL 218

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWL 243
           VWG    +   I   + +      D   +          A +HFK +D           +
Sbjct: 219 VWGE-TPEAGTIDAPIGRDP---RDRTRMAIIETASGKPARTHFKTLDVIDLGRAQVSLV 274

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLHARYMD 296
           + Q  TGRTHQ+RVH    G P++GD  Y  NF+      I+        +  LHA  + 
Sbjct: 275 QCQLETGRTHQIRVHFESEGHPLLGDPVYTRNFRRGRPQTIKAPLPIPFARQALHAVRLG 334

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           + HP  G+ +   A +P  + +  D+L    D +L
Sbjct: 335 IVHPASGQSMHWHAGVPDDLAELMDALEMDPDADL 369


>gi|302187286|ref|ZP_07263959.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. syringae 642]
          Length = 318

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 103/319 (32%), Positives = 169/319 (52%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 9   PGVQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRIPP-----VRVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y 
Sbjct: 121 LSFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G      + +   L+K +   G+ +  V         A++ FKV+  F      +E
Sbjct: 180 ALVRGNWATALKQVRAPLMKSNLRSGERMVEVNDE---GKEALTIFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   NF          +L+LHA  + +P P+G 
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHAIAGDTKYGDENFSREIRDLGGKRLFLHAYMLTVPMPDGS 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L + AP+     KT + L
Sbjct: 297 KLNVQAPVDDMWAKTVERL 315


>gi|225023856|ref|ZP_03713048.1| hypothetical protein EIKCOROL_00722 [Eikenella corrodens ATCC
           23834]
 gi|224943330|gb|EEG24539.1| hypothetical protein EIKCOROL_00722 [Eikenella corrodens ATCC
           23834]
          Length = 372

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 134/325 (41%), Gaps = 29/325 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD       P  +   L   ++ G V ++ +  +   R+  G+ + +  
Sbjct: 32  LTVPTDLAGQRLDAALAKLLPDYSRSRLSTWIKDGNVLLNGQVARPKERLIGGETLEVH- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                        I  S        + +   +++ED  + V NKPAG+ V   +G     
Sbjct: 91  -------------IQHSHETAAFTPEPMPLDIVFEDDSVIVLNKPAGLVVHPAAGNWSGT 137

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L      ++  +  + HRLD++TSG++VVA+T AA   L +  + R +++IY ++
Sbjct: 138 LLNGLLAHCPALAEIPRAGIVHRLDKDTSGLMVVAKTPAAQNSLVQQLQERSVKRIYRAV 197

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H       V      G   A++H KV++ + Q   ++E  
Sbjct: 198 ADGIVPFD-GKIDTLIGRDPHNRLKMAVV----GFGGKKAVTHIKVLERY-QSHSYIECT 251

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-----NFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH      P+  D  Y                   +  LHA  +   HPE
Sbjct: 252 LETGRTHQIRVHMREAKHPLAADPVYGNPRHPCSDAVKEAVLQLARQALHAYRLSFVHPE 311

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            G  +Q  APLP  +      L ++
Sbjct: 312 SGETVQFEAPLPEDIHHLLSVLRWE 336


>gi|210622438|ref|ZP_03293170.1| hypothetical protein CLOHIR_01118 [Clostridium hiranonis DSM 13275]
 gi|210154254|gb|EEA85260.1| hypothetical protein CLOHIR_01118 [Clostridium hiranonis DSM 13275]
          Length = 309

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 79/328 (24%), Positives = 141/328 (42%), Gaps = 37/328 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++  +VE DE+  RLD +  + +  ++   +QKI++  +V V+ K  K    ++    +
Sbjct: 8   DIREFLVEEDEDGDRLDVYLADQFVDMSRSYIQKIIKDKKVTVNGKVEKAKYLVKEEDKI 67

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            I      +  ++ +   ++               ++YED  I + NKP G+ V    G 
Sbjct: 68  VIEIPKPKVLEVVPQDIPIE---------------IVYEDDDIIIVNKPQGMVVHPAPGN 112

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                   I YH  G L S   +   +P + HR+D++TSGIL++A+   A   L E  + 
Sbjct: 113 YEGTLVNAILYHCKGNLSSI--NGVIRPGIVHRIDKDTSGILMIAKNNNAHNCLAEQLKD 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y  +   + K     +   + +          V          A++HF+VI+ F
Sbjct: 171 HSITREYEFICHSVFKEDNVTVDRPIGRNPKDRLKMAIV-----PNGKRAVTHFEVIERF 225

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  +  +  TGRTHQ+RVHA+ +  P+VGD  Y        +    N   LHA+ + 
Sbjct: 226 -NGYTHVRARLETGRTHQIRVHAMSINHPLVGDPVYGPKN----SKIKLNGQALHAKKLG 280

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP     ++  + LP +  K  + L 
Sbjct: 281 FIHPTTKEYVEFDSELPDYFQKLLEKLR 308


>gi|262374097|ref|ZP_06067374.1| 23S rRNA pseudouridylate synthase [Acinetobacter junii SH205]
 gi|262311108|gb|EEY92195.1| 23S rRNA pseudouridylate synthase [Acinetobacter junii SH205]
          Length = 310

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 98/317 (30%), Positives = 164/317 (51%), Gaps = 19/317 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +E  R+D +       +    + +++R GQVRV+KKR+K   R+  G  +R
Sbjct: 10  VTWFDVDEHQEGQRIDNFLFTRLKGVPKSRIYRLIREGQVRVNKKRIKAETRLSIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK    +      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETDAPVSDGVAQSLLSRVVYEDEGLLVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   +++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y ++
Sbjct: 123 YGLIEAMRAATGKKY--LELIHRIDRDTSGLVMISKKRSTLKLLQDLLREHKIKKTYAAI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     ++ I   LL+     G+    V    K    + + +KVI+ F +    +   
Sbjct: 181 VKGQVSLDQQLIDAPLLRYELANGERRVRVT---KEGKPSKTEWKVIERF-KAATLVHAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P++GD KY  N    +T P   +L LHA  +D+P+       
Sbjct: 237 PLSGRTHQIRVHGLSIGHPLIGDDKYGHN--TAYTGPEARRLCLHAMRLDIPNYPT---- 290

Query: 307 ITAPLPAHMVKTWDSLG 323
           I AP+P  M +  + L 
Sbjct: 291 IEAPMPEDMQQVINELR 307


>gi|16272361|ref|NP_438574.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae Rd
           KW20]
 gi|260580525|ref|ZP_05848353.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae RdAW]
 gi|1175639|sp|P44433|RLUC_HAEIN RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|1573385|gb|AAC22071.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|260092867|gb|EEW76802.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae RdAW]
          Length = 322

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 102/321 (31%), Positives = 170/321 (52%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++Q+G V
Sbjct: 11  SSVKMLTISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQTGDV 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV       + E+     S NL K +  L++ +L+ED  + + NKP+GI+V GGSG
Sbjct: 71  VRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDDCLIILNKPSGIAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   L++ +  + +   L HRLD++TSGIL++A+ R+A ++L E  R++ +QK Y 
Sbjct: 124 LNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYL 182

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++  + I   LLK     G+ +  V +       + + F + + +      ++
Sbjct: 183 ALVRGQWQSHIKVIQASLLKNELSSGERIVRVSEQ---GKPSETRFSIEERYI-NATLVK 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH  + G PI  D KY   +F         N+L+LHA  +   HP+ G
Sbjct: 239 ASPVTGRTHQIRVHTQYAGHPIALDDKYGDKDFDKQMNELGLNRLFLHAFSIRFEHPKNG 298

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L+  A L   M      L 
Sbjct: 299 ETLRFNASLDHQMKAILQKLR 319


>gi|309778048|ref|ZP_07672988.1| ribosomal large subunit pseudouridine synthase D
           [Erysipelotrichaceae bacterium 3_1_53]
 gi|308914185|gb|EFP59985.1| ribosomal large subunit pseudouridine synthase D
           [Erysipelotrichaceae bacterium 3_1_53]
          Length = 304

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 150/327 (45%), Gaps = 34/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  ++   +E  +R+D++       ++   +Q +L+ G + V++K  K N ++++  
Sbjct: 1   MREID-IIAAAEEAGVRIDKYISEQ-EELSRSRVQSLLQEGLILVNEKPAKANYKVKAQD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +                   D  + L    + ++  + YED  + V NKP  I V   +
Sbjct: 59  HITACF---------------DDEMELEARPEAMELDVRYEDEDVIVINKPKNIVVHPAA 103

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G L    D  G     +P + HR+D++T+G+L+VA+   A   L++  + +
Sbjct: 104 GNQTGTLVNGLLYHCKDLSGINGTLRPGIIHRIDKDTTGLLIVAKNDLAHASLSKQLQSK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + ++Y++LV G+ ++    I   + +        + V   N K A    +HF+VI+ F 
Sbjct: 164 TVNRLYYALVHGVIQHDFGTIDAPIGRDVK-DRQKMAVTSTNSKDAR---THFQVIERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E +  TGRTHQ+RVH  ++G P+VGD KY         +   N   LHA  +  
Sbjct: 219 ENYTLVECRLETGRTHQIRVHMQYIGHPVVGDEKYSYR-----KTMQTNGQLLHAHQLTF 273

Query: 298 PHPEGGRL-QITAPLPAHMVKTWDSLG 323
            HP  G +  + A LP       + L 
Sbjct: 274 QHPRTGEMITVEAELPKQFADILEELR 300


>gi|94499595|ref|ZP_01306132.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [Oceanobacter sp. RED65]
 gi|94428349|gb|EAT13322.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [Oceanobacter sp. RED65]
          Length = 318

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 95/323 (29%), Positives = 162/323 (50%), Gaps = 16/323 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  V  D    R+D +  +         + +I+R G+VRV+K R+K   +++ G VVR
Sbjct: 9   VQFEEVTADYVGQRIDNFLMSRIKGAPKSLVYRIIRKGEVRVNKGRIKPEYKVKLGDVVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP       +  E      S ++   ++ ++  +L+ED      NKP G++V GGSGI+
Sbjct: 69  IPP-----VKVKAEGDAAPISKDM---AEGIEQSILFEDDYFLAVNKPRGMAVHGGSGIS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWS 185
             +   L++ +  K ++  L HRLD++TSG+++VA+ R A     +  + ++ +QK Y +
Sbjct: 121 LGLIEVLRN-LRPKAKRLELVHRLDRDTSGVILVAKRRTALVAFHKMLQRKQGMQKRYLA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV+G      + +   L K     G+ +  V Q+      + + +  I+   + +  +  
Sbjct: 180 LVYGNWPKHLKDVEVPLKKNELKSGERLVKVAQD---GKPSHTRY-SIERKFKGYTLVNA 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +P TGRTHQ+RVH    G  IVGD KY  + +          +L+LHA+ +   HPE G 
Sbjct: 236 EPVTGRTHQIRVHCQFSGHNIVGDEKYATDEELQGARQQGARRLFLHAQSLRFKHPETGE 295

Query: 305 -LQITAPLPAHMVKTWDSLGFKY 326
            + I APL     +   SL  K+
Sbjct: 296 KMTIQAPLDEAFEQFLSSLDAKH 318


>gi|255065280|ref|ZP_05317135.1| ribosomal large subunit pseudouridine synthase D [Neisseria sicca
           ATCC 29256]
 gi|255050701|gb|EET46165.1| ribosomal large subunit pseudouridine synthase D [Neisseria sicca
           ATCC 29256]
          Length = 374

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 140/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLMPDYSRSRLTSWIKEGAVIVNDKPAQPKDKMIGGESISVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +L S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VLPSEENLAFKPEAMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y       +         +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNLRHPCSEPVKEAVKSLGARQALHAYRLSFVHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           + G  +   AP+P  +      L  + 
Sbjct: 310 KTGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|255021322|ref|ZP_05293370.1| Ribosomal large subunit pseudouridine synthase C [Acidithiobacillus
           caldus ATCC 51756]
 gi|254969185|gb|EET26699.1| Ribosomal large subunit pseudouridine synthase C [Acidithiobacillus
           caldus ATCC 51756]
          Length = 316

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 99/321 (30%), Positives = 161/321 (50%), Gaps = 14/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V++  V  +E   RLD +       +   ++ KILRSG+VRV+K R + +  +  G V
Sbjct: 4   NGVRHWQVTAEEAGQRLDNFLLRVLKGVPRSHIYKILRSGEVRVNKGRARPHYHLHLGDV 63

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+PPV +A    +             + +  L+  +L+ED ++ V +KPAG++V GGSG
Sbjct: 64  LRLPPVRSADPAAVPRLP--------EQLAVDLRERVLFEDDRVLVLDKPAGMAVHGGSG 115

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           I Y +   L+       ++  L HRLD++TSG L++++ R+A + L ++ R   + K Y 
Sbjct: 116 IRYGVIEALRQLRPDL-RELELVHRLDRDTSGCLLLSKRRSALRSLHQALREEAMDKRYL 174

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  K  +  +   L K     G+   +V+ +E     A + F   +        L 
Sbjct: 175 ALVGGRWKGAERVVKLPLRKNILQSGER--IVRVDEDQGKPARTRFYREEDLG-IATLLR 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +  TGRTHQ+RVH   +G P  GD KY    F G   +    +L+LHA ++  PHP   
Sbjct: 232 AELDTGRTHQIRVHLQAIGHPTAGDSKYGDETFNGAMRALGLRRLFLHAAFLAFPHPRDE 291

Query: 304 RL-QITAPLPAHMVKTWDSLG 323
           R+ ++ APLPA +      L 
Sbjct: 292 RIVRVEAPLPADLDAVLQRLR 312


>gi|237800339|ref|ZP_04588800.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. oryzae str. 1_6]
 gi|331023196|gb|EGI03253.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. oryzae str. 1_6]
          Length = 318

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 102/319 (31%), Positives = 170/319 (53%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V V  +    R+D +   +   +    + +I+R G+VRV+K R K   ++Q+G +
Sbjct: 9   PGVQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRIVRKGEVRVNKGRTKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRIPP-----VRVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL E+ R   + K Y 
Sbjct: 121 LSFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYM 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G     ++ +   LLK +   G+ +  V +       A++ FKV+  F      +E
Sbjct: 180 ALVRGNWAAAQKQVRAPLLKSNLRSGERMVEVNEE---GKEALTIFKVLRRFGDFATMVE 236

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +P TGRTHQ+RVH LH G  I GD KY   NF          +L+LHA  + +P P+G 
Sbjct: 237 AKPVTGRTHQIRVHTLHAGHAIAGDTKYGDENFSREIRDLGGKRLFLHAYMLTVPMPDGS 296

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +L + AP+     +T + L
Sbjct: 297 KLNVQAPVDEMWARTVERL 315


>gi|323343928|ref|ZP_08084155.1| ribosomal large subunit pseudouridine synthase D [Prevotella oralis
           ATCC 33269]
 gi|323095747|gb|EFZ38321.1| ribosomal large subunit pseudouridine synthase D [Prevotella oralis
           ATCC 33269]
          Length = 355

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 86/332 (25%), Positives = 150/332 (45%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +E +R+D++      H +   +Q+   +G V V+ + VK N +++   V+ +  
Sbjct: 25  LVVDKGQEPLRIDKYMSEKLQHSSRNRIQRAADAGFVHVNDRPVKSNYKVRPLDVITLML 84

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +  I+              ++ +   +++EDS++ V NKPAG+ V  G G  +  
Sbjct: 85  DRPRHDSTIE--------------AEDIPLDIVFEDSELMVINKPAGLVVHPGVGNFHGT 130

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+LV+A+T  A   L   F  +   + 
Sbjct: 131 LVNAIAWHLKDLKSFDPNDPEVGLVHRIDKDTSGLLVIAKTPMAKTKLGLQFFNKTTHRS 190

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + +        + V   + +    A++H++VI+ F      
Sbjct: 191 YNALVWGNFTEDEGRIEGNIARDPK-DRLRMTVFAPDSEIGKSAVTHYRVIERFG-YVTL 248

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQN------KLYL 290
           +E    TGRTHQ+R H  H+G P+ GD +Y             + + IQN      +  L
Sbjct: 249 VECILETGRTHQIRAHMKHIGHPLFGDERYGGTEILRGQRSSTYRAFIQNCFKLCSRQAL 308

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HAR +   HP  G+ +  T+ LPA M    D 
Sbjct: 309 HARTLGFAHPVTGKQMDFTSELPADMSMLVDK 340


>gi|153875465|ref|ZP_02003256.1| ribosomal large subunit pseudouridine synthase D [Beggiatoa sp. PS]
 gi|152068071|gb|EDN66744.1| ribosomal large subunit pseudouridine synthase D [Beggiatoa sp. PS]
          Length = 321

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 93/333 (27%), Positives = 153/333 (45%), Gaps = 36/333 (10%)

Query: 4   MTYVQYV--VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           MT +Q     +  +    RLD+   + +P  +   LQ+ +R G V V+    +  ++++ 
Sbjct: 1   MTQIQTFNAQIPPEMAGYRLDKALADLFPDYSRARLQQWIRGGYVLVNSISWRAKDKVKG 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G+ ++I   +                  ++     L   LLYED  I V NKPAG+ V  
Sbjct: 61  GEDIQITAQLEE---------------EVSWQPQTLPLTLLYEDKDILVVNKPAGLIVHP 105

Query: 122 GSGI-AYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G+G     +   L ++     Q PR  + HRLD++TSG+LVVAR+  A +HL E  + R 
Sbjct: 106 GAGHQQNTLVNALLNYAPELAQLPRAGIVHRLDKDTSGVLVVARSLPAHKHLVEQLQNRE 165

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             + Y ++V G          +  + +       + VVK+       AI+H++V+  + +
Sbjct: 166 FLREYKAIVIGALI--SGSTVDAPIGRHPTQRTRMAVVKK----GKPAITHYRVLQRY-R 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYL 290
              ++ +Q  TGRTHQ+RVH  H   P++GD  Y    +        F   ++   +  L
Sbjct: 219 VHTFIRVQLETGRTHQIRVHLAHKHYPLIGDSVYGGRLQIPPNSSDTFKEALRTFPRQAL 278

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           HA  + L HP  G  +Q TAPLP  M +    L
Sbjct: 279 HAERLGLTHPISGEMMQWTAPLPDDMQQLLLVL 311


>gi|296314698|ref|ZP_06864639.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           polysaccharea ATCC 43768]
 gi|296838532|gb|EFH22470.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           polysaccharea ATCC 43768]
          Length = 374

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 139/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   +R G V V+ K  +  +++  G+ +R+  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKPSQPKDKMIGGEQIRVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFMPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNLRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPNDIYHLLSVLRLEA 336


>gi|167765516|ref|ZP_02437580.1| hypothetical protein CLOSS21_00010 [Clostridium sp. SS2/1]
 gi|167712701|gb|EDS23280.1| hypothetical protein CLOSS21_00010 [Clostridium sp. SS2/1]
 gi|291558984|emb|CBL37784.1| ribosomal large subunit pseudouridine synthase D
           [butyrate-producing bacterium SSC/2]
          Length = 305

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 71/327 (21%), Positives = 136/327 (41%), Gaps = 32/327 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     + V ++    RLD         +    + K+ +  +  ++ K  K N + + G 
Sbjct: 1   MDETIEIKVTSEMAGKRLDVVLSEQCSDLTRSYINKLCKEERAALNGKTSKGNKKCKEGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +                +     L    + +   ++YED  + + NKP G+ V   +
Sbjct: 61  VITLQ---------------VPEPTELEILPEEMNLDIVYEDQDVILINKPKGMVVHPAA 105

Query: 124 GI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++G +    D         +P + HR+D++T+GIL+V +   A Q + +    
Sbjct: 106 GHYSGTLVNGLMAHCKDDLSGINGVLRPGIVHRIDKDTTGILIVCKNDMAHQSIAKQLYD 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y ++V+G  K ++  +   + +          V+        +A++H+KV+   
Sbjct: 166 HSITRKYHAIVYGNIKEEEGTVNAPIGRSLKDRKKMGIVM-----DGKHAVTHYKVLKRL 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F ++E Q  TGRTHQ+RVH   +  P++GD  Y        +        LHA+ + 
Sbjct: 221 KKGFTYIECQLETGRTHQIRVHMASIKHPLLGDDVYGPKK----SKYTLEGQCLHAKVLG 276

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G  ++   PLP +  K  + L
Sbjct: 277 FVHPRTGEYMEFEVPLPEYFEKLLNKL 303


>gi|322372447|ref|ZP_08046983.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           C150]
 gi|321277489|gb|EFX54558.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           C150]
          Length = 297

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 141/315 (44%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++     + +++G V V+ K  K    ++ G V+          
Sbjct: 7   EAGNRLDKALAD-LTELSRSQANEAIKAGTVLVNGKSAKAKYAVKEGDVIT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFL 133
           + + E+++L+        ++ +   ++YED+ + V NKP G+ V   +G      ++  +
Sbjct: 57  YELPEEEVLE------YKAEDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L+VA+   A   L    + ++  + Y ++V G
Sbjct: 111 YHVKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDKAHNALAAELKDKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +            K        A++ F V++ F   +  +E+Q  T
Sbjct: 171 NLPNDRGVIEAPIGRSDKDRKKQAVTAK-----GKPAVTRFTVLERFG-NYTLVELQLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G L + T
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLKGHGQFLHAKTLGFTHPTTGELVEFT 279

Query: 309 APLPAHMVKTWDSLG 323
           A  PA   +T + L 
Sbjct: 280 AEEPAIFKETLEKLR 294


>gi|83589720|ref|YP_429729.1| ribosomal large subunit pseudouridine synthase D [Moorella
           thermoacetica ATCC 39073]
 gi|83572634|gb|ABC19186.1| ribosomal large subunit pseudouridine synthase D [Moorella
           thermoacetica ATCC 39073]
          Length = 306

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 91/323 (28%), Positives = 149/323 (46%), Gaps = 32/323 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRI 67
            VVV  +    R+D W     P ++   +Q++L +G++ +    R+K N R++ G+ VR+
Sbjct: 2   EVVVPPEARGRRIDAWLAGELPEVSRSRIQQLLEAGEITLALPGRLKANYRLRGGERVRV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                           L     L    + +   +LYED  I V NKP G+ V    G   
Sbjct: 62  R---------------LPEPTLLAARPEAIPLDILYEDEDIIVVNKPQGMVVHPAPGSEG 106

Query: 127 -YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HRLD++TSGILV A+  AA + L    +   +++
Sbjct: 107 GTLVNALLYHCGDLSGINGVLRPGIVHRLDKDTSGILVAAKNDAAHRGLAAQIKDHSMKR 166

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY +LV G     +  +   + +   +    + V     K +  A++H++V++ F   + 
Sbjct: 167 IYLALVHGEVAEPRGRVEAPIGRH-PVDRQRMAVTL---KNSRPAVTHYRVVEHFP-GYT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            LE +  TGRTHQ+RVH   +G P+VGD KY    +  F  P      LHA  +   HP 
Sbjct: 222 LLEARLETGRTHQIRVHMAFIGHPVVGDPKYGPR-RCPFAVPG---QLLHAGCLGFVHPV 277

Query: 301 EGGRLQITAPLPAHMVKTWDSLG 323
            G  L+ T P P+  ++  + L 
Sbjct: 278 RGDYLEFTTPPPSIFLQVLEQLR 300


>gi|260063592|ref|YP_003196672.1| ribosomal large subunit pseudouridine synthase D [Robiginitalea
           biformata HTCC2501]
 gi|88783037|gb|EAR14210.1| ribosomal large subunit pseudouridine synthase D [Robiginitalea
           biformata HTCC2501]
          Length = 343

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 83/328 (25%), Positives = 141/328 (42%), Gaps = 35/328 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
              +  ++ +R+D++      +     +Q+  R G +R +++ +K N R++ G  +R+  
Sbjct: 21  FTADTGQKPLRVDKFLMTRIRNATRNKIQQAARDGNIRANEQVIKQNYRVKPGDTIRV-- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                 H   E  +L   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 79  ---LFEHPPYENLLLPEDIPLD---------IVYEDEVLLVVNKPAGMVVHPGHGNYTGT 126

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   +   L     +   +P L HR+D+ETSG+LV+A+T AA  +L   F  +  ++ Y 
Sbjct: 127 LVNALVHHLDQLPLNSDNRPGLVHRIDKETSGLLVIAKTEAAMANLARQFFDKTTRREYL 186

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG   +    +   + +           V  +      A++H++V +        + 
Sbjct: 187 ALVWGNVADDSGTVEGPIGRNPK--NRLQMQVFPDGSQGKEAVTHYRVEERLG-YVTLVS 243

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHA 292
            +  TGRTHQ+RVH  H+G  I  D +Y  +     TS             I  +  LHA
Sbjct: 244 CRLETGRTHQIRVHMQHIGHTIFNDSRYGGDRILKGTSFTKYKQFVENAFKILPRQALHA 303

Query: 293 RYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           R +   HP  G  L   AP+P  M    
Sbjct: 304 RTLGFTHPLSGKELDFEAPVPEDMAACI 331


>gi|94310295|ref|YP_583505.1| ribosomal large subunit pseudouridine synthase D [Cupriavidus
           metallidurans CH34]
 gi|93354147|gb|ABF08236.1| 23S rRNA pseudouridine synthase [Cupriavidus metallidurans CH34]
          Length = 403

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 142/331 (42%), Gaps = 32/331 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           Y+ V++     RLD+    H+   +   +Q+ +  G VRVD +  +    +Q GQ + + 
Sbjct: 59  YMEVDSASHGERLDKLLARHFSEFSRSRIQQWIEDGAVRVDGEPSRAKASVQMGQKIEVQ 118

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
           P                +  ++   ++ +   ++YED  + V NKPAG+ V   +G    
Sbjct: 119 PQA--------------APESMAFTAEDVPLDVVYEDDAMLVINKPAGLVVHPAAGNWSG 164

Query: 127 YHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             ++G L      ++  +  + HRLD+ETSG++VVART  A   L      R +++ Y +
Sbjct: 165 TVLNGLLHRDPSAARLPRAGIVHRLDKETSGLMVVARTLVAQTDLVRQLAARTVKRTYLA 224

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCW 242
           LVWG        I   + +      +   +   +      + +HF+ +        K   
Sbjct: 225 LVWGE-TPDDGTIDAPIGRDP---RERTRMAIVHTNSGKPSRTHFETLGTVPLGRGKVSM 280

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQ-NKLYLHARYM 295
           +  Q  TGRTHQ+RVH   +G P+VGD  Y                P+   +  LHA  +
Sbjct: 281 VMCQLETGRTHQIRVHFESIGHPLVGDPVYHKATQRGQRPAIRVPLPVPFTRQALHAYRL 340

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            L HP  GR +   A  P  +    D+L F+
Sbjct: 341 GLVHPVTGRKMSWEAEPPEDLQALIDALDFE 371


>gi|205373291|ref|ZP_03226095.1| YlyB [Bacillus coahuilensis m4-4]
          Length = 301

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 85/319 (26%), Positives = 149/319 (46%), Gaps = 33/319 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V  ++   R+D+         +   +Q+ ++ G V V+ ++ + N + Q+  V+ I   
Sbjct: 7   TVTQEQVGERIDKVVSTINSDWSRSQVQQWIKDGHVLVNMEQKRTNYKSQASDVITIE-- 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                  + E ++LD        ++ L   + YED  + V NKP G+ V    G      
Sbjct: 65  -------VPEAEVLDV------EAEDLNLDVYYEDQDVIVVNKPKGMVVHPAPGHYSGTL 111

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++G +    D  G     +P + HR+D++TSG+L+VA+   A +HL      + + + Y 
Sbjct: 112 VNGLMHHCKDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDVAHEHLVNQLVEKSVTRKYM 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+ ++    I   + + S      + +V Q      +A++HF+V D F Q +  +E
Sbjct: 172 ALVHGVIQHDYGTIDAPIGRDSK-DRQSMTIVDQ----GKHAVTHFEVKDRFEQ-YTLVE 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +   HP    
Sbjct: 226 CQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTMD-----IGGQALHAAVLGFIHPRTEE 280

Query: 305 -LQITAPLPAHMVKTWDSL 322
            L+ TAP+P+   +   +L
Sbjct: 281 YLEFTAPIPSEFNELLQNL 299


>gi|167630173|ref|YP_001680672.1| pseudouridine synthase, rlua family [Heliobacterium modesticaldum
           Ice1]
 gi|167592913|gb|ABZ84661.1| pseudouridine synthase, rlua family [Heliobacterium modesticaldum
           Ice1]
          Length = 369

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 87/321 (27%), Positives = 145/321 (45%), Gaps = 32/321 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V   E + R+D W        +  + Q  ++ G V +D   +K N R++ G V+ + P
Sbjct: 38  LTVTPAEADSRVDVWLVQKGLVPSRSHGQNWIKEGLVTLDGGPLKANYRLRPGDVIEVAP 97

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                  I+ E   L+               ++++D+ I V NKPAG+ V    G     
Sbjct: 98  PAPEAVEILPEDIPLE---------------IIFQDADIAVINKPAGLVVHPAEGHWSGT 142

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HR+D++TSG+LVVA+   A  HLTE  +  R+++ Y
Sbjct: 143 LVNALLYHIKDLSGINGELRPGIVHRIDKDTSGLLVVAKNDRAHIHLTEQVKDHRVRREY 202

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCW 242
            ++V G+   +   +   + +        + V+     G   AI+HF+V+  +  Q F  
Sbjct: 203 LAVVHGVIGAETGRVEAPIGRDPK-DRQRMAVIA----GGKSAITHFRVLARYPEQGFSL 257

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L  +  TGRTHQ+RVH  H+G P+ GD KY         +       LHA  ++  HP  
Sbjct: 258 LHCRLETGRTHQIRVHLAHIGHPVAGDPKYGPRK----AAFGLTGQALHAWKLEFVHPRS 313

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
           G  ++  A  P   V+   +L
Sbjct: 314 GEPMRFQADPPEPFVQVLQAL 334


>gi|149280326|ref|ZP_01886447.1| pseudouridylate synthase, 23S RNA-specific [Pedobacter sp. BAL39]
 gi|149228875|gb|EDM34273.1| pseudouridylate synthase, 23S RNA-specific [Pedobacter sp. BAL39]
          Length = 343

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 76/334 (22%), Positives = 148/334 (44%), Gaps = 42/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+D++      + +   +Q  + +G V V+ K VK + +++    + I  
Sbjct: 21  IVVDKGQSLLRVDKFLMGRMENASRNRIQNAIDAGNVLVNGKTVKSSYKVKPADEISI-- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
                 H  ++ ++    + L          ++YED+ + V NKPAG+ V  G       
Sbjct: 79  ---VFPHPPRDTEVYPEDIPLD---------IVYEDNDLLVVNKPAGMVVHPGYNNYTGT 126

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             + +A+H    L     ++G +P L HR+D++TSG+L++++       L + F    I 
Sbjct: 127 LVNALAFHF-EQLPQLPGNEG-RPGLVHRIDKDTSGLLLISKNEITMTKLAKQFFDHSIT 184

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +L WG    +   +  ++ +        V  V  +E+   ++++H+ V++      
Sbjct: 185 RKYIALAWGDIA-ENGTVTGFIGRSLK--NRIVMDVYDDEEKGKWSVTHYTVLERLG-YV 240

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------------PIQNKL 288
             +  Q  TGRTHQ+R H  H+G P+  D  Y  +     T+             I  + 
Sbjct: 241 TLISCQLETGRTHQIRAHMQHIGHPLFNDANYGGDKIVKGTTFNKYKQFVQNCFEIMPRQ 300

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            LHA+ +   HP   + ++  APLPA      + 
Sbjct: 301 SLHAQTLGFIHPTTKKYMEFEAPLPADFDGVLNK 334


>gi|150003134|ref|YP_001297878.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           vulgatus ATCC 8482]
 gi|254882415|ref|ZP_05255125.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           4_3_47FAA]
 gi|294778333|ref|ZP_06743757.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|319640483|ref|ZP_07995205.1| pseudouridine synthase [Bacteroides sp. 3_1_40A]
 gi|149931558|gb|ABR38256.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           vulgatus ATCC 8482]
 gi|254835208|gb|EET15517.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           4_3_47FAA]
 gi|294447809|gb|EFG16385.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|317387970|gb|EFV68827.1| pseudouridine synthase [Bacteroides sp. 3_1_40A]
          Length = 358

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 85/332 (25%), Positives = 147/332 (44%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK   +G +  + K VK + +++   V+ +  
Sbjct: 33  VVVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKSSYKVKPCDVLTVMM 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    +  I+   + L          ++YED+ + V NKPAG+ V  G G  +  
Sbjct: 93  -----DRPRYDNDIIPEDIPLD---------IVYEDNDLMVVNKPAGLVVHPGCGNYHGT 138

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+LVVA+T  A  HL   F  +  ++ 
Sbjct: 139 LVNAIAWHLKDNPKYDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRK 198

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG+ +N +  I   + +           V  +     +A++H++V++        
Sbjct: 199 YNALVWGVVENNEGTIEGNIGRNPK--DRMQMAVLSDPAQGKHAVTHYRVLERLG-YVTL 255

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  N   KG   S  +           +  L
Sbjct: 256 VECVLETGRTHQIRVHMKHIGHTLFNDERYGGNEILKGTHFSKYKQFVNNCFETCPRQAL 315

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G  +  T+PLP  M    D 
Sbjct: 316 HAMTLGFVHPRTGEEMFFTSPLPEDMTNLIDK 347


>gi|331001807|ref|ZP_08325329.1| hypothetical protein HMPREF0491_00191 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412781|gb|EGG92164.1| hypothetical protein HMPREF0491_00191 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 304

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 140/319 (43%), Gaps = 33/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            ++ E  + N R+D +   +    +   +Q +++ G+  +  K +K N R++ G +V + 
Sbjct: 5   EIIAEESDINKRIDVFLSKNLESFSRSYIQDLIKKGKATIGGKTIKANYRLREGDIVAL- 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                          +     L    + +   ++YED+ + + NKP G+ V   +G    
Sbjct: 64  --------------AIPKPEPLEILPENIPLDIVYEDNDVILVNKPKGMVVHPAAGHYSG 109

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             ++  L    D+        +P + HR+D +T+GI++V +   A QH+ +      I +
Sbjct: 110 TLVNALLYHCKDNLSGINGVLRPGIVHRIDMDTTGIIIVCKNDNAHQHIAKQLAEHSITR 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G  K  +  +   + + S      + V    +K    A++HFKV++     + 
Sbjct: 170 KYVAIVSGNIKEDEGVVDAAIAR-SKNDRKKMTV----DKDGKRAVTHFKVLERL-NNYT 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           ++E    TGRTHQ+RVH  ++  P++GD  Y    +            LHA+ +   HP 
Sbjct: 224 YIECVLETGRTHQIRVHMSYLHHPLLGDEVYSNKKENTK----LKGQCLHAKVLGFIHPS 279

Query: 302 GGR-LQITAPLPAHMVKTW 319
               ++  APLP +  +  
Sbjct: 280 TNEYMEFEAPLPEYFKEIL 298


>gi|23015589|ref|ZP_00055361.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 327

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 145/330 (43%), Gaps = 38/330 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           VE +E   RLDRW     P ++   ++ ++  G+V +D   +   + R++ GQ   +   
Sbjct: 14  VEPEEAATRLDRWLAARLPELSRTRIKALIEDGRVSLDATTISDASLRVKPGQCFTVE-- 71

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                        +         +  +   ++YED  + V +KPAG+ V    G      
Sbjct: 72  -------------VPPDAPAEPEAQDIALSVVYEDEDLIVIDKPAGMVVHPAPGNPDETL 118

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L    +S       ++P + HR+D++TSG+LV A+T AA + L   F    +++ Y
Sbjct: 119 VNALLAHCGESLAGIGGVKRPGIVHRIDKDTSGLLVAAKTDAAHRGLAAQFAEHSLERAY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CW 242
           W+LVWG P  ++  I   + +  +     + VVK    G   A++ ++V+  FA      
Sbjct: 179 WALVWGTPSPRQGEIEGNIGRNPN-DRKKMAVVKS---GGKPALTRYRVLKSFAGGAVSL 234

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF---------TSPIQNKLYLHAR 293
           +E +  TGRTHQ+RVH    G P++GD  Y                 +     +  LHA 
Sbjct: 235 VECRLATGRTHQIRVHMTAQGHPLIGDPVYGRIRGSRKVVLPPEVKESLTTFPRQALHAY 294

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            +   HP  G  ++  +P+PA +      L
Sbjct: 295 LLGFSHPTKGYEVRFESPIPADINALMRFL 324


>gi|319408111|emb|CBI81764.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           schoenbuchensis R1]
          Length = 340

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 91/353 (25%), Positives = 154/353 (43%), Gaps = 46/353 (13%)

Query: 11  VVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           + +      R+D+W    Y   ++   LQ ++R G ++VD + +K    ++Q  Q + + 
Sbjct: 5   ITDESALGQRIDQWLAKKYHNELSRSRLQTLIREGYLKVDGQLIKEPKTKLQPNQTIEL- 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                         I+    N+    + +   +L+ED  + V NKPAG+ V  G+G    
Sbjct: 64  --------------IIPPLKNVHLEGEAIVLDILFEDDHVIVINKPAGLVVHPGNGNWTG 109

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR---- 177
             ++  +    DS       ++P + HRLD+ TSG++VVA+   A + L+  F       
Sbjct: 110 TLVNALIHHCGDSLSGIGGVKRPGIVHRLDKNTSGVMVVAKNDFAHKSLSAQFSDHGRTC 169

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L+W  P+     I   L +  H       VV+     A +AI+HF +++ + 
Sbjct: 170 ALDRRYHALIWNAPRRNIGTIDVPLGRSPH-NRIKQTVVRHQNVHARHAITHFSLLEKYK 228

Query: 238 QKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------ 285
                      LE +  TGRTHQ+RVH  H+G P+VGD  Y   FK    +         
Sbjct: 229 TCADAEPFASLLECRLETGRTHQIRVHMAHIGHPLVGDTVYGNAFKTKANTLNSTIKNAI 288

Query: 286 ---NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
              N+  LHA  +   HP  G  +  ++P P  M +  +    K D N Y  +
Sbjct: 289 DQFNRQALHAVSLTFEHPAKGEIMSFSSPPPQDMAELINHFK-KLDWNFYPSQ 340


>gi|328952411|ref|YP_004369745.1| pseudouridine synthase, RluA family [Desulfobacca acetoxidans DSM
           11109]
 gi|328452735|gb|AEB08564.1| pseudouridine synthase, RluA family [Desulfobacca acetoxidans DSM
           11109]
          Length = 331

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 97/330 (29%), Positives = 155/330 (46%), Gaps = 34/330 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
             + VE +EE +RLD +     P  +   LQ+ +++G V+V+++  + +  ++ G  V +
Sbjct: 16  TTLDVEAEEEGLRLDHFLVRKMPSFSRARLQRWIKAGLVQVNQEERQPHYHMRKGDRVAV 75

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
            P      H+  E                +   +LYED  +   NKP G++V  G+G   
Sbjct: 76  SPPEVQRWHLAPEP---------------IPLKILYEDEDLLALNKPPGLTVHPGAGQSS 120

Query: 126 AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G    Q+P L HRLD++TSG++VVA+T  A Q L + F+ RR+ K
Sbjct: 121 GTLVNALLHHCPDLGGIGDVQRPGLVHRLDKDTSGVMVVAKTDRAHQALIKQFKNRRVDK 180

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LVWG     +  I   + +         H +    +    A + ++ +  +   F 
Sbjct: 181 RYLALVWGRFSENQGEIEEEIGRHPTQ----RHKMAVTSRRGRPAATSWRRLQEYPGPFS 236

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG--------NFTSPIQNKLYLHAR 293
           WLE++ HTGRTHQ+RVH   +G P+VGD  Y A  +             P+  +  LHA 
Sbjct: 237 WLELKLHTGRTHQIRVHLSSLGHPVVGDKIYGAGDRRLLVLPPELTELRPLVRRQALHAW 296

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            + L HP     L + APLP  + K  D L
Sbjct: 297 KLHLKHPCRDLELDLEAPLPEDLQKILDFL 326


>gi|73541961|ref|YP_296481.1| ribosomal large subunit pseudouridine synthase C [Ralstonia
           eutropha JMP134]
 gi|72119374|gb|AAZ61637.1| ribosomal large subunit pseudouridine synthase C [Ralstonia
           eutropha JMP134]
          Length = 352

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 104/330 (31%), Positives = 160/330 (48%), Gaps = 22/330 (6%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V YV ++   E  R+D +       +   ++ ++LRSG+VRV+K RV    R+Q G V
Sbjct: 19  PQVAYVTIDEGAEGQRIDNFLLKVSKGVPKSHIYRVLRSGEVRVNKGRVDATYRLQIGDV 78

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+           ++ + S             +L+ED+ + V NKPAG++V GGSG
Sbjct: 79  VRIPPM-----------RVAEPSQTTRHPVPAADFPVLFEDAHLLVINKPAGVAVHGGSG 127

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +A+ +   L+       +   L HRLD+ETSGILV+A+ R+A   L E  R   + K Y+
Sbjct: 128 VAFGVIEQLRKARPQ-AKFLELVHRLDRETSGILVLAKKRSALVDLHEQIRGNSMDKRYF 186

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           + V G   N ++ +   L K S   G+    V+++      + + F  ++ F   F  LE
Sbjct: 187 ACVAGEFPNNRQHVKLPLYKYSTPDGERRVRVQED---GLPSHTVFSRVEAFP-GFTLLE 242

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPH 299
            +  TGRTHQ+RVH  H G PI+GD KY               P   +++LHA  +   H
Sbjct: 243 AELKTGRTHQIRVHLAHSGYPIIGDEKYGDFALNKQLARAGARPGIKRMFLHAHRLTFVH 302

Query: 300 PEG-GRLQITAPLPAHMVKTWDSLGFKYDR 328
           P     L + APLP         L  + ++
Sbjct: 303 PGTREPLVVAAPLPDECTGFLQQLRSQSNQ 332


>gi|49475182|ref|YP_033223.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           henselae str. Houston-1]
 gi|49237987|emb|CAF27192.1| Ribosomal large subunit pseudouridine synthase D [Bartonella
           henselae str. Houston-1]
          Length = 334

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 90/345 (26%), Positives = 151/345 (43%), Gaps = 45/345 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           V   + + +    RLD+W    Y + ++   LQ ++R G ++VD + +K    +++S Q+
Sbjct: 2   VTQRITDENALGQRLDQWLAKQYHNVLSRSRLQALIREGYLKVDGQLIKEPKTKLKSNQI 61

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +            E   LD               +L+ED  + V NKPAG+ V  G+G
Sbjct: 62  IELTMPALRDAEPSGEAIALD---------------ILFEDDHVIVINKPAGLVVHPGNG 106

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +     S       ++P + HRLD+ TSG++VVA+   A + L+  F   
Sbjct: 107 NWTGTLVNALIHHCGKSLSGIGGVKRPGIVHRLDKNTSGVMVVAKNDLAHKSLSAQFFDH 166

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                + + Y +L+WG P      I   + +  H       VV      A +A++HF ++
Sbjct: 167 GRTSALDRRYHALIWGSPNRNVWTIDAPVGRSPH-NRTKQAVVYNQCLHARHAVTHFSLL 225

Query: 234 DCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-- 285
           + +            LE +  TGRTHQ+RVH  H+G P+VGD  Y   FK    +     
Sbjct: 226 EQYGTCADKTPFASLLECRLETGRTHQIRVHMAHIGHPLVGDTVYGNAFKTKSNTLNSII 285

Query: 286 -------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                  N+  LHA  +   HP  G+ +  ++PLP  M +    L
Sbjct: 286 KNAIDQFNRQALHAANLTFEHPATGKIMSFSSPLPQDMAELIKHL 330


>gi|163856053|ref|YP_001630351.1| ribosomal large subunit pseudouridine synthase C [Bordetella petrii
           DSM 12804]
 gi|163259781|emb|CAP42082.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           petrii]
          Length = 322

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 96/323 (29%), Positives = 161/323 (49%), Gaps = 20/323 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    V+ V V  + +  R+D +       +   ++ K +R G+VRV+K R++ + R+ +
Sbjct: 15  SSAPAVRLVEVGPEHDGQRIDNFLVRLCKGVPKSHIYKAIRGGEVRVNKGRIQADYRVAA 74

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PP+                +   ++     +  ++YED  + V +KPAG++V G
Sbjct: 75  GDVVRVPPLRL-------------PAPGESRPVPGAEFPVVYEDEALLVVDKPAGVAVHG 121

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+++ +   L++      +   L HRLD+ETSG+L++A+ R+A   L    R  R  K
Sbjct: 122 GSGVSFGVIEQLRAARPQ-ARFLELAHRLDRETSGLLMIAKKRSALLALHAMLREGRGDK 180

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   N ++ I   L K +   G+       + + A+  ++    +      + 
Sbjct: 181 HYLALVEGDWVNDRQHIRLALTKWTTQSGERRVRPDPDGQAAHTIVT----LKQRLGGYS 236

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGNFTSPIQNKLYLHARYMDLPHP 300
            ++ +  TGRTHQ+RVH    G PIVGD KY  +  +  F     N+++LHA  + LPHP
Sbjct: 237 LVDAELRTGRTHQIRVHLAASGFPIVGDDKYGTDETRARFARLGFNRMFLHAHQLTLPHP 296

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                L++TA LPA   K    L
Sbjct: 297 LTQEPLRLTAELPAACRKLLQQL 319


>gi|114570956|ref|YP_757636.1| ribosomal large subunit pseudouridine synthase D [Maricaulis maris
           MCS10]
 gi|114341418|gb|ABI66698.1| ribosomal large subunit pseudouridine synthase D [Maricaulis maris
           MCS10]
          Length = 335

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 84/343 (24%), Positives = 144/343 (41%), Gaps = 40/343 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M+ +   + +    ++   RLDRW       ++   L+ ++ +GQV VD   V   + ++
Sbjct: 1   MTDIAETRTLEATEEDAGQRLDRWLAASVESLSRSRLKALIEAGQVAVDGVAVTDPSAKV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            +G    +                +      T   + +   +L+ED  + V NKPAG+SV
Sbjct: 61  LAGSEYTVG---------------IPEPRADTPTPEPMDLDVLHEDDHLIVINKPAGLSV 105

Query: 120 QGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
              +G      + G L     S       ++P + HRLD+ETSG++VVA++  A + L+ 
Sbjct: 106 HPAAGNWTGTLVHGLLHHCAGSLSGIGGVERPGIVHRLDKETSGVMVVAKSDVAHKGLSI 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F    +++ Y +     P  K   IA  L + S     +      N +   +AI+++  
Sbjct: 166 QFARHTVERAYIAFTRNAPSPKAGRIATQLARSSRDRKKFEVPHDPNSEAGKHAITNYTT 225

Query: 233 IDCFAQ---------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF------- 276
           +  F Q             +E +  TGRTHQ+RVH  H+ CP++GD  Y           
Sbjct: 226 LKRFGQAEGAAIGTGMAAKVECRLETGRTHQIRVHMAHINCPLLGDPVYGQKRGRLLEYD 285

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             + T     +  LHA  +   HP  G  L+  + LP  M + 
Sbjct: 286 DDSGTLRAFRRQALHAAILGFEHPVTGEALRFESELPDDMKRV 328


>gi|212691724|ref|ZP_03299852.1| hypothetical protein BACDOR_01219 [Bacteroides dorei DSM 17855]
 gi|212665729|gb|EEB26301.1| hypothetical protein BACDOR_01219 [Bacteroides dorei DSM 17855]
          Length = 358

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 86/332 (25%), Positives = 147/332 (44%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK   +G +  + K VK + +++   V+ +  
Sbjct: 33  VVVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKSSYKVKPCDVLTVMM 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    +  I+   + L          ++YED+ + V NKPAG+ V  G G  +  
Sbjct: 93  -----DRPRYDNDIIPEDIPLD---------IVYEDNDLMVINKPAGLVVHPGCGNYHGT 138

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+LVVA+T  A  HL   F  +  ++ 
Sbjct: 139 LVNAIAWHLKDNPRYDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRK 198

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI +N +  I   + +           V  +     +A++H++V++        
Sbjct: 199 YNALVWGIVENNEGTIEGNIGRNPK--DRMQMAVLSDPAQGKHAVTHYRVLERLG-YVTL 255

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  N   KG   S  +           +  L
Sbjct: 256 VECVLETGRTHQIRVHMKHIGHTLFNDERYGGNEILKGTHFSKYKQFVNNCFETCPRQAL 315

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G  +  T+PLP  M    D 
Sbjct: 316 HAMTLGFVHPRTGEEMFFTSPLPEDMTNLIDK 347


>gi|332877311|ref|ZP_08445059.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
 gi|332684694|gb|EGJ57543.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
          Length = 362

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 150/332 (45%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +  ++ ++ MR+D++   H  + +   LQ+      + V+ + VK + +++    + I  
Sbjct: 36  LTADSGQKPMRIDKFLMEHLYNTSRNRLQRAAEQEFILVNGRPVKSSYKVKPLDEIVI-- 93

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
               L+    + +I+   + L          ++YED  + V +KPAG+ V  G G     
Sbjct: 94  ---LLDRPKYDNEIIAEDIPLD---------IVYEDEDLMVVDKPAGLVVHPGCGNYTGT 141

Query: 128 HIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++       D+    P      L HR+D++TSG+LVVA+   A  HL + F  +  +++
Sbjct: 142 LVNAIAWHLKDNPDYDPNDPTVGLVHRIDKDTSGLLVVAKNADAKTHLGKQFFNKTTKRL 201

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  + ++  I   + +        + V   + +   +A++H++V++ F      
Sbjct: 202 YNALVWGNFQEEEGRIEGNIARHPK-DRMQMAVFPPDSEIGKHAVTHYRVLENF-NYVTL 259

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYL 290
           +E +  TGRTHQ+R H  H+G P+  D +Y  N     T   +             +  L
Sbjct: 260 VECRLETGRTHQIRAHMKHIGHPLFNDERYGGNEILRGTQFSKYKQFIQNCFAVCPRQAL 319

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HAR +   HP  G  +  T+ LPA M    + 
Sbjct: 320 HARTLGFIHPRSGQEMYFTSELPADMTTLLER 351


>gi|167745608|ref|ZP_02417735.1| hypothetical protein ANACAC_00300 [Anaerostipes caccae DSM 14662]
 gi|167654920|gb|EDR99049.1| hypothetical protein ANACAC_00300 [Anaerostipes caccae DSM 14662]
          Length = 305

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 75/328 (22%), Positives = 136/328 (41%), Gaps = 31/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +   V   E   RLD      +P      LQK+ +   V VD    K N +++ G+
Sbjct: 1   MEQERQFTVSQKETGSRLDVCLAGRFPEFTRSYLQKLCKDSAVLVDDAEKKSNYKVREGE 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +                +     L+   + +   ++YED  I + NKP  + V    
Sbjct: 61  RVILK---------------VPKPTELSIKPEKMDLDIVYEDRDIILINKPKNMVVHPAP 105

Query: 124 GI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++G ++   D         +P + HR+D++T+GIL+V +   A Q L E  + 
Sbjct: 106 GHYEGTLVNGLMEHCRDELSGINGVLRPGIVHRIDKDTTGILIVCKNDMAHQCLAEQLKD 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y ++V    K +   +   + +           +  + +    A++H++V++  
Sbjct: 166 HTITRRYHAIVCHNIKEESGTVDAPIARSRKDRKK----MAIDREAGRRAVTHYRVLERL 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F ++E +  TGRTHQ+RVH   +G P++GD  Y        +        LHA+ + 
Sbjct: 222 KEGFTYIECRLETGRTHQIRVHMASIGHPLLGDTVYGPKK----SKYSLEGQCLHAKVLG 277

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP     ++    LPA+  +    LG
Sbjct: 278 FTHPRTKEYMEFEVGLPAYFEELLKRLG 305


>gi|332686651|ref|YP_004456425.1| ribosomal large subunit pseudouridine synthase D [Melissococcus
           plutonius ATCC 35311]
 gi|332370660|dbj|BAK21616.1| ribosomal large subunit pseudouridine synthase D [Melissococcus
           plutonius ATCC 35311]
          Length = 302

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 85/330 (25%), Positives = 144/330 (43%), Gaps = 35/330 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++ ++ E      R+D+         +   +Q+ L+   VRV+ K VK N ++Q   
Sbjct: 1   MENIKLIITEKTIG--RIDKVLSEELIAYSRSQIQQWLKDSLVRVNNKVVKANYKVQPAD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V I      +  +  E   LD               ++YED  + V NKP G+ V   +
Sbjct: 59  EVIIQLPKPKMMVVSPENIPLD---------------IVYEDQDVVVINKPQGMVVHPSA 103

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      +   L    D        +P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 104 GHFKGTMVHALLYHIKDLSSINDVIRPGIVHRIDKDTSGLLIVAKNNQAHEALAKQLKDK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I + Y +LV G   +++  I   + + S        ++    K    A++HFKV++ F 
Sbjct: 164 TILRKYIALVHGEVPHEQGTIDAPIGR-SKTNRKMQAII----KDGRSAVTHFKVLEKFT 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +      +LHA+ +  
Sbjct: 219 -GYTLIELQLETGRTHQIRVHMKYIGHPVAGDPVYGPK-----KTLKGEGQFLHAKVLGF 272

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLGFKY 326
            HP    R+   APLP     T   L   +
Sbjct: 273 THPTTHERMVFEAPLPEIFQNTLTKLRINH 302


>gi|308388890|gb|ADO31210.1| putative ribosomal large subunit pseudouridine synthase D
           [Neisseria meningitidis alpha710]
 gi|325136074|gb|EGC58684.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M0579]
 gi|325139918|gb|EGC62448.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis CU385]
          Length = 374

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 138/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LTHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|313893115|ref|ZP_07826692.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313442468|gb|EFR60883.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 307

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/321 (25%), Positives = 142/321 (44%), Gaps = 32/321 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   +V  ++E MRLD +        +   +Q +++ G V V  K  K N R+    V++
Sbjct: 1   MNEYIVSAEQEGMRLDVFLTEQMEG-SRSYIQSLIKGGHVIVGGKVGKANLRLTPNMVIQ 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSG 124
           +                +    ++    + +   +LYED  I + NK  G+ V    G+ 
Sbjct: 60  VE---------------IPEPESVEVKPEDIPLDVLYEDHDIIIVNKARGMVVHPAVGNY 104

Query: 125 IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L    D  G     +P + HRLD++TSG+++ A+  AA   L E  +    +
Sbjct: 105 SGTLVNALLFHCKDLSGINGEIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKEHSAK 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + YW+LV G    +K  I   + +        + VV +N K    A++HF+V++ +  + 
Sbjct: 165 RTYWALVQGNIVEEKGTIKAPIGRHPK-DRMKMAVVFENSKD---AVTHFRVLERYGHQ- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E    TGRTHQ+RVH  H+G P+V D  Y                 LH+R +D+ HP
Sbjct: 220 TLVECNLETGRTHQIRVHFAHIGHPVVNDPFYGYRR----MDFPIEGQALHSRSLDVKHP 275

Query: 301 EGGR-LQITAPLPAHMVKTWD 320
             G  +   AP+PA      +
Sbjct: 276 ITGEDMHFEAPVPADFEACLE 296


>gi|265755351|ref|ZP_06090121.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_33FAA]
 gi|263234493|gb|EEZ20083.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_33FAA]
          Length = 358

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 86/332 (25%), Positives = 147/332 (44%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK   +G +  + K VK + +++   V+ +  
Sbjct: 33  VVVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKSSYKVKPCDVLTVMM 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    +  I+   + L          ++YED+ + V NKPAG+ V  G G  +  
Sbjct: 93  -----DRPRYDNDIIPEDIPLD---------IVYEDNDLMVINKPAGLVVHPGCGNYHGT 138

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+LVVA+T  A  HL   F  +  ++ 
Sbjct: 139 LVNAIAWHLKDNPRYDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRK 198

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI +N +  I   + +           V  +     +A++H++V++        
Sbjct: 199 YNALVWGIVENNEGTIEGNIGRNPK--DRMQMAVLSDPAQGKHAVTHYRVLERLG-YVTL 255

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  N   KG   S  +           +  L
Sbjct: 256 VECVLETGRTHQIRVHMKHIGHTLFNDERYGGNEILKGTHFSKYKQFVNNCFETCPRQAL 315

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G  +  T+PLP  M    D 
Sbjct: 316 HAMTLGFVHPRTGEEMFFTSPLPEDMTNLIDK 347


>gi|154483515|ref|ZP_02025963.1| hypothetical protein EUBVEN_01219 [Eubacterium ventriosum ATCC
           27560]
 gi|149735425|gb|EDM51311.1| hypothetical protein EUBVEN_01219 [Eubacterium ventriosum ATCC
           27560]
          Length = 301

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 77/323 (23%), Positives = 145/323 (44%), Gaps = 36/323 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +V+ +  ++R+DR+     P ++   +QK+L+  ++ ++ K VK N ++Q    + I  
Sbjct: 5   FIVDEELFDIRIDRYLSELLPDVSRSFIQKLLKDNEILLNDKPVKANYKVQPSDKININI 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
                 +I+ E   LD               ++YED    + NKP  + V          
Sbjct: 65  PKPVEANIVAENIPLD---------------IIYEDDDFLIVNKPKDMVVHPAPGHYTGT 109

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             +G+ YH    L +   +   +P + HR+D++T+G L++ +   +   + E  ++  I 
Sbjct: 110 LVNGLMYHCKNHLSNI--NGVLRPGIVHRIDKDTTGALIICKNDYSHNFIAEQLKVHSIT 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y  +V G+ K++   I   + +      +    +  N K    A++H+KV+  F  K+
Sbjct: 168 RKYVGIVQGVVKDESGTINAPIGRHPVNRKE----MAINHKNGKEAVTHYKVLKRF-DKY 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++E Q  TGRTHQ+RVH   +  P++GD  Y      N          LHA+ +   HP
Sbjct: 223 TFMEFQLETGRTHQIRVHMASIHHPLLGDTVYNH----NKCPFKLEGQCLHAKTIGFIHP 278

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                ++  AP+P +M      L
Sbjct: 279 TTKEYVEFEAPIPEYMEHLLKIL 301


>gi|299067008|emb|CBJ38203.1| Ribosomal large subunit pseudouridine synthase C [Ralstonia
           solanacearum CMR15]
          Length = 346

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 100/322 (31%), Positives = 164/322 (50%), Gaps = 19/322 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D +  R+D +       +   ++ +ILRSG+VRV+K R+    R+  G +VR
Sbjct: 25  VAYVEIGEDAQGQRIDNFLMRLAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLNLGDLVR 84

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A                  +     +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 85  IPPLRVAQQS--------PGQAEAARAVPAAEFTILHEDTHLLVIDKPAGVAVHGGSGVA 136

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++ 
Sbjct: 137 FGVIEQLRR-SRPEAKFLELVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFAA 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  ++++ I + L K +   G+    V+ +      + + F  +  F   +  LE +
Sbjct: 196 VKGVWPHQRQHIKSPLFKYTTPEGERRVRVQAD---GQPSHTVFNRVGVFG-PYTLLEAE 251

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H G PI+GD KY              SP   +++LHA  + L HP+
Sbjct: 252 LKTGRTHQIRVHLAHAGFPILGDDKYGDFALNKALSRANASPRLARMFLHAHTLRLTHPQ 311

Query: 302 GGRL-QITAPLPAHMVKTWDSL 322
            G +    APLPA      ++L
Sbjct: 312 SGEIVTFKAPLPAECAAFLNAL 333


>gi|237708677|ref|ZP_04539158.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           9_1_42FAA]
 gi|229457377|gb|EEO63098.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           9_1_42FAA]
          Length = 357

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 84/332 (25%), Positives = 145/332 (43%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK   +G +  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKSSYKVKPCDVLTVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                ++ I                + +   ++YED+ + V NKPAG+ V  G G  +  
Sbjct: 92  DRPRYDNAI--------------IPEDIPLDIVYEDNDLMVINKPAGLVVHPGCGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+LVVA+T  A  HL   F  +  ++ 
Sbjct: 138 LVNAIAWHLKDNPRYDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRK 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI +N +  I   + +           V  +     +A++H++V++        
Sbjct: 198 YNALVWGIVENNEGTIEGNIGRNPK--DRMQMAVLSDPAQGKHAVTHYRVLERLG-YVTL 254

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  N   KG   S  +           +  L
Sbjct: 255 VECVLETGRTHQIRVHMKHIGHTLFNDERYGGNEILKGTHFSKYKQFVNNCFETCPRQAL 314

Query: 291 HARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           HA  +   HP     +  T+PLP  M    D 
Sbjct: 315 HAMTLGFVHPRTSEEMFFTSPLPEDMTNLIDK 346


>gi|28211276|ref|NP_782220.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           tetani E88]
 gi|28203716|gb|AAO36157.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           tetani E88]
          Length = 307

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 82/324 (25%), Positives = 146/324 (45%), Gaps = 32/324 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++  +V+ + EN RLD +   +    +   ++K+     + V+ +  K N +++ G +V
Sbjct: 4   KIEKFLVKEEFENERLDLFIVENLKDKSRSFIKKLSDDKGIMVNDEIKKVNYKVKCGDIV 63

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           ++               +L     +    + +   +LYED  I V NKP G+ V  G G 
Sbjct: 64  KV---------------LLPKEEGIYLEKENMDLNILYEDEDIIVINKPQGMVVHPGVGN 108

Query: 126 A--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++G L            ++P + HR+D++TSGILV+A+T  A +HL    +   +
Sbjct: 109 TKGTLVNGLLAHCKSLSNINGEERPGIVHRIDKDTSGILVIAKTNRAHEHLANQLKDHSM 168

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            ++Y +L  G+ K     I   L +      D +     +E     A++H+KVI+ +   
Sbjct: 169 LRVYMALTEGVIKEDMGTIDKDLGRNP---SDRIKFAVVDE--GKRAVTHYKVINRYNNN 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E +  TGRTHQ+RVH  ++G PIVGD  Y    +            LHA+ +   H
Sbjct: 224 -SLIECRLETGRTHQIRVHMSYIGHPIVGDPTYGYKRQ----KFKLKGQMLHAKKLGFIH 278

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G  ++  + +P    K  + L
Sbjct: 279 PTNGEYMEFDSEIPEEFKKILEIL 302


>gi|323144879|ref|ZP_08079445.1| rRNA pseudouridylate synthase C [Succinatimonas hippei YIT 12066]
 gi|322415346|gb|EFY06114.1| rRNA pseudouridylate synthase C [Succinatimonas hippei YIT 12066]
          Length = 335

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 165/319 (51%), Gaps = 13/319 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V Y  V  D+   RLD +       +    + +ILR G+VRV+KKR + + ++ +G  +
Sbjct: 26  KVSYKTVTADDAGQRLDNYLLRILKGVPRSMIYRILRRGEVRVNKKRAEPSYKLCAGDEI 85

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  +         ++  S NL    + LK  + +E+  + V +KPAGI+  GGSGI
Sbjct: 86  RVPPVRVSTA------PVIIPSANLHSVQN-LKDRICFENEALIVVDKPAGIAAHGGSGI 138

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + +   L++          L HRLD+ETSG L+VA+ R+A ++L E FR R I+K Y +
Sbjct: 139 EFGLIEALRALRPEFSF-LELAHRLDRETSGCLIVAKRRSALRNLHEQFRSRVIKKRYLT 197

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G    + + +   L++     G+ +  V+ N K    + + F +++        +  
Sbjct: 198 LVPGKWDRRLKLVEAPLVRNELRSGERM--VEVNFKSGAPSATGFDIVEELND-ATLMAA 254

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            PHTGRTHQ+RVH  ++  P+ GD KY +  F     +    +++LHA  +    P  G+
Sbjct: 255 MPHTGRTHQIRVHCAYVKHPVGGDVKYGSEEFNDRLKALGLKRMFLHAAKITFTDPVSGK 314

Query: 305 -LQITAPLPAHMVKTWDSL 322
            L++ APLP  + K  + L
Sbjct: 315 LLKVEAPLPDELRKIVEIL 333


>gi|323466424|gb|ADX70111.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 310

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/329 (25%), Positives = 147/329 (44%), Gaps = 35/329 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  M     + VEN+    RLD++     P ++   ++++++  ++ V+ K  K + +IQ
Sbjct: 5   MIKMPKKYELQVENEYG--RLDKFVSEQIPDLSRTRVKELVKEKEILVNHKVEKVSYKIQ 62

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  + I         ++ E   LD               ++YED  + V NKP G+ V 
Sbjct: 63  AGDKIEINVPAVKPLDVVPENIPLD---------------IVYEDEDVIVVNKPQGMVVH 107

Query: 121 GGSGIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G   H   +  L    D     +G +P + HR+D++TSG+L++A+   A + L +  
Sbjct: 108 PAPGHPDHTLVNALLYHTQDLAQSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQL 167

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             +  ++IYW++V G    +   I   + +  +       V     +    A++HFKV+ 
Sbjct: 168 AHKTNKRIYWAIVHGNFGEENGVIDAPIGRNPYDRKKMAVV-----ENGKKAVTHFKVL- 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              + +  +E Q  TGRTHQ+RVH  ++G  + GD  Y         +   N  +LHA+ 
Sbjct: 222 RQFKGYSLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPR-----KTLKGNGQFLHAKV 276

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP  G+ L+ T   P     T   L
Sbjct: 277 LGFKHPRTGKWLEFTVEPPKIFQDTLAQL 305


>gi|315126331|ref|YP_004068334.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
 gi|315014845|gb|ADT68183.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
          Length = 319

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 102/327 (31%), Positives = 166/327 (50%), Gaps = 16/327 (4%)

Query: 1   MSLMT--YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR 58
           MS  T   V +V +  D    R+D +   H   +    + KILR G+VRV+KKR+K   +
Sbjct: 1   MSEKTGLQVTFVTINEDHLGQRIDNFLITHLKGVPKSAVYKILRKGEVRVNKKRIKPVYK 60

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +Q   V+RIPP+      + + ++ + S ++       L+  +L+ED  + V NKP+G++
Sbjct: 61  LQLDDVIRIPPI-----RVSEREEFVPSKLDKVTR---LEDYILFEDKYLMVINKPSGMA 112

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           V GGSG++Y +   L+     + +   L HRLD++TSG L++A+ R+    L E  R + 
Sbjct: 113 VHGGSGLSYGLIEALRVLRPEE-RSLELVHRLDRDTSGCLLIAKRRSVLTALHEQLREKT 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K YW+LV G   +K + +   L K +   G+ V  V   E     + + FKV++ F  
Sbjct: 172 MEKNYWALVEGQWDSKTKNVTEGLRKNTLKSGERVVRVDNTE--GKPSHTRFKVLERFND 229

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDL 297
               ++  P TGRTHQ+RVH    G  I  D KY    F  +      N+L+LHA  +  
Sbjct: 230 -CSLVQASPVTGRTHQIRVHTQCQGHAIACDDKYGDQGFDESMRKRGLNRLFLHAHDLSF 288

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLG 323
            HP+    +++ APL   +      L 
Sbjct: 289 YHPKNETTMRVEAPLDKALSSCLVKLR 315


>gi|299142141|ref|ZP_07035274.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           C735]
 gi|298576230|gb|EFI48103.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           C735]
          Length = 360

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 142/332 (42%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++     P+ +   +Q+   SG + V+ K VK N +++ G V+ +  
Sbjct: 30  VEVDMGQTPVRIDKFLAEKNPYQSRNRIQQAADSGFIHVNDKPVKSNYKVRPGDVITLML 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                +  I               ++ +   ++YED  + V NK AG+ V  G+G     
Sbjct: 90  DRPKHDTSI--------------VAEDIPLDIVYEDDALMVINKQAGMVVHPGAGNFTGT 135

Query: 128 HIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            I+            D+   +  L HR+D++TSG+LVVA+T  A   L + F  +   + 
Sbjct: 136 LINAVAWHLKDLESFDANDPEVGLVHRIDKDTSGLLVVAKTADAKSALGKQFFNKTTHRS 195

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG   + +  I   + +        + V   +      A++H++VI+ F      
Sbjct: 196 YNALVWGNLIDDEGTIEGNIARDPK-NRLRMKVFSPDSGIGKNAVTHYRVIERFG-YTTL 253

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSP----------IQNKLYL 290
           +E    TGRTHQ+R H  H+G P+  D  Y      +G  +S           +  +  L
Sbjct: 254 VECILETGRTHQIRAHMKHIGHPLFADATYGGEQVLRGQRSSTYKAFIQNCFKLCPRQAL 313

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA+ +   HP  GR +   +  P    +    
Sbjct: 314 HAKTLGFVHPLTGRQMDFDSEWPDDFSQLIAK 345


>gi|124006632|ref|ZP_01691464.1| pseudouridine synthase, RluD [Microscilla marina ATCC 23134]
 gi|123987787|gb|EAY27478.1| pseudouridine synthase, RluD [Microscilla marina ATCC 23134]
          Length = 360

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 152/330 (46%), Gaps = 35/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +E +R+D++  +  P+I     Q  +R G V+V+ + VK N +++   ++ I  
Sbjct: 40  IVVDKGQEPVRIDKFLMDRVPNITRNKTQNAIREGFVKVNDQEVKPNYKVRPEDIIII-- 97

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----SG 124
              +L    +E +++   + +          ++YED  + V +K AG+ V          
Sbjct: 98  ---SLPEPPRESEVVPEDIPIN---------IVYEDDDLLVVHKEAGMVVHPAYNNWTGT 145

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   +    K+  +++  +P L HR+D++TSG+LVVA++  A QHL + F    I++ Y+
Sbjct: 146 LVNALAYHFKNLPENRDGRPGLVHRIDKDTSGLLVVAKSEHALQHLAKQFFDHTIERTYY 205

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG PK +   I   L +        V           +A++H+KV+    +    ++
Sbjct: 206 ALVWGEPKQEAGTIDVNLGRSLK--DRRVTAAFPEGDFGRHAVTHYKVLKNL-RYVSLVQ 262

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHA 292
               TGRTHQ+R H  H+G P+  D  Y  +     T              +  +  LHA
Sbjct: 263 CNLETGRTHQIRAHMKHLGHPLFNDATYGGDKILKGTVFSKYRAFVENCFKVMPRQALHA 322

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP   + +Q  + LP    K  + 
Sbjct: 323 KSLGFVHPTTQKFIQFDSELPKDFQKAMEK 352


>gi|319943487|ref|ZP_08017769.1| ribosomal large subunit pseudouridine synthase C [Lautropia
           mirabilis ATCC 51599]
 gi|319743302|gb|EFV95707.1| ribosomal large subunit pseudouridine synthase C [Lautropia
           mirabilis ATCC 51599]
          Length = 343

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 94/338 (27%), Positives = 158/338 (46%), Gaps = 20/338 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+  T +Q++ V+   E  RLD +       +    + +++R G+VRVD +RVK   R+ 
Sbjct: 10  MAQTTPIQWLTVDEGHEGQRLDNYLLAMLRGVPKTRIYRMIRKGEVRVDGRRVKAEQRVA 69

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ VR+PP+ +     ++               D     +L+ED  + V +K  G++V 
Sbjct: 70  AGERVRVPPLASVPQTALR-----PGPARGGPKLDDRHIRILFEDEHLLVVDKSEGLAVH 124

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSGI+  +   L++     GQ   L HRLD++TSG+LV+A+ R+A   L   F    ++
Sbjct: 125 GGSGISAGLIERLRA-TRPPGQFLELAHRLDRDTSGLLVIAKRRSALLALHRMFAAGEVK 183

Query: 181 KIYWSLVWGIP-KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           K Y ++V G   + +   +   LL+     G+    V         + + F+ +      
Sbjct: 184 KRYLAIVKGHWGRPRPVLVQFPLLRYLTPAGERRVRVDVQ---GQPSATRFRRLQALDFG 240

Query: 240 FC--------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYL 290
                      LE +  TGRTHQ+RVH  H G PI+GD KY              N+++L
Sbjct: 241 GTPGLPPHGALLECELLTGRTHQIRVHLAHGGHPILGDEKYGDFTLNKVLDDMGANRMFL 300

Query: 291 HARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYD 327
           HA ++++ HP+   +  + AP+PA         G   D
Sbjct: 301 HAFHLEMKHPKKEEMLVLDAPMPAAFEALLARFGVTAD 338


>gi|83592447|ref|YP_426199.1| ribosomal large subunit pseudouridine synthase D [Rhodospirillum
           rubrum ATCC 11170]
 gi|83575361|gb|ABC21912.1| ribosomal large subunit pseudouridine synthase D [Rhodospirillum
           rubrum ATCC 11170]
          Length = 343

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 81/323 (25%), Positives = 141/323 (43%), Gaps = 35/323 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V+ +    RLD+W     P ++   LQ+++   +V V+ + + + + R++ GQ VR+   
Sbjct: 29  VDAEAAGQRLDKWLATVIPTLSRARLQQLIGEKRVSVNGQTIGEGSRRVKPGQTVRVE-- 86

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                            +  T   + +   ++YED  + V +K AG+ V  G G   H  
Sbjct: 87  -------------EPPPIAATPQPEAIALTVVYEDDDLIVIDKAAGMVVHPGPGNPDHTL 133

Query: 130 -DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            +  L     S       ++P + HRLD++TSG+++ A+T  A   L E F    + + Y
Sbjct: 134 VNALLAHCGPSLSGIGGERRPGIVHRLDKDTSGLMIAAKTDLAHHGLAEQFACHSLTREY 193

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             LVWG P+     I   L +          V     +G   A++H++V+         +
Sbjct: 194 LCLVWGRPRPAAGSIDAPLGRHPTQRKKMAVV----SRGGKRALTHYRVVGDVEGIASIV 249

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQN--KLYLHARYMD 296
           +    TGRTHQ+RVH  H+G P++GD  Y          G+ +  I    +  LH+ ++ 
Sbjct: 250 KCTLSTGRTHQVRVHMAHIGHPLLGDAVYGHRNIPKKLPGDLSERIARLTRQALHSFHLG 309

Query: 297 LPHPEGGR-LQITAPLPAHMVKT 318
             HP  G  L+  + LP  +   
Sbjct: 310 FLHPRTGESLEFLSELPLDISAV 332


>gi|315038468|ref|YP_004032036.1| pseudouridine synthase [Lactobacillus amylovorus GRL 1112]
 gi|325956884|ref|YP_004292296.1| pseudouridine synthase [Lactobacillus acidophilus 30SC]
 gi|312276601|gb|ADQ59241.1| pseudouridine synthase [Lactobacillus amylovorus GRL 1112]
 gi|325333449|gb|ADZ07357.1| pseudouridine synthase [Lactobacillus acidophilus 30SC]
 gi|327183663|gb|AEA32110.1| pseudouridine synthase [Lactobacillus amylovorus GRL 1118]
          Length = 302

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 152/326 (46%), Gaps = 35/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     + V  DE   RLD++     P ++   ++++++   + V++K+ K + ++Q+G 
Sbjct: 1   MPKKYLLEV-KDEHG-RLDKFVSEQIPDLSRTRVKELIQDDNILVNQKKEKVSYKVQAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         ++ E   LD               ++YED  + V NKP G+ V    
Sbjct: 59  QIEVNVPAVKPLDVVPEDIPLD---------------IVYEDDDVIVVNKPQGMVVHPAP 103

Query: 124 GIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G + H   +  L    D     +G +P + HR+D++TSG+L++A+   A + L +    +
Sbjct: 104 GHSDHTLVNALLYHTKDLAKSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++IYW++V G    +   I   + +  +     + VV++       AI+HFKV+  F 
Sbjct: 164 TNKRIYWAIVHGNFSEENGTIDAPIGRNPY-DRKKMAVVER----GKKAITHFKVLKQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G  + GD  Y         +   N  +LHA+ +  
Sbjct: 218 KGYSLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPR-----KTLKGNGQFLHAKVLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G+ ++ +   P    +T   L
Sbjct: 273 KHPRTGKWMEFSVEPPQIFQETLAQL 298


>gi|207724162|ref|YP_002254560.1| ribosomal large subunit pseudouridine synthase d protein [Ralstonia
           solanacearum MolK2]
 gi|206589372|emb|CAQ36334.1| ribosomal large subunit pseudouridine synthase d protein [Ralstonia
           solanacearum MolK2]
          Length = 370

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 89/335 (26%), Positives = 144/335 (42%), Gaps = 32/335 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V +       RLD+      P  +   LQ+ + +G VRV    V+    +  G  + + P
Sbjct: 53  VQIPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVRPRAAVCGGDRIEVVP 112

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
              A      E   +   ++L          ++YED  + V NKPAG+ V   +G     
Sbjct: 113 QRAAD-----ENAFVAEPIDLD---------VVYEDDTLLVINKPAGLVVHPAAGNWSGT 158

Query: 128 HIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  +  + G  +  + HRLD+ETSG++VVART  A   L    + R +++ Y +L
Sbjct: 159 VLNGLLHRYPQAAGLPRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLAL 218

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWL 243
           VWG    +   I   + +      D   +          A +HFK +D           +
Sbjct: 219 VWGE-TPEAGTIDAPIGRDP---RDRTRMAIIETASGKPARTHFKTLDVIDLGRAQVSLV 274

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLHARYMD 296
           + Q  TGRTHQ+RVH    G P++GD  Y  NF+      I+        +  LHA  + 
Sbjct: 275 QCQLETGRTHQIRVHFESEGHPLLGDPVYTRNFRRGQPQTIKAPLPIPFARQALHAVRLG 334

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           + HP  G+ +   A +P  + +  D+L    D +L
Sbjct: 335 IVHPASGQSMHWHAGVPDDLAELMDALEMDSDVDL 369


>gi|27467790|ref|NP_764427.1| hypothetical protein SE0872 [Staphylococcus epidermidis ATCC 12228]
 gi|251810627|ref|ZP_04825100.1| pseudouridylate synthase RluD [Staphylococcus epidermidis
           BCM-HMP0060]
 gi|282876372|ref|ZP_06285239.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|293366838|ref|ZP_06613514.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|27315334|gb|AAO04469.1|AE016746_259 conserved hypothetical protein [Staphylococcus epidermidis ATCC
           12228]
 gi|251805787|gb|EES58444.1| pseudouridylate synthase RluD [Staphylococcus epidermidis
           BCM-HMP0060]
 gi|281295397|gb|EFA87924.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|291319139|gb|EFE59509.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|329729961|gb|EGG66352.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU144]
 gi|329736346|gb|EGG72618.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU028]
 gi|329736639|gb|EGG72905.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU045]
          Length = 305

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 80/324 (24%), Positives = 147/324 (45%), Gaps = 33/324 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    + ++E  +   R+D+   +     +   LQ  ++ G V+V+ K +K N +++   
Sbjct: 1   MENYNFNIIEQSQVGQRIDKLVSDLNKDWSRSQLQDWIKEGLVKVNGKVIKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           ++ E++++++ +      + L   + YED  + V  KP G+ V    
Sbjct: 61  KI-----------VVTEKEVVEADIK----PENLNLDIYYEDEDVAVVYKPKGMVVHPSP 105

Query: 124 GI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A +HL E    +
Sbjct: 106 GHYSGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRHLVEQLMSK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 TVKRKYTALVHGNIPHDYGTIDAPIGRN-KNDRQSMAVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +      +   LHA  +  
Sbjct: 220 KDYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPKKTLD-----IDGQALHAGIIGF 274

Query: 298 PHPEG-GRLQITAPLPAHMVKTWD 320
            HP     ++  A LP    K  D
Sbjct: 275 EHPVTHEYIEKHATLPNDFEKLLD 298


>gi|17545760|ref|NP_519162.1| ribosomal large subunit pseudouridine synthase C protein [Ralstonia
           solanacearum GMI1000]
 gi|17428054|emb|CAD14743.1| probable ribosomal large subunit pseudouridine synthase c protein
           [Ralstonia solanacearum GMI1000]
          Length = 331

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 100/322 (31%), Positives = 162/322 (50%), Gaps = 19/322 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D +  R+D +       +   ++ +ILRSG+VRV+K R+    R+  G +VR
Sbjct: 10  VAYVEIGEDAQGQRIDNFLMRLAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLNLGDLVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A                  +     +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 70  IPPLRIAQQS--------PGQAEAARAVPAAEFTILHEDTHLLVIDKPAGVAVHGGSGVA 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++ 
Sbjct: 122 FGVIEQLRR-SRPEAKFLELVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFAA 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  ++++ I   L K S   G+    V+ +      + + F  +  F   +  LE +
Sbjct: 181 VKGVWPHQRQHIKAPLFKYSTPEGERRVRVQAD---GQPSHTVFNRVGVFG-PYTLLEAE 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H G PI+GD KY              SP   +++LHA  + L HP+
Sbjct: 237 LKTGRTHQIRVHLAHAGFPILGDDKYGDFALNKALSRANASPRLARMFLHAHTLRLTHPQ 296

Query: 302 GGRL-QITAPLPAHMVKTWDSL 322
            G +    APLPA      ++ 
Sbjct: 297 SGEIVTFKAPLPAECAAFLNAF 318


>gi|229592115|ref|YP_002874234.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens SBW25]
 gi|229363981|emb|CAY51520.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens SBW25]
          Length = 319

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 99/317 (31%), Positives = 169/317 (53%), Gaps = 13/317 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLLEVSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP       + +  + +  +  L +    L++ +++ED+K+ V NKP GI+V GGSG+ 
Sbjct: 71  VPP-----VRVPERDEPVPLAQGLLQR---LEASIVFEDNKLIVINKPCGIAVHGGSGLN 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y +L
Sbjct: 123 FGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHTALRGDGVDKRYMAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   L K +   G+ +  V   ++    A++ FKV+  F      +E +
Sbjct: 182 VRGNWASSIKSVRAPLQKSNLRSGERMVEV---DEEGKEALTLFKVLRRFGDFATMVEAK 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           P TGRTHQ+RVH LH G  I GD KY    F          +L+LHA  + +P P+GG L
Sbjct: 239 PVTGRTHQIRVHTLHAGHCIAGDTKYGDEGFSKEIRDLGGKRLFLHAYMLTVPLPDGGEL 298

Query: 306 QITAPLPAHMVKTWDSL 322
           ++ AP+     KT + L
Sbjct: 299 KLQAPVDEMWAKTVERL 315


>gi|311695112|gb|ADP97985.1| pseudouridine synthase, RluA family [marine bacterium HP15]
          Length = 352

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 98/318 (30%), Positives = 171/318 (53%), Gaps = 15/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+V V+ D E  R+D +       +    + +++R G+VRV+K RVK ++R+++G  VR
Sbjct: 39  VQWVTVDEDNEGQRVDNFLLAQLRGVPKSIIYRVIRKGEVRVNKGRVKPDSRVRTGDQVR 98

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        I  ++  D     ++    ++S +++E+ ++ V NKP+GI+V GGSG++
Sbjct: 99  IPP--------ITRKEKPDQVAPGSRVQGVMESAVVFENEQMLVVNKPSGIAVHGGSGLS 150

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+S   +  +   L HRLD++TSG+++VA+ R+A ++L +  R +RI+K Y +L
Sbjct: 151 FGLIEVLRSARPT-AKFLELVHRLDRDTSGLIMVAKKRSALRYLQDELRQKRIRKHYHAL 209

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G      + +   LL+     G+    V   +     +++ F+ ++ +A  +  +E  
Sbjct: 210 VAGDWPASVDRVDVPLLRYEMPNGERRVKV---DAAGKASLTTFRCLEHYA-GYSLVEAS 265

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH+   G PI GD KY  +     F S    +L LHAR ++   P  G  
Sbjct: 266 PITGRTHQIRVHSAWAGHPIAGDDKYMDDVSLKAFRSIGGQRLMLHARALEFTLPVSGEA 325

Query: 305 LQITAPLPAHMVKTWDSL 322
           +++ AP           L
Sbjct: 326 MRLEAPYDDAFNDVLRKL 343


>gi|295706351|ref|YP_003599426.1| pseudouridine synthase [Bacillus megaterium DSM 319]
 gi|294804010|gb|ADF41076.1| pseudouridine synthase [Bacillus megaterium DSM 319]
          Length = 304

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 141/324 (43%), Gaps = 33/324 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++  V+  ++   R+D+         +   +Q+ ++ G  +V+ K VK N + ++G 
Sbjct: 1   MNVIET-VINEEQAGERIDKVLSTVNAEWSRSQVQQWIKEGHAKVNDKTVKGNYKCKTGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I                +     L   ++ +   + YED  + V NKP G+ V    
Sbjct: 60  AIIIE---------------VPELEELDVVAEEMDLDIYYEDQDVLVVNKPRGMVVHPAP 104

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHHSGTLVNGLMAHCKDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDLAHESLVSQLVAK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V GI  +    I   + +        + V  +N +    A++HF V+  F 
Sbjct: 165 TVTRRYKAIVHGIIAHDHGTIDAPIGRD-KQDRQSMTVTDENSRD---AVTHFTVLQRF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY         +   +   LHA  +  
Sbjct: 220 KDFSLVECKLETGRTHQIRVHMKYIGFPLAGDPKYGPK-----KTLPIDGQALHAGVLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWD 320
            HP     ++  AP P    +  +
Sbjct: 275 IHPRTNEYMEFEAPAPKEFNEMLE 298


>gi|225018395|ref|ZP_03707587.1| hypothetical protein CLOSTMETH_02342 [Clostridium methylpentosum
           DSM 5476]
 gi|224948813|gb|EEG30022.1| hypothetical protein CLOSTMETH_02342 [Clostridium methylpentosum
           DSM 5476]
          Length = 308

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 141/328 (42%), Gaps = 32/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     V+VE ++   RLD++     P      LQK++   QVR + + +   +++++G+
Sbjct: 1   MPKDFCVLVEPEQAGERLDKFLPTVLPGYTRSALQKLIEGEQVRCEGEPLNKKHKLRAGE 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         ++ E+  LD               +LYEDS + V NKP  + V   +
Sbjct: 61  TISVTIPDPEPLDVLPEEIPLD---------------ILYEDSDLLVVNKPKHMVVHPAA 105

Query: 124 G--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  L     S        +P + HR+D++TSG+L+VA+   A   L    + 
Sbjct: 106 GNYTGTLVNALLHHCRGSLSGINGVIRPGIVHRIDKDTSGLLIVAKNDQAHVGLAAQIKE 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
               + Y ++V+G        +   + +           +    K +  A++H++V+  +
Sbjct: 166 HSFDRTYEAVVYGKFVESTGTVDKPIGRSEKDRKK----MCVTTKNSKPAVTHYEVLGEY 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q F  L ++  TGRTHQ+RVH   +G P+ GD  Y                 LHAR + 
Sbjct: 222 GQ-FTHLRLRLETGRTHQIRVHMASIGHPVAGDPVYGPKK----CITELEGQCLHARSIG 276

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSLG 323
             HP  G RL   + LP++ V   D + 
Sbjct: 277 FVHPGTGERLSFESELPSYFVSFLDKIR 304


>gi|160892655|ref|ZP_02073445.1| hypothetical protein CLOL250_00185 [Clostridium sp. L2-50]
 gi|156865696|gb|EDO59127.1| hypothetical protein CLOL250_00185 [Clostridium sp. L2-50]
          Length = 305

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 78/323 (24%), Positives = 141/323 (43%), Gaps = 31/323 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +  + +  + R+D+   +++ + +   L+K+L  G + V+ K+ K + +I SG  + I  
Sbjct: 6   IEADENWTDKRVDKGLADYFDNYSRSFLKKLLDDGNILVNDKKAKPSLKIASGDRIDITI 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
              A   I  E   LD               ++YED  I + NKP G+ V    G     
Sbjct: 66  PSIASVEIEPENIPLD---------------IVYEDEDIIIVNKPKGMVVHPAPGHYSGT 110

Query: 128 HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++G +  + DS        +P + HR+D +T+G+LVV +  AA   L+E   +  I + 
Sbjct: 111 LVNGLMYHFKDSLSGINGELRPGIVHRIDMDTTGLLVVCKNDAAHNFLSEQLAVHSITRK 170

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y+++ +      +  +   + +           +  N K    A++H+KV+      FC 
Sbjct: 171 YYAICFNYFTEDEGIVDLPIGRHPTDRKK----MAVNYKNGRNAVTHYKVLKKLKNNFCL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E Q  TGRTHQ+RVH  ++  P++GD  Y    +            LHA  +   HP  
Sbjct: 227 IECQLETGRTHQIRVHMSYIKHPLLGDAIYGPKNQPYH----LQGQTLHAGVLGFIHPST 282

Query: 303 GR-LQITAPLPAHMVKTWDSLGF 324
              ++ ++ LP +  K    L  
Sbjct: 283 KEYVEFSSELPEYFQKLLKQLEL 305


>gi|240013591|ref|ZP_04720504.1| RluD [Neisseria gonorrhoeae DGI18]
 gi|240117408|ref|ZP_04731470.1| RluD [Neisseria gonorrhoeae PID1]
 gi|240120661|ref|ZP_04733623.1| RluD [Neisseria gonorrhoeae PID24-1]
 gi|268603103|ref|ZP_06137270.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae PID1]
 gi|268587234|gb|EEZ51910.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           gonorrhoeae PID1]
 gi|317163748|gb|ADV07289.1| RluD [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 374

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 137/327 (41%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     +  VK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAAVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+ GD  Y        +        +  +  LHA  +   HP
Sbjct: 250 LGTGRTHQIRVHMREANHPLAGDPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +    P+P  +      L  + 
Sbjct: 310 ESGETVSFETPIPDDIYHLLSVLRLEA 336


>gi|228478264|ref|ZP_04062872.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           salivarius SK126]
 gi|228249943|gb|EEK09213.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           salivarius SK126]
          Length = 296

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 74/315 (23%), Positives = 141/315 (44%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++     + +++G V V+ K  K    ++ G V+          
Sbjct: 7   EAGNRLDKALAD-LTELSRSQANEAIKAGTVLVNGKSAKAKYAVKEGDVIT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFL 133
           + + E+++L+        ++ +   ++YED+ + V NKP G+ V   +G      ++  +
Sbjct: 57  YELPEEEVLE------YKAEDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++V G
Sbjct: 111 YHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +            K        A++ F V++ F   +  +E+Q  T
Sbjct: 171 NLPNDRGVIEAPIGRSDKDRKKQAVTAK-----GKPAVTRFTVLERFG-NYTLVELQLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G L + T
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLKGHGQFLHAKTLGFTHPTTGELVEFT 279

Query: 309 APLPAHMVKTWDSLG 323
           A  PA   +T + L 
Sbjct: 280 AEEPAIFKETLEKLR 294


>gi|312962573|ref|ZP_07777063.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens WH6]
 gi|311283153|gb|EFQ61744.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens WH6]
          Length = 319

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 99/317 (31%), Positives = 169/317 (53%), Gaps = 13/317 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + V  +    R+D +       +    + +ILR G+VRV+K R+K   ++Q+G +VR
Sbjct: 11  VQLLEVSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDIVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP       + +  + +  +  L +    L++ +++ED+K+ V NKP GI+V GGSG+ 
Sbjct: 71  VPP-----VRVPERDEPVPLAQGLLQR---LEASIVFEDNKLIVINKPCGIAVHGGSGLN 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y +L
Sbjct: 123 FGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHTALRGDGVDKRYMAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +  + +   L K +   G+ +  V   ++    A++ FKV+  F      +E +
Sbjct: 182 VRGNWASSIKSVRAPLQKSNLRSGERMVEV---DEEGKEALTLFKVLRRFGDFATMVEAK 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           P TGRTHQ+RVH LH G  I GD KY    F          +L+LHA  + +P P+GG L
Sbjct: 239 PVTGRTHQIRVHTLHAGHCIAGDTKYGDEGFSKEIRDLGGKRLFLHAYMLTVPLPDGGEL 298

Query: 306 QITAPLPAHMVKTWDSL 322
           ++ AP+     KT + L
Sbjct: 299 KLQAPVDEMWAKTVERL 315


>gi|161869644|ref|YP_001598812.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis 053442]
 gi|161595197|gb|ABX72857.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis 053442]
          Length = 392

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 139/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 48  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 106

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 107 -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 153

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 154 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAV 213

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 214 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y        +        +  +  LHA  +   HP
Sbjct: 268 LETGRTHQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 327

Query: 301 EGGRLQ-ITAPLPAHMVKTWDSLGFKY 326
           + G  +   AP+P  +      L  + 
Sbjct: 328 KTGETRSFEAPIPNDIYHLLSVLRLEA 354


>gi|160938833|ref|ZP_02086184.1| hypothetical protein CLOBOL_03727 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437796|gb|EDP15556.1| hypothetical protein CLOBOL_03727 [Clostridium bolteae ATCC
           BAA-613]
          Length = 294

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 71/315 (22%), Positives = 144/315 (45%), Gaps = 31/315 (9%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E+++R+D++     P ++   +QK+L+SGQV V+ + +K +  +     + +        
Sbjct: 2   EDHVRIDKYLAEACPDLSRSYIQKLLKSGQVLVNGQGIKASYIVVEDDRIELE------- 54

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFL 133
                   +  +V     ++ +   +LYED  + + NKP G+ V   +G   H   +G +
Sbjct: 55  --------VPEAVEPEIDAEPMDLDILYEDQDLILINKPKGMVVHPAAGHYSHTLVNGLM 106

Query: 134 KSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               D         +P + HR+D +T+G+++  +   A   +    +   I + Y ++V 
Sbjct: 107 YHCKDQLSGINGVMRPGIVHRIDMDTTGVIIACKNDMAHSSIAAQLKEHSITRRYQAIVH 166

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+    +  +   + +   +    + +  QN K    A++H++V++ F +++  +E +  
Sbjct: 167 GVIAEDEGTVDAPIGRH-PVERKKMSINYQNGKN---AVTHYRVLNRF-RQYTHVECRLE 221

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH   +  P++GD  Y                 LHA  +   HP  G  ++ 
Sbjct: 222 TGRTHQIRVHMASIRHPLLGDAVYGP---ARCPISGLCGQTLHAGILGFIHPRTGEYMEF 278

Query: 308 TAPLPAHMVKTWDSL 322
           +APLP +  K   +L
Sbjct: 279 SAPLPDYFEKLLRTL 293


>gi|303249693|ref|ZP_07335898.1| 23S rRNA pseudouridylate synthase C [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|302651505|gb|EFL81656.1| 23S rRNA pseudouridylate synthase C [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
          Length = 321

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 162/319 (50%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q      
Sbjct: 11  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQP----- 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 66  -DDVVRVPPVRVAEKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+ +  V    +    + + F + + +A     ++  
Sbjct: 183 VRGQWQAHTKVIKAPLLKNELASGERIVRV---SEEGKPSETRFSIEERYA-NATLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 298

Query: 305 LQITAPLPAHMVKTWDSLG 323
           + ITAPL   +      L 
Sbjct: 299 MLITAPLDKTLKGVLAKLR 317


>gi|327385684|gb|AEA57158.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Lactobacillus casei BD-II]
          Length = 306

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 85/334 (25%), Positives = 143/334 (42%), Gaps = 42/334 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    +  E      R+D+    H        +QK L+ G V V+ +  K N ++ SG 
Sbjct: 1   MTSTFTITTEQG----RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQPTKANYKVASGD 56

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ I                +  +  L    + +   ++YED ++ V +KP G+ V    
Sbjct: 57  VIAIS---------------IPEAKPLEAIPEPIPLDIVYEDDQVIVVDKPQGMVVHPAP 101

Query: 124 GIAYHIDGFLKSWVDSKG--------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G   H DG L + +             +P + HR+D++TSG+L+VA+T  A   L+   +
Sbjct: 102 G---HPDGTLVNGLLYHTDLPGINGVIRPGIVHRIDKDTSGLLMVAKTEKAQLSLSAQLK 158

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +   + Y +LV G  K  +  I   L +          V         +A++HF+V++ 
Sbjct: 159 AKTSIREYLALVHGTFKEDEGTIDAPLGRDPRDRKRQAVVA-----AGRHAVTHFQVLER 213

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F + + +++    TGRTHQ+RVH  ++  P+ GD  Y         +      +LHA  +
Sbjct: 214 F-EHYTFIKCILETGRTHQIRVHMAYIHHPVAGDPLYGPK-----RTLPGKGQFLHAAKL 267

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
              HP  G+ L   AP+P    KT   L    D+
Sbjct: 268 GFVHPTTGQLLVFEAPVPPIFEKTLADLRAGIDK 301


>gi|325206453|gb|ADZ01906.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M04-240196]
          Length = 374

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 139/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T +A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           + G  +   AP+P  +      L  + 
Sbjct: 310 KTGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|294501002|ref|YP_003564702.1| pseudouridine synthase [Bacillus megaterium QM B1551]
 gi|294350939|gb|ADE71268.1| pseudouridine synthase [Bacillus megaterium QM B1551]
          Length = 304

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 141/324 (43%), Gaps = 33/324 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++  V+  ++   R+D+         +   +Q+ ++ G  +V+ K VK N + ++G 
Sbjct: 1   MNVIET-VINEEQAGERIDKVLSTVNAEWSRSQVQQWIKEGHAKVNDKTVKGNYKCKTGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I                +     L   ++ +   + YED  + V NKP G+ V    
Sbjct: 60  AIIIE---------------VPELEELDVVAEEMDLDIYYEDQDVLVVNKPRGMVVHPAP 104

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 105 GHHSGTLVNGLMAHCKDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDLAHESLVSQLVAK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  +    I   + +        + V  +N +    A++HF V+  F 
Sbjct: 165 TVTRRYKAIVHGVIAHDHGTIDAPIGRD-KQDRQSMTVTDENSRD---AVTHFTVLQRF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E +  TGRTHQ+RVH  ++G P+ GD KY         +   +   LHA  +  
Sbjct: 220 KDFSLVECKLETGRTHQIRVHMKYIGFPLAGDPKYGPK-----KTLPIDGQALHAGVLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWD 320
            HP     ++  AP P    +  +
Sbjct: 275 IHPRTNEYMEFEAPAPKEFNEMLE 298


>gi|254673628|emb|CBA09173.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis alpha275]
          Length = 374

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 138/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LIHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|317472795|ref|ZP_07932106.1| RluA family pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
 gi|316899714|gb|EFV21717.1| RluA family pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 305

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 75/328 (22%), Positives = 136/328 (41%), Gaps = 31/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +   V   E   RLD      +P      LQK+ +   V VD    K N +++ G+
Sbjct: 1   MEQERQFTVSQKETGSRLDVCLAGRFPEFTRSYLQKLCKDSAVLVDDAEKKSNYKVREGE 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +                +     L+   + +   ++YED  I + NKP  + V    
Sbjct: 61  RVILK---------------VPKPTELSIKPEKMDLDIVYEDRDIILINKPKNMVVHPAP 105

Query: 124 GI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++G ++   D         +P + HR+D++T+GIL+V +   A Q L E  + 
Sbjct: 106 GHYEGTLVNGLMEHCRDELSGINGVLRPGIVHRIDKDTTGILIVCKNDMAHQCLAEQLKD 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y ++V+   K +   +   + +           +  + +    A++H++V++  
Sbjct: 166 HTITRRYHAIVYHNIKEESGTVDAPIARSRKERKK----MAIDREAGRRAVTHYRVLERL 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F ++E    TGRTHQ+RVH   +G P++GD  Y        +        LHA+ + 
Sbjct: 222 KEGFTYIECSLETGRTHQIRVHMASIGHPLLGDTVYGPKK----SKYSLEGQCLHAKVLG 277

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP     ++    LPA+  +    LG
Sbjct: 278 FTHPRTKEYMEFEVGLPAYFEELLKRLG 305


>gi|224476300|ref|YP_002633906.1| putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus carnosus subsp. carnosus TM300]
 gi|222420907|emb|CAL27721.1| putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus carnosus subsp. carnosus TM300]
          Length = 305

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 76/329 (23%), Positives = 141/329 (42%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT   Y + E ++   R+D+         +   +Q  ++   V V+ K+VK N++++   
Sbjct: 1   MTEFNYEITEAEQAGQRIDKLLPEFNSDWSRSQIQDWIKEDLVTVNGKKVKANHKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                   +V      + L   + YEDS + +  KP G+ V    
Sbjct: 61  KIEVT---------------EKETVEADIKPENLNLDIYYEDSDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A ++L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRNLVEQLMAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G   +    I   + +      D   +   ++     A++HF V++ F 
Sbjct: 166 TVTRKYTALVHGNIPHDYGTIDAPIGRDKK---DRQSMAVVDD--GKDAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLVECELETGRTHQIRVHMKYIGHPLVGDPKYGPKKTMD-----IGGQALHAGVIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  ++    LP    +    +  +
Sbjct: 275 EHPVTGEYIERKTDLPEDFKQVLTDIRLR 303


>gi|220928062|ref|YP_002504971.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|219998390|gb|ACL74991.1| pseudouridine synthase, RluA family [Clostridium cellulolyticum
           H10]
          Length = 304

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 86/325 (26%), Positives = 152/325 (46%), Gaps = 32/325 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++  D + +R+D W   +    +   +QK+   G V  +  +VK N R+++   ++
Sbjct: 1   MKEFILNCDTDGVRIDSWLAGNLEDYSRSYIQKLCLDGNVWANGIQVKSNYRVKTDDNIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSG 124
           +          + E +ILD         + +   ++YED  I V NKP G+ V    G+ 
Sbjct: 61  VN---------VPEAEILDV------EPEDIPLDIVYEDKHIIVINKPKGMVVHPAVGNY 105

Query: 125 IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  +K   DS        +P + HR+D++TSG+LVVA++  A + L+E  +   I
Sbjct: 106 TGTLVNALMKHCGDSLSDINGVIRPGIVHRIDKDTSGLLVVAKSNIAHERLSEKLKTHDI 165

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +LV GI       I   + +   +    + V   N +    AI+HFKV++ F Q 
Sbjct: 166 KREYIALVDGIIYENSGKIDAPIGRN-PVERKKMCV---NTENGRNAITHFKVLERF-QN 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
             +LE++  TGRTHQ+RVH  ++  PI+GD  Y    +   T        LHA  +   H
Sbjct: 221 ATYLELKLETGRTHQIRVHMAYINHPIIGDMVYGRRKQKYKT----KGQVLHAWRLSFQH 276

Query: 300 P-EGGRLQITAPLPAHMVKTWDSLG 323
           P  G  ++    +P +  +    L 
Sbjct: 277 PITGEEVKFETAVPEYFQRILSQLR 301


>gi|116494944|ref|YP_806678.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
 gi|227535056|ref|ZP_03965105.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|301066507|ref|YP_003788530.1| 23S RNA-specific pseudouridylate synthase [Lactobacillus casei str.
           Zhang]
 gi|116105094|gb|ABJ70236.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           casei ATCC 334]
 gi|227187271|gb|EEI67338.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|300438914|gb|ADK18680.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           str. Zhang]
          Length = 306

 Score =  266 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 85/334 (25%), Positives = 143/334 (42%), Gaps = 42/334 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    +  E      R+D+    H        +QK L+ G V V+ +  K N ++ SG 
Sbjct: 1   MTSTFTITTEQG----RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQPTKANYKVASGD 56

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ I                +  +  L    + +   ++YED ++ V +KP G+ V    
Sbjct: 57  VIAIS---------------IPEAKPLEAIPEPIPLDIVYEDDQVIVVDKPQGMVVHPAP 101

Query: 124 GIAYHIDGFLKSWVDSKG--------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G   H DG L + +             +P + HR+D++TSG+L+VA+T  A   L+   +
Sbjct: 102 G---HPDGTLVNGLLYHTDLPGINGVIRPGIVHRIDKDTSGLLMVAKTEKAQLSLSAQLK 158

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +   + Y +LV G  K  +  I   L +          V         +A++HF+V++ 
Sbjct: 159 AKTSIREYLALVHGTFKEDEGTIDAPLGRDPRDRKRQAVVA-----DGRHAVTHFQVLER 213

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F + + +++    TGRTHQ+RVH  ++  P+ GD  Y         +      +LHA  +
Sbjct: 214 F-EHYTFIKCILETGRTHQIRVHMAYIHHPVAGDPLYGPK-----RTLPGKGQFLHAAKL 267

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
              HP  G+ L   AP+P    KT   L    D+
Sbjct: 268 GFVHPTTGQLLVFEAPVPPIFEKTLADLRAGIDK 301


>gi|313204538|ref|YP_004043195.1| ribosomal large subunit pseudouridine synthase d [Paludibacter
           propionicigenes WB4]
 gi|312443854|gb|ADQ80210.1| ribosomal large subunit pseudouridine synthase D [Paludibacter
           propionicigenes WB4]
          Length = 356

 Score =  266 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 85/335 (25%), Positives = 152/335 (45%), Gaps = 41/335 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV+  +  +R+D+   N   + +   +Q+   +G + V+ K VK N RI+   ++ I  
Sbjct: 29  FVVDKGQAMVRIDKHLVNCMSNTSRNRIQEAADAGNILVNGKPVKSNYRIKPYDIISI-- 86

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L++   + +I+   + +          ++YED  I + NK   + V  G G   + 
Sbjct: 87  ---VLSYPPSQFEIIPQDIPIN---------IVYEDDDIILVNKQPNLVVHPGFG---NF 131

Query: 130 DGFLKSWV----------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           DG L + +          D+   +  L HR+D++TSG++++A+T  A  HL + F  +  
Sbjct: 132 DGTLLNAIAWHLKDHPEFDANDSRIGLVHRIDKDTSGLILIAKTEEAKAHLGKQFFNKTT 191

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Q+ Y +LVWG  K  +  I   L +       +    +     A +A++H+KV++ FA  
Sbjct: 192 QRRYHALVWGNVKEDEGTIVGALARDPRDRMLFTVFPEGENPLAKHAVTHYKVLERFA-Y 250

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNK 287
              +E +  TGRTHQ+RVH  H+G  +  D +Y  +     T+             I  +
Sbjct: 251 VTLVECRLETGRTHQIRVHMKHIGHTLFNDERYGGHIILKGTNTAMYKAFVKNCFYICPR 310

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
             LHA+ +   HP  G  +   + LP  M +  D 
Sbjct: 311 QALHAKTLGFVHPRTGEFMHFESELPDDMQELIDK 345


>gi|237724045|ref|ZP_04554526.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D4]
 gi|229437505|gb|EEO47582.1| ribosomal large subunit pseudouridine synthase D [Bacteroides dorei
           5_1_36/D4]
          Length = 357

 Score =  266 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 85/332 (25%), Positives = 146/332 (43%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK   +G +  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQSQVRVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKSSYKVKPCDVLTVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    +  I+   + L          ++YED+ + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYDNDIIPEDIPLD---------IVYEDNDLMVINKPAGLVVHPGCGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+LVVA+T  A  HL   F  +  ++ 
Sbjct: 138 LVNAIAWHLKDNPRYDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRK 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI +N +  I   + +           V  +     +A++H++V++        
Sbjct: 198 YNALVWGIVENNEGTIEGNIGRNPK--DRMQMAVLSDPAQGKHAVTHYRVLERLG-YVTL 254

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  N   KG   S  +           +  L
Sbjct: 255 VECVLETGRTHQIRVHMKHIGHTLFNDERYGGNEILKGTHFSKYKQFVNNCFETCPRQAL 314

Query: 291 HARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           HA  +   HP     +  T+PLP  M    D 
Sbjct: 315 HAMTLGFVHPRTSEEMFFTSPLPEDMTNLIDK 346


>gi|15676602|ref|NP_273746.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis MC58]
 gi|34395832|sp|Q9K0B0|RLUD_NEIMB RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|7225933|gb|AAF41121.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis MC58]
 gi|316983681|gb|EFV62662.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis H44/76]
 gi|325200611|gb|ADY96066.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis H44/76]
          Length = 374

 Score =  266 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 138/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LTHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           E G  +   AP+P  +      L  + 
Sbjct: 310 ESGETVSFEAPIPNDIYHLLSVLRLEA 336


>gi|90407030|ref|ZP_01215220.1| Predicted pseudouridylate synthase, Rlu family protein
           [Psychromonas sp. CNPT3]
 gi|90311901|gb|EAS39996.1| Predicted pseudouridylate synthase, Rlu family protein
           [Psychromonas sp. CNPT3]
          Length = 303

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 96/315 (30%), Positives = 160/315 (50%), Gaps = 18/315 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +    R+D + + H   +    + +I+R G+VRV+KKR+K + ++Q G +VRIPP
Sbjct: 2   LEISQENAKQRIDNFLRLHLKGVPKSLIYRIIRKGEVRVNKKRIKPDYKLQPGDIVRIPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  +  + +   K+             L+S ++YED  + + NKP+GI+V GGSG+++  
Sbjct: 62  VKVSAENPLPSPKL--------NAIAQLESRIVYEDDALLILNKPSGIAVHGGSGLSFGA 113

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++ +    +   L HRLD+ TSG L++A+ R+  + L E  R + + K Y +LV G
Sbjct: 114 IEGLRA-LRPDARFLELVHRLDKATSGCLLIAKKRSMLRALHEQLRNKTMNKQYLALVKG 172

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               K   +   LLK S         V +       A + FK++  +      +E  P T
Sbjct: 173 SWDKKDRSVKEPLLKDSQNS------VVKVSALGKQAETRFKIMQRY-HGATLVEASPVT 225

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQI 307
           GRTHQ+RVH    G  I GD +Y A  F     +   N+L+LHA ++   HP    ++ +
Sbjct: 226 GRTHQIRVHCACKGHNIAGDDRYGAPEFSKKMQALGLNRLFLHAAHITFYHPVLEKKMTV 285

Query: 308 TAPLPAHMVKTWDSL 322
           +APL A +    + L
Sbjct: 286 SAPLCAPLAALLEKL 300


>gi|312886031|ref|ZP_07745658.1| ribosomal large subunit pseudouridine synthase D [Mucilaginibacter
           paludis DSM 18603]
 gi|311301488|gb|EFQ78530.1| ribosomal large subunit pseudouridine synthase D [Mucilaginibacter
           paludis DSM 18603]
          Length = 347

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 73/332 (21%), Positives = 148/332 (44%), Gaps = 38/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+D++  +   + +   +Q  +  G V V+ K +K + +++   V+ +  
Sbjct: 21  IVVDKGQSLLRIDKFLMHRVENASRNRIQNAIELGNVLVNDKAIKSSYKVKPLDVISV-- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIAY 127
               L H  ++ ++   ++ L          ++YED  + V NKPAG+ V  G  +    
Sbjct: 79  ---VLPHPPRDTEVYPENIPLD---------IVYEDDDVLVVNKPAGLVVHPGYNNYTGT 126

Query: 128 HIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++G +  +     +     +P L HR+D++TSG+L++++   +   L   F    I + 
Sbjct: 127 LVNGLVYHFQQLPTLPGNDGRPGLVHRIDKDTSGLLLISKNERSMTWLARQFYEHTIARK 186

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +     +  ++ +   I    V  +  + +   ++++H++V+         
Sbjct: 187 YLALVWGDLEID-GTVTGYIGRS--IKDRRVMSIYDDPEKGKWSVTHYRVLQRMT-YVTL 242

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYL 290
           +E +  TGRTHQ+R H  H+G P+  D  Y  +     T              +  +  L
Sbjct: 243 IECELETGRTHQIRAHMKHIGHPLFSDATYGGDHILKGTLFNKYKQFVENCFALMPRQAL 302

Query: 291 HARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           HA+ +   HP    R+   APLP   V   + 
Sbjct: 303 HAQTLGFVHPTARKRVHFEAPLPQDFVAVLEK 334


>gi|294674881|ref|YP_003575497.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Prevotella ruminicola 23]
 gi|294472042|gb|ADE81431.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Prevotella ruminicola 23]
          Length = 347

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 85/332 (25%), Positives = 151/332 (45%), Gaps = 40/332 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  +  +R+D++   H PH +   +Q+   +G + V++K VK N +++ G ++ +    
Sbjct: 25  VDKGQVPIRIDKYLVEHQPHSSRNRIQQAADAGFIHVNEKPVKSNYKVRPGDIITLMLDR 84

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------- 124
              +  I+ + I                 ++YED+ + V NKPAG+ V  G G       
Sbjct: 85  PHYDTTIEPEDI--------------PLEVVYEDADLMVINKPAGMVVHPGCGNFNGTLV 130

Query: 125 --IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             IA+H+     +  D    +  L HR+D++TSG+LVVA+T  A   L + F  +   + 
Sbjct: 131 NAIAWHLKDL--ASYDPNDPEVGLVHRIDKDTSGLLVVAKTPDAKTSLGKQFFNKTTHRS 188

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + +        + V   + +    A++H+KV++ +      
Sbjct: 189 YNALVWGNFVEDEGRIEGNIGRDPK-DRLRMEVFPPDSEIGKPAVTHYKVMERYG-YVTL 246

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKLYL 290
           +E    TGRTHQ+R H  H+G P+  D +Y      +G  T+           +  +  L
Sbjct: 247 VECILETGRTHQIRAHMKHIGHPLFADERYGGTELLRGERTASYKAYIQNCFKLCPRQVL 306

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA+ +   HP  G+ +  T+  PA M    D 
Sbjct: 307 HAKTLGFVHPTTGKQMDFTSEWPADMAALIDK 338


>gi|190151234|ref|YP_001969759.1| ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|307246812|ref|ZP_07528878.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307251150|ref|ZP_07533072.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|307253568|ref|ZP_07535436.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|307255795|ref|ZP_07537597.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|307257984|ref|ZP_07539737.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|307260247|ref|ZP_07541955.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|307264584|ref|ZP_07546167.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
 gi|189916365|gb|ACE62617.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|306852283|gb|EFM84522.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|306856816|gb|EFM88950.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|306858948|gb|EFM90993.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|306861258|gb|EFM93250.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|306863531|gb|EFM95461.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|306865694|gb|EFM97574.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|306870113|gb|EFN01874.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
          Length = 326

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 162/319 (50%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q      
Sbjct: 16  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQP----- 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  -DDVVRVPPVRVAEKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 128

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 129 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 187

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+ +  V    +    + + F + + +A     ++  
Sbjct: 188 VRGQWQAHTKVIKAPLLKNELASGERIVRV---SEEGKPSETRFSIEERYA-NATLVKAS 243

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 244 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 303

Query: 305 LQITAPLPAHMVKTWDSLG 323
           + ITAPL   +      L 
Sbjct: 304 MLITAPLDKTLKGVLAKLR 322


>gi|319898406|ref|YP_004158499.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           clarridgeiae 73]
 gi|319402370|emb|CBI75909.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           clarridgeiae 73]
          Length = 335

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 89/345 (25%), Positives = 157/345 (45%), Gaps = 46/345 (13%)

Query: 8   QYVVVENDEE-NMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           Q++   N+     R+D+W    Y   I+   LQ ++R G +++D + +K    +++S Q+
Sbjct: 3   QHITNTNENACGQRIDQWLAKQYKGEISRSRLQTLIREGHLKIDGQLIKEPKTKLKSNQI 62

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +               I+ +  +     + L   + +ED  + V NKPAG+ V  G+G
Sbjct: 63  IEL---------------IIPAPNDARPQGEALALDIFFEDDHVIVINKPAGLVVHPGNG 107

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +    DS       ++P + HRLD++TSG++V+A+   A ++L   F   
Sbjct: 108 NWTGTLVNALIYHCSDSLSGIGGIKRPGIVHRLDKDTSGVMVIAKNDIAHRNLNAQFADH 167

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                + + Y +++WG P      I  +L + SH       VV      A +AI+HF ++
Sbjct: 168 GRTSALDRRYHAIIWGSPNRNIATIDTFLARSSH-DRTKRAVVHSEHANARHAITHFSLL 226

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQ 285
           + +            LE +  TGRTHQ+RVH  H+G P++GD  Y   F  K N   P+ 
Sbjct: 227 EKYGTCNDTTPFASLLECRLETGRTHQIRVHMAHIGHPLIGDKVYGNAFKTKSNVLDPVI 286

Query: 286 -------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                  N+  LHA  +   HP  G  +  ++P P  +    + L
Sbjct: 287 KNKIDQFNRQALHATSLTFEHPVNGEIMSFSSPFPKDLADLINHL 331


>gi|303236145|ref|ZP_07322746.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
 gi|302483651|gb|EFL46645.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
          Length = 360

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 83/332 (25%), Positives = 149/332 (44%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V+  +E +R+D++      H +   +QK   +G + V+ K VK N +++   ++ +  
Sbjct: 35  LIVDKGQEPVRVDKYIFEKMQHSSRNRIQKAADAGCIYVNDKPVKSNYKVRPDDIITLML 94

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                ++ I+ ++I                 ++YED +I V NKPAG+ V  G+G     
Sbjct: 95  DRPKHDNTIEAEEI--------------PLDIVYEDDEIMVINKPAGLVVHPGAGNFHGT 140

Query: 128 HIDGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            I+       D K   P      L HR+D++TSG+L++A+T  A   L + F  +   + 
Sbjct: 141 LINAIAWHLKDLKDFDPNDPAVGLVHRIDKDTSGLLLIAKTPDAKTFLGKQFFNKTTHRS 200

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + +        + V          A++H++V++ F      
Sbjct: 201 YNALVWGNLVEDEGRIEGNIGRDPK-DRLRMAVFPPESGIGKNAVTHYRVLERFG-YTTL 258

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKLYL 290
           +E +  TGRTHQ+R H  H+G P+  D +Y      +G  T+           + N+  L
Sbjct: 259 VECRLETGRTHQIRAHMKHIGHPLFADERYGGMEILRGERTAAYKAYIKNCLKLCNRQAL 318

Query: 291 HARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           HAR +   HP    ++  T+ LP  +    D 
Sbjct: 319 HARTLGFIHPRTHEQMDFTSELPEDLGAVIDK 350


>gi|83745881|ref|ZP_00942938.1| Ribosomal large subunit pseudouridine synthase D [Ralstonia
           solanacearum UW551]
 gi|207743017|ref|YP_002259409.1| ribosomal large subunit pseudouridine synthase d protein [Ralstonia
           solanacearum IPO1609]
 gi|83727571|gb|EAP74692.1| Ribosomal large subunit pseudouridine synthase D [Ralstonia
           solanacearum UW551]
 gi|206594414|emb|CAQ61341.1| ribosomal large subunit pseudouridine synthase d protein [Ralstonia
           solanacearum IPO1609]
          Length = 370

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 89/335 (26%), Positives = 143/335 (42%), Gaps = 32/335 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V +       RLD+      P  +   LQ+ + +G VRV    V+    +  G  + + P
Sbjct: 53  VQIPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVRPREAVCGGDRIEVVP 112

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
              A      E   +   ++L          ++YED  + V NKPAG+ V   +G     
Sbjct: 113 QRAAD-----ENAFVAEPIDLD---------VVYEDDTLLVINKPAGLVVHPAAGNWSGT 158

Query: 128 HIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  +  + G  +  + HRLD+ETSG++VVART  A   L    + R +++ Y +L
Sbjct: 159 VLNGLLHRYPQAAGLPRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLAL 218

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWL 243
           VWG    +   I   + +      D   +          A +HFK +D           +
Sbjct: 219 VWGE-TPEAGTIDAPIGRDP---RDRTRMAIIETASGKPARTHFKTLDVIDLGRAQVSLV 274

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLHARYMD 296
           + Q  TGRTHQ+RVH    G P++GD  Y  NF+      I+        +  LHA  + 
Sbjct: 275 QCQLETGRTHQIRVHFESEGHPLLGDPVYTRNFRRGQPQTIKAPLPVPFARQALHAVRLG 334

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           + HP  G+ +   A +P  +    D+L    D +L
Sbjct: 335 IVHPASGQSMHWHAGVPDDLADLMDALEMDSDVDL 369


>gi|71280214|ref|YP_269010.1| ribosomal large subunit pseudouridine synthase C [Colwellia
           psychrerythraea 34H]
 gi|71145954|gb|AAZ26427.1| ribosomal large subunit pseudouridine synthase C [Colwellia
           psychrerythraea 34H]
          Length = 360

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 96/320 (30%), Positives = 173/320 (54%), Gaps = 14/320 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V+++ +++++   R+D +       +   +L +++R G++RV+KKR+K   ++     
Sbjct: 50  PKVRFITIDSEDAGQRIDNFLLRTLKGVPKSHLYRLMRKGEIRVNKKRIKPVYKLLIDDE 109

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRI P+      + +E+  + + +++  +   L+  +L+ED ++ V NKP+G++V GGSG
Sbjct: 110 VRIAPI-----RVSEEKDAVSTGLHIVAN---LEKQILFEDDRLIVINKPSGMAVHGGSG 161

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++ +  + +   L HRLD++TSG L+VA+ R+  +HL E FR + +QK Y 
Sbjct: 162 LSFGLIEALRA-LRPEARMLELVHRLDRDTSGCLMVAKKRSTLRHLHEQFRDKNVQKFYH 220

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G    K   + + L K     G+ V VV  + +    + + F+V++ + +    + 
Sbjct: 221 ALVKGHWPTKLTRVTDALKKNDLKSGERVVVV--DNQLGKESETRFRVLERY-RGATLVR 277

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             P TGRTHQ+RVH    G  I  D KY    F     S    +L+LHA  ++  HP   
Sbjct: 278 AFPVTGRTHQIRVHCQTSGHSIAMDAKYGHEEFDEQMKSKGLKRLFLHAASIEFTHPNTE 337

Query: 304 -RLQITAPLPAHMVKTWDSL 322
            RL+I APL A + K    L
Sbjct: 338 QRLKIEAPLEASLEKLLSKL 357


>gi|126209339|ref|YP_001054564.1| 23S rRNA pseudouridylate synthase C [Actinobacillus
           pleuropneumoniae L20]
 gi|126098131|gb|ABN74959.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
          Length = 321

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 162/319 (50%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q      
Sbjct: 11  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQP----- 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 66  -DDVVRVPPVRVAEKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLRKKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+ +  V    +    + + F + + +A     ++  
Sbjct: 183 VRGQWQAHTKVIKAPLLKNELASGERIVRV---SEEGKPSETRFSIEERYA-NATLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 298

Query: 305 LQITAPLPAHMVKTWDSLG 323
           + ITAPL   +      L 
Sbjct: 299 MLITAPLDKTLKGVLAKLR 317


>gi|17546347|ref|NP_519749.1| ribosomal large subunit pseudouridine synthase D protein [Ralstonia
           solanacearum GMI1000]
 gi|34395802|sp|Q8XYX8|RLUD_RALSO RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|17428644|emb|CAD15330.1| probable ribosomal large subunit pseudouridine synthase d protein
           [Ralstonia solanacearum GMI1000]
          Length = 358

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 91/340 (26%), Positives = 147/340 (43%), Gaps = 34/340 (10%)

Query: 7   VQYVVVE--NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           ++ ++VE        RLD+      P  +   LQ+ + +G VRV    V+    +  G  
Sbjct: 36  IEPIIVEIPEALHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVRPRAAVCGGDR 95

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + + P          E   +   V+L          ++YED  + V NKPAG+ V   +G
Sbjct: 96  IEVVPQRADD-----ENAFVAEPVDLD---------VVYEDDTLLVINKPAGLVVHPAAG 141

Query: 125 I--AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                 ++G L  +  + G  +  + HRLD+ETSG++VVART  A   L    + R +++
Sbjct: 142 NWSGTVLNGLLHRYPQAAGLPRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKR 201

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-- 239
            Y +LVWG    +   I   + +      D   +          A +HFK +D       
Sbjct: 202 TYLALVWGE-TPEAGTIDAPIGRDP---RDRTRMAIIETASGKPARTHFKTLDVVDLGRA 257

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLH 291
               ++ Q  TGRTHQ+RVH    G P++GD  Y  NF+      I+        +  LH
Sbjct: 258 QVSLVQCQLETGRTHQIRVHFESEGHPLLGDPVYTRNFRRGRPQTIKAPLPAPFARQALH 317

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           A  + L HP  G+ +   A +P  + +  D+L    D +L
Sbjct: 318 AVRLGLVHPASGQSVHWHAGVPDDLAELMDALEMDPDVDL 357


>gi|329120429|ref|ZP_08249095.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327462113|gb|EGF08441.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 435

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 97/326 (29%), Positives = 164/326 (50%), Gaps = 25/326 (7%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V   E   RLD +       +   ++ +++R+G+VR++KKR K  +RI +G +VRI
Sbjct: 115 RPLAVAEHEAGQRLDNYLIKILKGVPKSHIWRMIRAGEVRLNKKRCKPESRIAAGDIVRI 174

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PPV  A      E+    +           +  ++YED  + V +KPAG++V GGSG+++
Sbjct: 175 PPVRVAERQKPSEKAAAPAR----------EFDIVYEDDALLVIDKPAGVAVHGGSGVSF 224

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   ++     + +   L HRLD++TSG+L++A+ R+A   L E+ R    +KIY +L 
Sbjct: 225 GVIEQIRRAR-PEARYLELVHRLDKDTSGLLMIAKKRSALVKLHEAIRNDHPKKIYLALG 283

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------- 238
            G  +N +  +   L K +   G+ +  V ++    + A + FKV++ F+          
Sbjct: 284 AGRLENDRFHVRLPLFKYTGAAGEKMVRVSED---GHSAHTVFKVLNRFSDGLLHRVGLS 340

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDL 297
               +E    TGRTHQ+RVH    GCPI GD +Y               +++LHA  + L
Sbjct: 341 NLTLVEATLKTGRTHQIRVHMQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHAAELHL 400

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSL 322
            HP  G +L + APLP  + +    L
Sbjct: 401 DHPLTGEKLVLKAPLPQDLAQFLAVL 426


>gi|116626305|ref|YP_828461.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Solibacter usitatus Ellin6076]
 gi|116229467|gb|ABJ88176.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 296

 Score =  265 bits (678), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 90/321 (28%), Positives = 148/321 (46%), Gaps = 35/321 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
              +  +   R+D+W   H P  +   +Q+ ++S +VRV+   VK +  +++   V + P
Sbjct: 3   FTADPADTGQRIDQWLHAHLPDFSRSRIQEWIKSARVRVNGAAVKTSYTLRAADAVEVEP 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
                               L   ++ +   +LYED+ +   +KPAG+ V  G+G+    
Sbjct: 63  ---------------ADPPPLNATAEDIPLRILYEDADVVAIDKPAGMVVHAGAGVHSGT 107

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L  +    G     +P + HRLD+ TSG+L+VA+  AA Q L   F  R I+K+Y
Sbjct: 108 LVNALLHRFATLSGVGGPLRPGIVHRLDRFTSGVLLVAKNDAAHQKLAAQFSGREIEKVY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFC 241
            +LV G  K +   I         I  D VH  +   +      A S ++V+  F   F 
Sbjct: 168 LALVHGTVKPETGRIERP------IARDPVHRARMTARLAEGRAAWSEYRVLRRFPD-FT 220

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE++  TGRTHQ+RVH   +  P+VGD  Y A  +     P+  + +LHA  +    P 
Sbjct: 221 LLEVRIGTGRTHQIRVHLASIRHPVVGDTLYGAPAQ-----PLLGRYFLHAHRIRFHLPS 275

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
           G  + I +PLP  +     +L
Sbjct: 276 GREMLIESPLPPDLEAWLGTL 296


>gi|307262378|ref|ZP_07544024.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|306867926|gb|EFM99756.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
          Length = 326

 Score =  265 bits (678), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 161/319 (50%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q      
Sbjct: 16  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQP----- 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  -DDVVRVPPVRVAEKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 128

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  +     L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 129 FGVIEALRA-LRPQAHFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 187

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+ +  V    +    + + F + + +A     ++  
Sbjct: 188 VRGQWQAHTKVIKAPLLKNELASGERIVRV---SEEGKPSETRFSIEERYA-NATLVKAS 243

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 244 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 303

Query: 305 LQITAPLPAHMVKTWDSLG 323
           + ITAPL   +      L 
Sbjct: 304 MLITAPLDKTLKGVLAKLR 322


>gi|300691371|ref|YP_003752366.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Ralstonia solanacearum PSI07]
 gi|299078431|emb|CBJ51083.2| Ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Ralstonia solanacearum PSI07]
          Length = 358

 Score =  265 bits (678), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 88/335 (26%), Positives = 142/335 (42%), Gaps = 32/335 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V +       RLD+      P  +   LQ+ + +G VRV    V+    +  G  V + P
Sbjct: 41  VAIPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVRPRAAVCGGDRVEVVP 100

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
              A                    ++ +   ++YED  + V NKPAG+ V   +G     
Sbjct: 101 QRAADES--------------AFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGT 146

Query: 128 HIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  + ++ +  +  + HRLD+ETSG++VVART  A   L    + R +++ Y +L
Sbjct: 147 VLNGLLHRYPEAAELPRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLAL 206

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWL 243
           VWG    +   I   + +      D   +          A +HFK +D           +
Sbjct: 207 VWGE-TPEAGTIDAPIGRDP---RDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLV 262

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLHARYMD 296
             Q  TGRTHQ+RVH    G P++GD  Y  NF+      I+        +  LHA  + 
Sbjct: 263 RCQLETGRTHQIRVHFESEGHPLLGDPVYTRNFRRGQPQTIKAPLPVPFARQALHAVRLG 322

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           L HP  G+ +   A +P  + +  D+L    D +L
Sbjct: 323 LVHPASGQSIHWHAGVPDDLAELMDALEMDPDADL 357


>gi|330815964|ref|YP_004359669.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           gladioli BSR3]
 gi|327368357|gb|AEA59713.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           gladioli BSR3]
          Length = 342

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 105/326 (32%), Positives = 162/326 (49%), Gaps = 24/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  V V  +    R+D +       +   ++ +ILRSG+VRV+K R+    R+  G VV
Sbjct: 24  QVSMVEVGEEAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAYGDVV 83

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP+  A     +E   + ++          +  +++ED  + V NKPAG++V GGSG+
Sbjct: 84  RIPPIRIAAADPSRESVPVPAA----------EFAVVFEDEAMLVINKPAGVAVHGGSGV 133

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L+     + +   L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y++
Sbjct: 134 SFGVIEQLREAR-PEARFLELVHRLDRETSGILMIAKKRSALVGLHEQIRDNRMDKRYYA 192

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G           +   L K S   G+    V+ +      + + F +ID ++  + +
Sbjct: 193 AVHGEWAADWGRRRAVKVPLFKYSTPDGERRVRVQDD---GLPSHTVFNLIDRWSD-YAF 248

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           LE +  TGRTHQ+RVH  H+G PIVGD KY               P   +++LHA  + L
Sbjct: 249 LEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARANARPSLKRMFLHAYRLKL 308

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLP    +  D L
Sbjct: 309 AHPLSGETLQFDAPLPDECRRFLDQL 334


>gi|332879773|ref|ZP_08447463.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
 gi|332682292|gb|EGJ55199.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
          Length = 353

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 82/326 (25%), Positives = 153/326 (46%), Gaps = 35/326 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
             +E +R+D++  N   +     +Q+  + G + V+ + VK N+R+++   V++      
Sbjct: 37  KGQEPLRVDKFLMNFVENATRNKVQQAAKQGNIFVNGQPVKSNHRVKANDEVKVY----- 91

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDG 131
             H   E  ++  ++ L          ++YED  + V NKPAG+ V  G G      I+ 
Sbjct: 92  FAHPPHEDLLIPENIPLQ---------IVYEDDSLLVVNKPAGMVVHPGHGNYSGTLINA 142

Query: 132 FL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +   ++  ++   +P L HR+D++TSG+LV+A+T  A  HLT+ F  +  ++ Y +LVW
Sbjct: 143 LVYHFENLPNNSSNRPGLVHRIDKDTSGLLVIAKTEEAMLHLTQQFFHKTTEREYIALVW 202

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  +  +  +   + +  H+       V  +      A++H+KV++ F      +  +  
Sbjct: 203 GNVEADEGTVRGHIGR--HLKDRLQMDVFPDGSHGKEAVTHYKVLERFG-YVTLVSCRLE 259

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLHARYMD 296
           TGRTHQ+RVH  H+G  +  D +Y  +     T+  +             +  LHA+ + 
Sbjct: 260 TGRTHQIRVHMKHIGHTLFNDERYGGDKILKGTTFAKYKQFVDNCFSVLPRQALHAKTLG 319

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDS 321
             HP  G  L+  + LPA M    + 
Sbjct: 320 FEHPVSGEYLRFDSELPADMQACIEK 345


>gi|260577148|ref|ZP_05845125.1| pseudouridine synthase, RluA family [Rhodobacter sp. SW2]
 gi|259020622|gb|EEW23941.1| pseudouridine synthase, RluA family [Rhodobacter sp. SW2]
          Length = 349

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 112/341 (32%), Positives = 180/341 (52%), Gaps = 25/341 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V+ + V  DE   RLDRWFK  +P +    ++K+ R+GQVRVD  R K ++R+  G 
Sbjct: 1   MSAVKLLTVSGDEGEQRLDRWFKRRFPQLTQGAVEKMCRTGQVRVDGARAKASDRVVPGM 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+PP+ ++       +  + ++      +  ++S +L++D  I V NKP G+  QGGS
Sbjct: 61  EIRVPPLPDSEAPSRPLRDGVSAA-----DTKMIQSCVLFKDEHIIVLNKPPGLPSQGGS 115

Query: 124 G-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           G    H+DG  ++      ++P+L HRLD++TSG+L++ART   A+ L+E+FR R  +KI
Sbjct: 116 GQGDRHVDGLTEALKFGYKERPKLVHRLDKDTSGVLILARTDRVARALSEAFRHRNTRKI 175

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGG----DYVHVVKQNE----KGANYAISHFKVID 234
           YW+LV G+P  ++  I   L+K    G     + +  +   +      A  A + + V+ 
Sbjct: 176 YWALVAGVPHPRQGSIKYALMKAPGHGRGGEGEKMLCIHPAKTADYPDAKRAQTDYFVLW 235

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV---------GDHKYCANFKGNFTSPIQ 285
               +  W+ ++P TGRTHQLR H   MG PI+          D+     +       I 
Sbjct: 236 FLGSRLSWVALEPITGRTHQLRAHMAEMGHPILGDGKYGGGGADNL-GDGWGAQVGGDIS 294

Query: 286 NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
            KL+LHAR + + HP     +   A LP HM KTW +  + 
Sbjct: 295 RKLHLHARSLSVEHPITKAMMTFVAQLPEHMAKTWKTFDWN 335


>gi|257866108|ref|ZP_05645761.1| pseudouridylate synthase [Enterococcus casseliflavus EC30]
 gi|257872439|ref|ZP_05652092.1| pseudouridylate synthase [Enterococcus casseliflavus EC10]
 gi|257800042|gb|EEV29094.1| pseudouridylate synthase [Enterococcus casseliflavus EC30]
 gi|257806603|gb|EEV35425.1| pseudouridylate synthase [Enterococcus casseliflavus EC10]
          Length = 302

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 82/323 (25%), Positives = 151/323 (46%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q  V+  +E+  R+D+      P+ +   +Q+ L+   V +  + V+ N ++++G  + I
Sbjct: 4   QIEVIIKEEKG-RVDKVLAERLPNHSRSQIQQWLKEDAVTLKGETVRANYKVKAGDHLII 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                     + E +++D         + +   ++Y+D+ + V NKP G+ V   +G   
Sbjct: 63  Q---------VPEPEVVDL------QPENIPLTIVYQDADVAVINKPQGMVVHPSAGHPN 107

Query: 128 --HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D        +P + HR+D++TSG+L++A+   A + L +  + +   +
Sbjct: 108 GTLVNALLYHMDDLSTINDVVRPGIVHRIDKDTSGLLMIAKNDQAHESLAKQLKDKTSLR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + S +      V+    +    A++HF V++ F Q F 
Sbjct: 168 KYVALVHGTISHEKGTINAPIGR-SKVNRKMQAVI----ENGKPAVTHFTVLERFEQ-FT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   HP 
Sbjct: 222 LVELQLETGRTHQIRVHMQYIGFPLAGDPLYGPK-----RTLKGNGQFLHAKLLGFTHPT 276

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            G  L   APLP     T   L 
Sbjct: 277 TGESLVFEAPLPELFADTLKKLR 299


>gi|269798295|ref|YP_003312195.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269094924|gb|ACZ24915.1| pseudouridine synthase, RluA family [Veillonella parvula DSM 2008]
          Length = 305

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 85/321 (26%), Positives = 143/321 (44%), Gaps = 32/321 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   +V  ++E MRLD +        +   +Q +++ G V V  K  K N R+    V+R
Sbjct: 1   MNEYIVSAEQEGMRLDVFLTEQMEG-SRSYIQSLIKGGHVTVGGKVGKANLRLTPDTVIR 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSG 124
           +                +    ++    + +    LYED  I + NKP G+ V    G+ 
Sbjct: 60  VE---------------IPEPESIEVKPEDIPLDYLYEDHDIVIVNKPRGMVVHPAVGNY 104

Query: 125 IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L    D  G     +P + HRLD++TSG+++VA+  AA   L E  +    +
Sbjct: 105 SGTLVNALLFHCKDLSGINGEIRPGIVHRLDKDTSGVMMVAKNDAAHIGLAEQVKAHSAR 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + YW+LV G    +K  I   + +        + VV +N K    A++HFKV+  +  + 
Sbjct: 165 RTYWALVQGNIVEEKGTIKAPIGRHPK-DRMKMAVVFENSKD---AVTHFKVLARYGHQ- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E    TGRTHQ+RVH +++G P+V D  Y                 LH++ +D+ HP
Sbjct: 220 TLVECNLETGRTHQIRVHFVYIGHPVVNDPFYGYRR----MDFPIEGQALHSKSLDVKHP 275

Query: 301 -EGGRLQITAPLPAHMVKTWD 320
             G  +   AP+PA      +
Sbjct: 276 ITGEEMHFEAPVPADFKACLE 296


>gi|229552260|ref|ZP_04440985.1| pseudouridylate synthase [Lactobacillus rhamnosus LMS2-1]
 gi|258539670|ref|YP_003174169.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
 gi|229314396|gb|EEN80369.1| pseudouridylate synthase [Lactobacillus rhamnosus LMS2-1]
 gi|257151346|emb|CAR90318.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
          Length = 306

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 87/334 (26%), Positives = 146/334 (43%), Gaps = 42/334 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+    +  E+     R+D+    H        +QK L+ G V V+   VK N ++ +G 
Sbjct: 1   MSDTFTITTESG----RIDKIITAHETTHTRSQVQKWLQDGLVTVNGNPVKANFKVTAGD 56

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VV +                +     L   ++ +   ++YED ++ V NKP G+ V    
Sbjct: 57  VVTVT---------------IPEVKPLKAVAEPIPLEIVYEDDQVIVVNKPQGMVVHPAP 101

Query: 124 GIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G   H DG L + +    +        +P + HR+D++TSG+L+VA+T AA   L+   +
Sbjct: 102 G---HPDGTLVNGLLYHTKLPGINGVIRPGIVHRIDKDTSGLLMVAKTEAAQLSLSAQLK 158

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +   + Y +LV G  K  +  I   L +          V         +A++HF+V++ 
Sbjct: 159 AKTSIREYLALVHGTFKEDEGTIDAPLGRDPRDRKRQAVVA-----DGRHAVTHFQVLER 213

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F   +  ++    TGRTHQ+RVH  ++  P+ GD  Y         +   +  +LHA  +
Sbjct: 214 FT-NYTLVKCILDTGRTHQIRVHMAYIHHPVAGDPLYGPK-----RTLPGHGQFLHAAKL 267

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
              HP  G+ L  TAP+P    KT   L    D+
Sbjct: 268 GFVHPVTGKLLTFTAPVPPIFEKTLTDLRAGIDK 301


>gi|270290265|ref|ZP_06196490.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
 gi|304384921|ref|ZP_07367267.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici DSM 20284]
 gi|270281046|gb|EFA26879.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
 gi|304329115|gb|EFL96335.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici DSM 20284]
          Length = 302

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 79/330 (23%), Positives = 142/330 (43%), Gaps = 34/330 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  + + +   +    RLD+    +   +    +Q +++ GQ+ V+        +++   
Sbjct: 1   MKEINFTI--EESAKGRLDKVIAENVADLTRSQVQSLIKKGQILVNDVPTTNRYQVKPND 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V I                L   V +    + +   ++YED  + V NKP G+ V    
Sbjct: 59  QVIIK---------------LPDPVAIDVQPEKMDLDIVYEDDDVIVVNKPQGMVVHPAP 103

Query: 124 GIAY--HIDGFLKS--WVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G  +   ++G L         G+ +P + HR+D++TSG+L+VA+   A   L++  + + 
Sbjct: 104 GHDHGTLVNGLLAHTPLATINGELRPGIVHRIDKDTSGLLMVAKNDQALVSLSKQLKDKT 163

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            Q+ YW++V G  K     I   + + S      + +     +    A++HFKV++ F +
Sbjct: 164 NQRKYWAIVHGNIKEDTGTINAPIGR-SKKDRKKMAI----NEEGRPAVTHFKVLERFGE 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +E Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   
Sbjct: 219 -YTLIECQLETGRTHQIRVHLKYIGHPVAGDPLYGPR-----KTLKGNGQFLHAKLLGFK 272

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
           HP  G  +      PA    T   L    D
Sbjct: 273 HPRTGEEMVFEVDPPAIFQATLKKLRAISD 302


>gi|90021267|ref|YP_527094.1| ribosomal large subunit pseudouridine synthase C [Saccharophagus
           degradans 2-40]
 gi|89950867|gb|ABD80882.1| ribosomal large subunit pseudouridine synthase C [Saccharophagus
           degradans 2-40]
          Length = 321

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 102/329 (31%), Positives = 168/329 (51%), Gaps = 16/329 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   VQ++ V  DE   RLD +       +    + +++R G+VRV+K R K   ++  G
Sbjct: 1   MAQNVQFLTVSEDEAGQRLDNYLLARLKGVPKSLIYRVIRKGEVRVNKGRAKPERKLAGG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKH-SDFLKSILLYEDSKIYVFNKPAGISVQG 121
            VVR+PPV  A +            V ++K     L + ++ ++    V NKPAG++V G
Sbjct: 61  DVVRVPPVRVAES---------PEPVPISKTLKGVLDNAVIADEPGYLVVNKPAGLAVHG 111

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQ 180
           GSG+   +   L+           L HRLD++TSG ++VA+ R+  ++L E FR  +RI 
Sbjct: 112 GSGVTLGLIEALRQAFPQYSY-LELVHRLDRDTSGCILVAKKRSMLRYLQELFRGEKRIH 170

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G   +++  +   LL+K    G+ +  V  + K +    + F V+  F +  
Sbjct: 171 KRYLALVIGRWPSRRNLVDAPLLRKELQSGERIVRVSLDGKPSK---TEFNVVQRFGESA 227

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPH 299
             +E +P TGRTHQ+RVHA H G P+VGD KY    F  +      N+L+LHA  +   +
Sbjct: 228 TLVEARPITGRTHQIRVHAQHQGHPLVGDPKYGNEVFDLSVKKLGVNRLFLHAAGLSFKN 287

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
            +G ++ I  PLPA +     +    +++
Sbjct: 288 ADGEQVNIEVPLPAELQSVVAAFDGHFNQ 316


>gi|313903976|ref|ZP_07837356.1| pseudouridine synthase, RluA family [Eubacterium cellulosolvens 6]
 gi|313471125|gb|EFR66447.1| pseudouridine synthase, RluA family [Eubacterium cellulosolvens 6]
          Length = 311

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 146/323 (45%), Gaps = 30/323 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
              VE ++E+ R+D +  +    ++   +QKIL+ G V V+ K VK N ++         
Sbjct: 5   TFTVETEDEDTRVDAYLASQIDRMSRSYIQKILKQGGVLVNGKAVKPNYKVCEDD----- 59

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                     + +  +  +  L   ++ +   +LYED  + + NKP  + V   +G   H
Sbjct: 60  ----------RIEIEIPENEELDIEAEDIPLDILYEDDDVLIVNKPKDMVVHPAAGHYEH 109

Query: 129 I--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              +  L    D         +P + HR+D++T+G LV+ +  AA Q L     +  I +
Sbjct: 110 TLVNALLFHCRDRLSGINGVMRPGIVHRIDKDTTGALVICKNDAAHQSLAAQLAVHSITR 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G  K++   +   + + ++     + VV  ++    +A++H KV+    + + 
Sbjct: 170 RYRAIVAGNFKDETFTVEGNIGRSAN-DRKKMAVVSPDK--GKHAVTHVKVLQNL-KGYA 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           ++E +  TGRTHQ+RVH  H+G P++GD  Y                 LHA  +   HP 
Sbjct: 226 YVECELETGRTHQIRVHMAHIGHPLLGDEIYGPK---KCPVKGLQGQTLHAMVLGFQHPS 282

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
               ++ TAPLP +  +    LG
Sbjct: 283 TNEYVEFTAPLPEYFEELLRKLG 305


>gi|157363878|ref|YP_001470645.1| RluA family pseudouridine synthase [Thermotoga lettingae TMO]
 gi|157314482|gb|ABV33581.1| pseudouridine synthase, RluA family [Thermotoga lettingae TMO]
          Length = 298

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 88/319 (27%), Positives = 148/319 (46%), Gaps = 35/319 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           + VE  E N+RLD +     P  I+   +Q+ ++ G+V V+    K N R++ G VV+I 
Sbjct: 1   MTVEKSEVNLRLDLFLLQRIPKAISRSFVQRAIKEGKVTVNDVIRKPNYRVKFGDVVKIS 60

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIA 126
                         I  ++ +++   + ++  ++YED  I V NKPAG+ V         
Sbjct: 61  --------------IPSNAQSISIEPEPIQIGVIYEDEDIIVVNKPAGMIVHPIPSHNSG 106

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D KG     +P + HRLD++TSG++VVA+   A  +L+  F+ R++ K+
Sbjct: 107 TLVNALLYHCKDLKGIGGELRPGIVHRLDKDTSGVMVVAKNDFAHHNLSNQFKDRKVFKM 166

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G  ++ +  I   + +        +       +    A++H+KVI  F      
Sbjct: 167 YLALVSGKVEHLEGDIQISIARHP-----VLRTKMAASEIGRIAVTHYKVIKYFEHATLL 221

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +   P TGRTHQ+RVH   +  PI+GD  Y             ++  LHA  +   HP  
Sbjct: 222 MAF-PKTGRTHQIRVHMKCINHPILGDKLYGKGS-------GASRQMLHATKLGFYHPRT 273

Query: 303 GR-LQITAPLPAHMVKTWD 320
              ++  APLP    +T  
Sbjct: 274 HEWIEFIAPLPEDFKETIR 292


>gi|270292963|ref|ZP_06199174.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           M143]
 gi|270278942|gb|EFA24788.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           M143]
          Length = 299

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 147/324 (45%), Gaps = 34/324 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +    RLD+   +    ++     + +++GQV V+ +  K    +Q G +V      
Sbjct: 3   IKIETGGQRLDKALSD-LTELSRSLANEQIKAGQVLVNGQVKKAKYTVQEGDIVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ +   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDIPLDIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           ++ TA +P    +T + L    DR
Sbjct: 276 MEFTADIPEIFKETLERLRKNEDR 299


>gi|257875741|ref|ZP_05655394.1| pseudouridylate synthase [Enterococcus casseliflavus EC20]
 gi|257809907|gb|EEV38727.1| pseudouridylate synthase [Enterococcus casseliflavus EC20]
          Length = 302

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 82/323 (25%), Positives = 151/323 (46%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q  V+  +E+  R+D+      P+ +   +Q+ L+   V +  + V+ N ++++G  + I
Sbjct: 4   QIEVIIKEEKG-RVDKVLAERLPNHSRSQIQQWLKEDAVTLMGETVRANYKVKAGDHLII 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                     + E +++D         + +   ++Y+D+ + V NKP G+ V   +G   
Sbjct: 63  Q---------VPEPEVVDL------QPENIPLTIVYQDADVAVINKPQGMVVHPSAGHPN 107

Query: 128 --HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D        +P + HR+D++TSG+L++A+   A + L +  + +   +
Sbjct: 108 GTLVNALLYHMDDLSTINDVVRPGIVHRIDKDTSGLLMIAKNDQAHESLAKQLKDKTSLR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + S +      V+    +    A++HF V++ F Q F 
Sbjct: 168 KYVALVHGTISHEKGTINAPIGR-SKVNRKMQAVI----ENGKPAVTHFTVLERFEQ-FT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   HP 
Sbjct: 222 LVELQLETGRTHQIRVHMQYIGFPLAGDPLYGPK-----RTLKGNGQFLHAKLLGFTHPT 276

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            G  L   APLP     T   L 
Sbjct: 277 TGESLVFEAPLPELFADTLKKLR 299


>gi|254804587|ref|YP_003082808.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis alpha14]
 gi|254668128|emb|CBA04722.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis alpha14]
          Length = 374

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 139/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIIYEDDTVIVVNKPAGLVVHPAAGNWTGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T  A   L +  + R +++IY ++
Sbjct: 136 LLNGLLAHCPELSQVPRAGIVHRLDKETSGLMVVAKTLPAQNSLVQHLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y        +        +  +  LHA  +   HP
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 309

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           + G  +   AP+P  +      L  + 
Sbjct: 310 KTGETVSFEAPIPDDIYHLLSVLRLEA 336


>gi|302391670|ref|YP_003827490.1| ribosomal large subunit pseudouridine synthase D [Acetohalobium
           arabaticum DSM 5501]
 gi|302203747|gb|ADL12425.1| ribosomal large subunit pseudouridine synthase D [Acetohalobium
           arabaticum DSM 5501]
          Length = 308

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 84/332 (25%), Positives = 165/332 (49%), Gaps = 31/332 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  +  ++++++ + RLD++       ++   +QK++ +G+V V+K+  K + R+Q G 
Sbjct: 1   MSEEREYIIDDNDVDQRLDKFLAYQNEELSRSYIQKLIDNGEVTVNKEEKKNSYRLQVGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V++               I+     +    + +   ++ ED  I V NK A + V    
Sbjct: 61  EVKL---------------IIPQPEEVEIKPESIPLEVIAEDEDIVVINKQADLVVHPAP 105

Query: 124 GI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    +  G     +P + HRLD++TSG +V A+   A ++L + F+ R
Sbjct: 106 GHKQGTLVNALLYHCDNLSGINGEIRPGIVHRLDKDTSGAIVAAKNDQAHRNLVKQFKER 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           R +KIY +LV G  K+ K  I   + +  +     + V K+N   +  A++ F+V++ F 
Sbjct: 166 RTEKIYLALVEGNIKHNKAKIDAAIGRDPY-NRKRMAVTKRN---SKQAVTRFEVLERFG 221

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             + W++++  TGRTHQ+RVH  ++  P+VGD  Y  N +        ++  LHA  +  
Sbjct: 222 -NYTWVKLKLETGRTHQIRVHMSYIDNPVVGDRLYGYNKQQLNV----HRQLLHAYQLGF 276

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
            HP   + ++ TA +P+ + +  + L  + +R
Sbjct: 277 NHPRRNKWVEFTAEMPSDIKQILEKLRSEKNR 308


>gi|113868540|ref|YP_727029.1| pseudouridylate synthase, 23S RNA-specific [Ralstonia eutropha H16]
 gi|113527316|emb|CAJ93661.1| pseudouridylate synthase, 23S RNA-specific [Ralstonia eutropha H16]
          Length = 334

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 110/325 (33%), Positives = 167/325 (51%), Gaps = 21/325 (6%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V YV ++   E  R+D +       +   ++ ++LRSG+VRV+K R+    R+QSG V
Sbjct: 19  PQVAYVTIDEGSEGQRIDNFLLKVAKGVPKSHIYRVLRSGEVRVNKGRIDATYRLQSGDV 78

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+  A +          +  +  +H    +  +L+ED+++ V NKPAG++V GGSG
Sbjct: 79  VRIPPMRVANS----------AQSDNAQHVPAGEFPVLFEDAQLLVINKPAGVAVHGGSG 128

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +A+ +   L+     + +   L HRLD+ETSGILV+A+ R+A  HL E  R   + K Y+
Sbjct: 129 VAFGVIEQLRR-SRPEAKFLELVHRLDRETSGILVLAKKRSALVHLHEQIRGSAMDKRYF 187

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           + V G   N ++ +   L K S   G+    V+ +      + + F  ++ F Q F  LE
Sbjct: 188 ACVAGEFPNARQHVKLPLYKYSTPDGERRVRVQAD---GLASHTVFNRVEAF-QGFTLLE 243

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPH 299
            +  TGRTHQ+RVH  H G PIVGD KY           +   P   +++LHA  +   H
Sbjct: 244 AELKTGRTHQIRVHLAHSGFPIVGDEKYGDFSLNKALARSGARPGLKRMFLHAHRLVFIH 303

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  G  L + APLP   V     L 
Sbjct: 304 PATGEPLAVEAPLPDECVGFLQQLR 328


>gi|307293091|ref|ZP_07572937.1| pseudouridine synthase, RluA family [Sphingobium chlorophenolicum
           L-1]
 gi|306881157|gb|EFN12373.1| pseudouridine synthase, RluA family [Sphingobium chlorophenolicum
           L-1]
          Length = 316

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 145/333 (43%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     +    +   ++ MRLD+      P ++   L+ ++  GQV    +    + ++ 
Sbjct: 1   MVPGVSIIEATIGEAQDGMRLDKALAELVPDLSRERLKALIVDGQVTSSGRAPNPSLKVT 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            GQ   I                L   V     +  +   +++ED+ + V +KPAG+ V 
Sbjct: 61  MGQAFAI---------------ALPPPVEAEAVAQNIPLAIVHEDADLIVIDKPAGLVVH 105

Query: 121 GGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
             +G      ++  L              +P + HR+D++TSG+LVVA++  A + L + 
Sbjct: 106 PAAGNLDGTLVNALLHHCQGQLSGIGGVARPGIVHRIDKDTSGLLVVAKSDRAHEGLAQQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F    I ++Y ++V+G P+     + +W+ +      D   +    E    +A++H++ +
Sbjct: 166 FAAHSIDRLYAAIVYGAPQPAAGTVDSWIGRSD---ADRKKMAVCREGRGKHAVTHYRTL 222

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG---NFTSPIQNKLYL 290
           +   +    +E +  TGRTHQ+RVH   +G P++GD  Y    KG      +    +  L
Sbjct: 223 EKL-RGAALVECRLETGRTHQVRVHMTQLGHPLIGDPVYGKERKGFKSILETLGFKRQAL 281

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           HA+ +   HP  G  L   + LPA M +    L
Sbjct: 282 HAKRLGFIHPVTGEALSFDSQLPADMQELLSEL 314


>gi|294011927|ref|YP_003545387.1| ribosomal large subunit pseudouridine synthase D [Sphingobium
           japonicum UT26S]
 gi|292675257|dbj|BAI96775.1| ribosomal large subunit pseudouridine synthase D [Sphingobium
           japonicum UT26S]
          Length = 320

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 81/341 (23%), Positives = 153/341 (44%), Gaps = 42/341 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV------K 54
           M     +    +   ++ MRLD+      P ++   L+ ++  GQV    +         
Sbjct: 1   MVSGVSIIEATIGEAQDGMRLDKALAELVPDLSRERLKALIAEGQVT--GRPAHAGRSPN 58

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
            + ++ +GQ   I               +L   +     +  +   +++ED+ + V +KP
Sbjct: 59  PSMKVAAGQAFAI---------------VLPPPMEAEAVAQDIPLAIVHEDADLIVIDKP 103

Query: 115 AGISVQGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
           AG+ V   +G         + +H  G L         +P + HR+D++TSG+LVVA++  
Sbjct: 104 AGLVVHPAAGNLDGTLVNALLHHCQGRLSGI--GGVARPGIVHRIDKDTSGLLVVAKSDR 161

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           A + L + F+   I ++Y ++V+G+P+     + +W+ +      D   +    E    +
Sbjct: 162 AHEGLAQQFKAHSIDRLYAAIVYGVPQPAAGTVDSWIGRSD---ADRKKMAVHREGRGKH 218

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG---NFTS 282
           A++H++ ++   +    +E +  TGRTHQ+RVH  H+G P++GD  Y    KG      +
Sbjct: 219 AVTHYRTMERL-RGAAMVECRLETGRTHQVRVHMAHLGHPLIGDPVYGRERKGFKSILET 277

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              N+  LHA+ +   HP  G  L   + LPA M +    L
Sbjct: 278 LGFNRQALHAKRLGFIHPVTGEALSFDSKLPADMQELLSEL 318


>gi|89891672|ref|ZP_01203175.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BBFL7]
 gi|89516007|gb|EAS18671.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BBFL7]
          Length = 349

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 77/330 (23%), Positives = 145/330 (43%), Gaps = 33/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
               + +E +R+D++  N   +     +Q+ ++ G VRV+ + VK N ++++G  +R+  
Sbjct: 24  FTASDGQEPLRVDKYLMNFIENATRSKIQQSIKDGAVRVNDEVVKSNYKVKAGDHIRV-- 81

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                 H   E  ++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 82  ---LFKHPPHENLLVPEDIPLD---------IVYEDDTLVVVNKPAGMVVHPGHGNYSGT 129

Query: 128 HIDGFLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            I+  +       ++   +P L HR+D++TSG+LVVA+T  A  +L+  F  +  ++ Y 
Sbjct: 130 LINALIHHFDNLPNNSSNRPGLVHRIDKDTSGLLVVAKTEHAMSYLSAQFAAKTSEREYV 189

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++VWG    +   +   + +             +       A++H+ VI+        + 
Sbjct: 190 AIVWGNFDEQSGTVEGNIGRHPKNRLQNYVWSGEEAFKGKPAVTHWSVIEGLG-YVTMIS 248

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHA 292
            +  TGRTHQ+RVH  H+G  +  D +Y  +     TS             I  +  LHA
Sbjct: 249 CKLETGRTHQIRVHMKHIGHTLFNDERYGGDKILKGTSFTKYKQFVDNCMKILPRQALHA 308

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP   + +  +  +P  M+   + 
Sbjct: 309 KTLGFEHPVTKKWMSFSCDIPDDMMNCIEK 338


>gi|46143747|ref|ZP_00134463.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
          Length = 326

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 162/319 (50%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q      
Sbjct: 16  VQFFTISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQP----- 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  -DDVVRVPPVRVAEKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 128

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 129 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLRKKVVQKDYLAL 187

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+ +  V    +    + + F + + +A     ++  
Sbjct: 188 VRGQWQAHTKVIKAPLLKNELASGERIVRV---SEEGKPSETRFSIEERYA-NATLVKAS 243

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 244 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 303

Query: 305 LQITAPLPAHMVKTWDSLG 323
           + ITAPL   +      L 
Sbjct: 304 MLITAPLDKTLKGVLAKLR 322


>gi|307944601|ref|ZP_07659941.1| ribosomal large subunit pseudouridine synthase D [Roseibium sp.
           TrichSKD4]
 gi|307772350|gb|EFO31571.1| ribosomal large subunit pseudouridine synthase D [Roseibium sp.
           TrichSKD4]
          Length = 341

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 94/341 (27%), Positives = 156/341 (45%), Gaps = 46/341 (13%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRI 67
            + V+ D+   RLD         ++   +Q +++ G+V VD  K V+  +R+  GQ + +
Sbjct: 17  TLKVDADDHGKRLDAVLAGQIASLSRNRIQTLIKGGEVTVDGRKIVEPKHRVNEGQTLTL 76

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           L    +     + +   ++YED  + V +KPAG+ V  G+G   
Sbjct: 77  T---------------LPEPEDPDPKGENIPLSIIYEDDHLIVVDKPAGLVVHPGAGNLT 121

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-- 178
              ++  +    DS       ++P + HR+D++TSG+LVVA+T  A Q L+E F      
Sbjct: 122 GTLVNALIHHCGDSLSGIGSVKRPGIVHRIDKDTSGLLVVAKTDQAHQGLSEQFADHGKT 181

Query: 179 --IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             +++ Y +LVWG P + K  I   L + S      + VVK       +AI+ ++V + F
Sbjct: 182 GPLERAYSALVWGAPSSLKGTINANLAR-SQANRQKIAVVKT---AGRHAITRWQVKERF 237

Query: 237 AQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQ--- 285
            +K        +E +  TGRTHQ+RVH  H+G P++GD  Y A FK        P++   
Sbjct: 238 GEKDTEALASLMECRLETGRTHQIRVHMAHIGHPLIGDMDYGAGFKTKTKRLEDPLKTTI 297

Query: 286 ---NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
               +  LHA  +   HP  G  L+  +P P        +L
Sbjct: 298 NTFTRQALHAGLLAFAHPVSGETLRFESPFPTDFNALLSTL 338


>gi|255692432|ref|ZP_05416107.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           finegoldii DSM 17565]
 gi|260621900|gb|EEX44771.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           finegoldii DSM 17565]
          Length = 357

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 83/333 (24%), Positives = 149/333 (44%), Gaps = 39/333 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEGGFVMANGKPVKSSYKVKPLDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +I+   + LT         ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYENEIIPEDIPLT---------IVYEDPYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNALAWHMKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKTTKRK 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFC 241
           Y +LVWGI +  +  I   + +      D + +   ++     +A++H++V++       
Sbjct: 198 YRALVWGIVEQDEGTIIGNIARNPK---DRMQMAVMSDPTVGKHAVTHYRVLERLG-YVT 253

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLY 289
            +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +  
Sbjct: 254 LVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPRQA 313

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           LHA  +   HP  G  +  T+ LP  M +  + 
Sbjct: 314 LHAMTLGFVHPVTGEEMHFTSELPDDMTRLIEK 346


>gi|319781137|ref|YP_004140613.1| pseudouridine synthase, RluA family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317167025|gb|ADV10563.1| pseudouridine synthase, RluA family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 346

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 92/338 (27%), Positives = 155/338 (45%), Gaps = 46/338 (13%)

Query: 10  VVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
           +V + D    RLD+W      P ++   +Q ++R G V VD K +     ++  G+ V +
Sbjct: 19  LVADADAAGQRLDQWLAARLGPDMSRSRVQMLIRQGAVSVDGKLIDETKRKMAPGESVSV 78

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           +          + +   +LYED ++ V NKPAG+ V  G+G   
Sbjct: 79  T---------------MPEPEPAEPQGENIALDVLYEDDELIVINKPAGLVVHPGAGNWT 123

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--- 177
              ++  +    DS       ++P + HRLD+ETSG++VVA+T  A + L+E+F      
Sbjct: 124 GTLVNALIHHCGDSLSGIGGVRRPGIVHRLDKETSGVMVVAKTDRAHKSLSEAFADHGLT 183

Query: 178 -RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             +++ Y +LVWGIP+     +   L + +        VV +    A +A++HF V + F
Sbjct: 184 GDLERAYLALVWGIPQRPTGRVDAPLGRAA--DRVRRAVVPEGRDDARHAVTHFAVQERF 241

Query: 237 AQ------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQN- 286
            +          +E +  TGRTHQ+RVH  H+G P++GD  Y   F+        P+++ 
Sbjct: 242 GESQQEFATASMVECRLETGRTHQIRVHMAHIGHPVIGDPDYGQAFRTKANRLPEPLKSQ 301

Query: 287 -----KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
                +  LHA  +   HP     ++  APLP  M + 
Sbjct: 302 VKAFPRQALHAWLLAFRHPTTHLTMRFEAPLPRDMEEL 339


>gi|104774018|ref|YP_618998.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103423099|emb|CAI97824.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
          Length = 303

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 150/325 (46%), Gaps = 34/325 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   +  +E   RLD++       ++   +++++++G++ V+ K+ K + ++Q   ++++
Sbjct: 3   REYELTAEESGQRLDKYLAGEMTDLSRSRIKELVQAGEILVNGKKSKVSYKVQKDDLIQV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                          I+     L   ++ +   ++YED  + V NKP G+ V   +G   
Sbjct: 63  ---------------IVLPLEPLKLEAENIPLDIVYEDKDVIVVNKPQGMVVHPAAGHPS 107

Query: 128 HI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H   +  L    D     +G +P + HR+D++TSG+L+VA+  AA + L +    +  ++
Sbjct: 108 HTLVNALLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G    ++  I   + +          V K        A++HFKV++ + Q + 
Sbjct: 168 QYLAIVHGNFA-EEGTIDAPIGRNPKDRKQMAVVEK-----GKSAVTHFKVLEQY-QGYS 220

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +    P 
Sbjct: 221 LVECQLETGRTHQIRVHMAYIGHPLAGDPLYGPR-----KTLPGHGQFLHAKTLGFEQPS 275

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            G  L+ +   P    +T   L  K
Sbjct: 276 TGEWLEFSVQPPEIFQQTVADLRKK 300


>gi|187928999|ref|YP_001899486.1| pseudouridine synthase [Ralstonia pickettii 12J]
 gi|309782614|ref|ZP_07677336.1| ribosomal large subunit pseudouridine synthase D [Ralstonia sp.
           5_7_47FAA]
 gi|187725889|gb|ACD27054.1| pseudouridine synthase, RluA family [Ralstonia pickettii 12J]
 gi|308918589|gb|EFP64264.1| ribosomal large subunit pseudouridine synthase D [Ralstonia sp.
           5_7_47FAA]
          Length = 370

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 86/335 (25%), Positives = 144/335 (42%), Gaps = 32/335 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +       RLD+      P  +   LQ+ + +G VR+  + V+    I  G  + + P
Sbjct: 53  IEIPETMHGERLDKALAKLLPDYSRSRLQQWIDAGAVRLRGEVVRPRAAISGGDRIEVVP 112

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
              A      E   +   ++L          ++YED  + V NKPAG+ V   +G     
Sbjct: 113 QRAAD-----ENAFVAEPIDLD---------VVYEDDTLLVINKPAGLVVHPAAGNWSGT 158

Query: 128 HIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  + D+ +  +  + HRLD++TSG++VVART  A   L    + R +++ Y +L
Sbjct: 159 VLNGLLHRYPDAVELPRAGIVHRLDKDTSGLMVVARTLPAQTDLVRQLQARTVKRTYLAL 218

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWL 243
           VWG    ++  I   + +      D   +          A +HFK +D           +
Sbjct: 219 VWGE-TPEEATIDAPIGRDP---RDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLV 274

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLHARYMD 296
             Q  TGRTHQ+RVH    G P++GD  Y  NF+      I+        +  LHA  + 
Sbjct: 275 RCQLETGRTHQIRVHFESEGHPLLGDPVYTRNFRRGQPQTIKAQLPVPFTRQALHAVRLG 334

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           L HP  G+ +   A +P       ++L    D ++
Sbjct: 335 LVHPASGKSVHWEAGVPDDFADLLEALDLDPDADV 369


>gi|116253506|ref|YP_769344.1| ribosomal large subunit pseudouridine synthase D [Rhizobium
           leguminosarum bv. viciae 3841]
 gi|115258154|emb|CAK09255.1| putative ribosomal large subunit pseudouridine synthase D
           [Rhizobium leguminosarum bv. viciae 3841]
          Length = 341

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 83/345 (24%), Positives = 156/345 (45%), Gaps = 45/345 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           + V+  ++    RLD W         +   ++ +++ GQV +  + V     ++++G   
Sbjct: 12  RKVLTADETAEGRLDAWLTAQVGEEFSRSRIKALIKDGQVLLRGEPVTDPQRKVRTGDSF 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +                L    + T   + +   +L+ED  + V +KP+G+ V  G+G 
Sbjct: 72  ELT---------------LPEPEDPTPQGEDIPLDILHEDDDVIVISKPSGLVVHPGAGN 116

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  +    D+       ++P + HRLD++T+G++VVA+   A +HL+  F    
Sbjct: 117 WTGTLVNALIHHCSDTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHG 176

Query: 179 ----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y ++VWG P+     +   L + +        V + + + A+ AI+H++VI+
Sbjct: 177 RTMPLERAYQAIVWGRPRTLSGTVDAPLGRATG-DRTRRAVKRPDSQDADEAITHYQVIE 235

Query: 235 CFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
            F +K         +E +  TGRTHQ+RVH  H+G P++GD  Y A FK       +   
Sbjct: 236 RFHEKPDATAFASLVECRLETGRTHQIRVHMAHIGHPLLGDTVYGAGFKTKANLLPEEIR 295

Query: 286 ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                  +  LHA  +   HP  G  +    PLP  MV+  ++L 
Sbjct: 296 KVVNGFGRQALHAFMLQFEHPRTGEIMHFEVPLPDDMVELVEALR 340


>gi|219849171|ref|YP_002463604.1| pseudouridine synthase, RluA family [Chloroflexus aggregans DSM
           9485]
 gi|219543430|gb|ACL25168.1| pseudouridine synthase, RluA family [Chloroflexus aggregans DSM
           9485]
          Length = 310

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 88/321 (27%), Positives = 152/321 (47%), Gaps = 32/321 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + ++V ++    R+DR+     P ++   +Q+++  G V    +  + +  +  G ++ +
Sbjct: 15  RELIVPSEASGQRIDRFLAASMPDLSRTQVQRLIEQGMVLYAGRPTRASQPLHPGTIIHV 74

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                           +   V +    + +   ++YED+ + V NKPAG+ V    G   
Sbjct: 75  T---------------IPPPVPVELMPESIPLDIVYEDADVAVINKPAGMVVHPAPGHPR 119

Query: 126 AYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++  L  + D   S   +P + HRLD++TSG+LV+AR  AA + L E  + RR++KI
Sbjct: 120 GTLVNALLARYPDLAISGEVRPGIVHRLDRDTSGLLVIARHDAALRALVEQQQARRMRKI 179

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G P      I   + +        + VV         A +H++VI  F   +  
Sbjct: 180 YQALVVGRPP-VCGTIDAPIGRDPR-DRLRMAVVA----DGRPARTHYRVIATFGD-YSL 232

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           LE+Q  TGRTHQ+RVH  H+G PIVGD  Y        +     + +LHA  +   HP  
Sbjct: 233 LEVQLETGRTHQIRVHLRHLGYPIVGDPVYGPRR----SHLRLTRQFLHAGQLGFFHPRD 288

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
           G+  + TAPLP+ +    +++
Sbjct: 289 GQWREFTAPLPSDLSSVLNAM 309


>gi|260438385|ref|ZP_05792201.1| ribosomal large subunit pseudouridine synthase D [Butyrivibrio
           crossotus DSM 2876]
 gi|292808971|gb|EFF68176.1| ribosomal large subunit pseudouridine synthase D [Butyrivibrio
           crossotus DSM 2876]
          Length = 316

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 82/335 (24%), Positives = 155/335 (46%), Gaps = 40/335 (11%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPH----INFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
             +  + ++  +E  R+D++  +         +   +QK++ +G V V+ K  K   +I 
Sbjct: 7   EDIIELNIDKTQEGERIDKFLSDMLSSDERTYSRSYIQKLIEAGNVCVNDKNTKTGYKIS 66

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
              ++++        +I+ E   LD               ++YED  I + NKP G+ V 
Sbjct: 67  YNDLIKVMIPYLEDINIVAENIPLD---------------IVYEDDDIILVNKPKGMVVH 111

Query: 121 GGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
             +G         + YH    L     +   +P + HR+D++T+GI+V  +  AA   L+
Sbjct: 112 PSAGHYTGTLVNALMYHCSNNLSGI--NGVMRPGIVHRIDKDTTGIIVACKNDAAHISLS 169

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           E  +   I + Y+++     K K+  +   + +   +    + +   N K    A++H++
Sbjct: 170 EQLKEHNITRYYYAICHNCFKEKEGTVDAPIGRH-PVERKKMAI---NYKNGKKAVTHYE 225

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V++ F + F +++ +  TGRTHQ+RVH   +  P++GD+ YC N K  F    Q    LH
Sbjct: 226 VLENF-RNFAYIKCKLETGRTHQIRVHMASISHPLLGDNVYC-NAKCPFELEGQT---LH 280

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           A  +   HP  G+ ++ +APLP +  K  D L  +
Sbjct: 281 AGVLGFIHPRTGKYMEFSAPLPEYFEKILDILRNR 315


>gi|332361351|gb|EGJ39155.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1056]
          Length = 298

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 146/322 (45%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E+     RLD+        ++     + ++ G++ V+ +  K    ++ G V+   
Sbjct: 2   EVRIESSVAGQRLDKAVAE-LTDLSRSLANEQIKDGRILVNGQVKKAKYAVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++         + +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELPEPEVVE------YVPEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-YSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA +PA   +T + L 
Sbjct: 275 GEVLEFTAEVPAVFQETLEKLR 296


>gi|171778236|ref|ZP_02919442.1| hypothetical protein STRINF_00281 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171282936|gb|EDT48360.1| hypothetical protein STRINF_00281 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 298

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 139/315 (44%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++       ++ G V V+ K VK    ++ G VV          
Sbjct: 7   EAGARLDKALAD-LTDLSRSQANDEIKKGTVLVNGKAVKAKYAVKVGDVVT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFL 133
           + + E+++L+        ++ +   ++YED  + V  KP G+ V   +G      ++  +
Sbjct: 57  YEVPEEEVLE------YKAENIPLDIVYEDEDVAVVYKPQGMVVHPSAGHTSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++V G
Sbjct: 111 YHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDTAHNALAAELKDKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +            K        A++HFKV++ F   +  +E+   T
Sbjct: 171 NIPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTHFKVLERFG-NYTLVELTLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   HP+ G  +  T
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLKGNGQFLHAQTLGFTHPKTGETMTFT 279

Query: 309 APLPAHMVKTWDSLG 323
           A +P    +T + L 
Sbjct: 280 AEVPVIFKETLEKLR 294


>gi|148654435|ref|YP_001274640.1| RluA family pseudouridine synthase [Roseiflexus sp. RS-1]
 gi|148566545|gb|ABQ88690.1| ribosomal large subunit pseudouridine synthase D [Roseiflexus sp.
           RS-1]
          Length = 316

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 149/327 (45%), Gaps = 29/327 (8%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   V ++VVE   E  RLDR+  +H P ++    Q+++ + QV ++ ++ + +  + +G
Sbjct: 1   MSAEVLHLVVEAANEGDRLDRYVADHVPDLSRTYAQRLIEAAQVLLNNRQARPSTPVHAG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V +                L +   +   ++ L   ++YED  + V +KPA + V   
Sbjct: 61  DTVTVH---------------LPAPQPVGLVAEPLPLQIVYEDRDVVVIDKPASMVVHPA 105

Query: 123 SGIA--YHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G      ++  +  + +   +   +P + HRLD++TSG+LV AR   A + L    + R
Sbjct: 106 PGHDRGTLVNALIARYPEMAINGDMRPGIVHRLDRDTSGLLVAARNERALRSLQAQQQAR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + KIY ++V G     +  I   + +        + VV     G   A +H++V++   
Sbjct: 166 TMLKIYLAVVEGRMPELEGVIDAPIARH-PTDRVRMAVVA----GGRPARTHWRVLEDLG 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E +  TGRTHQ+RVH      PI+GD  Y         +    + +LHA  +  
Sbjct: 221 E-YTLIEARLETGRTHQIRVHCASRNRPILGDPLYGPKRPR--ATFGLTRQFLHAHRLGF 277

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
             P GG  ++ T+PLPA +      L 
Sbjct: 278 KLPSGGEWVEFTSPLPADLEAALARLR 304


>gi|260101276|ref|ZP_05751513.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           helveticus DSM 20075]
 gi|260084917|gb|EEW69037.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           helveticus DSM 20075]
          Length = 306

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 148/329 (44%), Gaps = 35/329 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  M     + VEN+    RLD++     P ++   ++++++  ++ V+ K  K + +IQ
Sbjct: 1   MIKMPKKYELQVENEYG--RLDKFISEQIPDLSRTRVKELVKEKEILVNHKVEKVSYKIQ 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  + I         ++ E   LD               ++YED  + V NKP G+ V 
Sbjct: 59  AGDKIEINVPAVKPLDVVPENIPLD---------------IVYEDEVVIVVNKPQGMVVH 103

Query: 121 GGSGIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G   H   +  L    D     +G +P + HR+D++TSG+L++A+   A + L +  
Sbjct: 104 PAPGHPDHTLVNALLYHTQDLAQSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQL 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             +  ++IYW++V G    +   I   + +  +       V     +    A++HFKV+ 
Sbjct: 164 AHKTNKRIYWAIVHGNFGEENGVIDAPIGRNLYDRKKMAVV-----ENGKKAVTHFKVLK 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F + +  +E Q  TGRTHQ+RVH  ++G  + GD  Y         +   N  +LHA+ 
Sbjct: 219 QF-KGYSLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPR-----KTLKGNGQFLHAKV 272

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP  G+ L+ T   P     T   L
Sbjct: 273 LGFKHPRTGKWLEFTVEPPKIFQDTLAQL 301


>gi|322515396|ref|ZP_08068389.1| ribosomal large subunit pseudouridine synthase C [Actinobacillus
           ureae ATCC 25976]
 gi|322118578|gb|EFX90808.1| ribosomal large subunit pseudouridine synthase C [Actinobacillus
           ureae ATCC 25976]
          Length = 356

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 166/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  + +DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q      
Sbjct: 46  VQFFTISDDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQEND--- 102

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 103 ---VVRVPPVRVAEKNEAPISTKLNKVAE-LEQQILYEDDVMLVINKPSGIAVHGGSGLS 158

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A ++L E  R + +QK Y +L
Sbjct: 159 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRNLHEQLREKVVQKDYLAL 217

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+ +  V    +    + + F + + +A     ++  
Sbjct: 218 VRGQWQSHVKVIRAPLLKNELASGERIVKV---SEEGKLSETRFAIEERYA-NATLVKAS 273

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +   ++L+LHA  +   HP+ G  
Sbjct: 274 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAVGLHRLFLHAYSIRFEHPKTGEE 333

Query: 305 LQITAPLPAHMVKTWDSLG 323
           + ITAPL   +      L 
Sbjct: 334 MLITAPLDKTLKGVLAKLR 352


>gi|125717901|ref|YP_001035034.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK36]
 gi|125497818|gb|ABN44484.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Streptococcus sanguinis SK36]
 gi|327474176|gb|EGF19586.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK408]
          Length = 298

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 146/322 (45%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E      RLD+        ++     + ++ G++ V+ +  K    ++ G V+   
Sbjct: 2   EVRIEASVAGQRLDKAVAE-LTDLSRSLANEQIKDGRILVNGQAKKAKYAVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++        ++ +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELPEPEVVE------YVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIQDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-YSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA +PA   +T + L 
Sbjct: 275 GEVLEFTAEVPAIFQETLEKLR 296


>gi|311104735|ref|YP_003977588.1| ribosomal large subunit pseudouridine synthase C [Achromobacter
           xylosoxidans A8]
 gi|310759424|gb|ADP14873.1| ribosomal large subunit pseudouridine synthase C [Achromobacter
           xylosoxidans A8]
          Length = 325

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 93/318 (29%), Positives = 154/318 (48%), Gaps = 20/318 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V V+ ++   RLD +       +   ++ K +R G+VR++K R   + R+  G VVR
Sbjct: 23  VRMVEVDAEQAGQRLDNFLARLCKGVPKTHIYKAIRGGEVRINKGRTSADYRVAEGDVVR 82

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+                     +     +  +++ED  + V +KPAG++V GGSG++
Sbjct: 83  IPPLRL-------------PDPGKPRPVPGAEFPVVFEDEALLVVDKPAGVAVHGGSGVS 129

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++      +   L HRLD+ETSG+L+VA+ R+A   L    R  +  K Y +L
Sbjct: 130 FGVIEQLRAARPG-AKFLELVHRLDRETSGLLMVAKKRSALLALHAMLREGKGDKHYLAL 188

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   N ++ I   L K +   G+    V  + + A+  ++    +      +  ++ +
Sbjct: 189 VEGDWVNDRQHIKLGLSKWTTQSGERRVKVDPDGQSAHTIVT----LKQRLGGYSLVDAE 244

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
             TGRTHQ+RVH    G PIVGD KY  +  +  F      +++LHA  + L HP  G  
Sbjct: 245 LRTGRTHQIRVHLAASGFPIVGDDKYGRDEVRAEFARMGFGRMFLHAHQLTLAHPVTGEP 304

Query: 305 LQITAPLPAHMVKTWDSL 322
           L +TA LP    +    L
Sbjct: 305 LTLTAELPPACRQILKQL 322


>gi|221633017|ref|YP_002522242.1| pseudouridine synthase, RluA family [Thermomicrobium roseum DSM
           5159]
 gi|221156507|gb|ACM05634.1| pseudouridine synthase, RluA family [Thermomicrobium roseum DSM
           5159]
          Length = 322

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 86/320 (26%), Positives = 150/320 (46%), Gaps = 29/320 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +   E   RLD+   +    ++   +Q++++ G + V+ +  K   R++ G  + +  
Sbjct: 13  LQISEREHGERLDKLIASRVTGMSRSFVQQLMKRGAILVNGEPCKPAQRVRYGDRLEVY- 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                        +           +FL   ++YED  I VF+KP GI      G  +  
Sbjct: 72  -------------LPPVEPPTDLEPEFLPIPVIYEDDDIIVFDKPPGIVTHPAPGHEHGT 118

Query: 129 IDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   LK+           +P + HRLD++TSG+LVVA+T AA   L E ++ R + K Y 
Sbjct: 119 LVNALKAIRPDLQVQPSHRPGIVHRLDKDTSGLLVVAKTEAARLALLEQWQSRSVVKKYT 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+ +     I   + +   +    + VV         AI+HF+V++ F +    L+
Sbjct: 179 ALVHGVVEPDSGTIDAPISRD-PVERTKMAVVSW----GRPAITHFRVLERF-RCATLLD 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TGRTHQ+RVH   +G P+VGD +Y  +       P   + +LHARY+   HP  G+
Sbjct: 233 VTIETGRTHQIRVHCAFIGHPVVGDSQYGGHRPFCVPVP---RQFLHARYLRFVHPTTGQ 289

Query: 305 -LQITAPLPAHMVKTWDSLG 323
            +++  PLP  +    ++L 
Sbjct: 290 AIELETPLPYDLRTVLEALR 309


>gi|237748962|ref|ZP_04579442.1| ribosomal large subunit pseudouridine synthase D [Oxalobacter
           formigenes OXCC13]
 gi|229380324|gb|EEO30415.1| ribosomal large subunit pseudouridine synthase D [Oxalobacter
           formigenes OXCC13]
          Length = 342

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 78/316 (24%), Positives = 139/316 (43%), Gaps = 35/316 (11%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +   RLD+         +   LQ+ +  G + V+ ++ +    +   + + + P +   +
Sbjct: 37  DGGQRLDKLVAGRLSQYSRSRLQRWIEDGHITVNGEKAQAKQTVIGDEEICVIPQLAEED 96

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                         L    + +   +++ED+ I V NKPA + V   +G   +  G L +
Sbjct: 97  --------------LAFTPEAVDFPVVFEDNAILVVNKPASLVVHPAAG---NWSGTLLN 139

Query: 136 ---WVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              + D K     +  + HRLD+ETSG++VVA+T  A   L    + R +++ Y +LVWG
Sbjct: 140 GLLYRDPKSATVPRAGIVHRLDKETSGVMVVAKTIEAQTDLVRQLQARTVKREYLALVWG 199

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQKFCWLEMQ 246
               +   I   + +      D V +   + +    A++HF+ I    C       ++ +
Sbjct: 200 -DTPQSGTIDEPIGRHP---RDRVKMAVIHTQSGKPAVTHFRKIAEGVCNNMNVSLVKCR 255

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL- 305
             TGRTHQ+RVH   +G P+VGD  Y  +   +    +  +  LHA  + L HP    + 
Sbjct: 256 LETGRTHQIRVHLQSIGFPLVGDPVYGKSHLAS----VFPRQALHAFRLGLIHPCTKEVC 311

Query: 306 QITAPLPAHMVKTWDS 321
           + TAPLP  M    + 
Sbjct: 312 EWTAPLPQDMKALLEQ 327


>gi|331266599|ref|YP_004326229.1| 23S rluA family pseudouridine synthase [Streptococcus oralis Uo5]
 gi|326683271|emb|CBZ00889.1| 23S rluA family pseudouridine synthase [Streptococcus oralis Uo5]
          Length = 299

 Score =  264 bits (676), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 147/324 (45%), Gaps = 34/324 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +    RLD+        ++     + +++GQV V+ +  K    +Q G +V      
Sbjct: 3   IKIETGGQRLDKALSE-LTELSRSLANEQIKAGQVLVNGQAKKAKYTVQEGDIVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ +   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F+V++ F   +  LE+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFQVLERFGD-YSLLEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           L+ TA +P    +T + L    +R
Sbjct: 276 LEFTADIPEIFKETLERLRKTENR 299


>gi|160885528|ref|ZP_02066531.1| hypothetical protein BACOVA_03528 [Bacteroides ovatus ATCC 8483]
 gi|260172152|ref|ZP_05758564.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D2]
 gi|293371714|ref|ZP_06618125.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|299147380|ref|ZP_07040445.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_23]
 gi|315920461|ref|ZP_07916701.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D2]
 gi|156109150|gb|EDO10895.1| hypothetical protein BACOVA_03528 [Bacteroides ovatus ATCC 8483]
 gi|292633411|gb|EFF51981.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|298514658|gb|EFI38542.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_23]
 gi|313694336|gb|EFS31171.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D2]
          Length = 357

 Score =  264 bits (676), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 82/333 (24%), Positives = 150/333 (45%), Gaps = 39/333 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +I+  ++ LT         ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYENEIIPENIPLT---------IVYEDPYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNALAWHMKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRK 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFC 241
           Y +LVWG+ +  +  I   + +      D + +   ++     +A++H++V++       
Sbjct: 198 YRALVWGVMEQDEGTIVGNIARNP---RDRMQMAVMSDPTVGKHAVTHYRVLERLG-YVT 253

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLY 289
            +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +  
Sbjct: 254 LVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPRQA 313

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           LHA  +   HP  G  +  T+ LP  M +  + 
Sbjct: 314 LHAMTLGFVHPVTGEEMYFTSELPDDMTRLIEK 346


>gi|291533845|emb|CBL06958.1| ribosomal large subunit pseudouridine synthase D [Megamonas
           hypermegale ART12/1]
          Length = 304

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 143/322 (44%), Gaps = 33/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +  DE   RLD +      + +  ++QK++  G + V+ +  + N ++++   + 
Sbjct: 2   IKTYTIS-DEIGTRLDVFLAGQEDNPSRASIQKMITDGAITVNNQVKRANYKLKANDQIT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +               + +    +    + +   +LYED+ I V NK  G+ V   +G+ 
Sbjct: 61  M---------------VFEPPTEIEVKPENIPLDILYEDNDIIVINKARGMVVHPAAGVY 105

Query: 126 -AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  L    D         +P + HRLD++TSG++VVA+   A   L      +  
Sbjct: 106 SGTLVNALLYHCHDELSGINGKIRPGIVHRLDKDTSGVMVVAKNDFAHNDLALQIGSKTA 165

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G    +K  I N  + +  I    + VV     G   A + F V++ + + 
Sbjct: 166 IKEYVALVHGNITEEKGII-NGNIGRHPIDRKKMAVVT---NGGKPATTVFHVLERY-KN 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
             +++ +  TGRTHQ+RVH  ++G P++GD KYC N K  F         LH+  + + H
Sbjct: 221 CTFVQCRLLTGRTHQIRVHMAYIGHPLIGDPKYC-NSKNKFN---IEGQALHSLNLKIIH 276

Query: 300 PEG-GRLQITAPLPAHMVKTWD 320
           P     +  TAP+P  M     
Sbjct: 277 PRTKEEMTFTAPIPEDMENLLK 298


>gi|269836533|ref|YP_003318761.1| pseudouridine synthase, RluA family [Sphaerobacter thermophilus DSM
           20745]
 gi|269785796|gb|ACZ37939.1| pseudouridine synthase, RluA family [Sphaerobacter thermophilus DSM
           20745]
          Length = 313

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 90/332 (27%), Positives = 156/332 (46%), Gaps = 33/332 (9%)

Query: 3   LMTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           LM     +V  V  +E+  RLDR        I+    Q ++++G V V+ +  +   RI 
Sbjct: 5   LMEDAVRIVLDVAAEEDGERLDRLIAARVAEISRSYAQSLVKAGDVYVNGEPARPARRIH 64

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + I               +           +++   ++YED  + +F+KPAG+   
Sbjct: 65  EGDTIEI--------------LLPPVPEPDDLTPEYIPVPVIYEDDDVIIFDKPAGLVTH 110

Query: 121 GGSGIAY-HIDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G  +  +   +K+          G++P + HRLD++TSG++VVA+   A ++L + +
Sbjct: 111 PAPGHEHGTLVNVVKALRPDVPLLMGGKRPGIVHRLDKDTSGLIVVAKNEEARRYLVQQW 170

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R + K Y +LV G+ +  +  I   + +        + VV         A++HF+V++
Sbjct: 171 QQRDVVKRYIALVHGVIRENEGTIDAPISRDPR-NRKRMAVV----PNGRPAVTHFRVLE 225

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F +    L +Q  TGRTHQ+RVH L +G PIVGD  Y       F  PI  + +LHA Y
Sbjct: 226 RF-RDATLLNVQIETGRTHQIRVHMLFIGHPIVGDQMYGKRP---FRIPIA-RQFLHASY 280

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +    PE GR +++   LPA + +  + L  +
Sbjct: 281 LKFSLPESGRPIEVETALPADLREVLERLRAE 312


>gi|169350183|ref|ZP_02867121.1| hypothetical protein CLOSPI_00927 [Clostridium spiroforme DSM 1552]
 gi|169292966|gb|EDS75099.1| hypothetical protein CLOSPI_00927 [Clostridium spiroforme DSM 1552]
          Length = 306

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 148/326 (45%), Gaps = 34/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  +V   +  N RLD+    +   ++   +Q+++  G V V+ K  K + + +   
Sbjct: 1   MEKINLLV--ENNNNYRLDKIIALNMEELSRTQIQEMIGRGLVLVNGKVEKASYKTKLND 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I                ++ + +L   ++ +   ++YED  + V +KP G+ V    
Sbjct: 59  QIEIT---------------IEDNSDLEIEAEDIPLNVVYEDKDVIVIDKPTGMIVHPSP 103

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           GI     ++  L    D  G     +P + HR+D+ETSG+L+VA+   A + L+E  +  
Sbjct: 104 GITSGTLVNALLFHCKDLSGINGVNRPGIVHRIDKETSGLLMVAKNDIAHRFLSEQLKDH 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G+  + +  I   + +  +     + V K N K    AI++F V+  + 
Sbjct: 164 SVTRRYVALVHGLIPHVQGKIDAPIGRNPN-DRQSMCVTKNNSKN---AITNFTVLKRY- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    +E +  TGRTHQ+RVH  ++G P+ GD KY             +  +LHA+ +  
Sbjct: 219 KNMSLIECRLETGRTHQIRVHMSYIGYPVYGDPKYGYRKDD-----CSHGQFLHAKKLGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP     ++  + LP +     D L
Sbjct: 274 IHPTTKEYMEFESELPDYFKAKLDEL 299


>gi|332360785|gb|EGJ38592.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK355]
          Length = 298

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 77/322 (23%), Positives = 145/322 (45%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E      RLD+        ++     + ++ GQ+ V+ +  K    ++ G VV   
Sbjct: 2   EVRIEASIAGQRLDKAVAE-LTDLSRSLANEQIKDGQILVNGQAKKAKYAVKEGDVV--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++        ++ +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELSEPEVVE------YVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHAALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-YTL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA  PA   +T D L 
Sbjct: 275 GEVLEFTAEAPAIFQETLDKLR 296


>gi|313901079|ref|ZP_07834567.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
 gi|312954037|gb|EFR35717.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
          Length = 304

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 76/327 (23%), Positives = 150/327 (45%), Gaps = 34/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++ ++   ++   R+D++       ++   +Q +L  G + V++  VK N ++++  
Sbjct: 1   MREIK-IIAAAEDAGARIDKYISEQ-EDLSRSRVQALLAEGSILVNQNAVKANYKVKADD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +                 + +  + +    + ++  + YED  + V NKP  I V   +
Sbjct: 59  CIT---------------AVFNDEMEMEARPEKMELDVRYEDEDVIVINKPKNIVVHPAA 103

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G L    D  G     +P + HR+D++T+G+L++A+   A   L++  + +
Sbjct: 104 GNQSGTLVNGLLYHCKDLSGINGTLRPGIVHRIDKDTTGLLIIAKNDLAHASLSKQLQSK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + ++Y++LV G+ ++    I   + +        + V   N K A    +HF+VI+ F 
Sbjct: 164 TVNRLYYALVHGVIQHDFGTIDAPIGRDVK-DRQKMAVTATNSKDAR---THFQVIERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E +  TGRTHQ+RVH  ++G P+VGD KY         +   N   LHA  +  
Sbjct: 219 ENYTLVECRLETGRTHQIRVHMQYIGHPVVGDEKYSYR-----KTMQTNGQLLHAHQLTF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  + + A LP       + L 
Sbjct: 274 QHPRTGEVMTVEAELPKQFADILEELR 300


>gi|291519437|emb|CBK74658.1| ribosomal large subunit pseudouridine synthase D [Butyrivibrio
           fibrisolvens 16/4]
          Length = 305

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 80/324 (24%), Positives = 143/324 (44%), Gaps = 35/324 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     ++ E  +E +R+D++     P  +    QK + +G V V+ K++K   + + G 
Sbjct: 1   MDEFTIIIEEPSDEGIRIDKYLAAALPEKSRSYYQKAIDNGFVLVNGKQIKSKYQTKLGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I+ E   +D               +LYEDS + V NKP G+ V    
Sbjct: 61  EIIVSIEPVKEIDILPEDIPID---------------ILYEDSDVIVVNKPKGMVVHPAP 105

Query: 124 GI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  +    DS        +P + HR+D  T+G L+V +   A   +    ++
Sbjct: 106 GHYSGTLVNALMYHCKDSLSGINGEIRPGIVHRIDMNTTGSLLVCKNDKAHNDIAAQIKV 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + +IY  +V G  K ++  I   + +        + VV         AI+H+ V++ +
Sbjct: 166 HSVNRIYKGIVVGNFKEEEGTINANIGRNPK-DRKKMAVVS----DGREAITHYTVLEQY 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F +++ +  TGRTHQ+RVH  H+G P++GD  Y    KG           LHA+ + 
Sbjct: 221 -KGFSYVQFKLETGRTHQIRVHMAHIGHPLLGDDVYGKPVKG------LEGQTLHAQTLG 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTW 319
              P  G  +++ APLPA+  +  
Sbjct: 274 FVQPTTGEYVEVNAPLPAYFEELL 297


>gi|302035761|ref|YP_003796083.1| 23S rRNA pseudouridine synthase [Candidatus Nitrospira defluvii]
 gi|300603825|emb|CBK40157.1| 23S rRNA pseudouridine synthase [Candidatus Nitrospira defluvii]
          Length = 321

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 151/326 (46%), Gaps = 30/326 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            +VV   E + R+D +  N  P  +   LQ+++  G++ ++ + ++ + +I+ G  +R+ 
Sbjct: 10  EIVVTGGESSKRIDVFLANRDPTFSRSALQRLIGEGRILINGQTIRPSQKIKPGDRIRLE 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                          +     L    + +   +L+ED+++ V +KPAG+ V    G    
Sbjct: 70  ---------------VPRPEPLDLKPEAIPFDILHEDAELLVLHKPAGLVVHPAPGNWSG 114

Query: 127 YHIDGFLKSWVDSK--------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             ++  L  +  S          ++P L HRLD+ETSG++V+A+T  A + L   F++  
Sbjct: 115 TLVNALLHHFATSGVTPSHIGGKERPGLVHRLDKETSGVMVIAKTDQAHRALAAQFKLHT 174

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I ++Y +L+WG+PK     I   + + +     +     +       + + ++V + + +
Sbjct: 175 ITRVYEALIWGVPKKGHGLIELAIGRDTKERKKFSARTTKP----KPSATDYQVEERYGK 230

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              ++ + P TGRTHQLRVH   +  PI+GD  Y      +       ++ LHAR +   
Sbjct: 231 IAAYVRLFPRTGRTHQLRVHLTSIDHPILGDKTYGGAKVMSVAGVTIPRVMLHARTLGFT 290

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP GG   +   P P  M +  D L 
Sbjct: 291 HPNGGEYHEFDVPCPPDMEQVQDLLR 316


>gi|331269364|ref|YP_004395856.1| RluA family pseudouridine synthase [Clostridium botulinum
           BKT015925]
 gi|329125914|gb|AEB75859.1| pseudouridine synthase, RluA family [Clostridium botulinum
           BKT015925]
          Length = 304

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 84/326 (25%), Positives = 151/326 (46%), Gaps = 38/326 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            +  ++  +  N RLD +  N     +   +QK+++ G V+V+ K  K N +++    V 
Sbjct: 3   TKEFIIHENLVNCRLDLFISNSLEGKSRSYIQKLIQEGHVKVNGKDKKSNYKLKLHDSVV 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---- 122
           +       N+I KE K +        + + ++  +LYED+ I V NK  G+ V       
Sbjct: 63  V-------NNIEKEDKKI--------NPENIEMDILYEDNDIIVINKSQGMVVHPATSNY 107

Query: 123 -----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                + + YH D  L +  D    +P + HR+D++TSG+LVVA+   A + L E  +  
Sbjct: 108 SGTLVNALLYHCD-TLSTLNDDT--RPGIVHRIDKDTSGVLVVAKNNKAHEILAEQLKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y ++V GI K +   +   L +          V     +G   A++H++V+  F 
Sbjct: 165 SMKREYIAVVEGIVKEENGLVDEPLGRNPKDRIKMAVV-----EGGKNAVTHYEVLKRFK 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    ++    TGRTHQ+RVH  ++G P+VGD  Y    +        N   LHA+ +  
Sbjct: 220 KN-TLVKCILETGRTHQIRVHMSYIGHPLVGDPMYGFKKQ----RFKLNGQMLHAKKLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP   + ++  + LP +  +    L
Sbjct: 275 IHPTTEKYIEFESDLPQYYKEILLKL 300


>gi|120437019|ref|YP_862705.1| ribosomal large subunit pseudouridine synthase D [Gramella forsetii
           KT0803]
 gi|117579169|emb|CAL67638.1| ribosomal large subunit pseudouridine synthase D [Gramella forsetii
           KT0803]
          Length = 354

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 75/330 (22%), Positives = 145/330 (43%), Gaps = 33/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V E  +  +R+D++  N   +     +QK  +SG + V+   VK N +++ G  V++  
Sbjct: 26  FVAEVGQNPLRVDKYLMNFIENATRNKIQKAAKSGNIYVNGDTVKQNYKVKGGDTVQVMF 85

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                 +++                + +   ++YED  + V NK AG+ V  G G     
Sbjct: 86  EHPPYEYLL--------------VPEDIPLDIVYEDDTLLVVNKQAGMVVHPGHGNYSGT 131

Query: 128 HIDGFLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            I+  +       ++   +P L HR+D++TSG+LVVA+T  A  HL++ F  +  ++ Y 
Sbjct: 132 LINALVHHFDNLPNNSSDRPGLVHRIDKDTSGLLVVAKTEEAMAHLSKQFFDKSSEREYV 191

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++VWG    ++  I   + +        +     + +    A++H+KV++        + 
Sbjct: 192 AIVWGNLAEEEGTIEGNIGRNPRNRLQNIVFEGDDVENGKAAVTHYKVLERLG-YVTLVA 250

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHA 292
            +  TGRTHQ+RVH  ++G  +  D +Y  +     T+             I  +  LHA
Sbjct: 251 CKLETGRTHQIRVHMKYIGHTLFNDERYGGDRILKGTTFTKYKQFVDNCFKILPRQALHA 310

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP+    +   + +P  MV   + 
Sbjct: 311 KTLGFVHPKTEEWMSFNSDIPQDMVDCIEK 340


>gi|241663187|ref|YP_002981547.1| pseudouridine synthase [Ralstonia pickettii 12D]
 gi|240865214|gb|ACS62875.1| pseudouridine synthase, RluA family [Ralstonia pickettii 12D]
          Length = 370

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 87/335 (25%), Positives = 144/335 (42%), Gaps = 32/335 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V +       RLD+      P  +   LQ+ + +G VR+  + V+    I  G  + + P
Sbjct: 53  VEIPEAMHGERLDKALAKLLPDYSRSRLQQWIDAGAVRLHGEVVRPRAAISGGDRIEVVP 112

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
              A      E   +   ++L          ++YED  + V NKPAG+ V   +G     
Sbjct: 113 QRAAD-----ENAFVAEPIDLD---------VVYEDDTLLVINKPAGLVVHPAAGNWSGT 158

Query: 128 HIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  + D+ +  +  + HRLD++TSG++VVART  A   L    + R +++ Y +L
Sbjct: 159 VLNGLLHRYPDAVELPRAGIVHRLDKDTSGLMVVARTLPAQTDLVRQLQARTVKRTYLAL 218

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWL 243
           VWG    ++  I   + +      D   +          A +HFK +D           +
Sbjct: 219 VWGE-TPEEATIDAPIGRDP---RDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLV 274

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLHARYMD 296
             Q  TGRTHQ+RVH    G P++GD  Y  NF+      I+        +  LHA  + 
Sbjct: 275 RCQLETGRTHQIRVHFESEGHPLLGDPVYTRNFRRGQPQTIKAPLPVPFARQALHAVRLG 334

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           L HP  G+ +   A +P       ++L    D ++
Sbjct: 335 LVHPASGKSVHWEAGVPDDFADLLEALDLDPDADV 369


>gi|73541038|ref|YP_295558.1| ribosomal large subunit pseudouridine synthase D [Ralstonia
           eutropha JMP134]
 gi|72118451|gb|AAZ60714.1| ribosomal large subunit pseudouridine synthase D [Ralstonia
           eutropha JMP134]
          Length = 403

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 141/331 (42%), Gaps = 32/331 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V++     RLD+    H+   +   LQ+ + SG VRVD +  +  + +Q G  + + 
Sbjct: 59  TLEVDSVAHGERLDKLLARHFSEFSRSRLQQWIESGAVRVDGEVRRPRDAVQMGNRIEVQ 118

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
           P     +     + +                 ++YED  + V +KPAG+ V   +G    
Sbjct: 119 PQAAPESQAFAPEDVA--------------LDVVYEDDALLVIDKPAGLVVHPAAGNWSG 164

Query: 127 YHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             ++G L     +    +  + HRLD+ETSG++VVART  A   L    + R +++ Y +
Sbjct: 165 TVLNGLLHRDPTAAALPRAGIVHRLDKETSGLMVVARTLTAQTDLVRQLQARTVKRTYLA 224

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCW 242
           LVWG    ++  I   + +      +   +   +      + +HF+ +            
Sbjct: 225 LVWGRIY-EEGTIDAPIGRDP---RERTRMAIVHTNSGKPSRTHFRTLATVPLGRSFVSM 280

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQ-NKLYLHARYM 295
           +  Q  TGRTHQ+RVH   +G P+VGD  Y                P+   +  LHA  +
Sbjct: 281 VRCQLETGRTHQIRVHFESIGHPLVGDPVYYRATQRGQRPAIRVPLPVPFERQALHAFKL 340

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            L HP  G+ +  TAP P  +    D+L F 
Sbjct: 341 GLVHPVTGKTVSWTAPPPEDLQALIDALDFS 371


>gi|149182321|ref|ZP_01860799.1| ribosomal large subunit pseudouridine synthase D [Bacillus sp.
           SG-1]
 gi|148849940|gb|EDL64112.1| ribosomal large subunit pseudouridine synthase D [Bacillus sp.
           SG-1]
          Length = 303

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 81/329 (24%), Positives = 140/329 (42%), Gaps = 37/329 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  M +    +V  +E+++RLD+         +   +Q+ ++ G V+V+  +VK N +  
Sbjct: 1   METMEH----IVREEEKSVRLDKVLTQLEEKWSRSQVQQWIKDGNVKVNGSQVKTNYKCA 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
               + I                +     L    + +   + +ED+ + V NKP G+ V 
Sbjct: 57  IEDKIIIS---------------IPEPEELDVVPENMDLDIYFEDADVIVVNKPRGMVVH 101

Query: 121 GGSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L E  
Sbjct: 102 PAPGHPSGTLVNGLMAHCKDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDLAHEKLVEQL 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             + + + Y ++V GI  +    I   L +      +   V          A++HF V++
Sbjct: 162 VNKTVTRKYKAIVHGIIPHDHGTIDAPLGRDPKDRQNMAVV-----DSGRDAVTHFNVLE 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F   F ++E +  TGRTHQ+RVH  ++G P+ GD KY      +          LHA  
Sbjct: 217 RFTD-FTYVECKLETGRTHQIRVHMKYIGYPLAGDPKYGPRKTLDL-----GGQALHAAV 270

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP  G  L+  A  P     T   L
Sbjct: 271 LGFIHPRTGEYLEFEAEPPEVFRHTLQKL 299


>gi|23098941|ref|NP_692407.1| hypothetical protein OB1486 [Oceanobacillus iheyensis HTE831]
 gi|22777169|dbj|BAC13442.1| hypothetical conserved protein [Oceanobacillus iheyensis HTE831]
          Length = 303

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 84/323 (26%), Positives = 143/323 (44%), Gaps = 34/323 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  Q++ V   +   R+D+         +   +Q  +  G V V+   VK N +   G 
Sbjct: 1   MTKSQHI-VTEQQGKTRVDKLLTQLLADQSRSQIQGWIDEGLVEVNGVSVKANYKCVEGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +                  +  +  L    + +   ++YEDS + V NKP G+ V   +
Sbjct: 60  ALTWE---------------IPETKPLILEPENIPLDVVYEDSDVIVINKPKGMVVHPSA 104

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      +   L    D  G    ++P + HR+D++TSG+LVVA+   A Q L++  + +
Sbjct: 105 GHQTGTLVHALLYHCDDLSGINGIERPGIVHRIDKDTSGLLVVAKNDVAHQKLSDQLQQK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           ++++ Y ++V G   +    I   + +        + VV         AI+HF+VI+ F 
Sbjct: 165 QLKRKYVAIVHGEIGHDTGLIDAPIGRDPK-DRQKMAVVD----NGKSAITHFRVIERFP 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             + ++E Q  TGRTHQ+RVH  ++G P+VGD KY      N      +   LHA+ +  
Sbjct: 220 D-YTFVECQLETGRTHQIRVHMQYIGFPLVGDPKYSQRKTMNV-----DGQALHAKEIGF 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTW 319
            HP+ G  L+  A  P    +  
Sbjct: 274 YHPKTGEWLEFDANPPEIFTEAL 296


>gi|34497273|ref|NP_901488.1| pseudouridine synthase [Chromobacterium violaceum ATCC 12472]
 gi|34103129|gb|AAQ59492.1| pseudouridine synthase [Chromobacterium violaceum ATCC 12472]
          Length = 312

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 98/318 (30%), Positives = 157/318 (49%), Gaps = 19/318 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V+ ++   RLD + +     +   ++ +ILRSG+VRV+K RV  + R+ +G ++R
Sbjct: 9   VTFLEVDAEDAGQRLDNYLQRLLKGVPKSHIYRILRSGEVRVNKGRVDASYRVAAGDMLR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A                  K        ++YED  + V +KPAG++V GGSG++
Sbjct: 69  IPPIRVAERA--------------EKTVPAATFPVVYEDDALLVIDKPAGVAVHGGSGVS 114

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD+ETSG+L++A+ R+A   L +  R     K Y +L
Sbjct: 115 FGVIEQLRRA-HPEWRYLELVHRLDRETSGLLMLAKKRSALTRLHDMMRDNVPDKRYLAL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G      + +   L K     G+   V         YA ++F +   + + F  +E  
Sbjct: 174 ATGHWPENVKQVKLPLYKFHTPDGER-RVKIAEGDDGQYAHTNFSIQQRYTE-FTLVEAH 231

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
             TGRTHQ+RVH    GC I GD KY    +          +++LHA+ + LPHP  G  
Sbjct: 232 LRTGRTHQIRVHMQANGCAIAGDEKYGDFAYNKELARRGLKRMFLHAKSLTLPHPLTGAT 291

Query: 305 LQITAPLPAHMVKTWDSL 322
           L++ APLP  + K   SL
Sbjct: 292 LKLEAPLPPELQKFLKSL 309


>gi|295132692|ref|YP_003583368.1| ribosomal large subunit pseudouridine synthase D [Zunongwangia
           profunda SM-A87]
 gi|294980707|gb|ADF51172.1| ribosomal large subunit pseudouridine synthase D [Zunongwangia
           profunda SM-A87]
          Length = 352

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 79/330 (23%), Positives = 150/330 (45%), Gaps = 33/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            + E  +  +R+D++  N+        +QK  + G + V+   VK N ++++G VV++  
Sbjct: 25  FIAEKGQNPLRVDKYLMNYIEKATRNKIQKAAKDGNIYVNDVPVKQNYKVKAGDVVQVM- 83

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                 H   E  +   ++ L          ++YED  + V NKPAG+ V  G G     
Sbjct: 84  ----FEHPPYEFLLTPENIPLD---------IVYEDDTLLVVNKPAGMVVHPGHGNYSGT 130

Query: 128 HIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            I+  +   ++  ++   +P L HR+D++TSG+LV+A+T  A  HL++ F  +  ++ Y 
Sbjct: 131 LINALVYHFENLPNNSSDRPGLVHRIDKDTSGLLVIAKTEHAMAHLSKQFFDKTSEREYI 190

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++VWG  +  +  +   + +             ++ +    A++H KV++ F      + 
Sbjct: 191 AIVWGNVEEDEGTVEGNIGRHPKNRLQNTVYEGEDAEKGKPAVTHLKVLERFG-YVTLVA 249

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHA 292
            +  TGRTHQ+RVH  H+G  +  D +Y        T+             I  +  LHA
Sbjct: 250 CKLETGRTHQIRVHMKHIGHTLFNDERYGGEKILKGTTFTKYKQFVENCFKILPRQALHA 309

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP+ G  +   + LP  M+   + 
Sbjct: 310 KTLGFTHPKTGEWMSFNSDLPEDMLGAIEK 339


>gi|289209195|ref|YP_003461261.1| pseudouridine synthase [Thioalkalivibrio sp. K90mix]
 gi|288944826|gb|ADC72525.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. K90mix]
          Length = 319

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 86/344 (25%), Positives = 144/344 (41%), Gaps = 38/344 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +   +  +E   RLD      +P  +   L + L+ G + V+  + K    +Q G+
Sbjct: 1   MNEPRSAELPEEEAGQRLDAALARLFPEYSRSQLTQWLKEGALTVNGGQPKPRTPVQGGE 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V + P                 +  L    + +   +++ED  + V NKPAG+ V   +
Sbjct: 61  HVVLEP---------------PEAPVLEAEPEPIALDIVHEDPAVLVINKPAGLVVHPAA 105

Query: 124 GI--AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G      ++  L    + S+  +  + HRLD++T+G++VVART  A   L    + R + 
Sbjct: 106 GHRAGTLVNALLHHDPNLSQLPRAGVVHRLDKDTTGLMVVARTPQAQTALVRQLQQRTVH 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQK 239
           + Y +LV G        + +    +  IG   V   +Q    G   A++H++V + F   
Sbjct: 166 REYRALVQG-------RVISGATIEEPIGRHPVDRKRQAVTGGGKPAVTHYRVAERFP-A 217

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG--------NFTSPIQNKLYLH 291
              L ++  TGRTHQ+RVH  H+  PIVGD  Y    +                 +  LH
Sbjct: 218 HTLLNVRLETGRTHQIRVHMAHIRHPIVGDPAYGGRPRPVRGMGEAAKAALAAFRRQALH 277

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           A  ++  HP+ G  L   AP+P        +L  + DR     R
Sbjct: 278 AARLEFEHPDSGEVLAFEAPVPEDFEALLAAL--RTDREADHDR 319


>gi|209550662|ref|YP_002282579.1| pseudouridine synthase [Rhizobium leguminosarum bv. trifolii
           WSM2304]
 gi|209536418|gb|ACI56353.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 341

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 85/345 (24%), Positives = 155/345 (44%), Gaps = 45/345 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           + V+  ++    RLD W         +   ++ +++ GQV +  + V     ++++G   
Sbjct: 12  RKVLTADETAEGRLDAWLTAQVGEEFSRSRIKALIKDGQVSLRGEPVTDPQRKVRNGDSF 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            I                L    + T   + +   +L+ED  + V +KP+G+ V  GSG 
Sbjct: 72  EIT---------------LPEPEDPTPQGEDIPLDILHEDEDLIVISKPSGLVVHPGSGN 116

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  +    D+       ++P + HRLD++T+G++VVA+   A +HL+  F    
Sbjct: 117 WTGTLVNALIHHCGDTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHG 176

Query: 179 ----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y ++VWG P++    +   L + +        V + +   A+ AI+H++VI+
Sbjct: 177 RTMPLERAYQAVVWGRPRSLTGTVDAPLGRATG-DRTRRAVKRPDSHDADEAITHYEVIE 235

Query: 235 CFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
            F +          +E    TGRTHQ+RVH  H+G P++GD  Y A FK       +   
Sbjct: 236 RFQENPDATALASLVECHLETGRTHQIRVHMAHIGHPLLGDTVYGAGFKTKANRLPEEVR 295

Query: 286 ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 N+  LHA  +   HP  G  +    PLP  MV+  ++L 
Sbjct: 296 KVVNGFNRQALHAFMLQFEHPRTGELMHFEVPLPDDMVELVEALR 340


>gi|300691996|ref|YP_003752991.1| ribosomal large subunit pseudouridine synthase C [Ralstonia
           solanacearum PSI07]
 gi|299079056|emb|CBJ51718.1| Ribosomal large subunit pseudouridine synthase C [Ralstonia
           solanacearum PSI07]
          Length = 346

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 98/322 (30%), Positives = 164/322 (50%), Gaps = 19/322 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D +  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 25  VAYVEIGEDAQGQRIDNFLMRLAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 84

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++  +         +     +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 85  IPP--------LRIAQQSAQQAEAARAVPAAEFTILHEDTHLLVIDKPAGVAVHGGSGVA 136

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++ 
Sbjct: 137 FGVIEQLRQ-SRPEAKFLELVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFAA 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  ++++ I   L K +   G+    V+ +      + + F  +  F   +  LE +
Sbjct: 196 VKGLWPHQRQHIKAPLFKYTTPEGERRVRVQAD---GQPSHTVFNKVGVFG-PYTLLEAE 251

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H G PI+GD KY              SP   +++LHA  + L HP+
Sbjct: 252 LKTGRTHQIRVHLAHAGFPILGDDKYGDFALNKALSRANASPRLARMFLHAHTLRLTHPQ 311

Query: 302 GGRL-QITAPLPAHMVKTWDSL 322
            G +    APLPA      ++ 
Sbjct: 312 SGEIVTFKAPLPAECAAFLNAF 333


>gi|187477608|ref|YP_785632.1| ribosomal large subunit pseudouridine synthase C [Bordetella avium
           197N]
 gi|115422194|emb|CAJ48718.1| ribosomal large subunit pseudouridine synthase C [Bordetella avium
           197N]
          Length = 319

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 103/318 (32%), Positives = 158/318 (49%), Gaps = 20/318 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ V V+  +E  RLD +       +   ++ K +R G+VRV+K R+  + R+  G VVR
Sbjct: 17  VRMVEVDAGQEGQRLDNFLLRLCKGVPKSHIYKAIRGGEVRVNKGRISADYRLVVGDVVR 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+                     K     +  ++YED  + V NKPAG++V GGSG++
Sbjct: 77  VPPLRL-------------PDPGQPKPVPASEFPVVYEDDAMLVINKPAGVAVHGGSGVS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++    + +   L HRLD+ETSG+L++A+ R+A   L    R  R  K Y +L
Sbjct: 124 FGVIEQLRAAR-PEARFLELVHRLDRETSGLLMIAKKRSALLALHAMLREGRGSKRYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   N ++ I   L K +   G+    V  + + A+  IS    +      +  +E +
Sbjct: 183 VEGDWVNDRQHIRLALSKWTTQSGERRVKVDPDGQTAHTVIS----LKQRFGDYSLVEAE 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
             TGRTHQ+RVH    G PIVGD KY  +  +  F     N+++LHA  + L HP  G  
Sbjct: 239 LRTGRTHQIRVHLAASGFPIVGDDKYGTDETRALFARQGFNRMFLHAYQLTLDHPLTGEP 298

Query: 305 LQITAPLPAHMVKTWDSL 322
           L +TA LPA   K    L
Sbjct: 299 LSLTAELPAICSKLLHQL 316


>gi|160900713|ref|YP_001566295.1| RluA family pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160366297|gb|ABX37910.1| pseudouridine synthase, RluA family [Delftia acidovorans SPH-1]
          Length = 362

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 101/321 (31%), Positives = 159/321 (49%), Gaps = 21/321 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V++D    RLD +   H   +   ++ +I+RSG+VR++K RV    R+ +G +VR
Sbjct: 50  VRLIEVDDDSAGQRLDNFLIRHLKGVPKTHVYRIIRSGEVRINKGRVSAETRVSTGDIVR 109

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +       +K+ + +       DF     L ED  +   +KPAG++V GGSG++
Sbjct: 110 IPPVRIS-------EKVAEKAERPAPARDFPS---LLEDEHLIAIDKPAGVAVHGGSGVS 159

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD+ETSGIL+VA+ R+A  HL + FR R   K Y +L
Sbjct: 160 FGVIEQLRQARPQS-RFLELVHRLDRETSGILLVAKKRSALTHLQDQFRERETGKTYLAL 218

Query: 187 VWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK------ 239
           V G      + I   L K     G+  V V   ++     +++  +V    A +      
Sbjct: 219 VQGTWPANHKVIDLPLHKYLQADGERRVRVTTADDPDGMRSVTLVRVRSTLAPQPLLGLP 278

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDL 297
               LE+   TGRTHQ+RVH    G PI GD KY   +           +++LHA  +  
Sbjct: 279 AMSLLEVTIKTGRTHQIRVHLSSQGHPIAGDDKYGDFDLNRRLQKQGLKRMFLHAWRLQF 338

Query: 298 PHP-EGGRLQITAPLPAHMVK 317
            HP  G R+++ A LP  + +
Sbjct: 339 THPASGERVELRAELPEELAR 359


>gi|319900222|ref|YP_004159950.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           helcogenes P 36-108]
 gi|319415253|gb|ADV42364.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           helcogenes P 36-108]
          Length = 355

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 78/332 (23%), Positives = 145/332 (43%), Gaps = 38/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 31  VVVDKGQVMMRVDKYLFDRLTNASRNRIQKAADAGFVMANGKPVKSSYKVKPQDVITVMM 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +++   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 91  -----DRPRYENEVIPEDIPLN---------IVYEDKHLMVVNKPAGLVVHPGHGNYHGT 136

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 137 LVNAIAWHMKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKTTKRR 196

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +  +  +   + +      D + +    +    +A++H++V++        
Sbjct: 197 YRALVWGNVEQDEGTVVGNIGRNPK---DRMQMTVLPDDQGKHAVTHYRVLERLG-YVTL 252

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +     T   +             +  L
Sbjct: 253 VECILETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFDTCPRQAL 312

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA  +   HP     +  T+ LP  M +  D 
Sbjct: 313 HAMTLGFVHPVTKEAMDFTSELPDDMARLIDK 344


>gi|262375074|ref|ZP_06068308.1| 23S rRNA pseudouridylate synthase [Acinetobacter lwoffii SH145]
 gi|262310087|gb|EEY91216.1| 23S rRNA pseudouridylate synthase [Acinetobacter lwoffii SH145]
          Length = 318

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 96/319 (30%), Positives = 162/319 (50%), Gaps = 18/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  ++  R+D +  +    +    + +++R GQVRV+KKR+K   ++  G  +R
Sbjct: 10  VTWFEVDEHQDGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLAIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++    K +  L + ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDESAAPVSDKVAQGLLARVIYEDEGLMVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y ++
Sbjct: 123 YGLIEGLRAATGKKY--LELIHRIDRDTSGLVMISKKRSVLKTLQDMLREHKIKKTYAAV 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     K+ I   L +     G+    V  + K    + + + V + F      +   
Sbjct: 181 VKGQVSLDKQLIDAPLHRYELANGER--RVCVSPKEGKESKTQWNVQERFMH-ATLVYAS 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P+VGD KY    +  +  P   +L LHA  +D+P    G   
Sbjct: 238 PLSGRTHQIRVHGLSIGHPLVGDEKYG--HETEYRGPKPRRLCLHAMRLDIP----GYPA 291

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I APLP  M      L  +
Sbjct: 292 IEAPLPEDMQSLVAQLRAQ 310


>gi|42520290|ref|NP_966205.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Drosophila melanogaster]
 gi|42410028|gb|AAS14139.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Drosophila melanogaster]
          Length = 307

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 110/323 (34%), Positives = 180/323 (55%), Gaps = 16/323 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++  ++ +++E+D  N+RLDR+ +  +P +    ++K LR G ++V+  + K ++R+ SG
Sbjct: 1   MLQSIKTILIEDD--NVRLDRYIRRIFPDLKQSVIEKSLRKGLIKVNDCKAKSSDRVNSG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q + +   +N + +   ++K  +  VNL      L+  +LYED  I   NKPAG+ VQGG
Sbjct: 59  QTITLK-HLNYIENANSDRKYNEKLVNL------LRENILYEDEYILAINKPAGVIVQGG 111

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             +   +   L      +G+  ++ HRLD++TSG+++ AR    A++L E F+ RR++K 
Sbjct: 112 VKVKISMSDLLDQIR--EGETFKIVHRLDRDTSGVIIFARNANVARYLMEEFKGRRVKKT 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L  GIP      I   L+KK   G + V V   +E     A +HF +I        +
Sbjct: 170 YLALTSGIPSKDSGTIDYPLVKKYVSGQEKVVV---DENSPQNATTHFSIIAKSKHNVAY 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L++QP TGRTHQLR H  H+ CPI+GD KY    K  F   I NK++LH+  + L  P  
Sbjct: 227 LKLQPITGRTHQLRAHLAHINCPILGDGKYGG--KKAFIDGIANKIHLHSHSLSLKLPNN 284

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
             + ITAP+  H+ K+ ++L F 
Sbjct: 285 KEITITAPITKHIEKSIEALFFD 307


>gi|57866712|ref|YP_188346.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           epidermidis RP62A]
 gi|242242479|ref|ZP_04796924.1| pseudouridylate synthase RluD [Staphylococcus epidermidis W23144]
 gi|57637370|gb|AAW54158.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus epidermidis RP62A]
 gi|242234053|gb|EES36365.1| pseudouridylate synthase RluD [Staphylococcus epidermidis W23144]
 gi|319401509|gb|EFV89719.1| pseudouridine synthase, RluA family protein [Staphylococcus
           epidermidis FRI909]
          Length = 305

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 79/324 (24%), Positives = 147/324 (45%), Gaps = 33/324 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    + ++E  +   R+D+   +     +   LQ  ++ G V+V+ K +K N +++   
Sbjct: 1   MGNYNFNIIEQSQVGQRIDKLVSDLNKDWSRSQLQDWIKEGLVKVNGKVIKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           ++ E++++++ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  KI-----------VVTEKEVVEADIK----PENLNLDIYYEDEDVAIVYKPKGMVVHPSP 105

Query: 124 GI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A +HL E    +
Sbjct: 106 GHYSGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRHLVEQLMSK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 TVKRKYTALVHGNIPHDYGTIDAPIGRN-KNDRQAMAVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPKKTLD-----IGGQALHAGIIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWD 320
            HP   + ++  A LP    K  D
Sbjct: 275 EHPVTHKYIEKHATLPNDFEKLLD 298


>gi|303252739|ref|ZP_07338900.1| 23S rRNA pseudouridylate synthase C [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|302648389|gb|EFL78584.1| 23S rRNA pseudouridylate synthase C [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
          Length = 321

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 162/319 (50%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q      
Sbjct: 11  VQFFTISEDEVGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQP----- 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 66  -DDVVRVPPVRVAEKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 124 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+ +  V +       + + F + + +A     ++  
Sbjct: 183 VRGQWQAHTKVIKAPLLKNELASGERIVRVSEK---GKPSETRFSIEERYA-NATLVKAS 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 239 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 298

Query: 305 LQITAPLPAHMVKTWDSLG 323
           + ITAPL   +      L 
Sbjct: 299 MLITAPLDKTLKGVLAKLR 317


>gi|257869391|ref|ZP_05649044.1| pseudouridylate synthase [Enterococcus gallinarum EG2]
 gi|257803555|gb|EEV32377.1| pseudouridylate synthase [Enterococcus gallinarum EG2]
          Length = 301

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 146/327 (44%), Gaps = 36/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     VV+   EE  R+D+   +     +   +Q+ L+ G V      ++ N ++++G 
Sbjct: 1   MNNQIEVVI--HEEKGRVDKVLADRL-EASRSQIQQWLKEGAVTCQGDPIRANYKVKAGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I                +    +L    + +   ++Y+D  + V NKP G+ V   +
Sbjct: 58  QLVIQ---------------VPEPESLDLEPEDIPLTIVYQDQDVAVINKPQGMVVHPSA 102

Query: 124 GIAY--HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D        +P + HR+D++TSG+L++A+   A + L +  + +
Sbjct: 103 GHPNGTLVNALLYHMTDLSSINDVVRPGIVHRIDKDTSGLLMIAKNDHAHEALAKQLKDK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G   ++K  I   + + S +      V    ++    A++HF V++ F 
Sbjct: 163 TSLRKYVALVHGNISHEKGTINAPIGR-SKVNRKMQAV----QEDGKPAVTHFTVLERFD 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q F  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +  
Sbjct: 218 Q-FTLVELQLETGRTHQIRVHMQYIGFPLAGDPVYGPK-----KTLKGNGQFLHAKLLGF 271

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +   APLP    +T   L 
Sbjct: 272 THPTTGESMVFEAPLPELFEETLKKLR 298


>gi|326800939|ref|YP_004318758.1| pseudouridine synthase [Sphingobacterium sp. 21]
 gi|326551703|gb|ADZ80088.1| pseudouridine synthase, RluA family [Sphingobacterium sp. 21]
          Length = 348

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 73/332 (21%), Positives = 149/332 (44%), Gaps = 38/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+D++  +   + +   +Q  + +  V V+ + VK + +++ G ++ +  
Sbjct: 24  IVVDKGQTLLRIDKFLMHRVENASRNRVQNAIEAENVLVNNRPVKSSYKVKPGDLITV-- 81

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIAY 127
               L H  ++ +I   ++ L          + YED  + + NKPAG+ V  G  +    
Sbjct: 82  ---VLPHPPRDTEIYPENIPLD---------IRYEDDDLLIVNKPAGMVVHPGYNNYTGT 129

Query: 128 HIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++  +  +     +     +P L HR+D++TSG+LV+A+      +L + F    IQ+ 
Sbjct: 130 LVNALVYHFNQLPQLPGNDGRPGLVHRIDKDTSGLLVIAKNEWTITNLAKQFFDHTIQRK 189

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  + +   ++ ++ +        V  V +NE    ++++H++V++        
Sbjct: 190 YLALVWGDLQ-ENGTVSGYIGRSLK--DRRVMSVYENEDKGKWSVTHYRVLERLG-YVTL 245

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYL 290
           +E Q  TGRTHQ+R H   +G P+  D  Y  +     T              I  +  L
Sbjct: 246 IECQLETGRTHQIRAHMQSIGHPLFNDTLYGGDKILKGTVFTKYKQFVDNCFSILPRQAL 305

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA+ +   HP+    +   + +P       D 
Sbjct: 306 HAKSLGFTHPKSKELMHFESDIPDDFAICLDK 337


>gi|317478569|ref|ZP_07937726.1| RluA family pseudouridine synthase [Bacteroides sp. 4_1_36]
 gi|316905210|gb|EFV27007.1| RluA family pseudouridine synthase [Bacteroides sp. 4_1_36]
          Length = 356

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 146/332 (43%), Gaps = 38/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQEMMRVDKYLFDRLTNSSRNRIQKAADAGFVMANGKAVKSSYKVKPMDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +++   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYENEVIPEDIPLD---------IVYEDKYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNAIAWHMKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKTTKRR 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +  +  +   + +      D + +    +    +A++H++V+         
Sbjct: 198 YRALVWGNVEQDEGTVVGNIGRNP---RDRMQMTVLPDDQGKHAVTHYRVLKRLG-YVTL 253

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +     T   +             +  L
Sbjct: 254 VECILETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFDTCPRQAL 313

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G  +  T+ LP  M +  D 
Sbjct: 314 HAMTLGFVHPVTGEEMYFTSELPDDMTRLIDK 345


>gi|225025072|ref|ZP_03714264.1| hypothetical protein EIKCOROL_01961 [Eikenella corrodens ATCC
           23834]
 gi|224942164|gb|EEG23373.1| hypothetical protein EIKCOROL_01961 [Eikenella corrodens ATCC
           23834]
          Length = 323

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 95/330 (28%), Positives = 158/330 (47%), Gaps = 26/330 (7%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V Y+ V+      RLD +       +   ++ +I+R G+VRV+KKR   ++R+ +G  
Sbjct: 7   NSVNYLSVDEAAAGQRLDNFLIRLLKGVPKSHIHRIIRGGEVRVNKKRAAADSRLAAGDE 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+  A      E  +              +  +++ED  + V +KP+G++V GGSG
Sbjct: 67  VRIPPIRLAQKAEQAEAAVPPR-----------EFDIVFEDEHLLVVDKPSGVAVHGGSG 115

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L+       +   L HRLD++TSG+LVVA+ R+A   L E++R  + +K+Y 
Sbjct: 116 VSFGVIEQLRRARPQ-ARYLELVHRLDKDTSGLLVVAKKRSALVKLHEAWRNDKPKKVYL 174

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ------ 238
           +L  G        +   L K +   G+ +  V    +    A + F+V++ F        
Sbjct: 175 ALGMGAWPQGVRQVKLPLFKYTGAAGEKMVRV---SEEGQSAHTLFRVLESFGGAPLHAV 231

Query: 239 ---KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARY 294
                  +E    TGRTHQ+RVH     CPI GD +Y               +++LHA  
Sbjct: 232 GLSALSLMEATLRTGRTHQIRVHMQSQNCPIAGDERYGDYTANRRLKKLGLKRMFLHAHR 291

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           ++L HP  G  L +TAPLP  + +  + L 
Sbjct: 292 LELEHPASGETLVLTAPLPEELRQMLEGLR 321


>gi|114321699|ref|YP_743382.1| ribosomal large subunit pseudouridine synthase D [Alkalilimnicola
           ehrlichii MLHE-1]
 gi|114228093|gb|ABI57892.1| ribosomal large subunit pseudouridine synthase D [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 313

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 88/332 (26%), Positives = 144/332 (43%), Gaps = 35/332 (10%)

Query: 5   TYVQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           T +++ ++++  +   RLD+      P  +   +Q+ +R G VR++    +  +++ +GQ
Sbjct: 3   TRIEHDILIDEQQTGQRLDQALAALLPDYSRSRIQQWIREGAVRLEGTAPRPRDKVAAGQ 62

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V I   +     +  E                +   + YED  + V +KPAG+ V  G+
Sbjct: 63  QVTIRAELEEEQRVSAEP---------------IPLRIQYEDRHLLVIDKPAGLVVHPGA 107

Query: 124 GIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G     +   L        + PR  + HRLD++TSG++VVAR+ AA   L    + R ++
Sbjct: 108 GNREGTLQNALLHHDPQLAELPRSGIVHRLDKDTSGLMVVARSLAAHTALVAQLQARSVR 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV G P      +   + +        + VV++       A +H++V +  A   
Sbjct: 168 REYLALVNGCPVA-GGTVEAPIGRHPR-DRKRMAVVER----GRPATTHYRVEERLA-AH 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--------GNFTSPIQNKLYLHA 292
             L     TGRTHQ+RVH  H G P+VGD  Y    +                 +  LHA
Sbjct: 221 TLLRCFLETGRTHQIRVHMAHAGYPLVGDPVYGGRLRLPPRATEAQRQALRAFQRQALHA 280

Query: 293 RYMDLPHPE-GGRLQITAPLPAHMVKTWDSLG 323
             + L HPE G RL   APLP  M      L 
Sbjct: 281 ARLALDHPESGERLSWEAPLPEDMAALLACLR 312


>gi|325143909|gb|EGC66219.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M01-240013]
          Length = 356

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 139/327 (42%), Gaps = 30/327 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ + +  
Sbjct: 12  LTVPLELAGGRLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKPSQPKDKMIGGEQICVT- 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 71  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGT 117

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    + S+  +  + HRLD+ETSG++VVA+T +A   L    + R +++IY ++
Sbjct: 118 LLNGLLAHCPELSQIPRAGIVHRLDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAV 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   A++H KV++ +     ++E  
Sbjct: 178 ANGIVP-FDGKIETQIGRDPH-NRLKMAVVKF---GGKPAVTHVKVLERY-LAHSYIECS 231

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
             TGRTHQ+RVH      P+  D  Y        +        +  +  LHA  +   HP
Sbjct: 232 LETGRTHQIRVHMREANHPLAADPVYGNPRHPCGDTVKEAVKSLGARQALHAYRLSFTHP 291

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
           + G  +   AP+P  +      L  + 
Sbjct: 292 KTGETVSFEAPIPDDIYHLLSVLRLEA 318


>gi|313496998|gb|ADR58364.1| RluA family pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 352

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 94/345 (27%), Positives = 155/345 (44%), Gaps = 38/345 (11%)

Query: 2   SLMTYVQYV--VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           S M+ +  +   V ++    RLD+     +   +   L   ++ G++ VD   V+  + +
Sbjct: 31  SSMSEIIQLSAEVPSELGGQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLV 90

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G ++ +     A    I E   LD               ++YED  I V NKPAG+ V
Sbjct: 91  HGGSLLTLEAEQEAQGEWIAEDIELD---------------IVYEDDHILVINKPAGLVV 135

Query: 120 QGGSGIA--YHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +G A    ++  L    D     +  + HRLD++T+G++VVA+T  A   L E  + 
Sbjct: 136 HPAAGHASGTLLNALLHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTLQAQTKLVEQMQA 195

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R++ +IY  +V G+       I   + +    GG    +   +  G   A+SH++V+  F
Sbjct: 196 RKVSRIYECIVIGVV-TAGGKIDAPIGRH---GGMRQRMAVTD--GGKPAVSHYRVLKRF 249

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKL 288
            +    + ++  TGRTHQ+RVH  H+G P+VGD  Y   F+     SP          + 
Sbjct: 250 -RSHTHVRVKLETGRTHQIRVHMAHVGFPLVGDQTYGGRFRIPPAASPTMVEAVKTFPRQ 308

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            LHAR++ L HP  G  ++  +PLP   V     L    DR  +I
Sbjct: 309 ALHARFLALAHPITGEVMKWESPLPDDFVWLLSLL--NQDRESFI 351


>gi|238762184|ref|ZP_04623156.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           kristensenii ATCC 33638]
 gi|238699531|gb|EEP92276.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           kristensenii ATCC 33638]
          Length = 319

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 99/322 (30%), Positives = 165/322 (51%), Gaps = 14/322 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEIQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGERMVKVSSE---GKPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F G       ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDGQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLGFKY 326
           ++I APL   +      L  K 
Sbjct: 296 MRIEAPLDNQLRHCLAVLRKKA 317


>gi|168180134|ref|ZP_02614798.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
 gi|226948812|ref|YP_002803903.1| RluA family pseudouridine synthase [Clostridium botulinum A2 str.
           Kyoto]
 gi|182669142|gb|EDT81118.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
 gi|226841647|gb|ACO84313.1| pseudouridine synthase, RluA family [Clostridium botulinum A2 str.
           Kyoto]
          Length = 305

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 85/326 (26%), Positives = 148/326 (45%), Gaps = 33/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  + VE + +N+RLD +    +   +   LQ I+  G V V+ K  K N +++   
Sbjct: 1   MEKIN-LQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVRD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   ++YED  + V NKP  + V    
Sbjct: 60  NIEVN---------------IPEPKLLQIEPEDINLDIIYEDKDVIVVNKPQEMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G+     ++  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+  
Sbjct: 105 GVYSGTLVNALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I ++Y +LV GI K+++  I   + +   +    + VV    K   +A++H+KVI+ F 
Sbjct: 165 SISRVYMALVEGIIKDEQGTIEAPIGRH-PVDRIKMAVV----KDGRHAVTHYKVIERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    +E +  TGRTHQ+RVH  H+  P+VGD  Y    +            LHA+ +  
Sbjct: 219 KNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQ----RFNLKGQMLHAKLLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP   + ++  + LP +  K    L
Sbjct: 275 IHPTTRQYVEFESELPEYFKKIIKIL 300


>gi|160902202|ref|YP_001567783.1| RluA family pseudouridine synthase [Petrotoga mobilis SJ95]
 gi|160359846|gb|ABX31460.1| pseudouridine synthase, RluA family [Petrotoga mobilis SJ95]
          Length = 319

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 87/320 (27%), Positives = 144/320 (45%), Gaps = 25/320 (7%)

Query: 12  VENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VE ++E  RLD +     P  I+   +Q  +  GQ+ V+  + K + +++ G  ++I   
Sbjct: 8   VEREDEQKRLDIYIAQKMPIEISRNLIQNAITKGQITVNGSQKKPHYKVKQGDEIQIDFH 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
              L    KE+ IL  ++ L          +LYED ++ V NKPAG+ V     I     
Sbjct: 68  --ELVEETKEENILPENIPLN---------ILYEDEELIVINKPAGLIVHPTPSIKTGTL 116

Query: 129 IDGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  +    D         +  + HRLD+ETSG+LVVA+   +   L++ F+ R+  K Y
Sbjct: 117 VNALMHHVKDLDKTMQDPNRLGIVHRLDKETSGVLVVAKNAFSHHLLSKEFKERKTMKYY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G  K K+  I   L +   +      V          AI+ +K +  F      +
Sbjct: 177 LAIVEGTLKEKEGEINLPLGRHPILRHKRAVVY-----NGKEAITEYKTLKEFGDLATLV 231

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++  TGRTHQ+RVH  ++G P++GD  Y  N           +  LHA  +   HP+  
Sbjct: 232 WIRLRTGRTHQIRVHFKYIGNPLIGDSLYGKNKIEKNLQIPVGRQMLHALKLGFYHPKTK 291

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             ++  APLP        +L
Sbjct: 292 EWMEFLAPLPDDFKNLLITL 311


>gi|299066639|emb|CBJ37832.1| Ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Ralstonia solanacearum CMR15]
          Length = 353

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 90/340 (26%), Positives = 146/340 (42%), Gaps = 34/340 (10%)

Query: 7   VQYVVVE--NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           ++ +VVE        RLD+      P  +   LQ+ + +G VRV    V+    +  G  
Sbjct: 31  IEPIVVEIPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVRPRAAVCGGDR 90

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + + P          E   +   ++L          ++YED  + V NKPAG+ V   +G
Sbjct: 91  IEVVPQRADD-----ENAFVAEPIDLD---------VVYEDDTLLVINKPAGLVVHPAAG 136

Query: 125 I--AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                 ++G L  +  + G  +  + HRLD+ETSG++VVART  A   L    + R +++
Sbjct: 137 NWSGTVLNGLLHRYPQAAGLPRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKR 196

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-- 239
            Y +LVWG    +   I   + +      D   +          A +HFK +D       
Sbjct: 197 TYLALVWGE-TPEAGTIDAPIGRDP---RDRTRMAIIETASGKPARTHFKTLDVVDLGRA 252

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLH 291
               ++ Q  TGRTHQ+RVH    G P++GD  Y  NF+      I+        +  LH
Sbjct: 253 QVSLVQCQLETGRTHQIRVHFESEGHPLLGDPVYTRNFRRGRPQTIKAPLPAPFARQALH 312

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           A  + L HP  G  +   A +P  + +  ++L    D +L
Sbjct: 313 AVRLGLVHPASGHSVHWHAGVPDDLAELMEALEMDPDVDL 352


>gi|241764488|ref|ZP_04762509.1| pseudouridine synthase, RluA family [Acidovorax delafieldii 2AN]
 gi|241366072|gb|EER60669.1| pseudouridine synthase, RluA family [Acidovorax delafieldii 2AN]
          Length = 353

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 79/328 (24%), Positives = 133/328 (40%), Gaps = 25/328 (7%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
           + ++ V V   +   RLDR   +  P  +   LQ++L  G V ++ ++  K   R+++G 
Sbjct: 44  SELRRVEVNAAQHGSRLDRALVDLVPEFSRSYLQQLLSQGLVALNGQQATKAAARVKAGD 103

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +       +   +               + L   ++YED+ + V NKPAG+ V    
Sbjct: 104 TLTVEMRPTLQSQAFR--------------PEALPIDVVYEDAHLLVVNKPAGLVVHPAP 149

Query: 124 GI--AYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G      ++G L          +  + HRLD++TSG++VVAR R     L      R + 
Sbjct: 150 GNWGGTLLNGLLARDAKAQLVPRAGIVHRLDKDTSGLMVVARDRTTMDALVRMIAARTVH 209

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++                + +       + VV  +      A +  + +       
Sbjct: 210 RQYLAIAHRPWTGVPNRAVQAPIGRDPRNRLRMAVVNLDTHAGKPARTDIRWLAGNDLG- 268

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           CW+E   HTGRTHQ+RVH   +G P+V D  Y              +  LHA  +   HP
Sbjct: 269 CWVECTLHTGRTHQIRVHMASLGHPLVADALYGGAPAAGL-----QRQALHAYRLSFTHP 323

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             G+ L+  APLP  M +     G  Y+
Sbjct: 324 VSGQALEFRAPLPDDMRRALAEWGLGYN 351


>gi|324991250|gb|EGC23184.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK353]
          Length = 298

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 145/322 (45%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E      RLD+        ++     + ++ G + V+ +  K    ++ G V+   
Sbjct: 2   EVRIEASVAGQRLDKAVAE-LTDLSRSLANEQIKDGWILVNGQAKKAKYAVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++        ++ +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELPEPEVVE------YVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIQDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKSALTRFQVLERFGD-YSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA +PA   +T + L 
Sbjct: 275 GEVLEFTAEVPAIFQETLEKLR 296


>gi|306831623|ref|ZP_07464781.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325978527|ref|YP_004288243.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|304426408|gb|EFM29522.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325178455|emb|CBZ48499.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 298

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 76/315 (24%), Positives = 141/315 (44%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RLD+   +    ++       ++ G V V+ K VK    ++ G VV          
Sbjct: 7   EAGVRLDKALAD-LTELSRSQANDEIKKGTVLVNGKAVKAKYAVKVGDVVT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGFL 133
           + + ++++L+ +      ++ +   ++YED  + V NKP G+ V    G      ++  +
Sbjct: 57  YEVPKEEVLEYT------AENIPLDIIYEDDDVAVVNKPQGMVVHPSVGHTSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++V G
Sbjct: 111 YHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +            K        A++HFKV++ F   +  +E+   T
Sbjct: 171 NIPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTHFKVLERFG-NYTLVELTLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  L  T
Sbjct: 225 GRTHQIRVHMAYIGYPVAGDPLYGPR-----KTLKGDGQFLHAQTLGFTHPTTGETLTFT 279

Query: 309 APLPAHMVKTWDSLG 323
           A  PA   +T ++L 
Sbjct: 280 AEAPAIFKETLENLR 294


>gi|293365185|ref|ZP_06611902.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           oralis ATCC 35037]
 gi|307703723|ref|ZP_07640664.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
 gi|291316635|gb|EFE57071.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           oralis ATCC 35037]
 gi|307622558|gb|EFO01554.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
          Length = 299

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 148/324 (45%), Gaps = 34/324 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +    RLD+   +    ++     + +++GQV V+ +  K    +Q G +V      
Sbjct: 3   IKIETGGQRLDKALSD-LTELSRSLANEQIKAGQVLVNGQAKKAKYTVQDGDIVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAENLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F+V++ F   +  LE+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFQVLERFGD-YSLLEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           L+ TA +P    +T + L    +R
Sbjct: 276 LEFTADIPEIFKETLERLRKTENR 299


>gi|254448982|ref|ZP_05062436.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium HTCC5015]
 gi|198261376|gb|EDY85667.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium HTCC5015]
          Length = 353

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 86/338 (25%), Positives = 157/338 (46%), Gaps = 41/338 (12%)

Query: 4   MTYVQY----VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M+  Q     + + ++    RLD+     +P  +   LQ+ L+ G + +D + +   +++
Sbjct: 1   MSETQTHHHQLSIPDEHAGQRLDKVLSALFPDFSRSRLQQWLKDGCITLDGQVLPGKHKV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G+++R                     ++    +  +  ++LYED  I V +KPAG+ V
Sbjct: 61  DGGELLR-------------ADFPEQEDLSGAVEAQDIPLVVLYEDDDILVVDKPAGMVV 107

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKP------RLTHRLDQETSGILVVARTRAAAQHLTES 173
              +G   + DG L++ +     +        + HRLD++TSG+LVVAR  +A Q L   
Sbjct: 108 HPAAG---NPDGTLQNALLFYAPELAGVPRSGIVHRLDKDTSGLLVVARNHSAHQSLVAQ 164

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + R + +IY ++V+G+P      +   + +  H G      V+Q   G   A++H++V 
Sbjct: 165 LQERSVSRIYEAIVFGVPV-SGGRVEGNIGR--HPGDRKKMAVRQV--GGKEAVTHYRV- 218

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQ------ 285
           +   +    +  Q  TGRTHQ+RVH  H+G P+VGD  Y    +  G+    +       
Sbjct: 219 EAKYRHHSHVRCQLETGRTHQIRVHMSHIGFPLVGDPVYGGRLRLPGDIEDSLLACLKRF 278

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           ++  LHA  + L HP  G  ++  +P+P  M +    L
Sbjct: 279 DRQALHAAELGLIHPRSGEAMRWESPMPEDMDELLFEL 316


>gi|238021276|ref|ZP_04601702.1| hypothetical protein GCWU000324_01175 [Kingella oralis ATCC 51147]
 gi|237868256|gb|EEP69262.1| hypothetical protein GCWU000324_01175 [Kingella oralis ATCC 51147]
          Length = 371

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 81/323 (25%), Positives = 135/323 (41%), Gaps = 29/323 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  D   +RLD       P  +   +   ++ G+V  + +      ++  G+ + +    
Sbjct: 30  VPIDLAGLRLDAALAKMLPDYSRSRIAGWIKDGEVLCNGQPASPKTKLIGGEQLAVN--- 86

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
                      I  S        + +   ++YED  + V NKPAG+ V   +G      +
Sbjct: 87  -----------IQPSQETQAYTPEAMPLDIVYEDDSVLVLNKPAGLVVHPAAGNWTGTLL 135

Query: 130 DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +G L    + S+  +  + HRLD++TSG++VVA+T  A  HL +  + R +++IY ++  
Sbjct: 136 NGLLAHASELSQVPRAGIVHRLDKDTSGLMVVAKTLPAQNHLVQQLQSRSVKRIYRAIAD 195

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           GI       I   + +  H     + VVK    G   AI+H KV++ + Q   ++E    
Sbjct: 196 GIVPFD-GKIETQIGRDPH-NRLKMAVVKF---GGKEAITHVKVLERY-QAHSYIECSLE 249

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKG-----NFTSPIQNKLYLHARYMDLPHPEGG 303
           TGRTHQ+RVH      P+ GD  Y                   +  LHA  +   HP+  
Sbjct: 250 TGRTHQIRVHLREARHPLAGDPVYGNPRHPCSPEVKAEVKALARQALHAYRLSFVHPKTN 309

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
             L   AP+P  M      L  +
Sbjct: 310 ETLSFEAPMPDDMYHLLSVLRLE 332


>gi|193215325|ref|YP_001996524.1| pseudouridine synthase, RluA family [Chloroherpeton thalassium ATCC
           35110]
 gi|193088802|gb|ACF14077.1| pseudouridine synthase, RluA family [Chloroherpeton thalassium ATCC
           35110]
          Length = 346

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 81/335 (24%), Positives = 135/335 (40%), Gaps = 39/335 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V  ++   R+D++      +     +Q+ +   +V V+ K +K N ++     + + 
Sbjct: 25  TLQVAPNQARERIDKFLTRQVENATRNKVQEAIEESRVLVNGKPIKSNYKVCPNDEIFVI 84

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG------- 121
                   +  E   LD               +++ED  + V NKPAG+ V         
Sbjct: 85  FTHPPAPDLEPENIPLD---------------IVFEDEFLLVINKPAGMVVHPAYANWTG 129

Query: 122 --GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + YH    L      +  +P + HRLD++TSG++VVA+  A    L + F  R  
Sbjct: 130 TLAGAVLYHTQNRLSE-TGKEALRPGIVHRLDKDTSGLIVVAKDDATHYALAKQFAERTT 188

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +KIY +LVWG PK     I   + + S      +       +    AI+ ++V + F   
Sbjct: 189 EKIYTALVWGCPKPPSGTIQTNIWR-SKRDRKIMANYPFESETGKPAITDYEVKEDF-HW 246

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-----------IQNKL 288
           F  L++Q HTGRTHQ+R H  H+G  I  D  Y          P           +  + 
Sbjct: 247 FSLLDLQLHTGRTHQIRAHLQHLGHAIFSDEVYGGKSVRKLGFPQSEAFVRNLFQVIPRQ 306

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            LHA+ +   HP     +   A LP  M +    +
Sbjct: 307 ALHAKKLGFKHPATENFVTFEASLPEDMEQAIQKI 341


>gi|160888049|ref|ZP_02069052.1| hypothetical protein BACUNI_00457 [Bacteroides uniformis ATCC 8492]
 gi|270295585|ref|ZP_06201786.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|156862548|gb|EDO55979.1| hypothetical protein BACUNI_00457 [Bacteroides uniformis ATCC 8492]
 gi|270274832|gb|EFA20693.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 356

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 79/332 (23%), Positives = 147/332 (44%), Gaps = 38/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E +R+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQEMVRVDKYLFDRLTNSSRNRIQKAADAGFVMANGKAVKSSYKVKPMDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +++   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYENEVIPEDIPLD---------IVYEDKYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNAIAWHMKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFFNKTTKRR 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +  +  +   + +      D + +    +    +A++H++V++        
Sbjct: 198 YRALVWGNVEQDEGTVVGNIGRNP---RDRMQMTVLPDDQGKHAVTHYRVLERLG-YVTL 253

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +     T   +             +  L
Sbjct: 254 VECILETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFDTCPRQAL 313

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G  +  T+ LP  M +  D 
Sbjct: 314 HAMTLGFVHPVTGEEMYFTSELPDDMTRLIDK 345


>gi|115351042|ref|YP_772881.1| RluA family pseudouridine synthase [Burkholderia ambifaria AMMD]
 gi|115281030|gb|ABI86547.1| pseudouridine synthase, RluA family [Burkholderia ambifaria AMMD]
          Length = 334

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 99/326 (30%), Positives = 157/326 (48%), Gaps = 23/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++ +    R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +V
Sbjct: 16  QVSMLEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDIV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + +    +                +LYED  + V NKPAG++V GGSG+
Sbjct: 76  RVPPVRVAAADLARADTPIVPPAQFE---------VLYEDDAMLVINKPAGVAVHGGSGV 126

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y++
Sbjct: 127 AFGVIEQMRQAR-PRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFA 185

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
              G  ++       +   L K S   G+    V+ +      + + F +++ +   +  
Sbjct: 186 CGHGEWQSDWGRRRAVKAPLFKYSTAEGERRVRVQDD---GLPSHTVFNLLERWPD-YAL 241

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PI GD KY               P   +++LHA  + L
Sbjct: 242 VEAELKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANAQPSLKRMFLHAHRLKL 301

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLP    +  D L
Sbjct: 302 AHPLTGEPLQFDAPLPDECRRFLDQL 327


>gi|237719675|ref|ZP_04550156.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_2_4]
 gi|229450944|gb|EEO56735.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_2_4]
          Length = 357

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 82/333 (24%), Positives = 150/333 (45%), Gaps = 39/333 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +I+  ++ LT         ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYENEIIPENIPLT---------IVYEDPYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNALAWHMKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRR 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFC 241
           Y +LVWG+ +  +  I   + +      D + +   ++     +A++H++V++       
Sbjct: 198 YRALVWGVVEQDEGTIVGNIARNPK---DRMQMAVMSDPTVGKHAVTHYRVLERLG-YVT 253

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLY 289
            +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +  
Sbjct: 254 LVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPRQA 313

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           LHA  +   HP  G  +  T+ LP  M +  + 
Sbjct: 314 LHAMTLGFVHPVTGEEMYFTSELPDDMTRLIEK 346


>gi|327489656|gb|EGF21448.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1058]
          Length = 298

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 139/322 (43%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E      RLD+        ++     + ++ G++ V+ +  K    ++ G V+   
Sbjct: 2   EVRIEASAAGQRLDKAVAE-LTDLSRSLANEQIKDGRILVNGQAKKAKYAVKEGDVISYE 60

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                +   + E   L+               ++Y+D  + V NKP G+ V   +G    
Sbjct: 61  QPEPEVVEYVPEDIPLE---------------IVYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-YTL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA +P    +T + L 
Sbjct: 275 GEVLEFTAEVPVIFQETLEKLR 296


>gi|329964664|ref|ZP_08301718.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
 gi|328525064|gb|EGF52116.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
          Length = 356

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 148/332 (44%), Gaps = 38/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDRGQEMMRVDKYLFDRLTNASRNRIQKAADAGFVMANGKPVKSSYKVKPQDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +++   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYENEVIPEDIPLN---------IVYEDRCLMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  HL   F  +  ++ 
Sbjct: 138 LVNAIAWHMKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTHLGNQFFNKTTKRR 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +  +  +   + +      D + +   ++    +A++H++V++        
Sbjct: 198 YRALVWGNVEQDEGTVVGNIGRNPK---DRMQMAVLSDDQGKHAVTHYRVLERLG-YVTL 253

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +     T   +             +  L
Sbjct: 254 VECILETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFETCPRQAL 313

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G  +  T+ +P  M +  D 
Sbjct: 314 HAMTLGFVHPVTGEEMYFTSEMPDDMTRLIDK 345


>gi|288905537|ref|YP_003430759.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
 gi|288732263|emb|CBI13830.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus gallolyticus UCN34]
          Length = 298

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 76/315 (24%), Positives = 141/315 (44%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RLD+   +    ++       ++ G V V+ K VK    ++ G VV          
Sbjct: 7   EAGVRLDKALAD-LTELSRSQANDEIKKGTVLVNGKAVKAKYAVKVGDVVT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL 133
           + + ++++L+ +      ++ +   ++YED  + V NKP G+ V    G      ++  +
Sbjct: 57  YEVPKEEVLEYT------AENIPLDIIYEDDDVAVVNKPQGMVVHPSVGHMSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++V G
Sbjct: 111 YHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +            K        A++HFKV++ F   +  +E+   T
Sbjct: 171 NIPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTHFKVLERFG-NYTLVELTLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  L  T
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLKGHGQFLHAQTLGFTHPTTGETLTFT 279

Query: 309 APLPAHMVKTWDSLG 323
           A  PA   +T ++L 
Sbjct: 280 AEAPAIFKETLENLR 294


>gi|238018931|ref|ZP_04599357.1| hypothetical protein VEIDISOL_00791 [Veillonella dispar ATCC 17748]
 gi|237864415|gb|EEP65705.1| hypothetical protein VEIDISOL_00791 [Veillonella dispar ATCC 17748]
          Length = 307

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 84/321 (26%), Positives = 140/321 (43%), Gaps = 32/321 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   +V  +++ MRLD +   H    +   +Q +++ G + V  K  K N R+    VVR
Sbjct: 1   MNEYIVNAEQDGMRLDVFLTEHMEG-SRSYIQSLIKGGHITVGAKVGKANLRLTPNAVVR 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSG 124
           +                +    ++    + +   +LYED  I + NK  G+ V    G+ 
Sbjct: 60  VE---------------IPEPESVEVKPEDIPLDVLYEDHDIIIVNKQRGMVVHPAVGNY 104

Query: 125 IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L    D  G     +P + HRLD++TSG+++ A+  AA   L E  +    +
Sbjct: 105 SGTLVNALLYHCKDLSGINGEIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKEHSAK 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV G    +K  I   + +        + VV +N K    A++HF V++ F  + 
Sbjct: 165 RTYLALVQGNIVEEKGTIKAPIGRHPK-DRMKMAVVFENSKD---AVTHFNVVERFGHQ- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E    TGRTHQ+RVH  H+G P+V D  Y                 LH+R +D+ HP
Sbjct: 220 TLVECNLETGRTHQIRVHFAHIGHPVVNDPFYGYRR----MDFPIEGQALHSRSLDVKHP 275

Query: 301 EGGR-LQITAPLPAHMVKTWD 320
             G  +   APLP       +
Sbjct: 276 ITGESMHFEAPLPDDFKACLE 296


>gi|220931776|ref|YP_002508684.1| ribosomal large subunit pseudouridine synthase D [Halothermothrix
           orenii H 168]
 gi|219993086|gb|ACL69689.1| ribosomal large subunit pseudouridine synthase D [Halothermothrix
           orenii H 168]
          Length = 308

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 84/322 (26%), Positives = 153/322 (47%), Gaps = 31/322 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++EE  R+D++       ++   +QK++ + +V V+ + VK + ++  G  +R+    
Sbjct: 10  VSSEEEGKRIDKYLSKLNKDLSRSYIQKLIDNDKVLVNGESVKRSFKVNRGDHIRL---- 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
                      I+    +       +   ++YED  I V NK AG+ V    G     + 
Sbjct: 66  -----------IIPPPEDSGIKPVEMDLDIIYEDKDILVLNKNAGLVVHPAPGNHENTLV 114

Query: 131 GFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             L ++ D+        +P + HRLD++TSG++V+A+   + + L E F+ R+ +K Y +
Sbjct: 115 NALIAYCDNLSTISGVNRPGIVHRLDKDTSGVMVIAKNDISHRKLVEQFKQRKTKKYYRT 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L+ G    K+  I   + +  H     + V +   K +  A+++FKV++ F +   ++E+
Sbjct: 175 LLKGELPYKEGKIDAPIGRDPH-DRKKMAVTR---KNSKKAVTYFKVLEFF-RDHSYVEV 229

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +  TGRTHQ+RVH  +MG P+VGD  Y              +  LHA  +   HP   + 
Sbjct: 230 ELKTGRTHQIRVHFSYMGFPVVGDSIYGKKR----NRLQATRQLLHAYRLGFYHPRNDKW 285

Query: 305 LQITAPLPAHMVKTWDSLGFKY 326
           ++  A LP    K  D L  K+
Sbjct: 286 VEYKASLPDDFKKALDILENKF 307


>gi|307248951|ref|ZP_07530961.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|306854562|gb|EFM86755.1| Ribosomal large subunit pseudouridine synthase C [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
          Length = 326

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 162/319 (50%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ+  +  DE   RLD +       +    + +I+R G+VRV+K R+K   ++Q      
Sbjct: 16  VQFFTISEDEVGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRIKPEYKLQP----- 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E+     S  L K ++ L+  +LYED  + V NKP+GI+V GGSG++
Sbjct: 71  -DDVVRVPPVRVAEKNEAPISTKLNKVAE-LEDQILYEDEVMLVINKPSGIAVHGGSGLS 128

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HR+D++TSGIL+VA+ R+A + L E  R + +QK Y +L
Sbjct: 129 FGVIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRSLHEQLREKVVQKDYLAL 187

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + I   LLK     G+ +  V +       + + F + + +A     ++  
Sbjct: 188 VRGQWQAHTKVIKAPLLKNELASGERIVRVSEK---GKPSETRFSIEERYA-NATLVKAS 243

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVH  + G PI  D KY  A F     +    +L+LHA  +   HP+ G  
Sbjct: 244 PVTGRTHQIRVHTQYAGHPIALDDKYGEAEFDSKMKAAGLQRLFLHAYSIRFEHPKTGEE 303

Query: 305 LQITAPLPAHMVKTWDSLG 323
           + ITAPL   +      L 
Sbjct: 304 MLITAPLDKTLKGVLAKLR 322


>gi|213961970|ref|ZP_03390235.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           sputigena Capno]
 gi|213955323|gb|EEB66640.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           sputigena Capno]
          Length = 350

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 152/330 (46%), Gaps = 35/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
                 +E +R+D++  N   +     +Q+  + G + V+ + VK N+R+++  VV++  
Sbjct: 28  FTAGKGQEPLRVDKFLMNFVENATRNKVQQAAKQGNIFVNGEPVKANHRVKANDVVKV-- 85

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
               L+H   E  ++  ++ L          ++YED  + V NKPAG+ V  G G     
Sbjct: 86  ---LLSHPPHEDLLVPENIPLN---------IVYEDDALLVVNKPAGMVVHPGHGNYSGT 133

Query: 128 HIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            I+  +   +   ++   +P L HR+D++TSG+LV+A+T  A  HLT+ F  +  Q+ Y 
Sbjct: 134 LINALVYHFEHLPNNSSNRPGLVHRIDKDTSGLLVIAKTEEAMLHLTQQFFYKTTQREYI 193

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG  +  +  +   + +  H+       V  +      A++H+KV++ F      + 
Sbjct: 194 ALVWGNIEEDEGTVRGHIGR--HLKDRLQMDVFPDGSHGKEAVTHYKVLERFG-YVTLVS 250

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLHA 292
            +  TGRTHQ+RVH  H+G  +  D +Y  +     T+  +             +  LHA
Sbjct: 251 CRLETGRTHQIRVHLKHIGHTLFNDERYGGDKILKGTTFAKYKQFVENCFAVLPRQALHA 310

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP     +   + LP  M    + 
Sbjct: 311 KTLGFEHPLTHEFMSFDSELPDDMQACIEK 340


>gi|118581597|ref|YP_902847.1| RluA family pseudouridine synthase [Pelobacter propionicus DSM
           2379]
 gi|118504307|gb|ABL00790.1| ribosomal large subunit pseudouridine synthase D [Pelobacter
           propionicus DSM 2379]
          Length = 315

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 87/328 (26%), Positives = 150/328 (45%), Gaps = 35/328 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V   D E +RLD +  +         +Q+++ SG + VD + V+ + +++ G+ + I  
Sbjct: 3   LVFPVDSEPVRLDLFLSSQLASETRSTIQRLIESGNIMVDGREVRPSLKLKGGESISIQ- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                         L   V      + +   +LYED  + V NKPAG+ V  G G     
Sbjct: 62  --------------LPEPVAARPLPESIPLEVLYEDGDLIVINKPAGMVVHPGPGNSSGT 107

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HRLD+ TSG++VVA+   + Q L+  F +  I++IY
Sbjct: 108 LVNALLAHCTDLSGIGGELRPGIVHRLDKGTSGVMVVAKNDRSHQALSAQFSVHSIKRIY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV+G P+     +   + +          + +Q      +A++ ++V   + +  C +
Sbjct: 168 QALVYGSPQQDSGRLEGQIGRHPTDRLRRSGLARQ----GKHAVTRWRVRGRYGR-ICLM 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQN-------KLYLHARYM 295
           E++  TGRTHQ+RVH    G P++GD  Y    +  N T P          +  LHAR +
Sbjct: 223 ELRLETGRTHQIRVHMSEAGFPLLGDPLYPDGGRFNNLTDPRLRKLITTLARQALHARTL 282

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSL 322
              HP  G  L+ +  +PA M    + L
Sbjct: 283 GFIHPASGNYLEFSVDMPADMAALLEYL 310


>gi|194289464|ref|YP_002005371.1| 23S rRNA pseudouridine synthase [Cupriavidus taiwanensis LMG 19424]
 gi|193223299|emb|CAQ69304.1| 23S rRNA pseudouridine synthase [Cupriavidus taiwanensis LMG 19424]
          Length = 418

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 138/330 (41%), Gaps = 32/330 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V++     RLD+    H+   +   LQ+ + SG VRVD +  +  + +Q G  + + P
Sbjct: 66  LEVDSASHGERLDKLLARHFSEFSRSRLQQWIESGAVRVDGQVRRPRDAVQMGNRIEVQP 125

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                      + +                 ++YED  + V NKPAG+ V   +G     
Sbjct: 126 QAAPEASAFAPEDV--------------PLDVVYEDDTLLVINKPAGLVVHPAAGNWSGT 171

Query: 128 HIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L     +    +  + HRLD+ETSG++VVART  A   L    + R +++ Y +L
Sbjct: 172 VLNGLLHRDPGAASLPRAGIVHRLDKETSGLMVVARTLTAQTDLVRQLQARTVKRTYIAL 231

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWL 243
           VWG     +  I   + +      +   +          + +HF+ +            +
Sbjct: 232 VWGR-TYDEGTIDAPIGRDP---RERTRMAIVQTASGKPSRTHFRTLATVPLGRGFVSMV 287

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQ-NKLYLHARYMD 296
             +  TGRTHQ+RVH   +G P+VGD  Y                P+   +  LHA  + 
Sbjct: 288 MCKLETGRTHQIRVHFESIGHPLVGDPVYFRATQRGQRPAIRVPLPVPYERQALHAYKLG 347

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           L HP  G+ +  TA  P  +    D+L F+
Sbjct: 348 LVHPATGKHMSWTAQPPEDLQALIDALDFE 377


>gi|332162113|ref|YP_004298690.1| 23S rRNA pseudouridylate synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|325666343|gb|ADZ42987.1| 23S rRNA pseudouridylate synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
          Length = 319

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 99/322 (30%), Positives = 165/322 (51%), Gaps = 14/322 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +  N    +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLNKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEIQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGERMVKVSSE---GKPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDSQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLGFKY 326
           ++I APL   +      L  K 
Sbjct: 296 MRIEAPLDNQLRHCLAVLRKKA 317


>gi|240850017|ref|YP_002971410.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           grahamii as4aup]
 gi|240267140|gb|ACS50728.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           grahamii as4aup]
          Length = 334

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 89/341 (26%), Positives = 150/341 (43%), Gaps = 45/341 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           + +      RLD+W    Y ++ +   LQ ++R G +++D + +K    +++  Q++ + 
Sbjct: 6   ITDEGALGQRLDQWLAKQYHNVFSRSRLQTLIREGYLKIDGQFIKEPKTKLRPKQIIELA 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                      E   LD               +L+ED  I V NKPAG+ V  G+G    
Sbjct: 66  MPDLRDAEPSAEAIALD---------------ILFEDDHIIVINKPAGLVVHPGNGNWTG 110

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR---- 177
             ++  +    +S       ++P + HRLD+ TSG+++VA+   A + L+  F       
Sbjct: 111 TLVNALIYHCGNSLSGIGGVKRPGIVHRLDKNTSGVMIVAKNDLAHKSLSAQFSDHGRTC 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L+WG P      I   L +  H       + KQN   A +A++HF +++ + 
Sbjct: 171 ALDRRYHALIWGTPHRNVWTIDASLGRSPHNRTKQAVIHKQN-PYARHAVTHFSLLEKYG 229

Query: 238 QKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-------- 283
                      LE +  TGRTHQ+RVH  H+G P++GD  Y   FK    +         
Sbjct: 230 SHADSTSFASLLECRLETGRTHQIRVHMAHIGHPLIGDTVYGNAFKTKSNAFNPTIRNAI 289

Query: 284 -IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              N+  LHA  +   HP  G+ +  +APLP  M K     
Sbjct: 290 DQFNRQALHAASLSFEHPSTGKVMSFSAPLPQDMAKLIKHF 330


>gi|29349120|ref|NP_812623.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|253571283|ref|ZP_04848690.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           1_1_6]
 gi|298386817|ref|ZP_06996372.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           1_1_14]
 gi|29341027|gb|AAO78817.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|251839236|gb|EES67320.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           1_1_6]
 gi|298260491|gb|EFI03360.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           1_1_14]
          Length = 357

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 81/332 (24%), Positives = 145/332 (43%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +I+  ++ L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYENEIIPENIPLN---------IVYEDPYVMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNALAWHMKDIPEYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRR 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +  +  I   + +           V  +     +A++H++V++        
Sbjct: 198 YRALVWGNVEQDEGTIVGSIARNPK--DRMQMAVMSDPSMGKHAVTHYRVLERLG-YVTL 254

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +  L
Sbjct: 255 VECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPRQAL 314

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G  +  T+ LP  M +  + 
Sbjct: 315 HAMTLGFVHPVTGEEMYFTSELPDDMTRLIEK 346


>gi|33597841|ref|NP_885484.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           parapertussis 12822]
 gi|33602743|ref|NP_890303.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           bronchiseptica RB50]
 gi|33574270|emb|CAE38602.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           parapertussis]
 gi|33577185|emb|CAE35742.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           bronchiseptica RB50]
          Length = 321

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 93/323 (28%), Positives = 157/323 (48%), Gaps = 20/323 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +    V+ + +  + +  R+D +       +   ++ K +R G+VRV+K R+    R+  
Sbjct: 14  TTPPAVRMLAIGPEHDGQRIDNFLLRLCKGVPKSHIYKAIRGGEVRVNKGRISAEYRLVE 73

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PP+                     +     +  ++YED  + V +KPAG++V G
Sbjct: 74  GDVVRVPPLRL-------------PDPGAARPVPGAEFPVVYEDDALLVIDKPAGVAVHG 120

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+++ +   L++      +   L HRLD+ETSG+L++A+ R+A   L    R  +  K
Sbjct: 121 GSGVSFGVIEQLRAARPQ-ARFLELVHRLDRETSGLLMLAKKRSALLALHAMLREGKGDK 179

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   N ++ I   L K +   G+    V Q  + A+  ++    +      + 
Sbjct: 180 HYLALVEGDWVNDRQHIRLALTKWTTQSGERRVRVDQAGQAAHTIVT----LRKRFGGYS 235

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-KGNFTSPIQNKLYLHARYMDLPHP 300
            ++ +  TGRTHQ+RVH    G PIVGD KY  +  +  F      +++LHA  + LPHP
Sbjct: 236 LVDAELRTGRTHQIRVHLASSGFPIVGDDKYGTDETRAAFARRGFGRMFLHAHQLTLPHP 295

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  L++TA LP   +K    L
Sbjct: 296 LTGETLRLTADLPPACLKLLKQL 318


>gi|199598373|ref|ZP_03211792.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|258508458|ref|YP_003171209.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus GG]
 gi|199590692|gb|EDY98779.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|257148385|emb|CAR87358.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus GG]
 gi|259649771|dbj|BAI41933.1| pseudouridylate synthase [Lactobacillus rhamnosus GG]
          Length = 306

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 87/334 (26%), Positives = 145/334 (43%), Gaps = 42/334 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+    +  E+     R+D+    H        +QK L+ G V V+   VK N ++ +G 
Sbjct: 1   MSDTFTITTESG----RIDKIITAHETTHTRSQVQKWLQDGLVTVNGNPVKANFKVTAGD 56

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VV +                +     L   ++ +   ++YED ++ V NKP G+ V    
Sbjct: 57  VVTVT---------------IPEVKPLKAVAEPIPLEIVYEDDQVIVVNKPQGMVVHPAP 101

Query: 124 GIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G   H DG L + +    +        +P + HR+D++TSG+L+VA+T AA   L+   +
Sbjct: 102 G---HPDGTLVNGLLYHTKLPGINGVIRPGIVHRIDKDTSGLLMVAKTEAAQLSLSAQLK 158

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +   + Y +LV G  K  +  I   L +          V         +A++HF+V++ 
Sbjct: 159 AKTSIREYLALVHGTFKEDEGTIDAPLGRDPRDRKRQAVVA-----DGRHAVTHFQVLER 213

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F   +  ++    TGRTHQ+RVH  +   P+ GD  Y         +   +  +LHA  +
Sbjct: 214 FT-NYTLVKCILDTGRTHQIRVHMAYTHHPVAGDPLYGPK-----RTLPGHGQFLHAAKL 267

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
              HP  G+ L  TAP+P    KT   L    D+
Sbjct: 268 GFVHPVTGKLLTFTAPVPPIFEKTLTDLRAGIDK 301


>gi|302670833|ref|YP_003830793.1| pseudouridine synthase RluA family protein [Butyrivibrio
           proteoclasticus B316]
 gi|302395306|gb|ADL34211.1| pseudouridine synthase RluA family [Butyrivibrio proteoclasticus
           B316]
          Length = 309

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 75/331 (22%), Positives = 149/331 (45%), Gaps = 32/331 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M   +     +V ++ + MR+D+        ++   ++K++   +V  + K VK +  + 
Sbjct: 1   MESKSEFFEFIVTDEYDGMRIDKLISELIDSLSRTYIKKLIDDKKVSCNGKVVKASFHVS 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
               + +      +  I+ +   LD               ++YED+ + V NKP  + V 
Sbjct: 61  ENDEIVMEIPPIEIPQILPQDIPLD---------------IIYEDNDVVVVNKPKDMVVH 105

Query: 121 GGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
             +G      ++  +    D+        +P + HR+D++T+G +++ +   A Q + E 
Sbjct: 106 PAAGHYKDTLVNAIMYHCKDNLSGINGVMRPGIVHRIDKDTTGSVIICKNDNAHQSIAEQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            +   I ++Y ++ +G+ K  +  +   + + S      + VV     G  YA +H++V+
Sbjct: 166 LKEHSINRVYHAICYGVIKEDEGDVTAPIGR-SVNDRKKMAVV----PGGKYASTHYRVL 220

Query: 234 DCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
             F    F ++E +  TGRTHQ+RVH  H+G P++GD  Y +     F +   N   LHA
Sbjct: 221 KRFPEDGFTYIECKLQTGRTHQIRVHMSHIGHPLLGDEVYASGRHSKFKT---NGQCLHA 277

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + +   HP  G  ++  APLP +     + L
Sbjct: 278 KTLGFIHPVSGEYIETDAPLPEYFNHLLNVL 308


>gi|294788953|ref|ZP_06754193.1| ribosomal large subunit pseudouridine synthase D [Simonsiella
           muelleri ATCC 29453]
 gi|294483055|gb|EFG30742.1| ribosomal large subunit pseudouridine synthase D [Simonsiella
           muelleri ATCC 29453]
          Length = 391

 Score =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 148/336 (44%), Gaps = 31/336 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V N+   MRLD       P  +   +   ++ G V  + +     +++  G+ + I    
Sbjct: 51  VPNELAGMRLDAALAKMLPDYSRSRITTWIKDGLVLCNNQEASPKDKLIGGEELHI---- 106

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
                     +I  S  N     + +   +++ED  + V NKPAG+ V   +G      +
Sbjct: 107 ----------QIQQSDENQAFEPELMDLDIVFEDDAVIVLNKPAGLVVHPAAGNWTGTLL 156

Query: 130 DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +G L    + S+  +  + HRLD++TSG++VVA+T     HL +  + R +++IY ++  
Sbjct: 157 NGLLAHCPELSQVPRAGIVHRLDKDTSGLMVVAKTLPVQNHLVQQLQNRSVKRIYRAVAD 216

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+       I   + +  H     + VVK    G   AI+H KV++ + Q   ++E    
Sbjct: 217 GVVP-FDGKIETLIGRDPH-NRLKMAVVKF---GGKEAITHVKVLERY-QSHSYIECSLE 270

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------KLYLHARYMDLPHPEG 302
           TGRTHQ+RVH      P+ GD  Y  N +   + P+++      +  LHA  +   HP+ 
Sbjct: 271 TGRTHQIRVHMREARHPLAGDLVYG-NPRHVCSQPVKDAVKKLARQALHAYRLSFVHPKS 329

Query: 303 GR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            + +   AP+P  M      L  +   +  + +   
Sbjct: 330 DQSVSFEAPIPDDMYYLLSVLRLESGLDSSLSKEIE 365


>gi|160872397|ref|ZP_02062529.1| ribosomal large subunit pseudouridine synthase C [Rickettsiella
           grylli]
 gi|159121196|gb|EDP46534.1| ribosomal large subunit pseudouridine synthase C [Rickettsiella
           grylli]
          Length = 315

 Score =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 96/322 (29%), Positives = 165/322 (51%), Gaps = 14/322 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +QY+ +  D    RLD +  +    +    L +I+R G++R+ KKRVK + R+Q G 
Sbjct: 1   MQTIQYLTITKDYSGQRLDNFLISRLKGLPKSRLYRIIRKGELRIYKKRVKPDYRLQEGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++R+PP+  +L+ +  ++K+L+      K + FL+  +++ED  + V NKP+G++V GGS
Sbjct: 61  IIRVPPL--SLSGLPTKKKVLNE-----KQAKFLEKTIIFEDKHLLVLNKPSGMAVHGGS 113

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           GI   +    +  +  + +   L HRLD+ETSG L++A+ R+  + L E  R+  I+K Y
Sbjct: 114 GITLGVIEAFR-LIRPQLKFLELVHRLDRETSGCLLMAKKRSILKELHELLRLNGIKKTY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G        +A  L K     G+ +  V   +     +++ F +   ++     +
Sbjct: 173 IALVSGHWPPSLLSVAEPLYKNQRQSGERMVRV---QPEGKRSLTKFSIQQYYSDS-TLV 228

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
              P TGRTHQ+RVHA  +  PI+GD KY               +L+LHA  +    P  
Sbjct: 229 TATPITGRTHQIRVHAQCVNHPIIGDEKYGNKEINKKMRQLGCKRLFLHASELVFTLPSQ 288

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
            + L + A LP  + +  + L 
Sbjct: 289 EKTLTLQAKLPEDLNRLLNQLR 310


>gi|124516586|gb|EAY58094.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Leptospirillum rubarum]
          Length = 339

 Score =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 78/340 (22%), Positives = 152/340 (44%), Gaps = 43/340 (12%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           ++++Y +++ V   E+  RLD +   +        +Q++L    V ++      +++++ 
Sbjct: 14  NILSYREFL-VPRGEQPKRLDIYLSKNCLGFTRSRVQRLLEEKLVTINDIYPASSHKVRG 72

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  +R+               ++    + T   + ++  +LYED  + V +KP G+ V  
Sbjct: 73  GDRIRV---------------LIPPPRSQTAQPENIRLEILYEDEDLIVISKPPGLVVHP 117

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ----------------KPRLTHRLDQETSGILVVART 163
             G      ++G L  +     +                +  L HRLDQ+TSG++VV +T
Sbjct: 118 APGHSSGTLVNGLLFHFQSQGDEQKKGEPEEEEEAERPLRAGLVHRLDQDTSGVMVVGKT 177

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
            +    L   F+ R + K Y +LV GI   K+  I   + + +H    +        +  
Sbjct: 178 ESVVLDLMNQFKDRSVSKKYLALVKGILPKKRGEINAPIGRSTHDRKKFTVR-----QDG 232

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
             +++ ++V++ + + +  LE+   TGRTHQ+RVH  ++G P++GD  Y +    N   P
Sbjct: 233 KPSVTRYRVLETYHENYSLLEVTLLTGRTHQIRVHFRYLGFPLLGDAVYGSKGTENKNFP 292

Query: 284 IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
              +  LHA  +   HP    +++  APLP   V   + L
Sbjct: 293 ---RQMLHAWKLSFQHPSSNSKMEFEAPLPPDFVSALERL 329


>gi|91216414|ref|ZP_01253381.1| ribosomal large subunit pseudouridine synthase [Psychroflexus
           torquis ATCC 700755]
 gi|91185552|gb|EAS71928.1| ribosomal large subunit pseudouridine synthase [Psychroflexus
           torquis ATCC 700755]
          Length = 345

 Score =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 75/327 (22%), Positives = 146/327 (44%), Gaps = 33/327 (10%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
              +E +R+D++  N   +     +Q+  + G + V+   VK N ++++G  V++     
Sbjct: 22  SKGQEPLRVDKFLMNFIENATRNKVQQAAKDGNIYVNGIPVKQNYKVKAGDEVKV----- 76

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHID 130
            L +   E  +    + L          ++YED  + V NK AG+ V  G G      I+
Sbjct: 77  LLAYPPYENLLTPEDIPLD---------IVYEDDALLVVNKAAGMVVHPGHGNYSGTLIN 127

Query: 131 GFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             +   ++  ++   +P L HR+D++TSG+LVVA+T AA  +L+  F  +  ++ Y ++ 
Sbjct: 128 ALVYHFENLPNNSSDRPGLVHRIDKDTSGLLVVAKTEAAMAYLSRQFFHKTSKREYVAIA 187

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           WG    ++  I   + +        +  +  +      A++H+KVI+        +  Q 
Sbjct: 188 WGNLNEEEGTIEGNIGRNPKNRLQNIVYLGDDADQGKPAVTHYKVIERLG-YVTLISCQL 246

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHARYM 295
            TGRTHQ+RVH  H+G  +  D +Y  +     T+             +  +  LHA+ +
Sbjct: 247 ETGRTHQIRVHLKHIGHTLFNDERYGGDKILKGTTFTKYKQFVDNCFKVLPRQALHAKKL 306

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDS 321
              HP     ++  + +P  M +  + 
Sbjct: 307 AFEHPTTKEWMEFNSEIPEDMTQCIER 333


>gi|315612946|ref|ZP_07887857.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis ATCC 49296]
 gi|315315056|gb|EFU63097.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis ATCC 49296]
          Length = 299

 Score =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 148/324 (45%), Gaps = 34/324 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +    RLD+   +    ++     + +++GQV V+ +  K    +Q G +V      
Sbjct: 3   IKIETGGQRLDKALSD-LTELSRSLANEQIKAGQVLVNGQVKKAKYIVQEGDIV------ 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 56  ---AYHVPEPEVLE------YVAENLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F+V++ F   +  LE+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFQVLERFGD-YSLLEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           L+ TA +P    +T + L    +R
Sbjct: 276 LEFTADIPEIFKETLERLRKTENR 299


>gi|154496189|ref|ZP_02034885.1| hypothetical protein BACCAP_00473 [Bacteroides capillosus ATCC
           29799]
 gi|150274744|gb|EDN01808.1| hypothetical protein BACCAP_00473 [Bacteroides capillosus ATCC
           29799]
          Length = 304

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 78/328 (23%), Positives = 135/328 (41%), Gaps = 38/328 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + +  D    R+D++     P ++    QK+L  G V +    VK N +   G  + 
Sbjct: 1   MTPLTLRADRVGERVDQFLSRQLPQLSRSAAQKLLEEGAVTLKGLPVKKNYKTAEGDELV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +                L   V +      +   ++YED  + V NKP G+ V   +G  
Sbjct: 61  LS---------------LPDPVEVDVVPQDIPLDVVYEDGDVIVINKPVGMVVHPAAG-- 103

Query: 127 YHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            H DG L + +               +P + HR+D++TSG+++ A++  A   L E  + 
Sbjct: 104 -HPDGTLVNALLYHCGKSLSGINGELRPGIVHRIDRDTSGLIIAAKSDFAHLALAEQLQD 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + + Y ++  G  K  +  +   + +             Q       A++H+ V++ F
Sbjct: 163 HSLYREYEAVAVGGFKEDEGTVRAPIARHPTDRKKMAVNFLQ----GREAVTHYTVLERF 218

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           +     L+ +  TGRTHQ+RVH  H+G P++GD  Y +        P      LHAR + 
Sbjct: 219 S-GCTHLQCRLETGRTHQIRVHMAHIGHPLLGDTVYGSKKP----YPGLAGQCLHARRLS 273

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLG 323
             HP  G R+ +  PLP       D L 
Sbjct: 274 FVHPRTGERMTVECPLPDWFEAVLDKLR 301


>gi|30248520|ref|NP_840590.1| rluD; ribosomal large subunit pseudouridine synthase D
           [Nitrosomonas europaea ATCC 19718]
 gi|34395760|sp|Q82WZ5|RLUD_NITEU RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|30138406|emb|CAD84416.1| rluD; ribosomal large subunit pseudouridine synthase D
           [Nitrosomonas europaea ATCC 19718]
          Length = 344

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 141/322 (43%), Gaps = 28/322 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V ++   +RLD+      P  +   LQ  +    V VD        ++  G+ +R+ 
Sbjct: 33  ELTVPDNLAGLRLDQALAQLLPQWSRSRLQGWIEQKCVSVDSAAATCKQKVWGGESIRVI 92

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
                 +               +  ++ +   +L+ED  + + +KPAG+ V  G+G  + 
Sbjct: 93  AGQTENDQ--------------SHQAEAIPLKILFEDDHLIIIDKPAGLVVHPGNGNWHG 138

Query: 128 HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   L +      Q PR  + HRLD++T+G+LVVA+T  A   L    + R +++ Y +
Sbjct: 139 TLLNALLNHAPQLSQVPRAGIVHRLDKDTTGLLVVAKTIEAQFDLARQLQQRTVKRHYLA 198

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  +     + +  + +  I    + VV    +    A +H++V++ F      L  
Sbjct: 199 LVLGKLEKDG--VVDAPIGRHPIHRTRMAVV----QNGKPARTHYRVLEKFT-ASTLLHC 251

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI---QNKLYLHARYMDLPHPEG 302
              TGRTHQ+RVH L +G P+ GD  Y        T+       +  LHA  ++L HP  
Sbjct: 252 SLETGRTHQIRVHLLSIGHPLAGDPVYGRTSPDPSTADAVVRLPRQALHAWQLELTHPHS 311

Query: 303 GRL-QITAPLPAHMVKTWDSLG 323
           G++    +PLP  M     ++ 
Sbjct: 312 GQILLWESPLPDDMAALLQAIR 333


>gi|119478176|ref|ZP_01618232.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [marine gamma
           proteobacterium HTCC2143]
 gi|119448685|gb|EAW29929.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [marine gamma
           proteobacterium HTCC2143]
          Length = 328

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 103/328 (31%), Positives = 170/328 (51%), Gaps = 25/328 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V +     R+D +   H   +    + +ILR G+VRV+K RVK   R+  G ++R
Sbjct: 16  VTFLEVTDAHAGQRIDNFLLRHLKGVPKSRIYRILRKGEVRVNKSRVKAEYRLCDGDLLR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP       I   +     SV+L++    L + +LYED ++ + NKP+G++V GGSGI+
Sbjct: 76  IPP-----VRISDAKPAESVSVSLSR---LLSNSILYEDDRLLIINKPSGLAVHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L+  +  + +   L HRLD++TSG +++A+ R+  +HL E  R  +I K Y +L
Sbjct: 128 QGLIEALR-VLRPEARFLELVHRLDRDTSGCVMIAKKRSMLRHLHEQLRSGKIDKRYLAL 186

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    K+  +   LLK S   G+ +  V         +I+ F V++ +AQ    +E +
Sbjct: 187 VSGRWPQKRRVVNEPLLKNSLQSGERMVNV---APEGKKSITEFSVVERYAQ-ATLVEAK 242

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           P TGRTHQ+RVHA + GCP++GD KY       +F      +L+LHA  + +P P     
Sbjct: 243 PITGRTHQIRVHAQYAGCPLLGDDKYGNPAACRDFKKRGLRRLFLHAASLKVPLP----- 297

Query: 306 QITAPLPAHMVKTWDSLGFKYDRNLYIK 333
                 P+ +    + L  + D +  + 
Sbjct: 298 ------PSDLADAPEFLMVRADLDAELS 319


>gi|15966478|ref|NP_386831.1| putative ribosomal large subunit pseudouridine synthase protein
           [Sinorhizobium meliloti 1021]
 gi|307300485|ref|ZP_07580265.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti BL225C]
 gi|307318350|ref|ZP_07597785.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti AK83]
 gi|15075749|emb|CAC47304.1| Putative ribosomal large subunit pseudouridine synthase
           [Sinorhizobium meliloti 1021]
 gi|306896032|gb|EFN26783.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti AK83]
 gi|306904651|gb|EFN35235.1| pseudouridine synthase, RluA family [Sinorhizobium meliloti BL225C]
          Length = 343

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 86/345 (24%), Positives = 151/345 (43%), Gaps = 46/345 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           + V+   D+   RLD +         +   ++ ++  G V ++   V     ++  G   
Sbjct: 12  RKVLTAGDDAAGRLDAFLTEALAGEFSRNRIKSLIEQGAVSINGATVTEPKRKVHPGDSF 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           RI                L    +     + +   +LYED+ + V  KPAG+ V  G+G 
Sbjct: 72  RI---------------ALPEPEDPEPKGEAIPLDVLYEDADLIVLVKPAGLVVHPGAGN 116

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  +    DS       ++P + HRLD++TSG++VVA+  AA +HL++ F    
Sbjct: 117 WTGTLVNALIHHCGDSLSGIGGVKRPGIVHRLDKDTSGVMVVAKNDAAHRHLSDQFADHG 176

Query: 179 ----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y ++VWG P+  K  I   L +          V +++   A  AI+H++V++
Sbjct: 177 RNGPLERAYRAVVWGRPRQLKGKIDAPLGRAG--DRTKRAVKREDSDDAREAITHYEVVE 234

Query: 235 CFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
            + +K         +E    TGRTHQ+RVH  H+G P++GD  Y A F+       +   
Sbjct: 235 RYHEKPDGTSLASTVECHLETGRTHQIRVHMAHIGHPLIGDPDYGAAFRTKANLLPEPAR 294

Query: 286 ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                  +  LHA  +   HP  G  +    P+PA M +   +L 
Sbjct: 295 AAVNRFPRQALHAFMLQFEHPATGETMHFETPVPADMQELIAALR 339


>gi|120609862|ref|YP_969540.1| RluA family pseudouridine synthase [Acidovorax citrulli AAC00-1]
 gi|120588326|gb|ABM31766.1| pseudouridine synthase, RluA family [Acidovorax citrulli AAC00-1]
          Length = 399

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 101/319 (31%), Positives = 160/319 (50%), Gaps = 21/319 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++V V+ +    RLD +       +   ++ +I+RSG+VR++K R   + R+++G VVR
Sbjct: 81  VRWVEVDAESAGQRLDNFLIRELKGVPKTHVYRIIRSGEVRINKGRAAADTRVEAGDVVR 140

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +     K ++   +           +  LL ED  +   +KPAG++V GGSG++
Sbjct: 141 VPPVRISDKVAAKAERPAPAR----------EFPLLLEDEHLVALDKPAGVAVHGGSGVS 190

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD+ETSGIL+VA+ R+A  HL + FR R   K Y +L
Sbjct: 191 FGVIEQLRQARPQ-ARFLELVHRLDRETSGILLVAKKRSALTHLQDQFRERETGKTYLAL 249

Query: 187 VWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK------ 239
           V G    + + I   L K     G+  V V  +++     +I+  KV      +      
Sbjct: 250 VSGEWPERLKVIDAPLHKYLQADGERRVRVTTEDDPDGMRSITLVKVRSRVPARPAEGLP 309

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDL 297
               LE+   TGRTHQ+RVH    G PIVGD KY   +           +++LHA  +  
Sbjct: 310 AMALLEVTIKTGRTHQIRVHLASRGHPIVGDDKYGDFDLNRRVQKHGLRRMFLHAWRLQF 369

Query: 298 PHP-EGGRLQITAPLPAHM 315
            HP  G R+++ A LPA +
Sbjct: 370 SHPASGERIELHAELPAEL 388


>gi|297621774|ref|YP_003709911.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
 gi|297377075|gb|ADI38905.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
          Length = 310

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 85/327 (25%), Positives = 149/327 (45%), Gaps = 32/327 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +    + ++   +E   RLD+     YP   +   LQ ++    V ++ K VK   ++ +
Sbjct: 2   ITPDTETLMTTAEEAGKRLDKVLAERYPDAYSRSYLQWLIEENHVLLNHKPVKKRAKVAA 61

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + +  V+     +  E+  LD               +++ED  I V NKPAG+ V  
Sbjct: 62  GDRIDVCFVLAPEIELKPEKIFLD---------------IIHEDEAIIVVNKPAGLVVHP 106

Query: 122 GSG--IAYHIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G+G      ++G L   K   + +  +P + HRLD+ET+G+LV A+T  A   L E F  
Sbjct: 107 GAGNWTGTFVNGLLYHCKKLPEGETLRPGIVHRLDKETTGLLVAAKTAEAQHKLVELFSS 166

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           RR+ K Y ++  G P   K  +   + +   +    + +V    +G   +++H++ +   
Sbjct: 167 RRVYKEYIAVCVGNP--GKGTVDAPIARH-PVHRQKMAIV----EGGRRSVTHYETLKYD 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +++   TGRTHQ+RVH   +G P++GD  Y ++           +  LHA  + 
Sbjct: 220 VS-LSLVKLVLETGRTHQIRVHMKQIGFPVLGDPVYGSSAMNQ--KFQLGRQMLHAAKLI 276

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
            PHP  G  + + AP+P  M K    L
Sbjct: 277 FPHPVTGKEMVLEAPVPDEMAKVMARL 303


>gi|121605976|ref|YP_983305.1| RluA family pseudouridine synthase [Polaromonas naphthalenivorans
           CJ2]
 gi|120594945|gb|ABM38384.1| pseudouridine synthase, RluA family [Polaromonas naphthalenivorans
           CJ2]
          Length = 398

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 103/342 (30%), Positives = 165/342 (48%), Gaps = 25/342 (7%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           + +     V V+ D    RLD +       +   ++ +I+RSG+VRV+K R   + R+++
Sbjct: 44  TALPQATLVTVDEDYAGQRLDNFLIRQLKGVPKTHVYRIIRSGEVRVNKGRAHADTRVEA 103

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKH---------SDFLKSILLYEDSKIYVFN 112
           G +VR+PPV  +     K Q +      + +H         +   +  +L+ED  +   +
Sbjct: 104 GDIVRLPPVRTSERAEQKAQAMQSVMTEVARHGASSTVGGYAPAAEFPILFEDDFLLAID 163

Query: 113 KPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           KPAG++V GGSG+++ I   L+     +     L HRLD+ETSGIL++A+ R A + L E
Sbjct: 164 KPAGVAVHGGSGVSFGIIEQLR-MARPEADFLELVHRLDRETSGILLIAKRRMALKLLQE 222

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFK 231
            FR R   K+Y +LV G     +  I   L K     G+  V +V  +   A  +++  K
Sbjct: 223 QFRERETDKVYLALVSGNWPANQRVIDKALHKYLLPNGERRVKIVANDHPDAMRSVTLVK 282

Query: 232 VID-------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKG 278
           V           A  F  LE+   TGRTHQ+RVH    G PI GD KY       A  + 
Sbjct: 283 VKTPIAANPLAPATPFTLLEVTIKTGRTHQIRVHLAGEGHPIAGDDKYGDFELNKALQRS 342

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           +  S    +++LHA  +   HP+  + +Q+ A LP  + +  
Sbjct: 343 SAGSASLKRMFLHAWSLKFNHPKTRKAVQLQASLPEELQQFL 384


>gi|241662583|ref|YP_002980943.1| pseudouridine synthase [Ralstonia pickettii 12D]
 gi|240864610|gb|ACS62271.1| pseudouridine synthase, RluA family [Ralstonia pickettii 12D]
          Length = 344

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 100/322 (31%), Positives = 163/322 (50%), Gaps = 23/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  + E  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 29  VAYVEIGEEAEGQRIDNFLMRVAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 88

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+             +   V   +     +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 89  IPPLR------------IAQQVEAARPVPAAEFAILHEDTHLLVIDKPAGVAVHGGSGVA 136

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++ 
Sbjct: 137 FGVIEQLRQ-SRPDAKFLELVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFAA 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  +K++ I + L K +   G+    V+ +      + + F  +  F   +  LE +
Sbjct: 196 VKGVWPHKRQHIKSPLYKYTTPEGERRVRVQAD---GQASHTIFNKVGVFG-PYTLLEAE 251

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H G PI+GD KY              SP   +++LHA  + L HP 
Sbjct: 252 LKTGRTHQIRVHLAHAGFPILGDDKYGDFALNKALSRANASPRLARMFLHAHRLQLTHPH 311

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  +   APLPA      ++ 
Sbjct: 312 SGEVVTFNAPLPAECTDFLNAF 333


>gi|288940468|ref|YP_003442708.1| RluA family pseudouridine synthase [Allochromatium vinosum DSM 180]
 gi|288895840|gb|ADC61676.1| pseudouridine synthase, RluA family [Allochromatium vinosum DSM
           180]
          Length = 346

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 98/320 (30%), Positives = 160/320 (50%), Gaps = 17/320 (5%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           QYV V+   +  R+D +       +   +L ++LR G+VRV+K RVK   R+ +G VVRI
Sbjct: 37  QYVQVDTQADGQRIDNFLLRILKGVPRSHLYRLLRRGEVRVNKGRVKAEYRLCAGDVVRI 96

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP        I+  +    +         L+  +++ED ++ V +KP+G++V GGSG++Y
Sbjct: 97  PP--------IRLGESAPPARAPEAQLARLEGAIIHEDERLLVIDKPSGLAVHGGSGLSY 148

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L+      G++  L HRLD++TSG LVV + R+A + L    R   + K Y +L+
Sbjct: 149 GLIESLRQLRP--GRELELVHRLDRDTSGCLVVCKRRSALRELHALIREGGLDKRYLALI 206

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLE 244
            G     +  +   L K     G+ +  V+ + +G   A + F+ +  F    Q    +E
Sbjct: 207 LGELPRAELLVDAPLKKNVLSSGERL--VRVDAQGGKEARTRFRRLKRFAIDGQALTLVE 264

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGG 303
            +  TGRTHQ+RVHA H+G P+ GD KY               +L+LHA  +        
Sbjct: 265 AELITGRTHQIRVHAAHLGTPLAGDDKYGDEAANQRLKGYGLKRLFLHASALSFKLECMA 324

Query: 304 R-LQITAPLPAHMVKTWDSL 322
           R L++  PLP  + +  D+L
Sbjct: 325 RPLRLECPLPDELQQVLDAL 344


>gi|146300375|ref|YP_001194966.1| RluA family pseudouridine synthase [Flavobacterium johnsoniae
           UW101]
 gi|146154793|gb|ABQ05647.1| ribosomal large subunit pseudouridine synthase D [Flavobacterium
           johnsoniae UW101]
          Length = 347

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 84/328 (25%), Positives = 142/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V   +  +R+D++     P+     +Q     G + V+   VK N +++   V+ I    
Sbjct: 23  VPKGQAFLRIDKYLMYLIPNATRNKIQNAATDGNIFVNDIPVKSNYKVKPFDVITIM--- 79

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
             L+H   E  IL   + L          ++YED  + + NK  G+ V  G G     + 
Sbjct: 80  --LSHPPFENHILPEDIPLN---------IVYEDDALLLINKEPGMVVHPGHGNYTGTLV 128

Query: 131 GFLKSWVDS----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             L    D+      ++P L HR+D++TSG+LVVA+T AA  HL + F  +  ++ Y +L
Sbjct: 129 NALAHHFDNLPMNSSERPGLVHRIDKDTSGLLVVAKTEAAMTHLAKQFEAKTTEREYIAL 188

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           VWG    +   I   L +  H+       V  + +    AI+H+KV++ F      +  +
Sbjct: 189 VWGNVAAESGTIEGNLAR--HLKDRMQMAVFADPEIGKPAITHYKVLERFG-YVTLISCK 245

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLHARY 294
             TGRTHQ+R H  H+G P+  D +Y  +     T+  +             +  LHA+ 
Sbjct: 246 LETGRTHQIRAHMKHIGHPLFNDERYGGHLILKGTTFTKYKQFIENCFKALPRQALHAKT 305

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           +   HP  G  ++    LP       + 
Sbjct: 306 LGFVHPNTGELMRFDTELPQDFQDCIEK 333


>gi|134295142|ref|YP_001118877.1| RluA family pseudouridine synthase [Burkholderia vietnamiensis G4]
 gi|134138299|gb|ABO54042.1| pseudouridine synthase, RluA family [Burkholderia vietnamiensis G4]
          Length = 334

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 100/326 (30%), Positives = 157/326 (48%), Gaps = 23/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++ +    R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +V
Sbjct: 16  QVSMIEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLALGDLV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + + +  +                +LYED  + V NKPAG++V GGSG+
Sbjct: 76  RVPPVRVAAADLARAETPIVPPAQFD---------VLYEDDAMLVINKPAGVAVHGGSGV 126

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y++
Sbjct: 127 AFGVIEQMRQAR-PRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFA 185

Query: 186 LVWGIPKNKKE---CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
              G  +        +   L K S   G+    V+ +      + + F +I+ +   +  
Sbjct: 186 CGHGQWQPDWGRRRVVKAPLFKYSTAEGERRVRVQDD---GLPSHTVFNLIERWPD-YAL 241

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PI GD KY               P   +++LHA  + L
Sbjct: 242 VEAELKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANAQPSLKRMFLHAYRLKL 301

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLP    +  D L
Sbjct: 302 AHPLSGEPLQFDAPLPDECRRFLDQL 327


>gi|167586609|ref|ZP_02378997.1| pseudouridine synthase, RluA family protein [Burkholderia ubonensis
           Bu]
          Length = 334

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 100/326 (30%), Positives = 160/326 (49%), Gaps = 23/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  V ++      R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +V
Sbjct: 16  QVSMVEIDETAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAHGDIV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + +    +    +           +L+ED  + V +KPAG++V GGSG+
Sbjct: 76  RVPPVRMAAADLARADTPVVPPAHFD---------VLFEDDAMLVIDKPAGVAVHGGSGV 126

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   L+     + +   L HRLD+ETSG+L++A+ RAA   L E  R  R+ K Y++
Sbjct: 127 AFGVIEQLRQAR-PRAKFLELVHRLDRETSGVLMLAKKRAALVGLHEMIRENRMDKRYFA 185

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G  ++       +   L K +   G+    V+ +      + + F +++ +   +  
Sbjct: 186 CVHGEWQSDWGRRRAVKAPLFKYTTPEGERRVRVQDD---GLPSHTVFNLVERWPD-YAL 241

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-----PIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PI GD KY         S     P   +++LHA  + L
Sbjct: 242 VEAELKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALSRANAQPSLKRMFLHAHRLRL 301

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLP    +  D L
Sbjct: 302 AHPLTGEALQFDAPLPDECRRFLDQL 327


>gi|256819393|ref|YP_003140672.1| pseudouridine synthase, RluA family [Capnocytophaga ochracea DSM
           7271]
 gi|256580976|gb|ACU92111.1| pseudouridine synthase, RluA family [Capnocytophaga ochracea DSM
           7271]
          Length = 352

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 152/330 (46%), Gaps = 35/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
                 +E +R+D++  N   +     +Q+  + G + V+ + VK N+R+++   V++  
Sbjct: 29  FTAGKGQEPLRVDKFLMNFVENATRNKVQQAAKQGNIFVNGEPVKSNHRVKANDEVKV-- 86

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                 H   E  ++  ++ L          ++YED  + V NKPAG+ V  G G     
Sbjct: 87  ---LFPHPPHEDLLVPENIPLN---------IVYEDDSLLVVNKPAGMVVHPGHGNYSGT 134

Query: 128 HIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            I+  +   ++  ++   +P L HR+D++TSG+LVVA+T  A  HLT+ F  +  Q+ Y 
Sbjct: 135 LINALVYHFENLPNNSSNRPGLVHRIDKDTSGLLVVAKTEEAMLHLTQQFFNKTTQREYI 194

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG  +  +  +   + +  H+       V  +      A++H+KV++ F      + 
Sbjct: 195 ALVWGNIEEDEGTVCGHIGR--HLKDRLQMDVFPDGSHGKEAVTHYKVLERFG-YVTLIS 251

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLHA 292
            +  TGRTHQ+RVH  H+G  +  D +Y  +     T+  +             +  LHA
Sbjct: 252 CKLETGRTHQIRVHLKHIGHTLFNDERYGGDKILKGTTFAKYKQFVENCFAVLPRQALHA 311

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP   + L   + LP  M +  + 
Sbjct: 312 KTLGFEHPITHKYLSFDSELPNDMQQCIEK 341


>gi|253681471|ref|ZP_04862268.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum D str. 1873]
 gi|253561183|gb|EES90635.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum D str. 1873]
          Length = 304

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 87/326 (26%), Positives = 143/326 (43%), Gaps = 38/326 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            +  ++  +  N RLD +  N     +   +QK+++ G V+V+ K  K N +++    V 
Sbjct: 3   TKEFIIHENLVNCRLDVFISNSLEGKSRSYIQKLIQEGHVKVNGKDKKSNYKLKLHDSVI 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---- 122
           +  + N    I  E   LD               +LYED  I V NKP G+ V       
Sbjct: 63  VNNIENEFQKINPENIDLD---------------ILYEDKDIIVINKPQGMVVHPATSNY 107

Query: 123 -----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                +G+ YH D  L +  D    +P + HR+D++TSG+LVVA+   A + L E  +  
Sbjct: 108 SGTLVNGLLYHCD-TLSTLNDDT--RPGIVHRIDKDTSGVLVVAKNNKAHEVLAEQLKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV GI K     I   L +          V     +    AI+H++V+  F 
Sbjct: 165 SMKREYIALVEGILKKDNGFIDKPLGRNPKDRIKMAVV-----QEGKNAITHYEVLKRFK 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    ++    TGRTHQ+RVH  ++G P+VGD  Y    +            LHA+ +  
Sbjct: 220 KN-TLVKCILETGRTHQIRVHMSYIGHPLVGDPMYGFKKQ----RFKLKGQMLHAKKLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP     ++  + LP +  +    L
Sbjct: 275 IHPTTQEYIEFQSDLPKYYKEVLLKL 300


>gi|237746821|ref|ZP_04577301.1| ribosomal large subunit pseudouridine synthase D [Oxalobacter
           formigenes HOxBLS]
 gi|229378172|gb|EEO28263.1| ribosomal large subunit pseudouridine synthase D [Oxalobacter
           formigenes HOxBLS]
          Length = 342

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 81/311 (26%), Positives = 136/311 (43%), Gaps = 29/311 (9%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+    H P  +   +Q+ +  G V VD K  +    +   + + + P +   +
Sbjct: 37  EGGERLDKIVARHLPDYSRSRIQRWIEQGYVTVDGKAAQGKQTVVGDEEIVVLPQLAEED 96

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL 133
                         L    + +   +L+ED  I V NKPAG+ V   +G      ++G L
Sbjct: 97  --------------LAFVPEPVGFPVLFEDRDILVVNKPAGLVVHPAAGNWSGTLLNGLL 142

Query: 134 KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                S    +  + HRLD++TSG++VVA+T  A  HL    + R +++ Y +LVWG   
Sbjct: 143 HHLPKSAAIPRAGIVHRLDKDTSGLMVVAKTLEAQTHLVRQLQARTVRREYLALVWGE-T 201

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHT 249
                +   + +      D + +          A++H+++++   C   K   ++ +  T
Sbjct: 202 PVAGTVDQPIGRHPK---DRIKMAVLQTASGKPAVTHYRLLETGVCNGSKVSLVKCRLET 258

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QIT 308
           GRTHQ+RVH    G P+VGD  Y  +      S +  +  LHA  + L HP      +  
Sbjct: 259 GRTHQIRVHMQFSGFPLVGDPLYGKSR----LSAVFPRQALHAFRLGLLHPAKNEWNEWM 314

Query: 309 APLPAHMVKTW 319
           APLP+ M    
Sbjct: 315 APLPSDMRMLL 325


>gi|150009274|ref|YP_001304017.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           distasonis ATCC 8503]
 gi|255015880|ref|ZP_05288006.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_7]
 gi|256841839|ref|ZP_05547345.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           sp. D13]
 gi|262384161|ref|ZP_06077297.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_33B]
 gi|301311073|ref|ZP_07217002.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           20_3]
 gi|149937698|gb|ABR44395.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           distasonis ATCC 8503]
 gi|256736733|gb|EEU50061.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           sp. D13]
 gi|262295059|gb|EEY82991.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_33B]
 gi|300831136|gb|EFK61777.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           20_3]
          Length = 359

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 83/340 (24%), Positives = 148/340 (43%), Gaps = 37/340 (10%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S M      V +  +  +R+D++  +         +Q    +G + V+ K VK N R++ 
Sbjct: 27  SQMYEHFRFVADKGQSLLRVDKFLVDRMMGATRNRIQLAAEAGCILVNDKPVKSNYRVKP 86

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
             VV I      ++   +E +I+   + L          ++YED  + V NKPAG+ V  
Sbjct: 87  LDVVSI-----VMDRPRRELEIIPEDIPLN---------IVYEDDDLLVVNKPAGLVVHP 132

Query: 122 GSG-----IAYHIDGFLKS--WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G G     +   +  +LK   + D    +  L HR+D++TSG+LVVA+   A  +L+  F
Sbjct: 133 GHGNYTGTLVNALAYYLKDDPYYDPSDPRLGLVHRIDKDTSGLLVVAKRPEAKSNLSLQF 192

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             +  ++ Y +LVWGI +  +  I   + +           V         A++H+ V++
Sbjct: 193 FNKTTKRKYRALVWGIVQEDEGRIEGNIGRDPR--DRMQMTVFPEGDQGKTAVTHYTVLE 250

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP----------- 283
                   +E +  TGRTHQ+RVH  ++G  +  D +Y  +     T+            
Sbjct: 251 RLG-YVSLVECRLETGRTHQIRVHMKYIGHTLFNDERYGGHDILKGTTFTKYKQFVQNCF 309

Query: 284 -IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
            I  +  LHA+ +   HP  G  +   + +P+ M +  D 
Sbjct: 310 AICPRQALHAKTLGFVHPTTGEEMFFDSEIPSDMQQLIDR 349


>gi|326692704|ref|ZP_08229709.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           argentinum KCTC 3773]
          Length = 308

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 89/325 (27%), Positives = 152/325 (46%), Gaps = 31/325 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    + +   ++  R+D    N     +   L   ++SG+V V+ +RVK + ++ +G 
Sbjct: 1   MTD--KITINITDQTGRIDAILANQNLPYSRTVLANWVQSGEVLVNGQRVKRSYKVAAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ I P       I+ E   LD               ++YED+ + V NKP G+ V   +
Sbjct: 59  VISIQPPAVQPTEIVAEAMPLD---------------IVYEDADLLVVNKPQGMVVHPAA 103

Query: 124 GIA--YHIDGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G      ++G L     S      +P + HR+D++TSG+L+VA+   A Q L+   +  +
Sbjct: 104 GHTSGTLVNGLLHHAPLSTINGEFRPGIVHRIDRDTSGLLMVAKNDQAHQALSAQLKAHK 163

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             +IY++LV G  +     I   + + + I      V    ++G   A++HF+VI  +  
Sbjct: 164 NDRIYYALVRGEFEENTGTINAPIARHA-IDRKKQAV----QEGGREAVTHFEVIARYV- 217

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  L+++  TGRTHQ+RVH  ++G PIVGD  Y        +        LHA+ + L 
Sbjct: 218 GYTLLKVRLETGRTHQIRVHLTYIGHPIVGDPVYGG--AQKLSGVNLAGQLLHAKTLSLT 275

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
            P  G  L   + LPA+  +   +L
Sbjct: 276 QPTTGENLIFDSELPAYFEQALATL 300


>gi|322374526|ref|ZP_08049040.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           C300]
 gi|321280026|gb|EFX57065.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           C300]
          Length = 299

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 145/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +    RLD+   +    ++     + +++GQV V+ +  K    +Q G +V      
Sbjct: 3   IKIETGGQRLDKALSD-LTELSRSLANEQIKAGQVLVNGQAKKAKYTVQEGDIVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAENLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NSLMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+ TA +P    +T + L 
Sbjct: 276 LEFTADIPEIFKETLERLR 294


>gi|227904070|ref|ZP_04021875.1| pseudouridine synthase [Lactobacillus acidophilus ATCC 4796]
 gi|227868089|gb|EEJ75510.1| pseudouridine synthase [Lactobacillus acidophilus ATCC 4796]
          Length = 305

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 82/329 (24%), Positives = 146/329 (44%), Gaps = 35/329 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  M     + V N +   RLD++       ++   ++++++   + V++K  K + +IQ
Sbjct: 1   MKNMPKKYSLEVTN-QRG-RLDKFISEQLSDLSRTRVKELIQDQNILVNEKVEKVSYKIQ 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + I         I+ E   LD               ++YED  + V NKP G+ V 
Sbjct: 59  DGDKIEITVPAVKPLDIVAENIPLD---------------IVYEDDDVIVVNKPQGMVVH 103

Query: 121 GGSGIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G   H   +  L    D     +G +P + HR+D++TSG+L++A+   A + L +  
Sbjct: 104 PAPGHPDHTLVNALLYHTQDLAQSPEGFRPGIVHRIDKDTSGLLMIAKNATARESLEQQL 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             +  ++IYW++V G    ++  I   + +  +       V     +    AI+HFKV+ 
Sbjct: 164 ANKTNKRIYWAIVHGNFSEEQGSIDAPIGRNPYDRKKMAVV-----ENGKKAITHFKVLK 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F + +  +E Q  TGRTHQ+RVH  ++G  + GD  Y         +   N  +LHA+ 
Sbjct: 219 QF-KGYSLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPR-----KTLKGNGQFLHAKI 272

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP+ G+ L+ +   P         L
Sbjct: 273 LGFKHPKTGKWLEFSVEPPKIFQNMLIQL 301


>gi|293401501|ref|ZP_06645644.1| ribosomal large subunit pseudouridine synthase D
           [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305139|gb|EFE46385.1| ribosomal large subunit pseudouridine synthase D
           [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 305

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 146/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  V+V  +E   R+D++       ++   +Q++L+ G V V+    K N +I+   
Sbjct: 1   MREID-VIVTEEEAFQRIDKYISEKEDDLSRSRVQQLLQEGIVCVNGNACKANYKIKPKD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-- 121
            +                 +    + +    + +   + YED  + V NKP G+ V    
Sbjct: 60  HIT---------------AVFCDEIEMEAKPEQMDLDIRYEDHDVIVINKPKGMVVHPAV 104

Query: 122 GSGIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G+     ++G L    D  G     +P + HR+D++T+G+L+VA+   A   L++  + +
Sbjct: 105 GNQTGTLVNGLLYHCKDLSGINGVLRPGIVHRIDKDTTGLLIVAKNDKAHTALSKQLQNK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + ++Y++LV G+ ++    I   + +        + V   N   A  A +HFKVI+ FA
Sbjct: 165 TVNRLYYALVHGVIEHDFGTIDAPIGRDVK-DRQKMAVTATN---AKDARTHFKVIERFA 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +E +  TGRTHQ+RVH  ++  P+VGD KY         +       LHA  +  
Sbjct: 221 H-YTLVECRLETGRTHQIRVHMQYIKHPVVGDEKYSYR-----KTMQTQGQLLHAHQLTF 274

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLG 323
            HP    ++ + A LP       + L 
Sbjct: 275 VHPTTNEKITVEAELPKQFADILEELR 301


>gi|163846479|ref|YP_001634523.1| RluA family pseudouridine synthase [Chloroflexus aurantiacus
           J-10-fl]
 gi|222524258|ref|YP_002568729.1| pseudouridine synthase, RluA family [Chloroflexus sp. Y-400-fl]
 gi|172045876|sp|Q45826|Y901_CHLAA RecName: Full=Uncharacterized RNA pseudouridine synthase Caur_0901;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|163667768|gb|ABY34134.1| pseudouridine synthase, RluA family [Chloroflexus aurantiacus
           J-10-fl]
 gi|222448137|gb|ACM52403.1| pseudouridine synthase, RluA family [Chloroflexus sp. Y-400-fl]
          Length = 316

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 96/321 (29%), Positives = 155/321 (48%), Gaps = 32/321 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV   +   R+DR+     P ++   +Q+++  G V  D +  + +  ++ G V+++
Sbjct: 15  RVVVVPPTQTAERIDRFLAGAMPDLSRAQVQRLIEQGFVLYDGRSPRASQPVRPGAVIQL 74

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                    ++ E   LD               ++YED+ I V NKPAG+ V    G   
Sbjct: 75  TIPPPIPTELVAEPIPLD---------------VVYEDADIAVINKPAGMVVHPAPGHPR 119

Query: 126 AYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++  L  + D       +P + HRLD++TSG+LV+AR   A + L +  + RR++KI
Sbjct: 120 GTLVNALLARYPDLAIGGELRPGIVHRLDRDTSGLLVIARHDQAMRSLVDQQQARRMRKI 179

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G P  +   I   + +        + VV         A +H++++D F   +  
Sbjct: 180 YQALVIGRPP-ETGTIDAPIGRDPR-DRLRMAVV----PDGRPARTHYRLLDTFGD-YSL 232

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           LE+Q  TGRTHQ+RVH  H+G PIVGD  Y        +    ++ +LHA Y+ L HP  
Sbjct: 233 LEVQLETGRTHQIRVHLRHLGYPIVGDPVYGPRR----SHLHLSRQFLHAAYLGLVHPRS 288

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
           GR  + TAPLPA +      L
Sbjct: 289 GRWQEFTAPLPADLQIVLRQL 309


>gi|291614218|ref|YP_003524375.1| pseudouridine synthase, RluA family [Sideroxydans lithotrophicus
           ES-1]
 gi|291584330|gb|ADE11988.1| pseudouridine synthase, RluA family [Sideroxydans lithotrophicus
           ES-1]
          Length = 312

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 104/320 (32%), Positives = 164/320 (51%), Gaps = 21/320 (6%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V ++ ++   E  R+D +   H   +   ++ +ILR G+VRV+KKRV    R+Q G +
Sbjct: 7   ESVSWLEIDEGSEGQRIDNFLFRHLKGVPKSHVYRILR-GEVRVNKKRVDQTYRLQLGDI 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RIPP+  A      E + + ++          +  +LYED  +   NKP+G +V GGSG
Sbjct: 66  LRIPPIRVAEK---PESEYVPAT----------EFPILYEDEALLAINKPSGTAVHGGSG 112

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L+S      +   L HRLD+ETSG+L+VA+ R+A   L E  R     K Y+
Sbjct: 113 VSFGVIEQLRSARPQ-AKLLELVHRLDRETSGVLLVAKKRSALTGLHEIMREGNSDKRYF 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  KN K+ +   L K     G+   +V+++ + ++   +    +     +F  LE
Sbjct: 172 ALVLGQWKNAKQHVKLPLHKFDTPQGEKRVMVREDGQASHTIFT----LQQSWPEFTLLE 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEGG 303
            Q  TGRTHQ+RVH  H+G PI GD KY    +          +++LHA  +   HP  G
Sbjct: 228 AQLKTGRTHQIRVHLSHLGFPIAGDDKYGDFARNKELAKRGLKRMFLHAHSIAFNHPLTG 287

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             L ITAPLP  +    + L
Sbjct: 288 EPLSITAPLPPELQNFLNKL 307


>gi|123441934|ref|YP_001005917.1| 23S rRNA pseudouridylate synthase C [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122088895|emb|CAL11702.1| ribosomal large subunit pseudouridine synthase C [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|318606162|emb|CBY27660.1| ribosomal large subunit pseudouridine synthase C; LSU Psi955,
           Psi2504 and Psi2580 [Yersinia enterocolitica subsp.
           palearctica Y11]
          Length = 319

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 98/322 (30%), Positives = 164/322 (50%), Gaps = 14/322 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEIQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGERMVKVSSE---GKPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDSQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLGFKY 326
           ++I APL   +      L  K 
Sbjct: 296 MRIEAPLDNQLRHCLAVLRKKA 317


>gi|291542663|emb|CBL15773.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           bromii L2-63]
          Length = 306

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 72/316 (22%), Positives = 139/316 (43%), Gaps = 32/316 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +   +RLD++  +    ++      ++ +G V V+   V    ++  G +V +       
Sbjct: 9   ETSGVRLDKFISDANIDLSRSAAVNLIENGAVLVNDSVVSKKYKLSQGDIVVVN------ 62

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGF 132
                    +         ++ +   ++YED  + V NKP G+ V   +G      ++  
Sbjct: 63  ---------VPDPTPYEAKAENIPLDIVYEDECLLVVNKPKGMVVHPAAGNYDGTLVNAL 113

Query: 133 LKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           L    DS        +P + HR+D++TSG+L+VA+   + + L E  +     + Y S+V
Sbjct: 114 LYHCGDSLSGINGVLRPGIVHRIDKDTSGLLIVAKNDFSHRSLAEQIKEHSFTREYESIV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G  KN +  +   + +        + V+   EK +  A++H+ VI  + + +  ++ + 
Sbjct: 174 FGNLKNDEGTVDAPIGRNPK-DRKKMCVI---EKNSKNAVTHYSVITRY-KGYTHIKCKL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++G P+ GD  Y    +            LHAR +   HP+    ++
Sbjct: 229 ETGRTHQIRVHMAYIGHPVSGDKVYGVKNEKVDFE----GQCLHARKIGFIHPKTNEYIE 284

Query: 307 ITAPLPAHMVKTWDSL 322
            T+ LP +  K    L
Sbjct: 285 FTSELPDYFKKYLKKL 300


>gi|255321251|ref|ZP_05362417.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           radioresistens SK82]
 gi|262380064|ref|ZP_06073219.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           radioresistens SH164]
 gi|255301805|gb|EET81056.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           radioresistens SK82]
 gi|262298258|gb|EEY86172.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           radioresistens SH164]
          Length = 312

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 94/319 (29%), Positives = 162/319 (50%), Gaps = 19/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K  +++  G  VR
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAESKLAIGDQVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P+        K++  +  S    K +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAPIRFEP----KDETPVPVS---DKVAQGLLSRVIYEDEGLMVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y ++
Sbjct: 123 YGLIEGLRAATGKKY--LELVHRIDRDTSGLVMISKKRSVLKTLQDLLREHKIKKTYAAI 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     ++ I   L +     G+    V +  K +    + + V + F      +   
Sbjct: 181 VKGQVSLDQQLIDAPLYRYELANGERRVRVSKEGKDSK---TQWNVAERFMH-ATLVYAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P+VGD KY    +  +  P   +L LHA  +++P    G   
Sbjct: 237 PLSGRTHQIRVHGLSIGHPLVGDDKYG--HETEYKGPKPRRLCLHAIRLEIP----GYPT 290

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I APLP  M      L  +
Sbjct: 291 IEAPLPEDMQSLAAQLRAQ 309


>gi|126664287|ref|ZP_01735278.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BAL38]
 gi|126623707|gb|EAZ94404.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BAL38]
          Length = 346

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 154/331 (46%), Gaps = 43/331 (12%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
              +  +R+D++  N   +     +Q+   +G + V+   VK N ++++G VVR+     
Sbjct: 23  SKGQSALRVDKFLMNMIENTTRNKIQQAAENGSILVNDVAVKSNYKVKAGDVVRL----- 77

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-------- 124
            L H   EQ +   ++ L          ++YED ++ V NKPAG+ V  G G        
Sbjct: 78  VLAHPTYEQLLTPENIPLD---------IVYEDDQLLVINKPAGMVVHPGHGNYSGTLVN 128

Query: 125 -IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            +AYH +        +  ++P L HR+D++T+G+LVVA+T  A  +L++ F  +  ++ Y
Sbjct: 129 ALAYHFENL----PMNSSERPGLVHRIDKDTTGLLVVAKTELAMAYLSKQFAEKTSEREY 184

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LVWG  +  +  +   + +  H        V ++++    A++H+KV++ F      +
Sbjct: 185 VALVWGNIEEDEGTVEGNIGR--HDTNRMRMAVHESDEKGKPAVTHYKVLERFG-YVTLV 241

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLH 291
             Q  TGRTHQ+RVH  H+G  +  D +Y  +     T+  +             +  LH
Sbjct: 242 SCQLETGRTHQIRVHMKHIGHTLFNDERYGGDSILKGTTFTKYKQFVDNCFKVLPRQALH 301

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           A+ +   HP     L+   P+P  +    + 
Sbjct: 302 AKTLGFEHPITKEFLRFNTPIPQDLQDCIEK 332


>gi|326203544|ref|ZP_08193408.1| pseudouridine synthase, RluA family [Clostridium papyrosolvens DSM
           2782]
 gi|325986364|gb|EGD47196.1| pseudouridine synthase, RluA family [Clostridium papyrosolvens DSM
           2782]
          Length = 304

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 82/325 (25%), Positives = 152/325 (46%), Gaps = 32/325 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++E D + +R+D W   +    +   +QK+   G + V++ + K N +++ G  ++
Sbjct: 1   MKEFILECDTDGVRIDSWLAGNLEDYSRSYIQKLCLDGNIWVNEVQAKSNYKVKPGDNIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSG 124
           +          + + +ILD         + +   ++YED  I V NKP G+ V    G+ 
Sbjct: 61  VS---------VPDAEILDV------EPEDIPLDIVYEDKHIIVINKPKGMVVHPAVGNY 105

Query: 125 IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  +K   DS        +P + HR+D++TSG+LVVA++  A + L+E  +   I
Sbjct: 106 SGTLVNALMKHCGDSLSDINGVIRPGIVHRIDKDTSGLLVVAKSNIAHERLSEKLKTHDI 165

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +LV GI       I   + +   +    + V   N +    AI+HFKV++ F   
Sbjct: 166 KREYIALVDGIIYENSGKIDAPIGRH-PVERKKMSV---NTQNGRNAITHFKVLERFPS- 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
             +++++  TGRTHQ+RVH  ++  PI+GD  Y    +   T        LHA  +   H
Sbjct: 221 ATYVQLKLETGRTHQIRVHMSYINHPIIGDMVYGRRKQKFKT----KGQVLHAWRLSFQH 276

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  G  ++    +P +       L 
Sbjct: 277 PVTGEDMKFETAVPEYFQSILSQLR 301


>gi|189464334|ref|ZP_03013119.1| hypothetical protein BACINT_00675 [Bacteroides intestinalis DSM
           17393]
 gi|189438124|gb|EDV07109.1| hypothetical protein BACINT_00675 [Bacteroides intestinalis DSM
           17393]
          Length = 357

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 86/343 (25%), Positives = 156/343 (45%), Gaps = 39/343 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ I  
Sbjct: 33  VVVDRGQEMMRVDKYLFDRLTNASRNRIQKSAEAGFVMANNKPVKSSYKVKPMDVITIMM 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +++   + L          ++YED  + + NKPAG+ V  G G  +  
Sbjct: 93  -----DRPRYENEVIPEDIPLN---------IVYEDKYLMIVNKPAGLVVHPGHGNYHGT 138

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 139 LVNAIAWHMKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRR 198

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI +  +  I   + +      D + +    +    +A++H++V++        
Sbjct: 199 YRALVWGIVEQDEGTIIGNIGRNPK---DRMQMTVLPDDQGKHAVTHYRVLERLG-YVTL 254

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +  L
Sbjct: 255 VECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPRQAL 314

Query: 291 HARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL-GFKYDRNLY 331
           HA  +   HP  G  +  T+ +P  M +  D   G+  +R+L 
Sbjct: 315 HAMTLGFVHPATGEEMYFTSEMPDDMTQLIDKWRGYISNRDLE 357


>gi|21958555|gb|AAM85318.1|AE013778_4 hypothetical protein y1750 [Yersinia pestis KIM 10]
          Length = 341

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 99/319 (31%), Positives = 164/319 (51%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 29  VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 85

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 86  ---VVRVPPVRVAEREEVQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 141

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 142 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKSMQKDYLAL 200

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+ V  V         + + FK+ + F +    ++  
Sbjct: 201 VRGQWQSHCKAIQAPLLKNIMQSGERVVKVSSE---GKPSETRFKIEERF-EHATLVKAS 256

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 257 PVTGRTHQIRVHALHAGHPIAFDDRYGYREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 316

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++I APL   +     +L 
Sbjct: 317 MRIEAPLDNQLRHCLLALR 335


>gi|148545913|ref|YP_001266015.1| RluA family pseudouridine synthase [Pseudomonas putida F1]
 gi|148509971|gb|ABQ76831.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           putida F1]
          Length = 352

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 94/345 (27%), Positives = 155/345 (44%), Gaps = 38/345 (11%)

Query: 2   SLMTYVQYV--VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           S M+ +  +   V ++    RLD+     +   +   L   ++ G++ VD   V+  + +
Sbjct: 31  SSMSEIIQLSAEVPSELGGQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLV 90

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G ++ +     A    I E   LD               ++YED  I V NKPAG+ V
Sbjct: 91  HGGSLLALEAEQEAQGEWIAEDIELD---------------IVYEDDHILVINKPAGLVV 135

Query: 120 QGGSGIA--YHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +G A    ++  L    D     +  + HRLD++T+G++VVA+T  A   L E  + 
Sbjct: 136 HPAAGHASGTLLNALLHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTLQAQTKLVEQMQA 195

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R++ +IY  +V G+       I   + +    GG    +   +  G   A+SH++V+  F
Sbjct: 196 RKVSRIYECIVIGVV-TAGGKIDAPIGRH---GGMRQRMAVTD--GGKPAVSHYRVLKRF 249

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKL 288
            +    + ++  TGRTHQ+RVH  H+G P+VGD  Y   F+     SP          + 
Sbjct: 250 -RSHTHVRVKLETGRTHQIRVHMAHVGFPLVGDQTYGGRFRIPPAASPTMVEAVKTFPRQ 308

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            LHAR++ L HP  G  ++  +PLP   V     L    DR  +I
Sbjct: 309 ALHARFLALAHPITGEVMKWESPLPDDFVWLLSLL--NQDRESFI 351


>gi|261879908|ref|ZP_06006335.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bergensis DSM 17361]
 gi|270333420|gb|EFA44206.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bergensis DSM 17361]
          Length = 367

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 80/335 (23%), Positives = 142/335 (42%), Gaps = 42/335 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++      H +   +Q    +G + V+ + VK N +++   V+ +  
Sbjct: 37  VQVDAGQAPLRIDKFLAERMQHSSRNRIQTAADAGCIFVNDRPVKSNYKVRPLDVITLML 96

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +  I              H++ +   ++YED  + V NK AG+ V  G+G   + 
Sbjct: 97  GRPKHDSTI--------------HAEDIPLDIVYEDRDLMVVNKKAGMVVHPGAG---NF 139

Query: 130 DGFLKSWV----------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +G L + V          D       L HR+D++TSG+LVVA+T  A   L + F  +  
Sbjct: 140 NGTLINAVAWHLRDLDTFDPNDPNVGLVHRIDKDTSGLLVVAKTADAKTALGKQFYNKTT 199

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y +LVWG P   +  I   + +        + V   +      A++H++V++ F   
Sbjct: 200 HRSYHALVWGNPVADEGRIEGNIGRDPK-DRLRMKVFPPDSGIGKAAVTHYRVLERFG-Y 257

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQN------K 287
              ++    TGRTHQ+R H  HMG P+  D +Y             + + +QN      +
Sbjct: 258 VTLVQCVLETGRTHQIRAHMKHMGHPLFCDERYGGCEILRGQRSTTYKAFVQNCFKLCPR 317

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
             LHA+ +   HP  G  +   +  PA        
Sbjct: 318 QALHAKTLGFVHPRTGEQMDFDSEWPADFAALISK 352


>gi|16331032|ref|NP_441760.1| hypothetical protein slr1629 [Synechocystis sp. PCC 6803]
 gi|3915482|sp|P74346|Y1629_SYNY3 RecName: Full=Uncharacterized RNA pseudouridine synthase slr1629;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|1653527|dbj|BAA18440.1| slr1629 [Synechocystis sp. PCC 6803]
          Length = 327

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 92/316 (29%), Positives = 151/316 (47%), Gaps = 29/316 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V      +RLD+W     P ++    QK++ SGQV+ +    +  N  +++G  + +   
Sbjct: 25  VAEGTLGVRLDKWLAEQLPELSRSRCQKLIESGQVQRNGLVCQDKNLILKTGDRLVVN-- 82

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                        +   + L   +  +   +LYED ++ + NKPAG+ V  G G      
Sbjct: 83  -------------IPELIPLDVVAQNIPLDILYEDEQLIIINKPAGLVVHPGPGHPDGTV 129

Query: 130 -DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            +  L    D  G    Q+P + HRLD++T+G +VVA+T  A  +L    + +  +++YW
Sbjct: 130 VNALLAHCPDLAGIGGVQRPGIVHRLDKDTTGAMVVAKTELALHNLQVQLKEKTARRLYW 189

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +V+G PK  +  +   + +  H G      +   EKG   A++H+++++       WLE
Sbjct: 190 GIVYGSPKEIQGTVNLPVGR--HPGDRQKMGIVPVEKGGREAVTHWRLLERIG-NHSWLE 246

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            Q  TGRTHQ+RVH+  MG P+VGD+ Y +    N   P      LHA  + L HP  G 
Sbjct: 247 FQLETGRTHQIRVHSKQMGHPLVGDNLYTSPGSVNVNLPG---QALHAHQLSLIHPVSGE 303

Query: 305 -LQITAPLPAHMVKTW 319
            +   AP+PAH  K  
Sbjct: 304 IITAIAPMPAHFEKLL 319


>gi|313159132|gb|EFR58507.1| pseudouridine synthase, RluA family [Alistipes sp. HGB5]
          Length = 362

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 74/334 (22%), Positives = 138/334 (41%), Gaps = 41/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV +  +  +RLD++        +   +Q    SG + V+ K  K + +++    ++I  
Sbjct: 34  VVADKGQAPLRLDKFLTVRMEKCSRNRIQAAADSGSILVNGKAAKSSYKVKPLDRIQI-- 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               + +  +E +I+  ++ L          + YED  + + NKPAG+ V  G G     
Sbjct: 92  ---VMPYPRREVEIIPENIPLE---------IPYEDDDLLIVNKPAGLVVHPGHGNYSGT 139

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH+             +  L HR+D+ TSG+LVVA+   +   L + F    I 
Sbjct: 140 LVNALTYHLRNL--PLFQEGDMRAGLVHRIDKNTSGLLVVAKNEQSHARLAKQFFDHTIG 197

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG  +  +  I   + +           V ++     +A++H++V+  +    
Sbjct: 198 RRYVALVWGNFEEDEGTITGNIGRSPRDRQK--MFVFEDGSDGKHAVTHWRVLKRYG-YV 254

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKL 288
             +E +  TGRTHQ+RVH    G P+  D +Y  +     T+             +  + 
Sbjct: 255 TLVECRLETGRTHQIRVHMSWQGHPLFNDERYGGDRILKGTTFSKYKQFIENCFAVMPRH 314

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            LHA+ +   HP     +   + LP       + 
Sbjct: 315 ALHAQSLGFVHPMTHEAVYFESELPDDFRALLEK 348


>gi|307706435|ref|ZP_07643244.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK321]
 gi|307618145|gb|EFN97303.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK321]
          Length = 295

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 141/319 (44%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETAGLRLDKALSD-LTELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVTYH--- 58

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
                       L     L   ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 59  ------------LPEPEVLEYVAENLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G +
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGEI 275

Query: 306 -QITAPLPAHMVKTWDSLG 323
            + TA +P    +T + L 
Sbjct: 276 LEFTADIPEIFKETLERLR 294


>gi|165925607|ref|ZP_02221439.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|166008246|ref|ZP_02229144.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|167402395|ref|ZP_02307858.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167421825|ref|ZP_02313578.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|165922716|gb|EDR39867.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165992628|gb|EDR44929.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166960310|gb|EDR56331.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167048228|gb|EDR59636.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|262362323|gb|ACY59044.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           D106004]
          Length = 327

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 99/319 (31%), Positives = 164/319 (51%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 15  VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 71

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 72  ---VVRVPPVRVAEREEVQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 128 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKSMQKDYLAL 186

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+ V  V         + + FK+ + F +    ++  
Sbjct: 187 VRGQWQSHCKAIQAPLLKNIMQSGERVVKVSSE---GKPSETRFKIEERF-EHATLVKAS 242

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 243 PVTGRTHQIRVHALHAGHPIAFDDRYGYREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 302

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++I APL   +     +L 
Sbjct: 303 MRIEAPLDNQLRHCLLALR 321


>gi|309781165|ref|ZP_07675902.1| ribosomal large subunit pseudouridine synthase C [Ralstonia sp.
           5_7_47FAA]
 gi|308919986|gb|EFP65646.1| ribosomal large subunit pseudouridine synthase C [Ralstonia sp.
           5_7_47FAA]
          Length = 344

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 100/322 (31%), Positives = 163/322 (50%), Gaps = 23/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  + E  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 29  VAYVEIGEEAEGQRIDNFLMRVAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 88

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+             +   V   +     +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 89  IPPLR------------IAQQVEAARPVPAAEFTILHEDTHLLVIDKPAGVAVHGGSGVA 136

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++ 
Sbjct: 137 FGVIEQLRQ-SRPDAKFLELVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFAA 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  +K++ I + L K +   G+    V+ +      + + F  +  F   +  LE +
Sbjct: 196 VKGVWPHKRQHIKSPLYKYTTPEGERRVRVQAD---GQASHTIFNKVGVFG-PYTLLEAE 251

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H G PI+GD KY              SP   +++LHA  + L HP 
Sbjct: 252 LKTGRTHQIRVHLAHAGFPILGDDKYGDFALNKVLSRANASPRLARMFLHAHRLQLTHPH 311

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  +   APLPA      ++ 
Sbjct: 312 SGEVVTFNAPLPAECTDFLNAF 333


>gi|270308540|ref|YP_003330598.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Dehalococcoides sp. VS]
 gi|270154432|gb|ACZ62270.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Dehalococcoides sp. VS]
          Length = 302

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 80/316 (25%), Positives = 145/316 (45%), Gaps = 34/316 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            + +  RLD++       ++   +Q ++ SG V+V+ K  K + ++++G  + I      
Sbjct: 10  AESDGERLDKYIAQKETDLSRSFIQALIDSGHVQVNGKTAKPSLKLKNGDTITIEISPET 69

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDG 131
              +  E   L+               ++++D  + + NKP G++V    G   H  I+G
Sbjct: 70  PPELKAEDIPLE---------------IIFQDKDLLLINKPPGLTVHPAPGHPDHTLING 114

Query: 132 FLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L      +      +P + HRLD++TSG+L+VA+ R    +L+  F+ R ++K Y +LV
Sbjct: 115 VLALEPKMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRETLANLSAQFKERTVRKYYLTLV 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G     +  I   L +        + VV        +A + +KV+  + Q +  LE++ 
Sbjct: 175 KGELHPAEGFIEAPLGRD-PQNRQKIAVVS----NGRHARTGYKVL-RYIQGYSLLEVKL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH   +G P+ GD  Y              + +LHA  +    P  G+ ++
Sbjct: 229 ETGRTHQIRVHFAAIGHPVAGDAIYGQK------ETWLKRQFLHAHRLSFTLPSNGQTVE 282

Query: 307 ITAPLPAHMVKTWDSL 322
            T+PLP  + +T   L
Sbjct: 283 FTSPLPPDLEETLKIL 298


>gi|58698525|ref|ZP_00373428.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Drosophila ananassae]
 gi|225630144|ref|YP_002726935.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia sp. wRi]
 gi|225677282|ref|ZP_03788264.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Muscidifurax uniraptor]
 gi|58534967|gb|EAL59063.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Drosophila ananassae]
 gi|225590674|gb|EEH11919.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Muscidifurax uniraptor]
 gi|225592125|gb|ACN95144.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia sp. wRi]
          Length = 307

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 111/323 (34%), Positives = 180/323 (55%), Gaps = 16/323 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++  ++ +++E+D  N+RLDR+ +  +P +    ++K LR G ++VD  + K ++R+ SG
Sbjct: 1   MLQSIKTILIEDD--NVRLDRYIRRIFPDLKQSVIEKSLRKGLIKVDDCKAKSSDRVNSG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q + +   +N + +   ++K  +  VNL      L+  +LYED  I   NKPAG+ VQGG
Sbjct: 59  QTITLK-HLNYIENANSDRKYNEKLVNL------LRENILYEDEYILAINKPAGVIVQGG 111

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             +   +   L      +G+  ++ HRLD++TSG+++ AR    A++L E F+ RR++K 
Sbjct: 112 VKVKISMSDLLDQIR--EGETFKIVHRLDRDTSGVIIFARNANVARYLMEEFKGRRVKKT 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L  GIP      I   L+KK   G + V V   +E     A +HF +I        +
Sbjct: 170 YLALTSGIPSKDSGTIDYPLVKKYVSGQEKVVV---DENSPQNATTHFSIIAKSKHNVAY 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L++QP TGRTHQLR H  H+ CPI+GD KY    K  F   I NK++LH+  + L  P  
Sbjct: 227 LKLQPITGRTHQLRAHLAHINCPILGDGKYGG--KKAFIDGIANKIHLHSHSLSLKLPNN 284

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
             + ITAP+  H+ K+ ++L F 
Sbjct: 285 KEITITAPITKHIEKSIEALFFD 307


>gi|206559376|ref|YP_002230137.1| ribosomal large subunit pseudouridine synthase C 2 [Burkholderia
           cenocepacia J2315]
 gi|206561222|ref|YP_002231987.1| ribosomal large subunit pseudouridine synthase C 1 [Burkholderia
           cenocepacia J2315]
 gi|198035414|emb|CAR51290.1| ribosomal large subunit pseudouridine synthase C 2 [Burkholderia
           cenocepacia J2315]
 gi|198037264|emb|CAR53186.1| ribosomal large subunit pseudouridine synthase C 1 [Burkholderia
           cenocepacia J2315]
          Length = 334

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 100/326 (30%), Positives = 160/326 (49%), Gaps = 23/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++ +    R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +V
Sbjct: 16  QVSMIEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + +    +    N           +LYED  + V +KPAG++V GGSG+
Sbjct: 76  RVPPVRVAAADLARADTPVVPPANFD---------VLYEDDAMLVIDKPAGVAVHGGSGV 126

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y++
Sbjct: 127 AFGVIEQMRQAR-PRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFA 185

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
              G  +        +   L K S   G+    V+++      + + F ++D +   +  
Sbjct: 186 CAHGEWQPDWGRRRAVKAPLFKYSTPEGERRVRVQED---GLASHTVFNLVDRWP-NYVL 241

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PI GD KY               P   +++LHA  + L
Sbjct: 242 VEAELKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANAQPSLKRMFLHAHRLKL 301

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA   +  D L
Sbjct: 302 AHPLTGEALQFDAPLPAECRRFLDQL 327


>gi|298376939|ref|ZP_06986893.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_19]
 gi|298265923|gb|EFI07582.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_19]
          Length = 359

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 82/340 (24%), Positives = 148/340 (43%), Gaps = 37/340 (10%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S M      V +  +  +R+D++  +         +Q    +G + V+ K VK N R++ 
Sbjct: 27  SQMYEHFRFVADKGQSLLRVDKFLVDRMMGATRNRIQLAAEAGCILVNDKPVKSNYRVKP 86

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
             VV +      ++   +E +I+   + L          ++YED  + V NKPAG+ V  
Sbjct: 87  LDVVSV-----VMDRPRRELEIIPEDIPLN---------IVYEDDDLLVVNKPAGLVVHP 132

Query: 122 GSG-----IAYHIDGFLKS--WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G G     +   +  +LK   + D    +  L HR+D++TSG+LVVA+   A  +L+  F
Sbjct: 133 GHGNYTGTLVNALAYYLKDDPYYDPSDPRLGLVHRIDKDTSGLLVVAKRPEAKSNLSLQF 192

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             +  ++ Y +LVWGI +  +  I   + +           V         A++H+ V++
Sbjct: 193 FNKTTKRKYRALVWGIVQEDEGRIEGNIGRDPR--DRMQMTVFPEGDQGKTAVTHYTVLE 250

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP----------- 283
                   +E +  TGRTHQ+RVH  ++G  +  D +Y  +     T+            
Sbjct: 251 RLG-YVSLVECRLETGRTHQIRVHMKYIGHTLFNDERYGGHDILKGTTFTKYKQFVQNCF 309

Query: 284 -IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
            I  +  LHA+ +   HP  G  +   + +P+ M +  D 
Sbjct: 310 AICPRQALHAKTLGFVHPTTGEEMFFDSEIPSDMQQLIDR 349


>gi|262370010|ref|ZP_06063337.1| 23S rRNA pseudouridylate synthase [Acinetobacter johnsonii SH046]
 gi|262315049|gb|EEY96089.1| 23S rRNA pseudouridylate synthase [Acinetobacter johnsonii SH046]
          Length = 312

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 97/319 (30%), Positives = 162/319 (50%), Gaps = 19/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   ++  G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLSIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK  +++    K +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDENAAPVSDKVAQSLLSRVVYEDEGLMVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y ++
Sbjct: 123 YGLIEGLRAATGKKY--LELIHRIDRDTSGLVMISKKRSVLKSLQDMLREHKIKKTYAAV 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+    K+ I   L +     G+    V    K +    + + V + F      +   
Sbjct: 181 VKGVVSLDKQLIDAPLHRYELANGERRVRVSSEGKESK---TQWNVAERFMH-ATLVYAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P+VGD KY    +  +  P   +L LHA  +D+P    G   
Sbjct: 237 PLSGRTHQIRVHGLSIGHPLVGDDKYG--HETEYKGPKPRRLCLHAMRLDIP----GYAP 290

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I APLP  M      L  +
Sbjct: 291 IEAPLPEDMQSIVAQLRAQ 309


>gi|225181681|ref|ZP_03735121.1| pseudouridine synthase, RluA family [Dethiobacter alkaliphilus AHT
           1]
 gi|225167662|gb|EEG76473.1| pseudouridine synthase, RluA family [Dethiobacter alkaliphilus AHT
           1]
          Length = 312

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 87/324 (26%), Positives = 145/324 (44%), Gaps = 30/324 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           ++ V+      RLD     H   +    +QK++    V+VD K  K N R+++G+ V + 
Sbjct: 5   FITVDEVLAGERLDVAVSRHVEELTRARVQKLIAEDYVQVDGKPQKANYRLRAGETVEVT 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                   I  E+  LD               +LYED  + V NKP G+ +   +G A  
Sbjct: 65  VPEVKPAEIAAEKIDLD---------------ILYEDQDVLVLNKPKGLVIHPAAGHAGG 109

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    D  G     +P + HRLD++TSG++VVA+   A   L+  F+   + + 
Sbjct: 110 TLVNALLHHCDDLSGIGGEARPGIVHRLDKDTSGVMVVAKNDRAHLSLSRQFKAHSVTRE 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G P  ++  I   + +      +   +     +    A++HFKV+D F + + +
Sbjct: 170 YVAIVHGEPAVEQGTIDAAIARHPK---ERKKMALTTAEKGRRAVTHFKVLDRFGE-YSY 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L ++  TGRTHQ+RVH   +G P+VGD  Y    +        +   LHAR +   HP  
Sbjct: 226 LALRLETGRTHQIRVHLSSLGHPVVGDPVYGYKKQ----KFKLSGQALHARLLGFNHPTD 281

Query: 303 GR-LQITAPLPAHMVKTWDSLGFK 325
            R L+     P    +  + L  K
Sbjct: 282 HRYLEFAGEPPEEFRRLLNLLRGK 305


>gi|91789509|ref|YP_550461.1| pseudouridine synthase RluD [Polaromonas sp. JS666]
 gi|91698734|gb|ABE45563.1| Pseudouridine synthase, RluD [Polaromonas sp. JS666]
          Length = 378

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 101/335 (30%), Positives = 162/335 (48%), Gaps = 26/335 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+ D    RLD +   H   +   ++ +I+RSG+VR++K R + + R+++G +VR+PP
Sbjct: 31  VTVDEDYAGQRLDNFLIRHLKGVPKTHVYRIIRSGEVRINKGRAQADTRLEAGDIVRLPP 90

Query: 70  VINALNHIIKEQKILDS------SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V  +     K Q + +       S  +  ++   +  +L+ED  +   +KPAG++V GGS
Sbjct: 91  VRTSERADQKAQAMAEEVARHGASSTVGGYAPSREFPVLFEDDFLLAIDKPAGVAVHGGS 150

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+++ +   L+     +     L HRLD+ETSGIL++A+ R A + L E FR R   K+Y
Sbjct: 151 GVSFGVIEQLR-MARPQADFLELVHRLDRETSGILLIAKRRMALKLLQEQFRERETDKVY 209

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGG-----DYVHVVKQNEKGANYAISHFKVIDCF-- 236
            +LV G        I   L K    GG       V VV  +      +++  KV   F  
Sbjct: 210 LALVSGNWPANHRVIDKALHKYLLPGGAGEGERRVKVVPNDHPDGMRSVTLVKVKSAFAA 269

Query: 237 -----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQ 285
                   F  LE+   TGRTHQ+RVH  + G PI GD KY       +  K        
Sbjct: 270 LPAAPGTPFTLLEVTIKTGRTHQIRVHLANEGHPIAGDDKYGDFELNKSLQKSVAGGAPL 329

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
            +++LHA  +   HP+  + + +  PLP  + +  
Sbjct: 330 KRMFLHAWSLKFNHPKTRKTIHLETPLPDELQQFL 364


>gi|317121731|ref|YP_004101734.1| ribosomal large subunit pseudouridine synthase D [Thermaerobacter
           marianensis DSM 12885]
 gi|315591711|gb|ADU51007.1| ribosomal large subunit pseudouridine synthase D [Thermaerobacter
           marianensis DSM 12885]
          Length = 321

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 83/320 (25%), Positives = 143/320 (44%), Gaps = 30/320 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            VV       RLD +        +    +Q+++RS Q+RV+ +  + + R++ G+ V + 
Sbjct: 17  FVVPASAAGERLDVFLAGQDSLELTRSAIQRLIRSQQIRVNGRPARPSRRLEPGEEVVVE 76

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
               A + ++ E   LD               ++YED+ + V NKP G  V    G    
Sbjct: 77  LPAPAPSGVVAEPLPLD---------------VVYEDADVVVLNKPRGWVVHPAPGHPQG 121

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +  L  + + +G     +P + HRLD++T+G+LVVAR+  A + L    + R + + 
Sbjct: 122 TLANALLARYPEMEGVGGPGRPGIVHRLDRDTTGLLVVARSPLAYRELVRQLKERGVHRE 181

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G P+ ++  +   + +   +    + V+     G   A +HF+V++   + +  
Sbjct: 182 YLALVRGSPEVREGTVDAPIGRH-PVDRKRMAVL---PGGGRPARTHFEVVERAGR-YTL 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L     TGRTHQ+RVH   +G P+ GD  Y                 LHA  +  PHP  
Sbjct: 237 LRCWLDTGRTHQIRVHLAFIGLPVAGDPVYGGRRAEG--ELGLEGQALHATRLAFPHPRD 294

Query: 303 GR-LQITAPLPAHMVKTWDS 321
           GR +  T P PA   +  + 
Sbjct: 295 GRPMDFTVPPPADFQRALER 314


>gi|297617022|ref|YP_003702181.1| pseudouridine synthase [Syntrophothermus lipocalidus DSM 12680]
 gi|297144859|gb|ADI01616.1| pseudouridine synthase, RluA family [Syntrophothermus lipocalidus
           DSM 12680]
          Length = 305

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 146/324 (45%), Gaps = 32/324 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
             + VV+E   E  RLDR+       ++   ++ ++  G V V  +  K   RI+ G ++
Sbjct: 2   ETRDVVIEGSHEGERLDRFLAETLCDVSRSQVKNLIDEGLVLVGGRPQKPGYRIRKGDII 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           ++         ++ ++               +   ++YED  + V +KP G+ V    G 
Sbjct: 62  QVRIPAARETGLVAQE---------------MPLNIVYEDRDLVVIDKPQGLVVHPAHGH 106

Query: 126 --AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++  L    D  G     +P + HRLD++TSG++VVA+   A + L +  + R+I
Sbjct: 107 WEGTLVNALLYRVKDLSGINGELRPGIVHRLDKDTSGLMVVAKNDQAHRDLADQIKARKI 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y ++V G+ +     I   + + S      + VV++       A++H+ V+  + + 
Sbjct: 167 RREYVAVVHGVIRENSGTIDAPIGR-SPSDRKKMAVVRE----GRPAVTHYTVLRRY-RD 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +  +  TGRTHQ+RVH  ++  P+VGD  Y  +     +        LHA Y+   H
Sbjct: 221 YTLVRARLETGRTHQIRVHFAYIRHPVVGDQVYGPSR----SRFELKGQALHACYLAFYH 276

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P     L+  +P P ++ +    L
Sbjct: 277 PTTKELLEFDSPFPPYVQELLRQL 300


>gi|237715324|ref|ZP_04545805.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D1]
 gi|262405165|ref|ZP_06081715.1| conserved hypothetical protein [Bacteroides sp. 2_1_22]
 gi|294643535|ref|ZP_06721341.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|294807042|ref|ZP_06765861.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|298482426|ref|ZP_07000612.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D22]
 gi|229444633|gb|EEO50424.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D1]
 gi|262356040|gb|EEZ05130.1| conserved hypothetical protein [Bacteroides sp. 2_1_22]
 gi|292641110|gb|EFF59322.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|294445741|gb|EFG14389.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|295088097|emb|CBK69620.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           xylanisolvens XB1A]
 gi|298271405|gb|EFI12980.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D22]
          Length = 357

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 82/333 (24%), Positives = 149/333 (44%), Gaps = 39/333 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEGGFVMANGKPVKSSYKVKPLDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +I+   + LT         ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYENEIIPEDIPLT---------IVYEDPYVMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNALAWHMKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRR 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFC 241
           Y +LVWG+ +  +  I   + +      D + +   ++     +A++H++V++       
Sbjct: 198 YRALVWGVVEQDEGTIVGNIARNPK---DRMQMAVMSDPTVGKHAVTHYRVLERLG-YVT 253

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLY 289
            +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +  
Sbjct: 254 LVECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPRQA 313

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           LHA  +   HP  G  +  T+ LP  M +  + 
Sbjct: 314 LHAMTLGFVHPVTGEEMYFTSELPDDMTRLIEK 346


>gi|149371695|ref|ZP_01891111.1| ribosomal large subunit pseudouridine synthase D [unidentified
           eubacterium SCB49]
 gi|149355322|gb|EDM43882.1| ribosomal large subunit pseudouridine synthase D [unidentified
           eubacterium SCB49]
          Length = 348

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 78/337 (23%), Positives = 145/337 (43%), Gaps = 34/337 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      V +  ++ +R+D++  N   +     +QK  + G + V+   VK N ++++  
Sbjct: 17  MHEHFRFVADKGQQPLRVDKYLMNRVENATRSKIQKAAKEGNIFVNNVIVKSNYKVKAND 76

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VV +                      L    + +   ++YED  + V NK  G+ V  G 
Sbjct: 77  VVTV--------------LFAHPPYELLLTPEDIDIDIVYEDDDLLVVNKQPGMVVHPGH 122

Query: 124 GI--AYHIDGFLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G      I+  +       ++   +P L HR+D++TSG+LVVA+T  A  HL + F  + 
Sbjct: 123 GNYSGTLINALIHHIDNLPNNSSNRPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKT 182

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++ Y +LVWG  ++ +  I   + +       + V + +  E+    A++HFKV++ F 
Sbjct: 183 TEREYVALVWGNIEDDEGTIEGHIGRHPKNRLQNTVFLDEDAEEKGKAAVTHFKVLERFG 242

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQ 285
                +  +  TGRTHQ+RVH   +G  +  D +Y        T+             + 
Sbjct: 243 -YVTLVSCKLETGRTHQIRVHMKFIGHTLFNDERYGGEKILKGTTFSKYKQFVDNCFKVL 301

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            +  LHAR +   HP  G  ++  + +P  +    + 
Sbjct: 302 PRQALHARTLGFVHPTTGEMMRFESKVPQDIEDCLEK 338


>gi|254245933|ref|ZP_04939254.1| Ribosomal large subunit pseudouridine synthase C [Burkholderia
           cenocepacia PC184]
 gi|124870709|gb|EAY62425.1| Ribosomal large subunit pseudouridine synthase C [Burkholderia
           cenocepacia PC184]
          Length = 341

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 100/326 (30%), Positives = 159/326 (48%), Gaps = 23/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++ +    R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +V
Sbjct: 23  QVSMIEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLV 82

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + +    +    N           +LYED  + V +KPAG++V GGSG+
Sbjct: 83  RVPPVRVAAADLARADTPVVPPANFD---------VLYEDDAMLVIDKPAGVAVHGGSGV 133

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y++
Sbjct: 134 AFGVIEQMRQAR-PRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFA 192

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
              G  +        +   L K S   G+    V+ +      + + F ++D +   +  
Sbjct: 193 CAHGEWQPDWGRRRAVKAPLFKYSTPEGERRVRVQDD---GLASHTVFNLVDRWPD-YVL 248

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PI GD KY               P   +++LHA  + L
Sbjct: 249 VEAELKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANAQPSLKRMFLHAHRLKL 308

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA   +  D L
Sbjct: 309 AHPLTGEALQFDAPLPAECRRFLDQL 334


>gi|120553810|ref|YP_958161.1| RluA family pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120323659|gb|ABM17974.1| ribosomal large subunit pseudouridine synthase D [Marinobacter
           aquaeolei VT8]
          Length = 325

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 87/350 (24%), Positives = 154/350 (44%), Gaps = 42/350 (12%)

Query: 1   MSLMTYVQ-YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M+    +     V  +  + RLD+      P  +   LQ  ++SG + V+ K  K  +++
Sbjct: 1   MTSENRITGQFTVPPELSDKRLDQAAAELMPEHSRSRLQSWIKSGALTVNGKSRKPRDKV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  + +                 +  V +T  ++ +   ++YED  + V NKPAG+ V
Sbjct: 61  MMGDSLALD---------------AEPEVQVTWEAEPISLDIVYEDEHLLVINKPAGLVV 105

Query: 120 QGGSGIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              +G   H DG L + + +         +  + HRLD++TSGI+VVAR+  A   L + 
Sbjct: 106 HPAAG---HTDGTLVNALLNYAPEVENLPRAGIVHRLDKDTSGIMVVARSLIAHTSLVDQ 162

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + R + + Y ++V G          +  + +       + VV         A++H++++
Sbjct: 163 LQTRTMGREYEAVVVGALT--GGATVDAPIGRHPQDRKRMAVVS----SGKPAVTHYRLL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------- 285
           + FA     +  +  +GRTHQ+RVH  H+  P+VGD  Y    +    +  +        
Sbjct: 217 ERFA-AHTLVRCKLESGRTHQIRVHMAHVRHPLVGDPAYGGRLRLPKGTTEELRDVLAAF 275

Query: 286 NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            +  LHAR + L HPE G +     PLP  MV   ++L  K+ R L  + 
Sbjct: 276 TRQALHARQLTLEHPETGEILSWEVPLPEDMVHLIEALR-KHARELEERD 324


>gi|322387558|ref|ZP_08061167.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           infantis ATCC 700779]
 gi|321141425|gb|EFX36921.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           infantis ATCC 700779]
          Length = 297

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 147/321 (45%), Gaps = 34/321 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+    K    +Q G V+      
Sbjct: 3   IKIETGGIRLDKALSD-LTELSRSLANEQIKSGQVLVNGHVKKAKYTVQEGDVIT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + I E ++L+        ++ +   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YQIPEPEVLE------YVAEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHMALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F+V++ F   +  LE+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFQVLERFGD-YTLLEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L+ TA +P    +T + L  +
Sbjct: 276 LEFTADIPEIFKQTLEKLRNE 296


>gi|291543962|emb|CBL17071.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus sp.
           18P13]
          Length = 304

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 86/326 (26%), Positives = 144/326 (44%), Gaps = 39/326 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ V++  D   MRLD+W     P ++   +Q ++  G V  + K    N +++ G  + 
Sbjct: 1   MREVMLTADGSGMRLDKWLTEQLPELSRSGVQHLIEQGAVLCNGKPAAKNLKLREGDGLL 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +              +I D +         L   ++YED  + V NKP G+ V   +G  
Sbjct: 61  V--------------QIPDPAPLEDVQPQNLPLEIVYEDEALLVVNKPKGMVVHPAAG-- 104

Query: 127 YHIDGFLKSWVDSKGQ----------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            H DG L + +    Q          +P + HR+D+ TSG+L+VA+T  A QHL E  + 
Sbjct: 105 -HPDGTLVNALLYHCQGRLSTINGVIRPGIVHRIDKNTSGLLMVAKTDFAHQHLAEQIKG 163

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
               + Y ++  G  +     +   + + S      + V    EK A +A++H+ V+  F
Sbjct: 164 HSFTREYEAIACGRFREPSGTVDAPIGR-STADRQKMCV---TEKNARHAVTHYAVLTQF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           A K   +  +  TGRTHQ+RVH  ++G PI GD  Y          P      LHA+ + 
Sbjct: 220 A-KHAHIRCRLETGRTHQIRVHMRYIGHPIYGDDVYGTAV------PGLEGQCLHAKKIG 272

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDS 321
             HP  G  ++  + LP + V+    
Sbjct: 273 FVHPVSGAYMEFDSALPDYFVQALKK 298


>gi|296876327|ref|ZP_06900379.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 15912]
 gi|296432617|gb|EFH18412.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 15912]
          Length = 296

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 142/319 (44%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +    RLD+   +  P ++     + ++ G+V V+    K    ++ G ++      
Sbjct: 3   IKIEVAGARLDKALADLTP-LSRAVANEQIKEGKVLVNGTVKKAKYTVKEGDII------ 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
                    Q  +     ++  ++ L   ++YED  + V NKP G+ V   +G      +
Sbjct: 56  ---------QYEVPEVEEVSYEAEDLPLDIVYEDQDVVVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSG+L+VA+   A   L E  + ++  + YW+
Sbjct: 107 NALLYHIKDLSGINGELRPGIVHRIDKDTSGLLMVAKNDQAHVALAEELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F+V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGMIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFQVLERFG-NYTLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +      +LHAR +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDPAYGPK-----KTLKGQGQFLHARTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+ TA +PA   KT + L 
Sbjct: 276 LEFTAEVPAIFEKTLEDLR 294


>gi|167031685|ref|YP_001666916.1| RluA family pseudouridine synthase [Pseudomonas putida GB-1]
 gi|166858173|gb|ABY96580.1| pseudouridine synthase, RluA family [Pseudomonas putida GB-1]
          Length = 352

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 94/345 (27%), Positives = 155/345 (44%), Gaps = 38/345 (11%)

Query: 2   SLMTYVQYV--VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           S M+ +  +   V ++    RLD+     +   +   L   ++ G++ VD   V+  + +
Sbjct: 31  SSMSEIIQLSAEVPSELGGQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLV 90

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G ++ +     A    I E   LD               ++YED  I V NKPAG+ V
Sbjct: 91  YGGSLLALEAEQEAQGEWIAEDIELD---------------IVYEDDHIMVINKPAGLVV 135

Query: 120 QGGSGIA--YHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +G A    ++  L    D     +  + HRLD++T+G++VVA+T  A   L E  + 
Sbjct: 136 HPAAGHASGTLLNALLHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTLQAQTKLVEQMQA 195

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R++ +IY  +V G+       I   + +    GG    +   +  G   A+SH++V+  F
Sbjct: 196 RKVSRIYECIVIGVV-TAGGKIDAPIGRH---GGMRQRMAVTD--GGKPAVSHYRVLKRF 249

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKL 288
            +    + ++  TGRTHQ+RVH  H+G P+VGD  Y   F+     SP          + 
Sbjct: 250 -RSHTHVRVKLETGRTHQIRVHMAHVGFPLVGDQTYGGRFRIPPAASPTMVEAVKTFPRQ 308

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            LHAR++ L HP  G  ++  +PLP   V     L    DR  +I
Sbjct: 309 ALHARFLALAHPITGEIMKWESPLPDDFVWLLSLL--NQDRESFI 351


>gi|157370141|ref|YP_001478130.1| 23S rRNA pseudouridylate synthase C [Serratia proteamaculans 568]
 gi|157321905|gb|ABV41002.1| pseudouridine synthase, RluA family [Serratia proteamaculans 568]
          Length = 320

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 98/322 (30%), Positives = 164/322 (50%), Gaps = 14/322 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +  VQ + + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G 
Sbjct: 5   IPAVQLITISDDEAGQRIDNFLLARLKGVPKSMIYRIVRKGEVRVNKGRIKAEYKLAPGD 64

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                 V+      + E++    S  L K +  L   +LYED  + + NKP+G +V GGS
Sbjct: 65  ------VVRVPPVRVAEREDAPVSAKLDKVA-ALAHCILYEDDHLLLLNKPSGTAVHGGS 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y
Sbjct: 118 GLSFGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G  ++  + +   LLK     G+ +  V         + + FKV + F +    +
Sbjct: 177 LALVRGEWQSHCKAVQAPLLKNILQSGERIVRVSSE---GKPSETRFKVEERF-EHATLV 232

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +  P TGRTHQ+RVHALH G PI  D +Y    F          +L+LHA  +   HP  
Sbjct: 233 KASPITGRTHQIRVHALHAGHPIAFDDRYGDREFDRQLAGTGLKRLFLHAAALRFEHPGT 292

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  ++I AP+ A +      L 
Sbjct: 293 GETMRIEAPMDAELRHCLQVLR 314


>gi|322391774|ref|ZP_08065239.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           peroris ATCC 700780]
 gi|321145254|gb|EFX40650.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           peroris ATCC 700780]
          Length = 297

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 74/321 (23%), Positives = 148/321 (46%), Gaps = 34/321 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G V+      
Sbjct: 3   IKIETGGVRLDKALSD-LTELSRSLANEQIKSGQVLVNGQLKKAKYSVQEGDVIT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ +   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YQVPEPEVLE------YVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F+V++ F   +  LE+
Sbjct: 167 IVHGNIPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFRVLERFGD-YTLLEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           ++ T+ +P    +T + L  +
Sbjct: 276 MEFTSDIPEIFKQTLEKLRNE 296


>gi|153808958|ref|ZP_01961626.1| hypothetical protein BACCAC_03259 [Bacteroides caccae ATCC 43185]
 gi|149128291|gb|EDM19510.1| hypothetical protein BACCAC_03259 [Bacteroides caccae ATCC 43185]
          Length = 357

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 81/332 (24%), Positives = 145/332 (43%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               ++    E +I+   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 90  ---VMDRPRYENEIIPEDIPLN---------IVYEDKYVMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNALAWHMKDVPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRK 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +  +  I   + +           V  +     +A++H++V++        
Sbjct: 198 YRALVWGTVEQDEGTIVGNIARNPK--DRMQMAVMSDPAVGKHAVTHYRVLERLG-YVTL 254

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +  L
Sbjct: 255 VECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPRQAL 314

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G  +  T+ LP  M +  + 
Sbjct: 315 HAMTLGFVHPVTGEEMYFTSELPDDMARLIEK 346


>gi|257468836|ref|ZP_05632930.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
          Length = 342

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 86/336 (25%), Positives = 154/336 (45%), Gaps = 34/336 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M  +     V  + +++  R+D +            +QKI+  G V +  K+V K  N++
Sbjct: 30  MENIKETITVYADENDKGKRIDSFLNEVIDDATRSYIQKIIDGGYVEITGKKVTKSGNKL 89

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +  + + +          I E +ILD         + +   ++YED  I V NK   + V
Sbjct: 90  KGTETITVN---------IPEDEILDV------IPENIPLNIIYEDKDIVVINKAPDMVV 134

Query: 120 QGGSGI--AYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G      ++  L    D    +   +P + HRLD++TSG++VVA+   A   L++ 
Sbjct: 135 HPAHGNYNGTLVNALLYHIKDLSTINGVIRPGIVHRLDKDTSGVIVVAKNDEAHSTLSDM 194

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ + ++K Y  +  GI K+K   I   + + S      + VV  N K    AIS+++++
Sbjct: 195 FKEKTLEKTYICIAKGIFKDKSGRIETLIGRDSR-DRKKMAVVDINGKN---AISNYEIL 250

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D   + F  ++++  TGRTHQ+RVH  ++  PI+GD  Y ++ +G        +  LHA 
Sbjct: 251 D-EEKNFSLVKVRIETGRTHQIRVHMKYLNHPILGDSVYGSSGEGA------KRQMLHAY 303

Query: 294 YMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDR 328
            +   HP     +++TA +P    K     G   D+
Sbjct: 304 RLKFTHPVTKKEMEVTADIPEDFKKAAKFAGVNIDK 339


>gi|45442052|ref|NP_993591.1| 23S rRNA pseudouridylate synthase C [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108807929|ref|YP_651845.1| 23S rRNA pseudouridylate synthase C [Yersinia pestis Antiqua]
 gi|108812199|ref|YP_647966.1| 23S rRNA pseudouridylate synthase C [Yersinia pestis Nepal516]
 gi|145599137|ref|YP_001163213.1| 23S rRNA pseudouridylate synthase C [Yersinia pestis Pestoides F]
 gi|149366507|ref|ZP_01888541.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           CA88-4125]
 gi|161484824|ref|NP_669067.2| 23S rRNA pseudouridylate synthase C [Yersinia pestis KIM 10]
 gi|162420400|ref|YP_001607836.1| 23S rRNA pseudouridylate synthase C [Yersinia pestis Angola]
 gi|165938469|ref|ZP_02227026.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166214606|ref|ZP_02240641.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167427006|ref|ZP_02318759.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|218928727|ref|YP_002346602.1| 23S rRNA pseudouridylate synthase C [Yersinia pestis CO92]
 gi|229841579|ref|ZP_04461738.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229843691|ref|ZP_04463834.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229894436|ref|ZP_04509618.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Pestoides A]
 gi|229902524|ref|ZP_04517643.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Nepal516]
 gi|270490299|ref|ZP_06207373.1| pseudouridine synthase, RluA family [Yersinia pestis KIM D27]
 gi|294504206|ref|YP_003568268.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Z176003]
 gi|34395806|sp|Q8ZFU1|RLUC_YERPE RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|45436915|gb|AAS62468.1| ribosomal large subunit pseudouridine synthaseC [Yersinia pestis
           biovar Microtus str. 91001]
 gi|108775847|gb|ABG18366.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Nepal516]
 gi|108779842|gb|ABG13900.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Antiqua]
 gi|115347338|emb|CAL20236.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           CO92]
 gi|145210833|gb|ABP40240.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Pestoides F]
 gi|149290881|gb|EDM40956.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           CA88-4125]
 gi|162353215|gb|ABX87163.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Angola]
 gi|165913584|gb|EDR32204.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166204213|gb|EDR48693.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167053985|gb|EDR63813.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|229680570|gb|EEO76667.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Nepal516]
 gi|229689299|gb|EEO81362.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229697945|gb|EEO87992.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229703455|gb|EEO90472.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Pestoides A]
 gi|262366257|gb|ACY62814.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           D182038]
 gi|270338803|gb|EFA49580.1| pseudouridine synthase, RluA family [Yersinia pestis KIM D27]
 gi|294354665|gb|ADE65006.1| ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           Z176003]
 gi|320014732|gb|ADV98303.1| Ribosomal large subunit pseudouridine synthase C [Yersinia pestis
           biovar Medievalis str. Harbin 35]
          Length = 320

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 99/319 (31%), Positives = 164/319 (51%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEVQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKSMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+ V  V         + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAIQAPLLKNIMQSGERVVKVSSE---GKPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHALHAGHPIAFDDRYGYREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++I APL   +     +L 
Sbjct: 296 MRIEAPLDNQLRHCLLALR 314


>gi|186683943|ref|YP_001867139.1| RluA family pseudouridine synthase [Nostoc punctiforme PCC 73102]
 gi|186466395|gb|ACC82196.1| pseudouridine synthase, RluA family [Nostoc punctiforme PCC 73102]
          Length = 345

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 80/316 (25%), Positives = 146/316 (46%), Gaps = 29/316 (9%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINA 73
           D +  R+DR+     P ++   +Q+++  G V+++ K        ++ G  + +      
Sbjct: 45  DTKGDRIDRFLSQELPDLSRSRIQQLIEQGNVQLNDKVCTSKKINVKLGDRITLE----- 99

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDG 131
                     +  +  L   ++ +   +LYED ++ + NKPAG+ V    G      ++ 
Sbjct: 100 ----------IPEAQPLELLAEDIPLDILYEDDQLLILNKPAGLVVHPAPGHPDGTLVNA 149

Query: 132 FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    +  G    Q+P + HRLD++T+G + +A+T  A  HL    + +  ++ Y  +V
Sbjct: 150 LLAHCPNLPGIGGVQRPGIVHRLDKDTTGAIAIAKTEVAHHHLQAQLKAKTARREYLGVV 209

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G PK +   I   + +  H        +   E+G   A++H++V++     F  +  Q 
Sbjct: 210 YGAPKVESGTIDLPIGR--HPQDRKKMAIMPIEQGGRSAVTHWQVLERLG-NFTLIRFQL 266

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-Q 306
            TGRTHQ+RVH+  +G PIVGD  Y +   G+      +   LHA  + L HP  G + +
Sbjct: 267 ETGRTHQIRVHSAKIGHPIVGDPIYSS---GHSVGVNLSGQALHAWRLRLQHPLSGEMIE 323

Query: 307 ITAPLPAHMVKTWDSL 322
           +TA  P    K  + L
Sbjct: 324 VTATPPTQFTKLLEML 339


>gi|116629656|ref|YP_814828.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           ATCC 33323]
 gi|238854259|ref|ZP_04644603.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri 202-4]
 gi|311110701|ref|ZP_07712098.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri MV-22]
 gi|116095238|gb|ABJ60390.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri ATCC 33323]
 gi|238833070|gb|EEQ25363.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri 202-4]
 gi|311065855|gb|EFQ46195.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri MV-22]
          Length = 304

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 152/327 (46%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT   ++V+E  EE  RLD+        ++   +++++    + V+ K  K + ++Q+G 
Sbjct: 1   MTENYHLVIE--EEKGRLDKVIAEKLKDLSRTKIKELVNDKNILVNHKAEKVSYKVQAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I                +  +  L+  +  L   ++YED+ + V NKP G+ V   +
Sbjct: 59  SIDIT---------------VPPAKPLSLEAQNLNLDIVYEDADVIVVNKPQGMVVHPSA 103

Query: 124 GIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +G L    +     +G +P + HR+D++TSG+L+VA+   A + L +    +
Sbjct: 104 GHPDHTLVNGLLYHTHELADSPEGFRPGIVHRIDKDTSGLLMVAKNDKARESLEKQLAEK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++ Y ++V G  + K   I   + +  +         K        A++HF V++ F 
Sbjct: 164 INKREYLAIVHGNFETKNGVIDAPIGRNPNNRKQMAVNPK-----GKAAVTHFTVLEQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  ++    TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +  
Sbjct: 218 KDYSLVKCILETGRTHQIRVHMKYIGHPLAGDPLYGPK-----KTLAGHGQFLHAKTLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
             P   + L+ +APLPA   K  ++L 
Sbjct: 273 YQPSTHKWLEFSAPLPAIFEKQLENLR 299


>gi|294787877|ref|ZP_06753121.1| ribosomal large subunit pseudouridine synthase C [Simonsiella
           muelleri ATCC 29453]
 gi|294484170|gb|EFG31853.1| ribosomal large subunit pseudouridine synthase C [Simonsiella
           muelleri ATCC 29453]
          Length = 334

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 100/327 (30%), Positives = 166/327 (50%), Gaps = 20/327 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V+  +   RLD +       +   ++Q+I+RSG+VR++K R K ++RIQ G VVR
Sbjct: 15  VNHLTVQEHDAEQRLDNYLIKILKGVPKSHIQRIIRSGEVRLNKGRAKPDSRIQIGDVVR 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A       +K+        K+    +  +++ED  + V NKPAG++V GGSG++
Sbjct: 75  IPPIRVA-------EKLPPHFSGSLKNIPAREFDIVFEDDALIVINKPAGVAVHGGSGVS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+    ++     L HRLD++TSG+L++A+ R A   L E  R    +K+Y +L
Sbjct: 128 FGVIEQLRQARPNESY-LELVHRLDKDTSGLLMIAKKRRALVKLHEMLRNDHPKKVYLAL 186

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC----- 241
             G  + +   I   ++K +   G+ +  V  NE+    A + F+V++ F+         
Sbjct: 187 GVGTWQPENRHIKLPIVKYTGAAGEKMVRV-GNEEDGQSAYTIFRVLNTFSGSLTHSVGI 245

Query: 242 ----WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                ++    TGRTHQ+RVH     CPI GD +Y               +++LHA  + 
Sbjct: 246 SALSLVQATLKTGRTHQIRVHMQSQDCPIAGDERYGDYQANKRLQKLGLKRMFLHAYELI 305

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSL 322
           L HP  G RL + A LPA +    + L
Sbjct: 306 LDHPISGERLHLKAELPAELQDFLNDL 332


>gi|187928001|ref|YP_001898488.1| pseudouridine synthase [Ralstonia pickettii 12J]
 gi|187724891|gb|ACD26056.1| pseudouridine synthase, RluA family [Ralstonia pickettii 12J]
          Length = 344

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 101/322 (31%), Positives = 163/322 (50%), Gaps = 23/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV +  D E  R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR
Sbjct: 29  VAYVEIGEDAEGQRIDNFLMRVAKGVPKSHIYRILRSGEVRVNKGRIDAEYRLKLGDLVR 88

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+             +   V   +     +  +L+ED+ + V +KPAG++V GGSG+A
Sbjct: 89  IPPLR------------IAQQVEAARPVPAAEFTILHEDTHLLVIDKPAGVAVHGGSGVA 136

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD+ETSG+L++A+ R+A   L E  R  ++ K Y++ 
Sbjct: 137 FGVIEQLRQ-SRPDAKFLELVHRLDRETSGVLLLAKKRSALVALHEQIREGQLDKRYFAA 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  +K++ I + L K +   G+    V+ +      + + F  +  F   +  LE +
Sbjct: 196 VKGVWPHKRQHIKSPLHKYTTPEGERRVRVQAD---GQASHTIFNKVGVFG-PYTLLEAE 251

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H G PI+GD KY              SP   +++LHA  + L HP 
Sbjct: 252 LKTGRTHQIRVHLAHAGFPILGDDKYGDFALNKALSRANASPRLARMFLHAHRLQLTHPH 311

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  +   APLPA      ++ 
Sbjct: 312 SGEVVTFNAPLPAECTDFLNAF 333


>gi|158320450|ref|YP_001512957.1| RluA family pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158140649|gb|ABW18961.1| pseudouridine synthase, RluA family [Alkaliphilus oremlandii
           OhILAs]
          Length = 308

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 86/334 (25%), Positives = 149/334 (44%), Gaps = 34/334 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +  V+E D +N RLD +    Y  ++   +QK+++   ++V+ K  K    I+ G 
Sbjct: 1   MEQERLRVLEEDVDN-RLDLYISEQYEELSRSYIQKLIKDHHIKVNGKIEKAKYMIKLGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I                L     +T   + +   ++YED  + V +KP G+ V    
Sbjct: 60  EIEIN---------------LPQVEEVTIEPENIPLTIVYEDEDVIVVDKPQGMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  L    +         +P + HR+D++TSG+LVVA+  AA + L E FR 
Sbjct: 105 GNYSGTLVNALLFHCKNQLSDVNGPMRPGIVHRIDKDTSGLLVVAKNNAAHEILAEQFRA 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
               + Y ++V G  + K+  +   + +          +         +A++HFKV++ F
Sbjct: 165 HTNTRKYHAIVVGNIREKEAAVDAPIGRHPVDRLKRAVM-----NDGKHAVTHFKVLEVF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F ++E +  TGRTHQ+RVH  ++G P+VGD  Y A      +        LHA+   
Sbjct: 220 -RDFTYIEAKLETGRTHQIRVHLSYIGNPLVGDPLYGAKS----SKFNLKGQILHAKVFG 274

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
             HP+    ++ T+ LP +  K    L   Y R 
Sbjct: 275 FIHPKTKEYMEFTSDLPEYFNKVLRVLRNNYSRE 308


>gi|332525768|ref|ZP_08401915.1| RluA family pseudouridine synthase [Rubrivivax benzoatilyticus JA2]
 gi|332109325|gb|EGJ10248.1| RluA family pseudouridine synthase [Rubrivivax benzoatilyticus JA2]
          Length = 305

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 97/319 (30%), Positives = 155/319 (48%), Gaps = 19/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V+ +    RLD +   H   +   ++ +++RSG+VRV+K R   + R+ +G  +R
Sbjct: 1   MQRITVDEESAGQRLDNFLLRHLKGVPKTHVYRVIRSGEVRVNKGRASADTRVAAGDEIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+  A           +               +L+ED  +    KPAG++V GGSG++
Sbjct: 61  VPPMRIAEKPAAAAVPAREFP-------------VLFEDEHLLAIAKPAGVAVHGGSGVS 107

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L+       +   L HRLD+ETSG+L++A+ R+A   L + FR R   K Y +L
Sbjct: 108 SGVIEQLRRAR-PDARFLELVHRLDKETSGVLLLAKKRSALTALQDQFRARDTGKNYLAL 166

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G+   K + +   L K +   G+  V VV  +   A  +I+  + +      +  LE+
Sbjct: 167 VVGVWPKKLKVLDLALHKGTDAAGERHVRVVAADAPDARRSITVVRSVRAVG-PYSLLEI 225

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
              TGRTHQ+RVH  H G PIVGD KY   A  K         +++LHA  +   HP  G
Sbjct: 226 GLKTGRTHQIRVHLAHSGHPIVGDPKYGDFALNKTVAREKRFARMFLHAVELAFDHPASG 285

Query: 303 GRLQITAPLPAHMVKTWDS 321
            R+ + APLP        +
Sbjct: 286 ERITLHAPLPPECETLLAA 304


>gi|309800529|ref|ZP_07694680.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           infantis SK1302]
 gi|308115840|gb|EFO53365.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           infantis SK1302]
          Length = 297

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 150/321 (46%), Gaps = 34/321 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIERGGIRLDKALSD-LTELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ +   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YQVPEPEVLE------YVAEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +           VK        A++ F+V++ F   +  LE+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTVK-----GKPAVTRFQVLERFGD-YTLLEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP+ G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPKTGET 275

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           ++ TA +P    +T + L  +
Sbjct: 276 MEFTADIPDIFKQTLEKLRKE 296


>gi|329667353|gb|AEB93301.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           johnsonii DPC 6026]
          Length = 304

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 149/326 (45%), Gaps = 35/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    +V+  D+E  RLD+        ++   +++++    + V+ K  K + ++QSG 
Sbjct: 1   MTKNYKLVI--DDEKGRLDKVIAEKITDLSRTKIKELVNDKNILVNNKAEKVSYKVQSGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +                +     L+  ++ L   ++YEDS + V NKP G+ V   +
Sbjct: 59  VIDVT---------------IPPVKPLSLEAENLHLDIVYEDSDVIVVNKPQGMVVHPSA 103

Query: 124 GIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +G L    D     +G +P + HR+D++TSG+L++A+   A + L +    +
Sbjct: 104 GHPDHTLVNGLLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMIAKNDKARESLEKQLAEK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++ Y ++V G  + K   I   + +  +         K        A++HF V++ F 
Sbjct: 164 INKREYLAIVHGNFEVKNGVINAPIGRNPNNRKQMAVNPK-----GKAAVTHFTVLEQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  ++    TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +  
Sbjct: 218 KNYSLVKCVLETGRTHQIRVHMKYIGHPLAGDPLYGPK-----KTLSGHGQFLHAKTLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
             P     L+ +APLP    K   +L
Sbjct: 273 YQPSTNEWLEFSAPLPTIFEKQLKNL 298


>gi|160900458|ref|YP_001566040.1| RluA family pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160366042|gb|ABX37655.1| pseudouridine synthase, RluA family [Delftia acidovorans SPH-1]
          Length = 356

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 78/331 (23%), Positives = 140/331 (42%), Gaps = 31/331 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQ 63
             ++ + V   +  +R D+         +   LQ++L  G V ++ +  VK   ++ +G 
Sbjct: 44  AELREITVPPAQHGLRADKVLAECVAEFSRSYLQQLLAQGAVTLNGRVLVKPATKVAAGD 103

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                  +  ++    + +   ++YED  + V NKPAG+ V    
Sbjct: 104 RMVLEMR--------------PTQQSMAFQPEDMALDVVYEDEHLLVVNKPAGLVVHPAP 149

Query: 124 GIAYHIDGFLKSWVDSKGQKPR------LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +  G L + +  +  K R      + HRLD++TSG++VVAR+RAA   L      R
Sbjct: 150 G---NWTGTLLNGLLGRDPKAREVPRAGIVHRLDKDTSGLMVVARSRAAMDALVAMIAAR 206

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L       +K    +  + +       + VV   +     A +   ++    
Sbjct: 207 DVSRQYLALAHKAWGPRKHREVDAPIGRDPRNRLRMAVVDLAQHAGKTARTDIDLL-AGN 265

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++   +    HTGRTHQ+RVH   +G P+V D  Y     G        +  LHA  +  
Sbjct: 266 EEVSLVRCTLHTGRTHQIRVHMASLGHPLVADAVYGGKEAGGMA-----RQALHAFRLAF 320

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            HP  G+ L + APLP  M +  ++ G  Y+
Sbjct: 321 THPMTGQALVLRAPLPPDMAQALENWGLSYN 351


>gi|319403704|emb|CBI77289.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           rochalimae ATCC BAA-1498]
          Length = 333

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 84/345 (24%), Positives = 151/345 (43%), Gaps = 45/345 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           +   +   +    R+D+W    Y   ++   LQ ++R G +++D + +K    +++S Q+
Sbjct: 1   MTQHITNENACGQRIDQWLAKQYKGELSRSRLQTLIREGYLKIDGQLIKEPKTKLKSNQI 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +                + +        + L   +L+ED+ I V NKPAG+ V  G+G
Sbjct: 61  IELT---------------IPTPNEAQPQGEALVLDILFEDNHIIVINKPAGLVVHPGNG 105

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++G +    DS       ++P + HRLD++TSG++V+A+   A ++L   F   
Sbjct: 106 NWTGTLVNGLIYHCRDSLSGIGGIKRPGIVHRLDKDTSGVMVIAKNDLAHRNLNAQFADH 165

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                + + Y +++WG P      I  +L + S        VV      A  AI+HF ++
Sbjct: 166 GRTSALDRRYHAVIWGSPNRNIATIDTFLARSSR-DRTKRTVVHSEYAHARRAITHFSLL 224

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-- 285
           + +            LE +  TGRTHQ+RVH  H+G P++GD  Y   FK    +     
Sbjct: 225 EKYGTCNDTTSLASLLECRLETGRTHQIRVHMSHIGHPLIGDKVYGNAFKTKSNTLDPEI 284

Query: 286 -------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                  N+  LHA  +   HP     +  ++P P  +    + L
Sbjct: 285 KNTIDQFNRQALHATSLTFEHPANSEIMSFSSPFPKDLADLLNHL 329


>gi|86358939|ref|YP_470831.1| pseudouridylate synthase, ribosomal large subunit D protein
           [Rhizobium etli CFN 42]
 gi|86283041|gb|ABC92104.1| pseudouridylate synthase, ribosomal large subunit D protein
           [Rhizobium etli CFN 42]
          Length = 354

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 87/346 (25%), Positives = 154/346 (44%), Gaps = 45/346 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ V+  ++    RLD W         +   ++ +++ GQV +  ++V     +++ G  
Sbjct: 24  IRKVLTADETAEGRLDAWLTAQVGEDFSRSRIKALIKDGQVSLRGEQVTDPQRKVRVGDS 83

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
             I                L    + T   + +   +L+ED  + V +KPAG+ V  GSG
Sbjct: 84  FEIT---------------LPEPEDPTPKGEDIPLEILHEDDDLIVISKPAGLVVHPGSG 128

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +    D+       ++P + HRLD++T+G++VVA+   A +HL+  F   
Sbjct: 129 NWTGTLVNALIHHCGDTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDVAHRHLSLQFADH 188

Query: 178 R----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                +++ Y ++VWG P+     I   L + +        V + + + A+ AI+H++VI
Sbjct: 189 GRTMPLERAYRAVVWGRPRTLSGTIDAPLGRATG-DRTRRAVKRPDSQDADAAITHYEVI 247

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-- 285
           + F +          +E    TGRTHQ+RVH  H+G P+VGD  Y A F+       +  
Sbjct: 248 ERFQENPDATALASLVECHLETGRTHQIRVHMAHIGHPLVGDTVYGAGFRTKANLLPEEI 307

Query: 286 -------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                   +  LHA  +   HP  G  +    PLP  MVK   +L 
Sbjct: 308 RKVVNGFGRQALHAFMLQFEHPRTGELMHFEVPLPDDMVKLVAALR 353


>gi|325298577|ref|YP_004258494.1| pseudouridine synthase, RluA family [Bacteroides salanitronis DSM
           18170]
 gi|324318130|gb|ADY36021.1| pseudouridine synthase, RluA family [Bacteroides salanitronis DSM
           18170]
          Length = 360

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 140/332 (42%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+D++      + +   +Q    +G V  + K VK + +++   V+ +  
Sbjct: 35  VTVDKGQAPVRIDKYLFERIVNASRNRIQTAADNGYVMANGKPVKSSYKVKPLDVLTVMM 94

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E  I+   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 95  -----DRPRYENDIIPEDIPLD---------IVYEDDDLMVVNKPAGLVVHPGCGNYHGT 140

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+LV+A+T  A  HL   F  +  ++ 
Sbjct: 141 LVNAIAWHLRNVPTYDPNDPQVGLVHRIDKDTSGLLVIAKTPDAKTHLGMQFYNKTTKRE 200

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI    +  I   + +           V  +     +A++H++V++        
Sbjct: 201 YNALVWGIIDEDEGTIEGNIGRNPK--DRMQMAVMSDPTQGKHAVTHYQVLERLG-YVTL 257

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYL 290
           ++    TGRTHQ+RVH  H+G  +  D +Y  +     T              I  +  L
Sbjct: 258 VKCVLETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFAICPRQAL 317

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA+ +   HP  G  L  T+ LP  M    + 
Sbjct: 318 HAKTLGFVHPRTGKELFFTSELPEDMTHLLEK 349


>gi|328946167|gb|EGG40312.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1087]
          Length = 298

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 146/322 (45%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E      RLD+       +++     + ++ G++ V+ +  K    ++ G ++   
Sbjct: 2   EVRIEASVAGQRLDKAVAE-LTYLSRSLANEQIKDGRILVNGQAKKAKYAVKEGDIIY-- 58

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                  + + E ++++        ++ +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 59  -------YELPEPEVVE------YVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIQDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTSFQVLERFGD-YSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA +PA   +T + L 
Sbjct: 275 GEVLEFTAEVPAIFQETLEKLR 296


>gi|312866736|ref|ZP_07726950.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
 gi|311097817|gb|EFQ56047.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
          Length = 296

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 142/319 (44%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +    RLD+   +  P ++     + ++ G+V V+    K    ++ G ++      
Sbjct: 3   IKIEVAGARLDKALADLTP-LSRAVANEQIKEGKVLVNGTVKKAKYTVKEGDII------ 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
                    Q  +     ++  ++ L   ++YED  + V NKP G+ V   +G      +
Sbjct: 56  ---------QYEVPEVEEVSYEAEDLPLDIVYEDQDVVVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSG+L+VA+   A   L E  + ++  + YW+
Sbjct: 107 NALLYHVKDLSGINGELRPGIVHRIDKDTSGLLMVAKNDQAHVALAEELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F+V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGMIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFQVLERFG-NYTLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +      +LHAR +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDPAYGPK-----KTLKGQGQFLHARTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+ TA +PA   KT + L 
Sbjct: 276 LEFTAEVPAIFEKTLEDLR 294


>gi|320546984|ref|ZP_08041285.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equinus ATCC 9812]
 gi|320448386|gb|EFW89128.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equinus ATCC 9812]
          Length = 298

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 140/315 (44%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++       ++   V V+ K VK    ++ G VV          
Sbjct: 7   EAGARLDKALAD-LTELSRSQANDEIKKETVLVNGKAVKAKYAVKVGDVVT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGFL 133
           + + E+++L+ +      ++ +   ++YED  + V NKP G+ V    G      ++  +
Sbjct: 57  YEVPEEEVLEYT------AENIPLDIIYEDEDVAVVNKPQGMVVHPSVGHTSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L++A+  AA   L    + ++  + Y ++V G
Sbjct: 111 YHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDAAHNALAAELKDKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +            K        A++HFKV++ F   +  +E+   T
Sbjct: 171 NIPNDRGVIEAPIGRSDKDRKKQAVTAK-----GKPAVTHFKVLERFGS-YTLVELTLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP+ G  +  T
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLKGHGQFLHAQTLGFTHPKTGETITFT 279

Query: 309 APLPAHMVKTWDSLG 323
           A +P    +T + L 
Sbjct: 280 AEVPEIFKETLEKLR 294


>gi|224825454|ref|ZP_03698559.1| pseudouridine synthase, RluA family [Lutiella nitroferrum 2002]
 gi|224602375|gb|EEG08553.1| pseudouridine synthase, RluA family [Lutiella nitroferrum 2002]
          Length = 362

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 135/330 (40%), Gaps = 29/330 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           +  Q   V       RLD       P  +   L + ++ G V +D K      ++  G+ 
Sbjct: 20  SATQQFDVPLSLAGERLDAALAKLLPDYSRSRLTQWVKDGHVLLDGKPAAPKTKLLGGEH 79

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +               +  +   L  H + ++  ++YED  I + NKPAG+ V   +G
Sbjct: 80  IEV--------------AVQQTEEQLAYHPEAIELPIVYEDDHIIIINKPAGLVVHPAAG 125

Query: 125 --IAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                 ++G L      +   +  + HRLD+ETSG++VVA+T  A   L    + R +++
Sbjct: 126 NWTGTLLNGLLHHCPALTHVPRAGIVHRLDKETSGLMVVAKTIPAQTELVRQMQARSVKR 185

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY ++  G+       I   + +  H     + VVK    G   AI+H +V+  F     
Sbjct: 186 IYRAIADGVVPFD-GKIETLIGRDPH-NRMRMAVVKF---GGKQAITHVRVLATFPS-HS 239

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-----NFTSPIQNKLYLHARYMD 296
           ++E +  TGRTHQ+RVH      P+ GD  Y                   +  LHA  + 
Sbjct: 240 YIECRLETGRTHQIRVHMREARHPLAGDPLYGNPRHTMPDEIEEAVKALGRQALHAYSLT 299

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           L HP  G  +   A LP  M      LG +
Sbjct: 300 LTHPATGKEMTWKAKLPDDMKHLLAVLGGE 329


>gi|227823294|ref|YP_002827266.1| putative ribosomal large subunit pseudouridine synthase D
           [Sinorhizobium fredii NGR234]
 gi|227342295|gb|ACP26513.1| putative ribosomal large subunit pseudouridine synthase D
           [Sinorhizobium fredii NGR234]
          Length = 352

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 86/345 (24%), Positives = 151/345 (43%), Gaps = 47/345 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           + +  + +    RLD +         +   ++ ++  G V ++   V +   ++  G   
Sbjct: 23  KVLTADENAAG-RLDAFLTEALSGEFSRNRIKALIEQGAVSINGVTVLEPKRKVHPGDRF 81

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            I                L +  +     + +   +LYED  + V  KPAG+ V  G+G 
Sbjct: 82  EIT---------------LPAPEDPEPKGEDIPIDVLYEDDDLIVLVKPAGLVVHPGAGN 126

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  +    DS       ++P + HRLD+ETSG++VVA+  AA +HL++ F    
Sbjct: 127 WTGTLVNALIHHCGDSLSGIGGVRRPGIVHRLDKETSGVMVVAKNDAAHRHLSDQFADHG 186

Query: 179 ----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y ++VWG P+  K  I   L +          V ++    A  AI+H++V++
Sbjct: 187 RTGPLERAYQAVVWGRPRQLKGTINAALGRAG--DRTKRAVKREESDDAREAITHYEVVE 244

Query: 235 CFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
            + +K         +E    TGRTHQ+RVH  H+G P++GD  Y A F+       +   
Sbjct: 245 RYHEKPDGTCLAATVECHLETGRTHQIRVHMAHIGNPLIGDPDYGAAFRTKANLLPETAR 304

Query: 286 ------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
                 ++  LHA  +   HP  G  +   APLPA M +   +L 
Sbjct: 305 SVVNRFSRQALHAFMLQFEHPSSGDTMHFEAPLPADMQELVAALR 349


>gi|307708571|ref|ZP_07645035.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           mitis NCTC 12261]
 gi|307615320|gb|EFN94529.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           mitis NCTC 12261]
          Length = 295

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 146/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G +V      
Sbjct: 3   IKIETGGLRLDKALSD-LTELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDIVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAENLPLDIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++ TA +P    +T + L 
Sbjct: 276 MEFTADIPEIFKETLERLR 294


>gi|258423760|ref|ZP_05686646.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus A9635]
 gi|257845992|gb|EEV70020.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus A9635]
          Length = 305

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 139/327 (42%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +++   
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I+ E                L   + YED  + V  KP G+ V    
Sbjct: 61  HIVVTEKEVVEADILPEN---------------LNLDIYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 GIAYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +   +G +    D  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKDLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAPIGRN-KNDRQSMAVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLD-----IGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  A LP       D++ 
Sbjct: 275 EHPVTGEYIERHAELPQDFEDLLDTIR 301


>gi|153948793|ref|YP_001400547.1| 23S rRNA pseudouridylate synthase C [Yersinia pseudotuberculosis IP
           31758]
 gi|152960288|gb|ABS47749.1| ribosomal large subunit pseudouridine synthase C [Yersinia
           pseudotuberculosis IP 31758]
          Length = 320

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 99/319 (31%), Positives = 164/319 (51%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEVQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKSMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+ V  V         + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAIQAPLLKNIMQSGERVVKVSSE---GKPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHALHAGHPIAFDDRYGDRAFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++I APL   +     +L 
Sbjct: 296 IRIEAPLDNQLRHCLLALR 314


>gi|192359429|ref|YP_001982148.1| pseudouridine synthase Rlu family protein [Cellvibrio japonicus
           Ueda107]
 gi|190685594|gb|ACE83272.1| pseudouridine synthase, RluA family subfamily [Cellvibrio japonicus
           Ueda107]
          Length = 349

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 94/325 (28%), Positives = 165/325 (50%), Gaps = 19/325 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+++ ++ +    RLD +       +    +  ++R G+VRV+K R + + ++ +G +VR
Sbjct: 35  VRFLTIDAELAGQRLDNFLMAQLKGVPKSRIYNLVRKGEVRVNKGRSRPDYKLCAGDLVR 94

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A   +    K  +  V L      L   +L+E+  + V NKP G++V GGSG+ 
Sbjct: 95  VPPVRTAEARVAAPAKAGNQLVAL------LDQSVLFENEGLLVINKPPGLAVHGGSGVN 148

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR---RIQKIY 183
             +   L+     + +   L HRLD++TSG ++VA+ R+  +HL  + R +   +I+K+Y
Sbjct: 149 LGLIETLRQMR-PEARYLELVHRLDRDTSGCIMVAKKRSYLRHLQAALRDKVEGQIEKVY 207

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G    +   +   LL+      +    V  +      +++ F VI  + Q F  +
Sbjct: 208 CALVVGHWPARLHQVNAPLLRTEVGADERYVRVHPD---GKPSLTLFNVIQRY-QGFTLV 263

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEG 302
           E +P TGRTHQ+RVHA H G  +VGD KY  +    +  +    +L+LHA  +    P  
Sbjct: 264 EARPVTGRTHQIRVHARHAGHGLVGDEKYGDDDINLHMRNQGIKRLFLHASSLGFCLPGE 323

Query: 303 GRLQ-ITAPLPAHMVK---TWDSLG 323
            ++  + APLP  + +     +SLG
Sbjct: 324 AQMTWVEAPLPQDLAQPLSCLESLG 348


>gi|16801023|ref|NP_471291.1| hypothetical protein lin1957 [Listeria innocua Clip11262]
 gi|16414458|emb|CAC97187.1| lin1957 [Listeria innocua Clip11262]
 gi|313618258|gb|EFR90322.1| ribosomal large subunit pseudouridine synthase D [Listeria innocua
           FSL S4-378]
          Length = 302

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 82/323 (25%), Positives = 143/323 (44%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++E      R+D+         +   +Q +L++G + V+ +  K N ++Q G  +R 
Sbjct: 4   ETLIIEESHARERVDKVIAEMM-EKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIRY 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                    I+ E   LD               + +ED  + V NKP G+ V   +G A 
Sbjct: 63  EAREPEELEILAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHAS 107

Query: 127 -YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 108 GTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + +      + VV+        A +HF+VI+     + 
Sbjct: 168 EYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVIERLP-GYT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH  ++G P+ GD KY         +   N  +LHA  +   HP 
Sbjct: 222 LINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTIKGNGQFLHAAKLGFDHPT 276

Query: 302 G-GRLQITAPLPAHMVKTWDSLG 323
              R+   APLP    +   SL 
Sbjct: 277 TNERMTFEAPLPDSFEQALKSLR 299


>gi|322389731|ref|ZP_08063278.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 903]
 gi|321143570|gb|EFX39001.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 903]
          Length = 296

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 142/319 (44%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +    RLD+   +  P ++     + ++ G+V V+    K    ++ G ++      
Sbjct: 3   IKIEVAGARLDKALADLTP-LSRAVANEQIKEGKVLVNGTVKKAKYTVKEGDII------ 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
                    Q  +     ++  ++ L   ++YED  + V NKP G+ V   +G      +
Sbjct: 56  ---------QYEVPEVEEVSYEAEDLPLDIVYEDQDVVVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HR+D++TSG+L++A+   A   L E  + ++  + YW+
Sbjct: 107 NALLYHVKDLSGINGELRPGIVHRIDKDTSGLLMIAKNDQAHVALAEELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F+V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGMIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFQVLERFG-NYTLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +      +LHAR +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDPAYGPK-----KTLKGQGQFLHARTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+ TA +PA   KT + L 
Sbjct: 276 LEFTAEVPAIFEKTLEDLR 294


>gi|126668127|ref|ZP_01739089.1| ribosomal large subunit pseudouridine synthase C [Marinobacter sp.
           ELB17]
 gi|126627397|gb|EAZ98032.1| ribosomal large subunit pseudouridine synthase C [Marinobacter sp.
           ELB17]
          Length = 331

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 97/329 (29%), Positives = 172/329 (52%), Gaps = 19/329 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +V V+ D +  RLD +       +    + +I+R G+VR++K RVK + R+++G  VR
Sbjct: 15  VLWVTVDEDNDGQRLDNFLMAQLRGVPKSIIYRIVRKGEVRINKGRVKPDTRVKTGDQVR 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV+         ++ +  +    +    +++ +++E+ ++ V NKP+GI+V GGSG++
Sbjct: 75  IPPVVR--------KEKVPQAAPGDRVQAVIEAAVVFENEQLLVVNKPSGIAVHGGSGLS 126

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++      +   L HRLD++TSG+++VA+ R+A ++L +  R R I+K Y +L
Sbjct: 127 FGLIEVLRAGRPQ-ARFLELVHRLDRDTSGLVMVAKKRSALRYLQDELRHRHIRKHYHAL 185

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        +A  LL+     G+    V   +     +++ F+ ++ +   +  +E  
Sbjct: 186 VSGDWPAGMGKVAQPLLRYEMPNGERRVKV---DSSGKESLTLFRCLERY-DGYSLVEAS 241

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHP----- 300
           P TGRTHQ+RVHA   G PI GD KY  +     F +   ++L LHAR ++L  P     
Sbjct: 242 PVTGRTHQIRVHATFAGHPIAGDDKYMDDASLKAFRALGGSRLMLHARALELSLPPDSDG 301

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           +   L++ AP           L  +  RN
Sbjct: 302 QSPALKLEAPYDNAFAAALQKLAARTGRN 330


>gi|324995685|gb|EGC27597.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK678]
          Length = 298

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 144/322 (44%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E+     RLD+        ++     + ++ GQ+ V+ +  K    ++ G V+   
Sbjct: 2   EVRIESSVAGQRLDKAVAE-LTDLSRSLANEQIKDGQILVNGQAKKAKYAVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++         + +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELPEPEVVE------YVPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIQDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHLALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-YSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAQTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA +P    +T   L 
Sbjct: 275 GEVLEFTAEVPVIFQETLKKLR 296


>gi|229829077|ref|ZP_04455146.1| hypothetical protein GCWU000342_01162 [Shuttleworthia satelles DSM
           14600]
 gi|229792240|gb|EEP28354.1| hypothetical protein GCWU000342_01162 [Shuttleworthia satelles DSM
           14600]
          Length = 306

 Score =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 136/319 (42%), Gaps = 31/319 (9%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E  +R+DR+  +H    +  ++QK++  G V V+    + + ++Q    + +      L
Sbjct: 11  EESGLRIDRYLADHLDGQSRNSIQKLIEEGLVLVNGNACRASYKLQEKDQIFVSVPDAVL 70

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGF 132
             +  E+  LD               +LYED ++ + NKP  + V    G      ++  
Sbjct: 71  TELRPERIPLD---------------ILYEDDQLLIVNKPKEMVVHPAPGHNTGTLVNAI 115

Query: 133 LKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +              +P + HR+D  T+G L+V +T AA + +    +   + ++Y ++V
Sbjct: 116 MYHCGKELSGINGEIRPGIVHRIDMNTTGSLIVCKTDAAHRFIASQIKEHSVHRVYRAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G     +  I   + +           +    K    AI+H++ +      F ++E + 
Sbjct: 176 YGHLNPTEGTIRTSIGRDPRDRKK----MSVGVKNGRQAITHYRELARLRNNFSYVEFEL 231

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH   +G PI+GD  Y        +    +   LHA  +   HP   R ++
Sbjct: 232 ETGRTHQIRVHMASIGHPILGDQVYGPKK----SPYHLDGQTLHAMTIGFVHPTSKRYVE 287

Query: 307 ITAPLPAHMVKTWDSLGFK 325
            TAPLP +       LG +
Sbjct: 288 FTAPLPEYFQHLLAILGEE 306


>gi|189462984|ref|ZP_03011769.1| hypothetical protein BACCOP_03686 [Bacteroides coprocola DSM 17136]
 gi|189430266|gb|EDU99250.1| hypothetical protein BACCOP_03686 [Bacteroides coprocola DSM 17136]
          Length = 355

 Score =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 81/332 (24%), Positives = 143/332 (43%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +Q    +G V  + K VK + +++   V+ +  
Sbjct: 31  VVVDKGQTPVRIDKYLFERIVNASRNRIQTAADAGFVMANGKPVKSSYKVKPLDVLTVMM 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E  I+   + L          ++YED+ + V NKPAG+ V  G G  +  
Sbjct: 91  -----DRPRYENDIIPEDIPLD---------IVYEDNDLMVINKPAGLVVHPGCGNYHGT 136

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D    +  L HR+D++TSG+LVVA+T  A   L   F  +  ++ 
Sbjct: 137 LVNAIAWHLRDVPSYDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTSLGMQFYNKTTKRE 196

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI +  +  I   + +           V  +     +A++H++V++        
Sbjct: 197 YNALVWGIVEEDEGTITGNIGRNPK--DRMQMAVMSDPTQGKHAVTHYQVLERLG-YVTL 253

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYL 290
           ++    TGRTHQ+RVH  H+G  +  D +Y  +     T              I  +  L
Sbjct: 254 VKCVLETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDICPRQAL 313

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA+ +   HP  G  +  T+ LP  M +  D 
Sbjct: 314 HAKTLGFVHPRTGKEMFFTSELPEDMTRLLDK 345


>gi|82750802|ref|YP_416543.1| hypothetical protein SAB1061 [Staphylococcus aureus RF122]
 gi|82656333|emb|CAI80750.1| conserved hypothetical protein [Staphylococcus aureus RF122]
          Length = 305

 Score =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 140/329 (42%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +++   
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I+ E                L   + YED  + V  KP G+ V    
Sbjct: 61  HIVVTEKEVVEADILPEN---------------LNLDIYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 GIAYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +   +G +    +  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRELVEQLMDK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAPIGRN-KNDRQSMAVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLD-----IGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  ++  A LP       D++  +
Sbjct: 275 EHPVTGEYIERHAELPQDFEDLLDTIRKR 303


>gi|51596800|ref|YP_070991.1| 23S rRNA pseudouridylate synthase C [Yersinia pseudotuberculosis IP
           32953]
 gi|186895871|ref|YP_001872983.1| 23S rRNA pseudouridylate synthase C [Yersinia pseudotuberculosis
           PB1/+]
 gi|51590082|emb|CAH21716.1| ribosomal large subunit pseudouridine synthase C [Yersinia
           pseudotuberculosis IP 32953]
 gi|186698897|gb|ACC89526.1| pseudouridine synthase, RluA family [Yersinia pseudotuberculosis
           PB1/+]
          Length = 320

 Score =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 99/319 (31%), Positives = 164/319 (51%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEVQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKSMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+ V  V         + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAIQAPLLKNIMQSGERVVKVSSE---GKPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++I APL   +     +L 
Sbjct: 296 IRIEAPLDNQLRHCLLALR 314


>gi|317495177|ref|ZP_07953547.1| RluA family pseudouridine synthase [Gemella moribillum M424]
 gi|316914599|gb|EFV36075.1| RluA family pseudouridine synthase [Gemella moribillum M424]
          Length = 299

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 82/313 (26%), Positives = 148/313 (47%), Gaps = 38/313 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D++ +     ++  N+Q ++  G ++VD K +K N +++ G  + I         ++
Sbjct: 14  ERIDKFLQKELSELSRTNIQNLISEGYIKVDGKEIKTNFKLKDGNEITIEYKEPEELDVV 73

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K+   +D               ++YEDS + V NK  G+ V   +G   H DG L + + 
Sbjct: 74  KQDIPVD---------------IVYEDSDLIVVNKAKGMVVHPSAG---HRDGTLVNALL 115

Query: 139 SKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +        +P + HR+D++TSG+LVVA+   A   L+E    + +++ Y++LV G 
Sbjct: 116 FHSELSSINGTIRPGIVHRIDKDTSGLLVVAKNDKAHVKLSEMIANKDVKRKYYALVHGS 175

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K+    I   + +      +   +          +I+HFKV++ F +K+  +E +  TG
Sbjct: 176 IKHDYGTIDAPIARNPKERKEMAII-----DEGKPSITHFKVVERF-EKYTLIECELETG 229

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++  P+VGD  Y      N      N   LH++ ++  HP  G  L    
Sbjct: 230 RTHQIRVHMKYINHPLVGDPVYGPRKTLNA-----NGQALHSKSIEFNHPITGEHLYFET 284

Query: 310 PLPAHMVKTWDSL 322
           P+P +M+     L
Sbjct: 285 PIPQYMLDIMAKL 297


>gi|107022188|ref|YP_620515.1| pseudouridine synthase, RluD [Burkholderia cenocepacia AU 1054]
 gi|116689134|ref|YP_834757.1| RluA family pseudouridine synthase [Burkholderia cenocepacia
           HI2424]
 gi|105892377|gb|ABF75542.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           cenocepacia AU 1054]
 gi|116647223|gb|ABK07864.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           cenocepacia HI2424]
          Length = 334

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 100/326 (30%), Positives = 159/326 (48%), Gaps = 23/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++ +    R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +V
Sbjct: 16  QVSMIEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + +    +    N           +LYED  + V +KPAG++V GGSG+
Sbjct: 76  RVPPVRVAAADLARADTPVVPPANFD---------VLYEDDAMLVIDKPAGVAVHGGSGV 126

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y++
Sbjct: 127 AFGVIEQMRQAR-PRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFA 185

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
              G  +        +   L K S   G+    V+ +      + + F ++D +   +  
Sbjct: 186 CAHGEWQPDWGRRRAVKAPLFKYSTPEGERRVRVQDD---GLASHTVFNLVDRWPD-YVL 241

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PI GD KY               P   +++LHA  + L
Sbjct: 242 VEAELKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANAQPSLKRMFLHAHRLKL 301

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA   +  D L
Sbjct: 302 AHPLTGEALQFDAPLPAECRRFLDQL 327


>gi|325295189|ref|YP_004281703.1| pseudouridine synthase, RluA family [Desulfurobacterium
           thermolithotrophum DSM 11699]
 gi|325065637|gb|ADY73644.1| pseudouridine synthase, RluA family [Desulfurobacterium
           thermolithotrophum DSM 11699]
          Length = 313

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 80/329 (24%), Positives = 152/329 (46%), Gaps = 35/329 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
            +VV+++++  RLD++  +    I+    + ++  G+V ++ + VK  + +++ G+ V  
Sbjct: 3   EIVVDSEKKGKRLDQFIAS-IADISRSQAKNLIEDGEVSINGRIVKKPSYKVKEGETVSF 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                           +   + L    + +   ++YED  + V NKPAG+ V    G   
Sbjct: 62  E---------------IPEPIPLDLQPENIPLDIVYEDKDVIVINKPAGLVVHPAPGHYS 106

Query: 126 AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D +G     +P + HRLD++T+G+LVVA+   A Q L E F+ R + +
Sbjct: 107 GTLVNALLYYCKDFQGINGTLRPGIVHRLDKDTAGLLVVAKNDLAQQSLIEQFKRRTVGR 166

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKF 240
            Y +LV GI + + + I   + +       +      N      AI+++ V++ F     
Sbjct: 167 FYRALVLGIFEKQHDRIVVPIGRDKFDRKKF----SPNTTSPKEAITNYWVLESFPTHNV 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-----KLYL-HARY 294
             ++ +  TGRTHQ+RVH  H+G P++GD  Y           ++      +++   A Y
Sbjct: 223 SDIKCKLETGRTHQIRVHMSHIGHPLLGDKTYGYKPSRIKDETLRRLIDEMRMHALCAYY 282

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +   HP   + ++    LP +M K  D L
Sbjct: 283 LGFKHPRTEKWIEFEIDLPENMKKVLDFL 311


>gi|293396582|ref|ZP_06640858.1| ribosomal large subunit pseudouridine synthase C [Serratia
           odorifera DSM 4582]
 gi|291420846|gb|EFE94099.1| ribosomal large subunit pseudouridine synthase C [Serratia
           odorifera DSM 4582]
          Length = 319

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 97/319 (30%), Positives = 163/319 (51%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + + +DE   R+D +       +    + +I+R G+VRV+K R+K   ++ +G    
Sbjct: 8   VQLITISDDEAGQRIDNFLLARLKGVPKSMIYRIVRKGEVRVNKGRIKAEYKLAAGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++    S  L K +  L + +LYED  + + NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEAPVSAKLDKVA-ALANCILYEDDHLLLLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FKV + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNILQSGERIVRVSSE---GKPSETRFKVEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH LH G PI  D +Y    F          +L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHTLHAGHPIAFDDRYGDREFDRQLAGTGLKRLFLHAAALRFEHPGTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+I AP+   +      L 
Sbjct: 296 LRIEAPMDDELRHCLQVLR 314


>gi|42519111|ref|NP_965041.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           johnsonii NCC 533]
 gi|41583398|gb|AAS09007.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           johnsonii NCC 533]
          Length = 304

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 149/327 (45%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    +V+  D+E  RLD+        ++   +++++    + V+ K  K + ++QSG 
Sbjct: 1   MTKNYKLVI--DDEKGRLDKVIAEKITDLSRTKIKELVNDKNILVNNKAEKVSYKVQSGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +                +     L+  ++ L   ++YEDS + V NKP G+ V   +
Sbjct: 59  VIDVT---------------IPPVKPLSLEAENLHLDIVYEDSDVIVVNKPQGMVVHPSA 103

Query: 124 GIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +G L    D     +G +P + HR+D++TSG+L++A+   A + L +    +
Sbjct: 104 GHPDHTLVNGLLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMIAKNDKARESLEKQLAEK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++ Y ++V G  + K   I   + +  +         K        A++HF V++ F 
Sbjct: 164 INKREYLAIVHGNFEVKNGVINAPIGRNPNNRKQMAVNPK-----GKAAVTHFTVLEQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  ++    TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +  
Sbjct: 218 KNYSLVKCVLETGRTHQIRVHMKYIGHPLAGDPLYGPK-----KTLSGHGQFLHAKTLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
             P     L+ +APLP    K   +L 
Sbjct: 273 YQPSTNEWLEFSAPLPTIFEKQLKNLR 299


>gi|154252611|ref|YP_001413435.1| RluA family pseudouridine synthase [Parvibaculum lavamentivorans
           DS-1]
 gi|154156561|gb|ABS63778.1| pseudouridine synthase, RluA family [Parvibaculum lavamentivorans
           DS-1]
          Length = 482

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 85/358 (23%), Positives = 151/358 (42%), Gaps = 57/358 (15%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPH---------INFVNLQKILRSGQVRVDKKR--- 52
              + V V  ++   RLD++                ++   +++++  GQV  ++K    
Sbjct: 132 AETRAVTVTAEDAGARLDKYLTEALGDKGEGDAPATLSRARMRQLIEQGQVSREEKAGAP 191

Query: 53  ---VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIY 109
                 + R+++G+ + +                +            +   ++YED+ + 
Sbjct: 192 KLLTDPSYRVKAGERLSVS---------------VPPPTPAKPAGQAIPLEIVYEDADLI 236

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVV 160
           V  KPAG+ V    G        + + V   G+         +P + HRLD+ETSG++VV
Sbjct: 237 VVMKPAGLVVHPAPG--NPDMTLVNALVAHCGETLSGIGGEKRPGIVHRLDKETSGLMVV 294

Query: 161 ARTRAAAQHLTESFRMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           A+T  A Q L+  F       ++ + Y +L WG+P+ +K  +   + + SH       V 
Sbjct: 295 AKTDRAHQGLSAQFAAHGRDGKLTRAYTALTWGVPQTRKGTVDANIARSSHNRSKMATVR 354

Query: 217 KQNEK-GANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            + E+ G   AI+H+ V   +A      +E +  TGRTHQ+RVH   +G P++GD  Y  
Sbjct: 355 DRGEETGGRIAITHYTVKTDYADGLVAEVECRLETGRTHQIRVHMTALGHPLLGDATYGT 414

Query: 275 NFKGN---------FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
             K                 N+  LHA ++   HP  G ++   APLP  M +   +L
Sbjct: 415 GMKSRKSKLSPEAQAALERLNRQALHAHHLGFEHPVAGEKMSFDAPLPEDMQELVRAL 472


>gi|332975054|gb|EGK11960.1| ribosomal large subunit pseudouridine synthase C [Kingella kingae
           ATCC 23330]
          Length = 334

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 96/327 (29%), Positives = 165/327 (50%), Gaps = 21/327 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ ++  E   RLD +       +   ++ +I+R+G+VRV+K RVK + RI++  +VR
Sbjct: 9   VNHITIQEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRVNKGRVKPDYRIENKDLVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+       I E+ +  S  N    +   +  +++ED  + V NKP+G++V GGSG++
Sbjct: 69  IPPIR------IAEKDVSGSLKNAPIPAR--EFDIVFEDDAMIVINKPSGVAVHGGSGVS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD++TSG+L++A+ R+A   L E  R    +KIY +L
Sbjct: 121 FGVIEQLRQ-SRPDAKYLELVHRLDRDTSGLLMIAKKRSALVKLHEMLRNDHPKKIYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-------- 238
             G  + +   +   L+K +   G+ +  V  +      A + F+V++ F+         
Sbjct: 180 GVGTWQPENRHVKLPLIKYTGANGEKMVRVGSDA-DGQSAHTIFRVLNTFSGSLMHSVGI 238

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +E    TGRTHQ+RVH     CPI GD +Y               +++LHA  ++
Sbjct: 239 SALSLVEATLKTGRTHQIRVHMQSQNCPIAGDERYGDYQANKRLQKLGLKRMFLHAFVLE 298

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSL 322
           L HP  G +L + A LP  +    D+L
Sbjct: 299 LNHPLTGEKLHLKADLPKELQNLLDNL 325


>gi|332366655|gb|EGJ44398.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1059]
          Length = 298

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 145/322 (45%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E      RLD+        ++     + ++ G++ V+ +  K    ++ G V+   
Sbjct: 2   EVRIEASVVGQRLDKAVAE-LTDLSRSLAHEQIKDGRILVNGQVKKAKYAVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++        ++ +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELPEPEVVE------YVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIQDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKAKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-YSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA  PA   +T + L 
Sbjct: 275 GEVLEFTAEAPAIFQETLEKLR 296


>gi|330685506|gb|EGG97159.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU121]
          Length = 305

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 143/323 (44%), Gaps = 33/323 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +Y + +++    RLD+         +   +Q  ++   V+V+ K VK N +++   
Sbjct: 1   METYEYTITDSNHVGQRLDKVLPELNSGWSRSQIQDWIKEDLVKVNDKVVKPNYKVKQND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           ++ EQ+++++ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  NI-----------VVTEQEVVEADI----TPENLNLDIFYEDDDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    +  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    +   + +      D   +   ++     A++HF V++ F 
Sbjct: 166 SVKRKYIALVHGNIPHDYGTVDAPIGRNKK---DRQAMAVVDD--GKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLIECELETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLD-----IGGQALHAGVIGF 274

Query: 298 PHPEG-GRLQITAPLPAHMVKTW 319
            HP     ++ TA LP       
Sbjct: 275 EHPVTHEYIERTAELPQEFEDLL 297


>gi|170700219|ref|ZP_02891235.1| pseudouridine synthase, RluA family [Burkholderia ambifaria
           IOP40-10]
 gi|170134852|gb|EDT03164.1| pseudouridine synthase, RluA family [Burkholderia ambifaria
           IOP40-10]
          Length = 316

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 99/322 (30%), Positives = 157/322 (48%), Gaps = 23/322 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++ +    R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +VR+PP
Sbjct: 2   IEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDIVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A   + +    +    +           +LYED  + V NKPAG++V GGSG+A+ +
Sbjct: 62  VRVAAADLARADTPIVPPAHFE---------VLYEDDAMLVINKPAGVAVHGGSGVAFGV 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y++   G
Sbjct: 113 IEQMRQAR-PRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFACGHG 171

Query: 190 IPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             ++       +   L K S   G+    V+    G   + + F +++ +   +  +E +
Sbjct: 172 EWQSDWGRRRAVKAPLFKYSTAEGERRVRVQD---GGLPSHTVFNLLERWPD-YALVEAE 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H+G PI GD KY               P   +++LHA  + L HP 
Sbjct: 228 LKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANAQPSLKRMFLHAHRLKLAHPL 287

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  LQ  APLP    +  D L
Sbjct: 288 TGEPLQFDAPLPDECRRFLDQL 309


>gi|325104837|ref|YP_004274491.1| ribosomal large subunit pseudouridine synthase D [Pedobacter
           saltans DSM 12145]
 gi|324973685|gb|ADY52669.1| ribosomal large subunit pseudouridine synthase D [Pedobacter
           saltans DSM 12145]
          Length = 342

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 74/333 (22%), Positives = 143/333 (42%), Gaps = 40/333 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  + ++R+D++      + +   +Q  +  G V V+ K +K + +I+    + I  
Sbjct: 21  VVVDKGQSSIRIDKFLMVRLENASRNKIQNAIEQGNVLVNGKAIKPSYKIKPLDDISI-- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI---- 125
               L H  ++ ++    + +          ++YED+ + + NK AG+ V  G G     
Sbjct: 79  ---VLPHPPRDTEVYPEDIPID---------IIYEDNDVVLVNKVAGMVVHPGYGNWSGT 126

Query: 126 ----AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                 H    L     + G +P L HR+D++TSG+LV+++   +   L + F    I++
Sbjct: 127 LVNALTHHFSQLPQLPGNDG-RPGLVHRIDKDTSGLLVISKNEKSMASLAKQFFDHSIKR 185

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LVWG        I+ ++ +   I    V  +  + +   ++++H+KV+        
Sbjct: 186 KYLALVWGDLPED-GIISGYIGRS--IKDRKVMDLYDDPEKGKWSVTHYKVVKRL-NYVT 241

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLY 289
            +E Q  TGRTHQ+R H   +G P+  D  Y  +     T   +             +  
Sbjct: 242 LIECQLETGRTHQIRAHMKAIGHPLFNDTAYGGDKIRKGTIFAKYKQFIDNCFAVMPRQA 301

Query: 290 LHARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           LHA+ +   HP     +   + LP    +  + 
Sbjct: 302 LHAKSLGFIHPTTKKEVYFESELPDDFSQVLEK 334


>gi|329728841|gb|EGG65262.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 305

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 140/329 (42%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +++   
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I+ E                L   + YED  + V  KP G+ V    
Sbjct: 61  HIVVTEKEVVEADILPEN---------------LNLDIYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 GIAYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +   +G +    +  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAPIGRN-KNDRQSMAVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KNYTLVECQLETGRTHQIRVHMRYIGFPLVGDPKYGPKKTLD-----IGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  ++  A LP       D++  +
Sbjct: 275 EHPVTGEYIERHAELPQDFEDLLDTIRKR 303


>gi|282916446|ref|ZP_06324208.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus D139]
 gi|283770258|ref|ZP_06343150.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
 gi|282319886|gb|EFB50234.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus D139]
 gi|283460405|gb|EFC07495.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
 gi|298694490|gb|ADI97712.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           ED133]
          Length = 305

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 79/329 (24%), Positives = 140/329 (42%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +++   
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I+ E                L   + YED  + V  KP G+ V    
Sbjct: 61  HIVVTEKEVVEADILPEN---------------LNLDIYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 GIAYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +   +G +    D  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKDLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAPIGRN-KNDRQSMAVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLD-----IGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  ++  A LP       D++  +
Sbjct: 275 EHPVTGEYIERHAELPQDFEDLLDTIRKR 303


>gi|315224831|ref|ZP_07866652.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           ochracea F0287]
 gi|314945234|gb|EFS97262.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           ochracea F0287]
          Length = 352

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 152/330 (46%), Gaps = 35/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
                 +E +R+D++  N   +     +Q+  + G + V+ + VK N+R+++   V++  
Sbjct: 29  FTAGKGQEPLRVDKFLMNFVENATRNKVQQAAKQGNIFVNGEPVKSNHRVKANDEVKV-- 86

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                 H   E  ++  ++ L          ++YED  + V NKPAGI V  G G     
Sbjct: 87  ---LFPHPPHEDLLVPENIPLN---------IVYEDDSLLVVNKPAGIVVHPGHGNYSGT 134

Query: 128 HIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            I+  +   ++  ++   +P L HR+D++TSG+LVVA+T  A  HLT+ F  +  Q+ Y 
Sbjct: 135 LINALVYHFENLPNNSSNRPGLVHRIDKDTSGLLVVAKTEEAMLHLTQQFFNKTTQREYI 194

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG  +  +  +   + +  H+       V  +      A++H+KV++ F      + 
Sbjct: 195 ALVWGNIEEDEGTVCGHIGR--HLKDRLQMDVFPDGSHGKEAVTHYKVLERFG-YVTLIS 251

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLHA 292
            +  TGRTHQ+RVH  H+G  +  D +Y  +     T+  +             +  LHA
Sbjct: 252 CKLETGRTHQIRVHLKHIGHTLFNDERYGGDKILKGTTFAKYKQFVENCFAVLPRQALHA 311

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP   + L   + LP  M +  + 
Sbjct: 312 KTLGFEHPITHKYLSFDSELPNDMQQCIEK 341


>gi|323464710|gb|ADX76863.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus pseudintermedius ED99]
          Length = 305

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 147/325 (45%), Gaps = 33/325 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    + + +      R+D+         +   LQ+ ++ G + V+ K VK N +++ G 
Sbjct: 1   MEKHIFNIEDATHHLQRIDKILPEFNSEWSRSQLQEWIKEGLIEVNGKAVKSNYKLKLGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I            E++++++ +     ++ L   + YED  + +  KP G+ V    
Sbjct: 61  RIEIT-----------EKEVVEADI----QAENLNLDIYYEDDDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    +  G     +P + HR+D++TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKNLSGINSEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVEQLMAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   ++   I   + +        + VV         A++HF VI+ F 
Sbjct: 166 TVKRKYIALVHGHIPHEFGTIDAPIGRN-KNDRQSMAVVD----DGKEAVTHFNVIETF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E +  TGRTHQ+RVH  ++G P+VGD KY         +       LHA  +  
Sbjct: 220 KNYTLVECELETGRTHQIRVHMKYIGYPLVGDPKYGPK-----KTLEIGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDS 321
            HP+ G  ++  APLPA      + 
Sbjct: 275 EHPKTGEYIERFAPLPAEFEAVIEQ 299


>gi|260221244|emb|CBA29613.1| Ribosomal large subunit pseudouridine synthase D [Curvibacter
           putative symbiont of Hydra magnipapillata]
          Length = 335

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 79/329 (24%), Positives = 142/329 (43%), Gaps = 31/329 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVR 66
           +   ++      RLDR         +   LQ+++ SG V+V+ K V K + +++ G+ + 
Sbjct: 23  RSFTLDASLHGERLDRALAFSVQEFSRSYLQQLIESGFVQVNGKVVTKTSGKVKVGEELT 82

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +              ++  +  +     + +   +++ED  + V NKPAG+ V    G  
Sbjct: 83  V--------------ELKPTPQSQAFKPEPMALDVVHEDEHVLVINKPAGLVVHPAPG-- 126

Query: 127 YHIDGFLKSWVDSKGQKP------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            +  G L + + +            + HRLD++TSG++VVAR+R A   L  +   R + 
Sbjct: 127 -NWSGTLLNGLLAYSPHAALVPRAGIVHRLDKDTSGLMVVARSRTAMDALVNAIAAREVS 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y+++        +    +  + +       + VV    +    A + F +I   +Q  
Sbjct: 186 RQYFAIAHKTWPWTRLKEVDAPIGRDPRNRLRMAVVDLVHQSGKEARTDFSLI-SNSQVA 244

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           CW+    HTGRTHQ+RVH  H+G P+V D  Y     G  T     +  LHA  +   HP
Sbjct: 245 CWVRCILHTGRTHQIRVHMAHIGHPLVADAVYGGAVLGEMT-----RQALHACRLAFKHP 299

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
             G  L+     P+  +     LG  Y++
Sbjct: 300 VSGESLEFECGPPSDFMALCAELGLGYNQ 328


>gi|319892189|ref|YP_004149064.1| Ribosomal large subunit pseudouridine synthase D [Staphylococcus
           pseudintermedius HKU10-03]
 gi|317161885|gb|ADV05428.1| Ribosomal large subunit pseudouridine synthase D [Staphylococcus
           pseudintermedius HKU10-03]
          Length = 305

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 147/325 (45%), Gaps = 33/325 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    + + +      R+D+         +   LQ+ ++ G + V+ K VK N +++ G 
Sbjct: 1   MEKHIFNIEDATHHLQRIDKILPEFNSEWSRSQLQEWIKEGLIEVNGKAVKSNYKLKLGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I            E++++++ +     ++ L   + YED  + +  KP G+ V    
Sbjct: 61  RIEIT-----------EKEVVEADI----QAENLNLDIYYEDDDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    +  G     +P + HR+D++TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKNLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVEQLMAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   ++   I   + +        + VV         A++HF VI+ F 
Sbjct: 166 TVKRKYIALVHGHIPHEFGTIDAPIGRN-KNDRQSMAVVD----DGKEAVTHFNVIETF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E +  TGRTHQ+RVH  ++G P+VGD KY         +       LHA  +  
Sbjct: 220 KNYTLVECELETGRTHQIRVHMKYIGYPLVGDPKYGPK-----KTLEIGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDS 321
            HP+ G  ++  APLPA      + 
Sbjct: 275 EHPKTGEYIERFAPLPAEFEAVIEQ 299


>gi|329769635|ref|ZP_08261039.1| hypothetical protein HMPREF0433_00803 [Gemella sanguinis M325]
 gi|328838390|gb|EGF87999.1| hypothetical protein HMPREF0433_00803 [Gemella sanguinis M325]
          Length = 299

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 84/313 (26%), Positives = 150/313 (47%), Gaps = 38/313 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D++ +N    ++  N+Q ++  G ++VD   VK N +++   V+ I         ++
Sbjct: 14  ERIDKFLQNELSDLSRTNIQNLISEGYIKVDGNTVKTNYKLKESNVITIDYKEPEELDVV 73

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K+   +D               ++YED+ + + NKP G+ V   +G   H DG L + + 
Sbjct: 74  KQDIPVD---------------IVYEDNDLLIVNKPKGMVVHPSAG---HKDGTLVNALL 115

Query: 139 SKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +        +P + HR+D++TSG+L+VA+   A   L+E    + +++ Y++LV G 
Sbjct: 116 YHCELSSINGTIRPGIVHRIDKDTSGLLIVAKNDKAHVKLSEMIANKEVKRKYYALVHGS 175

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K+    I   + +      +   +          +I+HFKVID F +K+  +E +  TG
Sbjct: 176 IKHDYGTIDAPIARNPKERKEMAVI-----DEGKPSITHFKVIDRF-EKYTLIECELETG 229

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++  P+VGD  Y      N      N   LH++ ++  HP  G  L    
Sbjct: 230 RTHQIRVHMKYINHPLVGDPVYGPRKTLNT-----NGQSLHSKSIEFNHPITGEHLYFET 284

Query: 310 PLPAHMVKTWDSL 322
            +P++MV T   L
Sbjct: 285 EIPSYMVDTMAKL 297


>gi|163867809|ref|YP_001609013.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           tribocorum CIP 105476]
 gi|161017460|emb|CAK01018.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           tribocorum CIP 105476]
          Length = 334

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 90/341 (26%), Positives = 150/341 (43%), Gaps = 45/341 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           V +    + RLD+W    Y   ++   LQ ++R G +++D + +K    +++  Q++ + 
Sbjct: 6   VTDEGALDQRLDQWLAKQYHDVLSRSRLQTLIREGCLKIDGQFIKEPKTKLKPNQIIELE 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                      E   LD               +LYED  + V NKPAG+ V  G+G    
Sbjct: 66  MPNLRDAEPSAEAIALD---------------ILYEDDHVIVINKPAGLVVHPGNGNWTG 110

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR---- 177
             ++  +    +S       ++P + HRLD+ TSG++VVA+   A + L+  F       
Sbjct: 111 TLVNALIYHCGNSLSGIGGVKRPGVVHRLDKNTSGVMVVAKNDLAHKSLSAQFSDHGRTC 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L+WG P      I   L +  H       VV +    A +A++HF +++ + 
Sbjct: 171 ALDRRYHALIWGTPHRNVWTIDASLGRSPH-NRTKQAVVHKQTPHARHAVTHFSLLEKYG 229

Query: 238 QKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------- 282
                      LE +  TGRTHQ+RVH  H+G P++GD  Y   FK    +         
Sbjct: 230 THADSTSFASLLECRLETGRTHQIRVHMAHIGHPLIGDTVYGNAFKTKSNTLNPTLKNAI 289

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              N+  LHA  +   HP  G+ +  +APLP  M +    L
Sbjct: 290 DQFNRHALHAASLTFEHPSSGKVISFSAPLPQDMAQLIKHL 330


>gi|120554793|ref|YP_959144.1| RluA family pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120324642|gb|ABM18957.1| ribosomal large subunit pseudouridine synthase C [Marinobacter
           aquaeolei VT8]
          Length = 317

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 97/322 (30%), Positives = 170/322 (52%), Gaps = 15/322 (4%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           + T VQ++ V+ D    R+D +       +    + +I+R G+VRV+K RVK ++R+  G
Sbjct: 1   MATEVQWITVDEDMAGQRVDNFLLARLRGVPKSIVYRIVRKGEVRVNKGRVKPDSRLNPG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VVRIPP++         Q   +     ++    +++ +++E+ ++ V NKP+GI+V GG
Sbjct: 61  DVVRIPPLVQ--------QARAEQPKPGSRVQGVMEAAVVFENDEMLVVNKPSGIAVHGG 112

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+++ +   L+S   ++ +   L HRLD++TSG+++VA+ R+A + L +  R +RI+K 
Sbjct: 113 SGLSFGLIEVLRSAR-TEARFLELVHRLDRDTSGLVMVAKKRSALRFLQDELRQKRIRKY 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G      + +A  LL+     G+    V    +    +++ F  +  F Q +  
Sbjct: 172 YHALVVGSWPENVDRVAEPLLRFEMPNGERRVRV---SEEGKSSLTLFTCLQRF-QGYSL 227

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPE 301
           +E  P TGRTHQ+RVH+   G PI GD KY  +     F +    +L LHAR ++   P 
Sbjct: 228 VEASPVTGRTHQIRVHSAWAGHPIAGDDKYMDDASLKAFRAIGGQRLMLHARALEFSLPG 287

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  +++ A          + L
Sbjct: 288 SGEPMRLEAVYDGPFSGVLEEL 309


>gi|238789119|ref|ZP_04632908.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           frederiksenii ATCC 33641]
 gi|238722883|gb|EEQ14534.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           frederiksenii ATCC 33641]
          Length = 319

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 98/322 (30%), Positives = 164/322 (50%), Gaps = 14/322 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLLDGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEIQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGERMVKVSSE---GKPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLGFKY 326
           ++I APL   +      L  K 
Sbjct: 296 MRIEAPLDNQLRHCLSVLRKKA 317


>gi|307704906|ref|ZP_07641797.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
 gi|307621520|gb|EFO00566.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
          Length = 295

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 144/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G V+      
Sbjct: 3   IKIETGGLRLDKALSD-LTELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVIT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ +   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           Q  TGRTHQ+RVH  ++G P+ GD  Y                +LHA+ +   HP  G +
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPRKTLKGL-----GQFLHAKTLGFTHPRTGEI 275

Query: 306 -QITAPLPAHMVKTWDSLG 323
            + TA +P    +T + L 
Sbjct: 276 LEFTADIPEIFKETLERLR 294


>gi|306825452|ref|ZP_07458792.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|304432390|gb|EFM35366.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
          Length = 299

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 149/324 (45%), Gaps = 34/324 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + +++GQV V+ +  K    +Q G +V      
Sbjct: 3   IKIERGGLRLDKALSD-LTELSRSLANEQIKAGQVLVNGQVKKAKYTVQEGDIVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ +   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDIPLDIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F+V++ F   +  LE+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFQVLERFGD-YSLLEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G +
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGEI 275

Query: 306 -QITAPLPAHMVKTWDSLGFKYDR 328
            + TA +P    +T + L    +R
Sbjct: 276 LEFTADIPEIFKETLERLRKTENR 299


>gi|289435186|ref|YP_003465058.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
 gi|289171430|emb|CBH27974.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
 gi|313632720|gb|EFR99690.1| ribosomal large subunit pseudouridine synthase D [Listeria
           seeligeri FSL N1-067]
 gi|313637301|gb|EFS02795.1| ribosomal large subunit pseudouridine synthase D [Listeria
           seeligeri FSL S4-171]
          Length = 303

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 82/325 (25%), Positives = 144/325 (44%), Gaps = 34/325 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++E      R+D+         +   +Q +L+SG + V+ +  K N ++Q G  + +
Sbjct: 4   EKLIIEESHARERIDKAVAE-LTGKSRSAIQIMLKSGDITVNGEIAKPNYKVQVGDEIYL 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                    ++ E   LD               + +ED  + V NKP G+ V   +G A 
Sbjct: 63  EVREPEELEVLAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHAS 107

Query: 127 -YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 108 GTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + +      + VV+        A +HF+VI+     + 
Sbjct: 168 EYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVIERLP-GYT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH  ++G P+ GD KY         +   N  YLHA  +   HP 
Sbjct: 222 LINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTIKGNGQYLHAAKLGFDHPT 276

Query: 302 G-GRLQITAPLPAHMVKTWDSLGFK 325
              R+   APLP+   K    L  +
Sbjct: 277 TNERMTFEAPLPSSFEKALKMLREE 301


>gi|325570254|ref|ZP_08146120.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           casseliflavus ATCC 12755]
 gi|325156737|gb|EGC68911.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           casseliflavus ATCC 12755]
          Length = 302

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 79/323 (24%), Positives = 147/323 (45%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q  V+  +E+  R+D+      P  +   +Q+ L+   V ++ + V+ N ++++G  + I
Sbjct: 4   QIEVIIKEEKG-RVDKVLAERLPDHSRSQVQQWLKEDAVTLEGETVRANYKVKAGDHLVI 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           +     +    + +   ++Y+D+ + V NKP G+ V   +G   
Sbjct: 63  Q---------------VPEPEVVGLEPENIPLTIVYQDADVAVINKPQGMVVHPSAGHPN 107

Query: 128 --HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D        +P + HR+D++TSG+L++A+   A + L +  + +   +
Sbjct: 108 GTLVNALLYHMDDLSTINDVVRPGIVHRIDKDTSGLLMIAKNDQAHESLAKQLKDKTSLR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + S +      V+    +    A++HF V++ F Q F 
Sbjct: 168 KYVALVHGNISHEKGTINAPIGR-SKVNRKMQAVI----ENGKPAVTHFTVLERFDQ-FT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   HP 
Sbjct: 222 LVELQLETGRTHQIRVHMQYIGFPLAGDPIYGPK-----RTLKGNGQFLHAKLLGFAHPA 276

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            G  +   APLP     T   L 
Sbjct: 277 TGESMVFEAPLPELFADTLKKLR 299


>gi|238927877|ref|ZP_04659637.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
 gi|238884210|gb|EEQ47848.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
          Length = 299

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 86/318 (27%), Positives = 142/318 (44%), Gaps = 31/318 (9%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
            +D    RLD +     P ++    Q+++  G V VD +R K N ++   ++V       
Sbjct: 4   TSDRVGERLDVFLVRQMPALSRSYAQRLIAGGNVAVDGERRKANFKLSGAEMVVCTLPPA 63

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HID 130
               I  E   LD               +LYED+ I V NK  G+ V   +G+     ++
Sbjct: 64  EETEICAEDIPLD---------------ILYEDADIIVINKRRGMVVHPAAGVHTGTLVN 108

Query: 131 GFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             L    D  G     +P + HRLD++TSG++V A+   A  +L    R +  ++ Y ++
Sbjct: 109 ALLHHCSDLSGINGALRPGIVHRLDKDTSGVMVAAKNDMAHHYLARQIRDKEARREYRAI 168

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G    +   I   + +        + +V++N      A +HF+V++ F   + ++  +
Sbjct: 169 VYGNIVERAGVITGDIGRH-PTDRKKMAIVREN---GRPATTHFEVLERFGD-YTFVACR 223

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
             TGRTHQ+RVH   +G P+VGD KY A               LH+  + L HP     +
Sbjct: 224 LETGRTHQIRVHMTSIGHPLVGDTKYTAKKNP----FAITGQALHSLTLTLTHPRTQEEM 279

Query: 306 QITAPLPAHMVKTWDSLG 323
             TAPLPA M +   +L 
Sbjct: 280 TFTAPLPADMEEILHTLR 297


>gi|150024746|ref|YP_001295572.1| 23S rRNA pseudouridine synthase [Flavobacterium psychrophilum
           JIP02/86]
 gi|149771287|emb|CAL42756.1| Probable 23S rRNA pseudouridine synthase [Flavobacterium
           psychrophilum JIP02/86]
          Length = 347

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/330 (24%), Positives = 148/330 (44%), Gaps = 35/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V    +  +R+D++  +   +     +Q+   SG + V+   VK N +++   VV I  
Sbjct: 21  FVATKGQSILRIDKYLMHLLENATRNKIQQAATSGNIFVNNIPVKSNYKVKPFDVVTIM- 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+H   E ++    + L          ++YED  + + NKPAG+ V  G G     
Sbjct: 80  ----LSHPPFENRVDPEDIPLD---------IVYEDDALLLINKPAGLVVHPGHGNYTGT 126

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   +    ++   +  ++P L HR+D++T+G+LV+A+T  A  HL + F  +  ++ Y 
Sbjct: 127 LVNALAFHFQNLPLNSSERPGLVHRIDKDTTGLLVIAKTEQAMTHLAKQFENKTSEREYI 186

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++VWG  +  +  I   L +  H+       V  + +    AI+H+KV++ F      + 
Sbjct: 187 AIVWGNVQKDEGTIEGNLAR--HLKDRMQMAVFADPEIGKPAITHYKVLERFG-YITVIS 243

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHA 292
            +  TGRTHQ+R H  H+G P+  D +Y  +     T+             I  +  LHA
Sbjct: 244 CKLETGRTHQIRAHLKHIGHPLFNDERYGGHLILKGTTFTKYKQFIDNCFKILPRQALHA 303

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP     ++    LP+ M +    
Sbjct: 304 KTLGFEHPTTKEMMRFDTNLPSDMQECIQK 333


>gi|74317581|ref|YP_315321.1| ribosomal large subunit pseudouridine synthase C [Thiobacillus
           denitrificans ATCC 25259]
 gi|74057076|gb|AAZ97516.1| pseudouridine synthase, RluD [Thiobacillus denitrificans ATCC
           25259]
          Length = 322

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 102/318 (32%), Positives = 160/318 (50%), Gaps = 14/318 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + ++   ++ RLD +       +    + K++R G+VR++  RV    R++ G  VR
Sbjct: 11  VRRLKIDEGADDQRLDNYLMARLKGVPKSRIYKLVRGGEVRINGGRVDVGYRLKVGDEVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A         ++  + +L +    L  ++LY D  +   NKPAG++V GGSGI+
Sbjct: 71  IPPVRMAA-------PVITPATHLPQGGLRLLPLILYRDDALIALNKPAGMAVHGGSGIS 123

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L+     + +   L HRLD+ETSG+L+VA  R A   L  + R  +I+K Y +L
Sbjct: 124 RGVIEQLR-LELPECRYMELVHRLDRETSGVLLVALKRRALVGLHAAMRDGKIEKRYLTL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   N  + +   L K+    G+    V+        A + F+ +  +A+ F  LE +
Sbjct: 183 VAGRWPNPLQHVKLPLHKRVTEEGEKRVTVRDT---GQTAHTIFRRLRGYAE-FTLLEAE 238

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
             TGRTHQ+RVH  H+G PI GD KY               +++LHA  +   HP  G R
Sbjct: 239 LKTGRTHQIRVHTSHLGFPIAGDDKYGDFELNKRLAKRGLKRMFLHAAKLAFAHPISGER 298

Query: 305 LQITAPLPAHMVKTWDSL 322
           + I APLPA +    D+L
Sbjct: 299 MTIEAPLPADLATFLDTL 316


>gi|291514728|emb|CBK63938.1| ribosomal large subunit pseudouridine synthase D [Alistipes shahii
           WAL 8301]
          Length = 361

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 78/331 (23%), Positives = 138/331 (41%), Gaps = 39/331 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI-P 68
           V  +  +  MRLD++      H +   +Q    SG + V+ K  K + +++    ++I  
Sbjct: 33  VTADKGQTPMRLDKFLTVRMEHCSRNRIQAAADSGNILVNGKAAKSSYKVKPLDRIQIVM 92

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAY 127
           P       ++ E   LD               + YED  + + +KPAG+ V  G G  + 
Sbjct: 93  PYPRREVELVAEDIPLD---------------IPYEDQWLLLVDKPAGLVVHPGVGNYSG 137

Query: 128 HIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            +   L   ++ +G       +  L HR+D+ TSG+LV+A+       L + F    IQ+
Sbjct: 138 TLVNALMHHLNKQGIPAEEQNRAGLVHRIDKNTSGLLVIAKDEQTHARLAKQFFDHTIQR 197

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LVWG     +  I   + +           V  +     +A++H+KV+  +     
Sbjct: 198 RYVALVWGNFDEDEGTITGNIGRSPKDRQK--MFVFADGSDGKHAVTHWKVLKRYG-YVT 254

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL----------- 290
            +E +  TGRTHQ+RVH   +G P+  D +Y  +     T+  + + ++           
Sbjct: 255 LVECRLETGRTHQIRVHMAWIGHPLFNDERYGGDRILKGTTFAKYRQFIENCFAVMPRHA 314

Query: 291 -HARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
            HAR +   HP     +   +PLPA      
Sbjct: 315 LHARLLGFEHPATHENVLFESPLPADFQSLL 345


>gi|297208159|ref|ZP_06924590.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|283470407|emb|CAQ49618.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ST398]
 gi|296887402|gb|EFH26304.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|302332801|gb|ADL22994.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus JKD6159]
 gi|323440971|gb|EGA98678.1| putative RNA pseudouridylate synthase [Staphylococcus aureus O11]
 gi|323442288|gb|EGA99918.1| putative RNA pseudouridylate synthase [Staphylococcus aureus O46]
          Length = 305

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 140/329 (42%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +++   
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I+ E                L   + YED  + V  KP G+ V    
Sbjct: 61  HIVVTEKEVVEADILPEN---------------LNLDIYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 GIAYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +   +G +    +  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAPIGRN-KNDRQSMAVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLD-----IGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  ++  A LP       D++  +
Sbjct: 275 EHPVTGEYIERHAELPQDFEDLLDTIRKR 303


>gi|322376434|ref|ZP_08050927.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           M334]
 gi|321282241|gb|EFX59248.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           M334]
          Length = 296

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 146/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETGGLRLDKALSD-LTELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAENLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQGVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPSTGET 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+ TA +P    +T + L 
Sbjct: 276 LEFTADIPELFKETLERLR 294


>gi|238022130|ref|ZP_04602556.1| hypothetical protein GCWU000324_02036 [Kingella oralis ATCC 51147]
 gi|237866744|gb|EEP67786.1| hypothetical protein GCWU000324_02036 [Kingella oralis ATCC 51147]
          Length = 328

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 96/328 (29%), Positives = 156/328 (47%), Gaps = 25/328 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V   E   RLD +       +   ++ +I+R G+VRV+K R K + R+ +G  VR
Sbjct: 9   VNHISVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRGGEVRVNKGRAKPDYRVAAGDCVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A  ++    K +             +  +++ED  + V NKP+GI+V GGSG++
Sbjct: 69  IPPIRVAEKNVSDSLKTVPPR----------EFEIIFEDDALLVINKPSGIAVHGGSGVS 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     +     L HRLD++TSG+L++A+ R+A   L E  R    +KIY +L
Sbjct: 119 FGVIEQLRQAR-PEANYLELVHRLDKDTSGLLMIAKKRSALVKLHEMLRNDHPKKIYLAL 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC----- 241
             G  + +   +   L+K +   G+ +  V         A + F+V+D F+         
Sbjct: 178 GVGAWQPENRHVRLPLVKYTGAAGEKMVRV---GDEGQSAHTIFRVLDTFSGCLTHSVGI 234

Query: 242 ----WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +E    TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 235 SALSLVEATLKTGRTHQIRVHMQASGCPIAGDERYGDYQANRRLQKLGLKRMFLHAHRLV 294

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           L HP  G  L + A LP  + +    L 
Sbjct: 295 LAHPLSGETLDLVAGLPEELERVLGRLA 322


>gi|239636325|ref|ZP_04677327.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus warneri L37603]
 gi|239597680|gb|EEQ80175.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus warneri L37603]
          Length = 305

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 143/323 (44%), Gaps = 33/323 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +Y + +++    RLD+         +   +Q  ++   V+V+ K VK N +++   
Sbjct: 1   METYEYTITDSNHVGQRLDKVLPELNSDWSRSQIQDWIKEDLVKVNDKVVKPNYKVKQND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           ++ EQ+++D+ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  NI-----------VVTEQEVVDADI----TPENLNLDIYYEDDDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    +  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    +   + +      D   +   ++     A++HF V++ F 
Sbjct: 166 SVKRKYVALVHGNIPHDYGTVDAPIGRNKK---DRQAMAVVDD--GKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLIECELETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLD-----IGGQALHAGVIGF 274

Query: 298 PHPEG-GRLQITAPLPAHMVKTW 319
            HP     ++ TA LP       
Sbjct: 275 EHPVTHEYIERTAELPQEFEDLL 297


>gi|241206033|ref|YP_002977129.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859923|gb|ACS57590.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 341

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 83/347 (23%), Positives = 156/347 (44%), Gaps = 49/347 (14%)

Query: 8   QYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           + V+  ++    RLD W         +   ++ +++ GQV +  + V     ++++G   
Sbjct: 12  RKVLTADESAEGRLDAWLTAQVGEEFSRSRIKALIKDGQVFLRGEPVTDPQRKVRTGDSF 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +                L    + T   + +   +L+ED  + V +KP+G+ V  G+G 
Sbjct: 72  ELT---------------LPEPEDPTPQGEDIPLDILHEDDDVIVISKPSGLVVHPGAGN 116

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                   + +H    L        ++P + HRLD++T+G++VVA+   A +HL+  F  
Sbjct: 117 WTGTLVNALIHHCSNTLSGI--GGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFAD 174

Query: 177 RR----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
                 +++ Y ++VWG P++    +   L + +        V + + + A+ AI+H++V
Sbjct: 175 HGRTMPLERAYQAVVWGRPRSLSGMVDAPLGRATG-DRTRRAVKRPDSQDADEAITHYQV 233

Query: 233 IDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ- 285
           ++ F +K         +E +  TGRTHQ+RVH  H+G P++GD  Y A FK       + 
Sbjct: 234 VERFHEKPDATAFASLVECRLETGRTHQIRVHMAHIGHPLLGDTVYGAGFKTKANLLPEE 293

Query: 286 --------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                    +  LHA  +   HP  G  +    PLP  MV+  ++L 
Sbjct: 294 IRKIVNGFGRQALHAFMLQFEHPRTGEIMHFEVPLPDDMVELVEALR 340


>gi|116492705|ref|YP_804440.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           pentosaceus ATCC 25745]
 gi|116102855|gb|ABJ67998.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           pentosaceus ATCC 25745]
          Length = 300

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 81/325 (24%), Positives = 145/325 (44%), Gaps = 38/325 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q+  V +D+E+ RLD+   NHYP +    +Q +++  Q+ V++       ++    V+ +
Sbjct: 3   QFSFVVSDQESGRLDKVVTNHYPDLTRSKIQNLIKQEQILVNQAPTTNRYKVSENDVIDV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           L   V ++   + +   +++ED  + V NKP G+ V    G   
Sbjct: 63  T---------------LPDPVEVSVKPEKMNLDIVFEDDDVIVVNKPQGMVVHPAPG--- 104

Query: 128 HIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           H +G L + +             +P + HR+D++TSG+L+VA+   A   L+   + +  
Sbjct: 105 HENGTLVNGLLDHAPLATVNGELRPGIVHRIDKDTSGLLMVAKNDQAMLSLSAQLKAKTN 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Q+ Y ++V G  K +   I   + + S      + +V    +    A++HFKV++ F   
Sbjct: 165 QRKYLAIVHGNFKEEAGTINAPIGR-SKKDRKKMAIV----EDGRPAVTHFKVLERFTD- 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +E +  TGRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   H
Sbjct: 219 YTLIECELETGRTHQIRVHLKYIGHPVAGDPLYGPR-----NTLKGNGQFLHAKLLGFKH 273

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLG 323
           P  G  L      P     T   L 
Sbjct: 274 PRTGEELVFEVDPPQIFQDTLSKLR 298


>gi|22299081|ref|NP_682328.1| ribosomal large subunit pseudouridine synthase D
           [Thermosynechococcus elongatus BP-1]
 gi|22295263|dbj|BAC09090.1| ribosomal large subunit pseudouridine synthase D
           [Thermosynechococcus elongatus BP-1]
          Length = 308

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 151/328 (46%), Gaps = 32/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           MT      VE      RLD +    +P  +    Q++++ G VR++ +   + N  +  G
Sbjct: 1   MTTSLTFKVEKG--GNRLDTFLAQQHPEFSRSRWQQLIQQGHVRLNGQVCDRKNQPLSGG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           +V+ +               +L +   L    + L   +LYED ++ + NKP  + V   
Sbjct: 59  EVLEV---------------VLPTPEPLDLVPEPLPLSILYEDEELLILNKPVDLVVHPA 103

Query: 123 SGIAY--HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G ++   + G L    D  G    Q+P + HRLD++TSG++VVA+T  A  HL +  + 
Sbjct: 104 PGHSHGTLVHGLLAHCPDLTGIGGVQRPGIVHRLDKDTSGVMVVAKTEFALHHLQQQLKT 163

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R++Q+ Y  +V+G P+  +  +   L +      D   +     +    AI+H+ V + F
Sbjct: 164 RQMQRHYLGVVYGQPREDRGTVITPLGRHP---VDRKKMAVVPPEKGRTAITHWYVKERF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    +E +  TGRTHQ+RVHA H+G P++GD  Y          P      LHA  + 
Sbjct: 221 -RHCALVEFRLETGRTHQIRVHAAHLGWPLLGDPLYGRGSPLKVKLPG---QALHAYRLQ 276

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           L HP  G  +   APLP H+ +    L 
Sbjct: 277 LQHPRSGQEIVAIAPLPDHLERLLQRLR 304


>gi|323351668|ref|ZP_08087322.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis VMC66]
 gi|322122154|gb|EFX93880.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis VMC66]
          Length = 298

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 146/322 (45%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E    + RLD+        ++     + ++ G++ V+ +  K    ++ G V+   
Sbjct: 2   EVRIEASVASQRLDKAVAE-LTDLSRSLAHEQIKDGRILVNGQAKKAKYAVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++        ++ +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELPEPEVVE------YVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIQDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFG-NYSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 G-RLQITAPLPAHMVKTWDSLG 323
           G  L+ TA +PA   +T   L 
Sbjct: 275 GEELEFTAEVPAIFQETLAKLR 296


>gi|149376750|ref|ZP_01894508.1| 23S rRNA pseudouridylate synthase C [Marinobacter algicola DG893]
 gi|149358989|gb|EDM47455.1| 23S rRNA pseudouridylate synthase C [Marinobacter algicola DG893]
          Length = 313

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 97/321 (30%), Positives = 170/321 (52%), Gaps = 15/321 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ VVV+ D    R+D +       +    + +I+R G+VRV+K RVK + R+ +G  VR
Sbjct: 1   MRKVVVDEDNHGQRVDNYLMAQIRDVPRSIIYRIIRKGEVRVNKGRVKPDTRLNTGDEVR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        +  ++     V  ++    ++S +++E+ ++ V NKP+GI+V GGSG+ 
Sbjct: 61  IPP--------VTRKEKPAQVVPGSRVQGVMQSAVVFENDQMLVVNKPSGIAVHGGSGLD 112

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++    + +   L HRLD++TSG+++VA+ R+A ++L +  R +RI+K Y +L
Sbjct: 113 FGLIEVLRAAR-PEARFLELVHRLDRDTSGLVMVAKKRSALRYLQDELRHKRIRKHYHAL 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G      + ++  LL+     G+    V   +     +++ F+V++ F+  +  +E  
Sbjct: 172 VAGDWPGSVKKVSEPLLRFELGSGERRVRV---DDAGKDSLTRFRVLESFS-GYTLVEAS 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH+   G PI GD KY  +     F S    +L LHAR +D   P  G  
Sbjct: 228 PVTGRTHQIRVHSAWAGHPIAGDDKYMDDVSLRAFRSAGGQRLMLHARALDFTLPPSGES 287

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           + + AP      +    L  +
Sbjct: 288 VHLEAPYDEAFGELMAKLAAR 308


>gi|227824343|ref|ZP_03989175.1| pseudouridine synthase [Acidaminococcus sp. D21]
 gi|226904842|gb|EEH90760.1| pseudouridine synthase [Acidaminococcus sp. D21]
          Length = 311

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/317 (25%), Positives = 147/317 (46%), Gaps = 32/317 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
             ++ +R D +  +    ++  +LQ  +  G V  + K VK + +++ G V  +      
Sbjct: 15  EKDQGLRADCYLADVL-DLSRSSLQHDMEKGLVTKEGKPVKASYKVKLGDVFTV------ 67

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
                    ++  +V+L    + +   +LYED  + V NKP G+ V   +G      ++ 
Sbjct: 68  ---------VIPPAVSLEAEPEPIPLAILYEDEDVIVVNKPRGMVVHPAAGNYTGTLVNA 118

Query: 132 FLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    D  G     +P + HRLD++TSG++V A+   A   L++  + +  ++ Y ++V
Sbjct: 119 LLYHCKDLSGINGVVRPGIVHRLDKDTSGVMVCAKNDRAHLSLSQQIKDKEAKRTYIAVV 178

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  K+ +  I   L+ +       + VV     G   A++ ++V++ + + F  +  + 
Sbjct: 179 RGNIKDDRGHIET-LIDRDPKDRMRMAVV---PSGGRLAVTDYEVLERYGR-FTVVRCRL 233

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++G P+VGD KY    +   T    +   LH+  +   HP  G+ + 
Sbjct: 234 QTGRTHQIRVHMTYLGHPLVGDPKY----QPQKTCFSIDGQALHSETLTFRHPRTGKIMS 289

Query: 307 ITAPLPAHMVKTWDSLG 323
            TAPLP  M      L 
Sbjct: 290 FTAPLPGDMETILTRLR 306


>gi|306833765|ref|ZP_07466891.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           bovis ATCC 700338]
 gi|304424102|gb|EFM27242.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           bovis ATCC 700338]
          Length = 298

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 76/315 (24%), Positives = 141/315 (44%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RLD+   +    ++       ++ G V V+ K VK    ++ G VV          
Sbjct: 7   EAGIRLDKALAD-LTELSRSQANDEIKKGTVLVNGKAVKAKYAVKVGDVVT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGFL 133
           + + ++++L+ +      ++ +   ++YED+ + V NKP G+ V    G      ++  +
Sbjct: 57  YEVPKEEVLEYT------AENIPLDIIYEDADVAVVNKPQGMVVHPSVGHTSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++V G
Sbjct: 111 YHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDTAHNALAAELKDKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +            K        A++HFKV++ F   +  +E+   T
Sbjct: 171 TIPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTHFKVLERFG-NYTLVELTLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   HP  G  L   
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLKGNGQFLHAQTLGFTHPTTGETLTFM 279

Query: 309 APLPAHMVKTWDSLG 323
           A  PA   +T ++L 
Sbjct: 280 AEAPAIFKETLENLR 294


>gi|153953824|ref|YP_001394589.1| pseudouridine synthase [Clostridium kluyveri DSM 555]
 gi|219854440|ref|YP_002471562.1| hypothetical protein CKR_1097 [Clostridium kluyveri NBRC 12016]
 gi|146346705|gb|EDK33241.1| Predicted pseudouridine synthase [Clostridium kluyveri DSM 555]
 gi|219568164|dbj|BAH06148.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 305

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 84/325 (25%), Positives = 150/325 (46%), Gaps = 33/325 (10%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++  +V +DEEN+RLD +   H    +   +Q ++    V V+ +  K N + ++G  +
Sbjct: 2   KIRNFLVNDDEENLRLDLFICKHIQDKSRSYIQNLIEDNLVEVNHRMKKSNYKTKTGDNI 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           ++                L  +V L    + +K  +LYEDS + V NKP G+ V   SG+
Sbjct: 62  KVS---------------LPDAVELNIKGEDIKLDILYEDSDVIVVNKPQGMIVHPASGV 106

Query: 126 --AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  L    +         +P + HR+D++TSGILV+A+   +   L+E  +   
Sbjct: 107 YTGTLVNALLNHCREDLSGINGIARPGIVHRIDKDTSGILVIAKNDMSHNKLSEQLKDHS 166

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + + Y +LV GI K +K  +   + +          V     +G   A++H++VI  F +
Sbjct: 167 MTREYIALVEGIIKEEKGSLDKPIGRHKKDKIKMAVV-----EGGKRAVTHYEVIKRFKE 221

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  ++    TGRTHQ+RVH  ++G P+VGD  Y    +            LHA+ +   
Sbjct: 222 -YTLVKCILETGRTHQIRVHMCYLGHPVVGDPVYGYKKQ----KFNLKGQLLHAQKLGFI 276

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSL 322
           HP  G  ++    +P +  +  D L
Sbjct: 277 HPGTGTYMEFQVEVPEYFKRIIDIL 301


>gi|323141904|ref|ZP_08076765.1| pseudouridine synthase, RluA family [Phascolarctobacterium sp. YIT
           12067]
 gi|322413651|gb|EFY04509.1| pseudouridine synthase, RluA family [Phascolarctobacterium sp. YIT
           12067]
          Length = 314

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 85/324 (26%), Positives = 143/324 (44%), Gaps = 32/324 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   E   R D         +   N+QK+L  G+     K +K N +++ G  + +
Sbjct: 12  QRLIITEQEAGQRADVGLAAML-ELTRSNMQKLLEEGRAVRGSKVLKSNYKLRLGDEIDV 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           L     L    + +   ++YED  + V NK  G+ V   +G   
Sbjct: 71  T---------------LPEPQPLDVQPENIPLDIIYEDEDVVVVNKARGMVVHPAAGNLN 115

Query: 128 --HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    +  G     +P + HRLD++TSGI++ A+  AA   L++  + +  Q+
Sbjct: 116 GTLVNALLYHCKNLSGINGVIRPGIVHRLDKDTSGIMICAKNDAAHLSLSQQIQAKTAQR 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G  K     I   L+ +       + VVK   +G   A++ ++V++ F  K+ 
Sbjct: 176 TYLAVVRGNIKTDSGVIET-LIARDKNDRKKMAVVK---EGGRDAVTEYEVLERFG-KYT 230

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH  ++G P+VGD KY        T        LH++ ++  HP 
Sbjct: 231 IVRCRLRTGRTHQIRVHMEYLGYPLVGDPKYSP----MKTPFSIQGQALHSQTLEFTHPR 286

Query: 302 GG-RLQITAPLPAHMVKTWDSLGF 324
            G RL   APLP  M K    L  
Sbjct: 287 TGERLSFEAPLPEDMHKIVTRLRL 310


>gi|330999175|ref|ZP_08322894.1| rRNA pseudouridylate synthase [Parasutterella excrementihominis YIT
           11859]
 gi|329575375|gb|EGG56919.1| rRNA pseudouridylate synthase [Parasutterella excrementihominis YIT
           11859]
          Length = 389

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 164/331 (49%), Gaps = 19/331 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V +  V+   +  RLD +  +    +    + +++RSG+VRV+K R   + R+QSG  
Sbjct: 71  PKVIFKKVDESNDGQRLDNFLLSQLKGVPKSLIYRVVRSGEVRVNKGRAHVDTRLQSGDE 130

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+     +  KE +     + L++        +L+ED  I V +KPAG++  GGSG
Sbjct: 131 VRIPPIR----YTEKESEHSAPPLKLSEMPP-----ILFEDQNIMVVDKPAGMASHGGSG 181

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           I+Y +   +++          L HRLD+ TSG+LV+A+TR A   L E  R   + K Y 
Sbjct: 182 ISYGLIERMRASRPEL-PFLELVHRLDRGTSGVLVLAKTRKALVRLHEMIREGEMHKAYQ 240

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  +N ++     L K     G+    V+ + +    + S F++ + F      +E
Sbjct: 241 ALVKGDWQNDRQHAKFPLFKYVTPSGER--RVRVDPENGLPSHSIFRLKERFG-PVSLVE 297

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPH 299
           +   TGRTHQ+RVHA  +G P+VGD KY                   +++LH+  +   H
Sbjct: 298 VDLLTGRTHQIRVHAAELGFPLVGDEKYGDFAFNDEVAHGLLGVPFKRMFLHSGKICFHH 357

Query: 300 P-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           P  G  L+I APLP   V+  + L  +  +N
Sbjct: 358 PITGEELEIEAPLPKDCVELIEVLEQRKAQN 388


>gi|198277498|ref|ZP_03210029.1| hypothetical protein BACPLE_03720 [Bacteroides plebeius DSM 17135]
 gi|198269996|gb|EDY94266.1| hypothetical protein BACPLE_03720 [Bacteroides plebeius DSM 17135]
          Length = 356

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 78/332 (23%), Positives = 141/332 (42%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV+  +  +R+D++      + +   +Q    +G V  + K VK + +++   V+ +  
Sbjct: 33  TVVDKGQAPVRIDKYLFERIVNASRNRIQMAADNGFVMANGKPVKSSYKVKPLDVLTVMM 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E  I+   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 93  -----DRPRYENDIIPEDIPLN---------IVYEDDDLMVINKPAGLVVHPGCGNYHGT 138

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        +    +  L HR+D++TSG+LVVA+T  A   L   F  +  ++ 
Sbjct: 139 LVNAIAWHLRDVPTYNPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTSLGLQFYNKTTKRE 198

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI +  +  I   + +           V  + +   +A++H++V++        
Sbjct: 199 YNALVWGIVEQDEGTITGNIGRNPR--DRMQMAVMSDPEQGKHAVTHYQVLERLG-YVTL 255

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------------PIQNKLYL 290
           ++    TGRTHQ+RVH  H+G  +  D +Y  +     T              I  +  L
Sbjct: 256 VKCVLETGRTHQIRVHMKHIGHTLFNDERYGGHEILKGTHFSKYKQFVNNCFEICPRQAL 315

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA+ +   HP  G  +  T+ LP  M    + 
Sbjct: 316 HAKTLGFVHPRTGEEMFFTSELPEDMTCLLER 347


>gi|254429310|ref|ZP_05043017.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881]
 gi|196195479|gb|EDX90438.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881]
          Length = 317

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 100/321 (31%), Positives = 167/321 (52%), Gaps = 17/321 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V +V ++      RLD +   H   +    + +I+RSG+VR++K R K   R+ SG V
Sbjct: 9   NRVTFVTIDEGRHGQRLDNFLFTHLKGVPKSRVYRIIRSGEVRINKGRAKQTTRLASGDV 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+  + +                  ++ L+   +YED ++++FNKP+G++V GGSG
Sbjct: 69  VRIPPIRTSESA--------APPAVSEGLAERLRRACVYEDDQLFIFNKPSGLAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  +   L+     + +   L HRLD++TSG+++VAR R+  + L    +  +++K YW
Sbjct: 121 VSLGLIEALRVMYPDEKEM-ELVHRLDRDTSGLIMVARRRSFLRKLQRLMQGGQVEKRYW 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            L  G  K K+  +   LLK  +     V V ++       +++H+++++ FAQ    +E
Sbjct: 180 LLCQGF-KGKERTLDAPLLKMMNGNERIVRVSRE----GKPSVTHYRLLERFAQ-AQLVE 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
               TGRTHQ+RVH+   G P++GD KY  A  +       + +L LHAR +   HP  G
Sbjct: 234 ATLETGRTHQIRVHSQFGGFPLLGDDKYGIAKGEALLAEIGRRRLCLHARTLVFVHPNTG 293

Query: 304 -RLQITAPLPAHMVKTWDSLG 323
            RL +TAPL         +L 
Sbjct: 294 KRLTVTAPLDDDYEAILTALR 314


>gi|238795959|ref|ZP_04639471.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           mollaretii ATCC 43969]
 gi|238720164|gb|EEQ11968.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           mollaretii ATCC 43969]
          Length = 319

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 99/322 (30%), Positives = 164/322 (50%), Gaps = 14/322 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEIQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L++A+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLIAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ V  V         + + FKV + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGERVVKVSSE---GKPSETRFKVEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLGFKY 326
           ++I APL   +      L  K 
Sbjct: 296 MRIEAPLDNQLRHCLLMLRKKA 317


>gi|238783756|ref|ZP_04627775.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           bercovieri ATCC 43970]
 gi|238715307|gb|EEQ07300.1| Ribosomal large subunit pseudouridine synthase C [Yersinia
           bercovieri ATCC 43970]
          Length = 319

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 100/321 (31%), Positives = 164/321 (51%), Gaps = 14/321 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEIQISAKLDKVA-VLADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ V  V         + + FKV + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGERVVKVSSE---GKPSETRFKVEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNTGET 295

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           ++I APL   +      L  K
Sbjct: 296 MRIEAPLDNQLRHCLLILRKK 316


>gi|325285479|ref|YP_004261269.1| pseudouridine synthase, RluA family [Cellulophaga lytica DSM 7489]
 gi|324320933|gb|ADY28398.1| pseudouridine synthase, RluA family [Cellulophaga lytica DSM 7489]
          Length = 344

 Score =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 147/331 (44%), Gaps = 36/331 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV    +E +R+D++  N   +     +QK  + G + V+   VK N ++++G  +R+  
Sbjct: 20  VVAAKGQEPLRIDKFLMNFIENATRSQIQKAAKDGHIWVNNVLVKQNYKVKAGDDIRVMF 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                  ++                + +   ++YED  + V NKPAG+ V  G G     
Sbjct: 80  SHPPYEFLL--------------QPEDIPLDIVYEDDVLLVVNKPAGMVVHPGHGNYSGT 125

Query: 128 HIDGFLKS----WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            I+  L        ++   +P L HR+D++TSG+LVVA+T AA   L++ F  +  ++ Y
Sbjct: 126 LINALLHHCKVDLPNNSSDRPGLVHRIDKDTSGLLVVAKTEAAMTFLSKQFFDKTSEREY 185

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++VWG  +  +  I   L +        +HV  + ++G   AI+H+KV++        +
Sbjct: 186 VAIVWGNVEADEGTIEGHLGRHPK-NRLQMHVFPEGDQG-KEAITHYKVLERLG-YVTVI 242

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLH 291
             +  TGRTHQ+RVH  H+G  +  D +Y        T+             I  +  LH
Sbjct: 243 SCKLETGRTHQIRVHMKHIGHTLFNDERYGGERILKGTTFTKYKQFVENAFKILPRQALH 302

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           A+ +   HP     +Q    +P  M    + 
Sbjct: 303 AKTLGFVHPVTKELMQFNTEIPEDMASVIEK 333


>gi|238758384|ref|ZP_04619561.1| Ribosomal large subunit pseudouridine synthase C [Yersinia aldovae
           ATCC 35236]
 gi|238703288|gb|EEP95828.1| Ribosomal large subunit pseudouridine synthase C [Yersinia aldovae
           ATCC 35236]
          Length = 322

 Score =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 101/325 (31%), Positives = 164/325 (50%), Gaps = 14/325 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLVDGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEVQLSPKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKNMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +   + +   LLK     G+ V  V         + + FKV + F +    ++  
Sbjct: 180 VRGQWQAHCKAVQAPLLKNIMQSGERVVKVSSE---GKPSETRFKVEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNSGET 295

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRN 329
           ++I APL   +      L  K   N
Sbjct: 296 MRIEAPLDNQLRHCLLILRKKAAEN 320


>gi|327470139|gb|EGF15603.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK330]
          Length = 298

 Score =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 144/322 (44%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E+     RLD+        ++     + ++ G + V+ +  K    ++ G V+   
Sbjct: 2   EVRIESSVAGQRLDKAVAE-LTDLSRSLANEQIKDGLILVNGQAKKAKYAVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++        ++ +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELPESEVVE------YVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   F  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-FSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA  P    +T + L 
Sbjct: 275 GEVLEFTAEAPVIFQETLEKLR 296


>gi|222086840|ref|YP_002545374.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221724288|gb|ACM27444.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 343

 Score =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 81/345 (23%), Positives = 148/345 (42%), Gaps = 45/345 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           + V+  ++    RLD W        ++   +Q ++++  V ++   V     +++ G + 
Sbjct: 14  RKVLTADETAEGRLDAWLTAQMDEELSRSRVQALIKANAVLLNGTPVTDAKRKVRPGDIY 73

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            I                +    + T   + +   +L+ED  + V +KPAG+ V  G+G 
Sbjct: 74  EIS---------------MPEPEDPTPQGEDIPLDVLFEDDDVIVISKPAGLVVHPGAGN 118

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  +    DS       ++P + HRLD++T+G++VVA+   A +HL+  F    
Sbjct: 119 WTGTLVNALIHHCGDSLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHG 178

Query: 179 ----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y ++VWG P+     +   L + +        V +     A+ AI+H++VI+
Sbjct: 179 RTTPLERAYQAIVWGRPRQLVGTVNAPLGRATG-DRTRRSVKRPGSPDADEAITHYEVIE 237

Query: 235 CFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
            F +          ++    TGRTHQ+RVH  H+G P++GD  Y   FK           
Sbjct: 238 RFHEAPDATALASLIDCHLETGRTHQIRVHMAHIGHPLLGDAAYGGGFKTKANLLPDAAR 297

Query: 286 ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                  +  LHA  +   HP  G  +   APLP  M +    L 
Sbjct: 298 EAVNRFPRQALHAYLLQFEHPRTGEVMHFEAPLPDDMEELAAILR 342


>gi|281420977|ref|ZP_06251976.1| ribosomal large subunit pseudouridine synthase D [Prevotella copri
           DSM 18205]
 gi|281404895|gb|EFB35575.1| ribosomal large subunit pseudouridine synthase D [Prevotella copri
           DSM 18205]
          Length = 387

 Score =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 77/332 (23%), Positives = 145/332 (43%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+ +++ +R+D++  +   + +   +Q+   +G + V+ K VK N +++   +V +  
Sbjct: 56  VQVDANQDPVRIDKYLADKMAYQSRNRIQQAADAGFIHVNGKPVKSNYKVRPNDLVTLML 115

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                   IK ++I                 ++YED ++ V NK AG+ V  G+G  +  
Sbjct: 116 DRPRHETSIKPEEIA--------------INVVYEDDQLMVVNKEAGMVVHPGAGNFHGT 161

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+   +  L HR+D++TSG+LVVA+T  A   L + F  +   + 
Sbjct: 162 LIQAVAWHLRDMPEFDANDPEVGLVHRIDKDTSGLLVVAKTPTAKNALGKQFFNKTTHRS 221

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + +        + V   +      A++H+KV++ F      
Sbjct: 222 YNALVWGNIVEDEGRIEGNIGRDPK-NRLRMKVFDPDSGIGKTAVTHYKVLERFG-YTTL 279

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQN------KLYL 290
           ++    TGRTHQ+R H  H+G P+  D  Y            ++ + IQN      +  L
Sbjct: 280 VQCVLETGRTHQIRAHMKHIGHPLFMDETYGGTEILRGQRSSSYKAFIQNCFKLCPRQAL 339

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA+ +   HP    ++   +  P    +  + 
Sbjct: 340 HAKTLGFVHPTTKQQMDFDSEWPNDFRQLIEK 371


>gi|239631456|ref|ZP_04674487.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           paracasei subsp. paracasei 8700:2]
 gi|239525921|gb|EEQ64922.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           paracasei subsp. paracasei 8700:2]
          Length = 306

 Score =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 85/334 (25%), Positives = 143/334 (42%), Gaps = 42/334 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    +  E      R+D+    H        +QK L+ G V V+ +  K N ++ SG 
Sbjct: 1   MTSTFTITTEQG----RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQPTKANYKVASGD 56

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ I                +  +  L    + +   ++YED ++ V +KP G+ V    
Sbjct: 57  VIAIS---------------IPEAKPLEAIPEPIPLDIVYEDDQVIVVDKPQGMVVHPAP 101

Query: 124 GIAYHIDGFLKSWVDSKG--------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G   H DG L + +             +P + HR+D++TSG+L+VA+T  A   L+   +
Sbjct: 102 G---HPDGTLVNGLLYHTDLPGINGVIRPGIVHRIDKDTSGLLMVAKTEKAQLSLSAQLK 158

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +   + Y +LV G  K  +  I   L +          V         +A++HF+V++ 
Sbjct: 159 AKTSIREYLALVHGTFKEDEGTIDAPLGRDPRDRKRQAVVA-----DGRHAVTHFQVLER 213

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F + + +++    TGRTHQ+RVH  ++  P+ GD  Y        T P +   +LHA  +
Sbjct: 214 F-EHYTFIKCILETGRTHQIRVHMAYIHHPVAGDPLYGPKR----TLPGEG-QFLHAAKL 267

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
              HP   + L    P+P    KT   L    D+
Sbjct: 268 GFVHPTTSQLLVFETPVPPIFEKTLADLRAGIDK 301


>gi|329116866|ref|ZP_08245583.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
 gi|326907271|gb|EGE54185.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
          Length = 295

 Score =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 76/315 (24%), Positives = 145/315 (46%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++       +++G V V+ +  K    +++G ++          
Sbjct: 7   EAGSRLDKAIAD-LTELSRGQANDAIKAGIVLVNGQAAKAKYSVKAGDIIT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFL 133
           + I+E+++LD        ++ +   ++YED  + + NKP G+ V   +G +     +  L
Sbjct: 57  YEIQEEEVLD------YQAEDIPLDVVYEDEDLAIINKPQGMVVHPSAGHSSGTMVNALL 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D  G     +P + HR+D++TSG+L+VA+  AA + L +  + ++  + Y ++V G
Sbjct: 111 YQIKDLSGINGVVRPGIVHRIDKDTSGLLMVAKNDAAHRALADELKAKKSLRKYLAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +          + +        A++ F+VI+ F   +  +E+   T
Sbjct: 171 NLPNDRGIIEAPIGRSEKDRKKQAVIAR-----GKEAVTRFQVIERFGD-YTLVELTLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ + L HP  G  +  T
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLPGNGQFLHAQTLGLTHPRTGEVMTFT 279

Query: 309 APLPAHMVKTWDSLG 323
           A  P    +T + L 
Sbjct: 280 AEPPLIFQQTIEKLR 294


>gi|166367953|ref|YP_001660226.1| ribosomal large subunit pseudouridine synthase D [Microcystis
           aeruginosa NIES-843]
 gi|166090326|dbj|BAG05034.1| ribosomal large subunit pseudouridine synthase D [Microcystis
           aeruginosa NIES-843]
          Length = 308

 Score =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 153/328 (46%), Gaps = 32/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M  +   V    E   RLD W  +H P ++   LQK++  G ++++ +     N ++  G
Sbjct: 1   MNQLNLEVAGKKE---RLDAWMGSHLPDLSRSRLQKLIEQGYIQLNGQICTNKNTKVGQG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             ++I                +  S  L   ++ ++  +LYED  + + NKPA + V   
Sbjct: 58  DRLKIT---------------IPDSQPLELTAEAIELDILYEDDYLIIINKPADLVVHPA 102

Query: 123 SGIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++  L    +  G    Q+P + HRLD++T+G +V+A+T  A QHL    + 
Sbjct: 103 PGHESGTLVNALLHHCPNLAGIGGIQRPGIVHRLDKDTTGAIVIAKTDQAHQHLQAQLKT 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           +  ++ Y +LV G+PK++   I   + +  H        +   EKG   A++H++V +  
Sbjct: 163 KTARREYIALVHGVPKSETGTIDLPIGR--HRSDRQKMAIIAVEKGGRNAVTHWQVKERL 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  +E +  TGRTHQ+RVH+ H+G PI+GD  Y +        P      LHA  + 
Sbjct: 221 G-NYTLMEFRLETGRTHQIRVHSSHIGHPILGDPLYSSGRSIGINLPG---QLLHAHRLI 276

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           L HP  G  L+  APLPA   K    L 
Sbjct: 277 LVHPVTGESLEAIAPLPAIFPKVLAILR 304


>gi|261367025|ref|ZP_05979908.1| ribosomal large subunit pseudouridine synthase D [Subdoligranulum
           variabile DSM 15176]
 gi|282571143|gb|EFB76678.1| ribosomal large subunit pseudouridine synthase D [Subdoligranulum
           variabile DSM 15176]
          Length = 310

 Score =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 83/333 (24%), Positives = 142/333 (42%), Gaps = 35/333 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++ +         RLD W       I+   LQ ++   +V  D + V    ++  G 
Sbjct: 1   MEPIE-ITAGPQTAG-RLDAWLAGQCEGISRNALQTLIEQERVTKDGRPVNKKEKVCPGA 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V  +                L     +      +   ++YED+ + V NKP G+ V    
Sbjct: 59  VYLLQ---------------LPDPKPIEAVPQDIPLSIVYEDNDLIVVNKPKGMVVHPAP 103

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + YH  G L         +P + HR+D++TSG+LVVA+   A Q L+   
Sbjct: 104 GNPDGTLVNALLYHCAGQLSGI--GGAIRPGIVHRIDKDTSGLLVVAKNDVAHQALSSQM 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            +  I ++Y ++V+G  K  +  +  WL +        + V+ +N  GA YA + ++V++
Sbjct: 162 SVHSIHRVYHAIVYGNLKEDEGFVEAWLGRDPR-DRKKMAVLSENTTGARYAYTGWRVLE 220

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F   F ++  +  TGRTHQ+RVH   +G P+ GD  Y         +       LHA+ 
Sbjct: 221 RFG-NFTYIACKLKTGRTHQIRVHMASIGHPLAGDVVYGPRNCIKSLA----GQCLHAKE 275

Query: 295 MDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
           +   HP     +Q  +PLPA+     + L  ++
Sbjct: 276 LGFVHPSTENWMQFDSPLPAYFTDFLNRLRKEH 308


>gi|255009930|ref|ZP_05282056.1| ribosomal large subunit pseudouridine synthase [Bacteroides
           fragilis 3_1_12]
 gi|313147717|ref|ZP_07809910.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis 3_1_12]
 gi|313136484|gb|EFR53844.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis 3_1_12]
          Length = 357

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 83/343 (24%), Positives = 150/343 (43%), Gaps = 38/343 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    + +I+   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYDNEIIPEDIPLN---------IVYEDKYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNAIAWHLKDNSDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRR 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI    +  +   + +           V  +     +A++H++V++        
Sbjct: 198 YRALVWGIVDQNEGTVVGSIARNPK--DRMQMAVMPDPAQGKHAVTHYRVLERLG-YVTL 254

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +  L
Sbjct: 255 VECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPRQAL 314

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL-GFKYDRNLY 331
           HA  +   HP  G  +  T+ LP  M +  +   G+  +R+L 
Sbjct: 315 HAMTLGFVHPVTGEEMHFTSELPDDMTRLIEKWRGYISNRDLE 357


>gi|300361720|ref|ZP_07057897.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri JV-V03]
 gi|300354339|gb|EFJ70210.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           gasseri JV-V03]
          Length = 304

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 150/327 (45%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    +V+E ++   RLD+        ++   +++++    + V+ K  K + ++Q+G 
Sbjct: 1   MTENYQLVIEKEKG--RLDKVIAEKIKDLSRTKIKELVNDKNILVNNKAEKVSYKVQAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I                +  +  L+  +  L   ++YED+ + V NKP G+ V   +
Sbjct: 59  LIDIT---------------VPPAKPLSLEAQNLNLDIVYEDADVIVVNKPQGMVVHPSA 103

Query: 124 GIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +G L          +G +P + HR+D++TSG+L+VA+   A + L +    +
Sbjct: 104 GHPDHTLVNGLLYHTHKLADSPEGFRPGIVHRIDKDTSGLLMVAKNDKARESLEKQLAEK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++ Y ++V G  + K   I   + +  +         K        A++HF V++ F 
Sbjct: 164 INKREYLAIVHGNFETKNGVIDAPIGRNPNNRKQMAVNPK-----GKAAVTHFTVLEQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  ++    TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA  +  
Sbjct: 218 KDYSLVKCVLETGRTHQIRVHMKYIGHPLAGDPLYGPK-----KTLTGHGQFLHAETLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
             P   + L+ +APLPA   K  ++L 
Sbjct: 273 YQPSTHKWLEFSAPLPAIFEKQLENLR 299


>gi|218781210|ref|YP_002432528.1| pseudouridine synthase, RluA family [Desulfatibacillum alkenivorans
           AK-01]
 gi|218762594|gb|ACL05060.1| pseudouridine synthase, RluA family [Desulfatibacillum alkenivorans
           AK-01]
          Length = 321

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 92/336 (27%), Positives = 147/336 (43%), Gaps = 35/336 (10%)

Query: 4   MTYVQY--VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           MT  Q     V+N E+  RLD +   H  +++     +++R G V VDK   K +  ++ 
Sbjct: 1   MTGDQTYQFKVQNKEQGQRLDAFVPVHCKNLSRNACARLIRQGLVTVDKSVKKPSYVLKP 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G++V +                +         +  +   +LYED  I   NKP G+ V  
Sbjct: 61  GEMVSVT---------------VPEPETADIVAQDMDLAILYEDRDIVAVNKPPGMVVHP 105

Query: 122 GSGIAYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G + +   +  L    D  G    Q+P + HRLD+ETSG+++ A+  AA   L+E   
Sbjct: 106 APGHSSNTLVNALLAHCKDLSGIGGVQRPGIVHRLDKETSGVILAAKNDAAHAGLSEQLA 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            RR++K Y +L  G+ K     I   L +      D   +          A+S + V + 
Sbjct: 166 QRRVEKFYLALAHGVIKEDTGVIDLPLARHP---SDRKRMHVSTPAKGREALSLWTVKER 222

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-------TSPIQNKL 288
           F     ++++Q  TGRTHQ+RVH   +  P++GD  Y    K           +P   + 
Sbjct: 223 FLD-ATYVKVQIKTGRTHQIRVHLAALHHPVIGDTVYGGRKKRGRLPASVLGKAPPPERQ 281

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            LHA  +   HP  G  L +TAPLP  M +  ++L 
Sbjct: 282 MLHAHIVSFTHPVTGEKLTLTAPLPQDMAQLLEALR 317


>gi|163786072|ref|ZP_02180520.1| ribosomal large subunit pseudouridine synthase D [Flavobacteriales
           bacterium ALC-1]
 gi|159877932|gb|EDP71988.1| ribosomal large subunit pseudouridine synthase D [Flavobacteriales
           bacterium ALC-1]
          Length = 343

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 141/328 (42%), Gaps = 33/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  ++ +R+D++  N   +     +Q   + G + ++   VK N +++    V +    
Sbjct: 22  VDKGQQPLRIDKYLMNFVENATRNKIQSAAKDGCIFINNSPVKSNYKVKPNDFVTV---- 77

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IA 126
               H   E  ++   + +          ++YED  + V NKPAG+ V  G G     + 
Sbjct: 78  -KFKHPPHENLLIAEDIPID---------VVYEDDDLLVVNKPAGMVVHPGHGNYSGTLI 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +    ++  ++   +P L HR+D++TSG+LVVA+T  A  HL+  F  +  ++ Y +L
Sbjct: 128 NALIFHFENLPNNSSDRPGLVHRIDKDTSGLLVVAKTEQAMAHLSNQFAKKTSEREYVAL 187

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           VWG     +  I   + +           +         AI+H+KVI+        +  +
Sbjct: 188 VWGNMTEDEGIIEGNIGRHPKNRLQNTVYLDDEADKGKPAITHYKVIERLG-YVTLVSCK 246

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHARY 294
             TGRTHQ+RVH  H+G  +  D +Y        T+             I  +  LHAR 
Sbjct: 247 LETGRTHQIRVHMKHIGHTLFNDARYGGERILKGTTFSKYKQFVENCFKILPRQALHART 306

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           +   HP  G  L+  + +P  + +  + 
Sbjct: 307 LGFEHPTTGEFLRFESEIPEDIAQCIEK 334


>gi|227892505|ref|ZP_04010310.1| pseudouridylate synthase [Lactobacillus ultunensis DSM 16047]
 gi|227865626|gb|EEJ73047.1| pseudouridylate synthase [Lactobacillus ultunensis DSM 16047]
          Length = 305

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 82/326 (25%), Positives = 150/326 (46%), Gaps = 35/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     + V  DE   RLD++     P ++   ++++++   + V+ K  K + ++Q+G 
Sbjct: 1   MPKKYLLEV-KDEHG-RLDKFVSEQVPDLSRTRVKELIQDKNILVNNKSEKVSYKVQAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +         ++ E   LD               ++YED  + V NKP G+ V    
Sbjct: 59  CVLVNVPAVKPLDVVPENIPLD---------------IVYEDDDVIVVNKPQGMVVHPAP 103

Query: 124 GIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +  L    D     +G +P + HR+D++TSG+L++A+   A + L +    +
Sbjct: 104 GHPDHTLVNALLYHTKDLAQSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++IYW++V G    +   I   L+ ++      + VV    +    A++HFKV++ F 
Sbjct: 164 TNKRIYWAIVHGNFGEEGGTIDA-LIGRNPYDRKKMAVV----ENGKKAVTHFKVLEQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E Q  TGRTHQ+RVH  ++G  + GD  Y         +   +  +LHA+ +  
Sbjct: 218 KGFSLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPR-----KTLKGHGQFLHAKVLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP+ G+ ++ +   P     T   L
Sbjct: 273 RHPQSGKWMEFSVEPPKIFQDTLAQL 298


>gi|325696405|gb|EGD38295.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK160]
          Length = 298

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 144/322 (44%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V++E      RLD+        ++     + ++ G++ V+ +  K    ++ G ++   
Sbjct: 2   EVIIEASVVGQRLDKAVAE-LTDLSRSLANEQIKDGRILVNGQAKKAKYAVKEGDIIY-- 58

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                  + + E ++++         + +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 59  -------YELPEPEVVE------YVPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKSALTRFQVLERFGD-YSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA +PA   +T   + 
Sbjct: 275 GEVLEFTAEVPAIFQETLAKMR 296


>gi|326405195|ref|YP_004285277.1| ribosomal large subunit pseudouridine synthase D [Acidiphilium
           multivorum AIU301]
 gi|325052057|dbj|BAJ82395.1| ribosomal large subunit pseudouridine synthase D [Acidiphilium
           multivorum AIU301]
          Length = 332

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 80/329 (24%), Positives = 136/329 (41%), Gaps = 37/329 (11%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
              +   RLDR+  +    ++   L+ ++ +G V  D   ++  +  ++ G +  +    
Sbjct: 17  TEADGGERLDRFLASRLSEMSRSRLKALIEAGTVTCDGAVIRLPSAAVRPGAIYTVALPP 76

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
                                    L   +LYEDS + V +KPAG+ V    G      +
Sbjct: 77  AIP---------------AAPQGQALDLTVLYEDSDLIVIDKPAGLVVHPAPGNPDGTLV 121

Query: 130 DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +  +    DS       ++P + HRLD++TSG++V A+T  A   L+ +F  R + + Y 
Sbjct: 122 NALIAHCGDSLAGIGGERRPGIVHRLDKDTSGVMVAAKTELALNALSAAFAARDLDREYL 181

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L WG P+  +  I   + +        + VV    +G   A++H++ +  F      L 
Sbjct: 182 ALCWGAPQPAEGEIEGPIGRDPR-DRKRMAVV---ARGGKPALTHYRTLRRFGLGATLLA 237

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NKLYLHARYM 295
            +  TGRTHQ+RVH    G P+VGD  Y        +   Q          +  LHA  +
Sbjct: 238 CRLATGRTHQIRVHLASRGHPLVGDPVYLRRRPAAASQMQQPQRDFLLDFPRQALHAATL 297

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
              HP  G +L+  A  PA +      LG
Sbjct: 298 GFAHPRSGAKLRFEAAPPADLATLLSHLG 326


>gi|15924187|ref|NP_371721.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus subsp. aureus Mu50]
 gi|15926780|ref|NP_374313.1| hypothetical protein SA1040 [Staphylococcus aureus subsp. aureus
           N315]
 gi|57651766|ref|YP_186072.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus COL]
 gi|88194903|ref|YP_499703.1| hypothetical protein SAOUHSC_01163 [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|148267688|ref|YP_001246631.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150393746|ref|YP_001316421.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp.
           aureus JH1]
 gi|151221320|ref|YP_001332142.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus str.
           Newman]
 gi|156979518|ref|YP_001441777.1| hypothetical protein SAHV_1187 [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|221141987|ref|ZP_03566480.1| hypothetical protein SauraJ_10200 [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|253315555|ref|ZP_04838768.1| hypothetical protein SauraC_05302 [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
 gi|253731814|ref|ZP_04865979.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|253733565|ref|ZP_04867730.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|255005984|ref|ZP_05144585.2| hypothetical protein SauraM_05925 [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|257795747|ref|ZP_05644726.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9781]
 gi|258415971|ref|ZP_05682241.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9763]
 gi|258419718|ref|ZP_05682685.1| pseudouridylate synthase [Staphylococcus aureus A9719]
 gi|258438760|ref|ZP_05689913.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9299]
 gi|258444534|ref|ZP_05692863.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus A8115]
 gi|258447633|ref|ZP_05695777.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus A6300]
 gi|258449475|ref|ZP_05697578.1| pseudouridine synthase [Staphylococcus aureus A6224]
 gi|258452494|ref|ZP_05700500.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A5948]
 gi|258454854|ref|ZP_05702818.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A5937]
 gi|262048100|ref|ZP_06020987.1| hypothetical protein SAD30_1876 [Staphylococcus aureus D30]
 gi|262051832|ref|ZP_06024048.1| hypothetical protein SA930_1382 [Staphylococcus aureus 930918-3]
 gi|269202811|ref|YP_003282080.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282892683|ref|ZP_06300918.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8117]
 gi|282919979|ref|ZP_06327708.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|282927537|ref|ZP_06335153.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|284024121|ref|ZP_06378519.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 132]
 gi|295407135|ref|ZP_06816936.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|296275218|ref|ZP_06857725.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus MR1]
 gi|297245979|ref|ZP_06929838.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8796]
 gi|304381241|ref|ZP_07363894.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|13700996|dbj|BAB42292.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           N315]
 gi|14246967|dbj|BAB57359.1| similar to ribosomal large subunit psudouridine synthase D
           [Staphylococcus aureus subsp. aureus Mu50]
 gi|57285952|gb|AAW38046.1| ribosomal large subunit pseudouridine synthases, RluD subfamily
           [Staphylococcus aureus subsp. aureus COL]
 gi|87202461|gb|ABD30271.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           NCTC 8325]
 gi|147740757|gb|ABQ49055.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149946198|gb|ABR52134.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus JH1]
 gi|150374120|dbj|BAF67380.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus str.
           Newman]
 gi|156721653|dbj|BAF78070.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253724413|gb|EES93142.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|253728619|gb|EES97348.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|257789719|gb|EEV28059.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9781]
 gi|257839307|gb|EEV63781.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9763]
 gi|257844303|gb|EEV68685.1| pseudouridylate synthase [Staphylococcus aureus A9719]
 gi|257848019|gb|EEV72012.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9299]
 gi|257850027|gb|EEV73980.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus A8115]
 gi|257853824|gb|EEV76783.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus A6300]
 gi|257857463|gb|EEV80361.1| pseudouridine synthase [Staphylococcus aureus A6224]
 gi|257859712|gb|EEV82554.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A5948]
 gi|257863237|gb|EEV86001.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A5937]
 gi|259160233|gb|EEW45261.1| hypothetical protein SA930_1382 [Staphylococcus aureus 930918-3]
 gi|259163666|gb|EEW48221.1| hypothetical protein SAD30_1876 [Staphylococcus aureus D30]
 gi|262075101|gb|ACY11074.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|269940689|emb|CBI49070.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus TW20]
 gi|282590540|gb|EFB95617.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|282594695|gb|EFB99679.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|282764680|gb|EFC04805.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8117]
 gi|285816879|gb|ADC37366.1| Ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus 04-02981]
 gi|294967988|gb|EFG44016.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|297177143|gb|EFH36397.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8796]
 gi|302751019|gb|ADL65196.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus str. JKD6008]
 gi|304340224|gb|EFM06165.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|312829590|emb|CBX34432.1| pseudouridine synthase, RluA family protein [Staphylococcus aureus
           subsp. aureus ECT-R 2]
 gi|315130988|gb|EFT86972.1| hypothetical protein CGSSa03_05574 [Staphylococcus aureus subsp.
           aureus CGS03]
 gi|320140988|gb|EFW32835.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|329313865|gb|AEB88278.1| Pseudouridine synthase [Staphylococcus aureus subsp. aureus T0131]
 gi|329724740|gb|EGG61245.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21189]
 gi|329727173|gb|EGG63629.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21172]
          Length = 305

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 140/329 (42%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +++   
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I+ E                L   + YED  + V  KP G+ V    
Sbjct: 61  HIVVTEKEVVEADILPEN---------------LNLDIYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 GIAYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +   +G +    +  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAPIGRN-KNDRQSMAVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLD-----IGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  ++  A LP       D++  +
Sbjct: 275 EHPVTGEYIERHAELPQDFEDLLDTIRKR 303


>gi|325267840|ref|ZP_08134490.1| ribosomal large subunit pseudouridine synthase C [Kingella
           denitrificans ATCC 33394]
 gi|324980721|gb|EGC16383.1| ribosomal large subunit pseudouridine synthase C [Kingella
           denitrificans ATCC 33394]
          Length = 326

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 106/336 (31%), Positives = 169/336 (50%), Gaps = 25/336 (7%)

Query: 1   MSLMTY--VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR 58
           M  ++   V ++ V+  E   RLD +       +   ++ +I+R+G+VRV+K R K   R
Sbjct: 1   MPTISKDLVNHICVQEHESAQRLDNYLIKILKGVPKSHIHRIIRAGEVRVNKGRAKPETR 60

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           IQ+G ++RIPPV  A       +K   SS+       F    ++YED  + V NKP+G++
Sbjct: 61  IQTGDLIRIPPVRTA-------EKTAKSSLQPVPARHF---EIVYEDDALLVVNKPSGVA 110

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           V GGSG+++ +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E  R   
Sbjct: 111 VHGGSGVSFGVIEQLRRAR-PEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEMLRNDH 169

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            +KIYW+L  G  +     +   L+K +   G+ +  V   E     A + F+V+D F+ 
Sbjct: 170 PKKIYWALGVGTWQPALRHVRLPLVKYTGAAGEKMVRVGSAE-DGQSAHTVFRVLDTFSG 228

Query: 239 KF---------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKL 288
           +            +E    TGRTHQ+RVH    GCPI GD +Y               ++
Sbjct: 229 ERPHSVGVSALSLVEATLKTGRTHQIRVHMQASGCPIAGDERYGDYQANRRLQKLGLKRM 288

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
           +LHA  ++L HP  G +L + A LP  + +  D L 
Sbjct: 289 FLHAYSLELDHPLTGEKLVLQAALPDDLQRFLDGLR 324


>gi|171057282|ref|YP_001789631.1| RluA family pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170774727|gb|ACB32866.1| pseudouridine synthase, RluA family [Leptothrix cholodnii SP-6]
          Length = 322

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 102/327 (31%), Positives = 153/327 (46%), Gaps = 22/327 (6%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V++  V+      RLD +            + +I+RSG+VRV+K R   + R+  G  
Sbjct: 9   PQVRHFQVDEAGAGQRLDNFLMRELKGAPKTLVYRIIRSGEVRVNKGRAGADTRLAIGDD 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP+  +      E  +                 +L ED  +    KPAG++V GGSG
Sbjct: 69  VRVPPLRLSERPDPAESTVPPREFP-----------ILLEDEHLLAIAKPAGVAVHGGSG 117

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L+       +   L HRLD+ETSGIL+VA+ R+A   L + FR R   K Y 
Sbjct: 118 VSFGVIEQLRRARPQ-ARFLELVHRLDKETSGILLVAKKRSALTALQDQFRQRDTGKTYA 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +LV G     K+ I   L K +  GG+  V  V  +      +IS  +V+  F   +  L
Sbjct: 177 ALVIGDWPENKKVIDVALHKYTDAGGERRVRAVAADHPDGRRSISLVQVLKRF-DGYTLL 235

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLHARYMD 296
           ++   TGRTHQ+RVH    G PIVGD KY         +  +        +++LHAR + 
Sbjct: 236 DVTIKTGRTHQIRVHLQQAGHPIVGDDKYGDFALNKAMARGEAVAGCRFERMFLHARRLA 295

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSL 322
             HP  G R+++ A LPA      DS 
Sbjct: 296 FDHPASGERIELEAALPAECATLLDSF 322


>gi|170023919|ref|YP_001720424.1| 23S rRNA pseudouridylate synthase C [Yersinia pseudotuberculosis
           YPIII]
 gi|169750453|gb|ACA67971.1| pseudouridine synthase, RluA family [Yersinia pseudotuberculosis
           YPIII]
          Length = 320

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 99/319 (31%), Positives = 164/319 (51%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEVQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKSMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + I   LLK     G+ V  V         + + FK+ + F +    ++  
Sbjct: 180 VRGQWQSHCKAIQAPLLKNIMQSGERVVKVSSE---GKPSETRFKIEERF-EHATLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  
Sbjct: 236 PVTGRTHQIRVHALHAGHPIAFDDRYGDREFDQQLQGTGLHRLFLHAAALRFEHPNTGAT 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++I APL   +     +L 
Sbjct: 296 MRIEAPLDNQLRHCLLALR 314


>gi|74316828|ref|YP_314568.1| ribosomal large subunit pseudouridine synthase D [Thiobacillus
           denitrificans ATCC 25259]
 gi|74056323|gb|AAZ96763.1| pseudouridine synthase, RluD [Thiobacillus denitrificans ATCC
           25259]
          Length = 318

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 86/327 (26%), Positives = 144/327 (44%), Gaps = 26/327 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V+ +V+ + +  +RLD+      P  +   +Q  +R+ ++ VD        ++  G+ V
Sbjct: 12  DVRELVIPDAQGGLRLDQALSALLPEFSRNRIQNWIRARKIVVDDAWGTTKMKVSGGESV 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+              ++           + +   ++YEDS + V NKP G+ V  GSG 
Sbjct: 72  RV--------------QVEPDPGATPDAPEAIPLDVVYEDSMLLVINKPVGLVVHPGSGN 117

Query: 126 AY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               +   L   V    + PR  + HRLD++TSG+LVVA+T  A   L    + R +++ 
Sbjct: 118 RDGTLLNALLHRVPQVAELPRAGIVHRLDKDTSGLLVVAKTLRAHTDLVRQLQARTVKRE 177

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV+G   ++   +   L +  H                  A++H+ V++ F      
Sbjct: 178 YLALVYGEV-DRGGTVDAPLARDPHNRTKRTV-----HSLGKEAVTHYDVVERFP-GITL 230

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L  +  TGRTHQ+RVH  H+G P+VGD  Y A+ + +   P   +  LHA  + L HP  
Sbjct: 231 LRCKLETGRTHQIRVHMQHVGHPLVGDTVYSASRRSHLKIPF-PRQALHAEKLGLIHPVT 289

Query: 303 GR-LQITAPLPAHMVKTWDSLGFKYDR 328
           G  +    PLP        +L    D 
Sbjct: 290 GEFVHWECPLPPDFGSLLQALRDNTDW 316


>gi|223939777|ref|ZP_03631648.1| pseudouridine synthase, RluA family [bacterium Ellin514]
 gi|223891553|gb|EEF58043.1| pseudouridine synthase, RluA family [bacterium Ellin514]
          Length = 318

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 85/327 (25%), Positives = 141/327 (43%), Gaps = 31/327 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   VE    + RLD + +  +P ++   +Q+++  G ++V+ + +K  +  ++G+++ +
Sbjct: 7   ESFTVEVSLPSERLDTFLRERFPAVSRGTIQRLIEQGHIKVNGQTIKPTHHPRAGELIEV 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                              +       + +   +++EDS + V NK  G+ V   +G   
Sbjct: 67  YW---------------PEARPAEARPEDIPLDIIFEDSDLLVLNKAPGLVVHPAAGHEE 111

Query: 128 HI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           H   +  L              +P + HRLD+ETSG LVVA+  AA   L E F  R ++
Sbjct: 112 HTLVNALLHHCEGQLSGIGGVARPGIVHRLDKETSGCLVVAKNDAAHMALAEQFSGRTLE 171

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++V G        I   + +       +   +   +     A + +KV + F+   
Sbjct: 172 KTYLAIVCGEVVRNSGEIRASIARHPT----HRKRMTVTDGSGREAWTSYKVRERFS-GA 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF---TSPIQNKLYLHARYMDL 297
            WLE   HTGRTHQ+RVH  H+G PIVGD  Y           T     +  LHA  +  
Sbjct: 227 TWLEALLHTGRTHQIRVHFQHLGYPIVGDATYGTRQNKRLIEVTGYAAPRQMLHAWKLSF 286

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLG 323
            HP +G +L   AP PA       SL 
Sbjct: 287 LHPCKGKKLSFEAPWPADFQTALASLR 313


>gi|172060047|ref|YP_001807699.1| RluA family pseudouridine synthase [Burkholderia ambifaria MC40-6]
 gi|171992564|gb|ACB63483.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MC40-6]
          Length = 316

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 98/322 (30%), Positives = 157/322 (48%), Gaps = 23/322 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++ +    R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +VR+PP
Sbjct: 2   IEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDIVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A   + +    +                +LYED  + V NKPAG++V GGSG+A+ +
Sbjct: 62  VRVAAADLARADTPIVPPAQFE---------VLYEDDAMLVINKPAGVAVHGGSGVAFGV 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y++   G
Sbjct: 113 IEQMRQAR-PRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFACGHG 171

Query: 190 IPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             ++       +   L K S   G+    V+ +      + + F +++ + + +  +E +
Sbjct: 172 EWQSDWGRRRAVKAPLFKYSTAEGERRVRVQDD---GLPSHTVFNLLERWPE-YALVEAE 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H+G PI GD KY               P   +++LHA  + L HP 
Sbjct: 228 LKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANAQPSLKRMFLHAHRLKLAHPL 287

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  LQ  APLP    +  D L
Sbjct: 288 TGEPLQFDAPLPDECRRFLDQL 309


>gi|329114084|ref|ZP_08242848.1| Ribosomal large subunit pseudouridine synthase D [Acetobacter
           pomorum DM001]
 gi|326696623|gb|EGE48300.1| Ribosomal large subunit pseudouridine synthase D [Acetobacter
           pomorum DM001]
          Length = 337

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 76/335 (22%), Positives = 134/335 (40%), Gaps = 35/335 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             V  ++   R+DR+       ++   ++ ++  G ++ D               V I  
Sbjct: 21  FTVTPEQAGERIDRFLAAIMETLSRSRIKSLIEEGHLKCDG--------------VCIRE 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                   +K +  +  +       + +   +LYED  + V +KPAG+ V    G     
Sbjct: 67  PAAIARAGMKVELTIPPAAPAVPQGEDISFTVLYEDDDLIVLDKPAGLVVHPAPGNETGT 126

Query: 128 HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++G +    +S       ++P + HRLD++TSG++V A+T  A Q L+E F  RRI + 
Sbjct: 127 LVNGLIAHCGESLKGIGGERRPGIVHRLDKDTSGVMVAAKTEMAHQALSEDFAARRIDRT 186

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +  WG+P   +      + +           +    KG  +A++H++ +  F      
Sbjct: 187 YLAFCWGLPNPAEGDFEGAIGRDKRDRK----RMALTPKGGKWALTHYRTLQAFGTGAAL 242

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFTSPIQNKLYLHAR 293
           +  +  TGRTHQ+RVH    G P++GD  Y                  +    +  LHA 
Sbjct: 243 VACKLATGRTHQIRVHFSANGHPLIGDPLYLRRIPAASRVLPSAARAAALDFPRQALHAA 302

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +   HP  G  L    P+P  M     SL    +
Sbjct: 303 RLGFIHPRTGEKLLFETPMPEDMQALERSLKADQE 337


>gi|148653370|ref|YP_001280463.1| RluA family pseudouridine synthase [Psychrobacter sp. PRwf-1]
 gi|148572454|gb|ABQ94513.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter sp.
           PRwf-1]
          Length = 420

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 148/328 (45%), Gaps = 32/328 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V  ++   R+D+   + +   +   LQ  L+SG + V+    K   R++ G +VR+
Sbjct: 105 ELHTVTQEQAGQRIDKLAADMFTEHSRAQLQDWLKSGNLTVNDHNEKAKYRVKIGDIVRL 164

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
              +                 + +   + +K  ++YED  + V NKP G+ V  G+G   
Sbjct: 165 EAKLEQ---------------HGSDQPEDIKLDIIYEDDSVIVINKPVGMVVHPGAGNWS 209

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + +     +  L HR+D+ TSG+LV+ +T+AA   L E  + + + + Y 
Sbjct: 210 GTLVNGLLYHYPNQAHLPRAGLVHRIDKNTSGLLVIGKTKAAQLELQEQLKDKSVYRHYQ 269

Query: 185 SLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +V G  P   ++   +  + +       + V          AI+H   I   +  +  L
Sbjct: 270 CVVAGDAPSLARQRTIDAPIGRHRTQRTKMTVTS----TGKTAITHIMKITPLSDTYSLL 325

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL--------HARYM 295
           +++  TGRTHQ+RVH  H+G PI+GD  Y    +       + +  +        HA  +
Sbjct: 326 DVRLETGRTHQIRVHLSHIGHPIIGDDIYGNRQQLRAGLTPEQRQAIQSFPRQALHAYKL 385

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HPE G  +++TAPLP  +V+   +L
Sbjct: 386 GFIHPETGESIELTAPLPQDIVELAHTL 413


>gi|284052171|ref|ZP_06382381.1| ribosomal large subunit pseudouridine synthase D [Arthrospira
           platensis str. Paraca]
 gi|291568935|dbj|BAI91207.1| probable pseudouridine synthase [Arthrospira platensis NIES-39]
          Length = 308

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 87/325 (26%), Positives = 143/325 (44%), Gaps = 29/325 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           ++ +  E D EN RLDRW       ++   LQ ++ SG V V+          +Q G  +
Sbjct: 3   IELICEEQDGENQRLDRWLSERVQQLSRSRLQALISSGHVWVNNSPCTSKKATVQIGDRI 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           ++                +  ++ L   +  +   +LYED ++ + NKPAG+ V    G 
Sbjct: 63  QVE---------------IPPAIPLELKATNIPLDILYEDEELLIINKPAGLVVHPAPGH 107

Query: 126 AYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           A     +  L       G    Q+P + HRLD++T+G + +A+T  A QHL    + +  
Sbjct: 108 ANDTLVNALLAHCETLAGIGGVQRPGIVHRLDKDTTGAIAIAKTDHAHQHLQAQIQAKTA 167

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y  +++G+PK     I   + +  H        +    +G   AI+ ++V +     
Sbjct: 168 RRQYLGIIYGVPKTTSGVIDQPIGR--HHSDRKKMAIVPEHQGGRSAITRWQVQERLG-N 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +E +  TGRTHQ+RVH+  +G PIVGD  Y          P      LHA  + L H
Sbjct: 225 YTLIEFELETGRTHQIRVHSASIGHPIVGDRVYGKGRSVGVNLPG---QALHAWKLTLQH 281

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  G  ++  APLP  M      L 
Sbjct: 282 PTSGELIEAIAPLPHTMTTLLKVLR 306


>gi|226939996|ref|YP_002795069.1| RluC [Laribacter hongkongensis HLHK9]
 gi|226714922|gb|ACO74060.1| RluC [Laribacter hongkongensis HLHK9]
          Length = 312

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 92/318 (28%), Positives = 160/318 (50%), Gaps = 18/318 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  + +DE   RLD W       +   ++ +I+R G+VR++K R + + R+++G VVR
Sbjct: 9   VTFHTITDDEAGQRLDNWLIKILKGVPKSHVYRIVRGGEVRINKGRCQVDQRVETGDVVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+             +      T+        +++ED  + V +KP G++V GGSG++
Sbjct: 69  IPPIR------------IAERPAATRPVPAAAFPVVFEDDALLVIDKPCGVAVHGGSGVS 116

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++      +   L HRLD++TSG+L++A+ R+A   L +  R   + K Y +L
Sbjct: 117 FGVIEQLRAARPQ-AKFLELVHRLDRDTSGLLLIAKKRSALVALHDMIRRNMLDKRYLAL 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G     ++ +   L K +   G+    V+ +E G   + + F+++  FA     +E  
Sbjct: 176 GVGRWNPARKSVKKPLTKYTLPDGER--RVRVDEAGGQASHTDFRIVRSFA-GHTLIEAT 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
             TGRTHQ+RVH     CPI GD KY       +       +++LHA  + L HP  G+ 
Sbjct: 233 LQTGRTHQIRVHMQSADCPIAGDDKYGDYATNKDLARQGLKRMFLHAWQLRLQHPLTGQL 292

Query: 305 LQITAPLPAHMVKTWDSL 322
           L+  APLP  + +  ++L
Sbjct: 293 LEFRAPLPDELNRFIETL 310


>gi|225873450|ref|YP_002754909.1| pseudouridine synthase, RluA family [Acidobacterium capsulatum ATCC
           51196]
 gi|225793546|gb|ACO33636.1| pseudouridine synthase, RluA family [Acidobacterium capsulatum ATCC
           51196]
          Length = 355

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 101/347 (29%), Positives = 157/347 (45%), Gaps = 46/347 (13%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             +Q+  V  +    RLD W     P ++   ++ +L  GQV VD  + + + +++ G+ 
Sbjct: 24  PQIQHFTVPAEAAGQRLDAWLTTQLPDVSRSRVKLLLDDGQVTVDSLKERASLKLRGGES 83

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V +              +   +   L   ++ +   ++YED  + V NKPAG+ V  GSG
Sbjct: 84  VEV--------------RGEPAPPPLRAMAEDIPLDIIYEDKDLIVVNKPAGMMVHAGSG 129

Query: 125 IAYH--IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTES 173
                   G L + +  + +K         P + HRLD+ETSG+++VAR  AA Q L E 
Sbjct: 130 ATDSARNRGTLVNALLGRQEKLSKTGGDLRPGIVHRLDKETSGLIIVARNDAAHQRLAEM 189

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV- 232
           F  R I K Y +LV G     +  I   + +          +  +  +GA  AISH++V 
Sbjct: 190 FSQREIHKTYLALVHGHIAEDRGTINAAIARDVIRR---TRMTTRRTEGARTAISHYRVQ 246

Query: 233 --IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---------ANFKGNFT 281
             I+    KF  + ++  TGRTHQ+RVH   +G P+VGD  Y          AN      
Sbjct: 247 RRIETRWGKFTLVSVRIETGRTHQIRVHLSSIGHPVVGDTHYGAPTTIVLPVANRARRKQ 306

Query: 282 SPIQNKL-----YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            P    L     +LHA  +  PHP   + L + APLPA +V   + L
Sbjct: 307 LPAPEGLSLPRNFLHAAELKFPHPRSEKPLHLEAPLPAELVAFLEQL 353


>gi|118586926|ref|ZP_01544359.1| pseudouridylate synthases, 23S RNA-specific [Oenococcus oeni ATCC
           BAA-1163]
 gi|118432653|gb|EAV39386.1| pseudouridylate synthases, 23S RNA-specific [Oenococcus oeni ATCC
           BAA-1163]
          Length = 308

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 141/329 (42%), Gaps = 35/329 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     ++  +V  ++   RLD+     +   +   ++K++   +V V+ K V     +Q
Sbjct: 5   MKNKQILESTIV--NQSG-RLDKILATDFSAFSRNQIKKLIDQDRVIVNGKPVLAKYLVQ 61

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  V I         ++ E+  LD               ++YED  + V NKP G+ V 
Sbjct: 62  DGDHVVIKVPPVKKTELLPEKIPLD---------------IVYEDDDLIVVNKPQGMVVH 106

Query: 121 GGSGIAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             +G + H   +  L     S      +P + HR+D++TSG+L+VA+   A +HL+   +
Sbjct: 107 PSAGHSEHTLVNALLSHAPLSTINGEFRPGIVHRIDKDTSGLLMVAKNNFAHEHLSLDLK 166

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             +  + Y ++V G    K+  I   + +          V          AI+HFKV++ 
Sbjct: 167 SHKTGRKYLAIVHGNFSEKRGTIKAPIDRDPKNRQKQAVVA-----NGREAITHFKVLES 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F+  +  +E    TGRTHQ+RVH  ++G P+ GD  Y         +      YL A  +
Sbjct: 222 FS-NYSLIEAVLETGRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLPGRGQYLFASSL 275

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            L  P  G  L  +APLP +  K    L 
Sbjct: 276 SLTQPHTGKELSFSAPLPDYFQKMLLKLR 304


>gi|254252865|ref|ZP_04946183.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           dolosa AUO158]
 gi|124895474|gb|EAY69354.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           dolosa AUO158]
          Length = 341

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 99/331 (29%), Positives = 161/331 (48%), Gaps = 23/331 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++      R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +V
Sbjct: 23  QVSMIQIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAYGDLV 82

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + +    +    +           +LYED  + V +KPAG++V GGSG+
Sbjct: 83  RVPPVRVAAADLARADAPVVPPAHFD---------VLYEDDAMLVIDKPAGVAVHGGSGV 133

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++ +   L+     + +   L HRLD+ETSG+L++A+ RAA   L E  R  RI K Y++
Sbjct: 134 SFGVIEQLRQAR-PRAKFLELVHRLDRETSGVLMLAKKRAALVGLHEQIRENRIDKRYFA 192

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G  + +      +   L K +   G+    V+++      + + F +++ +   +  
Sbjct: 193 CVHGDWQAEWGRRRAVKAPLFKYTTPEGERRVRVQED---GLPSHTVFNLVERWPD-YAL 248

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PI GD KY               P   +++LHA  + +
Sbjct: 249 VEAELKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANAQPSLKRMFLHAHRLRV 308

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            HP  G  LQ  APLP    +  D L    D
Sbjct: 309 AHPLTGEALQFDAPLPDDCRRFLDQLRALRD 339


>gi|222149596|ref|YP_002550553.1| ribosomal large subunit pseudouridine synthase RluD subfamily
           [Agrobacterium vitis S4]
 gi|221736578|gb|ACM37541.1| ribosomal large subunit pseudouridine synthase RluD subfamily
           [Agrobacterium vitis S4]
          Length = 342

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 88/345 (25%), Positives = 152/345 (44%), Gaps = 47/345 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           + ++   D E  RLD W        ++   ++ ++  G V V+   V     +I+ G  +
Sbjct: 13  KELIAGEDAEG-RLDAWLAASLGGDLSRNRVKALIEQGAVFVNGTAVTEPKRKIKPGDQL 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            I                +    +     + +   +LYED  + V +KPAG+ V  G+G 
Sbjct: 72  VI---------------AMPEPEDPEPKGEDIPLTVLYEDKDLIVLSKPAGLVVHPGAGN 116

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  +    DS       ++P + HRLD+ETSG++VVA+   A +HL + F    
Sbjct: 117 WTGTLVNALIHHCGDSLSGIGGVKRPGIVHRLDKETSGVMVVAKNDIAHRHLADQFADHG 176

Query: 179 ----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y +LVWG P+  +  I   L +          V +++   A  AI+H++V++
Sbjct: 177 RSGPLERAYQALVWGRPRGLRGTIDAALGRAG--DRTKRTVKREDTDDAREAITHYQVME 234

Query: 235 CFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
            + +K         +E +  TGRTHQ+RVH  H+G P++GD +Y A FK           
Sbjct: 235 RYGEKPDATCLASLVECRLETGRTHQIRVHMAHIGHPLIGDPEYGAAFKTKANLLPDAAK 294

Query: 286 ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 ++  LHA  +   HP  G  +   AP+P  M     +L 
Sbjct: 295 AIVTNFHRQALHAYLLAFEHPTTGDVMHFAAPIPDDMETIIRALR 339


>gi|315282847|ref|ZP_07871166.1| ribosomal large subunit pseudouridine synthase D [Listeria marthii
           FSL S4-120]
 gi|313613517|gb|EFR87342.1| ribosomal large subunit pseudouridine synthase D [Listeria marthii
           FSL S4-120]
          Length = 302

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 143/323 (44%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++E      R+D+         +   +Q +L++G + V+ +  K N ++Q G  +  
Sbjct: 4   ETLIIEESHARERVDKVIAEMM-GKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                    ++ E   LD               + +ED  + V NKP G+ V   +G A 
Sbjct: 63  EAREPEELEVLAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHAS 107

Query: 127 -YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 108 GTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + +      + VV+        A +HF+V++     F 
Sbjct: 168 EYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVLERLP-GFT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH  ++G P+ GD KY         +   N  +LHA  +   HP 
Sbjct: 222 LINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTIKGNGQFLHAAKLGFDHPT 276

Query: 302 G-GRLQITAPLPAHMVKTWDSLG 323
              R+   APLP+   K   +L 
Sbjct: 277 TNERMTFEAPLPSSFEKALKTLR 299


>gi|303256986|ref|ZP_07343000.1| ribosomal large subunit pseudouridine synthase C [Burkholderiales
           bacterium 1_1_47]
 gi|302860477|gb|EFL83554.1| ribosomal large subunit pseudouridine synthase C [Burkholderiales
           bacterium 1_1_47]
          Length = 334

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 166/331 (50%), Gaps = 19/331 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V +  V+   +  RLD +  +    +    + +++RSG+VRV+K R   + R+QSG  
Sbjct: 16  PKVIFKKVDESNDGQRLDNFLLSQLKGVPKSLIYRVVRSGEVRVNKGRAHVDTRLQSGDE 75

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+     +  KE +     + L++        +L+ED  I V +KPAG++  GGSG
Sbjct: 76  VRIPPIR----YTEKESEHSAPPLKLSEMPP-----ILFEDQNIMVVDKPAGMASHGGSG 126

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           I+Y +   +++          L HRLD+ TSG+LV+A+TR A   L E  R   + K Y 
Sbjct: 127 ISYGLIERMRASRPEL-PFLELVHRLDRGTSGVLVLAKTRKALVRLHEMIREGEMHKTYQ 185

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  +N ++     L K     G+    V+ + +    + S F++ + F      +E
Sbjct: 186 ALVKGDWQNDRQHAKFPLFKYVTPSGER--RVRVDPENGLPSHSIFRLKERFG-PVSLVE 242

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-----NKLYLHARYMDLPH 299
           +   TGRTHQ+RVHA  +G P+VGD KY      +  +         +++LH+  +   H
Sbjct: 243 VDLLTGRTHQIRVHAAELGFPLVGDEKYGDFAFNDEVAHGSLGVPFKRMFLHSGKICFHH 302

Query: 300 P-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           P  G  L+I APLP   V+  + L  +  +N
Sbjct: 303 PITGEELEIEAPLPKDCVELIEVLEQRKAQN 333


>gi|291459221|ref|ZP_06598611.1| ribosomal large subunit pseudouridine synthase D [Oribacterium sp.
           oral taxon 078 str. F0262]
 gi|291418475|gb|EFE92194.1| ribosomal large subunit pseudouridine synthase D [Oribacterium sp.
           oral taxon 078 str. F0262]
          Length = 308

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 73/332 (21%), Positives = 147/332 (44%), Gaps = 39/332 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHIN--FVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           MT  + + VE +    RLDR+     P ++      ++++  G+V +D +  K + R++ 
Sbjct: 1   MTGTESIRVEAECAGERLDRYLSKR-PELSLSRSYAERLIGEGRVLLDGQAEKPSKRLRG 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G+ + I         I  E+  LD               ++YEDS++ + NKP G+ V  
Sbjct: 60  GEQISICFPEEKPTEIRAEEIPLD---------------IVYEDSELLLVNKPKGMVVHP 104

Query: 122 GSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTE 172
             G  +     + + +   G          +P + HR+D++T+G+L+V +   A + L E
Sbjct: 105 APG--HSGGTLVNALLGRPGPELSSINGVLRPGIVHRIDRDTTGLLLVCKKDRAHRALAE 162

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
             +   I + Y +++ G  +  +  +   + +            ++       A++H++V
Sbjct: 163 QLKEHTITRRYHAILCGRMREDEGKVDAPIGRSRRDRKKQAIDWER----GREAVTHYRV 218

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++ F++ +  +E +  TGRTHQ+RVH   +G P++GD  Y                 LHA
Sbjct: 219 LERFSE-YTLVECRLETGRTHQIRVHMASIGHPVLGDEVYGPRH----CPFRLEGQCLHA 273

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           + +   HP  G+ ++  +  PA+  +    L 
Sbjct: 274 KLLGFVHPVSGKYMEFDSEYPAYFEELLQKLR 305


>gi|225010881|ref|ZP_03701348.1| pseudouridine synthase, RluA family [Flavobacteria bacterium
           MS024-3C]
 gi|225004928|gb|EEG42883.1| pseudouridine synthase, RluA family [Flavobacteria bacterium
           MS024-3C]
          Length = 379

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 76/330 (23%), Positives = 144/330 (43%), Gaps = 35/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +    +E +R+D++  N   +     +Q+  + G + V+   VK N ++++G  +++  
Sbjct: 57  FIASKGQEPLRIDKYLMNFIENATRNKIQQAAKEGHIWVNDLVVKQNYKVKAGDQIKVMF 116

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                  ++                + +   ++YEDS + V NKP G+ V  G G     
Sbjct: 117 THPPYEFLL--------------TPEDIPLDVVYEDSDLMVVNKPPGMVVHPGHGNYSGT 162

Query: 128 HIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            I+  L   K    +  ++P L HR+D++TSG+LVVA+T  A  HL + F  +  ++ Y 
Sbjct: 163 LINALLFHVKDLPLNADERPGLVHRIDKDTSGLLVVAKTAKAMTHLAKQFFDKTSEREYV 222

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++VWG  + ++  +   + +  H        V  +      A++H+KV++        + 
Sbjct: 223 AIVWGNVEEEQGTVRGHIGR--HPKNRLQMAVFPDGDQGKEAVTHYKVMERLG-YVTLVS 279

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLHA 292
               TGRTHQ+R H  H+G  +  D +Y        T+  +             +  LHA
Sbjct: 280 CVLETGRTHQIRAHMKHIGHTLFNDERYGGEKILKGTTFTKYKQFVDNAFKALPRQALHA 339

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP  G  ++   P+P  MV   + 
Sbjct: 340 KTLGFVHPSSGELMRFNTPIPEDMVLCIEK 369


>gi|218131974|ref|ZP_03460778.1| hypothetical protein BACEGG_03597 [Bacteroides eggerthii DSM 20697]
 gi|217985850|gb|EEC52190.1| hypothetical protein BACEGG_03597 [Bacteroides eggerthii DSM 20697]
          Length = 357

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 81/332 (24%), Positives = 147/332 (44%), Gaps = 38/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 33  VVVDKGQEMMRVDKYLFDRLTNASRNRIQKAADAGFVMANDKPVKSSYKVKPLDVITVMM 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +++   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 93  -----DRPRYENEVIPEDIPLN---------IVYEDKFLMVVNKPAGLVVHPGHGNYHGT 138

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 139 LVNAIAWHMKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRR 198

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +  +  I   + +      D + +    +    +A++H++V++        
Sbjct: 199 YRALVWGNVEQDEGTIVGNVGRNPK---DRMQMTVLPDDQGKHAVTHYRVLERLG-YVTL 254

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +     T   +             +  L
Sbjct: 255 VECVLETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFAKYKQFVNNCFDTCPRQAL 314

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G  +  T+ LP  M +  D 
Sbjct: 315 HAMTLGFVHPVTGEEMYFTSELPDDMTRLIDK 346


>gi|114320585|ref|YP_742268.1| ribosomal large subunit pseudouridine synthase C [Alkalilimnicola
           ehrlichii MLHE-1]
 gi|114226979|gb|ABI56778.1| ribosomal large subunit pseudouridine synthase C [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 327

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 99/321 (30%), Positives = 151/321 (47%), Gaps = 18/321 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V+ V +  ++   R+D +       +    + ++LRSGQVRVD KR K   R+ +G+
Sbjct: 12  MSGVRQVRIGPEDAGQRVDNFLMRQLKGVPRSLIYRLLRSGQVRVDGKRTKPPRRLATGE 71

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPPV           +    +    +    L   +LYED ++ V +KP+G++V GGS
Sbjct: 72  TVRIPPVQT---------RAPQEATPPARLQGELAQRILYEDDRLLVIDKPSGLAVHGGS 122

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+A+ +   L+    S      L HRLD+ TSG L+VA+ R+A + L E  R   + K Y
Sbjct: 123 GLAWGLIEVLRQARPS-APFLELVHRLDRATSGCLMVAKRRSALRELHEQLRTGAVHKRY 181

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L+ G        +   L ++S   G       +       A + F+ +          
Sbjct: 182 LALLTGALGRGPIPVEAPLERRSGPAGG-----VRVASHGKLARTVFRAVARPG-GMTLA 235

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEG 302
           E    TGRTHQ+RVHA H+G PI GD +Y               +L+LHA  ++L  P  
Sbjct: 236 EADIATGRTHQIRVHAAHLGMPIAGDDRYGERAVNRRLRGLGLKRLFLHAHRLELSAPGT 295

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
           G+ L I APLP  +      L
Sbjct: 296 GQPLSIEAPLPDELAAVVAQL 316


>gi|326335706|ref|ZP_08201892.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           sp. oral taxon 338 str. F0234]
 gi|325692135|gb|EGD34088.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           sp. oral taxon 338 str. F0234]
          Length = 345

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 148/326 (45%), Gaps = 35/326 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
             +E +R+D++  N   + +   +Q+  + G + V+   VK N+R+++   V++      
Sbjct: 27  KGQEPLRVDKFLMNFVENASRNKVQQAAKDGNIFVNGVAVKSNHRVKANDEVKVMFAHPP 86

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDG 131
             +++                + +   ++YED ++ + NKPAG+ V  G G      I+G
Sbjct: 87  HEYLL--------------VPELIPLNIVYEDEELIIINKPAGLVVHPGHGNYQGTLING 132

Query: 132 FLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +        +   +P L HR+D++TSG+LVVA+T  A  HL + F  +  ++ Y +LVW
Sbjct: 133 LIYHFEQLPKNSSDRPGLVHRIDKDTSGLLVVAKTEEAMNHLAKQFFNKTSEREYIALVW 192

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G     +  I   + +  H        V  +      AI+H+KV++ F      +  +  
Sbjct: 193 GNIPEDEGTITGHIGR--HPKNRLQMTVFPDGSEGKEAITHYKVLERFG-YVTLVSCRLE 249

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------------PIQNKLYLHARYMD 296
           TGRTHQ+R H  ++G P+  D +Y  +     T+             +  +  LHA+ + 
Sbjct: 250 TGRTHQIRAHFTYIGHPLFNDERYGGDKILKGTTSTKYKQFVENCFKVLPRQALHAKTLG 309

Query: 297 LPHPEGGRL-QITAPLPAHMVKTWDS 321
           +  P  G++ +  + +P  M +  + 
Sbjct: 310 IEKPSTGQMLRFDSEIPQDMQECIEK 335


>gi|324993007|gb|EGC24927.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK405]
 gi|327462303|gb|EGF08630.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1]
          Length = 298

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 146/322 (45%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E    + RLD+        ++     + ++ G++ V+ +  K    ++ G V+   
Sbjct: 2   EVRIEASVASQRLDKAVAE-LTDLSRSLAHEQIKDGRILVNGQAKKAKYAVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++        ++ +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELPEPEVVE------YVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHINDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-YTL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA  PA   +T + L 
Sbjct: 275 GEVLEFTAEAPAIFQETLEKLR 296


>gi|116491102|ref|YP_810646.1| ribosomal large subunit pseudouridine synthase D [Oenococcus oeni
           PSU-1]
 gi|290890605|ref|ZP_06553676.1| hypothetical protein AWRIB429_1066 [Oenococcus oeni AWRIB429]
 gi|116091827|gb|ABJ56981.1| ribosomal large subunit pseudouridine synthase D [Oenococcus oeni
           PSU-1]
 gi|290479733|gb|EFD88386.1| hypothetical protein AWRIB429_1066 [Oenococcus oeni AWRIB429]
          Length = 304

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 141/329 (42%), Gaps = 35/329 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     ++  +V  ++   RLD+     +   +   ++K++   +V V+ K V     +Q
Sbjct: 1   MKNKQILESTIV--NQSG-RLDKILATDFSAFSRNQIKKLIDQDRVIVNGKPVLAKYLVQ 57

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  V I         ++ E+  LD               ++YED  + V NKP G+ V 
Sbjct: 58  DGDHVVIKVPPVKKTELLPEKIPLD---------------IVYEDDDLIVVNKPQGMVVH 102

Query: 121 GGSGIAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             +G + H   +  L     S      +P + HR+D++TSG+L+VA+   A +HL+   +
Sbjct: 103 PSAGHSEHTLVNALLSHAPLSTINGEFRPGIVHRIDKDTSGLLMVAKNNFAHEHLSLDLK 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             +  + Y ++V G    K+  I   + +          V          AI+HFKV++ 
Sbjct: 163 SHKTGRKYLAIVHGNFSEKRGTIKAPIDRDPKNRQKQAVVA-----NGREAITHFKVLES 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F+  +  +E    TGRTHQ+RVH  ++G P+ GD  Y         +      YL A  +
Sbjct: 218 FS-NYSLIEAVLETGRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLPGRGQYLFASSL 271

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            L  P  G  L  +APLP +  K    L 
Sbjct: 272 SLTQPHTGKELSFSAPLPDYFQKMLLKLR 300


>gi|311748762|ref|ZP_07722547.1| ribosomal large subunit pseudouridine synthase D [Algoriphagus sp.
           PR1]
 gi|126577297|gb|EAZ81545.1| ribosomal large subunit pseudouridine synthase D [Algoriphagus sp.
           PR1]
          Length = 344

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 77/335 (22%), Positives = 142/335 (42%), Gaps = 43/335 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++  ++N+R+D++      +     +Q+ + +G V V+ K  K N +I+    +++  
Sbjct: 22  ISIDKGQKNIRIDKFLSEKLANATRNKVQQAIDAGSVLVNGKPTKANYKIKPMDDIKVMM 81

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +  +  +KI              +  ++YED  + + NKPAG+ V    G   + 
Sbjct: 82  EKPPRDTEVYPEKI--------------ELDIIYEDKYLLIVNKPAGMVVHPAHG---NW 124

Query: 130 DGFLKSWVDSKGQ----------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            G L + +    Q          +P L HR+D++TSG+LV+A+   A  HL   F    I
Sbjct: 125 SGTLANALVYHFQDLPEMKGNEGRPGLVHRIDKDTSGLLVIAKQEEAMTHLASQFFHHTI 184

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y +LVWG PK  +  I   + + +      V  V  + +   +AI+H+KV+    + 
Sbjct: 185 DRTYIALVWGEPKEDEGTIEGNVGRSAK--NRKVMDVFPDGEQGKHAITHWKVLKRL-RY 241

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNK 287
              ++    TGRTHQ+R H  ++G P+  D  Y  +     T              +  +
Sbjct: 242 VSLIQCNLETGRTHQIRAHMKYIGHPLFNDAMYGGDKIRKGTQFSKYKTFVQNCFDLIPR 301

Query: 288 LYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
             LHA  +   HP    ++     LP       + 
Sbjct: 302 QALHAMSLGFIHPVSKEKVYYEVGLPKDFADVLEK 336


>gi|121604767|ref|YP_982096.1| RluA family pseudouridine synthase [Polaromonas naphthalenivorans
           CJ2]
 gi|120593736|gb|ABM37175.1| ribosomal large subunit pseudouridine synthase D [Polaromonas
           naphthalenivorans CJ2]
          Length = 344

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 80/330 (24%), Positives = 141/330 (42%), Gaps = 25/330 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQV 64
            +++V V  +    RLD+      P  +   LQ+++  G V V   K +K + ++++G  
Sbjct: 35  ELRHVSVPVESHGCRLDKALAGLVPEFSRSYLQQLIEDGGVLVKGLKAIKTSAKVKAGDE 94

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I       +   K ++              +   ++YED  + V NKPAG+ V    G
Sbjct: 95  LTIELRPTPQSQAFKPEE--------------MALDIVYEDRHLIVVNKPAGLVVHPAPG 140

Query: 125 I--AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                 ++G L     +    +  + HRLD++TSG++VVAR R     L      R + +
Sbjct: 141 NWSGTLLNGLLAHDPQASFMPRAGIVHRLDKDTSGLMVVARQRQTMDQLVSMIAARTVSR 200

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L  G  +  K       + +       + VV   +     A +   ++D  A+K C
Sbjct: 201 EYIALAHGTWEGAKTRQVEAPIGRDPRNRLRMAVVDLEKNSGKAASTVISLLD-NAEKHC 259

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++ + HTGRTHQ+RVH   +G P+V D  Y     G+       +  LHA  +   HP 
Sbjct: 260 LVKCKLHTGRTHQIRVHMAFLGHPLVSDEVYGGAVAGSL-----QRQALHACRLAFAHPV 314

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFKYDRNL 330
            G  ++  +  P  +       G +Y++ L
Sbjct: 315 TGAAMEFKSLPPPDLEMAIAGFGLRYNQAL 344


>gi|317401917|gb|EFV82523.1| pseudouridine synthase [Achromobacter xylosoxidans C54]
          Length = 321

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 97/325 (29%), Positives = 159/325 (48%), Gaps = 22/325 (6%)

Query: 2   SLM--TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           S M    V+ V V  +    RLD +       +   ++ K +R G+VRV+K R+  + R+
Sbjct: 12  SPMATPSVRMVEVGAEHAGQRLDNYLMRLCKGVPKTHIYKAIRGGEVRVNKGRISVDYRV 71

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G +VRIPP+                     +     +  +++ED  + V +KPAG++V
Sbjct: 72  AEGDMVRIPPLRL-------------PDPGKPRPVPAAEFPVVFEDDAMLVVDKPAGVAV 118

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++    + +   L HRLD+ETSG+L+VA+ R+A   L    R  R 
Sbjct: 119 HGGSGVSFGVIEQLRAAR-PEAKFLELVHRLDRETSGLLMVAKKRSALLALHAMLREGRS 177

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y++LV G   N ++ I   L K +   G+    V  + + A+  I+    +     +
Sbjct: 178 DKHYYALVEGDWVNDRQHIKLSLSKWTTQSGERRVKVDPDGQTAHTIIT----LKQRFGR 233

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
           +  ++ +  TGRTHQ+RVH    G PIVGD KY  +  +  F+     +++LHA  + L 
Sbjct: 234 YSLVDAELRTGRTHQIRVHLAASGFPIVGDDKYGHDEVRAEFSRMGFGRMFLHAHQLTLN 293

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  G  + +TA LP    K    L
Sbjct: 294 HPLTGEPMTLTAELPPACRKILKQL 318


>gi|16803883|ref|NP_465368.1| hypothetical protein lmo1843 [Listeria monocytogenes EGD-e]
 gi|47097693|ref|ZP_00235203.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|224500073|ref|ZP_03668422.1| hypothetical protein LmonF1_10499 [Listeria monocytogenes Finland
           1988]
 gi|224501356|ref|ZP_03669663.1| hypothetical protein LmonFR_02345 [Listeria monocytogenes FSL
           R2-561]
 gi|254829161|ref|ZP_05233848.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL N3-165]
 gi|254831556|ref|ZP_05236211.1| hypothetical protein Lmon1_09383 [Listeria monocytogenes 10403S]
 gi|254899460|ref|ZP_05259384.1| hypothetical protein LmonJ_06589 [Listeria monocytogenes J0161]
 gi|254912401|ref|ZP_05262413.1| conserved hypothetical protein [Listeria monocytogenes J2818]
 gi|254936728|ref|ZP_05268425.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|255027649|ref|ZP_05299635.1| hypothetical protein LmonocytFSL_17157 [Listeria monocytogenes FSL
           J2-003]
 gi|284802289|ref|YP_003414154.1| hypothetical protein LM5578_2045 [Listeria monocytogenes 08-5578]
 gi|284995431|ref|YP_003417199.1| hypothetical protein LM5923_1996 [Listeria monocytogenes 08-5923]
 gi|16411297|emb|CAC99921.1| lmo1843 [Listeria monocytogenes EGD-e]
 gi|47013931|gb|EAL04954.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|258601571|gb|EEW14896.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL N3-165]
 gi|258609325|gb|EEW21933.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|284057851|gb|ADB68792.1| hypothetical protein LM5578_2045 [Listeria monocytogenes 08-5578]
 gi|284060898|gb|ADB71837.1| hypothetical protein LM5923_1996 [Listeria monocytogenes 08-5923]
 gi|293590383|gb|EFF98717.1| conserved hypothetical protein [Listeria monocytogenes J2818]
          Length = 303

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 143/323 (44%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++E      R+D+         +   +Q +L++G + V+ +  K N ++Q G  +  
Sbjct: 4   ETLIIEESHARERVDKVIAEMM-GKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                    ++ E   LD               + +ED  + V NKP G+ V   +G A 
Sbjct: 63  EVREPEELEVLAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHAS 107

Query: 127 -YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 108 GTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + +      + VV+        A +HF+V++     + 
Sbjct: 168 EYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVLERLP-GYT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH  ++G P+ GD KY         +   N  +LHA  +   HP 
Sbjct: 222 LINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTIKGNGQFLHAAKLGFDHPT 276

Query: 302 G-GRLQITAPLPAHMVKTWDSLG 323
              R+   APLP+   K   SL 
Sbjct: 277 TNERMTFEAPLPSSFEKALKSLR 299


>gi|332799431|ref|YP_004460930.1| pseudouridine synthase, RluA family [Tepidanaerobacter sp. Re1]
 gi|332697166|gb|AEE91623.1| pseudouridine synthase, RluA family [Tepidanaerobacter sp. Re1]
          Length = 308

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 90/329 (27%), Positives = 148/329 (44%), Gaps = 32/329 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M       V  D+E  RLD +  +     +   L+K +  G ++V+   VK N R++   
Sbjct: 1   MDNKYAFTVTRDDEKKRLDIFLADKLQD-SRSFLKKGIVEGWIKVNGSIVKPNYRLRQED 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +  ++      + +   +++ED  I V NKP G+ V    
Sbjct: 60  QIIVT---------------VPQALQPLIDPEDIPLDIIFEDRDIVVINKPRGMVVYPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      I+  L    D   +    +P + HRLD++TSG++VVA+   A  +L++  + R
Sbjct: 105 GNYSGTLINALLNHTKDLSARGGTMRPGIVHRLDKDTSGVIVVAKNDTAHINLSKQLKSR 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K+Y +LVWG  +  K  I   + +   I    + V     K +  AI+HFKV++ F 
Sbjct: 165 EVKKVYQTLVWGKVQEDKATINAPIGRH-PIKRKEMAV---TTKNSKEAITHFKVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            +F +LE+   TGRTHQ+RVH   +G PIVGD  Y                 LHA  +  
Sbjct: 220 DEFTFLEVAIETGRTHQIRVHMKFIGHPIVGDPIYSRKK----VPFEIKGQALHAYKLGF 275

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP   + ++  APLP  M    + L  +
Sbjct: 276 CHPSNNQYMEFEAPLPDDMSLILNILRNR 304


>gi|329956079|ref|ZP_08296850.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
 gi|328524838|gb|EGF51892.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
          Length = 356

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 81/332 (24%), Positives = 147/332 (44%), Gaps = 38/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQEMMRVDKYLFDRLTNASRNRIQKAADAGFVMANDKPVKSSYKVKPLDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +++   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYENEVIPEDIPLD---------IVYEDKYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNAIAWHMKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRR 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +  +  I   + +      D + +    +    +A++H++V++        
Sbjct: 198 YRALVWGNVEQDEGTIIGNVGRNPK---DRMQMTVLPDDQGKHAVTHYRVLERLG-YVTL 253

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +     T   +             +  L
Sbjct: 254 VECILETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFDTCPRQAL 313

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G  +  T+ LP  M +  D 
Sbjct: 314 HAMTLGFVHPVTGEEMYFTSELPDDMSRLIDK 345


>gi|224536385|ref|ZP_03676924.1| hypothetical protein BACCELL_01259 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224521998|gb|EEF91103.1| hypothetical protein BACCELL_01259 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 357

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 86/343 (25%), Positives = 153/343 (44%), Gaps = 39/343 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ I  
Sbjct: 33  VVVDRGQEMMRVDKYLFDRLTNASRNRIQKSAEAGFVMANNKPVKSSYKVKPMDVITIMM 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 93  -----DRPRYENEVIPEDIPLN---------IIYEDKYLMVVNKPAGLVVHPGHGNYQGT 138

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 139 LVNAIAWHMKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGMQFFNKTTKRR 198

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +  +  I   + +      D + +    +    +A++H++V++        
Sbjct: 199 YRALVWGTVEQDEGTITGNIGRNP---RDRMQMTVLPDDQGKHAVTHYRVLERLG-YVTL 254

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +  L
Sbjct: 255 VECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPRQAL 314

Query: 291 HARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL-GFKYDRNLY 331
           HA  +   HP  G  +  T+ +P  M    D   G+  +R+L 
Sbjct: 315 HAMTLGFVHPATGEEMYFTSEMPEDMTLLIDKWRGYISNRDLE 357


>gi|121601705|ref|YP_988611.1| RluA family pseudouridine synthase [Bartonella bacilliformis KC583]
 gi|120613882|gb|ABM44483.1| pseudouridine synthase, RluA family [Bartonella bacilliformis
           KC583]
          Length = 336

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 92/345 (26%), Positives = 151/345 (43%), Gaps = 45/345 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           +   + + D    R+D+W   HY   ++   LQ ++R G +++D K V     +I+S Q 
Sbjct: 1   MTQQITDEDALGQRIDQWLAKHYQNELSRSRLQTLIREGYLKIDGKLVTEPKTKIKSNQT 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +                + +  N     + +   +L+ED  I V NKPAG+ V  G G
Sbjct: 61  IELT---------------IPTLNNAYPEGEAIPLHILFEDDHIIVVNKPAGLVVHPGHG 105

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +    DS       ++P + HRLD+ TSG++VVA+   A + L+  F   
Sbjct: 106 NWTGTLVNALIYHCGDSLSGIGGVRRPGIVHRLDKNTSGVIVVAKNDLAHKGLSAQFSDH 165

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                + + Y +L+WG P      I   L + +        V+  +   A +A++HF VI
Sbjct: 166 GRTGVLDRRYHALIWGSPNRNIGVITASLGR-ARYDRTKQAVIHSHNIYARHAVTHFSVI 224

Query: 234 DCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP---- 283
           + +            LE +  TGRTHQ+RVH  H+G P+VGD  Y   FK          
Sbjct: 225 EKYQTCADKIPFASLLECRLETGRTHQIRVHMAHIGHPLVGDTVYGNAFKTKSNRFDSTI 284

Query: 284 -----IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                + N+  LHA  +   HP  G  +  +APLP  M +  +  
Sbjct: 285 KEAIDLFNRQALHAASLTFEHPAKGNIMSFSAPLPQDMAELINHF 329


>gi|159029548|emb|CAO87700.1| rluD [Microcystis aeruginosa PCC 7806]
          Length = 308

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 151/328 (46%), Gaps = 32/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M  +   V    E   RLD W  +  P ++   LQK++  G ++++ +     N ++  G
Sbjct: 1   MNQLNLEVAGKKE---RLDAWMGSQLPDLSRSRLQKLIEQGYIQLNGQICTNKNTKVGQG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             ++I                +  S  L   ++ +   +LYED  + + NKPA + V   
Sbjct: 58  DRLKIT---------------IPDSQPLQLSAEAIDLDILYEDEYLIIINKPADLVVHPA 102

Query: 123 SGIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++  L    +  G    Q+P + HRLD++T+G +V+A+T  A QHL    + 
Sbjct: 103 PGHESGTLVNALLHHCPNLAGIGGIQRPGIVHRLDKDTTGAIVIAKTDQAHQHLQAQLKT 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           +  ++ Y +LV G+PK++   I   + +  H        +   EKG   A++H++V +  
Sbjct: 163 KTARREYMALVHGVPKSETGTIDLPISR--HRSDRQKMAIIAVEKGGRNAVTHWQVKERL 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  +E +  TGRTHQ+RVH+ H+G PI+GD  Y +        P      LHA  + 
Sbjct: 221 G-NYTLMEFRLETGRTHQIRVHSSHIGHPILGDPLYSSGRSIGINLPG---QLLHAYRLI 276

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           L HP  G  L+  APLPA   K    L 
Sbjct: 277 LIHPVTGESLEAIAPLPAIFPKVLAILR 304


>gi|147669825|ref|YP_001214643.1| ribosomal large subunit pseudouridine synthase D [Dehalococcoides
           sp. BAV1]
 gi|289433036|ref|YP_003462909.1| pseudouridine synthase [Dehalococcoides sp. GT]
 gi|146270773|gb|ABQ17765.1| ribosomal large subunit pseudouridine synthase D [Dehalococcoides
           sp. BAV1]
 gi|288946756|gb|ADC74453.1| pseudouridine synthase, RluA family [Dehalococcoides sp. GT]
          Length = 300

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 78/323 (24%), Positives = 149/323 (46%), Gaps = 34/323 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +  +    RLD++       ++   +Q+++ SG + V+ +  K + R+++G  + 
Sbjct: 1   MRTFKLVAETAGERLDKYITQKESGLSRSFIQELVSSGHILVNNQSAKPSLRLKTGDTIT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I       + +  E   L+               ++++D  + + NKP G++V    G  
Sbjct: 61  IEIPPETPSELKAENIPLE---------------IIFQDKDLLLINKPPGLTVHPAPGHP 105

Query: 127 YHI--DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            H   +G L    + +      +P + HRLD++TSG+L+VA+ R A  +L+  F+ R ++
Sbjct: 106 DHTLVNGVLALEPEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRQALANLSAQFKERTVR 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  +  +  I   L +        + VV        +A + +KV+  + Q +
Sbjct: 166 KYYLALVKGELRPAEGFIEAPLGRD-PQNRQKIAVVS----DGRHARTGYKVL-RYIQGY 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE++  TGRTHQ+RVH   +G P+ GD  Y              + +LHA  +    P
Sbjct: 220 SLLEVKLETGRTHQIRVHFAAIGHPVAGDAVYGQKESWV------KRQFLHAHRLSFALP 273

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G+ ++ T+PLP  + +    L
Sbjct: 274 SNGQVVEFTSPLPPDLEEALKIL 296


>gi|110833922|ref|YP_692781.1| ribosomal large subunit pseudouridine synthase C [Alcanivorax
           borkumensis SK2]
 gi|110647033|emb|CAL16509.1| Ribosomal large subunit pseudouridine synthase C [Alcanivorax
           borkumensis SK2]
          Length = 317

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 103/323 (31%), Positives = 169/323 (52%), Gaps = 17/323 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V +V ++      RLD +   H   +    + +I+RSG+VRV+K R K   R+ +G V
Sbjct: 9   NRVTFVTIDEGRHGQRLDNFLFTHLKGVPKSRVYRIIRSGEVRVNKGRAKQTTRLCTGDV 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP+  + +           +      ++ L+   +YED +++VFNKPAG++V GGSG
Sbjct: 69  VRVPPIRTSDS--------TAPAAVSEGLAERLRRACVYEDDQLFVFNKPAGLAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++  +   L+     + ++  L HRLD++TSG+++VAR R+  + L    +  +I+K YW
Sbjct: 121 VSLGLIEALRVMFPQE-RELELVHRLDRDTSGLIMVARRRSFLRKLQRLMQGGQIEKRYW 179

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            L  G  K K+  +   LLK  +     V V ++       +++HF++++ FAQ    +E
Sbjct: 180 LLCQGF-KGKERTLDAPLLKMMNGNERIVRVSRE----GKPSVTHFRLLERFAQ-AQLVE 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
               TGRTHQ+RVH+   G  ++GD KY  A  +       + +L LHAR +   HP  G
Sbjct: 234 ATLETGRTHQIRVHSQFGGFALLGDSKYGIAKGEALLAEIGRRRLCLHARTLVFVHPNTG 293

Query: 304 -RLQITAPLPAHMVKTWDSLGFK 325
            RL +TAPL         +L  K
Sbjct: 294 KRLTVTAPLDDDYEAILTALRSK 316


>gi|152996325|ref|YP_001341160.1| RluA family pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150837249|gb|ABR71225.1| pseudouridine synthase, RluA family [Marinomonas sp. MWYL1]
          Length = 323

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 97/317 (30%), Positives = 164/317 (51%), Gaps = 16/317 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+YV ++++    R+D +       +    +  +LR G++RV+KKR K + R+Q+  VVR
Sbjct: 14  VRYVTIDDNNTGQRIDNFLVTFLKGVPKGKIYNLLRKGEIRVNKKRTKPDYRLQNEDVVR 73

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I P++ A           D  V   +    ++S ++YED  + V NKP+G++V GGSG++
Sbjct: 74  IAPIVIAPES--------DKPVLSDRLKSEIESRIVYEDKGLIVINKPSGLAVHGGSGLS 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWS 185
           + +   ++     +     L HRLD++TSG+++VA+ RA  + L  + R +  +QK Y +
Sbjct: 126 FGLVEVIRQMRPLEKF-IELVHRLDRDTSGLIMVAKKRAVLKELHTALREKEGVQKTYLA 184

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV+G    +K  +   LLK     G+ V  V  +      +++ FK++    + +  +E 
Sbjct: 185 LVYGSWPKRKLQVNAPLLKNELQSGERVVRVHTD---GKESLTRFKLV-RQFEGYSLVEC 240

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +P TGRTHQ+RVH  + G PIVGD KY  A       +    +L LHA  +D+    G R
Sbjct: 241 EPVTGRTHQIRVHTQYAGYPIVGDEKYSPAESLKETRALGFKRLCLHATRLDI-MLNGER 299

Query: 305 LQITAPLPAHMVKTWDS 321
           +   APL        + 
Sbjct: 300 MLFEAPLDKEWQTLMNE 316


>gi|116627406|ref|YP_820025.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMD-9]
 gi|116100683|gb|ABJ65829.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMD-9]
          Length = 296

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 74/315 (23%), Positives = 141/315 (44%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++     + +++G V V+ K  K    ++ G V+          
Sbjct: 7   EAGNRLDKSLAD-LTELSRSQANEAIKAGTVLVNGKLAKAKYVVKEGDVIT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFL 133
           +++ E+++L+        ++ +   ++YED+ + V NKP GI V   +G      ++  +
Sbjct: 57  YVLPEEEVLE------YKAEDIPLDIIYEDADVAVVNKPQGIVVHPSAGHTSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++V G
Sbjct: 111 YHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +            K        A++ F V++ F   +  +E+Q  T
Sbjct: 171 NLPNDRGVIEAPIGRSDKDRKKQAVTAK-----GKPAVTRFTVLERFG-NYTLVELQLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G L + T
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLKGHGQFLHAKTLGFTHPTTGELVEFT 279

Query: 309 APLPAHMVKTWDSLG 323
           A  P    +T + L 
Sbjct: 280 AEEPIIFKETLEKLR 294


>gi|217964005|ref|YP_002349683.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HCC23]
 gi|290893028|ref|ZP_06556017.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J2-071]
 gi|217333275|gb|ACK39069.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HCC23]
 gi|290557388|gb|EFD90913.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J2-071]
 gi|307571425|emb|CAR84604.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes L99]
 gi|313608111|gb|EFR84172.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL F2-208]
          Length = 302

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 81/323 (25%), Positives = 143/323 (44%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++E      R+D+         +   +Q +L+SG + V+ +  K N ++Q G  +  
Sbjct: 4   ETLIIEESHARERVDKVIAEMM-GKSRSAIQLMLKSGDITVNGELAKPNYKVQVGDEIHY 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                    ++ E   LD               + +ED  + V NKP G+ V   +G A 
Sbjct: 63  EVREPEELEVLAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHAS 107

Query: 127 -YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 108 GTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + +      + VV+        A +HF+V++     + 
Sbjct: 168 EYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVLERLP-GYT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH  ++G P+ GD KY         +   N  +LHA  +   HP 
Sbjct: 222 LINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTIKGNGQFLHAAKLGFDHPT 276

Query: 302 G-GRLQITAPLPAHMVKTWDSLG 323
              R+   APLP+   K   SL 
Sbjct: 277 TNERMTFEAPLPSSFEKALKSLR 299


>gi|171317151|ref|ZP_02906353.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MEX-5]
 gi|171097718|gb|EDT42548.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MEX-5]
          Length = 316

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 99/327 (30%), Positives = 157/327 (48%), Gaps = 23/327 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++ +    R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +VR+PP
Sbjct: 2   IEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDIVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A   + +    +                +LYED  + V NKPAG++V GGSG+A+ +
Sbjct: 62  VRVAAADLARADTPIVPPAQFE---------VLYEDDAMLVINKPAGVAVHGGSGVAFGV 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y++   G
Sbjct: 113 IEQMRQAR-PRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFACGHG 171

Query: 190 IPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             ++       +   L K S   G+    V+ +      + + F +++ +   +  +E +
Sbjct: 172 EWQSDWGRRRAVKAPLFKYSTAEGERRVRVQDD---GLPSHTVFNLLERWPD-YALVEAE 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H+G PI GD KY               P   +++LHA  + L HP 
Sbjct: 228 LKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANAQPSLKRMFLHAHRLKLAHPL 287

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFKYD 327
            G  LQ  APLP    +  D L    D
Sbjct: 288 TGEPLQFDAPLPDECRRFLDQLRALRD 314


>gi|53711780|ref|YP_097772.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis YCH46]
 gi|60680012|ref|YP_210156.1| ribosomal large subunit pseudouridine synthase [Bacteroides
           fragilis NCTC 9343]
 gi|265765162|ref|ZP_06093437.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_16]
 gi|52214645|dbj|BAD47238.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis YCH46]
 gi|60491446|emb|CAH06196.1| ribosomal large subunit pseudouridine synthase [Bacteroides
           fragilis NCTC 9343]
 gi|263254546|gb|EEZ25980.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_16]
          Length = 357

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 84/343 (24%), Positives = 150/343 (43%), Gaps = 38/343 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    + +I+   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYDNEIIPEDIPLH---------IVYEDKYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNAIAWHLKDNPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGVQFFNKTTKRR 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI    +  I   + +           V  +     +A++H++V++        
Sbjct: 198 YRALVWGIVDQDEGTIVGSIARNPK--DRMQMAVMADPTQGKHAVTHYRVLERLG-YVTL 254

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +  L
Sbjct: 255 VECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPRQAL 314

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL-GFKYDRNLY 331
           HA  +   HP  G  +  T+ LP  M +  +   G+  +R+L 
Sbjct: 315 HAMTLGFVHPVTGEEMHFTSELPDDMTRLIEKWRGYISNRDLE 357


>gi|317474426|ref|ZP_07933700.1| RluA family pseudouridine synthase [Bacteroides eggerthii
           1_2_48FAA]
 gi|316909107|gb|EFV30787.1| RluA family pseudouridine synthase [Bacteroides eggerthii
           1_2_48FAA]
          Length = 356

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 147/332 (44%), Gaps = 38/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E MR+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQEMMRVDKYLFDRLTNASRNRIQKAADAGFVMANDKPVKSSYKVKPLDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +++   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYENEVIPEDIPLN---------IVYEDKFLMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        ++      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNAIAWHMKDIPDYNANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRR 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG  +  +  I   + +      D + +    +    +A++H++V++        
Sbjct: 198 YRALVWGNVEQDEGTIVGNVGRNPK---DRMQMTVLPDDQGKHAVTHYRVLERLG-YVTL 253

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +     T   +             +  L
Sbjct: 254 VECVLETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFAKYKQFVNNCFDTCPRQAL 313

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G  +  T+ LP  M +  D 
Sbjct: 314 HAMTLGFVHPVTGEEMYFTSELPDDMTRLIDK 345


>gi|55820603|ref|YP_139045.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMG 18311]
 gi|55736588|gb|AAV60230.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMG 18311]
 gi|312277926|gb|ADQ62583.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 296

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 72/315 (22%), Positives = 141/315 (44%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++     + +++G V V+ K  K    ++ G V+          
Sbjct: 7   EAGNRLDKSLAD-LTELSRSQANEAIKAGTVLVNGKSAKAKYVVKEGDVIT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFL 133
           +++ E+++L+        ++ +   ++YED+ + V NKP G+ V   +G      ++  +
Sbjct: 57  YVLPEEEVLE------YKAEDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++V G
Sbjct: 111 YHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +            K        A++ F V++ F   +  +E+Q  T
Sbjct: 171 NLPNDRGVIEAPIGRSDKDRKKQAVTAK-----GKPAVTRFTVLERFG-NYTLVELQLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G+L +  
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLKGHGQFLHAKTLGFTHPTTGKLVEFN 279

Query: 309 APLPAHMVKTWDSLG 323
           A  P    +T + L 
Sbjct: 280 AEEPIIFKETLEKLR 294


>gi|261749573|ref|YP_003257259.1| ribosomal large subunit pseudouridine synthase D [Blattabacterium
           sp. (Periplaneta americana) str. BPLAN]
 gi|261497666|gb|ACX84116.1| ribosomal large subunit pseudouridine synthase D [Blattabacterium
           sp. (Periplaneta americana) str. BPLAN]
          Length = 344

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 88/363 (24%), Positives = 168/363 (46%), Gaps = 46/363 (12%)

Query: 4   MTYVQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M+  ++   VE  ++ +R+D++ +    +I+   +QK   SG++ V++  +K N +I+  
Sbjct: 1   MSIKKFKFFVEKYQKTIRIDKFLRKSIQNISRNQIQKATNSGKILVNQCIIKKNYKIKPF 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +V            I    ILDS       ++ +   +LYED  I V NK AG+ V  G
Sbjct: 61  DLVE---------AEIYYPPILDSEYK-NIIAENIPLNILYEDEDILVINKAAGMVVHPG 110

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                     GI YH     + +      +  L HR+D++T+G+LV+A+   A ++L + 
Sbjct: 111 FGNEKGTLIHGIKYHFKNNHQLY------RLGLVHRIDKDTTGLLVLAKNEYAQKYLFQQ 164

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  + IQ+ Y +LVWG  + ++  I+ ++ +  +     + + ++N   + Y+++H+KV+
Sbjct: 165 FISKTIQRKYLALVWGNIQKQEGTISGFIGRDPN-NRKRMTLFQRNFYRSRYSVTHYKVL 223

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-------------GNF 280
           + F +   ++     TG+THQ+RVH  ++G P+  D  Y  +                  
Sbjct: 224 ERF-KYLTYVSCNLETGKTHQIRVHFKYLGHPLFNDSTYGGDKIFMKKYLSKKSIDFFKD 282

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           +  +  +  LHA  +   HP+  +   T  +P    K    L     RN Y      ++E
Sbjct: 283 SLNLLKRQALHAGSLSFIHPKNRKCHFTCSIPEDFKKVLQKL-----RNQYFITRSPEEE 337

Query: 341 CKQ 343
            K+
Sbjct: 338 YKR 340


>gi|241890118|ref|ZP_04777416.1| ribosomal large subunit pseudouridine synthase D [Gemella
           haemolysans ATCC 10379]
 gi|241863740|gb|EER68124.1| ribosomal large subunit pseudouridine synthase D [Gemella
           haemolysans ATCC 10379]
          Length = 299

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 82/313 (26%), Positives = 148/313 (47%), Gaps = 38/313 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D++ +     ++  N+Q ++  G ++VD   +K N +++ G V+ I         ++
Sbjct: 14  ERIDKFLQQELTDVSRTNIQNLISEGYIKVDGNNIKTNYKLKEGNVITIDYKEPEELDVV 73

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K+   +D               ++YED+ + + NK  G+ V    G   H DG L + + 
Sbjct: 74  KQDIPVD---------------IVYEDNDLIIVNKAKGMVVHPSVG---HKDGTLVNALL 115

Query: 139 SKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +        +P + HR+D++TSG+L+VA+   A   L+E    + +++ Y++LV G 
Sbjct: 116 FHSELSSINGTIRPGIVHRIDKDTSGLLIVAKNDKAHVKLSEMIANKDVKRKYYALVHGS 175

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K+    I   + +      +   +          +I+HFKVID F +K+  +E +  TG
Sbjct: 176 IKHDYGTIDAPIARNPKERKEMAII-----DEGKPSITHFKVIDRF-EKYTLIECELETG 229

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++  P+VGD  Y      N      N   LH++ ++  HP  G  L    
Sbjct: 230 RTHQIRVHMKYINHPLVGDPVYGPRKTLNT-----NGQALHSKSIEFNHPITGEHLYFET 284

Query: 310 PLPAHMVKTWDSL 322
            +P +MV+T   L
Sbjct: 285 EIPEYMVETMSKL 297


>gi|300087236|ref|YP_003757758.1| RluA family pseudouridine synthase [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
 gi|299526969|gb|ADJ25437.1| pseudouridine synthase, RluA family [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
          Length = 301

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 93/315 (29%), Positives = 150/315 (47%), Gaps = 33/315 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            D E  RLDR+     P  +  +LQ+++R G V V+ +  +  + ++ G  V +      
Sbjct: 13  ADREGWRLDRYLAEKLPDRSRASLQELIREGFVTVNGRPARPASPLKPGDRVTVE----- 67

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDG 131
                     L      T  ++ +   ++YED  + V +KPAG++     G      ++ 
Sbjct: 68  ----------LPPPAPTTATAEDIPLTVIYEDEDLAVIDKPAGLTTHPAPGHPAGTLLNA 117

Query: 132 FLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            L       DS   +P + HRLD++TSG++VVAR+R A   L++ FR R + K+Y +LV 
Sbjct: 118 LLSRFPELRDSGLDRPGIVHRLDKDTSGLMVVARSRQAHARLSDQFRNREVTKVYLALVR 177

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  +  +  I   + +        + V +Q       A S FKVI  F +    LE++ +
Sbjct: 178 GCVEPAEGIIEAAIGRHRTQ-RKKMTVSEQ----GREARSRFKVIRRF-RNHTLLEVRIY 231

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH   +G P++GD  Y A       SP   + +LHA  +   HP  GR +  
Sbjct: 232 TGRTHQIRVHLAAIGHPVIGDATYGAE------SPDFPRQFLHAHRLGFRHPTDGRKMSF 285

Query: 308 TAPLPAHMVKTWDSL 322
           T+ LPA +    + L
Sbjct: 286 TSELPADLAGPLERL 300


>gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudouridine synthase C [Herbaspirillum
           seropedicae SmR1]
 gi|300073996|gb|ADJ63395.1| ribosomal large subunit pseudouridine synthase C protein
           [Herbaspirillum seropedicae SmR1]
          Length = 355

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 99/324 (30%), Positives = 163/324 (50%), Gaps = 26/324 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ + + ++E   R+D +       +   ++ ++LRSG+VRV+K R+    R+  G V
Sbjct: 31  PQVQLLTISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLAEGDV 90

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP+           ++ +    +   ++F    +L EDS + V +KPAG++V GGSG
Sbjct: 91  VRVPPI-----------RVAEKQETVVPGAEF---RILLEDSHLLVIDKPAGVAVHGGSG 136

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++Y +   L++      +   L HRLD++TSG+L++A+ R+A  +L +  R     K Y+
Sbjct: 137 VSYGVIEQLRAARPQ-AKFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYF 195

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  KN ++ +   L K S   G+    V+ +      + + F ++  F   F  LE
Sbjct: 196 TLVQGDWKNARQHVKLPLFKYSTPDGERRVRVQAD---GQPSHTVFSLLRRFGD-FALLE 251

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC------ANFKGNFTSPIQNKLYLHARYMDLP 298
            +  TGRTHQ+RVH    G PIVGD KY       A  K +       +++LHA  +   
Sbjct: 252 AELKTGRTHQIRVHLSSSGFPIVGDDKYGDFALNKALQKADGRRIAFKRMFLHAWRISFR 311

Query: 299 HPEGG-RLQITAPLPAHMVKTWDS 321
           HPE G  + + A LP        S
Sbjct: 312 HPESGDTVTLKAGLPQECASFLRS 335


>gi|225858727|ref|YP_002740237.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae 70585]
 gi|225722071|gb|ACO17925.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae 70585]
          Length = 295

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 146/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETGGLRLDKALSD-LSELSRSFANEQIKSGQVLVNGQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G+ 
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGKT 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+  A +P    +T + L 
Sbjct: 276 LEFKADIPEIFKETLERLR 294


>gi|116873278|ref|YP_850059.1| ribosomal large subunit pseudouridine synthase [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|116742156|emb|CAK21280.1| Ribosomal large subunit pseudouridine synthase [Listeria welshimeri
           serovar 6b str. SLCC5334]
          Length = 302

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 82/323 (25%), Positives = 143/323 (44%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++E      R+D+         +   +Q +L++G + V+ +  K N ++Q G  +  
Sbjct: 4   ETLIIEESHARERVDKVIAEMM-GKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                    ++ E   LD               + +ED  + V NKP G+ V   +G A 
Sbjct: 63  EIREPEELEVLAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHAS 107

Query: 127 -YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 108 GTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + +      + VV+        A +HF+V++     + 
Sbjct: 168 EYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVLERLP-GYT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH  ++G P+ GD KY         +   N  YLHA  +   HP 
Sbjct: 222 LINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTIKGNGQYLHAAKLGFDHPT 276

Query: 302 G-GRLQITAPLPAHMVKTWDSLG 323
              R+   APLPA   K   SL 
Sbjct: 277 TNERMTFEAPLPASFEKALKSLR 299


>gi|220927321|ref|YP_002502623.1| RluA family pseudouridine synthase [Methylobacterium nodulans ORS
           2060]
 gi|219951928|gb|ACL62320.1| pseudouridine synthase, RluA family [Methylobacterium nodulans ORS
           2060]
          Length = 337

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 90/348 (25%), Positives = 154/348 (44%), Gaps = 48/348 (13%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQS 61
           + + V+   +   E   RLDR     +P ++   LQ ++R G VR+D   ++    R+  
Sbjct: 1   MESEVRVAEIPAGEAPERLDRALARTWPDLSRSRLQGLIREGGVRLDGAEIRDAAVRVAG 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           GQ V +                +  +   T  ++    I+ YED  + V +KP G+ V  
Sbjct: 61  GQTVAVT---------------VPPARPATPEAEERALIIPYEDDDLIVIDKPPGLVVHP 105

Query: 122 GSGIAYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
             G   H  G L + + +            ++P + HRLD++TSG+LVVA+   A   L+
Sbjct: 106 APG---HDSGTLVNALIAHCGASLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDMAHAALS 162

Query: 172 ESFRMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             F       ++++ Y +LVWG+P+ +   I   L + S    + + VV+  +    +AI
Sbjct: 163 LQFADHGRSGQLERAYLALVWGVPEPRAGRIDAALAR-SDSNREKIAVVRPEK--GRHAI 219

Query: 228 SHFKVIDCFA--QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-------- 277
           +H++        +    +  +  TGRTHQ+RVH  H G P++GD  Y A F+        
Sbjct: 220 THYRTEAVLGVREPVGLVRCRLETGRTHQIRVHLAHRGHPLLGDATYGAAFRTKAARLEP 279

Query: 278 -GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                     +  LHA  +   HP     L+  +PLPA + +   +LG
Sbjct: 280 EARAALDALGRQALHAAVLGFVHPRTNAFLRFESPLPADLARLVAALG 327


>gi|148261702|ref|YP_001235829.1| RluA family pseudouridine synthase [Acidiphilium cryptum JF-5]
 gi|146403383|gb|ABQ31910.1| ribosomal large subunit pseudouridine synthase D [Acidiphilium
           cryptum JF-5]
          Length = 332

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 79/329 (24%), Positives = 136/329 (41%), Gaps = 37/329 (11%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
              +   RLDR+  +    ++   L+ ++ +G V  D   ++  +  ++ G +  +    
Sbjct: 17  TEADGGERLDRFLASRLSEMSRSRLKALIEAGTVTCDGAVIRLPSAAVRPGAIYTVALPP 76

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
                                    L   +LYEDS + V +KPAG+ V    G      +
Sbjct: 77  AIP---------------AAPQGQALDLTVLYEDSDLIVIDKPAGLVVHPAPGNPDGTLV 121

Query: 130 DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +  +    DS       ++P + HRLD++TSG++V A+T  A   L+ +F  R + + Y 
Sbjct: 122 NALIAHCGDSLAGIGGERRPGIVHRLDKDTSGVMVAAKTELALNALSAAFAARDLDREYL 181

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L WG P+  +  I   + +        + VV    +G   A+++++ +  F      L 
Sbjct: 182 ALCWGAPQPAEGEIEGPIGRDPR-DRKRMAVV---ARGGKPALTYYRTLRRFGLGATLLA 237

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NKLYLHARYM 295
            +  TGRTHQ+RVH    G P+VGD  Y        +   Q          +  LHA  +
Sbjct: 238 CRLATGRTHQIRVHLASRGHPLVGDPVYLRRRPAAASQMQQPQRDFLLDFPRQALHAATL 297

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
              HP  G +L+  A  PA +      LG
Sbjct: 298 GFAHPRSGAKLRFEAAPPADLATLLSHLG 326


>gi|315303759|ref|ZP_07874262.1| ribosomal large subunit pseudouridine synthase D [Listeria ivanovii
           FSL F6-596]
 gi|313627868|gb|EFR96498.1| ribosomal large subunit pseudouridine synthase D [Listeria ivanovii
           FSL F6-596]
          Length = 302

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 82/323 (25%), Positives = 145/323 (44%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++E      R+D+         +   +Q +L++G + V  +  K N ++Q G  + +
Sbjct: 4   ETLIIEEKNARERIDKAVAE-LTGKSRSAIQIMLKNGDITVSGEIAKPNYKVQVGDEIHL 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                    ++ E   LD               + +ED  + V NKP G+ V   +G A 
Sbjct: 63  EVREPEELEVLAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHAS 107

Query: 128 HI--DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
               +  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 108 STLVNALLFHCKDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + +      + VV+        A +HF+VI+   + + 
Sbjct: 168 EYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVIERL-EGYT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            +  +  TGRTHQ+RVH  ++G P+ GD KY         +   N  +LHA  +   HP 
Sbjct: 222 LINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTLKGNGQFLHAAKLGFDHPA 276

Query: 301 EGGRLQITAPLPAHMVKTWDSLG 323
            G R+   APLP+  VK   +L 
Sbjct: 277 TGERMTFEAPLPSSFVKALKTLR 299


>gi|313675550|ref|YP_004053546.1| ribosomal large subunit pseudouridine synthase d [Marivirga
           tractuosa DSM 4126]
 gi|312942248|gb|ADR21438.1| ribosomal large subunit pseudouridine synthase D [Marivirga
           tractuosa DSM 4126]
          Length = 343

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 73/337 (21%), Positives = 146/337 (43%), Gaps = 43/337 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
             + V+  ++ +R+D++  +  P++    +QK ++ G V+V+   +K N ++     +RI
Sbjct: 19  HQIKVDPKQDLLRIDKFLMDRLPNVTRNKVQKAIKDGFVQVNGVTIKPNYKVHPDDNIRI 78

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                          + +   +     + +   ++YEDS + + NK AG+ V        
Sbjct: 79  --------------ALPEPPRDTEVKPENIPLDIVYEDSDLLIVNKEAGMVVHPAH---Q 121

Query: 128 HIDGFLKSWVDSKGQ----------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           + +G L + +    Q          +P L HR+D++TSG+LV+A+T  +   L + F   
Sbjct: 122 NWEGTLVNALAYHFQQLPEMQGNEGRPGLVHRIDKDTSGLLVIAKTEKSMTALAKQFFDH 181

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I++ Y++LVWG  ++++  I   L +        +            AI+H+KV++   
Sbjct: 182 SIERTYYALVWGELEDEEGTIDVNLGRSFK--DRRITDAFPEGDFGRTAITHYKVLERL- 238

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQ 285
           +    ++    TGRTHQ+R H  ++G P+  D  Y  +     T              I 
Sbjct: 239 RYVTLIQCNLETGRTHQIRAHMKYIGHPLFNDATYGGDRILKGTQFSKYKSFVDNCFKII 298

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            +  LHA+ +   HP   + +   + LP    +  + 
Sbjct: 299 PRQALHAKSLGFIHPSSNKSVHFESELPKDFEEVLEK 335


>gi|253564151|ref|ZP_04841608.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_2_5]
 gi|251947927|gb|EES88209.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_2_5]
 gi|301161553|emb|CBW21093.1| ribosomal large subunit pseudouridine synthase [Bacteroides
           fragilis 638R]
          Length = 357

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 84/343 (24%), Positives = 150/343 (43%), Gaps = 38/343 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +QK    G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQAMVRVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKSSYKVKPLDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    + +I+   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 92  -----DRPRYDNEIIPEDIPLH---------IVYEDKYLMVVNKPAGLVVHPGHGNYHGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNAIAWHLKDDPVYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGVQFFNKTTKRR 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI    +  I   + +           V  +     +A++H++V++        
Sbjct: 198 YRALVWGIVDQDEGTIVGSIARNPK--DRMQMAVMADPTQGKHAVTHYRVLERLG-YVTL 254

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +  L
Sbjct: 255 VECILETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDTCPRQAL 314

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL-GFKYDRNLY 331
           HA  +   HP  G  +  T+ LP  M +  +   G+  +R+L 
Sbjct: 315 HAMTLGFVHPVTGEEMHFTSELPDDMTRLIEKWRGYISNRDLE 357


>gi|58337436|ref|YP_194021.1| pseudouridine synthase [Lactobacillus acidophilus NCFM]
 gi|58254753|gb|AAV42990.1| pseudouridine synthase [Lactobacillus acidophilus NCFM]
          Length = 302

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 145/326 (44%), Gaps = 35/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     + V N +   RLD++       ++   ++++++   + V++K  K + +IQ G 
Sbjct: 1   MPKKYSLEVTN-QRG-RLDKFISEQLSDLSRTRVKELIQDQNILVNEKVEKVSYKIQDGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I         I+ E   LD               ++YED  + V NKP G+ V    
Sbjct: 59  KIEITVPAVKPLDIVAENIPLD---------------IVYEDDDVIVVNKPQGMVVHPAP 103

Query: 124 GIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +  L    D     +G +P + HR+D++TSG+L++A+   A + L +    +
Sbjct: 104 GHPDHTLVNALLYHTQDLAQSPEGFRPGIVHRIDKDTSGLLMIAKNATARESLEQQLANK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++IYW++V G    ++  I   + +  +       V     +    AI+HFKV+  F 
Sbjct: 164 TNKRIYWAIVHGNFSEEQGSIDAPIGRNPYDRKKMAVV-----ENGKKAITHFKVLKQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G  + GD  Y         +   N  +LHA+ +  
Sbjct: 218 KGYSLIECQLETGRTHQIRVHLDYIGHAVAGDPLYGPR-----KTLKGNGQFLHAKILGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP+ G+ L+ +   P         L
Sbjct: 273 KHPKTGKWLEFSVEPPKIFQNMLIQL 298


>gi|114797120|ref|YP_759725.1| RluA family pseudouridine synthase [Hyphomonas neptunium ATCC
           15444]
 gi|114737294|gb|ABI75419.1| pseudouridine synthase, RluA family [Hyphomonas neptunium ATCC
           15444]
          Length = 349

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 116/339 (34%), Positives = 179/339 (52%), Gaps = 27/339 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            +    V + E   RLDRW K    +     ++K+LR+GQ+RV+  R K N R+ +   V
Sbjct: 4   QIITETVSDKETGARLDRWIKRRM-NATQGQVEKLLRTGQIRVNGSRAKANTRLVTADEV 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R P          K       S    +  +FL+SI+++ED  +   NKPAG++VQGGSG 
Sbjct: 63  RFPIFAAEDAGARKAANAKQIS---EEDREFLRSIIIHEDDDMLAINKPAGLAVQGGSGQ 119

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             H+DG + + +D  G +P L HRLD++TSG+L++A+  AAA  LTE FR R + K+YW+
Sbjct: 120 GRHVDGLI-AGMDVDGHRPVLVHRLDKDTSGVLLLAKHPAAAARLTELFRSREMDKVYWA 178

Query: 186 LVWGIPKNKKECIANWLLK--------------------KSHIGGDYVHVVKQNEKGANY 225
           +  G+P  +   I  W++K                    +     + +    Q  +GA +
Sbjct: 179 VTVGVPSPQAGQIRCWMVKGVPDINEPSGYRPVDPYATKRRDGDRERMIRSAQGVEGARH 238

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           +I+ + V+     K  W+ M+P TGR HQLR H L M   I+GD+KY    +      + 
Sbjct: 239 SITDYVVVSTAGPKAAWVAMRPETGRMHQLRFHMLEMNTSILGDYKY--KSRREVPQGLA 296

Query: 286 NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
             L+LHAR + +P   G  ++I APLP HM +T+++LGF
Sbjct: 297 EGLHLHARALIIPREHGKPIKIVAPLPPHMKETFETLGF 335


>gi|333029726|ref|ZP_08457787.1| pseudouridine synthase, RluA family [Bacteroides coprosuis DSM
           18011]
 gi|332740323|gb|EGJ70805.1| pseudouridine synthase, RluA family [Bacteroides coprosuis DSM
           18011]
          Length = 355

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 80/334 (23%), Positives = 148/334 (44%), Gaps = 41/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V+  +  +R+D++  +   + +   +QK   +G V+V+   VK N +++  + + I  
Sbjct: 31  IIVDKGQSLVRIDKFLCDRIENASRNQVQKAAEAGFVKVNGNPVKSNYKVKPLEEITIYM 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                +    E +I+   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 91  -----DTPPHEIEIIPEDIPLN---------IVYEDDYLMVVNKPAGLVVHPGHGNYRGT 136

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               IA+H+     S  D+   +  L HR+D++TSG+LV+A+T  A   L   F  +  +
Sbjct: 137 LVNAIAWHMKN--NSCYDANDPRVGLVHRIDKDTSGLLVIAKTPEAKSKLGIQFFNKTTK 194

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG  + ++  I   + +           V  + +   +A++H+KV++      
Sbjct: 195 REYRALVWGNIEEEEGRIEGNIARNPK--DRLQMAVFADPEIGKHAVTHYKVLERLG-YV 251

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKL 288
             +  +  TGRTHQ+RVH  H+G  +  D +Y  +     T   +             + 
Sbjct: 252 TLVACRLETGRTHQIRVHMKHIGHVLFNDARYGGSDILRGTHFAKYKQFVENCFNICPRQ 311

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
            LHA  +   HP     +  T+ LP  M +    
Sbjct: 312 ALHALSLGFIHPVTNEEMFFTSELPDDMTELLAK 345


>gi|312130058|ref|YP_003997398.1| ribosomal large subunit pseudouridine synthase d [Leadbetterella
           byssophila DSM 17132]
 gi|311906604|gb|ADQ17045.1| ribosomal large subunit pseudouridine synthase D [Leadbetterella
           byssophila DSM 17132]
          Length = 347

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 147/334 (44%), Gaps = 40/334 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV++ +  MRLD++  +H  +I+   +Q  + +  V+V+   VK + +++    + I  
Sbjct: 24  IVVDSGQSMMRLDKYLSHHLKNISRNRIQNAIDTDSVKVNGSSVKSSYKVKPFDDISISI 83

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
           V +             S +        +   ++YED  + + NK   + V  G G     
Sbjct: 84  VRS-------------SRIPKEVIPQNIPLDIVYEDDDVLLVNKAQEMVVHPGHGNPDGT 130

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH  G L S  D +  +P L HR+D+ TSG+LV+A+   A Q L + F     +
Sbjct: 131 LVNALVYHF-GNLPSARDGE-IRPGLVHRIDKGTSGLLVIAKNEYALQFLAKQFADHTTE 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y++L+WG PK  K  I   + +        +  V    +    AI+H++V+    +  
Sbjct: 189 RTYYALIWGEPKEPKGTINAHIGRGFK--DRRISDVFPEGEYGKEAITHYEVLKSL-RYV 245

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTS----------PIQNKL 288
             ++    TGRTHQ+R H  ++G P+  D  Y  +   +G   S           I  + 
Sbjct: 246 SLIKCNLETGRTHQIRAHMKYLGHPLFNDAAYGGDRVLRGEIFSKYKQFVENCFEIIPRQ 305

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            LHA+ +   HP   + +Q  + LPA      D 
Sbjct: 306 ALHAKSLGFIHPTTKKWMQFDSELPADFQAVLDK 339


>gi|219670033|ref|YP_002460468.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
 gi|219540293|gb|ACL22032.1| pseudouridine synthase, RluA family [Desulfitobacterium hafniense
           DCB-2]
          Length = 334

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 134/314 (42%), Gaps = 32/314 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RLD          +   +Q ++  G V V+    K N ++++   + +         
Sbjct: 41  EGTRLDVGVTERV-GKSRSFIQGLIEEGHVLVNGAARKANYKVRAMDQIAV--------- 90

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
                 ++     L   ++ +   +LYED  + V NK  G+ V    G      ++  L 
Sbjct: 91  ------VIPPPRELKVEAENIPLEILYEDEDVLVVNKSQGMVVHPAPGAWTKTLVNALLY 144

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +  G     +P + HR+D++TSG+LVVA+   A Q L E  +   + + Y ++V G+
Sbjct: 145 HCRNLSGINGVLRPGIVHRIDKDTSGLLVVAKNDLAHQGLAEQIKAHSMARRYLAIVHGV 204

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                  +   + +        + VV QN   A  A++H++V++ F + F  LE +  TG
Sbjct: 205 VFEPSGTVEAPIGRD-PADRKKMAVVFQN---AKEAVTHYEVLERF-RDFTLLEARLETG 259

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++  P++GD  Y                 LHA+ +   HP  G  ++ +A
Sbjct: 260 RTHQIRVHMAYLKHPVLGDPLYGPRKNP----FGLQGQMLHAQLLGFQHPRSGEYMEFSA 315

Query: 310 PLPAHMVKTWDSLG 323
           P      K  + + 
Sbjct: 316 PASGMFQKVLEEIR 329


>gi|227890010|ref|ZP_04007815.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
 gi|227849454|gb|EEJ59540.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
          Length = 304

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 150/327 (45%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    +V++ ++   RLD+        ++   +++++    + V+ K  K + ++QSG 
Sbjct: 1   MTKNYKLVIDGEKG--RLDKVIAEKITDLSRTKIKELVNDKNILVNNKAEKVSYKVQSGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +                +     L+  ++ L   ++YEDS + V NKP GI V   +
Sbjct: 59  VIDVT---------------IPPVKPLSLEAENLHLDIVYEDSDVIVVNKPQGIVVHPSA 103

Query: 124 GIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +G L    D     +G +P + HR+D++TSG+L++A+   A + L +    +
Sbjct: 104 GHPDHTLVNGLLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMIAKNDRARESLEKQLAEK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++ Y ++V G  + K   I   + +  +         K        A++HF V++ F 
Sbjct: 164 INKREYLAIVHGNFEVKNGVINAPIGRNPNNRKQMAVNPK-----GKAAVTHFTVLEQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  ++    TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +  
Sbjct: 218 KNYSLVKCVLETGRTHQIRVHMKYIGHPLAGDPLYGPK-----KTLSGHGQFLHAKTLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
             P     L+ +APLP    K  ++L 
Sbjct: 273 YQPSTNEWLEFSAPLPTIFEKQLENLR 299


>gi|303231392|ref|ZP_07318126.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302513988|gb|EFL55996.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 305

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 82/315 (26%), Positives = 137/315 (43%), Gaps = 32/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++E  RLD +  +     +   +Q +++SG V V+ K  K N R+ +   + +    
Sbjct: 6   VSLEQEGKRLDVFLTDVMEG-SRSYIQSLIKSGHVLVNGKVGKANLRLNADSTISVDIPE 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHI 129
                I+ E   ++                LYED  I + NKP G+ V    G+     +
Sbjct: 65  PESVEILPEDIPVEY---------------LYEDHDIIIVNKPRGMVVHPAIGNYSGTLV 109

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HRLD++TSG+++ A+  AA   L E  +    ++ Y +
Sbjct: 110 NALLYHCKDLSGINGEIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKAHSAKRTYLA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G    +K  I   + +        + VV +N   +  A++HFKV++ +      +E 
Sbjct: 170 LVQGNIVEEKGIIKAPIGRHPK-DRMKMAVVFEN---SKEAVTHFKVLERYG-YHTLVEC 224

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
              TGRTHQ+RVH  H+G P+V D  Y             +   LH+  +D+ HP  G  
Sbjct: 225 VLETGRTHQIRVHFAHIGHPVVNDPFYGYRR----MDFPIDGQALHSHTLDVVHPITGEP 280

Query: 305 LQITAPLPAHMVKTW 319
           +   AP+P       
Sbjct: 281 MHFEAPVPEDFQNCI 295


>gi|288962534|ref|YP_003452829.1| ribosomal large subunit pseudouridine synthase D [Azospirillum sp.
           B510]
 gi|288914800|dbj|BAI76285.1| ribosomal large subunit pseudouridine synthase D [Azospirillum sp.
           B510]
          Length = 363

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 85/334 (25%), Positives = 146/334 (43%), Gaps = 42/334 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           + +     RLD+      P ++   +Q +L  G VR D + +   + R++ GQ+  +   
Sbjct: 46  IPDTAAGQRLDKALSAGLPDLSRSRVQALLEQGCVRGDGRTITDPSQRVKYGQIFELRMP 105

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
            +A    + +   LD               ++YED+ + V +KPAG+ V   +G      
Sbjct: 106 GSAAAEPLPQDIPLD---------------VVYEDADVLVVDKPAGLVVHPAAGNPDGTL 150

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L    DS       ++P + HRLD++TSG++VVA+   A   L++ F  R + + Y
Sbjct: 151 VNALLAHCGDSLSGIGGVRRPGIVHRLDKDTSGLMVVAKNDRAHHGLSDQFSDRTLSRTY 210

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LVWG+P   +  I   + + S      + VV     G   A + ++V+  F      +
Sbjct: 211 LALVWGVPNPTQGRIEGNIGRSS-ADRKKMAVVT---GGGKPAGTKYRVVKSFGMAASLV 266

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--------------KLY 289
           E    TGRTHQ+RVH  H+G P+VGD  Y     G       +              +  
Sbjct: 267 ECVLETGRTHQIRVHLTHIGHPLVGDPLYGRGRSGRPGGKFASLLPEAARGLLTGFPRQA 326

Query: 290 LHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSL 322
           LHA  +   HP  G +    + +PA + +   +L
Sbjct: 327 LHAAALTFRHPVSGEIVAFRSSIPADIHELIVTL 360


>gi|190570815|ref|YP_001975173.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Culex quinquefasciatus Pel]
 gi|213019659|ref|ZP_03335464.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Culex quinquefasciatus JHB]
 gi|190357087|emb|CAQ54492.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Culex quinquefasciatus Pel]
 gi|212994700|gb|EEB55343.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Culex quinquefasciatus JHB]
          Length = 307

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 115/323 (35%), Positives = 181/323 (56%), Gaps = 17/323 (5%)

Query: 4   MTY-VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M+  ++ ++VE++  N+RLDR+ +  +P++    ++K LR G ++VD    K ++R+ SG
Sbjct: 1   MSEGIKTILVEDN--NVRLDRYIRRIFPNLKQSAIEKSLRKGLIKVDNCTAKSSDRVSSG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q +    +I  L++I  E    D   N  K  + L+  +LYED  I   NKPAG+ VQGG
Sbjct: 59  QTI----MIRYLDYI--ENTNSDCKYN-EKLVNLLRENILYEDEYILAINKPAGVIVQGG 111

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             +   I   L    + +  K  + HRLD++TSG+++ AR  + A++L E F+ RRI+K 
Sbjct: 112 IKVKISISDLLDQIREREIFK--IVHRLDRDTSGVIIFARNASVAKYLMEEFKGRRIKKT 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L +GIP      I   L+KK   G + V V   +E     A +HF +I        +
Sbjct: 170 YLALTFGIPSKDNGTIDYPLVKKYISGQEKVVV---DEDSPQNATTHFLIIARLKHNVAY 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L++QP TGRTHQLR H  H+ CPI+GD KY    K  F   + N+++LH+  + L  P  
Sbjct: 227 LKLQPITGRTHQLRAHLAHINCPILGDGKYGG--KKAFIDGVANQIHLHSYSLSLKLPNN 284

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
             + ITAP+P H+ K+ ++L F 
Sbjct: 285 KEVTITAPVPKHIEKSIEALSFD 307


>gi|306829292|ref|ZP_07462482.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           mitis ATCC 6249]
 gi|304428378|gb|EFM31468.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           mitis ATCC 6249]
          Length = 299

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 148/324 (45%), Gaps = 34/324 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++ GQV V+ +  K    +Q G +V      
Sbjct: 3   IKIERGGLRLDKALSD-LTELSRSLANEQIKVGQVLVNGQAKKAKYTVQEGDIVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F+V++ F   +  LE+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFQVLERFGD-YSLLEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           L+ TA +P    +T + L    +R
Sbjct: 276 LEFTADIPEIFKETLERLRKAENR 299


>gi|224024580|ref|ZP_03642946.1| hypothetical protein BACCOPRO_01306 [Bacteroides coprophilus DSM
           18228]
 gi|224017802|gb|EEF75814.1| hypothetical protein BACCOPRO_01306 [Bacteroides coprophilus DSM
           18228]
          Length = 354

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 77/333 (23%), Positives = 145/333 (43%), Gaps = 39/333 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +  +R+D++      + +   +Q    +G V  + K VK + +++   V+ +  
Sbjct: 31  VVVDKGQSPVRIDKYLFERIVNASRNRIQTAADAGFVMANGKPVKSSYKVKPQDVLTVMM 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E  I+   + L          ++YED  + V NKPAG+ V  G G  +  
Sbjct: 91  -----DRPRYENDIIPEDIPLD---------VVYEDEDLMVINKPAGLVVHPGCGNYHGT 136

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        +    +  L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 137 LVNAIAWHLRDVPTYNPNDPQVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFYNKTTKRE 196

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFC 241
           Y +LVWGI +  +  I   + +      D + +   ++     +A++H++V++       
Sbjct: 197 YNALVWGIVEEDEGTITGNIGRNP---RDRMQMAVISDPTQGKHAVTHYQVLERLG-YVT 252

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLY 289
            ++    TGRTHQ+RVH  H+G  +  D +Y  +     T              I  +  
Sbjct: 253 LVKCVLETGRTHQIRVHMKHIGHVLFNDERYGGHEILKGTHFSKYKQFVNNCFDICPRQA 312

Query: 290 LHARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           LHA+ +   HP     +  T+ LP  M +  + 
Sbjct: 313 LHAKTLGFVHPRTKEEMFFTSELPEDMTRLLER 345


>gi|190893167|ref|YP_001979709.1| RNA-pseudouridylate synthase, ribosomal large subunit D [Rhizobium
           etli CIAT 652]
 gi|190698446|gb|ACE92531.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli CIAT 652]
          Length = 354

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 83/346 (23%), Positives = 157/346 (45%), Gaps = 45/346 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ V+  ++    RLD W         +   ++ +++ GQV +  + +     ++++G  
Sbjct: 24  IRKVLTADETAEGRLDAWLTAQLGEEFSRSRIKVLIKDGQVSMRGQLITDPQRKVRAGDS 83

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
             I                L    + T   + +   +LYED  + V +KPAG+ V  GSG
Sbjct: 84  FEIT---------------LPEPEDPTPQGEDIPLDILYEDDDLIVISKPAGLVVHPGSG 128

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +     +       ++P + HRLD++T+G++VVA+   A +HL+  F   
Sbjct: 129 NWTGTLVNALIHHCGATLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDVAHRHLSLQFADH 188

Query: 178 R----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                +++ Y ++VWG P++    +   L + +        V + + + A+ AI+H++VI
Sbjct: 189 GRTMPLERAYRAIVWGRPRSLTGTVDAPLGRATG-DRTRRAVKRPDSQDADEAITHYEVI 247

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-- 285
           + F +          +E +  TGRTHQ+RVH  H+G P++GD  Y A F+       +  
Sbjct: 248 ERFHETPDATALASLVECRLETGRTHQIRVHMAHIGHPLLGDTVYGAGFRTKANLLPEDI 307

Query: 286 -------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                  ++  LHA  +   HP  G  +    PLP  MV+  ++L 
Sbjct: 308 RKVVNRFDRQALHAFMLQFEHPRSGELMHFEVPLPDDMVELVEALR 353


>gi|325687371|gb|EGD29392.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK72]
          Length = 298

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 143/322 (44%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E      RLD+        ++     + ++ G++ V+ +  K    ++ G V+   
Sbjct: 2   EVRIEVSVVGQRLDKAVAE-LTDLSRSLAHEQIKDGRILVNGQVKKAKYAVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++        ++ +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELPEPEVVE------YVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L+VA+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIQDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-YSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y                +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPRKTLKGY-----GQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA +P    +T + L 
Sbjct: 275 GEVLEFTAEVPVIFQETLEKLR 296


>gi|57233860|ref|YP_182086.1| ribosomal large subunit pseudouridine synthase D [Dehalococcoides
           ethenogenes 195]
 gi|57224308|gb|AAW39365.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Dehalococcoides ethenogenes 195]
          Length = 300

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 77/316 (24%), Positives = 147/316 (46%), Gaps = 34/316 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            + +  RLD++       ++   +Q+++ +G ++V+ K  K + ++++G  + I      
Sbjct: 8   AESDGERLDKYITQKETDLSRSFIQELVEAGHIQVNGKNAKPSLKLKNGDTITIEIPPET 67

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDG 131
              +  E   L+               ++++D  + + NKP G++V    G   H  I+G
Sbjct: 68  PPELKAEDIPLE---------------IIFQDKDLLLINKPPGLTVHPAPGHPDHTLING 112

Query: 132 FLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    + +      +P + HRLD++TSG+L+VA+ R A  +L+  F+ R ++K Y +LV
Sbjct: 113 VLALEPEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNREALANLSAQFKERTVRKYYLTLV 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G     +  I   L +        + VV         A + +KV+  + Q +  LE++ 
Sbjct: 173 QGELHPAEGFIEAPLGRD-PQNRQKIAVVS----NGRPARTGYKVL-RYIQGYSLLEVKL 226

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH   +G P+ GD  Y              + +LHA  +    P  G+ ++
Sbjct: 227 ETGRTHQIRVHFAAIGHPVAGDAVYGQK------ETWLKRQFLHAHRLSFSLPSNGQNVE 280

Query: 307 ITAPLPAHMVKTWDSL 322
            ++PLP  + +   +L
Sbjct: 281 FSSPLPPDLEEALKTL 296


>gi|254495420|ref|ZP_05108344.1| ribosomal large subunit pseudouridine synthase D [Polaribacter sp.
           MED152]
 gi|85819775|gb|EAQ40932.1| ribosomal large subunit pseudouridine synthase D [Polaribacter sp.
           MED152]
          Length = 345

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 81/330 (24%), Positives = 154/330 (46%), Gaps = 35/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V  + +E +R+D++  N   +     +Q+  ++G V V+   VK N++++   VVR+  
Sbjct: 20  FVAADGQEPLRVDKFLMNFIENATRNKVQQAAKAGNVLVNDIAVKSNHKVKPKDVVRV-- 77

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L +   E  ++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 78  ---VLAYPPAENLLVAEDIPLD---------IIYEDDAVIVVNKPAGMVVHPGHGNYSGT 125

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   +   +++   +  ++P L HR+D++TSG+LVVA+T  A  HL++ F  R  +++Y+
Sbjct: 126 LVNGLIHHIENLPTNSNERPGLVHRIDKDTSGLLVVAKTEFAMAHLSKQFFDRTTERLYY 185

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG  +  +  I   + +           V  +     +A++HFKV++        ++
Sbjct: 186 ALVWGNIEEDEGRIEGNIGRSLK--NRLQMAVFPDGDFGKHAVTHFKVLERLT-YVTLVQ 242

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLHA 292
            +  TGRTHQ+R H  H+G  +  D +Y  +     T+  +             +  LHA
Sbjct: 243 CKLETGRTHQIRAHFKHIGHTLFNDERYGGDEILKGTTFTKYKQFVQNCFKVLPRQALHA 302

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP  G  L   + +P  + +  + 
Sbjct: 303 KTLGFTHPTTGEFLSFNSEIPDDISECLEK 332


>gi|113867448|ref|YP_725937.1| pseudouridylate synthase, 23S RNA-specific [Ralstonia eutropha H16]
 gi|113526224|emb|CAJ92569.1| pseudouridylate synthase, 23S RNA-specific [Ralstonia eutropha H16]
          Length = 396

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 142/342 (41%), Gaps = 38/342 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V++     RLD+    H+   +   LQ+ + SG VRVD    +  + +Q G  + I P
Sbjct: 47  LEVDSASHGERLDKLLARHFSEFSRSRLQQWIESGAVRVDGHVRRPRDAVQMGNRIEIQP 106

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +                   + +   ++YED  + V NKPAG+ V   +G   + 
Sbjct: 107 QAAPESS--------------AFSPEDVPLDVVYEDDTLLVINKPAGLVVHPAAG---NW 149

Query: 130 DGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G + + +  +        +  + HRLD+ETSG++VVAR+  A   L    + R +++ Y
Sbjct: 150 SGTVLNGLLHRDPGAALLPRAGIVHRLDKETSGLMVVARSLTAQTDLVRQLQARTVKRTY 209

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---F 240
            +LVWG     +  I   + +      +   +   +      + +HF+ +          
Sbjct: 210 IALVWGR-TYDEGTIDAPIGRDP---RERTRMAVVHTASGKPSRTHFRTLATVPLGRGFV 265

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY------CANFKGNFTSPIQ-NKLYLHAR 293
             +  +  TGRTHQ+RVH   +G P+VGD  Y                P+   +  LHA 
Sbjct: 266 SMVMCKLETGRTHQIRVHFESIGHPLVGDPAYFRATQRGQRPAVRAPLPVPYERQALHAY 325

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            + L HP  G R+  TA  P  +    D+L F+  +    + 
Sbjct: 326 QLGLVHPATGKRMSWTAQPPQDLQALIDALDFESAQADEDEE 367


>gi|284036309|ref|YP_003386239.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283815602|gb|ADB37440.1| pseudouridine synthase, RluA family [Spirosoma linguale DSM 74]
          Length = 348

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 80/335 (23%), Positives = 148/335 (44%), Gaps = 43/335 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+DR+  +   +     +Q  + +  VRV+ K  K + +I+   ++ +  
Sbjct: 20  IVVDKGQSLLRIDRFLMDRLQNATRTKIQAGIDAESVRVNDKPTKASYKIKPSDIITV-- 77

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
              +L H  +E  +   ++ +          +++ED  + V NKPAG+ V    G   + 
Sbjct: 78  ---SLPHPPRETDLKPENIPIN---------IVFEDDDLLVINKPAGMVVHPAHG---NW 122

Query: 130 DGFLKSWVDSKGQ----------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           DG L + +    Q          +P L HR+D++TSG++V+A+T  A  +L   F    I
Sbjct: 123 DGTLVNALVYHFQNLPTSRHGEVRPGLVHRIDKDTSGLMVIAKTEFAMTYLARQFFEHTI 182

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +L WG+P  +   I  ++ +   I    V  +  +E    +A++H+  ++     
Sbjct: 183 ERTYNALTWGVPNPQIGTITGFIGRS--IKDRKVQAIYDDESKGKWAVTHYTTLEDLG-Y 239

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------------PIQNK 287
              +E +  TGRTHQ+R H  H+G P+  D  Y  +     T              +  +
Sbjct: 240 VALVECKLETGRTHQIRAHFKHIGNPLFNDAMYGGDRILRGTPVGSYKAFVENAFKLLPR 299

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
             LHAR +   HP     LQ  + LP       + 
Sbjct: 300 QALHARSLGFKHPRTKEWLQFDSNLPDDFQAALNK 334


>gi|317063086|ref|ZP_07927571.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
 gi|313688762|gb|EFS25597.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
          Length = 313

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 86/336 (25%), Positives = 154/336 (45%), Gaps = 34/336 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M  +     V  + +++  R+D +            +QKI+  G V +  K+V K  N++
Sbjct: 1   MENIKETITVYADENDKGKRIDSFLNEVIDDATRSYIQKIIDGGYVEITGKKVTKSGNKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +  + + +          I E +ILD         + +   ++YED  I V NK   + V
Sbjct: 61  KGTETITVN---------IPEDEILDV------IPENIPLNIIYEDKDIVVINKAPDMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G      ++  L    D    +   +P + HRLD++TSG++VVA+   A   L++ 
Sbjct: 106 HPAHGNYNGTLVNALLYHIKDLSTINGVIRPGIVHRLDKDTSGVIVVAKNDEAHSTLSDM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ + ++K Y  +  GI K+K   I   + + S      + VV  N K    AIS+++++
Sbjct: 166 FKEKTLEKTYICIAKGIFKDKSGRIETLIGRDSR-DRKKMAVVDINGKN---AISNYEIL 221

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D   + F  ++++  TGRTHQ+RVH  ++  PI+GD  Y ++ +G        +  LHA 
Sbjct: 222 D-EEKNFSLVKVRIETGRTHQIRVHMKYLNHPILGDSVYGSSGEGA------KRQMLHAY 274

Query: 294 YMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDR 328
            +   HP     +++TA +P    K     G   D+
Sbjct: 275 RLKFTHPVTKKEMEVTADIPEDFKKAAKFAGVNIDK 310


>gi|21282809|ref|NP_645897.1| hypothetical protein MW1080 [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49486036|ref|YP_043257.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|300912239|ref|ZP_07129682.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|21204247|dbj|BAB94945.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49244479|emb|CAG42908.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|300886485|gb|EFK81687.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus TCH70]
          Length = 305

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 77/329 (23%), Positives = 139/329 (42%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +++   
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I+ E                L   + YED  + V  K  G+ V    
Sbjct: 61  HIVVTEKEVVEADILPEN---------------LNLDIYYEDDDVAVVYKTKGMVVHPSP 105

Query: 124 GIAYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +   +G +    +  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAPIGRN-KNDRQSMAVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLD-----IGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  ++  A LP       D++  +
Sbjct: 275 EHPVTGEYIERHAELPQDFEDLLDTIRKR 303


>gi|325694604|gb|EGD36513.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK150]
          Length = 298

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 144/322 (44%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E      RLD+        ++     + ++ G++ V+ +  K    ++ G V+   
Sbjct: 2   EVRIEASVAGQRLDKAVAE-LTDLSRSLANEQIKDGRILVNGQAKKAKYAVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++        ++ +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELPEPEVVE------YVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLSNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-YSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++  P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIEHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA +P    +T + L 
Sbjct: 275 GEVLEFTAEVPDIFQETLEKLR 296


>gi|218528997|ref|YP_002419813.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
 gi|218521300|gb|ACK81885.1| pseudouridine synthase, RluA family [Methylobacterium
           chloromethanicum CM4]
          Length = 343

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 91/345 (26%), Positives = 153/345 (44%), Gaps = 48/345 (13%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
             + +V++      RLDR     +  ++   LQ ++R G VR D   V+    ++ +G  
Sbjct: 20  EARSLVLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCDGIVVRDPARKVGAGCR 79

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +                + + +      + L   +++ED  + V +KPAG+ V   +G
Sbjct: 80  IDLS---------------VPAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPAAG 124

Query: 125 IAYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              H DG L + + +            ++P + HRLD++TSG+LVVA+   A Q L+  F
Sbjct: 125 ---HEDGTLVNRLIAHCGASLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQF 181

Query: 175 RMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
                   +++ Y +LVW +P+ +   I   L +  H   + + VV++ E     AI+H+
Sbjct: 182 ADHGRSGALERAYLALVWNVPEPRAGTIRANLARSRH-NREKIAVVREGE--GREAITHY 238

Query: 231 KVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GN 279
           +V D   +      L     TGRTHQ+RVH  H G P++GD  Y   FK           
Sbjct: 239 RVEDVHGEGGVTALLRCHLETGRTHQIRVHLSHRGHPLLGDAVYGGAFKTKAARLSEPAR 298

Query: 280 FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLG 323
                  +  LHA  +   HP  G RL+  +PLP    +   +LG
Sbjct: 299 AALDALGRQALHAVELGFLHPRSGERLRFESPLPEDFSRLLAALG 343


>gi|189499996|ref|YP_001959466.1| pseudouridine synthase, RluA family [Chlorobium phaeobacteroides
           BS1]
 gi|189495437|gb|ACE03985.1| pseudouridine synthase, RluA family [Chlorobium phaeobacteroides
           BS1]
          Length = 346

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 145/334 (43%), Gaps = 37/334 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V   ++ MR+D +      +     +Q+ +   +VRV+ K VK N +I+S   + I 
Sbjct: 24  TLQVAQTQKPMRIDVYLAQQVENATRNKVQEAISEHRVRVNGKTVKANYKIKSLDSIEIT 83

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIA 126
            +      +  E   +D               ++YED+ + V NK  G+ V    G+   
Sbjct: 84  FLRPPAPELAPEDIPVD---------------IIYEDNDLMVINKAPGMVVHPAFGNWTG 128

Query: 127 YHIDGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  L         +D+   +P + HRLD+ TSG+++VA+   A   L + F  R+++
Sbjct: 129 TLANAILHHLGTDAEKLDTTELRPGIVHRLDKNTSGLIIVAKHATALHRLAKQFAERQVE 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++VWG+P+  +  +   + + S      +       K    A++ ++V++   + F
Sbjct: 189 KKYQAIVWGVPEPPEGIVKTNIGR-SIRDRKVMTSYDFEGKEGKTAVTEYRVVENL-RYF 246

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----------SPIQNKLY 289
             +EM  HTGRTHQ+RVH  H+  PI+GD  Y      +                  +  
Sbjct: 247 SLVEMILHTGRTHQIRVHLKHINAPILGDETYGGAGVQSLPFSKSESFVKNLLERIPRQA 306

Query: 290 LHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           LHA  +    P    R+ ++AP P  M    D +
Sbjct: 307 LHAASLSFFQPTTRERITLSAPQPEDMQAALDKI 340


>gi|170723708|ref|YP_001751396.1| RluA family pseudouridine synthase [Pseudomonas putida W619]
 gi|169761711|gb|ACA75027.1| pseudouridine synthase, RluA family [Pseudomonas putida W619]
          Length = 352

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 93/345 (26%), Positives = 154/345 (44%), Gaps = 38/345 (11%)

Query: 2   SLMTYVQYV--VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           S M+ +  +   V ++    RLD+     +   +   L   ++ G++ VD   V+  + +
Sbjct: 31  SSMSEIIQLSAEVPSELGGQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDTV 90

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G ++ +     A    I E   LD               ++YED +I V NKPAG+ V
Sbjct: 91  HGGSMLALEAEQEAQGEWIAEDIELD---------------IVYEDDQIMVINKPAGLVV 135

Query: 120 QGGSGIA--YHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +G A    ++  L    D     +  + HRLD++T+G++VVA+T  A   L E  + 
Sbjct: 136 HPAAGHASGTLLNALLHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTLQAQTKLVEQLQS 195

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + +IY  +V G+       I   + +        + V     +G   A+SH++V+  F
Sbjct: 196 RTVSRIYECIVIGVV-TAGGKINAPIGRHGG-ARQRMAVT----EGGKPAVSHYRVLKRF 249

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKL 288
            +    + ++  TGRTHQ+RVH  H+G P+VGD  Y   F+     SP          + 
Sbjct: 250 -RSHTHVRVKLETGRTHQIRVHMAHVGFPLVGDQTYGGRFRIPPAASPTMVEAVKTFPRQ 308

Query: 289 YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            LHAR++ L HP  G R++  + LP   V     L    DR  +I
Sbjct: 309 ALHARFLALDHPTTGERMEWASELPDDFVWLLSLL--NQDREAFI 351


>gi|73749059|ref|YP_308298.1| ribosomal large subunit pseudouridine synthase D [Dehalococcoides
           sp. CBDB1]
 gi|73660775|emb|CAI83382.1| ribosomal large subunit pseudouridine synthase,RluD subfamily
           [Dehalococcoides sp. CBDB1]
          Length = 300

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 79/316 (25%), Positives = 146/316 (46%), Gaps = 34/316 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +    RLD++       ++   +Q+++ SG + V+ +  K + R+++G  + I      
Sbjct: 8   AETAGERLDKYITQKESGLSRSFIQELVSSGHILVNNQSAKPSLRLKTGDTITIEIPPET 67

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DG 131
            + +  E   L+               ++++D  + + NKP G++V    G   H   +G
Sbjct: 68  PSELKAEDIPLE---------------IIFQDKDLLLINKPPGLTVHPAPGHPDHTLVNG 112

Query: 132 FLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    + +      +P + HRLD++TSG+L+VA+ R A  +L+  F+ R I+K Y +LV
Sbjct: 113 VLALEPEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRQALANLSAQFKERTIRKYYLALV 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  +  +  I   L +        + VV        +A + +KV+  + Q +  LE++ 
Sbjct: 173 KGELRPAEGFIEAPLGRD-PQNRQKIAVVS----DGRHARTGYKVL-RYIQGYSLLEVKL 226

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH   +G P+ GD  Y              + +LHA  +    P  G+ ++
Sbjct: 227 ETGRTHQIRVHFAAIGHPVAGDAVYGQKESWV------KRQFLHAHRLSFALPSNGQVVE 280

Query: 307 ITAPLPAHMVKTWDSL 322
            T+PLP  + +    L
Sbjct: 281 FTSPLPPDLEEALKIL 296


>gi|262038336|ref|ZP_06011717.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           goodfellowii F0264]
 gi|261747640|gb|EEY35098.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           goodfellowii F0264]
          Length = 346

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 149/325 (45%), Gaps = 33/325 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V  ++ N R+D +       +    +Q++++ G V V+ K VK + +++    + I  
Sbjct: 42  VTVSTEKTNKRVDSFLSEK-TDLTRSRIQQLIKDGNVSVNNKSVKSSYKVEENDRIEI-- 98

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                        I+  +  +   ++ +   ++YED  I V NK AG+ V    G     
Sbjct: 99  -------------IIPEAEKVEIIAENIDINIIYEDKDIAVINKKAGMVVHPAHGNYSRT 145

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HRLD++TSG++VVA+   A   L E F+ + ++K Y
Sbjct: 146 LVNAILYHIKDLSGINGEIRPGIVHRLDKDTSGLIVVAKNDKAHIKLAEMFQKKEVKKTY 205

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +++ G    +   +   + + +      + V+K+N+KG   AI+++ VI    + F  +
Sbjct: 206 LAILKGKLNRESGRLETQIGRDA-DDRKKMSVLKENDKGKK-AITNYNVILSN-ELFTLV 262

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++   TGRTHQ+RVH  ++G PI+GD  Y            + +  LHA  ++  HP   
Sbjct: 263 KVYIETGRTHQIRVHMKYLGYPILGDQVYGRKDS-------EKRQMLHAYKLEFLHPVTE 315

Query: 304 R-LQITAPLPAHMVKTWDSLGFKYD 327
           + ++    +P        +   + D
Sbjct: 316 KPMKFIGEIPEDFKNALKNTKLEVD 340


>gi|306520956|ref|ZP_07407303.1| putative pseudouridylate synthase [Clostridium difficile QCD-32g58]
          Length = 453

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 144/328 (43%), Gaps = 33/328 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +M  V+  +V  +EE +RLD +       ++   +QKI++ G+V+V+ K  K    ++  
Sbjct: 150 IMDEVKEFLVLEEEEEVRLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKAKYLVKEE 209

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I          I E K+L+           +   ++YED  + + NKP  + V   
Sbjct: 210 DNIVIE---------IPEPKVLEV------LPQDIPIDIVYEDDDVLIINKPQDMVVHPA 254

Query: 123 SGIAYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G   +   +G L    D         +P + HR+D++TSG+L++A+   A   L E  +
Sbjct: 255 PGNYENTLVNGILYHCKDKLSSINGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLK 314

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I + Y  + +G+ K  K  +   + +          V     K    AI+HF+V++ 
Sbjct: 315 EHTITREYEFICYGVVKEDKITVDKPIGRNPKDRLKMAVV-----KDGKNAITHFEVVER 369

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F  KF  +  +  TGRTHQ+RVHAL +  P++GD  Y        T        LHA+ +
Sbjct: 370 F-DKFTHMRARLETGRTHQIRVHALSINHPLLGDFVYGPKE----TKFKLKGQTLHAKKL 424

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP     ++  + LP +  +    +
Sbjct: 425 GFIHPTTKEYIEFNSELPEYFKEAIKKI 452


>gi|85860531|ref|YP_462733.1| ribosomal large subunit pseudouridine synthase D [Syntrophus
           aciditrophicus SB]
 gi|85723622|gb|ABC78565.1| ribosomal large subunit pseudouridine synthase D [Syntrophus
           aciditrophicus SB]
          Length = 333

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 86/339 (25%), Positives = 150/339 (44%), Gaps = 36/339 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRI 59
           M  +  ++   V   E  +RLD +  +H    +   LQ+++ SG+V +  K  ++ + ++
Sbjct: 1   MKGVAPLREYRVTATESGLRLDLFLASHESGFSRARLQRLIESGRVTISGKAAIRASQKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G +V +                   +  L      +   +LYED  + V +KPAG+ V
Sbjct: 61  RTGDIVMLE---------------EPPATPLELIPQDIPLSILYEDHDLLVLDKPAGLVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              +G      ++  L    D  G     +P + HRLD++TSG+LVVA+T AA Q L   
Sbjct: 106 HPAAGHVSGTLVNALLFHCRDLAGIGGVMRPGIVHRLDKDTSGLLVVAKTDAAHQGLALQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+  ++ K Y +LV+G P+ K   I   + +           +    +    A + +++ 
Sbjct: 166 FKKHQVGKTYQALVYGDPREKTGQIDLPVGRHPVERKK----MSTKSRRGKEAATRWRIA 221

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG--------NFTSPIQ 285
           + F      L +   TGRTHQ+RVH   +G P+VGD  Y ++ +                
Sbjct: 222 ERFG-VATLLNVDIVTGRTHQIRVHLAAIGHPVVGDAVYGSSKRATTLTDPAVKGRLKEM 280

Query: 286 NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
           ++  LHA  +   HP   ++ +  APLPA M      L 
Sbjct: 281 SRQALHAARLSFTHPVTHKILEFHAPLPADMEDLCAFLR 319


>gi|89895611|ref|YP_519098.1| hypothetical protein DSY2865 [Desulfitobacterium hafniense Y51]
 gi|89335059|dbj|BAE84654.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 300

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 135/314 (42%), Gaps = 32/314 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RLD          +   +Q ++  G + V+    K N ++++   + +         
Sbjct: 7   EGTRLDVGVTERV-GKSRSFIQGLIEEGHILVNGAARKANYKVRAMDQITV--------- 56

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
                 ++     L   ++ +   +LYED  + V NKP G+ V    G      ++  L 
Sbjct: 57  ------VIPPPRELKVEAENIPLEVLYEDEDVLVVNKPQGMVVHPAPGAWTKTMVNALLY 110

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +  G     +P + HR+D++TSG+LVVA+   A Q L E  +   + + Y ++V G+
Sbjct: 111 HCRNLSGINGVLRPGIVHRIDKDTSGLLVVAKNDLAHQGLAEQIKAHSMARRYLAIVHGV 170

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                  +    + +       + VV QN   A  A++H++V++ F + F  LE +  TG
Sbjct: 171 VFEPSGTVDAP-VGRDPADRKKMAVVFQN---AKEAVTHYEVLERF-RDFTLLEARLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++  P++GD  Y                 LHA+ +   HP  G  ++ +A
Sbjct: 226 RTHQIRVHMAYLKHPVLGDPLYGPRKNP----FGLQGQMLHAQLLGFQHPRSGEYMEFSA 281

Query: 310 PLPAHMVKTWDSLG 323
           P      K  + + 
Sbjct: 282 PASGMFQKVLEEIR 295


>gi|307709119|ref|ZP_07645578.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
 gi|307620065|gb|EFN99182.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
          Length = 295

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 146/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETGGLRLDKALSD-LTELSRSLANEQIKSGQVLVNDQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ +   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+ TA +P    +T + L 
Sbjct: 276 LEFTADIPEIFKETLEKLR 294


>gi|90022196|ref|YP_528023.1| ribosomal large subunit pseudouridine synthase D [Saccharophagus
           degradans 2-40]
 gi|89951796|gb|ABD81811.1| ribosomal large subunit pseudouridine synthase D [Saccharophagus
           degradans 2-40]
          Length = 321

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 85/326 (26%), Positives = 144/326 (44%), Gaps = 34/326 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  +    RLD+   + +P  +   +Q+ ++SG++ VD K  K   ++  G+ + + P +
Sbjct: 11  VPQEMAGNRLDQVCADLFPDYSRSRIQQWIKSGKLLVDDKTGKAKQKVFGGENLVLEPEL 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                  +E + L   +NL          ++YED  I V NK AG+ V   +G      +
Sbjct: 71  Q------EEGEWLPEPINLN---------IVYEDEHILVINKQAGLVVHPAAGNWSGTLL 115

Query: 130 DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +G L          +  + HRLD++T+G++VVA++     HL    + R + + Y ++V 
Sbjct: 116 NGLLHHVPSLVNVPRAGIVHRLDKDTTGLMVVAKSLPTQTHLVAQLQARTVSRHYQAVVH 175

Query: 189 GIP--KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           G    K+K   +   + +          +    E     A++H++V+    Q F  + +Q
Sbjct: 176 GTFAAKDKLGTVDIAIGRHPTQRVKMAAL----ENSGKPAVTHYRVVKDL-QGFAHVHLQ 230

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANF--------KGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+G P+VGD  Y             G   +    +  LHA  + L 
Sbjct: 231 LETGRTHQIRVHMAHIGYPLVGDQVYGKKVPTKVRNHNPGAVHAEAFPRQALHAWRLSLV 290

Query: 299 HPEGGRLQI-TAPLPAHMVKTWDSLG 323
           HP         A LP  MV+  D L 
Sbjct: 291 HPVTEETVFWEADLPEDMVQLIDQLA 316


>gi|78185708|ref|YP_378142.1| pseudouridine synthase, RluD [Synechococcus sp. CC9902]
 gi|78170002|gb|ABB27099.1| ribosomal large subunit pseudouridine synthase D [Synechococcus sp.
           CC9902]
          Length = 339

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 92/313 (29%), Positives = 141/313 (45%), Gaps = 28/313 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +   +QK + +G VRV+ K+ K    ++ G  V++          
Sbjct: 39  PMRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKQGKAKTPLREGDQVQLWMPPPEPLPY 98

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
           +K Q               +   +L+ED  I V NK AG++V    G      ++G L  
Sbjct: 99  LKPQP--------------MDLDVLFEDEHIIVLNKSAGLTVHPAPGNKDGTLVNGLLHH 144

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++TSG +VVA+++ A   L    + R   + Y+++V G+P
Sbjct: 145 CPDLPGISGKLRPGIVHRLDKDTSGCIVVAKSQEALVKLQVQIQKRVASREYFAVVHGVP 204

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   + +       Y  V   +++   YA +H+ +I+ F   +  L  +  TGR
Sbjct: 205 DGDSGTIIGAVGRHPVDRKKYAVV---SDESGRYARTHWTLIERFGD-YSLLRFKLDTGR 260

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  H+  P+VGD  Y    K     P      LHA  + L HP  G R+   AP
Sbjct: 261 THQIRVHCAHINHPVVGDPTYSRCRKLPLDLPG---QALHAVQLGLDHPITGERMVFEAP 317

Query: 311 LPAHMVKTWDSLG 323
           LP  M K    L 
Sbjct: 318 LPPVMEKLLLVLR 330


>gi|17228018|ref|NP_484566.1| hypothetical protein alr0522 [Nostoc sp. PCC 7120]
 gi|9957317|gb|AAG09315.1| hypothetical protein [Nostoc sp. PCC 7120]
 gi|17129867|dbj|BAB72480.1| alr0522 [Nostoc sp. PCC 7120]
          Length = 312

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 85/332 (25%), Positives = 149/332 (44%), Gaps = 31/332 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSG 62
           M    Y+ VE D    R+DR+     P ++   +Q+++  G+V+V+ K        ++ G
Sbjct: 1   MLNEFYLEVEEDSA--RIDRYLAEELPDLSRSRIQQLIEQGKVQVNGKVCTSKKINLKVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +                +  +  L   ++ +   +LYED ++ + NKPAG+ V   
Sbjct: 59  DRITLE---------------VPEAQPLEIQAEDIPLDILYEDDQLLILNKPAGLVVHPA 103

Query: 123 SGIAY--HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G ++   ++  L    D  G    Q+P + HRLD++T+G + +A+T  A +H+    + 
Sbjct: 104 PGHSHGTLVNALLAHCPDLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKHIQAQLQA 163

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           +  ++ Y  +V+G PK     +   + +  H        V   E+G   AI+H+++ +  
Sbjct: 164 KTARREYLGVVYGAPKTASGKVDLPIGR--HPQDRKKMAVVPIEEGGRSAITHWQIQERL 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              F  +  Q  TGRTHQ+RVH+  MG PIVGD  Y +        P      LHA  + 
Sbjct: 222 G-NFTLIHFQLETGRTHQIRVHSAKMGHPIVGDPVYGSGRSVGVNLPG---QALHAWRLR 277

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L HP  G  ++ TA  P       + L  +  
Sbjct: 278 LQHPITGDWVEATATPPQSFTTLLEILRRRAS 309


>gi|34497647|ref|NP_901862.1| pseudouridine synthase D [Chromobacterium violaceum ATCC 12472]
 gi|34103503|gb|AAQ59865.1| pseudouridine synthase D [Chromobacterium violaceum ATCC 12472]
          Length = 363

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 79/330 (23%), Positives = 139/330 (42%), Gaps = 29/330 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           +  Q++ +       RLD       P  +   L + ++ G V+VD + V    ++  G+ 
Sbjct: 20  STTQHLEIPLSLCGERLDAALAKLLPDYSRSRLTQWVKDGLVKVDGQVVAPKTKMLGGEK 79

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +   +              ++  +    + +   +++ED  I V NKPAG+ V   +G
Sbjct: 80  LEVTLQL--------------TNEEMAFQPEPMDLPIVFEDEHILVINKPAGLVVHPAAG 125

Query: 125 I--AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                 ++G L      +   +  + HRLD++TSG++VVA+T  A   L    + R +++
Sbjct: 126 NWSGTLLNGLLHHCPALASVPRAGIVHRLDKDTSGLMVVAKTLPAQTELVRQLQARTVKR 185

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++  G+       I   + + ++     + V+K    G   AI+H +V++ FA    
Sbjct: 186 VYRAIADGVVP-FDGTIDANIGRDAN-NRLKMAVLKF---GGKPAITHIRVLERFAS-HS 239

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-----NFTSPIQNKLYLHARYMD 296
            +E +  TGRTHQ+RVH    G P+ GD  Y                   +  LHA  + 
Sbjct: 240 HVECKLETGRTHQIRVHMREAGHPLAGDPVYGNPRHKMDEEIAAGVKALGRQALHAFALA 299

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           L HP  G      APLP       D L   
Sbjct: 300 LVHPATGEERSWKAPLPDDFRALLDLLRGD 329


>gi|56964104|ref|YP_175835.1| pseudouridine synthase [Bacillus clausii KSM-K16]
 gi|56910347|dbj|BAD64874.1| pseudouridine synthase [Bacillus clausii KSM-K16]
          Length = 302

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 86/324 (26%), Positives = 151/324 (46%), Gaps = 32/324 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++  +    R+D+   + +   +   +Q+ +  G V V++K VK N+++Q G  V 
Sbjct: 1   MEQWIITKEHHEQRIDKVVVDLHGQASRTAVQRWINEGAVLVNEKEVKTNSKVQQGDKVT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +         ++ E   LD               ++YEDS + V NKP G+ V    G  
Sbjct: 61  LTEPAAQEVELLGEDIPLD---------------VVYEDSDVIVVNKPRGLVVHPAPGHE 105

Query: 127 --YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L    D  G     +P + HR+D++TSG+++ A+  AA +HL    + +  +
Sbjct: 106 SGTLVNALLFHCKDLSGINGEIRPGIVHRIDKDTSGLIMAAKHDAAHEHLAAQLKAKTTE 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G+  + K  I   + +        + V   N   +  A++HF + + F Q +
Sbjct: 166 RRYKAIVHGVIPHAKGTIDAPIGRDPK-DRQKMAVTHVN---SRPAVTHFSLEETFKQ-Y 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++  +  TGRTHQ+RVH  ++G P+ GD KY         +   N   LHA  +   HP
Sbjct: 221 SYISCELETGRTHQIRVHFNYIGHPLAGDPKYGPK-----KTLPINGQALHAETLGFTHP 275

Query: 301 EGG-RLQITAPLPAHMVKTWDSLG 323
             G RL+ +APLPA M K    L 
Sbjct: 276 RTGERLRFSAPLPAEMEKLLVDLR 299


>gi|189346997|ref|YP_001943526.1| pseudouridine synthase, RluA family [Chlorobium limicola DSM 245]
 gi|189341144|gb|ACD90547.1| pseudouridine synthase, RluA family [Chlorobium limicola DSM 245]
          Length = 354

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 83/335 (24%), Positives = 142/335 (42%), Gaps = 37/335 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V   +  MR+D++      +     +Q+ +   +V V+ + VK N RI+S   + I 
Sbjct: 28  TLQVSKVQIPMRIDKYLTQQVENATRNKVQEAIEEERVLVNGRPVKSNYRIKSCDTILIT 87

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
            +      +  E   +D               ++YEDS + V NK  G+ V    G    
Sbjct: 88  FLRPPAPELAPEDIPID---------------IVYEDSDLMVVNKEPGMVVHPAFGNWTG 132

Query: 128 -------HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                  H  G     +D+   +P + HRLD++TSG++++A+   A   L   F MR++Q
Sbjct: 133 TLANAILHHIGRDAESLDASELRPGIVHRLDKDTSGLIIIAKNPTALHRLARQFAMRQVQ 192

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY ++VWG+P  +   I   + + S      +           +AI+ + +++     F
Sbjct: 193 KIYKAIVWGVPDPRSGTILTNIGR-SKKNRKIMANYPYEGLDGKHAITDY-LVEENLHWF 250

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----------SPIQNKLY 289
             + +  HTGRTHQ+R H  H G PI+GD  Y                      I  +  
Sbjct: 251 SVVSLTLHTGRTHQIRAHMQHTGNPILGDETYGGTVIRTLPFSKSESFVTNLLEIMPRQA 310

Query: 290 LHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           LHA  +    P    +L  ++PLP  M +T + + 
Sbjct: 311 LHAETLSFSQPTTHEKLTFSSPLPTDMQRTLEKIR 345


>gi|293603991|ref|ZP_06686404.1| ribosomal large subunit pseudouridine synthase C [Achromobacter
           piechaudii ATCC 43553]
 gi|292817595|gb|EFF76663.1| ribosomal large subunit pseudouridine synthase C [Achromobacter
           piechaudii ATCC 43553]
          Length = 301

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 94/315 (29%), Positives = 155/315 (49%), Gaps = 20/315 (6%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+++    RLD +       +   ++ K +R G+VRV+K R+  + RI +G +VRIPP
Sbjct: 2   VEVDDEHAGQRLDNFLMRLCKGVPKTHIYKAIRGGEVRVNKGRISVDYRIVAGDIVRIPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +                     +     +  +++ED  + V +KPAG++V GGSG+++ +
Sbjct: 62  LRL-------------PDPGKPRPVPGAEFPVVFEDDALLVVDKPAGVAVHGGSGVSFGV 108

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++      +   L HRLD+ETSG+L+VA+ R+A   L    R  +  K Y +LV G
Sbjct: 109 IEQLRAAR-PDAKFLELVHRLDRETSGLLMVAKKRSALLALHAMLREGKGDKHYLALVEG 167

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N ++ I   L K +   G+    V  + + A+  I+    +      +  ++ +  T
Sbjct: 168 DWVNDRQHIKLGLSKWTTQSGERRVKVDPDGQTAHTIIT----LKQRFGGYSLVDAELRT 223

Query: 250 GRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           GRTHQ+RVH    G PIVGD KY   + +  F+     +++LHA  + L HP  G  + +
Sbjct: 224 GRTHQIRVHLAASGFPIVGDDKYGHDDVRAEFSRMGFGRMFLHAHQLTLAHPVTGESMTL 283

Query: 308 TAPLPAHMVKTWDSL 322
           TA LP    K    L
Sbjct: 284 TAELPPACRKILKQL 298


>gi|255022986|ref|ZP_05294972.1| hypothetical protein LmonocyFSL_05005 [Listeria monocytogenes FSL
           J1-208]
          Length = 302

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 143/323 (44%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++E      R+D+         +   +Q +L++G + V+ +  K N ++Q G  +  
Sbjct: 4   ETLIIEESHARERVDKVIAEMM-GKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                    ++ E   LD               + +ED  + V NKP G+ V   +G A 
Sbjct: 63  EVREPEELEVLAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHAS 107

Query: 127 -YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 108 GTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + +      + VV+        A +HF+V++     + 
Sbjct: 168 EYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVLERLP-GYT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++ +  TGRTHQ+RVH  ++G P+ GD KY         +   N  +LHA  +   HP 
Sbjct: 222 LIKCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTIKGNGQFLHAAKLGFDHPT 276

Query: 302 G-GRLQITAPLPAHMVKTWDSLG 323
              R+   APLP    K   SL 
Sbjct: 277 TNERMTFEAPLPNSFEKALKSLR 299


>gi|271500125|ref|YP_003333150.1| pseudouridine synthase, RluA family [Dickeya dadantii Ech586]
 gi|270343680|gb|ACZ76445.1| pseudouridine synthase, RluA family [Dickeya dadantii Ech586]
          Length = 320

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 105/324 (32%), Positives = 170/324 (52%), Gaps = 14/324 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ +  +E   R+D + +     +    + +ILR G+VRV+KKRVK   ++  G  +R
Sbjct: 8   VQFLTISAEEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRVKPEYKLLDGDEIR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +      E++    S +L K S  L + +LYED  + + NKP+G +V GGSG++
Sbjct: 68  IPPVRQS------EREEAAVSASLDKVS-ALANCILYEDDYLLLLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRAKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FKV + F      +   
Sbjct: 180 VRGQWQSHCKSVQAPLLKNVLQSGERIVRVNSE---GKPSETLFKVEERF-DCATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  H G PI  D +Y   +F          +L+LHA+ +   HP  G  
Sbjct: 236 PITGRTHQIRVHTQHAGHPIAFDDRYGDRDFDAQLADTGLKRLFLHAQALRFEHPHTGET 295

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           L+I APL A +      L  +  +
Sbjct: 296 LRIEAPLDAGLRHCLQVLRQRQSQ 319


>gi|221066026|ref|ZP_03542131.1| pseudouridine synthase, RluA family [Comamonas testosteroni KF-1]
 gi|220711049|gb|EED66417.1| pseudouridine synthase, RluA family [Comamonas testosteroni KF-1]
          Length = 358

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 141/328 (42%), Gaps = 31/328 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVR 66
           + + V  +    R+D+         +   LQ++L  G V ++ K + K + ++  G  +R
Sbjct: 43  RELTVAAEHHGQRVDKVLALGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLR 102

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +                  +  ++    + +   ++YED  + V NKPAG+ V    G  
Sbjct: 103 VEMR--------------PTQQSMAFQPEAMDLQVVYEDEDLLVINKPAGLVVHPAPG-- 146

Query: 127 YHIDGFLKSWVDSKGQKPR------LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            +  G L + + ++ +K R      + HRLD++TSG++VVAR R+    L +    R + 
Sbjct: 147 -NWTGTLLNGLLARDEKARQVPRAGIVHRLDKDTSGLMVVARNRSTMDALIKMIAAREVS 205

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +L      ++K    +  + +       + VV  N      A + F ++D  A   
Sbjct: 206 RQYLALAHKQWGSRKRREVDAPIGRDPRNRLRMAVVDLNLHPGKQARTDFDLLDGDA-AH 264

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +    HTGRTHQ+RVH   +G P++ D  Y    +G        +  LHA  +   HP
Sbjct: 265 SLVRCTLHTGRTHQIRVHMASLGHPLIADTLYGGQPEGGLE-----RQALHAFRLAFEHP 319

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYD 327
              + L   APLP  M    D  G +Y+
Sbjct: 320 VTKKPLVHHAPLPQDMAGALDLWGLRYN 347


>gi|296123932|ref|YP_003631710.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
 gi|296016272|gb|ADG69511.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
          Length = 345

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 94/331 (28%), Positives = 150/331 (45%), Gaps = 36/331 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + VE      R+D +    YP+ + V  Q+ +  G+V V+   VK + R++   V+    
Sbjct: 17  LTVEARAHGWRIDHYLSRLYPNFSRVAFQRTIEEGKVLVNGLPVKISRRLRVNDVIEFSL 76

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYH 128
                  +  E   LD               +LY+D  + V NK A + V  G G     
Sbjct: 77  PAEPDQRVQPEDIPLD---------------ILYDDEYLCVINKTANMIVHPGRGNYRGT 121

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           + G L+   DS        +  + HRLD++TSG+LVVA+     QHL+  F  R ++K Y
Sbjct: 122 LAGALQFHFDSLSDVAGQYRAGIVHRLDRDTSGVLVVAKDNTVHQHLSRQFEERSVEKEY 181

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++VWG  +   + +  + ++ S    + + V    +  A  A + ++V   F + F ++
Sbjct: 182 HAIVWGEMQFDADYVETY-VRVSFRNRERMMVCPPGD-NARQAATFYEVQQRF-RGFTYV 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-----------CANFKGNFTSPIQNKLYLHA 292
           ++QP TGRTHQLRVH  H+G PI+ D  Y                      + ++  LHA
Sbjct: 239 KLQPQTGRTHQLRVHMHHLGHPIIADRLYEGKTCVKLSDILPETPEEADETLIDRQALHA 298

Query: 293 RYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           R +   HP    R+   APLPA   KT D+L
Sbjct: 299 RRLAFNHPVTKKRMVFEAPLPADFQKTLDTL 329


>gi|183597510|ref|ZP_02959003.1| hypothetical protein PROSTU_00783 [Providencia stuartii ATCC 25827]
 gi|188023155|gb|EDU61195.1| hypothetical protein PROSTU_00783 [Providencia stuartii ATCC 25827]
          Length = 325

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 84/332 (25%), Positives = 153/332 (46%), Gaps = 41/332 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + +  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKPKEKVLGGEQILVDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +I   N    +   LD               ++YED  I V NKP G+ V  G+G     
Sbjct: 70  LIEEDNRWEPQDIPLD---------------VVYEDEDILVINKPRGLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + +     +  + HRLD++T+G++VVA+T  A   L ES ++R I + Y ++
Sbjct: 115 ILNALLHRYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAV 174

Query: 187 VWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             G        +E I+    K++H+    +            AI+H++V++ F +    L
Sbjct: 175 AVGRMTAGGMVEEPISRHPTKRTHMAVHPM---------GKPAITHYRVMEHF-RAHTRL 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYM 295
            ++  TGRTHQ+RVH  H+  P++GD  Y    +    +  +        ++  LHA  +
Sbjct: 225 RLRLETGRTHQIRVHMAHINHPLIGDPLYGGRPRPLKGASEEFFEVMRKFDRQALHATML 284

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
            L HP  G +++  APLP  MV+  ++L   Y
Sbjct: 285 RLYHPISGIQMEWHAPLPDDMVELIEALKADY 316


>gi|301155711|emb|CBW15179.1| 23S rRNA pseudouridylate synthase [Haemophilus parainfluenzae T3T1]
          Length = 326

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 165/319 (51%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  DE   R+D +       +    + +ILR G+VRV+K R+K   ++Q+G    
Sbjct: 13  VKMLTISEDEAGQRIDNYLLAKLKGVPKSLIYRILRKGEVRVNKGRIKPEYKLQNGD--- 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E+     S NL K +  L+S +L+ED  + V NKP+GI+V GGSG+ 
Sbjct: 70  ---VVRVPPVRVSEKNTAPISKNLNKVA-SLESHILFEDDCLLVLNKPSGIAVHGGSGLN 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+A ++L E  R++ +QK Y +L
Sbjct: 126 FGVIEALRA-LRPEARFLELVHRLDRDTSGILLVAKKRSALRNLHEQLRVKTVQKDYLAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V +       + + F + + + Q    ++  
Sbjct: 185 VRGQWQSHVKVVQAPLLKNELASGERIVKVSEQ---GKPSETRFSIEERY-QNATLVKAS 240

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP+ G  
Sbjct: 241 PVTGRTHQIRVHTQYAGHPIALDDKYGDKEFDKYMQDLGLNRLFLHAFSIRFEHPKTGET 300

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L++ A L   M      L 
Sbjct: 301 LRLNAQLDEKMKAILKKLR 319


>gi|332977603|gb|EGK14371.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter sp.
           1501(2011)]
          Length = 364

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 97/318 (30%), Positives = 158/318 (49%), Gaps = 23/318 (7%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V ++ V   +   R+D +       +   ++ K++RS +VR++ KR K  + ++ G V
Sbjct: 60  SQVNHLEVTRHQHGQRVDNFLLARLKGMPRAHIYKMIRSDEVRINNKRCKPYDNLERGDV 119

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRI PV  A     +E+ ++         +  L   ++YED  + V NKP+G++V GGSG
Sbjct: 120 VRIAPVRLAT----REKPVISEGF-----AKSLLERVVYEDEGLIVLNKPSGMAVHGGSG 170

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + + +   ++     K     L HR+D++TSG+L++A+ R+  + L E  R + IQK Y 
Sbjct: 171 LDFGVIEAMRDATSKKY--LELVHRIDKDTSGLLMIAKKRSTLKVLQEYLREKTIQKHYL 228

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI---DCFAQKFC 241
            +V G P      I   LL+ +   G+    V +N   A  + +  KV+   +   +   
Sbjct: 229 CIVKGQPALNDISIDAPLLRYTLASGERRVRVDKNSPDAKTSQTTCKVLARFEINGEPVS 288

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E  PHTGRTHQ+RVH  ++G PI+GD KY              +L LHA  +D+P  E
Sbjct: 289 LIEAMPHTGRTHQIRVHLAYLGHPILGDDKYHIQDTSGV-----RRLCLHAWQLDIPEYE 343

Query: 302 GGRLQITAPLPAHMVKTW 319
                I APLP  M    
Sbjct: 344 T----IKAPLPEDMQSLL 357


>gi|238754377|ref|ZP_04615733.1| Ribosomal large subunit pseudouridine synthase C [Yersinia ruckeri
           ATCC 29473]
 gi|238707410|gb|EEP99771.1| Ribosomal large subunit pseudouridine synthase C [Yersinia ruckeri
           ATCC 29473]
          Length = 320

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 98/315 (31%), Positives = 163/315 (51%), Gaps = 14/315 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +       +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++    S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREDAPVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +L
Sbjct: 121 FGVIEALRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ V  V         + + FKV + F +    ++  
Sbjct: 180 VRGQWQSHCKAVQAPLLKNIMQSGERVVKVSSE---GKPSETRFKVEERF-EHCTLVKAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVHALH G PI  D +Y   +F         ++L+LHA  +   HP+ G  
Sbjct: 236 PITGRTHQIRVHALHAGHPIAFDDRYGDRDFDLQLKGTGLHRLFLHAAALRFAHPDTGET 295

Query: 305 LQITAPLPAHMVKTW 319
           ++I APL   +    
Sbjct: 296 MRIEAPLDNQLRHCL 310


>gi|313623251|gb|EFR93499.1| ribosomal large subunit pseudouridine synthase D [Listeria innocua
           FSL J1-023]
          Length = 297

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 82/321 (25%), Positives = 142/321 (44%), Gaps = 34/321 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++E      R+D+         +   +Q +L++G + V+ +  K N ++Q G  +R   
Sbjct: 1   MIIEESHARERVDKVIAEMM-GKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIRYEA 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
                  I+ E   LD               + +ED  + V NKP G+ V   +G A   
Sbjct: 60  REPEELEILAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHASGT 104

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   + Y
Sbjct: 105 LVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREY 164

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G   ++K  I   + + +      + VV+        A +HF+VI+     +  +
Sbjct: 165 IALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVIERLP-GYTLI 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
             +  TGRTHQ+RVH  ++G P+ GD KY         +   N  +LHA  +   HP   
Sbjct: 219 NCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTIKGNGQFLHAAKLGFDHPTTN 273

Query: 303 GRLQITAPLPAHMVKTWDSLG 323
            R+   APLP    +   SL 
Sbjct: 274 ERMTFEAPLPDSFEQALKSLR 294


>gi|194366931|ref|YP_002029541.1| RluA family pseudouridine synthase [Stenotrophomonas maltophilia
           R551-3]
 gi|194349735|gb|ACF52858.1| pseudouridine synthase, RluA family [Stenotrophomonas maltophilia
           R551-3]
          Length = 329

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 84/344 (24%), Positives = 144/344 (41%), Gaps = 38/344 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  +V +     R D      +P  +   L + +++G V +D  + +  + ++ G+VV +
Sbjct: 10  RQAIVPDTSAGRRFDAVVAELFPEYSRSRLTEWIKNGDVLLDGAQARPRDPLRGGEVVTL 69

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             V+        E   LD               +L+ED  + V NKP G+ V  G+G   
Sbjct: 70  TVVLETQTDAQPEDIPLD---------------VLFEDEYLLVINKPVGLVVHPGAG--N 112

Query: 128 HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           H    + + +          +  + HRLD++TSG++VVA+T  A   L E    R + + 
Sbjct: 113 HSGTLVNALLFRDPSVAVLPRAGIVHRLDKDTSGVMVVAKTLEAQTALVEQLAARDVHRQ 172

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G         A+  + +       + V     +    A++H+++ + F +    
Sbjct: 173 YLAIVMGALVA--GGTADAPIDRHPRDRLKMGVR----EDGKEAVTHYRLRERF-RAHTA 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARY 294
           LE +  TGRTHQ+RVH  H+  PIVGD  Y    K                 +  LHA  
Sbjct: 226 LECRLETGRTHQIRVHMAHIRHPIVGDPLYGGALKLPKGASDELVAALRGFKRQALHAET 285

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           ++  HP  G  ++ TAP+PA M+     L    D     +R   
Sbjct: 286 LEFVHPITGETVRNTAPVPADMLHLLKVLREDSDAFAARERDRW 329


>gi|303229468|ref|ZP_07316258.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302516004|gb|EFL57956.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 305

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 82/315 (26%), Positives = 136/315 (43%), Gaps = 32/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++E  RLD +  +     +   +Q +++SG V V+ K  K N R+ +   + +    
Sbjct: 6   VSLEQEGKRLDVFLTDVMEG-SRSYIQSLIKSGHVLVNGKVGKANLRLNADSTISVDIPE 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHI 129
                I+ E   ++                LYED  I + NKP G+ V    G+     +
Sbjct: 65  PESVEILPEDIPVEY---------------LYEDHDIIIVNKPRGMVVHPAIGNYSGTLV 109

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HRLD++TSG+++ A+  AA   L E  +    ++ Y +
Sbjct: 110 NALLYHCKDLSGINGEIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKAHSAKRTYLA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G    +K  I   + +        + VV +N   +  A++HFKV++ +      +E 
Sbjct: 170 LVQGNIVEEKGIIKAPIGRHPK-DRMKMAVVFEN---SKEAVTHFKVLERYG-YHTLVEC 224

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
              TGRTHQ+RVH  H+G P+V D  Y                 LH+  +D+ HP  G  
Sbjct: 225 VLETGRTHQIRVHFAHIGHPVVNDPFYGYRR----MDFPIEGQALHSHTLDVVHPITGEP 280

Query: 305 LQITAPLPAHMVKTW 319
           +   AP+P       
Sbjct: 281 MHFEAPVPEDFQNCI 295


>gi|307131541|ref|YP_003883557.1| Ribosomal large subunit pseudouridine synthase C [Dickeya dadantii
           3937]
 gi|306529070|gb|ADM99000.1| Ribosomal large subunit pseudouridine synthase C [Dickeya dadantii
           3937]
          Length = 318

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 104/319 (32%), Positives = 167/319 (52%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ++ V ++E   R+D + +     +    + +ILR G+VRV+KKR+K   ++  G  VR
Sbjct: 8   VQFLTVSSEEAGQRIDNFLRTRLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLLDGDEVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  +      E++    S +L K S  L   +LYED  + + NKP+G +V GGSG++
Sbjct: 68  IPPVRQS------EREEPAVSASLDKVS-ALVDCILYEDDYLLLLNKPSGTAVHGGSGLS 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRGKGMQKDYLAL 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V         + + FKV + F      +   
Sbjct: 180 VRGQWQSHCKAVQAPLLKNVLQSGERIVRVNSE---GKPSETLFKVEERF-DCATLVRAS 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D +Y    F          +L+LHA  +   HP  G  
Sbjct: 236 PITGRTHQIRVHTQYAGHPIAFDDRYGDREFDAQLAGTGLKRLFLHALALRFEHPHTGET 295

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++I APL A +     +L 
Sbjct: 296 MRIEAPLDAGLRHCLQALR 314


>gi|163850438|ref|YP_001638481.1| RluA family pseudouridine synthase [Methylobacterium extorquens
           PA1]
 gi|163662043|gb|ABY29410.1| pseudouridine synthase, RluA family [Methylobacterium extorquens
           PA1]
          Length = 343

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 91/345 (26%), Positives = 152/345 (44%), Gaps = 48/345 (13%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
             + +V++      RLDR     +  ++   LQ ++R G VR D   V+    ++ +G  
Sbjct: 20  EARSLVLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCDGIVVRDPARKVGAGCR 79

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +                + + +      + L   +++ED  + V +KPAG+ V   +G
Sbjct: 80  IDLS---------------VPAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPAAG 124

Query: 125 IAYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              H DG L + + +            ++P + HRLD++TSG+LVVA+   A Q L+  F
Sbjct: 125 ---HEDGTLVNRLIAHCGASLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQF 181

Query: 175 RMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
                   +++ Y +LVW +P+ +   I   L +  H   + + VV+  E     AI+H+
Sbjct: 182 ADHGRSGALERAYLALVWNVPEPRAGTIRANLARSRH-NREKIAVVRDGE--GREAITHY 238

Query: 231 KVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GN 279
           +V D   +      L     TGRTHQ+RVH  H G P++GD  Y   FK           
Sbjct: 239 RVEDVHGEGGVTALLRCHLETGRTHQIRVHLSHRGHPLLGDAVYGGAFKTKAARLSEPAR 298

Query: 280 FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLG 323
                  +  LHA  +   HP  G RL+  +PLP    +   +LG
Sbjct: 299 AALDALGRQALHAVELGFLHPRSGERLRFESPLPEDFSRLLAALG 343


>gi|75909134|ref|YP_323430.1| ribosomal large subunit pseudouridine synthase D [Anabaena
           variabilis ATCC 29413]
 gi|75702859|gb|ABA22535.1| ribosomal large subunit pseudouridine synthase D [Anabaena
           variabilis ATCC 29413]
          Length = 312

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 148/328 (45%), Gaps = 31/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSG 62
           M    Y+ VE +    R+DR+     P ++   +Q+++  G+V+V+ K        ++ G
Sbjct: 1   MLNEFYLEVEENSA--RIDRYLAEELPDLSRSRIQQLIEQGKVQVNGKVCTSKKINLKVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +                +  +  L   ++ +   +LYED ++ + NKPAG+ V   
Sbjct: 59  DRITLE---------------VPEAQPLELQAEDIPLDILYEDDQLLILNKPAGLVVHPA 103

Query: 123 SGIAY--HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G ++   ++  L       G    Q+P + HRLD++T+G + +A+T  A +H+    + 
Sbjct: 104 PGHSHGTLVNALLAHCPHLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKHIQAQLQT 163

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           +  ++ Y  +V+G PK     +   + +  H        +   E+G   AI+H+++ +  
Sbjct: 164 KTARREYLGVVYGAPKTSSGKVDLPIGR--HPQDRKKMAIVPVEEGGRSAITHWQIQERL 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              F  +  Q  TGRTHQ+RVH+  +G PIVGD  Y +        P      LHA  + 
Sbjct: 222 G-NFTLIHFQLETGRTHQIRVHSAKIGHPIVGDPVYGSGRSVGVNLPG---QALHAWRLR 277

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           L HP  G  +++TA  P       + L 
Sbjct: 278 LQHPITGDWVEVTATPPQSFTTLLEILR 305


>gi|327460457|gb|EGF06794.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1057]
          Length = 298

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 145/322 (45%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E      RLD+        ++     + ++  ++ V+ +  K    ++ G V+   
Sbjct: 2   EVRIEASVAGQRLDKAVAE-LTDLSRSLAHEQIKDSRILVNGQAKKAKYAVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++        ++ +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELPEPEVVE------YVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ FA  +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFAD-YSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA +P    +T + L 
Sbjct: 275 GEVLEFTAEVPVIFQETLEKLR 296


>gi|209525222|ref|ZP_03273765.1| pseudouridine synthase, RluA family [Arthrospira maxima CS-328]
 gi|209494407|gb|EDZ94719.1| pseudouridine synthase, RluA family [Arthrospira maxima CS-328]
          Length = 308

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 86/325 (26%), Positives = 143/325 (44%), Gaps = 29/325 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           ++ +  + D EN RLD+W       ++   LQ ++ SG V ++          +Q G  +
Sbjct: 3   IELICEDKDGENQRLDKWLSERVHQLSRSRLQALISSGHVWINNSPCTSKKATVQIGDRI 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           ++                +  ++ L   +  +   +LYED ++ + NKPAG+ V    G 
Sbjct: 63  QVE---------------IPPAIPLELKATNIPLDILYEDEELLIINKPAGLVVHPAPGH 107

Query: 126 AYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                 +  L       G    Q+P + HRLD++T+G + +A+T  A QHL    + +  
Sbjct: 108 ENDTLVNALLAHCETLAGIGGVQRPGIVHRLDKDTTGAIAIAKTDHAHQHLQAQIQAKTA 167

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y  +++G+PK     I   + +  H        +    +G   AI+H+KV +     
Sbjct: 168 RRQYLGIIYGVPKTTSGVIDQPIGR--HPSDRQKMAIVPQHQGGRSAITHWKVKERLG-N 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +E +  TGRTHQ+RVH+  MG PIVGD  Y          P      LHA  + L H
Sbjct: 225 YTLIEFELETGRTHQIRVHSASMGHPIVGDRVYGKGRSVGVNLPG---QALHAWKLTLQH 281

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  G  ++  APLP  M      L 
Sbjct: 282 PTSGELIEAIAPLPHTMTTLLKVLR 306


>gi|78065696|ref|YP_368465.1| pseudouridine synthase, RluD [Burkholderia sp. 383]
 gi|77966441|gb|ABB07821.1| Pseudouridine synthase, RluD [Burkholderia sp. 383]
          Length = 334

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 99/326 (30%), Positives = 160/326 (49%), Gaps = 23/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++      R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +V
Sbjct: 16  QVSMLEIDESSVGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDIV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + + +  +    +           +L+ED  + V NKPAG++V GGSG+
Sbjct: 76  RVPPVRVAAADLARAEATIVPPAHFD---------VLFEDDAMLVINKPAGVAVHGGSGV 126

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++     + +   L HRLD+ETSG+L++A+ R A   L E  R  ++ K Y++
Sbjct: 127 AFGVIEQMRQAR-PRAKFLELVHRLDRETSGVLMLAKKRTALVGLHEQIRENKMDKRYFA 185

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G  ++       +   L K S   G+    V+ +      + + F ++D + + +  
Sbjct: 186 CVHGEWQSDWGRRRAVKAPLFKYSTPEGERRVRVQDD---GLPSHTVFNLVDLWPE-YAL 241

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           LE +  TGRTHQ+RVH  H+G PI GD KY               P   +++LHA  + L
Sbjct: 242 LEAELKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANAQPSLKRMFLHAYRLRL 301

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLP    +  D L
Sbjct: 302 AHPLTGEALQFDAPLPDECRRFLDQL 327


>gi|251772724|gb|EES53286.1| Ribosomal large subunit pseudouridine synthase, RluA family
           [Leptospirillum ferrodiazotrophum]
          Length = 313

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 84/320 (26%), Positives = 136/320 (42%), Gaps = 31/320 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  E   RLD +        +   +QKIL  G + V+ +    + +I+   ++ +    
Sbjct: 4   VDPGESKKRLDHFLAQTCLPFSRSRIQKILDEGLITVNGRIEPASYKIRGADIITVHIPP 63

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
            A +    E+               +   +LYED  + V NKP  + V    G       
Sbjct: 64  PAPSEDAPEE---------------MDLDILYEDEFLLVINKPPSLVVHPAPGHPNGTLL 108

Query: 130 DGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +G L      +        +  L HRLDQ TSG+LVV +      HL E FR R + K Y
Sbjct: 109 NGLLGHLSREEAGEGEGPARAGLVHRLDQNTSGLLVVGKKSEVVDHLMEQFRGRTVSKSY 168

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L  GIP +++  I   + + +     +         G   + + ++V+  + + +  L
Sbjct: 169 IALAIGIPPSRRGLIDAPIGRSNGDRKKFAVTS-----GGKPSQTRYRVMTAYREGYSLL 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
           ++   TGRTHQ+RVH  H+G P+ GD  Y    KG   + +  ++ LHA  +   HP  G
Sbjct: 224 DITLLTGRTHQIRVHMQHLGYPLAGDPVY--KKKGRKDNLLFPRIMLHAANLGFTHPITG 281

Query: 303 GRLQITAPLPAHMVKTWDSL 322
             L+  APLP  M      L
Sbjct: 282 EELKFHAPLPPDMQGALSQL 301


>gi|15900809|ref|NP_345413.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae TIGR4]
 gi|111658131|ref|ZP_01408829.1| hypothetical protein SpneT_02000697 [Streptococcus pneumoniae
           TIGR4]
 gi|148992939|ref|ZP_01822558.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP9-BS68]
 gi|149010429|ref|ZP_01831800.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP19-BS75]
 gi|168485879|ref|ZP_02710387.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CDC1087-00]
 gi|168490255|ref|ZP_02714454.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP195]
 gi|169834331|ref|YP_001694382.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae Hungary19A-6]
 gi|182683874|ref|YP_001835621.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CGSP14]
 gi|194398681|ref|YP_002037566.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae G54]
 gi|303259840|ref|ZP_07345815.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP-BS293]
 gi|303262254|ref|ZP_07348198.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP14-BS292]
 gi|303264676|ref|ZP_07350594.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS397]
 gi|303267177|ref|ZP_07353044.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS457]
 gi|303269425|ref|ZP_07355194.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS458]
 gi|14972404|gb|AAK75053.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae TIGR4]
 gi|147764910|gb|EDK71839.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP19-BS75]
 gi|147928391|gb|EDK79407.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP9-BS68]
 gi|168996833|gb|ACA37445.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae Hungary19A-6]
 gi|182629208|gb|ACB90156.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CGSP14]
 gi|183571050|gb|EDT91578.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CDC1087-00]
 gi|183571388|gb|EDT91916.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP195]
 gi|194358348|gb|ACF56796.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae G54]
 gi|301801775|emb|CBW34486.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           INV200]
 gi|302636577|gb|EFL67068.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP14-BS292]
 gi|302639045|gb|EFL69505.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP-BS293]
 gi|302641044|gb|EFL71422.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS458]
 gi|302643292|gb|EFL73572.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS457]
 gi|302645763|gb|EFL75992.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS397]
 gi|332073261|gb|EGI83740.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA17570]
 gi|332076208|gb|EGI86674.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA41301]
 gi|332204930|gb|EGJ18995.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA47901]
          Length = 295

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 146/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETGGLRLDKALSD-LSELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G+ 
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGKT 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+  A +P    +T + L 
Sbjct: 276 LEFKADIPEIFKETLERLR 294


>gi|300867006|ref|ZP_07111676.1| conserved hypothetical protein [Oscillatoria sp. PCC 6506]
 gi|300334989|emb|CBN56842.1| conserved hypothetical protein [Oscillatoria sp. PCC 6506]
          Length = 319

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 87/312 (27%), Positives = 142/312 (45%), Gaps = 28/312 (8%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
            RLD W  N  P ++   +Q ++  G V V+    K     +++G  + I          
Sbjct: 24  QRLDLWLSNELPDLSRSRIQNLILQGNVTVNDLICKSKKENVKNGDRIHI---------- 73

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
                 +  +  L    + +   +LYED  + + NKPAG+ V   +G      ++  L  
Sbjct: 74  -----AIPDAEPLDLKPEAIPLDILYEDESLIIINKPAGLVVHPAAGHPGGTLVNALLAH 128

Query: 136 WVDSK---GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              ++     +P + HRLD++TSG +VVA+T  A QHL    + +  ++ Y  +V+G  K
Sbjct: 129 CPLAEIGGVLRPGIVHRLDKDTSGAIVVAKTDFAHQHLQAQLKAKTARREYLGVVYGTLK 188

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +   I   + + S +    + VV   EKG   A++H+++ +     +  +  Q  TGRT
Sbjct: 189 TENGTIDLPIGRHS-VDRKKMAVVTI-EKGGRSAVTHWQIQERLG-NYTLIHFQLETGRT 245

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           HQ+RVHA  +G PIVGD  Y +N              LHA  + L HP  G  ++  APL
Sbjct: 246 HQIRVHAAQIGHPIVGDPVYSSNHDIGVNLTG---QALHAWRLKLQHPVSGELIEAIAPL 302

Query: 312 PAHMVKTWDSLG 323
           PA      + L 
Sbjct: 303 PAQFNTLLEVLR 314


>gi|305664420|ref|YP_003860707.1| ribosomal large subunit pseudouridine synthase D [Maribacter sp.
           HTCC2170]
 gi|88708437|gb|EAR00673.1| ribosomal large subunit pseudouridine synthase D [Maribacter sp.
           HTCC2170]
          Length = 341

 Score =  259 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 148/330 (44%), Gaps = 35/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +    +E +R+D++  N   +     +Q+  + G + V++K VK N ++++G  V++  
Sbjct: 20  FIASKGQEPLRVDKFLMNFIENATRNKIQQAAKDGHIWVNEKIVKQNYKVKAGDEVKV-- 77

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                 H   E  +   ++ L          ++YED  + V NKPAG+ V  G G     
Sbjct: 78  ---LFEHPPYELLLTPENIPLD---------IVYEDDVLLVVNKPAGMVVHPGHGNYTGT 125

Query: 128 HIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            I+  L    D   +   +P L HR+D++TSG+LVVA+T AA  HL + F  +  ++ Y 
Sbjct: 126 LINALLYHSKDLPVNSNDRPGLVHRIDKDTSGLLVVAKTEAAMTHLAKQFFDKTSEREYV 185

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG  +++   I   + +           V    +    A++H+ V++        + 
Sbjct: 186 ALVWGNVEDESGTIEGNIARNPK--NRLQMQVFPEGEQGKEAVTHYGVLERLG-YVTLVS 242

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHA 292
            +  TGRTHQ+RVH  ++G  +  D +Y  +     T+             I  +  LHA
Sbjct: 243 CKLETGRTHQIRVHMKYIGHTLFNDERYGGDKVLKGTTFTKYKQFVDNAFKILPRQALHA 302

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP  G  ++  + +P  M    D 
Sbjct: 303 KTLGFVHPVSGEMMRFDSEIPEDMSLCIDK 332


>gi|186475584|ref|YP_001857054.1| RluA family pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184192043|gb|ACC70008.1| pseudouridine synthase, RluA family [Burkholderia phymatum STM815]
          Length = 353

 Score =  259 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 99/327 (30%), Positives = 160/327 (48%), Gaps = 25/327 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + +++     R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +V
Sbjct: 19  QVSMLEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAHGDLV 78

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP+           +I  S       +      +L+ED  + V +KPAG++V GGSG+
Sbjct: 79  RVPPI-----------RIAKSDEPAHALAPSAHFDILFEDDHLLVIDKPAGVAVHGGSGV 127

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   L++      +   L HRLD+ETSG+L++A+ RAA  +L E  R  R+ K Y++
Sbjct: 128 AFGVIEQLRAARPQ-AKFLELVHRLDRETSGVLMLAKKRAALVNLHEQIRENRMDKRYYA 186

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G   +       +   L K     G+    V+ +      + + F +I+ +   +  
Sbjct: 187 CVHGEWASDWGRRRAVKEPLHKYLLPDGERRVRVQPD---GLPSHTVFNLIERWPD-YAL 242

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           LE +  TGRTHQ+RVH  H+G PIVGD KY              +    +++LHA  + L
Sbjct: 243 LEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARANANLGLKRMFLHAYRLKL 302

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G+ +Q  APLPA   +    L 
Sbjct: 303 THPASGQTVQFDAPLPAECKRFLAQLA 329


>gi|46908075|ref|YP_014464.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|47094208|ref|ZP_00231922.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|226224446|ref|YP_002758553.1| hypothetical protein Lm4b_01859 [Listeria monocytogenes Clip81459]
 gi|254826115|ref|ZP_05231116.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
 gi|254852749|ref|ZP_05242097.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|254931987|ref|ZP_05265346.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|300763844|ref|ZP_07073841.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
 gi|46881345|gb|AAT04641.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Listeria monocytogenes serotype 4b str. F2365]
 gi|47017415|gb|EAL08234.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|225876908|emb|CAS05617.1| unnamed protein product [Listeria monocytogenes serotype 4b str.
           CLIP 80459]
 gi|258606073|gb|EEW18681.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|293583538|gb|EFF95570.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|293595355|gb|EFG03116.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
 gi|300515580|gb|EFK42630.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
 gi|328466193|gb|EGF37350.1| hypothetical protein LM1816_11407 [Listeria monocytogenes 1816]
 gi|328473565|gb|EGF44402.1| hypothetical protein LM220_09240 [Listeria monocytogenes 220]
 gi|332312284|gb|EGJ25379.1| Pseudouridylate synthase [Listeria monocytogenes str. Scott A]
          Length = 303

 Score =  259 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 143/323 (44%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++E      R+D+         +   +Q +L++G + V+ +  K N ++Q G  +  
Sbjct: 4   ETLIIEESHARERVDKVIAEMM-GKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                    ++ E   LD               + +ED  + V NKP G+ V   +G A 
Sbjct: 63  EVREPEELEVLAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHAS 107

Query: 127 -YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 108 GTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + +      + VV+        A +HF+V++     + 
Sbjct: 168 EYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVLERLP-GYT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH  ++G P+ GD KY         +   N  +LHA  +   HP 
Sbjct: 222 LINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTIKGNGQFLHAAKLGFDHPT 276

Query: 302 G-GRLQITAPLPAHMVKTWDSLG 323
              R+   APLP+   K   SL 
Sbjct: 277 TKERMMFEAPLPSSFEKALKSLR 299


>gi|312865253|ref|ZP_07725481.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
 gi|311099364|gb|EFQ57580.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
          Length = 298

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 144/317 (45%), Gaps = 34/317 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           EE +RLD+   +   +++     + ++ G V V+ +  K    +++G V+          
Sbjct: 7   EEGLRLDKALAD-LSNLSRSQANQAIKDGSVLVNGRPKKAKYSVKAGDVISFEE------ 59

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL 133
               E+++LD        ++ L   ++YED  + V NKP G+ V    G      ++  L
Sbjct: 60  ---PEEEVLD------YQAENLPLEIVYEDQDLAVVNKPQGMVVHPSVGHSSGTLVNALL 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L+VA+   A Q L +  + ++  + Y ++V G
Sbjct: 111 YRIKDLSTINGVVRPGIVHRIDKDTSGLLMVAKNDQAHQALADELKAKKSLRKYLAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +            K        A++HF V++ F   +  LE++  T
Sbjct: 171 NLPNDRGKIEAPIGRSEKDRKKQAVTAK-----GRPAVTHFHVLERFG-NYSLLELRLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G+ L+ +
Sbjct: 225 GRTHQIRVHMAYIGHPLAGDPLYGPR-----KTLKGHGQFLHAQTLGFTHPRTGQVLEFS 279

Query: 309 APLPAHMVKTWDSLGFK 325
              PA   +T + L  +
Sbjct: 280 VQPPAIFQETLEKLRAR 296


>gi|291614496|ref|YP_003524653.1| pseudouridine synthase, RluA family [Sideroxydans lithotrophicus
           ES-1]
 gi|291584608|gb|ADE12266.1| pseudouridine synthase, RluA family [Sideroxydans lithotrophicus
           ES-1]
          Length = 331

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 139/325 (42%), Gaps = 30/325 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  +   +RLD+     +P  +   LQ  +  G V V+ K      ++  G+ + + P I
Sbjct: 25  VPMEHGGLRLDQALVKLFPEYSRSRLQDWVEQGLVTVNGKAGSVKQKVWGGEHISVSPQI 84

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
           +                    H++ +   ++YED  + + NKP G+ V  GSG      +
Sbjct: 85  HPSEQP--------------YHAEDIPLDIVYEDDAMLIINKPVGLVVHPGSGNWQGTLL 130

Query: 130 DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L      +   +  + HRLD++TSG++VVA++  A   L    + R +++ Y +LVW
Sbjct: 131 NALLHHAPQLADVPRAGIVHRLDKDTSGLMVVAKSLVAQTALVRQMQARSVKREYLALVW 190

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G   ++   I   + +          V     +    AI+H  + + F      +  +  
Sbjct: 191 GEL-DRDYTINVPIGRHPSQ-----RVKMATTESGKEAITHVGIEERFP-YCTLVRCRLE 243

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           TGRTHQ+RVH  H+G P++GD  Y         +         +  LHA  + L HP  G
Sbjct: 244 TGRTHQIRVHMTHIGHPLIGDAVYQRGTQKCSPQLRELLNGFPRQALHATQLALNHPVTG 303

Query: 304 -RLQITAPLPAHMVKTWDSLGFKYD 327
            R++  +PLP  M +  + +    D
Sbjct: 304 ERMEFHSPLPEDMEELLEQIDEASD 328


>gi|268319474|ref|YP_003293130.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
 gi|262397849|emb|CAX66863.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
          Length = 304

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 150/327 (45%), Gaps = 35/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    +V++ ++   RLD+        ++   +++++    + V+ K  K + ++QSG 
Sbjct: 1   MTKNYKLVIDGEKG--RLDKVITEKITDLSRTKIKELVNDKNILVNNKAEKVSYKVQSGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +                +     L+  ++ L   ++YEDS + V NKP G+ V   +
Sbjct: 59  VIDVT---------------IPPVKPLSLEAENLHLDIVYEDSDVIVVNKPQGMVVHPSA 103

Query: 124 GIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +G L    D     +G +P + HR+D++TSG+L++A+   A + L +    +
Sbjct: 104 GHPDHTLVNGLLYHTRDLADSPEGFRPGIVHRIDKDTSGLLMIAKNDRARESLEKQLAKK 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ++ Y ++V G  + K   I   + +  +         K        A++HF V++ F 
Sbjct: 164 INKREYLAIVHGNFEVKNGVINAPIGRNPNSRKQMAVNPK-----GKAAVTHFTVLEQF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  ++    TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +  
Sbjct: 218 KNYSLVKCVLETGRTHQIRVHMKYIGHPLAGDPLYGPK-----KTLSGHGQFLHAKTLGF 272

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
             P     L+ +APLP    K  ++L 
Sbjct: 273 YQPSTNEWLEFSAPLPTIFEKQLENLR 299


>gi|318040686|ref|ZP_07972642.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp.
           CB0101]
          Length = 404

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 86/313 (27%), Positives = 135/313 (43%), Gaps = 28/313 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW     P  +   +QK + SG VRV+    +    ++    V +          
Sbjct: 21  PMRLDRWLVAQRPEQSRARIQKFIESGYVRVNGVTGRAKTPLRQSDTVELWMPPPEPLPY 80

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
           +  Q+I                 +L+ED  + V NKPAG++V    G      ++G L  
Sbjct: 81  LMPQEI--------------PLDVLFEDEHLIVLNKPAGLTVHPAPGNKDGTLVNGLLHH 126

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +VVA+++ A   L    + R   + Y ++V G+P
Sbjct: 127 CPDLPGISGKLRPGIVHRLDKDTTGCIVVAKSQEALVKLQVQIQKRIASREYLAVVHGVP 186

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             +   I   + +       Y  V   ++    +A +H+ +++     +  +  +  TGR
Sbjct: 187 AAEHGTIVGAIGRHPADRKKYAVV---HDDSGRHACTHWTLVERLGD-YSLMRFKLDTGR 242

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH  H+G PIVGD  Y    K     P      LHA  + L HP    R+   AP
Sbjct: 243 THQIRVHCAHIGHPIVGDPVYSRCRKLPMALPG---QALHAFQLGLDHPISRERMLFEAP 299

Query: 311 LPAHMVKTWDSLG 323
           LP    K    L 
Sbjct: 300 LPEVFEKLLAVLR 312


>gi|300771291|ref|ZP_07081167.1| ribosomal large subunit pseudouridine synthase D [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|300761961|gb|EFK58781.1| ribosomal large subunit pseudouridine synthase D [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 348

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 140/332 (42%), Gaps = 38/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +  +R+D++  N   + +   +Q  + +G V V+   +K + +++   ++ +  
Sbjct: 22  IEVDKGQALLRIDKFLMNRVENASRNKIQNAIDAGSVLVNDSVIKSSYKVKPFDIISV-- 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
                        + D   +   + + +   +++ED ++ V NK AG+ V  G +     
Sbjct: 80  ------------VLPDPPRDTEVYPEDIPLDIIFEDDEVMVVNKVAGMVVHPGFNNYTGT 127

Query: 129 IDGFLKSWVDS------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   L    +          +P L HR+D++TSG+LV+A++  A  +L + F    I + 
Sbjct: 128 LVNALTHHFNQLPTMPGNAGRPGLVHRIDKDTSGLLVIAKSEWAMTYLAKQFFDHSIMRK 187

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++VWG        +  ++ +        V  +  + +   ++++H++V++        
Sbjct: 188 YVAMVWGDIAED-GTVTGYIGRNLK--DRRVMTMYDDSEKGKWSVTHYRVLERLG-YVTL 243

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYL 290
           +E Q  TGRTHQ+R H   +G P+  D  Y  +     T              +  +  L
Sbjct: 244 IECQLETGRTHQIRAHMQSIGHPLFNDVAYGGDRILKGTVFNKYRQFVENCFALLPRQAL 303

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA+ +   HP+    L    PLP       + 
Sbjct: 304 HAQVLGFEHPKSKEFLTFETPLPEDFRLALEK 335


>gi|159899422|ref|YP_001545669.1| RluA family pseudouridine synthase [Herpetosiphon aurantiacus ATCC
           23779]
 gi|159892461|gb|ABX05541.1| pseudouridine synthase, RluA family [Herpetosiphon aurantiacus ATCC
           23779]
          Length = 323

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 85/343 (24%), Positives = 146/343 (42%), Gaps = 29/343 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     +  + V   E   RLDR    + P ++   +Q+++    +RV+ +  K +  +Q
Sbjct: 1   MEPTANLTTIQVGEAEAGQRLDRLVSANMPDLSRTYVQQLITDLHIRVNGRGAKASLPVQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + I   +     I+ E   LD               ++YED+ + + NK AG+ V 
Sbjct: 61  IGDQIEIFLPLAKPTDIVAEDLPLD---------------VIYEDADVLLVNKAAGMVVH 105

Query: 121 GGSG--IAYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
              G      ++  L  +     S   +P + HRLD+ETSG+LV+A+   A   LTE   
Sbjct: 106 PAPGHTTGTLVNALLYRYPHLTTSGDLRPGIVHRLDKETSGLLVIAKHDQARMMLTEQQM 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            RR+ K Y +LV G  +     I   + +  +     + +         YA++H++V++ 
Sbjct: 166 ARRMHKKYLALVEGHWREPTGTIDAPIGRNPNNRLRMMVM-----PEGRYAVTHYQVLEV 220

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
               +  +     TGRTHQ+RVH  +   PI+ D  Y         +    + +LHA ++
Sbjct: 221 LG-PYSLVRATLETGRTHQIRVHFSYRNRPILNDALYGHRKPKE--TFGIERHFLHAYHL 277

Query: 296 DLPHPEGGRLQ-ITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
               P  G       PLPA + K   +L  +Y+  +Y   L  
Sbjct: 278 GFRLPSTGEWCSWEVPLPAELEKILTTLRTRYETIVYPDPLIE 320


>gi|94497522|ref|ZP_01304091.1| Pseudouridine synthase, RluD [Sphingomonas sp. SKA58]
 gi|94422939|gb|EAT07971.1| Pseudouridine synthase, RluD [Sphingomonas sp. SKA58]
          Length = 317

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 84/336 (25%), Positives = 149/336 (44%), Gaps = 35/336 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVR---VDKKRVKFNN 57
           M L   +    +   +  +RLDR   +  P ++   L+ ++  GQV    V   R+  + 
Sbjct: 1   MVLGDSIIEATIGPAQHGLRLDRALADLLPDLSRERLKTLIGDGQVHSAPV--GRISGSM 58

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           ++  GQ   I                L   V L   +  +   +++ED+ + V +KPAG+
Sbjct: 59  KVAEGQRFTIT---------------LPPPVPLDTVAQDIPLTIVHEDADLLVVDKPAGL 103

Query: 118 SVQGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHL 170
            V   +G      ++  L              +P + HR+D++TSG+LVVA+T  A + L
Sbjct: 104 VVHPAAGNLDGTLVNALLHHCAGQLSGIGGVARPGIVHRIDKDTSGLLVVAKTDRAHEGL 163

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              F+   I++ Y ++ +GIP      + +W+ +      D   +    E    +A++H+
Sbjct: 164 ARQFKDHSIERAYAAITYGIPVPPAGTVDSWIGRSD---ADRKKMAVHREGRGKHAVTHY 220

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG---NFTSPIQNK 287
           + +D   +    +E +  TGRTHQ+RVH  H+G P++GD  Y    KG      +    +
Sbjct: 221 RTLDRL-RGAALVECRLETGRTHQVRVHMAHIGHPLIGDPVYGRERKGFKSILETLGFRR 279

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             LHAR +   HP     L   + LPA + +   +L
Sbjct: 280 QALHARMLGFIHPVTDEPLMFESALPADVQELLSAL 315


>gi|86144060|ref|ZP_01062398.1| ribosomal large subunit pseudouridine synthase D [Leeuwenhoekiella
           blandensis MED217]
 gi|85829520|gb|EAQ47984.1| ribosomal large subunit pseudouridine synthase D [Leeuwenhoekiella
           blandensis MED217]
          Length = 344

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 79/334 (23%), Positives = 150/334 (44%), Gaps = 43/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
                 +E +R+D++  N         +Q+  ++G ++V+   VK N+++++  VVR+  
Sbjct: 22  FTAGKGQEPLRVDKFLMNFIEKATRNKIQQAAKNGNIQVNGAVVKQNHKVKANDVVRV-- 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                 H   E  +    + L          +++ED  + V NKPAG+ V  G G     
Sbjct: 80  ---LFEHPPYEFLLTPEDIPLD---------IVFEDDTLLVVNKPAGMVVHPGHGNYSGT 127

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH D       ++   +P L HR+D++TSG+LVVA+T  A  HL + F  +  +
Sbjct: 128 LINALIYHFDNL----PENSSGRPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTSE 183

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++VWG  +  +  +   + +  H      + V ++      A++H+KV++      
Sbjct: 184 REYIAIVWGNVEEDQGTVEGHIGR--HPKNRMQNTVYEDGDQGKEAVTHYKVLERLG-YV 240

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKL 288
             +  +  TGRTHQ+RVH  H+G  +  D +Y  +     T+             +  + 
Sbjct: 241 TKISCKLETGRTHQIRVHMKHIGHTLFNDERYGGDAILKGTTFTKYKQFVENCFKVLPRQ 300

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            LHA+ +   HP+ G  ++  + +P  M    + 
Sbjct: 301 ALHAKTLGFEHPKTGEWMRFDSAIPEDMEACIEK 334


>gi|87161600|ref|YP_493787.1| hypothetical protein SAUSA300_1090 [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|161509370|ref|YP_001575029.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|294848190|ref|ZP_06788937.1| RNA pseudouridine synthase ylyB [Staphylococcus aureus A9754]
 gi|87127574|gb|ABD22088.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|160368179|gb|ABX29150.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|294824990|gb|EFG41412.1| RNA pseudouridine synthase ylyB [Staphylococcus aureus A9754]
 gi|315198434|gb|EFU28763.1| pseudouridylate synthase RluD [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320144297|gb|EFW36063.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA177]
          Length = 305

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 77/329 (23%), Positives = 139/329 (42%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +++   
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I+ E                L   + YED  + V  KP G+ V    
Sbjct: 61  HIVVTEKEVVEADILPEN---------------LNLDIYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 GIAYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +   +G +    +  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKNLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAPIGRN-KNDRQSMAVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLD-----IGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP     ++  A LP       D++  +
Sbjct: 275 EHPVTSEYIERHAELPQDFEDLLDTIRKR 303


>gi|110639847|ref|YP_680057.1| ribosomal large subunit pseudouridine synthase D [Cytophaga
           hutchinsonii ATCC 33406]
 gi|110282528|gb|ABG60714.1| ribosomal large subunit pseudouridine synthase D [Cytophaga
           hutchinsonii ATCC 33406]
          Length = 348

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 86/334 (25%), Positives = 155/334 (46%), Gaps = 41/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV +  +  MR+D++  +   +     +Q  +    V+V+ K  K + +++ G V+ I  
Sbjct: 25  VVCDPGQSLMRIDKFLMSRIQYATRSRIQYGIEIDSVKVNDKSTKASYKVRPGDVITI-- 82

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
              +L H  +E  ++   + L          ++YED +I + NK  G+ V    G     
Sbjct: 83  ---SLPHPPREDVLIPEDIPLD---------IVYEDDQILIVNKKPGMVVHPAHGNWTGT 130

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +AYH +  L + V+ K  +P L HR+D++TSG+LV+A+T  A   + + F    I+
Sbjct: 131 LVNALAYHFEN-LPTHVNGK-IRPGLIHRIDKDTSGLLVIAKTDYAMTFMAKQFADHSIE 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y+++ WG+P  K   I N+L + +      +    +NE+    AI+H+K +  +    
Sbjct: 189 RTYYAICWGVPDPKSGTIKNYLGRSTK--DRKLVTTYENEEDGKLAITHYKTLAAY-HYV 245

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQN------KL 288
             ++    TGRTHQ+R H   +G  +  D  Y  N        G +   ++N      + 
Sbjct: 246 ALIQCNLETGRTHQIRAHMKSIGHSLFNDMSYGGNSVVKGTVTGKYKQFVENCFKLLPRQ 305

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
            LHA+ +   HP    ++Q  + LPA M    D 
Sbjct: 306 ALHAKTLGFIHPTTKEKMQFDSELPADMQAVLDK 339


>gi|224825744|ref|ZP_03698848.1| pseudouridine synthase, RluA family [Lutiella nitroferrum 2002]
 gi|224601968|gb|EEG08147.1| pseudouridine synthase, RluA family [Lutiella nitroferrum 2002]
          Length = 310

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 103/319 (32%), Positives = 155/319 (48%), Gaps = 22/319 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V   E   R+D +       +   ++ +ILRSG+VRV+K R+    R+Q+   +R
Sbjct: 9   VTFYTVGEAESGQRIDNFLVRLLKGVPKSHIYRILRSGEVRVNKGRIDAAYRLQADDQIR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A                    +      ++YED+ + V +KPAGI+V GGSG++
Sbjct: 69  LPPVRVAERQ--------------ENDAPATTFPVIYEDNALLVIDKPAGIAVHGGSGVS 114

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD+ETSG+L++A+ R+A   L +  R     K Y +L
Sbjct: 115 FGVIEQLRKAY-PEYRFLELVHRLDRETSGLLMLAKKRSALLKLHDMMRSSTPDKRYLAL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G  ++ K  +   L K ++  G+    V  N      A + FKV + FA  F  +E +
Sbjct: 174 GVGRWQDDK-HVKLPLFKFTNAEGERRVRVADN---GQSAHTIFKVQERFAD-FTLVEAR 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
             TGRTHQ+RVH    G PI GD KY  A            +++LHA  + LPHP  G  
Sbjct: 229 LRTGRTHQIRVHMAASGHPIAGDDKYGDAALNRELGRRGLRRMFLHAASLSLPHPLTGEP 288

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L   APLP  +    DSL 
Sbjct: 289 LSFQAPLPPELAHFLDSLR 307


>gi|170017468|ref|YP_001728387.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
 gi|169804325|gb|ACA82943.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
          Length = 307

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 89/328 (27%), Positives = 151/328 (46%), Gaps = 37/328 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    + + N+    R+D          +   L + L+ G + V++ +VK + ++ SG 
Sbjct: 1   MTEKITLEITNETG--RIDAVLAKKSLPYSRTVLAEWLQDGHIVVNQTQVKRSYKVNSGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I P       II E   LD               ++YED+ + V NKP G+ V   +
Sbjct: 59  LITILPPAVQNTEIIAENMPLD---------------IIYEDNDLLVVNKPQGMVVHPAA 103

Query: 124 GIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G   H  G L + +             +P + HR+D++TSG+L+VA+   A Q L+E  +
Sbjct: 104 G---HTSGTLVNALLYHAPLSTINGSFRPGIVHRIDRDTSGLLMVAKNDKAHQALSEQLK 160

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             + ++IY++LV G        I   L +   +      V    + G   AI+HF+V+  
Sbjct: 161 AHKNERIYYALVRGEFSEDSGTINAPLARH-KVDRKKQAV----QAGGREAITHFEVVTR 215

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           +   +  L+++  TGRTHQ+RVH  ++G PI+GD  Y +           N   LHA+ +
Sbjct: 216 YV-GYTLLKIRLETGRTHQIRVHMTYIGHPIIGDPVYGS--AQKLPHVTLNGQMLHAKTL 272

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            L  P  G  L   + LP++  K+  +L
Sbjct: 273 SLTQPTTGELLTFDSELPSYFTKSLATL 300


>gi|119945867|ref|YP_943547.1| pseudouridine synthase, RluA family protein [Psychromonas
           ingrahamii 37]
 gi|119864471|gb|ABM03948.1| ribosomal large subunit pseudouridine synthase C [Psychromonas
           ingrahamii 37]
          Length = 312

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 94/318 (29%), Positives = 167/318 (52%), Gaps = 18/318 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  +    R+D + + H   +    + +I+R G+VRV+KKR+K + ++Q+G  VR
Sbjct: 8   VRILEITQENAQQRIDNYLRLHLKGVPKSMIYRIVRKGEVRVNKKRIKPDYKLQTGDFVR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A  + +   K+             L+S ++YED  + + NKP+G++V GGSG+ 
Sbjct: 68  IPPVRVAKENALPSPKL--------NKIARLESQIVYEDDGLIILNKPSGLAVHGGSGLD 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + I   L++ +  + +   L HRLD+ TSG L++A+ R+  + L E  R + + K Y +L
Sbjct: 120 FGIIEGLRA-LRPESRFLELVHRLDKATSGCLLIAKKRSMLRALHEQLRNKTMNKQYHAL 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+ + K   +   LLKK+         + +  +    + + FK++  + Q    +E  
Sbjct: 179 VKGVWEKKWRSVTAPLLKKAQDS------IVKVSELGKASETRFKILQRY-QGATLVEAS 231

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH+   G  I  D +Y    F     +   N+L+LHA ++   HP   + 
Sbjct: 232 PVTGRTHQIRVHSASKGHNIACDDRYGDEQFSKEMQALGLNRLFLHAAHITFFHPVLEKQ 291

Query: 305 LQITAPLPAHMVKTWDSL 322
           + ++APL + +    + L
Sbjct: 292 MTVSAPLCSELTLLLEKL 309


>gi|124024982|ref|YP_001014098.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. NATL1A]
 gi|123960050|gb|ABM74833.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. NATL1A]
          Length = 326

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 88/312 (28%), Positives = 144/312 (46%), Gaps = 28/312 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +  ++QK + +G  RV+ K  K    ++ G ++++          
Sbjct: 26  PMRLDRWLVSQRAEQSRAHVQKFIEAGFARVNGKTGKAKTPVRPGDIIQLWVPPPEPLPY 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
           +K ++I                 +LYED  + V NK AG++V    G      ++G +  
Sbjct: 86  LKPEEI--------------DLDILYEDDHLIVINKTAGMAVHPAPGNKSGTLVNGLIHH 131

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +VVA+T+ A   L    + R   + Y ++V G  
Sbjct: 132 CPDLPGIGGKLRPGIVHRLDKDTTGCIVVAKTQEALVKLQIQIQKRVASRNYIAVVHGAI 191

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K+ +  I   + +       Y  V   +E+   YA +H+K+I+     F  L+ +  TGR
Sbjct: 192 KDNEGMIVGSIGRHPKDRKKYAVV---DEESGRYACTHWKLIENLG-NFSLLKFKLDTGR 247

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH+ H+G PI+GD  Y    K            LHA  + L HP    +++ TAP
Sbjct: 248 THQIRVHSAHIGHPIIGDQTYSRCKKLPIK---LGGQALHAIELGLIHPITLEKMKFTAP 304

Query: 311 LPAHMVKTWDSL 322
           LP    +    L
Sbjct: 305 LPEDFERLLKVL 316


>gi|117925422|ref|YP_866039.1| ribosomal large subunit pseudouridine synthase D [Magnetococcus sp.
           MC-1]
 gi|117609178|gb|ABK44633.1| ribosomal large subunit pseudouridine synthase D [Magnetococcus sp.
           MC-1]
          Length = 332

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 93/333 (27%), Positives = 151/333 (45%), Gaps = 43/333 (12%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72
            D+   RLD+    H+P +    LQ+ ++  +V VD +  K  + +++ GQ + I P   
Sbjct: 16  ADDAGQRLDKALCCHFPDLTRSTLQRWIKEERVIVDHEVAKLPSQKVRVGQHIIIYPSEP 75

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HID 130
             +  + E+  L+               +L+ED  + V NKPAG+ V  G+G+ +   ++
Sbjct: 76  EPSTALPEEIALE---------------ILFEDEHLIVLNKPAGMVVHPGAGVNHGTLVN 120

Query: 131 GFLKSWVDSKGQK-----------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             L                     P + HRLD+ETSGI+V A+   A  HL+  F  R I
Sbjct: 121 ALLYHCGTPDNPHGGLSGIGGVIRPGIVHRLDKETSGIMVAAKQDHAHIHLSRQFEQRTI 180

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y +L  GIP+  +  I   + +   I    + VV   E+G   A + +KV++   Q 
Sbjct: 181 GRRYLALTRGIPQPAQGRIEGAIGRH-PIHRTKMAVV---EQGGRAAATRYKVLEPLGQ- 235

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--------KLYLH 291
           F  +  +  +GRTHQ+RVH  H+G P+VGD  Y A  K     P  +        +  LH
Sbjct: 236 FALIRCRLESGRTHQIRVHMTHIGHPLVGDPLYGAQHKAPSHWPPLHRQRFDQFQRQALH 295

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
           A  +   HP  G  +    P PA   + +++L 
Sbjct: 296 AHTLTFIHPHTGEEMSFKRPPPADFRQLYETLA 328


>gi|307154024|ref|YP_003889408.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7822]
 gi|306984252|gb|ADN16133.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7822]
          Length = 305

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 89/325 (27%), Positives = 151/325 (46%), Gaps = 29/325 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
            + ++ ++  +RLD W     P ++   LQ ++  G +R++ K       ++Q G ++ +
Sbjct: 2   EITLQVEQGKLRLDVWLAQKIPDLSRSRLQNLIEQGNLRLNGKICTDKKTKVQQGDLLYL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                           +     L    + +   +LYED ++ + NKPAG+ V    G   
Sbjct: 62  ---------------FIPPVEPLNLQPEEIPLDVLYEDEQLIIINKPAGLVVHPAPGHEK 106

Query: 127 -YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    +  G    Q+P + HRLD++T+G LV+A+T  A QHL    + +  ++
Sbjct: 107 GTLVNALLSHCSNLAGIGGVQRPGIVHRLDKDTTGALVIAKTDYAHQHLQAQLKAKTARR 166

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y  +V+G+PK     I N  + +  I    + VV   EKG   AI+H+++ +     + 
Sbjct: 167 EYLGVVYGVPKTGSGTI-NLPIGRHPIERKKMAVVPL-EKGGRVAITHWEIRERLG-NYT 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH+  MG PIVGD  Y +   G       +   LHA  + L HP 
Sbjct: 224 LIHFRLETGRTHQIRVHSTAMGHPIVGDPVYSS---GRSIGVNLDGQVLHAWKLTLEHPL 280

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            G  ++  APLP    K    L  +
Sbjct: 281 SGAIIEAIAPLPETFTKLLSVLRSR 305


>gi|167764292|ref|ZP_02436419.1| hypothetical protein BACSTE_02677 [Bacteroides stercoris ATCC
           43183]
 gi|167698408|gb|EDS14987.1| hypothetical protein BACSTE_02677 [Bacteroides stercoris ATCC
           43183]
          Length = 356

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 145/332 (43%), Gaps = 38/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VVV+  +E +R+D++  +   + +   +QK   +G V  + K VK + +++   V+ +  
Sbjct: 32  VVVDKGQEMVRVDKYLFDRLTNASRNRIQKAADAGFVMANGKPVKSSYKVKPLDVITVMM 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +    E +++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 92  -----DRPRYENEVIPEDIPLD---------IVYEDKYLMVVNKPAGLVVHPGHGNYRGT 137

Query: 130 DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +W        D+      L HR+D++TSG+LV+A+T  A  +L   F  +  ++ 
Sbjct: 138 LVNAIAWHMKDIPDYDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRR 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + +      D + +    +    +A++H++V++        
Sbjct: 198 YRALVWGNVGQDEGTIVGNVGRNPK---DRMQMTVLPDDQGKHAVTHYRVLERLG-YVTL 253

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYL 290
           +E    TGRTHQ+RVH  H+G  +  D +Y  +     T   +             +  L
Sbjct: 254 VECVLETGRTHQIRVHMKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFDICPRQAL 313

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G  +  T+ LP  M +  D 
Sbjct: 314 HAMTLGFVHPVTGEEMYFTSELPDDMNRLLDK 345


>gi|298208169|ref|YP_003716348.1| ribosomal large subunit pseudouridine synthase D [Croceibacter
           atlanticus HTCC2559]
 gi|83848090|gb|EAP85960.1| ribosomal large subunit pseudouridine synthase D [Croceibacter
           atlanticus HTCC2559]
          Length = 356

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 84/335 (25%), Positives = 148/335 (44%), Gaps = 42/335 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
                 +E +R+D++  N   +     +QK  + G + V+   VK N ++++G  V++  
Sbjct: 31  FTASKGQEPLRVDKFLMNFIENATRNKIQKAAKEGNIYVNDAVVKQNYKVKAGDEVKV-- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                 H   E  +    + L          +++ED  + V NKPAG+ V  G G     
Sbjct: 89  ---LFEHPPYEMLLTPEDIPLN---------IVHEDDDVLVVNKPAGMVVHPGHGNYSGT 136

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + +H D       ++   +P L HR+D++TSG+LVVA+T  A  HL++ F  +   
Sbjct: 137 LINALVFHFDNL----PNNSSNRPGLVHRIDKDTSGLLVVAKTEHAMTHLSKQFFNKTSS 192

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           + Y +LVWG  ++ +  I   + +       + V +    ++    A++H+KVI+     
Sbjct: 193 REYIALVWGNVEDDQGTIEGHIGRHPKNRLQNTVFLEDDADEKGKPAVTHYKVIERLG-Y 251

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------K 287
              L  +  TGRTHQ+RVH  H+G  +  D +Y  +   KG   S  +           +
Sbjct: 252 VTLLSCKLETGRTHQIRVHLKHIGHTLFNDERYGGDKILKGTHFSKYKQFVDNCFKTLPR 311

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
             LHA+ +   HP  G  L   + +P  +    D 
Sbjct: 312 QALHAKTLGFEHPVSGEWLSFDSEIPKDISDCVDK 346


>gi|121999014|ref|YP_001003801.1| RluA family pseudouridine synthase [Halorhodospira halophila SL1]
 gi|121590419|gb|ABM62999.1| ribosomal large subunit pseudouridine synthase D [Halorhodospira
           halophila SL1]
          Length = 313

 Score =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 84/324 (25%), Positives = 136/324 (41%), Gaps = 34/324 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V       RLDR     +P  +   LQ+ +R+G + VD    +  + + +G+ + +    
Sbjct: 10  VPEGLAGQRLDRVLAALFPDYSRSRLQQWIRAGWITVDGAVRRPRDPVHAGEQISVDAEP 69

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                +  E                +   LLYED  + V +KPAG+ V  G+G      +
Sbjct: 70  EPETPLAPEP---------------IPLRLLYEDDHLLVVDKPAGLVVHPGAGNPGGTLV 114

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L      +   +  + HRLD+ETSG+LVVART AA   L    + R + + Y ++V 
Sbjct: 115 NALLHYDPGLEALPRAGIVHRLDKETSGVLVVARTYAAHHALVAQLQARTVGRGYQAVVV 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G P      +   + +        + VV    +    A++H++V + F      L+++  
Sbjct: 175 GRP-TAGGRVDAPIARHPR-DRKRMAVV----ETGRPAVTHYRVAERFT-AHTLLDVELE 227

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANF--------KGNFTSPIQNKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H   P+VGD  Y                      +  LHAR++ L HP
Sbjct: 228 TGRTHQIRVHMAHCRLPLVGDPVYGRRPVYPKGASETLRAVLDGFRRQALHARHLRLEHP 287

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  +   AP P    +  + L 
Sbjct: 288 RTGEAMHWEAPPPDDWERLLEVLR 311


>gi|329766891|ref|ZP_08258419.1| hypothetical protein HMPREF0428_00116 [Gemella haemolysans M341]
 gi|328837616|gb|EGF87241.1| hypothetical protein HMPREF0428_00116 [Gemella haemolysans M341]
          Length = 299

 Score =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 81/313 (25%), Positives = 147/313 (46%), Gaps = 38/313 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D++ +     ++  N+Q ++  G ++VD   +K N +++ G V+ I         ++
Sbjct: 14  ERIDKFLQQELTDVSRTNIQNLISEGYIKVDGNNIKTNYKLKDGNVITIEYKEPEELDVV 73

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K+   +D               ++YED  + + NK  G+ V    G   H DG L + + 
Sbjct: 74  KQDIPID---------------IVYEDDDLIIVNKAKGMVVHPSVG---HKDGTLVNALL 115

Query: 139 SKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +        +P + HR+D++TSG+L+VA+   A   L+E    + +++ Y++LV G 
Sbjct: 116 FHSELSSINGTIRPGIVHRIDKDTSGLLIVAKNDKAHVKLSEMIANKDVKRKYYALVHGS 175

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K+    I   + +      +   +          +I+HFKV+D F +K+  +E +  TG
Sbjct: 176 IKHDYGTIDAPIARNPKERKEMAVI-----DEGKLSITHFKVVDRF-EKYTLIECELETG 229

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++  P+VGD  Y      N      N   LH++ ++  HP  G  L    
Sbjct: 230 RTHQIRVHMKYINHPLVGDPVYGPRKTLNT-----NGQALHSKSIEFNHPITGEHLYFET 284

Query: 310 PLPAHMVKTWDSL 322
            +P +MV+T   L
Sbjct: 285 EIPEYMVETMSKL 297


>gi|289167775|ref|YP_003446044.1| 23S_rRNA pseudouridine synthase [Streptococcus mitis B6]
 gi|288907342|emb|CBJ22179.1| 23S rRNA pseudouridine synthase [Streptococcus mitis B6]
          Length = 295

 Score =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 147/319 (46%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +  ++RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETGSLRLDKALSD-LTELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ +   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAENIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDEAHLALAQDLKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGET 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+ TA +P    +T + L 
Sbjct: 276 LEFTADIPEIFKETLERLR 294


>gi|222054127|ref|YP_002536489.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
 gi|221563416|gb|ACM19388.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
          Length = 319

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 84/334 (25%), Positives = 151/334 (45%), Gaps = 36/334 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT ++ + V  + E  RLD +       +    +Q+++ SG + V+    K + +++ G+
Sbjct: 1   MTDIE-LTVPENTEAERLDSYIARTVETLTRAAVQRLMESGMITVNGMPPKPSLKLKGGE 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            ++I                +   V      + +   +LYED  + V NK AG+ V  G+
Sbjct: 60  QLKI---------------AVPPPVEAGPAPENIPLEILYEDRDLVVVNKGAGMVVHPGA 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HR+D++TSGILVVA+  A+   L+E FR  
Sbjct: 105 GNSGGTLVNALLGHCTDLSGIGGELRPGIVHRIDKDTSGILVVAKNDASHLALSEQFREH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I++IY ++V+G PK     + + ++ +  +    +       +   +A++H++VI  + 
Sbjct: 165 SIKRIYIAIVYGSPKTDSGRLES-IIGRHPVDRKRM---SGKARHGKHAVTHWRVIGRYP 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--------QNKLY 289
              C + ++  TGRTHQ+RVH    G P+VGD  Y    + +               +  
Sbjct: 221 -GMCLIRLRLETGRTHQIRVHLSEAGHPLVGDEVYGGGARLDSVKDPVLRRLIRELGRQA 279

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           LHA+ +   HP     L+    LP  M    + L
Sbjct: 280 LHAKTLGFVHPSTKEYLEFDTDLPRDMATIVEHL 313


>gi|223042001|ref|ZP_03612184.1| 23S rRNA pseudouridine synthase D [Actinobacillus minor 202]
 gi|223017199|gb|EEF15628.1| 23S rRNA pseudouridine synthase D [Actinobacillus minor 202]
          Length = 325

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 83/347 (23%), Positives = 149/347 (42%), Gaps = 39/347 (11%)

Query: 4   MTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           MT    +   V  D    RLD+     +P  +   L+  + + QV V+ K V K   ++ 
Sbjct: 1   MTQQITLTAEVSADLLGARLDQALAQLFPDYSRSRLKVWIENDQVWVNGKIVNKAREKVF 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+++ I   +                         +   ++YED  I V NKP  + V 
Sbjct: 61  GGELIEIQAEVEEEVRF---------------EPQNIPLNIVYEDDDIIVINKPKDLVVH 105

Query: 121 GGSGIAYHI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+G       +  L  +   ++  +  + HRLD++T+G++VVA+   A  HL  + + R
Sbjct: 106 PGAGNPDGTVLNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKNIPAQTHLVTALQKR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           RI + Y ++  GI   +   +   + +                     A++H+++++ F 
Sbjct: 166 RITREYEAIASGIM-TQGGKVDEPMARHPT-----KRTAMAVHPMGKPAVTHYRIMERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLY 289
           + +  L ++  TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  
Sbjct: 219 RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQLYGGXPRPPKGASEEFLTVLRGFQRQA 278

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
           LHA  + L HP  G  ++  APLP   V+  ++L  K D  LY  +L
Sbjct: 279 LHATMLRLEHPITGELMEWHAPLPDDFVELVEAL--KADYELYKDQL 323


>gi|148996979|ref|ZP_01824633.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP11-BS70]
 gi|168491017|ref|ZP_02715160.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae CDC0288-04]
 gi|168575592|ref|ZP_02721528.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae MLV-016]
 gi|237651118|ref|ZP_04525370.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CCRI 1974]
 gi|237821884|ref|ZP_04597729.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CCRI 1974M2]
 gi|307067586|ref|YP_003876552.1| 23S RNA-specific pseudouridylate synthase [Streptococcus pneumoniae
           AP200]
 gi|147756679|gb|EDK63719.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP11-BS70]
 gi|183574680|gb|EDT95208.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae CDC0288-04]
 gi|183578513|gb|EDT99041.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae MLV-016]
 gi|306409123|gb|ADM84550.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           pneumoniae AP200]
          Length = 295

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 146/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETGGLRLDKALSD-LTELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G+ 
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGKT 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+  A +P    +T + L 
Sbjct: 276 LEFKADIPEIFKETLERLR 294


>gi|124265850|ref|YP_001019854.1| ribosomal large subunit pseudouridine synthase C [Methylibium
           petroleiphilum PM1]
 gi|124258625|gb|ABM93619.1| ribosomal large subunit pseudouridine synthase C [Methylibium
           petroleiphilum PM1]
          Length = 320

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 95/325 (29%), Positives = 161/325 (49%), Gaps = 24/325 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ V  D    RLD +       +   ++ +I+RSG+VRV++ R   + R+ +G  +R
Sbjct: 1   MRHLTVGEDGAGQRLDNYLVKTLKGVPKTHVYRIIRSGEVRVNRGRAAADTRLAAGDELR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A      E++               +  +++ED  + V +KPAG++V GGSG++
Sbjct: 61  LPPVRMA---TPAEREAAPPR----------EFPVVHEDEHLLVIDKPAGVAVHGGSGVS 107

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD+ETSG+L++A+ R+A   L + FR R   K Y +L
Sbjct: 108 FGVIEQLRRARPQ-AKFLELVHRLDRETSGLLLLAKKRSALTRLQDQFRARETGKTYAAL 166

Query: 187 VWGIPKNKKECIANWLLKK-SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V G    + + I   L K     G   V V   +++    +I+  +V   +A  +  L++
Sbjct: 167 VPGAWPARHKVIDAPLHKYLDGAGERRVRVTGADDEDGQRSITLVQVAAAYA-GYTLLDV 225

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLHARYMDLP 298
              TGRTHQ+RVH  H G  IVGD KY         +  +       ++++LHAR +   
Sbjct: 226 TIKTGRTHQIRVHLAHAGHAIVGDDKYGDFALNKAFARGEAVPAVKFDRMFLHARRLRFE 285

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  G  +++ A LPA       +L
Sbjct: 286 HPASGETIELEAALPAECRLLLTAL 310


>gi|284048842|ref|YP_003399181.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
 gi|283953063|gb|ADB47866.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
          Length = 305

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 80/317 (25%), Positives = 138/317 (43%), Gaps = 32/317 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +E+ +R D +            +Q  ++ G+V  + K  K N +++ G V ++  +   
Sbjct: 9   PEEKGLRADVFLAARL-DCTRSAVQHDIQEGRVTRNGKPAKANTKVKEGDVFQVQVL--- 64

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
                         V+L    + +   +LYED  + V NKP G+ V   +G      ++ 
Sbjct: 65  ------------PPVDLEARPENIPLDILYEDQDVIVVNKPRGMVVHPAAGNPDGTLVNA 112

Query: 132 FLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    D  G     +P + HRLD++TSG+++ A+   A   L E  + +  ++ Y ++V
Sbjct: 113 LLYHCRDLSGINGVIRPGIVHRLDKDTSGVMICAKNDRAHLSLAEQIQKKEAKRTYLAIV 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  K+ +  I   L +          V      G  +A + ++V++ +  KF  +  + 
Sbjct: 173 RGNIKDDRGHIETQLDRDPRDRKKMAVV----PSGGRWAATDYEVLERYG-KFTVVRCRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++G P+VGD KYC       T    N   LH+  +   HP  G  + 
Sbjct: 228 LTGRTHQIRVHMTYIGHPLVGDPKYCPQK----TCFSINGQALHSEQLTFRHPRTGEWMT 283

Query: 307 ITAPLPAHMVKTWDSLG 323
             AP+P  M      L 
Sbjct: 284 FRAPVPEDMQTILTRLR 300


>gi|120610104|ref|YP_969782.1| ribosomal large subunit pseudouridine synthase D [Acidovorax
           citrulli AAC00-1]
 gi|120588568|gb|ABM32008.1| ribosomal large subunit pseudouridine synthase D [Acidovorax
           citrulli AAC00-1]
          Length = 339

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 77/331 (23%), Positives = 132/331 (39%), Gaps = 31/331 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
              + V     +   RLD+      P  +   LQ++L  G V V+ +   K + R+Q+G 
Sbjct: 30  AETRVVQASPAQHGARLDKALAELVPEFSRSYLQQLLGEGGVLVNGRAAAKPSARVQAGD 89

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +              ++  +  +     + +    +YED  + + NKPAG+ V    
Sbjct: 90  VLSV--------------ELRPTPQSQAFRPEAMALDTVYEDEHLRIVNKPAGLVVHPAP 135

Query: 124 GIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +  G L + +           +  + HRLD++TSG++VVAR R+    L      R
Sbjct: 136 G---NWSGTLLNGLLALDPRAGNVPRAGIVHRLDKDTSGLMVVARERSVMDALVRMIAAR 192

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L     +  +  +    + +       +  V         A +   V+D   
Sbjct: 193 EVSRQYLALGHRAWQGAQTRVVEEAIGRDPRNRLRMAAVDLAVHAGKPARTDIAVLDTCE 252

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
              C +    HTGRTHQ+RVH   +  P+V D  Y        +     +  LHA  +  
Sbjct: 253 NG-CLVHCTLHTGRTHQIRVHMAWLRHPLVADALYGGEPAAGLS-----RQALHAYRLAF 306

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            HP  G+ L   APLP  M     + G +Y+
Sbjct: 307 AHPVTGQPLLFHAPLPGDMAGALQAWGLRYN 337


>gi|332360722|gb|EGJ38531.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK49]
          Length = 298

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 75/322 (23%), Positives = 144/322 (44%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E      RLD+        ++     + ++ G++ V+ +  K    ++ G V+   
Sbjct: 2   EVRIEVSVVGQRLDKAVAE-LTFLSRSLANEQIKDGRILVNGQVKKAKYVVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + E ++++         + +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYELPEPEVVE------YVPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKNKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   F  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-FSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA +PA   +T   L 
Sbjct: 275 GEVLEFTAEVPAIFQETLKKLR 296


>gi|82703097|ref|YP_412663.1| pseudouridine synthase, RluD [Nitrosospira multiformis ATCC 25196]
 gi|82411162|gb|ABB75271.1| ribosomal large subunit pseudouridine synthase D [Nitrosospira
           multiformis ATCC 25196]
          Length = 318

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 82/331 (24%), Positives = 141/331 (42%), Gaps = 29/331 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            +++ +    +RLD+         +   LQ  +   +V VD        ++  G+ + + 
Sbjct: 2   ELIIPDHCAGLRLDQALAQLLAEWSRSRLQSWILEKRVSVDGACSLPRQKVWGGEKIVLS 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
           P  +                      + +   +++ED  I + +KPAG+ V  GSG    
Sbjct: 62  PARD--------------PAETAHEPEAIALDIVHEDHAIIIIDKPAGLVVHPGSGNWQG 107

Query: 127 YHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             ++  L       G  +  + HRLD+ETSG+LVVA+T  A   L    + R +++ Y +
Sbjct: 108 TLLNALLHHSPQLSGIPRSGIVHRLDKETSGLLVVAKTLEAQTSLVRQLQKRTVKREYLA 167

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LVWG   +      +  + +  +    + VV         A + ++V++ F      L  
Sbjct: 168 LVWGSVSSHGRV--DAPVGRHPVQRTRMAVVA----SGKEARTRYEVLEQFTD-CTLLRC 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ----NKLYLHARYMDLPHPE 301
              TGRTHQ+RVH   +G P+VGD  Y    K   ++ +Q     +  LHA  ++L HP+
Sbjct: 221 GLETGRTHQIRVHMQSLGHPLVGDPLYGGKAKKGSSATMQLAAFPRQALHAHKLELTHPQ 280

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFKYDRNLY 331
            G R+   APLP  M      L    D+  +
Sbjct: 281 NGQRMGWEAPLPEDMSNLLLMLQKARDKESH 311


>gi|260435696|ref|ZP_05789666.1| pseudouridylate synthase, 23S rRNA-specific [Synechococcus sp. WH
           8109]
 gi|260413570|gb|EEX06866.1| pseudouridylate synthase, 23S rRNA-specific [Synechococcus sp. WH
           8109]
          Length = 333

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 88/313 (28%), Positives = 138/313 (44%), Gaps = 28/313 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +   +QK + +G VRV+ K  K    ++ G  V++          
Sbjct: 36  PMRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKTGKAKTPLRQGDEVQLWMPPPEPLSY 95

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
           +K               + +   +L+ED  + V NKPAG++V    G      ++G L  
Sbjct: 96  LK--------------PEPMDLDVLFEDDHLIVLNKPAGLTVHPAPGNKDGTLVNGLLHH 141

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y+++V G+P
Sbjct: 142 CPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVRLQVQIQKRIASREYFAVVHGVP 201

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   + +       Y  V  +N     YA +H+ +++     +  L  +  TGR
Sbjct: 202 AGDSGTIVGPIGRHPADRKKYAVVSSEN---GRYACTHWTLVERLGD-YSLLRFKLDTGR 257

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH  HM  P+VGD  Y    K     P      LHA  + L HP    R+   AP
Sbjct: 258 THQIRVHCAHMNHPVVGDPTYSRCRKLPIELPG---QALHAVQLGLDHPITRERMVFEAP 314

Query: 311 LPAHMVKTWDSLG 323
           LP  M K    L 
Sbjct: 315 LPPVMEKLLGVLR 327


>gi|227540505|ref|ZP_03970554.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
 gi|227239587|gb|EEI89602.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
          Length = 348

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 67/332 (20%), Positives = 140/332 (42%), Gaps = 38/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  +  +R+D++  N   + +   +Q  + +G V V+   +K + +++   ++ +  
Sbjct: 22  IEVDKGQALLRIDKFLMNRVENASRNKIQNAIDAGSVLVNDSVIKSSYKVKPFDIISV-- 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
                        + D   +   + + +   +++ED ++ V NK AG+ V  G +     
Sbjct: 80  ------------VLPDPPRDTEVYPEDIPLDIMFEDDEVMVVNKVAGMVVHPGFNNYTGT 127

Query: 129 IDGFLKSWVDS------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   L    +          +P L HR+D++TSG+LV+A++  A  +L + F    I + 
Sbjct: 128 LVNALTHHFNQLPTMPGNAGRPGLVHRIDKDTSGLLVIAKSEWAMTYLAKQFFDHSIVRK 187

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++VWG        I  ++ +        V  +  + +   ++++H++V++        
Sbjct: 188 YVAMVWGDIAED-GTITGYIGRNLK--DRRVMTMYDDPEKGKWSVTHYRVLERLG-YVTL 243

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYL 290
           +E Q  TGRTHQ+R H   +G P+  D  Y  +     T              +  +  L
Sbjct: 244 IECQLETGRTHQIRAHMQSIGHPLFNDAAYGGDRILKGTVFNKYRQFVENCFALLPRQAL 303

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA+ +   HP+    L    PLP       + 
Sbjct: 304 HAQVLGFEHPKSKEFLTFETPLPEDFRLALEK 335


>gi|188580214|ref|YP_001923659.1| pseudouridine synthase, RluA family [Methylobacterium populi BJ001]
 gi|179343712|gb|ACB79124.1| pseudouridine synthase, RluA family [Methylobacterium populi BJ001]
          Length = 345

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 90/338 (26%), Positives = 151/338 (44%), Gaps = 48/338 (14%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           +      RLDR     +  ++   LQ ++R G V+ D   V+    ++ +G  + +    
Sbjct: 29  DEGSVPERLDRVLARAFDDLSRARLQALVRDGLVQCDGAVVRDPARKVGAGSRIDLT--- 85

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                       + + +      + L   +++ED  + V +KPAG+ V   +G   H DG
Sbjct: 86  ------------VPAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPAAG---HEDG 130

Query: 132 FLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR---- 177
            L + + +            ++P + HRLD++TSG+LVVA+   A Q L+  F       
Sbjct: 131 TLVNRLIAHCGASLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQFADHGRSG 190

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--IDC 235
            +++ Y +LVWG+P+ +   I   L +  H   + + VV+  E     AI+H++V  +  
Sbjct: 191 ALERAYLALVWGVPEPRAGTIRANLARSRH-NREKIAVVRDGE--GREAITHYRVEALPA 247

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--------- 286
                  L  +  TGRTHQ+RVH  H G P++GD  Y   FK       +          
Sbjct: 248 ADGVTALLRCRLETGRTHQIRVHLSHRGHPLLGDAVYGGAFKTKAARLAEPARDALTALA 307

Query: 287 KLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLG 323
           +  LHA  +   HP  G RL+  +PLPA   +   +LG
Sbjct: 308 RQALHAAELGFLHPRSGERLRFESPLPADFSRLLAALG 345


>gi|170732422|ref|YP_001764369.1| RluA family pseudouridine synthase [Burkholderia cenocepacia MC0-3]
 gi|169815664|gb|ACA90247.1| pseudouridine synthase, RluA family [Burkholderia cenocepacia
           MC0-3]
          Length = 316

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 99/322 (30%), Positives = 158/322 (49%), Gaps = 23/322 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++ +    R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR+PP
Sbjct: 2   IEIDENSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A   + +    +    N           +LYED  + V +KPAG++V GGSG+A+ +
Sbjct: 62  VRVAAADLARADTPVVPPANFD---------VLYEDDAMLVIDKPAGVAVHGGSGVAFGV 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++     + +   L HRLD+ETSGIL++A+ R A   L E  R  R+ K Y++   G
Sbjct: 113 IEQMRQAR-PRAKFLELVHRLDRETSGILMLAKKRTALVGLHEQIRENRMDKRYFACAHG 171

Query: 190 IPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             +        +   L K S   G+    V+ +      + + F ++D +   +  +E +
Sbjct: 172 EWQPDWGRRRAVKAPLFKYSTPEGERRVRVQDD---GLASHTVFNLVDRWPD-YVLVEAE 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H+G PI GD KY               P   +++LHA  + L HP 
Sbjct: 228 LKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANAQPSLKRMFLHAHRLKLAHPL 287

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  LQ  APLPA   +  D L
Sbjct: 288 TGEALQFDAPLPAECRRFLDQL 309


>gi|325273287|ref|ZP_08139564.1| RluA family pseudouridine synthase [Pseudomonas sp. TJI-51]
 gi|324101572|gb|EGB99141.1| RluA family pseudouridine synthase [Pseudomonas sp. TJI-51]
          Length = 320

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 92/343 (26%), Positives = 153/343 (44%), Gaps = 38/343 (11%)

Query: 4   MTYVQYV--VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M+ +  +   V ++    RLD+     +   +   L   ++ G++ VD   V+  + +  
Sbjct: 1   MSEIIQLSAEVPSELGGQRLDQVAAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLVHG 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + +     A    + E   LD               ++YED  I V NKPAG+ V  
Sbjct: 61  GSQLALQAEQEAQGEWVAEDIELD---------------IVYEDDHIMVINKPAGLVVHP 105

Query: 122 GSGIA--YHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            +G A    ++  L    D     +  + HRLD++T+G++VVA+T  A   L E  + R+
Sbjct: 106 AAGHASGTLLNALLHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTLQAQTKLVEQMQARK 165

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + +IY  +V G+       I   + +    GG    +   +  G   A+SH++V+  F +
Sbjct: 166 VSRIYECIVIGVV-TAGGKIDAPIGRH---GGMRQRMAVTD--GGKPAVSHYRVLKRF-R 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKLYL 290
               + ++  TGRTHQ+RVH  H+G P+VGD  Y   F+     SP          +  L
Sbjct: 219 SHTHVRVKLETGRTHQIRVHMAHVGFPLVGDQTYGGRFRIPPAASPTMVEAVKSFPRQAL 278

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           HAR++ L HP  G  ++  +PLP   V     L    DR  +I
Sbjct: 279 HARFLALAHPITGEVMKWESPLPDDFVWLLSLL--NQDRESFI 319


>gi|70732611|ref|YP_262374.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens Pf-5]
 gi|68346910|gb|AAY94516.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens Pf-5]
          Length = 353

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 90/344 (26%), Positives = 155/344 (45%), Gaps = 37/344 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    ++   V ++    RLD+     +   +   L   ++ G++ VD   ++  + + 
Sbjct: 34  MSDKIELR-AEVPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVH 92

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G ++ +     A    I +   LD               ++YED  I V NKPAG+ V 
Sbjct: 93  GGSILELTAEQEAQGEWIAQDIELD---------------IVYEDDDILVINKPAGLVVH 137

Query: 121 GGSGIAYHI--DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +G A     +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R
Sbjct: 138 PAAGHADGTLLNALLHHIPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVAQLQSR 197

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + +IY  +V G+     +   N  + +       + V+    +G   A+SH++V++ F 
Sbjct: 198 SVSRIYECIVIGVVTAGGKI--NAPIGRHGQQRQRMAVM----EGGKQAVSHYRVLERF- 250

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLY 289
           +    + ++  TGRTHQ+RVH  H+  P+VGD  Y   F+            ++N  +  
Sbjct: 251 RSHTHVRVKLETGRTHQIRVHMAHINFPLVGDPAYGGRFRIPPAASQTMVDSLKNFPRQA 310

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           LHAR+++L HP  G R+   +PLP   V     L  K DR  +I
Sbjct: 311 LHARFLELDHPTTGIRMSWESPLPDDFVWLLSLL--KQDREAFI 352


>gi|319405172|emb|CBI78777.1| ribosomal large subunit pseudouridine synthase D [Bartonella sp. AR
           15-3]
          Length = 333

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 83/341 (24%), Positives = 152/341 (44%), Gaps = 45/341 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           +   +    R+D+W    Y   ++   LQ ++R G +++D + +K    +++S Q++ + 
Sbjct: 5   ITNENACGQRIDQWLAKQYKEELSRSRLQTLIREGYLKIDGQLIKEPKIKLKSNQIIELT 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                          + +  +     + L   +L+ED+ + V NKPAG+ V  G+G    
Sbjct: 65  ---------------IPTPNDARPQGEALALDILFEDNHVIVINKPAGLVVHPGNGNWTG 109

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR---- 177
             ++  +    DS       ++P + HRLD++TSG++V+A+   A ++L   F       
Sbjct: 110 TLVNALIYHCSDSLSGIGGIKRPGIVHRLDKDTSGVMVIAKNDLAHRNLNAQFADHGRTS 169

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +++WG P      I  +L + S        VV      A  AI+HF +++ + 
Sbjct: 170 ALDRRYHAVIWGSPNRNIVTIDTFLARSSR-DRTKRSVVHSEHAHARRAITHFSLLEKYG 228

Query: 238 QK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------ 285
                      LE +  TGRTHQ+RVH  H+G P++GD  Y   FK    +         
Sbjct: 229 ACNDATSLASLLECRLETGRTHQIRVHMAHIGHPLIGDKVYGNAFKTKSNTLDPEIKNII 288

Query: 286 ---NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              N+  LHA  +   HP   + +  ++P P  +    +SL
Sbjct: 289 DQFNRQALHATSLTFEHPANRKIMSFSSPFPKDLTNLINSL 329


>gi|319406711|emb|CBI80344.1| ribosomal large subunit pseudouridine synthase D [Bartonella sp.
           1-1C]
          Length = 333

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 83/345 (24%), Positives = 154/345 (44%), Gaps = 45/345 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           +   +   +    R+D+W    Y   ++   LQ ++R G +++D + +K    +++S Q+
Sbjct: 1   MTQHITSENACGQRIDQWLAKQYKGELSRSRLQTLIREGYLKIDGQLIKEPKTKLKSNQI 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +                + +  +     + +   +L+ED+ I V NKPAG+ V  G+G
Sbjct: 61  IELT---------------IPTPNDAQPQGEAIALDILFEDNHIIVINKPAGLVVHPGNG 105

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++G +    DS       ++P + HRLD++TSG++V+A++  A ++L   F   
Sbjct: 106 NWTGTLVNGLIYHCRDSLSGIGGIKRPGIVHRLDKDTSGVMVIAKSDFAHRNLNAQFADH 165

Query: 178 R----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                + + Y +++WG P      I  +L + S        VV      A  AI+H  ++
Sbjct: 166 GRTSPLDRRYHAVIWGSPNRNIATIDTFLARSSR-DRTKRTVVHSEHAHARRAITHISLL 224

Query: 234 DCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-- 285
           + +            LE +  TGRTHQ+RVH  H+G P++GD  Y   FK    +     
Sbjct: 225 EKYGTCNDATSLASLLECRLETGRTHQIRVHMSHIGHPLIGDKVYGNAFKTKSNTLDPDI 284

Query: 286 -------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                  N+  LHA  +   HP   + +  ++P P  +V   + L
Sbjct: 285 KNIIDQFNRQALHATSLTFEHPANSQIMSFSSPFPKDLVDLLNHL 329


>gi|325689795|gb|EGD31799.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK115]
          Length = 298

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 143/322 (44%), Gaps = 34/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +E      RLD+        ++     + ++ G++ V+ +  K    ++ G ++   
Sbjct: 2   EVRIEASVVGQRLDKAVAE-LTDLSRSLANEQIKDGRILVNGQAKKAKYAVKEGDIIY-- 58

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                  + + E ++++         + +   ++Y+D  + V NKP G+ V   +G    
Sbjct: 59  -------YELPEPEVVE------YVPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKSALTRFQVLERFGD-YSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  L+ TA +PA   +T   + 
Sbjct: 275 GEVLEFTAEVPAIFQETLAKMR 296


>gi|194336853|ref|YP_002018647.1| pseudouridine synthase, RluA family [Pelodictyon
           phaeoclathratiforme BU-1]
 gi|194309330|gb|ACF44030.1| pseudouridine synthase, RluA family [Pelodictyon
           phaeoclathratiforme BU-1]
          Length = 349

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 84/335 (25%), Positives = 139/335 (41%), Gaps = 37/335 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V   +  MR+D++      +     +Q+ +  G+V V++ RVK N RI+S  V+ + 
Sbjct: 24  TLQVSRVQIPMRIDQYLTQQVENATRNKVQEAIEEGRVLVNENRVKSNYRIKSCDVIEMT 83

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
            +      +  E   ++               ++YED  + V NK AG+ V    G    
Sbjct: 84  FLRPPAPELTAENIPIE---------------IIYEDCDLMVVNKKAGMVVHPAFGNWTG 128

Query: 128 -------HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                  H  G     +D    +P + HRLD+ TSG+++VA+   A   L   F  R++ 
Sbjct: 129 TLANAILHHIGMDAEELDQAELRPGIVHRLDKNTSGLIIVAKNPIALHRLARQFAERKVI 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y ++VWG+P      I   + + S      +       +    AI+ + V++   Q F
Sbjct: 189 KVYKAIVWGVPDPAAGTITTNIGR-SKKDRKVMANFPFEGEYGKTAITDYSVMENL-QWF 246

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----------SPIQNKLY 289
             L ++ HTGRTHQ+R H  H+G  I+GD  Y                      +  +  
Sbjct: 247 SLLSLRLHTGRTHQIRAHLQHLGHQILGDVTYGGTILRTLPFSKSESFVKNLLELLPRQA 306

Query: 290 LHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           LHA  +    P     L  TAP+P  M    D + 
Sbjct: 307 LHAETLSFHQPISHEPLSFTAPMPEDMQHALDKIR 341


>gi|326316273|ref|YP_004233945.1| pseudouridine synthase, RluA family [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323373109|gb|ADX45378.1| pseudouridine synthase, RluA family [Acidovorax avenae subsp.
           avenae ATCC 19860]
          Length = 339

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 76/331 (22%), Positives = 132/331 (39%), Gaps = 31/331 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
              + V     +   RLD+      P  +   LQ++L  G V V+ +   K + R+Q+G 
Sbjct: 30  AETRVVQASPAQHGARLDKALAELVPEFSRSYLQQLLGEGGVLVNGRAAAKPSARVQAGD 89

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +              ++  +  +     + +    +YED  + + NKPAG+ V    
Sbjct: 90  VLSV--------------ELRPTPQSQAFRPEAMALDTVYEDEHLRIVNKPAGLVVHPAP 135

Query: 124 GIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +  G L + +           +  + HRLD++TSG++VVAR R+    L      R
Sbjct: 136 G---NWSGTLLNGLLSLDPRAGNVPRAGIVHRLDKDTSGLMVVARERSVMDALVRMIAAR 192

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L     +  +  +    + +       +  V         A +   V+D   
Sbjct: 193 EVSRQYLALGHRAWQGSQTRVVEEAIGRDPRNRLRMAAVDLAVHAGKPARTDLAVLDTCE 252

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
              C +    HTGRTHQ+RVH   +  P++ D  Y        +     +  LHA  +  
Sbjct: 253 DG-CLVHCTLHTGRTHQIRVHMAWLRHPLLADTLYGGEPAAGMS-----RQALHAYRLAF 306

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            HP  G+ L   APLP  M     + G +Y+
Sbjct: 307 AHPVTGQPLLFHAPLPGDMAGALQAWGLRYN 337


>gi|15902874|ref|NP_358424.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae R6]
 gi|116515398|ref|YP_816303.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae D39]
 gi|148988365|ref|ZP_01819812.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP6-BS73]
 gi|168482999|ref|ZP_02707951.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae CDC1873-00]
 gi|15458431|gb|AAK99634.1| 23S rRNA pseudouridine synthase (supresses ftsH(ts) mutants)
           [Streptococcus pneumoniae R6]
 gi|116075974|gb|ABJ53694.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae D39]
 gi|147926046|gb|EDK77120.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP6-BS73]
 gi|172043419|gb|EDT51465.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae CDC1873-00]
 gi|301794072|emb|CBW36476.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           INV104]
 gi|332201394|gb|EGJ15464.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA47368]
          Length = 295

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 146/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETGGLRLDKALSD-LSELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLVLAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G+ 
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGKT 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+  A +P    +T + L 
Sbjct: 276 LEFKADIPEIFKETLERLR 294


>gi|70729172|ref|YP_258908.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens Pf-5]
 gi|68343471|gb|AAY91077.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens Pf-5]
          Length = 318

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 98/320 (30%), Positives = 160/320 (50%), Gaps = 15/320 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ + V  +    R+D +       +    + +ILR G+VRV+K R+K   ++Q+G  
Sbjct: 9   PGVQLLEVSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGD- 67

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                    +          D  V L +     L++ +++ED  + V NKPAGI+V GGS
Sbjct: 68  --------VVRVPPVRVPERDEPVPLAQGLLQRLEASIVFEDKALIVINKPAGIAVHGGS 119

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+ + +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL  + R   + K Y
Sbjct: 120 GLNFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRY 178

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G      + +   LLK +   G+ +  V +       A++ FKV+  F      +
Sbjct: 179 MALVRGHWATAVKQVRAPLLKSNLRSGERMVEVNEE---GKEALTVFKVLRRFGDFATMV 235

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           E +P TGRTHQ+RVH LH G  I GD KY   +F          +L+LHA  + +P P+G
Sbjct: 236 EAKPVTGRTHQIRVHTLHAGHCIAGDSKYGDDDFTREIRELGGKRLFLHAYMLTVPLPDG 295

Query: 303 GRLQITAPLPAHMVKTWDSL 322
           G L++ AP+     KT + L
Sbjct: 296 GELKLQAPVDEMWAKTVERL 315


>gi|50083692|ref|YP_045202.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ADP1]
 gi|49529668|emb|CAG67380.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ADP1]
          Length = 310

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 92/319 (28%), Positives = 162/319 (50%), Gaps = 19/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +       +    + +++R GQVRV+KKR+K  +++  G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFTRLKGVPKSRIYRLIREGQVRVNKKRIKAESKLSIGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK    +    + +  L + ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDESDAPVSDQVAKSLLNRVVYEDEGLLVVNKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   +++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y +L
Sbjct: 123 YGLIEAMRAATGKKY--LELIHRIDRDTSGLVMISKKRSTLKLLQDLLREHKIRKTYAAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G     ++ I   LL+     G+    V    K    + + ++V + F +    +   
Sbjct: 181 VKGQVSLDQQLIDAPLLRYELSNGERRVRV---SKEGKPSKTEWRVAERFKE-ATLVYAS 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P +GRTHQ+RVH L +G P+VGD KY    +  ++ P   +L LHA  +++P    G   
Sbjct: 237 PLSGRTHQIRVHGLSIGHPLVGDDKYG--HQTVYSGPEARRLCLHAMRLEIP----GYPV 290

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I APL   +      L  +
Sbjct: 291 IEAPLAEDIQSVVAQLRAR 309


>gi|228475048|ref|ZP_04059776.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus hominis SK119]
 gi|314936640|ref|ZP_07843987.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           hominis subsp. hominis C80]
 gi|228271033|gb|EEK12421.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus hominis SK119]
 gi|313655259|gb|EFS19004.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           hominis subsp. hominis C80]
          Length = 305

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 76/331 (22%), Positives = 137/331 (41%), Gaps = 33/331 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +Y + +      R+D+   +     +   LQ  +++  V V+ K +K N +++   
Sbjct: 1   METYKYKIEDEALVGQRIDKLLSDFNSEWSRSQLQDWIKNDLVTVNGKIIKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +++         I+ E                L   + YED  + +  KP G+ V    
Sbjct: 61  EIQVTEKEVVEADILPEN---------------LNLDIYYEDKDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 TVKRKYTALVHGNIPHDYGTIDAPIGRNKK-DRQSMDVVD----DGKEAVTHFNVLEHFN 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 221 D-YTLIECQLETGRTHQIRVHMKYIGFPLVGDPKYGPRKTLD-----IGGQALHAGVIGF 274

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
            HP     ++  A LP       + +  +  
Sbjct: 275 KHPVTHEYIERHAELPQAFQSLLEDIRLRES 305


>gi|160945091|ref|ZP_02092317.1| hypothetical protein FAEPRAM212_02610 [Faecalibacterium prausnitzii
           M21/2]
 gi|158442822|gb|EDP19827.1| hypothetical protein FAEPRAM212_02610 [Faecalibacterium prausnitzii
           M21/2]
          Length = 310

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 141/324 (43%), Gaps = 29/324 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  +VE +    R+DR+       ++   LQ ++  G V+ + K V  + ++++G  V +
Sbjct: 4   REFIVEQETAGQRIDRFLSGEDTGLSRSALQALVAEGHVQCNGKAVAKSLKLKAGDTVLL 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           +  +  +      +   ++YED+ + V NKP G+ V    G   
Sbjct: 64  E---------------IPDAKPIEAVPQDIPLEIVYEDAHLLVVNKPKGMVVHPAPGNPD 108

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++  L     S        +P + HR+D++TSG+LVVA+  A    L++   +  ++
Sbjct: 109 GTLVNALLWHCKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVE 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V+G     +  +   L + S I    + V    E    YA + +KV++   + F
Sbjct: 169 RAYQTVVYGGFAQDEGFVEANLGR-SKIDRKKMAVYPATEPHTKYAYTGYKVLERLGE-F 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE +  TGRTHQ+RVH   +  P+ GD  Y      +      +   LHA+ +   HP
Sbjct: 227 TLLECRLKTGRTHQIRVHMASIHHPVAGDPVYGP----HNCITSLHGQCLHAKTLGFVHP 282

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  L+  + LP +      +L 
Sbjct: 283 ITGEQLRFDSELPDYFTHFLATLR 306


>gi|295105659|emb|CBL03203.1| ribosomal large subunit pseudouridine synthase D [Faecalibacterium
           prausnitzii SL3/3]
          Length = 310

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 141/324 (43%), Gaps = 29/324 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  +VE +    R+DR+       ++   LQ ++  G V+ + K V  + ++++G  V +
Sbjct: 4   REFIVEQETAGQRIDRFLSGEDTGLSRSALQALVAEGHVQCNGKTVAKSLKLKAGDTVLL 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           +  +  +      +   ++YEDS + V NKP G+ V    G   
Sbjct: 64  E---------------IPDAKPIEAVPQDIPLEIVYEDSHLLVVNKPKGMVVHPAPGNQD 108

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++  L     S        +P + HR+D++TSG+LVVA+  A    L++   +  ++
Sbjct: 109 GTLVNALLWHCKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVE 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V+G     +  +   L + S      + V   NE    YA + +KV++   + F
Sbjct: 169 RAYQTVVYGGFAQDEGFVEANLGR-SKTDRKKMAVYPANEPHTKYAYTGYKVLERLGE-F 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE +  TGRTHQ+RVH   +  P+ GD  Y      +      +   LHA+ +   HP
Sbjct: 227 TLLECRLKTGRTHQIRVHMASIHHPVAGDPVYGP----HNCITSLHGQCLHAKTLGFVHP 282

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  L+  + LP +      +L 
Sbjct: 283 ITGEQLRFDSELPDYFTHFLATLR 306


>gi|307824793|ref|ZP_07655016.1| pseudouridine synthase, RluA family [Methylobacter tundripaludum
           SV96]
 gi|307734151|gb|EFO05005.1| pseudouridine synthase, RluA family [Methylobacter tundripaludum
           SV96]
          Length = 314

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 78/335 (23%), Positives = 150/335 (44%), Gaps = 41/335 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT +    V  +   MRLD+     +   +   LQ  ++SG+V+V+   +K  +++  G+
Sbjct: 1   MTRLTE-EVPFEMAGMRLDQVLAELFADYSRSKLQSWVKSGRVQVNGLTLKPRDKLVGGE 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                 ++ + +T   + +   +++ED  + + NKPAG+ V    
Sbjct: 60  TIALD---------------AEAEIVITAEPEPIPLEIIFEDESLLIVNKPAGLVVHPAI 104

Query: 124 GIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   + +G L + + +         +  + HR+D+ETSG+L+VA+T  A   LT+  + R
Sbjct: 105 G---NWNGTLLNALLNHDSSLETLPRAGIVHRIDKETSGLLMVAKTLQAHNSLTQQLQDR 161

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I + Y ++  G        +   + +       Y        +   +A++H++V   F 
Sbjct: 162 DITREYLAITRGRM-TAGGTVDEPIGRHPTDRKRYAVR-----ENGKHAVTHYRVGQRFT 215

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLY 289
           +    ++++  TGRTHQ+RVH  H+  P++GD  Y   F+       Q         +  
Sbjct: 216 R-HTLVQVKLETGRTHQIRVHMAHIRFPLLGDQVYGGRFQMPPDCSEQLEKELRSFKRQA 274

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           LHA  + L HP     L+   PLP  M++  ++L 
Sbjct: 275 LHAAKLGLQHPVTDEYLEWEQPLPEDMIRLLEALA 309


>gi|49483360|ref|YP_040584.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257425250|ref|ZP_05601675.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 55/2053]
 gi|257427910|ref|ZP_05604308.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus subsp. aureus 65-1322]
 gi|257430543|ref|ZP_05606925.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus 68-397]
 gi|257433304|ref|ZP_05609662.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257436146|ref|ZP_05612193.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus M876]
 gi|282903750|ref|ZP_06311638.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C160]
 gi|282905514|ref|ZP_06313369.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282908489|ref|ZP_06316319.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WW2703/97]
 gi|282910769|ref|ZP_06318572.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WBG10049]
 gi|282913972|ref|ZP_06321759.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus M899]
 gi|282918894|ref|ZP_06326629.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C427]
 gi|282924017|ref|ZP_06331693.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|283957938|ref|ZP_06375389.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus A017934/97]
 gi|293501005|ref|ZP_06666856.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|293509964|ref|ZP_06668672.1| RNA pseudouridine synthase ylyB [Staphylococcus aureus subsp.
           aureus M809]
 gi|293526552|ref|ZP_06671237.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus M1015]
 gi|295427682|ref|ZP_06820314.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297591359|ref|ZP_06949997.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus MN8]
 gi|49241489|emb|CAG40175.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|257271707|gb|EEV03845.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 55/2053]
 gi|257274751|gb|EEV06238.1| ribosomal large subunit psudouridine synthase D [Staphylococcus
           aureus subsp. aureus 65-1322]
 gi|257278671|gb|EEV09290.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus 68-397]
 gi|257281397|gb|EEV11534.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257284428|gb|EEV14548.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus M876]
 gi|282313989|gb|EFB44381.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|282316704|gb|EFB47078.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C427]
 gi|282322040|gb|EFB52364.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus M899]
 gi|282325374|gb|EFB55683.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WBG10049]
 gi|282327551|gb|EFB57834.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WW2703/97]
 gi|282330806|gb|EFB60320.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282595368|gb|EFC00332.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C160]
 gi|283790087|gb|EFC28904.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus A017934/97]
 gi|290920624|gb|EFD97687.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus M1015]
 gi|291096010|gb|EFE26271.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|291466908|gb|EFF09426.1| RNA pseudouridine synthase ylyB [Staphylococcus aureus subsp.
           aureus M809]
 gi|295128040|gb|EFG57674.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297576245|gb|EFH94961.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus MN8]
 gi|312438426|gb|ADQ77497.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|315194083|gb|EFU24476.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus CGS00]
          Length = 305

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 139/329 (42%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + + ++  MR+D+         +   +Q  +++G V  + K VK N +++   
Sbjct: 1   METYEFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I+ E                L   + YED  + V  KP G+ V    
Sbjct: 61  HIVVTEKEVVEADILPEN---------------LNLDIYYEDDDVAVVYKPKGMVVHPSP 105

Query: 124 GIAYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +   +G +    D  G     +P + HR+D +TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTNTLVNGLMYQIKDLSGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYIALVHGNIPHDYGTIDAPIGRN-KNDRQSMAVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLVECQLETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLD-----IGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  ++  A L        D++  +
Sbjct: 275 EHPVTGEYIERHAELAQDFEDLLDTIRKR 303


>gi|332638853|ref|ZP_08417716.1| pseudouridine synthase [Weissella cibaria KACC 11862]
          Length = 304

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 79/328 (24%), Positives = 138/328 (42%), Gaps = 41/328 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + +V+  D+   RLD+   + +       +   +  G + V+    K    ++   
Sbjct: 1   MSE-ETLVIT-DQTG-RLDKVVADAFDDYTRTQVTGWINDGILTVNGAVKKAKYSVKPND 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            ++                 +  +V +    + +   ++YED  + V NKP G+ V    
Sbjct: 58  EIKFT---------------VPEAVEIDLQPEDIPLDIVYEDDDLLVVNKPQGMVVHPAL 102

Query: 124 GIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G   H  G L + +             +P + HR+D++TSG+L+VA+   A + L+   +
Sbjct: 103 G---HESGTLVNALMFHTPLSTINGVVRPGIVHRIDKDTSGLLMVAKNDKAHESLSAQLK 159

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            ++  + Y++LV G     +  I   L + S        V      G   A++HFKV+  
Sbjct: 160 DKKNLRQYYALVHGEFVENEGTIKAPLGRSSADRKKQAVVA-----GGRDAVTHFKVVKR 214

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F   +  L++   TGRTHQ+RVH  ++G P+ GD  Y         +   N  YLHA  +
Sbjct: 215 FV-GYTLLQVTLETGRTHQIRVHMAYIGHPVAGDPLYGPK-----KTLPGNGQYLHAATL 268

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            L  P  G  +   APLP +     D L
Sbjct: 269 GLTQPTTGEDMTFEAPLPDYFTAMLDQL 296


>gi|150397811|ref|YP_001328278.1| RluA family pseudouridine synthase [Sinorhizobium medicae WSM419]
 gi|150029326|gb|ABR61443.1| pseudouridine synthase, RluA family [Sinorhizobium medicae WSM419]
          Length = 343

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 87/346 (25%), Positives = 151/346 (43%), Gaps = 46/346 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           + V+   D+ + RLD +         +   ++ ++  G V V+   V     ++  G   
Sbjct: 12  RKVLTAGDDASGRLDAFLTEALGGEFSRNRIKGLIEQGAVSVNALTVTESKRKVHPGDTF 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           +I                L    +     + +   +LYED  + V  KPAG+ V  G+G 
Sbjct: 72  QI---------------ALPEPEDPEPKGEAITLDVLYEDQDLIVLVKPAGLVVHPGAGN 116

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  +    DS       ++P + HRLD++TSG++VVA+  AA +HL++ F    
Sbjct: 117 WTGTLVNALIHHCGDSLSGIGGVKRPGIVHRLDKDTSGVMVVAKNDAAHRHLSDQFADHG 176

Query: 179 ----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y ++VWG P+  K  I   L +          V + +   A  AI+H++V+D
Sbjct: 177 RNGPLERAYRAVVWGRPRQLKGTIDAPLGRAG--DRTKRAVKRDDSDDAREAITHYEVVD 234

Query: 235 CFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
            + +K         +E    TGRTHQ+RVH  H+G P++GD  Y A F+       +   
Sbjct: 235 RYHEKPDGTSLASAVECHLETGRTHQIRVHMAHIGHPLIGDPDYGAAFRTKANLLPEPAR 294

Query: 286 ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
                  +  LHA  +   HP  G  +   A +P+ M +  D+L  
Sbjct: 295 TAVNRFPRQALHAFMLQFEHPSTGETMHFEAAVPSDMQELVDALRM 340


>gi|254473085|ref|ZP_05086483.1| ribosomal large subunit pseudouridine synthase D [Pseudovibrio sp.
           JE062]
 gi|211957806|gb|EEA93008.1| ribosomal large subunit pseudouridine synthase D [Pseudovibrio sp.
           JE062]
          Length = 349

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 86/341 (25%), Positives = 153/341 (44%), Gaps = 46/341 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           +  E ++   RLD     H    +   LQ ++R+GQV++ ++ V +   R+ +G  + + 
Sbjct: 26  ITPEPEDTGRRLDAVLAAHIDDFSRNRLQALIRAGQVQIGQRTVLEPKYRVCAGDTITL- 84

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                         I+          + +   ++YED  + V +KPAG+ V  G+G    
Sbjct: 85  --------------IVPEPEAAEPQPEDIPLTIVYEDEDLIVIDKPAGLVVHPGAGNPTG 130

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--- 178
             ++  +     S       ++P + HR+D++T+G+LV+A+   A Q L   F       
Sbjct: 131 TLVNALIHHCGSSLSGIGGVKRPGIVHRIDKDTTGLLVIAKNDMAHQGLAAQFADHGRTG 190

Query: 179 -IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LVWG P   K  +   L + S      + V+K    G  +AI+H++V + F 
Sbjct: 191 PLERAYKALVWGAPTAAKGTVDANLAR-STANRQKISVLKT---GGRHAITHWQVQERFG 246

Query: 238 QK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQ---- 285
            +        +E +  TGRTHQ+RVH  H+G P++GD  Y + F+     F  P++    
Sbjct: 247 PQDEAAVASLIECRLETGRTHQIRVHMSHIGNPLIGDMDYGSGFRTKYNKFHEPLKTQLA 306

Query: 286 --NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              +  LHA  +   HP     ++  + LPA       SL 
Sbjct: 307 EFKRQALHAGLLAFAHPRTQEFMKFESELPADFAGILQSLR 347


>gi|72383396|ref|YP_292751.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. NATL2A]
 gi|72003246|gb|AAZ59048.1| ribosomal large subunit pseudouridine synthase D [Prochlorococcus
           marinus str. NATL2A]
          Length = 326

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 90/312 (28%), Positives = 143/312 (45%), Gaps = 28/312 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +  ++QK + +G  RV+ K  K    ++ G ++++          
Sbjct: 26  PMRLDRWLVSQRAEQSRAHIQKFIEAGFARVNGKTGKAKTPVRPGDIIQLWVPPPEPLPY 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
           +K ++I                 +LYED  + V NK AGI+V    G      ++G +  
Sbjct: 86  LKPEEI--------------DLDILYEDDHLIVINKTAGIAVHPAPGNKSGTLVNGLIHH 131

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +VVA+T+ A   L    + R   + Y ++V G  
Sbjct: 132 CPDLPGIGGKLRPGIVHRLDKDTTGCIVVAKTQEALVKLQIQIQKRVASRNYIAVVHGAI 191

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           KN +  I   + +       Y  V   +E+   YA +H+K+I      F  L+ +  TGR
Sbjct: 192 KNNEGMIVGSIGRHPKDRKKYAVV---DEESGRYACTHWKLIKNLG-NFSLLKFKLDTGR 247

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH+ H+G PI+GD  Y    K            LHA  + L HP    +++ TAP
Sbjct: 248 THQIRVHSAHIGHPIIGDQTYSRCKKLPIK---LGGQALHAIELGLIHPITLEKMKFTAP 304

Query: 311 LPAHMVKTWDSL 322
           LP    +    L
Sbjct: 305 LPEDFERLLKVL 316


>gi|315221340|ref|ZP_07863261.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
 gi|315189459|gb|EFU23153.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
          Length = 298

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 143/319 (44%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ +   +RLD+   +    ++  +  + +++GQ+ V+ +  K    +++G V+      
Sbjct: 3   VKVEIGGVRLDKAVAD-LTSLSRSHANEQIKNGQILVNGQVKKAKYAVKAGDVITYE--- 58

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
                       L     L   ++ L   ++Y+D  + V NK  G+ V   +G      +
Sbjct: 59  ------------LPEPEALEYVAENLPLDIVYQDEDVAVVNKAQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L E  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHIKLAEELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFG-NYTLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP+ G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPKTGEV 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++ TA  PA   +T + L 
Sbjct: 276 MEFTAEAPAIFQETLEKLR 294


>gi|190575601|ref|YP_001973446.1| putative ribosomal large subunit pseudouridine synthase D
           [Stenotrophomonas maltophilia K279a]
 gi|190013523|emb|CAQ47158.1| putative ribosomal large subunit pseudouridine synthase D
           [Stenotrophomonas maltophilia K279a]
          Length = 329

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 84/344 (24%), Positives = 144/344 (41%), Gaps = 38/344 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  +V +     R D      +P  +   L + +++G+V +D  +V+  + ++ G+VV +
Sbjct: 10  RQAIVPDTAAGRRFDAVVAELFPEYSRSRLTEWIKAGEVLLDGAQVRPRDPLRGGEVVTL 69

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             V+        E   LD               +L+ED  + V NKP G+ V  G+G   
Sbjct: 70  NVVLETQTDAQPEDIPLD---------------VLFEDEHLLVINKPVGLVVHPGAG--N 112

Query: 128 HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           H    + + +          +  + HRLD++TSG++VVA+T  A   L E    R + + 
Sbjct: 113 HSGTLVNALLFRDPSVAVLPRAGIVHRLDKDTSGVMVVAKTLEAQTALVEQLAARDVHRQ 172

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G         A+  + +       + V     +    AI+H+++ + F +    
Sbjct: 173 YLAIVMGALVA--GGTADAPIDRHPRDRLKMAVR----EDGKEAITHYRLRERF-RAHTA 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARY 294
           LE +  TGRTHQ+RVH  H+  PI+GD  Y    K                 +  LHA  
Sbjct: 226 LECRLETGRTHQIRVHMAHVRHPIIGDPLYGGALKLPKGASDELVAALRGFKRQALHAET 285

Query: 295 MDLPHPEGGRLQI-TAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           ++  HP  G L   TAP+P  M+     L    +     +R   
Sbjct: 286 LEFTHPITGELVRNTAPVPEDMLHLMKVLREDSEAFAARERDRW 329


>gi|298368341|ref|ZP_06979659.1| ribosomal large subunit pseudouridine synthase D [Neisseria sp.
           oral taxon 014 str. F0314]
 gi|298282344|gb|EFI23831.1| ribosomal large subunit pseudouridine synthase D [Neisseria sp.
           oral taxon 014 str. F0314]
          Length = 373

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 132/326 (40%), Gaps = 29/326 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D   +RLD       P  +   L   ++   V V+ K  +   ++  G+ + +  
Sbjct: 30  LTVPLDMAGLRLDSALAKLMPDYSRSRLATWIKEDLVIVNGKPARPKEKLIGGEFITVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                        +  S  +L    + +   ++YED  + V NK AG+ V   +G     
Sbjct: 89  -------------VRSSEESLAFLPEKMDLDIVYEDDTVIVVNKSAGLVVHPAAGNWSGT 135

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    +  +  +  + HRLD+ETSG++VVA+T  A   L    + R +++IY ++
Sbjct: 136 LLNGLLAHCPELGQIPRAGIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VVK    G   AI+H KV++ +     ++E  
Sbjct: 196 ANGIVP-FDGKIETLIGRDPH-NRLKMAVVKY---GGKPAITHVKVLERYP-AHSYIECS 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-----NFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH      P+  D  Y                   +  LHA  +   HP+
Sbjct: 250 LETGRTHQIRVHMREANHPLAADPIYGNPRHPCSEMVKEAVKALGRQALHAYRLSFLHPK 309

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFKY 326
             + +   A +P  M      L  + 
Sbjct: 310 TQKAVSFEAAIPEDMYHLLSVLRLEA 335


>gi|240137515|ref|YP_002961986.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Methylobacterium
           extorquens AM1]
 gi|240007483|gb|ACS38709.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Methylobacterium
           extorquens AM1]
          Length = 330

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 92/345 (26%), Positives = 154/345 (44%), Gaps = 48/345 (13%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
             + +V++      RLDR     +  ++   LQ ++R G VR D   V+    ++ +G  
Sbjct: 7   EARSLVLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCDGIVVRDPARKVGAGCR 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +                + + +      + L   +++ED  + V +KPAG+ V   +G
Sbjct: 67  INLS---------------VPAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPAAG 111

Query: 125 IAYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              H DG L + + +            ++P + HRLD++TSG+LVVA+   A Q L+  F
Sbjct: 112 ---HEDGTLVNRLIAHCGVSLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQF 168

Query: 175 RMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
                   +++ Y +LVW +P+ +   I   L +  H   + + VV+  E     AI+H+
Sbjct: 169 ADHGRSGALERAYLALVWNVPEPRAGTIRANLARSRH-NREKIAVVRDGE--GREAITHY 225

Query: 231 KVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GN 279
           +V D   +      L     TGRTHQ+RVH  H G P++GD  Y   FK           
Sbjct: 226 RVEDVHGEGGVTALLRCHLETGRTHQIRVHLSHRGHPLLGDAVYGGAFKTKAARLSEPAR 285

Query: 280 FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLG 323
               +  +  LHA  +   HP  G RL+  +PLPA   +   +LG
Sbjct: 286 AALDVLGRQALHAVELGFLHPRSGERLRFESPLPADFSRLLAALG 330


>gi|261253417|ref|ZP_05945990.1| ribosomal large subunit pseudouridine synthase C [Vibrio orientalis
           CIP 102891]
 gi|260936808|gb|EEX92797.1| ribosomal large subunit pseudouridine synthase C [Vibrio orientalis
           CIP 102891]
          Length = 300

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 96/309 (31%), Positives = 167/309 (54%), Gaps = 16/309 (5%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              R+D + +N    I    + +ILR G+VRV+KKR+K   ++++G +VRIPP       
Sbjct: 2   AGQRIDNFLRNQLKSIPKSMVYRILRKGEVRVNKKRIKAEYKLKAGDLVRIPP-----VT 56

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           I ++ +    S  L K ++ L+ ++++ED  + + NKP+G +V GGSG+ +     L++ 
Sbjct: 57  IEEKPEEAAPSTKLNKVAE-LEYMIIHEDDHMLILNKPSGTAVHGGSGLKFGAIEALRA- 114

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + ++K Y++LV G  K   +
Sbjct: 115 LRPEARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVKKFYFALVMGQWKANCK 174

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +   LLK        V+ + +       + + FK+++ FA+    ++  P TGRTHQ+R
Sbjct: 175 VVNAPLLKNE------VNSIVRVNPNGKPSETRFKILEKFAE-ATLIQASPITGRTHQIR 227

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           VH  + G PI  D +Y       +T     ++L+LHA  +   HP     ++I AP+   
Sbjct: 228 VHTQYTGHPIAWDDRYGDRRFDAYTGQVGLDRLFLHAANIKFQHPSNDEWMEINAPMEPK 287

Query: 315 MVKTWDSLG 323
           + K    L 
Sbjct: 288 LEKALVGLR 296


>gi|116333479|ref|YP_795006.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
 gi|116098826|gb|ABJ63975.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           brevis ATCC 367]
          Length = 307

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 78/326 (23%), Positives = 136/326 (41%), Gaps = 36/326 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ V   +    RLD+   +    ++    +  + +GQ+ VD   VK  ++ + G 
Sbjct: 1   METTEFQVTTTE----RLDKLVADAVATVSRSQAKLAIEAGQITVDGATVKPKDKPKVGA 56

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+                L     L    + +   ++YED+ + V NKP G+ V    
Sbjct: 57  TIRVS---------------LPDPEPLDLTPEDIPLEIVYEDADVLVVNKPQGMVVHPAP 101

Query: 124 GIAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G   H   +  L     S+     +P + HR+D++TSG+L+VA+   A Q L+   + + 
Sbjct: 102 GHPNHTLVNALLYHSPLSQINGTLRPGIVHRIDKDTSGLLMVAKNDHAHQSLSAQLQAKT 161

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             + Y ++V G  K +   I   L +          V          A++HF+V++ +  
Sbjct: 162 NLREYVAIVHGNIKEEDGVIRAPLGRSPKDRKKQAIVA-----DGRPAVTHFRVLERYG- 215

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  +  +  TGRTHQ+RVH  ++  P+ GD  Y                +LHAR +   
Sbjct: 216 TYTLIACRLETGRTHQIRVHMAYINHPVAGDPLYGPKKTLKGA-----GQFLHARELGFK 270

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
            P  G  L  TAP+P +  K    L 
Sbjct: 271 QPTTGEELVFTAPVPENFAKAVRHLR 296


>gi|261346208|ref|ZP_05973852.1| ribosomal large subunit pseudouridine synthase D [Providencia
           rustigianii DSM 4541]
 gi|282565514|gb|EFB71049.1| ribosomal large subunit pseudouridine synthase D [Providencia
           rustigianii DSM 4541]
          Length = 325

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 82/343 (23%), Positives = 157/343 (45%), Gaps = 43/343 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            +   +   RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + I  
Sbjct: 10  TIAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKAKEKVLGGEQISIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +I        +   LD               ++YED  I V NKP G+ V  G+G     
Sbjct: 70  LIEEDTRWEPQDIPLD---------------VVYEDEDILVINKPRGLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + + +   +  + HRLD++T+G++VVA+T  A  HL ++ + R I + Y ++
Sbjct: 115 ILNALLYRYPEIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAV 174

Query: 187 VWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             G        +E I+    K++H+    +            A++H+++++ F +    L
Sbjct: 175 AVGRMTAGGMVEEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RAHTRL 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYM 295
            ++  TGRTHQ+RVH  H+  P++GD  Y    +    +  +        ++  LHA  +
Sbjct: 225 RLRLETGRTHQIRVHMAHINHPLIGDQLYGGRPRPLKGATEEFFEVMRKFDRQALHATML 284

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            L HP  G +++  APLP  MV+  ++L  K D  L+   +  
Sbjct: 285 RLYHPISGIQMEWHAPLPDDMVELINAL--KADAELHKDNMDW 325


>gi|254556664|ref|YP_003063081.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254045591|gb|ACT62384.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 307

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 86/328 (26%), Positives = 134/328 (40%), Gaps = 34/328 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+  T  Q   +  D+   RLD+             + K++++ QV V+ +       ++
Sbjct: 1   MAGATTEQQFTIT-DQTG-RLDKVLAALQSVWTRSQVDKLIKTDQVTVNGQLEASKYHVK 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +         I  E   LD               ++YED  + V NKP G+ V 
Sbjct: 59  PGDEIVVAAQTVQQTTIEPENIPLD---------------IVYEDDDVLVVNKPQGMVVH 103

Query: 121 GGSGIAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
              G   H   +  L     S      +P + HR+D++TSG+L+VA+   A Q L    +
Sbjct: 104 PAPGHPNHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDRAHQSLAAQLK 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +   + Y +LV G+ K     I   L +          V     K    AI+HFKV+  
Sbjct: 164 AKTNLREYVALVHGVIKEDTGTINAPLGRSPKDRKKQAIV-----KTGRPAITHFKVLKR 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           + Q +  +  +  TGRTHQ+RVH   +G P+VGD  Y         +   +  +LHA+ +
Sbjct: 219 Y-QHYTLISCRLETGRTHQIRVHLQSIGHPLVGDPLYGPK-----KTIKGHGQFLHAKLL 272

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP  G  L   APLP     T   L
Sbjct: 273 GFKHPVTGDLLTFEAPLPPIFTTTLAKL 300


>gi|28378455|ref|NP_785347.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|308180606|ref|YP_003924734.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28271291|emb|CAD64195.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|308046097|gb|ADN98640.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 307

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 85/328 (25%), Positives = 134/328 (40%), Gaps = 34/328 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+  T  Q   +  D+   RLD+             + K++++ QV V+ +       ++
Sbjct: 1   MAGATTEQQFTIT-DQTG-RLDKVLAALQSVWTRSQVDKLIKTDQVTVNGQLEASKYHVK 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +         I  E   LD               ++YED  + V NKP G+ V 
Sbjct: 59  PGDEIVVAAQTVQQTTIEPENIPLD---------------IVYEDDDVLVVNKPQGMVVH 103

Query: 121 GGSGIAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
              G   H   +  L     S      +P + HR+D++TSG+L+VA+   A Q L    +
Sbjct: 104 PAPGHPNHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDRAHQSLAAQLK 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +   + Y +LV G+ K     I   L +          V     K    A++HFKV+  
Sbjct: 164 AKTNLREYVALVHGVIKEDTGTINAPLGRSPKDRKKQAIV-----KTGRPAVTHFKVLKR 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           + Q +  +  +  TGRTHQ+RVH   +G P+VGD  Y         +   +  +LHA+ +
Sbjct: 219 Y-QHYTLISCRLETGRTHQIRVHLQSIGHPLVGDPLYGPK-----KTIKGHGQFLHAKLL 272

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP  G  L   APLP     T   L
Sbjct: 273 GFKHPVTGDLLTFEAPLPPIFTTTLAKL 300


>gi|325579066|ref|ZP_08149022.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325159301|gb|EGC71435.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 326

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 99/319 (31%), Positives = 164/319 (51%), Gaps = 14/319 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + +  DE   R+D +       +    + +ILR G+VRV+K R+K   ++Q+G    
Sbjct: 13  VKMLTISEDEAGQRIDNYLLAKLKGVPKSLIYRILRKGEVRVNKGRIKPEYKLQNGD--- 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E+     S NL K +  L+S +L+ED  + V NKP+GI+V GGSG+ 
Sbjct: 70  ---VVRVPPVRVSEKNTAPISKNLNKVA-SLESHILFEDDCLLVLNKPSGIAVHGGSGLN 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  + +   L HRLD++TSGIL+VA+ R+  ++L E  R++ +QK Y +L
Sbjct: 126 FGVIEALRA-LRPEARFLELVHRLDRDTSGILLVAKKRSTLRNLHEQLRVKTVQKDYLAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  ++  + +   LLK     G+ +  V +       + + F + + + Q    ++  
Sbjct: 185 VRGQWQSHVKVVQAPLLKNELASGERIVKVSEQ---GKPSETRFAIEERY-QNATLVKAS 240

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           P TGRTHQ+RVH  + G PI  D KY    F         N+L+LHA  +   HP+ G  
Sbjct: 241 PVTGRTHQIRVHTQYAGHPIALDDKYGDKEFDKYMQDLGLNRLFLHAFSIRFEHPKTGET 300

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L++ A L   M      L 
Sbjct: 301 LRLNAQLDEKMKAILKKLR 319


>gi|15889714|ref|NP_355395.1| ribosomal large subunit pseudouridine synthase D [Agrobacterium
           tumefaciens str. C58]
 gi|15157624|gb|AAK88180.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Agrobacterium tumefaciens str. C58]
          Length = 340

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 81/345 (23%), Positives = 151/345 (43%), Gaps = 46/345 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           + V++  ++   R+D W        ++   L+ ++  G V ++ + V     ++  G  V
Sbjct: 12  RKVLIAGEDAEGRIDVWLVGEVGSDLSRSRLKALIEQGAVLLNGQPVTEPKKKVHPGDRV 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            I               ++    +     + +   + YED  + V  KPAG+ V  G+G 
Sbjct: 72  EI---------------VMPEPEDPVPQGEDIPLDVEYEDEDLIVLVKPAGLVVHPGAGN 116

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  +    DS       ++P + HRLD+ETSG++VVA+   A +HL   F    
Sbjct: 117 WTGTLVNALIYHCGDSLSGIGGVKRPGIVHRLDKETSGVMVVAKNDNAHRHLAAQFADHG 176

Query: 179 ----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y ++VWG P+  +  +   L + +        V  ++   A  AI+H++V++
Sbjct: 177 RTGPLERAYKAVVWGRPRTLRGTVDAALGRGT--DRTKRAVKNEDSFDAREAITHYEVME 234

Query: 235 CFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
            F +K         +E +  TGRTHQ+RVH  H+G P++GD +Y A F+       +   
Sbjct: 235 RFHEKPDASCLASMVECRLETGRTHQIRVHMAHIGHPLIGDPEYGAAFRTKANLLDEPAR 294

Query: 286 ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                  +  LHA  +   HP  G  ++    +P  M +   +L 
Sbjct: 295 STVNRFPRQALHAYLLAFEHPRTGEVMEFETDMPEDMEELVTALR 339


>gi|119513315|ref|ZP_01632353.1| Pseudouridine synthase, RluD [Nodularia spumigena CCY9414]
 gi|119462022|gb|EAW43021.1| Pseudouridine synthase, RluD [Nodularia spumigena CCY9414]
          Length = 309

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 143/317 (45%), Gaps = 29/317 (9%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINA 73
           +E   RLDR+   + P+++   +Q+++  G V ++++        +++G  + +      
Sbjct: 9   EETGERLDRYLSENLPNLSRSRIQQLIEQGNVHLNEQICTTKKITVKAGDRITLE----- 63

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDG 131
                     +     L   +  +   +LYED  + + NKPAG+ V    G      ++ 
Sbjct: 64  ----------IPEVQPLQVQAQDIPLDILYEDDHLLILNKPAGLVVHPAPGHPDGTLVNA 113

Query: 132 FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    +  G    Q+P + HRLD++T+G + +A+T  A   L    + +  ++ Y  +V
Sbjct: 114 LLAHCPNLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYHSLQAQLQAKTARREYLGVV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G PK +   I   + +  H        V   EKG   A++H+++++    +   +  Q 
Sbjct: 174 YGAPKTENGKIDEPIGR--HPQDRKKMAVVPIEKGGRNAVTHWQILERLGNQ-TLVLFQL 230

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH+  +G PIVGD  Y +    +      N   LHA  + L HP     ++
Sbjct: 231 ETGRTHQIRVHSAKIGHPIVGDPIYSS---AHSVGVKLNGQALHAWRLKLQHPISENLIE 287

Query: 307 ITAPLPAHMVKTWDSLG 323
           +TAP P       + L 
Sbjct: 288 VTAPPPQTFTTLLEILR 304


>gi|116074038|ref|ZP_01471300.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9916]
 gi|116069343|gb|EAU75095.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9916]
          Length = 343

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 87/323 (26%), Positives = 141/323 (43%), Gaps = 28/323 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +   +QK + +G VRV+ K  K    ++ G  V++          
Sbjct: 39  PMRLDRWLVSQRSEQSRARIQKFIDAGFVRVNGKTGKAKTPLRDGDEVQLWMPPPEPLPY 98

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
           +K               + +   +L+ED  + V NKPAG++V    G      ++G L  
Sbjct: 99  LK--------------PEPMDLDVLFEDDHLIVINKPAGLTVHPAPGNKDGTLVNGLLHH 144

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y ++V G+P
Sbjct: 145 CPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQVQIQKRIASREYMAVVHGLP 204

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           +     I   + +       Y  V   + +   YA +H+ +++     +  L  +  TGR
Sbjct: 205 QGDSGSIVGAIGRHPADRKKYAVV---SGESGRYACTHWTLVERLGD-YSLLRFKLDTGR 260

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH  HM  P+VGD  Y    K     P      LHA  + L HP    R+   AP
Sbjct: 261 THQIRVHCAHMNHPVVGDPTYSRCRKLPIDLPG---QALHAFQLGLDHPITRERMVFEAP 317

Query: 311 LPAHMVKTWDSLGFKYDRNLYIK 333
           LP  M K    L  +   ++   
Sbjct: 318 LPPVMEKLLSVLRRRAGVDMPPP 340


>gi|332884260|gb|EGK04528.1| hypothetical protein HMPREF9456_00855 [Dysgonomonas mossii DSM
           22836]
          Length = 355

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 147/332 (44%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V +  +  +R+D++   H   ++   +Q+   +  + V+   VK N RI+   V+ +  
Sbjct: 31  FVADKGQGMIRVDKYLAMHIVGVSRNRIQQAAEADCILVNNTPVKSNYRIKPLDVISV-- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYH 128
               +N   +E +I+   + L          ++YED  + V NKP G+ V  G G     
Sbjct: 89  ---VMNRPPRELEIIPEDIPLD---------VVYEDEDLMVINKPPGLVVHPGFGNYQGT 136

Query: 129 IDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   +   +      DSK  +  + HR+D++TSG+++VA+   A  HL+  F  +  ++ 
Sbjct: 137 MVNAIAYRLKDTPEYDSKDPRLGIVHRIDKDTSGLILVAKNAYAKTHLSAQFFNKTTKRQ 196

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG   + +  I   + +        +  V        +A++H+KV++        
Sbjct: 197 YIALVWGNISDDEGRIEANIGRSLK--NRMLMTVFPEADYGKHAVTHYKVLERLG-YVTL 253

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYL 290
           ++ +  TGRTHQ+RVH  H+G  +  D +Y  N     T+  +             +  L
Sbjct: 254 IQCRLETGRTHQIRVHMKHIGYTLFNDERYGGNEILKGTNFAKYKQFVQNCFNICPRQAL 313

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA+ +   HP  G  L   APLP  M +  + 
Sbjct: 314 HAQTLGFVHPRTGQELMFEAPLPDDMSQLVEK 345


>gi|157150916|ref|YP_001450379.1| RluA family pseudouridine synthase [Streptococcus gordonii str.
           Challis substr. CH1]
 gi|157075710|gb|ABV10393.1| pseudouridine synthase, RluA family [Streptococcus gordonii str.
           Challis substr. CH1]
          Length = 296

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 142/319 (44%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ ++  +RLD+   +    ++     + +++G++ V+    K    ++ G V+      
Sbjct: 3   VKVEQAGVRLDKAVAD-LTDLSRSLANEQIKTGKILVNGLVKKAKYTVKEGDVISYE--- 58

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
                       L     +   ++ +   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 59  ------------LPEIEEIEYVTENIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F+V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRTGEV 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+ TA +PA   +T   L 
Sbjct: 276 LEFTAGVPAIFQETLKKLR 294


>gi|163782801|ref|ZP_02177797.1| hypothetical protein HG1285_15736 [Hydrogenivirga sp. 128-5-R1-1]
 gi|159881922|gb|EDP75430.1| hypothetical protein HG1285_15736 [Hydrogenivirga sp. 128-5-R1-1]
          Length = 322

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 140/334 (41%), Gaps = 34/334 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M          V  ++   RLD +    YP ++   +++++  G   V+ K  K + R++
Sbjct: 1   MKRTAETLEFTVSEEQAGERLDTFLAKAYPELSRSYIKRLIEEGFALVEGKVRKPSYRVK 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  V +                +     L    + +   ++YED  + V  KP G+ V 
Sbjct: 61  EGDRVTLS---------------VPEPEPLEVKPEDIPIEVVYEDRDVVVIVKPCGLVVH 105

Query: 121 GGSGIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++  L    D       ++P + HRLD+ET+G++VVA+   + ++L E F
Sbjct: 106 PSPGYTSGTLVNALLYHIKDLSSIGGVERPGIVHRLDKETAGLMVVAKNDTSHRNLVEQF 165

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             RR +K+Y +LV G  K +   +   + +       +      +   +  A S F V++
Sbjct: 166 ASRRTEKLYRALVKGTVKEEHGILELPIGRHPFHRKKF----STSSPRSKPAKSEFWVLE 221

Query: 235 CFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL----- 288
            F   +   L+++ +TGRTHQ+RVH   +G PIVGD  Y   FK +      N+L     
Sbjct: 222 RFPGLELTLLKVKIYTGRTHQIRVHLSSIGHPIVGDTTYG--FKRSSVPEAINRLLGECN 279

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            L A  +   HP  GR L+     P         
Sbjct: 280 MLVAYKLGFYHPSSGRWLEFEIDDPEPFGSVLKE 313


>gi|259500628|ref|ZP_05743530.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
 gi|302191317|ref|ZP_07267571.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners AB-1]
 gi|259168012|gb|EEW52507.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
          Length = 311

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 144/328 (43%), Gaps = 33/328 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+++E  +RLD++   H   I+   +Q++++   +  +  + K + ++ +   + I  
Sbjct: 9   LVVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNGLQTKLSYKVNTNDKINIE- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                         + S   L+   + L   ++YED  + V NKP G+ V   +G   H 
Sbjct: 68  --------------IPSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHT 113

Query: 130 --DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             +G +    +     +  +P + HR+D++TSG+L++A+   A   L +    +  ++ Y
Sbjct: 114 LVNGLIYHTKNLAECDEIFRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINKREY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V    K+    I   + +       Y             AI+HF V++ F   +  +
Sbjct: 174 IAIVHANFKHSSGVIDAPIGRNP-----YQRQQMAVVASGKKAITHFTVLEQFP-GYSLV 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    TGRTHQ+RVH  ++G PI GD  Y      N      N  +LHA+ +   HP+  
Sbjct: 228 KCILETGRTHQIRVHMSYIGHPIAGDPLYGPKKTLN-----GNGQFLHAKTLGFYHPKTN 282

Query: 304 R-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           + L+ +   P    K    L  K   NL
Sbjct: 283 QWLEFSISEPQIFAKQLYLLRKKLTNNL 310


>gi|331654054|ref|ZP_08355054.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli M718]
 gi|331047436|gb|EGI19513.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli M718]
          Length = 326

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 146/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  +++   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEAMRADFEE 318


>gi|307544580|ref|YP_003897059.1| 23S rRNA pseudouridylate synthase C [Halomonas elongata DSM 2581]
 gi|307216604|emb|CBV41874.1| 23S rRNA pseudouridylate synthase C [Halomonas elongata DSM 2581]
          Length = 315

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 103/323 (31%), Positives = 163/323 (50%), Gaps = 15/323 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+    VQ+V V   +   R+D +            + +I+R G+VRV+KKRVK ++R+ 
Sbjct: 1   MADGRDVQWVEVTEGQAGQRVDNFLMTRLKGAPRSLIYRIVRKGEVRVNKKRVKADSRLA 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G VVRIPP+  A    ++E  + D+  NL      L   +L E     V NKP+G++V 
Sbjct: 61  TGDVVRIPPLKLAPREAVRE--VSDNLRNL------LAGSVLLEGRDWLVLNKPSGLAVH 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+   +   L+  V        L HRLD++TSG L++A++R A   L  + +   + 
Sbjct: 113 GGSGVKIGLIEALRQ-VREDLDFLELVHRLDRDTSGCLLLAKSRTALLTLNTALKRHEMT 171

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G    +++ ++  L +     G+    V  N      A + F V + FA   
Sbjct: 172 KRYLALVAGRWPARRDFVSARLDRFDAGNGERRVRVDAN---GKVARTRFAVRETFA-GA 227

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-QNKLYLHARYMDLPH 299
             +E +P TGRTHQ+RVHA H G P++GD KY +       +    ++L+LHA  +  P 
Sbjct: 228 TLMEAEPVTGRTHQIRVHAAHAGHPLLGDDKYGSREGQRLAARWDLSRLFLHASELTFPE 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDS 321
           P  G+ ++I APL   +      
Sbjct: 288 PTSGKPVKIRAPLGESLDAVLAR 310


>gi|33860753|ref|NP_892314.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus subsp. pastoris str.
           CCMP1986]
 gi|33633695|emb|CAE18652.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus subsp. pastoris str.
           CCMP1986]
          Length = 322

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 82/312 (26%), Positives = 139/312 (44%), Gaps = 28/312 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +  P  +   +Q  + +G V V+ K  K    +++G  ++I          
Sbjct: 26  PMRLDRWLVSKRPEQSRARIQYFINAGLVLVNYKTAKAKTPLKTGDNIQIWMPPPEPLIY 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
           +K +K              +   +L+ED  I V NK +G+ V    G      ++G L  
Sbjct: 86  LKPEK--------------MNLNILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLFH 131

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++TSG +VVA+++ +  +L    + +   + Y +++ G+P
Sbjct: 132 CKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQESLVNLQIQIKEKIASRNYIAVIHGVP 191

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
              +  I   + +       Y  V   +EK   YA +++K+++     +  +  +  TGR
Sbjct: 192 NTSEGKIVGHIGRDKLNRLKYAVV---DEKSGRYACTYWKLLERLG-NYSLMSFKLDTGR 247

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  H+  PI+GD  Y    K        +   LHA  + L HP  G  ++  A 
Sbjct: 248 THQIRVHCAHINHPILGDPLYGRCKKLPCK---LDGQALHAVELGLFHPINGEEMKFEAE 304

Query: 311 LPAHMVKTWDSL 322
           LP    K    L
Sbjct: 305 LPQEFQKLLRVL 316


>gi|309808015|ref|ZP_07701936.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           01V1-a]
 gi|308168744|gb|EFO70841.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           01V1-a]
          Length = 311

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 144/328 (43%), Gaps = 33/328 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+++E  +RLD++   H   I+   +Q++++   +  +  + K + ++ +   + I  
Sbjct: 9   LVVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNGLQTKLSYKVNTNDKINIE- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                         + S   L+   + L   ++YED  + V NKP G+ V   +G   H 
Sbjct: 68  --------------IPSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHT 113

Query: 130 --DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             +G +    +     +  +P + HR+D++TSG+L++A+   A   L +    +  ++ Y
Sbjct: 114 LVNGLIYHTKNLAECDEIFRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINKREY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V    K+    I   + +       Y             AI+HF V++ F   +  +
Sbjct: 174 IAIVHANFKHSSGVIDAPIGRNP-----YQRQQMAVVASGKKAITHFTVLEQFP-GYSLV 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    TGRTHQ+RVH  ++G PI GD  Y      N      N  +LHA+ +   HP+  
Sbjct: 228 KCVLETGRTHQIRVHMSYIGHPIAGDPLYGPKKTLN-----GNGQFLHAKTLGFYHPKTN 282

Query: 304 R-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           + L+ +   P    K    L  K   NL
Sbjct: 283 QWLEFSISEPQIFAKQLYLLRKKLTNNL 310


>gi|82545047|ref|YP_408994.1| 23S rRNA pseudouridine synthase D [Shigella boydii Sb227]
 gi|187732689|ref|YP_001881382.1| 23S rRNA pseudouridine synthase D [Shigella boydii CDC 3083-94]
 gi|81246458|gb|ABB67166.1| suppressor of ftsH mutation [Shigella boydii Sb227]
 gi|187429681|gb|ACD08955.1| ribosomal large subunit pseudouridine synthase D [Shigella boydii
           CDC 3083-94]
 gi|320177087|gb|EFW52104.1| Ribosomal large subunit pseudouridine synthase D [Shigella
           dysenteriae CDC 74-1112]
          Length = 326

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 146/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
              I        +   LD               ++YED  I V NKP  + V  G+G + 
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNLD 112

Query: 127 YHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPEDMVELIEVMRADFEE 318


>gi|313886881|ref|ZP_07820585.1| putative ribosomal large subunit pseudouridine synthase D
           [Porphyromonas asaccharolytica PR426713P-I]
 gi|312923678|gb|EFR34483.1| putative ribosomal large subunit pseudouridine synthase D
           [Porphyromonas asaccharolytica PR426713P-I]
          Length = 374

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 77/332 (23%), Positives = 143/332 (43%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+DR+  +  PH +   +Q   ++G + VD + VK N +++  + + +  
Sbjct: 47  VQVDPGQTPLRIDRFLVDRMPHTSRHRIQLAAKAGLIWVDGEPVKSNYKVKPLETITMM- 105

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                        +     + +   + +   ++YED ++ V NKPAG+ V  G G     
Sbjct: 106 -------------LAHPKQDWSITPEDIPLDIVYEDDQLLVVNKPAGMVVHPGHGNYSGT 152

Query: 125 IAYHIDGFLKS--WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           + + +  +L++    D       L HR+D++TSG+L+VA+   A   L   F ++   + 
Sbjct: 153 LVHALAYYLRNDPLYDPNDASVGLVHRIDKDTSGLLLVAKRTEAKIRLARQFFLKTTGRR 212

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + +        + V     +    A++H+  ++        
Sbjct: 213 YQALVWGKLDQPQGTIEGNIARDPR-DRTRMTVYPPTSEIGKPAVTHYTQLERLG-FVTL 270

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------------NFTSPIQNKLYL 290
           +  +  TGRTHQ+R H   +  P+ GD +Y  +               N    I  +  L
Sbjct: 271 IACELETGRTHQIRAHMKSIDHPLFGDERYGGDQILWGQRTSSYQQFVNNCLKICPRQAL 330

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G R+  +APLP  M +  D 
Sbjct: 331 HAETLAFDHPTTGERMHFSAPLPDDMRQLIDK 362


>gi|295396961|ref|ZP_06807083.1| ribosomal large subunit pseudouridine synthase D [Aerococcus
           viridans ATCC 11563]
 gi|294974814|gb|EFG50519.1| ribosomal large subunit pseudouridine synthase D [Aerococcus
           viridans ATCC 11563]
          Length = 322

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 83/322 (25%), Positives = 146/322 (45%), Gaps = 31/322 (9%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
            E+ +RLD++  N +   +   ++K ++   V V+ K  K +  + +G ++ +       
Sbjct: 19  GEDGLRLDQFVTNQFTDESRTTIKKWIKDKLVTVNGKVAKASQSLVNGDLIGV------- 71

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFL 133
                E+     +      ++ +   +++ED  I V NKPA + V    +     +   L
Sbjct: 72  -----EKPAPAEAEEFKPVAEKMALDIVFEDDDILVVNKPANLVVHPSVNHPTNTLVNGL 126

Query: 134 KSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              V   G          +P + HRLD++T+G+LVVA+++AA ++LT+     ++ +IY 
Sbjct: 127 LYHVQENGSQLAVGRESFRPGIVHRLDKDTTGLLVVAKSQAALENLTKQVANHQMTRIYA 186

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV+G        I   + +       +     +  +   +A++HF V   +   +  + 
Sbjct: 187 GLVYGEIFEAGGTIDAPIRRHEKDRLKF-----ETNEAGRHAVTHFTVKHRYV-GYTLVN 240

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            Q  TGRTHQ+RVHA  +  PIV D  Y   +K  F S   N   LHA  ++L HP  G 
Sbjct: 241 FQLETGRTHQIRVHANFINHPIVDDPLYARQYKERFFS--DNGQLLHAHRLELEHPVTGE 298

Query: 305 -LQITAPLPAHMVKTWDSLGFK 325
            +   AP+P H  +    L FK
Sbjct: 299 HMVFDAPIPDHFQEVLHQLTFK 320


>gi|302878469|ref|YP_003847033.1| pseudouridine synthase, RluA family [Gallionella capsiferriformans
           ES-2]
 gi|302581258|gb|ADL55269.1| pseudouridine synthase, RluA family [Gallionella capsiferriformans
           ES-2]
          Length = 319

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 98/320 (30%), Positives = 159/320 (49%), Gaps = 19/320 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V ++ ++   E  R+D +   H   +   ++ +ILR G+VRV+KKRV    R++ G +
Sbjct: 7   ESVTFLTIDESGEEQRIDNFLFRHLKGVPKSHVYRILR-GEVRVNKKRVDQTYRLKLGDL 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RIPPV  A    + E  I             L+  ++YED  + + NKP+G++V GGSG
Sbjct: 66  LRIPPVRVAQKQEVDEVYIP-----------ALELPVIYEDDALVIINKPSGLAVHGGSG 114

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   ++       +   L HRLD+ETSG+L++A+ R+A   + E  R     K Y 
Sbjct: 115 VSFGVIEQMRRARPQ-AKFLELVHRLDRETSGVLLLAKKRSALTAMHEIMREGVSDKRYL 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G   N ++ +   L K     G+   +V+   +G   + + F  +      +  LE
Sbjct: 174 TLVLGQWNNARQHVKLPLFKFDTPQGEKRVMVR---EGGQASHTIF-SLQKNWPGYSLLE 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGG 303
            Q  TGRTHQ+RVH  H+G PI GD KY    +          +++LHA  +   HP  G
Sbjct: 230 AQLKTGRTHQIRVHLSHLGFPIAGDDKYGDFARNRELMKQGLKRMFLHAHSISFSHPLTG 289

Query: 304 R-LQITAPLPAHMVKTWDSL 322
             + I+APLP  +      L
Sbjct: 290 EPMHISAPLPPELASFIAKL 309


>gi|33591688|ref|NP_879332.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           pertussis Tohama I]
 gi|33571331|emb|CAE44806.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           pertussis Tohama I]
 gi|332381081|gb|AEE65928.1| ribosomal large subunit pseudouridine synthase C [Bordetella
           pertussis CS]
          Length = 316

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 93/323 (28%), Positives = 157/323 (48%), Gaps = 20/323 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +    V+ + +  + +  R+D +       +   ++ K +R G+VRV+K R+    R+  
Sbjct: 9   TTPPAVRMLAIGPEHDGQRIDNFLLRLCKGVPKSHIYKAIRGGEVRVNKGRISAEYRLVE 68

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PP+                    T+     +  ++YED  + V +KPAG++V G
Sbjct: 69  GDVVRVPPLRL-------------PDPGATRPVPGAEFPVVYEDDALLVIDKPAGVAVHG 115

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+++ +   L++      +   L HRLD+ETSG+L++A+ R+A   L    R  +  K
Sbjct: 116 GSGVSFGVIEQLRAARPQ-ARFLELVHRLDRETSGLLMLAKKRSALLALHAMLREGKGDK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   N ++ I   L K +   G+    V Q  + A+  ++    +      + 
Sbjct: 175 HYLALVEGDWVNDRQHIRLALTKWTTQSGERRVRVDQAGQAAHTIVT----LRKRFGGYS 230

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHP 300
            ++ +  TGRTHQ+RVH    G PIVGD K   +  +  F      +++LHA  + LPHP
Sbjct: 231 LVDAELRTGRTHQIRVHLASSGFPIVGDDKCGTDEIRAAFARRGFGRMFLHAHQLTLPHP 290

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  L++TA LP   +K    L
Sbjct: 291 LTGETLRLTADLPPACLKLLKQL 313


>gi|311693418|gb|ADP96291.1| pseudouridine synthase, RluA family [marine bacterium HP15]
          Length = 325

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 88/341 (25%), Positives = 150/341 (43%), Gaps = 41/341 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV  +  + RLD+      P  +   LQ  ++SG + V+ +  K  +++     + +  
Sbjct: 11  FVVPPELSDRRLDQAAAELMPEHSRSRLQSWIKSGALTVNGEVRKPRDKVMLDDRLALDA 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
              A      E+  LD               ++YED  + V NKPAG+ V   +G   H 
Sbjct: 71  EPEAQVSWQAEEISLD---------------IVYEDEHLLVINKPAGLVVHPAAG---HA 112

Query: 130 DGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG L + + +         +  + HRLD++TSGI+VVAR+  A   L +  + R + + Y
Sbjct: 113 DGTLVNALLNYAPEVENLPRAGIVHRLDKDTSGIMVVARSLIAHTSLVDQLQTRTMGREY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G          +  + +       + VV         A++H+++++ FA     +
Sbjct: 173 EAVVVGTLT--GGATVDAPIGRHPRERKKMAVVA----SGKPAVTHYRLVERFA-AHTHV 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYM 295
             +  +GRTHQ+RVH  H+  P+VGD  Y    +    +  +        N+  LHAR +
Sbjct: 226 RCKLESGRTHQIRVHMAHVKHPLVGDPLYGGRLRLPKGTTDELREALSTFNRQALHARQL 285

Query: 296 DLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            L HPE G +     PLP  MV   ++L  K+ R L  +  
Sbjct: 286 TLEHPETGEILTWEVPLPEDMVALIEALR-KHARELETRDY 325


>gi|253581824|ref|ZP_04859048.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           varium ATCC 27725]
 gi|251836173|gb|EES64710.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           varium ATCC 27725]
          Length = 313

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 81/336 (24%), Positives = 151/336 (44%), Gaps = 34/336 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M  +     V    +++  R+D +            +QKI+  G V +  K+V K  N++
Sbjct: 1   MKNIKETITVSANENDKGKRIDSFLNEIIDDATRSYIQKIIDGGYVEITGKKVTKSGNKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +  +++ +    + + +++ E                +   ++YED  I + NK A + V
Sbjct: 61  KGTEIIVVNIPEDEILNVVPEN---------------IPLNIIYEDKDIVIINKTANMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G      ++  L    D    +   +P + HRLD++TSG++VVA+   A   L++ 
Sbjct: 106 HPAHGNYNGTLVNALLYQIKDLSTINGVIRPGIVHRLDKDTSGVIVVAKNDEAHSTLSDM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ + ++K Y  +  GI K+K   I   + +        + VV  N K    AIS+++V+
Sbjct: 166 FKEKTLEKTYICITKGIFKDKSGKIETLIGRDPK-DRKKMTVVDINGKN---AISNYEVL 221

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D   + F  ++++  TGRTHQ+RVH  ++  PI+GD  Y  + +G        +  LHA 
Sbjct: 222 D-EGKNFSLVKVRIETGRTHQIRVHMKYLNHPILGDSVYGNSNEG------ITRQMLHAY 274

Query: 294 YMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDR 328
            +   HP     + +TA +P    K     G   ++
Sbjct: 275 RLKFTHPVTKKEMIVTADIPEDFKKAAKFAGVDINK 310


>gi|116072001|ref|ZP_01469269.1| Pseudouridine synthase, RluD [Synechococcus sp. BL107]
 gi|116065624|gb|EAU71382.1| Pseudouridine synthase, RluD [Synechococcus sp. BL107]
          Length = 339

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 90/313 (28%), Positives = 141/313 (45%), Gaps = 28/313 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +   +QK + +G VRV+ K+ K    ++ G  V++          
Sbjct: 39  PMRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKQGKAKTPLREGDQVQLWMPPPEPLPY 98

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
           ++ Q               +   +L+ED  I V NK AG++V    G      ++G L  
Sbjct: 99  LRPQP--------------MDLDVLFEDEHIIVLNKSAGLTVHPAPGNKDGTLVNGLLHH 144

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++TSG +VVA+++ A   L    + R   + Y+++V G+P
Sbjct: 145 CPDLPGISGKLRPGIVHRLDKDTSGCIVVAKSQEALVKLQVQIQKRVASREYFAVVHGVP 204

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   + +       Y  V   +++   YA +H+ +++ F   +  L  +  TGR
Sbjct: 205 NGDSGTIIGAVGRHPVDRKKYAVV---SDESGRYARTHWFLVERFGD-YSLLRFKLDTGR 260

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
           THQ+RVH  H+  P+VGD  Y    K     P      LHA  + L HP  G R+   AP
Sbjct: 261 THQIRVHCAHINHPVVGDPTYSRCRKLPVDLPG---QALHAVQLGLDHPITGERMVFEAP 317

Query: 311 LPAHMVKTWDSLG 323
           LP  M K    L 
Sbjct: 318 LPPVMEKLLLVLR 330


>gi|254559695|ref|YP_003066790.1| ribosomal large subunit pseudouridine synthase D [Methylobacterium
           extorquens DM4]
 gi|254266973|emb|CAX22773.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Methylobacterium
           extorquens DM4]
          Length = 330

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 91/345 (26%), Positives = 153/345 (44%), Gaps = 48/345 (13%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
             + +V++      RLDR     +  ++   LQ ++R G VR D   V+    ++ +G  
Sbjct: 7   EARSLVLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCDGIVVRDPARKVGAGSR 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +                + + +      + L   +++ED  + V +KPAG+ V   +G
Sbjct: 67  IDLS---------------VPAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPAAG 111

Query: 125 IAYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              H DG L + + +            ++P + HRLD++TSG+LVVA+   A Q L+  F
Sbjct: 112 ---HEDGTLVNRLIAHCGVSLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQF 168

Query: 175 RMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
                   +++ Y +LVW +P+ +   I   L +  H   + + VV++ E     AI+H+
Sbjct: 169 ADHGRSGALERAYLALVWNVPEPRAGTIRANLARSRH-NREKIAVVREGE--GREAITHY 225

Query: 231 KVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GN 279
           +V D   +      L     TGRTHQ+RVH  H G P++GD  Y   FK           
Sbjct: 226 RVEDVHGEGGVTALLRCHLETGRTHQIRVHLSHRGHPLLGDRVYGGAFKTKAARLSEPAR 285

Query: 280 FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLG 323
                  +  LHA  +   HP  G RL+  +PLP    +   +LG
Sbjct: 286 AALDALGRQALHAVELGFLHPRSGERLRFESPLPEDFSRLLAALG 330


>gi|312872998|ref|ZP_07733058.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
 gi|325912701|ref|ZP_08175084.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
 gi|311091520|gb|EFQ49904.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
 gi|325478122|gb|EGC81251.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
          Length = 311

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 144/328 (43%), Gaps = 33/328 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+++E  +RLD++   H   I+   +Q++++   +  +  + K + ++ +   + I  
Sbjct: 9   LVVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNGLQTKLSYKVNTNDKINIE- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                         + S   L+   + L   ++YED  + V NKP G+ V   +G   H 
Sbjct: 68  --------------IPSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHT 113

Query: 130 --DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             +G +    +     +  +P + HR+D++TSG+L++A+   A   L +    +  ++ Y
Sbjct: 114 LVNGLIYHTKNLAKCDEIFRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINKREY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V    K+    I   + +       Y             AI+HF V++ F   +  +
Sbjct: 174 IAIVHANFKHSSGVIDAPIGRNP-----YQRQQMAVVASGKKAITHFTVLEQFP-GYSLV 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    TGRTHQ+RVH  ++G PI GD  Y      N      N  +LHA+ +   HP+  
Sbjct: 228 KCVLETGRTHQIRVHMSYIGHPIAGDPLYGPKKTLN-----GNGQFLHAKTLGFYHPKTN 282

Query: 304 R-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           + L+ +   P    K    L  K   NL
Sbjct: 283 QWLEFSISEPQIFAKQLYLLRKKLTNNL 310


>gi|332299970|ref|YP_004441891.1| pseudouridine synthase, RluA family [Porphyromonas asaccharolytica
           DSM 20707]
 gi|332177033|gb|AEE12723.1| pseudouridine synthase, RluA family [Porphyromonas asaccharolytica
           DSM 20707]
          Length = 376

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 77/332 (23%), Positives = 143/332 (43%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+DR+  +  PH +   +Q   ++G + VD + VK N +++  + + +  
Sbjct: 49  VQVDPGQTPLRIDRFLVDRMPHTSRHRIQLAAKAGLIWVDGEPVKSNYKVKPLETITMM- 107

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                        +     + +   + +   ++YED ++ V NKPAG+ V  G G     
Sbjct: 108 -------------LAHPKQDWSITPEDIPLDIVYEDDQLLVVNKPAGMVVHPGHGNYSGT 154

Query: 125 IAYHIDGFLKS--WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           + + +  +L++    D       L HR+D++TSG+L+VA+   A   L   F ++   + 
Sbjct: 155 LVHALAYYLRNDPLYDPNDASVGLVHRIDKDTSGLLLVAKRTEAKIRLARQFFLKTTGRR 214

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG     +  I   + +        + V     +    A++H+  ++        
Sbjct: 215 YQALVWGKLDQPQGTIEGNIARDPR-DRTRMTVYPPTSEIGKPAVTHYTQLERLG-FVTL 272

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------------NFTSPIQNKLYL 290
           +  +  TGRTHQ+R H   +  P+ GD +Y  +               N    I  +  L
Sbjct: 273 IACELETGRTHQIRAHMKSIDHPLFGDERYGGDQILWGQRTSSYQQFVNNCLKICPRQAL 332

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA  +   HP  G R+  +APLP  M +  D 
Sbjct: 333 HAETLAFDHPTTGERMHFSAPLPDDMRQLIDK 364


>gi|71898901|ref|ZP_00681068.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|71731313|gb|EAO33377.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
          Length = 328

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 88/342 (25%), Positives = 153/342 (44%), Gaps = 42/342 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V +     R D      +P  +   L + ++SG V ++   V+  + +  G+VVR+
Sbjct: 11  RQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVRPRDPVYGGEVVRL 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             V +     + +   LD               +LYED  ++V NKPAG+ V  G+G   
Sbjct: 71  QVVPDIRTDAVPQDIPLD---------------ILYEDEHVFVINKPAGLVVHPGAG--- 112

Query: 128 HIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + DG L + +  +        +  + HRLD++TSG++VVART  A   L E    R++ +
Sbjct: 113 NPDGTLVNALLHRDPALAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSSRQVHR 172

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V  +         N  +++       + V          A++H+++ + F +   
Sbjct: 173 QYLAVV--VSALVSGGTVNAAIERHPRDRLRMAV----SDTGKEAVTHYRLRERF-RAHT 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNKLYLHAR 293
            LE +  TGRTHQ+RVH  H+  PIVGD  Y  + K                 +  LHA 
Sbjct: 226 ALECRLDTGRTHQIRVHMAHLRHPIVGDRLYGGSLKLPKGGTDALVVMLRGFKRQALHAE 285

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            ++  HP G   ++I AP+P  + +   +L  + D  L+ +R
Sbjct: 286 VLEFLHPVGALPVRIVAPVPEDLCQLLAAL--REDSVLFFER 325


>gi|296536195|ref|ZP_06898317.1| ribosomal large subunit pseudouridine synthase D [Roseomonas
           cervicalis ATCC 49957]
 gi|296263477|gb|EFH09980.1| ribosomal large subunit pseudouridine synthase D [Roseomonas
           cervicalis ATCC 49957]
          Length = 343

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 134/332 (40%), Gaps = 37/332 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
            +     +   RLDR+       ++   ++ ++ +G V  D +     +  I++G    +
Sbjct: 26  TLTAGPADAGARLDRFLAAAIGTLSRSRVKALIEAGHVTRDGQPAGDPSEAIRTGATYVV 85

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
            P                     T  +  +   +L+ED  + V +KPAG+ V    G   
Sbjct: 86  APPAAQPA---------------TPQAQDIPLTILFEDRHLIVLDKPAGLVVHPAPGNQD 130

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++  L    +        ++P + HRLD++TSG++VVA++  A   L+ +F  R ++
Sbjct: 131 GTLVNALLAHAGEELTGIGGEKRPGIVHRLDKDTSGVMVVAKSEVAHTALSAAFASRDLE 190

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +L WG+P      +    + +       + VV +N     +A++ +     +    
Sbjct: 191 RAYLALAWGVPAPASGEVDAP-VGRHPTDRKRMAVVARN---GKHALTRYATERAWGTSC 246

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS---------PIQNKLYLH 291
             L  +  TGRTHQ+RVH  H+G P+VGD  Y                       +  LH
Sbjct: 247 ALLRCRLATGRTHQIRVHMAHIGHPLVGDPVYLRRLPATARGLPVAARDALLAFPRQALH 306

Query: 292 ARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           A  +   HP  G + + + PLP  M      L
Sbjct: 307 AESLGFHHPVTGEMLRFSTPLPPDMQALLALL 338


>gi|229824104|ref|ZP_04450173.1| hypothetical protein GCWU000282_01408 [Catonella morbi ATCC 51271]
 gi|229786458|gb|EEP22572.1| hypothetical protein GCWU000282_01408 [Catonella morbi ATCC 51271]
          Length = 309

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 89/320 (27%), Positives = 146/320 (45%), Gaps = 29/320 (9%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
             +   RLD+   +  P  +   +QKI++ G V V+ +  K N +++  + + +     A
Sbjct: 9   EGQAG-RLDKVLTDLLPGESRSTIQKIIKDGLVSVNGQEQKANFKLKGDETLLV-----A 62

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDG 131
             ++  E+  L          + +   ++YED  I V NKPAG+ V    G      ++G
Sbjct: 63  RRNLAVEEDSLPEP-------EAMDLDIIYEDEDILVINKPAGLVVHPSKGHLKGTLVNG 115

Query: 132 FLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            L          S   +P + HR+D++TSG+LVVA+  AA Q L +      +++ Y +L
Sbjct: 116 LLHYLNGNLSTGSDFYRPGIVHRIDKDTSGLLVVAKHNAAHQALADQLLNHDMRRSYIAL 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K  +  I   L +       +        K   YA++ F+V++ F +    L+++
Sbjct: 176 VHGQVKAPQGTIEAPLQRDPANRLRWTVA-----KEGKYALTRFQVMENF-ENATLLDLE 229

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR 304
             TGRTHQ+RVH   +G P+VGD  Y         S + +     LHA  + L HP  G 
Sbjct: 230 LETGRTHQIRVHLEFIGHPLVGDPVYRKGLDHIKGSLVHDMTGQLLHAYALKLQHPRSGE 289

Query: 305 -LQITAPLPAHMVKTWDSLG 323
            L+  APLP    +  D L 
Sbjct: 290 WLEFKAPLPRRFEEALDQLR 309


>gi|312143925|ref|YP_003995371.1| pseudouridine synthase, RluA family [Halanaerobium sp.
           'sapolanicus']
 gi|311904576|gb|ADQ15017.1| pseudouridine synthase, RluA family [Halanaerobium sp.
           'sapolanicus']
          Length = 304

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 151/319 (47%), Gaps = 32/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  E   R+D++  + +   +   +QK++   +++V+   V+ +  I+    +++    
Sbjct: 8   VDKSEAGKRVDKFLASQFDDFSRNYIQKLIEDSKIKVNSNPVQNSYLIKEADEIKV---- 63

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHID 130
                      I+D +   +  +  ++  ++YED  I + NK A + V    G     I 
Sbjct: 64  -----------IIDKAKKSSIKAVDIELDIIYEDQDIIIINKDADMVVHPAPGHYDDTIV 112

Query: 131 GFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             L ++ +        ++P + HRLD++TSG+L+VA+   + + L+  F+ R + K Y +
Sbjct: 113 NALLAYTNDLSAINGVKRPGIVHRLDKDTSGLLLVAKNDKSHKELSRQFKKREVDKYYLA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L+ GI   K   I   + +  +         ++++K    A+S FK+++ F +    +E+
Sbjct: 173 LLKGILPYKTGKIDAPIGRHPNQRKKMAVRKRKSKK----AVSRFKILESF-KNHTLVEV 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           +  TGRTHQ+RVH  ++G P+VGD KY +       S    +  LHA+ +   HP  G +
Sbjct: 228 KIETGRTHQIRVHFAYLGYPVVGDQKYGSK-----DSLGAKRQLLHAKRLLFKHPSTGKK 282

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++  A L A        L 
Sbjct: 283 VEFEAELKADFKDILTKLR 301


>gi|167771408|ref|ZP_02443461.1| hypothetical protein ANACOL_02774 [Anaerotruncus colihominis DSM
           17241]
 gi|167666048|gb|EDS10178.1| hypothetical protein ANACOL_02774 [Anaerotruncus colihominis DSM
           17241]
          Length = 306

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 87/326 (26%), Positives = 147/326 (45%), Gaps = 37/326 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Y   E  +  +R DRW  +    +     +QK+     VRV +K V  N+R++ G+   I
Sbjct: 5   YYTSEESDAGVRADRWLASAAEGLLTRSAIQKLCDCKAVRVGEKPVSKNDRLRGGETFII 64

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
                           +  +  L      +   ++YED  + V NKP G+ V    G   
Sbjct: 65  D---------------VPDAQPLDIVPQDIPIEIVYEDGDLLVVNKPKGMVVHPAPGHPN 109

Query: 125 ------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 + YH  G L S   +   +P + HR+D++TSG+L+VA+  AA   L E  +   
Sbjct: 110 GTLVNALLYHCQGRLSSI--NGVIRPGIVHRIDKDTSGLLIVAKNDAAHGTLAEQIKNHS 167

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             +IY ++V+G     +  +   + + S      + V  +N +G   A++H++V++   +
Sbjct: 168 FTRIYNAVVYGGFSTDEGTVDAPIGR-SQNDRKKMCVTDRNARG---AVTHYRVLERLGR 223

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F WL++   TGRTHQ+RVH  ++G P+ GD  Y        T    +   LHAR +   
Sbjct: 224 -FTWLKLCLETGRTHQIRVHMAYIGHPVAGDPIYGPQK----TITSLHGQCLHARVIGFH 278

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  ++ ++ LP +      SL 
Sbjct: 279 HPRTGVYMEFSSELPDYFSTFLTSLR 304


>gi|326316005|ref|YP_004233677.1| pseudouridine synthase, RluA family [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323372841|gb|ADX45110.1| pseudouridine synthase, RluA family [Acidovorax avenae subsp.
           avenae ATCC 19860]
          Length = 343

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 160/319 (50%), Gaps = 21/319 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++V V+ +    RLD +       +   ++ +I+RSG+VR++K R   + RI++G VVR
Sbjct: 25  VRWVEVDAESAGQRLDNFLIRELKGVPKTHVYRIIRSGEVRINKGRAAADTRIEAGDVVR 84

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +             +    + +   +  LL ED  +   +KPAG++V GGSG++
Sbjct: 85  VPPVRISDK----------VAARAERPAPAREFPLLLEDEHLIALDKPAGVAVHGGSGVS 134

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD+ETSGIL+VA+ R+A  HL + FR R   K Y +L
Sbjct: 135 FGVIEQLRQARPQ-ARFLELVHRLDRETSGILLVAKKRSALTHLQDQFRERETGKTYLAL 193

Query: 187 VWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK------ 239
           V G    + + I   L K   + G+  V V  +++     +I+  KV      +      
Sbjct: 194 VSGEWPERLKVIDAPLHKYLQVDGERRVRVTTEDDPDGMRSITLVKVRSRIPARPAEGLP 253

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDL 297
               LE+   TGRTHQ+RVH    G PI+GD KY   +           +++LHA  +  
Sbjct: 254 AMALLEVTIKTGRTHQIRVHLASRGHPILGDDKYGDFDLNRRVQKHGLRRMFLHAWRLQF 313

Query: 298 PHP-EGGRLQITAPLPAHM 315
            HP  G R+++ A LPA +
Sbjct: 314 SHPASGERVELHAELPADL 332


>gi|323704148|ref|ZP_08115727.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323536214|gb|EGB25986.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 306

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 85/332 (25%), Positives = 146/332 (43%), Gaps = 34/332 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+++  V  ++ E D+ + R+D +  +         L+K++    V+V+ K VK N +++
Sbjct: 1   MNIVNIVN-IIAEKDDVDKRIDSFLASEV-DYTRSYLKKLILDELVKVNGKSVKPNYKVR 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G V+ +         +  E   LD                        V NKP G+ V 
Sbjct: 59  EGDVINLNIPEAEEIDLKPENIPLDIIYEDDDII---------------VVNKPQGMVVH 103

Query: 121 GGSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++  L    +  G     +P + HRLD++TSG++VVA+   A   L+   
Sbjct: 104 PAPGNLSGTLVNALLYHCTNLSGINGELRPGIVHRLDKDTSGVMVVAKNDKAHLELSNQI 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R I K Y ++V G+ KN +  +   + +  HI    + VV    K   YA++ ++V++
Sbjct: 164 KNRTILKKYLAIVEGVIKNDEGAVEAPIGRD-HIERKKMAVV----KDGRYALTLYRVLE 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            +      +E    TGRTHQ+RVH  ++G PIVGD  Y    +        +   LH++ 
Sbjct: 219 RYKNN-SLVEAIIKTGRTHQIRVHMAYIGHPIVGDEVYGYKKQ----RFNLSGQVLHSKL 273

Query: 295 MDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           + L HP     ++  AP P +  K    L  K
Sbjct: 274 LGLVHPSKKVYMEFEAPTPEYFEKLMKVLKEK 305


>gi|323261040|gb|EGA44633.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
          Length = 295

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 101/300 (33%), Positives = 161/300 (53%), Gaps = 14/300 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
              +   P TGRTHQ+RVH  + G PI  D +Y    F         N+L+LHA  + L 
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDKQLADTGLNRLFLHAAALKLY 288


>gi|313890534|ref|ZP_07824162.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
 gi|313121051|gb|EFR44162.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
          Length = 299

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 79/315 (25%), Positives = 142/315 (45%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RLD+        ++     + ++ G V V+ + VK    ++SG  +          
Sbjct: 7   EAGLRLDKALAET-TDLSRSQANEQIKKGLVLVNGQAVKAKYNVKSGDNIT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL 133
           + + E+++LD        ++ L   ++YEDS + + NK  G+ V   +G      ++  +
Sbjct: 57  YQLPEEEVLD------YQAENLPIDIIYEDSDLAIINKAQGMVVHPSAGHSSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L+VA+   A Q L E  + ++  + Y ++V G
Sbjct: 111 YHIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDKAHQVLAEELKAKKSLRNYLAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +           VK        A++ F V++ F   +  LE+   T
Sbjct: 171 NLPNDRGMIEAPIGRSEKDRKKQSVTVK-----GKDAVTRFTVLERFGD-YTLLELSLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ + L HP  G  +  +
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLKGNGQFLHAQTLGLTHPSSGELMTFS 279

Query: 309 APLPAHMVKTWDSLG 323
           A  PA  +K  + L 
Sbjct: 280 AEPPAIFLKRLEQLR 294


>gi|146318440|ref|YP_001198152.1| YlyB [Streptococcus suis 05ZYH33]
 gi|145689246|gb|ABP89752.1| YlyB [Streptococcus suis 05ZYH33]
          Length = 309

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 71/311 (22%), Positives = 135/311 (43%), Gaps = 34/311 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+   +    ++     + +++GQV V+ +  K    +Q G V+            
Sbjct: 9   GIRLDKALSD-LTDLSRSVANEQIKAGQVLVNGQPKKAKYSVQVGDVLTYQ--------- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKS 135
                 +     +   ++ +   ++++D  + V NKP G+ V   +G      ++  L  
Sbjct: 59  ------IPEVEEIDYVAEDIPLEIVFQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALLYH 112

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HR+D++TSG+L++A+   A   L    + ++  + YW++V G  
Sbjct: 113 VKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIVHGNL 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            N +  I   + +            K        A++ F+V++ F   +  +E+   TGR
Sbjct: 173 PNDRGVIEAPIGRSEKDRKKQAVTAK-----GKEAVTRFQVLERFGD-YTLVELTLETGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  G  ++ TA 
Sbjct: 227 THQIRVHMAYIGHPVAGDEAYGPR-----KTLKGHGQFLHARTLGFTHPRTGEVVEFTAE 281

Query: 311 LPAHMVKTWDS 321
            PA   + W  
Sbjct: 282 APAIFQEHWKK 292


>gi|256851102|ref|ZP_05556491.1| pseudouridylate synthase [Lactobacillus jensenii 27-2-CHN]
 gi|260660526|ref|ZP_05861441.1| pseudouridylate synthase [Lactobacillus jensenii 115-3-CHN]
 gi|282933759|ref|ZP_06339114.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 208-1]
 gi|297205967|ref|ZP_06923362.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii JV-V16]
 gi|256616164|gb|EEU21352.1| pseudouridylate synthase [Lactobacillus jensenii 27-2-CHN]
 gi|260548248|gb|EEX24223.1| pseudouridylate synthase [Lactobacillus jensenii 115-3-CHN]
 gi|281302138|gb|EFA94385.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 208-1]
 gi|297149093|gb|EFH29391.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii JV-V16]
          Length = 301

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 73/327 (22%), Positives = 139/327 (42%), Gaps = 37/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + +V        RLD++   H   ++   +Q++L SG + V+ K+ K + ++ +  
Sbjct: 1   MADFELIVATK--AG-RLDKYISEH-SDLSRSRVQELLGSGDILVNGKQEKPSYKVANND 56

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +   V L    + +   ++YED  + V NKP G+ V   +
Sbjct: 57  QITVH---------------VPKLVPLNVEPEDIPLDIVYEDEDVIVVNKPQGMVVHPSA 101

Query: 124 GIAYHI--DGFLKS----WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +  +          +G +P + HR+D++TSG+L++A+   A   L      +
Sbjct: 102 GHPNHTLVNALMNHTKFLAASPEGFRPGIVHRIDKDTSGLLMIAKNANARTSLESQLAHK 161

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +++Y ++V G  K     I   + +          V     +G   A++HF V++ + 
Sbjct: 162 TNKRVYLAIVHGNFKEATGTIDAPIARNPKDRKKMAIV-----EGGKEAVTHFHVLEQYP 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +  Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +  
Sbjct: 217 -GYALVSCQLETGRTHQIRVHMKYIGHPLAGDPLYGPK-----KTLKGHGQFLHAKILGF 270

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
             P+ G+ L+     P    K    L 
Sbjct: 271 KQPKTGQWLEFQVDPPEIFQKELTYLR 297


>gi|241763829|ref|ZP_04761874.1| pseudouridine synthase, RluA family [Acidovorax delafieldii 2AN]
 gi|241366873|gb|EER61287.1| pseudouridine synthase, RluA family [Acidovorax delafieldii 2AN]
          Length = 336

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 100/319 (31%), Positives = 157/319 (49%), Gaps = 21/319 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V+ D    RLD +   H   +   ++ +I+RSG+VR++K R   + R+ +G VVR+
Sbjct: 23  RLVEVDEDSAGQRLDNFLLRHLKGVPKTHVYRIIRSGEVRINKGRANADTRLAAGDVVRL 82

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PPV  +     K ++   +           +  +L ED  +   +KPAG++V GGSG+++
Sbjct: 83  PPVRISDKVAEKAERPAPAR----------EFPVLLEDEHVIALDKPAGVAVHGGSGVSF 132

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L+    +  +   L HRLD+ETSGIL+VA+ R+A  HL + FR R   K Y +LV
Sbjct: 133 GVIEQLRQARPA-ARFLELVHRLDRETSGILLVAKKRSALTHLQDQFRERETGKTYLALV 191

Query: 188 WGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
            G     K+ I   L K     G+  V V   ++     +++  KV      +       
Sbjct: 192 TGDWPANKKVIDLPLHKYLQADGERRVRVTTADDPDGMRSVTLVKVRQAVPARPMQGLPA 251

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLP 298
              LE+   TGRTHQ+RVH    G PIVGD KY   +           +++LHA  +   
Sbjct: 252 MSLLEVTIKTGRTHQIRVHLASQGHPIVGDDKYGDFDLNKRLQKQGMRRMFLHAWRLQFM 311

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP  G R+ + A LP+ + 
Sbjct: 312 HPASGERVVLHAALPSELA 330


>gi|254491724|ref|ZP_05104903.1| pseudouridine synthase, RluA family [Methylophaga thiooxidans
           DMS010]
 gi|224463202|gb|EEF79472.1| pseudouridine synthase, RluA family [Methylophaga thiooxydans
           DMS010]
          Length = 320

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 81/343 (23%), Positives = 148/343 (43%), Gaps = 38/343 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    +Q + + ++   MRLD+     +P  +   L K +++G V VD+  ++  + + 
Sbjct: 1   MSEKIQLQEI-IPDELGGMRLDQALAKLFPDFSRGQLTKWIKAGDVTVDEAILRPRDSVI 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ V I   + + +               +  ++ +   +++ED  + + NKPAG+ V 
Sbjct: 60  GGENVIIDTELQSQDE--------------SWSAEPIALDIVHEDDDVIIINKPAGMVVH 105

Query: 121 GGSGIAYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G+G   H    + + +    Q     +  + HRLD+ T+G+L+VA+T  A   L    +
Sbjct: 106 PGAG--NHQGTLVNALLAHAPQLANIPRAGIVHRLDKATTGLLMVAKTLQAHNSLVSQLQ 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R +Q+ Y ++  G+       +   + +  HI    + +     +    AI+H++V   
Sbjct: 164 ARTVQREYQAIAIGVM-TAGGTVDEPIGRH-HIDRKRMAI----SQTGKPAITHYRVEQR 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNK 287
           F +    +  +  TGRTHQ+RVH  H+  P++GD  Y   FK                 +
Sbjct: 218 F-RAHTHIRCKLETGRTHQIRVHMAHIRHPLLGDQVYAGRFKMAKGMSENCREAVQGFRR 276

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
             LHA  +   HP  G  +   APLP  M      L    +R 
Sbjct: 277 QALHAGLLGFKHPASGEDVSWQAPLPEDMQTILKLLADDTNRE 319


>gi|331684250|ref|ZP_08384842.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli H299]
 gi|222034298|emb|CAP77039.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           LF82]
 gi|312947168|gb|ADR27995.1| 23S rRNA pseudouridine synthase D [Escherichia coli O83:H1 str. NRG
           857C]
 gi|331077865|gb|EGI49071.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli H299]
          Length = 326

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPEDMVELIEVMRADFEE 318


>gi|237737691|ref|ZP_04568172.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           mortiferum ATCC 9817]
 gi|229419571|gb|EEO34618.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           mortiferum ATCC 9817]
          Length = 318

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 87/335 (25%), Positives = 155/335 (46%), Gaps = 36/335 (10%)

Query: 4   MTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           M   + + V    +++  R+D++            +QKI+ +G V +  K++ K  N+++
Sbjct: 1   MDIKETLTVYANENDKGKRIDKFLNELIDDATRSYVQKIIDNGLVEIQGKKITKSGNKLK 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
             +++ +          I E ++LD +       + +   ++YEDS I V NK   + V 
Sbjct: 61  GTEIIVVN---------IPEDEVLDLT------PEDIPLDIIYEDSDIVVINKAPNLVVH 105

Query: 121 GGSGI--AYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++  L    D    +   +P + HRLD++TSG++VVA+   A   L+E F
Sbjct: 106 PAHGNYSGTLVNALLYHIKDLSTINGVIRPGIVHRLDKDTSGVIVVAKNDEAHGKLSEMF 165

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + + ++KIY  +  GI K K   I   + + S      + VV +N      AIS+++VID
Sbjct: 166 KEKTLEKIYVCIAKGIFKEKSGRIKTLIGRDSR-DRKKMAVVNEN---GKIAISNYEVID 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              +    ++++  TGRTHQ+RVH  H+  PI+GD  Y     G       ++  LHA  
Sbjct: 222 -EGKNHSLVKVRIETGRTHQIRVHMKHLNHPIMGDTTYGNGNDGA------DRQMLHAYR 274

Query: 295 MDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           +   HP     + + APLP    +    +G    +
Sbjct: 275 LKFIHPTKNTEMTVIAPLPEDFKRAAKHVGVDISK 309


>gi|294341011|emb|CAZ89406.1| Ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Thiomonas sp. 3As]
          Length = 329

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 98/335 (29%), Positives = 164/335 (48%), Gaps = 30/335 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V+ + V +  E  RLD +   H   +   ++ +I+RSG+VRV+  R   + ++QS   
Sbjct: 7   PQVRLLQVGDAGEGQRLDNFLARHLKGVPRSHIHRIVRSGEVRVNGGRASADQKLQSSDQ 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV  A               +  + +  L+  +++ED  +   NKP G++V GGSG
Sbjct: 67  VRIPPVRVA-------------QPDAPRAAPALQFPVVFEDDFLLAINKPEGVAVHGGSG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++   +  +   L HRLD++TSG+L++A+ R+A   L  + R R   K Y 
Sbjct: 114 VSFGVIEALRAARPT-AKFLELVHRLDRDTSGLLLIAKKRSALTTLHAALRERHADKRYL 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA------- 237
           +LV G+       I   L K     G+    V+ + +    + + F+  + FA       
Sbjct: 173 ALVAGLWTRGAVMIEAPLHKYLLANGER--RVRVDVQQGQESRTQFRSQEQFALPGLGPW 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQNKLYLH 291
                ++ +  TGRTHQ+RVH  H G PIVGD KY  +       +G    P   +++LH
Sbjct: 231 GGLSLMQARLLTGRTHQIRVHLAHCGHPIVGDDKYGDDSLNALLARGQAGVPPFRRMFLH 290

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           A  + + HP  G RL++ APLP +  +    L  +
Sbjct: 291 AESLAIAHPASGERLELRAPLPENCAQWLHHLRAQ 325


>gi|91788477|ref|YP_549429.1| ribosomal large subunit pseudouridine synthase D [Polaromonas sp.
           JS666]
 gi|91697702|gb|ABE44531.1| ribosomal large subunit pseudouridine synthase D [Polaromonas sp.
           JS666]
          Length = 344

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 71/333 (21%), Positives = 144/333 (43%), Gaps = 25/333 (7%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           S+   ++ V+V       RLDR      P  +   LQ+++ +  V+++ + V K + +++
Sbjct: 31  SVELELRRVMVPAGSHGARLDRALAGIVPEFSRSYLQQLIEAAVVQLNGRAVTKPSAKVK 90

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  + I              ++  +  +     + +   +++ED  + V +KPAG+ V 
Sbjct: 91  AGDELII--------------ELRPTPQSQAFKPEAMALDIVFEDPYLLVIDKPAGLVVH 136

Query: 121 GGSGI--AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
              G      ++G L     +    +  + HRLD++TSG++VVAR R A   L      R
Sbjct: 137 PAPGNWSGTLLNGLLARDPQASFLPRAGIVHRLDKDTSGLMVVARQRQAMDQLVSMIAAR 196

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L  G  +  +    +  + +       +  V   +     A++   ++    
Sbjct: 197 SVSREYIALAHGAWQGARTREVSAAIGRDPRNRLRMAAVDLEKNAGKPALTVISLLQ-NG 255

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++ C ++ + HTGRTHQ+RVH   +G P++ D  Y              +  LHA  +  
Sbjct: 256 ERHCLVKCKLHTGRTHQIRVHMALLGHPLISDGLYGGAVAAGLE-----RQALHACRLAF 310

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
            HP  G  ++  +P P  +      +G  Y+++
Sbjct: 311 EHPVTGAPMEFRSPPPPDLRAAIADVGLIYNQS 343


>gi|45440505|ref|NP_992044.1| 23S rRNA pseudouridine synthase D [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51595196|ref|YP_069387.1| 23S rRNA pseudouridine synthase D [Yersinia pseudotuberculosis IP
           32953]
 gi|145600172|ref|YP_001164248.1| 23S rRNA pseudouridine synthase D [Yersinia pestis Pestoides F]
 gi|162420770|ref|YP_001607807.1| 23S rRNA pseudouridine synthase D [Yersinia pestis Angola]
 gi|170025566|ref|YP_001722071.1| 23S rRNA pseudouridine synthase D [Yersinia pseudotuberculosis
           YPIII]
 gi|186894214|ref|YP_001871326.1| 23S rRNA pseudouridine synthase D [Yersinia pseudotuberculosis
           PB1/+]
 gi|229896561|ref|ZP_04511728.1| 23S rRNA pseudouridine synthase [Yersinia pestis Pestoides A]
 gi|45435362|gb|AAS60921.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Microtus str. 91001]
 gi|51588478|emb|CAH20086.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Yersinia pseudotuberculosis IP 32953]
 gi|145211868|gb|ABP41275.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           Pestoides F]
 gi|162353585|gb|ABX87533.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           Angola]
 gi|169752100|gb|ACA69618.1| pseudouridine synthase, RluA family [Yersinia pseudotuberculosis
           YPIII]
 gi|186697240|gb|ACC87869.1| pseudouridine synthase, RluA family [Yersinia pseudotuberculosis
           PB1/+]
 gi|229700339|gb|EEO88371.1| 23S rRNA pseudouridine synthase [Yersinia pestis Pestoides A]
          Length = 325

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 82/340 (24%), Positives = 148/340 (43%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V V+ K++ K   ++  G++V I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKVLGGELVAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I        ++  LD               ++YED+ I V NKP G+ V  G+G     
Sbjct: 70  QIEEDARWAPQEIPLD---------------IVYEDNDILVINKPRGLVVHPGAGNPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++
Sbjct: 115 VLNALLHYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGNM-TAGGRVDEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDSFIAILRGFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G +++  A LP  MV+  ++L  K D   +  ++  
Sbjct: 288 HPISGIQMEWHAALPEDMVELINAL--KADTEEFKDQMDW 325


>gi|218438495|ref|YP_002376824.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
 gi|218171223|gb|ACK69956.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7424]
          Length = 306

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 88/321 (27%), Positives = 148/321 (46%), Gaps = 29/321 (9%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           E ++  +RLDRW     P ++   LQ ++  G ++++          ++SG  + +    
Sbjct: 6   EVEQGKLRLDRWLAQKLPDLSRSRLQTLIEQGNLQLNGTICTDKKTLVKSGDRLHL---- 61

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
                      ++     L      +   +LYED ++ + NKPAG+ V    G      +
Sbjct: 62  -----------LIPPVKPLDLQPQDIPLDILYEDDQLIIINKPAGLVVHPSPGHEQGTLV 110

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    +  G    Q+P + HRLD++T+G LVVA+T  A  HL +  + +  ++ Y  
Sbjct: 111 NALLSHCSNLAGIGGVQRPGIVHRLDKDTTGALVVAKTDYAHHHLQQQLKAKTARREYLG 170

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V+G+PK     I N  + +  I    + VV   EKG   AI+H+++++     +  +  
Sbjct: 171 IVYGVPKTTSGKI-NLSIGRHPIERKKMAVVPL-EKGGREAITHWEILERLG-NYSLIYF 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +  TGRTHQ+RVH   M  PIVGD  Y +   G           LHA  + L HP  G  
Sbjct: 228 RLETGRTHQIRVHCQAMNHPIVGDPVYSS---GRSIGVNLAGQALHAWKLTLEHPLSGEI 284

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           ++  APLP+   K  + L  +
Sbjct: 285 IETIAPLPSTFTKLLEVLRSR 305


>gi|319939285|ref|ZP_08013648.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319811681|gb|EFW07957.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 298

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 143/319 (44%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ +   +RLD+   +  P ++  +  + +++GQ+ V+ +  K    +++G V+      
Sbjct: 3   VKVEIGGVRLDKAVADLTP-LSRSHANEQIKNGQILVNGQVKKAKYAVKAGDVITYE--- 58

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
                       L     L   ++ L   ++Y+D  + V NK  G+ V   +G      +
Sbjct: 59  ------------LPEPEALEYVAENLPLDIVYQDEDVAVVNKAQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L E  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHIKLAEELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFG-NYTLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP+    
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPKTAEV 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++ TA  PA   +T + L 
Sbjct: 276 MEFTAEAPAIFQETLEKLR 294


>gi|258647058|ref|ZP_05734527.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           tannerae ATCC 51259]
 gi|260853174|gb|EEX73043.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           tannerae ATCC 51259]
          Length = 360

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 87/334 (26%), Positives = 148/334 (44%), Gaps = 40/334 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV +  ++ +R+D++   H P  +   +Q+  ++G + ++ +  K N R++   VV +  
Sbjct: 33  VVADKGQQLLRVDKFLMAHLPDTSRNRIQQAAKAGFIHINGRPEKSNYRVKPHDVVTL-- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L+    E  I   ++ L          ++YED  + V NK AG+ V  G G     
Sbjct: 91  ---LLDRPRYENLIEPENIPLD---------IVYEDEALIVVNKSAGLVVHPGFGNYTGT 138

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +AYH+     +  D       L HR+D++TSG+LV+A+T  A   L   F  +  +
Sbjct: 139 LVNALAYHLKDV--ADYDPNDPGVGLVHRIDKDTSGLLVIAKTPDAKSKLGVQFFNKTTR 196

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG  K  +  I   + +  H     + V   +      A++H+KV+  F    
Sbjct: 197 RRYEALVWGNVKTDEGRIEGNIARDPH-DRLQMAVFAPDSGIGKPAVTHYKVLKRFG-YV 254

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF------KGNFTSPIQN------KL 288
             +E Q  TGRTHQ+R H  H+G P+  D +Y  +        G + S I+N      + 
Sbjct: 255 TLIECQLETGRTHQIRTHMRHIGHPLFNDARYGGDKVLRGTTSGAYNSFIRNCFEICPRQ 314

Query: 289 YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
            LHAR +   HP  G  +  +   P       + 
Sbjct: 315 ALHARTLGFKHPTTGEEMDFSVLPPQDFNGLIEK 348


>gi|71892188|ref|YP_277920.1| ribosomal large subunit (23S) pseudouridine synthase C [Candidatus
           Blochmannia pennsylvanicus str. BPEN]
 gi|71796294|gb|AAZ41045.1| ribosomal large subunit (23S) pseudouridine synthase C [Candidatus
           Blochmannia pennsylvanicus str. BPEN]
          Length = 338

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 104/331 (31%), Positives = 176/331 (53%), Gaps = 17/331 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ + ++    R+D +   +        + KI+R+G +R++KKR+KF  ++Q G ++R
Sbjct: 8   VHFIRISSNSSGQRIDNFLYTYLKVAPKSMIYKIIRTGAIRINKKRIKFQYKLQIGDLLR 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        I+  KI   ++   +   FL++I++YED  +   NKP G++  GGSG+ 
Sbjct: 68  IPP--------IRGIKINRFNMKYMEEVAFLQNIIIYEDDYLLALNKPTGVAAHGGSGLK 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++ +  K Q   L HRLD+ETSG+L+VA+ R A  +L E  R++ ++K Y +L
Sbjct: 120 FGVIEGLRA-LRPKAQFLELVHRLDRETSGVLLVAKRRTALVYLHEQLRLQNMKKEYLAL 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G      + ++  L KK+ +  +   VV  + +   ++ +HF++ + F     +L ++
Sbjct: 179 VHGRWNVNLQIVSVPLFKKNTL-LNSSRVVYIDSENGKFSTTHFQIKEYFDNVATFLAIK 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
           P TGRTHQ+RVH  +   PIVGD++Y        F     N+L+LHA  +   HP+   +
Sbjct: 238 PITGRTHQIRVHTQYASHPIVGDNRYGDYQSNTRFKRFGFNRLFLHASILRFIHPKTKKK 297

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
             I APL          L     RNL IK  
Sbjct: 298 FHIHAPLGQSFHNCLFFL-----RNLSIKNY 323


>gi|332522697|ref|ZP_08398949.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
 gi|332313961|gb|EGJ26946.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 299

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 82/315 (26%), Positives = 141/315 (44%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RLD+   N    ++     + ++ G V V+ + VK    ++SG  +          
Sbjct: 7   ETGLRLDKALAN-VTDLSRSQANEQIKKGLVLVNGQVVKAKYSVKSGDEIT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL 133
           + + E++ILD        ++ L   ++YEDS + + NK  G+ V   +G      ++  +
Sbjct: 57  YQLPEEEILD------YKAENLPIDIIYEDSDLAIVNKAQGMVVHPSAGHSSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L+VA+   A Q L E  + ++  + Y ++V G
Sbjct: 111 YHIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDKAHQVLAEELKAKKSLRKYLAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +           VK        A++ F V++ F   +  LE+   T
Sbjct: 171 NLPNDRGMIEAPIGRSEKDRKKQSVTVK-----GKDAVTRFTVLERFGD-YTLLELSLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+ GD  Y                +LHA+ + L HP  G  +  T
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPRKTLKGA-----GQFLHAQTLGLTHPTSGELMTFT 279

Query: 309 APLPAHMVKTWDSLG 323
           A  PA  +KT   L 
Sbjct: 280 AEPPAIFLKTLAHLR 294


>gi|238026595|ref|YP_002910826.1| Pseudouridine synthase, RluA family protein [Burkholderia glumae
           BGR1]
 gi|237875789|gb|ACR28122.1| Pseudouridine synthase, RluA family protein [Burkholderia glumae
           BGR1]
          Length = 316

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 100/322 (31%), Positives = 156/322 (48%), Gaps = 24/322 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V  D    R+D +       +   ++ +ILRSG+VRV+K R+    R+  G VVRIPP
Sbjct: 2   VEVGEDAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGDVVRIPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  A     +E   + +          ++  +L+ED  +   NKPAG++V GGSG+++ +
Sbjct: 62  IRVAAADPAREAAPVPA----------VEFEILFEDEALIAINKPAGVAVHGGSGVSFGV 111

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +++      +   L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y++   G
Sbjct: 112 IEQMRAAR-PNAKFLELVHRLDRETSGILMLAKKRSALVALHEQIRENRMDKRYYACAHG 170

Query: 190 IPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                      +   L K S   G+    V+ +      + + F +I+ +   +  +E +
Sbjct: 171 DWAADWGRRRAVKVPLFKYSTAEGERRVRVQDD---GLPSHTVFNLIERWPD-YALVEAE 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H+G PI GD KY               P   +++LHA  + L HP 
Sbjct: 227 LKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANARPSLKRMFLHAYRLKLAHPL 286

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  LQ  APLP    +  D L
Sbjct: 287 SGEPLQFDAPLPDECRRFLDQL 308


>gi|88802386|ref|ZP_01117913.1| ribosomal large subunit pseudouridine synthase D [Polaribacter
           irgensii 23-P]
 gi|88781244|gb|EAR12422.1| ribosomal large subunit pseudouridine synthase D [Polaribacter
           irgensii 23-P]
          Length = 346

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 153/330 (46%), Gaps = 35/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V    +E +R+D++  N   +     LQ+  ++G V V++  VK N++++   VVRI  
Sbjct: 20  FVASAGQEPLRVDKFLMNFIENATRSKLQQAAKAGNVLVNEISVKSNHKVKPNDVVRI-- 77

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L +   E  ++   + L          ++YED  + V NKPAG+ V  G G     
Sbjct: 78  ---VLAYPPAESLLVAEDIPLD---------IIYEDDTVIVVNKPAGMVVHPGHGNYSGT 125

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   +   +++   +  ++P L HR+D++TSG+LVVA+T  A  +L+  F  R  +++Y+
Sbjct: 126 LVNGLIHHIENLPTNSNERPGLVHRIDKDTSGLLVVAKTEFAMANLSRQFFERTTERLYY 185

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG     +  I   + +           V  +     +A+SH+KV++        +E
Sbjct: 186 ALVWGNVAEDEGRIEGNIGRSLK--NRLQMAVFPDGDFGKHAVSHYKVLERLT-YVTLVE 242

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHA 292
            +  TGRTHQ+R H  H+G  +  D +Y  +     T+             +  +  LHA
Sbjct: 243 CKLETGRTHQIRAHFKHIGHTLFNDERYGGDGVLKGTTFTKYKQFVHNCFKVLPRQALHA 302

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP+ G  +Q  + +P  +    + 
Sbjct: 303 KTLGFTHPKTGVFMQFNSEIPQDITNCLEK 332


>gi|297171550|gb|ADI22548.1| pseudouridylate synthases, 23S RNA-specific [uncultured
           Oceanospirillales bacterium HF0500_09M11]
          Length = 519

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 75/338 (22%), Positives = 145/338 (42%), Gaps = 41/338 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V+     +RLD+     +   +   LQ  ++ G + VD +  +  +++  G+ + +
Sbjct: 207 RTEQVDAQYAGIRLDQAAAELFDGFSRSRLQNWIKEGVLTVDGRAARPKDKLLGGEALTL 266

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           ++ +  +    + ++  ++Y+D  + V NKPAG+ V   +G   
Sbjct: 267 ---------------AVELAPEIDDQPEAIELPVIYQDQDLIVINKPAGLVVHPAAG--- 308

Query: 128 HIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H DG L + +           +  + HRLD++T+G++VVAR+  A   L    + + + +
Sbjct: 309 HADGTLLNGLLHLDDRLSSLPRAGIVHRLDRDTTGLMVVARSVEAHTGLVAQLQDKSLYR 368

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++  G+       +   + +   +      VV     G   A++H++V+D + +   
Sbjct: 369 EYQAIAMGVMTG-GGTVDAPMGRH-PVDRKRQAVVTH---GGKPAVTHYRVLDRY-RAHT 422

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNKLYLHAR 293
            ++++  TGRTHQ+RVH  H   P+VGD  Y    K    +            +  LHA 
Sbjct: 423 RVQVRLETGRTHQIRVHLAHRRYPLVGDPLYGGRLKQPAGATEALREALRGFRRQALHAF 482

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
            + L HP  G  ++  APLP         L  + DR  
Sbjct: 483 KLGLVHPASGEYMEFEAPLPEDFQTLVQVL--EADREA 518


>gi|300113280|ref|YP_003759855.1| RluA family pseudouridine synthase [Nitrosococcus watsonii C-113]
 gi|299539217|gb|ADJ27534.1| pseudouridine synthase, RluA family [Nitrosococcus watsonii C-113]
          Length = 319

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 85/335 (25%), Positives = 149/335 (44%), Gaps = 36/335 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + + ++    RLD+     +P  +   LQ+ ++ GQV+V+    +  + +Q G+ + +  
Sbjct: 9   ITLPSELAGKRLDQALAQVFPAYSRSRLQQWIKHGQVKVNDALARPRDTVQGGEWIVV-- 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                        I ++       S  L   ++YED  I V NKPAG+ V   +G     
Sbjct: 67  -------------IAEAEAETGWKSQPLPLEIIYEDEAIIVVNKPAGLVVHPAAGNRDGT 113

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L    +  +  +  + HRLD++TSG+LVVAR   A   L +  + RRI + Y ++
Sbjct: 114 LVNALLHHAPELERIPRAGIVHRLDKDTSGLLVVARNLVAHHGLIQQLQARRITREYQAI 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G+       I   + ++  +    + V+         A++H++V+  F +    +  +
Sbjct: 174 TVGVM-TSGGRIEAPI-QRHPVNRKRMAVIS----TGKPALTHYRVVSRF-RIHTHILCR 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+G P++GD  Y         S  +         +  LHA  + L 
Sbjct: 227 LETGRTHQIRVHLAHIGYPLLGDPTYGKRLHIPRESSEELSTALRHFKRQALHAARLGLV 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           HPE  + +   APLP  M      L  + DR  +I
Sbjct: 287 HPEKKQAMNWEAPLPEDMATMLALL--EQDRQHHI 319


>gi|331674037|ref|ZP_08374799.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA280]
 gi|331068776|gb|EGI40169.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA280]
          Length = 326

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 83/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  D +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIDVMRADFEE 318


>gi|329894956|ref|ZP_08270755.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC3088]
 gi|328922685|gb|EGG30020.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC3088]
          Length = 321

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 90/318 (28%), Positives = 160/318 (50%), Gaps = 13/318 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +V Y  ++ DE   RLD +    +  +    + K +R G+VRV+K R     ++  G  +
Sbjct: 12  HVVYHQIDADEAGQRLDNFLLRWFAQVPKSRVYKAIRGGEVRVNKGRANAMYKLLEGDDI 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP+      +       + ++      D ++  +LYED+   + NKP+G++V GGSG+
Sbjct: 72  RIPPLGERALQM-------EGALVAKHWLDSVERGVLYEDADFMIINKPSGLAVHGGSGL 124

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            Y +   L+  +  + ++  L HRLD++TSG +++A+  +A +HL    R R++ K Y +
Sbjct: 125 KYGLIEVLRQ-LRPEARRLELVHRLDRDTSGCIMIAKKNSALRHLHALLRDRKLTKRYHA 183

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV+G     +  +   L K +   G+ +  V +       A + F  ++ +      +E 
Sbjct: 184 LVFGKWPRAQRLVDAPLKKFALASGERIVRVNEE---GQKAKTEFATLNRYP-GLTLVEA 239

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-TSPIQNKLYLHARYMDLPHPEGGR 304
           +P TGRTHQ+RVHA H+G  ++GD KY          S    +L+LHA  ++L  P G  
Sbjct: 240 KPITGRTHQIRVHAAHLGHCLLGDDKYAHEAAQELAASVGLKRLFLHAASLELVAPSGKS 299

Query: 305 LQITAPLPAHMVKTWDSL 322
           L ++AP    + +  +  
Sbjct: 300 LTVSAPYDQELNEVLERC 317


>gi|269121652|ref|YP_003309829.1| pseudouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268615530|gb|ACZ09898.1| pseudouridine synthase, RluA family [Sebaldella termitidis ATCC
           33386]
          Length = 305

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 82/326 (25%), Positives = 151/326 (46%), Gaps = 34/326 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++ E  EE  RLD +       +    +Q++++ G + V+ K+ K + +++    + 
Sbjct: 1   MEKIIFEISEEGKRLDLYIAER-TELTRTRIQQLIKDGNINVNNKKSKPSYKVEKNDFIE 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +               I+     +    + +   +LYEDS I V +K AGI V    G  
Sbjct: 60  M---------------IIPDEKEIDLVPENINIKILYEDSDIAVIDKEAGIVVHPSHGHE 104

Query: 127 --YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  +    D  G     +P + HRLD++TSG+L++A+   A   L+E F    I+
Sbjct: 105 SGTLVNAVMYHIKDLSGINGEIRPGIVHRLDKDTSGLLIIAKNDTAHLRLSEMFGSSGIR 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +++ G    +   +   + +        + VVK N      AI++F+V+D   +KF
Sbjct: 165 KTYIAILKGKINKESGKLETLIGRDPK-DRKKMAVVKTN---GKTAITYFQVLD-KNEKF 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +++   TGRTHQ+RVH  ++G P++GD  Y  + K      I  +  LHA  ++  HP
Sbjct: 220 SLVKVNIQTGRTHQIRVHMKYLGYPVLGDSVYGRDNK------IAGRQMLHAYKLEFLHP 273

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFK 325
              + ++I + LP    K     G +
Sbjct: 274 VTQKAMKIISELPQDFEKALKETGLE 299


>gi|256420955|ref|YP_003121608.1| pseudouridine synthase, RluA family [Chitinophaga pinensis DSM
           2588]
 gi|256035863|gb|ACU59407.1| pseudouridine synthase, RluA family [Chitinophaga pinensis DSM
           2588]
          Length = 356

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 78/335 (23%), Positives = 138/335 (41%), Gaps = 40/335 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++ +  +E +R+D++  N         +Q+   +G V V+ K VK N ++++   + +  
Sbjct: 27  IIADKGQEPLRVDKFLMNRVEGATRNKIQQACDNGMVIVNDKPVKSNYKVKAHDRIVVYS 86

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYH 128
             N  N  +                + L   ++YED  + + NK  G+ V  G G     
Sbjct: 87  NKNPENTQV--------------IPEELPLNIIYEDEDLMIINKLPGMVVHPGCGNYTGT 132

Query: 129 IDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +   L  ++      P          L HR+D+ TSG+LVVA++  A   L + F    +
Sbjct: 133 LVNGLAWYLGDHTTTPAPEPSIPRFGLVHRIDKNTSGLLVVAKSEKAMNDLAKQFFDHTV 192

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Q+ Y +LVWG  +  +  I   + +  H     +       +    AI+H+KV++ F   
Sbjct: 193 QRRYLALVWGDFEEDEGTIEAHVGR--HQRFRKIMDAYPEGEYGKEAITHYKVLERF-NY 249

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------------PIQNK 287
              +E +  TGRTHQ+RVH  H+G  +  D  Y  +     T              I  +
Sbjct: 250 VTLIECRLETGRTHQIRVHMQHIGHSLFNDDTYNGDRILKGTVFAKYKQFVENCFEIMPR 309

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
             LHA+ +   HP   + +   +PLP       + 
Sbjct: 310 HALHAQTLGFIHPRTRKPIHFESPLPDDFKAVLEK 344


>gi|322385620|ref|ZP_08059264.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           cristatus ATCC 51100]
 gi|321270358|gb|EFX53274.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           cristatus ATCC 51100]
          Length = 300

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 151/326 (46%), Gaps = 34/326 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + ++     +RLD+   +    ++     + +++GQ+ V+ +  K    ++ G V+   
Sbjct: 2   ELKIDAVAAGLRLDKAVAD-LTELSRGLANEQIKNGQILVNGEAKKAKYAVKEGDVI--- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 ++ + + ++++        ++ L   ++Y+D  + V NKP G+ V   +G    
Sbjct: 58  ------SYEVPDPEVVE------YVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSG 105

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + 
Sbjct: 106 TLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHLALADELKDKKSLRK 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW++V G   N +  I   + +            K        A++ F+V++ F   +  
Sbjct: 166 YWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPALTRFQVLERFGD-YTL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 220 VELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRT 274

Query: 303 GR-LQITAPLPAHMVKTWDSLGFKYD 327
           G  L+ TA  P+  ++T + L   +D
Sbjct: 275 GEVLEFTAEAPSIFLETLEKLRKVHD 300


>gi|228471651|ref|ZP_04056425.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           gingivalis ATCC 33624]
 gi|228277070|gb|EEK15756.1| ribosomal large subunit pseudouridine synthase D [Capnocytophaga
           gingivalis ATCC 33624]
          Length = 343

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 150/326 (46%), Gaps = 35/326 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
             +E +R+D++  N   + +   +Q+  + G + V+   VK N+R+++   V++      
Sbjct: 22  KGQEPLRVDKFLMNFVENASRNKVQQAAKDGNIFVNGVAVKANHRVKANDEVKVM----- 76

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDG 131
             H   E  ++   + L          ++YED ++ + NKPAG+ V  G G      I+G
Sbjct: 77  FAHPPHEYLLVPEPIPLD---------IVYEDEELIIINKPAGLVVHPGHGNYQGTLING 127

Query: 132 FL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +   +    +   +P L HR+D++TSG+LVVA+T  A  HL + F  +  ++ Y +LVW
Sbjct: 128 LIYHFQHLPMNSSDRPGLVHRIDKDTSGLLVVAKTEEAMNHLAKQFFNKTSEREYVALVW 187

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G     +  I   + +  H        V  +      AI+H+KV++ F      +  +  
Sbjct: 188 GNLAQDEGTIIGHIGR--HPKNRLQMTVFPDGSEGKEAITHYKVLERFG-YVTIVSCRLE 244

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------------PIQNKLYLHARYMD 296
           TGRTHQ+R H  ++G P+  D +Y  +     T+             I  +  LHA+ + 
Sbjct: 245 TGRTHQIRAHFTYIGHPLFNDERYGGDKILKGTTSAKYKQFVENCFKILPRQALHAKTLG 304

Query: 297 LPHPEGGRL-QITAPLPAHMVKTWDS 321
           +  P  G++ +  + +P  M +  + 
Sbjct: 305 VEKPSTGQMLRFDSEIPQDMQQCIEK 330


>gi|309805623|ref|ZP_07699665.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
 gi|308165061|gb|EFO67302.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
          Length = 311

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 144/328 (43%), Gaps = 33/328 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+++E  +RLD++   H   I+   +Q++++   +  +  + K + ++ +   + I  
Sbjct: 9   LVVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNGLQTKLSYKVNTNDKINIE- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                         + S   L+   + L   ++YED  + V NKP G+ V   +G   H 
Sbjct: 68  --------------IPSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHT 113

Query: 130 --DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             +G +    +     +  +P + HR+D++TSG+L++A+   A   L +    +  ++ Y
Sbjct: 114 LVNGLIYHTKNLAKCDEILRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINKREY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V    K+    I   + +       Y             AI+HF V++ F   +  +
Sbjct: 174 IAIVHANFKHSSGVIDAPIGRNP-----YQRQQMAVVASGKKAITHFTVLEQFP-GYSLV 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    TGRTHQ+RVH  ++G PI GD  Y      N      N  +LHA+ +   HP+  
Sbjct: 228 KCVLETGRTHQIRVHMSYIGHPIAGDPLYGPKKTLN-----GNGQFLHAKTLGFYHPKTN 282

Query: 304 R-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           + L+ +   P    K    L  K   NL
Sbjct: 283 QWLEFSISEPQIFAKQLYLLRKKLTNNL 310


>gi|215487933|ref|YP_002330364.1| 23S rRNA pseudouridine synthase D [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218690713|ref|YP_002398925.1| 23S rRNA pseudouridine synthase D [Escherichia coli ED1a]
 gi|312965509|ref|ZP_07779741.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           2362-75]
 gi|215266005|emb|CAS10416.1| 23S rRNA pseudouridine synthase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218428277|emb|CAR09055.1| 23S rRNA pseudouridine synthase [Escherichia coli ED1a]
 gi|281179642|dbj|BAI55972.1| putative pseudouridine synthase [Escherichia coli SE15]
 gi|312289929|gb|EFR17817.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           2362-75]
          Length = 326

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEEMRADFEE 318


>gi|319779244|ref|YP_004130157.1| Ribosomal large subunit pseudouridine synthase C [Taylorella
           equigenitalis MCE9]
 gi|317109268|gb|ADU92014.1| Ribosomal large subunit pseudouridine synthase C [Taylorella
           equigenitalis MCE9]
          Length = 310

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 100/325 (30%), Positives = 160/325 (49%), Gaps = 20/325 (6%)

Query: 1   MSL-MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M++ +  V+YV V++  +  R+D +       +   ++ K +RSGQVRV+K RV    RI
Sbjct: 1   MTISLPSVKYVQVDDSSDGQRIDNFLIKFSKGVPKSHIYKAIRSGQVRVNKGRVNSECRI 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            +G  +RIPP       + +EQ                   +++ED    + NKPAG++V
Sbjct: 61  HTGDEIRIPPF-----RLPQEQPKSFIPTR--------NFDIIFEDDYFLIINKPAGVAV 107

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG++Y +   +++      +   L HRLD+ETSG+L++A+ R+A   L +  R  ++
Sbjct: 108 HGGSGVSYGVIEQIRT-SRPDSKFLELVHRLDKETSGLLIIAKKRSALVALQDMIRQSKL 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y++L+ G    K + I   L K     G+    VK + +   YA S  + ++   + 
Sbjct: 167 HKSYYALIKGNWPEKLKDIKLPLYKYLTPQGER--RVKVDAENGKYAHSKVRKVEKVGE- 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLP 298
           F  L +Q  TGRTHQ+RVH    G PIVGD KY  +    +      N+++LHA  +   
Sbjct: 224 FELLSVQILTGRTHQIRVHLRSSGFPIVGDEKYGDDALTLHVKKLGFNRMFLHAYILSFV 283

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSL 322
           HP    RL+    LP         L
Sbjct: 284 HPITEKRLEFKIDLPDDCKSLLKKL 308


>gi|303254977|ref|ZP_07341056.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS455]
 gi|302598057|gb|EFL65124.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS455]
          Length = 295

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 145/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETGGLRLDKALSD-LSELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G+ 
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGKT 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L   A +P    +T + L 
Sbjct: 276 LGFKADIPEIFKETLERLR 294


>gi|295100789|emb|CBK98334.1| ribosomal large subunit pseudouridine synthase D [Faecalibacterium
           prausnitzii L2-6]
          Length = 310

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 139/324 (42%), Gaps = 29/324 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  +VE +    R+DR+       ++   LQ ++  G V  + K +  + ++++G  + +
Sbjct: 4   REFIVEAEAAGQRIDRFLSGEDTGLSRSALQGLVAEGHVLCNGKSIAKSLKLKAGDTILL 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           +  +  +      +   ++YED  + V NKP G+ V    G   
Sbjct: 64  E---------------IPDAKPIEAVPQDIPLDIVYEDDHLLVVNKPKGMVVHPAPGNPD 108

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++  L     S        +P + HR+D++TSG+LVVA+  A    L++   +  ++
Sbjct: 109 GTLVNALLWHCKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVE 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V+G     +  +   L + S      + V   +E    YA + +KV++ F   F
Sbjct: 169 RAYQTVVYGGFAQDEGFVEANLGR-SKTDRKKMAVYPASEPHTKYAYTGYKVLERFG-GF 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE +  TGRTHQ+RVH   +  P+ GD  Y      +      +   LHA+ +   HP
Sbjct: 227 TLLECRLKTGRTHQIRVHMASIQHPVAGDPVYGP----HNCITRLHGQCLHAKTLGFIHP 282

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  L+  + LP +      SL 
Sbjct: 283 ITGEHLRFDSGLPEYFTHFIASLR 306


>gi|71276441|ref|ZP_00652717.1| Pseudouridine synthase, RluD [Xylella fastidiosa Dixon]
 gi|71901554|ref|ZP_00683637.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|170730991|ref|YP_001776424.1| pseudouridylate synthase [Xylella fastidiosa M12]
 gi|71162757|gb|EAO12483.1| Pseudouridine synthase, RluD [Xylella fastidiosa Dixon]
 gi|71728678|gb|EAO30826.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|167965784|gb|ACA12794.1| Pseudouridylate synthase [Xylella fastidiosa M12]
          Length = 331

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 88/342 (25%), Positives = 153/342 (44%), Gaps = 42/342 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V +     R D      +P  +   L + ++SG V ++   V+  + +  G+VVR+
Sbjct: 14  RQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVRPRDPVYGGEVVRL 73

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             V +     + +   LD               +LYED  ++V NKPAG+ V  G+G   
Sbjct: 74  QVVPDIRTDAVPQDIPLD---------------ILYEDEHVFVLNKPAGLIVHPGAG--- 115

Query: 128 HIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + DG L + +  +        +  + HRLD++TSG++VVART  A   L E    R++ +
Sbjct: 116 NPDGTLVNALLHRDPALAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSSRQVHR 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V  +         N  +++       + V          A++H+++ + F +   
Sbjct: 176 QYLAVV--VSALVSGGTVNAAIERHPRDRLRMAV----SDTGKEAVTHYRLRERF-RAHT 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNKLYLHAR 293
            LE +  TGRTHQ+RVH  H+  PIVGD  Y  + K                 +  LHA 
Sbjct: 229 ALECRLDTGRTHQIRVHMAHLRHPIVGDRLYGGSLKLPKGGTDALVAMLRGFKRQALHAE 288

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            ++  HP G   ++I AP+P  + +   +L  + D  L+ +R
Sbjct: 289 VLEFLHPVGALPVRIVAPVPEDLCQLLAAL--REDSALFFER 328


>gi|289422301|ref|ZP_06424151.1| ribosomal large subunit pseudouridine synthase D
           [Peptostreptococcus anaerobius 653-L]
 gi|289157246|gb|EFD05861.1| ribosomal large subunit pseudouridine synthase D
           [Peptostreptococcus anaerobius 653-L]
          Length = 320

 Score =  256 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 145/326 (44%), Gaps = 31/326 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V   +V +D+ + RLD +  + Y  I+   +QK+++  ++RV+ K  K + ++++G  +
Sbjct: 18  DVDVYIVSDDDADSRLDFYIASQYRDISRSYIQKLIKEDRIRVNSKIEKASYKVKTGDKI 77

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                +     L      +   ++YED  + V NK  G+ V    G 
Sbjct: 78  EVN---------------MPEPQALEIEPQDIGIDIVYEDDYLMVVNKQQGMVVHPAPGN 122

Query: 126 AYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 +  L    D         +P + HR+D+ TSG+LV+A+     Q L++ F++  
Sbjct: 123 PDRTLVNAVLFHCGDRLSSINGVIRPGIVHRIDKNTSGLLVIAKDNQTHQGLSDQFKVHS 182

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y  +  G  + +++ I   + +        + +VK N      A++HF++++ +  
Sbjct: 183 ITREYEMICIGNVEWQEKTIDGPIGRNPK-DRMKMAIVKTN---GKRAVTHFRLVENY-D 237

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  L  +  TGRTHQ+RVH   +  PI+GD+ Y    K            LHAR +   
Sbjct: 238 GYSHLSARLETGRTHQIRVHISSINRPILGDNLYGYKVKTFAKLEG---QCLHARKLGFI 294

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G+ ++  + LP +     + L 
Sbjct: 295 HPISGKYMEFDSDLPEYFEDVLNKLR 320


>gi|332654861|ref|ZP_08420603.1| ribosomal large subunit pseudouridine synthase D [Ruminococcaceae
           bacterium D16]
 gi|332516204|gb|EGJ45812.1| ribosomal large subunit pseudouridine synthase D [Ruminococcaceae
           bacterium D16]
          Length = 301

 Score =  256 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 74/321 (23%), Positives = 133/321 (41%), Gaps = 33/321 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  +++   E   RLD +  +    +     Q++L  G V    K +K N +   G VV 
Sbjct: 1   MTPLILTAQEGGERLDAFVASQVEDLTRSAAQRLLEQGAVTSGGKPLKKNAKTTPGMVVE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +               +L     +      +   ++YED  + V NKP G+ V    G  
Sbjct: 61  V---------------LLPDPQPVEIVPQNIPLDVVYEDDDVIVVNKPVGLVVHPAPGHP 105

Query: 126 -AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  L    DS        +P + HR+D++TSG+++ A+   A   L    +   +
Sbjct: 106 DGTLVNALLYHCGDSLSGINGELRPGIVHRIDRDTSGLIIAAKNDRAHLALAAQLQDHTL 165

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            ++Y ++  G  K  +  +   + +   +    + V    +     A++H+KV+  +   
Sbjct: 166 ARVYEAVAVGGFKEDRGTVNAPIGRH-PVDRKKMAV----DPKGRPAVTHWKVLGRYP-G 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              LE +  TGRTHQ+RVH  ++G P++GD  Y A        P      LHAR +   H
Sbjct: 220 CTHLECRLETGRTHQIRVHMAYLGHPLLGDTVYGAKKP----VPGLAGQCLHARRLRFIH 275

Query: 300 PEGGR-LQITAPLPAHMVKTW 319
           P  G+ +++  PLP       
Sbjct: 276 PTTGQPVEVECPLPEWFTNLL 296


>gi|88800777|ref|ZP_01116334.1| pseudouridine synthase [Reinekea sp. MED297]
 gi|88776483|gb|EAR07701.1| pseudouridine synthase [Reinekea sp. MED297]
          Length = 328

 Score =  256 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 79/335 (23%), Positives = 147/335 (43%), Gaps = 32/335 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T  +  +V N+    R D+     +   +   +Q+ ++ G++ V+ K +K  +++  G+ 
Sbjct: 7   TIKESQIVPNELGQKRFDQIAAQLFADYSRSRIQQWIKEGRLTVNGKTLKPRDKLIGGET 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +   + +      E                ++  ++YED +I V +KPAG+ V  G+G
Sbjct: 67  LTLDVTLESDERWEAEP---------------VELNVVYEDEQIIVIDKPAGLVVHPGAG 111

Query: 125 IAYHI--DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                  +G L  + +     +  + HRLD++T+G++VVART  A  HL    + R + +
Sbjct: 112 TPSGTVLNGLLYRYPELAAVPRAGIVHRLDKDTTGLMVVARTLTAQTHLAGQLQDRSMGR 171

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++L  G+       + N  + +       + V          AI+H++V   F +   
Sbjct: 172 EYYALCMGVMT--GGGVVNEPIDRHPKHRTKMAVAPTG--MGKDAITHYRVEQRF-RNHT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT--------SPIQNKLYLHAR 293
            +  +  TGRTHQ+RVH  H+G P+VGD  Y    +                 +  LHA 
Sbjct: 227 LVRCKLETGRTHQIRVHLSHIGYPLVGDPLYAGRSRLPKGISPEVMTVLKAFKRQALHAG 286

Query: 294 YMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYD 327
           Y++L HP    +    + LP   +   D+L  + D
Sbjct: 287 YLELIHPATDEMVSWESDLPEDFLGLLDALQEEVD 321


>gi|27262446|gb|AAN87504.1| Ribosomal large subunit pseudouridine synthase D [Heliobacillus
           mobilis]
          Length = 327

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 84/318 (26%), Positives = 140/318 (44%), Gaps = 32/318 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +E + RLD W  N     +  + Q  ++ G ++V+   VK N R++ G  + + P    
Sbjct: 31  PEEVDSRLDVWLVNRELVPSRTHGQNWIKEGLIKVEGMTVKANYRLRPGDRIEVVPAEPV 90

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDG 131
              II E   +D               ++Y+D+ + V NK AG+ V    G      ++ 
Sbjct: 91  STEIIPENIPID---------------IVYQDAHVAVINKSAGLVVHPAEGHTSGTLVNA 135

Query: 132 FLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    D  G     +P + HR+D++TSG+LVVA+   A  HL E  +   +++ Y ++V
Sbjct: 136 LLYHIKDLSGINGELRPGIVHRIDKDTSGLLVVAKHDEAHIHLAEQVKDHLVRREYLAIV 195

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQ 246
            GI   +   I   + +        + VV         +++H +V++ F +  F  +   
Sbjct: 196 HGIIGAETGRIDAPIGRDPK-DRQKMAVVS----SGKASVTHLRVLERFPESGFSLVRCN 250

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  ++G P+ GD KY         +       LHA  +D  HP  GR +
Sbjct: 251 LETGRTHQIRVHMAYIGHPVAGDPKYGPKK----AAFGLEGQALHAHRLDFTHPHDGREM 306

Query: 306 QITAPLPAHMVKTWDSLG 323
              A  P    K  ++L 
Sbjct: 307 TFQAEPPETFQKVLETLR 324


>gi|332753864|gb|EGJ84241.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           4343-70]
 gi|332997822|gb|EGK17432.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           K-218]
          Length = 326

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRSGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|123965457|ref|YP_001010538.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9515]
 gi|123199823|gb|ABM71431.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9515]
          Length = 320

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 84/312 (26%), Positives = 142/312 (45%), Gaps = 28/312 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +  P  +   +Q ++ +G V ++ K  K    +++G  ++I          
Sbjct: 26  PMRLDRWLVSKRPEQSRARIQNLINAGLVLINYKTAKAKTPLKTGDNIQIWMPPPEPLVY 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
           +K +K              +   +LYED  I V NK +G+ V    G      ++G L  
Sbjct: 86  LKPEK--------------MHLNILYEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLFH 131

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++TSG +VVA+++ +  +L    R +   + Y +++ G+P
Sbjct: 132 CKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQESLVNLQIQIRDKIASRNYIAVIHGVP 191

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
              +  I   + +   I      VV  +E    YA +++K+++ F   +  +  +  TGR
Sbjct: 192 NTSEGKIVGHIGRD-KINRLKYAVV--DENSGRYACTYWKLLERFG-NYSLMSFKLDTGR 247

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  ++  PI+GD  Y    K        +   LHA  + L HP  G  ++  A 
Sbjct: 248 THQIRVHCAYINHPILGDPLYGRCKKLPCK---LDGQALHAIELGLFHPINGEEMKFEAD 304

Query: 311 LPAHMVKTWDSL 322
           LP   VK    L
Sbjct: 305 LPQEFVKLLRIL 316


>gi|255036339|ref|YP_003086960.1| pseudouridine synthase, RluA family [Dyadobacter fermentans DSM
           18053]
 gi|254949095|gb|ACT93795.1| pseudouridine synthase, RluA family [Dyadobacter fermentans DSM
           18053]
          Length = 343

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 150/334 (44%), Gaps = 41/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V +  +  MRLD++   H  + +   +Q  + +  VRV+ +  K + +++   VV +  
Sbjct: 21  IVADKGQSLMRLDKYLNLHVANASRTKIQNGIEAEAVRVNGQPTKASYKVKPFDVVTL-- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------- 122
              +L    ++ +I+  ++ L          ++YED  + + NK AG+ V          
Sbjct: 79  ---SLPQPPRDTEIIPENLPLD---------IIYEDDVLLIVNKAAGMVVHPAFGNWTGT 126

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             +G+ YH    L +  + +G +P L HR+D++TSG+LV+A+T  A   L   F    I+
Sbjct: 127 LINGLVYHFQ-QLPTGRNGEG-RPGLVHRIDKDTSGLLVIAKTEFAMTFLASQFADHSIE 184

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +L+WG PK +K  I   + + +      V  V  +     +A++H++VI    +  
Sbjct: 185 RTYHALIWGEPKAEKGTITGHVGRSAR--DRRVMDVYVDGSQGKHAVTHYEVIK-PLRYV 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------------PIQNKL 288
             ++    TGRTHQ+R H  H+G PI  D  Y  +      S             + +  
Sbjct: 242 SLIKCNLETGRTHQIRAHMKHIGHPIFNDPMYGGDKILRGGSSGSFKAMVENAFGLISGQ 301

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            LHA+ +   HP   + +Q    LP       + 
Sbjct: 302 ALHAKSLGFIHPTTRKWIQFDTELPEGFRAILEK 335


>gi|148984670|ref|ZP_01817938.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP3-BS71]
 gi|149006397|ref|ZP_01830109.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP18-BS74]
 gi|225861177|ref|YP_002742686.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298231008|ref|ZP_06964689.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae str. Canada MDR_19F]
 gi|298254573|ref|ZP_06978159.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae str. Canada MDR_19A]
 gi|298503058|ref|YP_003724998.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|147762174|gb|EDK69136.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP18-BS74]
 gi|147923061|gb|EDK74176.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP3-BS71]
 gi|225727922|gb|ACO23773.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298238653|gb|ADI69784.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|301799912|emb|CBW32491.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           OXC141]
 gi|327389210|gb|EGE87555.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA04375]
 gi|332075542|gb|EGI86010.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA17545]
 gi|332202784|gb|EGJ16853.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA41317]
          Length = 295

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 145/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETGGLRLDKALSD-LSELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G  + GD  Y         +   +  +LHA+ +   HP  G+ 
Sbjct: 221 QLETGRTHQIRVHMAYIGHSVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGKT 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+  A +P    +T + L 
Sbjct: 276 LEFKADIPEIFKETLERLR 294


>gi|324005834|gb|EGB75053.1| pseudouridine synthase, RluA family [Escherichia coli MS 57-2]
          Length = 326

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYSPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|259046729|ref|ZP_05737130.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           adiacens ATCC 49175]
 gi|259036625|gb|EEW37880.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           adiacens ATCC 49175]
          Length = 308

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 86/327 (26%), Positives = 142/327 (43%), Gaps = 37/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT V   +    E+  RLD+        ++   +Q  L++G + V+ + VK N + QSG 
Sbjct: 1   MTSVFKKLKLELEKTQRLDKVLTGEL-GLSRTTIQSWLKAGLISVNGEVVKSNYKAQSGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V I         + KE+ ++      T   + +   +++ED  + V NKP+G+ V    
Sbjct: 60  EVTI---------LQKEEDVI------TIQPENIPLDIVFEDDSLIVVNKPSGMVVHPSK 104

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + YH +  L      +  +P L HR+D++TSG+LV+A+     Q L E  
Sbjct: 105 GHYSGTLVNALLYHSNS-LSDSTSEEIYRPGLVHRIDKDTSGLLVIAKNNDVHQKLAEQI 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
              ++ + Y ++V G   ++   +   L +        V      EKG   AI+HF+V+D
Sbjct: 164 AENKMNREYIAIVDGHFAHETGVVDAPLSRHQTNRLKRVV-----EKGGKNAITHFEVLD 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F+  +  +  +  TGRTHQ+R H   +  PIV D  Y    K       +   +LHAR 
Sbjct: 219 SFSD-YSLVSCRLETGRTHQIRAHMEFIKHPIVNDPLYHPKGKNA----TEFGQFLHART 273

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWD 320
           +   HP  G  L      P    +   
Sbjct: 274 LSFTHPLTGETLNFQVEPPKEFAEFIQ 300


>gi|293392744|ref|ZP_06637062.1| ribosomal large subunit pseudouridine synthase D [Serratia
           odorifera DSM 4582]
 gi|291424603|gb|EFE97814.1| ribosomal large subunit pseudouridine synthase D [Serratia
           odorifera DSM 4582]
          Length = 325

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 81/333 (24%), Positives = 142/333 (42%), Gaps = 35/333 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V+V+ K   K   ++  G+ V I
Sbjct: 8   TATVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVQVNGKTTNKPKEKVLGGETVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YEDS I V NKP  + V  G+G   
Sbjct: 68  DAQIEEEARWEPQDIPLD---------------IVYEDSDILVINKPRDLVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + +     +  + HRLD++T+G++VVA+T  A   L E+ ++R I + Y 
Sbjct: 113 GTVLNALLHYYPEIIDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A++H+++++ F +    L 
Sbjct: 173 AVAIGTM-TAGGTVEEPIARHST-----KRTHMAVHPMGKPAVTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMSHISHPLVGDPLYGGRPRPPKGASEAFITTLRGFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           L HP  G +++  APLP  MV   D+L    + 
Sbjct: 286 LYHPISGIQMEWHAPLPQDMVDLIDALKADTEE 318


>gi|124024488|ref|YP_001018795.1| pseudouridylate synthase specific to ribosomal large subunit
           [Prochlorococcus marinus str. MIT 9303]
 gi|123964774|gb|ABM79530.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9303]
          Length = 324

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 87/313 (27%), Positives = 137/313 (43%), Gaps = 28/313 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +  ++QK + +G VRV+    +    ++ G  V++          
Sbjct: 27  PMRLDRWLVSQRSEQSRSHIQKFIEAGLVRVNGITGRAKTPLRQGDEVQLWM-------- 78

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFLKS 135
                            + +   +L+ED  + V NKPAG++V    G      ++G L  
Sbjct: 79  ------PPPEPLPYLQPEAMHLDVLFEDRHLIVINKPAGLTVHPAPGNRNGTLVNGLLHH 132

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +V+A+++ A   L +  + R   + Y ++V G P
Sbjct: 133 CSDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQQQIQKRIASRNYLAVVHGAP 192

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
              +  I   + +       Y  V    E G  +A +H+ +++     +  L  Q  TGR
Sbjct: 193 TGDQGTIVAAIGRHPVDRKKYAVV---TEDGGRHACTHWTLVERLGD-YSLLRFQLDTGR 248

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  H+G PIVGD  Y    K     P      LHA  + L HP  G R+   AP
Sbjct: 249 THQIRVHCAHIGHPIVGDPIYSRCRKLPIDLPG---QILHAVQLGLDHPLTGERMVFEAP 305

Query: 311 LPAHMVKTWDSLG 323
           LP    K    L 
Sbjct: 306 LPDLFEKLLAVLR 318


>gi|170683711|ref|YP_001744779.1| 23S rRNA pseudouridine synthase D [Escherichia coli SMS-3-5]
 gi|218701106|ref|YP_002408735.1| 23S rRNA pseudouridine synthase D [Escherichia coli IAI39]
 gi|170521429|gb|ACB19607.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           SMS-3-5]
 gi|218371092|emb|CAR18921.1| 23S rRNA pseudouridine synthase [Escherichia coli IAI39]
          Length = 326

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDDDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|332999362|gb|EGK18947.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           VA-6]
          Length = 326

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NSEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|24113932|ref|NP_708442.1| 23S rRNA pseudouridine synthase D [Shigella flexneri 2a str. 301]
 gi|26248957|ref|NP_754997.1| 23S rRNA pseudouridine synthase D [Escherichia coli CFT073]
 gi|30063991|ref|NP_838162.1| 23S rRNA pseudouridine synthase D [Shigella flexneri 2a str. 2457T]
 gi|74313153|ref|YP_311572.1| 23S rRNA pseudouridine synthase D [Shigella sonnei Ss046]
 gi|110642757|ref|YP_670487.1| 23S rRNA pseudouridine synthase D [Escherichia coli 536]
 gi|110806535|ref|YP_690055.1| 23S rRNA pseudouridine synthase D [Shigella flexneri 5 str. 8401]
 gi|191174579|ref|ZP_03036074.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           F11]
 gi|218555174|ref|YP_002388087.1| 23S rRNA pseudouridine synthase D [Escherichia coli IAI1]
 gi|218696219|ref|YP_002403886.1| 23S rRNA pseudouridine synthase D [Escherichia coli 55989]
 gi|293411985|ref|ZP_06654708.1| rluD [Escherichia coli B354]
 gi|300940369|ref|ZP_07154957.1| pseudouridine synthase, RluA family [Escherichia coli MS 21-1]
 gi|300976568|ref|ZP_07173520.1| pseudouridine synthase, RluA family [Escherichia coli MS 200-1]
 gi|300986849|ref|ZP_07177832.1| pseudouridine synthase, RluA family [Escherichia coli MS 45-1]
 gi|301026354|ref|ZP_07189802.1| pseudouridine synthase, RluA family [Escherichia coli MS 69-1]
 gi|301050463|ref|ZP_07197345.1| pseudouridine synthase, RluA family [Escherichia coli MS 185-1]
 gi|306812486|ref|ZP_07446684.1| 23S rRNA pseudouridine synthase D [Escherichia coli NC101]
 gi|331648338|ref|ZP_08349426.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli M605]
 gi|331658744|ref|ZP_08359686.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA206]
 gi|331664161|ref|ZP_08365070.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA143]
 gi|54039250|sp|P65835|RLUD_SHIFL RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|54041741|sp|P65834|RLUD_ECOL6 RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|26109363|gb|AAN81565.1|AE016764_247 Ribosomal large subunit pseudouridine synthase D [Escherichia coli
           CFT073]
 gi|24053038|gb|AAN44149.1| ftsH mutation suppressor [Shigella flexneri 2a str. 301]
 gi|30042247|gb|AAP17972.1| ftsH mutation suppressor [Shigella flexneri 2a str. 2457T]
 gi|73856630|gb|AAZ89337.1| suppressor of ftsH mutation [Shigella sonnei Ss046]
 gi|110344349|gb|ABG70586.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           536]
 gi|110616083|gb|ABF04750.1| suppressor of ftsH mutation [Shigella flexneri 5 str. 8401]
 gi|190905152|gb|EDV64796.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           F11]
 gi|218352951|emb|CAU98750.1| 23S rRNA pseudouridine synthase [Escherichia coli 55989]
 gi|218361942|emb|CAQ99544.1| 23S rRNA pseudouridine synthase [Escherichia coli IAI1]
 gi|281602002|gb|ADA74986.1| Ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           2002017]
 gi|284922542|emb|CBG35629.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           042]
 gi|291468756|gb|EFF11247.1| rluD [Escherichia coli B354]
 gi|300297834|gb|EFJ54219.1| pseudouridine synthase, RluA family [Escherichia coli MS 185-1]
 gi|300308510|gb|EFJ63030.1| pseudouridine synthase, RluA family [Escherichia coli MS 200-1]
 gi|300395569|gb|EFJ79107.1| pseudouridine synthase, RluA family [Escherichia coli MS 69-1]
 gi|300407859|gb|EFJ91397.1| pseudouridine synthase, RluA family [Escherichia coli MS 45-1]
 gi|300454823|gb|EFK18316.1| pseudouridine synthase, RluA family [Escherichia coli MS 21-1]
 gi|305854524|gb|EFM54962.1| 23S rRNA pseudouridine synthase D [Escherichia coli NC101]
 gi|313648270|gb|EFS12714.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           2a str. 2457T]
 gi|315290937|gb|EFU50302.1| pseudouridine synthase, RluA family [Escherichia coli MS 153-1]
 gi|315298638|gb|EFU57893.1| pseudouridine synthase, RluA family [Escherichia coli MS 16-3]
 gi|323184529|gb|EFZ69903.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           1357]
 gi|323963904|gb|EGB59397.1| RluA family protein pseudouridine synthase [Escherichia coli M863]
 gi|323978453|gb|EGB73537.1| RluA family protein pseudouridine synthase [Escherichia coli
           TW10509]
 gi|324012460|gb|EGB81679.1| pseudouridine synthase, RluA family [Escherichia coli MS 60-1]
 gi|327252300|gb|EGE63972.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           STEC_7v]
 gi|330912359|gb|EGH40869.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           AA86]
 gi|331042085|gb|EGI14227.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli M605]
 gi|331053326|gb|EGI25355.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA206]
 gi|331058618|gb|EGI30596.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA143]
 gi|332754015|gb|EGJ84387.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           K-671]
 gi|332755617|gb|EGJ85980.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           2747-71]
 gi|332765571|gb|EGJ95784.1| 23S rRNA pseudouridine synthase [Shigella flexneri 2930-71]
 gi|333015902|gb|EGK35238.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           K-304]
          Length = 326

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|254994200|ref|ZP_05276390.1| hypothetical protein LmonocytoFSL_15395 [Listeria monocytogenes FSL
           J2-064]
          Length = 296

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 141/320 (44%), Gaps = 34/320 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++E      R+D+         +   +Q +L++G + V+ +  K N ++Q G  +  
Sbjct: 4   ETLIIEESHARERVDKVIAEMM-GKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                    ++ E   LD               + +ED  + V NKP G+ V   +G A 
Sbjct: 63  EVREPEELEVLAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHAS 107

Query: 127 -YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 108 GTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + +      + VV+        A +HF+V++     + 
Sbjct: 168 EYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVLERLP-GYT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH  ++G P+ GD KY         +   N  +LHA  +   HP 
Sbjct: 222 LINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTIKGNGQFLHAAKLGFDHPT 276

Query: 302 G-GRLQITAPLPAHMVKTWD 320
              R+   APLP+   K   
Sbjct: 277 TKERMMFEAPLPSSFEKALK 296


>gi|320102981|ref|YP_004178572.1| RluA family pseudouridine synthase [Isosphaera pallida ATCC 43644]
 gi|319750263|gb|ADV62023.1| pseudouridine synthase, RluA family [Isosphaera pallida ATCC 43644]
          Length = 432

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 87/335 (25%), Positives = 152/335 (45%), Gaps = 38/335 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
             VV++  E  RLD +  + +P  +   +QK++ +  V V+ K  + + +++ G  V + 
Sbjct: 97  EFVVKSKLEGRRLDTYLTSRFPDYSRSVIQKVIDANAVMVNGKPARASQKVREGDFVSLR 156

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
                          L    + T  +  +   ++YED  + + +KPAG+    G G    
Sbjct: 157 ---------------LPELWDGTIPAQDIPLTVIYEDQWLSIIDKPAGMVTHPGKGNWSG 201

Query: 128 HIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +   L+   D+  Q     +P + HRLD++T+G+L+VAR       L + F  R I+K 
Sbjct: 202 TVVNALQHRYDTLSQLAGSTRPGVVHRLDRDTTGLLIVARDDTIHGKLAQLFETRTIEKE 261

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++  GIP+  ++ I   L    H        ++    G   A + ++V++ F  +F  
Sbjct: 262 YLAICSGIPERDRDWIDQPLG--PHPTVREKMAIRGEADGGRPARTFYEVVERF-DRFAL 318

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-------------GNFTSPIQNKLY 289
           +  QP TGRTHQ+RVH  H+G PI+ D  Y    +              +    +  +  
Sbjct: 319 VRCQPLTGRTHQIRVHLTHVGLPILADKLYSGRDRITRGDLLGWQARGDDHDHVLLTRQA 378

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           LHA  +   HP  G  L+I +PLP  M +T ++L 
Sbjct: 379 LHAHRLKFLHPATGEPLEIRSPLPPDMAETLETLR 413


>gi|307132187|ref|YP_003884203.1| 23S rRNA pseudouridine synthase [Dickeya dadantii 3937]
 gi|306529716|gb|ADM99646.1| 23S rRNA pseudouridine synthase [Dickeya dadantii 3937]
          Length = 325

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 146/342 (42%), Gaps = 37/342 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   ++  +   +V+++ K V K   ++  G+ V I
Sbjct: 8   TATVAESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGKMVDKPKEKVLGGESVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +I                      +  +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  DALIEEDARW---------------EAQPISLDIVYEDEDILVINKPRDLVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + +     +  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHHYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A++H+++++ F +    L 
Sbjct: 173 AVAIGTM-TAGGTVEEPIARHST-----KRTHMAVHPMGKPAVTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F   ++N  +  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMAHINHPLVGDPLYGGRPRLPKGASEAFIETLRNFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           L HP  G  ++  APLP  MV+   +L  K D + +  +L  
Sbjct: 286 LYHPISGIEMEWHAPLPQDMVELIAAL--KADTDAFKDQLDW 325


>gi|303257043|ref|ZP_07343057.1| ribosomal large subunit pseudouridine synthase D [Burkholderiales
           bacterium 1_1_47]
 gi|302860534|gb|EFL83611.1| ribosomal large subunit pseudouridine synthase D [Burkholderiales
           bacterium 1_1_47]
          Length = 394

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 82/340 (24%), Positives = 143/340 (42%), Gaps = 37/340 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
           + ++   V  D +  RLD+   +    I+   L+ ++  G V+V+ K V K   ++  G 
Sbjct: 23  SKIETFEVTLDLDGERLDKVLASSLKDISRSRLKTLIEDGLVKVNGKTVDKPKEKMSFGD 82

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +              +I     ++   +  +   ++YED  I V NKPA + V   +
Sbjct: 83  EVSV--------------EIKPRLEDMDFIATPMDIDVVYEDDDILVINKPARLVVHPAA 128

Query: 124 GIAYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H D  L + + +         +  + HRLD++T+G++VVA+   A   L +  + R
Sbjct: 129 G---HWDDTLLNGLLAYNPIFRTLPRAGIVHRLDRDTTGLMVVAKNEKAMLDLVQQLQAR 185

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI---D 234
            +++ YW+L  G     K  I   + +      + +         A  A +H + I   +
Sbjct: 186 TVKREYWALTRGKAPADK-VIEAAIERDP---RNPLRFTIGKGGRAKPATTHIRCIDQKE 241

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP----IQNKLYL 290
              + F W+  +  TGRTHQ+RVH   +G P++GD  Y                 ++  L
Sbjct: 242 VKGKPFSWVACRLKTGRTHQIRVHMESIGLPLIGDPLYRNKLPKPKEDGSVLNSFDRQAL 301

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF-KYDR 328
           HA  + L HP     ++  A  P       D LGF  +DR
Sbjct: 302 HASRLGLIHPVTKETMEWFAEPPQDFRDLMDELGFGPWDR 341


>gi|299530513|ref|ZP_07043933.1| pseudouridine synthase, RluA family protein [Comamonas testosteroni
           S44]
 gi|298721489|gb|EFI62426.1| pseudouridine synthase, RluA family protein [Comamonas testosteroni
           S44]
          Length = 352

 Score =  256 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 79/328 (24%), Positives = 142/328 (43%), Gaps = 31/328 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVR 66
           + ++V  +    R+D+         +   LQ++L  G V ++ K + K + ++  G  +R
Sbjct: 43  RELMVGTEHHGQRVDKVLALGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLR 102

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +                  +  ++    + +   ++YED  + V NKPAG+ V    G  
Sbjct: 103 VEMR--------------PTQQSMAFQPETMDLQVVYEDEDLLVINKPAGLVVHPAPG-- 146

Query: 127 YHIDGFLKSWVDSKGQKPR------LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            +  G L + + ++ +K R      + HRLD++TSG++VVAR R+    L +    R + 
Sbjct: 147 -NWTGTLLNGLLARDEKARQVPRAGIVHRLDKDTSGLMVVARNRSTMDALIKMIAAREVS 205

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +L      ++K    +  + +       + VV  N      A + F ++D  A   
Sbjct: 206 RQYLALAHKQWGSRKRREVDAPIGRDPRNRLRMAVVDLNLHPGKQARTDFDLLDGDA-AH 264

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +    HTGRTHQ+RVH   +G P++ D  Y    +G        +  LHA  +   HP
Sbjct: 265 SLVRCTLHTGRTHQIRVHMASLGHPLIADTLYGGKPEGGLE-----RQALHAFRLAFEHP 319

Query: 301 EGGRLQIT-APLPAHMVKTWDSLGFKYD 327
              +  +  APLP  M    D  G +Y+
Sbjct: 320 VTKKPLVHYAPLPQDMAGALDLWGLRYN 347


>gi|293415867|ref|ZP_06658507.1| rluD [Escherichia coli B185]
 gi|291432056|gb|EFF05038.1| rluD [Escherichia coli B185]
          Length = 326

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 146/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  +++   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEAMRADFEE 318


>gi|300775211|ref|ZP_07085073.1| ribosomal large subunit pseudouridine synthase D [Chryseobacterium
           gleum ATCC 35910]
 gi|300505951|gb|EFK37087.1| ribosomal large subunit pseudouridine synthase D [Chryseobacterium
           gleum ATCC 35910]
          Length = 357

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 150/334 (44%), Gaps = 42/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V++ +E +R+D++   +  + +   + +  R+G V V+   VK N R++ G  + +  
Sbjct: 37  ITVDSKQEPLRIDKFLLIYRQNSSRNKISQTCRAGNVIVNGVAVKQNYRVKPGDQISV-- 94

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H  +E  I+   + +          ++YED  + V +K AG+ V  G G   + 
Sbjct: 95  ---LLAHPPRENVIIPQDIPVN---------IIYEDDDLVVVDKEAGMVVHPGFG---NW 139

Query: 130 DGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           DG L + +    +K           L HR+D++TSG+LV+A+   A   L + F  R  +
Sbjct: 140 DGTLVNALAYHFEKNGEKSDLDRVGLVHRIDKDTSGLLVIAKNEYALSFLAKQFFNRTTK 199

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           ++YW+ VWG  +  +  I   + +  H        V ++     +A++H+KV++ F +  
Sbjct: 200 RLYWAFVWGNLQEDEGTIRGHIGR--HPKNRMQMSVYEDGSQGKHAVTHYKVLERF-KYM 256

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------------PIQNKL 288
            W+E +  TGRTHQ+R H  H+G  +  D +Y  +      +             I  + 
Sbjct: 257 TWVECKLETGRTHQIRAHFRHIGHTLFNDERYEGHTPLRGVNLPKYKQFIKNVFEILPRH 316

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
            LHA  +   HP     L   +P+P  M      
Sbjct: 317 ALHAHTLGFIHPTTKKELYFESPMPKDMADAVKK 350


>gi|123441245|ref|YP_001005232.1| 23S rRNA pseudouridine synthase D [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332160281|ref|YP_004296858.1| 23S rRNA pseudouridine synthase D [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122088206|emb|CAL10994.1| ribosomal large subunit pseudouridine synthase D [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|318604491|emb|CBY25989.1| ribosomal large subunit pseudouridine synthase D [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325664511|gb|ADZ41155.1| 23S rRNA pseudouridine synthase D [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330863600|emb|CBX73710.1| ribosomal large subunit pseudouridine synthase D [Yersinia
           enterocolitica W22703]
          Length = 325

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 82/340 (24%), Positives = 147/340 (43%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V V+ K + K   ++  G++V I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDKVTVNGKTINKPKEKVLGGELVAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I        ++  LD               ++YED+ I V NKP G+ V  G+G     
Sbjct: 70  QIEEDARWAPQEIPLD---------------IVYEDNDILVINKPRGLVVHPGAGNPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++
Sbjct: 115 VLNALLYYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGNM-TAGGRVDEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFIAILRGFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G +++  A LP  MV+  ++L  K D   +  ++  
Sbjct: 288 HPISGIQMEWHAALPEDMVELINAL--KADTEEFKDQMDW 325


>gi|317049249|ref|YP_004116897.1| RluA family pseudouridine synthase [Pantoea sp. At-9b]
 gi|316950866|gb|ADU70341.1| pseudouridine synthase, RluA family [Pantoea sp. At-9b]
          Length = 326

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 143/342 (41%), Gaps = 37/342 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V V+   + K   ++  G+ V I
Sbjct: 8   TATVSEAQLGQRLDQTLAELFPDYSRSRIKEWILERRVSVNGTVIDKPKEKVLGGEQVSI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I                      +  +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  SAEIEEEQRW---------------EAQNIPLNIVYEDDDIIVINKPRDLVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  +       +  + HRLD++T+G++VVA+T  A  HL E+ ++R I + Y 
Sbjct: 113 GTVLNALLYHYPPIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVETLQLREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A +H+++++ F +    L 
Sbjct: 173 AVAIGTM-TAGGTVNEPMARHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMAHINHPLVGDPLYGGRPRPPKGASDAFIETLRGFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           L HP  G  ++  APLP  MV   D+L  K D N++  +L  
Sbjct: 286 LYHPITGIEMEWHAPLPQDMVDLIDAL--KADTNMFRDQLDW 325


>gi|206603460|gb|EDZ39940.1| pseudouridylate synthase, 23S RNA-specific [Leptospirillum sp.
           Group II '5-way CG']
          Length = 340

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 78/334 (23%), Positives = 143/334 (42%), Gaps = 42/334 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  +V   E+  RLD +   +        +Q++L    V ++      +++I+ G  +R+
Sbjct: 19  REFLVPRGEQPKRLDIYLSRNCLGFTRSRVQRLLEEKLVTINDIYPASSHKIRGGDRIRV 78

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                          ++    +     + +   +LYED  + V +KP G+ V    G A 
Sbjct: 79  ---------------LIPPPRSQAAQPEDIHLEILYEDDDLIVISKPPGLVVHPAPGHAS 123

Query: 127 -YHIDGFLKSWVDSKGQ----------------KPRLTHRLDQETSGILVVARTRAAAQH 169
              ++G L  +     +                +  L HRLDQ+TSG++VV ++      
Sbjct: 124 GTLVNGLLFHFQSQGDEQKKGEPEEEEEAERPLRAGLVHRLDQDTSGVMVVGKSETVVLD 183

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           L   F+ R + K Y +LV GI   K+  I   + + +H    +        +    +++ 
Sbjct: 184 LMNQFKDRSVSKKYLALVKGILPKKRGEINAPIGRSTHDRKKFAVR-----QDGKPSLTR 238

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           ++V++ + + +  LE+   TGRTHQ+RVH  H+G P++GD  Y +    N   P   +  
Sbjct: 239 YRVLETYHENYSLLEVTLLTGRTHQIRVHFRHLGFPLLGDAVYGSKGMENRNFP---RQM 295

Query: 290 LHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           LHA  +   HP    +++  APLP   V     L
Sbjct: 296 LHAWKLAFQHPRSAAKMEFEAPLPPDFVSAMKRL 329


>gi|312127570|ref|YP_003992444.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311777589|gb|ADQ07075.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           hydrothermalis 108]
          Length = 299

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 84/315 (26%), Positives = 154/315 (48%), Gaps = 35/315 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPPVINALNHII 78
           RLDR+            +QKI+  G V V++ + +K   +++SG ++++           
Sbjct: 9   RLDRYLSEALSK-TRSFVQKIIEEGNVLVNQTQVLKPAYKVKSGDIIKV----------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW 136
               ++     L+  +  +   ++YED  + V NKP G+ V  G+G   +   +  L  +
Sbjct: 57  ----VIPEPKQLSIVAQDINIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKF 112

Query: 137 VDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      +P + HRLD++TSG+LVVA+T  A   L+E+ +  +I++IY+++  G+ 
Sbjct: 113 RGRLSSINGVIRPGIVHRLDKDTSGLLVVAKTDEAHVKLSEALKSHQIKRIYYAICEGVL 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K     I   + +   +    + VV         A+++F+V++ F  K+ +++++  TGR
Sbjct: 173 KEDSGVINAPIGRH-PVNRLKMAVV----PNGKEAVTYFEVLERF-DKYTFVKLRLKTGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P++GD  Y    K  F    Q    LHA  ++  HP     L  +A 
Sbjct: 227 THQIRVHMSYIGYPLLGDGTYG-RAKNEFGVEGQV---LHAGEIEFVHPITSEVLHFSAE 282

Query: 311 LPAHMVKTWDSLGFK 325
           LP + +K  + L  K
Sbjct: 283 LPEYFLKILNILRSK 297


>gi|225856592|ref|YP_002738103.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae P1031]
 gi|225724891|gb|ACO20743.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae P1031]
          Length = 295

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 146/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETGGLRLDKALSD-LTELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +          + K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVIAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++  P+ GD  Y         +   +  +LHA+ +   HP  G+ 
Sbjct: 221 QLETGRTHQIRVHMAYIDHPVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGKT 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+  A +P    +T + L 
Sbjct: 276 LEFKADIPEIFKETLERLR 294


>gi|331701446|ref|YP_004398405.1| RluA family pseudouridine synthase [Lactobacillus buchneri NRRL
           B-30929]
 gi|329128789|gb|AEB73342.1| pseudouridine synthase, RluA family [Lactobacillus buchneri NRRL
           B-30929]
          Length = 302

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 76/317 (23%), Positives = 141/317 (44%), Gaps = 35/317 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +Y++   ++   RLD+        I+    + ++    ++++ + VK   +++SG  +++
Sbjct: 3   EYIIT--NQTG-RLDKVISELDSSISRSRAKNLIDDQHLKINGEPVKPKYQVKSGDKIQV 59

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             V                   ++   + +   ++YED  + V NKP G+ V    G   
Sbjct: 60  DSV---------------QPTPISLEPENMPLDIVYEDDDVIVVNKPQGMVVHPSPGHPD 104

Query: 128 HI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           H   +  L     S      +P + HR+D++TSG+L+VA+   A Q L++  + ++  + 
Sbjct: 105 HTLVNALLYHSPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDKAHQFLSQQLQAQKNLRK 164

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G  K     +   + +          V          A++HF+V++ FA  +  
Sbjct: 165 YVALVHGRIKEDSGVVNAPIGRSPKDRKKQAVVS-----DGRSAVTHFEVLERFAD-YTL 218

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +  +  TGRTHQ+RVH  ++G PIVGD  Y             N  +LHA+ +   HP  
Sbjct: 219 VACRLETGRTHQIRVHMKYIGHPIVGDPLYGPRKTIR-----GNGQFLHAQELGFEHPRT 273

Query: 303 GRLQ-ITAPLPAHMVKT 318
            +L   +APLP    +T
Sbjct: 274 HQLMIFSAPLPPIFEQT 290


>gi|270264067|ref|ZP_06192335.1| ribosomal large subunit pseudouridine synthase D [Serratia
           odorifera 4Rx13]
 gi|270042260|gb|EFA15356.1| ribosomal large subunit pseudouridine synthase D [Serratia
           odorifera 4Rx13]
          Length = 325

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 80/333 (24%), Positives = 139/333 (41%), Gaps = 35/333 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V+V+ K   K   ++  G+ V I
Sbjct: 8   TATVAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKTTNKPKEKVLGGETVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I                         +   ++YEDS I V NKP  + V  G+G   
Sbjct: 68  DAQIEEEARW---------------EPQDIALNIVYEDSDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y 
Sbjct: 113 GTVLNALLHYYPEIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A++H+++++ F +    L 
Sbjct: 173 AVAIGTM-TAGGTVEEPISRHST-----KRTHMAVHPMGKPAVTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASEAFIATLRGFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           L HP  G +++  APLP  MV   ++L    + 
Sbjct: 286 LYHPISGIQMEWHAPLPQDMVDLINALKVDTEE 318


>gi|296136842|ref|YP_003644084.1| pseudouridine synthase, RluA family [Thiomonas intermedia K12]
 gi|295796964|gb|ADG31754.1| pseudouridine synthase, RluA family [Thiomonas intermedia K12]
          Length = 329

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 98/335 (29%), Positives = 163/335 (48%), Gaps = 30/335 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V+ + V +  E  RLD +   H   +   ++ +I+RSG+VRV+  R   + ++QS   
Sbjct: 7   PQVRLLQVGDAGEGQRLDNFLARHLKGVPLSHIHRIVRSGEVRVNGGRASADQKLQSSDQ 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV  A     +              +  L+  +++ED  +   NKP G++V GGSG
Sbjct: 67  VRIPPVRVAQPDTPR-------------SAPALQFPIVFEDDFLLAINKPEGVAVHGGSG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L++   +  +   L HRLD++TSG+L++A+ R+A   L  + R R   K Y 
Sbjct: 114 VSFGVIEALRAARPT-AKFLELVHRLDRDTSGLLLIAKKRSALTTLHAALRERHADKRYL 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA------- 237
           +LV G+       I   L K     G+    V+ + +    + + F+  + FA       
Sbjct: 173 ALVAGLWTRGAVMIEAPLHKYLLANGER--RVRVDAQQGQESRTQFRSQEQFALPGLGPW 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQNKLYLH 291
                ++ +  TGRTHQ+RVH  H G PIVGD KY  +       +G    P   +++LH
Sbjct: 231 GGLSLMQARLLTGRTHQIRVHLAHCGHPIVGDDKYGDDSLNALLARGQAGVPPFRRMFLH 290

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           A  + + HP  G RL++ APLP +  +    L  +
Sbjct: 291 AESLTIAHPASGERLELRAPLPENCAQWLHHLRAQ 325


>gi|157156608|ref|YP_001463915.1| 23S rRNA pseudouridine synthase D [Escherichia coli E24377A]
 gi|191169060|ref|ZP_03030823.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           B7A]
 gi|193064062|ref|ZP_03045147.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           E22]
 gi|193071695|ref|ZP_03052596.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           E110019]
 gi|194430158|ref|ZP_03062659.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           B171]
 gi|209920071|ref|YP_002294155.1| 23S rRNA pseudouridine synthase D [Escherichia coli SE11]
 gi|256019585|ref|ZP_05433450.1| 23S rRNA pseudouridine synthase D [Shigella sp. D9]
 gi|260845276|ref|YP_003223054.1| 23S rRNA pseudouridine synthase [Escherichia coli O103:H2 str.
           12009]
 gi|260869276|ref|YP_003235678.1| 23S rRNA pseudouridine synthase [Escherichia coli O111:H- str.
           11128]
 gi|293448946|ref|ZP_06663367.1| rluD [Escherichia coli B088]
 gi|300819932|ref|ZP_07100115.1| pseudouridine synthase, RluA family [Escherichia coli MS 107-1]
 gi|300825129|ref|ZP_07105222.1| pseudouridine synthase, RluA family [Escherichia coli MS 119-7]
 gi|300922522|ref|ZP_07138631.1| pseudouridine synthase, RluA family [Escherichia coli MS 182-1]
 gi|301326710|ref|ZP_07220028.1| pseudouridine synthase, RluA family [Escherichia coli MS 78-1]
 gi|307315092|ref|ZP_07594676.1| pseudouridine synthase, RluA family [Escherichia coli W]
 gi|309794107|ref|ZP_07688531.1| pseudouridine synthase, RluA family [Escherichia coli MS 145-7]
 gi|331669346|ref|ZP_08370192.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA271]
 gi|331678588|ref|ZP_08379262.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli H591]
 gi|332280710|ref|ZP_08393123.1| ribosomal large subunit pseudouridine synthase D [Shigella sp. D9]
 gi|157078638|gb|ABV18346.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           E24377A]
 gi|190900901|gb|EDV60687.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           B7A]
 gi|192929297|gb|EDV82906.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           E22]
 gi|192954990|gb|EDV85492.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           E110019]
 gi|194411783|gb|EDX28104.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           B171]
 gi|209913330|dbj|BAG78404.1| putative pseudouridine synthase [Escherichia coli SE11]
 gi|257760423|dbj|BAI31920.1| 23S rRNA pseudouridine synthase [Escherichia coli O103:H2 str.
           12009]
 gi|257765632|dbj|BAI37127.1| 23S rRNA pseudouridine synthase [Escherichia coli O111:H- str.
           11128]
 gi|291322036|gb|EFE61465.1| rluD [Escherichia coli B088]
 gi|300421134|gb|EFK04445.1| pseudouridine synthase, RluA family [Escherichia coli MS 182-1]
 gi|300522401|gb|EFK43470.1| pseudouridine synthase, RluA family [Escherichia coli MS 119-7]
 gi|300527520|gb|EFK48582.1| pseudouridine synthase, RluA family [Escherichia coli MS 107-1]
 gi|300846633|gb|EFK74393.1| pseudouridine synthase, RluA family [Escherichia coli MS 78-1]
 gi|306905521|gb|EFN36055.1| pseudouridine synthase, RluA family [Escherichia coli W]
 gi|308122012|gb|EFO59274.1| pseudouridine synthase, RluA family [Escherichia coli MS 145-7]
 gi|315061909|gb|ADT76236.1| 23S rRNA pseudouridine synthase [Escherichia coli W]
 gi|323377510|gb|ADX49778.1| pseudouridine synthase, RluA family [Escherichia coli KO11]
 gi|323946277|gb|EGB42310.1| RluA family protein pseudouridine synthase [Escherichia coli H120]
 gi|324016579|gb|EGB85798.1| pseudouridine synthase, RluA family [Escherichia coli MS 117-3]
 gi|324120053|gb|EGC13929.1| RluA family protein pseudouridine synthase [Escherichia coli E1167]
 gi|331063014|gb|EGI34927.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli TA271]
 gi|331073418|gb|EGI44739.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli H591]
 gi|332103062|gb|EGJ06408.1| ribosomal large subunit pseudouridine synthase D [Shigella sp. D9]
          Length = 326

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISMLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|28199626|ref|NP_779940.1| ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa Temecula1]
 gi|34395764|sp|Q87AR7|RLUD_XYLFT RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|28057741|gb|AAO29589.1| ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa Temecula1]
          Length = 331

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 85/342 (24%), Positives = 151/342 (44%), Gaps = 42/342 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V +     R D      +P  +   L + ++SG V ++   V+  + +  G+VV +
Sbjct: 14  RQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVRPRDPVYGGEVVWL 73

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             + +     + +   LD               +LYED  ++V NKPAG+ V  G+G   
Sbjct: 74  QVMPDIRTDAVPQDIPLD---------------ILYEDEHVFVINKPAGLVVHPGAG--- 115

Query: 128 HIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + DG L + +  +        +  + HRLD++TSG++VVART  A   L E    R++ +
Sbjct: 116 NPDGTLVNALLHRDPALAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSSRQVHR 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V  +         N  +++       + V          A++H+++ + F +   
Sbjct: 176 QYLAVV--VSALVSGGTVNAAIERHPRDRLRMEV----SDTGKEAVTHYRLRERF-RAHT 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNKLYLHAR 293
            LE +  TGRTHQ+RVH  H+  PIVGD  Y  + K                 +  LHA 
Sbjct: 229 ALECRLDTGRTHQIRVHMAHLRHPIVGDRLYGGSLKLPKGGTDALVAMLRGFKRQALHAE 288

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            ++  HP     ++I AP+P  + +   +L  + D  L+ +R
Sbjct: 289 VLEFLHPVRALPVRIVAPVPEDLCQLLAAL--REDSALFFER 328


>gi|309803986|ref|ZP_07698068.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           11V1-d]
 gi|309807269|ref|ZP_07701239.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
 gi|309809874|ref|ZP_07703724.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
 gi|312871741|ref|ZP_07731829.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
 gi|312874168|ref|ZP_07734202.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
 gi|312875676|ref|ZP_07735677.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
 gi|315653539|ref|ZP_07906459.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
 gi|325912067|ref|ZP_08174465.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
 gi|329920256|ref|ZP_08277040.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
 gi|308163905|gb|EFO66170.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           11V1-d]
 gi|308166329|gb|EFO68538.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
 gi|308169826|gb|EFO71869.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
 gi|311088930|gb|EFQ47373.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
 gi|311090238|gb|EFQ48648.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
 gi|311092683|gb|EFQ51039.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
 gi|315488901|gb|EFU78543.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
 gi|325476017|gb|EGC79185.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
 gi|328936301|gb|EGG32749.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
          Length = 311

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 76/328 (23%), Positives = 143/328 (43%), Gaps = 33/328 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+++E  +RLD++   H   I+   +Q++++   +  +  + K + ++ +   + I  
Sbjct: 9   LVVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNGLQTKLSYKVNTNDKINIE- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                         +     L+   + L   ++YED  + V NKP G+ V   +G   H 
Sbjct: 68  --------------IPYPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHT 113

Query: 130 --DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             +G +    +     +  +P + HR+D++TSG+L++A+   A   L +    +  ++ Y
Sbjct: 114 LVNGLIYHTKNLAKCDEIFRPGIVHRIDKDTSGLLMIAKNATARISLEKQLANKINKREY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V    K+    I   + +       Y             AI+HF V++ F   +  +
Sbjct: 174 IAIVHDNFKHSSGVIDAPIGRNP-----YQRQQMAVVASGKKAITHFTVLEQFP-GYSLV 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    TGRTHQ+RVH  ++G PI GD  Y      N      N  +LHA+ +   HP+  
Sbjct: 228 KCVLETGRTHQIRVHMSYIGHPIAGDPLYGPKKTLN-----GNGQFLHAKTLGFYHPKTN 282

Query: 304 R-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           + L+ +   P    K    L  K   NL
Sbjct: 283 QWLEFSISEPQIFAKQLYLLRKKLTNNL 310


>gi|218706096|ref|YP_002413615.1| 23S rRNA pseudouridine synthase D [Escherichia coli UMN026]
 gi|293406104|ref|ZP_06650030.1| rluD [Escherichia coli FVEC1412]
 gi|298381836|ref|ZP_06991433.1| rluD [Escherichia coli FVEC1302]
 gi|300900220|ref|ZP_07118406.1| pseudouridine synthase, RluA family [Escherichia coli MS 198-1]
 gi|218433193|emb|CAR14092.1| 23S rRNA pseudouridine synthase [Escherichia coli UMN026]
 gi|291426110|gb|EFE99142.1| rluD [Escherichia coli FVEC1412]
 gi|298276976|gb|EFI18492.1| rluD [Escherichia coli FVEC1302]
 gi|300356255|gb|EFJ72125.1| pseudouridine synthase, RluA family [Escherichia coli MS 198-1]
          Length = 326

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPIYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|300767399|ref|ZP_07077311.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|300495218|gb|EFK30374.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 320

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 83/324 (25%), Positives = 134/324 (41%), Gaps = 35/324 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T  Q+++   D+   RLD+             + K++++ QV V+ +       ++ G  
Sbjct: 19  TEQQFMIT--DQTG-RLDKVLAALQSVWTRSQVDKLIKTDQVTVNGQLEASKYHVKPGDE 75

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +         I  E   LD               ++YED  + V NKP G+ V    G
Sbjct: 76  IVVAAQTVQQTTIEPENIPLD---------------IVYEDDDVLVVNKPQGMVVHPAPG 120

Query: 125 IAYHI--DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              H   +  L     S      +P + HR+D++TSG+L+VA+   A Q L    + +  
Sbjct: 121 HPNHTLVNALLYHSPLSTINGEFRPGIVHRIDKDTSGLLMVAKNDRAHQSLAAQLKAKTN 180

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y +LV G+ K     I   L +          +     K    A++HFKV+  + Q 
Sbjct: 181 LREYVALVHGVIKEDTGTINAPLGRSPKDRKKQAII-----KTGRPAVTHFKVLKRY-QH 234

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +  +  TGRTHQ+RVH   +G P+VGD  Y         +   +  +LHA+ +   H
Sbjct: 235 YTLISCRLETGRTHQIRVHLQSIGHPLVGDPLYGPK-----KTIKGHGQFLHAKLLGFKH 289

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G  L   APLP     T   L
Sbjct: 290 PVTGDLLTFEAPLPPIFTTTLAKL 313


>gi|148240684|ref|YP_001226071.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp. WH
           7803]
 gi|147849223|emb|CAK24774.1| Pseudouridylate synthase, 23S RNA-specific [Synechococcus sp. WH
           7803]
          Length = 333

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 86/317 (27%), Positives = 136/317 (42%), Gaps = 28/317 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +   +QK + +G VRV+    K    ++ G  V++          
Sbjct: 36  PMRLDRWLVSQRSEQSRARIQKFIDAGYVRVNGNTGKAKTPLRQGDEVQLWMPPPEPLPY 95

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
           +K               + +   +L+ED  + V NKPAG++V    G      ++G L  
Sbjct: 96  LK--------------PEAMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLHH 141

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y ++V G+P
Sbjct: 142 CPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQVQIQKRIASREYLAVVHGVP 201

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   + +       Y  V   + +   YA +H+ + +     +  L  +  TGR
Sbjct: 202 AGDSGTIVGAIGRHPADRKKYAVV---SGENGRYACTHWSLQERLGD-YSLLRFKLDTGR 257

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH  HM  P+VGD  Y    K     P      LHA  + L HP    R+   AP
Sbjct: 258 THQIRVHCAHMNHPVVGDPTYSRCRKLPIELPG---QALHAFQLGLDHPITRERMLFEAP 314

Query: 311 LPAHMVKTWDSLGFKYD 327
           LP  M K    L  +  
Sbjct: 315 LPPVMDKLLAVLRRRSS 331


>gi|313207050|ref|YP_004046227.1| ribosomal large subunit pseudouridine synthase d [Riemerella
           anatipestifer DSM 15868]
 gi|312446366|gb|ADQ82721.1| ribosomal large subunit pseudouridine synthase D [Riemerella
           anatipestifer DSM 15868]
 gi|315022556|gb|EFT35583.1| ribosomal large subunit pseudouridine synthase D [Riemerella
           anatipestifer RA-YM]
          Length = 352

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 148/334 (44%), Gaps = 42/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+ ++E +R+D++      + +   + +  R+G V V+   VK N R++ G  V +  
Sbjct: 31  LVVDKNQEPLRIDKYLLIFRQNSSRNKISQTCRAGNVVVNGTPVKQNYRVKPGDKVSV-- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H  +E  I+   + +          ++YED  + V +K AG+ V  G G   + 
Sbjct: 89  ---LLTHPPRENVIVPQDIPIN---------IVYEDDDLLVVDKEAGMVVHPGFG---NW 133

Query: 130 DGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           DG L + +    +K           L HR+D++TSG+LV+A+   A   L + F  R  +
Sbjct: 134 DGTLVNALAYHFEKNGLKTDLDRVGLVHRIDKDTSGLLVIAKNEYAMSFLAKQFFERTTK 193

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           ++YW+ VWG        I   + +           V ++     +A++H+KV++ F +  
Sbjct: 194 RLYWAFVWGNLAEDTGTIKGHIGRDLK--NRMQMAVYEDGSLGKHAVTHYKVLERF-RYM 250

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSP-----------IQNKL 288
            W+E +  TGRTHQ+R H  H+G  +  D +Y           P           +  + 
Sbjct: 251 TWVECKLETGRTHQIRAHFRHIGHTLFNDERYEGHQILRGINLPKYKQFVKNVFEVLPRH 310

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
            LHA  +   HP     +   +P+P  M +  + 
Sbjct: 311 ALHAHTLGFTHPTTKKEMYFESPMPQDMQQAVEK 344


>gi|78213965|ref|YP_382744.1| ribosomal large subunit pseudouridine synthase D [Synechococcus sp.
           CC9605]
 gi|78198424|gb|ABB36189.1| Pseudouridine synthase, RluD [Synechococcus sp. CC9605]
          Length = 333

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 88/313 (28%), Positives = 138/313 (44%), Gaps = 28/313 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +   +QK + +G VRV+ K  K    ++ G  V++          
Sbjct: 36  PMRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKTGKAKTPLRQGDEVQLWMPPPEPLPY 95

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
           +K               + +   +L+ED  + V NKPAG++V    G      ++G L  
Sbjct: 96  LK--------------PEPMDLDVLFEDDHLIVLNKPAGLTVHPAPGNKDGTLVNGLLHH 141

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y+++V G+P
Sbjct: 142 CPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVRLQVQIQKRIASREYFAVVHGVP 201

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   + +       Y  V  +N     YA +H+ +++     +  L  +  TGR
Sbjct: 202 GGDSGTIVGAIGRHPADRKKYAVVSSEN---GRYACTHWTLVERLGD-YSLLRFKLDTGR 257

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH  HM  P+VGD  Y    K     P      LHA  + L HP    R+   AP
Sbjct: 258 THQIRVHCAHMNHPVVGDPTYSRCRKLPIELPG---QALHAVQLGLDHPITRERMMFEAP 314

Query: 311 LPAHMVKTWDSLG 323
           LP  M K    L 
Sbjct: 315 LPPVMEKLLGVLR 327


>gi|330811803|ref|YP_004356265.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327379911|gb|AEA71261.1| Ribosomal large subunit pseudouridine synthase D [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 320

 Score =  255 bits (651), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 89/344 (25%), Positives = 155/344 (45%), Gaps = 37/344 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    ++   V ++    RLD+     +   +   L   ++ G++ VD   ++  + + 
Sbjct: 1   MSDKIELR-AEVPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVH 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G ++ +     A    + +   LD               ++YED  I V NKPAG+ V 
Sbjct: 60  GGAILELTAEQEAQGEWVAQDIALD---------------IVYEDDDILVINKPAGLVVH 104

Query: 121 GGSGIAYHI--DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +G A     +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R
Sbjct: 105 PAAGHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSR 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + +IY  +V G+     +   N  + +       + V+    +G   A+SH++V++ F 
Sbjct: 165 SVSRIYECIVIGVVTAGGKI--NAPIGRHGQQRQRMAVM----EGGKQAVSHYRVLERF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLY 289
           +    + ++  TGRTHQ+RVH  H+  P+VGD  Y   F+            ++N  +  
Sbjct: 218 RSHTHVRVKLETGRTHQIRVHMAHINFPLVGDPAYGGRFRIPPAASQTMVESLKNFPRQA 277

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           LHAR+++L HP  G R+   +PLP   V     L  K DR  +I
Sbjct: 278 LHARFLELDHPTTGKRMSWESPLPDDFVWLLTLL--KQDREAFI 319


>gi|83312285|ref|YP_422549.1| pseudouridylate synthase, 23S RNA-specific [Magnetospirillum
           magneticum AMB-1]
 gi|82947126|dbj|BAE51990.1| Pseudouridylate synthase, 23S RNA-specific [Magnetospirillum
           magneticum AMB-1]
          Length = 505

 Score =  255 bits (651), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 86/341 (25%), Positives = 148/341 (43%), Gaps = 41/341 (12%)

Query: 4   MTYVQYVV---VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M   Q +    VE +E   RLDRW     P ++   ++ ++  G+V +++  +   + R+
Sbjct: 181 MPVTQRLTPPAVEPEEAGTRLDRWLALRLPELSRTRIKGLMEDGRVSLEETTISDASLRV 240

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + GQ   +                +            +   ++YED  + V +KPAG+ V
Sbjct: 241 KPGQCFVVD---------------VPPDAPAQPEPQDIALTVVYEDEDLIVIDKPAGMVV 285

Query: 120 QGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    +S       ++P + HR+D++TSG+LV A+T AA + L  
Sbjct: 286 HPAPGNPDETLVNALLAHCGESLAGIGGVKRPGIVHRIDKDTSGLLVAAKTDAAHRGLAT 345

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F    +++ YW+LVWG P  ++  I   + +  +     + VVK    G   A++ ++V
Sbjct: 346 QFAAHTLERAYWALVWGTPSPRQGEIEGNIGRNPN-DRKKMAVVKS---GGKPALTRYRV 401

Query: 233 IDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQN--- 286
           +  FA      +E +  TGRTHQ+RVH    G P+VGD  Y      KG    P      
Sbjct: 402 LKSFAGGAVSLVECRLATGRTHQIRVHMTTQGHPLVGDPVYGRIRGHKGVVLPPEVKTAL 461

Query: 287 ----KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
               +  LHA  +   HP  G  ++  + +P  +      L
Sbjct: 462 IQFPRQALHAYLLGFSHPTKGYDVRFESGMPLDINALMQIL 502


>gi|312171425|emb|CBX79684.1| ribosomal large subunit pseudouridine synthase D [Erwinia amylovora
           ATCC BAA-2158]
          Length = 325

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 77/340 (22%), Positives = 144/340 (42%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ + + ++ V+   + K   ++  G+ + I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILNRRITVNGTTIDKPKEKVLGGEQISIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I                      +  +   ++YED  I V NKP  + V  G+G     
Sbjct: 70  EIEEEARW---------------EAQDIPLAIVYEDDDILVINKPRDLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   +   +  + HRLD++T+G++VVA+T  +  HL ++ + R I + Y ++
Sbjct: 115 VLNALLHHFPAIADVPRAGIVHRLDKDTTGLMVVAKTVPSQTHLVDALQRREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGRM-TAGGTVNEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHISHPLVGDPLYGGRPRPPKGASEAFIATLRAFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G  ++  APLP  MV+  D+L  K D   + ++L  
Sbjct: 288 HPISGIEMEWHAPLPQDMVELIDAL--KADTEAFKEQLDW 325


>gi|49083826|gb|AAT51150.1| PA4544 [synthetic construct]
          Length = 321

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 89/347 (25%), Positives = 156/347 (44%), Gaps = 43/347 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS M   +   V  +    RLD+     +P  +   L   ++ G++ VD   ++  + + 
Sbjct: 1   MSDMIQ-RAAEVPFELGGQRLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVH 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SG  + +     A    + +   L+               ++YED  I V +KPAG+ V 
Sbjct: 60  SGAQLVLEAEQEAQGEWLAQDIELE---------------IVYEDEHILVIDKPAGLVVH 104

Query: 121 GGSGIAYHIDGFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             +G   H DG L + +       +   +  + HRLD++T+G++VVA+T  A   L    
Sbjct: 105 PAAG---HQDGTLLNALLYHVPDIANVPRAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQL 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R + +IY ++V G+       I   + +   +    + VV         A+SH++V++
Sbjct: 162 QARSVSRIYEAIVIGVI-TSGGTIDAPIGRHG-VQRQKMAVVD----AGKVAVSHYRVLE 215

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--------GNFTSPIQN 286
            F +      ++  TGRTHQ+RVH  H+G P+VGD  Y   F+           T     
Sbjct: 216 RF-RAHTHTRVKLETGRTHQIRVHMSHIGYPLVGDPVYGGRFRIPPVASQTLVQTLREFP 274

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +  LHAR+++L HP  G R++  +PLP   +     L  + DR  ++
Sbjct: 275 RQALHARFLELDHPATGVRMKWESPLPEDFLWLLSLL--RQDREAFV 319


>gi|313901894|ref|ZP_07835313.1| ribosomal large subunit pseudouridine synthase D [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467835|gb|EFR63330.1| ribosomal large subunit pseudouridine synthase D [Thermaerobacter
           subterraneus DSM 13965]
          Length = 321

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 82/320 (25%), Positives = 138/320 (43%), Gaps = 30/320 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            VV       RLD +        +    +Q+++RS +V V+ +  + + R++ G+ V I 
Sbjct: 17  FVVPGSAAGERLDVFLAEQDGLDLTRSAIQRLIRSHRVWVNGRTARPSRRLEPGEEVVIE 76

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
               A + ++ E                L   ++YED  + V NKP G  V    G    
Sbjct: 77  LPEPAPSGVVPE---------------ALPLDVVYEDPDVVVLNKPRGWVVHPAPGHPQG 121

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +  L  + + +G     +P + HRLD++T+G+LVVAR+  A + L    + RR+ + 
Sbjct: 122 TLANALLARYPEMEGVGGPGRPGIVHRLDRDTTGLLVVARSPLAYRELVRQIKERRVHRE 181

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G P+ ++  +   + +        + V+     G   A +HF V++   + +  
Sbjct: 182 YLALVRGWPEVREGTVEAPIGRH-PADRTRMTVLTT---GGRPARTHFAVVEQVGR-YTL 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L     TGRTHQ+RVH   +G P+ GD  Y                 LHA  +   HP  
Sbjct: 237 LRCWLDTGRTHQIRVHLAFIGLPVAGDPVYGGRRAQG--ELGLEGQALHATRLAFAHPRD 294

Query: 303 GR-LQITAPLPAHMVKTWDS 321
           GR +  T P PA  +   + 
Sbjct: 295 GRPMDFTVPPPADFLAALER 314


>gi|332284960|ref|YP_004416871.1| ribosomal large subunit pseudouridine synthase C [Pusillimonas sp.
           T7-7]
 gi|330428913|gb|AEC20247.1| ribosomal large subunit pseudouridine synthase C [Pusillimonas sp.
           T7-7]
          Length = 322

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 103/318 (32%), Positives = 165/318 (51%), Gaps = 20/318 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++V + +++   R+D +       +   +L K +RSG+VRV+K R+  + R++ G  VR
Sbjct: 19  VRFVEIGDEQAGQRIDNFLLRICKGVPKSHLYKAIRSGEVRVNKGRIAADYRLELGDTVR 78

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+         E + +  +V            +++ED  + V NKPAG++V GGSG++
Sbjct: 79  VPPLRLPRPD---EPRRVPPAV----------FPVVFEDEAMVVVNKPAGVAVHGGSGVS 125

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++          L HRLD+ETSG+L++A+ R A   L +  R    +K Y +L
Sbjct: 126 FGVIEQLRAAR-PDAPFLELAHRLDRETSGLLIIAKKRKALLGLHDMMREGGGRKHYQAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   N K+ +   LLK     G+    V    K A+  I+    +     ++  L  +
Sbjct: 185 VVGDWVNDKQHLRQPLLKWLTASGERRVKVDAQGKVAHTIIT----LQKRYGRYSLLGAE 240

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
             TGRTHQ+RVH    G PIVGD KY ++  +  F     N+++LHA  ++LPHP  G  
Sbjct: 241 LRTGRTHQIRVHLASCGYPIVGDDKYGSDEVRAYFAGLGLNRMFLHACRLELPHPLTGEP 300

Query: 305 LQITAPLPAHMVKTWDSL 322
           L +TA LP   +KT D L
Sbjct: 301 LVLTADLPPVCLKTLDYL 318


>gi|325335513|gb|ADZ11787.1| Pseudouridylate synthase, 23S RNA-specific [Riemerella
           anatipestifer RA-GD]
          Length = 354

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 148/334 (44%), Gaps = 42/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+ ++E +R+D++      + +   + +  R+G V V+   VK N R++ G  V +  
Sbjct: 33  LVVDKNQEPLRIDKYLLIFRQNSSRNKISQTCRAGNVVVNGTPVKQNYRVKPGDKVSV-- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H  +E  I+   + +          ++YED  + V +K AG+ V  G G   + 
Sbjct: 91  ---LLTHPPRENVIVPQDIPIN---------IVYEDDDLLVVDKEAGMVVHPGFG---NW 135

Query: 130 DGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           DG L + +    +K           L HR+D++TSG+LV+A+   A   L + F  R  +
Sbjct: 136 DGTLVNALAYHFEKNGLKTDLDRVGLVHRIDKDTSGLLVIAKNEYAMSFLAKQFFERTTK 195

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           ++YW+ VWG        I   + +           V ++     +A++H+KV++ F +  
Sbjct: 196 RLYWAFVWGNLAEDTGTIKGHIGRDLK--NRMQMAVYEDGSLGKHAVTHYKVLERF-RYM 252

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSP-----------IQNKL 288
            W+E +  TGRTHQ+R H  H+G  +  D +Y           P           +  + 
Sbjct: 253 TWVECKLETGRTHQIRAHFRHIGHTLFNDERYEGHQILRGINLPKYKQFVKNVFEVLPRH 312

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
            LHA  +   HP     +   +P+P  M +  + 
Sbjct: 313 ALHAHTLGFTHPTTKKEMYFESPMPQDMQQAVEK 346


>gi|298292656|ref|YP_003694595.1| pseudouridine synthase [Starkeya novella DSM 506]
 gi|296929167|gb|ADH89976.1| pseudouridine synthase, RluA family [Starkeya novella DSM 506]
          Length = 348

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 80/340 (23%), Positives = 144/340 (42%), Gaps = 47/340 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIP 68
           +     +E +RLDR   NH P ++   LQ ++  G+V    + V   + ++  G+V  + 
Sbjct: 19  ITAGPQDEGLRLDRVLANHLPELSRTRLQALIAEGRVLRAGRPVAGGSAKVAPGEVFTVE 78

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                      +   LD               +++ED  + V +KPAG+ V    G    
Sbjct: 79  VPPPEPAEPEPQDIPLD---------------IVFEDDDLIVIDKPAGLVVHPAPGNPDG 123

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--- 178
             ++  L     S       ++P + HRLD++TSG++VVA+   A Q L   F       
Sbjct: 124 TLVNALLFHCGASLSGIGGVRRPGIVHRLDKDTSGLMVVAKNDRAHQKLAAQFADHGRTG 183

Query: 179 -IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y + VWG+P+     +   L +   +  + + V         +AI+H++ ++ + 
Sbjct: 184 PLERAYLAFVWGVPELPSGTVDAPLARH-PVSRERIAVRA----NGRFAITHWQRVEAYE 238

Query: 238 QK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS---------P 283
                     +E Q  TGRTHQ+RVH  H+G P++GD  Y    +               
Sbjct: 239 DTQGRPVASLVECQLETGRTHQIRVHMAHIGHPLLGDAVYGGGQRTKANRLSEEARTMLE 298

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              +  LHA  +   HP  G  +   + LPA +++  ++L
Sbjct: 299 TLGRQALHAARLGFEHPSTGEFMSFESELPADLMRLQEAL 338


>gi|222152892|ref|YP_002562069.1| RNA pseudouridylate synthase [Streptococcus uberis 0140J]
 gi|222113705|emb|CAR41656.1| putative RNA pseudouridylate synthase [Streptococcus uberis 0140J]
          Length = 296

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 73/315 (23%), Positives = 138/315 (43%), Gaps = 34/315 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RLD+   +    ++       ++ G V V+ + VK    ++ G ++         ++ 
Sbjct: 9   GARLDKALAD-LTDLSRSQANDEIKKGTVLVNGEPVKAKYTVKEGDII---------SYQ 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
           + E++ILD        ++ +   ++YED  + + NK  G+ V   +G      ++  L  
Sbjct: 59  LPEEEILD------YEAEDIPIEIVYEDEYLAIINKAQGMVVHPSAGHSSGTLVNALLYH 112

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D        +P + HR+D++TSG+L++A+   A   L +  + ++  + Y ++V G  
Sbjct: 113 IKDLSTINGVVRPGIVHRIDKDTSGLLMIAKNDKAHHILADELKAKKSLRKYLAIVHGNL 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            N +  I   + +            K        AI+ F+V++ F   F  +E+   TGR
Sbjct: 173 PNDRGMIEAPIGRSEKDRKKQAVTAK-----GKDAITRFQVVERFGD-FTLVELSLETGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAP 310
           THQ+RVH  ++G P+ GD  Y         +   N  +LHA+ +   HP  G +   TA 
Sbjct: 227 THQIRVHMAYIGHPVAGDPLYGPR-----KTLAGNGQFLHAQTLGFTHPSTGEMVTFTAE 281

Query: 311 LPAHMVKTWDSLGFK 325
            P    +T + L  +
Sbjct: 282 PPIIFRQTLEKLRNR 296


>gi|49473932|ref|YP_031974.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           quintana str. Toulouse]
 gi|49239435|emb|CAF25784.1| Ribosomal large subunit pseudouridine synthase D [Bartonella
           quintana str. Toulouse]
          Length = 334

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 88/345 (25%), Positives = 152/345 (44%), Gaps = 45/345 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQV 64
           V   + +      RLD+W    Y   ++   LQ ++R G +++D + + +   +++  Q+
Sbjct: 2   VTQQITDEGALGQRLDQWLTKQYHSALSRSRLQALIREGYLKIDGQLIHEPKTKLKPNQM 61

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +   I                 +     + +K  +L+ED  + V NK AG+ V  G+G
Sbjct: 62  IELTIPILR---------------DAKPSGEAIKLDILFEDDHVIVINKQAGLVVHPGNG 106

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +    DS       ++P + HRLD+ TSGI+VVA+   A ++L+  F   
Sbjct: 107 NLTGTLVNALIYHCGDSLSGIGGVKRPGIVHRLDKNTSGIMVVAKNDLAHKNLSAQFSDH 166

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                + + Y +L+WG P      I   L +  H       +  QN   A +A++HF ++
Sbjct: 167 GRTSALDRRYHALIWGSPNRNVWKIDAPLGRSPHNRTKQAVIYSQN-PHARHAVTHFSLL 225

Query: 234 DCFA------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQ 285
           + +            LE +  TGRTHQ+RVH  H+G P+VGD  Y      K N   PI 
Sbjct: 226 EKYGICSDKTSFASLLECRLETGRTHQIRVHMAHIGHPLVGDTVYGNACKTKSNMLKPII 285

Query: 286 -------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                  N+  LHA  +   HP  G+ +  ++P+P  M +     
Sbjct: 286 KNAIDQFNRQALHAASLTFEHPATGKIMSFSSPIPQDMAELIKHF 330


>gi|33866856|ref|NP_898415.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Synechococcus sp. WH 8102]
 gi|33639457|emb|CAE08841.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Synechococcus sp. WH 8102]
          Length = 331

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 87/313 (27%), Positives = 137/313 (43%), Gaps = 28/313 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +   +QK + +G VRV+ K  K    ++ G  V++          
Sbjct: 36  PMRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKTGKAKTPLRQGDEVQMWMPPPEPLPY 95

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
           +K               + +   +L+ED  + V NKPAG++V    G      ++G L  
Sbjct: 96  LK--------------PEPMALDVLFEDDHLIVINKPAGLTVHPAPGNKDGTLVNGLLHH 141

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y ++V G+P
Sbjct: 142 CPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQQALVRLQGQIQKRIASREYLAVVHGVP 201

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   + +       Y  V   N+    YA +H+ + +     +  L  +  TGR
Sbjct: 202 GGDSGTIVGAIGRHPADRKKYAVV---NDDSGRYACTHWTLQERLGD-YSLLRFKLDTGR 257

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  H+  P+VGD  Y    K     P      LHA  + L HP  G R+   AP
Sbjct: 258 THQIRVHCAHINHPVVGDPTYSRCRKLPMELPG---QALHAFQLGLDHPISGERMAFQAP 314

Query: 311 LPAHMVKTWDSLG 323
           LP  M +    L 
Sbjct: 315 LPPVMERLLGVLR 327


>gi|260856684|ref|YP_003230575.1| 23S rRNA pseudouridine synthase [Escherichia coli O26:H11 str.
           11368]
 gi|257755333|dbj|BAI26835.1| 23S rRNA pseudouridine synthase [Escherichia coli O26:H11 str.
           11368]
          Length = 326

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 146/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G++V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGELVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISMLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|220933994|ref|YP_002512893.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. HL-EbGR7]
 gi|219995304|gb|ACL71906.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. HL-EbGR7]
          Length = 315

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 89/336 (26%), Positives = 139/336 (41%), Gaps = 36/336 (10%)

Query: 1   MSLMTYVQYV--VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR 58
           MS    V ++   V       RLD      +P  +   +Q+ + +G VRVD +  +  + 
Sbjct: 1   MSGELEVIHLQGEVPEALSGQRLDAALARMFPSYSRSRIQQWMEAGWVRVDGETPRRRDT 60

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
              G  V I   + A +    E   L+               ++YED  + V NKP G+ 
Sbjct: 61  ALGGARVVIEARVEAASEDRAEDIPLE---------------VIYEDDSLLVINKPPGLV 105

Query: 119 VQGGSGIAY--HIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
               +G      ++  L    D     +  + HRLD+ETSG+LVVART  A   L    +
Sbjct: 106 THPAAGNREGTLVNALLHHAPDLAALPRAGIVHRLDKETSGLLVVARTLEAHTDLVRQLQ 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + + Y +LV G+         +  + +  +    + VV     G   AI+H++V + 
Sbjct: 166 ARTVGREYLALVQGVIVA--GGTVDAPIGRHPVDRKRMAVVA----GGKEAITHYRV-EA 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--------GNFTSPIQNK 287
                  L ++  TGRTHQ+RVH  H+  PIVGD  Y    K                 +
Sbjct: 219 RLPHHTLLRVRLETGRTHQIRVHMAHVHHPIVGDPVYGGRLKVPAGLSEADQAVLRGFRR 278

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
             LHA  ++L HP  G  +   AP+PA      ++L
Sbjct: 279 QALHAARLELVHPVTGEEMGWEAPMPADFAALLEAL 314


>gi|192360779|ref|YP_001983659.1| pseudouridine synthase Rlu family protein [Cellvibrio japonicus
           Ueda107]
 gi|190686944|gb|ACE84622.1| pseudouridine synthase, RluA family subfamily [Cellvibrio japonicus
           Ueda107]
          Length = 320

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 140/330 (42%), Gaps = 33/330 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V      MR D+     +P  +   LQ  ++ G + VD +  K  +++  G+ + +   +
Sbjct: 11  VPIQMNGMRFDQAASELFPDFSRSRLQGWIKDGLLTVDGRVAKPKDKLIGGETLALHAEL 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            A      E   LD               +++ED  + + NK AG+ V   +G      +
Sbjct: 71  EAQGDWEPEAIELD---------------IIHEDDDLLIINKQAGLVVHPAAGNYTGTLV 115

Query: 130 DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L          +  + HRLD++T+G++VVA+T  A   L      R + + Y ++  
Sbjct: 116 NALLNHAPSLVNIPRAGIVHRLDKDTTGLMVVAKTLEAHTDLVAQLADRSVSREYEAVAV 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G          +  + +  +    + V+ Q   G   A++H++V   +      + ++  
Sbjct: 176 GAMT--GGGTVDAPIGRHPLQRKLMAVLSQ---GGKRAVTHYRVAKRYPH-HTHIRVKLE 229

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+G P+VGD  Y   FK    +  Q         +  LHA  + L HP
Sbjct: 230 TGRTHQIRVHMAHVGHPLVGDQTYGNRFKIPKGANQQLIEALKHFPRQALHAFKLGLEHP 289

Query: 301 EGGRL-QITAPLPAHMVKTWDSLGFKYDRN 329
             G   + TAPLPA   K  D+L   Y + 
Sbjct: 290 GTGEYTEWTAPLPADFRKLLDALDQGYQQE 319


>gi|292493653|ref|YP_003529092.1| pseudouridine synthase [Nitrosococcus halophilus Nc4]
 gi|291582248|gb|ADE16705.1| pseudouridine synthase, RluA family [Nitrosococcus halophilus Nc4]
          Length = 321

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 83/335 (24%), Positives = 143/335 (42%), Gaps = 34/335 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             +  +    RLD+     +P  +   LQ+ ++ GQV+V+    +  + ++ G+ V +  
Sbjct: 9   TTLPPELAGKRLDQALACVFPAYSRSRLQQWIKQGQVKVNDAPARPRDTVRGGEWVVLM- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                          +    +   +  L   ++YED  I V NKPAG+ V   +G     
Sbjct: 68  --------------AEMETAVVWQAQPLPLEIVYEDEAIIVVNKPAGLVVHPAAGNRDGT 113

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L    + ++  +  + HRLD++TSG+LVVART  A   L +    RR+ + Y ++
Sbjct: 114 LVNALLNHAPELAEIPRAGIVHRLDKDTSGLLVVARTLTAHHGLVQQLHARRVTRQYRAI 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G+       I    + +  +    + VV         AI+H++V   F +    +  +
Sbjct: 174 AVGVMT--GGGIIEAPIHRHPVDRKRMAVVS----TGKPAITHYRVRARF-RAHTDVSCR 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+G P++GD  Y         S  +         +  LHA  + L 
Sbjct: 227 LETGRTHQIRVHLAHIGYPLLGDPTYGKRLHIPRESGEELSTALRHFKRQALHAARLGLL 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           HPE  + +   APLP  M      L     R+ + 
Sbjct: 287 HPERKQAMSWEAPLPEDMSTLLALLEQDRQRHAHP 321


>gi|239814386|ref|YP_002943296.1| pseudouridine synthase, RluA family [Variovorax paradoxus S110]
 gi|239800963|gb|ACS18030.1| pseudouridine synthase, RluA family [Variovorax paradoxus S110]
          Length = 370

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 95/326 (29%), Positives = 156/326 (47%), Gaps = 24/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ V+ +    RLD +   H   +   ++ +I+RSG+VR++K R +   RI++G V+R
Sbjct: 38  IKFITVDAESAGQRLDNFLFRHLKGVPKTHVYRIIRSGEVRINKGRAQAETRIEAGDVLR 97

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+  +            +    T  +   +  +L ED  +   +KPAG++V GGSG++
Sbjct: 98  LPPIRISPR----------AEEGATPPAPAREFPVLLEDDAVLAIDKPAGVAVHGGSGVS 147

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++      +   L HRLD+ETSGIL+VA+ R+A   L + FR R   K Y +L
Sbjct: 148 FGVIEQLRTARPG-AKFLELVHRLDRETSGILLVAKKRSALVALQDQFRERETGKTYLAL 206

Query: 187 VWGIPKNKKECIANWLLKKSHIGG------DYVHVVKQNEKGANYAISHFKVIDC----- 235
           V G     K+ +   L K    G         V VV ++   A  A++  +V+       
Sbjct: 207 VEGAWPANKKVLDAPLAKYLLPGDGAGAGERRVRVVAKDHPDAMRAVTLVRVLARLTLPG 266

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARY 294
            A     L +   TGRTHQ+RVH    G  I GD KY     +         +++LHA  
Sbjct: 267 DAAPLSLLAVTIKTGRTHQIRVHLASAGHAIAGDDKYGDFERQRVLQKLGLKRMFLHAWR 326

Query: 295 MDLPHP-EGGRLQITAPLPAHMVKTW 319
           +   HP  G R+ + A LP  +    
Sbjct: 327 LQFNHPATGERVALQAGLPPELHALM 352


>gi|223934286|ref|ZP_03626210.1| pseudouridine synthase, RluA family [Streptococcus suis 89/1591]
 gi|253751575|ref|YP_003024716.1| RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|253753476|ref|YP_003026617.1| RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|253755698|ref|YP_003028838.1| RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|330832720|ref|YP_004401545.1| RluA family pseudouridine synthase [Streptococcus suis ST3]
 gi|31364860|gb|AAP49462.1| YlyB [Streptococcus suis]
 gi|223897042|gb|EEF63479.1| pseudouridine synthase, RluA family [Streptococcus suis 89/1591]
 gi|251815864|emb|CAZ51475.1| putative RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|251818162|emb|CAZ55959.1| putative RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|251819722|emb|CAR45564.1| putative RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|292558226|gb|ADE31227.1| YlyB [Streptococcus suis GZ1]
 gi|319758010|gb|ADV69952.1| pseudouridine synthase, RluA family [Streptococcus suis JS14]
 gi|329306943|gb|AEB81359.1| pseudouridine synthase, RluA family [Streptococcus suis ST3]
          Length = 297

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 71/313 (22%), Positives = 136/313 (43%), Gaps = 34/313 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+   +    ++     + +++GQV V+ +  K    +Q G V+            
Sbjct: 9   GIRLDKALSD-LTDLSRSVANEQIKAGQVLVNGQPKKAKYSVQVGDVLTYQ--------- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKS 135
                 +     +   ++ +   ++++D  + V NKP G+ V   +G      ++  L  
Sbjct: 59  ------IPEVEEIDYVAEDIPLEIVFQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALLYH 112

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HR+D++TSG+L++A+   A   L    + ++  + YW++V G  
Sbjct: 113 VKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIVHGNL 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            N +  I   + +            K        A++ F+V++ F   +  +E+   TGR
Sbjct: 173 PNDRGVIEAPIGRSEKDRKKQAVTAK-----GKEAVTRFQVLERFGD-YTLVELTLETGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  G  ++ TA 
Sbjct: 227 THQIRVHMAYIGHPVAGDEAYGPR-----KTLKGHGQFLHARTLGFTHPRTGEVVEFTAE 281

Query: 311 LPAHMVKTWDSLG 323
            PA   +  + L 
Sbjct: 282 APAIFQEALEKLR 294


>gi|114566812|ref|YP_753966.1| pseudouridylate synthase [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
 gi|114337747|gb|ABI68595.1| ribosomal large subunit pseudouridine synthase D [Syntrophomonas
           wolfei subsp. wolfei str. Goettingen]
          Length = 305

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 147/329 (44%), Gaps = 32/329 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + ++V+ + E  RLD +       ++   ++ ++ +G++RVD K+ K + R+++G+
Sbjct: 1   MPRTEILLVDEEMEGERLDAFVTEQLDELSRSLVKTLIENGEIRVDSKQQKPSYRLKAGE 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                + +   L   +  +    +Y+D  I V +KP G+      
Sbjct: 61  EIIVE---------------IPAVRELKLKAQDIPLSFIYQDKDIAVIDKPKGMVAHPAH 105

Query: 124 GIAYHI--DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +   +  L    D  G     +P + HRLD++TSG++V+A+   A + L    +  
Sbjct: 106 GNWENTLVNALLFHLKDLSGINGELRPGIVHRLDKDTSGVMVIAKNDMAHRQLAAQIKDH 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I + Y +LV GI K     I   + + S      + V+     G   A+S+++V++   
Sbjct: 166 SINREYITLVHGIIKENLGSIEAPIGR-SKQDRKKMAVIA----GGRPAVSNYQVLERLG 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  L+++  TGRTHQ+RVH  ++  P+VGD  Y +  K        +   LHA  +  
Sbjct: 221 -NYTLLKVKLLTGRTHQIRVHFAYIKHPVVGDPLYGSGKKQ----LGLDTQALHAHLLGF 275

Query: 298 PHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
            HP  G   +  + LP +       L  K
Sbjct: 276 KHPSSGEYREFKSELPLYFECILSDLRNK 304


>gi|317968170|ref|ZP_07969560.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp.
           CB0205]
          Length = 325

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 91/314 (28%), Positives = 139/314 (44%), Gaps = 30/314 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNH 76
            MRLDRW     P  +   +QK + +G VRV+    +    ++    V +  P    L +
Sbjct: 21  PMRLDRWLVAQRPEQSRARIQKFIDAGYVRVNGVTGRAKTPLRLNDTVELWMPPPEPLPY 80

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
           +I +   LD               +LYED  + V NKPAG++V    G      ++G L 
Sbjct: 81  LIPQDIPLD---------------VLYEDEHLIVLNKPAGLTVHPAPGNKDGTLVNGLLH 125

Query: 135 SWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +VVA+++ A   L    + R   + Y ++V G 
Sbjct: 126 HCPDLPGIGGEMRPGIVHRLDKDTTGCIVVAKSQEALVKLQVQIQKRVASREYLAVVHGA 185

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      I   + +       Y  V   ++    +A +H+ +++     +  +  +  TG
Sbjct: 186 PAGDNGTIVGAIGRHPADRKKYAVV---HDGSGRHACTHWTLLERLGD-YALMRFKLDTG 241

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  H+G PIVGD  Y    K   T P      LHA  + L HP    R+   A
Sbjct: 242 RTHQIRVHCAHIGHPIVGDPVYSRCRKLPLTLPG---QALHAFQLGLDHPIRKDRMLFEA 298

Query: 310 PLPAHMVKTWDSLG 323
           PLP  M K    L 
Sbjct: 299 PLPEVMEKLLKLLR 312


>gi|148652292|ref|YP_001279385.1| RluA family pseudouridine synthase [Psychrobacter sp. PRwf-1]
 gi|148571376|gb|ABQ93435.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter sp.
           PRwf-1]
          Length = 364

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 98/317 (30%), Positives = 158/317 (49%), Gaps = 23/317 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V ++ V  ++   R+D +       +   ++ K++RS +VR++ KR K  + ++ G VV
Sbjct: 61  QVNHLEVTRNQHGQRIDNFLLARLKGMPRAHIYKMIRSDEVRINNKRCKPYDNLERGDVV 120

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RI PV  A     +E+ ++         +  L   ++YED  + V NKP+G++V GGSG+
Sbjct: 121 RIAPVKLAT----REKPVISEGF-----AKSLLERVVYEDEGLIVLNKPSGMAVHGGSGL 171

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + +   ++     K     L HR+D++TSG+L++A+ R+  + L E  R + IQK Y  
Sbjct: 172 DFGVIEAMRDATSKKY--LELVHRIDKDTSGLLMIAKKRSTLKVLQEYLREKTIQKHYLC 229

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCW 242
           LV G P   +  I   LL+ +   G+    V +    A  + +  KV+  F    +    
Sbjct: 230 LVKGQPALNEFEIDAPLLRYTVANGERRVKVDKANPEAKLSQTTCKVLARFKMNGEPVSL 289

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E  PHTGRTHQ+RVH  ++G PI+GD KY              +L LHA  +D+P  E 
Sbjct: 290 IEAMPHTGRTHQIRVHLAYLGHPILGDDKYNIKDTSGV-----RRLCLHAWQLDVPEYE- 343

Query: 303 GRLQITAPLPAHMVKTW 319
               I APLP  M    
Sbjct: 344 ---VIKAPLPEDMQSLL 357


>gi|292487319|ref|YP_003530191.1| ribosomal large subunit pseudouridine synthase D [Erwinia amylovora
           CFBP1430]
 gi|292900315|ref|YP_003539684.1| ribosomal large subunit pseudouridine synthase D [Erwinia amylovora
           ATCC 49946]
 gi|291200163|emb|CBJ47289.1| ribosomal large subunit pseudouridine synthase D [Erwinia amylovora
           ATCC 49946]
 gi|291552738|emb|CBA19783.1| ribosomal large subunit pseudouridine synthase D [Erwinia amylovora
           CFBP1430]
          Length = 325

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 77/340 (22%), Positives = 144/340 (42%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ + + ++ V+   + K   ++  G+ + I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILNRRITVNGTTIDKPKEKVLGGEQISIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I                      +  +   ++YED  I V NKP  + V  G+G     
Sbjct: 70  EIEEEARW---------------EAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   +   +  + HRLD++T+G++VVA+T  +  HL ++ + R I + Y ++
Sbjct: 115 VLNALLHHFPAIADVPRAGIVHRLDKDTTGLMVVAKTVPSQTHLVDALQRREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGRM-TAGGTVNEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHISHPLVGDPLYGGRPRPPKGASEAFIATLRAFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G  ++  APLP  MV+  D+L  K D   + ++L  
Sbjct: 288 HPISGIEMEWHAPLPQDMVELIDAL--KADTEAFKEQLDW 325


>gi|319792202|ref|YP_004153842.1| pseudouridine synthase, rlua family [Variovorax paradoxus EPS]
 gi|315594665|gb|ADU35731.1| pseudouridine synthase, RluA family [Variovorax paradoxus EPS]
          Length = 365

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 99/327 (30%), Positives = 157/327 (48%), Gaps = 25/327 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ V+ +    RLD +   H   +   ++ +I+RSG+VR++K RV+   RI+ G V+R
Sbjct: 32  IKFITVDAESAGQRLDNFLFRHLKGVPKTHVYRIIRSGEVRINKGRVQAETRIEVGDVLR 91

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +            +    T  +   +  +L ED  +   +KPAG++V GGSG++
Sbjct: 92  LPPVRISPR----------AEEGATSPAPAREFPVLLEDDAVLAIDKPAGVAVHGGSGVS 141

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L++      +   L HRLD+ETSGIL+VA+ R+A   L + FR R   K Y +L
Sbjct: 142 FGVIEQLRTARPG-AKFLELVHRLDRETSGILLVAKKRSALVALQDQFRERETGKTYLAL 200

Query: 187 VWGIPKNKKECIANWLLKKSHIGG-------DYVHVVKQNEKGANYAISHFKVIDC---- 235
           V G     K+ +   L K     G         V VV ++   A  AI+  +V+      
Sbjct: 201 VEGDWPANKKVLDAPLAKYLLPDGSGAGAGERRVRVVAKDHPDAMRAITLVRVLARLTLP 260

Query: 236 -FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHAR 293
             A     L +   TGRTHQ+RVH    G  I GD KY     +         +++LHA 
Sbjct: 261 GDATPLSLLAVTIKTGRTHQIRVHLASAGHAIAGDDKYGDFERQRTLQKLGLKRMFLHAW 320

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTW 319
            +   HP GG R+ + A LP  +    
Sbjct: 321 RLQFNHPAGGERVALQADLPPELHALM 347


>gi|319953859|ref|YP_004165126.1| ribosomal large subunit pseudouridine synthase d [Cellulophaga
           algicola DSM 14237]
 gi|319422519|gb|ADV49628.1| ribosomal large subunit pseudouridine synthase D [Cellulophaga
           algicola DSM 14237]
          Length = 363

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 147/330 (44%), Gaps = 35/330 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV    +E +R+D++  N   +     +Q+  R+G + V+  +VK N R+++G  VR+  
Sbjct: 37  VVASKGQEPLRVDKFLMNFIENAVRNKIQQAARAGHIWVNDIQVKQNYRVKAGDEVRV-- 94

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                 H   E  ++   + +          ++YED  + V NK  G+ V  G G     
Sbjct: 95  ---LFEHPPHEFLLVPEDIPIN---------IVYEDDVLMVVNKEPGMVVHPGHGNYSGT 142

Query: 128 HIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            I+  L    D   +  ++P L HR+D++TSG+LV+A+T  A   L++ F  +  ++ Y 
Sbjct: 143 LINALLHHTKDLAVNSNERPGLVHRIDKDTSGLLVIAKTDEAMTFLSKQFFDKTSEREYV 202

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LVWG  +  +  I   + +  H        V  + +    A++HFKV++        + 
Sbjct: 203 ALVWGNMEEDEGTIEGHVGR--HPSNRLQMTVFPDGEQGKDAVTHFKVLERLG-YLTLIS 259

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYLHA 292
            +  TGRTHQ+RVH  ++G  +  D +Y        T+             I  +  LHA
Sbjct: 260 CKLETGRTHQIRVHLKYIGHTLFNDERYGGERILKGTTFTKYKQFVDNAFKILPRQALHA 319

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           + +   HP     ++  + +P  M    D 
Sbjct: 320 KTLGFVHPVTKEFMRFDSEIPEDMANCIDK 349


>gi|182682370|ref|YP_001830530.1| RluA family pseudouridine synthase [Xylella fastidiosa M23]
 gi|182632480|gb|ACB93256.1| pseudouridine synthase, RluA family [Xylella fastidiosa M23]
 gi|307578653|gb|ADN62622.1| ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa subsp. fastidiosa GB514]
          Length = 327

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 85/342 (24%), Positives = 151/342 (44%), Gaps = 42/342 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V +     R D      +P  +   L + ++SG V ++   V+  + +  G+VV +
Sbjct: 10  RQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVRPRDPVYGGEVVWL 69

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             + +     + +   LD               +LYED  ++V NKPAG+ V  G+G   
Sbjct: 70  QVMPDIRTDAVPQDIPLD---------------ILYEDEHVFVINKPAGLVVHPGAG--- 111

Query: 128 HIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + DG L + +  +        +  + HRLD++TSG++VVART  A   L E    R++ +
Sbjct: 112 NPDGTLVNALLHRDPALAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSSRQVHR 171

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V  +         N  +++       + V          A++H+++ + F +   
Sbjct: 172 QYLAVV--VSALVSGGTVNAAIERHPRDRLRMEV----SDTGKEAVTHYRLRERF-RAHT 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNKLYLHAR 293
            LE +  TGRTHQ+RVH  H+  PIVGD  Y  + K                 +  LHA 
Sbjct: 225 ALECRLDTGRTHQIRVHMAHLRHPIVGDRLYGGSLKLPKGGTDALVAMLRGFKRQALHAE 284

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            ++  HP     ++I AP+P  + +   +L  + D  L+ +R
Sbjct: 285 VLEFLHPVRALPVRIVAPVPEDLCQLLAAL--REDSALFFER 324


>gi|300921138|ref|ZP_07137519.1| pseudouridine synthase, RluA family [Escherichia coli MS 115-1]
 gi|300411911|gb|EFJ95221.1| pseudouridine synthase, RluA family [Escherichia coli MS 115-1]
          Length = 326

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 139/333 (41%), Gaps = 35/333 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + +                     A++H+++++ F +    L 
Sbjct: 173 AVAIGHM-TAGGTVDEPISRHPS-----KRTHMAVHPMGKPAVTHYRIMEHF-RVHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 286 LYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|146283956|ref|YP_001174109.1| pseudouridine synthase [Pseudomonas stutzeri A1501]
 gi|145572161|gb|ABP81267.1| pseudouridine synthase [Pseudomonas stutzeri A1501]
 gi|327482283|gb|AEA85593.1| pseudouridine synthase [Pseudomonas stutzeri DSM 4166]
          Length = 324

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 91/347 (26%), Positives = 159/347 (45%), Gaps = 39/347 (11%)

Query: 1   MSLMTY--VQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN 57
           MS ++   +Q    V  D    RLD+     +   +   L   ++ G + VD   ++  +
Sbjct: 1   MSTISKQAIQLRAEVPFDLGGQRLDQVAAQLFSEHSRSRLAAWIKDGLLTVDGAVLRPRD 60

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
            + +G V+ +     A    + +   LD               ++YED +I V +KPAG+
Sbjct: 61  TVHAGAVLELSAEQQAQGEWVAQDIPLD---------------IVYEDDQILVIDKPAGL 105

Query: 118 SVQGGSGIAYHI--DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            V   +G A     +  L    D     +  + HRLD++T+G++VVA+T  A   L E  
Sbjct: 106 VVHPAAGHADGTLLNALLHHVPDLINVPRAGIVHRLDKDTTGLMVVAKTLQAQTRLVEQL 165

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R + +IY ++V G+       +   + +        + VV    +G   A+SH++V++
Sbjct: 166 QARSVSRIYEAIVIGVIIT-GGTVDAPIGRHGQQ-RQRMAVV----EGGKPAVSHYRVLE 219

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------N 286
            F +    + ++  TGRTHQ+RVH  H+G P+VGD  Y   F+     +P          
Sbjct: 220 RF-RSHTHVRVKLETGRTHQIRVHMTHLGYPLVGDPLYAGRFRIPPAANPTLVQTLREFP 278

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +  LHAR+++L HP  G R++  +PLP   V     L  + DR  ++
Sbjct: 279 RQALHARFLELDHPVTGQRMKWESPLPDDFVWLLTLL--QQDREAFV 323


>gi|261342024|ref|ZP_05969882.1| ribosomal large subunit pseudouridine synthase D [Enterobacter
           cancerogenus ATCC 35316]
 gi|288315680|gb|EFC54618.1| ribosomal large subunit pseudouridine synthase D [Enterobacter
           cancerogenus ATCC 35316]
          Length = 326

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 83/336 (24%), Positives = 150/336 (44%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVFGGEAVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP G+ V  G+G   
Sbjct: 68  NVEIEEDVRFEPQDIPLD---------------IVYEDDDILVINKPRGLVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  +       +  + HRLD++T+G++VVA+T  A  HL ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIIDVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVESLQLREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTSGGTVDEPISRHPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RIHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEEFISVLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G +++  AP+P  MV+  D++   ++ 
Sbjct: 283 MLRLYHPVTGIQMEWHAPIPQDMVELIDAMRADFEE 318


>gi|152986388|ref|YP_001350515.1| pseudouridine synthase [Pseudomonas aeruginosa PA7]
 gi|150961546|gb|ABR83571.1| pseudouridine synthase [Pseudomonas aeruginosa PA7]
          Length = 320

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 90/347 (25%), Positives = 155/347 (44%), Gaps = 43/347 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS M   +   V  +    RLD+     +P  +   L   ++ G++ VD    +  + + 
Sbjct: 1   MSDMIQ-RAAEVPFELGGQRLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAAARPRDIVH 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SG  + +     A    + +   LD               +++ED  I V +KPAG+ V 
Sbjct: 60  SGAQLVLEAEQEAQGEWVAQDIELD---------------IVHEDEHILVIDKPAGLVVH 104

Query: 121 GGSGIAYHIDGFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             +G   H DG L + +       +   +  + HRLD++T+G++VVA+T  A   L    
Sbjct: 105 PAAG---HQDGTLLNALLYHVPGIANVPRAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQL 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R + +IY ++V G+       I   + +   +    + VV         A+SH++V++
Sbjct: 162 QARSVSRIYEAIVIGVI-TSGGTIDAPIGRHG-VQRQKMAVVD----AGKVAVSHYRVLE 215

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--------GNFTSPIQN 286
            F +      ++  TGRTHQ+RVH  H+G P+VGD  Y   FK           T     
Sbjct: 216 RF-RAHTHTRVKLETGRTHQIRVHMSHIGYPLVGDPVYGGRFKIPPVASQTLVQTLREFP 274

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +  LHAR+++L HP  G R++  +PLP   +     L  + DR  ++
Sbjct: 275 RQALHARFLELDHPATGVRMKWESPLPEDFLWLLSLL--RQDREAFV 319


>gi|242373484|ref|ZP_04819058.1| pseudouridylate synthase RluD [Staphylococcus epidermidis
           M23864:W1]
 gi|242348847|gb|EES40449.1| pseudouridylate synthase RluD [Staphylococcus epidermidis
           M23864:W1]
          Length = 305

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 71/324 (21%), Positives = 143/324 (44%), Gaps = 33/324 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + +  +   R+D+         +   LQ  ++   V+V+ K +K N +++   
Sbjct: 1   METYEFKITDESQVGQRIDKLLSEMNDEWSRSQLQDWIKEDLVKVNDKVIKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           I+ E++++++ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  HI-----------IVTEKEVVEADI----QPEDLNLDIYYEDEDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    +   + +        + +V         A++HF V++ F 
Sbjct: 166 TVKRKYTALVHGNIPHDYGTVDAPIGRN-KNDRQAMAIVD----DGKDAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLIECELETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLD-----IGGQALHAGVIGF 274

Query: 298 PHPEG-GRLQITAPLPAHMVKTWD 320
            HP     ++ ++ LP       +
Sbjct: 275 EHPVTHEYIERSSELPKEFKDLLE 298


>gi|157369129|ref|YP_001477118.1| 23S rRNA pseudouridine synthase D [Serratia proteamaculans 568]
 gi|157320893|gb|ABV39990.1| pseudouridine synthase, RluA family [Serratia proteamaculans 568]
          Length = 325

 Score =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 80/333 (24%), Positives = 139/333 (41%), Gaps = 35/333 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   ++  +   +V+V+ K + K   ++  G+ V I
Sbjct: 8   TATVAESQLGQRLDQALAELFPDYSRSRIKDWILDNRVQVNGKTINKPKEKVLGGETVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I                         +   ++YEDS I V NKP  + V  G+G   
Sbjct: 68  DAQIEEDARW---------------EPQDIALNIVYEDSDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y 
Sbjct: 113 GTVLNALLHYYPEIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQARDITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A++H+++++ F +    L 
Sbjct: 173 AVAIGTM-TAGGTVEEPISRHST-----KRTHMAVHPMGKPAVTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDAFIATLRGFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           L HP  G +++  APLP  MV   ++L    + 
Sbjct: 286 LYHPISGIQMEWHAPLPQDMVDLINALKADTEE 318


>gi|264677097|ref|YP_003277003.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
 gi|262207609|gb|ACY31707.1| pseudouridine synthase, RluA family [Comamonas testosteroni CNB-2]
          Length = 346

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 103/324 (31%), Positives = 158/324 (48%), Gaps = 21/324 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V+ D    RLD +   H   +   ++ +I+RSG+VR++K RV    R+Q G VVR
Sbjct: 34  VRLIEVDEDSAGQRLDNFLMRHLKGVPKTHVYRIIRSGEVRINKGRVSAETRVQPGDVVR 93

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +        K+ + +       DF     L +D  +   +KPAG++V GGSG++
Sbjct: 94  LPPVRIS-------DKVAEKAERPAPAKDFPA---LLDDEHMIALSKPAGVAVHGGSGVS 143

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD+ETSGIL+VA+ R+A  +L + FR R   K Y +L
Sbjct: 144 FGVIEQLRQAR-PDAKFLELVHRLDRETSGILLVAKKRSALINLQDQFRERETGKTYLAL 202

Query: 187 VWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK------ 239
           V G     K+ I   L K     G+  V V   ++     +I+  KV      +      
Sbjct: 203 VQGAWPANKKVIDLPLHKYLQADGERRVRVTTADDPDGMRSITLVKVRKLIEPRPLQGLP 262

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDL 297
               LE+   TGRTHQ+RVH    G PIVGD KY   +           +++LHA  +  
Sbjct: 263 AMSLLEVTIKTGRTHQIRVHLSSQGHPIVGDDKYGDFDLNRRVQKQGLKRMFLHAWRLQF 322

Query: 298 PHP-EGGRLQITAPLPAHMVKTWD 320
            HP  G R+++ A LP  +    +
Sbjct: 323 NHPASGERVELRAELPPELADFVN 346


>gi|330999930|ref|ZP_08323628.1| ribosomal large subunit pseudouridine synthase D [Parasutterella
           excrementihominis YIT 11859]
 gi|329573337|gb|EGG54949.1| ribosomal large subunit pseudouridine synthase D [Parasutterella
           excrementihominis YIT 11859]
          Length = 409

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/340 (24%), Positives = 143/340 (42%), Gaps = 37/340 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
           + ++   V  D +  RLD+   +    I+   L+ ++  G V+V+ K V K   ++  G 
Sbjct: 38  SKIETFEVTLDLDGERLDKVLASSLKDISRSRLKTLIEDGLVKVNGKTVDKPKEKMSFGD 97

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +              +I     ++   +  +   ++YED  I V NKPA + V   +
Sbjct: 98  EVSV--------------EIKPRLEDMDFIATPMDIDVVYEDDDILVINKPARLVVHPAA 143

Query: 124 GIAYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H D  L + + +         +  + HRLD++T+G++VVA+   A   L +  + R
Sbjct: 144 G---HWDDTLLNGLLAYNPIFRTLPRAGIVHRLDRDTTGLMVVAKNEKAMLDLVQQLQAR 200

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI---D 234
            +++ YW+L  G     K  I   + +      + +         A  A +H + I   +
Sbjct: 201 TVKREYWALTRGKAPADK-VIEAAIERDP---RNPLRFTIGKGGRAKPATTHIRCIDQKE 256

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP----IQNKLYL 290
              + F W+  +  TGRTHQ+RVH   +G P++GD  Y                 ++  L
Sbjct: 257 VKGKPFSWVACRLKTGRTHQIRVHMESIGLPLIGDPLYRNKLPKPKEDGSVLNSFDRQAL 316

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF-KYDR 328
           HA  + L HP     ++  A  P       D LGF  +DR
Sbjct: 317 HASRLGLIHPVTKETMEWFAEPPQDFRDLMDELGFGPWDR 356


>gi|146306004|ref|YP_001186469.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           mendocina ymp]
 gi|145574205|gb|ABP83737.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           mendocina ymp]
          Length = 324

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 151/334 (45%), Gaps = 36/334 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  ++   RLD+     +   +   L   ++ G++ VD    +  + + +G  + +   
Sbjct: 14  IVPFEQGGQRLDQVAAQLFGEFSRSRLSTWIKDGRLTVDGAVARPRDTVHAGSTLVLDAE 73

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
             A    +               +  ++  ++YED  + V +KPAG+ V   +G A    
Sbjct: 74  QEAQGEWV---------------AQDIELNIVYEDEHLLVIDKPAGLVVHPAAGHADGTL 118

Query: 130 -DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L    D     +  + HRLD++T+G++VVA+T  A  +L E  + R + +IY  + 
Sbjct: 119 LNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTLQAQTNLVEQLQKRSVSRIYECIC 178

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+       I   + + S      + V      G   AISH++V++ + +    + ++ 
Sbjct: 179 IGVI-TAGGTIDAPIGRSSSQ-RQRMAVTD----GGKPAISHYRVLERY-RSHTHVRVKL 231

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+G P+VGD  Y   F+    +            +  LHAR+++L H
Sbjct: 232 ETGRTHQIRVHMSHVGYPLVGDPVYAGRFRIPPAASQSLVQSLKEFPRQALHARFLELDH 291

Query: 300 P-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           P  G R++  +PLP  +V     L  + DR  ++
Sbjct: 292 PATGKRMKWESPLPDDLVWLLTLL--RQDREAFV 323


>gi|49259508|pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine
           Synthase Rlud From Escherichia Coli
 gi|118138510|pdb|2IST|A Chain A, Crystal Structure Of Rlud From E. Coli
          Length = 325

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 81/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 7   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I + NKP  + V  G+G   
Sbjct: 67  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIIINKPRDLVVHPGAGNPD 111

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 112 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 171

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 172 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 222 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 281

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 282 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 317


>gi|16130515|ref|NP_417085.1| 23S rRNA pseudouridine synthase; specific to U1911, U1915, and
           U1917 [Escherichia coli str. K-12 substr. MG1655]
 gi|89109396|ref|AP_003176.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           W3110]
 gi|157162070|ref|YP_001459388.1| 23S rRNA pseudouridine synthase D [Escherichia coli HS]
 gi|170019127|ref|YP_001724081.1| 23S rRNA pseudouridine synthase D [Escherichia coli ATCC 8739]
 gi|170082199|ref|YP_001731519.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|188493998|ref|ZP_03001268.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           53638]
 gi|194439337|ref|ZP_03071415.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           101-1]
 gi|238901755|ref|YP_002927551.1| 23S rRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|253772510|ref|YP_003035341.1| 23S rRNA pseudouridine synthase D [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254037671|ref|ZP_04871729.1| 23S rRNA pseudouridine synthase D [Escherichia sp. 1_1_43]
 gi|254162565|ref|YP_003045673.1| 23S rRNA pseudouridine synthase D [Escherichia coli B str. REL606]
 gi|256024877|ref|ZP_05438742.1| 23S rRNA pseudouridine synthase D [Escherichia sp. 4_1_40B]
 gi|297516262|ref|ZP_06934648.1| 23S rRNA pseudouridine synthase D [Escherichia coli OP50]
 gi|300905086|ref|ZP_07122893.1| pseudouridine synthase, RluA family [Escherichia coli MS 84-1]
 gi|300930681|ref|ZP_07146065.1| pseudouridine synthase, RluA family [Escherichia coli MS 187-1]
 gi|301305760|ref|ZP_07211847.1| pseudouridine synthase, RluA family [Escherichia coli MS 124-1]
 gi|301644036|ref|ZP_07244054.1| pseudouridine synthase, RluA family [Escherichia coli MS 146-1]
 gi|307139315|ref|ZP_07498671.1| 23S rRNA pseudouridine synthase D [Escherichia coli H736]
 gi|331643311|ref|ZP_08344442.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli H736]
 gi|2507541|sp|P33643|RLUD_ECOLI RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|1236631|gb|AAA92957.1| SfhB [Escherichia coli]
 gi|1788946|gb|AAC75643.1| 23S rRNA pseudouridine synthase; specific to U1911, U1915, and
           U1917 [Escherichia coli str. K-12 substr. MG1655]
 gi|85675474|dbj|BAA16479.2| 23S rRNA pseudouridine synthase [Escherichia coli str. K12 substr.
           W3110]
 gi|157067750|gb|ABV07005.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           HS]
 gi|169754055|gb|ACA76754.1| pseudouridine synthase, RluA family [Escherichia coli ATCC 8739]
 gi|169890034|gb|ACB03741.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|188489197|gb|EDU64300.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           53638]
 gi|194421699|gb|EDX37708.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           101-1]
 gi|226839295|gb|EEH71316.1| 23S rRNA pseudouridine synthase D [Escherichia sp. 1_1_43]
 gi|238859758|gb|ACR61756.1| 23S rRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|242378190|emb|CAQ32965.1| 23S rRNA pseudouridine synthase [Escherichia coli BL21(DE3)]
 gi|253323554|gb|ACT28156.1| pseudouridine synthase, RluA family [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253974466|gb|ACT40137.1| 23S rRNA pseudouridine synthase [Escherichia coli B str. REL606]
 gi|253978633|gb|ACT44303.1| 23S rRNA pseudouridine synthase [Escherichia coli BL21(DE3)]
 gi|260448330|gb|ACX38752.1| pseudouridine synthase, RluA family [Escherichia coli DH1]
 gi|300403013|gb|EFJ86551.1| pseudouridine synthase, RluA family [Escherichia coli MS 84-1]
 gi|300461455|gb|EFK24948.1| pseudouridine synthase, RluA family [Escherichia coli MS 187-1]
 gi|300839014|gb|EFK66774.1| pseudouridine synthase, RluA family [Escherichia coli MS 124-1]
 gi|301077610|gb|EFK92416.1| pseudouridine synthase, RluA family [Escherichia coli MS 146-1]
 gi|309702976|emb|CBJ02307.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           ETEC H10407]
 gi|315137214|dbj|BAJ44373.1| 23S rRNA pseudouridine synthase D [Escherichia coli DH1]
 gi|315253122|gb|EFU33090.1| pseudouridine synthase, RluA family [Escherichia coli MS 85-1]
 gi|323935610|gb|EGB31930.1| RluA family protein pseudouridine synthase [Escherichia coli E1520]
 gi|323941386|gb|EGB37570.1| RluA family protein pseudouridine synthase [Escherichia coli E482]
 gi|323960546|gb|EGB56175.1| RluA family protein pseudouridine synthase [Escherichia coli H489]
 gi|323971461|gb|EGB66697.1| RluA family protein pseudouridine synthase [Escherichia coli TA007]
 gi|331036782|gb|EGI09006.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Escherichia coli H736]
 gi|332344465|gb|AEE57799.1| ribosomal large subunit pseudouridine synthase [Escherichia coli
           UMNK88]
          Length = 326

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 81/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I + NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIIINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|257453790|ref|ZP_05619068.1| ribosomal large subunit pseudouridine synthase D [Enhydrobacter
           aerosaccus SK60]
 gi|257448717|gb|EEV23682.1| ribosomal large subunit pseudouridine synthase D [Enhydrobacter
           aerosaccus SK60]
          Length = 380

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 76/333 (22%), Positives = 143/333 (42%), Gaps = 37/333 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q   V +++   R+D+     +   +   ++  L SG++ V+    K   R++   ++ 
Sbjct: 66  IQNYTVNSEQIGERIDKIAALVFSDYSREQIKNWLESGELTVNGAAQKPKYRLKPNDMLV 125

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SG 124
           +   + A    + E   LD               +LYED  + V NKP G+ V  G  +G
Sbjct: 126 LKASLTAQQQDLPENIPLD---------------ILYEDEAVLVINKPVGLVVHPGAGNG 170

Query: 125 IAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               ++  L  + DS+   +  L HR+D+ETSG++V+A+   +  HL    + + + ++Y
Sbjct: 171 SGTLVNALLFHYPDSRTLPRAGLVHRIDKETSGLMVIAKDSQSQLHLINQLKDKSVYRLY 230

Query: 184 WSLVWGIPKN--KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            ++V        +   I   + +          V          A++H + I   +    
Sbjct: 231 QAIVLASAAELARHRTIDAPIGRHPTQRTKMAVVSS-----GKPAVTHLEKITAISDAVS 285

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-----------KLYL 290
            + ++  TGRTHQ+RVH  ++G P++GD  Y A  K        +           +  L
Sbjct: 286 LVSVRLETGRTHQIRVHLSNLGFPLLGDPLYGAARKNAILLKTLDDDQKHIVQQFQRQAL 345

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           HA  +   HP+ G  +++ A LP  M +  D+L
Sbjct: 346 HAYELGFIHPKTGEPIKVQARLPEDMQQLLDTL 378


>gi|189423553|ref|YP_001950730.1| pseudouridine synthase [Geobacter lovleyi SZ]
 gi|189419812|gb|ACD94210.1| pseudouridine synthase, RluA family [Geobacter lovleyi SZ]
          Length = 326

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 149/336 (44%), Gaps = 36/336 (10%)

Query: 4   MTYVQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M    Y + V  +    RLD +       ++   +Q+++  GQV + + + + + ++  G
Sbjct: 1   METTYYCIEVPAEAAGQRLDAFLATRLTDLSRAAVQRLIDDGQVLLTEGKPRSSMKLAGG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + + +     A    + EQ  LD               +LYED  + V NK AG++V  G
Sbjct: 61  EQITVEIPPPAPAVPLAEQIPLD---------------VLYEDHDLIVINKSAGMTVHPG 105

Query: 123 SGIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G+     ++  L    D  G     +P + HRLD+ TSG+LVVA+   A + L E F  
Sbjct: 106 AGVDSGTLVNALLGHCTDLSGIGGEIRPGIVHRLDKGTSGVLVVAKNDIAHRGLAEQFAA 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I+++YW+L++G P      ++N + +           +    K    A ++++V++ F
Sbjct: 166 HSIKRLYWALIYGSPNEDTGKVSNSIGRHPTD----RLRMSGKAKHGKEATTNWRVLERF 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQ------NKL 288
                 ++++  TGRTHQ+RVH      P++GD  Y     F     + ++       + 
Sbjct: 222 G-AASLVQLRLETGRTHQIRVHLSEANMPLLGDPLYPDGGRFNNLKDTRLKGMISHLGRQ 280

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            LHAR +   HP  G+ L+ ++  P         L 
Sbjct: 281 ALHARVLGFIHPLTGQYLEFSSEPPEDFSGILAYLR 316


>gi|168494358|ref|ZP_02718501.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae CDC3059-06]
 gi|221231700|ref|YP_002510852.1| RNA pseudouridylate synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225854435|ref|YP_002735947.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae JJA]
 gi|183575636|gb|EDT96164.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae CDC3059-06]
 gi|220674160|emb|CAR68683.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           ATCC 700669]
 gi|225722558|gb|ACO18411.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Streptococcus pneumoniae JJA]
          Length = 295

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 145/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETGGLRLDKALSD-LSELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLVLAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G  + GD  Y         +   +  +LHA+ +   HP  G+ 
Sbjct: 221 QLETGRTHQIRVHMAYIGHSVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGKT 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+  A +P    +T + L 
Sbjct: 276 LEFKADIPEIFKETLERLR 294


>gi|325293793|ref|YP_004279657.1| ribosomal large subunit pseudouridine synthase D [Agrobacterium sp.
           H13-3]
 gi|325061646|gb|ADY65337.1| ribosomal large subunit pseudouridine synthase D [Agrobacterium sp.
           H13-3]
          Length = 340

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 81/345 (23%), Positives = 150/345 (43%), Gaps = 46/345 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           + V++  ++   R+D W        ++   L+ ++  G V ++   V     ++     V
Sbjct: 12  RKVLIAGEDAEGRIDVWLAGEVGGDLSRSRLKALIEQGAVLLNGTPVTEPKKKVHPHDRV 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            I               ++    +     + +   + YED  + V  KPAG+ V  G+G 
Sbjct: 72  EI---------------VMPEPEDPEPKGEDIPLDVEYEDDDLIVLVKPAGLVVHPGAGN 116

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  +    DS       ++P + HRLD+ETSG++VVA+   A +HL   F    
Sbjct: 117 WTGTLVNALIYHCGDSLSGIGGVKRPGIVHRLDKETSGVMVVAKNDNAHRHLAAQFADHG 176

Query: 179 ----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y ++VWG P+  +  I   L + +        V +++   A  AI+H++V++
Sbjct: 177 RTGPLERAYKAVVWGRPRTLRGTIDAALGRGA--DRTKRAVKREDTDDAREAITHYEVME 234

Query: 235 CFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
            F +K         +E +  TGRTHQ+RVH  H+G P++GD +Y A F+       +   
Sbjct: 235 RFHEKADASCLASMVECRLETGRTHQIRVHMAHIGHPLIGDPEYGAAFRTKANLLEEPAR 294

Query: 286 ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                  +  LHA  +   HP  G  ++    +P  M +   +L 
Sbjct: 295 STVNRFPRQALHAYLLAFEHPRTGEVMEFETDMPDDMEELLIALR 339


>gi|15599740|ref|NP_253234.1| pseudouridine synthase [Pseudomonas aeruginosa PAO1]
 gi|116052689|ref|YP_793005.1| pseudouridine synthase [Pseudomonas aeruginosa UCBPP-PA14]
 gi|218893639|ref|YP_002442508.1| pseudouridine synthase [Pseudomonas aeruginosa LESB58]
 gi|254238708|ref|ZP_04932031.1| pseudouridine synthase [Pseudomonas aeruginosa C3719]
 gi|254244558|ref|ZP_04937880.1| pseudouridine synthase [Pseudomonas aeruginosa 2192]
 gi|296391365|ref|ZP_06880840.1| pseudouridine synthase [Pseudomonas aeruginosa PAb1]
 gi|313107189|ref|ZP_07793388.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           aeruginosa 39016]
 gi|12231021|sp|P33640|RLUD_PSEAE RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|9950788|gb|AAG07932.1|AE004868_3 pseudouridine synthase [Pseudomonas aeruginosa PAO1]
 gi|115587910|gb|ABJ13925.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|126170639|gb|EAZ56150.1| pseudouridine synthase [Pseudomonas aeruginosa C3719]
 gi|126197936|gb|EAZ61999.1| pseudouridine synthase [Pseudomonas aeruginosa 2192]
 gi|218773867|emb|CAW29681.1| pseudouridine synthase [Pseudomonas aeruginosa LESB58]
 gi|310879890|gb|EFQ38484.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           aeruginosa 39016]
          Length = 320

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 89/347 (25%), Positives = 156/347 (44%), Gaps = 43/347 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS M   +   V  +    RLD+     +P  +   L   ++ G++ VD   ++  + + 
Sbjct: 1   MSDMIQ-RAAEVPFELGGQRLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVH 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SG  + +     A    + +   L+               ++YED  I V +KPAG+ V 
Sbjct: 60  SGAQLVLEAEQEAQGEWLAQDIELE---------------IVYEDEHILVIDKPAGLVVH 104

Query: 121 GGSGIAYHIDGFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             +G   H DG L + +       +   +  + HRLD++T+G++VVA+T  A   L    
Sbjct: 105 PAAG---HQDGTLLNALLYHVPDIANVPRAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQL 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R + +IY ++V G+       I   + +   +    + VV         A+SH++V++
Sbjct: 162 QARSVSRIYEAIVIGVI-TSGGTIDAPIGRHG-VQRQKMAVVD----AGKVAVSHYRVLE 215

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--------GNFTSPIQN 286
            F +      ++  TGRTHQ+RVH  H+G P+VGD  Y   F+           T     
Sbjct: 216 RF-RAHTHTRVKLETGRTHQIRVHMSHIGYPLVGDPVYGGRFRIPPVASQTLVQTLREFP 274

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +  LHAR+++L HP  G R++  +PLP   +     L  + DR  ++
Sbjct: 275 RQALHARFLELDHPATGVRMKWESPLPEDFLWLLSLL--RQDREAFV 319


>gi|238760705|ref|ZP_04621826.1| Ribosomal large subunit pseudouridine synthase D [Yersinia aldovae
           ATCC 35236]
 gi|238701078|gb|EEP93674.1| Ribosomal large subunit pseudouridine synthase D [Yersinia aldovae
           ATCC 35236]
          Length = 325

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 83/340 (24%), Positives = 147/340 (43%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V V+ K + K   ++  G++V I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDKVTVNGKTINKPKEKVLGGELVAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I        ++  LD               ++YEDS I V NKP G+ V  G+G     
Sbjct: 70  QIEEDARWAPQEIPLD---------------IVYEDSDILVINKPRGLVVHPGAGNPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++
Sbjct: 115 VLNALLYYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGNM-TAGGRVDEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDSFISILRGFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G +++  A LP  MV+  ++L  K D   +  ++  
Sbjct: 288 HPISGIQMEWHAALPKDMVELINAL--KADTEEFKDQMDW 325


>gi|264679430|ref|YP_003279337.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
 gi|262209943|gb|ACY34041.1| pseudouridine synthase, RluA family [Comamonas testosteroni CNB-2]
          Length = 352

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 79/328 (24%), Positives = 142/328 (43%), Gaps = 31/328 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVR 66
           + ++V  +    R+D+         +   LQ++L  G V ++ K + K + ++  G  +R
Sbjct: 43  RELMVGTEHHGQRVDKVLALGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLR 102

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +                  +  ++    + +   ++YED  + V NKPAG+ V    G  
Sbjct: 103 VEMR--------------PTQQSMAFQPETMDLQVVYEDEDLLVINKPAGLVVHPAPG-- 146

Query: 127 YHIDGFLKSWVDSKGQKPR------LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            +  G L + + ++ +K R      + HRLD++TSG++VVAR R+    L +    R + 
Sbjct: 147 -NWTGTLLNGLLARDEKARQVPRAGIVHRLDKDTSGLMVVARNRSTMDALIKMIAAREVS 205

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +L      ++K    +  + +       + VV  N      A + F ++D  A   
Sbjct: 206 RQYLALAHKQWGSRKHREVDAPIGRDPRNRLRMAVVDLNLHPGKQARTDFDLLDGDA-AH 264

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +    HTGRTHQ+RVH   +G P++ D  Y    +G        +  LHA  +   HP
Sbjct: 265 SLVRCTLHTGRTHQIRVHMASLGHPLIADTLYGGQPEGGLE-----RQALHAFRLAFEHP 319

Query: 301 EGGRLQIT-APLPAHMVKTWDSLGFKYD 327
              +  +  APLP  M    D  G +Y+
Sbjct: 320 VTKKPLVHYAPLPQDMAGALDLWGLRYN 347


>gi|326791366|ref|YP_004309187.1| pseudouridine synthase [Clostridium lentocellum DSM 5427]
 gi|326542130|gb|ADZ83989.1| pseudouridine synthase, RluA family [Clostridium lentocellum DSM
           5427]
          Length = 304

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 79/329 (24%), Positives = 150/329 (45%), Gaps = 35/329 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   ++++V  N E   R+D++    +P      +QK +  G + V++K +    ++++ 
Sbjct: 1   MAEKIEHIV--NSEAKGRVDKYLAEVFPEYTRSFIQKQIEKGGILVNQKVINSKYQVKAD 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +                +   + +    + +   ++YED  + + NKP  + V   
Sbjct: 59  DHIIMT---------------IPDPIEVDIIPEPIDIEIVYEDDDLMIVNKPQDMVVHPA 103

Query: 123 SGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G      ++G L    D         +P + HR+D++TSG+L++A+   A   L+E  +
Sbjct: 104 PGNYSGTLVNGLLYHCKDKLSGINGEIRPGIVHRIDKDTSGLLMIAKNDKAHLGLSELLK 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I + Y ++V+G  K  +  I   + + S      + +V+       YA + +KV++ 
Sbjct: 164 DHHITRKYHAIVYGGFKEDEGTIEEPIGR-STQDRKKMAIVR----DGRYAKTDYKVLER 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F Q F ++E+  HTGRTHQ+RVH  H+G P++GD  Y         S   NK  LHA+ +
Sbjct: 219 FKQ-FTYIELTLHTGRTHQIRVHMKHIGHPLLGDPVYGP----TKMSFGINKQMLHAKVI 273

Query: 296 DLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
              HP     +   + LP + V+  D L 
Sbjct: 274 GFTHPITHKEMYFESELPDYFVRVIDKLR 302


>gi|163794483|ref|ZP_02188454.1| Pseudouridylate synthase, 23S RNA-specific [alpha proteobacterium
           BAL199]
 gi|159180207|gb|EDP64730.1| Pseudouridylate synthase, 23S RNA-specific [alpha proteobacterium
           BAL199]
          Length = 349

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 140/327 (42%), Gaps = 42/327 (12%)

Query: 20  RLDRWFKNHYPH------INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72
           R+DRW             ++   L+ ++  G++ V+   +   ++ ++ G   RI     
Sbjct: 37  RIDRWLARCLEDRETDPPLSRNRLKTLILDGRLFVNGATITDPSSPVKPGATYRID---- 92

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
                      +  +      +  L   ++YED+ + V +KPAG++V    G      ++
Sbjct: 93  -----------VPEATPAIPEAQDLPLTVVYEDAALIVIDKPAGMTVHPAPGAPKDTLVN 141

Query: 131 GFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             +    DS       ++P + HR+D++TSG+LVVA+T AA   L   F    I + Y +
Sbjct: 142 ALIAHCGDSLSGIGGVKRPGIVHRIDKDTSGLLVVAKTDAAHHALAARFADHSIDRAYRA 201

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L WG P      I   + +      D + +  + E     A++HF+ +  F +    LE 
Sbjct: 202 LCWGRPIPPAGRIEGAIGRHP---RDRIRMAVRPEGSGKAAVTHFRTVRAFNEAATLLEC 258

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NKLYLHARYMD 296
           +  TGRTHQ+RVH  H+G P+VGD  Y            +         ++  LHA  + 
Sbjct: 259 RLETGRTHQIRVHLTHIGHPLVGDPVYGRGRSAKLGGLPEETRDRLHGFSRQALHAAVLG 318

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G  L+  +PLP  +    D L
Sbjct: 319 FNHPITGEPLRFESPLPEDLAALIDDL 345


>gi|189502073|ref|YP_001957790.1| hypothetical protein Aasi_0665 [Candidatus Amoebophilus asiaticus
           5a2]
 gi|189497514|gb|ACE06061.1| hypothetical protein Aasi_0665 [Candidatus Amoebophilus asiaticus
           5a2]
          Length = 341

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 147/332 (44%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  ++  R+D++  +  P+ +   +Q  + +  + V+    K N +I+    ++I  
Sbjct: 19  ITVDPGQKPYRIDKFLIDRLPNTSRNKIQLAIDNQFILVNGIPTKANYKIRPYDKIQI-- 76

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
               L +  +  +++  ++ L          ++YED  + V +KPAG+ V  G +     
Sbjct: 77  ---VLPNPPRNNELIPENIPLD---------IVYEDEALMVVHKPAGMVVHPGYNNWTGT 124

Query: 129 IDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   L  + D+         +P L HR+D++TSG+LVVA+T A+   L + F    I + 
Sbjct: 125 LVNALIYYFDNLPTAPNNIGRPGLVHRIDKDTSGLLVVAKTEASLIALAKQFYDHSIART 184

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y++L+WG P+ +   I +  L +S      V      EKG   A++H++V++   +    
Sbjct: 185 YYALIWGEPETETGTI-DINLDRSLQDRRIVAPYTNPEKG-KRAVTHYQVVERL-RYVSL 241

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------------IQNKLYL 290
           ++    TGRTHQ+R H  HMG PI  D  Y  +                    I  +  L
Sbjct: 242 VKCTLETGRTHQIRAHMKHMGHPIFADAAYGGHEIVKGEQFSKYKSFVENCFQIMPRQAL 301

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA  +   HP     +   +PLP       + 
Sbjct: 302 HAYSLGFIHPTTQENMYFESPLPTDFQTVLNR 333


>gi|254523997|ref|ZP_05136052.1| ribosomal large subunit pseudouridine synthase D [Stenotrophomonas
           sp. SKA14]
 gi|219721588|gb|EED40113.1| ribosomal large subunit pseudouridine synthase D [Stenotrophomonas
           sp. SKA14]
          Length = 329

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 84/345 (24%), Positives = 146/345 (42%), Gaps = 40/345 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  +V +     R D      +P  +   L + +++G V +D  +V+  + ++ G+VV +
Sbjct: 10  RQAIVPDTAAGRRFDAVVAELFPEYSRSRLTEWIKAGDVLLDGAQVRPRDPLRGGEVVTL 69

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             V+        E   LD               +L+ED  + V NKP G+ V  G+G   
Sbjct: 70  TVVLETQTDAQPEDIPLD---------------VLFEDEHLLVINKPVGLVVHPGAG--N 112

Query: 128 HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           H    + + +          +  + HRLD++TSG++VVA+T  A   L E    R + + 
Sbjct: 113 HSGTLVNALLFRDPSVAVLPRAGIVHRLDKDTSGVMVVAKTLEAQTALVEQLAARDVHRQ 172

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G         A+  + +       + V     +    AI+H+++ + F +    
Sbjct: 173 YLAIVMGALVA--GGTADAPIDRHPRDRLKMAVR----EDGKEAITHYRLRERF-RAHTA 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARY 294
           LE +  TGRTHQ+RVH  H+  PI+GD  Y    K                 +  LHA  
Sbjct: 226 LECRLETGRTHQIRVHMAHVRHPIIGDPLYGGALKLPKGASDELVAALRGFKRQALHAET 285

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           ++  HP  G  ++ TAP+P  M+     L  + D   +  R   +
Sbjct: 286 LEFTHPITGEPVRNTAPVPEDMLHLMKVL--RDDSEAFAARERDR 328


>gi|194435119|ref|ZP_03067355.1| ribosomal large subunit pseudouridine synthase D [Shigella
           dysenteriae 1012]
 gi|194416650|gb|EDX32783.1| ribosomal large subunit pseudouridine synthase D [Shigella
           dysenteriae 1012]
 gi|332089232|gb|EGI94339.1| ribosomal large subunit pseudouridine synthase D [Shigella
           dysenteriae 155-74]
          Length = 326

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHM 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|33864373|ref|NP_895933.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9313]
 gi|33641153|emb|CAE22283.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9313]
          Length = 324

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 92/314 (29%), Positives = 142/314 (45%), Gaps = 30/314 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNH 76
            MRLDRW  +     +  ++QK + +G VRV+    +    ++ G  V +  P    L +
Sbjct: 27  PMRLDRWLVSQRSEQSRSHIQKFIEAGLVRVNGITGRAKTPLRQGDEVELWMPPPEPLPY 86

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFLK 134
           +  E+  LD               +L+ED  + V NKPAG++V    G      ++G L 
Sbjct: 87  LQPEEMPLD---------------VLFEDRHLIVINKPAGLTVHPAPGNRNGTLVNGLLH 131

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D  G     +P + HRLD++T+G +V+A+++ A   L E  + R   + Y ++V G 
Sbjct: 132 HCSDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQEQIQKRIASRNYLAVVHGA 191

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P   +  I   + +       Y  V    E G  +A +H+ +++  A  +  L  +  TG
Sbjct: 192 PSGDQGTIVAAIGRHPVDRKKYAVV---TEDGGRHACTHWTLVERLAD-YSLLRFKLDTG 247

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           RTHQ+RVH  H+G PIVGD  Y    K     P      LHA  + L HP    R+   A
Sbjct: 248 RTHQIRVHCAHIGHPIVGDPIYSRCRKLPMDLPG---QILHAVQLGLDHPLTRERMIFEA 304

Query: 310 PLPAHMVKTWDSLG 323
           PLP    K    L 
Sbjct: 305 PLPDLFEKLLTVLR 318


>gi|52307928|gb|AAU38428.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 327

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 81/340 (23%), Positives = 145/340 (42%), Gaps = 36/340 (10%)

Query: 1   MSLMTYVQ-YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNR 58
           M  M  +     V+  +   RLD+     +P  +   L+  +    V ++ K       +
Sbjct: 1   MIFMAQITMSAEVQPHQMGQRLDQTLAELFPDYSRSRLKTWIEDELVLLNGKVANIPREK 60

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +  G+ V I   I   N                     +   ++YED  I V NKP    
Sbjct: 61  VYGGEQVEITVEIEDENRF---------------EPQNIPLNIVYEDDDILVINKPKDFV 105

Query: 119 VQGGSGIAYHI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           V  G+G       +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  + +
Sbjct: 106 VHPGAGNPNGTVLNALLYHYPQITEVPRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRALQ 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R+I + Y ++ +GI   K   +   + +           +         A++H++V++ 
Sbjct: 166 KRKITREYEAIAFGIM-TKGGTVDEPMSRHPT-----KRTLMAVHPMGKPAVTHYRVMEH 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--K 287
           F + +  L ++  TGRTHQ+RVH  H+  P++GD  Y    +        F S ++N  +
Sbjct: 220 F-RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEEFMSVLRNFQR 278

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
             LHA  + L HP  G  ++  APLP   V+  ++L   Y
Sbjct: 279 QALHAIMLRLEHPITGELMEWHAPLPEDFVELVNALKADY 318


>gi|221068709|ref|ZP_03544814.1| pseudouridine synthase, RluA family [Comamonas testosteroni KF-1]
 gi|220713732|gb|EED69100.1| pseudouridine synthase, RluA family [Comamonas testosteroni KF-1]
          Length = 346

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 103/324 (31%), Positives = 158/324 (48%), Gaps = 21/324 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V+ D    RLD +   H   +   ++ +I+RSG+VR++K RV    R+Q G VVR
Sbjct: 34  VRLIEVDEDSAGQRLDNFLMRHLKGVPKTHVYRIIRSGEVRINKGRVSAETRVQPGDVVR 93

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +        K+ + +       DF     L +D  +   +KPAG++V GGSG++
Sbjct: 94  LPPVRIS-------DKVAEKAERPAPAKDFPA---LLDDEHMLALSKPAGVAVHGGSGVS 143

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+       +   L HRLD+ETSGIL+VA+ R+A  +L + FR R   K Y +L
Sbjct: 144 FGVIEQLRQAR-PDAKFLELVHRLDRETSGILLVAKKRSALINLQDQFRERETGKTYLAL 202

Query: 187 VWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK------ 239
           V G     K+ I   L K     G+  V V   ++     +I+  KV      +      
Sbjct: 203 VQGAWPANKKVIDLPLHKYLQADGERRVRVTTADDPDGMRSITLVKVRKLIEPRPLQGLP 262

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDL 297
               LE+   TGRTHQ+RVH    G PIVGD KY   +           +++LHA  +  
Sbjct: 263 AMSLLEVTIKTGRTHQIRVHLSSQGHPIVGDDKYGDFDLNRRVQKQGLKRMFLHAWRLQF 322

Query: 298 PHP-EGGRLQITAPLPAHMVKTWD 320
            HP  G R+++ A LP  +    +
Sbjct: 323 NHPASGERVELRAELPPELADFVN 346


>gi|222111813|ref|YP_002554077.1| RluA family pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221731257|gb|ACM34077.1| pseudouridine synthase, RluA family [Acidovorax ebreus TPSY]
          Length = 339

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 102/322 (31%), Positives = 156/322 (48%), Gaps = 21/322 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V+ +    RLD +   H   +   ++ +I+RSG+VR++K R   + R+  G +VR+
Sbjct: 22  RIVEVDAESAGQRLDNFLIRHLKGVPKTHVYRIIRSGEVRLNKGRTSADARVAPGDLVRL 81

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PPV  +        K+LD +       +F    +L ED  +   +KPAG +V GGSG+++
Sbjct: 82  PPVRVS-------DKVLDKAERPAPAREF---PILLEDEHLIAIDKPAGTAVHGGSGVSF 131

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L+       +   L HRLD+ETSGIL+VA+ R+A  HL + FR R   K Y +LV
Sbjct: 132 GVIEQLRQARPQ-ARFLELVHRLDRETSGILLVAKKRSALTHLQDQFRGRETGKTYLALV 190

Query: 188 WGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
            G     K+ I   L K     G+  V V   ++     +++  KV    A +       
Sbjct: 191 TGHWPANKKVIDTPLHKYLQEDGERRVRVTTPDDPDGMRSVTLVKVRSQLAPRPLQGLPA 250

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLP 298
              LE+   TGRTHQ+RVH    G PI GD KY   +           +++LHA  +   
Sbjct: 251 MSLLEVTIKTGRTHQIRVHLSSQGHPIAGDDKYGDFDLNRRLQKQGLKRMFLHAWRLQFD 310

Query: 299 HP-EGGRLQITAPLPAHMVKTW 319
           HP  G RL++ A LP  +    
Sbjct: 311 HPASGERLELRAELPPELTAFL 332


>gi|24379309|ref|NP_721264.1| putative pseudouridylate synthase [Streptococcus mutans UA159]
 gi|24377230|gb|AAN58570.1|AE014926_13 putative pseudouridylate synthase [Streptococcus mutans UA159]
          Length = 296

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 78/318 (24%), Positives = 141/318 (44%), Gaps = 34/318 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E  E  +RLD+   +    ++     + +++G V V+ K  K    ++ G ++      
Sbjct: 3   IEIKEAGVRLDKALAD-LTDLSRSQASEQIKAGLVLVNGKTQKAKYAVKEGDII------ 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHI 129
               H  + Q+ +     L   +  +   ++YED  + V NKP G+ V    G      +
Sbjct: 56  ----HYERPQEEV-----LDCVAQNIPLEIVYEDEDVAVINKPQGMVVHPSVGHPSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D        +P + HR+D++TSG+L++A+   A Q L +  + ++  + Y +
Sbjct: 107 NALLFHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDQAHQALAKELKEKKSLRQYIA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   N +  I   + +            K        A++HFKV++ F Q +  +E+
Sbjct: 167 LVHGNLPNDRGVIEAPIGRSEKDRKKQTVTAK-----GKPAVTHFKVLERFGQ-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
              TGRTHQ+RVH  ++G P+ GD  Y         +      +LHA+ +   HP+ G  
Sbjct: 221 TLETGRTHQIRVHMAYIGHPVAGDPLYAPK-----KTLKGQGQFLHAKTLGFTHPKTGEL 275

Query: 305 LQITAPLPAHMVKTWDSL 322
           +Q T  +P    +  D L
Sbjct: 276 MQFTTEVPVIFQEVLDHL 293


>gi|22124820|ref|NP_668243.1| 23S rRNA pseudouridine synthase D [Yersinia pestis KIM 10]
 gi|108808759|ref|YP_652675.1| 23S rRNA pseudouridine synthase D [Yersinia pestis Antiqua]
 gi|108810984|ref|YP_646751.1| 23S rRNA pseudouridine synthase D [Yersinia pestis Nepal516]
 gi|153997673|ref|ZP_02022773.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           CA88-4125]
 gi|165926534|ref|ZP_02222366.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165936735|ref|ZP_02225302.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166010204|ref|ZP_02231102.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166213045|ref|ZP_02239080.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167398582|ref|ZP_02304106.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167421637|ref|ZP_02313390.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167423313|ref|ZP_02315066.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|167470273|ref|ZP_02334977.1| 23S rRNA pseudouridine synthase D [Yersinia pestis FV-1]
 gi|218930302|ref|YP_002348177.1| 23S rRNA pseudouridine synthase D [Yersinia pestis CO92]
 gi|229838893|ref|ZP_04459052.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229899460|ref|ZP_04514603.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229901200|ref|ZP_04516323.1| 23S rRNA pseudouridine synthase [Yersinia pestis Nepal516]
 gi|270489385|ref|ZP_06206459.1| pseudouridine synthase, RluA family [Yersinia pestis KIM D27]
 gi|294504991|ref|YP_003569053.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           Z176003]
 gi|34395805|sp|Q8ZBV7|RLUD_YERPE RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|21957646|gb|AAM84494.1|AE013693_10 suppressor of ftsH mutation [Yersinia pestis KIM 10]
 gi|108774632|gb|ABG17151.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           Nepal516]
 gi|108780672|gb|ABG14730.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           Antiqua]
 gi|115348913|emb|CAL21870.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           CO92]
 gi|149289310|gb|EDM39390.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           CA88-4125]
 gi|165915384|gb|EDR33994.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|165921462|gb|EDR38659.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165991111|gb|EDR43412.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166205832|gb|EDR50312.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166960556|gb|EDR56577.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167051086|gb|EDR62494.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167057483|gb|EDR67229.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|229681925|gb|EEO78018.1| 23S rRNA pseudouridine synthase [Yersinia pestis Nepal516]
 gi|229687862|gb|EEO79935.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229695259|gb|EEO85306.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|262363056|gb|ACY59777.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           D106004]
 gi|262366980|gb|ACY63537.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           D182038]
 gi|270337889|gb|EFA48666.1| pseudouridine synthase, RluA family [Yersinia pestis KIM D27]
 gi|294355450|gb|ADE65791.1| ribosomal large subunit pseudouridine synthase D [Yersinia pestis
           Z176003]
 gi|320016469|gb|ADW00041.1| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 325

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/340 (24%), Positives = 148/340 (43%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V V+ K++ K   ++  G++V I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKVLGGELVAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I        ++  LD               ++YED+ I V NKP G+ V  G+G     
Sbjct: 70  QIEEDARWAPQEIPLD---------------IVYEDNDILVINKPRGLVVHPGAGNPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++
Sbjct: 115 VLNALLHYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGNM-TAGGRVDEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDSFIAILRGFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G +++  A LP  MV+  ++L  K D   +  ++  
Sbjct: 288 HPIRGIQMEWHAALPEDMVELINAL--KADTEEFKDQMDW 325


>gi|227888161|ref|ZP_04005966.1| 23S rRNA pseudouridine synthase [Escherichia coli 83972]
 gi|227834801|gb|EEJ45267.1| 23S rRNA pseudouridine synthase [Escherichia coli 83972]
 gi|307554609|gb|ADN47384.1| 23S rRNA pseudouridine synthase [Escherichia coli ABU 83972]
          Length = 326

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 81/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V ++ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLINGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|212712902|ref|ZP_03321030.1| hypothetical protein PROVALCAL_03999 [Providencia alcalifaciens DSM
           30120]
 gi|212684447|gb|EEB43975.1| hypothetical protein PROVALCAL_03999 [Providencia alcalifaciens DSM
           30120]
          Length = 325

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/343 (23%), Positives = 156/343 (45%), Gaps = 43/343 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            +   +   RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + I  
Sbjct: 10  TIAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKAKEKVLGGEQISIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +I        +   LD               ++YED  I + NKP  + V  G+G     
Sbjct: 70  LIEEDTRWEPQDIPLD---------------VVYEDEDILIINKPRDLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + + +   +  + HRLD++T+G++VVA+T  A  HL E+ + R I + Y ++
Sbjct: 115 ILNALLYRYPEIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAV 174

Query: 187 VWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             G        +E I+    K++H+    +            A++H++V++ F +    L
Sbjct: 175 AVGRMTAGGMVEEPISRHPTKRTHMAVHPM---------GKPAVTHYRVMEHF-RAHTRL 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYM 295
            ++  TGRTHQ+RVH  H+  P++GD  Y    +    +  +        ++  LHA  +
Sbjct: 225 RLRLETGRTHQIRVHMAHINHPLIGDQLYGGRPRPLKGATEEFLEVMRKFDRQALHATML 284

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            L HP  G +++  APLP  MV+  ++L  K D  L+   +  
Sbjct: 285 RLYHPITGIQMEWHAPLPDDMVELIEAL--KADTELHKDDMDW 325


>gi|330501971|ref|YP_004378840.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           mendocina NK-01]
 gi|328916257|gb|AEB57088.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           mendocina NK-01]
          Length = 327

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 87/350 (24%), Positives = 155/350 (44%), Gaps = 42/350 (12%)

Query: 1   MSLMTYVQ------YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK 54
           M  MT +         +V  ++   RLD+     +   +   L   ++ G++ VD    +
Sbjct: 1   MPKMTSINKQLIQLQAIVPFEQGGQRLDQVAAQLFGEYSRSRLSTWIKEGRLTVDGAVAR 60

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
             + + +G  + +     A    I               +  ++  ++YED  + V +KP
Sbjct: 61  PRDTVHAGSTLVLDAEQEAQGEWI---------------AQDIELNIVYEDEHMLVIDKP 105

Query: 115 AGISVQGGSGIAYHI--DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           AG+ V   +G A     +  L    D     +  + HRLD++T+G++VVA+T  A  +L 
Sbjct: 106 AGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTLQAQTNLV 165

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           E  + R + +IY  +  G+       I   + + S      + V      G   AISH++
Sbjct: 166 EQLQKRTVSRIYECICIGVI-TAGGTIDAPIGRSSSQ-RQRMAVTD----GGKPAISHYR 219

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ----- 285
           V++ + +    + ++  TGRTHQ+RVH  H+G P+VGD  Y   F+     SP       
Sbjct: 220 VLERY-RSHTHVRVKLETGRTHQIRVHMTHVGYPLVGDPVYAGRFRIPPAASPTLVQSLK 278

Query: 286 --NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
              +  LHAR+++L HP  G R++  + LP  +V     L  + DR  ++
Sbjct: 279 EFPRQALHARFLELDHPATGQRMKWESELPDDLVWLLTLL--RQDREAFV 326


>gi|15803118|ref|NP_289149.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 EDL933]
 gi|12517018|gb|AAG57707.1|AE005490_2 suppressor of ftsH mutation [Escherichia coli O157:H7 str. EDL933]
          Length = 326

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 144/336 (42%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                 L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTXLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|51892381|ref|YP_075072.1| 23S rRNA pseudouridine synthase [Symbiobacterium thermophilum IAM
           14863]
 gi|51856070|dbj|BAD40228.1| 23S rRNA pseudouridine synthase [Symbiobacterium thermophilum IAM
           14863]
          Length = 304

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 140/331 (42%), Gaps = 38/331 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           ++   +  +E + R+D +        ++   +Q ++  GQV ++    K    +  G V+
Sbjct: 1   MREYRITAEEGHPRIDVFLAGRPEIGLSRSRIQALIDEGQVTLNGAMPKARQAVNPGDVI 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +         ++ E   LD               ++YED  I V NK  G+ V   +G 
Sbjct: 61  VVRVPDPEPMELVPEDIPLD---------------IVYEDEDILVVNKQRGLVVHPAAG- 104

Query: 126 AYHIDGFLKSWVDSK---------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             H  G L   +  K           +P + HRLD++T+G+LVVA++  A   L E  R 
Sbjct: 105 --HWTGTLVHALLDKVDDLEGIGGELRPGIVHRLDKDTTGLLVVAKSERAMASLQEQIRD 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             +Q++YW+LV G        I   + +           +  N K    A+++F+V++ +
Sbjct: 163 HMVQRVYWALVHGNSMPDTGRIEAPIGRHPRDRK----RMAVNPKTGRDAVTYFRVLERY 218

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  LE +  TGRTHQ+RVH   +G P+VGD  Y                 LHAR + 
Sbjct: 219 -RGYALLECRLETGRTHQIRVHLSFIGHPVVGDPLYGPRKP----HLGMPPQALHARQLS 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
             HP  G  ++ T   PA M+     L  + 
Sbjct: 274 FRHPASGEWMEFTVDPPADMMAVVQRLREEA 304


>gi|292490642|ref|YP_003526081.1| pseudouridine synthase [Nitrosococcus halophilus Nc4]
 gi|291579237|gb|ADE13694.1| pseudouridine synthase, RluA family [Nitrosococcus halophilus Nc4]
          Length = 325

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 107/322 (33%), Positives = 164/322 (50%), Gaps = 15/322 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    V+ V ++ ++   R+D +  +    +    + + LR G+VRV+K RV  + R++ 
Sbjct: 7   SSTPRVRLVEIQLEQAGQRIDNFLLSQLKGVPKSRIYRCLRRGEVRVNKSRVASSYRLEQ 66

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VRIPP+   ++H   ++ +  S ++L      ++S LLYED  + + NKPAGI+V  
Sbjct: 67  GDQVRIPPLR--VSHPSVKEPVAPSLLHL------IESSLLYEDKHLLILNKPAGIAVHS 118

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GS I+Y +   L+  +  +     L HRLD+ETSG L+VA+TR+    L    R + I K
Sbjct: 119 GSSISYGVIETLRH-LRPEAPFLELVHRLDRETSGCLMVAKTRSTLLALQSMQREQLIHK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G        +   LLK     G+ V  V         A SHF       ++  
Sbjct: 178 RYLALVKGRWPRNIGQVNLPLLKNILQSGERVVKV---SATGKPAASHFHP-KQLYKEAT 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            +E+   TGRTHQ+RVHA H+G P+ GD KY    F     +    +L+LHA  +    P
Sbjct: 234 LMEITLETGRTHQIRVHAAHLGHPLGGDEKYGDPAFNKRLRNLGLRRLFLHADQLSFTPP 293

Query: 301 EGGR-LQITAPLPAHMVKTWDS 321
           EG + L+ITAPLP  +     +
Sbjct: 294 EGKKLLKITAPLPEELSAVLKA 315


>gi|307243485|ref|ZP_07525636.1| pseudouridine synthase, RluA family [Peptostreptococcus stomatis
           DSM 17678]
 gi|306493129|gb|EFM65131.1| pseudouridine synthase, RluA family [Peptostreptococcus stomatis
           DSM 17678]
          Length = 310

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 79/320 (24%), Positives = 145/320 (45%), Gaps = 31/320 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ D    RLD +  + Y  I+   +QK+++ G V V+++  K + +++ G  + I    
Sbjct: 13  VDQDSAGKRLDVFIADQYQDISRSYVQKLIKDGLVLVNEEVKKASYKLEEGDRMEI---- 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
                       +     L   +  +   ++YED  + + NKP G+ V    G      +
Sbjct: 69  -----------AMPEPEVLEVLAQDIDLDIVYEDDDLLIVNKPQGMVVHPAPGNPDGTLV 117

Query: 130 DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +  +    D         +P + HR+D+ TSG+LVVA+  A+ Q L + F++  I + Y 
Sbjct: 118 NAIMYHCKDKLSSINGVIRPGIVHRIDKNTSGLLVVAKNNASHQGLADQFKLHSITREYE 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +  G     +  I   + +          +    + G  +A++HF VI+   + + +++
Sbjct: 178 MVCIGGVNWDQMTIDKNIGRNPKDRLKMAVL----DTGGRHAVTHFTVIEHL-EGYTYMK 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQ+RVH+ ++  PI+GD  Y    K       Q    LHAR +   HP  G 
Sbjct: 233 AKLETGRTHQIRVHSNYLRHPILGDTLYGYQVKKFSKLEGQT---LHARKLGFVHPRTGE 289

Query: 305 -LQITAPLPAHMVKTWDSLG 323
            ++ T+ LP +  K  D++ 
Sbjct: 290 YMEFTSDLPDYFKKILDTIR 309


>gi|261493667|ref|ZP_05990186.1| 23S rRNA pseudouridine synthase D [Mannheimia haemolytica serotype
           A2 str. BOVINE]
 gi|261494334|ref|ZP_05990828.1| 23S rRNA pseudouridine synthase D [Mannheimia haemolytica serotype
           A2 str. OVINE]
 gi|261309983|gb|EEY11192.1| 23S rRNA pseudouridine synthase D [Mannheimia haemolytica serotype
           A2 str. OVINE]
 gi|261310667|gb|EEY11851.1| 23S rRNA pseudouridine synthase D [Mannheimia haemolytica serotype
           A2 str. BOVINE]
          Length = 325

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 83/347 (23%), Positives = 146/347 (42%), Gaps = 39/347 (11%)

Query: 4   MTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           MT  + +   +  D    RLD+     +P  +   ++  + S  V+V+   V K   ++ 
Sbjct: 1   MTQQKILTAEITADLLGARLDQALAQLFPDYSRSRIKVWIESDLVKVNGNIVNKAREKVF 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ V I   I                         +   ++YED  I V NKP  + V 
Sbjct: 61  GGETVEITAEIEEEIRF---------------EPQDIPLNIVYEDDDIIVINKPKDLVVH 105

Query: 121 GGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+G     +   L  +     + PR  + HRLD++T+G++VVA+   A  HL  + + R
Sbjct: 106 PGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRLDKDTTGLMVVAKNIPAQTHLVTALQKR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           RI + Y ++  GI   +   +   + +                     A++H+++++ F 
Sbjct: 166 RITREYEAIASGIM-TQGGKVDEPMARHPT-----KRTAMAVHPMGKPAVTHYRIMERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLY 289
           + +  L ++  TGRTHQ+RVH  H+  P++GD  Y    +    +            +  
Sbjct: 219 RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQLYGGRPRPPKGASDSFLSVLRGFQRQA 278

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
           LHA  + L HP  G  ++  APLP   ++   +L  K D  LY  +L
Sbjct: 279 LHATMLRLEHPITGEMMEWHAPLPDDFIELIQAL--KADYELYKDQL 323


>gi|188994625|ref|YP_001928877.1| ribosomal large subunit pseudouridine synthase [Porphyromonas
           gingivalis ATCC 33277]
 gi|188594305|dbj|BAG33280.1| ribosomal large subunit pseudouridine synthase [Porphyromonas
           gingivalis ATCC 33277]
          Length = 365

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 145/332 (43%), Gaps = 36/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V +  +  +R+D++  +   +     +Q+   +G + V+ + VK N RI+ G VV +  
Sbjct: 35  TVADPGQTLIRIDKFLVDRMNNATRSRIQQAAEAGAIFVNGRPVKSNYRIKPGDVVTL-- 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYH 128
                       ++L     L    + +   ++YED  + V NKPAG+ V  G G     
Sbjct: 93  ------------ELLRPRRELEIIPEDIPLDIVYEDDVLLVINKPAGLVVHPGHGNYTGT 140

Query: 129 IDGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   L  ++    +         L HR+D++TSG+LVVA+   A   L + F  +   + 
Sbjct: 141 LVNALAYYLREDPEYDPMDPSLGLVHRIDKDTSGLLVVAKRAEAKSDLCKQFYYKTTHRS 200

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWG        I   + +        + V   +      A++H++V++  A    W
Sbjct: 201 YRALVWGRFDYPIGTITGNIGRDLK-DRLQMAVFPPDGDIGKPAVTHYQVLEELA-YVSW 258

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           +E +  TGRTHQ+R H  H+G  +  D +Y  +   +GN T+  +           +  L
Sbjct: 259 IECRLETGRTHQIRAHMKHIGHTLFADERYGGDQILRGNNTANYRRFVQNCLAICPRQAL 318

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA+ +   HP  G  +Q  + +PA +    + 
Sbjct: 319 HAKTLGFRHPVTGVEMQFDSDIPADLTTLLER 350


>gi|315924170|ref|ZP_07920396.1| ribosomal large subunit pseudouridine synthase D [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315622572|gb|EFV02527.1| ribosomal large subunit pseudouridine synthase D [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 307

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 84/327 (25%), Positives = 145/327 (44%), Gaps = 32/327 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++  V  +E+NMRLD       P+++   L++++  G ++VD    K   R+++ +
Sbjct: 1   MNQKEHY-VHEEEKNMRLDVLCAQICPNLSRQYLKELIVDGDIQVDFANKKPAYRLKADE 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I                +   V      + +   ++YED  + V NKP+G+ V   S
Sbjct: 60  RIVIK---------------IPDPVPCQVMPESIDLDIVYEDGDVIVVNKPSGMVVHPAS 104

Query: 124 GI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  +    D  G     +P + HR+D++TSGILVVA+   A +HL       
Sbjct: 105 GTQSGTLVNALMAHTKDLSGINGVNRPGIVHRIDKDTSGILVVAKNDLAHRHLARQLAEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G        +    + +  +    + VV    +    A++HF+VI+   
Sbjct: 165 SMVRQYVALVKGNIVENSGTVDMP-VGRHPVDRVRMAVV----ENGKSAVTHFEVIERLG 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F ++  +  TGRTHQ+RVH   +G PI GD  Y  +    F +   +   LHAR +  
Sbjct: 220 D-FTYVAFRLETGRTHQIRVHMQAIGHPIAGDPVYGGDKHLPFKT---DGQLLHARELGF 275

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP     ++  A LP    K  + L 
Sbjct: 276 IHPRTKAFMRFEASLPEIFQKVLNQLR 302


>gi|313667509|ref|YP_004047793.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           lactamica ST-640]
 gi|313004971|emb|CBN86399.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           lactamica 020-06]
          Length = 330

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 156/322 (48%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIAVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRAAEKEMPSERRAAVPAREFD---------IVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V ++      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVRLPLFKYTGAQGEKMVRVSED---GQAAHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A LP  + +
Sbjct: 298 LNHPLTGEPLVLKAELPPDLAQ 319


>gi|15837541|ref|NP_298229.1| ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa 9a5c]
 gi|34395837|sp|Q9PET9|RLUD_XYLFA RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|9105864|gb|AAF83749.1|AE003933_1 ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa 9a5c]
          Length = 331

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 88/342 (25%), Positives = 152/342 (44%), Gaps = 42/342 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V +     R D      +P  +   L + ++SG V ++   V+  + +  G+VVR+
Sbjct: 14  RQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVRPRDPVYGGEVVRL 73

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             V +     + +   LD               +LYED  ++V NKPAG+ V  G+G   
Sbjct: 74  QVVPDIRTDAVPQDIPLD---------------ILYEDEHVFVLNKPAGLVVHPGAG--- 115

Query: 128 HIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + DG L + +  +        +  + HRLD++TSG++VVART  A   L E    R++ +
Sbjct: 116 NPDGTLVNALLHRDPALAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSSRQVHR 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V  +         N  +++       + V          A++H+++ + F +   
Sbjct: 176 QYLAVV--VSALVSGGTVNAAIERHPRDRLRMAV----SDTGKEAVTHYRLRERF-RAHT 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNKLYLHAR 293
            LE +  TGRTHQ+RVH  H+  PIVGD  Y  + K                 +  LHA 
Sbjct: 229 ALECRLDTGRTHQIRVHMAHLRHPIVGDRLYGGSLKLPKVGTDALVVMLRGFKRQALHAE 288

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            ++  HP G   ++I AP+P  + +    L  + D  L+ +R
Sbjct: 289 VLEFLHPVGALPVRIVAPVPEDLCQLLAVL--REDSALFFER 328


>gi|15832711|ref|NP_311484.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str.
           Sakai]
 gi|168752065|ref|ZP_02777087.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4113]
 gi|168758664|ref|ZP_02783671.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4401]
 gi|168762387|ref|ZP_02787394.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4501]
 gi|168771700|ref|ZP_02796707.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4486]
 gi|168773478|ref|ZP_02798485.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4196]
 gi|168778572|ref|ZP_02803579.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4076]
 gi|168789497|ref|ZP_02814504.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC869]
 gi|168801712|ref|ZP_02826719.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC508]
 gi|195940189|ref|ZP_03085571.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str.
           EC4024]
 gi|208808732|ref|ZP_03251069.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4206]
 gi|208812778|ref|ZP_03254107.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4045]
 gi|208821085|ref|ZP_03261405.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4042]
 gi|209396635|ref|YP_002272067.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4115]
 gi|217326855|ref|ZP_03442938.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. TW14588]
 gi|254794542|ref|YP_003079379.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str.
           TW14359]
 gi|261227479|ref|ZP_05941760.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261255673|ref|ZP_05948206.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291283867|ref|YP_003500685.1| Ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O55:H7 str. CB9615]
 gi|34395799|sp|Q8X9F0|RLUD_ECO57 RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|13362928|dbj|BAB36880.1| suppressor of ftsH mutation [Escherichia coli O157:H7 str. Sakai]
 gi|187770638|gb|EDU34482.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4196]
 gi|188014009|gb|EDU52131.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4113]
 gi|189003176|gb|EDU72162.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4076]
 gi|189354550|gb|EDU72969.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4401]
 gi|189359603|gb|EDU78022.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4486]
 gi|189367297|gb|EDU85713.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4501]
 gi|189370886|gb|EDU89302.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC869]
 gi|189376176|gb|EDU94592.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC508]
 gi|208728533|gb|EDZ78134.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4206]
 gi|208734055|gb|EDZ82742.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4045]
 gi|208741208|gb|EDZ88890.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4042]
 gi|209158035|gb|ACI35468.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. EC4115]
 gi|209762678|gb|ACI79651.1| suppressor of ftsH mutation [Escherichia coli]
 gi|209762680|gb|ACI79652.1| suppressor of ftsH mutation [Escherichia coli]
 gi|209762682|gb|ACI79653.1| suppressor of ftsH mutation [Escherichia coli]
 gi|209762684|gb|ACI79654.1| suppressor of ftsH mutation [Escherichia coli]
 gi|209762686|gb|ACI79655.1| suppressor of ftsH mutation [Escherichia coli]
 gi|217319222|gb|EEC27647.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O157:H7 str. TW14588]
 gi|254593942|gb|ACT73303.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           TW14359]
 gi|290763740|gb|ADD57701.1| Ribosomal large subunit pseudouridine synthase D [Escherichia coli
           O55:H7 str. CB9615]
 gi|320640778|gb|EFX10276.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str.
           G5101]
 gi|320646123|gb|EFX15068.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H- str.
           493-89]
 gi|320651420|gb|EFX19821.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H- str. H
           2687]
 gi|320657025|gb|EFX24848.1| 23S rRNA pseudouridine synthase D [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320662689|gb|EFX30033.1| 23S rRNA pseudouridine synthase D [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|320667506|gb|EFX34430.1| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 326

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|114331227|ref|YP_747449.1| pseudouridine synthase, RluA family protein [Nitrosomonas eutropha
           C91]
 gi|114308241|gb|ABI59484.1| ribosomal large subunit pseudouridine synthase D [Nitrosomonas
           eutropha C91]
          Length = 342

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 78/324 (24%), Positives = 144/324 (44%), Gaps = 30/324 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             +  ++  ++   +RLD+      P  +   LQ+ +   +V VD        +I  G++
Sbjct: 28  EDIIELIAPDNLAGLRLDQVLAQLLPQWSRSRLQRWIGEDRVSVDGSAGSTRQKIWGGEI 87

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +   +   +               +  ++ +   ++YED  + V +KPAG+ V  G+G
Sbjct: 88  IHVTAGLVESDQ--------------SHQAEAIPLSIIYEDDHLIVIDKPAGLVVHPGNG 133

Query: 125 IAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             +  +   L +      Q PR  + HRLD++T+G+LVVA+T  A   L    + R +++
Sbjct: 134 NWHGTLLNALLNHAPQLSQVPRAGIVHRLDKDTTGLLVVAKTIEAQLDLVRQLQQRTVKR 193

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKF 240
            Y++L  G        I    L  + IG   VH  +    K    A +++++++ F    
Sbjct: 194 HYFALALG-------GIEKDGLVDAPIGRHPVHRTRMAVVKNGKPARTYYRILEKFV-AC 245

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDL 297
             L+    TGRTHQ+RVH + +G P+ GD  Y    ++           +  LHAR ++L
Sbjct: 246 TLLQCSLETGRTHQIRVHLMSIGHPLAGDPVYGKISSDPPTADAIVHLPRQALHARQLEL 305

Query: 298 PHPEGGR-LQITAPLPAHMVKTWD 320
            HP  G+ +   + LP  M +   
Sbjct: 306 THPNSGQIMHWESSLPDDMSRLLQ 329


>gi|87123536|ref|ZP_01079387.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9917]
 gi|86169256|gb|EAQ70512.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9917]
          Length = 329

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 89/313 (28%), Positives = 138/313 (44%), Gaps = 28/313 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +   +QK + +G VRV+ K  K    ++ G  V++          
Sbjct: 36  PMRLDRWLVSQRSEQSRARIQKFIDAGFVRVNGKTGKAKTPLRQGDAVQLWMPPPEPLPY 95

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
           +K               + +   +L+ED  + V NKPAG++V    G      ++G L  
Sbjct: 96  LK--------------PEPMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLHH 141

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y ++V G+P
Sbjct: 142 CPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQLQIQKRIASREYLAVVHGVP 201

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           +     I   + +       Y  V   + +   YA +H+ + +  A  +  L  +  TGR
Sbjct: 202 RGDSGTIVGAIGRHPADRKKYAVV---SGENGRYACTHWSLQERLAD-YSLLRFKLDTGR 257

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH  HM  P+VGD  Y    K     P      LHA  + L HP    RL   AP
Sbjct: 258 THQIRVHCAHMNHPVVGDPTYSRCRKLPVELPG---QALHAFQLGLDHPITRERLLFEAP 314

Query: 311 LPAHMVKTWDSLG 323
           LP  M K    L 
Sbjct: 315 LPPVMEKLLAVLR 327


>gi|238765380|ref|ZP_04626304.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           kristensenii ATCC 33638]
 gi|238696422|gb|EEP89215.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           kristensenii ATCC 33638]
          Length = 325

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 83/340 (24%), Positives = 147/340 (43%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V VD K + K   ++  G++V I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I        ++  LD               ++YED+ I V NKP G+ V  G+G     
Sbjct: 70  QIEEDARWAPQEIPLD---------------IVYEDNDILVINKPRGLVVHPGAGNPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++
Sbjct: 115 VLNALLYYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGNM-TAGGRVDEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFIAILRGFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G +++  A LP  MV+  ++L  K D   +  ++  
Sbjct: 288 HPISGIQMEWHAALPEDMVELINAL--KADTEEFKDQMDW 325


>gi|218547883|ref|YP_002381674.1| 23S rRNA pseudouridine synthase D [Escherichia fergusonii ATCC
           35469]
 gi|218355424|emb|CAQ88032.1| 23S rRNA pseudouridine synthase [Escherichia fergusonii ATCC 35469]
 gi|324111235|gb|EGC05217.1| RluA family protein pseudouridine synthase [Escherichia fergusonii
           B253]
          Length = 326

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 82/333 (24%), Positives = 145/333 (43%), Gaps = 41/333 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I   
Sbjct: 11  VSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HI 129
           I        +   LD               ++YED  I V NKP  + V  G+G     +
Sbjct: 71  IEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPDGTV 115

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y ++ 
Sbjct: 116 LNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVA 175

Query: 188 WGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            G         E I+    K++H+    +            A++H+++++ F +    L 
Sbjct: 176 IGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 286 LYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|21232518|ref|NP_638435.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. ATCC 33913]
 gi|66767398|ref|YP_242160.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. 8004]
 gi|34395783|sp|Q8P682|RLUD_XANCP RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|21114309|gb|AAM42359.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. ATCC 33913]
 gi|66572730|gb|AAY48140.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. 8004]
          Length = 331

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 84/347 (24%), Positives = 150/347 (43%), Gaps = 40/347 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L + ++  VV +     R D      +P  +   L + ++SG   +D +  +  + ++ G
Sbjct: 9   LDSSLRQAVVPDSAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGETARPRDTLRGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +                +   +LYED  + V +KPAG+ V  G
Sbjct: 69  ETVQVQVVLETQTHAAPQD---------------IPLNVLYEDDHVLVIDKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +  +        +  + HRLD++TSG++VVART  A   L E    
Sbjct: 114 AG---NPDGTLVNALLFRDPNLAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSA 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + + Y ++V G         A+  + +       + V          A++H+++ + F
Sbjct: 171 RDVHRQYLAVVVGAL--VSGGTADAPIDRHPRDRLKMAVRD----DGRDAVTHYRLRERF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNKL 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y    K    +            + 
Sbjct: 225 -RAHTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDTLVAELRGFKRQ 283

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  ++  HP  G  ++ +AP+P  + +   +L     R   + R
Sbjct: 284 ALHAETLEFLHPVSGEPIRASAPVPEDLQRLMSALREDSARAAELAR 330


>gi|146312715|ref|YP_001177789.1| 23S rRNA pseudouridine synthase D [Enterobacter sp. 638]
 gi|145319591|gb|ABP61738.1| ribosomal large subunit pseudouridine synthase D [Enterobacter sp.
           638]
          Length = 326

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 81/336 (24%), Positives = 150/336 (44%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K       ++  G+VV I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVMVNGKVWDTPKEKVLGGEVVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I+                     +  +   ++YED  I V NKP G+ V  G+G   
Sbjct: 68  NAEIDEEVRF---------------EAQDIPLTIVYEDDDILVINKPRGLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPITDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        +E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTSGGTVEEPISRHPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RIHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMSHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  +++   ++ 
Sbjct: 283 MLRLYHPITGIEMEWHAPIPQDMVELIEAMRADFEE 318


>gi|312875944|ref|ZP_07735934.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311797425|gb|EFR13764.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 300

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 78/318 (24%), Positives = 154/318 (48%), Gaps = 35/318 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD++            +QKI+  G V V++ + +K   +++SG ++++           
Sbjct: 9   RLDKYLSEALSK-TRSFVQKIIEEGNVWVNQTQVLKPAYKVKSGDIIKV----------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW 136
               ++     L+  +  +   ++YED  + V NKP G+ V  G+G   +   +  L  +
Sbjct: 57  ----VIPEPKQLSLVAQDIDIEVVYEDEHLAVINKPCGMVVHPGTGNFENTLVNALLHKF 112

Query: 137 VDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      +P + HRLD++TSG+L+VA+T  A   L+E+ +  +I++IY+++  G+ 
Sbjct: 113 SGRLSSINGVIRPGIVHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVL 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K     I   + +   +    + VV         A+++F+V++ F  K+ +++++  TGR
Sbjct: 173 KEDSGVINAPIGRH-PVNRLKMAVV----PNGKEAVTYFEVLERF-DKYTFIKLRLKTGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P++GD  Y                 LHA  ++  HP   + L  +A 
Sbjct: 227 THQIRVHMSYIGYPLLGDSSYGR----AKNEFGVQGQVLHAGEIEFVHPITSKVLHFSAD 282

Query: 311 LPAHMVKTWDSLGFKYDR 328
           LP + V+  + L  + ++
Sbjct: 283 LPEYFVEILNMLRNRNNK 300


>gi|325496332|gb|EGC94191.1| 23S rRNA pseudouridine synthase D [Escherichia fergusonii ECD227]
          Length = 326

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 82/333 (24%), Positives = 145/333 (43%), Gaps = 41/333 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I   
Sbjct: 11  VSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HI 129
           I        +   LD               ++YED  I V NKP  + V  G+G     +
Sbjct: 71  IEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPDGTV 115

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y ++ 
Sbjct: 116 LNALLYYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVA 175

Query: 188 WGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            G         E I+    K++H+    +            A++H+++++ F +    L 
Sbjct: 176 IGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 286 LYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|192288803|ref|YP_001989408.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           TIE-1]
 gi|192282552|gb|ACE98932.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           TIE-1]
          Length = 334

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 95/343 (27%), Positives = 150/343 (43%), Gaps = 53/343 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           VVV  DE + RLDR      P ++   L+ ++  G+V +    V+        G+ + I 
Sbjct: 11  VVVAGDEGSQRLDRVLAARCPELSRSRLKALILDGRVAIAGTPVRDPAYHASPGETITID 70

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                      E   LD               ++YED+ I V NKP G+ V   +G   H
Sbjct: 71  VPPPVPAEPAGEAIALD---------------IVYEDADIIVLNKPRGLVVHPAAG---H 112

Query: 129 IDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR- 177
             G L + + +            ++P + HRLD++T+G++V A+   A Q L+  F    
Sbjct: 113 ETGTLVNALIAHCGASLSGIGGVRRPGIVHRLDKDTTGLMVAAKNDKAHQSLSAQFADHG 172

Query: 178 ---RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y + VWG+P  K   I   + +  H   + + V     +G   AI+H++V++
Sbjct: 173 RTGELRRGYLAFVWGVPGRKYGTIDAPIDRHPH-AREKMAVR----QGGREAITHWEVLE 227

Query: 235 CFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNF 280
            FA K        +  Q  TGRTHQ+RVH  H+G P++GD  Y  +FK         G  
Sbjct: 228 NFAGKDGKPVAALIACQLETGRTHQIRVHLAHLGHPLLGDDVYGPHFKTKANQLAPAGRA 287

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 +  LHA  + L HP  G  L   +PLPA +     +L
Sbjct: 288 ALAGLGRQALHAYLLTLEHPSTGEVLTWESPLPADLAHLQAAL 330


>gi|238785831|ref|ZP_04629800.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           bercovieri ATCC 43970]
 gi|238713244|gb|EEQ05287.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           bercovieri ATCC 43970]
          Length = 325

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 142/328 (43%), Gaps = 35/328 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V VD K + K   ++  G++V I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVTIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I        ++  LD               ++YEDS I V NKP G+ V  G+G     
Sbjct: 70  QIEEDARWAPQEIPLD---------------IVYEDSDILVINKPRGLVVHPGAGNPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++
Sbjct: 115 VLNALLYYYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGNM-TAGGRVDEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFITILRGFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           HP  G +++  A LP  MV+  ++L   
Sbjct: 288 HPISGIQMEWHAALPEDMVELINALKAD 315


>gi|295677198|ref|YP_003605722.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1002]
 gi|295437041|gb|ADG16211.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1002]
          Length = 349

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 99/327 (30%), Positives = 159/327 (48%), Gaps = 24/327 (7%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +
Sbjct: 23  EQVSLIEIDDRSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDL 82

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP+  A +          +              +L+ED  + V +KPAG++V GGSG
Sbjct: 83  VRVPPIRVAQS----------NQAAAHVPVPAAGFQILFEDEHLLVIDKPAGVAVHGGSG 132

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +A+ +   ++       +   L HRLD+ETSGIL++A+ RAA  +L E  R  R+ K Y+
Sbjct: 133 VAFGVIEQMREARPQ-AKFLELVHRLDRETSGILMLAKKRAALVNLHEQIRDNRMDKRYY 191

Query: 185 SLVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           + V G   +       +   L K     G+    V+ +      + + F ++D +   + 
Sbjct: 192 ACVHGEWASDWGRRRAVKEPLHKYLTSDGERRVRVQTD---GLASHTIFNLVDRWPD-YA 247

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMD 296
            LE +  TGRTHQ+RVH  H+G PIVGD KY               P   +++LHA  + 
Sbjct: 248 LLEAELKTGRTHQIRVHLQHLGLPIVGDAKYGDFALNKALARANAKPGIKRMFLHAYRLK 307

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
           L HP  G  LQ+ APLPA      + L
Sbjct: 308 LTHPATGAPLQLEAPLPADCRGFIEQL 334


>gi|307127518|ref|YP_003879549.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae 670-6B]
 gi|306484580|gb|ADM91449.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae 670-6B]
          Length = 295

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 145/319 (45%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV      
Sbjct: 3   IKIETGGLRLDKALSD-LSELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVT----- 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
               + + E ++L+        ++ L   ++Y+D  + V NKP G+ V   +G      +
Sbjct: 57  ----YHVPEPEVLE------YVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEASIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G  + GD  Y         +   +  +LHA+ +   HP  G+ 
Sbjct: 221 QLETGRTHQIRVHMAYIGHSVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGKT 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+  A +P    +T + L 
Sbjct: 276 LEFKADIPEIFKETLERLR 294


>gi|268317176|ref|YP_003290895.1| pseudouridine synthase, RluA family [Rhodothermus marinus DSM 4252]
 gi|262334710|gb|ACY48507.1| pseudouridine synthase, RluA family [Rhodothermus marinus DSM 4252]
          Length = 355

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 87/370 (23%), Positives = 143/370 (38%), Gaps = 66/370 (17%)

Query: 1   MSLMTYVQYVVVENDE-ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNR 58
           M L      + V     E  RLD +        +   +Q+ +R G+V V+   V K    
Sbjct: 1   MELQEVCIQLEVPPGYREGGRLDAYLARFLAQASRTKIQRGIREGRVTVNGVVVQKPAYT 60

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +Q G V+ +  +      I+ E   LD               ++YED  + V NK AG+ 
Sbjct: 61  VQPGDVITLRILRPPPVEIVPEPIPLD---------------IVYEDPYLIVVNKQAGLV 105

Query: 119 VQGGSGIAY-HIDGFLKSWVDS-------------------------------KGQKPRL 146
           V    G     +   L  ++ S                               +  +P +
Sbjct: 106 VHPARGNRSGTLVNALLYYIGSGPVRFDEEDDLPEDDEIGLSMVSTGPTEAKLEAPRPGI 165

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G++VVA+       L   F  R I + Y ++VWG+P   +  I   + +  
Sbjct: 166 VHRLDKDTTGLIVVAKDDVTHTGLARQFEHRTIARTYLAIVWGVPDPPRGRIEAAIGRDP 225

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               D   +    +     A++H++V++        +  +  TGRTHQ+RVHA H+G P+
Sbjct: 226 ---RDRQRMAVVPDDRGKRAVTHYEVVEALP-AAALVRFKLETGRTHQIRVHARHIGHPV 281

Query: 267 VGDHKYCAN---------FKGNFTSPI---QNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +GD  Y             +  F   +     +  LHA  +   HP  G  L+  APLP 
Sbjct: 282 LGDPTYGGRTIRYGPHTPRRRAFYDQLFARLTRQALHAHTLGFRHPRTGEWLEFEAPLPE 341

Query: 314 HMVKTWDSLG 323
            M    + L 
Sbjct: 342 DMACALEQLR 351


>gi|238791395|ref|ZP_04635034.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           intermedia ATCC 29909]
 gi|238729528|gb|EEQ21043.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           intermedia ATCC 29909]
          Length = 325

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 84/340 (24%), Positives = 146/340 (42%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V VD K + K   ++  G++V I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I        +   LD               ++YED+ I V NKP G+ V  G+G     
Sbjct: 70  QIEEDARWAPQDIPLD---------------IVYEDNDILVINKPRGLVVHPGAGNPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           I   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++
Sbjct: 115 ILNALLYYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGNM-TAGGRVDEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFISILRGFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G +++  A LP  MV+  ++L  K D   +  ++  
Sbjct: 288 HPISGIQMEWHAALPEDMVELINAL--KADTEEFKDQMDW 325


>gi|312135180|ref|YP_004002518.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           owensensis OL]
 gi|311775231|gb|ADQ04718.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           owensensis OL]
          Length = 300

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 79/318 (24%), Positives = 155/318 (48%), Gaps = 35/318 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLDR+            +QKI+  G V V++ +V K   ++++G ++++           
Sbjct: 9   RLDRYLSEALSK-TRSFIQKIIEEGNVWVNQTQVFKPAYKVRNGDIIKV----------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW 136
               ++     L+  +  +   ++YED  + V NKP G+ V  G+G   +   +  L  +
Sbjct: 57  ----VIPEPKQLSLVAQDIDIDVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKF 112

Query: 137 VDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      +P + HRLD++TSG+LVVA+T  A   L+E+ +  +I++IY+++  G+ 
Sbjct: 113 SGRLSSINGVIRPGIVHRLDKDTSGLLVVAKTDEAHIKLSEALKSHQIKRIYYAICEGVL 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K     +   + +   +    + VV         A+++F+V++ F  K+ +++++  TGR
Sbjct: 173 KEDSGVVDAPIGRH-PVNRLKMAVV----PNGKEAVTYFEVLERF-DKYTFVKLRLKTGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P++GD+ Y                 LHA  ++  HP   + L  +A 
Sbjct: 227 THQIRVHMSYIGYPLLGDNTYGR----AKNEFGVQGQVLHAGEIEFVHPITSKVLHFSAD 282

Query: 311 LPAHMVKTWDSLGFKYDR 328
           LP + V+  + L  + ++
Sbjct: 283 LPEYFVEILNMLRNRNNK 300


>gi|126666670|ref|ZP_01737647.1| Pseudouridylate synthases, 23S RNA-specific [Marinobacter sp.
           ELB17]
 gi|126628715|gb|EAZ99335.1| Pseudouridylate synthases, 23S RNA-specific [Marinobacter sp.
           ELB17]
          Length = 325

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 81/339 (23%), Positives = 146/339 (43%), Gaps = 41/339 (12%)

Query: 1   MSLMTYVQ-YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS    +    V+     + RLD+      P  +   LQ  ++SG + V+  + K  +++
Sbjct: 1   MSAENRIIASFVIPPKLSDKRLDQAAAELMPEHSRSRLQSWVKSGALTVNGGQCKPRDKV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  + +                 +    +T  ++ +   ++YED  I + NKPAG+ V
Sbjct: 61  MLGDKLELD---------------AEPEAQVTWQAEAITLDIVYEDEHILIINKPAGLVV 105

Query: 120 QGGSGIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              +G   H DG L + + +         +  + HRLD++TSG++VVAR+  A   L   
Sbjct: 106 HPAAG---HADGTLVNAILNIAPEVENLPRAGIVHRLDKDTSGVMVVARSLIAHTSLVNQ 162

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + R + + Y ++V G          +  + +       + VV    K    A++H++VI
Sbjct: 163 LQTRTMGREYEAVVVGTLT--GGATVDAPIGRHPTERKRMAVV----KSGKPAVTHYRVI 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------- 285
           + F+     +  +  +GRTHQ+RVH  H+  P+VGD  Y    +    +  +        
Sbjct: 217 ERFS-AHTHVRCKLESGRTHQIRVHLTHVKHPLVGDPVYGGRLRLPKGTTEELREVLSGF 275

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           ++  LHAR + L HP+ G  +    PLP        +L 
Sbjct: 276 HRQALHARQLTLEHPQTGETMSWDVPLPEDFQLLLAALR 314


>gi|309379094|emb|CBX22225.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 330

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 96/327 (29%), Positives = 156/327 (47%), Gaps = 24/327 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIAVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPAREFD---------IVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  +      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVRLPLFKYTGAQGEKMVRVSGD---GQAAHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
           L HP  G  L + A LP  + +    L
Sbjct: 298 LNHPLTGEPLALKAELPPDLAQFAAML 324


>gi|71907635|ref|YP_285222.1| ribosomal large subunit pseudouridine synthase C [Dechloromonas
           aromatica RCB]
 gi|71847256|gb|AAZ46752.1| ribosomal large subunit pseudouridine synthase C [Dechloromonas
           aromatica RCB]
          Length = 334

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 103/337 (30%), Positives = 156/337 (46%), Gaps = 18/337 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V +V V  +E   RLD +       +   ++ +ILRSG+VRV+ KRV    R+  G  
Sbjct: 7   NSVTHVEVGEEELGQRLDNFLIRRCKGVPKSHIYRILRSGEVRVNSKRVDATYRLCVGDN 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RIPP+  A     +  +     V+L          ++YED  + + +KP GI+V GGSG
Sbjct: 67  IRIPPIRIAERPQNEVDEAAKERVDLP---------IIYEDEAMLIIDKPEGIAVHGGSG 117

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--RIQKI 182
           +++ +   L+       +   L HRLD+ETSG+L+V + R A   L + FR       K 
Sbjct: 118 VSFGVIEALRRQRPQ-AKFLELAHRLDRETSGVLLVGKKRLALTALHDMFREHGAGADKR 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  LV G   N  + +   L K    GG+    V   +     + + F+++  + +    
Sbjct: 177 YLVLVKGRWMNNTQHVKLPLHKYLTEGGERRVSV---DAQGKASHTVFRLLARWPE-ASL 232

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPE 301
           LE Q  TGRTHQ+RVH  H+G PI+GD KY               ++ LHA  M   HP 
Sbjct: 233 LEAQLKTGRTHQIRVHLAHLGFPILGDEKYGDFALNKALKRDGLKRMALHAWRMVFQHPL 292

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
               L+  APLP  +     +L  +  R    + L S
Sbjct: 293 TAVPLECIAPLPEGVGNYIAALDGQSPREFSAENLES 329


>gi|313114073|ref|ZP_07799625.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310623482|gb|EFQ06885.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 310

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 73/324 (22%), Positives = 139/324 (42%), Gaps = 29/324 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  VVE +    R+DR+       ++   LQ ++  G V  + + V  + ++++G  + +
Sbjct: 4   REFVVEQETAGQRIDRFLSGEDTGLSRSALQALVADGHVLCNGRLVAKSLKLKAGDTIVL 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           +  +  +      +   ++YED  + V NKP G+ V    G   
Sbjct: 64  E---------------IPDAKPIEAVPQDIPLEIVYEDEHLLVVNKPKGMVVHPAPGNPD 108

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++  L     S        +P + HR+D++TSG+LVVA+  A    L++   +  ++
Sbjct: 109 GTLVNALLWHCKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVE 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V+G     +  + + L + S      + V   +E    YA + ++V++     F
Sbjct: 169 RAYRTIVYGGFAQDEGFVESNLGR-SKTDRKKMAVYPASEPHTKYAYTGYQVLERL-NNF 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE +  TGRTHQ+RVH   +  P+ GD  Y      +      +   LHA+ +   HP
Sbjct: 227 TMLECRLKTGRTHQIRVHMASIQHPVAGDPVYGP----HNCITSLHGQCLHAKTLGFVHP 282

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  L+  + LP +      +L 
Sbjct: 283 ITGEHLRFDSELPEYFTHFLATLR 306


>gi|309389006|gb|ADO76886.1| ribosomal large subunit pseudouridine synthase D [Halanaerobium
           praevalens DSM 2228]
          Length = 303

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 85/321 (26%), Positives = 158/321 (49%), Gaps = 33/321 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  ++  R+D++   ++  ++   +QK+++  +++V+ + +  + +I +   + +  
Sbjct: 6   LTVKKKDQGQRIDKYLAKYFKDLSRSFIQKLIKEKEIKVNNRVIDKSYKIINNDFIELK- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                   +KEQ+    +V        +K  ++YED  I V NK A   V    G     
Sbjct: 65  --------LKEQESKVKAV-------AMKLDIVYEDQDIIVINKDADRVVHPAPGHYNDT 109

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           I   L + VD+       ++P + HRLD++TSG+L+VA+   + + L + F+ R + K Y
Sbjct: 110 IVNGLLACVDNLSAINGIKRPGIVHRLDKDTSGLLIVAKNDKSHKSLAKQFKARTVDKYY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++L+ G    KK  I   + +  +     + V K++ K    AIS FK+I+ F   +  +
Sbjct: 170 FALIEGNLAYKKGKIEAPIGRDPNH-RKKMAVRKRHSKN---AISRFKIIEEF-NHYTLV 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
           E++  TGRTHQ+RVH  ++G PIVGD KY +    N       +  LHA+ + + HP   
Sbjct: 225 EVKIETGRTHQIRVHFSYLGHPIVGDQKYGSKNNLNV-----KRQLLHAKKLFIKHPISQ 279

Query: 303 GRLQITAPLPAHMVKTWDSLG 323
            +++  A L     K    L 
Sbjct: 280 QKMKFEAELKDDFQKVLTKLR 300


>gi|240949469|ref|ZP_04753809.1| 23S rRNA pseudouridine synthase D [Actinobacillus minor NM305]
 gi|240296042|gb|EER46703.1| 23S rRNA pseudouridine synthase D [Actinobacillus minor NM305]
          Length = 325

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 81/347 (23%), Positives = 148/347 (42%), Gaps = 39/347 (11%)

Query: 4   MTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           MT    +   V  D    RLD+     +P  +   L+  + + QV V+ K V K   ++ 
Sbjct: 1   MTQQITLTAEVSADLLGARLDQALAQLFPDYSRSRLKVWIENDQVWVNGKIVNKAREKVF 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+++ +   +                         +   ++YED  I V NKP  + V 
Sbjct: 61  GGELIEVQAEVEEEVRF---------------EPQNIPLNIVYEDDDIIVINKPKDLVVH 105

Query: 121 GGSGIAYHI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+G       +  L  +   ++  +  + HRLD++T+G++VVA+   A  HL  + + R
Sbjct: 106 PGAGNPDGTVLNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKNIPAQTHLVTALQKR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I + Y ++  GI   +   +   + +                     A++H+++++ F 
Sbjct: 166 HITREYEAIASGIM-TQGGKVDEPMARHPT-----KRTAMAVHPMGKPAVTHYRIMERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLY 289
           + +  L ++  TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  
Sbjct: 219 RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQLYGGRPRPPKGASEEFLSVLRGFQRQA 278

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
           LHA  + L HP  G  ++  APLP   V+  ++L  K D  LY  +L
Sbjct: 279 LHATMLRLEHPITGELMEWHAPLPDDFVELVEAL--KADYELYKDQL 323


>gi|154492071|ref|ZP_02031697.1| hypothetical protein PARMER_01702 [Parabacteroides merdae ATCC
           43184]
 gi|154087857|gb|EDN86902.1| hypothetical protein PARMER_01702 [Parabacteroides merdae ATCC
           43184]
          Length = 359

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 78/332 (23%), Positives = 136/332 (40%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V +  +  +R+D++  +         +Q    +G +  + K VK N R++   VV I  
Sbjct: 35  FVADRGQSLLRVDKFLVDRMFGATRNRIQSAADAGCIMANGKPVKSNYRVKPEDVVTIMM 94

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYH 128
                                    + +   ++YED  + V +KPAG+ V  G G     
Sbjct: 95  TR--------------PPRTFEILPENIPIKIVYEDDDLLVVDKPAGLVVHPGHGNYTGT 140

Query: 129 IDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   L  ++      D       L HR+D++TSG+LVVA+   A  HL+  F  +  ++ 
Sbjct: 141 LVNALAWYLKDDPTYDPNDPALGLVHRIDKDTSGLLVVAKKPEAKAHLSMQFFHKTTKRE 200

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI +  +  I   + +           V         A++H+ V++        
Sbjct: 201 YRALVWGIVREDEGRIEGNIGRNPR--DRMQMTVFPEGDQGKTAVTHYSVLERLG-YVTL 257

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           ++ +  TGRTHQ+RVH  ++G  +  D +Y  N   KG  +S  +           +  L
Sbjct: 258 VKCRLETGRTHQIRVHMKYIGHTLFNDERYGGNEILKGTTSSKYKQFVDNCFAICPRQAL 317

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA+ +   HP  G  +   + +PA M    D 
Sbjct: 318 HAKTLGFVHPTTGEEMFFDSEIPADMTALIDK 349


>gi|283786206|ref|YP_003366071.1| ribosomal large subunit pseudouridine synthase D [Citrobacter
           rodentium ICC168]
 gi|282949660|emb|CBG89279.1| ribosomal large subunit pseudouridine synthase D [Citrobacter
           rodentium ICC168]
          Length = 326

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 81/336 (24%), Positives = 148/336 (44%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+VV I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDRRVLVNDKICDKPKEKVLGGEVVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I+                 +      +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  DAEIDE---------------EIRFEPQDIPLDIVYEDDDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  D++   ++ 
Sbjct: 283 MLRLYHPVSGIEMEWHAPIPQDMVELIDAMRADFEE 318


>gi|149377766|ref|ZP_01895499.1| Pseudouridylate synthase, 23S RNA-specific [Marinobacter algicola
           DG893]
 gi|149357938|gb|EDM46427.1| Pseudouridylate synthase, 23S RNA-specific [Marinobacter algicola
           DG893]
          Length = 325

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 82/343 (23%), Positives = 150/343 (43%), Gaps = 46/343 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  +  + RLD+      P  +   LQ  ++SG + V+ K  K  +++  G  + +    
Sbjct: 13  VPPEHSDRRLDQAAAELMPEHSRSRLQGWIKSGALTVNGKSCKPRDKVMLGDRLELD--- 69

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                        +    ++  ++ +   ++YED  + V NKPAG+ V   +G   H DG
Sbjct: 70  ------------AEPEAQVSWEAESIDLDIVYEDEHLLVINKPAGLVVHPAAG---HADG 114

Query: 132 FLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L + + +         +  + HRLD++TSGI+VVAR+  A   L +  + R + + Y +
Sbjct: 115 TLVNALLNHAPEVENLPRAGIVHRLDKDTSGIMVVARSLIAHTSLVDQLQTRTMGREYEA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G          +  + +       + VV         A++H+++++ FA     +  
Sbjct: 175 IVVGTLT--GGSTVDAPIGRHPRERKKMAVV----PTGKPAVTHYRLVERFA-AHTHVRC 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDL 297
           +  +GRTHQ+RVH  H+  P+VGD +Y    +    +  +         +  LHAR + L
Sbjct: 228 KLESGRTHQIRVHMAHVKHPLVGDPQYGGRLRLPKGTTDELREVLASFQRQALHARQLTL 287

Query: 298 PHPEGGRL-QITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQD 339
            HP+ G +     PLP  +     +L        ++K L S D
Sbjct: 288 EHPQTGEILTWEVPLPDDIEGLLAALR------KHVKELESHD 324


>gi|238790742|ref|ZP_04634503.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           frederiksenii ATCC 33641]
 gi|238721183|gb|EEQ12862.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           frederiksenii ATCC 33641]
          Length = 325

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 83/340 (24%), Positives = 147/340 (43%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V VD K++ K   ++  G++V I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVTVDGKKINKPKEKVLGGELVAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I        +   LD               ++YED+ I V NKP G+ V  G+G     
Sbjct: 70  QIEEDARWAPQDIPLD---------------IVYEDNDILVINKPRGLVVHPGAGNPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++
Sbjct: 115 VLNALLHYYPKIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGNM-TAGGRVDEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFISILRGFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G +++  A LP  MV+  ++L  K D   +  ++  
Sbjct: 288 HPISGIQMEWHAALPEDMVELINAL--KADTEEFKDQMDW 325


>gi|77461057|ref|YP_350564.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens Pf0-1]
 gi|77385060|gb|ABA76573.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens Pf0-1]
          Length = 320

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 87/344 (25%), Positives = 154/344 (44%), Gaps = 37/344 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    ++   V ++    RLD+     +   +   L   ++ G++ VD   ++  + + 
Sbjct: 1   MSDKIELR-AEVPSELGGQRLDQVAAQLFAEHSRSRLSAWIKEGRLTVDGAVIRPRDIVH 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G ++ +     A    + +   LD               ++YED  I V NKPAG+ V 
Sbjct: 60  GGAILELTAEQEAQGEWVAQDIELD---------------IVYEDDDILVINKPAGLVVH 104

Query: 121 GGSGIAYHI--DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +G A     +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R
Sbjct: 105 PAAGHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTKLVAQLQSR 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + +IY  +V G+     +   N  + +       + V+    +G   A+SH++V++ F 
Sbjct: 165 SVSRIYECIVIGVVTAGGKI--NAPIGRHGQQRQRMAVM----EGGKPAVSHYRVLERF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLY 289
           +    + ++  TGRTHQ+RVH  H+  P+VGD  Y   F+    +            +  
Sbjct: 218 RSHTHVRVKLETGRTHQIRVHMAHINFPLVGDPAYGGRFRIPPAASQTMVESLKHFPRQA 277

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           LHAR+++L HP  G R+   +PLP  +V     L  K DR  ++
Sbjct: 278 LHARFLELDHPTTGERMSWESPLPEDLVWLLTLL--KQDREAFV 319


>gi|238752927|ref|ZP_04614389.1| Ribosomal large subunit pseudouridine synthase D [Yersinia rohdei
           ATCC 43380]
 gi|238708835|gb|EEQ01091.1| Ribosomal large subunit pseudouridine synthase D [Yersinia rohdei
           ATCC 43380]
          Length = 325

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 83/340 (24%), Positives = 147/340 (43%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   ++  +   +V VD K++ K   ++  G++V I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKDWILDDKVTVDGKKINKPKEKVLGGELVAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I        ++  LD               ++YED+ I V NKP G+ V  G+G     
Sbjct: 70  QIEEDARWAPQEIPLD---------------IVYEDNDILVINKPRGLVVHPGAGNPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++
Sbjct: 115 VLNALLYYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGNM-TAGGRVDEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFISILRGFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G +++  A LP  MV+  ++L  K D   +  ++  
Sbjct: 288 HPISGIQMEWHAALPEDMVELINAL--KADTEEFKDQMDW 325


>gi|254780610|ref|YP_003065023.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Candidatus Liberibacter asiaticus str. psy62]
 gi|254040287|gb|ACT57083.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Candidatus Liberibacter asiaticus str. psy62]
          Length = 340

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 87/350 (24%), Positives = 150/350 (42%), Gaps = 47/350 (13%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           + ++  ++ +     R+DRW         +   ++ ++ +G + ++    K  N ++  G
Sbjct: 9   SSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
               I                + ++  L    + +   +LYED  I V NKPAG+ V   
Sbjct: 69  DSFLIT---------------VPAAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPA 113

Query: 123 SG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            G         + YH    L S   +  ++P + HRLD++T+G++VVA+   A Q L+E 
Sbjct: 114 PGNWTGTLVNALLYHCHNNLSSI--NGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQ 171

Query: 174 FRMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           F       R+++ Y+++VWGIP      I   L +          V   ++K A+ AI+H
Sbjct: 172 FVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGR-CKSNRLRRAVKGIDDKTADSAITH 230

Query: 230 FKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           ++ I+ + +        L+    TGRTHQ+RVH  H G P++GD  Y   FK        
Sbjct: 231 YQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNN 290

Query: 286 N---------KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           N         +  LHA  +   HP   + +    P+P  M+     L  K
Sbjct: 291 NAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTVIRKLNEK 340


>gi|319763867|ref|YP_004127804.1| pseudouridine synthase, rlua family [Alicycliphilus denitrificans
           BC]
 gi|330823869|ref|YP_004387172.1| RluA family pseudouridine synthase [Alicycliphilus denitrificans
           K601]
 gi|317118428|gb|ADV00917.1| pseudouridine synthase, RluA family [Alicycliphilus denitrificans
           BC]
 gi|329309241|gb|AEB83656.1| pseudouridine synthase, RluA family [Alicycliphilus denitrificans
           K601]
          Length = 339

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 100/322 (31%), Positives = 156/322 (48%), Gaps = 21/322 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V+ +    RLD +   H   +   ++ +I+RSG+VR++K R   + R+ +G  VR+
Sbjct: 22  RIVEVDAESAGQRLDNFLIRHLKGVPKTHVYRIIRSGEVRLNKGRTSADARVAAGDRVRL 81

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PPV  +        K+ D +       +F    +L ED  +   +KPAG++V GGSG+++
Sbjct: 82  PPVRVS-------DKVQDKAERPAPAREF---PILLEDEHLIALDKPAGVAVHGGSGVSF 131

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L+     + +   L HRLD+ETSGIL+VA+ R+A +HL + FR R   K Y +LV
Sbjct: 132 GVIEQLRQARQ-EARFLELVHRLDRETSGILLVAKRRSALKHLQDQFRERETGKTYLALV 190

Query: 188 WGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
            G     K+ I   L K     G+  V V    +     +I+  KV      +       
Sbjct: 191 PGAWPANKKVIDLPLHKYLQEDGERRVRVTTPQDSDGMRSITLVKVHSHLPARPLQGLPA 250

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLP 298
              LE+   TGRTHQ+RVH    G PI GD KY   +           +++LHA  +   
Sbjct: 251 MSLLEVTIKTGRTHQIRVHLASQGHPIAGDDKYGDFDLNRRLQKQGLRRMFLHAWRLQFD 310

Query: 299 HP-EGGRLQITAPLPAHMVKTW 319
           HP  G R+++ A LP  +    
Sbjct: 311 HPASGERMELRAELPPELAAFL 332


>gi|238854437|ref|ZP_04644777.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 269-3]
 gi|260664477|ref|ZP_05865329.1| pseudouridylate synthase [Lactobacillus jensenii SJ-7A-US]
 gi|282932582|ref|ZP_06338003.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 208-1]
 gi|313472076|ref|ZP_07812568.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 1153]
 gi|238832930|gb|EEQ25227.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 269-3]
 gi|239530107|gb|EEQ69108.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 1153]
 gi|260561542|gb|EEX27514.1| pseudouridylate synthase [Lactobacillus jensenii SJ-7A-US]
 gi|281303278|gb|EFA95459.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii 208-1]
          Length = 301

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 137/311 (44%), Gaps = 34/311 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++   H   ++   +Q++L SG + V+ K+ K + ++  G  + +            
Sbjct: 14  RLDKYISEH-SDLSRSRVQELLTSGDILVNSKQEKPSYKVAIGDKISVH----------- 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKS-- 135
               +   V L    + +   ++YED+ + V NKP G+ V   +G   H   +  +    
Sbjct: 62  ----VPKLVPLNVEPEDIPLDIVYEDNDVIVVNKPQGMVVHPSAGHPNHTLVNALMNHTK 117

Query: 136 --WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 +G +P + HR+D++TSG+L++A+   A + L      +  +++Y ++V G  K 
Sbjct: 118 ELAASPEGFRPGIVHRIDKDTSGLLMIAKNTQARESLESQLAHKTNKRVYLAIVHGNFKE 177

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               I   + +          V     +    A++HFKV++ +   +  +  Q  TGRTH
Sbjct: 178 ASGTIDAPIARNPKERKKMAVV-----ESGKAAVTHFKVLEQYP-NYALVSCQLETGRTH 231

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Q+RVH  ++G P+ GD  Y         +   +  +LHA+ +    P+ G+ L+     P
Sbjct: 232 QIRVHMKYIGHPLAGDPLYGPK-----KTLKGHGQFLHAKILGFKQPKTGQWLEFQVEPP 286

Query: 313 AHMVKTWDSLG 323
               K    L 
Sbjct: 287 EIFQKKLTYLR 297


>gi|146296933|ref|YP_001180704.1| RluA family pseudouridine synthase [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145410509|gb|ABP67513.1| ribosomal large subunit pseudouridine synthase D
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 300

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 79/318 (24%), Positives = 154/318 (48%), Gaps = 35/318 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD++            +QKI+  G V V++ +V K   +++SG ++++           
Sbjct: 9   RLDKYLSEALSK-TRSFVQKIIEEGNVWVNQSQVLKPAYKVKSGDIIKV----------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW 136
               ++     L+  +  +   ++YED  + V NKP G+ V  G+G   +   +  L  +
Sbjct: 57  ----VIPEPKQLSLVAQDIDIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKF 112

Query: 137 VDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      +P + HRLD++TSG+L+VA+T  A   L+E+ +  +I++IY+++  G+ 
Sbjct: 113 SGRLSSINGVIRPGIVHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVL 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K     I   + +   +    + VV         A+++F+V++ F  K+ +++++  TGR
Sbjct: 173 KEDSGVINAPIGRH-PVNRLKMAVV----PNGKEAVTYFEVLERF-DKYTFIKLRLKTGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P++GD  Y                 LHA  ++  HP   + L  +A 
Sbjct: 227 THQIRVHMSYIGYPLLGDSSYGR----AKNEFGVQGQVLHAGEIEFVHPITSKVLHFSAD 282

Query: 311 LPAHMVKTWDSLGFKYDR 328
           LP + ++  + L  K ++
Sbjct: 283 LPEYFLEILNILRNKNNK 300


>gi|326795265|ref|YP_004313085.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326546029|gb|ADZ91249.1| pseudouridine synthase, RluA family [Marinomonas mediterranea
           MMB-1]
          Length = 324

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 92/317 (29%), Positives = 161/317 (50%), Gaps = 16/317 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V++V ++ +    R+D +       +    +  +LR G++RV+KKR K + R+QSG +
Sbjct: 14  TKVRFVDIDENNHGQRIDNFLITELKGLPKGKIYNLLRKGEIRVNKKRTKPDYRLQSGDI 73

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRI P++          +  D           ++S ++YED  + V NKP+G++V GGSG
Sbjct: 74  VRIAPLVL--------PERADKPTVAEGLKAQIESRIIYEDKGLLVVNKPSGLAVHGGSG 125

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIY 183
           +++ +   ++     +     L HRLD++TSG++++A+ R+  + L E+ R +  +QK Y
Sbjct: 126 LSFGLVEVVRQMRPLEKF-VELVHRLDRDTSGLIMIAKRRSVLKLLHEALREKSGVQKTY 184

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G    +K+ +   LLK     G+ V  V         +++ F ++    + F  +
Sbjct: 185 LALVHGAWSKRKQKVDAPLLKNELKSGERVVRVN---PEGKESLTRFNLV-REFEGFSLI 240

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + +P TGRTHQ+RVH    G  IVGD KY  +            +L LHA  +++ + EG
Sbjct: 241 QCEPVTGRTHQIRVHTQFAGHSIVGDDKYTSSELNKQTKEMGFKRLCLHATRLEIDY-EG 299

Query: 303 GRLQITAPLPAHMVKTW 319
            +L + APL        
Sbjct: 300 EKLILEAPLDDEWKALM 316


>gi|258511286|ref|YP_003184720.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478012|gb|ACV58331.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 314

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 89/337 (26%), Positives = 166/337 (49%), Gaps = 43/337 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPH----INFVNLQKILRSGQVRVDK-KRVKF 55
           M    +VQY  V  ++   RLDRW  +        ++   +Q+ L  G +R  +  R+K 
Sbjct: 1   MRPAIHVQY-EVSAEDAGERLDRWLTDRLQEDDIEVSRTQVQRWLDDGFIRRARPGRLKA 59

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           ++ +++G +  +          + E++ L+         D +  ++ YED  + V +KP 
Sbjct: 60  SDPVEAGDLYEVD---------VPEEEPLEL-----VPDDGVPFVVAYEDDDVIVVDKPR 105

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAA 166
           G+ V  G+G   H+ G L + + ++G          +P + HR+D++TSG++V A++  A
Sbjct: 106 GVVVHPGAG---HMRGTLVNGLLARGTPLCTLAGALRPGVVHRIDKDTSGLVVFAKSDRA 162

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
            + L E+FR   +++ Y ++  G   +++  I   + +        + V     +G   A
Sbjct: 163 YRALVEAFRAHDVEREYVAIAHGRMPHREGTIDMPIARD-PADRQRMAVR----QGGKRA 217

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++HF+V++ FA K+ +L ++  TGRTHQ+RVH   +G PI GD  Y         +   +
Sbjct: 218 VTHFEVLESFA-KYSYLRLRLETGRTHQIRVHLAAIGHPIAGDPVYGPRH-----TLPID 271

Query: 287 KLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
              LHAR +   HP+G RL+  + +P+ M +  D L 
Sbjct: 272 GQALHARTLGFTHPDGRRLRFESAVPSDMARLLDGLR 308


>gi|258543199|ref|YP_003188632.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256634277|dbj|BAI00253.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256637337|dbj|BAI03306.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-03]
 gi|256640389|dbj|BAI06351.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-07]
 gi|256643446|dbj|BAI09401.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-22]
 gi|256646501|dbj|BAI12449.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-26]
 gi|256649554|dbj|BAI15495.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-32]
 gi|256652540|dbj|BAI18474.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-01-42C]
 gi|256655598|dbj|BAI21525.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-12]
          Length = 337

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 76/331 (22%), Positives = 135/331 (40%), Gaps = 37/331 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVRIP 68
             V  ++   R+DR+       ++   ++ ++  G +  D   ++    I ++G  V + 
Sbjct: 21  FTVTPEQAGERIDRFLAATMETLSRSRIKSLIEEGHLACDGVCIREPAAIARAGMEVVLT 80

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                          +  +       + +   +LYED  + V +KPAG+ V    G    
Sbjct: 81  ---------------IPPAAPAVPQGEDISFTVLYEDDDLIVLDKPAGLVVHPAPGNETG 125

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             ++G +    +S       ++P + HRLD++TSG++V A+T  A Q L+E F  RRI +
Sbjct: 126 TLVNGLIAHCGESLKGIGGERRPGIVHRLDKDTSGVMVAAKTEMAHQALSEDFAARRIDR 185

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +  WG+P   +      + +           +    KG  +A++H++ +  F     
Sbjct: 186 AYLAFCWGLPNPAEGDFEGAIGRDKRDRK----RMALTPKGGKWALTHYRTLQAFGTGAA 241

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFTSPIQNKLYLHA 292
            +  +  TGRTHQ+RVH    G P++GD  Y                  +    +  LHA
Sbjct: 242 LVACKLATGRTHQIRVHFSANGHPLIGDPLYLRRIPAASRVLPSAARAAALDFPRQALHA 301

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +   HP  G  L    P+P  M     SL
Sbjct: 302 ARLGFIHPRTGEKLLFETPMPEDMQVLERSL 332


>gi|188534767|ref|YP_001908564.1| 23S rRNA pseudouridine synthase D [Erwinia tasmaniensis Et1/99]
 gi|188029809|emb|CAO97690.1| Ribosomal large subunit pseudouridine synthase D [Erwinia
           tasmaniensis Et1/99]
          Length = 325

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 78/340 (22%), Positives = 143/340 (42%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   ++ V+   + K   ++  G+ + I  
Sbjct: 10  TVSESQLGQRLDQALAELFPDYSRSRIKEWILDRRITVNDTIIDKPKEKVLGGEQISIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I                      +  +   ++YED  I V NKP  + V  G+G     
Sbjct: 70  EIEEEARW---------------EAQDIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   +   +  + HRLD++T+G++VVA+T  A  HL ++ + R I + Y ++
Sbjct: 115 VLNALLYHFPAIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGRM-TAGGTVDQPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHISHPLVGDPLYGGRPRPPKGASEAFITTLRAFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G  ++  APLP  MV   D+L  K D  ++ ++L  
Sbjct: 288 HPISGIEMEWHAPLPQDMVDLIDAL--KADTEMFKEQLDW 325


>gi|322831462|ref|YP_004211489.1| pseudouridine synthase, RluA family [Rahnella sp. Y9602]
 gi|321166663|gb|ADW72362.1| pseudouridine synthase, RluA family [Rahnella sp. Y9602]
          Length = 325

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 143/333 (42%), Gaps = 35/333 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   ++  +   +V V+ K+V K   ++  G+ + I
Sbjct: 8   TATVAESQLGQRLDQALAELFPDYSRSRIKDWILEDRVTVNGKKVTKPKEKVLGGEAIAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I      + +   LD               ++YED+ I V NKP  + V  G+G   
Sbjct: 68  DAQIEEEARWLPQDIALD---------------IVYEDTDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +  +    PR  + HRLD++T+G++VVA++  A  HL  + + R I + Y 
Sbjct: 113 GTVLNALLHYYPAIIDVPRCGIVHRLDKDTTGLMVVAKSVPAQTHLVTALQAREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A +H+++++ F +    L 
Sbjct: 173 AVAIGTM-TAGGTVNEPIARHST-----KRTHMAVHPTGKPATTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQN------KLYLHARYMD 296
           ++  +GRTHQ+RVH  H+  P++GD  Y    +     + P  N      +  LHA  + 
Sbjct: 226 LRLESGRTHQIRVHMAHINHPLLGDQLYGGRPRLPKGASEPFINMLRGFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           L HP  G +++  AP+P  MV   ++L    + 
Sbjct: 286 LYHPVTGIQMEWHAPIPQDMVDLINALKADTEE 318


>gi|332529427|ref|ZP_08405386.1| pseudouridine synthase RluD [Hylemonella gracilis ATCC 19624]
 gi|332041073|gb|EGI77440.1| pseudouridine synthase RluD [Hylemonella gracilis ATCC 19624]
          Length = 322

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 95/319 (29%), Positives = 156/319 (48%), Gaps = 15/319 (4%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+ +    RLD +       +   ++ +I+RSG+VRV+K R     R+QSG  VR+PP
Sbjct: 1   MTVDEESAGQRLDNFLLRQLKGVPKTHVYRIIRSGEVRVNKGRANAETRVQSGDAVRLPP 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  +     K       ++     +   +  +L+ED  +   +KPAG++V GGSG+++ +
Sbjct: 61  LRLSERAADK-----AEAMAHGGGAPGREFPVLFEDEAVLAVDKPAGVAVHGGSGVSFGV 115

Query: 130 DGFLKSWV----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              L++          +   L HRLD+ETSGIL++A+ R+A + L + FR R   K Y +
Sbjct: 116 IEQLRTARGYGQAGGAKFLELVHRLDRETSGILLLAKKRSALKALQDQFRERETGKTYLA 175

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           LV G     K+ +   L K     G+  V VV +++     A++  KV    +     LE
Sbjct: 176 LVSGRWPQSKKVLDKPLHKYLLEDGERRVRVVAKDDPEGMRAVTLVKVRQA-SDTHSLLE 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMDLPHP- 300
           +   TGRTHQ+RVH    G  I GD KY     N      +    +++LHA  +   HP 
Sbjct: 235 VTIKTGRTHQIRVHLASEGHAIAGDDKYGDFELNRVLQKGASPLKRMFLHAWRLQFTHPV 294

Query: 301 EGGRLQITAPLPAHMVKTW 319
            G R+++ + LP  +    
Sbjct: 295 SGERIELMSALPTDLTPYL 313


>gi|91211928|ref|YP_541914.1| 23S rRNA pseudouridine synthase D [Escherichia coli UTI89]
 gi|91073502|gb|ABE08383.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           UTI89]
 gi|294490521|gb|ADE89277.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           IHE3034]
 gi|307625854|gb|ADN70158.1| 23S rRNA pseudouridine synthase D [Escherichia coli UM146]
          Length = 326

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQSLHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|312796112|ref|YP_004029034.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           rhizoxinica HKI 454]
 gi|312167887|emb|CBW74890.1| Ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70)
           [Burkholderia rhizoxinica HKI 454]
          Length = 373

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 82/350 (23%), Positives = 140/350 (40%), Gaps = 33/350 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V       RLD+     +P  +   LQ  + +G+V +D    +    +  G  VR+ P +
Sbjct: 33  VPPALAGERLDKVLARLFPTFSRSRLQTWIDAGRVTLDGAPARLRQSVPLGATVRLVPDL 92

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                             L    + +   ++YED  + V +KPAG+ V   +G      +
Sbjct: 93  L--------------PQALAFAPEPVPLPIVYEDETLVVIDKPAGLVVHPAAGNWSGTLL 138

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +G L  + D+ G  +  + HRLD++TSG++VVART AA   L    + R +++ Y +  W
Sbjct: 139 NGLLHRYPDAAGLPRAGIVHRLDKDTSGLMVVARTLAAQTDLVRQLQARTVKRRYIAFAW 198

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEM 245
           G+      CI   + +      +   +          A +HFK +       Q    L  
Sbjct: 199 GV-TPPSGCIDAPIGRDP---RERTRMAVLAGAAGKAARTHFKTVATGVWSGQPVSRLLC 254

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHPEG 302
              TGRTHQ+RVH  H G P++GD  Y           +     +  LHA  + L HP  
Sbjct: 255 DLETGRTHQIRVHLAHTGHPLLGDPLYGRVRNARQRPALPAGFARQALHAWRLALVHPAT 314

Query: 303 -GRLQITAPLPAHMVKTWDSLGF-----KYDRNLYIKRLYSQDECKQNIL 346
              +   + +P  + +    L            +   R ++ D+   +I+
Sbjct: 315 HAPVAWRSAMPQDLAQLAAVLELTDPPDDQAETIDFARQHAYDDEGGSIV 364


>gi|270157796|ref|ZP_06186453.1| RluA family pseudouridine synthase [Legionella longbeachae D-4968]
 gi|289163935|ref|YP_003454073.1| Ribosomal large subunit pseudouridine synthase [Legionella
           longbeachae NSW150]
 gi|269989821|gb|EEZ96075.1| RluA family pseudouridine synthase [Legionella longbeachae D-4968]
 gi|288857108|emb|CBJ10923.1| Ribosomal large subunit pseudouridine synthase [Legionella
           longbeachae NSW150]
          Length = 318

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 113/324 (34%), Positives = 169/324 (52%), Gaps = 17/324 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V Y  + N+EE  RLD +       +   ++ +I+R+G+VRV+KKR + N+R+ +G 
Sbjct: 1   MSEVSYKEISNEEEGQRLDNYLIRVLKGVPKSHIYRIIRAGEVRVNKKRAQINSRLHAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VRIPPV       + E K +    NL K    L+  +++EDS + V NKPAGI+V GGS
Sbjct: 61  SVRIPPVR------VSEPKEVFVGNNLAKR---LQESIIFEDSSLLVINKPAGIAVHGGS 111

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G++  +   L+           L HRLD+ETSG L++A+ R+  + +      R +QK Y
Sbjct: 112 GLSLGVIEALRKTRSDLAY-LELIHRLDKETSGCLLLAKKRSVLRAIHALLEAREVQKTY 170

Query: 184 WSLVWGIPKNKKECIA-NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           W+L+    + KK  I    L K     G+ +  VK+  K +  A   FK+++ + Q  CW
Sbjct: 171 WALLTHRWEGKKRVIVQAALEKNILKSGERIVKVKEEGKASETA---FKLLENYEQ-ACW 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPE 301
           +E  P TGRTHQ+RVH+ H+G  IVGD KY A           QN+L+LHAR +      
Sbjct: 227 VEASPKTGRTHQIRVHSAHLGHVIVGDKKYGALAGQVEGIDNQQNRLFLHARSIQFE-LN 285

Query: 302 GGRLQITAPLPAHMVKTWDSLGFK 325
           G +    A        T   L  +
Sbjct: 286 GKKHLFQADADEQFSTTLKQLRAR 309


>gi|82778018|ref|YP_404367.1| 23S rRNA pseudouridine synthase D [Shigella dysenteriae Sd197]
 gi|309789452|ref|ZP_07684038.1| ribosomal large subunit pseudouridine synthase D [Shigella
           dysenteriae 1617]
 gi|81242166|gb|ABB62876.1| suppressor of ftsH mutation [Shigella dysenteriae Sd197]
 gi|308922695|gb|EFP68216.1| ribosomal large subunit pseudouridine synthase D [Shigella
           dysenteriae 1617]
          Length = 326

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 147/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNSKLCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 127 YHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A + L ES + R I + Y 
Sbjct: 113 STVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQRRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  +++   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEAMRADFEE 318


>gi|32423742|gb|AAP81266.1| pseudouridine synthase [Pseudomonas aeruginosa PA14]
          Length = 320

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 89/347 (25%), Positives = 156/347 (44%), Gaps = 43/347 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS M   +   V  +    RLD+     +P  +   L   ++ G++ VD   ++  + + 
Sbjct: 1   MSDMIQ-RAAEVPFELGGQRLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVH 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SG  + +     A    + +   L+               ++YED  I V +KPAG+ V 
Sbjct: 60  SGAQLVLEAEQEAQGEWLAQDIELE---------------IVYEDEHILVIDKPAGLVVH 104

Query: 121 GGSGIAYHIDGFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             +G   H DG L + +       +   +  + HRLD++T+G++VVA+T  A   L    
Sbjct: 105 PAAG---HQDGTLLNALLYHVPDIANVPRAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQL 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R + +IY ++V G+       I   + +   +    + VV         A+SH++V++
Sbjct: 162 QARSVSRIYEAIVIGVI-TSGGTIDAPIGRHG-VQRQKMAVVD----AGKVAVSHYRVLE 215

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--------GNFTSPIQN 286
            F +      ++  TGRTHQ+RVH  H+G P+VGD  Y   F+           T     
Sbjct: 216 RF-RAHTHTRVKLETGRTHQIRVHMSHIGYPLVGDPVYGGRFRIPPVASQTLVQTLREFP 274

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +  LHAR+++L HP  G R++  +PLP   +     L  + DR  ++
Sbjct: 275 RQALHARFLELDHPATGVRMKWESPLPEEFLWLLSLL--RQDREAFV 319


>gi|150390556|ref|YP_001320605.1| RluA family pseudouridine synthase [Alkaliphilus metalliredigens
           QYMF]
 gi|149950418|gb|ABR48946.1| pseudouridine synthase, RluA family [Alkaliphilus metalliredigens
           QYMF]
          Length = 310

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 142/327 (43%), Gaps = 37/327 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            +Q+  V  ++E +RLD +    Y  ++   +QK+++   V VD +  K    ++ GQV+
Sbjct: 2   EIQHFCVLEEDEGVRLDIYIAEQYDDLSRSYIQKVIKDNGVTVDGRPEKNRYIVKVGQVI 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +                L  +  L   +  +   ++YED  + V NKP  + V    G 
Sbjct: 62  VVS---------------LPEAKELEVTAQNIPLDIVYEDDDLLVVNKPQDMVVHPAPGN 106

Query: 125 --------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                   + YH  G L S   +   +P + HR+D++TSG+L+VA+   A Q L+E  + 
Sbjct: 107 YENTMVNALLYHCKGKLSSI--NGIIRPGIVHRIDKDTSGLLMVAKNNHAHQFLSEQLKD 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
               + Y  +  G  K ++  I   + +          +      G   A++H +V++ F
Sbjct: 165 HSTTRKYHGISVGTIKEERATINAPIARHQTDRLKMAVLA-----GGRNAVTHIQVLNRF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                ++E Q  TGRTHQ+RVH  ++G P++GD  Y        +        LHA+ + 
Sbjct: 220 GD-HTYMEAQLETGRTHQIRVHLGYIGHPLLGDFVYGHKK----SKFNLKGQVLHAKTLG 274

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
             HP     ++  A LP +  K    L
Sbjct: 275 FIHPTKKTYMEFNAALPTYFEKLLRVL 301


>gi|170766082|ref|ZP_02900893.1| ribosomal large subunit pseudouridine synthase D [Escherichia
           albertii TW07627]
 gi|170125228|gb|EDS94159.1| ribosomal large subunit pseudouridine synthase D [Escherichia
           albertii TW07627]
          Length = 326

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 81/336 (24%), Positives = 144/336 (42%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSEKQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+   A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIVDVPRAGIVHRLDKDTTGLMVVAKNVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  +++   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELVEAMRADFEE 318


>gi|312958894|ref|ZP_07773413.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens WH6]
 gi|311286664|gb|EFQ65226.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens WH6]
          Length = 320

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 87/344 (25%), Positives = 153/344 (44%), Gaps = 37/344 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    ++   V ++    RLD+     +   +   L   ++ G++ VD   ++  + + 
Sbjct: 1   MSDKIELR-AEVPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVH 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G ++ +     A    + +   LD               ++YED  I V NKPAG+ V 
Sbjct: 60  GGAILELTAEQEAQGEWVAQDIELD---------------IVYEDDDILVINKPAGLVVH 104

Query: 121 GGSGIAYHI--DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +G A     +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R
Sbjct: 105 PAAGHADGTLLNALLHHIPDIINVPRCGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSR 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + +IY  +V G+     +   N  + +       + V+    +G   A+SH++V++ F 
Sbjct: 165 SVSRIYECIVIGVVVAGGKI--NAPIGRHGQQRQRMAVM----EGGKQAVSHYRVLERF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLY 289
           +    + ++  TGRTHQ+RVH  H+  P+VGD  Y   F+    +            +  
Sbjct: 218 RSHTHVRVKLETGRTHQIRVHMAHINFPLVGDPAYGGRFRIPPAASQTMVESLKTFPRQA 277

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           LHAR+++L HP  G R+   +PLP   V     L  K DR  ++
Sbjct: 278 LHARFLELDHPTSGQRMSWESPLPDDFVWLLSLL--KQDREAFV 319


>gi|268593137|ref|ZP_06127358.1| ribosomal large subunit pseudouridine synthase D [Providencia
           rettgeri DSM 1131]
 gi|291311410|gb|EFE51863.1| ribosomal large subunit pseudouridine synthase D [Providencia
           rettgeri DSM 1131]
          Length = 325

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 81/343 (23%), Positives = 155/343 (45%), Gaps = 43/343 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            +   +   RLD+     +P  +   +++ + + +V+V+ K + K   ++   + + I  
Sbjct: 10  TIAESQLGQRLDQALAELFPDYSRSRIKEWILADRVQVNGKVINKPKEKVFGSEQILIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +I   N                     +   ++YED  I + NKP  + V  G+G     
Sbjct: 70  LIEEDNRW---------------EPQDIPLNVIYEDEDILIINKPRDLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + + +   +  + HRLD++T+G++VVA+T  A  HL E+ + R I + Y ++
Sbjct: 115 ILNALLYRYPEIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAV 174

Query: 187 VWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             G        +E I+    K++H+    +            A++H++V++ F +    L
Sbjct: 175 AVGRMTAGGMVEEPISRHPTKRTHMAVHPM---------GKPAVTHYRVMEHF-RAHTRL 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYM 295
            ++  TGRTHQ+RVH  H+  P++GD  Y    +    +  +        ++  LHA  +
Sbjct: 225 RLRLETGRTHQIRVHMAHINHPLIGDPLYGGRPRPLKGATEEFLEVMRNFDRQALHATML 284

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            L HP  G +++  APLP  MVK  ++L  K D  L+   +  
Sbjct: 285 RLYHPISGIQMEWHAPLPDDMVKLIEAL--KADTELHKDDMDW 325


>gi|170077579|ref|YP_001734217.1| 23S rRNA-specific pseudouridylate synthase [Synechococcus sp. PCC
           7002]
 gi|169885248|gb|ACA98961.1| 23S rRNA-specific pseudouridylate synthase [Synechococcus sp. PCC
           7002]
          Length = 308

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 81/329 (24%), Positives = 150/329 (45%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSG 62
           MT  Q + ++ +    RLD+W     P ++   LQ+++  GQV++++   +    +++ G
Sbjct: 1   MTE-QILELKVEGAGERLDQWLAQQLPELSRSRLQRLIEQGQVQLNEAPCQSKKTKLKVG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +                + +   +    + +   +L+ED    + NKPAG+ V   
Sbjct: 60  DRLILK---------------IPAPATMALAPEAMDLDILFEDEHFLIVNKPAGMVVHPA 104

Query: 123 SG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G      + G L    ++       Q+P + HRLD++T+G + +A+T  A QHL    +
Sbjct: 105 PGNYTGTLVHGLLAHCGENLAGIGGVQRPGIVHRLDKDTTGAIAIAKTDQAHQHLQAQIK 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +  ++ Y  +V+G P+N         + +       + V    ++    A++H+++++ 
Sbjct: 165 AKTARREYMGIVYGCPRNDAAGTIEAPIARHKGDRKKMAV----DETGRPAVTHWEIMER 220

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
               +  L  +  TGRTHQ+RVH+ HMG PI+GD  Y +N    F         LHAR +
Sbjct: 221 LG-NYSLLYYKLETGRTHQIRVHSAHMGNPIIGDPLYTSN---KFDKVKLTGQALHARKL 276

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            + HP  G  ++  APLP    K    L 
Sbjct: 277 IVKHPVTGETIEAIAPLPTEFEKLLQFLR 305


>gi|148243331|ref|YP_001228488.1| pseudouridylate synthases, 23S RNA-specific [Synechococcus sp.
           RCC307]
 gi|147851641|emb|CAK29135.1| Pseudouridylate synthases, 23S RNA-specific [Synechococcus sp.
           RCC307]
          Length = 316

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 84/316 (26%), Positives = 135/316 (42%), Gaps = 28/316 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +  P  +   +QK + +G VRV+    +    ++ G  +++          
Sbjct: 21  PMRLDRWLVSQRPEQSRARIQKFIEAGYVRVNGTTGRAKTPLRHGDEIKLWM-------- 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
                            + +   +L+ED  + V NKPAG++V    G      ++G L  
Sbjct: 73  ------PPPEPLPYLQPEPMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLHH 126

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y ++V G+P
Sbjct: 127 CPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQQALVKLQVQIQKRVASREYLAVVHGVP 186

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             +   I   + +       Y  V   N     YA +H+ + +     +  L  +  TGR
Sbjct: 187 AGESGTIVGAIGRHPVDRKKYAVVSSDN---GRYACTHWSLQERLGD-YSLLRFKLDTGR 242

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  H   P+VGD  Y    K     P      LHA  + L HP  G R+   AP
Sbjct: 243 THQIRVHCAHRNHPVVGDPTYSRCRKLPIELPG---QALHAVQLGLDHPITGERMVFEAP 299

Query: 311 LPAHMVKTWDSLGFKY 326
           LP  + K    L  + 
Sbjct: 300 LPEVLEKLLAVLRKRA 315


>gi|253998975|ref|YP_003051038.1| RluA family pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|253985654|gb|ACT50511.1| pseudouridine synthase, RluA family [Methylovorus sp. SIP3-4]
          Length = 333

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 99/315 (31%), Positives = 157/315 (49%), Gaps = 16/315 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+      R+D +       +   ++ +ILRSG+VRV+ KR+    R+Q G +VR+PP
Sbjct: 23  LTVDEGSAGQRIDNFLTKTLKGVPKSHVYRILRSGEVRVNSKRIDATYRLQLGDLVRVPP 82

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +      + +E + +         +   +  +++ED  + V +KPAG +V GGSG++  +
Sbjct: 83  IRVQPQPVAEETRPV---------AARFEEAVIFEDEAMLVIDKPAGFAVHGGSGVSRGV 133

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+       +   L HRLD+ETSG+L+VA+ R+A   L E+ R   + K Y  LV G
Sbjct: 134 IEQLR-LERPHAKFLELVHRLDRETSGVLMVAKKRSALVGLHEAMRANHMDKRYLMLVSG 192

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             K KK+ +   L K     G+    V   E+    + + F +   + + F  LE Q  T
Sbjct: 193 DWKEKKKRVVLALQKHVTANGERKVTV---EEEGQNSETIFHLKKSYGE-FTLLEAQLIT 248

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           GRTHQLRV   H+G PI GD KY               +++LH+    + HP  G +L++
Sbjct: 249 GRTHQLRVQLAHLGFPIAGDDKYGDFALNKALQKRGLKRMFLHSAETGIRHPLSGDKLKL 308

Query: 308 TAPLPAHMVKTWDSL 322
            APLPA +     SL
Sbjct: 309 IAPLPAALQAFLTSL 323


>gi|152981207|ref|YP_001353037.1| ribosomal large subunit pseudouridine synthase C [Janthinobacterium
           sp. Marseille]
 gi|151281284|gb|ABR89694.1| ribosomal large subunit pseudouridine synthase C [Janthinobacterium
           sp. Marseille]
          Length = 339

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 100/325 (30%), Positives = 163/325 (50%), Gaps = 26/325 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V + +++   R+D +       +   ++ ++LRSG+VRV+K R+    R+  G +
Sbjct: 29  AQVQLVTINDEDAGQRIDNFLLRICKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLVEGDI 88

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+           +I + + +    ++F    +L ED+ + V +KPAG++V GGSG
Sbjct: 89  VRIPPI-----------RIAEKAPSTAPGAEF---KILLEDNHLLVIDKPAGVAVHGGSG 134

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++Y +   L++      +   L HRLD++TSG+LV+A+ R+A  +L E  R     K Y 
Sbjct: 135 VSYGVIEQLRAAR-PDAKFLELVHRLDRDTSGVLVLAKKRSALTNLHEQIRGGEPDKRYL 193

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  KN ++ I   L K +   G+    V+ +      + + F +I  +   F  LE
Sbjct: 194 VLVHGDWKNARQHIKLPLHKYTTPEGERRVRVQAD---GMESHTVFNLIQRYG-PFSLLE 249

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANF------KGNFTSPIQNKLYLHARYMDLP 298
            +  TGRTHQ+RVH    G  I GD KY          K +       +++LHA  +   
Sbjct: 250 AELKTGRTHQIRVHLASSGFAIAGDDKYGDFALNRDLQKADGERVALKRMFLHAHQITFI 309

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HPE G+ + + APLP    +   SL
Sbjct: 310 HPESGKPVTLNAPLPPECERFLKSL 334


>gi|282892065|ref|ZP_06300542.1| hypothetical protein pah_c205o103 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498107|gb|EFB40449.1| hypothetical protein pah_c205o103 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 319

 Score =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 87/322 (27%), Positives = 142/322 (44%), Gaps = 35/322 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            +++  E  +RLD+   + Y  + +    Q ++  G V ++ + VK   +   G  V + 
Sbjct: 12  FIIQEMEAGIRLDKVLADRYKSNGSRTYFQMLIEKGLVLLNGEPVKKRFKPNVGDDVELF 71

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                   +I EQ               +   +LYED  + + NKP G+ V    G    
Sbjct: 72  FAAAPEIDLIPEQ---------------IPLNILYEDEHLLIINKPVGMVVHPAPGNWTG 116

Query: 127 YHIDGFLKSWVDS------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             ++  L     S         +P + HRLD+ETSG+LV A+T +  Q L E F  R++ 
Sbjct: 117 TFVNALLYHCGYSLSDASVDSIRPGIVHRLDKETSGVLVAAKTLSVQQKLMELFAARQVY 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW++  G P N   C  NW + +  I    + V     +    A++  + ++    + 
Sbjct: 177 KEYWAICLGNPGN---CELNWPIGRHPIHRKQMTVR----EDGKEALTFCETLE-VGNEI 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           C  ++   TGRTHQ+RVH  H G PI+GD  Y +  K         +  LHAR +   HP
Sbjct: 229 CLAKLILSTGRTHQIRVHLKHKGHPILGDSIYGS--KQVNMRYRAERQMLHARKLAFIHP 286

Query: 301 EG-GRLQITAPLPAHMVKTWDS 321
               ++++ APLPA M +    
Sbjct: 287 ITQQKIEVEAPLPADMEECLRK 308


>gi|91775965|ref|YP_545721.1| ribosomal large subunit pseudouridine synthase D [Methylobacillus
           flagellatus KT]
 gi|91709952|gb|ABE49880.1| ribosomal large subunit pseudouridine synthase D [Methylobacillus
           flagellatus KT]
          Length = 356

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 83/338 (24%), Positives = 145/338 (42%), Gaps = 34/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS       + +  +   MRLD+  +   P  +   +Q  ++ G V +D +      ++ 
Sbjct: 1   MSHTATPITLTITQELGGMRLDQALQRLMPEHSRSRIQGWIKDGLVTIDDETPTAKFKVW 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ V+I P                +   L    + +   +++ED  I V NKPAG+ V 
Sbjct: 61  GGEQVQIKPQA--------------TPEALAFEPENIPLEVVFEDEHILVINKPAGMVVH 106

Query: 121 GGSGI--AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +G      ++  L      K   +  + HRLD++TSG+LVVA+T AA  +L    + R
Sbjct: 107 PAAGNWSGTLLNALLYHAPQLKDVPRAGIVHRLDKDTSGLLVVAKTLAAQTNLVRQLQAR 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y ++VWG    +   +   + +  H     + V +        A++H++V+D F+
Sbjct: 167 TVKREYRTIVWGQVW-RNGKVDQPIGRHPH-ARTKMAVNRM----GKPAVTHYEVLDRFS 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---------KL 288
               ++     TGRTHQ+RVH  H+  PIVGD  Y             N         + 
Sbjct: 221 -VHTYMRCLLETGRTHQIRVHMQHLKAPIVGDPVYGIRGILPLRHISDNLRNVLLEFKRQ 279

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            LHA  + L HP  G  ++    L A M    +++  +
Sbjct: 280 ALHAIRLGLKHPVSGEPMEWQVELAADMKILLEAIRAE 317


>gi|296111936|ref|YP_003622318.1| pseudouridine synthase [Leuconostoc kimchii IMSNU 11154]
 gi|295833468|gb|ADG41349.1| pseudouridine synthase [Leuconostoc kimchii IMSNU 11154]
          Length = 308

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 86/312 (27%), Positives = 141/312 (45%), Gaps = 35/312 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D          +   L + L++G + V+  +VK + ++  G  + I P   A   II 
Sbjct: 15  RIDAILAKEDLQYSRTTLAEWLQNGHILVNNNKVKRSYKVSVGDTISIFPPEVASTEIIA 74

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   LD               ++YED+ I V NKP G+ V   +G   H  G L + +  
Sbjct: 75  EDIPLD---------------IVYEDNDILVVNKPQGMVVHPAAG---HSSGTLVNALLH 116

Query: 140 KGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      +P + HR+D++TSG+L+VA+   A + L+   +  +  +IY++LV G  
Sbjct: 117 HAPLSTINGTFRPGIVHRIDRDTSGLLMVAKNDVAHKALSAQLKAHKNDRIYYALVRGEF 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   + +   +      V      G   AI+HF+V+  +   F  L+++  TGR
Sbjct: 177 SEDSGTINAPIGRH-PVDRKRQAVQV----GGREAITHFEVVHRYV-GFTLLKVRLETGR 230

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
           THQ+RVH  ++G PIVGD  Y    K    S +     LHA+ + L  P  G  L+  + 
Sbjct: 231 THQIRVHLTYIGHPIVGDPVYGNAQKLADVSLM--GQLLHAKTLSLTQPTTGEELRFDSS 288

Query: 311 LPAHMVKTWDSL 322
           LP +  +   +L
Sbjct: 289 LPTYFQEALATL 300


>gi|161510965|ref|YP_089013.2| 23S rRNA pseudouridine synthase D [Mannheimia succiniciproducens
           MBEL55E]
          Length = 324

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 79/328 (24%), Positives = 142/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+  +   RLD+     +P  +   L+  +    V ++ K       ++  G+ V I   
Sbjct: 10  VQPHQMGQRLDQTLAELFPDYSRSRLKTWIEDELVLLNGKVANIPREKVYGGEQVEITVE 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           I   N                     +   ++YED  I V NKP    V  G+G      
Sbjct: 70  IEDENRF---------------EPQNIPLNIVYEDDDILVINKPKDFVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  + + R+I + Y ++ 
Sbjct: 115 LNALLYHYPQITEVPRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRALQKRKITREYEAIA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +GI   K   +   + +           +         A++H++V++ F + +  L ++ 
Sbjct: 175 FGIM-TKGGTVDEPMSRHPT-----KRTLMAVHPMGKPAVTHYRVMEHF-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +        F S ++N  +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEEFMSVLRNFQRQALHAIMLRLEH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGELMEWHAPLPEDFVELVNALKADY 315


>gi|119897905|ref|YP_933118.1| ribosomal large subunit pseudouridine synthase C [Azoarcus sp.
           BH72]
 gi|119670318|emb|CAL94231.1| ribosomal large subunit pseudouridine synthase C [Azoarcus sp.
           BH72]
          Length = 319

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 92/320 (28%), Positives = 150/320 (46%), Gaps = 22/320 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++  ++      R+D +       +   ++ +ILR G+VRV+ +RV+   R+  G  VR
Sbjct: 10  VRHERIDEASAGQRIDNFLLRLAKGVPKSHVYRILRGGEVRVNGRRVQPTYRLALGDEVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+             L                +++ED  + V +KP+G +V GGSG++
Sbjct: 70  VPPLR------------LAEPTRSAPAPAGKPLPVVFEDDALLVVDKPSGKAVHGGSGVS 117

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++      +   L HRLD+ETSG+L+VA+ R+A   L +  R  +++K Y +L
Sbjct: 118 YGVIEQLRTQRPEL-RMLELAHRLDRETSGLLIVAKKRSALTALHDMMREGQVEKRYLTL 176

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   N  + +   LLK     G+    V         A S  +++  +A  +  LE++
Sbjct: 177 VPGRWMNPMQHVKAPLLKYLTPEGERRVRVSDE---GKPAHSIVRLVQRWAD-YSLLEVE 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
             TGRTHQ+RVH  H+G P+ GD KY               +++LHA  +   HP  G  
Sbjct: 233 LKTGRTHQIRVHLTHLGFPLCGDDKYGDFALNKRLEGEGLRRMFLHAASLRFHHPLTGEL 292

Query: 305 LQITAPLPAH---MVKTWDS 321
           L   A LP      V   D+
Sbjct: 293 LAFEAALPDDLRGFVALLDT 312


>gi|322514978|ref|ZP_08067990.1| ribosomal large subunit pseudouridine synthase D [Actinobacillus
           ureae ATCC 25976]
 gi|322119031|gb|EFX91195.1| ribosomal large subunit pseudouridine synthase D [Actinobacillus
           ureae ATCC 25976]
          Length = 325

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 78/338 (23%), Positives = 144/338 (42%), Gaps = 37/338 (10%)

Query: 4   MTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           MT    +   V  D    RLD+     +P+ +   L+  + S  V+V+   V K   ++ 
Sbjct: 1   MTQQMTLTAKVSADLLGARLDQALAQLFPYYSRSRLKVWIESDLVKVNGNIVNKAREKVF 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+++ +   I                         +   ++YED  I V NKP  + V 
Sbjct: 61  GGELIEVQAEIEEEVRF---------------EPQDIPLNIVYEDDDILVINKPKDLVVH 105

Query: 121 GGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+G     +   L  +     + PR  + HRLD++T+G++VVA+   A  HL  + + R
Sbjct: 106 PGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRLDKDTTGLMVVAKNIPAQTHLVTALQKR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           RI + Y ++  G+   +   +   + +                     A++H+++++ F 
Sbjct: 166 RITREYEAVTSGVM-TQGGKVDEPMARHPT-----KRTAMAVHPMGKPAVTHYRIMERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLY 289
           + +  L ++  TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  
Sbjct: 219 RNYTRLRLRLETGRTHQIRVHMTHIAHPLLGDQLYGGRPRPPKGASEEFLAVLRGFQRQA 278

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           LHA  + L HP  G  ++  APLP   ++  ++L   Y
Sbjct: 279 LHATMLRLEHPITGELMEWHAPLPDDFIELIEALKADY 316


>gi|296113828|ref|YP_003627766.1| RluA family pseudouridine synthase [Moraxella catarrhalis RH4]
 gi|295921522|gb|ADG61873.1| RluA family pseudouridine synthase [Moraxella catarrhalis RH4]
 gi|326562171|gb|EGE12499.1| RluA family pseudouridine synthase [Moraxella catarrhalis 7169]
 gi|326564465|gb|EGE14691.1| RluA family pseudouridine synthase [Moraxella catarrhalis 46P47B1]
 gi|326565646|gb|EGE15809.1| RluA family pseudouridine synthase [Moraxella catarrhalis 12P80B1]
 gi|326572296|gb|EGE22291.1| RluA family pseudouridine synthase [Moraxella catarrhalis BC8]
 gi|326574310|gb|EGE24257.1| RluA family pseudouridine synthase [Moraxella catarrhalis O35E]
 gi|326574892|gb|EGE24822.1| RluA family pseudouridine synthase [Moraxella catarrhalis 101P30B1]
 gi|326576218|gb|EGE26133.1| RluA family pseudouridine synthase [Moraxella catarrhalis CO72]
          Length = 382

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 89/327 (27%), Positives = 162/327 (49%), Gaps = 27/327 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V ++ V N+++  R+D +       +   +L K++RS ++R++ KR K ++++  G V
Sbjct: 58  SRVNFLTVTNNQDGQRVDNFLLARLKGLPRSHLYKLIRSDEIRINGKRCKAHDKLYMGDV 117

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+ P+  +    ++E  I+   +     +  L   +++ED  + V NKP G++V GGSG
Sbjct: 118 VRVAPIRLS----VREAPIISEEL-----AKGLLERIIFEDDGLIVLNKPHGMAVHGGSG 168

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            ++ I   ++  +  K     L HR+D++TSG+L++A+ R+  + L E FR + IQK Y 
Sbjct: 169 ESFGIIEAMRLAMGKKY--LELIHRIDKDTSGLLLIAKKRSTLKILQEQFRKKTIQKRYL 226

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVI---DCF 236
            LV G  +  +  I   LL+ +   G+    V     ++  + A  +++  K +      
Sbjct: 227 CLVMGHVQADEMVIDVPLLRYTLANGERRVKVAHLNEQKAGEYAKASLTKIKTLLRFKKD 286

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +   P TGRTHQ+RVH  H+G  ++GD KY    + N  +P   +L LHA  + 
Sbjct: 287 GCPVSLVLAMPATGRTHQIRVHMAHIGHALLGDDKY----QNNPLAPKVGRLCLHAWQLG 342

Query: 297 LP----HPEGGRLQITAPLPAHMVKTW 319
           +     H         AP+   M +  
Sbjct: 343 MTNDDGHTVTRPQNFVAPVADDMAQLL 369


>gi|118594941|ref|ZP_01552288.1| Pseudouridine synthase, RluD [Methylophilales bacterium HTCC2181]
 gi|118440719|gb|EAV47346.1| Pseudouridine synthase, RluD [Methylophilales bacterium HTCC2181]
          Length = 324

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 101/319 (31%), Positives = 163/319 (51%), Gaps = 13/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V+Y ++    E  ++D +      ++   ++ K+LRSGQVRV+KKR+K + R+  G  
Sbjct: 7   NSVRYELIGEGSEGQKIDNFLIKTLKNVPKSHIYKLLRSGQVRVNKKRIKTDFRLSLGDS 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP  +  + +     I      L + S      +++ED  + V NKP G++V GGSG
Sbjct: 67  VRIPPFTSPKSEVKTPISIKPEQALLIEKS------IIHEDDALIVINKPCGLAVHGGSG 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           I+Y +   L+       +   L HR+D+ETSGI+++A+ R     + +  R + I K Y 
Sbjct: 121 ISYGLIELLRK-SRPDARFLELVHRIDKETSGIILIAKKRPVLVDIHKQMRDKSIHKKYQ 179

Query: 185 SLVWGIPKNKKECIANWLLK-KSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFC 241
            +V G  + K+  +   L+K     G   V V+ Q +   G+  + S F +   F Q  C
Sbjct: 180 VIVNGKWQKKQLIVDLNLIKTSDEEGQKKVRVISQEDVVGGSKVSRSVFFLKQAFDQFSC 239

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
             E++  TGRTHQ+RVH  H+G  IVGD KY   +           +++LHA  +   HP
Sbjct: 240 L-EVKLVTGRTHQIRVHLSHLGFSIVGDDKYGDFSLNKRHAKLGFKRMFLHACELGFRHP 298

Query: 301 EGGR-LQITAPLPAHMVKT 318
             G  + +TAP+P+  +K 
Sbjct: 299 LSGEDIFLTAPIPSDFIKL 317


>gi|300948988|ref|ZP_07163044.1| pseudouridine synthase, RluA family [Escherichia coli MS 116-1]
 gi|300957377|ref|ZP_07169594.1| pseudouridine synthase, RluA family [Escherichia coli MS 175-1]
 gi|300315880|gb|EFJ65664.1| pseudouridine synthase, RluA family [Escherichia coli MS 175-1]
 gi|300451545|gb|EFK15165.1| pseudouridine synthase, RluA family [Escherichia coli MS 116-1]
          Length = 326

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 80/336 (23%), Positives = 144/336 (42%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I + NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIIINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++ VA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMAVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|198283980|ref|YP_002220301.1| RluA family pseudouridine synthase [Acidithiobacillus ferrooxidans
           ATCC 53993]
 gi|218668096|ref|YP_002426617.1| ribosomal large subunit pseudouridine synthase C [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198248501|gb|ACH84094.1| pseudouridine synthase, RluA family [Acidithiobacillus ferrooxidans
           ATCC 53993]
 gi|218520309|gb|ACK80895.1| ribosomal large subunit pseudouridine synthase C [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 317

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 101/323 (31%), Positives = 164/323 (50%), Gaps = 14/323 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V+   V + E   RLD +       +   ++ KILRSG+VRV+K R + +  +  G V
Sbjct: 4   NGVRQWQVTDAEAGQRLDNFLLRVMKGVPRSHIYKILRSGEVRVNKGRARPHYHLAEGDV 63

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+PPV  A           D +V        L++ +LYEDS + V +KP+G++V GGSG
Sbjct: 64  LRLPPVRVA--------APSDPAVLPAYLQGQLEAAVLYEDSHLLVLDKPSGLAVHGGSG 115

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L+  +    ++  L HRLD++TSG L+ ++ R+A + L E+ R   ++K Y 
Sbjct: 116 LSWGVIEALRQ-LRPDARELELVHRLDRDTSGCLIFSKKRSALRALHEALRAGLMEKRYL 174

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            L  G  + +   +   L K +   G+ +  V   E     A +HF  ++ F +    L+
Sbjct: 175 VLAAGDWQGEARSVRLALRKNTLQSGERMVRVDPVE--GKAAHTHFLPLERF-RGAVLLQ 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
               TGRTHQ+RVH   +G  + GD KY  A F     +    +L+LHA  +   HP+ G
Sbjct: 232 ADLDTGRTHQIRVHLQAIGHAVAGDEKYGDAAFNQRLRALGLRRLFLHAALVAFRHPQDG 291

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
           R ++I APLPA +      L  +
Sbjct: 292 RPMRIEAPLPADLQAILTPLRKE 314


>gi|312793558|ref|YP_004026481.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312180698|gb|ADQ40868.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 300

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 78/318 (24%), Positives = 154/318 (48%), Gaps = 35/318 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD++            +QKI+  G V V++ + +K   +++SG ++++           
Sbjct: 9   RLDKYLSEALSK-TRSFVQKIIEEGNVWVNQTQVLKPAYKVKSGDIIKV----------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW 136
               ++     L+  +  +   ++YED  + V NKP G+ V  G+G   +   +  L  +
Sbjct: 57  ----VIPEPKQLSLVAQDIDIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKF 112

Query: 137 VDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      +P + HRLD++TSG+L+VA+T  A   L+E+ +  +I++IY+++  G+ 
Sbjct: 113 RGRLSSINGVIRPGIVHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVL 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K     I   + +   +    + VV         A+++F+V++ F  K+ +++++  TGR
Sbjct: 173 KEDSGVINAPIGRH-PVNRLKMAVV----PNGKEAVTYFEVLERF-DKYTFIKLRLKTGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P++GD  Y                 LHA  ++  HP   + L  +A 
Sbjct: 227 THQIRVHMSYIGYPLLGDSSYGR----AKNEFGVQGQVLHAGEIEFVHPITSKVLHFSAD 282

Query: 311 LPAHMVKTWDSLGFKYDR 328
           LP + V+  + L  + ++
Sbjct: 283 LPEYFVEILNMLRNRNNK 300


>gi|319786173|ref|YP_004145648.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317464685|gb|ADV26417.1| pseudouridine synthase, RluA family [Pseudoxanthomonas suwonensis
           11-1]
          Length = 326

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 81/330 (24%), Positives = 141/330 (42%), Gaps = 34/330 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V ++    R D      +P  +   L   ++SG   +D +  +  + ++ G+ V +
Sbjct: 9   RQATVPDEAAGRRFDAVLAELFPEYSRSRLAAWIKSGDALLDGQPARPRDAVKGGETVSL 68

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
             V       + E   LD               +LY+D  ++V +KPAG+ V  G+G   
Sbjct: 69  AEVSEIQTEAVAEDIPLD---------------VLYQDEHLFVLDKPAGLVVHPGAGNPA 113

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++  L          +  + HRLD++TSG++VVART  A   L      R +++ Y 
Sbjct: 114 GTLVNALLHRDPGLAALPRAGIVHRLDKDTSGVMVVARTLQAHTGLVAQLAAREVRRQYV 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G         AN  + +       + V     +    A++H+++ + F +    LE
Sbjct: 174 AVVVGAL--VSGGTANAPIDRHPRDRLRMAVR----EDGRDAVTHYRLRERF-RAHTALE 226

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMD 296
            +  TGRTHQ+RVH  H+  PIVGD  Y    K           +     +  LHA  ++
Sbjct: 227 CRLETGRTHQIRVHMQHLRHPIVGDPLYGGPLKLPRGATEDLVASLRGFGRQALHAEVLE 286

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
             HP  G ++++ APLP  M++    L   
Sbjct: 287 FQHPVTGAQVRVEAPLPKDMLELLRVLRED 316


>gi|257095460|ref|YP_003169101.1| RluA family pseudouridine synthase [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257047984|gb|ACV37172.1| pseudouridine synthase, RluA family [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 375

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 136/319 (42%), Gaps = 26/319 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPV 70
           V       RLD+         +   LQ  +R G+V V     V+   R+  G+ + +   
Sbjct: 33  VPTACGGQRLDQVLARLLSQHSRSRLQDWIREGRVAVGGAVTVEPRFRLWGGETIALTES 92

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
            +        ++I                 +++ED  + V +K AG+ V  GSG      
Sbjct: 93  TDERAEASAPEEI--------------PLRIVFEDDTLIVLDKQAGLVVHPGSGNWRGTL 138

Query: 129 IDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++G L      ++  +  + HRLD++T+G++VVA+T  A   L    + R +++ Y +LV
Sbjct: 139 LNGLLHHAPQLARVPRAGIVHRLDKDTTGLMVVAKTLEAQTDLVRQLQARSVKRCYQALV 198

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI +     I +  + +       + VV     G   A +H++V++ F      +E   
Sbjct: 199 RGIVEGAG--IVDAPIGRHPTVRTRMAVVS----GGRPARTHYRVLERFV-ACTLIECAL 251

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH   +  P+VGD  Y           +  +  LHA  + L HP  G+ + 
Sbjct: 252 ETGRTHQIRVHMTSIAHPLVGDPIYGGGASRVPQGAVFPRQALHACRLALVHPASGKAML 311

Query: 307 ITAPLPAHMVKTWDSLGFK 325
             + +PA M    D L  +
Sbjct: 312 WRSGVPADMAALIDRLRLE 330


>gi|242240266|ref|YP_002988447.1| pseudouridine synthase [Dickeya dadantii Ech703]
 gi|242132323|gb|ACS86625.1| pseudouridine synthase, RluA family [Dickeya dadantii Ech703]
          Length = 325

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 80/345 (23%), Positives = 148/345 (42%), Gaps = 43/345 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V+  +   RLD+     +P  +   ++  +   +V+++   + K   ++  G+ V I
Sbjct: 8   TATVDESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGNVIDKPKEKVLGGESVSI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +I                      +  ++  ++YED  I V NKP  + V  G+G   
Sbjct: 68  TAIIEEDVRW---------------DAQPIQLDIVYEDEDILVINKPRDLVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  +   +   +  + HRLD++T+G++VVA+   A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHHYPAIADVPRAGIVHRLDKDTTGLMVVAKNVPAQTRLVESLQAREITREYE 172

Query: 185 SLVWGIPKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E IA    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVANGTMTAGGSVAEPIARHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RAHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHINHPLVGDPLYGGRPRFPKGASDEFLTVLRHFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            + L HP     ++  APLP  MV+   +L  K D   +  +L  
Sbjct: 283 MLRLYHPISCIEMEWHAPLPQDMVELIAAL--KADTEAFKDQLDW 325


>gi|238798952|ref|ZP_04642415.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           mollaretii ATCC 43969]
 gi|238717181|gb|EEQ09034.1| Ribosomal large subunit pseudouridine synthase D [Yersinia
           mollaretii ATCC 43969]
          Length = 325

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 142/328 (43%), Gaps = 35/328 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V VD K + K   ++  G++V I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I        ++  LD               ++YEDS I V NKP G+ V  G+G     
Sbjct: 70  QIEEDARWAPQEIPLD---------------IVYEDSDILVINKPRGLVVHPGAGNPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++
Sbjct: 115 VLNALLYYYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGNM-TAGGRVDEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDSFIAILRGFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           HP  G +++  A LP  MV+  ++L   
Sbjct: 288 HPISGIQMEWHAALPEDMVELINALKAD 315


>gi|254467985|ref|ZP_05081391.1| ribosomal large subunit pseudouridine synthase C [beta
           proteobacterium KB13]
 gi|207086795|gb|EDZ64078.1| ribosomal large subunit pseudouridine synthase C [beta
           proteobacterium KB13]
          Length = 306

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 104/318 (32%), Positives = 175/318 (55%), Gaps = 18/318 (5%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            +Q++ ++   E+ R+D +    +  +   ++ KI+R+G+VRV+KKRVK   +++   VV
Sbjct: 5   QIQHIDIDESSEDQRIDNFLFKTFKDVPKNHIFKIIRNGEVRVNKKRVKTLYKLKINDVV 64

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP    +  I K++K         K SD  K  ++YED  + V NKP+G++V GGSGI
Sbjct: 65  RIPP----IEFIEKKEK---------KPSDNFKPHIIYEDEWLLVVNKPSGLAVHGGSGI 111

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + +   ++  +  + +   L HR+D+ TSG++V+A+ R+A + + E FR ++I+K Y  
Sbjct: 112 DFGLIEHMRH-IKPEYKFLELVHRIDKNTSGVIVIAKKRSALRSMQELFRNKKIKKNYLV 170

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G   +KK+ ++  L KK    G +V+VV+   +G   + S F ++    QK   L  
Sbjct: 171 AVKGNWDSKKKEVSLRLEKKQTSEGHHVNVVEDPLRG-KLSKSIFYLVKQM-QKQSLLSA 228

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           Q  TGRTHQ+RV    +G P++GD KY          S    +++LHA  +   HP    
Sbjct: 229 QIITGRTHQIRVQLAFLGFPVLGDDKYGDFALNKKLQSSGLKRMFLHAHKLSFFHPFTEE 288

Query: 305 -LQITAPLPAHMVKTWDS 321
            +++TA LP  + K +D 
Sbjct: 289 KVELTADLPIELRKFFDE 306


>gi|116511823|ref|YP_809039.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. cremoris SK11]
 gi|116107477|gb|ABJ72617.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. cremoris SK11]
          Length = 301

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 143/323 (44%), Gaps = 33/323 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  + +++RLD+   N     +   L +++++ +V V+ +  K   ++++G  +    
Sbjct: 4   IKITEENKDLRLDKALANQ-TEYSRSLLTELIKNDKVFVNNEAKKAKYKVKTGDRIEFE- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
                         +  +  L   ++ L   ++YEDS + V NKP G+ V   +G A   
Sbjct: 62  --------------IPQAEVLDVAAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGT 107

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  +    D        +P + HR+D++TSG+L++A+   A + L    + +  ++ Y
Sbjct: 108 LVNAIMYHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G   N K  I   + +          V      G   A++HF+V++ F   +  +
Sbjct: 168 LAIVHGELANDKGTIEAPIGRNLKDRKKQAVVS-----GGKPAVTHFEVLERFV-GYTLI 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++  TGRTHQ+RVH  ++G P+ GD  Y      N T       +LHA  +   HP  G
Sbjct: 222 ALRLETGRTHQIRVHMHYIGHPVAGDPLYGP----NKTLTPNKGQFLHAETLGFEHPTSG 277

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
             ++     P    +  + L  +
Sbjct: 278 ELMEFQVDAPDLFKEQLEKLREQ 300


>gi|76810444|ref|YP_334298.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 1710b]
 gi|76579897|gb|ABA49372.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 1710b]
          Length = 477

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 95/326 (29%), Positives = 153/326 (46%), Gaps = 22/326 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++      R+D +       +   ++ +ILRSG+VRV+K R+    R+  G   
Sbjct: 158 QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGD-- 215

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                       ++      +           +  +L+ED  I V NKPAG++V GGSG+
Sbjct: 216 ------VVRVPPVRVAAADLARAAGPAPVPAAEFEILFEDDAIIVLNKPAGVAVHGGSGV 269

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y++
Sbjct: 270 AFGVIEQMRHAR-PHAKFLELAHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRYFA 328

Query: 186 LVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G       ++  +   L K +   G+    V+++      + + F ++D +   +  
Sbjct: 329 CVHGDWAADWGRRRVVKAPLFKYATPDGERRVRVQED---GLPSHTVFNLVDRWPD-YAL 384

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PIVGD KY               P   +++LHA  + L
Sbjct: 385 VEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARANAVPSIKRMFLHAHRLRL 444

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA   +  D L
Sbjct: 445 AHPLTGEPLQFDAPLPAECRQFIDQL 470


>gi|326566216|gb|EGE16368.1| RluA family pseudouridine synthase [Moraxella catarrhalis 103P14B1]
          Length = 382

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 88/327 (26%), Positives = 161/327 (49%), Gaps = 27/327 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V ++ V N+++  R+D +       +   +L K++RS ++R++ KR K ++++  G V
Sbjct: 58  SRVNFLTVTNNQDGQRVDNFLLARLKGLPRSHLYKLIRSDEIRINGKRCKAHDKLYMGDV 117

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+ P+  +    ++E  I+   +     +  L   +++ED  + V NKP G++V GGSG
Sbjct: 118 VRVAPIRLS----VREAPIISEEL-----AKGLLERIIFEDDGLIVLNKPHGMAVHGGSG 168

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            ++ I   ++  +  K     L HR+D++TSG+L++A+ R+  + L E FR + I K Y 
Sbjct: 169 ESFGIIEAMRLAMGKKY--LELIHRIDKDTSGLLLIAKKRSTLKILQEQFRTKTIHKQYL 226

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVI---DCF 236
            LV G  +  +  I   LL+ +   G+    V     ++  + A  +++  K +      
Sbjct: 227 CLVMGHVQADEMVIDVPLLRYTLANGERRVKVAHLNEQKAGEHAKASLTKIKTLLRFKKD 286

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +   P TGRTHQ+RVH  H+G  ++GD KY    + N  +P   +L LHA  + 
Sbjct: 287 GCPVSLVLAMPATGRTHQIRVHMAHIGHALLGDDKY----QNNPLAPKVGRLCLHAWQLG 342

Query: 297 LP----HPEGGRLQITAPLPAHMVKTW 319
           +     H         AP+   M +  
Sbjct: 343 MTNDDGHTVTRPQNFVAPVADDMAQLL 369


>gi|71735208|ref|YP_273032.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|257481618|ref|ZP_05635659.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           tabaci ATCC 11528]
 gi|289626965|ref|ZP_06459919.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           aesculi str. NCPPB3681]
 gi|289651379|ref|ZP_06482722.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           aesculi str. 2250]
 gi|298485413|ref|ZP_07003502.1| Ribosomal large subunit pseudouridine synthase D [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|71555761|gb|AAZ34972.1| Ribosomal large subunit pseudouridine synthase D(Pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|298160063|gb|EFI01095.1| Ribosomal large subunit pseudouridine synthase D [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|320326249|gb|EFW82303.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           glycinea str. B076]
 gi|320330673|gb|EFW86650.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330869191|gb|EGH03900.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           aesculi str. 0893_23]
 gi|330891573|gb|EGH24234.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. mori str. 301020]
 gi|330901397|gb|EGH32816.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. japonica str. M301072PT]
 gi|330954255|gb|EGH54515.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae Cit 7]
 gi|330971944|gb|EGH72010.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. aceris str. M302273PT]
 gi|331008769|gb|EGH88825.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           tabaci ATCC 11528]
          Length = 320

 Score =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 87/333 (26%), Positives = 150/333 (45%), Gaps = 36/333 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLELIAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
            A    + +   LD               ++YED +I V NKPAG+ V   +G A     
Sbjct: 71  EAQGEWVAQDIELD---------------IIYEDDQILVINKPAGLVVHPAAGHADGTLL 115

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R + +IY  +V 
Sbjct: 116 NALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVI 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+       I   + +        + V+    +G   A+SH++V++ F +    + ++  
Sbjct: 176 GVV-TAGGKIDAPIGRHGQQ-RQRMAVM----EGGKQAVSHYRVLERF-RSHTHVRVKLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P+VGD  Y   F+    + +          +  LHAR+++L HP
Sbjct: 229 TGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFLELDHP 288

Query: 301 EGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
             G R+   +PLP   V     L  K DR  +I
Sbjct: 289 TTGKRMSWESPLPDDFVWLLSLL--KQDREAFI 319


>gi|326567130|gb|EGE17252.1| RluA family pseudouridine synthase [Moraxella catarrhalis BC1]
          Length = 382

 Score =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 89/327 (27%), Positives = 162/327 (49%), Gaps = 27/327 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V ++ V N+++  R+D +       +   +L K++RS ++R++ KR K ++++  G V
Sbjct: 58  SRVNFLTVTNNQDGQRVDNFLLARLKGLPRSHLYKLIRSDEIRINGKRCKAHDKLYMGDV 117

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+ P+  +    ++E  I+   +     +  L   +++ED  + V NKP G++V GGSG
Sbjct: 118 VRVAPIRLS----VREAPIISEEL-----AKGLLERIIFEDDGLIVLNKPHGMAVHGGSG 168

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            ++ I   ++  +  K     L HR+D++TSG+L++A+ R+  + L E FR + IQK Y 
Sbjct: 169 ESFGIIEAMRLAMGKKY--LELIHRIDKDTSGLLLIAKKRSTLKILQEQFRKKTIQKRYL 226

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVI---DCF 236
            LV G  +  +  I   LL+ +   G+    V     ++  + A  +++  K +      
Sbjct: 227 CLVMGHVQADEMVIDVPLLRYTLANGERRVKVAHLNEQKAGEYAKASLTKIKTLLRFKKD 286

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +   P TGRTHQ+RVH  H+G  ++GD KY    + N  +P   +L LHA  + 
Sbjct: 287 GCPVSLVLAMPATGRTHQIRVHMAHIGHALLGDDKY----QNNPLAPKVGRLCLHAWQLG 342

Query: 297 LP----HPEGGRLQITAPLPAHMVKTW 319
           +     H         AP+   M +  
Sbjct: 343 MTNDDGHTVTRPQNFVAPVADDMAQLL 369


>gi|317493978|ref|ZP_07952395.1| RluA family pseudouridine synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918305|gb|EFV39647.1| RluA family pseudouridine synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 326

 Score =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 84/336 (25%), Positives = 149/336 (44%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + I
Sbjct: 8   TATVTESQLGHRLDQALAELFPDYSRSRIKEWILDDRVKVNGKIINKPKEKVLGGEEIAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +I        +   LD               ++YEDS I V NKP  + V  G+G   
Sbjct: 68  DALIEEEARWEPQNIPLD---------------IVYEDSDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             I   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y 
Sbjct: 113 GTILNALLYYYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        +E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGTMTAGGTVEEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RAHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHISHPLVGDPLYGGRPRPPKGASEEFITILRGFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G +++  APLP  MV    +L    + 
Sbjct: 283 MLRLYHPISGIQMEWHAPLPQDMVDLITALQADTEE 318


>gi|83719283|ref|YP_442243.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           thailandensis E264]
 gi|83653108|gb|ABC37171.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           thailandensis E264]
          Length = 477

 Score =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 94/326 (28%), Positives = 150/326 (46%), Gaps = 22/326 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++      R+D +       +   ++ +ILRSG+VRV+K R+    R+  G   
Sbjct: 158 QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGD-- 215

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                       ++      +           +  +L+ED  I   NKPAG++V GGSG+
Sbjct: 216 ------VVRVPPVRVAAADLARAAGPAPVPAAEFEILFEDDAIIALNKPAGVAVHGGSGV 269

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y++
Sbjct: 270 AFGVIEQMRHAR-PHAKFLELVHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRYFA 328

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G           +   L K +   G+    V+++      + + F ++D +   +  
Sbjct: 329 CVHGDWAADWGRRRAVKAPLFKYATPDGERRVRVQED---GLPSHTVFNLVDRWPD-YAL 384

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PIVGD KY               P   +++LHA  + L
Sbjct: 385 VEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARASAVPSIKRMFLHAHRLRL 444

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA   +  D L
Sbjct: 445 AHPLTGEPLQFDAPLPAECRQFLDQL 470


>gi|302185255|ref|ZP_07261928.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           syringae 642]
          Length = 320

 Score =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 87/333 (26%), Positives = 150/333 (45%), Gaps = 36/333 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLELVAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
            A    + +   LD               ++YED +I V NKPAG+ V   +G A     
Sbjct: 71  EAQGEWVAQDIELD---------------IIYEDDQILVINKPAGLVVHPAAGHADGTLL 115

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R + +IY  +V 
Sbjct: 116 NALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVI 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+       I   + +        + V+    +G   A+SH++V++ F +    + ++  
Sbjct: 176 GVV-TAGGKIDAPIGRHGQQ-RQRMAVM----EGGKQAVSHYRVLERF-RSHTHVRVKLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P+VGD  Y   F+    + +          +  LHAR+++L HP
Sbjct: 229 TGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFLELDHP 288

Query: 301 EGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
             G R+   +PLP   V     L  K DR  +I
Sbjct: 289 TTGKRMSWESPLPDDFVWLLSLL--KQDREAFI 319


>gi|290580687|ref|YP_003485079.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
 gi|254997586|dbj|BAH88187.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
          Length = 296

 Score =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 78/318 (24%), Positives = 141/318 (44%), Gaps = 34/318 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E  E  +RLD+   +    ++     + +++G V V+ K  K    ++ G ++      
Sbjct: 3   IEIKEAGVRLDKALAD-LTDLSRSQASEQIKAGLVWVNGKTQKAKYAVKEGDII------ 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHI 129
               H  + Q+ +     L   +  +   ++YED  + V NKP G+ V    G      +
Sbjct: 56  ----HYERPQEEV-----LDCVAQNIPLEIVYEDEDVAVINKPQGMVVHPSVGHPSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D        +P + HR+D++TSG+L++A+   A Q L +  + ++  + Y +
Sbjct: 107 NALLFHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDQAHQALAKELKEKKSLRQYIA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G   N +  I   + +            K        A++HFKV++ F Q +  +E+
Sbjct: 167 LVHGNLPNDRGVIEAPIGRSEKDRKKQTVTAK-----GKPAVTHFKVLERFDQ-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
              TGRTHQ+RVH  ++G P+ GD  Y         +      +LHA+ +   HP+ G  
Sbjct: 221 TLETGRTHQIRVHMAYIGHPVAGDPLYAPK-----KTLKGQGQFLHAKTLGFTHPKTGEL 275

Query: 305 LQITAPLPAHMVKTWDSL 322
           +Q T  +P    +  D L
Sbjct: 276 MQFTTEVPVIFQEVLDHL 293


>gi|170744872|ref|YP_001773527.1| RluA family pseudouridine synthase [Methylobacterium sp. 4-46]
 gi|168199146|gb|ACA21093.1| pseudouridine synthase, RluA family [Methylobacterium sp. 4-46]
          Length = 336

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 86/348 (24%), Positives = 151/348 (43%), Gaps = 48/348 (13%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQS 61
           +   V+   +       RLDR     +P ++   LQ ++R G VR+D   ++    ++  
Sbjct: 1   MENEVRVSEIPAGGAPERLDRALARLWPDLSRNRLQGLIREGGVRLDGAEIRDGAVKVAG 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           GQ V +                +  ++  T  +      ++YED  + V +KPAG+ V  
Sbjct: 61  GQRVAV---------------AVPQALPATPAAQARDLAIVYEDDDLIVIDKPAGLVVHP 105

Query: 122 GSGIAYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
             G   H DG L + + +            ++P + HRLD++TSG+LVVA+   A   L+
Sbjct: 106 APG---HPDGTLVNALIAHCGASLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHAGLS 162

Query: 172 ESFRMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             F        +++ Y +LVWG+P  +   I   L +      + + VV+  +    +A+
Sbjct: 163 LQFADHGRSGMLERAYLALVWGVPAPRNGTIDAALARSER-NREKIAVVRPEQ--GRHAV 219

Query: 228 SHFKVIDCFA--QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---------NF 276
           +H++        +    +  +  TGRTHQ+RVH  H G P++GD  Y A         + 
Sbjct: 220 THYRTEAVLGAREPVGQIRCRLETGRTHQIRVHLAHRGHPLLGDRTYGAAFRTKAARLDP 279

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +         +  LHA  +   HP     L+  +PLPA + +   +LG
Sbjct: 280 EAREALDALGRQALHAAVLGFVHPRSHAVLRFESPLPADLARLVAALG 327


>gi|326560261|gb|EGE10649.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis 7169]
 gi|326570229|gb|EGE20274.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis BC8]
 gi|326570966|gb|EGE20990.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis BC7]
          Length = 355

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 146/322 (45%), Gaps = 30/322 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD+   + +   +  NL+K +  GQ+ V+ K VK    ++ G ++ +  V 
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVKPKYAVKVGDILTLEAVH 107

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            + +  + E   +D               ++YED  + + NKPAG+ V  G+G      +
Sbjct: 108 ESHSEDLPENIDID---------------IIYEDEAVIIINKPAGMVVHPGAGNRTGTLV 152

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L  +       +  L HR+D++T+G+LV+ART++A   L +  + + + + Y  +  
Sbjct: 153 NALLYHFPKQAHLPRAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIAL 212

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQP 247
           G        +       + IG    H  K   K     A++H        +++  L++  
Sbjct: 213 GAVHE----VLRHAQIDAPIGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHL 268

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPE 301
            TGRTHQ+RVH  ++G P+VGD  Y  + +   +   +       +  LHA  +   HP 
Sbjct: 269 KTGRTHQIRVHLSYVGHPLVGDPVYGTSPRSGLSDRQRCAILDFGRQALHAYMLGFIHPV 328

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++  APLP  M +  + L
Sbjct: 329 TGEAMKFHAPLPKDMQQLIEIL 350


>gi|315498779|ref|YP_004087583.1| pseudouridine synthase, rlua family [Asticcacaulis excentricus CB
           48]
 gi|315416791|gb|ADU13432.1| pseudouridine synthase, RluA family [Asticcacaulis excentricus CB
           48]
          Length = 334

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 88/334 (26%), Positives = 149/334 (44%), Gaps = 41/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           +V+ +D    RLDR      P ++   LQ ++  G +  D + +    ++ ++G      
Sbjct: 22  LVLTSDMAGDRLDRALLPLLPDLSRARLQALISDGHLSHDGQTIADGKHKARAG------ 75

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                       +  + + V+    +  L   +LYED+ + V NKPAG++     G A  
Sbjct: 76  ----------LYRLFVPAPVSAIPEAQNLPLEVLYEDAHLIVVNKPAGMAAHPAPGTADG 125

Query: 129 IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + + +   G+         +P + HRLD++TSG++V A++ AA + L+E F    I
Sbjct: 126 --TLVNALLFHCGESLSGIGGVLRPGIVHRLDKDTSGVMVAAKSDAAHRGLSELFSRHDI 183

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y +LV G PK     +   + +  H     + V+K    G   AISH++ ++ F  +
Sbjct: 184 DRAYEALVRGAPKTASGTVTTRIGRSPH-DRKKMAVLKS---GGREAISHYRTLNSFGGE 239

Query: 240 ---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-----KLYLH 291
                 +     TGRTHQ+RVH  ++GCP +GD  Y +       +         +  LH
Sbjct: 240 KPVAARVRCTLETGRTHQIRVHMAYLGCPCLGDPVYGSGAPHRAVAEALKTLSFARQALH 299

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
           A ++   HP  G RL   APLPA M     +L  
Sbjct: 300 AAHLGFVHPVTGERLAFEAPLPADMADLLSALKL 333


>gi|91784729|ref|YP_559935.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           xenovorans LB400]
 gi|91688683|gb|ABE31883.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           xenovorans LB400]
          Length = 323

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 96/322 (29%), Positives = 156/322 (48%), Gaps = 24/322 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR+PP
Sbjct: 2   IEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  A            S              +++ED  + V +KPAG++V GGSG+A+ +
Sbjct: 62  IRVAQ----------PSEAAAQAPVPAAHFRIIFEDEHLLVIDKPAGVAVHGGSGVAFGV 111

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++       +   L HRLD+ETSGIL++A+ R+A  +L E  R  ++ K Y++ V G
Sbjct: 112 IEQMREARPQ-AKFLELVHRLDRETSGILMLAKKRSALVNLHEQIRENKMDKRYYACVHG 170

Query: 190 IPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
              +       +   L K     G+    V+ +      + + F +ID + + +  LE +
Sbjct: 171 EWASDWGRRRAVREPLHKYLTADGERRVRVQPD---GLASHTVFNLIDRWPE-YALLEAE 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H+G PIVGD KY              +P   +++LHA  + L HP 
Sbjct: 227 LKTGRTHQIRVHLQHLGLPIVGDAKYGDFALNKALARANANPGLKRMFLHAYRLKLTHPA 286

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  LQ  APLP         L
Sbjct: 287 TGEPLQFEAPLPPECRSFIAQL 308


>gi|88705138|ref|ZP_01102850.1| Ribosomal large subunit pseudouridine synthase C [Congregibacter
           litoralis KT71]
 gi|88700833|gb|EAQ97940.1| Ribosomal large subunit pseudouridine synthase C [Congregibacter
           litoralis KT71]
          Length = 309

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 98/322 (30%), Positives = 157/322 (48%), Gaps = 16/322 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V+Y+ V+   E  RLD +     P +    L + +R G++RV+K RVK + R+  G 
Sbjct: 1   MSAVRYLTVDERGEGQRLDNYVLRECPAVPKTRLYRAMRKGEIRVNKGRVKPDRRLALGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VVR+PP        +   +  +         + L + +++ED  +   NKP+GI+V GGS
Sbjct: 61  VVRLPP--------LSTPEPRERGAAPPGWQERLGARVVFEDEHLLAINKPSGIAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKI 182
           G+ + +   L++      +   L HRLD+ETSG+++VA+  AA + L E  R + +I K 
Sbjct: 113 GLQFGLIETLRTMRPG-AKFLELVHRLDRETSGLILVAKKPAALRALHELLRQKGKIDKR 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L  G        +   L +     G+    V    K    +I+ F+ I         
Sbjct: 172 YLALAEGAWPRHLRLVEAPLKRFERQSGERQVKV---AKDGKPSITEFR-IKRSFSAATL 227

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +E +P TGRTHQ+RVHALH G P++GD KY     +G        +L+LHA+ +      
Sbjct: 228 VEARPLTGRTHQIRVHALHGGHPLLGDGKYQSEKGEGLARKLGLKRLFLHAQSLSFE-LN 286

Query: 302 GGRLQITAPLPAHMVKTWDSLG 323
             R ++TAPL   +      L 
Sbjct: 287 DQRYELTAPLDEELESILIKLA 308


>gi|157148106|ref|YP_001455425.1| 23S rRNA pseudouridine synthase D [Citrobacter koseri ATCC BAA-895]
 gi|157085311|gb|ABV14989.1| hypothetical protein CKO_03916 [Citrobacter koseri ATCC BAA-895]
          Length = 326

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 80/336 (23%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVSI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                            +    +      +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  N---------------AEIDEEIRFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKGASEAFISTLRQFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  D +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIDVMRADFEE 318


>gi|326575838|gb|EGE25761.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis CO72]
          Length = 355

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 146/322 (45%), Gaps = 30/322 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD+   + +   +  NL+K +  GQ+ V+ K VK    ++ G ++ +  V 
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVKPKYAVKVGDILTLEAVH 107

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            + +  + E   +D               ++YED  + + NKPAG+ V  G+G      +
Sbjct: 108 ESHSEDLPENIDID---------------IIYEDEAVIIINKPAGMVVHPGAGNRTGTLV 152

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L  +       +  L HR+D++T+G+LV+ART++A   L +  + + + + Y  +  
Sbjct: 153 NALLYHFPKQAHLPRAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIAL 212

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQP 247
           G        +       + IG    H  K   K     A++H        +++  L++  
Sbjct: 213 GAVHE----VLRHAQIDAPIGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHL 268

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPE 301
            TGRTHQ+RVH  ++G P+VGD  Y  + +   +   +       +  LHA  +   HP 
Sbjct: 269 KTGRTHQIRVHLSYVGHPLVGDPVYGTSPRAGLSDRQRCAILDFGRQALHAYMLGFIHPV 328

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++  APLP  M +  + L
Sbjct: 329 TGEAMKFHAPLPKDMQQLIEVL 350


>gi|332668251|ref|YP_004451039.1| RluA family pseudouridine synthase [Haliscomenobacter hydrossis DSM
           1100]
 gi|332337065|gb|AEE54166.1| pseudouridine synthase, RluA family [Haliscomenobacter hydrossis
           DSM 1100]
          Length = 366

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 78/339 (23%), Positives = 147/339 (43%), Gaps = 45/339 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V+ ++  +R+D++  +    ++   +Q  +++G V V+ + +K N +I+ GQ + +
Sbjct: 27  RIIEVDGNQSPLRIDKFLMDRIGEVSRNRVQNAIKTGSVLVNDQEIKPNFKIKPGQKITL 86

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
               +  +              L      +   ++YED  + V NKP G+ V  G G   
Sbjct: 87  ILPKSTTD-------------KLRIVPQNIPLNVVYEDEDLLVVNKPPGLVVHPGVG--- 130

Query: 128 HIDGFLKSWVDSK-------------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           H  G L + +                 ++  L HR+D+ TSG+LVVA+   A  HL + F
Sbjct: 131 HFKGTLVNALAYHLRLDPNQISTGNFQERVGLVHRIDKNTSGLLVVAKNEFALSHLAKQF 190

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               I++ Y +LVWG P+  +  I   + +      D+   V        +A++H++V++
Sbjct: 191 FYHTIERTYNALVWGEPEEDRGTINAHVGRHPRFRKDF--TVFPEGDQGKWAVTHYQVLE 248

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ------- 285
                   ++    TGRTHQ+RVH  ++G  +  D KY  +   KG   S  +       
Sbjct: 249 RL-YYVSLIKCTLETGRTHQIRVHLKYLGHTLFNDEKYGGDEILKGTIFSKYKIFVDHMF 307

Query: 286 ---NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
               +  LHA+ +   HP   + +   + LP       +
Sbjct: 308 DVLPRHALHAKSLGFIHPRTNKFMHFDSDLPDDFKVAME 346


>gi|152981261|ref|YP_001353083.1| ribosomal large subunit pseudouridine synthase D [Janthinobacterium
           sp. Marseille]
 gi|151281338|gb|ABR89748.1| ribosomal large subunit pseudouridine synthase D [Janthinobacterium
           sp. Marseille]
          Length = 342

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 80/315 (25%), Positives = 137/315 (43%), Gaps = 29/315 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+      P  +   LQ+ +  G V VD +  +    +   + V I P     +  
Sbjct: 48  GVRLDKVLSTLVPQYSRSRLQQWIDGGHVSVDGEVARAKMTVYGDEKVVIYPQPAPEDEA 107

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
            K               + +   +++ED+++ V NKPAG+ V   +G      ++G L  
Sbjct: 108 FK--------------PEAMDLAIVHEDAEMLVINKPAGLVVHPAAGNWSGTLLNGLLHY 153

Query: 136 WVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                G  +  + HRLD++TSG++VVA+T  A   L    + R +++ Y +LVWG P N 
Sbjct: 154 LPSISGVPRAGIVHRLDKDTSGLMVVAKTLIAHTDLVRQLQARTVKREYLALVWGTP-NI 212

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGR 251
              I   + +      D + +       A  A++HF+ +       +    +  +  TGR
Sbjct: 213 TGKIDASIGRH---ARDRIKMAVSENLTAKPAVTHFQRLATGMLDGRPVSLMLCRLETGR 269

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH   +G  +VGD  Y         + +  +  LHAR + L HP  G  ++ ++ 
Sbjct: 270 THQIRVHMQSIGFALVGDGLYGKQH----LTTVFPRQALHARRLGLIHPVSGEAVEWSSE 325

Query: 311 LPAHMVKTWDSLGFK 325
           LP    +     G K
Sbjct: 326 LPQDFAELIARAGIK 340


>gi|326568395|gb|EGE18475.1| RluA family pseudouridine synthase [Moraxella catarrhalis BC7]
          Length = 382

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 89/327 (27%), Positives = 163/327 (49%), Gaps = 27/327 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V ++ V N+++  R+D +       +   +L K++RS ++R++ KR K ++++  G V
Sbjct: 58  SRVNFLTVTNNQDGQRVDNFLLARLKGLPRSHLYKLIRSDEIRINGKRCKAHDKLYMGDV 117

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+ P+  +    ++E  I+   +     +  L   +++ED+ + V NKP G++V GGSG
Sbjct: 118 VRVAPIRLS----VREAPIISEEL-----AKGLLERIIFEDNGLIVLNKPHGMAVHGGSG 168

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            ++ I   ++  +  K     L HR+D++TSG+L++A+ R+  + L E FR + IQK Y 
Sbjct: 169 ESFGIIEAMRLAMGKKY--LELIHRIDKDTSGLLLIAKKRSTLKILQEQFRKKTIQKRYL 226

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVI---DCF 236
            LV G  +  +  I   LL+ +   G+    V     ++  + A  +++  K +      
Sbjct: 227 CLVMGHVQADEMVIDVPLLRYTLANGERRVKVAHLNEQKAGEYAKASLTKIKTLLRFKKD 286

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +   P TGRTHQ+RVH  H+G  ++GD KY    + N  +P   +L LHA  + 
Sbjct: 287 GCPVSLVLAMPATGRTHQIRVHMAHIGHALLGDDKY----QNNPLAPKVGRLCLHAWQLG 342

Query: 297 LP----HPEGGRLQITAPLPAHMVKTW 319
           +     H         AP+   M +  
Sbjct: 343 MTNDDGHTVTRPQNFVAPVADDMAQLL 369


>gi|312795518|ref|YP_004028440.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           rhizoxinica HKI 454]
 gi|312167293|emb|CBW74296.1| Ribosomal large subunit pseudouridine synthase C (EC 4.2.1.70)
           [Burkholderia rhizoxinica HKI 454]
          Length = 336

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 98/325 (30%), Positives = 153/325 (47%), Gaps = 26/325 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V++     R+D +       +   ++ +ILRSG+VRV+K RV  + R++ G +VR
Sbjct: 17  VSWLNVDDASAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDASYRLEHGDIVR 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+  A               +    +      +LYED  +   +KPAGI+V GGSG++
Sbjct: 77  VPPIRVA------------QPAHSPVSAPAATFPVLYEDDCLIALDKPAGIAVHGGSGVS 124

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   +++      +   L HRLD+ETSG+L++A+ RAA   L E  R  R+ K Y + 
Sbjct: 125 FGVIEQMRAARPG-ARMLELVHRLDRETSGVLLLAKKRAALVGLHEQIREGRLDKRYLAC 183

Query: 187 VWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             G           +   L K     G+    V+ +  G   + + F +       +  L
Sbjct: 184 ARGAWPADWGVRRAVKAPLHKYLTADGERRVRVQPDGLG---SHTVFNLRQRLGD-YLLL 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLP 298
           E +  TGRTHQ+RVH  H+G PIVGD KY       N       P   +++LHA  + + 
Sbjct: 240 EAELKTGRTHQIRVHLAHLGLPIVGDDKYGDFSLNKNLARPGVRPGLRRMFLHAWRLSIQ 299

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSL 322
           HP  G  L   APLPA        L
Sbjct: 300 HPASGAPLSFEAPLPAECDNFLQQL 324


>gi|66043991|ref|YP_233832.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           B728a]
 gi|63254698|gb|AAY35794.1| Pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           B728a]
          Length = 320

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 87/333 (26%), Positives = 150/333 (45%), Gaps = 36/333 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGALRPRDIVHGGAVLELIAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
            A    + +   LD               ++YED +I V NKPAG+ V   +G A     
Sbjct: 71  EAQGEWVAQDIELD---------------IIYEDDQILVINKPAGLVVHPAAGHADGTLL 115

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R + +IY  +V 
Sbjct: 116 NALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVI 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+       I   + +        + V+    +G   A+SH++V++ F +    + ++  
Sbjct: 176 GVV-TAGGKIDAPIGRHGQQ-RQRMAVM----EGGKQAVSHYRVLERF-RSHTHVRVKLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P+VGD  Y   F+    + +          +  LHAR+++L HP
Sbjct: 229 TGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFLELDHP 288

Query: 301 EGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
             G R+   +PLP   V     L  K DR  +I
Sbjct: 289 TTGKRMSWESPLPDDFVWLLSLL--KQDREAFI 319


>gi|319787308|ref|YP_004146783.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317465820|gb|ADV27552.1| pseudouridine synthase, RluA family [Pseudoxanthomonas suwonensis
           11-1]
          Length = 319

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 97/328 (29%), Positives = 154/328 (46%), Gaps = 21/328 (6%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S     + V V  D +  RLD +            + K++RSGQVRV+  R K   ++  
Sbjct: 5   SPRAGARTVTVPEDRDGQRLDNFLLGQLKGAPRSLVYKLVRSGQVRVNGGRAKAERKLAG 64

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VRIPP        ++ +   +           +++ +++ED++I V +KP+G++  G
Sbjct: 65  GDEVRIPP--------VRVETEAERGTPAPGLLQRMEASIVFEDARILVIDKPSGVASHG 116

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM----R 177
           GSGI++     L++     GQ   L HRLD++TSGILVVA+ R+A   L    R      
Sbjct: 117 GSGISFGAIETLRALRP--GQTLELAHRLDRDTSGILVVAKKRSALAELQALMREGGSGG 174

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I+K Y +L+ G   +    +   L      GG+    V Q       ++SHF+ ++   
Sbjct: 175 GIRKRYLTLLAGRMPDGTMSVDAPLHVGLRQGGERHVQVNQ---AGKPSVSHFRALERRG 231

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYM 295
               + E++  TGRTHQ+RVHA H+G P+ GD KY                +L+LHA  +
Sbjct: 232 -GQSYCEVRIETGRTHQIRVHAQHIGHPVAGDDKYGDPEVNRRLRDKAGLRRLFLHAASL 290

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           +     G     + APLP  + +  D L
Sbjct: 291 EFALDAGRTPYTLNAPLPPELREVLDRL 318


>gi|225075563|ref|ZP_03718762.1| hypothetical protein NEIFLAOT_00576 [Neisseria flavescens
           NRL30031/H210]
 gi|224953108|gb|EEG34317.1| hypothetical protein NEIFLAOT_00576 [Neisseria flavescens
           NRL30031/H210]
          Length = 328

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 99/322 (30%), Positives = 167/322 (51%), Gaps = 25/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   EE  RLD +       +   ++ +I+R+G+VR++KKR K +NRIQ+G  VR
Sbjct: 9   VSLIAVAEHEEGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDNRIQAGDTVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      I ++Q+  +S     +  +     ++YED  + V NKP+G++V GGSG++
Sbjct: 69  IPPI-----RIAEKQRPSESQAAPAREFE-----IVYEDDALLVINKPSGVAVHGGSGVS 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++     + +   L HRLD++TSG+L++A+ R+A   L E+ R    +KIY +L
Sbjct: 119 FGVIEQIRRAR-PEARYLELVHRLDKDTSGLLMIAKKRSALVKLHEAIRNDHPKKIYLAL 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   N +  +   L K +   G+ +  V ++      A + F+V++ F+         
Sbjct: 178 GVGRLPNDRFHVKLPLFKYTGAQGEKMVRVSED---GQSAHTIFRVLNRFSDGLLHQVGL 234

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
               ++E    TGRTHQ+RVH     CPI GD +Y               +++LHA  + 
Sbjct: 235 SDLTFVEATLKTGRTHQIRVHLQSQDCPIAGDERYGDYQANKRLQKLGLKRMFLHASELH 294

Query: 297 LPHP-EGGRLQITAPLPAHMVK 317
           L HP  G +L + APLP  + +
Sbjct: 295 LAHPLTGEKLILKAPLPQELAQ 316


>gi|296113272|ref|YP_003627210.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis RH4]
 gi|295920966|gb|ADG61317.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis RH4]
 gi|326566421|gb|EGE16571.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis BC1]
          Length = 355

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 145/322 (45%), Gaps = 30/322 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD+   + +   +  NL+K +  GQ+ V+ K VK    ++ G ++ +  V 
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVKPKYAVKVGDILTLEAVH 107

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            + +  + E   +D               ++YED  + + NKPAG+ V  G+G      +
Sbjct: 108 ESHSEDLPENIDID---------------IIYEDEAVIIINKPAGMVVHPGAGNRTGTLV 152

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L  +       +  L HR+D++T+G+LV+ART++A   L    + + + + Y  +  
Sbjct: 153 NALLYHFPKQAHLPRAGLVHRIDKDTTGLLVIARTKSAQLSLINQLKDKSVYRHYQCIAL 212

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQP 247
           G        +       + IG    H  K   K     A++H        +++  L++  
Sbjct: 213 GAVHE----VLRHAQIDAPIGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHL 268

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPE 301
            TGRTHQ+RVH  ++G P+VGD  Y  + +   +   +       +  LHA  +   HP 
Sbjct: 269 KTGRTHQIRVHLSYVGHPLVGDPVYGTSPRSGLSDRQRCAILDFGRQALHAYMLGFIHPV 328

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++  APLP  M +  + L
Sbjct: 329 TGEAMKFHAPLPKDMQQLIEIL 350


>gi|161870862|ref|YP_001600036.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis 053442]
 gi|161596415|gb|ABX74075.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis 053442]
 gi|325141211|gb|EGC63711.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis CU385]
 gi|325145393|gb|EGC67670.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M01-240013]
          Length = 330

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 156/322 (48%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V ++      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSED---GQSAHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A LP  + +
Sbjct: 298 LNHPLTGEPLVLKAELPPDLAQ 319


>gi|238756473|ref|ZP_04617780.1| Ribosomal large subunit pseudouridine synthase D [Yersinia ruckeri
           ATCC 29473]
 gi|238705322|gb|EEP97732.1| Ribosomal large subunit pseudouridine synthase D [Yersinia ruckeri
           ATCC 29473]
          Length = 325

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 142/328 (43%), Gaps = 35/328 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V VD K + K   ++  G++V I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDDKVSVDGKTINKPKEKVLGGEIVAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I        ++  LD               ++YEDS I V NKP G+ V  G+G     
Sbjct: 70  QIEEAARWEPQEIPLD---------------IVYEDSDILVINKPRGLVVHPGAGNPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++
Sbjct: 115 VLNALLYYYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A++H+++++ F +    L ++
Sbjct: 175 AIGKM-TAGGLVDEPISRHST-----KRTHMAVHPMGKPAVTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPRGASDNFITVLRGFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           HP  G +++  A LP  M++   +L   
Sbjct: 288 HPISGVQMEWHAALPEDMIELITALKAD 315


>gi|187924897|ref|YP_001896539.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187716091|gb|ACD17315.1| pseudouridine synthase, RluA family [Burkholderia phytofirmans
           PsJN]
          Length = 341

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 97/326 (29%), Positives = 159/326 (48%), Gaps = 24/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +V
Sbjct: 16  QVSMIEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP+  A       Q  + ++             +++ED  + V +KPAG++V GGSG+
Sbjct: 76  RVPPIRVAQPSETATQAPVPAAH----------FKIIFEDEHLLVIDKPAGVAVHGGSGV 125

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ R+A  +L E  R  ++ K Y++
Sbjct: 126 AFGVIEQMREARPQ-AKFLELVHRLDRETSGILMLAKKRSALVNLHEQIRENKMDKRYYA 184

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G   +       +   L K     G+    V+ +      + + F +ID + + +  
Sbjct: 185 CVHGDWASDWGRRRAVKEPLHKYLTADGERRVRVQPD---GLASHTVFNLIDRWPE-YAL 240

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           LE +  TGRTHQ+RVH  H+  PIVGD KY               P   +++LHA  + L
Sbjct: 241 LEAELKTGRTHQIRVHLQHLELPIVGDAKYGDFALNKALARANAKPGLKRMFLHAYRLKL 300

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA        L
Sbjct: 301 THPATGAPLQFEAPLPAECRSFIAQL 326


>gi|314933372|ref|ZP_07840737.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           caprae C87]
 gi|313653522|gb|EFS17279.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           caprae C87]
          Length = 305

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 71/324 (21%), Positives = 143/324 (44%), Gaps = 33/324 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + +      R+D++        +   LQ  ++   V+V+ K +K N +++   
Sbjct: 1   MEKHEFKITDERRVGQRIDKFLSESNDAWSRSQLQDWIKEDLVKVNDKVIKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           I+ E++++++ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  HI-----------IVTEKEVVEADI----QPEDLDLDIYYEDDDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    +  G     +P + HR+D++TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKNLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMNK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    +   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYTALVHGNIPHDYGTVDAPIGRN-KNDRQAMAVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLIECELETGRTHQIRVHMKYIGFPLVGDPKYGPKKTLD-----IGGQALHAGVIGF 274

Query: 298 PHPEG-GRLQITAPLPAHMVKTWD 320
            HP     ++ ++ LP       +
Sbjct: 275 DHPVTHEYIERSSELPNDFKDLLE 298


>gi|330977498|gb|EGH77444.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. aptata str. DSM 50252]
          Length = 320

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 87/333 (26%), Positives = 150/333 (45%), Gaps = 36/333 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLELIAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
            A    + +   LD               ++YED +I V NKPAG+ V   +G A     
Sbjct: 71  EAQGEWVAQDIELD---------------IIYEDDQILVINKPAGLVVHPAAGHADGTLL 115

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R + +IY  +V 
Sbjct: 116 NALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVI 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+       I   + +        + V+    +G   A+SH++V++ F +    + ++  
Sbjct: 176 GVV-TAGGKIDAPIGRHGQQ-RQRMAVM----EGGKQAVSHYRVLERF-RSHTHVRVKLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P+VGD  Y   F+    + +          +  LHAR+++L HP
Sbjct: 229 TGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFLELDHP 288

Query: 301 EGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
             G R+   +PLP   V     L  K DR  +I
Sbjct: 289 TTGKRISWESPLPDDFVWLLSLL--KQDREAFI 319


>gi|53728774|ref|ZP_00135229.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
 gi|126208592|ref|YP_001053817.1| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae
           L20]
 gi|165976548|ref|YP_001652141.1| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|190150449|ref|YP_001968974.1| ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|303253303|ref|ZP_07339452.1| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307246037|ref|ZP_07528119.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307248145|ref|ZP_07530173.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|307250378|ref|ZP_07532326.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|307255019|ref|ZP_07536837.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|307257175|ref|ZP_07538947.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|307259455|ref|ZP_07541180.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|307261604|ref|ZP_07543272.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|126097384|gb|ABN74212.1| ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
 gi|165876649|gb|ABY69697.1| pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 3
           str. JL03]
 gi|189915580|gb|ACE61832.1| ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|302647985|gb|EFL78192.1| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306852972|gb|EFM85195.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|306855322|gb|EFM87497.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|306857588|gb|EFM89696.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|306861892|gb|EFM93868.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|306864337|gb|EFM96248.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|306866391|gb|EFM98254.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|306868727|gb|EFN00536.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
          Length = 325

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 80/338 (23%), Positives = 142/338 (42%), Gaps = 37/338 (10%)

Query: 4   MTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           MT    +   V  D    RLD+     +P  +   ++  + S  V+V+   V K   ++ 
Sbjct: 1   MTQQMTLTAEVTADLLGCRLDQALAQLFPDYSRSRIKVWIESDLVKVNGIVVNKAREKVF 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ V I   I                         +   ++YED  I V NKP  + V 
Sbjct: 61  GGEQVEIQAEIEEEIRF---------------EPQDIPLNIVYEDDDIIVINKPKDLVVH 105

Query: 121 GGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+G     +   L  +     + PR  + HRLD++T+G++VVA+   A  HL  + + R
Sbjct: 106 PGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRLDKDTTGLMVVAKNIPAQTHLVTALQKR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           RI + Y ++  G+   +   +   + +                     A++H+++++ F 
Sbjct: 166 RITREYEAVASGVM-TQGGKVDEPMARHPT-----KRTAMAVHPMGKPAVTHYRIMERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLY 289
           + +  L ++  TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  
Sbjct: 219 RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQLYGGRPRPPKGASEEFLAVLRGFQRQA 278

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           LHA  + L HP  G  ++  APLP   V+  ++L   Y
Sbjct: 279 LHATMLRLEHPITGELMEWHAPLPDDFVELIEALKADY 316


>gi|78224625|ref|YP_386372.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           metallireducens GS-15]
 gi|78195880|gb|ABB33647.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           metallireducens GS-15]
          Length = 319

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 83/335 (24%), Positives = 148/335 (44%), Gaps = 36/335 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           + T  +++     E   RLD++       +    +Q+++  G+V VD K  K + +++ G
Sbjct: 1   MDTTYEFIAPGEGEAG-RLDQFVARSVEGMTRSTVQRLIDEGRVTVDGKVEKPSLKLRGG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + + +     A                    ++ +  ++L+EDS + V NK AG+ V  G
Sbjct: 60  ERIVVAVPPPAPA---------------VPEAEEIPLVILHEDSDLVVVNKSAGMVVHPG 104

Query: 123 SGI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G      ++  L    D  G     +P + HR+D++T+G+LVVA+   + + L   FR 
Sbjct: 105 AGTPGGTLVNALLAHCTDLSGIGGEIRPGIVHRIDKDTTGVLVVAKNDRSHEGLARQFRE 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I++IY +LV+G PK     I   + +           +    K   +A++H+KV+  +
Sbjct: 165 HTIKRIYLALVFGSPKTDTGRIEGAIGRHPTD----RLRMSGKAKHGKHAVTHWKVLARY 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQN-------KL 288
                 L ++  TGRTHQ+RVH    G P+VGD  Y       +   P+         + 
Sbjct: 221 P-GMTLLRLRLETGRTHQIRVHLAESGHPLVGDEVYGGAGRANDLRDPVLKKLVRELGRQ 279

Query: 289 YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            LHA+ +   HP  G  ++    LP  M +    L
Sbjct: 280 ALHAKTLGFIHPASGSYVEFDTELPDDMARIITYL 314


>gi|218767110|ref|YP_002341622.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis Z2491]
 gi|121051118|emb|CAM07389.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis Z2491]
 gi|254672162|emb|CBA04981.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis alpha275]
          Length = 330

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 156/322 (48%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V ++      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSED---GQSAHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A LP  + +
Sbjct: 298 LNHPLTGEPLVLKAELPPDLAQ 319


>gi|169335052|ref|ZP_02862245.1| hypothetical protein ANASTE_01458 [Anaerofustis stercorihominis DSM
           17244]
 gi|169257790|gb|EDS71756.1| hypothetical protein ANASTE_01458 [Anaerofustis stercorihominis DSM
           17244]
          Length = 301

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 157/323 (48%), Gaps = 30/323 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++  +V  +++N+R D++  +     +  +L+K+ + G+V ++ ++VK + ++ +G+ V
Sbjct: 2   EIKEFIVTEEKQNIRCDKFLSDKLEDFSRESLKKLFKEGEVFLNDEKVKPSRKLIAGERV 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           ++          + E ++LD        ++ +   ++YED  + + +KP G+ V   +G 
Sbjct: 62  KVN---------LPEPEVLDV------IAENIPINIVYEDEDVVIVDKPQGMVVHPANGN 106

Query: 126 A--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++  +    D        +P + HR+D++TSG+L++A+   A  HL   F+   I
Sbjct: 107 HSGTLVNALMYHVKDLSSINGVIRPGIVHRIDKDTSGLLIIAKNDNAHNHLAVQFKEHSI 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++  GI       I   + +   I    + V + N   +  A++HF VI  +  K
Sbjct: 167 NRRYKTICHGIIHENSGTIDAPIGRD-KIKRKEMCVTQSN---SKRAVTHFDVIKRY-DK 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           + +L++   TGRTHQ+RVH  ++  P++GD  Y   F      P + +L  HA  +   H
Sbjct: 222 YTFLDVHLETGRTHQIRVHLKYISHPVIGDKVYG--FNSQIDRPFKGQLL-HAYKLGFIH 278

Query: 300 PEGGR-LQITAPLPAHMVKTWDS 321
           P+    ++  + LP +  +  D 
Sbjct: 279 PKTNEYMEFNSELPDYFYELLDR 301


>gi|107099793|ref|ZP_01363711.1| hypothetical protein PaerPA_01000811 [Pseudomonas aeruginosa PACS2]
          Length = 317

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 86/336 (25%), Positives = 152/336 (45%), Gaps = 42/336 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  +    RLD+     +P  +   L   ++ G++ VD   ++  + + SG  + +    
Sbjct: 8   VPFELGGQRLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVHSGAQLVLEAEQ 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A    + +   L+               ++YED  I V +KPAG+ V   +G   H DG
Sbjct: 68  EAQGEWLAQDIELE---------------IVYEDEHILVIDKPAGLVVHPAAG---HQDG 109

Query: 132 FLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L + +       +   +  + HRLD++T+G++VVA+T  A   L    + R + +IY +
Sbjct: 110 TLLNALLYHVPDIANVPRAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEA 169

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+       I   + +   +    + VV         A+SH++V++ F +      +
Sbjct: 170 IVIGVI-TSGGTIDAPIGRHG-VQRQKMAVVD----AGKVAVSHYRVLERF-RAHTHTRV 222

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--------GNFTSPIQNKLYLHARYMDL 297
           +  TGRTHQ+RVH  H+G P+VGD  Y   F+           T     +  LHAR+++L
Sbjct: 223 KLETGRTHQIRVHMSHIGYPLVGDPVYGGRFRIPPVASQTLVQTLREFPRQALHARFLEL 282

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            HP  G R++  +PLP   +     L  + DR  ++
Sbjct: 283 DHPATGVRMKWESPLPEDFLWLLSLL--RQDREAFV 316


>gi|254427100|ref|ZP_05040807.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881]
 gi|196193269|gb|EDX88228.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881]
          Length = 324

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 77/330 (23%), Positives = 144/330 (43%), Gaps = 39/330 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V+ +    R+D+     +   +   LQ  +++G + V+  + K   ++   + + +
Sbjct: 11  RTEQVKPEHAGQRVDQVAAELFDGFSRSRLQTWIKNGVLTVNGAKTKPKEKLTGNESLTL 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           ++    L      +   ++Y+D  + V NKP G+ V   +G   
Sbjct: 71  E---------------VEIEPELDDQPQSIDLDVVYQDDDLIVINKPTGLVVHPAAG--- 112

Query: 128 HIDGFLKSWVDSKGQKP------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H DG L + +    ++        + HRLD++T+G++VVAR+  A Q L    + + + +
Sbjct: 113 HADGTLLNGLLHLDERLNSLPRAGIVHRLDRDTTGLMVVARSLEAHQSLVAQLQDKSLFR 172

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++  G+     +   +  + +  +      VVK    G   A++H++V+D + +   
Sbjct: 173 QYEAIAVGVMTGGGKV--DAPMGRHPVDRKKQAVVKT---GGKNAVTHYRVLDRY-RAHT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +++Q  TGRTHQ+RVH  H   P+VGD  Y    K    +            +  LHAR
Sbjct: 227 RIQVQLETGRTHQIRVHMAHRNYPLVGDPLYGGRLKQPAGATEALRQALHKFPRQALHAR 286

Query: 294 YMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
            + L HP  G   +  APLPA M     +L
Sbjct: 287 KLGLIHPATGEYREFEAPLPADMTGLIAAL 316


>gi|303250129|ref|ZP_07336331.1| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307252760|ref|ZP_07534651.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|302651192|gb|EFL81346.1| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306859792|gb|EFM91814.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
          Length = 325

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 80/338 (23%), Positives = 142/338 (42%), Gaps = 37/338 (10%)

Query: 4   MTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           MT    +   V  D    RLD+     +P  +   ++  + S  V+V+   V K   ++ 
Sbjct: 1   MTQQMTLTAKVTADLLGCRLDQALAQLFPDYSRSRIKVWIESDLVKVNGIVVNKAREKVF 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ V I   I                         +   ++YED  I V NKP  + V 
Sbjct: 61  GGEQVEIQAEIEEEIRF---------------EPQDIPLNIVYEDDDIIVINKPKDLVVH 105

Query: 121 GGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+G     +   L  +     + PR  + HRLD++T+G++VVA+   A  HL  + + R
Sbjct: 106 PGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRLDKDTTGLMVVAKNIPAQTHLVTALQKR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           RI + Y ++  G+   +   +   + +                     A++H+++++ F 
Sbjct: 166 RITREYEAVASGVM-TQGGKVDEPMARHPT-----KRTAMAVHPMGKPAVTHYRIMERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLY 289
           + +  L ++  TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  
Sbjct: 219 RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQLYGGRPRPPKGASEEFLAVLRGFQRQA 278

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           LHA  + L HP  G  ++  APLP   V+  ++L   Y
Sbjct: 279 LHATMLRLEHPITGELMEWHAPLPDDFVELIEALKADY 316


>gi|206900390|ref|YP_002251511.1| pseudouridylate synthase, 23S RNA-specific [Dictyoglomus
           thermophilum H-6-12]
 gi|206739493|gb|ACI18551.1| pseudouridylate synthase, 23S RNA-specific [Dictyoglomus
           thermophilum H-6-12]
          Length = 303

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 74/318 (23%), Positives = 141/318 (44%), Gaps = 33/318 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++   R+D++       ++   +Q ++  G ++V++K VK + +++ G  + +       
Sbjct: 11  EDGGERIDKYLSQKIS-LSRSQIQDLIDKGLIKVNEKEVKSSYKVKVGDKIEV------- 62

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGF 132
                   I+            +   ++YED  I + NKP G+ V    G      ++  
Sbjct: 63  --------IVPPPEETEIKPQDIPIEIVYEDDDIVIINKPKGMVVHPAHGHYNDTLVNAL 114

Query: 133 LKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L    D  G     +P + HRLD++T+G+L++A+   + Q L+E  + R +++ YW++  
Sbjct: 115 LYRIKDLSGIGGEIRPGIVHRLDKDTTGLLIIAKNDVSHQRLSEQLKNRILKRTYWAICE 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G    +++ +   L +   I    + +V         AI++FKV++ F + +  +     
Sbjct: 175 GEIPWEEKRVEAPLGRH-PIDRKRMAIV----PYGKLAITNFKVLERF-KGYTLISADLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+RVH  H+G PI+GD  Y    K            LHA+ +   HP     ++ 
Sbjct: 229 TGRTHQIRVHISHLGFPILGDEVYGRIDK----RFGVRGQLLHAKKISFIHPTKNVPMEF 284

Query: 308 TAPLPAHMVKTWDSLGFK 325
              LP    +    L  K
Sbjct: 285 EIDLPEEFKRVLSFLREK 302


>gi|85058561|ref|YP_454263.1| 23S rRNA pseudouridine synthase D [Sodalis glossinidius str.
           'morsitans']
 gi|84779081|dbj|BAE73858.1| ribosomal large subunit pseudouridine synthase D [Sodalis
           glossinidius str. 'morsitans']
          Length = 326

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 87/352 (24%), Positives = 150/352 (42%), Gaps = 45/352 (12%)

Query: 4   MTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQ 60
           M   Q++   V   +   RLD+     +P  +   ++  +  G VRV+++       ++ 
Sbjct: 1   MAQYQHLTGTVSESQLGQRLDQALAELFPDYSRSRIKAWILDGLVRVNRRVTAVPKEKML 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ V I   I                      +  +   ++YED  I V NKP  + V 
Sbjct: 61  GGESVEIQAFIEEAPRW---------------EAQAIPLNIVYEDDDILVINKPRDLVVH 105

Query: 121 GGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+G A   +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R
Sbjct: 106 PGAGNADGTVLNALLHYFPPIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAR 165

Query: 178 RIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            I + Y ++  G        ++ IA    K++H+    +            A++++++++
Sbjct: 166 EITREYEAVAIGTMTAGGTLEQPIARHATKRTHMAVHPM---------GKPAVTNYRIME 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG--------NFTSPIQN 286
            F +    L ++  TGRTHQ+RVH  H+  P+VGD  Y    +         N      +
Sbjct: 217 HF-RAHTRLRLRLETGRTHQIRVHMAHINHPLVGDPLYGGRSRPPKGASDAFNEVLRSFD 275

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           +  LHA  + L HP     ++  APLP  MV    +L  K D  L+   +  
Sbjct: 276 RQALHATLLRLYHPITSIEMEWHAPLPQDMVALIAAL--KADTELFKDSMDW 325


>gi|326576921|gb|EGE26827.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis O35E]
          Length = 355

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 146/322 (45%), Gaps = 30/322 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD+   + +   +  NL+K +  GQ+ V+ K VK    ++ G ++ +  V 
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVKPKYAVKVGDILTLEAVH 107

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            + +  + E   +D               ++YED  + + NKPAG+ V  G+G      +
Sbjct: 108 ESHSEDLPENIDID---------------IIYEDEAVIIINKPAGMVVHPGAGNRTGTLV 152

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L  +       +  L HR+D++T+G+LV+ART++A   L +  + + + + Y  +  
Sbjct: 153 NALLYHFPKQAHLPRAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCVAL 212

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQP 247
           G        +       + IG    H  K   K     A++H        +++  L++  
Sbjct: 213 GAVHE----VLRHAQIDAPIGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHL 268

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPE 301
            TGRTHQ+RVH  ++G P+VGD  Y  + +   +   +       +  LHA  +   HP 
Sbjct: 269 KTGRTHQIRVHLSYVGHPLVGDPVYGTSPRSGLSDRQRCAILDFGRQALHAYMLGFIHPV 328

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++  APLP  M +  + L
Sbjct: 329 TGEAMKFHAPLPKDMQQLIEIL 350


>gi|88809823|ref|ZP_01125329.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 7805]
 gi|88786207|gb|EAR17368.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 7805]
          Length = 327

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 85/315 (26%), Positives = 139/315 (44%), Gaps = 28/315 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +   +QK + +G VRV+ +  K    ++ G  V++          
Sbjct: 33  PMRLDRWLVSQRREQSRARIQKFIDAGLVRVNGRTGKAKTPLRQGDEVQLWMPPPEPLPY 92

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
           +K               + +   +L+ED  + V NKPAG++V    G      ++G L  
Sbjct: 93  LK--------------PEAMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLHH 138

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +V+A+++ A   L    + R   + Y ++V G+P
Sbjct: 139 CPDLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQVQIQKRIASREYLAVVHGVP 198

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   + +       Y  V   + +   +A +H+ + +     +  L  +  TGR
Sbjct: 199 SGDSGTIVGAIGRHPVDRKKYAVV---STESGRFACTHWSLQERLGD-YSLLRFKLDTGR 254

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH  HM  P+VGD  Y    K     P      LHA  + L HP    R+   AP
Sbjct: 255 THQIRVHCAHMNHPVVGDPTYSRCRKLPIELPG---QALHAFQLGLDHPISRERMLFEAP 311

Query: 311 LPAHMVKTWDSLGFK 325
           LP  MV+  + L  +
Sbjct: 312 LPGVMVRLLNKLRNR 326


>gi|218265033|ref|ZP_03478645.1| hypothetical protein PRABACTJOHN_04355 [Parabacteroides johnsonii
           DSM 18315]
 gi|218221638|gb|EEC94288.1| hypothetical protein PRABACTJOHN_04355 [Parabacteroides johnsonii
           DSM 18315]
          Length = 359

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 77/332 (23%), Positives = 137/332 (41%), Gaps = 37/332 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V +  +  +R+D++  +         +Q    +G +  + K VK N R++   VV I  
Sbjct: 35  FVADRGQSLLRVDKFLVDRMFGATRNRIQSAADAGCIMANGKPVKSNYRVKPEDVVTIMM 94

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYH 128
                                    + +   ++YED  + V +KPAG+ V  G G     
Sbjct: 95  TR--------------PPRTFEILPENIPIKIVYEDDDLLVVDKPAGLVVHPGHGNYTGT 140

Query: 129 IDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   L  ++      D       L HR+D++TSG+LVVA+   A  +L+  F  +  ++ 
Sbjct: 141 LVNALAWYLKDDPTYDPNDPALGLVHRIDKDTSGLLVVAKKPEAKANLSMQFFHKTTKRE 200

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LVWGI ++ +  I   + +           V         A++H+ V++        
Sbjct: 201 YRALVWGIVRDDEGRIEGNIGRNPR--DRMQMTVFPEGDQGKTAVTHYSVLERLG-YVTL 257

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQN----------KLYL 290
           ++ +  TGRTHQ+RVH  ++G  +  D +Y  N   KG  +S  +           +  L
Sbjct: 258 VKCRLETGRTHQIRVHMKYIGHTLFNDERYGGNEILKGTTSSKYKQFVDNCFAICPRQAL 317

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           HA+ +   HP  G  +   + +PA M    D 
Sbjct: 318 HAKTLGFVHPSTGEEMFFDSEIPADMTALIDK 349


>gi|294085986|ref|YP_003552746.1| pseudouridine synthase [Candidatus Puniceispirillum marinum
           IMCC1322]
 gi|292665561|gb|ADE40662.1| pseudouridine synthase, RluA family [Candidatus Puniceispirillum
           marinum IMCC1322]
          Length = 335

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 99/324 (30%), Positives = 169/324 (52%), Gaps = 16/324 (4%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++  +  DE+  RLDR  +   P +    ++K+LR+G +R+D  + K  +R+  GQ +R+
Sbjct: 11  RFETISEDEDGSRLDRVLRRLIPGLAQGQIEKMLRNGLIRIDGAKAKSASRVAVGQQIRL 70

Query: 68  PPVINALNHIIKE------QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           P  I+AL  +         + +   S+           +++ E       NKP+G++VQG
Sbjct: 71  PISIDALATVKPAANKMSAKALGAPSIGGAPLQKTFDDMVIGEGKGWLALNKPSGLAVQG 130

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G+G   H+DG L +     G + RL HR+D++TSG+L++A+T  +A+ LT++F    I+K
Sbjct: 131 GTGTKQHVDGMLAALAARGGDRLRLVHRIDKDTSGVLLLAKTLQSARSLTDAFHKHAIEK 190

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L  G+P  ++  +   + K     G+ +      +     A + F+ +D   +K  
Sbjct: 191 TYLALCMGLPP-EEGAVKQAISKLPGKSGERMVA----DDDGQSAHTLFRRVDHAGRKLT 245

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + ++P TGRTHQLR+H   +G  I GD KY      +    +  +L+LHA  + LP   
Sbjct: 246 LMALRPLTGRTHQLRIHMALIGHVICGDGKYGG-VDAHPGGMVARQLHLHAWQLKLPD-- 302

Query: 302 GGRLQITAPLPAHMVKTWDSLGFK 325
            G+L ITAP   HMV + D+LG  
Sbjct: 303 -GKL-ITAPPSPHMVTSLDALGLS 324


>gi|56478105|ref|YP_159694.1| ribosomal large subunit pseudouridine synthase D [Aromatoleum
           aromaticum EbN1]
 gi|56314148|emb|CAI08793.1| ribosomal large subunit pseudouridine synthase D [Aromatoleum
           aromaticum EbN1]
          Length = 306

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 137/320 (42%), Gaps = 25/320 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  D   +R+D+     +P  +   LQ  L+SG+V +D  +     ++  G+ + +  
Sbjct: 5   LTIPADCAGLRVDQALARLFPSHSRSRLQGWLKSGRVSLDGDQPDAKFKVWGGESLEVDA 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                      + I                ++++ED +I V +KP G+ V  GSG     
Sbjct: 65  APPPEAAAEAPEDI--------------PLVVVHEDEEILVIDKPVGLVVHPGSGNWSGT 110

Query: 128 HIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L          +  + HRLD++TSG+LVVA+T  +   L    + R +++ Y +L
Sbjct: 111 LLNALLHHAPQLAAVPRAGIVHRLDKDTSGLLVVAKTLESQTALVRQLQARTVRRHYLAL 170

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V          +   + +        + VV    +    A++ ++  + FA+    +E Q
Sbjct: 171 VHRAVAGA-GMVEAPIGRHPTQ-RTRMAVV----QSGRAAVTRYRPRERFAR-VTLVECQ 223

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
             TGRTHQ+RVH  ++G P+VGD  Y     G+       +  LHA  + L HP  G  +
Sbjct: 224 LETGRTHQIRVHMAYIGHPLVGDATYGLRRSGSPVLDAFARQALHAFRLGLLHPASGAEM 283

Query: 306 QITAPLPAHMVKTWDSLGFK 325
              +PLP        SL  +
Sbjct: 284 TWESPLPEDFEALLASLREE 303


>gi|320354569|ref|YP_004195908.1| RluA family pseudouridine synthase [Desulfobulbus propionicus DSM
           2032]
 gi|320123071|gb|ADW18617.1| pseudouridine synthase, RluA family [Desulfobulbus propionicus DSM
           2032]
          Length = 302

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 139/315 (44%), Gaps = 26/315 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V + ++  RLD +     P  +   + K++ +  V V+ ++VK   R+   +++ +    
Sbjct: 2   VTSGDQGQRLDHYLIRQLPEQSRSAIGKLIGAAHVLVNGQQVKAGYRLHQDEIITVSF-- 59

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHI 129
                          + +L    + +   +L+ED  + V  KP G+ V    G G    +
Sbjct: 60  -------------PPTPSLDLAPEKIDFSILFEDEHLLVIGKPPGLVVHPACGHGGGTLV 106

Query: 130 DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            G L    D       +P + HRLD++TSG+++VA++  + + L   F+ R+I K Y +L
Sbjct: 107 HGLLYHCQDLPALDAGRPGIVHRLDKDTSGVMLVAKSERSLRSLMADFKNRKIHKTYHAL 166

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           +   P+ ++  +   + +             Q      YA +H++V++ F   +C +E+ 
Sbjct: 167 LLRSPREREGRLVAPIGRHPVDRKKMAIRPDQ----GKYAATHWRVLESFINGWCLVEIG 222

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
             TGRTHQ+RVH   +  P+ GD  Y    +         +  LHA  +   HP     +
Sbjct: 223 IETGRTHQIRVHMASLRAPVAGDALYGGRVERGAPIK-PPRQMLHASTLRFHHPLTNEEM 281

Query: 306 QITAPLPAHMVKTWD 320
            +TAPL A M    +
Sbjct: 282 CLTAPLWADMQDILN 296


>gi|153948512|ref|YP_001402171.1| 23S rRNA pseudouridine synthase D [Yersinia pseudotuberculosis IP
           31758]
 gi|152960007|gb|ABS47468.1| ribosomal large subunit pseudouridine synthase D [Yersinia
           pseudotuberculosis IP 31758]
          Length = 327

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 83/341 (24%), Positives = 148/341 (43%), Gaps = 37/341 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V V+ K++ K   ++  G++V I  
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKVLGGELVAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I        ++  LD               ++YED+ I V NKP G+ V  G+G     
Sbjct: 70  QIEEDARWAPQEIPLD---------------IVYEDNDILVINKPRGLVVHPGAGNPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y ++
Sbjct: 115 VLNALLHYYPEIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEM 245
             G        +   + + S                   A +H+++++ F A     L +
Sbjct: 175 AIGNM-TAGGRVDEPISRHST-----KRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRL 228

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDL 297
           +  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L
Sbjct: 229 RLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDSFIAILRGFDRQALHATMLRL 288

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            HP  G +++  A LP  MV+  ++L  K D   +  ++  
Sbjct: 289 YHPISGIQMEWHAALPEDMVELINAL--KADTEEFKDQMDW 327


>gi|229588326|ref|YP_002870445.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens SBW25]
 gi|229360192|emb|CAY47049.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens SBW25]
          Length = 320

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 87/344 (25%), Positives = 154/344 (44%), Gaps = 37/344 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    ++   V ++    RLD+     +   +   L   ++ G++ VD   ++  + + 
Sbjct: 1   MSDKIELR-AEVPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVH 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G ++ +     A    + +   LD               ++YED  I V NKPAG+ V 
Sbjct: 60  GGAILELTAEQEAQGEWVAQDIELD---------------IVYEDDDILVINKPAGLVVH 104

Query: 121 GGSGIAYHI--DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +G A     +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R
Sbjct: 105 PAAGHADGTLLNALLHHVPDIINVPRCGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSR 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + +IY  +V G+     +   N  + +       + V+    +G   A+SH++V++ F 
Sbjct: 165 SVSRIYECIVIGVVVAGGKI--NAPIGRHGQQRQRMAVM----EGGKQAVSHYRVLERF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLY 289
           +    + ++  TGRTHQ+RVH  H+  P+VGD  Y   F+    +            +  
Sbjct: 218 RSHTHVRVKLETGRTHQIRVHMAHINFPLVGDPAYGGRFRIPPAASATMVESLKTFPRQA 277

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           LHAR+++L HP  G R+   +PLP  +V     L  K DR  ++
Sbjct: 278 LHARFLELDHPTSGKRMSWESPLPDDLVWLLSLL--KQDREAFV 319


>gi|83648561|ref|YP_436996.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83636604|gb|ABC32571.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 319

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 77/332 (23%), Positives = 142/332 (42%), Gaps = 34/332 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q ++V  +    RLD       P  +   +Q  ++ G +RV+ K+VK   ++  G  V +
Sbjct: 7   QSLIVPAELGEQRLDMAASELMPEYSRSRIQNWIKQGALRVNGKQVKPKEKVIEGDQVEL 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              + A      +   LD               +++ED  + V NK A   V   +G + 
Sbjct: 67  DVELEAQGDWEAQPIALD---------------VVFEDEHLLVINKQADFVVHPAAGHSD 111

Query: 128 HI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L      S+  +  + HRLD++T+G++V+A+T  A   L E  + R + + Y 
Sbjct: 112 GTVVNAVLHHCPALSELPRAGIVHRLDKDTTGLMVIAKTLIAHNSLVEQLQAREMGREYE 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +V+G        +    + +       + V +    G   A++H+++I  + + F  L 
Sbjct: 172 CVVYGELT--GGGVVEAAIGRHPQNRQKMAVTR----GGKDAVTHYRLIRRW-RGFTHLR 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+   I+GD  Y +  +       +         +  LHA+ ++
Sbjct: 225 LKLETGRTHQIRVHMAHIHHSILGDPLYGSRPRLPKGLSAETIEYLQTFGRQALHAKALE 284

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           L HP  G  L     LP  M+   + L  + +
Sbjct: 285 LSHPVTGELLSWEVGLPEDMINLLNRLDSEEE 316


>gi|262282338|ref|ZP_06060106.1| pseudouridine synthase [Streptococcus sp. 2_1_36FAA]
 gi|262261629|gb|EEY80327.1| pseudouridine synthase [Streptococcus sp. 2_1_36FAA]
          Length = 296

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 140/319 (43%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ ++   RLD+   +    ++     + +++G++ V+    K    ++ G V+      
Sbjct: 3   VKVEQAGARLDKAVAD-LTDLSRSLANEQIKTGKILVNGLVKKAKYTVKEGDVISYELPE 61

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
                 + E   L+               ++Y+D  + V NKP G+ V   +G      +
Sbjct: 62  VEEVEYVPEDIPLE---------------IVYQDEDVAVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L++A+   A   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F+V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAK-----GKSALTRFQVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHGQFLHARTLGFTHPRTGEV 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+ TA +PA   +T   L 
Sbjct: 276 LEFTAEVPAIFQETLKKLR 294


>gi|123967748|ref|YP_001008606.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. AS9601]
 gi|123197858|gb|ABM69499.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. AS9601]
          Length = 319

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 85/315 (26%), Positives = 139/315 (44%), Gaps = 28/315 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +  P  +   +Q  + SG V V+ K  K    +++G  ++I          
Sbjct: 26  PMRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNIQIWMPPPEPLIY 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
           +K +K              +   +L+ED  I V NK +G+ V    G      ++G L  
Sbjct: 86  LKPEK--------------MDLNILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLFH 131

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++TSG +VVA+++ A  +L +  + +   + Y +++ G P
Sbjct: 132 CKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAP 191

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +++  I   + +       Y  V    E    YA +++K+ + F   +  +  +  TGR
Sbjct: 192 NSEEGQIVGNIGRDKLNRLKYKVV---EETSGRYACTYWKLEERFG-NYSLMSFKLDTGR 247

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  H+  PIVGD  Y    K        +   LHA  + L HP  G  +   + 
Sbjct: 248 THQIRVHCAHINHPIVGDPLYGRCKKLPCK---LDGQALHAIKLGLIHPINGKEMIFESE 304

Query: 311 LPAHMVKTWDSLGFK 325
           LP    K    L  K
Sbjct: 305 LPLDFQKLLSVLKIK 319


>gi|148262954|ref|YP_001229660.1| RluA family pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146396454|gb|ABQ25087.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           uraniireducens Rf4]
          Length = 320

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 92/336 (27%), Positives = 156/336 (46%), Gaps = 40/336 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ +  EN E   RLD +       +     Q+++ +GQ+ VD    K + +++ G+
Sbjct: 1   MENVELIFPENSEI-ERLDSFIARSVNGMTRATAQRLIEAGQITVDGHPQKPSLKLKGGE 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +   V     ++ +   +L+ED  + V NK AG+ V  G+
Sbjct: 60  RLMVT---------------IPPPVAAEPAAETIPLEILFEDRNLVVVNKAAGMVVHPGA 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HR+D++TSG+LVVA++ AA Q L E F+  
Sbjct: 105 GNSGGTLVNALLGHCTDLSGIGGELRPGIVHRIDKDTSGVLVVAKSDAAHQSLAEQFKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDC 235
            I+++Y +LV+G PK+ K  +       SHIG   V   + + K     +A++H++V+  
Sbjct: 165 TIKRVYLALVYGAPKDDKGRLE------SHIGRHPVDRKRMSGKAKHGKHAVTHWRVVGR 218

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--------QNK 287
           + +    L ++  TGRTHQ+RVH    G P+VGD  Y    +    S            +
Sbjct: 219 Y-RGITLLRLRLETGRTHQIRVHLSEAGYPLVGDDVYGGGSRLATVSDTLLRKLIKDLGR 277

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             LHA+ +   HP  G  L+    LP  M +  + L
Sbjct: 278 QALHAKTLGFIHPVTGEYLEFDTELPDDMARIVEYL 313


>gi|145588577|ref|YP_001155174.1| RluA family pseudouridine synthase [Polynucleobacter necessarius
           subsp. asymbioticus QLW-P1DMWA-1]
 gi|145046983|gb|ABP33610.1| ribosomal large subunit pseudouridine synthase C [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 339

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 97/324 (29%), Positives = 150/324 (46%), Gaps = 8/324 (2%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S    V    +  +E   RLD +       +   ++ +I+RSG+VRV+KKR +   R+  
Sbjct: 14  SAPPAVHLQTIGPEEAGQRLDNYLLRWAKGVPKSHVYRIIRSGEVRVNKKRAEPTTRLVE 73

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV  A    +       +      +SD +   +L+ED  + + NKPAG++V G
Sbjct: 74  GDVVRVPPVRIAEPAQMAAVNTAQTKSRAQGYSDKMP--ILFEDEALLIVNKPAGLAVHG 131

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSGIA  +   L+           L HRLD++TSG+L++A+ R+A   L    R  +  K
Sbjct: 132 GSGIALGVIETLRITRPELKF-LELVHRLDRDTSGVLLLAKKRSALVELHRQIREGQTDK 190

Query: 182 IYWSLVWGIPKNKKEC--IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            Y+ L  G  +   +   +   L K     G+    V  +   ++ A+   +V       
Sbjct: 191 RYYLLAHGEIEQGAQVMQLKYPLHKYLLANGERRVRVDPDGLPSHTALRVTQVFKREGAA 250

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
               E Q  TGRTHQ+RVH L +G  I+GD KY    +         +LYLHA      H
Sbjct: 251 ITLAEAQLKTGRTHQIRVHLLKLGHAILGDDKYGFEDQDKLLK--SKRLYLHAHLAGFTH 308

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G  ++I +PLP+       + 
Sbjct: 309 PRTGEKMRIESPLPSEFAAMMKTF 332


>gi|94970372|ref|YP_592420.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Koribacter versatilis Ellin345]
 gi|94552422|gb|ABF42346.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Koribacter versatilis Ellin345]
          Length = 333

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 93/344 (27%), Positives = 158/344 (45%), Gaps = 42/344 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   Q++ V  D+ N+RLD++  +H P ++   +Q ++   ++ VD K  K + +++  +
Sbjct: 1   MDGAQHIQVSADDANIRLDQYLVSHLPDVSRARVQALIDDEKILVDGKSSKPSYKLRGSE 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +                      L    + +   ++YED  + V NKPAG+ V  G+
Sbjct: 61  VIDVVGEYQ--------------PPPLRAIPEDIPLDVVYEDDDLAVINKPAGMMVHVGA 106

Query: 124 GIAYHI-------DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           G            +  L  +          +P + HRLD+ETSG++VVA+   A + L E
Sbjct: 107 GATEEERNRGTLVNALLYRFRALSEVGGDMRPGIVHRLDKETSGLIVVAKNDVAHRKLAE 166

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F  RR+ K Y +LV G PK  K  I   + +           +     G   A+SH++V
Sbjct: 167 QFSSRRVHKKYVALVHGWPKKLKGTINLPIARDM----SRRTRMTTRGSGGRDALSHYEV 222

Query: 233 ---IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--- 286
              I+    KF  +E++  TGRTHQ+RVH   +G P+VGD  Y A  +   T  ++    
Sbjct: 223 KEKIESPYGKFALVEVKIETGRTHQIRVHMASLGHPVVGDTLYGAPGELRVTKALKGMPS 282

Query: 287 ------KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 + +LHA  ++L  P  G+ L+    +PA +    ++L 
Sbjct: 283 KMASLERNFLHAAEIELQQPATGKALRFVTKVPAALEDFAETLR 326


>gi|126695551|ref|YP_001090437.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9301]
 gi|126542594|gb|ABO16836.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9301]
          Length = 319

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 85/315 (26%), Positives = 139/315 (44%), Gaps = 28/315 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +  P  +   +Q  + SG V V+ K  K    +++G  ++I          
Sbjct: 26  PMRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNIQIWMPPPEPLIY 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
           +K +K              +   +L+ED  I V NK +G+ V    G      ++G L  
Sbjct: 86  LKPEK--------------MDLNILFEDEHIIVINKQSGLIVHPAPGNKSGTLVNGLLFH 131

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++TSG +VVA+++ A  +L +  + +   + Y +++ G P
Sbjct: 132 CKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAP 191

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +++  I   + +       Y  V    E    YA +++K+ + F   +  +  +  TGR
Sbjct: 192 NSEEGQIVGHIGRDKLNRLKYKVV---EETSGRYARTYWKLEERFG-NYSLMSFKLDTGR 247

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  H+  PIVGD  Y    K        +   LHA  + L HP  G  +   + 
Sbjct: 248 THQIRVHCAHINHPIVGDPLYGRCKKLPCK---LDGQALHAIKLGLIHPINGKEMIFESE 304

Query: 311 LPAHMVKTWDSLGFK 325
           LP    K    L  K
Sbjct: 305 LPLDFQKLLSVLKVK 319


>gi|257454043|ref|ZP_05619317.1| ribosomal large subunit pseudouridine synthase C [Enhydrobacter
           aerosaccus SK60]
 gi|257448521|gb|EEV23490.1| ribosomal large subunit pseudouridine synthase C [Enhydrobacter
           aerosaccus SK60]
          Length = 365

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 95/326 (29%), Positives = 165/326 (50%), Gaps = 28/326 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V Y+ V   + + R+D +       +   ++  ++RS ++RV+ KR K ++++Q   V
Sbjct: 54  AKVNYLTVTRQQHDQRVDNFLLGRLKGLPRSHVYNMIRSDEIRVNGKRCKPHDKLQRNDV 113

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRI P+  A     +E+ ++         +  L   ++YED  + V NKP+G++V GGSG
Sbjct: 114 VRIAPIKLAT----REKPVISPDF-----AQSLLERIVYEDEGLIVLNKPSGMAVHGGSG 164

Query: 125 IAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++   G +++  ++ G+K   L HR+D++TSG+L++A+ R+  + L E  R + +QK Y
Sbjct: 165 ESF---GVIEAMREATGKKYLELVHRIDKDTSGLLMIAKKRSTLKTLQEHLREKTLQKTY 221

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIG------GDYVHVVKQNEKGANYAISHFKVI---D 234
             LV G   ++ + I   LLK +         G+    V    + +  + +   V+   +
Sbjct: 222 LCLVVGWISSETQTIDKPLLKYTLPATQEGKSGERRVKVDVKSEDSKPSQTQINVLQKFE 281

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              QK   +E +P TGRTHQ+RVH   +G P++GD KY  N        +  +L LHA  
Sbjct: 282 LNGQKVSLIEAKPLTGRTHQIRVHLASIGHPLLGDDKYNPNVAKG--DKMVRRLCLHAYQ 339

Query: 295 MDLPHPEGGRLQITAPLPAHMVKTWD 320
           + +P  E     ITA LP  M    +
Sbjct: 340 LAIPEYET----ITAELPVDMQNLIE 361


>gi|209517244|ref|ZP_03266089.1| pseudouridine synthase, RluA family [Burkholderia sp. H160]
 gi|209502380|gb|EEA02391.1| pseudouridine synthase, RluA family [Burkholderia sp. H160]
          Length = 349

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 98/326 (30%), Positives = 157/326 (48%), Gaps = 24/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +V
Sbjct: 24  QVSLLEIDDSSAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLV 83

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP+  A  +       + +              +L+ED  + V +KPAG++V GGSG+
Sbjct: 84  RVPPIRVAQPNEAAAHVPVPAG----------GFHILFEDEHLLVIDKPAGVAVHGGSGV 133

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ RAA  +L E  R  R+ K Y++
Sbjct: 134 AFGVIEQMREARPQ-AKFLELVHRLDRETSGILMLAKKRAALVNLHEQIRENRMDKRYYA 192

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G           +   L K     G+    V+ +      + + F ++D +   +  
Sbjct: 193 CVHGEWATDWGRRRAVKEPLHKYLTADGERRVRVQAD---GLASHTIFNLVDRWPD-YAL 248

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           LE +  TGRTHQ+RVH  H+  PIVGD KY               P   +++LHA  + L
Sbjct: 249 LEAELKTGRTHQIRVHLQHLALPIVGDAKYGDFALNKALARANAKPGIKRMFLHAYRLKL 308

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL 322
            HP  G  LQ+ APLPA        L
Sbjct: 309 THPATGAPLQLEAPLPADCRGFIQQL 334


>gi|298372061|ref|ZP_06982051.1| ribosomal large subunit pseudouridine synthase D [Bacteroidetes
           oral taxon 274 str. F0058]
 gi|298274965|gb|EFI16516.1| ribosomal large subunit pseudouridine synthase D [Bacteroidetes
           oral taxon 274 str. F0058]
          Length = 357

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 79/335 (23%), Positives = 136/335 (40%), Gaps = 41/335 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV+  +  +R+D++  N    ++    Q     G + V+   VK + R++    + I  
Sbjct: 30  IVVDKGQGLIRIDKYLTNLLGGVSRTRFQNAADFGFITVNGDTVKSSYRVKPLDEIVISL 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                ++ I  Q I                 +++ED  I V NK   + V  G G   ++
Sbjct: 90  ETPPSDYTIVPQDI--------------PLSVVFEDDDIMVVNKTPDMVVHPGVG---NL 132

Query: 130 DGFLKSWV----------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           DG L + +          D    +  L HR+D++TSG+L++A+   A   L + F+ +  
Sbjct: 133 DGTLLNAIAWYLRDNPKFDVNNPRVGLVHRIDKDTSGLLLIAKNEQAKSFLGKQFQDKTT 192

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +LVWGI K     +   L +       +          A +A++H++V+  F + 
Sbjct: 193 KRTYNALVWGIVKEDNGTVDGALARNPKDRMQFCVFDPDENPLAKHAVTHYRVLRRF-KY 251

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NK 287
              LE    TGRTHQ+RVH  H+G  +  D +Y  N         +             +
Sbjct: 252 TTLLECNLETGRTHQIRVHMKHIGHTLFNDERYGGNEILFGERTAKYKQFVGNCFEVCPR 311

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
             LHA+ +   HP  G  L     LP       D 
Sbjct: 312 QALHAKTLGFVHPTTGEELFFDTELPHDFQALLDK 346


>gi|15676125|ref|NP_273256.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis MC58]
 gi|7225419|gb|AAF40655.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis MC58]
 gi|316985120|gb|EFV64072.1| pseudouridine synthase, RluA family protein [Neisseria meningitidis
           H44/76]
 gi|325143210|gb|EGC65550.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis 961-5945]
 gi|325197484|gb|ADY92940.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis G2136]
 gi|325199409|gb|ADY94864.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis H44/76]
          Length = 330

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 155/322 (48%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  +      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSAD---GQSAHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A LP  + +
Sbjct: 298 LNHPLTGEPLVLKAELPPDLAQ 319


>gi|302035759|ref|YP_003796081.1| 23S rRNA pseudouridine synthase [Candidatus Nitrospira defluvii]
 gi|300603823|emb|CBK40155.1| 23S rRNA pseudouridine synthase [Candidatus Nitrospira defluvii]
          Length = 320

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 139/319 (43%), Gaps = 23/319 (7%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
              ++   E+  RLD +     P ++   LQ+++ +G VRV+    K + RI++G V+  
Sbjct: 3   TEFIISAGEQPKRLDVFLVQREPKLSRAALQRMITAGWVRVNSHIAKSSQRIRAGDVIVF 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                A   I  E + L+               +L+ED    V NKPAGI      G   
Sbjct: 63  DTPQPAPLRIAGETQQLE---------------VLFEDHACLVLNKPAGIVTHPSPGHWS 107

Query: 128 HI--DGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   +  L       G   P + HRLD++TSG++VVA+T  A + L+E F    I + Y 
Sbjct: 108 NTLLNALLDHCARGGGAATPGVVHRLDKDTSGVMVVAKTEEAHRKLSEQFERHSITRQYE 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+P   +  I   L    H          Q       A++ ++V + F +    L 
Sbjct: 168 ALVVGVPAQSEGRIEAALGPDRHHPKRTSTQTLQP----KPAVTDYRVEEVFDKVAARLV 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           + PHTGRTHQ+R H   +G PI+GD  Y     G        ++ LHAR +   HP  G 
Sbjct: 224 LSPHTGRTHQIRAHLHVIGHPILGDRSYGGERVGAIAGYEIPRVMLHARTLGFRHPATGL 283

Query: 305 L-QITAPLPAHMVKTWDSL 322
             + TA +P         L
Sbjct: 284 YGEWTADVPPDFQAVRQGL 302


>gi|261391734|emb|CAX49183.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C; rRNA pseudouridylate synthase C) [Neisseria
           meningitidis 8013]
          Length = 330

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 156/322 (48%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V ++      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVRLPLFKYTGAQGEKMVRVSED---GQSAHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A LP  + +
Sbjct: 298 LNHPLTGEPLVLKAELPPDLAQ 319


>gi|125624328|ref|YP_001032811.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. cremoris MG1363]
 gi|124493136|emb|CAL98100.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. cremoris MG1363]
 gi|300071111|gb|ADJ60511.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. cremoris NZ9000]
          Length = 301

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 73/323 (22%), Positives = 144/323 (44%), Gaps = 33/323 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  + +++RLD+   N     +   L +++++ +V V+ +  K   ++++G  +    
Sbjct: 4   IKITEENKDLRLDKALANQ-TEYSRSLLTELIKNDKVFVNNEAKKAKYKVKTGDRI---- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
                      Q  +  +  L   ++ L   ++YEDS + V NKP G+ V   +G A   
Sbjct: 59  -----------QFEIPQAEVLDVVAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGT 107

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  +    D        +P + HR+D++TSG+L++A+   A + L    + +  ++ Y
Sbjct: 108 LVNAIMYHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G   N K  I   + +          V      G   A++HF+V++ F   +  +
Sbjct: 168 LAIVHGELANDKGTIEAPIGRNLKDRKKQAVVS-----GGKPAVTHFEVLEGFV-GYTLI 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++  TGRTHQ+RVH  ++G P+ GD  Y      N T       +LHA  +   HP  G
Sbjct: 222 ALRLETGRTHQIRVHMHYIGHPVAGDPLYGP----NKTLTPNKGQFLHAETLGFEHPTSG 277

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
             ++     P    +  + L  +
Sbjct: 278 ELMEFQVDAPDLFKEQLEKLREQ 300


>gi|158425878|ref|YP_001527170.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
 gi|158332767|dbj|BAF90252.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
          Length = 354

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 87/342 (25%), Positives = 147/342 (42%), Gaps = 48/342 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           + V  ++  +R DR+     P ++   LQK++  G+V V  + V     R+ +G    + 
Sbjct: 33  LTVGPEDAGLRADRFLAARLPDLSRTRLQKLVADGRVSVGGRVVGDPAERVNAGDEWTVR 92

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                    + E+               +   + YED  + V +KPAG+ V    G    
Sbjct: 93  VPAPEPAAPVPEK---------------MDLSIAYEDDFLIVVDKPAGLVVHPAPGNWSG 137

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--- 178
             ++G L     S       ++P + HRLD++TSG+LVVA+T AA   L   F       
Sbjct: 138 TLVNGLLAHCGASLSGIGGVKRPGIVHRLDKDTSGLLVVAKTDAAHAGLAAQFADHGRTG 197

Query: 179 -IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y++ VWG+P +++  +   +    H        V+Q+      AI+H++ ++ FA
Sbjct: 198 PLERAYYAFVWGVP-DQRGTVDAPI--DRHPTHRQKMAVRQS---GREAITHWERLEVFA 251

Query: 238 QK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFTSP 283
                     +E Q  TGRTHQ+RVH  H+G P++GD  Y   F+               
Sbjct: 252 GADGAPLASLIECQLETGRTHQIRVHLAHVGHPLLGDEVYGQGFRTKASRLPEGARALLA 311

Query: 284 IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF 324
              +  LHA  +   HP     L   +PLP  + +  D+L  
Sbjct: 312 ALGRQALHAARLGFAHPVTDEELLFESPLPEDLARLRDALAL 353


>gi|254976188|ref|ZP_05272660.1| putative pseudouridylate synthase [Clostridium difficile QCD-66c26]
 gi|255093577|ref|ZP_05323055.1| putative pseudouridylate synthase [Clostridium difficile CIP
           107932]
 gi|255315322|ref|ZP_05356905.1| putative pseudouridylate synthase [Clostridium difficile QCD-76w55]
 gi|255517989|ref|ZP_05385665.1| putative pseudouridylate synthase [Clostridium difficile QCD-97b34]
 gi|255651105|ref|ZP_05398007.1| putative pseudouridylate synthase [Clostridium difficile QCD-37x79]
          Length = 315

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 144/328 (43%), Gaps = 33/328 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +M  V+  +V  +EE +RLD +       ++   +QKI++ G+V+V+ K  K    ++  
Sbjct: 12  IMDEVKEFLVLEEEEEVRLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKAKYLVKEE 71

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I          I E K+L+           +   ++YED  + + NKP  + V   
Sbjct: 72  DNIVIE---------IPEPKVLEV------LPQDIPIDIVYEDDDVLIINKPQDMVVHPA 116

Query: 123 SGIAYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G   +   +G L    D         +P + HR+D++TSG+L++A+   A   L E  +
Sbjct: 117 PGNYENTLVNGILYHCKDKLSSINGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLK 176

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I + Y  + +G+ K  K  +   + +          V     K    AI+HF+V++ 
Sbjct: 177 EHTITREYEFICYGVVKEDKITVDKPIGRNPKDRLKMAVV-----KDGKNAITHFEVVER 231

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F  KF  +  +  TGRTHQ+RVHAL +  P++GD  Y        T        LHA+ +
Sbjct: 232 F-DKFTHMRARLETGRTHQIRVHALSINHPLLGDFVYGPKE----TKFKLKGQTLHAKKL 286

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP     ++  + LP +  +    +
Sbjct: 287 GFIHPTTKEYIEFNSELPEYFKEAIKKI 314


>gi|257439832|ref|ZP_05615587.1| ribosomal large subunit pseudouridine synthase D [Faecalibacterium
           prausnitzii A2-165]
 gi|257197741|gb|EEU96025.1| ribosomal large subunit pseudouridine synthase D [Faecalibacterium
           prausnitzii A2-165]
          Length = 314

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 73/324 (22%), Positives = 142/324 (43%), Gaps = 29/324 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  +VE +    R+DR+       ++   LQ ++  G V  + K    + ++++G ++ +
Sbjct: 4   REYIVEAEGAGQRIDRFLSGEDTGLSRSALQGLVAEGHVLCNGKAPAKSLKLKAGDIILL 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           +  +  +      +   ++YED+ + V NKP G+ V    G   
Sbjct: 64  E---------------IPDAKPIEAVPQEIPLDIIYEDAHLLVVNKPKGMVVHPAPGNPD 108

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++  L     S        +P + HR+D++TSG+LVVA+  A    L++   +  ++
Sbjct: 109 GTLVNALLWHCKGSLSGIGGEIRPGIVHRVDKDTSGLLVVAKDDATHIGLSQQMAVHSVE 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V+G     +  + + L + S      + V   +E    YA + +KV++   + F
Sbjct: 169 RAYNTIVYGGFAQDEGFVESNLGR-SKTDRKKMAVYPASEPHTKYAYTGYKVLERLGE-F 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE +  TGRTHQ+RVH   +  P+ GD  Y      +      +   LHA+ +   HP
Sbjct: 227 TMLECRLKTGRTHQIRVHMASIHHPVAGDPVYGP----HNCITSLHGQCLHAKTLGFIHP 282

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  L+  + LP +  +   +L 
Sbjct: 283 ITGEHLRFDSELPDYFTRFLTTLR 306


>gi|158335489|ref|YP_001516661.1| RluA family pseudouridine synthase [Acaryochloris marina MBIC11017]
 gi|158305730|gb|ABW27347.1| pseudouridine synthase, RluA family [Acaryochloris marina
           MBIC11017]
          Length = 328

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 85/316 (26%), Positives = 141/316 (44%), Gaps = 34/316 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHII 78
           R+DRW  N    ++  ++QK++  G V+++ K        +Q G  V +           
Sbjct: 14  RIDRWLANQVDSLSRSHIQKLIEQGHVQINHKICTSKKYALQIGDQVEVH---------- 63

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFLKSW 136
                + +   L    + +   +L+ED  + + NKPAG+ V    G A    + G L   
Sbjct: 64  -----IPAPQPLALEPEPMDLEILFEDDHLLIVNKPAGLVVHPAPGHATGTLVHGLLAHC 118

Query: 137 VDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            D +G         ++P + HRLD++T+G ++VA+T  A QHL      +   + Y  LV
Sbjct: 119 QDGQGSTLSGIGGVERPGIVHRLDKDTTGAIMVAKTNQAHQHLQAQIAAKTALREYVGLV 178

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G P      +   + +  H        V   E+G   A++H++++      +  ++ + 
Sbjct: 179 YGRPSALTGRMEFPIGR--HRSDRIKMAVVPEEQGGKVAVTHWQILQPLG-NYALVKFRL 235

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH   MG PIVGD  Y    +G       +   LHA  + L HP     + 
Sbjct: 236 ETGRTHQIRVHCAQMGWPIVGDPLYS---RGRSLKVNLSGQVLHAWRLSLKHPVFHTEIS 292

Query: 307 ITAPLPAHMVKTWDSL 322
           + APLP   VK  + L
Sbjct: 293 VQAPLPIDFVKLLNRL 308


>gi|297568585|ref|YP_003689929.1| pseudouridine synthase, RluA family [Desulfurivibrio alkaliphilus
           AHT2]
 gi|296924500|gb|ADH85310.1| pseudouridine synthase, RluA family [Desulfurivibrio alkaliphilus
           AHT2]
          Length = 324

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 89/329 (27%), Positives = 145/329 (44%), Gaps = 35/329 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDK-----KRVKFNNRIQS 61
            VV   E   RLD            +    LQ ++R G+VRV+        +K    +++
Sbjct: 11  FVVAPHEAGRRLDLVLATRAAGSAELTRSRLQSLIRQGRVRVESAGVEAGPLKPGMLLKA 70

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  V +         ++ E+               ++   LYED  I V  KP G+ V  
Sbjct: 71  GDRVDLQVPPPEATELVAEE---------------VEFTPLYEDEDILVLVKPPGLVVHP 115

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      + G L    +  G     +P + HRLD++TSG LVVA+   A  +L + F+
Sbjct: 116 ADGHRQGTLVHGLLHHCRNLSGISGQLRPGIVHRLDKDTSGCLVVAKNDLAHHNLVQQFK 175

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R ++K Y +L+ GI       +   + +   +    + V +   +G   A++H++V   
Sbjct: 176 GREVEKTYQALLRGILAEDTGQVVLPIGRH-PVHRKKMAVRR---EGGREAVTHWRVRQR 231

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F+  +  +E+   TGRTHQ+RVH   +G P+ GD  Y  N + +    I ++ +LHA  +
Sbjct: 232 FSAGYTLVELLLETGRTHQIRVHMAALGHPLAGDRLYGRNPEKDMPYGI-DRQWLHAWRL 290

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
              HP  G RL  TAPL   +  + D L 
Sbjct: 291 AFNHPRSGRRLTFTAPLWVDLQASLDRLR 319


>gi|117624818|ref|YP_853731.1| 23S rRNA pseudouridine synthase D [Escherichia coli APEC O1]
 gi|218559515|ref|YP_002392428.1| 23S rRNA pseudouridine synthase D [Escherichia coli S88]
 gi|237706817|ref|ZP_04537298.1| 23S rRNA pseudouridine synthase D [Escherichia sp. 3_2_53FAA]
 gi|115513942|gb|ABJ02017.1| 23S rRNA pseudouridine synthase [Escherichia coli APEC O1]
 gi|218366284|emb|CAR04036.1| 23S rRNA pseudouridine synthase [Escherichia coli S88]
 gi|226899857|gb|EEH86116.1| 23S rRNA pseudouridine synthase D [Escherichia sp. 3_2_53FAA]
 gi|315284807|gb|EFU44252.1| pseudouridine synthase, RluA family [Escherichia coli MS 110-3]
 gi|323951205|gb|EGB47081.1| RluA family protein pseudouridine synthase [Escherichia coli H252]
 gi|323957037|gb|EGB52763.1| RluA family protein pseudouridine synthase [Escherichia coli H263]
          Length = 326

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 81/336 (24%), Positives = 145/336 (43%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ + I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQMAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVDEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQSLHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|222529363|ref|YP_002573245.1| RluA family pseudouridine synthase [Caldicellulosiruptor bescii DSM
           6725]
 gi|222456210|gb|ACM60472.1| pseudouridine synthase, RluA family [Caldicellulosiruptor bescii
           DSM 6725]
          Length = 300

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 82/318 (25%), Positives = 158/318 (49%), Gaps = 35/318 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLDR+            +QKI+  G V V++++V K   +++SG ++++           
Sbjct: 9   RLDRYLSEALSK-TRSFVQKIIEEGNVWVNQRQVLKPAYKVKSGDIIKV----------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW 136
               ++     L+  +  +   ++YED  + V NKP G+ V  G+G   +   +  L  +
Sbjct: 57  ----VIPEPKQLSLVAQDIDIEVVYEDEHLSVINKPRGMVVHPGAGNFENTLVNALLHKF 112

Query: 137 VDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      +P + HRLD++TSG+LVVA+T  A   L+E+ +  +I++IY+++  G+ 
Sbjct: 113 KGRLSSINGVIRPGIVHRLDKDTSGLLVVAKTDEAHIKLSEALKSHQIKRIYYAICEGVL 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K     +   + +   +    + +V         A+++F+V++ F  K+ +++++  TGR
Sbjct: 173 KEDSGVVDAPIGRH-PVNRLKMAIV----PNGKEAVTYFEVLERF-DKYTFVKLRLKTGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P++GD  Y    K  F    Q    LHA  ++  HP   + L  +A 
Sbjct: 227 THQIRVHMSYIGYPLLGDGIYG-RAKNEFGVEGQV---LHAGEIEFVHPITSKVLHFSAD 282

Query: 311 LPAHMVKTWDSLGFKYDR 328
           LP + V+  + L  + ++
Sbjct: 283 LPEYFVEILNMLRNRNNK 300


>gi|304393319|ref|ZP_07375247.1| ribosomal large subunit pseudouridine synthase D [Ahrensia sp.
           R2A130]
 gi|303294326|gb|EFL88698.1| ribosomal large subunit pseudouridine synthase D [Ahrensia sp.
           R2A130]
          Length = 365

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 88/349 (25%), Positives = 158/349 (45%), Gaps = 50/349 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQV 64
           ++ ++V + ++  R+D++   + P  ++   +Q ++R G V ++ +     + +I +G V
Sbjct: 35  MEVLIVSHVDDGKRVDKFISANAPDDLSRARVQALVRQGNVTINGELPRGTSTKISNGDV 94

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR                ++    +     + +   +L+ED  + V  KPAG+ V    G
Sbjct: 95  VRF---------------LMPPPEDAIPQPENIPLDILHEDDDLIVLIKPAGMVVHPAPG 139

Query: 125 ---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                    + +H DG L        ++P + HRLD++TSG++VVA++  A   L E F 
Sbjct: 140 NWSGTLVNALLHHCDGNLSGI--GGVKRPGIVHRLDKDTSGVMVVAKSYRAHIDLQEQFA 197

Query: 176 MRR----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
                  +++ YW+L WG P   K  +   L+ +         VV++    A +AI+H++
Sbjct: 198 DHGRTGPLERAYWALAWGAPPRMKGKVDT-LIGRHPTRRVQRAVVEEGAPDAKHAITHYE 256

Query: 232 VIDCFAQ-------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           V+  F             +E +  TGRTHQ+RVH  H+G P++GD +Y   +        
Sbjct: 257 VVKRFEDAERSGEAMASLIECKLETGRTHQIRVHLTHLGNPLLGDPEYGRAYANRIVRLP 316

Query: 285 Q---------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                     N+  LHAR +   HP  G  ++ TA   + M    DS+G
Sbjct: 317 HKAQSLFAEFNRQALHARTLGFRHPATGETMRFTAEPTSDMQALIDSIG 365


>gi|114775485|ref|ZP_01451053.1| ribosomal large subunit pseudouridine synthase C [Mariprofundus
           ferrooxydans PV-1]
 gi|114553596|gb|EAU55977.1| ribosomal large subunit pseudouridine synthase C [Mariprofundus
           ferrooxydans PV-1]
          Length = 315

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 99/316 (31%), Positives = 162/316 (51%), Gaps = 18/316 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  DE+  RLDR    H    +   + +++R G VR++KKR K    + +G  V +P 
Sbjct: 11  LTIGADEDGSRLDRVLSRHLGAGHRALILRLIRKGNVRLNKKRCKPETHVAAGDQVFLPV 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +   + + +      + V+ +         +LYED  + V NKPAG+ V GGSG   H 
Sbjct: 71  SLREPDTMER------APVSASLLGKMASIPVLYEDDSLLVVNKPAGMVVHGGSG---HE 121

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            G +++   S+G    RL HRLD++TSG+L++A+   A + LTESFR R +QK Y++L+ 
Sbjct: 122 AGLIEALKQSRGLDDLRLAHRLDRDTSGVLLMAKHLDALRRLTESFRERDMQKTYFALIA 181

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEM 245
           G P      +++ L K    GG+ + V   + +    +++ ++V+   +     +  + +
Sbjct: 182 GHPYAHAGRMSSNLAKGVVRGGERMVV---DSEEGKASVTDYQVMIEYERHGFPYAMVAL 238

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGR 304
            PH+GRTHQLRV   H G PI+GD KY    +   + S     L LHA  +   HP  G+
Sbjct: 239 NPHSGRTHQLRVQLQHEGHPILGDGKYGEKAQLAAYKSLGGKGLMLHAWRLRFTHPVSGK 298

Query: 305 -LQITAPLPAHMVKTW 319
            L+  AP P +     
Sbjct: 299 SLECKAPWPDNWSALL 314


>gi|227513366|ref|ZP_03943415.1| pseudouridylate synthase [Lactobacillus buchneri ATCC 11577]
 gi|227524509|ref|ZP_03954558.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
 gi|227083239|gb|EEI18551.1| pseudouridylate synthase [Lactobacillus buchneri ATCC 11577]
 gi|227088319|gb|EEI23631.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
          Length = 303

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 82/310 (26%), Positives = 136/310 (43%), Gaps = 32/310 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+      P I+    +K++  G V V+  + K     +    + I  V      I  
Sbjct: 13  RLDKIVSKLDPEISRSRAKKMIEDGDVIVNDSKKKPKYETKVSDTILIKDVKPETVSIKP 72

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWV 137
           E   LD               ++YED  + V NKP G+ V   +G   H   +  L    
Sbjct: 73  ENMPLD---------------IVYEDEDVIVVNKPQGMVVHPSAGHPNHTLVNALLFHSP 117

Query: 138 DSK---GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            S      +P + HR+D++TSG+L+VA+   A + L++  + ++  + Y +LV G  K  
Sbjct: 118 LSSINGEYRPGIVHRIDKDTSGLLMVAKNDMAHKALSKQLKAKKNLRKYVALVHGRIKED 177

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I   + +          V          AI+HF+V++ F + +  ++ +  TGRTHQ
Sbjct: 178 SGVIKAPIGRSPKDRKKQAIVA-----DGRPAITHFEVMERF-EDYTLIDCRLETGRTHQ 231

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPA 313
           +RVH  ++G PIVGD  Y         +   +  +LHA+ +   HP   +L   +AP+P 
Sbjct: 232 IRVHMQYIGHPIVGDPLYGPK-----KTIKGHGQFLHAQELGFEHPRNHKLMIFSAPIPE 286

Query: 314 HMVKTWDSLG 323
              KT  +L 
Sbjct: 287 IFEKTLRTLR 296


>gi|300173082|ref|YP_003772248.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299887461|emb|CBL91429.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 308

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 86/312 (27%), Positives = 143/312 (45%), Gaps = 35/312 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D          +   L + L++G + V+  +VK   ++ +G  + I         II 
Sbjct: 15  RIDAILAKENLPYSRTTLAEWLQTGHILVNGVQVKRAYKVTTGDTITILQPEVITTEIIA 74

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   LD               ++YED  I V NKP G+ V   +G   H  G L + +  
Sbjct: 75  EDIPLD---------------IIYEDDDILVVNKPQGMVVHPAAG---HSSGTLVNALLF 116

Query: 140 KGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      +P + HR+D++TSG+L+VA+   A Q L+   +  +  +IY++LV G  
Sbjct: 117 HAPLSTINGEFRPGIVHRIDRDTSGLLMVAKNDQAHQGLSAQLKAHKNDRIYYALVRGEF 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I N  + +  +      V    ++G   AI+HF+VI+ +   +  L+++  TGR
Sbjct: 177 VENSGTI-NAPINRHKVDRKKQAV----QEGGREAITHFEVIERYV-GYTLLKVRLETGR 230

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
           THQ+RVH  ++G P+VGD  Y +    N      N   LHA+ + L  P+ G  L+  + 
Sbjct: 231 THQIRVHMTYIGHPVVGDPVYGS--AQNLAGVKLNGQMLHAKTLSLTQPKTGEELRFDSA 288

Query: 311 LPAHMVKTWDSL 322
           LPA+      +L
Sbjct: 289 LPAYFKDALATL 300


>gi|261378098|ref|ZP_05982671.1| ribosomal large subunit pseudouridine synthase C [Neisseria cinerea
           ATCC 14685]
 gi|269145550|gb|EEZ71968.1| ribosomal large subunit pseudouridine synthase C [Neisseria cinerea
           ATCC 14685]
          Length = 330

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 96/322 (29%), Positives = 155/322 (48%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +              +YED  + V NKP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARVFEA---------VYEDDALLVVNKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-------- 238
             G   +    +   L K +   G+ +  V ++      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSED---GQAAHTVFRVLSRFSDGILHSVGL 237

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A LP  + +
Sbjct: 298 LNHPLTGEPLVLKAELPPDLAQ 319


>gi|70726718|ref|YP_253632.1| hypothetical protein SH1717 [Staphylococcus haemolyticus JCSC1435]
 gi|68447442|dbj|BAE05026.1| unnamed protein product [Staphylococcus haemolyticus JCSC1435]
          Length = 305

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 74/329 (22%), Positives = 144/329 (43%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ +   +    R+D+         +   +Q +++   V V++K +K N +++   
Sbjct: 1   MKTHEFKIENQELVGQRIDKLLPEFNNEWSRSQIQDLIKEDLVTVNEKVIKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++           I+ E++++++ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  LI-----------IVTEKEVVEADI----QPENLNLDIYYEDEDVAIVYKPKGMVVHPSP 105

Query: 124 GI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L E    +
Sbjct: 106 GHYSGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMDK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    I   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYTALVHGNIPHDYGTIDAPIGRNEK-DRQSMDVVD----NGKEAVTHFNVLEHFN 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 221 D-YTLIECQLETGRTHQIRVHMKYIGFPLVGDPKYGPRKTLD-----IGGQALHAGVIGF 274

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
            HP     ++  A LP       + +  +
Sbjct: 275 EHPVTHEYIERQAELPKEFETLLEDIRLR 303


>gi|319638921|ref|ZP_07993679.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317399825|gb|EFV80488.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 328

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 97/322 (30%), Positives = 161/322 (50%), Gaps = 25/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   EE  RLD +       +   ++ +I+R+G+VR++KKR K +NRIQ+G  VR
Sbjct: 9   VSLIAVAEHEEGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDNRIQAGDTVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A      E +   +           +  ++YED  + V NKP+G++V GGSG++
Sbjct: 69  IPPIRTAEKQRPSESQAAPAR----------EFDIVYEDDALLVINKPSGVAVHGGSGVS 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++     + +   L HRLD++TSG+L++A+ R+A   L E+ R    +KIY +L
Sbjct: 119 FGVIEQIRRAR-PEARYLELVHRLDKDTSGLLMIAKKRSALVKLHEAIRNDHPKKIYLAL 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   N +  +   L K +    + +  V ++      A + F+V++ F+         
Sbjct: 178 GVGRLPNDRFHVKLPLFKYTGAQDEKMVRVSED---GQSAHTIFRVLNRFSDGLLHQVGL 234

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +E    TGRTHQ+RVH     CPI GD +Y               +++LHA  + 
Sbjct: 235 SDLTLVEATLKTGRTHQIRVHLQSQDCPIAGDERYGDYQANKRLQKLGLKRMFLHASELH 294

Query: 297 LPHP-EGGRLQITAPLPAHMVK 317
           L HP  G +L + APLP  + +
Sbjct: 295 LAHPLTGEKLILKAPLPQELAQ 316


>gi|323526881|ref|YP_004229034.1| RluA family pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323383883|gb|ADX55974.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1001]
          Length = 345

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 98/326 (30%), Positives = 162/326 (49%), Gaps = 24/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +V
Sbjct: 20  QVSVIEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLV 79

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP+  A +     Q  + S+          +  +++ED  + V +KPAG++V GGSG+
Sbjct: 80  RVPPIRVAQHDEAAAQAPVPSA----------QFKIIFEDEHLLVIDKPAGVAVHGGSGV 129

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ R+A  +L +  R  R+ K Y++
Sbjct: 130 AFGVIEQMREARPQ-AKFLELVHRLDRETSGILMLAKKRSALVNLHDQIRENRMDKRYYA 188

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G   +       +   L K     G+    V+ +      + + F +ID + + +  
Sbjct: 189 CVHGEWASDWGRRRAVREPLHKYVTADGERRVRVQAD---GLASHTVFNLIDRWPE-YAL 244

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           LE +  TGRTHQ+RVH  H+  PIVGD KY               P   +++LHA  + L
Sbjct: 245 LEAELKTGRTHQIRVHLQHLELPIVGDAKYGDFALNKALARANAKPALKRMFLHAYRLKL 304

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL 322
            HP  G  LQ+ APLPA        L
Sbjct: 305 THPATGAPLQLEAPLPAECRNFIAQL 330


>gi|237801870|ref|ZP_04590331.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. oryzae str. 1_6]
 gi|330962679|gb|EGH62939.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. maculicola str. ES4326]
 gi|331024728|gb|EGI04784.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. oryzae str. 1_6]
          Length = 320

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 87/333 (26%), Positives = 150/333 (45%), Gaps = 36/333 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLELIAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
            A    + +   LD               ++YED +I V NKPAG+ V   +G A     
Sbjct: 71  EAQGEWVAQDIELD---------------IIYEDDQILVINKPAGLVVHPAAGHADGTLL 115

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R + +IY  +V 
Sbjct: 116 NALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVI 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+       I   + +        + V+    +G   A+SH++V++ F +    + ++  
Sbjct: 176 GVV-TAGGKIDAPIGRHGQQ-RQRMAVM----EGGKQAVSHYRVLERF-RSHTHVRVKLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P+VGD  Y   F+    + +          +  LHAR+++L HP
Sbjct: 229 TGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFLELDHP 288

Query: 301 EGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
             G R+   +PLP   V     L  K DR  +I
Sbjct: 289 ITGKRMSWESPLPDDFVWLLSLL--KQDREAFI 319


>gi|304316700|ref|YP_003851845.1| pseudouridine synthase [Thermoanaerobacterium thermosaccharolyticum
           DSM 571]
 gi|302778202|gb|ADL68761.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 306

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 80/329 (24%), Positives = 143/329 (43%), Gaps = 34/329 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M++   +  ++ E D+ + R+D +  +         L+K++  G V+V+   +K N +++
Sbjct: 1   MNIADRIN-IIAEKDDVDKRIDSFLASEL-DYTRSYLKKLILDGLVKVNGLLIKPNYKLK 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  V +         +  E   LD                          NKP G+ V 
Sbjct: 59  EGDSVDVNIPEAEEIDLSPENIPLDIIYEDDDIIVI---------------NKPQGMVVH 103

Query: 121 GGSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      ++  L    +  G     +P + HRLD++TSG++VVA+   A   L+   
Sbjct: 104 PAPGNYSGTLVNALLYHCKNLSGINGELRPGIVHRLDKDTSGVMVVAKNDKAHLDLSNQI 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R I K Y ++V G+ K+ +  I   + +  H+    + V     +   YA++ +KV++
Sbjct: 164 KERTILKKYIAIVEGVIKDDEGSIEAPIGRD-HVERKKMAVT----EDGRYALTLYKVLE 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            +      +E    TGRTHQ+RVH  ++G PIVGD  Y    K  F         LH++ 
Sbjct: 219 RYKNN-SLIEATIKTGRTHQIRVHMSYIGHPIVGDEVYGYK-KQRFNLLG---QALHSKL 273

Query: 295 MDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           + L HP     ++  AP+P +  +  + L
Sbjct: 274 LGLVHPSKKIYMEFEAPIPEYFERLINIL 302


>gi|302879313|ref|YP_003847877.1| pseudouridine synthase, RluA family [Gallionella capsiferriformans
           ES-2]
 gi|302582102|gb|ADL56113.1| pseudouridine synthase, RluA family [Gallionella capsiferriformans
           ES-2]
          Length = 326

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 139/326 (42%), Gaps = 30/326 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V + V+ N    +RLD+      P  +   LQ+ +   QV +D K      ++  G+ +
Sbjct: 12  DVIHFVIPNSSAGLRLDQVLATLLPEYSRSRLQEWVTLNQVLLDGKPAISKQKVWGGEKL 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            + P +                      ++ +   ++YED  + V NKP G+ V  GSG 
Sbjct: 72  AVLPQVTQSEQP--------------YQAEDIPLDIVYEDDDLLVINKPVGLVVHPGSGN 117

Query: 126 --AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                ++  L  W + +   +  + HRLD++TSG+LVVA+T  +  +L    + R +++ 
Sbjct: 118 WQGTLLNALLHHWPELALVPRAGIVHRLDKDTSGLLVVAKTLISQTNLVRQLQERSVKRE 177

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G   +      +  + +       + VV    +    A++H+KV +        
Sbjct: 178 YLALVHGELSH--GGYVDQPIGRHPSNRVKMAVV----ETGKDAVTHYKV-ERTFPSCTL 230

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-----NFTSPIQNKLYLHARYMDL 297
           L     TGRTHQ+RVH  ++  P+VGD  Y    +              +  LHA  + L
Sbjct: 231 LRCTLETGRTHQIRVHMTYLKHPLVGDSVYLKGPQKCVLQLRDVLTRFPRQALHATRLAL 290

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSL 322
            HP  G R++   PLP  M +    +
Sbjct: 291 EHPISGERMEWHVPLPDDMQQLLRQI 316


>gi|73662884|ref|YP_301665.1| pseudouridylate synthase [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72495399|dbj|BAE18720.1| putative pseudouridylate synthase [Staphylococcus saprophyticus
           subsp. saprophyticus ATCC 15305]
          Length = 305

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 71/327 (21%), Positives = 138/327 (42%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   Q+ +   ++   R+D+    ++   +   +Q  +++  V+V+ + +K N + +   
Sbjct: 1   MDIHQFKIENPEDTGQRIDKLLPEYHSEWSRTQIQDWIKASLVKVNDQVIKSNYKTKMND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                   +V      + L   + YED  + +  KP G+ V   +
Sbjct: 61  HIVVT---------------EKETVEADIQPENLNLDIYYEDDDVAIVYKPKGMVVHPSA 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    +  G     +P + HR+D++TSG+L+VA+   A + L +    +
Sbjct: 106 GHYTGTLVNGLMYQMKNLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVDQLVNK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G   +    +   + +        + VV         A++HF V++ F 
Sbjct: 166 TVTRKYVALVHGKIPHDYGTVDAPIGRN-KNDRQSMDVVD----DGKEAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            K+  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 NKYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPKKTLD-----IGGQALHAGIIGF 274

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLG 323
            HP     ++ +  LP    +    L 
Sbjct: 275 EHPVTHEYIEKSTALPEDFEQLLSELR 301


>gi|310766696|gb|ADP11646.1| 23S rRNA pseudouridine synthase D [Erwinia sp. Ejp617]
          Length = 325

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 81/340 (23%), Positives = 143/340 (42%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ + +  + V+   + K   ++  G+ + I  
Sbjct: 10  TVAESQLGHRLDQALAELFPDYSRSRIKEWILNRHITVNGVIIDKPKEKVLGGEQISIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I        +   LD               ++YED  I V NKP  + V  G+G     
Sbjct: 70  EIEEEARWEAQDIPLD---------------IVYEDDDILVINKPRDLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   +   +  + HRLD++T+G++VVA+T  A  HL +S + R I + Y ++
Sbjct: 115 VLNALLHHFPAIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDSLQRREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGRM-TAGGTVDQPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHISHPLVGDPLYGGRPRPPKGASEAFIATLRAFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G  ++  APLP  MV   D+L  K D   + ++L  
Sbjct: 288 HPISGIEMEWHAPLPQDMVDLIDAL--KADTEAFKEQLDW 325


>gi|296313302|ref|ZP_06863243.1| ribosomal large subunit pseudouridine synthase [Neisseria
           polysaccharea ATCC 43768]
 gi|296840180|gb|EFH24118.1| ribosomal large subunit pseudouridine synthase [Neisseria
           polysaccharea ATCC 43768]
          Length = 330

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 96/322 (29%), Positives = 155/322 (48%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +              +YED  + V NKP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARVFEA---------VYEDDALLVVNKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V ++      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSED---GQAAHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A LP  + +
Sbjct: 298 LNHPLTGEPLVLKAELPPDLAQ 319


>gi|296284607|ref|ZP_06862605.1| pseudouridine synthase D large subunit [Citromicrobium
           bathyomarinum JL354]
          Length = 314

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 80/319 (25%), Positives = 137/319 (42%), Gaps = 30/319 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
              RLD+   +    ++   ++ ++  GQV V  KR    + ++ +G    I        
Sbjct: 13  APARLDKALADA-TDLSRERIKGLIADGQVSVGGKRATSPSAKVAAGTPFTI-------- 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                   L +   L      +  ++ YED+ + V +KPAG+ V   +G      ++  L
Sbjct: 64  -------ALPAPTPLEAEPQDIPLVVAYEDAHLIVVDKPAGMVVHPAAGNRDGTLVNALL 116

Query: 134 KSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                        ++P + HR+D++TSG+LVVA+T AA + L   F    I + Y ++  
Sbjct: 117 YHCRGQLSGINGVERPGIVHRIDKDTSGLLVVAKTDAAHEGLARQFADHSISRRYVAVCA 176

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G P+  +  I   L +        + V+        +A++H++    F      LE +  
Sbjct: 177 GQPRPAEGTIDARLGRSDR-DRKKMAVLDPQSTRGKHAVTHYRTTKTFG-VASILECRLE 234

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT---SPIQNKLYLHARYMDLPHP-EGGR 304
           TGRTHQ+RVH   +G P++GD +Y  + K            +  LHA  +   HP  G R
Sbjct: 235 TGRTHQVRVHCASIGHPLLGDPQYGRDPKALRPIIEKLAFRRQALHAASLGFIHPATGER 294

Query: 305 LQITAPLPAHMVKTWDSLG 323
           L+  A LP  M +  D + 
Sbjct: 295 LEFRADLPRDMGELIDEIA 313


>gi|330988806|gb|EGH86909.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           lachrymans str. M301315]
          Length = 320

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 87/333 (26%), Positives = 151/333 (45%), Gaps = 36/333 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLELIAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
            A    + +   LD               ++YED +I V NKPAG+ V   +G A     
Sbjct: 71  EAQGEWVAQDIELD---------------IIYEDDQILVINKPAGLVVHPAAGHADGTLL 115

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R + +IY  +V 
Sbjct: 116 NALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVI 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+       I   + +        + V+    +G   A+SH++V++ F +    + ++  
Sbjct: 176 GVV-TAGGKIDAPIGRHGQQ-RQRMAVM----EGGKQAVSHYRVLERF-RSHTHVRVKLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P+VGD  Y   F+    + +          +  LHAR+++L HP
Sbjct: 229 TGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFLELDHP 288

Query: 301 EGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
             G R+   +PLP  +V     L  K DR  +I
Sbjct: 289 TTGKRMSWESPLPDDLVWLLSLL--KQDREAFI 319


>gi|157412550|ref|YP_001483416.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9215]
 gi|157387125|gb|ABV49830.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9215]
          Length = 319

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 85/315 (26%), Positives = 139/315 (44%), Gaps = 28/315 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +  P  +   +Q  + SG V V+ K  K    +++G  ++I          
Sbjct: 26  PMRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNIQIWMPPPEPLIY 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
           +K +K              +   +L+ED  I V NK +G+ V    G      ++G L  
Sbjct: 86  LKPEK--------------MDLNILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLFH 131

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++TSG +VVA+++ A  +L +  + +   + Y +++ G P
Sbjct: 132 CKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAP 191

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +++  I   + +       Y  V    E    YA +++K+ + F   +  +  +  TGR
Sbjct: 192 NSEEGQIVGNIGRDKLNRLKYKVV---EETSGRYACTYWKLEERFG-NYSLMSFKLDTGR 247

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  H+  PIVGD  Y    K        +   LHA  + L HP  G  +   + 
Sbjct: 248 THQIRVHCAHINHPIVGDPLYGRCKKLPCK---LDGQALHAIKLGLIHPINGKEMIFESE 304

Query: 311 LPAHMVKTWDSLGFK 325
           LP    K    L  K
Sbjct: 305 LPLDFQKLLSVLKVK 319


>gi|311278476|ref|YP_003940707.1| pseudouridine synthase, RluA family [Enterobacter cloacae SCF1]
 gi|308747671|gb|ADO47423.1| pseudouridine synthase, RluA family [Enterobacter cloacae SCF1]
          Length = 326

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 80/335 (23%), Positives = 147/335 (43%), Gaps = 41/335 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKMCDKPKEKVLGGENVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I                      +  +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEDVRF---------------EAQDIPLNIVYEDDDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        ++ I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVEQPISRHPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDQLYGGRPRPPKGASDEFITALRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            + L HP  G  ++  AP+P  MV   D++   ++
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVDLIDAMRADFE 317


>gi|259909396|ref|YP_002649752.1| 23S rRNA pseudouridine synthase D [Erwinia pyrifoliae Ep1/96]
 gi|224965018|emb|CAX56548.1| Ribosomal large subunit pseudouridine synthase D [Erwinia
           pyrifoliae Ep1/96]
 gi|283479469|emb|CAY75385.1| ribosomal large subunit pseudouridine synthase D [Erwinia
           pyrifoliae DSM 12163]
          Length = 325

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 80/340 (23%), Positives = 143/340 (42%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ + +  + V+   + K   ++  G+ + I  
Sbjct: 10  TVAESQLGHRLDQALAELFPDYSRSRIKEWILNRHITVNGVIIDKPKEKVLGGEQISIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I        +   LD               ++YED  I V NKP  + V  G+G     
Sbjct: 70  EIEEEARWEAQDIPLD---------------IVYEDEDILVVNKPRDLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   +   +  + HRLD++T+G++VVA+T  A  HL ++ + R I + Y ++
Sbjct: 115 VLNALLHHFPAIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGRM-TAGGTVDQPISRHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHISHPLVGDPLYGGRPRPPKGASEAFIATLRAFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G  ++  APLP  MV   D+L  K D   + ++L  
Sbjct: 288 HPISGIEMEWHAPLPQDMVDLIDAL--KADTEAFKEQLDW 325


>gi|121607091|ref|YP_994898.1| RluA family pseudouridine synthase [Verminephrobacter eiseniae
           EF01-2]
 gi|121551731|gb|ABM55880.1| ribosomal large subunit pseudouridine synthase D [Verminephrobacter
           eiseniae EF01-2]
          Length = 344

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 85/330 (25%), Positives = 140/330 (42%), Gaps = 31/330 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQV 64
            ++ + +   +   R+DR      P  +   LQ++L  G V ++ + V K  +R+ +G  
Sbjct: 36  ELRQMQIGARQHAARIDRALVELVPEFSRSYLQQLLAQGGVSLNGRPVRKAASRVNAGDR 95

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V +       +   + Q               +   ++YED+ + V NKPAG+ V    G
Sbjct: 96  VVLEMRPTVQSQAFRPQP--------------MDIDVVYEDAHLLVLNKPAGLVVHPAPG 141

Query: 125 IAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              H    L + + ++        +  + HRLD++TSG++VVAR RA    L      R+
Sbjct: 142 ---HWSATLLNGLLARDANALLLPRAGIVHRLDKDTSGLMVVARDRATMDALVAQIARRQ 198

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           +Q+ Y +L  G     +       + +       + VV         A +    +D   Q
Sbjct: 199 VQRQYLALAHGAWSGPRSRSVQAPIGRDPRNRLRMAVVDLARHAGKCARTDVLCLDATPQ 258

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             CWL+ + HTGRTHQ+RVH   +  P+VGD  Y     G        +  LHA  +   
Sbjct: 259 G-CWLQCRLHTGRTHQIRVHMASLQHPLVGDGLYGGAPLGAL-----QRQALHAERLAFV 312

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           HP  G+ LQ  A +P  M +   S G  Y+
Sbjct: 313 HPATGQALQFHAEVPQDMQQALSSWGLGYN 342


>gi|114707402|ref|ZP_01440299.1| Prenyl group binding site (CAAX box):RNA-binding S4:Pseudouridine
           synthase:Pseudouridine synthase, Rlu:Pseudouridine
           [Fulvimarina pelagi HTCC2506]
 gi|114537283|gb|EAU40410.1| Prenyl group binding site (CAAX box):RNA-binding S4:Pseudouridine
           synthase:Pseudouridine synthase, Rlu:Pseudouridine
           [Fulvimarina pelagi HTCC2506]
          Length = 339

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 85/351 (24%), Positives = 149/351 (42%), Gaps = 43/351 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQ 63
             +   VE +E  MR+D +      P ++   +Q ++R+G V V          R++ G+
Sbjct: 2   ETREYTVEAEEAGMRIDAFLAGRCSPELSRARIQSLIRAGDVTVGGVDTAAAKRRVKEGE 61

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +                + +        + +   +++ED+ + V +KPAG+ V  G 
Sbjct: 62  AVALR---------------VPAPAEPEPEPEDIPLTIVFEDADLVVVDKPAGLVVHPGP 106

Query: 124 GI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  L    +        ++P + HRLD++TSG+LV+A+T  A + L E F  
Sbjct: 107 GNWSGTLVNALLHYCGEELSGINGVKRPGIVHRLDKDTSGLLVIAKTDMAHRSLAEQFAA 166

Query: 177 R----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
                R+ + Y ++VWG P      I   L + S        VV   +  A  AI+ +++
Sbjct: 167 HGSDGRMVRSYRAIVWGTPVPAVGRIETMLGRSSS-DRLKRDVVAATQPDARQAITDYRI 225

Query: 233 IDCFAQKF----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------ 282
           +    +        +E +  TGRTHQ+RVH  H+G P++GD  Y + F     +      
Sbjct: 226 LAGAGRAAGAEASLVECRLATGRTHQIRVHMAHIGHPLIGDVVYASGFASKAKALEEPAR 285

Query: 283 ---PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
                  +  LHA  +   HP  G   + ++ LP  M +   +LG     N
Sbjct: 286 TTVEAFRRQALHAAELGFVHPVTGDAKRFSSDLPTDMRELAAALGIALSGN 336


>gi|33519868|ref|NP_878700.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Blochmannia floridanus]
 gi|33504213|emb|CAD83475.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Blochmannia floridanus]
          Length = 322

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 101/321 (31%), Positives = 165/321 (51%), Gaps = 14/321 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           + ++ V +     R+D +   +   +    + +++R G+VRV+KKR+KF  R++ G +++
Sbjct: 8   LHWLKVSDHCAGQRVDNFLSFYLKTVPKSMIYRMIRIGKVRVNKKRIKFQYRLKIGDLLK 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SG 124
           IP         IK  KI  S +       FL++ ++YED  + V NKP+GISV GG  + 
Sbjct: 68  IP--------AIKYVKIRQSCMCNISEMMFLQNTVIYEDEHLLVLNKPSGISVHGGGDNK 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +  +I   L+  +  K +   L HRLD++TSG+L++A++R     L E  R+++IQK Y 
Sbjct: 120 LQLNIIDALR-MLRPKIRFLWLVHRLDRDTSGLLLIAKSRIVLIKLHEQLRLQKIQKTYL 178

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V+G        I+  L KK     + ++VV  + K    A + F+V + F      L 
Sbjct: 179 AIVYGSWDTHITSISAPLFKKKDYIKN-INVVFIDSKFGKLAQTCFQVKERFKNIATLLN 237

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEGG 303
           + P TGRTHQ+RVH  +  CPI+GDH Y        F     N+L+LHA  +   HP   
Sbjct: 238 IIPITGRTHQIRVHTQYAQCPIIGDHVYGKQKVNVQFKKLGWNRLFLHASTLCFIHPCTE 297

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             + I+AP+          L 
Sbjct: 298 EKMNISAPVDQSFYDCLSFLR 318


>gi|240081627|ref|ZP_04726170.1| RluC [Neisseria gonorrhoeae FA19]
 gi|268597722|ref|ZP_06131889.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae FA19]
 gi|268551510|gb|EEZ46529.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae FA19]
          Length = 330

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 153/322 (47%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +    + +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKGYIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V NKP+G++V GGSG+ 
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFE---------VVYEDDALLVVNKPSGVAVHGGSGVG 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-------- 238
             G   +    +   L K +   G+ +  V ++      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSED---GQSAHTVFRVLSRFSDGILHGVGL 237

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A  P  + +
Sbjct: 298 LNHPLTGEPLVLKAEPPPDLAQ 319


>gi|119492077|ref|ZP_01623530.1| Pseudouridine synthase, RluD [Lyngbya sp. PCC 8106]
 gi|119453287|gb|EAW34452.1| Pseudouridine synthase, RluD [Lyngbya sp. PCC 8106]
          Length = 319

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 84/336 (25%), Positives = 142/336 (42%), Gaps = 37/336 (11%)

Query: 4   MTYVQYVVVENDEENM--------RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VK 54
           M   Q + +   E+N         RLDRW       ++   +Q ++  G V V++K  V 
Sbjct: 1   MNSEQTITLTVSEQNQTTLEPQNYRLDRWLSESLETLSRSRIQTLISQGHVTVNQKVCVS 60

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
               ++ G  + +                +  +  L   +  +   +LYED  + + NK 
Sbjct: 61  KKLTLKRGDHIEVK---------------IPPNEPLELEAVDIPLDILYEDEHLIIINKQ 105

Query: 115 AGISVQGGSGIAYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQ 168
           AG+ V   +G       +  L       G    ++P + HRLD++T+G +VVA+T  + Q
Sbjct: 106 AGLVVHPSAGHVNDTLVNALLAHCDTLAGIGGVERPGIVHRLDKDTTGAIVVAKTDFSLQ 165

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            L +  + +  Q+ Y  +V+G  K     I   + +  H+       V   E+G   AI+
Sbjct: 166 SLQQQIKNKTAQRQYLGVVYGSHKADFGTIEQPIGR--HLADRKKMAVVTIERGGRNAIT 223

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
           H+++ +     +  +     TGRTHQ+RVH+  +G PIVGD  Y +   G       +  
Sbjct: 224 HWQIQERLG-NYSLILFTLETGRTHQIRVHSNFIGHPIVGDLDYSS---GRSVGVNLSGQ 279

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            LHA  + L HP     ++  APLP  M      L 
Sbjct: 280 ALHAWKLKLQHPVTEEWIEAIAPLPEEMNTLLQVLR 315


>gi|59802102|ref|YP_208814.1| RluC [Neisseria gonorrhoeae FA 1090]
 gi|194099977|ref|YP_002003116.1| RluC [Neisseria gonorrhoeae NCCP11945]
 gi|239997984|ref|ZP_04717908.1| RluC [Neisseria gonorrhoeae 35/02]
 gi|240015038|ref|ZP_04721951.1| RluC [Neisseria gonorrhoeae DGI18]
 gi|240113908|ref|ZP_04728398.1| RluC [Neisseria gonorrhoeae MS11]
 gi|240116640|ref|ZP_04730702.1| RluC [Neisseria gonorrhoeae PID18]
 gi|240122106|ref|ZP_04735068.1| RluC [Neisseria gonorrhoeae PID24-1]
 gi|240124728|ref|ZP_04737614.1| RluC [Neisseria gonorrhoeae SK-92-679]
 gi|240129077|ref|ZP_04741738.1| RluC [Neisseria gonorrhoeae SK-93-1035]
 gi|254494662|ref|ZP_05107833.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae 1291]
 gi|260439599|ref|ZP_05793415.1| RluC [Neisseria gonorrhoeae DGI2]
 gi|268593835|ref|ZP_06128002.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae 35/02]
 gi|268599970|ref|ZP_06134137.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae MS11]
 gi|268602307|ref|ZP_06136474.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae PID18]
 gi|268683306|ref|ZP_06150168.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae SK-92-679]
 gi|268687455|ref|ZP_06154317.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae SK-93-1035]
 gi|291042839|ref|ZP_06568580.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae DGI2]
 gi|293398142|ref|ZP_06642347.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae F62]
 gi|59718997|gb|AAW90402.1| putative ribosomal large subunit pseudouridine synthase C
           [Neisseria gonorrhoeae FA 1090]
 gi|193935267|gb|ACF31091.1| RluC [Neisseria gonorrhoeae NCCP11945]
 gi|226513702|gb|EEH63047.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae 1291]
 gi|268547224|gb|EEZ42642.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae 35/02]
 gi|268584101|gb|EEZ48777.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae MS11]
 gi|268586438|gb|EEZ51114.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae PID18]
 gi|268623590|gb|EEZ55990.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae SK-92-679]
 gi|268627739|gb|EEZ60139.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae SK-93-1035]
 gi|291013273|gb|EFE05239.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae DGI2]
 gi|291611405|gb|EFF40475.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae F62]
 gi|317165428|gb|ADV08969.1| RluC [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 330

 Score =  251 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 154/322 (47%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +    + +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKGYIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V NKP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFE---------VVYEDDALLVVNKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-------- 238
             G   +    +   L K +   G+ +  V ++      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSED---GQSAHTVFRVLSRFSDGILHGVGL 237

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A  P  + +
Sbjct: 298 LNHPLTGEPLVLKAEPPPDLAQ 319


>gi|297182616|gb|ADI18775.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF4000_36I10]
          Length = 319

 Score =  251 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 141/323 (43%), Gaps = 39/323 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V+ ++    RLD+     +P  +   LQ  ++SG++ V+  + +  ++I  G+ +R+   
Sbjct: 10  VIPDELAGSRLDQAVAQLFPDYSRSRLQSWIKSGELTVNGSQYRPRDKIMGGEEIRVGAE 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +        +Q               +   L YED  + V NKP G+ V   +G   H D
Sbjct: 70  LQDEGDWQPQQ---------------IDFGLFYEDEHLLVLNKPVGLVVHPAAG---HYD 111

Query: 131 GFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + +           +  + HRLD++TSG++VVA+T  A   L +  + R + + Y 
Sbjct: 112 GTLVNALIEHCPGLAQLPRAGIVHRLDKDTSGLMVVAKTLEAHTSLVKQLQARNVHREYE 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV+G+     +      + +       + VV+    G   AI+H+++I+ F   F  + 
Sbjct: 172 ALVYGVMTGGGKVDE--PMGRHPQQRKKMAVVR---AGGKEAITHYRIIERFTH-FSHVR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
               TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHAR ++
Sbjct: 226 CLLETGRTHQIRVHMAHIKHPLIGDALYAGRLRQPKGASELLIETLRTFRRQALHARKLE 285

Query: 297 LPHPEGGRL-QITAPLPAHMVKT 318
           L HP    L      LP    + 
Sbjct: 286 LIHPATDELVSWETDLPDDFQRL 308


>gi|148827314|ref|YP_001292067.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae PittGG]
 gi|148718556|gb|ABQ99683.1| SfhB [Haemophilus influenzae PittGG]
          Length = 324

 Score =  251 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 141/328 (42%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGEKIEITVE 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +        E                +   ++YED  I V NKP  + V  G+G      
Sbjct: 70  VEDETRFEPEN---------------IPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLSH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|253996250|ref|YP_003048314.1| RluA family pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253982929|gb|ACT47787.1| pseudouridine synthase, RluA family [Methylotenera mobilis JLW8]
          Length = 368

 Score =  251 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 83/336 (24%), Positives = 144/336 (42%), Gaps = 40/336 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +T + ++ + +D   +RLD   +   P  +   LQ  ++SG V VD K      ++  G+
Sbjct: 9   LTNLIHLTISSDLGGLRLDVALQRLLPEHSRSRLQSWIKSGLVTVDGKASTAKTKVWGGE 68

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +   +   +     Q I                 ++YED  I V NKPAG+ V   +
Sbjct: 69  KVSVDVQVKPESRAFIAQDI--------------PLDIVYEDDHILVVNKPAGMVVHPAA 114

Query: 124 GIAYHIDGFLKSWVDSKGQKPR------LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   + DG L + +     +        + HRLD+ETSG+LVVA+T  A  HL    + R
Sbjct: 115 G---NWDGTLLNALLFHAPQLHDVPRAGIVHRLDKETSGLLVVAKTLNAQTHLVRQLQAR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y ++VWG    +   +   L +        + + +        AI+ +++++ F+
Sbjct: 172 TVKREYRAIVWGQLW-RNGVVDQPLGRDPR-SRTKMAINRM----GKPAITRYEILERFS 225

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NKL 288
               +L     TGRTHQ+RVH  H+  P+VGD  Y         +  Q         ++ 
Sbjct: 226 -VQTYLRCNLETGRTHQIRVHMQHLKAPLVGDPVYGFRGIVPIRAMTQTLRDAVSQFHRQ 284

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            LHA  + L HP     ++    L   M    +++ 
Sbjct: 285 ALHAIKLGLVHPATNEFMEWQIELADDMKVLLEAMR 320


>gi|255101761|ref|ZP_05330738.1| putative pseudouridylate synthase [Clostridium difficile QCD-63q42]
 gi|255307629|ref|ZP_05351800.1| putative pseudouridylate synthase [Clostridium difficile ATCC
           43255]
          Length = 315

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 145/328 (44%), Gaps = 33/328 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +M  V+  +V  +EE +RLD +       ++   +QKI++ G+V+V+ K  K    ++  
Sbjct: 12  IMDEVKEFLVLEEEEEVRLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKARYLVKEE 71

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I          I E K+L+           +   ++YED  + + NKP  + V   
Sbjct: 72  DNIVIE---------IPEPKVLEV------LPQDIPIDIVYEDDDVLIINKPQDMVVHPA 116

Query: 123 SGIAYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G   +   +G L    D         +P + HR+D++TSG+L++A+   A   L E  +
Sbjct: 117 PGNYENTLVNGILYHCKDKLSSINGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLK 176

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I + Y  + +G+ K  K  +   + +          V     K    AI+HF+V++ 
Sbjct: 177 EHTITREYEFICYGVVKEDKITVDKPIGRNPKDRLKMAVV-----KDGKNAITHFEVVER 231

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F  KF  +  +  TGRTHQ+RVHAL +  P++GD+ Y        T        LHA+ +
Sbjct: 232 F-DKFTHMRARLETGRTHQIRVHALSINHPLLGDYVYGPKE----TKFKLKGQTLHAKKL 286

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP     ++  + LP +  +    +
Sbjct: 287 GFIHPTTKEYIEFNSELPEYFKEVIKKI 314


>gi|260220730|emb|CBA28584.1| Ribosomal large subunit pseudouridine synthase C [Curvibacter
           putative symbiont of Hydra magnipapillata]
          Length = 361

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 102/332 (30%), Positives = 159/332 (47%), Gaps = 21/332 (6%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ V V+ D    RLD +       +   ++ +I+RSG+VRV+K R   + R+  G V
Sbjct: 18  SQVKSVTVDEDSAGQRLDNFLMRELKGVPKTHVYRIIRSGEVRVNKGRASADTRLAVGDV 77

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+PPV  +      EQK    +  + +        +L+ED      +KPAG++V GGSG
Sbjct: 78  IRLPPVRTSER---AEQKTAAMAEQVGRFVPAKDFPVLFEDDHFLAVDKPAGVAVHGGSG 134

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +++ +   L+     K     L HRLD+ETSGIL+VA+ R+A ++L + FR R   K Y 
Sbjct: 135 VSFGVIEQLR-MARPKATFLELVHRLDRETSGILLVAKKRSALKNLQDQFRERETGKTYL 193

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFA------ 237
           +LV G     K+ +   L K     G+  V VV ++   A  ++S  KV           
Sbjct: 194 ALVAGQWPANKKVLDKSLQKYLLADGERRVRVVAKDHPDAMPSLSLVKVHSVTPAARTAQ 253

Query: 238 ----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKL 288
               + +  LE+   TGRTHQ+RVH    G  IVGD KY           +  +    ++
Sbjct: 254 TPQQKVYSLLEVTIKTGRTHQIRVHLASEGMGIVGDDKYGDFDLNKALARDDGALALKRM 313

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           +LHA      HP  G R+ +   LP  + +  
Sbjct: 314 FLHAWRFQCNHPATGERVVLQTGLPPELARFL 345


>gi|254491706|ref|ZP_05104885.1| pseudouridine synthase, RluA family [Methylophaga thiooxidans
           DMS010]
 gi|224463184|gb|EEF79454.1| pseudouridine synthase, RluA family [Methylophaga thiooxydans
           DMS010]
          Length = 318

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 91/321 (28%), Positives = 155/321 (48%), Gaps = 15/321 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            VQ++ +   +   R+D +       +    + + +R G+VRV+K R+K   +IQ+G +V
Sbjct: 10  KVQFIEISPSQAGQRIDNFLLTLEKGVPKSRIYRAIRKGEVRVNKGRIKQTYKIQAGDIV 69

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP+      + + +     S +L +    L   +++ED  + V NKP+G++V  GS I
Sbjct: 70  RVPPL-----RVAEREAPTHVSESLRQQ---LLQDIIFEDDSMLVLNKPSGLAVHAGSQI 121

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +    +           L HRLD++TSG L++A++R +  +L +     +I K Y +
Sbjct: 122 QVGVIEAFRIIKPELAF-LELVHRLDRDTSGCLLLAKSRDSLLNLQQQMLSDQIDKRYLT 180

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L+ GI  N +E +   LLK +   G+ +  V  + K A        +           E+
Sbjct: 181 LLKGILPNAEELVEQPLLKNTVSSGERMVKVTPDGKRAKT----LFIRQQDLSLAQLTEV 236

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           + +TGRTHQ+RVHA     P+ GD KY    F     S    +L+LHA  + + HP  G 
Sbjct: 237 KLYTGRTHQIRVHAAWTQHPVAGDDKYGDREFNKTLKSFGLKRLFLHAWRLGIRHPVSGE 296

Query: 305 -LQITAPLPAHMVKTWDSLGF 324
            +Q+ APLP  + +    L  
Sbjct: 297 PMQLEAPLPTALQQVITKLEL 317


>gi|551786|gb|AAA23442.1| orfX [Escherichia coli]
          Length = 285

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 99/296 (33%), Positives = 160/296 (54%), Gaps = 16/296 (5%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAITADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHA 292
              +   P TGRTHQ+RVH  + G PI  D +Y     + +        N+L+LHA
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHA 284


>gi|309792569|ref|ZP_07687031.1| RluA family pseudouridine synthase [Oscillochloris trichoides DG6]
 gi|308225383|gb|EFO79149.1| RluA family pseudouridine synthase [Oscillochloris trichoides DG6]
          Length = 299

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 83/316 (26%), Positives = 142/316 (44%), Gaps = 28/316 (8%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           E      RLDR+     P ++   +Q ++ +GQV V+ + V+ ++ ++ G +V +     
Sbjct: 2   EAQAAGHRLDRFVAQALPDLSRSFVQHLIAAGQVLVNAQAVRPSHALRHGDLVSVTVPPA 61

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HID 130
               ++ E                +   ++YED+ + V  KPAG+ V    G      ++
Sbjct: 62  QPVALVPE---------------AIPLHVVYEDADVVVVEKPAGMVVHPAPGHPNGTLVN 106

Query: 131 GFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             L  + D       +P + HRLD  TSG+LVVAR   A +HLT     R+++KIY ++ 
Sbjct: 107 ALLARYPDMQVGGDLRPGIVHRLDAGTSGLLVVARHDQALRHLTALQHARQMRKIYLAVA 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  K  +  I   + +  H       +          A +H++V +     +  LE++ 
Sbjct: 167 EGRFKQAEGLIDAPVGRHPHD-----RLRMAVTPTGREARTHYRVCEELG-NYTLLELRL 220

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH  H+G PI+GD  Y    +    +    + +LHA  +     +G   + 
Sbjct: 221 ETGRTHQIRVHLQHLGRPILGDPLYG--VRKGRPTFGLERQFLHAHCLGFQLLDGSWREF 278

Query: 308 TAPLPAHMVKTWDSLG 323
           T+PLPA +      L 
Sbjct: 279 TSPLPADLQAVLVKLR 294


>gi|104783634|ref|YP_610132.1| 23S rRNA pseudouridine synthase [Pseudomonas entomophila L48]
 gi|95112621|emb|CAK17349.1| 23S rRNA pseudouridine synthase [Pseudomonas entomophila L48]
          Length = 320

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 89/346 (25%), Positives = 159/346 (45%), Gaps = 44/346 (12%)

Query: 4   MTYVQYV--VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M+ +  +   V ++    RLD+     +   +   L   ++ G++ VD   ++  + + S
Sbjct: 1   MSEIIQLSAEVPSELGGQRLDQVAAQLFSEYSRSRLSSWIKDGRLTVDGAVLRPRDTVHS 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G ++ +     A    + +   LD               ++YED +I V NKPAG+ V  
Sbjct: 61  GSILALEAEQEAQGEWVAQDIELD---------------IVYEDDQILVINKPAGLVVHP 105

Query: 122 GSGIAYHIDGFLKSWVDS------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +G   H DG L + +           +  + HRLD++T+G++VVA+T  A  +L +  +
Sbjct: 106 AAG---HPDGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTLQAQTNLVDQLQ 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + +IY  +V G+       I   + +    GG+   +   +  G   A+SH++V+  
Sbjct: 163 KRSVSRIYECIVVGVVIA-GGKIDAPIGRH---GGERQRMAVTD--GGKPAVSHYRVLKR 216

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NK 287
           F +    + ++  TGRTHQ+RVH  H+G P+VGD  Y   F+    + +          +
Sbjct: 217 F-RSHTHVRVKLETGRTHQIRVHMAHVGYPLVGDQTYGVRFRIPPAASVAMVEAVKNFPR 275

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
             LHAR++ L HP  G R++  +PLP   +     L    DR  +I
Sbjct: 276 QALHARFLALDHPTTGERMEWASPLPDDFLWLLSLL--NDDRESFI 319


>gi|284929127|ref|YP_003421649.1| ribosomal large subunit pseudouridine synthase D [cyanobacterium
           UCYN-A]
 gi|284809586|gb|ADB95291.1| ribosomal large subunit pseudouridine synthase D [cyanobacterium
           UCYN-A]
          Length = 316

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 83/324 (25%), Positives = 157/324 (48%), Gaps = 35/324 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINA 73
           +++  R+DRW   H  +I+   +QK++++G + ++ K  K    ++ +G  + +      
Sbjct: 8   EDKGDRIDRWLSKHILNISRARIQKLIQAGNIILNNKICKTKKEQLIAGDCLEV------ 61

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDG 131
                     + S   L    + +   +LYED  + + NK AG+ V    G      +  
Sbjct: 62  ---------FVPSPKKLELIPEAIPLDVLYEDKYLIIINKVAGMVVHPSPGHENGTLVHA 112

Query: 132 FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            L    D  G    Q+P + HRLD++T+G +V+A+T    QHL +  R R +++ Y +++
Sbjct: 113 LLHHCRDLSGIGEVQRPGIVHRLDKDTTGTIVIAKTDFVHQHLQKQIRDRVVEREYLAII 172

Query: 188 WGIPKNKK-------ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            G+ KN++       + + +  + +  I    + V+  +EK    A++++K+++     +
Sbjct: 173 HGVLKNRENNDNVVNKGVIDLPIGRHLIDRKKMAVM-PSEKNGRKAVTYWKILERLG-NY 230

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +  +  TGRTHQ+RVH+  +GCPI+GD  Y +N   N      +   LHA  + L HP
Sbjct: 231 SMVNFKLGTGRTHQIRVHSSFLGCPILGDPLYSSNHSFNIN---LSGQALHAHKLSLIHP 287

Query: 301 -EGGRLQITAPLPAHMVKTWDSLG 323
               +++ITA  P    K   +L 
Sbjct: 288 VSSNKIEITANPPIEFTKLLKTLR 311


>gi|307730549|ref|YP_003907773.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1003]
 gi|307585084|gb|ADN58482.1| pseudouridine synthase, RluA family [Burkholderia sp. CCGE1003]
          Length = 345

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 97/326 (29%), Positives = 161/326 (49%), Gaps = 24/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +V
Sbjct: 20  QVSVIEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLV 79

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP+  A +     Q  + S+          +  +++ED  + V +KPAG++V GGSG+
Sbjct: 80  RVPPIRVAQHDEAAAQAPVPSA----------QFKIIFEDEHLLVIDKPAGVAVHGGSGV 129

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ R+A  +L +  R  ++ K Y++
Sbjct: 130 AFGVIEQMREARPQ-AKFLELVHRLDRETSGILMLAKKRSALVNLHDQIRENKMDKRYYA 188

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G   +       +   L K     G+    V+ +      + + F +ID +   +  
Sbjct: 189 CVHGDWASDWGRRRAVKEPLHKYLTADGERRVRVQAD---GLASHTVFNLIDRWPD-YAL 244

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           LE +  TGRTHQ+RVH  H+  PIVGD KY               P   +++LHA  + L
Sbjct: 245 LEAELKTGRTHQIRVHLQHLELPIVGDAKYGDFALNKALARANAKPGLKRMFLHAYRLKL 304

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL 322
            HP  G  LQ+ APLPA        L
Sbjct: 305 THPATGAPLQLEAPLPAECRNFIAQL 330


>gi|271501679|ref|YP_003334705.1| pseudouridine synthase, RluA family [Dickeya dadantii Ech586]
 gi|270345234|gb|ACZ77999.1| pseudouridine synthase, RluA family [Dickeya dadantii Ech586]
          Length = 325

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 80/342 (23%), Positives = 145/342 (42%), Gaps = 37/342 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   ++  +   +V+++   V +   ++  G+ V I
Sbjct: 8   TATVAESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGNMVDRPKEKVLGGESVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +I                      +  +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  DALIEEDARW---------------EAQPISLDIVYEDDDILVINKPRDLVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + + +   +  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHHYPEIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A++H+++++ F +    L 
Sbjct: 173 AVAIGTM-TAGGTVDEPIARHST-----KRTHMAVHPMGKPAVTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +        F   ++N  +  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMAHINHPLVGDPLYGGRPRLPKGASDEFIETLRNFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           L HP  G +++  APLP  MV    +L  K D   +  +L  
Sbjct: 286 LYHPISGIQMEWHAPLPQDMVDLIAAL--KADTEAFKDQLDW 325


>gi|301154795|emb|CBW14258.1| 23S rRNA pseudouridine synthase [Haemophilus parainfluenzae T3T1]
          Length = 324

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 78/339 (23%), Positives = 148/339 (43%), Gaps = 37/339 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M  MT      ++ ++   RLD+     +P  +   L+  + + QV+++ +       ++
Sbjct: 1   MPQMTL--TAEIQPEQMGQRLDQTLAELFPEYSRSRLKTWIEAKQVKMNGEIADIPRAKV 58

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G+ + I   +   N                     +   ++YED  I V NKP  + V
Sbjct: 59  YGGEQIEISVEVEDENRF---------------EPQNIPLNIVYEDDDIIVINKPKDLVV 103

Query: 120 QGGSGIAYHI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             G+G       +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + 
Sbjct: 104 HPGAGNPDGTVLNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQK 163

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R+I + Y ++  GI   K   +   + + +         +         A++H+++++ F
Sbjct: 164 RKITREYEAVASGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENF 217

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KL 288
            + +  L ++  TGRTHQ+RVH  H+  P++GD  Y    +        FT  ++N  + 
Sbjct: 218 -RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEAFTEVLRNFKRQ 276

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            LHA  + L HP  G  ++  APLP   V+   +L   Y
Sbjct: 277 ALHAVMLRLAHPITGETMEWYAPLPDDFVELLHALKADY 315


>gi|149173826|ref|ZP_01852455.1| ribosomal large subunit pseudouridine synthase [Planctomyces maris
           DSM 8797]
 gi|148847356|gb|EDL61690.1| ribosomal large subunit pseudouridine synthase [Planctomyces maris
           DSM 8797]
          Length = 342

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 92/336 (27%), Positives = 146/336 (43%), Gaps = 40/336 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + VE      R+D +    YP+   V  Q  ++   V V+   VK   R++    V + 
Sbjct: 18  EITVEARAHGWRIDHYLCRLYPNYTRVLFQTAIKQEAVLVNGLPVKAARRMRVNDRVSVR 77

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAY 127
                 N +  E   +D               ++YED  I + NKP+ + V  G G  A 
Sbjct: 78  LPELPDNRLPPEDIPID---------------IVYEDDWIAIINKPSDMIVHPGKGNYAG 122

Query: 128 HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            + G L+   D         +P + HRLD+ TSGI+VVA+       L+  F  R +QK 
Sbjct: 123 TLAGALQYHFDQLSDVAGQYRPGIVHRLDRNTSGIMVVAKDNQVHAKLSAQFEKRDVQKE 182

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++VWG  +   + I  ++    H       +V      A  A ++++VI+ + Q F +
Sbjct: 183 YRAIVWGRMEFDTDYIDTFMCV--HPRAREKMIVCDEGGNARNAFTYYEVIERY-QAFTY 239

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP---------------IQNK 287
           + ++P TGRTHQLRVH  H+G  IV D  Y  +      S                +  +
Sbjct: 240 VRLKPRTGRTHQLRVHMQHIGHSIVADRVYGGHKSLKMKSLGIQAEADAAELESDVLIER 299

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             LHA  ++  HP+ G+ ++  APLP  M  T  +L
Sbjct: 300 QALHAYCLEFFHPQSGKPMKFEAPLPEDMQNTLAAL 335


>gi|167837371|ref|ZP_02464254.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           thailandensis MSMB43]
          Length = 335

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 100/326 (30%), Positives = 160/326 (49%), Gaps = 22/326 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++      R+D +       +   ++ +ILRSG+VRV+K R+    R+  G VV
Sbjct: 16  QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGDVV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + +   +        +        +L+ED  I   NKPAG++V GGSG+
Sbjct: 76  RVPPVRVAAADLARAAGLAPVPAAAFE--------ILFEDDAIIALNKPAGVAVHGGSGV 127

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y++
Sbjct: 128 AFGVIEQMRHAR-PHAKFLELAHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRYFA 186

Query: 186 LVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G       ++  +   L K +   G+    V+++      + + F ++D +   +  
Sbjct: 187 CVHGDWAADWGRRRTVKAPLFKYATPDGERRVRVQED---GLPSHTVFNLVDRWPD-YAL 242

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PIVGD KY              +P   +++LHA  +  
Sbjct: 243 VEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALSRANAAPSIKRMFLHAHRLRF 302

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA   +  D L
Sbjct: 303 AHPLTGEPLQFDAPLPAECRQFLDQL 328


>gi|308048517|ref|YP_003912083.1| ribosomal large subunit pseudouridine synthase D [Ferrimonas
           balearica DSM 9799]
 gi|307630707|gb|ADN75009.1| ribosomal large subunit pseudouridine synthase D [Ferrimonas
           balearica DSM 9799]
          Length = 323

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 79/333 (23%), Positives = 143/333 (42%), Gaps = 39/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           V+ + +   RLD+     +P  +   +++ + + +V ++ K V K   ++  G+ V I  
Sbjct: 10  VISDSQLGQRLDQALAECFPDYSRSRIKEWILAERVSLNGKTVAKPREKVMGGEAVLIQ- 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                          +    +      +   ++YED  I V NKPA + V  G+G   H 
Sbjct: 69  --------------AEFEEEVAAKPQDIALDIVYEDDDILVINKPADLVVHPGAG--NHD 112

Query: 130 DGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              L + +      +   +  + HRLD++T+G++VVA+T  A  HL    + R I + Y 
Sbjct: 113 GTVLNALLHHCPSIANVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVAQLQAREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G+       +   + +                +    A++H+++ + F +    L 
Sbjct: 173 AIALGVM-TAGGHVDEPIGRHPQ-----RRTHMAVTELGKPAVTHYRIREKF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG--------NFTSPIQNKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+G P+VGD  Y    +                N+  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMAHLGHPLVGDPLYSGRPRPVKGWSEELREFLRRFNRQALHAAMLR 285

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           L HP  G  +Q TAP+P  MV+  + L    + 
Sbjct: 286 LEHPITGEMMQWTAPIPDDMVRLTELLRRDTEE 318


>gi|119476934|ref|ZP_01617215.1| Pseudouridine synthase, RluD [marine gamma proteobacterium
           HTCC2143]
 gi|119449741|gb|EAW30978.1| Pseudouridine synthase, RluD [marine gamma proteobacterium
           HTCC2143]
          Length = 318

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 86/332 (25%), Positives = 144/332 (43%), Gaps = 33/332 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
              V    E  RLD+     +P  +   LQ  ++SG++ VD +  K   ++QSG+++ + 
Sbjct: 8   TATVPEGLEGSRLDQIAAQLFPDYSRARLQIWIKSGELTVDGEAKKSREKLQSGELLELR 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
            V+                      ++ +   ++YED  + V NKPAG+ V  GSG A  
Sbjct: 68  AVVEDEERW---------------DAESMDLDIVYEDEALLVVNKPAGLVVHPGSGNASG 112

Query: 127 YHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             ++  L    D +   +  + HRLD++TSGI+VVA+T AA   L    + R + ++Y +
Sbjct: 113 TLLNALLAHLPDIASVPRAGIVHRLDKDTSGIMVVAKTLAAQNSLVNQLQARTVSRVYEA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V+G        +    + +       + V+     G   A +H+++I  F    C +  
Sbjct: 173 VVFGSLT--GGGVVRADIGRHPRQRTKMAVLAI---GGKEATTHYRLIKRF-NNHCHIRC 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDL 297
              TGRTHQ+RVH  H+   +VGD  Y    +    +  +         +  LHAR + L
Sbjct: 227 MLETGRTHQIRVHMAHIKHALVGDPVYAGRPRIPKGASEELINGLRGFGRQALHARKLSL 286

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
            HP     +    PL   MVK    L  +   
Sbjct: 287 IHPLSNEEVSWEIPLVDDMVKLIALLAAEDSE 318


>gi|326562905|gb|EGE13192.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis 46P47B1]
 gi|326563654|gb|EGE13906.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis 103P14B1]
 gi|326573262|gb|EGE23230.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis 101P30B1]
          Length = 355

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 145/322 (45%), Gaps = 30/322 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD+   + +   +  NL+  +  GQ+ V+ K VK    ++ G ++ +  V 
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKNFIDEGQLTVNGKVVKPKYAVKVGDILTLEAVH 107

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            + +  + E   +D               ++YED  + + NKPAG+ V  G+G      +
Sbjct: 108 ESHSEDLPENIDID---------------IIYEDEAVIIINKPAGMVVHPGAGNRTGTLV 152

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L  +       +  L HR+D++T+G+LV+ART++A   L +  + + + + Y  +  
Sbjct: 153 NALLYHFPKQAHLPRAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIAL 212

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQP 247
           G        +       + IG    H  K   K     A++H        +++  L++  
Sbjct: 213 GAVHE----VLRHAQIDAPIGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHL 268

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPE 301
            TGRTHQ+RVH  ++G P+VGD  Y  + +   +   +       +  LHA  +   HP 
Sbjct: 269 KTGRTHQIRVHLSYVGHPLVGDPVYGTSPRSGLSDRQRCAILDFGRQALHAYMLGFIHPV 328

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++  APLP  M +  + L
Sbjct: 329 TGEAMKFHAPLPKDMQQLIEIL 350


>gi|320528439|ref|ZP_08029601.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
 gi|320131353|gb|EFW23921.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
          Length = 304

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 144/329 (43%), Gaps = 34/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    ++V  +++   RLD++  ++   ++   +Q++   G + V+ K  K ++++ +G 
Sbjct: 1   MAKQTWIV--SEDTKERLDKYLSSN-TELSRTRVQQLADDGMIFVNGKVAKSSSKVVTGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +      +    I+ E   LD               +LYED  I V NKP G+ V    
Sbjct: 58  EISCDVPEDRPVDILPENIPLD---------------ILYEDHDIIVINKPKGMVVHPAP 102

Query: 124 GIAYHI--DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   +   +  L    D  G     +P + HR+D++T+G +V  +   A + + +    +
Sbjct: 103 GNYSNTMVNALLYHCKDLSGINGVIRPGIVHRIDKDTTGCIVACKNDKAHEAIAKQLENK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              ++Y ++V G   +    I   + +           +K  E+ +  A +HF V++ F 
Sbjct: 163 TCHRVYKTIVVGNITHDDGLIDAPIGRDPRD----RQRMKVTEENSRDARTHFHVLERF- 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
               +LE +  TGRTHQ+R H  ++  P++GD KY        T        LHA  + L
Sbjct: 218 NVATYLECRLETGRTHQIRAHMKYINHPVMGDDKYGKPCPYMDT----QGQVLHASELTL 273

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  +   APLP++  K  + L  +
Sbjct: 274 VHPTTGETMTFHAPLPSYFEKLLEILRKR 302


>gi|227115223|ref|ZP_03828879.1| 23S rRNA pseudouridine synthase D [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 325

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 80/345 (23%), Positives = 148/345 (42%), Gaps = 43/345 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V+++   + K   ++  G+ V I
Sbjct: 8   TATVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVINKPKEKVLGGESVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +I                      +  +K  ++YED  I V NKP  + V  G+G   
Sbjct: 68  DALIEEEARW---------------EAQDIKLDIVYEDEDILVINKPRDLVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + +     +  + HRLD++T+G++VVA+T  A   L E+ + R I + Y 
Sbjct: 113 GTVLNALLHHYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYE 172

Query: 185 SLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        ++ IA    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGSMTAGGMVEQPIARHATKRTHMAVHPM---------GKPAVTHYRIMEHF-RAHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHINHPLVGDQLYGGRPRPPKGASEDFIETLRGFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            +   HP  G  ++  A LP  MV   ++L  K D   +  +L  
Sbjct: 283 MLRFYHPITGIHMEWHAELPQDMVDLINAL--KADTEAFKDQLDW 325


>gi|261364850|ref|ZP_05977733.1| ribosomal large subunit pseudouridine synthase [Neisseria mucosa
           ATCC 25996]
 gi|288566895|gb|EFC88455.1| ribosomal large subunit pseudouridine synthase [Neisseria mucosa
           ATCC 25996]
          Length = 332

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 159/322 (49%), Gaps = 23/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RIQ+G ++R
Sbjct: 11  VSLITVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIQTGDLLR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A      E +               +  ++YED  + V +KPAG++V GGSG++
Sbjct: 71  IPPVRTAEKQRSSENRAQAVPAR--------EFDIIYEDDALLVIDKPAGVAVHGGSGVS 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++     + +   L HRLD++TSG+L++A+ R+A   L E+ R    +KIY +L
Sbjct: 123 FGVIEQIRRAR-PEARYLELVHRLDKDTSGLLMIAKKRSALVKLHEAIRNDHPKKIYLAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-------- 238
             G   N    +   L K +   G+ +  V ++      A + F V++ F+         
Sbjct: 182 GVGKLPNDSFHVKLPLFKYTGAQGEKMVRVSED---GQSAHTIFHVLNRFSDDLLHQVGL 238

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                ++    TGRTHQ+RVH     CPI GD +Y               +++LHA  + 
Sbjct: 239 SHLTLVQATLKTGRTHQIRVHLQSQQCPIAGDERYGDYQANKRLQKLGLKRMFLHAAELH 298

Query: 297 LPHP-EGGRLQITAPLPAHMVK 317
           L HP  G +L + APLP  + +
Sbjct: 299 LNHPLTGEKLILKAPLPQELAQ 320


>gi|332184772|gb|AEE27026.1| Ribosomal large subunit pseudouridine synthase [Francisella cf.
           novicida 3523]
          Length = 307

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 103/318 (32%), Positives = 166/318 (52%), Gaps = 13/318 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V +D  + R+D +  + +  +    + + +R G++RV+KKRVK  +RI +G 
Sbjct: 1   MNKVELIEVPDDVIDQRIDNFLLSRFSCLPKSLIYRWIRKGELRVNKKRVKQTSRISAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           GI   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GINSGLVERLRQ-LRPKARRLDLVHRLDKETSGCVILAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G    K   I   L  K     D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHGHWDKKIITIDLPL--KRTETKDGQRVVKVDSKDGKRALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPE- 301
           E++  TGRTHQ+RVH   MG PIV D KY  N K         +KL LHA  ++    + 
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFNTKDQSLLEKGVDKLLLHAGKLEFYDEKQ 289

Query: 302 GGRLQITAPLPAHMVKTW 319
             ++ +TA L +   K  
Sbjct: 290 NKQISVTAALDSRFEKFI 307


>gi|260583810|ref|ZP_05851558.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           elegans ATCC 700633]
 gi|260158436|gb|EEW93504.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           elegans ATCC 700633]
          Length = 301

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 82/314 (26%), Positives = 136/314 (43%), Gaps = 33/314 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E++ RLD+       H     +Q+ L+SG V V+ + VK N + + G  V I        
Sbjct: 13  EKSERLDKILTKELSH-TRSVIQQWLKSGFVSVNGEVVKANYKAKDGDHVTIQ------- 64

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLK 134
                   ++    LT  ++ +   +++ED  + V NKP+G+ V    G +   +   L 
Sbjct: 65  --------IEEEEELTVLAENIPLEIVFEDEHLLVINKPSGMVVHPSKGHSTGTLVNALL 116

Query: 135 SWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             VD      +  +P + HR+D++TSG+LVVA+T  A   L+       + + Y ++V G
Sbjct: 117 YHVDQLSKGSESYRPGIVHRIDKDTSGLLVVAKTPQAHVGLSNQLMDHSMTRSYVAIVEG 176

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             ++    +   L +  H       + +  +K    AI+HF VI    +      +   T
Sbjct: 177 SFEHITGTVDAPLARDPHN-----RLKRCVQKEGKQAITHFTVIQALKETSVL-RLNLET 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
           GRTHQ+R H   +  PI+ D  Y  N K       +   YLHA  +   HP    +L   
Sbjct: 231 GRTHQIRAHMDFIHHPILNDPMYHPNGKNA----TEFGQYLHAETLGFVHPITQEKLYFE 286

Query: 309 APLPAHMVKTWDSL 322
           +PLP    +    L
Sbjct: 287 SPLPKEFEEMIQEL 300


>gi|308274565|emb|CBX31164.1| Uncharacterized RNA pseudouridine synthase ylyB [uncultured
           Desulfobacterium sp.]
          Length = 335

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 82/324 (25%), Positives = 139/324 (42%), Gaps = 34/324 (10%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           +     +RLD    ++ P  +      ++  G++ V  +  K   +++ G  +       
Sbjct: 28  DESVSGIRLDIVVSSYIPLCSRSIAASLINKGKITVCNQIKKQGYKVKFGDKIT------ 81

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHID 130
                      +     ++   + ++  +LYEDS I V NKP GI      G      ++
Sbjct: 82  ---------GTIPDPEPVSFLPEPIELNILYEDSDIIVINKPPGIVAHPAPGHYSGTLVN 132

Query: 131 GFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             L    D  G     +P + HRLD++TSG LVVA+   +  +L   F+ RRI+K Y +L
Sbjct: 133 ALLFHCPDLTGIGGEIRPGIVHRLDKDTSGALVVAKNDISHTNLCLQFKERRIRKKYLAL 192

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           VWG P++    I   + +        + V+ +  K    A + +KVI+ + +     E+ 
Sbjct: 193 VWGNPEHDSGSITLPIGRH-PSNRKKMSVLTRKPK---TAETLWKVIERY-KSVSLWEID 247

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-------PIQNKLYLHARYMDLPH 299
             TGRTHQ+RVH   +  P++GD  Y    K +              +  LHA  +   H
Sbjct: 248 LKTGRTHQIRVHCAAIKHPVIGDQVYGNRPKLSVDLKNTQDFYKQIKRQMLHAWKIGFMH 307

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P   + ++  APLP  M +   SL
Sbjct: 308 PVTNKTMEFEAPLPDDMKELISSL 331


>gi|254805759|ref|YP_003083980.1| ribosomal large subunit pseudouridine synthase [Neisseria
           meningitidis alpha14]
 gi|254669301|emb|CBA08284.1| ribosomal large subunit pseudouridine synthase [Neisseria
           meningitidis alpha14]
          Length = 330

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 154/322 (47%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +              +YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFEA---------VYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  +      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSAD---GQSAHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A LP  + +
Sbjct: 298 LNHPLTGEPLVLKAELPPDLAQ 319


>gi|21672612|ref|NP_660679.1| ribosomal large subunit pseudouridine synthase [Buchnera aphidicola
           str. Sg (Schizaphis graminum)]
 gi|25091178|sp|Q8K9J8|RLUC_BUCAP RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|21623244|gb|AAM67890.1| ribosomal large subunit pseudouridine synthase [Buchnera aphidicola
           str. Sg (Schizaphis graminum)]
          Length = 314

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 98/321 (30%), Positives = 169/321 (52%), Gaps = 16/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V  + +  D  N R+D + +    ++    + +I+R+G++R++KKR+K + +++ G  
Sbjct: 6   TSVSIIYINEDMINQRIDNFLQKKLKNVPRSMIYRIIRTGKIRINKKRIKPDYKLKIGDK 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RIPP+      I+ E+K   SS+  T++   L + +LYED+ + + NKP+GI+V GGSG
Sbjct: 66  LRIPPI-----KILCEKK---SSLLTTEYKKNLLNNILYEDNYLLIINKPSGIAVHGGSG 117

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           I   +  + +     +     L HR+D++TSG+L++A+ R +   L +  R +++QK Y 
Sbjct: 118 INLGVIEYFRKIRPLEKF-LELVHRIDRDTSGVLMLAKKRRSLLSLHKQIREKKVQKKYI 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+       ++  LLK          ++    K    A ++FK I         + 
Sbjct: 177 ALVHGLWPLSLRKVSEPLLKTHLKNKQRKILIN---KEGKPAETYFK-IKKQYLFTTLVS 232

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG--NFTSPIQNKLYLHARYMDLPHPEG 302
           + P TGRTHQ+RVH LH G PI+ D +Y               N+L LHA  ++  HPE 
Sbjct: 233 ITPKTGRTHQIRVHTLHAGHPILFDKRYGKRDLDCNIKNKTKINRLLLHATSINFIHPET 292

Query: 303 G-RLQITAPLPAHMVKTWDSL 322
           G ++ I APL  +     ++L
Sbjct: 293 GKKMHIVAPLDVYFKNYLNTL 313


>gi|227510357|ref|ZP_03940406.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
 gi|227190009|gb|EEI70076.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
          Length = 303

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 83/310 (26%), Positives = 137/310 (44%), Gaps = 32/310 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+      P I+    +K++  G + V+  + K     ++   + I  V      I  
Sbjct: 13  RLDKIVSMLDPEISRSRAKKMIEDGDIIVNDSKKKPKYETKASDTLLIKDVKPETVSIKP 72

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWV 137
           E   LD               ++YED  + V NKP G+ V   +G   H   +  L    
Sbjct: 73  ENMPLD---------------IVYEDEDVIVVNKPQGMVVHPSAGHPNHTLVNALLFHSP 117

Query: 138 DSK---GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            S      +P + HR+D++TSG+L+VA+   A + L++  + ++  + Y +LV G  K  
Sbjct: 118 LSSINGEYRPGIVHRIDKDTSGLLMVAKNDMAHKALSKQLKAKKNLRKYVALVHGRIKED 177

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I   + +          V          AI+HF+V++ F Q +  +E +  TGRTHQ
Sbjct: 178 SGVIKAPIARSPKDRKKQAIVA-----DGRPAITHFEVMERF-QDYTLIECRLETGRTHQ 231

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPA 313
           +RVH  ++G PIVGD  Y         +   +  +LHA+ +   HP   +L   +AP+P 
Sbjct: 232 IRVHMQYIGHPIVGDPLYGPK-----KTIKGHGQFLHAQELGFEHPRTHQLMIFSAPIPE 286

Query: 314 HMVKTWDSLG 323
              KT  +L 
Sbjct: 287 IFEKTLRTLR 296


>gi|229845163|ref|ZP_04465297.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae 6P18H1]
 gi|229811874|gb|EEP47569.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae 6P18H1]
          Length = 324

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 144/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLVH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|121634072|ref|YP_974317.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis FAM18]
 gi|120865778|emb|CAM09507.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis FAM18]
 gi|308388417|gb|ADO30737.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis alpha710]
 gi|319411317|emb|CBY91728.1| ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C; rRNA pseudouridylate synthase C) [Neisseria
           meningitidis WUE 2594]
 gi|325133121|gb|EGC55793.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M6190]
 gi|325139089|gb|EGC61635.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis ES14902]
          Length = 330

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 155/322 (48%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  +      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSAD---GQSAHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A LP  + +
Sbjct: 298 LNHPLTGEPLVLKAELPLDLAQ 319


>gi|291618565|ref|YP_003521307.1| RluD [Pantoea ananatis LMG 20103]
 gi|291153595|gb|ADD78179.1| RluD [Pantoea ananatis LMG 20103]
 gi|327394946|dbj|BAK12368.1| ribosomal large subunit pseudouridine synthase D RluD [Pantoea
           ananatis AJ13355]
          Length = 326

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 79/342 (23%), Positives = 142/342 (41%), Gaps = 37/342 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ + + +V V+     K   ++  G+ V I
Sbjct: 8   TATVSESQLGQRLDQTLAELFPDYSRSRIKEWILNQRVSVNGTVTDKPKEKVLGGERVTI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP    V  G+G   
Sbjct: 68  DAEIEEEQRWEPQNIPLD---------------IVYEDEDIIVINKPRDFVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  +   +   +  + HRLD++T+G++VVA+T  A  HL ++ + R I + Y 
Sbjct: 113 GTVLNALLHHYPAIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A++H+++++ F +    L 
Sbjct: 173 AVAIGTM-TAGGTVDEPISRHST-----KRTHMSVHPMGKPAVTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMSHINHPLVGDPLYGGRPRPPKGASEDFITTLRGFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           L HP  G  ++  A +P  M+   D+L  K D  ++  +L  
Sbjct: 286 LYHPISGIEMEFHAAIPQDMIDLIDAL--KADTEMFKDQLDW 325


>gi|240124400|ref|ZP_04737356.1| RluC [Neisseria gonorrhoeae PID332]
 gi|268683027|ref|ZP_06149889.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae PID332]
 gi|268623311|gb|EEZ55711.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae PID332]
          Length = 330

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 154/322 (47%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +    + +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKGYIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V NKP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFE---------VVYEDDALLVVNKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-------- 238
             G   +    +   L K +   G+ +  V ++      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSED---GQSAHTVFRVLSHFSDGILHGVGL 237

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A  P  + +
Sbjct: 298 LNHPLTGEPLVLKAEPPPDLAQ 319


>gi|296158256|ref|ZP_06841088.1| pseudouridine synthase, RluA family [Burkholderia sp. Ch1-1]
 gi|295891592|gb|EFG71378.1| pseudouridine synthase, RluA family [Burkholderia sp. Ch1-1]
          Length = 323

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 96/322 (29%), Positives = 155/322 (48%), Gaps = 24/322 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +VR+PP
Sbjct: 2   IEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +  A            S              +++ED  + V +KPAG++V GGSG+A+ +
Sbjct: 62  IRVAQ----------PSEAAAQAPVPAAHFKIIFEDEHLLVIDKPAGVAVHGGSGVAFGV 111

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++       +   L HRLD+ETSGIL++A+ R+A  +L E  R  ++ K Y++ V G
Sbjct: 112 IEQMREARPQ-AKFLELVHRLDRETSGILMLAKKRSALVNLHEQIRENKMDKRYYACVHG 170

Query: 190 IPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
              +       +   L K     G+    V+ +      + + F +ID + + +  LE +
Sbjct: 171 EWASDWGRRRAVKEPLHKYLTADGERRVRVQPD---GLASHTVFNLIDRWPE-YALLEAE 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H+G PIVGD KY               P   +++LHA  + L HP 
Sbjct: 227 LKTGRTHQIRVHLQHLGLPIVGDAKYGDFALNKALARANAKPGLKRMFLHAYRLKLTHPA 286

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  LQ  APLP         L
Sbjct: 287 TGEPLQFDAPLPPECRSFIAQL 308


>gi|170695400|ref|ZP_02886545.1| pseudouridine synthase, RluA family [Burkholderia graminis C4D1M]
 gi|170139591|gb|EDT07774.1| pseudouridine synthase, RluA family [Burkholderia graminis C4D1M]
          Length = 345

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 97/326 (29%), Positives = 162/326 (49%), Gaps = 24/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +V
Sbjct: 20  QVSVIEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLV 79

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP+  A +        + S+          +  +++ED  + V +KPAG++V GGSG+
Sbjct: 80  RVPPIRVAQHDETVPSAPVPSA----------EFRIIFEDEHLLVIDKPAGVAVHGGSGV 129

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++     + +   L HRLD+ETSGIL++A+ R+A  +L +  R  R+ K Y++
Sbjct: 130 AFGVIEQMRQ-SRPQAKFLELVHRLDRETSGILMLAKKRSALVNLHDQIRENRMDKRYYA 188

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G   +       +   L K     G+    V+ +      + + F +ID +   +  
Sbjct: 189 CVHGEWASDWGRRRAVKEPLHKYLTADGERRVRVQAD---GLASHTVFNLIDRWPD-YAL 244

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           LE +  TGRTHQ+RVH  H+  PIVGD KY           +   P   +++LHA  + L
Sbjct: 245 LEAELKTGRTHQIRVHLQHLELPIVGDAKYGDFALNKALARSNAKPGLKRMFLHAYRLKL 304

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSL 322
            HP  G  LQ+ APLPA        L
Sbjct: 305 THPATGAPLQLEAPLPAECRNFIAQL 330


>gi|310659174|ref|YP_003936895.1| ribosomal large subunit pseudouridine synthase, rlud subfamily
           [Clostridium sticklandii DSM 519]
 gi|308825952|emb|CBH21990.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium sticklandii]
          Length = 306

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 69/331 (20%), Positives = 140/331 (42%), Gaps = 33/331 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +Y +V+ +EE++RLD +  +    ++   +Q +++  +V V+ K  K + ++   
Sbjct: 1   MIEEKKYFIVDEEEEDLRLDVFISSALSDLSRTYIQSLIKDKKVTVNDKIEKSSYKVAQL 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I               ++  +  L   ++ +   +LYED  + V  K  G+ V  G
Sbjct: 61  DNICI---------------LIPPAKELVIEAEDIPIEILYEDEDLAVVYKERGMVVHPG 105

Query: 123 SGIAYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +G A H   +  +  +           +P + HR+D++TSG+L++A++  A + L+E  +
Sbjct: 106 AGNANHTLVNALMYHFKGQLSSINGIIRPGIVHRIDKDTSGLLMIAKSDIAHRGLSEQLK 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              +Q+ Y  +  G  K  +  I   + +      D + +   ++    +A++H   I  
Sbjct: 166 EHTVQRTYTFICHGNIKADEFTIDAPIGRNP---RDRMKMAVVSD--GKHAVTHITKIKS 220

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             + + +      TGRTHQ+RVH    G P+VGD  Y      + +        LHA+ +
Sbjct: 221 N-ENYSYAMANLETGRTHQIRVHMASKGLPLVGDTLYGP----HNSKFKAQGQLLHAKTL 275

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
              HP  G  +      P             
Sbjct: 276 GFVHPVTGEFMLFEKEEPEIFKSFLQRFLLD 306


>gi|329902613|ref|ZP_08273174.1| Ribosomal large subunit pseudouridine synthase D [Oxalobacteraceae
           bacterium IMCC9480]
 gi|327548721|gb|EGF33364.1| Ribosomal large subunit pseudouridine synthase D [Oxalobacteraceae
           bacterium IMCC9480]
          Length = 355

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 83/325 (25%), Positives = 138/325 (42%), Gaps = 30/325 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++ + +   +   RLD+      P  +   +Q+ +  G V VD K  +    +   +
Sbjct: 35  MPPIE-LDLTPGDCGDRLDKVVARLVPQFSRSRMQQWIDDGFVTVDGKVGRTRMTVYGDE 93

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + + P     +     ++              +   ++YED  I V NKPAG+ V  GS
Sbjct: 94  HIVVLPQAAPEDTAFAPEE--------------MALNIVYEDEAIIVVNKPAGLVVHPGS 139

Query: 124 GI--AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G      ++G L  W    G  +  + HRLD++TSG++VVA+T      L      R ++
Sbjct: 140 GNWSGTLLNGLLHYWPALIGVPRAGIVHRLDKDTSGLMVVAKTLEVHTDLVRQLAARTVK 199

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FA 237
           + Y++LVWG P N    I   + +      D + +       A  AI+HF+ I+      
Sbjct: 200 REYFALVWGTP-NLSGTIDASMGRHP---RDRIRMAVLESMSAKPAITHFERIESGLLDR 255

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    +  +  TGRTHQ+RVH   +G  +VGD  Y         +P  ++  L AR + L
Sbjct: 256 RPVSLMRCRLETGRTHQIRVHMQSIGFALVGDTLYGKQH----LAPAFHRQALQARRLGL 311

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDS 321
            HP  G  ++   PL         S
Sbjct: 312 VHPVTGEDVEWRVPLADDFAALIAS 336


>gi|77406381|ref|ZP_00783442.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
 gi|77175005|gb|EAO77813.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
          Length = 296

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 72/314 (22%), Positives = 135/314 (42%), Gaps = 34/314 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             +RLD+   ++   ++     + ++ G V V+ +  K    +Q G  +           
Sbjct: 8   AGVRLDKALADN-SELSRSQANEEIKKGIVLVNGQVKKAKYTVQEGDRITFD-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
            I ++++LD        ++ +   ++Y+D  + V NKP G+ V   +G      ++  + 
Sbjct: 59  -IPKKEVLD------YQAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+   A Q L E  + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        A++ F V++ F   +  +E+   TG
Sbjct: 172 LPNDQGVIEAPIGRSDKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YTLVELSLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +      +LHA+ +   HP  G  L  + 
Sbjct: 226 RTHQIRVHMAYIGHPLAGDPVYGPR-----KTLGGKGQFLHAQTLGFTHPSNGENLIFSV 280

Query: 310 PLPAHMVKTWDSLG 323
            +P     T D L 
Sbjct: 281 EVPEIFQTTLDKLR 294


>gi|258593870|emb|CBE70211.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [NC10 bacterium 'Dutch sediment']
          Length = 314

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 92/327 (28%), Positives = 147/327 (44%), Gaps = 34/327 (10%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++ ++ +     +RLDR+       +    +Q+++++G+V VD +  K +     GQ +
Sbjct: 5   EIRELIADISAGGLRLDRYLSTA-TGLPRSQIQRLIKAGRVLVDGRCPKASAIAHPGQQI 63

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +       + +  E   LD               +LYED+ + V NKPAG+ V    G 
Sbjct: 64  SLSIPPPQPSTLTPEPIPLD---------------ILYEDTDMLVLNKPAGLVVHPAPGH 108

Query: 126 A--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                +   L    D  G    ++P + HRLD+ETSG++VVA+T  A   L   F+ RR+
Sbjct: 109 HSGTLVHAILYHCPDLPGIGEERRPGIVHRLDKETSGVMVVAKTDTAMASLATQFKGRRV 168

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  K  +  IA  + +      D   +  +  KG   A+++++VI      
Sbjct: 169 QKTYIALVHGEVKQPQGQIAADIGRHE---RDRKRMAVRTRKG-REAVTNYRVIKRLG-G 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT------SPIQNKLYLHAR 293
              LE+QP TGRTHQ+RVH   +G P+VGD  Y    +               +  LHA 
Sbjct: 224 LTLLELQPQTGRTHQIRVHLSAIGHPVVGDKVYGGRREKKCRVLSVECRVKTERHLLHAW 283

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTW 319
            + L HP     ++  APLP       
Sbjct: 284 KLGLFHPRTDVWMEFEAPLPPDFTSRL 310


>gi|257058664|ref|YP_003136552.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8802]
 gi|256588830|gb|ACU99716.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8802]
          Length = 318

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 88/323 (27%), Positives = 150/323 (46%), Gaps = 32/323 (9%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINAL 74
           ++  R+D W   +   I+  +LQK++  G + ++ +       ++ SG  +++       
Sbjct: 17  DKGDRIDLWLSQNLDQISRSHLQKLIEQGNIYLNNQVCLNKKTKVNSGDRLQVFLPPPEP 76

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGF 132
             +  E   LD               +LYED  + + NK AG+ V    G      + G 
Sbjct: 77  LELQPEPIPLD---------------ILYEDDSLIIINKSAGLVVHPAPGHTTGTLVHGL 121

Query: 133 LKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L    +  G    Q+P + HRLD++T+G +VVA+T  A QHL    + +  ++ Y  +V+
Sbjct: 122 LYHCPNLVGIGGIQRPGIVHRLDKDTTGAIVVAKTDYAHQHLQAQLKAKTARREYLGVVY 181

Query: 189 GIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           G+P+++   +  I   + +  H G      V   E G   AI+H+++++     +  +E 
Sbjct: 182 GVPRHEDTHQGTINVPIGR--HRGDRKKMAVVPVENGGREAITHWQIVERLG-NYTLVEF 238

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           +  TGRTHQ+RVH+ ++G PIVGD  Y +   G       +   LHA  + L HP  G  
Sbjct: 239 RLETGRTHQIRVHSSYIGHPIVGDPLYSS---GGSVGVNLSGQALHAYRLILEHPVTGNT 295

Query: 305 LQITAPLPAHMVKTWDSLGFKYD 327
           ++  APLPA   K    L  K  
Sbjct: 296 IEAIAPLPAEFTKLLTLLRQKLS 318


>gi|167750498|ref|ZP_02422625.1| hypothetical protein EUBSIR_01474 [Eubacterium siraeum DSM 15702]
 gi|167656424|gb|EDS00554.1| hypothetical protein EUBSIR_01474 [Eubacterium siraeum DSM 15702]
          Length = 303

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 73/312 (23%), Positives = 132/312 (42%), Gaps = 33/312 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             R D++       I       ++  G   V+ K    N ++++G  V +         I
Sbjct: 11  GERTDKFLALQDTGITRSAAAALIEQGCCLVNGKIAAKNQKLKTGDTVTLDVPEAQPADI 70

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
           + E   LD               ++YEDS + V NKP G+ V    G      ++  +  
Sbjct: 71  LPENIPLD---------------IVYEDSDLLVVNKPKGMVVHPAPGHYSGTLVNALMYH 115

Query: 136 WVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             DS        +P + HR+D++TSG+L+VA+   A   L E  ++    + Y ++V G+
Sbjct: 116 CGDSLSGINGVIRPGIVHRIDRDTSGLLIVAKNDTAHNILAEQIKVHSFTREYMAVVQGV 175

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K     +   + +        + V  +N   +  A++H+ V +   +    + ++  TG
Sbjct: 176 IKED-GTVDAPIGRH-KTDRKKMCVTTEN---SREAVTHYFV-EQTYRNNTLVRLRLETG 229

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQ+RVH  ++G P+ GD  Y      N +        LHA+ +   HP+G  ++  + 
Sbjct: 230 RTHQIRVHMAYIGHPVTGDEVYG-----NGSPKWLCGQCLHAKKIGFIHPDGRYMEFDSE 284

Query: 311 LPAHMVKTWDSL 322
           LP +  K   +L
Sbjct: 285 LPDYFKKLLANL 296


>gi|78778581|ref|YP_396693.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9312]
 gi|78712080|gb|ABB49257.1| ribosomal large subunit pseudouridine synthase D [Prochlorococcus
           marinus str. MIT 9312]
          Length = 319

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 86/315 (27%), Positives = 139/315 (44%), Gaps = 28/315 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +  P  +   +Q  + SG V V+ K  K    +++G  V+I          
Sbjct: 26  PMRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNVQIWMPPPEPLIY 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
           +K +K              +   +L+ED  I V NK +G+ V    G      ++G L  
Sbjct: 86  LKPEK--------------MDLNILFEDKHIIVINKQSGLIVHPAPGHKSGTLVNGLLFH 131

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++TSG +VVA+++ A  +L +  + +   + Y +++ G P
Sbjct: 132 CKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAP 191

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +++  I   + +       Y  V    E    YA +++K+ + F   +  +  +  TGR
Sbjct: 192 NSEEGQIVGHIGRDKLNRLKYKVV---EETTGRYACTYWKLEERFG-NYSLMSFKLDTGR 247

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  H+  PIVGD  Y    K        +   LHA  + L HP  G  +   + 
Sbjct: 248 THQIRVHCAHINHPIVGDPLYGRCKKLPCQ---LDGQALHAIKLGLIHPINGKEMIFESE 304

Query: 311 LPAHMVKTWDSLGFK 325
           LP    K    L  K
Sbjct: 305 LPLDFQKLLRVLKVK 319


>gi|76787790|ref|YP_330006.1| ribosomal large subunit pseudouridine synthase A [Streptococcus
           agalactiae A909]
 gi|77408235|ref|ZP_00784979.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
 gi|77412105|ref|ZP_00788430.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|76562847|gb|ABA45431.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus agalactiae A909]
 gi|77161861|gb|EAO72847.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77173176|gb|EAO76301.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
          Length = 296

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 73/314 (23%), Positives = 135/314 (42%), Gaps = 34/314 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             +RLD+   ++   ++     + ++ G V V+ +  K    +Q G  +           
Sbjct: 8   AGVRLDKALADN-SELSRSQANEEIKKGIVLVNGQVKKAKYTVQEGDRITFD-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
            I ++++LD        ++ +   ++Y+D  + V NKP G+ V   +G      ++  + 
Sbjct: 59  -IPKEEVLD------YQAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+   A Q L E  + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        AI+ F V++ F   +  +E+   TG
Sbjct: 172 LPNDRGVIEAPIGRSDKDRKKQAVTAK-----GKPAITRFHVLERFGD-YTLVELSLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +      +LHA+ +   HP  G  L  + 
Sbjct: 226 RTHQIRVHMAYIGHPLAGDPVYGPR-----KTLGGKGQFLHAQTLGFTHPSNGENLIFSV 280

Query: 310 PLPAHMVKTWDSLG 323
            +P     T D L 
Sbjct: 281 EVPEIFQTTLDKLR 294


>gi|251788633|ref|YP_003003354.1| pseudouridine synthase, RluA family [Dickeya zeae Ech1591]
 gi|247537254|gb|ACT05875.1| pseudouridine synthase, RluA family [Dickeya zeae Ech1591]
          Length = 325

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 78/342 (22%), Positives = 143/342 (41%), Gaps = 37/342 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   ++  +   +V+++   V +   ++  G+ V I
Sbjct: 8   TATVAESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGNTVDRPKEKVLGGESVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +I                      +  +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  DALIEEEARW---------------EAQPISLDIVYEDDDILVINKPRDLVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  +   +   +  + HRLD++T+G++VVA+T  A   L ES + R I + Y 
Sbjct: 113 GTVLNALLHHYPAIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A++H+++++ F +    L 
Sbjct: 173 AVAIGTM-TAGGTVDEPIARHST-----KRTHMAVHPMGKPAVTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P++GD  Y    +        F   ++N  +  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMAHINHPLIGDPLYGGRPRLPKGASDTFIETLRNFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           L HP  G  ++  A LP  MV    +L  K D + +  +L  
Sbjct: 286 LYHPISGIEMEWHAALPQDMVDLIAAL--KADTDAFKDQLDW 325


>gi|319947181|ref|ZP_08021415.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
 gi|319747229|gb|EFV99488.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
          Length = 296

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 139/319 (43%), Gaps = 34/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  +    RLD+        ++     + ++ G++ V+ +  K    ++ G V+      
Sbjct: 3   VRVEVAGARLDKAVSE-LTELSRGLANEQIKEGKILVNGQVKKAKYTVKEGDVISYE--- 58

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
                       +     +T  ++ +   ++Y+D+ + V NKP G+ V   +G      +
Sbjct: 59  ------------VPQMEEVTYEAEDIPLEIVYQDADVVVVNKPQGMVVHPSAGHTSGTLV 106

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +    D  G     +P + HR+D++TSG+L+VA+  AA   L +  + ++  + YW+
Sbjct: 107 NALMYHIKDLSGINGELRPGIVHRIDKDTSGLLMVAKNDAAHVALADELKAKKSLRKYWA 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   N +  I   + +            K        A++ F V++ F   +  +E+
Sbjct: 167 IVHGNLPNDRGVIEAPIGRSDKDRKKQAVTAK-----GKPALTRFHVLERFGD-YSLVEL 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G  
Sbjct: 221 QLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----RTLKGHGQFLHAKTLGFTHPRTGEV 275

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++ +  +P    KT + L 
Sbjct: 276 MEFSVEVPEVFQKTLEQLR 294


>gi|312898193|ref|ZP_07757584.1| pseudouridine synthase, RluA family [Megasphaera micronuciformis
           F0359]
 gi|310620690|gb|EFQ04259.1| pseudouridine synthase, RluA family [Megasphaera micronuciformis
           F0359]
          Length = 306

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 82/329 (24%), Positives = 143/329 (43%), Gaps = 37/329 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M ++T V    V + +  +R+D +       I+      ++++G+V +  + +K N R+ 
Sbjct: 1   MEVITSV----VTDKDTGIRVDIYVARAL-DISRSYAGNLIKNGKVSMRNRILKANYRVA 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + I                 D + +LT  ++ +   ++YED  I + NK  G+ V 
Sbjct: 56  EGDEIVIE---------------KDEAEDLTVEAENIPLDIVYEDKDIIIVNKARGMVVH 100

Query: 121 GGSGIAY--HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
             +G      ++  L              +P + HRLD++TSG++V A+T AA + L E 
Sbjct: 101 PAAGNPNGTLVNALLWHCGGELSGINGVIRPGIVHRLDKDTSGLMVAAKTDAAHKSLAEQ 160

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            +    ++ Y +LV G     K  I   L +      D V +   N K    AI+HF V+
Sbjct: 161 IKSHTARRTYVALVHGNIVEAKGRIDAPLGRHPK---DRVKMA-VNMKDGKDAITHFTVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F   +  ++ +  TGRTHQ+RVH  ++G P+V D  Y         +       LH+ 
Sbjct: 217 ERFG-NYTLVQCRLETGRTHQIRVHMAYIGHPVVNDPLYGYKRD----AFPIEGQALHSC 271

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            +DL HP   + +   AP P        +
Sbjct: 272 ALDLVHPITKQAMHFEAPWPNDFKAVVQA 300


>gi|315121810|ref|YP_004062299.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Candidatus Liberibacter solanacearum CLso-ZC1]
 gi|313495212|gb|ADR51811.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Candidatus Liberibacter solanacearum CLso-ZC1]
          Length = 340

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 79/336 (23%), Positives = 136/336 (40%), Gaps = 43/336 (12%)

Query: 14  NDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVI 71
           N+E   R+DRW   +     +   ++ ++ +G + ++    +  + ++  G+   I    
Sbjct: 18  NNEAEGRIDRWLAINLKEKFSRSYVKTLILNGAISINGVVSINPSRKVVPGESFFIDVPQ 77

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
               +I  E   LD               +LYED  I V NK AG+ V    G      +
Sbjct: 78  LQQLNIAAENIPLD---------------ILYEDDDIIVINKQAGLVVHPAPGNWTGTLV 122

Query: 130 DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK--- 181
           +  L    ++       ++P + HRLD++T+G +VVA+   A Q L+E F    +     
Sbjct: 123 NALLHHCNNNLSGINGIKRPGIVHRLDKDTTGTMVVAKNDIAHQRLSEQFADHGLHMGLK 182

Query: 182 -IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK- 239
             Y+++VWG+P      I   L +          V +  +K  + A++ ++ ++ + +  
Sbjct: 183 RSYYAMVWGVPSPDSGTINAPLGR-CKSNRLRRAVKRIEDKTGDRAVTRYQTVEIYNKNS 241

Query: 240 ---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF---------TSPIQNK 287
                 L     TGRTHQ+RVH  H G PI+GD  Y   FK                  +
Sbjct: 242 NFAASLLRCDLETGRTHQIRVHMAHKGYPIIGDPLYGKGFKTKENIVNHSTKSAILSLAR 301

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             LHA  +   HP   + +    P+P  M      L
Sbjct: 302 QALHAYSLSFTHPCKNKDMNFKTPIPEDMSNVIKEL 337


>gi|325981765|ref|YP_004294167.1| pseudouridine synthase, RluA family [Nitrosomonas sp. AL212]
 gi|325531284|gb|ADZ26005.1| pseudouridine synthase, RluA family [Nitrosomonas sp. AL212]
          Length = 326

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 104/334 (31%), Positives = 171/334 (51%), Gaps = 23/334 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  +T +    V+ D ++ R+D +    + ++   +L +++RSGQVRV+ KR+  N R++
Sbjct: 1   MESITSITKERVKEDGDDQRIDNFLFKRFRNVPKNHLYQLVRSGQVRVNGKRIDANYRLR 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G +VRIPPV       +    I           +F     LYED  +   +KP+G++V 
Sbjct: 61  LGDMVRIPPVKIETKDSLNRTAIT--------CLNFFSFTHLYEDDAVLAIDKPSGMAVH 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGS +++ +   L++  +   +   L HRLD+ETSG+L++A+ R+A   L    R   ++
Sbjct: 113 GGSNVSFGVIEQLRAQ-NPSWKFLELVHRLDRETSGVLLLAKKRSALVELHRQIREGLVE 171

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN---YAISHFKVIDCFA 237
           K Y  +V G  +N K+ +   L K     G+    V  + +  N    + S FK +D   
Sbjct: 172 KHYLVMVKGKWRNAKQHVRLILDKYVTASGERRVAVVTSIRPGNKPMPSHSIFK-LDKSW 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--------ANFKGNFTSPIQNKLY 289
             F  L+ Q  TGRTHQ+RVH  H+G PI+GD KY         A   G+  S +  +++
Sbjct: 231 DNFSLLDAQIKTGRTHQIRVHLAHLGFPILGDDKYGNFEINKRLAKGGGDGKSKLM-RMF 289

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           LHA  + + HP  G R+ + +PL + + K  D L
Sbjct: 290 LHAHSLQITHPVSGQRINLRSPLSSDLQKFIDDL 323


>gi|283835694|ref|ZP_06355435.1| ribosomal large subunit pseudouridine synthase D [Citrobacter
           youngae ATCC 29220]
 gi|291068911|gb|EFE07020.1| ribosomal large subunit pseudouridine synthase D [Citrobacter
           youngae ATCC 29220]
          Length = 326

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 81/336 (24%), Positives = 148/336 (44%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+     K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGHLCDKPKEKVLGGEQVSI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I+       +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIDEEVRFEPQDIPLD---------------IVYEDDDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        +E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVEEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKGASDEFISVLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEE 318


>gi|254526037|ref|ZP_05138089.1| pseudouridylate synthase, 23S rRNA-specific [Prochlorococcus
           marinus str. MIT 9202]
 gi|221537461|gb|EEE39914.1| pseudouridylate synthase, 23S rRNA-specific [Prochlorococcus
           marinus str. MIT 9202]
          Length = 319

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 85/315 (26%), Positives = 139/315 (44%), Gaps = 28/315 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +  P  +   +Q  + SG V V+ K  K    +++G  ++I          
Sbjct: 26  PMRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNIQIWMPPPEPLIY 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
           +K +K              +   +L+ED  I V NK +G+ V    G      ++G L  
Sbjct: 86  LKPEK--------------MDLNILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLFH 131

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++TSG +VVA+++ A  +L +  + +   + Y +++ G P
Sbjct: 132 CKDLPGINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAP 191

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +++  I   + +       Y  V    E    YA +++K+ + F   +  +  +  TGR
Sbjct: 192 NSEEGQIVGNIGRDKLNRLKYKVV---EETSGRYACTYWKLEERFG-NYSLMSFKLDTGR 247

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  H+  PIVGD  Y    K        +   LHA  + L HP  G  +   + 
Sbjct: 248 THQIRVHCAHINHPIVGDPLYGRCKKLPCK---LDGQALHAIKLGLIHPINGKEMIFKSE 304

Query: 311 LPAHMVKTWDSLGFK 325
           LP    K    L  K
Sbjct: 305 LPLDFQKLLSVLKVK 319


>gi|167570710|ref|ZP_02363584.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           oklahomensis C6786]
          Length = 335

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 105/326 (32%), Positives = 159/326 (48%), Gaps = 22/326 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + +++     R+D +       +   ++ +ILRSG+VRV+K RV    R+  G VV
Sbjct: 16  QVSLIEIDDGAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAHGDVV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + +            +        +L+ED  I   NKPAG++V GGSG+
Sbjct: 76  RVPPVRVAAADLARAAGPGPVPAAAFE--------ILFEDDAIIALNKPAGVAVHGGSGV 127

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y++
Sbjct: 128 AFGVIEQMRHAR-PHAKFLELVHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRYFA 186

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G           +   L K S   G+    V+++      + + F ++DC+   +  
Sbjct: 187 CVHGEWAPDWGRRRAVKAPLFKYSTPDGERRVRVQED---GLPSHTVFNLVDCWPD-YAL 242

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           LE +  TGRTHQ+RVH  H+G PIVGD KY               P   +++LHA  + L
Sbjct: 243 LEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARANAVPSLKRMFLHAHRLRL 302

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA   +  D L
Sbjct: 303 AHPLTGEPLQFDAPLPAECRQFLDQL 328


>gi|255656576|ref|ZP_05401985.1| putative pseudouridylate synthase [Clostridium difficile QCD-23m63]
 gi|296449972|ref|ZP_06891736.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           difficile NAP08]
 gi|296878353|ref|ZP_06902361.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           difficile NAP07]
 gi|296261242|gb|EFH08073.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           difficile NAP08]
 gi|296430651|gb|EFH16490.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           difficile NAP07]
          Length = 315

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 83/328 (25%), Positives = 145/328 (44%), Gaps = 33/328 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           LM  V+  +V  +EE +RLD +       ++   +QKI++ G+V+V+ K  K    ++  
Sbjct: 12  LMYEVKEFLVLEEEEEVRLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKIEKAKYLVKEE 71

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I          I E K+L+           +   ++YED  + + NKP  + V   
Sbjct: 72  DNIVIE---------IPEPKVLEV------VPQDIPIDIVYEDDDVLIINKPQDMVVHPA 116

Query: 123 SGIAYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G   +   +G L    D         +P + HR+D++TSG+L++A+   A   L E  +
Sbjct: 117 PGNYENTLVNGILYHCKDKLSSINGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLK 176

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I + Y  + +G+ K  K  +   + +          V     K    AI+HF+V++ 
Sbjct: 177 EHTITREYEFICYGVVKENKITVDKPIGRNPKDRLKMAVV-----KDGKNAITHFEVVER 231

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F  KF  +  +  TGRTHQ+RVHAL +  P++GD+ Y        T        LHA+ +
Sbjct: 232 F-DKFTHMRAKLETGRTHQIRVHALSINHPLLGDYVYGPKE----TKFKLKGQTLHAKKL 286

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              HP     ++  + LP +  +    +
Sbjct: 287 GFIHPTTKEYIEFNSELPEYFKEVIKKI 314


>gi|217968192|ref|YP_002353698.1| pseudouridine synthase, RluA family [Dictyoglomus turgidum DSM
           6724]
 gi|217337291|gb|ACK43084.1| pseudouridine synthase, RluA family [Dictyoglomus turgidum DSM
           6724]
          Length = 303

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 149/330 (45%), Gaps = 36/330 (10%)

Query: 4   MTYVQYVV-VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M   +Y + VE + E  R+D++     P ++   +Q ++    ++V++K +K + +++ G
Sbjct: 1   MEKQRYEIYVEGESE--RIDKYLSKKVP-LSRSQIQDLIEKELIKVNEKPIKNSYKVKLG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +               I+   V        +   ++YED  + + NKP G+ V   
Sbjct: 58  DRIEV---------------IIPPPVETEVKPQDIPIEIVYEDEDMVIINKPKGMVVHPA 102

Query: 123 SGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++  L    D  G     +P + HRLD++T+G+L++A+   + Q L+E  + 
Sbjct: 103 HGHYNDTLVNALLYRVKDLSGIGGELRPGIIHRLDKDTTGLLIIAKNDLSHQKLSEQLKN 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R +++ YW+L  G    +++ I   + +   I    + +V         AI++FKV++ F
Sbjct: 163 RTLRRTYWALCEGEIPWEEKRIEAPIGRH-PINRKKMAIV----PYGKIAITNFKVLERF 217

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +     TGRTHQ+RVH  H+G PIVGD  Y    K            LHA+ + 
Sbjct: 218 -KGYTLISADLETGRTHQIRVHISHLGFPIVGDEVYGRIDK----KFGVKGQLLHAKKVS 272

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
             HP  G  ++    LP    K    L  K
Sbjct: 273 FIHPTKGIPMEFEIDLPEEFKKVLTLLREK 302


>gi|145633599|ref|ZP_01789327.1| SfhB [Haemophilus influenzae 3655]
 gi|229847288|ref|ZP_04467391.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae 7P49H1]
 gi|144985805|gb|EDJ92419.1| SfhB [Haemophilus influenzae 3655]
 gi|229809831|gb|EEP45554.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae 7P49H1]
          Length = 324

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 144/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|301632247|ref|XP_002945202.1| PREDICTED: ribosomal large subunit pseudouridine synthase D-like
           [Xenopus (Silurana) tropicalis]
          Length = 341

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 137/327 (41%), Gaps = 31/327 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQV 64
            V+ + V   +  +RLD+      P ++   LQ++L  G V +D     K  +++++G  
Sbjct: 25  EVRSLFVGPGQHGLRLDKALAELVPELSRSYLQQLLAQGLVCLDGAASRKPAHKVKAGDA 84

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +       +   K + +    V              +ED+ + V NKPAG+ V    G
Sbjct: 85  LVVEIRPTQQSQAFKPEPVPVPVV--------------FEDAHLLVVNKPAGLVVHPAPG 130

Query: 125 IAYHIDGFLKSWVDSKGQKP------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              H  G L + +  +  K        + HRLD++TSG++VVAR R     L      R+
Sbjct: 131 ---HWSGTLLNGLMGRDPKAMLLPRAGIVHRLDKDTSGLMVVARERTTMDALVRLIAQRQ 187

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           +++ Y +L   + +       +  L +       + VV   +     A + F+ +     
Sbjct: 188 VRRQYLALGHCVWRGGGLRTVDAALGRDPRNRLRMAVVDLAQHAGKPARTDFEYLAGNDL 247

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             C +    HTGRTHQ+RVH L MG P+V D  Y  +           +  LHA  +   
Sbjct: 248 G-CLVRCTLHTGRTHQIRVHMLSMGHPLVADVLYGGSAAAGLA-----RQALHADRLAFV 301

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGF 324
           HP  G+ L+  APLP  M +     G 
Sbjct: 302 HPVTGQALEFHAPLPEDMQQALVQWGL 328


>gi|92113717|ref|YP_573645.1| ribosomal large subunit pseudouridine synthase C [Chromohalobacter
           salexigens DSM 3043]
 gi|91796807|gb|ABE58946.1| ribosomal large subunit pseudouridine synthase C [Chromohalobacter
           salexigens DSM 3043]
          Length = 315

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 98/323 (30%), Positives = 162/323 (50%), Gaps = 15/323 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+    VQ+V V   +   R+D + +          + +I+R G++RV+KKRVK + R++
Sbjct: 1   MAEGRDVQWVEVSEGQVGQRIDNFLRTRLKGAPKSLIYRIVRKGEIRVNKKRVKADYRLE 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G +VRIPP+  A    ++E  + D   NL      L   +L E     V NKPAG++V 
Sbjct: 61  LGDLVRIPPLRLAPEEAVRE--VSDGLRNL------LAGSVLVEGPAWLVINKPAGLAVH 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+   +   L+   D       L HRLD++TSG L++A++R A   L ++ +  ++ 
Sbjct: 113 GGSGVKIGLIEALRQVRDDLDF-LELVHRLDRDTSGCLLLAKSRTALVTLNQALKAHQMD 171

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G    ++E ++  L +     G+    V   +     + + F V + F++  
Sbjct: 172 KQYLALVQGRWPTRREFVSARLDRFDAGNGERRVRV---DSQGKVSRTRFAVREAFSR-V 227

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPH 299
             +E +P TGRTHQ+RVHA H G  ++GD KY           ++  +L+LH+  +  P 
Sbjct: 228 TLIEAEPVTGRTHQIRVHAAHAGHALLGDDKYGTREGARLARELKLERLFLHSNALTFPE 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDS 321
           P  GR + + APL   +      
Sbjct: 288 PSSGRPVHVKAPLGETLEAVLAR 310


>gi|241758991|ref|ZP_04757103.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           flavescens SK114]
 gi|241320812|gb|EER57045.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           flavescens SK114]
          Length = 328

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 100/322 (31%), Positives = 166/322 (51%), Gaps = 25/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   EE  RLD +       +   ++ +I+R+G+VR++KKR K +NRIQ+G  VR
Sbjct: 9   VSLIAVAEHEEGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDNRIQAGDTVR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+      I ++Q+  +S     +  D     ++YED  + V NKP+GI+V GGSG++
Sbjct: 69  IPPI-----RIAEKQRPSESQAAPAREFD-----IVYEDDALLVINKPSGIAVHGGSGVS 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++     + +   L HRLD++TSG+L++A+ R+A   L E+ R    +KIY +L
Sbjct: 119 FGVIEQIRRAR-PEARYLELVHRLDKDTSGLLMIAKKRSALVKLHEAIRNDHPKKIYLAL 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   N +  +   L K +   G+ +  V ++      A + F+V++ F+         
Sbjct: 178 GVGRLPNNRFHVKLPLFKYTGAQGEKMVRVSED---GQSAHTIFRVLNRFSDGLLHQVGL 234

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
               ++E    TGRTHQ+RVH     CPI GD +Y               +++LHA  + 
Sbjct: 235 SDLTFVEATLKTGRTHQIRVHLQSQDCPIAGDERYGDYQANKRLQKLGLKRMFLHASELH 294

Query: 297 LPHP-EGGRLQITAPLPAHMVK 317
           L HP  G +L +  PLP  + +
Sbjct: 295 LAHPLTGEKLILKTPLPQELAQ 316


>gi|223043754|ref|ZP_03613797.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus capitis SK14]
 gi|222442851|gb|EEE48953.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus capitis SK14]
          Length = 305

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 71/324 (21%), Positives = 142/324 (43%), Gaps = 33/324 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++ + +  +   R+D++        +   LQ  ++   V+V+ K +K N +++   
Sbjct: 1   METHEFKITDETQVGQRIDKFLSESNDAWSRSQLQDWIKEDLVKVNDKVIKSNYKVKLND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           I+ E++++++ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  HI-----------IVTEKEVVEADI----QPEDLDLDIYYEDDDVAIVYKPKGMVVHPSP 105

Query: 124 G--IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    +  G     +P + HR+D++TSG+L+VA+   A + L E    +
Sbjct: 106 GHYTGTLVNGLMYQIKNLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRGLVEQLMAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV     +    +   + +        + VV         A++HF VI+ F 
Sbjct: 166 SVKRKYTALVHDNIPHDYGTVDAPIGRN-KNDRQAMAVVD----DGKEAVTHFNVIEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E +  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLIECELETGRTHQIRVHMKYIGYPLVGDPKYGPKRTLD-----IGGQALHAGVIGF 274

Query: 298 PHPEG-GRLQITAPLPAHMVKTWD 320
            HP     ++ +  LP       +
Sbjct: 275 EHPVTHEYIERSTNLPNDFKDLLE 298


>gi|260684170|ref|YP_003215455.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260687829|ref|YP_003218963.1| putative pseudouridylate synthase [Clostridium difficile R20291]
 gi|260210333|emb|CBA64669.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260213846|emb|CBE05842.1| putative pseudouridylate synthase [Clostridium difficile R20291]
          Length = 303

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 143/327 (43%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V  +EE +RLD +       ++   +QKI++ G+V+V+ K  K    ++   
Sbjct: 1   MDEVKEFLVLEEEEEVRLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKAKYLVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I          I E K+L+           +   ++YED  + + NKP  + V    
Sbjct: 61  NIVIE---------IPEPKVLEV------LPQDIPIDIVYEDDDVLIINKPQDMVVHPAP 105

Query: 124 GIAYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G   +   +G L    D         +P + HR+D++TSG+L++A+   A   L E  + 
Sbjct: 106 GNYENTLVNGILYHCKDKLSSINGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKE 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y  + +G+ K  K  +   + +          V     K    AI+HF+V++ F
Sbjct: 166 HTITREYEFICYGVVKEDKITVDKPIGRNPKDRLKMAVV-----KDGKNAITHFEVVERF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
             KF  +  +  TGRTHQ+RVHAL +  P++GD  Y        T        LHA+ + 
Sbjct: 221 -DKFTHMRARLETGRTHQIRVHALSINHPLLGDFVYGPKE----TKFKLKGQTLHAKKLG 275

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP     ++  + LP +  +    +
Sbjct: 276 FIHPTTKEYIEFNSELPEYFKEAIKKI 302


>gi|300023530|ref|YP_003756141.1| pseudouridine synthase [Hyphomicrobium denitrificans ATCC 51888]
 gi|299525351|gb|ADJ23820.1| pseudouridine synthase, RluA family [Hyphomicrobium denitrificans
           ATCC 51888]
          Length = 344

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 88/354 (24%), Positives = 155/354 (43%), Gaps = 48/354 (13%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
            +    ++   RLDRW       ++   +Q ++R G V  D   ++     ++ G   R+
Sbjct: 12  ELTAAAEDAGQRLDRWLAQKIEDLSRARIQALIRDGYVS-DGGTIREARTPVKPGITYRV 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                           L  +       + L   ++YED+ + V +KP G+ V   +G A 
Sbjct: 71  E---------------LPPASEPDVAGETLPLSIVYEDADLIVIDKPTGLVVHPAAGHAS 115

Query: 127 -YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--- 177
              ++  +    DS       ++P + HRLD++TSG+LVVA+T AA Q L + F+     
Sbjct: 116 GTLVNALIAHCGDSLSGIGGVKRPGIVHRLDKDTSGLLVVAKTDAAHQGLADQFKSHGRD 175

Query: 178 -RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI--- 233
            R+ + Y + VWG     K  I+  L + S      + VV+   +    A +H++V+   
Sbjct: 176 GRLFRSYLAFVWGRLPLPKGTISARLGR-SQANRTKIAVVR--GEAGRSATTHYEVLQVF 232

Query: 234 --DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------ 285
             +        + +   TGRTHQ+RVH  H+G P++GD  Y + F+    S  +      
Sbjct: 233 PGERSTGDVSLVRLVLETGRTHQIRVHLAHIGHPVLGDAVYGSGFRTRLASLKEAARAAA 292

Query: 286 ---NKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
              ++  LHA  ++  HP    +L+ ++ LPA +     ++ F        KRL
Sbjct: 293 SELSRQALHAETLEFEHPTSLKKLKFSSELPADLSDL--AIAFAATEKPKKKRL 344


>gi|260582391|ref|ZP_05850183.1| pseudouridylate synthase [Haemophilus influenzae NT127]
 gi|260094542|gb|EEW78438.1| pseudouridylate synthase [Haemophilus influenzae NT127]
          Length = 324

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 72/328 (21%), Positives = 144/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   S+  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPISEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|329297086|ref|ZP_08254422.1| RluA family pseudouridine synthase [Plautia stali symbiont]
          Length = 326

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 83/333 (24%), Positives = 139/333 (41%), Gaps = 35/333 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V V+   + K   ++  G+ V I
Sbjct: 8   TATVSKAQLGQRLDQTLAELFPDYSRSRIKEWILERRVSVNGTIIDKPKEKVLGGERVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  DAEIEEEQRWEAQNIPLD---------------IVYEDDHILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L     +    PR  + HRLD++T+G++VVA+T  A  HL E+ ++R I + Y 
Sbjct: 113 GTVLNVLLYHYPAIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVETLQLREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A +H+++++ F +    L 
Sbjct: 173 AVAIGTM-TAGGTVNEPMARHST-----KRTHMAVHPMGKPATTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMAHIKHPLVGDPLYGGRPRPPKGASEAFISTLRGFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           L HP  G  ++  APLP  MV   D+L    D 
Sbjct: 286 LYHPITGIEMEWHAPLPQDMVDLIDALKADTDE 318


>gi|162533081|ref|YP_001621404.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213971041|ref|ZP_03399161.1| Ribosomal large subunit pseudouridine synthase D(Pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           tomato T1]
 gi|301384235|ref|ZP_07232653.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. tomato Max13]
 gi|302059468|ref|ZP_07251009.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. tomato K40]
 gi|302134990|ref|ZP_07260980.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. tomato NCPPB 1108]
 gi|118201618|gb|ABK79681.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213924149|gb|EEB57724.1| Ribosomal large subunit pseudouridine synthase D(Pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           tomato T1]
 gi|330878989|gb|EGH13138.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
 gi|330966362|gb|EGH66622.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. actinidiae str. M302091]
 gi|331018389|gb|EGH98445.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. lachrymans str. M302278PT]
          Length = 320

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 87/333 (26%), Positives = 150/333 (45%), Gaps = 36/333 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLELIAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
            A    + +   LD               ++YED +I V NKPAG+ V   +G A     
Sbjct: 71  EAQGEWVAQDIELD---------------IIYEDDQILVINKPAGLVVHPAAGHADGTLL 115

Query: 130 DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R + +IY  +V 
Sbjct: 116 NALLHHVPDIVNVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVI 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+       I   + +        + V+    +G   A+SH++V++ F +    + ++  
Sbjct: 176 GVV-TAGGKIDAPIGRHGQQ-RQRMAVM----EGGKQAVSHYRVLERF-RSHTHVRVKLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P+VGD  Y   F+    + +          +  LHAR+++L HP
Sbjct: 229 TGRTHQIRVHMAHVNYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFLELDHP 288

Query: 301 EGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
             G R+   +PLP   V     L  K DR  +I
Sbjct: 289 ITGKRMSWESPLPDDFVWLLSLL--KQDREAFI 319


>gi|22537512|ref|NP_688363.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           agalactiae 2603V/R]
 gi|76797703|ref|ZP_00779971.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
 gi|77414617|ref|ZP_00790757.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
 gi|22534392|gb|AAN00236.1|AE014254_16 ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 2603V/R]
 gi|76586927|gb|EAO63417.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
 gi|77159330|gb|EAO70501.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
          Length = 296

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 72/314 (22%), Positives = 135/314 (42%), Gaps = 34/314 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             +RLD+   ++   ++     + ++ G V V+ +  K    +Q G  +           
Sbjct: 8   AGVRLDKALADN-SELSRSQANEEIKKGIVLVNGQVKKAKYTVQEGDRITFD-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
            I ++++LD        ++ +   ++Y+D  + V NKP G+ V   +G      ++  + 
Sbjct: 59  -IPKEEVLD------YQAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+   A Q L E  + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        AI+ F V++ F   +  +E+   TG
Sbjct: 172 LPNDRGVIEAPIGRSDKDRKKQAVTAK-----GKPAITRFHVLERFGD-YTLVELSLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +      +LHA+ +   HP  G  L  + 
Sbjct: 226 RTHQIRVHMAYIGHPLAGDPVYGPR-----KTLGGKGQFLHAQTLGFTHPSNGENLIFSV 280

Query: 310 PLPAHMVKTWDSLG 323
            +P     T + L 
Sbjct: 281 EVPEIFQTTLEKLR 294


>gi|312622398|ref|YP_004024011.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202865|gb|ADQ46192.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 299

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 85/315 (26%), Positives = 154/315 (48%), Gaps = 35/315 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPPVINALNHII 78
           RLDR+            +QKI+  G V V++ + +K   +++SG ++++           
Sbjct: 9   RLDRYLSEALSK-TRSFVQKIIEEGNVWVNQIQVLKPAYKVKSGDIIKV----------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW 136
               ++     L+  +  +   +LYED  + V NKP G+ V  G+G   +   +  L  +
Sbjct: 57  ----VIPEPKQLSLVAQEIDIEVLYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKF 112

Query: 137 VDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      +P + HRLD++TSG+LVVA+T  A   L+E+ +  +I++IY+++  G+ 
Sbjct: 113 SGRLSSINGVIRPGIVHRLDKDTSGLLVVAKTDEAHIKLSEALKSHQIKRIYYAICEGVL 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K     I   + +   +    + VV         A+++F+V++ F  K+ +++++  TGR
Sbjct: 173 KEDSGVINAPIGRH-PVNRLKMAVV----PNGKEAVTYFEVLERF-DKYTFIKLRLKTGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P++GD  Y    K  F    Q    LHA  ++  HP     L  +A 
Sbjct: 227 THQIRVHISYIGYPLLGDGIYG-RAKNEFGVEGQV---LHAGEIEFVHPITSEVLHFSAE 282

Query: 311 LPAHMVKTWDSLGFK 325
           LP + +K  + L  K
Sbjct: 283 LPEYFLKILNILRSK 297


>gi|168182405|ref|ZP_02617069.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
 gi|237794814|ref|YP_002862366.1| RluA family pseudouridine synthase [Clostridium botulinum Ba4 str.
           657]
 gi|182674415|gb|EDT86376.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
 gi|229261378|gb|ACQ52411.1| pseudouridine synthase, RluA family [Clostridium botulinum Ba4 str.
           657]
          Length = 305

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 87/326 (26%), Positives = 151/326 (46%), Gaps = 33/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  + VE + +N+RLD +    +   +   LQ I+  G V V+ K+ K N +++ G 
Sbjct: 1   MEKI-SLQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDEGNVLVNNKKKKRNYKLKVGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +K  ++YED  + V NKP  + V    
Sbjct: 60  NIEVN---------------IPEPKLLEIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G+     ++  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+  
Sbjct: 105 GVYSGTLVNALLNHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I ++Y +LV GI K+++  I   + +   +    + VV    K   +A++H+KVI+ F 
Sbjct: 165 SISRVYMALVEGIIKDEQGTIEAPIGRH-PVDRIKMAVV----KDGRHAVTHYKVIERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    +E +  TGRTHQ+RVH  H+  P+VGD  Y    +            LHA+ +  
Sbjct: 219 KNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQ----RFNLKGQMLHAKLLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP   + ++  + LP +  K    L
Sbjct: 275 IHPTTRQYVEFESELPEYFKKIIKIL 300


>gi|297538120|ref|YP_003673889.1| RluA family pseudouridine synthase [Methylotenera sp. 301]
 gi|297257467|gb|ADI29312.1| pseudouridine synthase, RluA family [Methylotenera sp. 301]
          Length = 363

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 80/334 (23%), Positives = 142/334 (42%), Gaps = 34/334 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + + ND   +RLD   +   P  +   LQ  ++ G V VDK       ++  G+ V + 
Sbjct: 14  TLTISNDLGGLRLDVALQRMLPEHSRSRLQTWIKEGLVTVDKLPSTSKTKVWGGEQVVVQ 73

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                 N+                 ++ +   +++ED  I + NKPAG+ V   +G    
Sbjct: 74  VQAKPENY--------------AYVAEDIPLDIVFEDDHIIIINKPAGMVVHPAAGNWSG 119

Query: 127 YHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             ++  L    + K   +  + HRLD++TSGILVVA+T AA  +L    + R +++ Y +
Sbjct: 120 TLLNALLFHAPELKDVPRAGIVHRLDKDTSGILVVAKTLAAQTNLVRQLQARTVKREYRA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +VWG     +  + +  + +       + + +        AI+ +++++ F+    +L  
Sbjct: 180 IVWGQLW--RNGVVDQAIGRDPRSRTKMALNRM----GKPAITRYEILERFS-VQTYLRC 232

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NKLYLHARYMD 296
              TGRTHQ+RVH   +  PIVGD  Y            Q         N+  LHA  + 
Sbjct: 233 NLETGRTHQIRVHMQSLKAPIVGDPVYGFRGIIPIRVMTQTLRDEVSQFNRQALHAIKLG 292

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           L HP     ++    L   M    +++  +  RN
Sbjct: 293 LMHPATNEFMEWQIELADDMKALLEAMRHEDPRN 326


>gi|282900595|ref|ZP_06308537.1| Pseudouridine synthase, RluD [Cylindrospermopsis raciborskii
           CS-505]
 gi|281194395|gb|EFA69350.1| Pseudouridine synthase, RluD [Cylindrospermopsis raciborskii
           CS-505]
          Length = 326

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 83/316 (26%), Positives = 145/316 (45%), Gaps = 29/316 (9%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINAL 74
           ++  RLDR+  +  P ++   +Q ++  G V+V+ K     N  +  G+ + +       
Sbjct: 30  QKTQRLDRYLSSVIPDLSRSRIQDLIEQGYVQVNGKVCYSKNITLDGGEYLEVEIPPVQA 89

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGF 132
             ++ +   LD               +LYED ++ + NKPAG+ V    G      +   
Sbjct: 90  AQLVAQDIPLD---------------ILYEDEQLLILNKPAGLVVHPAPGHLEGTLVHAL 134

Query: 133 LKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L    +  G    Q+P + HRLD++T+G + +A+T  A + L    + +  ++ Y  +V+
Sbjct: 135 LAHCPNLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKQLQLQLQSKIARREYLGVVY 194

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G PK++   I   + +  H        +   E+G   AI+++ + +     +  +  Q  
Sbjct: 195 GAPKSESGTIDLPIGR--HPQQRKKMAIVPVEQGGRNAITNWHIKERLG-NYTLIHFQLE 251

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH+  MG PIVGD  Y +        P      LHA  + L HP  G  +++
Sbjct: 252 TGRTHQIRVHSAKMGHPIVGDPVYSSGRSVGVNLPG---QALHAWQLKLQHPTSGEWVEV 308

Query: 308 TAPLPAHMVKTWDSLG 323
           TAPLP  + K  + L 
Sbjct: 309 TAPLPDSLTKLIEVLR 324


>gi|298251897|ref|ZP_06975700.1| pseudouridine synthase, RluA family [Ktedonobacter racemifer DSM
           44963]
 gi|297546489|gb|EFH80357.1| pseudouridine synthase, RluA family [Ktedonobacter racemifer DSM
           44963]
          Length = 317

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 78/316 (24%), Positives = 140/316 (44%), Gaps = 27/316 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE+++   RLDR+  +    ++   +Q+++    V V+ K  K    ++    V      
Sbjct: 17  VESEQVGQRLDRFLVSVLDGVSRSGVQQLIADALVLVNGKVSKPGYVLRLKDRVT----- 71

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                     +   +S         L   +++ED  + + NK AG+ V    G      +
Sbjct: 72  --------ALRATPASQMKQVTPQNLPLEVVFEDDDLLIVNKAAGMVVHPAPGNYEGTLV 123

Query: 130 DGFLKSWV----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  +  +     D    +P + HRLD++TSG+L+VA+   +   L E  +  +I K Y +
Sbjct: 124 NALVAHYPELQQDEGDMRPGIIHRLDKDTSGLLMVAKNAQSQAALIEQMKQHKIIKRYLA 183

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  +  +  I   + + +     +  ++         A++HF+V+  F +K   + +
Sbjct: 184 LVEGNVELDQGSIDAPIGRDTR----HRQMMAVTLTEGRDAVTHFRVLQRF-RKHTLVLV 238

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH   +  P+ GD  Y +  +    +      +LHA  ++L HP  G  
Sbjct: 239 QIVTGRTHQIRVHFQAIKHPVAGDQTYGSGHR--IPNVKLEHQFLHAYQLELTHPRTGES 296

Query: 305 LQITAPLPAHMVKTWD 320
           L I APLP  + K  D
Sbjct: 297 LHIEAPLPPDLQKVLD 312


>gi|240017486|ref|ZP_04724026.1| RluC [Neisseria gonorrhoeae FA6140]
 gi|240118863|ref|ZP_04732925.1| RluC [Neisseria gonorrhoeae PID1]
 gi|268604570|ref|ZP_06138737.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae PID1]
 gi|268588701|gb|EEZ53377.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           gonorrhoeae PID1]
          Length = 330

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 154/322 (47%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +    + +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKGYIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V NKP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFE---------VVYEDDALLVVNKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-------- 238
             G   +    +   L K +   G+ +  V ++      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSED---GQSAHTVFRVLSRFSDGILHGVGL 237

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGG-RLQITAPLPAHMVK 317
           L HP  G  L + A  P  + +
Sbjct: 298 LNHPLTGDPLVLKAEPPPDLAQ 319


>gi|54298185|ref|YP_124554.1| ribosomal large subunit pseudouridine synthase [Legionella
           pneumophila str. Paris]
 gi|53751970|emb|CAH13394.1| Ribosomal large subunit pseudouridine synthase [Legionella
           pneumophila str. Paris]
          Length = 315

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 109/324 (33%), Positives = 169/324 (52%), Gaps = 17/324 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V Y  + ++E+  RLD +       +   ++ +I+R G+VR++KKR + N+R+Q G 
Sbjct: 1   MSEVSYKEIGSEEDGQRLDNYLIRILKGVPKSHIYRIIRGGEVRINKKRAQANSRLQIGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+    +      K +  S NL K    LK  +++EDS + V NKPAGI+V GGS
Sbjct: 61  SIRIPPIRMTDS------KEIFVSDNLAKR---LKDSIIFEDSSLLVINKPAGIAVHGGS 111

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G++  +   L+           L HRLD+ETSG L++A+ R+  + +      R +QKIY
Sbjct: 112 GLSLGVIEALRKTRHDLSY-LELVHRLDRETSGCLLLAKKRSTLRAIQALLEAREVQKIY 170

Query: 184 WSLVWGIPKNKKE-CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           W+L+      KK+  I   L K +   G+ V  V   +K    + + FK+++ + Q  CW
Sbjct: 171 WALLTHRWDGKKKITITAPLEKNTLKSGERVVSV---QKDGKASETDFKLLENYHQ-ACW 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPE 301
           +E  P TGRTHQ+RVH+ + G  IVGD KY +           QN+LYLHAR +   +  
Sbjct: 227 VEASPKTGRTHQIRVHSAYFGHVIVGDGKYGSKVGEVEGIDYQQNRLYLHARSIQF-NLN 285

Query: 302 GGRLQITAPLPAHMVKTWDSLGFK 325
           G      A +      T   L  +
Sbjct: 286 GVMHVFQADVDDGFGNTLKQLRAR 309


>gi|218667498|ref|YP_002424927.1| ribosomal large subunit pseudouridine synthase D [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|218519711|gb|ACK80297.1| ribosomal large subunit pseudouridine synthase D [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 319

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 85/341 (24%), Positives = 150/341 (43%), Gaps = 34/341 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS  +    +++  ++   RLD       P  +   +Q +LR G++ VD    K + R++
Sbjct: 1   MSDDSTGLPMILPEEQAGERLDTVLSQLLPETSRSRIQALLRDGRILVDGTPEKPSARVR 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ V +       ++ + E                L   +L+ED+ I V +KPAG    
Sbjct: 61  GGEQVMVDWPQIEPSNWLAEG---------------LPLHILHEDADILVLHKPAGQLTH 105

Query: 121 GGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+G A   +   + + V      PR  + HRLD++T+G+LVVA+T  A Q L +     
Sbjct: 106 PGAGHADGTLVNGVLAHVPENAYLPRGGIVHRLDKDTTGLLVVAKTEMARQSLIDQLGDH 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LV G        +   + + +    D + +  +++     A + +++++ F 
Sbjct: 166 TMHREYLALVTGAMTG-GGRVDAPIGRHAQ---DRLRMTVRDD--GRPAQTDYRLVERFP 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--------KGNFTSPIQNKLY 289
           +   +L ++  TGRTHQ+RVH  H+G P+VGD  Y             G        +  
Sbjct: 220 R-HSYLRLRLATGRTHQIRVHMTHIGHPLVGDPVYGGRMTVPKGLDEAGLARWRQFRRQA 278

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           LHA  + L HP  G  +   +PLP  M +    L    D +
Sbjct: 279 LHAWRLRLYHPASGELMTWESPLPDDMTELLALLRHARDGD 319


>gi|319760323|ref|YP_004124261.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Blochmannia vafer str. BVAF]
 gi|318039037|gb|ADV33587.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Blochmannia vafer str. BVAF]
          Length = 333

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 77/336 (22%), Positives = 153/336 (45%), Gaps = 36/336 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVV 65
           ++ +VV+      RLD       P  +   +++ + + +V ++ +  V    ++ SG+++
Sbjct: 11  IKPIVVQIAYSGKRLDWVLSELLPQFSRSQIKRWIINKKVVINNQISVLPKKKVISGEII 70

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I  + N          ++  +++L          ++YED+ I V NKP+ + V    G+
Sbjct: 71  EINDINNDSTSDCNNNILIPQNISLN---------IVYEDNDILVINKPSNMVVHP--GV 119

Query: 126 AYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             + D  L + +          ++  +  RLD++T+G++++A+T  A  +L +SF+M+++
Sbjct: 120 KNNKDTVLNALLYRYPSIMQISKQAGIVQRLDKDTTGLMIIAKTYLAYTNLLQSFKMKQV 179

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y ++V G        I+  + + S                   A++ + V++ F + 
Sbjct: 180 IKEYDAVVCGTFSYNAGIISQPIRRHS-----INRTCMTVHPHGKPAVTRYSVVESFGRT 234

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------------NK 287
           +  + +   TGRTHQ+RVH  ++  P+VGD KY   FK + T  +             N+
Sbjct: 235 YSRIRVYLETGRTHQIRVHMAYINHPVVGDVKYGIKFKNSTTGKLSISDDVSICLSSFNR 294

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
             LHA  + L HP    ++    PLP  M+K    L
Sbjct: 295 QALHACKLQLVHPITRLKMHWIVPLPEDMLKLVTVL 330


>gi|237729509|ref|ZP_04559990.1| 23S rRNA pseudouridine synthase D [Citrobacter sp. 30_2]
 gi|226908115|gb|EEH94033.1| 23S rRNA pseudouridine synthase D [Citrobacter sp. 30_2]
          Length = 326

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 81/336 (24%), Positives = 149/336 (44%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ +   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNDQLCDKPKEKVLGGERVSI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I+       +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIDEEVRFEPQDIPLD---------------IVYEDDDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        +E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVEEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKGASDEFISVLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G  ++  AP+P  MV+  + +   ++ 
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVQLIEVMRADFEE 318


>gi|269926450|ref|YP_003323073.1| pseudouridine synthase, RluA family [Thermobaculum terrenum ATCC
           BAA-798]
 gi|269790110|gb|ACZ42251.1| pseudouridine synthase, RluA family [Thermobaculum terrenum ATCC
           BAA-798]
          Length = 313

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 75/317 (23%), Positives = 136/317 (42%), Gaps = 28/317 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++  ++   RLD    +    ++   +Q+ +  G + V+    K + +++ G  + I  
Sbjct: 14  LIISPEDVGERLDTLLAHKLESVSRSQVQRAIEQGTILVNDHPSKPSYKLREGDRILI-- 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                   +   ++    V L      L+  ++YED KI V +KPAG+ V    G   + 
Sbjct: 72  --------LTIPRVPQGEVALIPSYVDLR--VVYEDDKIIVIDKPAGMVVHPSPGHYDNT 121

Query: 130 --DGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +  +  + D   Q   +P + HRLD++TSG+++VAR      +L    + R+I K Y 
Sbjct: 122 LVNALIARYPDLLKQPTDRPGIVHRLDKDTSGLIIVARDLDTLNYLQGQMKARKIFKEYT 181

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            L  G     +  I   + +          +      G   A++ +  I     K+    
Sbjct: 182 LLCCGALDPPEGRIEAPIGRDLRDRTKMSVIA-----GGKEAVTEYSTIQSLG-KYTLAI 235

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +P TGRTHQ+RVH   +G PI GD  Y      N      N+ +LHA  + +  P G  
Sbjct: 236 ARPITGRTHQIRVHFAAIGHPIAGDPIYG-----NCRLEGLNRQFLHASRLGVVMPNGEY 290

Query: 305 LQITAPLPAHMVKTWDS 321
            +  +PLP  + ++ + 
Sbjct: 291 KEWHSPLPEDLRQSLEK 307


>gi|77166008|ref|YP_344533.1| pseudouridine synthase, RluD [Nitrosococcus oceani ATCC 19707]
 gi|254436382|ref|ZP_05049888.1| pseudouridine synthase, RluA family [Nitrosococcus oceani AFC27]
 gi|76884322|gb|ABA59003.1| ribosomal large subunit pseudouridine synthase D [Nitrosococcus
           oceani ATCC 19707]
 gi|207088072|gb|EDZ65345.1| pseudouridine synthase, RluA family [Nitrosococcus oceani AFC27]
          Length = 319

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 142/322 (44%), Gaps = 34/322 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + + ++    RLD+     +P  +   LQ+ ++ GQV+V+    +  + +Q G+ + +  
Sbjct: 9   ITLPSELAGKRLDQALAQVFPAYSRSRLQQWIKHGQVKVNDAPARPRDTVQGGEWIVVM- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                          ++   +   S  L   + YED  I V NKPAG+ V   +G     
Sbjct: 68  --------------AEAEAEVIWKSQPLPLEIRYEDEAIIVVNKPAGLVVHPAAGNRDGT 113

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L    +  +  +  + HRLD++TSG+LVVAR   A   L    + R+I + Y ++
Sbjct: 114 LVNALLHHAPELERIPRAGIVHRLDKDTSGLLVVARNLVAHHGLVRQLQARQITREYQAI 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G+       I   + ++  +    + V+         A++H++V++ F +    +  +
Sbjct: 174 TVGVMTG-GGRIEAPI-QRHPVHRKRMAVIS----TGKPALTHYRVLNRF-RVHTHVSCR 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+G  ++GD  Y         S  +         +  LHA  + L 
Sbjct: 227 LETGRTHQIRVHLAHIGYSLLGDPTYGKRLHIPRESSEKLSTALRHFKRQALHAARLGLV 286

Query: 299 HPEGGR-LQITAPLPAHMVKTW 319
           HPE  R ++  +PLP  M    
Sbjct: 287 HPEKKREMRWESPLPEDMATLL 308


>gi|325203319|gb|ADY98772.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M01-240355]
 gi|325205289|gb|ADZ00742.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M04-240196]
          Length = 330

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 94/322 (29%), Positives = 155/322 (48%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  +      A + F+ ++ F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSAD---GQSAHTVFRALNRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A LP  + +
Sbjct: 298 LNHPLTGEPLVLKAELPPDLAQ 319


>gi|294664687|ref|ZP_06730020.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
 gi|292605540|gb|EFF48858.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
          Length = 328

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 95/326 (29%), Positives = 156/326 (47%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++     D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPP--------VRTNDEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRALRP--NQSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L+ G   +    +   L      GG+    V         ++SHF++++      
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFRLLERRG-GH 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G P+ GD KY      K         +L+LHA  ++  
Sbjct: 242 SYCEVRIETGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAASLEFA 301

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     ++APL   + +  D LG
Sbjct: 302 LDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|281204012|gb|EFA78208.1| Probable ribosomal large subunit pseudouridine synthase C protein
           [Polysphondylium pallidum PN500]
          Length = 702

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 119/368 (32%), Positives = 179/368 (48%), Gaps = 55/368 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV----DKKR--VKFNNRIQSGQVV 65
           V  D + MR+DRW  NHYP I    L K +RS ++ V    + +R  V+ N+R+ +GQ V
Sbjct: 329 VVEDLDGMRVDRWVSNHYPVITHSLLCKWIRSNKISVSDSLNGERKQVELNDRLVTGQWV 388

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +P        +   ++    +    +    ++  +LY+D ++ + NKP G+SVQGG+G+
Sbjct: 389 NVPMKALKEQRLADRKEPTKYARLSDEEIKEIRDSVLYKDDQLLIINKPQGLSVQGGTGL 448

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-------- 177
             H+D  +        + PRL HRLD+ETSGIL++ARTR AA  + + F M+        
Sbjct: 449 KKHLDMMMSHLKFELEEAPRLCHRLDRETSGILILARTRKAATAMADKFEMKLKRRTTRQ 508

Query: 178 -------------------------------------RIQKIYWSLVWGIPKNKKECIAN 200
                                                 I+K YW+L+   P  K+  I  
Sbjct: 509 DRDKKDKQKKDGSGSGSSSKKDKDRSGGEDEELRDDNGIRKTYWALLTSTPNPKEGRIRA 568

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K    G + V   K+   GA  AI+ +KV++       ++ + P TGRTHQLRVH  
Sbjct: 569 PLKKVVQDGEEMVIATKETGDGAKLAITEYKVVESSLTNASFVSLWPETGRTHQLRVHCA 628

Query: 261 HMG-CPIVGDHKYCANFKGNFTSPIQNK--LYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
            +   PIVGD KY  N    F S +  K  L+LHAR ++  HPE   ++ + APLP ++ 
Sbjct: 629 SILSSPIVGDKKYGKNDSVAFQSVLGKKIPLHLHARRVEFFHPETNKKIDVVAPLPKNLE 688

Query: 317 KTWDSLGF 324
            +WD LGF
Sbjct: 689 NSWDMLGF 696


>gi|89901092|ref|YP_523563.1| pseudouridine synthase RluD [Rhodoferax ferrireducens T118]
 gi|89345829|gb|ABD70032.1| ribosomal large subunit pseudouridine synthase D [Rhodoferax
           ferrireducens T118]
          Length = 334

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 77/331 (23%), Positives = 138/331 (41%), Gaps = 31/331 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQV 64
            ++ +V  + +   RLDR      P  +   LQ+++  G V ++   + K + R+++  V
Sbjct: 26  ELRQLVFGSVQHGQRLDRALVELVPEFSRSYLQQLIDLGGVTINGIVIHKPSTRVKAADV 85

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
             I              ++  +  +     + +   +++ED  + V NKPAG+ V    G
Sbjct: 86  GTI--------------ELRPTPQSQAFKPETMALNVVFEDEHLMVINKPAGLVVHPAPG 131

Query: 125 IAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              +  G L + + ++        +  + HRLD++TSG++VVARTR     L  S   R 
Sbjct: 132 ---NWSGTLLNGLLARDAKAMNLPRAGIVHRLDKDTSGLMVVARTRPVMDALIRSIAARE 188

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + + Y +L  G     +    N  + +       + VV         A +  +++    Q
Sbjct: 189 VSRQYVALAHGPWTGNRRVEINAPIGRDPRNRLRMAVVDLARNPGKLARTDVELLQNCDQ 248

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             CW+    HTGRTHQ+RVH   +G P+V D  Y    +         +  LHA  +   
Sbjct: 249 G-CWVLCTLHTGRTHQIRVHMAMIGHPLVADVLYGGRAEAGM-----QRQALHACRLAFT 302

Query: 299 HPEG-GRLQITAPLPAHMVKTWDSLGFKYDR 328
           HP     +   A LP  +     + G  Y++
Sbjct: 303 HPVTLESMVFQASLPVDLNLALANWGLSYNQ 333


>gi|52842505|ref|YP_096304.1| ribosomal large subunit (23S rRNA) pseudouridine synthase C
           [Legionella pneumophila subsp. pneumophila str.
           Philadelphia 1]
 gi|52629616|gb|AAU28357.1| ribosomal large subunit (23S rRNA) pseudouridine synthase C
           [Legionella pneumophila subsp. pneumophila str.
           Philadelphia 1]
          Length = 317

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 109/325 (33%), Positives = 168/325 (51%), Gaps = 17/325 (5%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
            M+ V Y  + ++E   RLD +       +   ++ +I+R G+VR++KKR + ++R+Q G
Sbjct: 2   TMSEVSYKEIGSEENGQRLDNYLIRILKGVPKSHIYRIIRGGEVRINKKRAQASSRLQIG 61

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +RIPP+    +      K +  S NL K    LK  +++EDS + V NKPAGI+V GG
Sbjct: 62  DSIRIPPIRMTDS------KEIFVSDNLAKR---LKDSIIFEDSSLLVINKPAGIAVHGG 112

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG++  +   L+           L HRLD+ETSG L++A+ R+  + +      R +QKI
Sbjct: 113 SGLSLGVIEALRKTRHDLSY-LELVHRLDRETSGCLLLAKKRSTLRAIQALLEAREVQKI 171

Query: 183 YWSLVWGIPKNKKE-CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           YW+L+      KK+  I   L K +   G+ V  V   +K    + + FK+++ + Q  C
Sbjct: 172 YWALLTHRWDGKKKITITAPLEKNTLKSGERVVSV---QKDGKASETDFKLLENYHQ-AC 227

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHP 300
           W+E  P TGRTHQ+RVH+ + G  IVGD KY A           QN+LYLHAR +   + 
Sbjct: 228 WVEASPKTGRTHQIRVHSAYFGHVIVGDEKYGAKVGEVEGIDYQQNRLYLHARSIQF-NL 286

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFK 325
            G      A +      T   L  +
Sbjct: 287 NGVMHVFQADVDDGFGNTLKQLRAR 311


>gi|55822493|ref|YP_140934.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus CNRZ1066]
 gi|55738478|gb|AAV62119.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus CNRZ1066]
          Length = 292

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 68/296 (22%), Positives = 134/296 (45%), Gaps = 33/296 (11%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +    ++     + +++G V V+ K  K    ++ G V+          
Sbjct: 7   EAGNRLDKSLAD-LTELSRSQANEAIKAGTVLVNGKSAKAKYVVKEGDVIT--------- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFL 133
           +++ E+++L+        ++ +   ++YED+ + V NKP G+ V   +G      ++  +
Sbjct: 57  YVLPEEEVLE------YKAEDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALM 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L++A+   A   L    + ++  + Y ++V G
Sbjct: 111 YHVKDLSSINGVVRPGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N +  I   + +            K        A++ F V++ F   +  +E+Q  T
Sbjct: 171 NLPNDRGVIEAPIGRSDKDRKKQAVTAK-----GKPAVTRFTVLERFG-NYTLVELQLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           GRTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ +   HP  G+L
Sbjct: 225 GRTHQIRVHMAYIGHPVAGDPLYGPR-----KTLKGHGQFLHAKTLGFTHPTTGKL 275


>gi|307611132|emb|CBX00776.1| ribosomal large subunit pseudouridine synthase [Legionella
           pneumophila 130b]
          Length = 315

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 109/324 (33%), Positives = 169/324 (52%), Gaps = 17/324 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V Y  + ++E+  RLD +       +   ++ +I+R G+VR++KKR + N+R+Q G 
Sbjct: 1   MSEVSYKEIGSEEDGQRLDNYLIRILKGVPKSHIYRIIRGGEVRINKKRAQANSRLQIGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+    +      K +  S NL K    LK  +++EDS + V NKPAGI+V GGS
Sbjct: 61  SIRIPPIRMTDS------KEIFVSDNLAKR---LKDSIIFEDSSLLVINKPAGIAVHGGS 111

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G++  +   L+           L HRLD+ETSG L++A+ R+  + +      R +QKIY
Sbjct: 112 GLSLGVIEALRKTRHDLSY-LELVHRLDRETSGCLLLAKKRSTLRAIQALLEAREVQKIY 170

Query: 184 WSLVWGIPKNKKE-CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           W+L+      KK+  I   L K +   G+ V  V   +K    + + FK+++ + Q  CW
Sbjct: 171 WALLTHRWDGKKKITITAPLEKNTLKSGERVVSV---QKDGKASETDFKLLENYHQ-ACW 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPE 301
           +E  P TGRTHQ+RVH+ + G  IVGD KY +           QN+LYLHAR +   +  
Sbjct: 227 VEASPKTGRTHQIRVHSAYFGHVIVGDEKYGSKVGEVEGIDYQQNRLYLHARSIQF-NLN 285

Query: 302 GGRLQITAPLPAHMVKTWDSLGFK 325
           G      A +      T   L  +
Sbjct: 286 GVMHVFQADVDDGFGDTLKQLRAR 309


>gi|327484563|gb|AEA78970.1| Ribosomal large subunit pseudouridine synthase C LSU Psi955,
           Psi2504 and Psi2580 [Vibrio cholerae LMA3894-4]
          Length = 321

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 91/270 (33%), Positives = 157/270 (58%), Gaps = 13/270 (4%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++LV G    + + +   LLK        V+ + +       + + F++++ FA+   
Sbjct: 177 YYYALVMGHWDAECKVVNAPLLKNE------VNSIVRVNSNGKPSETRFRILEKFAE-AT 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            ++  P TGRTHQ+RVH  +MG PI  D +
Sbjct: 230 LVQASPVTGRTHQIRVHTQYMGHPIAWDDR 259


>gi|291530266|emb|CBK95851.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           siraeum 70/3]
          Length = 304

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 74/312 (23%), Positives = 132/312 (42%), Gaps = 33/312 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             R D++       I       ++  G   V+ K    N ++++G  V +         I
Sbjct: 12  GERTDKFLALQDTGITRSAAAALIEQGCCLVNGKIAAKNQKLKTGDTVTLDVPEAQPADI 71

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
           + E   LD               ++YEDS + V NKP G+ V    G      ++  +  
Sbjct: 72  LPENIPLD---------------IVYEDSDLLVVNKPKGMVVHPAPGHYSGTLVNALMYH 116

Query: 136 WVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             DS        +P + HR+D++TSG+L+VA+   A   L E  ++    + Y ++V G+
Sbjct: 117 CGDSLSGINGVIRPGIVHRIDRDTSGLLIVAKNDTAHNILAEQIKVHSFTREYMAVVQGV 176

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K     +   + +        + V  +N   +  AI+H+ V +   +    + ++  TG
Sbjct: 177 IKED-GTVDAPIGRH-KTDRKKMCVTTEN---SREAITHYFV-EQTYRNNTLVRLRLETG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQ+RVH  ++G P+ GD  Y      N +        LHA+ +   HP+G  ++  + 
Sbjct: 231 RTHQIRVHMAYIGHPVTGDEVYG-----NGSPKWLCGQCLHAKKIGFIHPDGRYMEFDSD 285

Query: 311 LPAHMVKTWDSL 322
           LP +  K   +L
Sbjct: 286 LPDYFKKLLANL 297


>gi|298492053|ref|YP_003722230.1| pseudouridine synthase, RluA family ['Nostoc azollae' 0708]
 gi|298233971|gb|ADI65107.1| pseudouridine synthase, RluA family ['Nostoc azollae' 0708]
          Length = 329

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 83/333 (24%), Positives = 150/333 (45%), Gaps = 32/333 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSG 62
           MT +  +V    +   RLD +  +   +++   LQ+++  G V ++ +        ++ G
Sbjct: 21  MTVINLLV---SQNTQRLDLYLSSELQNLSRSRLQQLIEQGHVLLNDQVCTSKKVNVKVG 77

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +                + S   L   ++ +   +LYED ++ + NKPAG+ V   
Sbjct: 78  DRICVE---------------IPSLQPLKLVAEDIPLDILYEDEQLLILNKPAGLVVHPA 122

Query: 123 SGI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++  L    +  G    Q+P + HRLD++T+G + +A+T  A QHL    + 
Sbjct: 123 PGHLDGTLVNALLAHCANLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYQHLQAQLQA 182

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           +  ++ Y  +V+G+PK +   I   + +  H        +   E+G   AI+H+++ +  
Sbjct: 183 KTARREYLGVVYGVPKTESGIINLPISR--HPQDRKKMAIVPTEQGGRTAITHWQIRERL 240

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           +  +  +  Q  TGRTHQ+RVH+  +G PIVGD  Y A               LHA  + 
Sbjct: 241 S-NYTLIHFQLETGRTHQIRVHSAKIGHPIVGDSVYGAGRSVGVNLAGH---ALHAWQLK 296

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           L HP  G  +Q+TA  P       + L  + +R
Sbjct: 297 LQHPISGDWIQVTASPPQTFTTLLEVLRRRSER 329


>gi|67920300|ref|ZP_00513820.1| Pseudouridine synthase, RluD [Crocosphaera watsonii WH 8501]
 gi|67857784|gb|EAM53023.1| Pseudouridine synthase, RluD [Crocosphaera watsonii WH 8501]
          Length = 313

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 150/328 (45%), Gaps = 36/328 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           + VEN  +  RLD W  N    I+   +QK++  G + ++ +       +++ G  +++ 
Sbjct: 5   LTVEN--QGDRLDIWLSNQLTDISRSRIQKLIEQGNITLNNEVCPNKKIKLKIGDRLQVN 62

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                          +     L    + +   +LYED ++ + NK A + V    G    
Sbjct: 63  ---------------IPEPQPLELQPEPIPLDILYEDEQLIIINKSANLVVHPAPGHETG 107

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             +   L    +  G    Q+P + HRLD++T+G +VVA+T  A Q+L    + R  ++ 
Sbjct: 108 TLVHALLYHCSNLAGIGGVQRPGIVHRLDKDTTGAIVVAKTDFAHQNLQFQIKNRTAKRE 167

Query: 183 YWSLVWGIPKNKKE------CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           Y  +++G+  N+++       + N  + +  +    + VV + EK    A++++++I+  
Sbjct: 168 YLGIIYGVLNNEEDENNRDKGMINLPIGRHPVDRKRMAVVPR-EKPGREAVTYWEIIERL 226

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  ++    TGRTHQ+RVH+ + G PIVGD  Y  N          +   LHA  + 
Sbjct: 227 G-NYSLVKFILETGRTHQIRVHSSYFGNPIVGDPLYSNNRSLKMN---LSGQALHAHKLT 282

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           L HP    +++  APLP   +K  + L 
Sbjct: 283 LTHPITSEKIEAIAPLPDEFIKLLNYLR 310


>gi|254496550|ref|ZP_05109419.1| hypothetical protein LDG_0200 [Legionella drancourtii LLAP12]
 gi|254354229|gb|EET12895.1| hypothetical protein LDG_0200 [Legionella drancourtii LLAP12]
          Length = 321

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 83/332 (25%), Positives = 142/332 (42%), Gaps = 30/332 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V  +  N R+D    +  P  +   +   ++SG V +++K  K  ++   G  + I
Sbjct: 7   KQLTVPREYHNQRIDSVLAHLLPDYSRSQISNWIKSGAVILNQKPCKPKDKALDGDQITI 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              +N  ++                  + +   +++ED ++ V NKPA + V  G+G   
Sbjct: 67  SVDLNLTDNNFD-----------HCAPEAIPLNVVFEDDELLVLNKPANMVVHPGAGNRE 115

Query: 128 HI--DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           H   +  L          +  + HRLD++T+G+LVVA+T  A   L    + R IQ+ Y 
Sbjct: 116 HTLVNALLHHAPSLHHLPRAGIIHRLDKDTTGLLVVAKTLTAHTSLIRQMQAREIQRHYV 175

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G        I     +        + V++Q       AI+H+ V     Q +  L+
Sbjct: 176 TLVQGHV-ISGGTIETGFGRHPR-NRLKMAVLEQ----GREAITHYTV-KKQYQDYTLLD 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    K    +  +         +  LHA  + 
Sbjct: 229 VKLMTGRTHQIRVHLTHINHPVVGDQLYGGRMKVPANASQELRTLIQEFKRQALHACSLA 288

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
             HP+    L  TAPLP       ++L   Y+
Sbjct: 289 FFHPKTEQELTFTAPLPDDFQLLLNTLDEHYE 320


>gi|148359833|ref|YP_001251040.1| ribosomal large subunit (23S rRNA) pseudouridine synthase C
           [Legionella pneumophila str. Corby]
 gi|296107879|ref|YP_003619580.1| ribosomal large subunit pseudouridine synthase C [Legionella
           pneumophila 2300/99 Alcoy]
 gi|148281606|gb|ABQ55694.1| ribosomal large subunit (23S rRNA) pseudouridine synthase C
           [Legionella pneumophila str. Corby]
 gi|295649781|gb|ADG25628.1| ribosomal large subunit pseudouridine synthase C [Legionella
           pneumophila 2300/99 Alcoy]
          Length = 315

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 109/324 (33%), Positives = 168/324 (51%), Gaps = 17/324 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V Y  + ++E   RLD +       +   ++ +I+R G+VR++KKR + N+R+Q G 
Sbjct: 1   MSEVSYKEIGSEENGQRLDNYLIRILKGVPKSHIYRIIRGGEVRINKKRAQANSRLQIGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+    +      K +  S NL K    LK  +++EDS + V NKPAGI+V GGS
Sbjct: 61  SIRIPPIRMTDS------KEIFVSDNLAKR---LKDSIIFEDSSLLVINKPAGIAVHGGS 111

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G++  +   L+           L HRLD+ETSG L++A+ R+  + +      R +QKIY
Sbjct: 112 GLSLGVIEALRKTRHDLSY-LELVHRLDRETSGCLLLAKKRSTLRAIQALLEAREVQKIY 170

Query: 184 WSLVWGIPKNKKE-CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           W+L+      KK+  I   L K +   G+ V  V   +K    + + FK+++ + Q  CW
Sbjct: 171 WALLTHRWDGKKKITITAPLEKNTLKSGERVVSV---QKDGKASETDFKLLENYHQ-ACW 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPE 301
           +E  P TGRTHQ+RVH+ + G  IVGD KY +           QN+LYLHAR +   +  
Sbjct: 227 VEASPKTGRTHQIRVHSAYFGHVIVGDGKYGSKVGEVEGIDYQQNRLYLHARSIQF-NLN 285

Query: 302 GGRLQITAPLPAHMVKTWDSLGFK 325
           G      A +      T   L  +
Sbjct: 286 GVMHVFQADVDDGFGNTLKQLRAR 309


>gi|194476821|ref|YP_002049000.1| Pseudouridine synthase, RluD [Paulinella chromatophora]
 gi|171191828|gb|ACB42790.1| Pseudouridine synthase, RluD [Paulinella chromatophora]
          Length = 315

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 95/318 (29%), Positives = 145/318 (45%), Gaps = 30/318 (9%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVIN 72
           +D   MRLDRW     P  +   +QK + +G VRV+  +      ++ G  V+I  P  +
Sbjct: 17  SDLVPMRLDRWLALKRPEQSRSRIQKFIYAGLVRVNGIKSSTKTPLRQGDQVQIWMPPPD 76

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HID 130
            L ++I +   LD               +L+ED  + V NKPA ++V    G  Y   ++
Sbjct: 77  LLPYLIPQHIPLD---------------ILFEDQYLIVVNKPADLTVHPAPGNKYGTLVN 121

Query: 131 GFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           G L    D  G     +P + HRLD+ T+G +V+A+T+     L    + R + + Y  +
Sbjct: 122 GLLFHCSDLMGIGGEMRPGVVHRLDKSTTGCIVIAKTKEILAALQLQIQNRVVSREYIGI 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+P   K  I   L +  H      + V  NEKG  YA +H+ +I+ +   +  L  +
Sbjct: 182 VHGVPATNKGTIIGKLGR--HPVNRKRYAVLVNEKG-RYACTHWCLIERWGD-YSLLRFK 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRL 305
             TGRTHQ+R+H  H+G PI+GD  Y    +        N   LHA  +   HP    R+
Sbjct: 238 LDTGRTHQIRIHCSHIGYPIIGDQYYSKQRRLPLA---FNGQALHAVELSFNHPVNSDRM 294

Query: 306 QITAPLPAHMVKTWDSLG 323
              APLP    K   S  
Sbjct: 295 VFHAPLPKIFEKLLTSFR 312


>gi|149916264|ref|ZP_01904785.1| NAD(P) transhydrogenase subunit alpha [Roseobacter sp. AzwK-3b]
 gi|149809924|gb|EDM69775.1| NAD(P) transhydrogenase subunit alpha [Roseobacter sp. AzwK-3b]
          Length = 348

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 89/344 (25%), Positives = 141/344 (40%), Gaps = 50/344 (14%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L +++  G V V+   V    +RI  G  + I        
Sbjct: 17  RLDKALSRDVPEDAALSRTRLARLIAEGAVSVNGTPVTDPKSRISEGDSIAITVPQAQDT 76

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
           HI  E   LD               +++ED  + V +KPAG+ V    G      ++  L
Sbjct: 77  HIAAESIPLD---------------IVFEDDDLIVIDKPAGMVVHPAPGSPGGTLVNALL 121

Query: 134 KSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               D+       ++P + HR+D++TSG+LVVA++  A   L   F    +++ Y ++V+
Sbjct: 122 HHCGDTLSGVGGMKRPGIVHRIDKDTSGLLVVAKSDRAHHGLAAQFEDHSVERYYRAVVY 181

Query: 189 GIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCF 236
           G+P      +           N +   S +        KQ    +G  +A++  +V+D F
Sbjct: 182 GVPDAADPRLRGLRGVSFETGNIIKITSGLARHRTDRQKQAVTFEGGRHAVTRARVVDTF 241

Query: 237 AQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------- 285
            Q      +E    TGRTHQ+RVH  H G  +VGD  Y    K    +  +         
Sbjct: 242 GQPPVAALMECWLETGRTHQIRVHMAHAGHGLVGDPVYGGRRKLPLRALSEAGLKAARDF 301

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
            +  LHA  +   HP  G  L+  APLP  M    D+L     R
Sbjct: 302 PRQALHAAVLGFVHPVSGEALEFEAPLPDDMTALIDALRATPSR 345


>gi|261856619|ref|YP_003263902.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261837088|gb|ACX96855.1| pseudouridine synthase, RluA family [Halothiobacillus neapolitanus
           c2]
          Length = 340

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 84/345 (24%), Positives = 154/345 (44%), Gaps = 41/345 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + +++  +    RLD+     +P  +   +Q  ++SG++ +D +  +    +  G+
Sbjct: 1   MHLEETLLIPPECAGQRLDQALAKCWPDYSRSRIQDWIKSGEILLDGEVARPRATVLGGE 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +   I      + +   LD               ++YED  I V NK   I V   +
Sbjct: 61  SVELLAEIEEAVAAVPQDIPLD---------------IIYEDDAIIVLNKSPDIVVHPAA 105

Query: 124 GIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   + DG L + +           +  + HRLD++TSG++VVA+T AA + L E+   R
Sbjct: 106 G---NPDGTLVNALLFHDPSLVSVPRAGVVHRLDKQTSGVMVVAKTLAAHKILVENLAAR 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +I++ Y ++V G        +   + +            +        A++H++V+  + 
Sbjct: 163 KIRREYDTVVMGHVVA-GGTVDAPIGRHPRD-----RQRQAVTATGKRAVTHYRVLQHYG 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLY 289
           ++  WL +Q  TGRTHQ+RVH  H+  P++GD  Y    +    +            +  
Sbjct: 217 EQ-TWLRVQLETGRTHQIRVHMAHIRHPVIGDPVYGGRPRIPPRASTALIDVLRHFERQA 275

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
           LHARY+ L HP  G +++  AP+P  M +    L  +Y  NL+ +
Sbjct: 276 LHARYLTLAHPVTGTQMRFEAPMPDDMRELIALLT-EYRDNLHRR 319


>gi|170756442|ref|YP_001781114.1| RluA family pseudouridine synthase [Clostridium botulinum B1 str.
           Okra]
 gi|169121654|gb|ACA45490.1| pseudouridine synthase, RluA family [Clostridium botulinum B1 str.
           Okra]
          Length = 305

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 87/326 (26%), Positives = 151/326 (46%), Gaps = 33/326 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +  + VE + +N+RLD +    +   +   LQ I+  G V V+ K+ K N +++ G 
Sbjct: 1   MEKI-SLQVEKEFDNVRLDLYLSKIFEDKSRSYLQGIIDQGSVLVNNKKKKRNYKLKVGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +K  ++YED  + V NKP  + V    
Sbjct: 60  NIEVN---------------IPEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAP 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G+     ++  L    D  G     +P + HR+D++TSGILVVA+   +  +L   F+  
Sbjct: 105 GVYSGTLVNALLHHCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I ++Y +LV GI K+++  I   + +   +    + VV    K   +A++H+KVI+ F 
Sbjct: 165 SISRVYMALVEGIIKDEQGTIEAPIGRH-PVDRIKMAVV----KDGRHAVTHYKVIERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    +E +  TGRTHQ+RVH  H+  P+VGD  Y    +            LHA+ +  
Sbjct: 219 KNHTLVECRLETGRTHQIRVHMSHIMHPLVGDPVYGYKKQ----RFNLKGQMLHAKLLGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP   + ++  + LP +  K    L
Sbjct: 275 IHPTTEQYVEFESELPEYFKKIIKIL 300


>gi|294634724|ref|ZP_06713255.1| ribosomal large subunit pseudouridine synthase D [Edwardsiella
           tarda ATCC 23685]
 gi|291091854|gb|EFE24415.1| ribosomal large subunit pseudouridine synthase D [Edwardsiella
           tarda ATCC 23685]
          Length = 326

 Score =  249 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 82/345 (23%), Positives = 149/345 (43%), Gaps = 43/345 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V V+   + K   ++  G+ + I
Sbjct: 8   TATVTESQLGQRLDQALAELFPDYSRSRIKEWILEDRVSVNGIIINKPKEKVLGGEHIAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +I   N    +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  DALIEEENRWEAQDIALD---------------IVYEDEDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPQIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        +E IA    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGTMTAGGTVREPIARHPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RAHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHINHPLVGDQLYGGRPRPPRDASPEFIQTLRAFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            + L HP  G  ++  AP+P  M +    +  + D   +   +  
Sbjct: 283 MLRLYHPISGIEMEWHAPIPEDMQRLIAVM--QEDAETFKDEMDW 325


>gi|290476241|ref|YP_003469141.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Xenorhabdus bovienii SS-2004]
 gi|289175574|emb|CBJ82377.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Xenorhabdus bovienii SS-2004]
          Length = 325

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 81/343 (23%), Positives = 150/343 (43%), Gaps = 43/343 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +   +   +++ +   +V+V+ K + K   ++  G+V+ I  
Sbjct: 10  TVAETQLGQRLDQALAELFSDYSRSRIKEWILDNKVQVNGKLINKPKEKVLGGEVISIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +I                         ++  ++YED  I V NKP  + V  G+G     
Sbjct: 70  IIEEDARW---------------EPQDIELNIVYEDDDILVINKPRDLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   +   +  + HRLD++T+G++V+A+T  A   L ES ++R I + Y ++
Sbjct: 115 VLNALLYRYPAIADVPRAGIVHRLDKDTTGLMVIAKTVPAQTRLVESLQLREITREYEAI 174

Query: 187 VWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             G        +E I+    K++H+    +            A++H++V++ F +    L
Sbjct: 175 ALGCMTAGGMVEEPISRHPTKRTHMAVHPM---------GKSAVTHYRVMEHF-RAHTRL 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYM 295
            ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA  +
Sbjct: 225 RLRLETGRTHQIRVHMAHIKHPLVGDPLYGGRPRPLKGASDEFREVMRNFDRQALHATML 284

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            L HP  G  ++  A LP  MVK  D +  K D   +   +  
Sbjct: 285 RLYHPISGIEMEWHAELPDDMVKLIDVM--KADAETFKDEMDW 325


>gi|16761516|ref|NP_457133.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|16765978|ref|NP_461593.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|29142987|ref|NP_806329.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|62181235|ref|YP_217652.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|167553892|ref|ZP_02347635.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|167992440|ref|ZP_02573538.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|168234182|ref|ZP_02659240.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|168239430|ref|ZP_02664488.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           SL480]
 gi|168244683|ref|ZP_02669615.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|168262167|ref|ZP_02684140.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|168464166|ref|ZP_02698083.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|168822474|ref|ZP_02834474.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|194446496|ref|YP_002041926.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194447791|ref|YP_002046668.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194471474|ref|ZP_03077458.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194737121|ref|YP_002115673.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197247406|ref|YP_002147565.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197262464|ref|ZP_03162538.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197363556|ref|YP_002143193.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|198242257|ref|YP_002216673.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200389193|ref|ZP_03215805.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|204929503|ref|ZP_03220577.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|207858012|ref|YP_002244663.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|213051815|ref|ZP_03344693.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213424875|ref|ZP_03357625.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
 gi|213585773|ref|ZP_03367599.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213619387|ref|ZP_03373213.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
 gi|213646598|ref|ZP_03376651.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213850144|ref|ZP_03381042.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|224584515|ref|YP_002638313.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|238909508|ref|ZP_04653345.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|289824162|ref|ZP_06543757.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|54039251|sp|P65837|RLUD_SALTI RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|54041742|sp|P65836|RLUD_SALTY RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|25322403|pir||AC0832 pseudouridylate synthase (EC 4.2.1.70) - Salmonella enterica subsp.
           enterica serovar Typhi (strain CT18)
 gi|16421209|gb|AAL21552.1| pseudouridine synthase [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
 gi|16503817|emb|CAD05842.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29138619|gb|AAO70189.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|62128868|gb|AAX66571.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Salmonella enterica subsp. enterica serovar
           Choleraesuis str. SC-B67]
 gi|194405159|gb|ACF65381.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194406095|gb|ACF66314.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|194457838|gb|EDX46677.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194712623|gb|ACF91844.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|195633435|gb|EDX51849.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197095033|emb|CAR60579.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|197211109|gb|ACH48506.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
 gi|197240719|gb|EDY23339.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197287851|gb|EDY27239.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           SL480]
 gi|197936773|gb|ACH74106.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|199606291|gb|EDZ04836.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|204321222|gb|EDZ06422.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205321769|gb|EDZ09608.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|205329256|gb|EDZ16020.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|205331842|gb|EDZ18606.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|205336483|gb|EDZ23247.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|205341144|gb|EDZ27908.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|205349079|gb|EDZ35710.1| ribosomal large subunit pseudouridine synthase D [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|206709815|emb|CAR34167.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|224469042|gb|ACN46872.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|261247856|emb|CBG25685.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267994803|gb|ACY89688.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301159209|emb|CBW18724.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312913652|dbj|BAJ37626.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320087095|emb|CBY96863.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
 gi|322614488|gb|EFY11419.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322621447|gb|EFY18300.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322624308|gb|EFY21141.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322629393|gb|EFY26171.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322633633|gb|EFY30375.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322638324|gb|EFY35022.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322639762|gb|EFY36445.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322647376|gb|EFY43872.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322650454|gb|EFY46864.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322656053|gb|EFY52353.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322661447|gb|EFY57672.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322662647|gb|EFY58855.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322667020|gb|EFY63195.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322671389|gb|EFY67512.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322677604|gb|EFY73667.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322681570|gb|EFY77600.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322683970|gb|EFY79980.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|322715721|gb|EFZ07292.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323130996|gb|ADX18426.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323195539|gb|EFZ80717.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323197912|gb|EFZ83035.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323203090|gb|EFZ88122.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323205331|gb|EFZ90306.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323210519|gb|EFZ95403.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323218200|gb|EGA02912.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323221534|gb|EGA05947.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323223754|gb|EGA08059.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323230963|gb|EGA15081.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323234685|gb|EGA18771.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323238724|gb|EGA22774.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323241423|gb|EGA25454.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323246879|gb|EGA30846.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323253278|gb|EGA37108.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323257074|gb|EGA40783.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323260453|gb|EGA44064.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323264490|gb|EGA47996.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323269625|gb|EGA53078.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326624429|gb|EGE30774.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332989587|gb|AEF08570.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 326

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 80/335 (23%), Positives = 149/335 (44%), Gaps = 41/335 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ + + +V V+ +   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I+                 +   +  +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  DAEIDE---------------EIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVNEPISRHPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            + L HP  G  ++  AP+P  MV   D++   ++
Sbjct: 283 MLRLYHPVSGIEMEWHAPIPQDMVDLIDAMRADFE 317


>gi|190575132|ref|YP_001972977.1| putative ribosomal large subunit pseudouridine synthase C
           [Stenotrophomonas maltophilia K279a]
 gi|190013054|emb|CAQ46686.1| putative ribosomal large subunit pseudouridine synthase C
           [Stenotrophomonas maltophilia K279a]
          Length = 324

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 95/323 (29%), Positives = 154/323 (47%), Gaps = 20/323 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   ++++G  VR
Sbjct: 16  VRMITVPADRAGQRLDNFLLGQLKGAPRSLVYKLVRSGQVRVNGGRAKAERKLEAGDEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP       + +E   +       +    L+  +++ED+++   NKP G++  GGSGI+
Sbjct: 76  VPP-----VRLTEEGDKVGPPEAFMRR---LEQAIVFEDARLLALNKPTGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR---IQKIY 183
           +     L++     GQ   L HRLD++TSG+L+VA+ R+A   L    R      I+K Y
Sbjct: 128 FGAIETLRALRP--GQTLELVHRLDRDTSGLLIVAKKRSALSELQALLREDHGAGIRKRY 185

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L+ G   +    +   L      GG+    V         +ISHF+V++       + 
Sbjct: 186 LTLLAGRMPDGVMTVDAPLHVGLRQGGERHVQVNAI---GKESISHFRVLERRG-GHSYC 241

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPE 301
           E++  TGRTHQ+RVHA H+G P+ GD KY                +L+LHA  ++    +
Sbjct: 242 EVRIETGRTHQIRVHAQHLGHPVAGDDKYGDPAVNKRLREQIGLKRLFLHAASLEFALDD 301

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
           G     + APL   +V+  D L 
Sbjct: 302 GKSPYVLNAPLADELVEALDRLR 324


>gi|144897894|emb|CAM74758.1| ribosomal large subunit pseudouridine synthase D [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 327

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 83/332 (25%), Positives = 140/332 (42%), Gaps = 42/332 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQ--VVRIP 68
           V  DE   RLD+W     P ++   ++ ++   +V    + +   + R++ GQ  VV IP
Sbjct: 14  VTTDEAGSRLDKWLSARLPDLSRTRIKGLIDDSRVSAAGQTITDASARVKPGQCFVVAIP 73

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P   A                       +   + YED  + V +KP G+ V    G   H
Sbjct: 74  PERPA-----------------DPLPQAMDLSVAYEDDDLIVIDKPPGLVVHPAPGSPDH 116

Query: 129 I--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              +  L    +S       ++P + HR+D++TSG+LVVA+   A   L E F +  +++
Sbjct: 117 TLVNALLAHCGESLSGIGGVKRPGIVHRIDKDTSGLLVVAKNDRAHHGLAEQFSVHSLER 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF- 240
            Y +LVWG+P   +  I   + + S      + +V     G   A++ ++V+  FA    
Sbjct: 177 AYRALVWGVPMPAQGEIHGNIGR-SPQDRKKMAIVSH---GGKPALTRYRVLRSFAGGAV 232

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---------KGNFTSPIQNKLYLH 291
             +E +  TGRTHQ+RVH   +G P+VGD  Y             +         +  LH
Sbjct: 233 SLVECRLATGRTHQIRVHMTSIGHPLVGDQTYGRARSTKVKHLPDQARLALLEFPRQALH 292

Query: 292 ARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           A  +   HP  G + +  + +P    +    L
Sbjct: 293 ASVLGFIHPNSGVMLKFESQIPDDFNELVSLL 324


>gi|126700216|ref|YP_001089113.1| putative pseudouridylate synthase [Clostridium difficile 630]
 gi|115251653|emb|CAJ69486.1| putative pseudouridylate synthase, RluC/RluD family [Clostridium
           difficile]
          Length = 303

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 144/327 (44%), Gaps = 33/327 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+  +V  +EE +RLD +       ++   +QKI++ G+V+V+ K  K    ++   
Sbjct: 1   MDEVKEFLVLEEEEEVRLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKVEKARYLVKEED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I          I E K+L+           +   ++YED  + + NKP  + V    
Sbjct: 61  NIVIE---------IPEPKVLEV------LPQDIPIDIVYEDDDVLIINKPQDMVVHPAP 105

Query: 124 GIAYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G   +   +G L    D         +P + HR+D++TSG+L++A+   A   L E  + 
Sbjct: 106 GNYENTLVNGILYHCKDKLSSINGVIRPGIVHRIDKDTSGLLMIAKNNYAHNFLAEQLKE 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y  + +G+ K  K  +   + +          V     K    AI+HF+V++ F
Sbjct: 166 HTITREYEFICYGVVKEDKITVDKPIGRNPKDRLKMAVV-----KDGKNAITHFEVVERF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
             KF  +  +  TGRTHQ+RVHAL +  P++GD+ Y        T        LHA+ + 
Sbjct: 221 -DKFTHMRARLETGRTHQIRVHALSINHPLLGDYVYGPKE----TKFKLKGQTLHAKKLG 275

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP     ++  + LP +  +    +
Sbjct: 276 FIHPTTKEYIEFNSELPEYFKEVIKKI 302


>gi|309972703|gb|ADO95904.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae R2846]
          Length = 324

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 72/328 (21%), Positives = 144/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   S+  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPISEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|51246582|ref|YP_066466.1| ribosomal large subunit pseudouridine synthase D [Desulfotalea
           psychrophila LSv54]
 gi|50877619|emb|CAG37459.1| related to ribosomal large subunit pseudouridine synthase D
           [Desulfotalea psychrophila LSv54]
          Length = 327

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 87/324 (26%), Positives = 151/324 (46%), Gaps = 33/324 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++   RLD++     P ++   +    +   V VD +  K + R++ G+ V      
Sbjct: 23  VSYNQRGTRLDQFLAFSLPDVSRALITLSNKKELVLVDDEVKKSSYRLKEGETVTC---- 78

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HI 129
                       L  +  L+     +    +YED  + V +KP GI V  G+G      +
Sbjct: 79  -----------ALWQAPPLSLEPQQVDFESIYEDDSLLVLSKPPGIVVHPGNGNTEGTLV 127

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            G L    +  G     +P + HRLD++TSG +VVA+   + + L +SF+ R++ K+Y +
Sbjct: 128 HGLLYHCREIGGVGDAIRPGIVHRLDKDTSGAMVVAKDERSLRTLVDSFKERQVYKVYHA 187

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQKFCW 242
           LV GIPK  +  I   + + S +    + +   +E+   +A ++++V++        +  
Sbjct: 188 LVCGIPKKYEGRIVAPIGRHS-VHRQKMAI---SERTGKFAATNWQVVEVFETKDGPYSL 243

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L +   TGRTHQ+RVH   +GCPI GD  Y +  +     P   +  LHA  + LPHP  
Sbjct: 244 LRVHIETGRTHQIRVHMSSIGCPIAGDQVYGSKRQN----PAFARQMLHASRLRLPHPVT 299

Query: 303 GR-LQITAPLPAHMVKTWDSLGFK 325
           GR +  TAPL     +  + + + 
Sbjct: 300 GRTMSFTAPLWQDFQEVLEDMDWS 323


>gi|170752009|ref|YP_001758269.1| RluA family pseudouridine synthase [Methylobacterium radiotolerans
           JCM 2831]
 gi|170658531|gb|ACB27586.1| pseudouridine synthase, RluA family [Methylobacterium radiotolerans
           JCM 2831]
          Length = 334

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 84/337 (24%), Positives = 147/337 (43%), Gaps = 47/337 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINAL 74
           E  +RLDR     +P ++   LQ ++R+GQV+ D       + ++ +G  + +     A 
Sbjct: 15  EGGVRLDRALVALFPDLSRARLQDLIRTGQVQRDGLPALDPSGKVAAGAHIVLRVPPAAP 74

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
              + E   L                ++YED  + V +KPAG+ V    G   H  G L 
Sbjct: 75  AEPVAEAADLP---------------IVYEDDDLIVIDKPAGLVVHPAPG---HESGTLV 116

Query: 135 SWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR----IQ 180
           + + +            ++P + HRLD++TSG++VVA+   A Q LT  F        ++
Sbjct: 117 NALIAHCGASLSGIGGVRRPGIVHRLDKDTSGLIVVAKNDTAHQGLTAQFADHGRSGPLE 176

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++VWG+P+ +   I   L +          +   ++    +A++H+ V + + +  
Sbjct: 177 RAYAAVVWGLPQPRAGTIQANLARSRF---HREKIAVVSDASGRHAVTHYAVAEAYGE-A 232

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFTSPIQNKLYLH 291
             +  +  TGRTHQ+RVH  H G P++GD  Y   F+                  +  LH
Sbjct: 233 ALVRCRLETGRTHQIRVHLAHRGHPLLGDTVYGGAFRTKAARLSSEARAALTALGRQALH 292

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
           A  +   HP  G  L+  +PLP  M     +L  + +
Sbjct: 293 AELLGFSHPRTGTTLRFESPLPPDMTALVQALRAEEN 329


>gi|134301269|ref|YP_001121237.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis WY96-3418]
 gi|134049046|gb|ABO46117.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis WY96-3418]
          Length = 309

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 99/320 (30%), Positives = 164/320 (51%), Gaps = 13/320 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIEVTEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G    K   I   L  K     D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHGHWDKKIIKIDLPL--KRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP-HPE 301
           E++  TGRTHQ+RVH   MG PIV D KY  A           ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVKTWDS 321
             ++ +TA L +   K    
Sbjct: 290 NKQISVTAALDSRFEKFIQE 309


>gi|325577679|ref|ZP_08147954.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325160424|gb|EGC72550.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 324

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 76/337 (22%), Positives = 147/337 (43%), Gaps = 36/337 (10%)

Query: 4   MTYVQYV-VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQS 61
           M  +     ++ ++   RLD+     +P  +   L+  + + QV+++ +       ++  
Sbjct: 1   MPQITLTAEIQPEQMGQRLDQTLAELFPEYSRSRLKTWIEAKQVKMNGEIADIPRAKVYG 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G+ + I   +   N                     +   ++YED  I V NKP  + V  
Sbjct: 61  GEQIEISVEVEDENRF---------------EPQNIPLNIVYEDDDIIVINKPKDLVVHP 105

Query: 122 GSGIAYHI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G+G       +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R+
Sbjct: 106 GAGNPDGTVLNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRK 165

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y ++  GI   K   +   + + +         +         A++H+++++ F +
Sbjct: 166 ITREYEAVASGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENF-R 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQN--KLYL 290
            +  L ++  TGRTHQ+RVH  H+  P++GD  Y    +        FT  ++N  +  L
Sbjct: 219 NYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASKAFTEVLRNFKRQAL 278

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HA  + L HP  G  ++  APLP   V+   +L   Y
Sbjct: 279 HAVMLRLAHPITGEMMEWYAPLPDDFVELLHALKADY 315


>gi|325129115|gb|EGC51964.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis N1568]
          Length = 330

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 95/322 (29%), Positives = 154/322 (47%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +              +YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFEA---------VYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  +      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSAD---GQSAHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L + A LP  + +
Sbjct: 298 LNHPLTGEPLVLKAELPLDLAQ 319


>gi|215919036|ref|YP_338280.2| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           RSA 493]
 gi|206583921|gb|AAZ22628.2| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           RSA 493]
          Length = 327

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 88/331 (26%), Positives = 151/331 (45%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   +++  Q + I  
Sbjct: 15  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEA 74

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 75  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 119

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y ++
Sbjct: 120 LINALLHYDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAI 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+            + +  I    + VV    +    AI+HF++I  + +    + +Q
Sbjct: 180 VKGVLI--SGRTIEAPVGRHPIHRTRMAVV----EFGRPAITHFRIIKRY-RAHTHIRVQ 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQ------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+ GD  Y +      + + P+Q       +  LHA  +   
Sbjct: 233 LETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHAATLQFS 292

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           HP   R +   APLPA M    + L   Y +
Sbjct: 293 HPVDQRPMACHAPLPADMAHLLECLEDDYSQ 323


>gi|332184383|gb|AEE26637.1| Ribosomal large subunit pseudouridine synthase D [Francisella cf.
           novicida 3523]
          Length = 331

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 75/317 (23%), Positives = 136/317 (42%), Gaps = 28/317 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K    +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDIAINEQFEQFSRAQIQKWLKEGSIIVNGQATKPKYIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E                +K  ++YED  I V +KP  + V  G+G   
Sbjct: 72  NVELLPTNEWIAED---------------IKLNIIYEDDDIIVIDKPVNMVVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + D  K  +  + HRLD++TSG++V A++  A  +L +    R++ + Y 
Sbjct: 117 GTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + + S      + +  +       AI+H+  I+ +   F  LE
Sbjct: 177 AIVEGEIY-QQGTINQPIGRDS-TNRTKMAINHR----GKEAITHYTPIEVY-DGFTLLE 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            Q  TGRTHQ+RVH   +  P+VGD  Y   +            +  LHA  +   HP+ 
Sbjct: 230 CQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITTPTRQALHAYKLSFIHPKT 289

Query: 303 GRL-QITAPLPAHMVKT 318
            ++ +  + LP  M+  
Sbjct: 290 AKIVKFKSKLPEDMLNL 306


>gi|313201079|ref|YP_004039737.1| RluA family pseudouridine synthase [Methylovorus sp. MP688]
 gi|312440395|gb|ADQ84501.1| pseudouridine synthase, RluA family [Methylovorus sp. MP688]
          Length = 312

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 99/315 (31%), Positives = 157/315 (49%), Gaps = 16/315 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+      R+D +       +   ++ +ILRSG+VRV+ KR+    R+Q G +VR+PP
Sbjct: 2   LTVDEGSAGQRIDNFLTKTLKGVPKSHVYRILRSGEVRVNSKRIDATYRLQLGDLVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +      + +E + +         +   +  +++ED  + V +KPAG +V GGSG++  +
Sbjct: 62  IRVQPQPVAEESRPV---------AARFEEAVIFEDEAMLVIDKPAGFAVHGGSGVSRGV 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+       +   L HRLD+ETSG+L+VA+ R+A   L E+ R   + K Y  LV G
Sbjct: 113 IEQLR-LERPHAKFLELVHRLDRETSGVLMVAKKRSALVGLHEAMRANHMDKRYLMLVSG 171

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             K KK+ +   L K     G+    V   E+    + + F +   + + F  LE Q  T
Sbjct: 172 DWKEKKKRVVLALQKHVTANGERKVTV---EEEGQNSETIFHLKKSYGE-FTLLEAQLIT 227

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           GRTHQLRV   H+G PI GD KY               +++LH+    + HP  G +L++
Sbjct: 228 GRTHQLRVQLAHLGFPIAGDDKYGDFALNKALQKRGLKRMFLHSAETGIRHPLSGDKLKL 287

Query: 308 TAPLPAHMVKTWDSL 322
            APLPA +     SL
Sbjct: 288 IAPLPAALQAFLTSL 302


>gi|290968210|ref|ZP_06559753.1| pseudouridine synthase, RluA family [Megasphaera genomosp. type_1
           str. 28L]
 gi|290781692|gb|EFD94277.1| pseudouridine synthase, RluA family [Megasphaera genomosp. type_1
           str. 28L]
          Length = 305

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 82/321 (25%), Positives = 136/321 (42%), Gaps = 37/321 (11%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
              +E +RLD +       ++    Q +++ G VRV     K N R++ GQ + +    +
Sbjct: 9   TPADEGVRLDVYVARMLS-VSRTYAQDLIKKGLVRVQDNMGKANCRLEDGQCITVSFSPS 67

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-------- 124
           A+               L+   + +   +LYED+ I V NK  G+ V    G        
Sbjct: 68  AV---------------LSAEPENIPLHILYEDAHIIVVNKARGMVVHPAPGNPSGTLVN 112

Query: 125 -IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + YH  G L     +   +P + HRLD++TSG++VVA+T  A + L    +     + Y
Sbjct: 113 ALLYHCGGELSGI--NGVIRPGIVHRLDKDTSGVMVVAKTDPAHRGLAAQIKAHTAHRTY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G    ++  I   + +           +    KG   A +HF V+  + + + WL
Sbjct: 171 WALVHGNIAEERGTIEAPIGRHPKDRIK----MAVTFKGGREATTHFHVLQRYGE-YTWL 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +  TGRTHQ+RVH  ++  P+V D  Y                 LH+R +D  HP  G
Sbjct: 226 ACRLETGRTHQIRVHLAYIRHPVVNDPVYGYKRD----DFPIQGQVLHSRCLDFVHPVTG 281

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             + + AP  A      + + 
Sbjct: 282 EPMHVEAPPAADFSACLERIR 302


>gi|283780614|ref|YP_003371369.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
 gi|283439067|gb|ADB17509.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
          Length = 355

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 90/335 (26%), Positives = 151/335 (45%), Gaps = 41/335 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN--NRIQSGQVVR 66
            +VVE  E + RLD++        + + L++++ +G V ++  R K     R+ +G  V 
Sbjct: 38  ELVVEEREADGRLDQFLALRLHRYSRMQLRRVIDAGGVLLNGSRAKVKVAYRVSTGDRVS 97

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I               +L    +   + + +   +L+ED  +   NKP G+ V    G  
Sbjct: 98  I---------------VLPEMPSAGPNPEKIPLDILFEDEHLIAVNKPPGMVVHPARG-- 140

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            H  G L S +    Q         +P + HRLD++TSG+++VA+T      L   F  R
Sbjct: 141 -HWSGTLTSALAFHFQQLSTVGGQHRPGIVHRLDRDTSGVIIVAKTDPVHFSLAAQFADR 199

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              K Y+++  G+P   ++ ++  +    H        ++     +  A + F V++ FA
Sbjct: 200 TTAKEYFAITAGVPDRDRDVVSQPIGI--HPFHREKMAIRPGHSTSRDAETMFHVLERFA 257

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--------FKGNFTSPIQNKLY 289
           Q    +E  P TGRTHQ+RVH  H+  P++ D  Y            +   T  + N+  
Sbjct: 258 QHAA-VECLPKTGRTHQIRVHLAHVRTPVLCDKLYGGRAEITQGELVRDGSTEVVLNRQA 316

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           LHAR + + HP+ G RL I APLPA + +  D L 
Sbjct: 317 LHARKLSINHPKTGERLTIEAPLPADLQRVLDLLR 351


>gi|89075039|ref|ZP_01161480.1| putative ribosomal large subunit pseudouridine synthase D
           [Photobacterium sp. SKA34]
 gi|89049126|gb|EAR54691.1| putative ribosomal large subunit pseudouridine synthase D
           [Photobacterium sp. SKA34]
          Length = 324

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 88/332 (26%), Positives = 145/332 (43%), Gaps = 35/332 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++  MRLD+     YP  +   ++  + +G V V+   V K   ++  G+ + I  
Sbjct: 10  TVGENQLGMRLDQVIAQLYPDYSRSRIKDWILNGMVSVNGDVVKKPREKMMGGEELFIQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I      + +   LD               ++YED  I V NKP    V  G+G     
Sbjct: 70  EIEDEVRWVAQDIPLD---------------IVYEDDDILVINKPRDFVVHPGAGTPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           I   L  +  S  + PR  + HRLD++T+G++VVA+T  A   L  + + R+I + Y +L
Sbjct: 115 ILNALLHYCPSLAEVPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEAL 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        I   + + S        +     +    AI+H++V + F ++   + ++
Sbjct: 175 AIGQMTG-GGTIEKPIGRHST-----KRICMAVHEMGKDAITHYRVAERF-REHTRIVLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  +M  P++GD  Y    +    +  +        ++  LHAR + L 
Sbjct: 228 LETGRTHQIRVHMSYMSHPLIGDVIYGGRPRPPRDASPEFIQALRAFDRQALHARMLRLD 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           HP  G  ++  APLP  MV   D L      N
Sbjct: 288 HPITGEKMEWHAPLPIDMVAMIDILRKDTQEN 319


>gi|68248781|ref|YP_247893.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae 86-028NP]
 gi|145635280|ref|ZP_01790983.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           influenzae PittAA]
 gi|68056980|gb|AAX87233.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           influenzae 86-028NP]
 gi|145267424|gb|EDK07425.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           influenzae PittAA]
          Length = 324

 Score =  249 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 72/328 (21%), Positives = 144/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVFGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   S+  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPISEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEIMEWYAPLPDDFVELLNALKADY 315


>gi|148825561|ref|YP_001290314.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae PittEE]
 gi|148715721|gb|ABQ97931.1| SfhB [Haemophilus influenzae PittEE]
          Length = 324

 Score =  249 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 144/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMDRHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|167855786|ref|ZP_02478539.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           parasuis 29755]
 gi|167853065|gb|EDS24326.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           parasuis 29755]
          Length = 325

 Score =  249 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 144/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V +D    RLD+     +P  +   ++  + S  V V+ K V K   ++  G+++ I   
Sbjct: 11  VTSDLLGARLDQALAQLFPDYSRSRIKVWIESDLVSVNGKIVNKAREKVFGGELIEIQAE 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           I                         +   ++YED  I V NKP  + V  G+G      
Sbjct: 71  IEEEIRF---------------EPQNIPLNIVYEDDDILVINKPKDLVVHPGAGNPDGTV 115

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   ++  +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++ 
Sbjct: 116 LNALLHHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVTALQKREITREYEAVA 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   +   +   + +                     A++H+++++ F + +  L ++ 
Sbjct: 176 SGIM-TQGGKVDEPMARHPT-----KRTAMAVHPMGKPAVTHYRIMERF-RNYTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +      G F   ++N  +  LHA  + L H
Sbjct: 229 ETGRTHQIRVHMAHIAHPLLGDQLYGGRPRPPKGASGEFLEVLRNFKRQALHATMLRLHH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 289 PITGELMEWHAPLPDDFVELIEALKADY 316


>gi|209965021|ref|YP_002297936.1| ribosomal large subunit pseudouridine synthase D, putative
           [Rhodospirillum centenum SW]
 gi|209958487|gb|ACI99123.1| ribosomal large subunit pseudouridine synthase D, putative
           [Rhodospirillum centenum SW]
          Length = 364

 Score =  249 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 81/335 (24%), Positives = 143/335 (42%), Gaps = 39/335 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHY--PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
             V V       RLD+   +      ++   L+ ++  G V    + +   + R++ GQ+
Sbjct: 46  HQVEVAAGRAGDRLDKVLSDALGGAGLSRSRLRSLIDQGCVSSGGETIDDASRRVKPGQI 105

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V +               ++ ++         +   +++ED  + V +K A + V   +G
Sbjct: 106 VEV---------------LVPAAEPAVPLPQAIPLAIVHEDEDLLVIDKAAEMVVHPAAG 150

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  L    D        ++P + HRLD+ TSG+LV A+T  A Q LT  F  R
Sbjct: 151 NPDGTLVNALLAHCGDRLSGIGGVRRPGIVHRLDKGTSGLLVAAKTDRAHQGLTAQFADR 210

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++VWG+P  ++  I   + +        + V+    +G   A++ ++V+  F 
Sbjct: 211 SLSRTYLAVVWGVPAAREGVIEGNIGRHPG-DRKRMAVL---SRGGKPAVTRYRVVRSFG 266

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQN------KL 288
                +E +  TGRTHQ+RVH  H+G P+VGD  Y       KG    P+        + 
Sbjct: 267 LLASLVECKLLTGRTHQIRVHMAHVGHPLVGDPLYGRLRPPRKGTAPEPVLRALAGFPRQ 326

Query: 289 YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            LHA  ++  HP    +L  TA LP  +      L
Sbjct: 327 ALHAAALEFRHPASDLKLGFTAALPEDLAGLIQGL 361


>gi|326565266|gb|EGE15451.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis 12P80B1]
          Length = 355

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 145/322 (45%), Gaps = 30/322 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  ++  +RLD+   + +   +  NL+  +  GQ+ V+ K VK    ++ G ++ +  V 
Sbjct: 48  VSTEQIGIRLDKLCADIFGGFSRANLKNFIDEGQLMVNGKVVKPKYAVKVGDILTLEAVH 107

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
            + +  + E   +D               ++YED  + + NKPAG+ V  G+G      +
Sbjct: 108 ESHSEDLPENIDID---------------IIYEDEAVIIINKPAGMVVHPGAGNRTGTLV 152

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L  +       +  L HR+D++T+G+LV+ART++A   L +  + + + + Y  +  
Sbjct: 153 NALLYHFPKQAHLPRAGLVHRIDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIAL 212

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQP 247
           G        +       + IG    H  K   K     A++H        +++  L++  
Sbjct: 213 GAVHE----VLRHAQIDAPIGRHSTHRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHL 268

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPE 301
            TGRTHQ+RVH  ++G P+VGD  Y  + +   +   +       +  LHA  +   HP 
Sbjct: 269 KTGRTHQIRVHLSYVGHPLVGDPVYGTSPRSGLSDRQRCAILDFGRQALHAYMLGFIHPV 328

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  ++  APLP  M +  + L
Sbjct: 329 TGEAMKFHAPLPKDMQQLIEIL 350


>gi|288934030|ref|YP_003438089.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|288888759|gb|ADC57077.1| pseudouridine synthase, RluA family [Klebsiella variicola At-22]
          Length = 326

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 78/335 (23%), Positives = 146/335 (43%), Gaps = 41/335 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+     K   ++  G+ + I
Sbjct: 8   TATVTENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGSIGDKPKEKVLGGEHIAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I                         +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  DVEIEEEARF---------------QPQDIPLNIVYEDDDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTIPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        +E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTSGGTVEEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RIHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMSHITHPLVGDQVYGGRPRPPKGASEEFITALRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            + L HP  G  ++  AP+P  MV+  +++   ++
Sbjct: 283 MLRLYHPITGIEMEWHAPIPQDMVELIEAMRADFE 317


>gi|134095276|ref|YP_001100351.1| 23S rRNA pseudouridylate synthase [Herminiimonas arsenicoxydans]
 gi|133739179|emb|CAL62228.1| Ribosomal large subunit pseudouridine synthase C (rRNA-uridine
           isomerase C) (rRNA pseudouridylate synthase C)
           [Herminiimonas arsenicoxydans]
          Length = 326

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 101/319 (31%), Positives = 160/319 (50%), Gaps = 26/319 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            +  +E   R+D +       +   ++ ++LRSG+VRV+K R+    R+  G VVRIPP+
Sbjct: 22  TISEEEAGQRIDNFLLRICKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLTEGDVVRIPPI 81

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                      +I + + +    ++F    +L ED+ + V +KPAG++V GGSG++Y + 
Sbjct: 82  -----------RIAEKAPSTAPGAEF---KILLEDNHLLVIDKPAGVAVHGGSGVSYGVI 127

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L++      +   L HRLD++TSG+LV+A+ R+A  +L E  R     K Y  LV G 
Sbjct: 128 EQLRAAR-PDAKFLELVHRLDRDTSGVLVLAKKRSALTNLHEQIRGGEPDKRYLVLVHGD 186

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            KN ++ I   L K S   G+    V+ +      + + F +I  + + F  LE +  TG
Sbjct: 187 WKNARQHIKLALHKYSTADGERRVRVQAD---GMESHTIFNLIQRYGE-FALLEAELKTG 242

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANF------KGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           RTHQ+RVH    G  I GD KY          K N       +++LHA  +   HPE G+
Sbjct: 243 RTHQIRVHLASSGFAIAGDDKYGDFALNRELQKANGERVALKRMFLHAHQITFIHPESGK 302

Query: 305 -LQITAPLPAHMVKTWDSL 322
            + + APLP    +   SL
Sbjct: 303 PVTLNAPLPPECERFLKSL 321


>gi|212212777|ref|YP_002303713.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           CbuG_Q212]
 gi|212011187|gb|ACJ18568.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           CbuG_Q212]
          Length = 327

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 88/331 (26%), Positives = 150/331 (45%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   ++   Q + I  
Sbjct: 15  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVWENQFIEIEA 74

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 75  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 119

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y ++
Sbjct: 120 LINALLHYDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAI 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+            + +  I    + VV    +    AI+HF++I  + +    + +Q
Sbjct: 180 VKGVLI--SGRTIEAPVGRHPIHRTRMAVV----EFGRPAITHFRIIKRY-RAHTHIRVQ 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQ------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+ GD  Y +      + + P+Q       +  LHA  +   
Sbjct: 233 LETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHAATLQFS 292

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           HP   R +   APLPA M    + L   Y +
Sbjct: 293 HPVDQRPMACHAPLPADMAHLLECLEDDYSQ 323


>gi|205353701|ref|YP_002227502.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205273482|emb|CAR38459.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|326628807|gb|EGE35150.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 326

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 143/332 (43%), Gaps = 35/332 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ + + +V V+ +   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I+                 +   +  +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  DAEIDE---------------EIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + +                     A++H+++++ F +    L 
Sbjct: 173 AVAIGHM-TAGGTVNEPIGRHPT-----KRTHMSVHPMGKPAVTHYRIMEHF-RVHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
           L HP  G  ++  AP+P  MV   D++   ++
Sbjct: 286 LYHPVSGIEMEWHAPIPQDMVDLIDAMRADFE 317


>gi|254373560|ref|ZP_04989047.1| hypothetical protein FTCG_01516 [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|151571285|gb|EDN36939.1| hypothetical protein FTCG_01516 [Francisella novicida GA99-3549]
          Length = 309

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 99/320 (30%), Positives = 164/320 (51%), Gaps = 13/320 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIEVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G    K   I   L  K     D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHGHWDKKIIRIDLPL--KRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP-HPE 301
           E++  TGRTHQ+RVH   MG PIV D KY  A           ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAGKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVKTWDS 321
             ++ +TA L +   K    
Sbjct: 290 NKQISVTAALDSRFEKFIQE 309


>gi|166712251|ref|ZP_02243458.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 328

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 97/326 (29%), Positives = 157/326 (48%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++  +  D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPP--------VRVNEEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRALRP--NQNLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y SL+ G   +    +   L      GG+    V         ++SHFK+++      
Sbjct: 186 KRYLSLLIGRMPDGVMSVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFKLLERRG-GH 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G P+ GD KY      K         +L+LHA  ++  
Sbjct: 242 SYCEVRIETGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAASLEFA 301

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     ++APL   + +  D LG
Sbjct: 302 LDAGQTPYVLSAPLAPELAEALDQLG 327


>gi|71907236|ref|YP_284823.1| ribosomal large subunit pseudouridine synthase D [Dechloromonas
           aromatica RCB]
 gi|71846857|gb|AAZ46353.1| ribosomal large subunit pseudouridine synthase D [Dechloromonas
           aromatica RCB]
          Length = 318

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 83/319 (26%), Positives = 140/319 (43%), Gaps = 26/319 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           + V +     RLD+      P  +   LQ  +R   V+VD K       ++  G+ + + 
Sbjct: 19  LTVPDASYGRRLDQVLAELLPQHSRNRLQGWVREACVQVDGKPETEPKRKMMGGEKLLVS 78

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
              +  N                +  + +   +++ED  + V NKPAG+ V  GSG    
Sbjct: 79  EPEDVRNQP--------------ELPEDIPLDVVFEDETLLVINKPAGLVVHPGSGNWSG 124

Query: 127 YHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             ++  L      +   +  + HRLD++TSG+LVVA+T  A   L    + R +++IY +
Sbjct: 125 TLMNALLHHVPGIEVVPRAGIVHRLDKDTSGLLVVAKTLEAQTDLVRQLQARTVRRIYLA 184

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L  G  K  +  +   + +  H        +    +G   AI++ ++++ F     ++E 
Sbjct: 185 LAAGAMK-HEGTVNEPIGR--HPSQRIKMAIVPENRGGKPAITNIRILEAFT-YTTFVEC 240

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
              TGRTHQ+RVH   +  P+VGD  Y    K N   P   +  LHA  + L HP  G +
Sbjct: 241 SLETGRTHQIRVHMAAIHHPLVGDQVYG---KHNPKLPEFPRQALHATRLGLVHPLTGLK 297

Query: 305 LQITAPLPAHMVKTWDSLG 323
           +Q   P+P  M    D+L 
Sbjct: 298 MQWEVPMPEDMRNLLDNLR 316


>gi|298370246|ref|ZP_06981562.1| ribosomal large subunit pseudouridine synthase C [Neisseria sp.
           oral taxon 014 str. F0314]
 gi|298281706|gb|EFI23195.1| ribosomal large subunit pseudouridine synthase C [Neisseria sp.
           oral taxon 014 str. F0314]
          Length = 332

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 96/322 (29%), Positives = 163/322 (50%), Gaps = 23/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RIQ+G ++R
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIQAGDLLR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A      E ++  +           +  ++YED  + V NKP+G +V GGSG++
Sbjct: 71  IPPVRTAEKQRPSENRVQAAPAR--------EFDIVYEDDALLVINKPSGTAVHGGSGVS 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++     + +   L HRLD++TSG+L++A+ R+A   L E+ R  R +KIY +L
Sbjct: 123 FGVIEQIRRAR-PEARYLELVHRLDKDTSGLLMIAKKRSALVRLHEAIRNDRPKKIYLAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-------- 238
             G  +N +  +   L K +   G+ +  V ++      A + F+V++ F+         
Sbjct: 182 GVGRLENDRFHVKLPLFKYTGAQGEKMVRVSED---GQSAHTVFRVLNRFSDGLLHQAGL 238

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +E    TGRTHQ+RVH     CPI GD +Y               +++LHA  + 
Sbjct: 239 SHLTLVEATLKTGRTHQIRVHLQSQHCPIAGDERYGDYQANKRLQKLGLKRMFLHASELH 298

Query: 297 LPHP-EGGRLQITAPLPAHMVK 317
           L HP  G +L + A LP  + +
Sbjct: 299 LDHPLTGEKLVLKADLPQELQQ 320


>gi|171913853|ref|ZP_02929323.1| pseudouridine synthase, RluA family protein [Verrucomicrobium
           spinosum DSM 4136]
          Length = 303

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 82/317 (25%), Positives = 136/317 (42%), Gaps = 30/317 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           + + V E+     RLD + +   P ++   LQ +++ G + ++ K  K N  ++ G  + 
Sbjct: 1   MDFTVNESAPAKQRLDHYLQGELPDMSRTRLQGLIKDGHILLNGKAAKPNTPLKQGDRIT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +                +   V        +   +L+ED  I V NKP G+ V   +G  
Sbjct: 61  ME---------------VPDPVPTEVVPQDIPLNVLFEDEHIIVINKPDGLVVHPAAGNP 105

Query: 125 IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L    +  G     +P + HRLD+ETSG +V A+   A   LTE+F  R + 
Sbjct: 106 DGTLVNALLFHCKNLSGIGGELRPGIVHRLDKETSGCMVAAKHDLAHTRLTEAFSQRDLT 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY + V G P +    I N + +      D   +     +    A++ +  +    Q  
Sbjct: 166 KIYLAAVNGTPSSSSGRIENRIGRHP---VDRKRMALVTGEAGKEALTEWDRVAVH-QGC 221

Query: 241 CWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
             +  +  TGRTHQ+RVH    +GCPI+GD  Y    +     P   +L LHA  ++  H
Sbjct: 222 ALIRCRLLTGRTHQIRVHMKEALGCPILGDTIYAQIQRQLIKMP---RLMLHAWKLEFQH 278

Query: 300 PEGG-RLQITAPLPAHM 315
           P     L+  AP+P   
Sbjct: 279 PITKLGLKFEAPVPEAF 295


>gi|320539057|ref|ZP_08038731.1| putative 23S rRNA pseudouridine synthase [Serratia symbiotica str.
           Tucson]
 gi|320030897|gb|EFW12902.1| putative 23S rRNA pseudouridine synthase [Serratia symbiotica str.
           Tucson]
          Length = 325

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 83/342 (24%), Positives = 142/342 (41%), Gaps = 37/342 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V+V+ K   K   ++  G++V I
Sbjct: 8   TATVAESQLGQRLDQAMAELFPDYSRSRIKEWILDDRVQVNGKTANKPKEKVLGGEIVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP    V  G+G   
Sbjct: 68  AAQIEEDPRWEPQDIALD---------------VVYEDCDILVINKPRDRVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y 
Sbjct: 113 GTVLNALLHYYPKIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQEREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A++H+++++ F +    L 
Sbjct: 173 AVAIGTM-TAGGTVDEPISRHSTKRTHMAVYPM-----GKPAVTHYRILEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMSHINHPLVGDPLYGGRPRSPKGASEAFISTLRGFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           L HP  G +++  APLP  MV     L  K D   +  ++  
Sbjct: 286 LYHPISGIQMEWHAPLPQDMVDLITVL--KADTEKFKDKMDW 325


>gi|218281133|ref|ZP_03487668.1| hypothetical protein EUBIFOR_00229 [Eubacterium biforme DSM 3989]
 gi|218217647|gb|EEC91185.1| hypothetical protein EUBIFOR_00229 [Eubacterium biforme DSM 3989]
          Length = 304

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 141/325 (43%), Gaps = 33/325 (10%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
             + + ++ D +  RLD+         +   ++ +L  G V V++K +K + ++     +
Sbjct: 2   ETRILKIDEDTKLDRLDKVLAEKL-DFSRKRIKDLLDEGNVLVNQKVMKASYKVCVNDEI 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +         ++ E   LD               ++YED  I V NKP G+ V    G 
Sbjct: 61  EVSIPELDSTQVLPEPIDLD---------------IVYEDHDIIVINKPKGMVVHPAPGH 105

Query: 126 --AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++  L    D  G     +P + HR+D++TSG+LVVA+   A + L++  + +  
Sbjct: 106 YSGTLVNALLYHCKDLSGINGVMRPGIVHRIDKDTSGLLVVAKNDKAHEALSQQLQDKTC 165

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V     ++   I   + +        + V   N K    AI+HF V++ F+ K
Sbjct: 166 HREYVAIVHKPFTHEYGTIHAPIGRDEK-DRQKMAVTANNSKD---AITHFSVLENFS-K 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           F +++ Q  TGRTHQ+RVH  ++  PI GD KY         +   N   LHA  ++  H
Sbjct: 221 FAYIKCQLETGRTHQIRVHMQYIEHPIAGDPKYGPR-----KTIQANGQLLHACALEFVH 275

Query: 300 PEG-GRLQITAPLPAHMVKTWDSLG 323
           P    ++    PL     K  + L 
Sbjct: 276 PTTHEKMHFEVPLEPTFEKVLNELR 300


>gi|218245618|ref|YP_002370989.1| RluA family pseudouridine synthase [Cyanothece sp. PCC 8801]
 gi|218166096|gb|ACK64833.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8801]
          Length = 318

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 88/323 (27%), Positives = 149/323 (46%), Gaps = 32/323 (9%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINAL 74
           ++  R+D W   +   I+  +LQK++  G + ++ +       ++  G  +++       
Sbjct: 17  DKGDRIDLWLSQNLDQISRSHLQKLIEQGNIYLNNQVCLNKKTKVNLGDRLQVFLPPPEP 76

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGF 132
             +  E   LD               +LYED  + + NK AG+ V    G      + G 
Sbjct: 77  LELQPEPIPLD---------------ILYEDDSLIIINKSAGLVVHPAPGHTSGTLVHGL 121

Query: 133 LKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L    +  G    Q+P + HRLD++T+G +VVA+T  A QHL    + +  ++ Y  +V+
Sbjct: 122 LYHCPNLVGIGGVQRPGIVHRLDKDTTGAIVVAKTDYAHQHLQAQLKAKTARREYLGVVY 181

Query: 189 GIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           G+P++K   +  I   + +  H G      V   E G   AI+H+++++     +  +E 
Sbjct: 182 GVPRHKDTHQGTINVPIGR--HRGDRKKMAVVPVENGGREAITHWQIVERLG-NYTLVEF 238

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           +  TGRTHQ+RVH+ ++G PIVGD  Y +   G       +   LHA  + L HP  G  
Sbjct: 239 RLETGRTHQIRVHSSYIGHPIVGDPLYSS---GGSVGVNLSGQALHAYRLILEHPVTGNT 295

Query: 305 LQITAPLPAHMVKTWDSLGFKYD 327
           ++  APLPA   K    L  K  
Sbjct: 296 IEAIAPLPAEFTKLLTLLRQKLS 318


>gi|56708307|ref|YP_170203.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis SCHU S4]
 gi|110670778|ref|YP_667335.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis FSC198]
 gi|224457427|ref|ZP_03665900.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|254370790|ref|ZP_04986795.1| hypothetical protein [Francisella tularensis subsp. tularensis
           FSC033]
 gi|254875128|ref|ZP_05247838.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|54113047|gb|AAV29157.1| NT02FT0135 [synthetic construct]
 gi|56604799|emb|CAG45878.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis SCHU S4]
 gi|110321111|emb|CAL09261.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis FSC198]
 gi|151569033|gb|EDN34687.1| hypothetical protein FTBG_00600 [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254841127|gb|EET19563.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|282159538|gb|ADA78929.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. tularensis NE061598]
          Length = 332

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 74/321 (23%), Positives = 134/321 (41%), Gaps = 28/321 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E                +   +++ED  I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWIAED---------------INLKIIFEDDDIIVIDKPVNMIVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + D  K  +  + HRLD++TSG++V A++  A  +L +    R++ + Y 
Sbjct: 117 GTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    K+  I   + +            +        AI+H+  I+ +   F  +E
Sbjct: 177 AIVEGEIY-KQGTINQPIGRDPTNRTKMAINYR-----GKEAITHYTSIEVY-DGFTLIE 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            Q  TGRTHQ+RVH   +  P+VGD  Y   +         I  +  LHA  +   HP  
Sbjct: 230 CQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITIPTRQALHAYKLSFIHPTT 289

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
            ++ +  + LP  M+     L
Sbjct: 290 AKMVKFKSKLPEDMLNLKAQL 310


>gi|145641509|ref|ZP_01797087.1| SfhB [Haemophilus influenzae R3021]
 gi|145273800|gb|EDK13668.1| SfhB [Haemophilus influenzae 22.4-21]
          Length = 324

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 72/328 (21%), Positives = 144/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   S+  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPISEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPIGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|78047980|ref|YP_364155.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
 gi|78036410|emb|CAJ24101.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
          Length = 328

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 95/326 (29%), Positives = 157/326 (48%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++  +  D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPP--------VRINEEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRALRP--NQSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L+ G   +    +   L      GG+    V         ++SHF++++      
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFRLLERRG-GH 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G P+ GD KY      K         +L+LHA  ++  
Sbjct: 242 SYCEVRIETGRTHQIRVHAQHLGHPVAGDEKYGEADVNKRLRDQLGLKRLFLHAASLEFA 301

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     ++APL   + +  D LG
Sbjct: 302 LDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|91206061|ref|YP_538416.1| ribosomal large subunit pseudouridine synthase RluD subfamily
           protein [Rickettsia bellii RML369-C]
 gi|157826559|ref|YP_001495623.1| ribosomal large subunit pseudouridine synthase RluD subfamily
           protein [Rickettsia bellii OSU 85-389]
 gi|91069605|gb|ABE05327.1| Ribosomal large subunit pseudouridine synthase RluD subfamily
           protein [Rickettsia bellii RML369-C]
 gi|157801863|gb|ABV78586.1| Ribosomal large subunit pseudouridine synthase RluD subfamily
           protein [Rickettsia bellii OSU 85-389]
          Length = 312

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 73/328 (22%), Positives = 145/328 (44%), Gaps = 40/328 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPV 70
           V  +   +RLD+       +++   +QK ++S  V+++   +  ++  ++   ++     
Sbjct: 6   VPTELSGLRLDKALSQLLENVSRNQIQKAIKSSCVQINNVIILDSDILVKENDIILFSFK 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                              LT  +  +K  ++YED  + V NK AG++V  G+G  +H D
Sbjct: 66  ---------------EPEELTIEAADIKLDIVYEDEDLIVINKAAGMTVHPGAG--HHDD 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD++T+G++VVA+   A   L      R++ + 
Sbjct: 109 TLVNALLHHTRNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVVRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFC 241
           Y +LVWG+    +  I N + + S      + ++K    G   A++++K ++  +     
Sbjct: 169 YKALVWGVINPLEGTIKNNIGR-SRSDRQKMTILKY---GGKEAVTYYKTLELFYGGSIS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +E +  TGRTHQ+RV   H+   +VGD  Y  N +    +P +         +  LH+ 
Sbjct: 225 MVECKLATGRTHQIRVQLSHLKHSVVGDQIYGNNDRKINHAPPELKAKLLDFKRQALHSW 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           Y+   HP     ++ +  LP  M     
Sbjct: 285 YLSFTHPTSNEVMEFSCELPKDMEGVIK 312


>gi|54295134|ref|YP_127549.1| ribosomal large subunit pseudouridine synthase [Legionella
           pneumophila str. Lens]
 gi|53754966|emb|CAH16454.1| Ribosomal large subunit pseudouridine synthase [Legionella
           pneumophila str. Lens]
          Length = 315

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 109/324 (33%), Positives = 169/324 (52%), Gaps = 17/324 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V Y  + ++E+  RLD +       +   ++ +I+R G+VR++KKR + N+R+Q G 
Sbjct: 1   MSEVSYKEIGSEEDGQRLDNYLIRILKGVPKSHIYRIIRGGEVRINKKRAQANSRLQIGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +RIPP+    +      K +  S NL K    LK  +++EDS + V NKPAGI+V GGS
Sbjct: 61  SIRIPPIRMTDS------KEIFVSDNLAKR---LKDSIIFEDSSLLVINKPAGIAVHGGS 111

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G++  +   L+           L HRLD+ETSG L++A+ R+  + +      R +QKIY
Sbjct: 112 GLSLGVIEALRKTRHDLSY-LELVHRLDRETSGCLLLAKKRSTLRAIHALLEAREVQKIY 170

Query: 184 WSLVWGIPKNKKE-CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           W+L+      KK+  I   L K +   G+ V  V   +K    + + FK+++ + Q  CW
Sbjct: 171 WALLTHRWDGKKKITITAPLEKNTLKSGERVVSV---QKDGKASETDFKLLENYHQ-ACW 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPE 301
           +E  P TGRTHQ+RVH+ + G  IVGD KY +           QN+LYLHAR +   +  
Sbjct: 227 VEASPKTGRTHQIRVHSAYFGHVIVGDEKYGSKVGEVEGIDYQQNRLYLHARSIQF-NLN 285

Query: 302 GGRLQITAPLPAHMVKTWDSLGFK 325
           G      A +      T   L  +
Sbjct: 286 GVMHVFQADVDDGFGNTLKQLRAR 309


>gi|261856344|ref|YP_003263627.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261836813|gb|ACX96580.1| pseudouridine synthase, RluA family [Halothiobacillus neapolitanus
           c2]
          Length = 346

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 106/335 (31%), Positives = 162/335 (48%), Gaps = 24/335 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP----HINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           V+ V V+      R+D +           +    + +ILR+G+VRV+ +R K   R+ +G
Sbjct: 19  VRRVTVDAHYAGQRIDNFLLRELGATHGEVPRSLIYRILRTGEVRVNSQRAKPTTRLATG 78

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             VRIPP+   L    +E   + S+  L + +D    +++YED  +   NKPAG++V GG
Sbjct: 79  DEVRIPPL--KLQSPSQESAGVISANWLARAAD----MIVYEDEALLAVNKPAGLAVHGG 132

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQK 181
           S I + +   ++      G+K  L HR+D++TSG+L++A+TRA    L   FR     +K
Sbjct: 133 SNIPFGLIELMRQHT-GLGEKLELAHRIDRDTSGLLILAKTRATLHSLQTQFRPEGHAEK 191

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G   +K + +   L K    G    H V+ N +G   A++HF V+    +   
Sbjct: 192 QYLAIVHGHWPDKLKRVDAPLEKWQGEGES--HRVQVNPQG-KEAVTHFAVLAAN-KNAT 247

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-------IQNKLYLHARY 294
            L  Q  TGRTHQ+RVH  H   PIVGD KY          P        +  L LHA  
Sbjct: 248 LLRAQLETGRTHQIRVHTAHENHPIVGDEKYGQREWDKRLFPSTGASARRRPPLLLHAYR 307

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           + L HP+  + LQ+TAP+P         L      
Sbjct: 308 LMLTHPQTEQPLQLTAPIPDKWRSLAQQLNLTLPE 342


>gi|227329204|ref|ZP_03833228.1| 23S rRNA pseudouridine synthase D [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 325

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 80/345 (23%), Positives = 147/345 (42%), Gaps = 43/345 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V+++     K   ++  G+ V I
Sbjct: 8   TATVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVTNKPKEKVLGGESVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +I                      +  +K  ++YED  I V NKP  + V  G+G   
Sbjct: 68  DALIEEEARW---------------EAQDIKLDIVYEDQDILVINKPRDLVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + +     +  + HRLD++T+G++VVA+T  A   L E+ + R I + Y 
Sbjct: 113 GTVLNALLHHYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYE 172

Query: 185 SLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        ++ IA    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGSMTAGGMVEQPIARHATKRTHMAVHPM---------GKPAVTHYRIMEHF-RAHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHINHPLVGDQLYGGRPRPPKGASEDFIEMLRGFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            +   HP  G  ++  A LP  MV   D+L  K D   +  +L  
Sbjct: 283 MLRFYHPITGIHMEWHAELPQDMVDLIDAL--KADTEAFKDQLDW 325


>gi|197284293|ref|YP_002150165.1| 23S rRNA pseudouridine synthase D [Proteus mirabilis HI4320]
 gi|227357802|ref|ZP_03842150.1| ribosomal large subunit pseudouridine synthase D [Proteus mirabilis
           ATCC 29906]
 gi|194681780|emb|CAR40996.1| ribosomal large subunit pseudouridine synthase D [Proteus mirabilis
           HI4320]
 gi|227161912|gb|EEI46930.1| ribosomal large subunit pseudouridine synthase D [Proteus mirabilis
           ATCC 29906]
          Length = 325

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 79/334 (23%), Positives = 146/334 (43%), Gaps = 41/334 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V + +   RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + +  
Sbjct: 10  TVADSQLGQRLDQALAELFPDYSRSRIKEWILDNRVQVNDKIINKPKEKMLGGEKIEVDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +I                         +   ++YED  I V NKP  + V  G+G     
Sbjct: 70  LIEEDVRW---------------EPQNIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + +     +  + HRLD++T+G++VVA+T  A  HL E+ + R I + Y ++
Sbjct: 115 VLNALLYRYPEIVNVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAV 174

Query: 187 VWGIPKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             G         E I+    K++H+    +            A++H++V++ F +    L
Sbjct: 175 ATGRMTAGGLVNEPISRHPTKRTHMAVHPM---------GKPAVTHYRVMEHF-RAHTRL 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG--------NFTSPIQNKLYLHARYM 295
            ++  TGRTHQ+RVH  H+  P++GD  Y    +           T    ++  LHA  +
Sbjct: 225 RLRLETGRTHQIRVHMAHIHHPLIGDQLYGGRPRPLKGASEEFRETLRRFDRQALHATML 284

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            L HP  G  ++  APLP  MV+    L    ++
Sbjct: 285 RLYHPITGIEMEWHAPLPDDMVELIRVLKVDAEQ 318


>gi|83644955|ref|YP_433390.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83632998|gb|ABC28965.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 315

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 89/308 (28%), Positives = 150/308 (48%), Gaps = 13/308 (4%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V +++  +  RLD +       +    + KI+R G+VR++K R K   +++ G  VRI
Sbjct: 13  RVVTIDSGSDGQRLDNFLVRELKGVPKGKIYKIIRKGEVRINKGRCKPETKLKDGDQVRI 72

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP+  +    + E  I    + L   S       L+E+ ++ + NKP G++V GGSG+++
Sbjct: 73  PPIRVSEGDSL-EPVIPAGLIELVSQST------LFENDELLIINKPCGVAVHGGSGVSF 125

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L++      +   L HRLD++TSG+LV+A+ R A     +  +  R++KIY + V
Sbjct: 126 GVIEILRAARQDI-RFLELAHRLDRDTSGVLVLAKKRRALVQFHDMLKTGRVEKIYHAWV 184

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G     K  I   L K     G+ +  V ++      + + F+V+         +E QP
Sbjct: 185 CGKWPKHKSVITAPLKKNVLRSGERMVNVSED---GKPSETRFRVL-YSGAGRTLVEAQP 240

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGGRLQ 306
            TGRTHQ+RVHA   G PI+GD KYC +     +      +L LHA  + +  P+    +
Sbjct: 241 ITGRTHQIRVHAKFAGHPIIGDDKYCDSETNRVYRDMGVKRLCLHAYSLRMSWPDRPEQK 300

Query: 307 ITAPLPAH 314
           I       
Sbjct: 301 IVCEWDED 308


>gi|294625341|ref|ZP_06703977.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
 gi|292600359|gb|EFF44460.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
          Length = 328

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 95/326 (29%), Positives = 156/326 (47%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLRGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++     D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPP--------VRTNDEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRALRP--NQSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L+ G   +    +   L      GG+    V         ++SHF++++      
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFRLLERRG-GH 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G P+ GD KY      K         +L+LHA  ++  
Sbjct: 242 SYCEVRIETGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAASLEFA 301

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     ++APL   + +  D LG
Sbjct: 302 LDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|260598975|ref|YP_003211546.1| 23S rRNA pseudouridine synthase D [Cronobacter turicensis z3032]
 gi|260218152|emb|CBA32977.1| Ribosomal large subunit pseudouridine synthase D [Cronobacter
           turicensis z3032]
          Length = 328

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 84/344 (24%), Positives = 148/344 (43%), Gaps = 42/344 (12%)

Query: 1   MSLMTYVQYV-VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNR 58
           M +   VQ    V   +   RLD+     +P  +   +++ +   +V V+ +       +
Sbjct: 1   MYMAQRVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNDQMCDTPKEK 60

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +  G+ V I   I        +   LD               ++YED  I V NKP  + 
Sbjct: 61  VLGGERVAINAEIEEEARFEPQDIPLD---------------IVYEDDDILVINKPRDLV 105

Query: 119 VQGGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFR 175
           V  G+G     +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ +
Sbjct: 106 VHPGAGNPDGTVLNALLHYYPPIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQ 165

Query: 176 MRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           +R I + Y ++  G         E I+    K++H+    +            A++H+++
Sbjct: 166 LREITREYEAVAIGHMTAGGTVSEPISRHPTKRTHMSVHPM---------GKPAVTHYRI 216

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------- 285
           ++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +          
Sbjct: 217 MEHF-RIHTRLRLRLETGRTHQIRVHMAHITHPLVGDQLYGGRPRPPKGASEAFIQALRK 275

Query: 286 -NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            ++  LHA  + L HP  G  ++  AP+P  MV   D+L   ++
Sbjct: 276 FDRQALHATMLRLYHPVSGILMEWHAPIPQDMVDLIDALRADFE 319


>gi|325927798|ref|ZP_08189023.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           perforans 91-118]
 gi|325541788|gb|EGD13305.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           perforans 91-118]
          Length = 328

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 96/326 (29%), Positives = 157/326 (48%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++  +  D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPP--------VRINEEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRALRP--NQSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L+ G   +    +   L      GG+    V         ++SHFK+++      
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFKLLERRG-GH 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G P+ GD KY      K         +L+LHA  ++  
Sbjct: 242 SYCEVRIETGRTHQIRVHAQHLGHPVAGDEKYGEADVNKRLRDQLGLKRLFLHAASLEFA 301

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     ++APL   + +  D LG
Sbjct: 302 LDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|237809510|ref|YP_002893950.1| pseudouridine synthase, RluA family [Tolumonas auensis DSM 9187]
 gi|237501771|gb|ACQ94364.1| pseudouridine synthase, RluA family [Tolumonas auensis DSM 9187]
          Length = 326

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 80/331 (24%), Positives = 142/331 (42%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
            +E   E  RLD+   + +   +   L++ +  G+V++D K       ++  GQ V I  
Sbjct: 10  TIEPHHEGKRLDQVLADLFTDYSRTRLKEWILGGKVQLDGKVCLLPKEKVMGGQQVEIAT 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  L   ++YED  + V +KPAG+ V  G+G     
Sbjct: 70  ELEDDTRW---------------QAQDLPLNIVYEDEHLLVIDKPAGLVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + D ++  +  + HRLD+ET+G++VVA+T  A   L  + + RRI + Y ++
Sbjct: 115 VLNALLHRYPDIAEVPRAGIVHRLDKETTGLMVVAKTIPAQIRLVYALQKRRITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        +   + + S         +         AI+H++V + F +    L  +
Sbjct: 175 VVGHM-TAGGTVDEPISRHSTQ-----RTMMAVNPMGKPAITHYRVAERF-RAHTRLRCR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+   +VGD  Y    +    + ++         +  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMAHINHALVGDPVYGGRLRPIRNASVELSDFLRTFRRQALHATMLRLT 287

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  ++  +P+P  MV+  + L      
Sbjct: 288 HPITGEEMEWHSPIPDDMVQLIEVLRLDSAE 318


>gi|56707234|ref|YP_169130.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis SCHU S4]
 gi|110669704|ref|YP_666261.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis FSC198]
 gi|118498217|ref|YP_899267.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. novicida U112]
 gi|194324401|ref|ZP_03058174.1| pseudouridine synthase, RluA family [Francisella tularensis subsp.
           novicida FTE]
 gi|224456294|ref|ZP_03664767.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|254369904|ref|ZP_04985913.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica FSC022]
 gi|254369919|ref|ZP_04985927.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis FSC033]
 gi|254375025|ref|ZP_04990505.1| ribosomal large subunit pseudouridine synthase C [Francisella
           novicida GA99-3548]
 gi|254874072|ref|ZP_05246782.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|56603726|emb|CAG44688.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis SCHU S4]
 gi|110320037|emb|CAL08071.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis FSC198]
 gi|118424123|gb|ABK90513.1| ribosomal large subunit pseudouridine synthase C [Francisella
           novicida U112]
 gi|151568165|gb|EDN33819.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis FSC033]
 gi|151572743|gb|EDN38397.1| ribosomal large subunit pseudouridine synthase C [Francisella
           novicida GA99-3548]
 gi|157122874|gb|EDO66991.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica FSC022]
 gi|194321466|gb|EDX18951.1| pseudouridine synthase, RluA family [Francisella tularensis subsp.
           novicida FTE]
 gi|254840071|gb|EET18507.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|282158342|gb|ADA77733.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis NE061598]
          Length = 309

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 99/320 (30%), Positives = 164/320 (51%), Gaps = 13/320 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIEVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G    K   I   L  K     D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHGHWDKKIIKIDLPL--KRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP-HPE 301
           E++  TGRTHQ+RVH   MG PIV D KY  A           ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVKTWDS 321
             ++ +TA L +   K    
Sbjct: 290 NKQISVTAALDSRFEKFIQE 309


>gi|206577750|ref|YP_002237068.1| ribosomal large subunit pseudouridine synthase D [Klebsiella
           pneumoniae 342]
 gi|290510910|ref|ZP_06550279.1| ribosomal large subunit pseudouridine synthase D [Klebsiella sp.
           1_1_55]
 gi|206566808|gb|ACI08584.1| ribosomal large subunit pseudouridine synthase D [Klebsiella
           pneumoniae 342]
 gi|289775903|gb|EFD83902.1| ribosomal large subunit pseudouridine synthase D [Klebsiella sp.
           1_1_55]
          Length = 326

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/335 (23%), Positives = 146/335 (43%), Gaps = 41/335 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+     K   ++  G+ + I
Sbjct: 8   TATVTENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGNIGDKPKEKVLGGEHIAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I                         +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  DVEIEEEARF---------------QPQDIPLNIVYEDDDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTIPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        +E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTSGGTVEEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RIHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMSHITHPLVGDQVYGGRPRPPKGASEEFITALRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            + L HP  G  ++  AP+P  MV+  +++   ++
Sbjct: 283 MLRLYHPITGIEMEWHAPIPQDMVELIEAMRADFE 317


>gi|332678953|gb|AEE88082.1| Ribosomal large subunit pseudouridine synthase C [Francisella cf.
           novicida Fx1]
          Length = 309

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 99/320 (30%), Positives = 164/320 (51%), Gaps = 13/320 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIEVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G    K   I   L  K     D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHGHWDKKIIKIDLPL--KRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP-HPE 301
           E++  TGRTHQ+RVH   MG PIV D KY  A           ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAGKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVKTWDS 321
             ++ +TA L +   K    
Sbjct: 290 NKQISVTAALDSRFEKFIQE 309


>gi|21242847|ref|NP_642429.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21108337|gb|AAM36965.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 328

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 96/326 (29%), Positives = 156/326 (47%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++     D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPP--------VRINDEDDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRALRP--NQSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L+ G   +    +   L      GG+    V         ++SHFK+++      
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFKLLERRG-GH 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G P+ GD KY      K         +L+LHA  ++  
Sbjct: 242 SYCEVRIETGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAASLEFA 301

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     ++APL   + +  D LG
Sbjct: 302 LDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|165923990|ref|ZP_02219822.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           RSA 334]
 gi|165916576|gb|EDR35180.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           RSA 334]
          Length = 323

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 88/331 (26%), Positives = 151/331 (45%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   +++  Q + I  
Sbjct: 11  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEA 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 71  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 115

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y ++
Sbjct: 116 LINALLHYDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAI 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+            + +  I    + VV    +    AI+HF++I  + +    + +Q
Sbjct: 176 VKGVLI--SGRTIEAPVGRHPIHRTRMAVV----EFGRPAITHFRIIKRY-RAHTHIRVQ 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQ------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+ GD  Y +      + + P+Q       +  LHA  +   
Sbjct: 229 LETGRTHQIRVHMAHIHHPVAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHAATLQFS 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           HP   R +   APLPA M    + L   Y +
Sbjct: 289 HPVDQRPMACHAPLPADMAHLLECLEDDYSQ 319


>gi|330446994|ref|ZP_08310645.1| 23S rRNA pseudouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328491185|dbj|GAA05142.1| 23S rRNA pseudouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 324

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 83/332 (25%), Positives = 142/332 (42%), Gaps = 35/332 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +  MRLD+     YP  +   ++  + +G V V+ K V K   ++  G+ + I  
Sbjct: 10  TVGESQLGMRLDQVVAELYPDYSRSRIKDWILNGMVSVNGKVVKKPREKMMGGEELFIQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I      + +   LD               ++YED  I V NKP    V  G+G     
Sbjct: 70  EIEDEVRWVAQDIPLD---------------IVYEDDDILVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L      ++  +  + HRLD++T+G++VVA+T  A   L  + + R+I + Y +L
Sbjct: 115 VLNALLHHCPSLAEVPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEAL 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S              +    AI+H++V + F ++   + ++
Sbjct: 175 AIGQMTG-GGTVEKPIGRHST-----KRTCMAVHEMGKDAITHYRVAERF-REHTRIVLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHAR + L 
Sbjct: 228 LETGRTHQIRVHMSYLSHPLIGDVTYGGRPRPPRNASPEFIQALRAFDRQALHARMLRLD 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           HP  G  ++  APLP  MV   D L      N
Sbjct: 288 HPITGEKMEWHAPLPNDMVAMIDILRKDTLEN 319


>gi|253689512|ref|YP_003018702.1| pseudouridine synthase, RluA family [Pectobacterium carotovorum
           subsp. carotovorum PC1]
 gi|251756090|gb|ACT14166.1| pseudouridine synthase, RluA family [Pectobacterium carotovorum
           subsp. carotovorum PC1]
          Length = 325

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/342 (22%), Positives = 141/342 (41%), Gaps = 37/342 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V+++     K   ++  G+ V I
Sbjct: 8   TATVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVTNKPKEKVLGGESVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +I                      +  +K  ++YED  I V NKP  + V  G+G   
Sbjct: 68  DALIEEEARW---------------EAQDIKLDIVYEDQDILVINKPRDLVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + +     +  + HRLD++T+G++VVA+T  A   L E+ + R I + Y 
Sbjct: 113 GTVLNALLHHYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A++H+++++ F +    L 
Sbjct: 173 AVAIGSM-TAGGMVDQPIARHST-----KRTHMAVHPMGKPAVTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMAHINHPLVGDQLYGGRPRPPRGASEAFIETLRGFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
             HP  G  ++  A LP  MV   D+L  K D   +  +L  
Sbjct: 286 FYHPITGIHMEWHAELPQDMVDLIDAL--KADTEEFKDQLDW 325


>gi|332992387|gb|AEF02442.1| ribosomal large subunit pseudouridine synthase D [Alteromonas sp.
           SN2]
          Length = 327

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 81/332 (24%), Positives = 148/332 (44%), Gaps = 35/332 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
               +   +RLD+   + +P  +   L+  ++ G V VD + +    +++Q  +VV +  
Sbjct: 13  TTGAEHFGLRLDQVLADLFPEYSRSKLKTWIQGGNVSVDGQVITVPRHKMQMDEVVTVS- 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                          +  + +T  +  +   ++YED  I V NK A + V  G+G     
Sbjct: 72  --------------AEIEIQVTSQAQDIALDIVYEDEHILVINKSADLVVHPGAGNPSGT 117

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L    D  K  +  + HRLD++T+G++VVA+T  A  HL +  + R + + Y ++
Sbjct: 118 VLNALLNHVPDIDKVPRAGIVHRLDKDTTGLMVVAKTLPAQTHLVDQLQTRVMSREYEAV 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + +  H        V++N      A++HF+VI+ F + +  L ++
Sbjct: 178 AMGTMVA-GGVVDEPIGR--HATKRTHMAVREN---GKPAVTHFRVIEKF-RAYTHLRLK 230

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P++GD  Y    +       +F + ++   +  LHA  + L 
Sbjct: 231 LETGRTHQIRVHMAHIKHPLLGDPTYSGRPRLPKGASDDFVNTLRGFQRQALHAAQLSLY 290

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           HPE    +   APLP  M     ++      N
Sbjct: 291 HPETEEWMTWQAPLPQDMQDLLAAVRLDSKEN 322


>gi|194366450|ref|YP_002029060.1| RluA family pseudouridine synthase [Stenotrophomonas maltophilia
           R551-3]
 gi|194349254|gb|ACF52377.1| pseudouridine synthase, RluA family [Stenotrophomonas maltophilia
           R551-3]
          Length = 324

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 96/323 (29%), Positives = 153/323 (47%), Gaps = 20/323 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   ++++G  VR
Sbjct: 16  VRMITVPADRAGQRLDNFLLGQLKGAPRSLVYKLVRSGQVRVNGGRAKAERKLEAGDEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  +        +  D +         L+  +++ED+++   NKP G++  GGSGI+
Sbjct: 76  VPPVRLS--------EEGDKAGPPEAFMRRLEQAIVFEDARLLALNKPTGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR---IQKIY 183
           +     L++     GQ   L HRLD++TSG+L+VA+ R+A   L    R      I+K Y
Sbjct: 128 FGAIETLRALRP--GQTLELVHRLDRDTSGLLIVAKKRSALSELQALLREDHGAGIRKRY 185

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L+ G   +    +   L      GG+    V         +ISHF+V++       + 
Sbjct: 186 LTLLAGRMPDGVMTVDAPLHVGLRQGGERHVQVNAI---GKESISHFRVLERRG-GHSYC 241

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPE 301
           E++  TGRTHQ+RVHA H+G P+ GD KY                +L+LHA  ++     
Sbjct: 242 EVRIETGRTHQIRVHAQHLGHPVAGDDKYGDPAVNKRLREQIGLKRLFLHAASLEFALDA 301

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
           G     + APL   +V+  D L 
Sbjct: 302 GKTPYVLNAPLADELVEALDRLR 324


>gi|113954535|ref|YP_731894.1| 23S RNA-specific pseudouridylate synthase [Synechococcus sp.
           CC9311]
 gi|113881886|gb|ABI46844.1| 23S RNA-specific pseudouridylate synthase [Synechococcus sp.
           CC9311]
          Length = 295

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 85/314 (27%), Positives = 140/314 (44%), Gaps = 28/314 (8%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDRW  +     +   +QK + +G VRV+ K  K    +++G  V++          +
Sbjct: 1   MRLDRWLVSQRSEQSRSRIQKFIDAGYVRVNGKTGKAKTPLRNGDQVQLWMPPPEPLPYL 60

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
           K               + +   +L+ED  + V NKPAG++V    G      ++G L   
Sbjct: 61  K--------------PEPMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLHHC 106

Query: 137 VDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            D  G     +P + HRLD++T+G +VVA+++ A   L    + R   + Y ++V G+P+
Sbjct: 107 QDLPGISGKLRPGVVHRLDKDTTGCIVVAKSQEALVRLQAQIQQRIASREYLAVVHGVPQ 166

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +   I   + +       Y  V   ++    YA +H+ + +     +  L  +  TGRT
Sbjct: 167 GESGTIIGAIGRHPVDRKKYAVV---SDDSGRYARTHWTLQERLGD-YSLLRFKLDTGRT 222

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPL 311
           HQ+RVH  H+   +VGD  Y    K     P      LHA  + L HP    R+   AP+
Sbjct: 223 HQIRVHCAHINHAVVGDITYSRCRKLPVELPG---QALHAFQLGLDHPITKERMLFEAPV 279

Query: 312 PAHMVKTWDSLGFK 325
           P+ M K    L  +
Sbjct: 280 PSVMEKLLIVLRKR 293


>gi|254415358|ref|ZP_05029119.1| pseudouridine synthase, RluA family [Microcoleus chthonoplastes PCC
           7420]
 gi|196177833|gb|EDX72836.1| pseudouridine synthase, RluA family [Microcoleus chthonoplastes PCC
           7420]
          Length = 330

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 84/340 (24%), Positives = 139/340 (40%), Gaps = 47/340 (13%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVIN 72
           N E + RLDR+     P ++   +QK++  G V+++          IQ G  + +     
Sbjct: 8   NQENSDRLDRYLAQQLPDLSRSRIQKLIEEGNVQLNHNLCTSKKATIQPGDSIHLT---- 63

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HID 130
                      +  +  L    + +   +LYED +I + NKPA + V    G      ++
Sbjct: 64  -----------IPDAKPLDLKPEAIPLDILYEDDQILIVNKPANLVVHPAPGHENGTLVN 112

Query: 131 GFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             L    +  G    Q+P + HRLD++T+G + +A+T  A  HL    + +  ++ Y  +
Sbjct: 113 ALLAHCPNLAGIGGVQRPGIVHRLDKDTTGAIAIAKTDHAHHHLQAQLKAKTARRDYLGV 172

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G P  +   I   + +  H        V   EKG   AI+H+++ +     +  +  Q
Sbjct: 173 VYGSPATETGTINFPIGR--HPSDRKKMAVVPLEKGGRSAITHWQIKERLG-NYTLIHFQ 229

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE----- 301
             TGRTHQ+RVH  H+G PI+GD  Y          P      LHA  + L HP      
Sbjct: 230 LETGRTHQIRVHTAHIGHPIIGDPVYSKGRDIGVNLPG---QALHAWRLQLQHPNTIARP 286

Query: 302 --------------GGRLQITAPLPAHMVKTWDSLGFKYD 327
                         G  +++ APLP         L  +  
Sbjct: 287 LSPNQGDQRTGNKPGDWIEVIAPLPPAFSTLLTVLRRRAS 326


>gi|50085931|ref|YP_047441.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter sp. ADP1]
 gi|49531907|emb|CAG69619.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter sp. ADP1]
          Length = 350

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 142/327 (43%), Gaps = 36/327 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++ D    R+D+     +   +   L++ ++ G + V+ + VK   R +  +++ +  
Sbjct: 41  VQLDPDYLGQRIDQVAATVWNEFSREKLKQWMKDGHLLVNGEVVKPKYRCEGNELLTLNV 100

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
            + A      E   LD               ++YED  I V NKPAG+ V  G+G     
Sbjct: 101 ELEAQTTSQPENIPLD---------------IVYEDQDILVINKPAGMVVHPGAGNPSGT 145

Query: 128 HIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L  +  + +  +  L HR+D++TSG+LVVA+   A   L++    + + +IY  +
Sbjct: 146 LVNALLYHYPKAVELSRAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLADKSVYRIYDLV 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEM 245
           V+G        I         I    V  +K     G   A++H+ V + F Q F  ++ 
Sbjct: 206 VYGN-------IIAGGTIDEQIKRHPVDRIKMAILPGGREAVTHYNVKERF-QHFTRVQA 257

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDL 297
           Q  TGRTHQ+RVH  ++G  +VGD  Y         A+ +   T     +  LHA  + L
Sbjct: 258 QLETGRTHQIRVHFSYIGHGLVGDPVYMSRVRVPAGASERLGQTLRGFKRQALHASKLGL 317

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLG 323
            HP     +   AP P    +  + L 
Sbjct: 318 VHPRTQEEMMFEAPWPEDFTQLLEVLR 344


>gi|149202314|ref|ZP_01879287.1| Pseudouridine synthase, RluD [Roseovarius sp. TM1035]
 gi|149144412|gb|EDM32443.1| Pseudouridine synthase, RluD [Roseovarius sp. TM1035]
          Length = 342

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 90/344 (26%), Positives = 147/344 (42%), Gaps = 50/344 (14%)

Query: 15  DEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           D+   RLD+      P    ++   L ++L  G VRV+   V     R+Q+G ++ I   
Sbjct: 12  DDPPQRLDKALVRDVPEAAVLSRTRLARLLEEGAVRVNGAVVSEAKARVQAGDLIEIVVP 71

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
               +H+  E   L+               ++YED  + V NKPAG+ V    G      
Sbjct: 72  EARESHMAPEAIALE---------------VVYEDDDLIVVNKPAGMVVHPAPGSPEGTL 116

Query: 129 IDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L    DS       ++P + HR+D+ETSG+LVVA++ AA Q L   F    +++ Y
Sbjct: 117 VNALLHHCGDSLSGVGGAKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQFEAHSVERQY 176

Query: 184 WSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE--KGANYAISHFK 231
            ++V+G+P+     +           N L   + +        +Q    +G  +A++  +
Sbjct: 177 RAVVYGVPEASDPRLRGLRGISFEPGNILRIATRLARHKTDRQRQAVLFEGGRHAVTRAR 236

Query: 232 VIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNF 280
           VI+ F        +E    TGRTHQ+RVH  + G  ++GD  Y    K         G  
Sbjct: 237 VIESFGTPGVAALMECWLETGRTHQIRVHMAYAGHGLIGDPVYGGRRKLKEKALLPAGVA 296

Query: 281 TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            +    +  LHA  +   HP  G  L+  A LP  M+    +L 
Sbjct: 297 AAQEFPRQALHAAVLGFVHPGTGAALRFEADLPQDMLALLSALR 340


>gi|145637336|ref|ZP_01792996.1| SfhB [Haemophilus influenzae PittHH]
 gi|145269428|gb|EDK09371.1| SfhB [Haemophilus influenzae PittHH]
          Length = 324

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 72/328 (21%), Positives = 144/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   S+  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPISEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNAREDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|167581129|ref|ZP_02374003.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           thailandensis TXDOH]
          Length = 335

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 94/326 (28%), Positives = 151/326 (46%), Gaps = 22/326 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++      R+D +       +   ++ +ILRSG+VRV+K R+    R+  G   
Sbjct: 16  QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGD-- 73

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                       ++      +    +      +  +L+ED  I   NKPAG++V GGSG+
Sbjct: 74  ------VVRVPPVRVAAADLARAAGSAPVPAAEFEILFEDDAIIALNKPAGVAVHGGSGV 127

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y++
Sbjct: 128 AFGVIEQMRHAR-PHAKFLELVHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRYFA 186

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G           +   L K +   G+    V+++      + + F ++D +   +  
Sbjct: 187 CVHGDWAADWGRRRAVKAPLFKYATPDGERRVRVQED---GLPSHTVFNLVDRWPD-YAL 242

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PIVGD KY               P   +++LHA  + L
Sbjct: 243 VEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARASAVPSIKRMFLHAHRLRL 302

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA   +  D L
Sbjct: 303 AHPLTGEPLQFDAPLPAECRQFLDQL 328


>gi|208780244|ref|ZP_03247586.1| pseudouridine synthase, RluA family [Francisella novicida FTG]
 gi|208743893|gb|EDZ90195.1| pseudouridine synthase, RluA family [Francisella novicida FTG]
          Length = 309

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 99/320 (30%), Positives = 164/320 (51%), Gaps = 13/320 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIEVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G    K   I   L  K     D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHGHWDKKIIKIDLPL--KRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP-HPE 301
           E++  TGRTHQ+RVH   MG PIV D KY  A           ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDRGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVKTWDS 321
             ++ +TA L +   K    
Sbjct: 290 NKQISVTAALDSRFEKFIQE 309


>gi|212218242|ref|YP_002305029.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           CbuK_Q154]
 gi|212012504|gb|ACJ19884.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           CbuK_Q154]
          Length = 327

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 87/331 (26%), Positives = 150/331 (45%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   +++  Q + I  
Sbjct: 15  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEA 74

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 75  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 119

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y ++
Sbjct: 120 LINALLHYDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAI 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+            + +  I    + VV    +    AI+HF++I  + +    + +Q
Sbjct: 180 VKGVLI--SGRTIEAPVGRHPIHRTRMAVV----EFGRPAITHFRIIKRY-RAHTHIRVQ 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQ------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+ GD  Y +      + + P+Q       +  LH   +   
Sbjct: 233 LETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHGATLQFS 292

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           HP   R +   APLPA M    + L   Y +
Sbjct: 293 HPVDQRPMACHAPLPADMAHLLECLEDDYSQ 323


>gi|167627646|ref|YP_001678146.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017]
 gi|167597647|gb|ABZ87645.1| Lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017]
          Length = 328

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/339 (23%), Positives = 143/339 (42%), Gaps = 34/339 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++  D    R+D      +   +   +QK ++ G + V+ K  K  + +   + V I
Sbjct: 12  QKIMMHPDHAGKRIDSTINELFEQFSRSQIQKWIKDGLITVNGKTTKSKHILLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  + E                +   +++ED+ I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWLAED---------------IDLNIVFEDNDIIVIDKPIDMVVHPGAGNMT 116

Query: 126 AYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + +  K  +  + HRLD++TSG++V A++  A  +L +    R++ + Y 
Sbjct: 117 GTISNALLHKYPNQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLSERKVSRKYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWL 243
           ++V G    +             IG D  +  K         AI+H+K I+ +   F  +
Sbjct: 177 AIVEGEIYEEGTI-------NQPIGRDLNNRTKMTINHKGKEAITHYKPIEVY-DGFTLI 228

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E Q  TGRTHQ+RVH   +  P+VGD  Y   +           N+  LHA  +   HP 
Sbjct: 229 ECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLDKVGIENINRQALHAYKLSFMHPT 288

Query: 302 GGRL-QITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQD 339
             ++ +  + LP  M+    +L  +  + +     Y +D
Sbjct: 289 SQKIVRFKSKLPEDML----NLKLELQQTIEFYDDYEED 323


>gi|85373063|ref|YP_457125.1| pseudouridine synthase D large subunit [Erythrobacter litoralis
           HTCC2594]
 gi|84786146|gb|ABC62328.1| pseudouridine synthase D large subunit [Erythrobacter litoralis
           HTCC2594]
          Length = 322

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 77/314 (24%), Positives = 134/314 (42%), Gaps = 30/314 (9%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHII 78
           RLD+        ++   ++ +++ G V VD       + +   G    I           
Sbjct: 24  RLDKALAEA-SGLSRERVKALMQGGAVLVDGDPATNPSAKGSEGTPYTIT---------- 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW 136
                L  +V+       +K  +++ED  + V NKPAG+ V   +G      ++  L   
Sbjct: 73  -----LPPTVDPEAQPQDIKLDVVFEDEHLLVVNKPAGMVVHPAAGNPDGTLVNALLHHC 127

Query: 137 VDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      +P + HR+D++TSG+LVVA+T  A + L   F    I + Y +L  G P
Sbjct: 128 RGQLSGINGVARPGIVHRIDKDTSGLLVVAKTDNAHEGLAAQFAEHTINRRYLALCAGHP 187

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
              +  I   + +        +  + ++     +A++H+K +    +    +E +  TGR
Sbjct: 188 NPAEGTIEGRIGRSER-DRKKMAPLPEDSSRGKHAVTHYKTLRRL-RDCALIECRLETGR 245

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGN---FTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           THQ+RVH   +G P++GD  Y  + KG           +  LHA  +   HP  G+ ++ 
Sbjct: 246 THQVRVHCQSIGHPLLGDPTYGRDPKGLRPILKELGFARQALHAAMLGFEHPVTGQWVEF 305

Query: 308 TAPLPAHMVKTWDS 321
           TA LPA M +  D 
Sbjct: 306 TADLPADMQELIDE 319


>gi|253996195|ref|YP_003048259.1| RluA family pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253982874|gb|ACT47732.1| pseudouridine synthase, RluA family [Methylotenera mobilis JLW8]
          Length = 340

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 100/325 (30%), Positives = 163/325 (50%), Gaps = 21/325 (6%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           ++ ++   E  R+D +       +   ++ +ILRSG+VRV+KKR+  + R+  G VVR+P
Sbjct: 23  FLTIDEASEGQRIDNFLTKTLKGVPKSHVYRILRSGEVRVNKKRIDADFRLSLGDVVRVP 82

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P  +           ++ + +    +   +  ++YED  + V +K AG +V GGSGI+  
Sbjct: 83  PTRST---------AVEKTESAVPVTSKFEQAVIYEDDAMLVIDKAAGFAVHGGSGISRG 133

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +   L+     + +   L HRLD+ETSG+L++A+ R+A   L E+ R  +  K Y  LV 
Sbjct: 134 VIEQLR-LERPRAKFLELVHRLDRETSGVLMLAKKRSALVALHEAIRNNQTDKRYLVLVQ 192

Query: 189 GIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGA----NYAISHFKVIDCFAQ----K 239
           G     K+ +   L K     G+  V+VV    K        + + F+++  F+     K
Sbjct: 193 GEWLEPKKRVVLDLQKYVLPNGERRVNVVTDVSKDKFGERQTSETMFRLLKNFSHPVIGK 252

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLP 298
           F  LE Q  TGRTHQLRV   H+G PIVGD KY   +           +++LH+    + 
Sbjct: 253 FSLLEAQLVTGRTHQLRVQLAHLGFPIVGDDKYGDFDLNKFLAKHGLKRMFLHSSVTKIR 312

Query: 299 HPEG-GRLQITAPLPAHMVKTWDSL 322
           HP    +L++ AP+PA + K    L
Sbjct: 313 HPLTAEKLELIAPVPAELNKFLIKL 337


>gi|254514408|ref|ZP_05126469.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium NOR5-3]
 gi|219676651|gb|EED33016.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium NOR5-3]
          Length = 309

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 93/321 (28%), Positives = 153/321 (47%), Gaps = 16/321 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V+++ V+   +  RLD +     P I    L + +R G++RV+K R K + R+  G 
Sbjct: 1   MSGVRFLTVDERSDGQRLDNYILRECPGIPKTRLYRAMRKGEIRVNKGRAKPDQRLMLGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+              +         + L + +++ED  +   NKP+GI+V GGS
Sbjct: 61  RVRLPPLSTPPPR--------EPGAAPPGWQERLATSVVFEDDHLLAINKPSGIAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQKI 182
           G+ + +   L++      +   L HRLD+ETSG+++VA+  AA + L E  R   +I K 
Sbjct: 113 GLQFGLIETLRAMR-PHARFLELVHRLDRETSGLVLVAKKPAALRALHEQLRAQGKIDKR 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L  G        +   L +     G+ +  V    K    + + F++ + FA     
Sbjct: 172 YLALAEGAWPRHLRLVEAPLQRFERKSGERMVKV---AKEGKASTTEFRIRESFAD-VTL 227

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPE 301
           LE +P TGRTHQ+RVHA H G  ++GD KY       +T  +Q  +L+LHA  +      
Sbjct: 228 LEARPLTGRTHQIRVHAQHAGHALLGDGKYQTANGEAYTRKLQLKRLFLHAESLSFV-LN 286

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
             R  + APL   + +     
Sbjct: 287 EQRYALNAPLDQELSQVLKKC 307


>gi|172038237|ref|YP_001804738.1| pseudouridine synthase [Cyanothece sp. ATCC 51142]
 gi|171699691|gb|ACB52672.1| pseudouridine synthase [Cyanothece sp. ATCC 51142]
          Length = 314

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 86/328 (26%), Positives = 151/328 (46%), Gaps = 36/328 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           + VEN  +  RLD W  N    I+  ++Q+++  G + ++ +       +++ G  ++I 
Sbjct: 5   LTVEN--KGNRLDLWLSNQLTDISRSHIQRLIEQGNIILNNEVCTNKKIKVKIGDRLQIN 62

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                          L     L    + L   +LYED ++ + NKPA + V    G    
Sbjct: 63  ---------------LPEPKPLELKPEPLPLDILYEDEQLIIINKPANLVVHPAPGHETG 107

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + G L    +  G    Q+P + HRLD++T+G +VVA+T  A Q+L    + +  ++ 
Sbjct: 108 TLVHGLLYHCSNLAGIGGVQRPGIVHRLDKDTTGAMVVAKTDFAHQNLQAQIKNKTAKRE 167

Query: 183 YWSLVWGIPKNKK------ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           Y  +++G+  N++      + I N  + +  I    + VV   EK    AI+H+++++  
Sbjct: 168 YLGIIYGVLTNQEDKENSHQGIINLPIGRHPIDRKKMAVVPL-EKRGREAITHWEILERL 226

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  ++    TGRTHQ+RVH+ + G PIVGD  Y  N          +   LHA  + 
Sbjct: 227 G-NYSLVKFTLETGRTHQIRVHSSYYGNPIVGDPLYSTNRSLKMN---LSGQALHAHKLT 282

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           L HP    +++  APLP  + K    L 
Sbjct: 283 LTHPITSEKIEAIAPLPDELTKLLTYLR 310


>gi|319745315|gb|EFV97632.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           agalactiae ATCC 13813]
          Length = 296

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 72/314 (22%), Positives = 135/314 (42%), Gaps = 34/314 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             +RLD+   ++   ++     + ++ G V V+ +  K    +Q G  +           
Sbjct: 8   AGVRLDKALADN-SELSRSQANEEIKKGIVLVNGQVKKAKYTVQEGDRITFD-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
            I ++++LD        ++ +   ++Y+D  + V NKP G+ V   +G      ++  + 
Sbjct: 59  -IPKEEVLD------YQAENIPLDIIYQDDDVAVVNKPQGMVVHSSAGHSSGTLVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+   A Q L E  + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        AI+ F V++ F   +  +E+   TG
Sbjct: 172 LPNDRGVIEAPIGRSDKDRKKQAVTAK-----GKPAITRFHVLERFGD-YTLVELSLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +      +LHA+ +   HP  G  L  + 
Sbjct: 226 RTHQIRVHMAYIGHPLAGDPVYGPR-----KTLGGKGQFLHAQTLGFTHPSNGENLIFSV 280

Query: 310 PLPAHMVKTWDSLG 323
            +P     T + L 
Sbjct: 281 EVPEIFQTTLEKLR 294


>gi|261820451|ref|YP_003258557.1| 23S rRNA pseudouridine synthase D [Pectobacterium wasabiae WPP163]
 gi|261604464|gb|ACX86950.1| pseudouridine synthase, RluA family [Pectobacterium wasabiae
           WPP163]
          Length = 325

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 79/345 (22%), Positives = 148/345 (42%), Gaps = 43/345 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V+++   + K   ++  G+ V I
Sbjct: 8   TATVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVINKPKEKVLGGESVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +I                      +  +K  ++YED  I V NK   + V  G+G   
Sbjct: 68  DALIEEEARW---------------EAQDIKLDIVYEDQDILVINKSRDLVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + +     +  + HRLD++T+G++VVA+T  A   L E+ + R I + Y 
Sbjct: 113 GTVLNALLHHYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYE 172

Query: 185 SLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        ++ IA    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGSMTAGGMVEQPIARHATKRTHMAVHPM---------GKPAVTHYRIMEHF-RAHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMSHINHPLVGDQLYGGRPRPPKGASDDFIETLRGFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            +   HP  G +++  A LP  MV   ++L  K D   +  +L  
Sbjct: 283 MLRFYHPITGIQMEWHAALPQDMVDLIEAL--KADTEAFKDQLDW 325


>gi|156932863|ref|YP_001436779.1| 23S rRNA pseudouridine synthase D [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156531117|gb|ABU75943.1| hypothetical protein ESA_00660 [Cronobacter sakazakii ATCC BAA-894]
          Length = 326

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 81/335 (24%), Positives = 144/335 (42%), Gaps = 41/335 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V V+ +       ++  G+ V I
Sbjct: 8   TATVSESQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGQMCDTPKEKVLGGERVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I V NKP  + V  G+G   
Sbjct: 68  NAEIEEEARFEPQDIPLD---------------IVYEDDDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVSEPISRHPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RIHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDQLYGGRPRPPKGASEAFIQALRKFDRQALHAT 282

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            + L HP  G  ++  AP+P  MV   D+L   ++
Sbjct: 283 MLRLYHPISGILMEWHAPIPQDMVDLIDALRADFE 317


>gi|56478533|ref|YP_160122.1| ribosomal large subunit pseudouridine synthase C [Aromatoleum
           aromaticum EbN1]
 gi|56314576|emb|CAI09221.1| ribosomal large subunit pseudouridine synthase C [Aromatoleum
           aromaticum EbN1]
          Length = 318

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 91/315 (28%), Positives = 153/315 (48%), Gaps = 19/315 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V+      R+D +       +   ++ +ILRSG+VRV+  RV    R+     +R
Sbjct: 9   VRRERVDEAAAGQRIDNYLLRICKGVPKSHVYRILRSGEVRVNGGRVAPTYRLAENDEIR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+             L                +++ED  + V +KP+G +V GGSG++
Sbjct: 69  IPPIR------------LAEKTTSGPAPAGEPLPVVFEDEALLVVDKPSGKAVHGGSGVS 116

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+S      +   L HR+D+ETSG+LV+A+ R+A   L +  R  R++K Y +L
Sbjct: 117 FGVIEQLRSQR-PDARLLELAHRIDRETSGLLVIAKKRSALTALHDMMREGRVEKRYLTL 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   N  + I   L K     G+    V  + K ++  +   +++  +++ F  LE++
Sbjct: 176 VPGRWANPLQHIKEPLFKYLTAEGERRVRVSGDGKASHSIV---RLVRRWSR-FSLLEVE 231

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
             TGRTHQ+RVH  H+G P+ GD KY       +  +    +++LHA  +   HP  G  
Sbjct: 232 LKTGRTHQIRVHLAHLGFPLCGDDKYGDFALNKSLEAEGLKRMFLHAARLSFAHPLTGEA 291

Query: 305 LQITAPLPAHMVKTW 319
           + +TA LPA +    
Sbjct: 292 ITLTADLPAELQSFL 306


>gi|189349901|ref|YP_001945529.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           multivorans ATCC 17616]
 gi|189333923|dbj|BAG42993.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           multivorans ATCC 17616]
          Length = 334

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 101/326 (30%), Positives = 157/326 (48%), Gaps = 23/326 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++      R+D +       +   ++ +ILRSG+VRV+K RV    R+  G VV
Sbjct: 16  QVSMIQIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDVV 75

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PPV  A   + +    +                +L+ED  + V +KPAG++V GGSG+
Sbjct: 76  RVPPVRVAAADLARADAPIVPPAQFD---------VLFEDDAMLVIDKPAGVAVHGGSGV 126

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   L+     + +   L HRLD+ETSG+L++A+ R A   L E  R  RI K Y++
Sbjct: 127 AFGVIEQLRQAR-PRAKFLELVHRLDRETSGVLMLAKKRTALVALHEQIRENRIDKRYFA 185

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G  +        +   L K +   G+    V+ +      + + F +++ +   +  
Sbjct: 186 CVHGEWQADWGRRRAVKAPLFKYTTADGERRVRVQDD---GLASHTVFNLVERWPD-YAL 241

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PIVGD KY               P   +++LHA  + L
Sbjct: 242 VEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARANAQPSLKRMFLHAHRLRL 301

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA      D L
Sbjct: 302 AHPLSGDALQFDAPLPAECRHFLDQL 327


>gi|289667068|ref|ZP_06488143.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. musacearum NCPPB4381]
          Length = 331

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 85/347 (24%), Positives = 152/347 (43%), Gaps = 40/347 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L   ++  +V ++    R D      +P  +   L + ++SG   +D    +  + ++ G
Sbjct: 9   LEPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +                +   +LYED ++ V +KPAG+ V  G
Sbjct: 69  ESVQVQVVLETQTHAAPQD---------------IPLSVLYEDEQVLVIDKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +       +   +  + HRLD++TSG++VVART  A   L E    
Sbjct: 114 AG---NPDGTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSA 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + + Y ++V G         AN  + +       + V          A++H+++ + F
Sbjct: 171 RDVHRQYLAVVVGAL--VSGGTANAPIDRHPRDRLKMAVRD----DGRDAVTHYRLRERF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKL 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y    K    +  +         + 
Sbjct: 225 -RAHTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQ 283

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  ++  HP  G  ++ +AP+PA + +   +L     R   + R
Sbjct: 284 ALHAETLEFRHPVSGEPVRASAPVPADLQRLMTALREDSARAAEMAR 330


>gi|260912661|ref|ZP_05919147.1| ribosomal large subunit pseudouridine synthase D [Pasteurella
           dagmatis ATCC 43325]
 gi|260633039|gb|EEX51204.1| ribosomal large subunit pseudouridine synthase D [Pasteurella
           dagmatis ATCC 43325]
          Length = 324

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 75/328 (22%), Positives = 140/328 (42%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V+  +   RLD+     +P  +   L+  +    V V+ + V     ++  G+ + I   
Sbjct: 10  VQLSQMGQRLDQTLAELFPDYSRSRLKTWIEDELVLVNGEVVILPRAKVYGGEQIEITVE 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           I   +  + E                L   ++YED  I V NKP    V  G+G      
Sbjct: 70  IEEDSRFMPEN---------------LPLNIVYEDDDILVINKPKDFVVHPGAGNPTGTV 114

Query: 129 IDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L  +   ++  +  + HRLD++T+G++V+A+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPQIAEVPRAGIVHRLDKDTTGLMVIAKTIPAQTKLVRDLQKRKITREYEAIA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + +                     AI+H+++++ F + +  L ++ 
Sbjct: 175 SGIM-TKGGMVDQPMARHPT-----KRTQMAVHPMGKPAITHYRIMERF-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEEFMAVLRDFKRQALHAIMLRLKH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   ++  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPEDFIQLVEALKADY 315


>gi|313884116|ref|ZP_07817882.1| pseudouridine synthase, RluA family [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620563|gb|EFR31986.1| pseudouridine synthase, RluA family [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 314

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 146/319 (45%), Gaps = 37/319 (11%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            D+   RLD+        ++   +Q +++ G V V+ +  K N ++   +++ +      
Sbjct: 17  EDQSG-RLDKVLVEE-SELSRTQIQSLIKQGLVTVNGQVEKANYKLSGQELIEMQ----- 69

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--------- 124
               + E+++L+        +  +   ++YED  + V NK AG+ V    G         
Sbjct: 70  ----VPEEEVLE------IEAQAIPLDIIYEDDDLLVINKEAGMVVHPSKGHPRDTLVNA 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + YH    L +  DS   +P L HR+D++TSG+LVVA+   + ++L++      + +IY+
Sbjct: 120 LVYHFGNHLAAGSDS--YRPGLVHRIDKDTSGLLVVAKNNESHRYLSQQLMDHTLGRIYY 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G  + K+  I   L +       Y       +     A + F+V++ +      ++
Sbjct: 178 CLVEGQMEVKQGSIEIPLARDPKNRLKY-----HADAQGKPAWTDFEVLESYPS-ASLIQ 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQ+R H  H+G PI+GD  Y  +    +  P     +LHA ++   HP    
Sbjct: 232 AELKTGRTHQIRAHFEHIGHPIIGDPVYNRDSLNLW--PTDQGQFLHAGHIHFIHPRSHE 289

Query: 305 -LQITAPLPAHMVKTWDSL 322
            ++  APLPA  +   + L
Sbjct: 290 LIEFHAPLPASFINLQNHL 308


>gi|152971444|ref|YP_001336553.1| 23S rRNA pseudouridine synthase D [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238896040|ref|YP_002920776.1| 23S rRNA pseudouridine synthase D [Klebsiella pneumoniae
           NTUH-K2044]
 gi|262043838|ref|ZP_06016928.1| ribosomal large subunit pseudouridine synthase D [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|330012968|ref|ZP_08307538.1| ribosomal large subunit pseudouridine synthase D [Klebsiella sp. MS
           92-3]
 gi|150956293|gb|ABR78323.1| 23S rRNA pseudouridine synthase [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238548358|dbj|BAH64709.1| 23S rRNA pseudouridine synthase [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|259038808|gb|EEW39989.1| ribosomal large subunit pseudouridine synthase D [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|328533634|gb|EGF60346.1| ribosomal large subunit pseudouridine synthase D [Klebsiella sp. MS
           92-3]
          Length = 326

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/335 (23%), Positives = 146/335 (43%), Gaps = 41/335 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+     K   ++  G+ + I
Sbjct: 8   TATVTENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGTIGDKPKEKVLGGERIAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I                         +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  DVEIEEEARF---------------QPQDIPLNIVYEDDDIIVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTIPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        +E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVEEPISRHPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RIHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMSHITHPLVGDQVYGGRPRPPKGASEEFITALRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            + L HP  G  ++  AP+P  MV+  +++   ++
Sbjct: 283 MLRLYHPISGIEMEWHAPIPQDMVELIEAMRADFE 317


>gi|37525235|ref|NP_928579.1| 23S rRNA pseudouridine synthase D [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36784662|emb|CAE13562.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (uracil hydrolyase) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 325

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 80/344 (23%), Positives = 147/344 (42%), Gaps = 43/344 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             V   +   RLD+     +P  +   ++  +   +V+V+ K + K   ++  G+ + I 
Sbjct: 9   TTVAESQLGQRLDQALAELFPDYSRSRIKDWILDDRVQVNGKLINKPKEKVLGGEEIAID 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            +I                         +   ++YED  I V NK   + V  G+G    
Sbjct: 69  AIIEEDARW---------------EPQNIALNIVYEDDDILVINKSRDLVVHPGAGNPDG 113

Query: 129 I--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +  L  + + +   +  + HRLD++T+G++V+A+T  A   L ES ++R I + Y +
Sbjct: 114 TVLNALLYHYPEIADVPRAGIVHRLDKDTTGLMVIAKTVPAQTRLVESLQLREITREYEA 173

Query: 186 LVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           +  G        +E I+    K++H+    +            AI+H++V++ F +    
Sbjct: 174 VATGRMTAGGMVEEPISRHPTKRTHMAVHPM---------GKPAITHYRVMEHF-RAHTR 223

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARY 294
           L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA  
Sbjct: 224 LRLRLETGRTHQIRVHMAHISHPLVGDPLYGGRPRPLKGASDEFREVMRNFDRQALHATM 283

Query: 295 MDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           + L HP  G  ++  A LP  MV    +L  K D   +   +  
Sbjct: 284 LRLYHPITGIEMEWHAELPDDMVMLIKAL--KADAEAFKDEMDW 325


>gi|317401792|gb|EFV82407.1| pseudouridine synthase [Achromobacter xylosoxidans C54]
          Length = 336

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 74/327 (22%), Positives = 131/327 (40%), Gaps = 31/327 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q V V +     RLD+      P  +   LQ  + +G V+V+    K    +  G  + +
Sbjct: 33  QLVTVPSGTRADRLDKVLAGLLPDHSRSRLQGWIEAGNVQVNGAPGKVRQTVGPGDEIAV 92

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                             +   L    + +   ++ E     V NKPAG+ V  G+G   
Sbjct: 93  WAQ--------------PAPEALAFAPEAIDFPVVDESPDWIVVNKPAGLVVHPGAGNWS 138

Query: 126 AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + + ++  +  + HRLD++TSG++VVAR   A  HL    + R + + Y 
Sbjct: 139 GTLLNGLLHRYPELAQVARAGIVHRLDKDTSGLMVVARNEIAQTHLVRQLQARSMGREYV 198

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC----FAQKF 240
           +L  G        +   + +   +    V +  +       A++H+            + 
Sbjct: 199 ALAHG-WLAAAGKVDRPIGRDPRV---PVRMSVERPVAPKPAVTHYAPARRGQIDPGGRA 254

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +  +  TGRTHQ+RVH   +G P++ D  Y              +  LHAR +    P
Sbjct: 255 TEVVCRLETGRTHQIRVHLASLGHPLLADTIYGGKNIA-----GAQRQMLHARALHFDDP 309

Query: 301 EG-GRLQITAPLPAHMVKTWDSLGFKY 326
            G G +Q  AP+PA M    +++ +  
Sbjct: 310 GGRGEVQFAAPVPADMTLVQEAIAWNA 336


>gi|145628474|ref|ZP_01784274.1| SfhB [Haemophilus influenzae 22.1-21]
 gi|144978944|gb|EDJ88630.1| SfhB [Haemophilus influenzae 22.1-21]
          Length = 324

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 143/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V ++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVNLNDRIANIPREKVFGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++   +     + +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDDTRFEPENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLSH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|77166295|ref|YP_344820.1| pseudouridine synthase, RluD [Nitrosococcus oceani ATCC 19707]
 gi|254435147|ref|ZP_05048654.1| pseudouridine synthase, RluA family [Nitrosococcus oceani AFC27]
 gi|76884609|gb|ABA59290.1| ribosomal large subunit pseudouridine synthase C [Nitrosococcus
           oceani ATCC 19707]
 gi|207088258|gb|EDZ65530.1| pseudouridine synthase, RluA family [Nitrosococcus oceani AFC27]
          Length = 324

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 102/319 (31%), Positives = 163/319 (51%), Gaps = 14/319 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V+ + +  ++   R+D +  +    +    + + LR G+VRV+K R+  + R+Q G  
Sbjct: 10  AQVRILKIHLEQAGQRIDNFLFSQLKGVPKSRIYRCLRKGEVRVNKSRIASSYRLQQGDQ 69

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP+  + + + +                 +K+ LLYED ++ + NKPA I V GGSG
Sbjct: 70  VRVPPLRVSHSPLKRPIA--------HSLLLLIKNSLLYEDKELLMLNKPARIPVHGGSG 121

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++Y I   L+  +  +     L HRLD+ETSG L+VA+TR+A   L    + + I K Y 
Sbjct: 122 VSYGIIEALR-ILRPEAAFLELVHRLDRETSGCLMVAKTRSALLTLQAMQQKQLIHKRYL 180

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  +   + +   LLK   I      +VK N  G   AISHF     +  +   +E
Sbjct: 181 ALVKGRWRKNVQRVDLPLLKN--ILRSEERIVKVNSAG-KPAISHFYPKLFYGGEATLME 237

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +   TGRTHQ+RVHA H+G P+ GD KY  ++F         ++L+LHA  +    PEG 
Sbjct: 238 VTLETGRTHQIRVHAAHLGHPLGGDEKYGDSSFNKQLRCMGLHRLFLHASQLTFTLPEGK 297

Query: 304 R-LQITAPLPAHMVKTWDS 321
           + ++  APLP  +     +
Sbjct: 298 KTIKAAAPLPKELNAVLQT 316


>gi|289662940|ref|ZP_06484521.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. vasculorum NCPPB702]
          Length = 331

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 85/347 (24%), Positives = 152/347 (43%), Gaps = 40/347 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L   ++  +V ++    R D      +P  +   L + ++SG   +D    +  + ++ G
Sbjct: 9   LEPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +                +   +LYED ++ V +KPAG+ V  G
Sbjct: 69  ESVQVQVVLETQTHAAPQD---------------IPLSVLYEDEQVLVIDKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +       +   +  + HRLD++TSG++VVART  A   L E    
Sbjct: 114 AG---NPDGTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSA 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + + Y ++V G         AN  + +       + V          A++H+++ + F
Sbjct: 171 RDVHRQYLAVVVGAL--VSGGTANAPIDRHPRDRLKMAVRD----DGRDAVTHYRLRERF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKL 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y    K    +  +         + 
Sbjct: 225 -RAHTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQ 283

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  ++  HP  G  ++ +AP+PA + +   +L     R   + R
Sbjct: 284 ALHAETLEFLHPVSGEPVRASAPVPADLQRLMTALREDSARAAEMAR 330


>gi|320160390|ref|YP_004173614.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
 gi|319994243|dbj|BAJ63014.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
          Length = 310

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 150/331 (45%), Gaps = 32/331 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQS 61
           +   V     E  +E  RLD++   H+P ++   +Q ++R G VRV  K V K    +++
Sbjct: 1   MQDQVFVFTCEPHQEG-RLDKFLVAHFPELSRSQIQGLIRDGFVRVSGKTVQKTGFLVEA 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G+ V I                +      +   + +   +++E+  + + NKPAG+ V  
Sbjct: 60  GKEVEIR---------------IPPPQPTSLEPEPIPLEVIFENQDLLLVNKPAGMVVHP 104

Query: 122 GSGIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +G      +   L    + +G    ++P + HRLD++TSG++++A+   A + L + FR
Sbjct: 105 SAGHDRGTLVHAALAHIPELEGIHGEERPGVVHRLDKDTSGLILLAKNDRAHRWLQDQFR 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           +R++QK Y +LV G P      I   + +      +   +     +    A+S +   + 
Sbjct: 165 LRKVQKTYLALVDGRPPTPTGRIEAPIGRDPK---NRQRMAVVPPEKGREAVSEYFTREV 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F      LE+ P TGRTHQ+RVH   +GCP+ GD  Y         +   N+ +LHA  +
Sbjct: 222 FPS-HTLLEVHPLTGRTHQIRVHLAFIGCPVAGDLIYGHKH----ATVSLNRHFLHAYRL 276

Query: 296 DLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            +  P E       APLP+ + +    L  +
Sbjct: 277 TIQLPGESSPRTFEAPLPSELEQVLQVLRGR 307


>gi|188585950|ref|YP_001917495.1| pseudouridine synthase, RluA family [Natranaerobius thermophilus
           JW/NM-WN-LF]
 gi|179350637|gb|ACB84907.1| pseudouridine synthase, RluA family [Natranaerobius thermophilus
           JW/NM-WN-LF]
          Length = 328

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 84/324 (25%), Positives = 147/324 (45%), Gaps = 29/324 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            ++ +  +E +RLD +       ++    + ++ +  V V+   VK +  I SG VV++ 
Sbjct: 15  ELIPKEKDEGLRLDLYLSEQIEDLSRSKAKMLINNNSVMVNDNWVKASYSITSGDVVKV- 73

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                      + +++ S + L   S  +   ++YED  + V NKP  + V  G+G    
Sbjct: 74  -----------DTQLIQSEITLIPQS--IPLDIVYEDEYLLVVNKPRNMVVHPGAGNYRD 120

Query: 127 YHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    +    +  ++P + HRLD++TSG+LVVA+       L+E  + RR+ + 
Sbjct: 121 TMVNALLYHCQNLSDGTSYERPGIVHRLDKDTSGLLVVAKQNETHDILSEEIKNRRVART 180

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF--AQKF 240
           Y +LV G    KK  I   + +        + VV     G   AI+  +++  F   +K 
Sbjct: 181 YLALVIGDFSKKKATIDLPIGRDPR-NRKKMAVVH----GGKRAITKVEMLRSFQNPEKI 235

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPH 299
            +L+    TGRTHQ+RVH  H+G P++GD  Y     K            LH+  +   H
Sbjct: 236 SYLKCSLETGRTHQIRVHLSHLGYPLLGDPVYRGKTGKNVDIDKNLTGQALHSFSLAFTH 295

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P   + +   APLP+ M+     L
Sbjct: 296 PVFKKTMVFRAPLPSDMMNLISKL 319


>gi|58581220|ref|YP_200236.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae KACC10331]
 gi|58425814|gb|AAW74851.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae KACC10331]
          Length = 335

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 84/347 (24%), Positives = 151/347 (43%), Gaps = 40/347 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L   ++  +V ++    R D      +P  +   L + ++SG   +D    +  + ++ G
Sbjct: 13  LDPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGG 72

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +                +   +LYED ++ V +KPAG+ V  G
Sbjct: 73  ESVQVQVVLETQTHAAPQD---------------IPLSVLYEDEQVLVIDKPAGLVVHPG 117

Query: 123 SGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +       +   +  + HRLD++TSG++V+ART  A   L E    
Sbjct: 118 AG---NPDGTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVLARTVQAQTALVEQLSA 174

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + + Y ++V G         AN  + +       + V          A++H+++ + F
Sbjct: 175 RDVHRQYLAVVVGAL--VSGGTANAPIDRHPRDRLKMAVRD----DGRDAVTHYRLRERF 228

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKL 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y    K    +  +         + 
Sbjct: 229 -RAHTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQ 287

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  +   HP  G  ++ +AP+PA + +   +L     R   + R
Sbjct: 288 ALHAETLQFLHPVSGEPVRASAPVPADLQRLMTALREDSARAAELAR 334


>gi|50122269|ref|YP_051436.1| 23S rRNA pseudouridine synthase D [Pectobacterium atrosepticum
           SCRI1043]
 gi|49612795|emb|CAG76245.1| ribosomal large subunit pseudouridine synthase D [Pectobacterium
           atrosepticum SCRI1043]
          Length = 325

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 82/345 (23%), Positives = 149/345 (43%), Gaps = 43/345 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V+++   + K   ++  G+ V I
Sbjct: 8   TATVAESQLGQRLDQALAELFPDYSRSRIKEWILDNRVQINGNVINKPKEKVLGGESVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +I                      +  +K  ++YED  I V NKP  + V  G+G   
Sbjct: 68  DALIEEEARW---------------EAQDIKLDIVYEDQDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L E+ + R I + Y 
Sbjct: 113 GTVLNALLHYYPEIVDVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYE 172

Query: 185 SLVWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G        ++ IA    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGSMTAGGMVEQPIARHATKRTHMAVHPM---------GKPAVTHYRIMEHF-RAHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMSHIDHPLVGDQLYGGRPRPPKGASDDFIEMLRGFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            +   HP  G +++  A LP  MV   D+L  K D   +  +L  
Sbjct: 283 MLRFYHPITGIQMEWHAALPQDMVDLIDAL--KADTAAFQDQLNW 325


>gi|39933445|ref|NP_945721.1| pseudouridine synthase RluD [Rhodopseudomonas palustris CGA009]
 gi|39647291|emb|CAE25812.1| possible pseudouridine synthases [Rhodopseudomonas palustris
           CGA009]
          Length = 407

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 149/343 (43%), Gaps = 53/343 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           VVV  DE + RLDR      P ++   L+ ++  G+V +    V+        G+ + I 
Sbjct: 84  VVVAGDEGSQRLDRVLAARCPELSRSRLKALILDGRVAIAGTPVRDPAYHASPGETITID 143

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                      E   LD               ++YED+ I V NKP G+ V   +G   H
Sbjct: 144 VPPPVPAEPAGEAIALD---------------IVYEDADIIVLNKPRGLVVHPAAG---H 185

Query: 129 IDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR- 177
             G L + + +            ++P + HRLD++T+G++V A+   A Q L+  F    
Sbjct: 186 ETGTLVNALIAHCGASLSGIGGVRRPGIVHRLDKDTTGLMVAAKNDKAHQSLSAQFADHG 245

Query: 178 ---RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y + VWG+P  K   I   + +  H   + + V     +    AI+H++V++
Sbjct: 246 RTGELRRGYLAFVWGVPGRKYGTIDAPIDRHPH-AREKMAVR----QSGREAITHWEVLE 300

Query: 235 CFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNF 280
            F+ K        +  Q  TGRTHQ+RVH  H+G P++GD  Y  +FK         G  
Sbjct: 301 NFSGKDGKPVAALIACQLETGRTHQIRVHLAHLGHPLLGDDVYGPHFKTKANQLAPAGRA 360

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 +  LHA  + L HP  G  L   +PLPA +     +L
Sbjct: 361 ALAGLGRQALHAYLLTLEHPSTGEVLTWESPLPADLAHLQAAL 403


>gi|300722272|ref|YP_003711556.1| pseudouridine synthase [Xenorhabdus nematophila ATCC 19061]
 gi|297628773|emb|CBJ89351.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Xenorhabdus nematophila ATCC 19061]
          Length = 325

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 82/343 (23%), Positives = 152/343 (44%), Gaps = 43/343 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           +V   +   RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + I  
Sbjct: 10  IVAGSQLGQRLDQALAELFPDYSRSRIKEWILDNKVQVNGKLINKPKEKMLGGEDISIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +I                         ++  ++YED  I V NKP  + V  G+G     
Sbjct: 70  IIEEDARW---------------EPQDIELNVVYEDDDILVINKPRDLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   +   +  + HRLD++T+G++VVA+T  A   L ES ++R I + Y ++
Sbjct: 115 VLNALLYRYPKIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAI 174

Query: 187 VWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             G        +E I+    K++H+    +            AI+H++V++ F +    L
Sbjct: 175 ALGCMTAGGMVEEPISRHPTKRTHMAVHPM---------GKPAITHYRVLEHF-RAHTRL 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYM 295
            ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA  +
Sbjct: 225 RLRLETGRTHQIRVHMAHIKHPLVGDQLYGGRPRPLKGASDEFREVMRNFDRQALHATML 284

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            L HP  G  ++  APLP  MV+  + +  K D   +   +  
Sbjct: 285 RLYHPITGIEMEWHAPLPDDMVRLIEVM--KADAETFKDEMDW 325


>gi|289665912|ref|ZP_06487493.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 328

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 96/326 (29%), Positives = 155/326 (47%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++  +  D +         L++ +++ED+++   NKP G++  GGSGI+
Sbjct: 76  IPP--------VRVNEEGDKAAPPPSFMARLEAAIVFEDARLLALNKPTGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRALRP--NQSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L+ G   +    +   L      GG+    V         ++SHFK+++      
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFKLLERRG-GH 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G P+ GD KY      K         +L+LHA  ++  
Sbjct: 242 SYCEVRIETGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAASLEFA 301

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     ++APL   + +  D LG
Sbjct: 302 LDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|16272141|ref|NP_438344.1| 23S rRNA pseudouridine synthase D [Haemophilus influenzae Rd KW20]
 gi|260580943|ref|ZP_05848767.1| sfhB protein [Haemophilus influenzae RdAW]
 gi|1175998|sp|P44445|RLUD_HAEIN RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|1573131|gb|AAC21845.1| sfhB protein (sfhB) [Haemophilus influenzae Rd KW20]
 gi|260092432|gb|EEW76371.1| sfhB protein [Haemophilus influenzae RdAW]
          Length = 324

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 143/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +    +  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPIVEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|294781868|ref|ZP_06747200.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Fusobacterium sp. 1_1_41FAA]
 gi|294481679|gb|EFG29448.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Fusobacterium sp. 1_1_41FAA]
          Length = 318

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 75/338 (22%), Positives = 146/338 (43%), Gaps = 36/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V  + E MRLD++            L+K++ +  V+++ K +  N  ++
Sbjct: 1   MENIKEKFEFEVSPEYEGMRLDKYLAEQIEEATRSYLEKLIDNSYVKINSKVINKNGRKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +SG+ + I                +    N+   ++ +   +++E+    + NK   + V
Sbjct: 61  KSGEKIEIS---------------IPEEENIDIEAENIPLDIVFENDDFILVNKKYNMVV 105

Query: 120 QGGSGIAY-HIDGFLKSWVDSK-----GQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     +   L  + ++        +P + HRLD++TSG+++VA+   A   L   
Sbjct: 106 HPAYGNYNGTLVNALLYYTNNLSSVNGNIRPGIIHRLDKDTSGLILVAKNNFAHAKLASM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           F  + I K Y  +V G   ++  +  I N + + +      + VVK+N      AIS+++
Sbjct: 166 FTDKTIHKTYLCIVKGNFSDENLEGRIENLIGRDTK-DRKKMAVVKEN---GKLAISNYR 221

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V++   + +  +E+   TGRTHQ+RVH   +  PI+GD  Y +  K         +  LH
Sbjct: 222 VVEQV-KDYSLVEVLIETGRTHQIRVHMKSINHPILGDVIYGSEDKN------IKRQMLH 274

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A  ++  +P +      T  L    ++    L F  D+
Sbjct: 275 AFKLEFLNPLDNKEYTFTGKLFDDFIEVAKRLNFNIDK 312


>gi|54114079|gb|AAV29673.1| NT02FT1763 [synthetic construct]
          Length = 309

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 99/320 (30%), Positives = 163/320 (50%), Gaps = 13/320 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELFEVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G    K   I   L  K     D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHGHWDKKIIKIDLPL--KRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP-HPE 301
           E++  TGRTHQ+RVH   MG PIV D KY  A           ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVKTWDS 321
             ++ +TA L +   K    
Sbjct: 290 NKQISVTAALDSRFEKFIQE 309


>gi|25011477|ref|NP_735872.1| hypothetical protein gbs1435 [Streptococcus agalactiae NEM316]
 gi|24413015|emb|CAD47094.1| unknown [Streptococcus agalactiae NEM316]
          Length = 296

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 73/314 (23%), Positives = 135/314 (42%), Gaps = 34/314 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             +RLD+   ++   ++     + ++ G V V+ +  K    +Q G  +           
Sbjct: 8   AGVRLDKALADN-SELSRSQANEEIKKGIVLVNGQVKKAKYTVQEGDRITFD-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
            I ++++LD        ++ +   ++Y+D  + V NKP G+ V   +G      ++  + 
Sbjct: 59  -IPKEEVLD------YQAENISLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+   A Q L E  + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        AI+ F V++ F   +  +E+   TG
Sbjct: 172 LPNDRGVIEAPIGRSDKDRKKQAVTAK-----GKPAITRFHVLERFGD-YTLVELSLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +      +LHA+ +   HP  G  L  + 
Sbjct: 226 RTHQIRVHMAYIGHPLAGDSVYGPR-----KTLEGKGQFLHAQTLGFTHPSNGENLIFSV 280

Query: 310 PLPAHMVKTWDSLG 323
            +P     T D L 
Sbjct: 281 EVPEIFQTTLDKLR 294


>gi|289668996|ref|ZP_06490071.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 328

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 95/326 (29%), Positives = 155/326 (47%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++  +  D +         L++ +++ED+++   NKP G++  GGSGI+
Sbjct: 76  IPP--------VRVNEEGDKAAPPPSFMARLEAAIVFEDARLLALNKPTGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+++VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRALRP--NQSLELVHRLDRDTSGLVIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L+ G   +    +   L      GG+    V         ++SHFK+++      
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFKLLERRG-GH 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G P+ GD KY      K         +L+LHA  ++  
Sbjct: 242 SYCEVRIETGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAASLEFA 301

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     ++APL   + +  D LG
Sbjct: 302 LDAGKTPYVLSAPLAPELAEALDQLG 327


>gi|56750446|ref|YP_171147.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 6301]
 gi|81299921|ref|YP_400129.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 7942]
 gi|56685405|dbj|BAD78627.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 6301]
 gi|81168802|gb|ABB57142.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 7942]
          Length = 313

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 93/332 (28%), Positives = 153/332 (46%), Gaps = 34/332 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           MS    ++   V ++    RLDRW    +PH++   LQK++ +GQ+RV+ +   +   + 
Sbjct: 1   MSDRLQLEITEVPSE----RLDRWLAQQWPHLSRARLQKLIAAGQLRVNGEVCDQKRWQP 56

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G  + +         +  E+  LD               +LYED+ + + NK  G+ V
Sbjct: 57  RLGDRLELEMPPTEAIALAPEEIPLD---------------ILYEDADLLIVNKAVGMVV 101

Query: 120 QGGSGIAY--HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
              +G      +   L    DS       Q+P + HRLD++T+G +VVA+T AA   L +
Sbjct: 102 HPAAGHDTGTLVHALLAHCGDSLTGIGGEQRPGIVHRLDKDTTGAMVVAKTEAALLSLQD 161

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
             R +  Q+ Y  +V+G P+     +   + +  H+       V   E+G  +A++H++V
Sbjct: 162 QIRQKTAQREYLGVVFGSPRQDSGQVEEPIGR--HLRDRKRMAVVPIERGGRWALTHWQV 219

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            +     +  L  +  TGRTHQ+RVH+ HMG P+VGD  Y     G           LHA
Sbjct: 220 RERLG-NYALLHYRLATGRTHQIRVHSHHMGHPLVGDPLYG---NGRSLGVNLQGQALHA 275

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             + L HP  G  + + APLPA   +    L 
Sbjct: 276 WRLSLQHPRTGEVIAVEAPLPAEFQRLLRVLR 307


>gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudouridine synthase D [Herbaspirillum
           seropedicae SmR1]
 gi|300075092|gb|ADJ64491.1| ribosomal large subunit pseudouridine synthase D protein
           [Herbaspirillum seropedicae SmR1]
          Length = 370

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 143/336 (42%), Gaps = 29/336 (8%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           +++    RLD+      P  +   +Q+ +  G V V+    K    +   ++V + P   
Sbjct: 47  DDEVIGQRLDKVLSGLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAPQSV 106

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHID 130
             +                   + +   +L+ED  + V NKPAG+ V   +G      ++
Sbjct: 107 PSDQP--------------YGPEPMALDILHEDKALIVLNKPAGLVVHPAAGNWSGTLLN 152

Query: 131 GFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           G L      +K  +  + HRLD++TSGI+VVA+T AA   L    + R +++ Y +LVWG
Sbjct: 153 GLLHHCPALAKVPRAGIVHRLDKDTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVWG 212

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQ 246
           +P+     I   + +      D + +       A  A++H++ +   +   +    +  +
Sbjct: 213 LPQ-LSGTINAPMARHP---RDRIKMAVSQSMRAKPAVTHYRRLATGEIDRKPVSLIHCR 268

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL- 305
             TGRTHQ+RVH   +G P+VGD  Y      +    +  +  L A  + L HP  G+  
Sbjct: 269 LETGRTHQIRVHLQSLGFPLVGDALYGK----HHLVSVFPRQALLAGRLGLLHPSTGKFR 324

Query: 306 QITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDEC 341
           Q  APLP  +V      G      +  +     DE 
Sbjct: 325 QWAAPLPEDIVALLQRAGIDPALAVIPEMSDEPDEV 360


>gi|154705997|ref|YP_001424165.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           Dugway 5J108-111]
 gi|154355283|gb|ABS76745.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           Dugway 5J108-111]
          Length = 323

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 88/331 (26%), Positives = 151/331 (45%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   +++  Q + I  
Sbjct: 11  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEA 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 71  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 115

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y ++
Sbjct: 116 LINALLHYDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKTMKARQIVREYEAI 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+            + +  I    + VV    +    AI+HF++I  + +    + +Q
Sbjct: 176 VKGVLI--SGRTIEAPVGRHPIHRTRMAVV----EFGRPAITHFRIIKRY-RAHTHIRVQ 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQ------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+ GD  Y +      + + P+Q       +  LHA  +   
Sbjct: 229 LETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHAATLQFS 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           HP   R +   APLPA M    + L   Y +
Sbjct: 289 HPVDQRPMACHAPLPADMAHLLECLEDDYSQ 319


>gi|145631295|ref|ZP_01787067.1| SfhB [Haemophilus influenzae R3021]
 gi|144983080|gb|EDJ90580.1| SfhB [Haemophilus influenzae R3021]
          Length = 324

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 144/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGERLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +    +  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPIVEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +        ++         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRILMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|304389009|ref|ZP_07371056.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis ATCC 13091]
 gi|304337143|gb|EFM03330.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis ATCC 13091]
 gi|325131027|gb|EGC53753.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis OX99.30304]
 gi|325135123|gb|EGC57750.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M13399]
 gi|325137030|gb|EGC59626.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M0579]
 gi|325202968|gb|ADY98422.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M01-240149]
 gi|325207234|gb|ADZ02686.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis NZ-05/33]
          Length = 330

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 94/322 (29%), Positives = 154/322 (47%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +             ++YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFD---------VVYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  +      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVKLPLFKYTGAQGEKMVRVSAD---GQSAHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L +   LP  + +
Sbjct: 298 LNHPLTGEPLVLKVGLPPDLAQ 319


>gi|319898141|ref|YP_004136338.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae F3031]
 gi|317433647|emb|CBY82032.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae F3031]
          Length = 324

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 143/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +    +  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPIVEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|84623138|ref|YP_450510.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae MAFF 311018]
 gi|84367078|dbj|BAE68236.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae MAFF 311018]
          Length = 331

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 84/347 (24%), Positives = 151/347 (43%), Gaps = 40/347 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L   ++  +V ++    R D      +P  +   L + ++SG   +D    +  + ++ G
Sbjct: 9   LDPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +                +   +LYED ++ V +KPAG+ V  G
Sbjct: 69  ESVQVQVVLETQTHAAPQD---------------IPLSVLYEDEQVLVIDKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +       +   +  + HRLD++TSG++V+ART  A   L E    
Sbjct: 114 AG---NPDGTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVLARTVQAQTALVEQLSA 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + + Y ++V G         AN  + +       + V          A++H+++ + F
Sbjct: 171 RDVHRQYLAVVVGAL--VSGGTANAPIDRHPRDRLKMAVRD----DGRDAVTHYRLRERF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKL 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y    K    +  +         + 
Sbjct: 225 -RAHTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQ 283

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  +   HP  G  ++ +AP+PA + +   +L     R   + R
Sbjct: 284 ALHAETLQFLHPVSGEPVRASAPVPADLQRLMTALREDSARAAELAR 330


>gi|218961736|ref|YP_001741511.1| Pseudouridylate synthase, 23S RNA-specific [Candidatus Cloacamonas
           acidaminovorans]
 gi|167730393|emb|CAO81305.1| Pseudouridylate synthase, 23S RNA-specific [Candidatus Cloacamonas
           acidaminovorans]
          Length = 351

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 82/354 (23%), Positives = 152/354 (42%), Gaps = 46/354 (12%)

Query: 16  EENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +E  RLD++          +   ++ ++   ++ V+   VK +  ++ G  V I      
Sbjct: 19  QEMQRLDKFLAELKIQELYSRTFIEHLIEEDRILVNLTPVKKSYLLKEGDEVIIN----- 73

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDG 131
                     L     +      +   ++YED  + + NK AG+ V  G G      ++ 
Sbjct: 74  ----------LPEPEPMNVLPQDIPLDVVYEDEYLAIINKKAGMIVHPGFGNPEGTLVNA 123

Query: 132 FLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            L  + ++     +  +P + HRLD+ TSG++++A+       L++ F  R I+K Y+++
Sbjct: 124 ILYRFGENLSSGKEFNRPGIVHRLDRGTSGLIIIAKNDLTHAKLSDMFARREIKKTYFAI 183

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GIP+ +K  I  +L +      +   +   NE    YA++H+K I  +   F  +E+ 
Sbjct: 184 TTGIPEPEKGEIETYLARS---NKNPRTICVTNE--GRYALTHYKTIKTW-HYFALVEIN 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-------------IQNKLYLHAR 293
           P TGR HQ+RVH  H+  PI+GD  Y +        P                +  LH+ 
Sbjct: 238 PATGRMHQIRVHFAHIRYPILGDLLYNSRRYVQSLVPQNMKKKVTELLVNHLRRQALHSW 297

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLG--FKYDRNLYIKRLYSQDECKQN 344
            ++  HP  G  + ++AP+P  +  T + L   F  D +     L   +E   +
Sbjct: 298 KLEFFHPITGYPISVSAPIPDDIQYTLNWLDNNFSIDTDTSDANLILNEEINND 351


>gi|58582695|ref|YP_201711.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84624582|ref|YP_451954.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|58427289|gb|AAW76326.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84368522|dbj|BAE69680.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 328

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 95/326 (29%), Positives = 156/326 (47%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRMLKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++  +  D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPP--------VRVNEEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRALRP--NQNLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L+ G   +    +   L      GG+    V         ++SHF +++      
Sbjct: 186 KRYLTLLIGRMPDGVMSVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFTLLERRG-GH 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G P+ GD KY      K         +L+LHA  ++  
Sbjct: 242 SYCEVRIETGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAASLEFA 301

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     ++APL   + +  D LG
Sbjct: 302 LDAGQTPYVLSAPLAPELAEALDQLG 327


>gi|295099509|emb|CBK88598.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           cylindroides T2-87]
          Length = 305

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 69/325 (21%), Positives = 132/325 (40%), Gaps = 33/325 (10%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
             +  +++++   +R+D+   +     +   ++ IL  G + V+    K +  +Q G  +
Sbjct: 2   ETREFIIDDENAKIRVDKAVASLL-DFSRKRVKDILDEGNILVNGSPCKASYILQEGDHL 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                +    +L    + +   ++YED  + V NKP G+ V    G 
Sbjct: 61  LVN---------------IPEVQSLEVLPENIPLNIVYEDDDVIVINKPKGMVVHPAFGH 105

Query: 126 --AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++  +    D  G     +P + HR+D++TSG+LVV +   A   L+E    +  
Sbjct: 106 VSGTLVNALMYHCKDLSGINGVMRPGIVHRIDKDTSGLLVVCKNDKAHLALSEQLSNKTC 165

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V     ++   I   + +        + V   N   +  AI+HF V++ F + 
Sbjct: 166 HREYLAIVHHPFSHEHGTINAPIGRDEK-DRQKMAVTANN---SKEAITHFTVLENF-KD 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +  +  TGRTHQ+RVH  ++  PI GD KY      +      N   LHA  ++  H
Sbjct: 221 YALVRCRLETGRTHQIRVHMQYIKHPIAGDPKYGHRKTIDT-----NGQLLHACKLEFIH 275

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P     +   A          + L 
Sbjct: 276 PTTKEYMSFEAEPDQTFKNILEKLR 300


>gi|21243943|ref|NP_643525.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           axonopodis pv. citri str. 306]
 gi|294625813|ref|ZP_06704430.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 11122]
 gi|34395784|sp|Q8PHN2|RLUD_XANAC RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|21109553|gb|AAM38061.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           axonopodis pv. citri str. 306]
 gi|292599888|gb|EFF44008.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 11122]
          Length = 331

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 83/344 (24%), Positives = 148/344 (43%), Gaps = 34/344 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L   ++  +V ++    R D      +P  +   L + ++SG   +D +  +  + ++ G
Sbjct: 9   LDPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGEMARPRDTLRGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +                +   +LYED ++ V +KPAG+ V  G
Sbjct: 69  ESVQVQVVLETQTHAAPQD---------------IPLSVLYEDEQVLVIDKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +G           + D   +   +  + HRLD++TSG++VVART  A   L E    R +
Sbjct: 114 AGNPDRTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSAREV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G         AN  + +       + V          A++H+++ + F + 
Sbjct: 174 HRQYLAVVVGAL--VSGGTANAPIDRHPRDRLKMAVRD----DGRDAVTHYRLRERF-RA 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLH 291
              LE +  TGRTHQ+RVH  H+  PIVGD  Y    K    +  +         +  LH
Sbjct: 227 HTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQALH 286

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           A  ++  HP  G  ++ +AP+PA + +    L     R   + R
Sbjct: 287 AETLEFLHPVSGEPVRASAPVPADLQRLMTVLREDSARAAELAR 330


>gi|89257067|ref|YP_514429.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica LVS]
 gi|115315423|ref|YP_764146.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica OSU18]
 gi|167009454|ref|ZP_02274385.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           FSC200]
 gi|254368306|ref|ZP_04984325.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica 257]
 gi|89144898|emb|CAJ80243.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica LVS]
 gi|115130322|gb|ABI83509.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           OSU18]
 gi|134254115|gb|EBA53209.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica 257]
          Length = 309

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 99/320 (30%), Positives = 164/320 (51%), Gaps = 13/320 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIDVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G    K   I   L  K     D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHGHWDKKIIKIDLPL--KRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP-HPE 301
           E++  TGRTHQ+RVH   MG PIV D KY  A           ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVKTWDS 321
             ++ +TA L +   K    
Sbjct: 290 NKQISVTAALDSRFEKFIQE 309


>gi|153209393|ref|ZP_01947379.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           'MSU Goat Q177']
 gi|120575364|gb|EAX31988.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           'MSU Goat Q177']
          Length = 323

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 87/331 (26%), Positives = 150/331 (45%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   +++  Q + I  
Sbjct: 11  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEA 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 71  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 115

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y ++
Sbjct: 116 LINALLHYDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAI 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+            + +  I    + VV    +    AI+HF++I  + +    + +Q
Sbjct: 176 VKGVLI--SGRTIEAPVGRHPIHRTRMAVV----EFGRPAITHFRIIKRY-RAHTHIRVQ 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQ------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+ GD  Y +      + + P+Q       +  LH   +   
Sbjct: 229 LETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHGATLQFS 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           HP   R +   APLPA M    + L   Y +
Sbjct: 289 HPVDQRPMACHAPLPADMAHLLECLEDDYSQ 319


>gi|118497849|ref|YP_898899.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. novicida U112]
 gi|254374659|ref|ZP_04990140.1| hypothetical protein FTDG_00834 [Francisella novicida GA99-3548]
 gi|118423755|gb|ABK90145.1| ribosomal large subunit pseudouridine synthase D [Francisella
           novicida U112]
 gi|151572378|gb|EDN38032.1| hypothetical protein FTDG_00834 [Francisella novicida GA99-3548]
          Length = 332

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 133/321 (41%), Gaps = 28/321 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E                +   +++ED  I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWIAED---------------INLKIIFEDDDIIVIDKPVNMIVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + D  K  +  + HRLD++TSG++V A++  A  +L +    R++ + Y 
Sbjct: 117 GTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +            +        AI+H+  I+ +   F  +E
Sbjct: 177 AIVEGEIY-QQGTINQPIGRDPTNRTKMAINYR-----GKEAITHYTPIEVY-DGFTLIE 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            Q  TGRTHQ+RVH   +  P+VGD  Y   +            +  LHA  +   HP  
Sbjct: 230 CQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITTPTRQALHAYKLSFIHPTT 289

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
            ++ +  + LP  M+     L
Sbjct: 290 AKMVKFKSKLPEDMLNLKAQL 310


>gi|188577474|ref|YP_001914403.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           oryzae pv. oryzae PXO99A]
 gi|188521926|gb|ACD59871.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           oryzae pv. oryzae PXO99A]
          Length = 313

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 95/326 (29%), Positives = 156/326 (47%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 1   MRMLKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++  +  D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 61  IPP--------VRVNEEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 112

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 113 FGAIETLRALRP--NQNLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGIT 170

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y SL+ G   +    +   L      GG+    V         ++SHF +++      
Sbjct: 171 KRYLSLLIGRMPDGVMSVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFTLLERRG-GH 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G P+ GD KY      K         +L+LHA  ++  
Sbjct: 227 SYCEVRIETGRTHQIRVHAQHLGHPVAGDDKYGEADVNKRLRDQLGLKRLFLHAASLEFA 286

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     ++APL   + +  D LG
Sbjct: 287 LDAGQTPYVLSAPLAPELAEALDQLG 312


>gi|89256088|ref|YP_513450.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. holarctica LVS]
 gi|115314564|ref|YP_763287.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           OSU18]
 gi|167010773|ref|ZP_02275704.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           FSC200]
 gi|169656565|ref|YP_001428170.2| RNA pseudouridine synthase, RluA family protein [Francisella
           tularensis subsp. holarctica FTNF002-00]
 gi|254367416|ref|ZP_04983442.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. holarctica 257]
 gi|254369095|ref|ZP_04985107.1| hypothetical protein FTAG_00024 [Francisella tularensis subsp.
           holarctica FSC022]
 gi|290954527|ref|ZP_06559148.1| RNA pseudouridine synthase, RluA family protein [Francisella
           tularensis subsp. holarctica URFT1]
 gi|295312043|ref|ZP_06802858.1| RNA pseudouridine synthase, RluA family protein [Francisella
           tularensis subsp. holarctica URFT1]
 gi|89143919|emb|CAJ79138.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. holarctica LVS]
 gi|115129463|gb|ABI82650.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           OSU18]
 gi|134253232|gb|EBA52326.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. holarctica 257]
 gi|157122045|gb|EDO66185.1| hypothetical protein FTAG_00024 [Francisella tularensis subsp.
           holarctica FSC022]
 gi|164551633|gb|ABU61214.2| RNA pseudouridine synthase, RluA family protein [Francisella
           tularensis subsp. holarctica FTNF002-00]
          Length = 332

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 134/321 (41%), Gaps = 28/321 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E                +   +++ED  I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWIAED---------------INLKIIFEDDDIIVIDKPVNMIVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + D  K  +  + HRLD++TSG++V A++  A  +L +    R++ + Y 
Sbjct: 117 GTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +            +        AI+++  I+ +   F  +E
Sbjct: 177 AIVEGEIY-QQGTINQPIGRDPTNRTKMAINYR-----GKEAITYYTPIEVY-DGFTLIE 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            Q  TGRTHQ+RVH   +  P+VGD  Y   +         I  +  LHA  +   HP  
Sbjct: 230 CQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITIPTRQALHAYKLSFIHPTT 289

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
            ++ +  + LP  M+     L
Sbjct: 290 AKMVKFKSKLPEDMLNLKAQL 310


>gi|282896340|ref|ZP_06304362.1| Pseudouridine synthase, RluD [Raphidiopsis brookii D9]
 gi|281198836|gb|EFA73715.1| Pseudouridine synthase, RluD [Raphidiopsis brookii D9]
          Length = 323

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 82/316 (25%), Positives = 146/316 (46%), Gaps = 29/316 (9%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINAL 74
           ++  RLDR+  +  P ++   +Q ++  G V+V+ K     N  +  G+ + +       
Sbjct: 27  QKTQRLDRYLSSVIPDLSRSRIQDLIEQGYVQVNGKVCYSKNITLDGGEYLEVEVPPVQA 86

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGF 132
             ++ +   LD               +LYED ++ + NKPAG+ V    G      +   
Sbjct: 87  AQLVAQDIPLD---------------ILYEDEQLLILNKPAGLVVHPAPGHLEGTLVHAL 131

Query: 133 LKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           L    +  G    Q+P + HRLD++T+G + +A+T  A + L    + +  ++ Y  +V+
Sbjct: 132 LAHCPNLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYKQLQLQLQSKTARREYLGVVY 191

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G PK++   +   + +  H        +   E+G   AI+++ + +     +  +  Q  
Sbjct: 192 GAPKSESGTMDLPIGR--HPQQRKKMAIVPVEQGGRNAITNWYIKERLG-NYTLIHFQLE 248

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH+  MG PIVGD  Y +        P      LHA  + L HP  G+ +++
Sbjct: 249 TGRTHQIRVHSAKMGHPIVGDPVYSSGRSVGVNLPG---QALHAWQLKLQHPTSGKWVEV 305

Query: 308 TAPLPAHMVKTWDSLG 323
           TAPLP  + K  + L 
Sbjct: 306 TAPLPDSLTKLIEVLR 321


>gi|219871128|ref|YP_002475503.1| 23S rRNA pseudouridine synthase D [Haemophilus parasuis SH0165]
 gi|219691332|gb|ACL32555.1| 23S rRNA pseudouridine synthase D [Haemophilus parasuis SH0165]
          Length = 325

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 144/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V +D    RLD+     +P  +   ++  + S  V V+ K V K   ++  G+++ I   
Sbjct: 11  VTSDLLGARLDQALAQLFPDYSRSRIKVWIESDLVSVNGKIVNKAREKVFGGELIEIQAE 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           I                         +   ++YED  I V NKP  + V  G+G      
Sbjct: 71  IEEEIRF---------------EPQNIPLNIVYEDDDILVINKPKDLVVHPGAGNPDGTV 115

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   ++  +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++ 
Sbjct: 116 LNALLHHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVTALQRREITREYEAVA 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   +   +   + +                     A++H+++++ F + +  L ++ 
Sbjct: 176 SGIM-TQGGKVDEPMARHPT-----KRTAMAVHPMGKPAVTHYRIMERF-RNYSRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +      G F   ++N  +  LHA  + L H
Sbjct: 229 ETGRTHQIRVHMAHIAHPLLGDQLYGGRPRPPKGASGEFLEVLRNFKRQALHATMLRLHH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 289 PITGELMEWHAPLPDDFVELIEALKADY 316


>gi|300718035|ref|YP_003742838.1| ribosomal large subunit pseudouridine synthase D [Erwinia
           billingiae Eb661]
 gi|299063871|emb|CAX60991.1| Ribosomal large subunit pseudouridine synthase D [Erwinia
           billingiae Eb661]
          Length = 325

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 77/340 (22%), Positives = 140/340 (41%), Gaps = 37/340 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V V+   + K   ++   + + I  
Sbjct: 10  TVSESQLGQRLDQALAELFPDYSRSRIKEWILDRRVTVNGVIIDKPKEKVLGSEQIAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I                      +  +   ++YED  I V NKP G+ V  G+G     
Sbjct: 70  EIEEEARW---------------EAQDIPLDIVYEDEDILVINKPRGLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   +   +  + HRLD++T+G++VVA+T  A  HL ES ++R I + Y ++
Sbjct: 115 VLNALLHHFPAIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVESLQLREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S                   A +H+++++ F +    L ++
Sbjct: 175 AIGRM-TAGGTVDEPISRHST-----KRTHMAVHPTGKPATTHYRIMEHF-RVHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMAHINHPLVGDQLYGGRPRPPKGASESFIAMLRKFDRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           HP  G  ++  APLP  MV     +  K D   +  ++  
Sbjct: 288 HPISGIEMEWHAPLPQDMVDLIAEM--KADTAEFKDQMDW 325


>gi|134095125|ref|YP_001100200.1| pseudouridine synthase [Herminiimonas arsenicoxydans]
 gi|133739028|emb|CAL62076.1| Ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Herminiimonas arsenicoxydans]
          Length = 318

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 83/316 (26%), Positives = 136/316 (43%), Gaps = 29/316 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+      P  +   LQ+ + +G V VD +  +    +   + V I P     +  
Sbjct: 24  GVRLDKVLSTLVPQYSRSRLQQWIDAGHVSVDGEIARAKMTVYGDEKVVIYPQPAPEDEA 83

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
            K               + +   + YED+ I V +KPAG+ V   +G      ++G L  
Sbjct: 84  FK--------------PEAMDLNIAYEDAAILVIDKPAGLVVHPAAGNWSGTLLNGLLHY 129

Query: 136 WVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                G  +  + HRLD++TSG++VVA+T  A   L    + R +++ Y +LVWG P N 
Sbjct: 130 LPAIAGVPRAGIVHRLDKDTSGLMVVAKTLVAHTDLVRQLQARTVKREYLALVWGTP-NV 188

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGR 251
              +   + + S    D V +       A  A++HF+ +       +    +  Q  TGR
Sbjct: 189 SGKVDTSIGRHS---RDRVKMAVSENLTAKPALTHFQRLATGMLDGRPVSLMMCQLETGR 245

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
           THQ+RVH   +G  +VGD  Y         + +  +  LHAR + L HP  G  ++ ++ 
Sbjct: 246 THQIRVHMQSIGFALVGDALYGKQH----LTTVFPRQALHARRLGLVHPVSGAAVEWSSE 301

Query: 311 LPAHMVKTWDSLGFKY 326
           LP          G K 
Sbjct: 302 LPQDFADLIARSGIKA 317


>gi|254373204|ref|ZP_04988693.1| hypothetical protein FTCG_00787 [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|151570931|gb|EDN36585.1| hypothetical protein FTCG_00787 [Francisella novicida GA99-3549]
          Length = 332

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 133/321 (41%), Gaps = 28/321 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E                +   +++ED  I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWIAED---------------INLKIIFEDDDIIVIDKPVNMIVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + D  K  +  + HRLD++TSG++V A++  A  +L +    R++ + Y 
Sbjct: 117 GTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +            +        AI+H+  I+ +   F  +E
Sbjct: 177 AIVEGEIY-QQGTINQPIGRDPTNRTKMAINYR-----GKEAITHYTPIEVY-DGFTLIE 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            Q  TGRTHQ+RVH   +  P+VGD  Y   +            +  LHA  +   HP  
Sbjct: 230 CQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAIKTPTRQALHAYKLSFIHPTT 289

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
            ++ +  + LP  M+     L
Sbjct: 290 AKMVKFKSKLPEDMLNLKAQL 310


>gi|145639768|ref|ZP_01795370.1| SfhB [Haemophilus influenzae PittII]
 gi|145271136|gb|EDK11051.1| SfhB [Haemophilus influenzae PittII]
 gi|309750408|gb|ADO80392.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae R2866]
          Length = 324

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 143/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +    +  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPIVEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPIGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|166713128|ref|ZP_02244335.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzicola BLS256]
          Length = 331

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 85/347 (24%), Positives = 153/347 (44%), Gaps = 40/347 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L   ++  +V ++    R D      +P  +   L + ++SG   +D    +  + ++ G
Sbjct: 9   LDPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +                +   +LYED+++ V +KPAG+ V  G
Sbjct: 69  ESVQVQVVLETQTHAAPQD---------------IALSVLYEDAQVLVIDKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +       +   +  + HRLD++TSG++VVART  A   L E    
Sbjct: 114 AG---NPDGTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSA 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + + Y ++V G         AN  + +       + V          A++H+++ + F
Sbjct: 171 RDVHRQYLAVVVGAL--VSGGTANAPIDRHPRDRLKMAVRD----DGRDAVTHYRLRERF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKL 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y    K    +  +         + 
Sbjct: 225 -RAHTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQ 283

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  ++  HP  G  ++ +AP+PA + +   +L     R   + R
Sbjct: 284 ALHAETLEFLHPVSGEPVRASAPVPADLQRLMTALREDSARAAELAR 330


>gi|325916249|ref|ZP_08178530.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325537543|gb|EGD09258.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 331

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 86/347 (24%), Positives = 152/347 (43%), Gaps = 40/347 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
               ++  +V ++    R D      +P  +   L + ++SG   +D +  +  + ++ G
Sbjct: 9   TDPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGEMARPRDTLRGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +                +   +LYED ++ V +KPAG+ V  G
Sbjct: 69  ESVQLQVVLETQTHAAPQD---------------IPLSVLYEDDQVLVIDKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +  +        +  + HRLD+ETSG++VVART  A   L E    
Sbjct: 114 AG---NPDGTLVNALLFRDPALSAVPRAGVVHRLDKETSGVMVVARTVQAQTALVEQLSA 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + + Y ++V G         AN  + +       + V          A++H+++ + F
Sbjct: 171 RDVHRQYLAVVVGAL--VSGGTANAPIDRHPRDRLKMAVRD----DGRDAVTHYRLRERF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKL 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y    K    +            + 
Sbjct: 225 -RAHTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDDLVHELRTFKRQ 283

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  ++  HP  G+ ++ TAP+PA + +   +L     R   + R
Sbjct: 284 ALHAETLEFLHPVSGQPVRATAPVPADLQRLMTALREDSARAAELAR 330


>gi|188575741|ref|YP_001912670.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae PXO99A]
 gi|188520193|gb|ACD58138.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae PXO99A]
          Length = 333

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 84/347 (24%), Positives = 151/347 (43%), Gaps = 40/347 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L   ++  +V ++    R D      +P  +   L + ++SG   +D    +  + ++ G
Sbjct: 11  LDPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGG 70

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +                +   +LYED ++ V +KPAG+ V  G
Sbjct: 71  ESVQVQVVLETQTHAAPQD---------------IALSVLYEDEQVLVIDKPAGLVVHPG 115

Query: 123 SGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +       +   +  + HRLD++TSG++V+ART  A   L E    
Sbjct: 116 AG---NPDGTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVLARTVQAQTALVEQLSA 172

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + + Y ++V G         AN  + +       + V          A++H+++ + F
Sbjct: 173 RDVHRQYLAVVVGAL--VSGGTANAPIDRHPRDRLKMAVRD----DGRDAVTHYRLRERF 226

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKL 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y    K    +  +         + 
Sbjct: 227 -RAHTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQ 285

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  +   HP  G  ++ +AP+PA + +   +L     R   + R
Sbjct: 286 ALHAETLQFLHPVSGEPVRASAPVPADLQRLMTALREDSARAAELAR 332


>gi|198282733|ref|YP_002219054.1| RluA family pseudouridine synthase [Acidithiobacillus ferrooxidans
           ATCC 53993]
 gi|198247254|gb|ACH82847.1| pseudouridine synthase, RluA family [Acidithiobacillus ferrooxidans
           ATCC 53993]
          Length = 310

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 83/332 (25%), Positives = 147/332 (44%), Gaps = 34/332 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++  ++   RLD       P  +   +Q +LR G++ VD    K + R++ G+ V +  
Sbjct: 1   MILPEEQAGERLDTVLSQLLPETSRSRIQALLRDGRILVDGTPEKPSARVRGGEQVMVDW 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                ++ + E                L   +L+ED+ I V +KPAG     G+G A   
Sbjct: 61  PQIEPSNWLAEG---------------LPLHILHEDADILVLHKPAGQLTHPGAGHADGT 105

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   + + V      PR  + HRLD++T+G+LVVA+T  A Q L +      + + Y +L
Sbjct: 106 LVNGVLAHVPENAYLPRGGIVHRLDKDTTGLLVVAKTEMARQSLIDQLGDHTMHREYLAL 165

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        +   + + +    D + +  +++     A + +++++ F +   +L ++
Sbjct: 166 VTGAMTG-GGRVDAPIGRHAQ---DRLRMTVRDD--GRPAQTDYRLVERFPR-HSYLRLR 218

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANF--------KGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+G P+VGD  Y             G        +  LHA  + L 
Sbjct: 219 LATGRTHQIRVHMTHIGHPLVGDPVYGGRMTVPKGLDEAGLARWRQFRRQALHAWRLRLY 278

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           HP  G  +   +PLP  M +    L    D +
Sbjct: 279 HPASGELMTWESPLPDDMTELLALLRHARDGD 310


>gi|325918635|ref|ZP_08180739.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325535142|gb|EGD07034.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 328

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 95/325 (29%), Positives = 156/325 (48%), Gaps = 23/325 (7%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VRI
Sbjct: 17  RILKVPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVRI 76

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP        ++  +  D +   +     L++ +++ED+++   NKP+G++  GGSGI++
Sbjct: 77  PP--------VRVTEEGDKAAPPSSFLARLEAAIVFEDARLLALNKPSGVASHGGSGISF 128

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQK 181
                L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I K
Sbjct: 129 GAIETLRALRP--NQTLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITK 186

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L+ G   +    +   L      GG+    V         ++SHFK+++       
Sbjct: 187 RYLTLLVGRMPDGVMTVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFKLLERRG-GHS 242

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLPH 299
           + E++  TGRTHQ+RVHA H+G P+ GD KY      K         +L+LHA  ++   
Sbjct: 243 YCEVRIETGRTHQIRVHAQHLGHPVAGDDKYGEAEVNKRLRDQLGLKRLFLHAASLEFAL 302

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLG 323
             G     ++APL   + +  D LG
Sbjct: 303 DAGKTPYVLSAPLAPELAEALDRLG 327


>gi|163802429|ref|ZP_02196322.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. AND4]
 gi|159173730|gb|EDP58545.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. AND4]
          Length = 325

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 74/331 (22%), Positives = 142/331 (42%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V V+ + V K   R+  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVHVNGEVVTKPRTRVMGGEEITLQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  I V NKP    V  G+G     
Sbjct: 70  ELEDEERW---------------EAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDCT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + D ++  +  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLHHYPDIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S         +         A++H++V + F ++   + ++
Sbjct: 175 AIGRM-TAGGKVEQPIGRHST-----KRTLMAVAPLGKPAVTHYRVAERF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDTAYGGRARIPTGASEELTAMIRGFDRQALHAVMLRFE 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  L+  AP+P  MV+  +SL    + 
Sbjct: 288 HPITGEELEFHAPIPDDMVEMTESLRKDTEE 318


>gi|88707052|ref|ZP_01104748.1| Ribosomal large subunit pseudouridine synthase D [Congregibacter
           litoralis KT71]
 gi|88698702|gb|EAQ95825.1| Ribosomal large subunit pseudouridine synthase D [Congregibacter
           litoralis KT71]
          Length = 312

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 80/320 (25%), Positives = 143/320 (44%), Gaps = 33/320 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RLD+     +P  +   LQ  +RSG++R+D  + +  + I+ G+V+ +   + +    
Sbjct: 2   GARLDQAAAQLFPEFSRARLQSWIRSGELRLDGTKGRPRDAIRGGEVLSLNAELES---- 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFLKS 135
                       ++  ++ L   ++YED ++ V +KPAG+ V  G+G      ++  L  
Sbjct: 58  -----------EVSWTAEALPLEIVYEDEELLVIDKPAGLVVHPGAGNHNGTLVNALLNH 106

Query: 136 WVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             D +   +  + HRLD+ETSG+LVVA T  A + L    + + +Q+ Y+++V G+P   
Sbjct: 107 RPDLEAIPRGGIVHRLDKETSGLLVVAATLNAHRSLVAQLQKKDVQREYFAIVRGVPSG- 165

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              +   + +          V      G   A++H+++   FAQ     ++Q  TGRTHQ
Sbjct: 166 GGRVEAAIGRHPRQRTKMAVVAA----GGKPAVTHYRIARRFAQYTAL-DVQLETGRTHQ 220

Query: 255 LRVHALHMGCPIVGDHKYCANF--------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           +RVH  H G P++GD  Y            +         +  LHA+ +   HP  G   
Sbjct: 221 IRVHMAHRGYPLLGDPVYGGRLQLPRGASERLAAALRGFRRQALHAQRLSFVHPGSGDHC 280

Query: 307 -ITAPLPAHMVKTWDSLGFK 325
              +PL   +      L  +
Sbjct: 281 SFESPLSDDLEALLQVLAEE 300


>gi|313201439|ref|YP_004040097.1| RluA family pseudouridine synthase [Methylovorus sp. MP688]
 gi|312440755|gb|ADQ84861.1| pseudouridine synthase, RluA family [Methylovorus sp. MP688]
          Length = 354

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 81/341 (23%), Positives = 146/341 (42%), Gaps = 42/341 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRI 59
           M+  T +  +++  D   +RLD+  +   P  +   LQ+ ++ G V ++  + V    ++
Sbjct: 1   MTQTTPI-TLIIPQDLGGLRLDQALQKLLPEHSRSRLQQWIKDGLVTLEPAQAVTAKTKV 59

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G+ +++    +   H                 ++ +   + YED  I V NKPAG+ V
Sbjct: 60  WGGERLQVQVQPSPDEH--------------AFEAEDIPLDVQYEDEHILVINKPAGLVV 105

Query: 120 QGGSGIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              +G   +  G L + +           +  + HRLD++TSG+LVVA+T  A   L   
Sbjct: 106 HPAAG---NWSGTLLNALLHHAPVVKDLPRAGIVHRLDKDTSGLLVVAKTLTAQTSLVRQ 162

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + R +++ Y ++VWG    +   I   + +  H             +    A++ ++V+
Sbjct: 163 LQARTVKREYRAIVWGQVW-QNGRIDQPIGRHPH-----ARTKMAINRNGKPAVTRYEVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------- 286
           + FA    +L     TGRTHQ+RVH  H+  P+VGD  Y            Q+       
Sbjct: 217 ERFA-VHTYLRCNLETGRTHQIRVHMQHLKAPLVGDPVYGLGGIVPLRMMPQHLRDTVLN 275

Query: 287 --KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
             +  LHA  + L HP  G  ++    LPA M    +++  
Sbjct: 276 FGRQALHAVKLGLIHPASGEFMEWQVELPADMKSLLEAMRL 316


>gi|39995193|ref|NP_951144.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           sulfurreducens PCA]
 gi|39981955|gb|AAR33417.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           sulfurreducens PCA]
 gi|298504197|gb|ADI82920.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           sulfurreducens KN400]
          Length = 322

 Score =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 82/337 (24%), Positives = 146/337 (43%), Gaps = 35/337 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M        + V  + E  RLD++       I     Q+++  G+V VD +  K + +++
Sbjct: 1   MERQDERYDLSVPTEGEAERLDQFVARSVQGITRSAAQRLIEEGRVTVDDRLEKPSLKLR 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+               +    +         ++ +  ++L+ED  + V +KPAG+ V 
Sbjct: 61  GGE---------------RVVVTVPPPAPAVPEAEEIPLVVLHEDGDVVVVDKPAGMVVH 105

Query: 121 GGSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             +G      ++  L    D  G     +P + HR+D++TSG+LVVA++  A + L+  F
Sbjct: 106 PAAGNPGGTLVNALLAHCTDLSGIGGEIRPGIVHRIDKDTSGVLVVAKSDRAHESLSRQF 165

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               ++++Y +LV+G P+  K  I   + +            +       +A++H++V  
Sbjct: 166 HDHTVKRVYLALVYGSPREDKGRIEGAIGRHPTDRKKMSGAARH----GKHAVTHWRVAA 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPI-------QN 286
            F      L ++  TGRTHQ+RVH    G P+VGD  Y    +  N   P+         
Sbjct: 222 RFT-GVTLLRLRLETGRTHQIRVHMAEAGFPLVGDEVYGGAGRINNLRDPVLRKLIRELG 280

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +  LHA+ +   HP  G  L+    LP  M +  D L
Sbjct: 281 RQALHAKTLGFVHPVTGEYLEFDTELPEDMARIIDYL 317


>gi|156503277|ref|YP_001429342.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica FTNF002-00]
 gi|290954356|ref|ZP_06558977.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica URFT1]
 gi|295312220|ref|ZP_06803020.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica URFT1]
 gi|156253880|gb|ABU62386.1| pseudouridine synthase, Rlu family protein [Francisella tularensis
           subsp. holarctica FTNF002-00]
          Length = 309

 Score =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 99/320 (30%), Positives = 164/320 (51%), Gaps = 13/320 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIDVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQTSRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMTVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +++V G    K   I   L  K     D   VVK + K    A++    +      F  L
Sbjct: 172 YAIVHGHWDKKIIKIDLPL--KRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP-HPE 301
           E++  TGRTHQ+RVH   MG PIV D KY  A           ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVKTWDS 321
             ++ +TA L +   K    
Sbjct: 290 NKQISVTAALDSRFEKFIQE 309


>gi|332678564|gb|AEE87693.1| Ribosomal large subunit pseudouridine synthase D [Francisella cf.
           novicida Fx1]
          Length = 332

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 133/321 (41%), Gaps = 28/321 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E                +   +++ED  I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWIAED---------------INLKIIFEDDDIIVIDKPVNMIVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + D  K  +  + HRLD++TSG++V A++  A  +L +    R++ + Y 
Sbjct: 117 GTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +            +        AI+H+  I+ +   F  +E
Sbjct: 177 AIVEGEIY-QEGTINQPIGRDPTNRTKMAINYR-----GKEAITHYTPIEVY-DGFTLIE 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            Q  TGRTHQ+RVH   +  P+VGD  Y   +            +  LHA  +   HP  
Sbjct: 230 CQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAIKTPTRQALHAYKLSFIHPTT 289

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
            ++ +  + LP  M+     L
Sbjct: 290 AKMVKFKSKLPEDMLNLKAQL 310


>gi|253999417|ref|YP_003051480.1| RluA family pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|253986096|gb|ACT50953.1| pseudouridine synthase, RluA family [Methylovorus sp. SIP3-4]
          Length = 353

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 81/341 (23%), Positives = 146/341 (42%), Gaps = 42/341 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRI 59
           M+  T +  +++  D   +RLD+  +   P  +   LQ+ ++ G V ++  + V    ++
Sbjct: 1   MTQTTPI-TLIIPQDLGGLRLDQALQKLLPEHSRSRLQQWIKDGLVTLEPAQAVTAKTKV 59

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G+ +++    +   H                 ++ +   + YED  I V NKPAG+ V
Sbjct: 60  WGGERLQVQVQPSPDEH--------------AFEAEDIPLDVQYEDEHILVINKPAGLVV 105

Query: 120 QGGSGIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              +G   +  G L + +           +  + HRLD++TSG+LVVA+T  A   L   
Sbjct: 106 HPAAG---NWSGTLLNALLHHAPVVKDLPRAGIVHRLDKDTSGLLVVAKTLTAQTSLVRQ 162

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + R +++ Y ++VWG    +   I   + +  H             +    A++ ++V+
Sbjct: 163 LQARTVKREYRAIVWGQVW-QNGRIDQPIGRHPH-----ARTKMAINRNGKPAVTRYEVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------- 286
           + FA    +L     TGRTHQ+RVH  H+  P+VGD  Y            Q+       
Sbjct: 217 ERFA-VHTYLRCNLETGRTHQIRVHMQHLKAPLVGDPVYGLGGIVPLRMMPQHLRDTILN 275

Query: 287 --KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
             +  LHA  + L HP  G  ++    LPA M    +++  
Sbjct: 276 FGRQALHAVKLGLIHPASGEFMEWQVELPADMKSLLEAMRL 316


>gi|254431057|ref|ZP_05044760.1| pseudouridylate synthase, 23S rRNA-specific [Cyanobium sp. PCC
           7001]
 gi|197625510|gb|EDY38069.1| pseudouridylate synthase, 23S rRNA-specific [Cyanobium sp. PCC
           7001]
          Length = 320

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 87/315 (27%), Positives = 138/315 (43%), Gaps = 28/315 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW     P  +   +QK + +G VRV+    +    ++ G  V +          
Sbjct: 21  PMRLDRWLVAQRPEQSRARIQKFIEAGYVRVNGVTGRAKTPLRHGDRVEVWM-------- 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
                           +  +   +LYED+ + V NKPAG++V    G      ++G L  
Sbjct: 73  ------PPPEPLPYLVAQAMPLDVLYEDAHLIVLNKPAGLTVHPAPGNKDGTLVNGLLHH 126

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +VVA+++ A  +L    + R   + Y  +V G P
Sbjct: 127 CPDLPGIGGELRPGIVHRLDKDTTGCIVVAKSQEALVNLQVQIQKRIASRDYLGVVHGQP 186

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 +   + +       Y  V   ++    +A +H++V +     +  L  +  TGR
Sbjct: 187 AADHGTVIGAIGRHPADRKKYAVV---SDASGRHACTHWQVQERLGD-YALLRFKLDTGR 242

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH+ HMG PIVGD  Y    +     P      LHA  + L HP    RL + AP
Sbjct: 243 THQIRVHSAHMGHPIVGDPVYSRCRRLPLALPG---QALHAVRLGLDHPITRERLVLEAP 299

Query: 311 LPAHMVKTWDSLGFK 325
           LPA   +  + L  +
Sbjct: 300 LPAVFEQLLERLRSR 314


>gi|85707640|ref|ZP_01038706.1| pseudouridine synthase D large subunit [Erythrobacter sp. NAP1]
 gi|85689174|gb|EAQ29177.1| pseudouridine synthase D large subunit [Erythrobacter sp. NAP1]
          Length = 317

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 141/328 (42%), Gaps = 30/328 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVR 66
           + ++  + +   RLD+   +    ++   +Q ++  G V +  K V   + ++      R
Sbjct: 4   EEIITGSIQVPARLDKALADA-TELSRARVQALIAEGAVEIAGKAVTSASVKVTENTPFR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           I                + + V     +  +   + +ED  + V NKPAG+ V   +G  
Sbjct: 63  IT---------------VPAVVEAEAQAQDIALDVAFEDEDLIVVNKPAGMVVHPAAGNP 107

Query: 125 IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  L              +P + HR+D++TSG+LVVA++ AA + L   F    +
Sbjct: 108 DGTLVNALLHHCRGQLSGIGGVARPGIVHRIDKDTSGLLVVAKSDAAHEGLAAQFAEHSV 167

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++  G P   +  I   L + S      + V+ +N     +AI+H+KV+      
Sbjct: 168 HRRYLAVCGGHPSPAEGTINERLGR-SDANRKKMAVLPKNSSRGKHAITHYKVLKPIG-A 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---KGNFTSPIQNKLYLHARYMD 296
              +E +  TGRTHQ+RVH   +G  ++GD  Y       K   +     +  LHA  + 
Sbjct: 226 AALIECRLETGRTHQVRVHCASIGHALLGDPIYGRTPKVLKPLLSQLKFARQALHAAELG 285

Query: 297 LPHPE-GGRLQITAPLPAHMVKTWDSLG 323
             HP  G  L+ +A LPA M +  D LG
Sbjct: 286 FIHPILGSELRFSADLPADMQELIDELG 313


>gi|126032015|gb|ABN71573.1| putative pseudouridylate synthase [uncultured bacterium]
          Length = 353

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 81/330 (24%), Positives = 138/330 (41%), Gaps = 35/330 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + ++      RLD+      P ++   LQ+ + +G V V+   V+  + +  G VV++ 
Sbjct: 34  TLRIDERYAGERLDKALAFLIPDVSRSRLQQWVVAGAVTVNGGAVRARHTLTFGDVVKVT 93

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P                +        + +   +++ED  I V NKP  + V   +G   H
Sbjct: 94  PQ--------------PAPDAAAYKPEPMPLEVIFEDDAILVLNKPPKLVVHPAAG---H 136

Query: 129 IDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             G L + + +         +  + HRLD +TSG++VVA+T AA   L    + R + + 
Sbjct: 137 WSGTLLNGLLAYAPTLIDVPRAGIVHRLDADTSGLMVVAKTLAAQTDLVRQLQSRTVTRE 196

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQK 239
           YW+LV G+P  +   I   + +      + +       + A  A +H+  +D        
Sbjct: 197 YWALVLGVPSQR-GVIDAAIGRDP---RNPLRFKVSTTEAAKPARTHYATLDSTKNAGAD 252

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ----NKLYLHARYM 295
             WL  +  TGRTHQ+RVH  H+G P++GD  Y            +    ++  LHA  +
Sbjct: 253 ISWLACRLETGRTHQIRVHLEHVGHPLIGDPVYRRRLPPRGEPAARWKEFDRQALHACRL 312

Query: 296 DLPHPEG-GRLQITAPLPAHMVKTWDSLGF 324
            L HP    RL       A + +    LGF
Sbjct: 313 ALDHPVSRQRLNWFHSPAADLAQLMHELGF 342


>gi|332141865|ref|YP_004427603.1| ribosomal large subunit pseudouridine synthase D [Alteromonas
           macleodii str. 'Deep ecotype']
 gi|327551887|gb|AEA98605.1| ribosomal large subunit pseudouridine synthase D [Alteromonas
           macleodii str. 'Deep ecotype']
          Length = 327

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 85/330 (25%), Positives = 150/330 (45%), Gaps = 33/330 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
            E     +RLD+   + +P  +   L+  ++ G V V+            G+V+ +P   
Sbjct: 14  TEAAHFGLRLDQVLADLFPEYSRSKLKTWIQDGNVSVN------------GEVITVPRHK 61

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
             ++ ++  Q  +D  V +T  +  +   ++YED  I V NKPA + V  G+G     + 
Sbjct: 62  MQMDELVTVQAEMD--VQVTSEAQDIALDIVYEDEHILVINKPADLVVHPGAGNPSGTVL 119

Query: 131 GFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             L + V    + PR  + HRLD++T+G++VVA+T  A  HL +  + R + + Y ++  
Sbjct: 120 NALLNHVPEIDKVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVDQLQRREVSREYEAIAL 179

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        I +  + +      ++ V +        AI+HF+VI+ F + +  L ++  
Sbjct: 180 GTMVA--GGIVDEPIGRHATKRTHMAVREM----GKPAITHFRVIEKF-RAYTHLRLKLE 232

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L HP
Sbjct: 233 TGRTHQIRVHMAHIKHPLLGDQVYGGRPRLPKGASEDFIGVLRGFQRQALHAAQLSLFHP 292

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           E    +   APLP  M     ++    + N
Sbjct: 293 ETEEWMTWKAPLPQDMQDLLKAVKKDTEDN 322


>gi|289547904|ref|YP_003472892.1| pseudouridine synthase [Thermocrinis albus DSM 14484]
 gi|289181521|gb|ADC88765.1| pseudouridine synthase, RluA family [Thermocrinis albus DSM 14484]
          Length = 324

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 76/316 (24%), Positives = 144/316 (45%), Gaps = 32/316 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
             +    VE  +   RLD++    YP  +   +++++  G V VD + V K + +++ G+
Sbjct: 7   EEILEFRVEEHQAGKRLDQFLAEAYPDFSRSYIKELVEGGYVLVDGQVVYKPSRKVKGGE 66

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VV +                +     L+  ++ +   +LYED  + V  KP G+ V    
Sbjct: 67  VVVLC---------------VPKVEPLSLPAEDIPLEILYEDDDLAVVVKPCGLVVHPSP 111

Query: 124 GIA--YHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L  W D     +  +P + HRLD+ T G++VVA+   A + L E F  R
Sbjct: 112 GYTSGTLVNALLFRWRDLPTVGEWYRPGIVHRLDRNTMGVMVVAKRELAHRRLAEQFEKR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF- 236
           ++ K+Y +LV G+ +  +  ++  L +       +        +    AI+H+KV+  + 
Sbjct: 172 KVLKVYRALVKGLVERDEGTLSMPLARDPRHRKRFTV-----SEKGRDAITHYKVLKRYR 226

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHAR 293
           +     LE++ +TGRTHQ+RVH   +G P++GD  Y    ++        +     L + 
Sbjct: 227 SLSVSLLEIRIYTGRTHQIRVHMAGIGHPVLGDRIYGYVPSSLPQEINEAMGECHMLVSY 286

Query: 294 YMDLPHPEGGR-LQIT 308
            +   HP  G+ ++ +
Sbjct: 287 RLGFYHPVSGQWMEFS 302


>gi|90580377|ref|ZP_01236184.1| putative ribosomal large subunit pseudouridine synthase D [Vibrio
           angustum S14]
 gi|90438679|gb|EAS63863.1| putative ribosomal large subunit pseudouridine synthase D [Vibrio
           angustum S14]
          Length = 324

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 84/332 (25%), Positives = 143/332 (43%), Gaps = 35/332 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++  MRLD+     YP  +   ++  + +G V V+   V K   ++  G+ + I  
Sbjct: 10  TVGENQLGMRLDQVIAQLYPDYSRSRIKDWILNGMVSVNGDVVKKPREKMMGGEELFIQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I      + +   LD               ++YED  I V NKP    V  G+G     
Sbjct: 70  EIEDEVRWVAQDIPLD---------------IVYEDDDILVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L      ++  +  + HRLD++T+G++VVA+T  A   L  + + R+I + Y +L
Sbjct: 115 VLNALLHHCPSLAEVPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEAL 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        I   + + S        +     +    AI+H++V + F ++   + ++
Sbjct: 175 AIGQMTG-GGTIEKPIGRHST-----KRICMAVHEMGKDAITHYRVAERF-REHTRIVLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  +M  P++GD  Y    +    +  +        ++  LHAR + L 
Sbjct: 228 LETGRTHQIRVHMSYMSHPLIGDVIYGGRPRPPRDASPEFIQALRAFDRQALHARMLRLD 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           HP  G  ++  APLP  MV   D L      N
Sbjct: 288 HPITGEKMEWHAPLPIDMVAMIDILRKDTQEN 319


>gi|78048898|ref|YP_365073.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325929044|ref|ZP_08190199.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           perforans 91-118]
 gi|78037328|emb|CAJ25073.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325540577|gb|EGD12164.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           perforans 91-118]
          Length = 331

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 81/344 (23%), Positives = 151/344 (43%), Gaps = 34/344 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L   ++  +V ++    R D      +P  +   L + ++SG   +D +  +  + ++ G
Sbjct: 9   LDPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGEMARPRDTLRGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +                +   +LYED ++ V +KPAG+ V  G
Sbjct: 69  ESVQLQVVLETQTHAAPQD---------------IPLSVLYEDEQVLVIDKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +G           + D   +   +  + HRLD++TSG++VVART  A   L E    R +
Sbjct: 114 AGNPDQTLVNALLFRDPALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSAREV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G        +   + +      D + +  +++     A++H+++ + F + 
Sbjct: 174 HRQYLAVVVGALV-SGGTVNAPIDRHP---RDRLKMAVRDD--GRDAVTHYRLRERF-RA 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLH 291
              LE +  TGRTHQ+RVH  H+  PIVGD  Y    K    +  +         +  LH
Sbjct: 227 HTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRSFKRQALH 286

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           A  ++  HP  G  ++ +AP+PA + +    L     R   + R
Sbjct: 287 AETLEFLHPVSGEPVRASAPVPADLQRLMTVLREDSARAAELAR 330


>gi|114799098|ref|YP_762171.1| RluA family pseudouridine synthase [Hyphomonas neptunium ATCC
           15444]
 gi|114739272|gb|ABI77397.1| pseudouridine synthase, RluA family [Hyphomonas neptunium ATCC
           15444]
          Length = 341

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 78/352 (22%), Positives = 134/352 (38%), Gaps = 48/352 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSG 62
           M  +  +  E  +   RLD +       I+    + ++  G V V           ++ G
Sbjct: 1   MNQI-VITSEAADAGQRLDAFLGARAEGISRSRAKTLIEEGAVTVGGAVETNPRAPVKKG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V  +                +   V     ++ +   +L+ED+ + + NK AG++V   
Sbjct: 60  LVYAVN---------------MPPPVPAMPEAEAIPLEILFEDAHLVILNKAAGMAVHPA 104

Query: 123 SG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G      ++  L             ++P + HRLD+ TSG++V A+T +A   L   F 
Sbjct: 105 PGSQTGTLVNALLHHCQGQLSGIGGVERPGIVHRLDKLTSGVMVAAKTESAHTGLAALFE 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I ++Y ++  G P+     I   + +              +   A +A++H+K ++ 
Sbjct: 165 RHDIDRVYRAVTRGAPRPLSGTIEAAIARSESDRKKMSVHRNPDSPAARHAVTHYKAVET 224

Query: 236 FAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF----------- 276
           F  K           LE +  TGRTHQ+RVH  H G P++GD  Y               
Sbjct: 225 FGYKDRATRLPAAALLECRLETGRTHQIRVHMAHSGAPLIGDPVYGRQAGIMAWKAPGSE 284

Query: 277 ----KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
               K    +   ++  LHA  +   HP  G  L+  APLP  M     +L 
Sbjct: 285 ARYDKALAAARAFSRQALHAAVLGFVHPITGETLRYEAPLPEDMTGLIAALR 336


>gi|254482837|ref|ZP_05096074.1| pseudouridine synthase, RluA family [marine gamma proteobacterium
           HTCC2148]
 gi|214036918|gb|EEB77588.1| pseudouridine synthase, RluA family [marine gamma proteobacterium
           HTCC2148]
          Length = 312

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 81/318 (25%), Positives = 135/318 (42%), Gaps = 33/318 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +N RLD+     +P  +   LQ  ++ G + VD K+++  +++  G  + I         
Sbjct: 2   DNERLDQIAAKLFPDYSRSRLQTWIKKGDLLVDGKQLRTRDKVFYGAQLSID-------- 53

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKS 135
                   +    +      +   ++YED+ I V NKPAG+ V   +G     +   L +
Sbjct: 54  -------TEPEQAVGWQPQNIDLDIIYEDAHILVVNKPAGLVVHPAAGHPDGTLVNALLA 106

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 Q PR  + HRLD ETSGI+V A++  A Q L    + R +++ Y ++  G+   
Sbjct: 107 HSPEMAQLPRGGIVHRLDMETSGIMVAAKSLLAHQDLVSQLQERTVRREYVAVCIGVMTG 166

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               +   + +          +V     G   AI+H++V   +      + +   TGRTH
Sbjct: 167 -GGTVDEPMGRHPKQRKKMAVLVV----GGKPAITHYRVTKRYGH-HTRIAVNLETGRTH 220

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-R 304
           Q+RVH  H   P+VGD  Y    +    +  +         +  LHAR + L HPE G  
Sbjct: 221 QIRVHMAHKHYPLVGDPTYGGRPRIPKGASEELIAALRGFPRQALHARALGLFHPETGEE 280

Query: 305 LQITAPLPAHMVKTWDSL 322
           +    PLP  +    D L
Sbjct: 281 MNFECPLPTDLQGLLDVL 298


>gi|62260278|gb|AAX77894.1| unknown protein [synthetic construct]
          Length = 367

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 74/321 (23%), Positives = 134/321 (41%), Gaps = 28/321 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 38  QNIIMHPKDAGKRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 97

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E                +   +++ED  I V +KP  + V  G+G   
Sbjct: 98  NIELLPTNEWIAED---------------INLKIIFEDDDIIVIDKPVNMIVHPGAGNPT 142

Query: 126 AYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + D  K  +  + HRLD++TSG++V A++  A  +L +    R++ + Y 
Sbjct: 143 GTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYL 202

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    K+  I   + +            +        AI+H+  I+ +   F  +E
Sbjct: 203 AIVEGEIY-KQGTINQPIGRDPTNRTKMAINYR-----GKEAITHYTSIEVY-DGFTLIE 255

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            Q  TGRTHQ+RVH   +  P+VGD  Y   +         I  +  LHA  +   HP  
Sbjct: 256 CQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITIPTRQALHAYKLSFIHPTT 315

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
            ++ +  + LP  M+     L
Sbjct: 316 AKMVKFKSKLPEDMLNLKAQL 336


>gi|302871828|ref|YP_003840464.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302574687|gb|ADL42478.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 303

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 151/318 (47%), Gaps = 35/318 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPPVINALNHII 78
           RLDR+            +QKI+  G V V++ + +K   +++SG ++RI           
Sbjct: 9   RLDRYLSEVLSK-TRSFVQKIIEEGNVWVNQTQVLKPAYKVRSGDIIRI----------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW 136
               ++     L+  +  +   ++YED  + V NKP G+ V  G+G   +   +  L  +
Sbjct: 57  ----VIPEPKQLSLVAQDIDIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKF 112

Query: 137 VDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      +P + HRLD++TSG+L+VA+T  A   L+E+ +  +I++IY+++  G+ 
Sbjct: 113 SGKLSSINGVIRPGIVHRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVL 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K     +   + +   +    + V+         A+++F+V++ +  K+ +++++  TGR
Sbjct: 173 KEDSGVVDAPIGRH-PVNRLKMAVI----PNGKQAVTYFEVLERY-DKYTFVKLRLKTGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P++GD  Y  +              LHA  +   HP     L  +  
Sbjct: 227 THQIRVHMSYIGYPLLGDSTYGRSK----NEFGIQGQVLHAGEIKFVHPITSDVLHFSTE 282

Query: 311 LPAHMVKTWDSLGFKYDR 328
           LP + ++  + L  +  +
Sbjct: 283 LPEYFLEILNILRSRNSK 300


>gi|33592279|ref|NP_879923.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           pertussis Tohama I]
 gi|33571924|emb|CAE41444.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           pertussis Tohama I]
 gi|332381696|gb|AEE66543.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           pertussis CS]
          Length = 320

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 129/325 (39%), Gaps = 31/325 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD+      P  +   LQ  + +G V V+  + K    +  G V+ +  
Sbjct: 19  LTVPPDTPADRLDKVLAGLLPGHSRSRLQGWIEAGYVLVNGAQAKVRQAVGPGDVLSVWE 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                +     + +                 ++ E     V +KPAG+    G+G     
Sbjct: 79  QPAPESRAFAPEPVA--------------FDVVAESPDWIVVDKPAGLVTHPGAGNWSGT 124

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  + + ++  +  + HRLD++TSG++VVAR   A  HL    + R + + Y +L
Sbjct: 125 LLNGLLHRYPELARVARAGIVHRLDKDTSGLMVVARNERAQTHLVRQLQARTMGRQYIAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC----FAQKFCW 242
             G        +   + + + +    V +  +       A++HF            +   
Sbjct: 185 AHG-WLGAAGTVDRPIGRDARV---PVRMSVERPIAPKPAVTHFDPRRRGCAEGGARVSE 240

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +  +  TGRTHQ+RVH   +G P++ D  Y        T     +  LHAR +    P G
Sbjct: 241 VLCRLETGRTHQIRVHLASLGHPLLADTLYGGKPLAGAT-----RQMLHARALHFDDPGG 295

Query: 303 -GRLQITAPLPAHMVKTWDSLGFKY 326
            G +   A +PA M    ++L +  
Sbjct: 296 AGEVSFEAGVPADMSDVQEALAWNA 320


>gi|53720057|ref|YP_109043.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei K96243]
 gi|53725726|ref|YP_102318.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           mallei ATCC 23344]
 gi|67641115|ref|ZP_00439900.1| pseudouridine synthase, RluA family [Burkholderia mallei GB8 horse
           4]
 gi|121600497|ref|YP_993794.1| RluA family pseudouridine synthase [Burkholderia mallei SAVP1]
 gi|124385930|ref|YP_001028742.1| RluA family pseudouridine synthase [Burkholderia mallei NCTC 10229]
 gi|126448075|ref|YP_001081352.1| RluA family pseudouridine synthase [Burkholderia mallei NCTC 10247]
 gi|126452060|ref|YP_001067109.1| RluA family pseudouridine synthase [Burkholderia pseudomallei
           1106a]
 gi|134277927|ref|ZP_01764642.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 305]
 gi|167000755|ref|ZP_02266562.1| pseudouridine synthase, RluA family [Burkholderia mallei PRL-20]
 gi|167739572|ref|ZP_02412346.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 14]
 gi|167825182|ref|ZP_02456653.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 9]
 gi|167846678|ref|ZP_02472186.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei B7210]
 gi|167895267|ref|ZP_02482669.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 7894]
 gi|167911901|ref|ZP_02498992.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 112]
 gi|167919896|ref|ZP_02506987.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei BCC215]
 gi|217420690|ref|ZP_03452195.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 576]
 gi|226199879|ref|ZP_03795429.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pakistan 9]
 gi|237813217|ref|YP_002897668.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           MSHR346]
 gi|242315815|ref|ZP_04814831.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106b]
 gi|254178644|ref|ZP_04885299.1| pseudouridine synthase, RluA family [Burkholderia mallei ATCC
           10399]
 gi|254184188|ref|ZP_04890778.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1655]
 gi|254191223|ref|ZP_04897727.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pasteur 52237]
 gi|254195717|ref|ZP_04902143.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei S13]
 gi|254199211|ref|ZP_04905577.1| pseudouridine synthase, RluA family [Burkholderia mallei FMH]
 gi|254205518|ref|ZP_04911870.1| pseudouridine synthase, RluA family [Burkholderia mallei JHU]
 gi|254259234|ref|ZP_04950288.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1710a]
 gi|254357685|ref|ZP_04973958.1| pseudouridine synthase, RluA family [Burkholderia mallei
           2002721280]
 gi|52210471|emb|CAH36454.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei K96243]
 gi|52429149|gb|AAU49742.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           mallei ATCC 23344]
 gi|121229307|gb|ABM51825.1| pseudouridine synthase, RluA family [Burkholderia mallei SAVP1]
 gi|124293950|gb|ABN03219.1| pseudouridine synthase, RluA family [Burkholderia mallei NCTC
           10229]
 gi|126225702|gb|ABN89242.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106a]
 gi|126240945|gb|ABO04038.1| pseudouridine synthase, RluA family [Burkholderia mallei NCTC
           10247]
 gi|134251577|gb|EBA51656.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 305]
 gi|147748807|gb|EDK55881.1| pseudouridine synthase, RluA family [Burkholderia mallei FMH]
 gi|147752961|gb|EDK60026.1| pseudouridine synthase, RluA family [Burkholderia mallei JHU]
 gi|148026812|gb|EDK84833.1| pseudouridine synthase, RluA family [Burkholderia mallei
           2002721280]
 gi|157938895|gb|EDO94565.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pasteur 52237]
 gi|160699683|gb|EDP89653.1| pseudouridine synthase, RluA family [Burkholderia mallei ATCC
           10399]
 gi|169652462|gb|EDS85155.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei S13]
 gi|184214719|gb|EDU11762.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1655]
 gi|217396102|gb|EEC36119.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 576]
 gi|225927935|gb|EEH23972.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pakistan 9]
 gi|237503168|gb|ACQ95486.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           MSHR346]
 gi|238521978|gb|EEP85425.1| pseudouridine synthase, RluA family [Burkholderia mallei GB8 horse
           4]
 gi|242139054|gb|EES25456.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106b]
 gi|243063307|gb|EES45493.1| pseudouridine synthase, RluA family [Burkholderia mallei PRL-20]
 gi|254217923|gb|EET07307.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1710a]
          Length = 335

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 95/326 (29%), Positives = 153/326 (46%), Gaps = 22/326 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++      R+D +       +   ++ +ILRSG+VRV+K R+    R+  G   
Sbjct: 16  QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGD-- 73

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                       ++      +           +  +L+ED  I V NKPAG++V GGSG+
Sbjct: 74  ------VVRVPPVRVAAADLARAAGPAPVPAAEFEILFEDDAIIVLNKPAGVAVHGGSGV 127

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y++
Sbjct: 128 AFGVIEQMRHAR-PHAKFLELAHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRYFA 186

Query: 186 LVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G       ++  +   L K +   G+    V+++      + + F ++D +   +  
Sbjct: 187 CVHGDWAADWGRRRVVKAPLFKYATPDGERRVRVQED---GLPSHTVFNLVDRWPD-YAL 242

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PIVGD KY               P   +++LHA  + L
Sbjct: 243 VEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARANAVPSIKRMFLHAHRLRL 302

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA   +  D L
Sbjct: 303 AHPLTGEPLQFDAPLPAECRQFIDQL 328


>gi|251793936|ref|YP_003008668.1| 23S rRNA pseudouridine synthase D [Aggregatibacter aphrophilus
           NJ8700]
 gi|247535335|gb|ACS98581.1| ribosomal large subunit pseudouridine synthase D [Aggregatibacter
           aphrophilus NJ8700]
          Length = 324

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 73/329 (22%), Positives = 135/329 (41%), Gaps = 35/329 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
            V+  +   RLD+     +P  +   L+  +    V V+         ++   + + I  
Sbjct: 9   TVQPQQMGQRLDQTLAELFPDYSRSRLKTWIEDDLVLVNGVVQNVPRTKVYGDEHIEITV 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
            I        E                +   ++YED  I V NKP  + V  G+G     
Sbjct: 69  EIEDETRFEPEN---------------IPLNIVYEDDDILVINKPKDLVVHPGAGNPKGT 113

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++
Sbjct: 114 VLNALLYHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAV 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI   K   +   + +                     A++H+++++ F + +  L ++
Sbjct: 174 ACGIM-TKGGTVDEPMARHPT-----KRTHMAVHPMGKPAVTHYRIMERF-RDYTRLRLR 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  LHA  + L 
Sbjct: 227 LETGRTHQIRVHMAHLAHPLLGDQTYGGRPRPPKNASEELMNVLRNFKRQALHAIMLRLQ 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HP  G  ++  APLP   V+   +L   Y
Sbjct: 287 HPISGEMMEWYAPLPEDFVELITALKADY 315


>gi|322411546|gb|EFY02454.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. dysgalactiae ATCC 27957]
          Length = 297

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 76/314 (24%), Positives = 138/314 (43%), Gaps = 34/314 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V++          
Sbjct: 8   SGQRLDKALADLSP-LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVIQFE-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
            + E+++L+        +  +   ++YED  + + NKP G+ V   +G      ++  + 
Sbjct: 59  -LPEEEVLE------YQAQVIPLDIIYEDEALAIINKPQGMVVHPSAGHPSGTMVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+T  A Q L    + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDEAHQALAAELKAKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        A++ F V++ F   +  +E+Q  TG
Sbjct: 172 LPNDRGMIEAPIGRSEKDRKKQAVTAK-----GKEAVTRFTVLERFGD-YSLVELQLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +   +  +LHA  + L HP  G  +  T 
Sbjct: 226 RTHQIRVHMAYIGHPVAGDPLYGPR-----KTLSGHGQFLHAETLGLTHPLTGEDMLFTV 280

Query: 310 PLPAHMVKTWDSLG 323
             PA   KT   L 
Sbjct: 281 APPAIFQKTLQQLR 294


>gi|301168827|emb|CBW28418.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae 10810]
          Length = 324

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 142/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NK   + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKSKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +    +  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPIVEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|113475517|ref|YP_721578.1| ribosomal large subunit pseudouridine synthase D [Trichodesmium
           erythraeum IMS101]
 gi|110166565|gb|ABG51105.1| ribosomal large subunit pseudouridine synthase D [Trichodesmium
           erythraeum IMS101]
          Length = 316

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 89/334 (26%), Positives = 148/334 (44%), Gaps = 29/334 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RI 59
           MS  + +   V    E   RLD W       ++  ++QK++  G V+V+ +        +
Sbjct: 1   MSDESPIILEVNSEYEITQRLDIWLSQQMLELSRSHIQKLISQGNVKVNDQLCTSKKAIV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G                K   ++   + L   ++ +   +LYED  + + NKPAG+ V
Sbjct: 61  HQGD---------------KIILVIPPPIPLAIEANDIPLDILYEDDALLIINKPAGLVV 105

Query: 120 QGGSGIAY--HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G +    ++  L       G    Q+P + HRLD++T+G ++VA+T  A QHL   
Sbjct: 106 HPAPGHSEGTLVNALLAHCDSLAGIGGVQRPGIVHRLDKDTTGAIMVAKTDHAYQHLQAQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + +  ++ Y  +V+G PK     I   + +  H        V   E+G   A++H++V 
Sbjct: 166 LQAKTARREYLGVVYGSPKTDSGIINLPIGR--HRVDRKKMAVTPVERGGKIAVTHWEVK 223

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           +     F  +  +  TGRTHQ+RVH+  +G PIVGD  Y    KG           LHA 
Sbjct: 224 ERLG-NFSMILFRLETGRTHQIRVHSAQVGYPIVGDTIYG---KGRSVGVNLTGQVLHAW 279

Query: 294 YMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKY 326
            ++L HP  G L +  APLP   +   + L  ++
Sbjct: 280 RLELQHPVSGELVEAIAPLPEDFLTLVEVLRKRF 313


>gi|15839195|ref|NP_299883.1| pseudouridylate synthase [Xylella fastidiosa 9a5c]
 gi|9107828|gb|AAF85403.1|AE004067_10 pseudouridylate synthase [Xylella fastidiosa 9a5c]
          Length = 330

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 96/327 (29%), Positives = 159/327 (48%), Gaps = 25/327 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ VVV  +    RLD +  +    +    + K++RSGQVRV+  RVK   ++  G  +R
Sbjct: 18  VRIVVVPAEHSGQRLDNFLLSKLKGVPRSLIYKLVRSGQVRVNGGRVKAERKLDGGDEIR 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      +I+++ I+  S         +++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 78  LPPL-----RLIQDRAIVAPSAAFLAR---MEAAIVFEDARLLALNKPSGMASHGGSGIS 129

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--------RR 178
           Y +   ++       Q+  L HRLD++TSG+L++A+ RAA   L    R         R 
Sbjct: 130 YGVIEAMRILRPK--QELELVHRLDRDTSGLLIMAKKRAALIELQALMREASVNGKEGRG 187

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y +L+ G   N    +   L      GG+    V  + K +    S F++++    
Sbjct: 188 IAKRYLTLLSGRMPNGVMSVDAPLHINLRQGGERHVRVHHDGKPSK---SRFRLLERRG- 243

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMD 296
              + E+   TGRTHQ+RVHA H+G P+ GD KY                +L+LHA  ++
Sbjct: 244 GQSYCEVLIETGRTHQIRVHAQHLGHPVTGDDKYGDQEVNRRLRDQIGLQRLFLHAVSLE 303

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
                G     + APL   +V   D L
Sbjct: 304 FALDAGSTPYVLNAPLAEDLVAALDRL 330


>gi|153834660|ref|ZP_01987327.1| ribosomal large subunit pseudouridine synthase D [Vibrio harveyi
           HY01]
 gi|156973324|ref|YP_001444231.1| 23S rRNA pseudouridine synthase D [Vibrio harveyi ATCC BAA-1116]
 gi|148868912|gb|EDL67970.1| ribosomal large subunit pseudouridine synthase D [Vibrio harveyi
           HY01]
 gi|156524918|gb|ABU70004.1| hypothetical protein VIBHAR_01005 [Vibrio harveyi ATCC BAA-1116]
          Length = 325

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 73/331 (22%), Positives = 144/331 (43%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L +G+V+V+ + V K   R+  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTRVMGGEEITLQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  I V NKP    V  G+G     
Sbjct: 70  ELEDEERW---------------EAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + D ++  +  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLHHYPDIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S         +         A++H++V + F ++   + ++
Sbjct: 175 AIGRM-TAGGKVDKPIGRHST-----KRTLMAVAPMGKPAVTHYRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDTAYGGRARIPTGASEELTEMIRGFDRQALHAVMLRFD 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  L+  AP+P  MV+  ++L    + 
Sbjct: 288 HPVTGEELEFHAPVPDDMVEMTEALRKDTEE 318


>gi|325921639|ref|ZP_08183476.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           gardneri ATCC 19865]
 gi|325547873|gb|EGD18890.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           gardneri ATCC 19865]
          Length = 328

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 95/326 (29%), Positives = 155/326 (47%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPQDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++  +  D +   +     L++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 76  IPP--------VRVNEEGDKAAPPSAFMARLEAAIVFEDARLLALNKPSGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   +    R       R I 
Sbjct: 128 FGAIETLRALRP--NQTLELVHRLDRDTSGLLIVAKKRSALTEMQALMREDDRVQGRGIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L+ G   +    +   L      GG+    V         ++SHFK+++      
Sbjct: 186 KRYLTLLVGRMPDGVMTVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFKLLERRG-GH 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G P+ GD KY      K         +L+LHA  ++  
Sbjct: 242 SYCEVRIETGRTHQIRVHAQHLGHPVAGDDKYGEAEVNKRLRDQLGLKRLFLHAASLEFA 301

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     + APL   +    D LG
Sbjct: 302 LDAGKAPYVLNAPLAPELADALDRLG 327


>gi|93005955|ref|YP_580392.1| pseudouridine synthase, RluD [Psychrobacter cryohalolentis K5]
 gi|92393633|gb|ABE74908.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter
           cryohalolentis K5]
          Length = 396

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 78/337 (23%), Positives = 140/337 (41%), Gaps = 33/337 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V++ V+E DE  +R+D+     +   + V LQ  +  G +  +    K   R+++G ++
Sbjct: 80  DVKHTVIE-DEAGLRIDKLASKIFTDFSRVQLQGWVSDGSLLYNGSIQKPKIRVKAGDIL 138

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +   +   +    E   +D               ++YED  + V NKP G+ V  G+G 
Sbjct: 139 HLSTTLEQHSEDQPEDIAID---------------VVYEDDDVLVINKPVGMVVHPGAGN 183

Query: 125 -IAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                ++  L  +       +  L HR+D++TSG+L++ +T+ A   L E  + + + + 
Sbjct: 184 QTGTLVNALLYHYPQQHHLPRAGLVHRIDKDTSGLLLIGKTKPAQLALMEQLKDKSVYRH 243

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFC 241
           Y  +V G        ++      + IG       K         A++H   +      +C
Sbjct: 244 YQCVVAG----DAASLSRHRRIDAPIGRHRNQRTKMTVMTAGREAVTHLLNVTALNGNYC 299

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL--------HAR 293
            L++   TGRTHQ+RVH  H+  PIVGD  Y    +         +  +        HA 
Sbjct: 300 LLDIGLETGRTHQIRVHLSHITYPIVGDRVYGGRRQLRAGLTEAQRQAINNFPRQALHAY 359

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
            +   HP  G  +++T P+P  M +    L   YD  
Sbjct: 360 TLGFVHPTTGEDVEVTTPMPEDMQQLMAVLSDGYDEE 396


>gi|33602573|ref|NP_890133.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           bronchiseptica RB50]
 gi|33577012|emb|CAE34092.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           bronchiseptica RB50]
          Length = 320

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 129/325 (39%), Gaps = 31/325 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD+      P  +   LQ  + +G V V+  + K    +  G V+ +  
Sbjct: 19  LTVPPDTPADRLDKVLAGLLPGHSRSRLQGWIEAGYVLVNGAQAKVRQAVGPGDVLSVWE 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                +     + +                 ++ E     V +KPAG+    G+G     
Sbjct: 79  QPAPESRAFAPEPVA--------------FDVVAESPDWIVVDKPAGLVTHPGAGNWSGT 124

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  + + ++  +  + HRLD++TSG++VVAR   A  HL    + R + + Y +L
Sbjct: 125 LLNGLLHRYPELARVARAGIVHRLDKDTSGLMVVARNELAQTHLVRQLQARTMGRQYIAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC----FAQKFCW 242
             G        +   + + + +    V +  +       A++HF            +   
Sbjct: 185 AHG-WLGAAGTVDRPIGRDARV---PVRMSVERPIAPKPAVTHFDPRRRGCAEGGARVSE 240

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +  +  TGRTHQ+RVH   +G P++ D  Y        T     +  LHAR +    P G
Sbjct: 241 VLCRLETGRTHQIRVHLASLGHPLLADTLYGGKPLAGAT-----RQMLHARALHFDDPGG 295

Query: 303 -GRLQITAPLPAHMVKTWDSLGFKY 326
            G +   A +PA M    ++L +  
Sbjct: 296 SGEVSFEAGVPADMSDVQEALAWNA 320


>gi|160947739|ref|ZP_02094906.1| hypothetical protein PEPMIC_01674 [Parvimonas micra ATCC 33270]
 gi|158446873|gb|EDP23868.1| hypothetical protein PEPMIC_01674 [Parvimonas micra ATCC 33270]
          Length = 310

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 74/335 (22%), Positives = 139/335 (41%), Gaps = 33/335 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++Y+     ++ +R D +      +++  ++QK+++   V V+ K +K N  ++ G 
Sbjct: 1   MAELKYI----SDKKIRCDVFLSEKISNLSRTSIQKLIKGKLVFVNGKNIKPNVILEIGD 56

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     +T  ++ +   ++YED  I + NKP  + V    
Sbjct: 57  EITVS---------------IPDKKEITLVAEDIDLDIVYEDDYIIIINKPRNMVVHPAV 101

Query: 124 GIAYHI--DGFLKSWVDS--KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           G   H   +  L     S    ++P + HRLD++T+G+++ A+       L E F  R I
Sbjct: 102 GNEKHTLVNALLNHCKLSMINSERPGIVHRLDKDTTGLIICAKDDETHLKLVEMFANREI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y ++  G    +   I   + +           +    K    AI+ + V+     K
Sbjct: 162 NKKYLAICNGSFSKENGLIDKPIGRDEKDRKK----MSVKSKSGKAAITEYNVL-ISNLK 216

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +++  HTGRTHQ+RVH   +  PI+GD  Y    +        N   LH+ Y++  H
Sbjct: 217 YSLVDVTLHTGRTHQIRVHFSSLNHPIIGDETYGKKNEKIKA----NGQMLHSYYLEFSH 272

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
           P     L  T     +     +  G K++  L  K
Sbjct: 273 PITDENLSFTVLPDEYFFSILNKTGLKFNEELLCK 307


>gi|322437152|ref|YP_004219364.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX9]
 gi|321164879|gb|ADW70584.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX9]
          Length = 371

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 89/343 (25%), Positives = 150/343 (43%), Gaps = 47/343 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++    +     MRLD +     P I+   +Q ++ +GQV+VD    K   +++ G+ + 
Sbjct: 47  IRSFPADVAAAGMRLDAYLAQALPDISRARVQILIEAGQVKVDGAVPKAKAKLKGGETIE 106

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           I                      L    + +   ++YED  + V NKPAG+ V  G+G  
Sbjct: 107 IEGQPQLE--------------PLHAIPEDIPLQIVYEDEYLAVVNKPAGMMVHAGAGST 152

Query: 125 ------------IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLT 171
                       + +H+     S     G+ +P + HRLD++TSG++VVA+     + L 
Sbjct: 153 DDERNRGTLVNAVLFHMGKTADSLSGVGGELRPGIVHRLDKQTSGLIVVAKDDVTHRRLG 212

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISH 229
           E F  RR+ K Y +L  G  K     ++        I  D V  ++   +      A+SH
Sbjct: 213 EMFSERRVSKTYLTLAHGELKKADTTVSLP------IARDLVRRIRMTTRRGDGRSAVSH 266

Query: 230 FKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF------KGNF 280
           F V++       KF ++E++  TGRTHQ+RVH   +G P+VGD  Y A        + N 
Sbjct: 267 FHVLERLDTPYGKFTFVEVKIETGRTHQIRVHLQSLGHPVVGDTLYGAPHVVRLTKEPNV 326

Query: 281 TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
                 + +LHA  +   HP     ++  APL   +V+  + +
Sbjct: 327 EPLELERNFLHAARLAFVHPRTEEEMEFEAPLAEELVEFLEKI 369


>gi|241668214|ref|ZP_04755792.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25015]
 gi|254876749|ref|ZP_05249459.1| ribosomal large subunit pseudouridine synthase D [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|254842770|gb|EET21184.1| ribosomal large subunit pseudouridine synthase D [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
          Length = 328

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 75/318 (23%), Positives = 135/318 (42%), Gaps = 30/318 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++  D    R+D      +   +   +QK ++ G + V+ K  K  + +   + V I
Sbjct: 12  QKIMMHPDHAGKRIDSTINELFEQFSRSQIQKWIKDGLITVNGKTTKSKHILLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  + E                +   +++ED+ I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWLAED---------------IDLNIVFEDNDIIVIDKPIDMVVHPGAGNMT 116

Query: 126 AYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + +  K  +  + HRLD++TSG++V A++  A  +L +    R++ + Y 
Sbjct: 117 GTISNALLHKYPNQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLSERKVSRKYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWL 243
           ++V G    +             IG D  +  K         AI+H+K I+ +   F  +
Sbjct: 177 AIVEGEIYEEGTI-------NQPIGRDINNRTKMTINHKGKEAITHYKPIEVY-DGFTLI 228

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           E Q  TGRTHQ+RVH   +  P+VGD  Y   +           N+  LHA  +   HP 
Sbjct: 229 ECQLETGRTHQIRVHMKSIKHPLVGDQTYNKSSTKLDKVGIENINRQALHAYKLSFIHPT 288

Query: 302 GGRL-QITAPLPAHMVKT 318
             ++ +  + LP  M+  
Sbjct: 289 SQKIVRFKSKLPEDMLNL 306


>gi|239948112|ref|ZP_04699865.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Rickettsia endosymbiont of Ixodes scapularis]
 gi|239922388|gb|EER22412.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Rickettsia endosymbiont of Ixodes scapularis]
          Length = 310

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 145/326 (44%), Gaps = 40/326 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V N+  N+RLD+       +++   +QK ++S  V+V+   +   +  ++   V+     
Sbjct: 6   VPNELNNIRLDKALSQLLENVSRNQIQKSIKSSCVQVNDVIISDPDVLVKENDVILFSFK 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                              L   +  +   ++YED  + V NK AG++V  G+G  +H D
Sbjct: 66  ---------------EPEELKIAAANIALDIIYEDDDLIVINKAAGMTVHPGAG--HHDD 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD+ T+G++VVA+   A   L      R++ + 
Sbjct: 109 TLVNALLYHTKNLSDIGSSERPGIVHRLDKNTTGLMVVAKNNKAHMLLANQIEQRQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFC 241
           Y +LVWG+    +  I N + + S      + ++K    G   A++H+K ++  ++    
Sbjct: 169 YKALVWGVINPLEGVIKNNIGR-SRSDRQKMTILKY---GGKEAVTHYKTLELFYSGTIS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP +         +  LH+ 
Sbjct: 225 MVECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAHSPPELKAKLIDFKRQALHSW 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKT 318
           Y+   HP     ++ +  LP  M + 
Sbjct: 285 YLSFTHPTSNEIMEFSCELPRDMGRL 310


>gi|254283218|ref|ZP_04958186.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium NOR51-B]
 gi|219679421|gb|EED35770.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium NOR51-B]
          Length = 319

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 136/328 (41%), Gaps = 34/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  D    RLD+     +P  +   L+  ++ G++ VD   ++  +++     + +    
Sbjct: 11  VPADLHGARLDQASAELFPDYSRSRLKTWIQEGKLTVDGVVLRPKDKVALDNQLEL---- 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
                      I ++   +    + L   + YED  + V NKPAG+ V   +G     + 
Sbjct: 67  -----------IAEAEAEVAWSGESLPLDICYEDDDVIVVNKPAGLVVHPAAGHPTGTLV 115

Query: 131 GFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             L +      Q+PR  + HRLD++TSG++ VA++  A + L      R + + Y +L  
Sbjct: 116 NALLAHAPELQQQPRGGIVHRLDKDTSGVMFVAKSHRAHRSLVTQLSARSVTREYAALCS 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        I   + +        + VV         AI+HF+V + F + F  L++   
Sbjct: 176 GQLVA-GGTIDQPIGRH-PTARTKMAVVS----DGKPAITHFRVANRF-EHFTQLQVNLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDLPHP 300
           TGRTHQ+RVH      P+VGD  Y    +          S + +  +  LHAR +   HP
Sbjct: 229 TGRTHQIRVHMAWCRHPLVGDPVYGGRLRIPAGISDRLKSALADFQRQALHARSLGFDHP 288

Query: 301 -EGGRLQITAPLPAHMVKTWDSLGFKYD 327
             G R+Q  A LP         L  +  
Sbjct: 289 ATGERMQFDANLPDDFRGLLAVLEAESP 316


>gi|167619213|ref|ZP_02387844.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           thailandensis Bt4]
 gi|257138436|ref|ZP_05586698.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           thailandensis E264]
          Length = 335

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 94/326 (28%), Positives = 150/326 (46%), Gaps = 22/326 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++      R+D +       +   ++ +ILRSG+VRV+K R+    R+  G   
Sbjct: 16  QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGD-- 73

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                       ++      +           +  +L+ED  I   NKPAG++V GGSG+
Sbjct: 74  ------VVRVPPVRVAAADLARAAGPAPVPAAEFEILFEDDAIIALNKPAGVAVHGGSGV 127

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y++
Sbjct: 128 AFGVIEQMRHAR-PHAKFLELVHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRYFA 186

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G           +   L K +   G+    V+++      + + F ++D +   +  
Sbjct: 187 CVHGDWAADWGRRRAVKAPLFKYATPDGERRVRVQED---GLPSHTVFNLVDRWPD-YAL 242

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PIVGD KY               P   +++LHA  + L
Sbjct: 243 VEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARASAVPSIKRMFLHAHRLRL 302

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA   +  D L
Sbjct: 303 AHPLTGEPLQFDAPLPAECRQFLDQL 328


>gi|239618296|ref|YP_002941618.1| pseudouridine synthase, RluA family [Kosmotoga olearia TBF 19.5.1]
 gi|239507127|gb|ACR80614.1| pseudouridine synthase, RluA family [Kosmotoga olearia TBF 19.5.1]
          Length = 311

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 82/323 (25%), Positives = 140/323 (43%), Gaps = 30/323 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  +V N E+  RLD++     P   +   +Q+ ++ G V V+ ++ K + R++SG +V 
Sbjct: 3   EEQIVTNREDGWRLDKFLSEKAPQWVSRTAIQRHIKDGGVLVNGEKKKASYRVKSGDIVT 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSG 124
                             +     T   + +   ++YED  I V NKP  + V       
Sbjct: 63  YT--------------FPEKVEPGTVEPENIPLNIIYEDHDIIVVNKPPDMIVHPVHNKT 108

Query: 125 IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L    D +G     +P + HRLD+ETSG++VVA+   A   L + F+ R  +
Sbjct: 109 SGTLVNALLNYCNDLQGIGGIMRPGIVHRLDKETSGVIVVAKNDRAHNSLVQQFKARTTE 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++  G    + E   N+ L +  +    + V          + + FK I  F    
Sbjct: 169 KYYLAIARGKTPLQGEI--NFSLARHPVNRLKMTV----SATGKESHTLFKTITYFGNIA 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +  +P TGRTHQ+RVH   +G P++GD  Y  +           +  LHA  + + HP
Sbjct: 223 SLVLAKPKTGRTHQIRVHFKEIGHPLLGDKLYGRHKDDIIL--GAERHMLHALQISIHHP 280

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  +   A +P  M+K   +L
Sbjct: 281 RTGEKMTFVARVPEDMLKVIRNL 303


>gi|269962553|ref|ZP_06176901.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio harveyi 1DA3]
 gi|269832748|gb|EEZ86859.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio harveyi 1DA3]
          Length = 325

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 72/331 (21%), Positives = 145/331 (43%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L +G+V+V+ + V K   ++  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTKVMGGEEITLQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  I V NKP    V  G+G     
Sbjct: 70  ELEDEERW---------------EAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + D ++  +  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLHHYPDIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S         +        +A++H++V + F ++   + ++
Sbjct: 175 AIGRM-TAGGKVDKPIGRHST-----KRTLMAVAPMGKHAVTHYRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDTAYGGRARIPTGASQELTEMIRGFDRQALHAVMLRFE 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  L+  AP+P  MV+  ++L    + 
Sbjct: 288 HPVTGEELEFHAPVPDDMVEMTEALRKDTEE 318


>gi|121998031|ref|YP_001002818.1| RluA family pseudouridine synthase [Halorhodospira halophila SL1]
 gi|121589436|gb|ABM62016.1| ribosomal large subunit pseudouridine synthase C [Halorhodospira
           halophila SL1]
          Length = 325

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 97/328 (29%), Positives = 149/328 (45%), Gaps = 13/328 (3%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V++  V  DE   R+D +       +    + ++LR GQVRVD  R K   R+ +G+V
Sbjct: 6   PKVRHHQVLADEAGQRIDNFLLRQLKGVPRSRVYRLLRKGQVRVDGGRAKPTRRLSAGEV 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPPV             L   +        L+  +LYED ++ V +KP+G++V GGS 
Sbjct: 66  VRIPPVSGQRQTSQPASGGLPDGLEAR-----LRRGVLYEDERLLVLDKPSGLAVHGGST 120

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +   +   L+           L HRLDQETSG L++A+ R+  + L E  R  +++K Y 
Sbjct: 121 VRLGLVEALRGLRPDL-PFIELVHRLDQETSGCLMLAKRRSTLRRLHEQLRQGKVEKHYT 179

Query: 185 SLVWGIPKNKKE-CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +L+ G  +      +   L +      +    V    K    A++ F     + Q    +
Sbjct: 180 TLLVGPLRGVTPLRVDAPLERLPGAPRERQVRV---SKQGRAAVTEFLRKQSWPQ-ATLV 235

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEG 302
             +  TGRTHQ+RVHA H+G P+ GD +Y               +L+LHA  + L HP+ 
Sbjct: 236 TARLETGRTHQIRVHARHIGHPVAGDERYGDRGANATMRDYGLRRLFLHASSLRLQHPDT 295

Query: 303 GR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           G  L I APL   +    + L    D  
Sbjct: 296 GEPLCIEAPLSDELKAVLERLSHSQDEE 323


>gi|254477672|ref|ZP_05091058.1| ribosomal large subunit pseudouridine synthase D [Ruegeria sp. R11]
 gi|214031915|gb|EEB72750.1| ribosomal large subunit pseudouridine synthase D [Ruegeria sp. R11]
          Length = 344

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 91/356 (25%), Positives = 146/356 (41%), Gaps = 50/356 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M   +   V  +    RLD+      P    ++   L +++ +GQ+ VD K V     R+
Sbjct: 1   MASRRIEFVIAENPPKRLDKAVSRDVPEEATLSRTRLARLIEAGQLEVDGKIVTDAKARV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G  + I       +HI  E   L+               +++ED  + V NKPAG+ V
Sbjct: 61  EEGATISITVEEAEDSHIGPEDIPLE---------------VIFEDDDLIVINKPAGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    D+       ++P + HR+D+ETSG+LVVA++ AA Q L  
Sbjct: 106 HPAPGTPSGTLVNALLHHCGDNLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F    +++ Y ++ +G+P      +           N L   + +        KQ    
Sbjct: 166 QFEKHTVERYYRAVCYGVPDGNDPRLRGVKGASFEPGNILKLTTQLARHKTDRQKQAVLF 225

Query: 221 KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK- 277
           +G  +AI+  +++D F        +E    TGRTHQ+RVH  H G  +VGD  Y    K 
Sbjct: 226 QGGRHAITRARIVDSFGTPPVVALIECWLETGRTHQIRVHMAHAGHGLVGDPVYGGKRKL 285

Query: 278 --------GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
                            +  LHA  +   HP  G  ++  APLP  M    D+L  
Sbjct: 286 AAKALSTQAAAAVQGFPRQALHAAVLGFVHPVSGEDMRFEAPLPQDMATLLDTLAL 341


>gi|261867120|ref|YP_003255042.1| 23S rRNA pseudouridine synthase D [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412452|gb|ACX81823.1| ribosomal large subunit pseudouridine synthase D [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 324

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 73/329 (22%), Positives = 136/329 (41%), Gaps = 35/329 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
            V++ +   RLD+     +P  +   L+  +    V V+        +++   + + I  
Sbjct: 9   TVQSHQMGQRLDQTLAELFPDYSRSRLKTWIEEDLVLVNGVVQNVPRSKVYGDEQIEITV 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I        E                +   ++YED  I V NKP  + V  G+G     
Sbjct: 69  EIEDETRFEPEN---------------IPLNIVYEDDDILVINKPKDLVVHPGAGNPSGT 113

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++
Sbjct: 114 VLNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKIIREYEAV 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI   K   +   + +                     A++H+++++ F + +  L ++
Sbjct: 174 ACGIM-TKGGTVDEPMARHPT-----KRTHMAVHPMGKPAVTHYRIMERF-RDYTRLRLR 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  LHA  + L 
Sbjct: 227 LETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEELMSVLRNFKRQALHAVMLRLQ 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HP  G  ++  APLP   V+   +L   Y
Sbjct: 287 HPISGEMMEWYAPLPEDFVELITALKADY 315


>gi|283769500|ref|ZP_06342396.1| pseudouridine synthase, RluA family [Bulleidia extructa W1219]
 gi|283103768|gb|EFC05154.1| pseudouridine synthase, RluA family [Bulleidia extructa W1219]
          Length = 303

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 82/322 (25%), Positives = 145/322 (45%), Gaps = 34/322 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +VVE     +RLD++  +H   ++   LQ +++  QV V+ K VK + ++    ++  
Sbjct: 4   RRLVVEK--SGLRLDKYVSDHC-ELSRSFLQDLIKEQQVLVNGKAVKSSYKVNLEDIIEF 60

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGI 125
                     ++E +++   + L          +LYED  + V NK  G+ V    G   
Sbjct: 61  ------AVPDLEEIEVIPQDIPLN---------VLYEDEDVIVVNKEKGMVVHPSLGHQD 105

Query: 126 AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HR+D++TSG LV+A+   A   L++    +   +
Sbjct: 106 GTLVNALLFHCQDLSGINGKIRPGIVHRIDKDTSGCLVIAKNDVAHIALSKQIETKEAYR 165

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y  +V G  +++   I   + +        + VV +N + A    +HF V+  F Q + 
Sbjct: 166 EYRLIVHGNIQHEDGLIDAPIGRDPK-DRQRMAVVAENSRPAK---THFHVLKRFGQ-YT 220

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +L     TGRTHQ+RVH  ++  P++GD KY +      +        LHA  +   HP 
Sbjct: 221 YLSCLLETGRTHQIRVHMKYIQHPVLGDEKYGS----ACSFYETKGQVLHAHTLKFKHPI 276

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
            G  ++  APLP +     D L
Sbjct: 277 TGKEMEFIAPLPTYFTDVLDYL 298


>gi|254785221|ref|YP_003072649.1| ribosomal large subunit pseudouridine synthase D [Teredinibacter
           turnerae T7901]
 gi|237685566|gb|ACR12830.1| ribosomal large subunit pseudouridine synthase D [Teredinibacter
           turnerae T7901]
          Length = 333

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 81/307 (26%), Positives = 134/307 (43%), Gaps = 34/307 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+     +P  +   LQ+ ++ G++ V+ +  K   ++  G+ +R+  +       + 
Sbjct: 36  RLDQVAAELFPEFSRARLQQWIKQGRLTVNGEPAKPKLKLAGGECLRLSVLEEPQGEWLP 95

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSW- 136
           E   LD               ++YED  I V NKPAG+ V   +G      ++G +    
Sbjct: 96  EPIPLD---------------VVYEDEAILVLNKPAGLVVHPAAGNYTGTLLNGLIHHRQ 140

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             S   +  + HRLD++TSG++VVA+T AA  +L    + R +++ Y +L  G    +  
Sbjct: 141 AQSLLPRAGIVHRLDKDTSGLMVVAKTTAAQNNLVAQLQARTVKREYEALAIGEV--RSS 198

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              +  + +       + VV         A++H+  +  F   F  L +Q  TGRTHQ+R
Sbjct: 199 GFVDAPIGRHPTNRTRMAVVS----SGKPAVTHYTALARF-DGFTHLRLQLETGRTHQIR 253

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQN--------KLYLHARYMDLPHPEGGR-LQI 307
           VH  H+G P+VGD  Y             +        +  LHA  + L HP  G  LQ 
Sbjct: 254 VHMAHLGYPLVGDPVYGRRLPAKLLRENPDLVPLSSLPRQALHAVQLGLQHPASGEYLQW 313

Query: 308 TAPLPAH 314
             PL   
Sbjct: 314 QVPLAED 320


>gi|319789350|ref|YP_004150983.1| pseudouridine synthase, RluA family [Thermovibrio ammonificans
           HB-1]
 gi|317113852|gb|ADU96342.1| pseudouridine synthase, RluA family [Thermovibrio ammonificans
           HB-1]
          Length = 314

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 141/327 (43%), Gaps = 37/327 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            RLD++       I+    ++I+  G V+V+ K V K   +++ G+ V            
Sbjct: 9   QRLDQFVAEA-AQISRSQAKEIIEKGLVKVNGKTVQKPAYKVKEGERVEFE--------- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
                 +     +    + +   ++YED  + V NKPAG+ V    G      ++  L  
Sbjct: 59  ------VPEPEPIEVKPEAIPLEVIYEDQDVIVINKPAGMVVHPAPGHYSGTLVNALLHH 112

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G++VVA+   A Q L E F+ R + + Y +L++GIP
Sbjct: 113 CKDLGGIGGALRPGIVHRLDKDTAGLIVVAKNDLAQQSLIEQFKNRSVGRFYRALIYGIP 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTG 250
           K + + I   + +       +      N      AI+++ VI+ F       ++ +  TG
Sbjct: 173 KREHDRIVLPIGRDKFDRKKF----SPNTTSPKEAITNYWVIEKFPEHNVAEIKCKLETG 228

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------YLHARYMDLPHPEGG 303
           RTHQ+RVH  ++G P++GD  Y              +L        L A Y+   HP  G
Sbjct: 229 RTHQIRVHMSNLGHPLLGDRTYGYKP-SRIEDEKLRRLIDEMGMHALCAYYLAFDHPRTG 287

Query: 304 -RLQITAPLPAHMVKTWDSLGFKYDRN 329
            R++    LP    +  + L   Y   
Sbjct: 288 KRMEFEVELPKGYQRVLNYLKGFYSTE 314


>gi|161830503|ref|YP_001596932.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           RSA 331]
 gi|161762370|gb|ABX78012.1| ribosomal large subunit pseudouridine synthase D [Coxiella burnetii
           RSA 331]
          Length = 323

 Score =  246 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 87/331 (26%), Positives = 150/331 (45%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++  +    RLD+     +P  +   LQ  +R G V+VD  ++ K   +++  Q + I  
Sbjct: 11  IIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEIEA 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            +      + +   LD               ++YED  + V NKP G+ V  G+G+    
Sbjct: 71  QLEPNERWVPQPIPLD---------------VIYEDETLLVINKPVGLIVHPGAGVRDQT 115

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +  S    PR  + HRLD++TSG+L++ART A+   L ++ + R+I + Y ++
Sbjct: 116 LINALLHYDPSLSVVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAI 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+            + +  I    + VV    +    AI+HF++I  + +    + +Q
Sbjct: 176 VKGVLI--SGRTIEAPVGRHPIHRTRMAVV----EFGRPAITHFRIIKRY-RAHTHIRVQ 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQ------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+ GD  Y +      + + P+Q       +  LHA  +   
Sbjct: 229 LETGRTHQIRVHMAHIHHPLAGDPVYGSHVGIPVHLSDPLQTALKTLKRQALHAATLQFS 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           HP   R +   AP PA M    + L   Y +
Sbjct: 289 HPVDQRPMACHAPPPADMAHLLECLEDDYSQ 319


>gi|126439038|ref|YP_001059822.1| RluA family pseudouridine synthase [Burkholderia pseudomallei 668]
 gi|167903651|ref|ZP_02490856.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei NCTC 13177]
 gi|126218531|gb|ABN82037.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 668]
          Length = 335

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 95/326 (29%), Positives = 153/326 (46%), Gaps = 22/326 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + ++      R+D +       +   ++ +ILRSG+VRV+K R+    R+  G   
Sbjct: 16  QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGD-- 73

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                       ++      +           +  +L+ED  I V NKPAG++V GGSG+
Sbjct: 74  ------VVRVPPVRVAAADLARAAGPAPVPAAEFEILFEDDAIIVLNKPAGVAVHGGSGV 127

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ R+A   L E  R  R+ K Y++
Sbjct: 128 AFGVIEQMRHAR-PHAKFLELAHRLDRETSGILMLAKKRSALVGLHEQIRENRMDKRYFA 186

Query: 186 LVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G       ++  +   L K +   G+    V+++      + + F ++D +   +  
Sbjct: 187 CVHGDWAADWGRRRVVRAPLFKYATPDGERRVRVQED---GLPSHTVFNLVDRWPD-YAL 242

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+RVH  H+G PIVGD KY               P   +++LHA  + L
Sbjct: 243 VEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARANAVPSIKRMFLHAHRLRL 302

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G  LQ  APLPA   +  D L
Sbjct: 303 AHPLTGEPLQFDAPLPAECRQFIDQL 328


>gi|294085882|ref|YP_003552642.1| pseudouridine synthase [Candidatus Puniceispirillum marinum
           IMCC1322]
 gi|292665457|gb|ADE40558.1| pseudouridine synthase, RluA family [Candidatus Puniceispirillum
           marinum IMCC1322]
          Length = 341

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 139/333 (41%), Gaps = 44/333 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPH----INFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQV 64
           +    +    R+D++   H       ++   ++ ++   ++  D +     ++ ++    
Sbjct: 14  ITAPAEAVAQRIDKFLAEHLDDDGQSLSRSRIKALILDKRLLEDGRTLADPSSTVKP--- 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
                       +      L   V+ T  ++ +   +LYED+ I V NKPAG+ V    G
Sbjct: 71  ------------LCHYALELPPPVDATPKAENIPLDVLYEDAHIIVLNKPAGMVVHPAPG 118

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +    DS        +P + HRLD++TSG+++ A+T AA   LT  F   
Sbjct: 119 SLTGTLVNALIAHCGDSLTGIGGVMRPGIVHRLDKDTSGVMMAAKTDAAHHTLTSMFAAH 178

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +LVWG   ++   +   L + +H         +       +AI+H++V+    
Sbjct: 179 DLDRRYHALVWGTGVDRDGMVDAPLGRSTHDRKKQAVNPR-----GRHAITHWRVMRTLP 233

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-----------GNFTSPIQN 286
                +E    TGRTHQ+RVH  H+G P++GD  Y    +           G       N
Sbjct: 234 PFGSLVECTLETGRTHQIRVHMAHIGYPVIGDPLYGRAPRAGQMPDTRARTGLAQMRAFN 293

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           +  LHA ++   HP  G  L  TAP+P  M   
Sbjct: 294 RQALHAAHLGFEHPITGEALAFTAPMPPDMASL 326


>gi|27904809|ref|NP_777935.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
 gi|34395769|sp|Q89AH2|RLUC_BUCBP RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|27904207|gb|AAO27040.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
          Length = 315

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 102/321 (31%), Positives = 174/321 (54%), Gaps = 15/321 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           +   ++ +  + E  R+D + +  +  + F  + KI+R+GQ+R++KKR+  N +++ G  
Sbjct: 6   SSTHFLNITENSEKQRIDNFLRKTFKRLPFNLICKIIRTGQIRINKKRINQNYKLKLGDS 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+    +      K +  +  L+       +++LYED+   + NKP+G+SV  GSG
Sbjct: 66  VRIPPITIQSDS----NKKIKLNTRLSI---IFNNMILYEDNYFLILNKPSGMSVHSGSG 118

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           I Y +   L+  +    +   L HRLD++TSG+L++A+ R+  ++L E  R ++I+K Y 
Sbjct: 119 INYGMIENLR-ILRPYNRYLDLVHRLDRDTSGVLIIAKKRSILRNLHEQLREKKIKKKYV 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+  +  + I+  LLK S       ++VK + KG   +I+HF +   + +    + 
Sbjct: 178 ALVHGVWPDILKSISKPLLKTS--SRKNKNIVKIDPKG-KESITHFNIKKKYTKN-TLIS 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEG 302
           + P TGRTHQ+RVH LH+  PIV D KY       F       N+L LHA  ++  HP+ 
Sbjct: 234 ITPITGRTHQIRVHLLHLNYPIVLDAKYGIKKLDYFIKNKFNINRLLLHAESINFFHPKR 293

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
            + + ITAPL         +L
Sbjct: 294 KKNILITAPLDYVFKTVLKNL 314


>gi|294666973|ref|ZP_06732202.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 10535]
 gi|292603262|gb|EFF46684.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 10535]
          Length = 331

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 83/344 (24%), Positives = 148/344 (43%), Gaps = 34/344 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L   ++  +V ++    R D      +P  +   L + ++SG   +D +  +  + ++ G
Sbjct: 9   LDPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGEMARPRDTLRGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H   +                +   +LYED ++ V +KPAG+ V  G
Sbjct: 69  ESVQVQVVLETQTHAAPQD---------------IPLSVLYEDEQVLVIDKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +G           + D   +   +  + HRLD++TSG++VVART  A   L E    R +
Sbjct: 114 AGNPDRTLVNALLFRDPALASVPRSGVVHRLDKDTSGVMVVARTVQAQTALVEQLSAREV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G         AN  + +       + V          A++H+++ + F + 
Sbjct: 174 HRQYLAVVVGAL--VSGGTANAPIDRHPRDRLKMAVRD----DGRDAVTHYRLRERF-RA 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLH 291
              LE +  TGRTHQ+RVH  H+  PIVGD  Y    K    +  +         +  LH
Sbjct: 227 HTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGATDELVHELRTFKRQALH 286

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           A  ++  HP  G  ++ +AP+PA + +    L     R   + R
Sbjct: 287 AETLEFLHPVSGEPVRASAPVPADLQRLMTVLREDSARAAELAR 330


>gi|28897333|ref|NP_796938.1| 23S rRNA pseudouridine synthase D [Vibrio parahaemolyticus RIMD
           2210633]
 gi|153839761|ref|ZP_01992428.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus AQ3810]
 gi|260876296|ref|ZP_05888651.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus AN-5034]
 gi|260895103|ref|ZP_05903599.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus Peru-466]
 gi|260903277|ref|ZP_05911672.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus AQ4037]
 gi|34395767|sp|Q87S65|RLUD_VIBPA RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|28805542|dbj|BAC58822.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|149746714|gb|EDM57702.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus AQ3810]
 gi|308088909|gb|EFO38604.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus Peru-466]
 gi|308092904|gb|EFO42599.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus AN-5034]
 gi|308107949|gb|EFO45489.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus AQ4037]
 gi|328472095|gb|EGF42972.1| 23S rRNA pseudouridine synthase D [Vibrio parahaemolyticus 10329]
          Length = 325

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 72/331 (21%), Positives = 142/331 (42%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V+V+ + V K   ++  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVQVNGEVVTKPRTKVMGGEEITLQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  I V NKP    V  G+G     
Sbjct: 70  ELEDEERW---------------EAQDIPLDIVYEDDDIIVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + D ++  +  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLHHYPDIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S         +         A++H++V + F ++   + ++
Sbjct: 175 AIGRM-TAGGKVDQPIGRHST-----KRTLMAVAPLGKPAVTHYRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDTAYGGRARIPTGASQELTDMIRGFDRQALHAVMLRFE 287

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  L+  AP+P  MV   ++L    + 
Sbjct: 288 HPITGEELEFHAPVPDDMVAMTEALRKDTEE 318


>gi|322641590|gb|EFY38228.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
          Length = 274

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 94/276 (34%), Positives = 151/276 (54%), Gaps = 13/276 (4%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  EAGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R + +
Sbjct: 114 HGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGM 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A  
Sbjct: 173 QKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA-F 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              +   P TGRTHQ+RVH  + G PI  D +Y   
Sbjct: 229 ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDR 264


>gi|297183890|gb|ADI20012.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium EB000_65A11]
          Length = 318

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 84/324 (25%), Positives = 144/324 (44%), Gaps = 35/324 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  D    RLD      +P  +   LQ  +++G++ VD ++ K  +++  G++V I   
Sbjct: 10  IVPEDLAFNRLDHVASALFPQYSRSRLQTWIKNGELVVDGQKRKSKDKVTGGELVAIQ-- 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                          S++  T  +  +   + YED  + V NKP+G+ V  G+G      
Sbjct: 68  --------------SSAIETTYEAQAIPLNVAYEDEHLLVVNKPSGLVVHPGAGNFDGTL 113

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++G L       G  +  + HRLD++T+G+LVVA+T     HL +  + R + +IY ++V
Sbjct: 114 LNGLLHHAEQLNGIPRAGIVHRLDKDTTGLLVVAKTLTTQHHLVQQLQARSVSRIYDAVV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G    +   +   + + +               G   AI+H+KV+  F +    +E+  
Sbjct: 174 YGSL-TRSGKVDQPIGRHTTQRTKMAIR-----PGGKPAITHYKVVRNFGE-HSHIELAL 226

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH   +  P++GD+ Y   FK                 +  LHAR + L H
Sbjct: 227 ETGRTHQIRVHMQSISHPLIGDNTYGGGFKEPAHKDSGLLKALREFKRPALHARELKLIH 286

Query: 300 PEG-GRLQITAPLPAHMVKTWDSL 322
           P     +   A +P  M    D L
Sbjct: 287 PATEEEMHWCAEIPVDMQTLLDDL 310


>gi|253990666|ref|YP_003042022.1| 23S rRNA pseudouridine synthase D [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782116|emb|CAQ85280.1| ribosomal large subunit pseudouridine synthase D [Photorhabdus
           asymbiotica]
          Length = 325

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 79/343 (23%), Positives = 150/343 (43%), Gaps = 43/343 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + I  
Sbjct: 10  TVAESQLGQRLDQALAEMFPDYSRSRIKEWILGDRVQVNGKLINKPKEKVLGGEEISIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +I                         ++  ++YED  I V NKP  + V  G+G     
Sbjct: 70  IIEEDARW---------------EPQNIELNIVYEDDDILVINKPRDLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + + +   +  + HRLD++T+G++V+A+T  A   L ES ++R I + Y ++
Sbjct: 115 VLNALLYRYPEIADVPRAGIVHRLDKDTTGLMVIAKTVPAQTRLVESLQLREITREYEAV 174

Query: 187 VWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             G        +E I+    K++H+    +            AI+ ++V++ F +    L
Sbjct: 175 ATGRMTAGGIVEEPISRHPTKRTHMAVHPM---------GKPAITRYRVMEHF-RAHTRL 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYM 295
            ++  TGRTHQ+RVH  H+   +VGD  Y    +    +  +        ++  LHA  +
Sbjct: 225 RLRLETGRTHQIRVHMAHISHSLVGDPLYGGRPRPLKGASDEFREVMRNFDRQALHATML 284

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
            L HP  G  ++  A LP  MV   ++L  K D  ++   +  
Sbjct: 285 RLYHPITGIEMEWHAELPEDMVILINAL--KADAEVFKDDMDW 325


>gi|237653101|ref|YP_002889415.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|237624348|gb|ACR01038.1| pseudouridine synthase, RluA family [Thauera sp. MZ1T]
          Length = 319

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 94/318 (29%), Positives = 151/318 (47%), Gaps = 19/318 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++  ++      R+D +       +   ++ +ILRSG+VRV+ +RV+   R+Q G  VR
Sbjct: 11  VRHERIDEAAAGQRIDNYLLRIAKGVPKSHVYRILRSGEVRVNGRRVQQTYRLQEGDEVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+             +    +           ++YED  + V +KP+G +V GGSG++
Sbjct: 71  IPPIR------------IAEPTHAAPAPAGKPLPVVYEDEALLVIDKPSGKAVHGGSGVS 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L+       +   L HRLD+ETSG+L+VA+ R+A   L +  R   ++K Y +L
Sbjct: 119 YGVIEQLRVQRPEL-RMLELAHRLDRETSGLLIVAKKRSALTALHDMMREGSVEKRYLTL 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   N  + +   L K     G+    V    K A+  +     +    + +  LE++
Sbjct: 178 VPGRWSNPLQHVKVPLHKYLTAEGERRVRVADEGKAAHSIV----RLVRRWRDYSLLEVE 233

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
             TGRTHQ+RVH  H+G  + GD KY               +++LHA  + L HP  G  
Sbjct: 234 LKTGRTHQIRVHLAHLGFALCGDDKYGDFALNKRLEVEGLRRMFLHAAKLRLAHPLTGAP 293

Query: 305 LQITAPLPAHMVKTWDSL 322
           L   +PLPA +    D L
Sbjct: 294 LAFDSPLPADLQTFLDRL 311


>gi|226328713|ref|ZP_03804231.1| hypothetical protein PROPEN_02608 [Proteus penneri ATCC 35198]
 gi|225201899|gb|EEG84253.1| hypothetical protein PROPEN_02608 [Proteus penneri ATCC 35198]
          Length = 325

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 148/334 (44%), Gaps = 41/334 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V + +   RLD+     +P  +   +++ +   +V+V+ K + K   ++  G+ + I  
Sbjct: 10  TVADSQLGQRLDQALAEMFPDYSRSRIKEWILDNRVQVNDKIINKPKEKMLGGEKIEIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +I                         +   ++YED  I V NKP  + V  G+G     
Sbjct: 70  LIEEDVRW---------------EPQNIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + + +   +  + HRLD++T+G++VVA+T  A  HL E+ + R I + Y ++
Sbjct: 115 VLNALLYRYPEIANVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAV 174

Query: 187 VWGIPKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             G         E I+    K++H+    +            A++H++V++ F +    L
Sbjct: 175 ATGRMTAGGLVNEPISRHPTKRTHMAVHPM---------GKPAVTHYRVMEHF-RAHTRL 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG--------NFTSPIQNKLYLHARYM 295
            ++  TGRTHQ+RVH  H+   ++GD  Y    +           T  + ++  LHA  +
Sbjct: 225 RLRLETGRTHQIRVHMAHIHHALIGDQLYAGRPRPLKGASDELRETLRLFDRQALHATML 284

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            L HP  G  ++  APLP  MVK  D L    ++
Sbjct: 285 RLYHPITGIEMEWHAPLPDDMVKLIDVLKADVEQ 318


>gi|312881916|ref|ZP_07741679.1| 23S rRNA pseudouridine synthase D [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309370434|gb|EFP97923.1| 23S rRNA pseudouridine synthase D [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 325

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 76/331 (22%), Positives = 143/331 (43%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L+  L  G+V+VD + V K   ++  G+V+ +  
Sbjct: 10  TVKDAQLGQRLDQAIAELFSDFSRSRLKDWLLDGKVQVDGEVVTKPRTKVMGGEVIVLHA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  I V NKP G  V  G+G     
Sbjct: 70  ELEDEERW---------------EAQDIPLDIVYEDDDIIVINKPRGFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + D ++  +  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLHHFPDIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S         +         A++H++V + F ++   + ++
Sbjct: 175 AIGRM-TAGGRVEQPIGRHST-----KRTLMAVAPLGKPAVTHYRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPRGATPELAEKIRQFDRQALHAVMLKFE 287

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  L+  AP+P  MV   D+L    + 
Sbjct: 288 HPITGEELEFHAPVPDDMVAMSDALRTDIEE 318


>gi|146338456|ref|YP_001203504.1| pseudouridine synthase [Bradyrhizobium sp. ORS278]
 gi|146191262|emb|CAL75267.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Bradyrhizobium sp. ORS278]
          Length = 384

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 79/350 (22%), Positives = 143/350 (40%), Gaps = 58/350 (16%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV------DKKRVKFNNRIQSG 62
            ++V  DE + RLDR      P ++   L+ ++ +GQV +                + +G
Sbjct: 55  TIIVAGDEGSPRLDRVLAARLPELSRSRLKALILAGQVSLTSDSFGSGAVRDPAYHVTTG 114

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I                +  +V     ++ +   ++YED  I V +KP+G+ V   
Sbjct: 115 DTITID---------------VPEAVAPEPQAEAIPLQIIYEDDDIIVIDKPSGLVVHPA 159

Query: 123 SGIAYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           +G   H  G L + + +            ++P + HRLD++T+G++VVA+   A   L+ 
Sbjct: 160 AG---HETGTLVNALIAHCGASLSGIGGVKRPGIVHRLDKDTTGLMVVAKNDMAHASLSA 216

Query: 173 SFRMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            F        +++ Y +  WG+P      I   + +  H         K        AI+
Sbjct: 217 QFADHGRTGAMERGYLAFAWGVPHRPHGTINAAIDRHPHARDKMAVRAK-----GREAIT 271

Query: 229 HFKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------ 277
           H++V + F  +        +     TGRTHQ+RVH  H+G P++GD  Y  +FK      
Sbjct: 272 HYEVQESFTGRDGKPVASLIACHLETGRTHQIRVHLAHLGHPLLGDAVYGPHFKTKANQL 331

Query: 278 ---GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                       +  LHA  + + HP  G  ++  + LP  +    ++L 
Sbjct: 332 SERARAALDSLGRQALHAYLLVIEHPRTGDIMRWESELPEDLSLLGEALR 381


>gi|319941549|ref|ZP_08015875.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
 gi|319804919|gb|EFW01761.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
          Length = 339

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 99/322 (30%), Positives = 152/322 (47%), Gaps = 20/322 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V YV++  D +  RLD +       +   ++ +++R+G+VRV KKR K   ++  G VVR
Sbjct: 25  VSYVLIGEDADGQRLDNFLFRIAKGVPKGHVYRVIRAGEVRVSKKRAKAETKLMLGDVVR 84

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  A            +              +LYED  I +  KPAGI+  GGSGI+
Sbjct: 85  IPPMRVAQK---------PAGTPPAAPLAQGVLPVLYEDRHILIVLKPAGIAAHGGSGIS 135

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    +     L HRLD+ETSG +V+A+TR A   + +  +   ++K Y  L
Sbjct: 136 YGLIERLRATRPEE-PMLELCHRLDKETSGAIVIAKTRKALVRMHDLMKEGGVEKHYKLL 194

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   N+++ +   L +     G+              A + F V++ F     +L+ +
Sbjct: 195 VKGDWVNERQHVKVPLERYLLPSGERRVRASSE---GMSAHTIFTVLERFGS-VTYLDAE 250

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVHAL  G P+ GD KY                   +++LHA  +   HP 
Sbjct: 251 LKTGRTHQIRVHALSQGFPLAGDDKYGDFAFNRECTHGLLGAPLKRMFLHAWKLRFAHPV 310

Query: 302 GGRL-QITAPLPAHMVKTWDSL 322
            G L  ITAPLP  +     +L
Sbjct: 311 TGELVDITAPLPEELSAVISAL 332


>gi|134301739|ref|YP_001121707.1| pseudouridine synthase, RluA family protein [Francisella tularensis
           subsp. tularensis WY96-3418]
 gi|134049516|gb|ABO46587.1| pseudouridine synthase, RluA family protein [Francisella tularensis
           subsp. tularensis WY96-3418]
          Length = 317

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 73/315 (23%), Positives = 130/315 (41%), Gaps = 28/315 (8%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
             +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I   +  
Sbjct: 3   PKDAGKRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEINIELLP 62

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
            N  I E                +   +++ED  I V +KP  + V  G+G       + 
Sbjct: 63  TNEWIAED---------------INLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNT 107

Query: 132 FLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            L  + D  K  +  + HRLD++TSG++V A++  A  +L +    R++ + Y ++V G 
Sbjct: 108 LLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGE 167

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              K+  I   + +            +        AI+H+  I+ +   F  +E Q  TG
Sbjct: 168 IY-KQGTINQPIGRDPTNRTKMAINYR-----GKEAITHYTPIEVY-DGFTLIECQLETG 220

Query: 251 RTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QI 307
           RTHQ+RVH   +  P+VGD  Y   +         I  +  LHA  +   HP   ++ + 
Sbjct: 221 RTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITIPTRQALHAYKLSFIHPTTAKMVKF 280

Query: 308 TAPLPAHMVKTWDSL 322
            + LP  M+     L
Sbjct: 281 KSKLPEDMLNLKAQL 295


>gi|87118928|ref|ZP_01074826.1| ribosomal large subunit pseudouridine synthase C [Marinomonas sp.
           MED121]
 gi|86165319|gb|EAQ66586.1| ribosomal large subunit pseudouridine synthase C [Marinomonas sp.
           MED121]
          Length = 322

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 92/319 (28%), Positives = 168/319 (52%), Gaps = 16/319 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V+   ++ +  + R+D +       +    +  +LR G++RV+KKRVK + RI SG +
Sbjct: 12  PKVKINTIDENNHDQRIDNYLMAQLKGVPKGRIYNLLRKGEIRVNKKRVKPDTRIYSGDI 71

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRI P++         +   ++S    K    ++S ++YED+ + V NKP+G++V GGSG
Sbjct: 72  VRIAPIVV--------EPPKEASPVPHKLMQLIESRIVYEDAGLMVVNKPSGLAVHGGSG 123

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIY 183
           + + +   ++  + SK +   L HRLD++TSG++++++ R+  + L  + R +  +QK Y
Sbjct: 124 LNFGLVEVVRQ-LRSKEKSIELVHRLDRDTSGLIMISKKRSVLKQLHAALREKEGVQKTY 182

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV+G    +K+ +   LLK     G+ +  V         +++ FK++    + +  +
Sbjct: 183 QALVYGSWPKRKQQVNAPLLKNELKSGERIVKVHTE---GKESLTRFKLL-RQFEGYSLV 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEG 302
           E +P TGRTHQ+RVH LH G PIVGD KY  + +      +   +L LHA  +D+     
Sbjct: 239 ECEPVTGRTHQIRVHTLHAGYPIVGDDKYSPSEQNKEAKGLGFKRLCLHAAKLDI-MLND 297

Query: 303 GRLQITAPLPAHMVKTWDS 321
            R+ +  P+        + 
Sbjct: 298 QRILVEVPIDDEWRNAMNQ 316


>gi|308187865|ref|YP_003931996.1| ribosomal large subunit pseudouridine synthase D [Pantoea vagans
           C9-1]
 gi|308058375|gb|ADO10547.1| ribosomal large subunit pseudouridine synthase D [Pantoea vagans
           C9-1]
          Length = 325

 Score =  246 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 77/333 (23%), Positives = 133/333 (39%), Gaps = 35/333 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V V+   V     ++  G++V I
Sbjct: 8   TATVSESQLGQRLDQTLAELFPDYSRSRIKEWILDRRVTVNGVMVDTPKEKVLGGELVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I                         L   ++YED  I V NKP    V  G+G   
Sbjct: 68  DAEIEEAQRW---------------EPQNLPLDIVYEDEDIIVINKPRDFVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  +       +  + HRLD++T+G++VVA+T  A  HL +S + R I + Y 
Sbjct: 113 GTVLNALLHHYPAIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDSLQRREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A++H+++++ F +    L 
Sbjct: 173 AVAIGNM-TAGGTVEQPISRHST-----KRTHMAVHPMGKPAVTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMSHISHPLVGDPLYGGRPRPPKGASEAFITTLRGFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           L HP  G  ++  A LP  MV    +L    + 
Sbjct: 286 LYHPISGIEMEFHAALPQDMVDLIAALKADTEE 318


>gi|304399171|ref|ZP_07381038.1| pseudouridine synthase, RluA family [Pantoea sp. aB]
 gi|304353225|gb|EFM17605.1| pseudouridine synthase, RluA family [Pantoea sp. aB]
          Length = 325

 Score =  246 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 77/333 (23%), Positives = 133/333 (39%), Gaps = 35/333 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V   +   RLD+     +P  +   +++ +   +V V+   V     ++  G++V I
Sbjct: 8   TATVSESQLGQRLDQTLAELFPDYSRSRIKEWILDRRVTVNGVMVDTPKEKVLGGELVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I                         L   ++YED  I V NKP    V  G+G   
Sbjct: 68  DAEIEEAQRW---------------EPQDLPLDIVYEDEDIIVINKPRDFVVHPGAGNPD 112

Query: 128 HI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  +       +  + HRLD++T+G++VVA+T  A  HL +S + R I + Y 
Sbjct: 113 GTVLNALLHHYPAIMDVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDSLQRREITREYE 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        +   + + S                   A++H+++++ F +    L 
Sbjct: 173 AVAIGNM-TAGGTVEQPISRHST-----KRTHMAVHPMGKPAVTHYRIMEHF-RAHTRLR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--------TSPIQNKLYLHARYMD 296
           ++  TGRTHQ+RVH  H+  P+VGD  Y    +           T    ++  LHA  + 
Sbjct: 226 LRLETGRTHQIRVHMSHISHPLVGDPLYGGRPRPPKGASEAFITTLRGFDRQALHATMLR 285

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           L HP  G  ++  A LP  MV    +L    + 
Sbjct: 286 LYHPISGIEMEFHAALPQDMVDLIAALKADTEE 318


>gi|118594976|ref|ZP_01552323.1| pseudouridine synthase D [Methylophilales bacterium HTCC2181]
 gi|118440754|gb|EAV47381.1| pseudouridine synthase D [Methylophilales bacterium HTCC2181]
          Length = 349

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 87/353 (24%), Positives = 158/353 (44%), Gaps = 39/353 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           + +  + +++  +   +R+D      +P  +   +Q  +R G ++VD + +    +I  G
Sbjct: 1   MASNKKDILMPQELSGLRIDAAIHKIFPEYSRGRIQAWIRDGHIKVDGQSLAPKKKIIGG 60

Query: 63  QVVRIPPVI-NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           + + I     + L     E  I+++               +YED  I V NKPAG+ V  
Sbjct: 61  ENISIDFQPDDELKQFEAEDMIIEA---------------VYEDDHILVINKPAGLVVHP 105

Query: 122 GSGI--AYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G+G      ++G L  + ++K   +  + HRLD++TSG++VV++T  A QHL +  + + 
Sbjct: 106 GAGNWSGTLLNGLLHHFPENKVLARAGIVHRLDKDTSGLMVVSKTEVAQQHLIKQLQNKT 165

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCF 236
           +++ Y  +VWG             + K  IG      VK   N+     +++H++V++ F
Sbjct: 166 VKREYRCIVWGQVWKNG-------VVKEPIGRHPTVRVKMAVNKIHGKESVTHYEVLERF 218

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---------K 287
                +L     TGRTHQ+RVH  H+  PIVGD  Y            Q+         +
Sbjct: 219 GH-HSYLRCNLETGRTHQIRVHMSHVQAPIVGDPVYGIKKIIPVRELSQDLKDEVFGFPR 277

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQD 339
             LHA  + L HP     ++    LP  M K  + +  + +++     L  +D
Sbjct: 278 QALHAIGLGLIHPATNEFMRWDIDLPDDMKKLLELIRAEPNKSPKPFTLSDED 330


>gi|262273643|ref|ZP_06051456.1| ribosomal large subunit pseudouridine synthase D [Grimontia
           hollisae CIP 101886]
 gi|262222058|gb|EEY73370.1| ribosomal large subunit pseudouridine synthase D [Grimontia
           hollisae CIP 101886]
          Length = 325

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 75/329 (22%), Positives = 143/329 (43%), Gaps = 36/329 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V  ++   RLD+     +P  +   +++ + + +V VD + V K   ++  G+V+ +  
Sbjct: 10  TVNENQLGQRLDQALAELFPDYSRSRIKEWILADKVSVDGEIVNKPRLKMMGGEVIVVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I                      +  +   ++YED  I V NKP  + V  G+G     
Sbjct: 70  EIEDEQRF---------------EAQDIPLNIVYEDDDIIVINKPRDLVVHPGAGCPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWS 185
             +G L  + D ++  +  + HRLD++T+G++VVA+       L  + + R+   + Y +
Sbjct: 115 VLNGLLYHYPDIAEVPRAGIVHRLDKDTTGLMVVAKNIPTQTRLVRALQKRKKFTREYEA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G        I   + + S       H+  Q  +    AI+H++V++ F +    L +
Sbjct: 175 IALGNMTG-GGMIEKPIGRHST---KRTHMAVQ--ELGKPAITHYRVVEHF-RAHTRLRL 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDL 297
           +  TGRTHQ+RVH  ++  P+VGD  Y    +    +  +        ++  LHA  + +
Sbjct: 228 RLETGRTHQIRVHMAYLNHPLVGDPLYGGRPRPPRNAGDKLIQTLRQFDRQALHAAMLRI 287

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP     ++  AP+P  MV   + L   
Sbjct: 288 EHPTTKEVMEWHAPIPDDMVNLTEVLRAD 316


>gi|19745906|ref|NP_607042.1| hypothetical protein spyM18_0889 [Streptococcus pyogenes MGAS8232]
 gi|19748060|gb|AAL97541.1| conserved hypothetical protein [Streptococcus pyogenes MGAS8232]
          Length = 296

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 78/316 (24%), Positives = 134/316 (42%), Gaps = 34/316 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V+           
Sbjct: 8   SGQRLDKALADLSP-LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVICFE-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLK 134
                  L     L   +  +   ++YED  + + NKP G+ V   +G       +  + 
Sbjct: 59  -------LPKEEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSETMVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+T AA Q LTE  + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDAAHQALTEELKAKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        A++ F V++ F   +  +E+Q  TG
Sbjct: 172 LPNDRGMIEAPIGRSEKDRKKQAVTAK-----GKEAVTRFTVLERFGD-YSLVELQLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ + L HP  G  +  T 
Sbjct: 226 RTHQIRVHMAYIGHPVAGDPLYGPR-----KTLSGHGQFLHAKTLGLTHPMTGKEMIFTV 280

Query: 310 PLPAHMVKTWDSLGFK 325
             P    K    L  K
Sbjct: 281 EAPEIFQKVLKLLRKK 296


>gi|171463620|ref|YP_001797733.1| pseudouridine synthase, RluA family [Polynucleobacter necessarius
           subsp. necessarius STIR1]
 gi|171193158|gb|ACB44119.1| pseudouridine synthase, RluA family [Polynucleobacter necessarius
           subsp. necessarius STIR1]
          Length = 344

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 137/328 (41%), Gaps = 32/328 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +       RLD+      P  +   L+  + +G V VD K  K    ++ G+ +++ P
Sbjct: 23  LEIPLKMAGERLDKVLVGTLPDYSRNRLKTWVEAGAVMVDGKVTKARYLLRGGESIKVFP 82

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                          +       + + +   ++YED  I V NKP G+ V   +G     
Sbjct: 83  Q--------------EMPEQFAFNPEDIPLDVVYEDGDIIVINKPPGLVVHPAAGNWSGT 128

Query: 128 HIDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  + + K   +  + HRLD++TSG++VVART  A   L    + R + + Y + 
Sbjct: 129 LLNGLLFRYPELKMFPRAGIVHRLDKDTSGLMVVARTSQAQTSLVRQLQDRTVGRRYLAW 188

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDC---FAQKFC 241
           VWG   ++ + +A+       +G D    +K          A + F+ +           
Sbjct: 189 VWGDAPSQGKVLAS-------VGRDQRDRLKMAAGSPQGKPAATLFRRLSKGLVQETPVT 241

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE +  TGRTHQ+RVH   +G P+VGD  Y     G   +    +  LHA  + L HP 
Sbjct: 242 LLECRLETGRTHQIRVHFESLGFPLVGDPVYRKKTPGAANNLEFKRQALHAFALSLQHPA 301

Query: 302 GGRLQ--ITAPLPAHMVKTWDSLGFKYD 327
              +      P P  +++    LG   +
Sbjct: 302 RNEVMTWFRLP-PQDILELLPQLGMSEE 328


>gi|127513878|ref|YP_001095075.1| RluA family pseudouridine synthase [Shewanella loihica PV-4]
 gi|126639173|gb|ABO24816.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           loihica PV-4]
          Length = 323

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 140/325 (43%), Gaps = 35/325 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPV 70
           +   +   RLD+     +P  +   +++ +++G V VD     K   ++  GQ + I   
Sbjct: 11  ITATQTGQRLDQTLAELFPDYSRTRIKEWIQAGAVYVDGMVQTKPREKVLEGQEIEIEAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           +                  +   +  +   ++YED  I V NK AG+ V  G+G      
Sbjct: 71  LKE---------------EIKAEAQAIDLDIVYEDDHIIVINKQAGLVVHPGAGNSDGTL 115

Query: 129 IDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L    +     +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 MNALLHHCPEIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        + +  + +      ++ V          +++H++V + F +    L ++ 
Sbjct: 176 SGTMTA--GGVVDEPIARHPTKRTHMAV----HHSGRPSVTHYRVAEKF-RAHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+G  +VGD  Y    +    +  +         +  LHA  ++L H
Sbjct: 229 ETGRTHQIRVHMAHIGHILVGDPVYGGRPRPPKKATPELMEALNGFKRQALHAVRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P     +   AP+P  MV    +L 
Sbjct: 289 PFTCEIMSWQAPIPEDMVALTRALR 313


>gi|237738860|ref|ZP_04569341.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           2_1_31]
 gi|229423963|gb|EEO39010.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           2_1_31]
          Length = 315

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 74/338 (21%), Positives = 147/338 (43%), Gaps = 36/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V  + E MRLD++            L+K++ +  V+++ K +  N  ++
Sbjct: 1   MENIKEKFEFEVSPEYEGMRLDKYLAEQIEEATRSYLEKLIDNSYVKINSKVINKNGRKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +SG+ + I                +    N+   ++ +   +++E+    + NK   + V
Sbjct: 61  KSGEKIEIS---------------IPEEENIDIEAENIPLDIVFENDDFILVNKKYNMVV 105

Query: 120 QGGSG-IAYHIDGFLKSWVDSK-----GQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     +   L  + ++        +P + HRLD++TSG+++VA+   A   L   
Sbjct: 106 HPAYGNYTGTLVNALLYYTNNLSSVNGNIRPGIIHRLDKDTSGLILVAKNNFAHAKLASM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           F  + I K Y  +V G   ++  +  I N + + +      + VVK+N      AIS+++
Sbjct: 166 FTDKTIHKTYLCIVKGNFSDENLEGRIENLIGRDTK-DRKKMAVVKEN---GKLAISNYR 221

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V++   + +  +E+   TGRTHQ+RVH   +  PI+GD  Y +  K         +  LH
Sbjct: 222 VVEQV-KDYSLVEVLIETGRTHQIRVHMKSINHPILGDVIYGSEDKNV------KRQMLH 274

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A  ++  +P +      T  L    ++   +L F  ++
Sbjct: 275 AFKLEFLNPLDNKEYTFTGKLFDDFIEVAKNLKFDINK 312


>gi|33597725|ref|NP_885368.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           parapertussis 12822]
 gi|33574153|emb|CAE38483.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           parapertussis]
          Length = 320

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 129/325 (39%), Gaps = 31/325 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD+      P  +   LQ  + +G V V+  + K    +  G V+ +  
Sbjct: 19  LTVPPDTPADRLDKVLAGLLPGHSRSRLQGWIEAGYVLVNGAQAKVRQAVGPGDVLSVWE 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                +     + +                 ++ E     V +KPAG+    G+G     
Sbjct: 79  QPAPESRAFAPEPVA--------------FDVVAESPDWIVVDKPAGLVTHPGAGNWSGT 124

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  + + ++  +  + HRLD++TSG++VVAR   A  HL    + R + + Y +L
Sbjct: 125 LLNGLLHRYPELARVARAGIVHRLDKDTSGLMVVARNELAQTHLVRQLQARTMGRQYIAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC----FAQKFCW 242
             G        +   + + + +    V +  +       A++HF            +   
Sbjct: 185 AHG-WLGAAGTVDRPIGRDARV---PVRMSVERPIAPKPAVTHFDPRRRGCAEGGARVSE 240

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +  +  TGRTHQ+RVH   +G P++ D  Y        T     +  LHAR +    P G
Sbjct: 241 VLCRLETGRTHQIRVHLASLGHPLLADTLYGGKPLAGAT-----RQMLHARALHFGDPGG 295

Query: 303 -GRLQITAPLPAHMVKTWDSLGFKY 326
            G +   A +PA M    ++L +  
Sbjct: 296 AGEVSFEAGVPADMSDVQEALAWNA 320


>gi|319775954|ref|YP_004138442.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae F3047]
 gi|329123818|ref|ZP_08252376.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           aegyptius ATCC 11116]
 gi|317450545|emb|CBY86762.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae F3047]
 gi|327469305|gb|EGF14776.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           aegyptius ATCC 11116]
          Length = 324

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 142/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEI--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 67  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 114

Query: 130 -DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +    +  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPIVEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + + +         +         A++H+++++ + + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHAT-----KRTLMAVHPMGKPAVTHYRIMENY-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGR HQ+RVH  H+  P++GD  Y    +    +            +  LHA  + L H
Sbjct: 228 ETGRMHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEDFMEVLRNFKRQALHAVMLRLAH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V+  ++L   Y
Sbjct: 288 PITGEMMEWYAPLPDDFVELLNALKADY 315


>gi|239996651|ref|ZP_04717175.1| ribosomal large subunit pseudouridine synthase D [Alteromonas
           macleodii ATCC 27126]
          Length = 327

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 81/322 (25%), Positives = 146/322 (45%), Gaps = 33/322 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
            E     +RLD+   + +P  +   L+  ++ G V V+            G+V+ +P   
Sbjct: 14  TEAAHFGLRLDQVLADLFPEYSRSKLKTWIQDGNVAVN------------GEVITVPRHK 61

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
             ++ ++  Q  +D  V +T  +  +   ++YED  I V NKPA + V  G+G       
Sbjct: 62  MQMDELVTVQAEMD--VQVTSEAQDIALNIVYEDEHILVINKPADLVVHPGAGNPSGTVL 119

Query: 130 DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L    +  K  +  + HRLD++T+G++VVA+T  A  HL +  + R + + Y ++  
Sbjct: 120 NALLNHCPEIDKVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVDQLQRREMSREYEAVAL 179

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        I +  + +      ++ V +        A++HF+VI+ F + +  L ++  
Sbjct: 180 GTMVA--GGIVDAPIGRHATKRTHMAVREM----GKPAVTHFRVIEKF-RAYTHLRLKLE 232

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  LHA  + L HP
Sbjct: 233 TGRTHQIRVHMAHIKHPLLGDQVYGGRPRLPKGASEEFIAALRGFQRQALHAAQLSLFHP 292

Query: 301 EGGR-LQITAPLPAHMVKTWDS 321
           E    +   APLP  M     +
Sbjct: 293 ETEEWMTWKAPLPQDMQDLLKA 314


>gi|329849859|ref|ZP_08264705.1| ribosomal large subunit pseudouridine synthase D [Asticcacaulis
           biprosthecum C19]
 gi|328841770|gb|EGF91340.1| ribosomal large subunit pseudouridine synthase D [Asticcacaulis
           biprosthecum C19]
          Length = 335

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 85/336 (25%), Positives = 147/336 (43%), Gaps = 43/336 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQ-V 64
           V    V  DE   RLDR    H+P ++   LQ ++  G++  +   +    ++ + G   
Sbjct: 20  VLTATVTADEAGDRLDRALTVHFPDLSRARLQALIAEGRLSHNGAVITDGKHKARPGDYS 79

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + IP +I+A                       +   +L+ED  + V NK  G++     G
Sbjct: 80  LSIPALISA-----------------NPEPQDIPLDILFEDEHLIVINKAPGMAAHPAPG 122

Query: 125 IAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                   + + +   G+         +P + HRLD++TSG++V A++  A + L+E F 
Sbjct: 123 TRDG--TLVNALLFHCGESLSGIGGVLRPGIVHRLDKDTSGVMVAAKSDVAHRSLSELFG 180

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I + Y ++V G P+     + N  + +SH     + V++    G   AI+H+++ + 
Sbjct: 181 RHDIDREYKAVVRGAPRYVSGTV-NTRIGRSHHDRKKMAVLR---GGGREAITHYRLEEV 236

Query: 236 FAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-----QNK 287
           F         L  +  TGRTHQ+RVH  H+GCP +GD  Y +         I       +
Sbjct: 237 FGTVKPLAALLSCRLETGRTHQIRVHMAHLGCPCLGDPVYGSGAPAREVQEIVRDLEFGR 296

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             LHA  +   HP  G  L+  A +P  MV+  ++L
Sbjct: 297 QALHAGLLGFVHPITGEKLKFKAKMPDDMVQLVEAL 332


>gi|323342856|ref|ZP_08083088.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322463968|gb|EFY09162.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 308

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 88/331 (26%), Positives = 146/331 (44%), Gaps = 34/331 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  +  +  ++VE   + MR+D++        +   LQ  +++G + V+   VK N R++
Sbjct: 1   MKEVKNMNKLIVEEMFDGMRIDQYMALAVTDYSRSVLQTWIKNGNITVNGNVVKPNLRLK 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
              VV              E +I +  +++      L   ++YED  I V NKP G+ V 
Sbjct: 61  EDDVV--------------EYEITEEQISIVPVPMDLD--IVYEDDAILVVNKPKGLIVH 104

Query: 121 GGSGIAYHI---DGFLKS---WVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                        G L       D  G+ +P + HR+D++T+G+LVVA+T  A + L E 
Sbjct: 105 PSPSTLNQPTLVHGLLAHTTQLSDLNGELRPGIVHRIDKDTTGLLVVAKTNEAHEILVED 164

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + R I + Y ++V    K++   +   + +        + V  QN   +  A++HF + 
Sbjct: 165 LKQRLISREYVAIVHHQFKHQSATVDAPIGRDPK-NRQRMAVTDQN---SKQAVTHFYLA 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F   F  L  +  TGRTHQ+RVHA ++  PIVGD  Y             N   LHA+
Sbjct: 221 ERFND-FSVLRCKLDTGRTHQIRVHAQYIKHPIVGDQTYSYKNTWET-----NGQCLHAQ 274

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            + L HP     +   A LP  M    + + 
Sbjct: 275 KLTLTHPVSKEVMTFEAELPQTMKDVIEEIR 305


>gi|295687954|ref|YP_003591647.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
 gi|295429857|gb|ADG09029.1| pseudouridine synthase, RluA family [Caulobacter segnis ATCC 21756]
          Length = 340

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 140/332 (42%), Gaps = 38/332 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
             V+  +    RLD+     +P ++   LQ ++  G++  + + V   + + ++G  V +
Sbjct: 26  TAVLPAELAGQRLDKALAPLFPDLSRARLQALIAEGRLSAEGQPVTDASRKAKAGTYVLL 85

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                           +   +      + +   +LYED+ + V +KPAG++     G   
Sbjct: 86  ----------------VPPPIPADPEPEAIPLTVLYEDAHLIVVDKPAGMAAHPAPGSLT 129

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++  L    DS        +P + HRLD++TSG++V A++ AA + L+  F    I 
Sbjct: 130 GTLVNALLHHCGDSLSGVGGVARPGIVHRLDKDTSGVMVAAKSDAAHKGLSALFATHDID 189

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK- 239
           ++Y +L  G P      I   L + S      + V++    G   A++H++V   F  + 
Sbjct: 190 RLYIALTRGAPSPPAGTITTQLGR-SPGDRKKMAVLRS---GGREAVTHYRVEAAFGPQE 245

Query: 240 ---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLH 291
                 +  +  TGRTHQ+RVH    G P +GD  Y      A  +    +    +  LH
Sbjct: 246 KPLAARVACRLETGRTHQIRVHMASKGSPCLGDPVYGTGQPAAAVREAIQAAGLKRQALH 305

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           A  +   HP  G  L+   PLP  M     SL
Sbjct: 306 AAVLGFVHPITGEALRFETPLPEDMAALQKSL 337


>gi|56414629|ref|YP_151704.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|56128886|gb|AAV78392.1| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
          Length = 326

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 80/335 (23%), Positives = 149/335 (44%), Gaps = 41/335 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ + + +V V+ +   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I+                 +   +  +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  DAEIDE---------------EIRFEAQDIPLDIVYEDDDILVINKPRDLVVHLGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVNEPISRHPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA 
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHAT 282

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            + L HP  G  ++  AP+P  MV   D++   ++
Sbjct: 283 MLRLYHPVSGIEMEWHAPIPQDMVDLIDAMRADFE 317


>gi|115522842|ref|YP_779753.1| RluA family pseudouridine synthase [Rhodopseudomonas palustris
           BisA53]
 gi|115516789|gb|ABJ04773.1| ribosomal large subunit pseudouridine synthase D [Rhodopseudomonas
           palustris BisA53]
          Length = 327

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 84/346 (24%), Positives = 154/346 (44%), Gaps = 53/346 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVV 65
           +  + V  DE  +RLDR      P ++   L+ ++ +G+V + +         + +G  +
Sbjct: 1   MLEITVAGDEGAVRLDRVLALRAPELSRSRLKALILAGRVAIGETPLCDPAYHVGAGDTI 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I                +  ++      + +   +++ED  I V +KP G+ V   +G 
Sbjct: 61  TID---------------VPPAIAAEPAGEPIALDIVHEDDDIIVIDKPRGLVVHPAAG- 104

Query: 126 AYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             H  G L + + +            ++P + HRLD++T+G++V A+   A Q L+  F 
Sbjct: 105 --HETGTLVNALIAHCGASLSGIGGVRRPGIVHRLDKDTTGLMVAAKNDRAHQSLSAQFA 162

Query: 176 MR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
                  +++ Y++ VWG+P      I   + +  H   + + V     +G   AI+H++
Sbjct: 163 DHGRTGALRRGYYAFVWGVPNRPHGTIDAPIDRHPH-NREKMAVR----EGGRDAITHWE 217

Query: 232 VIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------- 279
           V++ FA +        +  Q  TGRTHQ+RVH  H+G P++GD  Y  +FK         
Sbjct: 218 VLETFAGRSGKPVASLIACQLETGRTHQIRVHLAHIGHPLLGDGVYGPHFKTKASALPPA 277

Query: 280 --FTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
                    +  LHA  + L HP  G + + T+ LPA + K  ++L
Sbjct: 278 ARAALEALGRQALHAYLLVLEHPSSGEIREWTSDLPADLAKLQNAL 323


>gi|304414306|ref|ZP_07395674.1| 23S rRNA pseudouridine synthase [Candidatus Regiella insecticola
           LSR1]
 gi|304283520|gb|EFL91916.1| 23S rRNA pseudouridine synthase [Candidatus Regiella insecticola
           LSR1]
          Length = 325

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 87/328 (26%), Positives = 151/328 (46%), Gaps = 41/328 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V   +   RLD+     +P  +   +++ + +  V V+ K++     R+   + V I  
Sbjct: 10  TVAESQIGQRLDQALAELFPDYSRSRIKEWILADCVLVNGKKINTPKGRVLGSESVTINA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I      I +Q               +   ++YED+ I V NKP G+ V  G+G A   
Sbjct: 70  EIKENVRSIPQQ---------------IPLNIVYEDNDILVINKPRGLVVHPGAGNADGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           I   L  +  +    PR  + HRLD++T+G++VVA+T  A  HL E+ + R+I + Y ++
Sbjct: 115 ILNALLHYYPAISNVPRAGIIHRLDKDTTGLMVVAKTVPAQTHLVEALQARKITREYEAI 174

Query: 187 VWGIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             G        +E IA    K++H+    +            A++H+++++ F +    L
Sbjct: 175 AIGNMIAGGAVEEPIARHASKRTHMAVHPM---------GKPAVTHYRIMEHF-RAHTHL 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQ-----NKLYLHARYM 295
            ++  TGRTHQ+RVH   +  P+VGD  Y +     KG   + I+     ++  LHA  +
Sbjct: 225 RLRLETGRTHQIRVHMSFIRHPLVGDPLYGSRACHPKGASDAFIKILRGFDRQALHASML 284

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            L HP  G  ++  A LP  +V    +L
Sbjct: 285 RLKHPISGIEMEWRAALPQDIVDLISAL 312


>gi|110833337|ref|YP_692196.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
 gi|110646448|emb|CAL15924.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
          Length = 323

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 76/330 (23%), Positives = 143/330 (43%), Gaps = 39/330 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V+ +    R+D+     +   +   LQ  +++G + V+  + K   ++   + + +
Sbjct: 11  RTEQVKPEHAGQRVDQVAAELFEGFSRSRLQTWIKNGVLTVNGAQTKPKEKLTGNESLTL 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           ++    L      +   ++Y+D  + V NKP G+ V   +G   
Sbjct: 71  E---------------VEIEPELDDQPQSIDLDVVYQDDDLIVINKPTGLVVHPAAG--- 112

Query: 128 HIDGFLKSWVDSKGQKP------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           H DG L + +    ++        + HRLD++T+G++VVAR+  A Q L    + + + +
Sbjct: 113 HADGTLLNGLLHLDERLNSLPRAGIVHRLDRDTTGLMVVARSLEAHQSLVAQLQDKSLFR 172

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++  G+     +   +  + +  +      VVK    G   A++H++V+D + +   
Sbjct: 173 QYEAIAVGVMTGGGKV--DAPMGRHPVDRKKQAVVKT---GGKNAVTHYRVLDRY-RAHT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +++Q  TGRTHQ+RVH  H   P+VGD  Y    K    +            +  LHAR
Sbjct: 227 RIQVQLETGRTHQIRVHMAHRNYPLVGDPLYGGRLKQPAGATEALRQALHKFPRQALHAR 286

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            + L HP  G   +  A LPA M     +L
Sbjct: 287 KLGLIHPARGEYCEFQAELPADMTSLIVAL 316


>gi|15674865|ref|NP_269039.1| hypothetical protein SPy_0827 [Streptococcus pyogenes M1 GAS]
 gi|50914002|ref|YP_059974.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|71910451|ref|YP_282001.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
 gi|94988324|ref|YP_596425.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|306827571|ref|ZP_07460852.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes ATCC 10782]
 gi|13622001|gb|AAK33760.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS]
 gi|50903076|gb|AAT86791.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|71853233|gb|AAZ51256.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
 gi|94541832|gb|ABF31881.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|304430223|gb|EFM33251.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes ATCC 10782]
          Length = 296

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 77/316 (24%), Positives = 134/316 (42%), Gaps = 34/316 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V+           
Sbjct: 8   SGQRLDKALADLSP-LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVICFE-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
                  L     L   +  +   ++YED  + + NKP G+ V   +G      ++  + 
Sbjct: 59  -------LPKEEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+T AA Q L E  + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        A++ F V++ F   +  +E+Q  TG
Sbjct: 172 LPNDRGMIEAPIGRSEKDRKKQAVTAK-----GKEAVTRFTVLERFGD-YSLVELQLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ + L HP  G  +  T 
Sbjct: 226 RTHQIRVHMAYIGHPVAGDPLYGPR-----KTLSGHGQFLHAKTLGLTHPMTGKEMIFTV 280

Query: 310 PLPAHMVKTWDSLGFK 325
             P    K    L  K
Sbjct: 281 EAPEIFQKVLKLLRKK 296


>gi|251782204|ref|YP_002996506.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|242390833|dbj|BAH81292.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
          Length = 297

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 76/314 (24%), Positives = 133/314 (42%), Gaps = 34/314 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V++          
Sbjct: 8   SGQRLDKALADLSP-LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVIQFE-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
                  L     L   +  +   ++YED  + + NKP G+ V   +G      ++  + 
Sbjct: 59  -------LPKEEVLEYQAQDIPLNIIYEDEALAIINKPQGMVVHPSAGHPSGTMVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+T  A Q L    + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDEAHQALAAELKAKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        A++ F V++ F   +  +E+Q  TG
Sbjct: 172 LPNDRGMIEAPIGRSEKDRKKQAVTAK-----GKEAVTRFTVLERFGD-YSLVELQLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +   +  +LHA  + L HP  G  +  T 
Sbjct: 226 RTHQIRVHMAYIGHPVAGDPLYGPR-----KTLSGHGQFLHAETLGLTHPLTGEDMLFTV 280

Query: 310 PLPAHMVKTWDSLG 323
             PA   KT   L 
Sbjct: 281 APPAIFQKTLQQLR 294


>gi|229587213|ref|YP_002845714.1| Ribosomal large subunit pseudouridine synthases RluD subfamily
           protein [Rickettsia africae ESF-5]
 gi|228022263|gb|ACP53971.1| Ribosomal large subunit pseudouridine synthases RluD subfamily
           protein [Rickettsia africae ESF-5]
          Length = 313

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 76/327 (23%), Positives = 144/327 (44%), Gaps = 40/327 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V ++   +RLD+   +   +++   +QK ++  QV V+   +   +  ++   ++     
Sbjct: 6   VPHELNGIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFK 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                              L   +  +   ++YED  + V NK AG++V  G+G  +H D
Sbjct: 66  ---------------EPEELKIATANVALDIIYEDDDLIVINKAAGMTVHPGAG--HHDD 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD++T+G++VVA+   A   L      R++ + 
Sbjct: 109 TLVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FC 241
           Y  LVWG+    +  I N + + S      + ++K    G   A++H+K ++ F +    
Sbjct: 169 YKVLVWGVINPLEGVIKNNIGR-SRSDRQKMTILKY---GGKEAVTHYKTLELFYKGSIS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +E +  TGRTHQ+RV   H+   IVGD  Y  N +    SP +         +  LH+ 
Sbjct: 225 MVECKLSTGRTHQIRVQLSHLKHSIVGDQTYGNNDRKIAHSPPELKAKLIDFKRQALHSW 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTW 319
           Y+   HP     ++ +  LP  M +  
Sbjct: 285 YLSFTHPTSNEIMEFSCELPRDMEEII 311


>gi|331004934|ref|ZP_08328347.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC1989]
 gi|330421258|gb|EGG95511.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC1989]
          Length = 333

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 157/333 (47%), Gaps = 40/333 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  +V + +   R+D+   + +   +   +Q+ ++ G + VD ++ +  +++ SG+++ +
Sbjct: 7   EQCIVPDTDAGKRVDQVAASLFQQYSRSRIQEWIKQGTILVDGQKCRSKDKLLSGEMITL 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
              +   +  + +   +D                +Y D  I + NKPAG+ V  G+G+  
Sbjct: 67  AVELIEDDRWLPQDIAIDE---------------VYSDEHIIIINKPAGLVVHPGAGMPD 111

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + +     +  + HRLD++T+G++VVAR+  A   L +  + R + + Y 
Sbjct: 112 GTLLNGLLFHYPELSTLPRAGIVHRLDKDTTGLMVVARSLLAHTSLVQQLQDRSLGREYE 171

Query: 185 SLVWG-----------IPKNKKECIANWLLKKSHIGGDYVH-VVKQNEKGANYAISHFKV 232
           ++V G           I ++  + I   ++ +SH  G Y     + + +    AI+H+++
Sbjct: 172 AVVMGELTGGGVIDKPIGRHPTQRIKMAVIDRSHRRGGYSDESSRPDSQAGKEAITHYRL 231

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------- 285
           +  F+  +  +  Q  TGRTHQ+RVH  H   P+VGD  Y    K    + ++       
Sbjct: 232 LKRFS-GYTHIACQLETGRTHQIRVHLAHSNHPLVGDPVYLTRQKWVAGTVVELKSILTA 290

Query: 286 -NKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
             +  LHAR + L HP+ G  L+  + LP  M 
Sbjct: 291 FTRQALHARKLTLVHPQSGDTLEWESELPKDMQ 323


>gi|15603584|ref|NP_246658.1| 23S rRNA pseudouridine synthase D [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|20139708|sp|Q9CKA6|RLUD_PASMU RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|12722131|gb|AAK03803.1| SfB [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 324

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 73/325 (22%), Positives = 138/325 (42%), Gaps = 35/325 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINA 73
            +   RLD+     +P  +   L+  +    V V+   V     ++  G+ + I      
Sbjct: 13  SQLGQRLDQALAELFPDYSRSRLKTWIEQNLVHVNGDVVNVPRAKVYGGEQIEI------ 66

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DG 131
                    +++   +     + L   ++YED  I V NKP    V  G+G A     + 
Sbjct: 67  ---------VVEIDDDTRFEPENLPLNIVYEDDDILVINKPKDFVVHPGAGNASGTVLNA 117

Query: 132 FLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            L  +   ++  +  + HRLD++T+G++V+A+T  A   L    + R+I + Y ++  GI
Sbjct: 118 LLYHYPAIAEVPRAGIVHRLDKDTTGLMVIAKTIPAQTKLVRDLQKRKITREYEAIACGI 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              K   +   + +                     A++H+++++ F + +  L ++  TG
Sbjct: 178 M-TKGGMVDQPMARHPT-----KRTHMAVHPMGKPAVTHYRIMERF-RNYTRLRLRLETG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEG 302
           RTHQ+RVH  H+  P++GD  Y    +    +  +         +  LHA  + L HP  
Sbjct: 231 RTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEELMQTLRDFKRQALHAIMLRLAHPIT 290

Query: 303 GR-LQITAPLPAHMVKTWDSLGFKY 326
           G  ++  APLP   V+  ++L   Y
Sbjct: 291 GELMEWHAPLPTDFVELVEALKADY 315


>gi|119946871|ref|YP_944551.1| pseudouridine synthase, RluA family protein [Psychromonas
           ingrahamii 37]
 gi|119865475|gb|ABM04952.1| ribosomal large subunit pseudouridine synthase D [Psychromonas
           ingrahamii 37]
          Length = 322

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 86/327 (26%), Positives = 153/327 (46%), Gaps = 38/327 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V + +   RLD+   + +P  +   +++ + +  V++D + + +   ++ +GQ V +  V
Sbjct: 11  VTDQQLGFRLDQAVASLFPDYSRTRIKEWILADMVKIDGEVINRPREKVYTGQTVGVQAV 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +                  +   +  +K  ++YED  I V NKPAG+ V  G+G      
Sbjct: 71  LED---------------EVVFKAQKIKLEIVYEDDDILVINKPAGLVVHPGAGNPDGTV 115

Query: 130 -DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +    +  +  + HRLD++T+G++VVA+T  A  HL  S + R I + Y ++ 
Sbjct: 116 LNALLHHFPQIIEVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVTSLQAREITREYEAIA 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEM 245
            G               ++ IG D VH VK   N  G  +A++H++V + + +    L +
Sbjct: 176 MG-------GFTAGGFVEAPIGRDKVHRVKMAVNSTGGKHALTHYRVSEKY-RAHTRLRL 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDL 297
           +  TGRTHQ+RVH +H+G  + GD  Y    +           T     +  LHA  + L
Sbjct: 228 RLETGRTHQIRVHMMHIGHVLTGDPVYGGRPRPPKGASEALLATLRGFRRQALHATMLRL 287

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++  APLPA M +  ++L 
Sbjct: 288 AHPITGEIMEWHAPLPADMAELAEALR 314


>gi|71275230|ref|ZP_00651517.1| Pseudouridine synthase, RluD [Xylella fastidiosa Dixon]
 gi|71899549|ref|ZP_00681705.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|170731225|ref|YP_001776658.1| pseudouridylate synthase [Xylella fastidiosa M12]
 gi|71164039|gb|EAO13754.1| Pseudouridine synthase, RluD [Xylella fastidiosa Dixon]
 gi|71730678|gb|EAO32753.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|167966018|gb|ACA13028.1| pseudouridylate synthase [Xylella fastidiosa M12]
          Length = 330

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 96/327 (29%), Positives = 159/327 (48%), Gaps = 25/327 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ VVV  +    RLD +  +    +    + K++RSGQVRV+  RVK   ++  G  VR
Sbjct: 18  VRIVVVPAEHSGQRLDNFLLSKLKGVPRSLIYKLVRSGQVRVNGGRVKAERKLDGGDEVR 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      +I+++ I+  S         +++ +++ED+++   NKP+G++  GGSG++
Sbjct: 78  LPPL-----RLIQDRAIVAPSAAFLAR---MEAAIVFEDARLLALNKPSGMASHGGSGVS 129

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--------RR 178
           Y +   ++       Q+  L HRLD++TSG+L++A+ RAA   L    R         R 
Sbjct: 130 YGVIEAMRILRPK--QELELVHRLDRDTSGLLIMAKKRAALIELQALMREASVNGKEGRG 187

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y +L+ G   N    +   L      GG+    V  + K +    S F++++    
Sbjct: 188 IAKRYLTLLSGRMPNGVMSVDAPLHINLRHGGERHVRVHHDGKPSK---SRFRLLERRG- 243

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMD 296
              + E+   TGRTHQ+RVHA H+G P+ GD KY                +L+LHA  ++
Sbjct: 244 GQSYCEVLIETGRTHQIRVHAQHLGHPVTGDDKYGDQEVNRKLRDQIGLQRLFLHAVSLE 303

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
                G     + APL   +V   D L
Sbjct: 304 FALDAGSTPYVLNAPLAEDLVAALDRL 330


>gi|254521304|ref|ZP_05133359.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219718895|gb|EED37420.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 307

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 94/319 (29%), Positives = 152/319 (47%), Gaps = 20/319 (6%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  D    RLD +            + K++RSGQVRV+  R K   ++++G  VR+PP
Sbjct: 2   ITVPADRAGQRLDNFLLGQLKGAPRSLVYKLVRSGQVRVNGGRAKAERKLEAGDEVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                   ++  +  D +         L+  +++ED+++   NKP G++  GGSGI++  
Sbjct: 62  --------VRLTEEGDKAGPPEAFMRRLEQAIVFEDARLLALNKPTGVASHGGSGISFGA 113

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR---IQKIYWSL 186
              L++     GQ   L HRLD++TSG+L+VA+ R+A   L    R      I+K Y +L
Sbjct: 114 IETLRALRP--GQTLELVHRLDRDTSGLLIVAKKRSALSELQALLREDHGAGIRKRYLTL 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           + G   +    +   L      GG+    V         +ISHF+V++       + E++
Sbjct: 172 LTGRMPDGVMTVDAPLHVGLRQGGERHVQVNAI---GKESISHFRVLERRG-GHSYCEVR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG- 303
             TGRTHQ+RVHA H+G P+ GD KY                +L+LHA  ++    +G  
Sbjct: 228 IETGRTHQIRVHAQHLGHPVAGDDKYGDPVVNKRLREQIGLKRLFLHAASLEFALDDGKS 287

Query: 304 RLQITAPLPAHMVKTWDSL 322
              + APL   +V+  D L
Sbjct: 288 PYVLNAPLADELVEALDRL 306


>gi|239815171|ref|YP_002944081.1| pseudouridine synthase, RluA family [Variovorax paradoxus S110]
 gi|239801748|gb|ACS18815.1| pseudouridine synthase, RluA family [Variovorax paradoxus S110]
          Length = 327

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 142/332 (42%), Gaps = 31/332 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
           + ++   V   E   RLDR      P  +   LQ+++ +G V +  + + K +  +++GQ
Sbjct: 18  SELRPFTVGPTEHGQRLDRALAALVPEFSRNYLQQLIEAGAVELQGRTLLKASATVRAGQ 77

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
              I              ++  +  +     + +  + ++ED  + + +KPAG+ V    
Sbjct: 78  TGHI--------------ELRPTPQSQAFRPEPMDIVTVHEDEHLRIIDKPAGLVVHPAP 123

Query: 124 GIAYHIDGFLKSWVDSKGQKP------RLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H  G L + + +   K        + HRLD++TSG++VVARTRAA   +      R
Sbjct: 124 G---HWSGTLLNGLLALDPKAALLPRAGIVHRLDRDTSGLMVVARTRAAMDAMVALIAAR 180

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +L             +  + +       + VV         A +  + +D  A
Sbjct: 181 EVKRQYLALGHKPWAGAAARQVDAPIGRDPRNRLRMAVVDLERHAGKTARTLIERLDSNA 240

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q  C +     TGRTHQ+RVH   +G P+VGD  Y              +  LHA  +  
Sbjct: 241 Q-ACAVRCTLETGRTHQIRVHMASIGHPLVGDALYGGAPAAGL-----GRQALHAFRLAF 294

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            HP     L++ +  PA +V+ + +LG  Y+R
Sbjct: 295 VHPVTQAALELRSLPPADLVQAFQALGLDYNR 326


>gi|327539710|gb|EGF26317.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica WH47]
          Length = 333

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 78/344 (22%), Positives = 149/344 (43%), Gaps = 53/344 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  VV       R+D +        +   ++  +++    VD + ++ + ++++GQ VR
Sbjct: 1   MREFVVPESANGFRIDLFLTQSCDGYSRSQIRDAVQNDGAEVDGRIIRPSYKVKAGQKVR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                 A +  + E   LD               +LYED  + V NKPAG+ V    G  
Sbjct: 61  FRVPPPASDDTVPENIPLD---------------ILYEDDGLVVINKPAGMVVHPARG-- 103

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            +  G L S +  + Q         +P + HRLD++TSG++VVA+  A   +L   +  R
Sbjct: 104 -NWTGTLTSALAFRFQSLSDVGGPTRPGIVHRLDRDTSGVIVVAKNNAVHLNLAAQWHDR 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +QK Y ++ +G     ++ I   + +  +        +++    +  A + ++V++   
Sbjct: 163 LVQKEYTAITFGRLDRDRDWIHASIGRHPYQRDK--QAIREGHATSKTASTFYEVVERHG 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA----------------------N 275
           +    ++++P TGRTHQ+RVH  H+GCPI+ D  Y                         
Sbjct: 221 R-VTRVDVRPKTGRTHQIRVHLAHIGCPILCDRLYGGHSELSRSQIRRLAGTEVATPGVK 279

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
                   + ++  LHA+ +   +P+ G  + +TAPLP  +   
Sbjct: 280 PTPEGEEILLSRQALHAKALTFTNPQTGKEMTLTAPLPPDLQAV 323


>gi|260771109|ref|ZP_05880036.1| ribosomal large subunit pseudouridine synthase D [Vibrio furnissii
           CIP 102972]
 gi|260613706|gb|EEX38898.1| ribosomal large subunit pseudouridine synthase D [Vibrio furnissii
           CIP 102972]
 gi|315179286|gb|ADT86200.1| 23S rRNA pseudouridine synthase D/large subunit [Vibrio furnissii
           NCTC 11218]
          Length = 324

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 73/332 (21%), Positives = 139/332 (41%), Gaps = 35/332 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +   RLD+     +   +   L++ L  G+V V+   V K   ++  G+ + +  
Sbjct: 10  TVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKVMVNGNVVTKPRTKVMGGEAITVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  I V NKP  + V  G+G     
Sbjct: 70  ELEDEQRW---------------EAQDIPLNIVYEDDDIIVINKPRDLVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R I + Y ++
Sbjct: 115 VLNALLFHFPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRELQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        I   + + S         +         A++H++V + F ++   + ++
Sbjct: 175 AIGKM-TAGGMIDKPIGRHST-----KRTLMAVSPLGKPAVTHYRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGATQELTDMIRGFDRQALHAVMLRFE 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           HP  G  L+  AP+P  MV+  ++L      N
Sbjct: 288 HPITGEPLEFHAPVPDDMVEMTEALREDAQLN 319


>gi|71899934|ref|ZP_00682081.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|71730297|gb|EAO32381.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
          Length = 330

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 97/327 (29%), Positives = 159/327 (48%), Gaps = 25/327 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ VVV  +    RLD +  +    +    + K++RSGQVRV+  RVK   ++  G  VR
Sbjct: 18  VRIVVVPAEHSGQRLDNFLLSKLKGVPRSLIYKLVRSGQVRVNGGRVKAERKLDGGDEVR 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      +I+++ I+  S         +++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 78  LPPL-----RLIQDRAIVAPSAAFLAR---MEAAIVFEDARLLALNKPSGMASHGGSGIS 129

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--------RR 178
           Y +   ++       Q+  L HRLD++TSG+L++A+ RAA   L    R         R 
Sbjct: 130 YGVIEAMRILRPK--QELELVHRLDRDTSGLLIMAKKRAALIELQALMREASVNGKEGRG 187

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y +L+ G   N    +   L      GG+    V  + K +    S F++++    
Sbjct: 188 IAKRYLTLLSGRMPNGVMSVDAPLHINLRHGGERHVRVHHDGKPSK---SRFRLLERRG- 243

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMD 296
              + E+   TGRTHQ+RVHA H+G P+ GD KY                +L+LHA  ++
Sbjct: 244 GQSYCEVLIETGRTHQIRVHAQHLGHPVTGDDKYGDQEVNRKLRDQIGLQRLFLHAVSLE 303

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
                G     + APL   +V   D L
Sbjct: 304 FALDAGSTPYVLNAPLAEDLVAALDRL 330


>gi|32477768|ref|NP_870762.1| ribosomal large subunit pseudouridine synthase [Rhodopirellula
           baltica SH 1]
 gi|32448322|emb|CAD77839.1| ribosomal large subunit pseudouridine synthase [Rhodopirellula
           baltica SH 1]
          Length = 334

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 78/344 (22%), Positives = 149/344 (43%), Gaps = 53/344 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  VV       R+D +        +   ++  +++    VD + ++ + ++++GQ VR
Sbjct: 2   MREFVVPESANGFRIDLFLTQSCDGYSRSQIRDAVQNDGAEVDGRIIRPSYKVKAGQKVR 61

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                 A +  + E   LD               +LYED  + V NKPAG+ V    G  
Sbjct: 62  FRVPPPASDDTVPENIPLD---------------ILYEDDGLVVINKPAGMVVHPARG-- 104

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            +  G L S +  + Q         +P + HRLD++TSG++VVA+  A   +L   +  R
Sbjct: 105 -NWTGTLTSALAFRFQSLSDVGGPTRPGIVHRLDRDTSGVIVVAKNNAVHLNLAAQWHDR 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +QK Y ++ +G     ++ I   + +  +        +++    +  A + ++V++   
Sbjct: 164 LVQKEYTAITFGRLDRDRDWIHASIGRHPYQRDK--QAIREGHATSKTASTFYEVVERHG 221

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA----------------------N 275
           +    ++++P TGRTHQ+RVH  H+GCPI+ D  Y                         
Sbjct: 222 R-VTRVDVRPKTGRTHQIRVHLAHIGCPILCDRLYGGHSELSRSQIRRLAGTEVATPGVK 280

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
                   + ++  LHA+ +   +P+ G  + +TAPLP  +   
Sbjct: 281 PTPEGEEILLSRQALHAKALTFTNPQTGKEMTLTAPLPPDLQAV 324


>gi|121611690|ref|YP_999497.1| RluA family pseudouridine synthase [Verminephrobacter eiseniae
           EF01-2]
 gi|121556330|gb|ABM60479.1| pseudouridine synthase, RluA family [Verminephrobacter eiseniae
           EF01-2]
          Length = 334

 Score =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 89/321 (27%), Positives = 144/321 (44%), Gaps = 19/321 (5%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V+      RLD +       +   ++ +I+RSGQVR++K R   + R+Q+G +VR+
Sbjct: 23  RLVQVDGASAGQRLDNFLLRQLKGVPKTHVYRIIRSGQVRINKGRAHADTRVQAGDMVRL 82

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP+  +             +      +   +  +L+ED  +   +KPAG++V GGSG+++
Sbjct: 83  PPLRISD----------AVAQKAEHPAPAREFPILWEDEHLIAIDKPAGVAVHGGSGVSF 132

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L+           L HRLD+ETSGIL+VA+ R+A  HL    R R   K Y +LV
Sbjct: 133 GVIEQLRQAR-PDAPFLELVHRLDRETSGILLVAKKRSALTHLQAQLRARTTGKTYLALV 191

Query: 188 WGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWL--- 243
            G     +  I   L K     G+  V V   ++     +I+  +    +  +       
Sbjct: 192 AGAWPAHQRVIDLPLHKYLQADGERRVRVTTADDPHGMRSITLVRPRGSWPARAGLPALQ 251

Query: 244 --EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
             E+   TGRTHQ+RVH    G  I GD KY               +++LHA  +   HP
Sbjct: 252 LLEVTIKTGRTHQIRVHLASQGHAIAGDDKYGDFELNKRMQKQGLKRMFLHAWRLQFKHP 311

Query: 301 EGGR-LQITAPLPAHMVKTWD 320
             G  + + A L   +    +
Sbjct: 312 ASGEPVALHAELAPELADLVN 332


>gi|254670429|emb|CBA06026.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis alpha153]
          Length = 330

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 94/322 (29%), Positives = 153/322 (47%), Gaps = 24/322 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + V   E   RLD +       +   ++ +I+R+G+VR++KKR K ++RI  G  VR
Sbjct: 11  VSLIGVAEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVR 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPPV  A   +  E++    +              +YED  + V +KP+G++V GGSG++
Sbjct: 71  IPPVRVAEKEMPSERRAAVPARAFEA---------VYEDDALLVIDKPSGVAVHGGSGVS 121

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   L+     + +   L HRLD++TSG+L+VA+ R+A   L E+ R    +KIY +L
Sbjct: 122 FGVIEQLRRAR-PEARYLELVHRLDKDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------- 239
             G   +    +   L K +   G+ +  V  +      A + F+V+  F+         
Sbjct: 181 GVGKLPDDNFHVRLPLSKYTGAQGEKMVRVSAD---GQSAHTVFRVLSRFSDGILHGVGL 237

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
                +     TGRTHQ+RVH    GCPI GD +Y               +++LHA  + 
Sbjct: 238 SHLTLVRATLKTGRTHQIRVHLQSQGCPIAGDERYGDYQANRRLQKLGLKRMFLHASELH 297

Query: 297 LPHPEGGR-LQITAPLPAHMVK 317
           L HP  G  L +   LP  + +
Sbjct: 298 LNHPLTGEPLVLKVGLPPDLAQ 319


>gi|325921580|ref|ZP_08183425.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           gardneri ATCC 19865]
 gi|325547934|gb|EGD18943.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           gardneri ATCC 19865]
          Length = 331

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 83/347 (23%), Positives = 150/347 (43%), Gaps = 40/347 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           L   ++  +V ++    R D      +P  +   L + ++SG   ++ +  +  + ++ G
Sbjct: 9   LDPSIRQAIVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLNGEMARPRDTLRGG 68

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V++  V+    H                    +   +LYED ++ V +KPAG+ V  G
Sbjct: 69  ESVQVQVVLEIQTH---------------SEPQDIPLSVLYEDDQVLVIDKPAGLVVHPG 113

Query: 123 SGIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G   + DG L + +  +        +  + HRLD++TSG++VVART  A   L E    
Sbjct: 114 AG---NPDGTLVNALLFRDPALAAVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSA 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + + Y ++V G         AN  + +       + V          A++H+++ + F
Sbjct: 171 RDVHRQYLAVVVGAL--VSGGTANAPIDRHPRDRLKMAVRD----DGRDAVTHYRLRERF 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKL 288
            +    LE +  TGRTHQ+RVH  H+  PIVGD  Y    K    +  +         + 
Sbjct: 225 -RAHTALECRLETGRTHQIRVHMAHLKSPIVGDPLYGGALKLPKGASDELVHELRTFKRQ 283

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            LHA  ++  HP  G  ++ +AP+P  + +   +L     R     R
Sbjct: 284 ALHAETLEFLHPVSGEPVRASAPVPVDLQRLMTALREDSVRAAEQAR 330


>gi|94676891|ref|YP_588880.1| ribosomal large subunit pseudouridine synthase C [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
 gi|94220041|gb|ABF14200.1| ribosomal large subunit pseudouridine synthase C [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
          Length = 322

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 94/306 (30%), Positives = 151/306 (49%), Gaps = 16/306 (5%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   R+D + +     +    + +I+R G+VR++KKR+K   ++QSG  +R+PP      
Sbjct: 17  EAGQRIDNFLRTKLKGVPKSLIYRIIRKGEVRINKKRIKPQYKLQSGDQIRLPP------ 70

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
             +    I        K    L   +LYED  I V NKPAG +V GG  +++ +   L++
Sbjct: 71  --VWRNNITQLFSPQLKKVAVLADTILYEDDYILVLNKPAGTAVHGGYKLSFGVIEGLRA 128

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    +   L HRLD++TSG L+VA+ R+A + + E  RM+ I K Y +LV G  ++  
Sbjct: 129 -LWPFAKFLELIHRLDRDTSGALLVAKKRSALRLMHEQLRMKNINKHYLALVRGQWESD- 186

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +   L+KK    G ++  V  + K +      F  I+        +   P TGRTHQ+
Sbjct: 187 TVVEVPLMKKIQSNGKHIVQVSSDGKMSKT----FFKIEENFTIATLVNASPITGRTHQI 242

Query: 256 RVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
           RVH+ + G PI  D +Y  N F         ++L+LHA  +   HP  G + +I APL  
Sbjct: 243 RVHSQYAGHPIAFDDRYGDNEFDQQLKKCGLSRLFLHAVALSFKHPISGEILRIEAPLDE 302

Query: 314 HMVKTW 319
            ++   
Sbjct: 303 SLLNCL 308


>gi|187931011|ref|YP_001890995.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. mediasiatica FSC147]
 gi|187711920|gb|ACD30217.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. mediasiatica FSC147]
          Length = 309

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 100/320 (31%), Positives = 164/320 (51%), Gaps = 13/320 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V  D  + R+D +  + +  +    + + +R G++RV+KKRVK  +R+ +G 
Sbjct: 1   MNKVELIEVAEDVIDQRIDNFLLSRFSRLPKSLIYRWIRKGELRVNKKRVKQISRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP   +L    K  KI  S      H DFL+  +LYE+    + +KP+G++V GGS
Sbjct: 61  IVRVPPF--SLEEDSKPIKISQS------HLDFLEQRILYENDDYIIVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           +S+V G    K   I   L  K     D   VVK + K    A++    +      F  L
Sbjct: 172 YSIVHGHWDKKIIKIDLPL--KRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLL 229

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP-HPE 301
           E++  TGRTHQ+RVH   MG PIV D KY  A           ++L LHA  ++     +
Sbjct: 230 EIKLETGRTHQIRVHTKAMGHPIVADKKYGFATKDQLLLDKGVDRLLLHAAKLEFYDDKQ 289

Query: 302 GGRLQITAPLPAHMVKTWDS 321
             ++ +TA L +   K    
Sbjct: 290 NKQISVTAALDSRFEKFIQE 309


>gi|171463176|ref|YP_001797289.1| pseudouridine synthase, RluA family [Polynucleobacter necessarius
           subsp. necessarius STIR1]
 gi|171192714|gb|ACB43675.1| pseudouridine synthase, RluA family [Polynucleobacter necessarius
           subsp. necessarius STIR1]
          Length = 335

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 95/319 (29%), Positives = 144/319 (45%), Gaps = 8/319 (2%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V   ++  +E   RLD +       +   ++ +I+RSG+VRV+KKR +   R+  G VVR
Sbjct: 20  VHLQIIGPEEAGQRLDNYLLRWAKGVPKSHVYRIIRSGEVRVNKKRAEPTTRLIEGDVVR 79

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A    +    +  +      H    K  +L+ED  + + NKPAG++V GGSGIA
Sbjct: 80  LPPVRIAEPAQMA--AVNSAQTKFRAHGYSDKMPILFEDEALLIVNKPAGLAVHGGSGIA 137

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L+           L HRLD++TSG+L +A+ R+A   L    R  +  K Y+ L
Sbjct: 138 LGVIETLRITRPELKF-LELVHRLDRDTSGVLFLAKKRSALVELHRQIREDQADKRYYLL 196

Query: 187 VWGIPKNKKEC--IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
             G      +   +   L K     G+    V  +   ++ A+   K +          E
Sbjct: 197 AHGEIVQGAQTMQLKYPLHKYLLPNGERRVRVDPDGLPSHTALRVTKALKREGAAITLAE 256

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            Q  TGRTHQ+RVH   +G  I+GD KY              +LYLHA      HP  G 
Sbjct: 257 AQLKTGRTHQIRVHLQKLGHAILGDDKYGFEDLDKVIK--SKRLYLHAHLAGFTHPRTGE 314

Query: 305 -LQITAPLPAHMVKTWDSL 322
            ++I +PLP        + 
Sbjct: 315 KMRIESPLPPEFTAMMKTF 333


>gi|289551021|ref|YP_003471925.1| Ribosomal large subunit pseudouridine synthase D [Staphylococcus
           lugdunensis HKU09-01]
 gi|289180553|gb|ADC87798.1| Ribosomal large subunit pseudouridine synthase D [Staphylococcus
           lugdunensis HKU09-01]
          Length = 305

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 76/329 (23%), Positives = 144/329 (43%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT     V +      R+D+   ++    +   +Q  ++   V V+ K +K N +++   
Sbjct: 1   MTTHSIEVTDTRHTGQRIDKLLSDYNHDWSRSQIQDWIKHELVIVNGKAIKANYKVKLHD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I            E++++D+ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  SIVIT-----------EKEVVDADI----QPENLNLDIYYEDKDVAIVYKPKGMVVHPSP 105

Query: 124 GI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L +    +
Sbjct: 106 GHYSGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRSLVDQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    +   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYTALVHGNIPHDYGTVDAPIGRNKK-DRQSMDVVD----DGKDAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPKKTLD-----IGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  ++  A LP    +  + +  +
Sbjct: 275 EHPVTGEYIERQAALPDAFEQLLEDIRKR 303


>gi|194323822|ref|ZP_03057598.1| pseudouridine synthase, RluA family [Francisella tularensis subsp.
           novicida FTE]
 gi|208779913|ref|ZP_03247257.1| pseudouridine synthase, RluA family [Francisella novicida FTG]
 gi|194322186|gb|EDX19668.1| pseudouridine synthase, RluA family [Francisella tularensis subsp.
           novicida FTE]
 gi|208744368|gb|EDZ90668.1| pseudouridine synthase, RluA family [Francisella novicida FTG]
          Length = 317

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 71/315 (22%), Positives = 129/315 (40%), Gaps = 28/315 (8%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
             +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I   +  
Sbjct: 3   PKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEINIELLP 62

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
            N  I E                +   +++ED  I V +KP  + V  G+G       + 
Sbjct: 63  TNEWIAED---------------INLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNA 107

Query: 132 FLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            L  + D  K  +  + HRLD++TSG++V A++  A  +L +    R++ + Y ++V G 
Sbjct: 108 LLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGE 167

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              ++  I   + +            +        AI+H+  I+ +   F  +E Q  TG
Sbjct: 168 IY-QQGTINQPIGRDPTNRTKMAINYR-----GKEAITHYTPIEVY-DGFTLIECQLETG 220

Query: 251 RTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QI 307
           RTHQ+RVH   +  P+VGD  Y   +            +  LHA  +   HP   ++ + 
Sbjct: 221 RTHQIRVHMKSIKHPLVGDQTYNKSSTKLEKLAITTPTRQALHAYKLSFIHPTTAKMVKF 280

Query: 308 TAPLPAHMVKTWDSL 322
            + LP  M+     L
Sbjct: 281 KSKLPEDMLNLKAQL 295


>gi|254304341|ref|ZP_04971699.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148324533|gb|EDK89783.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 316

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 76/338 (22%), Positives = 143/338 (42%), Gaps = 36/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V  + E MRLD++            L+K++ +  V+V+ K +K N  ++
Sbjct: 1   MENIKEKFEFEVSFEYEGMRLDKYLSEQIEEATRSYLEKLIDNNFVKVNSKIIKKNGRKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +SG+ + +               ++    N+   ++ +   ++YE+    V NK  G+ V
Sbjct: 61  KSGEKIEV---------------LIPEEENIDIEAENIPLDVVYENDDFIVINKNYGMVV 105

Query: 120 QGGSG-IAYHIDGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     +   L  + +     +   +P + HRLD++TSG++++A+   A   L   
Sbjct: 106 HPAYGNYTGTLVNALLYYTNNLSSVNGNIRPGIIHRLDKDTSGLILIAKNNFAHAKLASM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           F  + I K Y  +V G    +     I N + +        + VVK+N      AIS+++
Sbjct: 166 FIDKTIHKTYLCIVKGNFSEENLSGRIENLIGRDIK-DRKKMAVVKEN---GKIAISNYR 221

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           VI+   + +  +E+   TGRTHQ+RVH   +   I+GD  Y    K         +  LH
Sbjct: 222 VIEQV-EGYSLVEVAIETGRTHQIRVHMKSINHVILGDSVYGTEDKN------IKRQMLH 274

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A  ++  +P +         L    ++    L F  ++
Sbjct: 275 AYKLEFLNPLDNKEYVFKGKLFDDFIEVAKKLKFNIEK 312


>gi|156740304|ref|YP_001430433.1| RluA family pseudouridine synthase [Roseiflexus castenholzii DSM
           13941]
 gi|156231632|gb|ABU56415.1| pseudouridine synthase, RluA family [Roseiflexus castenholzii DSM
           13941]
          Length = 315

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 78/324 (24%), Positives = 142/324 (43%), Gaps = 29/324 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++VE  +E  RLDR+     P ++    + ++   +V ++ ++V+  + ++ G VV +  
Sbjct: 9   LIVEAADEGHRLDRYIAGKVPDLSRTYARHLIEDARVLLNNRQVRPASPVRVGDVVTVQ- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                         L     +   ++ L   ++YED  + V +KPAGI V    G     
Sbjct: 68  --------------LPEPQPVGLVAEALPLQIVYEDDDVVVIDKPAGIVVHPAPGHNRGT 113

Query: 128 HIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            ++  +  + +   S   +P + HRLD++TSG+LV AR   A   L    + RR+ KIY 
Sbjct: 114 LVNALIARYPEMAISGDLRPGIVHRLDRDTSGLLVAARNDRALHSLQAQQQARRMLKIYL 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +V G        I   + +      D V +      G   A +H++V++   + +  +E
Sbjct: 174 VVVEGRMNESGGVIDAPIARHPT---DRVRMAVM--AGGRPARTHWRVLEELGE-YALIE 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
            +  TGRTHQ+RVH      P++ D  Y         +    + +LHA  +    P  G 
Sbjct: 228 ARLETGRTHQIRVHFASRNRPVLADPLYGPKRPR--ATFGLTRQFLHAHRLGFALPSSGA 285

Query: 304 RLQITAPLPAHMVKTWDSLGFKYD 327
            ++ T+PLP  +      L  + +
Sbjct: 286 WVEFTSPLPDDLAAALARLRQRAN 309


>gi|187477717|ref|YP_785741.1| ribosomal large subunit pseudouridine synthase D [Bordetella avium
           197N]
 gi|115422303|emb|CAJ48827.1| ribosomal large subunit pseudouridine synthase D [Bordetella avium
           197N]
          Length = 320

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 132/323 (40%), Gaps = 31/323 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  D    RLD+      P  +   LQ  + +G V V+ +  K    +  G V+ +  
Sbjct: 19  IFIPPDVPADRLDKVLAGLMPGHSRSRLQGWIEAGHVLVNGQAAKVRQPVGPGDVLTVWE 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                           +  +L    + +   ++   S   V NKPAG+    G+G     
Sbjct: 79  Q--------------PAPESLAFSPEPVDFDVIDSSSDWIVVNKPAGLVTHPGAGNWTGT 124

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L  + + S+  +  + HRLD++TSG++VVAR   A  HL    + R + + Y +L
Sbjct: 125 LLNGLLHRFPELSRVARAGIVHRLDKDTSGLMVVARNELAQTHLVRQLQARSMGREYLAL 184

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF----KVIDCFAQKFCW 242
             G        +   + + + +    V +  +    A  AI+H+    +      ++   
Sbjct: 185 AHGWLAGA-GTVDRPIGRDARV---PVRMSVERPIAAKPAITHYLPQRRGEAQEGERVTE 240

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +  +  TGRTHQ+RVH   +G P++ D  Y        T     +  LHAR +    P G
Sbjct: 241 VICRLETGRTHQIRVHLASLGHPLLADTIYGGRALAGAT-----RQMLHARALHFDDPGG 295

Query: 303 -GRLQITAPLPAHMVKTWDSLGF 324
            G +   A LP  M     +L +
Sbjct: 296 RGEVTFEAALPPDMQAVQGALIW 318


>gi|256822306|ref|YP_003146269.1| RluA family pseudouridine synthase [Kangiella koreensis DSM 16069]
 gi|256795845|gb|ACV26501.1| pseudouridine synthase, RluA family [Kangiella koreensis DSM 16069]
          Length = 324

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 79/340 (23%), Positives = 142/340 (41%), Gaps = 35/340 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M+  +     + +      RLD      +   +   +Q+ +++G V+V+ + +  N  ++
Sbjct: 1   MTTQSIALRHIFDEKVYGKRLDAALSQQFSEYSRSRIQEWIQNGFVKVNDEVITSNKYKM 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
              + + I   I        E                +   ++YED  + V NKPAG+ V
Sbjct: 61  AGFEDIEINAEIEVAGEWKPE---------------AIDLDIVYEDDALLVINKPAGLVV 105

Query: 120 QGGSGIAYHI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             G+G       +  L    D +   +  + HR+D+ET+G+LVVA+T AA   L E  + 
Sbjct: 106 HPGAGNQDGTMVNALLHHCPDLANLPRAGIIHRIDKETTGLLVVAKTIAAHTSLVEQLQN 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R   + Y ++V  +       I   + +          V          AI+H++V++ F
Sbjct: 166 RAFTREYDAVVNRVMV-SGGTIDKPIGRHPTKRTSMAVVA-----DGKRAITHYRVVEKF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKL 288
                 L+++  TGRTHQ+RVH  ++  P++GD  Y   ++       +         + 
Sbjct: 220 LD-HTHLKLRLETGRTHQIRVHMAYLKFPLIGDPLYSGRYRVPTRITPELRNTVDNFKRQ 278

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            LHA  + L HPE    ++  AP+P  M +  D L    D
Sbjct: 279 ALHASLLGLQHPETDEYIEWRAPMPQDMARLLDDLRVNRD 318


>gi|15672980|ref|NP_267154.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis Il1403]
 gi|281491492|ref|YP_003353472.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
 gi|12723945|gb|AAK05096.1|AE006334_2 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
 gi|281375210|gb|ADA64723.1| Ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
 gi|326406542|gb|ADZ63613.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis CV56]
          Length = 301

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 144/323 (44%), Gaps = 33/323 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  + + +RLD+   N     +   L +++++ +V V+ +  K   +++ G  +    
Sbjct: 4   IKINEENKGLRLDKALANQ-TEYSRSLLTELIKNDKVFVNSEAKKAKYKVKVGDRIEFE- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
                   + E ++LD        ++ L   ++YEDS + V NKP G+ V   +G A   
Sbjct: 62  --------VPEAEVLD------IVAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGT 107

Query: 128 HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  +    D        +P + HR+D++TSG+L++A+   A + L    + +  ++ Y
Sbjct: 108 LVNAIMYHIKDLSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G   N K  I   + +          V      G   A++HF+V++ F   +  +
Sbjct: 168 LAIVHGEIANDKGTIEAPIGRNLKDRKKQAVVS-----GGKPAVTHFEVLERF-YGYTLI 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++  TGRTHQ+RVH  ++G P+ GD  Y      N T       +LHA  +   HP  G
Sbjct: 222 ALRLETGRTHQIRVHMNYIGHPVAGDPLYGP----NKTLTPNKGQFLHAETLGFDHPTTG 277

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
             ++     P    +  + L  +
Sbjct: 278 EFMEFQVDAPEIFNEQLEKLREQ 300


>gi|21910093|ref|NP_664361.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28896209|ref|NP_802559.1| hypothetical protein SPs1297 [Streptococcus pyogenes SSI-1]
 gi|71903284|ref|YP_280087.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94994123|ref|YP_602221.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|21904284|gb|AAM79164.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28811460|dbj|BAC64392.1| conserved hypothetical protein [Streptococcus pyogenes SSI-1]
 gi|71802379|gb|AAX71732.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94547631|gb|ABF37677.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
          Length = 296

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 77/316 (24%), Positives = 134/316 (42%), Gaps = 34/316 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V+           
Sbjct: 8   SGQRLDKALADLSP-LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVICFE-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
                  L     L   +  +   ++YED  + + NKP G+ V   +G      ++  + 
Sbjct: 59  -------LPKEEVLEYQAQNIPLDIIYEDDTLAIINKPQGMVVHPSAGHPSGTMVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+T AA Q L E  + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        A++ F V++ F   +  +E+Q  TG
Sbjct: 172 LPNDRGMIEAPIGRSEKDRKKQAVTAK-----GKEAVTRFTVLERFGD-YSLVELQLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ + L HP  G  +  T 
Sbjct: 226 RTHQIRVHMAYIGHPVAGDPLYGPR-----KTLSGHGQFLHAKTLGLTHPMTGKEMIFTV 280

Query: 310 PLPAHMVKTWDSLGFK 325
             P    K    L  K
Sbjct: 281 EAPEIFQKVLKLLRKK 296


>gi|212550472|ref|YP_002308789.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
 gi|212548710|dbj|BAG83378.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
          Length = 342

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 87/353 (24%), Positives = 157/353 (44%), Gaps = 51/353 (14%)

Query: 8   QYVVVENDEEN-MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            +  V N E+  +R+D++  +     +   +Q+    G +  +   +K N +++ G ++ 
Sbjct: 8   HFRFVANKEQGFLRVDKFLVDKIIGTSRNRIQQAANVGSICANNHPIKSNYKVKPGDIIT 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I      +N   +E +I   ++ L          ++YED  + V +KPA + V  G    
Sbjct: 68  I-----VMNQPHREVEIAPENIPLN---------IVYEDDDVIVVDKPAELVVHPGH--- 110

Query: 127 YHIDGFLKSWVDSKGQ----------------KPRLTHRLDQETSGILVVARTRAAAQHL 170
            +  G L + +                     +  L HR+D+ TSG+LV A+   A  +L
Sbjct: 111 DNYTGTLVNAIAGYYSSTTSSIIQSTFYNEDFRSGLVHRIDKGTSGLLVFAKNLNAKTNL 170

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              F  + I++ YW++VWG  K ++E I   + +  H     +  V  N      AI+H+
Sbjct: 171 DMQFFRKTIRRNYWAVVWGNVKKEEETIKCNIGRNLH--NRMLMDVFPNNNHGKPAITHY 228

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FKGNFTSPIQ--- 285
           KV++ F +    +E    TGRTHQ+RVH  ++G  +  D +Y  N   KGN  +  +   
Sbjct: 229 KVLERF-EYVTLIECSLETGRTHQIRVHMKYIGHVLFNDRRYGGNEILKGNHHTKYKQFV 287

Query: 286 -------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNL 330
                   +  LHAR +   HP+ G  + + +PLP  M+   +     + +NL
Sbjct: 288 QNCFAICQRQALHARVLGFTHPKTGKEILLESPLPKDMILLIERWR-NFSKNL 339


>gi|165933873|ref|YP_001650662.1| ribosomal large subunit pseudouridine synthase D [Rickettsia
           rickettsii str. Iowa]
 gi|165908960|gb|ABY73256.1| ribosomal large subunit pseudouridine synthase D [Rickettsia
           rickettsii str. Iowa]
          Length = 313

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 76/327 (23%), Positives = 144/327 (44%), Gaps = 40/327 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V ++   +RLD+   +   +++   +QK ++  QV V+   +   +  ++   ++     
Sbjct: 6   VPHELNGIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFK 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 I      LD               ++YED  + V NK AG++V  G+G  +H D
Sbjct: 66  EPEELKIAAANVALD---------------IIYEDDDLIVINKAAGMTVHPGAG--HHDD 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD++T+G++VVA+   A   L      +++ + 
Sbjct: 109 TLVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQKQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FC 241
           Y  LVWG+    +  I N + + S      + ++K    G   A++H+K ++ F +    
Sbjct: 169 YKVLVWGVINPLEGVIKNNIGR-SRSDRQKMTILKY---GGKEAVTHYKTLELFYKGSIS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP +         +  LH+ 
Sbjct: 225 MVECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAYSPPELKAKLIDFKRQALHSW 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTW 319
           Y+   HP     ++ +  LP  M +  
Sbjct: 285 YLSFTHPTSNEIMEFSCELPRDMEEII 311


>gi|99081958|ref|YP_614112.1| ribosomal large subunit pseudouridine synthase D [Ruegeria sp.
           TM1040]
 gi|99038238|gb|ABF64850.1| ribosomal large subunit pseudouridine synthase D [Ruegeria sp.
           TM1040]
          Length = 337

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 87/349 (24%), Positives = 141/349 (40%), Gaps = 50/349 (14%)

Query: 14  NDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
            D    RLD+      P    ++   L +++ SG V VD  R     +R+  G ++ I  
Sbjct: 3   ADNPPKRLDKAIARDVPEEANLSRTRLARLIESGGVFVDGARANDAKSRVAEGALIVITV 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                +HI  E   LD               +++ED+ + V NKPAG+ V    G     
Sbjct: 63  EEAEDSHIGPEDIPLD---------------VIHEDADLIVINKPAGMVVHPAPGSPSGT 107

Query: 128 HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++  L             ++P + HR+D+ETSG+LVVA++ AA Q L   F    +++ 
Sbjct: 108 LVNALLHHCGADLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQFERHTVERY 167

Query: 183 YWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE--KGANYAISHF 230
           Y ++ +G+P      +           N L   + +        +Q    +G  +A++  
Sbjct: 168 YQAVCYGVPDGNDPRLRGVRGTSFEPGNILKITTQLARHKTDRQRQAVLFEGGRHAVTRA 227

Query: 231 KVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GN 279
           ++I+ F        +E    TGRTHQ+RVH  H G  ++GD  Y    K         G 
Sbjct: 228 RIIEAFGAPAAASLVECWLETGRTHQIRVHMAHAGHGLLGDPTYGGKRKISPKALSAAGL 287

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
                  +  LHA  +   HP  G  ++  APLP  M     +L     
Sbjct: 288 AAINSFQRQALHAAVLGFEHPVSGEMMRFEAPLPEDMQALIAALRIPAS 336


>gi|139473995|ref|YP_001128711.1| RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo]
 gi|134272242|emb|CAM30494.1| putative RNA pseudouridylate synthase [Streptococcus pyogenes str.
           Manfredo]
          Length = 296

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 78/316 (24%), Positives = 135/316 (42%), Gaps = 34/316 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V+           
Sbjct: 8   SGQRLDKALADLSP-LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVICFE-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
                  L     L   +  +   ++YED  + + NKP G+ V   +G      ++  + 
Sbjct: 59  -------LPKEEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+T AA Q LTE  + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDAAHQVLTEELKAKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        A++ F V++ F   +  +E+Q  TG
Sbjct: 172 LPNDRGMIEAPIGRSEKDRKKQAVTAK-----GKEAVTRFTVLERFGD-YSLVELQLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ + L HP  G  +  T 
Sbjct: 226 RTHQIRVHMAYIGHPVAGDPLYGPR-----KTLSGHGQFLHAKTLGLTHPMTGKEMIFTV 280

Query: 310 PLPAHMVKTWDSLGFK 325
             P    K    L  K
Sbjct: 281 EAPEIFQKVLKLLRKK 296


>gi|291166433|gb|EFE28479.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Filifactor alocis ATCC 35896]
          Length = 293

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 79/310 (25%), Positives = 135/310 (43%), Gaps = 33/310 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  ++ P I+   +QK++   +V V+ K  K +  ++S   + I           
Sbjct: 1   MRLDQFISSNLPSISRSYIQKLIDEKRVLVNGKYEKKSFLLKSFDNIEIY---------- 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW 136
                +    ++    + +   +L+ED  I + NK  G+ V    G   H   +  L   
Sbjct: 51  -----IPEPKSIEISPENIPLNILFEDKDILIVNKEKGMVVHPAPGNYSHTLVNAILYHC 105

Query: 137 VDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             +  +     +P + HR+D++TSGILV+A+   A Q L+E F+   IQ+ Y  + +G  
Sbjct: 106 KGNLSEINGYIRPGIVHRIDKDTSGILVIAKNNDAHQFLSEQFKEHSIQREYQLITFGNI 165

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K     I   + +          V          AI+H  VI+ F  K  +L+ +  TGR
Sbjct: 166 KTTHLSIEQPIGRNPKNRLQMAVV-----PNGKPAITHLTVIENFKDK-TYLKARLETGR 219

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P++GD  Y                 LHA Y+   HP   + ++  +P
Sbjct: 220 THQIRVHCTYIGHPLLGDSLY----TNRKCEYQLQGQTLHAGYLGFVHPTSKKFIEFYSP 275

Query: 311 LPAHMVKTWD 320
           LP +      
Sbjct: 276 LPEYFSHILR 285


>gi|262067278|ref|ZP_06026890.1| pseudouridine synthase, RluA family [Fusobacterium periodonticum
           ATCC 33693]
 gi|291379004|gb|EFE86522.1| pseudouridine synthase, RluA family [Fusobacterium periodonticum
           ATCC 33693]
          Length = 315

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 75/338 (22%), Positives = 147/338 (43%), Gaps = 36/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V  + E MRLD++            L+K++ +  V+++ K +  N  ++
Sbjct: 1   MENIKEKFEFEVNPEYEGMRLDKYLAEQIEEATRSYLEKLIDNSYVKINSKIINKNGRKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +SG+ V I                +    N+   ++ +   +++E+    + NK   + V
Sbjct: 61  KSGEKVEIS---------------IPEEENIDIEAENIPLDIVFENDDFILVNKKYNMVV 105

Query: 120 QGGSG-IAYHIDGFLKSWVDSK-----GQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     +   L  + ++        +P + HRLD++TSG+++VA+   A   L   
Sbjct: 106 HPAYGNYTGTLVNALLYYTNNLSSVNGNIRPGIIHRLDKDTSGLILVAKNNFAHAKLASM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           F  + I K Y  +V G   ++  +  I N + + +      + +VK+N      AIS+++
Sbjct: 166 FTDKTIHKTYLCIVKGNFSDENLEGRIENLIGRDTK-DRKKMAIVKEN---GKLAISNYR 221

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V++   + +  +E+   TGRTHQ+RVH   +  PI+GD  Y +  K         +  LH
Sbjct: 222 VVEQV-KDYSLVEVLIETGRTHQIRVHMKSINHPILGDVIYGSEDKNV------KRQMLH 274

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A  ++  +P +    + T  L    ++    L F  D+
Sbjct: 275 AFKLEFLNPLDNKEYRFTGKLFDDFIEVAKKLNFNIDK 312


>gi|157829144|ref|YP_001495386.1| hypothetical protein A1G_07185 [Rickettsia rickettsii str. 'Sheila
           Smith']
 gi|157801625|gb|ABV76878.1| hypothetical protein A1G_07185 [Rickettsia rickettsii str. 'Sheila
           Smith']
          Length = 313

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 144/327 (44%), Gaps = 40/327 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V ++   +RLD+   +   +++   +QK ++  QV V+   +   +  ++   ++     
Sbjct: 6   VPHELNGIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFK 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 I      LD               ++YED  + V NK AG++V  G+G  +H D
Sbjct: 66  EPEELKIAAANVALD---------------IIYEDDDLIVINKAAGMTVHPGAG--HHDD 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD++T+G++VVA+   A   L      +++ + 
Sbjct: 109 TLVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQKQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FC 241
           Y  LVWG+    +  I N + + S      + ++K    G   A++H+K I+ F +    
Sbjct: 169 YKVLVWGVINPLEGVIKNNIGR-SRSDRQKMTILKY---GGKEAVTHYKTIELFYKGSIS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP +         +  LH+ 
Sbjct: 225 MVECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAYSPPELKAKLIDFKRQALHSW 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTW 319
           Y+   HP     ++ +  LP  M +  
Sbjct: 285 YLSFTHPTSNEIMEFSCELPRDMEEII 311


>gi|296269399|ref|YP_003652031.1| pseudouridine synthase, RluA family [Thermobispora bispora DSM
           43833]
 gi|296092186|gb|ADG88138.1| pseudouridine synthase, RluA family [Thermobispora bispora DSM
           43833]
          Length = 310

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 86/324 (26%), Positives = 141/324 (43%), Gaps = 28/324 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V    E  RLD      +   +      ++ +G V VD      ++R+++GQ
Sbjct: 1   MGEQRSLPVPEGLEGERLDAALSRLF-GFSRTRAADLIAAGDVLVDGAVPSKSDRLRAGQ 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +           + + I   S             +LYED  I V NKPAG++     
Sbjct: 60  WLDVTIPPPPAPPAPRLEPIPGMS-------------ILYEDEDIIVINKPAGVAAHPTV 106

Query: 124 G-IAYHIDGFLK---SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L      V + G  ++  + HRLD  T+G +VVA++  A   L  +F+ R
Sbjct: 107 GWTGPTVLGGLLGAGHRVSTSGAAERQGIVHRLDANTTGAMVVAKSELAYARLKRAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +++K Y ++V G     +  I   +    H  GD    V     G   AI+H+  I+ F 
Sbjct: 167 KVEKRYHAMVQGHMDPLRGTIDAPI--DRHPSGDGRFAVV---AGGKEAITHYDTIEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    L+++  TGRTHQ+RVH   +G P VGD  Y A+        + N+ +LHA  +  
Sbjct: 221 RAASLLDVKIETGRTHQIRVHLSALGHPCVGDFMYGADPTLAAKLGV-NRQWLHAITLAF 279

Query: 298 PHPEGGR-LQITAPLPAHMVKTWD 320
            HP  G  +  TA  P  + ++  
Sbjct: 280 EHPVTGEWMSFTAEYPDDLARSLK 303


>gi|126738738|ref|ZP_01754434.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           SK209-2-6]
 gi|126719919|gb|EBA16626.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           SK209-2-6]
          Length = 344

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 88/355 (24%), Positives = 144/355 (40%), Gaps = 50/355 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M+  Q   V  +    RLD+      P    ++   L +++ +G + VD   V     RI
Sbjct: 1   MSSRQIEFVITENPPKRLDKAVSRDVPEEAALSRTRLARLIEAGSLLVDGVVVLDPKARI 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  + I       +HI  E   L+               ++YED  + V NKPAG+ V
Sbjct: 61  AEGAQISITVEEAEDSHIGPEDIPLE---------------VIYEDDDLIVINKPAGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    +        ++P + HR+D+ETSG+LVVA+T AA Q L  
Sbjct: 106 HPAPGTPSGTLVNALLHHCGEKLSGVGGVKRPGIVHRIDKETSGLLVVAKTDAAHQGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F    +++ Y ++ +G+P      +           N L   + +        +Q    
Sbjct: 166 QFEKHTVERYYRAVCYGVPDGNDPRLRGVKGASFESGNILKLTTQLARHKHDRQRQAVLF 225

Query: 221 KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +G  +A++  ++++ F        +E    TGRTHQ+RVH  H G  ++GD  Y    K 
Sbjct: 226 QGGRHAVTRARIVEPFGNPGTAALIECWLETGRTHQIRVHMTHAGHSLIGDPTYGGKRKL 285

Query: 279 NFTSPIQ---------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              +             +  LHA  +   HP  G  ++  APLP  M +  D L 
Sbjct: 286 AAKALSLAGISAVQSFPRQALHAAVLGFTHPVSGEAMRFEAPLPDDMEELIDKLR 340


>gi|149926440|ref|ZP_01914701.1| pseudouridine synthase [Limnobacter sp. MED105]
 gi|149824803|gb|EDM84017.1| pseudouridine synthase [Limnobacter sp. MED105]
          Length = 335

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 91/318 (28%), Positives = 152/318 (47%), Gaps = 8/318 (2%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++   ++ RLD +  N    +   ++ +I+RSG+VR+++KR +   ++  G VVR+PP
Sbjct: 15  LEIDEKHQDQRLDNFLCNVCKGVPKSHVFRIIRSGEVRINRKRAEAKTKLCVGDVVRVPP 74

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +       +    +                 +L+ED  + V NKP+G++V GGSG ++ +
Sbjct: 75  IKVVEKQDLDSLSLSAGLNKTQLLKAAADLPILFEDEHLLVVNKPSGMAVHGGSGSSFGL 134

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +++      Q   L HR+D+ETSGIL++++ R+A + L E  R R  +K Y +LV G
Sbjct: 135 IECIRALRAETHQDLELVHRIDRETSGILIISKKRSALRKLQEQLRARSWKKYYKTLVLG 194

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQ 246
                   +   LLK      +    V  +E G   A + FKVI C+   +     ++ Q
Sbjct: 195 HWPEALRQVDLPLLK--TQSSEKEARVFVDESGDK-ACTKFKVIQCYKSSYSSFTLIQAQ 251

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
             TGRTHQ+RVH      PI GD +Y               +++LHA  + L HP     
Sbjct: 252 ILTGRTHQIRVHTSANKFPIAGDDRYGNFEMNKQLARQGLKRMFLHAARLQLVHPATNET 311

Query: 305 LQITAPLPAHMVKTWDSL 322
           + + APL   +     SL
Sbjct: 312 IVLEAPLAPELDGFLKSL 329


>gi|329120441|ref|ZP_08249106.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327461899|gb|EGF08229.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 373

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 80/334 (23%), Positives = 141/334 (42%), Gaps = 29/334 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V VD K  +  +++  G+ + +  
Sbjct: 30  LTVPLEMAGQRLDAALAALLPDYSRSRLAGWIKEGAVAVDGKAARPKDKLIGGETLAV-- 87

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                       ++ + +  L    + +   ++YED  + V +KPAG+ V   +G     
Sbjct: 88  ------------RVRERNETLAFTPEPMDLDIVYEDDSVMVLDKPAGLVVHPAAGNWSGT 135

Query: 128 HIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L      +   +  + HRLD++TSG++VVA+T AA   L    + R +++IY ++
Sbjct: 136 LLNGLLAYCPALQNVPRAGIVHRLDKDTSGLMVVAKTLAAQTDLVRQMQARSVKRIYRAV 195

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI       I   + +  H     + VV     G   A++H KV++ +     ++E  
Sbjct: 196 ADGIVPFD-GKIETLIGRDPH-NRTKMAVV---GFGGKEAVTHVKVLERY-LAHSYIECA 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-----NFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH      P+ GD  Y                   +  LHA  +   HP+
Sbjct: 250 LETGRTHQIRVHMREARHPLAGDPVYGNLRHPASDIVKTAVRGLGRQALHAYRLSFAHPQ 309

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
            G  ++  APLPA +      L  +   +  + R
Sbjct: 310 SGETMRFEAPLPADIHHLLSVLRLESGMDSPLSR 343


>gi|187931810|ref|YP_001891795.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. mediasiatica FSC147]
 gi|187712719|gb|ACD31016.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. mediasiatica FSC147]
          Length = 332

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 134/321 (41%), Gaps = 28/321 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +++   +   R+D      +   +   +QK L+ G + V+ +  K  + +   + V I
Sbjct: 12  QNIIMHPKDAGKRIDVAINEQFEQFSRAQIQKWLKEGSITVNGRATKPKHIVLGDEEVEI 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
              +   N  I E                +   +++ED  I V +KP  + V  G+G   
Sbjct: 72  NIELLPTNEWIAED---------------INLKIIFEDDDIIVIDKPVNMIVHPGAGNPT 116

Query: 126 AYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L  + D  K  +  + HRLD++TSG++V A++  A  +L +    R++ + Y 
Sbjct: 117 GTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYL 176

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +            +        AI+H+  I+ +   F  +E
Sbjct: 177 AIVEGEIY-QQGTINQPIGRDPTNRTKMAINYR-----GKEAITHYTPIEVY-DGFTLIE 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--GNFTSPIQNKLYLHARYMDLPHPEG 302
            Q  TGRTHQ+RVH   +  P+VGD  Y  +          I  +  LHA  +   HP  
Sbjct: 230 CQLETGRTHQIRVHMKSIKHPLVGDQTYNKSLTKLEKLAITIPTRQALHAYKLSFIHPTI 289

Query: 303 GRL-QITAPLPAHMVKTWDSL 322
            ++ +  + LP  M+     L
Sbjct: 290 AKMVKFKSKLPEDMLNLKAQL 310


>gi|161525362|ref|YP_001580374.1| RluA family pseudouridine synthase [Burkholderia multivorans ATCC
           17616]
 gi|221201329|ref|ZP_03574368.1| pseudouridine synthase, RluA family [Burkholderia multivorans
           CGD2M]
 gi|221208809|ref|ZP_03581807.1| pseudouridine synthase, RluA family [Burkholderia multivorans CGD2]
 gi|221214111|ref|ZP_03587084.1| pseudouridine synthase, RluA family [Burkholderia multivorans CGD1]
 gi|160342791|gb|ABX15877.1| pseudouridine synthase, RluA family [Burkholderia multivorans ATCC
           17616]
 gi|221166288|gb|EED98761.1| pseudouridine synthase, RluA family [Burkholderia multivorans CGD1]
 gi|221171265|gb|EEE03714.1| pseudouridine synthase, RluA family [Burkholderia multivorans CGD2]
 gi|221178597|gb|EEE11005.1| pseudouridine synthase, RluA family [Burkholderia multivorans
           CGD2M]
          Length = 316

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 100/322 (31%), Positives = 156/322 (48%), Gaps = 23/322 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++      R+D +       +   ++ +ILRSG+VRV+K RV    R+  G VVR+PP
Sbjct: 2   IQIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDVVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A   + +    +                +L+ED  + V +KPAG++V GGSG+A+ +
Sbjct: 62  VRVAAADLARADAPIVPPAQFD---------VLFEDDAMLVIDKPAGVAVHGGSGVAFGV 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+     + +   L HRLD+ETSG+L++A+ R A   L E  R  RI K Y++ V G
Sbjct: 113 IEQLRQAR-PRAKFLELVHRLDRETSGVLMLAKKRTALVALHEQIRENRIDKRYFACVHG 171

Query: 190 IPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             +        +   L K +   G+    V+ +      + + F +++ +   +  +E +
Sbjct: 172 EWQADWGRRRAVKAPLFKYTTADGERRVRVQDD---GLASHTVFNLVERWPD-YALVEAE 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             TGRTHQ+RVH  H+G PIVGD KY               P   +++LHA  + L HP 
Sbjct: 228 LKTGRTHQIRVHLAHLGLPIVGDAKYGDFALNKALARANAQPSLKRMFLHAHRLRLAHPL 287

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            G  LQ  APLPA      D L
Sbjct: 288 SGDALQFDAPLPAECRHFLDQL 309


>gi|238651091|ref|YP_002916949.1| ribosomal large subunit pseudouridine synthase D [Rickettsia
           peacockii str. Rustic]
 gi|238625189|gb|ACR47895.1| ribosomal large subunit pseudouridine synthase D [Rickettsia
           peacockii str. Rustic]
          Length = 313

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 144/327 (44%), Gaps = 40/327 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V ++   +RLD+   +   +++   +QK ++  QV V+   +   +  ++   ++     
Sbjct: 6   VPHELNGIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFK 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 I      LD               ++YED  + V NK AG++V  G+G  +H D
Sbjct: 66  EPEELKIAAANVALD---------------IIYEDDDLIVINKAAGMTVHPGAG--HHDD 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD++T+G++VVA+   A   L      R++ + 
Sbjct: 109 TLVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FC 241
           Y  LVWG+    +  I N + + S      + ++K    G   A++H+K ++ F +    
Sbjct: 169 YKVLVWGVINPLEGVIKNNIGR-SRSDRQKMTILKY---GGKEAVTHYKTLELFYKGSIS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP +         +  LH+ 
Sbjct: 225 MVECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAHSPPELKAKLIDFKRQALHSW 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTW 319
           Y+   HP     ++ +  LP  M +  
Sbjct: 285 YLSFTHPTSNEIMEFSCELPRDMEEII 311


>gi|116751075|ref|YP_847762.1| RluA family pseudouridine synthase [Syntrophobacter fumaroxidans
           MPOB]
 gi|116700139|gb|ABK19327.1| ribosomal large subunit pseudouridine synthase D [Syntrophobacter
           fumaroxidans MPOB]
          Length = 344

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 89/334 (26%), Positives = 142/334 (42%), Gaps = 35/334 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ +E+  RLD +     P  +   +QK++R G+V V+   VK +  I+SG  + +    
Sbjct: 14  VDVEEKLRRLDVFLSARSPDCSRSQVQKLIREGRVTVNGLPVKASYEIRSGDCIAVW--- 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HI 129
             L   + E  +    + L          +L+ED  + V NK  G+ V  G+G      +
Sbjct: 71  --LPEAVGEDSLQPRPMPLE---------ILFEDDDVLVLNKAPGVIVHPGAGHEEGTLV 119

Query: 130 DGFLKSW----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            G L            ++P + HRLD+ TSG L+VA++  A   L   F+   + K Y +
Sbjct: 120 HGLLAHCSRLASRGAPRRPGIVHRLDRGTSGALMVAKSERAYLELIRQFKHHEVGKEYLA 179

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV+G        I   + +   +    + V+   EKG   A+S +KV   + +    L +
Sbjct: 180 LVYGTMAGASGEIRTGMGRH-PVDRKRMAVL---EKGGREAVSQWKVAVAWGE-VSLLRV 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NKLYLHARYMD 296
              TGRTHQ+RVH  HM  P+VGD  Y    +                 ++  LHA  + 
Sbjct: 235 VIKTGRTHQIRVHLSHMQHPVVGDETYGGGKRKARAVKSDVLRELLMEVDRQMLHAVGLA 294

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
             HP  G  L  TAPLP       + +     + 
Sbjct: 295 FRHPVSGADLSFTAPLPPDFAGLLERIRISLQKE 328


>gi|85711025|ref|ZP_01042085.1| Pseudouridylate synthase [Idiomarina baltica OS145]
 gi|85694938|gb|EAQ32876.1| Pseudouridylate synthase [Idiomarina baltica OS145]
          Length = 322

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 142/325 (43%), Gaps = 35/325 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           +V       RLD+     +P  +   ++K +  G+V VD + + K   +++ G +V I  
Sbjct: 10  IVPESLAGKRLDQILAELFPDYSRSRMKKWITEGKVSVDAQVIEKPREKLEFGALVAIDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
            +                      +  ++  ++YED  I + NKPAG+ V  G+G     
Sbjct: 70  ELEREER---------------YQAQPIELDIVYEDEDILIINKPAGLVVHPGAGAPDGT 114

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    D     +  + HRLD++T+G++VVAR   A   L +  + R I + Y ++
Sbjct: 115 LLNGLLHYDPDIDHVPRAGIIHRLDKDTTGLMVVARNIPAQTQLVDMMQKREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G+       + +  + +      ++ VV         A++H++V++ F +    L ++
Sbjct: 175 CNGVMTA--GGMVDEPIGRHPTKRTHMAVVS----SGKPAVTHYRVVERF-RAHTLLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLP 298
             +GRTHQ+RVH  H+  P+VGD  Y    +           +    ++  LHA  + L 
Sbjct: 228 LESGRTHQIRVHMAHIRHPLVGDLTYGGRPRPPKQASDEFLASLRGFSRQALHAAKLSLH 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP  G  +   AP P   V    S+
Sbjct: 288 HPITGDWMSFEAPRPDDFVALIQSM 312


>gi|34581099|ref|ZP_00142579.1| sfhB protein homolog [Rickettsia sibirica 246]
 gi|28262484|gb|EAA25988.1| sfhB protein homolog [Rickettsia sibirica 246]
          Length = 313

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 144/327 (44%), Gaps = 40/327 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V ++   +RLD+   +   +++   +QK ++  QV V+   +   +  ++   ++     
Sbjct: 6   VPHELNGIRLDKVLSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFK 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 I      LD               ++YED  + V NK AG++V  G+G  +H D
Sbjct: 66  EPEELKIAAANVALD---------------IIYEDDDLIVINKAAGMTVHPGAG--HHDD 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD++T+G++VVA+   A   L      R++ + 
Sbjct: 109 TLVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FC 241
           Y  LVWG+    +  I N + + S      + ++K    G   A++H+K ++ F +    
Sbjct: 169 YKVLVWGVINPLEGIIKNNIGR-SRSDRQKMTILKY---GGKEAVTHYKTLELFYKGSIS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP +         +  LH+ 
Sbjct: 225 MVECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAHSPPELKAKLIDFKRQALHSW 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTW 319
           Y+   HP     ++ +  LP  M +  
Sbjct: 285 YLSFTHPTSNEIMEFSCELPRDMEEII 311


>gi|146328697|ref|YP_001210177.1| ribosomal large subunit pseudouridine synthase, RluD [Dichelobacter
           nodosus VCS1703A]
 gi|146232167|gb|ABQ13145.1| ribosomal large subunit pseudouridine synthase, RluD [Dichelobacter
           nodosus VCS1703A]
          Length = 322

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 136/330 (41%), Gaps = 38/330 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +V+++   +RLD+    +YP  +    Q  + +G V ++    K  + + +G  +    
Sbjct: 12  FIVDHNNHALRLDQVLARNYPEFSRNRWQDAINAGTVLLNGAAAKSKSLVCAGDQIT--- 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                        +L   +     +  L   +LY D  I V NKPAG+ V    G   H 
Sbjct: 69  ------------GVLTQEIQTEDSAQNLPLNILYADDDIIVINKPAGLVVHPAVG--NHD 114

Query: 130 DGFLKSWVDSKGQKPRL-----THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +  L + +    Q   L      HRLD++TSG +V+A +  A   L    + R + +IY 
Sbjct: 115 NTLLNALLYHFPQTKHLPRSGIVHRLDKDTSGAMVIAHSARAHTDLVRQLQNRSMGRIYL 174

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV+G      + I   + + +                   AI+H+++ + + Q    L 
Sbjct: 175 ALVYGYI-TAGDTIDLPIGRHAKDRLKMAVR-----PDGKPAITHYRIEERW-QTLTLLR 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--------KGNFTSPIQNKLYLHARYMD 296
           +Q  TGRTHQ+RVH  H   P+VGD  Y A                    +  LHA  + 
Sbjct: 228 VQLETGRTHQIRVHLSHHRHPLVGDKLYGARPFLASSLTELQRQALAEFPRQALHAVELH 287

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           L HP     ++ TAPLP  M + +  L  +
Sbjct: 288 LHHPATNEIMRFTAPLPDDMTQLFTILRAQ 317


>gi|285018394|ref|YP_003376105.1| pseudouridine synthase (rna-uridine isomerase) (rna pseudouridylate
           synthase) protein [Xanthomonas albilineans GPE PC73]
 gi|283473612|emb|CBA16115.1| probable pseudouridine synthase (rna-uridine isomerase) (rna
           pseudouridylate synthase) protein [Xanthomonas
           albilineans]
          Length = 330

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 156/328 (47%), Gaps = 23/328 (7%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V+ + V  D    R+D +            + K++RSGQVRV+  R K   +++ G  
Sbjct: 16  SAVRILKVPEDRAGQRVDNFLLGQLKGAPRSLIYKLMRSGQVRVNGGRTKAERKLEVGDE 75

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP        ++ Q+  + +       + L++ ++YED+++   NKP+G++  GGSG
Sbjct: 76  VRIPP--------VRLQEEGEKTAPPAAFMERLEAAIVYEDARLLALNKPSGVASHGGSG 127

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT------ESFRMRR 178
           I++     L++      Q   L HRLD++TSG+L+VA+ R+A   L       +  + R 
Sbjct: 128 ISFGAIETLRALRP--NQTLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDQVQGRG 185

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y +L+ G   +    +   L      GG+    V         ++SHF++++    
Sbjct: 186 IGKRYLTLLVGRLPDGTMTVEVPLHIGLRQGGERHVQV---HAAGKPSLSHFRMLERRG- 241

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMD 296
              + E++  TGRTHQ+RVHA H+G P+ GD KY                +L+LHA  ++
Sbjct: 242 GHSYCEVRIETGRTHQIRVHAQHLGYPVAGDDKYGDPEVNKRLREHIGLKRLFLHAASLE 301

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLG 323
                G     + APL   + +    LG
Sbjct: 302 FTLDGGKAPYLLNAPLADELSEALSRLG 329


>gi|330993274|ref|ZP_08317210.1| Ribosomal large subunit pseudouridine synthase D [Gluconacetobacter
           sp. SXCC-1]
 gi|329759676|gb|EGG76184.1| Ribosomal large subunit pseudouridine synthase D [Gluconacetobacter
           sp. SXCC-1]
          Length = 323

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 134/328 (40%), Gaps = 36/328 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           V+   D+   R DR+       ++   ++ ++ SG +  +   ++     +++G    I 
Sbjct: 10  VIATADDAGQRTDRFIATATGALSRSRVKALMESGHLLRNGSPLRDPAEPVRAGMCYEIH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IA 126
                          L  ++  T     +   +LYED  + V +KPAG+ V    G    
Sbjct: 70  ---------------LPPAIPATPQGQDIALDILYEDRDLIVLDKPAGMVVHPAPGNEDG 114

Query: 127 YHIDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             ++  L    +S       ++P + HRLD++TSGI+V A+T  A Q L+ +F  RRI +
Sbjct: 115 TLVNALLAHCGESLTGIGGEKRPGIVHRLDKDTSGIMVAAKTELAHQALSLAFAERRIDR 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++ WG+P   +      + +      D   +      G   A++H++VI+ F     
Sbjct: 175 AYQAICWGLPVPAQGSFDGAIGRDR---RDRKRMAVIANGGGKQALTHYRVIETFHGGLA 231

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI---------QNKLYLHA 292
            +E +  TGRTHQ+RVH  H G  +VGD  Y                       +  LHA
Sbjct: 232 HVECRLATGRTHQIRVHFAHAGHALVGDPVYLRRIPAAARGLPVAARDAALDFPRQALHA 291

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           R +   HP  G  L      PA      
Sbjct: 292 RRLGFVHPRSGEQLLFETAPPADFTTLL 319


>gi|209542655|ref|YP_002274884.1| RluA family pseudouridine synthase [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209530332|gb|ACI50269.1| pseudouridine synthase, RluA family [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 322

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 79/341 (23%), Positives = 139/341 (40%), Gaps = 37/341 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M+  T    +  E +    R DR+  +    ++   ++ ++  G V  D   ++   + +
Sbjct: 1   MTDDTQPIRLTPETEHAGQRTDRFLADMVGTLSRSRVKALMEGGHVLRDGHVLREPADPV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G    I                +  ++  T  +  +   +LYEDS + V +KPAG+ V
Sbjct: 61  RAGLCYEIR---------------MPPAIPATPRAQAIPFAILYEDSDLIVLDKPAGLVV 105

Query: 120 QGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    DS       ++P + HRLD++TSG++VVA+T  A   L++
Sbjct: 106 HPAPGNEDGTLVNALLAHCGDSLTGIGGERRPGIVHRLDKDTSGVMVVAKTEQAHTALSD 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           +F  R I + Y +L WGI           + +        + VV     G  +A++H++ 
Sbjct: 166 AFAARDIDRTYLALAWGILSPASGTFEGAIGRDRR-DRKRMAVVTH---GGKHAMTHYRT 221

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------ 286
           +  F      +E +  TGRTHQ+RVH    G P+VGD  Y         +  ++      
Sbjct: 222 LHSFHGGISSVECRLATGRTHQIRVHFSTSGHPLVGDPVYLRRIPAAARALPEDARRAAL 281

Query: 287 ---KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              +  LHA  +   HP  G  L      P         + 
Sbjct: 282 DFPRQALHAARLGFTHPRTGESLLFETAPPDDFKTLLAKIA 322


>gi|114561852|ref|YP_749365.1| pseudouridine synthase, RluA family protein [Shewanella
           frigidimarina NCIMB 400]
 gi|114333145|gb|ABI70527.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           frigidimarina NCIMB 400]
          Length = 324

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 76/331 (22%), Positives = 147/331 (44%), Gaps = 35/331 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +  +RLD+     +P  +   +++ + SG + +D   V K   ++   Q+V +   
Sbjct: 11  ITAIQTGLRLDQALAGLFPDYSRTRIKEWILSGAITIDGITVDKPREKVFESQLVEVTAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--H 128
           +                  ++  +  +   ++YED  I V NK AG+ V  G+G A    
Sbjct: 71  LEE---------------EVSAKAQNIDLNIVYEDDHILVINKQAGLVVHPGAGNADGTL 115

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L    D +   +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 MNALLYHCPDIEHVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQARDIVREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        +   + + +        +      G   +++H++V + F +    L ++ 
Sbjct: 176 LGTM-TAGGTVDEPIERHATRRTQMAVI-----HGGRPSVTHYRVSEKF-RAHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            +GRTHQ+RVH  H+G  +VGD  Y    +   ++  +         +  LHA  ++L H
Sbjct: 229 ESGRTHQIRVHMAHIGHELVGDPVYGGRPRPPKSASPEFFELLKNFKRQALHAVRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           P     +   AP+P  MV+   +L    + N
Sbjct: 289 PFTCEIMTWHAPIPDDMVELTKALRVDTELN 319


>gi|225868421|ref|YP_002744369.1| RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
 gi|225701697|emb|CAW99033.1| putative RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
          Length = 296

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 74/315 (23%), Positives = 133/315 (42%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +  P ++       ++  +V V+    K    +Q G  +          
Sbjct: 7   ESGHRLDKALADLTP-LSRSQANDQIKQKRVLVNGSPKKAKYIVQVGDCISYH------- 58

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                   +    +L   +  +   ++Y+D  + + NKP G+ V   +G      ++  L
Sbjct: 59  --------IPEESSLDYQAQDIPLDIVYQDDVLAIINKPQGMVVHPSAGHSTGTLVNALL 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L+VA+T  A Q L +  + ++  + Y ++V G
Sbjct: 111 YHVKDLSSINGVIRPGIVHRIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I   + +            K        A++ FKV++ F + +  +E+Q  T
Sbjct: 171 NLPKDRGVIEAPIGRSDKDRKKQTVTAK-----GKEALTRFKVLERFGR-YSLVELQLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +   N  +LHA+ + L HP  G  L  T
Sbjct: 225 GRTHQIRVHMAYIGHPLAGDPLYGPR-----KTLAGNGQFLHAQTLGLTHPVTGEELVFT 279

Query: 309 APLPAHMVKTWDSLG 323
              P    +T + L 
Sbjct: 280 VEPPEIFQRTLEQLR 294


>gi|254423656|ref|ZP_05037374.1| pseudouridine synthase, RluA family [Synechococcus sp. PCC 7335]
 gi|196191145|gb|EDX86109.1| pseudouridine synthase, RluA family [Synechococcus sp. PCC 7335]
          Length = 309

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 83/326 (25%), Positives = 139/326 (42%), Gaps = 35/326 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            VE      RLDRW  ++    +   +Q+++  G V V+ +   +    + +G  + +  
Sbjct: 6   TVEAG-APERLDRWLADNVEAFSRNRVQQLIEQGAVSVNGEVCDRKKELVTAGDYIILSV 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  +  E   LD               +LYED ++ + NKPAG+ V    G A   
Sbjct: 65  PEAQPYELTPEDIPLD---------------ILYEDDQLLIVNKPAGMVVHPAPGHATG- 108

Query: 130 DGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + + +   G         Q+P + HRLD+ T+G +VVA+T  A  +L +  + +  +
Sbjct: 109 -TLVHALLFYCGEQLTGVGGVQRPGIVHRLDKNTTGAMVVAKTETALCNLQQQIQAKTAK 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y  +V G PK ++  I   + +  H        +   E G   AI+H+K ++     +
Sbjct: 168 REYLGIVNGAPKAEQGTIDQPIGR--HPKHRKKMSILPVESGGRTAITHWKTVERLG-NY 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +  Q  TGRTHQ+RVH+ ++G PI+GD  Y +        P      LHA  + L HP
Sbjct: 225 TLIHFQLETGRTHQIRVHSAYLGLPIIGDPDYGSTRFPGVKLPG---QALHAFRLTLSHP 281

Query: 301 EGG-RLQITAPLPAHMVKTWDSLGFK 325
                +   APLP         L  +
Sbjct: 282 ITQAVVSAEAPLPDQWKILLGQLRSR 307


>gi|113460513|ref|YP_718577.1| 23S rRNA pseudouridine synthase D [Haemophilus somnus 129PT]
 gi|112822556|gb|ABI24645.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           somnus 129PT]
          Length = 321

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 72/328 (21%), Positives = 139/328 (42%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           ++      RLD+     +P  +   L+  +    V+V+ + +     ++  G++V +   
Sbjct: 7   IQPQHMGQRLDQTLAELFPDYSRSRLKTWIEGDLVKVNGEIINVARTKVYGGELVELCVE 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           I   +    E                L   ++YED  I V NKP    V  G+G      
Sbjct: 67  IEEESRFEPEN---------------LPLNIVYEDEHILVINKPKDFVVHPGAGNQRGTV 111

Query: 130 -DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +    +  +  + HRLD++T+G++VVA+T  A   L +  + R+I + Y ++ 
Sbjct: 112 LNALLYHYPKIVEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVQDLQKRKIIREYEAVA 171

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G+   +   +   + +                     A++H+++++ F + +  L ++ 
Sbjct: 172 FGVM-TQGGKVDQPMSRHPT-----KRTQMAVHPLGKPAVTHYRIMERF-RNYTRLRLRL 224

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  LHA  + L H
Sbjct: 225 ETGRTHQIRVHMAHISHPLLGDQTYGGRPRPPKNASEEFMQVMRDFKRQALHAIMLRLTH 284

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V   ++L   Y
Sbjct: 285 PITGEIMEWEAPLPDDFVTLINALKADY 312


>gi|89093551|ref|ZP_01166499.1| pseudouridine synthase [Oceanospirillum sp. MED92]
 gi|89082241|gb|EAR61465.1| pseudouridine synthase [Oceanospirillum sp. MED92]
          Length = 322

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 139/323 (43%), Gaps = 34/323 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +D    RLD+     +P  +   LQ  ++ G + V+ +  K   ++  G+ + I   +
Sbjct: 11  VTDDLVGKRLDQAVAQLFPDYSRSRLQGWIKDGSLTVNGEVKKPREKLLGGEAIAIDANL 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHI 129
             +     +   LD               ++YED  I V NKPAG+ V    G      +
Sbjct: 71  EVIEDHKPQNIPLD---------------IVYEDEHILVINKPAGLVVHPAVGHRDGTLL 115

Query: 130 DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L    D ++  +  + HRLD +T+G++VVA+T AA   L E  + R + + Y ++V 
Sbjct: 116 NALLYHCPDIAQVPRAGIVHRLDMDTTGLMVVAKTIAAQTELVEQLQERSMGREYEAVVN 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+       +   + + S      + VV         A++H++V+    +    + ++  
Sbjct: 176 GVMTG-GGVVDEPMGRHSK-NRQKMAVVGV----GKEAVTHYRVLKKL-RSHTHIRLKLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P+VGD  Y   F+       +         +  LHA+ ++L HP
Sbjct: 229 TGRTHQIRVHMSHINYPLVGDQMYGGRFRLPKGCSDEMMDALRDFKRQALHAKKLELWHP 288

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
             G L      LP  +      L
Sbjct: 289 HSGELVSWEVDLPEDIQNLLAVL 311


>gi|167625160|ref|YP_001675454.1| RluA family pseudouridine synthase [Shewanella halifaxensis
           HAW-EB4]
 gi|167355182|gb|ABZ77795.1| pseudouridine synthase, RluA family [Shewanella halifaxensis
           HAW-EB4]
          Length = 324

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 78/334 (23%), Positives = 144/334 (43%), Gaps = 35/334 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +   RLD+   + +P  +   +++ + +G V +D +   K   ++  GQVV +   
Sbjct: 11  ITATQTGQRLDQTLADLFPDYSRTRIKEWILAGSVFIDGEVSDKPRFKVLEGQVVTVGAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           +                      ++ +   ++YED  I + NK AG+ V  G+G      
Sbjct: 71  LEEETK---------------AQAEAIDLDIIYEDDHILIINKQAGLVVHPGAGNQDGTL 115

Query: 129 IDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L          +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 MNALLHHCPGIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        I   +  +      ++ VV         A++H++V + F +    L ++ 
Sbjct: 176 TGTI-ISGGTIDEPI-DRHPTKRTHMAVVH----NGKPAMTHYRVAEKF-RAHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            +GRTHQ+RVH  H+G  +VGD  Y    +    +            +  LHA  ++L H
Sbjct: 229 ESGRTHQIRVHMAHIGHVLVGDPVYAGRPRPPKGAAPDFFETYMGFRRQALHAVRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           P     +   AP+P  MVK   +L    + N  +
Sbjct: 289 PFTCEIMSWQAPIPDDMVKLTRALRKDTEDNPLV 322


>gi|91794214|ref|YP_563865.1| pseudouridine synthase, RluD [Shewanella denitrificans OS217]
 gi|91716216|gb|ABE56142.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           denitrificans OS217]
          Length = 324

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 76/331 (22%), Positives = 141/331 (42%), Gaps = 35/331 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +  +RLD+     +P  +   +++ + SG V VD  +V K   ++   Q + I   
Sbjct: 11  ITATQTGLRLDQALAELFPDYSRTRIKEWILSGAVYVDGVKVDKPREKVLESQQIEIEAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--H 128
                              +   +  +   ++YED  I + NK AG+ V  G+G A    
Sbjct: 71  FEE---------------EVKAKAQAIDLNIVYEDDHIIIVNKQAGLVVHPGAGNADGTL 115

Query: 129 IDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L      +   +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 MNALLHHCPAIEMVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREIVREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        +   + +               + G   +++H++V + F +    L ++ 
Sbjct: 176 LGTM-TAGGTVDEPIERHPT-----KRTQMSVQHGGRPSVTHYRVSEKF-RAHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            +GRTHQ+RVH  ++G  +VGD  Y    K    +  +         +  LHA  ++L H
Sbjct: 229 ESGRTHQIRVHMDYIGHVLVGDPVYGGRPKPPKNASPEFFDILKNFGRQALHAVRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           P     +   AP+P  MV    +L    + N
Sbjct: 289 PYTHEIMSWQAPIPEDMVMLTKALRKDTEEN 319


>gi|315634974|ref|ZP_07890255.1| ribosomal large subunit pseudouridine synthase D [Aggregatibacter
           segnis ATCC 33393]
 gi|315476236|gb|EFU66987.1| ribosomal large subunit pseudouridine synthase D [Aggregatibacter
           segnis ATCC 33393]
          Length = 324

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 73/329 (22%), Positives = 135/329 (41%), Gaps = 35/329 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
            V+  +   RLD+     +P  +   L+  +    V V+         ++   + + I  
Sbjct: 9   TVQPQQMGQRLDQTLAELFPDYSRSRLKTWIEEDLVLVNGVVQNVPRTKVYGDEHIEITV 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
            I        E                +   ++YED  I V NKP  + V  G+G     
Sbjct: 69  EIEDETRFEPE---------------AIPLNIVYEDEDILVINKPKDLVVHPGAGNPKGT 113

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++
Sbjct: 114 VLNALLYHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAV 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI   K   +   + +                     A++H+++++ F + +  L ++
Sbjct: 174 ACGIM-TKGGTVDEPMARHPT-----KRTHMAVHPMGKPAVTHYRIMERF-RDYTRLRLR 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  LHA  + L 
Sbjct: 227 LETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEELMEVLRNFKRQALHAVMLRLQ 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HP  G  ++  APLP   V+   +L   Y
Sbjct: 287 HPISGEMMEWYAPLPDDFVELVTALKADY 315


>gi|254230257|ref|ZP_04923648.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. Ex25]
 gi|262395163|ref|YP_003287017.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. Ex25]
 gi|269966583|ref|ZP_06180664.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio alginolyticus
           40B]
 gi|151937237|gb|EDN56104.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. Ex25]
 gi|262338757|gb|ACY52552.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. Ex25]
 gi|269828768|gb|EEZ83021.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio alginolyticus
           40B]
          Length = 325

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 71/331 (21%), Positives = 142/331 (42%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V+V+ + V K   ++  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVQVNGEVVTKPRTKVMGGEEITLQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   +++ED  I V NKP    V  G+G     
Sbjct: 70  ELEDEERW---------------EAQDIPLDIVFEDDDIIVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + D ++  +  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLHHYPDIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S         +         A++H++V + F ++   + ++
Sbjct: 175 AIGRM-TAGGKVDQPIGRHST-----KRTLMAVAPMGKPAVTHYRVAERF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDIAYGGRARIPTGASEELTAMIRGFDRQALHAVMLRFE 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  L+  AP+P  MV   ++L    + 
Sbjct: 288 HPITGEVLEFHAPVPDDMVAMTEALRQDTEE 318


>gi|285017490|ref|YP_003375201.1| pseudouridine synthase [Xanthomonas albilineans GPE PC73]
 gi|283472708|emb|CBA15213.1| probable pseudouridine synthase protein [Xanthomonas albilineans]
          Length = 335

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 141/327 (43%), Gaps = 34/327 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +     R D      +P  +   L + ++SG   +D    +  + ++ G++  +  V+
Sbjct: 22  VPDHAAGRRFDAVLAELFPEYSRSRLAEWIKSGDALLDGAPARPRDPLRGGEIASLHAVL 81

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
           +   H + E   L+               +LYED ++ V NKPAG+ V  G+G      +
Sbjct: 82  DTQTHALPEDIALE---------------VLYEDDQVIVLNKPAGLVVHPGAGNPGGTLV 126

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L          +  + HRLD++TSG +VVART  A   L      R++ + Y +LV 
Sbjct: 127 NALLYRDPGLSALPRAGIVHRLDKDTSGAMVVARTLQAHTALVAQLAARQVHRQYLALVV 186

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G         AN  + +       + V     +    A++H+++ + F +    LE +  
Sbjct: 187 GAL--VSGGTANAPIDRHPRDRLRMAVR----EDGRDALTHYRLRERF-RAHTALECRLE 239

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQ------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  PI+GD  Y            P+        +  LHA  ++  HP
Sbjct: 240 TGRTHQIRVHMAHLKHPIIGDPLYGGPLKLPKGAADPLIAELRGFKRQALHAEILEFKHP 299

Query: 301 -EGGRLQITAPLPAHMVKTWDSLGFKY 326
             G  +++TA +PA + +   +L    
Sbjct: 300 LHGEPVRVTAAVPADLQRLLAALRADA 326


>gi|322418237|ref|YP_004197460.1| RluA family pseudouridine synthase [Geobacter sp. M18]
 gi|320124624|gb|ADW12184.1| pseudouridine synthase, RluA family [Geobacter sp. M18]
          Length = 319

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 90/339 (26%), Positives = 150/339 (44%), Gaps = 40/339 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++ +    D +  RLD +     P +      +++ +G   V+ ++ K   R++ G+
Sbjct: 1   MEPIE-LTFPCDADPERLDSFISRSVPELTRSAALRLIETGFATVNGQKQKPALRLKGGE 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VV +               I+          + +   +LYED+ + V NK AG+ V  G+
Sbjct: 60  VVTV---------------IVPPPTPAEPQPEEIPLEILYEDADVVVVNKGAGMVVHPGA 104

Query: 124 GIAY--HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G A    ++  L    D  G     +P + HR+D++TSG LV+A++  A   L E F++ 
Sbjct: 105 GNAEGTLVNALLAHCKDLSGIGGELRPGIVHRIDKDTSGTLVIAKSDRAHNGLAEQFKVH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDC 235
            I++IY +LV+G PK ++  I       S IG   V   K + K      AI+H++V + 
Sbjct: 165 SIKRIYLALVYGSPKEERGHIE------SVIGRHPVERKKMSGKARHGKNAITHWRV-EA 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQN-------K 287
                  + ++  TGRTHQ+RVH    G P++ D  Y    +      P+         +
Sbjct: 218 RYPGITLVRLKLETGRTHQIRVHLSEAGHPLLADEVYGGGSRLAQLKDPVLKQMIKAMGR 277

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
             LHA+ +   HP  G  L+  A LP  M      L  K
Sbjct: 278 QALHAKTLGFLHPVTGEYLEFDAELPPDMAGIIAYLEEK 316


>gi|15893233|ref|NP_360947.1| pseudouridylate synthase [Rickettsia conorii str. Malish 7]
 gi|15620450|gb|AAL03848.1| sfhB protein homolog [Rickettsia conorii str. Malish 7]
          Length = 313

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 144/327 (44%), Gaps = 40/327 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V ++   +RLD+   +   + +   +QK ++  QV V+   +   +  ++   ++     
Sbjct: 6   VPHELNGIRLDKALSSLLENASRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFK 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 I      LD               ++YED  + V NK AG++V  G+G  +H D
Sbjct: 66  EPEELKIAAANVALD---------------IIYEDDDLIVINKAAGMTVHPGAG--HHDD 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD++T+G++VVA+   A   L      R++ + 
Sbjct: 109 TLVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FC 241
           Y  LVWG+    +  I N + + S      + ++K    G   A++H+K+++ F +    
Sbjct: 169 YKVLVWGVINPLEGVIKNNIGR-SRSDRQKMTILKY---GGKEAVTHYKILELFYKGSIS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP +         +  LH+ 
Sbjct: 225 MVECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAHSPPELKAKLIDFKRQALHSW 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTW 319
           Y+   HP     ++ +  LP  M +  
Sbjct: 285 YLSFTHPTSNEIMEFSCELPRDMEEII 311


>gi|325108531|ref|YP_004269599.1| pseudouridine synthase [Planctomyces brasiliensis DSM 5305]
 gi|324968799|gb|ADY59577.1| pseudouridine synthase, RluA family [Planctomyces brasiliensis DSM
           5305]
          Length = 336

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 84/338 (24%), Positives = 161/338 (47%), Gaps = 38/338 (11%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T V++ V+  +E ++RLD W  +H    +    QK +++G++RV+ ++VK + R++ G+ 
Sbjct: 12  TQVEHEVL-AEEVDLRLDAWLSSHSAGHSRSQWQKAIQAGEIRVNGQKVKPSYRLRIGEK 70

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS- 123
           +                  L            +   +LY+D  + V NKPA + V  G  
Sbjct: 71  IS---------------GQLKVVAAPVVAPAPIALDILYQDEHLVVVNKPAHLIVHPGKA 115

Query: 124 ----GIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                +A  +        ++ G+  P + HRLD++TSG++V+A      ++L+  F  R 
Sbjct: 116 NYGGTLANALVHHFNQLSETGGEHRPGIVHRLDRDTSGVIVIALNNRVHENLSAQFADRT 175

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y ++VWG  +   + I   +  ++H       +V   +  A  A + ++ ++ F +
Sbjct: 176 VEKEYRAIVWGKVEFDADIIETHV--RTHSKHREKMIVCGPDPEARQATTFYETLERF-R 232

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------------ 286
            F +L++ P TGRTHQLRVH  ++  PIV D  Y  + +   +  +++            
Sbjct: 233 GFSYLKLLPKTGRTHQLRVHLQYLRHPIVADRLYGGHPQLALSELLESKEHMTEDRVLIE 292

Query: 287 KLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +  LHA  +   HP    R++  +P+P  M +T D++ 
Sbjct: 293 RQALHAHRLQFTHPVTEERVEFISPIPDDMQRTLDAMR 330


>gi|72161527|ref|YP_289184.1| ribosomal large subunit pseudouridine synthase D [Thermobifida
           fusca YX]
 gi|71915259|gb|AAZ55161.1| ribosomal large subunit pseudouridine synthase D [Thermobifida
           fusca YX]
          Length = 309

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 81/329 (24%), Positives = 143/329 (43%), Gaps = 28/329 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + + V +  E  RLD      +  ++     +++  G V VD      ++R+ +G 
Sbjct: 1   MSDHRSMPVPDGLEGDRLDTAIARLF-GLSRTRAAELIAEGNVLVDGAPAAKSDRVNAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-- 121
            + I                        +        ++YED+ I V +KPAG+      
Sbjct: 60  WLDITLPPPPNPPA-------------PRPEPVPGMRIVYEDADIVVVDKPAGVVAHPTI 106

Query: 122 GSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      +DG L + V        ++  + HRLD  T+G++VVA++  A   L  +F+ R
Sbjct: 107 GWSGPTVVDGLLAAGVAVATSGAAERQGIVHRLDANTTGLMVVAKSEIAYSSLKRAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K+Y +LV G P   +  I   +    H  GD    V     G   +++H+  ++ F 
Sbjct: 167 TVEKVYHALVQGHPDPLRGTIDAPI--DRHPSGDGRFAVV---AGGRPSVTHYTTLEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    LE+   TGRTHQ+RVH   +  P VGD  Y A+        + ++ +LHA  +  
Sbjct: 221 RAASLLEIDLETGRTHQIRVHMSAIRHPCVGDTLYGADPTLAERLGV-HRQWLHAIRLAF 279

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
            HP    R++ T+  P  + K+ + L  +
Sbjct: 280 THPTQYRRVEFTSSYPEDLAKSLEILRAE 308


>gi|320449663|ref|YP_004201759.1| ribosomal large subunit pseudouridine synthase D [Thermus
           scotoductus SA-01]
 gi|320149832|gb|ADW21210.1| ribosomal large subunit pseudouridine synthase D [Thermus
           scotoductus SA-01]
          Length = 308

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 154/328 (46%), Gaps = 41/328 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
           E +RLD+        ++    Q+ +  G+V+V +K V K + R++  +V+ +PP      
Sbjct: 10  EGVRLDQAVAEAC-GVSRSRAQEWIAQGRVQVGEKVVEKPSYRLKGEEVLVVPPEEKPFV 68

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL 133
                                L   +LYED  + V NKPAG+      G+     ++  L
Sbjct: 69  A-----------------PQDLAIPVLYEDEDLLVLNKPAGLLTHPAPGVYTGTVVNALL 111

Query: 134 KSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             +         +  +P + HRLD++TSG+LVVA+   A + L  +FR R + K Y ++ 
Sbjct: 112 GRYFPLQEAERPEEVRPGIVHRLDKDTSGVLVVAKHGGALEALARAFRDRLVMKRYLAIT 171

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G PK  +  +   + +   +    +HV         YA + F+++      +  +E +P
Sbjct: 172 EGHPK--EGTLIAPIGRH-PVERHKMHV---GGIAPRYAETEFRILATAG-PYALVEARP 224

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
           HTGRTHQ+RVH  ++  PI+GD  Y         SP   +  LHA  + +PHP  GR L+
Sbjct: 225 HTGRTHQIRVHLKYLRAPILGDELYGR------PSPHIPRQALHAYELRIPHPRTGRFLE 278

Query: 307 ITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
             AP+P  MVK W +LG ++   + ++ 
Sbjct: 279 FRAPVPRDMVKAWGALGGEWPEGIILED 306


>gi|152997613|ref|YP_001342448.1| RluA family pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150838537|gb|ABR72513.1| pseudouridine synthase, RluA family [Marinomonas sp. MWYL1]
          Length = 327

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 144/328 (43%), Gaps = 33/328 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V  D    R D+     +   +   +Q  ++ G ++VD K  K   ++  G+VV 
Sbjct: 6   VKEAQVPFDLGGNRFDQIATELFSDYSRSRIQSWIKEGVLKVDGKITKPKEKLFGGEVVT 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSG 124
           +  VI A                    +  +   ++YED  I + NKPAG+ V    G+ 
Sbjct: 66  LDIVIEAQEE---------------HEAQAMDLDVVYEDDDIMIINKPAGLVVHPAVGNR 110

Query: 125 IAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               ++  L    ++    +  + HRLD+ET+G++VVA+T AA   L    + R + + Y
Sbjct: 111 DGTLMNAILHHAPETAHIPRAGIVHRLDKETTGLMVVAKTLAAQTDLVMQLQERSMGREY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++  G+       + +  + +         V   N K    A++H+++++ F +    +
Sbjct: 171 EAVSIGVMT--GGGVVDEPIGRHPHNRQKQAVEPVNGKD---AVTHYRLVERF-KNHTHI 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYM 295
            ++  TGRTHQ+RVH   +  P+VGD +Y    K       +         +  LHA+ +
Sbjct: 225 RLKLETGRTHQIRVHMAFIQYPLVGDPQYGGRLKMPKACSPELQDELRHFRRQALHAKKL 284

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +L HP  G  ++    LP  M K  D+L
Sbjct: 285 ELSHPITGEWMEWEIDLPDDMKKLLDAL 312


>gi|78485714|ref|YP_391639.1| pseudouridine synthase, RluD [Thiomicrospira crunogena XCL-2]
 gi|78364000|gb|ABB41965.1| ribosomal large subunit pseudouridine synthase D [Thiomicrospira
           crunogena XCL-2]
          Length = 352

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 82/348 (23%), Positives = 155/348 (44%), Gaps = 36/348 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPPV 70
           +  D+   RLD      +   +   +Q  +R+G V +D  +  K N ++   + V +   
Sbjct: 10  IPTDKMGHRLDAVLAELFSDYSRNRIQDWIRAGLVTLDGVEHKKPNFKVFGDESVVL--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                       + +    ++  +  +   ++YED  I V NKPAG+ V  G+G      
Sbjct: 67  ------------LAEIEDEVSYQAQDIPIEVVYEDEDILVLNKPAGLVVHPGAGNPDGTL 114

Query: 129 IDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L  +    +  +  + HRLD+ETSG++VVA+   A  HL E  +   ++++Y ++V
Sbjct: 115 LNALLFHYETIREVPRAGIVHRLDKETSGLMVVAKNVPAQTHLVEQLQQHDVERVYDAIV 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        I+  + +        + V+     G   A SH++V++ F ++   + ++ 
Sbjct: 175 VGKM-ISGGTISKPIGRH-PTDRKRMAVLTV---GGKPATSHYRVLERF-REHTHVRVKL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQ--NKLYLHARYMDLPH 299
            TGRTHQ+RVH  ++G P+VGD  Y    +        F   ++   +  LHA  + L H
Sbjct: 229 ETGRTHQIRVHMAYLGFPLVGDPVYAGRLRIPQQMMPEFADYLRGFKRQALHAGQLSLTH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYD--RNLYIKRLYSQDECKQN 344
           P  G+ ++    +P  M++  D L    +  + +      S DE   +
Sbjct: 289 PRTGKTMKWKVSMPDDMLELIDILRDDMEDFQAMKYGDRMSYDEYDYD 336


>gi|270159531|ref|ZP_06188187.1| ribosomal large subunit pseudouridine synthase D [Legionella
           longbeachae D-4968]
 gi|289165671|ref|YP_003455809.1| Ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Legionella longbeachae
           NSW150]
 gi|269987870|gb|EEZ94125.1| ribosomal large subunit pseudouridine synthase D [Legionella
           longbeachae D-4968]
 gi|288858844|emb|CBJ12758.1| Ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Legionella longbeachae
           NSW150]
          Length = 321

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 72/332 (21%), Positives = 138/332 (41%), Gaps = 30/332 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + +  +  N R+D    +     +   +   ++ G + ++ +  K  ++++ G ++ I
Sbjct: 7   KQLTIPREYHNQRIDTALAHLLSDYSRSQISNWIKCGSIMLNHQSCKPKDKVEDGDLIDI 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
               N  +  ++               + +   ++YED  + V NKPA + V  G+G   
Sbjct: 67  NVNFNKTDTNLE-----------HCIPEEIPLNIIYEDDDVLVLNKPANMVVHPGAGNKE 115

Query: 128 HI--DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           H   +  L          +  + HRLD++T+G+L++A+T  A   L    + R I++ Y 
Sbjct: 116 HTLVNALLHHSPSLIHLPRAGIVHRLDKDTTGLLIIAKTLPAHTSLIRQMQAREIKRHYI 175

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G        I     +          +    ++    AI+H+ V       F  L+
Sbjct: 176 TLVQGHI-ISGGTIDTGFGRHPRN-----RLKMAVQEHGRQAITHYAV-KKQYHDFTLLD 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           +   TGRTHQ+RVH  ++  P+VGD  Y    +    +P           +  LHAR + 
Sbjct: 229 VNLMTGRTHQIRVHLAYIHHPVVGDPLYGTRMRFPSQAPEHLRTLFQNFKRQALHARTLS 288

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
             HP+    L + AP+P       ++L   Y+
Sbjct: 289 FYHPKTEKELTLMAPIPDDFKLLLNTLDEHYE 320


>gi|261212185|ref|ZP_05926471.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. RC341]
 gi|262401594|ref|ZP_06078160.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. RC586]
 gi|260838793|gb|EEX65444.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. RC341]
 gi|262352011|gb|EEZ01141.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp. RC586]
          Length = 324

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 145/332 (43%), Gaps = 35/332 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +   RLD+     +   +   L++ L  G++ V+ + + K   ++  G+V+ +  
Sbjct: 10  TVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVITKPRMKVMGGEVIVVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  L   ++YED  I V NKP    V  G+G A   
Sbjct: 70  ELEDEQRW---------------EAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADST 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A  HL  + + R + + Y ++
Sbjct: 115 VLNALLFHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVRALQKRDVTREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + + S         +        +A++H++V + F ++   L ++
Sbjct: 175 VIGTM-TAGGMIDKPIGRHST-----KRTLMSVSPMGKHAVTHYRVAEHF-REHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGASEELTEMIRGFDRQALHAVMLKFE 287

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           HP  G  L+  AP+P  MV+   +L     +N
Sbjct: 288 HPITGEELEFHAPVPDDMVEMTLALREDAKQN 319


>gi|262163884|ref|ZP_06031623.1| ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           VM223]
 gi|262027412|gb|EEY46078.1| ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           VM223]
          Length = 324

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 77/333 (23%), Positives = 144/333 (43%), Gaps = 37/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +   RLD+     +   +   L++ L  G++ V+ + V K   ++  G+V+ +  
Sbjct: 10  TVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVVTKPRTKVMGGEVIVVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  L   ++YED  I V NKP    V  G+G A   
Sbjct: 70  ELEDEQRW---------------EAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  + + R + + Y ++
Sbjct: 115 VLNALLFHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + + S         +        +A++H++V + F ++   L ++
Sbjct: 175 VIGTM-TAGGMIDKPIGRHST-----KRTLMSVSPMGKHAVTHYRVAEHF-REHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGASEELTAMIRNFDRQALHAVMLKFE 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNL 330
           HP  G  L+  AP+P  MV    +L  + D  L
Sbjct: 288 HPITGEELEFHAPVPDDMVTM--TLALREDSKL 318


>gi|103487227|ref|YP_616788.1| pseudouridine synthase, RluD [Sphingopyxis alaskensis RB2256]
 gi|98977304|gb|ABF53455.1| ribosomal large subunit pseudouridine synthase D [Sphingopyxis
           alaskensis RB2256]
          Length = 376

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 147/334 (44%), Gaps = 28/334 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     +  V + +    +RLDR      P+++   L+ +++ G+V VD           
Sbjct: 59  MLGDDEILTVTLGDTAAGLRLDRALAEALPNLSRERLKSLIKGGRV-VD----------A 107

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G ++  P    A    I  +  + +++     +  L  ++ YED+ + V +KPAG+ V 
Sbjct: 108 HGAILWDPAAKAAPPATI--EIRVPAALPAHNAAQDLDLVIAYEDAHLIVIDKPAGMVVH 165

Query: 121 GGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
             +G      ++  L              +P + HR+D++TSG++V A+   A + L + 
Sbjct: 166 PAAGNLDGTMVNALLHHCAGQLSGIGGVARPGIVHRIDKDTSGLIVAAKHDKAHEGLAKQ 225

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F    I + Y ++  G P      +   L + S      + VV        +A++H++ +
Sbjct: 226 FAAHSIDRRYLAIATGRPMPANGTVDAALGR-SATNRKKMAVVAAGR--GKHALTHYRTV 282

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKLYL 290
           +   Q    +E +  TGRTHQ+RVH  H+G P+VGD  Y    K       +    +  L
Sbjct: 283 EPL-QGATLIECRLETGRTHQVRVHMAHIGHPLVGDPVYGRARKPLSDVLKARNFARQAL 341

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           HA ++   HP  G R+ + + LPA M +  D L 
Sbjct: 342 HAAHLGFIHPVTGNRIALDSELPADMRELIDELR 375


>gi|304320252|ref|YP_003853895.1| putative ribosomal large subunit pseudouridine synthase protein
           [Parvularcula bermudensis HTCC2503]
 gi|303299154|gb|ADM08753.1| putative ribosomal large subunit pseudouridine synthase protein
           [Parvularcula bermudensis HTCC2503]
          Length = 338

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 79/351 (22%), Positives = 139/351 (39%), Gaps = 48/351 (13%)

Query: 4   MTYVQYV--VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQ 60
           M+  + +   V   +   RLD+W  +     +   ++ ++  G +  D         +++
Sbjct: 1   MSDTEPLSFTVAEADVGARLDKWIADQTDAYSRARIKALIEGGALTKDAAPFTDPKWKLR 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+V  +               +     + T   + +   +L+ED  + V NKPAG+ V 
Sbjct: 61  QGEVFTL---------------VPPPPEDPTPKPEDIPLTVLFEDGDLIVINKPAGLVVH 105

Query: 121 GGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
             +G      ++  L    D+        +P + HRLD++TSG++V+A+   A Q L+  
Sbjct: 106 PAAGNWTGTLVNALLHHCGDTLSGIGGVIRPGIVHRLDKDTSGVMVIAKNDHAHQGLSAL 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F    I + Y +L  G P+     I  W L +S      + VV  +      AI+HF  +
Sbjct: 166 FAAHDIDRAYLALCEGSPRPTSGTIT-WPLARSSGDRKKMTVVGVDRPEGKEAITHFARL 224

Query: 234 DCFAQK---------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---------AN 275
           D +               +E +  TGRTHQ+RVH  H+G P++GD  Y           +
Sbjct: 225 DAYGIGRAKLPGDALASLVECRLETGRTHQIRVHMSHIGHPLLGDPVYGRSGLAGLKPGD 284

Query: 276 FKGNFTSPIQ---NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              +    +     +  LHA  +   HP  G  L    P P       ++ 
Sbjct: 285 PAADHALGLLRRFRRQALHAVELGFDHPVTGEALHFRQPPPHDFSTLVEAF 335


>gi|269468168|gb|EEZ79867.1| pseudouridylate synthase, 23S RNA-specific [uncultured SUP05
           cluster bacterium]
          Length = 303

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 93/321 (28%), Positives = 151/321 (47%), Gaps = 25/321 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+   E  RLD +   H   +   ++ +++R G+VRV+K R K   ++Q   VVR
Sbjct: 3   VSFKTVDEFSEGQRLDNYLLKHLKGVPKSHIYRVIRKGEVRVNKGRKKAEYKLQLDDVVR 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+  + +  +         V        L   +LYED  + + NKP+G++V  GSG+A
Sbjct: 63  IPPIRVSESIQV---------VVSDSLKQLLSDAILYEDKGLLIINKPSGLAVHSGSGVA 113

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
               G +++      +   L HRLD+ TSG+L++A+ R+  ++L E     +++K Y +L
Sbjct: 114 ---VGVIEALRGMYKEPVELVHRLDRSTSGVLLIAKKRSVLKNLHEQLSQHQMEKRYTAL 170

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWL 243
           V G    K+  I   L + S         V  + KG   A+SHF+ +  F         +
Sbjct: 171 VKGTWSKKRHTIDAPLYQNS-------RGVVIDAKG-KQAVSHFQPLKNFHNDEFEASLV 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEG 302
           E+   TGR HQ+R HA + G  I  D KY    F     +    +L+LHA  +   +P  
Sbjct: 223 EVLIETGRMHQIRAHAKYAGHSIAFDDKYGDKIFDTQVKAKGLKRLFLHAHQLTFANPLT 282

Query: 303 GRLQ-ITAPLPAHMVKTWDSL 322
             +Q + APL   +      L
Sbjct: 283 SEIQKVKAPLSKDLEDFLAKL 303


>gi|110679108|ref|YP_682115.1| ribosomal large subunit pseudouridine synthase D [Roseobacter
           denitrificans OCh 114]
 gi|109455224|gb|ABG31429.1| ribosomal large subunit pseudouridine synthase D [Roseobacter
           denitrificans OCh 114]
          Length = 342

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 90/355 (25%), Positives = 146/355 (41%), Gaps = 50/355 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKR-VKFNNRI 59
           M+  Q   V ++    RLD+      P    ++   L +++  G V VD         R+
Sbjct: 1   MSVRQIQFVIDEAPPPRLDKALARDVPVEAALSRTRLARLIDEGGVLVDGVVQSNAKARV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            +G  + I       +HI+ E   LD               +++EDS + V NKPAG+ V
Sbjct: 61  AAGAQITIQVQQAQDSHILPEDIALD---------------VIHEDSDLIVVNKPAGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L             ++P + HR+D++TSG+LVVA++ AA   L  
Sbjct: 106 HPAPGTPSGTLVNALLSHCGADLSGVGGLKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F+   +++ Y  LV+G P      +           N L   + +        +Q    
Sbjct: 166 QFQAHTVERYYNCLVYGAPDANDPRLRGVKGARFEAGNILKLTTQLARHKTDRQRQAVLF 225

Query: 221 KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +G  +A++  + ++ F        +E    TGRTHQ+RVH  H G  +VGD  Y    K 
Sbjct: 226 QGGRHAVTRARSLERFGTPPVLTLMECWLETGRTHQIRVHMAHAGHALVGDPTYGGKRKL 285

Query: 279 NFTSPIQ---------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              S  +         N+  LHA  +   HP  G  L+  APLP  M +  ++L 
Sbjct: 286 PAKSLPETALEAVKCFNRQALHAAVLGFEHPVTGEHLRFEAPLPQDMAQLLNTLR 340


>gi|330814384|ref|YP_004358623.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Pelagibacter sp. IMCC9063]
 gi|327487479|gb|AEA81884.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Pelagibacter sp. IMCC9063]
          Length = 327

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 86/345 (24%), Positives = 147/345 (42%), Gaps = 44/345 (12%)

Query: 4   MTYVQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQS 61
           MT  +Y   V  ++   R+D++     P  +   + K+++ G + ++ + ++  + ++  
Sbjct: 1   MTDKKYKFTVSEEQNLKRVDQFIVEELPTFSRTKISKLIKEGALLINNEPIEERSKKVSF 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  V +                +   V        +   ++YED  + V NKP G+ V  
Sbjct: 61  GDEVELS---------------VPEPVPTDLKPQNIPLDVVYEDDDLLVINKPIGMVVHP 105

Query: 122 GSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G+G      ++  L    ++        +P + HR+D++TSG+LVVA+   A   L + F
Sbjct: 106 GAGNPDGTLVNALLHHCKENLSGINGELRPGIVHRIDKDTSGLLVVAKNDIAHNVLAKQF 165

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               IQ+ Y + VWG+PK     I   L+ +S      +     + K    AI+++K ++
Sbjct: 166 EDHSIQRTYLAFVWGMPKPIHGRIET-LIGRSKYNRQKMSAEVGSGKD---AITNYKTLE 221

Query: 235 CFAQKF----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ----- 285
            F  K       +E +  TGRTHQ+RVH  H G PI+GD  Y    +       Q     
Sbjct: 222 VFKGKTIPDISLIECRLETGRTHQIRVHLAHQGNPILGDQMYGKKVRKIRDLDEQLSILL 281

Query: 286 ---NKLYLHARYMDLPHPEG-GRLQITAPLPAH---MVKTWDSLG 323
              N   LHA+ +   HP+    L  T  LP     + K    LG
Sbjct: 282 ENINFQALHAQSLGFLHPKSDKELFFTTELPKDLLNLQKMLKKLG 326


>gi|296117562|ref|ZP_06836146.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           ammoniagenes DSM 20306]
 gi|295969293|gb|EFG82534.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           ammoniagenes DSM 20306]
          Length = 308

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 137/325 (42%), Gaps = 28/325 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V+ + V    + +R+D         ++     ++   G V V+   V  ++R+ +GQ V
Sbjct: 4   EVRTLPVPEGNDGLRIDAALAKML-GLSRTVAAELCAEGAVLVNGTTVSKSDRLTAGQWV 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +     A   + KE+ +                 ++Y D  I   NKP G++     G 
Sbjct: 63  EVTLPEPAAPLVPKEELVE-------------GMDVVYSDDDIIAVNKPVGVAAHPSVGW 109

Query: 125 IAYHIDGFLKSWV-----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R +
Sbjct: 110 DGPTVIGGLAAAGFRISNSGPPERKGIVHRLDVGTSGVMVVASSERAYTALKNAFKERTV 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G+P      I   + +    G  +        +   +AI+H+ +I+ F ++
Sbjct: 170 HKTYHALVQGLPDPIVGTIDAPIGRHPSSGWKFAV-----TEDGKHAITHYSLIEAF-RE 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L++   TGRTHQ+RVH    G P  GD  Y ++   +    +  + +LHA  +   H
Sbjct: 224 ASLLDVHLETGRTHQIRVHMSATGHPCCGDPMYGSDPNLSKRLGLI-RQWLHAVKLGFEH 282

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  GR ++I    P  +    D L 
Sbjct: 283 PGTGRWIEIETSYPDDLQHALDVLR 307


>gi|258624747|ref|ZP_05719681.1| Ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           VM603]
 gi|258583034|gb|EEW07849.1| Ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           VM603]
          Length = 324

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 77/333 (23%), Positives = 144/333 (43%), Gaps = 37/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +   RLD+     +   +   L++ L  G++ V+ + V K   ++  G+V+ +  
Sbjct: 10  TVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVVTKPRTKVMGGEVIVVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  L   ++YED  I V NKP    V  G+G A   
Sbjct: 70  ELEDEQRW---------------EAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  + + R + + Y ++
Sbjct: 115 VLNALLFHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + + S         +        +A++H++V + F ++   L ++
Sbjct: 175 VIGTM-TAGGMIDKPIGRHST-----KRTLMSVSPMGKHAVTHYRVAEHF-REHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGASEELTAMIRNFDRQALHAVMLKFK 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNL 330
           HP  G  L+  AP+P  MV    +L  + D  L
Sbjct: 288 HPITGEELEFHAPVPDDMVTM--TLALREDSKL 318


>gi|71065814|ref|YP_264541.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter
           arcticus 273-4]
 gi|71038799|gb|AAZ19107.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter
           arcticus 273-4]
          Length = 400

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 74/333 (22%), Positives = 138/333 (41%), Gaps = 34/333 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V  +E  +R+D+     +   + V LQ  +  G +  +    K   R+++G V+ +  +
Sbjct: 88  TVTEEEAGLRIDKLASKIFIDFSRVQLQGWVSDGSLLYNGSVQKPKIRVKAGDVLHLSTI 147

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
           +   +    E   +D               ++YED ++ V NKP G+ V  G+G      
Sbjct: 148 LEQHSADQPEDIAID---------------VVYEDDEVLVINKPVGMVVHPGAGNQAGTL 192

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L  +       +  L HR+D++TSG+L++ +T+ A   L E  + + + + Y  +V
Sbjct: 193 VNALLYHYPQHHHLPRAGLVHRIDKDTSGLLLIGKTKPAQLALMEQLKDKSVYRHYQCVV 252

Query: 188 WGIPKN--KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            G   +  +   I   + +  +       +          A++H   +      +C L++
Sbjct: 253 AGDAASLLRHRRIDAPIGRHRNQRTKMTVMT-----AGREAVTHLLNVTALNGNYCLLDV 307

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL--------HARYMDL 297
              TGRTHQ+RVH  H+  PIVGD  Y    +         +  +        HA  +  
Sbjct: 308 GLETGRTHQIRVHLSHITYPIVGDRVYGGRRQLRAGLTEAQRQAINNFPRQALHAYILGF 367

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
            HP  G  +++T P+P  M +    L   YD  
Sbjct: 368 VHPTTGEDIEVTTPMPEDMQQLMAVLSDGYDAE 400


>gi|28199848|ref|NP_780162.1| pseudouridylate synthase [Xylella fastidiosa Temecula1]
 gi|182682599|ref|YP_001830759.1| RluA family pseudouridine synthase [Xylella fastidiosa M23]
 gi|28057969|gb|AAO29811.1| pseudouridylate synthase [Xylella fastidiosa Temecula1]
 gi|182632709|gb|ACB93485.1| pseudouridine synthase, RluA family [Xylella fastidiosa M23]
 gi|307578881|gb|ADN62850.1| pseudouridylate synthase [Xylella fastidiosa subsp. fastidiosa
           GB514]
          Length = 330

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 96/327 (29%), Positives = 158/327 (48%), Gaps = 25/327 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ VVV  +    RLD +  +    +    + K++RSGQVRV+  RVK   ++  G  VR
Sbjct: 18  VRIVVVPAEHSGQRLDNFLLSKLKGVPRSLIYKLVRSGQVRVNGGRVKAERKLDGGDEVR 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      +I+++ I+  S         +++ +++ED+++   NKP+G++  GGSGI+
Sbjct: 78  LPPL-----RLIQDRAIVAPSAAFLAR---MEAAIVFEDARLLALNKPSGMASHGGSGIS 129

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--------RR 178
           Y +   ++       Q+  L HRLD++TSG+L++A+ RA    L    R         R 
Sbjct: 130 YGVIEAMRILRPK--QELELVHRLDRDTSGLLIMAKKRAVLIELQALMREASVNGKEGRG 187

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y +L+ G   N    +   L      GG+    V  + K +    S F++++    
Sbjct: 188 IAKRYLTLLSGRMPNGVMSVDAPLHINLRHGGERHVRVHHDGKPSK---SRFRLLERRG- 243

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMD 296
              + E+   TGRTHQ+RVHA H+G P+ GD KY                +L+LHA  ++
Sbjct: 244 GQSYCEVLIETGRTHQIRVHAQHLGHPVTGDDKYGDQEVNRKLRDQIGLQRLFLHAVSLE 303

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
                G     + APL   +V   D L
Sbjct: 304 FALDAGSTPYVLNAPLAEDLVAALDRL 330


>gi|56460291|ref|YP_155572.1| 23S rRNA pseudouridine synthase D [Idiomarina loihiensis L2TR]
 gi|56179301|gb|AAV82023.1| Pseudouridylate synthase [Idiomarina loihiensis L2TR]
          Length = 322

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 142/331 (42%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           +V       RLD+     +P  +   L+  +  G+V +D K + K   ++ +G +V +  
Sbjct: 10  IVTESLAGKRLDQALAELFPDYSRSRLKSWITDGKVTIDTKVIEKPREKVVAGALVAVDA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I        +   LD               ++YED  I V NKPAG+ V  G+G     
Sbjct: 70  EIEGEERHAAQPVELD---------------IVYEDDDILVINKPAGLVVHPGAGAPDRT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +G L          +  + HRLD++T+G++VVAR   A   L    + R I + Y ++
Sbjct: 115 LLNGLLHYDPQLDLVPRAGIIHRLDKDTTGLMVVARNVPAQTQLVSMMQDRDITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G+       + +  + +      ++ VV    +    A++H++V+D + +    L ++
Sbjct: 175 CNGVMTA--GGMVDQPIGRHPTKRTHMAVV----QSGKPAVTHYRVLDRY-RAHTLLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             +GRTHQ+RVH  H+  P+VGD  Y    +    +  +        N+  LHA  + L 
Sbjct: 228 LESGRTHQIRVHMAHIRHPLVGDLTYGGRPRPPKQAEDRLLQTLRGFNRQALHAASLGLH 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  L+   P P       + L   ++R
Sbjct: 288 HPITGDWLEFNVPRPTDFQYLIEELRVDHER 318


>gi|157962983|ref|YP_001503017.1| RluA family pseudouridine synthase [Shewanella pealeana ATCC
           700345]
 gi|157847983|gb|ABV88482.1| pseudouridine synthase, RluA family [Shewanella pealeana ATCC
           700345]
          Length = 323

 Score =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 80/335 (23%), Positives = 139/335 (41%), Gaps = 37/335 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +   RLD+   + +P  +   +++ + SG V +D +   K   ++  GQVV I   
Sbjct: 11  ITATQTGQRLDQTLADLFPDYSRTRIKEWILSGSVFIDGETSDKPRFKVLEGQVVTIGAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
           +                      ++ +   ++YED  I V NK AG+ V  G+G      
Sbjct: 71  LEEET---------------KAEAEAIDLDIIYEDDHILVINKQAGLVVHPGAGNQSGTL 115

Query: 129 IDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L          +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 MNALLHHCPGIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVTALQAREITREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQ 246
            G        I         I                  A++H++V + F +    L ++
Sbjct: 176 TG-------TIIAGGTVDEPIDRHPTKRTHMAVVHNGKPAMTHYRVAEKF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             +GRTHQ+RVH  H+G  +VGD  Y    +    +            +  LHA  ++L 
Sbjct: 228 LESGRTHQIRVHMAHIGHVLVGDPVYAGRPRPPKGAAPDFFETYMGFRRQALHAVRLELA 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           HP     +   AP+P  MVK   +L    + N  +
Sbjct: 288 HPFTCEIMSWQAPIPEDMVKLTRALRKDTEENPTV 322


>gi|195978250|ref|YP_002123494.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
 gi|195974955|gb|ACG62481.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
          Length = 296

 Score =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 74/315 (23%), Positives = 133/315 (42%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +  P ++       ++  +V V+    K    +Q G  +          
Sbjct: 7   ESGHRLDKALADLTP-LSRSQANDQIKQKRVLVNGSPKKAKYIVQVGDCISYH------- 58

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                   +    +L   +  +   ++Y+D  + + NKP G+ V   +G      ++  L
Sbjct: 59  --------IPEESSLDYQAQDIPLDIVYQDDVLVIINKPQGMVVHPSAGHSTGTLVNALL 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L+VA+T  A Q L +  + ++  + Y ++V G
Sbjct: 111 YHVKDLSSINGVIRPGIVHRIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I   + +            K        A++ FKV++ F + +  +E+Q  T
Sbjct: 171 NLPKDRGVIEAPIGRSDKDRKKQTVTAK-----GKEALTRFKVLERFGR-YSLVELQLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
           GRTHQ+RVH  ++G P+ GD  Y      +      N  +LHA+ + L HP  G  L  T
Sbjct: 225 GRTHQIRVHMAYIGHPLAGDPLYGPRKTLD-----GNGQFLHAQTLGLTHPVTGEELVFT 279

Query: 309 APLPAHMVKTWDSLG 323
              P    +T + L 
Sbjct: 280 VEPPEIFQRTLEQLR 294


>gi|284030831|ref|YP_003380762.1| pseudouridine synthase, RluA family [Kribbella flavida DSM 17836]
 gi|283810124|gb|ADB31963.1| pseudouridine synthase, RluA family [Kribbella flavida DSM 17836]
          Length = 309

 Score =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 144/327 (44%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + ++V +     RLD      +  ++     +++ +G V+VD      + R+ +G 
Sbjct: 1   MSDSRTLMVPDGLAGERLDAALSRLF-GVSRTKAAELIEAGLVQVDGAPAAKSARVSAGV 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ +      L     E  ++  +V            ++++D +I V +KP G++     
Sbjct: 60  LLDV-----ELPAPPGEVTVVPETVE--------NLRIVHDDDEIVVVDKPVGVAAHPSP 106

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L             ++  + HRLD  TSG++VVA+T  +   L  +F+ R
Sbjct: 107 GWTGPTVIGHLAGAGFSISTSGAAERKGIVHRLDVGTSGLMVVAKTEYSYTVLKRAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++KIY +LV G P      +   +    H   DY   V     G   +I+H++ ++ F 
Sbjct: 167 TVKKIYHALVQGHPDPFTGTVDAPI--DRHPNHDYKFGVVA---GGKPSITHYETLEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    LE+   TGRTHQ+RVH   +G P  GD  Y A+        + ++ +LHA  +  
Sbjct: 221 RYATLLEITLETGRTHQIRVHMSAIGHPCCGDLTYGADPVLAERLEL-SRQWLHAMRLGF 279

Query: 298 PHPEGGRL-QITAPLPAHMVKTWDSLG 323
            HP  G   + T+  P  + +  D L 
Sbjct: 280 THPGSGEYTEFTSQYPDDLDQALDRLA 306


>gi|163742953|ref|ZP_02150336.1| ribosomal large subunit pseudouridine synthase D [Phaeobacter
           gallaeciensis 2.10]
 gi|161383636|gb|EDQ08022.1| ribosomal large subunit pseudouridine synthase D [Phaeobacter
           gallaeciensis 2.10]
          Length = 344

 Score =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 87/355 (24%), Positives = 146/355 (41%), Gaps = 50/355 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M   +   V  +    RLD+      P    ++   L +++ +GQ++V+   V     ++
Sbjct: 1   MARRRIEFVIAENPPKRLDKAVSRDVPEEATLSRTRLARLIEAGQLQVNGTVVSDAKAKV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G ++ I       +HI  E   L+               ++YED  + V NKP G+ V
Sbjct: 61  DEGALIEITIEEAEDSHIGPEDIPLE---------------VIYEDDDLIVINKPTGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    D+       ++P + HR+D+ETSG+LVVA++  A Q L  
Sbjct: 106 HPAPGTPSGTLVNALLHHCGDNLSGVGGVKRPGIVHRIDKETSGLLVVAKSDVAHQGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F    +++ Y ++ +G+P      +           N L   + +        +Q    
Sbjct: 166 QFEKHTVERYYRAICYGVPDANDPRLRGVKGTSFEPGNILKLTTQLARHKTDRQRQAVLF 225

Query: 221 KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +G  +AI+  +++D F        +E    TGRTHQ+RVH  H G  +VGD  Y    K 
Sbjct: 226 QGGRHAITRARIVDSFGTPPVVALIECWLETGRTHQIRVHMAHAGHGLVGDPVYGGKRKL 285

Query: 279 NFTSPIQN---------KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              S  ++         +  LHA  +   HP  G  ++  APLP  M      LG
Sbjct: 286 AAKSLPEDTAAAIQAFPRQALHAAVLGFIHPVTGDAMRFEAPLPEDMAHLLQKLG 340


>gi|94990203|ref|YP_598303.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94543711|gb|ABF33759.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
          Length = 296

 Score =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 77/316 (24%), Positives = 134/316 (42%), Gaps = 34/316 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V+           
Sbjct: 8   SGQRLDKALADLSP-LSRGQANDQIKQGLVLVNDQQKKAKYTVQAGDVICFE-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
                  L     L   +  +   ++YED  + + NKP G+ V   +G      ++  + 
Sbjct: 59  -------LPKEEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+T AA Q L E  + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        A++ F V++ F   +  +E+Q  TG
Sbjct: 172 LPNDRGMIEAPIGRSEKDRKKQAVTAK-----GKEAVTRFTVLERFGD-YSLVELQLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ + L HP  G  +  T 
Sbjct: 226 RTHQIRVHMAYIGHPVAGDPLYGPR-----KTLSGHGQFLHAKTLGLTHPMTGKEMIFTV 280

Query: 310 PLPAHMVKTWDSLGFK 325
             P    K    L  K
Sbjct: 281 EAPEIFQKVLKLLRKK 296


>gi|157826322|ref|YP_001494042.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Rickettsia akari str. Hartford]
 gi|157800280|gb|ABV75534.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Rickettsia akari str. Hartford]
          Length = 329

 Score =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 145/329 (44%), Gaps = 40/329 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V N+  N+RLD+        I+   +QK +++ QV V+   +   +  ++   V+     
Sbjct: 6   VPNELNNIRLDKALSQLLEKISRNQIQKAIKNSQVLVNDVIISDPDVLVKENDVILF--- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                              L   +  +   ++YED  + V NK AG++V  G+G  +H D
Sbjct: 63  ------------AFKEPEELKIAAVNIALDIIYEDDDLIVINKAAGMTVHPGAG--HHDD 108

Query: 131 GFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +             +P + HRLD++T+G++VVA+   A   L      R++ + 
Sbjct: 109 TLVNALLYHTKNLSDIGSAARPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFC 241
           Y +LVWG+       I N + + S +    + ++K    G   A++H+K ++  +     
Sbjct: 169 YKALVWGVINPLAGVIKNNIGR-SRVERQKMSILKY---GGKEAVTHYKTLELFYGGTIS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQ-------NKLYLHAR 293
            +E + +TGRTHQ+RV   H+   +VGD  Y  N +    +SP          +  LH+ 
Sbjct: 225 MVECRLNTGRTHQIRVQLSHVKHSVVGDQTYGNNDRKIAHSSPALKAKLIDFKRQALHSW 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           Y+   HP   + ++ +  LP  M     +
Sbjct: 285 YLSFTHPTSNKIMEFSCELPRDMEAIIAT 313


>gi|325288855|ref|YP_004265036.1| ribosomal large subunit pseudouridine synthase D [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964256|gb|ADY55035.1| ribosomal large subunit pseudouridine synthase D [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 312

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 78/326 (23%), Positives = 138/326 (42%), Gaps = 33/326 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
            Y Q++ VE   E +RLD          +   ++ ++  G+V V+ +  K N RI++   
Sbjct: 10  AYEQWLAVEGKPE-VRLDVCLTEK-TGTSRSFIRNMIEEGRVLVNGETKKANYRIRAEDK 67

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I                L     L      +   ++YED  + V NKP G+ V    G
Sbjct: 68  IGIN---------------LPKPRELKVVPQQIPLEIIYEDDDLLVVNKPQGMVVHPAPG 112

Query: 125 I--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           +     ++  L    D  G     +P + HR+D++TSG+LVVA+   +   L    +  +
Sbjct: 113 VWEGTLVNALLYHCRDLSGINGIIRPGIVHRIDKDTSGLLVVAKNDESHNQLAGQLKEHK 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           +Q+ Y ++V G+       I   + +          V K     +  A++H++V + F  
Sbjct: 173 MQRKYLAVVHGVLSEPSGTIDAPIGRDPKDRKKMAVVFKH----SRPAVTHYEVEERF-I 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  ++    TGRTHQ+RVH  ++  P++GD  Y                 LHA  +   
Sbjct: 228 GYTKIKAVLETGRTHQIRVHMAYIRNPVLGDPLYGPKK----NILGLTGQVLHAHTLAFL 283

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP GG+ ++ +A  P   ++  D L 
Sbjct: 284 HPRGGKLMEFSADPPREFLEAVDKLR 309


>gi|299136326|ref|ZP_07029510.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX8]
 gi|298602450|gb|EFI58604.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX8]
          Length = 446

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 89/339 (26%), Positives = 155/339 (45%), Gaps = 39/339 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   VE   + MRLD +     P I+   +  ++  GQV VD    K   +++ G+++ 
Sbjct: 118 VRSFTVEPAAKEMRLDAYLAKAIPDISRARVVLLIEKGQVTVDGNPGKGKQKLKGGEMIE 177

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I              +       L    + +   ++YED  + V +K AG+ V  G+G +
Sbjct: 178 I--------------EGEPRPEPLHAQPEDIPLTIVYEDDDLAVVDKAAGMMVHAGAGDS 223

Query: 127 YHIDGFLKSWVD----------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               G L + +           S   +P + HRLD++TSG++VVA+  +  + L+E F  
Sbjct: 224 ERNRGTLVNALLFHMGKSLSQVSGDLRPGIVHRLDKQTSGLIVVAKNDSTHRKLSEMFSE 283

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVID 234
           RR++K+Y +LV G          +  ++   I  D V  ++   +  G   A+SH++V++
Sbjct: 284 RRLRKVYLALVHGWIAPATGAQDSGTIQL-PISRDLVRRIRMTTRRSGGRSAVSHWRVLE 342

Query: 235 CFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--------ANFKGNFTSP 283
             +    KF  +E++  TGRTHQ+RVH   +G P+VGD  Y            +      
Sbjct: 343 KISGPYGKFSLVEVRIETGRTHQIRVHMQAIGHPVVGDFLYGAPHRINPIGGPQAEVEGF 402

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
              + +LHA  ++  HP  G  L + A LP  +V+  + 
Sbjct: 403 ALERNFLHAAELEFVHPRTGEKLALDAALPEELVQVLER 441


>gi|226943324|ref|YP_002798397.1| Pseudouridine synthase [Azotobacter vinelandii DJ]
 gi|226718251|gb|ACO77422.1| Pseudouridine synthase [Azotobacter vinelandii DJ]
          Length = 336

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 87/324 (26%), Positives = 147/324 (45%), Gaps = 34/324 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  +    RLD+     +   +   L   ++ G++ VD   ++  + +  G ++ +    
Sbjct: 28  VPVELGGQRLDQVAAQLFAEHSRSRLAAWIKDGRLTVDGAALRPRDIVHGGALLELDAEQ 87

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
            A    I               +  ++  +++ED +I V NKPAG+ V   +G A   + 
Sbjct: 88  QAQGEWI---------------AQAIELDIVHEDEQILVLNKPAGLVVHPAAGHADGTLL 132

Query: 131 GFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             L   V      PR  + HRLD++T+G++VVA+T  A   L E  + R + +IY ++V 
Sbjct: 133 NALLHHVPGLVNVPRAGIVHRLDKDTTGLMVVAKTLQAQTRLVEQLQKRSVSRIYEAIVV 192

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+         +  + +       + VV    +G   A+SH++V++ F +      ++  
Sbjct: 193 GVITA--GATIDAPIGRHGQQRQRMAVV----EGGKPAVSHYRVLERF-RAHTHARIKLE 245

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+G  +VGD  Y   F+     SP          +  LHAR+++L HP
Sbjct: 246 TGRTHQIRVHMAHVGYSLVGDPVYGGRFRIPPAASPTLVQALREFPRQALHARFLELDHP 305

Query: 301 -EGGRLQITAPLPAHMVKTWDSLG 323
             G RL+  APLP   V     L 
Sbjct: 306 ASGERLKWEAPLPDDFVWLLTLLR 329


>gi|117921609|ref|YP_870801.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           ANA-3]
 gi|117613941|gb|ABK49395.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           ANA-3]
          Length = 323

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 142/325 (43%), Gaps = 35/325 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +  +RLD+     +P  +   +++ + S  V VD   V K   ++   Q + I   
Sbjct: 11  ISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVYVDGVIVNKPREKVFELQRIEINAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--H 128
           +    H   +   LD               ++YED  I V NK AG+ V  G+G A    
Sbjct: 71  LEEEVHAAAQAIELD---------------IVYEDDDILVINKQAGLVVHPGAGNADGTL 115

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L    + +   +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 MNALLHHCPNIEHVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        +   + +         H+   +      A++H++V + F +    L ++ 
Sbjct: 176 LGTM-TAGGTVDEPIGRHPT---KRTHMAVHHS--GKPAVTHYRVAEKF-RNHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            +GRTHQ+RVH  ++G  +VGD  Y    K    +  +         +  LHA  ++L H
Sbjct: 229 ESGRTHQIRVHMAYIGHVLVGDPVYGGRPKPPKAASPEFFEILKNFKRQALHAVRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P     +  TAP+P  MV    +L 
Sbjct: 289 PVTCEIMSWTAPIPEDMVILTKALR 313


>gi|319794365|ref|YP_004156005.1| pseudouridine synthase, rlua family [Variovorax paradoxus EPS]
 gi|315596828|gb|ADU37894.1| pseudouridine synthase, RluA family [Variovorax paradoxus EPS]
          Length = 322

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 78/332 (23%), Positives = 139/332 (41%), Gaps = 31/332 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
           + ++  VV       RLDR      P  +   LQ+++ +G V    + + K +  +++GQ
Sbjct: 13  SELRPFVVSEALHGQRLDRALAALVPEFSRSYLQQLIEAGAVEFQGRTLTKASATVRAGQ 72

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
             RI              ++  +  +     + +  + ++ED  + + +KPAG+ V    
Sbjct: 73  AGRI--------------ELRPTPQSQAFRPEPMDLVTVFEDEHLRIVDKPAGLVVHPAP 118

Query: 124 GIAYHIDGFLKSWVDSKGQKP------RLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H  G L + + +   K        + HRLD++TSG++VVARTRAA   L      R
Sbjct: 119 G---HWSGTLLNGLLALDPKAVLLPRAGIVHRLDRDTSGLMVVARTRAAMDALVALIAAR 175

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y ++             +  + +       + VV         A +  + +D  +
Sbjct: 176 EVKRQYLAIGHKPWVGAAARQVDAPIGRDPRNRLRMAVVDLERHSGKTARTLIERLDSHS 235

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +  C +     TGRTHQ+RVH   +G P+VGD  Y         +    +  LHA  +  
Sbjct: 236 EG-CVVRCTLETGRTHQIRVHMASIGHPLVGDALYGG-----APAVGLARQALHAFRLAF 289

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            HP     L+  +  P  +V+   S G  Y+R
Sbjct: 290 VHPVTQAALEFHSLPPPDLVQALQSWGLDYNR 321


>gi|237740892|ref|ZP_04571373.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           4_1_13]
 gi|229431189|gb|EEO41401.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           4_1_13]
          Length = 314

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 76/338 (22%), Positives = 142/338 (42%), Gaps = 36/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V ++ E MRLD++            L+K++ +  V+++ K +  N  ++
Sbjct: 1   MENIKEKFEFEVSSEYEGMRLDKYLSKQIEEATRSYLEKLIDNNYVKINSKVINKNGRKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G+ + +                +    N+   ++ +   ++YE+    V NK  G+ V
Sbjct: 61  KLGEKIEVS---------------IPKEENIDIEAENISLDIVYENDDFIVINKSYGMVV 105

Query: 120 QGGSG-IAYHIDGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G  +  +   L  + +     +   +P + HRLD++TSG+++VA+   A   L   
Sbjct: 106 HPAYGNYSGTLVNALLYYTNNLSSINGNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           F  + I K Y  +V G    +     I N + + S      + VVK+N      AIS++K
Sbjct: 166 FTDKTIHKTYLCIVKGNFSEENLNGRIENLIGRDSK-DRKKMAVVKEN---GKTAISNYK 221

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           VI+     +  +E+   TGRTHQ+RVH   +   I+GD  Y    K         +  LH
Sbjct: 222 VIEQV-DGYSLVEIAIETGRTHQIRVHMKSINHVILGDSTYGNEDKNV------KRQMLH 274

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A  ++  +P +         L    ++    L F  ++
Sbjct: 275 AYKLEFLNPLDNKEYIFKGRLFDDFIEVAKKLRFNIEK 312


>gi|316931592|ref|YP_004106574.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           DX-1]
 gi|315599306|gb|ADU41841.1| pseudouridine synthase, RluA family [Rhodopseudomonas palustris
           DX-1]
          Length = 334

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 92/344 (26%), Positives = 149/344 (43%), Gaps = 53/344 (15%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
            V V  DE + RLDR      P ++   L+ ++  G+V +    V+        G+ + I
Sbjct: 10  EVTVAGDEGSARLDRVLAARCPELSRSRLKALILDGRVAIAGNPVRDPAYHASPGETITI 69

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                A      E   LD               + +ED+ I V NKP G+ V   +G   
Sbjct: 70  DVPPPAPAEPAGEAIALD---------------IAHEDADIIVLNKPRGLVVHPAAG--- 111

Query: 128 HIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           H  G L + + +            ++P + HRLD++T+G++VVA+   A Q L+  F   
Sbjct: 112 HETGTLVNALIAHCGASLSGIGGVRRPGIVHRLDKDTTGLMVVAKNDRAHQSLSAQFADH 171

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                +++ Y++ VWG+P      I   + +  H   + + V     +G   AI+H++V+
Sbjct: 172 GRTGELRRGYFAFVWGVPGRTYGTIDAPIDRHPH-AREKMAVR----QGGREAITHWEVL 226

Query: 234 DCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT------- 281
           + FA K        +  Q  TGRTHQ+RVH  H+G P++GD  Y  +FK           
Sbjct: 227 ESFAGKDGKPVASLIACQLETGRTHQIRVHLAHIGHPLLGDDVYGPHFKTKANQLAPAAR 286

Query: 282 --SPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
                  +  LHA  + L HP  G +    +PLPA +     +L
Sbjct: 287 AALAQLGRQALHAYLLTLEHPSTGEILTWESPLPADLAHLQAAL 330


>gi|87300810|ref|ZP_01083652.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 5701]
 gi|87284681|gb|EAQ76633.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 5701]
          Length = 315

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 87/313 (27%), Positives = 133/313 (42%), Gaps = 28/313 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW     P  +   +QK + +G VRV+    +    ++    V++          
Sbjct: 21  PMRLDRWLVAQRPEQSRARIQKFIDAGYVRVNGVTGRAKTPLRLHDEVQLWMPPPEPLP- 79

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
                              +   +L+ED+ + V NKPAG++V    G      ++G L  
Sbjct: 80  -------------YLLPQPIPLDVLFEDAHLIVLNKPAGLTVHPAPGNRDGTLVNGLLHH 126

Query: 136 WVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +VVA+++ A   L    + R   + Y ++V G P
Sbjct: 127 CPDLPGIGGEMRPGIVHRLDKDTTGCIVVAKSQEALVRLQVQIQKRVASREYLAVVHGAP 186

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   + +       Y  V    E+   +A +H+ +I+     +  L  +  TGR
Sbjct: 187 AASSGTIVGAIGRHPADRKKYAVVA---EEKGRFACTHWTLIERLGD-YSLLRFRLDTGR 242

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH  H+G PIVGD  Y    K     P      LHA  + L HP  G RL   AP
Sbjct: 243 THQIRVHCAHIGHPIVGDVTYSRCRKLPLELPG---QALHAVALGLDHPISGERLAFEAP 299

Query: 311 LPAHMVKTWDSLG 323
           LP    +    L 
Sbjct: 300 LPEPFERLLHLLR 312


>gi|311104863|ref|YP_003977716.1| ribosomal large subunit pseudouridine synthase D [Achromobacter
           xylosoxidans A8]
 gi|310759552|gb|ADP15001.1| ribosomal large subunit pseudouridine synthase D [Achromobacter
           xylosoxidans A8]
          Length = 332

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 73/327 (22%), Positives = 131/327 (40%), Gaps = 31/327 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q+V V +     RLD+      P  +   LQ  + +G V V+ +  K    +  G  + +
Sbjct: 29  QFVTVPSSTRADRLDKVLAGLLPEHSRGRLQGWIEAGNVHVNGRPGKVRQTVGPGDELTV 88

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P                +  +L    + +   ++ E     V NKPAG+    G+G   
Sbjct: 89  WPQ--------------PAPESLAFAPEPVDFAVVDESPDWIVVNKPAGLVTHPGAGNWS 134

Query: 126 AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + + ++  +  + HRLD++TSG++VVAR   A  HL    + R + + Y 
Sbjct: 135 GTLLNGLLYRYPELTQVARAGIVHRLDKDTSGLMVVARNETAQTHLVRQLQARSMGREYV 194

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC----FAQKF 240
           +L  G        +   + + S +    V +  +       AI+H+            + 
Sbjct: 195 ALAHG-WLAAAGKVDRPIGRDSRV---PVRMSVERPVAPKPAITHYAPARRGEADPGGRV 250

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +  +  TGRTHQ+RVH   +G P++ D  Y              +  LHAR +    P
Sbjct: 251 TEVVCRLETGRTHQIRVHMASLGHPLLADTLYGGK-----NIVGAQRQMLHARALHFEDP 305

Query: 301 EG-GRLQITAPLPAHMVKTWDSLGFKY 326
            G G ++  A +P  M    + + +  
Sbjct: 306 GGRGEVEFAAAVPPDMGLVQEEIAWNA 332


>gi|77358713|ref|YP_338279.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           RSA 493]
 gi|161830459|ref|YP_001596417.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           RSA 331]
 gi|212213029|ref|YP_002303965.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           CbuG_Q212]
 gi|71066703|gb|AAZ22625.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           RSA 493]
 gi|161762326|gb|ABX77968.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           RSA 331]
 gi|212011439|gb|ACJ18820.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           CbuG_Q212]
          Length = 308

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 102/318 (32%), Positives = 160/318 (50%), Gaps = 15/318 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +   V +++     RLD +       +    + + +R G+VRV+K+RV  + R+  G +V
Sbjct: 2   HTTPVTIDDAHAGQRLDNFLITRLKGVPSTRIYRAIRKGEVRVNKRRVGADYRLVVGDLV 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPPV  A     K+   +D  + ++     L+  +LYE++ + V +KPAG+ V GGSGI
Sbjct: 62  RIPPVQMAA---PKKPATVDEKLLIS-----LEMRILYEEADLLVIDKPAGLPVHGGSGI 113

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +   L+     K +   L HRLD+ETSG L+VA+ R+    L      R++ K Y  
Sbjct: 114 QGGVIEALRIMR-PKVRLLELVHRLDRETSGCLMVAKKRSTLVALHTLLTQRKVIKQYLL 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  +  +  +   L K     G+ +  V   EK    A++ F+ +  F Q    +E 
Sbjct: 173 LVKGQWQGGECRVEVPLKKNRLQSGERMVKV---EKEGKSAVTVFRPLKIFEQ-ASLIEA 228

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +P TGRTHQ+RVHA H+G PI GD KY    F     +    +L+LH+  + L   E  R
Sbjct: 229 KPLTGRTHQIRVHAAHLGYPIAGDEKYGDKVFNREMRNYGLRRLFLHSAGI-LCQWEDKR 287

Query: 305 LQITAPLPAHMVKTWDSL 322
           L + A L + ++K    L
Sbjct: 288 LGVCAILDSELMKCLTQL 305


>gi|58038975|ref|YP_190939.1| ribosomal large subunit pseudouridine synthase D [Gluconobacter
           oxydans 621H]
 gi|58001389|gb|AAW60283.1| Ribosomal large subunit pseudouridine synthase D [Gluconobacter
           oxydans 621H]
          Length = 322

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 78/340 (22%), Positives = 136/340 (40%), Gaps = 38/340 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           MS       +VV+      R DR   +    ++   ++ ++ SG + V+ K V +    +
Sbjct: 1   MSDPVSPFRLVVDASTAGQRADRALADAIGTVSRSRVKALIESGNLSVNGKTVCEPAETL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G  + +          + EQ               +   +LYED  + V +K AG+  
Sbjct: 61  RDGMEMVLTFPAPTPARPVAEQ---------------IPLNILYEDDDLIVLDKQAGLVT 105

Query: 120 QGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    +        ++P + HRLD++TSG++VVA+T      L+E
Sbjct: 106 HPAPGNETGTLVNALLGHCGEGFEGIGGEKRPGIVHRLDKDTSGLMVVAKTAMVHNALSE 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           +F  R I + Y +L WG+   + E   +  + +       + VV     G   A++ FK+
Sbjct: 166 AFAARDIDRAYLALAWGLLPAEGEF--DGSIGRDKRDRKRMAVV---GSGGKVALTRFKL 220

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------ 286
           I+ +      +E +  TGRTHQ+RVH  + G P++GD  Y            Q+      
Sbjct: 221 IEPYQAAVSLIECRLATGRTHQIRVHLSNAGHPLLGDPVYLRRIPAAARGLSQDAKEAAL 280

Query: 287 ---KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              +  LHA  +   HP   + L      P         L
Sbjct: 281 DFPRQALHATRLGFIHPRTKKQLSFETAPPEDFQALKKRL 320


>gi|257093130|ref|YP_003166771.1| RluA family pseudouridine synthase [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257045654|gb|ACV34842.1| pseudouridine synthase, RluA family [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 328

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 107/332 (32%), Positives = 165/332 (49%), Gaps = 22/332 (6%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V   ++  +E   RLD         +   ++  I+RSGQVRV+ +R + + R+Q+G V
Sbjct: 7   SSVTQALITENEHGQRLDNLLLKQCKGVPKSHVYSIVRSGQVRVNGRRAEVSYRLQTGDV 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RIPP+  A     +EQ+I+  +         +   +LYED  + + +KPAGI+V GGSG
Sbjct: 67  LRIPPLRIAR----REQEIVAGA------EFNVDLPVLYEDDGLLIIDKPAGIAVHGGSG 116

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI----- 179
            ++ +   L+       +   L HRLD+ETSGIL+V + R+A   L E FR         
Sbjct: 117 ESFGVIEALRRQRPQ-ARFLELAHRLDRETSGILLVGKKRSALLALHEMFRDGGGGGRGA 175

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y  LV G   +    +   LLK     G+    V    +    + + F+++  + + 
Sbjct: 176 DKRYQVLVAGRWMDPVRNVRVPLLKYLQPSGERRVRV---SEAGKASHTVFRLLARW-EH 231

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLP 298
           F  LE    TGRTHQ+RVH  H+G P+ GD KY               +++LHA  M LP
Sbjct: 232 FSLLEAHLKTGRTHQIRVHLAHLGYPVAGDEKYGDFALNRVLARDGLKRMFLHAWTMRLP 291

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           +P  GR L + APLP  + +  DSL  K  ++
Sbjct: 292 NPLDGRDLVVEAPLPVVLRRFLDSLSAKEKQD 323


>gi|269958655|ref|YP_003328442.1| putative pseudouridylate synthase [Anaplasma centrale str. Israel]
 gi|269848484|gb|ACZ49128.1| putative pseudouridylate synthase [Anaplasma centrale str. Israel]
          Length = 327

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 142/334 (42%), Gaps = 34/334 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSG 62
           M  V  + V  + +  R+D+        I+    Q ++  GQV +  + +  N    ++G
Sbjct: 1   MKSVHEICVTKEGDQQRIDKLISCAL-EISRNRAQGLIAGGQVTISGRVINDNSYLTKTG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V  I   +   + +     I                 ++YED  + V +K   I+V  G
Sbjct: 60  DVYTIVTAVQKPSTLSPNYDI--------------DLKVVYEDHDVIVIDKDPYIAVHPG 105

Query: 123 SGIAYHI--DGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +GI +H   +  L  +           +P + HRLD++TSG++V A+T  A   L+E   
Sbjct: 106 NGIEHHTITNALLARFGAGLQSVGSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELA 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +  +K Y ++ WGIP  K+  I   +     +    + +++    G   A + ++V   
Sbjct: 166 NQGFKKEYLAVAWGIPCPKRGVIHTNI----RVKRSDITMMEAANSGGKPAKTEYEVEQE 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLY 289
             +    +    HTGRTHQ+RVH  H+G  IVGD KY  N K    S +        +  
Sbjct: 222 LGEVASLIRCTLHTGRTHQIRVHMSHIGHSIVGDQKYGKNCKKCMRSGVPPDVKNFRRQA 281

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           LHA  +   HP  G+ ++ T+     M +   +L
Sbjct: 282 LHASLLGFRHPSTGKYIEFTSKPADDMQQLISAL 315


>gi|15606824|ref|NP_214204.1| hypothetical protein aq_1758 [Aquifex aeolicus VF5]
 gi|3915479|sp|O67638|Y1758_AQUAE RecName: Full=Uncharacterized RNA pseudouridine synthase aq_1758;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2984062|gb|AAC07603.1| hypothetical protein aq_1758 [Aquifex aeolicus VF5]
          Length = 316

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 145/325 (44%), Gaps = 34/325 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           ++ V    VE +EE  RLD++    YP  +   ++K+++ G V V+ + V K + +++ G
Sbjct: 3   ISEVLEFKVEGEEE--RLDKFLARAYPDFSRSYIKKLVKEGLVYVNGEEVRKPSRKLREG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V +                +     L    + +   ++YED  I V  KP G+ V   
Sbjct: 61  ERVILH---------------VPEPEPLDVKPENIPINIIYEDEDIAVVEKPCGLVVHPS 105

Query: 123 SGIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++  L    D       ++P + HRLD+ET+G++V+A+   A ++L   F+ 
Sbjct: 106 PGYTSGTLVNALLYHIKDLSSIGGVERPGIVHRLDKETAGVMVIAKNNTAHRNLVRQFQE 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R+ +K Y  LV G+ K     I   + +   +      V K+       A++ + V+  +
Sbjct: 166 RKTEKFYKVLVKGLVKKDYGAIDTPIARH-PVDRKRFWVRKE----GKEALTEYWVLKRY 220

Query: 237 AQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHA 292
            + +   L+++ HTGRTHQ+RVH   +G P++GD  Y    ++      S +     L A
Sbjct: 221 EKYEITLLKVKIHTGRTHQIRVHFASIGHPVLGDRTYGFKSSSVPKELLSLMGECNMLIA 280

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMV 316
            ++   HP  G  +      P    
Sbjct: 281 YHLGFYHPTKGEWMVFEIEEPETFK 305


>gi|120603012|ref|YP_967412.1| RluA family pseudouridine synthase [Desulfovibrio vulgaris DP4]
 gi|120563241|gb|ABM28985.1| dephospho-CoA kinase / ribosomal large subunit pseudouridine
           synthase D [Desulfovibrio vulgaris DP4]
          Length = 541

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 87/349 (24%), Positives = 148/349 (42%), Gaps = 39/349 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVR 66
           + V     N RLDR+      H  ++   +++ +R GQ  VD       + R++SGQ V 
Sbjct: 17  LTVPAGMRNERLDRFLGEALSHTDLSREKIKRAIRDGQCTVDGTVCTTPSTRLRSGQRVE 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--- 123
           +     A     +E  +                 +++ D  + V +KPAG++V       
Sbjct: 77  LAIAPAATAVEPEEGDL----------------TIIHRDEHLLVIDKPAGLTVHPCPSCP 120

Query: 124 --GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + + +     +    +G +P + HR+D++TSG+L+VA +      L+E+F  R ++K
Sbjct: 121 EGTLVHRLVHHFDALRAQEGFRPGIVHRIDKDTSGLLLVALSEGVRLKLSEAFAERTVEK 180

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQ-K 239
            Y +LV G+P    E         + IG    H V+    KG   A S ++V+    +  
Sbjct: 181 EYLALVHGVPPATGEV-------DAPIGRHPTHKVRMAVVKGGKPARSEWRVLHAAPEGH 233

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-KLYLHARYMDLP 298
           +  + ++ H+GRTHQ+RVH  H G P+ GD  Y               +  LHA  +   
Sbjct: 234 YALVAVRIHSGRTHQIRVHMAHAGFPLWGDQLYGPGTPARLREQGYGARQMLHAWRLAFT 293

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL 346
           HP  G RL+ T P P        +L     R +    +     C ++ L
Sbjct: 294 HPVTGERLRFTCPPPQDFPDLAVALA----RRMTRVVITGSPGCGKSAL 338


>gi|46579437|ref|YP_010245.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Desulfovibrio vulgaris str. Hildenborough]
 gi|46448851|gb|AAS95504.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Desulfovibrio vulgaris str. Hildenborough]
 gi|311233254|gb|ADP86108.1| pseudouridine synthase, RluA family [Desulfovibrio vulgaris RCH1]
          Length = 541

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 87/349 (24%), Positives = 149/349 (42%), Gaps = 39/349 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVR 66
           + V     N RLDR+      H  ++   +++ +R GQ  VD       + R++SGQ V 
Sbjct: 17  LTVPAGMRNERLDRFLGEALSHTDLSREKIKRAIRDGQCTVDGTVCTTPSTRLRSGQRVE 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--- 123
           +     A     +E  +                 +++ D  + V +KPAG++V       
Sbjct: 77  LAIAPAATAVEPEEGDL----------------TIIHRDEHLLVIDKPAGLTVHPCPSCP 120

Query: 124 --GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + + +     +    +G +P + HR+D++TSG+L+VA +      L+E+F  R ++K
Sbjct: 121 EGTLVHRLVHHFDALRAQEGFRPGIVHRIDKDTSGLLLVALSEGVRLKLSEAFAERTVEK 180

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQ-K 239
            Y +LV G+P    E         + IG    H V+    KG   A S ++V+    +  
Sbjct: 181 EYLALVHGVPPATGEV-------DAPIGRHPTHKVRMAVVKGGKPARSEWRVLHAAPEGH 233

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-KLYLHARYMDLP 298
           +  + ++ H+GRTHQ+RVH  H G P+ GD  Y               +  LHA ++   
Sbjct: 234 YALVAVRIHSGRTHQIRVHMAHAGFPLWGDQLYGPGTPARLREQGYGARQMLHAWHLAFT 293

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNIL 346
           HP  G RL+ T P P        +L     R +    +     C ++ L
Sbjct: 294 HPVTGERLRFTCPPPQDFPDLAIALA----RRMTRVVITGSPGCGKSAL 338


>gi|163747421|ref|ZP_02154773.1| ribosomal large subunit pseudouridine synthase D [Oceanibulbus
           indolifex HEL-45]
 gi|161379274|gb|EDQ03691.1| ribosomal large subunit pseudouridine synthase D [Oceanibulbus
           indolifex HEL-45]
          Length = 348

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 90/355 (25%), Positives = 149/355 (41%), Gaps = 50/355 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M++ +   +  D    RLD+      P    ++   L +++  G V VD   V     ++
Sbjct: 1   MSHRRIDFILGDSPPARLDKALARDVPEAANLSRTRLGRLIEEGAVTVDGAVVHDPRAKV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             GQVV+I     A +HI+ E                +   +++ED  + V +KPAG+ V
Sbjct: 61  AEGQVVQIKVEEAAESHILPED---------------IPLSVVFEDDDLIVIDKPAGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    D        ++P + HR+D++T+G+LVVA++ AA   L  
Sbjct: 106 HPAPGSPSGTLVNALLAHCGDDLSGVGGMKRPGIVHRIDKDTTGLLVVAKSDAAHHGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F    +++ Y +LV+G+P      +           N L   + +        +Q    
Sbjct: 166 QFEKHTVERYYQTLVYGVPDANDPRLRGVKGASFEAGNILRMTTQLARHKTDRQRQAVLF 225

Query: 221 KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +G  +A++  + I+ F        LE    TGRTHQ+RVH  H G  +VGD  Y    K 
Sbjct: 226 QGGRHAVTRARTIERFGTPPVLALLECWLETGRTHQIRVHMSHAGHGLVGDATYGGRRKL 285

Query: 279 NFTSPIQ---------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             T+  +          +  LHA  +   HP  G  L+  APLP+ M    + L 
Sbjct: 286 AKTALPEATADAIRAFPRQALHAAVLGFEHPVTGENLRFEAPLPSDMAALLNLLR 340


>gi|154707769|ref|YP_001424927.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           Dugway 5J108-111]
 gi|161349250|ref|ZP_02096635.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           'MSU Goat Q177']
 gi|165920598|ref|ZP_02219569.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           RSA 334]
 gi|212218908|ref|YP_002305695.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           CbuK_Q154]
 gi|154357055|gb|ABS78517.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           Dugway 5J108-111]
 gi|164601538|gb|EDQ95142.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           'MSU Goat Q177']
 gi|165916800|gb|EDR35404.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           RSA 334]
 gi|212013170|gb|ACJ20550.1| ribosomal large subunit pseudouridine synthase C [Coxiella burnetii
           CbuK_Q154]
          Length = 308

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 102/318 (32%), Positives = 160/318 (50%), Gaps = 15/318 (4%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +   V +++     RLD +       +    + + +R G+VRV+K+RV  + R+  G +V
Sbjct: 2   HTTPVTIDDAHAGQRLDNFLITRLKGVPSTRIYRAIRKGEVRVNKRRVGADYRLVVGDLV 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPPV  A     K+   +D  + ++     L+  +LYE++ + V +KPAG+ V GGSGI
Sbjct: 62  RIPPVQMAA---PKKPATVDEKLLIS-----LEMRILYEEADLLVIDKPAGLPVHGGSGI 113

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +   L+     K +   L HRLD+ETSG L+VA+ R+    L      R++ K Y  
Sbjct: 114 QGGLIEALRIMR-PKVRLLELVHRLDRETSGCLMVAKKRSTLVALHTLLTQRKVIKQYLL 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G  +  +  +   L K     G+ +  V   EK    A++ F+ +  F Q    +E 
Sbjct: 173 LVKGQWQGGECRVEVPLKKNRLQSGERMVKV---EKEGKSAVTVFRPLKIFEQ-ASLIEA 228

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +P TGRTHQ+RVHA H+G PI GD KY    F     +    +L+LH+  + L   E  R
Sbjct: 229 KPLTGRTHQIRVHAAHLGYPIAGDEKYGDKVFNREMRNYGLRRLFLHSAGI-LCQWEDKR 287

Query: 305 LQITAPLPAHMVKTWDSL 322
           L + A L + ++K    L
Sbjct: 288 LGVCAILDSELMKCLTQL 305


>gi|152977723|ref|YP_001343352.1| 23S rRNA pseudouridine synthase D [Actinobacillus succinogenes
           130Z]
 gi|150839446|gb|ABR73417.1| pseudouridine synthase, RluA family [Actinobacillus succinogenes
           130Z]
          Length = 324

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 78/328 (23%), Positives = 143/328 (43%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V++ +   RLD+     +P  +   L+  +    VRV+         ++  G+ + I   
Sbjct: 10  VQSHQMGQRLDQTLAELFPDYSRSRLKTWIEGNLVRVNGNIQNIPRTKVLGGEQIEIRAE 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +    H   E   LD               ++YED  I V NKP    V  G+G      
Sbjct: 70  VEEETHYEPENLPLD---------------IVYEDDHILVLNKPKNFVVHPGAGNPRGTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++ 
Sbjct: 115 LNALLYHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G+   K   +   + +                     A++H+++++ F + +  L ++ 
Sbjct: 175 FGVM-TKGGKVDEPMARHPT-----KRTAMAVHPMGKPAVTHYRIMEHF-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +       +F+  ++N  +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPRNASEHFSEVLRNFQRQALHAIMLRLEH 287

Query: 300 P-EGGRLQITAPLPAHMVKTWDSLGFKY 326
           P  GG ++  APLP    +   +L   Y
Sbjct: 288 PISGGLMEWFAPLPDDFAELIAALKEDY 315


>gi|332530535|ref|ZP_08406474.1| pseudouridine synthase, RluA family protein [Hylemonella gracilis
           ATCC 19624]
 gi|332040010|gb|EGI76397.1| pseudouridine synthase, RluA family protein [Hylemonella gracilis
           ATCC 19624]
          Length = 361

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 84/344 (24%), Positives = 144/344 (41%), Gaps = 50/344 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-----KFNNRIQSGQVVR 66
           +  +    RLDR      P  +   LQ+++ +G V +  +       K  +++++G+V  
Sbjct: 23  IPPELHGQRLDRALSELVPEFSRSYLQQLIEAGAVTLGPQPSQLVVRKSAHKVRAGEVGT 82

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I              ++  +  +     + +   +++ED+ + V +KPAG+ V    G  
Sbjct: 83  I--------------ELRPTPQSQAFKPEVMDLDIVHEDAHLLVIHKPAGLVVHPAPG-- 126

Query: 127 YHIDGFLKSWVDSKGQ----------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            +  G L + +  + Q          +  + HRLD++TSG++VVARTR A + L      
Sbjct: 127 -NWSGTLLNGLLGRDQGRGEVAAQLPRAGIVHRLDKDTSGLMVVARTRVAMEALVRMIAA 185

Query: 177 RRIQKIYWSLVW----GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           R + + Y +L      G         A   + +       + VV         A++ F++
Sbjct: 186 REVSRQYLALAHRAWNGPVLRDVGGAAQEGIGRDPANRLRMAVVDLARHPGKPALTTFEL 245

Query: 233 I--------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           +        +  AQ  C L    HTGRTHQ+RVHA  +G P++GD  Y            
Sbjct: 246 LGNAAPRPDEGLAQGACLLRCTLHTGRTHQIRVHAASIGHPLLGDGVYGG-----APVVG 300

Query: 285 QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             +  LHA  + L HP  G  L   AP P  + K   +LG  Y+
Sbjct: 301 LRRQALHAWRLALRHPVSGEALVFHAPPPDDLAKACAALGLDYN 344


>gi|256846833|ref|ZP_05552288.1| pseudouridylate synthase [Fusobacterium sp. 3_1_36A2]
 gi|256717799|gb|EEU31357.1| pseudouridylate synthase [Fusobacterium sp. 3_1_36A2]
          Length = 316

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 76/338 (22%), Positives = 142/338 (42%), Gaps = 36/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V ++ E MRLD++            L+K++ +  V+++ K +  N  ++
Sbjct: 1   MENIKEKFEFEVSSEYEGMRLDKYLSKQIEEATRSYLEKLIDNNYVKINSKVINKNGRKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G+ + +                +    N+   ++ +   ++YE+    V NK  G+ V
Sbjct: 61  KLGEKIEVS---------------IPKEENIDIEAENISLDIVYENDDFIVINKSYGMVV 105

Query: 120 QGGSG-IAYHIDGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G  +  +   L  + +     +   +P + HRLD++TSG+++VA+   A   L   
Sbjct: 106 HPAYGNYSGTLVNALLYYTNNLSSINGNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           F  + I K Y  +V G    +     I N + + S      + VVK+N      AIS++K
Sbjct: 166 FTDKTIHKTYLCIVKGNFSEENLNGRIENLIGRDSK-DRKKMAVVKEN---GKTAISNYK 221

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           VI+     +  +E+   TGRTHQ+RVH   +   I+GD  Y    K         +  LH
Sbjct: 222 VIEQV-DGYSLVEIAIETGRTHQIRVHMKSINHVILGDSTYGNEDKNV------KRQMLH 274

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A  ++  +P +         L    ++    L F  ++
Sbjct: 275 AYKLEFLNPLDNKEYIFKGRLFDDFIEVAKRLRFNIEK 312


>gi|209559192|ref|YP_002285664.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
 gi|209540393|gb|ACI60969.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
          Length = 296

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 76/316 (24%), Positives = 132/316 (41%), Gaps = 34/316 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V+           
Sbjct: 8   SGQRLDKALADLSP-LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVICFE-------- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
                  L     L   +  +   ++YED  + +  KP G+ V    G      ++  + 
Sbjct: 59  -------LPKEEVLEYQAQNIPLDIIYEDDTLAIITKPQGMVVHPSGGHPSGTMVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+T AA Q L E  + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        A++ F V++ F   +  +E+Q  TG
Sbjct: 172 LPNDRGMIEAPIGRSEKDRKKQAVTAK-----GKEAVTRFTVLERFGD-YSLVELQLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +   +  +LHA+ + L HP  G  +  T 
Sbjct: 226 RTHQIRVHMAYIGHPVAGDPLYGPR-----KTLSGHGQFLHAKTLGLTHPMTGKEMIFTV 280

Query: 310 PLPAHMVKTWDSLGFK 325
             P    K    L  K
Sbjct: 281 EAPEIFQKVLKLLRKK 296


>gi|53804663|ref|YP_113451.1| ribosomal large subunit pseudouridine synthase D [Methylococcus
           capsulatus str. Bath]
 gi|53758424|gb|AAU92715.1| ribosomal large subunit pseudouridine synthase D [Methylococcus
           capsulatus str. Bath]
          Length = 334

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 75/334 (22%), Positives = 140/334 (41%), Gaps = 40/334 (11%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + +    + +    +RLD+     +P  +   LQ  ++ G   +D  +V    ++  G+ 
Sbjct: 23  SRILTTEIPHHLAGLRLDQALAVLFPDFSRARLQTWIKDGHALLDGIQVAPRQKLLGGER 82

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V +                 ++   +   ++ +   +++ D  I+V +KPAG+ V   +G
Sbjct: 83  VELR---------------AEADAAVECEAEAIPLTVVHADESIFVIDKPAGLVVHPAAG 127

Query: 125 IAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              H  G L++ +           +  + HRLD++TSG+LVVART  A + L +  + R 
Sbjct: 128 ---HPAGTLQNALLHLDPALAAIPRCGIVHRLDKDTSGLLVVARTLEAHKSLVDQLKDRS 184

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + + Y +LV G+       +   + +       +             +++H++V + F  
Sbjct: 185 VNREYLALVQGMV-TAGATVDEPIGRHPADRKRFAVR-----PDGRESVTHYRVEERF-L 237

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNKLYL 290
               L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +            +  L
Sbjct: 238 HHTLLRVRLETGRTHQIRVHMAHLHHPLVGDPVYGGRARIPAAADPVLIDVLRGFRRQAL 297

Query: 291 HARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLG 323
           HA  + L HPE GG +   +PLP         L 
Sbjct: 298 HAARLGLIHPEKGGEMAWESPLPPDFDALLRLLR 331


>gi|92112630|ref|YP_572558.1| ribosomal large subunit pseudouridine synthase D [Chromohalobacter
           salexigens DSM 3043]
 gi|91795720|gb|ABE57859.1| ribosomal large subunit pseudouridine synthase D [Chromohalobacter
           salexigens DSM 3043]
          Length = 325

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 72/328 (21%), Positives = 131/328 (39%), Gaps = 34/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +    +RLD+     +   +   L+  ++SG +  D    +  +++  G+ + +   +
Sbjct: 17  VPDTMIGLRLDQAAAELFADFSRERLKAWIKSGALTRDGAPARPKDKLFGGERLTLEATL 76

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
                                    +   +++ED  + V +KPAG+ V   +G      +
Sbjct: 77  EEDTRFAP---------------QAMALSIVHEDDDVLVIDKPAGLVVHPAAGNPDGTLL 121

Query: 130 DGFLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L       +  +  + HRLD++T+G++VVA+T AA   L E  + R + + Y ++V 
Sbjct: 122 NALLHHAPGQMQLPRAGIVHRLDKDTTGLMVVAKTLAAHASLVEQLQARTVSREYDAVVT 181

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        +   + +                     A++H++V++ F      +  +  
Sbjct: 182 GRM-TAGGSVDAPIGRHPKDRKRQAV-----TPSGKPAVTHYRVVERFP-AHTHVRCRLE 234

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H   P++GD  Y    K    +            +  LHAR +   HP
Sbjct: 235 TGRTHQIRVHMAHRRFPLIGDPVYAGRLKMPAGATDALKDVLRHFPRQALHARKLAFVHP 294

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             G  L   APLP  M+   D L    D
Sbjct: 295 GTGETLTFRAPLPDDMLMLLDFLRDAAD 322


>gi|323127056|gb|ADX24353.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis ATCC 12394]
          Length = 297

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 77/314 (24%), Positives = 133/314 (42%), Gaps = 34/314 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V+           
Sbjct: 8   SGQRLDKALADLSP-LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVI----------- 55

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
               Q  L     L   +  +   ++YED  + + NKP G+ V   +G      ++  + 
Sbjct: 56  ----QFELPKEEVLEYQAQDIPLNIIYEDEALAIINKPQGMVVHPSAGHPSGTMVNALMY 111

Query: 135 SWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              D        +P + HR+D++TSG+L+VA+T  A Q L    + ++  + Y ++V G 
Sbjct: 112 HIKDLSSINGVVRPGIVHRIDKDTSGLLMVAKTDEAHQALAAELKAKKSLRKYLAIVHGN 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N +  I   + +            K        A++ F V++ F   +  +E+Q  TG
Sbjct: 172 LPNDRGMIEAPIGRSEKDRKKQAVTAK-----GKEAVTRFTVLERFGD-YSLVELQLETG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  ++G P+ GD  Y         +   +  +LHA  + L HP  G  +  T 
Sbjct: 226 RTHQIRVHMAYIGHPVAGDPLYGPR-----KTLSGHGQFLHAETLGLTHPLTGEDMLFTV 280

Query: 310 PLPAHMVKTWDSLG 323
             PA   KT   L 
Sbjct: 281 APPAIFHKTLQQLR 294


>gi|309812701|ref|ZP_07706445.1| pseudouridine synthase, RluA family [Dermacoccus sp. Ellin185]
 gi|308433396|gb|EFP57284.1| pseudouridine synthase, RluA family [Dermacoccus sp. Ellin185]
          Length = 309

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 82/326 (25%), Positives = 146/326 (44%), Gaps = 26/326 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V+ + V    E  R+D          +     ++   G V VD KRV  + R+ +G 
Sbjct: 1   MSEVKSLFVPEGLEGERVDAAIARLL-GFSRTRAAELAAEGAVSVDGKRVAKSERVSAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +             +      +N           ++++D++I V +KPAG++     
Sbjct: 60  WLEVAMPERTGPREATPRVEPVPGMN-----------IVHDDTEIVVVDKPAGVAAHPSV 108

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  +  RLD  TSG++VVA++  A   L ++FR R
Sbjct: 109 GWDGPDVVGGLAAAGYRISTSGAPERQGIVQRLDVGTSGLMVVAKSERAYTLLKQAFRDR 168

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G+P   +  I   + +  H   DY   V  +      +++H+++++ F 
Sbjct: 169 TVDKTYHALVQGLPDPIEGTIDAPIGR--HPNHDYKFAVMDS---GRASVTHYELLEAF- 222

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    LE+   TGRTHQ+RVH   M  P VGD  Y ++        ++ + +LHA  +  
Sbjct: 223 RSASLLEIHLETGRTHQIRVHVSAMHHPCVGDPLYGSDPTLAKKLGLE-RQWLHAVELGF 281

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSL 322
            HP  G R+  T+P PA + +  D +
Sbjct: 282 DHPGSGERVTFTSPYPADLQRALDRI 307


>gi|254448155|ref|ZP_05061618.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium HTCC5015]
 gi|198262281|gb|EDY86563.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium HTCC5015]
          Length = 321

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 93/320 (29%), Positives = 162/320 (50%), Gaps = 20/320 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            Q + V ++    R+D +   ++  +    + ++LR G+VRV+  R K   +++SG ++R
Sbjct: 12  TQKLTVPDEAVGQRIDNFLMGYWKGVPRSRVYRVLRKGEVRVNGGRKKPIYKLKSGDLLR 71

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV       I+ Q   +      +    +   +L+ED ++ V NKP+G++   GSG+ 
Sbjct: 72  LPPVR------IEPQGETEVPAGAWRE---IAQRILFEDERLLVINKPSGMAAHAGSGVP 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + I   +       G++  L HRLD+ETSG L++A+ R+    L +SFR R   K Y +L
Sbjct: 123 FGIAEAVHQH-HCDGKRTELVHRLDRETSGCLLLAKGRSVLNVLQDSFRQRETHKQYLAL 181

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWL 243
           + G  K  +    +  L+K+ + G+ + VV   ++    A+S F+ +  +          
Sbjct: 182 LVGDLKGSRRV--DLALQKTKLSGEAMVVV---DEAGKSALSDFEPLAHYPWNDRTLTLA 236

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            +  HTGRTHQ+RVHA  +G P++GD KY       +       +L+LHA  +  P  EG
Sbjct: 237 RVTIHTGRTHQIRVHARALGLPLLGDDKYGDERLNRDAKRQGLKRLFLHAESIRFP-LEG 295

Query: 303 GRLQITAPLPAHMVKTWDSL 322
             L   APL A + +  ++L
Sbjct: 296 QTLYFEAPLDADLEQFINAL 315


>gi|157376631|ref|YP_001475231.1| lysozyme [Shewanella sediminis HAW-EB3]
 gi|157319005|gb|ABV38103.1| Lysozyme [Shewanella sediminis HAW-EB3]
          Length = 323

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 80/334 (23%), Positives = 150/334 (44%), Gaps = 35/334 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPV 70
           +   +   RLD+   + +P  +   +++ +++G V +D    +K   ++  GQV+++   
Sbjct: 11  ITATQTGQRLDQTLADLFPDYSRTRIKEWIQAGWVYIDGTVSIKPREKVLEGQVIQV--- 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                 +++E K    +++L          ++YED  I V NK AG+ V  G+G      
Sbjct: 68  ---EATLVEETKAKAQAIDLD---------IVYEDDHILVINKQAGLVVHPGAGNSDGTL 115

Query: 129 IDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L    +     +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 MNALLHHCPNIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G          +  + +      ++ VV         A++H++V + F +    L ++ 
Sbjct: 176 QGSLI--SGGTVDEPIDRHPTKRTHMAVVH----NGKPAMTHYRVAEKF-RAHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            +GRTHQ+RVH  H+G  +VGD  Y    +       +         +  LHA  ++L H
Sbjct: 229 ESGRTHQIRVHMSHIGHTLVGDPVYGGRPRPPKGVSPEFFEIYMGFKRQALHAIRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           P     +   AP+P  MV    +L      N  I
Sbjct: 289 PYTCEIMSWQAPVPEDMVILTKALRQDTLENPSI 322


>gi|58617275|ref|YP_196474.1| SfhB protein homolog (peudouridylate synthase) [Ehrlichia
           ruminantium str. Gardel]
 gi|58416887|emb|CAI28000.1| SfhB protein homolog (peudouridylate synthase) [Ehrlichia
           ruminantium str. Gardel]
          Length = 324

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 84/332 (25%), Positives = 152/332 (45%), Gaps = 32/332 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVR 66
           + + ++N EEN RLD++      +I+   +Q+++++ ++ +  K VK NN I +   +  
Sbjct: 4   KKIFIQNGEENKRLDKFIALKL-NISRNRVQQLIQNNKIYLFNKIVKDNNHITKVNDIYY 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           I       N  I                  +   +LYED  I + NK  GI+V  G+G  
Sbjct: 63  INMPTQEHNCSITPNI-------------NIPITILYEDQDIIIINKEPGITVHPGAGTK 109

Query: 126 -AYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++G +  +        K  +P + HRLD++TSG++V+AR   +   L++    ++I
Sbjct: 110 DDTLVNGLIAHYGSTLSYIGKASRPGIVHRLDKDTSGLMVIARNEHSYYFLSDLLSKKQI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++VWGIP  K   I N +   +      +  V  ++     AI+ +  I  FA  
Sbjct: 170 KKEYLAVVWGIPNPKCNIIKNHI--DTKSNNKQMMTVTHSQNKGKLAITEYNTIQTFASI 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQNKLYLHA 292
              ++ + +TGRTHQ+RVH  ++G  I+GD KY  N        + +       +  LHA
Sbjct: 228 ATLVKCRIYTGRTHQIRVHMSYIGNSIIGDQKYGKNDSKIAKYAQQSTIINTLKRQALHA 287

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
             +   HP     ++  + +P  +    + L 
Sbjct: 288 HKLGFIHPTTNTYIEFNSDIPNDIQILLNELA 319


>gi|293390711|ref|ZP_06635045.1| ribosomal large subunit pseudouridine synthase D [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951245|gb|EFE01364.1| ribosomal large subunit pseudouridine synthase D [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 324

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 73/329 (22%), Positives = 136/329 (41%), Gaps = 35/329 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
            V++ +   RLD+     +P  +   L+  +    V V+        +++   + + I  
Sbjct: 9   TVQSHQMGQRLDQTLAELFPDYSRSCLKTWIEEDLVLVNGVVQNVPRSKVYGDEQIEITV 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I        E                +   ++YED  I V NKP  + V  G+G     
Sbjct: 69  EIEDETRFEPEN---------------IPLNIVYEDDDILVINKPKDLVVHPGAGNPSGT 113

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R+I + Y ++
Sbjct: 114 VLNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAV 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GI   K   +   + +                     A++H+++++ F + +  L ++
Sbjct: 174 ACGIM-TKGGMVDEPMARHPT-----KRTHMAVHPMGKPAVTHYRIMERF-RDYTRLRLR 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  LHA  + L 
Sbjct: 227 LETGRTHQIRVHMAHIAHPLLGDQTYGGRPRPPKNASEELMSVLRNFKRQALHAVMLRLQ 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HP  G  ++  APLP   V+   +L   Y
Sbjct: 287 HPISGEMMEWYAPLPEDFVELITALKADY 315


>gi|91775675|ref|YP_545431.1| pseudouridine synthase, RluD [Methylobacillus flagellatus KT]
 gi|91709662|gb|ABE49590.1| Pseudouridine synthase, RluD [Methylobacillus flagellatus KT]
          Length = 326

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 95/321 (29%), Positives = 155/321 (48%), Gaps = 16/321 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V  + ++   E  R+D +       +   ++ +ILRSG+VRV+ KRV  + ++  G  VR
Sbjct: 16  VNLLTIDEASEGQRVDNFLAKILKGVPKSHIYRILRSGEVRVNSKRVDSSCKLNLGDQVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PPV  A        +           +   +  +++ED  + V +KPAG +V GGSGI+
Sbjct: 76  VPPVRMAQPQAESVAR---------PQASRFEGAIIFEDEALLVIDKPAGFAVHGGSGIS 126

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L+       +   L HRLD+ETSG+L++A+ R A  +L ++ R  +  K Y  L
Sbjct: 127 RGVIEQLR-LERPHAKFLELVHRLDRETSGVLLLAKKRVALVNLHDAIRNNQTDKRYLVL 185

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   ++K  +   L K     G+    V+   + ++        +     +F  LE Q
Sbjct: 186 VHGKWTDQKRRVKLPLHKFVLPSGERRVAVQDGGQNSDT----IFYLRKPLGEFTLLEAQ 241

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
             TGRTHQLRV   H+G PI GD KY       +       +++LH+   +L HP  G +
Sbjct: 242 LVTGRTHQLRVQLSHLGFPIAGDDKYGDFALNKSLQKRGLKRMFLHSAETNLRHPVSGEK 301

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           L++ APLP  + K  + L  +
Sbjct: 302 LKLIAPLPDELNKFIEMLSVE 322


>gi|113971328|ref|YP_735121.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           MR-4]
 gi|114048565|ref|YP_739115.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           MR-7]
 gi|113886012|gb|ABI40064.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           MR-4]
 gi|113890007|gb|ABI44058.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           MR-7]
          Length = 323

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 142/325 (43%), Gaps = 35/325 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +  +RLD+     +P  +   +++ + S  V VD   V K   ++   Q + I   
Sbjct: 11  ISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVYVDGVMVNKPREKVFELQRIEINAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--H 128
           +    H   +   LD               ++YED  I V NK AG+ V  G+G A    
Sbjct: 71  LEEEVHAAAQAIELD---------------IVYEDDDILVINKQAGLVVHPGAGNADGTL 115

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L    + +   +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 MNALLHHCPNIEHVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        +   + +         H+   +      A++H++V + F +    L ++ 
Sbjct: 176 LGTM-TAGGTVDEPIGRHPT---KRTHMAVHHS--GKPAVTHYRVAEKF-RNHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            +GRTHQ+RVH  ++G  +VGD  Y    K    +  +         +  LHA  ++L H
Sbjct: 229 ESGRTHQIRVHMAYIGHVLVGDPVYGGRPKPPKAASPEFFEILKNFKRQALHAVRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P     +  TAP+P  MV    +L 
Sbjct: 289 PVTCEIMSWTAPIPEDMVILTKALR 313


>gi|315658516|ref|ZP_07911388.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           lugdunensis M23590]
 gi|315496845|gb|EFU85168.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           lugdunensis M23590]
          Length = 305

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 75/329 (22%), Positives = 145/329 (44%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT     + +      R+D+   ++    +   +Q  ++   V V+ K +K N++++   
Sbjct: 1   MTTHSIEITDTRHTGQRIDKLLSDYNHDWSRSQIQDWIKHELVIVNGKAIKANHKVKLHD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I            E++++D+ +      + L   + YED  + +  KP G+ V    
Sbjct: 61  SIVIT-----------EKEVVDADI----QPENLNLDIYYEDKDVAIVYKPKGMVVHPSP 105

Query: 124 GI--AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L +    +
Sbjct: 106 GHYSGTLVNGLMYQIKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRSLVDQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +++ Y +LV G   +    +   + +        + VV         A++HF V++ F 
Sbjct: 166 SVKRKYTALVHGNIPHDYGTVDAPIGRNKK-DRQSMDVVD----DGKDAVTHFNVLEHF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E Q  TGRTHQ+RVH  ++G P+VGD KY      +          LHA  +  
Sbjct: 220 KDYTLIECQLETGRTHQIRVHMKYIGYPLVGDPKYGPKKTLD-----IGGQALHAGLIGF 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  ++  A LP    +  + +  +
Sbjct: 275 EHPVTGEYIERQAALPDAFEQLLEDIRKR 303


>gi|149187050|ref|ZP_01865357.1| pseudouridine synthase D large subunit [Erythrobacter sp. SD-21]
 gi|148829339|gb|EDL47783.1| pseudouridine synthase D large subunit [Erythrobacter sp. SD-21]
          Length = 318

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 72/331 (21%), Positives = 134/331 (40%), Gaps = 31/331 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M+  + +         RLD+   +    ++   ++ ++  G V +  K  +  + ++  G
Sbjct: 1   MSSAEVLTGTLSSAG-RLDKALADA-TGLSRERVKGLIADGVVEIAGKAARSASAKVAEG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           +   I                L     L   +  +   +++ED+ + V NKPAG+ V   
Sbjct: 59  ERYFI---------------ALPPPEPLETVAQDIPLDVVFEDAYLLVVNKPAGMVVHPA 103

Query: 123 SG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +G      ++  L              +P + HR+D++TSG+LVVA++ AA + L + F 
Sbjct: 104 AGNPDGTLVNALLHHCAGRLSGINGVARPGIVHRIDKDTSGLLVVAKSDAAHEGLAKQFA 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I + Y +   G P      ++  + +        + V+  +     +A++H++ +  
Sbjct: 164 DHSITRRYLAACAGHPNPPSGTVSGRIGRSDR-DRKKMAVLPDDSTRGKHAVTHYETVRR 222

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPIQNKLYLHA 292
                  +E +  TGRTHQ+RVH   +G  ++GD  Y    K       S    +  LHA
Sbjct: 223 L-NHAALIECRLETGRTHQVRVHCASIGHALLGDPVYGRTPKPLRATLESLDFQRQALHA 281

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +   HP  G  L   A LP  M +    L
Sbjct: 282 ARLGFIHPISGESLDFCAELPPDMSELMREL 312


>gi|254995115|ref|ZP_05277305.1| sfhb-like protein [Anaplasma marginale str. Mississippi]
          Length = 328

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 143/334 (42%), Gaps = 34/334 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSG 62
           M  V  V V  +++  R+D+        I+    Q ++  GQV +  + +  N    ++G
Sbjct: 1   MKCVHEVCVTKEDDQQRIDKLISCAL-EISRNRAQGLIAGGQVTISGRVINNNSYLTKTG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V  I   +   + +     I                 ++YED  + V +K   I+V  G
Sbjct: 60  DVYTIVTAVQKPSTLSPNYDI--------------DLKVVYEDHDVIVIDKDPYIAVHPG 105

Query: 123 SGIAYHI--DGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +GI +H   +  L  +           +P + HRLD++TSG++V A+T  A   L+E   
Sbjct: 106 NGIEHHTITNALLARFGAGLQSVGSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELA 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +  +K Y ++ WGIP  K+  I   +     +    + +++    G   A + ++V   
Sbjct: 166 NQGFKKEYLAVAWGIPCPKRGVIHTNI----RVKRSDITMMEAANSGGKPAKTEYEVEQE 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLY 289
             +    +    HTGRTHQ+RVH  H+G  IVGD KY  N K    S +        +  
Sbjct: 222 LGEVASLIRCTLHTGRTHQIRVHMSHIGHSIVGDQKYGKNCKKCMRSGVPPDVKNFRRQA 281

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           LHA  +   HP  G+ ++ T+     + +   +L
Sbjct: 282 LHASLLGFRHPSTGKYIEFTSKPADDIQQLISAL 315


>gi|260775124|ref|ZP_05884022.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260608825|gb|EEX34987.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 325

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 143/326 (43%), Gaps = 35/326 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V+V+ + + K   ++  G+++ +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLVDGKVQVNGEVITKPRTKVMGGEIITLQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  I V NKP    V  G+G     
Sbjct: 70  ELEDEERW---------------EAQDIPLDIVYEDDDIMVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + D ++  +  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLHHYPDIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S         +         A++H++V + F ++   + ++
Sbjct: 175 AIGRM-TAGGRVEQPIGRHST-----KRTLMAVSPMGKPAVTHYRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDSAYGGRARIPSGASEELAEMIRKFDRQALHAVMLKFD 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  L+  AP+P  MV+  ++L 
Sbjct: 288 HPVTGEELEFHAPVPDDMVEMAEALR 313


>gi|258620374|ref|ZP_05715412.1| Ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           VM573]
 gi|262172216|ref|ZP_06039894.1| ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           MB-451]
 gi|258587253|gb|EEW11964.1| Ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           VM573]
 gi|261893292|gb|EEY39278.1| ribosomal large subunit pseudouridine synthase D [Vibrio mimicus
           MB-451]
          Length = 324

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 77/333 (23%), Positives = 144/333 (43%), Gaps = 37/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +   RLD+     +   +   L++ L  G++ V+ + V K   ++  G+V+ +  
Sbjct: 10  TVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVVTKPRTKVMGGEVIVVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  L   ++YED  I V NKP    V  G+G A   
Sbjct: 70  ELEDEQRW---------------EAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  + + R + + Y ++
Sbjct: 115 VLNALLFHFPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + + S         +        +A++H++V + F ++   L ++
Sbjct: 175 VIGTM-TAGGMIDKPIGRHST-----KRTLMSVSPMGKHAVTHYRVAEHF-REHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGASEELTAMIRNFDRQALHAVMLKFE 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNL 330
           HP  G  L+  AP+P  MV    +L  + D  L
Sbjct: 288 HPITGEELEFHAPVPDDMVTM--TLALREDSKL 318


>gi|330831468|ref|YP_004394420.1| ribosomal large subunit pseudouridine synthase D [Aeromonas veronii
           B565]
 gi|328806604|gb|AEB51803.1| Ribosomal large subunit pseudouridine synthase D [Aeromonas veronii
           B565]
          Length = 326

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 74/325 (22%), Positives = 140/325 (43%), Gaps = 35/325 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72
           + +   RLD+     +P  +   +++ +   +V +D +       +I +GQ V +   + 
Sbjct: 13  DHQFGQRLDQALAELFPDYSRTRIKEWILQDRVTLDGQVANTPREKILAGQQVHVNVELE 72

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--D 130
                                +  ++  ++YED  I V +KPAG+ V  G+G       +
Sbjct: 73  DDTRW---------------DAQDIELNIVYEDEHILVIDKPAGLVVHPGAGTPDGTILN 117

Query: 131 GFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             L  +   ++  +  + HRLD++T+G++VVA+T  A  HL E+ + R+I + Y ++  G
Sbjct: 118 ALLHRYPGIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQARQITREYEAIAIG 177

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   +   + +          V          +++H++V + F +    L ++  T
Sbjct: 178 HM-TAGGTVDAPIGRHPTQRTHMAVV-----PNGRPSVTHYRVHEKF-RGHTRLRLRLET 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPE 301
           GRTHQ+RVH  H+  P+VGD  Y    +    +  +        N+  LHA  + L HP 
Sbjct: 231 GRTHQIRVHMAHIKHPLVGDPAYGGRLRPLRNATPELTQALRNFNRQALHATMLQLAHPI 290

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            G  +Q  +  P  MV+  + L   
Sbjct: 291 TGEVMQWHSATPQDMVELMEVLRAD 315


>gi|288940534|ref|YP_003442774.1| RluA family pseudouridine synthase [Allochromatium vinosum DSM 180]
 gi|288895906|gb|ADC61742.1| pseudouridine synthase, RluA family [Allochromatium vinosum DSM
           180]
          Length = 326

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 88/337 (26%), Positives = 147/337 (43%), Gaps = 38/337 (11%)

Query: 2   SLMTYV--QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           SL T +  + + VE D    RLDR      P  +   LQ+ + +GQV VD +  +  +++
Sbjct: 3   SLSTEIIRRSLRVEPDLAGGRLDRVLAQLLPEFSRGRLQQWIEAGQVLVDDRPCRVRDKV 62

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G+ +RI            E  ++D           +   L+YED  + V +KPAG+ V
Sbjct: 63  WGGESIRIE----------AELAVVDE-----HRPQAIALDLVYEDEHLLVIDKPAGLVV 107

Query: 120 QGGSG--IAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +G      ++  L    + +   +  + HRLD++T+G++VVART  A   L E  + 
Sbjct: 108 HPAAGNPDGTLLNALLHHAPELATLPRAGIVHRLDKDTTGLMVVARTLQAHCALVEQLQR 167

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDC 235
           R + + Y +LV G        +      ++ IG      VK    G    AI+H++V++ 
Sbjct: 168 RIVHREYRALVLG-------TLVAGGRVEAPIGRHPTQRVKMAVVGNGREAITHYRVLES 220

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NK 287
           +      L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       +         +
Sbjct: 221 YP-GHTLLAVELETGRTHQIRVHMTHIHHPLVGDTTYGGRPRPPRGCRPELAAALQSFPR 279

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
             LHA  + L HP  G  +    P+ + +    D   
Sbjct: 280 QALHAIRLGLIHPATGAEMHWEVPMASDLEALLDLFR 316


>gi|145589104|ref|YP_001155701.1| RluA family pseudouridine synthase [Polynucleobacter necessarius
           subsp. asymbioticus QLW-P1DMWA-1]
 gi|145047510|gb|ABP34137.1| ribosomal large subunit pseudouridine synthase D [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 318

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 83/319 (26%), Positives = 134/319 (42%), Gaps = 32/319 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD+      P  +   L+  + +G V VD K  K    ++ G+ V++ P       
Sbjct: 2   AGERLDKVLAGSLPDYSRNRLKAWVEAGAVMVDGKVTKARYLLRGGESVKVFPQ------ 55

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
                   +         + +   ++YED  I V NKP G+ V   +G      ++G L 
Sbjct: 56  --------EMPEQFAFSPENIPLEVVYEDDSIIVINKPPGLVVHPAAGNWSGTLLNGLLH 107

Query: 135 SWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            + + K   +  + HRLD++TSG++VVART  A   L    + R + + Y + VWG   +
Sbjct: 108 RFPELKSLPRAGIVHRLDKDTSGLMVVARTAHAQTALVRQLQERTVGRRYLAWVWGDAPS 167

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDC---FAQKFCWLEMQPH 248
           + + +A+       +G D    +K          A + F+ I            LE +  
Sbjct: 168 QGKVLAS-------VGRDQRDRLKMAAGSPQGKPAATLFRRIAKGNVENAPVALLECRLE 220

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-- 306
           TGRTHQ+RVH   +G P+VGD  Y     G   +   ++  LHA  + L HP    LQ  
Sbjct: 221 TGRTHQIRVHLESLGFPLVGDPVYRKKAPGVAKALSFDRQALHAFALSLQHPVTQELQTW 280

Query: 307 ITAPLPAHMVKTWDSLGFK 325
              P P  ++     +G  
Sbjct: 281 FRLP-PVDLINLLPQVGMS 298


>gi|163750158|ref|ZP_02157401.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Shewanella benthica KT99]
 gi|161330215|gb|EDQ01197.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Shewanella benthica KT99]
          Length = 324

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 76/331 (22%), Positives = 136/331 (41%), Gaps = 35/331 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +   RLD+     +P  +   +++ +  G V +D     K   ++  GQ + +   
Sbjct: 11  ITATQTGQRLDQTLAELFPDYSRTRIKEWILDGSVTIDGNVSNKPREKVLEGQEIEVGAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           +                   T  +  +   ++YED  I V NK AG+ V  G+G      
Sbjct: 71  LVE---------------ETTAKAQAIDLNIVYEDDHILVINKQAGLVVHPGAGNSDGTL 115

Query: 129 IDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L          +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 LNALLHHCPGIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        +   + +          V+         A++HF+V + F +    L ++ 
Sbjct: 176 MGSL-ISGGTVDEPIDRHPTKRTHMAVVLS-----GKPAMTHFRVAEKF-RAHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            +GRTHQ+RVH  H+G  +VGD  Y    +       +         +  LHA  ++L H
Sbjct: 229 ESGRTHQIRVHMAHLGHTLVGDPVYGGRPRPPKAVTPEFFEIFMGFKRQALHAIRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           P     +   AP+P  MV    +L    + N
Sbjct: 289 PYTCEIMSWQAPVPEDMVILTKALRKDTEDN 319


>gi|90422129|ref|YP_530499.1| pseudouridine synthase RluD [Rhodopseudomonas palustris BisB18]
 gi|90104143|gb|ABD86180.1| ribosomal large subunit pseudouridine synthase D [Rhodopseudomonas
           palustris BisB18]
          Length = 391

 Score =  241 bits (616), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 85/351 (24%), Positives = 149/351 (42%), Gaps = 59/351 (16%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-----------N 57
            V V  DE  +RLDR      P ++   L+ ++ +GQVR+  +    +            
Sbjct: 59  EVTVAGDEGAVRLDRVLALRAPELSRSRLKALILAGQVRL--RPADASAALPTPLRDPAY 116

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
            +++G  + I                +  +V      + +   ++YED  I V +KP G+
Sbjct: 117 HVEAGDTITID---------------VPPAVAAEPAGEAIALDIVYEDDDIIVIDKPKGL 161

Query: 118 SVQGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHL 170
            V   +G      ++  +    +S       ++P + HRLD++T+G++VVA+   A + L
Sbjct: 162 VVHPAAGHETGTLVNALIAHCGNSLSGIGGVRRPGIVHRLDKDTTGLMVVAKNDKAHKSL 221

Query: 171 TESFRMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           +E F        +++ Y + +WG P      +   +  +     + + V      G   A
Sbjct: 222 SEQFADHGRTNEMRRGYKAFIWGAPNRPHGTVDAPI-DRHPFAREKMAVRD----GGREA 276

Query: 227 ISHFKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           ++H++V D F  +        L  Q  TGRTHQ+RVH  H+G P++GD  Y  +FK    
Sbjct: 277 VTHWEVEDTFLGRGGKPVVSLLACQLETGRTHQIRVHLAHIGHPLLGDGVYGPHFKTKAN 336

Query: 282 ---------SPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
                         +  LHA  + L HP  G + + TA LPA +     +L
Sbjct: 337 ALNLPAQAALAALGRQALHAYLLALEHPVSGEILEWTAELPADLALLRTAL 387


>gi|254509457|ref|ZP_05121534.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus 16]
 gi|219547619|gb|EED24667.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus 16]
          Length = 326

 Score =  241 bits (616), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 71/327 (21%), Positives = 143/327 (43%), Gaps = 36/327 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L +G+V+V+ + V K   ++  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTKVMGGEEIILQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  I V NKP G  V  G+G     
Sbjct: 70  ELEDEERW---------------EAQDIPLDIVYEDDDILVINKPRGFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES-FRMRRIQKIYWS 185
             +  L  + + ++  +  + HRLD++T+G++VVA+T  A   L  +  + R   + Y +
Sbjct: 115 VLNALLHHYPNIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFVREYEA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G        I   + + S         +         A++H++V + F ++   + +
Sbjct: 175 IAIGRM-TAGGRIEQPIGRHST-----KRTLMAVSPMGKPAVTHYRVAEHF-REHTRIRL 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDL 297
           +  TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +  
Sbjct: 228 RLETGRTHQIRVHMSYLQHPLLGDSAYGGRARIPSGATEELAEKIRSFDRQALHAVMLKF 287

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLG 323
            HP  G  ++  AP+P  MV+  ++L 
Sbjct: 288 EHPITGEEVEFHAPVPDDMVEMAEALR 314


>gi|259415714|ref|ZP_05739634.1| ribosomal large subunit pseudouridine synthase D [Silicibacter sp.
           TrichCH4B]
 gi|259347153|gb|EEW58930.1| ribosomal large subunit pseudouridine synthase D [Silicibacter sp.
           TrichCH4B]
          Length = 345

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 89/355 (25%), Positives = 142/355 (40%), Gaps = 50/355 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M   +   V  D    RLD+      P    ++   L +++ SG V VD         R+
Sbjct: 1   MASRRIEFVIADNPPKRLDKAIARDVPEEANLSRTRLARLIESGGVEVDGAVASDAKARV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  + I       +HI  E   LD               ++YED+ + V NKPAG+ V
Sbjct: 61  LEGAQIVITVEDAEESHIGPEDIALD---------------VIYEDADLIVINKPAGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L             ++P + HR+D+ETSG+LVVA++ AA Q L  
Sbjct: 106 HPAPGSPSGTLVNALLHHCGADLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F    +++ Y ++ +G+P      +           N L   + +        +Q    
Sbjct: 166 QFERHSVERYYQAVCYGVPDANDPRLRGVRGASFEPGNILKLTTQLARHKTDRQRQAVLF 225

Query: 221 KGANYAISHFKVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK- 277
           +G  +A++  ++I+ F        +E    TGRTHQ+RVH  H G  ++GD  Y    K 
Sbjct: 226 EGGRHAVTRARIIEAFGAPAAASLVECWLETGRTHQIRVHMAHAGHGLLGDPTYGGKRKI 285

Query: 278 --------GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                   G       ++  LHA  +   HP  G  ++  APLP  M     +L 
Sbjct: 286 SPKALSAAGLVAINNFHRQALHAAVLGFEHPVSGEMMRFEAPLPEDMQALIAALR 340


>gi|301328545|ref|ZP_07221606.1| pseudouridine synthase, RluA family [Escherichia coli MS 78-1]
 gi|300844937|gb|EFK72697.1| pseudouridine synthase, RluA family [Escherichia coli MS 78-1]
          Length = 283

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 98/292 (33%), Positives = 159/292 (54%), Gaps = 16/292 (5%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
            + +ILR G+VRV+KKR+K   ++++G  VRIPPV       + E++    S +L K + 
Sbjct: 1   MIYRILRKGEVRVNKKRIKPEYKLEAGDEVRIPPVR------VAEREEEAVSPHLQKVA- 53

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L  ++LYED  I V NKP+G +V GGSG+++ +   L++ +  + +   L HRLD++TS
Sbjct: 54  ALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTS 112

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+VA+ R+A + L E  R + +QK Y +LV G  ++  + +   LLK     G+ +  
Sbjct: 113 GVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVR 172

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
           V Q       + + FKV + +A     +   P TGRTHQ+RVH  + G PI  D +Y   
Sbjct: 173 VSQE---GKPSETRFKVEERYA-FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDR 228

Query: 275 --NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             + +        N+L+LHA  +   HP  G  ++I AP+   + +    L 
Sbjct: 229 EFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKLR 280


>gi|30249427|ref|NP_841497.1| rluC; ribosomal large subunit pseudouridine synthase C
           [Nitrosomonas europaea ATCC 19718]
 gi|30138790|emb|CAD85367.1| rluC; ribosomal large subunit pseudouridine synthase C
           [Nitrosomonas europaea ATCC 19718]
          Length = 343

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 103/324 (31%), Positives = 159/324 (49%), Gaps = 23/324 (7%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++   E+ R+D +       I   ++ ++LRSGQVRV+ KR+  + R+Q G  VRIPPVI
Sbjct: 29  IDETAESQRIDNFLIRSLKGIPRRHIYQLLRSGQVRVNSKRIDASYRLQLGDKVRIPPVI 88

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            ++             V+        +  +LY+D  + V +KPAGI+V GGSGI++ +  
Sbjct: 89  RSVK-----------PVSSQGVYRTDRFNILYQDDHLLVIDKPAGIAVHGGSGISHGVIE 137

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L+       +   L HRLD+ETSGIL++AR R +   L    R   ++K Y +LV G  
Sbjct: 138 QLRGQ-HPDWKFLELVHRLDRETSGILLLARKRQSLLELHRQIREGTVEKHYLTLVRGKW 196

Query: 192 KNKKECIANWLLKKSHIGGDYVHVV---KQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           KN  + +   L K     G+    V   + ++  A  A + F  +    + F  L+ +  
Sbjct: 197 KNSVQNVRLPLNKYLTAAGERRVAVAAGRNDQDKAQQAHTLF-TLQKAWEDFSLLDAELK 255

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           TGRTHQ+RVH  H+G PI GD KY          K +    +  +++LHA      HP  
Sbjct: 256 TGRTHQIRVHLAHLGFPIAGDDKYGDFGLNKQLQKDDGKGQVLRRMFLHASAFTCTHPVT 315

Query: 303 GR-LQITAPLPAHMVKTWDSLGFK 325
           G  L++ APLP  +     +L   
Sbjct: 316 GDLLRLEAPLPDELRVFLRNLDLN 339


>gi|90417173|ref|ZP_01225100.1| Pseudouridine synthase, RluD [marine gamma proteobacterium
           HTCC2207]
 gi|90330949|gb|EAS46210.1| Pseudouridine synthase, RluD [marine gamma proteobacterium
           HTCC2207]
          Length = 324

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 132/324 (40%), Gaps = 34/324 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V + +   RLD+     +   +   LQ  ++SG++ VD ++     ++  G+ + +   
Sbjct: 20  TVSSADCGRRLDQIAAELFSDYSRSRLQLWIKSGELTVDGQQQPPKFKLLGGETIAVSAQ 79

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           + A                    ++ +   +++ED  I V NKP    V   +G      
Sbjct: 80  LKAEGDW---------------QAEDIPLNIVFEDEHIIVINKPTNFVVHPAAGNREGTL 124

Query: 130 -DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L      K   +  + HRLD++T+G++VVA+T AA   L    + R + + Y S+V
Sbjct: 125 LNALLFHCPQLKSVPRAGIVHRLDKDTTGLMVVAKTLAAHTDLVAQLQARTVSREYESVV 184

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+       +   + +          V     +    A +H+KV+  F     ++ ++ 
Sbjct: 185 SGVMTG-GGLVDQPIGRHPKQ-----RVKMAVVRDGKEARTHYKVVKRF-DGHTYIRLKL 237

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFK--------GNFTSPIQNKLYLHARYMDLPH 299
            TGRTHQ+RVH   +  PIVGD  Y   F+           +     +  LHAR + L H
Sbjct: 238 ETGRTHQIRVHMASIKYPIVGDDTYGGRFRIHKGVSDQLRDSLQYFGRQALHARALGLVH 297

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G  +     LP  M     +L
Sbjct: 298 PASGEYVNWETELPEDMQNLLLAL 321


>gi|145297342|ref|YP_001140183.1| ribosomal large subunit pseudouridine synthase D [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142850114|gb|ABO88435.1| ribosomal large subunit pseudouridine synthase D [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 326

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 73/325 (22%), Positives = 140/325 (43%), Gaps = 35/325 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72
           + +   RLD+     +P  +   +++ +   +V +D +       ++ +GQ V +   + 
Sbjct: 13  DHQFGQRLDQALAELFPDYSRTRIKEWILQDRVTLDGQVANTPREKVLAGQQVHVDVELE 72

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--D 130
                                +  +   ++YED  I V +KPAG+ V  G+G       +
Sbjct: 73  DDTRW---------------DAQDIALNIVYEDEHILVIDKPAGLVVHPGAGTPDGTILN 117

Query: 131 GFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             L  + D ++  +  + HRLD++T+G++VVA+T  A  HL E+ + R+I + Y ++  G
Sbjct: 118 ALLHRYPDIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQARQITREYEAIAIG 177

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   +   + +          V          +++H++V + F +    L ++  T
Sbjct: 178 HM-TAGGTVDAPIGRHPTQRTHMAVV-----PNGRPSVTHYRVHEKF-RGHTRLRLRLET 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPE 301
           GRTHQ+RVH  H+  P+VGD  Y    +    +  +        N+  LHA  + L HP 
Sbjct: 231 GRTHQIRVHMSHIKHPLVGDPAYGGRLRPLRNATPELTLALRNFNRQALHATMLQLAHPI 290

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            G  +Q  +P P  M+   + +   
Sbjct: 291 TGEVMQWHSPTPQDMLDLMEVMRAD 315


>gi|323136929|ref|ZP_08072009.1| pseudouridine synthase, RluA family [Methylocystis sp. ATCC 49242]
 gi|322397690|gb|EFY00212.1| pseudouridine synthase, RluA family [Methylocystis sp. ATCC 49242]
          Length = 339

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 88/342 (25%), Positives = 147/342 (42%), Gaps = 51/342 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYP----HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
            +V  +    RLDR+          H++   ++ ++ SG+V +    ++    ++ +G  
Sbjct: 18  FLVAPEAAGARLDRFLAERPEIVDAHLSRSRIKALIESGRVSLRGAAIRDPAKKLAAGDA 77

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V +            E+  LD               ++YED+ + V +KPAG+ V   SG
Sbjct: 78  VSLDVPPPEPAEPQAEEIALD---------------IVYEDAHLIVIDKPAGLVVHPASG 122

Query: 125 IAYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              H  G L + + +            +KP + HR+D++T+G+LVVA+T AA   L+  F
Sbjct: 123 ---HESGTLVNALIAHCGESLSGVGGVKKPGIVHRIDKDTTGLLVVAKTDAAHHGLSRLF 179

Query: 175 RMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
                   + + Y + VWG+P      I   L + S I  + + VV   E     AI+H+
Sbjct: 180 ADHGRTLSLTREYLAFVWGVPDRAHGTIETSLGRHS-IQREKMAVV--PEARGREAITHW 236

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFT 281
           + +  +      +  Q  TGRTHQ+RVH  H+G P++GD  Y A FK             
Sbjct: 237 EKVADYG-VASLVRCQLETGRTHQIRVHMAHIGHPLIGDSTYGAGFKTKVAKLPEAARAA 295

Query: 282 SPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                +  LHA  +   HP  G  +  T+ LP  +     +L
Sbjct: 296 VEKLGRQALHAATLGFEHPITGEEMMFTSELPDDLAALMAAL 337


>gi|254467318|ref|ZP_05080729.1| ribosomal large subunit pseudouridine synthase D [Rhodobacterales
           bacterium Y4I]
 gi|206688226|gb|EDZ48708.1| ribosomal large subunit pseudouridine synthase D [Rhodobacterales
           bacterium Y4I]
          Length = 341

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 88/352 (25%), Positives = 150/352 (42%), Gaps = 52/352 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           +++V+ EN     RLD+      P    ++   L +++  G + VD   V+     + +G
Sbjct: 6   IEFVIAEN--PPKRLDKAVSRDVPEEAALSRTRLARLIGEGALTVDGAVVQDPKANVAAG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V+ I       +HI  E   L+               +++ED  + V NKPAG+ V   
Sbjct: 64  AVIAIEVEEAEDSHIGPEDIPLE---------------IVFEDDDLIVINKPAGMVVHPA 108

Query: 123 SGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G      ++  L  +  +       ++P + HR+D+ETSG+LVVA++ AA Q L   F 
Sbjct: 109 PGSPSGTLVNALLHHFGGNLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQFE 168

Query: 176 MRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE--KGA 223
              +++ Y ++ +G+P      +           N L   +H+        +Q    +G 
Sbjct: 169 KHTVERYYQAICYGVPDGNDPRLRGVKGASFEPGNILKLTTHLARHKTDRQRQAVLFQGG 228

Query: 224 NYAISHFKVIDCFAQKFC--WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            +A++  ++ + F    C   +E    TGRTHQ+RVH  H G  +VGD  Y    K    
Sbjct: 229 RHAVTRARICESFGNPPCAALIECWLETGRTHQIRVHMAHAGHSLVGDPTYGGRRKLPAK 288

Query: 282 SPIQ---------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +  +          +  LHA  +   HP  G  L+  APLP  M +   +L 
Sbjct: 289 ALSEEAQEAVRAFPRQALHAAVLGFGHPVSGEPLRFEAPLPQDMAELLAALR 340


>gi|261250364|ref|ZP_05942940.1| ribosomal large subunit pseudouridine synthase D [Vibrio orientalis
           CIP 102891]
 gi|260939480|gb|EEX95466.1| ribosomal large subunit pseudouridine synthase D [Vibrio orientalis
           CIP 102891]
          Length = 326

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 69/327 (21%), Positives = 142/327 (43%), Gaps = 36/327 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V+V+ + + K   ++  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVKVNGEVISKPRTKVMGGEEIILQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  + V NKP G  V  G+G     
Sbjct: 70  ELEDEERW---------------EAQDIPLDIVYEDDDLLVINKPRGFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES-FRMRRIQKIYWS 185
             +  L  + + ++  +  + HRLD++T+G++VVA+T  A   L  +  + R   + Y +
Sbjct: 115 VLNALLHHYPNIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFVREYEA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G        +   + + S         +         AI+H++V + F ++   + +
Sbjct: 175 IAIGRM-TAGGRVEQPIGRHST-----KRTLMAVTPTGKPAITHYRVAEHF-REHTRIRL 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDL 297
           +  TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +  
Sbjct: 228 RLETGRTHQIRVHMSYLQHPLLGDTAYGGRARIPSGASEELANHIRSFDRQALHAVMLKF 287

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLG 323
            HP  G  ++  AP+P  MV+  ++L 
Sbjct: 288 EHPITGEEVEFHAPVPDDMVEMAEALR 314


>gi|163738662|ref|ZP_02146076.1| riboflavin synthase subunit alpha [Phaeobacter gallaeciensis BS107]
 gi|161387990|gb|EDQ12345.1| riboflavin synthase subunit alpha [Phaeobacter gallaeciensis BS107]
          Length = 344

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 87/355 (24%), Positives = 146/355 (41%), Gaps = 50/355 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M   +   V  +    RLD+      P    ++   L +++ +GQ++V+   V     ++
Sbjct: 1   MARRRIEFVIAENPPKRLDKAVSRDVPEEATLSRTRLARLIEAGQLQVNGTVVSDAKAKV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G ++ I       +HI  E   L+               ++YED  + V NKP G+ V
Sbjct: 61  DEGALIEITIEEAEDSHIGPEDIPLE---------------VIYEDDDLIVINKPTGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    D+       ++P + HR+D+ETSG+LVVA++  A Q L  
Sbjct: 106 HPAPGTPSGTLVNALLHHCGDNLSGVGGVKRPGIVHRIDKETSGLLVVAKSDVAHQGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F    +++ Y ++ +G+P      +           N L   + +        +Q    
Sbjct: 166 QFEKHTVERYYRAICYGVPDANDPRLRGVKGTSFEPGNILKLTTQLARHKTDRQRQAVLF 225

Query: 221 KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +G  +AI+  +++D F        +E    TGRTHQ+RVH  H G  +VGD  Y    K 
Sbjct: 226 QGGRHAITRARIVDSFGTPPVVALIECWLETGRTHQIRVHMAHGGHGLVGDPVYGGKRKL 285

Query: 279 NFTSPIQN---------KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              S  ++         +  LHA  +   HP  G  ++  APLP  M      LG
Sbjct: 286 AAKSLPEDTAAAIQAFPRQALHAAVLGFIHPVTGDAMRFEAPLPEDMAHLLQKLG 340


>gi|27363948|ref|NP_759476.1| 23S rRNA pseudouridine synthase D [Vibrio vulnificus CMCP6]
 gi|320157325|ref|YP_004189704.1| ribosomal large subunit pseudouridine synthase D [Vibrio vulnificus
           MO6-24/O]
 gi|34395776|sp|Q8DEV0|RLUD_VIBVU RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|27360065|gb|AAO09003.1| Ribosomal large subunit pseudouridine synthase D [Vibrio vulnificus
           CMCP6]
 gi|319932637|gb|ADV87501.1| ribosomal large subunit pseudouridine synthase D [Vibrio vulnificus
           MO6-24/O]
          Length = 325

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 72/331 (21%), Positives = 141/331 (42%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V VD   V K   ++  G+V+ +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVTVDGNVVTKPRTKVMGGEVITV-- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                        + +    +   +  +   ++YED  I V NKP    V  G+G     
Sbjct: 68  -------------LAELEDEVRWEAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L    + ++  +  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLFHCPEVAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + +         +         A++HF+V + F ++   + ++
Sbjct: 175 AIGRM-TAGGKVDKPIGRHAT-----KRTLMAVSPMGKPAVTHFRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +           ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDAAYGGRARIPAGASEDVTAMIRNFDRQALHAVMLRFE 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  ++  AP+P  MV+  ++L      
Sbjct: 288 HPITGEEMEFHAPVPDDMVELTETLRRDAQE 318


>gi|27382447|ref|NP_773976.1| pseudouridine synthase-like protein [Bradyrhizobium japonicum USDA
           110]
 gi|27355618|dbj|BAC52601.1| blr7336 [Bradyrhizobium japonicum USDA 110]
          Length = 335

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 82/344 (23%), Positives = 146/344 (42%), Gaps = 53/344 (15%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
            VVV  DE + RLDR      P ++   L+ ++ +G V +    V+     +  G  + I
Sbjct: 11  EVVVAGDEGSARLDRVLAARLPDLSRSRLKALILAGAVSLKASAVRDPAYHVSHGDTIII 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           +  +       + +   +++ED  I V NKP G+ V   +G   
Sbjct: 71  D---------------VPEAAPAEPKGEEIALDIVFEDDDIIVINKPRGLVVHPAAG--- 112

Query: 128 HIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           H  G L + + +            ++P + HRLD++T+G++VVA+   A   L+  F   
Sbjct: 113 HETGTLVNALIAHCGSTLSGIGGVRRPGIVHRLDKDTTGLMVVAKNDLAHASLSAQFADH 172

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                +++ Y +  WG+P   +  +   +  +     + + V     +G   A++H++++
Sbjct: 173 GRTGAMRRGYMAFAWGVPGRHRGTVDAPI-DRHPYAREKMAVR----QGGREAVTHWEIL 227

Query: 234 DCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI---- 284
           + F  +        L  +  TGRTHQ+RVH  H+G P++GD  Y  +FK           
Sbjct: 228 ESFPGRDGKPIAALLACELETGRTHQIRVHLAHIGHPLMGDAVYGPHFKTKANQLAPESQ 287

Query: 285 -----QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                  +  LHA  + L HP  G  L   APLP  ++    +L
Sbjct: 288 AALATLGRQALHAYLLVLEHPRTGELLHWEAPLPEDLLLLRSAL 331


>gi|323491101|ref|ZP_08096291.1| 23S rRNA pseudouridine synthase D [Vibrio brasiliensis LMG 20546]
 gi|323314648|gb|EGA67722.1| 23S rRNA pseudouridine synthase D [Vibrio brasiliensis LMG 20546]
          Length = 326

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 71/327 (21%), Positives = 142/327 (43%), Gaps = 36/327 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V+V+ + V K   ++  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVQVNGEVVTKPRTKVMGGEEIILQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  I V NKP G  V  G+G     
Sbjct: 70  ELEDEERW---------------EAQDIPLDIVYEDDDILVINKPRGFIVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES-FRMRRIQKIYWS 185
             +  L  + + ++  +  + HRLD++T+G++VVA+T  A   L  +  + R   + Y +
Sbjct: 115 VLNALLHHYPNIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFTREYEA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G        I   + + S         +         A++H++V + F ++   + +
Sbjct: 175 IAIGRM-TAGGRIEQPIGRHST-----KRTLMAVSPMGKPAVTHYRVAEHF-REHTRIRL 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDL 297
           +  TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +  
Sbjct: 228 RLETGRTHQIRVHMSYLQHPLLGDSAYGGRARIPAGASEELATMIRQFDRQALHAVMLKF 287

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLG 323
            HP  G  ++  AP+P  MV+  ++L 
Sbjct: 288 EHPITGEEVEFHAPVPDDMVEMAEALR 314


>gi|90408473|ref|ZP_01216632.1| Ribosomal large subunit pseudouridine synthase D [Psychromonas sp.
           CNPT3]
 gi|90310405|gb|EAS38531.1| Ribosomal large subunit pseudouridine synthase D [Psychromonas sp.
           CNPT3]
          Length = 322

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 142/326 (43%), Gaps = 38/326 (11%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINAL 74
           +   RLD+     +P  +   +++ +    V++D   V +   ++ +GQ V +   +   
Sbjct: 15  QLGFRLDKALAALFPDYSRTRIKEWILDDLVKIDDVTVNRPREKVYTGQQVEVNATLED- 73

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGF 132
                          +  H   +   +++ED  I V NKPAG+ V  G+G       +  
Sbjct: 74  --------------EVVFHPQNIPLDIIFEDEHILVINKPAGLVVHPGAGNPDGTVLNAL 119

Query: 133 LKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L  + +  +  +  + HRLD++T+G++V+A+T  A  HL  S + R I + Y ++  G  
Sbjct: 120 LHHYPEIVEVPRAGIVHRLDKDTTGLMVIAKTVPAQTHLVTSLQAREITREYDAIAMG-- 177

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHT 249
                C       ++ IG D  + VK      G  +A++H++V + + +    L ++  T
Sbjct: 178 -----CFTAGGRVEAPIGRDKANRVKMAVATVGGKHAVTHYRVAEKY-RAHTRLRLRLET 231

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKG--------NFTSPIQNKLYLHARYMDLPHPE 301
           GRTHQ+RVH  H+G  + GD  Y    +           T     +  LHA  + L HP 
Sbjct: 232 GRTHQIRVHMSHIGHVLAGDPVYGGRPRPPKGASESLTTTLRAFKRQALHAIMLRLEHPI 291

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFKY 326
            G  ++  AP+P  M +    L    
Sbjct: 292 TGEIMEWHAPVPDDMKELAAVLRADA 317


>gi|332290082|ref|YP_004420934.1| 23S rRNA pseudouridine synthase D [Gallibacterium anatis UMN179]
 gi|330432978|gb|AEC18037.1| 23S rRNA pseudouridine synthase D [Gallibacterium anatis UMN179]
          Length = 324

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 77/337 (22%), Positives = 144/337 (42%), Gaps = 37/337 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+  +   RLD+     +P  +   ++  + +G V+VD K V     ++   + + +   
Sbjct: 10  VQPHQLGQRLDQTLAELFPEYSRSRIKTWIEAGLVQVDDKIVTVPKEKVFGTEQIIMQAE 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           I        +   LD               ++YED  I V NK   + V  G+G   +  
Sbjct: 70  IEEDTRFTPQNIPLD---------------IVYEDEHILVINKSKDLVVHPGAGNPDNTV 114

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  + + R+I + Y ++ 
Sbjct: 115 LNALLYHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIEAQTKLVRALQKRQITREYEAIA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI   K   +   + +                     A++H+++++ F + +  L ++ 
Sbjct: 175 SGIM-TKGGTVDQPMARHPT-----KRTHMAIHPLGKPAVTHYRIMERF-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  ++  P++GD  Y    K    +            +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAYIAHPLLGDQTYGGRPKPPKGASEALLEVLRQFQRQALHAIMLRLEH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
           P     ++  APLP   V+  ++L  K D  L+   L
Sbjct: 288 PISRELMEWYAPLPDDFVELVNAL--KTDYELHKDEL 322


>gi|226943601|ref|YP_002798674.1| Pseudouridine synthase, RluC [Azotobacter vinelandii DJ]
 gi|226718528|gb|ACO77699.1| Pseudouridine synthase, RluC [Azotobacter vinelandii DJ]
          Length = 278

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 98/289 (33%), Positives = 164/289 (56%), Gaps = 15/289 (5%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK-HS 94
            + +ILR G+VRV+K R+K   ++Q+G +VR+PP+  A           D  V L +   
Sbjct: 1   MIYRILRKGEVRVNKGRIKPEYKLQAGDLVRVPPLRLAER---------DEPVPLAQGLL 51

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           + L++ +++ED  + V NKPAGI+V GGSG+++ +   L+  +  + +   L HRLD++T
Sbjct: 52  ERLEAAIVHEDKSLIVLNKPAGIAVHGGSGLSHGVIEALRQ-LRPEARDLELVHRLDRDT 110

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L++A+ R+  +HL E+ R   + K Y +LV G   + ++ ++  L K +   G+ + 
Sbjct: 111 SGLLMIAKKRSMLRHLHEALRGDGVDKRYLALVRGAWPSARKQVSAPLQKNTLRSGERMV 170

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V   ++    A++ F+V+  F      +E +P TGRTHQ+RVHA H G PI GD KY  
Sbjct: 171 EV---DEEGREALTLFRVLRRFGDFATLVEAKPVTGRTHQIRVHARHAGHPIAGDAKYGD 227

Query: 275 N-FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
             F     +    +L+LHA  + +P PEGG L++ AP+     +  + L
Sbjct: 228 ETFTREIRALGGKRLFLHAYSLAVPLPEGGELRLEAPVDEMWAQALERL 276


>gi|182677345|ref|YP_001831491.1| RluA family pseudouridine synthase [Beijerinckia indica subsp.
           indica ATCC 9039]
 gi|182633228|gb|ACB94002.1| pseudouridine synthase, RluA family [Beijerinckia indica subsp.
           indica ATCC 9039]
          Length = 346

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 83/329 (25%), Positives = 150/329 (45%), Gaps = 48/329 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPH----INFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVV 65
           VV  +E   RLDR+           ++ + ++ ++  G V VD + R+  +  +++GQ++
Sbjct: 19  VVGAEEAGQRLDRFLAERTETGAAFLSRMRIKTLIEQGHVSVDGEARLTASASVRAGQII 78

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                +  +      +  L   ++YED+ + V +KPAG+ V   +G 
Sbjct: 79  EL---------------AVPPAKEAVPVAQDLPLNIVYEDAGLVVLDKPAGLVVHPAAGH 123

Query: 126 A--YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR- 177
           A    ++  +    +S       ++P + HRLD++TSG+LV A+T A  Q L   F    
Sbjct: 124 AQGTLVNALMAHCGESLSGIGGVKRPGIVHRLDKDTSGLLVAAKTDAVHQGLARLFADHG 183

Query: 178 ---RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               + + Y + VWG+P  +   I   L + +    +   VV ++     +A++H++V++
Sbjct: 184 QNLHLVREYLAFVWGVPARQSGRIEAALGRHA-QDRERQAVVSEDV--GRHAVTHWEVLE 240

Query: 235 CFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN---FTSPIQ-- 285
            F +K       +  Q  TGRTHQ+RVH  H+G P++GD  Y   FK      + P Q  
Sbjct: 241 VFQRKGKPVASLIACQLETGRTHQIRVHMAHIGHPLLGDPLYGKGFKSKSAILSPPAQEA 300

Query: 286 ----NKLYLHARYMDLPHP-EGGRLQITA 309
                +  LHA  +   HP  G  +   +
Sbjct: 301 LRQLGRQALHAAQLGFEHPITGEEMLFES 329


>gi|160872393|ref|ZP_02062525.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Rickettsiella grylli]
 gi|159121192|gb|EDP46530.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Rickettsiella grylli]
          Length = 325

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 77/325 (23%), Positives = 143/325 (44%), Gaps = 33/325 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  D    RLD+     +P  +   LQ+ +   +V VD +  +  ++I+ G  + I   
Sbjct: 13  IVPEDLAEKRLDQILSQLFPAYSRTRLQQWIHDKRVLVDNEFKRPRDKIKPGAKITI--- 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--H 128
                       + +    +   ++ L   +++ED  + V NKPAG+ V  G+G  +   
Sbjct: 70  ------------VANLHEAIDWEAENLPLDIIFEDDALVVINKPAGLVVHPGAGNRHKTL 117

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L      K   +  +  RLD++TSG+L++ +   A   L +  + R +++ Y +++
Sbjct: 118 VNALLHHLPALKKLPRAGIIQRLDKDTSGLLIIPKILNAHTQLVKQLQARTMKREYTAII 177

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+       I   + +   +       +   E     A+SH++VI+ F      + +Q 
Sbjct: 178 QGLLIA-GGSINAPIGRHPKLRKK----MAVTENHGKPAVSHYRVIERF-NHHTLINVQL 231

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQ-------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P+VGD  Y   F      SP+        ++  LHA  + + H
Sbjct: 232 ETGRTHQIRVHMAHIHHPLVGDKTYSGRFHLPKKASPLLIHCLHHFSRQALHAHCLGITH 291

Query: 300 PEG-GRLQITAPLPAHMVKTWDSLG 323
           P     ++  +PLP  M +    L 
Sbjct: 292 PISLKPMEWHSPLPEDMKQLIHCLR 316


>gi|294786018|ref|ZP_06751305.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_27]
 gi|294486355|gb|EFG33718.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_27]
          Length = 316

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 77/338 (22%), Positives = 142/338 (42%), Gaps = 36/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V ++ E MRLD++            L+K++ +  V+++ K +  N  ++
Sbjct: 1   MENIKENFEFEVSSEYEGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G+ + I                +    N+   ++ +   ++YE+    V NK  G+ V
Sbjct: 61  KLGEKIEIS---------------IPEEENIDIEAENISLDIVYENDDFIVINKSYGMVV 105

Query: 120 QGGSG-IAYHIDGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G  +  +   L  + +     +   +P + HRLD++TSG+++VA+   A   L   
Sbjct: 106 HPAYGNYSGTLVNALLYYTNNLSSINGNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           F  + I K Y  +V G    +     I N + + S      + VVK+N      AIS++K
Sbjct: 166 FTDKTIHKTYLCIVKGNFSEENLNGRIENLIGRGSK-DRKKMAVVKEN---GKTAISNYK 221

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           VI+     +  +E+   TGRTHQ+RVH   +   I+GD  Y    K         +  LH
Sbjct: 222 VIEQV-DGYSLVEIAIETGRTHQIRVHMKSINHVILGDSTYGNEDKNV------KRQMLH 274

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A  ++  +P +         L    ++    L F  ++
Sbjct: 275 AYKLEFLNPLDNKEYIFKGRLFDDFIEVAKRLKFNIEK 312


>gi|260495646|ref|ZP_05815770.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_33]
 gi|260196829|gb|EEW94352.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_33]
          Length = 328

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 75/338 (22%), Positives = 143/338 (42%), Gaps = 36/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V ++ E MRLD++            L+K++ +  V+++ K +  N  ++
Sbjct: 1   MENIKEKFEFEVNSEYEGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G+ + +                +    N+    + +   ++YE++   V NK  G+ V
Sbjct: 61  KLGEKIEVS---------------IPEEENIDIEPENIPLDIVYENNDFIVINKNYGMVV 105

Query: 120 QGGSG-IAYHIDGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     +   L  + +     +   +P + HRLD++TSG+++VA++  A   L   
Sbjct: 106 HPAYGNYTGTLVNALLYYTNNLSSINGNIRPGIIHRLDKDTSGLILVAKSNYAHAKLASM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           F  + I K Y  +V G    +     I N + + S      + VVK+N      AIS++K
Sbjct: 166 FIDKTIHKTYLCIVKGNFSEENLSGRIENLIGRDSK-DRKKMAVVKEN---GKIAISNYK 221

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V++   + +  +E+   TGRTHQ+RVH   +   I+GD  Y    K         +  LH
Sbjct: 222 VVEQV-EGYSLVEVAIETGRTHQIRVHMKSINHVILGDFVYGNEDKNV------KRQMLH 274

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A  ++  +P +         L    ++    L F  ++
Sbjct: 275 AYKLEFLNPLDNKEYVFKGKLFDDFIEIAKKLKFNIEK 312


>gi|121587761|ref|ZP_01677521.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           2740-80]
 gi|121730333|ref|ZP_01682696.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           V52]
 gi|147673459|ref|YP_001216201.1| 23S rRNA pseudouridine synthase D [Vibrio cholerae O395]
 gi|153215116|ref|ZP_01949823.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           1587]
 gi|153801880|ref|ZP_01956466.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MZO-3]
 gi|153818725|ref|ZP_01971392.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           NCTC 8457]
 gi|153826766|ref|ZP_01979433.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MZO-2]
 gi|153829371|ref|ZP_01982038.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           623-39]
 gi|229525359|ref|ZP_04414764.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           bv. albensis VL426]
 gi|229530513|ref|ZP_04419901.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           12129(1)]
 gi|254224983|ref|ZP_04918597.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           V51]
 gi|254291985|ref|ZP_04962765.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           AM-19226]
 gi|262170005|ref|ZP_06037695.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC27]
 gi|262191805|ref|ZP_06049976.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           CT 5369-93]
 gi|297580830|ref|ZP_06942756.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC385]
 gi|121547988|gb|EAX58068.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           2740-80]
 gi|121627915|gb|EAX60491.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           V52]
 gi|124114907|gb|EAY33727.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           1587]
 gi|124122591|gb|EAY41334.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MZO-3]
 gi|125622370|gb|EAZ50690.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           V51]
 gi|126510747|gb|EAZ73341.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           NCTC 8457]
 gi|146315342|gb|ABQ19881.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           O395]
 gi|148875154|gb|EDL73289.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           623-39]
 gi|149739417|gb|EDM53657.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MZO-2]
 gi|150422124|gb|EDN14091.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           AM-19226]
 gi|227012534|gb|ACP08744.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           O395]
 gi|229332286|gb|EEN97774.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           12129(1)]
 gi|229338940|gb|EEO03957.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           bv. albensis VL426]
 gi|262021739|gb|EEY40450.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC27]
 gi|262032292|gb|EEY50859.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           CT 5369-93]
 gi|297535246|gb|EFH74081.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC385]
 gi|327483506|gb|AEA77913.1| Ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           LMA3894-4]
          Length = 324

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 76/333 (22%), Positives = 145/333 (43%), Gaps = 37/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G++ V+   + K   ++  G+V+ +  
Sbjct: 10  TVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  L   ++YED  I V NKP    V  G+G A   
Sbjct: 70  ELEDEQRW---------------EAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  + + R + + Y ++
Sbjct: 115 VLNALLFHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + + S         +        +A++H++V + F ++   L ++
Sbjct: 175 VIGTM-TAGGMIDKPIGRHST-----KRTLMSVSPMGKHAVTHYRVAEHF-REHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGATEELTEMIRDFDRQALHAVMLKFE 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNL 330
           HP  G  L+  AP+P  MV+   +L  + D  L
Sbjct: 288 HPVTGEELEFHAPVPDDMVEM--TLALREDAKL 318


>gi|91227645|ref|ZP_01261922.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           alginolyticus 12G01]
 gi|91188424|gb|EAS74718.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           alginolyticus 12G01]
          Length = 325

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 73/331 (22%), Positives = 142/331 (42%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V+VD + V K   ++  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVQVDGEVVTKPRTKVMGGEEITLQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  I V NKP    V  G+G     
Sbjct: 70  ELEDEERW---------------EAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + D ++  +  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLHHYPDIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S         +         A++H++V + F ++   + ++
Sbjct: 175 AIGRM-TAGGKVDQPIGRHST-----KRTLMAVAPMGKPAVTHYRVAERF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDIAYGGRARIPTGASEELTAMIRGFDRQALHAVMLRFE 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  L+  AP+P  MV   ++L    + 
Sbjct: 288 HPITGEVLEFHAPVPDDMVVMTEALRQDTEE 318


>gi|15640728|ref|NP_230358.1| 23S rRNA pseudouridine synthase D [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|153822744|ref|ZP_01975411.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           B33]
 gi|227080889|ref|YP_002809440.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           M66-2]
 gi|229505673|ref|ZP_04395183.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           BX 330286]
 gi|229508754|ref|ZP_04398247.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           B33]
 gi|229519496|ref|ZP_04408939.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC9]
 gi|229608691|ref|YP_002879339.1| 23S rRNA pseudouridine synthase D [Vibrio cholerae MJ-1236]
 gi|254851039|ref|ZP_05240389.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MO10]
 gi|255743834|ref|ZP_05417790.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholera
           CIRS 101]
 gi|262156053|ref|ZP_06029172.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           INDRE 91/1]
 gi|298500820|ref|ZP_07010623.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MAK 757]
 gi|34395835|sp|Q9KU20|RLUD_VIBCH RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|9655151|gb|AAF93874.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|126519727|gb|EAZ76950.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           B33]
 gi|227008777|gb|ACP04989.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           M66-2]
 gi|229344185|gb|EEO09160.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC9]
 gi|229354278|gb|EEO19208.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           B33]
 gi|229357896|gb|EEO22813.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           BX 330286]
 gi|229371346|gb|ACQ61769.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MJ-1236]
 gi|254846744|gb|EET25158.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MO10]
 gi|255738465|gb|EET93854.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholera
           CIRS 101]
 gi|262030089|gb|EEY48734.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           INDRE 91/1]
 gi|297540601|gb|EFH76659.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           MAK 757]
          Length = 324

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 76/333 (22%), Positives = 145/333 (43%), Gaps = 37/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G++ V+   + K   ++  G+V+ +  
Sbjct: 10  TVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  L   ++YED  I V NKP    V  G+G A   
Sbjct: 70  ELEDEQRW---------------EAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  + + R + + Y ++
Sbjct: 115 VLNALLFHYSPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + + S         +        +A++H++V + F ++   L ++
Sbjct: 175 VIGTM-TAGGMIDKPIGRHST-----KRTLMSVSPMGKHAVTHYRVAEHF-REHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGATEELTEMIRDFDRQALHAVMLKFE 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNL 330
           HP  G  L+  AP+P  MV+   +L  + D  L
Sbjct: 288 HPVTGEELEFHAPVPDDMVEM--TLALREDAKL 318


>gi|326796213|ref|YP_004314033.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326546977|gb|ADZ92197.1| pseudouridine synthase, RluA family [Marinomonas mediterranea
           MMB-1]
          Length = 327

 Score =  241 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 78/336 (23%), Positives = 148/336 (44%), Gaps = 37/336 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V  +    R D+     +   +   +Q  ++ G + VD K  K   ++  G+VV 
Sbjct: 6   VKEAQVPFESSGQRFDQITTELFQDFSRSRIQAWIKEGALLVDGKACKAKEKLLGGEVV- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                 +L+  ++EQ+           +  +   ++YED  I V NKPAG+ V    G  
Sbjct: 65  ------SLDVALEEQE--------AHEAQDIPIDIVYEDEHILVINKPAGLVVHPAVGHR 110

Query: 127 YHI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                +  L    + +   +  + HRLD+ET+G++VVA+T  A   L    + R + + Y
Sbjct: 111 EGTLLNAILHHAPETAHVPRAGIVHRLDKETTGLMVVAKTLQAQTDLVAQLQERSMGREY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++  G+       + +  + +       + V   + K    A++H++++  F +    +
Sbjct: 171 EAITIGVMT--GGGMVDEPIGRHPTNRQRMAVEPIHGKD---ALTHYRLLKRF-KNHTHI 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYM 295
            ++  TGRTHQ+RVH  H+  P++GD +Y    K       +         +  LHA+ +
Sbjct: 225 RLKLETGRTHQIRVHMSHIQYPLLGDPQYSGRLKMPKACGEELQITLRNFRRQALHAKRL 284

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           +L HP  G  ++    LP  M +  + L    DR++
Sbjct: 285 ELNHPFTGDWMEWEVDLPDDMAELLEVL----DRDM 316


>gi|254282586|ref|ZP_04957554.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium NOR51-B]
 gi|219678789|gb|EED35138.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium NOR51-B]
          Length = 315

 Score =  241 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 94/322 (29%), Positives = 159/322 (49%), Gaps = 21/322 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V  +E   RLD +       +    L + +R G+VRV+K R K + R+++G  VR+
Sbjct: 9   RLVTVTEEESGQRLDNYLLRTLQGVPKTRLYRAVRKGEVRVNKGRAKVDLRLKAGDTVRL 68

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP       ++  Q    + V+         SI+L + + +   NKP+G++V GGSG+  
Sbjct: 69  PP-------LVASQPKGPAPVSGRWRKAIGGSIVL-DTADLLALNKPSGLAVHGGSGVDV 120

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L++    + +   L HRLD++TSG+++VA+  +  + L    R   I K Y  LV
Sbjct: 121 GLIESLRAMFPEQ-RYLELVHRLDRDTSGLILVAKRASVLRDLHAQLRDGEIDKRYQCLV 179

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G      + +   L + S   G+    V  +      +++ F+V++ F Q    LE +P
Sbjct: 180 SGRWPAYLKQVDGPLERYSLASGERRVRVSVD---GKPSLTRFRVLERF-QDATLLEAKP 235

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-QNKLYLHARYMDLP---HPEGG 303
            +GRTHQ+RVHAL  G PI+GD KY        T+ +  N+L+LHA  +      HP   
Sbjct: 236 VSGRTHQIRVHALQAGHPILGDAKYSNAESEALTAAVTANRLFLHAESLRFKLGDHP--- 292

Query: 304 RLQITAPLPAHMVKTWDSLGFK 325
             +++APL + +    + L  +
Sbjct: 293 -CELSAPLDSSLRAVLERLRSR 313


>gi|332295618|ref|YP_004437541.1| pseudouridine synthase, RluA family [Thermodesulfobium narugense
           DSM 14796]
 gi|332178721|gb|AEE14410.1| pseudouridine synthase, RluA family [Thermodesulfobium narugense
           DSM 14796]
          Length = 319

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 89/324 (27%), Positives = 145/324 (44%), Gaps = 39/324 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            RLD++  N     +     K+++ G VRV+ K V K +  ++    + +          
Sbjct: 23  ERLDQFLLNATKEESRSYYSKLIKEGLVRVNDKIVEKPSFIVKPYDKITL---------- 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                 L     L    D L   +LYED  I V NK   + V  G G     +  L + +
Sbjct: 73  -----FLKPKEPLYIEYDKLNITVLYEDDYIIVINKERNMVVHPGPG--NFRNTILNALI 125

Query: 138 DSKG-------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           +S         ++P + HRLD+ET+G+L++A++    + L+E F+ R+++K Y +LV+G 
Sbjct: 126 NSINKDEFTDQERPGIVHRLDKETTGVLIIAKSEKIMRKLSEQFKNRQVKKTYLALVYGD 185

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQP 247
              K+  I+  + K+S I    + V          A + + VI+      Q    L++  
Sbjct: 186 VNYKEGFISMPI-KRSKIHRQKMEVNL----SGKVAFTEYSVINKGIFEKQIVSLLKVNI 240

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-Q 306
            TGRTHQ+RVH  ++G PIVGD KY      N        + LHA  ++  HP   ++  
Sbjct: 241 FTGRTHQIRVHMSYIGHPIVGDKKYSTKSCKNCPE-----IALHALKIEFLHPITNKIVS 295

Query: 307 ITAPLPAHMVKTWDSLGFKYDRNL 330
             APLP  +          YD +L
Sbjct: 296 FKAPLPQDLQDFLKRCNINYDLDL 319


>gi|229512403|ref|ZP_04401877.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           TMA 21]
 gi|229350553|gb|EEO15499.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           TMA 21]
          Length = 324

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 76/333 (22%), Positives = 145/333 (43%), Gaps = 37/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G++ V+   + K   ++  G+V+ +  
Sbjct: 10  TVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  L   ++YED  I V NKP    V  G+G A   
Sbjct: 70  ELEDEQRW---------------EAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  + + R + + Y ++
Sbjct: 115 VLNALLFHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + + S         +        +A++H++V + F ++   L ++
Sbjct: 175 VIGTM-TAGGMIDKPIGRHST-----KRTLMSVSPMGKHAVTHYRVAEHF-REHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGASEELTEMIRGFDRQALHAVMLKFE 287

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
           HP  G  L+  AP+P  MV+   +L  + D  L
Sbjct: 288 HPITGEELEFHAPVPDDMVEM--TLALREDAKL 318


>gi|332307416|ref|YP_004435267.1| pseudouridine synthase, RluA family [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332174745|gb|AEE23999.1| pseudouridine synthase, RluA family [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 327

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 138/332 (41%), Gaps = 35/332 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           VV       RLD+     +P  +   ++  + + QV +D + V K   ++   +++ I  
Sbjct: 13  VVPQTLLGKRLDQALAEMFPDYSRSRIKDWILADQVSIDGQIVNKPREKLLGEELIEIDA 72

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I                      +  +   ++YED  I V NKP  + V  G+G A   
Sbjct: 73  SIEIQER---------------HSAQEIDLNIVYEDEHILVINKPTNLVVHPGAGNANGT 117

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L    D +   +  + HRLD++T+G++VVA+T  A  HL E  + R I + Y ++
Sbjct: 118 ILNALLSHVPDIASVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVEKLQAREISREYEAV 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G        +   + +      +   V     +    A++H++V     +    L ++
Sbjct: 178 VYGNLIA-GGSVDEPIGRHPTKRTNMAVV-----QSGKPALTHYRV-KHKYRAHTHLRLK 230

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             +GRTHQ+RVH  H+  P+VGD  Y    +    +            +  LHA  ++L 
Sbjct: 231 LESGRTHQIRVHMAHLRHPLVGDQAYGGRPRLPKAASEVMIETIRGFKRQALHAIQLELE 290

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           HP  G  +   APLP   V   D L     +N
Sbjct: 291 HPITGEWMSFQAPLPDDFVNLLDVLKEDTAQN 322


>gi|33239671|ref|NP_874613.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus subsp. marinus str.
           CCMP1375]
 gi|33237196|gb|AAP99265.1| 23S RNA-specific pseudouridylate synthase [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
          Length = 318

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 85/313 (27%), Positives = 138/313 (44%), Gaps = 28/313 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +   +QK +  G V V+  + K    +++G  +++          
Sbjct: 26  PMRLDRWLVSQRSEQSRARIQKFIEDGLVLVNGIQGKSKTPLRTGDEIQLWVPPPEPLPY 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKS 135
           +K QK              +   +++EDS I V NKPAG++V    G       +G L  
Sbjct: 86  LKPQK--------------MHLDIIFEDSHIIVINKPAGLTVHPAPGNKDRTLVNGLLHH 131

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +V+A+++ A  +L    + R   + Y +LV G+P
Sbjct: 132 CTDLPGINGKLRPGIVHRLDKDTTGCIVIAKSQEALVNLQVQIQKRIASRRYIALVHGVP 191

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
              K  I+  + +       Y  V   N+     A +H+++ +     +  L  +  TGR
Sbjct: 192 HGDKGIISAPIGRHPIDRKKYAVV---NDGSGRDACTHWELKERLGD-YSLLSFKLETGR 247

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH+ H+G PI+GD  Y    K            LHA  + L HP     +   AP
Sbjct: 248 THQIRVHSAHIGHPILGDPTYSRCKK---LPTKLTGQVLHAIQLGLQHPISKTDILFEAP 304

Query: 311 LPAHMVKTWDSLG 323
           LP   +     L 
Sbjct: 305 LPDTFLNVLSVLR 317


>gi|300112960|ref|YP_003759535.1| RluA family pseudouridine synthase [Nitrosococcus watsonii C-113]
 gi|299538897|gb|ADJ27214.1| pseudouridine synthase, RluA family [Nitrosococcus watsonii C-113]
          Length = 324

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 103/323 (31%), Positives = 164/323 (50%), Gaps = 14/323 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V+ + +  ++   R+D +  +H   +    + + LR G+VRV+K R+  + R+Q G  
Sbjct: 10  AQVRILEIHLEQVGQRIDNFLFSHLKGVPKSRIYRCLRRGEVRVNKSRITSSYRLQQGDQ 69

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP+   ++H   ++ I    + L K+S      LLYED ++ + +KPAGI V GGSG
Sbjct: 70  VRIPPLR--VSHPPLKRPIAHFLLFLIKNS------LLYEDKELLILDKPAGIPVHGGSG 121

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           ++Y I   L++ +  +     L HRLD+ETSG L++A+TR     L    + + I K Y 
Sbjct: 122 VSYGIIEVLRA-LRPEATFLELVHRLDRETSGCLMIAKTRGTLLTLQAMQQKQLIHKRYL 180

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  +   + +   LLK   I      +VK        A S F     +  +   +E
Sbjct: 181 ALVKGRWRKNVQRVDLPLLKN--ISRSKERIVKV-SPAGKPAASRFYPKLFYRDEATLVE 237

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +   TGRTHQ+RVHA H+G P+ GD KY  + F          +L+LHA  +    PEG 
Sbjct: 238 VALETGRTHQIRVHATHLGHPLGGDEKYGDSTFNKRLRYLGLRRLFLHASQLIFTLPEGK 297

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
           + ++  APLP  +    ++   K
Sbjct: 298 KTIKTIAPLPEELNAVMEAYAIK 320


>gi|37678897|ref|NP_933506.1| 23S rRNA pseudouridine synthase D [Vibrio vulnificus YJ016]
 gi|37197638|dbj|BAC93477.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
          Length = 325

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 72/331 (21%), Positives = 141/331 (42%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G+V VD   V K   ++  G+V+ +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLDGKVTVDGNVVTKPRTKVMGGEVITV-- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                        + +    +   +  +   ++YED  I V NKP    V  G+G     
Sbjct: 68  -------------LAELEDEVRWEAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L    + ++  +  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLFHCPEVAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRHITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + +         +         A++HF+V + F ++   + ++
Sbjct: 175 AIGRM-TAGGKVDKPIGRHAT-----KRTLMAVSPMGKPAVTHFRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +           ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDAAYGGRARIPAGASEDVTAMIRNFDRQALHAVMLRFE 287

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  ++  AP+P  MV+  ++L      
Sbjct: 288 HPITGEEMEFHAPVPDDMVELTETLRRDAQE 318


>gi|83955695|ref|ZP_00964275.1| ribosomal large subunit pseudouridine synthase D [Sulfitobacter sp.
           NAS-14.1]
 gi|83839989|gb|EAP79165.1| ribosomal large subunit pseudouridine synthase D [Sulfitobacter sp.
           NAS-14.1]
          Length = 344

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 88/357 (24%), Positives = 149/357 (41%), Gaps = 50/357 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M++ Q      D    RLD+      P    ++   L ++L  G V+VD   V    +R 
Sbjct: 1   MSHRQITFTIADSPPPRLDKALARDVPEDANLSRTRLGRLLEQGAVQVDGTVVTDPRSRA 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++GQ + +       +HI+ E+  L+               +++ED+ + V NKPAG+ V
Sbjct: 61  EAGQQITVDVEEAEDSHILAEEIPLE---------------VVFEDADLIVINKPAGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    D        ++P + HR+D++TSG+LVVA++ AA   L +
Sbjct: 106 HPAPGSPSGTLVNALLAHCGDDLSGVGGMKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAK 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F    +++ Y +LV+G+P      +           N L   + +        +Q    
Sbjct: 166 QFEKHTVERYYQALVYGVPDANDPRLRGVKGASFEPGNILKLTTQLARHRTDRQRQAVFF 225

Query: 221 KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +G  +A++  + +           +E    TGRTHQ+RVH  H G  +VGD  Y    K 
Sbjct: 226 QGGRHAVTRARTVARLGNPEVLALMECWLETGRTHQIRVHMAHAGHALVGDPTYGGKRKL 285

Query: 279 NFTSPIQ---------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
              +             +  LHA  +   HP  G  ++  APLP  M     +LG+ 
Sbjct: 286 AKGAVSDAAAEAVRSFPRQALHAAVLGFDHPVTGDYVRFEAPLPGDMTDLLGALGYD 342


>gi|260771763|ref|ZP_05880681.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           metschnikovii CIP 69.14]
 gi|260613055|gb|EEX38256.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           metschnikovii CIP 69.14]
          Length = 324

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 142/332 (42%), Gaps = 35/332 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +   RLD+     +   +   L++ L  G++ V+   V K   ++  G+ + +  
Sbjct: 10  TVKESQLGQRLDQAVAELFVDFSRSRLKEWLLDGKITVNGTVVTKPRTKVMGGECITV-- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L  +  EQ+     + L          ++YED  I V NKP    V  G+G     
Sbjct: 68  ----LAELEDEQRWEAQDIPLN---------IVYEDDDILVINKPRDFVVHPGAGTPDRT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L    + R I + Y ++
Sbjct: 115 VLNALLFHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRDLQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        I   + + S         +    +    A++H++V + F ++   + ++
Sbjct: 175 AIGKM-TAGGMIDKPIGRHST-----KRTLMAVNQMGKPAVTHYRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMAYLQHPLLGDSAYGGRARIPKGATPELTEMIRAFDRQALHAVMLKFE 287

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           HP  G  L+  AP+P  MV   ++L      N
Sbjct: 288 HPITGEELEFHAPVPDDMVIMTEALREDAKLN 319


>gi|229519979|ref|ZP_04409409.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           TM 11079-80]
 gi|229343031|gb|EEO08019.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           TM 11079-80]
          Length = 324

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 76/333 (22%), Positives = 145/333 (43%), Gaps = 37/333 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G++ V+   + K   ++  G+V+ +  
Sbjct: 10  TVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  L   ++YED  I V NKP    V  G+G A   
Sbjct: 70  ELEDEQRW---------------EAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  + + R + + Y ++
Sbjct: 115 VLNALLFHYPPIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + + S         +        +A++H++V + F ++   L ++
Sbjct: 175 VIGTM-TAGGMIDKPIGRHST-----KRTLMSVSPMGKHAVTHYRVAEHF-REHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMAYLQHPLLGDTAYGGRARIPKGATEELTEMIRDFDRQALHAVMLKFD 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNL 330
           HP  G  L+  AP+P  MV+   +L  + D  L
Sbjct: 288 HPVTGEELEFHAPVPDDMVEM--TLALREDAKL 318


>gi|197103876|ref|YP_002129253.1| ribosomal large subunit pseudouridine synthase d [Phenylobacterium
           zucineum HLK1]
 gi|196477296|gb|ACG76824.1| ribosomal large subunit pseudouridine synthase d [Phenylobacterium
           zucineum HLK1]
          Length = 326

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 83/336 (24%), Positives = 141/336 (41%), Gaps = 37/336 (11%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V    V  +    R+D+      P ++   LQ +L  G+V      V    + Q+G  
Sbjct: 9   SEVLTAEVPAELAGERIDKALAGLLPTLSRARLQALLAEGRVTRGGAPVDAKAKAQAG-- 66

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
                              +          + +   +L+ED+ + V +KPAG+++    G
Sbjct: 67  --------------AYAIAVPPPEPAEPQPEAIPLTVLFEDAHLIVVDKPAGMAMHPAPG 112

Query: 125 IA--YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  L    DS        +P + HR+D+ETSG++V A+T AA Q L+  F   
Sbjct: 113 SERGTLVNALLAHCGDSLSGIGGVARPGVVHRIDKETSGVVVAAKTDAAHQGLSALFAAH 172

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I+++Y +L  G P+ ++  I   + + +H     + +VK    G  +A++H+ V   F 
Sbjct: 173 DIERVYIALTRGAPRPERGVIEGAIARSAH-DRKKMALVKS---GGRHAVTHYAVERVFG 228

Query: 238 QK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-----KL 288
            +       +  +  TGRTHQ+RVH    G P +GD  Y +                 + 
Sbjct: 229 PQERPLAARVACRLETGRTHQIRVHLASKGTPCLGDPTYGSGPPAEAVREAIRQAGLARQ 288

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            LHA  +   HP  G+ L+  +PLPA M      LG
Sbjct: 289 ALHAAVLGFRHPVSGQALRFESPLPADMAALEVLLG 324


>gi|218295180|ref|ZP_03496016.1| pseudouridine synthase, RluA family [Thermus aquaticus Y51MC23]
 gi|218244383|gb|EED10908.1| pseudouridine synthase, RluA family [Thermus aquaticus Y51MC23]
          Length = 307

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 96/332 (28%), Positives = 156/332 (46%), Gaps = 41/332 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
           E +RLD+        ++    Q  +  G+VRV +K V K   R++               
Sbjct: 7   EGLRLDQAVAEAL-GVSRARAQAWILEGRVRVGEKVVDKPAYRLKG-------------- 51

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL 133
              +E  +           + L   +LYED  + V NKP G+      G+     ++  L
Sbjct: 52  ---EEVVVEPKEERPLVVPEDLPLPILYEDEDLLVLNKPPGLLTHPAPGVYTGTVVNALL 108

Query: 134 KSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             + + K        +P + HRLD++TSG+LVVA+   A + L+++FR R + K Y +L 
Sbjct: 109 GRYYEPKAVERPEMVRPGIVHRLDKDTSGVLVVAKHGGALEALSQAFRDRLVMKRYLALT 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G PK  +  +   + +   +    +HV         YA +HF+V+   A     +E +P
Sbjct: 169 EGHPK--EGTLIAPIGRH-PVERHKMHV---GGVAPRYAETHFQVLAT-AGPHALVEARP 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-Q 306
           HTGRTHQ+RVH  H+  PI+GD  Y         SP+  +  LHA  + LPHP  GR+ +
Sbjct: 222 HTGRTHQIRVHLKHLRAPILGDEVYGKK------SPVIPRQALHAYELRLPHPRTGRILE 275

Query: 307 ITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             AP+PA M + W++LG  +   + + R  ++
Sbjct: 276 FLAPVPADMARAWEALGGAWPEGIALNRETTE 307


>gi|119775737|ref|YP_928477.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119768237|gb|ABM00808.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           amazonensis SB2B]
          Length = 324

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 80/331 (24%), Positives = 142/331 (42%), Gaps = 35/331 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +  +RLD+     +P  +   L++ +  G V VD   V K   ++   QV+ I   
Sbjct: 11  ISATQTGLRLDQAIAELFPDYSRTRLKEWILGGNVYVDGVVVTKPREKVLESQVIEIEAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--H 128
           +                      +  +   ++YED  I V NK AG+ V  G+G A    
Sbjct: 71  LEEEVAA---------------EAQEIDLDIVYEDDHILVINKQAGLVVHPGAGNADGTL 115

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L    + +   +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 MNALLHHCPEIEHVPRAGIIHRLDKDTTGLMVVAKTVEAQTHLVAALQARDITREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        +   + +         H+   +      +++H++V + F +    L ++ 
Sbjct: 176 LGTM-TAGGTVDAPIGRHPT---KRTHMAVHHS--GRPSVTHYRVAEKF-RAHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+G  +VGD  Y    K    +  +         +  LHA  ++L H
Sbjct: 229 ETGRTHQIRVHMAHIGHVLVGDPVYGGRPKPPKNASPEFFEVLKNFTRQALHAVRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           P     +   AP+P  MV    +L    + N
Sbjct: 289 PVTMEIMSFNAPIPEDMVLLTKALRKDTEAN 319


>gi|297538696|ref|YP_003674465.1| RluA family pseudouridine synthase [Methylotenera sp. 301]
 gi|297258043|gb|ADI29888.1| pseudouridine synthase, RluA family [Methylotenera sp. 301]
          Length = 343

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 102/325 (31%), Positives = 161/325 (49%), Gaps = 21/325 (6%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           ++ V+   E  R+D +       +   ++ +ILRSG+VRV+KKR+  + R+  G VVR+P
Sbjct: 27  FLTVDEASEGQRVDNFLTKTLKGVPKSHVYRILRSGEVRVNKKRIDADFRLTIGDVVRVP 86

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P+            I++            ++ ++YED  I V +KPAG +V GGSG++  
Sbjct: 87  PIRAT---------IVEHVETAVPAVSKFENTIIYEDDAILVIDKPAGFAVHGGSGVSRG 137

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +   ++     K +   L HRLD+ETSG+L++A+ R+A   L E+ R  +  K Y  LV 
Sbjct: 138 VIEQMR-LERPKAKFLELVHRLDRETSGVLMLAKKRSALVALHEAIRNNQTDKRYLMLVR 196

Query: 189 GIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGA----NYAISHFKVIDCFAQ----K 239
           G     K+ +   L K     G+  V+VV    K        + + FK++  ++     K
Sbjct: 197 GEWLEAKKRVVLDLQKYLLPNGERRVNVVTDVSKDKYNERQTSETMFKLLKNYSHPVLGK 256

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLP 298
           F  LE Q  TGRTHQLRV   H+G  IVGD KY       +       +++LH+    + 
Sbjct: 257 FSLLEAQLVTGRTHQLRVQLAHLGFQIVGDDKYGDFAVNKSLVKSGLKRMFLHSSVTKIR 316

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSL 322
           HP    +L++ APLP  + K    L
Sbjct: 317 HPLTNDKLELVAPLPPELSKFLVKL 341


>gi|168334458|ref|ZP_02692629.1| putative pseudouridylate synthase [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 304

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 73/330 (22%), Positives = 137/330 (41%), Gaps = 40/330 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     + + N+  ++R+D++     P      +QK +  G + ++ K      RI++G 
Sbjct: 1   MNDKLLLTI-NNIADIRVDKFLTEQLPQYTRSYIQKQIELGLLLINGKVAPARTRIKTGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           I   +  LD               ++YEDS I + NKP  + V   +
Sbjct: 60  TIEFTIAPPREVDITPSEIKLD---------------IIYEDSDILIVNKPKNMVVHPSA 104

Query: 124 GIAYHIDGFLKSWVDSKGQ----------KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           G   H +  L + +    +          +P + HR+D++T+G+L+VA+   +   L++ 
Sbjct: 105 G---HYNDTLVNALLFYAKDSLSGINGEIRPGIVHRIDKDTTGLLMVAKNDHSHVFLSDL 161

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            +   I++ Y +LV+G  K     I   + +          V     +    A++  +V+
Sbjct: 162 LKDHNIERKYNALVYGNIKEDFFTIDRPIARNPKDRKKMAIV-----ENGRRAVTECRVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F      +E+   TGRTHQ+RVH   +G P++GD  Y  +              LHAR
Sbjct: 217 ERFG-NATHIELSLQTGRTHQIRVHLTSIGHPLLGDPLYGRSKH----LFNLQTQMLHAR 271

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +   HP   + ++  + LP   + T   L
Sbjct: 272 VLGFIHPSSQQFMRFESVLPTEFLHTIGRL 301


>gi|257056703|ref|YP_003134535.1| ribosomal large subunit pseudouridine synthase D [Saccharomonospora
           viridis DSM 43017]
 gi|256586575|gb|ACU97708.1| ribosomal large subunit pseudouridine synthase D [Saccharomonospora
           viridis DSM 43017]
          Length = 308

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 145/325 (44%), Gaps = 28/325 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  + MR+D         ++   + ++  SG V +D K    ++R+ +G ++ +
Sbjct: 4   RMLPVPDGLDGMRVDVGLAKLL-GLSRTVVAELAASGDVLIDGKVASKSDRLTAGDLLEV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
                    + +     + S    +        +L+ED  I V +KP G++V    G   
Sbjct: 63  T--------LPEPDTPAEVSAEPVE-----GLRILHEDDDIVVVDKPVGVAVHPSPGWTG 109

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              +       L+       ++  + HRLD  T+G++VVA++  A   L  +F+ R + K
Sbjct: 110 PTVVGGLAAAGLRISTSGAAERQGVVHRLDAGTTGVMVVAKSEHAYSVLKRAFKERTVSK 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G P   +  I   + +       +  V      G   +I+H++VI+ F +   
Sbjct: 170 GYHALVQGHPDPTRGTIDAPIDRHPRYDYKFAVVT-----GGKPSITHYEVIEAF-RAAS 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++Q  TGRTHQ+RVH   M  P VGD  Y A+        +  + +LHAR +   HP 
Sbjct: 224 LVDVQLETGRTHQIRVHFSAMRHPCVGDLTYGADPVLARRLGL-TRQWLHARTLGFAHPA 282

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            GR ++ T+  PA +    D L  +
Sbjct: 283 DGRWVEFTSEYPADLAAALDILRAE 307


>gi|33151686|ref|NP_873039.1| 23S rRNA pseudouridine synthase D [Haemophilus ducreyi 35000HP]
 gi|34395836|sp|Q9L7A7|RLUD_HAEDU RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|33147907|gb|AAP95428.1| pseudouridine synthase [Haemophilus ducreyi 35000HP]
          Length = 325

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 82/348 (23%), Positives = 147/348 (42%), Gaps = 39/348 (11%)

Query: 4   MTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           MT    +   +  D    RLD+     +P  +   ++  + +  V+V+   V +   ++ 
Sbjct: 1   MTQQMTLTAEISADLLGYRLDQALAQLFPDYSRSRIKVWIENDLVKVNGIIVNRARGKVF 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ + I   I                         +   +++ED  I + NKP  + V 
Sbjct: 61  GGEQIEIQAEIEEEIRF---------------EPQNIPLNIVHEDDDIIIINKPKNLVVH 105

Query: 121 GGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+G     +   L  +     + PR  + HRLD++T+G++VVA+   A  HL  + + R
Sbjct: 106 PGAGNPDGTVLNALLYYYPPIAEVPRAGIIHRLDKDTTGLMVVAKNIPAQTHLVTALQKR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           RI + Y ++  GI   +   +   + +                     AI+H+++++ F 
Sbjct: 166 RITREYEAIASGIM-TQGGKVDEPMARHPT-----KRTAMAVHPMGKPAITHYRIMERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLY 289
           + +  L ++  TGRTHQ+RVH  H+  P++GD  Y    +    S            +  
Sbjct: 219 RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQLYGGRPRPPKGSSEAFLTVLRAFQRQA 278

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLY 336
           LHA  + L HP  G  ++  APLPA  V+  ++L   Y R  Y + LY
Sbjct: 279 LHATMLRLEHPINGELIECHAPLPADFVELIEALKTDYQR--YKEDLY 324


>gi|114327513|ref|YP_744670.1| ribosomal large subunit pseudouridine synthase D [Granulibacter
           bethesdensis CGDNIH1]
 gi|114315687|gb|ABI61747.1| ribosomal large subunit pseudouridine synthase D [Granulibacter
           bethesdensis CGDNIH1]
          Length = 330

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 146/334 (43%), Gaps = 39/334 (11%)

Query: 9   YVVVE--NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
            + V    D    R+DR+   H P ++   L+ ++ SG V  D + V+     ++ G + 
Sbjct: 12  EITVSAAPDAVPERIDRFLAIHLPDMSRSRLKSLIESGAVHRDGQSVRGPAEMVRPGSLY 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
           R+                L +       +  +   +L+ED  + V +KPAG+ V    G 
Sbjct: 72  RLR---------------LPTPAPAIPIAQHIAFPILFEDDDLIVLDKPAGMVVHPAPGS 116

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  L    ++       ++P + HRLD++TSG++VVA+T  A   L+  F  R 
Sbjct: 117 PDGTLVNALLAYCGENLPGIGGEKRPGIVHRLDKDTSGVMVVAKTEFALAALSALFAARD 176

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++++Y +L WG+   ++  I   + +        + +V+    G   A++H++ +  +  
Sbjct: 177 LERLYTALAWGVLTPREGDIEGAIGRDPR-DRKRMAIVRH---GGKPALTHYRAMATWYD 232

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---------KLY 289
               +E +  TGRTHQ+RVH    G PI+GD  Y         S  Q+         +  
Sbjct: 233 AVTRMECKLATGRTHQIRVHLSANGHPIIGDPVYLRRIPAVAKSLDQDVKNALLDFPRQA 292

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           LHA  +   HP  G  L+   PLP  M+   D L
Sbjct: 293 LHAGVLGFRHPRTGENLRFETPLPEDMMSLIDLL 326


>gi|56416931|ref|YP_154005.1| sfhb-like protein [Anaplasma marginale str. St. Maries]
 gi|255003281|ref|ZP_05278245.1| sfhb-like protein [Anaplasma marginale str. Puerto Rico]
 gi|56388163|gb|AAV86750.1| sfhb-like protein [Anaplasma marginale str. St. Maries]
          Length = 327

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 143/334 (42%), Gaps = 34/334 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSG 62
           M  V  V V  +++  R+D+        I+    Q ++  GQV +  + +  N    ++G
Sbjct: 1   MKCVHEVCVTKEDDQQRIDKLISCAL-EISRNRAQGLIAGGQVTISGRVINNNSYLTKTG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V  I   +   + +     I                 ++YED  + V +K   I+V  G
Sbjct: 60  DVYTIVTAVQKPSTLSPNYDI--------------DLKVVYEDHDVIVIDKDPYIAVHPG 105

Query: 123 SGIAYHI--DGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +GI +H   +  L  +           +P + HRLD++TSG++V A+T  A   L+E   
Sbjct: 106 NGIEHHTITNALLARFGAGLQSVGSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELA 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +  +K Y ++ WGIP  K+  I   +     +    + +++    G   A + ++V   
Sbjct: 166 NQGFKKEYLAVAWGIPCPKRGVIHTNI----RVKRSDITMMEAANSGGKPAKTEYEVEQE 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLY 289
             +    +    HTGRTHQ+RVH  H+G  IVGD KY  N K    S +        +  
Sbjct: 222 LGEVASLIRCTLHTGRTHQIRVHMSHIGHSIVGDQKYGKNCKKCMRSGVPPDVKNFRRQA 281

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           LHA  +   HP  G+ ++ T+     + +   +L
Sbjct: 282 LHASLLGFRHPSTGKYIEFTSKPADDIQQLISAL 315


>gi|87119407|ref|ZP_01075304.1| ribosomal large subunit pseudouridine synthase D [Marinomonas sp.
           MED121]
 gi|86164883|gb|EAQ66151.1| ribosomal large subunit pseudouridine synthase D [Marinomonas sp.
           MED121]
          Length = 322

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 144/328 (43%), Gaps = 33/328 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   V  +    R D      +   +   +Q  ++ G + VD K+ K   ++  G+V+ 
Sbjct: 6   VKEAQVPFELNGQRFDLIATELFSDYSRSRIQAWIKEGVLLVDGKKSKAKEKLFVGEVIS 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +  ++  ++    E   LD               ++YED  I V NKP+G+ V    G  
Sbjct: 66  LETLVEDIDDHQPEDIPLD---------------IVYEDEDILVVNKPSGLVVHPAVGHR 110

Query: 126 -AYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               ++  L    +S    +  + HRLD+ET+G++VVA+T AA   L    + R + + Y
Sbjct: 111 SGTLMNAILFHCPESAHVPRAGIVHRLDKETTGLMVVAKTLAAQTELVSQLQDRSMGREY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++  GI         N  + +       + V   N K    A++H++++  F +    +
Sbjct: 171 EAVAIGIMT--GGGTVNEPIGRHPQNRQKMAVEPLNGKD---AVTHYRLLQRF-KNHTHI 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYM 295
            ++  TGRTHQ+RVH  H+  P++GD +Y    K            +QN  +  LHA+ +
Sbjct: 225 RLKLETGRTHQIRVHMSHIQFPLLGDPQYAGRMKMPKACIPELRDELQNFRRQALHAKRL 284

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +L HP  G  ++    LP  M    + L
Sbjct: 285 ELSHPITGEFMEWEVDLPDDMKHLIELL 312


>gi|159902752|ref|YP_001550096.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9211]
 gi|159887928|gb|ABX08142.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9211]
          Length = 327

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 90/312 (28%), Positives = 139/312 (44%), Gaps = 28/312 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRW  +     +   +QK +  G V+V++K  K    ++ G  +++          
Sbjct: 26  PMRLDRWLVSQRSEQSRARIQKFINEGLVKVNEKIGKAKTPLRQGDEIKLWLPPPEPLPY 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
           +K +KI                 +LYED  + V NK AGI+V    G      ++G L  
Sbjct: 86  LKPEKI--------------SLDILYEDKYLIVINKQAGIAVHPAPGNKFGTLVNGLLHH 131

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HRLD++T+G +VVA+T+ A  +L +  + R   +IY ++V G+P
Sbjct: 132 CNDLPGISGKLRPGIVHRLDKDTTGCIVVAKTQEALVNLQKQIQTRVASRIYLAIVHGVP 191

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K  K  I   + +       Y  V  +    A YA +H+++ +     +  L  +  TGR
Sbjct: 192 KGDKGTIIGAIGRHPVDRKKYAVVTNEM---ARYACTHWELKERLGD-YSLLSFKLDTGR 247

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  H G PI+GD  Y    K        +   LHA  + L HP     +   AP
Sbjct: 248 THQIRVHCAHFGHPILGDQTYSRCKK---LPNGVSSQVLHAVKLGLKHPHNNETMLFEAP 304

Query: 311 LPAHMVKTWDSL 322
           LP         L
Sbjct: 305 LPNTFKNVLTRL 316


>gi|238897770|ref|YP_002923449.1| pseudouridine synthase [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
 gi|229465527|gb|ACQ67301.1| pseudouridine synthase [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
          Length = 325

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 72/340 (21%), Positives = 143/340 (42%), Gaps = 37/340 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIP 68
             V   +   RLDR     +P  +   +++ + + QV V+   +     ++  G+ + I 
Sbjct: 9   TTVCESQLGQRLDRALAELFPTYSRSRIKEWILAHQVTVNGITKSIPKEKVLGGEHIEIH 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I      + ++               +   ++YED+ I V NKP+G+ V  G+G   H
Sbjct: 69  TYIEENKRWMPQK---------------IPLNIIYEDTDILVINKPSGLVVHPGAGNPDH 113

Query: 129 I--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +  L  + D +   +  + HRLD++T+G++V+A+T  A   L ++ + R + + Y +
Sbjct: 114 TILNALLDYYPDITHVPRAGIVHRLDKDTTGLMVIAKTLRAQTSLVDALQARLVTREYEA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G        I   + +                     A++H++++  F +    L +
Sbjct: 174 IAVGHI-TAGGSINEPIARH-----KSKRTHMAVHPLGKSAVTHYRILQHF-RAHTRLRL 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDL 297
           +  TGRTHQ+RVH  ++  P+VGD  Y    +    +  +         +  LHA  + L
Sbjct: 227 RLETGRTHQIRVHFSYIHHPLVGDPLYGRRLRQPKGALEKLIETLSAFKRQALHATMLRL 286

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLY 336
            HP     ++  A LP  M+    +L    D+  + ++  
Sbjct: 287 HHPITQIEMEWHADLPQDMLDLISAL--NADQEAFCQKEE 324


>gi|167644317|ref|YP_001681980.1| RluA family pseudouridine synthase [Caulobacter sp. K31]
 gi|167346747|gb|ABZ69482.1| pseudouridine synthase, RluA family [Caulobacter sp. K31]
          Length = 351

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 86/323 (26%), Positives = 133/323 (41%), Gaps = 31/323 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  D    RLD+      P ++   LQ ++ +GQV +          +  G   R  P
Sbjct: 33  IELGADLAGQRLDKALATAAPELSRARLQALIAAGQVSL----------VVEGAAPRAMP 82

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
              A       + ++          + +   +LYED+ + V +KPAG++     G     
Sbjct: 83  DGKAKAPAGLYEVVVPPPTAAEPLPENIPLSVLYEDAHLIVIDKPAGMAAHPAPGCETGT 142

Query: 128 HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++  L     S        +P + HRLD+ETSG++V A+T AA Q L+  F    I ++
Sbjct: 143 LVNALLFHCGASLSGIGGVARPGIVHRLDKETSGVMVAAKTDAAHQGLSALFAKHDIDRM 202

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--- 239
           Y +L  G P      I   L + S      + V+K    G   AI+H++V   F      
Sbjct: 203 YLALTRGAPHPVVGTIITQLGR-SPGDRKKMAVLKS---GGREAITHYRVEKSFGPPDKP 258

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHAR 293
               +  +  TGRTHQ+RVH    G P +GD  Y A       K   T    ++  LHA 
Sbjct: 259 LASRVACRLETGRTHQIRVHMASKGSPCLGDPVYGAGAPAAPVKAALTEIGFSRQALHAA 318

Query: 294 YMDLPHPEGGR-LQITAPLPAHM 315
            +   HP     L+   PLP  M
Sbjct: 319 VLGFVHPITRELLRFETPLPPDM 341


>gi|226941139|ref|YP_002796213.1| RluD [Laribacter hongkongensis HLHK9]
 gi|226716066|gb|ACO75204.1| RluD [Laribacter hongkongensis HLHK9]
          Length = 349

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 86/326 (26%), Positives = 140/326 (42%), Gaps = 34/326 (10%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
             + + + +     RLD       P  +   L + ++ G VRVD   V    ++   GQ 
Sbjct: 16  DTRVLTIPDTLAGDRLDAALAALMPDQSRSRLTQWIKDGHVRVDGSTVTVPRSKTVLGQQ 75

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V +            EQ  LD    +    + ++  ++YED +I V NKPAG+    G+G
Sbjct: 76  VEVD-----------EQLSLDE---MAFAPEDIEIPVIYEDRQILVVNKPAGLVTHPGNG 121

Query: 125 I--AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                 ++G L    + +   +  + HRLD++TSG++VVA+T AA   L    + R +++
Sbjct: 122 NWSGTLLNGLLYRVPELAHVPRAGIVHRLDKDTSGLMVVAKTVAAQLDLIRQLQARTVKR 181

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQK 239
            Y ++  G        +A  +     IG D    VK      G   AI+H + ++ F + 
Sbjct: 182 HYRAIACGN-------VAGDITIDKAIGRDPKTRVKMAVVAFGGKPAITHVRPLEMF-EH 233

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-----NKLYLHARY 294
              +E +  TGRTHQ+RVH   +GCP+ GD  Y            +      +  LHA  
Sbjct: 234 HTLVECRLETGRTHQIRVHMASIGCPLAGDPLYGNPRLPASPEVREAINDFGRQALHAAK 293

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTW 319
           + L HPE  + +     LP  M    
Sbjct: 294 LALIHPESKKPVGWKTRLPQDMQYLL 319


>gi|148552990|ref|YP_001260572.1| ribosomal large subunit pseudouridine synthase D [Sphingomonas
           wittichii RW1]
 gi|148498180|gb|ABQ66434.1| ribosomal large subunit pseudouridine synthase D [Sphingomonas
           wittichii RW1]
          Length = 321

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 78/338 (23%), Positives = 138/338 (40%), Gaps = 32/338 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV-RVDKKRVK-FNNR 58
           M+      + VV  D E  RLDR      P ++   L+ ++ SGQV   D    +    +
Sbjct: 1   MTGGKSTLHAVVPQDAEGWRLDRALAAALPTLSRERLKALISSGQVSHADGALARDPAMK 60

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +  G    +               I+         +  +  ++ YED  + V +KPAG+ 
Sbjct: 61  VAPGARFAV---------------IVPDPAPAHNAAQDIPLVVAYEDEHLIVIDKPAGLV 105

Query: 119 VQGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           V   +G      ++  L     S       ++P + HR+D++TSG++V A+T  A   L 
Sbjct: 106 VHPAAGNPDGTLVNALLHHCRGSLSGIGGVERPGIVHRIDKDTSGLMVAAKTDPAHVGLA 165

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    I + Y ++V G P+     +   L + +    D   +    +     A++H+ 
Sbjct: 166 AQFARHSIDRRYRAIVAGTPRLAAGTVDAPLARST---ADRKKIAIVADGRGKRAVTHYS 222

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKL 288
           VI+   ++   +E +  TGRTHQ+RVH   +G P++GD  Y       +        ++ 
Sbjct: 223 VIE-PLRRAALVECRLETGRTHQVRVHMASLGHPLLGDPVYGRSRPEHRELLNRLKFHRQ 281

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
            LHA  +   HP     L   + +P  M   +  L  +
Sbjct: 282 ALHAARLGFIHPVTSAALSFDSEIPQDMQDLFSELRVR 319


>gi|323497826|ref|ZP_08102840.1| 23S rRNA pseudouridine synthase D [Vibrio sinaloensis DSM 21326]
 gi|323317173|gb|EGA70170.1| 23S rRNA pseudouridine synthase D [Vibrio sinaloensis DSM 21326]
          Length = 326

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 73/327 (22%), Positives = 142/327 (43%), Gaps = 36/327 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L +G+V+V+ + V K   ++  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKEWLLAGKVQVNGEVVTKPRTKVMGGEEIILQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +        +   LD               ++YED  I V NKP G  V  G+G     
Sbjct: 70  ELEDEERWEAQDIPLD---------------IVYEDDDILVINKPRGFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES-FRMRRIQKIYWS 185
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  +  + R   + Y +
Sbjct: 115 VLNALLHHYPSIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFVREYEA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G        +   + + S         +         AI+H++V + F ++   + +
Sbjct: 175 IAIGRM-TAGGRVEQPIGRHST-----KRTLMAVSPMGKPAITHYRVAEHF-REHTRIRL 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDL 297
           +  TGRTHQ+RVH  ++  P++GD  Y    +    +           ++  LHA  +  
Sbjct: 228 RLETGRTHQIRVHMSYLQHPLLGDSAYGGRARIPSGASNELAEKIRGFDRQALHAVMLKF 287

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLG 323
            HP  G  ++  AP+P  MV+  ++L 
Sbjct: 288 EHPITGEEVEFHAPVPDDMVEMAEALR 314


>gi|297172749|gb|ADI23715.1| pseudouridylate synthases, 23S RNA-specific [uncultured
           Oceanospirillales bacterium HF4000_21D01]
          Length = 321

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 79/323 (24%), Positives = 140/323 (43%), Gaps = 34/323 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  D    RLD+     +P  +   LQ  ++ G + V+ +R++  +R+ +G  + +   +
Sbjct: 11  VPQDLSGYRLDQIAAKLFPDYSRARLQIWIKDGSLLVNARRLRPRDRLHAGDKLEVNAEL 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHI 129
               + + E   LD               +++ED  + + NKPA + V    G G    +
Sbjct: 71  PVQENWLAEPMALD---------------IVFEDDCLIIVNKPANMVVHPASGHGDGTLL 115

Query: 130 DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +G L       +  +  + HRLD++T+G++VVA+T A+   L    + R I + Y ++V 
Sbjct: 116 NGLLHHHNALQQLPRAGIVHRLDKDTTGLMVVAKTLASHAALVNQMQARGIAREYEAVVQ 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+       +   L +          +     +    A++H++VI  + +    LE++  
Sbjct: 176 GVLTG-GGTVDAALGRHPVNRKKRAVL-----EIGQRAVTHYRVIKRY-RSHTHLEVKLD 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT--------SPIQNKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  PIVGD  Y    +                 +  LHAR + L HP
Sbjct: 229 TGRTHQIRVHMAHLNHPIVGDPMYGGRQRIPAACSEELIHCLKAFKRQALHARRLALHHP 288

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G+ +   +  P  MV     L
Sbjct: 289 GNGKLMSWESATPPDMVSLIYEL 311


>gi|304413613|ref|ZP_07395057.1| 23S rRNA pseudouridylate synthase [Candidatus Regiella insecticola
           LSR1]
 gi|304283704|gb|EFL92098.1| 23S rRNA pseudouridylate synthase [Candidatus Regiella insecticola
           LSR1]
          Length = 294

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 106/301 (35%), Positives = 160/301 (53%), Gaps = 13/301 (4%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
               +    + +I+R G+VRV+K R+K   ++Q+G  VRIPPV       + E++    S
Sbjct: 4   RLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLQNGDRVRIPPVR------VAERETRTLS 57

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           V L K S  L   +L+ED  + + NKP GI+V GGSG+ + +   L++ +  + +   L 
Sbjct: 58  VKLNKIS-SLPDRILFEDDALLILNKPFGIAVHGGSGVDFGVIEALRA-LRPEARFLELV 115

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG+L++A+ R+A + L E  R+++IQK Y +LV G   +  + +   LLK   
Sbjct: 116 HRLDRDTSGVLLIAKKRSALRALHEQLRLKKIQKDYLALVKGHWPSSCKKVQAPLLKNVL 175

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             G  V  V         + +HFKV + F +    L+  P TGRTHQ+RVH LH G PI 
Sbjct: 176 QNGGRVVKVSSE---GKVSETHFKVEERF-EYATLLKASPITGRTHQIRVHTLHSGHPIA 231

Query: 268 GDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
            D++Y    F  +      N+L+LHA  +   HP GG L I APL   +      L  K 
Sbjct: 232 FDNRYGDREFDRHLQDTGLNRLFLHAATLCCQHPLGGTLSIEAPLDDQLRHCLQILRKKS 291

Query: 327 D 327
            
Sbjct: 292 P 292


>gi|188991778|ref|YP_001903788.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. B100]
 gi|167733538|emb|CAP51742.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris]
          Length = 327

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 93/326 (28%), Positives = 153/326 (46%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRTGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++  +  D +   +     L++ +++ED+++   NKP G++  GGSGI+
Sbjct: 76  IPP--------VRLTEEGDKAAPPSAFQARLEAAIVFEDARLLALNKPTGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRALRP--NQTLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVDGRSIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L+ G   +    +   L      GG+    V         ++SHF++++      
Sbjct: 186 KRYLTLLVGRMPDGVMSVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFRLLERRG-GH 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G  + GD KY                +L+LHA  ++  
Sbjct: 242 SYCEVRIETGRTHQIRVHAQHLGHAVAGDDKYGDPEVNKRLRDQVGLRRLFLHAASLEFS 301

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     + APL   + +  D LG
Sbjct: 302 LDNGKTPYVLNAPLAPELAEALDRLG 327


>gi|57239260|ref|YP_180396.1| pseudouridylate synthase [Ehrlichia ruminantium str. Welgevonden]
 gi|58579223|ref|YP_197435.1| SfhB protein homolog (peudouridylate synthase) [Ehrlichia
           ruminantium str. Welgevonden]
 gi|57161339|emb|CAH58262.1| ribosomal large subunit pseudouridine synthase D [Ehrlichia
           ruminantium str. Welgevonden]
 gi|58417849|emb|CAI27053.1| SfhB protein homolog (peudouridylate synthase) [Ehrlichia
           ruminantium str. Welgevonden]
          Length = 324

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 84/332 (25%), Positives = 151/332 (45%), Gaps = 32/332 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVR 66
           + + ++N EEN RLD++      +I+   +Q+++++ ++ +  K VK NN I +   +  
Sbjct: 4   KKIFIQNGEENKRLDKFIALKL-NISRNKVQQLIQNNKIYLFNKIVKDNNHITKVNDIYY 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           I       N  I                  +   +LYED  I + NK  GI+V  G+G  
Sbjct: 63  INMPTQEHNCSITPNI-------------NIPITILYEDQDIIIINKEPGITVHPGAGTK 109

Query: 126 -AYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++G +  +        K  +P + HRLD++TSG++V+AR   +   L++    ++I
Sbjct: 110 DDTLVNGLIAHYGSTLSYIGKASRPGIVHRLDKDTSGLMVIARNEHSYYFLSDLLSKKQI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++VWGIP  K   I N +   +      +  V  +      AI+ +  I  FA  
Sbjct: 170 KKEYLAVVWGIPNPKCNIIKNHI--DTKSNNKQMMTVTHSRNKGKLAITEYNTIQTFASI 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQNKLYLHA 292
              ++ + +TGRTHQ+RVH  ++G  I+GD KY  N        + +       +  LHA
Sbjct: 228 ATLVKCRIYTGRTHQIRVHMSYIGNSIIGDQKYGKNDSKIAKYAQQSTIINTLKRQALHA 287

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
             +   HP     ++  + +P  +    + L 
Sbjct: 288 HKLGFIHPTTNTYIEFNSDIPNDIQILLNELA 319


>gi|320105613|ref|YP_004181203.1| RluA family pseudouridine synthase [Terriglobus saanensis SP1PR4]
 gi|319924134|gb|ADV81209.1| pseudouridine synthase, RluA family [Terriglobus saanensis SP1PR4]
          Length = 441

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 91/376 (24%), Positives = 155/376 (41%), Gaps = 74/376 (19%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++    +     +RLD +     P I+   +Q ++  GQVRVD K  K   ++  G+ +
Sbjct: 74  DIRSFSADAAAAGLRLDAYLAKAMPDISRGRVQLLIEQGQVRVDGKTAKNKLKLLGGERI 133

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I              +       L   ++ +   ++YED  + V +KPAG+ V  GSG+
Sbjct: 134 EI--------------EGEPRPAPLKAMAEDIPLKIVYEDEHMAVIDKPAGMMVHAGSGL 179

Query: 126 AY--HIDGFLKSWVDSKGQ----------KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                  G L + +               +P + HRLD++TSG+++VA+     + L E 
Sbjct: 180 TDDARSGGTLVNALLHHFNVNLSSVGGELRPGIVHRLDKQTSGLIMVAKNDRTHRALGEM 239

Query: 174 FRMRRIQKIYWSLVWGIP--------KNKKECIANWLLKKS------------------- 206
           F  R ++K Y +LV G          +     I   + +                     
Sbjct: 240 FSDRSLEKRYLALVHGEVGAKARGNAERDHGTINLPIGRDPIRRTRMTTRSRQSWMTTES 299

Query: 207 --------HIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQL 255
                       + +   K  E  A  A+SH++V++     A KF  LE+   TGRTHQ+
Sbjct: 300 PGTPSKLHPEEREPMKEPKLYE--ARAAVSHYEVLERLDTSAGKFTLLEVLIETGRTHQI 357

Query: 256 RVHALHMGCPIVGDHKYCA-------NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           RVH   +G P+VGD  Y A       +   +       + +LHA+ + L HP  G  L++
Sbjct: 358 RVHMQAIGHPVVGDTLYGAPARIVGLHRPEDGDGATLPRNFLHAKELHLAHPITGEDLEL 417

Query: 308 TAPLPAHMVKTWDSLG 323
            A +PA +++  + L 
Sbjct: 418 EAEIPADLIELLNRLR 433


>gi|146328747|ref|YP_001209889.1| ribosomal large subunit pseudouridine synthase, RluC [Dichelobacter
           nodosus VCS1703A]
 gi|146232217|gb|ABQ13195.1| ribosomal large subunit pseudouridine synthase, RluC [Dichelobacter
           nodosus VCS1703A]
          Length = 313

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 93/315 (29%), Positives = 156/315 (49%), Gaps = 16/315 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V ++ V   +   R+D + + ++P +    + ++LR G+VR +KKRVK  ++I +G V+R
Sbjct: 9   VHFMTVSAADAGQRVDNFIRKYHPALPKSRIYQMLRKGEVRRNKKRVKPTDKICAGDVIR 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+INA           D ++ +      +++ +LYED    + NKPAGI V GGSG  
Sbjct: 69  LPPIINAQRA--------DVAIPIYWQKR-IEAAVLYEDDHFLILNKPAGIVVHGGSGHE 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +   ++S          L HRLD +TSG+LV+ + R A      +     ++K YW+L
Sbjct: 120 FGVIDVVRSIWGENY--AELAHRLDGDTSGVLVLGKHRQALNAFQTAMNEGTVEKRYWAL 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+   ++  +   L K      + + V +   + A +A + F V+  + Q    +E  
Sbjct: 178 VDGVWTREEAEVVVHLTKAPLNVREKMQVSEL--ENAQFARTWFYVLQRW-QDATLMEAV 234

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
             TGRTHQ+RV A H    I GD KY    F         + L+LHAR +   + +   +
Sbjct: 235 LDTGRTHQIRVSAAHCQHAIAGDKKYGKREFNDLVRKKGFHGLFLHAREIKFCY-QNQTI 293

Query: 306 QITAPLPAHMVKTWD 320
            + APL   M +  +
Sbjct: 294 HVMAPLTEAMQQLLE 308


>gi|85704967|ref|ZP_01036067.1| ribosomal large subunit pseudouridine synthase D [Roseovarius sp.
           217]
 gi|85670289|gb|EAQ25150.1| ribosomal large subunit pseudouridine synthase D [Roseovarius sp.
           217]
          Length = 342

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 84/344 (24%), Positives = 144/344 (41%), Gaps = 50/344 (14%)

Query: 15  DEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           D+   RLD+      P    ++   L ++L  G V+V+   ++    R+ +G ++ I   
Sbjct: 12  DDPPQRLDKALSRDVPEEATLSRTRLARLLEEGAVQVNGAVMRDAKARVTAGDLIEI--- 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                       ++  +      ++ +   ++YED  + V NKPAG+ V    G      
Sbjct: 69  ------------LVPEARESHISAEAIALTVVYEDDDLIVINKPAGMVVHPAPGSPEGTL 116

Query: 129 IDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L    DS       ++P + HR+D++TSG+LVVA++ AA Q L   F    +++ Y
Sbjct: 117 VNALLHHCGDSLSGVGGSKRPGIVHRIDKDTSGLLVVAKSDAAHQGLAAQFEAHSVERSY 176

Query: 184 WSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE--KGANYAISHFK 231
            ++V G+P      +           N L   + +        KQ    +G  +A++  +
Sbjct: 177 RAVVNGVPDAGDPRLRGLPGISFEAGNILRIATRLARHKTDRQKQAVLFEGGRHAVTRAR 236

Query: 232 VIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---- 285
           VI+ F        +E    TGRTHQ+RVH  H G  ++GD  Y    K +  +       
Sbjct: 237 VIESFGTPGVVSLMECWLETGRTHQIRVHMAHAGHGLIGDPVYGGRRKLSEKALSATAVA 296

Query: 286 -----NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
                 +  LHA  +   HP  G  L+  A LP  M     +L 
Sbjct: 297 AARDFPRQALHAAVLGFVHPVSGMALRFEAALPEDMTTLIAALR 340


>gi|315126099|ref|YP_004068102.1| 23S rRNA pseudouridine synthase D [Pseudoalteromonas sp. SM9913]
 gi|315014613|gb|ADT67951.1| 23S rRNA pseudouridine synthase D [Pseudoalteromonas sp. SM9913]
          Length = 325

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 79/336 (23%), Positives = 139/336 (41%), Gaps = 36/336 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPV 70
           V  D    RLD+     +P  +   ++  +   ++ VD +       ++  G+VV +   
Sbjct: 11  VPTDLGGKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEIFNTPREKLLGGEVVAVETT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HI 129
           I A                    +  +K  ++YED  I V NKP G+ V  G+G     +
Sbjct: 71  IEA---------------PREYEAQDIKLNIVYEDDDILVINKPMGLVVHPGAGNPDGTV 115

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSL 186
              L  +       PR  + HRLD++T+G++VVA+T  A  HL ++ + R    + Y +L
Sbjct: 116 LNALLHYYPEIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTHLVKALQKRENFTREYEAL 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + +              +    AI+H++V + F +    L ++
Sbjct: 176 CNGTM-TAGGMVEKPIGRHATQ-----RTHMAVHEMGKPAITHYRVAEKF-RAHTRLRLR 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +         +  LHA  + + 
Sbjct: 229 LETGRTHQIRVHMAYLNHPLIGDQSYGGRPRPPKGATPELFELLRSFKRQALHAVKLSIA 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
           HP  G  +   AP+P  MV+   +L      N  I 
Sbjct: 289 HPITGEMMTWQAPIPDDMVQMTQALREDTKANPDIA 324


>gi|126733181|ref|ZP_01748928.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           CCS2]
 gi|126716047|gb|EBA12911.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           CCS2]
          Length = 341

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 85/341 (24%), Positives = 141/341 (41%), Gaps = 54/341 (15%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L K++  G V VD   V    +RI  G VV +   +   +
Sbjct: 17  RLDKALGRDVPDDASLSRSRLAKLIAEGAVSVDGAVVTDPRHRIAEGSVVEVTVAMAEES 76

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           HI+ E   LD               +++ED  + V NKPAG+ V    G        + +
Sbjct: 77  HIVGEDIPLD---------------VVFEDDDLIVVNKPAGMVVHPAPGTPNG--TLVNA 119

Query: 136 WVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            +   G+         +P + HR+D+ET+G+LV A++  A  HL + F    +++ Y ++
Sbjct: 120 LIHHCGETLSGVGGMKRPGIVHRIDKETTGLLVAAKSDRAHHHLADQFAAHTVERRYLAV 179

Query: 187 VWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVID 234
            +G+P      +           N L  ++ +G       +Q        +A++  ++++
Sbjct: 180 CYGLPDQNDPRLRGIKGTSFEPGNILKIQTFLGRHRTDRQRQAVSFTAGRHAVTRSRIVE 239

Query: 235 CFAQKFC--WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFTSP 283
                 C   +E    TGRTHQ+RVH  H G  ++GD  Y    K         G     
Sbjct: 240 GLGNPACAALIECWLETGRTHQIRVHMAHCGHALIGDPVYGGRRKLSQKAIGEVGVEAVA 299

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             ++  LHA  +   HP  G  LQ  A +P  M     +LG
Sbjct: 300 AFSRQALHAATLGFEHPVSGEFLQFEAEIPQDMRDLLRALG 340


>gi|226226809|ref|YP_002760915.1| ribosomal large subunit pseudouridine synthase D [Gemmatimonas
           aurantiaca T-27]
 gi|226090000|dbj|BAH38445.1| ribosomal large subunit pseudouridine synthase D [Gemmatimonas
           aurantiaca T-27]
          Length = 329

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 81/317 (25%), Positives = 141/317 (44%), Gaps = 35/317 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD    +H   ++      ++ +G V V+  R K + + ++G VVR+         
Sbjct: 17  AGGRLDLLVADH-ASVSRTQAATLIANGNVLVNGAREKASYKGETGDVVRVTIPPPPGRD 75

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           I+ EQ  LD               ++YED  + V +K AG+ V    G   +  G L + 
Sbjct: 76  IVAEQIPLD---------------VVYEDEHLLVVDKAAGMVVHPAPG---NWTGTLVNA 117

Query: 137 VDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +  +G+         +  L HRLD++TSG+LVVA++ AA + L+ +   R++ + Y ++ 
Sbjct: 118 LLGRGEPLAEGGGEDRAGLVHRLDKDTSGLLVVAKSDAAHRTLSSALAARQVTRRYAAVC 177

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           WG    ++  +   + +        + +V    +    + + F  +  F      L    
Sbjct: 178 WGHLAEERITVEKPIARDPR-DRTRMAIV----QSGKASRTDFTRLARF-DSVDLLRAHL 231

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
           HTGRTHQ+RVH    G P+VGD  Y              + +LHA ++   HP  G  + 
Sbjct: 232 HTGRTHQIRVHLASTGHPVVGDDTYGGGGGRRLALLPPRRHFLHAAWLRFRHPISGDLID 291

Query: 307 ITAPLPAHMVKTWDSLG 323
           + +PLPA +  +  +LG
Sbjct: 292 LRSPLPADLRTSLAALG 308


>gi|254486310|ref|ZP_05099515.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           GAI101]
 gi|214043179|gb|EEB83817.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           GAI101]
          Length = 344

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 89/356 (25%), Positives = 148/356 (41%), Gaps = 50/356 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M++ +   +  D    RLD+      P    ++   L +++  G V+VD   V     RI
Sbjct: 1   MSHRRISFIIADTPPPRLDKALARDVPEDANLSRTRLGRLIADGSVQVDGIVVTDPRARI 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             GQ + +       +HI+ E   L+               +++EDS + V NKPAG+ V
Sbjct: 61  FEGQEITVDVEEAEDSHILAESIPLE---------------VVFEDSDLIVINKPAGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    D        ++P + HR+D++TSG+LVVA++ AA   L +
Sbjct: 106 HPAPGSPSGTLVNALLAHCGDDLSGVGGMKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAK 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F    +++ Y +LV+G+P      +           N L   + +        +Q    
Sbjct: 166 QFEKHTVERYYQALVYGVPDANDPRLRGIKGTSFEPGNILKMTTQLARHRTDRQRQAVLF 225

Query: 221 KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +G  +A++  + I  +        +E    TGRTHQ+RVH  H G  +VGD  Y    K 
Sbjct: 226 QGGRHAVTRARTISRYGTPPVLALMECWLETGRTHQIRVHMAHAGHSLVGDPTYGGKRKL 285

Query: 279 NFTSPIQ---------NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
             T+  +          +  LHA  +   HP  G + +  APLP  M    D +  
Sbjct: 286 PKTALPEIASDAVRAFPRQALHAAVLGFEHPVTGEMVRFEAPLPRDMTDLLDLVAL 341


>gi|21231531|ref|NP_637448.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66768413|ref|YP_243175.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|21113212|gb|AAM41372.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66573745|gb|AAY49155.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
          Length = 327

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 93/326 (28%), Positives = 153/326 (46%), Gaps = 23/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V  D    RLD +            + K++RSGQVRV+  R K   +++ G+ VR
Sbjct: 16  VRILKVPEDRTGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAKAERKLEGGEEVR 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP        ++  +  D +   +     L++ +++ED+++   NKP G++  GGSGI+
Sbjct: 76  IPP--------VRLTEEGDKAAPPSAFQARLEAAIVFEDARLLALNKPTGVASHGGSGIS 127

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM------RRIQ 180
           +     L++      Q   L HRLD++TSG+L+VA+ R+A   L    R       R I 
Sbjct: 128 FGAIETLRALRP--NQTLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVDGRSIT 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L+ G   +    +   L      GG+    V         ++SHF++++      
Sbjct: 186 KRYLTLLVGRMPDGVMSVDAPLHIGLRQGGERHVQVNAI---GKPSLSHFRLLERRG-GH 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLP 298
            + E++  TGRTHQ+RVHA H+G  + GD KY                +L+LHA  ++  
Sbjct: 242 SYCEVRIETGRTHQIRVHAQHLGHAVAGDDKYGDPEVNKRLRDQVGLRRLFLHAASLEFA 301

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
              G     + APL   + +  D LG
Sbjct: 302 LDNGKTPYVLNAPLAPELAEALDRLG 327


>gi|170728051|ref|YP_001762077.1| RluA family pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169813398|gb|ACA87982.1| pseudouridine synthase, RluA family [Shewanella woodyi ATCC 51908]
          Length = 323

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 79/331 (23%), Positives = 142/331 (42%), Gaps = 35/331 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPV 70
           +   +   RLD+     YP  +   +++ +++G V +D     K   ++  GQ + I   
Sbjct: 11  ITATQTGQRLDQTLAELYPDYSRTRIKEWIQAGWVYIDGVVSTKPREKVLEGQEIAI--- 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                  +KE+            +  +   ++YED  I V NK AG+ V  G+G      
Sbjct: 68  ----EATLKEETAA--------KAQAIDLDIVYEDDHIIVINKQAGLVVHPGAGNQDGTL 115

Query: 129 IDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L          +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 MNALLHHCPGIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAVV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G          +  + +      ++ VV         A++H++V + F +    L ++ 
Sbjct: 176 LGTLI--SGGTVDEPIDRHPTKRTHMAVVH----NGKPAMTHYRVAEKF-RAHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            +GRTHQ+RVH  H+G  +VGD  Y    +       +         +  LHA  ++L H
Sbjct: 229 ESGRTHQIRVHMSHIGHTLVGDPVYGGRPRPPKGVTPEFFETYMGFKRQALHAIRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           P     +   AP+P  MV    +L    + N
Sbjct: 289 PYTFEIMSWQAPVPEDMVTLTRALRKDTEEN 319


>gi|297161299|gb|ADI11011.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces bingchenggensis BCW-1]
          Length = 312

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 77/331 (23%), Positives = 141/331 (42%), Gaps = 27/331 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V+VD      ++R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAIARMF-GFSRTKAAELAAAGKVQVDGSVAGKSDRVS 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +     A    I  + +                 ++++D  I V +KP G++  
Sbjct: 60  GGAWLEVEMPQAAPPVRIVAEPVE-------------GMEIVHDDEHIVVVDKPVGVAAH 106

Query: 121 GGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G     + G L +           ++  + HRLD  TSG++VVA++  A   L + F
Sbjct: 107 PSPGWTGPTVIGGLAAAGFRVSTSGAAERQGIVHRLDVGTSGLMVVAKSELAYTLLKQQF 166

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R + K Y +LV G P      I   + +  H   DY   V         +++H+ +I+
Sbjct: 167 RERTVDKRYQALVQGHPDPLSGTIDAPIGR--HPQHDYKWAVTAE---GKPSVTHYDLIE 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA  
Sbjct: 222 AF-RAASLLDIKLETGRTHQIRVHMAAHRHPCVGDLTYGADPTLAKRLQL-TRQWLHAVR 279

Query: 295 MDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           +   HP GG ++  +  P  + +  D++   
Sbjct: 280 LGFEHPGGGWVEFESRYPDDLQRALDTVRAD 310


>gi|209886260|ref|YP_002290117.1| ribosomal large subunit pseudouridine synthase D [Oligotropha
           carboxidovorans OM5]
 gi|209874456|gb|ACI94252.1| ribosomal large subunit pseudouridine synthase D [Oligotropha
           carboxidovorans OM5]
          Length = 366

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 77/346 (22%), Positives = 148/346 (42%), Gaps = 53/346 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVR 66
           + +      ++ RLDR        ++   L+ ++ +G V +    V+    ++++G+ + 
Sbjct: 41  RSITAAASGKSQRLDRLLAEQIDDLSRTRLKALILAGHVSLGDTVVRDPAYQVKAGEAIT 100

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I                +  +V+     + +   ++YED  I V +K  G+ V   +G  
Sbjct: 101 IE---------------VPPAVDPEPVGENIPLDIVYEDDDIIVLDKQRGLVVHPAAG-- 143

Query: 127 YHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            H +G L + + +            ++P + HRLD++T+G++V+A+   A Q LT  F  
Sbjct: 144 -HENGTLVNALIAHCGASLSGIGGVKRPGIVHRLDKDTTGLMVIAKNDHAHQSLTAQFAD 202

Query: 177 R----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
                 +++ Y + VWG+P   +  I   +  +     + + V          AI+H+++
Sbjct: 203 HGRTGELRRGYLAFVWGVPARPRGTIDQPI-DRHPFAREKMAVRA----SGRQAITHWEM 257

Query: 233 IDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-- 285
           ++ FA +        L  Q  TGRTHQ+RVH  H G P++GD  Y + F+       +  
Sbjct: 258 LESFAGRDGKPLAALLACQLETGRTHQIRVHLSHAGHPLIGDDVYGSGFRTKVNQLAEPA 317

Query: 286 -------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                   +  LHA  + + HP  G  L+  + LP  +      L 
Sbjct: 318 KIAVTTLGRQALHAYLLQIEHPTTGEVLEWQSELPEDLAHLQALLR 363


>gi|117618510|ref|YP_858498.1| ribosomal large subunit pseudouridine synthase D [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117559917|gb|ABK36865.1| ribosomal large subunit pseudouridine synthase D [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 326

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 71/325 (21%), Positives = 143/325 (44%), Gaps = 35/325 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72
           + +   RLD+     +P  +   +++ +   +V +D +       ++ +GQ V +     
Sbjct: 13  DHQFGQRLDQALAELFPDYSRTRIKEWILQDRVTLDGQVANTPREKVLAGQKVHVD---- 68

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--D 130
                      ++ + +    +  ++  ++YED  I V +KPAG+ V  G+G       +
Sbjct: 69  -----------VELADDTRWDAQNIELNIVYEDEHILVIDKPAGLVVHPGAGTPDGTILN 117

Query: 131 GFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             L  +   ++  +  + HRLD++T+G++VVA+T  A  HL E+ + R+I + Y ++  G
Sbjct: 118 ALLHRYPAIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVEALQARQITREYEAIAIG 177

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   +   + +          V          +++H++V + F +    L ++  T
Sbjct: 178 HM-TAGGTVDAPIGRHPTQRTHMAVV-----PNGRESVTHYRVHEKF-RGHTRLRLRLET 230

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPE 301
           GRTHQ+RVH  H+  P+VGD  Y    +    +  +        ++  LHA  + L HP 
Sbjct: 231 GRTHQIRVHMAHIKHPLVGDPAYGGRLRLLRNATPELTEALRGFHRQALHATMLKLAHPI 290

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            G  ++  +P P  M+   + L   
Sbjct: 291 TGEVMEWHSPTPQDMLDLMEVLRAD 315


>gi|332297938|ref|YP_004439860.1| pseudouridine synthase, RluA family [Treponema brennaborense DSM
           12168]
 gi|332181041|gb|AEE16729.1| pseudouridine synthase, RluA family [Treponema brennaborense DSM
           12168]
          Length = 318

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 145/330 (43%), Gaps = 37/330 (11%)

Query: 10  VVVENDEENMRLDRWF------KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           V V       RLD++       +     +N   L K + +G + V+ +  K + +I+ G 
Sbjct: 6   VTVPAASAAERLDKYLISCESVQQQCAGLNRSKL-KAIATG-ITVNGRDAKLSTKIRPGD 63

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-- 121
            + +    N  +HI  E   LD               ++YED  + V NK  G+      
Sbjct: 64  SIVVDWADNIPDHIDPEDIPLD---------------IIYEDGNVAVVNKKQGMVTHPAL 108

Query: 122 GSGIAYHIDGFLKSW----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G+     ++  L  W    V    ++P + HRLD++TSG+++  + R + + L   FR R
Sbjct: 109 GNWSGTLVNALLFHWNRESVAQTARRPGIVHRLDKDTSGLIITGKNRESEEWLQAQFRDR 168

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           R++K Y ++V G P +    I   +++       +    +   +   +A + ++ I C+ 
Sbjct: 169 RVKKEYIAIVAGRPPHASGTIKTQIIRDPRNRKRFK--AETGTENGKFAHTQYRCIACYG 226

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  + +Q  TGRTHQ+RVH  ++GCPI+GD  Y    +          L LH+R + +
Sbjct: 227 S-FSLMRLQLKTGRTHQIRVHMKYLGCPILGDPLYGNKTQ----LFPDATLMLHSRLLSI 281

Query: 298 PHPEGGRL-QITAPLPAHMVKTWDSLGFKY 326
             P      +  AP+P    K   +L  KY
Sbjct: 282 RLPGQAAFSEFKAPVPRRFKKVLKTLHGKY 311


>gi|241667739|ref|ZP_04755317.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25015]
 gi|254876283|ref|ZP_05248993.1| ribosomal large subunit pseudouridine synthase C [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|254842304|gb|EET20718.1| ribosomal large subunit pseudouridine synthase C [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
          Length = 309

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 94/316 (29%), Positives = 161/316 (50%), Gaps = 14/316 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  VQ + V +D    R+D +  + +  +    + + +R G++RV+KKRVK   R+ +G 
Sbjct: 1   MNKVQLIEVTDDVIEQRIDNFLISKFSRLPKSLIYRWIRKGELRVNKKRVKQTTRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP     N        L+ +     H DFL+  +LYE     V +KP+G++V GGS
Sbjct: 61  IVRVPPFSLEEN--------LEIAKVSKSHLDFLEQRILYETDDYIVVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKERKVNKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++LV G    K + I   L +     G    +VK +++    A++    +      +  L
Sbjct: 172 YALVHGHWDEKVDAIDLPLSRTETKDGQR--IVKVDKREGKRALTRILAVQKIGD-YSLL 228

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEG 302
           E++  TGRTHQ+RVH   MG PIV D KY          +   +KL LHA  ++    + 
Sbjct: 229 EIKLETGRTHQIRVHTRAMGHPIVADKKYGYMIDDEKLLAKGVDKLLLHAGKLEFYDEKQ 288

Query: 303 GR-LQITAPLPAHMVK 317
            + + I A L +   +
Sbjct: 289 QKLISIEAKLDSRFDE 304


>gi|163856156|ref|YP_001630455.1| ribosomal large subunit pseudouridine synthase D [Bordetella petrii
           DSM 12804]
 gi|163259884|emb|CAP42185.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           petrii]
          Length = 324

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 71/325 (21%), Positives = 129/325 (39%), Gaps = 30/325 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q++ V       RLD+         +   LQ  + +G V+V+    K    +  G V+ +
Sbjct: 22  QFITVPAGTRADRLDKILAALLDGHSRSRLQGWIEAGWVQVNGAPAKVRQVVGPGDVLAV 81

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                             +  +L    + +   ++ E     V +KPAG+    G+G   
Sbjct: 82  WEQ--------------PAPESLAFTPEPIAFAVVAESPDWIVVDKPAGLVTHPGAGNWS 127

Query: 126 AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + + ++  +  + HRLD++TSG++VVAR   A  HL    + R + + Y 
Sbjct: 128 GTLLNGLLHRYPELARVARAGIVHRLDKDTSGLMVVARNELAQTHLVRQLQARSMGREYI 187

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFC 241
           +L  G        +   + + + +    V +  +       AI+H+  +           
Sbjct: 188 ALAHG-WLPVAGKVDRPIGRDARV---PVRMSVERPIAPKPAITHYAPLRRGRAPDGPVT 243

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            +  +  TGRTHQ+RVH   +G P++ D  Y        T     +  LHAR +    P 
Sbjct: 244 EVACRLETGRTHQIRVHLASLGHPLLADTLYGGRLTAGAT-----RQMLHARALHFDDPG 298

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFK 325
            GG     A  P  M +  ++L + 
Sbjct: 299 GGGPAAFRADPPDDMRQVQEALQWS 323


>gi|148257971|ref|YP_001242556.1| ribosomal large subunit pseudouridine synthase D [Bradyrhizobium
           sp. BTAi1]
 gi|146410144|gb|ABQ38650.1| ribosomal large subunit pseudouridine synthase D [Bradyrhizobium
           sp. BTAi1]
          Length = 326

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 82/345 (23%), Positives = 144/345 (41%), Gaps = 53/345 (15%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRI 67
            V+V  DE + RLDR      P ++   L+ ++ +GQV +           + SG  + I
Sbjct: 2   TVIVAGDEGSPRLDRVLAARLPELSRSRLKALILAGQVSLSTGAVRDPAYHVASGDTITI 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           +  +      ++ +   ++YED  I V +KPAG+ V   +G   
Sbjct: 62  D---------------VPEAAPPEPKAEAIPLHVVYEDDDIVVLDKPAGLVVHPAAG--- 103

Query: 128 HIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           H  G L + + +            ++P + HRLD++T+G++VVA+   A   L+  F   
Sbjct: 104 HETGTLVNALIAHCGASLSGIGGVKRPGIVHRLDKDTTGLMVVAKNDHAHASLSAQFADH 163

Query: 178 ----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                +++ Y +  WG+P      I   L +  H   D + V  +       AI+H++V 
Sbjct: 164 GRTGAMERGYLAFSWGLPHRPHGTINAPLDRHPH-ARDKMAVRPR----GREAITHYEVQ 218

Query: 234 DCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GN 279
           + F  +        +     TGRTHQ+RVH  H+G  ++GD  Y  +FK           
Sbjct: 219 ESFVGRDGKPVASLIACHLETGRTHQIRVHLAHLGHTLLGDAVYGPHFKTKANQLAPGAR 278

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
                  +  LHA  + + HP  G + +  + LP  +    ++L 
Sbjct: 279 AALEALGRQALHAYLLVIEHPRTGEILRWESELPEDLSLLREALR 323


>gi|225870653|ref|YP_002746600.1| RNA pseudouridylate synthase [Streptococcus equi subsp. equi 4047]
 gi|225700057|emb|CAW94108.1| putative RNA pseudouridylate synthase [Streptococcus equi subsp.
           equi 4047]
          Length = 296

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 73/315 (23%), Positives = 132/315 (41%), Gaps = 34/315 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +  P ++       ++  +V V+    K    +Q G  +          
Sbjct: 7   ESGHRLDKALADLTP-LSRSQANDQIKQKRVLVNGLPKKAKYIVQVGDCISYH------- 58

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                   +    +L   +  +   ++Y+D  + + NKP G+ V   +G      ++  L
Sbjct: 59  --------IPEESSLDYQAQDIPLDIVYQDDVLAIINKPQGMVVHPSAGHSTGTLVNALL 110

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               D        +P + HR+D++TSG+L+VA+T  A Q L +  + ++  + Y ++V G
Sbjct: 111 YHIKDLSSINGVIRPGIVHRIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I   + +            K        A++ FKV++ F   + ++E+Q  T
Sbjct: 171 NLPKDRGVIEAPIGRSEKDRKKQTVTAK-----GKEALTLFKVLERFGH-YTFVELQLET 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
           GRTHQ+RVH  ++G P+ GD  Y         +      +LHA+ + L HP  G  L  T
Sbjct: 225 GRTHQIRVHMAYIGHPLAGDPLYGPR-----KTLAGKGQFLHAQTLGLTHPVTGEELVFT 279

Query: 309 APLPAHMVKTWDSLG 323
              P    +T + L 
Sbjct: 280 VEPPEIFQRTLEQLR 294


>gi|258645705|ref|ZP_05733174.1| ribosomal large subunit pseudouridine synthase D [Dialister invisus
           DSM 15470]
 gi|260403074|gb|EEW96621.1| ribosomal large subunit pseudouridine synthase D [Dialister invisus
           DSM 15470]
          Length = 308

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 81/320 (25%), Positives = 137/320 (42%), Gaps = 38/320 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQVVRIPPV 70
           V   +E  RLD++ K     +    +QK +++G V  + KK +  N  +  G  +     
Sbjct: 8   VSVADEGKRLDQFLKER-TGLTRSEVQKWIKAGNVSLLPKKMIHSNYHVSEGDRISFFWE 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------ 124
                 +I +   LD               +LYED+ + V NK  G+ V  G+G      
Sbjct: 67  EKKKQELIGQNIPLD---------------ILYEDNDMIVINKRRGVVVHPGAGNTEGTL 111

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + +H    L+S  D   ++P + HRLD++TSG++V A++  A   L +     + Q+
Sbjct: 112 VNALLFHCGEQLRSVGDP--ERPGIVHRLDKDTSGVMVAAKSERAYGILQKEIASHKAQR 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  +     I   L + +     +        +    A++HF VI+     + 
Sbjct: 170 CYIALVHGQMEGDTGVIRLPLGRSTKDRMKW----DVLHETGRPAVTHFHVIEYLPH-YS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           W+E +  TGRTHQ+RVH  H+   +V D  Y                 LH+  ++L HP 
Sbjct: 225 WIECKLETGRTHQIRVHMAHIRHAVVNDPLYG----WKKDHFPIKGQALHSHTLELCHPI 280

Query: 302 GGR-LQITAPLPAHMVKTWD 320
            G  +   AP+P  M+   +
Sbjct: 281 TGEVMHFEAPVPEDMINCLN 300


>gi|256028259|ref|ZP_05442093.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
 gi|289766191|ref|ZP_06525569.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
 gi|289717746|gb|EFD81758.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
          Length = 328

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 75/338 (22%), Positives = 143/338 (42%), Gaps = 36/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V +  E MRLD++            L+K++ +  V+++ K +  N  ++
Sbjct: 1   MENIKEKFEFEVNSKYEGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G+ + +               ++    N+    + +   ++YE++   V NK  G+ V
Sbjct: 61  KLGEKIEV---------------LIPEEENIDIEPENIPLDIVYENNDFIVINKNYGMVV 105

Query: 120 QGGSG-IAYHIDGFLKSWVDSK-----GQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     +   L  + ++        +P + HRLD++TSG+++VA++  A   L   
Sbjct: 106 HPAYGNYTGTLVNALLYYTNNLSSINGNIRPGIIHRLDKDTSGLILVAKSNYAHAKLASM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           F  + I K Y  +V G    +     I N + + S      + VVK+N      AIS++K
Sbjct: 166 FIDKTIHKTYLCIVKGNFSEENLSGRIENLIGRDSK-DRKKMAVVKEN---GKIAISNYK 221

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V++   + +  +E+   TGRTHQ+RVH   +   I+GD  Y    K         +  LH
Sbjct: 222 VVEQV-EGYSLVEVAIETGRTHQIRVHMKSINHVILGDSVYGNEDKNV------KRQMLH 274

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A  ++  +P +         L    ++    L F  ++
Sbjct: 275 AYKLEFLNPLDNKEYVFKGKLFDDFIEIAKKLKFNIEK 312


>gi|284044971|ref|YP_003395311.1| pseudouridine synthase [Conexibacter woesei DSM 14684]
 gi|283949192|gb|ADB51936.1| pseudouridine synthase, RluA family [Conexibacter woesei DSM 14684]
          Length = 299

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 131/323 (40%), Gaps = 32/323 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     + V  +    RLD +     P  +    Q+++ +G V VD       +++ +G+
Sbjct: 1   MPAPLTLEVGAEAAGERLDLFLAQ--PLGSRARAQRLIDAGLVTVDGAARPKRHKVSAGE 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V + P                  V   + S      + +ED  + + +KPAG+ V    
Sbjct: 59  RVEVTP----------------EPVVDVEPSGDAPFAVAWEDEHLLIVDKPAGVVVHPAP 102

Query: 124 GIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G          +   + G+ P    + HRLD++TSG+L+VA+T  A + L      R + 
Sbjct: 103 GNRTGTLSQALAGRAAGGEDPSRAGIVHRLDRDTSGLLIVAKTEEAHRELKRMIEARDVT 162

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV G P  +   I   + +   +       +         A +HF+ ++      
Sbjct: 163 REYVALVEGTPPARSGTIDAPIGRDRRV----RTRMSTETDDPRDARTHFR-LERALPDS 217

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L +   TGRTHQ+RVH   +G P+VGD +Y              + +LHA  +   HP
Sbjct: 218 ALLRVTLETGRTHQIRVHLEAIGHPVVGDPEYG-----RAGRFGLERQFLHAARLAFAHP 272

Query: 301 -EGGRLQITAPLPAHMVKTWDSL 322
               ++ +++PLP  +      L
Sbjct: 273 LRDEQVDVSSPLPPDLAAVLAQL 295


>gi|109897660|ref|YP_660915.1| RluA family pseudouridine synthase [Pseudoalteromonas atlantica
           T6c]
 gi|109699941|gb|ABG39861.1| ribosomal large subunit pseudouridine synthase D [Pseudoalteromonas
           atlantica T6c]
          Length = 327

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 85/332 (25%), Positives = 139/332 (41%), Gaps = 35/332 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           VV       RLD+     +P  +   ++  + + QV VD + V K   ++   +++ I  
Sbjct: 13  VVPQTLLGKRLDQALAEMFPDYSRSRIKDWILADQVAVDGQIVNKPREKLLGEELIEIDA 72

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            I                      +  ++  ++YED  I V NKP  + V  G+G A   
Sbjct: 73  SIEIQER---------------HSAQEIELNIVYEDEHILVINKPTNLVVHPGAGNASGT 117

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           I   L S V      PR  + HRLD++T+G++VVA+T  A  HL E  + R I + Y ++
Sbjct: 118 ILNALLSHVPEIASVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVEKLQAREISREYEAV 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G        +   + +          V     +    A++H++V     +    L ++
Sbjct: 178 VYGNLIA-GGSVDEPIGRHPTKRTSMAVV-----QSGKPALTHYRV-KHKYRAHTHLRLK 230

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             +GRTHQ+RVH  H+  P+VGD  Y    +    +            +  LHA  ++L 
Sbjct: 231 LESGRTHQIRVHMAHLRHPLVGDQAYGGRPRLPKAASELMIETIRGFKRQALHAIQLELE 290

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           HP  G  +   APLP   V   D L     +N
Sbjct: 291 HPITGEWMSFQAPLPDDFVNLLDVLKEDTAQN 322


>gi|313679572|ref|YP_004057311.1| ribosomal large subunit pseudouridine synthase d [Oceanithermus
           profundus DSM 14977]
 gi|313152287|gb|ADR36138.1| ribosomal large subunit pseudouridine synthase D [Oceanithermus
           profundus DSM 14977]
          Length = 306

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 100/321 (31%), Positives = 152/321 (47%), Gaps = 38/321 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + E  RLD+        ++    Q  + +G VRV  + V    R  +G+ V +       
Sbjct: 8   EAEGERLDQALARAL-GVSRARAQAWISAGHVRVAGEVVTKPARRLAGERVEVEVPPEPP 66

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGF 132
             +  E                L   +LYED  + V NKPAG+      G+     ++  
Sbjct: 67  ARVEAED---------------LTVEILYEDEDMVVVNKPAGMVTHPAPGVTRGTLVNAL 111

Query: 133 LKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           L  WV+  G+  +P + HRLD+ETSG++VVAR  AA + L ++F+ R + K Y +L  G+
Sbjct: 112 LGRWVEPGGEPVRPGIVHRLDKETSGVIVVARHEAALRRLADAFKQRFVFKRYVALTEGV 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPH 248
           P N            + IG   VH  K +  G  A YA + F+V+   A+    +E +PH
Sbjct: 172 PANTTVI--------APIGRHPVHRFKMHTGGIKARYAETDFEVVAT-AEGRALVEARPH 222

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QI 307
           TGRTHQ+RVH  H+  PI  D  Y         SP   +L LHA  + +PHP+ G++   
Sbjct: 223 TGRTHQIRVHLKHLHTPIWADPLYGK------PSPFIGRLALHAYELRVPHPKSGKILSF 276

Query: 308 TAPLPAHMVKTWDSLGFKYDR 328
           TAP+P  M + W++ G  +  
Sbjct: 277 TAPVPEDMARGWEAAGGVWPE 297


>gi|19704707|ref|NP_604269.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
 gi|296327673|ref|ZP_06870215.1| RluA family pseudouridine synthase [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
 gi|19715021|gb|AAL95568.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
 gi|296155204|gb|EFG95979.1| RluA family pseudouridine synthase [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
          Length = 319

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 74/338 (21%), Positives = 143/338 (42%), Gaps = 36/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V ++ E MRLD++            L+K++ +  V+V+ K +  N  ++
Sbjct: 6   MENIKEKFEFEVNSEYEGMRLDKYLSEQIEEATRSYLEKLIDNNFVKVNSKIINKNGRKL 65

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G+ + +               ++    N+    + +   ++YE+    + NK  G+ V
Sbjct: 66  KLGEKIEV---------------LIPEEENIDIEPENIPLNIVYENDDFILINKSYGMVV 110

Query: 120 QGGSG-IAYHIDGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     +   L  + +     +   +P + HRLD++TSG+++VA+   A   L   
Sbjct: 111 HPAYGNYTGTLVNALLYYTNNLSSVNGNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASM 170

Query: 174 FRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           F  + I K Y  +V G    +     I N + + S      + +VK+N      AIS++K
Sbjct: 171 FIDKTIHKTYLCIVKGNFSEENLSGRIENLIGRDSK-DRKKMTIVKEN---GKIAISNYK 226

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V++   + +  +E+   TGRTHQ+RVH   +   I+GD  Y    K         +  LH
Sbjct: 227 VVEQV-EGYSLVEVAIETGRTHQIRVHMKSINHVILGDSVYGTEDKNV------KRQMLH 279

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A  ++  +P +  +      L    ++    L F  ++
Sbjct: 280 AYKLEFLNPLDNKKYIFKGKLFDDFIEVAKRLKFNIEK 317


>gi|315226968|ref|ZP_07868756.1| pseudouridylate synthase [Parascardovia denticolens DSM 10105]
 gi|315121100|gb|EFT84232.1| pseudouridylate synthase [Parascardovia denticolens DSM 10105]
          Length = 337

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 72/328 (21%), Positives = 139/328 (42%), Gaps = 18/328 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+   +  D   +R D+        ++     +++  GQ RV+ + V  + +I  G  + 
Sbjct: 8   VRSFEMGEDSFGLRFDQALSRIL-GLSRSQAARLIADGQARVEGRSVPKSGQILPGDFIL 66

Query: 67  IPPVI----NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           +         +   I    +          +       ++YED  + V +KPAG++    
Sbjct: 67  VSSAGSTAGPSGVRIFTGSQTSKDEKAAGPNQAEASLPIVYEDDDLVVVDKPAGMASHPA 126

Query: 123 SGIA-YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +G A   +   L++            +P +  RLD  TSG+++V ++  A   + E F  
Sbjct: 127 AGWAGPTVVEALQALDKDLSRVDSDIRPGIVSRLDAGTSGLMLVCKSDRAFVAMKEQFAR 186

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++K Y +LV G     +  +   + +++        +          AI+H+ V++  
Sbjct: 187 HQVKKTYQTLVQGHIAQDRATVEAPIARQTGASSFRFAI----SPDGKPAITHWDVLERL 242

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 L +   TGRTHQ+RVH   +G P++GD  Y AN +        N+ +LH+  ++
Sbjct: 243 P-GATLLSINLETGRTHQIRVHLSSLGHPLIGDTLYGANPRL-AEELGLNRQWLHSIRLE 300

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP GGR + + +PLP  +    + L 
Sbjct: 301 FTHPVGGRTIHLESPLPDDLSHALEVLR 328


>gi|294142197|ref|YP_003558175.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           violacea DSS12]
 gi|293328666|dbj|BAJ03397.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           violacea DSS12]
          Length = 324

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 78/331 (23%), Positives = 140/331 (42%), Gaps = 35/331 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +   RLD+   + +P  +   +++ +  G V +D     K   ++  GQ+V +   
Sbjct: 11  ITATQTGQRLDQTLADLFPDYSRTRIKEWILDGSVTIDGDVSNKPREKVLEGQIVVVGAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           +                   T  +  +   ++YED  I V NK AG+ V  G+G      
Sbjct: 71  LVE---------------ETTAKAQAIDLNIVYEDDHILVINKQAGLVVHPGAGNSDGTL 115

Query: 129 IDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L          +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 LNALLHHCPGIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G          +  + +      ++ VV         A++HF+V + F +    L ++ 
Sbjct: 176 LGSLI--SGGTVDEPIDRHPTKRTHMAVVY----SGKPAMTHFRVAEKF-RAHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            +GRTHQ+RVH  H+G  +VGD  Y    +       +         +  LHA  ++L H
Sbjct: 229 ESGRTHQIRVHMAHLGHTLVGDPVYGGRPRPPKAVTPEFFDVYMNFKRQALHAIRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           P     +   AP+P  MV    +L    + N
Sbjct: 289 PYTCEIMSWQAPVPEDMVILTKALRKDTEDN 319


>gi|224065743|ref|XP_002301949.1| predicted protein [Populus trichocarpa]
 gi|222843675|gb|EEE81222.1| predicted protein [Populus trichocarpa]
          Length = 444

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 88/362 (24%), Positives = 148/362 (40%), Gaps = 65/362 (17%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V++     RLD W  +    I+   +Q  ++SG V V+ K + K ++ +++G  V     
Sbjct: 87  VDSKSGKSRLDSWISSRISGISRARVQSSIKSGLVSVNGKVIDKVSHNVKAGDKVNC--- 143

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--H 128
                       ++     L    + +   ++YED  + V NKPA + V    G A    
Sbjct: 144 ------------VISELQPLRAEPENIPLDIVYEDENVLVVNKPAHMVVHPAPGNATGTL 191

Query: 129 IDGFLKSWV-------------------DSKGQ---------KPRLTHRLDQETSGILVV 160
           ++G L                       D +G          +P + HRLD+ TSG+LVV
Sbjct: 192 VNGILHHCSLPTVSSQEVLSGAEDVSDDDDEGLCSSSYAASVRPGIVHRLDKGTSGLLVV 251

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+   +  HL+E F++  I+++Y SL  G+P      I   + +          +V+ N 
Sbjct: 252 AKDEHSHAHLSEQFKLHTIKRVYVSLTCGVPAPMAGRIDVPIGRDVSNRIRMAAIVEPNR 311

Query: 221 KGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA----- 274
             A +A S +KVI+         +E +  TGRTHQ+R HA ++G P++GD  Y       
Sbjct: 312 GQARHAASRYKVIEILAGGGSALVEWRLETGRTHQIRAHAKYIGIPLLGDEVYGGTQNMA 371

Query: 275 -NFKGNFTSPIQNKL-----------YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
            +   + T P  ++             LHA  +   HP  G  +  + P P    +    
Sbjct: 372 LSLLRSRTQPSCHRQLSLSLSGLERPCLHALALGFTHPCTGKEIHFSCPPPPDFTEILSQ 431

Query: 322 LG 323
           L 
Sbjct: 432 LR 433


>gi|218290459|ref|ZP_03494579.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|218239480|gb|EED06675.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
          Length = 314

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 85/334 (25%), Positives = 161/334 (48%), Gaps = 37/334 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPH----INFVNLQKILRSGQVRVDK-KRVKF 55
           M    +VQY  V  ++   RLDRW  +        ++   +Q+ +  G VR  +  R+K 
Sbjct: 1   MRPAIHVQY-EVSAEDAGERLDRWLTDRLQEDEIEVSRTQVQRWISDGCVRRARPGRLKA 59

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           ++ +++G +  +          + E++ ++ +         +   + YED  + V +KP 
Sbjct: 60  SDPVEAGDLYEVD---------VPEEEPMELA-----PDAGVPFAVAYEDDDVVVVDKPR 105

Query: 116 GISVQGGSGI--AYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           G+ V  G+G      ++G L         +   +P + HR+D++TSG++V A++  A + 
Sbjct: 106 GVVVHPGAGHMRGTLVNGLLARGTQLCTLAGAMRPGVVHRIDKDTSGLVVFAKSDRAYRW 165

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           L E+FR   +++ Y ++  G   +++  I   + +        + V     +G   A++H
Sbjct: 166 LVEAFRAHDVEREYVAIAHGRMSHREGTIDMPIARD-PADRQRMAVR----QGGKRAVTH 220

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           F+V++ FA K+ +L ++  TGRTHQ+RVH   +G PI GD  Y         +   +   
Sbjct: 221 FEVLESFA-KYSYLRLRLETGRTHQIRVHLAAIGHPIAGDPVYGPRH-----TLPIDGQA 274

Query: 290 LHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
           LHAR +   HP+G RL+  + +P+ M +  D L 
Sbjct: 275 LHARTLGFTHPDGRRLRFESAIPSDMARLLDGLR 308


>gi|219682262|ref|YP_002468646.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. Tuc7 (Acyrthosiphon pisum)]
 gi|219621995|gb|ACL30151.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. Tuc7 (Acyrthosiphon pisum)]
 gi|311086084|gb|ADP66166.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. LL01 (Acyrthosiphon pisum)]
 gi|311086657|gb|ADP66738.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. TLW03 (Acyrthosiphon pisum)]
 gi|311087242|gb|ADP67322.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. JF99 (Acyrthosiphon pisum)]
 gi|311087761|gb|ADP67840.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. JF98 (Acyrthosiphon pisum)]
          Length = 314

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 173/319 (54%), Gaps = 16/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + +  +  N R+D + ++ +  +    + +I+R+G++R++KKR+K + +++ G +++
Sbjct: 8   ISIIYINKEMLNQRIDNFMRSKFKSVPKSMIYRIIRTGKIRINKKRIKPHYKLKIGDILK 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+    +        + ++     HS  L + +LYEDS + + NKP+GI+V GGSG+ 
Sbjct: 68  IPPIKILCD--------IKNTFFPLNHSTNLLNRILYEDSHLLIINKPSGIAVHGGSGLN 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +  + +  +    +   L HR+D++TSG+L++A+ R +   L E  R ++I+K Y +L
Sbjct: 120 FGVIEYFRK-LRPLNKFLELVHRIDRDTSGVLILAKKRTSLVSLHEQLREKKIKKEYIAL 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  +  + I+  LLK        + ++   +K    + ++F++   F+     L + 
Sbjct: 179 VHGLWPDHIKKISEPLLKIQFKNKQKMVLI---DKKGKPSETYFQIKKKFSSS-TLLSII 234

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGG- 303
           P TGRTHQ+RVHALH G PI  D +Y  N        +   N+L LH+  +   HP+ G 
Sbjct: 235 PKTGRTHQIRVHALHAGHPIFFDKRYGKNNLDADIKNNHKINRLLLHSSGVHFIHPKNGN 294

Query: 304 RLQITAPLPAHMVKTWDSL 322
           ++ I APL        +++
Sbjct: 295 KIYIKAPLDIDFQNYLNTI 313


>gi|291563387|emb|CBL42203.1| pseudouridine synthase, RluA family [butyrate-producing bacterium
           SS3/4]
          Length = 332

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 85/344 (24%), Positives = 148/344 (43%), Gaps = 35/344 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +V+E +E   RLD++   +    +     K++R   + ++ K+ + N ++  G VV+
Sbjct: 1   MREIVIEKNEAGQRLDKFLAKYMNEASKSFFYKMMRKKNITLNGKKCEGNEKLAEGDVVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          + E  I   S    +    +   +LYED +I + NKPAG+  Q      
Sbjct: 61  L---------FLAEDTIEKFSSVQVQEVKKVDLDILYEDDEIILVNKPAGMLSQKAKETD 111

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  +L  ++   G+         +P + +RLD+ TSGI+   ++ A  Q L+  F+ R
Sbjct: 112 ESLVEYLIDYLLGSGKLTESGLRAFRPSVCNRLDRNTSGIVAAGKSLAGLQMLSGVFKDR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV----HVVKQNEKGA----NYAISH 229
            I K Y  LV G  ++ K  +  WLLK        +       +   +G         + 
Sbjct: 172 SIHKYYQCLVSGEIRDVK-TVDGWLLKDEKKNQVRILTEAEAKRFGGRGGDEEPKRIRTK 230

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           ++ I    + F  L++   TGR+HQ+R H   +G PIVGD KY    K N +        
Sbjct: 231 YEPIATDGR-FTLLKVTLLTGRSHQIRAHLASLGHPIVGDFKYGGVSKVNPSGRTVKYQL 289

Query: 290 LHARYMDLP---HPE---GGRLQITAPLPAHMVKTWDSLGFKYD 327
           LH+  ++ P    P     GR+   APLP +        G +  
Sbjct: 290 LHSYRLEFPKLAEPFVYLSGRV-FEAPLPGYFGSVLKETGIRSP 332


>gi|59711171|ref|YP_203947.1| 23S rRNA pseudouridine synthase D [Vibrio fischeri ES114]
 gi|59479272|gb|AAW85059.1| 23S rRNA pseudouridine synthase [Vibrio fischeri ES114]
          Length = 324

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 73/344 (21%), Positives = 148/344 (43%), Gaps = 42/344 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +   RLD+     +   +   +++ L +G + V+ + V K   ++  G+ + +  
Sbjct: 10  TVKESQLGQRLDQAAAELFSDFSRSRIKEWLLAGNMTVNGEVVTKARLKVMGGEEITVKA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +      + +   LD               ++YED  + V NKP    V  G+G     
Sbjct: 70  ELEDEERWLAQDIPLD---------------IVYEDDDLLVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + + ++  +  + HRLD++T+G++VVA+T  A   L  + + R+I + Y ++
Sbjct: 115 VLNALLFHYPNIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRKITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + +  +        +    +    A++H++V + F +    + ++
Sbjct: 175 VVGRM-TAGGMIEKPIGRHPN-----KRTLMAVHELGKDAVTHYRVAEHF-RIHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P+VGD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLVGDTAYGGRARIPKGASQELIDMIRGFDRQALHAAMLRFE 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDEC 341
           HP  G  ++  AP+P  M+    +L          +RL  ++E 
Sbjct: 288 HPITGETMEFHAPIPDDMIALSQALRDD-------ERLMHEEEY 324


>gi|332185831|ref|ZP_08387578.1| pseudouridine synthase, RluA family protein [Sphingomonas sp. S17]
 gi|332014189|gb|EGI56247.1| pseudouridine synthase, RluA family protein [Sphingomonas sp. S17]
          Length = 315

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 137/323 (42%), Gaps = 33/323 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           +    +  RLDR   +  P ++   L+ ++ SG V  +    +    R  +G + ++   
Sbjct: 12  IAPTADGWRLDRALADAVPTLSRERLKVLIASGAVTREGVMARDPAKRAAAGDLFQV--- 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHI 129
                        + +       +  +  ++ YED  + V +KPAG+ V   +G +   +
Sbjct: 69  ------------AVPAPTPAHNEAQDIPLVIAYEDEHLIVIDKPAGLVVHPAAGNLDGTL 116

Query: 130 DGFLKSWVDSK------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              L  +            +P + HR+D++TSG++V A+T    + L + F    I + Y
Sbjct: 117 VNALLHYCGGSLSGIGGVARPGIVHRIDKDTSGLMVAAKTDRTHEGLAKQFAAHSIDRRY 176

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++  GIP+     +   L + S      V +V    +G   A++H++ I+        +
Sbjct: 177 RAITGGIPRPADGTVDAPLAR-SPQNRKKVAIV----QGGKRAVTHYRTIEKL-NNAALV 230

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHP 300
           E +  TGRTHQ+RVH   +G  ++GD  Y       K         +  LHA ++   HP
Sbjct: 231 ECRLETGRTHQVRVHMQSLGHALLGDPVYGRTKGAQKALLDELDFRRQALHAAHLGFIHP 290

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
             G  L   +P+PA M + +  L
Sbjct: 291 ISGNALAFESPMPADMQELFSRL 313


>gi|262195687|ref|YP_003266896.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262079034|gb|ACY15003.1| pseudouridine synthase, RluA family [Haliangium ochraceum DSM
           14365]
          Length = 322

 Score =  239 bits (609), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 82/324 (25%), Positives = 143/324 (44%), Gaps = 30/324 (9%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVI 71
            +DE   RLD++       ++   +++++  G V+VD   V K   ++Q G+ V +    
Sbjct: 17  PDDEPRARLDQFLTACELALSRSQVKRLIDEGAVQVDGAEVRKPGFKLQGGEAVEV---- 72

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                       L +   L      +   + YED  I V +KPAG+ V    G      +
Sbjct: 73  -----------ALPAPQPLAAEPQAIPLDICYEDEHIIVVDKPAGLVVHPAPGHPDGTLV 121

Query: 130 DGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D  G     +P + HRLD++TSG++V  +T  A   + E+F+  R+++ Y +
Sbjct: 122 NALLAHCHDLSGIGGALRPGIVHRLDKDTSGVMVATKTEIAHHAMVETFQAHRLERAYLA 181

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V   P+  +  I+    +       +   V +       AI+ ++V   F +    +  
Sbjct: 182 VVAPPPEPPRGTISTLHGRHPVHRKKFSGRVSR----GKQAITQYRVERVFGRLAAEVRC 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI---QNKLYLHARYMDLPHPEG 302
           Q  TGRTHQ+RVH   MG P++GD  Y   ++    +P+     +  LHA  +   HP  
Sbjct: 238 QLETGRTHQIRVHLSEMGAPLIGDVLYGRRYRDGVLAPLARALGRQALHATLLAFAHPVT 297

Query: 303 G-RLQITAPLPAHMVKTWDSLGFK 325
           G  L+   P PA M    ++L  +
Sbjct: 298 GAPLRFERPPPADMQTLIEALAAR 321


>gi|167627177|ref|YP_001677677.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017]
 gi|167597178|gb|ABZ87176.1| Lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017]
          Length = 309

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 94/316 (29%), Positives = 161/316 (50%), Gaps = 14/316 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  VQ + V +D    R+D +  + +  +    + + +R G++RV+KKRVK   R+ +G 
Sbjct: 1   MNKVQLIEVADDVIEQRIDNFLISKFSRLPKSLIYRWIRKGELRVNKKRVKQTTRVSAGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VR+PP     N        L+ +     H DFL+  +LYE     V +KP+G++V GGS
Sbjct: 61  IVRVPPFSLEEN--------LEIAKVSKSHLDFLEQRILYETDDYIVVDKPSGMAVHGGS 112

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+   +   L+  +  K ++  L HRLD+ETSG +++A+  ++  +  + F+ R++ KIY
Sbjct: 113 GVNSGLVERLRQ-LRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKERKVNKIY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++LV G    K + I   L +     G    +VK +++    A++    +      +  L
Sbjct: 172 YALVHGHWDEKVDAIDLPLSRTETKDGQR--IVKVDKREGKRALTRILAVQKIGD-YSLL 228

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEG 302
           E++  TGRTHQ+RVH   MG PIV D KY          +   +KL LHA  ++    + 
Sbjct: 229 EIKLETGRTHQIRVHTRAMGHPIVADKKYGYMVDDKKLLAKGVDKLLLHAGKLEFYDEKQ 288

Query: 303 GR-LQITAPLPAHMVK 317
            + + I A L +   +
Sbjct: 289 QKLISIEAKLDSRFDE 304


>gi|311113351|ref|YP_003984573.1| ribosomal large subunit pseudouridine synthase D [Rothia
           dentocariosa ATCC 17931]
 gi|310944845|gb|ADP41139.1| ribosomal large subunit pseudouridine synthase D [Rothia
           dentocariosa ATCC 17931]
          Length = 324

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 144/325 (44%), Gaps = 36/325 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV----DKKRVKFNNRIQSGQVVRI 67
           V      MRLD         I        +R G VRV    ++ ++  ++++ +G+ V +
Sbjct: 16  VSEALVGMRLDAALAGAL-EIPRTRASGWIRDGHVRVVQCGNELKIGKSHKLSAGETVFV 74

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                     I+ +K+                 ++Y D  I V +KPAG++     G  +
Sbjct: 75  NAPAPRDLADIQPEKV-------------DGFGIVYCDDDIVVVDKPAGVAAHPSHG--W 119

Query: 128 HIDGFLKSWVDSK--------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           H    L + +            ++  + HRLD  TSG++VVAR+  A   L  +F+ R +
Sbjct: 120 HGPTVLSALLGEGVTVATSGAAERQGIVHRLDVGTSGLMVVARSERAYTELKRAFKDRTV 179

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K+Y +LV G+P      I   + +  H G ++   V ++      +I++++ ++ F   
Sbjct: 180 EKVYHTLVQGLPDPLMGTIDAPIGR--HPGHEWKFAVIED---GRSSITYYETLESFGS- 233

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E+   TGRTHQ+RVH   +  P  GD  Y A+ + +    +  + +LHA  +   H
Sbjct: 234 ASLVEVHLETGRTHQIRVHFSSLRHPCCGDLTYGADPRFSAELGL-TRQWLHAHRLGFTH 292

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLG 323
           P  G R++  +P P  +    ++L 
Sbjct: 293 PTTGERVEFESPYPQDLDYALEALR 317


>gi|302546161|ref|ZP_07298503.1| RluA family RNA pseudouridine synthase [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302463779|gb|EFL26872.1| RluA family RNA pseudouridine synthase [Streptomyces himastatinicus
           ATCC 53653]
          Length = 313

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 77/333 (23%), Positives = 141/333 (42%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V+VD      ++R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAIARMF-GFSRTKAAELAAAGKVQVDGSVAGKSDRVS 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPQAAAPVQIVAEP--------------VEGMEIVHDDDDIVVIAKPVGVAA 105

Query: 120 QGGSGIAYHID------GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G +             +       ++  + HRLD  TSG++VVA++  A   L + 
Sbjct: 106 HPSPGWSGTTVIGGLAAAGFRIATSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKQQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R ++K Y +LV G P      I   + +  H   DY   V  +      +++H+ +I
Sbjct: 166 FRERTVEKRYHALVQGHPDPLSGTIDAPIGR--HPQHDYKWAVTAD---GKPSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAF-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTLAKRLKL-TRQWLHAM 278

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
            +   HP  G  ++  +P P  + +  D +  +
Sbjct: 279 RLGFEHPSDGSWIEFESPYPDDLQRALDIVRAE 311


>gi|116618468|ref|YP_818839.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
 gi|116097315|gb|ABJ62466.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
          Length = 312

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 83/317 (26%), Positives = 135/317 (42%), Gaps = 36/317 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D+   R+D          +   L   L  G + V+  +VK + ++ SG  + I P     
Sbjct: 11  DQAG-RVDAVLSKENLSYSRTTLSNWLVDGTILVNNHKVKRSYKVVSGDTISITPPETQE 69

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             I  E   LD                        V NKP G+ V   +G   H  G L 
Sbjct: 70  TKIEAENIPLDIIYEDDDII---------------VVNKPQGMVVHPAAG---HSSGTLV 111

Query: 135 SWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +             +P + HR+D++TSG+L+VA+   A + L+E  +  + Q++Y++L
Sbjct: 112 NALLHHSPLSTINGEFRPGIVHRIDRDTSGLLMVAKNDKAHRSLSEQLKSHKNQRVYYAL 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + +   I      V+    +G   A++HF+V+  +   +  L++ 
Sbjct: 172 VRGEFTEDSGTIEAPIGRH-KIDRKKQAVI----EGGREAVTHFRVLKRYV-GYTLLKVS 225

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
             TGRTHQ+RVH  ++G P+VGD  Y    K + T    N   LHA+ + L  P  G  L
Sbjct: 226 LETGRTHQIRVHMSYIGHPVVGDPVYGTAQKLDGTQ--LNGQLLHAKTLTLEQPTTGDEL 283

Query: 306 QITAPLPAHMVKTWDSL 322
              +PLP +      +L
Sbjct: 284 SFDSPLPDYFQFALSTL 300


>gi|317486057|ref|ZP_07944910.1| RluA family pseudouridine synthase [Bilophila wadsworthia 3_1_6]
 gi|316922684|gb|EFV43917.1| RluA family pseudouridine synthase [Bilophila wadsworthia 3_1_6]
          Length = 532

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 83/317 (26%), Positives = 138/317 (43%), Gaps = 40/317 (12%)

Query: 19  MRLDRWFKNHYP--HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           MRLDR+         ++   +++ +R G   VD       + ++ +GQ + +       +
Sbjct: 1   MRLDRFLGEALREQDVSREKVKRAIRDGGCLVDGAVCTDVSAKVGAGQSIELRMEAEPTS 60

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-----GIAYHID 130
              +E ++                 +LY+D+ + V NKPAG++V          + + + 
Sbjct: 61  VQPEEGELE----------------ILYQDAWLAVLNKPAGMTVHPAPSCPDGTLVHRLV 104

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
               S    +G +P + HRLD++TSG++ VA T  A   L+E+F  R I+K Y +LV G+
Sbjct: 105 ARFPSLRAQEGFRPGIVHRLDKDTSGLICVALTEEARMRLSEAFAAREIRKEYLALVQGV 164

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P      +   L +        V V     K    A S ++V+    Q +  LE++  TG
Sbjct: 165 PAPA-GTVDAPLGRHPT-----VKVKVAVAKNGKEARSEWRVL-HKGQGYSLLEVRIFTG 217

Query: 251 RTHQLRVHALHMGCPIVGDHKYCAN--------FKGNFTSPIQNKLYLHARYMDLPHP-E 301
           RTHQ+RVH  H+G P+ GD  Y                      +  LHA ++   HP  
Sbjct: 218 RTHQIRVHMAHIGHPLWGDKLYGRGGQVLTPPVPGVLLKHDPAPRQMLHAWHLSFIHPFT 277

Query: 302 GGRLQITAPLPAHMVKT 318
           G ++  T P P   V+T
Sbjct: 278 GEKMAFTCPPPEDFVQT 294


>gi|40889481|pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
           Pseudouridine Synthase Rlud
          Length = 349

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 80/336 (23%), Positives = 139/336 (41%), Gaps = 41/336 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ +   +V V+ K   K   ++  G+ V I
Sbjct: 31  TATVSENQLGQRLDQALAEXFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAI 90

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I        +   LD               ++YED  I + NKP  + V  G+G   
Sbjct: 91  NAEIEEEARFEPQDIPLD---------------IVYEDEDIIIINKPRDLVVHPGAGNPD 135

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G+ VVA+T  A   L ES + R I + Y 
Sbjct: 136 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLXVVAKTVPAQTRLVESLQRREITREYE 195

Query: 185 SLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H     +            A++H+++ + F +   
Sbjct: 196 AVAIGHXTAGGTVDEPISRHPTKRTHXAVHPM---------GKPAVTHYRIXEHF-RVHT 245

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    +           ++  LHA 
Sbjct: 246 RLRLRLETGRTHQIRVHXAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT 305

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
            + L HP  G   +  AP+P   V+  +     ++ 
Sbjct: 306 XLRLYHPISGIEXEWHAPIPQDXVELIEVXRADFEE 341


>gi|237745359|ref|ZP_04575840.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           7_1]
 gi|229432588|gb|EEO42800.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           7_1]
          Length = 314

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 74/338 (21%), Positives = 143/338 (42%), Gaps = 36/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V ++ + MRLD++            L+K++ +  V+++ K +  N  ++
Sbjct: 1   MENIKEKFEFEVNSEYKGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G+ + +                +    N+    + +   ++YE++   V NK  G+ V
Sbjct: 61  KLGEKIEVS---------------IPEEENIDIEPENIPLDIVYENNDFIVINKNYGMVV 105

Query: 120 QGGSG-IAYHIDGFLKSWVDSK-----GQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     +   L  + ++        +P + HRLD++TSG+++VA++  A   L   
Sbjct: 106 HPAYGNYTGTLVNALLYYTNNLSSINGNIRPGIIHRLDKDTSGLILVAKSNYAHAKLASM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           F  + I K Y  +V G    +     I N + + S      + VVK+N      AIS++K
Sbjct: 166 FIDKTIHKTYLCIVKGNFSEENISGRIENLIGRDSK-DRKKMAVVKEN---GKIAISNYK 221

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V++   + +  +E+   TGRTHQ+RVH   +   I+GD  Y    K         +  LH
Sbjct: 222 VVEQV-EGYSLVEVAIETGRTHQIRVHMKSINHVILGDSVYGNEDKNV------KRQMLH 274

Query: 292 ARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           A  ++  +P +         L    ++    L F  ++
Sbjct: 275 AYKLEFLNPLDNKEYVFKGKLFDDFIEIAKKLKFNIEK 312


>gi|83319260|ref|YP_424375.1| ribosomal large subunit pseudouridine synthase A [Mycoplasma
           capricolum subsp. capricolum ATCC 27343]
 gi|83283146|gb|ABC01078.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma capricolum subsp. capricolum ATCC 27343]
          Length = 322

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 77/331 (23%), Positives = 150/331 (45%), Gaps = 24/331 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP--HINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQ 63
           +  + + +    +RLD+           +   +QK+++   + V+ + +  NN  ++   
Sbjct: 1   MNKITLNSVNTTLRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITSNNFLVKPNS 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I      L+  I + K      N+TK+ D +   ++Y+D  + V NK   I+V    
Sbjct: 61  QIIITIKDPVLDPNITKNKDPVLDPNITKNKD-IDLNIIYQDDDLLVINKQNNITVHPS- 118

Query: 124 GIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +    +  + + + S  +        +P + HR+D++T+G+L+VA+     + L+E F+
Sbjct: 119 -LNNTNNTIVNALLASDVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKTHKLLSEMFK 177

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             +I K Y ++V G+ K  K  I   + + S      + V     K + +AI+ F+V++ 
Sbjct: 178 NHQIYKEYLAIVTGVIKPNKGLIDAPIGR-SQTDRKKMSV---TAKNSKHAITTFEVVER 233

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F +    ++ Q  TGRTHQ+RVH  ++  P++ D  Y       FT       YLHA  +
Sbjct: 234 FLKN-TLIKCQIQTGRTHQIRVHFNYINHPVLNDPIYGKK-HQEFTDFG---QYLHAYKL 288

Query: 296 DLPHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
              HP     +++ +PLP         L  +
Sbjct: 289 KFTHPITKKEIELISPLPKEFDDKIKELRGE 319


>gi|15616954|ref|NP_240167.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. APS (Acyrthosiphon pisum)]
 gi|219681707|ref|YP_002468093.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. 5A (Acyrthosiphon pisum)]
 gi|257471403|ref|ZP_05635402.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. LSR1 (Acyrthosiphon pisum)]
 gi|11387076|sp|P57430|RLUC_BUCAI RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|25322330|pir||E84970 pseudouridylate synthase (EC 4.2.1.70) [imported] - Buchnera sp.
           (strain APS)
 gi|10039019|dbj|BAB13053.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. APS (Acyrthosiphon pisum)]
 gi|219624550|gb|ACL30705.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. 5A (Acyrthosiphon pisum)]
          Length = 314

 Score =  239 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 171/319 (53%), Gaps = 16/319 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + +  +  N R+D + ++ +  +    + +I+R+G++R++KKR+K + +++ G +++
Sbjct: 8   ISIIYINKEMLNQRIDNFMRSKFKSVPKSMIYRIIRTGKIRINKKRIKPHYKLKIGDILK 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP+    +        + ++     HS  L + +LYEDS + + NKP+GI+V GGSG+ 
Sbjct: 68  IPPIKILCD--------IKNTFFPLNHSTNLLNRILYEDSHLLIINKPSGIAVHGGSGLN 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +  + +           L HR+D++TSG+L++A+ R +   L E  R ++I+K Y +L
Sbjct: 120 FGVIEYFRKLRPLNKF-LELVHRIDRDTSGVLILAKKRTSLVSLHEQLREKKIKKEYIAL 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  +  + I+  LLK        + ++   +K    + ++F++   F+     L + 
Sbjct: 179 VHGLWPDHIKKISEPLLKIQFKNKQKMVLI---DKKGKPSETYFQIKKKFSSS-TLLSII 234

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGG- 303
           P TGRTHQ+RVHALH G PI  D +Y  N        +   N+L LH+  +   HP+ G 
Sbjct: 235 PKTGRTHQIRVHALHAGHPIFFDKRYGKNDLDADIKNNHKINRLLLHSSGVHFIHPKNGN 294

Query: 304 RLQITAPLPAHMVKTWDSL 322
           ++ I APL        +++
Sbjct: 295 KIYIKAPLDIDFQNYLNTI 313


>gi|46445989|ref|YP_007354.1| 23S RNA-specific pseudouridine synthase D [Candidatus
           Protochlamydia amoebophila UWE25]
 gi|46399630|emb|CAF23079.1| probable 23S RNA-specific pseudouridine synthase D [Candidatus
           Protochlamydia amoebophila UWE25]
          Length = 318

 Score =  239 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 135/326 (41%), Gaps = 33/326 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
             V  +++  DE   RLD+     +    +    Q ++    + V+   VK    +Q G 
Sbjct: 7   EEVDLLIISEDEVGERLDKVLARRFNAKYSRTYFQFLIDKHLILVNGIAVKKRTLLQEGD 66

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +  + +  ++++ E                +   +LYED  + V NKPAG+ V    
Sbjct: 67  EVEVQFLASPESNLMPEN---------------IPLSILYEDEHLLVINKPAGMVVHPAP 111

Query: 124 GIAY-HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G         L  +           +P + HRLD+ TSG+LV A+T    Q L E F  R
Sbjct: 112 GNWSGTFVNALLYYCQKLPLLPDTIRPGIVHRLDKGTSGLLVAAKTLETQQKLIELFASR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           ++ K Y ++  G P + +       + +  I    + V+         AIS  K +  ++
Sbjct: 172 KVYKAYLAICIGRPADGE---IQAPIGRHPIHRKQMAVI----PTGKPAISFCKTLG-WS 223

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            K  +++++  TGRTHQ+RVH  + G PI+GD  Y       + S       LHA  +  
Sbjct: 224 DKLSFVQIEIATGRTHQIRVHMKYRGSPILGDPLYGQISLNQYYSVPH--QLLHAAVLRF 281

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSL 322
            HP     L+   P P  MV+    +
Sbjct: 282 QHPISLENLEFCTPPPPEMVRLIKKI 307


>gi|153853142|ref|ZP_01994551.1| hypothetical protein DORLON_00536 [Dorea longicatena DSM 13814]
 gi|149753928|gb|EDM63859.1| hypothetical protein DORLON_00536 [Dorea longicatena DSM 13814]
          Length = 272

 Score =  239 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 80/294 (27%), Positives = 131/294 (44%), Gaps = 31/294 (10%)

Query: 42  RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
           + G V+V++K VK N R+  G  V +         I+ E   LD               +
Sbjct: 2   KEGYVKVNQKPVKSNYRLSFGDSVEVTLPEAKEPDIVPENIPLD---------------I 46

Query: 102 LYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDS-----KGQKPRLTHRLDQET 154
           LYED  I + NKP  + V    G      ++  +    D         +P + HR+D +T
Sbjct: 47  LYEDQDIIMINKPKQMVVHPAPGHYSGTLVNALMYHCGDELSGINGCMRPGIVHRIDMDT 106

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +G LVV +   A Q L+E  ++  I++IY ++V G  K     +   + +          
Sbjct: 107 TGSLVVCKNDKAHQSLSEQLKVHSIRRIYVAIVHGNIKEDSGTVNAPIGRHPTDRKKMST 166

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                 K    A++H+KV++ F   + +++ +  TGRTHQ+RVH   +G P+VGD  Y  
Sbjct: 167 HC----KNGRDAVTHYKVLERFGD-YTYIQCELETGRTHQIRVHMASIGHPLVGDEVYGP 221

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
                          LHAR + + HP  G+ L++ APLP + ++  D L   Y+
Sbjct: 222 K---KCPFKGLQGQTLHARTLGIIHPTTGKYLEVNAPLPEYFIELLDRLRNIYN 272


>gi|221135103|ref|ZP_03561406.1| RluA family pseudouridine synthase [Glaciecola sp. HTCC2999]
          Length = 330

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 147/331 (44%), Gaps = 37/331 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
           +V+  + + RLD+   + +P  +   L++ + +G V+VD + V     ++Q  + + I  
Sbjct: 16  IVDQTQFDKRLDQVLADLFPEYSRSKLKEWILAGFVKVDDEVVTVARQKMQGDEQIDIHA 75

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           VI               +V +      ++  +++ED  + V NKPAG+ V  G+G A   
Sbjct: 76  VI---------------AVQVLNTPQNIELDIVFEDEHVLVINKPAGLVVHPGAGNADGT 120

Query: 130 --DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L    + +   +  + HRLD++T+G++VVA+T  A  +L E  + R + + Y +L
Sbjct: 121 VLNALLAHHPEIENIPRAGIVHRLDKDTTGLMVVAKTLIAQTYLVEQLQTRVMSREYEAL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEM 245
           V G        +         IG           +     A +H+++ + F +    L +
Sbjct: 181 VMG-------TMVAGGFVDEPIGRHPTKRTSMAVRATGKEATTHYRIKEKF-RAHTHLRL 232

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KLYLHARYMDL 297
           +  +GRTHQ+RVH  H+  P+VGD  Y    +        F   ++N  +  LHA  +  
Sbjct: 233 KLESGRTHQIRVHMAHIRHPLVGDQLYGGRPRMPKAASEAFMQALRNFKRQALHAAQLSF 292

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            HP     L   APLP   V+  + +    D
Sbjct: 293 AHPITEDWLTFNAPLPDDFVQLLEDVRADTD 323


>gi|119470041|ref|ZP_01612846.1| 23S rRNA pseudouridine synthase [Alteromonadales bacterium TW-7]
 gi|119446751|gb|EAW28024.1| 23S rRNA pseudouridine synthase [Alteromonadales bacterium TW-7]
          Length = 325

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 78/337 (23%), Positives = 141/337 (41%), Gaps = 36/337 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V  D    RLD+     +P  +   ++  +   ++ VD + +     ++  G+V+ +   
Sbjct: 11  VPTDLGGKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEILNTPRTKLLGGEVLNVETT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           I A    + +                +   ++YED  I V NKP G+ V  G+G      
Sbjct: 71  IEAPREYLAQN---------------IDLNIVYEDDHILVINKPMGLVVHPGAGNPDGTV 115

Query: 130 -DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSL 186
            +  L  + D     +  + HRLD++T+G++VVA+T  A  HL ++ + R    + Y +L
Sbjct: 116 LNALLHHYPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTHLVKALQKRENFTREYEAL 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + +              +    AI+H++V + F +    L ++
Sbjct: 176 CNGTM-TAGGMVEKPIGRHATQ-----RTHMAVHEMGKPAITHYRVAEKF-RAHTRLRLR 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  Q         +  LHA  + + 
Sbjct: 229 LETGRTHQIRVHMAYLNHPLIGDQSYNGRPRPPKGATPQLFELLRSFKRQALHAVKLSIA 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           HP  G  +   AP+P  MV+   +L      N  I R
Sbjct: 289 HPITGEMMTWQAPIPDDMVEMTLALREDTQANPDIDR 325


>gi|120599938|ref|YP_964512.1| RluA family pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|146292126|ref|YP_001182550.1| RluA family pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|120560031|gb|ABM25958.1| ribosomal large subunit pseudouridine synthase D [Shewanella sp.
           W3-18-1]
 gi|145563816|gb|ABP74751.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           putrefaciens CN-32]
 gi|319425422|gb|ADV53496.1| pseudouridine synthase, RluA family [Shewanella putrefaciens 200]
          Length = 324

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 141/325 (43%), Gaps = 35/325 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +  +RLD+     +P  +   +++ + S  V VD   V K   ++   Q + I   
Sbjct: 11  ISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVYVDGVIVNKPREKVFELQQIEIAAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--H 128
           +    H                 +  ++  ++YED  I V NK AG+ V  G+G A    
Sbjct: 71  LEEEVHAA---------------AQAIELNIVYEDDHILVINKQAGLVVHPGAGNADGTL 115

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L    D +   +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 MNALLHHCPDIEHVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        +   + +         H+   +      A++H++V + F +    L ++ 
Sbjct: 176 MGTMTG-GGTVDEPIGRHPT---KRTHMAVHHS--GKPAVTHYRVAEKF-RNHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            +GRTHQ+RVH  ++G  +VGD  Y    K    +  +         +  LHA  ++L H
Sbjct: 229 ESGRTHQIRVHMEYIGHVLVGDPVYGGRPKPPKAASPEFFEILKNFKRQALHAVRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P     +   AP+P  MV    +L 
Sbjct: 289 PVSCEIMSWQAPIPEDMVILTKALR 313


>gi|257063802|ref|YP_003143474.1| pseudouridine synthase, RluA family [Slackia heliotrinireducens DSM
           20476]
 gi|256791455|gb|ACV22125.1| pseudouridine synthase, RluA family [Slackia heliotrinireducens DSM
           20476]
          Length = 320

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 75/339 (22%), Positives = 139/339 (41%), Gaps = 36/339 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +    +Y+ V+   + MRLD +      +       K + +G+V ++    + +  +++G
Sbjct: 1   MDVQTEYLYVDETGDGMRLDAFLAKEGAYTTRSAAAKRVAAGEVSINGVAARKSATVKAG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VV     I+                     S  +   + YED ++ V +K AG+     
Sbjct: 61  DVVEYQVFIDPRV--------------FDLESADIPLDVRYEDDQVLVISKQAGLVTHPA 106

Query: 123 SGI---AYHIDGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
            G       ++  +          V  +  +  + HRLD++TSG+++ A+T  A Q L E
Sbjct: 107 DGHPQQDTLVNALIHHCGRENLCNVQGEQDRLGIVHRLDRDTSGLMLAAKTNEAGQKLME 166

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
               R + + Y +LV G    +   +   + +      D + +   +   A  A++ F V
Sbjct: 167 DIADRDVDRHYLALVHGWIPLETGLVDAPIGRSD---RDRLRMCVSDRDNARDAMTSFSV 223

Query: 233 IDCFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +  F        +  ++ +  TGRTHQ+RVH  ++  P VGD  Y      N      ++
Sbjct: 224 VKRFEAGRNDDGYTLIDCKLFTGRTHQIRVHMEYIKHPCVGDPVYGWAKHDNL---GLDR 280

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
            +LH+  +   HP  G RLQ    LPA + +  D L  +
Sbjct: 281 QFLHSYKLAFTHPTTGERLQFEDTLPADLQRVIDELEAR 319


>gi|114331690|ref|YP_747912.1| pseudouridine synthase, RluA family protein [Nitrosomonas eutropha
           C91]
 gi|114308704|gb|ABI59947.1| ribosomal large subunit pseudouridine synthase C [Nitrosomonas
           eutropha C91]
          Length = 354

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 99/321 (30%), Positives = 151/321 (47%), Gaps = 23/321 (7%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+   E  R+D +       I   ++ ++LRSGQVRV+ KR+    R+     VRIPPV+
Sbjct: 40  VDETAEGQRIDNFLIKALKDIPRRHIYQLLRSGQVRVNSKRIDAGYRLLLNDKVRIPPVL 99

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                       L   ++        +   LY+D  + V NKPAG +V GGSGI+Y +  
Sbjct: 100 K-----------LAKPISRQAPYRAEQFDTLYQDDYLLVINKPAGTAVHGGSGISYGVIE 148

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L+       +   L HRLD+ETSG+L++AR R     L +  R   ++K Y +LV G  
Sbjct: 149 QLRKQR-PDWKFLELVHRLDRETSGVLLLARKRQTLLELHKQIREGTVRKHYLTLVRGKW 207

Query: 192 KNKKECIANWLLKKSHIGGDYVHVV---KQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           KN  + +   L K     G+    +   + +      A + F  +    + F  L+ +  
Sbjct: 208 KNSLQNVRLPLYKYLTAEGERRVAIATGRNDHDKVQQAYTLFA-LQKNWEAFSLLDAELK 266

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           TGRTHQ+RVH  H+G PI GD KY          K + +  +  +++LHA      HP  
Sbjct: 267 TGRTHQIRVHLAHLGFPIAGDDKYGDFGLNRQLQKDDGSGLVLKRMFLHASVFVCTHPVT 326

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
           G  L++ APLP  +     +L
Sbjct: 327 GELLRLEAPLPDELRVFLRNL 347


>gi|157964996|ref|YP_001499820.1| ribosomal large subunit pseudouridine synthases RluD subfamily
           protein [Rickettsia massiliae MTU5]
 gi|157844772|gb|ABV85273.1| Ribosomal large subunit pseudouridine synthases RluD subfamily
           protein [Rickettsia massiliae MTU5]
          Length = 313

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 144/327 (44%), Gaps = 40/327 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V ++  ++RLD+   +   +++   +QK ++  QV V+   +   +  ++   ++     
Sbjct: 6   VPHELNDIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFK 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 I      LD               ++YED  + V NK AG++V  G+G  +H D
Sbjct: 66  EPEELKIAAANVALD---------------IIYEDDDLIVINKAAGMTVHPGAG--HHDD 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD++T+G++VVA+   A   L      R++ + 
Sbjct: 109 TLVNALLHHTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FC 241
           Y  LVWG+    +  I N + + S      + ++K    G   A++H+K ++ F +    
Sbjct: 169 YKVLVWGVINPLEGVIKNNIGR-SRSDRQKMTILKY---GGKEAVTHYKTLELFYKGSIS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +E +  TGRTHQ+RV   H+   +VGD  Y  N +    SP +         +  LH+ 
Sbjct: 225 MVECKLSTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKIAHSPPELKAKLIDFKRQALHSW 284

Query: 294 YMDLPHPEGGRLQ-ITAPLPAHMVKTW 319
           Y+   HP    +   +  LP  M +  
Sbjct: 285 YLSFTHPTSNEIMAFSCKLPRDMEEII 311


>gi|269101904|ref|ZP_06154601.1| ribosomal large subunit pseudouridine synthase D [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268161802|gb|EEZ40298.1| ribosomal large subunit pseudouridine synthase D [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 324

 Score =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 81/339 (23%), Positives = 145/339 (42%), Gaps = 37/339 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V + +   RLD+     YP  +   ++  + +G+V VD + + K   ++  G+ + I  
Sbjct: 10  TVNDSQLGKRLDQVIAELYPDYSRTRIKDWILAGKVAVDGEIIDKPRIKMMGGEQLVINA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I                      +  +   ++YED  I V NKP    V  G+G     
Sbjct: 70  EIEDEVRW---------------EAQDIPLDIVYEDDDIIVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L      ++  +  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLWHCPSLAEVPRAGIVHRLDKDTTGLMVVAKTVQAQTRLVRALQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S              +    AI+H++V + F ++   + ++
Sbjct: 175 AMGKMTG-GGTVEKAIGRHST-----KRTCMAVHELGKPAITHYRVAEHF-REHTRIVLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P+VGD  Y    +    +  +        ++  LHAR + L 
Sbjct: 228 LETGRTHQIRVHMSYLTHPLVGDATYGGRPRPPRNASDELIQALRAFDRQALHARMLRLT 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLY 336
           HP  G  ++  APLP  MV   D L  + D+ L  +  Y
Sbjct: 288 HPITGELMEWHAPLPNDMVAMIDIL--RKDKELNDEDDY 324


>gi|164687826|ref|ZP_02211854.1| hypothetical protein CLOBAR_01470 [Clostridium bartlettii DSM
           16795]
 gi|164603101|gb|EDQ96566.1| hypothetical protein CLOBAR_01470 [Clostridium bartlettii DSM
           16795]
          Length = 307

 Score =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 141/325 (43%), Gaps = 33/325 (10%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++  +V  +EE  RLD +  +    ++   +QKI++  +V+V+ K  K    ++    V
Sbjct: 7   EIREFLVLGEEEGDRLDVYLSSQLGEMSRSYIQKIIKDKKVKVNGKIEKAKYAVKEDDSV 66

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I      L  +I +   +D               ++YED  + + NKP  + V    G 
Sbjct: 67  VIEIPAPKLLEVIPQDIPID---------------IVYEDDDLLIVNKPQDMVVHPAPGN 111

Query: 126 AYHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             +   +  L    D+        +P + HR+D++TSGIL++A+   A   L E  +   
Sbjct: 112 YENTLVNAILYHCKDNLSSINGVIRPGIVHRIDKDTSGILMIAKNNNAHNSLAEQLKDHS 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y  +  G+ K  K  +   + +          V     K    A++HF+VI  + +
Sbjct: 172 ITREYEFICHGVVKEDKITVDRPIGRNPKDRLKMAIV-----KDGKRAVTHFEVIKRY-E 225

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F  ++    TGRTHQ+RVHA  +G P++GD  Y        +        LHAR +   
Sbjct: 226 NFTHMKANLETGRTHQIRVHAASIGHPLLGDPIYGPKN----SKIKCKGQTLHARKLGFI 281

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP   + ++  + LP + V+  + +
Sbjct: 282 HPTTKQYVEFNSDLPDYFVEILNKI 306


>gi|148358865|ref|YP_001250072.1| ribosomal large subunit pseudouridine synthase D [Legionella
           pneumophila str. Corby]
 gi|296106912|ref|YP_003618612.1| ribosomal large subunit pseudouridine synthase D [Legionella
           pneumophila 2300/99 Alcoy]
 gi|148280638|gb|ABQ54726.1| ribosomal large subunit pseudouridine synthase D, RluD [Legionella
           pneumophila str. Corby]
 gi|295648813|gb|ADG24660.1| ribosomal large subunit pseudouridine synthase D [Legionella
           pneumophila 2300/99 Alcoy]
          Length = 321

 Score =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 136/327 (41%), Gaps = 30/327 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q + V  +  N R+D       P  +   +   +++G V ++    K  ++   G ++ I
Sbjct: 7   QQLSVPRELHNQRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCKPKDKALGGDLITI 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                          I+++  NL K  + +   ++YEDS++ V NKPAG+ V  G+G   
Sbjct: 67  NVN----------HTIVNTDFNLCK-PENIPIQIIYEDSEVIVVNKPAGLVVHPGAGNKE 115

Query: 128 HI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           H   +  L    +     +  + HRLD++T+G+L+VA+   +   L    + R I++ Y 
Sbjct: 116 HTLVNALLHHCPELQLLPRAGIIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYL 175

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G        I     +        + V          A++H+  I+   + F  L 
Sbjct: 176 TLVHGYV-ISGGTIDTGFGRHPK-NRLKMAVTDF----GRQAVTHYN-INKHYKDFTLLN 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           +   TGRTHQ+RVH  ++  P+VGD  Y    K    +            +  LHA  + 
Sbjct: 229 VSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKFPPNADEAILSVLKQFKRQALHACSIS 288

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
             HP     + + A LP       ++L
Sbjct: 289 FCHPVKNTEITLNALLPDDFELLLNTL 315


>gi|291295265|ref|YP_003506663.1| pseudouridine synthase RluA family [Meiothermus ruber DSM 1279]
 gi|290470224|gb|ADD27643.1| pseudouridine synthase, RluA family [Meiothermus ruber DSM 1279]
          Length = 327

 Score =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 95/345 (27%), Positives = 151/345 (43%), Gaps = 53/345 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
             +RLD+       + +    Q+ + +G V V  K V K + +++ G+ V + P      
Sbjct: 7   SGVRLDQALAFE-ANTSRAKAQEWIEAGLVTVGGKVVTKPSYKLR-GETVEVEPPPPQPA 64

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI---------- 125
            +  E                +   +LYED  + V NKPAG+      G+          
Sbjct: 65  SVAAED---------------IPLHILYEDPDLIVINKPAGMITHPAPGVYSGTLVNAIL 109

Query: 126 -----------AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                      +    G L      +  +P + HRLD+ TSG++VVAR  AA + L E+F
Sbjct: 110 GRFGLDLSLGESEEEGGLLLQAQKPELIRPGIVHRLDKGTSGVIVVARHEAAHRRLAEAF 169

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             R + K Y +L  GIP+   E + +  + +  +    +HV       A +A + F+V+ 
Sbjct: 170 AGRSVYKRYIALTVGIPR---EGLLSAPIGRHPVDRTRMHV---GGVAARHAQTEFEVL- 222

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
             A+    +    HTGRTHQ+RVH  H+  PI+GD  Y         S +  +  LHA  
Sbjct: 223 AVAEPHALVSAILHTGRTHQIRVHLKHLHAPILGDEVYGK------PSELIARQALHAYE 276

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           + L HP  G+ L   AP+PA MV  W SLG  +  +L  +   ++
Sbjct: 277 LRLQHPRTGKYLHFVAPIPADMVWAWVSLGGAWPEDLQTENPRAE 321


>gi|149907608|ref|ZP_01896355.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Moritella sp. PE36]
 gi|149809278|gb|EDM69207.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Moritella sp. PE36]
          Length = 326

 Score =  238 bits (607), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 80/333 (24%), Positives = 136/333 (40%), Gaps = 35/333 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           VV   +   RLD+     +P  +   L++ + +G V ++    VK   ++Q G  + +  
Sbjct: 10  VVAEHQVGQRLDQVLAEMFPDYSRTRLKEWILAGFVNLNGNVVVKAREKMQYGDKIILN- 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                          +    +      L  +++YED  I V NKPAG  V  G+G     
Sbjct: 69  --------------AEVDEEVRYEPQDLPLVIVYEDDDILVINKPAGFVVHPGAGNPDGT 114

Query: 130 --DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + D     +  + HRLD++T+G++V+A+T  A  HL  + + RRI + Y ++
Sbjct: 115 VLNALLFHYPDIIDVPRAGIVHRLDKDTTGLMVIAKTIPAQTHLVTALQARRITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        +   + + +                   A +H++V + + +    L ++
Sbjct: 175 VSGTM-TAGGFVDEPIGRHAT-----KRTQMAVRPLGKPAKTHYRVAEKY-RAHSLLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLP 298
             +GRTHQ+RVH  H+  PIVGD  Y    K                 +  LHAR + L 
Sbjct: 228 LESGRTHQIRVHMTHIMHPIVGDTVYAGRPKPPSNATDTLILALRGFGRQALHARMLKLE 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           HP  G  +   A  P+ M      L      N+
Sbjct: 288 HPVTGEMMMWRAERPSDMNTLIHILREDTALNM 320


>gi|329895229|ref|ZP_08270893.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC3088]
 gi|328922467|gb|EGG29809.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC3088]
          Length = 317

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 75/327 (22%), Positives = 135/327 (41%), Gaps = 40/327 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V  +    RLD+     +P  +   LQ+ ++SG + VD    K    +    V+ +   
Sbjct: 10  IVPIELHRKRLDQVAAALWPEFSRGKLQEWIKSGALLVDGNTAKPKQSVDVDSVLTLSAD 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +    H                    +   ++YED  + V NKP G+ V   +G   + D
Sbjct: 70  LEPAVHW---------------QPQAIPMDIVYEDEDVIVVNKPVGLVVHPAAG---NWD 111

Query: 131 GFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + + +         +  + HRLD++TSG++VVA+T  +   L E+ + R + + Y 
Sbjct: 112 GTLVNALLAHDASLEQVPRAGVVHRLDKDTSGLMVVAKTLQSHTALVEALQQREVSRQYI 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G        + +  + +       + VV         A +H+  +    + F  L 
Sbjct: 172 AIAHGSMT--GGGVVDAPIGRHPTMRQKMAVVA----SGKPARTHY-SLGQRFKHFTELH 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           ++  TGRTHQ+RVH  H   P+VGD  Y    +    S  +         +  LHA+ + 
Sbjct: 225 LKLETGRTHQIRVHMAHKKHPLVGDSVYGGRARVPGNSAPELVNAIREFPRQALHAKALA 284

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP     +   AP+P  M +  ++L
Sbjct: 285 FFHPISDEWMSFDAPIPDDMQQLLETL 311


>gi|86137869|ref|ZP_01056445.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           MED193]
 gi|85825461|gb|EAQ45660.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           MED193]
          Length = 346

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 84/354 (23%), Positives = 149/354 (42%), Gaps = 52/354 (14%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRIQS 61
            +++++   ++   RLD+      P    ++   L +++ +G + VD   V+    R+  
Sbjct: 5   QIEFII--AEDPPKRLDKAVSRDVPAEATLSRTRLARLIEAGSLTVDGVVVQDAKARVAE 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G V+ I       +HI  E   LD               +++ED  + V NKP+G+ V  
Sbjct: 63  GAVITITVEEAEDSHIGPEDIALD---------------VIFEDDDLIVINKPSGMVVHP 107

Query: 122 GSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             G      ++  L    ++       ++P + HR+D+ETSG+LVVA++ AA Q L   F
Sbjct: 108 APGTPSGTLVNALLHHCGENLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQF 167

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE--KG 222
               +++ Y ++ +G+P      +           N L   + +        +Q    +G
Sbjct: 168 EKHTVERYYRAICYGVPDANDPRLRGVKGTSFEPGNILKLTTQLARHKHDRQRQAVLFQG 227

Query: 223 ANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             +A++  ++++ F        +E    TGRTHQ+RVH  H G  +VGD  Y    K   
Sbjct: 228 GRHAVTRARIVEPFGAPPVVALIECWLETGRTHQIRVHMTHAGHGLVGDPTYGGKRKLAA 287

Query: 281 TSPIQ---------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
            S             +  LHA  +   HP  G  ++  APLP  M    ++L  
Sbjct: 288 KSLATTAIAAVQSFPRQALHAAVLGFVHPVSGAEMRFEAPLPQDMSDLIETLRL 341


>gi|212636674|ref|YP_002313199.1| pseudouridine synthase RluD [Shewanella piezotolerans WP3]
 gi|212558158|gb|ACJ30612.1| Pseudouridine synthase, RluD [Shewanella piezotolerans WP3]
          Length = 328

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 138/325 (42%), Gaps = 35/325 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           + + +   RLD+   + +P  +   +++ + SG V +D     K   ++  GQ + +   
Sbjct: 16  ITSIQTGQRLDQTLADLFPDYSRTRIKEWILSGAVSIDGNVSDKPRTKVLEGQEIIVLAT 75

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
           +                   +  ++ +   ++YED  I V NK AG+ V  G+G      
Sbjct: 76  LEE---------------ETSAKAEAIDLDIVYEDDHILVINKQAGLVVHPGAGNQDGTL 120

Query: 129 IDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L          +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 121 MNALLHHCPGIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVTALQAREITREYEAIV 180

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        IA   + +                    A++H++V + F +    L ++ 
Sbjct: 181 QG------GIIAGGTVDEPIDRHPTKRTHMAVVHNGKPAMTHYRVAEKF-RAHTRLRLRL 233

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            +GRTHQ+RVH  ++G  +VGD  Y    +    +            +  LHA  ++L H
Sbjct: 234 ESGRTHQIRVHMAYIGHVLVGDPVYAGRPRPPKGAAPDFFETYMGFKRQALHAIRLELAH 293

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P     +   AP+P  MVK   +L 
Sbjct: 294 PFTCEIMSWQAPVPDDMVKLTKALR 318


>gi|301629906|ref|XP_002944074.1| PREDICTED: ribosomal large subunit pseudouridine synthase C-like
           [Xenopus (Silurana) tropicalis]
          Length = 541

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 97/332 (29%), Positives = 148/332 (44%), Gaps = 28/332 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V+ +    RLD +       +   ++ +I+RSG+VRV++ R     R+  G  VR+
Sbjct: 27  RLVAVDAESSGQRLDNFLLRQLKGVPKTHVYRIIRSGEVRVNRGRASAGTRVAEGDQVRL 86

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PPV  +    +K              +      LL ED ++   +KPAG++V GGSG+++
Sbjct: 87  PPVRVSEKVALKAG----------HPAPARAFALLLEDEQLIAIDKPAGVAVHGGSGVSF 136

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L+           L HRLD+ETSGIL+VA+ R+A   L + FR R   K Y +LV
Sbjct: 137 GVIEQLRQARPQ-APFLELVHRLDRETSGILLVAKKRSALHQLQDQFRERATGKTYLALV 195

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQK------- 239
            G      + I   L K     G+    V   E      A++  K+      +       
Sbjct: 196 QGSWPAAHKVIDLPLHKYLLPDGERRVRVTTPENPDGMRALTLVKLRAHLPPRPLQGLPA 255

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLP 298
              LE+   TGRTHQ+RVH    G PIVGD KY   +           +++LHA  +   
Sbjct: 256 MTLLEVTIKTGRTHQIRVHLASQGHPIVGDDKYGDFDLNKRLPQQGLKRMFLHAWRL--- 312

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
           HP          +P H  + +D + F +D  L
Sbjct: 313 HPPWEPT-----MPDHRPRRFDLIAFDWDGTL 339


>gi|197335573|ref|YP_002155322.1| ribosomal large subunit pseudouridine synthase D [Vibrio fischeri
           MJ11]
 gi|197317063|gb|ACH66510.1| ribosomal large subunit pseudouridine synthase D [Vibrio fischeri
           MJ11]
          Length = 324

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 73/344 (21%), Positives = 148/344 (43%), Gaps = 42/344 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +   RLD+     +   +   +++ L +G + V+ + V K   ++  G+ + +  
Sbjct: 10  TVKESQLGQRLDQAAAELFSDFSRSRIKEWLLAGNMTVNGEVVTKARLKVMGGEEITVKA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +      + +   LD               ++YED  + V NKP    V  G+G     
Sbjct: 70  ELEDEERWLAQDISLD---------------IVYEDDDLLVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + + ++  +  + HRLD++T+G++VVA+T  A   L  + + R+I + Y ++
Sbjct: 115 VLNALLFHYPNIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRKITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + +  +        +    +    A++H++V + F +    + ++
Sbjct: 175 VVGRM-TAGGMIEKPIGRHPN-----KRTLMAVHELGKDAVTHYRVAEHF-RIHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P+VGD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLVGDTAYGGRARIPKGASQELIDMIRGFDRQALHAAMLRFE 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDEC 341
           HP  G  ++  AP+P  M+    +L          +RL  ++E 
Sbjct: 288 HPITGETMEFHAPIPDDMIALSQALRDD-------ERLMHEEEY 324


>gi|83941136|ref|ZP_00953598.1| ribosomal large subunit pseudouridine synthase D [Sulfitobacter sp.
           EE-36]
 gi|83846956|gb|EAP84831.1| ribosomal large subunit pseudouridine synthase D [Sulfitobacter sp.
           EE-36]
          Length = 344

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 87/357 (24%), Positives = 149/357 (41%), Gaps = 50/357 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M++ Q      D    RLD+      P    ++   L ++L  G V+VD   V    +R 
Sbjct: 1   MSHRQITFTIADSPPPRLDKALARDVPEDANLSRTRLGRLLEQGAVQVDGTVVTDPRSRA 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++GQ + +       +HI+ E+  L+               +++ED+ + V NKPAG+ V
Sbjct: 61  EAGQQITVDVEEAEDSHILAEEIPLE---------------VVFEDADLIVINKPAGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    D        ++P + HR+D++TSG+LVVA++ AA   L +
Sbjct: 106 HPAPGSPSGTLVNALLAHCGDDLSGVGGMKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAK 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F    +++ Y +LV+G+P      +           N L   + +        +Q    
Sbjct: 166 QFEKHTVERYYQALVYGVPDANDPRLRGVKGASFEPGNILKLTTQLARHRTDRQRQAVFF 225

Query: 221 KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +G  +A++  + +           +E    TGRTHQ+RVH  H G  +VGD  Y    K 
Sbjct: 226 QGGRHAVTRARTVARLGNPEVLALMECWLETGRTHQIRVHMAHAGHALVGDPTYGGKRKL 285

Query: 279 NFTSPIQ---------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
              +             +  LHA  +   HP  G  ++  APLP  M     ++G+ 
Sbjct: 286 AKGAVSDAAAEAVRSFPRQALHAAVLGFDHPVTGDYVRFEAPLPGDMTDLLGAVGYD 342


>gi|54297242|ref|YP_123611.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Legionella pneumophila
           str. Paris]
 gi|53751027|emb|CAH12438.1| Ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Legionella pneumophila
           str. Paris]
          Length = 321

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 137/327 (41%), Gaps = 30/327 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q + V  +  N R+D       P  +   +   +++G V ++    K  ++   G ++ I
Sbjct: 7   QQLSVPRELHNQRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCKPKDKALGGDLITI 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       +  I+++  NL K  + +   ++YEDS++ V NKPAG+ V  G+G   
Sbjct: 67  NV----------DHTIVNTDFNLCK-PENIPIQIIYEDSEVIVVNKPAGLVVHPGAGNKE 115

Query: 128 HI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           H   +  L    +     +  + HRLD++T+G+L+VA+   +   L    + R I++ Y 
Sbjct: 116 HTLVNALLHHCPELQLLPRAGIIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYL 175

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G        I     +        + V          A++H+  I+   + F  L 
Sbjct: 176 TLVHGYV-ISGGTIDTGFGRHPK-NRLKMAVTDF----GRQAVTHYN-INKHYKDFTLLN 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           +   TGRTHQ+RVH  ++  P+VGD  Y    K    +            +  LHA  + 
Sbjct: 229 VSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKFPPNADEAILSVLKQFKRQALHACSIS 288

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
             HP     + + A LP       ++L
Sbjct: 289 FCHPVKNTEITLNALLPDDFELLLNTL 315


>gi|261417496|ref|YP_003251179.1| pseudouridine synthase, RluA family [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261373952|gb|ACX76697.1| pseudouridine synthase, RluA family [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302326984|gb|ADL26185.1| ribosomal large subunit pseudouridine synthase D [Fibrobacter
           succinogenes subsp. succinogenes S85]
          Length = 424

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 87/352 (24%), Positives = 155/352 (44%), Gaps = 47/352 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +VE      R+D++      +++  ++QK++ +G+V+V   +V  N R+++G  V +  +
Sbjct: 4   IVEEKHNGERIDKFLVGVMENVSRTDVQKLIEAGEVKVGGGKVSKNFRVETGMAVVVEKM 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA---- 126
           I   +  ++ + I                 ++YED  I V NKP  + V  G+G++    
Sbjct: 64  IEKESSTLEPEDI--------------PLNIVYEDDDIVVINKPRNLVVHPGNGVSKGTL 109

Query: 127 -----YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                YH    L +   +   +P + HRLD++T G++VVA+  AA +HL      R + +
Sbjct: 110 AAALLYHFKENLSTV--NGPLRPGIVHRLDKDTPGLMVVAKNDAAHRHLAHQLETRTLHR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LVWG P++ +  I   + +          V     KG   + +H+ V   F     
Sbjct: 168 TYNALVWGCPRDLEGTIDAPIGRNPKNRLKMAVV-----KGGKESRTHY-VAKQFFAIAT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNK-----------LY 289
            LE+Q  +GRTHQ+RVH+ + G P+VGD  Y   +   N   P+                
Sbjct: 222 LLELQLESGRTHQIRVHSRYTGHPVVGDPLYDGRDESLNRVPPLMKPVAEKVLEIAPAQL 281

Query: 290 LHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           L A  ++L HP    +L    P+          L  +   +  +   Y ++E
Sbjct: 282 LQAVKIELIHPRTNKKLTFKVPMEEPFANVLKLLKKECPASAPV---YDEEE 330


>gi|269127123|ref|YP_003300493.1| pseudouridine synthase, RluA family [Thermomonospora curvata DSM
           43183]
 gi|268312081|gb|ACY98455.1| pseudouridine synthase, RluA family [Thermomonospora curvata DSM
           43183]
          Length = 309

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 79/324 (24%), Positives = 138/324 (42%), Gaps = 28/324 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V    +  R+D      +  ++     +++ +G V VD + V  ++R+  G 
Sbjct: 1   MADVRSLPVPEGLDGERVDAALARLF-GLSRSRAAELIAAGDVLVDGRTVVKSDRLHGGG 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-- 121
            + +             + +                 +LYED  I V +KP G++     
Sbjct: 60  WLEVTLPPPPAPPRPVAEPVP-------------GMTILYEDEHIVVVSKPVGVAAHPTI 106

Query: 122 GSGIAYHIDGFLKS----WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      + G L +          ++  + HRLD  T+G +VVA++  A   L  +F+ R
Sbjct: 107 GWNGPTVLGGLLGAGHTVATSGAAERQGIVHRLDANTTGAMVVAKSEIAYSRLKRAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           R+ K Y +LV G P   +  I   +    H  GD    V     G   +I+H+  ++ F 
Sbjct: 167 RVDKRYHALVQGHPDPLRGTIDAPI--DRHPSGDGRFAVV---AGGRPSITHYDTLEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    LE+   TGRTHQ+RVH   +  P VGD  Y A+        +  + +LHA  + L
Sbjct: 221 RAASLLEIDLETGRTHQIRVHMSAVRHPCVGDLLYGADPTLAARLGV-KRQWLHAIRLGL 279

Query: 298 PHPEGGR-LQITAPLPAHMVKTWD 320
            HP  G  ++  +P P  + ++ +
Sbjct: 280 EHPTTGEWMEFESPYPEDLTRSLE 303


>gi|227494657|ref|ZP_03924973.1| possible pseudouridylate synthase [Actinomyces coleocanis DSM
           15436]
 gi|226831839|gb|EEH64222.1| possible pseudouridylate synthase [Actinomyces coleocanis DSM
           15436]
          Length = 304

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 137/327 (41%), Gaps = 32/327 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ ++Y+ V +   N R+D         ++     K++   +VRV+   V  ++R+   +
Sbjct: 1   MSDIRYLPVPDGLANERIDSALSRML-GLSRSAAGKLIDDEKVRVNGVVVAKSHRLSINE 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++                   D      K +  +   ++YED  + V NKP G++  GG 
Sbjct: 60  IIE-----------------ADLEPPALKPAPIVGMDIVYEDEDLVVVNKPVGVAAHGGP 102

Query: 124 G------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      I        +       ++  + HRLD  TSG + VA++  A   L  +F+ R
Sbjct: 103 GWDGPTVIDNLEAAGFRISTSGPPERKGIVHRLDVGTSGAMAVAKSELAYTKLKHAFKER 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           R+ K Y +LV G P   K  I   + +  H   ++   V     G   AI+H++  +   
Sbjct: 163 RVHKTYHALVSGHPDPAKGTIDAPIAR--HPSKEWRMAVV---AGGRPAITHYQTQELLP 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                L++   TGRTHQ+RVH   +G P VGD  Y A+ K         + +LH+  +  
Sbjct: 218 -GAALLDITLETGRTHQIRVHFSAIGHPCVGDTFYGADQKQ-ADQLGLTRQWLHSVELQF 275

Query: 298 PHPEGGRL-QITAPLPAHMVKTWDSLG 323
            HP    L  + AP    + K  + L 
Sbjct: 276 VHPRTNALTTVKAPYTEDLSKALEQLR 302


>gi|326803607|ref|YP_004321425.1| putative ribosomal large subunit pseudouridine synthase D
           [Aerococcus urinae ACS-120-V-Col10a]
 gi|326650706|gb|AEA00889.1| putative ribosomal large subunit pseudouridine synthase D
           [Aerococcus urinae ACS-120-V-Col10a]
          Length = 315

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 142/329 (43%), Gaps = 34/329 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
            ++++RLDR+        +   + + +++GQV+V+K+ VK + R+     + +       
Sbjct: 10  GDQSLRLDRYLSQRLDSYSRSEIAQWIKTGQVKVNKQVVKPSYRLNPMDKISL------- 62

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFL 133
                    ++    L    + L   ++YED  + V NK  G+ V    G ++  +   L
Sbjct: 63  --------AIEEEQKLPIEGESLDLDIVYEDKDLLVINKAKGMVVHPSKGHLSGTLVNAL 114

Query: 134 KSWVDSK---------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            ++               +P + HRLD++TSG++VVA++  A Q L E     ++ + Y 
Sbjct: 115 LAYAQKNHFTLSDLGDYYRPGIVHRLDKDTSGLMVVAKSDPAYQALLEDLANHQLDRKYL 174

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L++G   +K+  I   L +      D +  V   +     A++HFK I    + +  L 
Sbjct: 175 ALIYGHLPDKQGTIDIPLRRHPK---DRMRYV--GDPLGKEAVTHFKQI-AQVENYALLR 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +   TGRTHQ+R H  ++  P+V D  Y   ++  F S  Q    LHA  +   HP    
Sbjct: 229 LSLETGRTHQIRAHLAYLDHPVVDDPLYAKAYQQRFFS--QQGQCLHAYGLSFNHPITKE 286

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           +L      P   +         YD +L  
Sbjct: 287 KLSFQVKPPKTFMNILHKALPNYDLHLEK 315


>gi|258544039|ref|ZP_05704273.1| ribosomal large subunit pseudouridine synthase C [Cardiobacterium
           hominis ATCC 15826]
 gi|258520667|gb|EEV89526.1| ribosomal large subunit pseudouridine synthase C [Cardiobacterium
           hominis ATCC 15826]
          Length = 311

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 93/320 (29%), Positives = 145/320 (45%), Gaps = 17/320 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V ++ V  D+   RLD + +  YP +    + ++LR G+VRV+KKR K   R+ +G  
Sbjct: 4   SRVHFLTVTADDAGQRLDNFLRKRYPALPKSRIYQMLRRGEVRVNKKRAKPELRVAAGDE 63

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +R+PP+ +A                     + +   +LYED    + NKPAGI+V GGS 
Sbjct: 64  LRLPPLADATR---------PPQDVPAFWCERIAGAVLYEDDDFLMLNKPAGIAVHGGSE 114

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             Y +   ++    +      L HRLD++TSG+LV+ + RAA        +   ++K Y 
Sbjct: 115 QPYGVIDAVRQVWGAGY--AELAHRLDRDTSGVLVLGKNRAALAGFQALMQAGGVEKRYL 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            LV G        +   L K    GG+ + V          A + F+++  FA     LE
Sbjct: 173 CLVDGHWNPATREVRLHLAKAQLQGGERMVV---GAADGQEARTRFRLLQTFAD-ASLLE 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
               TGRTHQ+RV   H G  I GD KY   +F           ++LHA ++   + +  
Sbjct: 229 ATLDTGRTHQIRVSVQHRGHGIAGDDKYGKRDFNRAMRKRGYKGMFLHAAHIAFAY-DAR 287

Query: 304 RLQITAPLPAHMVKTWDSLG 323
            + + APLPA        L 
Sbjct: 288 AIAVEAPLPAPAAHLLTLLR 307


>gi|126729199|ref|ZP_01745013.1| putative Pseudouridine synthase, Rlu [Sagittula stellata E-37]
 gi|126710189|gb|EBA09241.1| putative Pseudouridine synthase, Rlu [Sagittula stellata E-37]
          Length = 342

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 82/354 (23%), Positives = 139/354 (39%), Gaps = 55/354 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQ 63
           +  VV   +   RLD+      P    ++   L +++  G V  D   +     ++  G 
Sbjct: 3   RLRVVIAADPPQRLDKALARDVPEAAALSRTRLGRLIAEGAVTRDGALLTDPKAKVAEGD 62

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ I                +  + +    +  +   +++ED+ + V NKPAG+ V    
Sbjct: 63  VLEI---------------AVPEAEDYDVVAQDIPLEIVFEDADLLVVNKPAGMVVHPAP 107

Query: 124 GI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G      ++  L  +          ++P + HR+D++TSG+LVVA++  A   L   F  
Sbjct: 108 GTPDGTLVNALLHHFGGELSGVGGEKRPGIVHRIDKDTSGLLVVAKSDRAHHGLARQFEK 167

Query: 177 RRIQKIYWSLVWGIPK---------------NKKECIANWLLKKSHIGGDYVHVVKQNEK 221
              ++ Y ++V G+P                          L +         V    + 
Sbjct: 168 HTARRAYLAVVHGVPDVADPRLMGTRGVSAGAGGGITITSGLARHKTDRQRQAVFFVGQ- 226

Query: 222 GANYAISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN--FK 277
              +AI+H +V++ F    C   +E +  TGRTHQ+RVH  H G  +VGD  Y      K
Sbjct: 227 -GRHAITHARVLETFGAPECLALVECRLETGRTHQIRVHMAHAGHALVGDSTYGGRRKLK 285

Query: 278 GNFTSPIQ-------NKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           G+  SP         ++  LHA  +   HP     +   APLPA M     +L 
Sbjct: 286 GSALSPEAFAVASAFDRQALHAAELGFVHPVTEEEMLFEAPLPADMRDLLAALR 339


>gi|157804237|ref|YP_001492786.1| type II citrate synthase [Rickettsia canadensis str. McKiel]
 gi|157785500|gb|ABV74001.1| type II citrate synthase [Rickettsia canadensis str. McKiel]
          Length = 325

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 70/327 (21%), Positives = 144/327 (44%), Gaps = 40/327 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V ++   +RLD+       +++   +QK ++  QV V+   +   +  ++   ++     
Sbjct: 6   VPHELNGIRLDKALSLLLKNVSRNQIQKAVKDSQVLVNDIIISDPDVLVKENDIILFSFK 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                              L   +  +   ++YE+  + V NK AG++V    G+ +H D
Sbjct: 66  ---------------EPEELKIEAANIALDIIYENDDLIVINKAAGMTVHP--GLGHHND 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD++T+G++VVA+   A   L      R++ + 
Sbjct: 109 TLVNALLHYTKNLSDIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFC 241
           Y +L+WG+    +  I N + + S      + ++K    G   A++H+K ++  +     
Sbjct: 169 YKALIWGVINPLEGVIQNNIGR-SRSDRQKMTILKY---GGKEAVTHYKTLELFYGGTIS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +E + +TGRTHQ+RV   H+   +VGD  Y  N +    SP +         +  LH+ 
Sbjct: 225 MVECKLNTGRTHQIRVQLSHLKHSVVGDQTYGNNDRKVAHSPPELKAKLIDFKRQALHSW 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTW 319
           Y+   +P   + ++ +  LP  M +  
Sbjct: 285 YLSFTNPTSNKIMEFSCKLPRDMEEII 311


>gi|170718793|ref|YP_001783975.1| 23S rRNA pseudouridine synthase D [Haemophilus somnus 2336]
 gi|168826922|gb|ACA32293.1| pseudouridine synthase, RluA family [Haemophilus somnus 2336]
          Length = 324

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 73/328 (22%), Positives = 139/328 (42%), Gaps = 35/328 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           ++      RLD+     +P  +   L+  +    V+V+ + +     ++  G++V I   
Sbjct: 10  IQPQHMGQRLDQTLAELFPDYSRSRLKTWIEGDLVKVNGEIINVARTKVYGGELVEICVE 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           I   +    E                L   ++YED  I V NKP    V  G+G      
Sbjct: 70  IEEESRFEPEN---------------LPLNIVYEDEHILVINKPKDFVVHPGAGNQRGTV 114

Query: 130 -DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +    +  +  + HRLD++T+G++VVA+T  A   L +  + R+I + Y ++ 
Sbjct: 115 LNALLYHYPKIVEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVQDLQKRKIIREYEAVA 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G+   +   +   + +                     A++H+++++ F + +  L ++ 
Sbjct: 175 FGVM-TQGGKVDQPMSRHPT-----KRTQMAVHPLGKPAVTHYRIMERF-RNYTRLRLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  LHA  + L H
Sbjct: 228 ETGRTHQIRVHMAHISHPLLGDQTYGGRPRPPKNASEEFMQVMRDFKRQALHAIMLCLTH 287

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           P  G  ++  APLP   V   ++L   Y
Sbjct: 288 PITGEIMEWEAPLPDDFVTLINALKADY 315


>gi|332876323|ref|ZP_08444096.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6014059]
 gi|322507012|gb|ADX02466.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 1656-2]
 gi|323516880|gb|ADX91261.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332735474|gb|EGJ66528.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6014059]
          Length = 350

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 140/326 (42%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++      R+D+     +   +   L++ ++ G + V+   VK   R +  + + +  
Sbjct: 41  VQLDESYLGQRIDQVAAMLWSEFSREKLKQWMKEGHLLVNGNIVKPKYRCEGNETLTLNV 100

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
            + A  +   E   LD               ++YED  I V NKP G+ V  G+G     
Sbjct: 101 ELEAQTNSQPENIPLD---------------IVYEDEDILVINKPVGMVVHPGAGNTSGT 145

Query: 128 HIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L     S +  +  L HR+D++TSG+LVVA+   A   L++    + + +IY  +
Sbjct: 146 LVNALLYHSPKSAELSRAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLGDKSVYRIYDLV 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            +G        I   + K+  +    + ++     G   A++H+ V + F + F  ++ Q
Sbjct: 206 TYGNIIA-GGTIDEPI-KRHPVDRVKMAIL----PGGRDAVTHYNVKERF-RDFTRVQAQ 258

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  ++G  +VGD  Y         A+     T     +  LHA  + L 
Sbjct: 259 LETGRTHQIRVHFSYIGHGLVGDQVYMNRVRIPAGASELLIETLRGFKRQALHAAKLGLK 318

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +   AP P    +  + L 
Sbjct: 319 HPRTGEEMLFEAPWPEDFTQLVNVLR 344


>gi|260434078|ref|ZP_05788049.1| ribosomal large subunit pseudouridine synthase D [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260417906|gb|EEX11165.1| ribosomal large subunit pseudouridine synthase D [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 347

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 88/351 (25%), Positives = 146/351 (41%), Gaps = 52/351 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           +++V+   +    RLD+      P    ++   L +++  G V VD K V     ++  G
Sbjct: 6   IEFVI--AEAPPPRLDKALSRDVPADESLSRTRLARLIEEGAVAVDGKLVTDAKAKVAEG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V I       +HI  E   LD               +++ED+ + V NKPAG+ V   
Sbjct: 64  AAVCITVSEADESHIGPEDIPLD---------------IVHEDADLIVINKPAGLVVHPA 108

Query: 123 SGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G      ++  L    D        ++P + HR+D++TSG+LVVA++ AA Q L   F 
Sbjct: 109 PGSPSGTLVNALLHHCGDDLSGVGGVKRPGIVHRIDKDTSGLLVVAKSDAAHQGLAAQFE 168

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANW----------LLKKSHIGGDYVHVVKQNE--KGA 223
              +++ Y +L +G+P      +             +   + +        KQ     G 
Sbjct: 169 AHSVERYYRALCYGVPDANDPRLRGIKGVSFEPGNVMRITTQLARHKHDRQKQAVLFHGG 228

Query: 224 NYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            +A++  +V++ F Q      +E    TGRTHQ+RVH  H G  +VGD  Y    K +  
Sbjct: 229 RHAVTRARVVEVFGQPGAVSLIECWLETGRTHQIRVHMAHAGHGLVGDPVYGGKRKLSAR 288

Query: 282 SPIQN---------KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           S   +         +  LHA  +   HP  G  ++  AP+P  M     +L
Sbjct: 289 SFGADAAEAVRSFPRQALHAAVLGFEHPVTGAGMRFEAPIPQDMQALISAL 339


>gi|83815887|ref|YP_445314.1| ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber DSM 13855]
 gi|83757281|gb|ABC45394.1| ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber DSM 13855]
          Length = 349

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 80/356 (22%), Positives = 136/356 (38%), Gaps = 64/356 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           E +    R+D++    YP  +   +Q+ ++ G ++V+   VK +  ++ G  +       
Sbjct: 3   ETETGGPRIDKYLTRFYPEASRTKIQRAIKKGHLKVNGTDVKKSYGVEPGDEIVFR---- 58

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-------- 124
                      L     +    + +   +++E   + V NKPAG+ V    G        
Sbjct: 59  -----------LIRKPPMQAEPEAIPLDVVHEGDDLLVVNKPAGMVVHPAPGHRSGTLVH 107

Query: 125 -IAYHIDG-----------------------FLKSWVDSKGQKPRLTHRLDQETSGILVV 160
            + +H+DG                        L    D    +P + HRLD+ TSG+LVV
Sbjct: 108 ALLHHVDGGEVAADDERDEVSEDEVGLSLVNALPQSPDHPVVRPGIVHRLDKGTSGLLVV 167

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+   A Q L E F+   + + Y ++VWG        I   + +  H       +    E
Sbjct: 168 AKRGRAHQPLAEQFKAHTVDRRYRAIVWGRFAPSDGTIEGAIGRDPH---HRQRMAVVPE 224

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               +A +H++ ++  A     +E +  TGRTHQ+RVHA   G P++GD KY        
Sbjct: 225 DEGKWARTHYETVETHAH-TSVVEFELETGRTHQIRVHARAQGHPLLGDPKYGGQRVRYG 283

Query: 281 TSPIQNKLYL------------HARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           T     + +             HA  +   HP    RL+  A  P    +    L 
Sbjct: 284 TQSGTRRTFYDQLFETLPHPALHAYRLGFDHPTTEERLRFEADPPPAWRRVLRELR 339


>gi|39938617|ref|NP_950383.1| pseudouridylate synthase [Onion yellows phytoplasma OY-M]
 gi|39721726|dbj|BAD04216.1| pseudouridylate synthases [Onion yellows phytoplasma OY-M]
          Length = 303

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 88/325 (27%), Positives = 147/325 (45%), Gaps = 32/325 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +  ++   E   RLD +   H  ++N    QK++ + QV V+ K  K +  +++  
Sbjct: 1   MNEKKEFLISASEAFQRLDHFLLTHI-NLNKSQCQKLILAQQVLVNSKPAKKSYLLKAQD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ +                   SVNL +    L   ++YED  + V NKPA +      
Sbjct: 60  LITVIIPQT------------QESVNL-QTPQNLNLDIIYEDPYLAVINKPANLVAHPSL 106

Query: 124 GIAYHI--DGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                   +G L    +      Q+P + HRLD+ T+G+L++A+    +  L  +F+ R+
Sbjct: 107 SFQETTLVNGLLYQFATLSHVDTQRPGIVHRLDKNTTGLLIIAKNNDVSDKLQIAFQQRK 166

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I KIYW+L+ G  +  K  I   + +  H       +          A++HFK +  F+ 
Sbjct: 167 ITKIYWALIEGFLE-DKGTIKLPIGRNPHNRLKMQVI-----PDGKTAVTHFKTLQRFSH 220

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F  +E    TGRTHQLR H   +  PI+GD  Y +    +  +P+    +LHA+ +   
Sbjct: 221 -FSLMEFNLETGRTHQLRAHFSFLKRPIIGDLLYGS---SHHITPL--GQFLHAKMLKFN 274

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP   + L + APLPA+  K   SL
Sbjct: 275 HPITNQNLILEAPLPANFEKLLQSL 299


>gi|332535270|ref|ZP_08411072.1| ribosomal large subunit pseudouridine synthase D [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332035301|gb|EGI71805.1| ribosomal large subunit pseudouridine synthase D [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 325

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 80/337 (23%), Positives = 137/337 (40%), Gaps = 36/337 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPV 70
           V  +    RLD+     +P  +   ++  +   ++ VD +       ++  G+VV +   
Sbjct: 11  VPTELGGKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEIFNTPREKLLGGEVVSVETT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HI 129
           I A                    +  +K  ++YED  I V NKP G+ V  G+G     +
Sbjct: 71  IEA---------------PREYEAQDIKLNIVYEDDDILVINKPMGLVVHPGAGNPNGTV 115

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSL 186
              L  +       PR  + HRLD++T+G++VVA+T  A  HL  + + R    + Y +L
Sbjct: 116 LNALLHYYPEIINVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVTALQKRENFTREYEAL 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + +                +    AI+H++V + F +    L ++
Sbjct: 176 CNGTM-TAGGMVEKAIGRHPTQ-----RTHMAVHELGKPAITHYRVAEKF-RAHTRLRLR 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P++GD  Y    +    +  +         +  LHA  + + 
Sbjct: 229 LETGRTHQIRVHMAHLNHPLIGDQSYGGRPRPPKGATPELFELLRSFRRQALHAVKLSIA 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           HP  G  +   AP+P  MV    +L      N  I R
Sbjct: 289 HPITGEMMTWQAPIPDDMVAMTHALREDTKANPDIDR 325


>gi|308751621|gb|ADO45104.1| pseudouridine synthase, RluA family [Hydrogenobacter thermophilus
           TK-6]
          Length = 326

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 140/325 (43%), Gaps = 32/325 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
            VV+ + +  RLD +    Y   +   +QK++  G V VD K +K  + R+++GQ +   
Sbjct: 14  FVVDQEAQGKRLDLFLTEAYGEFSRSYVQKLIEDGFVLVDDKEIKKPSRRLKAGQKITFY 73

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                   ++ E    D               ++YED  I V  KP G+ V    G    
Sbjct: 74  IPQVEPLEVLPEDIPFD---------------VVYEDEDILVLIKPCGLVVHPSPGYSSG 118

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    +  G    ++P + HRLD+ T+G++VVA++  A + L E F  RR+ K 
Sbjct: 119 TLVNALLFRIKELSGIGGKERPGIVHRLDKNTAGLMVVAKSDKAHRSLVEEFMQRRVLKR 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFC 241
           Y +LV G+ +     +   + +       +  V     +    A + ++VI  F   +  
Sbjct: 179 YHALVSGLLREDSGTVEKSIGRHPVDRKKFSVV-----EDGKPAKTEYEVIKRFEKHRIT 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLP 298
           +L+++ HTGRTHQ+RVH   +G P++GD  Y    ++      + +     L +  +   
Sbjct: 234 FLDVRIHTGRTHQIRVHLSFIGHPVLGDKTYGFKTSSVDRKILNLMGECHMLVSYQLGFY 293

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP   + +      P       + L
Sbjct: 294 HPITKKWMDFQIEDPKPFRDVLNFL 318


>gi|16124708|ref|NP_419272.1| ribosomal large subunit pseudouridine synthase d [Caulobacter
           crescentus CB15]
 gi|221233422|ref|YP_002515858.1| ribosomal large subunit pseudouridine synthase D [Caulobacter
           crescentus NA1000]
 gi|13421626|gb|AAK22440.1| ribosomal large subunit pseudouridine synthase d [Caulobacter
           crescentus CB15]
 gi|220962594|gb|ACL93950.1| ribosomal large subunit pseudouridine synthase D [Caulobacter
           crescentus NA1000]
          Length = 342

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 79/324 (24%), Positives = 135/324 (41%), Gaps = 38/324 (11%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVI 71
             +    RLD+     +P ++   LQ ++  G++  D + V   + + ++G V  +    
Sbjct: 32  PENLAGQRLDKVLAPLFPDLSRARLQALIAEGRLTFDGETVADASRKARAG-VYSL---- 86

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                      ++          + L   +LYED+ + V +K AG++V    G      +
Sbjct: 87  -----------VVPPPAPADPEPEALPLSILYEDAHLIVVDKAAGMAVHPAPGTYNGTLV 135

Query: 130 DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +  L     S        +P + HRLD++TSG++V A++ AA + L+  F    I ++Y 
Sbjct: 136 NALLHHCGASLSGVGGVARPGIVHRLDKDTSGVMVAAKSDAAHRGLSTLFATHDIDRLYV 195

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK----F 240
           +L  G P      I   + + S      + V++    G   AI+H++V   F        
Sbjct: 196 ALTRGAPNPPTGTIQTQIGR-SPGDRKKMAVLR---AGGREAITHYRVEAAFGPADRPLA 251

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYM 295
             +  +  TGRTHQ+RVH    G P +GD  Y      A  +    +    +  LHA  +
Sbjct: 252 ARVACRLETGRTHQIRVHMASKGSPCLGDPVYGAAQPAAAVRERIEAAGLRRQALHAAVL 311

Query: 296 DLPHPEGGR-LQITAPLPAHMVKT 318
              HP  G  L+   PLPA M   
Sbjct: 312 GFVHPITGETLRFETPLPADMDAL 335


>gi|311895525|dbj|BAJ27933.1| putative ribosomal large subunit pseudouridine synthase D
           [Kitasatospora setae KM-6054]
          Length = 312

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 73/333 (21%), Positives = 146/333 (43%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS+    + + V +  E  RLD      +   +     ++   G+V +D      ++R+ 
Sbjct: 1   MSIAAQTRSLPVPDGLEGERLDAALARMF-GFSRTKAAELAAEGKVTLDGAVAGKSDRVT 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK-SILLYEDSKIYVFNKPAGISV 119
           +G  + +              +I   +  +   ++ ++   ++++D  + V +KP G++ 
Sbjct: 60  AGSWLEV--------------EIPAPAAPVQIVAEAVEGMRIIHDDDHVVVIDKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSGI+VVA++  A   L   
Sbjct: 106 HPSPGWTGPTVIGGLAAAGYRISTSGAAERQGVVHRLDVGTSGIMVVAKSERAYTDLKRQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  R  +K Y +LV G P      +   + +  H   D+   V ++      +++H+ +I
Sbjct: 166 FHDRVTEKKYNALVQGHPDPLSGTVDAPIGR--HPSSDWKWAVTRD---GKPSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + + +    L+++  TGRTHQ+RVH   +  P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAY-RAASLLDIKLETGRTHQIRVHMSALRHPCVGDLTYGADPTLAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +   HPE GR ++ ++  P  +    D++  +
Sbjct: 279 SLGFEHPEDGRWVEFSSDYPEDLQHALDTIAAE 311


>gi|254468337|ref|ZP_05081743.1| ribosomal large subunit pseudouridine synthase D [beta
           proteobacterium KB13]
 gi|207087147|gb|EDZ64430.1| ribosomal large subunit pseudouridine synthase D [beta
           proteobacterium KB13]
          Length = 346

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 85/344 (24%), Positives = 148/344 (43%), Gaps = 34/344 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+   + + +++       RLD    N  P  +   +Q ++++  + ++   V  N ++ 
Sbjct: 1   MTNTDFNKKLIIPATFFGSRLDAVLSNLVPEFSRSKIQSMIKNDLIFLNGSHVSQNYKVV 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ + I  VI     +I E   LD               ++YED  I V NKP  + V 
Sbjct: 61  GGEEIVINGVIEDEIDVIAENISLD---------------IVYEDDDILVLNKPYNLVVH 105

Query: 121 GGSGIAYHI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            GSG A     +G L    D  K  +  + HRLD++T+G++VVA+   +  +L    + +
Sbjct: 106 PGSGNANGTLLNGLLYYNKDLEKLPRGGIVHRLDKDTTGLMVVAKNEESQNNLISQLQSK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++VWG     K  +    + +       + V K N K    A +  ++++ F 
Sbjct: 166 SVYREYRAIVWGQIWQNK--VIQKPIGRHPRQRTKMAVTKVNGKD---AETKLEILERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-------ANFKGNFTSPIQN--KL 288
               ++     TGRTHQ+RVH L    PIVGD  Y         N + +    I+N  + 
Sbjct: 220 NYHTYVRCLLKTGRTHQIRVHMLDNNSPIVGDKDYGLKKIIPTKNMEMDLLKSIKNFDRQ 279

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDRNLY 331
            LHA  + L HP+    ++ T  LP  M +    +      N +
Sbjct: 280 ALHAIALGLIHPKTNKEMKWTIDLPEDMKELLSVIRKDSVENDF 323


>gi|227833472|ref|YP_002835179.1| pseudouridylate synthase [Corynebacterium aurimucosum ATCC 700975]
 gi|227454488|gb|ACP33241.1| pseudouridylate synthase [Corynebacterium aurimucosum ATCC 700975]
          Length = 307

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 139/327 (42%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V    + MR+D         I+   + ++  +G V +D   V  + R+ +G 
Sbjct: 1   MRESRRLPVPEGLDGMRVDAALAKLL-GISRARVSQLCAAGDVEIDGAAVGKSERLNAGG 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         I KE+ +                 +LY D  I    KP G++     
Sbjct: 60  WIDVMMPAPEEPLIPKEELVE-------------GMDVLYADEDIICVCKPVGVAAHPTL 106

Query: 124 G-IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L++   +       ++  + HRLD  TSG++VVA +  A   L  +FR R
Sbjct: 107 GWDGPTVIGGLRAAGYALADAGPTERKGIVHRLDVGTSGVMVVAASERAYSQLKNAFRER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +QK Y ++V G+P      I   + +    G  +  V          A++H+K+++ F 
Sbjct: 167 TVQKTYHAVVQGLPDPIVGTIDAPIGRHPSAGWKFGVV-----DDGKPAVTHYKLLEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++   LE+   TGRTHQ+RVH    G P VGD  Y  +        + N+ +LHA  +  
Sbjct: 221 REASLLEVHLETGRTHQIRVHMSATGHPCVGDPMYGCDPNLAKRVGL-NRQWLHAVELGF 279

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G+  + TAP P  +    + L 
Sbjct: 280 THPGTGKWFECTAPYPEDLKHAVEVLR 306


>gi|294787462|ref|ZP_06752715.1| ribosomal large subunit pseudouridine synthase D [Parascardovia
           denticolens F0305]
 gi|294484818|gb|EFG32453.1| ribosomal large subunit pseudouridine synthase D [Parascardovia
           denticolens F0305]
          Length = 325

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 71/321 (22%), Positives = 136/321 (42%), Gaps = 18/321 (5%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI-- 71
            D   +R D+        ++     +++  GQ RV+ + V  + +I  G  + +      
Sbjct: 3   EDSFGLRFDQALSRIL-GLSRSQAARLIADGQARVEGRSVPKSGQILPGDFILVSSAGST 61

Query: 72  --NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YH 128
              +   I    +          +       ++YED  + V +KPAG++    +G A   
Sbjct: 62  AGPSGVRIFTGSQTSKDEKAAGPNQAEASLPIVYEDDDLVVVDKPAGMASHPAAGWAGPT 121

Query: 129 IDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +   L++            +P +  RLD  TSG+++V ++  A   + E F   +++K Y
Sbjct: 122 VVEALQALDKDLSRVDSDIRPGIVSRLDAGTSGLMLVCKSDRAFVAMKEQFARHQVKKTY 181

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G     +  +   + +++        +          AI+H+ V++        L
Sbjct: 182 QTLVQGHIAQDRATVEAPIARQTGASSFRFAI----SPDGKPAITHWDVLERLP-GATLL 236

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +   TGRTHQ+RVH   +G P++GD  Y AN +        N+ +LH+  ++  HP GG
Sbjct: 237 SINLETGRTHQIRVHLSSLGHPLIGDTLYGANPRL-AEELGLNRQWLHSIRLEFTHPVGG 295

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
           R + + +PLP  +    + L 
Sbjct: 296 RTIHLESPLPDDLSHALEVLR 316


>gi|255004408|ref|ZP_05279209.1| sfhb-like protein [Anaplasma marginale str. Virginia]
          Length = 340

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 142/334 (42%), Gaps = 34/334 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSG 62
           M  V  V V  + +  R+D+        I+    Q ++  GQV +  + +  N    ++G
Sbjct: 1   MKCVHEVCVTKEGDQQRIDKLISCAL-EISRNRAQGLIAGGQVTISGRVINNNSYLTKTG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V  I   +   + +     I                 ++YED  + V +K   I+V  G
Sbjct: 60  DVYTIVTAVQKPSTLSPNYDI--------------DLKVVYEDHDVIVIDKDPYIAVHPG 105

Query: 123 SGIAYHI--DGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +GI +H   +  L  +           +P + HRLD++TSG++V A+T  A   L+E   
Sbjct: 106 NGIEHHTITNALLARFGAGLQSVGSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELA 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +  +K Y ++ WGIP  K+  I   +     +    + +++    G   A + ++V   
Sbjct: 166 NQGFKKEYLAVAWGIPCPKRGVIHTNI----RVKRSDITMMEAANSGGKPAKTEYEVEQE 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLY 289
             +    +    HTGRTHQ+RVH  H+G  IVGD KY  N K    S +        +  
Sbjct: 222 LGEVASLIRCTLHTGRTHQIRVHMSHIGHSIVGDQKYGKNCKKCMRSGVPPDVKNFRRQA 281

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           LHA  +   HP  G+ ++ T+     + +   +L
Sbjct: 282 LHASLLGFRHPSTGKYIEFTSKPADDIQQLISAL 315


>gi|56696292|ref|YP_166649.1| ribosomal large subunit pseudouridine synthase D [Ruegeria pomeroyi
           DSS-3]
 gi|56678029|gb|AAV94695.1| ribosomal large subunit pseudouridine synthase D [Ruegeria pomeroyi
           DSS-3]
          Length = 342

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 85/355 (23%), Positives = 143/355 (40%), Gaps = 50/355 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M   +   V       RLD+      P    ++   L +++  G V VD + V     R+
Sbjct: 1   MQSTRLEFVIAAAPPPRLDKALSRDVPETAALSRTRLARLITEGAVSVDGQVVTDPKARV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  V I       +HI  E                +  +++YED  + V +KPAG+ V
Sbjct: 61  VEGAQVAIALTEAEESHIAPE---------------AIPLVVVYEDDDLIVIDKPAGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    D+       ++P + HR+D++TSG+LVVA++ AA   L  
Sbjct: 106 HPAPGTPSGTLVNALLAHCGDNLSGVGGVKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F     ++ Y +L +G+P      +           N L   + +        +Q    
Sbjct: 166 QFAAHSAERHYTALCYGVPDGSDPRLRGVKGASFEPGNILRLTTQLTRHPTDRQRQAVVF 225

Query: 221 KGANYAISHFKVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            G  +A++  +V++ F Q      ++    TGRTHQ+RVH  H G  ++GD  Y    K 
Sbjct: 226 HGGRHAVTRARVVESFGQPAAVSLIDCWLETGRTHQIRVHMAHAGHGLLGDPVYGGRRKL 285

Query: 279 NFTS---------PIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
           +  +             +  LHA  +   HP  G +L  +APLP  + +  + L 
Sbjct: 286 SPRALSPEAVDAIGAFPRQALHAAVLGFEHPLSGEKLSFSAPLPDDLERLLEVLR 340


>gi|260364018|ref|ZP_05776749.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus K5030]
 gi|308115630|gb|EFO53170.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           parahaemolyticus K5030]
          Length = 325

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 73/331 (22%), Positives = 142/331 (42%), Gaps = 35/331 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L+    +G+V+V+ + V K   ++  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAIAELFADFSRSRLKDGCWTGKVQVNGEVVTKPRTKVMGGEEITLQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +        +   LD               ++YED  I V NKP    V  G+G     
Sbjct: 70  ELEDEERWEAQDIPLD---------------IVYEDDDIIVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  + D ++  +  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLHHYPDIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S         +         A++H++V + F ++   + ++
Sbjct: 175 AIGRM-TAGGKVDQPIGRHST-----KRTLMAVAPLGKPAVTHYRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDTAYGGRARIPTGASQELTDMIRGFDRQALHAVMLRFE 287

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           HP  G  L+  AP+P  MV   ++L    + 
Sbjct: 288 HPITGEELEFHAPVPDDMVAMTEALRKDTEE 318


>gi|224368793|ref|YP_002602954.1| RluD1 [Desulfobacterium autotrophicum HRM2]
 gi|223691509|gb|ACN14792.1| RluD1 [Desulfobacterium autotrophicum HRM2]
          Length = 313

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 89/322 (27%), Positives = 144/322 (44%), Gaps = 30/322 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +       RLD    +         + + +  G + V   R K   R++ G+VV    
Sbjct: 5   IEISEALMGRRLDLVVADVVHDTTRGAVVRAIEKGLILVSGNRKKPAYRVKPGEVVC--- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                          +S +     ++ +    L+ED  I V NKPAG+ V  G+G     
Sbjct: 62  ----------GSLGSESEIESKPRAESISLDFLHEDQWIVVVNKPAGMVVHPGAGNSSGT 111

Query: 128 HIDGFLKS---WVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            ++  L       D+    P    + HRLD++TSG +VVA+++ A + L + FR RR++K
Sbjct: 112 LLNALLHHFPSLTDTHCDPPLRGGIVHRLDKDTSGTIVVAKSKKAYEFLQKEFRFRRVEK 171

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L  GI    +  I   + +   I    + V   N + A  A + ++V+   A    
Sbjct: 172 RYIALATGIITETQGRITLPIGRH-PIHRKRMAV---NTERARPAETLWRVLGQMA-GHT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            L++   TGRTHQ+RVH   +G P+ GD  Y    K +  +P   +  LHA  +   HP 
Sbjct: 227 LLDVGLKTGRTHQIRVHFRALGHPLAGDRVYGFRGKQSARAP---RQMLHAGTLGFRHPW 283

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
            G R++ TAPLP  MV+  + L
Sbjct: 284 SGKRVEFTAPLPEDMVEVLERL 305


>gi|299134311|ref|ZP_07027504.1| pseudouridine synthase, RluA family [Afipia sp. 1NLS2]
 gi|298591058|gb|EFI51260.1| pseudouridine synthase, RluA family [Afipia sp. 1NLS2]
          Length = 347

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 76/349 (21%), Positives = 144/349 (41%), Gaps = 59/349 (16%)

Query: 11  VVENDEEN------MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQ 63
           ++             RLDR        ++   L+ ++ +G V +    V+    ++++ +
Sbjct: 19  IITAGAAGKSPGQSQRLDRVLAEQVEDLSRTRLKALIVAGHVSIGGAPVQDPAYQVKADE 78

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +  +V      + +   ++YED  + V NKP G+ V   +
Sbjct: 79  TIIVE---------------VPPAVAPEPEGENIPLNIVYEDDDLLVLNKPKGLVVHPAA 123

Query: 124 GIAYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           G   H  G L + + +            ++P + HRLD++T+G++VVA+   A Q LT  
Sbjct: 124 G---HETGTLVNALIAHCGTSLSGIGGVKRPGIVHRLDKDTTGLMVVAKNDRAHQSLTAQ 180

Query: 174 FRMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           F        +++ Y + VWG P      I   +  +     + + V     +G  +A++H
Sbjct: 181 FADHGRTGALRRGYMAFVWGAPSRSHGTIDQPI-DRHPFAREKMAVR----QGGRHAVTH 235

Query: 230 FKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           +++++ F  +        L  Q  TGRTHQ+RVH  H G P++GD  Y + F+       
Sbjct: 236 WEMLESFEGRDGKPLAALLACQLETGRTHQIRVHLGHAGHPLIGDDVYGSGFRTKANQLG 295

Query: 285 ---------QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                      +  LHA  + + HP  G  +   + LP  +V    +L 
Sbjct: 296 TPAKTAVAALGRQALHAYLLQIEHPATGEIMNWQSGLPEDLVLLQSALR 344


>gi|86747580|ref|YP_484076.1| pseudouridine synthase RluD [Rhodopseudomonas palustris HaA2]
 gi|86570608|gb|ABD05165.1| ribosomal large subunit pseudouridine synthase D [Rhodopseudomonas
           palustris HaA2]
          Length = 324

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 83/342 (24%), Positives = 145/342 (42%), Gaps = 51/342 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           +VV  DE + RLDR      P ++   L+ ++  G+V +    V+        G+ + I 
Sbjct: 1   MVVAGDEGSSRLDRVLATRCPALSRSRLKVLILDGRVAIAGSAVRDPAYHASPGETITID 60

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                      E   L+               +++ED  I V NKP G+ V   +G  + 
Sbjct: 61  VPPPVAPEPEGEAIALE---------------IVHEDDDIIVINKPRGLVVHPAAG--HE 103

Query: 129 IDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-- 177
               + + +   G+         +P + HRLD++T+G++V A+   A Q L+  F     
Sbjct: 104 TGTLVNALIAHCGESLSGIGGVRRPGIVHRLDKDTTGLMVAAKNDRAHQSLSAQFADHGR 163

Query: 178 --RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              +++ Y++ VWG+P   +  I   +  +     + + V      G   AI+H++V++ 
Sbjct: 164 TGELRRGYYAFVWGVPNRARGTIEAPI-DRHPYAREKMAVRD----GGREAITHWEVLET 218

Query: 236 F-----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFT 281
           F      +    +  Q  TGRTHQ+RVH  H+G P++GD  Y  +FK             
Sbjct: 219 FTGRSGGEIVSLIACQLETGRTHQIRVHLAHLGHPLLGDDVYGPHFKTKASQLSPAARAA 278

Query: 282 SPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                +  LHA  + L HP  G  +   + LPA + +   +L
Sbjct: 279 LADLGRQALHAYLLVLEHPSSGEVMAWESGLPADLARLKAAL 320


>gi|154245928|ref|YP_001416886.1| RluA family pseudouridine synthase [Xanthobacter autotrophicus Py2]
 gi|154160013|gb|ABS67229.1| pseudouridine synthase, RluA family [Xanthobacter autotrophicus
           Py2]
          Length = 377

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 84/363 (23%), Positives = 145/363 (39%), Gaps = 70/363 (19%)

Query: 9   YVVVENDEENMRLDRWFKNHY----PHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQ 63
            V +  ++   RLDR          P ++   +Q+++  G+V V  + V     R+ +  
Sbjct: 32  TVQIAAEDAGERLDRVLARRLALEAPELSRTRIQRLVTEGRVSVSGRVVGDAAGRVNAAD 91

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V  +                L         ++ L   +++ED+ + V +KPAG+ V    
Sbjct: 92  VYTL---------------FLPPPEAAEPVAENLPLTIVFEDAHLVVIDKPAGLVVHPAP 136

Query: 124 GIA--YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G A    ++  L    DS       ++P + HR+D++TSG+LVVA++  A + L   F  
Sbjct: 137 GHASGTLVNALLYHCGDSLSGIGGVRRPGIVHRIDKDTSGLLVVAKSDLAHKGLAAQFAD 196

Query: 177 RR----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFK 231
                 +++ Y + VWG+P+             + I     H  K   +     AI+H++
Sbjct: 197 HGRTGPLERAYLAFVWGVPEAHGSV-------DAPIDRHPSHRQKMAVRLSGRNAITHWE 249

Query: 232 VIDCFAQK---------------------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           V + F                           +E +  TGRTHQ+RVH  H+G P++GD 
Sbjct: 250 VQEAFVGHGRTHLRNKGQVKGEVKMEEGVASLIECRLETGRTHQIRVHMAHVGHPLLGDE 309

Query: 271 KYCANFKGNFTSPIQN---------KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            Y   F+   T   ++         +  LHA  +   HP  G  L   + LP  +    +
Sbjct: 310 VYGQGFRTKETLLPEDAREHLARLGRQALHAARLGFAHPVTGETLSFESQLPEDLAALAE 369

Query: 321 SLG 323
            LG
Sbjct: 370 VLG 372


>gi|108757849|ref|YP_631549.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108461729|gb|ABF86914.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 346

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 82/324 (25%), Positives = 144/324 (44%), Gaps = 36/324 (11%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             +    R+D++    +P +    +  ++ +G V  D +  K   R++ G+++ +     
Sbjct: 12  PPEARGERVDQYLARAFPDLTRSRIHGLIEAGHVLADGQPAKPARRLRGGELLVLH---- 67

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHID 130
                      + + V     ++ L   LL+ED  + V +K AG+ V  G+G A    ++
Sbjct: 68  -----------IPAPVPAVPLAEELPLALLHEDRDLVVVDKAAGMVVHPGAGHASGTLVN 116

Query: 131 GFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             L    D  G     +P + HRLD++T+G LVVA+   A   L ++F+ R ++K Y +L
Sbjct: 117 ALLHRVKDLAGVGGELRPGIVHRLDKDTTGCLVVAKNEQALVALQKAFKTRAVEKTYLAL 176

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLE 244
           V G+P  +      +       G   +H  +     K    AI+ ++V++ F      +E
Sbjct: 177 VHGVPPAEGRIETLY-------GRHPIHRQRFTGKVKEGKNAITEYRVLETF-DGAALVE 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF----TSPIQNKLYLHARYMDLPHP 300
           +   TGRTHQ+RVH    G P++ D  Y A  K             +  LHA  +   HP
Sbjct: 229 VDLLTGRTHQIRVHLSEAGHPLLCDALYGAGRKAKGAAAEAQERLGRQALHAWRLSFAHP 288

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G+ L++ AP+PA +      L 
Sbjct: 289 RTGKVLKLEAPIPADLEAALTLLR 312


>gi|148244244|ref|YP_001218938.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Vesicomyosocius okutanii HA]
 gi|146326071|dbj|BAF61214.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 303

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 90/324 (27%), Positives = 152/324 (46%), Gaps = 26/324 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V +  ++   +  RLD +       +   ++ +++R G+VRV+K R K   ++    
Sbjct: 1   MS-VSFQTIDEFSQGQRLDNYLLKILKGVPKSHIYRVIRKGEVRVNKGRKKSEYKLNLDD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VRIPP+  +    +     L            L + +LYED  + + NKP+G++V  GS
Sbjct: 60  IVRIPPIKVSTTKSMYTSDGLKK---------ILTNAILYEDKGLLIINKPSGLAVHSGS 110

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+     G +++      +   L HRLD+ TSG+L+VA+ R   ++L E      I+K Y
Sbjct: 111 GV---NVGVIEALRQMYKEPIELVHRLDRATSGVLLVAKKRLVLKNLHEQLNQHTIEKHY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---F 240
            +LV G+   K   I   L   S          K + KG  Y++SHF  +  F  +    
Sbjct: 168 IALVKGVWSKKIHTINAPLYNNS-------RYTKVDAKG-KYSVSHFHPLKNFNIENFSA 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPH 299
             + +   TGRTHQ+RVHA ++G  +  D+KY    F          +L+LH+  +   +
Sbjct: 220 SLVNISIETGRTHQIRVHAKYVGHALACDNKYGDKEFDRQVKFKGLKRLFLHSNQLIFIN 279

Query: 300 PEGGRLQ-ITAPLPAHMVKTWDSL 322
           P    +Q + APLP  + +    L
Sbjct: 280 PLTNDIQKVNAPLPIELEEFLAKL 303


>gi|193076604|gb|ABO11275.2| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 17978]
          Length = 350

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 139/326 (42%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++      R+D+     +   +   L++ ++ G + V+   VK   R +  + + +  
Sbjct: 41  VQLDESYLGQRIDQVAAMVWSEFSREKLKQWMKEGHLLVNGNIVKPKYRCEGNETLTLNV 100

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            + A  +   E   LD               ++YED  I V NKP G+ V  G+G     
Sbjct: 101 ELEAQTNSQPENIPLD---------------IVYEDEDILVINKPVGMVVHPGAGNTSST 145

Query: 130 --DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L     S +  +  L HR+D++TSG+LVVA+   A   L++    + + +IY  +
Sbjct: 146 LVNALLYHSPKSAELSRAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLGDKSVYRIYDLV 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            +G        I   + K+  +    + ++     G   A++H+ V + F + F  ++ Q
Sbjct: 206 TYGNIIA-GGTIDEPI-KRHPVDRVKMAIL----PGGRDAVTHYNVKERF-RDFTRVQAQ 258

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  ++G  +VGD  Y         A+     T     +  LHA  + L 
Sbjct: 259 LETGRTHQIRVHFSYIGHGLVGDQVYMNRVRIPAGASELLIETLRGFKRQALHAAKLGLK 318

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +   AP P    +  + L 
Sbjct: 319 HPRTGEEMLFEAPWPEDFTQLVNVLR 344


>gi|329122166|ref|ZP_08250773.1| ribosomal large subunit pseudouridine synthase D [Dialister
           micraerophilus DSM 19965]
 gi|327466804|gb|EGF12327.1| ribosomal large subunit pseudouridine synthase D [Dialister
           micraerophilus DSM 19965]
          Length = 307

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 82/323 (25%), Positives = 142/323 (43%), Gaps = 34/323 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSG-QVRVDKKRVKFNNRIQSGQVV 65
           +    V+  ++ MRLD++ K     +    +QK ++ G  + +  + V+ N  I   + +
Sbjct: 3   IHIYEVDEKQDGMRLDQFLKE-VSGLTRSEVQKWIKEGYAISLPNRMVRSNYHISDKEKI 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +          +I ++  LD               +LYED  I V NK  G+ V  G+G 
Sbjct: 62  QFSWEEKKEIELIPQKIKLD---------------ILYEDEHIIVINKSRGMVVHPGAGN 106

Query: 126 AYHI--DGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             +   +  L    +S     +  +P + HRLD++TSG++V  ++  A + +        
Sbjct: 107 IDNTLVNALLYHCGESLLKVGEKTRPGIVHRLDKDTSGVMVAVKSDIAYEKVKNEIATHE 166

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            ++ Y +LV G  +     I   L +       +        K    AI+HF V++    
Sbjct: 167 AKRTYLTLVHGQMEGPDGKIDLPLGRSLKDRMKW----DVQPKTGKNAITHFHVLEFMP- 221

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           K+  LE +  TGRTHQ+RVH  ++G P++ D  Y    K NF         LH+  ++L 
Sbjct: 222 KYSLLECKLETGRTHQIRVHMSYIGHPVINDPLYG-RKKDNFP---IQGQALHSFTLELK 277

Query: 299 HPEGGR-LQITAPLPAHMVKTWD 320
           HP  G+ ++  APLP  M K  +
Sbjct: 278 HPLTGKIMKFEAPLPEDMKKCLE 300


>gi|288818020|ref|YP_003432367.1| pseudouridine synthase [Hydrogenobacter thermophilus TK-6]
 gi|288787419|dbj|BAI69166.1| pseudouridine synthase [Hydrogenobacter thermophilus TK-6]
          Length = 318

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 140/325 (43%), Gaps = 32/325 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
            VV+ + +  RLD +    Y   +   +QK++  G V VD K +K  + R+++GQ +   
Sbjct: 6   FVVDQEAQGKRLDLFLTEAYGEFSRSYVQKLIEDGFVLVDDKEIKKPSRRLKAGQKITFY 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                   ++ E    D               ++YED  I V  KP G+ V    G    
Sbjct: 66  IPQVEPLEVLPEDIPFD---------------VVYEDEDILVLIKPCGLVVHPSPGYSSG 110

Query: 127 YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++  L    +  G    ++P + HRLD+ T+G++VVA++  A + L E F  RR+ K 
Sbjct: 111 TLVNALLFRIKELSGIGGKERPGIVHRLDKNTAGLMVVAKSDKAHRSLVEEFMQRRVLKR 170

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFC 241
           Y +LV G+ +     +   + +       +  V     +    A + ++VI  F   +  
Sbjct: 171 YHALVSGLLREDSGTVEKSIGRHPVDRKKFSVV-----EDGKPAKTEYEVIKRFEKHRIT 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLP 298
           +L+++ HTGRTHQ+RVH   +G P++GD  Y    ++      + +     L +  +   
Sbjct: 226 FLDVRIHTGRTHQIRVHLSFIGHPVLGDKTYGFKTSSVDRKILNLMGECHMLVSYQLGFY 285

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP   + +      P       + L
Sbjct: 286 HPITKKWMDFQIEDPKPFRDVLNFL 310


>gi|255522642|ref|ZP_05389879.1| hypothetical protein LmonocFSL_15771 [Listeria monocytogenes FSL
           J1-175]
          Length = 279

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 72/302 (23%), Positives = 133/302 (44%), Gaps = 33/302 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++E      R+D+         +   +Q +L++G + V+ +  K N ++Q G  +  
Sbjct: 4   ETLIIEESHARERVDKVIAEMM-GKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                    ++ E   LD               + +ED  + V NKP G+ V   +G A 
Sbjct: 63  EVREPEELEVLAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHAS 107

Query: 127 -YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 108 GTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + +      + VV+        A +HF+V++     + 
Sbjct: 168 EYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVLERLP-GYT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  TGRTHQ+RVH  ++G P+ GD KY         +   N  +LHA  +   HP 
Sbjct: 222 LINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTIKGNGQFLHAAKLGFDHPT 276

Query: 302 GG 303
             
Sbjct: 277 TK 278


>gi|284007738|emb|CBA73551.1| 23S rRNA pseudouridine synthase D [Arsenophonus nasoniae]
          Length = 325

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 144/325 (44%), Gaps = 41/325 (12%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72
             +   RLD+     +P  +   +++ +   +V V+ K + +   ++   + + I  +I 
Sbjct: 13  ESQLGQRLDQALAELFPDYSRSRIKEWILDNRVLVNGKIINRPKEKVFGSEQIAIDVLIE 72

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--D 130
                           ++      +   ++YED +I V NKP  + V  G+G       +
Sbjct: 73  E---------------DMRWQPQNIPLNIVYEDDEILVINKPRDLVVHPGAGNPDGTVLN 117

Query: 131 GFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             L  + +     +  + HRLD++T+G++V+A+T  A  HL E+ + R I + Y ++V G
Sbjct: 118 ALLYRYPEIINVPRAGIVHRLDKDTTGLMVIAKTIPAQTHLVEALQRREITREYEAVVNG 177

Query: 190 IPK---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                    E IA    K++H+    +            AI+H++V++ F +    L ++
Sbjct: 178 RMTAGGTVDEPIARHPTKRTHMAIHPM---------GKPAITHYRVMEHF-RAHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             +GRTHQ+RVH  H+  P+VGD  Y    +       +        N+  LHA  + L 
Sbjct: 228 LESGRTHQIRVHMAHINHPLVGDPVYGGRPRPLKGVSEEFRQIMSNFNRQALHATMLRLY 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSL 322
           HP  G  ++  A +PA MV   + L
Sbjct: 288 HPLTGIEMEWHADIPADMVILINIL 312


>gi|118602128|ref|YP_903343.1| ribosomal large subunit pseudouridine synthase C [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
 gi|118567067|gb|ABL01872.1| ribosomal large subunit pseudouridine synthase C [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
          Length = 303

 Score =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 97/324 (29%), Positives = 156/324 (48%), Gaps = 26/324 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ + + +V+   E  RLD +       +   ++ +++R G VRV+K R K + ++    
Sbjct: 1   MS-ISFQIVDEFSEGQRLDNYLLKILKGVPKSHICRVIRKGWVRVNKGRKKVSYKLILND 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +VRIPP+  +   IIK   I DS   L   +       LYED  + + NKP+G+SV  GS
Sbjct: 60  IVRIPPIKVS---IIKSIYISDSLKKLLIDAK------LYEDKGLLIINKPSGLSVHSGS 110

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+     G +++      +   L HRLD+ TSG+L++A+ R+  ++L E      ++K Y
Sbjct: 111 GVD---VGIIEALRQIYKKPIELVHRLDRATSGVLLIAKKRSVLKNLHEQLSQHTVEKRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---F 240
            +LV G+   K   I   L + S     Y+ V    +    YAISHF+ +  F+      
Sbjct: 168 TALVKGVWSKKCHTIDAPLYQNSR----YIMV----DAKGKYAISHFQPLKNFSDGGFSA 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPH 299
             +E+   TGRTHQ+RVHA + G  +  D KY    F          +L+LHA      +
Sbjct: 220 SLVEISIETGRTHQIRVHAKYAGHALACDDKYGDKEFDRQVKFKGLKRLFLHAHQFIFTN 279

Query: 300 PEGGRLQ-ITAPLPAHMVKTWDSL 322
           P    +Q + A LP  + +    L
Sbjct: 280 PLTNDIQKVNASLPVELEEFLAKL 303


>gi|93005114|ref|YP_579551.1| pseudouridine synthase, RluD [Psychrobacter cryohalolentis K5]
 gi|92392792|gb|ABE74067.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter
           cryohalolentis K5]
          Length = 343

 Score =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 100/314 (31%), Positives = 163/314 (51%), Gaps = 23/314 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V Y+ V   + + RLD +  N    +   ++ K++RS ++RV+ KR K ++R+Q   VV
Sbjct: 37  KVNYLEVTRHQHDQRLDNFLLNRLKGLPKPHIYKMIRSDEIRVNNKRCKAHDRVQREDVV 96

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RI PV+ A           +  +  T+ +  L + ++YED  + V NKP+GI+V GGSG+
Sbjct: 97  RIAPVVLATR---------EKPIISTEFAKSLLARVVYEDEGLIVLNKPSGIAVHGGSGL 147

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++     K     L HR+D++TSG+L++++ R+A + L +    + IQK Y  
Sbjct: 148 AFGVIEAMREVTGKKY--LELVHRIDKDTSGLLMISKKRSALKVLQQHLVDKTIQKHYLC 205

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCW 242
           +  G P   ++ I   LL+ +   G+    V   +     + +   V   F    Q    
Sbjct: 206 IAKGQPALNEQRIDASLLRYTLASGERRVKVDTQDPQTKESQTDIVVHGRFMIAEQPVSL 265

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +P TGRTHQ+RVH  H+G  I+GD KY  + K        ++L LHA  +D+P    
Sbjct: 266 IEAKPLTGRTHQIRVHLAHIGHAILGDDKYHVHDKSGV-----HRLCLHAWRLDIP---- 316

Query: 303 GRLQITAPLPAHMV 316
           G   ITAPLP  M+
Sbjct: 317 GYETITAPLPEEML 330


>gi|253702050|ref|YP_003023239.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251776900|gb|ACT19481.1| pseudouridine synthase, RluA family [Geobacter sp. M21]
          Length = 319

 Score =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 142/328 (43%), Gaps = 36/328 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++ +   +D +  RLD +   + P +      +++ +G   V+  + K   +++ G 
Sbjct: 1   MEPIE-LTFPSDSDPERLDSFISRNVPELTRSAALRLIETGFATVNGSKQKPALKLKGG- 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                            Q ++   V      + +   +LYED ++ V NK AG+ V  G+
Sbjct: 59  --------------EVVQVVVPPPVPAEPQPEEIPIEVLYEDGELVVVNKGAGMVVHPGA 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HR+D++TSG LVVA++  A   L E F+  
Sbjct: 105 GNPEGTLVNALLAHCKDLSGIGGELRPGIVHRIDKDTSGTLVVAKSDRAHNALAEQFKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I+++Y +LV+G PK  K  I + + +           +    +    A++H++V+  + 
Sbjct: 165 TIKRVYLALVYGSPKEDKGRIESSIGRHPTDRKK----MSAKARHGKQAVTHWRVVARYP 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--------QNKLY 289
                + ++  TGRTHQ+RVH    G P++ D  Y    + +               +  
Sbjct: 221 -GITLIRLRLETGRTHQIRVHMSEAGHPLLADEVYGGTGRLSGVQDPVLKQMIKSMGRQA 279

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMV 316
           LHA+ +   HP  G+ L+    LP  M 
Sbjct: 280 LHAKTLGFLHPVSGKYLEFDTELPPDMA 307


>gi|313891514|ref|ZP_07825127.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
 gi|313120091|gb|EFR43270.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
          Length = 307

 Score =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 82/318 (25%), Positives = 141/318 (44%), Gaps = 34/318 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSG-QVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V+  ++ MRLD++ K     +    +QK ++ G  + +  + V+ N  I   + ++    
Sbjct: 8   VDEKQDGMRLDQFLKE-VSGLTRSEVQKWIKEGYAISLPNRMVRSNYHISDKEKIQFSWE 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                 +I ++  LD               +LYED  I V NK  G+ V  G+G   +  
Sbjct: 67  EKKEIELIPQKIKLD---------------ILYEDEHIIVINKSRGMVVHPGAGNIDNTL 111

Query: 130 -DGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            +  L    +S     +  +P + HRLD++TSG++V  ++  A + +         ++ Y
Sbjct: 112 VNALLYHCGESLLKVGEKTRPGIVHRLDKDTSGVMVAVKSDIAYEKVKNEIATHEAKRTY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G  +     I   L +       +        K    AI+HF V++    K+  L
Sbjct: 172 LTLVHGQMEGPDGKIDLPLGRSLKDRMKW----DVQPKTGKNAITHFHVLEFMT-KYSLL 226

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E +  TGRTHQ+RVH  ++G P++ D  Y    K NF         LH+  ++L HP  G
Sbjct: 227 ECKLETGRTHQIRVHMSYIGHPVINDPLYG-RKKDNFP---IQGQALHSFTLELKHPLTG 282

Query: 304 R-LQITAPLPAHMVKTWD 320
           + ++  APLP  M K  +
Sbjct: 283 KIMKFEAPLPEDMKKCLE 300


>gi|227431875|ref|ZP_03913898.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
 gi|227352342|gb|EEJ42545.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
          Length = 312

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 82/317 (25%), Positives = 133/317 (41%), Gaps = 36/317 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D+   R+D          +   L   L  G + V+  +VK + ++ SG  + I P     
Sbjct: 11  DQAG-RVDAVLSKENLSYSRTTLSNWLVDGTILVNNHKVKRSYKVVSGDTISITPPETQE 69

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             I  E   LD                        V NKP G+ V   +G   H  G L 
Sbjct: 70  TKIEAENIPLDIIYEDDDII---------------VVNKPQGMVVHPAAG---HSSGTLV 111

Query: 135 SWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +             +P + HR+D++TSG+L+VA+   A   L+E  +  + Q++Y++L
Sbjct: 112 NALLHHSPLSTINGEFRPGIVHRIDRDTSGLLMVAKNDKAHHSLSEQLKSHKNQRVYYAL 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + +   I      V+    +G   A++HF+V+  +   +  L++ 
Sbjct: 172 VRGEFTEDSGTIEAPIGRH-KIDRKKQAVI----EGGREAVTHFRVLKRYV-GYTLLKVN 225

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
             TGRTHQ+RVH  ++G P+VGD  Y    K +      N   LHA+ + L  P  G  L
Sbjct: 226 LETGRTHQIRVHMSYIGHPVVGDPVYGTAQKLDGIQ--LNGQLLHAKTLTLEQPTTGDEL 283

Query: 306 QITAPLPAHMVKTWDSL 322
              +PLP +      +L
Sbjct: 284 SFDSPLPDYFQFALSTL 300


>gi|307610038|emb|CBW99572.1| ribosomal large subunit pseudouridine synthase D [Legionella
           pneumophila 130b]
          Length = 321

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 135/327 (41%), Gaps = 30/327 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q + V  +  N R+DR      P  +   +   +++G V ++    K  ++   G ++ I
Sbjct: 7   QQLSVPRELHNQRVDRVIARLLPEYSRSLISNWIKTGAVTLNNLPCKPKDKALGGDLITI 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                 +N          +  N  K  + +   ++YEDS++ V NKPAG+ V  G+G   
Sbjct: 67  NVDHTMVN----------TDFNFCK-PENIPIQIIYEDSEVIVVNKPAGLVVHPGAGNKE 115

Query: 128 HI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           H   +  L    +     +  + HRLD++T+G+L+VA+   +   L    + R I++ Y 
Sbjct: 116 HTLVNALLHHCPELQLLPRAGIIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYL 175

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G        I     +        + V          A++H+  I+   + F  L 
Sbjct: 176 TLVHGYV-ISGGTIDTGFGRHPK-NRLKMAVTDF----GRQAVTHYN-INKHYKDFTLLN 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           +   TGRTHQ+RVH  ++  P+VGD  Y    K    +            +  LHA  + 
Sbjct: 229 VSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKFPPNADEAILSVLKQFKRQALHACSIS 288

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
             HP     + + A LP       ++L
Sbjct: 289 FCHPVKNTEITLNALLPDDFELLLNTL 315


>gi|68171180|ref|ZP_00544587.1| Pseudouridine synthase, RluD [Ehrlichia chaffeensis str. Sapulpa]
 gi|67999411|gb|EAM86053.1| Pseudouridine synthase, RluD [Ehrlichia chaffeensis str. Sapulpa]
          Length = 323

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 77/331 (23%), Positives = 154/331 (46%), Gaps = 32/331 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVR 66
           + + +++ +EN RLD++  +   +I+   +Q++++  ++ +    ++ NN I +   +  
Sbjct: 4   KKIFIKSGDENNRLDKFIASKL-NISRNQVQQLIKDSKILLFDTIIRDNNHITKVNDIYN 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I      ++  I               + ++   ++YED  I + NK  GI+V  G+G  
Sbjct: 63  ISIPTKTISDTIT-------------PNHYIPISVVYEDHDIIIINKAPGITVHPGAGTN 109

Query: 127 YHI--DGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            +   +  +  + +S     K  +P + HRLD++TSG++V+A+   +   L++    ++I
Sbjct: 110 NNTLVNALVAHYGNSLSHVGKATRPGIIHRLDKDTSGLMVIAKNEKSYYFLSDLLLKKQI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++VWG+P  K   I N++  K       +  V         AI+ ++    F+  
Sbjct: 170 KKEYLAVVWGLPNPKSNTIKNYICVKP--NNKQMMTVTHLPHKGKLAITEYQTQKSFSNI 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQNKLYLHA 292
              ++ + HTGRTHQ+RVH  ++G  I+GD KY  N        K +       +  LHA
Sbjct: 228 ASLIKCRIHTGRTHQIRVHMSYIGNSIIGDQKYGKNNSKSVKYAKQSTIINTLKRQALHA 287

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
             +   HP     ++  + +P  +    D L
Sbjct: 288 YKLGFTHPTSNTYIEFHSDIPNDIQMLIDEL 318


>gi|255019802|ref|ZP_05291878.1| Ribosomal large subunit pseudouridine synthase D [Acidithiobacillus
           caldus ATCC 51756]
 gi|254970731|gb|EET28217.1| Ribosomal large subunit pseudouridine synthase D [Acidithiobacillus
           caldus ATCC 51756]
          Length = 320

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 140/326 (42%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +    RLD   K   P ++   LQ +L+ G V VD    + + RI+ G+ V +  
Sbjct: 10  LTLPVEGAGQRLDAVLKELLPELSRSRLQTLLQQGSVLVDGSAHRPSYRIRGGEGVVLH- 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                         L  +      ++ +   +++EDS++ V +KPAG++   G+G     
Sbjct: 69  --------------LPQTPAEHWQAEAMDLTIVHEDSQLLVIDKPAGLATHPGAGRPRGT 114

Query: 128 HIDGFLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L     + +  +  + HRLD +TSG+LVVA+T  A Q L      R + + Y +L
Sbjct: 115 LANAVLAHCPANERLPRAGIVHRLDMDTSGLLVVAKTELARQSLIAQLADRSMHREYLAL 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        +   + +      D + +  +  +    A + +++++ F +    L ++
Sbjct: 175 VQGALTG-GGHVEAPIGRHPQ---DRLRMTVR--RDGRPARTDYRLVERFPR-HSLLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANF--------KGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  H+G P+VGD  Y             G        +  LHA  + L 
Sbjct: 228 LATGRTHQIRVHMRHLGHPLVGDPLYGGRPILPAGLGAAGLARWQAFRRQALHAWRLILE 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HPE G   Q    +P  M +    L 
Sbjct: 288 HPESGDTCQWEVAMPTDMDELLQVLR 313


>gi|319942386|ref|ZP_08016700.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
 gi|319804074|gb|EFW00982.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
          Length = 363

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 141/330 (42%), Gaps = 26/330 (7%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNH 76
             RLD+    H P ++   L K++ +G V+++     K   +   G  + +         
Sbjct: 45  GERLDKVLAAHLPDVSRARLAKLIENGSVKLNGAVTTKIRAKATEGDEIELL-------- 96

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
              E   LD ++     S F++  ++YED  I V NKPAG+ V  G+G      ++G L 
Sbjct: 97  ---EPPKLDEALAFEPQS-FVEFEVIYEDPSIIVVNKPAGLVVHPGAGNPDGTLLNGLLY 152

Query: 135 SWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            + + K   +  + HRLD++T+G++VVART AA  +L    + R +++ YW+L  G    
Sbjct: 153 HFPELKDVPRAGIVHRLDRDTTGLMVVARTLAAQTNLVRQLQERTVKREYWALTMGTAAE 212

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTG 250
               +   + +       +          A  A +  + +           W+  +  TG
Sbjct: 213 D-FVVDVPIGRDPKSRIRFKGFPGSTGVRAKPARTRARAVGWSSVDGIPASWVACRLDTG 271

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTS----PIQNKLYLHARYMDLPHP-EGGRL 305
           RTHQ+RVH      P++GD  Y     G           ++  LHA  + L HP  G  +
Sbjct: 272 RTHQIRVHLTGEDLPLIGDQLYRGRAPGIAVKVENFLEFHRQALHASRLGLIHPATGEEM 331

Query: 306 QITAPLPAHMVKTWDSLGF-KYDRNLYIKR 334
           +     P  M+   + LGF  +DR + +  
Sbjct: 332 EWFVEPPEDMIDLMEQLGFGPWDRPVTVFE 361


>gi|54310131|ref|YP_131151.1| 23S rRNA pseudouridine synthase D [Photobacterium profundum SS9]
 gi|90414902|ref|ZP_01222867.1| putative ribosomal large subunit pseudouridine synthase D
           [Photobacterium profundum 3TCK]
 gi|46914570|emb|CAG21349.1| putative ribosomal large subunit pseudouridine synthase D
           [Photobacterium profundum SS9]
 gi|90324016|gb|EAS40610.1| putative ribosomal large subunit pseudouridine synthase D
           [Photobacterium profundum 3TCK]
          Length = 324

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 79/332 (23%), Positives = 140/332 (42%), Gaps = 35/332 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V + +  MRLD+     YP  +   +++ +    V V+ + V K   ++  G+ + I  
Sbjct: 10  TVNDSQLGMRLDQVIAELYPDYSRSRVKEWILKNMVSVNGEIVNKPRLKMMGGEELFIKA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            I      + +   LD               ++YED  I V NKP    V  G+G     
Sbjct: 70  EIEDEVRWVAQDIPLD---------------IVYEDEHILVINKPRDFVVHPGAGTPDRT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L      ++  +  + HRLD++T+G++VVA+T  A   L  + + R+I + Y ++
Sbjct: 115 VLNALLFHCPALAEVPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + +        +     +    AI+H++V + F +    + ++
Sbjct: 175 AMGKMTG-GGTVEKPIGRHAT-----KRICMAVHELGKPAITHYRVAEHFREHTRLV-LR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  +M  P+VGD  Y    +                ++  LHAR + L 
Sbjct: 228 LETGRTHQIRVHMSYMSHPLVGDAIYGGRPRPPRHASDELILALRSFDRQALHARMLRLS 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
           HP  G  ++  APLP  ++   D L      N
Sbjct: 288 HPITGELMEWRAPLPNDILAMIDILRKDKIEN 319


>gi|169634097|ref|YP_001707833.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter baumannii
           SDF]
 gi|169796974|ref|YP_001714767.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter baumannii
           AYE]
 gi|213156621|ref|YP_002318282.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB0057]
 gi|215484435|ref|YP_002326668.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB307-0294]
 gi|239501205|ref|ZP_04660515.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB900]
 gi|260555735|ref|ZP_05827955.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 19606]
 gi|301346835|ref|ZP_07227576.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB056]
 gi|301594459|ref|ZP_07239467.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB059]
 gi|332855566|ref|ZP_08435940.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6013150]
 gi|169149901|emb|CAM87794.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter baumannii
           AYE]
 gi|169152889|emb|CAP01927.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter baumannii]
 gi|213055781|gb|ACJ40683.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB0057]
 gi|213987395|gb|ACJ57694.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB307-0294]
 gi|260410646|gb|EEX03944.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 19606]
 gi|332727390|gb|EGJ58823.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6013150]
          Length = 350

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 140/326 (42%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++      R+D+     +   +   L++ ++ G + V+   VK   R +  + + +  
Sbjct: 41  VQLDESYLGQRIDQVAAMVWSEFSREKLKQWMKEGHLLVNGNIVKPKYRCEGNETLTLNV 100

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
            + A  +   E   LD               ++YED  I V NKP G+ V  G+G     
Sbjct: 101 ELEAQTNSQPENIPLD---------------IVYEDEDILVINKPVGMVVHPGAGNTSGT 145

Query: 128 HIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L     S +  +  L HR+D++TSG+LVVA+   A   L++    + + +IY  +
Sbjct: 146 LVNALLYHSPKSAELSRAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLGDKSVYRIYDLV 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            +G        I   + K+  +    + ++     G   A++H+ V + F + F  ++ Q
Sbjct: 206 TYGNIIA-GGTIDEPI-KRHPVDRVKMAIL----PGGRDAVTHYNVKERF-RDFTRVQAQ 258

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  ++G  +VGD  Y         A+     T     +  LHA  + L 
Sbjct: 259 LETGRTHQIRVHFSYIGHGLVGDQVYMNRVRIPAGASELLIETLRGFKRQALHAAKLGLK 318

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +   AP P    +  + L 
Sbjct: 319 HPRTGEEMLFEAPWPEDFTQLVNVLR 344


>gi|126173261|ref|YP_001049410.1| RluA family pseudouridine synthase [Shewanella baltica OS155]
 gi|152999620|ref|YP_001365301.1| RluA family pseudouridine synthase [Shewanella baltica OS185]
 gi|160874239|ref|YP_001553555.1| RluA family pseudouridine synthase [Shewanella baltica OS195]
 gi|217974428|ref|YP_002359179.1| RluA family pseudouridine synthase [Shewanella baltica OS223]
 gi|304410382|ref|ZP_07392000.1| pseudouridine synthase, RluA family [Shewanella baltica OS183]
 gi|307304474|ref|ZP_07584224.1| pseudouridine synthase, RluA family [Shewanella baltica BA175]
 gi|125996466|gb|ABN60541.1| ribosomal large subunit pseudouridine synthase D [Shewanella
           baltica OS155]
 gi|151364238|gb|ABS07238.1| pseudouridine synthase, RluA family [Shewanella baltica OS185]
 gi|160859761|gb|ABX48295.1| pseudouridine synthase, RluA family [Shewanella baltica OS195]
 gi|217499563|gb|ACK47756.1| pseudouridine synthase, RluA family [Shewanella baltica OS223]
 gi|304350866|gb|EFM15266.1| pseudouridine synthase, RluA family [Shewanella baltica OS183]
 gi|306911876|gb|EFN42300.1| pseudouridine synthase, RluA family [Shewanella baltica BA175]
 gi|315266473|gb|ADT93326.1| pseudouridine synthase, RluA family [Shewanella baltica OS678]
          Length = 324

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 141/325 (43%), Gaps = 35/325 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           +   +  +RLD+     +P  +   +++ + S  V VD   V K   ++   Q + I   
Sbjct: 11  ISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVHVDGVVVNKPREKVYELQQILIDAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--H 128
           +    H                 +  +   ++YED  I V NK AG+ V  G+G A    
Sbjct: 71  LEEEVHAA---------------AQAIDLDIVYEDDDIIVINKQAGLVVHPGAGNADGTL 115

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           ++  L    D +   +  + HRLD++T+G++VVA+T  A  HL  + + R I + Y ++V
Sbjct: 116 MNALLHHCPDIEHVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        +   + +  H+       V  +      A++H++V + F +    L ++ 
Sbjct: 176 MGTMTG-GGTVDEPIGR--HLTKRTHMAVLHS---GKPAVTHYRVAEKF-RNHTRLRLRL 228

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
            +GRTHQ+RVH  ++G  +VGD  Y    K    +  +         +  LHA  ++L H
Sbjct: 229 ESGRTHQIRVHMEYIGHVLVGDPVYGGRPKPPKAASPEFFDILKNFKRQALHAVRLELAH 288

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P     +   AP+P  MV    +L 
Sbjct: 289 PVSCEIMSWQAPIPEDMVILTKALR 313


>gi|301511995|ref|ZP_07237232.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB058]
          Length = 350

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 140/326 (42%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++      R+D+     +   +   L++ ++ G + V+   VK   R +  + + +  
Sbjct: 41  VQLDESYLGQRIDQVAAMVWSEFSREKLKQWMKEGHLLVNGNIVKPKYRCEGNETLTLNV 100

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
            + A  +   E   LD               ++YED  I V NKP G+ V  G+G     
Sbjct: 101 ELEAQTNSQPENIPLD---------------IVYEDEDILVINKPVGMVVHPGAGNTSGT 145

Query: 128 HIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L     S +  +  L HR+D++TSG+LVVA+   A   L++    + + +IY  +
Sbjct: 146 LVNALLYHSPKSAELSRAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLGDKSVYRIYDLV 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            +G        I   + K+  +    + ++     G   A++H+ V + F + F  ++ Q
Sbjct: 206 TYGNIIA-GGTIDEPI-KRHPVDRVKMAIL----PGGRDAVTHYNVKERF-RDFTRVQAQ 258

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  ++G  +VGD  Y         A+     T     +  LHA  + L 
Sbjct: 259 LETGRTHQIRVHFSYIGHGLVGDQVYMNRVRIPAGASELLIETLRGFKRQALHAAKLGLK 318

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +   AP P    +  + L 
Sbjct: 319 HPRTGEEMLFEAPWPEDFTQLVNVLR 344


>gi|52841563|ref|YP_095362.1| ribosomal large subunit pseudouridine synthase D, RluD [Legionella
           pneumophila subsp. pneumophila str. Philadelphia 1]
 gi|52628674|gb|AAU27415.1| ribosomal large subunit pseudouridine synthase D, RluD [Legionella
           pneumophila subsp. pneumophila str. Philadelphia 1]
          Length = 321

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 76/327 (23%), Positives = 136/327 (41%), Gaps = 30/327 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q + V  +  N R+D       P  +   +   +++G V ++    K  ++   G ++ I
Sbjct: 7   QQLSVPRELHNQRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCKPKDKALGGDLITI 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       +  I+++  N  K  + +   ++YEDS++ V NKPAG+ V  G+G   
Sbjct: 67  NV----------DHTIVNTDFNYCK-PENIPIQIIYEDSEVIVVNKPAGLVVHPGAGNKE 115

Query: 128 HI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           H   +  L    +     +  + HRLD++T+G+L+VA+   +   L    + R I++ Y 
Sbjct: 116 HTLVNALLHHCPELQLLPRAGIIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYL 175

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G        I     +        + V          A++H+  I+   + F  L 
Sbjct: 176 TLVHGYV-ISGGTIDTGFGRHPK-NRLKMAVTDF----GRQAVTHYN-INKHYKDFTLLN 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           +   TGRTHQ+RVH  ++  P+VGD  Y    K    +            +  LHA  + 
Sbjct: 229 VSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKFPPNADEAILSVLKQFKRQALHACSIS 288

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
             HP     + + A LP       ++L
Sbjct: 289 FCHPVKNTEITLNALLPDDFELLLNTL 315


>gi|197119760|ref|YP_002140187.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           bemidjiensis Bem]
 gi|197089120|gb|ACH40391.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           bemidjiensis Bem]
          Length = 319

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 76/328 (23%), Positives = 141/328 (42%), Gaps = 36/328 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++ +   +D +  RLD +     P +      +++ +G   V+  + K   +++ G+
Sbjct: 1   MEPIE-LTFPSDSDPERLDSFISRSVPELTRSAALRLIETGFATVNGSKQKPALKLKGGE 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                            Q ++          + +   +LYED+++ V NK AG+ V  G+
Sbjct: 60  ---------------VVQVVVPPPTPAEPQPEEIPIEVLYEDAELVVVNKGAGMVVHPGA 104

Query: 124 GI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HR+D++TSG LVVA+   A   L E F+  
Sbjct: 105 GNPEGTLVNALLAHCKDLSGIGGELRPGIVHRIDKDTSGTLVVAKCDRAHNALAEQFKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I+++Y +LV+G PK  K  I + + +           +    +    A++H++V+  + 
Sbjct: 165 SIKRVYLALVYGSPKEDKGRIESTIGRHPTDRKK----MSAKARHGKQAVTHWRVVARYP 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--------QNKLY 289
                + ++  TGRTHQ+RVH    G P++ D  Y    + +               +  
Sbjct: 221 -GITLIRLRLETGRTHQIRVHMSEAGHPLLADEVYGGTGRLSGVQDPVLKQMIKSMGRQA 279

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMV 316
           LHA+ +   HP  G+ L+    LP  M 
Sbjct: 280 LHAKTLGFLHPVSGKYLEFDTELPPDMA 307


>gi|86158324|ref|YP_465109.1| ribosomal large subunit pseudouridine synthase D [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|85774835|gb|ABC81672.1| ribosomal large subunit pseudouridine synthase D [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 353

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 82/337 (24%), Positives = 143/337 (42%), Gaps = 43/337 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V  +    RLD       P ++   +Q+++ +G+V+VD +  K + R++ G+ + +
Sbjct: 24  RTLHVPPELAGARLDAALVRLAPELSRARVQRLVEAGRVQVDGRAAKASARLRGGEAIAL 83

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                  + ++               +  L   +L+ED+ + V +K  G+ V    G  +
Sbjct: 84  EIPPPEPSGLV---------------AQDLPLAVLHEDADLIVLDKAPGMVVHPARGTPH 128

Query: 128 HI--DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +  L           D    +  L HRLD++TSG LVVA+T AA   L   ++ R 
Sbjct: 129 STVVNALLHRLGLPAAAGPDGALPRLGLVHRLDKDTSGCLVVAKTEAALAALQAQWKGRS 188

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA--NYAISHFKVIDCF 236
           ++K+Y +L  G           +       G      ++   + A    AI+ ++V + F
Sbjct: 189 VEKVYLALCHGALAAAGRLDTPY-------GRHPRDRLRFTGRLASSRRAITEWRVREAF 241

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP---------IQNK 287
                  E+  HTGRTHQ+RVH    G P++GD  Y    +    +P            +
Sbjct: 242 GPAASLAEVTLHTGRTHQIRVHLSEAGHPLLGDAVYGGTRREARLAPDDPARRAAEAVGR 301

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
             LHA  + L HP  G RL + AP+PA +    + L 
Sbjct: 302 QALHALRLGLDHPRTGRRLVVEAPVPADLRAALEILR 338


>gi|114763109|ref|ZP_01442535.1| ribosomal large subunit pseudouridine synthase D [Pelagibaca
           bermudensis HTCC2601]
 gi|114544162|gb|EAU47171.1| ribosomal large subunit pseudouridine synthase D [Roseovarius sp.
           HTCC2601]
          Length = 343

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 83/356 (23%), Positives = 138/356 (38%), Gaps = 52/356 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M     +++  +    RLD+      P    ++   L K++  G V    + +     ++
Sbjct: 1   MDKALRIIIG-EAPPARLDKALARDVPEAAALSRTRLAKLIAEGAVTRGGEVLSDPKVKV 59

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  + I       +HI  E   LD               +++ED  + V NKPAG+ V
Sbjct: 60  AEGDEIVIAVPQAEESHIGPEDIPLD---------------IVWEDDDLVVVNKPAGMVV 104

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L  +           +P + HR+D++TSG+LVVA++  A   L  
Sbjct: 105 HPAPGTPTGTLVNALLHHFGGKLSGVGGVARPGIVHRIDKDTSGLLVVAKSDRAHHGLAA 164

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-------------DYVHVVKQN 219
            F      + Y ++ +G+P      +          GG             D        
Sbjct: 165 QFEAHSADRAYRAICYGVPNQGDPRLLGTRGVSVEPGGVLCIQSGLARHKTDRQRQAVFF 224

Query: 220 EKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +    +A++  +V++ F        LE +  TGRTHQ+RVH  H G  +VGD  Y    K
Sbjct: 225 DGQGRHAVTRARVLESFGAPPAMALLECRLETGRTHQIRVHMAHAGHGLVGDPVYGGRRK 284

Query: 278 GNFTSPIQ---------NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
               +  +         ++  LHA  +   HP  G RL+  APLPA M    ++L 
Sbjct: 285 PPVKAIGEAVATEVAGFDRQALHAAELGFDHPATGERLRFEAPLPADMQSLLEALR 340


>gi|307543919|ref|YP_003896398.1| pseudouridine synthase [Halomonas elongata DSM 2581]
 gi|307215943|emb|CBV41213.1| pseudouridine synthase, RluA family [Halomonas elongata DSM 2581]
          Length = 338

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 69/311 (22%), Positives = 128/311 (41%), Gaps = 34/311 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           + +     RLD+     +   +   L+  ++SG + VD    K  +++  G+++ +   +
Sbjct: 30  IPDSMAGFRLDQAAAELFSDFSRERLKAWIKSGALTVDGGPAKPKDKVYGGEMLALVAEL 89

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
                   E   L+               +++ED ++ V +KP G+ V   +G      +
Sbjct: 90  EDDARFEPEDIPLE---------------VVFEDDEVLVIDKPPGLVVHPAAGNPDGTLL 134

Query: 130 DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +G L      +   +  + HRLD++TSG++VVA+T  A   L E  + R + + Y ++  
Sbjct: 135 NGLLHHCPSLAMVPRAGIVHRLDKDTSGLMVVAKTLVAQTALVEQLQARTVSREYDAVAV 194

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        +   + +                     A++H++VI+ F +    +  +  
Sbjct: 195 GAM-TAGGTLDAPIGRHPRDRKRQAVNAS-----GKPAVTHYRVIERF-RAHTHVRCRLE 247

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNKLYLHARYMDLPHP 300
           TGRTHQ+RVH  H+  P+VGD  Y    K    +            +  LHAR +   HP
Sbjct: 248 TGRTHQIRVHMAHLRYPLVGDPVYGGRLKLPAGAGDTLKEVLREFPRQALHARKLAFVHP 307

Query: 301 EGG-RLQITAP 310
             G  +   AP
Sbjct: 308 TSGATMTFRAP 318


>gi|257466280|ref|ZP_05630591.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|315917437|ref|ZP_07913677.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|313691312|gb|EFS28147.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
          Length = 318

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 74/329 (22%), Positives = 139/329 (42%), Gaps = 37/329 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V  +++  RLD + K   P      L+K++  G V  ++K +  N  ++
Sbjct: 1   MRRIVENYEYQVGEEDQGKRLDLFLKEQLPEATRSYLEKLITEGYVLCNEKVITKNGRKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +  +V+++         I+ E   LD               ++YED  + V NK A + V
Sbjct: 61  KGKEVIQLAIPEEEKMEIVAENIPLD---------------IVYEDKYLLVVNKQANMVV 105

Query: 120 QG--GSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G+     ++  L    ++        +P + HRLD++T+G+++VA+       L  
Sbjct: 106 HPALGNYSGTLVNALLYYCKENLSDMNGVIRPGIVHRLDKDTTGLIIVAKNNQVHSKLAL 165

Query: 173 SFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            F+ + I+K Y ++V G    + K+  +   + + S           Q       AIS++
Sbjct: 166 MFQEKTIRKTYVAIVKGRFSEEKKEGRLETLITRDSKDRKKMTVSQIQ----GKKAISNY 221

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           +V+     K   +E++  TGRTHQ+RVH  ++  PI+GD  Y              +  L
Sbjct: 222 RVL-LDGDKHSLVEVKIETGRTHQIRVHMKYLNHPILGDIVYGQE------DTKCKRQML 274

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           HA  ++  HP     + +   LP   ++ 
Sbjct: 275 HAYRLEFIHPITEEAICLEGKLPEDFIEA 303


>gi|258405122|ref|YP_003197864.1| pseudouridine synthase, RluA family [Desulfohalobium retbaense DSM
           5692]
 gi|257797349|gb|ACV68286.1| pseudouridine synthase, RluA family [Desulfohalobium retbaense DSM
           5692]
          Length = 547

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 87/325 (26%), Positives = 145/325 (44%), Gaps = 37/325 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHI--NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVR 66
            VVE  E   RLD++  +    +  +   + + +R  +VRV      +   ++ +GQ V 
Sbjct: 15  FVVEAGEAGKRLDKFLSDRLADLGVSRSRISQWIRQERVRVAGALCLQGKTKVLNGQKVV 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +                L  S+      +     ++Y D  + V NK AG++V  G+G  
Sbjct: 75  L----------------LAPSLQSGIKPEVGPVEVVYSDPDVVVVNKAAGVTVHPGTGCE 118

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + +H+           G++P + HRLD++TSG+L VA   +A   LT SF  R + K
Sbjct: 119 SGTLVHHLAALYPELARFDGERPGVVHRLDKDTSGLLTVALNESARLALTRSFARREVDK 178

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-F 240
            Y +LV G P+ +   + + L +        + VV    +G   A++ FK +        
Sbjct: 179 EYLTLVHGRPEAE-GTVDHPLGRD-PQSKIRMAVV---PRGGKEALTRFKRVWTSPDGRV 233

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKL----YLHARY 294
             L ++  TGRTHQ+RVH  ++G P+VGD  Y    +  F  + P+  +L     LHA  
Sbjct: 234 SLLRVRILTGRTHQIRVHMAYLGFPLVGDALYGPQAQAAFQRSRPLLARLAKHHMLHAWR 293

Query: 295 MDLPHPEGGRL-QITAPLPAHMVKT 318
           +  PHP  GR+      +P  M + 
Sbjct: 294 LAFPHPRSGRMVCCEQAMPKAMWRL 318


>gi|295695962|ref|YP_003589200.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
 gi|295411564|gb|ADG06056.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
          Length = 308

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 84/322 (26%), Positives = 140/322 (43%), Gaps = 33/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           + VV+ +E   RLDR+        +   +Q  +  G+VRV ++ VK ++R++ G+     
Sbjct: 12  WFVVDPEEAGERLDRFLAERLADTSRSQIQGWIDEGRVRVGERPVKASHRVRPGE----- 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                                L    + +   +++ED  + V +KP G+ V    G    
Sbjct: 67  ----------DVLVEPPEPEPLELVPEPIPLKIVFEDEDVVVVDKPRGLVVHPAPGHSRG 116

Query: 127 YHIDGFLKSW----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + G L             +P + HR+D++TSG+LV A+T  A   L + F    + + 
Sbjct: 117 TLVHGLLAHCGRLSRLGGSLRPGIVHRIDRDTSGLLVAAKTDLAYMGLAKQFHDHTVDRE 176

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G+  +    +   + +  H+      V     +G   A++HF VI+ FA+    
Sbjct: 177 YLALVHGVVPHDHGTVDAPVGRHPHLRQQMAVV-----RGGRPAVTHFIVIERFAR-ATL 230

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L ++  TGRTHQ+RVH   +G P++GD KY         S       LHA  +   HP  
Sbjct: 231 LRLRLETGRTHQIRVHMEFIGFPVIGDPKYGPR-----RSLGMKGQALHAAVLGFDHPRT 285

Query: 303 G-RLQITAPLPAHMVKTWDSLG 323
           G R++  +PLP  M      L 
Sbjct: 286 GERVRFESPLPEDMRDLIAELR 307


>gi|308177850|ref|YP_003917256.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
 gi|307745313|emb|CBT76285.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
          Length = 314

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 85/330 (25%), Positives = 151/330 (45%), Gaps = 28/330 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           +S  T +  ++V+ D+   RLD +       I       + +  QV+V+ + +  + RI+
Sbjct: 2   ISNGTAIHELLVDPDDAGARLDAYIARVL-QIPRTLASSLCKDSQVQVNGRTISKSLRIK 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +     A    IK +K+ +               ++ +D    V +KP G++  
Sbjct: 61  VGDQLVVTIPPQADPLEIKVEKVEE-------------LKIIADDDDYVVIDKPVGVAAH 107

Query: 121 GGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G +   + G L +           ++  + HRLD  TSG++VVA+T  A   L  +F
Sbjct: 108 PSPGWVGPTVVGALMAEGYNITTSGAAERQGIVHRLDVGTSGLMVVAKTERAYTELKRAF 167

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R  +KIY ++V G+P   +  I   + +  H G D+   V     G   +++H+KVI+
Sbjct: 168 KERTPKKIYHAVVQGLPDPLQGTIDAPIGR--HPGHDWKFAVLD---GGRDSVTHYKVIE 222

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F +    +E+   TGRTHQ+RVH    G P VGD  Y A+ K      +  + +LHA+ 
Sbjct: 223 AFGR-ASLVEVHLETGRTHQIRVHFSAFGHPCVGDQTYGADPKLGAALGL-TRQWLHAKR 280

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +   HP  G+ ++  +  PA +    + L 
Sbjct: 281 LGFSHPVSGQWVEYESEYPADLDGAVELLR 310


>gi|88657737|ref|YP_507302.1| ribosomal large subunit pseudouridine synthase A [Ehrlichia
           chaffeensis str. Arkansas]
 gi|88599194|gb|ABD44663.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Ehrlichia chaffeensis str. Arkansas]
          Length = 337

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 78/331 (23%), Positives = 155/331 (46%), Gaps = 32/331 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVR 66
           + + +++ +EN RLD++  +   +I+   +Q++++  ++ +    ++ NN I +   +  
Sbjct: 18  KKIFIKSGDENNRLDKFIASKL-NISRNQVQQLIKDSKILLFDTIIRDNNHITKVNDIYN 76

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I   I  ++  I               + ++   ++YED  I + NK  GI+V  G+G  
Sbjct: 77  ISIPIKTISDTIT-------------PNHYIPISVVYEDHDIIIINKAPGITVHPGAGTN 123

Query: 127 YHI--DGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            +   +  +  + +S     K  +P + HRLD++TSG++V+A+   +   L++    ++I
Sbjct: 124 NNTLVNALVAHYGNSLSHVGKATRPGIIHRLDKDTSGLMVIAKNEKSYYFLSDLLLKKQI 183

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++VWG+P  K   I N++  K       +  V         AI+ ++    F+  
Sbjct: 184 KKEYLAVVWGLPNPKSNTIKNYICVKP--NNKQMMTVTHLPHKGKLAITEYQTQKSFSNI 241

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQNKLYLHA 292
              ++ + HTGRTHQ+RVH  ++G  I+GD KY  N        K +       +  LHA
Sbjct: 242 ASLIKCRIHTGRTHQIRVHMSYIGNSIIGDQKYGKNNSKSVKYAKQSTIINTLKRQALHA 301

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
             +   HP     ++  + +P  +    D L
Sbjct: 302 YKLGFTHPTSNTYIEFHSYIPNDIQMLIDEL 332


>gi|71064834|ref|YP_263561.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter
           arcticus 273-4]
 gi|71037819|gb|AAZ18127.1| ribosomal large subunit pseudouridine synthase C [Psychrobacter
           arcticus 273-4]
          Length = 338

 Score =  236 bits (602), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 99/314 (31%), Positives = 163/314 (51%), Gaps = 23/314 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V Y+ V   + + RLD +  N    +   ++ K++RS ++RV+ KR K ++R+Q   VV
Sbjct: 32  KVNYLEVTRHQHDQRLDNFLLNRLKGLPKPHIYKMIRSDEIRVNNKRCKAHDRVQREDVV 91

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RI PV+ A           +  +  T+ +  L + ++YED  + V NKP+GI+V GGSG+
Sbjct: 92  RIAPVVLATR---------EKPIISTEFAKSLLARVVYEDEGLIVLNKPSGIAVHGGSGL 142

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            + +   ++     K     L HR+D++TSG+L++++ R+A + L +    + IQK Y  
Sbjct: 143 DFGVIEAMREVTGKKY--LELVHRIDKDTSGLLMISKKRSALKVLQQHLVDKTIQKHYLC 200

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCW 242
           +  G P   ++ I   LL+ +   G+    V   +     + +   V   F    Q    
Sbjct: 201 IAKGQPALNEQRIDAPLLRYTLASGERRVKVDAQDPQTKESQTDIVVHGRFTIAEQPVSL 260

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +P TGRTHQ+RVH  H+G  I+GD+KY  + K        ++L LHA  +D+P    
Sbjct: 261 IEAKPLTGRTHQIRVHLAHIGHAILGDNKYHVHDKSGV-----HRLCLHAWRLDIP---- 311

Query: 303 GRLQITAPLPAHMV 316
           G   ITAPLP  M+
Sbjct: 312 GYDTITAPLPDEML 325


>gi|294507190|ref|YP_003571248.1| Ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber M8]
 gi|294343518|emb|CBH24296.1| Ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber M8]
          Length = 379

 Score =  236 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 79/351 (22%), Positives = 136/351 (38%), Gaps = 64/351 (18%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             R+D++    YP  +   +Q+ ++ G ++V+   VK +  ++ G  +            
Sbjct: 38  GPRIDKYLTRFYPEASRTKIQRAIKKGHLKVNGADVKKSYGVEPGDEIVFR--------- 88

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYH 128
                 L     +    + +   +++ED  + V NKPAG+ V    G         + +H
Sbjct: 89  ------LIRKPPMQAEPEAIPLDVVHEDDDLLVVNKPAGMVVHPAPGHRSGTLVHALLHH 142

Query: 129 IDG-----------------------FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
           +DG                        L    D    +P + HRLD+ TSG+LVVA+   
Sbjct: 143 VDGGEVAADDERDEVSEDEVGLSLVNALPQSPDHPVVRPGIVHRLDKGTSGLLVVAKRGR 202

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           A Q L E F+   + + Y ++VWG        I   + +  H       +         +
Sbjct: 203 AHQPLAEQFKAHTVDRRYRAIVWGHFAPSDGTIEGAIGRDPH---HRQRMAVVPGDEGKW 259

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           A +H++ ++ +A     +E +  TGRTHQ+RVHA   G P++GD KY        T   +
Sbjct: 260 ARTHYETVETYAH-TSVVEFELETGRTHQIRVHARAQGHPLLGDPKYGGQRVRYGTQSGK 318

Query: 286 NKLYL------------HARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            + +             HA  +   HP    RL+  A  P    +    L 
Sbjct: 319 RRAFYDQLFGTLPHPALHAYRIGFDHPIMEDRLRFEADPPPAWRRVLRELR 369


>gi|320333612|ref|YP_004170323.1| RluA family pseudouridine synthase [Deinococcus maricopensis DSM
           21211]
 gi|319754901|gb|ADV66658.1| pseudouridine synthase, RluA family [Deinococcus maricopensis DSM
           21211]
          Length = 323

 Score =  236 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 84/320 (26%), Positives = 139/320 (43%), Gaps = 41/320 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD          +   +   + +G+VRV+ +   K + +++ G+ + +      L H+ 
Sbjct: 15  RLDAVLAG-LADSSRSQVSAWIDAGRVRVNGQVTTKSSLKLRGGETLIVDVPPPVLAHVE 73

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFLKSW 136
            E   LD               +LYED  +   NKP G++     G+     ++  L   
Sbjct: 74  PENVPLD---------------VLYEDDALIAINKPPGMTTHPAPGVTTGTLVNALLGRM 118

Query: 137 --------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                       G +P + HRLD++TSG++VVA+T  A   L ++F+ R  +K Y +L  
Sbjct: 119 PLPEQDGARGPDGYRPGIVHRLDKDTSGVIVVAKTVEAHAKLADAFKARETRKTYLALAG 178

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----AQKFCWLE 244
           G    +K    +  + +  +    + V   N + A    + F  +        Q    + 
Sbjct: 179 GSWSAQKPLNIDAPIGRHPVDRQRMTVGGVNPREAQ---TRFVPLAAHPNGRGQTLALVR 235

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +P TGRTHQLRVH  H G PI+GD  Y         S +  +  LHA  + +PHP  G 
Sbjct: 236 CEPRTGRTHQLRVHLQHAGSPILGDAVYGR------ASDVMPRQALHAWALVIPHPTTGE 289

Query: 305 -LQITAPLPAHMVKTWDSLG 323
            L + AP+P  M++ W + G
Sbjct: 290 PLHLHAPVPDDMLQAWVAFG 309


>gi|332868375|ref|ZP_08438121.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6013113]
 gi|332733434|gb|EGJ64615.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6013113]
          Length = 350

 Score =  236 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 141/326 (43%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++      R+D+     +   +   L++ ++ G + V+   VK   R +  +++ +  
Sbjct: 41  VQLDESYLGQRIDQVAAMVWSEFSREKLKQWMKEGHLLVNGNIVKPKYRCEGNEMLTLNV 100

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
            + A  +   E   LD               ++YED  I V NKP G+ V  G+G     
Sbjct: 101 ELEAQTNSQPENIPLD---------------IVYEDEDILVINKPVGMVVHPGAGNTSGT 145

Query: 128 HIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L     S +  +  L HR+D++TSG+LVVA+   A   L++    + + +IY  +
Sbjct: 146 LVNALLYHSPKSAELSRAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLGDKSVYRIYDLV 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            +G        I   + K+  +    + ++     G   A++H+ V + F + F  ++ Q
Sbjct: 206 TYGNIIA-GGTIDEPI-KRHPVDRVKMAIL----PGGRDAVTHYNVKERF-RDFTRVQAQ 258

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  ++G  +VGD  Y         A+     T     +  LHA  + L 
Sbjct: 259 LETGRTHQIRVHFSYIGHGLVGDQVYMNRVRIPAGASELLIETLRGFKRQALHAAKLGLK 318

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +   AP P    +  + L 
Sbjct: 319 HPRTGEEMLFEAPWPEDFTQLVNVLR 344


>gi|296135788|ref|YP_003643030.1| pseudouridine synthase, RluA family [Thiomonas intermedia K12]
 gi|295795910|gb|ADG30700.1| pseudouridine synthase, RluA family [Thiomonas intermedia K12]
          Length = 342

 Score =  236 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 135/328 (41%), Gaps = 24/328 (7%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V   VV   +   RLD+     +   +   LQ+   +G VR+  +     ++ ++G+ 
Sbjct: 29  STVLEAVVPEADAGQRLDKVLAAQFSQYSRSRLQQWCEAGLVRMGAQVAGVRDKARAGET 88

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RI               +     +     + L   +++ED+ + V NKPAG+ V   +G
Sbjct: 89  LRI--------------AVPALPEDTAFAPEDLPLNVVFEDADLAVLNKPAGLVVHPAAG 134

Query: 125 I--AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                 ++G L  + ++ G  +  + HRLD++TSG++V ART  A   L    + R I +
Sbjct: 135 NWSGTLLNGLLARYPETAGLPRAGIVHRLDKDTSGLMVTARTLEAQTELVRRLQARTIHR 194

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L WG    +   +   + +  H        V    K A    +    +D       
Sbjct: 195 QYLALAWGSVS-RAFNVEAPIGR--HPRDRLRMAVVHGGKPARTDFTPLAELDTRWGPLT 251

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            L  + H+GRTHQ+RVH       +V D  Y    + +       +  LHA  +   HP 
Sbjct: 252 ALRCKLHSGRTHQIRVHLQFAKLEMVADSVYGGRLRPDLP---LQRQALHAARLAFAHPL 308

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
               +   AP+P  +   WD+ G + D 
Sbjct: 309 NDKPMDFIAPIPDDIASFWDACGGEMDE 336


>gi|162447675|ref|YP_001620807.1| ribosomal large subunit pseudouridine synthase, RluA-like protein
           [Acholeplasma laidlawii PG-8A]
 gi|161985782|gb|ABX81431.1| ribosomal large subunit pseudouridine synthase, RluA-like protein
           [Acholeplasma laidlawii PG-8A]
          Length = 297

 Score =  236 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 143/327 (43%), Gaps = 40/327 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +++ + E  +   RLD +       +N   +  +++ G V V+    K   ++++   + 
Sbjct: 1   MKFKITEQTDS--RLDHFLVAS-TELNRSQITTLIKDGLVMVNGLTTKAGYKLKNSDEIT 57

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---- 122
           +        + +K + I                 ++YED  I V NKP G+ V       
Sbjct: 58  LNLEAKEETNPLKPKNI--------------DLNIVYEDDDIMVINKPKGLVVHPSETFS 103

Query: 123 -----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                SG+ +H D    S  +    +P + HR+D++TSG+++VA+T  A + L +  +  
Sbjct: 104 ETTLVSGLLHHTDTL--STHNDDPLRPGILHRIDKDTSGLILVAKTNEAHKILAQDLKSH 161

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I++ Y +LV G+  + K  I   + +   I      V          AI+HF+V+  F 
Sbjct: 162 DIKREYIALVEGVLDHNKGVIDAPIARHPKIRTKMAVVA-----TGKPAITHFEVMRTF- 215

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    L  +  TGRTHQ+RVH  ++  P+ GD  Y    K      +++   LHA  ++ 
Sbjct: 216 RDHTLLHCKLETGRTHQIRVHLAYIKHPVTGDPLYGTKAK-----ILKDGQLLHAFRLEF 270

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP   + + + APLP        +LG
Sbjct: 271 VHPITKKVMMLEAPLPPEFESYLVTLG 297


>gi|94501303|ref|ZP_01307824.1| Pseudouridylate synthases, 23S RNA-specific [Oceanobacter sp.
           RED65]
 gi|94426574|gb|EAT11561.1| Pseudouridylate synthases, 23S RNA-specific [Oceanobacter sp.
           RED65]
          Length = 322

 Score =  236 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 77/333 (23%), Positives = 142/333 (42%), Gaps = 34/333 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV N+  N RLD+     +P  +   LQ  ++ G++++D    K  +++  G+ + +
Sbjct: 7   ETVVVPNELGNRRLDQIAAQLFPDYSRARLQSWIKDGELKIDGAVRKPKDKLIGGETLTL 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              + A    I E                +   ++YED  I V +KPA + V   +G   
Sbjct: 67  DVTLQAEGEWIAED---------------IDFPIVYEDEHIIVIDKPADLVVHPAAGNLT 111

Query: 128 HIDGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                         +   +  + HRLD++T+G++VVA+T  A  HL E  + R++ + Y 
Sbjct: 112 GTLLNGLLHHCPSLETIPRAGIVHRLDKDTTGLMVVAKTLQAQNHLVEQLQSRQMGREYE 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +++ G        I+  + + S                   AI+H++V+  +      + 
Sbjct: 172 AVIQGKMTG-GGKISEPIARHSKD-----RTKMAVHPTGKEAITHYRVVKQYP-AHTHIR 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQ------NKLYLHARYMD 296
           ++  TGRTHQ+RVH  HM  P+VGD  Y     F    +  ++       +  LHA  ++
Sbjct: 225 VKLETGRTHQIRVHMAHMQHPLVGDATYGGKVRFPKGLSQELREVLREFPRQALHAVKLE 284

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           L HP     +     LP    +  + L +  ++
Sbjct: 285 LHHPATNELMSWQVSLPDDFEELLEELNYDAEQ 317


>gi|294339951|emb|CAZ88314.1| Ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Thiomonas sp. 3As]
          Length = 342

 Score =  236 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 135/328 (41%), Gaps = 24/328 (7%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V   VV   +   RLD+     +   +   LQ+   +G VR+  +     ++ ++G+ 
Sbjct: 29  STVLEAVVPEADAGQRLDKVLAAQFSQYSRSRLQQWCEAGLVRMGAQVAGVRDKARAGET 88

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +RI               +     +     + L   +++ED+ + V NKPAG+ V   +G
Sbjct: 89  LRI--------------AVPALPEDTAFAPEDLPLNVVFEDADLAVLNKPAGLVVHPAAG 134

Query: 125 I--AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                 ++G L  + ++ G  +  + HRLD++TSG++V ART  A   L    + R I +
Sbjct: 135 NWSGTLLNGLLARYPETAGLPRAGIVHRLDKDTSGLMVTARTLEAQTELVRRLQARTIHR 194

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L WG    +   +   + +  H        V    K A    +    +D       
Sbjct: 195 QYLALAWGSVS-RAFNVEAPIGR--HPRDRLRMAVVHGGKPARTDFTPLAELDTRWGPLT 251

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            L  + H+GRTHQ+RVH       +V D  Y    + +       +  LHA  +   HP 
Sbjct: 252 ALRCKLHSGRTHQIRVHLQFAKLEMVADSVYGGRLRPDLP---LQRQALHAARLAFAHPL 308

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
               +   AP+P  +   WD+ G + D 
Sbjct: 309 NDKPMDFIAPIPDDIASFWDACGGEMDE 336


>gi|256394870|ref|YP_003116434.1| pseudouridine synthase [Catenulispora acidiphila DSM 44928]
 gi|256361096|gb|ACU74593.1| pseudouridine synthase, RluA family [Catenulispora acidiphila DSM
           44928]
          Length = 312

 Score =  236 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 146/332 (43%), Gaps = 28/332 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  M+ ++ + + +  E  RLD      +  ++     ++   G+VRVD      ++R++
Sbjct: 1   MVAMSDLRSLPIPDGLEGERLDAALARMF-GLSRTRAAELAAEGRVRVDGSEAGKSDRVR 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + I     A    +K + +                 ++++D  I V +KP G++  
Sbjct: 60  GGAWLEIELPAAADPVAVKAEAVE-------------GMRIVHDDEDIVVIDKPVGVAAH 106

Query: 121 GGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G +   + G L +           ++  + HRLD  TSG++VVA++  A   L ++F
Sbjct: 107 PSPGWLGTTVVGGLAAAGYRISTSGASERQGVVHRLDVGTSGLMVVAKSERAYTLLKQAF 166

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R + K Y +LV G P   +  +   + +  H    +  V     +G   +++H++ I+
Sbjct: 167 RDRTVDKRYHTLVQGHPDPMRGTVDAPIGRHPHHDYKFAVV-----RGGKDSVTHYETIE 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            + +    L ++  TGRTHQ+RVH   +  P VGD +Y A+        +  + +LHA  
Sbjct: 222 AY-RAATLLAIKLETGRTHQIRVHMAALRHPCVGDLQYGADPTLGERLGL-GRQWLHAVS 279

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +   HP  G  +Q  +  P  +    D +  +
Sbjct: 280 LGFEHPGTGEWVQYDSQYPDDLQHALDLIAAE 311


>gi|222475297|ref|YP_002563714.1| Ribosomal large subunit pseudouridine synthase D (rluD) [Anaplasma
           marginale str. Florida]
 gi|222419435|gb|ACM49458.1| Ribosomal large subunit pseudouridine synthase D (rluD) [Anaplasma
           marginale str. Florida]
          Length = 321

 Score =  236 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 140/326 (42%), Gaps = 34/326 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPV 70
           V  +++  R+D+        I+    Q ++  GQV +  + +  N    ++G V  I   
Sbjct: 3   VTKEDDQQRIDKLISCAL-EISRNRAQGLIAGGQVTISGRVINNNSYLTKTGDVYTIVTA 61

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   + +     I                 ++YED  + V +K   I+V  G+GI +H  
Sbjct: 62  VQKPSTLSPNYDI--------------DLKVVYEDHDVIVIDKDPYIAVHPGNGIEHHTI 107

Query: 130 -DGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            +  L  +           +P + HRLD++TSG++V A+T  A   L+E    +  +K Y
Sbjct: 108 TNALLARFGAGLQSVGSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++ WGIP  K+  I   +     +    + +++    G   A + ++V     +    +
Sbjct: 168 LAVAWGIPCPKRGVIHTNI----RVKRSDITMMEAANSGGKPAKTEYEVEQELGEVASLI 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDL 297
               HTGRTHQ+RVH  H+G  IVGD KY  N K    S +        +  LHA  +  
Sbjct: 224 RCTLHTGRTHQIRVHMSHIGHSIVGDQKYGKNCKKCMRSGVPPDVKNFRRQALHASLLGF 283

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G+ ++ T+     + +   +L
Sbjct: 284 RHPSTGKYIEFTSKPADDIQQLISAL 309


>gi|149190361|ref|ZP_01868634.1| 23S rRNA pseudouridine synthase D [Vibrio shilonii AK1]
 gi|148835850|gb|EDL52814.1| 23S rRNA pseudouridine synthase D [Vibrio shilonii AK1]
          Length = 324

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 73/339 (21%), Positives = 145/339 (42%), Gaps = 37/339 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   L++ L  G++ V+ + + K   ++  G+++ +  
Sbjct: 10  TVKDSQLGQRLDQAVAELFADFSRSRLKEWLLDGKIAVNGEVITKPRTKVMGGELITVQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
            +                      +  +   ++YED  I V NKP    V  G+G     
Sbjct: 70  ELEDEERF---------------EAQDIPLNIVYEDDDIIVINKPRDFVVHPGAGTPDGT 114

Query: 129 IDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L     +  + PR  + HRLD++T+G++VVA+T  A   L  + + R I + Y ++
Sbjct: 115 VLNALLHHFPAIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + S         +    +    A++H++V + F ++   + ++
Sbjct: 175 AIGKM-TAGGMVDKAIGRHST-----KRTLMAVNELGKPAVTHYRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDSAYGGRARIPRGASEELTHMIRSFDRQALHAVMLKFA 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLY 336
           HP  G  +   AP+P  MV   ++L  + D  L  +  Y
Sbjct: 288 HPVTGEEMTFHAPIPDDMVVMTEAL--REDAKLNKEEDY 324


>gi|29832675|ref|NP_827309.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           avermitilis MA-4680]
 gi|29609795|dbj|BAC73844.1| putative pseudouridylate synthase [Streptomyces avermitilis
           MA-4680]
          Length = 314

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 138/333 (41%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVLVDGTVVGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  + V  KP G++ 
Sbjct: 60  GGAWLEVEMPQAPAPVQIVAEP--------------VEGMEIVHDDDDVLVIVKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWSGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ R + K Y +LV G P      I   + +  H   DY   V         +++H+ +I
Sbjct: 166 FKERTVDKRYHALVQGHPDPTSGTIDAPIGR--HPNHDYKWAVTAE---GKPSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAF-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTLGKRLGL-TRQWLHAV 278

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +   HP  G  ++     PA + +  D +  +
Sbjct: 279 RLGFEHPGDGEWVEFACDYPADLQQALDKVREE 311


>gi|225850427|ref|YP_002730661.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Persephonella marina EX-H1]
 gi|225645814|gb|ACO04000.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Persephonella marina EX-H1]
          Length = 319

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 75/338 (22%), Positives = 151/338 (44%), Gaps = 35/338 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M+    +   +V+ + +  RLD++  + YP  +    QK+++ G V  D K +K  + ++
Sbjct: 1   MNHKDEILSFMVDEEYDRKRLDQFLSSVYPEYSRSYFQKLIKDGYVFEDGKDIKKPSYKV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + GQ + +               ++     L    + +   +L+ED  I V  KPAG+ V
Sbjct: 61  RKGQEITL---------------VIPPPETLEIKPENIPVDILFEDEDIAVVYKPAGMVV 105

Query: 120 QGGSGIA--YHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G      ++  L  + +       ++  + HRLD++T+G++++A++  A + L + 
Sbjct: 106 HPSPGHTSGTLVNALLYHFRNISEYGGKERAGIVHRLDKDTAGLMIIAKSEFAHKELQKQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ R + K Y ++V GI +N    I   + +  +        +         A++ + V 
Sbjct: 166 FQERTVDKRYIAVVTGIVQNDHGFIDLPIGRSIYNRKK----MGTEATNLRDALTEYWVK 221

Query: 234 DCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLY 289
           +    +    ++++ HTGRTHQ+RVH   +G P+  D  Y    +  +      I ++  
Sbjct: 222 NRSEKENLTVVDIKLHTGRTHQIRVHFSAIGHPLFNDKVYGFKKSQLRSEKMRSISDQTL 281

Query: 290 LH---ARYMDLPHPEGGR-LQIT-APLPAHMVKTWDSL 322
            H   A  +   HP  G  + IT   LP H+ K  +++
Sbjct: 282 YHALLAYRIAFDHPRTGEKIDITLQKLPEHISKVIEAI 319


>gi|291280358|ref|YP_003497193.1| ribosomal large subunit pseudouridine synthase D [Deferribacter
           desulfuricans SSM1]
 gi|290755060|dbj|BAI81437.1| ribosomal large subunit pseudouridine synthase D [Deferribacter
           desulfuricans SSM1]
          Length = 288

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 74/309 (23%), Positives = 132/309 (42%), Gaps = 30/309 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D +        +     KI++ G V V+ K VK +  +  G  + +           
Sbjct: 1   MRIDTYLSEVI-GKSRSFCSKIIKKGLVLVNNKTVKPSYNVNLGDEILVK---------- 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW 136
                +     L      +   ++YE+    + NKPAG+ V    G   +   +  L  +
Sbjct: 50  -----IPQEEKLDLKPANIPLNIIYENQYYLIINKPAGLCVHPAPGNFDNTLVNALLYHF 104

Query: 137 V--DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
              D    +P + HRLD++TSG+++VA+ R   + ++E F+ R + K Y ++ +G PK  
Sbjct: 105 QINDDNDVRPGIVHRLDKDTSGLILVAKNRDVREKMSEMFKEREVDKKYLAICYGNPKWD 164

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  + N + +   +    + VV    +   YA +   V+  +   F   +++ +TGRTHQ
Sbjct: 165 EILVENSIGRH-PVDRKKMAVV----ENGRYAKTKITVLKRYDNIF-LADVKIYTGRTHQ 218

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPA 313
           +RVH  ++GCPI+GD  Y              +  LHA Y+    P     +     +  
Sbjct: 219 IRVHCSYLGCPIIGDKVYGNKLSNKIR---FERQALHAYYLAFDCPFTKEKKIFEIDMSE 275

Query: 314 HMVKTWDSL 322
            M     SL
Sbjct: 276 DMKAFLGSL 284


>gi|71280552|ref|YP_270573.1| 23S rRNA pseudouridine synthase D [Colwellia psychrerythraea 34H]
 gi|71146292|gb|AAZ26765.1| ribosomal large subunit pseudouridine synthase D [Colwellia
           psychrerythraea 34H]
          Length = 324

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 77/344 (22%), Positives = 143/344 (41%), Gaps = 42/344 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
           +V       R D+     +P  +   ++  + +GQV+V+   +     ++  G+ + I  
Sbjct: 10  IVPESCLGKRFDQSLAIMFPDYSRSRIKDWILAGQVKVNGDVLLIPREKMYGGEEIDINA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
            + A                +   +  +   ++YED  I V NKPAG+ V  G+G     
Sbjct: 70  KVEA---------------EIRFEAQNIPLNIVYEDDYILVINKPAGLVVHPGAGNPDGT 114

Query: 128 HIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L  +       +  + HRLD++T+G++VVA+T AA  +L ++ ++R I + Y ++
Sbjct: 115 LLNALLHHYPALNVVPRAGIVHRLDKDTTGLMVVAKTIAAQTNLVDALQLREITREYEAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G+       +   + + S                   +++H++V++ +         +
Sbjct: 175 ANGVM-TAGGLVDEPIGRHSTKRTQMAVSYI-----GRPSVTHYRVMEKYRLHTRLRL-R 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  H+  P+VGD  Y    +    S            +  LHA  + L 
Sbjct: 228 LETGRTHQIRVHMSHITHPLVGDPVYGGRPRPPKNSTEALLMKLRSFKRQALHAAMLSLF 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDEC 341
           HP  G  +   A LP   V+  + L           +L +QDE 
Sbjct: 288 HPITGEEMTWHAELPEDFVELIELLQED-------NKLNAQDEY 324


>gi|167719292|ref|ZP_02402528.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei DM98]
          Length = 318

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 72/286 (25%), Positives = 120/286 (41%), Gaps = 24/286 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRV     K    +  G  + +
Sbjct: 51  RTVDVPLALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIEL 110

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P +                       + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 111 LPELLPEQL--------------AFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 156

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 157 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYF 216

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +L WG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 217 ALAWGRMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVS 272

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            +     TGRTHQ+RVH  H+G P++GD  Y    +         +
Sbjct: 273 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARRQALGRAAAGR 318


>gi|257462225|ref|ZP_05626642.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
 gi|317059894|ref|ZP_07924379.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
 gi|313685570|gb|EFS22405.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
          Length = 318

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 76/328 (23%), Positives = 141/328 (42%), Gaps = 35/328 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +        +  ++  RLD + K   P      L+K++  G V+ D+K +  N  ++
Sbjct: 1   MRAIIESYRYQAQEKDQGKRLDLFLKEQLPEATRSYLEKLIAEGYVKCDEKVITKNGKKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +  + +++                +     +   ++ L   ++YED  + V NK A + V
Sbjct: 61  KGKEAIQVS---------------IPEEEEMKMEAEKLPLDIVYEDEYLLVINKAANMVV 105

Query: 120 QG--GSGIAYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G+     ++  L    +S        +P + HRLD++T+G++VVA+       L  
Sbjct: 106 HPALGNYTGTLVNALLYYCKESLSDVNGTLRPGIVHRLDKDTTGLIVVAKNNQIHHRLAL 165

Query: 173 SFRMRRIQKIYWSLVWGIP-KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
            F+ + IQK Y ++V G   + KKE     L+ +       + V + +      A+SH+K
Sbjct: 166 MFQEKTIQKTYLAIVKGRFSEEKKEGDLVTLIARDRKDRKKMAVSQSH---GKKAVSHYK 222

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V+    +K   +E+   TGRTHQ+RVH  ++  PI+GD  Y             ++  LH
Sbjct: 223 VL-WNGEKHSLVEVNIKTGRTHQIRVHMKYLNHPILGDAVYGQE------DLQCSRQMLH 275

Query: 292 ARYMDLPHPEG-GRLQITAPLPAHMVKT 318
           A  ++  HP     +     LP   ++ 
Sbjct: 276 AYRLEFVHPVTKEEMCFEGKLPEDFLEA 303


>gi|197122384|ref|YP_002134335.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196172233|gb|ACG73206.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 353

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 80/335 (23%), Positives = 138/335 (41%), Gaps = 39/335 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V  +    RLD       P ++   +Q+++ +G V+VD +  K + R++ G+ + +
Sbjct: 24  RTLHVPPELAGTRLDAALVRLAPELSRARVQRLVEAGLVQVDGRGAKASARLRGGEAIAL 83

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           L         +  L   +L+ED+ + V +K  G+ V    G  +
Sbjct: 84  E---------------LPPPEPSGLVAQDLPLAVLHEDADLIVLDKAPGMVVHPARGTPH 128

Query: 128 HI--DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +  L           D    +  L HRLD++TSG LVVA+T AA   L   ++ R 
Sbjct: 129 STVVNALLHRLGLPGAAGPDGALPRLGLVHRLDKDTSGCLVVAKTEAALAALQAQWKGRS 188

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K+Y +L  G    +   +     +       +   V      +  A++ ++V + F  
Sbjct: 189 VEKVYLALCHGALAPE-GRLDTPYGRHPRDRLRFTGRVT----SSRRAVTEWRVREAFGA 243

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NKLY 289
                E+  HTGRTHQ+RVH    G P++ D  Y    +    +P            +  
Sbjct: 244 AASLAEVTLHTGRTHQIRVHLSEAGHPLLADAVYGGTRREARLAPADPARRAAEAVGRQA 303

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           LHA  +   HP  G RL + APLPA +    + L 
Sbjct: 304 LHALRLGFDHPRTGRRLVVEAPLPADLRAAIEVLR 338


>gi|294101951|ref|YP_003553809.1| pseudouridine synthase, RluA family [Aminobacterium colombiense DSM
           12261]
 gi|293616931|gb|ADE57085.1| pseudouridine synthase, RluA family [Aminobacterium colombiense DSM
           12261]
          Length = 326

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 88/323 (27%), Positives = 144/323 (44%), Gaps = 34/323 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR--VKFNNRIQSGQVVR 66
            +  + DEE  R+D +       +    +QK++R G V +   R  +K   ++ +   + 
Sbjct: 22  TLTPQGDEEGKRIDAFLAEEL-GLTRSYVQKLIRLGNVEISGIRRALKPALKVTAEMAIH 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I               ++  +  L    + +K  ++YED  I V NKPAG+ V    G  
Sbjct: 81  I---------------VVPPAETLEIEPEPVKFGIIYEDPYIIVVNKPAGLVVHPAPGNW 125

Query: 127 Y--HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           +   + G L  + D +      +P + HRLD  TSG+LVVART    Q+L   FR R ++
Sbjct: 126 HGTLVHGLLYKYRDMRKFDEEVRPGIVHRLDSGTSGLLVVARTPKILQNLQNQFRSRSVE 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L  G  +     I   + +          ++         A++ ++++    QK+
Sbjct: 186 KKYLALSCGKLRKAAGFIEEPIGRSQRN-----RLMMTVTDTGRPALTEYRILWTH-QKY 239

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            ++E   HTGRTHQ+RVH  H GCPIVGD  Y        T     +++LHA  +   HP
Sbjct: 240 SFIECTLHTGRTHQIRVHLKHRGCPIVGDGLYGTKQSLQRTP---GRMFLHAWKLAFDHP 296

Query: 301 EGG-RLQITAPLPAHMVKTWDSL 322
             G R+   A LP  +     ++
Sbjct: 297 INGSRMSFRACLPQELSLFLKNI 319


>gi|184157114|ref|YP_001845453.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|183208708|gb|ACC56106.1| Pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
          Length = 350

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 139/326 (42%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++      R+D+     +   +   L++ ++ G + V+   VK   R +  + + +  
Sbjct: 41  VQLDESYLGQRIDQVAAMLWSEFSREKLKQWMKEGHLLVNGNIVKPKYRCEGNETLTLNV 100

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
            + A  +   E   LD               ++YED  I V NKP G+ V  G+G     
Sbjct: 101 ELEAQTNSQPENIPLD---------------IVYEDEDILVINKPVGMVVHPGAGNTSGT 145

Query: 128 HIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L     S +  +  L HR+D++TSG+LVVA    A   L++    + + +IY  +
Sbjct: 146 LVNALLYHSPKSAELSRAGLVHRIDKDTSGLLVVANNLEAQFSLSKQLGDKSVYRIYDLV 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            +G        I   + K+  +    + ++     G   A++H+ V + F + F  ++ Q
Sbjct: 206 TYGNIIA-GGTIDEPI-KRHPVDRVKMAIL----PGGRDAVTHYNVKERF-RDFTRVQAQ 258

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  ++G  +VGD  Y         A+     T     +  LHA  + L 
Sbjct: 259 LETGRTHQIRVHFSYIGHGLVGDQVYMNRVRIPAGASELLIETLRGFKRQALHAAKLGLK 318

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +   AP P    +  + L 
Sbjct: 319 HPRTGEEMLFEAPWPEDFTQLVNVLR 344


>gi|303326647|ref|ZP_07357089.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Desulfovibrio sp. 3_1_syn3]
 gi|302862635|gb|EFL85567.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Desulfovibrio sp. 3_1_syn3]
          Length = 524

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 91/325 (28%), Positives = 149/325 (45%), Gaps = 36/325 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           M  ++ +++  D    RLDR  ++  P ++   LQK + +G+  VD   V + + + + G
Sbjct: 1   MNRIE-LLITADTAGRRLDRVLRDAAPGLSRAALQKAVLAGRCLVDGLPVSRPDAKTRPG 59

Query: 63  QVV--RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           Q V   +PP  NAL+                   +     LL++D  + V NKPAG++V 
Sbjct: 60  QRVLLELPPTENALS------------------PEEGHLELLWQDESLVVCNKPAGLTVH 101

Query: 121 GGSGIAYHID-----GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                  H       G        +G +P + HRLD++TSG+L+VA T  A   L+ +F 
Sbjct: 102 PCPSCPEHTLVQRLLGRFPQLGRLEGLRPGIVHRLDKDTSGLLLVALTEPARLALSAAFA 161

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-D 234
            R + K Y +LV G+P  + EC    L +  H        V    +G   A + +K + +
Sbjct: 162 RREVHKEYLALVSGLPPEQGEC-REPLGR--HPTAKIKMAVLPETRGGKPAHTTWKRLWN 218

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              Q+   L ++ HTGRTHQ+RVH  H+G P++GD  Y           +  +  LHA +
Sbjct: 219 TPDQRVSLLAVRIHTGRTHQIRVHLAHLGHPLLGDKLYAPAP----VRELAPRQMLHAWH 274

Query: 295 MDLPHPE-GGRLQITAPLPAHMVKT 318
           +   HP+ G  +    P P  + + 
Sbjct: 275 LAFSHPDSGEEMHFACPPPDDLPQA 299


>gi|77359880|ref|YP_339455.1| 23S rRNA pseudouridine synthase D [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874791|emb|CAI86012.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 325

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 80/337 (23%), Positives = 139/337 (41%), Gaps = 36/337 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPV 70
           V  D    RLD+     +P  +   ++  +   ++ VD +       ++  G+V+ +   
Sbjct: 11  VPTDLGGKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEIFNTPRTKLLGGEVLNVETT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HI 129
           I A    I               +  +K  ++YED  I V NKP G+ V  G+G     +
Sbjct: 71  IEAPREYI---------------AQDIKLDIVYEDDDILVINKPMGLVVHPGAGNPDGTV 115

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSL 186
              L  +       PR  + HRLD++T+G++VVA+T  A  HL  + + R    + Y +L
Sbjct: 116 LNALLHYHPEIINVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVTALQKRENFTREYEAL 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + +              +    AI+H++V + F +    L ++
Sbjct: 176 CNGTM-TAGGMVEKPIGRHATQ-----RTHMDVHEQGKPAITHYRVAEKF-RAHTRLRLR 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +         +  LHA  + + 
Sbjct: 229 LETGRTHQIRVHMAYLNHPLIGDQSYGGRPRPPKGATPELFELLRSFKRQALHAVKLSIA 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           HP  G  +   AP+P  MV    +L      N  I R
Sbjct: 289 HPITGEMMTWQAPIPDDMVAMTLALREDTKANPDIDR 325


>gi|302875571|ref|YP_003844204.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
 gi|307690100|ref|ZP_07632546.1| pseudouridine synthase, RluA family protein [Clostridium
           cellulovorans 743B]
 gi|302578428|gb|ADL52440.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
          Length = 298

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 80/324 (24%), Positives = 132/324 (40%), Gaps = 31/324 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M       +  ++E M++  +      + +    +    +  +  + K +K N  +++G 
Sbjct: 1   MENKITFNITKEDEGMKIKEFL-KLKNNFSSRFCRASALAKNIFANNKVIKLNYVLKAGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +         I  E                +   + YEDS I V NKP  I V    
Sbjct: 60  VIEVKLNKEESQDIEPEN---------------IPLKVAYEDSDIIVLNKPPFIVVHPTK 104

Query: 124 GIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              Y  +   L  +   KG+    RL  RLD  TSG+++VA+ + +   L         +
Sbjct: 105 NYPYGTLANGLLYYFKEKGENCIVRLVSRLDMNTSGLIIVAKNQFSHMSLQRDMNKEEFK 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++V G  +     I   + K+       +   +        +I+H+KVI+ ++   
Sbjct: 165 KQYLAIVHGKMEADFGTIDLPIYKEEDEPIKRIIDDR-----GQRSITHYKVIETYS-NA 218

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L++   TGRTHQ+RVH  H+GCPI GD  Y              +  LHA  +  PHP
Sbjct: 219 QLLKLTLETGRTHQIRVHLSHLGCPIFGDSLYG-----ELEDQYIKRQALHAFSLSFPHP 273

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             GR + I A LPA M +  + L 
Sbjct: 274 RDGRIINIEAELPADMSELLEKLR 297


>gi|115372593|ref|ZP_01459900.1| ribosomal large subunit pseudouridine synthase C [Stigmatella
           aurantiaca DW4/3-1]
 gi|115370314|gb|EAU69242.1| ribosomal large subunit pseudouridine synthase C [Stigmatella
           aurantiaca DW4/3-1]
          Length = 330

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 89/324 (27%), Positives = 147/324 (45%), Gaps = 16/324 (4%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E D   MRLD++ +    ++   +L K++R  +VRV+ KR +    + +G V+ I    
Sbjct: 15  IEEDSVGMRLDKYLRKRLANMPTSHLFKMIRVKKVRVNGKRAQPEQLLAAGDVIAIRGDE 74

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHID 130
             L       + L         S+    ++L ED  +   +KP+G++V  GSGI    + 
Sbjct: 75  QQLLGPAPGGERLPPPPPPVDPSEL---VILLEDDWMMAVDKPSGMAVHTGSGITGGTLV 131

Query: 131 GFLKSWVDSKGQK----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++++++  K  +        HRLD+ETSG+++VA+ R A  H TE F   R +K Y +L
Sbjct: 132 DYVRAYLGPKAVRNDFTASPAHRLDRETSGVILVAKRRPAMVHFTEVFTESRARKRYVTL 191

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   L +                     A++ +KVI   + +   L   
Sbjct: 192 VKGKMPQDSGVIDLPLSEHQQTAESKARR----GVNMQEALTRWKVI-RQSSEAALLSCA 246

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
             TGRTHQ+R H   +G P+ GD KY   A  +         +L+LHA  ++ PHP  GG
Sbjct: 247 IETGRTHQIRRHLAAVGHPVAGDRKYGDFAFNRDVRARWGLKRLFLHAERIEFPHPQHGG 306

Query: 304 RLQITAPLPAHMVKTWDSLGFKYD 327
           ++ + A LP  +  T      +  
Sbjct: 307 KVTVEARLPPELKDTLKRAALEPS 330


>gi|83949443|ref|ZP_00958176.1| ribosomal large subunit pseudouridine synthase D [Roseovarius
           nubinhibens ISM]
 gi|83837342|gb|EAP76638.1| ribosomal large subunit pseudouridine synthase D [Roseovarius
           nubinhibens ISM]
          Length = 341

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 84/355 (23%), Positives = 141/355 (39%), Gaps = 50/355 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M   Q V         RLD+      P   H++   L +++  G V V+    +   +R+
Sbjct: 1   MASTQVVFTIAANPPPRLDKALSRDVPEEAHLSRTRLARLVEEGAVSVNGAEARDVKSRV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  V I   +   + I+ E   LD               ++YED+ + V NKPAG+ V
Sbjct: 61  AEGDEVVITVPVAEESDILPENIPLD---------------IVYEDADLLVVNKPAGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L             ++P + HR+D++TSG+LVVA++  A   L  
Sbjct: 106 HPAPGTPRGTLVNALLHHCGGDLSGVGGVRRPGIVHRIDKDTSGLLVVAKSDQAHHGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANW----------LLKKSHIGGDYVHVVKQNE-- 220
            F     +++Y ++V+G+P      +             L   + +        KQ    
Sbjct: 166 QFEAHSAERVYQAIVYGVPDAADPRLGGLRGVGFEPGNVLRITTQLARHRTDRQKQAVLF 225

Query: 221 KGANYAISHFKVIDCFAQKFC--WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-- 276
            G  +A++  +V +          +E +  TGRTHQ+RVH  + G  ++GD  Y      
Sbjct: 226 DGGKHAVTRAQVTERLGDPASVALIECRLETGRTHQIRVHLAYAGHGLLGDPVYGGRRGL 285

Query: 277 -------KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                  +   T    N+  LHA ++ + HP  G  L+  A LP  M     +L 
Sbjct: 286 PKRGFSAEAAETLATFNRQALHAGHLGVIHPASGEPLRFDARLPEDMAGLLAALR 340


>gi|149200603|ref|ZP_01877608.1| 23S rRNA/tRNA pseudouridine synthase [Lentisphaera araneosa
           HTCC2155]
 gi|149136305|gb|EDM24753.1| 23S rRNA/tRNA pseudouridine synthase [Lentisphaera araneosa
           HTCC2155]
          Length = 323

 Score =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 97/335 (28%), Positives = 147/335 (43%), Gaps = 32/335 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Y    VV+   E  RLDR+     P  +   LQK L+ G   + +   K N R+    V+
Sbjct: 7   YTHSWVVDEFNECQRLDRYISQQLPEYSRTFLQKSLKDGAFELVRSGAKINARMSEN-VI 65

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
               V   +     E  +L   + L          ++YED  I V NKPAG+ V  G+G 
Sbjct: 66  EGDFVHYKMPEEADESTLLPEDIELD---------IIYEDDDILVVNKPAGMVVHPGAGN 116

Query: 125 -IAYHIDGFL------KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                ++  L       S +D    +P + HRLD+ETSG+++VA++      L+ SF  R
Sbjct: 117 YTGTLVNALLGRDLDTFSAMDDGSSRPGIVHRLDKETSGVIIVAKSAKNLDKLSRSFARR 176

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ----NEKGANYAISHFKVI 233
            ++K Y +L  G  +  ++ I       SHIG    +  K     +      AISH+KV+
Sbjct: 177 DVEKYYVALCRGTIRVGRDTIT------SHIGRSRSNRQKMENTNDSNRGKEAISHYKVL 230

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                    ++++  TGRTHQ+RVH   +  P+VGD  Y         SP  ++  LHA 
Sbjct: 231 -ADNNGATLVKLKIDTGRTHQIRVHMSGINHPVVGDKLYGVRRLDEKESP--DRHILHAW 287

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
              + HP     +  TAPL        D  G ++D
Sbjct: 288 RTRIIHPGTQEIMTFTAPLHDDFKSVCDKFGIEFD 322


>gi|310779318|ref|YP_003967651.1| pseudouridine synthase, RluA family [Ilyobacter polytropus DSM
           2926]
 gi|309748641|gb|ADO83303.1| pseudouridine synthase, RluA family [Ilyobacter polytropus DSM
           2926]
          Length = 313

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 78/336 (23%), Positives = 144/336 (42%), Gaps = 34/336 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRI 59
           M        +  EN ++  RLD +    + ++    +QK++    + ++ K + K  N++
Sbjct: 1   MKNYKEQDTIYAENSDKGKRLDAFVNESFDYLTRSYIQKLIEQRDIIIEGKEKNKSGNKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +  + + +          I E ++LD           +    +YED  + V NK   + V
Sbjct: 61  KGNEKILVR---------IPEDEMLD------IEPQDIPIEKVYEDKDLVVINKAPDMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G      ++  + +  D        +P + HRLD+ TSG++V+A+   +   L++ 
Sbjct: 106 HPAPGNYSGTLVNALMHNIKDLSNINGVIRPGIVHRLDKNTSGLIVIAKNDFSHLKLSDM 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ + I K Y  +  GI   K   I N + +        + VV   +K    AIS++K++
Sbjct: 166 FKNKDISKTYICICKGIFSEKTGRIENLIGRNPK-NRKTMTVV---QKNGKNAISNYKIL 221

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D     F  +E++  TGRTHQ+RVH   +  PI+GD  Y         S I  +  LHA 
Sbjct: 222 DEAGD-FSLVEVKIETGRTHQIRVHMKSINHPILGDEVYGK------PSKICKRQMLHAY 274

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
            ++  HP  G ++ +   +P          G   ++
Sbjct: 275 RLEFHHPLSGEKMTVFGEIPEDFKNAAKKTGLDINK 310


>gi|331696640|ref|YP_004332879.1| RluA family pseudouridine synthase [Pseudonocardia dioxanivorans
           CB1190]
 gi|326951329|gb|AEA25026.1| pseudouridine synthase, RluA family [Pseudonocardia dioxanivorans
           CB1190]
          Length = 312

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 82/324 (25%), Positives = 149/324 (45%), Gaps = 25/324 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++ + V +  + MR+D         ++   +  +   G+V VD +    ++R+ +G  +
Sbjct: 5   ELRSLPVPDGLDGMRVDAGLSRLL-GLSRTVVATLAEEGRVAVDGRAAGKSDRLAAGGWL 63

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            I      L    +E   +   V +          +L+ED  I V +KP G++     G 
Sbjct: 64  EI-----ELPDPERESDGITGPVEVV-----AGLTILHEDDDIVVVDKPVGVAAHPSPGW 113

Query: 125 IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + G L +           ++  + HRLD  T+G++VVA++ +A   L  +F+ R +
Sbjct: 114 TGPTVVGGLAALGVRVATSGAAERQGIVHRLDAGTTGVMVVAKSESAYSELKRAFKERTV 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y ++V G P   +  I   +    H   D+   V    +G   +++H+  I+ F + 
Sbjct: 174 DKRYHAVVQGHPDPSRGTIDAPI--DRHPRHDWRFAVV---EGGRPSVTHYDTIEAF-RA 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+++  TGRTHQ+RVH   M  P VGD  Y A+        + ++ +LHAR +   H
Sbjct: 228 ASLLDIRLETGRTHQIRVHFSAMRHPCVGDLTYGADPTLAKRLHL-DRQWLHARELGFAH 286

Query: 300 P-EGGRLQITAPLPAHMVKTWDSL 322
           P +G R++ T+P PA + +  D L
Sbjct: 287 PADGRRVEFTSPYPADLARALDLL 310


>gi|310823803|ref|YP_003956161.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309396875|gb|ADO74334.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 321

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 89/324 (27%), Positives = 147/324 (45%), Gaps = 16/324 (4%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E D   MRLD++ +    ++   +L K++R  +VRV+ KR +    + +G V+ I    
Sbjct: 6   IEEDSVGMRLDKYLRKRLANMPTSHLFKMIRVKKVRVNGKRAQPEQLLAAGDVIAIRGDE 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHID 130
             L       + L         S+    ++L ED  +   +KP+G++V  GSGI    + 
Sbjct: 66  QQLLGPAPGGERLPPPPPPVDPSEL---VILLEDDWMMAVDKPSGMAVHTGSGITGGTLV 122

Query: 131 GFLKSWVDSKGQK----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++++++  K  +        HRLD+ETSG+++VA+ R A  H TE F   R +K Y +L
Sbjct: 123 DYVRAYLGPKAVRNDFTASPAHRLDRETSGVILVAKRRPAMVHFTEVFTESRARKRYVTL 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   L +                     A++ +KVI   + +   L   
Sbjct: 183 VKGKMPQDSGVIDLPLSEHQQTAESKARR----GVNMQEALTRWKVI-RQSSEAALLSCA 237

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
             TGRTHQ+R H   +G P+ GD KY   A  +         +L+LHA  ++ PHP  GG
Sbjct: 238 IETGRTHQIRRHLAAVGHPVAGDRKYGDFAFNRDVRARWGLKRLFLHAERIEFPHPQHGG 297

Query: 304 RLQITAPLPAHMVKTWDSLGFKYD 327
           ++ + A LP  +  T      +  
Sbjct: 298 KVTVEARLPPELKDTLKRAALEPS 321


>gi|257452410|ref|ZP_05617709.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|317058953|ref|ZP_07923438.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|313684629|gb|EFS21464.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
          Length = 318

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 73/329 (22%), Positives = 137/329 (41%), Gaps = 37/329 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           M  +       V  +++  RLD + K   P      L+K++  G V  ++K +  N  ++
Sbjct: 1   MRRIVENYEYQVGEEDQGKRLDLFLKEQLPEATRSYLEKLITEGYVLCNEKVITKNGKKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +  +V+++         I+ E   LD               ++YED  + V NK A + V
Sbjct: 61  KGKEVIQLAIPEEEEMEIVAENIPLD---------------IVYEDKYLLVVNKQANMVV 105

Query: 120 QG--GSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G+     ++  L    ++        +P + HRLD++T+G+++VA+       L  
Sbjct: 106 HPALGNYSGTLVNALLYYCKENLSDMNGVIRPGIVHRLDKDTTGLIIVAKNNQVHSKLAL 165

Query: 173 SFRMRRIQKIYWSLVWGIPKN--KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            F+ + I+K Y ++V G      K+  +   + +             Q       AIS++
Sbjct: 166 MFQEKTIRKTYVAIVKGRFSEERKEGRLETLITRDPKDRKKMTVSQIQ----GKKAISNY 221

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           +V+     K   +E++  TGRTHQ+RVH  ++  PI+GD  Y              +  L
Sbjct: 222 RVL-LDGDKHSLVEVKIETGRTHQIRVHMKYLNHPILGDIVYGQE------DTKCKRQML 274

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           HA  ++  HP     + +   LP   ++ 
Sbjct: 275 HAYRLEFIHPITEEAICLEGKLPEDFIEA 303


>gi|293604136|ref|ZP_06686544.1| ribosomal large subunit pseudouridine synthase D [Achromobacter
           piechaudii ATCC 43553]
 gi|292817361|gb|EFF76434.1| ribosomal large subunit pseudouridine synthase D [Achromobacter
           piechaudii ATCC 43553]
          Length = 343

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 128/325 (39%), Gaps = 31/325 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q V V +     RLD+      P  +   LQ  + SG V V+    K    +  G  + +
Sbjct: 40  QRVTVPSSTRADRLDKVLAGLLPDHSRSRLQGWIESGNVHVNGAPGKIRQTVGPGDQLLV 99

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                             +        + ++  ++ E +   V NKPAG+    G+G   
Sbjct: 100 WAQ--------------PAPDARAFTPEPVEFTVVDESADWIVVNKPAGLVTHPGAGNWS 145

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + +     +  + HRLD++TSG++VVAR   A  HL    + R + + Y 
Sbjct: 146 GTLLNGLLYRYPELAAVARAGIVHRLDKDTSGLMVVARNEKAQTHLVRQLQARSMGREYI 205

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC----FAQKF 240
           +L  G        +   + +   +    + +  +       AI+++            + 
Sbjct: 206 ALAHG-WLAAAGRVDRAIGRDPRV---PIRMSVERPVAPKPAITNYAPARRGQVDPGGRV 261

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +  +  TGRTHQ+RVH   +G P++ D  Y        T     +  LHAR +    P
Sbjct: 262 TEVVCRLETGRTHQIRVHMASLGHPLLADTIYGGKNIAGAT-----RQMLHARALHFDDP 316

Query: 301 EG-GRLQITAPLPAHMVKTWDSLGF 324
            G G +Q  A +PA M    +++ +
Sbjct: 317 GGSGDVQFAAEVPADMALVQETIAW 341


>gi|85714567|ref|ZP_01045554.1| pseudouridine synthase, RluD [Nitrobacter sp. Nb-311A]
 gi|85698452|gb|EAQ36322.1| pseudouridine synthase, RluD [Nitrobacter sp. Nb-311A]
          Length = 351

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 84/354 (23%), Positives = 144/354 (40%), Gaps = 64/354 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK------------RVKFNN 57
           VVV  +E + RLDR    H P ++   L+ ++ +G V V KK                  
Sbjct: 17  VVVTGNEGSARLDRVLAVHSPDLSRSRLKSLILAGHVSVVKKASAAERTSGPPSVSDPAY 76

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
            +  G  + I                +   ++     + +   ++YED+ + V NKP G+
Sbjct: 77  HVAPGDTITIR---------------VPPPISAKPQGEAIALDIVYEDNDLIVINKPKGL 121

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAA 167
            V  G+G   H  G L + + +             +P + HRLD++T+G++V A+  AA 
Sbjct: 122 VVHPGAG---HQAGTLVNALIAHCGGSLSGIGGVCRPGIVHRLDKDTTGLMVAAKNDAAH 178

Query: 168 QHLTESFRMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
           + L+  F        +++ Y + VWG+P      I   +  +     + + V      G 
Sbjct: 179 KSLSTQFADHGRTGAMRRGYLAFVWGLPNRPHGTIDAPI-DRHPYAREKMAVRA----GG 233

Query: 224 NYAISHFKVIDCFAQKF-----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             AI+H+ V+  F           L  +  TGRTHQ+RVH  H G P++GD  Y ++F+ 
Sbjct: 234 REAITHWDVVQAFDDPAGKSVAALLACRLATGRTHQIRVHLAHAGHPLMGDGVYGSHFRT 293

Query: 279 NFTSPI---------QNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
                            +  LHA  + + HP  G + +    LP  +     +L
Sbjct: 294 KANHLGPRAAAALSALGRQALHASLLVIEHPRTGEILRWETGLPEDLALLRSAL 347


>gi|296114958|ref|ZP_06833603.1| pseudouridine synthase, RluA family protein [Gluconacetobacter
           hansenii ATCC 23769]
 gi|295978476|gb|EFG85209.1| pseudouridine synthase, RluA family protein [Gluconacetobacter
           hansenii ATCC 23769]
          Length = 323

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 72/341 (21%), Positives = 139/341 (40%), Gaps = 36/341 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M+     + V+    +   R DR+  +    ++   ++ ++ +G +  D   ++   + +
Sbjct: 1   MTQDIQPEPVIATVGDAGQRTDRFMADTIGTLSRSRIKALMEAGHLLRDGVVLRDPADPV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G    +                + ++   T     +   +L+ED  + V +KPAG+ V
Sbjct: 61  RAGMRYELR---------------VPAAAPATPQGQDIALDVLFEDRDLIVLDKPAGLVV 105

Query: 120 QGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    DS       ++P + HRLD++TSG++V A+T  A   L+ 
Sbjct: 106 HPAPGNEDGTLVNALLGHCGDSLTGIGGERRPGIVHRLDKDTSGVMVAAKTELAHHALSA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           +F  R I++ Y ++ WG+           + +      +   +   +  G  +A++H++ 
Sbjct: 166 AFASRDIERAYQAVCWGVLAPTTGSFDGAIGRDR---RERKRMAVISNGGGKHALTHYRT 222

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------ 286
           +D F      +E +  TGRTHQ+RVH  H G  +VGD  Y             +      
Sbjct: 223 LDTFHGSLSHVECKLATGRTHQIRVHFAHAGHALVGDPTYLRRIPAAARGLPADARATAL 282

Query: 287 ---KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
              +  LHA  +   HP  G  L    P P        ++G
Sbjct: 283 DFPRQALHAARLGFVHPRTGAHLLFETPPPHDFQDLLAAIG 323


>gi|167823889|ref|ZP_02455360.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei 9]
          Length = 318

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 73/285 (25%), Positives = 121/285 (42%), Gaps = 24/285 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V V       RLD+     +P  +   LQ+ + S +VRV     K    +  G  + +
Sbjct: 51  RTVDVPLALAGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAKIRQPVPLGATIEL 110

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
            P +                       + +   ++YED  I V +KPAG+ V   +G   
Sbjct: 111 LPELLPEQL--------------AFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWS 156

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++G L  + D+ G  +  + HRLD+ETSG++VVART AA   L    + R +++ Y+
Sbjct: 157 GTLLNGLLHRYADAAGLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYF 216

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFC 241
           +L WG     +  I   + +      +   +          A +HF+ +D      Q   
Sbjct: 217 ALAWGRMP-DEGTIDAPIGRDP---RERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVS 272

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
            +     TGRTHQ+RVH  H+G P++GD  Y         +P+  
Sbjct: 273 AIHCDLETGRTHQIRVHCAHVGHPLLGDPVYGRARGKRSVAPLPG 317


>gi|118602363|ref|YP_903578.1| ribosomal large subunit pseudouridine synthase D [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
 gi|118567302|gb|ABL02107.1| ribosomal large subunit pseudouridine synthase D [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
          Length = 314

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 82/341 (24%), Positives = 146/341 (42%), Gaps = 39/341 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSL++    V++ N     R+D       P+ + V +   ++SG   +  K  K   ++ 
Sbjct: 1   MSLLS----VIIPNRFIGQRIDAAMAQMLPNYSRVKITYWIKSGDALIHHKTFKPKEKVL 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+V+ +   I   N  + +  ++D               ++YED  I + NKP  +   
Sbjct: 57  GGEVITLSIKIEKTNAWLAQDIVID---------------VVYEDEAIIIVNKPVNLVTH 101

Query: 121 GG-SGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G S     +   L  +  S     +  + HRLD+ TSG++VVAR+  A ++LT   +  
Sbjct: 102 PGVSNWTGTLANALLHYDSSLANLDRAGIVHRLDKNTSGLMVVARSEYAQKYLTRQLQTH 161

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I + Y ++V+G        +   + +          + +   +    A++H++VI+ FA
Sbjct: 162 SISREYSAIVYGHM-ISGGTVDKPIGRDPKD-----RIRQTVTESGKDALTHYRVIERFA 215

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLY 289
                +++   TGRTHQ+RVH   +G P++ D  Y    +    +  Q        N+  
Sbjct: 216 H-HTHVKVMLETGRTHQIRVHLSFIGHPLIADPMYGGKIRFPKKADKQLKNSLKNFNRQT 274

Query: 290 LHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           LHA+ + L HP     +    PLP  M      L  K+D N
Sbjct: 275 LHAKKLTLIHPTSTELMSWKVPLPQDMQDLLQVLA-KFDAN 314


>gi|83859151|ref|ZP_00952672.1| ribosomal large subunit pseudouridine synthase d [Oceanicaulis
           alexandrii HTCC2633]
 gi|83852598|gb|EAP90451.1| ribosomal large subunit pseudouridine synthase d [Oceanicaulis
           alexandrii HTCC2633]
          Length = 310

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 74/328 (22%), Positives = 136/328 (41%), Gaps = 48/328 (14%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  ++    + ++  G + VD + +   + +++ G V R+                
Sbjct: 1   MAAIWEDLSRSRCKALVEQGCLFVDGEALTDPSAKVREG-VYRLD--------------- 44

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---------IAYHIDGFLK 134
           + + V  T   + +   +L+ED  + V NKPAG++V   +G         + +H  G L 
Sbjct: 45  VPAPVEATPKPEDIPLEVLFEDDHLIVINKPAGMAVHPAAGNWTGTLVHALLFHCAGSLS 104

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++P + HRLD++TSG++V A+T  A Q L+  F    +++ Y +     P+ +
Sbjct: 105 GI--GGVERPGIVHRLDKDTSGVMVAAKTDKAHQGLSAQFAAHTVERAYLAFTRSAPQPR 162

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ---------KFCWLEM 245
              I   L + SH       +     +   +AI++++ +  F Q             +  
Sbjct: 163 TGRIETRLARSSHDRKKMAVIDAPGSQAGKHAITNYETLATFGQEPGKSVGHPMCALVRC 222

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-------ANFKGNFTSPIQNKLYLHARYMDLP 298
           +  TGRTHQ+RVH  H+GCP++GD  Y        A            +  LHA  +   
Sbjct: 223 RLETGRTHQIRVHMAHIGCPLLGDPVYGRGRSTPLAKLDSGKDFKDFRRQALHAAVLGFD 282

Query: 299 HPEGGR-LQITAPLPAHMVKT---WDSL 322
           HP  G  ++    LP  M +     + L
Sbjct: 283 HPVTGEQVRFETELPKDMQRLQGFLERL 310


>gi|304309991|ref|YP_003809589.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium HdN1]
 gi|301795724|emb|CBL43923.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium HdN1]
          Length = 318

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 77/339 (22%), Positives = 150/339 (44%), Gaps = 41/339 (12%)

Query: 4   MTYVQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           MT +Q+   + +D    RLD+     +P  +   LQ+ ++ G + ++++      ++  G
Sbjct: 1   MTQIQHQATIPDDLSGKRLDQAAAQLFPDYSRARLQEWIKMGALTINQQVGVAKEKVIGG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + + +   + A   +  +   LD               +++ED  + + NKPAG+ V  G
Sbjct: 61  EQLFLSVELQADERVKPQNISLD---------------IVHEDDSLLIINKPAGLVVHPG 105

Query: 123 SGIAYHIDGFLKSWVDSKGQKP------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           SG   H +G L + + +   K        L HR+D++T+G+LVVA+T  A   L    + 
Sbjct: 106 SG---HSEGTLVNALVNHAPKLAELPRAGLVHRIDKDTTGLLVVAKTLEAHTDLVAQLQA 162

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + +++ Y ++  G+       +   + +          V          A++H++V+  +
Sbjct: 163 KLVKREYEAIAQGVMTG-GGKVDAPIGRHPTQRTKQAVVSS-----GREAVTHYRVVARY 216

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------GNFTSPIQN--KL 288
            +    + +   TGRTHQ+RVH  H+  P++GD  Y    +        F   +Q   + 
Sbjct: 217 -RAHTHIRLALETGRTHQIRVHMAHIHYPLLGDPDYGGRLRLPKAASPEFIEALQGFRRQ 275

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            LHA+ + L HPE G  +    PLP   V+   ++   +
Sbjct: 276 ALHAQRLALHHPESGDWVAWEVPLPEDFVQLLAAIKADH 314


>gi|324999316|ref|ZP_08120428.1| ribosomal large subunit pseudouridine synthase [Pseudonocardia sp.
           P1]
          Length = 310

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 79/327 (24%), Positives = 146/327 (44%), Gaps = 26/327 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++ + V +  + MR+D         ++   +  +   G+++VD +    ++R+  G 
Sbjct: 1   MGELRSMPVPDGLDGMRIDAGLSRLL-GLSRTVVAGLAEEGRIQVDGRDAGKSDRLPGGS 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +     A   +I+    + + ++           +L++D  I V +KP G++     
Sbjct: 60  WLEVELPDAAAPAVIEGPAEVVAGLS-----------VLHDDEDIVVVDKPVGVAAHPSP 108

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  + HRLD  T+G++VVA +  A   L  +F+ R
Sbjct: 109 GWTGPTVTGGLAALGYRLSTSGAAERQGIVHRLDVGTTGVMVVATSEHAYTALKRAFKER 168

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y ++V G P      I   +    H   DY   V Q   G   +I+H+  I+ F 
Sbjct: 169 TVEKRYHAVVQGHPDPSSGTIDAPI--DRHPRHDYRFAVLQ---GGKPSITHYDTIEAF- 222

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    L++   TGRTHQ+RVH   +  P VGD  Y A+        + ++ +LHAR +  
Sbjct: 223 RSASLLDVHLETGRTHQIRVHFSALRHPCVGDLTYGADPTLAKRVGL-SRQWLHARTLGF 281

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  GR ++ T+P P  +     +L 
Sbjct: 282 EHPADGRYVEFTSPYPDDLASALAALR 308


>gi|254757932|ref|ZP_05209959.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Australia 94]
          Length = 249

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 124/269 (46%), Gaps = 27/269 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHTSGTLVNGLMHHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++V G+  + K  I   + +               ++   +A++HF+V++ F 
Sbjct: 166 TVTRRYKAIVHGVIPHDKGTIDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF- 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           + F  +E +  TGRTHQ+RVH  ++G P+
Sbjct: 220 KDFTLVECRLETGRTHQIRVHMKYIGYPL 248


>gi|327404084|ref|YP_004344922.1| ribosomal large subunit pseudouridine synthase D [Fluviicola
           taffensis DSM 16823]
 gi|327319592|gb|AEA44084.1| ribosomal large subunit pseudouridine synthase D [Fluviicola
           taffensis DSM 16823]
          Length = 342

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 86/337 (25%), Positives = 150/337 (44%), Gaps = 44/337 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
              +  +E++R+D++  +  P+ +   +Q   +SG V V+   VK N +I+    V I  
Sbjct: 21  FTADLGQESVRIDKYLLDRMPNTSRNKIQSAAKSGSVVVNGSSVKSNYKIKPKDEVTI-- 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
               L + ++E +++   + +          ++YED ++ V NKP  + V  G G     
Sbjct: 79  ---VLPYPVRELELIAQDIPID---------IVYEDDEVIVVNKPPNMVVHPGYGNYTGT 126

Query: 125 ----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + YH D   +  +D  G +P L HRLD+ T+G++VVA+T  A  +L + F  R  +
Sbjct: 127 LVNALVYHFDNLPERKLDYFG-RPGLVHRLDKHTTGVMVVAKTEDALTNLAKQFYDRTTE 185

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LVWG  +     I   L +   +    V  V        +A++H KV+  +    
Sbjct: 186 RRYQALVWGDVEEDM-RIEGNLGRS--LNNRKVMTVFPEGDYGKHAVTHVKVLKRYGL-V 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS------------PIQNKL 288
             +E +  TGRTHQ+R H    G P+  D +Y  +     T+             +    
Sbjct: 242 TLIECKLETGRTHQIRTHLKWKGYPLFHDLEYGGDRIVRGTTHDKYKQFISNCFDLIPGQ 301

Query: 289 YLHARYMDLPHPEGGRL-QITAPLP---AHMVKTWDS 321
            LHA+ +   HP+ G   Q    LP     +++ WD 
Sbjct: 302 ALHAKSLGFQHPKTGEWKQFETDLPLGFQDLLQKWDR 338


>gi|317052412|ref|YP_004113528.1| pseudouridine synthase, RluA family [Desulfurispirillum indicum S5]
 gi|316947496|gb|ADU66972.1| pseudouridine synthase, RluA family [Desulfurispirillum indicum S5]
          Length = 313

 Score =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 80/337 (23%), Positives = 148/337 (43%), Gaps = 36/337 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQS 61
           + +    + V+    + RLD++        +    QK++  G V+V+   + K +  +Q 
Sbjct: 1   MKSSRHELTVD---ASRRLDQFLAAT-ELFSRSMAQKLVAQGHVQVNGTVIEKASYSLQP 56

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +V +       +  +  Q+I                 + YED  + V NKPAG+ V  
Sbjct: 57  GDLVCVQQPAPVDHATVVGQEI--------------PLNIWYEDESLLVVNKPAGMVVHP 102

Query: 122 GSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            +G   A  ++  +    D         +P + HRLD++TSG+++VA+T  A Q L   F
Sbjct: 103 AAGNYDATLVNALVHYLGDGLPAIGGVLRPGIVHRLDKDTSGLMLVAKTEVAHQRLVSMF 162

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             + I + Y +L  G   +    I   + +        + +V+ ++     A +H+++++
Sbjct: 163 AAKEIDRCYLALCHGSL-DDSGVIEGNIGRDPK-DRKRMAIVEADK--GKTARTHYRLLE 218

Query: 235 ---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
              C  Q    +E +  TGRTHQ+RVH   +  P++GD  Y    +  + S    +  LH
Sbjct: 219 KFFCHQQWVSLIECRLDTGRTHQIRVHLRSVQRPLLGDQVYGVKKEPGYVS--MRRQALH 276

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           +  + L HP  G  +++  PLP  M    +SL  +  
Sbjct: 277 SASLCLQHPISGEVVELQCPLPEDMRDQVESLRRRSS 313


>gi|271964386|ref|YP_003338582.1| RluA family pseudouridine synthase [Streptosporangium roseum DSM
           43021]
 gi|270507561|gb|ACZ85839.1| RluA family pseudouridine synthase [Streptosporangium roseum DSM
           43021]
          Length = 309

 Score =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 137/327 (41%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  E  RLD      +   +     +++ SG V VD      ++R+ +G 
Sbjct: 1   MAEQRSLPVPDGLEGERLDAALSRLF-GFSRTRAAELIVSGDVLVDGSPAAKSDRVHAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         +   + +                 ++YED  I V NKP G++    +
Sbjct: 60  WLDVTLPPPPTAPMPVAEPVP-------------GMKIVYEDDDIVVVNKPIGVAAHPTT 106

Query: 124 G-IAYHIDGFLK---SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L      V + G  ++  + HRLD  T+G +VVA++  A  HL  +F+ R
Sbjct: 107 GWTGPTVIGGLLGTGHRVATSGAAERQGIVHRLDANTTGAMVVAKSEHAYSHLKRAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G P   +  +   +    H  GD    V     G   +++H+  I+ F 
Sbjct: 167 TVDKRYHALVQGHPDPLRGTVDAPI--DRHPSGDGRFAVV---AGGKESVTHYDTIEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    L+++  TGRTHQ+RVH   +  P VGD  Y A+        +  + +LHA  +  
Sbjct: 221 RAASLLDIKLETGRTHQIRVHMSALRHPCVGDMMYGADPTLAARLGV-TRQWLHAVSLAF 279

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +  T   P  +      +G
Sbjct: 280 EHPATGEWVSFTTDYPDDLAHALKIVG 306


>gi|163733966|ref|ZP_02141407.1| ribosomal large subunit pseudouridine synthase D [Roseobacter
           litoralis Och 149]
 gi|161392502|gb|EDQ16830.1| ribosomal large subunit pseudouridine synthase D [Roseobacter
           litoralis Och 149]
          Length = 342

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 89/355 (25%), Positives = 144/355 (40%), Gaps = 50/355 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           M+  Q   V ++   +RLD+      P    ++   L +++  G V VD         RI
Sbjct: 1   MSVRQIQFVIDEAPPLRLDKALARDVPVEAALSRTRLARLIDEGGVWVDGVVQHNPKARI 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           ++G  V I       +HI+ E   LD               +++ED+ + V NKPAG+ V
Sbjct: 61  EAGAQVTIHVQEAQDSHILPEDIPLD---------------IIHEDADLIVVNKPAGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    D        ++P + HR+D++TSG+LVVA++ AA   L  
Sbjct: 106 HPAPGTPSGTLVNALLAHCGDDLSGVGGLKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F+   +++ Y  LV+G P      +           N L   + +        +Q    
Sbjct: 166 QFQAHTVERYYNCLVYGAPDANDPRLRGVKGARFEAGNILKMTTQLARHKTDRQRQAVLF 225

Query: 221 KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +G  +A++  + ++ +        +E    TGRTHQ+RVH  H G  +VGD  Y    K 
Sbjct: 226 QGGRHAVTRARSVERYGTPPVLTLMECWLETGRTHQIRVHMAHAGHALVGDPTYGGKRKL 285

Query: 279 NFTSPIQ---------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              S             +  LHA  +   HP  G  L+  A LP  M +    L 
Sbjct: 286 PAKSLPDATLEAVKCFKRQALHAAVLGFEHPVSGEHLRFEAALPDDMAQLLGILR 340


>gi|281357295|ref|ZP_06243784.1| pseudouridine synthase, RluA family [Victivallis vadensis ATCC
           BAA-548]
 gi|281316326|gb|EFB00351.1| pseudouridine synthase, RluA family [Victivallis vadensis ATCC
           BAA-548]
          Length = 323

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 81/330 (24%), Positives = 144/330 (43%), Gaps = 35/330 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
              +E  +   RLDR      P  +   LQ+++R G V+ D   ++     +++G  + +
Sbjct: 7   TFQIEAGDAGTRLDRCLSRLIPGESRSFLQRLIRDGLVKADGVALEVPRYPVRAGMSIAV 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                                     ++  +  +LYED  + V +KPAG+ V   +G   
Sbjct: 67  ELPEEES---------------PEPAAEPFEFPILYEDDVMLVIDKPAGVVVHPAAGNPT 111

Query: 126 AYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              ++  L  +     Q      +P + HRLD++TSG L VA+T  A   L+ +F  R  
Sbjct: 112 GTVVNALLGRYPQLAEQLACTTSRPGIVHRLDKDTSGCLAVAKTANAQFKLSTAFAGRET 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---F 236
           +K Y ++  G+P  +   ++  L+ +  +    + VV   E+    AI+ ++V       
Sbjct: 172 RKTYLAITRGVPIRRSGELST-LIGRHPVSRQKMAVV---ERNGKLAITRYRVEYTGMLD 227

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
             +   L ++  TGRTHQ+RVH   +G P++GD  Y              +  LHA  + 
Sbjct: 228 GVEIGVLAVRILTGRTHQIRVHLASLGVPVLGDAVYGGARTAVAGVE---RQLLHAWKLC 284

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           +PHP  G  ++ TAP P  + +  + +G K
Sbjct: 285 VPHPATGTPMEFTAPPPEDIRRILERIGVK 314


>gi|254419052|ref|ZP_05032776.1| pseudouridine synthase, RluA family [Brevundimonas sp. BAL3]
 gi|196185229|gb|EDX80205.1| pseudouridine synthase, RluA family [Brevundimonas sp. BAL3]
          Length = 339

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 91/331 (27%), Positives = 141/331 (42%), Gaps = 45/331 (13%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSG-QVVRIPPVIN 72
           D   +RLD+     +P ++   LQ +L  G VR D   +   + + Q G  VV +PPV  
Sbjct: 27  DAPGVRLDKALAEAFPTLSRARLQALLAEGAVRRDGLVLTAGSAKAQPGLYVVALPPVAP 86

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
           A                 T   + +   +LYED+ + V +KPAG++     G      ++
Sbjct: 87  A-----------------TPQPEAIPLTVLYEDADLIVIDKPAGMAAHPAPGCETGTLVN 129

Query: 131 GFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             L    DS        +P + HRLD++TSG++V A+T  A Q L+  F    I++ Y +
Sbjct: 130 ALLAHCGDSLSGIGGVARPGIVHRLDKDTSGVMVAAKTDRAHQGLSALFATHDIERTYIA 189

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------ 239
           L  G P   +  I   + + +      + V+K    G   AI+ + V   F +       
Sbjct: 190 LTRGAPSPSRGRIETRIGRSTG-DRKKIAVLK---AGGREAITDYVVQAIFGEPAKASGA 245

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-----GNFTSPIQNKLYLHA 292
                +    HTGRTHQ+RVH    G PI+GD  Y +                 +  LHA
Sbjct: 246 PLAARVACTLHTGRTHQIRVHLSSKGSPILGDATYGSGSPAAAVRAVVAEAGLARQALHA 305

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +   HP  G  L+   P PA MV+  ++L
Sbjct: 306 AVLGFVHPVTGETLRFETPPPADMVR-LEAL 335


>gi|255261883|ref|ZP_05341225.1| ribosomal large subunit pseudouridine synthase D [Thalassiobium sp.
           R2A62]
 gi|255104218|gb|EET46892.1| ribosomal large subunit pseudouridine synthase D [Thalassiobium sp.
           R2A62]
          Length = 341

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 80/342 (23%), Positives = 137/342 (40%), Gaps = 50/342 (14%)

Query: 16  EENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           +   RLD+      P    ++   + K+L SG V ++   +     ++     + +    
Sbjct: 13  DPPKRLDKAIARDVPADASLSRSRIAKLLASGDVALNGAVLTDPRAKVAEDDEITVTLPD 72

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
            A +H+  E   LD               L++ED  + V NKP+G+ V    G      +
Sbjct: 73  AAESHMGPEDIPLD---------------LVFEDDDLIVINKPSGMVVHPAPGSPSGTLV 117

Query: 130 DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           +  +    DS       ++P + HR+D+ETSG+LVVA++  A   L   F    +++ Y 
Sbjct: 118 NALMHHCGDSLSGVGGEKRPGIVHRIDKETSGLLVVAKSDKAHHGLAAQFEAHTVERYYR 177

Query: 185 SLVWGIPKNKKECIANWLLKK----------SHIGGDYVHVVKQNE--KGANYAISHFKV 232
           ++V+G+P +    +                 + +        +Q        +A++  +V
Sbjct: 178 AVVYGVPDSNDPRLRGIRGVNFERSNIMKITTQLARHKTDRQRQAVLFGNGRHAVTRARV 237

Query: 233 IDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFT 281
           ++ F Q      +E    TGRTHQ+RVH  H G  +VGD  Y    K         G   
Sbjct: 238 VERFGQPVVASLVECWLETGRTHQIRVHMTHAGHNLVGDPTYGGRRKLSPKAINAAGFEA 297

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
                +  LHA  +   HP  G + +  APLP  M     +L
Sbjct: 298 VASFPRQALHAAVLGFKHPVTGEMVRFEAPLPDDMADLLCAL 339


>gi|54294221|ref|YP_126636.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Legionella pneumophila
           str. Lens]
 gi|53754053|emb|CAH15526.1| Ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Legionella pneumophila
           str. Lens]
          Length = 321

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 73/327 (22%), Positives = 133/327 (40%), Gaps = 30/327 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q + V  +  N R+D       P  +   +   +++G V ++    K  ++   G ++ I
Sbjct: 7   QQLSVPRELHNQRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCKPKDKALGGDLITI 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           +D++       + +   ++YEDS++ V NKPA + V  G+G   
Sbjct: 67  NV-----------DYTIDNTDFNLCKPENIPIQIVYEDSEVIVVNKPASLVVHPGAGNKE 115

Query: 128 HI--DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           H   +  L    +     +  + HRLD++T+G+L+VA+   +  +L    + R I++ Y 
Sbjct: 116 HTLVNALLHHCPELQLLPRAGIIHRLDKDTTGLLIVAKNLISHTYLIRQMQNREIKRHYL 175

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G        I     +        + V          A++H+  I+   + F  L 
Sbjct: 176 TLVHGYV-ISGGTIDTGFGRHPK-NRLKMAVTDF----GRQAVTHYN-INKHYKDFTLLN 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           +   TGRTHQ+RVH  ++  P+VGD  Y    K    +            +  LHA  + 
Sbjct: 229 VSLMTGRTHQIRVHMNYINHPVVGDQLYGGRMKFPPNADEAILSVLKQFKRQALHACSIS 288

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
             HP     + + A LP       ++L
Sbjct: 289 FCHPVKNTEITLNALLPDDFELLLNTL 315


>gi|254442724|ref|ZP_05056200.1| pseudouridine synthase, RluA family [Verrucomicrobiae bacterium
           DG1235]
 gi|198257032|gb|EDY81340.1| pseudouridine synthase, RluA family [Verrucomicrobiae bacterium
           DG1235]
          Length = 307

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 135/324 (41%), Gaps = 25/324 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+      V       R+D+     +P  +  + Q+   S  V +D   +    ++  G+
Sbjct: 1   MSEPVSWEVPEGVYKARIDKLLSEAFPDHSRSDFQRAFDSDLVTLDGAPIAKKQKVSEGE 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V                  + +   L      +   +++ED  + V NKPAG+ V  G+
Sbjct: 61  IVTF---------------AMPTVQKLDMSPIDMDLEVIFEDEHMVVVNKPAGLVVHPGA 105

Query: 124 GIAY--HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           G        G L             ++P + HRLD+ETSG+++ A+T  A + L+E F+ 
Sbjct: 106 GPDEPTLAHGLLHHCQGQLSGIGGVERPGIVHRLDRETSGLIMAAKTDVAHRALSELFQS 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K Y +L  GIP+     +   + ++       + V  +    A  A + + ++  +
Sbjct: 166 RSLVKEYSALCCGIPELMSGTVERPI-ERHPTQRHKMRVGFEGRGRAREAKTDWTLVKAY 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +C L  + HTGRTHQ+RVH   +   I+GD  Y      N     + ++ LH+ Y+ 
Sbjct: 225 DAGYCHLRCRIHTGRTHQIRVHLKSIRHIILGDAVYGYRPLPNLPKQPE-RVMLHSCYLK 283

Query: 297 LPHPEGG-RLQITAPLPAHMVKTW 319
             HP  G  L + A  PA      
Sbjct: 284 FDHPLTGSELVLEAKPPADFQSYL 307


>gi|212702767|ref|ZP_03310895.1| hypothetical protein DESPIG_00797 [Desulfovibrio piger ATCC 29098]
 gi|212673824|gb|EEB34307.1| hypothetical protein DESPIG_00797 [Desulfovibrio piger ATCC 29098]
          Length = 531

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 84/316 (26%), Positives = 145/316 (45%), Gaps = 31/316 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V       RLD+      P ++   +Q+ + +G  R+D   V   + ++++GQ V +  +
Sbjct: 13  VAGALVGQRLDKALCGLLPELSRAAVQRAITAGACRIDGMPVATASLKLKAGQAVCLD-L 71

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
            +  N +  E + +D               +L++D  + + NKPAG++V        +  
Sbjct: 72  PDTANELRAEDEAVD---------------ILWQDEHLLLCNKPAGLTVHPCPSCPENTL 116

Query: 130 -DGFLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L       + +G +P + HRLD++TSG+L+VA        ++E+F  R + K Y +
Sbjct: 117 VQRLLHHFPRLREQEGLRPGVVHRLDKDTSGLLLVALDEPTRLRMSEAFARREVHKEYLA 176

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLE 244
           LV G+P     C     L +       + VV +N +G   A S ++V+    +K F  + 
Sbjct: 177 LVGGVPPQTGTC--REPLGRHPTAKVKMAVVPEN-RGGKTAHSDWRVLWSSPRKDFSLVA 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
           ++ HTGRTHQ+RVH  H+G P++GD  Y                 LHA ++   HP  G 
Sbjct: 234 VRIHTGRTHQIRVHMAHVGHPLLGDALYAPAPVAARAPR----QMLHAWHISFCHPLSGE 289

Query: 304 RLQITAPLPAHMVKTW 319
            L+   P P  M++T 
Sbjct: 290 ELEFFCPPPGDMIQTI 305


>gi|88856520|ref|ZP_01131177.1| ribosomal large subunit pseudouridine synthase [marine
           actinobacterium PHSC20C1]
 gi|88814174|gb|EAR24039.1| ribosomal large subunit pseudouridine synthase [marine
           actinobacterium PHSC20C1]
          Length = 301

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 128/321 (39%), Gaps = 29/321 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V       R+D          +     ++   G V ++   V  ++R+ +   + +  V 
Sbjct: 3   VPEGLAGQRVDAALAKLL-GFSRTFAAEVAEEGGVTMNGVVVGKSDRLSAEAWLEVSWVS 61

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
            +   I+                      ++Y+D  I V +KPAG++     G     + 
Sbjct: 62  KSEPQIVP--------------VVLDTLGIVYDDEHIVVIDKPAGVAAHPSIGWDGVTVL 107

Query: 131 GFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           G L             ++  + HRLD  TSG++VVA++  A   L  +F  R + KIY S
Sbjct: 108 GALAGAGYRISTSGAAERAGIVHRLDAGTSGLMVVAKSELAYTELKRAFHDREVNKIYHS 167

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G P      I   + +  H G  +   V     G   +I+H++ ++ F      +E+
Sbjct: 168 IVQGHPDPLMGTIDAPIGR--HPGSSWKFAVVA---GGKDSITHYETLEAFPS-ASLVEV 221

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
           Q  TGRTHQ+RVH      P VGD  Y A+   +    +  + +LHA  +   HP     
Sbjct: 222 QLETGRTHQIRVHMAAQRHPCVGDTMYGADPTISAKLGL-TRQWLHAHKLGFVHPATREP 280

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           +   +P PA +    + L   
Sbjct: 281 VTFESPYPADLQAALEVLRGD 301


>gi|328881776|emb|CCA55015.1| Ribosomal large subunit pseudouridine synthase D [Streptomyces
           venezuelae ATCC 10712]
          Length = 313

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 140/333 (42%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    ++ + V +  E  R+D      +   +     ++  +G+V+VD   V  + R+ 
Sbjct: 1   MSTSPEIRTLPVPDGLEGERVDAAIARMF-GFSRTKAAELAAAGKVQVDGSVVGKSERVS 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPGAAAPVQIVAEP--------------VEGMEIVHDDDDIVVIMKPIGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ R + K Y +LV G P      I   + +  H   DY   V  +      +++H+ +I
Sbjct: 166 FKERTVDKRYHALVQGHPDPMSGTIDAPIGR--HPNHDYKWAVTAD---GKPSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + + +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAY-RSASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTIAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            +   HP +G  ++  +  P  + K  D +  +
Sbjct: 279 RLGFEHPGDGSWVEFASTYPEDLQKALDRIAAE 311


>gi|78356492|ref|YP_387941.1| pseudouridine synthase, RluD [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
 gi|78218897|gb|ABB38246.1| dephospho-CoA kinase / ribosomal large subunit pseudouridine
           synthase D [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
          Length = 578

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 85/337 (25%), Positives = 140/337 (41%), Gaps = 41/337 (12%)

Query: 12  VENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           V       R DR+         I+   +Q+ +  GQ+ +D         +++SGQ +   
Sbjct: 45  VSPQAAGERADRFIAAALAGDAISRGKIQRAISDGQLLIDNTVCTSPKTKLKSGQHIVFS 104

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS----- 123
               A     +E ++                 +LY D+ + V NKPAG++V         
Sbjct: 105 MEAPAACVSPEEGELE----------------VLYRDAHMLVINKPAGLTVHPAPSCPEG 148

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + + +          +G +P + HR+D++TSG+L++A T  A   L+++F  RRI K Y
Sbjct: 149 TLVHRLLHHFPELEAQEGFRPGIVHRIDKDTSGLLLIALTEKARLALSDAFAGRRIHKEY 208

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---- 239
            +LV GIP+     I    + +       + VV+    G   A+S ++V+          
Sbjct: 209 LALVKGIPEGDSGEIDAP-VGRHPTHKTRMAVVR----GGREALSTWRVLLADPHGGGGT 263

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN------FTSPIQNKLYLHA 292
            +  + ++ HTGRTHQ+RVH  H G P+ GD  Y               +    +  LHA
Sbjct: 264 GWTLVAVRIHTGRTHQIRVHMQHTGHPLWGDALYGGMPGREELQTTPALAQTATRQMLHA 323

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
             +   HP  G  +Q T P PA        LG +  R
Sbjct: 324 WKISFDHPVTGAPMQFTLPPPADFGTLIRDLGSRCQR 360


>gi|84688066|ref|ZP_01015925.1| ribosomal large subunit pseudouridine synthase D [Maritimibacter
           alkaliphilus HTCC2654]
 gi|84663916|gb|EAQ10421.1| ribosomal large subunit pseudouridine synthase D [Rhodobacterales
           bacterium HTCC2654]
          Length = 344

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 86/344 (25%), Positives = 141/344 (40%), Gaps = 52/344 (15%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L K++  G V    + +     ++  G+V+ I   +   +
Sbjct: 17  RLDKALARDVPEAANLSRSRLAKLIAEGAVMRAGEVLTDAKAKVTEGEVIEITVPVAEES 76

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL 133
           H+  E   LD               +++ED  + V NKPAG+ V    G      ++  L
Sbjct: 77  HMRPEAIALD---------------VVWEDHDLIVVNKPAGMVVHPAPGTPSGTLVNALL 121

Query: 134 KSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               D        ++P + HR+D++TSG+LVVA+T AA   L   F    +++ Y +LV+
Sbjct: 122 HHCGDDLSGVGGEKRPGIVHRIDKDTSGLLVVAKTDAAHHGLAAQFEKHTVERHYRALVY 181

Query: 189 GIPKN-------------KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           G+P               ++  I     + +    D          G  +AI+  +V++ 
Sbjct: 182 GMPDLADPRLKGVRGVSFEQGGIVKITTQLARHKTDRQKQAV-TWSGGRHAITRARVVET 240

Query: 236 FAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------- 285
           F +      L+    TGRTHQ+RVH  H G  +VGD  Y    K + ++           
Sbjct: 241 FGRPPSVSLLDCWLETGRTHQIRVHMAHAGHGLVGDPVYGGRRKPSESALGAEAAKALWG 300

Query: 286 -NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             +  LHA  +   HP     L+  A LP  M    + LG K D
Sbjct: 301 FERQALHAATLGFEHPVTKEQLRFEARLPDDMAGLIEVLGAKPD 344


>gi|296445496|ref|ZP_06887453.1| pseudouridine synthase, RluA family [Methylosinus trichosporium
           OB3b]
 gi|296257062|gb|EFH04132.1| pseudouridine synthase, RluA family [Methylosinus trichosporium
           OB3b]
          Length = 338

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 83/338 (24%), Positives = 147/338 (43%), Gaps = 47/338 (13%)

Query: 12  VENDEENMRLDRWFKNHYPH-----INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           V  +    RLDR+     P      ++   L+ ++  G++ +     +    ++ +G  V
Sbjct: 18  VPPEAAGTRLDRFLAER-PEIVAASLSRTRLKALIEDGRLTIGPAPTRDAARKLAAGDRV 76

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                +          + +   + +ED+ + V +KPAG+ V    G 
Sbjct: 77  SL---------------AVPPPQPPEPQPENIPLDIRFEDAHLIVVDKPAGLVVHPAHGH 121

Query: 126 A--YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  L    DS       +KP + HR+D++TSG+LVVA+T AA + L+  F    
Sbjct: 122 ESGTLVNALLGHCGDSLSGIGGVKKPGIVHRIDKDTSGLLVVAKTDAAHKGLSRLFEDHG 181

Query: 179 ----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               + + Y + VWG+P+  +  +   + + S I  + + VV  +E+    AI+H+++I+
Sbjct: 182 RSLGLMREYLAFVWGVPERARGTVEAPIGRHS-IQRERMAVV--SEERGREAITHWELIE 238

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFTSPIQ 285
            F      +  +  TGRTHQ+RVH  H+G P++GD  Y A FK                 
Sbjct: 239 SFG-VVSLVACRLETGRTHQIRVHMAHIGHPLIGDATYGAGFKTKTALLAPAARAVVEAL 297

Query: 286 NKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
            +  LHA  +  PHP     L   + LPA +     +L
Sbjct: 298 GRQALHAATLGFPHPATREELLFESELPADLTALRAAL 335


>gi|262369409|ref|ZP_06062737.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           johnsonii SH046]
 gi|262315477|gb|EEY96516.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           johnsonii SH046]
          Length = 350

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 142/323 (43%), Gaps = 34/323 (10%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           +      R+D+     +   +   L++ L+ G + V+   VK   + +  +++ +   + 
Sbjct: 44  DETYLGQRIDQVAATIWSEFSREKLKQWLKEGHLLVNGNSVKPKYKCEGFELLTLEVELE 103

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHID 130
           A    + E   LD               ++YED  I V NKP G+ V  G+G      ++
Sbjct: 104 AQTRSLPEDIPLD---------------IVYEDDDIIVVNKPVGMVVHPGAGNSSGTLVN 148

Query: 131 GFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             L  +  S +  +  L HR+D++TSG+LVVA+   A   L++    + + ++Y  +V+G
Sbjct: 149 ALLHHYPKSAELTRAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLAKKTVYRVYDLIVYG 208

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   +   + K+  +    + V+     G   A++H+ V + F Q F  ++ +  T
Sbjct: 209 NVIA-GGTVDEPI-KRHPVDRVKMAVL----PGGKDAVTHYNVKERF-QHFTRIQARLET 261

Query: 250 GRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           GRTHQ+RVH  ++G  +VGD  Y         A    + T     +  LHA  + L HP 
Sbjct: 262 GRTHQIRVHFSYIGFGLVGDPVYMPRVRVPAGATELLDETLRGFRRQALHAAELGLKHPR 321

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G  +   AP PA +    D L 
Sbjct: 322 TGEEMLFKAPWPADLATLVDVLR 344


>gi|289208370|ref|YP_003460436.1| pseudouridine synthase [Thioalkalivibrio sp. K90mix]
 gi|288944001|gb|ADC71700.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. K90mix]
          Length = 328

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 87/320 (27%), Positives = 154/320 (48%), Gaps = 16/320 (5%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V    +  RLD +       +    + +++R G +RVD +R K   R+  G  VR+
Sbjct: 15  RTLSVTERGDGQRLDNFLLRELKGVPKSLIYRLVRKGAIRVDGRRAKVTQRLSVGSEVRV 74

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P     L+     ++ +   V      D L+  +L+ED ++ V +KP+G++V GGSG+A+
Sbjct: 75  P----DLDRPEAVERDIPPGV-----LDRLRRSILHEDDQVLVLDKPSGLAVHGGSGLAF 125

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            I   ++      G +  L HRLD+ETSG L++A++R+  Q    + R  R++K Y +L 
Sbjct: 126 GIIEAMRQLRP--GSELELGHRLDRETSGCLLLAKSRSGLQDFHAALREGRVEKRYLALQ 183

Query: 188 WGIPKNKKECIANWLLK--KSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLE 244
            G   + +  + +  +   +   G   +   +  + + A  AIS F  ++ +   F   E
Sbjct: 184 VGAFPSDQPIVCDEPIASSRGPDGKRRMRAGEDADPESARSAISQFVPLERYGS-FQLAE 242

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++  TGRTHQ+RVH   +G P+ GDH Y   +           +L+LHA+ +        
Sbjct: 243 VRIGTGRTHQIRVHGQAIGHPVGGDHDYGLPDANRVLRGAGLKRLFLHAQALQYEDSASE 302

Query: 304 RLQITAPLPAHMVKTWDSLG 323
               +APLP  +    D+L 
Sbjct: 303 SHVYSAPLPDELQSILDALA 322


>gi|282882144|ref|ZP_06290785.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus
           lacrimalis 315-B]
 gi|281298174|gb|EFA90629.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus
           lacrimalis 315-B]
          Length = 295

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 77/318 (24%), Positives = 143/318 (44%), Gaps = 36/318 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ +    RLD +       ++   ++ ++ + +V V+KK VK   ++    V+      
Sbjct: 6   VDKENFGQRLDVYLAKLV-DLSRSQIKNLIDNEKVLVNKKNVKAGYKLSEDDVIS----- 59

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHI 129
                       L+   +    ++ +   ++YED  I V +KP  + V  G+G      +
Sbjct: 60  ------------LEYPKDNKPFAEKIDFNVIYEDEYIAVISKPQDLVVHIGAGNSSGTLV 107

Query: 130 DGFLK----SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +G L        D    +P + HRLD+ TSG++++A+   A  +L + F+  +I+K Y +
Sbjct: 108 NGLLYKFKNQLSDLDPLRPGIVHRLDKNTSGLMIIAKNNQAHINLVDQFKNSQIKKYYLA 167

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G  K  +  I    + ++      + VV    K +  AI+ +K +  F Q++  L +
Sbjct: 168 IVHG--KTPESGIIAEPIGRNPNDRKKMAVVY---KNSKQAITKYKKLKEF-QEYSLLNI 221

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
              TGRTHQ+RVH  ++G P++GD  Y         S   +K  LH+  +   HP    +
Sbjct: 222 NLLTGRTHQIRVHMAYIGYPVLGDIIYGRK-----NSLKIDKQMLHSYKLIFNHPITNQK 276

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++ T   P    K  D +
Sbjct: 277 MEFTDEFPIRFKKFIDKI 294


>gi|197294534|ref|YP_001799075.1| Pseudouridine synthase [Candidatus Phytoplasma australiense]
 gi|171853861|emb|CAM11823.1| Pseudouridine synthase [Candidatus Phytoplasma australiense]
          Length = 302

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 75/327 (22%), Positives = 145/327 (44%), Gaps = 36/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +  ++    +  RLD +  +     N    QK++ + +V V++K  K N  +++  
Sbjct: 1   MKATKNFLISEKNKMQRLDHFLVSQ-TTWNKSQCQKLIAAKKVLVNQKPTKKNYLLKNQD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ IP              +  + +N+ K  + L   ++YEDS + V NKP+ + V    
Sbjct: 60  LITIP------------TTVFKTPLNIQKPYN-LNLEVVYEDSDLAVINKPSNLIVHPS- 105

Query: 124 GIAYHIDGFLKSWVDS-------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            +++     + + +            +P + HRLD+ T+G++++A+    +Q L  +F  
Sbjct: 106 -LSFEGITLVNALLHQFSSLSNIDTPRPGIVHRLDKNTTGLMLIAKNDNTSQKLQTAFSQ 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I+K+YW L+ G  +N+   I   + +  +       +          A++HFK +   
Sbjct: 165 RTIKKVYWGLIEGFLENE-GTINLPIARNPNDRLKMTVL-----PNGKEAVTHFKTLKRL 218

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              F  ++    TGRTHQ+R H  ++  P++GD  Y +              +LHA+ + 
Sbjct: 219 -NNFSLMQFVLETGRTHQIRAHLSYLKKPLLGDKLYGSKHYNT-----DEGQFLHAKELI 272

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWDSL 322
             HP     + + APLP +  K  D L
Sbjct: 273 FKHPISFQEINLQAPLPLNFQKLLDKL 299


>gi|168700598|ref|ZP_02732875.1| ribosomal large subunit pseudouridine synthase [Gemmata
           obscuriglobus UQM 2246]
          Length = 354

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 78/331 (23%), Positives = 152/331 (45%), Gaps = 46/331 (13%)

Query: 17  ENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINAL 74
           E MRLD++ + H     +   +Q+ + SG V ++ + V K + +++    + +       
Sbjct: 40  EGMRLDQYVQLHLGADWSRSVVQRAIESGGVLLNGRPVLKPSYKVRKNDRLHVT------ 93

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                    +    +     + +   +LY+D  + + NKPA + V    G   +  G L 
Sbjct: 94  ---------MPEPTHEIPVPEDIPLDILYQDEWLALVNKPADMVVHPAKG---NWSGTLV 141

Query: 135 SWVDSKGQ----------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +    +          +  + HRLD++TSG+++VA+     + L   F  R++ K Y 
Sbjct: 142 NALQWHFREHLSTGAGHLRAGIVHRLDKDTSGVILVAKDDLTHRDLAMQFESRKVFKEYV 201

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G  +   + I   L    +   D + ++   +  A +A+S+++V++ F + F  ++
Sbjct: 202 AIAAGELERDSDYIEGALKMHPY---DRLKMIVSTDPDAKHALSYYEVLERF-RGFTLVK 257

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-----------SPIQNKLYLHAR 293
           +QP TGRTHQ+RVH LH+GC ++ D  Y    +   +             +  +  LHA 
Sbjct: 258 VQPRTGRTHQIRVHLLHVGCAVLADKIYGGRAQVKLSEIAPGTPPAEDEVLLGRQALHAF 317

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            +   HP  G+ ++  APLP  M +T D+L 
Sbjct: 318 RLRFQHPRTGQWIEAEAPLPPDMRRTLDALR 348


>gi|8575702|gb|AAF78056.1|AF263561_1 23S rRNA pseudouridine synthase [secondary endosymbiont of
           Glycaspis brimblecombei]
          Length = 314

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 72/326 (22%), Positives = 139/326 (42%), Gaps = 35/326 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72
             +   RLD+     +P  +   +++ +   +V+V+ K + +   ++   + + I  +I 
Sbjct: 2   ESQLGQRLDQTLAELFPDYSRSRIKEWILDNRVQVNGKIINRPKEKVFGSEQIAIDVLIE 61

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--D 130
                           ++      +   ++YED +I V NKP  + V  G+G       +
Sbjct: 62  E---------------DMRWQPQNIPLNIVYEDDEIIVINKPRDLVVHPGAGNPDGTVLN 106

Query: 131 GFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             L  + +     +  + HRLD++T+G++V+A+T  A  HL E+ ++R I + Y ++V G
Sbjct: 107 ALLYRYPEIINVPRAGIVHRLDKDTTGLMVIAKTIPAQTHLVEALQLREITREYEAVVNG 166

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   +   + +                     AI+H++V++ F +    L ++  +
Sbjct: 167 RM-TAGGTVDEPIARHPT-----KRTHMAIHPLGKPAITHYRVMEHF-RAHTRLRLRLES 219

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKG--------NFTSPIQNKLYLHARYMDLPHPE 301
           GRTHQ+RVH  H+  P+VGD  Y    +                ++  LHA  + L HP 
Sbjct: 220 GRTHQIRVHMAHINHPLVGDPVYGGRPRPLKGVSEEFRQVMNNFDRQALHATMLRLYHPR 279

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFKY 326
            G  ++  A +PA MV   + L    
Sbjct: 280 TGIEMEWHADIPADMVILINILKADA 305


>gi|88811115|ref|ZP_01126371.1| ribosomal large subunit pseudouridine synthase D [Nitrococcus
           mobilis Nb-231]
 gi|88791654|gb|EAR22765.1| ribosomal large subunit pseudouridine synthase D [Nitrococcus
           mobilis Nb-231]
          Length = 315

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 79/328 (24%), Positives = 136/328 (41%), Gaps = 34/328 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
              ++   +   R DR     +P  +   LQ  L+SG + VD   ++  + +  G+ VR+
Sbjct: 7   HTAIIPIAQAGQRFDRALATIFPQYSRSRLQAWLKSGAITVDTTVLRAKDLVCGGEQVRL 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
             ++     +  E                +   ++YED  + V +KP  + V  G+G A 
Sbjct: 67  SVLLEEEGAVAAEP---------------IALRIVYEDDSLLVIDKPPSLIVHPGAGHAG 111

Query: 127 -YHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +  L       G  +  + HRLD+ TSG++VVAR   A + L E  + R +++ Y 
Sbjct: 112 GTLQNALLHYDPRLAGLPRAGIVHRLDKGTSGLMVVARNLTAHKLLVEQLQARSVKRDYL 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV  +        A   + +       + V     +    A++HF+V++ FA     L 
Sbjct: 172 ALVSAVVT--SGGRATAAIGRHRRDRTRMAVR----QDGRAAVTHFRVVERFA-AHTLLR 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
               TGRTHQ+RVH   +  P+VGD  Y    +    +  +         +  LHA  + 
Sbjct: 225 CSLETGRTHQIRVHMAWLRQPVVGDPVYGGRTRLPKGASEELKTALSGFRRQALHALELR 284

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           L HP   + +   +PLPA      + L 
Sbjct: 285 LVHPATEQAVGWHSPLPADYAYLLEVLR 312


>gi|300814696|ref|ZP_07094946.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
 gi|300511169|gb|EFK38419.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
          Length = 295

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 140/323 (43%), Gaps = 36/323 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +    V+ +    RLD +       ++   ++ ++ + +V V+ K VK   ++    V+ 
Sbjct: 1   MDTFKVDKENFGQRLDVYLAKLV-DLSRSQIKNLIDNEKVLVNNKNVKAGYKLSEDDVIS 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
                            L+   +    ++ +   ++YED  I V +KP  + V  G+G  
Sbjct: 60  -----------------LEYPKDSKPFAEKIDFNVIYEDDYIAVISKPQDLVVHIGAGNS 102

Query: 126 -AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++G L  + +        +P + HRLD+ TSG++++A+   A  +L + F+  +I+
Sbjct: 103 SGTLVNGLLYKFKNQLSNLDPLRPGIVHRLDKNTSGLMIIAKNNQAHINLVDQFKNSQIK 162

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++V G    +   I   + +  +       V     K +  AI+ +K +  F Q++
Sbjct: 163 KYYLAIVHGK-TPESGIIEEPIGRNPNDRKKMAVVY----KNSKQAITKYKKLKEF-QEY 216

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L +   TGRTHQ+RVH  ++G P++GD  Y         S   +K  LH+  +   HP
Sbjct: 217 SLLNINLLTGRTHQIRVHMAYIGYPVLGDIIYGRK-----NSFKIDKQMLHSYKLIFNHP 271

Query: 301 EG-GRLQITAPLPAHMVKTWDSL 322
               +++     P    K  D +
Sbjct: 272 ITNQKMEFKDEFPIRFKKFIDKI 294


>gi|330805203|ref|XP_003290575.1| hypothetical protein DICPUDRAFT_81306 [Dictyostelium purpureum]
 gi|325079283|gb|EGC32890.1| hypothetical protein DICPUDRAFT_81306 [Dictyostelium purpureum]
          Length = 583

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 110/381 (28%), Positives = 164/381 (43%), Gaps = 66/381 (17%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-------------RVKFNNR 58
           V  D E MR+DRW  +  P +    + K LR+  +  + +             ++KFN++
Sbjct: 196 VTRDMEGMRVDRWISHKLPILPHSLVCKWLRNKIIYKENEEFKQNSTSELKRHKMKFNDK 255

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           ++ G  +  P       H+    +    +         +K  +LY+D  + V NKP G+S
Sbjct: 256 VEVGSWIYFPSQALLDQHMADINEPTKYTRLSDDEIKEIKESVLYKDEHLLVLNKPQGLS 315

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR--- 175
           VQGGSG+  H+D  L      K + P+L HRLD+ TSGIL++ R+R AA  + E F    
Sbjct: 316 VQGGSGLKKHLDMMLNHLRFEKSENPKLVHRLDKATSGILILGRSRLAATAMAEKFELKL 375

Query: 176 ------------------------------------------MRRIQKIYWSLVWGIPKN 193
                                                      + I+K YW+L+ G PK 
Sbjct: 376 VSSKKKEKEKFNKDNERENKKNSSKKKKDTKDEEIDDDEDLENKGIKKTYWALIAGAPKP 435

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           ++  I   L K    G + V    +   GA  AI+ +KVI        ++ + P TGRTH
Sbjct: 436 REGRIRAPLKKVMIGGEEKVIPALKIGDGAKLAITEYKVIQSSLDNQSFVALWPETGRTH 495

Query: 254 QLRVHALH-MGCPIVGDHKYCANFKGNFTSPIQN------KLYLHARYMDLPHPEGGR-L 305
           QLRVH    +  PI+GD KY             N      KL+LHAR +   HP   + +
Sbjct: 496 QLRVHCASVLNAPIIGDTKYGNKLVNESIKTFLNSASSSLKLHLHARRIQFIHPFTNKPI 555

Query: 306 QITAPLPAHMVKTWDSLGFKY 326
            I APLP  + ++W   GF Y
Sbjct: 556 DIIAPLPPSLKESWKKFGFNY 576


>gi|226953430|ref|ZP_03823894.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (uracil hydrolyase) [Acinetobacter sp. ATCC
           27244]
 gi|294649580|ref|ZP_06726999.1| ribosomal large subunit pseudouridine synthase D family protein
           [Acinetobacter haemolyticus ATCC 19194]
 gi|226835813|gb|EEH68196.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (uracil hydrolyase) [Acinetobacter sp. ATCC
           27244]
 gi|292824519|gb|EFF83303.1| ribosomal large subunit pseudouridine synthase D family protein
           [Acinetobacter haemolyticus ATCC 19194]
          Length = 361

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 140/326 (42%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++ +    R+D+     +   +   L++ ++ G + V+   VK   R +  +++ +  
Sbjct: 52  VQLDENYLGQRIDQVAALVWNEFSREKLKQWMKDGHLLVNGNIVKPKYRCEGNELLTLEV 111

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
            + A                 +   + +   ++YED  I V NK  G+ V  G+G     
Sbjct: 112 ELEAQT---------------SSQPENIPLNIVYEDDDIIVINKDVGMVVHPGAGNPTGT 156

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L      ++  +  L HR+D++TSG+LVVA+   A   L++    + + ++Y  +
Sbjct: 157 LVNALLYHAPKLAELARAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLAKKTVYRVYDLV 216

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G        I   + K+  +    + ++     G   A++H+ V + F + F  ++ Q
Sbjct: 217 VYGNIIA-GGTIDEPI-KRHPVDRVKMAIL----PGGRDAVTHYNVKERF-RDFTRVQAQ 269

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  ++G  +VGD  Y         A+           +  LHA  + L 
Sbjct: 270 LETGRTHQIRVHFSYLGHGLVGDPVYVNRVRFPAGASATLTDMLRGFKRQALHAAKLGLV 329

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  +   AP P    +  + L 
Sbjct: 330 HPRTGEDMMFEAPWPEDFTQLVEVLR 355


>gi|153002938|ref|YP_001377263.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152026511|gb|ABS24279.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 339

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 78/326 (23%), Positives = 141/326 (43%), Gaps = 24/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +    +  D    RLD+  +     +   ++ K+ R+ ++RV+  R K    + +G VV 
Sbjct: 1   MLTFTISEDAAGQRLDKLVRKALRDVPLSHVYKMFRTRKIRVNGGRGKAEQLVAAGDVVV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I           +E+ +          +  +   +L+ED+ +   +KPAG++   G+GI+
Sbjct: 61  I--------RGDEERLLARQEPEPGARAGAVTFGVLHEDADVLAVDKPAGLAAHPGTGIS 112

Query: 127 YHIDGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR- 178
                 +          +     KP   HRLD++TSG+++VA+ R     LTE F     
Sbjct: 113 GATLVEMARAHLGTPADLPPTEFKPSPAHRLDRDTSGVVLVAKNRKTMVRLTELFTDGAD 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y +LV G    +   I   L +                     A++ +KV+    +
Sbjct: 173 VKKTYLALVKGKMPREAGTIDLPLAEHEQTARSKAAR----GVNLQEALTRWKVVSAMKE 228

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMD 296
               L +   TGRTHQ+R H   +G P++GD +Y      +         +++LHA  ++
Sbjct: 229 -ASLLAVTIETGRTHQIRRHLEAVGHPVLGDRRYGDFPTNRAARQRWGLRRMFLHAWRLE 287

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDS 321
           LPHP  G  L++ APLP  +++    
Sbjct: 288 LPHPTTGAPLRLEAPLPGELLEALSR 313


>gi|325067131|ref|ZP_08125804.1| pseudouridine synthase, RluA family protein [Actinomyces oris K20]
          Length = 306

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 148/325 (45%), Gaps = 29/325 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V +  +  R+D         ++   ++ +  +G+VR   + +  ++R+++G+++ 
Sbjct: 3   VRLLPVPDGFDGERVDAALAR-MTGLSRSRVEDLCEAGEVRRGGETLAKSSRLRAGELLE 61

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-I 125
           +          + + + ++      +  +     LLYED  I V +KPAG++     G  
Sbjct: 62  VD---------LPDPRPVEPVATPVEGME-----LLYEDEDIVVVDKPAGVAAHPSMGWD 107

Query: 126 AYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + G LK+           ++  +  RLD  TSG+++VA+   A   L  +FR   + 
Sbjct: 108 GPDVLGALKAMHVRVATSGAAERQGIVSRLDVGTSGVMIVAKGERAYSVLKRAFREHTVD 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y +LV G        I   + +  H   ++   +    +G   +I+H+ VI+      
Sbjct: 168 KVYHALVQGHLDPSSGTIDAPIGR--HPSREWKMAII---EGGRESITHYDVIEAMP-GA 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           C  E+   TGRTHQ+RVH   +G P VGD  Y A+   +  + +  + +LHAR + + HP
Sbjct: 222 CLAEIHLETGRTHQIRVHMAAVGHPCVGDATYGADPAISARTGLI-RQWLHARELGIAHP 280

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGF 324
             G  +  T+  P  +V   D L  
Sbjct: 281 ITGEHMVFTSDYPDDLVHALDVLRL 305


>gi|258653360|ref|YP_003202516.1| pseudouridine synthase [Nakamurella multipartita DSM 44233]
 gi|258556585|gb|ACV79527.1| pseudouridine synthase, RluA family [Nakamurella multipartita DSM
           44233]
          Length = 308

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 84/327 (25%), Positives = 144/327 (44%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V +    MRLD         ++   + +++ +G V VD   V  ++R+    
Sbjct: 1   MPDVRRLPVPDGLAGMRLDAGVARLL-GLSRTTVAEMIDAGDVLVDGVPVARSSRMALDT 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I          ++ Q +   S             +LY D+ I V +KP G++     
Sbjct: 60  WLEITLPEPDRPPAVQAQVVDGLS-------------VLYRDADIVVVDKPVGVAAHPSP 106

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L             ++  + HRLD  T+G++VVA +  A   L  +F+ R
Sbjct: 107 GWTGPTVLGALAGLGIAVSTSGSAERQGIVHRLDVGTTGVMVVALSERAYTTLKAAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + KIY +LV G P      I   + +  H   D+   V     G   +++H++ ++ F 
Sbjct: 167 TVDKIYHALVQGHPDPSAGTIDAPIGR--HPSSDWKFAVV---AGGKDSVTHYETLEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    L++   TGRTHQ+RVH   +  P VGD  Y A+        +Q + +LHAR +  
Sbjct: 221 RAASLLQVHLETGRTHQIRVHFAAVRHPCVGDRTYGADPTLADRLGLQ-RQWLHARTLGF 279

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP+ GR ++ T+P PA +    + L 
Sbjct: 280 AHPDDGRWVEFTSPYPADLAHALEVLA 306


>gi|148244467|ref|YP_001219161.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Vesicomyosocius okutanii HA]
 gi|146326294|dbj|BAF61437.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 314

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 83/342 (24%), Positives = 148/342 (43%), Gaps = 45/342 (13%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSL++    +++ N   N R+D       P+ +   +   ++SG   + +K  K   ++ 
Sbjct: 1   MSLLS----IIIPNRFINQRVDVAMAQMLPNYSRTKITYWIKSGNALIHRKTFKPKEKVL 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G++V +       N  + E   +D               ++YEDS+I + NKP G+   
Sbjct: 57  GGEMVNLLIKTKKANSWLAEDAAID---------------VVYEDSEIIIVNKPVGLVTH 101

Query: 121 GGSGIAYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            G   A +  G L + +           +  + HRLD+ TSG++VVAR+  A ++LT+  
Sbjct: 102 PG---ASNWTGTLANALLHYDSSLANLDRAGIVHRLDKNTSGLMVVARSEYAQKYLTKQL 158

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +   I + Y ++V+G        +   + +          + +   K   YA++H+++I+
Sbjct: 159 QTHSISREYSAIVYGYM-ISGGSVDAPIGRDPKD-----RIKQAVVKDGKYALTHYRIIE 212

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------N 286
            F      ++    TGRTHQ+RVH   +G P++ D  Y         +  Q        N
Sbjct: 213 RFTH-HTHVKAILETGRTHQIRVHLSFIGHPLIADPIYGGKVYFPKKADKQLTKALKNFN 271

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           +  LHA+ + L HP  G  +    PLP  M      L  K+D
Sbjct: 272 RQTLHAKKLTLTHPISGELMSWKMPLPQDMQDLLQILA-KFD 312


>gi|227504711|ref|ZP_03934760.1| possible pseudouridylate synthase [Corynebacterium striatum ATCC
           6940]
 gi|227198721|gb|EEI78769.1| possible pseudouridylate synthase [Corynebacterium striatum ATCC
           6940]
          Length = 307

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 139/327 (42%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V    E MR D         I+      +  +G V VD   V  ++R+++G 
Sbjct: 1   MRESRRLPVPEGLEGMRADAALAKLI-GISRGKAADLCAAGDVEVDGTIVGKSDRLEAGG 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         + KE+ +                 +LY D  +   +KP G++     
Sbjct: 60  WIDVMMPAPEEPLVPKEELVE-------------GMDVLYADDDVICVHKPVGVAAHPTL 106

Query: 124 GIA-YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L++           ++  + HRLD  TSG++VVA +  A   L  +F+ R
Sbjct: 107 GWEGPTVIGGLRAAGYQLADAGPTERKGIVHRLDVGTSGVMVVAASERAYSQLKAAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y ++V G+P      I   + +    G  +  V      G  +A++H+K+++ F 
Sbjct: 167 TVTKTYHAVVQGLPDPIVGTIDAPIGRHPSSGWKFAVV-----DGGKHAVTHYKLLEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++   LE+   TGRTHQ+RVH    G P VGD  Y  +        +  + +LHA  +  
Sbjct: 221 REASLLEVHLETGRTHQIRVHMSATGHPCVGDPMYGCDPNLAKRVGLI-RQWLHAVSLGF 279

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G+  ++TAP P  +    + L 
Sbjct: 280 IHPGTGKHFEVTAPYPEDLRHALEVLR 306


>gi|227503303|ref|ZP_03933352.1| pseudouridylate synthase [Corynebacterium accolens ATCC 49725]
 gi|306836462|ref|ZP_07469436.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           accolens ATCC 49726]
 gi|227075806|gb|EEI13769.1| pseudouridylate synthase [Corynebacterium accolens ATCC 49725]
 gi|304567655|gb|EFM43246.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           accolens ATCC 49726]
          Length = 308

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 83/324 (25%), Positives = 149/324 (45%), Gaps = 28/324 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++   +    E MR D         ++     ++   G V VD + +  + R+ SGQVV
Sbjct: 4   QLRSFPIPEGLEGMRADAALAKLL-GLSRSATAQLCAEGGVTVDSQELGKSERLASGQVV 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +         + + +K L     L +  D     +LY D+ I   +KP G++     G 
Sbjct: 63  SV--------LLPEPEKPLLPREELVEGMD-----VLYSDADIICVHKPVGVAAHPSVGW 109

Query: 125 IAYHIDGFLKSW---VDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + G L++    V S G  ++  + HRLD  TSG++VVA +  A   L  +F+ R +
Sbjct: 110 DGPTVIGGLRAAGYNVASLGPTERQGIVHRLDVGTSGVMVVASSGRAYSALKHAFKHRTV 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++V G+P   +  I   + +    G  +  +          A++H+++I+ F ++
Sbjct: 170 KKTYHAVVQGLPDPIEGTIDAPIGRHPKSGWKFAVL-----DDGKAAVTHYRLIEAF-RE 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E+   TGRTHQ+RVH    G P VGD  Y +N + +    ++ + +LHA  +   H
Sbjct: 224 ASLIEVHLETGRTHQIRVHMSATGHPCVGDPMYGSNPQLSARLGLE-RQWLHAVQLGFTH 282

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G+  +  AP P  + +  + L
Sbjct: 283 PGTGKWFEARAPYPDDLQQALERL 306


>gi|254294738|ref|YP_003060761.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254043269|gb|ACT60064.1| pseudouridine synthase, RluA family [Hirschia baltica ATCC 49814]
          Length = 369

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 76/351 (21%), Positives = 141/351 (40%), Gaps = 61/351 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           +V   +    RLD+W     P ++    + I+  G V +D   +    +++ +     I 
Sbjct: 23  IVAPAEFAGERLDKWLPIAAPELSRSRAKAIIEKGDVLLDDTAITSPKHKVIADGRYVI- 81

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                         ++   ++     + +   +L+ED  + + NKPAG+ V    G    
Sbjct: 82  --------------LMPPPLDAEPLPEDIPLDVLFEDEHLIILNKPAGLVVHPAPGSTSG 127

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             ++  L              +P + HRLD++TSG++V A+T  A   L+  F+   +++
Sbjct: 128 TLVNALLHHCAGQLPGIGGVARPGIVHRLDKDTSGVMVAAKTEFAHTGLSSLFQAHFMER 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN----------------EKGANY 225
            Y ++  G P+     I   + + S      + VV+++                E+   +
Sbjct: 188 AYLAVTRGAPRPLLGKIETRIAR-STTDRKKMAVVRESRLSASAEWHGESEEDYEQKGKH 246

Query: 226 AISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--AN 275
           AI+++KV++ F +             E +  TGRTHQ+RVH  H+G P++GD  Y     
Sbjct: 247 AITNYKVLEQFGRIDATSGLPAATLTECRLETGRTHQIRVHMAHIGAPLLGDQTYGRYRG 306

Query: 276 FKGNFTSPI----------QNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            K + + P             +  LHA  +   HP  G  L+     P  M
Sbjct: 307 LKAHGSGPAFETATHACKEFKRQALHAAILGFEHPVTGENLRFEVEPPEDM 357


>gi|209694254|ref|YP_002262182.1| 23S rRNA pseudouridine synthase D [Aliivibrio salmonicida LFI1238]
 gi|208008205|emb|CAQ78349.1| ribosomal large subunit pseudouridine synthase D [Aliivibrio
           salmonicida LFI1238]
          Length = 324

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 72/339 (21%), Positives = 146/339 (43%), Gaps = 37/339 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   +++ + +G + V+ + + K   ++  G+ + +  
Sbjct: 10  TVKDSQLGQRLDQAAAELFSDFSRSRIKEWVLAGSISVNGEVITKARVKMMGGEEIVVKA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +      + +   L+               ++YED  I V NKP  + V  G+G     
Sbjct: 70  ELEDEERWLAQDIPLE---------------IVYEDDDILVINKPRDLVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  + + R+I + Y ++
Sbjct: 115 ILNALLFHYPSIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRKITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   + +           +    +    A++H++V + F +    L ++
Sbjct: 175 VLGRM-TAGGMIEKPIGRHPQ-----KRTLMAVHELGKDAVTHYRVAEHF-RIHTRLRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH   +  P+VGD  Y    +    +  +        N+  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSFLQHPLVGDTAYGGRARIPKGASQELIDMIRGFNRQALHAAMLRFD 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLY 336
           HP  G  ++  AP+P  ++    +L  + D  L  +  Y
Sbjct: 288 HPITGEVMEFHAPIPDDIIALAQAL--RDDERLLHEEEY 324


>gi|269219521|ref|ZP_06163375.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 848 str. F0332]
 gi|269211100|gb|EEZ77440.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 848 str. F0332]
          Length = 309

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 74/327 (22%), Positives = 139/327 (42%), Gaps = 30/327 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++  V +     R+D         ++       ++ G+  +D      ++R+ SG 
Sbjct: 1   MPERRFYPVPDGLSGDRIDSVLSR-MTGLSRSVCAAAVQKGEAWIDGAVASKSDRVPSGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ I               ++    +L         + LYED  + V +KPAG++     
Sbjct: 60  VLEI---------------LVPDPPSLEPRPSAEGIVRLYEDEDVVVVDKPAGMAAHPSL 104

Query: 124 G------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  +   +   +K       ++  + HRLD  T+G +VVA++ AA   L  +FR R
Sbjct: 105 NFEGPDVLGTLMAEGVKLTTHGPQERKGIVHRLDVGTTGCMVVAKSEAAYSALKRAFRDR 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K+Y +LV G P      I   + + +     +   V+ +      +++H++ ++  A
Sbjct: 165 AVEKVYHALVQGHPDPMSGTIEAPIGRDNR--RQWKMAVRAD---GRPSVTHYEALEAMA 219

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                LE++  TGRTHQ+RVH   M  P VGD  Y A+   +    +  + +LHA  +  
Sbjct: 220 -GASLLEVRLETGRTHQIRVHMSAMSHPCVGDDMYGADPTLSARLGL-TRQWLHAVRLGF 277

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +   AP P  +  + +++ 
Sbjct: 278 EHPTSGEWVAFAAPYPEDLQNSLEAMR 304


>gi|91974839|ref|YP_567498.1| pseudouridine synthase RluD [Rhodopseudomonas palustris BisB5]
 gi|91681295|gb|ABE37597.1| ribosomal large subunit pseudouridine synthase D [Rhodopseudomonas
           palustris BisB5]
          Length = 426

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 85/343 (24%), Positives = 146/343 (42%), Gaps = 51/343 (14%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
            VVV  DE + RLDR      P ++   L+ ++  G+V +    V+       SG+ + I
Sbjct: 102 EVVVAGDEGSPRLDRVLATRCPALSRSRLKALILDGRVAIRGAPVRDPAYHAASGETITI 161

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       E   L+               +++ED  I V +KP G+ V   +G  +
Sbjct: 162 DVPPPVAPEPAGEAIALE---------------IVHEDDDIIVIDKPRGLVVHPAAG--H 204

Query: 128 HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR- 177
                + + +   G+         +P + HRLD++T+G++V A+   A Q L+  F    
Sbjct: 205 ETGTLVNALIAHCGESLSGIGGVRRPGIVHRLDKDTTGLMVAAKNDRAHQSLSAQFADHG 264

Query: 178 ---RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               +++ Y++ VWG P   +  I   + +  H   + + V      G   AI+H++V++
Sbjct: 265 RTGELRRGYYAFVWGAPNRIRGTIDAPIDRHPH-AREKMAVRD----GGREAITHWEVLE 319

Query: 235 CF-----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNF 280
            F      +    +  Q  TGRTHQ+RVH  H+G P++GD  Y  +FK            
Sbjct: 320 TFTGRSGGEIVSLIACQLETGRTHQIRVHLAHIGHPLLGDDVYGPHFKTKASQLRPDARA 379

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSL 322
                 +  LHA  + L HP  G +    + LPA + +   +L
Sbjct: 380 ALTDLGRQALHAYLLVLEHPSTGEVVAWESGLPADLKRLKAAL 422


>gi|328950026|ref|YP_004367361.1| pseudouridine synthase, RluA family [Marinithermus hydrothermalis
           DSM 14884]
 gi|328450350|gb|AEB11251.1| pseudouridine synthase, RluA family [Marinithermus hydrothermalis
           DSM 14884]
          Length = 318

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 93/339 (27%), Positives = 154/339 (45%), Gaps = 41/339 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           V V    E +RLD+         +    Q  + +G VRVD   V K   R++ G+ V + 
Sbjct: 4   VEVRFSAEGVRLDQAVAER-TGASRAKAQAWIAAGYVRVDGVPVTKPGKRLK-GETVEVV 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
              +    +  EQ+ L+               +LYED  + V NKP G++     G+   
Sbjct: 62  APPDPPPRVAPEQRDLE---------------ILYEDEDMVVVNKPPGMATHPAPGLTSG 106

Query: 127 YHIDGFLKSWVDSKGQ-------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             ++  +  +  +  +       +P + HRLD++TSG++VV R  AA + L ++F+ R +
Sbjct: 107 TLVNALMGRYAQAAVEGEPPEQVRPGIVHRLDRDTSGVIVVGRHDAAVRRLADAFKNRFV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y ++  G P           + +  +    +HV   N   A YA + F ++      
Sbjct: 167 FKRYVAITVGQPPEMTLV---APIGRHPVERHKMHVSGVN---ARYAETDFSLLATV-DG 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              ++ +PHTGRTHQ+RVH  H+  PI+GD  Y         SP  ++  LHA  + +PH
Sbjct: 220 HALVDARPHTGRTHQIRVHLKHLYAPILGDELYGK------PSPYISRQALHAYELRIPH 273

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           P  GR +   AP+P  MV  W++LG ++   L    +  
Sbjct: 274 PRSGRIMTFVAPVPRDMVAAWEALGGRWPDGLERADVAP 312


>gi|323700732|ref|ZP_08112644.1| pseudouridine synthase, RluA family [Desulfovibrio sp. ND132]
 gi|323460664|gb|EGB16529.1| pseudouridine synthase, RluA family [Desulfovibrio desulfuricans
           ND132]
          Length = 562

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 85/333 (25%), Positives = 143/333 (42%), Gaps = 35/333 (10%)

Query: 11  VVENDEENMRLDRWFKNHY--PHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
            V   +   RLD+++        ++   ++  + SG   VD +   K N ++  GQV  I
Sbjct: 13  TVTLSDAGTRLDKFWGRELAGEGVSRGRVKGWIESGLALVDGEVTTKGNLKLARGQVAVI 72

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GI 125
                       E   L  +      S  +++  +YED  + V  KPAG++V        
Sbjct: 73  -------RAAAPEADPLGPASPPEPVSGDIEA--VYEDEHMLVIVKPAGLTVHPAPSEPG 123

Query: 126 AYHIDGFLKSWVD-------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              ++  +  W D          Q+P + HRLD++TSG++ VART +A   L+ SF    
Sbjct: 124 PTLVNLLIHQWPDIAAENSGMDPQRPGIVHRLDKDTSGLMAVARTESARLALSASFAGHE 183

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             K+Y +LV G P+  +  I   + +       +  ++    KG   A S ++V+    +
Sbjct: 184 TFKVYLALVHGRPELAEGVIDAPMGRHPT----HKTLMAVLPKGGREARSDYRVLWTGPR 239

Query: 239 K-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQNKLYLH 291
                  ++ HTGRTHQ+RVH  H+G P++GD  Y          + +  + +  +  LH
Sbjct: 240 GLASLAAVRIHTGRTHQIRVHMAHIGHPLIGDAAYGPRENAEWSRRPDRLAGLAPRQMLH 299

Query: 292 ARYMDLPHPEGGR--LQITAPLPAHMVKTWDSL 322
           A Y+ +PHP  G    +  AP P         L
Sbjct: 300 AFYLSVPHPVTGEPVTRWLAP-PEDFRALLAGL 331


>gi|254461389|ref|ZP_05074805.1| ribosomal large subunit pseudouridine synthase D [Rhodobacterales
           bacterium HTCC2083]
 gi|206677978|gb|EDZ42465.1| ribosomal large subunit pseudouridine synthase D [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 341

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 78/345 (22%), Positives = 138/345 (40%), Gaps = 50/345 (14%)

Query: 14  NDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
            ++   RLD+      P    ++   + K+L +G + ++         +I +G  V I  
Sbjct: 11  QEDPPARLDKALSRDVPESASLSRTRIAKLLDAGAITINGAVQTDPKAKITAGAQVDIT- 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                         ++ +V+     + +   ++YED  + V NKPAG+ V    G     
Sbjct: 70  --------------VEEAVDSHIEPEDIPLDVMYEDDDLIVVNKPAGMVVHPAPGTPSGT 115

Query: 128 HIDGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            ++  L  +          ++P + HR+D+ET+G+LVVA++ AA   L   F     ++ 
Sbjct: 116 LVNALLHHFAGKLSGVGGSKRPGVVHRIDKETTGLLVVAKSDAAHHGLAAQFAAHTAERA 175

Query: 183 YWSLVWGIPKNKKECIANW----------LLKKSHIGGDYVHVVKQNE--KGANYAISHF 230
           Y ++  G P+     I             L   + +        +Q    +   +A++  
Sbjct: 176 YLAVTQGAPEASDPRIRGVRGVSFETGGVLKVTTQLARHKHDRQRQAVLFENGRHAVTRA 235

Query: 231 KVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GN 279
           + I+ F    C   +E +  TGRTHQ+RVH  H+G  ++GD  Y    K         G 
Sbjct: 236 RTIERFGNPHCLALVECRLETGRTHQIRVHMAHVGHGLLGDPTYGGRRKLPAKALSEVGL 295

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             +   N+  LHA  +   HP  G  L+  A LP  +      L 
Sbjct: 296 EAAKTFNRQALHAAVLGFEHPISGELLRFEADLPDDIAVLLQKLR 340


>gi|297183636|gb|ADI19762.1| hypothetical protein [uncultured gamma proteobacterium EB000_37F04]
          Length = 322

 Score =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 133/325 (40%), Gaps = 34/325 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V +  D   +RLD    + +P  +   L + +++G+++ + +  +  +++     + + P
Sbjct: 14  VDIPADLHGIRLDAAAAHLFPDFSRSRLAEWIKAGRLQRNHQASRPKDKVAVDDQLLLWP 73

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                     E   LD               +LYED  + V NKPAG+ V   +G     
Sbjct: 74  ETEDRVEWAPEPLPLD---------------ILYEDEHVIVLNKPAGLVVHPATGHQTGT 118

Query: 128 HIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++G L    +     +  + HRLD++TSG+++ AR+  A + L      R + ++Y ++
Sbjct: 119 LVNGLLAHAPEMSALPRGGIVHRLDKDTSGVMLAARSAIAHKSLVAQLADRSVSRLYSAV 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        I   + +        + VV    +    + +H+++   F+     L + 
Sbjct: 179 CRGTFTG-GGTIDAPIGRH-PTSRLKMAVV----EDGKPSRTHYRIEKRFS-AHTHLSVS 231

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH      P+VGD  Y         A+ +         +  LHAR +   
Sbjct: 232 LETGRTHQIRVHLAWRKHPLVGDPVYAGRAMRPAGASDQLVAALTGFRRQALHARRLTFL 291

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP+    +    P+PA M      L
Sbjct: 292 HPQSQDSMTFETPIPADMAGLLGCL 316


>gi|282862147|ref|ZP_06271210.1| pseudouridine synthase, RluA family [Streptomyces sp. ACTE]
 gi|282563172|gb|EFB68711.1| pseudouridine synthase, RluA family [Streptomyces sp. ACTE]
          Length = 313

 Score =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 142/333 (42%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    V+ + V +  E  R+D      +   +     ++  +G+V+VD      + R+ 
Sbjct: 1   MSTYPEVRTLPVPDGLEGERVDAVISRLF-GFSRTKAAELAAAGKVQVDGAVAGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPQAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKAQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R ++K Y +LV G P      I   + +  H   DY   V         +++H+ +I
Sbjct: 166 FRDRVVEKKYHALVQGHPDPMSGTIDAPIGR--HPQHDYKWAVTAE---GKPSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + + +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAY-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTMAKRLGL-GRQWLHAV 278

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            +   HP +GG ++ ++  P  + +  +++  +
Sbjct: 279 RLGFEHPADGGWVEFSSGYPDDLEQALETIAAE 311


>gi|256384025|gb|ACU78595.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           mycoides subsp. capri str. GM12]
 gi|256384857|gb|ACU79426.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           mycoides subsp. capri str. GM12]
 gi|296455719|gb|ADH21954.1| ribosomal large subunit pseudouridine synthase D [synthetic
           Mycoplasma mycoides JCVI-syn1.0]
          Length = 310

 Score =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 144/319 (45%), Gaps = 36/319 (11%)

Query: 19  MRLDRWFKNHYP--HINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVRIPPVINALN 75
           +RLD+           +   +QK+++   + V+ + +  NN + +    + I        
Sbjct: 13  LRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITNNNFVVKPNSQITITI------ 66

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
               +  ILD ++     +D +   ++Y+D  + V NK   I+V     ++   +  + +
Sbjct: 67  ----KDPILDPNL---VKNDEIDLDIIYQDDDLLVINKQNNITVHPS--LSNTNNTIVNA 117

Query: 136 WVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            + S  +        +P + HR+D++T+G+L+VA+     + L+E F+  +I K Y ++V
Sbjct: 118 LLASDVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKTHKLLSEMFKNHQIYKEYLAIV 177

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+ K  K  I   + + S I    + V     K +  AI+ F+V++ F +    ++ Q 
Sbjct: 178 SGVIKPNKGLIDAPIGR-SQIDRKKMSV---TAKNSKQAITTFEVVERFLKN-TLVKCQI 232

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  ++  P++ D  Y       FT       YLHA  +   HP     ++
Sbjct: 233 QTGRTHQIRVHFNYINHPVLNDPVYGKK-HQEFTDFG---QYLHAYKLRFTHPITKKEIE 288

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           + +PLP         L  +
Sbjct: 289 LISPLPKEFDDKIKELRGE 307


>gi|84515394|ref|ZP_01002756.1| ribosomal large subunit pseudouridine synthase D [Loktanella
           vestfoldensis SKA53]
 gi|84510677|gb|EAQ07132.1| ribosomal large subunit pseudouridine synthase D [Loktanella
           vestfoldensis SKA53]
          Length = 349

 Score =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 84/339 (24%), Positives = 144/339 (42%), Gaps = 50/339 (14%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P+   ++   L +++  G V VD + V     RI  G  V +   +   +
Sbjct: 23  RLDKALGRDVPNDAALSRSRLARLIADGAVAVDGQVVTDPRFRIAEGAQVAVTVAVAVES 82

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFL 133
           HI  +   LD               +++ED  + V NKPAG+ V    G A    ++  +
Sbjct: 83  HIEAQDITLD---------------VVFEDDDLIVINKPAGMVVHPAPGTADGTLVNALI 127

Query: 134 KSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               DS       ++P + HR+D++TSG+LVVA++  A  HL + F    +++ Y ++ +
Sbjct: 128 HHCGDSLSGVGGLKRPGIVHRIDKDTSGLLVVAKSDRAHHHLADQFADHTVERRYIAVCY 187

Query: 189 GIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCF 236
           G+P+     +           N L  ++ +G       +Q        +A++  +++   
Sbjct: 188 GVPEANDPRLRGIKGTSFEPGNILKIQTQLGRHRTDRQRQAVSFTAGRHAVTRVRILAAL 247

Query: 237 AQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFTSPIQ 285
                   +E    TGRTHQ+RVH  H G  ++GD  Y +  K         G       
Sbjct: 248 GAMPVAALVECWLETGRTHQIRVHLAHCGHALIGDPTYGSRRKMSPKALGEAGVAAVAAF 307

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            +  LHA  +   HP     L+ +APLPA M     ++G
Sbjct: 308 PRQALHAATLGFVHPVTEEFLEFSAPLPADMQALLAAMG 346


>gi|319943653|ref|ZP_08017934.1| ribosomal large subunit pseudouridine synthase D [Lautropia
           mirabilis ATCC 51599]
 gi|319742886|gb|EFV95292.1| ribosomal large subunit pseudouridine synthase D [Lautropia
           mirabilis ATCC 51599]
          Length = 332

 Score =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 70/323 (21%), Positives = 138/323 (42%), Gaps = 33/323 (10%)

Query: 10  VVVENDE-ENMRLDRWFKN----HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           +V++  E +  RLD++           I+   +Q+ +  G VRVD++    + R++  + 
Sbjct: 17  LVIDAREGQGQRLDQFLTRYLQERLDGISRTRIQRWIALGAVRVDQQVRLPSLRLKGVES 76

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + + P     +                   D +   ++++D+ I V +KPAG+      G
Sbjct: 77  IEVEPQPLESDTAFA--------------PDPVPLAIVHQDADITVIDKPAGLVTHPAPG 122

Query: 125 IAYH--IDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              +  ++G L +   + +  +  + HRLD++TSG+LV AR+  A   LT     R++ +
Sbjct: 123 NWRNTLMNGLLHADPKAARLPRAGIVHRLDRDTSGLLVCARSERAFASLTAQLASRQMGR 182

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++  G     +  +   + +      + + +          A +H++++        
Sbjct: 183 RYLAIACGQ-TPAQGTVEGNIGRDE---RNRLRMAVVQPPAGKPARTHYRLLAASPDAEA 238

Query: 242 W-LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +  +  +GRTHQ+RVH  H+G P+VGD  Y       F      +  LHA  + L HP
Sbjct: 239 AAILCKLESGRTHQIRVHMAHIGHPLVGDTLYGGKPLAGFA-----RQALHAWQLQLIHP 293

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
              +     AP+P  ++     L
Sbjct: 294 ATQQSQVFVAPIPPDLLTLAAEL 316


>gi|51473455|ref|YP_067212.1| pseudouridine synthase [Rickettsia typhi str. Wilmington]
 gi|81692307|sp|Q68XB2|RLUC_RICTY RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|51459767|gb|AAU03730.1| Pseudouridine synthase [Rickettsia typhi str. Wilmington]
          Length = 303

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 89/301 (29%), Positives = 151/301 (50%), Gaps = 11/301 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  QV V+ ++ + N R++ G  + I    N      +
Sbjct: 12  RLDKYLKRLYPSLTQGVIEKALRQKQVTVNFQKAEANLRVKEGDTIFINDYFNLPVTQHE 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                D+ + L K    L   L+YED  +   NKPA ++ QGGS I   ID  LK +++ 
Sbjct: 72  TLVFADAEIKLAKK--ILTDYLIYEDDHLIAINKPASLATQGGSKINLSIDSALK-YLNY 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G   +L HRLD+ETSG+L++A+   ++  L ++F+ + + K Y+++ +G P      + 
Sbjct: 129 QGADFKLVHRLDKETSGLLLIAKNYLSSVKLHDAFKEKLVIKKYFAITYGRPVKNVGIVK 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + + K     G    +   +      AI+++K++         +E  P TGR HQLR+HA
Sbjct: 189 SNIGKSK---GRMFKITDIDSDNGKLAITYYKLLKSLNNNLFLIEFMPVTGRMHQLRLHA 245

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
             +GCPI+GD KY          P    ++LHA  + L     G  +++ A LP +  + 
Sbjct: 246 QLLGCPILGDDKYG----NKEVMPYSKYMFLHANNIYLSESIVGKEIKLEAKLPFYFTRR 301

Query: 319 W 319
            
Sbjct: 302 L 302


>gi|325263985|ref|ZP_08130718.1| ribosomal large subunit pseudouridine synthase C [Clostridium sp.
           D5]
 gi|324031023|gb|EGB92305.1| ribosomal large subunit pseudouridine synthase C [Clostridium sp.
           D5]
          Length = 331

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 84/328 (25%), Positives = 145/328 (44%), Gaps = 22/328 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V ++E   RLD+    +        L K+LR   + ++ K+   N ++  G  ++
Sbjct: 1   MQQITVGDNEAGQRLDKLLAKYLREAPKSFLYKMLRKKNITLNGKKASGNEKLLRGDEIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +     + K    +  L + S      ++YEDS I + NKPAG+  Q  +   
Sbjct: 61  LFLADETIAKFAGDAKPHAENGMLNRLSYGESLNIIYEDSHIILINKPAGMLSQKAADTD 120

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   L +++   G          +P + +RLD+ TSG++   ++    Q L+  F+ R
Sbjct: 121 VSLVEHLTAYLLRSGALTEDEMRTFRPSVCNRLDRNTSGMVAAGKSLQGLQELSRLFKDR 180

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  LV G   N+   I  +L K +    + VH+    E+G+    + F+ +    
Sbjct: 181 TLGKYYHCLVKGEV-NETSHIHGFLKKDAE--NNQVHITAGQEEGSTAIETEFRPLKS-G 236

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                LE+   TG+THQ+R H   +G PI+GD+KY      +   ++       LHA  +
Sbjct: 237 NDVTLLEVHLITGKTHQIRAHLASVGHPILGDYKYGDRRLNDRCRSAYGLKHQLLHAYRI 296

Query: 296 DLPHPEG------GRLQITAPLPAHMVK 317
             P  EG      GR +  APLPA   K
Sbjct: 297 TFPALEGPLAGLSGR-EFLAPLPAEFQK 323


>gi|326771685|ref|ZP_08230970.1| ribosomal large subunit pseudouridine synthase D [Actinomyces
           viscosus C505]
 gi|326637818|gb|EGE38719.1| ribosomal large subunit pseudouridine synthase D [Actinomyces
           viscosus C505]
          Length = 306

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 77/325 (23%), Positives = 148/325 (45%), Gaps = 29/325 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V +  +  R+D         ++   ++ +  +G+VR   + +  ++R+++G+++ 
Sbjct: 3   VRLLPVPDGFDGERVDAALAR-MTGLSRSRVEDLCEAGEVRRGGETLAKSSRLRAGELLE 61

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-I 125
           +          + + + ++      +  +     LLYED  I V +KPAG++     G  
Sbjct: 62  VD---------LPDPRPVEPVATPVEGME-----LLYEDEDIVVVDKPAGVAAHPSMGWD 107

Query: 126 AYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + G LK+           ++  +  RLD  TSG+++VA+   A   L  +FR   + 
Sbjct: 108 GPDVLGALKAMHVQVATSGAAERQGIVSRLDVGTSGVMIVAKGERAYSVLKRAFREHTVD 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y +LV G        I   + +  H   ++   +    +G   +I+H+ VI+      
Sbjct: 168 KVYHALVQGHLDPSSGTIDAPIGR--HPSREWKMAII---EGGRESITHYDVIEAMP-GA 221

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           C  E+   TGRTHQ+RVH   +G P VGD  Y A+   +  + +  + +LHAR + + HP
Sbjct: 222 CLAEIHLETGRTHQIRVHMAAVGHPCVGDATYGADPVMSARTGLI-RQWLHARELGIAHP 280

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGF 324
             G  +  T+  P  +V   + L  
Sbjct: 281 ITGEHMVFTSDYPDDLVHALNVLRL 305


>gi|160934208|ref|ZP_02081595.1| hypothetical protein CLOLEP_03079 [Clostridium leptum DSM 753]
 gi|156866881|gb|EDO60253.1| hypothetical protein CLOLEP_03079 [Clostridium leptum DSM 753]
          Length = 319

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 135/303 (44%), Gaps = 26/303 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V  ++   RLD++    Y  +    L K +R+  ++++ KR + ++RIQ G ++ 
Sbjct: 1   MRQITVGKNDAGQRLDKFLTKTYTKLPQSMLYKGIRTKNIKLNGKRCQISSRIQEGDIIS 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          +KE+    +               +YED  I + NK  G+ V       
Sbjct: 61  LY---------LKEEFFEQTPTEYDFLKAPKVVDCVYEDENILLLNKKPGLLVHPDEN-- 109

Query: 127 YHIDGF---LKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           YH D     ++ ++  KG+          P L +R+D+ TSGI++ A+   A + L +  
Sbjct: 110 YHFDSLIARVQHYLYEKGEYQPQNENSFAPALVNRIDRNTSGIVIAAKNAEALRILNDKM 169

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R + K Y  +V G  + K + +  +L K      + V++  +   GA    + ++ + 
Sbjct: 170 RKRELHKYYLCVVHGKMEKKSDLLVGYLEKNE--SKNRVYISARPFPGAKTIQTKYRTLQ 227

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              +K+  LE+   TGRTHQ+R H   +G P+VGD KY  N +   +      L  +   
Sbjct: 228 -QKEKYSLLEVDLLTGRTHQIRAHMASIGHPLVGDGKYGKNTQNRESRYKWQALCSYKLV 286

Query: 295 MDL 297
            D 
Sbjct: 287 FDF 289


>gi|218886014|ref|YP_002435335.1| pseudouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|218756968|gb|ACL07867.1| pseudouridine synthase, RluA family [Desulfovibrio vulgaris str.
           'Miyazaki F']
          Length = 558

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 85/364 (23%), Positives = 150/364 (41%), Gaps = 45/364 (12%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPH----------INFVNLQKILRSGQVRVDKKRVK 54
           T      V  +    RLDR+  +              ++   +++ +R G   V  +   
Sbjct: 11  TRTHSFTVAPEHAGQRLDRFLGDAMAEQRERDGHGDAVSREKVKRAIRDGAATVQGRACT 70

Query: 55  -FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
             N R++ GQ V +   + A     ++  +                 +LY D+ I V +K
Sbjct: 71  VPNTRVEPGQTVTLTLAVPAAKVTPEDGDLA----------------VLYRDAAIAVLDK 114

Query: 114 PAGISVQGGS-----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           PAG++V          + + +          +G +P + HR+D++TSG+L+VA T A   
Sbjct: 115 PAGLTVHPCPSCPEGTLVHRLVRHFPELAAQEGFRPGIVHRIDKDTSGLLLVALTEAVRL 174

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            L+ +F  R++ K Y +LV G+PK + E      + +  +    + VV +N +G   A S
Sbjct: 175 ELSRAFAERQVHKEYLALVHGVPKAQGEL--EAPIGRHPLHKVKMAVVPEN-RGGKPARS 231

Query: 229 HFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----FKGNFTSP 283
            ++V+       F  + ++  TGRTHQ+RVH  H+G P+  D  Y  +            
Sbjct: 232 AWRVLLADPDGRFALVAVRIFTGRTHQIRVHMAHLGHPLWQDAVYGPSEAVAPAAGELPD 291

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECK 342
              +  LHA  +   HPE  R +  T P P        +L  +  R +    +     C 
Sbjct: 292 FPPRQMLHAWRLSFRHPETDRDMHFTCPPPPDFA----ALALRLSRRMQRVVVTGSPGCG 347

Query: 343 QNIL 346
           ++ L
Sbjct: 348 KSAL 351


>gi|220917166|ref|YP_002492470.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219955020|gb|ACL65404.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 352

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 79/335 (23%), Positives = 138/335 (41%), Gaps = 39/335 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V  +    RLD       P ++   +Q+++ +G V+VD +  K + R++ G+ + +
Sbjct: 24  RTLHVPPELAGTRLDAALVRLAPDLSRARVQRLVEAGLVQVDGRGAKASARLRGGEAIAL 83

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           L         +  L   +L+ED+ + V +K  G+ V    G  +
Sbjct: 84  E---------------LPPPEPSGLVAQDLPLAVLHEDADLIVLDKAPGMVVHPARGTPH 128

Query: 128 HI--DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +  L           D    +  L HRLD++TSG LVVA+T AA   L   ++ R 
Sbjct: 129 STVVNALLHRLGLPGAAGPDGGLPRLGLVHRLDKDTSGCLVVAKTEAALAALQAQWKGRS 188

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K+Y +L  G    +   +     +       +   V      +  A++ ++V + F  
Sbjct: 189 VEKVYLALCHGALAPE-GRLDTPYGRHPRDRLRFTGRVT----SSRRALTEWRVREAFGA 243

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NKLY 289
                E+  HTGRTHQ+RVH    G P++ D  Y    +    +P            +  
Sbjct: 244 AASLAEVTLHTGRTHQIRVHLSEAGHPLLADAVYGGTRREARLAPADPARRAAEAVGRQA 303

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           LHA  +   HP  G RL + AP+PA +    + L 
Sbjct: 304 LHALRLGFDHPRTGRRLVVEAPVPADLRAAIEILR 338


>gi|300741275|ref|ZP_07071296.1| RNA pseudouridine synthase, RluA family [Rothia dentocariosa M567]
 gi|300380460|gb|EFJ77022.1| RNA pseudouridine synthase, RluA family [Rothia dentocariosa M567]
          Length = 302

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 78/318 (24%), Positives = 143/318 (44%), Gaps = 36/318 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRV----DKKRVKFNNRIQSGQVVRIPPVINAL 74
           MRLD         I        +R G VRV    ++ ++  ++++ +G+ V +       
Sbjct: 1   MRLDAALAGAL-EIPRTRASGWIRDGHVRVVQRGNELKIGKSHKLSAGETVFVNAPAPRD 59

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
              I+ +K+                 ++Y D  I V +KPAG++     G  +H    L 
Sbjct: 60  LADIQPEKV-------------DGFGIVYCDDDIVVVDKPAGVAAHPSHG--WHGPTVLS 104

Query: 135 SWVDSK--------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +            ++  + HRLD  TSG++VVAR+  A   L  +F+ R ++K+Y +L
Sbjct: 105 ALLGEGVTVATSGAAERQGIVHRLDVGTSGLMVVARSERAYTELKRAFKDRTVEKVYHTL 164

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+P      I   + +  H G ++   V ++      +I+H++ ++ F      +E+ 
Sbjct: 165 VQGLPDPLMGTIDAPIGR--HPGHEWKFAVIED---GRSSITHYETLESFGS-ASLVEVH 218

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
             TGRTHQ+RVH   +  P  GD  Y A+ + +    +  + +LHA  +   HP  G R+
Sbjct: 219 LETGRTHQIRVHFSSLRHPCCGDLTYGADPRFSAELGL-TRQWLHAHRLGFTHPTTGERV 277

Query: 306 QITAPLPAHMVKTWDSLG 323
           +  +P P  +    ++L 
Sbjct: 278 EFESPYPQDLDYALEALR 295


>gi|254510211|ref|ZP_05122278.1| ribosomal large subunit pseudouridine synthase D [Rhodobacteraceae
           bacterium KLH11]
 gi|221533922|gb|EEE36910.1| ribosomal large subunit pseudouridine synthase D [Rhodobacteraceae
           bacterium KLH11]
          Length = 344

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 84/339 (24%), Positives = 134/339 (39%), Gaps = 50/339 (14%)

Query: 20  RLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L +++  G V VD   V     ++     + I       +
Sbjct: 17  RLDKALARDVPAEESLSRTRLARLIGEGAVTVDGAVVDDPKAKVAEDAQIAITVAEAEDS 76

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFL 133
           HI  E   LD               ++YED  + V NKPAG+ V    G      ++  L
Sbjct: 77  HIGPEDIPLD---------------VVYEDDDLIVINKPAGMVVHPAPGSPNGTLVNALL 121

Query: 134 KSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               D        ++P + HR+D+ETSG+LVVA++ AA   L   F    +++ Y ++ +
Sbjct: 122 HHCGDDLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHHGLAAQFEAHSVERYYRAVCY 181

Query: 189 GIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCF 236
           G+P      +           N +   + +        KQ     G  +A++  ++++ F
Sbjct: 182 GVPDANDPRLRGIKGVSFEPGNIMRLTTQLARHKTDRQKQAVLFHGGRHAVTRSRIVEVF 241

Query: 237 AQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------- 285
                   +E    TGRTHQ+RVH  H G  +VGD  Y    K    +            
Sbjct: 242 GNPGAISLVECWLETGRTHQIRVHMAHAGHGLVGDPVYGGKRKLAARAFAPTAVEAVQAF 301

Query: 286 NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            +  LHA  +   HP  G  L+  APLP  M +    L 
Sbjct: 302 PRQALHAAVLGFEHPVSGADLRFEAPLPEDMERLLSELR 340


>gi|50365205|ref|YP_053630.1| 23S rRNA/tRNA pseudouridine synthase [Mesoplasma florum L1]
 gi|50363761|gb|AAT75746.1| 23S rRNA/tRNA pseudouridine synthase [Mesoplasma florum L1]
          Length = 311

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 141/330 (42%), Gaps = 37/330 (11%)

Query: 12  VENDEENMRLDRWFKNHY---PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV-VRI 67
           ++ + E +RLD++  +        +   +Q +++ G V V+       N    G + + I
Sbjct: 3   IKANVEKVRLDKYLVDALAESTEYSRSYIQTLIKDGNVIVNGNVETKQNFNLIGDIEIEI 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                  + I  E+  LD               ++YED  I V NKP  + V  G+G   
Sbjct: 63  NIPEVKTSTINPEKIDLD---------------IVYEDDDILVVNKPNNMVVHPGAGNTE 107

Query: 128 HI--DGFL---KSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +  L     ++ + G  ++P + HR+D++T+G+L+VA+   + Q LTE  +   I 
Sbjct: 108 GTMVNALLGRDAEFLSTIGGVERPGIVHRIDKQTTGLLIVAKNDKSHQVLTEMLKNHEIY 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LVWG  K  K  I   + +  +     +       K + YA+++F+VI     K 
Sbjct: 168 KEYVALVWGEIKEDKGIIDAPIGRHQNDRKKMM----VTSKNSKYAVTNFEVIKRL-DKT 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             ++    TGRTHQ+RVH   +  PIV D  Y    +            LHA  ++  HP
Sbjct: 223 TLVKCAIETGRTHQIRVHFNFIKHPIVNDPSYGKLAEKQTDF----GQMLHAYKLEFLHP 278

Query: 301 EGGRL-QITAPLPAHMV-KTWDSLGFKYDR 328
               + ++ A LP     K     G + D 
Sbjct: 279 ITKEMVKLKAELPKEFTDKILQEGGVENDW 308


>gi|239978958|ref|ZP_04701482.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces albus J1074]
 gi|291450838|ref|ZP_06590228.1| ribosomal large subunit pseudouridine synthase [Streptomyces albus
           J1074]
 gi|291353787|gb|EFE80689.1| ribosomal large subunit pseudouridine synthase [Streptomyces albus
           J1074]
          Length = 314

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 79/335 (23%), Positives = 141/335 (42%), Gaps = 30/335 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVLVDGAAVGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPAAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIVKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L + 
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKQQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R + K Y +LV G P      I   + +  H   DY   V         +++H+ +I
Sbjct: 166 FRERTVDKRYHALVQGHPDPMSGTIDAPIGR--HPQHDYKWAVTAE---GKPSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + + +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAY-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTLAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYD 327
            +   HP  G   + ++  PA +    D++  + +
Sbjct: 279 RLGFEHPADGSWAEFSSEYPADLQHALDTVRAESN 313


>gi|71891968|ref|YP_277698.1| pseudouridine synthase [Candidatus Blochmannia pennsylvanicus str.
           BPEN]
 gi|71796074|gb|AAZ40825.1| pseudouridine synthase [Candidatus Blochmannia pennsylvanicus str.
           BPEN]
          Length = 343

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 150/332 (45%), Gaps = 37/332 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           ++ ++V+  +   RLD       P+ +   ++  + S +V V+ + V     ++  G+ +
Sbjct: 27  IKPMIVQESQSGKRLDCILSELLPNYSRSKIKCWILSKKVNVNNQTVIIPKKKMMGGEFI 86

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I  ++N  N+ I  Q I                 ++YED  I V NK   + V  G+G 
Sbjct: 87  EIKDIVNIDNNNIVPQDI--------------PLDIVYEDDDIVVINKAKNMVVHPGAG- 131

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             H    L + +          +  +  RLD++T+G++VVA+   A   L   F+ R+I 
Sbjct: 132 -NHSGTILNALLYKYPAITEVFRSGIVQRLDKDTTGLMVVAKNMIAYHSLLRLFKKRKII 190

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++V G   + +  I N  +++  +    + V          AI+H+ +I+ F   +
Sbjct: 191 REYEAVVLGNFLHNEGTI-NQPIRRHAVHRTRMTVNPM----GKSAITHYSIIESFG-MY 244

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--------NFKGNFTSPIQNKLYLHA 292
             + ++  TGRTHQ+RVH  ++  P++GDHKY          +   N    + N+  LHA
Sbjct: 245 TRIRVRLETGRTHQIRVHMAYINHPLLGDHKYGKSTYFIKGISDTVNDCLHVLNRQALHA 304

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
             + L HP    +++   PLP  ++K  + L 
Sbjct: 305 ATLQLCHPITRIKMKWDVPLPKDIIKLINILR 336


>gi|50955140|ref|YP_062428.1| ribosomal large subunit pseudouridine synthase [Leifsonia xyli
           subsp. xyli str. CTCB07]
 gi|50951622|gb|AAT89323.1| ribosomal large subunit pseudouridine synthase [Leifsonia xyli
           subsp. xyli str. CTCB07]
          Length = 306

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 77/323 (23%), Positives = 135/323 (41%), Gaps = 29/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   + +    +R+D          +     ++  SG V VD +    ++R+ +G  + +
Sbjct: 4   RSFPIPDGLGGVRVDAGLAKLL-GFSRSFAAEVAESGGVTVDGREAGKSDRLPAGSWLDV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                      +E +I+   V+        +  +++ED  I V +KPAG++     G   
Sbjct: 63  TWQPR------EEPRIVPIVVS--------ELTIVHEDDDIVVLDKPAGVAAHPSIGWEG 108

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  + HRLD  TSG++VVA++  A   L  +F  R ++K
Sbjct: 109 PTVLGALAAAGFRISTSGAPERAGIVHRLDAGTSGLMVVAKSEHAYTVLKRAFHDRTVEK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY ++V G P      I   + +       +  V      G   +++H++ I+ F     
Sbjct: 169 IYHAVVQGHPDPLTGTIDAPIGRHPKSDWRFAVVA-----GGKPSVTHYETIEAFP-AAS 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE+   TGRTHQ+RVH      P VGD  Y A+   +    +  + +LHA  +   HP 
Sbjct: 223 LLEIHLETGRTHQIRVHMSAQRHPCVGDAMYGADPTLSARLGL-TRQWLHAVQLAFAHPA 281

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            G  +  T   PA      D L 
Sbjct: 282 TGEWVTFTTAYPADFRNALDILR 304


>gi|307297424|ref|ZP_07577230.1| pseudouridine synthase, RluA family [Thermotogales bacterium
           mesG1.Ag.4.2]
 gi|306916684|gb|EFN47066.1| pseudouridine synthase, RluA family [Thermotogales bacterium
           mesG1.Ag.4.2]
          Length = 310

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 74/324 (22%), Positives = 144/324 (44%), Gaps = 30/324 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +Q ++V + E+  RLD+      P   +   +Q+ +++ +V V+ +  K + +++ G+ +
Sbjct: 2   LQEIIVSSREDGWRLDKVVVEKAPPWVSRTFVQRQIKNSKVFVNSRPRKPSYKVKIGESI 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GS 123
                            + +     +   + +   +++ED  I V NK  GI V      
Sbjct: 62  TF--------------DLPEKPKVASVEPEAIPLKIVFEDRDIIVVNKDPGIIVHPLPRK 107

Query: 124 GIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++  L    D +G     +P + HRLD++TSGI++VA+   A   L+  F+ R  
Sbjct: 108 QTGTLVNALLYHCKDLQGIGGVTRPGIVHRLDKDTSGIIIVAKNDLAHVSLSSQFKSRLT 167

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G      +   ++ + +  +    + V     +    ++++F+ +  F+  
Sbjct: 168 AKEYIALVRGKTPPFGKI--DYSIARHPVNRLKMSV----NENGKESLTYFQTLSNFSSI 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + ++P TGRTHQ+RVH    G P++GD  Y    +         +  LHA  + + H
Sbjct: 222 ASLIIVRPRTGRTHQIRVHMKEKGFPLLGDAVYGKAREDEI--FGIKRQMLHAMKLTVSH 279

Query: 300 PEGG-RLQITAPLPAHMVKTWDSL 322
           P  G R+   A LP  M +   +L
Sbjct: 280 PRSGIRMTFIARLPEDMKEAIVNL 303


>gi|289426144|ref|ZP_06427890.1| pseudouridine synthase, RluA family [Propionibacterium acnes SK187]
 gi|289153309|gb|EFD02024.1| pseudouridine synthase, RluA family [Propionibacterium acnes SK187]
          Length = 306

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 138/322 (42%), Gaps = 29/322 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +  ++V +  +  R+D         ++   +  ++  G V +D ++V + + R+ +GQ++
Sbjct: 1   MSVLLVPDGLDGERVDVA-AARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQML 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +          I  Q +               + ++++DS I V +KPAG++     G 
Sbjct: 60  DVDLCDPVATPSITPQIVE-------------GTRIIHDDSDIVVVDKPAGVAAHPSLGW 106

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + +              ++  +  RLD  TSG++VVA++  A   L ++FR R +
Sbjct: 107 EGPSVVEHLAAAGFAISTSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y +LV G P      I   + +          V      G  ++++H++ ++ F + 
Sbjct: 167 DKVYLALVQGHPDPFTGTIDAPIGRDHRHDWKMAIV-----DGGRHSVTHYETVEAF-RH 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L++   TGRTHQ+RVH   +  P  GD  Y  +        ++ + +LHA  +   H
Sbjct: 221 ATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLYGCDPALAKELGLE-RQWLHAGELSFTH 279

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  +   A LPA +    D
Sbjct: 280 PGSGEWVTFHADLPADLQNALD 301


>gi|302533940|ref|ZP_07286282.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp. C]
 gi|302442835|gb|EFL14651.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp. C]
          Length = 313

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 78/332 (23%), Positives = 136/332 (40%), Gaps = 28/332 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++   G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAIARMF-GFSRTKAAELAAEGKVSVDGSVVGKSERVH 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +            E       V L          ++++D  + V  KP G++  
Sbjct: 60  GGAWLEV------------EMPAPPRPVELVAEP-VPGMEIIHDDDDVVVIMKPVGVAAH 106

Query: 121 GGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G     + G L +           ++  + HRLD  TSG++ VA++  A   L   F
Sbjct: 107 PSPGWTGTTVIGGLAAAGYRISTSGASERQGIVHRLDVGTSGLMAVAKSERAYTSLKNQF 166

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R + K Y +LV G P      I   + +  H   DY   V Q+      +++H+ +I+
Sbjct: 167 RERVVDKRYHALVQGHPDPMSGTIDAPIGR--HPSADYKWAVTQD---GKASVTHYDLIE 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F +    L+++  TGRTHQ+RVH      P VGD  Y A+           + +LHA  
Sbjct: 222 AF-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPT-VAKRLGLTRQWLHAVR 279

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +   HP  G+ ++  +  PA +    D +  +
Sbjct: 280 LGFEHPADGQWVEFESGYPADLQHALDVIRAE 311


>gi|217978454|ref|YP_002362601.1| pseudouridine synthase, RluA family [Methylocella silvestris BL2]
 gi|217503830|gb|ACK51239.1| pseudouridine synthase, RluA family [Methylocella silvestris BL2]
          Length = 342

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 78/343 (22%), Positives = 137/343 (39%), Gaps = 44/343 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYP----HINFVNLQKILRSGQVRVDKKRVK-FNNRIQS 61
           V    V       RLDR+           ++   L+ ++  G V V+   V   +  +++
Sbjct: 15  VHSFAVAPGRAGERLDRFLAAETAAAGADLSRTRLKTLIEGGHVSVNGVIVTEASFAVRA 74

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           GQ                    +  +       + +   + +ED  + V +KPAG+ V  
Sbjct: 75  GQ---------------ALAVAVPPAAEPIPAGEAIALDIRFEDEHLLVLDKPAGLVVHP 119

Query: 122 GSGIA--YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G+G      ++  +    DS       ++P + HRLD++TSG++VVA+T  A Q L   F
Sbjct: 120 GAGHESGTLVNALIAHCGDSLSGIGGVKRPGIVHRLDKDTSGLMVVAKTDRAHQGLARLF 179

Query: 175 RMRR----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
                   + + Y + VWG P      +   L +   +  + + +V         A++H+
Sbjct: 180 ADHGRTLPLLREYLAFVWGAPDRASGLVDAPLGRH-PVDREKIAIVAAAR--GRRAVTHW 236

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP------- 283
           ++++    +   L  +  TGRTHQ+RVH   +G P++GD  Y   FK             
Sbjct: 237 RLLEQLGPEVAALACRLETGRTHQIRVHMASLGWPLLGDPVYGRGFKTKAGRLPPEAQAA 296

Query: 284 --IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
                +  LHAR +   HP  G  L   +  P  M +   +L 
Sbjct: 297 LIALGRQALHARALGFEHPVTGAALAFESDPPPDMAELQAALR 339


>gi|237756115|ref|ZP_04584689.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium yellowstonense SS-5]
 gi|237691719|gb|EEP60753.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium yellowstonense SS-5]
          Length = 318

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 84/336 (25%), Positives = 144/336 (42%), Gaps = 37/336 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M  +    VE +  N RLD++    YP  +    Q ++ +G V +D   VK  + ++++G
Sbjct: 1   MEEIISFKVEEEFSNKRLDQFLALVYPEYSRSFYQNLIENGFVLLDNSPVKKPSTKVKTG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
           Q   I         I  E   L+               + YED  + V  KP G+ V   
Sbjct: 61  QEFTIIIPPPEPLEIEPENIPLE---------------ICYEDEDLAVVYKPPGMVVHPS 105

Query: 122 -GSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++  L  + +       ++  + HRLD++T+G+L+VA+T  A + L + F+ 
Sbjct: 106 VGHTSGTLVNALLYHFKNVSQYQGKERAGIVHRLDKDTAGLLIVAKTEFAHKELQKMFQD 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I K Y ++V GI K     I   + + S      +  V  N K    A++ + V   F
Sbjct: 166 REIDKKYKAIVSGIVKKDHGLIDLPIGR-SIYNRQKMGTVSTNLKD---ALTEYWVEKRF 221

Query: 237 A-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLH- 291
                  ++++ HTGRTHQ+RVH   +G P+  D  Y    +N        + +KL  H 
Sbjct: 222 EKHNLTLVDIKLHTGRTHQIRVHFSAIGHPLFNDFVYGFKKSNLSSELAKNLSDKLNYHA 281

Query: 292 --ARYMDLPHPEGGRL---QITAPLPAHMVKTWDSL 322
             A  +   HP   ++   ++ + LP  + +    L
Sbjct: 282 LVAYKLTFRHPRTSQILNVELKS-LPKEIEEILQEL 316


>gi|73667158|ref|YP_303174.1| ribosomal large subunit pseudouridine synthase D [Ehrlichia canis
           str. Jake]
 gi|72394299|gb|AAZ68576.1| ribosomal large subunit pseudouridine synthase D [Ehrlichia canis
           str. Jake]
          Length = 323

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 79/331 (23%), Positives = 149/331 (45%), Gaps = 32/331 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVR 66
           + + ++ +E N RLD+   N   + +   +Q++++  +V + +      N+  +   +  
Sbjct: 4   KKIFIKIEEANNRLDKLIANKL-NTSRNQVQQLIKDSKVSLFNNIITDNNHTTKVNDIYI 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I      +++ I               +  +   +LYED  I + NK +GI+V  G+G  
Sbjct: 63  INIPTKEISNTI-------------IPNHSIPISVLYEDHDIIIINKTSGITVHPGAGTK 109

Query: 127 YHI--DGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            +   +  +  + ++     K  +P + HRLD++TSG++V+A+   +   L+E    ++I
Sbjct: 110 NNTLVNALVAHYGNALSTVGKATRPGIIHRLDKDTSGLMVIAKNEKSYYFLSELLLKKQI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++VWG P  K   I N++  K       +  V         AI+ +K    F+  
Sbjct: 170 KKEYLAVVWGSPNPKNNTIQNYICVKP--NNKQMMAVTHLSHKGKLAITEYKTKQNFSNI 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQNKLYLHA 292
              ++ + HTGRTHQ+RVH  H+G  I+GD KY  N        K +       +  LHA
Sbjct: 228 ASLIKCRIHTGRTHQIRVHMSHIGNSIIGDQKYGKNNSKITKYAKQSTIINTLKRQALHA 287

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
             +   HP     ++  A +P  +    + L
Sbjct: 288 YKLGFIHPTKNTYIEFRADIPHDIQTLINEL 318


>gi|88608500|ref|YP_506438.1| ribosomal large subunit pseudouridine synthase C [Neorickettsia
           sennetsu str. Miyayama]
 gi|88600669|gb|ABD46137.1| ribosomal large subunit pseudouridine synthase C [Neorickettsia
           sennetsu str. Miyayama]
          Length = 305

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 95/313 (30%), Positives = 152/313 (48%), Gaps = 11/313 (3%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +VEND    RLD++ ++ +       LQK LR   VR++   VK +  +  G  + 
Sbjct: 1   MRSFIVEND--CRRLDKYLRDTFGQFPQSALQKALRKKAVRLNNSVVKASAAVLKGDSLT 58

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +    +E     S V  +K  +F+ S++LYED  +   +KP G  VQ G GI 
Sbjct: 59  LSANFLQILSSPREIPSDSSKVVDSKFVEFIASLMLYEDENVLAISKPFGFPVQSGYGIT 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             ID  +KS       + R+ HRLD+ T+G+L+ A+T  AA+ L   F  R ++K Y ++
Sbjct: 119 ASIDNAMKS----INPEYRVVHRLDKHTTGVLIFAKTLDAARELWRLFSNRLVKKSYLAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K KK  +  ++ K    G + +     N     +AI+ F VI  F +    +E+ 
Sbjct: 175 VIGELKEKKGVVDCYINKVLFKGEEVMQC--NNIGNGEHAITQFHVIKKF-KNTSLIELF 231

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P TGR HQ+R     +G P++ D KY    K      +  KL LHA  ++     G  ++
Sbjct: 232 PLTGRKHQIRSQMASIGHPVLNDGKYG-RRKAFLEWSVNKKLCLHACEIEFE-LFGKVIK 289

Query: 307 ITAPLPAHMVKTW 319
           +TA LP H  +  
Sbjct: 290 VTAELPVHFAENL 302


>gi|313813196|gb|EFS50910.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL025PA1]
          Length = 306

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 137/322 (42%), Gaps = 29/322 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +  ++V +  +  R+D         ++   +  ++  G V +D ++V + + R+ +GQ++
Sbjct: 1   MSVLLVPDGLDGERVDVA-AARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQML 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +          I  Q +                 ++++DS I V +KPAG++     G 
Sbjct: 60  DVDLCDPVATPSITPQIVE-------------GMWIIHDDSDIVVVDKPAGVAAHPSLGW 106

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + +              ++  +  RLD  TSG++VVA++  A   L ++FR R +
Sbjct: 107 EGPSVVEHLAAAGFAISTSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y +LV G P      I   + +          V      G  ++++H++ ++ F + 
Sbjct: 167 DKVYLALVQGHPDPFTGTIDAPIGRDHRHDWKMAIV-----DGGRHSVTHYETVEAF-RH 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L++   TGRTHQ+RVH   +  P  GD  Y  +        ++ + +LHA  +   H
Sbjct: 221 ATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLYGCDPALAKELGLE-RQWLHAGELSFTH 279

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  +   A LPA +    D
Sbjct: 280 PGSGEWVTFHADLPADLQNALD 301


>gi|119505582|ref|ZP_01627653.1| pseudouridine synthase [marine gamma proteobacterium HTCC2080]
 gi|119458525|gb|EAW39629.1| pseudouridine synthase [marine gamma proteobacterium HTCC2080]
          Length = 324

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 74/324 (22%), Positives = 137/324 (42%), Gaps = 34/324 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  +    R D+     +P  +   LQ  + +G + +D    +  +++  GQ++ +   +
Sbjct: 15  ISRELHGSRFDQAAATLFPEFSRSRLQSYIGAGTLTLDGHAARAKDKVAQGQLLVLAAAV 74

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
                   + + LD               +++ED  + V NKPAG+ V   +G A   + 
Sbjct: 75  EPAVSWSGDSRPLD---------------IIFEDEHVLVVNKPAGVVVHPAAGHADGTLV 119

Query: 131 GFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             L  +     Q PR  + HRLD++T+GI+ VAR+  A Q L +    R ++++Y ++  
Sbjct: 120 NSLIGYAPELEQLPRGGIVHRLDKDTTGIMFVARSYLAHQSLVKQLAARSVKRVYAAVCR 179

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        +   + + S +       V     G   AI+H+++ + F        +   
Sbjct: 180 GALSG-GGSVDAPIGRHSSVRTRMAVTV-----GGKPAITHYRIAERFKHHTALS-VSLE 232

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP 300
           TGRTHQ+RVH      P++GD  Y    +    +  +        ++  LHA+ +   HP
Sbjct: 233 TGRTHQIRVHLASRNNPLIGDPVYGGRPRPPAAASTELQTMLRTFSRQALHAQTLAFDHP 292

Query: 301 EGG-RLQITAPLPAHMVKTWDSLG 323
             G R Q   PLP  +++    L 
Sbjct: 293 ATGQRCQFETPLPEDLLQLLSVLR 316


>gi|313791774|gb|EFS39885.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL110PA1]
 gi|313802139|gb|EFS43371.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL110PA2]
 gi|313838471|gb|EFS76185.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL086PA1]
 gi|314963072|gb|EFT07172.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL082PA1]
 gi|315077536|gb|EFT49594.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL053PA2]
 gi|315080320|gb|EFT52296.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL078PA1]
 gi|327452876|gb|EGE99530.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL092PA1]
          Length = 306

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 138/322 (42%), Gaps = 29/322 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +  ++V +  +  R+D         ++   +  ++  G V +D ++V + + R+ +GQ++
Sbjct: 1   MSVLLVPDGLDGERVDVA-AARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQML 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +      +   I  Q +                 ++++DS I V +KPAG++     G 
Sbjct: 60  DVDLCDPVVTPSITPQIVE-------------GMRIIHDDSDIVVVDKPAGVAAHPSLGW 106

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + +              ++  +  RLD  TSG++VVA++  A   L ++FR R +
Sbjct: 107 EGPSVVEHLAAAGFAISTSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y +LV G P      I   + +          V      G  ++++H++ ++ F + 
Sbjct: 167 DKVYLALVQGHPDPFTGTIDAPIGRDHRHDWKMAIV-----DGGRHSVTHYETVEAF-RH 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L++   TGRTHQ+RVH   +  P  GD  Y  +        ++ + +LHA  +   H
Sbjct: 221 ATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLYGCDPALAKELGLE-RQWLHAGELSFTH 279

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  +   A LPA +    D
Sbjct: 280 PGSGEWVTFHADLPADLQNALD 301


>gi|294678331|ref|YP_003578946.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           capsulatus SB 1003]
 gi|294477151|gb|ADE86539.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           capsulatus SB 1003]
          Length = 347

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 78/357 (21%), Positives = 137/357 (38%), Gaps = 50/357 (14%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVKF- 55
           MS +  ++  + +  D    RLD+      P    ++   L +++  G V  D   +   
Sbjct: 1   MSDIAAHLLRIEIGEDPA-ERLDKALAALVPEEAALSRSRLARLIAEGAVTRDGVAITDQ 59

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
             ++  G+V  I                ++    +   +  +   +L+ED  + V +KPA
Sbjct: 60  KAKVAPGEVYMI---------------AVEPPRAVETLAQDIPLTVLWEDEDLIVIDKPA 104

Query: 116 GISVQGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQ 168
           G+ V    G      ++  L  +           +P + HR+D+ETSG+LVVA++  A  
Sbjct: 105 GMVVHPAPGSEDGTLVNALLHHFGGRLSGIGGEARPGIVHRIDKETSGLLVVAKSDRAHH 164

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK----------SHIGGDYVHVVKQ 218
            L   F    + + Y +LV G+P      +                 S +        +Q
Sbjct: 165 GLAAQFEKHTVHRHYTALVQGVPSAADPRLRGIRGVNFEQGGILKITSQLARHPTDRQRQ 224

Query: 219 NE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                G  +A++  + ++ F      ++    TGRTHQ+RVH  H+G  +VGD  Y    
Sbjct: 225 AVLFTGGRHAVTRARTVEAFGGVAALMDCWLETGRTHQIRVHMAHVGHGLVGDPTYGGKR 284

Query: 277 KGNFTSPIQ---------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           K +  +             +  LHA  +   HP  G  L  T+PLP        +L 
Sbjct: 285 KLSVRAVGAAAAEAVANFPRQALHATTLGFTHPVTGEELSFTSPLPEDFEALLATLR 341


>gi|85057870|ref|YP_456786.1| ribosomal large subunit pseudouridine synthase D [Aster yellows
           witches'-broom phytoplasma AYWB]
 gi|84789975|gb|ABC65707.1| ribosomal large subunit pseudouridine synthase D [Aster yellows
           witches'-broom phytoplasma AYWB]
          Length = 306

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 87/325 (26%), Positives = 146/325 (44%), Gaps = 32/325 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +  ++   E   RLD +   H  ++N    QK++ + QV V+ K  K +  ++   
Sbjct: 1   MNEKKEFLISASEAFQRLDHFLSAHI-NLNKSQCQKLILAQQVLVNTKSSKKSYLLKPQD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ +                   S+NL +    L   ++YED  + V NKPA + V    
Sbjct: 60  LITVIIPQTH------------ESINL-QTPQNLNLDIIYEDPYLAVINKPANLVVHPSL 106

Query: 124 GIAYHI--DGFLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                   +G L           Q+P + HRLD+ T+G+L+VA+T   +  L  +F+ R+
Sbjct: 107 SFQKTTLVNGLLHQFNTLSHIDTQRPGIVHRLDKNTTGLLIVAKTNDVSDKLQIAFQQRK 166

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I KIYW+L+ G  +  K  I   + + +H       +          A++HFK +  F+ 
Sbjct: 167 ITKIYWALIEGFLE-DKGIIKLPIGRNNHNRLKMQVM-----PDGKTAVTHFKTLQRFSH 220

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F  +E    TGRTHQLR H   +  PIVGD  Y +    +  +P+    +LH++ +   
Sbjct: 221 -FSLMECNLETGRTHQLRAHFSFLKHPIVGDLLYDS---SHHITPL--GQFLHSKILKFN 274

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP   + L + APLP +  K   + 
Sbjct: 275 HPITNQNLILEAPLPTNFEKLLKTF 299


>gi|320531632|ref|ZP_08032574.1| pseudouridine synthase, RluA family [Actinomyces sp. oral taxon 171
           str. F0337]
 gi|320136161|gb|EFW28167.1| pseudouridine synthase, RluA family [Actinomyces sp. oral taxon 171
           str. F0337]
          Length = 306

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 79/331 (23%), Positives = 145/331 (43%), Gaps = 33/331 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS     + + V +  +  R+D         ++   +  +  +G VR + + +  + R+ 
Sbjct: 1   MST----RLLPVPDGFDGERVDAALAR-MTGLSRSRVGDLCEAGGVRRNGEDLAKSARLH 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+++ +          + + + ++      +  +     LLYED  I V +KPAG++  
Sbjct: 56  AGELLEVD---------LPDPRPVEPVATPVEGME-----LLYEDEDIVVVDKPAGVAAH 101

Query: 121 GGSG-IAYHIDGFLKSWV-----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G     + G LK+           ++  +  RLD  TSG+++VA+   A   L  +F
Sbjct: 102 PSMGWDGPDVLGALKAMRVRVATSGAAERQGIVSRLDVGTSGVMIVAKGERAYSVLKRAF 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R   + K+Y +LV G        I   + +  H   ++   +    +G   +I+H+ VI+
Sbjct: 162 REHTVDKVYHALVQGHLDPSSGTIEAPIGR--HPSREWKMAII---EGGRESITHYDVIE 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                 C  E+   TGRTHQ+RVH   +G P VGD  Y A+      + +  + +LHAR 
Sbjct: 217 AMP-GACLAEIHLETGRTHQIRVHMAAVGHPCVGDATYGADPAMTARTGLI-RQWLHARE 274

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           + + HP  G  +  T+  PA +    D L  
Sbjct: 275 LGIAHPITGEHMVFTSGYPADLTHALDVLRL 305


>gi|15604676|ref|NP_221194.1| pseudouridylate synthase [Rickettsia prowazekii str. Madrid E]
 gi|3861371|emb|CAA15270.1| SFHB PROTEIN HOMOLOG (sfhB) [Rickettsia prowazekii]
 gi|292572507|gb|ADE30422.1| Ribosomal large subunit pseudouridine synthases RluD subfamily
           protein [Rickettsia prowazekii Rp22]
          Length = 313

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/327 (21%), Positives = 140/327 (42%), Gaps = 40/327 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPV 70
           V  +  N RLD+        ++   +QK +++  V+V+   +  ++  ++    +     
Sbjct: 6   VPKELNNTRLDKALSLLLKKVSRNQVQKAIKNYCVQVNGVIISDSDVLVKENDTILFSFK 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                              L   +  +   ++YED  + V NK AG++V    GI +H +
Sbjct: 66  ---------------EPEELKITAANITLDIIYEDDDLIVINKAAGMTVHP--GIRHHDN 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD++T+G++VVA+       L    + R++ + 
Sbjct: 109 TLVNALLHHTKYLSDIGSAERPGIVHRLDKDTTGLMVVAKNNKTHILLANQIKQRQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFC 241
           Y +LVWG+    +  I N  + ++      + ++K    G   A++++K ++  +     
Sbjct: 169 YKALVWGVINPLEGIIKN-NVGRNRNNRKKMTILKY---GGKKAVTYYKTLELFYGGTLS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +E +  TGRTHQ+RV   ++   +VGD  Y  N +    SP +         +  LH+ 
Sbjct: 225 MVECKLSTGRTHQIRVQLSNLKHSVVGDQTYGNNNRKIINSPPKLKAKLIAFKRQALHSW 284

Query: 294 YMDLPHPEGGRLQ-ITAPLPAHMVKTW 319
           Y+   HP    +   +  LP  M +  
Sbjct: 285 YLSFTHPTSNDIMAFSCELPRDMQEII 311


>gi|289426834|ref|ZP_06428560.1| pseudouridine synthase, RluA family [Propionibacterium acnes J165]
 gi|295130343|ref|YP_003581006.1| Ribosomal large subunit pseudouridine synthase D [Propionibacterium
           acnes SK137]
 gi|289159923|gb|EFD08101.1| pseudouridine synthase, RluA family [Propionibacterium acnes J165]
 gi|291376668|gb|ADE00523.1| Ribosomal large subunit pseudouridine synthase D [Propionibacterium
           acnes SK137]
 gi|313772526|gb|EFS38492.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL074PA1]
 gi|313807256|gb|EFS45743.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL087PA2]
 gi|313809762|gb|EFS47483.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL083PA1]
 gi|313818302|gb|EFS56016.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL046PA2]
 gi|313820064|gb|EFS57778.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL036PA1]
 gi|313823127|gb|EFS60841.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL036PA2]
 gi|313825596|gb|EFS63310.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL063PA1]
 gi|313830671|gb|EFS68385.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL007PA1]
 gi|313833891|gb|EFS71605.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL056PA1]
 gi|314925486|gb|EFS89317.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL036PA3]
 gi|314960263|gb|EFT04365.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL002PA2]
 gi|314968093|gb|EFT12192.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL037PA1]
 gi|314973673|gb|EFT17769.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL053PA1]
 gi|314976266|gb|EFT20361.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL045PA1]
 gi|314978249|gb|EFT22343.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL072PA2]
 gi|314983525|gb|EFT27617.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL005PA1]
 gi|314987713|gb|EFT31804.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL005PA2]
 gi|314990192|gb|EFT34283.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL005PA3]
 gi|315084579|gb|EFT56555.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL027PA2]
 gi|315085915|gb|EFT57891.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL002PA3]
 gi|315088667|gb|EFT60643.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL072PA1]
 gi|315096293|gb|EFT68269.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL038PA1]
 gi|327325929|gb|EGE67719.1| RNA pseudouridine synthase, RluA family [Propionibacterium acnes
           HL096PA2]
 gi|327330628|gb|EGE72374.1| RNA pseudouridine synthase, RluA family [Propionibacterium acnes
           HL097PA1]
 gi|327332198|gb|EGE73935.1| RNA pseudouridine synthase, RluA family [Propionibacterium acnes
           HL096PA3]
 gi|327442820|gb|EGE89474.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL013PA2]
 gi|327446191|gb|EGE92845.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL043PA2]
 gi|327447826|gb|EGE94480.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL043PA1]
 gi|328753730|gb|EGF67346.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL020PA1]
 gi|328760574|gb|EGF74142.1| RNA pseudouridine synthase, RluA family [Propionibacterium acnes
           HL099PA1]
 gi|332675185|gb|AEE72001.1| pseudouridylate synthase [Propionibacterium acnes 266]
          Length = 306

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 137/322 (42%), Gaps = 29/322 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +  ++V +  +  R+D         ++   +  ++  G V +D ++V + + R+ +GQ++
Sbjct: 1   MSVLLVPDGLDGERVDVA-AARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQML 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +          I  Q +                 ++++DS I V +KPAG++     G 
Sbjct: 60  DVDLCDPVATPSITPQIVE-------------GMRIIHDDSDIVVVDKPAGVAAHPSLGW 106

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + +              ++  +  RLD  TSG++VVA++  A   L ++FR R +
Sbjct: 107 EGPSVVEHLAAAGFAISTSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y +LV G P      I   + +          V      G  ++++H++ ++ F + 
Sbjct: 167 DKVYLALVQGHPDPFTGTIDAPIGRDHRHDWKMAIV-----DGGRHSVTHYETVEAF-RH 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L++   TGRTHQ+RVH   +  P  GD  Y  +        ++ + +LHA  +   H
Sbjct: 221 ATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLYGCDPALAKELGLE-RQWLHAGELSFTH 279

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  +   A LPA +    D
Sbjct: 280 PGSGEWVTFHADLPADLQNALD 301


>gi|148978562|ref|ZP_01815014.1| 23S rRNA pseudouridine synthase D [Vibrionales bacterium SWAT-3]
 gi|145962351|gb|EDK27632.1| 23S rRNA pseudouridine synthase D [Vibrionales bacterium SWAT-3]
          Length = 324

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/334 (20%), Positives = 143/334 (42%), Gaps = 35/334 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   +++ L  G+V+VD + + K   ++  G+ + +  
Sbjct: 10  TVKSSQLGQRLDQAVAELFTDFSRSRIKEWLLDGKVQVDGEVITKPRVKVMGGEEIILQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   +++ED  + V NKP    V  G+G     
Sbjct: 70  ELEDEERW---------------EAQDIPLDIVFEDEHLLVINKPRDFVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  +   RRI + Y ++
Sbjct: 115 VLNALLHHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + +         +    +    A++H++V + F ++   + ++
Sbjct: 175 AIGKM-TAGGMVEKGISRHAT-----KRTLMAVNETGKPAVTHYRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDIAYGGRARIPKGASEELTKMIRAFDRQALHAVMLKFV 287

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLY 331
           HP  G  ++  AP+P  MV   ++L      NL 
Sbjct: 288 HPITGEEVEFHAPVPNDMVVMAEALRVDARDNLE 321


>gi|226356664|ref|YP_002786404.1| ribosomal large subunit pseudouridine synthase D [Deinococcus
           deserti VCD115]
 gi|226318654|gb|ACO46650.1| putative ribosomal large subunit pseudouridine synthase D
           [Deinococcus deserti VCD115]
          Length = 321

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 135/328 (41%), Gaps = 41/328 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD          +   +   +  G V+V+ + V K + +++ G+ + + P       + 
Sbjct: 13  RLDAVLAA-LSGASRSQVAAWIAGGHVKVEGQPVTKVSLKLRGGERIDVSPPALPDARVE 71

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL--- 133
            E   LD               ++YED  +   NKP G+      G+     ++  L   
Sbjct: 72  AEDLPLD---------------VIYEDDYLIAVNKPPGMVTHPAPGVLSGTLVNALLGRM 116

Query: 134 -----KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                  +    G +P + HRLD++TSG++VVA+T  A   L  +F+ R  +K Y ++  
Sbjct: 117 PLPEQPDYDSEAGYRPGIVHRLDKDTSGVIVVAKTVGAHARLAAAFKDRETRKTYLAIAA 176

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF----CWLE 244
           G  +          + +  +    + V          A + F  +             + 
Sbjct: 177 GQWRADGPARVEAPIGRHPVQRQRMTV---GGANPREAQTLFTPLAAHPDGHGRTLALVR 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            QP TGRTHQ+RVH  H+G PI+GD  Y        +S    +  LHA ++ +PHP  GR
Sbjct: 234 AQPRTGRTHQIRVHLAHLGSPILGDAVYGR------SSETMLRHALHAHFLSVPHPGTGR 287

Query: 305 -LQITAPLPAHMVKTWDSLGFKYDRNLY 331
            L + AP P  M+  W +LG     +L 
Sbjct: 288 LLHLHAPAPDDMLNAWIALGGAMPSDLE 315


>gi|306841397|ref|ZP_07474100.1| pseudouridine synthase, RluA family [Brucella sp. BO2]
 gi|306288582|gb|EFM59931.1| pseudouridine synthase, RluA family [Brucella sp. BO2]
          Length = 294

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 79/305 (25%), Positives = 142/305 (46%), Gaps = 44/305 (14%)

Query: 47  RVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
            +D    +    +++ G  + I               +L          + +   +LYED
Sbjct: 2   TIDGAPARETKQKLREGMNIAI---------------VLPEPEPAEPQGENIPLDILYED 46

Query: 106 SKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGIL 158
             + V NKPAG+ V  G+G      ++  +    DS       ++P + HRLD++TSG++
Sbjct: 47  DDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLSGIGGIRRPGIVHRLDKDTSGVM 106

Query: 159 VVARTRAAAQHLTESFRMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           VVA+   A +HL+E F        +++ Y +LVWG+ +  +  +  +L + SH       
Sbjct: 107 VVAKNNRAHRHLSEQFADHGRTGDLERAYLALVWGMTERPQGTVDAYLGR-SHRDRTKQA 165

Query: 215 VVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           VV++  + A +AI+H+  ++ F+ +         +E +  TGRTHQ+RVH  H+G P+VG
Sbjct: 166 VVREEREDARHAITHYATVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVG 225

Query: 269 DHKYCANFK---GNFTSPIQ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           D  Y + +K        P++      ++  LHA  +   HP     ++  APLP  M + 
Sbjct: 226 DMDYGSAYKTKANKLPEPLKQAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPDDMEQL 285

Query: 319 WDSLG 323
            ++  
Sbjct: 286 LENFR 290


>gi|77462967|ref|YP_352471.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides 2.4.1]
 gi|77387385|gb|ABA78570.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides 2.4.1]
          Length = 349

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 81/344 (23%), Positives = 139/344 (40%), Gaps = 52/344 (15%)

Query: 15  DEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           ++   RLD+      P    ++   L K++  G VR++   V     ++  GQV  I   
Sbjct: 17  EDPPDRLDKALVREAPEEAALSRSRLMKLIGEGAVRLEGAPVTDPKAKVAEGQVYEI--- 73

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                        LD+   +    + +   +++ED  + V +KP G+ V    G      
Sbjct: 74  ------------ALDAPAEVEARPEAIPLSVVWEDEDLIVIDKPVGMVVHPAPGQWTGTL 121

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L    +S       ++P + HR+D++TSG+LVVA+T  A Q L   F    +++ Y
Sbjct: 122 VNALLHHCGESLSGIGGEKRPGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRY 181

Query: 184 WSLVWGIPKN-------------KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            +LV G+P+              +   +       +    D        E G  +A++  
Sbjct: 182 LALVHGVPEVSDPRLRGVRGTSFEPGGVLRIATGLARHRTDRQRQAVTFE-GGRHAVTRA 240

Query: 231 KVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
           ++++ F        +E +  TGRTHQ+RVH  H G  ++GD  Y    K +  +      
Sbjct: 241 RLLERFGMPSVLALVECRLETGRTHQIRVHMAHAGHGLIGDQTYGGRRKLSPKALGAEAA 300

Query: 286 ------NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                  +  LHA  +   HP  G  L   +PLPA M      L
Sbjct: 301 AAAEAFPRQALHAASLGFRHPVSGEELSFESPLPADMASLLSLL 344


>gi|42561113|ref|NP_975564.1| ribosomal large subunit pseudouridylate synthase D [Mycoplasma
           mycoides subsp. mycoides SC str. PG1]
 gi|42492610|emb|CAE77206.1| ribosomal large subunit pseudouridylate synthase D [Mycoplasma
           mycoides subsp. mycoides SC str. PG1]
 gi|301320622|gb|ADK69265.1| pseudouridine synthase, RluA family [Mycoplasma mycoides subsp.
           mycoides SC str. Gladysdale]
          Length = 310

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 142/319 (44%), Gaps = 36/319 (11%)

Query: 19  MRLDRWFKNHYP--HINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALN 75
           +RLD+           +   +QK+++   + V+ + +  NN  ++    + I        
Sbjct: 13  LRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITNNNFLVKPNSQITITI------ 66

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
               +  ILD ++     +D +   ++Y+D  + V NK   I+V     +    +  + +
Sbjct: 67  ----KDPILDPNL---VKNDEIDLDIIYQDDDLLVINKQNNITVHPS--LNNTNNTIVNA 117

Query: 136 WVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            + S  +        +P + HR+D++T+G+L+VA+     + L+E F+  +I K Y ++V
Sbjct: 118 LLASDVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKTHKLLSEMFKNHQIYKEYLAIV 177

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+ K  K  I   + + S      + V     K +  AI+ F+V++ F +    ++ Q 
Sbjct: 178 TGVIKPNKGLIDAPIGR-SQTDRKKMSV---TAKNSKQAITTFEVVERFFKN-TLVKCQI 232

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  ++  P++ D  Y       FT       YLHA  +   HP     ++
Sbjct: 233 QTGRTHQIRVHFNYINHPVLNDPVYGKK-HQEFTDFG---QYLHAYKLKFTHPITKKEIE 288

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           + +PLP         L  +
Sbjct: 289 LISPLPKEFDDKIKELRGE 307


>gi|86148440|ref|ZP_01066731.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp.
           MED222]
 gi|218708594|ref|YP_002416215.1| 23S rRNA pseudouridine synthase D [Vibrio splendidus LGP32]
 gi|85833794|gb|EAQ51961.1| ribosomal large subunit pseudouridine synthase D [Vibrio sp.
           MED222]
 gi|218321613|emb|CAV17565.1| ribosomal large subunit pseudouridine synthase D [Vibrio splendidus
           LGP32]
          Length = 324

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 68/334 (20%), Positives = 143/334 (42%), Gaps = 35/334 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   +++ L  G+++VD + + K    +  G+ + +  
Sbjct: 10  TVKSSQLGQRLDQAVAELFTDFSRSRIKEWLLDGKIQVDGEVITKPRTIVLGGEAIILQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  + V NKP  + V  G+G     
Sbjct: 70  ELADEERW---------------EAQDIPLDIVYEDDDLLVINKPRDLVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  +   RRI + Y ++
Sbjct: 115 ILNALLFHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + +         +    +    A++H++V + F ++   + ++
Sbjct: 175 AIGKM-TAGGVVEKGISRHAT-----KRTLMDVNELGKPAVTHYRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDIAYGGRARIPKGASEELTTMIRSFDRQALHAVMLKFV 287

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLY 331
           HP  G  ++  AP+P  MV   ++L      N+ 
Sbjct: 288 HPITGEEVEFHAPVPNDMVVMAEALRVDARENIE 321


>gi|325283365|ref|YP_004255906.1| pseudouridine synthase, RluA family [Deinococcus proteolyticus MRP]
 gi|324315174|gb|ADY26289.1| pseudouridine synthase, RluA family [Deinococcus proteolyticus MRP]
          Length = 319

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 92/345 (26%), Positives = 142/345 (41%), Gaps = 46/345 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           MT  Q           RLD          +   +   + +G+V V+ K   K +++++ G
Sbjct: 1   MTEPQQTQTYTATAG-RLDAVAAELTGE-SRSQVALWIAAGRVEVEGKAATKASHKLRGG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + + I P                   +L+   + +   +LYED  +   NKP G+     
Sbjct: 59  EALHISP---------------PPPADLSVQPEQVPLDVLYEDDALIAVNKPPGMVTHPA 103

Query: 123 SGI--AYHIDGFLKSWVDSK--------GQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
            G+     ++  L      +        G +P + HRLD++TSG++VVA+T  A   L+ 
Sbjct: 104 PGVVSGTLVNALLGRLELPQQSDHDSPAGYRPGIVHRLDKDTSGVIVVAKTVQAHAALSA 163

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY--AISHF 230
           SF+ R  QK+Y ++  G  K +           + IG   V   K    GAN   A + F
Sbjct: 164 SFKARETQKVYLAIAAGEWKAQ-----TPAKVDAPIGRHPVQRQKMTVGGANPRDAQTRF 218

Query: 231 KVIDCFAQKF----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
             +             +  +P TGRTHQ+RVH  H+G PIVGD  Y         S    
Sbjct: 219 VPLSHHPDGHGRTLALVRCEPRTGRTHQIRVHLAHLGSPIVGDAVYGRE------SQAMP 272

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           +  LHA  + LPHP     L +TAP P  ++  W +LG      L
Sbjct: 273 RQALHAWQLTLPHPVTQEPLHLTAPPPDDLLDAWVALGGHLPTEL 317


>gi|297194901|ref|ZP_06912299.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           pristinaespiralis ATCC 25486]
 gi|297152522|gb|EFH31815.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           pristinaespiralis ATCC 25486]
          Length = 313

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 79/330 (23%), Positives = 140/330 (42%), Gaps = 30/330 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V+VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVQVDGSVVGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPQAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIVKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L + 
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGASERQGIVHRLDVGTSGLMVVAKSERAYTLLKQQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R + K Y +LV G P      I   + +  H   DY   V         +++H+ +I
Sbjct: 166 FRERVVDKRYHALVQGHPDPLSGTIDAPIGR--HPTADYKWAVTAE---GKPSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAF-RAASLLDIKLETGRTHQIRVHMAAHRHPCVGDLTYGADPTMAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +   HP  G+ ++  +  P  + +  D +
Sbjct: 279 RLGFEHPSDGQWVEYESTYPDDLQQALDRI 308


>gi|320185010|gb|EFW59792.1| Ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           CDC 796-83]
 gi|332091934|gb|EGI97012.1| ribosomal large subunit pseudouridine synthase D [Shigella boydii
           3594-74]
          Length = 300

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 139/317 (43%), Gaps = 41/317 (12%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
            +P  +   +++ +   +V V+ K   K   ++  G+ V I   I        +   LD 
Sbjct: 1   MFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLD- 59

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPR 145
                         ++YED  I V NKP  + V  G+G +   +   L  +       PR
Sbjct: 60  --------------IVYEDEDIIVINKPRDLVVHPGAGNLDGTVLNALLHYYPPIADVPR 105

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIAN 200
             + HRLD++T+G++VVA+T  A   L ES + R I + Y ++  G         E I+ 
Sbjct: 106 AGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISR 165

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K++H+    +            A++H+++++ F +    L ++  TGRTHQ+RVH  
Sbjct: 166 HPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMA 215

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPL 311
           H+  P+VGD  Y    +    +           ++  LHA  + L HP  G  ++  AP+
Sbjct: 216 HITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPI 275

Query: 312 PAHMVKTWDSLGFKYDR 328
           P  MV+  + +   ++ 
Sbjct: 276 PEDMVELIEVMRADFEE 292


>gi|153853839|ref|ZP_01995195.1| hypothetical protein DORLON_01186 [Dorea longicatena DSM 13814]
 gi|149753589|gb|EDM63520.1| hypothetical protein DORLON_01186 [Dorea longicatena DSM 13814]
          Length = 296

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 142/322 (44%), Gaps = 32/322 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M      ++   E+ +R++++ +   Y   N   ++++ +S  + V+         + +G
Sbjct: 1   MNRTIEYLITEKEDGLRIEQFLRRKGYSGQNLAEIKRMPKS--ILVNGVHYYMRQTLTAG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++++       +  I   +I                 ++YED  I V NKPAG+ +   
Sbjct: 59  DILKVIICETKCSEKIPPVEI--------------PLDIIYEDEDIIVINKPAGMPIHPS 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRL---THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               Y+      +W   K  KP +    +RLD++TSG+ VV++   +   L+   + R +
Sbjct: 105 MNNYYNSLANALAWYYQKQDKPFIFRCCNRLDRDTSGLTVVSKHLVSGSILSTMTKNREV 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G        I   L +K     + +     + +    AI+H+K+I   A  
Sbjct: 165 HREYLAVVKGRVTPSSGTICAPLARKEGTIIERM----VDFEHGEEAITHYKLI-REANG 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + ++  TGRTHQ+R+H  ++G P++GD+ Y  + +         +  LH+ +M+  H
Sbjct: 220 HSLVSLKLETGRTHQIRIHMKYLGFPLIGDYLYNPDME------HMTRQALHSHHMEFAH 273

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  +  TAPLPA M     
Sbjct: 274 PITGEWMSFTAPLPADMANVLK 295


>gi|312114651|ref|YP_004012247.1| pseudouridine synthase [Rhodomicrobium vannielii ATCC 17100]
 gi|311219780|gb|ADP71148.1| pseudouridine synthase, RluA family [Rhodomicrobium vannielii ATCC
           17100]
          Length = 358

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 86/362 (23%), Positives = 152/362 (41%), Gaps = 64/362 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV-RVDKKR-----VKFNNRIQSGQVVR 66
             D+  +RLDR+  +     + V LQ+++R+G V R+   R        + +++ G    
Sbjct: 14  SEDDAGVRLDRFLASRIETQSRVRLQELIRAGHVVRLAAGRDAETSTDPSAKVRLGDTFE 73

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +                   + N     + ++  ++YED+ + V +KPAG+ V  G+G  
Sbjct: 74  VT---------------TPPAENYAVEGEAIELNVVYEDASLIVIDKPAGLVVHPGAGNP 118

Query: 127 Y--HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-- 177
               ++  +    DS        +P + HRLD+ TSG++VVA+T  A + L+  F     
Sbjct: 119 NGTLVNALIAHCGDSLSGIGGVTRPGIVHRLDKNTSGLMVVAKTDKAHRSLSAQFADHGR 178

Query: 178 --RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--- 232
              +++ Y +LVWG P+     I   + +  H G      V +N  G   A + +     
Sbjct: 179 TGALRREYLALVWGEPQPTSGRIEARIAR--HAGSRIKMAVVRN--GGREAATIYATERV 234

Query: 233 ------------IDCFAQKFCWL--EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                       +  + +         +  TGRTHQ+RVH  H+G P+VGD  Y A F+ 
Sbjct: 235 FRLGNVESQSAAMGKWNKTATLSVLRCKLETGRTHQVRVHLAHIGVPLVGDSVYGAGFRT 294

Query: 279 NFTSPI---------QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
              +             +  LHA  +   HP   + L   +PLP  + +  ++L  ++D 
Sbjct: 295 KALALPDEAARNFACAERQALHAAGLRFEHPSSRKVLSFESPLPEDIAQLCNAL-ERFDA 353

Query: 329 NL 330
            L
Sbjct: 354 KL 355


>gi|56551646|ref|YP_162485.1| RluA family pseudouridine synthase [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241761227|ref|ZP_04759315.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|260752766|ref|YP_003225659.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis NCIMB
           11163]
 gi|59803028|sp|P50513|RLUD_ZYMMO RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|56543220|gb|AAV89374.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241374134|gb|EER63631.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|258552129|gb|ACV75075.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
          Length = 317

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 136/327 (41%), Gaps = 29/327 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + V +  +    RLDR   +    ++   L+ ++ SG V  + +          G +VR
Sbjct: 3   TEQVTLTEEMIGWRLDRALASLITRLSRERLKNLISSGCVS-NSQ----------GALVR 51

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            P               L    +       +   +++ED  + V NKPAG+ V   +G  
Sbjct: 52  DPAFKIKSLDCFTVDIPLPRPAH--NEPQDIPLEIVFEDEHLLVVNKPAGMVVHPAAGNY 109

Query: 127 YHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            +   +  L              +P + HR+D++TSG+LVVA+T  A   L   F    I
Sbjct: 110 DNTLVNALLYHCAGKLSGIGGVARPGIVHRIDKDTSGLLVVAKTDPAHAGLAAQFADHSI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G P   +  +   L + S +    + +V         A++H+++I    + 
Sbjct: 170 NRRYRAIVDGHPSL-QGHVDAPLARSS-VNRQKMAIVSDGR--GKRAVTHYRMI-TPLKN 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN---FTSPIQNKLYLHARYMD 296
              +E +  TGRTHQ+RVH   +G  ++GD  Y  + K +     S    +  LHA ++ 
Sbjct: 225 ASLIECRLETGRTHQVRVHMSSIGHSLLGDPVYGRSKKAHHALLQSLAFQRQALHAAHLG 284

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G+ +   A +P  M   +  L
Sbjct: 285 FIHPISGKQVDFDAEMPQDMQLLFKML 311


>gi|312880111|ref|ZP_07739911.1| ribosomal large subunit pseudouridine synthase D [Aminomonas
           paucivorans DSM 12260]
 gi|310783402|gb|EFQ23800.1| ribosomal large subunit pseudouridine synthase D [Aminomonas
           paucivorans DSM 12260]
          Length = 344

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 83/319 (26%), Positives = 144/319 (45%), Gaps = 33/319 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPV 70
           V    ++ RLD +        +     K++R GQV V    RVK + ++  G  V     
Sbjct: 40  VSPSYQDHRLDYFLSREL-GTSRAFSTKLIRDGQVSVSWCPRVKPSMKVLPGGSVT---- 94

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                       ++     L    + +   ++YED+ + V +KPAG+ V    G      
Sbjct: 95  -----------AVVPPPEELDLVPEDVPFRVVYEDADLIVVDKPAGLVVHPAPGHWRGTL 143

Query: 129 IDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + G L  + D +     ++P + HRLD  TSG+LVVAR   A + L   F+ R ++K Y 
Sbjct: 144 VHGLLFRYPDMEALNGVRRPGIVHRLDATTSGLLVVARNGLAMEELVRCFKQRTLRKEYL 203

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L  G P+  +  I   + +        + ++    +G   +++ ++ +    +    L 
Sbjct: 204 ALAHGRPQLPEGEIRLPIGRDPK-NRKRMTIL----EGGRDSLTRYRTLWTRGR-ISLLL 257

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            Q  TGRTHQ+RVH   +GCP+VGD  Y    +  F     ++++LHA  +   HP  G 
Sbjct: 258 CQLCTGRTHQIRVHLKALGCPLVGDRVYAPGRETPFHP---DRVFLHAWKLGFSHPRTGE 314

Query: 305 -LQITAPLPAHMVKTWDSL 322
            L   +PLP  +++  ++L
Sbjct: 315 PLLFRSPLPPDLLEALEAL 333


>gi|304404905|ref|ZP_07386565.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
 gi|304345784|gb|EFM11618.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
          Length = 317

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 141/326 (43%), Gaps = 37/326 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINF---VNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V VE  +   ++    +     ++      + K+   G   V+ KRV  ++R+ +G ++
Sbjct: 11  TVTVEERDHGQQVRTVLERRL-GVSRKLLSRV-KLTELGL-TVNGKRVYTSDRVSTGDLL 67

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           ++       + I+ E   ++               +++ED  + + NKPAGI V    G 
Sbjct: 68  QVRMEKERSDDILPEPIPIE---------------VVFEDDDLLIVNKPAGIIVHPTHG- 111

Query: 126 AYHIDGFLK----SWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             H  G L      +   +G+  + R  HRLD+ TSG++V+A+T    Q L+E  +   I
Sbjct: 112 --HYTGTLANGVVHYWQERGEIVRFRPIHRLDEHTSGLVVIAKTPYVHQQLSEQLQAGTI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y + V+G P+  +  +   + +           ++        +++H++ I  + + 
Sbjct: 170 EKRYLAFVYGKPEPSEGTVNEPIDRDPERPH-----IRIVTPEGYPSVTHYETIAQYNEG 224

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               + +   TGRTHQ+RVH   +GCP++GD  Y              +  LHA  +   
Sbjct: 225 TASCVRLNLETGRTHQIRVHMKFLGCPLIGDDMYGREEGHGPADEKARRQALHAESIAFT 284

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLG 323
           HP    R+   APLP  + +    LG
Sbjct: 285 HPMTAERMTWKAPLPEDLQQLAHFLG 310


>gi|262373260|ref|ZP_06066539.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           junii SH205]
 gi|262313285|gb|EEY94370.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           junii SH205]
          Length = 349

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 140/326 (42%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++ +    R+D+     +   +   L++ ++ G + V+   VK   R +  +++ +  
Sbjct: 40  IQLDEEYLGQRIDQVAAMVWSEFSREKLKQWMKDGHLLVNGNIVKPKYRCEGNELLTLEV 99

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
            + A                 T   + +   ++YED  I V NK  G+ V  G+G     
Sbjct: 100 ELEAQT---------------TSQPENIPLNVVYEDDDIIVINKEVGMVVHPGAGNPSGT 144

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L      ++  +  L HR+D++TSG+LV+A+   A   L++    + + ++Y  +
Sbjct: 145 LVNALLYHAPKLAELSRAGLVHRIDKDTSGLLVIAKNLEAQFSLSKQLAKKTVYRVYDLV 204

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G        I   + K+  +    + ++     G   A++H+ V + F + F  ++ Q
Sbjct: 205 VYGNIIA-GGTIDEPI-KRHPVDRVKMAIL----PGGREAVTHYNVKERF-RDFTRVQAQ 257

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  ++G  +VGD  Y    +    +            +  LHA  + L 
Sbjct: 258 LETGRTHQIRVHFSYLGYGLVGDPVYVNRVRLPAGASETLIDMLRSFKRQALHAAKLGLV 317

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +   AP P    +  + L 
Sbjct: 318 HPRTGEEMMFEAPWPEDFKQLVEVLR 343


>gi|55980377|ref|YP_143674.1| ribosomal large subunit pseudouridine synthase D [Thermus
           thermophilus HB8]
 gi|55771790|dbj|BAD70231.1| ribosomal large subunit pseudouridine synthase D [Thermus
           thermophilus HB8]
          Length = 308

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 87/324 (26%), Positives = 147/324 (45%), Gaps = 41/324 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
           E +RLD+        ++    Q  +++G+VRV  + V K   R++               
Sbjct: 7   EGVRLDQAVAEALS-VSRAKAQAWIQAGRVRVGDRVVLKPAYRLKG-------------- 51

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLK 134
              +E  +           + L   +LYED  +   NKP G+      G+ +  +   L 
Sbjct: 52  ---EEVAVEPVEEAPMVLPEDLPIPILYEDEDVLALNKPPGLLTHPAPGVYSGTVVNLLL 108

Query: 135 SWVDSKGQK-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +      +K       P + HRLD++TSG+LVVA+     + L  +FR R + K Y ++ 
Sbjct: 109 ARYYGPVEKGPPELVRPGIVHRLDKDTSGVLVVAKHGGVLEGLARAFRDRLVMKRYLAIT 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G P  ++  +   + +         H +      A YA + F+V+   A  +  +E +P
Sbjct: 169 EGHP--REGVLIAPIGRHPRE----RHKMHVGGLAARYAETEFQVLAT-AGPYALVEARP 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-Q 306
           HTGRTHQ+RVH  ++G PI+GD  Y         SP   +  LHA  + +PHP  GR+ +
Sbjct: 222 HTGRTHQIRVHLKYLGAPILGDELYGRK------SPHIGRQALHAYELRIPHPRTGRILE 275

Query: 307 ITAPLPAHMVKTWDSLGFKYDRNL 330
           + AP+P  M   W++LG ++   +
Sbjct: 276 LLAPVPQDMAAAWEALGGRWPEEV 299


>gi|254391608|ref|ZP_05006807.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           clavuligerus ATCC 27064]
 gi|294812119|ref|ZP_06770762.1| Pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|326440725|ref|ZP_08215459.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces clavuligerus ATCC 27064]
 gi|197705294|gb|EDY51106.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           clavuligerus ATCC 27064]
 gi|294324718|gb|EFG06361.1| Pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
          Length = 313

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 79/333 (23%), Positives = 139/333 (41%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTLPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVLVDGAAVGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPQAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIVKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L + 
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKQQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R + K Y +LV G P      I   + +  H   DY   V         +++H+ ++
Sbjct: 166 FRDRTVDKRYHALVQGHPDPMSGTIDAPIGR--HPNHDYKWAVTAE---GKPSVTHYDLL 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAF-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTMAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +   HP  GR ++  +  P  +    D +  +
Sbjct: 279 RLGFEHPSDGRWVEYESGYPDDLRLALDKIAEE 311


>gi|239617850|ref|YP_002941172.1| pseudouridine synthase, RluA family [Kosmotoga olearia TBF 19.5.1]
 gi|239506681|gb|ACR80168.1| pseudouridine synthase, RluA family [Kosmotoga olearia TBF 19.5.1]
          Length = 299

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 93/308 (30%), Positives = 150/308 (48%), Gaps = 32/308 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHII 78
           RLD++ ++  P +   ++ K+LR G VRV+ KR+K  +  +  G VV +    N     I
Sbjct: 18  RLDKFLRHVLPDLKLSSIYKLLRKGNVRVNGKRIKAPSYELSLGDVVAVNYRGN-----I 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWV 137
           +  K L  S  L  H+  L   +LYED      +KPAG++V  G G+    +   L ++ 
Sbjct: 73  EYLKRLKESRELIPHN--LPIKILYEDESFLAVDKPAGLAVHPGKGVQIVTLIEGLLAYG 130

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              G KP L HRLD+ TSG+L+VA++  AA+ LT  FR +RI K Y +LV G+P+  +  
Sbjct: 131 KRNGFKPFLVHRLDKHTSGVLLVAKSPQAARELTAMFREKRIDKRYVTLVKGLPEKSRAY 190

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + +                         S + V   ++    +LE++  TG+ HQ+R 
Sbjct: 191 LKDVI-------------------DGLREESEYIVKKAYS-GCSFLEVRLFTGKKHQIRR 230

Query: 258 HALHMGCPIVGDHKYCAN-FKGNFTSPIQ-NKLYLHARYMDLPHPEGG-RLQITAPLPAH 314
               +G P+VGD  Y    F  NF    +  + +LH   M   HP+ G  +++ + LP  
Sbjct: 231 QMAKIGHPVVGDDVYGDREFNRNFKKRYELKRYFLHCMKMGFIHPKTGHYVEVLSELPDD 290

Query: 315 MVKTWDSL 322
           + K  + L
Sbjct: 291 LKKVLEKL 298


>gi|124267192|ref|YP_001021196.1| ribosomal large subunit pseudouridine synthase D [Methylibium
           petroleiphilum PM1]
 gi|124259967|gb|ABM94961.1| ribosomal large subunit pseudouridine synthase D [Methylibium
           petroleiphilum PM1]
          Length = 334

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 133/320 (41%), Gaps = 38/320 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           V+      RLDRW        +  +LQ ++  GQVR+D + V    R + +GQ + I   
Sbjct: 26  VDAGAHGERLDRWLATLAGEFSRNHLQTLIEGGQVRIDGQTVTARARRVSAGQQIEIT-- 83

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                       +L +  +     + +   +++ED+ + V +KPAG+ V    G   +  
Sbjct: 84  ------------LLPTPESQAFRPEPVALPVVFEDAHLLVIDKPAGLVVHPAPG---NWS 128

Query: 131 GFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + + + +         +  + HRLD++TSG++VVA+T  A   L  +   R + + Y 
Sbjct: 129 GTVLNGLLAHHAGAAALPRAGIVHRLDKDTSGLMVVAKTLPAMTSLVRAIAAREVHREYL 188

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWL 243
           +LV G+ +     +         IG D V  +K     G   A +  ++I         +
Sbjct: 189 ALVHGVLRQAVFSVDAP------IGRDPVSRIKMAVLAGGRTARTDVELIAAR-DAVSAV 241

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
               HTGRTHQ+RVH    G  ++ D  Y        T     +  LHA  +   HP   
Sbjct: 242 RCTLHTGRTHQIRVHMASRGHALLADALYGGRPGLGLT-----RQALHAHRLGFVHPASL 296

Query: 303 GRLQITAPLPAHMVKTWDSL 322
             ++ +A  P  +   W  +
Sbjct: 297 QPIEFSAVPPDDLRAAWQQI 316


>gi|315103148|gb|EFT75124.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL050PA2]
          Length = 306

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 136/322 (42%), Gaps = 29/322 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +  ++V +  +  R+D         ++   +  ++  G V +D + V + + R+ +GQ++
Sbjct: 1   MSVLLVPDGLDGERVDVA-AARMSGVSRSRISSLIEDGGVFLDGQLVSRASVRVATGQML 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +          I  Q +                 ++++DS I V +KPAG++     G 
Sbjct: 60  DVDLCDPVATPSITPQIVE-------------GMRIIHDDSDIVVVDKPAGVAAHPSLGW 106

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + +              ++  +  RLD  TSG++VVA++  A   L ++FR R +
Sbjct: 107 EGPSVVEHLAAAGFAISTSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y +LV G P      I   + +          V      G  ++++H++ ++ F + 
Sbjct: 167 DKVYLALVQGHPDPFTGTIDAPIGRDHRHDWKMAIV-----DGGRHSVTHYETVEAF-RH 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L++   TGRTHQ+RVH   +  P  GD  Y  +        ++ + +LHA  +   H
Sbjct: 221 ATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLYGCDPALAKELGLE-RQWLHAGELSFTH 279

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  +   A LPA +    D
Sbjct: 280 PGSGEWVTFHADLPADLQNALD 301


>gi|313827835|gb|EFS65549.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL063PA2]
 gi|315108225|gb|EFT80201.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL030PA2]
          Length = 306

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 137/322 (42%), Gaps = 29/322 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +  ++V +  +  R+D         ++   +  ++  G V +D ++V + + R+ +GQ++
Sbjct: 1   MSVLLVPDGLDGERVDVA-AARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVAAGQML 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +          I  Q +                 ++++DS I V +KPAG++     G 
Sbjct: 60  DVDLCDPVATPSITPQIVE-------------GMRIIHDDSDIVVVDKPAGVAAHPSLGW 106

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + +              ++  +  RLD  TSG++VVA++  A   L ++FR R +
Sbjct: 107 EGPSVVEHLAAAGFAISTSGAPERQGIVQRLDVGTSGLMVVAKSEHAYILLKQAFRDRTV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y +LV G P      I   + +          V      G  ++++H++ ++ F + 
Sbjct: 167 DKVYLALVQGHPDPFTGTIDAPIGRDHRHDWKMAIV-----DGGRHSVTHYETVEAF-RH 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L++   TGRTHQ+RVH   +  P  GD  Y  +        ++ + +LHA  +   H
Sbjct: 221 ATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLYGCDPALAKELGLE-RQWLHAGELSFTH 279

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  +   A LPA +    D
Sbjct: 280 PGSGEWVTFHADLPADLQNALD 301


>gi|302342169|ref|YP_003806698.1| pseudouridine synthase, RluA family [Desulfarculus baarsii DSM
           2075]
 gi|301638782|gb|ADK84104.1| pseudouridine synthase, RluA family [Desulfarculus baarsii DSM
           2075]
          Length = 317

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 84/325 (25%), Positives = 134/325 (41%), Gaps = 36/325 (11%)

Query: 13  ENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
             +    RLD           +   +Q++LR G V VD +  K   +++ GQ + +    
Sbjct: 9   PPEAAAQRLDVALLGLLGDDFSRAQVQRLLRDGLVLVDGQAAKAAQKLRPGQAIAVRLPD 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HI 129
              + +I                  +   +L+ED  + + NKP G+ V    G A    +
Sbjct: 69  PEPSELIP---------------MAMDLAILHEDEDLIIINKPPGLVVHPSPGHAEGTLV 113

Query: 130 DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            G L             +P + HRLD++TSG LV A+   A + L   F   R+QK Y +
Sbjct: 114 HGLLHHCGGLAEVGGKLRPGIVHRLDKDTSGALVAAKNDRAHRGLVARFAAGRVQKEYLA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G P  K+  + + + +     GD   +  Q  +    A+S ++V   F +    L +
Sbjct: 174 LVHGRPA-KRGRVDSGIGRHP---GDRKRMSSQGSRT-KPALSQWRVCRSFGE-ASLLRV 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-------NFTSPIQNKLYLHARYMDLP 298
             HTGRTHQ+RVH    G P++GD  Y A  +                +  LHA  +   
Sbjct: 228 NIHTGRTHQIRVHLSEAGHPVLGDQTYGARRRDAALPDPVAAALRQAGRQMLHAVVLSFE 287

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP   + + +TAPLPA       + 
Sbjct: 288 HPISAQIIHVTAPLPADYRAVLRAC 312


>gi|84393596|ref|ZP_00992349.1| ribosomal large subunit pseudouridine synthase D [Vibrio splendidus
           12B01]
 gi|84375805|gb|EAP92699.1| ribosomal large subunit pseudouridine synthase D [Vibrio splendidus
           12B01]
          Length = 324

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 68/332 (20%), Positives = 142/332 (42%), Gaps = 35/332 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V++ +   RLD+     +   +   +++ L  G+++VD + + K    +  G+ + +  
Sbjct: 10  TVKSSQLGQRLDQAVAELFTDFSRSRIKEWLLDGKIQVDGEVITKPRTIVLGGEAIILQA 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +                      +  +   ++YED  + V NKP  + V  G+G     
Sbjct: 70  ELADEERW---------------EAQDIPLDIVYEDDDLLVINKPRDLVVHPGAGTPDGT 114

Query: 130 --DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   ++  +  + HRLD++T+G++VVA+T  A   L  +   RRI + Y ++
Sbjct: 115 ILNALLFHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        +   + + +         +    +    A++H++V + F ++   + ++
Sbjct: 175 AIGKM-TAGGVVEKGISRHAT-----KRTLMDVNELGKPAVTHYRVAEHF-REHTRIRLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P++GD  Y    +    +  +        ++  LHA  +   
Sbjct: 228 LETGRTHQIRVHMSYLQHPLLGDIAYGGRARIPKGASEELTTMIRSFDRQALHAVMLKFV 287

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           HP  G  ++  AP+P  MV   ++L      N
Sbjct: 288 HPITGEEVEFHAPVPNDMVVMAEALRVDAREN 319


>gi|323188383|gb|EFZ73674.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           RN587/1]
          Length = 300

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 138/317 (43%), Gaps = 41/317 (12%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
            +P  +   +++ +   +V V+ K   K   ++  G+ V I   I        +   LD 
Sbjct: 1   MFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLD- 59

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPR 145
                         ++YED  I V NKP  + V  G+G     +   L  +       PR
Sbjct: 60  --------------IVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPR 105

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIAN 200
             + HRLD++T+G++VVA+T  A   L ES + R I + Y ++  G         E I+ 
Sbjct: 106 AGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISR 165

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K++H+    +            A++H+++++ F +    L ++  TGRTHQ+RVH  
Sbjct: 166 HPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMA 215

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPL 311
           H+  P+VGD  Y    +    +           ++  LHA  + L HP  G  ++  AP+
Sbjct: 216 HITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPI 275

Query: 312 PAHMVKTWDSLGFKYDR 328
           P  MV+  + +   ++ 
Sbjct: 276 PQDMVELIEEMRADFEE 292


>gi|126461841|ref|YP_001042955.1| RluA family pseudouridine synthase [Rhodobacter sphaeroides ATCC
           17029]
 gi|126103505|gb|ABN76183.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides ATCC 17029]
          Length = 349

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 81/344 (23%), Positives = 138/344 (40%), Gaps = 52/344 (15%)

Query: 15  DEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           ++   RLD+      P    ++   L K++  G VR++   V     ++  GQV  I   
Sbjct: 17  EDPPDRLDKALVREAPEEAALSRSRLMKLIGEGAVRLEGAPVTDPKAKVAEGQVYEI--- 73

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                        LD+   +    + +   +++ED  + V +KP G+ V    G      
Sbjct: 74  ------------ALDAPAEVEARPEAIPLSVVWEDEDLIVIDKPVGMVVHPAPGQWTGTL 121

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L    +S       ++P + HR+D++TSG+LVVA+T  A Q L   F    +++ Y
Sbjct: 122 VNALLHHCGESLSGIGGEKRPGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRY 181

Query: 184 WSLVWGIPKN-------------KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            +LV G+P+              +   +       +    D        E G  +A++  
Sbjct: 182 LALVHGVPEVSDPRLRGVRGTSFEPGGVLRIATGLARHRTDRQRQAVTFE-GGRHAVTRA 240

Query: 231 KVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GN 279
           ++++ F        +E +  TGRTHQ+RVH  H G  ++GD  Y    K           
Sbjct: 241 RLLERFGTPPVLALVECRLETGRTHQIRVHMAHAGHGLIGDQTYGGRRKLSPKALGPEAA 300

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             +    +  LHA  +   HP  G  L   +PLPA M      L
Sbjct: 301 AAAEAFPRQALHAASLGFRHPVSGEELSFESPLPADMAGLLSLL 344


>gi|331703570|ref|YP_004400257.1| ribosomal large subunit pseudouridylatesynthase D [Mycoplasma
           mycoides subsp. capri LC str. 95010]
 gi|328802125|emb|CBW54279.1| Ribosomal large subunit pseudouridylatesynthase D [Mycoplasma
           mycoides subsp. capri LC str. 95010]
          Length = 310

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 142/319 (44%), Gaps = 36/319 (11%)

Query: 19  MRLDRWFKNHYP--HINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALN 75
           +RLD+           +   +QK+++   + V+ + +  NN  ++    + I        
Sbjct: 13  LRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITNNNFLVKPNSQITITI------ 66

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
               +  ILD ++     ++ +   ++Y+D  + V NK   I+V     +    +  + +
Sbjct: 67  ----KDPILDPNL---VKNEDIDLDIVYQDDDLLVINKQNNITVHPS--LNNTNNTIVNA 117

Query: 136 WVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            + S  +        +P + HR+D++T+G+L+VA+     + L+E F+  +I K Y ++V
Sbjct: 118 LLASDVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKTHKLLSEMFKNHQIYKEYLAIV 177

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+ K  K  I   + + S      + V     K +  AI+ F+V++ F +    ++ Q 
Sbjct: 178 TGVIKPNKGLIDAPIGR-SQTDRKKMSV---TAKNSKQAITTFEVVERFLKN-TLVKCQI 232

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  ++  P++ D  Y       FT       YLHA  +   HP     ++
Sbjct: 233 QTGRTHQIRVHFNYINHPVLNDPVYGKK-HQEFTDFG---QYLHAYKLKFTHPITKKEIE 288

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           + +PLP         L  +
Sbjct: 289 LISPLPKEFDDKIKELRGE 307


>gi|50842255|ref|YP_055482.1| pseudouridylate synthase [Propionibacterium acnes KPA171202]
 gi|50839857|gb|AAT82524.1| pseudouridylate synthase [Propionibacterium acnes KPA171202]
 gi|315107090|gb|EFT79066.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL030PA1]
          Length = 306

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 137/322 (42%), Gaps = 29/322 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +  ++V +  +  R+D         ++   +  ++  G V +D ++V + + R+ +GQ++
Sbjct: 1   MSVLLVPDGLDGERVDVA-AARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQML 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +          I  + +                 ++++DS I V +KPAG++     G 
Sbjct: 60  DVDLCDPVATPSITPRIVE-------------GMRIIHDDSDIVVVDKPAGVAAHPSLGW 106

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + +              ++  +  RLD  TSG++VVA++  A   L ++FR R +
Sbjct: 107 EGPSVVEHLAAAGFAISTSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y +LV G P      I   + +          V      G  ++++H++ ++ F + 
Sbjct: 167 DKVYLALVQGHPDPFTGTIDAPIGRDHRHDWKMAIV-----DGGRHSVTHYETVEAF-RH 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L++   TGRTHQ+RVH   +  P  GD  Y  +        ++ + +LHA  +   H
Sbjct: 221 ATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLYGCDPALAKELGLE-RQWLHAGELSFTH 279

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  +   A LPA +    D
Sbjct: 280 PGSGEWVTFHADLPADLQNALD 301


>gi|326333482|ref|ZP_08199724.1| RNA pseudouridine synthase, RluA family [Nocardioidaceae bacterium
           Broad-1]
 gi|325948727|gb|EGD40825.1| RNA pseudouridine synthase, RluA family [Nocardioidaceae bacterium
           Broad-1]
          Length = 313

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 136/319 (42%), Gaps = 28/319 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + ++V +  E  R+D      +  ++     +++  G V VD   V  ++R+ +G ++  
Sbjct: 9   RTLLVPDGLEGERVDAAMARLF-GLSRTRAAELIADGLVTVDGSAVAKSDRVSAGSMLDA 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
                A    IK + +                 ++Y+D    V +KP G++V    G   
Sbjct: 68  TIPSQADPLEIKPEIVE-------------GIKIIYDDDAFVVIDKPVGVAVHPSPGWQG 114

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              + +      +       ++  +  RLD  TSG++V+A++  A   L  +FR R + K
Sbjct: 115 QTVVGHLAAAGFRISTSGAKEREGIVQRLDVGTSGVMVIAKSEHAYSVLKNAFRQRTVDK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G P   +  I   + +      DY   V+ +     ++++H++ ++   +   
Sbjct: 175 TYHALVQGHPDPLEGTIDAPIGRNPKY--DYKFAVRAD---GRHSVTHYETLEAH-RFAS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L++   TGRTHQ+RVH   +  P VGD  Y A+        ++ + +LHA  +   HPE
Sbjct: 229 LLKIHLETGRTHQIRVHMSALKHPCVGDLTYGADPALARRVGLE-RQWLHAVQLGFDHPE 287

Query: 302 GGR-LQITAPLPAHMVKTW 319
            G  +   +  P  +    
Sbjct: 288 TGEYVTFESTYPDDLQHAL 306


>gi|256829592|ref|YP_003158320.1| RluA family pseudouridine synthase [Desulfomicrobium baculatum DSM
           4028]
 gi|256578768|gb|ACU89904.1| pseudouridine synthase, RluA family [Desulfomicrobium baculatum DSM
           4028]
          Length = 526

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 81/330 (24%), Positives = 149/330 (45%), Gaps = 37/330 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           +  YV+ V V   +   RLD +++       +    +Q  ++ G+ R++ +   K   R+
Sbjct: 1   MQEYVEKVGVA--DVGQRLDVFWQTCLEEEGVGRSRVQAWIKDGRARINGQVCSKAATRL 58

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             GQ + + P            +  DSSV      D     + + D  + V NK   ++V
Sbjct: 59  MPGQTLTLAP------------EYTDSSV----VPDDGPLNVFFADEDLVVVNKTPAMTV 102

Query: 120 QGGSGIA-----YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                +A     + +     + +   G++P + HRLD++TSG++V+A + +A   LT++F
Sbjct: 103 HPAPSVAEPTLVHRVAHHFPALLSQSGERPGIVHRLDKDTSGLIVLALSESARLSLTQAF 162

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             R + K Y +LV G+P +    ++  L +   I    + VV   E+G   A + F+++ 
Sbjct: 163 ASREVYKEYLALVAGVP-DSSGTVSLALGRHPSI-KTRMAVV---ERGGRAAETRFELLW 217

Query: 235 CFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             A +    + ++  TGRTHQ+RVH   +G P++GD  Y        T+    +  LHA 
Sbjct: 218 SAADRSASLVRVRIMTGRTHQIRVHMAALGHPLLGDAVYADKQ----TAARAPRQMLHAW 273

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +   HP     ++  AP P   ++    L
Sbjct: 274 QLRFEHPRSFESMEFCAPPPDDFLQVLREL 303


>gi|255505900|ref|ZP_05348786.3| pseudouridine synthase, RluA family [Bryantella formatexigens DSM
           14469]
 gi|255265256|gb|EET58461.1| pseudouridine synthase, RluA family [Bryantella formatexigens DSM
           14469]
          Length = 342

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 82/348 (23%), Positives = 137/348 (39%), Gaps = 25/348 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++V  +E   RLD+    +        L K+LR   + ++ K+   N        +R
Sbjct: 1   MKEIIVRENEAGQRLDKLLARYLCQAPKSFLYKMLRKKNITLNGKKASGNEITAKEDCIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I                 + +  +       K  ++YED  I V NKPAG+  Q      
Sbjct: 61  IFLSDETYEKFSAG----EEAPPIRHTGALTKEQIIYEDGDILVLNKPAGMLSQKSRPED 116

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
              + +  S++   GQ          P + +RLD+ TSG+L+  ++ A  Q + E+ + R
Sbjct: 117 VSANEYFLSYLLETGQISAQELRTFHPSICNRLDRNTSGLLLAGKSLAGLQAMAEALKDR 176

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  LV G    K   +  +L+K        +      +K A    + +  +    
Sbjct: 177 SLHKYYLCLVSGSL-TKGARLEGFLVKDEAANKVKICATDMGDKEAKPISTQYVPLWTDG 235

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYM 295
            K   L++   TGR HQ+R H   +G PI+GD KY    K  +           LHA  M
Sbjct: 236 -KVTLLKIWLITGRAHQIRAHLSGIGHPIIGDGKYGDRRKNVYYEKTYHLKGQLLHAFQM 294

Query: 296 DLPHPEGGRL------QITAPLPAHMVKTWDSLGFK-YDRNLYIKRLY 336
            +P P  G L      +  APLP +  K     G    D + + +  +
Sbjct: 295 KMP-PLTGTLSRLSGQEFIAPLPENFRKILADAGCDTADTDAWRQTEF 341


>gi|293192338|ref|ZP_06609449.1| ribosomal large subunit pseudouridine synthase D [Actinomyces
           odontolyticus F0309]
 gi|292820253|gb|EFF79247.1| ribosomal large subunit pseudouridine synthase D [Actinomyces
           odontolyticus F0309]
          Length = 301

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 134/325 (41%), Gaps = 34/325 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +     R+D         ++     ++   G V V+      ++R+ +  ++ +    
Sbjct: 4   VPDALVGERVDAALARML-GLSRSRCAELAGDGHVLVNGVAAGKSDRLGALDIIEVT--- 59

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------I 125
                      I +     T  +D     +LY+D  I V +KP G++   G G      +
Sbjct: 60  -----------IPEPESKPTPVTDMA---ILYDDEDIVVVDKPVGVAAHTGPGWEGPTVL 105

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                   +       ++  + HRLD  TSG ++VA++  A   +  +F+ R I+K+Y +
Sbjct: 106 GNLEAAGYRITSYGPPERQGIVHRLDVGTSGAMMVAKSELAYTVMKRAFKERTIEKVYHA 165

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G        I   + +  H   ++   V     G   A++H+  ++  A      E+
Sbjct: 166 VVAGHLDPASGTIDAPIGR--HPSREWRMAVID---GGKRAVTHYDTLELMA-GAQLTEV 219

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
              TGRTHQ+RVH   +G P VGD  Y A+        +  + +LHA  +   HP  G  
Sbjct: 220 HLETGRTHQIRVHMAAVGHPCVGDTFYGADPTQAERLGL-TRQWLHAVRLGFAHPRTGMP 278

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRN 329
           + +++P P  +    + L  ++ RN
Sbjct: 279 MSVSSPYPDDLADALEEL--RHPRN 301


>gi|154509032|ref|ZP_02044674.1| hypothetical protein ACTODO_01549 [Actinomyces odontolyticus ATCC
           17982]
 gi|153798666|gb|EDN81086.1| hypothetical protein ACTODO_01549 [Actinomyces odontolyticus ATCC
           17982]
          Length = 301

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 134/325 (41%), Gaps = 34/325 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +     R+D         ++     ++   G V V+      ++R+ +  ++ +    
Sbjct: 4   VPDALVGERVDAALARML-GLSRSRCAELAGEGHVLVNGVAAGKSDRLGALDIIEVT--- 59

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------I 125
                      I +     T  +D     +LY+D  I V +KP G++   G G      +
Sbjct: 60  -----------IPEPESKPTPVTDMA---ILYDDEDIVVVDKPVGVAAHTGPGWEGPTVL 105

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                   +       ++  + HRLD  TSG ++VA++  A   +  +F+ R I+K+Y +
Sbjct: 106 GNLEAAGYRITSYGPPERQGIVHRLDVGTSGAMMVAKSELAYTVMKRAFKERTIEKVYHA 165

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G        I   + +  H   ++   V     G   A++H+  ++  A      E+
Sbjct: 166 VVAGHLDPASGTIDAPIGR--HPSREWRMAVID---GGKRAVTHYDTLELMA-GAQLTEV 219

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
              TGRTHQ+RVH   +G P VGD  Y A+        +  + +LHA  +   HP  G  
Sbjct: 220 HLETGRTHQIRVHMAAVGHPCVGDTFYGADPTQAERLGL-TRQWLHAVRLGFAHPRTGMP 278

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRN 329
           + +++P P  +    + L  ++ RN
Sbjct: 279 MSVSSPYPDDLADALEEL--RHPRN 301


>gi|282856468|ref|ZP_06265745.1| ribosomal large subunit pseudouridine synthase D [Pyramidobacter
           piscolens W5455]
 gi|282585708|gb|EFB90999.1| ribosomal large subunit pseudouridine synthase D [Pyramidobacter
           piscolens W5455]
          Length = 345

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 149/331 (45%), Gaps = 37/331 (11%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV---RVDKKRVKFN 56
           M  M   +  + V  ++   RLD +       ++    + ++  G V   +V  K+++  
Sbjct: 32  MEKMNGEIYELAVPEEDSGARLDLFLAGELS-LSRSRARSLIDGGAVSSGQV--KKIRPA 88

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
            +IQ GQ+ R+     A   I                +  +   ++YED  + V NKPAG
Sbjct: 89  FKIQPGQIYRVEIPEAAPAEI---------------AAQDMPFDVVYEDDDVIVVNKPAG 133

Query: 117 ISVQGGSG--IAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           + V  G+G      ++G +  + +        +P + HRLD  TSG++VVAR+ AA + L
Sbjct: 134 VVVHPGAGRPDGTLVNGLMFRYPEIGRIGDSVRPGIVHRLDVGTSGLMVVARSDAAFRGL 193

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
           TE+F+   + K Y  L  G  K  +  +   + +        + V          A++ +
Sbjct: 194 TEAFQAHEVLKEYLGLGVGALKAPEGTVDAPIGRDPR-NRLKMCVSW----DGRDAVTDY 248

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           KV+   A+    + ++ HTGRTHQ+RVH   +GC + GD  Y           ++++++L
Sbjct: 249 KVLWTRAR-CNLIRVRLHTGRTHQIRVHMRALGCSLDGDTLYGPKDPAQHI--LKDRVFL 305

Query: 291 HARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
           H+  +   HP  G RL+  APLP  ++    
Sbjct: 306 HSWRLGFRHPVSGERLEFRAPLPPELIAALR 336


>gi|255534470|ref|YP_003094841.1| Ribosomal large subunit pseudouridine synthase D [Flavobacteriaceae
           bacterium 3519-10]
 gi|255340666|gb|ACU06779.1| Ribosomal large subunit pseudouridine synthase D [Flavobacteriaceae
           bacterium 3519-10]
          Length = 352

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 151/334 (45%), Gaps = 42/334 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+  ++ +R+D++      +     + +  R+G V V+   VK N R++ G  + +  
Sbjct: 32  ITVDRGQQPLRIDKFLHIFRQNSTRNKISQSCRAGNVVVNGTAVKQNYRVKPGDRISV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L+   +E  I+   + L          ++YED  + V +K  G+ V  G G   + 
Sbjct: 90  ---LLSRPPRENVIIPQDIPLN---------IVYEDDDLVVVDKDPGMVVHPGHG---NW 134

Query: 130 DGFL---------KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           DG L         K+ V S   +  L HR+D++TSG+LV+A+   A  +L + F  R+ +
Sbjct: 135 DGTLINALAFHFEKNGVKSDLDRVGLVHRIDKDTSGLLVIAKNEYALSYLAKQFFDRKTK 194

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           ++YW+ VWG    +   I   + +  H+       V ++     +A++H+KV++ F +  
Sbjct: 195 RLYWAFVWGNLDQENGTITGNIGR--HLKNRMQMAVFEDGSLGKHAVTHYKVVERF-KYM 251

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSP-----------IQNKL 288
            W+E +  TGRTHQ+R H  H+G  +  D +Y           P           I  + 
Sbjct: 252 TWVECKLETGRTHQIRAHFKHIGHTLFNDERYEGNQILKGVNMPKYKQFIKNVFEILPRH 311

Query: 289 YLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDS 321
            LHA  +   HP     +   +P+PA M+   + 
Sbjct: 312 ALHAHTLGFIHPTKKEEMYFESPMPADMLGAVEK 345


>gi|326386900|ref|ZP_08208514.1| ribosomal large subunit pseudouridine synthase D [Novosphingobium
           nitrogenifigens DSM 19370]
 gi|326208580|gb|EGD59383.1| ribosomal large subunit pseudouridine synthase D [Novosphingobium
           nitrogenifigens DSM 19370]
          Length = 314

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 130/321 (40%), Gaps = 32/321 (9%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINA 73
           +E   RLD+        ++   ++ ++  G V V    ++  + +  +G    I   + A
Sbjct: 13  EESGQRLDKALAEG-SGLSRERVKALIEEGAVTVAGTPLRQPSAKSVAGTEWTIAVPVPA 71

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDG 131
                               +  +   ++YED+ + V +KPAG+ V   +G      ++ 
Sbjct: 72  AA---------------EAVAQDIPLTVVYEDADLIVVDKPAGMVVHPAAGNPDGTLVNA 116

Query: 132 FLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            L              +P + HR+D++TSG+LVVA+T  A + L   F    I + Y ++
Sbjct: 117 LLHHCRGQLSGIGGVARPGIVHRIDKDTSGLLVVAKTDVAHEGLARQFADHSIVRAYRAV 176

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G P      I   + + SH   D   +    E    +A++H++ ++        +E +
Sbjct: 177 TGGAPTPPAGTIRGAIARSSH---DRKKMALVEEGRGKHAVTHYRTLERL-DSSALVECR 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             TGRTHQ+RVH   +G  ++GD  Y    A  +   +     +  LHA  +   HP  G
Sbjct: 233 LETGRTHQVRVHLASIGHSLLGDPVYGRCPARLRPVLSRLEFRRQALHAAELGFVHPVSG 292

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
             L   +  P  M +    L 
Sbjct: 293 EHLHFVSATPVDMEQLIVELR 313


>gi|297180914|gb|ADI17118.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0070_03O15]
 gi|297181510|gb|ADI17697.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0130_23I23]
          Length = 305

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 78/321 (24%), Positives = 152/321 (47%), Gaps = 33/321 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +  N R+D +    +  ++   +Q ++  G+V V+ K V  + + +    + I   +
Sbjct: 8   IDEENANNRIDIFLSRKFDSLSRGIVQGLIDEGKVLVNGKTVDRDYKTKVDDQIEIEFDL 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHI 129
              N  + +                +   +++E++ + + +K AG++V  G+G   +  I
Sbjct: 68  ETNNADLPQD---------------INLNIVFENNDLLIIDKHAGLTVHPGAGQKDSTLI 112

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +G L  + D K   +  + HRLD++TSG++++ART  +  +LT+  + R+I++ Y++LV 
Sbjct: 113 NGLLYMYPDQKKIPRYGVVHRLDKDTSGLMIIARTLESHTNLTDLIQTRKIKRNYYALVH 172

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G P      I   + +          ++   ++G   AI+HFKV   F + F  L++   
Sbjct: 173 GQPIA-GNTIDKPIGRHPKN-----RLLFCVKEGGREAITHFKVHKKF-KNFSLLDVSLE 225

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLHARYMDLPHPE 301
           TGRTHQ+RVH  H+G PI GD  YC       ++  +        +  LHA  ++  + E
Sbjct: 226 TGRTHQIRVHMQHIGHPIAGDQSYCRIKNWKNSTENEINALNSLGRQSLHAYKLEFTYEE 285

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
                  + +P  + K  D L
Sbjct: 286 -KDFSFLSNIPEELQKVIDQL 305


>gi|146277612|ref|YP_001167771.1| RluA family pseudouridine synthase [Rhodobacter sphaeroides ATCC
           17025]
 gi|145555853|gb|ABP70466.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides ATCC 17025]
          Length = 349

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 80/336 (23%), Positives = 140/336 (41%), Gaps = 50/336 (14%)

Query: 15  DEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           ++   RLD+      P    ++   L K++  G VR+    V     R+  GQV  I   
Sbjct: 17  EDPPERLDKALAREAPEEAALSRSRLMKLIAEGAVRLKGVPVTDPKARVLEGQVYEI--- 73

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                       +  ++  +    + +   +++ED+ + V +KP G+ V    G      
Sbjct: 74  ------------VTGAAAEVEALPEAIPLSVVWEDADLIVIDKPVGMVVHPAPGQWTGTL 121

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L     S       ++P + HR+D++TSG+LVVA+T  A Q L   F    +++ Y
Sbjct: 122 VNALLHHCGASLSGIGGEKRPGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRY 181

Query: 184 WSLVWGIPKNKKECIANW----------LLKKSHIGGDYVHVVKQNE--KGANYAISHFK 231
            +LV G+P+     +             L   + I        +Q    +G  +A++  +
Sbjct: 182 LALVHGVPEPSDPRLRGIRGVSFEPGGVLRIATGIARHRTDRQRQAVTFEGGRHAVTRAR 241

Query: 232 VIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---- 285
           +++ F        +E +  TGRTHQ+RVH  H+G  ++GD  Y    K +  +       
Sbjct: 242 LLERFGTPPAAALVECRLETGRTHQIRVHMSHVGHGLIGDQTYGGRRKLSAKAVGAEAAQ 301

Query: 286 -----NKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
                 +  LHA  +   HP  G  L   +PLPA M
Sbjct: 302 AAEAFPRQALHAATLGFCHPVTGEDLSFESPLPADM 337


>gi|323167770|gb|EFZ53465.1| ribosomal large subunit pseudouridine synthase D [Shigella sonnei
           53G]
 gi|323173090|gb|EFZ58721.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           LT-68]
 gi|333001156|gb|EGK20726.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           K-272]
 gi|333015794|gb|EGK35131.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           K-227]
          Length = 300

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 138/317 (43%), Gaps = 41/317 (12%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
            +P  +   +++ +   +V V+ K   K   ++  G+ V I   I        +   LD 
Sbjct: 1   MFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLD- 59

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPR 145
                         ++YED  I V NKP  + V  G+G     +   L  +       PR
Sbjct: 60  --------------IVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPR 105

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIAN 200
             + HRLD++T+G++VVA+T  A   L ES + R I + Y ++  G         E I+ 
Sbjct: 106 AGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISR 165

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K++H+    +            A++H+++++ F +    L ++  TGRTHQ+RVH  
Sbjct: 166 HPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMA 215

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPL 311
           H+  P+VGD  Y    +    +           ++  LHA  + L HP  G  ++  AP+
Sbjct: 216 HITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPI 275

Query: 312 PAHMVKTWDSLGFKYDR 328
           P  MV+  + +   ++ 
Sbjct: 276 PQDMVELIEVMRADFEE 292


>gi|296393841|ref|YP_003658725.1| pseudouridine synthase [Segniliparus rotundus DSM 44985]
 gi|296180988|gb|ADG97894.1| pseudouridine synthase, RluA family [Segniliparus rotundus DSM
           44985]
          Length = 315

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 74/326 (22%), Positives = 132/326 (40%), Gaps = 26/326 (7%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T ++ + V      +RLD         ++     ++  +G   VD K  + ++R+  G  
Sbjct: 6   TALRSLPVPEGLVGLRLDAGLARLL-GVSRTKAAELADAGHALVDGKEARRSDRLVEGAW 64

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +                L + V            +L+ D  + V  KPA I+V    G
Sbjct: 65  LEVSV-----------PAALPAPVEEDVPEIIAGLNVLFSDEHVVVVEKPAEIAVHPSVG 113

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                + G LK+           ++  +  RLD  TSG++V+A +  A   L  +F+ R 
Sbjct: 114 WSGPTVVGGLKALGFRIATSGVAERQGVVQRLDVGTSGVMVLAASEHAYTVLKRAFKHRE 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y +LV G P      I   + K+   G  +             +++H+  ++ F Q
Sbjct: 174 VEKWYEALVQGHPDPSSGTIDAAIGKRPGPGWRFAVTT-----NGRPSVTHYDTLEAFGQ 228

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               + ++  TGRTHQ+RVH   +  P  GD  Y A+ K      +  + +LHAR +   
Sbjct: 229 -ASLVSIRLETGRTHQIRVHFSALRHPCCGDMLYGADPKLAARLGL-RRQWLHARKLSFA 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  GR +   + L   + +   +L 
Sbjct: 287 HPGDGRIMHFESELTEDLARALQTLR 312


>gi|300784875|ref|YP_003765166.1| ribosomal large subunit pseudouridine synthase D [Amycolatopsis
           mediterranei U32]
 gi|299794389|gb|ADJ44764.1| ribosomal large subunit pseudouridine synthase D [Amycolatopsis
           mediterranei U32]
          Length = 309

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 76/323 (23%), Positives = 141/323 (43%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  + MR+D         ++   + ++  SG V +D +    ++R+  G ++ I
Sbjct: 4   RMLPVPDGLDGMRVDAGLAKLL-GLSRTVVAELAESGDVLLDGRPAGKSDRLSGGGLLEI 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
                A    +  Q +                 +L++D  I V +KP G++V    G   
Sbjct: 63  TLPEPANPVEVVAQPV-------------DGMQILHDDDDIVVISKPVGVAVHPSPGWTG 109

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              +       L+       ++  + HRLD  T+G++VVA++  A   L  +F+ R + K
Sbjct: 110 PTVVGGLAAAGLRIATSGAAERQGVVHRLDAGTTGVMVVAKSEHAYTVLKRAFKERTVDK 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G P   +  I   +    H   DY   V Q   G   +++H++V++ F +   
Sbjct: 170 GYHAIVQGHPDPMRGTIDAPI--DRHPRHDYKFAVVQ---GGRPSVTHYEVVEAF-RAAS 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
              ++  TGRTHQ+RVH   +  P VGD  Y A+          ++ +LHA+ +   HP 
Sbjct: 224 LTHIKLETGRTHQIRVHFSALRHPCVGDLTYGADPVL-ARHLGLSRQWLHAKTLAFAHPA 282

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            GR ++  +  P  + K  + L 
Sbjct: 283 DGRWVEFESEYPDDLAKALEILR 305


>gi|225572187|ref|ZP_03781051.1| hypothetical protein RUMHYD_00481 [Blautia hydrogenotrophica DSM
           10507]
 gi|225040359|gb|EEG50605.1| hypothetical protein RUMHYD_00481 [Blautia hydrogenotrophica DSM
           10507]
          Length = 343

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 90/332 (27%), Positives = 148/332 (44%), Gaps = 31/332 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + ++ ++   RLD++            L K+LR   + ++KK+   N +++ G  V+
Sbjct: 1   MQQMDIKENDAGQRLDKYLSKLLFKAPKSFLYKMLRKKNITLNKKKASGNEKLKPGDQVQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +           ++             +D L+  +LYEDS++ + NKPAGI  Q      
Sbjct: 61  LFFSQETFEKFSRDD---------FYPTDDLQLEILYEDSQVMILNKPAGILSQKSRPED 111

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  ++ S++   GQ         +P + +RLD+ T+GI+   +T A+ Q L++ F  R
Sbjct: 112 VSLVEYMLSYLLESGQFTQTDFRTFRPGICNRLDRNTTGIVAAGKTLASLQSLSQMFHDR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  LV G    KK  I  +L K +    + V V     KGA    + ++ +   A
Sbjct: 172 TLEKYYLCLVKGKI-IKKNFIKGYLHKDTK--CNKVIVSSVPIKGAQPIETSYEPLTSNA 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYM 295
            K   L +   TGRTHQ+R H   +G PI+GD KY      +  F         LHA  +
Sbjct: 229 -KLTLLRVHLITGRTHQIRSHLASIGHPILGDPKYGDASWNQDYFRRYKLQHQVLHAVQL 287

Query: 296 DLPHPEG------GRLQITAPLPAHMVKTWDS 321
           + P  EG      GR    APLPA   +    
Sbjct: 288 NFPVMEGTLEHLSGR-HFFAPLPAQFTEILRQ 318


>gi|320011298|gb|ADW06148.1| pseudouridine synthase, RluA family [Streptomyces flavogriseus ATCC
           33331]
          Length = 313

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 79/333 (23%), Positives = 140/333 (42%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    V+ + V +  E  R+D      +   +     ++  +G+V+VD      + R+ 
Sbjct: 1   MSTYPEVRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVQVDGAVAGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWMEVEMPQAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKAQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R ++K Y +LV G P      I   + +  H   DY   V         +++H+ +I
Sbjct: 166 FRDRVVEKKYHALVQGHPDPMSGTIDAPIGR--HPQHDYKWAVTAE---GKPSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + + +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAY-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTLAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            +   HP +GG ++  +  P  +    D++  +
Sbjct: 279 RLGFEHPADGGWVEFESTYPDDLRHALDTIAAE 311


>gi|262277480|ref|ZP_06055273.1| ribosomal large subunit pseudouridine synthase D [alpha
           proteobacterium HIMB114]
 gi|262224583|gb|EEY75042.1| ribosomal large subunit pseudouridine synthase D [alpha
           proteobacterium HIMB114]
          Length = 325

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 76/336 (22%), Positives = 145/336 (43%), Gaps = 44/336 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
            VV+ + +  R+D+     YP I+   + KI+++  ++++ + +K  +++++SG  +   
Sbjct: 6   FVVDENFDQKRIDQVVAKQYPKISRSKVSKIIKTELLKLNGQILKDPSHKVKSGDQIEF- 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG------ 122
                       + +++ ++NL      L   +++ED  I + +KP G+ V  G      
Sbjct: 65  ------------ENLIEETINLIPKKMDLN--IIFEDQDIIIIDKPIGMVVHPGAGNYED 110

Query: 123 ---SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              +G+ YH    L     +   +P + HR+D++TSG+LVVA+   A   + + F    I
Sbjct: 111 TMVNGLLYHCKNNLSGM--NGEDRPGIVHRIDKDTSGLLVVAKNDQAHAFIAKQFEEHSI 168

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y   V+GI +     I   + +           V +       AI++++ ++ F   
Sbjct: 169 KRSYLVFVYGILRPLHGKIETLIGRNKTNRQKMSADVIR----GKDAITNYETLEVFKGN 224

Query: 240 ----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG--------NFTSPIQNK 287
                  ++    TGRTHQ+RVH  H G PI+GD  Y    K                 +
Sbjct: 225 KIPDISLVKCILETGRTHQIRVHMSHKGNPILGDQTYGKKIKKIRGIDQEFEEILKSLKR 284

Query: 288 LYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
             LHA  +   HP     +   + LP  + K  + L
Sbjct: 285 QALHAHTLGFIHPTTNEEVFFASELPDDLNKLKNRL 320


>gi|254441292|ref|ZP_05054785.1| pseudouridine synthase, RluA family [Octadecabacter antarcticus
           307]
 gi|198251370|gb|EDY75685.1| pseudouridine synthase, RluA family [Octadecabacter antarcticus
           307]
          Length = 344

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 81/355 (22%), Positives = 143/355 (40%), Gaps = 50/355 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M+    +    +    R+D+    + P    ++   L ++L  G V+V+   V     + 
Sbjct: 1   MSATTVLFTLAENPPARMDKALALNVPLDASLSRSRLMRLLADGAVQVNGAVVTDPRAKP 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  V I   I    H++ E   LD               +++ED  + V NKP G+ V
Sbjct: 61  VEGDAVEILVEIADDYHVLPEDIPLD---------------VVFEDDDLIVINKPTGMVV 105

Query: 120 QGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
               G      ++  L    D+       ++P + HR+D+ETSG+LVVA+T  A   L  
Sbjct: 106 HPAPGTPGGTLVNALLHHCGDALSGVGGEKRPGIVHRIDKETSGLLVVAKTDRAHHGLAA 165

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE-- 220
            F    +++ Y ++ +G+P +    +           N L  ++ +        KQ    
Sbjct: 166 QFEAHTVERHYRAICYGVPDSNDPRVRGIKGASFDPGNILKLQTQLARHKHDRQKQAVVW 225

Query: 221 KGANYAISHFKVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK- 277
               +A++  +++           ++    TGRTHQ+RVH  H G  ++GD  Y    K 
Sbjct: 226 HNGRHAVTRARIVQPLGNPAVAAVMDCWLETGRTHQIRVHMTHAGHGLIGDPTYGGRRKL 285

Query: 278 --------GNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
                   G   +    +  LHA  +   HP    + +  AP+PA M++   +LG
Sbjct: 286 SEKAVGEAGRIAAYTFPRQALHAATLGFQHPVSKEMLRFEAPMPADMIRLIAALG 340


>gi|323159115|gb|EFZ45108.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           E128010]
 gi|323177278|gb|EFZ62866.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           1180]
          Length = 300

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 138/317 (43%), Gaps = 41/317 (12%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
            +P  +   +++ +   +V V+ K   K   ++  G+ V I   I        +   LD 
Sbjct: 1   MFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLD- 59

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPR 145
                         ++YED  I V NKP  + V  G+G     +   L  +       PR
Sbjct: 60  --------------IVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPR 105

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIAN 200
             + HRLD++T+G++VVA+T  A   L ES + R I + Y ++  G         E I+ 
Sbjct: 106 AGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISR 165

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K++H+    +            A++H+++++ F +    L ++  TGRTHQ+RVH  
Sbjct: 166 HPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMA 215

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPL 311
           H+  P+VGD  Y    +    +           ++  LHA  + L HP  G  ++  AP+
Sbjct: 216 HITHPLVGDPVYGGRPRPPKGASEAFISMLRKFDRQALHATMLRLYHPISGIEMEWHAPI 275

Query: 312 PAHMVKTWDSLGFKYDR 328
           P  MV+  + +   ++ 
Sbjct: 276 PQDMVELIEVMRADFEE 292


>gi|260575494|ref|ZP_05843493.1| pseudouridine synthase, RluA family [Rhodobacter sp. SW2]
 gi|259022414|gb|EEW25711.1| pseudouridine synthase, RluA family [Rhodobacter sp. SW2]
          Length = 356

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 79/348 (22%), Positives = 138/348 (39%), Gaps = 50/348 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVR 66
           VV  ++   RLD+      P    ++   L K++  G V ++   V     R+  GQ   
Sbjct: 22  VVIGEDPPDRLDKALARQVPEDAALSRSRLMKMIADGDVTLEGVAVTNPKARVAEGQEYL 81

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +                L  +V++    + +   +++ED+ + V +KP G+ V    G  
Sbjct: 82  LR---------------LAPAVDIDAQPEDIPLTVVWEDADLIVVDKPVGMVVHPAPGSY 126

Query: 125 IAYHIDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  L    D+       ++P + HR+D++TSG+LVVA+T  A   L   F    +
Sbjct: 127 TGTLVNALLHHCGDTLSGVGGAKRPGIVHRIDKDTSGLLVVAKTDRAHHGLAAQFEAHSV 186

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKK----------SHIGGDYVHVVKQNE--KGANYAI 227
            + Y +LV G P      +                 +++        +Q        +A+
Sbjct: 187 TRHYIALVHGAPNAADPRLRGIRGVSFEPGGIVCIATNLARHKTDRQRQAVLFDSGRHAV 246

Query: 228 SHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           +  +V++ +        +E    TGRTHQ+RVH  H G  ++GD  Y    K    +  +
Sbjct: 247 TRVRVLESYGTPPVAALVECWLETGRTHQIRVHMSHAGHALLGDQTYGGRRKVAPKAVGE 306

Query: 286 ---------NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
                     +  LHA  +   HP  G  L  T+PLPA M     +L 
Sbjct: 307 AVAQAANDFPRQALHAASLGFVHPVSGEELLFTSPLPADMAALTAALR 354


>gi|255325321|ref|ZP_05366427.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           tuberculostearicum SK141]
 gi|255297886|gb|EET77197.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           tuberculostearicum SK141]
          Length = 308

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 143/325 (44%), Gaps = 28/325 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++   +    E MR D         ++     ++   G V +D + +  + R+ SG VV
Sbjct: 4   QMRSFPIPEGLEGMRADAALAKLL-GLSRSATAQLCAEGSVTIDSQELGKSERLTSGNVV 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +         + + +K L     L +  D     +LY D+ I   +KP G++     G 
Sbjct: 63  SV--------LLPEPEKPLLPREELVEGMD-----VLYNDADIICVHKPVGVAAHPSVGW 109

Query: 125 IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + G L++           ++  + HRLD  TSG++VVA +  A   L  +F+ R +
Sbjct: 110 DGPTVIGGLRAAGYTVASSGPTERKGIVHRLDVGTSGVMVVASSERAYSALKHAFKYRSV 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++V G+P   +  +   + +    G  +  +          A++H+ +I+ F ++
Sbjct: 170 KKTYHAVVQGLPDPIEGTVDAPIGRHPKSGWKFAVL-----DDGKAAVTHYSLIEAF-RE 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E+   TGRTHQ+RVH    G P VGD  Y ++        +Q + +LHA  +   H
Sbjct: 224 ASLIEVHLETGRTHQIRVHMSATGHPCVGDPMYGSDPNLAKRLGLQ-RQWLHAVKLGFTH 282

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  G+  +I AP PA +    + L 
Sbjct: 283 PGTGKWFEIEAPYPADLEHALEVLR 307


>gi|1143378|dbj|BAA09443.1| ORFX [Zymomonas mobilis]
          Length = 317

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 135/327 (41%), Gaps = 29/327 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + V +  +    RLDR   +    ++   L+ ++ SG V  + +          G +VR
Sbjct: 3   TEQVTLTEEMIGWRLDRALASLITRLSRERLKNLISSGCVS-NSQ----------GALVR 51

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            P               L    +       +   +++ED  + V NKPAG+ V   +G  
Sbjct: 52  DPAFKIKSLDCFTVDIPLPRPAH--NEPQDIPLEIVFEDEHLLVVNKPAGMVVHPAAGNY 109

Query: 127 YHI--DGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            +   +  L              +P + HR+D++TSG+LVVA+T  A   L   F    I
Sbjct: 110 DNTLVNALLYHCAGKLSGIGGVARPGIVHRIDKDTSGLLVVAKTDPAHAGLAAQFADHSI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G P   +  +   L + S +    + +V         A++H+ +I    + 
Sbjct: 170 NRRYRAIVDGNPSL-QGHVDAPLARSS-VNRQKMAIVSDGR--GKRAVTHYCMI-TPLKN 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN---FTSPIQNKLYLHARYMD 296
              +E +  TGRTHQ+RVH   +G  ++GD  Y  + K +     S    +  LHA ++ 
Sbjct: 225 ASLIECRLETGRTHQVRVHMSSIGHSLLGDPVYGRSKKAHHALLQSLAFQRQALHAAHLG 284

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP  G+ +   A +P  M   +  L
Sbjct: 285 FIHPISGKQVDFDAEMPQDMQLLFKML 311


>gi|311741553|ref|ZP_07715377.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           pseudogenitalium ATCC 33035]
 gi|311303723|gb|EFQ79802.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           pseudogenitalium ATCC 33035]
          Length = 308

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 143/325 (44%), Gaps = 28/325 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++   +    E MR D         ++     ++   G V +D + +  + R+ SG VV
Sbjct: 4   QMRSFPIPEGLEGMRADAALAKLL-GLSRSATAQLCAEGSVTIDSQELGKSERLTSGNVV 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +         + + +K L     L +  D     +LY D+ I   +KP G++     G 
Sbjct: 63  SV--------LLPEPEKPLLPREELVEGMD-----VLYNDADIICVHKPVGVAAHPSVGW 109

Query: 125 IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + G L++           ++  + HRLD  TSG++VVA +  A   L  +F+ R +
Sbjct: 110 DGPTVIGGLRAAGYTVASSGPTERKGIVHRLDVGTSGVMVVASSERAYSALKHAFKYRSV 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++V G+P   +  +   + +    G  +  +          AI+H+ +I+ F ++
Sbjct: 170 KKTYHAVVQGLPDPIEGTVDAPIGRHPKSGWKFAVL-----DDGKAAITHYSLIEAF-RE 223

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E+   TGRTHQ+RVH    G P VGD  Y ++        +Q + +LHA  +   H
Sbjct: 224 ASLIEVHLETGRTHQIRVHMSATGHPCVGDPMYGSDPNLAKRLGLQ-RQWLHAVKLGFTH 282

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  G+  +I AP PA +    + L 
Sbjct: 283 PGTGKWFEIEAPYPADLEHALEVLR 307


>gi|308178003|ref|YP_003917409.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
 gi|307745466|emb|CBT76438.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
          Length = 321

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 82/320 (25%), Positives = 151/320 (47%), Gaps = 19/320 (5%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             ++ +V++++    R++++ ++    +    + K++R GQ+RV+ K+V+   R+ +   
Sbjct: 16  AKIETIVIDSEHTGRRIEKYLRSALKSMPAGQMFKLMRKGQLRVNGKKVQEGYRLAANDK 75

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +P          +E +I      L +    L++ +++ED  + V +KPAGI V  G+ 
Sbjct: 76  ITLPAFHA---QPTREPRIEVPPALLKR----LRNTVVHEDEDVLVIDKPAGIPVHKGTD 128

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--IQKI 182
               +    +           L+HRLD++TSG+LV+A+T +  ++L E  R R   I++ 
Sbjct: 129 NPAGVIEAFRQLRPEL-PDLELSHRLDRDTSGLLVLAKTPSILRYLHEMLRDREDEIERH 187

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G        I   LL+ +    D +      +     A +   V     ++   
Sbjct: 188 YLALVAGSWNEDTAVIHTPLLRLA----DRMVA----DPTGQRAETRVWVQQRVGKRATI 239

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           L++Q  TGR HQ+RVH    G PI GD +Y  A F           L+LHA  + +P P+
Sbjct: 240 LDVQLMTGRKHQIRVHLQSEGHPIAGDDRYGFAKFNSRVEQLGGRGLFLHATKLVIPKPD 299

Query: 302 GGRLQITAPLPAHMVKTWDS 321
           G  L + AP+P    +   +
Sbjct: 300 GQELVVEAPMPQRWKQLLKA 319


>gi|297559888|ref|YP_003678862.1| pseudouridine synthase [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
 gi|296844336|gb|ADH66356.1| pseudouridine synthase, RluA family [Nocardiopsis dassonvillei
           subsp. dassonvillei DSM 43111]
          Length = 308

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 76/329 (23%), Positives = 142/329 (43%), Gaps = 28/329 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V+ + V +  E  RLD      +  ++     +I+  G V VD      ++R+ +G 
Sbjct: 1   MSDVRSLPVPDGLEGDRLDSAIARMF-GLSRTRAAEIIGDGGVLVDGSEAAKSDRVSAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-- 121
            + +         + + + +                 +++ED+ I V +KP G+      
Sbjct: 60  WLEVTLPPPPTAPVPRPEAVP-------------GMRIVHEDTDIIVVDKPVGVVAHPTV 106

Query: 122 GSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G L S V        ++  + HRLD  T+G++VVA++  A   L  +F+ R
Sbjct: 107 GWTGPSVLEGLLASGVQVATSGAAERQGIVHRLDANTTGLMVVAKSETAYSVLKRAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G P   +  +   + +     G +  V      G   +++H+   + F 
Sbjct: 167 TVDKHYHTLVQGHPDPLRGTVDAPIDRHPAGDGRWAVVA-----GGRPSVTHYDTQEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    LE++  TGRTHQ+RVH   +  P VGD  Y A+        +  + +LHA  +  
Sbjct: 221 RAASLLEIKLETGRTHQIRVHMSALRHPCVGDMLYGADPTLAERLGV-RRQWLHAVRLGF 279

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP   R ++ ++P P  +    ++L   
Sbjct: 280 DHPTEHRPVEFSSPYPDDLAAAVETLRED 308


>gi|239947789|ref|ZP_04699542.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           endosymbiont of Ixodes scapularis]
 gi|239922065|gb|EER22089.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           endosymbiont of Ixodes scapularis]
          Length = 303

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 88/301 (29%), Positives = 152/301 (50%), Gaps = 11/301 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++V+ + R++ G  + I    N      K
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNSQKVEASLRVKGGDKIFINDKFNLPVKQPK 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +    D+ + L K        L+YED  +   NKPAG++ QGGS I   ID  LK +++ 
Sbjct: 72  KLVFTDAEIKLAKK--ITTDYLIYEDDNLIAINKPAGLATQGGSKIKLSIDSALK-YLNY 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           KG   +L HRLD+ETSG+L++A+   ++  L + F+ + + K Y+++ +G P      + 
Sbjct: 129 KGADFKLVHRLDKETSGLLLIAKNYLSSVKLHDVFKEKLVVKTYFAVTYGKPIKNVGEVR 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + + K          +   + +    AI+++K++         +E  P TGR HQLR+H+
Sbjct: 189 SNIEKSK---RSTPKITDIDSENGKLAITYYKLLKPLDNNLFLIEFTPVTGRMHQLRLHS 245

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKT 318
             +GCPI+GD KY          P    ++LHA  + L     G  +++ A LP +  + 
Sbjct: 246 KLLGCPILGDDKYG----NKEIMPYSKYMFLHANNICLYEKIFGKEIKLEAKLPFYFTRH 301

Query: 319 W 319
            
Sbjct: 302 L 302


>gi|323156250|gb|EFZ42409.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           EPECa14]
          Length = 300

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 139/317 (43%), Gaps = 41/317 (12%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
            +P  +   +++ +   +V V+ K   K   ++  G++V I   I        +   LD 
Sbjct: 1   MFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGELVAINAEIEEEARFEPQDIPLD- 59

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPR 145
                         ++YED  I V NKP  + V  G+G     +   L  +       PR
Sbjct: 60  --------------IVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPR 105

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIAN 200
             + HRLD++T+G++VVA+T  A   L ES + R I + Y ++  G         E I+ 
Sbjct: 106 AGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISR 165

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K++H+    +            A++H+++++ F +    L ++  TGRTHQ+RVH  
Sbjct: 166 HPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMA 215

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPL 311
           H+  P+VGD  Y    +    +           ++  LHA  + L HP  G  ++  AP+
Sbjct: 216 HITHPLVGDPVYGGRPRPPKGASEAFISMLRKFDRQALHATMLRLYHPISGIEMEWHAPI 275

Query: 312 PAHMVKTWDSLGFKYDR 328
           P  MV+  + +   ++ 
Sbjct: 276 PQDMVELIEVMRADFEE 292


>gi|25028588|ref|NP_738642.1| putative ribosomal large subunit pseudouridine synthase
           [Corynebacterium efficiens YS-314]
 gi|259507644|ref|ZP_05750544.1| RluA family RNA pseudouridine synthase [Corynebacterium efficiens
           YS-314]
 gi|23493873|dbj|BAC18842.1| putative ribosomal large subunit pseudouridine synthase
           [Corynebacterium efficiens YS-314]
 gi|259164823|gb|EEW49377.1| RluA family RNA pseudouridine synthase [Corynebacterium efficiens
           YS-314]
          Length = 309

 Score =  229 bits (584), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 78/330 (23%), Positives = 140/330 (42%), Gaps = 30/330 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS  +  + + V      MR+D         I+     ++  +G V VD   V+ ++R+ 
Sbjct: 1   MSRQS--RTLPVPEGLAGMRVDAALSKLL-GISRTTAAELAEAGDVSVDGSAVRKSDRLV 57

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ +     A   + +E+ +                 +LY D  +   NKP G++  
Sbjct: 58  ADSMLDVLLPEPAQPLVPREEIVP-------------GLDILYADDDLIAVNKPVGVAAH 104

Query: 121 GGSGIA-YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G     + G L +           ++  +  RLD  TSG++VVA +      L  +F
Sbjct: 105 PTVGWEGPTVVGGLAAAGFRISTSGPPERKGIVQRLDVGTSGVMVVAASERGYTVLKRAF 164

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R +QK Y +LV G P   +  I   + +    G  +            +A++H++ I+
Sbjct: 165 RDRTVQKTYHALVQGHPDPTEGTIEAPIGRHPSSGWRFAVTT-----DGKHAVTHYETIE 219

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F Q+   +++   TGRTHQ+RVH   +  P  GD  Y ++   +    +  + +LHA  
Sbjct: 220 AF-QEATLVKVHLETGRTHQIRVHFSALHHPCCGDPMYGSDPALSERLGLI-RQWLHAVS 277

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +   HP  GR ++IT+P P  +    D L 
Sbjct: 278 LGFHHPADGRWMEITSPYPDDLQHALDVLR 307


>gi|46198348|ref|YP_004015.1| ribosomal large subunit pseudouridine synthase D [Thermus
           thermophilus HB27]
 gi|46195970|gb|AAS80388.1| ribosomal large subunit pseudouridine synthase D [Thermus
           thermophilus HB27]
          Length = 300

 Score =  229 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 87/322 (27%), Positives = 146/322 (45%), Gaps = 41/322 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MRLD+        ++    Q  +++G+VRV  + V K   R++                 
Sbjct: 1   MRLDQAVAEALS-VSRAKAQAWIQAGRVRVGDRVVLKPAYRLKG---------------- 43

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSW 136
            +E  +           + L   +LYED  +   NKP G+      G+ +  +   L + 
Sbjct: 44  -EEVAVEPVEEAPMVLPEDLPIPILYEDEDVLALNKPPGLLTHPAPGVYSGTVVNLLLAR 102

Query: 137 VDSKGQK-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                +K       P + HRLD++TSG+LVVA+     + L  +FR R + K Y ++  G
Sbjct: 103 YYGPVEKGPPELVRPGIVHRLDKDTSGVLVVAKHGGVLEGLARAFRDRLVMKRYLAITEG 162

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            P  ++  +   + +         H +      A YA + F+V+   A  +  +E +PHT
Sbjct: 163 HP--REGVLIAPIGRHPRE----RHKMHVGGLAARYAETEFQVLAT-AGPYALVEARPHT 215

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QIT 308
           GRTHQ+RVH  ++G PI+GD  Y         SP   +  LHA  + +PHP  GR+ ++ 
Sbjct: 216 GRTHQIRVHLKYLGAPILGDELYGRK------SPHIGRQALHAYELRIPHPRTGRILELL 269

Query: 309 APLPAHMVKTWDSLGFKYDRNL 330
           AP+P  M   W++LG ++   +
Sbjct: 270 APVPQDMAAAWEALGGRWPEEV 291


>gi|67459415|ref|YP_247039.1| ribosomal large subunit pseudouridine synthase [Rickettsia felis
           URRWXCal2]
 gi|75536169|sp|Q4UKQ3|RLUC_RICFE RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|67004948|gb|AAY61874.1| Ribosomal large subunit pseudouridine synthase [Rickettsia felis
           URRWXCal2]
          Length = 305

 Score =  229 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 89/301 (29%), Positives = 150/301 (49%), Gaps = 11/301 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R++ G  + I    N      +
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNSQKAEASLRVKGGDKIFINDKFNLPVKQPE 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +    D+ + L K        L+YED  +   NKPAG++ QGGS I   ID  LK +++ 
Sbjct: 72  KLVFTDAEIKLAKK--ITTDYLIYEDDNLIAINKPAGLATQGGSKINLSIDSALK-YLNY 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           KG   +L HRLD+ETSG+L++A+   +   L ++F+ + + K Y+++ +G P      + 
Sbjct: 129 KGADFKLVHRLDKETSGLLLIAKNYLSNVKLHDAFKEKLVVKTYFAVTYGKPIKNVGEVR 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + + K     G    +     +    AI+++K++         +E  P TGR HQLR+HA
Sbjct: 189 SNIEKSK---GSTPKITDIYSENGKLAITYYKLLKSLDNNLFLIEFTPVTGRMHQLRLHA 245

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKT 318
             +GCPIVGD KY          P    ++LHA  + L     G  + + A LP +    
Sbjct: 246 KLLGCPIVGDDKYG----NKEIMPYSKYMFLHANNICLSEKIFGKEINLEAKLPFYFTDK 301

Query: 319 W 319
           +
Sbjct: 302 F 302


>gi|329890476|ref|ZP_08268819.1| pseudouridine synthase, RluA family protein [Brevundimonas diminuta
           ATCC 11568]
 gi|328845777|gb|EGF95341.1| pseudouridine synthase, RluA family protein [Brevundimonas diminuta
           ATCC 11568]
          Length = 341

 Score =  229 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 135/331 (40%), Gaps = 45/331 (13%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVRIPPVIN 72
           D   +RLD+     +P ++   LQ +L  G V  D   V   + + Q G  VV +PPV  
Sbjct: 29  DAPGVRLDKALAEAFPTLSRARLQALLADGAVTRDGLTVSNGSAKAQPGLYVVALPPVAP 88

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHID 130
           A                 T   + +   +L+ED+ + V +K  G++     G      ++
Sbjct: 89  A-----------------TPQPEAIPLTVLFEDADLIVIDKAPGMAAHPAPGCETGTLVN 131

Query: 131 GFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             L    DS        +P + HRLD++TSG++V A++  A   L+  F    I++ Y +
Sbjct: 132 ALLAHCGDSLSGIGGVARPGIVHRLDKDTSGVMVAAKSDRAHAGLSALFAAHDIERTYVA 191

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------ 239
           L  G P  +K  I   + + S      + V++    G   AI+ + V   F +       
Sbjct: 192 LTRGAPSPEKGRIQTQIGRSSG-DRKKMAVLRS---GGREAITDYVVQQTFGRPAKASNA 247

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-----IQNKLYLHA 292
                +    HTGRTHQ+RVH    G P++GD  Y +                 +  LHA
Sbjct: 248 RLAARVACTLHTGRTHQIRVHMASKGAPLLGDPVYGSGSPAAAVRAAVEASGLKRQALHA 307

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +   HP  G  L+     P  M +  ++L
Sbjct: 308 AVLGFIHPVTGEALRFETAPPDDMQR-LEAL 337


>gi|301024188|ref|ZP_07187895.1| pseudouridine synthase, RluA family [Escherichia coli MS 196-1]
 gi|312973162|ref|ZP_07787335.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           1827-70]
 gi|299880530|gb|EFI88741.1| pseudouridine synthase, RluA family [Escherichia coli MS 196-1]
 gi|310333104|gb|EFQ00318.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           1827-70]
 gi|315615335|gb|EFU95969.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           3431]
          Length = 300

 Score =  229 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 77/317 (24%), Positives = 138/317 (43%), Gaps = 41/317 (12%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
            +P  +   +++ +   +V V+ K   K   ++  G+ V I   I        +   LD 
Sbjct: 1   MFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLD- 59

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPR 145
                         ++YED  I + NKP  + V  G+G     +   L  +       PR
Sbjct: 60  --------------IVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPR 105

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIAN 200
             + HRLD++T+G++VVA+T  A   L ES + R I + Y ++  G         E I+ 
Sbjct: 106 AGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISR 165

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K++H+    +            A++H+++++ F +    L ++  TGRTHQ+RVH  
Sbjct: 166 HPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMA 215

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPL 311
           H+  P+VGD  Y    +    +           ++  LHA  + L HP  G  ++  AP+
Sbjct: 216 HITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPI 275

Query: 312 PAHMVKTWDSLGFKYDR 328
           P  MV+  + +   ++ 
Sbjct: 276 PQDMVELIEVMRADFEE 292


>gi|220934527|ref|YP_002513426.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. HL-EbGR7]
 gi|219995837|gb|ACL72439.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. HL-EbGR7]
          Length = 323

 Score =  229 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 99/323 (30%), Positives = 153/323 (47%), Gaps = 12/323 (3%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           S  + V  V V + +   RLD +       +   ++ ++LR G+VRV+K R K   R+Q 
Sbjct: 6   SPPSKVTLVRVGSGQAGQRLDNFLLGQLKGVPKSHVYRLLRKGEVRVNKGRAKPEYRLQE 65

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  VRIPPV  A +     Q  L   +     ++ L+  +L ED  + V NKPAG++V G
Sbjct: 66  GDQVRIPPVRQAASPPDDSQMPLPGEL-----AETLRRAVLLEDEDLLVLNKPAGLAVHG 120

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+   +   ++  +  +     L HRLD+ETSG LV+A+ R A     E+ +   + K
Sbjct: 121 GSGVKLGLIEAMRR-LRPRADFLELAHRLDRETSGCLVLAKRREALLAFHEALKSGGVDK 179

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +L+ G+ +     I+  L +K   G        + ++   +A S F           
Sbjct: 180 HYVTLLAGVWQGGPRRISETLARK---GPRTQVRKVEVDEDGKHAESFFFP-RRHFVDAT 235

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
            + ++  TGRTHQ+RVHA H G P+ GD +Y    F          + +LHA  +    P
Sbjct: 236 LMGVEIGTGRTHQIRVHAAHEGFPVAGDSQYGDFEFNRRMKRLGLKRQFLHAETLRFHLP 295

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
              R  QI APLPA +    + L
Sbjct: 296 GHERPYQIQAPLPADLEAVLERL 318


>gi|220904866|ref|YP_002480178.1| pseudouridine synthase, RluA family [Desulfovibrio desulfuricans
           subsp. desulfuricans str. ATCC 27774]
 gi|219869165|gb|ACL49500.1| pseudouridine synthase, RluA family [Desulfovibrio desulfuricans
           subsp. desulfuricans str. ATCC 27774]
          Length = 525

 Score =  229 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 89/320 (27%), Positives = 144/320 (45%), Gaps = 32/320 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M+ +Q + +   +   RLDR      P ++   LQK++++G   VD    K    +++ G
Sbjct: 1   MSRLQ-LKITAGQAGKRLDRILGATVPELSRAALQKVVQAGCCTVDGLPEKRPAAKMRMG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q V +               + +    L      L+  LL++D  + V NKPAG++V   
Sbjct: 60  QTVTL--------------DLPEHPDRLQPEEGHLE--LLWQDDHLVVCNKPAGLTVHPC 103

Query: 123 S-----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  +   + G        +GQ+P + HRLD++TSG+LVVA T A    L  +F  R
Sbjct: 104 PSCPEQTLVQRLLGRFPQLSRLEGQRPGIVHRLDKDTSGLLVVALTEADCLALAAAFAER 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           ++ K Y +LV G+P  + +C    L +  H        V   ++G   A + ++ +    
Sbjct: 164 QVHKEYLALVSGLPPLEGQC-REPLGR--HPTAKIKMAVVPEDQGGRNAFTEWRRLWNTD 220

Query: 238 QK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 L ++ HTGRTHQ+RVH  H+G P++GD  Y      N       +  LHA  + 
Sbjct: 221 DGSVSLLAVRIHTGRTHQIRVHMTHLGYPLLGDRLYAPKAVQNMA----PRQMLHAWRLG 276

Query: 297 LPHPEGGR-LQITAPLPAHM 315
             HP  G  ++ T P P  M
Sbjct: 277 FTHPASGEDMRFTCPPPHDM 296


>gi|332088103|gb|EGI93228.1| ribosomal large subunit pseudouridine synthase D [Shigella boydii
           5216-82]
          Length = 300

 Score =  229 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 138/317 (43%), Gaps = 41/317 (12%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
            +P  +   +++ +   +V V+ K   K   ++  G+ V I   I        +   LD 
Sbjct: 1   MFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLD- 59

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPR 145
                         ++YED  I V NKP  + V  G+G     +   L  +       PR
Sbjct: 60  --------------IVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPR 105

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIAN 200
             + HRLD++T+G++VVA+T  A   L ES + R I + Y ++  G         E I+ 
Sbjct: 106 AGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISR 165

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K++H+    +            A++H+++++ F +    L ++  TGRTHQ+RVH  
Sbjct: 166 HPTKRTHMAVHPM---------GKPAVTHYRIMEHF-RVHMRLRLRLETGRTHQIRVHMA 215

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPL 311
           H+  P+VGD  Y    +    +           ++  LHA  + L HP  G  ++  AP+
Sbjct: 216 HITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPI 275

Query: 312 PAHMVKTWDSLGFKYDR 328
           P  MV+  + +   ++ 
Sbjct: 276 PQDMVELIEVMRADFEE 292


>gi|146282969|ref|YP_001173122.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           stutzeri A1501]
 gi|145571174|gb|ABP80280.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           stutzeri A1501]
          Length = 266

 Score =  229 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 95/276 (34%), Positives = 154/276 (55%), Gaps = 13/276 (4%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKI 108
           +K R+K   ++Q+G +VR+PP+  A      E + L   +      + L+S ++YED  +
Sbjct: 2   NKGRIKPEYKLQAGDLVRVPPLRLAERD---EPEPLAQGL-----LERLESAIVYEDKAL 53

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V NKPAGI+V GGSG++Y +   L+  +    ++  L HRLD++TSG+L+VA+ R+  +
Sbjct: 54  IVLNKPAGIAVHGGSGLSYGVIEALRQ-LRPDAKELELVHRLDRDTSGLLMVAKKRSMLR 112

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           HL ++ R   + K Y +LV G     K+ ++  LLK +   G+ +  V ++      A++
Sbjct: 113 HLHQALRGDGVDKRYMALVRGRWDTSKKQVSAPLLKNTLRSGERMVEVTED---GKEALT 169

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNK 287
            F+V+  F      +E +P TGRTHQ+RVHA H G  I GD KY   +F          +
Sbjct: 170 LFRVLRRFGDFATLVEAKPVTGRTHQIRVHARHAGHSIAGDSKYGDEDFTREVRELGGKR 229

Query: 288 LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
           L+LHA  + +P P+GG L + AP+     +T + LG
Sbjct: 230 LFLHAYALKVPLPDGGELTLEAPVDEVWARTLERLG 265


>gi|312196232|ref|YP_004016293.1| pseudouridine synthase, RluA family [Frankia sp. EuI1c]
 gi|311227568|gb|ADP80423.1| pseudouridine synthase, RluA family [Frankia sp. EuI1c]
          Length = 325

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 73/323 (22%), Positives = 136/323 (42%), Gaps = 27/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  + +RLD      +  ++      ++  GQV VD      ++R++ G  + +
Sbjct: 20  RSLPVPDGLDGLRLDAAIARMF-GLSRTVAAALVDDGQVSVDGAAPGRSDRVRGGAWLEV 78

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                       E       V     +      +++ED  + V +KP G++     G   
Sbjct: 79  ------------ELPPSPRPVTEVIATPVDGLTIVHEDDDLVVVDKPVGVAAHPAPGYTG 126

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  + HRLD  T+G++VVA++      L  +FR R + K
Sbjct: 127 PTVIGALAAAGYRISTSGAAERQGVVHRLDVGTTGVMVVAKSELGYAALKRAFREREVDK 186

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G P   +  +   + +     G +  V          +++H+ + + F +   
Sbjct: 187 RYRAVVQGHPDPLRGTVDAPIDRHPRKPGLFAVVA-----DGKPSVTHYDLEEAF-RAAS 240

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE++  TGRTHQ+RVH   +  P VGD  Y A+        +  + +LHA  +   HP 
Sbjct: 241 LLEVRLETGRTHQIRVHMSALRHPCVGDLAYGADPTLAEKLGL-RRQWLHAFQLSFEHPA 299

Query: 302 GGRL-QITAPLPAHMVKTWDSLG 323
            GRL   T+P P  + +  + L 
Sbjct: 300 DGRLVTFTSPDPPDLAEALERLR 322


>gi|257069409|ref|YP_003155664.1| pseudouridine synthase, RluA family [Brachybacterium faecium DSM
           4810]
 gi|256560227|gb|ACU86074.1| pseudouridine synthase, RluA family [Brachybacterium faecium DSM
           4810]
          Length = 318

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 80/317 (25%), Positives = 147/317 (46%), Gaps = 19/317 (5%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + ++V+ +    RLD++ ++    +    L ++LR G++RV+ ++ + N R+Q+G  + +
Sbjct: 16  RTLIVDVEHAGRRLDKFLRSRVKGVPAGLLFRLLRQGKLRVNGRKAQQNYRLQAGDEITV 75

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P +    +                     L+   L+ED  + + +KPAG++V  G+ +  
Sbjct: 76  PALRIDADAAP-------PPAVPPALIQQLRGTALHEDEDLLIIDKPAGVAVHRGTDVPA 128

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--IQKIYWS 185
            +   L+           L HRLD+ TSG+L +A++ +  ++L +  R R   I++ Y +
Sbjct: 129 GVIDALRQLRPEL-PDLELIHRLDRSTSGVLALAKSPSMLRYLHDLLRDREDEIERRYLA 187

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G    +   +   L ++ +            +     A +H  V   F  +   LE+
Sbjct: 188 LVAGHWPAETTILDAPLRREEN--------RVVVDPDGQRAETHVAVAQRFGNRATLLEV 239

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +  TGR HQ+RVH  H G PI GD +Y  + F     S     L+LHA  + +P P+G  
Sbjct: 240 RLLTGRKHQIRVHLQHAGHPIAGDDRYGDDAFNRRAASLGGTGLHLHAAELVIPRPDGTT 299

Query: 305 LQITAPLPAHMVKTWDS 321
           L +TAP P    +   +
Sbjct: 300 LAVTAPTPRRWEQLLRA 316


>gi|221195841|ref|ZP_03568894.1| ribosomal large subunit pseudouridine synthase D [Atopobium rimae
           ATCC 49626]
 gi|221184315|gb|EEE16709.1| ribosomal large subunit pseudouridine synthase D [Atopobium rimae
           ATCC 49626]
          Length = 338

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 74/337 (21%), Positives = 146/337 (43%), Gaps = 38/337 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQS 61
           +   V  ++V  + + +R+D +        +     K++  G+V ++   V   + ++  
Sbjct: 1   MAERVFDILVGPEGDGIRIDAFLAAQDELPSRSACAKLVEEGKVFINGTPVSSKSEKVLL 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + +         ++ +    +    L   +  +   + +ED  + V +K AG+    
Sbjct: 61  GDRLMV---------VLPKG---EPEAGLLVPNPDIPLDIRFEDQYLIVLSKQAGLVCHP 108

Query: 122 GSGIAYHIDGFLKSWVDSKG-----------QKPRLTHRLDQETSGILVVARTRAAAQHL 170
             G   HID  L + + +              +P + HRLD +TSG++V A++    + L
Sbjct: 109 SPG---HIDDTLANALVAHCGYEHLGLLQGEDRPGIVHRLDMDTSGLMVAAKSDEVQKAL 165

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            +  R+R + + Y  LV G     +  I   + +      D + +   +  GA  AI+ F
Sbjct: 166 QDLIRLRVLDRRYVVLVQGYVAPDEGTIETGIARSI---RDRLKMTVTDAPGAREAITTF 222

Query: 231 KVIDCF-----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           + ++ F      + +  LE   +TGRTHQ+RVH  H+G P+VGD  Y    K    +   
Sbjct: 223 RTLERFEAGRRGEGYSLLECHLYTGRTHQIRVHMRHVGHPVVGDQLYG--RKDERLNLGL 280

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
            + +LH+ ++   HP  G  +++T  LP  ++    S
Sbjct: 281 KRQFLHSWHIQFEHPVTGETIELTDSLPQDLLAALKS 317


>gi|323702975|ref|ZP_08114632.1| pseudouridine synthase, RluA family [Desulfotomaculum nigrificans
           DSM 574]
 gi|323532106|gb|EGB21988.1| pseudouridine synthase, RluA family [Desulfotomaculum nigrificans
           DSM 574]
          Length = 293

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 69/315 (21%), Positives = 130/315 (41%), Gaps = 33/315 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             V  D+    ++R  +     ++   L++  +   V +D + V  N R+  G ++ I  
Sbjct: 5   TTVCQDQAGWTVERVLRQGL-GVSRSLLRRAKQRRAVLLDGQPVNSNVRVAPGAILEISM 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAY 127
                + +                 + +   ++YED  I   +KP G+ V          
Sbjct: 64  QQEVSSIV----------------PEPMDLSIIYEDQDIMAVHKPPGMLVHPLTTEPTGT 107

Query: 128 HIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +G L  W+      + R  HR+D++TSG+++VAR     Q L        + + Y ++
Sbjct: 108 LANGVLYYWLQQGSPARFRPVHRIDRDTSGLVLVARNSYVHQQLQSQINQGLMCRRYLAM 167

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    +K  I   + +++      V            AI+H++V+   +     + ++
Sbjct: 168 VTGKLAKQKGTITAPIDREAGSLIKRVV-----TPAGKPAITHYRVLRQLSWG-SLVRVE 221

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  H+G P++GD  Y  +        +  +  LH  Y+   HP  G+ +
Sbjct: 222 LVTGRTHQVRVHMSHIGHPLLGDDLYGGDLS------LIKRQALHCAYLAFSHPVTGQLI 275

Query: 306 QITAPLPAHMVKTWD 320
           ++  PLP  M    +
Sbjct: 276 KLACPLPGDMKALLN 290


>gi|119503335|ref|ZP_01625419.1| ribosomal large subunit pseudouridine synthase C [marine gamma
           proteobacterium HTCC2080]
 gi|119460981|gb|EAW42072.1| ribosomal large subunit pseudouridine synthase C [marine gamma
           proteobacterium HTCC2080]
          Length = 320

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 92/318 (28%), Positives = 154/318 (48%), Gaps = 16/318 (5%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V++ VV  +E   RLD + +     +    + + +R G+VRVDK RVK + R+++G  V
Sbjct: 17  KVEWRVVLPEEAGQRLDNFLQRVRGGVPKTRIYRAIRKGEVRVDKGRVKPDTRLEAGVSV 76

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPP+                          L++ ++ E+S + V NKP G++V GGSGI
Sbjct: 77  RIPPLRVPEKAEA---------AGAAGWRTRLRASIIREESTLLVVNKPPGLAVHGGSGI 127

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +   L++  ++  +   L HRLD++TSG+L+VAR  +  ++L    R   I K Y  
Sbjct: 128 NVGLIETLRAMYETD-RYLELVHRLDRDTSGLLLVARRASTLRNLHVLLRSNGIDKRYLC 186

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G      + +   L K +   G+    V         +++ F+V+  ++     +E 
Sbjct: 187 LVNGRWPAHLKRVDAPLEKFALPSGERRVKV---AATGRQSLTTFRVVRRWSS-ATLVEA 242

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-QNKLYLHARYMDLPHPEGGR 304
           +P TGRTHQ+RVH  H G PI+GD KY           +   +L+LHA  ++    +   
Sbjct: 243 KPVTGRTHQIRVHCQHAGFPILGDAKYADEAAVRIADKLGLKRLFLHAASLNFR-LDDQN 301

Query: 305 LQITAPLPAHMVKTWDSL 322
             + A LP  + +  D++
Sbjct: 302 YSLEAGLPTELERLLDAI 319


>gi|73666929|ref|YP_302945.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia canis
           str. Jake]
 gi|72394070|gb|AAZ68347.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia canis
           str. Jake]
          Length = 308

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 103/315 (32%), Positives = 165/315 (52%), Gaps = 14/315 (4%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +Y  V+ D++++R+D++ +     I    ++K LR G V +D  +VK N RI++G V+ I
Sbjct: 4   KYYTVKEDDQDVRVDKFVRRVLK-IPQSLVEKFLRKGIVLLDNAKVKSNTRIKTGNVIYI 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                    I  ++     S  L    + + + +LYED  + + NKPAG+SVQGG+ +  
Sbjct: 63  KCNTIIGEEIHTKRICKTDSSYLI---NLISNSILYEDDDVLIINKPAGVSVQGGTKVRI 119

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            I   L    D  G+  R+ HRLD++TSGIL++AR   A++ +   F+ RR++K Y +L 
Sbjct: 120 SISDILDKIRD--GESMRIVHRLDKDTSGILMLARNARASRLIMHEFKNRRVEKKYLALT 177

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GIPKN    I + + KK H   ++   +         AI+ F V+         LE++P
Sbjct: 178 QGIPKNDVGEINHSITKKKH---NFYENIGTGNSIFQEAITSFFVLKKLPYDIGLLELKP 234

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGR HQ+R+H  H+GC I+GD KY           +Q  L+ H   +D+      +L  
Sbjct: 235 KTGRKHQIRIHLSHIGCSIIGDKKYGKFCNHVLNDHLQ--LHAHFLSIDI---GNKKLSF 289

Query: 308 TAPLPAHMVKTWDSL 322
           TAP+P +M  T  +L
Sbjct: 290 TAPMPDYMKDTIMNL 304


>gi|317490447|ref|ZP_07948929.1| RluA family pseudouridine synthase [Eggerthella sp. 1_3_56FAA]
 gi|316910440|gb|EFV32067.1| RluA family pseudouridine synthase [Eggerthella sp. 1_3_56FAA]
          Length = 344

 Score =  228 bits (582), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 68/341 (19%), Positives = 129/341 (37%), Gaps = 39/341 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ +   V   D+   RLD        + +     + +  G V V+   V   + +  G 
Sbjct: 1   MSRMLSYVAAPDDAGQRLDALLAARGLYPSRSAAARAVDDGLVFVNGAEVAKKHPVAPGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +            ++ Q I                 + +ED  + V +K  G+      
Sbjct: 61  TIVYQVEEPVEPGPLRGQPI--------------DLDIRFEDEDLIVLSKQVGLVCHPS- 105

Query: 124 GIAYHIDGFLKSWV------------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
               H DG L + +              +  +  + HRLD++TSG+++ A+       L 
Sbjct: 106 --VDHDDGTLVNALIYHCGAENLCNVQGEDDRLGIVHRLDRDTSGLMLAAKNDETGYALM 163

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              R R + + Y +LV G+  +    I   + +      +   +  ++   A  AI+ F+
Sbjct: 164 SDIRDRAVDRRYLALVHGVIAHDTGMIDAPIARAEK---ERTRMAVRDTPSAREAITTFR 220

Query: 232 VIDCFAQ-----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQ 285
           V++ F        +  ++ +  TGRTHQ+RVH  +   P+VGD  Y              
Sbjct: 221 VLERFEHGGRDDGYTLIDCKLFTGRTHQIRVHLEYAKHPLVGDPAYTSGAPSAPAADLGL 280

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           ++ +LH+  +   HP  G  L+    LP+ + +  D L  +
Sbjct: 281 DRQFLHSFQLSFQHPVTGEGLRFADNLPSDLQEALDDLASR 321


>gi|182439225|ref|YP_001826944.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces griseus subsp. griseus NBRC 13350]
 gi|326779877|ref|ZP_08239142.1| pseudouridine synthase, RluA family [Streptomyces cf. griseus
           XylebKG-1]
 gi|178467741|dbj|BAG22261.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces griseus subsp. griseus NBRC 13350]
 gi|326660210|gb|EGE45056.1| pseudouridine synthase, RluA family [Streptomyces cf. griseus
           XylebKG-1]
          Length = 313

 Score =  228 bits (582), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 139/333 (41%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    ++ + V +  E  R+D      +   +     ++  +G+V+VD      + R+ 
Sbjct: 1   MSTHPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVQVDGSVAGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPGAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKAQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R + K Y +LV G P      I   + +  H   DY   V         +++H+ +I
Sbjct: 166 FRDRVVDKKYHALVQGHPDPMSGTIDAPIGR--HPNHDYKWAVTAE---GKPSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + + +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAY-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTLAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
            +   HP  G  ++ ++  PA +    D++  +
Sbjct: 279 RLGFEHPSDGSWVEFSSTYPADLQHALDTISAE 311


>gi|262202888|ref|YP_003274096.1| pseudouridine synthase [Gordonia bronchialis DSM 43247]
 gi|262086235|gb|ACY22203.1| pseudouridine synthase, RluA family [Gordonia bronchialis DSM
           43247]
          Length = 308

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 139/327 (42%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  + MRLD         ++   +  +   G V VD   V  ++R+ +G 
Sbjct: 1   MRESRMLPVPDGLDGMRLDAALARML-GLSRTVVAGLADDGDVTVDGVAVGKSHRLAAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ +          ++   + D               ++Y DS I V +KP G++     
Sbjct: 60  LLHVTLPEPERPLQVEPTPVED-------------LDVIYHDSDIIVVDKPVGVAAHPSL 106

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  +  RLD  TSG++VVA +  A   L  +F+ R
Sbjct: 107 GWSGPTVLGALDAAGYRISTSGAPERQGIVSRLDVGTSGVMVVAVSERAYSVLKRAFKQR 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G        I   + +  H G D+   V  N      +I+H++ ++ FA
Sbjct: 167 TVDKGYHALVQGHLDPPTGTIDAPIGR--HPGSDWRFAVTAN---GKPSITHYETLEMFA 221

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                L++   TGRTHQ+RVH   +  P  GD  Y  +        + ++ +LHAR +  
Sbjct: 222 -AASLLDIHLETGRTHQIRVHFAALHHPCCGDPTYGGDPVLAKRLGL-DRQWLHARSLGF 279

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLG 323
            HP +G R++ T+P P  +    D L 
Sbjct: 280 AHPADGRRVEFTSPYPHDLQHALDVLR 306


>gi|325288659|ref|YP_004264840.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324964060|gb|ADY54839.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 295

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 77/322 (23%), Positives = 147/322 (45%), Gaps = 33/322 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           + +Y++Y  +  + + + ++ + K     I+   +QK+ R   + ++ K+V    ++++G
Sbjct: 1   MKSYLKY-TIAEEHQGLTVEEYLKKAL-QISGRKIQKLTRLTGILLNGKKVFLQKKLRAG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
            ++ +  + +    +  E   +D               +LYED  + V NKPAG+ V   
Sbjct: 59  DLLSVLSLQDRSYGVNPEAGAID---------------ILYEDESLIVLNKPAGLLVHPA 103

Query: 122 GSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           G   +  +  +L  +    G     R  HRLD++TSG LV A+       + +     +I
Sbjct: 104 GMTTSGTLANYLADYFRQLGVICTIRPLHRLDRDTSGCLVFAKGPVVQSKMEDLLAAGKI 163

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +L  G+    +  I+  +          +     +EKG+  AI+H++ +  F Q 
Sbjct: 164 KRTYLALAEGLIIPAEGTISAPIASDPAKPNRRM----VSEKGSQ-AITHYRKLKTFGQN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E+   TGRTHQ+RVH  ++G PI+GD  Y         SP+ ++  LHA  +   H
Sbjct: 219 -SLVELNLETGRTHQIRVHLAYLGHPILGDRMYGRK------SPLISRQALHAVKISFQH 271

Query: 300 PEGG-RLQITAPLPAHMVKTWD 320
           P     + + A LP   +K  +
Sbjct: 272 PVKETEICLEAKLPGDFLKCLE 293


>gi|297180551|gb|ADI16763.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0010_11B23]
          Length = 307

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 83/321 (25%), Positives = 150/321 (46%), Gaps = 33/321 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +  N R+D +  N+   I+   +Q+++  G+V ++ K  K N  ++   +V I   +
Sbjct: 8   IDEENSNNRVDIFLANNLDAISRGIVQQLISEGKVTINGKETKRNYLLKPSDIVEITFEL 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--I 129
            +               N    +  +   + +E+   +V NK +G++V  G+G   +  I
Sbjct: 68  ES---------------NGEDEAQDIPVDITFENDDFFVINKHSGLTVHPGAGQKDNTLI 112

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +G L    + +   +  L HRLD++TSG++V+A+   A   LTE  + + IQ+ Y++LV 
Sbjct: 113 NGILHIRKEQRDIPRYGLVHRLDKDTSGLMVLAKNLKAHTVLTELIQAKSIQRKYYALVH 172

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G P + K  I   + +  H     +  VK    G   AI+HFK I+   + F  L ++  
Sbjct: 173 GTPISGK-TIDLPIGR--HPKNRLLFCVKD---GGREAITHFK-IEKRFKNFSLLNVELE 225

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLHARYMDLPHPE 301
           TGRTHQ+RVH  H+G PI GD  Y +        P +        +  LH+  +     +
Sbjct: 226 TGRTHQIRVHLKHIGHPIAGDASYNSIKIWKDAIPKELEAINNLQRQALHSYSLKFQFLD 285

Query: 302 GGRLQITAPLPAHMVKTWDSL 322
             +    + +P  + KT + L
Sbjct: 286 -EKFFFESKIPDDLEKTMELL 305


>gi|227548930|ref|ZP_03978979.1| pseudouridine synthase [Corynebacterium lipophiloflavum DSM 44291]
 gi|227078955|gb|EEI16918.1| pseudouridine synthase [Corynebacterium lipophiloflavum DSM 44291]
          Length = 308

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 139/323 (43%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V    E MR+D+     +  ++     +++  G V +D  RV  ++R++SG ++ +
Sbjct: 6   RALPVPEGLEGMRVDQAVSKLF-GLSRSVAAELVAEGSVLIDASRVAKSDRVRSGALLEV 64

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                                   K        ++Y D  +   +KP G++     G   
Sbjct: 65  TL-------------PEPRQAPAPKAELVDGLSIIYSDDDVIAVDKPVGVAAHPTLGWEG 111

Query: 127 YHIDGFLKSWV-----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  +  RLD  TSG++VVA +      L  +F+ R + K
Sbjct: 112 PTVVGGLTAMGFTLPDAGPPERKGIVQRLDVGTSGVMVVANSVQGYSVLKRAFKERTVSK 171

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++V G+P      I   + +    G  +            +A++H+++++ F ++  
Sbjct: 172 LYHAVVQGLPDPIAGTIDAPIGRHPSSGWKFAVTS-----DGRHAVTHYELVEAF-REAS 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE++  TGRTHQ+RVH   +G P VGD  Y +N        +  + +LHA  +   HP 
Sbjct: 226 LLEIRLETGRTHQIRVHMSAVGHPCVGDPMYGSNPNLTMRVGLV-RQWLHATKLGFTHPR 284

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G  +++ +P PA +    + L 
Sbjct: 285 TGDYMEVESPYPADLAHALEVLR 307


>gi|320093965|ref|ZP_08025793.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 178 str. F0338]
 gi|319979099|gb|EFW10614.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 178 str. F0338]
          Length = 304

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 71/327 (21%), Positives = 130/327 (39%), Gaps = 32/327 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +     R+D         ++      +   G V ++ +    ++R+ +  
Sbjct: 1   MGEGRLLPVPDALVGERVDAALSRML-GMSRSKCADLAAQGAVTLNGRTAGKSDRLGAAD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I     A+  +                       +LY+D  I V +KP G++   G 
Sbjct: 60  IIGIDMPDPAVKAVP-----------------VTGMDILYDDEDIVVVDKPVGVAAHTGP 102

Query: 124 G------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      +        +       ++  + HRLD  TSG ++VA++  A   +  +F+ R
Sbjct: 103 GWEGPTVLGNLAAAGYRITTHGPPERQGIVHRLDVGTSGAMMVAKSELAYSVMKRAFKER 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K+Y ++V G        I   + +  H   ++   V     G   AI+H+  ++  A
Sbjct: 163 TVTKVYHAVVAGHLDPASGTIDAPIGR--HPSREWRMAVID---GGKRAITHYDTLEMMA 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
              C  E+   TGRTHQ+RVH   +G P VGD  Y A+  G        + +LHA  +  
Sbjct: 218 -GACLAEIHLETGRTHQIRVHMAAVGHPCVGDAFYGADP-GQAERLGLVRQWLHAVELSF 275

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLG 323
            HP  G    + +P P+ +    + L 
Sbjct: 276 AHPRTGAPTTVRSPYPSDLAAALEVLR 302


>gi|282854248|ref|ZP_06263585.1| pseudouridine synthase, RluA family [Propionibacterium acnes J139]
 gi|282583701|gb|EFB89081.1| pseudouridine synthase, RluA family [Propionibacterium acnes J139]
 gi|314923234|gb|EFS87065.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL001PA1]
 gi|314967001|gb|EFT11100.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL082PA2]
 gi|314980957|gb|EFT25051.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL110PA3]
 gi|315091688|gb|EFT63664.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL110PA4]
 gi|315093078|gb|EFT65054.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL060PA1]
 gi|327327821|gb|EGE69597.1| RNA pseudouridine synthase, RluA family [Propionibacterium acnes
           HL103PA1]
          Length = 306

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 135/322 (41%), Gaps = 29/322 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +  ++V +  +  R+D         ++   +  ++  G V +  + V + + R+ +GQ++
Sbjct: 1   MSVLLVPDGLDGERVDVA-AARMSGVSRSRISSLIEDGGVFLGGQLVSRASVRVATGQML 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +          I  Q +                 ++++DS I V +KPAG++     G 
Sbjct: 60  DVDLCDPVATPSITPQIVE-------------GMRIIHDDSDIVVVDKPAGVAAHPSLGW 106

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + +              ++  +  RLD  TSG++VVA++  A   L ++FR R +
Sbjct: 107 EGPSVVEHLAAAGFAISTSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y +LV G P      I   + +          V      G  ++++H++ ++ F + 
Sbjct: 167 DKVYLALVQGHPDPFTGTIDAPIGRDHRHDWKMAIV-----DGGRHSVTHYETVEAF-RH 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L++   TGRTHQ+RVH   +  P  GD  Y  +        ++ + +LHA  +   H
Sbjct: 221 ATLLKVHLETGRTHQIRVHMAAIKHPCCGDPLYGCDPALAKELGLE-RQWLHAGELSFTH 279

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  +   A LPA +    D
Sbjct: 280 PGSGEWVTFHADLPADLQNALD 301


>gi|328955606|ref|YP_004372939.1| pseudouridine synthase, RluA family [Coriobacterium glomerans PW2]
 gi|328455930|gb|AEB07124.1| pseudouridine synthase, RluA family [Coriobacterium glomerans PW2]
          Length = 350

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 80/333 (24%), Positives = 140/333 (42%), Gaps = 40/333 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPP 69
           VV+  E   RLD +              +++  G V VD   +   +  + SGQ V +  
Sbjct: 20  VVDATEAGQRLDAYLGGRRACPTRSACARLIERGAVSVDGAMQCSKSFIVLSGQRVDLAY 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  ++  + I                 + +ED  + V +K  G+    G G   H 
Sbjct: 80  SEQVEAAVVAGEPI--------------PLDIRFEDEYLIVLSKQRGLVCHPGHG---HD 122

Query: 130 DGFLKSWVDSKG-----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            G L + +                +P + HRLD++TSG+++ A+  A  + L +  R+R 
Sbjct: 123 SGTLANALVHHCGIDHLGTLQGEDRPGIVHRLDRDTSGLMLAAKDDATQRALQDLIRLRT 182

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA- 237
           + + Y +LV G+       I   L + S    D + +   ++  A  AI+ F+V++ F  
Sbjct: 183 LDRRYIALVHGVIARDAGTIDTGLARSS---RDRLKMAVSDDPAARQAITTFRVLERFDA 239

Query: 238 ----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
               + +  +E   +TGRTHQ+RVH  ++  PIVGD  Y    K         + +LH+ 
Sbjct: 240 ARGDEGYTLIECHLYTGRTHQIRVHMRYISHPIVGDPLYG--RKSKRAELGLTRQFLHSW 297

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            +   HP  G R+++T  LP  +  + D L  +
Sbjct: 298 RLRFTHPVSGERVEVTDTLPWDLAASLDDLAKR 330


>gi|289805597|ref|ZP_06536226.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 274

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 95/286 (33%), Positives = 154/286 (53%), Gaps = 16/286 (5%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           +VRV+KKR+K   +++SG  VRIPPV       + E++    S +L K +  L  ++LYE
Sbjct: 1   EVRVNKKRIKPEYKLESGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYE 53

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  I V NKP+G +V GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R
Sbjct: 54  DDHILVLNKPSGTAVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKR 112

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           +A + L E  R + +QK Y +LV G  ++  + +   LLK     G+ +  V Q      
Sbjct: 113 SALRSLHEQLREKGMQKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GK 169

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFT 281
            + + FKV + +A     +   P TGRTHQ+RVH  + G PI  D +Y     + +    
Sbjct: 170 PSETRFKVEERYA-FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEA 228

Query: 282 SPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
                +L+LHA  +   HP  G  ++I AP+   + +  + L  K 
Sbjct: 229 GTGLKRLFLHAAALKFTHPGTGDVMRIEAPMDKQLKRCLEVLRSKA 274


>gi|239906997|ref|YP_002953738.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Desulfovibrio magneticus RS-1]
 gi|239796863|dbj|BAH75852.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Desulfovibrio magneticus RS-1]
          Length = 554

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 92/330 (27%), Positives = 139/330 (42%), Gaps = 36/330 (10%)

Query: 15  DEENMRLDRWFKNHY--PHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVI 71
           D    RLD ++        I+   ++  + +G   VD +   K   +++ G+ + +    
Sbjct: 22  DAAGTRLDAFWSARLASEDISRAKVRAAIEAGLALVDGEICRKPGLKLRGGEALTL---- 77

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHI 129
             L     E K  D  + L           LY D  + V NKPAG+++   S       +
Sbjct: 78  -RLPETPSEAKAEDGELKL-----------LYLDGDVLVLNKPAGLTIHPASSQPDGTLV 125

Query: 130 DGFLKSWVDSK---GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +  L  + D +   G +P + HRLD++TSG+L+VA+T +A   L   F  RR+ K Y +L
Sbjct: 126 NRLLHHFPDMRAMAGDRPGIVHRLDKDTSGLLLVAQTESARLALAADFAERRVAKTYLAL 185

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEM 245
           V G P+     I   + +          V     KG   A S +K+           LE+
Sbjct: 186 VHGRPERSDGVIELPVGRDPKHPTKMAVVA----KGGREAKSSWKLAWTAPDGTASLLEV 241

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNFTSPIQNKLYLHARYMDLPH 299
              TGRTHQ+RVH   MG PIVGD  Y A        +G   + +  +  LHA  +   H
Sbjct: 242 AIATGRTHQIRVHMAAMGHPIVGDAVYGARQHSDWTRRGGAMARLAKRQMLHAWKLAFSH 301

Query: 300 P-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           P  G  L    P PA   +    LG +  R
Sbjct: 302 PGTGEELSFCQPPPADFWRLLLMLGRRCQR 331


>gi|182414827|ref|YP_001819893.1| RluA family pseudouridine synthase [Opitutus terrae PB90-1]
 gi|177842041|gb|ACB76293.1| pseudouridine synthase, RluA family [Opitutus terrae PB90-1]
          Length = 311

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 81/330 (24%), Positives = 140/330 (42%), Gaps = 34/330 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  Q   V +   + R D+         + V LQ+   +G V      +  +  + +G 
Sbjct: 1   MTP-QTYTVPDTIRHGRADKVLAAGVTEHSRVALQRSFDAGLVTRGGVPIGRDTTVTAGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +           I                +  +   +L+ED  +   NK AG+ V    
Sbjct: 60  TIEFSFAEIKPTEI---------------KAVDIPLTVLFEDKHMLAVNKAAGMVVHP-- 102

Query: 124 GIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G+A   D  + + +             ++P + HRLD+ET+G++VVA+T AA + L + F
Sbjct: 103 GVATSEDTLVHALLAHCAGSLSGIGGVERPGIVHRLDKETTGVIVVAKTDAAHRALADQF 162

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             R ++K Y +LV G+P+     I   + +   +    + V     +G   A + +++++
Sbjct: 163 ATRTLKKEYVALVAGVPRLLSGSIDRAIARH-PVHRHRMTV----GEGGRPARTDWELVE 217

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F      +  +  TGRTHQ+RVH   +G PI+GD  Y    +    +    ++ LHA +
Sbjct: 218 AFGDIGALVRCRIFTGRTHQIRVHLKSLGHPILGDALYGWKPEPRLATQPA-RVMLHAEH 276

Query: 295 MDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           + L HP  G  L + APLP   V     L 
Sbjct: 277 LVLTHPISGKELDLRAPLPKDFVAMIKELR 306


>gi|75676616|ref|YP_319037.1| pseudouridine synthase, RluD [Nitrobacter winogradskyi Nb-255]
 gi|74421486|gb|ABA05685.1| ribosomal large subunit pseudouridine synthase D [Nitrobacter
           winogradskyi Nb-255]
          Length = 351

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 83/353 (23%), Positives = 146/353 (41%), Gaps = 62/353 (17%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV------------KFNN 57
           VVV  DE  +RLDR    H P ++   L+ ++ +G V + KK                  
Sbjct: 17  VVVTGDEGAVRLDRVLAVHSPDLSRSRLKSLILAGHVSIVKKASVAERTEGPVPVRDPAY 76

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
            +  G  + I                +  +++     + +   ++YED  + V NKP G+
Sbjct: 77  HVAPGDTITIH---------------VPPAISAKPQGEAIALDIIYEDDDLIVINKPKGL 121

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQ 168
            V   +G  +H    + + +   G+         +P + HRLD++T+G++V A+  AA +
Sbjct: 122 VVHPAAG--HHTGTLVNALIAHCGETLSGIGGVCRPGIVHRLDKDTTGLMVAAKNDAAHK 179

Query: 169 HLTESFRMR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            L   F        +++ Y + VWG+P      +   +  +     + + V      G  
Sbjct: 180 SLGAQFADHGRTGAMRRGYLAFVWGLPNRSHGTVDAPI-DRHPYAREKMAVRA----GGR 234

Query: 225 YAISHFKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            AI+H++V   F  +        L  Q  TGRTHQ+RVH  H+G P++GD  Y  +F+  
Sbjct: 235 EAITHWEVRQAFNGRDGKPVAALLACQLATGRTHQIRVHLAHVGHPLMGDGVYGPHFRTK 294

Query: 280 FTSPIQ---------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +   +          +  LHA  + L HP   + L+    LP  +     +L
Sbjct: 295 VSHLGERAAAALSALGRQALHASLLVLEHPRTEKVLRWETGLPEDLSSLQMAL 347


>gi|226325122|ref|ZP_03800640.1| hypothetical protein COPCOM_02914 [Coprococcus comes ATCC 27758]
 gi|225206470|gb|EEG88824.1| hypothetical protein COPCOM_02914 [Coprococcus comes ATCC 27758]
          Length = 341

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 78/339 (23%), Positives = 151/339 (44%), Gaps = 22/339 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V  +E   RLD+    +  +     + K+LR   ++++ K+ + N ++  G  V 
Sbjct: 1   MQKITVSANEAGQRLDKLLGKYLSNAPMSFVYKMLRKKNIKLNGKKAQGNEKLTKGDQVE 60

Query: 67  IPPVINALNHII-KEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +    +                 +L +  +  ++  ++YED  I + NKP+G+  Q  + 
Sbjct: 61  VFLSDDTWQKFAGAPGAEKQLPADLARAMESSIRLSVIYEDPDILILNKPSGMLSQKAAP 120

Query: 125 IAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
               ++ ++ +++  KG          +P + +RLD+ TSG++   ++ A  Q L+E  R
Sbjct: 121 SDLSLNEYMIAYLLKKGDLKLAELATFRPSVCNRLDRNTSGLVTAGKSLAGLQQLSEILR 180

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R ++K Y ++V G+ K++++ I  +LLK        V ++K+ +  A    + +  +  
Sbjct: 181 DRTVKKYYLTIVDGVIKDRQK-IEGYLLKNEMTN--QVKILKEAKGEAKPIATEYIPLAD 237

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHAR 293
             Q+    ++   TGRTHQ+R H    G PI+GD KY      +            LHA 
Sbjct: 238 NGQQTIL-KVHLITGRTHQIRAHLSSTGHPIIGDSKYGNPKVNSIFRKKYALKYQLLHAW 296

Query: 294 YMDLPHPEGG-----RLQITAPLPAHMVKTWDSLGFKYD 327
            M  P  E         ++TAPLP          G +++
Sbjct: 297 KMQFPKREDALAKVSEKEVTAPLPEGFTTIIKGEGLEWE 335


>gi|269792594|ref|YP_003317498.1| pseudouridine synthase, RluA family [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100229|gb|ACZ19216.1| pseudouridine synthase, RluA family [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 320

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 80/316 (25%), Positives = 136/316 (43%), Gaps = 34/316 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPV 70
           V  D E  RLD         ++     K+++ G V+V    RVK + +++ G  V     
Sbjct: 24  VGEDGEGHRLDFVLSREI-GVSRSYASKLIKEGMVQVSWSPRVKPSLKVRVGGTVT---- 78

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                        L  S  L      +   ++Y+D  + V +KPAG+ V    G      
Sbjct: 79  -----------AQLPPSEELELEPQDVPFRVVYQDQDLVVVDKPAGLVVHPAPGHWRGTL 127

Query: 129 IDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + G L  + D    +  ++P + HRLD  TSG++VVAR   A + L  +F+ RR+ K+Y 
Sbjct: 128 VHGLLYRYPDLMELNGVKRPGIVHRLDATTSGLMVVARNGLAMEGLVRAFKDRRVGKVYL 187

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G  + +     +  + +       +  V         A++ ++VI      +  + 
Sbjct: 188 AMAAGTLRGEGSV--SLPIGRDPDNRKRMACVPW----GREALTRYRVIWSRG-GYSLVA 240

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
            Q  TGRTHQ+RVH   +G P+VGD  Y       F      +++LH+  ++  HP  G 
Sbjct: 241 CQIKTGRTHQIRVHMRSLGHPLVGDRIYGGPCPEGFP---LGRVFLHSWRLEFDHPRTGA 297

Query: 304 RLQITAPLPAHMVKTW 319
            +    PLP  +V+  
Sbjct: 298 PMSFICPLPPDLVRFI 313


>gi|157827593|ref|YP_001496657.1| ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           OSU 85-389]
 gi|157802897|gb|ABV79620.1| Ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           OSU 85-389]
          Length = 310

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 89/300 (29%), Positives = 155/300 (51%), Gaps = 11/300 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ +  YP +    ++K LR  Q+ V+ K+ + + R+  G  + I    N    I +
Sbjct: 21  RLDKYLRRLYPLLTQGVIEKALRQKQIIVNSKKAEASLRVVEGDEIFIHDKFNLP--IAQ 78

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             K++ +   +T         L+YED  I   NKPAG++ QGGS I   +D  LK +++S
Sbjct: 79  PTKLVFTDAEITLAKKITTEYLIYEDDNIIAINKPAGLATQGGSKINLSVDSALK-YLNS 137

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G   +L HRLD+ETSG+L++A+   ++  L ++F+ + ++K Y ++ +G P   +  + 
Sbjct: 138 QGADFKLVHRLDKETSGLLLIAKNYVSSVKLHDAFKEKLVEKTYLAVTYGKPIKDQGEVK 197

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + K     G    +   N+     AI+++K++         +E  P TGR HQLR+HA
Sbjct: 198 TNIEKSK---GSIPKITDINDNNGKLAITYYKLLKSLTNNLFLVEFIPITGRMHQLRLHA 254

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKT 318
             +GCPI GD+KY      +   P    ++LHA  + L     G  + + A LP++  + 
Sbjct: 255 KLLGCPIFGDNKYG----NDKLMPYSKYMFLHANNIVLSKKVFGKEVNLEAKLPSYFNRV 310


>gi|262184460|ref|ZP_06043881.1| pseudouridylate synthase [Corynebacterium aurimucosum ATCC 700975]
          Length = 292

 Score =  227 bits (580), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 80/312 (25%), Positives = 134/312 (42%), Gaps = 28/312 (8%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D         I+   + ++  +G V +D   V  + R+ +G  + +         I 
Sbjct: 1   MRVDAALAKLL-GISRARVSQLCAAGDVEIDGAAVGKSERLNAGGWIDVMMPAPEEPLIP 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWV 137
           KE+ +                 +LY D  I    KP G++     G     + G L++  
Sbjct: 60  KEELVE-------------GMDVLYADEDIICVCKPVGVAAHPTLGWDGPTVIGGLRAAG 106

Query: 138 DSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +       ++  + HRLD  TSG++VVA +  A   L  +FR R +QK Y ++V G+P 
Sbjct: 107 YALADAGPTERKGIVHRLDVGTSGVMVVAASERAYSQLKNAFRERTVQKTYHAVVQGLPD 166

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I   + +    G  +  V          A++H+K+++ F ++   LE+   TGRT
Sbjct: 167 PIVGTIDAPIGRHPSAGWKFGVV-----DDGKPAVTHYKLLEAF-REASLLEVHLETGRT 220

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           HQ+RVH    G P VGD  Y  +        + N+ +LHA  +   HP  G+  + TAP 
Sbjct: 221 HQIRVHMSATGHPCVGDPMYGCDPNLAKRVGL-NRQWLHAVELGFTHPGTGKWFECTAPY 279

Query: 312 PAHMVKTWDSLG 323
           P  +    + L 
Sbjct: 280 PEDLKHAVEVLR 291


>gi|297566959|ref|YP_003685931.1| pseudouridine synthase, RluA family [Meiothermus silvanus DSM 9946]
 gi|296851408|gb|ADH64423.1| pseudouridine synthase, RluA family [Meiothermus silvanus DSM 9946]
          Length = 315

 Score =  227 bits (580), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 94/337 (27%), Positives = 157/337 (46%), Gaps = 51/337 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
           + +RLD+         + V  Q+ +  G VRVD K V K + R++ G+ V + P      
Sbjct: 7   QGVRLDQALAYEAKT-SRVKAQEWIEMGIVRVDGKPVTKASYRLK-GEWVEVEPPPERPP 64

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFL 133
            +  E   L+               +LYED  + V NKPAG+      G+     ++  L
Sbjct: 65  SVEPENVPLE---------------ILYEDQDLVVVNKPAGMITHPAPGVTSGTLVNAIL 109

Query: 134 KSWVDSKG-----------------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             + + +G                  +P + HRLD++TSG+++VAR  AA + L+E+FR 
Sbjct: 110 GRYAELRGVLATQLEDEEAPPRPELIRPGIVHRLDKDTSGVILVARHEAAHRRLSEAFRG 169

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K Y ++  G P  K+   A  + +   +    +HV         YA + F+++   
Sbjct: 170 RSVYKRYLAITVGHP--KEGTFAAPIGRH-PVDRTRMHV---GGIAPRYAETDFEIL-AI 222

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           A ++  +    HTGRTHQ+RVH   +  PI+GD  Y         S +  +  LHA  + 
Sbjct: 223 AGEYALVSAILHTGRTHQIRVHLKALHAPILGDDVYGK------PSGLIARQALHAYELR 276

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           + HP  G+ L+ TAP+PA M   W++LG  + + + +
Sbjct: 277 IQHPRSGKYLEFTAPVPADMAGAWEALGGVWPQGIEL 313


>gi|261400963|ref|ZP_05987088.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           lactamica ATCC 23970]
 gi|269209209|gb|EEZ75664.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           lactamica ATCC 23970]
          Length = 295

 Score =  227 bits (580), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 90/297 (30%), Positives = 148/297 (49%), Gaps = 24/297 (8%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +   ++ +I+R+G+VR++KKR K ++RI  G  VRIPPV  A   +  E++    +    
Sbjct: 1   MPKSHIHRIIRAGEVRLNKKRCKPDSRIAEGDTVRIPPVRVAEKEMPSERRAAVPAREFD 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                    ++YED  + V +KP+G++V GGSG+++ +   L+     + +   L HRLD
Sbjct: 61  ---------IVYEDDALLVIDKPSGVAVHGGSGVSFGVIEQLRRAR-PEARYLELVHRLD 110

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L+VA+ R+A   L E+ R    +KIY +L  G   +    I   L K +   G+
Sbjct: 111 KDTSGLLMVAKKRSALVKLHEAIRNDHPKKIYLALGVGKLPDDNFHIKLPLFKYTGAQGE 170

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQ---------KFCWLEMQPHTGRTHQLRVHALHM 262
            +  V ++      A + F+V+  F+              +     TGRTHQ+RVH    
Sbjct: 171 KMVRVSED---GQSAHTVFRVLSRFSDGILHGVGLSHLTLVRATLKTGRTHQIRVHLQSQ 227

Query: 263 GCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           GCPI GD +Y               +++LHA  + L HP  G  L + A LP  + +
Sbjct: 228 GCPIAGDERYGDYQANRRLQKLGLKRMFLHASELHLNHPLTGEPLVLKAELPPDLAQ 284


>gi|239940558|ref|ZP_04692495.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces roseosporus NRRL 15998]
 gi|239987042|ref|ZP_04707706.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces roseosporus NRRL 11379]
 gi|291443991|ref|ZP_06583381.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           roseosporus NRRL 15998]
 gi|291346938|gb|EFE73842.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           roseosporus NRRL 15998]
          Length = 313

 Score =  227 bits (580), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 140/333 (42%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    ++ + V +  E  R+D      +   +     ++  +G+V+VD      + R+ 
Sbjct: 1   MSTHPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVQVDGSVAGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  I V  KP G++ 
Sbjct: 60  GGAWLEVEMPGAPAPVQIVAEP--------------VEGMEIVHDDDDIVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGTTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKAQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R + K Y +LV G P      I   + +  H   DY   V         +++H+ +I
Sbjct: 166 FRDRVVDKRYHALVQGHPDPMSGTIDAPIGR--HPNHDYKWAVTAE---GKPSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + + +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAY-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTLAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            +   HP +G  ++ ++  PA +    D++  +
Sbjct: 279 RLGFEHPADGSWVEFSSTYPADLQHALDTISAE 311


>gi|332670137|ref|YP_004453145.1| RluA family pseudouridine synthase [Cellulomonas fimi ATCC 484]
 gi|332339175|gb|AEE45758.1| pseudouridine synthase, RluA family [Cellulomonas fimi ATCC 484]
          Length = 312

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 75/330 (22%), Positives = 141/330 (42%), Gaps = 26/330 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+ + V +     R+D         ++     +I   G VRVD + V  ++R+ +G 
Sbjct: 1   MPEVRALPVPDGLAGERVDAALARLL-GLSRTRAAEIAADGGVRVDGREVGKSDRLLAGG 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                    + +    D +  +           +KP G++     
Sbjct: 60  WLEVEIPDPQGPAAPVVVPEPVPGMRIVHDDDDVVVV-----------DKPVGVAAHPSP 108

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  + HRLD  TSG++VVA++  A   L  +F+ R
Sbjct: 109 GWTGPTVVGALAAAGYRISTSGAAERQGVVHRLDVGTSGLMVVAKSEHAYTVLKRAFKER 168

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K+Y +LV G P+     I   + +  H   D+   V  +      +++H++V++   
Sbjct: 169 TVEKVYHALVQGHPEPTTGTIDAPIGR--HPSADWKFAVVAD---GKPSVTHYEVLEMLP 223

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +E+   TGRTHQ+RVH   +  P VGD  Y A+      + + ++ +LHA  +  
Sbjct: 224 S-ASLVEVHLETGRTHQIRVHFAALRHPCVGDLTYGADPSLAARTHL-SRQWLHAVRLGF 281

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            HP  G  L++T+  P  + +  ++LG  Y
Sbjct: 282 EHPGTGEWLEVTSEYPQDLARALETLGAGY 311


>gi|119961612|ref|YP_947480.1| RNA RluA family pseudouridine synthase [Arthrobacter aurescens TC1]
 gi|119948471|gb|ABM07382.1| putative RNA pseudouridine synthase, RluA family [Arthrobacter
           aurescens TC1]
          Length = 308

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 137/323 (42%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV  +    R+D         I+      ++  G V      +  + ++ +G V+ +
Sbjct: 3   RSVVVPEELAGARVDAGLARLL-DISRSAAALLISEGNVTSGGVPLGKSAKLVAGTVLDV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                                            +L +D    V +KP G++     G + 
Sbjct: 62  TVPER-------------PDPLEVVEEVVEGLKILLDDEDFVVIDKPVGVAAHPSPGWVG 108

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L             ++  + HRLD  TSG++VVA+T  A   L  +F+ R ++K
Sbjct: 109 PTVVGGLAGAGYRISTSGAPERAGIVHRLDVGTSGVMVVAKTEHAYTVLKRAFKERTVEK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++V G+P   +  I   + +  H G D+   V ++      +++H++V++ F  K  
Sbjct: 169 VYHAVVQGLPDPLEGTIDAPIGR--HPGHDWRFAVIED---GRPSVTHYEVLEAFG-KAT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+   TGRTHQ+RVH   +  P  GD  Y A+ +      +  + +LHAR +   HP 
Sbjct: 223 LVEVHLETGRTHQIRVHFSALRHPCAGDLTYGADPRLAANLGL-TRQWLHARQLGFTHPR 281

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            G  +++++  PA +    D L 
Sbjct: 282 TGDWVEVSSEYPADLQYALDLLA 304


>gi|149178869|ref|ZP_01857448.1| ribosomal large subunit pseudouridine synthase D [Planctomyces
           maris DSM 8797]
 gi|148842281|gb|EDL56665.1| ribosomal large subunit pseudouridine synthase D [Planctomyces
           maris DSM 8797]
          Length = 317

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 147/325 (45%), Gaps = 24/325 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++VE+  +  R+DR+   H+ + +   LQ+I+++G  +V+        R+  GQ + I  
Sbjct: 9   LIVEDYLDGARIDRFLSRHFRNYSTHRLQRIVQAGFAKVNGIPADPLQRVFRGQQINIR- 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYH 128
                         L    + T   + L   +LYED+ + + NKP G+     G+ ++  
Sbjct: 68  --------------LPEPPDKTYDPEPLPLEVLYEDAWLIIVNKPPGMIAHPAGNILSGT 113

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +   L+ ++D +       +P + HRLDQ TSGIL+VA+     + L+  F+  R+ K Y
Sbjct: 114 VANALQYYLDQQTGVRSLLRPGIVHRLDQFTSGILIVAKEHLGHRSLSIQFQQNRVSKSY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V   PK       + + +     G  +    +  + A  A + F+V++        +
Sbjct: 174 LAIVRDQPKQDLFENNDAIGEHPTQAGVCMTTHPEALR-AKAAFTRFEVVERLP-GHSLI 231

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              P TGR HQ+RVH   +G PI+ D  Y  + +      + ++  LHA  ++  HP   
Sbjct: 232 RAFPKTGRLHQIRVHLADLGFPIIADDFYGNDARLLDDRELISRQALHAEQIEFSHPVTS 291

Query: 304 -RLQITAPLPAHMVKTWDSLGFKYD 327
            R+ I+A +PA        +   + 
Sbjct: 292 LRMNISAGVPADFQLALQRIRSAWS 316


>gi|91205071|ref|YP_537426.1| ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           RML369-C]
 gi|122425980|sp|Q1RJX7|RLUC_RICBR RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|91068615|gb|ABE04337.1| Ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           RML369-C]
          Length = 301

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 89/300 (29%), Positives = 155/300 (51%), Gaps = 11/300 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ +  YP +    ++K LR  Q+ V+ K+ + + R+  G  + I    N    I +
Sbjct: 12  RLDKYLRRLYPLLTQGVIEKALRQKQIIVNSKKAEASLRVVEGDEIFIHDKFNLP--IAQ 69

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             K++ +   +T         L+YED  I   NKPAG++ QGGS I   +D  LK +++S
Sbjct: 70  PTKLVFTDAEITLAKKITTEYLIYEDDNIIAINKPAGLATQGGSKINLSVDSALK-YLNS 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G   +L HRLD+ETSG+L++A+   ++  L ++F+ + ++K Y ++ +G P   +  + 
Sbjct: 129 QGADFKLVHRLDKETSGLLLIAKNYVSSVKLHDAFKEKLVEKTYLAVTYGKPIKDQGEVK 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + K     G    +   N+     AI+++K++         +E  P TGR HQLR+HA
Sbjct: 189 TNIEKSK---GSIPKITDINDNNGKLAITYYKLLKSLTNNLFLVEFIPITGRMHQLRLHA 245

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKT 318
             +GCPI GD+KY      +   P    ++LHA  + L     G  + + A LP++  + 
Sbjct: 246 KLLGCPIFGDNKYG----NDKLMPYSKYMFLHANNIVLSKKVFGKEVNLEAKLPSYFNRV 301


>gi|317508658|ref|ZP_07966314.1| RluA family pseudouridine synthase [Segniliparus rugosus ATCC
           BAA-974]
 gi|316253061|gb|EFV12475.1| RluA family pseudouridine synthase [Segniliparus rugosus ATCC
           BAA-974]
          Length = 315

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 135/326 (41%), Gaps = 26/326 (7%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + ++ + V      +RLD         ++     ++  +G   +D K    ++R+ +G  
Sbjct: 6   SALRSLPVPEGLAGLRLDAGLARLL-GVSRTKAAELADAGHALIDGKEAGRSDRLVAGAW 64

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +         + ++   +   +N           +LY D  + V  KP  I+V    G
Sbjct: 65  LEVSVPSAPSAPVEEDAPEIIPGLN-----------VLYSDEHVVVVEKPPEIAVHPSVG 113

Query: 125 -IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                + G LK+           ++  +  RLD  TSG++V+A +  A   L  +F+ R 
Sbjct: 114 WSGPTVVGGLKALGFHIATTGVAERQGVVQRLDVGTSGVMVLAASEHAYTVLKRAFKHRE 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y +LV G P      I   + K+   G  +    +       ++++H+  I+ F  
Sbjct: 174 VEKWYEALVQGHPDPSSGTIDAPIGKRPGPGWRFAVTTE-----GRHSVTHYDTIEAFG- 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               + ++  TGRTHQ+RVH   +  P  GD  Y A+ K      +  + +LHAR +   
Sbjct: 228 AASLVSVKLETGRTHQIRVHFSALRHPCCGDMLYGADPKLAARLGL-RRQWLHARRLSFA 286

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G+ ++  + LP  +      L 
Sbjct: 287 HPADGKIMRFESELPQDLQHALGVLR 312


>gi|313672276|ref|YP_004050387.1| pseudouridine synthase, rlua family [Calditerrivibrio nitroreducens
           DSM 19672]
 gi|312939032|gb|ADR18224.1| pseudouridine synthase, RluA family [Calditerrivibrio nitroreducens
           DSM 19672]
          Length = 320

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 78/330 (23%), Positives = 149/330 (45%), Gaps = 31/330 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + + +D  + R+D +      + +    + ++  G V ++ K  K ++++ +G  + 
Sbjct: 16  IDKLDITSDSFSERIDIFLSEKL-NRSRSYFKNLIDEGLVTLNGKICKPSSKVVAGDHII 74

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +    ++++   KE                +   ++Y+     V NKPAG+ V    G  
Sbjct: 75  VLIPDDSIDLTPKE----------------IDFEVIYDSKWYAVINKPAGLVVHPAPGNT 118

Query: 125 IAYHIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
               ++G L   K+  D+   +P + HRLD++TSG+L++A+ R   Q ++E F+ R ++K
Sbjct: 119 TDTLVNGLLAKFKNIDDNDNVRPGIIHRLDKDTSGLLIIAKNRDVRQQMSELFQKREVKK 178

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++  G PKN    I N++ + S      + V+   + G   A+S  K++   +  F 
Sbjct: 179 VYLAVCMGEPKNDYYMIDNFIGR-SLTDRKKMAVL---QNGGKRAVSEVKILKRSSGIF- 233

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
              +  HTGRTHQ+RVH  ++  PI+GD  Y             N+  LHA  +      
Sbjct: 234 LASVAIHTGRTHQIRVHMSYLNYPILGDFLYGG---AKVMKYGINRQALHAYKISFFDFY 290

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
            G  +   A +P  +          +D NL
Sbjct: 291 LGREVSYIAEIPEDIKYLITKYRLDFDINL 320


>gi|94264419|ref|ZP_01288209.1| Pseudouridine synthase, RluD [delta proteobacterium MLMS-1]
 gi|93455176|gb|EAT05394.1| Pseudouridine synthase, RluD [delta proteobacterium MLMS-1]
          Length = 310

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 72/326 (22%), Positives = 138/326 (42%), Gaps = 38/326 (11%)

Query: 17  ENMRLDRWFKNHYPH--INFVNLQKILRSGQVRV------DKKRVKFNNR----IQSGQV 64
              RLD +         +    L+ ++R G V V       ++    + +    +++G  
Sbjct: 2   AGRRLDHFLAEQLQDQELTRSRLRGLIRQGLVTVVPATAAPEQAATPSRKAGLALKAGDR 61

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V +                + ++  +   +  +  ++LYED  + V +KP G+ V   +G
Sbjct: 62  VAVE---------------VPAAEPVALAAQEIPFVVLYEDGDLLVISKPPGVVVHPAAG 106

Query: 125 IA--YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 ++G L    D  G     +P + HRLD++TSG LVVA+   A + L   F+ R 
Sbjct: 107 HHRGTLVNGLLHHCRDLSGISGELRPGIVHRLDKDTSGCLVVAKNDRAHRDLLAQFKNRE 166

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++KIY +L+ G    ++  +   + +          +  +       A++H+++   F  
Sbjct: 167 VEKIYLALLSGKLAGEQGRVEGAIGRHPKQ---RQKMAVRPAGEGRAALTHWRLRQRFTA 223

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  + ++  +GRTHQ+RVH   +G P+ GD  Y    + +    I  + +LHA  +   
Sbjct: 224 GYTLVSLRLDSGRTHQIRVHMASLGHPVAGDALYGKGGERDRRYGI-TRQWLHAAELAFR 282

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLG 323
           HP  G  L+   PL   + +    L 
Sbjct: 283 HPVSGEPLRCRGPLWPDLEQVLAELA 308


>gi|302528436|ref|ZP_07280778.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           AA4]
 gi|302437331|gb|EFL09147.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           AA4]
          Length = 308

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 141/323 (43%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  + MR+D         ++   +  +  +G V +D +    ++R+ +G ++ +
Sbjct: 4   RMLPVPDGLDGMRVDAGLAKLL-GLSRTAVADLAAAGDVLLDGRPAGKSDRLAAGGLLEV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
                 L    +  +I+   V+  K        +L++D  I V +KP G++V    G   
Sbjct: 63  -----TLPEPERPAEIVAEPVDGMK--------ILHDDDDIVVISKPVGVAVHPSPGWTG 109

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              +       L+       ++  + HRLD  T+G++VVA++  A   L  +F+ R + K
Sbjct: 110 PTVVGGLAAAGLRISTSGAAERQGVVHRLDAGTTGVMVVAKSEHAYTVLKRAFKERTVDK 169

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G P   +  I   +    H   DY   V     G   +++H++V++ F +   
Sbjct: 170 GYHAVVQGHPDPTRGTIDAPI--DRHPRHDYKFAVV---AGGRPSVTHYEVVEAF-RAAS 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
              ++  TGRTHQ+RVH   +  P  GD  Y A+           + +LHAR +   HP 
Sbjct: 224 LAHVKLETGRTHQIRVHFSALRHPCAGDLTYGADPVL-ARKLGLTRQWLHARTLGFAHPA 282

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            GR ++  A  P  +    + L 
Sbjct: 283 DGRWVEFEAEYPDDLASALEILR 305


>gi|116670141|ref|YP_831074.1| ribosomal large subunit pseudouridine synthase D [Arthrobacter sp.
           FB24]
 gi|116610250|gb|ABK02974.1| ribosomal large subunit pseudouridine synthase D [Arthrobacter sp.
           FB24]
          Length = 308

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 78/323 (24%), Positives = 144/323 (44%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V  +    R+D         I+      ++  G V    K V  + ++ SG V+ +
Sbjct: 3   EKLTVPEELAGTRVDAGLARLM-GISRSQAATLIAEGNVSSGGKAVGKSLKLASGTVLEV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                    ++ E++  D    + +  + LK  +L +D    V +KP G++     G + 
Sbjct: 62  ---------VVPERR--DPLEIVEEVVEGLK--ILLDDEDFVVIDKPVGVAAHPSPGWVG 108

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L             ++  + HRLD  TSG +VVA++  A   L  +F+ R + K
Sbjct: 109 PTVVGGLAGLGYRISTSGAPERAGIVHRLDVGTSGAMVVAKSERAYTALKRAFKERTVDK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++V G+P      I   + +  H G D+   V ++      +++H++V++ F  K  
Sbjct: 169 VYHAVVQGLPDPLAGTIDAPIGR--HPGHDWRFAVIED---GRESVTHYEVLEAFG-KAS 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+   TGRTHQ+RVH   +  P  GD  Y A+ +   T  +  + +LHAR +    P 
Sbjct: 223 LVEVHLETGRTHQIRVHFSALRHPCAGDLTYGADPRLAATLGL-TRQWLHARQLGFDSPR 281

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G R+ +T+  P  +    + L 
Sbjct: 282 TGERVTVTSDYPQDLAYALEVLA 304


>gi|88857987|ref|ZP_01132629.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
 gi|88819604|gb|EAR29417.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
          Length = 325

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 74/339 (21%), Positives = 137/339 (40%), Gaps = 38/339 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V  +    RLD+   + +P  +   ++  +    V+++ +       ++   + V I   
Sbjct: 11  VPLELGGKRLDQILADLFPEYSRSRIKTWILDDMVQINGEIKNIPKEKLFGEEQVVISAT 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           I                      +  +   ++YED  I V NKPAG+ V  G+G A    
Sbjct: 71  IEPQRE---------------YEAQNIALNIVYEDDDILVINKPAGLVVHPGAGNADGTV 115

Query: 130 -DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSL 186
            +  L    + +   +  + HRLD++T+G++VVA+T  A   L  + + R    + Y ++
Sbjct: 116 LNALLHHCPEIANVPRAGIVHRLDKDTTGLMVVAKTIPAQTRLVANLQARYNFTREYEAI 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        I   + + +                   A++HF+V + F +    L ++
Sbjct: 176 CTGTM-TAGGMIDKPIGRHAT-----KRTHMDVTITGKPAVTHFRVAEKF-RSHTRLRLR 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLP 298
             TGRTHQ+RVH  ++  P+VGD  Y    +    +  +         +  LHA  + + 
Sbjct: 229 LETGRTHQIRVHMSYLTHPLVGDQSYNGRPRPPKKATPELFECLQKFRRQALHAVMLTIE 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLY 336
           HP  G  +   AP+P  M    + L  + D  L+ +  Y
Sbjct: 289 HPITGEMMTWHAPIPDDMQYLTEVL--RADTALHGREDY 325


>gi|183179760|ref|ZP_02957971.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MZO-3]
 gi|183013171|gb|EDT88471.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MZO-3]
          Length = 267

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 91/277 (32%), Positives = 155/277 (55%), Gaps = 15/277 (5%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKI 108
           +KKRVK   ++++G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  +
Sbjct: 2   NKKRVKAEYKLEAGDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHL 56

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            + NKP+G +V GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +
Sbjct: 57  LILNKPSGTAVHGGSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALR 115

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           HL   FR + +QK Y++LV G    + + +   LLK        V+ + +       + +
Sbjct: 116 HLQAQFREKTVQKYYYALVMGHWDAECKVVNAPLLKNE------VNSIVRVNPNGKPSET 169

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNK 287
            F++++ FA+    ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +
Sbjct: 170 RFRILEKFAE-ATLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIER 228

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           L+LHA  +   HP    +L+I APL AH+ +    + 
Sbjct: 229 LFLHAANIQFVHPASEKKLEIHAPLEAHLEQALTKMR 265


>gi|299144084|ref|ZP_07037164.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus sp.
           oral taxon 386 str. F0131]
 gi|298518569|gb|EFI42308.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus sp.
           oral taxon 386 str. F0131]
          Length = 304

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 86/325 (26%), Positives = 145/325 (44%), Gaps = 39/325 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V YV    + +N+R+DR+      +IN   ++K +  G + ++   VK     + G 
Sbjct: 9   MVKVNYVC---ESDNIRIDRYLVEKL-NINRSQIKKYIDFGNILINNSVVKAGYMTKIGD 64

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ +            E +IL          + +   ++YED  I V +KP  + V  GS
Sbjct: 65  IIDVSY----------EDEIL-------LLPEEIDFKIIYEDEHIAVISKPQNLVVHPGS 107

Query: 124 GIAYHI--DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +G L  + +        +P + HRLD++TSG++++A+T  A   L + F+  
Sbjct: 108 GNYNHTLVNGLLFKFKNLSNCGDKLRPGIVHRLDKDTSGLMIIAKTNLAYLKLVKDFKES 167

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +I+K Y ++V G  K  +  I N  + +       + V+ +N K    AI+ +K I    
Sbjct: 168 KIRKTYIAVVEG--KTDEFGIINEPIGRDPKNRKKMAVIYENSKN---AITEYKKI-REF 221

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  + +   TGRTHQ+RVH  ++  P++GD  Y    K        +K  LHA  +  
Sbjct: 222 NNFSLISINILTGRTHQIRVHLSYIKHPVLGDLTYGNKNKYK-----IDKQMLHAYRLKF 276

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDS 321
            HP  G  L     +P   VK    
Sbjct: 277 NHPITGEELSFEDDIPNRFVKFLSR 301


>gi|254796911|ref|YP_003081748.1| ribosomal large subunit pseudouridine synthase C [Neorickettsia
           risticii str. Illinois]
 gi|254590147|gb|ACT69509.1| ribosomal large subunit pseudouridine synthase C [Neorickettsia
           risticii str. Illinois]
          Length = 305

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 93/313 (29%), Positives = 150/313 (47%), Gaps = 11/313 (3%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  VVEND    RLD++ ++ +       LQK LR   V+++   VK +  +  G  + 
Sbjct: 1   MKSFVVEND--CRRLDKYLRDTFGPFPQSALQKALRKKAVKLNNVVVKASAAVLKGDSLT 58

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +    +E     S V  +K   F+ S++LYED  +   +KP G  VQ G GI 
Sbjct: 59  LSANFLQILSSPREIPSDSSKVVDSKFVKFIASLMLYEDENVLAIDKPFGFPVQSGYGIT 118

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             ID  +KS       + R+ HRLD+ T+G+L+ A+T  AA+ L   F  R ++K Y ++
Sbjct: 119 TSIDNAMKS----INPEYRVVHRLDKHTTGVLIFAKTLDAARELWRLFSNRLVKKRYLAI 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K KK  +  ++ K    G + +           +AI+ F VI  F +    +E+ 
Sbjct: 175 VIGELKEKKGAVDCYINKVLFKGEEVMQCNHIG--NGEHAITQFHVIKKF-KNASLIELF 231

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P TGR HQ+R     +G P++ D KY    +      +  KL LHA  ++     G  ++
Sbjct: 232 PLTGRKHQIRSQMASIGHPVLNDGKYG-RREAFLECSVNKKLCLHACEIEFE-LFGKIIK 289

Query: 307 ITAPLPAHMVKTW 319
           +TA LP H  +  
Sbjct: 290 VTAELPVHFAENL 302


>gi|195953891|ref|YP_002122181.1| pseudouridine synthase, RluA family [Hydrogenobaculum sp. Y04AAS1]
 gi|195933503|gb|ACG58203.1| pseudouridine synthase, RluA family [Hydrogenobaculum sp. Y04AAS1]
          Length = 308

 Score =  227 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 69/326 (21%), Positives = 143/326 (43%), Gaps = 36/326 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           + +  D    R+D    N Y  I+   +++I++   V ++ ++V K + ++    V+   
Sbjct: 4   IKITPDIAGERIDVLISNIYKDISREYIKRIIKENGVLINGEKVFKSSKKVFENDVLEFE 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                          +     L   +  +   +LYED+ + V  KP+G+    G G  + 
Sbjct: 64  ---------------IPPPKKLDVKAQDIHIDILYEDNDLAVVVKPSGMPSHTGPG--HD 106

Query: 129 IDGFLKSWVDSKG--------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            +  + + +   G        ++P + HRLD+ T G++V+A+   + Q L+  F+ + + 
Sbjct: 107 ENTLVNALLAKFGDLSVIGGVERPGIVHRLDRYTHGLMVIAKNDVSHQKLSLMFKNKEVD 166

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++V+GI + K++ I  ++ +       +     +       AI+ +  ++   +  
Sbjct: 167 KHYKAIVYGISRFKEQTIETFIRRHPTNRLKF-----EVANEGKLAITKY-SLEKPLKNA 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQNKLYLHARYMDL 297
             L+++ +TGRTHQ+RVH  ++G PIVGD  Y      F       I  +  L A  +  
Sbjct: 221 SLLDIKIYTGRTHQIRVHMSYIGHPIVGDTLYGYKHSYFDKTLEHMIGKRFLLVAYKLSF 280

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP+  + ++    +P +       L
Sbjct: 281 LHPKSQKPMEFEIDMPDYFKNVLKYL 306


>gi|296122834|ref|YP_003630612.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
 gi|296015174|gb|ADG68413.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
          Length = 325

 Score =  227 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 79/342 (23%), Positives = 147/342 (42%), Gaps = 38/342 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M++++  + V VE     +R+D +   H+       + +++ +G V +D +      R+ 
Sbjct: 1   MAILS--KTVTVEKYLAGVRVDSFLVKHFRSYTSWRILRMVAAGLVTIDGQVAATTQRVH 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            GQ V I         +  E   L+               +L+ED  + V NKPAG+   
Sbjct: 59  PGQQVTIQLTEPPDLFVPPEPTPLE---------------ILFEDDSLLVINKPAGLIAH 103

Query: 121 G-GSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             G      +   ++ ++D +      ++P + HRLD++TSG + + +   + + L+  F
Sbjct: 104 PTGEIPDGTLINAVQHYLDKQSTHPGLERPGIVHRLDRDTSGAMAICKEHLSHRLLSIQF 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           ++ RI K Y +LV G+  + +  I   + +        +   + +   A  + +  +V++
Sbjct: 164 QLGRISKSYLALVEGVLTDDQLVIDLPIGRAPGCSSALMS-CRADALEAQASKTSLRVVE 222

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC----------ANFKGNFTSPI 284
            F Q    +E +P TGR HQ+R+H   +G PIVGD  Y              +    S +
Sbjct: 223 RFPQ-HTLVEAKPRTGRMHQIRIHLATIGFPIVGDEFYLKGGEIRPLVWPESERVQVSLL 281

Query: 285 QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD--SLG 323
            N+  LHA  +   HP         APLP  + +  +   LG
Sbjct: 282 INRQALHAACLSFAHPLTNEWQDFQAPLPDDLRQAIELARLG 323


>gi|297170255|gb|ADI21292.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0010_09F21]
          Length = 305

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 144/329 (43%), Gaps = 39/329 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            +   ++    N RLD +  +    I+   +Q+++  G V V+   VK N +++    ++
Sbjct: 3   TKTFNIDEANINKRLDSFLSDILDDISRGLVQQLIEQGNVLVNDLEVKKNYKLRLNDQIQ 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +               IL     +      +   +++E+   Y+ NK AG++V  G+G  
Sbjct: 63  V---------------ILQFPEVIEDEPQNIPLDIVFENEDFYIINKQAGLTVHPGAG-- 105

Query: 127 YHIDGFLKSWVDSKGQKPR------LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              D  L + +    +K        + HRLD+ETSG++VVA+  ++   LT   + R I+
Sbjct: 106 -QKDNTLLNGLLHLNKKACELSRCGIVHRLDKETSGLMVVAKNHSSQTILTNLIKDRAIE 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y++LV G        I   + +  H     + +V Q  K +    +H+ V + + + F
Sbjct: 165 RKYYALVHGNV-ISGGTIDEPIER--HPKNRLIFIVDQEGKESK---THYLVKERY-ENF 217

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-------CANFKGNFTSPIQNKLYLHAR 293
             L+++  TGRTHQ+RVH  H+G PI GD +Y        ++ K           +LHA 
Sbjct: 218 SLLDVKLETGRTHQIRVHLKHIGFPIAGDKQYTKISNWKGSSEKELNVINSLKGQFLHAY 277

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
            +     +      +A LP ++      L
Sbjct: 278 SLAFLF-KNESFSFSAELPDYLTTVLKDL 305


>gi|332557842|ref|ZP_08412164.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides WS8N]
 gi|332275554|gb|EGJ20869.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides WS8N]
          Length = 349

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 81/344 (23%), Positives = 137/344 (39%), Gaps = 52/344 (15%)

Query: 15  DEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           ++   RLD+      P    ++   L K++  G VR++   V     ++  GQV  I   
Sbjct: 17  EDPPDRLDKALVREAPEEAALSRSRLMKLIGEGAVRLEGAPVTDPKAKVAEGQVYEI--- 73

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYH 128
                        LD+   +    + +   +++ED  + V +KP G+ V    G      
Sbjct: 74  ------------ALDAPAEVEARPEAIPLSVVWEDEDLIVIDKPVGMVVHPAPGQWTGTL 121

Query: 129 IDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           ++  L    +S       ++P + HR+D++TSG+LVVA+T  A Q L   F    +++ Y
Sbjct: 122 VNALLHHCGESLSGIGGEKRPGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRY 181

Query: 184 WSLVWGIPKN-------------KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            +LV G+P+              +   +       +    D        E G  +A++  
Sbjct: 182 LALVHGVPEVSDPRLRGVRGTSFEPGGVLRIATGLARHRTDRQRQAVTFE-GGRHAVTRA 240

Query: 231 KVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GN 279
           ++++ F        +E +  TGRTHQ+RVH  H G  ++GD  Y    K           
Sbjct: 241 RLLERFGMPSVLALVECRLETGRTHQIRVHMAHAGHGLIGDQTYGGRRKLSPKALGPEAA 300

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
             +    +  LHA  +   HP  G  L    PLPA M      L
Sbjct: 301 AAAEAFPRQALHAASLGFRHPVSGEELSFERPLPADMAGLLSLL 344


>gi|325831406|ref|ZP_08164660.1| pseudouridine synthase, RluA family [Eggerthella sp. HGA1]
 gi|325486660|gb|EGC89108.1| pseudouridine synthase, RluA family [Eggerthella sp. HGA1]
          Length = 344

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 68/341 (19%), Positives = 128/341 (37%), Gaps = 39/341 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ +   V   D+   RLD        + +     + +  G V V+   V   + +  G 
Sbjct: 1   MSRMLSYVAAPDDAGQRLDALLAARGLYPSRSAAARAVDDGLVFVNGAEVAKKHPVAPGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +            ++ Q I                 + +ED  + V +K  G+      
Sbjct: 61  TIVYQVEEPVEPGPLRGQPI--------------DLDIRFEDEDLIVLSKQVGLVCHPS- 105

Query: 124 GIAYHIDGFLKSWV------------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
               H DG L + +              +  +  + HRLD++TSG+++ A+       L 
Sbjct: 106 --VDHDDGTLVNALIYHCGAENLCNVQGEDDRLGIVHRLDRDTSGLMLAAKNDETGYALM 163

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              R R + + Y +LV G+  +    I   + +      +   +  ++   A  AI+ F+
Sbjct: 164 SDIRDRAVDRRYLALVHGVIAHDTGMIDAPIARAEK---ERTRMAVRDTPSAREAITTFR 220

Query: 232 VIDCFAQ-----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQ 285
           V++ F        +  ++ +  TGRTHQ+RVH  +   P+VGD  Y              
Sbjct: 221 VLERFEHGARDDGYTLIDCKLFTGRTHQIRVHLEYAKHPLVGDPAYTSGAPSAPAADLGL 280

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           ++ +LH+  +   HP  G  L+    LP  + +  D L  +
Sbjct: 281 DRQFLHSFQLSFQHPVTGESLRFADNLPVDLQEALDDLASR 321


>gi|321314645|ref|YP_004206932.1| putative RNA pseudouridine synthase [Bacillus subtilis BSn5]
 gi|320020919|gb|ADV95905.1| putative RNA pseudouridine synthase [Bacillus subtilis BSn5]
          Length = 302

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 86/319 (26%), Positives = 139/319 (43%), Gaps = 34/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            +++   ++   L    K      +   +Q  +   Q++V+ + V  N  ++ G  V I 
Sbjct: 9   EILINEKQDGQWLFSVLKTALK-ASKPVIQDWMSHQQIKVNHESVLNNMIVKKGDRVFID 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                 + +I E   LD               +LYED+ + + NKPAGI+      G   
Sbjct: 68  LQEIEASSVIPEYGELD---------------ILYEDNHMLIVNKPAGIATHPNEDGQTG 112

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +       G+  K R  HRLDQ+TSG +V A+ R A   L +    + +++ Y +
Sbjct: 113 TLANLIAYHYQINGETCKVRHVHRLDQDTSGAIVFAKHRLAHAILDQQLEKKTLKRTYTA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFA-QKFCWL 243
           +  G  + KK  I       S IG D  H  ++    G   A++HFKV+   A ++   +
Sbjct: 173 IAEGKLRTKKGTI------NSPIGRDRSHPTRRRVSPGGQTAVTHFKVMASNAKERLSLV 226

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E++  TGRTHQ+RVH   +G P+ GD  Y    K      + N+  LHA  +   HP   
Sbjct: 227 ELELETGRTHQIRVHMASIGHPLTGDSLYGGGSK------LLNRQALHANKVQAVHPITD 280

Query: 304 RLQI-TAPLPAHMVKTWDS 321
            L +  AP PA M     +
Sbjct: 281 ELIVAEAPFPADMKNLCRT 299


>gi|296332341|ref|ZP_06874802.1| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305673620|ref|YP_003865292.1| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296150259|gb|EFG91147.1| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305411864|gb|ADM36983.1| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 302

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 84/318 (26%), Positives = 144/318 (45%), Gaps = 34/318 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++   ++   L    K      +   +Q  +   QV+V+ + V  N  ++ G  V I  
Sbjct: 10  LLINEKQDGQWLFSVLKTALK-ASKPVIQDWMSHHQVKVNHESVLNNVIVKKGDRVFIDL 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
             +  + +I E   LD               +L+ED+ + + NKPAGI+      G    
Sbjct: 69  QESEESSVIPEYGELD---------------ILFEDNHMLIVNKPAGIATHPNEDGQTGT 113

Query: 129 IDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +       G+  K R  HRLDQ+TSG +V A+ R +   L +    + +++ Y ++
Sbjct: 114 LANLIAYHYQVNGEICKVRHVHRLDQDTSGAIVFAKHRLSHAILDQQLEKKTLKRTYTAI 173

Query: 187 VWGIPKNKKECIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLE 244
             G  K KK  I + + + +SH     V            A++HFKV+   A ++   +E
Sbjct: 174 TEGKLKTKKGTIDSPIGRDRSHPTRRRV------SPSGQTAVTHFKVVASNAKERLTLVE 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++  TGRTHQ+RVH   +G P++GD  Y    K      + N+  LHA+ +   HP  G 
Sbjct: 228 LELETGRTHQIRVHMASIGHPLIGDALYGGGSK------LLNRQALHAKKVQAVHPITGE 281

Query: 305 LQI-TAPLPAHMVKTWDS 321
           L +  AP PA +   +D+
Sbjct: 282 LIVAEAPFPADIENLFDT 299


>gi|15604128|ref|NP_220643.1| hypothetical protein RP258 [Rickettsia prowazekii str. Madrid E]
 gi|14423907|sp|Q9ZDR7|RLUC_RICPR RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|3860820|emb|CAA14720.1| unknown [Rickettsia prowazekii]
 gi|292571856|gb|ADE29771.1| Ribosomal large subunit pseudouridine synthase [Rickettsia
           prowazekii Rp22]
          Length = 303

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 87/301 (28%), Positives = 149/301 (49%), Gaps = 11/301 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + N R++ G  + I    N      +
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNFQKAEANLRVKVGDTIFINDYFNLPVTQHE 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                D+ + L K    L   L+YED  +   NKPA ++ QGGS I   ID  LK +++ 
Sbjct: 72  TLVFADAEIKLAKK--ILTDYLIYEDDHLIAINKPASLATQGGSKINLSIDSALK-YLNY 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G   +L HRLD+ETSG+L++A+   ++  L  +F+ + + K Y+++ +G P      + 
Sbjct: 129 QGADFKLVHRLDKETSGLLLIAKNYLSSVKLHNAFKEKLVIKKYFAITYGRPVKNVGTVK 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + + K          +   +      AI+++K++         +E  P TGR HQLR+HA
Sbjct: 189 SNIGKSK---RRLSKIANIDSDDGKLAITYYKLLKSLNNNLFLIEFMPVTGRMHQLRLHA 245

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
             +GCPI+GD KY          P    ++LHA  + L     G  +++ A LP +  + 
Sbjct: 246 QLLGCPILGDDKYG----NKEIMPYSKYMFLHANNIYLSETIVGKEIKLEAKLPFYFTRR 301

Query: 319 W 319
            
Sbjct: 302 I 302


>gi|253682097|ref|ZP_04862894.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum D str. 1873]
 gi|253561809|gb|EES91261.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           botulinum D str. 1873]
          Length = 302

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 77/332 (23%), Positives = 143/332 (43%), Gaps = 37/332 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     +  + VE + E +RL+ + K      +   ++K  R G+++V+    + +  + 
Sbjct: 1   MESKDNIIKLKVEIETEEIRLNHYLKEVAQCSSR-FIRKAAREGRIKVNGNNARLSYMLT 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  +V +         II E+               +   ++YED+ I V NKP GI V 
Sbjct: 60  NNDIVELQINRKEEQDIIPEK---------------MDLDIIYEDNDIIVVNKPKGIVVH 104

Query: 121 GGSGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                  H++G L + V       ++    RL +RLD +TSG++++A+   +   L+   
Sbjct: 105 PTK---RHLNGTLSNGVLYYFNDKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDM 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +     K Y ++V G        I   + +        +      ++    +I+ FKVI+
Sbjct: 162 QKDDFVKKYLAIVHGNFNEDSGVIDKPIYRVGEGTLKRII-----DERGQRSITLFKVIE 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            + +    +E+   TGRTHQ+RVH   +G PI GD  Y             ++  LHA  
Sbjct: 217 QY-KNASLVELTLETGRTHQIRVHLSSIGHPIYGDSLYGEEEPQ-----YIDRQALHAYK 270

Query: 295 MDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
           + +PHP+ G++ ++ + LP  M      L  +
Sbjct: 271 LQIPHPKDGKILKLESSLPEDMKNLIRKLSEE 302


>gi|91200050|emb|CAJ73092.1| similar to ribosomal large subunit pseudouridine synthase D
           [Candidatus Kuenenia stuttgartiensis]
          Length = 335

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 86/351 (24%), Positives = 157/351 (44%), Gaps = 51/351 (14%)

Query: 1   MSLM-----TYVQYVVVENDEEN--MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV 53
           M++M      +V+ V +E        R+DR+  + +P ++   +QK+++ G + V+   V
Sbjct: 1   MNIMLQESQAHVKEVTLEIKRVGESKRIDRFISSRFPDLSRTYIQKLVKEGAIVVNGNVV 60

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
           K +  I+ G V+      +A   + +E KI    + L          ++YED  + + NK
Sbjct: 61  KSSYFIKKGDVI------SATVPVPEETKITPEDIPLN---------IIYEDDYLMLINK 105

Query: 114 PAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTR 164
           P  + V    G   H  G L + V    Q         K  + HRLD++TSG+++V ++ 
Sbjct: 106 PYDMVVHPAGG---HPSGTLVNAVTFYCQNLSQINGPLKAGIVHRLDRDTSGVMLVIKSD 162

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           A   H+   F  R ++K Y+++V G        I N  + +  +    + V +   K   
Sbjct: 163 AVHSHIAMQFEKRLVKKEYFAVVEGEVAFDSNEI-NMPIGRHRVDRQKMAVRRDTGKN-- 219

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-------ANFK 277
            A S ++VI+ F + +  +++ P TGRTHQ+RVH   +G P+V D  Y        ++  
Sbjct: 220 -ATSVYEVIERF-RGYTLVKIMPKTGRTHQIRVHMQAIGHPVVADEMYSKYNACFRSDLL 277

Query: 278 GNFTSP----IQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLG 323
           G   +P    I  +  LHA  ++  HP    ++     +   +     +L 
Sbjct: 278 GKERAPDEGSIIERQALHAHRIEFFHPILNKQMAFQVDMAEDISFLVSALR 328


>gi|291519368|emb|CBK74589.1| pseudouridine synthase, RluA family [Butyrivibrio fibrisolvens
           16/4]
          Length = 311

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 144/320 (45%), Gaps = 24/320 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + ++  + N R D++ K   P+ +   + K+LR   + +++K+   + ++  G V++
Sbjct: 1   MKELRIDTGDSNQRFDKFLKRVLPNASTSFIYKMLRKKNITLNEKKADGSEKLNVGDVIK 60

Query: 67  IPPVINALNHI--IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           I         +  + E+  L  S+   K +      +++ED  + + NKPAG+  Q  S 
Sbjct: 61  IWFSDETFAKMAGVSERDELYYSIKEIKPN----INIVFEDDDMIIINKPAGVKSQKDSP 116

Query: 125 IAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
               I+    S++ +  Q          P + +RLD+ TSGI++ A+   AAQ L ++ +
Sbjct: 117 SDISINEMAISYMIASNQLSEESFKHFHPSVCNRLDRNTSGIVLFAKNLHAAQSLGQALK 176

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R  +K+Y ++V G   +K++ I  +L K      + V + K     +    + +  I  
Sbjct: 177 ERSCKKLYRAVVLGKVDSKQQ-IEGFLWKDE--ATNKVTISKNEIPDSKPIKTAYNPIKN 233

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
              KF  LE+   TGRTHQ+R H   +G PI+GD+KY                 LHA  +
Sbjct: 234 IGDKFTLLEIHLITGRTHQIRAHLASIGHPILGDNKYGNTIINKEQK--VRGQLLHAYSI 291

Query: 296 DLPHPEGGRLQITAPLPAHM 315
           +         +    LP   
Sbjct: 292 EF----ADERKFVCDLPGEF 307


>gi|238921072|ref|YP_002934587.1| ribosomal large subunit pseudouridine synthase D [Edwardsiella
           ictaluri 93-146]
 gi|238870641|gb|ACR70352.1| ribosomal large subunit pseudouridine synthase D [Edwardsiella
           ictaluri 93-146]
          Length = 300

 Score =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 76/308 (24%), Positives = 139/308 (45%), Gaps = 41/308 (13%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
            +P  +   +++ +  G+V V+   + K   ++  G+ + I  +I   N    +   LD 
Sbjct: 1   MFPDYSRSRIKEWILEGRVSVNGVIINKPKEKVLGGEHIAIDALIEEENRWEAQDIALD- 59

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVD-SKGQK 143
                         ++YED  I V NKP  + V  G+G       +  L  +   +   +
Sbjct: 60  --------------IVYEDEDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPQIADVPR 105

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIAN 200
             + HRLD++T+G++VVA+T  A   L ES ++R I + Y ++  G        +E IA 
Sbjct: 106 AGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGTMTAGGTVREPIAR 165

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K++H+    +            A++H+++++ F +    L ++  TGRTHQ+RVH  
Sbjct: 166 HPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMA 215

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPL 311
           H+  P+VGD  Y    +    +  +        ++  LHA  + L HP  G  ++  AP+
Sbjct: 216 HINHPLVGDPLYGGRPRPPRDASPEFIRVLREFDRQALHATMLRLYHPISGIEMEWHAPI 275

Query: 312 PAHMVKTW 319
           P  M +  
Sbjct: 276 PDDMQRLI 283


>gi|256379746|ref|YP_003103406.1| pseudouridine synthase, RluA family [Actinosynnema mirum DSM 43827]
 gi|255924049|gb|ACU39560.1| pseudouridine synthase, RluA family [Actinosynnema mirum DSM 43827]
          Length = 310

 Score =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 79/323 (24%), Positives = 144/323 (44%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  + MR+D         ++   +  +  SG V +D +    ++R+ +G  + +
Sbjct: 6   RTLPVPDGLDGMRVDAGLAKLL-GLSRTVIASLAESGDVVLDGRVAGKSDRLVAGSWLEL 64

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
              +      ++ Q +    +           I+L+ED  + V +KP G++V    G   
Sbjct: 65  T--LPEPERPVQVQAVPVEGM-----------IVLHEDDDVIVVDKPVGVAVHPSPGWTG 111

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  + HRLD  T+G++VVA++  A   L ++F+ R + K
Sbjct: 112 PTVVGGLAAAGVRVSTSGAAERQGVVHRLDVGTTGVMVVAKSEHAYSVLKQAFKDRTVDK 171

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y +LV G P   K  I   +    H   DY   V     G   +I+H++V++ F +   
Sbjct: 172 LYHALVQGHPDPIKGTIDAPI--DRHPKHDYKFAVM---AGGKPSITHYEVVEAF-RAAS 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L++   TGRTHQ+RVH   +  P VGD  Y A+          ++ +LHAR +   HP 
Sbjct: 226 LLDVHLETGRTHQIRVHFSALKHPCVGDLTYTADPVLAKRL-GMSRQWLHARRLGFHHPA 284

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            G  ++ T+  P  +      L 
Sbjct: 285 DGEWVEFTSEYPDDLDHALKLLR 307


>gi|172040870|ref|YP_001800584.1| pseudouridylate synthase D [Corynebacterium urealyticum DSM 7109]
 gi|171852174|emb|CAQ05150.1| pseudouridylate synthase D [Corynebacterium urealyticum DSM 7109]
          Length = 314

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 75/326 (23%), Positives = 139/326 (42%), Gaps = 26/326 (7%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +    MR+D         ++   +  +  +G +  + K +  ++R+ +GQ + +
Sbjct: 7   RMMPVPDGLAGMRVDAGLSKLL-GLSRTVVADLAAAGDITAEGKSLGKSDRLVAGQWLDV 65

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGI 125
                       E+ +      L +  D     +LY D  +   NKP G++     G   
Sbjct: 66  T-------LPAPERDLAAEPPQLVEGMD-----ILYSDDDVIAVNKPVGVAAHPTLGWEG 113

Query: 126 AYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                G   +          ++  +  RLD  TSG+++VA +  A  HL  +FR R +QK
Sbjct: 114 PTVTAGLAAAGFRISTSGPPERKGIVQRLDVGTSGVMIVAASERAYTHLKRAFRNREVQK 173

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY +LV G P      I   + +  H    +   V+ +     +A++H+  ++   ++  
Sbjct: 174 IYHALVQGHPDPTSGTIDAPIGR--HPSAGWRFAVRDD---GKHAVTHYDTLEAH-RQAS 227

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L +   TGRTHQ+RVH   +  P+ GD  Y ++   +    +  + +LHA  +   HP 
Sbjct: 228 LLRVNLETGRTHQIRVHFSSLHHPLCGDPMYGSDPALSEKLGLI-RQWLHAVSLRFEHPT 286

Query: 302 GGRLQITAPLPAHMVKTWDSLGFKYD 327
           G  +QI +P P  + +  D L    D
Sbjct: 287 GRMMQIDSPYPEDLQQALDRLREAND 312


>gi|222099185|ref|YP_002533753.1| Pseudouridine synthase [Thermotoga neapolitana DSM 4359]
 gi|221571575|gb|ACM22387.1| Pseudouridine synthase [Thermotoga neapolitana DSM 4359]
          Length = 271

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 70/284 (24%), Positives = 124/284 (43%), Gaps = 28/284 (9%)

Query: 47  RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
           +V+ +  K + +++ G++V +              ++ +     T   + +   +LYED 
Sbjct: 2   KVNGQIKKPSYKLKEGEIVEV--------------ELPEEPKEPTVQPEKIDLKILYEDR 47

Query: 107 KIYVFNKPAGISVQG--GSGIAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVV 160
            I V +KP  + V           ++  L    D +G     +P + HRLD+ETSG++VV
Sbjct: 48  DIIVIDKPGDMIVHPVPSKLSGTLVNAILYHCSDLQGVGGKLRPGIVHRLDKETSGVIVV 107

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+   A Q L+  F+ R+++K Y  L  G  K  +  +   L +        + V     
Sbjct: 108 AKNDLAHQSLSRQFKDRKVKKTYILLARGRIKEDEGTVELPLARHP-----VLRVKMTVS 162

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    AI+H++V+  F      +   P TGRTHQ+RVH   +G PI+GD  Y    +   
Sbjct: 163 ENGKEAITHYRVLKRFDDVATLVLAFPQTGRTHQIRVHMKSLGHPIMGDKIYGKYKEDEM 222

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 +  LHA  +   HP  G  ++  +P+P    +    + 
Sbjct: 223 --FGIKRQMLHALKLGFFHPRTGEWMEFVSPIPEDFKEAIRKIA 264


>gi|188996123|ref|YP_001930374.1| pseudouridine synthase, RluA family [Sulfurihydrogenibium sp.
           YO3AOP1]
 gi|188931190|gb|ACD65820.1| pseudouridine synthase, RluA family [Sulfurihydrogenibium sp.
           YO3AOP1]
          Length = 318

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 144/336 (42%), Gaps = 37/336 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           M  +    VE +  N RLD++    YP  +    Q ++ +  V +D   V K + ++++G
Sbjct: 1   MEEIISFKVEEEFSNKRLDQFLALVYPEYSRSFYQNLIENRFVLLDNNPVRKSSTKVKTG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
           Q   I         I  E   L+               + YED  + V  KP G+ V   
Sbjct: 61  QEFTIIIPPPEPLEIEPENIPLE---------------IYYEDEDLAVVYKPPGMVVHPS 105

Query: 122 -GSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++  L  + +       ++  + HRLD++T+G+L+VA++  A + L + F+ 
Sbjct: 106 VGHTSGTLVNALLYHFKNVSQYQGKERAGIVHRLDKDTAGLLIVAKSEFAHKELQKMFQD 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I K Y ++V GI K     I   + + S      +  V  N K    A++ + V   F
Sbjct: 166 REIDKKYKAIVSGIVKKDHGLIDLPIGR-SIYNRQKMGTVATNPKD---ALTEYWVEKRF 221

Query: 237 A-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLH- 291
                  ++++ HTGRTHQ+RVH   +G P+  D  Y    +N   +    + +KL  H 
Sbjct: 222 EKHNLTLVDIKLHTGRTHQIRVHFSAIGHPLFNDFVYGFKKSNLSSDLAKNLSDKLKYHA 281

Query: 292 --ARYMDLPHPEGGRL---QITAPLPAHMVKTWDSL 322
             A  +   HP   ++   ++ + LP  + +    L
Sbjct: 282 LVAYKLTFRHPRTNQMLSIELKS-LPKEIEEILQEL 316


>gi|288574921|ref|ZP_06393278.1| pseudouridine synthase, RluA family [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570662|gb|EFC92219.1| pseudouridine synthase, RluA family [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 340

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 85/323 (26%), Positives = 146/323 (45%), Gaps = 31/323 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVR 66
           + ++V  D + +RLD +  +    ++   +Q+++R G V+V   KRVK +  + +G+ +R
Sbjct: 33  EEILVPPDMDGVRLDAFLSDFL-GVSRTFIQRVIRDGYVKVFQGKRVKPSRSVLAGESLR 91

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
                            L     +    + +   ++YED  I V +KPAG+ V    G  
Sbjct: 92  FK---------------LPPPQRMDLVPEPVDFSVVYEDEDIIVVDKPAGVVVHPAPGHW 136

Query: 126 -AYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + G L  + D    +   +P + HRLD  TSG+L VAR   +   L  SFR R++ 
Sbjct: 137 RGTLVHGLLYRYPDIGTINDVVRPGIVHRLDSTTSGLLAVARNTESLNELQSSFRDRKVG 196

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L  G    ++  +   + +       Y   V  + K A    +    +    + +
Sbjct: 197 KFYLALSDGRVVGEEISLDAPIGRDR--NNRYRMTVTDDGKNAR---TDVYPLWNRGR-Y 250

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQNKLYLHARYMDLPH 299
            +L  + H+GRTHQ+RVH  H+G P+VGD  Y    K     P ++ +++LHA  + LPH
Sbjct: 251 SFLICELHSGRTHQIRVHLRHLGAPLVGDELYGFRKKARKNDPLLEGRVFLHAWKLVLPH 310

Query: 300 PEGGR-LQITAPLPAHMVKTWDS 321
           P  G  +   + LP  +      
Sbjct: 311 PRTGEIMNFRSVLPRDLSSVLSR 333


>gi|172039934|ref|YP_001799648.1| pseudouridylate synthase C [Corynebacterium urealyticum DSM 7109]
 gi|171851238|emb|CAQ04214.1| pseudouridylate synthase C [Corynebacterium urealyticum DSM 7109]
          Length = 313

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 84/325 (25%), Positives = 148/325 (45%), Gaps = 22/325 (6%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           +  Q ++V + + + RLD++ ++    +    L +++R+ Q+ V+  + K + R  +G  
Sbjct: 4   SEPQTLIVSDSQADRRLDKYIRSQVKGVPATVLFRMMRTKQITVNGAKCKPDQRTVAGDK 63

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V +P    AL     + K         + +  L   +++ED  + + NKPA I+V  GSG
Sbjct: 64  VHLP----ALEVAEAKPKPAGDRKAAEQLARRLSRHIVFEDDDLLIVNKPANIAVHVGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--RIQKI 182
           +   +   L+  +  + ++  L HRLD+ETSG+L+VA+     +HL    R     IQ+ 
Sbjct: 120 VKAGVIEALR-VLRPEDKELELAHRLDKETSGLLIVAKNSKMLRHLQSLLREGGEDIQRY 178

Query: 183 YWSLVWGIPKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++  G+ K        I   L                + +    A +   V   + + 
Sbjct: 179 YLAVAGGVLKKSGKQARRIDAPL-------RKTGAATVVDRRAGQQAETKLWVKKPWGRA 231

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLP 298
              +E+Q  TGR HQ+RVH  H+G PI+GD +Y         +    + L LHA  + +P
Sbjct: 232 GTLVEVQLLTGRKHQIRVHLQHLGHPIIGDSRYGDKAANQAAAEKGVRMLMLHASRLVIP 291

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLG 323
            P G  L + AP+P      W+ L 
Sbjct: 292 LPSGEELDVQAPMPP----AWNKLR 312


>gi|51474013|ref|YP_067770.1| pseudouridine synthase [Rickettsia typhi str. Wilmington]
 gi|51460325|gb|AAU04288.1| Pseudouridine synthase [Rickettsia typhi str. Wilmington]
          Length = 313

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 145/327 (44%), Gaps = 40/327 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPV 70
           +  +  N RLD+   +    ++   +QK +++  V+++   +  ++  ++    +     
Sbjct: 6   IPKELNNTRLDKALSSLLEKVSRNQVQKAIKNSCVQINDVIISDSDVLVKENDTILFSFK 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                              L   S  +   ++YED  + V NK AGI+V  G+   +H +
Sbjct: 66  ---------------EPEELKITSANITLDIIYEDDDLIVINKAAGITVHPGA--KHHDN 108

Query: 131 GFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +            ++P + HRLD+ET+G++VVA+   A   L +    R++ + 
Sbjct: 109 TLVNALLHHTKNLSDIGSAERPGIVHRLDKETTGLMVVAKNNKAHMLLAKQIEQRQVIRK 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFC 241
           Y +LVWG+  N  E I N  + ++      + ++K    G   A++H+K ++  +     
Sbjct: 169 YKALVWGVI-NPLEGIINNNIGRNRNNRKKMTILKY---GGKKAVTHYKTLELFYGGTLS 224

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHAR 293
            +E +  TGRTHQ+RV   ++   +VGD  Y  N +    SP +         +  LH+ 
Sbjct: 225 MVECKLSTGRTHQIRVQLSNLKHSVVGDQTYGNNNRKIINSPPKLKAKLIDFKRQALHSW 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTW 319
           Y+   HP   + ++ +  +P  M +  
Sbjct: 285 YLSFTHPTSNKIMEFSCAIPRDMQEII 311


>gi|260553983|ref|ZP_05826248.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           RUH2624]
 gi|260404869|gb|EEW98374.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           RUH2624]
          Length = 350

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 75/326 (23%), Positives = 141/326 (43%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++      R+D+     +   +   L++ L+ G + V+   VK  +R +         
Sbjct: 41  VQLDESYLGQRIDQVAAMVWSEFSREKLKQWLKDGHLLVNGNIVKPKHRCEG-------- 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
                         ++     T   + +   ++YED+ I V NKP G+ V  G+G     
Sbjct: 93  -------TELLTLEVELEAQTTSQPENIPLNIVYEDNDILVINKPVGMVVHPGAGNTSGT 145

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L  +   ++  +  L HR+D++TSG+LVVA+T  A   L++    + + ++Y  +
Sbjct: 146 LVNALLYHFPKLAELSRAGLVHRIDKDTSGLLVVAKTLEAQFSLSKQLANKSVYRVYDLV 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G        I   + K+  +    + ++     G   A++H+ V + F + F  ++ +
Sbjct: 206 VYGNIIA-GGTIDEPI-KRHPVDRVKMAIL----PGGRDAVTHYNVKERF-KDFTRVQAR 258

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  ++G  ++GD  Y         A+     T     +  LHA  + L 
Sbjct: 259 LETGRTHQIRVHFSYIGYGLIGDQVYMNRVRVPAGASELLIETLRGFKRQALHAAKLGLK 318

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +   AP P    +  + L 
Sbjct: 319 HPRTGEEMLFEAPWPEDFTQLVNVLR 344


>gi|257791310|ref|YP_003181916.1| pseudouridine synthase, RluA family [Eggerthella lenta DSM 2243]
 gi|257475207|gb|ACV55527.1| pseudouridine synthase, RluA family [Eggerthella lenta DSM 2243]
          Length = 344

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 68/341 (19%), Positives = 128/341 (37%), Gaps = 39/341 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ +   V   D+   RLD        + +     + +  G V V+   V   + +  G 
Sbjct: 1   MSRMLSYVAAPDDAGQRLDALLAARGLYPSRSAAARAVDDGLVFVNGAEVAKKHPVAPGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +            ++ Q I                 + +ED  + V +K  G+      
Sbjct: 61  TIVYQVEEPVEPGPLRGQPI--------------DLDIRFEDEDLIVLSKQVGLVCHPS- 105

Query: 124 GIAYHIDGFLKSWV------------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
               H DG L + +              +  +  + HRLD++TSG+++ A+       L 
Sbjct: 106 --VDHDDGTLVNALIYHCGAENLCNVQGEDDRLGIVHRLDRDTSGLMLAAKNDETGYALM 163

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              R R + + Y +LV G+  +    I   + +      +   +  ++   A  AI+ F+
Sbjct: 164 SDIRDRAVDRRYLALVHGVIAHDTGMIDAPIARAEK---ERTRMAVRDTPSAREAITTFR 220

Query: 232 VIDCFAQ-----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQ 285
           V++ F        +  ++ +  TGRTHQ+RVH  +   P+VGD  Y              
Sbjct: 221 VLERFEHGARDDGYTLIDCKLFTGRTHQIRVHLEYAKHPLVGDPAYTSGAPSAPAADLGL 280

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           ++ +LH+  +   HP  G  L+    LP  + +  D L  +
Sbjct: 281 DRQFLHSFQLSFQHPVTGEGLRFADNLPVDLQEALDDLASR 321


>gi|260425298|ref|ZP_05779278.1| ribosomal large subunit pseudouridine synthase D [Citreicella sp.
           SE45]
 gi|260423238|gb|EEX16488.1| ribosomal large subunit pseudouridine synthase D [Citreicella sp.
           SE45]
          Length = 345

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 74/349 (21%), Positives = 132/349 (37%), Gaps = 51/349 (14%)

Query: 11  VVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVR 66
           ++  +    RLD+      P    ++   L +++  G V    + +     R+  G  + 
Sbjct: 7   IIIGEAPPPRLDKALARDVPEEAALSRTRLARLIAEGAVTRAGEALTDPKARVAEGDEIL 66

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           I       +HI  E                +   +++ED  + V +KPAG+ V    G  
Sbjct: 67  ITVPQAEDSHIGPED---------------IPLSIVWEDEDLVVVDKPAGMVVHPAPGTP 111

Query: 126 -AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  L  +           +P + HR+D++TSG+LVVA++  A   L   F     
Sbjct: 112 SGTLVNALLHHFGGRLSGVGGVARPGIVHRIDKDTSGLLVVAKSDRAHHGLAAQFEAHSA 171

Query: 180 QKIYWSLVWGIPKN-------------KKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
            + Y ++V+G+P               +   +       +    D        +    +A
Sbjct: 172 DRAYLAVVYGVPDAGDPRLVGTRGVSMEPGGVIRIQSGLARHKTDRQRQAVYFDGQGRHA 231

Query: 227 ISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-- 282
            +   V++ F        ++ +  TGRTHQ+RVH  H G  +VGD  Y    K    +  
Sbjct: 232 TTRASVLETFGTPPAMALVQCRLETGRTHQIRVHMAHAGHGLVGDPVYGGRRKPPAKAIG 291

Query: 283 -------PIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
                     ++  LHA  +   HP  G RL+  +PLP  M    ++L 
Sbjct: 292 PVATEAVSGFSRQALHAAELGFDHPVTGERLRFESPLPDDMDALIEALR 340


>gi|108759922|ref|YP_634049.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108463802|gb|ABF88987.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 318

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 87/318 (27%), Positives = 144/318 (45%), Gaps = 18/318 (5%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E D   MRLD+  +   P++   +L K++R+ +VRV+ KR +    +  G V+ I    
Sbjct: 6   IEADTAGMRLDKHLRKRLPNVPVSHLFKMIRTKKVRVNGKRAQPEQLLSEGDVLTIRGDE 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHID 130
             L    +               D  + ++L ED  +   +KP+G++V  GSGI    + 
Sbjct: 66  QQLVGAER-----PKVDPPPPPVDPSRLVILREDDWLMAVDKPSGMAVHTGSGITGGTLV 120

Query: 131 GFLKSWVDSKGQK----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++++++  K  +        HRLD+ETSG+++VA+ R A  H TE F     +K Y +L
Sbjct: 121 DYVRAYLGPKAVRNDFAASPAHRLDRETSGVILVAKRRPAMVHFTEVFTHGLSRKRYLTL 180

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   L +                     A++ +KV+   ++    L   
Sbjct: 181 VKGKMPRDSGVIDLPLSEHQQTAESKARR----GVNMQAAVTRWKVVKQSSE-AALLSCA 235

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
             TGRTHQ+R H   +G P+ GD KY   A  +         +L+LHA  ++ PHPEGG 
Sbjct: 236 IETGRTHQIRRHLAAIGHPVAGDKKYGDFAFNRDVRARWGLKRLFLHAERIEFPHPEGGA 295

Query: 304 RLQITAPLPAHMVKTWDS 321
           ++ + APL   +      
Sbjct: 296 KVAVEAPLAVELRDVLKR 313


>gi|328865280|gb|EGG13666.1| putative ribosomal large subunit pseudouridine synthase C protein
           [Dictyostelium fasciculatum]
          Length = 720

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 103/382 (26%), Positives = 159/382 (41%), Gaps = 66/382 (17%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV---------------DKKRVKFN 56
           V  D   MR+DRW +  +P +    + K+LR   +                 DK+ ++ +
Sbjct: 331 VLPDLAKMRVDRWLRIQFPVMTHSLICKLLRKEVITATDEFHQNGLDDVAASDKRVLEQS 390

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           +R ++G  + IP        +   +               +++ +LY+D  + V NKP G
Sbjct: 391 DRTEAGSWIYIPAKYAKEQRVADRESPEKYIRLSDAEIAAIRNSILYKDDDLLVINKPPG 450

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT----- 171
           +SVQGG+G+  H+D  L        + PRL HRLD++TSGIL++ R R A   +      
Sbjct: 451 LSVQGGTGLKKHLDMMLSHLKFEADETPRLVHRLDKDTSGILILGRNRTATTAMADKFEQ 510

Query: 172 ----------------------------------------ESFRMRRIQKIYWSLVWGIP 191
                                                   E      I K YW+L+   P
Sbjct: 511 KLKRRSDREVKKEKKDKKDDSNNNNNNNYSSKKTTKTTVEEMKDDNSIIKTYWALLTSTP 570

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             ++  I   L K    G + V   K+   GA  AI+ ++VI+       ++ + P TGR
Sbjct: 571 NPREGRIRAPLQKIVENGQEKVVATKETGNGAKLAITEYRVIENSMADTSFVALWPETGR 630

Query: 252 THQLRVHALH-MGCPIVGDHKYCANFKGNFTSPIQNK---LYLHARYMDLPHP--EGGRL 305
           THQLRVH    +G PI+GD KY           + +K   L+LHAR +   HP      +
Sbjct: 631 THQLRVHCASILGSPIIGDVKYGGKKSTAPFENVFDKNIPLHLHARRVQFYHPINTNKLV 690

Query: 306 QITAPLPAHMVKTWDSLGFKYD 327
            + APLP  +  +W  LGF  D
Sbjct: 691 DVIAPLPPTLQDSWSILGFNPD 712


>gi|310815298|ref|YP_003963262.1| NAD(P) transhydrogenase subunit alpha [Ketogulonicigenium vulgare
           Y25]
 gi|308754033|gb|ADO41962.1| NAD(P) transhydrogenase subunit alpha [Ketogulonicigenium vulgare
           Y25]
          Length = 339

 Score =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 76/333 (22%), Positives = 139/333 (41%), Gaps = 48/333 (14%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L K+L  G +R+D   V+    R+  G +V I       +
Sbjct: 17  RLDKALARDVPEEASLSRSRLAKLLDEGAIRIDGTVVQDAKARVTEGALVEITIAEANES 76

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
           HI+                  +   ++YED  + V +KPAG+ V    G      ++  +
Sbjct: 77  HIV---------------GQDIPLNVVYEDDDLIVIDKPAGMVVHPAPGSPDGTLVNALI 121

Query: 134 KSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               +S       ++P + HR+D++TSG+LV A+T  A   L   F    I++ Y +L +
Sbjct: 122 HHCGESLSGVGGMKRPGIVHRIDKDTSGLLVAAKTDRAHHGLAALFEAHDIERRYLALCY 181

Query: 189 GIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCF 236
           G+       +           N L  ++ +        +Q    +G  +A++  +V++ +
Sbjct: 182 GVLSAADPRVRGLKGVNFELGNILKIQTRLDRHRTDRQRQAVIWEGGRHAVTRARVVEEY 241

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NK 287
                 +E    TGRTHQ+RVH  ++G  ++GD  Y    + +  S  +          +
Sbjct: 242 NGAASLIECWLETGRTHQIRVHMSYVGHGLIGDPTYGGRKRLSPKSLPEAAVAMAHDFPR 301

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
             LHA  +   HP  G  ++  +PLP  + +  
Sbjct: 302 QALHAATLGFVHPFTGEEMRFESPLPPDISQLI 334


>gi|134102271|ref|YP_001107932.1| ribosomal large subunit pseudouridine synthase [Saccharopolyspora
           erythraea NRRL 2338]
 gi|291003766|ref|ZP_06561739.1| ribosomal large subunit pseudouridine synthase [Saccharopolyspora
           erythraea NRRL 2338]
 gi|133914894|emb|CAM05007.1| ribosomal large subunit pseudouridine synthase [Saccharopolyspora
           erythraea NRRL 2338]
          Length = 310

 Score =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 144/327 (44%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ ++ + V +  + MR+D         ++   +  +  SG V +D      ++R+ +G 
Sbjct: 1   MSGLRTLPVPDGLDGMRVDAGLSKLL-GLSRTIVAGLAESGDVVLDGTPAGKSDRLVAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +            EQ +   +V +          +L++D  I V +KP G++V    
Sbjct: 60  WLEVT-------LPPAEQPLEVVAVPVE------GLRILHQDDDIVVVDKPIGVAVHPSP 106

Query: 124 G------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      +       ++       ++  + HRLD  T+G++VVA++  A   L  +F+ R
Sbjct: 107 GWEGPTVVGGLAAAGVRIATSGASERQGVVHRLDAGTTGVMVVAKSEHAYSTLKRAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G P   +  I   +    H   DY   V     G   +I+H++ ++ F 
Sbjct: 167 TVDKRYHALVQGHPDPSRGTIDAPI--DRHPRHDYKFAVV---AGGKPSITHYETVEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    ++++  TGRTHQ+RVH   +  P VGD  Y A+        + ++ +LHAR +  
Sbjct: 221 RAASLVDVKLETGRTHQIRVHFAAVRHPCVGDLTYGADPVLARRVGL-SRQWLHARSLGF 279

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  GR +   +  PA +    D L 
Sbjct: 280 EHPSDGRWVSFDSDYPADLAHAVDVLR 306


>gi|87201058|ref|YP_498315.1| ribosomal large subunit pseudouridine synthase D [Novosphingobium
           aromaticivorans DSM 12444]
 gi|87136739|gb|ABD27481.1| ribosomal large subunit pseudouridine synthase D [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 332

 Score =  226 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 73/317 (23%), Positives = 134/317 (42%), Gaps = 32/317 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNH 76
             RLD+   +    ++   ++ +L  G+VR+    V + + +   G    I         
Sbjct: 23  GQRLDKALADA-SGLSRERVKALLGEGRVRLGGAVVSQASLKPAEGTPFEIH-------- 73

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
                  +  +      +  +  ++++ED  + V +KPAG+ V   +G      ++  L 
Sbjct: 74  -------VPEAAPAEAIAQAIPLVVVHEDDALIVVDKPAGLVVHPAAGNPDGTLVNALLH 126

Query: 135 SWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                        +P + HR+D++TSG+LVVA+T AA + L   F    I + Y  +  G
Sbjct: 127 HCRGQLSGIGGVARPGIVHRIDKDTSGLLVVAKTDAAHEGLARQFADHSITRAYKCVTAG 186

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +P      +   + + SH   D   +   ++    +A++HF+ +    Q    +E +  T
Sbjct: 187 VPMPPSGTVRGAIARSSH---DRKKMALVDDGRGKHAVTHFRTLAAL-QGAALVECRLET 242

Query: 250 GRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
           GRTHQ+RVH   +G P++GD  Y    +  +        ++  LHA  +   HP  G  L
Sbjct: 243 GRTHQVRVHLASIGHPLLGDPVYGRTPSRLRPLLQRLGFHRQALHAAELGFIHPVTGAPL 302

Query: 306 QITAPLPAHMVKTWDSL 322
              +P P  M +    L
Sbjct: 303 HFASPTPVDMRELIVEL 319


>gi|295091829|emb|CBK77936.1| pseudouridine synthase, RluA family [Clostridium cf.
           saccharolyticum K10]
          Length = 345

 Score =  226 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 83/338 (24%), Positives = 141/338 (41%), Gaps = 30/338 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ V V  +E   RLD+    +        + K+LR   + ++ K+   + R+  G  +R
Sbjct: 1   MRLVTVTKNEAGQRLDKLLFKYMNLAGKSFVYKMLRKKNITLNGKKCDGSERLLEGDEIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          + E+ I   S    +    +K  ++YED  +   NKPAG+  Q      
Sbjct: 61  L---------FLSEETIEKFSEVKVQKVSRVKLEIVYEDEDVIFINKPAGMLSQKARDGD 111

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  +L +++   GQ         +P + +RLD+ TSG++   ++    Q L+   + R
Sbjct: 112 ESLVEYLIAYLMESGQLTKEELKSFRPSVCNRLDRNTSGLVAAGKSLPGLQELSRIIKDR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I K Y  LV G  K     I  WLLK        V V K+   G+    + +  +    
Sbjct: 172 SIGKYYLCLVKGQVKQPS-RIEGWLLKDERTNR--VEVTKEERGGSLPICTEYTPLLRSG 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYM 295
                L+++  TGR+HQ+R H   +GCP+VGD KY   A  +            LHA  +
Sbjct: 229 -AHTLLKVKLITGRSHQIRAHLASIGCPVVGDRKYGDPAENRKAREQFGVTGQLLHAAEL 287

Query: 296 DLPHPEGGRL------QITAPLPAHMVKTWDSLGFKYD 327
            +P    G L      +  APLP   +   +++    D
Sbjct: 288 VMPGELSGPLCRLRGRKFAAPLPEAFLTMAEAVFTDQD 325


>gi|118617189|ref|YP_905521.1| RluA family pseudouridine synthase [Mycobacterium ulcerans Agy99]
 gi|118569299|gb|ABL04050.1| pseudouridine synthase, RluA-family [Mycobacterium ulcerans Agy99]
          Length = 345

 Score =  226 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 139/326 (42%), Gaps = 28/326 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  + + V      MR+D         ++   +  I  +G V +D      ++R+ +G 
Sbjct: 1   MTGDRSMPVPEGLAGMRVDAGLARLL-GLSRSAVAVIAENGGVELDGVPAGKSDRLTAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          + E      +  +          +LY D  I   +KPA ++     
Sbjct: 60  WLHVQ---------LPEAPPPPENTPVEIEG----MTILYSDDDIVAVDKPAAVAAHASV 106

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R
Sbjct: 107 GWTGPTVLGGLAAAGYRISTSGVHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQR 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G P      I   + +  H GG++   V    K   ++++H+  ++ F 
Sbjct: 167 TVDKRYHALVQGHPDPSSGTIDAPIGR--HPGGEWKFAVT---KNGRHSLTHYDTVEAFV 221

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                L++   TGRTHQ+RVH   +  P  GD  Y A+ K      +Q + +LHAR +  
Sbjct: 222 -AASLLDVHLETGRTHQIRVHFAALHHPCCGDLVYGADPKLAKRLGLQ-RQWLHARSLAF 279

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSL 322
            HP +G R++I +P P  +    D L
Sbjct: 280 AHPADGRRVEIVSPYPPDLQHALDVL 305


>gi|281413199|ref|YP_003347278.1| pseudouridine synthase, RluA family [Thermotoga naphthophila
           RKU-10]
 gi|281374302|gb|ADA67864.1| pseudouridine synthase, RluA family [Thermotoga naphthophila
           RKU-10]
          Length = 304

 Score =  226 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 90/314 (28%), Positives = 138/314 (43%), Gaps = 34/314 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHII 78
           RLD++ +N    +    + K++R G+V V+KKRVK  +  ++ G VV +          +
Sbjct: 13  RLDKFLRNQLKDVPLSVIYKLIRKGKVYVNKKRVKDPSFELEEGDVVEL--------RYV 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWV 137
             + +   S         +K  +LYED    V NKP  I++  G G+    +   L  + 
Sbjct: 65  NLENLPKRSEKKDLTPVPMKLDVLYEDDHYLVLNKPPNIAIHPGKGVHVATLIEGLLHYG 124

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             KG  P L HRLD++TSG+LVVA+ R AA+ LTE F+ R I+K Y +LV G+P+N  + 
Sbjct: 125 QEKGFSPFLVHRLDKDTSGLLVVAKNREAARILTELFKGRNIEKEYVTLVRGVPENNMKL 184

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                                       A+S   V     +    L ++ HTGR HQ+R 
Sbjct: 185 TIPL--------------------DGQEAVSEI-VSVKPLKDVSLLRVKIHTGRKHQIRR 223

Query: 258 HALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAH 314
           H   +G P+VGD  Y                + +LH+  M    P         APLP  
Sbjct: 224 HLSQIGFPVVGDDTYGDRHFNIEFRKRYGLKRQFLHSYRMKFIDPWTEEEKDFRAPLPDD 283

Query: 315 MVKTWDSLGFKYDR 328
           ++   + L  + D 
Sbjct: 284 LLSVLNLLKERSDE 297


>gi|313665289|ref|YP_004047160.1| pseudouridine synthase, RluA family [Mycoplasma leachii PG50]
 gi|312949430|gb|ADR24026.1| pseudouridine synthase, RluA family [Mycoplasma leachii PG50]
          Length = 310

 Score =  226 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 71/321 (22%), Positives = 140/321 (43%), Gaps = 36/321 (11%)

Query: 19  MRLDRWFKNHYP--HINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
           +RLD+           +   +QK+++   + V+ + +   N  ++    + I      L+
Sbjct: 13  LRLDKLLVELLTSYDYSRSYIQKLIKEKCISVNDQIIINNNFLVKPNSEIVITIKDPILD 72

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
             + + K +D               ++Y+D  + V NK   I+V     +    +  + +
Sbjct: 73  TNLVKNKDID-------------LDIIYQDDDLLVINKQNNITVHPS--LNNTNNTIVNA 117

Query: 136 WVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            + S  +        +P + HR+D++T+G+L++A+     + L+E F+  RI K Y ++V
Sbjct: 118 LLASDVELSSINGELRPGIVHRIDKQTTGLLIIAKNDKTHKLLSEMFKSHRIYKEYLAIV 177

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+ K  K  I   + + S      + V     K +  AI+ F++++ F +    ++ Q 
Sbjct: 178 TGVIKPNKGLIDAPIGR-SQTDRKKMSV---TAKNSKQAITTFELVERFLKN-TLVKCQI 232

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  ++  P++ D  Y       FT       YLHA  +   HP     ++
Sbjct: 233 QTGRTHQIRVHFNYINHPVLNDPVYGKK-HQEFTDFG---QYLHAYKLKFTHPITKKEIE 288

Query: 307 ITAPLPAHMVKTWDSLGFKYD 327
           + +PLP         L  + +
Sbjct: 289 LISPLPKEFDDKIKELRGESN 309


>gi|291285956|ref|YP_003502772.1| pseudouridine synthase, RluA family [Denitrovibrio acetiphilus DSM
           12809]
 gi|290883116|gb|ADD66816.1| pseudouridine synthase, RluA family [Denitrovibrio acetiphilus DSM
           12809]
          Length = 302

 Score =  226 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 140/327 (42%), Gaps = 31/327 (9%)

Query: 4   MTYVQYVV-VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M+ ++  + +  +  NMRLD +  ++   I+    ++++    V+V+        +++SG
Sbjct: 1   MSGIEKTIKLNVETGNMRLDAYIADN-TDISRSFAERLVTDEFVKVNGVSKPKKYKVKSG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I      +  +   +               +   ++Y+  +  V NKPAGI+V   
Sbjct: 60  DSIVIDVPREEVPELTPVK---------------MDIEIIYDCDEFAVINKPAGITVHPA 104

Query: 123 SGIAYHI--DGFLKSW--VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            G A     +  L  +   D    +P + HRLD++TSG+++VA+ R + + L++ F  R 
Sbjct: 105 PGHADDTIVNAMLAEFDITDDNDLRPGIVHRLDKDTSGLMIVAKNRKSREVLSKVFADRD 164

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y ++ WG PK  +  I   + +        + V     +   Y+ S  +V+     
Sbjct: 165 IDKRYLAVCWGKPKELEFTIEQPIGRHYK-DRKRMCVR----EDGRYSKSGVRVLKQNNN 219

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            F   E++  TGRTHQ+RVH  H G P+ GD  Y              +  LH+  +   
Sbjct: 220 AF-LAEIRIFTGRTHQIRVHMSHAGFPLAGDVVYGHRQSLKLP---IKRQALHSFRLAFV 275

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGF 324
            P  G  +   +PLP  M +    L  
Sbjct: 276 SPFTGEDMVFESPLPLDMKELIIGLKL 302


>gi|206889653|ref|YP_002248865.1| pseudouridylate synthase, 23S RNA-specific [Thermodesulfovibrio
           yellowstonii DSM 11347]
 gi|206741591|gb|ACI20648.1| pseudouridylate synthase, 23S RNA-specific [Thermodesulfovibrio
           yellowstonii DSM 11347]
          Length = 315

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 88/342 (25%), Positives = 161/342 (47%), Gaps = 40/342 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS++     +  E  +E  RLD +  +   +I+    Q+ +    V+V+      + +I+
Sbjct: 1   MSIL-----LQTEKADEGKRLDIFISDKL-NISRAKAQEAIEKKFVKVNNYVKTKSYKIK 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
              ++ +    +           L++S  L   +  +   ++Y+D  + V +KPAG+ V 
Sbjct: 55  FNDLIEVSDEFSLK---------LENSEKLIPQN--IPIQVIYKDDYLIVLSKPAGMVVY 103

Query: 121 GGSGIAYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLT 171
             +G   H DG L + +    +K         P + HRLD++TSG++VVA        L 
Sbjct: 104 PCAG---HPDGTLMNALAYHVKKLANVGAPFRPGIVHRLDKDTSGVMVVALDDETYYKLV 160

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           E+F+ R I+K Y +LV+G  +   +      + ++      + +     K A  AI+ ++
Sbjct: 161 EAFKKREIKKEYLALVYGQLRGSGKITT--PVGRAIYDRKKMSI---KSKKAKEAITEWE 215

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQNKL 288
           VI  F + + +L+++  TGRTHQ+RVH   +G P++GD  Y        GN   P+ ++ 
Sbjct: 216 VIKNF-KNYTFLKVKILTGRTHQIRVHFSSIGHPVIGDKTYGRKTYIEIGNKKIPV-SRQ 273

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
            LHA  ++L HP   + LQ  A LP  +    + L  +Y+  
Sbjct: 274 MLHAHKIELIHPITEKLLQFEASLPDDIQYILNILEDRYESE 315


>gi|283798031|ref|ZP_06347184.1| pseudouridine synthase, RluA family [Clostridium sp. M62/1]
 gi|291074333|gb|EFE11697.1| pseudouridine synthase, RluA family [Clostridium sp. M62/1]
          Length = 345

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 83/338 (24%), Positives = 141/338 (41%), Gaps = 30/338 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ V V  +E   RLD+    +        + K+LR   + ++ K+   + R+  G  +R
Sbjct: 1   MRLVTVTKNEAGQRLDKLLFKYMNLAGKSFVYKMLRKKNITLNGKKCDGSERLLEGDEIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          + E+ I   S    +    +K  ++YED  +   NKPAG+  Q      
Sbjct: 61  L---------FLSEETIEKFSEVRVQKVSRVKLEIVYEDEDVIFINKPAGMLSQKARDGD 111

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  +L +++   GQ         +P + +RLD+ TSG++   ++    Q L+   + R
Sbjct: 112 ESLVEYLITYLMESGQLTKEELKSFRPSVCNRLDRNTSGLVAAGKSLPGLQELSRIIKDR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I K Y  LV G  K     I  WLLK        V V K+   G+    + +  +    
Sbjct: 172 SIGKYYLCLVKGQVKQPS-RIEGWLLKDERTNR--VEVTKEERGGSLPICTEYTPLLRSG 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYM 295
                L+++  TGR+HQ+R H   +GCP+VGD KY   A  +            LHA  +
Sbjct: 229 -AHTLLKVKLITGRSHQIRAHLASIGCPVVGDRKYGDPAENRKAREQFGVTGQLLHAAEL 287

Query: 296 DLPHPEGGRL------QITAPLPAHMVKTWDSLGFKYD 327
            +P    G L      +  APLP   +   +++    D
Sbjct: 288 VMPGELSGPLCRLRGRKFAAPLPEAFLTMAEAVFTDQD 325


>gi|302518516|ref|ZP_07270858.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           SPB78]
 gi|333027806|ref|ZP_08455870.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces sp. Tu6071]
 gi|302427411|gb|EFK99226.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           SPB78]
 gi|332747658|gb|EGJ78099.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces sp. Tu6071]
          Length = 313

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 79/333 (23%), Positives = 140/333 (42%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  V+ + V +  E  R+D      +   +     ++   G+V+VD   V  + R++
Sbjct: 1   MSAIPEVRTLPVPDGLEGERVDAALSRMF-GFSRTKAAELAAGGKVQVDGSVVGKSERVR 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  + V  KP G++ 
Sbjct: 60  GGAWLEVEMPRAAAPVQIVAEP--------------VEGMEIVHDDEDVVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGQTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKNQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR+R + K Y +LV G P      I   + +  H   DY   V         +++H+ +I
Sbjct: 166 FRVRTVDKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAE---GKASVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAF-RAASLLDVKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTLAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +   HP  G  ++  +  P  + +  D +  +
Sbjct: 279 RLGFTHPGTGDWVEYASDYPEDLQRALDRVRAE 311


>gi|323143512|ref|ZP_08078192.1| ribosomal large subunit pseudouridine synthase D [Succinatimonas
           hippei YIT 12066]
 gi|322416706|gb|EFY07360.1| ribosomal large subunit pseudouridine synthase D [Succinatimonas
           hippei YIT 12066]
          Length = 323

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 73/337 (21%), Positives = 144/337 (42%), Gaps = 34/337 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           M     + + ++  N RLD          +   L++ +  G+V VD   + K + ++ SG
Sbjct: 1   MPQNVILTITDEFHNKRLDAALGGLIDTHSRSTLREYIDEGKVAVDGVVITKPSIKVSSG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q+V +                +    +L      L   ++Y+D  I + NKP    V  G
Sbjct: 61  QIVSVT---------------IPDPEDLDAKPQDLPLDIIYQDDDILIINKPINFVVHPG 105

Query: 123 SGIAYH--IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +GI     ++  L  +  +    +  + HRLD++TSG++V+A ++ A Q LT++     +
Sbjct: 106 AGIKDGTVMNAVLYHFPQTSSLPRAGIVHRLDKDTSGLMVIALSQLAQQVLTKAIAKHDV 165

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++  G        I   + +  ++      +    E     A++H++V++ F + 
Sbjct: 166 VREYEAIAEGQI-TAGGTIDAPIGRDPYV---RTKMAVMPEGIGREAVTHYRVMERF-RA 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---------KLYL 290
              L ++  TGRTHQ+RVH   +  P++GD++Y            ++            L
Sbjct: 221 HTRLRLRLETGRTHQIRVHMASIHHPLLGDNQYGGKRLKMLPGADEDLANMLRNYRHQAL 280

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           HA +++  HP+    +    P+P  M +  + L   Y
Sbjct: 281 HAVHIEFAHPKTKENMSFDVPIPEEMSELIELLRKDY 317


>gi|296140324|ref|YP_003647567.1| pseudouridine synthase [Tsukamurella paurometabola DSM 20162]
 gi|296028458|gb|ADG79228.1| pseudouridine synthase, RluA family [Tsukamurella paurometabola DSM
           20162]
          Length = 308

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 140/327 (42%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  + +R+D         ++   + ++   G V +D   V  ++++++G 
Sbjct: 1   MRESRTMPVPDGLDGLRVDAGVARLL-GLSRTVVSELAAEGSVTLDGAPVGKSDKLRAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ +      L    +  +I+   V            +LY D  I V +KP G++     
Sbjct: 60  LLDV-----TLPEPARPLEIVAEPVP--------GMNILYSDDDIVVVDKPVGVAAHASV 106

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  + HRLD  TSG++ VA +  A   L  +F+ R
Sbjct: 107 GWTGPTVIGGLAAAGFRISTSGAPERQGIVHRLDVGTSGVMAVAVSERAYTVLKRAFKQR 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G P      I   + +  H   D+   V    K    +I+H+  I+ F 
Sbjct: 167 TVDKRYHALVQGHPDPMSGTIDAPIGR--HRSSDWKFAVT---KDGKPSITHYDTIEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q    L++   TGRTHQ+RVH   +  P  GD  Y ++        ++ + +LHAR +  
Sbjct: 221 QAATLLDVHLETGRTHQIRVHFAALHHPCCGDQTYGSDPVLAKKLGLE-RQWLHARTLGF 279

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  ++ T+P P  +    D L 
Sbjct: 280 THPTKGEYVEFTSPYPDDLQHALDVLR 306


>gi|297571262|ref|YP_003697036.1| pseudouridine synthase [Arcanobacterium haemolyticum DSM 20595]
 gi|296931609|gb|ADH92417.1| pseudouridine synthase, RluA family [Arcanobacterium haemolyticum
           DSM 20595]
          Length = 306

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 139/325 (42%), Gaps = 31/325 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +    + +     RLD         ++   +  ++ SG V +D      ++R+ +G +V 
Sbjct: 1   MNSYFIPDGFAGDRLDAALAK-MTGLSRSRIADLIASGDVYLDGVIPGKSDRVNAGAMVM 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I   I A   +  E   ++               +LYED  I V +KP G++        
Sbjct: 60  IN--IPAPASVEPELTPVEG------------MGVLYEDDDIIVVDKPVGVAAHASQNFE 105

Query: 127 YHID--GFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                   L + V        ++  + HRLD  T+G +VVA++  A   L  +FR R + 
Sbjct: 106 GPNVLGALLAAGVRLTTSGPQERMGIVHRLDVGTTGAMVVAKSELAYTMLKRAFRDRTVT 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQK 239
           KIY +LV G P      +         IG D+ H  K   +    ++++H+  I+  A  
Sbjct: 166 KIYHALVQGHPDPMNGTVEAP------IGRDHRHQWKMGVRADGKHSVTHYDTIEAMA-G 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              LE+   TGRTHQ+RVH   +  P VGD  Y A+ + +    ++ + +LHA  +   H
Sbjct: 219 ASLLEVHLETGRTHQIRVHMSALRHPCVGDDMYGADPRLSAKLGLE-RQWLHAVRLGFDH 277

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLG 323
           P  G  +++ +  PA +    D++ 
Sbjct: 278 PRTGHYIEVESAYPADLQHALDTMR 302


>gi|67459733|ref|YP_247357.1| ribosomal large subunit pseudouridine synthase D [Rickettsia felis
           URRWXCal2]
 gi|67005266|gb|AAY62192.1| Ribosomal large subunit pseudouridine synthases, RluD subfamily
           [Rickettsia felis URRWXCal2]
          Length = 385

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 78/374 (20%), Positives = 151/374 (40%), Gaps = 84/374 (22%)

Query: 12  VENDEENMRLDRWFKNHYPHI--------------------------------------- 32
           V ++  N+RLD+   + + ++                                       
Sbjct: 6   VPSELNNIRLDKALLHLFKNVQGNSENFRQDEFQGEPAERILTREYRRDLQNSLVSSFLN 65

Query: 33  ---NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
              +   +QK +++ QV V+   +   +  ++   V+                       
Sbjct: 66  YPVSRNQIQKAIKNSQVLVNDVIISDPDVLVKENDVILFSFK---------------EPE 110

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD--------SK 140
            L   +  +   ++YED  + V NK AG++V  G+G  +H D  + + +           
Sbjct: 111 ELKIAAANIALDIIYEDDDLIVINKAAGMTVHPGAG--HHDDTLVNALLYHTKNLSDIGS 168

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            ++P + HRLD++T+G++VVA+   A   L      R++ + Y +LVWG+    +  I N
Sbjct: 169 AERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKALVWGVINPLEGVIKN 228

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHA 259
            + + S +    + ++K    G   A++H+K ++ F +     +E +  TGRTHQ+RV  
Sbjct: 229 NIGR-SRVDRQKMTILKY---GGKEAVTHYKTLELFHKGTISMVECKLSTGRTHQIRVQL 284

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGGR-LQITAP 310
            H+   +VGD  Y  N +    S  +         +  LH+ Y+   HP     ++ +  
Sbjct: 285 SHLKHSVVGDQTYGNNDRKIAHSLPELKAKLIDFKRQALHSWYLSFTHPTSNEIMKFSCE 344

Query: 311 LPAHMVKTW--DSL 322
           LP  M +    D+L
Sbjct: 345 LPRDMEEIIATDAL 358


>gi|325522995|gb|EGD01421.1| RluA family pseudouridine synthase [Burkholderia sp. TJI49]
          Length = 279

 Score =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 84/292 (28%), Positives = 142/292 (48%), Gaps = 22/292 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + ++      R+D +       +   ++ +ILRSG+VRV+K RV    R+  G +VR+PP
Sbjct: 2   IEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAFGDLVRVPP 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           V  A   + +    +    +           +LYED  + V +KPAG++V GGSG+A+ +
Sbjct: 62  VRVAAADLARADAPVVPPAHFD---------VLYEDDAMLVIDKPAGVAVHGGSGVAFGV 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+     + +   L HRLD+ETSG+L++A+ R+A   L E  R  R+ K Y++   G
Sbjct: 113 IEQLRQAR-PRAKFLELVHRLDRETSGVLMLAKKRSALVGLHEQIRENRMDKRYYACGHG 171

Query: 190 IPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             +        +   L K +   G+    V+ +      + + F +++ +   +  +E +
Sbjct: 172 EWQPDWGRRRAVKAPLFKYTTPEGERRVRVQDD---GLASHTVFNLVERWPD-YALVEAE 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHAR 293
             TGRTHQ+RVH  H+G PI GD KY               P   +++LHA 
Sbjct: 228 LKTGRTHQIRVHLAHLGLPIAGDAKYGDFALNKALARANAQPSLKRMFLHAH 279


>gi|260654932|ref|ZP_05860420.1| ribosomal large subunit pseudouridine synthase D [Jonquetella
           anthropi E3_33 E1]
 gi|260630247|gb|EEX48441.1| ribosomal large subunit pseudouridine synthase D [Jonquetella
           anthropi E3_33 E1]
          Length = 301

 Score =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 135/321 (42%), Gaps = 30/321 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +VVE  +   RLD +       ++   + +++  G V    K VK +  + SG    +
Sbjct: 4   RRIVVEPSDAGNRLDLYLSGQL-ELSRSAVGRLISGGLVSGVGK-VKASRVVVSGDWFDV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                +   ++ +                +    +Y D  + V  K AGI+V  G+G   
Sbjct: 62  SMPEPSEESVVPQD---------------VPFRTVYADDWLAVVEKLAGIAVHPGAGRKD 106

Query: 126 AYHIDGFLKSW--VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              ++G +K++  +   G +P + HRLD  TSG++VVART  A   L   F  RR++K Y
Sbjct: 107 GTLVNGLVKTFGPLPGAGLRPGIVHRLDIGTSGLMVVARTPQAYLFLQREFSQRRVEKTY 166

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G     +  +   + +  +                  A++ ++ +          
Sbjct: 167 LALVHGWIPASQGTLDGPIGRSRYDRLKMAVRA-----DGRRAVTRYRTLWTRGS-LSLT 220

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +  TGRTHQ+RVH   +GC + GD  Y    K      ++ +++LHA  +   HP  G
Sbjct: 221 ACRIETGRTHQIRVHMASIGCYLDGDRLYGP--KDVSRHFLEGRVFLHAWRLSFHHPSDG 278

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
           R +   +PLP  ++     + 
Sbjct: 279 RTMNFRSPLPDELIGVLKKIR 299


>gi|221308760|ref|ZP_03590607.1| hypothetical protein Bsubs1_05088 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221313082|ref|ZP_03594887.1| hypothetical protein BsubsN3_05029 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221318008|ref|ZP_03599302.1| hypothetical protein BsubsJ_04973 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221322282|ref|ZP_03603576.1| hypothetical protein BsubsS_05074 [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|255767213|ref|NP_388802.2| RNA pseudouridine synthase [Bacillus subtilis subsp. subtilis str.
           168]
 gi|239938792|sp|P54604|YHCT_BACSU RecName: Full=Uncharacterized RNA pseudouridine synthase yhcT;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|225184840|emb|CAB12749.2| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|291483387|dbj|BAI84462.1| hypothetical protein BSNT_01587 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 302

 Score =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 85/319 (26%), Positives = 140/319 (43%), Gaps = 34/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            +++   ++   L    K      +   +Q  +   Q++V+ + V  N  ++ G  V I 
Sbjct: 9   EILINEKQDGQWLFSVLKTALK-ASKPVIQDWMSHQQIKVNHESVLNNMIVKKGDRVFID 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
              +  + +I E   LD               +L+ED+ + + NKPAGI+      G   
Sbjct: 68  LQESEASSVIPEYGELD---------------ILFEDNHMLIINKPAGIATHPNEDGQTG 112

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +       G+  K R  HRLDQ+TSG +V A+ R A   L +    + +++ Y +
Sbjct: 113 TLANLIAYHYQINGETCKVRHVHRLDQDTSGAIVFAKHRLAHAILDQQLEKKTLKRTYTA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFA-QKFCWL 243
           +  G  + KK  I       S IG D  H  ++    G   A++HFKV+   A ++   +
Sbjct: 173 IAEGKLRTKKGTI------NSPIGRDRSHPTRRRVSPGGQTAVTHFKVMASNAKERLSLV 226

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E++  TGRTHQ+RVH   +G P+ GD  Y    K      + N+  LHA  +   HP   
Sbjct: 227 ELELETGRTHQIRVHLASLGHPLTGDSLYGGGSK------LLNRQALHANKVQAVHPITD 280

Query: 304 RLQI-TAPLPAHMVKTWDS 321
            L +  AP PA M     +
Sbjct: 281 ELIVAEAPFPADMKNLCRT 299


>gi|118444250|ref|YP_878581.1| ribosomal large subunit pseudouridine synthase D [Clostridium novyi
           NT]
 gi|118134706|gb|ABK61750.1| ribosomal large subunit pseudouridine synthases, RluD subfamily
           [Clostridium novyi NT]
          Length = 301

 Score =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 149/329 (45%), Gaps = 37/329 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     +  + V+ DEE +RL+ + KNH    +   ++K  R G+++V+ + V+ +  ++
Sbjct: 1   MEEKNNILKIKVQIDEEEIRLNHYLKNHANCSSR-FIRKAAREGRIKVNNENVRLSYMLK 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  V+ +         I+ E+  LD               ++YED  I V NKP GI V 
Sbjct: 60  NDDVIELQINREENQDIVPEKMHLD---------------VIYEDKDIVVINKPKGIVVH 104

Query: 121 GGSGIAYHIDGFLKS----WVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                  H +G L +    +   K +    RL +RLD +TSG++++A+   +   L+   
Sbjct: 105 PTK---RHQNGTLSNGVLYYFKEKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDM 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +     K Y ++V G  K K   I   + +        V      ++    +++ FKV++
Sbjct: 162 QKDDFVKSYLAIVHGNLKEKSGVINKPIYRVGEGTLRRVI-----DERGQRSVTRFKVVE 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            + +    +E+   TGRTHQ+RVH   +G PI GD  Y             ++  LHA  
Sbjct: 217 SY-EDADLVELTLETGRTHQIRVHLSSIGHPIYGDSLYGKE-----EHEYIDRQALHAYK 270

Query: 295 MDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           + +PHP+ GR+ ++ + LP  M      L
Sbjct: 271 LQIPHPKDGRILKLESDLPDDMKNLISKL 299


>gi|148270918|ref|YP_001245378.1| RluA family pseudouridine synthase [Thermotoga petrophila RKU-1]
 gi|147736462|gb|ABQ47802.1| ribosomal large subunit pseudouridine synthase C [Thermotoga
           petrophila RKU-1]
          Length = 304

 Score =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 91/324 (28%), Positives = 139/324 (42%), Gaps = 34/324 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           V V  +    RLD++ +N    +    + K++R G+V V+ KRVK  +  ++ G VV   
Sbjct: 3   VEVTKENFYRRLDKFLRNQLKDVPLSVIYKLIRKGKVYVNGKRVKDPSFDLEEGDVVEF- 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-Y 127
                    +  + +   S         +K  +LYE     V NKP  I++  G G+   
Sbjct: 62  -------RYVNLENLPKRSEKKDLTPVPMKLDVLYEGKHYLVLNKPPNIAIHPGKGVHVA 114

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L  +   KG  P L HRLD++TSG+LVVA+ R AA+ LTE F+ R I+K Y +LV
Sbjct: 115 TLIEGLLHYGQEKGFSPFLVHRLDKDTSGLLVVAKDREAARILTELFKDRNIEKEYVTLV 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G P+N  +                             AIS    +    +    L ++ 
Sbjct: 175 RGTPENNMKITIPL--------------------DGQEAISEIVSVKSL-RDVSLLRVKI 213

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
           HTGR HQ+R H   +G P+VGD  Y      +         +L+LH+  M    P     
Sbjct: 214 HTGRKHQIRRHLSQIGFPVVGDDTYGDRHFNREFRKRYGLKRLFLHSYRMKFIDPWTEEE 273

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
               APLP  ++   + L  + D 
Sbjct: 274 KDFRAPLPDDLLSVLNFLEERSDE 297


>gi|33519652|ref|NP_878484.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Candidatus Blochmannia floridanus]
 gi|34395754|sp|P59838|RLUD_BLOFL RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|33517315|emb|CAD83700.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Candidatus Blochmannia floridanus]
          Length = 321

 Score =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 78/338 (23%), Positives = 159/338 (47%), Gaps = 39/338 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M  ++ ++V+  +   RLD       P  +   ++  + + +V V+ +       ++  G
Sbjct: 1   MVIIKPMIVQVHQSGYRLDYILSKLLPQYSRSQIKHWILNKKVVVNNQVSTLPRKKVVYG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           +++ I  + N  N I K + I+  ++ L          ++YED+ I V NK + + V  G
Sbjct: 61  ELIEIKYINN--NDICKSEDIVPQNIPLN---------IIYEDNDILVINKASNMVVHPG 109

Query: 123 SGIAYHIDGFLKSWVDSKGQ-------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G   H  G + + +  +         +  +  RLD++T+G++++A+T +A  +L  SF+
Sbjct: 110 IG---HYQGTVLNALLYRYPSILKISKQAGIVQRLDKDTTGLMIIAKTVSAYDNLLRSFK 166

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           +R++ K Y ++V+G   +    +   + ++      ++ V          A++++ V++ 
Sbjct: 167 LRKVVKEYDAIVYGKFTSNAGVVNQPM-RRHFAKRTFMSVHY----TGKSAVTYYSVVEE 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF----------KGNFTSPIQ 285
           F +    + +   TGRTHQ+RVH  ++  P+VGD KY  NF          + N      
Sbjct: 222 F-KAHSRVRINLKTGRTHQIRVHMAYINHPLVGDQKYKGNFSVFDIKKMSDELNNYLLDF 280

Query: 286 NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           N+  LHA  + L HP    +++  APLP  +++    L
Sbjct: 281 NRQALHACTLQLLHPITQVQMKWNAPLPQDILQLIAIL 318


>gi|168187890|ref|ZP_02622525.1| hypothetical RNA pseudouridine synthase YhcT [Clostridium botulinum
           C str. Eklund]
 gi|169294254|gb|EDS76387.1| hypothetical RNA pseudouridine synthase YhcT [Clostridium botulinum
           C str. Eklund]
          Length = 301

 Score =  225 bits (573), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 82/329 (24%), Positives = 150/329 (45%), Gaps = 37/329 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     V  + V+ ++E +RL+ + KN+    +   ++K  R G+++V+ + V+ +  ++
Sbjct: 1   MEEKNNVLKLKVQINDEEIRLNHYLKNYAKCSSR-FIRKAAREGRIKVNNENVRLSYMLK 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I         I+ E+               +K  ++YED  I V NKP  I V 
Sbjct: 60  NNDLIEIQINRKEEQDIVPEK---------------MKLDIIYEDEDIIVINKPKAIVVH 104

Query: 121 GGSGIAYHIDGFLKS----WVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                  H++G L +    +   K +    RL +RLD +TSG++++A+   +   L+   
Sbjct: 105 PTK---RHLNGTLSNGVLYYFKEKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDM 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +     K Y ++V G  + K   I   + +        V      ++    +I+ FKVI+
Sbjct: 162 QKDDFIKRYLAIVHGNLEEKSGVIDKPIYRVGEGTLKRVI-----DERGQKSITRFKVIE 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            + +    +E+   TGRTHQ+RVH   +G PI GD  Y             ++  LHA  
Sbjct: 217 SY-ENADLIELTLETGRTHQIRVHLSSIGHPIYGDALYGKE-----EHEYIDRQALHAYK 270

Query: 295 MDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           + +PHP+ GR+ ++ + LP  M    D L
Sbjct: 271 LQIPHPKDGRILKLQSDLPDDMKNLIDKL 299


>gi|300933336|ref|ZP_07148592.1| pseudouridylate synthase [Corynebacterium resistens DSM 45100]
          Length = 339

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 135/322 (41%), Gaps = 26/322 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +    MR+D         ++   + ++  S  V ++   V  ++R+ +G  + I
Sbjct: 33  RVLPVPDGLAGMRVDAGLSKLL-GLSRTVVAQLAESNDVLMEGAPVGKSDRLVAGAWLDI 91

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGI 125
                        + + +    L +  D     +LY D  + V +KP G++     G   
Sbjct: 92  T-------LPEPPRDLANEPPQLVEGMD-----ILYSDEDVIVVDKPVGVAAHPTLGWEG 139

Query: 126 AYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                G   +          ++  +  RLD  TSG +VVA +  A   L  +FR R + K
Sbjct: 140 PTVTAGLAAAGFRISTSGPPERKGIVQRLDVGTSGAMVVAASERAYSLLKRAFRDREVDK 199

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G P      I   + +  H    +   V+ +     +A++H+  ++   ++  
Sbjct: 200 TYHALVQGHPDPTSGTIDAPIAR--HPSAGWRFAVRDD---GKHAVTHYDTLEAH-RQAS 253

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L+++  TGRTHQ+RVH   +  P+VGD  Y ++        +  + +LHA  +  PHP 
Sbjct: 254 LLKVKLETGRTHQIRVHFSSLHHPLVGDPMYGSDPHLAEKLGLI-RQWLHAVELGFPHPS 312

Query: 302 GGRLQITAPLPAHMVKTWDSLG 323
           G  + I +P P  +    D L 
Sbjct: 313 GKWMTIESPYPKDLAVALDRLR 334


>gi|187250787|ref|YP_001875269.1| pseudouridine synthase [Elusimicrobium minutum Pei191]
 gi|186970947|gb|ACC97932.1| Pseudouridine synthase [Elusimicrobium minutum Pei191]
          Length = 299

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 73/333 (21%), Positives = 137/333 (41%), Gaps = 53/333 (15%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + +         RLD +   + P  +   +Q +++ G+V V+ K  K    +  G 
Sbjct: 1   MSNKETLTFSGTSA--RLDLFLSENKPDYSRGLIQNLIKQGKVTVNGKERKPAWPLAEGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V I                        ++   LK ++++ED  ++V NKP+G+ V   S
Sbjct: 59  NVEIEW-------------------PSVENKTGLKDLIIFEDKNMFVINKPSGMLVHPQS 99

Query: 124 GIAYHI-------DGFLKSWVDSKGQK--------PRLTHRLDQETSGILVVARTRAAAQ 168
            +           +  L S + +   K          L HRLD++TSG++++A+      
Sbjct: 100 PVWEENPAAAFIGEETLVSLILANPPKNFEKGITRAGLVHRLDKDTSGVMIIAKNSKTQD 159

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            + E F  R + K Y ++V G+  + K  I   + + +  GG       +  +    A++
Sbjct: 160 AMVEMFANREMHKTYEAIVCGVVPDDKGIINVPIGRVT--GGKI-----KASELGREAVT 212

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
            + V+    +    +++ P TGRT+QLRVH   +G P++GD  Y              +L
Sbjct: 213 EYSVLQRK-ETVSLMKLHPVTGRTNQLRVHMSWLGYPVLGDWLYKG--------ATAPRL 263

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
            LH++  +  HP     ++ T   P     +W 
Sbjct: 264 MLHSKSAEFEHPFTSKPVKFTVAPPKDFKDSWK 296


>gi|269123861|ref|YP_003306438.1| pseudouridine synthase, RluA family [Streptobacillus moniliformis
           DSM 12112]
 gi|268315187|gb|ACZ01561.1| pseudouridine synthase, RluA family [Streptobacillus moniliformis
           DSM 12112]
          Length = 297

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 71/308 (23%), Positives = 134/308 (43%), Gaps = 36/308 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D +            +Q++++S  + V+ K+ K + ++  G  + I           
Sbjct: 11  ERIDIYLSKKLDE-TRSRIQELIKSNNILVNGKKTKASYKVNFGDEIFID---------- 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW 136
                +     +      +   ++YED  + + NK AG+ V    G       +  +   
Sbjct: 60  -----IPLLKEVDIIPQDIDIDIVYEDKYLAIINKYAGMVVHPSKGHEEDTLVNAIMYKI 114

Query: 137 VDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            D  G     +P + HRLD+ TSG++++A+       L+E F+ + I+KIY+++V G   
Sbjct: 115 KDLSGINGDLRPGIVHRLDKNTSGLIIIAKDDKTHFKLSEMFKNKEIKKIYYAIVKGKVN 174

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            K   I   ++ ++      + VV         AI++F+VID   +KF  L++   TGRT
Sbjct: 175 KKSGRIET-MIGRNPNDRKKMAVVD----NGKLAITNFEVIDSN-EKFSLLKVDLETGRT 228

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPL 311
           HQ+RVH  H   PI+GD  Y    +        ++  LHA  ++  HP    ++ +    
Sbjct: 229 HQIRVHLSHFFFPILGDSVYGRKDE-------YDRQMLHAYMLNFIHPITLEKIDVIGNF 281

Query: 312 PAHMVKTW 319
            +  ++  
Sbjct: 282 HSDFLRAL 289


>gi|94676946|ref|YP_588650.1| ribosomal large subunit pseudouridine synthase D [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
 gi|94220096|gb|ABF14255.1| ribosomal large subunit pseudouridine synthase D [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
          Length = 319

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 79/324 (24%), Positives = 148/324 (45%), Gaps = 31/324 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNH 76
             RLD+         +   ++  +  G+V+V+ +  +  N +I  G++++I  +      
Sbjct: 18  PQRLDQAIAKLLADYSRSQIKGWILEGKVKVNDQVTILPNKKILGGEIIKISVM------ 71

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKS 135
                  ++        +  +   ++YED  I V NKP  + V  G+G +   I   L  
Sbjct: 72  -------IEREHEQYWKAQNIALNIVYEDDDIIVINKPRDMVVHSGAGNLDGTILNALLY 124

Query: 136 WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +  +    PR  + HRLD+ T+G+++V +T +A   L E  R R I + Y ++  GI  N
Sbjct: 125 YYPAIANVPRAGIVHRLDKNTTGLMIVGKTLSAQTKLVELLRTRSIIREYEAITIGIINN 184

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               +   + + +                   AI+H+ +I+ F +    L ++  TGRTH
Sbjct: 185 D-GTVEQPIARHAT-----KRTHMTVNPLGKPAITHYSIIERF-RAHTRLRLRLETGRTH 237

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTS----PIQNKLYLHARYMDLPHPEGGR-LQIT 308
           Q+RVH  +M   +VGD  Y ++ + + ++       N+  LHA  + L HP   R +++ 
Sbjct: 238 QIRVHMAYMNHHLVGDQLYRSSQQNHHSNIEVLRRFNRQALHATTLRLHHPITAREMELH 297

Query: 309 APLPAHMVKTWDSLGFKYDRNLYI 332
           A LP  MV+  ++L  + DR  ++
Sbjct: 298 AALPQDMVELVNAL--QEDRKNFL 319


>gi|299532487|ref|ZP_07045877.1| pseudouridine synthase, RluA family protein [Comamonas testosteroni
           S44]
 gi|298719434|gb|EFI60401.1| pseudouridine synthase, RluA family protein [Comamonas testosteroni
           S44]
          Length = 294

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 97/305 (31%), Positives = 149/305 (48%), Gaps = 21/305 (6%)

Query: 26  KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILD 85
             H   +   ++ +I+RSG+VR++K RV    R+Q G VVR+PPV  +       +K+ +
Sbjct: 1   MRHLKGVPKTHVYRIIRSGEVRINKGRVSAETRVQPGDVVRLPPVRIS-------EKVSE 53

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
            +       DF     L +D  +   +KPAG++V GGSG+++ +   L+       +   
Sbjct: 54  KAERPAPAKDFPA---LLDDEHMLALSKPAGVAVHGGSGVSFGVIEQLRQAR-PDAKFLE 109

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ETSGIL+VA+ R+A  +L + FR R   K Y +LV G     K+ I   L K 
Sbjct: 110 LVHRLDRETSGILLVAKKRSALINLQDQFRERETGKTYLALVQGAWPANKKVIDLPLHKY 169

Query: 206 SHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQK-------FCWLEMQPHTGRTHQLRV 257
               G+  V V   ++     +I+  KV      +          LE+   TGRTHQ+RV
Sbjct: 170 LQADGERRVRVTTADDPDGMRSITLVKVRKLIEPRPLQGLPAMSLLEVTIKTGRTHQIRV 229

Query: 258 HALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           H    G PIVGD KY   +           +++LHA  +   HP  G R+++ A LP  +
Sbjct: 230 HLSSQGHPIVGDDKYGDFDLNRRVQKQGLKRMFLHAWRLQFNHPASGERVELRAELPPEL 289

Query: 316 VKTWD 320
               +
Sbjct: 290 ADFVN 294


>gi|238897665|ref|YP_002923344.1| 23S rRNA pseudouridylate synthase [Candidatus Hamiltonella defensa
           5AT (Acyrthosiphon pisum)]
 gi|229465422|gb|ACQ67196.1| 23S rRNA pseudouridylate synthase [Candidatus Hamiltonella defensa
           5AT (Acyrthosiphon pisum)]
          Length = 281

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 158/290 (54%), Gaps = 14/290 (4%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
            L +ILR G+VRV+KKR+K   ++ +G ++RIPP+  A   II+ + I   S+   K   
Sbjct: 1   MLYRILRKGEVRVNKKRIKPCYKLLTGDMLRIPPIKTA---IIQNKPI---SIKCNKVV- 53

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L   +L+ED  I + NKP+G +V GGSG+++ +   L++    + +   L HRLD+ETS
Sbjct: 54  ALAQSILFEDPDILILNKPSGTAVHGGSGLSFGVIEALRALRPDQ-RFLHLVHRLDRETS 112

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GIL+VA+   A + L E  R++ ++K Y +LV G      + I   L K     G+ +  
Sbjct: 113 GILMVAKKPYALRSLNEQLRLKTMKKEYLALVAGDWPLSCKLIQAPLQKNILQNGERIVK 172

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-A 274
           V         + +HF++ + F      ++++P TGRTHQ+RVHALH G PIV D +Y   
Sbjct: 173 VSHQ---GKESQTHFEIEERFT-NTTLMKVRPLTGRTHQIRVHALHAGHPIVFDDRYGDP 228

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            F+        N+L+LHA  ++  HP  G  +QI APL   +      L 
Sbjct: 229 EFEKKLKGCHLNRLFLHALSLEFVHPHSGETIQIKAPLDNSLRHCLQFLR 278


>gi|332976359|gb|EGK13213.1| ribosomal large subunit pseudouridine synthase D [Desmospora sp.
           8437]
          Length = 270

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 71/290 (24%), Positives = 128/290 (44%), Gaps = 31/290 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R  +VRVD + VK N+R+Q G+ V +                +          + L   
Sbjct: 1   IREHRVRVDGRIVKSNHRLQGGEQVEV---------------AVPPPEEAEVKPEALPLE 45

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQET 154
           +++ED  + + NKP G+ V    G      ++  L    D  G     +P + HR+D++T
Sbjct: 46  VVFEDGDVIMVNKPRGMVVHPAPGSPSGTLVNALLAHCDDLSGIGGVLRPGIVHRIDKDT 105

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA+   A + L    +   + + Y +LV G   + +  +   + +  H    +  
Sbjct: 106 SGLIMVAKNDFAHRSLAAQLKNHTVDREYTALVQGNIPHDRGTVDAPIGRDPH----HRK 161

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +    +    A++HF+VI+ F++    +  +  TGRTHQ+RVH   +G P+VGD  Y  
Sbjct: 162 RMAVEHRHGKPAVTHFEVIERFSR-ATLIRCRLETGRTHQIRVHMKSIGHPLVGDPVYST 220

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            ++        +   LHAR +   HP  G R+     +P  M    +   
Sbjct: 221 RYR----DFPIDGQALHARLLGFDHPRTGERICRELEMPEDMRSLVEGFR 266


>gi|157828222|ref|YP_001494464.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           rickettsii str. 'Sheila Smith']
 gi|165932925|ref|YP_001649714.1| hypothetical protein RrIowa_0413 [Rickettsia rickettsii str. Iowa]
 gi|157800703|gb|ABV75956.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           rickettsii str. 'Sheila Smith']
 gi|165908012|gb|ABY72308.1| hypothetical protein RrIowa_0413 [Rickettsia rickettsii str. Iowa]
          Length = 303

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 85/301 (28%), Positives = 151/301 (50%), Gaps = 11/301 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + +  ++ G  + I    N      +
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNSQKAEASLSVKGGDKIFINDKFNLPVKQPE 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +    D+ + L K        L+Y D  +   NKPAG++ QGG+ I   ID  LK +++ 
Sbjct: 72  KLVFTDAEIKLAKK--ITTDYLIYADDNLIAINKPAGLATQGGTKINLSIDSALK-YLNY 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           KG   +L HRLD++TSG+L++A+   ++  L ++F+ + + K Y+++ +G P      + 
Sbjct: 129 KGTDFKLVHRLDKKTSGLLLIAKNYLSSVKLHDAFKEKLVVKTYFAVTYGKPIKNVGEVR 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + + K     G    +   + +    AI+++KV+         +E  P TGR HQLR+HA
Sbjct: 189 SNIEKSK---GSTPKITDIDSENGKLAITYYKVLKSLDNNLFLIEFTPVTGRMHQLRLHA 245

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKT 318
             +GCPI+GD KY          P    ++LHA  + L     G  +++ A LP +  + 
Sbjct: 246 KLLGCPILGDDKYG----NKAIMPYSKYMFLHAHNICLSEKIFGQEIKLEAKLPFYFTRR 301

Query: 319 W 319
            
Sbjct: 302 L 302


>gi|294055321|ref|YP_003548979.1| pseudouridine synthase, RluA family [Coraliomargarita akajimensis
           DSM 45221]
 gi|293614654|gb|ADE54809.1| pseudouridine synthase, RluA family [Coraliomargarita akajimensis
           DSM 45221]
          Length = 312

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 84/332 (25%), Positives = 142/332 (42%), Gaps = 32/332 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   V    V +  ++ R D+ F + +  I+   LQ+   +GQV  D + +    +I  G
Sbjct: 1   MARRVIEFRVPDGIQSGRADKLFASKFEDISRARLQRAFDAGQVSFDGEAIDKRFKINRG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++R                + +   N+      +   ++YEDS + V +KP G+    G
Sbjct: 61  GLLR--------------AVLDEPDANVGPRPVDMPLEIVYEDSCMVVVSKPVGMVTHPG 106

Query: 123 SGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           SG     D  + + +   G         ++P + HRLD+ETSG++ VA+T  A   L  +
Sbjct: 107 SGTGE--DTLVHALLHHTGGQLSSVGAPERPGIVHRLDKETSGLIAVAKTDLAHHKLASA 164

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  R   K Y +LV G P      +   + +        V      +     A + + V 
Sbjct: 165 FSERNTYKRYRALVLGSPMRSSGTVREPIGRHP-----VVRTRMAVQPNGRDAHTDWTVD 219

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F  +   +    HTGRTHQ+RVH  H   P++GD  Y              ++ LH+ 
Sbjct: 220 ERFGDRAALISCVIHTGRTHQIRVHMSHERLPLLGDTTYGFKP-NRLKGISVPRVMLHST 278

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            + LPHPE G+ L++ APLP    +  ++L  
Sbjct: 279 ELHLPHPETGKLLELNAPLPQDFERVIEALRL 310


>gi|150015406|ref|YP_001307660.1| RluA family pseudouridine synthase [Clostridium beijerinckii NCIMB
           8052]
 gi|149901871|gb|ABR32704.1| pseudouridine synthase, RluA family [Clostridium beijerinckii NCIMB
           8052]
          Length = 299

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 79/323 (24%), Positives = 144/323 (44%), Gaps = 29/323 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ ++  VV N E+  ++  + K     ++   ++      ++ V+ + VK N  +  G+
Sbjct: 1   MSILEKQVV-NIEKGTKIREYLKVEL-GLSTRLIRSASLGKRIFVNDEVVKMNRVLNEGE 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +++I    +    I  E+               +   ++YED  I V NK   + V    
Sbjct: 59  IIKIDLAKDESQDIAPEK---------------MDIDIVYEDEDILVVNKKPFMVVHPTK 103

Query: 124 GIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 +   + ++    GQ    RL  RLD  TSG++++A+ + +   L++     +++
Sbjct: 104 SYQSGTLANGVINYFMESGQNCIVRLVSRLDMNTSGLIIIAKNQFSHGMLSKEMSENKVE 163

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV GI K K+  I   + K   I      VV +       +I+H+KV++ + +  
Sbjct: 164 KKYLALVHGIMKEKQGTIDLPIYKPEGIENGIRRVVDER---GQRSITHYKVVEEYNES- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E +  TGRTHQ+RVH  H+G PI GD  Y    + +    +  +  LHA  +D   P
Sbjct: 220 SLVECKLETGRTHQIRVHLSHLGHPIYGDTLYGDGDEED----LIKRQALHAFGLDFKSP 275

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
             G +  + A LP  M +    L
Sbjct: 276 RSGEILSLRAELPDDMKELISKL 298


>gi|167757684|ref|ZP_02429811.1| hypothetical protein CLOSCI_00014 [Clostridium scindens ATCC 35704]
 gi|167664704|gb|EDS08834.1| hypothetical protein CLOSCI_00014 [Clostridium scindens ATCC 35704]
          Length = 305

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 134/322 (41%), Gaps = 32/322 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M  +    +   E  +R++++     Y   N   L+K+  S  V V+ + +  N R+ SG
Sbjct: 10  MDRILTYQIGPSEGGLRIEQFLLRRGYSLQNLTQLKKMKES--VLVNGQWLHLNRRLTSG 67

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I    +  +  I               +  L   ++YED  I V NKPAG+ +   
Sbjct: 68  DELVIHIQEHESSKNIP--------------AVNLSLDIVYEDEDIIVINKPAGMPIHPS 113

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHR---LDQETSGILVVARTRAAAQHLTESFRMRRI 179
                +      +W   +  K  +      LD++TSG+ VV++   +   L+     R +
Sbjct: 114 QNNYRNSLANALAWYYQEQGKAFVFRCANRLDRDTSGLTVVSKHMLSGNVLSSMAADRML 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++  G        I   L +K     +     +Q E     AI+H+ V+D     
Sbjct: 174 HREYLAICRGHITPSAGTIHAPLSRKPGSIIERTVDWEQGE----TAITHYCVVD-EKNG 228

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + ++  TGRTHQ+R+H  H+G P++GD+ Y  + +         +  LH+  +  PH
Sbjct: 229 HSLVSLRLETGRTHQIRIHMKHLGYPLIGDYLYNPDME------YIGRQALHSHKLSFPH 282

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  ++  APLP  M    D
Sbjct: 283 PITGEDMEFIAPLPEDMQSVLD 304


>gi|157964329|ref|YP_001499153.1| ribosomal large subunit pseudouridine synthase [Rickettsia
           massiliae MTU5]
 gi|157844105|gb|ABV84606.1| Ribosomal large subunit pseudouridine synthase [Rickettsia
           massiliae MTU5]
          Length = 306

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 87/301 (28%), Positives = 152/301 (50%), Gaps = 11/301 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R++ G  + I    N      +
Sbjct: 15  RLDKYLKRLYPLLTQGVIEKALRQKQITVNSQKTEASLRVKGGDKIFINDKFNLPVKQPE 74

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +    D+ + L K        L+Y D  +   NK AG++ QGGS I   ID  LK +++ 
Sbjct: 75  KLVFTDAEIKLAKK--ITTDYLIYADDNLIAINKLAGLATQGGSKINLSIDSALK-YLNY 131

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           KG   +L HRLD+ETSG+L++A+   ++  L ++F+ + + K Y+++ +G P      + 
Sbjct: 132 KGADFKLVHRLDKETSGLLLIAKNYLSSVKLHDAFKEKLVVKTYFAVTYGKPIKNVGEVR 191

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + + K     G    +   + + +  AI+++KV+         +E  P TGR HQLR+HA
Sbjct: 192 SNIEKSK---GSTPKITNIDSENSKLAITYYKVLKSLDNNLFLIEFTPVTGRMHQLRLHA 248

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKT 318
             +GCPI+GD KY          P    ++LHA  + L     G  +++ A LP +  + 
Sbjct: 249 RLLGCPILGDDKYG----NKEIMPYSKYMFLHANNICLSEKIFGKEIKLEAKLPFYFTRR 304

Query: 319 W 319
            
Sbjct: 305 L 305


>gi|295839444|ref|ZP_06826377.1| RluA family RNA pseudouridine synthase [Streptomyces sp. SPB74]
 gi|197698743|gb|EDY45676.1| RluA family RNA pseudouridine synthase [Streptomyces sp. SPB74]
          Length = 313

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 138/333 (41%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  V+ + V +  E  R+D      +   +     ++   G+V+VD   V  + R++
Sbjct: 1   MSAIPEVRTLPVPDGLEGERVDAALSRMF-GFSRTKAAELAAGGKVQVDGSVVGKSERVR 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E                    ++++D  + V  KP G++ 
Sbjct: 60  GGAWLEVEMPAAAAPVRIVAEP--------------VEGMEIVHDDEDVVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGPTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKNQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR+R + K Y +LV G P      I   + +  H   DY   V         +++H+ +I
Sbjct: 166 FRVRTVDKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAE---GKPSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +    L+++  TGRTHQ+RVH      P  GD  Y A+        +  + +LHA 
Sbjct: 221 EAF-RAASLLDVKLETGRTHQIRVHMAAHRHPCAGDLTYGADPTLAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
            +   HP  G   +  +  P  + +  D +  +
Sbjct: 279 RLGFTHPGTGDWAEYASDYPEDLQRALDRVRAE 311


>gi|90418990|ref|ZP_01226901.1| ribosomal large subunit pseudouridine synthase [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90337070|gb|EAS50775.1| ribosomal large subunit pseudouridine synthase [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 344

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 93/347 (26%), Positives = 150/347 (43%), Gaps = 52/347 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVD------KKRVKFNNRIQSG 62
            +VE+D   +RLD +        ++    Q ++  GQV VD       KR     ++ +G
Sbjct: 17  FLVEDDRAGIRLDAFVAAASDGALSRSRAQALIADGQVTVDDVTVTVGKR-----KLVAG 71

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           ++V +                +    +     + +   +++ED  + V +KPAG+ V  G
Sbjct: 72  EIVAVD---------------IPPPSDPEPLPEPIPLTIVFEDEHLVVIDKPAGLVVHPG 116

Query: 123 SG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G      ++  +    DS       ++P + HRLD++TSG+LVVA++ AA Q L + F 
Sbjct: 117 PGNWTGTLVNALIHHCGDSLSGVGGVKRPGIVHRLDKDTSGLLVVAKSDAAHQGLADQFA 176

Query: 176 MR----RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
                 R+ + Y +LVWG+P      I   L + S        VV  +   A +A++ F 
Sbjct: 177 AHGRDGRLSRAYLALVWGVPLRPSGTIDAALGR-STTDRVKRAVVAADRADARHAVTRFN 235

Query: 232 VIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
           ++            +E    TGRTHQ+RVH  H+G P+VGD  Y A F+           
Sbjct: 236 LVKASMLDDGIASLVECVLETGRTHQIRVHMAHIGHPLVGDDVYGAGFRSKSRRLEDDAR 295

Query: 286 ------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
                 ++  LHA  +   HP  G  L   A LPA MV+   + G  
Sbjct: 296 HVVERFDRQALHAFRLGFVHPVTGEDLAFQADLPADMVELCAAFGIS 342


>gi|42572121|ref|NP_974151.1| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|122215273|sp|Q3ECD0|PUS2_ARATH RecName: Full=RNA pseudourine synthase 2, chloroplastic; AltName:
           Full=RNA pseudouridylate synthase 2; AltName:
           Full=RNA-uridine isomerase 2; Flags: Precursor
 gi|332197669|gb|AEE35790.1| RNA pseudourine synthase 2 [Arabidopsis thaliana]
          Length = 430

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 84/363 (23%), Positives = 149/363 (41%), Gaps = 72/363 (19%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           +V+  +  +RLD W  +    ++   +Q  +R G V V+ + V K ++ ++SG  V    
Sbjct: 74  IVDAAKGKIRLDSWISSRINGVSRARVQSSIRLGLVTVNGRVVDKVSHNVKSGDEVNCT- 132

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                         +     L   ++ +   ++YED  + V NKPA + V    G     
Sbjct: 133 --------------ISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGT 178

Query: 128 HIDGFLKSWV--------------------------------DSKGQKPRLTHRLDQETS 155
            ++G L                                     +   +P + HRLD+ T+
Sbjct: 179 LVNGILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRPGIVHRLDKGTT 238

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LVVA+   +  HL E F++  I+++Y SL  G+P   +  I   + + S      +  
Sbjct: 239 GLLVVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPSPPQGRIEIPIGRDSS-NRIRMAA 297

Query: 216 VKQNEKG--ANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +    +G  A +A S +KVI+ FA      +E +  TGRTHQ+R HA +MG P++GD  Y
Sbjct: 298 IPGGVRGGRARHAASRYKVIETFAGGGSALVEWRLETGRTHQIRAHAKYMGVPLLGDEVY 357

Query: 273 CA--------------NFKGNFTSPIQNKL---YLHARYMDLPHPEGGRL-QITAPLPAH 314
                                    + +++    LHA  +   HP  G + + + P P+ 
Sbjct: 358 GGTKSMALSLLQKRVSRSDQEEIIELISRMDRPCLHAIVLGFTHPCTGEIVKFSCPPPSD 417

Query: 315 MVK 317
           + +
Sbjct: 418 LAE 420


>gi|1239996|emb|CAA65704.1| hypothetical protein [Bacillus subtilis subsp. subtilis str. 168]
          Length = 302

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 84/319 (26%), Positives = 139/319 (43%), Gaps = 34/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            +++   ++   L    K      +   +Q  +   Q++V+ + V  N  ++ G  V I 
Sbjct: 9   EILINEKQDGQWLFSVLKTALK-ASKPVIQDWMSHQQIKVNHESVLNNMIVKKGDRVFID 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
              +  + +I E   LD               +L+ED+ + + NKPAGI+      G   
Sbjct: 68  LQESEASSVIPEYGELD---------------ILFEDNHMLIINKPAGIATHPNEDGQTG 112

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +       G+  K R  HRLDQ+TSG +V A+ R A   L +    + +++ Y +
Sbjct: 113 TLANLIAYHYQINGETCKVRHVHRLDQDTSGAIVFAKHRLAHAILDQQLEKKTLKRTYTA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFA-QKFCWL 243
           +  G  + KK  I         IG D  H  ++    G   A++HFKV+   A ++   +
Sbjct: 173 IAEGKLRTKKGTI------NPPIGRDRSHPTRRRVSPGGQTAVTHFKVMASNAKERLSLV 226

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E++  TGRTHQ+RVH   +G P+ GD  Y    K      + N+  LHA  +   HP   
Sbjct: 227 ELELETGRTHQIRVHLASLGHPLTGDSLYGGGSK------LLNRQALHANKVQAVHPITD 280

Query: 304 RLQI-TAPLPAHMVKTWDS 321
            L +  AP PA M     +
Sbjct: 281 ELIVAEAPFPADMKNLCRT 299


>gi|194246668|ref|YP_002004307.1| Pseudouridine synthase [Candidatus Phytoplasma mali]
 gi|193807025|emb|CAP18461.1| Pseudouridine synthase [Candidatus Phytoplasma mali]
          Length = 299

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 146/324 (45%), Gaps = 34/324 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++ +++  E+ MRLD +      + +    QK++  G++ V+ K  K +  ++    +++
Sbjct: 4   EFFIIDV-EKGMRLDHFLNKKI-NFSKNRCQKLIILGKILVNNKPSKKSYILKENDHIKV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                 LN +                   L   ++YED  + V +KP  + +      + 
Sbjct: 62  FIPSTPLNVL---------------QPIDLNLEIIYEDEFLAVIDKPKNLVIHPSITFSG 106

Query: 127 -YHIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              I+G L   K++    G +P + HRLD++T+G+++VA++    Q L  S + R I++ 
Sbjct: 107 VTLINGLLFQIKNFRKMDGLRPGIVHRLDKDTTGLILVAKSEEIRQQLQLSIQKREIKRY 166

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           YW+L+ G  + + + I    + +       + VV    K    +I++FKV+  F   F  
Sbjct: 167 YWALIHGHLEKQGKII--LPIGRHPHNRIKMAVV----KNGKPSITYFKVLKYF-NNFSL 219

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E Q  TGRTHQ+RVH  ++   I+GD  Y                +LH++ ++  HP  
Sbjct: 220 IECQLETGRTHQIRVHLSYLKHHILGDKLYGLKENCYSNES----QFLHSKKIEFIHPIT 275

Query: 303 GR-LQITAPLPAHMVKTWDSLGFK 325
            + + + + LP         L  K
Sbjct: 276 KKNIFLESILPIGFQNVVKKLSIK 299


>gi|303245339|ref|ZP_07331623.1| pseudouridine synthase, RluA family [Desulfovibrio fructosovorans
           JJ]
 gi|302493188|gb|EFL53050.1| pseudouridine synthase, RluA family [Desulfovibrio fructosovorans
           JJ]
          Length = 551

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 137/327 (41%), Gaps = 36/327 (11%)

Query: 18  NMRLDRWFKNHY--PHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINAL 74
             RLD ++        +    ++  +  G+  VD     K   +++ G+ + +       
Sbjct: 21  GTRLDVFWTARLAGEDVTRARVRAAIEEGRATVDGAVCRKPGTKLRGGEALGLRL----- 75

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-----YHI 129
                       +++    ++     LL+ D+ + V +KPAG++V    G+        +
Sbjct: 76  -----------PALSSETEAEAGALKLLHADTDVIVLDKPAGLTVHPAPGLPEGTLVNRL 124

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                   D  G++P + HRLD++TSG+L+VA T +A Q L   F  RR++K Y +LV G
Sbjct: 125 LYRFPQLRDMAGERPGIVHRLDKDTSGLLLVALTESARQALAADFAARRVRKTYLALVHG 184

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPH 248
            P+     I   + +          V     KG   A S ++++          LE+   
Sbjct: 185 RPERDGGDIRLPIGRDPKHRAKMAVVA----KGGREARSRWRLVWSAPDAAASLLEVDIF 240

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT------SPIQNKLYLHARYMDLPHPEG 302
           TGRTHQ+RVH   +G PIVGD  Y A+ + ++       S +  +  LHA  +   HP  
Sbjct: 241 TGRTHQIRVHLAAIGHPIVGDAVYGASRQNDWKRRPGVLSGLATRQMLHAWKLSFTHPGT 300

Query: 303 GRLQ-ITAPLPAHMVKTWDSLGFKYDR 328
           G       P P    +    LG +  R
Sbjct: 301 GETCAYRCPPPPDFWRLVLLLGRRCQR 327


>gi|303287646|ref|XP_003063112.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226455748|gb|EEH53051.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 417

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 82/347 (23%), Positives = 134/347 (38%), Gaps = 63/347 (18%)

Query: 20  RLDRWFKNHYP------HINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72
           RLD +   H P       I    +   +++G V V+     K + R+  G V+R+     
Sbjct: 87  RLDAYIATHAPPSEGGGGITRARVVASIKAGLVDVNGVVARKASERVSPGDVIRV----- 141

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                      L  +       + +   + YED  + V NKPAG+ V    G   H  G 
Sbjct: 142 ----------ALKPTPPTEAAPEDIPLDVKYEDEHVLVVNKPAGMVVHPAPG---HSSGT 188

Query: 133 LKSWV------------------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           L + V                       +P + HRLD+ TSG++VVA+  AA   L E F
Sbjct: 189 LVNAVLFRCGCPAMRVASGNANTADGVARPGIVHRLDKGTSGLIVVAKNEAAHASLCEQF 248

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             R +++ Y ++  G P+  +  +   + +          V +        +  ++KV  
Sbjct: 249 ATRVVRRRYLAICLGSPEQGEGRVDAPIGRDPRDRLKMAVVRRSRGGRRAAS--NYKVRA 306

Query: 235 CFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT------------ 281
             A+     +E +  TGRTHQ+RVHA  +G PI+GD  Y     G               
Sbjct: 307 SLARGNASLVEWRLETGRTHQIRVHAREIGIPILGDETYGGAGNGAEERLRSKGAMTPAE 366

Query: 282 ----SPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
               + I  +  LHA+ +   HP  G  +   A  P    + +++L 
Sbjct: 367 AKRVAKISRRPMLHAQTLGFRHPRTGEEMDFKAEPPEDFAEVFEALR 413


>gi|325121171|gb|ADY80694.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           calcoaceticus PHEA-2]
          Length = 350

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 74/326 (22%), Positives = 139/326 (42%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++      R+D+     +   +   L++ L+ G + V+   VK  +R +         
Sbjct: 41  VQLDETYLGQRIDQVAALVWSEFSREKLKQWLKDGHLLVNGNIVKPKHRCEG-------- 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                         ++     T   + +   ++YED  I V NKP G+ V  G+G     
Sbjct: 93  -------TELLTLEVELEAQTTSQPENIPLNIVYEDDDILVINKPVGMVVHPGAGNSSGT 145

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L  +   ++  +  L HR+D++TSG+LVVA++  A   L++    + + ++Y  +
Sbjct: 146 LVNALLYHFPKLAELSRAGLVHRIDKDTSGLLVVAKSLEAQFSLSKQLANKTVYRVYDLV 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G        I   + K+  +    + ++     G   A++H+ V + F + F  ++ +
Sbjct: 206 VYGNIIA-GGTIDEPI-KRHPVDRVKMAIL----PGGRDAVTHYNVKERF-KDFTRVQAR 258

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  ++G  ++GD  Y         A+     T     +  LHA  + L 
Sbjct: 259 LETGRTHQIRVHFSYIGYGLIGDQVYMNRVRVPAGASELLIETLRGFKRQALHAAKLGLK 318

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +   AP P       + L 
Sbjct: 319 HPRTGEEMLFEAPWPEDFTHLVNVLR 344


>gi|311067404|ref|YP_003972327.1| putative RNA pseudouridine synthase [Bacillus atrophaeus 1942]
 gi|310867921|gb|ADP31396.1| putative RNA pseudouridine synthase [Bacillus atrophaeus 1942]
          Length = 303

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 78/316 (24%), Positives = 139/316 (43%), Gaps = 34/316 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            +++    +   L    K      +   +Q+ + +  ++V+ +    N  ++ G  + I 
Sbjct: 9   ELMITEKLDGQWLFSVLKTEVK-ASKPVIQEWMTTKSIKVNHEPAVHNFIVKKGDRLFID 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAY 127
               A +++I E   ++               +L+EDS + + NKPAG+       G   
Sbjct: 68  LQEKAESNVIPEYGEIE---------------ILFEDSHMLIVNKPAGMPTHPNEEGQTG 112

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +   + + G+  K R  HRLD +TSG +V A+ R A   L +    + +++ Y +
Sbjct: 113 TLANLIAYHLQANGEQTKVRHVHRLDLDTSGAVVFAKHRLAHAILDQQLEKKELKRTYIA 172

Query: 186 LVWGIPKNKKECIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWL 243
           L  G  K KK  I + + + +SH     V        G   A++HF+V     +      
Sbjct: 173 LAEGKLKPKKGTIDSPIGRDRSHPTRRRV------SPGGQAAVTHFRVKGYHPKAGLSLA 226

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E++  TGRTHQ+RVH   +G P+ GD  Y        ++ I ++  LHA+ +   HP  G
Sbjct: 227 ELELETGRTHQIRVHMASIGHPLTGDELYGG------STFILDRQALHAKKVQAVHPITG 280

Query: 304 RLQI-TAPLPAHMVKT 318
              I  APLPA + + 
Sbjct: 281 EFIIAEAPLPADLAEL 296


>gi|302382390|ref|YP_003818213.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
 gi|302193018|gb|ADL00590.1| pseudouridine synthase, RluA family [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 336

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 85/341 (24%), Positives = 136/341 (39%), Gaps = 46/341 (13%)

Query: 3   LMTYVQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
            +T  Q +VV  +      RLD+      P ++   LQ +L  G V  D   V   ++R 
Sbjct: 10  PITDDQVIVVHLDAGMVGDRLDKALARALPTLSRGRLQALLAQGAVSHDGAVVTDGSSRA 69

Query: 60  QSGQV-VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
             G   + +PPV+ A                    +  +   +LYED+ + V +KPAG++
Sbjct: 70  IPGDYDITVPPVMAA-----------------EPRAQAIPLTVLYEDADLIVIDKPAGMA 112

Query: 119 VQGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
                G      ++  L     +        +P + HRLD++TSG++V A++  A   L+
Sbjct: 113 AHPAPGTPDGTLVNALLHHCGATLSGIGGVARPGIVHRLDKDTSGVMVAAKSDRAHAGLS 172

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    I++ Y +L  G P      I   L+ +S      + V+K    G   AI+ + 
Sbjct: 173 ALFATHDIERTYIALTRGAPSPTLGRIET-LIGRSSSDRKKMAVLKS---GGRNAITDYV 228

Query: 232 VIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----FKG 278
           V   +A             +     TGRTHQ+RVH    G PI+GD  Y +       + 
Sbjct: 229 VQARYAVPAKPGAAPLAARVACTLQTGRTHQIRVHMASKGSPILGDATYGSGSPALSVRA 288

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
                   +  LHA  +   HP     L+    LPA M + 
Sbjct: 289 AIEQSGLTRQALHAAVLGFVHPVTDEALRFETSLPADMARL 329


>gi|121534542|ref|ZP_01666364.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
 gi|121306794|gb|EAX47714.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
          Length = 300

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 80/314 (25%), Positives = 133/314 (42%), Gaps = 32/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  +   + ++ + K      +   +QK+ R   + ++ K V    ++++   +R+    
Sbjct: 11  VSREHAGLTVENYLKQVL-QYSGRQIQKLTRHKGILLNGKTVYLQKKVKADDTLRVLISG 69

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHID 130
           ++   +  EQ  ++               +LYED  + V NKPA   V   GS  +  + 
Sbjct: 70  DSAYGVQPEQGPVE---------------ILYEDDYLLVINKPAYQLVHPTGSTTSGTLA 114

Query: 131 GFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +L   ++ +G     R  HRLD+ETSG ++ A+   +   L +    R +++ YW+LV 
Sbjct: 115 NYLAYHLEQRGIICTIRAVHRLDRETSGCIIFAKDAHSQFLLEQQLAARTLKRTYWALVK 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        I   +    H                + AI+H++ I  F      LE+   
Sbjct: 175 GSVSPPAGTIDAPIGPHPHFANRRAVTAH-----GDPAITHYQTIRSFPD-ATLLELILD 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  H+G PIVGD  Y         SP   +  LHA  +   H +  R L +
Sbjct: 229 TGRTHQIRVHLAHLGYPIVGDGMYGVR------SPWIGRQALHAVSVSFQHLQDQRELTV 282

Query: 308 TAPLPAHMVKTWDS 321
            APLPA      + 
Sbjct: 283 HAPLPADFTHAIEQ 296


>gi|315656560|ref|ZP_07909447.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii subsp. holmesii ATCC 35242]
 gi|315492515|gb|EFU82119.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii subsp. holmesii ATCC 35242]
          Length = 304

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 84/323 (26%), Positives = 145/323 (44%), Gaps = 29/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V      +R D         ++      +L SG V  D + +K ++++ +G ++ I
Sbjct: 3   RLLPVPEGLAGLRADIGLSRLL-GLSRAKAGALLESGAVIQDGETLKKSDQLAAGNLLEI 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                          I + +  + + +      +LY D  + V +KPAG++   G G   
Sbjct: 62  --------------DIPEPTGYVPEVTRVDNLGILYADDDLVVVDKPAGVAAHTGPGWEG 107

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L++           ++  + HRLD  TSG +VVA++  A   L   FR  R++K
Sbjct: 108 PTVVGALRAAGIRVSTSGPVEREGIVHRLDAGTSGAMVVAKSELAYGKLKNEFRYHRVEK 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY +L  G  K     I   + +    G ++   V     G   A++H+ VI+       
Sbjct: 168 IYTALATGGVKPPVGTIDAPIGRAP--GREFKMAVVS---GGKPAVTHYDVIEELP-GAT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L++Q  TGRTHQ+RVH   +G P+VGD +Y A+ K      ++ + +LHA  +   HP 
Sbjct: 222 LLKVQLETGRTHQIRVHLAAIGHPLVGDTEYGADRKTAARLGLE-RQWLHASRLAFKHPR 280

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G  + + APLPA +    + L 
Sbjct: 281 TGLEVAVQAPLPADLATAVELLR 303


>gi|114775487|ref|ZP_01451055.1| possible pseudouridine synthase [Mariprofundus ferrooxydans PV-1]
 gi|114553598|gb|EAU55979.1| possible pseudouridine synthase [Mariprofundus ferrooxydans PV-1]
          Length = 325

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 84/334 (25%), Positives = 136/334 (40%), Gaps = 39/334 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV--KFNNRIQSGQVVRI 67
           + V  +    RLD         ++   +Q +LR G VR     V  + + R+  G+   +
Sbjct: 13  ITVSTEASGKRLDAVLAAAC-ELSRSRIQTLLREGHVRTAGGSVISQASARVWEGERYLL 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           L     L    + L   +L+ED  + V NKPAGI V    G  +
Sbjct: 72  T---------------LPPVKPLILEPEDLPLDILFEDEHLIVLNKPAGIVVHPSHGHDH 116

Query: 128 --HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              +   L       G    ++P + HRLD++TSG LV+A++    Q L+E F    + +
Sbjct: 117 GTLVHALLHHCKTLPGINGVERPGIVHRLDKDTSGSLVIAKSEVVHQRLSEMFAEHNLNR 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +   G+P  + +CI   + +  H     + V          +I+   V +     F 
Sbjct: 177 QYIAWCRGVPSWRVKCIELPIGRHPHQ-RQKMAVTD----SGRESITDAAV-EHIFGPFS 230

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--------IQNKLYLHAR 293
            + +  HTGRTHQ+RVH  H   P++GD  Y  ++      P          ++  LHA 
Sbjct: 231 QMRLTLHTGRTHQIRVHMAHENLPVLGDPVYARSYHPGREIPEPARHAIATLSRQALHAE 290

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            ++  HP  G  +   APLP  +    D+L   Y
Sbjct: 291 LLEFDHPISGEPMSFRAPLPEDLTILHDALTKSY 324


>gi|114771661|ref|ZP_01449065.1| putative Pseudouridine synthase, Rlu [alpha proteobacterium
           HTCC2255]
 gi|114547733|gb|EAU50623.1| putative Pseudouridine synthase, Rlu [alpha proteobacterium
           HTCC2255]
          Length = 341

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 75/361 (20%), Positives = 144/361 (39%), Gaps = 56/361 (15%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYP---HINFVNLQKILRSGQVRVDKKRV-KFN 56
           MS   YV  + +  +    RLD+   +  P    ++   + K++  G V +  + + K  
Sbjct: 1   MSA-PYVVELTLGENPAP-RLDKALASVVPAEVTLSRSRITKLIAEGAVTLAGEPITKLK 58

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
            +  +G + RI                           + +   +++ED  + + NKPAG
Sbjct: 59  YKAPAGSIFRIVMPPVQDYE--------------NAQPENIPLDIVFEDDHLIIVNKPAG 104

Query: 117 ISVQGGSGIAY-HIDGFLKSWVDSK------GQKPRLTHRLDQETSGILVVARTRAAAQH 169
           + V    G     +   L  + D         ++P + HR+D++TSG+LVVA++ +A   
Sbjct: 105 MVVHPAPGSENGTLVNALLYYFDGNLSGVGGEKRPGIVHRIDKDTSGLLVVAKSDSAHAG 164

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWL---------------LKKSHIGGDYVH 214
           L + F    I + Y ++  G+P+     +A                  + +       + 
Sbjct: 165 LAKQFADHSISRRYLAVSKGVPQKSDPRLAGLRGVNFEDGGVIRVATNIARHKTDRKRMA 224

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV+       +AI+   V++ FA     +E    TGRTHQ+RVH  H+G  ++GD  Y  
Sbjct: 225 VVQD---AGRHAITRATVLENFAHSA-LMECWLETGRTHQIRVHFSHIGHGLIGDPIYGL 280

Query: 275 N---------FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
                      +        ++  LHA+ +   HP     +   + +P+ +++  + L  
Sbjct: 281 RKAMPGSVFEPEDMVIVKGFSRQALHAKSIGFIHPITKEYMNFDSDIPSDLIELIEILRK 340

Query: 325 K 325
           K
Sbjct: 341 K 341


>gi|325971290|ref|YP_004247481.1| pseudouridine synthase [Spirochaeta sp. Buddy]
 gi|324026528|gb|ADY13287.1| pseudouridine synthase, RluA family [Spirochaeta sp. Buddy]
          Length = 333

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 86/341 (25%), Positives = 147/341 (43%), Gaps = 53/341 (15%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     +  +VVEND E MRLD +       ++   L +      + ++ K VK +  ++
Sbjct: 1   MPTKERILEMVVENDSEAMRLDIYIATKQQSVSRSQLSE--EKTHLFLNGKEVKKSKLVK 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  +++    +    II +   LD               +LYED  + + NK  G+ V 
Sbjct: 59  AGDCIKVIYYEDFFEGIIAQDIPLD---------------VLYEDQDLLIINKKQGMVVH 103

Query: 121 GGSGIAYHIDGFLKSWVDSKGQ---------------------KPRLTHRLDQETSGILV 159
             +G   + D  + + +   GQ                     +P + HRLD++TSG+LV
Sbjct: 104 PAAG--NYEDTLVNALLFRYGQDFSPSLEDDEETEVESPDMALRPGIVHRLDKDTSGVLV 161

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR R + ++L++ F+ R   K+Y +L  G  K  +  I   L + S+   D       +
Sbjct: 162 IARNRQSHRNLSQQFKDRTTHKVYIALAKGNFKGTEGSIRANLKRDSN---DRKKFTTCS 218

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +     A + + V+    + F  + +   TGRTHQ+RVH   +G P+VGD  Y       
Sbjct: 219 DTEGRDARTDYTVL-RQYRDFALVRITLFTGRTHQIRVHFKSIGHPLVGDPVYGK----- 272

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
              P    L LHA  + +  P  G+ ++  AP+P    K  
Sbjct: 273 ---PEGLTLMLHALVLVVFSPSSGKQIRCVAPMPERFRKVL 310


>gi|15806790|ref|NP_295512.1| ribosomal large subunit pseudouridine synthase D [Deinococcus
           radiodurans R1]
 gi|6459564|gb|AAF11343.1|AE002020_2 ribosomal large subunit pseudouridine synthase D [Deinococcus
           radiodurans R1]
          Length = 338

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 83/324 (25%), Positives = 145/324 (44%), Gaps = 41/324 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD         ++   +   + +G V +D +   K + +++ G+ +R+ P       + 
Sbjct: 32  RLDAVVS-LLSGVSRSQVAGWIEAGLVEIDGRAASKASQKLRGGEALRVSPPPLPSAQVE 90

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL--- 133
            E   LD               +++ED  +   NKP G+      G+     ++  L   
Sbjct: 91  PEDVPLD---------------VIFEDEHLIAINKPPGMVTHPAPGVISGTLVNALLGRM 135

Query: 134 -----KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                + +    G +P + HRLD++TSG++VVA+T AA   L  +F+ R  +K Y ++  
Sbjct: 136 SLPEQQDFDGPDGYRPGIVHRLDKDTSGVIVVAKTVAAHARLAAAFKDRETKKTYLAIAA 195

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF----CWLE 244
           G  K ++    +  + +  I    + V      GA  A + F  +D            + 
Sbjct: 196 GAWKAERPVQVDAPIGRHQIQRQRMTV---GGAGAREAQTLFTPLDAHPDGHGRTLALVR 252

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            QP TGRTHQ+RVH  H+G PI+GD  Y         S I  +  LHA+++++PHP  G 
Sbjct: 253 AQPRTGRTHQIRVHLAHLGSPILGDAVYGR------ASEIMPRHALHAQFLEVPHPVSGD 306

Query: 305 L-QITAPLPAHMVKTWDSLGFKYD 327
           +  + A +P  ++  W  LG ++D
Sbjct: 307 ILHLQAAVPEDLLGAWVGLGGRWD 330


>gi|238650483|ref|YP_002916335.1| hypothetical protein RPR_02200 [Rickettsia peacockii str. Rustic]
 gi|238624581|gb|ACR47287.1| hypothetical protein RPR_02200 [Rickettsia peacockii str. Rustic]
          Length = 303

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 85/301 (28%), Positives = 152/301 (50%), Gaps = 11/301 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R++ G  + I    N      +
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNSQKAEASLRVKGGDKIFINDKFNLPVKQPE 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +    D+ + L   +      L+Y D  +   NKPAG++ QGG+ I   ID  LK +++ 
Sbjct: 72  KLVFTDAEIKLA--TKITTDYLIYADDNLIAINKPAGLATQGGTKINLSIDSALK-YLNY 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           KG   +L HRLD++TSG+L++A+   ++  L ++F+ + + K Y+++ +G P      + 
Sbjct: 129 KGTDFKLVHRLDKKTSGLLLIAKNYLSSVKLHDAFKEKLVVKTYFAVTYGKPIKNVGEVR 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + + K     G    +   + +    AI+++KV+         +E  P TGR HQLR+HA
Sbjct: 189 SNIEKSK---GSTPKITDIDSENGKLAITYYKVLKSLDNNLFLIEFTPVTGRMHQLRLHA 245

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKT 318
             +GCPI+GD KY          P    ++LHA  + L     G  +++ A LP +  + 
Sbjct: 246 KLLGCPILGDDKYG----NKEIMPYSKYMFLHANNICLSEKIFGQEIKLDAKLPFYFTRR 301

Query: 319 W 319
            
Sbjct: 302 L 302


>gi|15643702|ref|NP_228748.1| ribosomal large subunit pseudouridine synthase C [Thermotoga
           maritima MSB8]
 gi|222100610|ref|YP_002535178.1| Pseudouridine synthase [Thermotoga neapolitana DSM 4359]
 gi|4981478|gb|AAD36021.1|AE001757_14 ribosomal large subunit pseudouridine synthase C [Thermotoga
           maritima MSB8]
 gi|221573000|gb|ACM23812.1| Pseudouridine synthase [Thermotoga neapolitana DSM 4359]
          Length = 304

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 90/314 (28%), Positives = 139/314 (44%), Gaps = 34/314 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHII 78
           RLD++ +N    +    + K++R G+V V++KRVK  +  ++ G VV +          +
Sbjct: 13  RLDKFLRNQLKDVPLSVIYKLIRKGKVYVNRKRVKDPSFDLEEGDVVEL--------RYV 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWV 137
             + +   S         +K  +LYED    V NKP  I++  G G+    +   L  + 
Sbjct: 65  NLENLPKRSEKKDLTPVPMKLDVLYEDDHYLVLNKPPNIAIHPGKGVHVATLIEGLLYYG 124

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             KG  P L HRLD+ETSG+LVVA+ R AA+ LTE F+ R I+K Y +LV G+P+N  + 
Sbjct: 125 QEKGFSPFLVHRLDKETSGLLVVAKNREAARILTELFKGRNIEKEYVTLVRGVPENNMKI 184

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                                       A+S   V     +    L ++ HTGR HQ+R 
Sbjct: 185 TIPL--------------------DGQEAVSEI-VSVKPLKDVSLLRVKIHTGRKHQIRR 223

Query: 258 HALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAH 314
           H   +G P+VGD  Y      +         + +LH+  M    P         APLP  
Sbjct: 224 HLSQIGFPVVGDDTYGDRHFNREFRKRYGLKRQFLHSYRMKFIDPWTEEEKDFRAPLPDD 283

Query: 315 MVKTWDSLGFKYDR 328
           ++   + L  + D 
Sbjct: 284 LLSVLNLLEERSDE 297


>gi|153004820|ref|YP_001379145.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152028393|gb|ABS26161.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 293

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 77/304 (25%), Positives = 131/304 (43%), Gaps = 37/304 (12%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +Q+++  G+VRVD +  K + R++ G+ V +       + ++ ++               
Sbjct: 1   MQRLVEEGRVRVDGRAAKASARLRGGETVDVEIPPPEPSGLVAQE--------------- 45

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW-----VDSKGQKPRLTHR 149
           L   +LYED+ + V +K AG+ V    G  +    +  L          ++G +  L HR
Sbjct: 46  LPLAVLYEDADLLVLDKAAGMVVHPARGAPHSTVVNALLHRLGVGAAAPAEGLRLGLVHR 105

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG LVVA+T  A   L   F+ R ++K Y +L  G+   +   +     +     
Sbjct: 106 LDKDTSGCLVVAKTEPALAALQAQFKGRTVEKRYLALCHGLLAPE-GRLDTPYGRHPRDR 164

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             +   V    K A  A++ ++ ++ F       E+   TGRTHQ+RVH    G P++ D
Sbjct: 165 IRFTTRV----KSARRAVTEWRALESFPAGATLAEVTLLTGRTHQIRVHLAEAGHPLLAD 220

Query: 270 HKYCANFKGNFTSP---------IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
             Y    +     P            +  LHA  +   HP  G RL + APLP  + +  
Sbjct: 221 AVYGGTRREARLPPEHPVRLAAGAIGRQALHAARLAFDHPRTGRRLALEAPLPDDLRRGL 280

Query: 320 DSLG 323
             L 
Sbjct: 281 QVLR 284


>gi|196248006|ref|ZP_03146708.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
 gi|196212790|gb|EDY07547.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
          Length = 299

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 140/315 (44%), Gaps = 33/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +    +   L ++ + +   I+   L  I    G + V+ + V   + +++G+ + +   
Sbjct: 10  INEQHDGKLLRQFLQEN--GISRTALTDIKFHGGALYVNSRPVTVRHVLRAGETLSVVFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
               +  +                + +   ++YED  + V NKPAG++            
Sbjct: 68  PERTSDWM--------------DPEAMPLDIVYEDEYVLVVNKPAGLATIPSRHHPGGTL 113

Query: 129 IDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +G L  +   +      +  RLD++TSG+++VA+ R     L+   +  ++ + Y ++ 
Sbjct: 114 ANGLLHHYRQQQLDSTVHIITRLDRDTSGLVLVAKHRHVHHLLSTLQQKGQVTRTYEAVC 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+   ++  I   + +++        + ++  +    AI+HF+V++  +  + ++ ++ 
Sbjct: 174 HGVIDEEEGTIDAPIGRQND-----SIIAREVREDGKRAITHFRVLERLS-GYTYVSLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-Q 306
            TGRTHQ+RVH  ++G P+ GD  Y        +  I  +  LH+R +   HP   +L  
Sbjct: 228 ETGRTHQIRVHLAYLGHPLAGDELYGG------SREIIGRQALHSRQLSFFHPFARQLYT 281

Query: 307 ITAPLPAHMVKTWDS 321
            TAPLP  M +  ++
Sbjct: 282 FTAPLPDDMARLIEA 296


>gi|317154041|ref|YP_004122089.1| RluA family pseudouridine synthase [Desulfovibrio aespoeensis
           Aspo-2]
 gi|316944292|gb|ADU63343.1| pseudouridine synthase, RluA family [Desulfovibrio aespoeensis
           Aspo-2]
          Length = 596

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 78/344 (22%), Positives = 146/344 (42%), Gaps = 39/344 (11%)

Query: 1   MSLMTYVQY--VVVENDEENMRLDRWFKNHY--PHINFVNLQKILRSGQVRVDKKRV-KF 55
           MS     +    V  + +  +RLD+++        ++   +Q+ + SG   VD + V + 
Sbjct: 9   MSNEAEKRTWERVAPSSDCGLRLDKFWARELADEGVSRGRVQEWIESGLALVDGEVVTRG 68

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
            +++   + +RI     A +                  +   +  +++ED+ + V +K A
Sbjct: 69  KHKLAGRETLRIGDAGVAPSDDAA-------------QAVPGELEVVFEDAHVAVIDKRA 115

Query: 116 GISVQGGSG--IAYHIDGFLKSWVD-------SKGQKPRLTHRLDQETSGILVVARTRAA 166
           G++     G      ++  L  W D          Q+P + HRLD++TSG++VVA T   
Sbjct: 116 GLTTHPAPGEPGPTLVNHLLHRWPDVASDISGMDRQRPGIVHRLDKDTSGLMVVALTEGD 175

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
              L   F  RR++K+Y ++V G P      I   + +          V +    G   A
Sbjct: 176 RLRLAADFAGRRVRKVYLAVVLGRPAQPAGTIDAPMGRHPSQKTRMAVVAR----GGREA 231

Query: 227 ISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGN 279
           +S ++V+    +     + ++ HTGRTHQ+RVH  H+G P++GD  Y          + +
Sbjct: 232 VSDYRVLWTGPRGLASLVAVRIHTGRTHQIRVHMAHIGHPLLGDSAYGPRENVEWSRRPD 291

Query: 280 FTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
             + +  +  LHA ++   HP    R+ +    PA       +L
Sbjct: 292 RLAGLAPRQMLHAFHLSFRHPATCERVTLWRRPPADFCTLLAAL 335


>gi|256832316|ref|YP_003161043.1| pseudouridine synthase, RluA family [Jonesia denitrificans DSM
           20603]
 gi|256685847|gb|ACV08740.1| pseudouridine synthase, RluA family [Jonesia denitrificans DSM
           20603]
          Length = 313

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 141/326 (43%), Gaps = 26/326 (7%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V +     R+D         ++   +     +G V VD +     +RI  G V+ +
Sbjct: 6   RSFPVPDGLVGQRVDAALARML-GLSRSAILAAFDAGDVYVDGRPAAKGDRIVQGAVIDV 64

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                    ++ + + +D++ +  +    ++  ++++D  I V +KP G++     G   
Sbjct: 65  ---------VLPDPREVDATEDEPQPVPGMR--IVHDDEHIVVVDKPVGVAAHSAVGWSG 113

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  + HRLD  TSG++VVA++  A   L  +FR R + K
Sbjct: 114 PTVVGALAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSELAYTRLKRAFRERTVDK 173

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++V G P+  K  I   + +       +  +          +I+H++V++       
Sbjct: 174 VYHTVVQGHPEPTKGTIDAPIGRHPKAEFKFAVMA-----DGKRSITHYEVMEMLPS-AS 227

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            + +   TGRTHQ+RVH   M  P VGD  Y A+      + + ++ +LHA  +   HP 
Sbjct: 228 LVTVHLETGRTHQIRVHFSAMRHPCVGDSMYGADPTLARRTGL-DRQWLHAVELSFEHPA 286

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKY 326
            G R  + +  P  + +  D L   Y
Sbjct: 287 SGERFTVASEYPQDLQQALDVLRGDY 312


>gi|226360214|ref|YP_002777992.1| pseudouridine synthase RluD [Rhodococcus opacus B4]
 gi|226238699|dbj|BAH49047.1| pseudouridine synthase RluD [Rhodococcus opacus B4]
          Length = 308

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 143/328 (43%), Gaps = 30/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  E MR+D         ++   + ++   G V VD   V  ++R+ +G 
Sbjct: 1   MRETRSMPVPDGLEAMRVDAGLARLL-GLSRTAVAQLTEEGSVLVDGAPVGKSDRLSAGT 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGG 122
            + +              ++ +    LT  ++ ++ + +LY D  +   +KP G++    
Sbjct: 60  WLEV--------------ELPEPPRPLTIEAEPVEGMEILYADDDVVAVDKPVGVAAHAS 105

Query: 123 SG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ 
Sbjct: 106 VGWTGPTVIGGLAAAGFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTLLKRAFKQ 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I K Y +LV G P      I   + +  H   D+   V  +      +I+H+  ++ F
Sbjct: 166 RTIDKRYHALVQGHPDPSSGTIDAPIGR--HRSNDWKFAVTAD---GKPSITHYDTVEAF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q    L++   TGRTHQ+RVH   +  P  GD  Y A+ +      ++ + +LHAR + 
Sbjct: 221 -QAASLLDIHLETGRTHQIRVHFAALRHPCCGDLTYGADPRLAERLGLE-RQWLHARSLG 278

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  GR ++IT+  P  +      L 
Sbjct: 279 FAHPADGRWVEITSKYPKDLEDALGVLR 306


>gi|19553337|ref|NP_601339.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glutamicum ATCC 13032]
 gi|62390974|ref|YP_226376.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           glutamicum ATCC 13032]
 gi|145296099|ref|YP_001138920.1| hypothetical protein cgR_2020 [Corynebacterium glutamicum R]
 gi|21324908|dbj|BAB99531.1| Pseudouridylate synthases, 23S RNA-specific [Corynebacterium
           glutamicum ATCC 13032]
 gi|41326313|emb|CAF20475.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE D [Corynebacterium
           glutamicum ATCC 13032]
 gi|140846019|dbj|BAF55018.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 310

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 135/325 (41%), Gaps = 28/325 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V      MR+D         I+     ++  +G V VD   V  + R+ +  ++ +
Sbjct: 7   RTLPVPEGLAGMRVDAALSKLL-GISRTVAAELATAGDVSVDGAVVGKSERLVADSMLDV 65

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                A   + KE+ +                 +LY D  +   NKP G++     G   
Sbjct: 66  LLPEPAAPLMPKEEIVP-------------GLDILYSDDDVIAVNKPVGVAAHPTVGWEG 112

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  +  RLD  TSG++VVA +      L  +FR R + K
Sbjct: 113 PTVVGGLAAAGFRISTSGPPERKGIVQRLDVGTSGVMVVAASERGYTVLKRAFRDRTVDK 172

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G P      I   + +    G  +    +       +A++H++ ++ F Q+  
Sbjct: 173 TYHALVQGHPDPLTGTIEAPIGRHPSAGWRFAVTTE-----GKHAVTHYETLEAF-QEAT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L++   TGRTHQ+RVH   +  P  GD  Y ++   +    + N+ +LHA  +   HP 
Sbjct: 227 LLKIHLETGRTHQIRVHFSALHHPCCGDPMYGSDPALSERLGL-NRQWLHAVSLGFNHPA 285

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            GR ++I +P P  +    D L  +
Sbjct: 286 DGRWMEIVSPYPTDLQHALDVLREQ 310


>gi|218198893|gb|EEC81320.1| hypothetical protein OsI_24484 [Oryza sativa Indica Group]
          Length = 445

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 81/376 (21%), Positives = 139/376 (36%), Gaps = 80/376 (21%)

Query: 12  VENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           V   E   R+D W         ++   +Q  +R+G V V+ + V K ++ ++ G +V   
Sbjct: 65  VPAGEGRSRIDAWISARLGGGGVSRARIQASIRAGLVVVNGRPVSKVSHMVKGGDIVSCT 124

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
                          +     L    + +   ++YED  + V NKPA + V    G A  
Sbjct: 125 ---------------VSELQPLRAEPEDIPLDIVYEDDHLLVVNKPAHMVVHPAPGNANG 169

Query: 128 -HIDGFLKSW-----------------------------------------VDSKGQKPR 145
             ++  L                                            V     +P 
Sbjct: 170 TLVNAILHHCKISTFTCLARNSIDDECPDSSDDDIDVFDIDQFTTGEVSSEVREALVRPG 229

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+ TSG+LVVA+   +   L E F++  I+++Y SL  G P      I   + + 
Sbjct: 230 IVHRLDKGTSGLLVVAKDEHSHAQLAEQFKLHTIRRVYISLTCGAPNPNSGRIEVPIARD 289

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGC 264
            +     +       + A +A S +KV + FA      +E +  TGRTHQ+R HA ++G 
Sbjct: 290 PNNRIRMIATPGSGHRYARHAASRYKVREVFAGGGSALVEWRLETGRTHQIRAHAKYLGI 349

Query: 265 PIVGDHKYCANFKGNFTSP-----------------IQNKLYLHARYMDLPHPEGGRL-Q 306
           P++GD  Y        +                     ++  LHA  +   HP  G++ +
Sbjct: 350 PLLGDETYGGTKSMALSLLRPRTPSRYHCDLSNMISKIDRPCLHAALLGFKHPHSGKILE 409

Query: 307 ITAPLPAHMVKTWDSL 322
            + P P    +  + L
Sbjct: 410 FSCPPPDDFTEVLNEL 425


>gi|99034362|ref|ZP_01314387.1| hypothetical protein Wendoof_01000811 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 264

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 99/278 (35%), Positives = 151/278 (54%), Gaps = 14/278 (5%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           VD  + K ++R+ SGQ + +   +N + +   ++K  +  VNL      L+  +LYED  
Sbjct: 1   VDDCKAKSSDRVNSGQTITLK-HLNYIENANSDRKYNEKLVNL------LRENILYEDEY 53

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I   NKPAG+ VQGG  +   +   L      +G+  ++ HRLD++TSG+++ AR    A
Sbjct: 54  ILAINKPAGVIVQGGVKVKISMSDLLDQIR--EGETFKIVHRLDRDTSGVIIFARNANVA 111

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           ++L E F+ RR++K Y +L  GIP      I   L+KK   G + V V   +E     A 
Sbjct: 112 RYLMEEFKGRRVKKTYLALTSGIPSKDSGTIDYPLVKKYVSGQEKVVV---DENSPQNAT 168

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +HF +I        +L++QP TGRTHQLR H  H+ CPI+GD KY    K  F   I NK
Sbjct: 169 THFSIIAKSKHNVAYLKLQPITGRTHQLRAHLAHINCPILGDGKYGG--KKAFIDGIANK 226

Query: 288 LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           ++LH+  + L  P    + ITAP+  H+ K+ ++L F 
Sbjct: 227 IHLHSHSLSLKLPNNKEITITAPITKHIEKSIEALFFD 264


>gi|225849242|ref|YP_002729406.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225644151|gb|ACN99201.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 318

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 72/336 (21%), Positives = 140/336 (41%), Gaps = 37/336 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M  +    V  +   +RLD++    YP  +    Q ++  G +  + K +K  + +++ G
Sbjct: 1   MEEILTFKVNEEYAGLRLDQFLAKVYPEYSRSYYQDLIEKGFILKEDKPIKKPSLKVKVG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
           +   +               I+     L    + +   + YED  + V  KP G+ V   
Sbjct: 61  ESYTV---------------IIPPPQPLEVVPENIPLKVYYEDEDLAVVYKPPGMVVHPS 105

Query: 122 -GSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G      ++  L  + +       ++  + HRLD++T+G+++VA++    + L + F+ 
Sbjct: 106 VGHTSGTLVNALLYHFKNVSTYQGKERAGIVHRLDKDTAGLIIVAKSEFTHKELQKMFQN 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I K Y ++V GI K     I   + + S      +  V  N +    A++ + V   +
Sbjct: 166 REIDKRYKAIVVGIVKKDHGIIDLPIGR-SIYDRQKMGTVATNLRD---ALTEYWVEKRW 221

Query: 237 A-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLH- 291
                  ++++ HTGRTHQ+RVH   +G P++ D  Y    +    +    + N L  H 
Sbjct: 222 EKHNLTMVDIKLHTGRTHQIRVHFSAIGHPLLNDQVYGFKKSKLGSSLAVELSNILNYHA 281

Query: 292 --ARYMDLPHPEGGR---LQITAPLPAHMVKTWDSL 322
             A  +   HP   +   +Q+   LP  +    + L
Sbjct: 282 LVAYSLTFKHPRTNKDLHIQLE-KLPEPIPYIIEKL 316


>gi|225021946|ref|ZP_03711138.1| hypothetical protein CORMATOL_01978 [Corynebacterium matruchotii
           ATCC 33806]
 gi|305681500|ref|ZP_07404307.1| pseudouridine synthase, RluA family [Corynebacterium matruchotii
           ATCC 14266]
 gi|224945232|gb|EEG26441.1| hypothetical protein CORMATOL_01978 [Corynebacterium matruchotii
           ATCC 33806]
 gi|305659705|gb|EFM49205.1| pseudouridine synthase, RluA family [Corynebacterium matruchotii
           ATCC 14266]
          Length = 310

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 136/332 (40%), Gaps = 30/332 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS     + + V     +MR+D      +  ++      +   G V +D K    +++I 
Sbjct: 1   MS--RETRSLPVPEGLADMRVDVALSKLF-GLSRTVSADLATKGDVLIDGKPATKSDKIT 57

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +         + + QK L  +  L    +     +LY D  +   +KP G++  
Sbjct: 58  DGAWLEV--------LLPEPQKPLVPTEELVDGLE-----ILYADEDLIAVDKPVGVAAH 104

Query: 121 GGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G     + G L +           ++  +  RLD  TSG++VVA +      L  +F
Sbjct: 105 PTVGWDGPTVVGGLAAAGYRISTSGPPERNGIVQRLDVGTSGVMVVAASERGYSVLKRAF 164

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R + K Y +LV G        I   + +    G  +            +A++H++ ++
Sbjct: 165 KERTVSKTYHALVQGHMDPLAGTIEANIGRHPSSGWKFAVTS-----DGKHAVTHYETLE 219

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F      LE+   TGRTHQ+RVH   +  P  GD  Y A+ + +    + N+ +LHA  
Sbjct: 220 AFV-AASLLEVHLETGRTHQIRVHMSALHHPCCGDPMYGADPQLSARLGL-NRQWLHAVK 277

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +   HP  GR L+I +P P  +    + L  +
Sbjct: 278 LGFYHPADGRWLEIESPYPPDLRHALEVLRAE 309


>gi|157825473|ref|YP_001493193.1| ribosomal large subunit pseudouridine synthase C [Rickettsia akari
           str. Hartford]
 gi|157799431|gb|ABV74685.1| ribosomal large subunit pseudouridine synthase C [Rickettsia akari
           str. Hartford]
          Length = 303

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 89/298 (29%), Positives = 153/298 (51%), Gaps = 11/298 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R+ +G  + I    N      +
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNAQKAEASLRVNAGDKIFIKDKFNLPVKSPE 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +    D+ + L +        L+YED  +   NKPAG++ QGGS I   ID  LK +++ 
Sbjct: 72  KLVFTDAEIKLAQKITI--DYLIYEDDNLIAINKPAGLATQGGSKINLSIDSALK-YLNY 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           KG   +L HRLD+ETSG+L++A+   ++  L ++F+ + I K Y ++ +G P      + 
Sbjct: 129 KGADFKLVHRLDKETSGLLLIAKNYLSSVKLHDAFKEKLIVKTYCAITYGKPIKNVGEVR 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + + K     G    +   + + A  AI+++K++         +E  P TGR HQLR+H+
Sbjct: 189 SNIEKSK---GSTPKITDIDSENAKLAITYYKLLKSLDNNLFLIEFTPVTGRMHQLRLHS 245

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMV 316
             +GCPIVGD+KY          P    ++LH+  M L     G  +++ A LP +  
Sbjct: 246 KLLGCPIVGDNKYG----NKEIMPYSKYMFLHSNNMCLSEKIFGQEIKLEAKLPFYFT 299


>gi|283850426|ref|ZP_06367715.1| pseudouridine synthase, RluA family [Desulfovibrio sp. FW1012B]
 gi|283574452|gb|EFC22423.1| pseudouridine synthase, RluA family [Desulfovibrio sp. FW1012B]
          Length = 558

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 128/322 (39%), Gaps = 36/322 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHI--NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             +     RLD ++      +  +   ++  +  G   VD     K   +++ G+ + + 
Sbjct: 17  TTDGGVGTRLDVFWSARLADLEVSRARVRAAIEGGLATVDGADCRKPGLKLRGGETLTLN 76

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
               A   +                ++     +LY D ++ V +KP G++V    G+   
Sbjct: 77  LPQVASETV----------------AEAGSLRVLYADKELAVLDKPPGLTVHPAPGLPEG 120

Query: 127 YHIDGFLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             ++  L       +  G++P + HRLD++TSG+L+VA T      L   F  R++ K Y
Sbjct: 121 TLVNRLLHHFPGLREMAGERPGIVHRLDKDTSGLLMVALTEPVRLALAADFAARQVHKTY 180

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCW 242
            +LV G P  K   I   + +       Y   +    KG   A S ++ +          
Sbjct: 181 LALVHGRPDGKGGDIRLPIGRDPK----YRTKMAVPHKGGRPAHSRWRPVWTAPDGTASL 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQNKLYLHARYMD 296
           LE+   TGRTHQ+RVH   +G PI+GD  Y          +G   + + ++  LHA  + 
Sbjct: 237 LEVTIFTGRTHQIRVHMAAIGHPIIGDAVYGPHQHAAWKRRGGAIARLASRQMLHAWKLS 296

Query: 297 LPHPE-GGRLQITAPLPAHMVK 317
             HP        T P P    +
Sbjct: 297 FTHPVLKEPRSFTCPPPPDFWR 318


>gi|307331663|ref|ZP_07610770.1| pseudouridine synthase, RluA family [Streptomyces violaceusniger Tu
           4113]
 gi|306882689|gb|EFN13768.1| pseudouridine synthase, RluA family [Streptomyces violaceusniger Tu
           4113]
          Length = 322

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 74/327 (22%), Positives = 140/327 (42%), Gaps = 28/327 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           +S +  ++ + V +  E  R+D      +   +     ++  +G+V++D      ++R+ 
Sbjct: 10  VSTIPEIRTLPVPDGLEGERVDAAIARMF-GFSRTKAAELAAAGKVQLDGTVAGKSDRVS 68

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +      L       +++   V            ++++D  I V +KP G++  
Sbjct: 69  GGAWLEV-----ELPQAAPPVRVVAEPVE--------GMEIVHDDEDIVVVSKPVGVAAH 115

Query: 121 GGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G     + G L +           ++  + HRLD  TSG++VVA++  A   L ++F
Sbjct: 116 PSPGWTGPTVIGGLAAAGFRVSTSGAAERQGIVHRLDVGTSGLMVVAKSELAYSVLKQAF 175

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R + K Y +LV G P      I   + +  H   DY   V  +      +++H+ +I+
Sbjct: 176 RERTVDKRYHALVQGHPDPLSGTIDAPIGR--HPQHDYKWAVTAD---GKPSVTHYDLIE 230

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA  
Sbjct: 231 AF-RAASLLDIKLETGRTHQIRVHMAAHRHPCVGDLTYGADPTLAKRLKL-TRQWLHAMR 288

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWD 320
           +   HP  G  ++  +  P  +    D
Sbjct: 289 LGFEHPAHGEWVEFESAYPDDLRVALD 315


>gi|332283691|ref|YP_004415602.1| ribosomal large subunit pseudouridine synthase D [Pusillimonas sp.
           T7-7]
 gi|330427644|gb|AEC18978.1| ribosomal large subunit pseudouridine synthase D [Pusillimonas sp.
           T7-7]
          Length = 319

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 70/324 (21%), Positives = 127/324 (39%), Gaps = 30/324 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
             +V       RLD+      P  +   LQ  + +G V V+ +  +       G  + + 
Sbjct: 18  EFLVPYTALPERLDKVIARLIPEHSRSRLQGWIEAGHVLVNGQPGRVKQMANPGDKLVVW 77

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--A 126
                                L    + +   ++ + S   V NKPAG+    G+G    
Sbjct: 78  EQA--------------PPEALAFTPEDVDFQVVDQSSDWIVVNKPAGLVTHPGAGNWSG 123

Query: 127 YHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             ++G L  + + +   +  + HRLD++TSG+LVVAR   A  HL    + R + + Y +
Sbjct: 124 TLLNGLLYRYPELATVARAGIVHRLDKDTSGLLVVARHEKAQTHLIRQLQARSVSREYVA 183

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCW 242
           LV G+   +   +   + + + +    V +  +       A++H+  +            
Sbjct: 184 LVHGLL-TRPGSVKLAIGRDTRV---PVRMAVEPAIAPKPAVTHYAPVRAGRIDDAAVTE 239

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +  +  TGRTHQ+RVH + +  P+V D  Y     G  +     +  LHAR +       
Sbjct: 240 VACKLETGRTHQIRVHMMSLHHPLVADALYGGKALGGAS-----RQLLHARALSFDDYGS 294

Query: 303 G-RLQITAPLPAHMVKTWDSLGFK 325
           G R+   A L A   +  D + + 
Sbjct: 295 GQRVSFVASLAADFQQVLDDIAWN 318


>gi|118471435|ref|YP_887490.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           smegmatis str. MC2 155]
 gi|118172722|gb|ABK73618.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           smegmatis str. MC2 155]
          Length = 309

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 144/325 (44%), Gaps = 28/325 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
             + + V      MR+D         ++   +  +   G V +D      ++++ +G  +
Sbjct: 2   DTRSMPVPEGLAGMRVDAGLSRLL-GLSRTVVATLAEEGAVELDGAPAAKSDKLVAGAWL 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +         + +  K ++++       D     +LY D+ I   +KP G++     G 
Sbjct: 61  EV--------RLPEAPKPVENT-----PVDIEGMNILYSDADIVAVDKPPGVAAHATVGW 107

Query: 125 IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R +
Sbjct: 108 HGPTVLGGLAAAGFRISTSGIHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQRTV 167

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G P      I   + +  H G D+   V    +G  ++++H+  ++ F Q 
Sbjct: 168 EKRYHALVQGHPDPSSGTIDAPIGR--HRGHDWKFAVV---EGGRHSVTHYDTLEMF-QA 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+++  TGRTHQ+RVH   +  P  GD  Y A+        ++ + +LHAR +   H
Sbjct: 222 ASLLDIELETGRTHQIRVHFSALHHPCCGDLTYGADPTLAKRLGLE-RQWLHARSLAFAH 280

Query: 300 P-EGGRLQITAPLPAHMVKTWDSLG 323
           P +G R++IT+P P  +    D L 
Sbjct: 281 PADGRRVEITSPYPDDLQNALDLLR 305


>gi|256825466|ref|YP_003149426.1| ribosomal large subunit pseudouridine synthase D [Kytococcus
           sedentarius DSM 20547]
 gi|256688859|gb|ACV06661.1| ribosomal large subunit pseudouridine synthase D [Kytococcus
           sedentarius DSM 20547]
          Length = 309

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 142/327 (43%), Gaps = 26/327 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + VVV +  E  R+D         ++   +  I   G V +  K +   +R+ +G+
Sbjct: 1   MSDTRTVVVPDGLEGERVDAGLSRLL-GLSRNKVADIAAEGGVLMGSKALGKGDRLLAGE 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V +         +  E +       L          +++ED++I V +KPAG++     
Sbjct: 60  LVTVT--------LPPENQAPPV---LPSTESIPGLRVVHEDTEIIVVDKPAGVAAHPSV 108

Query: 124 G------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      +        +       ++  +  RLD  TSG++VVA++  A   L ++FR R
Sbjct: 109 GWKGPDVVGGLAAEGYRISTSGAAERQGIVQRLDVGTSGLMVVAKSERAYSVLKQAFRDR 168

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y +LV G+P   +  I   + +  H G DY   V  N      +I+H+++++   
Sbjct: 169 VVEKTYHTLVQGLPDPLQGTIDAPIGR--HPGHDYRFAVMSN---GRPSITHYELLEAH- 222

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    LE+   TGRTHQ+RVH   MG P  GD  Y A+        +  + +LHA  +  
Sbjct: 223 RAASLLEVHLETGRTHQIRVHFSAMGHPCAGDLTYGADPTLAKRLGLV-RQWLHAVELGF 281

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  G  +  T+     +    D L 
Sbjct: 282 THPGSGEWVTFTSEYSEDLQAAIDQLR 308


>gi|227497602|ref|ZP_03927823.1| possible pseudouridylate synthase [Actinomyces urogenitalis DSM
           15434]
 gi|226832928|gb|EEH65311.1| possible pseudouridylate synthase [Actinomyces urogenitalis DSM
           15434]
          Length = 304

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 136/324 (41%), Gaps = 29/324 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V +     R+D         ++   + ++   G VR+D   +  ++R+ +G ++ 
Sbjct: 1   MRLLPVPDGLVGERVDAALAR-MTGLSRSKVSELCAQGGVRMDGAVLGKSDRLVAGSLIE 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-I 125
           +               + D        +      L+YED  I V +KPAGI+     G  
Sbjct: 60  V--------------DLPDPRPLGPAPTPVDGMSLVYEDEDIVVVDKPAGIAAHPSMGWD 105

Query: 126 AYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + G LK+           ++  +  RLD  TSG ++VA+   A   L  +FR   + 
Sbjct: 106 GPDVLGALKAMHVQVATSGAAERQGIVSRLDVGTSGAMIVAKGERAYSVLKRAFREHEVD 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY +LV G        I   + +  H   ++   +     G   +++H+ VI+      
Sbjct: 166 KIYHALVQGHLDPSSGTIDAPIGR--HPSREWKMAIID---GGRESVTHYDVIESMP-AA 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
              E+   TGRTHQ+RVH   +G P VGD  Y A+   +  + +  + +LHA  + L HP
Sbjct: 220 DLAEIHLETGRTHQIRVHMSAVGHPCVGDETYGADAALSQRTGLV-RQWLHAHRLGLAHP 278

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  +   +P P  +V   + L 
Sbjct: 279 ITGEWMTFVSPYPDDLVHALEVLR 302


>gi|197301688|ref|ZP_03166758.1| hypothetical protein RUMLAC_00414 [Ruminococcus lactaris ATCC
           29176]
 gi|197299128|gb|EDY33658.1| hypothetical protein RUMLAC_00414 [Ruminococcus lactaris ATCC
           29176]
          Length = 340

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 77/332 (23%), Positives = 135/332 (40%), Gaps = 22/332 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++++ +E   R D++   +          K+LR   + ++ K+   N  ++    VR
Sbjct: 10  MKEIIIKKNEAGQRFDKFLAKYMSQAPKSFFYKMLRKKNITLNGKKAAGNEILELNDTVR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +       +      +        +  ++YED      NKPAG+  Q      
Sbjct: 70  LFLSDETIQKFSGTIQQSPGDPDWILAHAGKEPSIIYEDESTIFLNKPAGMLSQKAKPDD 129

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   L +++ + GQ          P + +RLD+ TSG++   +T  A Q L+E FR R
Sbjct: 130 ISMVEHLIAYLLNSGQISKEELRTFHPSVCNRLDRNTSGLIAAGKTLQALQQLSEMFRDR 189

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  LV G   +    I+ +L K        V V +     A+   + + +I    
Sbjct: 190 SLKKYYLCLVRGKVSSDS-HISGYLKKDPRTNR--VTVSRTPSAAASPIETEYHIIK-QT 245

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYM 295
           +    LE+   TG+THQ+R H   +G PI GD+KY               +   LHA  +
Sbjct: 246 KDVTLLEVHLITGKTHQIRAHLASIGHPIAGDYKYGNRAFNETLKKEYGLSSQLLHAYRL 305

Query: 296 DLPHPEGGRL------QITAPLPAHMVKTWDS 321
           + P   GG L      ++ APLP    K    
Sbjct: 306 NFP-KCGGDLSLLSGKELQAPLPPLFQKICQE 336


>gi|158522832|ref|YP_001530702.1| RluA family pseudouridine synthase [Desulfococcus oleovorans Hxd3]
 gi|158511658|gb|ABW68625.1| pseudouridine synthase, RluA family [Desulfococcus oleovorans Hxd3]
          Length = 329

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 142/331 (42%), Gaps = 38/331 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V     + +RLD      +   +  +   ++++G + VD +  K + ++   Q +    
Sbjct: 9   LVTSAGHDGLRLDTLVAGQW-DCSRHSAALLIKNGTILVDGRPQKPSYKVGVNQSITGRI 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--Y 127
                     E   L                LL+ED+ + V NKP G+ V    G     
Sbjct: 68  PSQKPEKPGPEPAPLP---------------LLFEDAFLLVVNKPPGLVVHPAPGHEGGT 112

Query: 128 HIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++  L  +       +  +P + HRLD+ TSG LVVA+T AA Q L++ F+ R+++K Y
Sbjct: 113 LVNRLLHHFPAIGTVGEPDRPGIVHRLDRNTSGALVVAKTAAAHQALSDMFKSRQVRKTY 172

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV+G  K+    +   + + S         +  +   A  A + +KV   F      L
Sbjct: 173 LALVYGQMKSTGGVVTLPIGRHSLERKK----MSVSSPQARPAETRWKVRKAFVD-ASLL 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTS-------PIQNKLYLHAR 293
           E++ HTGRTHQ+RVH   +  P+VGD  Y       + +F+S           +  LHA 
Sbjct: 228 ELEIHTGRTHQIRVHCTALQRPVVGDPTYPCKWTRKRQHFSSRASFELLNAAGRQMLHAW 287

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            ++  HP  G  +  TAPL   + +    L 
Sbjct: 288 RLEFDHPVTGAPMCFTAPLFEDIKEMLHLLR 318


>gi|229815199|ref|ZP_04445535.1| hypothetical protein COLINT_02245 [Collinsella intestinalis DSM
           13280]
 gi|229809209|gb|EEP44975.1| hypothetical protein COLINT_02245 [Collinsella intestinalis DSM
           13280]
          Length = 338

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 74/345 (21%), Positives = 139/345 (40%), Gaps = 43/345 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           M    +++V ++    RLD +        +     K++ +G V V+ +        +  G
Sbjct: 1   MAADVHLLVPSEAAGERLDAYLGAQDACPSRSACAKLVEAGAVAVNGETCLSKKQVVCEG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I              ++ +           +   + YED  + V +K  G+     
Sbjct: 61  DRISI--------------ELPEVREPGAIVPQAIPLDIRYEDDHLLVLSKQRGLVCHPA 106

Query: 123 SGIAYHIDGFLKSWVDSKG-----------QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
            G   H DG L + +                +P + HRLD++TSG+++ A+     + L 
Sbjct: 107 HG---HEDGTLANALVYHCGIEHLGTVQGEDRPGIVHRLDRDTSGLMLAAKDDETQRALQ 163

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              R R + + Y +LV G     +  I   + + +    D V +   ++  A  AI+ F+
Sbjct: 164 NLIRTRTLDRRYITLVHGEIVMDEGTINTGIARST---RDRVKMAVSDDPFARQAITTFQ 220

Query: 232 VIDCFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           V++ F      + +  +E   +TGRTHQ+RVH  H+  P+VGD  Y         +   +
Sbjct: 221 VLERFEPARGDEGYTLVECHLYTGRTHQIRVHMRHIHHPLVGDPLYGKG--NGRMNLDLD 278

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           + +LH+  +   HP  G  +     LP  +    + L   +DR+L
Sbjct: 279 RQFLHSWSVQFEHPITGEVVNCRDELPWDLAAALEEL---HDRSL 320


>gi|197303693|ref|ZP_03168730.1| hypothetical protein RUMLAC_02422 [Ruminococcus lactaris ATCC
           29176]
 gi|197297213|gb|EDY31776.1| hypothetical protein RUMLAC_02422 [Ruminococcus lactaris ATCC
           29176]
          Length = 295

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 74/321 (23%), Positives = 138/321 (42%), Gaps = 32/321 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M       +   E  +R++++ ++  Y + N   L+K+  S  + ++       + +  G
Sbjct: 1   MERTITYQISESEHGLRVEQYLRHKGYSYQNLTQLKKMPES--ILINGIWSYMRSTLSCG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +               I +S  +       L   ++YED  + V NKPAG+ +   
Sbjct: 59  DTLTVH--------------IQESEYSEHIPPVQLPLDIIYEDDDLLVVNKPAGMPIHPS 104

Query: 123 -SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            +     +   L  +   +G+    R T+RLD++TSG+ V+A+   ++  L+       I
Sbjct: 105 LNNYKNSLANALMYYYKEQGKPFIFRCTNRLDRDTSGLTVIAKHLVSSSILSFMAVRHEI 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G        I   L +     G  +   K + +   +A++H+KV+    Q 
Sbjct: 165 HREYLAIVRGAVSPASGTINAPLAR----TGSSIIERKVDFEHGEHAVTHYKVLKEQNQ- 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + +   TGRTHQ+RVH  ++G P+VGD+ Y  + +        N+  LH+  +   H
Sbjct: 220 HSLVSLILETGRTHQIRVHLQYLGHPLVGDYLYNPDME------YINRQALHSWKLSFIH 273

Query: 300 PEGGR-LQITAPLPAHMVKTW 319
           P  G  +   APLP  M K  
Sbjct: 274 PITGEAMHFEAPLPEDMRKVL 294


>gi|229586508|ref|YP_002845009.1| Ribosomal large subunit pseudouridine synthase [Rickettsia africae
           ESF-5]
 gi|228021558|gb|ACP53266.1| Ribosomal large subunit pseudouridine synthase [Rickettsia africae
           ESF-5]
          Length = 303

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 86/301 (28%), Positives = 152/301 (50%), Gaps = 11/301 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R++ G  + I    N      +
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNAQKAEASLRVKGGDKIFINDKFNLPVKQPE 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +    D+ + L K        L+Y D  +   NKPAG++ QGG+ I   ID  LK +++ 
Sbjct: 72  KLVFTDAEIKLAKK--ITTDYLIYADDNLIAINKPAGLATQGGTKINLSIDSALK-YLNY 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           KG   +L HRLD++TSG+L++A+   ++  L ++F+ + + K Y+++ +G P      + 
Sbjct: 129 KGADFKLVHRLDKKTSGLLLIAKNYLSSVKLHDAFKEKLVVKTYFAVTYGKPIKNVGEVR 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + + K     G  + +   + +    AI+++KV+         +E  P TGR HQLR+HA
Sbjct: 189 SNIEKSK---GSTLKITDIDSENGKLAITYYKVLKSLDNNLFLIEFTPVTGRMHQLRLHA 245

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKT 318
             +GCPI+GD KY          P    ++LHA  + L     G   ++ A LP +  + 
Sbjct: 246 KLLGCPILGDDKYG----NKEIMPYSKYMFLHANNICLSEKIFGQESKLEAKLPFYFTRR 301

Query: 319 W 319
            
Sbjct: 302 L 302


>gi|325981783|ref|YP_004294185.1| pseudouridine synthase, RluA family [Nitrosomonas sp. AL212]
 gi|325531302|gb|ADZ26023.1| pseudouridine synthase, RluA family [Nitrosomonas sp. AL212]
          Length = 285

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 76/307 (24%), Positives = 130/307 (42%), Gaps = 32/307 (10%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
            P+ +   LQ  +   ++ V+ +       +   + V I P+      I  E   +  ++
Sbjct: 1   MPNWSRSRLQTWIVEKRILVNGQIATAKQLVWGNEHVEIFPL-----KIAAESPFVAEAI 55

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKG-QKPR 145
           +L           + ED  + + NKPAG+    G+G      ++  L    + K   +  
Sbjct: 56  HLNT---------IEEDETLIIINKPAGLVTHPGNGNWQGTLLNALLHHAPELKNIPRAG 106

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+ T+G+LV+A+T AA   L    + R +++ Y +LV G  K             
Sbjct: 107 IVHRLDKNTTGLLVIAKTLAAQTSLVRQLQQRTVKRDYLALVLGEIKQAGNI-------D 159

Query: 206 SHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           + IG   +H  K         A ++++VI+ F +    L+    TGRTHQ+RVH   +G 
Sbjct: 160 APIGRHPIHRTKMTITSKGKPARTNYQVIENF-EGCTLLQCSLETGRTHQIRVHLNAIGH 218

Query: 265 PIVGDHKYCANFKGNFTSPIQ-----NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKT 318
            +VGD  Y         +  Q      +  LHA+ + L HP+  ++ Q  AP P  +   
Sbjct: 219 ALVGDPVYGGKPGKTARAIAQILTDFPRQALHAQKLALIHPKTEQINQWEAPTPEDINDL 278

Query: 319 WDSLGFK 325
              L  K
Sbjct: 279 LQILRKK 285


>gi|21672662|ref|NP_660729.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Sg (Schizaphis graminum)]
 gi|25009121|sp|Q8K9E9|RLUD_BUCAP RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|21623299|gb|AAM67940.1| ribosomal large subunit pseudouridine synthase d [Buchnera
           aphidicola str. Sg (Schizaphis graminum)]
          Length = 315

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 74/317 (23%), Positives = 137/317 (43%), Gaps = 36/317 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
              RLD+     +   +   L+K +    V ++ K   + + +I  G+ + I      L 
Sbjct: 16  SGKRLDQILSKLFMQYSRSCLKKWIIMNNVYINGKIENQPDKKILGGEKITIYSTDEKLP 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFL 133
             + +   L++               +YEDS I + NKP G+ V  G+G       +  L
Sbjct: 76  INLPQNIALNT---------------IYEDSNILIINKPPGLVVHPGAGNQDGTILNALL 120

Query: 134 KSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             + + S   +  + HRLD++TSG++V+A+T  +   L    + R+I + Y  ++ G   
Sbjct: 121 YRYTNISSIPRCGIIHRLDKDTSGLMVIAKTIFSYNKLVTLLKKRKIIRKYQGIIKGNMI 180

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I N+ + +      +  +    +     +I+H+K+I+ F +    +  +  TGRT
Sbjct: 181 --SGGIVNYPIMRHP----FKRICMTTDSLGKKSITHYKIINRF-KFHTHVSFRLETGRT 233

Query: 253 HQLRVHALHMGCPIVGDHKYCA---------NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           HQ+RVH LH+G P++GD  Y             +  +      +  LHA Y++  HP   
Sbjct: 234 HQIRVHMLHIGYPLLGDPLYGGIDYGCNYFQENRNIYRKFNLFRQALHADYIEFIHPFTQ 293

Query: 304 R-LQITAPLPAHMVKTW 319
           + +  +A LP  M    
Sbjct: 294 KVMSWSASLPQDMKDIL 310


>gi|161615592|ref|YP_001589557.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|161364956|gb|ABX68724.1| hypothetical protein SPAB_03373 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
          Length = 300

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 75/316 (23%), Positives = 141/316 (44%), Gaps = 41/316 (12%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
            +P  +   +++ + + +V V+ +   K   ++  G+ V I                 + 
Sbjct: 1   MFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAID---------------AEI 45

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPR 145
              +   +  +   ++YED  I V NKP  + V  G+G     +   L  +       PR
Sbjct: 46  DEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPR 105

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK---ECIAN 200
             + HRLD++T+G++VVA+T  A   L ES ++R I + Y ++  G         E I+ 
Sbjct: 106 AGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPISR 165

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K++H+    +            A++H+++++ F +    L ++  TGRTHQ+RVH  
Sbjct: 166 HPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMA 215

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPL 311
           H+  P+VGD  Y    +    +  +        ++  LHA  + L HP  G  ++  AP+
Sbjct: 216 HITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPVSGIEMEWHAPI 275

Query: 312 PAHMVKTWDSLGFKYD 327
           P  MV   D++   ++
Sbjct: 276 PQDMVDLIDAMRADFE 291


>gi|120403758|ref|YP_953587.1| RluA family pseudouridine synthase [Mycobacterium vanbaalenii
           PYR-1]
 gi|119956576|gb|ABM13581.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           vanbaalenii PYR-1]
          Length = 309

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 82/333 (24%), Positives = 149/333 (44%), Gaps = 32/333 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  + + V      MR+D         ++      I   G V +D  R   ++++ +G 
Sbjct: 1   MT-TRSMPVPEGLAGMRVDAGLARLL-GLSRTAAAAIAEEGGVELDGARAAKSDKLTAGA 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGG 122
            + +              ++ ++   +      ++ + +LY D  I   +KP G++    
Sbjct: 59  WLEV--------------RLPEAPAPVENTPVDIEGMGILYSDEDIVAVDKPPGVAAHAT 104

Query: 123 SG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ 
Sbjct: 105 VGWHGPTVLGGLAAAGFRISTSGIHERQGIVHRLDVGTSGVMVVALSERAYTALKRAFKQ 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R ++K Y +LV G P      I   + +  H G D+   V    +G  ++++H+  ++  
Sbjct: 165 RTVEKRYHALVQGHPDPSSGTIDAPIGR--HRGHDWKFAVV---EGGRHSVTHYDTLEAH 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q    L+++  TGRTHQ+RVH   +  P  GD  Y A+        ++ + +LHAR + 
Sbjct: 220 -QAASLLDIELETGRTHQIRVHFAALHHPCCGDLTYGADPTLAKKLGLE-RQWLHARSLA 277

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
             HP +G R++IT+P PA +    D L  ++DR
Sbjct: 278 FVHPADGRRIEITSPYPADLQHALDVLR-QHDR 309


>gi|289524245|ref|ZP_06441099.1| ribosomal large subunit pseudouridine synthase [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289502901|gb|EFD24065.1| ribosomal large subunit pseudouridine synthase [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 307

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 79/323 (24%), Positives = 139/323 (43%), Gaps = 35/323 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ D + +RLDR+ +  Y  +    + + +R G+V V+ ++   + R+  G  V +P   
Sbjct: 7   IDEDYDCVRLDRFLRKKYSEVPLGAIMRAIRKGRVTVNGEKTDPSYRLYRGDEVSVPF-- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  ++   L  S+N+          +++ D  + + NKPAG+  Q  S     +  
Sbjct: 65  -------EDPAKLKPSLNVADK----PLEVIFMDENVLIINKPAGLLSQPASNEDDSVVN 113

Query: 132 FLKSWVD--SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              + ++    G  P   HRLD+  SG++ +A    + + LT  FR RR+ K Y ++V G
Sbjct: 114 RALNLINKTKGGFIPTPAHRLDRNISGVMALALNFRSLRALTAMFRNRRVAKKYLAVVRG 173

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               +   I   L +      +       N+     + + +  +         + ++P T
Sbjct: 174 RLTGE-GVIEAPLERD-----ERFLKTVVNKGAGKRSATRYMSLSA-GNHASLVALEPIT 226

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM-----DLPHPEGGR 304
           GR+HQLRVH  H+G PIVGD KY  + K         +  LHA  +     DL +  G +
Sbjct: 227 GRSHQLRVHLSHIGHPIVGDVKYGDSGKEA------RRPMLHAYSLEIFGNDLSYLAGKK 280

Query: 305 LQITAPLPAHMVKTWDSLGFKYD 327
               APLPA +    +      D
Sbjct: 281 --FCAPLPADLAAVINLFDLSLD 301


>gi|304440211|ref|ZP_07400101.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus
           duerdenii ATCC BAA-1640]
 gi|304371260|gb|EFM24876.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus
           duerdenii ATCC BAA-1640]
          Length = 307

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 80/322 (24%), Positives = 138/322 (42%), Gaps = 35/322 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +VV++  E MRLD + K      +   + K +++  V V+   VK    I+   ++ +
Sbjct: 11  KTLVVQSQYEGMRLDIFLKEVL-DYSRSKINKEIKNKSVLVNGVSVKSGYIIKKNDIITL 69

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-- 125
                         +IL+  VNL       K  +L+ED  I V +KP  + V  G+G+  
Sbjct: 70  --------------EILEDQVNLEPQKIDFK--ILFEDEYIMVISKPENLVVHPGAGVFS 113

Query: 126 AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++G L   ++ K      +P + HRLD++TSG++++A+   A + L   F+   I K
Sbjct: 114 ETLVNGLLDYNINIKDIGEEDRPGIVHRLDKDTSGLMIIAKDALAYKKLVNMFKYGEIHK 173

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +++ G  +N+   +   + +       +  +       +  AIS F  I      F 
Sbjct: 174 EYIAILTGHLENE-IRVDEPIGRNPKDRKSFTVIYS----NSKNAISTFVPIKYM-NGFT 227

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
              +   TGRTHQ+RVHA ++  P++GD  Y         S       LHA  +   HP 
Sbjct: 228 LCRVIIETGRTHQIRVHARYLNHPVLGDSIYGYK-----NSLGIKTQLLHAYKLTFNHPI 282

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
            G  L      P    K  + +
Sbjct: 283 TGEELSFEDDFPDRFTKALEKI 304


>gi|313837447|gb|EFS75161.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL037PA2]
 gi|314929343|gb|EFS93174.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL044PA1]
 gi|314971654|gb|EFT15752.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL037PA3]
          Length = 306

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 137/322 (42%), Gaps = 29/322 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +  ++V +  +  R+D         ++   +  ++  G V +D ++V + + R+ +GQ++
Sbjct: 1   MSVLLVPDGLDGERVDVA-AARMSGVSRSRIGNLIEEGGVFLDGQQVSRASVRVTAGQML 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +          I  Q +                 ++++DS I V +KPAG++     G 
Sbjct: 60  DVDLSDPVSTPSITPQIVE-------------GMRIVHDDSDIVVVDKPAGVAAHPSLGW 106

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + +              ++  +  RLD  TSG++VVA++  A   L ++FR R +
Sbjct: 107 EGPSVVEHLAAAGFAISTSGLLERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRAV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y +LV G P      I   + +          V      G  ++++H++ ++ F + 
Sbjct: 167 DKVYLALVQGHPDPFAGTIDAPIGRDHRHDWKMAIV-----DGGRHSVTHYETVEAF-RH 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L++   TGRTHQ+RVH   +  P  GD  Y  +        ++ + +LHA  +   H
Sbjct: 221 ATLLKVHLETGRTHQIRVHMAAVKHPCCGDPLYGCDPALAKELGLE-RQWLHAAELSFAH 279

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  +   A LPA +    D
Sbjct: 280 PGSGEWVTFHADLPADLQHALD 301


>gi|318057566|ref|ZP_07976289.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           SA3_actG]
 gi|318081471|ref|ZP_07988794.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           SA3_actF]
          Length = 313

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 138/327 (42%), Gaps = 30/327 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  V+ + V +  E  R+D      +   +     ++   G+V+VD   V  + R++
Sbjct: 1   MSAIPEVRTLPVPDGLEGERVDAALSRMF-GFSRTKAAELAAGGKVQVDGSVVGKSERVR 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P+  A   I+ E                    ++++D  + V  KP G++ 
Sbjct: 60  GGAWLEVEMPLAAAPVQIVAEP--------------VEGMEIVHDDEDVVVIMKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGQTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKNQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR+R + K Y +LV G P      I   + +  H   DY   V         +++H+ +I
Sbjct: 166 FRVRTVDKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAE---GKASVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAF-RAASLLDVKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTLAKRLGL-TRQWLHAV 278

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTW 319
            +   HP  G  ++  +  P  + +  
Sbjct: 279 RLGFTHPGTGDWVEYASDYPEDLQRAL 305


>gi|297626700|ref|YP_003688463.1| Pseudouridylate synthase, Uncharacterized RNA pseudouridine
           synthase [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
 gi|296922465|emb|CBL57038.1| Pseudouridylate synthase, Uncharacterized RNA pseudouridine
           synthase [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
          Length = 306

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 137/325 (42%), Gaps = 29/325 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVV 65
           +  + V +  E  R+D         ++   +  ++  G+V +D    VK + R++ GQ +
Sbjct: 1   MSVLFVPDGLEGQRIDAA-AARMTGLSRSRVVDLIGEGKVLLDGSTVVKASERVRGGQTI 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I                  + V     +      ++++D+ I V +KPAG++     G 
Sbjct: 60  DIDLSE-------------PTRVARVTPAVVEGMRIVHDDADIVVVDKPAGVAAHPSVGW 106

Query: 126 AYHID------GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                         +       ++  + HRLD  TSG++VVA++  A   L  +FR R +
Sbjct: 107 DGPDVVSGLAGAGFRISTSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKRAFRDRTV 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G     +  I   + +  H G ++   V  +      +++H++ ++   + 
Sbjct: 167 DKYYLTLVQGHLDASEGTIGAPIGR--HPGSEWKFAVTAD---GRPSVTHYETVEMM-RG 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L +   TGRTHQ+RVH   +  P VGD  Y A+        ++ + +LHA  +   H
Sbjct: 221 ASLLRVHLETGRTHQIRVHFAALHHPCVGDPLYGADPVLAAQLGLE-RQWLHAADLGFVH 279

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  G  ++  +  PA +    ++L 
Sbjct: 280 PGNGEHVEYHSDPPADLQHALEALR 304


>gi|331091184|ref|ZP_08340025.1| hypothetical protein HMPREF9477_00668 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330404631|gb|EGG84170.1| hypothetical protein HMPREF9477_00668 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 320

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 79/331 (23%), Positives = 142/331 (42%), Gaps = 32/331 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + +  +E   RLD+    +        L K+LR   + ++ K+   N ++ +G  V+
Sbjct: 1   MQEIQIAANEAGQRLDKLLAKYLSEAPKSFLYKMLRKKNIVLNGKKASGNEKLVAGDSVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +    KE  +  S+  L          +LYED  I + NKPAG+  Q      
Sbjct: 61  LFLSDETIQKFSKEITVCKSNTKLD---------ILYEDDDILLVNKPAGMLSQKAEAKD 111

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   L S++   GQ         KP + +RLD+ TSG++V  ++    Q + + F+ R
Sbjct: 112 ISLVEHLISYLLESGQLTRENLKSFKPSICNRLDRNTSGLVVCGKSLKGLQTMGQLFKER 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +++K Y  +V G    +K+ +  +L+K      + V V       +    + ++ I    
Sbjct: 172 KLKKYYRCIVAGNV-TEKQYVKGYLIKDEK--KNQVTVSDTYFPESQEIETEYRPIQQLK 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYM 295
           Q    LE+   TG+THQ+R H    G  ++GD+KY +    +        +   LHA  +
Sbjct: 229 QG-TLLEVHLITGKTHQIRAHLASQGHAVIGDYKYGSREINDRYKKEYQLSHQLLHAYRL 287

Query: 296 DLPHPEGGRL------QITAPLPAHMVKTWD 320
           ++  P+   L         APLP    K  +
Sbjct: 288 EV--PKTKELPQLSEKMFVAPLPKQFQKIIE 316


>gi|293609056|ref|ZP_06691359.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292829629|gb|EFF87991.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 350

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 136/327 (41%), Gaps = 36/327 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++      R+D+     +   +   L++ L+ G + V+   VK  +R +         
Sbjct: 41  VQLDETYLGQRIDQVAALVWSEFSREKLKQWLKDGHLLVNGNIVKPKHRCEG-------- 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                         ++     T   + +   ++YED  I V NKP G+ V  G+G     
Sbjct: 93  -------TELLTLEVELEAQTTSQPENIPLNIVYEDDDILVINKPVGMVVHPGAGNSSGT 145

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L  +   ++  +  L HR+D++TSG+LVVA++  A   L++    + + ++Y  +
Sbjct: 146 LVNALLYHFPKLAELSRAGLVHRIDKDTSGLLVVAKSLEAQFSLSKQLANKTVYRVYDLV 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEM 245
           V+G        I         I    V  VK     G   A++H+ V + F + F  ++ 
Sbjct: 206 VYGN-------IIAGGTIDEQIKRHPVDRVKMAILPGGRDAVTHYNVKERF-KDFTRVQA 257

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDL 297
           +  TGRTHQ+RVH  ++G  ++GD  Y         A+     T     +  LHA  + L
Sbjct: 258 RLETGRTHQIRVHFSYIGYGLIGDQVYMNRVRVPAGASELLIETLRGFKRQALHAAKLGL 317

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLG 323
            HP  G  +   AP P       + L 
Sbjct: 318 KHPRTGEEMLFEAPWPEDFTHLVNVLR 344


>gi|15892267|ref|NP_359981.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           conorii str. Malish 7]
 gi|20139551|sp|Q92IS6|RLUC_RICCN RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|15619407|gb|AAL02882.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           conorii str. Malish 7]
          Length = 303

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 86/301 (28%), Positives = 150/301 (49%), Gaps = 11/301 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R++ G  + I    N      +
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQITVNAQKAEASLRVKGGDKIFINDKFNLPVKQPE 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +    D+ + L K        L+Y D  +   NKPAG++ QGG+ I   ID  LK +++ 
Sbjct: 72  KLVFTDAEIKLAKK--ITTDYLIYADDNLIAINKPAGLATQGGTKINLSIDSALK-YLNY 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           KG   +L HRLD++TSG+L++A+   ++  L  +F+ + + K Y+++ +G P      + 
Sbjct: 129 KGADFKLVHRLDKKTSGLLLIAKNYLSSVKLHNAFKEKLVVKTYFAVTYGKPIKNVGEVR 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + + K     G    +   + +    AI+++KV+         +E  P TGR HQLR+HA
Sbjct: 189 SNIEKSK---GSTPKITDIDSENGKLAITYYKVLKSLDNNLFLIEFTPVTGRMHQLRLHA 245

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKT 318
             +GCPI+GD KY          P    ++LHA  + L     G   ++ A LP +  + 
Sbjct: 246 KLLGCPILGDDKYG----NKEIMPYSKYMFLHANNICLSEKIFGQESKLEAKLPFYFTRR 301

Query: 319 W 319
            
Sbjct: 302 L 302


>gi|190571305|ref|YP_001975663.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Culex quinquefasciatus Pel]
 gi|213018702|ref|ZP_03334510.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Culex quinquefasciatus JHB]
 gi|190357577|emb|CAQ55016.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Culex quinquefasciatus Pel]
 gi|212995653|gb|EEB56293.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Culex quinquefasciatus JHB]
          Length = 315

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 79/323 (24%), Positives = 153/323 (47%), Gaps = 34/323 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + + ++E+ +RLD +      +I+    Q+++++ QV++    +  N+ I       +
Sbjct: 3   RTLNISSEEKKLRLDTYVAKKC-NISRSKAQRLIQNEQVKLLGIPIINNDHI-------V 54

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P    + H+I+     D S ++  + D +K  ++YED  I V +K + ++V  G+G   
Sbjct: 55  KPGEEYVVHLIQ----PDISTSIEPNYD-IKLDIVYEDDDIIVLSKQSRLTVHPGAGT-- 107

Query: 128 HIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + D  L + +   G+      +P + HRLD++TSG++V+A+   +   L+E    R+I++
Sbjct: 108 NNDTLLNAVIAHLGKIPYTNTRPGIVHRLDKDTSGLMVIAKNEQSHSFLSELLSNRKIKR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +++WG   N +  +   +  K         ++   +     AI+H+ V     Q   
Sbjct: 168 EYLAVIWGALPNLQGTVKTHIAPK----RSNKEMMCVTKTAGKLAITHYSVKKIIGQ-AS 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-------NKLYLHARY 294
            ++    TGRTHQ+RVH  H+G  +VGD  Y  N   +             N+  LHA  
Sbjct: 223 LVKCTLETGRTHQIRVHMSHIGHSVVGDQVYGKNSSKSEKHAKNSDFIRNFNRQALHAHT 282

Query: 295 MDLPHPEGGR-LQITAPLPAHMV 316
           + L HP+    ++  + LP  M 
Sbjct: 283 LGLYHPKSKEYIEFVSDLPQDMQ 305


>gi|282857614|ref|ZP_06266832.1| ribosomal large subunit pseudouridine synthase D [Pyramidobacter
           piscolens W5455]
 gi|282584552|gb|EFB89902.1| ribosomal large subunit pseudouridine synthase D [Pyramidobacter
           piscolens W5455]
          Length = 315

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 93/321 (28%), Positives = 143/321 (44%), Gaps = 27/321 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +   +E  RLD   +  +P +    + K  R G VR++ KR + N+R+  GQ V +P   
Sbjct: 7   ISRHDEGRRLDSVLRGMWPGVPLGAMMKYFRKGAVRLEGKRCQPNDRVLEGQHVWVPW-- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +E   +  +         L   ++Y D  + V NKPAG+  Q        +  
Sbjct: 65  -------EEPGTVGRAEMPDGTPRRLPLDVIYSDRCVMVVNKPAGLLSQPDVKGEDSVVT 117

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
               +       P+L HRLD+ TSG++ +A      + L E F+ RR  K YW++V G  
Sbjct: 118 RALGYAVDPEFPPQLVHRLDRNTSGVMALALDGPTTRALMECFKARRADKRYWAIVIGEL 177

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             +   I   LLK +        +V+ + KG   A++ +K +   +  F   E+   TGR
Sbjct: 178 PER-GRIDVPLLKDAD-----KKLVRVDPKGER-AVTEYKRL-TSSGAFSLAEVHLLTGR 229

Query: 252 THQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLP-------HPEGG 303
           THQ+RVH  H+G P++GD KY     KG   S    +  LHAR + L        H EG 
Sbjct: 230 THQIRVHMNHVGHPLLGDVKYGDFGSKGQLRSLGVKRPMLHARSLTLNGLPAFLSHLEGK 289

Query: 304 RLQITAPLPAHMVKTWDSLGF 324
                AP P  + +  + LGF
Sbjct: 290 --TFRAPAPDDLRRVMEKLGF 308


>gi|226313676|ref|YP_002773570.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226096624|dbj|BAH45066.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
          Length = 306

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 70/331 (21%), Positives = 135/331 (40%), Gaps = 38/331 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++  +    V+  +    +    +  Y  ++   L +    G +  +   V  N ++Q+G
Sbjct: 1   MLEELISFTVDEADAGQTVREVLQKRY-GVSRRLLIRAKFKGSITRNGVLVFVNEKLQAG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +     A                 T   + +   + YED  + V  KPAG+ V   
Sbjct: 60  DKIAVMVEEEAEE---------------TVAPEDMPLSIRYEDEDLMVIAKPAGLVVHP- 103

Query: 123 SGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                H  G L + +        + +K R  +RLD++TSG+++VA+ + A +  +   ++
Sbjct: 104 --TGNHPSGTLANGMIAYWKKRGENRKFRAVNRLDKDTSGLMIVAKNQWAHEQFSRMQQI 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R +Q+ Y ++V GI ++    I   +        +   + +Q       A++H++V+   
Sbjct: 162 RTLQRTYRAIVQGIVESDDGTINTPIG-----LAENSFITRQVRPDGQTAVTHYRVLAR- 215

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +   ++E++  TGRTHQ+RVH    G P+ GD  Y    +         +  LHA  + 
Sbjct: 216 GEGMSFVEVKLETGRTHQIRVHMSSEGHPLAGDDLYGGERE------HIGRQALHAWGLS 269

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
             HP  G  +    PLP  M +        Y
Sbjct: 270 FVHPRSGLAMSWEEPLPNDMEQLAQQFFPDY 300


>gi|298346986|ref|YP_003719673.1| putative pseudouridylate synthase [Mobiluncus curtisii ATCC 43063]
 gi|298237047|gb|ADI68179.1| possible pseudouridylate synthase [Mobiluncus curtisii ATCC 43063]
          Length = 304

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 83/323 (25%), Positives = 145/323 (44%), Gaps = 29/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V      +R D         ++      +L SG V  D + +K ++++ +G ++ I
Sbjct: 3   RLLPVPEGLAGLRADVGLSRLL-GLSRAKTGALLESGAVIQDGETLKKSDQLAAGNLLEI 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                          I + +  + + +      +LY D  + V +KPAG++   G G   
Sbjct: 62  --------------DIPEPTGYVPEVTRVDNLGILYADDDLVVVDKPAGVAAHTGPGWEG 107

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L++           ++  + HRLD  TSG +VVA++  A   L   FR  R++K
Sbjct: 108 PTVVGALRAAGIRVSTSGPVEREGIVHRLDAGTSGAMVVAKSELAYGKLKNEFRYHRVEK 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY +L  G  K     I   + +    G ++   V     G   A++H+ +I+       
Sbjct: 168 IYTALATGKVKPPVGTIDAPIGRAP--GREFKMAVVS---GGKPAVTHYDIIEELP-GAT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L++Q  TGRTHQ+RVH   +G P+VGD +Y A+ K      ++ + +LHA  +   HP 
Sbjct: 222 LLKVQLETGRTHQIRVHLAAIGHPLVGDTEYGADRKTAARLGLE-RQWLHASRLAFKHPR 280

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G  + + APLPA +    + L 
Sbjct: 281 TGLEVAVQAPLPADLATAVELLR 303


>gi|326382577|ref|ZP_08204268.1| pseudouridine synthase, RluA family protein [Gordonia neofelifaecis
           NRRL B-59395]
 gi|326198696|gb|EGD55879.1| pseudouridine synthase, RluA family protein [Gordonia neofelifaecis
           NRRL B-59395]
          Length = 308

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 141/327 (43%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +    MR+D         ++   +  +  +G + VD   V  ++++ +G 
Sbjct: 1   MRDSRAMPVPDGLHGMRVDAGVARVL-GLSRTVVATLADAGDITVDGVSVGKSHKLAAGS 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          ++   + D               ++Y DS I V +KPAG++     
Sbjct: 60  WLDVLLPEPEQPLTVEPTPVED-------------LEVIYHDSDIIVVDKPAGVAAHPSL 106

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R
Sbjct: 107 GWSGPTVIGALAAAGFRISTSGAHERQGIVHRLDAGTSGVMVVAASERAYTLLKRAFKQR 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G        I   + +  H G D+   V  N      +++H+  ++ FA
Sbjct: 167 TVDKRYHALVQGHLDPPSGTIDAPIGR--HPGSDWRFAVTAN---GRESVTHYDTLEMFA 221

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                L++   TGRTHQ+RVH   M  P  GD  Y A+ K      + ++ +LHAR +  
Sbjct: 222 -AASLLDVHLETGRTHQIRVHFSAMHHPCCGDPTYGADPKLAARLGL-DRQWLHARTLGF 279

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLG 323
            HP +G R++ TA  PA +    D L 
Sbjct: 280 AHPADGRRVEFTAEYPADLQHALDVLR 306


>gi|310820541|ref|YP_003952899.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309393613|gb|ADO71072.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 315

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 90/331 (27%), Positives = 140/331 (42%), Gaps = 32/331 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
                + VE  +   R+D +       ++   L+++   G VRV+ + VK    + +GQ 
Sbjct: 4   EKTHTLTVEPTKAGQRVDLFVGEAL-GLSRAKLKRLFEEGAVRVNGRAVKKGLLVSAGQH 62

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GS 123
           + +         +                      ++L+ED+ + V +KPAG        
Sbjct: 63  ILVEWEEETREAV---------------PDTGFPLVVLHEDAALVVVDKPAGRPSHPLKP 107

Query: 124 GIAYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G    +   L +      Q      +  L HRLD ETSG+L+ ARTR A Q L  +F  R
Sbjct: 108 GETGTVANALIARYPECAQASEDAREGGLCHRLDIETSGVLLAARTREAWQRLRTAFSGR 167

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G   ++ E      L+      D V      E+GA  A S F+V    +
Sbjct: 168 EVDKHYVALVTGPLADEGEI--EIPLRHHPRHPDRVEPALPGEEGAREAHSLFQV-QARS 224

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  +E++  TG  HQ+R H   +G P+VGD  Y          P  ++ +LHAR +  
Sbjct: 225 GDFSLVEVRILTGVLHQVRAHLAGIGAPLVGDSLYGGR-----EEPGLSRFFLHARALGF 279

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            HPE G RLQ+ +PLP  + +     G   D
Sbjct: 280 THPETGQRLQVESPLPQELAEVLRHHGLSAD 310


>gi|304389307|ref|ZP_07371272.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii subsp. curtisii ATCC 35241]
 gi|304327425|gb|EFL94658.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii subsp. curtisii ATCC 35241]
          Length = 304

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 83/323 (25%), Positives = 145/323 (44%), Gaps = 29/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V      +R D         ++      +L SG V  D + +K ++++ +G ++ I
Sbjct: 3   RLLPVPEGLAGLRADVGLSRLL-GLSRAKTGALLESGAVIQDGETLKKSDQLAAGNLLEI 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                          I + +  + + +      +LY D  + V +KPAG++   G G   
Sbjct: 62  --------------DIPEPTGYVPEATRVDNLGILYADDDLVVVDKPAGVAAHTGPGWEG 107

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L++           ++  + HRLD  TSG +VVA++  A   L   FR  R++K
Sbjct: 108 PTVVGALRAAGIRVSTSGPVEREGIVHRLDAGTSGAMVVAKSELAYGKLKNEFRYHRVEK 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY +L  G  K     I   + +    G ++   V     G   A++H+ +I+       
Sbjct: 168 IYTALATGKVKPPVGTIDAPIGRAP--GREFKMAVVS---GGKPAVTHYDIIEELP-GAT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L++Q  TGRTHQ+RVH   +G P+VGD +Y A+ K      ++ + +LHA  +   HP 
Sbjct: 222 LLKVQLETGRTHQIRVHLAAIGHPLVGDTEYGADRKTAARLGLE-RQWLHASRLAFKHPR 280

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G  + + APLPA +    + L 
Sbjct: 281 TGLEVAVQAPLPADLATAVELLR 303


>gi|117928240|ref|YP_872791.1| ribosomal large subunit pseudouridine synthase D [Acidothermus
           cellulolyticus 11B]
 gi|117648703|gb|ABK52805.1| ribosomal large subunit pseudouridine synthase D [Acidothermus
           cellulolyticus 11B]
          Length = 314

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 73/320 (22%), Positives = 132/320 (41%), Gaps = 27/320 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V    +  R+D         ++   +  ++ +GQVRVD      + R+ +G  + +
Sbjct: 9   RLLPVPEGLDGERVDVAIARLL-GLSRTRVADLIAAGQVRVDGVVPAKSARLAAGSWLEV 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           +                ++Y+D  I V +KPAG++     G   
Sbjct: 68  RVPRPGPPRPPVIPTPV------------ADMAVVYDDPDIVVVDKPAGVAAHPSPGWEG 115

Query: 128 HID--GFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                  L +          ++  + HRLD  TSG++VVA++  A   L  +FR R + K
Sbjct: 116 ATVLGALLAAGYRVATSGAAERQGIVHRLDVGTSGLMVVAKSERAYSTLKRAFREREVHK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY +LV G P   +  I   +    H   ++   V     G   +++H+  ++       
Sbjct: 176 IYHALVQGHPDPVRGTIDAPI--DRHPVHEFRFAVV---AGGKPSVTHYTTLEALP-AAS 229

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE++  TGRTHQ+RVH   +  P VGD  Y A+        + ++ +LHA  +   HP 
Sbjct: 230 LLEIELETGRTHQIRVHMAAIRHPCVGDLMYGADPTFAARLGL-DRQWLHAVRLRFTHPI 288

Query: 302 -GGRLQITAPLPAHMVKTWD 320
            G  +++T+  P  + +   
Sbjct: 289 LGSPIELTSSYPPDLDRALR 308


>gi|210633884|ref|ZP_03297899.1| hypothetical protein COLSTE_01816 [Collinsella stercoris DSM 13279]
 gi|210159053|gb|EEA90024.1| hypothetical protein COLSTE_01816 [Collinsella stercoris DSM 13279]
          Length = 338

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 78/345 (22%), Positives = 141/345 (40%), Gaps = 43/345 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           M    ++ V   +   RLD +        +     K++ +G V V+ +        +  G
Sbjct: 1   MASELHLAVSAADAGERLDSYLGAQSACPSRSACAKLVEAGSVAVNGETCLSKKQAVAEG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +      L  I +   I+  ++ L          + YED  + V +K  G+     
Sbjct: 61  DRICV-----ELPEIREPGAIVPQAIPLD---------IRYEDDYLIVLSKQRGLVCHPA 106

Query: 123 SGIAYHIDGFLKSWVDSKG-----------QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
            G   H DG L + +                +P + HRLD++TSG+++ A+     + L 
Sbjct: 107 HG---HEDGTLANALVHHCGIEHLGTVQGEDRPGIVHRLDRDTSGLMLAAKDDETQRELQ 163

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
              R R + + Y +LV G     +  I   + + +    D V +   ++  A  AI+ F+
Sbjct: 164 NLIRTRTLDRRYITLVHGEIVMDEGTINTGIARST---RDRVKMAVSDDPFARQAITTFQ 220

Query: 232 VIDCFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           V++ F      + +  +E   +TGRTHQ+RVH  H+  P+VGD  Y         +   +
Sbjct: 221 VLERFEPARGDEGYTLVECHLYTGRTHQIRVHMRHIHHPLVGDPLYGKG--NERMNLDLD 278

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           + +LH+  +   HP  G  +     LP  +    D L   +DR+L
Sbjct: 279 RQFLHSWSVQFEHPVTGETISCRDELPWDLAAALDEL---HDRSL 320


>gi|308068172|ref|YP_003869777.1| RNA pseudouridine synthase (RNA-uridine isomerase) [Paenibacillus
           polymyxa E681]
 gi|305857451|gb|ADM69239.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Paenibacillus polymyxa E681]
          Length = 319

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 87/341 (25%), Positives = 147/341 (43%), Gaps = 40/341 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRI 59
           MSL        +  +EE M L    +    +I+   + K+ L    + ++  RV  + ++
Sbjct: 1   MSLYYEPIVYTIPPEEEGMLLKTILQKRM-NISRKLISKLKLTEQGIMLNGTRVYISVKV 59

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +SG  V I       + I+ E                +   +L+ED  + V NK AG+ V
Sbjct: 60  KSGDQVEIRMERERSDDILPEP---------------IPFEILFEDEHLLVVNKAAGMIV 104

Query: 120 QGGSGIAYHIDGFLK----SWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G   H  G L      +  +KG+  + R  HRLDQET+G+LVVA+     QH++E 
Sbjct: 105 HPTHG---HYTGTLANGVVHYWQAKGELFRFRPVHRLDQETTGVLVVAKNPYVHQHISEQ 161

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                + K Y +LV G P+ ++  +   + +        +            A++ +K +
Sbjct: 162 MIAGTVDKRYTALVHGRPELQEGKVDGPIDRNPDNPHLRMV-----TPDGYPALTLYK-L 215

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-------CANFKGNFTSPIQN 286
           +        + ++  +GRTHQ+RVH  ++GCP++GD  Y           + +       
Sbjct: 216 EEVWNGGSRIGLKLESGRTHQIRVHMTYIGCPLIGDKMYRITPDDAAQRERYDQLDARMP 275

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
           +  LHA  + L HP  G RL   APLP  M +  + L  +Y
Sbjct: 276 RQALHASELSLEHPVTGERLTFYAPLPDDMAEMQELLRAQY 316


>gi|299771331|ref|YP_003733357.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           DR1]
 gi|298701419|gb|ADI91984.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           DR1]
          Length = 350

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 139/326 (42%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++      R+D+     +   +   L++ L+ G + V+   VK  +R +         
Sbjct: 41  VQLDETYLGQRIDQVAALVWNEFSREKLKQWLKDGHLLVNGNIVKPKHRCEG-------- 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                         ++     T   + +   ++YED  I V NKP G+ V  G+G     
Sbjct: 93  -------TELLTLEVELEAQTTSQPENIPLNIVYEDDDILVINKPVGMVVHPGAGNSSGT 145

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L  +   S+  +  L HR+D++TSG+LVVA++  A   L++    + + ++Y  +
Sbjct: 146 LVNALLYHFPKLSELSRAGLVHRIDKDTSGLLVVAKSLEAQFSLSKQLANKSVYRVYDLV 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G        I   + K+  +    + ++     G   A++H+ V + F + F  ++ +
Sbjct: 206 VYGNIIA-GGTIDEPI-KRHPVDRVKMAIL----PGGRDAVTHYNVKERF-KDFTRVQAR 258

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  ++G  ++GD  Y         A+     T     +  LHA  + L 
Sbjct: 259 LETGRTHQIRVHFSYIGYGLIGDQIYMNRVRVPAGASELLIDTLRGFKRQALHAAKLGLK 318

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +   AP P       D L 
Sbjct: 319 HPRTGEEMLFEAPWPEDFTHLVDVLR 344


>gi|138894383|ref|YP_001124836.1| ribosomal large subunit pseudouridine synthase D-like protein
           [Geobacillus thermodenitrificans NG80-2]
 gi|134265896|gb|ABO66091.1| ribosomal large subunit pseudouridine synthase D-like protein
           [Geobacillus thermodenitrificans NG80-2]
          Length = 299

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 63/315 (20%), Positives = 140/315 (44%), Gaps = 33/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +    +   L ++ + +   I+   L  I    G + V+ + V   + +++G+ + +   
Sbjct: 10  INEQHDGKLLRQFLQEN--GISRTALTDIKFHGGALYVNSRPVTVRHVLRAGETLSVVFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
               +  +                + +   ++YED  + V NKPAG++            
Sbjct: 68  PERTSDWM--------------DPEEMPLDIVYEDEYVLVVNKPAGLATIPSRHHPGGTL 113

Query: 129 IDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +G L  +   +      +  RLD++TSG+++VA+ R     L+   +  ++ + Y ++ 
Sbjct: 114 ANGLLHHYRQQQLDSTVHIITRLDRDTSGLVLVAKHRHVHHLLSTLQQKGQVTRTYEAVC 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+   ++  I   + +++        + ++  +    AI+HF+V++  +  + ++ ++ 
Sbjct: 174 HGVIDEEEGTIDAPISRQND-----SIIAREVREDGKRAITHFRVLERLS-GYTYVSLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-Q 306
            TGRTHQ+RVH  ++G P+ GD  Y        +  +  +  LH+R +   HP   +L  
Sbjct: 228 ETGRTHQIRVHLAYLGHPLAGDELYGG------SREMIGRQALHSRQLSFFHPFARQLYT 281

Query: 307 ITAPLPAHMVKTWDS 321
            TAPLP  M +  ++
Sbjct: 282 FTAPLPDDMARLIEA 296


>gi|115469990|ref|NP_001058594.1| Os06g0717400 [Oryza sativa Japonica Group]
 gi|75252835|sp|Q5Z8P2|PUS2_ORYSJ RecName: Full=RNA pseudourine synthase 2, chloroplastic; AltName:
           Full=RNA pseudouridylate synthase 2; AltName:
           Full=RNA-uridine isomerase 2; Flags: Precursor
 gi|53791796|dbj|BAD53590.1| ribosomal large subunit pseudouridine synthase-like [Oryza sativa
           Japonica Group]
 gi|54291043|dbj|BAD61720.1| ribosomal large subunit pseudouridine synthase-like [Oryza sativa
           Japonica Group]
 gi|113596634|dbj|BAF20508.1| Os06g0717400 [Oryza sativa Japonica Group]
 gi|215706335|dbj|BAG93191.1| unnamed protein product [Oryza sativa Japonica Group]
 gi|222636236|gb|EEE66368.1| hypothetical protein OsJ_22675 [Oryza sativa Japonica Group]
          Length = 445

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 81/376 (21%), Positives = 139/376 (36%), Gaps = 80/376 (21%)

Query: 12  VENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           V   E   R+D W         ++   +Q  +R+G V V+ + V K ++ ++ G +V   
Sbjct: 65  VPAGEGRSRIDAWISARLGGGGVSRARIQASIRAGLVVVNGRPVSKVSHMVKGGDIVSCT 124

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
            +                   L    + +   ++YED  + V NKPA + V    G A  
Sbjct: 125 VL---------------ELQPLRAEPEDIPLDIVYEDDHLLVVNKPAHMVVHPAPGNANG 169

Query: 128 -HIDGFLKSW-----------------------------------------VDSKGQKPR 145
             ++  L                                            V     +P 
Sbjct: 170 TLVNAILHHCKISTFTCLARNSIDDECPDSSDDDIDVFDIDQFTTGEVSSEVREALVRPG 229

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+ TSG+LVVA+   +   L E F++  I+++Y SL  G P      I   + + 
Sbjct: 230 IVHRLDKGTSGLLVVAKDEHSHAQLAEQFKLHTIRRVYISLTCGAPNPNSGRIEVPIARD 289

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGC 264
            +     +       + A +A S +KV + FA      +E +  TGRTHQ+R HA ++G 
Sbjct: 290 PNNRIRMIATPGSGHRYARHAASRYKVREVFAGGGSALVEWRLETGRTHQIRAHAKYLGI 349

Query: 265 PIVGDHKYCANFKGNFTSP-----------------IQNKLYLHARYMDLPHPEGGRL-Q 306
           P++GD  Y        +                     ++  LHA  +   HP  G++ +
Sbjct: 350 PLLGDETYGGTKSMALSLLRPRTPSRYHCDLSNMISKIDRPCLHAALLGFKHPHSGKILE 409

Query: 307 ITAPLPAHMVKTWDSL 322
            + P P    +  + L
Sbjct: 410 FSCPPPDDFTEVLNEL 425


>gi|154496245|ref|ZP_02034941.1| hypothetical protein BACCAP_00530 [Bacteroides capillosus ATCC
           29799]
 gi|150274328|gb|EDN01405.1| hypothetical protein BACCAP_00530 [Bacteroides capillosus ATCC
           29799]
          Length = 300

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 73/316 (23%), Positives = 135/316 (42%), Gaps = 33/316 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + V  D+   ++D   +     ++   ++  K L  G + +D  RV   +R+++GQ++ 
Sbjct: 8   TLTVAPDQSGWKVDALLRGTL-GLSGTVIRRVKWLEDG-ILLDGVRVTVGDRVRAGQILS 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +               + D+ V+           ++Y+D  + V NK  G++V  G G  
Sbjct: 66  V--------------VVGDTEVSGAIVPAPGPLDIVYQDQDVLVLNKAPGVAVHPGPGHY 111

Query: 126 AYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +  I  FL  +   +G        HRLD+ TSG+L+VA    A + L E       +++Y
Sbjct: 112 SDTIGNFLMDYYRKQGILADFHPVHRLDRGTSGLLLVALHGHAQEVLKEQLHSPSFRRVY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++  G P      I   + +      +   + +        A++H++ +     +   +
Sbjct: 172 LAVCEGAPNPPSGVIDAPIGRL-----EGSVLARTVRPDGQRAVTHYRTLRTVNDRA-LV 225

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++  TGRTHQ+RVH  H+G P+ GD  Y    +      +  +  LHA  +   HP  G
Sbjct: 226 RLELETGRTHQIRVHMAHLGHPLTGDFLYGTEDQS-----LIPRPALHAAELSFTHPITG 280

Query: 304 R-LQITAPLPAHMVKT 318
           + +  TAPLP  M   
Sbjct: 281 KTMAFTAPLPQDMAAL 296


>gi|269215565|ref|ZP_06159419.1| ribosomal large subunit pseudouridine synthase D [Slackia exigua
           ATCC 700122]
 gi|269131052|gb|EEZ62127.1| ribosomal large subunit pseudouridine synthase D [Slackia exigua
           ATCC 700122]
          Length = 316

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 77/336 (22%), Positives = 134/336 (39%), Gaps = 36/336 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ V VE   + MR+D +              + + +G+VRV+   V+ +  ++   VV 
Sbjct: 1   MEAVYVEGSFDGMRIDAFLAAVAAFPTRSAAARRVDAGEVRVNGVVVRKSFTVRISDVVE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
               ++A                L      +   + YED  + V +K AG+      G  
Sbjct: 61  YVVAMDARV--------------LELMPADIPLDIRYEDDDVLVLSKQAGLVTHPADGHP 106

Query: 127 YHI---DGFLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                 +  +          V  +  +  + HRLD++TSG+++ A+T AA   L E    
Sbjct: 107 EQDTLVNALIAHCGREKLCNVQGEQDRLGIVHRLDRDTSGLMLAAKTDAAGLRLMEDIAA 166

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + + Y +LV G        I   + +      D + +   + + A  A + F+V+  F
Sbjct: 167 RDVDRHYLALVHGWIPLDTGLIDAPIGRS---AKDRLRMCVSDRESARPASTSFRVVRRF 223

Query: 237 A-----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
                   +  ++ +  TGRTHQ+RVHA ++  P VGD  Y      N       + +LH
Sbjct: 224 EPSRRDDGYTLIDCKLFTGRTHQIRVHAEYIKHPCVGDPTYGWPKHDNL---GLERQFLH 280

Query: 292 ARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
           +  +   HP  G RL     LPA +    D L  + 
Sbjct: 281 SYRLAFTHPSTGARLSFEDGLPADLQAVVDELDARA 316


>gi|68536967|ref|YP_251672.1| pseudouridylate synthase [Corynebacterium jeikeium K411]
 gi|68264566|emb|CAI38054.1| pseudouridylate synthase [Corynebacterium jeikeium K411]
          Length = 313

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 88/322 (27%), Positives = 151/322 (46%), Gaps = 16/322 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           +  Q ++V + + + RLD++ ++H   +    L +++R+ Q+ V+  + K + R  +G  
Sbjct: 4   SEPQTLIVSDSQADRRLDKYIRSHVKGVPATVLFRLMRTKQITVNGAKCKPDQRTVAGDK 63

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+P    AL     +           + +  L   +++ED  + V NKPA I+V  GSG
Sbjct: 64  VRLP----ALEVARAKPPPAGDRKAAEQLARRLSRHIVFEDDALLVVNKPANIAVHVGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--RIQKI 182
           +   +   L+  +  K ++  L HRLD+ETSG+L+VA+     +HL E  R     IQ+ 
Sbjct: 120 VKAGVIEALR-VLRPKEKELELAHRLDKETSGLLIVAKKSKMLRHLQELLRTGGEDIQRY 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G  K          +     G         + +   +A +   V   +      
Sbjct: 179 YLAVVSGGVKRTGRQTQRIEVPLRKTG----AATVVDSRAGQWAETKMWVKKPWGTAGTL 234

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHPE 301
           +E+Q  TGR HQ+RVH  H+G PI+GD +Y         +    + L LHA  + +P P+
Sbjct: 235 VEVQLLTGRKHQIRVHLQHLGHPIIGDSRYGNPAANRAAAEKGVRMLMLHACRLVVPLPD 294

Query: 302 GGRLQITAPLPAHMVKTWDSLG 323
           G  L + AP+P      W+ L 
Sbjct: 295 GEVLDLHAPMPP----AWNKLR 312


>gi|300858799|ref|YP_003783782.1| hypothetical protein cpfrc_01382 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|300686253|gb|ADK29175.1| hypothetical protein cpfrc_01382 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|302331059|gb|ADL21253.1| Putative pseudouridine synthase [Corynebacterium pseudotuberculosis
           1002]
          Length = 307

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 79/329 (24%), Positives = 134/329 (40%), Gaps = 29/329 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V      MR+D         I+      +  +G V VD   V  ++RI  GQ
Sbjct: 1   MREHRSLPVPEGLAGMRVDAALSKLL-GISRTVAADLATAGDVLVDALPVGKSDRIAEGQ 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          + E K L     L +  D     +LY D  +   NKP G++     
Sbjct: 60  WLDVT---------LPETKDLTPREELVEGMD-----ILYSDDDLIAVNKPVGVAAHPTL 105

Query: 124 GIA-YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  +  RLD  TSG++V+A +      L  +F+ R
Sbjct: 106 GWEGPTVIGGLAAAGFRISTSGPPERKGIVQRLDVGTSGVMVIAASERGYSVLKRAFKER 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G        I   + +    G  +            +A++H++ ++ FA
Sbjct: 166 TVSKTYHALVQGHMDPFTGTIDAPIGRHPSAGWRFAVTS-----DGKHAVTHYETLEAFA 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    L++   TGRTHQ+RVH   +  P  GD  Y ++ K +    +  + +LHA  +  
Sbjct: 221 E-ASLLKIHLETGRTHQIRVHMSALHHPCCGDPMYGSDPKLSERLGL-TRQWLHAVSLGF 278

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  GR ++IT+P    +    D L   
Sbjct: 279 NHPADGRWMEITSPYSDDLQHALDILRED 307


>gi|291550323|emb|CBL26585.1| pseudouridine synthase, RluA family [Ruminococcus torques L2-14]
          Length = 342

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 82/340 (24%), Positives = 145/340 (42%), Gaps = 27/340 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + ++ +E   R+D++   +          K++R   + ++ K+   N +++ G V++
Sbjct: 1   MREISIQKNEAGQRMDKFLAKYLNKAPKSFFYKMMRKKNITLNGKKAVGNEQLKQGDVIK 60

Query: 67  IPPVINALNHII---KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +      + + I   +  K   SS         ++  +LYED      NKP G+  Q  S
Sbjct: 61  LFLAEETIENFIDHSQFSKKKASSARKQTAGKKVQLDILYEDEAAVFINKPVGMLSQKAS 120

Query: 124 GIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                +  +   ++   G+          P + +RLD+ TSGI+   +T  A Q L+E F
Sbjct: 121 PTDTSLVEYFIDYLLENGKITEEELHTFHPSVCNRLDRNTSGIVAAGKTLQALQGLSEMF 180

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAI---SH 229
           R R ++K Y  LV G  K  +  I  +L+K        V   K  E  K    A    + 
Sbjct: 181 RDRTLKKYYLCLVKGQVKENQ-RIHGYLVKNEKTNKVTVSQKKPAEQTKDGKEASAIDTE 239

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNK 287
           +KV+    ++   LE+   TG+THQ+R H   +G PI GD+KY      +          
Sbjct: 240 YKVLARN-RETTLLEVHLITGKTHQIRAHLASIGHPIAGDYKYGNRSFNDALKKEYGLRS 298

Query: 288 LYLHARYMDLPHPEGGRLQ------ITAPLPAHMVKTWDS 321
             LHA  ++ P    G ++      I AP+PA   +   +
Sbjct: 299 QLLHAYRLEFPENCEGDIKQLSGKIIKAPVPALFEQICKA 338


>gi|166030562|ref|ZP_02233391.1| hypothetical protein DORFOR_00225 [Dorea formicigenerans ATCC
           27755]
 gi|166029564|gb|EDR48321.1| hypothetical protein DORFOR_00225 [Dorea formicigenerans ATCC
           27755]
          Length = 296

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 68/316 (21%), Positives = 141/316 (44%), Gaps = 32/316 (10%)

Query: 11  VVENDEENMRLDRWFKN-HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++ D   +R++++ +   Y   N   ++++ +S  + V+         + +G  +++  
Sbjct: 8   IIDEDSAGLRVEQFLRRKRYSGQNLSEIKRMPKS--ILVNGVHYYMRQELSTGDHLQVRI 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
                +  I                  L   ++YED  + V NKPAG+ +    +     
Sbjct: 66  CETKNSEKIP--------------PTNLPLDIIYEDEDLLVLNKPAGMPIHPSLNNYTNS 111

Query: 129 IDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           I   L  +  S+G+    R  +RLD++TSG+ +V++   +   L++  + R + + Y ++
Sbjct: 112 IANALAYYFQSQGKPFIFRCCNRLDRDTSGLTIVSKHLVSGSILSDMTKYREVHREYLAI 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G     +  I   L +K    G  +     + +    A++H+KV+   A     + ++
Sbjct: 172 ARGSVTPSEGTIQAPLGRK----GGTIIERTVDWEHGEDAVTHYKVVK-EANGHSLVSLR 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+R+H  ++G P++GD+ Y  + +         +  LH+ +M+  HP  G  +
Sbjct: 227 LETGRTHQIRIHMKYLGYPLIGDYLYNPDME------YMTRQALHSHHMEFTHPITGEHM 280

Query: 306 QITAPLPAHMVKTWDS 321
             TAPLP  M +    
Sbjct: 281 SFTAPLPEDMARVMQE 296


>gi|315655527|ref|ZP_07908426.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii ATCC 51333]
 gi|315490182|gb|EFU79808.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii ATCC 51333]
          Length = 304

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 84/323 (26%), Positives = 144/323 (44%), Gaps = 29/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V      +R D         ++      +L SG V  D + +K ++++  G ++ I
Sbjct: 3   RLLPVPEGLAGLRADIGLSRLL-GLSRAKAGALLESGAVIQDGETLKKSDQLVVGNLLEI 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                          I + +  + + +      +LY D  + V +KPAG++   G G   
Sbjct: 62  --------------DIPEPTGYVPEVTRVDNLGILYADDDLVVVDKPAGVAAHTGPGWEG 107

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L++           ++  + HRLD  TSG +VVA++  A   L   FR  R++K
Sbjct: 108 PTVVGALRAAGIRVSTSGPVEREGIVHRLDAGTSGAMVVAKSELAYGKLKNEFRYHRVEK 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY +L  G  K     I   + +    G ++   V     G   A++H+ VI+       
Sbjct: 168 IYTALATGGVKPPVGTIDAPIGRAP--GREFKMAVVS---GGKPAVTHYDVIEELP-GAT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L++Q  TGRTHQ+RVH   +G P+VGD +Y A+ K      ++ + +LHA  +   HP 
Sbjct: 222 LLKVQLETGRTHQIRVHLAAIGHPLVGDTEYGADRKTAARLGLE-RQWLHASRLAFKHPR 280

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G  + + APLPA +    + L 
Sbjct: 281 TGLEVAVQAPLPADLATAVELLR 303


>gi|153814854|ref|ZP_01967522.1| hypothetical protein RUMTOR_01069 [Ruminococcus torques ATCC 27756]
 gi|331089624|ref|ZP_08338523.1| hypothetical protein HMPREF1025_02106 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145847885|gb|EDK24803.1| hypothetical protein RUMTOR_01069 [Ruminococcus torques ATCC 27756]
 gi|330404992|gb|EGG84530.1| hypothetical protein HMPREF1025_02106 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 347

 Score =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 85/348 (24%), Positives = 142/348 (40%), Gaps = 17/348 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + + ++E   R D++   +        L K+LR   + ++ K+   N  +  G  V+
Sbjct: 1   MKEIEINSNEAGQRFDKFLGKYLDQAPKSFLYKMLRKKNITLNGKKAAGNEILALGDNVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +    K  + +   V        +K  +LYED  +   NKP G+  Q  +   
Sbjct: 61  LFFSDETIKKFSKTSEEVFRPVQKNTAKSKVKLNVLYEDENVIFLNKPVGMLSQKANRED 120

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  +L  ++   GQ          P + +RLD+ TSGI+   +T +A Q L E FR R
Sbjct: 121 TSLVEYLIEYLLDSGQVTREELKTFHPAVCNRLDRNTSGIVAGGKTLSALQILNEMFRTR 180

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  LV G  K   + I  +L K +      V   K+  K A    + +  +   +
Sbjct: 181 SLEKYYLCLVSGKIK-DGQRICGYLKKNTKTNKVSVTKEKRETKEALPIETEYTPL-FVS 238

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYM 295
                L++   TG+THQ+R H   +G PI+GD+KY                   LHA  +
Sbjct: 239 DHVTLLKVHLITGKTHQIRAHLAAIGHPIIGDYKYGDFKINEAYKKKYGLKTQLLHAYQL 298

Query: 296 DLPHPEGGR----LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQD 339
             P  E  +     QI AP+P    K     G   +  +  KR    D
Sbjct: 299 CFPDVELVKNLPNRQIIAPVPDLFKKICIDKGVNNNGCMEFKRSSGFD 346


>gi|297530964|ref|YP_003672239.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|297254216|gb|ADI27662.1| pseudouridine synthase, RluA family [Geobacillus sp. C56-T3]
          Length = 304

 Score =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 66/323 (20%), Positives = 141/323 (43%), Gaps = 33/323 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++   +   L ++ + +   I+   L  I    G + VD + V   + +++G+ + +   
Sbjct: 10  IDEQHDGKLLRQFLQEN--GISRTALTDIKFHGGALLVDGRPVTVRHVLRAGETLSVVFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
               +  +               ++ +   +LYED  + V NKPAG++            
Sbjct: 68  PERTSDWM--------------DAEAMPLDILYEDDYVLVVNKPAGLATIPSRHHPGGTL 113

Query: 129 IDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +G L  +   +      +  RLD++TSG+++VA+ R     L+   +   + + Y ++ 
Sbjct: 114 ANGLLHHYRKQQLDSTVHIVTRLDRDTSGLVLVAKHRHVHHLLSALQQKGHVVRTYEAIC 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+    +  I   + ++S        + ++  +    A++HF+V++     + ++ ++ 
Sbjct: 174 HGVIVEDEGTIDAPIGRQSD-----SIIAREVREDGKPAVTHFRVLERL-YGYTYVSLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++G P+ GD  Y        +  +  +  LH+R +   HP  GR   
Sbjct: 228 ETGRTHQIRVHLAYLGHPLAGDELYGG------SREMIGRQALHSRQLSFFHPFAGRWYT 281

Query: 307 ITAPLPAHMVKTWDSLGFKYDRN 329
            +APLP  M    ++   +Y  +
Sbjct: 282 CSAPLPDDMELLIEATRRRYADD 304


>gi|319440272|ref|ZP_07989428.1| pseudouridylate synthase [Corynebacterium variabile DSM 44702]
          Length = 311

 Score =  222 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 135/322 (41%), Gaps = 26/322 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V      MR+D         ++   + ++  +G +  D K    ++R+  G  + +
Sbjct: 7   RMMPVPGGLAGMRVDAGLSKLL-GLSRTVVAELAEAGDIVQDGKTAGKSDRLVDGAWLDV 65

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGI 125
                  +   +  ++++               +LY D  + V +KP G++     G   
Sbjct: 66  TLPAPPRDLAAEPARVVEG------------MDILYSDDDVIVVDKPVGVAAHPTIGWEG 113

Query: 126 AYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                G   +          ++  + HRLD  TSG++ VA +  A   L  +FR R + K
Sbjct: 114 PTVTSGLAAAGYRISTSGPPERKGIVHRLDVGTSGVMAVAASERAYTVLKRAFRDRTVDK 173

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G P      I   + +    G  +       + G  +A++H++ I+ F ++  
Sbjct: 174 TYHALVQGHPDPTDGTIDAPIARHPGHGWKFAV-----QDGGRHAVTHYETIEAF-REAT 227

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +   TGRTHQ+RVH   +  P  GD  Y ++   +    +  + +LHA ++  PHP+
Sbjct: 228 LVRVHLETGRTHQIRVHFSALHHPCAGDPMYGSDPALSQRLGLV-RQWLHAVHLGFPHPD 286

Query: 302 GGRLQITAPLPAHMVKTWDSLG 323
           G  + I +P PA +    D L 
Sbjct: 287 GRWMDIESPYPADLQTALDRLR 308


>gi|56419366|ref|YP_146684.1| hypothetical protein GK0831 [Geobacillus kaustophilus HTA426]
 gi|56379208|dbj|BAD75116.1| hypothetical conserved protein [Geobacillus kaustophilus HTA426]
          Length = 303

 Score =  222 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 138/315 (43%), Gaps = 33/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++   +   L ++ + +   I+   L  I    G + VD + V   + +++G+ + +   
Sbjct: 10  IDEQHDGKLLRQFLQEN--GISRTALTDIKFHGGALLVDGRPVTVRHVLRAGETLSVVFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
               +  +               ++ +   +LYED  + V NKPAG++            
Sbjct: 68  PERTSDWM--------------DAEAMPLDILYEDDYVLVVNKPAGLATIPSRHHPGGTL 113

Query: 129 IDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +G L  +   +      +  RLD++TSG+++VA+ R     L+   +   + + Y ++ 
Sbjct: 114 ANGLLHHYRKQQLDSTVHIVTRLDRDTSGLVLVAKHRHVHHLLSALQQKGHVVRTYEAIC 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+    +  I   + ++S        + ++  +    A++HF+V++     + ++ ++ 
Sbjct: 174 HGVIVEDEGTIDAPIGRQSD-----SIIAREVREDGKPAVTHFRVLERL-YGYTYVSLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++G P+ GD  Y        +  +  +  LH+R +   HP  GR   
Sbjct: 228 ETGRTHQIRVHLAYLGHPLAGDELYGG------SREMIGRQALHSRQLSFFHPFAGRWYT 281

Query: 307 ITAPLPAHMVKTWDS 321
            +APLP  M    ++
Sbjct: 282 CSAPLPDDMELLIEA 296


>gi|317500368|ref|ZP_07958592.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|316898123|gb|EFV20170.1| pseudouridylate synthase [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 347

 Score =  222 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 136/326 (41%), Gaps = 17/326 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + + ++E   R D++   +        L K+LR   + ++ K+   N  +  G  V+
Sbjct: 1   MKEIEINSNEAGQRFDKFLGKYLDQAPKSFLYKMLRKKNITLNGKKAAGNEILALGDNVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +    K  + +   V        +K  +LYED  +   NKP G+  Q  +   
Sbjct: 61  LFFSDETIKKFSKTSEEVFRPVQKNTAKSKVKLNVLYEDENVIFLNKPVGMLSQKANRED 120

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  +L  ++   GQ          P + +RLD+ TSGI+   +T +A Q L E FR R
Sbjct: 121 TSLVEYLIEYLLDSGQVTREELKTFHPAVCNRLDRNTSGIVAGGKTLSALQILNEMFRTR 180

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  LV G  K   + I  +L K +      V   K+  K A    + +  +   +
Sbjct: 181 SLEKYYLCLVSGKIK-DGQRICGYLKKNTKTNKVSVTKEKRETKEALPIETEYTPL-FVS 238

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYM 295
                L++   TG+THQ+R H   +G PI+GD+KY                   LHA  +
Sbjct: 239 DHVTLLKVHLITGKTHQIRAHLAAIGHPIIGDYKYGDFKINEAYKKKYGLKTQLLHAYQL 298

Query: 296 DLPHPEGGR----LQITAPLPAHMVK 317
             P  E  +     QI AP+P    K
Sbjct: 299 CFPDVELVKNLPNRQIIAPVPDLFKK 324


>gi|325962959|ref|YP_004240865.1| ribosomal large subunit pseudouridine synthase D [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323469046|gb|ADX72731.1| ribosomal large subunit pseudouridine synthase D [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 308

 Score =  222 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 137/323 (42%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +VV  +    R D         ++      +L  G V    K +  + ++ +G V+++
Sbjct: 3   ERMVVTEEFGGARADAGLAALL-GVSRSVAASLLAEGHVLAKGKPLGKSAKLVAGDVLQV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                                            +L +D    V +KP G++     G + 
Sbjct: 62  SMPERR-------------DPLEVVEEVVEGLKILLDDEDFAVVDKPVGVAAHPSPGWVG 108

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L             ++  + HRLD  TSG++VVA++  A   L  +F+ R + K
Sbjct: 109 PTVVGGLAGAGYRISTSGSPERAGIVHRLDVGTSGVMVVAKSERAYTALKRAFKERSVDK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++V G+P      I   + +  H G D+   V ++      +I+H++V++ F  K  
Sbjct: 169 VYHAVVQGLPDPVVGTIDAPIGR--HPGHDWRFAVIED---GRPSITHYEVLEAFG-KAS 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+   TGRTHQ+RVH   +  P  GD  Y A+ +   T  +  + +LHAR +   HP 
Sbjct: 223 LVEVHLETGRTHQIRVHFSALRHPCAGDLTYGADPRLAATLGL-TRQWLHARELGFDHPV 281

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G R+++T+  P  +    + L 
Sbjct: 282 TGERVRVTSDYPQDLAFALEVLA 304


>gi|302868912|ref|YP_003837549.1| RluA family pseudouridine synthase [Micromonospora aurantiaca ATCC
           27029]
 gi|302571771|gb|ADL47973.1| pseudouridine synthase, RluA family [Micromonospora aurantiaca ATCC
           27029]
          Length = 314

 Score =  222 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 135/325 (41%), Gaps = 28/325 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
             + + V +  + MRLD+        ++      ++ +G   VD      + ++++G  +
Sbjct: 10  DTRSLPVPDGLDGMRLDQAVSRLL-GLSRTAAAGLIDAGDALVDGVARPNSYKVKAGSWL 68

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +     A                           ++Y D  I V +KP G++     G 
Sbjct: 69  EVTLPAPAAPPA-------------VVPQAVPGLTVVYADDDIVVVDKPVGVAAHPSPGW 115

Query: 125 IAYHIDGFLK---SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + G L      + + G  ++  + HRLD  T+GI+ VA++  A   L  +F+ R +
Sbjct: 116 TGPTVIGGLAGIGHRISTSGAAERQGVVHRLDVGTTGIMAVAKSERAYTALKRAFKYREV 175

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++V G P   +  I   + +  H    +  V      G   +I+H+  ++ F   
Sbjct: 176 EKRYHAVVQGHPDPLRGTIDAPIDRHPHHDYRWAVVS-----GGKPSITHYDTLEAFP-A 229

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+++  TGRTHQ+RVH   M  P VGD  Y A+   +    + ++ +LHAR +   H
Sbjct: 230 ASLLDVRLETGRTHQIRVHFSSMRHPCVGDLTYGADPTLSARLGL-SRQWLHARSLSFAH 288

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLG 323
           P  G  +   +  P  + +  + L 
Sbjct: 289 PGTGDEVTFVSEYPDDLARALEILR 313


>gi|261419065|ref|YP_003252747.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|319765882|ref|YP_004131383.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
 gi|261375522|gb|ACX78265.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC61]
 gi|317110748|gb|ADU93240.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC52]
          Length = 304

 Score =  222 bits (565), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 138/315 (43%), Gaps = 33/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++   +   L ++ + +   I+   L  I    G + VD + V   + +++G+ + +   
Sbjct: 10  IDEQHDGKLLRQFLQEN--GISRTALTDIKFHGGALLVDGRPVTVRHVLRAGETLSVVFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
               +  +               ++ +   +LYED  + V NKPAG++            
Sbjct: 68  PERTSDWM--------------DAEAMPLDILYEDDYVLVVNKPAGLATIPSRHHPGGTL 113

Query: 129 IDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +G L  +   +      +  RLD++TSG+++VA+ R     L+   +   + + Y ++ 
Sbjct: 114 ANGLLHHYRKQQLDSTVHIVTRLDRDTSGLVLVAKHRHVHHLLSALQQKGHVVRTYEAIC 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+    +  I   + ++S        + ++  +    A++HF+V++     + ++ ++ 
Sbjct: 174 HGVIVEDEGTIDAPIGRQSD-----SIIAREVREDGKPAVTHFRVLERL-YGYTYVSLRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++G P+ GD  Y        +  +  +  LH+R +   HP  GR   
Sbjct: 228 ETGRTHQIRVHLAYLGHPLAGDELYGG------SREMIGRQALHSRQLSFFHPFAGRWYT 281

Query: 307 ITAPLPAHMVKTWDS 321
            +APLP  M    ++
Sbjct: 282 CSAPLPDDMELLIEA 296


>gi|162148037|ref|YP_001602498.1| ribosomal large subunit pseudouridine synthase D [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|161786614|emb|CAP56196.1| putative ribosomal large subunit pseudouridine synthase D
           [Gluconacetobacter diazotrophicus PAl 5]
          Length = 295

 Score =  222 bits (565), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 73/310 (23%), Positives = 128/310 (41%), Gaps = 37/310 (11%)

Query: 32  INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           ++   ++ ++  G V  D   ++   + +++G    I                +  ++  
Sbjct: 5   LSRSRVKALMEGGHVLRDGHVLREPADPVRAGLCYEIR---------------MPPAIPA 49

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG-----QK 143
           T  +  +   +LYEDS + V +KPAG+ V    G      ++  L    DS       ++
Sbjct: 50  TPRAQAIPFAILYEDSDLIVLDKPAGLVVHPAPGNEDGTLVNALLAHCGDSLTGIGGERR 109

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD++TSG++VVA+T  A   L+++F  R I + Y +L WGI           + 
Sbjct: 110 PGIVHRLDKDTSGVMVVAKTEQAHTALSDAFAARDIDRTYLALAWGILSPASGTFEGAIG 169

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +        + VV     G  +A++H++ +  F      +E +  TGRTHQ+RVH    G
Sbjct: 170 RDRR-DRKRMAVVTH---GGKHAMTHYRTLHSFHGGISSVECRLATGRTHQIRVHFSTSG 225

Query: 264 CPIVGDHKYCANFKGNFTSPIQN---------KLYLHARYMDLPHPEGGR-LQITAPLPA 313
            P+VGD  Y         +  ++         +  LHA  +   HP  G  L      P 
Sbjct: 226 HPLVGDPVYLRRIPAAARALPEDARRAALDFPRQALHAARLGFTHPRTGESLLFETAPPD 285

Query: 314 HMVKTWDSLG 323
                   + 
Sbjct: 286 DFKTLLAKIA 295


>gi|220915194|ref|YP_002490498.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219953048|gb|ACL63432.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 339

 Score =  221 bits (564), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 84/330 (25%), Positives = 150/330 (45%), Gaps = 24/330 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + V  D    RLD+  +     +   ++ K+ R+ +VRV+ +R K +  +  G VV 
Sbjct: 1   MIQLTVTADAAGQRLDKLVRKALRDVPLSHVYKMFRTRKVRVNGQRGKADQLVAEGDVVV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I           +E+ +  ++      +  +   +L+ED+ +   +KPAG++   G+GI 
Sbjct: 61  I--------RGDEERLLAKAAPAAPGGAPRVTFGVLHEDADLLAVDKPAGLAAHPGTGIE 112

Query: 127 -YHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR- 178
              +    + ++ +         KP   HRLD++TSG+++VA+ R A   LTE+F     
Sbjct: 113 GATLVEMARGYLKTPDDLPPTEFKPSPAHRLDRDTSGVVLVAKHRKAMVRLTETFTSGEG 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y +LV G    +   I   L +                     A++ +KV+   A+
Sbjct: 173 VHKTYLALVKGKMPREAGTIDLPLSEHEQTSKSKAMR----GVNFQEALTRWKVVSA-AK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMD 296
           +   L +   TGRTHQ+R H   +G P+ GD +Y   A  +   T     ++ LHA  ++
Sbjct: 228 EISLLAVTIETGRTHQIRRHLEAVGHPVAGDRRYGDFAFNRTARTRWGLRRMGLHAWKLE 287

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           +PHP  G  L++ AP PA + +       K
Sbjct: 288 VPHPLTGAPLRLEAPFPAELAEVLSRANLK 317


>gi|15828769|ref|NP_326129.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Mycoplasma pulmonis UAB
           CTIP]
 gi|14089712|emb|CAC13471.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE D (PSEUDOURIDYLATE
           SYNTHASE) (URACIL HYDROLYASE) [Mycoplasma pulmonis]
          Length = 296

 Score =  221 bits (564), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 73/313 (23%), Positives = 140/313 (44%), Gaps = 38/313 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            R+D++  ++   I+  +++ ++    V V+ K + K N  ++    + +          
Sbjct: 10  ERIDKYISDN-SAISRNDIKSLILEKAVFVNGKVIQKPNFILKPDAEIEVI--------- 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
               K++D +++L    + +   ++YED  + V NKP+G+ V    G      ++G +  
Sbjct: 60  ----KVIDKTIDL--KPEKMDLDIVYEDEHLIVINKPSGLVVHPAPGHYSQTLVNGLIYH 113

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           + +   +    +P + HR+D++TSG+L++A+T    Q L +  +   I++ Y ++V G  
Sbjct: 114 FKNLSNENGLLRPGIVHRIDKDTSGLLIIAKTNQVHQLLAKMLKNHEIKRSYIAIVEGFF 173

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQKFCWLEMQPH 248
           +NK   + N  + +S      + +   N K    AI+H  +I       Q    +E Q  
Sbjct: 174 ENKIVHL-NLPIGRSQKDRKKMEITNNNSKN---AITHVYLIKQFYYEKQPLSLVECQLE 229

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           TGRTHQ+RVH  +   P+  D  Y  +F            YLHA  +   HP     L  
Sbjct: 230 TGRTHQIRVHLNYFKHPVWNDPLYGKSFSDY-------GQYLHAYKLFFVHPITNQELTF 282

Query: 308 TAPLPAHMVKTWD 320
             P+P    +  +
Sbjct: 283 EIPMPEEFQRIIN 295


>gi|153815705|ref|ZP_01968373.1| hypothetical protein RUMTOR_01942 [Ruminococcus torques ATCC 27756]
 gi|317501908|ref|ZP_07960092.1| RluA family Pseudouridine synthase [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|145846946|gb|EDK23864.1| hypothetical protein RUMTOR_01942 [Ruminococcus torques ATCC 27756]
 gi|316896588|gb|EFV18675.1| RluA family Pseudouridine synthase [Lachnospiraceae bacterium
           8_1_57FAA]
          Length = 295

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 71/321 (22%), Positives = 139/321 (43%), Gaps = 32/321 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M       + +  +N+R+D + + H Y   N   L+K+  S  +  + +       +Q+G
Sbjct: 1   MERTITYKITDSGQNIRIDSFLRKHGYSMQNLTLLKKMPES--ILKNGEWSYMQTTLQAG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++ +              +I + + +    +  L   ++YED  I V NK AG+ +   
Sbjct: 59  DILTV--------------RIQEETSSPNIPAVNLPIDIVYEDEDIIVINKAAGMPIHPS 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHR---LDQETSGILVVARTRAAAQHLTESFRMRRI 179
                +       W   +  KP +      LD++TSG+ VVA+   ++  L+      +I
Sbjct: 105 LNNYRNSLANALMWYYEQQNKPFIFRCTNRLDRDTSGLTVVAKHMVSSNILSSMTARHQI 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y ++V G     +  I   + +     G  +   K + +   +AI+H+  +      
Sbjct: 165 EREYLAIVRGHVTPFEGTINAPIGR----TGSSLIERKIDFENGEHAITHYHTV-FEKNG 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + +   TGRTHQ+RVH  H+G P++GD+ Y  + +      + ++  LH+  +   H
Sbjct: 220 LSLVSLILETGRTHQIRVHMKHLGFPLIGDYLYNPDME------LIDRQALHSHCLRFLH 273

Query: 300 PEGGR-LQITAPLPAHMVKTW 319
           P  GR +  TA LP  M + +
Sbjct: 274 PITGRQMTFTADLPEDMARLF 294


>gi|94987255|ref|YP_595188.1| pseudouridylate synthases, 23S RNA-specific [Lawsonia
           intracellularis PHE/MN1-00]
 gi|94731504|emb|CAJ54867.1| Pseudouridylate synthases, 23S RNA-specific [Lawsonia
           intracellularis PHE/MN1-00]
          Length = 541

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 78/314 (24%), Positives = 141/314 (44%), Gaps = 34/314 (10%)

Query: 19  MRLDRWFKNHY--PHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
           +RLD++  N+     ++   L+K++ SG  ++D K     + R++ G  + I  +   ++
Sbjct: 16  VRLDQFLYNNLCTHGVSRERLKKVIVSGGCKIDDKVCFSPSTRLKVGMHIFIQ-LPEVVS 74

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----SGIAYHID 130
            ++ E+  L+               +L+ D  + + NKP G++V        S + + + 
Sbjct: 75  ALLPEEGFLE---------------ILFSDEHLAIINKPPGLTVHPAPSCQESTLVHRLL 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            +    ++  G +P + HR+D++TSG+L +A T      L++ F  R+I K Y +LV G+
Sbjct: 120 KYFPKLIEQGGLRPGIVHRIDKDTSGLLCIALTEDTRLKLSKIFLDRKINKEYLALVHGV 179

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHT 249
           P  +   IA  L +          V          A + ++V+       +  L +   T
Sbjct: 180 PSME-GYIAVPLGRDPKT-----KVKVAVNPKGKPAHTEWRVLHRGKNDVYSILALTIQT 233

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
           GRTHQ+RVH  H+G P+VGD  Y         +   N+  LHA  +   HP  G ++   
Sbjct: 234 GRTHQIRVHMKHIGHPLVGDKLYAGGHVNK--TFQCNRQMLHAWKLSFEHPITGKKMNFL 291

Query: 309 APLPAHMVKTWDSL 322
            P P   + T   L
Sbjct: 292 CPPPKDFLDTVSLL 305


>gi|6721111|gb|AAF26765.1|AC007396_14 T4O12.25 [Arabidopsis thaliana]
          Length = 980

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 85/374 (22%), Positives = 155/374 (41%), Gaps = 68/374 (18%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF--------NNRIQSG 62
           +V+  +  +RLD W  +    ++   +Q  +R G V V+ + V          + + Q  
Sbjct: 598 IVDAAKGKIRLDSWISSRINGVSRARVQSSIRLGLVTVNGRVVDKVLTSKFDSSKKFQFC 657

Query: 63  QVVRIPPVINALNHIIKEQKILDSSV----NLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
             V I   +  ++H +K    ++ ++     L   ++ +   ++YED  + V NKPA + 
Sbjct: 658 NQVSISLTLFQVSHNVKSGDEVNCTISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMV 717

Query: 119 VQGGSG--IAYHIDGFLKSWV--------------------------------DSKGQKP 144
           V    G      ++G L                                     +   +P
Sbjct: 718 VHPAPGNPTGTLVNGILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRP 777

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HRLD+ T+G+LVVA+   +  HL E F++  I+++Y SL  G+P   +  I   + +
Sbjct: 778 GIVHRLDKGTTGLLVVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPSPPQGRIEIPIGR 837

Query: 205 KSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALH 261
            S      +  +    +G  A +A S +KVI+ FA      +E +  TGRTHQ+R HA +
Sbjct: 838 DSS-NRIRMAAIPGGVRGGRARHAASRYKVIETFAGGGSALVEWRLETGRTHQIRAHAKY 896

Query: 262 MGCPIVGDHKYCA--------------NFKGNFTSPIQNKL---YLHARYMDLPHPEGGR 304
           MG P++GD  Y                         + +++    LHA  +   HP  G 
Sbjct: 897 MGVPLLGDEVYGGTKSMALSLLQKRVSRSDQEEIIELISRMDRPCLHAIVLGFTHPCTGE 956

Query: 305 L-QITAPLPAHMVK 317
           + + + P P+ + +
Sbjct: 957 IVKFSCPPPSDLAE 970


>gi|315504618|ref|YP_004083505.1| pseudouridine synthase, rlua family [Micromonospora sp. L5]
 gi|315411237|gb|ADU09354.1| pseudouridine synthase, RluA family [Micromonospora sp. L5]
          Length = 314

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 135/325 (41%), Gaps = 28/325 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
             + + V +  + MRLD+        ++      ++ +G   VD      + ++++G  +
Sbjct: 10  DTRSLPVPDGLDGMRLDQAVSRLL-GLSRTAAAGLIDAGDALVDGVARPNSYKVKAGSWL 68

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +     A                           ++Y D  I V +KP G++     G 
Sbjct: 69  EVTLPAPAAPPA-------------VVPQAVPGLTVVYADDDIVVVDKPVGVAAHPSPGW 115

Query: 125 IAYHIDGFLK---SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + G L      + + G  ++  + HRLD  T+GI+ VA++  A   L  +F+ R +
Sbjct: 116 TGPTVIGGLAGIGHRISTSGAAERQGVVHRLDVGTTGIMAVAKSERAYTALKRAFKYREV 175

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++V G P   +  I   + +  H    +  V      G   +I+H+  ++ F   
Sbjct: 176 EKRYHAVVQGHPDPLRGTIDAPIDRHPHHDYRWAVVS-----GGKPSITHYDTLEAFP-A 229

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+++  TGRTHQ+RVH   M  P VGD  Y A+   +    + ++ +LHAR +   H
Sbjct: 230 ASLLDVRLETGRTHQIRVHFSSMRHPCVGDLTYGADPTLSARLGL-SRQWLHARSLSFAH 288

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLG 323
           P  G  +   +  P  + +  + L 
Sbjct: 289 PGTGDEVTFVSEYPDDLARALEILR 313


>gi|302206504|gb|ADL10846.1| Ribosomal large subunit pseudouridine synthase D [Corynebacterium
           pseudotuberculosis C231]
 gi|308276746|gb|ADO26645.1| Ribosomal large subunit pseudouridine synthase D [Corynebacterium
           pseudotuberculosis I19]
          Length = 307

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 79/329 (24%), Positives = 134/329 (40%), Gaps = 29/329 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V      MR+D         I+      +  +G V VD   V  ++RI  GQ
Sbjct: 1   MREHRSLPVPEGLAGMRVDAALSKLL-GISRTVAADLATAGDVLVDALPVGKSDRIAEGQ 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          + E K L     L +  D     +LY D  +   NKP G++     
Sbjct: 60  WLDVT---------LPETKDLTPREELVEGMD-----ILYSDDDLIAVNKPVGVAAHPTL 105

Query: 124 GIA-YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  +  RLD  TSG++V+A +      L  +F+ R
Sbjct: 106 GWEGPTVIGGLAAAGFRISTSGPPERKGIVQRLDVGTSGVMVIAASERGYSVLKRAFKER 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G        I   + +    G  +            +A++H++ ++ FA
Sbjct: 166 TVSKTYHALVQGHTDPFTGTIDAPIGRHPSAGWRFAVTS-----DGKHAVTHYETLEAFA 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    L++   TGRTHQ+RVH   +  P  GD  Y ++ K +    +  + +LHA  +  
Sbjct: 221 E-ASLLKIHLETGRTHQIRVHMSALHHPCCGDPMYGSDPKLSERLGL-TRQWLHAVSLGF 278

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  GR ++IT+P    +    D L   
Sbjct: 279 NHPADGRWMEITSPYSDDLQHALDILRED 307


>gi|126435691|ref|YP_001071382.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           JLS]
 gi|126235491|gb|ABN98891.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           JLS]
          Length = 304

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 80/319 (25%), Positives = 138/319 (43%), Gaps = 28/319 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V      MR+D         ++      I   G+V +D      ++R+ +G  + +    
Sbjct: 3   VPEGLGGMRVDAGLSRLL-GLSRTAAAAIAEDGRVDIDGAPAGKSDRLTAGAWLEVR--- 58

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
                 + E      +  +          +LY D  I   +KP G++     G     + 
Sbjct: 59  ------LPEAPPPVENTPVEIEG----MAVLYSDDDIVAVDKPPGVAAHATVGWHGPTVL 108

Query: 131 GFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R ++K Y +
Sbjct: 109 GGLAAAGFRISTSGIHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQRTVEKRYHA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G P      I   + +  H G D+   V    +G  ++++H+  ++ F Q    L++
Sbjct: 169 LVQGHPDPSSGTIDAPIGR--HRGHDWKFAVT---EGGRHSVTHYDTLEAF-QAASLLDI 222

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
           +  TGRTHQ+RVH   +  P  GD  Y A+        ++ + +LHAR +   HP +G R
Sbjct: 223 ELETGRTHQIRVHFAALHHPCCGDLTYGADPTLARRLGLE-RQWLHARSLAFAHPADGRR 281

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++IT+P PA +    D L 
Sbjct: 282 IEITSPYPADLQHALDVLR 300


>gi|312140126|ref|YP_004007462.1| tRNA-pseudouridine synthase i [Rhodococcus equi 103S]
 gi|311889465|emb|CBH48782.1| tRNA-pseudouridine synthase I [Rhodococcus equi 103S]
          Length = 308

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 140/328 (42%), Gaps = 30/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  + MR+D         ++   +  +   G V VD      ++R+ +G 
Sbjct: 1   MRETRSMPVPDGLDGMRVDAGLARLL-GLSRTAVATLTEEGAVLVDGAAAGKSDRLSAGT 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGG 122
            + +              ++ +    LT  ++ ++ + +LY D  I   +KP G++    
Sbjct: 60  WLEV--------------ELPEPPRPLTIEAEPVEGMEILYADDDIVAVDKPVGVAAHAS 105

Query: 123 SG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ 
Sbjct: 106 VGWTGPTVIGGLAAAGFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTVLKRAFKQ 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I K Y +LV G P      I   + +  H   D+   V  +      +++H+  ++ F
Sbjct: 166 RTIDKRYHALVQGHPDPSSGTIDAPIGR--HRSNDWKFAVTAD---GKPSVTHYDTVEAF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q    L++   TGRTHQ+RVH   +  P  GD  Y A+ +      ++ + +LHAR + 
Sbjct: 221 -QAASLLDIHLETGRTHQIRVHFSALRHPCCGDLTYGADPRLAERLGLE-RQWLHARSLG 278

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  G  ++IT+  P  +      L 
Sbjct: 279 FAHPADGHWVEITSDYPKDLQHALGVLR 306


>gi|257068273|ref|YP_003154528.1| ribosomal large subunit pseudouridine synthase D [Brachybacterium
           faecium DSM 4810]
 gi|256559091|gb|ACU84938.1| ribosomal large subunit pseudouridine synthase D [Brachybacterium
           faecium DSM 4810]
          Length = 308

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 73/329 (22%), Positives = 145/329 (44%), Gaps = 28/329 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + ++V +     R+D         ++      ++ +G V VD +    + R++ G 
Sbjct: 1   MSSSRLLMVPDGLAGERVDVGISRML-GLSRTRAADLVTAGHVLVDGRAPARSTRLEPGV 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V +          ++ Q     S             L+++D  I V +KP G++    +
Sbjct: 60  MVHVELPDEKPAVEVRPQIAEGMS-------------LIHQDDDIVVIDKPVGVAAHPSA 106

Query: 124 G------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      + +     ++       ++  +  RLD  TSG++VVART  A   L ++FR R
Sbjct: 107 GWSGPTVLGHLAAAGVEIRTSGDPERQGIVSRLDVGTSGLMVVARTERAYTTLKDAFRAR 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K+Y ++  G P   +  I   + +      DY   V+++     ++++H++ ++   
Sbjct: 167 EVGKVYHAICQGTPDQPRGTIEAPIGRSPQ--HDYKFAVRED---GKHSVTHYETLEEL- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q    L +   TGRTHQ+RVH   +  P+VGD  Y A+        +  + +LHA  +  
Sbjct: 221 QGATLLRIGLETGRTHQIRVHMSALHHPLVGDPLYGADPTLAERVGLI-RQWLHAMELTF 279

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  GR +  T+  P+ + +  ++L  +
Sbjct: 280 VHPATGREVTYTSQYPSDLAQALEALRGR 308


>gi|161502239|ref|YP_001569351.1| hypothetical protein SARI_00264 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160863586|gb|ABX20209.1| hypothetical protein SARI_00264 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 318

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 68/291 (23%), Positives = 128/291 (43%), Gaps = 34/291 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ + + +V V+ +   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I+                 +   +  +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  DAEIDE---------------EIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVNEPISRHPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +       + +L+   
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKAH--RKRLFPRC 271


>gi|160880920|ref|YP_001559888.1| RluA family pseudouridine synthase [Clostridium phytofermentans
           ISDg]
 gi|160429586|gb|ABX43149.1| pseudouridine synthase, RluA family [Clostridium phytofermentans
           ISDg]
          Length = 346

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 142/334 (42%), Gaps = 23/334 (6%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V+ + +  +E   RLD++   +          K+LR   + ++ K+ +   ++  G +
Sbjct: 16  NKVREITIVQNEAGQRLDKFLAKYLNKAPKSFFYKMLRKKNITLNGKKAEGAEKLIEGDI 75

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+      +    KE   LD+ VN       +K  +LYEDS + + NKP G+  Q    
Sbjct: 76  VRLFLAEETIESF-KESYQLDAKVN----QRAVKLDVLYEDSHVVIINKPIGMLSQRAKE 130

Query: 125 IAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
               +   L +++   G          KP + +RLD+ TSGI++  ++    Q ++   +
Sbjct: 131 SDVSLVELLIAYLLEMGSLTKEELSTFKPSVCNRLDRNTSGIVIAGKSLLGLQEMSAKLQ 190

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y  +V G    K   I  +L K        +     N+  ++Y  + ++ I  
Sbjct: 191 DRSLHKYYRCIVKGTM-TKGARINGYLAKDEKTNKVRITTNDPNDGESSYIETEYQPILS 249

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHAR 293
               +  LE+   TG+THQ+R H   +G PI+GD KY      K        +   LH+ 
Sbjct: 250 K-NGYTLLEVLLITGKTHQIRAHLSSIGHPIIGDTKYGDETLNKKMQKQYGLSHQLLHSY 308

Query: 294 YMDLPH--PEGGRL---QITAPLPAHMVKTWDSL 322
            ++ P+   E  +L   +I AP P        SL
Sbjct: 309 RLEFPNLPKELEKLSNQKIIAPYPKLFKNLEKSL 342


>gi|296164416|ref|ZP_06846990.1| RluA family RNA pseudouridine synthase [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295900198|gb|EFG79630.1| RluA family RNA pseudouridine synthase [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 308

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 83/329 (25%), Positives = 141/329 (42%), Gaps = 29/329 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  + + V      MR+D         ++      I   G V +D  +   ++R+  G 
Sbjct: 1   MTD-RSMPVPEGLAGMRVDAGLARLL-GLSRSAAAAIAEDGGVELDGVQAGKSDRLTGGA 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +++          + E      +  +    D     +LY D  I   +KPA ++     
Sbjct: 59  WLQVR---------LPEAPPPVENTPV----DIEGMTILYSDEDIVAVDKPAAVAAHASV 105

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R
Sbjct: 106 GWTGPTVLGGLAAAGYRITTSGVPERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G P      I   + +  H GG++   V  N     ++++H+  I+ F 
Sbjct: 166 TVDKRYHALVQGHPDPSSGTIDAPIGR--HRGGEWKFAVTTN---GRHSLTHYDTIEAFT 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                L++   TGRTHQ+RVH   +  P  GD  Y A+ K      ++ + +LHAR +  
Sbjct: 221 -AASLLDVHLETGRTHQIRVHFSALHHPCCGDLVYGADPKLAKRLGLE-RQWLHARSLSF 278

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            HP +G R++I +P PA +    D L  +
Sbjct: 279 AHPADGRRMEIVSPYPADLQHALDVLRAE 307


>gi|310820148|ref|YP_003952506.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309393220|gb|ADO70679.1| Pseudouridine synthase, RluA family [Stigmatella aurantiaca
           DW4/3-1]
          Length = 304

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 82/320 (25%), Positives = 147/320 (45%), Gaps = 26/320 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V  +    RLD+    H P ++    ++++  G VR+  K+ +   ++  G+ + +  
Sbjct: 1   MIVAREASGERLDKHLSKHVPGLSLERARQLIAQGNVRIRGKKCQPTRKLWGGEEIELS- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                   +   ++   +  +    +     +L++D  + + +KP G+ V+ G G A  +
Sbjct: 60  --------LPPPRVPQGTAAV----EGPGLPVLHDDPDMVIVDKPVGLVVEPGGG-APSV 106

Query: 130 DGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              L +           +P + HRLD+ETSG L+ ART AAA  L ++F+ +R+ K YW+
Sbjct: 107 VELLAAQRPPFDVEGVARPGVVHRLDRETSGCLMFARTDAAAAALDQAFQQKRVDKRYWT 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G    + E +     +       +   V    K A  A   F+V +   +    LE+
Sbjct: 167 LVLGE-TPEHERLEGPYGRDPQDPRKFTTRV----KSARRAALSFEVRERL-RGATLLEV 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +  TGRTHQ+RV     G P++GD  Y     + +  +    +  LHA  + +PHP  G 
Sbjct: 221 RLETGRTHQIRVQLSEAGFPVLGDSVYGPSEARAHPVAQALGRQALHALRLAVPHPSTGA 280

Query: 305 L-QITAPLPAHMVKTWDSLG 323
           L ++ APLP    K   +L 
Sbjct: 281 LVRVEAPLPEDFQKALAALR 300


>gi|213965290|ref|ZP_03393487.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           amycolatum SK46]
 gi|213952142|gb|EEB63527.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           amycolatum SK46]
          Length = 327

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 137/325 (42%), Gaps = 28/325 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
             + + V      MR+D         ++   +  +  +G + VD   V  ++R++    +
Sbjct: 21  ETRQMPVPPGLAGMRVDAGVAKLL-GLSRTAVADLAAAGDITVDGVSVGKSDRLEENAFL 79

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +         +   +K L     L +  D     +LY DS +   +KP G++     G 
Sbjct: 80  SV--------LLPPVEKPLVPKEELVEGMD-----VLYHDSDLVAVHKPVGVAAHPSVGW 126

Query: 126 A-YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + G L +           ++  + HRLD  TSG++VVA +      L  +F+ R +
Sbjct: 127 EGPTVIGGLAAAGFRISTSGPPERKGIVHRLDVGTSGVMVVACSERGYSVLKRAFKNREV 186

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G P      I   + +  H    +   V+Q+     +A++H++ ++ FA  
Sbjct: 187 SKTYHALVQGHPDPLSGTIDAPIGR--HPSAGWRFAVRQD---GKHAVTHYETLEAFA-P 240

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L++   TGRTHQ+RVH   +  P  GD  Y ++        + N+ +LHA  +   H
Sbjct: 241 ATLLKVNLETGRTHQIRVHFSALNHPCCGDPMYGSDPALAKRLGL-NRQWLHAVSLGFHH 299

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  GR ++I  P P  +    + L 
Sbjct: 300 PADGRWMEIECPYPDDLNHALEVLR 324


>gi|94984711|ref|YP_604075.1| pseudouridine synthase, RluD [Deinococcus geothermalis DSM 11300]
 gi|94554992|gb|ABF44906.1| Pseudouridine synthase, RluD [Deinococcus geothermalis DSM 11300]
          Length = 341

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 85/328 (25%), Positives = 139/328 (42%), Gaps = 41/328 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD    +    ++       +  GQV V    V K + +++ G+ +R+           
Sbjct: 33  RLDSVLAD-LTGVSRSQAAGWIAGGQVEVGGVVVQKASLKLKGGETLRVQ---------- 81

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKSW 136
                +    + T   + +   +LYED  +   NKP G+      G+     ++  L   
Sbjct: 82  -----VPPPPDATVSPEAVPLDVLYEDEHLIAVNKPPGMVTHPAPGVTSGTLVNALLGRL 136

Query: 137 --------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                   V   G +P + HRLD++TSG++VVA+T  A   L  +F+ R   K Y ++  
Sbjct: 137 TLPEQPGAVGPDGYRPGIVHRLDKDTSGVIVVAKTVEAHARLAAAFKDRSTHKTYLAIAA 196

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF----CWLE 244
           G+ K +     N  + +       + V      G   A + F  +             + 
Sbjct: 197 GMWKAQGPVSVNAPVGRHPTARQRMTV---GGVGPREAQTLFTPLATHPDGHGRTLALVR 253

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            QPHTGRTHQ+RVH  H+G PI+GD  Y         S +  +  LHA+++ LPHP  G 
Sbjct: 254 AQPHTGRTHQIRVHLAHLGSPILGDAVYGR------ASAVMPRHALHAQFLTLPHPVTGE 307

Query: 305 -LQITAPLPAHMVKTWDSLGFKYDRNLY 331
            L + AP+P  +++ W +LG      L 
Sbjct: 308 TLHLHAPVPDDLLRAWVALGGAVPAELE 335


>gi|189485617|ref|YP_001956558.1| pseudouridylate synthase [uncultured Termite group 1 bacterium
           phylotype Rs-D17]
 gi|170287576|dbj|BAG14097.1| pseudouridylate synthase [uncultured Termite group 1 bacterium
           phylotype Rs-D17]
          Length = 296

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 77/318 (24%), Positives = 136/318 (42%), Gaps = 29/318 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q  ++    E  R D +  + Y   +    QK+    +V V+ K +  +++++ G ++ 
Sbjct: 1   MQEKIIYEKFERERADSYLASIYKDYSRSYFQKLTDRQRVFVNDKIIPVSHKLKRGDIIT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I         I  E+  +D                        V NK +GI V    G  
Sbjct: 61  IEFEKEEKFQIKPEKIKIDIIYEDDDI---------------VVVNKRSGIVVHPSYG-- 103

Query: 127 YHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            H+ G L + +    +    P L HRLD++TSG++V A+T  A   +++  + R ++KIY
Sbjct: 104 -HLSGTLLNALMGYSAGKYNPYLIHRLDKDTSGVIVFAKTEKAKISISKQLQKRVVKKIY 162

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           ++ V G+    +  I   L +          +V  N      AI+ FKVI+     +  L
Sbjct: 163 YAAVKGVIAENRGIIKAPLGRSPKNRK----LVSVNPLAKKVAITEFKVIERK-DDYTLL 217

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +++  TGRTHQ+R H  ++  P++GD +Y     G        +  LHA  +   HP   
Sbjct: 218 KVRIITGRTHQIRSHMKYINHPVIGDKQYGG--PGTIGLKRCERQMLHAHNITFTHPSTS 275

Query: 304 R-LQITAPLPAHMVKTWD 320
           + ++  A LP  M   + 
Sbjct: 276 KTVKFIAQLPNDMKAIFK 293


>gi|329944572|ref|ZP_08292712.1| pseudouridine synthase, RluA family [Actinomyces sp. oral taxon 170
           str. F0386]
 gi|328530125|gb|EGF57008.1| pseudouridine synthase, RluA family [Actinomyces sp. oral taxon 170
           str. F0386]
          Length = 314

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 80/331 (24%), Positives = 145/331 (43%), Gaps = 33/331 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSL    + + V +  +  R+D         ++   +  +   G VR + + +  ++R+ 
Sbjct: 1   MSL----RLLPVPDGFDGERVDTALAR-MTGLSRSRVGDLCAHGDVRRNVEALTKSDRLH 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G ++ +          + + + ++      K        LLYED  I V +KPAG++  
Sbjct: 56  AGDLLEVD---------LPDPRPVEPVATPVK-----GMALLYEDEDIVVVDKPAGVAAH 101

Query: 121 GGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G     + G LK+           ++  +  RLD  TSG+++VA+   A   L  +F
Sbjct: 102 PSMGWDGPDVLGALKAMHVRVATSGAAERQGIVSRLDVGTSGVMIVAKGERAYSVLKRAF 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R   + K+Y +LV G        I   + +  H   ++   +    +G   +++H+ VI+
Sbjct: 162 REHMVDKVYHALVQGHLDPSHGTIDAPIGR--HPSREWKMAIV---EGGRESVTHYDVIE 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                 C  E+   TGRTHQ+RVH   +G P VGD  Y A+      + +  + +LHAR 
Sbjct: 217 AMP-GACLAEVHLETGRTHQIRVHMAAVGHPCVGDATYGADPVMTARTGLV-RQWLHARR 274

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           + + HP  G  +  T+  PA +V   D +  
Sbjct: 275 LGIAHPITGEHMVFTSDYPADLVHALDVMRL 305


>gi|295109974|emb|CBL23927.1| pseudouridine synthase, RluA family [Ruminococcus obeum A2-162]
          Length = 330

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 79/344 (22%), Positives = 143/344 (41%), Gaps = 33/344 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   + ++E   R D++      +       K+LR   + ++ K+   N ++++G  ++
Sbjct: 1   MKEFQITDNEAGQRFDKYLAKLLGNAPKSFFYKMLRKKNITLNGKKASGNEKLKNGDQIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    +      ++++   +  +L          +LYEDS I + +KP G+  Q      
Sbjct: 61  LFLSDDTFAKFSQQEQTARAVTDLD---------ILYEDSDILLISKPVGMLSQPDDTKE 111

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  +L  ++ + G           P + +RLD+ TSGI+   ++ A  Q L+  F  R
Sbjct: 112 PSLVEYLIGYLLNNGSITEEGLRTFHPSVCNRLDKNTSGIVAAGKSLAGLQELSSLFHDR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I K Y  +V GI  + K+ I  +L K + +    V + K   K A    + ++ +   +
Sbjct: 172 TIHKDYLCIVKGILTDNKQ-IRGYLYKDTKLN--KVTISKIKIKDAQPIETRYEPLGHTS 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYM 295
                L ++  TGRTHQ+R H    G P+ GD KY       +       N   LHA  +
Sbjct: 229 H-MTLLRVRLITGRTHQIRAHLASEGHPLAGDMKYGQKEFNRYFHEKYHLNHQLLHAYRL 287

Query: 296 DLPHPEGGRL------QITAPLPAHMVKTW--DSLGFKYDRNLY 331
             P    G+L         APLP   +     + L   Y  NL 
Sbjct: 288 TFP-ELTGKLATLSGKCFLAPLPKQFLTILKEEHLEESYYENLE 330


>gi|242097088|ref|XP_002439034.1| hypothetical protein SORBIDRAFT_10g030300 [Sorghum bicolor]
 gi|241917257|gb|EER90401.1| hypothetical protein SORBIDRAFT_10g030300 [Sorghum bicolor]
          Length = 441

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 82/377 (21%), Positives = 146/377 (38%), Gaps = 80/377 (21%)

Query: 12  VENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           V   E   R+D W         ++   +Q  +R+G V V+ + V K ++ ++ G +V   
Sbjct: 66  VPVGEGRSRIDAWISARLGGGGVSRARVQASIRAGLVAVNGRPVSKVSHTVKGGDLVSCT 125

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
                          +     L   ++ +   ++YED  + V NKPA + V    G A  
Sbjct: 126 ---------------VSELQPLRAEAEDIPLDIVYEDDHVLVVNKPAHMVVHPAPGNANG 170

Query: 128 -HIDGFLKSW-----------------------------------------VDSKGQKPR 145
             ++  L                                            V +   +P 
Sbjct: 171 TLVNAILHHCKISTFTCLARSSTGDECLDSSDDDIDVFNVDQFATEDASSEVRNALVRPG 230

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+ TSG+LVVA+   +   L E F++  I+++Y SL  G+P      I   + + 
Sbjct: 231 IVHRLDKGTSGLLVVAKDEHSHAQLAEQFKLHTIRRVYISLTCGVPNPNSGRIEASIARD 290

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            +     + +     + A +A S +KV + F       +E +  TGRTHQ+R HA ++G 
Sbjct: 291 PNNRIRMIAIAGSGHRYARHAASRYKVREVFVGGGSALVEWRLETGRTHQIRAHAKYIGI 350

Query: 265 PIVGDHKYCA---------------NFKGNFTSPIQ--NKLYLHARYMDLPHPEGGRL-Q 306
           P++GD  Y                  +  + ++ I   ++  LHA  +   HP  G++ +
Sbjct: 351 PLLGDETYGGTKSMALSLLRPRTPSKYHSDLSNLISKVDRPCLHAALLGFKHPHSGKILE 410

Query: 307 ITAPLPAHMVKTWDSLG 323
            + P P    +  D L 
Sbjct: 411 FSCPPPDDFSEVLDELR 427


>gi|332654559|ref|ZP_08420302.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Ruminococcaceae bacterium D16]
 gi|332516523|gb|EGJ46129.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Ruminococcaceae bacterium D16]
          Length = 301

 Score =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 85/322 (26%), Positives = 135/322 (41%), Gaps = 33/322 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + +      +++D   K H   ++   ++  K L  G + VD  RV      Q GQV+ 
Sbjct: 7   ELPITGALAGIKVDTLLKRHL-GLSGTVVRRIKWLEDG-ILVDGARVNTRFCPQEGQVLS 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +      L+   +   IL S   L          ++YED  + V NK  G+ V  G G  
Sbjct: 65  V-----RLSDPERRSGILPSPGPLD---------IVYEDGDVVVLNKAPGVPVHPGPGHY 110

Query: 126 AYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +  I  +L  + D +G +      HRLD+ TSG+LVVAR   A + L E        + Y
Sbjct: 111 SDTIGNYLLYYYDQEGTEGDFHPVHRLDRGTSGLLVVARHPHAQEVLKEQLHTDGFHREY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++  GI +     I   L  K     + +           +A +H++V+    ++   +
Sbjct: 171 LAVCEGILEPPVGTIEEPLGPKPGSLVEQMVR-----PDGKFARTHYEVVKA-GERCTLV 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +   TGRTHQ+RVH  H+G P+VGD  Y          P      LH+  +   HP  G
Sbjct: 225 RLVLDTGRTHQIRVHLAHLGHPLVGDFLYGKEEPERIPRP-----ALHSHRLTFRHPITG 279

Query: 304 -RLQITAPLPAHMVKTWDSLGF 324
             +  TAP+P  M +  +  G 
Sbjct: 280 QEMTFTAPVPQDMKRLLEQEGL 301


>gi|260578068|ref|ZP_05845990.1| RluA family RNA pseudouridine synthase [Corynebacterium jeikeium
           ATCC 43734]
 gi|258603808|gb|EEW17063.1| RluA family RNA pseudouridine synthase [Corynebacterium jeikeium
           ATCC 43734]
          Length = 323

 Score =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 69/318 (21%), Positives = 132/318 (41%), Gaps = 26/318 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +    MR+D         ++   + ++   G +  D+  V  ++R+ +G  + +    
Sbjct: 10  VPDGLAGMRVDSGLSKLL-GLSRTAVAELAADGDILQDQAPVGKSDRLVAGAWLDVTLPA 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHID 130
              +   +  + ++               +LY D  + V +KP G++     G     + 
Sbjct: 69  PPRDLAAEPARHVEG------------MDILYSDEDVIVVDKPVGVAAHPTVGWEGPTVT 116

Query: 131 GFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             L +           ++  +  RLD  TSG+++VA +  A   L  +FR R + K Y +
Sbjct: 117 SGLAAAGFRISTSGPPERKGIVQRLDVGTSGVMIVAASERAYTVLKNAFRDREVSKTYHA 176

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G P      I   + +    G  +        +   +AI+H+  ++   ++   LE+
Sbjct: 177 LVQGHPDPTSGTIDAPIGRHPSAGWRFSVR-----EDGKHAITHYDTLEAH-RQASLLEV 230

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +  TGRTHQ+RVH   +  P+ GD  Y ++ K      +  + +LHA  +  PHP+G   
Sbjct: 231 KLETGRTHQIRVHFSALHHPLCGDPMYGSDPKLAERLGLI-RQWLHAVELGFPHPDGSWK 289

Query: 306 QITAPLPAHMVKTWDSLG 323
            + +P P  +    D L 
Sbjct: 290 TVRSPYPEDLQLALDRLR 307


>gi|182419830|ref|ZP_02951070.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Clostridium butyricum 5521]
 gi|237666579|ref|ZP_04526564.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum E4 str. BoNT E BL5262]
 gi|182376378|gb|EDT73960.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Clostridium butyricum 5521]
 gi|237657778|gb|EEP55333.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum E4 str. BoNT E BL5262]
          Length = 301

 Score =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 75/326 (23%), Positives = 142/326 (43%), Gaps = 31/326 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS++       V   EE  ++  + K     ++   ++      ++ V+   VK N  I 
Sbjct: 1   MSILEKK----VTGIEEGTKIREYLKMEM-GLSTRLIRSASIDKRIFVNDIPVKMNRVIN 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+V++I    +    I  E+               +   ++YED  I V NK   + V 
Sbjct: 56  EGEVIKIDLAKDESQDIAPEK---------------MDIEIIYEDEDILVVNKKPFMVVH 100

Query: 121 GGSGIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                    +   + ++    GQ    RL  RLD  TSG++++A+ + +   L++     
Sbjct: 101 PTKSYQSGTLANGVINYFMESGQNCIVRLVSRLDMNTSGLIIIAKNQFSHGMLSKEMTEN 160

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           ++ K Y ++V GI +N++  I   + +   I    + +V +       +I+H+KVI+ + 
Sbjct: 161 KVTKRYLAVVHGILENEEGTIDRPIYRPEGIDFGIMRIVDER---GQRSITHYKVIEKY- 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    +E    TGRTHQ+RVH   +G PI GD  Y +   G+    + ++  LHA  +D 
Sbjct: 217 ENASLVECTLETGRTHQIRVHLSSIGHPIYGDSLYGS---GDEEQDLISRQALHAYSLDF 273

Query: 298 PHPEGGRL-QITAPLPAHMVKTWDSL 322
             P  G +  + + LP  +    + +
Sbjct: 274 RSPRTGEILSLKSNLPEDIKTLIEKI 299


>gi|298530973|ref|ZP_07018374.1| pseudouridine synthase, RluA family [Desulfonatronospira
           thiodismutans ASO3-1]
 gi|298508996|gb|EFI32901.1| pseudouridine synthase, RluA family [Desulfonatronospira
           thiodismutans ASO3-1]
          Length = 535

 Score =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 82/333 (24%), Positives = 141/333 (42%), Gaps = 38/333 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHI--NFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           M       V+  +   RLDR    + P    +   +Q  +R G + +D     K  +++ 
Sbjct: 1   MGEELLFTVQESQAGSRLDRLVMQNIPRPAPSRSRVQDWIRKGNILLDGTVCLKPAHKLS 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +GQ V++                L    N        K  ++Y D ++ V NKPAG+SV 
Sbjct: 61  AGQTVQV----------------LAREENEDLEPVAGKLDIVYMDREMVVLNKPAGLSVH 104

Query: 121 GGSGI-AYHIDGFLKS-----WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             S   A  +  +L        + +  Q+P + HRLD++T+G++V A  + A + L   F
Sbjct: 105 PSSSDPAPTLVHYLLYACPGLRLMTDRQRPGIVHRLDKDTTGLMVAALNQEAKEDLAGQF 164

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             RR+ K Y +LV G  K  +  I   L +                +    A + +KV+ 
Sbjct: 165 AGRRVHKTYLALVCGALKQDEGIINVPLARDQQ-----SRARVAPSREGRSARTAYKVLK 219

Query: 235 CFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQNK 287
                 +  +++Q  TGRTHQ+RVH  H+  P++GD  Y         +K  F S +  +
Sbjct: 220 RDPSGLWSLVQVQIFTGRTHQIRVHFSHLNHPVLGDRIYGGTDWDRFGWKKRFLSRLAKR 279

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
             LH+  + + HP   + L+  +  P   ++T 
Sbjct: 280 QLLHSSCLGIMHPVSRQWLEFISRPPRDFIRTL 312


>gi|108800058|ref|YP_640255.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           MCS]
 gi|119869184|ref|YP_939136.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           KMS]
 gi|108770477|gb|ABG09199.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           MCS]
 gi|119695273|gb|ABL92346.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           KMS]
          Length = 304

 Score =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 80/319 (25%), Positives = 137/319 (42%), Gaps = 28/319 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V      MR+D         ++      I   G V +D      ++R+ +G  + +    
Sbjct: 3   VPEGLGGMRVDAGLSRLL-GLSRTAAAAIAEDGGVDIDGAPAGKSDRLTAGAWLEVR--- 58

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
                 + E      +  +          +LY D  I   +KP G++     G     + 
Sbjct: 59  ------LPEAPPPVENTPVEIEG----MAVLYSDDDIVAVDKPPGVAAHATVGWHGPTVL 108

Query: 131 GFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R ++K Y +
Sbjct: 109 GGLAAAGFRISTSGIHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQRTVEKRYHA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G P      I   + +  H G D+   V    +G  ++++H+  ++ F Q    L++
Sbjct: 169 LVQGHPDPSSGTIDAPIGR--HRGHDWKFAVT---EGGRHSVTHYDTLEAF-QAASLLDI 222

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
           +  TGRTHQ+RVH   +  P  GD  Y A+        ++ + +LHAR +   HP +G R
Sbjct: 223 ELETGRTHQIRVHFAALHHPCCGDLTYGADPTLARRLGLE-RQWLHARSLAFAHPADGRR 281

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++IT+P PA +    D L 
Sbjct: 282 IEITSPYPADLQHALDVLR 300


>gi|310640966|ref|YP_003945724.1| pseudouridine synthase, rlua family protein [Paenibacillus polymyxa
           SC2]
 gi|309245916|gb|ADO55483.1| pseudouridine synthase, RluA family protein [Paenibacillus polymyxa
           SC2]
          Length = 319

 Score =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 86/341 (25%), Positives = 151/341 (44%), Gaps = 40/341 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRI 59
           MSL       ++  +EE M L    +    +I+   + K+ L    + ++  RV  + ++
Sbjct: 1   MSLYYEPIVYMIPPEEEGMLLKTILQKRM-NISRKLISKLKLTEQGIMLNGIRVYISVKV 59

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +SG  V I       + I+ E                +   +L+ED  + V NK AG+ V
Sbjct: 60  KSGDRVEIRMERERSDDILPEP---------------IPFEILFEDEHLLVVNKAAGMVV 104

Query: 120 QGGSGIAYHIDGFLK----SWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G   H  G L      +  +KG+  + R  HRLDQET+G+LVVA+     QH++E 
Sbjct: 105 HPTHG---HYTGTLANGVVHYWQAKGELFRFRPVHRLDQETTGVLVVAKNPYVHQHISEQ 161

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
                + K Y +LV G P+ ++  +   + +        +            A++ +K+ 
Sbjct: 162 MIAGTVDKRYTALVHGRPQQQEGRVDGPIDRNPDNPHLRMV-----TPDGYPALTLYKLE 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------- 286
           + ++     + ++  +GRTHQ+RVH  ++GCP++GD  Y           + +       
Sbjct: 217 EVWSGG-SRIGLKLESGRTHQIRVHMTYIGCPLIGDKMYRITPNDAVQRELYDQLDARMP 275

Query: 287 KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
           +  LHA  + L HP  G R+   APLP  M++  + L  +Y
Sbjct: 276 RQALHASELSLVHPVTGERMTFYAPLPDDMIRMQELLRAQY 316


>gi|221638823|ref|YP_002525085.1| Ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides KD131]
 gi|221159604|gb|ACM00584.1| Ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides KD131]
          Length = 322

 Score =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 130/324 (40%), Gaps = 49/324 (15%)

Query: 32  INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           ++   L K++  G VR++   V     ++  GQV  I                LD+   +
Sbjct: 10  LSRSRLMKLIGEGAVRLEGAPVTDPKAKVAEGQVYEI---------------ALDAPAEV 54

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG-----QK 143
               + +   +++ED  + V +KP G+ V    G      ++  L    +S       ++
Sbjct: 55  EARPEAIPLSVVWEDEDLIVIDKPVGMVVHPAPGQWTGTLVNALLHHCGESLSGIGGEKR 114

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN---------- 193
           P + HR+D++TSG+LVVA+T  A Q L   F    +++ Y +LV G+P+           
Sbjct: 115 PGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRYLALVHGVPEVSDPRLRGVRG 174

Query: 194 ---KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPH 248
              +   +       +    D        E G  +A++  ++++ F        +E +  
Sbjct: 175 TSFEPGGVLRIATGLARHRTDRQRQAVTFE-GGRHAVTRARLLERFGMPPVLALVECRLE 233

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFTSPIQNKLYLHARYMDLPH 299
           TGRTHQ+RVH  H G  ++GD  Y    K                  +  LHA  +   H
Sbjct: 234 TGRTHQIRVHMAHAGHGLIGDQTYGGRRKLSPKALGPEAAAAVEAFPRQALHAASLGFRH 293

Query: 300 P-EGGRLQITAPLPAHMVKTWDSL 322
           P  G  L   +PLPA M      L
Sbjct: 294 PVSGEELSFESPLPADMAGLLSLL 317


>gi|260589549|ref|ZP_05855462.1| ribosomal large subunit pseudouridine synthase D [Blautia hansenii
           DSM 20583]
 gi|331082975|ref|ZP_08332095.1| hypothetical protein HMPREF0992_01019 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540117|gb|EEX20686.1| ribosomal large subunit pseudouridine synthase D [Blautia hansenii
           DSM 20583]
 gi|330399970|gb|EGG79628.1| hypothetical protein HMPREF0992_01019 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 294

 Score =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 67/321 (20%), Positives = 146/321 (45%), Gaps = 32/321 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M  +    +  +     +  + K+     +   + ++ +    + V+ +       ++  
Sbjct: 1   MNRIFQYTITKENLPCTVGEFLKS--KEFSRQIIIQLKKTQKGILVNNEWAYVRTPLKVN 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +V I              ++L+ + +       L   ++YED  I + NKPA + V   
Sbjct: 59  DIVTI--------------RLLEEAPSEHIVPVALPLDIVYEDEDILLVNKPADMPVHPS 104

Query: 123 -SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            +     +   +  +   +G+    R  +RLD++T+G+L++A+   +A  L+   + R I
Sbjct: 105 INNYDNTLANGIAHYYQVQGETFVFRCINRLDRDTTGLLIIAKNALSASILSNQMKAREI 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V+GIPK + + I   + +K +   +       +      A+++++V+    + 
Sbjct: 165 HRTYLAVVFGIPKKEADTITAPIARKENSAIER----CVDFINGERAVTNYQVVASK-ED 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  L++   TGRTHQ+RVHA +MG P++GD+ Y  +F          ++ LH+  +   H
Sbjct: 220 YSLLKLSLETGRTHQIRVHAKYMGNPLLGDYLYNPDFSR------IQRVALHSYSLSFIH 273

Query: 300 PEGGR-LQITAPLPAHMVKTW 319
           P  G+ ++ +APLP  M   +
Sbjct: 274 PLTGQPMKFSAPLPEDMASLF 294


>gi|68535841|ref|YP_250546.1| pseudouridylate synthase [Corynebacterium jeikeium K411]
 gi|68263440|emb|CAI36928.1| pseudouridylate synthase [Corynebacterium jeikeium K411]
          Length = 323

 Score =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 69/318 (21%), Positives = 132/318 (41%), Gaps = 26/318 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +    MR+D         ++   + ++   G +  D+  V  ++R+ +G  + +    
Sbjct: 10  VPDGLAGMRVDSGLSKLL-GLSRTAVAELAADGDILQDQAPVGKSDRLVAGAWLDVTLPA 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHID 130
              +   +  + ++               +LY D  + V +KP G++     G     + 
Sbjct: 69  PPRDLAAEPARHVEG------------MDILYSDEDVIVVDKPVGVAAHPTVGWEGPTVT 116

Query: 131 GFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             L +           ++  +  RLD  TSG+++VA +  A   L  +FR R + K Y +
Sbjct: 117 SGLAAAGFRISTSGPPERKGIVQRLDVGTSGVMIVAASERAYTVLKNAFRDREVSKTYHA 176

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G P      I   + +    G  +        +   +AI+H+  ++   ++   LE+
Sbjct: 177 LVQGHPDPTSGTIDAPIGRHPSAGWRFSVR-----EDGKHAITHYDTLEAH-RQASLLEV 230

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +  TGRTHQ+RVH   +  P+ GD  Y ++ K      +  + +LHA  +  PHP+G   
Sbjct: 231 KLETGRTHQIRVHFSALHHPLCGDPMYGSDPKLAERLGLI-RQWLHAVELGFPHPDGSWK 289

Query: 306 QITAPLPAHMVKTWDSLG 323
            + +P P  +    D L 
Sbjct: 290 TVRSPYPEDLQLALDRLR 307


>gi|197120482|ref|YP_002132433.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196170331|gb|ACG71304.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 339

 Score =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 84/330 (25%), Positives = 150/330 (45%), Gaps = 24/330 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + V  D    RLD+  +     +   ++ K+ R+ +VRV+ +R K +  +  G VV 
Sbjct: 1   MIQLTVTADAAGQRLDKLVRKALRDVPLSHVYKMFRTRKVRVNGQRGKADQLVAEGDVVV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I           +E+ +  ++      +  +   +L+ED+ +   +KPAG++   G+GI 
Sbjct: 61  I--------RGDEERLLAKAAPAAPGGAPRVTFGVLHEDADLLAVDKPAGLAAHPGTGIE 112

Query: 127 -YHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR- 178
              +    + ++ +         KP   HRLD++TSG+++VA+ R A   LTE+F     
Sbjct: 113 GATLVEMARGYLRTPDDLPPTEFKPSPAHRLDRDTSGVVLVAKHRKAMVRLTETFTSGEG 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y +LV G    +   I   L +                     A++ +KV+   A+
Sbjct: 173 VHKTYLALVKGKMPREAGTIDLPLSEHEQTSRSKALR----GVNFQEALTRWKVVSA-AK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMD 296
           +   L +   TGRTHQ+R H   +G P+ GD +Y   A  +   T     ++ LHA  ++
Sbjct: 228 EISLLAVTIETGRTHQIRRHLEAVGHPVAGDRRYGDFAFNRTARTRWGLRRMGLHAWKLE 287

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           +PHP  G  L++ AP PA + +       K
Sbjct: 288 VPHPLTGAPLRLEAPFPAELAEVLSRANLK 317


>gi|16125533|ref|NP_420097.1| ribosomal large subunit pseudouridine synthase D [Caulobacter
           crescentus CB15]
 gi|221234280|ref|YP_002516716.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus NA1000]
 gi|13422619|gb|AAK23265.1| ribosomal large subunit pseudouridine synthase D [Caulobacter
           crescentus CB15]
 gi|220963452|gb|ACL94808.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus NA1000]
          Length = 270

 Score =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 84/251 (33%), Positives = 130/251 (51%), Gaps = 4/251 (1%)

Query: 79  KEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            + K  ++ + LT       +S +LYED  I V NKPAG+S QGG   A+ +D  L ++ 
Sbjct: 13  AKPKASETPIALTPDEIAAAQSWVLYEDETIIVLNKPAGLSSQGGRIKAHTLDDLLWAFA 72

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +P+L HRLD++TSG+++ A+T+ AA  L ++   +R +K Y ++V G P+ K   
Sbjct: 73  RPNRPRPKLVHRLDRDTSGVILTAKTKPAAAMLGKALEAKRFRKSYLAIVAGAPEPKGGM 132

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I + L ++S     Y+ V + +   A  A S ++ +         +E+ P TGR HQLRV
Sbjct: 133 IDSPLRRESIGREAYMRVCEPDHPDAETARSRYRTLAHNGL-AALVELSPDTGRMHQLRV 191

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
           H   +G P+ GD +Y              +L LHA  +  PHP GG  +I APLP   V 
Sbjct: 192 HMASIGRPLAGDSRYGGAL--MLGGVPAPRLMLHAASLAFPHPLGGERKILAPLPPDFVS 249

Query: 318 TWDSLGFKYDR 328
             ++LG     
Sbjct: 250 MLEALGLPVPE 260


>gi|111018085|ref|YP_701057.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
 gi|110817615|gb|ABG92899.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
          Length = 302

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 79/320 (24%), Positives = 140/320 (43%), Gaps = 30/320 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +  E MR+D         ++   + ++   G V VD   V  ++R+ +G  + +    
Sbjct: 3   VPDGLEAMRVDAGLARLL-GLSRTAVAQLTEEGSVLVDGAPVGKSDRLSAGAWLEV---- 57

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG-IAYHI 129
                     ++ +    LT  ++ ++ + +LY D  +   +KP G++     G     +
Sbjct: 58  ----------ELPEPPRPLTIEAEPVEGMEILYADDDVVAVDKPVGVAAHASVGWTGPTV 107

Query: 130 DGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R I K Y 
Sbjct: 108 IGGLAAAGFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTLLKRAFKQRTIDKRYH 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G P      I   + +  H   D+   V  +      +I+H+  ++ F Q    L+
Sbjct: 168 ALVQGHPDPSSGTIDAPIGR--HRSNDWKFAVTAD---GKPSITHYDTVEAF-QAASLLD 221

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TGRTHQ+RVH   +  P  GD  Y A+ +      ++ + +LHAR +   HP  GR
Sbjct: 222 IHLETGRTHQIRVHFAALRHPCCGDLTYGADPRLAERLGLE-RQWLHARSLGFAHPADGR 280

Query: 305 -LQITAPLPAHMVKTWDSLG 323
            ++IT+  P  +      L 
Sbjct: 281 WVEITSKYPKDLEDALGVLR 300


>gi|240167932|ref|ZP_04746591.1| RluA family pseudouridine synthase [Mycobacterium kansasii ATCC
           12478]
          Length = 308

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 78/326 (23%), Positives = 144/326 (44%), Gaps = 30/326 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V      +R+D         ++   +  I   G V++D      ++R+ SG  +++
Sbjct: 4   RSMPVPEGLAGLRVDAGLARLL-GLSRSAVAAIAEGGGVQLDGVPAGKSDRLTSGAWLQV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG-I 125
                         ++ ++   L      ++ + +LY D  I   +KPA ++     G  
Sbjct: 63  --------------RLPEAPPPLENTPVDIEGMTILYSDDDIVAVDKPAAVAAHASVGWT 108

Query: 126 AYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R ++
Sbjct: 109 GPTVLGGLAAAGYRITTSGVHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKHRTVE 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G P      I   + +  H G ++   V  N     ++++H+  I+ F    
Sbjct: 169 KRYHALVQGHPDPSSGTIDAPIGR--HPGPEWKFAVTTN---GRHSVTHYDTIEAFV-AA 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L+++  TGRTHQ+RVH   +  P  GD  Y A+ K      ++ + +LHAR +   HP
Sbjct: 223 SLLDIELETGRTHQIRVHFAALRHPCCGDLVYGADPKLAKKLGLE-RQWLHARSLAFAHP 281

Query: 301 -EGGRLQITAPLPAHMVKTWDSLGFK 325
            +G R++I +P P  +    D L  +
Sbjct: 282 ADGRRIEIVSPYPPDLQHALDVLRAE 307


>gi|302141717|emb|CBI18920.3| unnamed protein product [Vitis vinifera]
          Length = 433

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 86/367 (23%), Positives = 143/367 (38%), Gaps = 70/367 (19%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V +D   +RLD W  +    I+   +Q  +RSG V V+ + V K ++ I++G  V     
Sbjct: 70  VNSDSGKLRLDSWISSRIIGISRARVQSSIRSGLVSVNDRIVDKVSHVIRAGDKVNCT-- 127

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YH 128
                        +     L    + +   ++YED  + V NKPA + V    G A    
Sbjct: 128 -------------ISELQPLRAEPEDIPLDIVYEDEHVLVVNKPAHMVVHPAPGNASGTL 174

Query: 129 IDGFLKSW--------------------------------VDSKGQKPRLTHRLDQETSG 156
           ++G L                                         +P + HRLD+ TSG
Sbjct: 175 VNGILHHCSLPTVALPNRDSEEDDISDDEFNSFAAGQNCGTCETNIRPGIVHRLDKGTSG 234

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LVVA+   +  HL+E F++  I ++Y SL  G+P      +   + +  +       V 
Sbjct: 235 LLVVAKDEHSHAHLSEQFKLHSIHRVYISLTSGVPTPLSGRVEIPVGRDPNNRIRMTAVP 294

Query: 217 KQNEKG-ANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             +  G A +A S +KVI+   A     +E +  TGRTHQ+R HA ++G P++GD  Y  
Sbjct: 295 GPSNSGQARHAASRYKVIEILAAGGSALVEWRLETGRTHQIRAHAKYLGIPLLGDEVYGG 354

Query: 275 NFKGNFTSP-----------------IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
                 +                     ++  LHA  +   HP+ G+ +  +   P    
Sbjct: 355 TKNMALSLLRPRIPSSHHGQLAQLVSRLDRPCLHAVALGFNHPKTGKNVHFSCQPPEDFA 414

Query: 317 KTWDSLG 323
           +    L 
Sbjct: 415 EILSWLR 421


>gi|328759180|gb|EGF72796.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL025PA2]
          Length = 285

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 67/300 (22%), Positives = 128/300 (42%), Gaps = 28/300 (9%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
              ++   +  ++  G V ++ ++V + + R+ +GQ++ +          I  Q +    
Sbjct: 1   MSGVSRSRISSLIEDGGVFLNGQQVSRASVRVATGQMLDVDLCDPVATPSITPQIVE--- 57

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------IAYHIDGFLKSWVDSKG 141
                        ++++DS I V +KPAG++     G      + +              
Sbjct: 58  ----------GMRIIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTSGAP 107

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           ++  +  RLD  TSG++VVA++  A   L ++FR R + K+Y +LV G P      I   
Sbjct: 108 ERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTIDAP 167

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +          V      G  ++++H++ ++ F +    L++   TGRTHQ+RVH   
Sbjct: 168 IGRDHRHDWKMAIV-----DGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAA 221

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           +  P  GD  Y  +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 222 IKHPCCGDPLYGCDPALAKELGLE-RQWLHAGELSFTHPGSGEWVTFHADLPADLQNALD 280


>gi|167771608|ref|ZP_02443661.1| hypothetical protein ANACOL_02980 [Anaerotruncus colihominis DSM
           17241]
 gi|167666248|gb|EDS10378.1| hypothetical protein ANACOL_02980 [Anaerotruncus colihominis DSM
           17241]
          Length = 338

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 69/306 (22%), Positives = 133/306 (43%), Gaps = 24/306 (7%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           SL   ++   +  ++   R+D++     P +    L K +R+ +++++ KR + + R+ +
Sbjct: 13  SLEDVMREFQINGNDAGQRVDKFLTKAVPLLPQSMLYKAIRTKRIKLNGKRCEISTRLCT 72

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + +    +  +        L S   +          ++YED  I + NKPAG+ V  
Sbjct: 73  GDQLTLYLNDSFFDSRDGAFSFLRSPAAID---------IIYEDENILLVNKPAGLVVHE 123

Query: 122 GSGI----------AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
                          +  +  + +  +     P L +R+D+ T+GI++ A+  AA + L 
Sbjct: 124 DEHQSSDTLINRIQHHLYNCGVYNPAEENSFAPALCNRIDRNTAGIVIAAKNAAALRILN 183

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           E  + R +QK+Y  +V G    + + +  +L K +      V V           ++H++
Sbjct: 184 EKIKARELQKLYLCIVHGTMPKESDTLKAFLRKDARTN--TVAVYDHPIPDGRTILTHYR 241

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V+     +   LE+   TGRTHQ+R H  H+G P++GD KY  N   + T        L 
Sbjct: 242 VV-AQKDRLSLLEIDLLTGRTHQIRAHLAHIGHPLLGDAKYGRNRDNHKT--GLKHQALC 298

Query: 292 ARYMDL 297
           A  +  
Sbjct: 299 AYKLTF 304


>gi|42525117|ref|NP_970497.1| pseudouridylate synthase [Bdellovibrio bacteriovorus HD100]
 gi|39577328|emb|CAE81151.1| Pseudouridylate synthase [Bdellovibrio bacteriovorus HD100]
          Length = 319

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 83/336 (24%), Positives = 138/336 (41%), Gaps = 47/336 (13%)

Query: 17  ENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
             +RLD+      P I        +L S  V ++ K  K +  I+   ++ I        
Sbjct: 2   SGLRLDKAMA-LIPEIGTRSRASHLLESNSVLLNGKPAKASVAIKENDLIEIQ------- 53

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                   L            LK  +L+ED  + V NKPAG+ V   +G A+  D  + +
Sbjct: 54  --------LPEPEPTELQPFDLKLDVLFEDEDLIVINKPAGLVVHPAAGHAH--DTLVNA 103

Query: 136 WVDSKG--------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +            ++P + HRLD+ETSGI+V+A+   A + LT  F+ R   +IY+++ 
Sbjct: 104 LIHHTDDLSMKFGEERPGIVHRLDKETSGIIVIAKNDKAHESLTSQFKERSTHRIYYAVC 163

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG----------ANYAISHFKVIDCFA 237
            G  +     + ++L +       Y  V+  + K             +A++HF+V+   +
Sbjct: 164 LGTARTLSGSVRSFLARHPVDRKRYASVLGDDRKPLTDPNDDPGLGKWAVTHFEVLQRKS 223

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK--------GNFTSPIQNKLY 289
               +L+++  TGRTHQ+RVH    G PI GD  Y A+ K                 +  
Sbjct: 224 -GMSYLKLKLETGRTHQIRVHMSESGLPIAGDTLYGADRKIKSIEARATQEDLRTLPRFL 282

Query: 290 LHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF 324
           LHA  +   HP    R+  T   P  ++      G 
Sbjct: 283 LHAAELGFTHPRTKERMFFTKDWPEDVLVLIKKWGL 318


>gi|187934581|ref|YP_001884790.1| pseudouridine synthase, RluA family [Clostridium botulinum B str.
           Eklund 17B]
 gi|187722734|gb|ACD23955.1| pseudouridine synthase, RluA family [Clostridium botulinum B str.
           Eklund 17B]
          Length = 298

 Score =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 77/315 (24%), Positives = 139/315 (44%), Gaps = 29/315 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V N +  +++  + K     ++   ++   +  ++ V+   V+ N  I++G +++I    
Sbjct: 8   VSNIDGKIKIREYLKEKL-DLSTRLIRSASKDQRIYVNNSAVRMNYMIKNGDIIKIDLNR 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
           N   +I  E+  LD               ++YED  + V NK   I V          + 
Sbjct: 67  NESQNINPEKIDLD---------------IVYEDEDVLVINKQPFIIVHPTKNFQSGTLA 111

Query: 131 GFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             +  +     Q    RL  RLD  TSG++++A+ + +   L++  + + +QK Y ++V 
Sbjct: 112 NGILYYFQETNQNCIVRLVSRLDMNTSGLIIIAKNQFSHSRLSKDMKEK-LQKRYLAIVH 170

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  + K+  I   + K   I    + VV +       +I+H+KVI+ F      +E    
Sbjct: 171 GNLEEKEGTIDLPIYKPEGIEYGSMRVVDER---GQRSITHYKVIESFEGGD-LVECLLE 226

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           TGRTHQ+RVH  H+G PI GD  Y    + N    +  +  LHA  ++   P     L +
Sbjct: 227 TGRTHQIRVHLSHLGHPIYGDELYGVGAEEN----LIKRQALHAYGLNFASPRSLKELSL 282

Query: 308 TAPLPAHMVKTWDSL 322
            A LP  M +  + +
Sbjct: 283 RAELPDDMKELLEKI 297


>gi|330718578|ref|ZP_08313178.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc fallax KCTC
           3537]
          Length = 258

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 74/278 (26%), Positives = 125/278 (44%), Gaps = 35/278 (12%)

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
           K + ++  G ++ I P       I  E                +   ++YED  + V NK
Sbjct: 2   KQSYKVNKGDIIVITPPKVQATTIEPE---------------AIPLNIVYEDDDLLVVNK 46

Query: 114 PAGISVQGGSGIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRA 165
           P G+ V   +G   H  G L + +             +P + HR+D++TSG+L+VA+   
Sbjct: 47  PQGMVVHPSAG---HSSGTLVNALLHHAPLSTINGEFRPGIVHRIDRDTSGLLMVAKNDT 103

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           A Q L+   +  + Q+IY++LV G  K     +   + +   I      +V         
Sbjct: 104 AHQALSAQLKAHKNQRIYYALVRGEFKENSGTVNAPIARH-KIDRKKQAIVS----DGKP 158

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           A++HF+V+  +   +  L+++  TGRTHQ+RVH  ++G PIVGD  Y    K    +   
Sbjct: 159 AVTHFEVVQRYV-GYTLLKVRLETGRTHQIRVHMTYIGHPIVGDPVYGNAPK--MPNVTL 215

Query: 286 NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           +   LHA+ + L  P     L   +PLP +  +  D+L
Sbjct: 216 HGQLLHAKTLSLMQPTTQAELTFDSPLPVYFQQALDTL 253


>gi|110802739|ref|YP_699398.1| pseudouridylate synthase family protein, yabo [Clostridium
           perfringens SM101]
 gi|110683240|gb|ABG86610.1| pseudouridine synthase, RluA family [Clostridium perfringens SM101]
          Length = 298

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 140/332 (42%), Gaps = 41/332 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS++       +  + +  ++  + K     ++   ++      +++VD   VK N  ++
Sbjct: 1   MSILESK----ITKEYDKRKIREFLKEEL-GLSSRLIRSAAIDKRIKVDGVAVKMNYVVK 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ ++I        +I  E+               +   ++YEDS I V NK   + V 
Sbjct: 56  TGEEIKIELSKKESQNIEPEK---------------MDIEIVYEDSDILVLNKKPFMVVH 100

Query: 121 GGSGIAYHIDGFLKS----WVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                  H +G L +    +     Q    RL  RLD  TSG++++ + + A   L+   
Sbjct: 101 PTRS---HPNGTLANGILYYFKESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEM 157

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +  + QK Y ++V G  + K+  I   + + +      V      ++    +I+H+KVI+
Sbjct: 158 KTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV-----DERGQESITHYKVIE 212

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            +      +E    TGRTHQ+RVH   +G PI GD  Y             ++  LHA  
Sbjct: 213 SY-NGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTE-----DEEFISRQALHAYG 266

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +D   P+  + L + A LP  M +  + L  K
Sbjct: 267 LDFYSPKTKKSLSLRADLPEDMKELINKLKNK 298


>gi|54023755|ref|YP_117997.1| putative RNA pseudouridine synthase [Nocardia farcinica IFM 10152]
 gi|54015263|dbj|BAD56633.1| putative RNA pseudouridine synthase [Nocardia farcinica IFM 10152]
          Length = 308

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 143/328 (43%), Gaps = 30/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  + MR+D         ++   +  +   G V++D      ++R+ +G 
Sbjct: 1   MRETRAMPVPDGLDGMRVDAGLSRLL-GLSRTAVAALTAEGSVQLDGVPAGKSDRLTAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGG 122
            + +              +  +    LT  +  ++ + +LY D  I   +KP G++   G
Sbjct: 60  WLEV--------------EFPEPKRELTVEAAPVEGMKILYADDDIVAVDKPVGVAAHTG 105

Query: 123 SG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G     + G L +           ++  + HRLD  TSG++VVA++  A   L  +F+ 
Sbjct: 106 VGWSGPTVVGGLAAAGYRISTSGAHERQGIVHRLDVGTSGVMVVAQSEHAYTVLKRAFKQ 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K Y +LV G P      I   + +    G D+   V  +      +++H+  I+ F
Sbjct: 166 RTVSKRYHALVQGHPDPSSGTIDAPIGRAR--GNDWKFAVTAD---GRPSVTHYDTIEAF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q    L++   TGRTHQ+RVH   +  P  GD  Y A+ +      +Q + +LHAR + 
Sbjct: 221 -QAASLLDIHLETGRTHQIRVHFSAIRHPCCGDLTYGADPRLAERLGLQ-RQWLHARTLG 278

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  GR L+IT+  P  +    D L 
Sbjct: 279 FHHPADGRWLEITSEYPDDLRHALDVLR 306


>gi|289640971|ref|ZP_06473141.1| pseudouridine synthase, RluA family [Frankia symbiont of Datisca
           glomerata]
 gi|289509286|gb|EFD30215.1| pseudouridine synthase, RluA family [Frankia symbiont of Datisca
           glomerata]
          Length = 340

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 73/323 (22%), Positives = 138/323 (42%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  + +RLD      +  ++     +++  GQ  VD      ++R+ +G+ + +
Sbjct: 36  RALPVPDGLDGLRLDAVIARMF-GLSRTAAAQLVDDGQASVDGTVRGRSDRVGAGEWLDV 94

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                     +  + +                +++++D  I V +KP G++     G   
Sbjct: 95  RLPPPPNPVRVAAEPVP-------------GLLVIHDDDDIVVVSKPIGVAAHPAPGFTG 141

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  + HRLD  T+GI+VVA++  A   L  +FR R ++K
Sbjct: 142 PTVIGGLAAAGYRVATSGAAERQGVVHRLDVGTTGIMVVAKSERAYTALKRAFRDREVEK 201

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY +LV G P      +   + +     G +  V      G   +++H+   + F +   
Sbjct: 202 IYRALVQGHPDPSSGTVDAPIDRHPRKPGLFAVVA-----GGKPSVTHYDTEEAF-RAAS 255

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L ++  TGRTHQ+RVH   +  P VGD  Y A+        +  + +LHA  +   HP 
Sbjct: 256 LLSVRLETGRTHQIRVHMSALRHPCVGDLAYGADPVLAGRLGLA-RQWLHAAQLSFAHPA 314

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            GR +  T+P P  + +    L 
Sbjct: 315 DGRKVTFTSPDPPDLAEAVAVLR 337


>gi|219682312|ref|YP_002468696.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Tuc7 (Acyrthosiphon pisum)]
 gi|219622045|gb|ACL30201.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Tuc7 (Acyrthosiphon pisum)]
 gi|311086711|gb|ADP66792.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. TLW03 (Acyrthosiphon pisum)]
 gi|311087807|gb|ADP67886.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. JF98 (Acyrthosiphon pisum)]
          Length = 312

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 82/316 (25%), Positives = 138/316 (43%), Gaps = 35/316 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
              RLD      +   +   L+K++   QV V++  V + + +I  G+++ I P    L 
Sbjct: 16  SGQRLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKILGGEILTIHPFSKDLL 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFL 133
             I E   LD               ++YEDS I + NKPAG+ V  GSG       +  L
Sbjct: 76  VDIPENIFLD---------------IVYEDSDILIINKPAGLVVHPGSGNKSGTILNALL 120

Query: 134 KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             + +SK   +  + HRLD++TSG++V+A+   +  HL    + ++I + Y  +V G   
Sbjct: 121 YHYKNSKDLPRAGIVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGIVHGKMI 180

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I   +++  +                  +++H+KV+  F +    + ++  TGRT
Sbjct: 181 A-GGTINKPIMRHYN-----RRTCMMVHHLGKPSVTHYKVLSRF-KFHTHIAIRLETGRT 233

Query: 253 HQLRVHALHMGCPIVGDHKYCA--------NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           HQ+RVH LH+  P+VGD  Y            K         +  LHA ++ L HP    
Sbjct: 234 HQIRVHMLHIKYPLVGDPCYSGFKIQSNYRKDKKTNKIYKFPRQALHANHLSLHHPIKKN 293

Query: 305 -LQITAPLPAHMVKTW 319
            +  T PLP  + +  
Sbjct: 294 VMSWTVPLPQDIQELL 309


>gi|150020811|ref|YP_001306165.1| RluA family pseudouridine synthase [Thermosipho melanesiensis
           BI429]
 gi|149793332|gb|ABR30780.1| pseudouridine synthase, RluA family [Thermosipho melanesiensis
           BI429]
          Length = 293

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 85/323 (26%), Positives = 133/323 (41%), Gaps = 38/323 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           ++V  +    RLD++ +    ++    + KI+R G+V V+ KRVK  + R++ G  + I 
Sbjct: 1   MIVNENNYYSRLDKFLRKQLQNMPLSAIYKIIRKGKVLVNGKRVKEPSFRLEIGDEIEIK 60

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-Y 127
                 N     Q I             +   +LYED  + + NKPAGI +  G G    
Sbjct: 61  EETTKYNREKNNQII----------PIKMDFEILYEDENLLIINKPAGIPIHPGKGTHIA 110

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L  +       P L HRLD+ TSG+ VVA+    A+ L E    R ++K+Y +L 
Sbjct: 111 TLIEGLMYYGKEHNFTPYLVHRLDKHTSGVFVVAKNVNTARELNEIISSRAVEKVYTTLC 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLE 244
            G  K K E I   L                       A++ ++    F      F  L 
Sbjct: 171 VGEMK-KSEVIKIPL-------------------DGKNAVTIYEKQKQFKSGLGYFSLLR 210

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEG 302
           +Q  TGR HQ+R H   +G P++GD  Y                + +LH   M L +   
Sbjct: 211 VQIKTGRKHQIRKHLSLIGHPVIGDDLYGDKKLNRKFKQKYALKRYFLHCSMMLLYY-ND 269

Query: 303 GRLQITAPLPAHMVKTWDSLGFK 325
             ++I APLP  +     +L  +
Sbjct: 270 KEIRINAPLPNDLKDVLKNLKME 292


>gi|157803478|ref|YP_001492027.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           canadensis str. McKiel]
 gi|157784741|gb|ABV73242.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           canadensis str. McKiel]
          Length = 303

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 86/301 (28%), Positives = 151/301 (50%), Gaps = 11/301 (3%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD++ K  YP +    ++K LR  Q+ V+ ++ + + R+  G  + I    N      +
Sbjct: 12  RLDKYLKRLYPLLTQGVIEKALRQKQIIVNARKAEASLRVIDGDKIFISDKFNLPVKQPE 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +    D+ + L K        L+YED  +   NKPAG++ QGGS I   ID  LK +++ 
Sbjct: 72  KLVFTDAEIKLAKK--ITTDYLIYEDDNLIAINKPAGLATQGGSKINLSIDSALK-YLNY 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           KG   +L HRLD+ETSG+L++A+   ++    ++F+ + + K Y+++ +G P      + 
Sbjct: 129 KGADFKLVHRLDKETSGLLLIAKNYLSSIKFHDAFKDKLVVKTYFAVTYGKPIKNVGEVR 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + + K     G    +   + +    AI+++K++         +E  P TG+ HQLR+HA
Sbjct: 189 SNIEKSK---GSTRKITDIDSENGKLAITYYKLLKSLDNNLFLIEFTPITGKMHQLRLHA 245

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
             +GCPI+GD KY          P    ++LHA ++ L     G  + + A LP +  + 
Sbjct: 246 KLLGCPILGDDKYG----NKEIMPYSQYMFLHANHICLSEKVFGTEINLEAKLPFYFTRR 301

Query: 319 W 319
            
Sbjct: 302 L 302


>gi|239917851|ref|YP_002957409.1| ribosomal large subunit pseudouridine synthase D [Micrococcus
           luteus NCTC 2665]
 gi|239839058|gb|ACS30855.1| ribosomal large subunit pseudouridine synthase D [Micrococcus
           luteus NCTC 2665]
          Length = 320

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 75/334 (22%), Positives = 144/334 (43%), Gaps = 34/334 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD------KKRVKFNNRIQ 60
            + + V   E   R+D    + +  ++   L      G VR +       + +  + +  
Sbjct: 8   TERLQVAEAEAGRRVDAVLADAF-GVSRSLLADWFSRGLVRAESRSGRRDRVLAKSAKAV 66

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ + +    +     ++ +++   S             +LYED  +   +KP G++  
Sbjct: 67  AGETLAVDVPDDPDPLEVRAERVDALS-------------ILYEDDDLVAVDKPTGVAAH 113

Query: 121 GGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G +   + G L +           ++  + HRLD  T+G++VVA+T  A   + + F
Sbjct: 114 PSPGWVGPTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQF 173

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R  +K+Y ++V GIP      +   + +  H G  +   V  +      +++H++ ++
Sbjct: 174 RERVPEKVYHAVVQGIPDPLSGTVDAPIGR--HPGHHWKFAVLDD---GRPSVTHYETLE 228

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F +    LE+   TGRTHQ+RVH   +  P VGD  Y A+ +      +  + +LHA  
Sbjct: 229 VFGRG-TLLEVHLETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGL-TRQWLHAHR 286

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           +  PHP  G  + IT+P P  +     +L    D
Sbjct: 287 LAFPHPVTGEPVTITSPYPDDLAHALAALRGDED 320


>gi|294668132|ref|ZP_06733239.1| ribosomal large subunit pseudouridine synthase [Neisseria elongata
           subsp. glycolytica ATCC 29315]
 gi|291309840|gb|EFE51083.1| ribosomal large subunit pseudouridine synthase [Neisseria elongata
           subsp. glycolytica ATCC 29315]
          Length = 297

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 89/297 (29%), Positives = 149/297 (50%), Gaps = 23/297 (7%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +   ++ +I+R+G+VR++KKR K ++RIQ+G ++RIPPV  A      E +   +     
Sbjct: 1   MPKSHIHRIIRAGEVRLNKKRCKPDSRIQTGDLLRIPPVRTAEKQRPSENRAQAAPAR-- 58

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                 +  ++YED  + V +KPAG +V GGSG+++ +   ++     + +   L HRLD
Sbjct: 59  ------EFTIIYEDDALLVIDKPAGTAVHGGSGVSFGVIEQIRRAR-PEARYLELVHRLD 111

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG+L++A+ R A   L E+ R    QKIY +L  G   N    +   L K +   G+
Sbjct: 112 KDTSGLLMIAKKRNALVKLHEAIRNDHPQKIYLALGVGKLPNDSFHVKLPLFKYTGAQGE 171

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQK---------FCWLEMQPHTGRTHQLRVHALHM 262
            +  V ++      A + F+V++ F+              ++    TGRTHQ+RVH    
Sbjct: 172 KMVRVSED---GQSAHTIFRVLNRFSDGLLHQVGLSHLTLVQATLKTGRTHQIRVHLQSQ 228

Query: 263 GCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
            CPI GD +Y               +++LHA  + L HP  G  L + A LP  + +
Sbjct: 229 QCPIAGDERYGDYQANKRLQKLGLKRMFLHAAELHLDHPLTGEPLHLKAELPQELAQ 285


>gi|238060235|ref|ZP_04604944.1| 50S ribosomal pseudouridine synthase D [Micromonospora sp. ATCC
           39149]
 gi|237882046|gb|EEP70874.1| 50S ribosomal pseudouridine synthase D [Micromonospora sp. ATCC
           39149]
          Length = 311

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 73/323 (22%), Positives = 139/323 (43%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  + MRLD+     +  ++      ++ +G   VD      ++++++G  + +
Sbjct: 9   RSLPVPDGLDGMRLDQAVSRLF-GLSRTAAANLVDAGDALVDGVARPNSHKVKTGSWLDV 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                A    +  Q +                 ++Y D  I V +KP G++     G   
Sbjct: 68  TLPTPAAPPTMVPQAVP-------------GLTVVYADDDIVVVDKPVGVAAHPSPGWTG 114

Query: 127 YHIDGFLK---SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L      + + G  ++  + HRLD  T+GI+VVA++  A   L  +F+ R ++K
Sbjct: 115 PTVIGGLAGIGHRISTSGAAERQGVVHRLDVGTTGIMVVAKSEQAYTALKRAFKYREVEK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G P   +  I   + +  H    +  V      G   +I+H+  ++ F     
Sbjct: 175 RYHAVVQGHPDPLRGTIDAPIDRHPHHDYRWAVVS-----GGKPSITHYDTLEAFPS-AS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L+++  TGRTHQ+RVH   +  P VGD  Y A+   +    +  + +LHAR +   HP 
Sbjct: 229 LLDVRLETGRTHQIRVHFSSLRHPCVGDVTYGADPTLSARLGL-GRQWLHARSLSFLHPR 287

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G  +   +  P  + +    L 
Sbjct: 288 TGDEVTFVSDYPDDLDRALRILR 310


>gi|225389034|ref|ZP_03758758.1| hypothetical protein CLOSTASPAR_02779 [Clostridium asparagiforme
           DSM 15981]
 gi|225044909|gb|EEG55155.1| hypothetical protein CLOSTASPAR_02779 [Clostridium asparagiforme
           DSM 15981]
          Length = 342

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 77/331 (23%), Positives = 138/331 (41%), Gaps = 27/331 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q ++V  +E   RLD+    +        L K++R   + ++ K+   + R+  G  +R
Sbjct: 1   MQTLIVTPNEAGQRLDKLLAKYMNQAGKGFLYKMMRKKNITLNGKKCDGSERLGEGDEIR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +            S        + K  ++YEDS I V NKPAG+  Q      
Sbjct: 61  LFLADETIAKFTGGGAAKPIS------GYYPKPDIIYEDSHILVVNKPAGLLSQKAREDD 114

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             ++  + +++   G+         +P + +RLD+ TSG++V  R+ A  Q +   F+ R
Sbjct: 115 TSLNEAILNYLIDSGRMPVEQLRTFRPSICNRLDRNTSGLVVAGRSLAGLQVMNAVFKDR 174

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I K Y  +V G  K K+  IA +L K      + V +     + +   ++ +  +  + 
Sbjct: 175 SIHKYYQCIVKGSLKEKQ-LIAGFLRKDE--ASNTVDIYPLEVENSVPIMTEYLPL-AWG 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
             F  L++   TGR+HQ+R H   +G PI+GD KY                   LH+  +
Sbjct: 231 GGFTLLQVTLITGRSHQIRAHLASIGHPILGDFKYGDRSVNEEMKKRYGLRAQLLHSWKL 290

Query: 296 DLPHPEGGRL------QITAPLPAHMVKTWD 320
            +P      L      +  APLP    +  +
Sbjct: 291 VMPEDLAVPLDYLAGREFFAPLPEKFNRVLE 321


>gi|168212841|ref|ZP_02638466.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE
           str. F4969]
 gi|170715523|gb|EDT27705.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE
           str. F4969]
          Length = 298

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 139/332 (41%), Gaps = 41/332 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS++       +  + +  ++  + K     ++   ++      +++VD   VK N  ++
Sbjct: 1   MSILESK----ITKEYDKRKIREFLKEEL-GLSSRLIRSAAIDKRIKVDGVAVKMNYVVK 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ ++I        +I  E+               +   ++YEDS I V NK   + V 
Sbjct: 56  TGEEIKIELSKKESQNIEPEK---------------MDIEIVYEDSDILVLNKKPFMVVH 100

Query: 121 GGSGIAYHIDGFLKS----WVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                  H +G L +    +     Q    RL  RLD  TSG++++ + + A   L+   
Sbjct: 101 PTRS---HPNGTLANGILYYFKESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEM 157

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +  + QK Y ++V G  + K+  I   + + +      V      ++    +I+H+KVI+
Sbjct: 158 KTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV-----DERGQESITHYKVIE 212

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            +      +E    TGRTHQ+RVH   +G PI GD  Y             ++  LHA  
Sbjct: 213 SY-NGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTE-----DEEFISRQALHAYG 266

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +D   P+    L + A LP  M +  + L  K
Sbjct: 267 LDFYSPKTKEPLSLRADLPEDMKELINKLKNK 298


>gi|262199978|ref|YP_003271187.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262083325|gb|ACY19294.1| pseudouridine synthase, RluA family [Haliangium ochraceum DSM
           14365]
          Length = 303

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 83/317 (26%), Positives = 142/317 (44%), Gaps = 31/317 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           MS+        V +++   RLD+      P ++    + +L  G V VD+ RVK  + ++
Sbjct: 1   MSIRARTVRFEVADEDVGKRLDQLLAARVPELSRRMARTLLDIGGVFVDRTRVKVASRKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + GQ V +         + +  K +             +  +++ED  + V +KPAG+  
Sbjct: 61  RPGQSVEVHLG----GALERATKEVGKEARKRDSRALPRFKIVFEDRDLVVVDKPAGLLS 116

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                      G L + +  + ++  + HR+D +TSG+LV A+TR A QHL+E FR  +I
Sbjct: 117 APTP---ESDLGNLAALLRERRERVYVVHRIDLQTSGLLVFAKTRRANQHLSERFREHQI 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y ++V G P      I   L                       A +H +V+    ++
Sbjct: 174 ERAYTAVVAGAPVEDTFTIDLPLR-------------------GRRATTHLQVLQRIGER 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+ +  TGRTHQ+R+H L  G P++GD +Y        T P   ++ LHAR +   H
Sbjct: 215 AAVLDARLETGRTHQIRLHCLQRGYPVLGDPQYGERMSDELTPP---RMALHARVLGFEH 271

Query: 300 PEGGR-LQITAPLPAHM 315
           P  G   +  + LPA +
Sbjct: 272 PRSGEARRFESELPADL 288


>gi|88658198|ref|YP_507572.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           chaffeensis str. Arkansas]
 gi|88599655|gb|ABD45124.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           chaffeensis str. Arkansas]
          Length = 307

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 98/322 (30%), Positives = 169/322 (52%), Gaps = 21/322 (6%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +M+  +Y +VE D+ N+R+D++ +     I    ++K LR G V +D  +VK + RI++G
Sbjct: 1   MMS--KYYIVEEDDHNIRIDKFIRRILK-IPQSLVEKFLRKGVVLLDNTKVKSDVRIKAG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKH--SDFLKSILLYEDSKIYVFNKPAGISVQ 120
            V+ +       + +I E+K +              +++ ++YED  + + NKPAGISVQ
Sbjct: 58  NVICV-----RYDRVIYERKQIRKICKADSDFLVHLIRNSVVYEDDDVLIINKPAGISVQ 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GG+ +   I   +    D +  K  + HRLD++TSGIL++AR    ++ +   F+ RR++
Sbjct: 113 GGTKVKISISDIVDKIRDGESMK--IVHRLDKDTSGILMLARNARISRLIMHEFKNRRVE 170

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +L  GIPKN    I + ++K        + + K N+     A++ F V+       
Sbjct: 171 KKYLALTQGIPKNDIGQINHSIIKN----KRSLSLDKVNDSYLQEAVTSFSVLKKLPYGI 226

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE++P TGR HQ+R+H  H+GC I+GD KY    +      +Q    LHA ++ +   
Sbjct: 227 GLLELKPITGRKHQIRIHLSHIGCSIIGDKKYGKFCEHVLNDNLQ----LHAYFLSINIG 282

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
           E  ++  T P+P++M      L
Sbjct: 283 E-KKIDFTVPVPSYMKDAIMQL 303


>gi|239826305|ref|YP_002948929.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239806598|gb|ACS23663.1| pseudouridine synthase, RluA family [Geobacillus sp. WCH70]
          Length = 298

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 67/319 (21%), Positives = 140/319 (43%), Gaps = 39/319 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +   EE   +  + K     I+   L  I    G + VD++ V   +R+  G+ +R+  
Sbjct: 9   TITEKEEGKLVREFLKEQ--GISKTALTDIKFHGGAIFVDEQPVTVRHRLCCGETLRVLF 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSG 124
              + +  +                + +   ++YED  + V NKP  ++        G  
Sbjct: 67  PKESPSEGM--------------MPEAIPLDIVYEDEYVLVVNKPPFMATIPSREHPGGT 112

Query: 125 IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +A   +  L  +   + +    +  RLD++TSG+++VA+ R     L+   +  ++ + Y
Sbjct: 113 LA---NALLYHYKKQQLESTIHVVTRLDRDTSGLVLVAKHRHVHHLLSTLQQQGKVTRCY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++  G     +  I   + +KS        + ++  K    A++HF+V+  F +++ ++
Sbjct: 170 EAICHGCLVEDEGTIDAPIARKSD-----SIIEREVRKDGQRAVTHFRVLQRF-REYTYV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++  TGRTHQ+RVH  H+G P+ GD  Y  + +        ++  LH++ +   HP   
Sbjct: 224 SLRLETGRTHQIRVHLAHIGHPLAGDELYGGSREA------ISRQALHSKELSFFHPIKR 277

Query: 304 RL-QITAPLPAHMVKTWDS 321
           ++   + PLP  M +  + 
Sbjct: 278 KIYTFSCPLPDDMKQLMER 296


>gi|126640893|ref|YP_001083877.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 17978]
          Length = 293

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 76/307 (24%), Positives = 132/307 (42%), Gaps = 34/307 (11%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           +   +   L++ ++ G + V+   VK   R +  + + +   + A  +   E   LD   
Sbjct: 3   WSEFSREKLKQWMKEGHLLVNGNIVKPKYRCEGNETLTLNVELEAQTNSQPENIPLD--- 59

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDS-KGQKPR 145
                       ++YED  I V NKP G+ V  G+G       +  L     S +  +  
Sbjct: 60  ------------IVYEDEDILVINKPVGMVVHPGAGNTSSTLVNALLYHSPKSAELSRAG 107

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HR+D++TSG+LVVA+   A   L++    + + +IY  + +G        I   + K+
Sbjct: 108 LVHRIDKDTSGLLVVAKNLEAQFSLSKQLGDKSVYRIYDLVTYGNIIA-GGTIDEPI-KR 165

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
             +    + ++     G   A++H+ V + F + F  ++ Q  TGRTHQ+RVH  ++G  
Sbjct: 166 HPVDRVKMAIL----PGGRDAVTHYNVKERF-RDFTRVQAQLETGRTHQIRVHFSYIGHG 220

Query: 266 IVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
           +VGD  Y         A+     T     +  LHA  + L HP  G  +   AP P    
Sbjct: 221 LVGDQVYMNRVRIPAGASELLIETLRGFKRQALHAAKLGLKHPRTGEEMLFEAPWPEDFT 280

Query: 317 KTWDSLG 323
           +  + L 
Sbjct: 281 QLVNVLR 287


>gi|281413656|ref|ZP_06245398.1| ribosomal large subunit pseudouridine synthase D [Micrococcus
           luteus NCTC 2665]
          Length = 320

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 76/328 (23%), Positives = 134/328 (40%), Gaps = 22/328 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + + V   E   R+D    + +  ++   L      G VR      +  +R      V 
Sbjct: 8   TERLQVAEAEAGRRVDAVLADAF-GVSRSLLADWFSRGLVR---AESRSGHR----DRVL 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-I 125
                      +      D      +        +LYED  +   +KP G++     G +
Sbjct: 60  AKSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDDDLVAVDKPTGVAAHPSPGWV 119

Query: 126 AYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + G L +           ++  + HRLD  T+G++VVA+T  A   + + FR R  +
Sbjct: 120 GPTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPE 179

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y ++V GIP      +   + +  H G  +   V  +      +++H++ ++ F +  
Sbjct: 180 KVYHAVVQGIPDPLSGTVDAPIGR--HPGHHWKFAVLDD---GRPSVTHYETLEVFGRG- 233

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE+   TGRTHQ+RVH   +  P VGD  Y A+ +      +  + +LHA  +  PHP
Sbjct: 234 TLLEVHLETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGL-TRQWLHAHRLAFPHP 292

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             G  + IT+P P  +     +L    D
Sbjct: 293 VTGEPVTITSPYPDDLAHALAALRGDED 320


>gi|310778176|ref|YP_003966509.1| pseudouridine synthase [Ilyobacter polytropus DSM 2926]
 gi|309747499|gb|ADO82161.1| pseudouridine synthase [Ilyobacter polytropus DSM 2926]
          Length = 289

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 91/310 (29%), Positives = 156/310 (50%), Gaps = 25/310 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++ +  + RLD++ +  Y  IN   + K++R G+++V+ K+VK N R+Q G +V++  + 
Sbjct: 5   IDKNFHDTRLDKYIRKKYEGINLTEIFKLIRKGRIKVNGKKVKQNYRLQDGDIVKVFYMG 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                    +K +D S    K ++++K  ++YED  + +FNK   + +  GSG  Y +  
Sbjct: 65  GE----TAVKKFIDLS---PKETEYIKKGIVYEDEDVLLFNKSPNMVMHKGSGHDYGLSE 117

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            LKS+   +       +R+D+ TSG+++ A+     + L+E  R   I K Y+ LV G  
Sbjct: 118 MLKSYYQREDFT--FINRIDKATSGLIIGAKNLPMTRKLSEDMRDGNINKRYYILVEGRV 175

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             ++  I ++L K       +V  +++ EKGA  +IS+FKV+    +    LE    TGR
Sbjct: 176 DREEFQIKSYLKKTDT----HVVELEKYEKGAKESISYFKVVQR-GKNRTILEGTLGTGR 230

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           THQLRVH  ++G PIVGD KY  N +G         L+ H   +         +++  PL
Sbjct: 231 THQLRVHLANLGHPIVGDAKYGENTRGEMC------LFSHYTEI-----LSLGIKVDLPL 279

Query: 312 PAHMVKTWDS 321
           P         
Sbjct: 280 PEVFKNKLTK 289


>gi|332525786|ref|ZP_08401930.1| ribosomal large subunit pseudouridine synthase D [Rubrivivax
           benzoatilyticus JA2]
 gi|332109340|gb|EGJ10263.1| ribosomal large subunit pseudouridine synthase D [Rubrivivax
           benzoatilyticus JA2]
          Length = 317

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 128/321 (39%), Gaps = 38/321 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           VV+      RLDR   +     +  +LQ ++  G VRVD +     + R+++GQ V +  
Sbjct: 20  VVDTARHGERLDRVLVSIAGEFSRSHLQHLIELGHVRVDGQPASTASRRVKAGQRVEV-- 77

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                       +++ +  +       +   +LYED  + V +KPAG+ V    G   + 
Sbjct: 78  ------------ELVPTDESRAFRPQPMALAILYEDEHLLVLDKPAGLVVHPAPG---NW 122

Query: 130 DGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G L + + +         +  + HRLD++TSG+++V ++  A   L      R + + Y
Sbjct: 123 SGTLLNGLLAHHAAAATLPRAGIVHRLDKDTSGVMMVGKSLPAVTALVRDIAARDVHRRY 182

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L  G    ++    +  + +  +    + VV         A +  + +         +
Sbjct: 183 LALAHGAVATQR---IDAPVGRDPVSRVRMAVVA----SGKPARTDVECL-AQHDGVSAV 234

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
               HTGRTHQ+RVH    G  +V D  Y              +  LHA  ++L HP   
Sbjct: 235 RCTLHTGRTHQIRVHLASRGHALVADTLYGGRPALGMA-----RQALHAVRLELEHPLTR 289

Query: 303 GRLQITAPLPAHMVKTWDSLG 323
             L    P PA     W ++ 
Sbjct: 290 APLSFVCPPPADFSAAWRAIA 310


>gi|303238360|ref|ZP_07324895.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
 gi|302594064|gb|EFL63777.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
          Length = 322

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 75/312 (24%), Positives = 131/312 (41%), Gaps = 27/312 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q +++  D  N R+D+  K  YP++    + K  R   V+V+  RVK +     G  V 
Sbjct: 1   MQTLIIAEDSSNKRIDKVLKEKYPNMPQNFMYKAFRKKDVKVNGIRVKEDYIANLGDKVE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  +           +IL+          F    ++YED  + + NK  GI V      A
Sbjct: 61  VYII----------DEILEGKSISEPTDYFKAFTVIYEDKNLLIVNKKQGIPVHPDKDQA 110

Query: 127 YHID-GFLKSWVDSK-------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            +     + +++  K       G  P L HRLD+ T G++++A+   A + + E  + + 
Sbjct: 111 ENTLIDLVTAYIREKEVTSKTSGFSPALCHRLDRNTGGLIIIAKNNEALKVMLEKIKNKE 170

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID---- 234
           ++K Y  LV G  +  +  +  +L K        V++     + +   I+ +K +     
Sbjct: 171 VKKYYQCLVRGKMEKPQGILKAYLEKDER--KSRVYINDYKTRNSLEIITKYKTLSIIDN 228

Query: 235 -CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                    LE++  TGRTHQ+R H  ++G PIVGD KY  N              L A 
Sbjct: 229 ITADDSASLLEVELVTGRTHQIRAHMSYIGHPIVGDGKYGDNTLNRTLK--AKYQALWAY 286

Query: 294 YMDLPHPEGGRL 305
            +     +GG +
Sbjct: 287 KLKFEFSKGGGI 298


>gi|154685381|ref|YP_001420542.1| YhcT [Bacillus amyloliquefaciens FZB42]
 gi|154351232|gb|ABS73311.1| YhcT [Bacillus amyloliquefaciens FZB42]
          Length = 302

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 72/314 (22%), Positives = 135/314 (42%), Gaps = 34/314 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            +++        L    K+ +   +   + + +    ++V++   K N  +++G  + I 
Sbjct: 9   ELLITEKHAGQWLFSVLKSEF-QASKPVITEWMNQESIQVNRTPTKNNIILKTGDRLFID 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                 + +  E               + +  +L+ED+ + + NKPAG+           
Sbjct: 68  LQEKTGSSVTPE---------------YGEPDILFEDNHMLIANKPAGMPTHPNEEGQTG 112

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   ++ +  K R  HRLD++TSG +V A+ R A   L      + +++ Y +
Sbjct: 113 TLSNLIAYHFHINGEQAKVRHVHRLDRDTSGAVVFAKHRLAHAILDRQLETKTLKRTYIA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVH-VVKQNEKGANYAISHFKVIDCFAQ-KFCWL 243
              G    KK  +       S IG D  H V ++   G   A++H+KV D     +    
Sbjct: 173 AAEGKVTPKKGTV------DSPIGRDRSHSVRRRVSPGGQAAVTHYKVKDYHPGAQLTLA 226

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
           E++  TGRTHQ+RVH   +G P+ GD  Y        +  + ++  LHA+ + + HP  G
Sbjct: 227 ELELETGRTHQIRVHMASIGHPLAGDDLYGG------SRTLFHRQALHAKKVSVVHPISG 280

Query: 303 GRLQITAPLPAHMV 316
             +   AP+PA + 
Sbjct: 281 EEIVAEAPMPADLA 294


>gi|253577780|ref|ZP_04855052.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850098|gb|EES78056.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 341

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 79/337 (23%), Positives = 137/337 (40%), Gaps = 28/337 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++E +E   R D++              K+LR   + ++ K+   N ++  G  ++
Sbjct: 1   MKEFIIEENEAGQRFDKYLAKLLREAPKSFFYKMLRKKNITLNGKKATGNEKLLKGDTIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +       +      +   +   L          ++YED  I + NKPAG+  Q      
Sbjct: 61  LFLSDETFDKFAGSSQAARAYCELD---------IVYEDPDIIIINKPAGMLSQPAYDGE 111

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  +L  ++  KG          +P + +RLD+ TSG++   ++ A  Q L+  F  R
Sbjct: 112 PSLVEYLTGYLLKKGDLTEEQLKTFRPSVCNRLDRNTSGMVCAGKSLAGLQFLSRIFHDR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  L  G  + K + I  +L K        V V +Q  K +    + +  +    
Sbjct: 172 TLHKYYICLTKGKIE-KPDHIRGYLHKDKKTN--KVIVSRQEFKDSLPIETKYCPLGSNG 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMD 296
            K   LE++  TGRTHQ+R H    G P++GD KY  + F   +         LHA  + 
Sbjct: 229 -KITLLEVELITGRTHQIRAHLAGTGHPLLGDTKYGDSEFNKQYIRHGVRHQLLHAYRLV 287

Query: 297 LPHPEGGRLQITAPLPAHMVKTW--DSLGFKYDRNLY 331
           +  PE  +    AP P    K    ++L   Y  NL 
Sbjct: 288 I--PETDQ-TFVAPAPELFCKIIKEENLEEAYHENLE 321


>gi|15617005|ref|NP_240218.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. APS (Acyrthosiphon pisum)]
 gi|219681757|ref|YP_002468143.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. 5A (Acyrthosiphon pisum)]
 gi|257471459|ref|ZP_05635458.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. LSR1 (Acyrthosiphon pisum)]
 gi|11387080|sp|P57481|RLUD_BUCAI RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|25322332|pir||H84976 pseudouridylate synthase (EC 4.2.1.70) [imported] - Buchnera sp.
           (strain APS)
 gi|10039070|dbj|BAB13104.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. APS (Acyrthosiphon pisum)]
 gi|219624600|gb|ACL30755.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. 5A (Acyrthosiphon pisum)]
          Length = 312

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 82/316 (25%), Positives = 137/316 (43%), Gaps = 35/316 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
              RLD      +   +   L+K++   QV V++  V + + +I  G+ + I P    L 
Sbjct: 16  SGQRLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKILGGETLTIHPFSKDLL 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFL 133
             I E   LD               ++YEDS I + NKPAG+ V  GSG       +  L
Sbjct: 76  VDIPENIFLD---------------IVYEDSDILIINKPAGLVVHPGSGNKSGTILNALL 120

Query: 134 KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             + +SK   +  + HRLD++TSG++V+A+   +  HL    + ++I + Y  +V G   
Sbjct: 121 YHYKNSKDLPRAGIVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGIVHGKMI 180

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I   +++  +                  +++H+KV+  F +    + ++  TGRT
Sbjct: 181 A-GGTINKPIMRHYN-----RRTCMMVHHLGKPSVTHYKVLSRF-KFHTHIAIRLETGRT 233

Query: 253 HQLRVHALHMGCPIVGDHKYCA--------NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           HQ+RVH LH+  P+VGD  Y            K         +  LHA ++ L HP    
Sbjct: 234 HQIRVHMLHIKYPLVGDPCYSGFKIQSNYRKDKKTNKIYKFPRQALHANHLSLHHPIKKN 293

Query: 305 -LQITAPLPAHMVKTW 319
            +  T PLP  + +  
Sbjct: 294 VMSWTVPLPQDIQELL 309


>gi|18311104|ref|NP_563038.1| hypothetical protein CPE2122 [Clostridium perfringens str. 13]
 gi|168215749|ref|ZP_02641374.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
 gi|18145787|dbj|BAB81828.1| conserved hypothetical protein [Clostridium perfringens str. 13]
 gi|182382353|gb|EDT79832.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
          Length = 298

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 140/332 (42%), Gaps = 41/332 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS++       +  + +  ++  + K     ++   ++      +++VD   VK N  ++
Sbjct: 1   MSILESK----ITKEYDKRKIREFLKEEL-GLSSRLIRSAAIDKRIKVDGVAVKMNYVVK 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ ++I        +I  E+               +   ++YEDS I V NK   + V 
Sbjct: 56  TGEEIKIELSKKESQNIEPEK---------------MDIEIVYEDSDILVLNKKPFMVVH 100

Query: 121 GGSGIAYHIDGFLKS----WVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                  H +G L +    +     Q    RL  RLD  TSG++++ + + A   L+   
Sbjct: 101 PTRS---HPNGTLANGILYYFKESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEM 157

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +  + QK Y ++V G  + K+  I   + + +      V      ++    +I+H+KVI+
Sbjct: 158 KTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV-----DERGQESITHYKVIE 212

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            +      +E    TGRTHQ+RVH   +G PI GD  Y    +        ++  LHA  
Sbjct: 213 SY-NGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDED-----FISRQALHAYG 266

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +D   P+    L + A LP  M +  + L  K
Sbjct: 267 LDFYSPKTKEPLSLRADLPEDMKELINKLKNK 298


>gi|291301467|ref|YP_003512745.1| pseudouridine synthase RluA family [Stackebrandtia nassauensis DSM
           44728]
 gi|290570687|gb|ADD43652.1| pseudouridine synthase, RluA family [Stackebrandtia nassauensis DSM
           44728]
          Length = 312

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 71/323 (21%), Positives = 139/323 (43%), Gaps = 27/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V+V +  + +R+D+     +  ++     +++ +G+V VD +    + R+ +G  + +
Sbjct: 7   REVLVPDGLDGLRIDQVISRLF-GLSRTVAAELVSAGEVTVDGQECMKSTRVAAGGQLSV 65

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--- 124
                       E ++++               ++Y D  I V +KP G++     G   
Sbjct: 66  LLPEPPKPASAPEPELVEG------------LAVIYSDDDIAVVDKPVGVAAHSSPGWNG 113

Query: 125 ---IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              +A       +  V    ++  + HRLD  TSG++ VA++  A   L  +F+ R + K
Sbjct: 114 PTVVAGLAAAGHRISVHGPPERQGIVHRLDVGTSGLMAVAKSERAYSALKRAFKQREVDK 173

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +++ G P   +  I   + +  H G D+   V+    G   +I+H+  ++ F     
Sbjct: 174 RYRTVIQGHPDPLRGTIDAPIAR--HPGHDFKFAVR---AGGRASITHYDTLEAFP-AAS 227

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L++Q  TGRTHQ+RVH   +  P VGD  Y A+     +     + +LHA  +   HP 
Sbjct: 228 LLDVQLETGRTHQIRVHFSALRHPCVGDLIYGADPTL-ASKLGLTRQWLHAYRLGFIHPG 286

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
             + ++     P  +      L 
Sbjct: 287 TAKPVEFRCEDPPDLAHALRVLR 309


>gi|183982375|ref|YP_001850666.1| RluA family pseudouridine synthase [Mycobacterium marinum M]
 gi|183175701|gb|ACC40811.1| pseudouridine synthase, RluA-family [Mycobacterium marinum M]
          Length = 303

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 135/319 (42%), Gaps = 28/319 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V      MR+D         ++   +  I  +G V +D      ++R+ +G  + +    
Sbjct: 3   VPEGLAGMRVDAGLARLL-GLSRSAVAVIAENGGVELDGVPAGKSDRLTAGAWLHVQ--- 58

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
                 + E      +  +          +LY D  I   +KPA ++     G     + 
Sbjct: 59  ------LPEAPPPPENTPVEIEG----MTILYSDDDIVAVDKPAAVAAHASVGWTGPTVL 108

Query: 131 GFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R + K Y +
Sbjct: 109 GGLAAAGYRISTSGVHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQRTVDKRYHA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G P      I   + +  H GG++   V    K   ++++H+  ++ F      L++
Sbjct: 169 LVQGHPDPSSGTIDAPIGR--HPGGEWKFAVT---KNGRHSLTHYDTVEAFV-AASLLDV 222

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
              TGRTHQ+RVH   +  P  GD  Y A+ K      +Q + +LHAR +   HP +G R
Sbjct: 223 HLETGRTHQIRVHFAALHHPCCGDLVYGADPKLAKRLGLQ-RQWLHARSLAFAHPADGRR 281

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++I +P P  +    D L 
Sbjct: 282 VEIVSPYPPDLQHALDVLR 300


>gi|86156486|ref|YP_463271.1| ribosomal large subunit pseudouridine synthase C [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|85772997|gb|ABC79834.1| ribosomal large subunit pseudouridine synthase C [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 339

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 148/330 (44%), Gaps = 24/330 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + V  D    RLD+  +     +   ++ K+ R+ +VRV+  R K +  +  G VV 
Sbjct: 1   MIQLTVSADAAGQRLDKLVRKALRDVPLSHVYKMFRTRKVRVNGARGKADQVVAEGDVVV 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I           +E+ +  ++      +  +   +L+ED+ +   +KPAG++   G+GI 
Sbjct: 61  I--------RGDEERLLAKAAPAAPGGAPRVTFGVLHEDADLLAVDKPAGLAAHPGTGIE 112

Query: 127 -YHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR- 178
              +    + ++ +         KP   HRLD++TSG+++VA+ R A   L E+F     
Sbjct: 113 GATLVEMARGYLKTPDDLPPTEFKPSPAHRLDRDTSGVVLVAKHRKAMVRLGETFTTGEG 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y +LV G    +   I   L +                     A++ +KV+   A+
Sbjct: 173 VHKTYLALVKGKMPREAGTIDLPLSEHEQTSKSKAMR----GVNFQEALTRWKVVSA-AK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMD 296
           +   L +   TGRTHQ+R H   +G P+ GD +Y   A  +   T     ++ LHA  ++
Sbjct: 228 EISLLAVTIETGRTHQIRRHLEAVGHPVAGDRRYGDFAFNRTARTRWGLRRMGLHAWRLE 287

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           +PHP  G  L++ AP PA + +       K
Sbjct: 288 VPHPLTGAPLRLEAPFPAELAEVLSRANLK 317


>gi|168205929|ref|ZP_02631934.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
 gi|170662629|gb|EDT15312.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
          Length = 298

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 138/332 (41%), Gaps = 41/332 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS++       +  + +  ++  + K     ++   ++      +++VD   VK N  ++
Sbjct: 1   MSILESK----ITKEYDKRKIREFLKEEL-GLSSRLIRSAAIDKRIKVDGVAVKMNYVVK 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ ++I        +I  E+               +   ++YEDS I V NK   + V 
Sbjct: 56  TGEEIKIELSKKESQNIEPEK---------------MDIEIVYEDSDILVLNKKPFMVVH 100

Query: 121 GGSGIAYHIDGFLKS----WVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                  H +G L +    +     Q    RL  RLD  TSG++++ + + A   L+   
Sbjct: 101 PTRS---HPNGTLANGILYYFKESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEM 157

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +  + QK Y ++V G    K+  I   + + +      V      ++    +I+H+KVI+
Sbjct: 158 KTDKFQKRYLAIVHGNLAEKEGTINRPIYRPAEDTIKRVV-----DERGQESITHYKVIE 212

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            +      +E    TGRTHQ+RVH   +G PI GD  Y             ++  LHA  
Sbjct: 213 SY-NGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTE-----DEEFISRQALHAYG 266

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +D   P+    L + A LP  M +  + L  K
Sbjct: 267 LDFYSPKTKEPLSLRADLPEDMKELINKLKNK 298


>gi|311086138|gb|ADP66220.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. LL01 (Acyrthosiphon pisum)]
          Length = 312

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 82/316 (25%), Positives = 138/316 (43%), Gaps = 35/316 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
              RLD      +   +   L+K++   QV V++  V + + +I  G+++ I P    L 
Sbjct: 16  SGQRLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKILGGEILTIHPFSKDLL 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFL 133
             I E   LD               ++YEDS I + NKPAG+ V  GSG       +  L
Sbjct: 76  VDIPENIFLD---------------IVYEDSDILIINKPAGLVVHPGSGNKSGTILNALL 120

Query: 134 KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             + +SK   +  + HRLD++TSG++V+A+   +  HL    + ++I + Y  +V G   
Sbjct: 121 YHYKNSKDLPRAGIVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGVVHGKMI 180

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I   +++  +                  +++H+KV+  F +    + ++  TGRT
Sbjct: 181 A-GGTINKPIMRHYN-----RRTCMMVHHLGKPSVTHYKVLSRF-KFHTHIAIRLETGRT 233

Query: 253 HQLRVHALHMGCPIVGDHKYCA--------NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           HQ+RVH LH+  P+VGD  Y            K         +  LHA ++ L HP    
Sbjct: 234 HQIRVHMLHIKYPLVGDPCYSGFKIQSNYRKDKKTNKIYKFPRQALHANHLSLHHPIKKN 293

Query: 305 -LQITAPLPAHMVKTW 319
            +  T PLP  + +  
Sbjct: 294 VMSWTVPLPQDIQELL 309


>gi|125973321|ref|YP_001037231.1| RluA family pseudouridine synthase [Clostridium thermocellum ATCC
           27405]
 gi|256005428|ref|ZP_05430391.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281417524|ref|ZP_06248544.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|125713546|gb|ABN52038.1| pseudouridine synthase, RluA family [Clostridium thermocellum ATCC
           27405]
 gi|255990568|gb|EEU00687.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281408926|gb|EFB39184.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|316940446|gb|ADU74480.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           1313]
          Length = 318

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 67/333 (20%), Positives = 130/333 (39%), Gaps = 41/333 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V+ +     +    K     ++   ++K+ R G++  + + V  N  +    ++ +   
Sbjct: 6   TVDKETSGKTVKHILKKQLK-LSERLIKKLKRQGKILCNNRPVYVNAVVCENDIIEVDLD 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHI 129
            +     I                + +   ++YED  +   NK  GI V    S     +
Sbjct: 65  FDDSGIFI--------------QPEDIPIDIIYEDEFLIALNKQPGIVVHPTCSHPGGTL 110

Query: 130 DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              +   +  KG  +K R   RLD++TSGI++ A+     + L      +   K Y  +V
Sbjct: 111 ANAVAFHLQKKGIVKKIRPVIRLDRDTSGIIIFAKNPYCQEFLIRQMNDKTFIKEYIGIV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
             + +N    I   + +K         +++      + A++H+ V++        ++ + 
Sbjct: 171 HKVLENDNGTIDLPIARKPG-----SIMLRHISPDGDPAVTHYTVLERL-NGATLVKFRL 224

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANF----------------KGNFTSPIQNKLYLH 291
            TGRTHQ+RVH   +G P++GD  Y                      + TS I  +  LH
Sbjct: 225 ETGRTHQIRVHCQAIGHPLLGDTLYPFEDTPYSLSGNNPHITQANTPSITSGIITRQALH 284

Query: 292 ARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
           ++     HP   ++ +ITAP+P  M    + L 
Sbjct: 285 SQRAVFLHPFTKKILEITAPIPEDMKSALEILR 317


>gi|262280059|ref|ZP_06057844.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           calcoaceticus RUH2202]
 gi|262260410|gb|EEY79143.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           calcoaceticus RUH2202]
          Length = 350

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 74/326 (22%), Positives = 138/326 (42%), Gaps = 34/326 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V ++      R+D+     +   +   L++ L+ G + V+   VK  +R +         
Sbjct: 41  VQLDESYLGQRIDQVAALVWNEFSREKLKQWLKDGHLLVNGNIVKPKHRCEG-------- 92

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
                         ++     T   + +   ++YED  I V NKP G+ V  G+G     
Sbjct: 93  -------TELLTLEVELEAQTTSQPENIPLNIVYEDDDILVINKPVGMVVHPGAGNSSGT 145

Query: 128 HIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            ++  L  +   S+  +  L HR+D++TSG+LVVA++  A   L++    + + ++Y  +
Sbjct: 146 LVNALLYHFPKLSELSRAGLVHRIDKDTSGLLVVAKSLEAQFSLSKQLANKSVYRVYDLV 205

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V+G        I   + K+  +    + ++     G   A++H+ V + F + F  ++ +
Sbjct: 206 VYGNIIA-GGTIDEPI-KRHPVDRVKMAIL----PGGRDAVTHYNVKERF-RDFTRVQAR 258

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLP 298
             TGRTHQ+RVH  ++G  ++GD  Y         A+     T     +  LHA  + L 
Sbjct: 259 LETGRTHQIRVHFSYIGYGLIGDQIYMNRVRVPAGASELLIDTLRGFKRQALHAAKLGLK 318

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP  G  +    P P       + L 
Sbjct: 319 HPRTGEEMLFEVPWPEDFTHLVNVLR 344


>gi|182623983|ref|ZP_02951771.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
 gi|177910876|gb|EDT73230.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
          Length = 298

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 141/332 (42%), Gaps = 41/332 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS++       +  + +  ++  + K     ++   ++      +++VD   VK N  ++
Sbjct: 1   MSILESK----ITKEYDKRKIREFLKEEL-GLSSRLIRSAAIDKRIKVDGVAVKMNYVVK 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ ++I        +I  E+               +   ++YEDS I V NK   + V 
Sbjct: 56  TGEEIKIELSKKESQNIEPEK---------------MDIEIVYEDSDILVLNKKPFMVVH 100

Query: 121 GGSGIAYHIDGFLKS----WVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                  H +G L +    +     Q    RL  RLD  TSG++++ + + A   L+   
Sbjct: 101 PTRS---HPNGTLANGILYYFKESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEM 157

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +  + QK Y ++V G  + K+  I   + + +      V      ++    +I+H+KVI+
Sbjct: 158 KTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV-----DERGQESITHYKVIE 212

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            + +    +E    TGRTHQ+RVH   +G PI GD  Y    +        ++  LHA  
Sbjct: 213 SY-EGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTEDED-----FISRQALHAYG 266

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +D   P+    L + A LP  M +  + L  K
Sbjct: 267 LDFYSPKTKEPLSLRADLPEDMKELINKLKNK 298


>gi|311087296|gb|ADP67376.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. JF99 (Acyrthosiphon pisum)]
          Length = 312

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 81/316 (25%), Positives = 138/316 (43%), Gaps = 35/316 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
              RLD      +   +   L+K++   QV V++  V + + +I  G+++ I P    L 
Sbjct: 16  SGQRLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKILGGEILTIHPFSKDLL 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFL 133
             I E   LD               ++YEDS I + NKPAG+ V  GSG       +  L
Sbjct: 76  VDIPENIFLD---------------IVYEDSDILIINKPAGLVVHPGSGNKSGTILNALL 120

Query: 134 KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             + +S+   +  + HRLD++TSG++V+A+   +  HL    + ++I + Y  +V G   
Sbjct: 121 YHYKNSRDLPRAGIVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGIVHGKMI 180

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I   +++  +                  +++H+KV+  F +    + ++  TGRT
Sbjct: 181 A-GGTINKPIMRHYN-----RRTCMMVHHLGKPSVTHYKVLSRF-KFHTHIAIRLETGRT 233

Query: 253 HQLRVHALHMGCPIVGDHKYCA--------NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           HQ+RVH LH+  P+VGD  Y            K         +  LHA ++ L HP    
Sbjct: 234 HQIRVHMLHIKYPLVGDPCYSGFKIQSNYRKDKKTNKIYKFPRQALHANHLSLHHPIKKN 293

Query: 305 -LQITAPLPAHMVKTW 319
            +  T PLP  + +  
Sbjct: 294 VMSWTVPLPQDIQELL 309


>gi|291542920|emb|CBL16030.1| pseudouridine synthase, RluA family [Ruminococcus bromii L2-63]
          Length = 317

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 134/303 (44%), Gaps = 28/303 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + ++ ++ N RLD++ +  +  +    + K +R   ++V+ K+      ++ G V+ 
Sbjct: 1   MRTLEIKKNDANQRLDKFLQKRFKTLPKSLMYKYIRKKCIKVNGKKCDIQTMLKEGDVLT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                         ++     +   K  D     ++YED  + + +K  GI V       
Sbjct: 61  FYIKDEFFE---ASEQKSYEFMKAPKTFD-----IVYEDENLILIDKKPGIIVHPDKN-- 110

Query: 127 YHIDGF---LKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           YH D     ++ ++  KG+          P L +R+D+ T GI++ A+   + + L    
Sbjct: 111 YHFDSLVARVQHYLYDKGEYNPDEEKAFAPALVNRIDRNTGGIVIAAKNADSLRILNAKM 170

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R ++K Y  L++G PK   + +  ++ K      + V V K   +G+    + ++++D
Sbjct: 171 KTRELEKYYLCLLYGKPKKDSDTLHGYMTKNE--SKNKVTVFKNEVEGSKEIKTKYEILD 228

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
               KF   E++  TGRTHQ+R H   +G P+VGD KY    KG           L++  
Sbjct: 229 FNG-KFSLAEIELLTGRTHQIRAHMASIGHPLVGDTKYG---KGKKAPDSIKYQALYSYK 284

Query: 295 MDL 297
           +  
Sbjct: 285 LKF 287


>gi|313888344|ref|ZP_07822015.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus
           harei ACS-146-V-Sch2b]
 gi|312845747|gb|EFR33137.1| ribosomal large subunit pseudouridine synthase D [Peptoniphilus
           harei ACS-146-V-Sch2b]
          Length = 297

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 140/324 (43%), Gaps = 36/324 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Y     V+ +   +RLD++ +     IN   ++K +  G + ++  +VK    ++    +
Sbjct: 2   YKNTFNVDKESVGLRLDKFLEEIL-EINRSQIKKNIVDGNILLNNNKVKAGYNLKLDDEI 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                 +   + +   + +   +LYED  + V +KP  + V  G+G 
Sbjct: 61  TV-----------------EYEDDFSLSPEKIDFDVLYEDDYLAVISKPQELVVHPGAGN 103

Query: 126 --AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                ++G L  + +        +P + HRLD++TSG++++A+   A   L E F+ R+I
Sbjct: 104 KSGTLVNGLLYKFKELSNPIDNDRPGIVHRLDKDTSGLMLIAKKDEAYYKLVEMFKNRQI 163

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y ++  G      +      + +       + V+ +N   +  A + FKV+  F  K
Sbjct: 164 DKHYLAICHGNIYEDFDV--KAPIGRDPNNRIKMRVIDEN---SKEAYTSFKVLKNF-DK 217

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  L++  HTGRTHQ+RVH  ++  P+VGD  Y    K        +K  LHA  +   H
Sbjct: 218 YTLLDVHLHTGRTHQIRVHLAYVNHPVVGDEVYGIKNK-----FKISKQLLHAYKLKFNH 272

Query: 300 P-EGGRLQITAPLPAHMVKTWDSL 322
           P  G  L+I    P       +  
Sbjct: 273 PISGEELEIIDKFPVRFEDFINKF 296


>gi|303249294|ref|ZP_07335526.1| pseudouridine synthase, RluA family [Desulfovibrio fructosovorans
           JJ]
 gi|302489300|gb|EFL49257.1| pseudouridine synthase, RluA family [Desulfovibrio fructosovorans
           JJ]
          Length = 323

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 90/322 (27%), Positives = 141/322 (43%), Gaps = 35/322 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           + T VQ   V   E   +L ++        +    LQK +R+GQVR+D KR K  +R+ +
Sbjct: 1   MKTPVQNFTVAEAEGGQKLLQYLARRLDGAVPPTALQKFIRTGQVRIDGKRCKPFDRVAA 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           GQ+VR+PP        IKE +   +     +  D     +L+ED +I V  KPAG+ V  
Sbjct: 61  GQIVRMPPYE------IKEPRNSPAKTAAPRGHDL---DILHEDDEILVIVKPAGLPVHP 111

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG  + +   L++       +P   HRLD++T+G+L+VA++  A + + E+       K
Sbjct: 112 GSGHPFALTSILRARYPDAPFRPTPAHRLDRDTTGVLLVAKSYRALRAIHEAMTTGTAHK 171

Query: 182 IYWSLVWGIP----KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            Y + VWG       N    + + L K+   G + V    +   G   A+   +++    
Sbjct: 172 DYLAWVWGEWTLGEANDWVTLRDRLAKEGGPGRERV----EPSAGGKDAVCKVRLLGVM- 226

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +E++  TGRT Q+R      G PIVGD KY               + LHA  + L
Sbjct: 227 DTASLVEVRLETGRTQQIRAQLASRGAPIVGDPKYGGGPP---------PMRLHAWRVVL 277

Query: 298 PHPEGGRLQITAPLPAHMVKTW 319
           P          A  P      W
Sbjct: 278 PDAA-----FCA--PPDWEAPW 292


>gi|242279048|ref|YP_002991177.1| pseudouridine synthase, RluA family [Desulfovibrio salexigens DSM
           2638]
 gi|242121942|gb|ACS79638.1| pseudouridine synthase, RluA family [Desulfovibrio salexigens DSM
           2638]
          Length = 549

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 74/328 (22%), Positives = 137/328 (41%), Gaps = 36/328 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
             E  + N RLD+++        I+   ++  +++G   ++ K  K  N ++   + + +
Sbjct: 19  TAEFSDRNTRLDKFWGTALEEEGISRGKVKDWIKAGFAEINGKICKKPNQKLMGNEELTL 78

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS---- 123
                  + + +E                L   ++Y D KI V NKPAG++         
Sbjct: 79  KGEAELTSLVPEE----------------LPLEIIYNDGKIAVINKPAGLTTHPAPSCPT 122

Query: 124 -GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             + + +        D    +P + HRLD+ TSG++ VA        ++ +F  R + K 
Sbjct: 123 GTLVHRMIHHFPEIRDMDEWRPGIVHRLDKFTSGLITVALNEHDRLAMSTAFADREVNKA 182

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFC 241
           Y ++V G+PK +   I   + +          V+    KG   A S ++V+    A +  
Sbjct: 183 YLAIVHGVPKREFGEIDQPMGRHPVHKTKMAVVL----KGGRDARSEYEVLWSDPAGRAS 238

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQNKLYLHARYM 295
            ++++ +TGRTHQ+RVH  H+G P+VGD  Y +             + +  +  LHA  +
Sbjct: 239 LVKVKIYTGRTHQIRVHMAHIGHPLVGDQVYGSMPHAIWEQDQPQLAKLAERQMLHAYSL 298

Query: 296 DLPHPEG-GRLQITAPLPAHMVKTWDSL 322
              HP+    L  T   P   +    +L
Sbjct: 299 SFTHPDSEEELSFTQAPPEDFINMLKAL 326


>gi|323341916|ref|ZP_08082149.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322464341|gb|EFY09534.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 298

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 73/317 (23%), Positives = 139/317 (43%), Gaps = 31/317 (9%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ +    +R+D +   H   ++   +  +++ G +  +    K N + +    +     
Sbjct: 5   IITSKTLGLRIDHFLNEHL-DLSRSKIASMIKDGTILCNDMPTKANYKTKLNDCIT---- 59

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHI 129
             A  + IK   I    +++          ++YED  + V NKP G+ V  G+G+ +  +
Sbjct: 60  --ASTYQIKTLDIEPVKMDID---------VVYEDEYLLVVNKPRGLVVHPGNGVKSDTL 108

Query: 130 DGFLKSWVDSK---GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
              L  +++S      +P L HR+D+ TSG+LV+A+     Q L E    + + + Y++L
Sbjct: 109 LHGLLYYLNSNCDHYIRPGLVHRIDRNTSGLLVIAKDDKTHQFLAEQLLDKTMNRTYYAL 168

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+       I   +            ++  N+  +  A +HF+ I+ +      +  +
Sbjct: 169 VHGVLPQAHVLIDAPIG----PDKSNTKIMTVNQARSKPARTHFEKIETYINS-SLICCK 223

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVHALH   P+ GD +Y      +     +   YL A  ++  HP+  + +
Sbjct: 224 LETGRTHQIRVHALHANIPLHGDPQYGHPSDTD-----KTGQYLCAARLEFVHPKYLKLM 278

Query: 306 QITAPLPAHMVKTWDSL 322
           Q   PLP +       L
Sbjct: 279 QFEIPLPRYFQDKITEL 295


>gi|295394748|ref|ZP_06804963.1| ribosomal large subunit pseudouridine synthase D [Brevibacterium
           mcbrellneri ATCC 49030]
 gi|294972344|gb|EFG48204.1| ribosomal large subunit pseudouridine synthase D [Brevibacterium
           mcbrellneri ATCC 49030]
          Length = 308

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 73/323 (22%), Positives = 134/323 (41%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + ++V    E  R+D         ++      +  SG V VD  +V  + R+ +G  + +
Sbjct: 3   RSILVPEGLEGERVDTALSRLL-GLSRSVAAGMAESGDVEVDGVKVPKSMRVTTGARIDV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                     I  + +   +             ++Y+D    V +KP G++    +G   
Sbjct: 62  TMPKPKEPLSIVAEPVPGMN-------------VIYDDDAFVVVDKPVGVAAHAAAGWSG 108

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  + HRLD  TSG++VVA+   A   L  +F+ R + K
Sbjct: 109 PTVIGGLAAAGYQIATSGAAERQGIVHRLDVGTSGVMVVAKGEHAYSVLKRAFKNRTVDK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G+P      I   + +     G Y            +A++H++V++ + +   
Sbjct: 169 TYHALVQGLPDPVVGTIEAPIGRHPRKDGLYAVRT-----DGKHAVTHYEVLEAY-RSAS 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E++  TGRTHQ+RVH      P  GD  Y A+        + N+ +LHA  +   HPE
Sbjct: 223 LVEVKLETGRTHQIRVHMSATKRPCCGDLPYGADPVLAQKLGL-NRQWLHAVKLGFEHPE 281

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            G  ++  +  P  +    + L 
Sbjct: 282 TGEYVEFESDYPEDLATALERLR 304


>gi|217077277|ref|YP_002334995.1| ribosomal large subunit pseudouridine synthase C [Thermosipho
           africanus TCF52B]
 gi|217037132|gb|ACJ75654.1| ribosomal large subunit pseudouridine synthase C [Thermosipho
           africanus TCF52B]
          Length = 293

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 82/317 (25%), Positives = 141/317 (44%), Gaps = 32/317 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           ++V  +    RLD++ +    ++    + K++R+G+++V+ K+VK  + +I+ G  + I 
Sbjct: 1   MIVTEENYYSRLDKFLRKKLLNLPLSAIYKLIRTGKIKVNGKKVKNPSYKIEIGDEITIE 60

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-Y 127
             I+  N  I   K++   ++L          ++YED+ I + NKPAGI +  G G    
Sbjct: 61  EDISKYNREI-NNKVVPIKMDLD---------IVYEDNDILIINKPAGIPIHPGKGTHIA 110

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L  +   K   P L HRLD+ TSGIL++A+   +A+ L +    R I+K Y +L 
Sbjct: 111 TLIEGLIYYGQEKNFTPHLVHRLDKHTSGILIIAKNTQSARELGDIIAGRSIKKEYIALC 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    K+  I   L               +N++     I+  KV      +F  L +  
Sbjct: 171 KGKLS-KEGKIDIPL---------------ENKQALTTFITQ-KVYKTHLGEFSLLNVNI 213

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGGRL 305
            TGR HQ+R H   +  PI+GD  Y                + +LH   M+    +   +
Sbjct: 214 KTGRKHQIRKHLSLINHPIIGDDVYGDKKLNREFKREYGLKRYFLHCHSMEFYF-KNKHI 272

Query: 306 QITAPLPAHMVKTWDSL 322
             TAPL   +     +L
Sbjct: 273 AATAPLSKDLKNVLKNL 289


>gi|91762258|ref|ZP_01264223.1| pseudouridylate synthase [Candidatus Pelagibacter ubique HTCC1002]
 gi|91718060|gb|EAS84710.1| pseudouridylate synthase [Candidatus Pelagibacter ubique HTCC1002]
          Length = 326

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 80/341 (23%), Positives = 150/341 (43%), Gaps = 40/341 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M     ++V  DE N+RLD +       I+   ++ ++   +++++ + +   + ++ SG
Sbjct: 1   MEKNINLIVGEDENNLRLDVFINKRENLISRSRIKNLILKEKLKINDQIINSPSKKVLSG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +                +      +      K  ++YED  + + NKPAGI +  G
Sbjct: 61  DEINLQ---------------IPEPKEASLKPYNFKLQIVYEDDDLLIINKPAGIIMHPG 105

Query: 123 SG-IAYHIDGFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +G     I   L  +            +P + HR+D++TSG++V+A+     ++L+  F 
Sbjct: 106 AGNYDETIVNALMHYNKDSLSTIGDELRPGIVHRIDKDTSGLIVIAKNNETHENLSHQFS 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I ++Y  L+WG  +     I  ++ + S    +   +   N KG   AI+++K I+ 
Sbjct: 166 EHTITRVYQLLIWGKLRPSSGKIDTFITRSSK---NRQMMEVSNSKG-KRAITNYKTIEI 221

Query: 236 FAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGD------HKYCANFKGNFTSPI- 284
           F          +E +  TGRTHQ+RVH  HMG  I+GD      +K   N   N  + I 
Sbjct: 222 FENDKTPTLSLVECRLETGRTHQIRVHMTHMGNSIMGDGKYKKKYKKLKNIDTNLENLIY 281

Query: 285 -QNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
             ++ +LHA+ +   HP    ++  T+ LP  +      L 
Sbjct: 282 KLDRQFLHAQTLGFIHPRTNEKMVFTSILPQELENILVLLR 322


>gi|289522930|ref|ZP_06439784.1| ribosomal large subunit pseudouridine synthase D [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289503954|gb|EFD25118.1| ribosomal large subunit pseudouridine synthase D [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 299

 Score =  219 bits (558), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 93/328 (28%), Positives = 151/328 (46%), Gaps = 38/328 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     VVV ++    RLD          +   +Q+ +R           K + +++   
Sbjct: 1   MAEKVEVVVSDEFIGERLDVAVSK-ITARSRSQIQRAMREAGF-------KPSMKVREAM 52

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                 D     T   + +   +LYED+ I + +KPA + V    
Sbjct: 53  NLELSFH--------------DEEKEATLEPEPVNFEVLYEDADIIIIDKPAPLVVHPAV 98

Query: 124 GIAY--HIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G  Y   + G +  +    DS  ++P + HRLD  TSG++V+AR   + Q LT++F+ R 
Sbjct: 99  GHWYGTLVHGLVYRYPELADSDMRRPGIVHRLDAGTSGLMVIARNLFSKQKLTDAFKARS 158

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y +LV+G P  +K  IA+ + +        + VV     G   A++ ++V+     
Sbjct: 159 VKKEYLALVYGSPNKEKGTIASPIGRHPK-NRLKMAVVS----GGREAVTEYEVLWSN-D 212

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           KF +L    HTGRTHQ+RVH   MGCPIVGD  Y  N K  +    +++ +LHA  +  P
Sbjct: 213 KFSFLRCTIHTGRTHQIRVHLKDMGCPIVGDRLYGCNLKAEWVP--KDRFFLHAWKLAFP 270

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           HP  GR +   + LP  + K    LG +
Sbjct: 271 HPRDGRIMSFRSFLPLELKKAL--LGAR 296


>gi|119717276|ref|YP_924241.1| ribosomal large subunit pseudouridine synthase D [Nocardioides sp.
           JS614]
 gi|119537937|gb|ABL82554.1| ribosomal large subunit pseudouridine synthase D [Nocardioides sp.
           JS614]
          Length = 312

 Score =  219 bits (558), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 72/330 (21%), Positives = 140/330 (42%), Gaps = 28/330 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS     + + V       R+D      +  ++     +++ +G V VD   V  ++R+ 
Sbjct: 1   MSRDADHRVLSVPEGLAGERVDAALARMF-GLSRTRGAELIAAGNVLVDGAPVGKSDRVL 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  V +   + A    +  + +                 +L++D  I V +KP G++V 
Sbjct: 60  PGSTVAVTIPVEADPLAVVPEVVE-------------GIKILHDDDDIVVIDKPVGVAVH 106

Query: 121 GGSG------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      + +      +       ++  +  RLD  TSG++V+ ++  A   L  +F
Sbjct: 107 PSPGWSGPTVVGHLAGAGFRISTSGAPERQGIVQRLDVGTSGVMVICKSEHAYSVLKNAF 166

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R + K+Y +LV G P   +  I   + +  H   DY   V  +     ++++H++ ++
Sbjct: 167 RRRTVDKVYHALVQGHPDPLEGTIDAPIGR--HPKADYKFAVMAD---GRHSVTHYETLE 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              +    LE+   TGRTHQ+RVH   +  P VGD  Y A+        ++ + +LHA  
Sbjct: 222 AH-RFASLLEIHLETGRTHQIRVHMAALKHPCVGDPTYGADPSLARRVGLE-RQWLHAVR 279

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +   HPE G+ ++  +  P  +    + + 
Sbjct: 280 LGFEHPETGKQVEYESEYPEDLAHALEVIR 309


>gi|110800540|ref|YP_696800.1| RluA family pseudouridine synthase [Clostridium perfringens ATCC
           13124]
 gi|168208824|ref|ZP_02634449.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
 gi|110675187|gb|ABG84174.1| pseudouridine synthase, RluA family [Clostridium perfringens ATCC
           13124]
 gi|170713119|gb|EDT25301.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
          Length = 298

 Score =  219 bits (558), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 141/332 (42%), Gaps = 41/332 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS++       +  + +  ++  + K     ++   ++      +++VD   VK N  ++
Sbjct: 1   MSILESK----ITKEYDKRKIREFLKEEL-GLSSRLIRSAAIDKRIKVDGVAVKMNYVVK 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ ++I        +I  E+               +   ++YEDS I V NK   + V 
Sbjct: 56  TGEEIKIELSKKESQNIEPEK---------------MDIEIVYEDSDILVLNKKPFMVVH 100

Query: 121 GGSGIAYHIDGFLKS----WVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                  H +G L +    +     Q    RL  RLD  TSG++++ + + A   L+   
Sbjct: 101 PTRS---HPNGTLANGILYYFKESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEM 157

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +  + QK Y ++V G  + K+  I   + + +      V      ++    +I+H+KVI+
Sbjct: 158 KTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV-----DERGQESITHYKVIE 212

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            + +    +E    TGRTHQ+RVH   +G PI GD  Y             ++  LHA  
Sbjct: 213 SY-KGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTE-----DEEFISRQALHAYG 266

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +D   P+  + L + A LP  M +  + L  K
Sbjct: 267 LDFYSPKTKKPLSLRADLPEDMKELINKLKNK 298


>gi|169346799|ref|ZP_02865750.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
 gi|169297081|gb|EDS79203.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
          Length = 298

 Score =  219 bits (558), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 140/332 (42%), Gaps = 41/332 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS++       +  + +  ++  + K     ++   ++      +++VD   VK N  ++
Sbjct: 1   MSILESK----ITKEYDKRKIREFLKEEL-GLSSRLIRSAAIDKRIKVDGVSVKMNYVVK 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ ++I        +I  E+               +   ++YEDS I V NK   + V 
Sbjct: 56  TGEEIKIELSKKESQNIEPEK---------------MDIEIVYEDSDILVLNKKPFMVVH 100

Query: 121 GGSGIAYHIDGFLKS----WVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                  H +G L +    +     Q    RL  RLD  TSG++++ + + A   L+   
Sbjct: 101 PTRS---HPNGTLANGILYYFKESNQDCIVRLVSRLDMNTSGLIIIGKNQYAHMVLSNEM 157

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +  + QK Y ++V G  + K+  I   + + +      V      ++    +I+H+KVI+
Sbjct: 158 KTDKFQKRYLAIVHGNLEEKEGTINRPIYRPAEDTIKRVV-----DERGQESITHYKVIE 212

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            +      +E    TGRTHQ+RVH   +G PI GD  Y             ++  LHA  
Sbjct: 213 SY-NGADLVECLLETGRTHQIRVHLSSLGHPIFGDSLYGTE-----DEEFISRQALHAYG 266

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +D   P+  + L + A LP  M +  + L  K
Sbjct: 267 LDFYSPKTKKPLSLRADLPEDMKELINKLKNK 298


>gi|302846594|ref|XP_002954833.1| RNA pseudouridine synthase mitochondrial precursor [Volvox carteri
           f. nagariensis]
 gi|300259808|gb|EFJ44032.1| RNA pseudouridine synthase mitochondrial precursor [Volvox carteri
           f. nagariensis]
          Length = 343

 Score =  219 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 72/356 (20%), Positives = 124/356 (34%), Gaps = 71/356 (19%)

Query: 26  KNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                 ++   +Q  + +G V V+ +   K + ++++G  V                  L
Sbjct: 1   AARTQDVSRAKIQASIAAGLVLVNGQPAAKASQQLKAGDCVVCR---------------L 45

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ--GGSGIAYHIDGFLKSW------ 136
                +    + +   + YED  + V NKP+G+ V    G      ++  L         
Sbjct: 46  QPPPPMQALPEAIPLDIKYEDDHVIVVNKPSGMVVHVAPGHHHGTLVNALLHHCALPALD 105

Query: 137 ----------------------------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
                                         S   +P + HRLD+ TSG+LVVA+T  A  
Sbjct: 106 LDSSLDLDPDLGTGIGTSSSSSCSTSSLSSSSCLRPGIVHRLDKGTSGLLVVAKTEVALT 165

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            L   F+ R + ++Y S+  G P      +   + +        +            A S
Sbjct: 166 RLQAQFKARTVDRLYDSITVGCPVQPNGRVETNICRDPR-DRKRMAAAPYGSGRGRTAGS 224

Query: 229 HFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS----- 282
           ++ V+          +  +  TGRTHQ+RVHA ++G P++GD  Y         +     
Sbjct: 225 NYTVMAPLAGGGAALVRWKLDTGRTHQIRVHAKYIGHPLLGDDTYGGTAPAALAAVSRGS 284

Query: 283 -----------PIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
                          +  LHAR +   HP  G RL    P+P   ++    LG + 
Sbjct: 285 SLDSLSSLEVVEQLGRPALHARTLGFTHPVTGARLSFEQPVPEDFLRALRGLGMEA 340


>gi|42780396|ref|NP_977643.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 10987]
 gi|42736315|gb|AAS40251.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus ATCC 10987]
          Length = 297

 Score =  219 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 66/317 (20%), Positives = 134/317 (42%), Gaps = 39/317 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ EE   +  + K     I+   L  I    G + V+ +      ++Q+G+ +R+   
Sbjct: 10  IDSAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRYQLQAGEELRVFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 68  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPAGSV 113

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 114 A---NALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID  A     + 
Sbjct: 171 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EDGQRAVTHFRVIDS-ANHKTHVS 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 225 LELDTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 278

Query: 304 RLQITAPLPAHMVKTWD 320
            +  T P+P+ M     
Sbjct: 279 EMSFTTPIPSDMQAVLR 295


>gi|313764724|gb|EFS36088.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL013PA1]
 gi|313815789|gb|EFS53503.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL059PA1]
 gi|314915215|gb|EFS79046.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL005PA4]
 gi|314918556|gb|EFS82387.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL050PA1]
 gi|314919819|gb|EFS83650.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL050PA3]
 gi|314931834|gb|EFS95665.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL067PA1]
 gi|314955990|gb|EFT00388.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL027PA1]
 gi|314958385|gb|EFT02488.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL002PA1]
 gi|315098276|gb|EFT70252.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL059PA2]
 gi|315101033|gb|EFT73009.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL046PA1]
 gi|327451042|gb|EGE97696.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL087PA3]
 gi|327453603|gb|EGF00258.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL083PA2]
 gi|328753075|gb|EGF66691.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL087PA1]
          Length = 285

 Score =  219 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 68/300 (22%), Positives = 128/300 (42%), Gaps = 28/300 (9%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
              ++   +  ++  G V +D ++V + + R+ +GQ++ +          I  Q +    
Sbjct: 1   MSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQMLDVDLCDPVATPSITPQIVE--- 57

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG------IAYHIDGFLKSWVDSKG 141
                        ++++DS I V +KPAG++     G      + +              
Sbjct: 58  ----------GMRIIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTSGAP 107

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           ++  +  RLD  TSG++VVA++  A   L ++FR R + K+Y +LV G P      I   
Sbjct: 108 ERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTIDAP 167

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +          V      G  ++++H++ ++ F +    L++   TGRTHQ+RVH   
Sbjct: 168 IGRDHRHDWKMAIV-----DGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAA 221

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           +  P  GD  Y  +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 222 IKHPCCGDPLYGCDPALAKELGLE-RQWLHAGELSFTHPGSGEWVTFHADLPADLQNALD 280


>gi|295401674|ref|ZP_06811641.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111991|ref|YP_003990307.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
 gi|294976294|gb|EFG51905.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311217092|gb|ADP75696.1| pseudouridine synthase, RluA family [Geobacillus sp. Y4.1MC1]
          Length = 300

 Score =  219 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 68/321 (21%), Positives = 136/321 (42%), Gaps = 39/321 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V   +E   +  + K +   I+   L  I    G + V+ + V   +R+  G+ +R+  
Sbjct: 10  IVTKQDEGKLIREFLKEN--GISKTALIDIKFHGGAIYVNDQPVTVRHRLGEGETLRVVF 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +  +                + +   ++YED  + V NKP  ++         H 
Sbjct: 68  PPELPSEGMA--------------PEAIPLDIVYEDEHVIVVNKPPFMATIPSR---EHP 110

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G L + +    +K        +  RLD++TSG++++A+ R     L+   +  ++ + Y
Sbjct: 111 GGTLANALLYHYEKQQLTSTIHVVTRLDRDTSGLVLIAKHRHIHHLLSTLQKQGKVARRY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++  G     +  I   + +KS        + ++  +    A++HF+V+  F + +  L
Sbjct: 171 EAICHGRVSKDEGTIDAPIARKSD-----SIIAREVREDGQRAVTHFRVLQRF-RDYTHL 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  H+G P+ GD  Y  +          ++  LH++ +   HP   
Sbjct: 225 SLQLETGRTHQIRVHLAHIGHPLAGDELYGGSRNA------IDRQALHSKELSFFHPLKK 278

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
           +    + PLP  M +  + L 
Sbjct: 279 QAYTFSCPLPDDMQRLIERLR 299


>gi|170289613|ref|YP_001739851.1| RluA family pseudouridine synthase [Thermotoga sp. RQ2]
 gi|170177116|gb|ACB10168.1| pseudouridine synthase, RluA family [Thermotoga sp. RQ2]
          Length = 304

 Score =  219 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 88/324 (27%), Positives = 142/324 (43%), Gaps = 34/324 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           + V  +    RLD++ +N         + K++R G+V V+ KRV+     ++ G  V I 
Sbjct: 3   IDVTRENFYRRLDKFLRNTLKDFPLSTIYKLIRKGKVYVNGKRVRDPGFDLEEGDTVEIK 62

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-Y 127
             +N  N   +  K   + V        +K  +++E+    V NKPAGI++  G G+   
Sbjct: 63  -YVNLENLPKRSDKKDLTPVP-------MKLDIIHENDNYLVLNKPAGIAIHPGKGVHVA 114

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L  +   +G +P L HRLD++TSG+L+VA+ R AA+ LTE FR R ++K Y +LV
Sbjct: 115 TLIEGLLYYGQEQGFEPFLVHRLDKDTSGLLIVAKNREAARVLTEMFRGRNMEKEYIALV 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+P+N  +                             A+S   V     +    L ++ 
Sbjct: 175 KGVPENNLKITIPL--------------------DGQEAVSEI-VSVKPLKNVSLLRVKI 213

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
           HTGR HQ+R H   +G P+VGD  Y      +         + +LH+  M    P     
Sbjct: 214 HTGRKHQIRRHLSQIGFPVVGDDTYGDRQFNREFRRKYALKRHFLHSYRMRFFDPWAEEE 273

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
               APL   ++     L  + D 
Sbjct: 274 KDFKAPLTEDLLNVLTLLEERSDE 297


>gi|167645618|ref|YP_001683281.1| pseudouridine synthase [Caulobacter sp. K31]
 gi|167348048|gb|ABZ70783.1| pseudouridine synthase [Caulobacter sp. K31]
          Length = 286

 Score =  219 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 88/253 (34%), Positives = 137/253 (54%), Gaps = 5/253 (1%)

Query: 78  IKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           + + K  D+ +NLT     F KS++++ED  ++V NKPAG+S QGG   A+ +D  L + 
Sbjct: 30  VAKPKASDTPINLTPEEIAFTKSLVIHEDDSVFVLNKPAGLSSQGGRIQAHTLDDLLWAL 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKK 195
                 +PRL HRLD++TSG+++ ART+ AA  L ++   +R +K YW++V  G P+ + 
Sbjct: 90  ARRDRPRPRLIHRLDRDTSGVILTARTKPAATFLGKALMGKRFRKTYWAIVTPGAPEPRG 149

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I + L ++S     Y+ V + +   A  A S ++ +    +    +E+ P TGR HQL
Sbjct: 150 GQIDSPLRRESIGREAYMRVCEADHPDAETARSRYRTLAA-TEGAALVELSPDTGRMHQL 208

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           RVH   +G PI GD +Y              +L LHA  +  PHPEGG  +I+AP+P  M
Sbjct: 209 RVHMASIGRPIAGDSRYGGAL--MLGGAPVPRLMLHAANLVFPHPEGGERRISAPIPDDM 266

Query: 316 VKTWDSLGFKYDR 328
                 LG +   
Sbjct: 267 RAILAKLGLEIPE 279


>gi|25026884|ref|NP_736938.1| putative ribosomal large subunit pseudouridine synthase C
           [Corynebacterium efficiens YS-314]
 gi|259506052|ref|ZP_05748954.1| ribosomal large subunit pseudouridine synthase C [Corynebacterium
           efficiens YS-314]
 gi|23492164|dbj|BAC17138.1| putative ribosomal large subunit pseudouridine synthase C
           [Corynebacterium efficiens YS-314]
 gi|259166340|gb|EEW50894.1| ribosomal large subunit pseudouridine synthase C [Corynebacterium
           efficiens YS-314]
          Length = 304

 Score =  219 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 87/318 (27%), Positives = 153/318 (48%), Gaps = 28/318 (8%)

Query: 1   MSLMTYVQ----YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN 56
           M++ T ++     V +       RLD++ + H   +    + + LR+G+++V+ ++ K +
Sbjct: 1   MAMETKLKPTFVEVEIPEAHAGRRLDKYLRAHLKGVPASLIFRQLRTGKIKVNGRKAKPD 60

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
            R Q G ++++      L   + E     +S+  TK  + + + +++ED+ + V NKPA 
Sbjct: 61  YRTQPGDMLKM------LQMDLPENLPPPASLP-TKLLNQIDNGIIHEDADLIVLNKPAD 113

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR- 175
           I+V  G+G+A  +   L+     +     L HRLD ETSG+L+VA+T A  +H+ +  R 
Sbjct: 114 IAVHTGTGVAGGVIEALRQLRPGEA-DLELAHRLDHETSGLLMVAKTPAMLRHIQQLLRE 172

Query: 176 -MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             R + + Y  LV G   +    +   L               +       A++ F+V  
Sbjct: 173 DDRALSRRYALLVRGRWPDHLTAVDAPL--------QRTDTTVRVHPDGQSALTFFEVER 224

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F  +   ++ +  TGR HQ+RVHA H G PI+GD KY               L+LHA  
Sbjct: 225 RFGNRATLVKARLTTGRKHQIRVHARHAGHPIIGDRKYGDPRARATH------LFLHAAE 278

Query: 295 MDLPHPEGGRLQITAPLP 312
           + +P P+G   + +APLP
Sbjct: 279 LTVPMPDGMTREFSAPLP 296


>gi|218509234|ref|ZP_03507112.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli Brasil 5]
          Length = 274

 Score =  219 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 70/280 (25%), Positives = 130/280 (46%), Gaps = 35/280 (12%)

Query: 20  RLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           RLD W         +   ++ +++ GQV +  + +     +++ G    I          
Sbjct: 5   RLDAWLTAQLGEEFSRSRIKVLIKDGQVSMRGQLITDPQRKVRVGDSFEIT--------- 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKS 135
                 L    + T   + +   +LYED  + V +KPAG+ V  GSG      ++  +  
Sbjct: 56  ------LPEPEDPTPRGEDIPLDILYEDDDLIVISKPAGLVVHPGSGNWTGTLVNALIHH 109

Query: 136 WVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR----IQKIYWSL 186
              +       ++P + HRLD++T+G++VVA+   A +HL+  F        +++ Y ++
Sbjct: 110 CGATLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDVAHRHLSLQFADHGRTMPLERAYQAI 169

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------F 240
           VWG P++    +   L + +        V + + + A+ AI+H++VI+ F +        
Sbjct: 170 VWGRPRSLTGTVDAPLGRATG-DRTRRAVKRPDSQDADQAITHYEVIERFHETPDATALA 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             +E +  TGRTHQ+RVH  H+G P++GD  Y A F+   
Sbjct: 229 SLVECRLETGRTHQIRVHMAHIGHPLLGDTVYGAGFRTKA 268


>gi|325264047|ref|ZP_08130779.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Clostridium sp. D5]
 gi|324030531|gb|EGB91814.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Clostridium sp. D5]
          Length = 296

 Score =  219 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 72/324 (22%), Positives = 140/324 (43%), Gaps = 38/324 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ----VRVDKKRVKFNNRI 59
           M  +    +  +++ +R++++ +      +    Q ++   +    V V+    + N R+
Sbjct: 1   MDRILIYNIRKNDDGLRVEQYLRRQ--GYSR---QNLVELKKMPQSVLVNGCFCRLNERL 55

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            +   + +               I +   +L      L   ++YED  I V NKPAG+ V
Sbjct: 56  ANHNTLTVH--------------IQERESSLQILPVLLPLDIIYEDEDIIVINKPAGMPV 101

Query: 120 QGG-SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  +  +   L  +   +G+    R T+RLD++TSG+ V+A+   ++  L+     
Sbjct: 102 HPSMNNYSNTLANGLAWYYQEQGKPFIFRCTNRLDRDTSGLTVIAKHMLSSNILSRMTVR 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I + Y ++V G  +  +  I   L +K    G  +      E G   A++H+  ++  
Sbjct: 162 HEITREYLAVVRGSVRPSEGIICAPLSRKP---GSIIERTVDFENGEK-AVTHYHAVE-E 216

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 + +   TGRTHQ+R+H  ++G P++GD+ Y  + +         +  LH+  + 
Sbjct: 217 KNGHSLVSLVLETGRTHQIRIHMKYLGFPLIGDYLYNPDME------YIQRQALHSCRLA 270

Query: 297 LPHPEGGR-LQITAPLPAHMVKTW 319
             HP  G  L+ TAPLP  M K  
Sbjct: 271 FSHPITGEKLEFTAPLPDDMQKVL 294


>gi|239908533|ref|YP_002955275.1| pseudouridine synthase [Desulfovibrio magneticus RS-1]
 gi|239798400|dbj|BAH77389.1| pseudouridine synthase [Desulfovibrio magneticus RS-1]
          Length = 339

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 90/343 (26%), Positives = 146/343 (42%), Gaps = 47/343 (13%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           + T VQ++ V   E   +L ++      P +    LQK +R+GQVR+D KR K  +R+  
Sbjct: 1   MKTPVQHITVTAAEAGQKLLQYLARRLGPGLPLAALQKCIRTGQVRLDGKRCKPFDRVAQ 60

Query: 62  GQVVRIPPVINALNHIIKEQ---------------------KILDSSVNLTKHSDFLKSI 100
           GQVVR+PP                                 K   S+ + T         
Sbjct: 61  GQVVRVPPFELDEAGPAGGALGAPELAAVPTGRPKPGPLSVKTSPSAAHRTGGRAMPALE 120

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED ++ V  KPAG+ V  GSG  + +   L +       KP   HRLD++T+G+L+V
Sbjct: 121 ILHEDDELLVVVKPAGLPVHPGSGHTFALTTLLHAHAPHAPFKPTPAHRLDRDTTGLLLV 180

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIP----KNKKECIANWLLKKSHIGGDYVHVV 216
           A++    + L E+ +   ++K Y++ VWG      +N+   + + L K    G + V   
Sbjct: 181 AKSYRRLRALHEAMQDGTLRKDYFAWVWGKWLLGEENEWVTMRDALAKSGGPGRERVTA- 239

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               +    A++  ++I   A     +E++  TGRTHQ+R      G P+VGD KY    
Sbjct: 240 ---GEDGKEAVAKVRLISR-APTASLVEVRLETGRTHQIRAQLASRGYPLVGDAKYGGG- 294

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
                 P   +L+     +    PE         +P      W
Sbjct: 295 ------PTPLRLHAWRVIL----PEEAYC-----VPPDWEAPW 322


>gi|331083782|ref|ZP_08332891.1| hypothetical protein HMPREF0992_01815 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330403207|gb|EGG82767.1| hypothetical protein HMPREF0992_01815 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 337

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 75/334 (22%), Positives = 142/334 (42%), Gaps = 29/334 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +VV+  E   RLD++   +        L K+LR   + ++ K+   N ++Q    ++
Sbjct: 1   MKQLVVKEIESGQRLDKFLGKYLKEAPKSFLYKMLRKKNITLNGKKATGNEKLQPNDEIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    + L     E+          K S   +  ++YE++ +   NKP G+  Q      
Sbjct: 61  LFLSDDTLEKFCGEE----------KSSSRTELDIVYENNHVLFVNKPVGMLSQKAEKED 110

Query: 127 YHIDGFLKSWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  ++  ++         D +  +P + +RLD+ TSGI+   +T    Q +++ F+ R
Sbjct: 111 VSLVEYITGYLLEEKFLTKEDLRTFRPGVCNRLDRNTSGIVAAGKTVQGLQEMSQWFKER 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G  + +   +  +L K      + V V  +  +G+    + ++ +    
Sbjct: 171 NLHKYYLTLVKGKVE-RPAHVKGYLWKDEK--KNKVAVFPEKREGSLPIETKYEPLGISK 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                L+++  TGR+HQ+R H   +G P++GD KY +  K              LHA  +
Sbjct: 228 NGDTLLKVELLTGRSHQIRSHLAGLGHPVIGDWKYGSKEKNENFRKKYGIEFQLLHAWKL 287

Query: 296 DLPHPEG--GRL---QITAPLPAHMVKTWDSLGF 324
             P  EG    L    ITA +P    K     G 
Sbjct: 288 SFPKTEGILKELSLKTITADVPEKFQKALKGEGL 321


>gi|260587780|ref|ZP_05853693.1| pseudouridylate synthase [Blautia hansenii DSM 20583]
 gi|260542045|gb|EEX22614.1| pseudouridylate synthase [Blautia hansenii DSM 20583]
          Length = 337

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 75/334 (22%), Positives = 143/334 (42%), Gaps = 29/334 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +VV+  E   RLD++   +        L K+LR   + ++ K+   N ++Q    ++
Sbjct: 1   MKQLVVKEIESGQRLDKFLGKYLKEAPKSFLYKMLRKKNITLNGKKATGNEKLQPNDEIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    + L     E+          K S   +  ++YE++ +   NKP G+  Q      
Sbjct: 61  LFLSDDTLEKFCGEE----------KSSSRTELDIVYENNHVLFVNKPVGMLSQKAEKED 110

Query: 127 YHIDGFLKSWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  ++  ++         D +  +P + +RLD+ TSGI+   +T    Q +++ F+ R
Sbjct: 111 VSLVEYITGYLLEEKFLTKEDLRTFRPGVCNRLDRNTSGIVAAGKTVQGLQEMSQWFKER 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G  + +   +  +L K      + V V ++  +G+    + ++ +    
Sbjct: 171 NLHKYYLTLVKGKVE-RPAHVKGYLWKDEK--KNKVAVFQEKREGSLPIETKYEPLGISK 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYM 295
                L+++  TGR+HQ+R H   +G P++GD KY +  K              LHA  +
Sbjct: 228 NGDTLLKVELLTGRSHQIRSHLAGLGHPVIGDWKYGSKEKNENFRKKYGIEFQLLHAWKL 287

Query: 296 DLPHPEG--GRL---QITAPLPAHMVKTWDSLGF 324
             P  EG    L    ITA +P    K     G 
Sbjct: 288 SFPKTEGILKELSLKTITADVPEKFQKALKGEGL 321


>gi|240144135|ref|ZP_04742736.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis L1-82]
 gi|257203836|gb|EEV02121.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis L1-82]
 gi|291538917|emb|CBL12028.1| Pseudouridylate synthases, 23S RNA-specific [Roseburia intestinalis
           XB6B4]
          Length = 329

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 73/330 (22%), Positives = 134/330 (40%), Gaps = 22/330 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +  +E   R D++ K    +     + K+LR   + ++ K+     ++  G  ++
Sbjct: 1   MREFKINENEAGQRFDKYLKKLLGNAPGSFIYKMLRKKNITLNGKKADGTEKLNQGDDIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFL-----KSILLYEDSKIYVFNKPAGISVQG 121
           +                      L   S        K  ++YED  +   NKP G+  Q 
Sbjct: 61  LFFSDETFEKFSGSGTPDSEFEALKVLSREFTSGKRKLPVVYEDKDVIFINKPTGMLSQK 120

Query: 122 GSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTE 172
                   + ++ +++ +KG+         +P + +RLD+ TSG+L   +T    Q + +
Sbjct: 121 AKPEDISANEYILAYLIAKGELTESSFRTFRPSICNRLDRNTSGLLAAGKTLKGLQEMAK 180

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           + + R +QK Y  +V G  K     +  +L K        +   K +E       + +K 
Sbjct: 181 ALKERSVQKYYRCIVKGTVKEAS-YLKGYLQKDESSNQVLIRRTKPSEGEWLPIETEYKP 239

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYL 290
           I C    +   E+   TGR+HQ+R H   +G PI+GD+KY  +    +   +       L
Sbjct: 240 IRCMG-GYTEFEVHLMTGRSHQIRAHLASIGHPIIGDYKYGDSGVNVYFKKNARITSQLL 298

Query: 291 HARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           HA        E GR +ITAP  A   + W+
Sbjct: 299 HASRFVF---EDGR-EITAPCGAEFERAWN 324


>gi|152967132|ref|YP_001362916.1| pseudouridine synthase [Kineococcus radiotolerans SRS30216]
 gi|151361649|gb|ABS04652.1| pseudouridine synthase, RluA family [Kineococcus radiotolerans
           SRS30216]
          Length = 307

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 133/326 (40%), Gaps = 28/326 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  E  R+D         ++      I  +G V VD + V  ++R+ +G 
Sbjct: 1   MPEQRSLPVPDGLEGERVDAALSRLL-GLSRTRAADIAAAGHVLVDGRAVGKSDRLTAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +             ++I   ++        +                P G++     
Sbjct: 60  WLEVEVPDAPGAPTAVAERIEGLTIVHDDDDLVVVDK-------------PVGVAAHPSP 106

Query: 124 G-IAYHIDGFLK-----SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L             ++  + HRLD  TSG++VVA++  A   L  +F+ R
Sbjct: 107 GWTGPTVVGGLMGAGYTIATSGSAERQGVVHRLDVGTSGLMVVAKSEHAYSALKRAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K+Y +LV G P   +  I   + +  H GG Y   V         +++H++V++ F 
Sbjct: 167 TVEKVYHALVQGHPDPLRGTIDAPIGR--HPGGTYKFAVTAE---GKPSVTHYEVLEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +     E+   TGRTHQ+RVH   +  P VGD  Y A+        +  + +LHA  +  
Sbjct: 221 RAAALCEVHLETGRTHQIRVHFSALRHPCVGDLNYGADPTLAARLGL-TRQWLHAVRLGF 279

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSL 322
            HP  G+ ++ T+  P  +    + L
Sbjct: 280 EHPGTGQAVEFTSSYPEDLATALERL 305


>gi|58617049|ref|YP_196248.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Gardel]
 gi|58416661|emb|CAI27774.1| Ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Gardel]
          Length = 305

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 92/315 (29%), Positives = 160/315 (50%), Gaps = 16/315 (5%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +Y  ++ D   +R+DR+ +     I    ++K LR+  + +D  +VK N ++  G V+ +
Sbjct: 3   KYYTIQEDNLGVRIDRFIRKELR-IPQSLIEKFLRNRIILLDGLKVKSNTKLNVGNVIYV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++    +S +L +    +   ++YED  + V NKP+G+SVQGGS +  
Sbjct: 62  QNECIISKEKKDKKVCKLASESLVR---LICDNIVYEDDNVLVINKPSGVSVQGGSKVKI 118

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            I   L S     G+  ++ HRLD+ TSGIL++AR    ++ +   F+ R+++K Y +L 
Sbjct: 119 SISDVLDSIR--IGESMKIVHRLDKSTSGILMLARNSRVSRLIMNEFKDRKVKKKYLALT 176

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GIP +    I   ++KK H        +++N      A++ F  +         L++QP
Sbjct: 177 CGIPDDDCGQIDYPIVKKKH-----GITLEKNMSFVQQAVTMFSTLRKLPNDIGLLDLQP 231

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGR HQ+R+H  H+GCPIVGD KY         + +Q    LHA ++ + + +G  + I
Sbjct: 232 ITGRKHQIRIHLSHIGCPIVGDVKYGKICDNISNNYLQ----LHAYFLSI-NIDGKEISI 286

Query: 308 TAPLPAHMVKTWDSL 322
           T P+P++M      L
Sbjct: 287 TIPMPSYMQNIILQL 301


>gi|332704325|ref|ZP_08424413.1| Dephospho-CoA kinase [Desulfovibrio africanus str. Walvis Bay]
 gi|332554474|gb|EGJ51518.1| Dephospho-CoA kinase [Desulfovibrio africanus str. Walvis Bay]
          Length = 556

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 79/320 (24%), Positives = 135/320 (42%), Gaps = 36/320 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIP 68
           V   +    RLD +         +   +Q+ ++ G   V+ K   K + R++ G+ V + 
Sbjct: 14  VAGPNAAGKRLDVFLGEQVGDGFSRGRVQEWIKIGLASVNGKPWTKPSLRLRGGENVCLL 73

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS----- 123
                     ++  +                 +LY D  + V NKPAG++          
Sbjct: 74  GRAEGNCLTPEQGDLA----------------VLYRDDWLLVLNKPAGLTTHPAPSCPEG 117

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + + +            ++P + HRLD++TSG+LVVA T  A   L E F  RR+ K+Y
Sbjct: 118 TLVHRLLHHFPELAALDSERPGIVHRLDKDTSGLLVVALTERARLALAEDFAERRVDKVY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCW 242
            +LV G P+++ +   +  + +       + V+K   KG   A S ++++       F  
Sbjct: 178 LALVHGRPQDRGDI--DLPMGRHPTHKTRMAVLK---KGGRPARSAYEMLWSSRDGRFSL 232

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQNKLYLHARYMD 296
           L ++  TGRTHQ+RVH   +G PI+GD  Y        +    +   +  +  LHA  + 
Sbjct: 233 LRVRIFTGRTHQIRVHLAAIGHPIIGDSVYGPGPFAGWDKDLPWARLLAKRQMLHAHRLR 292

Query: 297 LPHPEGGR-LQITAPLPAHM 315
           L HP  GR L   +  P   
Sbjct: 293 LAHPADGRELVFVSTPPKDF 312


>gi|145224223|ref|YP_001134901.1| RluA family pseudouridine synthase [Mycobacterium gilvum PYR-GCK]
 gi|315444557|ref|YP_004077436.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           Spyr1]
 gi|145216709|gb|ABP46113.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           gilvum PYR-GCK]
 gi|315262860|gb|ADT99601.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           Spyr1]
          Length = 309

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 80/333 (24%), Positives = 146/333 (43%), Gaps = 32/333 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  + + V +    MR+D         ++      I   G V +D      ++++ +G 
Sbjct: 1   MT-TRSMPVPDGLAGMRVDAGLARLL-GLSRTAAAAIAEEGGVDIDGAPAAKSDKLVAGA 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGG 122
            + +              ++      +      ++ + +LY D  I   +KP G++    
Sbjct: 59  WLEV--------------RLPPPPAPVENTPVDIEGMGILYSDDDIVAVDKPPGVAAHAT 104

Query: 123 SG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ 
Sbjct: 105 VGWHGPTVLGGLAAAGFRISTSGIHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQ 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R ++K Y +LV G P      I   + +  H G D+   V ++     ++I+H+  ++  
Sbjct: 165 RTVEKRYHALVQGHPDPSSGTIDAPIGR--HRGHDWKFAVVED---GRHSITHYDTLEAH 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q    L+++  TGRTHQ+RVH   +  P  GD  Y A+        ++ + +LHAR + 
Sbjct: 220 -QAASLLDIELETGRTHQIRVHFAALHHPCCGDLTYGADPTLAKKLGLE-RQWLHARSLA 277

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
             HP +G R++ T+P PA +    D L  ++DR
Sbjct: 278 FAHPADGRRVEFTSPYPADLQHALDVLR-RHDR 309


>gi|266624507|ref|ZP_06117442.1| pseudouridylate synthase [Clostridium hathewayi DSM 13479]
 gi|288863645|gb|EFC95943.1| pseudouridylate synthase [Clostridium hathewayi DSM 13479]
          Length = 320

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 76/328 (23%), Positives = 144/328 (43%), Gaps = 31/328 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++V  +E   RLD+    +        L K++R   + ++ K+   + ++ +G  VR
Sbjct: 1   MRSLIVTENESGQRLDKLLAKYLNLAGKGFLYKMMRKKNITLNGKKCDGSEKLVTGDEVR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +            SV+  +    +   ++YED  I + NKP+G+  Q      
Sbjct: 61  LFFSDETIGKF---------SVHTLQEVKKVNLQIIYEDDHILLVNKPSGMLSQKAKDSD 111

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  ++  ++ S GQ         +P + +RLD+ TSG++V  ++    Q ++  F+ R
Sbjct: 112 ESLVEYIIDYLVSSGQLSTEQLKSFRPSVCNRLDRNTSGLVVAGKSLPGLQIMSAVFKDR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  +V G     K+ I  +L K S      V +     +G+   ++ ++ +   A
Sbjct: 172 SLHKYYRCVVKGSV-TDKQVITGFLKKDSVTN--QVTITAAEVEGSVPVMTEYEPLG-QA 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYM 295
           +    L ++  TGRTHQ+R H   +G PI+GD KY ++   +            LH+  +
Sbjct: 228 EGCTLLSVKLITGRTHQIRAHLASIGHPILGDFKYGSSAVNEEAKKRWNIRSQMLHSCTV 287

Query: 296 DLPH-PE-----GGRLQITAPLPAHMVK 317
             P  PE      G+   +APLP    K
Sbjct: 288 TFPELPEPLAYLSGK-TFSAPLPQTFRK 314


>gi|108758809|ref|YP_633659.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108462689|gb|ABF87874.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 306

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 90/322 (27%), Positives = 141/322 (43%), Gaps = 27/322 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q V V  +    RLDR+     P IN    + ++ SG VR+  KR +   ++  G+ + +
Sbjct: 4   QKVQVPREAAGERLDRFLSKQVPGINLERARALIDSGAVRIRGKRCQPTRKLWGGEEIEL 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                         +  +        S+     +L++DS + + NKP GI V+   G A 
Sbjct: 64  --------------ERPEPRAASVAASEGPVLPVLHDDSALVIVNKPPGIVVEP-EGRAA 108

Query: 128 HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            + G L +           +P + HRLD+ETSG L  ART  AA  L  SF+ +R+ K Y
Sbjct: 109 SVVGLLAAQRPPFDVEGLAQPGVVHRLDRETSGCLAFARTDTAAAALLRSFQEKRVDKRY 168

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           W+LV G P   +  +     +       +   V      A  A   F+V + FA     L
Sbjct: 169 WTLVLGQPPA-QGRLEGPYARDPADPRRFTTRV----PSARRAALSFEVRERFAD-AALL 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           E+   TGRTHQ+RV     G P++ D  Y     + +  +    +  LHA  ++LP P  
Sbjct: 223 EVDLDTGRTHQVRVQLSEAGFPVLADSLYGPPEARAHAAARALGRQALHAFTLELPSPAT 282

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G+ +++ APLP    +    L 
Sbjct: 283 GQPVRVEAPLPEDFQRALTVLR 304


>gi|224542885|ref|ZP_03683424.1| hypothetical protein CATMIT_02079 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524215|gb|EEF93320.1| hypothetical protein CATMIT_02079 [Catenibacterium mitsuokai DSM
           15897]
          Length = 322

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 84/334 (25%), Positives = 154/334 (46%), Gaps = 32/334 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +V++  +++ R+D++ K          + K+LR   V+V+ KRVK N  + SG  V 
Sbjct: 1   MKKLVIDQYDDHQRIDKYLKKVLVQAPSSLIYKMLRKKDVKVNGKRVKENYILHSGDEVE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
           +          + E K  + +  LT +   +   ++YED+ I + +KPAG+ V    +  
Sbjct: 61  L---------FLYEDKFKEYTKPLTIYELPITFKVVYEDAHILIVDKPAGLLVHEDINES 111

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +   + +++  KG+          P   HRLD+ TSG+++  +   A Q L    + 
Sbjct: 112 VNTLSNQVLTYLHQKGEYDPEKNISFTPGPVHRLDRNTSGLVIFGKDMRALQDLNTMMKT 171

Query: 177 RR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           R+ I+K Y ++  G  K+    ++ ++ K    G   +++VK++  GA    +   V+  
Sbjct: 172 RQGIEKKYLTIAMGHMKDA--TLSGYVKKNEDEG--KMYLVKKDTPGALSMKTIVHVLKR 227

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHAR 293
            +     +E+Q  TGRTHQ+R+H    G P++GD KY      K        N  +LHA 
Sbjct: 228 CS-TCSLVEVQLITGRTHQIRIHLSATGHPVMGDSKYGDFEWNKEVKKKFHLNHQFLHAY 286

Query: 294 YMDLPHPEG-----GRLQITAPLPAHMVKTWDSL 322
            +   +P G         +T+ LP  + K    L
Sbjct: 287 RLTFVNPIGSMSYLKGKTVTSQLPEQLEKIQKEL 320


>gi|71083312|ref|YP_266031.1| pseudouridylate synthase [Candidatus Pelagibacter ubique HTCC1062]
 gi|71062425|gb|AAZ21428.1| pseudouridylate synthase [Candidatus Pelagibacter ubique HTCC1062]
          Length = 326

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 80/341 (23%), Positives = 149/341 (43%), Gaps = 40/341 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M     ++V  DE N+RLD +       I+   ++ ++   +++++ + +   + ++ SG
Sbjct: 1   MEKNINLIVGEDENNLRLDVFINKRENLISRTRIKNLILKEKLKINDQIINSPSKKVLSG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +                +      +      K  ++YED  + + NKPAGI +  G
Sbjct: 61  DEINLQ---------------IPEPKEASLKPYNFKLQIVYEDDDLLIINKPAGIIMHPG 105

Query: 123 SG-IAYHIDGFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +G     I   L  +            +P + HR+D++TSG++V+A+     ++L+  F 
Sbjct: 106 AGNYDETIVNALMHYNKDSLSTIGDELRPGIVHRIDKDTSGLIVIAKNNETHENLSHQFS 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I ++Y  L+WG  +     I  ++ + S    +   +   N KG   AI+++K I+ 
Sbjct: 166 EHTITRVYQLLIWGKLRPSSGKIDTFITRSSK---NRQMMEVSNSKG-KRAITNYKTIEI 221

Query: 236 FAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGD------HKYCANFKGNFTSPI- 284
           F          +E +  TGRTHQ+RVH  HMG  I+GD      +K   N   N  + I 
Sbjct: 222 FENDKTPTLSLVECRLETGRTHQIRVHMTHMGNSIMGDGKYKKKYKKLKNIDTNLENLIY 281

Query: 285 -QNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
             ++ +LHA+ +   HP     +  T+ LP  +      L 
Sbjct: 282 KLDRQFLHAQTLGFIHPRTNEEMVFTSILPQELENILVLLR 322


>gi|89067930|ref|ZP_01155374.1| ribosomal large subunit pseudouridine synthase D [Oceanicola
           granulosus HTCC2516]
 gi|89046528|gb|EAR52584.1| ribosomal large subunit pseudouridine synthase D [Oceanicola
           granulosus HTCC2516]
          Length = 341

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 80/339 (23%), Positives = 134/339 (39%), Gaps = 50/339 (14%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   L +++  G VR++   V     R+  G  V I        
Sbjct: 17  RLDKALARDVPEDAALSRSRLARLVPDGAVRINGVVVTDVKARLGEGDAVEI-------- 68

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                   LD  V+     + +   ++YED ++ V NKPAG+ V    G      ++  +
Sbjct: 69  -------ALDIPVDSDMGGEPIPLDVVYEDDELIVINKPAGMVVHPAPGSPDGTLVNALI 121

Query: 134 KSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               +S       ++P + HR+D++TSG+LV A+T  A   L   F    +++ Y +L +
Sbjct: 122 HHCGESLSGVGGLRRPGIVHRIDKDTSGLLVAAKTDRAHHGLAAQFEAHDVERHYQALCF 181

Query: 189 GIPKNKKECIA----------NWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCF 236
           G+P      +           N L  ++ +        +Q        +A++  + ++ F
Sbjct: 182 GLPDAADPRLRGIRGTSFEPGNILKIQTQLARHKTDRQRQAVVWSNGRHAVTRARRVETF 241

Query: 237 AQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFTSPIQ 285
                   +E    TGRTHQ+RVH  H G  +VGD  Y    K                 
Sbjct: 242 GGPPVVARIECWLETGRTHQIRVHMAHAGHGLVGDPVYGGKRKIAKGAVSEAAMRALATF 301

Query: 286 NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
            +  LHA  +   HP  G L +  A +PA M +    L 
Sbjct: 302 PRQALHAATLGFKHPVTGELKRFAADMPADMTELCALLR 340


>gi|313904059|ref|ZP_07837439.1| pseudouridine synthase, RluA family [Eubacterium cellulosolvens 6]
 gi|313471208|gb|EFR66530.1| pseudouridine synthase, RluA family [Eubacterium cellulosolvens 6]
          Length = 370

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 91/374 (24%), Positives = 162/374 (43%), Gaps = 60/374 (16%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +  +  + RLD++ + + P      L K LR   + ++  +      +  G VVR
Sbjct: 1   MREIRIGREIASQRLDKFLQRYLPEAGTGLLYKQLRKKNITLNGGKAGGKELLSEGDVVR 60

Query: 67  IPPVINALNHI-----------IKEQKILDSSVNLTKH---------------------- 93
           I      L  +             + +    S N TK+                      
Sbjct: 61  IWFSEETLEKLSGGKGVSFSGTPADDRRALESENGTKNVTGGNVSRRTAGKKSPDKRTDR 120

Query: 94  -----SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ------ 142
                      +++YED  I + NKPAGI  Q        ++  L+S++  KG+      
Sbjct: 121 KQKRVKRLTPEMIVYEDEDIILINKPAGILSQKAKPEDVSLNEMLQSYLFEKGELTEGKL 180

Query: 143 ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
               P + +R+D+ TSG+++ A+  AAA+ ++E  R R +QK Y++LV G  K +KE + 
Sbjct: 181 KFYSPSVVNRIDRNTSGLVLGAKNLAAAREMSEMLRNRTLQKYYYALVNGQVK-EKEHVR 239

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            WL+K      + V +      GA+   + ++ +    +++  L ++  TG+THQ+R H 
Sbjct: 240 AWLVKDK--AKNQVKIYDHPVDGADLIETVYEPMAKV-ERYTLLRVELLTGKTHQIRAHL 296

Query: 260 LHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEG------GRLQITAPL 311
             +G  +VGD KY      + T      ++ +LHA  +  P  +G      GR    APL
Sbjct: 297 SFIGHSLVGDVKYGQKSMNSATREHTGLSRQFLHAEKVIFPDTDGALKSLSGR-CFRAPL 355

Query: 312 PAHMVKTWDSLGFK 325
           PA + KT +  G +
Sbjct: 356 PADLQKTLEIFGIR 369


>gi|154504965|ref|ZP_02041703.1| hypothetical protein RUMGNA_02475 [Ruminococcus gnavus ATCC 29149]
 gi|153794848|gb|EDN77268.1| hypothetical protein RUMGNA_02475 [Ruminococcus gnavus ATCC 29149]
          Length = 321

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 135/327 (41%), Gaps = 30/327 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + +   E   R D+    +        L K+LR   + ++ K+   N ++  G  V+
Sbjct: 1   MQEIKITEQEAGQRFDKLLGKYLNKAPKSFLYKMLRKKNITLNGKKASGNEKLAKGDCVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +      QK  ++    T  S      +LYED  I + NKP G+  Q  +   
Sbjct: 61  LFLSDETI------QKFSETFSGYTNVS----LDILYEDEDIILINKPVGMLSQKAARSD 110

Query: 127 YHIDGFLKSWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   L S++         D +  +P + +RLD+ TSGI+   ++ A  Q L++ F  R
Sbjct: 111 ESLVEHLISYLIQSHALTEEDLRTFRPSICNRLDRNTSGIVAAGKSMAGLQSLSQMFHDR 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I K Y  L  GI +     +  WL K        V ++ Q   G+   I+ ++ I    
Sbjct: 171 TIGKYYLCLTAGIIEKPS-RVEGWLFKDERTN--KVEILFQERPGSARIITEYRPIKSH- 226

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYM 295
                LE+   TG+THQ+R H   +G P++GDHKY A+                LHA  +
Sbjct: 227 DGVTLLEVHLITGKTHQIRAHLASVGHPLIGDHKYGASQINREYEQKYHLQSQLLHAARL 286

Query: 296 DLPHPEG-----GRLQITAPLPAHMVK 317
             P          + + TAPLP    +
Sbjct: 287 QFPVCTQTLCNVSKKEFTAPLPKQFYR 313


>gi|108757756|ref|YP_630767.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108461636|gb|ABF86821.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 316

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 83/332 (25%), Positives = 144/332 (43%), Gaps = 32/332 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + +  + V+ D+   R+D +       ++   L+++  +G V+V+ +  K    + +GQ 
Sbjct: 4   SKLHTLTVDADKAGQRVDLFIGEAL-GLSRARLKRLFEAGAVKVNGRPAKKGLTLTAGQH 62

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--G 122
           + +              ++ + S      +DF    +L+ED  +   +KPAG        
Sbjct: 63  IAV--------------EVEEESREAVPDADF-PLTVLHEDDSLVFVDKPAGRPSHPLQS 107

Query: 123 SGIAYHIDGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                  +  +  + +        ++  L HRLD ETSG++V ARTR A   + E+F  R
Sbjct: 108 GETGTVANALVARYPECALASLDAREGGLCHRLDVETSGVVVAARTRDAWNAVREAFGSR 167

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G P   +  I   L +      D V       + A  A+S F V+    
Sbjct: 168 AVDKRYLALVTG-PLTDEGDIDLPL-RHHPRHPDRVEPAPYGAEDARDAVSKFTVLSRSG 225

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + F  +E++  TG  HQ+R H   +G PIVGD  Y         +P   + +LHAR + L
Sbjct: 226 E-FSVVEVKILTGVLHQVRAHLAGIGAPIVGDSLYGGR-----EAPELGRFFLHARSLGL 279

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
            HP+  R + + +PLP  +    +  G    R
Sbjct: 280 THPQTRRNMTVHSPLPPELRAELERRGLPLPR 311


>gi|330836420|ref|YP_004411061.1| pseudouridine synthase, RluA family [Spirochaeta coccoides DSM
           17374]
 gi|329748323|gb|AEC01679.1| pseudouridine synthase, RluA family [Spirochaeta coccoides DSM
           17374]
          Length = 329

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 90/354 (25%), Positives = 147/354 (41%), Gaps = 55/354 (15%)

Query: 4   MTYVQYVVVENDEEN-MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M +V   +V +D +   R+D +       ++   +     S ++ V+ + VK +  I  G
Sbjct: 1   MCHVFESIVPDDADGKQRVDAYLAAA-SGVSRSIIGDA--SSRIMVNGREVKRSKAIAPG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V +    N   +I  +   LD               +LYED  I   +KP GI V  G
Sbjct: 58  DAVILYWQENPPGNIEPQDIPLD---------------ILYEDDDILFIDKPQGIVVHPG 102

Query: 123 SGIAYHID----------GFLKSWVDSKGQ-----------------KPRLTHRLDQETS 155
           +G                 F++++                       +P + HRLD++TS
Sbjct: 103 AGNPDGTVVNALVFRYGPDFIRAYGGQDEHEDAGDETDEAVDRTDFLRPGIVHRLDKDTS 162

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V+ARTR A  ++   F      K Y +LV G  K+ +  I   L +  +   D    
Sbjct: 163 GVMVIARTRLAHGYMARQFSEHTAVKHYIALVEGSMKDDEGVIITNLARDRN---DRKKF 219

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                K    A + ++V+  +      L ++  TGRTHQ+RVH  H+G P+VGD  Y   
Sbjct: 220 RVSTGKEGKRAETRWRVVARYG-VCTLLRIRIMTGRTHQIRVHMAHLGHPVVGDGVYGGR 278

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
            K          L LHAR +D+  P  GR L+I+AP+P   ++     G  + +
Sbjct: 279 RKSFPGVT----LMLHARLLDVSRPSDGRHLKISAPVPQRFIELVHEAGGSFPQ 328


>gi|126698644|ref|YP_001087541.1| putative pseudouridylate synthase [Clostridium difficile 630]
 gi|115250081|emb|CAJ67901.1| putative pseudouridylate synthase [Clostridium difficile]
          Length = 300

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 74/313 (23%), Positives = 135/313 (43%), Gaps = 32/313 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +EE M L     +   + +  +L K+ R   V V+    K + ++ SG ++ +       
Sbjct: 16  NEEEMTLKEVLLDKL-NFSVRSLSKMKREKSVLVNGVYKKPSLKVYSGDLIEVKIYEEKA 74

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFL 133
           N                     L   ++Y+D  I + NKP  + V    S     I   +
Sbjct: 75  N----------------FEPQDLNLQIIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGI 118

Query: 134 KSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             ++D++ +  K R  +RLD  TSG+++VA+   A   L+ +    +++K Y ++V GI 
Sbjct: 119 SYYIDNQKENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGII 178

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K  +  I   + + +      +      ++    +++H+KVI+   +    LE+   TGR
Sbjct: 179 KENEGTIDEPIYRPTEDSIKRII-----DERGQSSVTHYKVIERL-ENATVLEVSLETGR 232

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH  H+G  I+GD  Y           + N+  LHA  ++   P    +L+  A 
Sbjct: 233 THQIRVHMAHIGHGIIGDELYGY-----VDEELINRQALHAYKLEFEQPRTKEKLKFKAD 287

Query: 311 LPAHMVKTWDSLG 323
           +P  M +    L 
Sbjct: 288 IPEDMKELISKLR 300


>gi|291545928|emb|CBL19036.1| pseudouridine synthase, RluA family [Ruminococcus sp. SR1/5]
          Length = 322

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/342 (22%), Positives = 142/342 (41%), Gaps = 37/342 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++  +E   R D++              +      + ++ K+   N ++ SG  V+
Sbjct: 1   MKEFIINENEAGQRFDKYLAKLLREAPKSFFLQNDEEKNITLNGKKATGNEKLFSGDHVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          + ++     S N +         ++YED  I + NKPAG+  Q      
Sbjct: 61  L---------FLSDETFEKFSGNDSAPRAHYALDIIYEDENILLINKPAGMLSQPADDGT 111

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  +L  ++   G          +P + +RLD+ TSG++   ++ +  Q L+  F+ R
Sbjct: 112 PSLVEYLTGYLLKNGSLTENDLRTFRPSVCNRLDRNTSGLIAAGKSLSGLQELSGMFKSR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  LV G+ K ++  I  +L K      + V + KQ ++ A    + +  +    
Sbjct: 172 ELHKYYLCLVEGVLKEER-YIKGYLAKDKK--SNKVTIYKQEKENALPVETKYYPLGTNG 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            +   L+++  TGR HQ+R H    G  IVGD KY    K            LH+  M+ 
Sbjct: 229 TR-TLLKVELITGRAHQIRAHLASEGHSIVGDPKYGKADKK------LKGQLLHSFRMEF 281

Query: 298 PHPEG------GRLQITAPLPAHMVKTW--DSLGFKYDRNLY 331
           P  +G      G++  TAPLP   ++T   + L   Y  NL 
Sbjct: 282 PSMKGSLSYLSGKV-FTAPLPEIFLRTLKEEKLEESYYENLE 322


>gi|300853931|ref|YP_003778915.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           ljungdahlii DSM 13528]
 gi|300434046|gb|ADK13813.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           ljungdahlii DSM 13528]
          Length = 299

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 146/324 (45%), Gaps = 31/324 (9%)

Query: 4   MTYVQYV-VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           MT  + V  V+  +E ++L R++      ++   ++    SG++ ++ KRVK N+ ++SG
Sbjct: 1   MTENKIVFTVDEKDEGLKL-RYYLQRVQRLSGRLIKGAALSGRIEINNKRVKLNHIVKSG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + + +  V     ++  E+               +   + YED  + V NK  GI V   
Sbjct: 60  ESISLNLVKEESQNVEPEK---------------MDIEVAYEDDDLIVVNKRPGIVVHPT 104

Query: 123 SGIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                  +   L  +   KG+    RL  RLD +TSG+++V + + A   L    +    
Sbjct: 105 RSYPSGTLANGLMYYFKEKGEDCIVRLVSRLDMDTSGLIIVGKNQFAHMALARDMKSEEF 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +++ G  K  +  I   + ++       +      ++    +I+H+KVI  F   
Sbjct: 165 EKSYIAVIHGKMKENEGTIDLPIYRQEGEDIRRII-----DERGQKSITHYKVIKDFKND 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L++   TGRTHQ+RVH  ++G P+ GD  Y       +     N+  LHA  +  PH
Sbjct: 220 Q-LLKLTLETGRTHQIRVHLSYLGHPLYGDTLYGKEDDSMY----INRQALHAYRLKFPH 274

Query: 300 PEGGRL-QITAPLPAHMVKTWDSL 322
           P G ++ ++   +P  ++K  + +
Sbjct: 275 PRGNKILELETAIPEDILKLIEKI 298


>gi|255305986|ref|ZP_05350158.1| putative pseudouridylate synthase [Clostridium difficile ATCC
           43255]
          Length = 300

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 74/313 (23%), Positives = 134/313 (42%), Gaps = 32/313 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +EE M L         + +  +L K+ R   V V+    K + ++ SG ++ +       
Sbjct: 16  NEEEMTLKEVLLAKL-NFSVRSLSKMKREKSVLVNGVYKKPSLKVYSGDLIEVKIYEEKA 74

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFL 133
           N                     L   ++Y+D  I + NKP  + V    S     I   +
Sbjct: 75  N----------------FEPQDLNLQIIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGI 118

Query: 134 KSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             ++D++ +  K R  +RLD  TSG+++VA+   A   L+ +    +++K Y ++V GI 
Sbjct: 119 SYYIDNQKENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGII 178

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K  +  I   + + +      +      ++    +++H+KVI+   +    LE+   TGR
Sbjct: 179 KENEGTIDEPIYRPTEDSIKRII-----DEIGQSSVTHYKVIERL-ENATVLEVSLETGR 232

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH  H+G  I+GD  Y           + N+  LHA  ++   P    +L+  A 
Sbjct: 233 THQIRVHMAHIGHGIIGDELYGY-----VDEELINRQALHAYKLEFEQPRTKEKLKFKAD 287

Query: 311 LPAHMVKTWDSLG 323
           +P  M +    L 
Sbjct: 288 IPEDMKELISKLR 300


>gi|325674393|ref|ZP_08154081.1| RluA family RNA pseudouridine synthase [Rhodococcus equi ATCC
           33707]
 gi|325554653|gb|EGD24327.1| RluA family RNA pseudouridine synthase [Rhodococcus equi ATCC
           33707]
          Length = 302

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 76/320 (23%), Positives = 137/320 (42%), Gaps = 30/320 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +  + MR+D         ++   +  +   G V VD      ++R+ +G  + +    
Sbjct: 3   VPDGLDGMRVDAGLARLL-GLSRTAVATLTEEGAVLVDGAAAGKSDRLSAGTWLEV---- 57

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG-IAYHI 129
                     ++ +    LT  ++ ++ + +LY D  I   +KP G++     G     +
Sbjct: 58  ----------ELPEPPRPLTIEAEPVEGMEILYADDDIVAVDKPVGVAAHASVGWTGPTV 107

Query: 130 DGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R I K Y 
Sbjct: 108 IGGLAAAGFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTVLKRAFKQRTIDKRYH 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G P      I   + +  H   D+   V  +      +++H+  ++ F Q    L+
Sbjct: 168 ALVQGHPDPSSGTIDAPIGR--HRSNDWKFAVTAD---GKPSVTHYDTVEAF-QAASLLD 221

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TGRTHQ+RVH   +  P  GD  Y A+ +      ++ + +LHAR +   HP  G 
Sbjct: 222 IHLETGRTHQIRVHFSALRHPCCGDLTYGADPRLAERLGLE-RQWLHARSLGFAHPADGH 280

Query: 305 -LQITAPLPAHMVKTWDSLG 323
            ++IT+  P  +      L 
Sbjct: 281 WVEITSDYPKDLQHALGVLR 300


>gi|295696843|ref|YP_003590081.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
 gi|295412445|gb|ADG06937.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
          Length = 327

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 76/335 (22%), Positives = 138/335 (41%), Gaps = 52/335 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE  +   ++    +     ++   ++  +    +R + +    + R+ +G ++ I    
Sbjct: 11  VEARDHGRQVREVLQGRL-QVSRRLVRLAITQNGIRRNGRPAYLSERVSAGDILEIRWGE 69

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
              + ++ E    ++               LYED  + V NKP G+ V    G+A     
Sbjct: 70  TPSDDVLPEPIPFET---------------LYEDEDVLVVNKPPGMLVHPTKGVAAGTLA 114

Query: 130 DGFLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRM------------ 176
           +G + +W  +   +P R  +RLD++TSG++++A+ + A Q L+   R             
Sbjct: 115 NGVVYAWRLTGSYRPFRPLNRLDRDTSGLVLIAKNQFAHQRLSRDLRFVEGGRSPVFGAD 174

Query: 177 --------RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
                   RR+ + Y +LV G     +  I   + +  + G        Q       A +
Sbjct: 175 EAERLDGVRRVHREYAALVQGRVVADRGWIDLPIDRDPNHGNRR-----QVAPAGRRART 229

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
            F+V +         +++  TGRTHQ+RVH   +G P++GD  Y         SP   + 
Sbjct: 230 RFEVAERVGNAAYL-KVRLQTGRTHQIRVHLAELGHPVIGDTLYGE------PSPWIERQ 282

Query: 289 YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            LHA  +   HP  G R+Q+TAP    M + W  L
Sbjct: 283 ALHAERLVFDHPRTGKRIQVTAPWFPDMAELWRRL 317


>gi|323484810|ref|ZP_08090167.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323401916|gb|EGA94257.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 333

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 138/332 (41%), Gaps = 31/332 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q V +  +E   RLD+    +        + K+LR   + ++ K+   + ++  G  V+
Sbjct: 1   MQVVKITKNEAGQRLDKLLAKYLNLAGKSFIYKMLRKKNITLNGKKCDGSEKLSEGDEVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          + ++ I   S    +     K  ++YED  I + NKP+G+  Q      
Sbjct: 61  L---------FLSDETIEKFSEVKIQKVRKRKLDVVYEDDDIILINKPSGMLSQKAKETD 111

Query: 127 YHIDGFLKSWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  +L  ++         D +  KP + +RLD+ TSGI++  ++    Q ++E+ + R
Sbjct: 112 ESLVEYLIQYLLDGGKLTKEDMRQFKPSVCNRLDRNTSGIVIAGKSLPGLQLMSEAIKER 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVID 234
            I K Y  +V G     KE I  +L K            + + + +K A    + ++ + 
Sbjct: 172 TIGKYYLCIVKGSVAGPKE-IDGYLKKNEKTNQVTVLKANELCREDKDALPIRTQYRPLC 230

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHA 292
              +    LE++  TGR+HQ+R H   +G PI GD+KY      +            LHA
Sbjct: 231 SDGR-HTLLEVKLITGRSHQIRAHLASIGHPIAGDYKYGDPAVNREARDKYAVQSQMLHA 289

Query: 293 RYMDLPHPEGGRL------QITAPLPAHMVKT 318
             + +P      L      + TA  P   ++ 
Sbjct: 290 WRLVMPKELREPLAGLGGREFTAKPPEEFMRM 321


>gi|255326239|ref|ZP_05367325.1| ribosomal large subunit pseudouridine synthase D [Rothia
           mucilaginosa ATCC 25296]
 gi|255296693|gb|EET76024.1| ribosomal large subunit pseudouridine synthase D [Rothia
           mucilaginosa ATCC 25296]
          Length = 328

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 74/304 (24%), Positives = 133/304 (43%), Gaps = 35/304 (11%)

Query: 33  NFVNLQKILRSGQVRV--DKKRVK--FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
                   +R G V V  + K VK   + ++ +G  V +          I+ +K+     
Sbjct: 40  PRTRTSGWIRDGHVTVTNNGKTVKIGKSYKLSAGDEVVVDAPAPRDLADIRPEKV----- 94

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------- 140
                       +++ D  I V +KPAG++     G  +H    + + +           
Sbjct: 95  --------DGFRIVHLDDDIVVVDKPAGVAAHPSPG--WHGPTVISALMGEGISVATSGA 144

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            ++  + HRLD  TSG++VVAR+  A   L  +F+ R + K+Y +LV G+P   +  I  
Sbjct: 145 AERQGIVHRLDVGTSGLMVVARSERAYTELKRAFKERTVDKVYHTLVQGLPDPLRGTIDA 204

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H G ++   V ++      +I+H+ V++ F      +E+   TGRTHQ+RVH  
Sbjct: 205 PIGR--HPGNEWKFAVVED---GRNSITHYDVLEAFG-PASLVEVHLETGRTHQIRVHFS 258

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
            +  P  GD  Y A+ + +    +  + +LHA  +   HP  G R+  T+  P  +    
Sbjct: 259 ALRHPCCGDLTYGADPRFSAELGL-TRQWLHAHRLGFDHPGTGERVTFTSEYPLDLSYAL 317

Query: 320 DSLG 323
            +L 
Sbjct: 318 TALR 321


>gi|323691883|ref|ZP_08106137.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
 gi|323504090|gb|EGB19898.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
          Length = 333

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 138/332 (41%), Gaps = 31/332 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q V +  +E   RLD+    +        + K+LR   + ++ K+   + ++  G  V+
Sbjct: 1   MQVVKITKNEAGQRLDKLLAKYLNLAGKSFIYKMLRKKNITLNGKKCDGSEKLSEGDEVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          + ++ I   S    +     K  ++YED  I + NKP+G+  Q      
Sbjct: 61  L---------FLSDETIEKFSEVKIQKVRKRKLDVVYEDDDIILINKPSGMLSQKAKETD 111

Query: 127 YHIDGFLKSWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  +L  ++         D +  KP + +RLD+ TSGI++  ++    Q ++E+ + R
Sbjct: 112 ESLVEYLIQYLLDGGKLTKEDMRQFKPSVCNRLDRNTSGIVIAGKSLPGLQLMSEAIKER 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD---YVHVVKQNEKGANYAISHFKVID 234
            I K Y  +V G     KE I  +L K            + + + +K A    + ++ + 
Sbjct: 172 TIGKYYLCIVKGSVAGPKE-IDGYLKKNEKTNQVTVLKANELCREDKDALPIRTQYRPLC 230

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHA 292
              +    LE++  TGR+HQ+R H   +G PI GD+KY      +            LHA
Sbjct: 231 SDGR-HTLLEVKLITGRSHQIRAHLASIGHPIAGDYKYGDPAVNREARDKYAVQSQMLHA 289

Query: 293 RYMDLPHPEGGRL------QITAPLPAHMVKT 318
             + +P      L      + TA  P   ++ 
Sbjct: 290 WRLVMPKELREPLAGLGGREFTAKPPEEFMRM 321


>gi|253577230|ref|ZP_04854549.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251843344|gb|EES71373.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 321

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 133/327 (40%), Gaps = 47/327 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINF---VNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           V   E+   +    +     I+      + K+   G V ++ +RV  +  +++G  V + 
Sbjct: 13  VPAAEDGWTVKSVLQRRM-GISRKLLSRI-KLTERG-VMLNGERVYISVPVKAGDTVSVS 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                   I+ E    D               ++YED  + + NK AG+ V    G   H
Sbjct: 70  LEKETSTDILPEPIPFD---------------IVYEDEALLIVNKAAGLIVHPTHG---H 111

Query: 129 IDGFLKS----WVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             G L +    +   KG+K R    HRLDQETSG++ +A+     QH++E      + K 
Sbjct: 112 YTGTLANGVVYYWQEKGEKFRFRPVHRLDQETSGLIAIAKNAYVHQHISEQLIAGEVTKK 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +LV G P   +  I   + +        +            +++++KV + +      
Sbjct: 172 YTALVHGCPAVPEGTIDGPIDRDPAEPHRRIV-----TPSGYPSLTYYKVAEAYGDGA-R 225

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ----------NKLYLHA 292
           +E++  TGRTHQ+RVH   +G P++GD  Y         +P +           +  LHA
Sbjct: 226 VELRLGTGRTHQIRVHMTSIGHPLIGDKFYGMPGLAELPAPARERIARLDAAIGRQALHA 285

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKT 318
             +   HP  G  L   + LP  M+K 
Sbjct: 286 SELGFRHPLTGEALTFKSELPEDMLKL 312


>gi|299470964|emb|CBN79948.1| Pseudouridine synthase, RluD [Ectocarpus siliculosus]
          Length = 489

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 85/338 (25%), Positives = 133/338 (39%), Gaps = 48/338 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + + VE  E   RLD +     P  +      + + G V V  K  K + +++ GQ V 
Sbjct: 103 TEMLTVEEGEGGKRLDSFLGARMPEQSRSYFGGLCQLGMVLVGGKTAKKSVKVEEGQEVE 162

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  +I               S  L+   + +   +LYED +I   +KPAG+ V    G  
Sbjct: 163 VRFII---------------SPELSLQGEDIPLDILYEDDEIIAVSKPAGMVVHPAPGSW 207

Query: 127 Y-HIDGFLKSWVDSKG------------------------QKPRLTHRLDQETSGILVVA 161
                  L   ++  G                         +P + HRLD+ T+G+L+ A
Sbjct: 208 NGTFVNALVFHLEKSGADGNGLGVAEAAFQSVPDGEHNPSLRPGIVHRLDKGTTGVLLAA 267

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L E F  RRI K Y ++  G P  K   I   + +        +  V   + 
Sbjct: 268 KNPTMQAKLAELFAQRRISKSYLAVCVGNP-GKAATIDVPIGRHPR-DRQRMVAVPTIQP 325

Query: 222 G--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--K 277
              +  A+S    +  F  K    E+   TGRTHQ+RVH  H   P++GD  Y  N   +
Sbjct: 326 NIRSRRALSVVTTV-AFDGKLSVAEVSIETGRTHQIRVHLQHRRTPVLGDEVYGNNDWNR 384

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
               S    +  LHAR ++  HP  G  + + APLP+ 
Sbjct: 385 RLRQSTGLTRPLLHARSLEFKHPNTGEVVSLAAPLPSD 422


>gi|110004584|emb|CAK98921.1| probable pseudouridine synthase d protein [Spiroplasma citri]
          Length = 306

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 75/331 (22%), Positives = 142/331 (42%), Gaps = 44/331 (13%)

Query: 9   YVVVENDEENMRLDRWFKNHYPH----INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
            ++V +     R+D+   +++       +   +Q++++  +V+V+ + V+ N   Q G  
Sbjct: 5   TLIVSSSA---RIDKILTDYFKTNTTPFSRTKIQELIKQEKVQVNGQVVRANYVSQIGDH 61

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V I       + +                   +   +LYEDS + V +KP  + V    G
Sbjct: 62  VIIEFPSAKASELTP---------------LAIPLTILYEDSYLMVIDKPNNLVVHPAPG 106

Query: 125 IAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
              H +  L + + ++G         Q+P + HR+D++T+G L++A+       L +  +
Sbjct: 107 ---HQNDTLVNALLARGVQWSTASGEQRPGIVHRIDRQTTGTLIIAKNDVVHHQLQQQIQ 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +++Q+ Y +LV G     +  I   + +  +     V       K +  A+++  VI+ 
Sbjct: 164 TKQLQRRYLALVHGQIIENRAKIDAPIGRDPNNRKKMV----VTAKNSKKALTNIVVIER 219

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F   + ++E +  +GRTHQ+R H  ++  PIVGD  Y        +       YLHA  +
Sbjct: 220 FND-YTYIECELESGRTHQIRAHLKYINHPIVGDPLYGTVADKKESF----GQYLHAYQL 274

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
              HP     L ITA LP    +    L  K
Sbjct: 275 RFIHPVTKESLTITAALPQEFEQRLAILRAK 305


>gi|262376643|ref|ZP_06069871.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           lwoffii SH145]
 gi|262308353|gb|EEY89488.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           lwoffii SH145]
          Length = 350

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 74/324 (22%), Positives = 129/324 (39%), Gaps = 36/324 (11%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           +      R+D+     +   +   L++ ++ G + V+ + VK   +    + + +   + 
Sbjct: 44  DETYIGQRIDQIAAMVWNDFSREKLKQWIKDGNLLVNGQPVKPKFKSDGFETLTLNVELE 103

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHID 130
           A    + E   LD                          NKP G+ V  G+G      ++
Sbjct: 104 AQTRSLPEDIPLDIIYEDDDIIVI---------------NKPVGMVVHPGAGNSSGTLVN 148

Query: 131 GFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             L  +  S +  +  L HR+D++TSG+LVVA+   A   L++    + + ++Y  +V+G
Sbjct: 149 ALLHHYPKSAELARAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLEKKSVYRLYDLVVYG 208

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPH 248
                   I         I    V  VK     G   A++H+ V + F Q F  ++ +  
Sbjct: 209 N-------IIAGGTIDEPIKRHPVDRVKMTVLPGGKDAVTHYNVKERF-QHFTRVQARLE 260

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLPHP 300
           TGRTHQ+RVH  ++G  +VGD  Y         A+   + T     +  LHA  + L HP
Sbjct: 261 TGRTHQIRVHFSYIGFGLVGDQVYMPRVRMPAGASQLLDDTLRGFKRQALHAVQLGLTHP 320

Query: 301 EG-GRLQITAPLPAHMVKTWDSLG 323
                +   AP P       + L 
Sbjct: 321 RTKEEMTFEAPWPEDFANLVEVLR 344


>gi|15618629|ref|NP_224915.1| pseudouridine synthase [Chlamydophila pneumoniae CWL029]
 gi|15836251|ref|NP_300775.1| pseudouridine synthase [Chlamydophila pneumoniae J138]
 gi|16752321|ref|NP_444579.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           pneumoniae AR39]
 gi|33242078|ref|NP_877019.1| ribosomal large subunit pseudouridine synthase A [Chlamydophila
           pneumoniae TW-183]
 gi|4377023|gb|AAD18858.1| predicted Pseudouridine Synthase [Chlamydophila pneumoniae CWL029]
 gi|7188966|gb|AAF37922.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           pneumoniae AR39]
 gi|8979091|dbj|BAA98926.1| pseudouridine synthase [Chlamydophila pneumoniae J138]
 gi|33236588|gb|AAP98676.1| ribosomal large subunit pseudouridine synthase A [Chlamydophila
           pneumoniae TW-183]
 gi|269302507|gb|ACZ32607.1| pseudouridine synthase, RluA family [Chlamydophila pneumoniae
           LPCoLN]
          Length = 325

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 86/327 (26%), Positives = 143/327 (43%), Gaps = 36/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSG 62
           M  V    V  +    RLD++    +P  +    Q+ + SG V+++ +   +   R+  G
Sbjct: 1   MKTVTSFTVCKENSG-RLDKYLTEVHPKYSRAFYQEHILSGLVQINGQINTRVATRLNCG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +V I               I +    L    + +    +YED  I V NKP  + V   
Sbjct: 60  DIVTI--------------DIQEKEELLELLPEAIPLDKVYEDGMILVINKPRDMVVHPA 105

Query: 123 SG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            G         + + I   LK     +  +P + HRLD++TSG+++ A+TR A +  +E 
Sbjct: 106 PGHFHGTLVHALLHEIGERLKEEFPEEPWRPGIVHRLDKDTSGLIITAKTRQAKKVFSEL 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  +R++K Y ++  G P  +   I   + +  +   +     +        A++H +V+
Sbjct: 166 FSTKRLKKSYLAVCIGKP--RSTTIHTHISRHQNKRKEMTVSSQ-----GKEAVTHCQVL 218

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F  K  ++ + P TGRTHQLRVH  H+G PI+GD  Y        +S   +K  LHA 
Sbjct: 219 -AFNGKLSFVALSPETGRTHQLRVHMKHLGTPILGDPVYG--IPSMNSSYGLDKQQLHAY 275

Query: 294 YMDLPHPEGGRLQ-ITAPLPAHMVKTW 319
            +D  HPE  +   + A LP  M    
Sbjct: 276 SVDFTHPETRQFCSLKAGLPEDMRSLL 302


>gi|210615565|ref|ZP_03290663.1| hypothetical protein CLONEX_02881 [Clostridium nexile DSM 1787]
 gi|210150232|gb|EEA81241.1| hypothetical protein CLONEX_02881 [Clostridium nexile DSM 1787]
          Length = 323

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 73/331 (22%), Positives = 140/331 (42%), Gaps = 30/331 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q ++V  +E   RLD+    +        L K+LR   + ++ K+   N ++  G  V+
Sbjct: 1   MQEIIVAANEAGQRLDKMLAKYLNEAPKSFLYKMLRKKNIVLNGKKATGNEKLAVGDSVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +              + +    N+      +   ++YED  + + NKP G+  Q  +   
Sbjct: 61  LFL----------ADETIAKFSNIHAVHTNVTLDIIYEDENVLLINKPVGMLSQKAAADD 110

Query: 127 YHIDGFLKSWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   + S++         + +  +P + +RLD+ TSG++   ++ A  Q +   F+ R
Sbjct: 111 ESLVEHIISYMLETRQLTEEELRKFRPSVCNRLDRNTSGLVAAGKSLAGLQEMGTLFKNR 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  LV G  K   + ++ +L+K        V V K  +       + ++ +    
Sbjct: 171 SLRKYYRCLVAGEVK-HSQSVSGYLVKDEKTN--KVTVSKAEKGDCLPIETEYEPLWSNG 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYM 295
            K+ +LE+   TGRTHQ+R H   +G PI+GD+KY +    +            LHA  +
Sbjct: 228 -KYTYLEVHLITGRTHQIRAHLASIGYPIIGDYKYGSKKVNDRLKEQYGLKSQLLHAYRL 286

Query: 296 DLPHPEGG-----RLQITAPLPAHMVKTWDS 321
           ++P   G        +  APLP        +
Sbjct: 287 EMPACTGELSNLSERKFVAPLPKLFQNILKA 317


>gi|167464208|ref|ZP_02329297.1| pseudouridine synthase, RluA family protein [Paenibacillus larvae
           subsp. larvae BRL-230010]
 gi|322383741|ref|ZP_08057492.1| pseudouridylate synthase-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
 gi|321151953|gb|EFX44896.1| pseudouridylate synthase-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
          Length = 310

 Score =  217 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 137/325 (42%), Gaps = 36/325 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V  +++ M L    +     ++   L ++ L    + V+  R   + ++++G +V +   
Sbjct: 11  VPPEDDGMLLKSIIQKRLK-VSRKLLSRLKLTEKGIMVNGTRQYISVKVKTGDLVELRME 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
               + I+                  +   +L+ED ++ V NK AG+ V    G   H  
Sbjct: 70  QETSDDILP---------------QSIPLNILHEDEQLLVLNKEAGMIVHPTHG---HYV 111

Query: 131 GFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             + + V           + R  HRLDQETSG+L +A+     Q ++E   M  + K Y 
Sbjct: 112 NTVANAVVFHWQQKGICHRFRPVHRLDQETSGVLAIAKNPYVHQQISEQMMMHALDKQYL 171

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV+G+ K  +  + + + +           ++        A++H++V+         + 
Sbjct: 172 ALVYGVVKEDRGTLDDPIDRNKDNPH-----IRTVTPSGYPAVTHYEVLKRM-NGATLVR 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +   TGRTHQ+RVH  H+G P++GD  Y        G  T  + ++  LHA  +   HP 
Sbjct: 226 LWLETGRTHQIRVHMQHLGHPLLGDKLYRLEQFEQLGEKTKKLISRHALHAESLGFVHPG 285

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFK 325
            G ++  TA LP  M       GF 
Sbjct: 286 TGQKVTFTASLPKDMAHVIKEWGFS 310


>gi|195644818|gb|ACG41877.1| RNA binding protein [Zea mays]
          Length = 439

 Score =  217 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 84/377 (22%), Positives = 142/377 (37%), Gaps = 80/377 (21%)

Query: 12  VENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           V   E   R+D W         ++   +Q  +R+G V V+ + V K ++ ++ G +V   
Sbjct: 63  VPVGEGRSRVDAWISARLGGGGVSRARVQASIRAGLVAVNGRPVSKVSHTVKGGDLVSCT 122

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                          +     L   ++ +   ++YED  + V NKPA + V    G A  
Sbjct: 123 ---------------VSELQPLRAEAEDIPLDIVYEDDHVLVVNKPAHMVVHPAPGNAKG 167

Query: 127 YHIDGFLKSW-----------------------------------------VDSKGQKPR 145
             ++  L                                            V +   +P 
Sbjct: 168 TLVNAILHHCKISTFTCLARSSAGDECPDSSDEDTDVFHVDQFAAEDVSSEVRNALVRPG 227

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+ TSG+LVVA+   +   L E F++  I+++Y SL  G P      I   + + 
Sbjct: 228 IVHRLDKGTSGLLVVAKDEHSHARLAEQFKLHTIRRVYISLTCGAPNPNSGRIEASIARD 287

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGC 264
            +       +     + A  A S +KV + FA      +E +  TGRTHQ+R HA ++G 
Sbjct: 288 PNNRIRMTAIAGSGHRYARNAASRYKVREVFAGGGSALVEWRLETGRTHQIRAHAKYIGI 347

Query: 265 PIVGDHKYCA-----------NFKGNFTSPIQN------KLYLHARYMDLPHPEGGR-LQ 306
           P++GD  Y                  + S + N      +  LHA  +   HP  G+ L+
Sbjct: 348 PLLGDETYGGTQSMALSLLRPRSPSKYHSGLSNLLSKVDRPCLHAASLGFKHPRSGKVLE 407

Query: 307 ITAPLPAHMVKTWDSLG 323
            + P P   ++    L 
Sbjct: 408 FSCPPPDDFLEVLGELR 424


>gi|189219158|ref|YP_001939799.1| pseudouridylate synthase, 23S RNA-specific [Methylacidiphilum
           infernorum V4]
 gi|189186016|gb|ACD83201.1| Pseudouridylate synthase, 23S RNA-specific [Methylacidiphilum
           infernorum V4]
          Length = 325

 Score =  217 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 83/348 (23%), Positives = 151/348 (43%), Gaps = 45/348 (12%)

Query: 2   SLMTYVQYVVVENDE----ENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFN 56
           S M     + +   E       RLD +  +   +++   ++K + SG +R+ +   ++ +
Sbjct: 3   SFMDEADSLSIPKTEMEKGVGQRLDLFLSSLL-NVSRNKIKKKILSGDLRLKNGAVLEPS 61

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           +RI+  + + I   +                +     ++ +   +LYED +I + NK  G
Sbjct: 62  HRIRGIEEIEIRGGLT-------------EEIPSLPKAEEIALEILYEDEEILIVNKQRG 108

Query: 117 ISVQGGSGIAYHIDGFL-KSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAA 167
           + V    G   H  G L  S +   G+        +P + HRLD++TSG++V+A+T  + 
Sbjct: 109 MVVHPSCG---HWSGTLVNSLLFHYGESLPGSSLLRPGIVHRLDKDTSGVMVIAKTERSL 165

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           + L   F  R +QK+Y  L        +      + + +      + V +        A 
Sbjct: 166 KSLLLQFSQRTVQKVYLCLCKNRFPYLRYSFEANIHRHAS-DRKKMAVHRLK---GKTAE 221

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           + F ++   +Q   +L+ +P +GRTHQ+RVH  H+G PI+GD  Y    +          
Sbjct: 222 TRFTLLFASSQ-ASFLKCEPVSGRTHQIRVHLSHLGFPIIGDPLYGKGVRK-----YPFP 275

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           L LHA  + + HP  G +++  APLP    +  D   F Y RN   + 
Sbjct: 276 LLLHAYALKIEHPRSGKKIEFMAPLPQDFKEALD---FFYGRNFSWEE 320


>gi|119384947|ref|YP_916003.1| RluA family pseudouridine synthase [Paracoccus denitrificans
           PD1222]
 gi|119374714|gb|ABL70307.1| ribosomal large subunit pseudouridine synthase D [Paracoccus
           denitrificans PD1222]
          Length = 341

 Score =  217 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 81/358 (22%), Positives = 141/358 (39%), Gaps = 51/358 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  +  + +       RLD+      P    ++   L K++  G V         +  + 
Sbjct: 1   MAEI-LITIPEGLS-ERLDKALALAAPEQAALSRSRLAKLIAEGAVL------GPSGPVT 52

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+V          ++ ++    + +   L    + +   + YED+++ V +KPAG+ V 
Sbjct: 53  DGKV-----RAETGDYRVR----IVAPEPLEAQPEPIPLAVAYEDAELIVVDKPAGMVVH 103

Query: 121 GGSG--IAYHIDGFLKSWVDS-----KGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              G      ++  L     S        +P + HR+D+ETSG+LVVA+T  A Q L   
Sbjct: 104 PAPGAPSGTLVNALLAHCAGSLSGIGGAARPGIVHRIDKETSGLLVVAKTDRAHQGLARQ 163

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANW----------LLKKSHIGGDYVHVVKQNE--K 221
           F     ++ Y ++  G+       +             L   + IG       +Q    +
Sbjct: 164 FADHTARRRYLAIAHGMIDPADARLRGLPGVGFEPGGVLRIATLIGRHPGDRQRQAVSFQ 223

Query: 222 GANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              +A++  +V++ F        +E +  TGRTHQ+RVH  H G  +VGD  Y  N + +
Sbjct: 224 NGRHAVTRARVVETFGTPPAAMLVECRLETGRTHQIRVHMAHAGLGLVGDPVYGGNRRAS 283

Query: 280 FTSPIQ---------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
             +             +  LHA  +   HP  G+ L   +PLPA M     +L    D
Sbjct: 284 ARALGADAAAAVAAFPRQALHAAELGFEHPVSGQTLTFASPLPADMAGLLATLRKAAD 341


>gi|308172908|ref|YP_003919613.1| RNA pseudouridine synthase [Bacillus amyloliquefaciens DSM 7]
 gi|307605772|emb|CBI42143.1| putative RNA pseudouridine synthase [Bacillus amyloliquefaciens DSM
           7]
 gi|328552548|gb|AEB23040.1| RNA pseudouridine synthase [Bacillus amyloliquefaciens TA208]
 gi|328910948|gb|AEB62544.1| putative RNA pseudouridine synthase [Bacillus amyloliquefaciens
           LL3]
          Length = 302

 Score =  217 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 140/319 (43%), Gaps = 34/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            +++        L    K+ +   +   + + +    ++V++   K N  +++G  + I 
Sbjct: 9   ELLITEKHAGQWLFSVLKSEF-QASKPVITEWMNQESIQVNRTSPKNNIILKTGDRLFID 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                 + ++ E               + ++ +L+EDS + + NKPAG+           
Sbjct: 68  LQEKTDSTVVPE---------------YGEAEILFEDSHMLIANKPAGMPTHPNEEGQTG 112

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   ++ +  K R  HRLD++TSG +V A+ R A   L      + +++ Y +
Sbjct: 113 TLSNLIAYHFQINGEQAKVRHVHRLDRDTSGAVVFAKHRLAHAILDRQLETKTLKRTYIA 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVH-VVKQNEKGANYAISHFKVIDCFAQ-KFCWL 243
              G  K KK  +       S IG D  H V ++   G   A++H+KV       +   +
Sbjct: 173 AAEGKVKPKKGTV------DSPIGRDRSHSVRRRVSPGGQAAVTHYKVKGYHPGAQLSLV 226

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
           E++  TGRTHQ+RVH   +G P+ GD  Y  +        + ++  LHA+ + + HP  G
Sbjct: 227 ELELETGRTHQIRVHMASIGHPLAGDELYGGSRA------LFHRQALHAKKVSVVHPISG 280

Query: 303 GRLQITAPLPAHMVKTWDS 321
             +   AP+PA +    ++
Sbjct: 281 EEIVAEAPMPADLAHFAET 299


>gi|302386355|ref|YP_003822177.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
 gi|302196983|gb|ADL04554.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
          Length = 320

 Score =  217 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 147/331 (44%), Gaps = 31/331 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q ++V  +E   RLD+    +        L K++R   + ++ K+   + ++  G  V+
Sbjct: 1   MQSLIVSQNEAGQRLDKLLSKYLNLAEKSFLYKMMRKKNITLNGKKCDGSEKLVQGDEVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          + ++ I   S         +   +LYED  I + NKPAG+  Q      
Sbjct: 61  L---------FLSDETIGKFSQIKLPEVRKVSLNILYEDEHILLINKPAGMLSQKARESD 111

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  ++ +++ S G+         +P + +RLD+ TSG++V  ++ A  Q ++ +F+ R
Sbjct: 112 ESLVEYMINYLVSNGRLSTEQLRSFRPSVCNRLDRNTSGLVVGGKSLAGLQLMSAAFKDR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I K Y  +V G   +++  I  +L K      + V V KQ   G+   ++ ++ +    
Sbjct: 172 SIHKYYQCVVKGHISDRQ-VITGYLTKSE--ASNQVTVHKQPVTGSVPIVTEYEPVQYHG 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYM 295
           + +  L +   TGRTHQ+R H   +G PIVGD+KY  +        +   +   LH+  +
Sbjct: 229 E-YTLLRITLITGRTHQIRAHLSSIGYPIVGDYKYGNSRVNEEAKKLYHIHSQLLHSYQV 287

Query: 296 DLPH-PE-----GGRLQITAPLPAHMVKTWD 320
             P  PE      GR    APLP    K   
Sbjct: 288 IFPELPEPLAYLSGR-TFIAPLPKTFSKICK 317


>gi|217077318|ref|YP_002335036.1| ribosomal large subunit pseudouridine synthase D [Thermosipho
           africanus TCF52B]
 gi|217037173|gb|ACJ75695.1| ribosomal large subunit pseudouridine synthase D [Thermosipho
           africanus TCF52B]
          Length = 245

 Score =  217 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 67/252 (26%), Positives = 112/252 (44%), Gaps = 15/252 (5%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDS 139
           +  +    +    + +   +LYED  I V NK AG+             ++  +    D 
Sbjct: 2   EFPEKPKEVEILPENIPLDILYEDKDIVVVNKSAGMITHPTPSFTSGTLVNALMYHCKDF 61

Query: 140 KGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +G     +P + HRLD++TSG++VVA+   A Q L++ F+ R  +K+Y ++V GI K   
Sbjct: 62  QGISGELRPGIVHRLDKDTSGVIVVAKNDKAHQSLSKQFKDRVTEKVYAAIVKGIVKKDY 121

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   + +   +      V          A+++FKV+  F +    +   P TGRTHQ+
Sbjct: 122 GTIEVPVGRNPVVRTKMAAVDW-----GKNALTYFKVLRRF-KDATLVFAYPKTGRTHQI 175

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           R+H  ++G P++GD  Y +  K         +  LHA  +   HP     +   APLP  
Sbjct: 176 RIHMKYIGHPLLGDELYGSGKKDEIY--GATRQMLHALRLSFYHPTTEEKMTFVAPLPED 233

Query: 315 MVKTWDSLGFKY 326
             +    L   Y
Sbjct: 234 FKRVLKILSEIY 245


>gi|323356542|ref|YP_004222938.1| pseudouridylate synthase, 23S RNA-specific [Microbacterium
           testaceum StLB037]
 gi|323272913|dbj|BAJ73058.1| pseudouridylate synthase, 23S RNA-specific [Microbacterium
           testaceum StLB037]
          Length = 307

 Score =  217 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 73/323 (22%), Positives = 134/323 (41%), Gaps = 29/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +++ V +  +  R+D+         +     +I  +G V VD + V  ++R+++G  + +
Sbjct: 4   RHLPVPDGLDGTRVDQALAKML-GFSRTFAAEIADAGGVSVDGRTVARSDRLRAGGWLSV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                    I+   ++ D  +        +               KPAG++     G   
Sbjct: 63  EWEPKREPEIVP-VEVADLGIVWDDDDIVVVD-------------KPAGVAAHPSVGWEG 108

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  + HRLD  TSG++VVA+T  A   L  +F+ R + K
Sbjct: 109 PTVLGALAAAGFRIATSGPAERRGVVHRLDAGTSGLMVVAKTERAYTLLKSAFKEREVDK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY ++V G P      I   + +  H    +  V          +++H++ ++ F +   
Sbjct: 169 IYHAVVQGHPDPLSGTIDAPIGRHPHHSWKFAVV-----PDGKDSVTHYETLEAFPR-AS 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE+   TGRTHQ+RVH      P VGD  Y A+   +    ++ + +LHA  +   HP 
Sbjct: 223 LLEIHLETGRTHQIRVHMAAHRHPCVGDPLYGADPTLSARLGLE-RQWLHAHRLAFTHPA 281

Query: 302 GGRLQ-ITAPLPAHMVKTWDSLG 323
            G      +  PA + K  + L 
Sbjct: 282 TGEWVGFESAYPADLAKALEILR 304


>gi|52079396|ref|YP_078187.1| putative pseudouridine synthase YhcT [Bacillus licheniformis ATCC
           14580]
 gi|52784756|ref|YP_090585.1| YhcT [Bacillus licheniformis ATCC 14580]
 gi|319646823|ref|ZP_08001052.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
 gi|52002607|gb|AAU22549.1| putative Pseudouridine synthase YhcT [Bacillus licheniformis ATCC
           14580]
 gi|52347258|gb|AAU39892.1| YhcT [Bacillus licheniformis ATCC 14580]
 gi|317391411|gb|EFV72209.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
          Length = 305

 Score =  217 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 77/332 (23%), Positives = 140/332 (42%), Gaps = 32/332 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+   +  +   +       L  + K      +   +Q  + + +V+V+ K V  N R++
Sbjct: 1   MNQKNHGLFFSADIRHHGELLYAYLKREAK-ASKPVIQYWIANEKVKVNHKSVNHNVRLE 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SG  V I       + I+ E               + +  +L+ED  + + NKPAG++  
Sbjct: 60  SGDSVMIDLREEEESGIVPE---------------YGELPVLFEDDHMLIVNKPAGMATH 104

Query: 121 GG-SGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
              +G    +   +  +    G+  K R  HRLD++TSG +V A+ R A   L E  + +
Sbjct: 105 PNEAGQTGTLSNLVAFYFQMNGEERKVRHVHRLDKDTSGAVVFAKHRLAHALLDEQLQRK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y ++  G  + K   I+  + +  H       V ++       A++HF+     +
Sbjct: 165 ELARTYVAVAEGKFRKKTGTISAPIGRDKHHP-----VRRRVSHSGQPAVTHFESKGYDS 219

Query: 238 QK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           +       +Q  TGRTHQ+RVH   +G P+ GD  Y        +  +  +  LHA  ++
Sbjct: 220 RHDVTLCRLQLETGRTHQIRVHLASIGHPLSGDTLYGG------SKGLFQRQALHAIEIN 273

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
           + HP    R+ + APLP  +      L    D
Sbjct: 274 VTHPITKERVTVAAPLPDDLKDEIGRLFGTVD 305


>gi|327399178|ref|YP_004340047.1| RluA family pseudouridine synthase [Hippea maritima DSM 10411]
 gi|327181807|gb|AEA33988.1| pseudouridine synthase, RluA family [Hippea maritima DSM 10411]
          Length = 301

 Score =  217 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 75/322 (23%), Positives = 135/322 (41%), Gaps = 37/322 (11%)

Query: 4   MTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M   + V+  ++    + R+D+        I    +Q  ++ G ++V  + +  + +++ 
Sbjct: 3   MQSSEIVIERIDEVYVDKRVDKVVSEIL-EIPRNQVQNYIKDGFIKVCSRFISKSYKLKY 61

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + I               I+    N     +     +L+ED  + V  KPAGI V  
Sbjct: 62  GDCLSI---------------IIPPPKNNKIEPNDAPIKILFEDEDVVVVEKPAGIVVHP 106

Query: 122 GSGIAY-HIDGFLKSW---VDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G+      +   LK     + S G   R  + HR+D++TSG++V+A+   A   L + F 
Sbjct: 107 GAACEDVSVVSALKYRGVRLSSIGAPLRGGVVHRIDKDTSGVIVLAKNDRAHFFLAKQFF 166

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I++ Y  +V    K     I   + +       +  V     +    AI+ +K++  
Sbjct: 167 EHSIERRYIGVVGCHLKQNSGEIDKPIGRHPKNRKLFAVV-----ENGKEAITFYKLLKR 221

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             + +  +  +  TGRTHQ+RVH  ++GCP+VGD  Y    K         +  LHA  +
Sbjct: 222 L-ENYDVVMFKLQTGRTHQIRVHMKYLGCPLVGDATYGGVLKE------IKRQALHAFVL 274

Query: 296 DLPHPEGGR-LQITAPLPAHMV 316
              HP  G+ L+  + LP  M 
Sbjct: 275 GFRHPWSGKFLKFYSKLPEDMR 296


>gi|290961167|ref|YP_003492349.1| RNA pseudouridine synthase [Streptomyces scabiei 87.22]
 gi|260650693|emb|CBG73809.1| putative RNA pseudouridine synthase [Streptomyces scabiei 87.22]
          Length = 314

 Score =  217 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 136/327 (41%), Gaps = 18/327 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVTVDGSVVGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E       + +    D +  I+       +     +G +V
Sbjct: 60  GGAWLEVEMPQAPAPVQIVAEPV---EGMEIVHDDDDVVVIVKPVGVAAHPSPGWSGPTV 116

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GG   A +             ++  + HRLD  TSG++ VA++  A   L   F+ R +
Sbjct: 117 IGGLAAAGYRIST-----SGAAERQGIVHRLDVGTSGLMTVAKSERAYTSLKRQFKERTV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G P      I   + +  H   DY   V         +++H+ +I+ F + 
Sbjct: 172 DKRYHALVQGHPDPTSGTIDAPIGR--HPNHDYKWAVTAE---GKPSVTHYDLIEAF-RA 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+++  TGRTHQ+RVH      P VGD  Y A+        I  + +LHA  +   H
Sbjct: 226 ASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADPTLAKRLGI-TRQWLHAVRLGFEH 284

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFK 325
           P  G  ++  +  PA + K  D +  +
Sbjct: 285 PGDGEWVEFESDYPADLQKALDKVREE 311


>gi|255100096|ref|ZP_05329073.1| putative pseudouridylate synthase [Clostridium difficile QCD-63q42]
          Length = 300

 Score =  217 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 74/313 (23%), Positives = 135/313 (43%), Gaps = 32/313 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +EE M L     +   + +  +L K+ R   V V+    K + ++ SG ++ +       
Sbjct: 16  NEEEMTLKEVLLDKL-NFSVRSLSKMKREKSVLVNGVYKKPSLKVYSGDLIEVKIDEEKA 74

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFL 133
           N                     L   ++Y+D  I + NKP  + V    S     I   +
Sbjct: 75  N----------------FEPQDLNLQIIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGI 118

Query: 134 KSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             ++D++ +  K R  +RLD  TSG+++VA+   A   L+ +    +++K Y ++V GI 
Sbjct: 119 SYYIDNQKENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGII 178

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K  +  I   + + +      +      ++    +++H+KVI+   +    LE+   TGR
Sbjct: 179 KENEGTIDEPIYRPTEDSIKRII-----DERGQSSVTHYKVIERL-ENATVLEVSLETGR 232

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH  H+G  I+GD  Y           + N+  LHA  ++   P    +L+  A 
Sbjct: 233 THQIRVHMAHIGHGIIGDELYGY-----VDEELINRQALHAYKLEFEQPRTKEKLKFKAD 287

Query: 311 LPAHMVKTWDSLG 323
           +P  M +    L 
Sbjct: 288 IPEDMKELISKLR 300


>gi|302550785|ref|ZP_07303127.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           viridochromogenes DSM 40736]
 gi|302468403|gb|EFL31496.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           viridochromogenes DSM 40736]
          Length = 314

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 77/333 (23%), Positives = 137/333 (41%), Gaps = 30/333 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++   G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAGGKVTVDGSVVGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   ++ E       + +    D +               KP G++ 
Sbjct: 60  GGAWLEVEMPQAPAPVQVVAEPV---EGMEIVHDDDDVVV-----------IAKPVGVAA 105

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  TSG++VVA++  A   L   
Sbjct: 106 HPSPGWTGPTVIGGLAAAGYRISTSGAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQ 165

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ R + K Y +LV G P      I   + +  H   DY   V  +      +++H+ +I
Sbjct: 166 FKERTVDKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAD---GKPSVTHYDLI 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +    L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA 
Sbjct: 221 EAF-RAASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADPTLAKRLHL-TRQWLHAV 278

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +   HP  G+ ++  +  PA + K  D +  +
Sbjct: 279 RLGFEHPGDGQWVEFASDYPADLQKALDQVREE 311


>gi|269958889|ref|YP_003328678.1| ribosomal large subunit pseudouridine synthase C [Anaplasma
           centrale str. Israel]
 gi|269848720|gb|ACZ49364.1| ribosomal large subunit pseudouridine synthase C [Anaplasma
           centrale str. Israel]
          Length = 299

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 97/316 (30%), Positives = 162/316 (51%), Gaps = 23/316 (7%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  +VE     +R+DR+ +   P +    ++++LR G++ ++  +V+ + R+ +G V+ I
Sbjct: 3   REYLVEEACFGVRVDRYLRGLLPGVTQSFIERLLRRGEILLNNTKVRSSARVSNGDVLSI 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                A   +++E++I    +      D + + +LYED  +   NKPAG+SVQGGS +  
Sbjct: 63  KH---ADRIVMREKEI--RRLQHVPLLDLISNNILYEDQNVIAINKPAGVSVQGGSKVGV 117

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            I   L       G   R+ HRLD++TSG+LV+AR    A+ L   FR RR+QK Y ++ 
Sbjct: 118 SIGDLLDKIRP--GGCCRIVHRLDKDTSGVLVLARDLDVARCLAREFRERRVQKEYIAIT 175

Query: 188 WGIPKNKKECIANWLL-KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            G+P +    +   +  K     G+ +      EK A    S  +V+      F  + ++
Sbjct: 176 KGVPHSASGEVNTPIFYKVQSATGERML-----EKDAKTFFSVTRVL----GNFAVVLLR 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P TGR HQLR+H   +GCPIVGD KYC        +     L+LHA  +      G +L 
Sbjct: 227 PVTGRKHQLRIHMSQIGCPIVGDSKYCKCGPVEKET-----LHLHASLLTFE-LMGRKLS 280

Query: 307 ITAPLPAHMVKTWDSL 322
           I+A +P +M +  ++L
Sbjct: 281 ISAGMPGYMEEKINTL 296


>gi|57239048|ref|YP_180184.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Welgevonden]
 gi|58578991|ref|YP_197203.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Welgevonden]
 gi|57161127|emb|CAH58040.1| putative ribosomal large subunit pseudouridine synthase C
           [Ehrlichia ruminantium str. Welgevonden]
 gi|58417617|emb|CAI26821.1| Ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Welgevonden]
          Length = 305

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 92/315 (29%), Positives = 158/315 (50%), Gaps = 16/315 (5%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +Y  ++ D   +R+DR+ +     I    ++K LR+  + +D  +VK N ++  G V+ +
Sbjct: 3   KYYTIQEDNLGVRIDRFIRKELR-IPQSLIEKFLRNRIILLDGLKVKSNTKLNVGNVIYV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++    +S +L K    +   ++YED  + V NKP+G+SVQGGS +  
Sbjct: 62  QNECIISKEKKDKKVCKFASESLVK---LICDNIVYEDDNVLVINKPSGVSVQGGSKVKI 118

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            I   L S     G+  ++ HRLD+ TSGIL++AR    ++ +   F+ R+++K Y +L 
Sbjct: 119 SISDVLDSIR--IGESMKIVHRLDKSTSGILMLARNARVSRLIMNEFKDRKVKKKYLALT 176

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GIP +    I   ++KK H        +++N      A++ F  +         L++QP
Sbjct: 177 CGIPDDDFGQIDYPIVKKKH-----GITLEKNMSFMQQAVTMFSTLRKLPNDIGLLDLQP 231

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGR HQ+R+H   +GCPIVGD KY           +Q    LHA ++ + + +G  + I
Sbjct: 232 ITGRKHQIRIHLSRIGCPIVGDVKYGKICDSISNDYLQ----LHAYFLSI-NIDGKEISI 286

Query: 308 TAPLPAHMVKTWDSL 322
           T P+P++M      L
Sbjct: 287 TIPMPSYMQNIILQL 301


>gi|329889164|ref|ZP_08267507.1| RNA pseudouridylate synthase family protein [Brevundimonas diminuta
           ATCC 11568]
 gi|328844465|gb|EGF94029.1| RNA pseudouridylate synthase family protein [Brevundimonas diminuta
           ATCC 11568]
          Length = 241

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 83/239 (34%), Positives = 131/239 (54%), Gaps = 4/239 (1%)

Query: 87  SVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
            V+LT+     ++S +++ED+ +  FNKP+G+S QGG   A  +D  L ++  S G++P 
Sbjct: 6   PVSLTEDEIAAVRSWVVHEDAHLIAFNKPSGLSSQGGRIQANTLDDLLWAFARSNGKRPE 65

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD++TSG+++ A+T+ AA    ++ +MR+ QK Y +LV   P+ K   I + L ++
Sbjct: 66  LVHRLDRDTSGVILAAKTKPAAGFFGKAMQMRKFQKTYLALVAAAPEPKSGRITSALRRE 125

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                 Y+ VV  +  GA  A S ++ +         +E+ P TGR HQLRVH   +G P
Sbjct: 126 EIGRESYMRVVDFDAPGAQGAASGYRTLASSEDGAV-VELSPETGRMHQLRVHMASIGRP 184

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           +VGD +Y       F      +L LHA  +  PHP+GGR+ + AP P        + G 
Sbjct: 185 LVGDVRYGGAL--TFAGRAAPRLMLHAAKLSFPHPDGGRVTVEAPEPEDFAALRAAAGL 241


>gi|118476779|ref|YP_893930.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|196044122|ref|ZP_03111358.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|225863156|ref|YP_002748534.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|118416004|gb|ABK84423.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|196024761|gb|EDX63432.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|225788401|gb|ACO28618.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
          Length = 297

 Score =  216 bits (551), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 136/318 (42%), Gaps = 39/318 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I  + G + V+ +     +++Q G+ +RI   
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFQGGAIEVNGQHASVRHQLQVGEELRIFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 68  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPSGSV 113

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 114 A---NALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID  A     + 
Sbjct: 171 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVS 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 225 LELDTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 278

Query: 304 RLQITAPLPAHMVKTWDS 321
            +  TA +P+ M +    
Sbjct: 279 EMSFTAMIPSDMQEVLRQ 296


>gi|254520209|ref|ZP_05132265.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
 gi|226913958|gb|EEH99159.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
          Length = 298

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 139/327 (42%), Gaps = 38/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR----SGQVRVDKKRVKFNNRI 59
           M+ ++ + V  + E  ++  + K      +      ++R      ++ VD K VK N  +
Sbjct: 1   MSTIKRI-VSKEHEGRKIREFLKEELGLSSR-----LIRSASIDKRIFVDNKAVKMNYVL 54

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +  + V I  V     +I  E   +D               ++YED  I V NK   + V
Sbjct: 55  KRSEEVLIDLVKEETQNIDPENIPID---------------IVYEDEDIIVVNKGPNMVV 99

Query: 120 QGGSGIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                     +   L  +     QK   RL  RLD +TSG++++A+ + A   L++   +
Sbjct: 100 HPTKRYQSGTLANALMYYFKESNQKCIVRLVSRLDMDTSGLIIIAKNQYAHMELSKEMTL 159

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             ++K Y ++V G  +N +  I   + +    G     + +  ++    +I+H+KVI+ F
Sbjct: 160 NNVEKRYLTVVHGHMENDEGTIDLPIYRPEEEG----TIRRVVDERGQRSITHYKVIERF 215

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +E    TGRTHQ+RVH   +G PI GD  Y     G     I ++  LHA  +D
Sbjct: 216 KDSD-LVECLLETGRTHQIRVHLSSLGHPIWGDTLYGYEEDGE----IISRQALHAYGLD 270

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWDSL 322
              P     L + A +P  + K  + L
Sbjct: 271 FKSPRTKKELSLRARVPDDIEKLVEYL 297


>gi|159045150|ref|YP_001533944.1| ribosomal large subunit pseudouridine synthase D [Dinoroseobacter
           shibae DFL 12]
 gi|157912910|gb|ABV94343.1| ribosomal large subunit pseudouridine synthase D [Dinoroseobacter
           shibae DFL 12]
          Length = 347

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 83/340 (24%), Positives = 138/340 (40%), Gaps = 52/340 (15%)

Query: 1   MSLMTYV-QYVVVE-NDEENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKR-VK 54
           MS +    + + VE   +   RLDR      P    ++   L K++ +G VR   +    
Sbjct: 1   MSGIPEASEEITVEVQPDPPPRLDRALARDVPEGLGLSRSRLVKLIEAGDVRRGAEVLAS 60

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
              R+ +G V+ +     A   ++ E   LD               +++ED+ + V NKP
Sbjct: 61  PKARVAAGDVLTLRLGAPAEVPLVAEAIPLD---------------VIFEDADLIVVNKP 105

Query: 115 AGISVQGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAA 167
           AG+ V    G      ++  +    DS       ++P + HR+D++TSG+LVVA++  A 
Sbjct: 106 AGMVVHPAPGSPAGTLVNALMHHCGDSLSGIGGEKRPGIVHRIDKDTSGLLVVAKSDHAH 165

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-------------DYVH 214
           Q L   F    +++IY +LV G+P+     +    + +   GG             D   
Sbjct: 166 QGLAAQFAAHSVERIYDALVHGVPEASDPRLRGLPMVRFEPGGVLCLRASLARHRTDRQR 225

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                E    +A++  +V   F        L     TGRTHQ+RVH  H+G  ++GD  Y
Sbjct: 226 QAVVAEGQGRHAVTRARVEARFGDPAGVAHLACWLETGRTHQIRVHLAHIGHGLLGDPVY 285

Query: 273 CAN---------FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                        +    +    +  LHAR +   HP  G
Sbjct: 286 GGRKRLSAKAFSPQALAAAEAFPRQALHARTLGFVHPVTG 325


>gi|330469278|ref|YP_004407021.1| RluA family pseudouridine synthase [Verrucosispora maris AB-18-032]
 gi|328812249|gb|AEB46421.1| RluA family pseudouridine synthase [Verrucosispora maris AB-18-032]
          Length = 314

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 67/323 (20%), Positives = 138/323 (42%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  + MRLD+     +  ++      ++ +G+  VD      ++++++G  + +
Sbjct: 12  RSLPVPDGLDGMRLDQAVARLF-GLSRTAAAALVDAGEALVDGAVRPNSHKVRAGAWLEV 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                A   +                       ++Y D  I V +KP G++     G   
Sbjct: 71  TLPAPAAAPV-------------VVPQAVPGLRVVYADDDIVVVDKPVGVAAHPSPGWTG 117

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +   +       ++  + HRLD  T+G++VVA++  A   L  +F+ R ++K
Sbjct: 118 PTVIGGLAAIGHTIATSGAAERQGVVHRLDVGTTGVMVVAKSEQAYSALKRAFKYREVEK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G     +  I   + +  H    +  V          +I+H+  ++ F     
Sbjct: 178 RYHAVVQGHLDPLRGTIDAPIDRHPHHDYRWAVVS-----DGKPSITHYDTLEAFPS-AS 231

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++  TGRTHQ+RVH   +  P VGD  Y A+   +    + ++ +LHAR +   HP 
Sbjct: 232 LVDVRLETGRTHQIRVHFSTLRHPCVGDLTYGADPTLSARLKL-DRQWLHARELSFEHPR 290

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G  ++  +  P  + +  + L 
Sbjct: 291 TGDEVRFVSDYPDDLGRALEILR 313


>gi|88810811|ref|ZP_01126068.1| ribosomal large subunit pseudouridine synthase C [Nitrococcus
           mobilis Nb-231]
 gi|88792441|gb|EAR23551.1| ribosomal large subunit pseudouridine synthase C [Nitrococcus
           mobilis Nb-231]
          Length = 314

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 80/324 (24%), Positives = 150/324 (46%), Gaps = 15/324 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ V ++ E  RLD +       +    + ++LR GQVRV+  RV+   R++ G  +R
Sbjct: 1   MRHIQVASEYEGQRLDNFLLRELKGLPRTRVYRLLRQGQVRVNGGRVRPEYRLRRGDRLR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +PP+      +              +    ++  +LYE+ ++ + +KP+G++V GGSG+A
Sbjct: 61  LPPMRLQEREL--------GGAPSARILQRIEQAILYENEQLLILDKPSGLAVHGGSGLA 112

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   +++          L HRLD++TSG L++A+ R   + +    R  R++K Y +L
Sbjct: 113 YGVIEAIRARRPGT-LPLDLAHRLDRDTSGCLIIAKRRETLRQIHALMRSNRVEKRYLAL 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           + G   +    +   L ++   G   +    Q   G   A++ F  I+   + +  +++ 
Sbjct: 172 LRGKLASAM-RVEAPLERRPGQG---LLQPVQVSIGGRQALTVFHPIERH-RGWTLVDVM 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            HTGR HQ+RVHA + G P+ GD +Y               +L+LHA  +    P   +L
Sbjct: 227 LHTGRMHQIRVHAAYSGYPVAGDARYGDPQANRTLRRFGLRRLFLHASRVAFALPGQDKL 286

Query: 306 QITAPLPAHMVKTWDSLGFKYDRN 329
            + A L   +      L       
Sbjct: 287 VVQAALSEELAAVLQYLRENASAE 310


>gi|254974610|ref|ZP_05271082.1| putative pseudouridylate synthase [Clostridium difficile QCD-66c26]
 gi|255092002|ref|ZP_05321480.1| putative pseudouridylate synthase [Clostridium difficile CIP
           107932]
 gi|255313736|ref|ZP_05355319.1| putative pseudouridylate synthase [Clostridium difficile QCD-76w55]
 gi|255516418|ref|ZP_05384094.1| putative pseudouridylate synthase [Clostridium difficile QCD-97b34]
 gi|255649516|ref|ZP_05396418.1| putative pseudouridylate synthase [Clostridium difficile QCD-37x79]
 gi|306519647|ref|ZP_07405994.1| putative pseudouridylate synthase [Clostridium difficile QCD-32g58]
          Length = 300

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 73/313 (23%), Positives = 135/313 (43%), Gaps = 32/313 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +EE M L     +   + +  +L K+ +   V V+    K + ++ SG ++ +       
Sbjct: 16  NEEEMTLKEVLLDKL-NFSVRSLSKMKKEKSVLVNGVYKKPSLKVYSGDLIEVKIDEEKA 74

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFL 133
           N                     L   ++Y+D  I + NKP  + V    S     I   +
Sbjct: 75  N----------------FEPQDLNLQIIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGI 118

Query: 134 KSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             ++D++ +  K R  +RLD  TSG+++VA+   A   L+ +    +++K Y ++V GI 
Sbjct: 119 SYYIDNQKENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGII 178

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K  +  I   + + +      +      ++    +++H+KVI+   +    LE+   TGR
Sbjct: 179 KENEGTIDEPIYRPTEDSIKRII-----DERGQSSVTHYKVIERL-ENATVLEVSLETGR 232

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH  H+G  I+GD  Y           + N+  LHA  ++   P    +L+  A 
Sbjct: 233 THQIRVHMAHIGHGIIGDELYGY-----VDEELINRQALHAYKLEFEQPRTKEKLKFKAD 287

Query: 311 LPAHMVKTWDSLG 323
           +P  M +    L 
Sbjct: 288 IPEDMKELISKLR 300


>gi|162454208|ref|YP_001616575.1| ribosomal large subunit pseudouridine synthase D [Sorangium
           cellulosum 'So ce 56']
 gi|161164790|emb|CAN96095.1| ribosomal large subunit pseudouridine synthase D [Sorangium
           cellulosum 'So ce 56']
          Length = 345

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 78/341 (22%), Positives = 142/341 (41%), Gaps = 46/341 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHI----NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           V++ +   RLD+   +         +   +Q+ + +G+V VD +  + +  +++  +V +
Sbjct: 14  VDDGDPRDRLDKLVVHLLERAGHAASRAAVQRWIAAGRVLVDGEPARASVAVRASALVEV 73

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
            P   + +    E  ++                ++YED  + V +KPAG+ V    G A 
Sbjct: 74  RPEEPSPSPTAAEPDVVIP--------------VVYEDEHLLVIDKPAGLVVHPARGHAS 119

Query: 127 -YHIDGFLK----SWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
              ++G L     +   +  +      +P + HRLD+ TSG+LVVA+     + L + F 
Sbjct: 120 GTLVNGLLALPGFALAPADPRDPMGHVRPGIVHRLDRGTSGLLVVAKDEPTREALKDRFA 179

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA--------NYAI 227
              I++ Y ++V G  ++      + L  +            +   GA          A+
Sbjct: 180 RHAIEREYAAIVAGEARDAT---YDTLHGRHPTDRLRFTSWIRGGAGAPGSHVAAPRRAV 236

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG-CPIVGDHKYCANFKG---NFTSP 283
           +H +VI+        +     TGRTHQ+RVH    G  P++GD  Y    K       + 
Sbjct: 237 THVRVIERLGDAATVVACSLETGRTHQIRVHLAERGRTPVLGDPLYGKPPKKPAVRAIAE 296

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              +  LHAR +   HP   + ++  + LPA M K  D L 
Sbjct: 297 ELGRQALHARVLGFIHPATQKPVRWESALPADMRKALDQLR 337


>gi|157363528|ref|YP_001470295.1| RluA family pseudouridine synthase [Thermotoga lettingae TMO]
 gi|157314132|gb|ABV33231.1| pseudouridine synthase, RluA family [Thermotoga lettingae TMO]
          Length = 294

 Score =  216 bits (550), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 87/325 (26%), Positives = 140/325 (43%), Gaps = 38/325 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQS 61
           +   +  + +  +    RLD++ +N    +    + K+LR+G V+V+ K V+     +  
Sbjct: 1   MENKIVELSINEENSYRRLDKFLRNELKAVPLSEIYKLLRTGCVQVNGKTVRKPYTELYV 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  V I   +                      S  LK  +LYED  + + NK AGI++  
Sbjct: 61  GDKVTIKADLAVYRQ------------KKDLPSIPLKLDILYEDDNLLILNKKAGITIHP 108

Query: 122 G-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                +  +   L  +   KG KP L HRLD++TSG+LV+A+    A+ L+  FR R ++
Sbjct: 109 SEKTRSTTLIQGLHFYGAKKGFKPHLVHRLDRDTSGVLVIAKNVKTARTLSHMFRNRLVK 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G        I   L                     + A++ +KV++ F +  
Sbjct: 169 KEYITLVSGKIFGD-GFIDKPL-------------------DGSEALTEYKVLENF-RDT 207

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLP 298
             L +  HTGRTHQ+R H   +G P+VGD  Y             N  + +LH   +   
Sbjct: 208 SLLRVILHTGRTHQIRKHFALIGNPVVGDILYGDKKVNELFKKKHNLRRQFLHCIRISFT 267

Query: 299 HP-EGGRLQITAPLPAHMVKTWDSL 322
           +P E G + I APLP  + +    L
Sbjct: 268 NPSEPGVISIKAPLPDDLERVIKGL 292


>gi|167041415|gb|ABZ06167.1| putative RNA pseudouridylate synthase [uncultured marine
           microorganism HF4000_006O13]
          Length = 320

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 84/325 (25%), Positives = 155/325 (47%), Gaps = 13/325 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  +     V+V  D++ MRLD +       +    + +++R G+VR++ KR K  +R+ 
Sbjct: 1   MKDLGINNKVIVSRDDDGMRLDNYLIKIIKGMPKSRIYRMIRKGEVRINSKRAKPRSRVH 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
               VRIPP        + E K   SSV        + +I+++E+    + NKP+G++V 
Sbjct: 61  VNDTVRIPPYA------VNEPKTNVSSVRKD-DFRRINNIVIFENDSFLLVNKPSGLAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSGI   +   L+S+ + + +   L HRLD++TSG L+V++ ++  + L E FR  +++
Sbjct: 114 GGSGIHLGLIELLRSFREKRNEHLELVHRLDKDTSGCLLVSKKKSKLRKLHEYFREGKVK 173

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y  L+ G        I   L   +      + V   + K A    + F +++ + +  
Sbjct: 174 KTYLGLMVGKFTQTVYEIDQPLKIITTPENGRLAVPDDSGKKAK---TKFFLMEKY-KNS 229

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
              +++P TG+THQ+R HA +M  P+  D++Y        +     +L+LHA  +  P  
Sbjct: 230 ALFKIEPITGKTHQIRAHAKYMKTPLAADNRYGIQPDQIVSEFGLTRLFLHAESITFPGL 289

Query: 301 EGGR--LQITAPLPAHMVKTWDSLG 323
                     + L   +++  + L 
Sbjct: 290 SSTENTFSFKSKLDTKLIEVLEKLR 314


>gi|311742786|ref|ZP_07716595.1| ribosomal large subunit pseudouridine synthase D [Aeromicrobium
           marinum DSM 15272]
 gi|311314414|gb|EFQ84322.1| ribosomal large subunit pseudouridine synthase D [Aeromicrobium
           marinum DSM 15272]
          Length = 313

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 76/321 (23%), Positives = 133/321 (41%), Gaps = 29/321 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V    +  R+D         ++     +++  G V +D  R   + R+  G V+  
Sbjct: 10  KVISVPEGLDGERVDVALAR-LTGLSRSRASELVADGHVLLDGHRPAKSERVLFGAVL-- 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                       E  I    V            +++ED  I V +KP G++   G G   
Sbjct: 67  ------------EATIPAPPVVEVVPIPVDALSIVHEDDDIVVVDKPVGVAAHPGVGWTG 114

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  + HRLD  TSG++ VA++  A   L ++FR R + K
Sbjct: 115 PTVLGALAARGYRISTSGAPERQGIVHRLDVGTSGLMAVAKSEHAYTVLKQAFRDRVVDK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y SLV G P      I   + +  H   D+   V+ +      +++H+  ++   +   
Sbjct: 175 TYHSLVQGHPDPHTGTIDAPIAR--HPKHDFKFTVRAD---GRASVTHYATLEAH-RYAS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L ++  TGRTHQ+RVH   +  P VGD  Y A+        ++ + +LHA  +   HP 
Sbjct: 229 LLTIKLETGRTHQIRVHMAAIKHPCVGDPLYGADPTLAARVGLE-RQWLHALGLGFDHPR 287

Query: 302 GG-RLQITAPLPAHMVKTWDS 321
            G R+   +  PA +    D+
Sbjct: 288 TGERVDFASTYPADLQAALDT 308


>gi|13508031|ref|NP_109980.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           pneumoniae M129]
 gi|2501680|sp|P75485|Y292_MYCPN RecName: Full=Uncharacterized RNA pseudouridine synthase MG209
           homolog; AltName: Full=RNA pseudouridylate synthase;
           AltName: Full=RNA-uridine isomerase
 gi|1674240|gb|AAB96191.1| ribosomal large subunit pseudouridine synthase D-like protein
           [Mycoplasma pneumoniae M129]
          Length = 309

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 77/331 (23%), Positives = 133/331 (40%), Gaps = 29/331 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSG 62
           M     V         RLD +      +++ V + K++  G V V+ K++  N   +Q  
Sbjct: 1   MEQTFSVTTA-----QRLDTFLATLL-NLSRVKVAKLIVDGLVSVNGKKITKNGWLVQPE 54

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V +                L   V +          +LYED +I V NKP G+     
Sbjct: 55  DRVHVNWSEE-----------LFEKVPVEVQPYDFPLDILYEDEQIMVVNKPNGLISHPT 103

Query: 123 SGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           S      +  L  +      Q   L HRLD++TSG++++A+ +++  HL +  + R +++
Sbjct: 104 S--FNESESLLGAALFHCNHQPVFLVHRLDRDTSGVIMLAKNQSSLLHLQKQLQQRVMKR 161

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV     +    I+  L +        +  V  +   A  A + F V++   +K  
Sbjct: 162 YYLALVHFPLDSLSGTISAPLERVG--NNKVMWKVGNSSNKAKNAFTKFTVLN-QNEKAA 218

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++ +  TGRTHQ+RVH   +  P+  D  Y    +       +   YLHA+ +   HP 
Sbjct: 219 LIKCELLTGRTHQIRVHLQFIKHPVYNDPLYGLKSEQA----TEYGQYLHAQQISFIHPT 274

Query: 302 -GGRLQITAPLPAHMVKTWDSLGFKYDRNLY 331
               +   A L        D+L  K   +LY
Sbjct: 275 LNKEMGFEAQLDKTFSDKLDNLNLKIANSLY 305


>gi|329120908|ref|ZP_08249540.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
 gi|327471367|gb|EGF16818.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
          Length = 328

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 82/317 (25%), Positives = 145/317 (45%), Gaps = 16/317 (5%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E  +L ++     P  +   + K LR   +  + K+   N  I+SG V+ I      L 
Sbjct: 10  DEGQKLIKFLFKLLPGASKSLIYKSLRKKNILYNNKKANGNEIIKSGDVIEIWFSDETLE 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           +  K++       N+ K S   K I+LYE+  I V NKP G+  Q        ++ +L  
Sbjct: 70  NFSKKESKEILKGNIEKFS--FKDIILYENEDIIVVNKPKGMLSQRDISRQKSLNDYLLE 127

Query: 136 WVDSK---GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           ++ +    G KP + +RLD+ TSG L+ A+T   A+ + E  +   I K Y  LV+G  K
Sbjct: 128 YIKNSNYSGFKPSICNRLDKNTSGTLICAKTFKIAREINELIKNHVINKKYLCLVFGDIK 187

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHT 249
           +    + ++L K   +  +   V  + ++G     +   VI           +LE+   T
Sbjct: 188 DDL-YLKDYLFKN--VENNKAIVSNEKKEGFLEIKTKVHVIKSFKLHEYPVTFLEVTLLT 244

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP--HPEGG--R 304
           G+ HQ+R H  ++G PI+GD KY  N     +  ++  +  LH+  ++ P  H       
Sbjct: 245 GKFHQIRAHLSYIGHPILGDRKYGNNESLEISKILEIGRQLLHSYSIEFPENHCLKELSG 304

Query: 305 LQITAPLPAHMVKTWDS 321
           ++I AP+P  ++   + 
Sbjct: 305 MKIKAPIPKDIMCILNK 321


>gi|188590633|ref|YP_001919968.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str.
           Alaska E43]
 gi|188500914|gb|ACD54050.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str.
           Alaska E43]
          Length = 298

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 80/315 (25%), Positives = 141/315 (44%), Gaps = 29/315 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V N E  +++  + K     ++   ++   +  ++ V+   V+ N  I++G V++I    
Sbjct: 8   VSNVEGKIKIREYLKEKL-DLSTRLIRSASKDQRIYVNNSVVRMNYMIKNGDVIKIDLNK 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
           N   +I  E+  LD               ++YED  + V NK   I V          + 
Sbjct: 67  NESQNINPEKIDLD---------------IVYEDDDVLVINKQPFIIVHPTKNFQSGTLA 111

Query: 131 GFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             +  +     Q    RL  RLD  TSG++++A+ + +   L++  + + +QK Y ++V 
Sbjct: 112 NGILYYFQETNQNCIVRLVSRLDMNTSGLIIIAKNQFSHSRLSKDMKEK-LQKRYLAIVH 170

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  + K+  I   + K    G +Y      +E+G   +I+H+KVI+ F      +E    
Sbjct: 171 GNLEEKEGTIDLPIYK--PEGIEYGSRRVIDERG-QRSITHYKVIESFEGGD-LVECLLE 226

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           TGRTHQ+RVH  H+G PI GD  Y    + N    +  +  LHA  +D   P     L +
Sbjct: 227 TGRTHQIRVHLSHLGHPIYGDELYGVGLEEN----LIKRQALHAYGLDFESPRSLKPLSL 282

Query: 308 TAPLPAHMVKTWDSL 322
            A LP  + +  + +
Sbjct: 283 RADLPDDIKELLEKI 297


>gi|301633483|gb|ADK87037.1| pseudouridine synthase, RluA family [Mycoplasma pneumoniae FH]
          Length = 309

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 77/331 (23%), Positives = 133/331 (40%), Gaps = 29/331 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSG 62
           M     V         RLD +      +++ V + K++  G V V+ K++  N   +Q  
Sbjct: 1   MEQTFSVTTA-----QRLDTFLATLL-NLSRVKVAKLIVDGLVSVNGKKITKNGWLVQPE 54

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V +                L   V +          +LYED +I V NKP G+     
Sbjct: 55  DRVHVNWSEE-----------LFEKVPVEVQPYDFPLDILYEDEQIMVVNKPNGLISHPT 103

Query: 123 SGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           S      +  L  +      Q   L HRLD++TSG++++A+ +++  HL +  + R +++
Sbjct: 104 S--FNESESLLGAALFHCNHQPVFLVHRLDRDTSGVIMLAKNQSSLLHLQKQLQQRVMKR 161

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV     +    I+  L +        +  V  +   A  A + F V++   +K  
Sbjct: 162 YYLALVHFPLDSLSGTISAPLERVG--NNKVMWKVGNSSNKAKNAFTKFTVLN-QNEKAA 218

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++ +  TGRTHQ+RVH   +  P+  D  Y    +       +   YLHA+ +   HP 
Sbjct: 219 LIKCELLTGRTHQIRVHLQFIKHPVYNDPLYGLKGEQA----TEYGQYLHAQQISFIHPT 274

Query: 302 -GGRLQITAPLPAHMVKTWDSLGFKYDRNLY 331
               +   A L        D+L  K   +LY
Sbjct: 275 LNKEMGFEAQLDKTFSDKLDNLNLKIANSLY 305


>gi|255311484|ref|ZP_05354054.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 6276]
          Length = 335

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 79/328 (24%), Positives = 145/328 (44%), Gaps = 32/328 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQ 63
           T V   V++      RLD+   ++    +    Q+ +  G+VRV+ +   + ++ +  G 
Sbjct: 9   TAVFSFVIDEQLTG-RLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGD 67

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VV +              ++++     +   + +    +YED  I V NKP  + V    
Sbjct: 68  VVEV--------------ELIEEKEPSSLIPEDIPLDKVYEDDMILVINKPRDMVVHPAP 113

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + + I   LK     +  +P + HRLD++TSG+L+  +TR A    +E F
Sbjct: 114 GHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKALYSELF 173

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             ++++K+Y ++    P  +   + +  + +  +    + V+  + +G   AI+H  V+ 
Sbjct: 174 ATKQVKKLYVAICINAPSQE---LIHTRIARHPLKRKEMTVLSTHAEGGKEAITHCHVLA 230

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              +    + + P TGRTHQLRVH  H+G PI+GD  Y             +K  LHA  
Sbjct: 231 TNGR-LSVVALYPETGRTHQLRVHMKHLGTPILGDPVYG--IPSINFRYGLDKQQLHAYS 287

Query: 295 MDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           +   HPE   R+++   LP  M    + 
Sbjct: 288 LVFAHPESAERVKLVTKLPDDMTSLIEK 315


>gi|229183506|ref|ZP_04310730.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BGSC 6E1]
 gi|228599916|gb|EEK57512.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BGSC 6E1]
          Length = 292

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 136/318 (42%), Gaps = 39/318 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I  + G + V+ +     +++Q G+ +RI   
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFQGGAIEVNGQHASVRHQLQVGEELRIFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPSGSV 108

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 109 A---NALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID  A     + 
Sbjct: 166 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVS 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 220 LELDTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 273

Query: 304 RLQITAPLPAHMVKTWDS 321
            +  TA +P+ M +    
Sbjct: 274 EMSFTAMIPSDMQEVLRQ 291


>gi|291550480|emb|CBL26742.1| pseudouridine synthase, RluA family [Ruminococcus torques L2-14]
          Length = 295

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 68/321 (21%), Positives = 135/321 (42%), Gaps = 32/321 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M       +  + + +R++++ ++  Y + N   L+K+  S  +  +       + + +G
Sbjct: 1   MDRTINYQITEEADGLRIEQFLRHQGYSYQNITQLKKMPES--ILKNGVWEYMRSLLATG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++ +               I ++  +       L   ++YED  I V NKPAG+ +   
Sbjct: 59  DILTVH--------------IQENESSPNIPPVELPLSIIYEDEDILVVNKPAGMPIHPS 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHR---LDQETSGILVVARTRAAAQHLTESFRMRRI 179
                +       W  ++  KP +      LD++TSG+ V+A+   ++  L+       I
Sbjct: 105 LNNYENSLANGLMWYYTEQGKPFIFRCTNRLDRDTSGLTVIAKHLISSSILSSMGARHEI 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y ++V G        I   L +     G  +   K + K    A++H+KV++     
Sbjct: 165 KREYLAIVRGSVTPPSGTIDAPLAR----TGSSMIERKVDFKHGERAVTHYKVVE-EKNG 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + +   TGRTHQ+RVH  ++G P+VGD+ Y  + +        ++  LH+  +   H
Sbjct: 220 HSLVSLILETGRTHQIRVHMQYLGFPLVGDYLYNPDME------YIHRQALHSWKLSFIH 273

Query: 300 PEGGR-LQITAPLPAHMVKTW 319
           P     ++ TA LP  M    
Sbjct: 274 PITKEPMEFTAELPEDMKNIL 294


>gi|269978156|ref|ZP_06185106.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           mulieris 28-1]
 gi|306818529|ref|ZP_07452252.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           mulieris ATCC 35239]
 gi|307700922|ref|ZP_07637947.1| pseudouridine synthase, RluA family [Mobiluncus mulieris FB024-16]
 gi|269933665|gb|EEZ90249.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           mulieris 28-1]
 gi|304648702|gb|EFM46004.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           mulieris ATCC 35239]
 gi|307613917|gb|EFN93161.1| pseudouridine synthase, RluA family [Mobiluncus mulieris FB024-16]
          Length = 306

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 144/323 (44%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V      +R D         ++     +IL  G V + +  +K ++ +QSG+ + +
Sbjct: 3   RVLPVPEGLTGLRADVGLAKLL-GLSRAKAGEILAQGGVAMGETVLKKSDALQSGETLEV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
              I+   ++ +   +                 LLYED+ + V +KPAG++   G G   
Sbjct: 62  TAPIHPKVYVPEVTPVP-------------GLKLLYEDADLVVVDKPAGVAAHTGPGWDG 108

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L++           ++  + HRLD  TSG +VVA++  A   L  +FR  R++K
Sbjct: 109 PTVVGALRAAGVRISTSGPVEREGIVHRLDAGTSGAMVVAKSELAYGKLKNAFRYHRVEK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY ++  GI K     I   + +    G ++   V     G   A++H+   +       
Sbjct: 169 IYLAVARGILKPSLGTIDAPIGRAP--GREFKMAVVV---GGKPAVTHYDTAESLP-GAT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
              +Q  TGRTHQ+RVH   +G P++GD +Y A+ K      ++ + +LHA  +   HP 
Sbjct: 223 LARVQLETGRTHQIRVHFAAIGHPLLGDTEYGADAKQAVRLGLE-RQWLHASRLVFKHPR 281

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G  + + +PLP+ +      L 
Sbjct: 282 TGIEIAMDSPLPSDLQGVLAVLR 304


>gi|251778694|ref|ZP_04821614.1| pseudouridine synthase, RluA family [Clostridium botulinum E1 str.
           'BoNT E Beluga']
 gi|243083009|gb|EES48899.1| pseudouridine synthase, RluA family [Clostridium botulinum E1 str.
           'BoNT E Beluga']
          Length = 298

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 80/315 (25%), Positives = 141/315 (44%), Gaps = 29/315 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V N E  +++  + K     ++   ++   +  ++ V+   V+ N  I++G V++I    
Sbjct: 8   VSNVEGKIKIREYLKEKL-DLSTRLIRSASKDQRIYVNNSAVRMNYMIKNGDVIKIDLNK 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
           N   +I  E+  LD               ++YED  + V NK   I V          + 
Sbjct: 67  NESQNINPEKIDLD---------------IVYEDDDVLVINKQPFIIVHPTKNFQSGTLA 111

Query: 131 GFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             +  +     Q    RL  RLD  TSG++++A+ + +   L++  + + +QK Y ++V 
Sbjct: 112 NGILYYFQETNQNCIVRLVSRLDMNTSGLIIIAKNQFSHSRLSKDMKEK-LQKRYLAIVH 170

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  + K+  I   + K    G +Y      +E+G   +I+H+KVI+ F      +E    
Sbjct: 171 GNLEEKEGTIDLPIYK--PEGIEYGSRRVIDERG-QRSITHYKVIESFEGGD-LVECLLE 226

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           TGRTHQ+RVH  H+G PI GD  Y    + N    +  +  LHA  +D   P     L +
Sbjct: 227 TGRTHQIRVHLSHLGHPIYGDELYGVGLEEN----LIKRQALHAYGLDFESPRSLKPLSL 282

Query: 308 TAPLPAHMVKTWDSL 322
            A LP  + +  + +
Sbjct: 283 RADLPDDIKELLEKI 297


>gi|297544995|ref|YP_003677297.1| RluA family pseudouridine synthase [Thermoanaerobacter mathranii
           subsp. mathranii str. A3]
 gi|296842770|gb|ADH61286.1| pseudouridine synthase, RluA family [Thermoanaerobacter mathranii
           subsp. mathranii str. A3]
          Length = 285

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 77/317 (24%), Positives = 142/317 (44%), Gaps = 38/317 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV  +E+ + L+ + +N       + + K    G++ V+  +      +Q G V+ +  
Sbjct: 3   LVVGENEKGVILENFLRNRGFSKRLIRIYKW--QGEILVNGIKSNVKRILQPGDVIDL-- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                  I+ E              + L   + YED +I + NKPA + V    G     
Sbjct: 59  -------ILPEND-------SNIAPEKLDLDICYEDEEILIVNKPANMVVHPTKGYQSGT 104

Query: 129 IDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +  +   KG K   R  +RLD+ TSG++V A+      +L      + + K+Y+++
Sbjct: 105 LANGVAWYFKDKGLKALIRPVNRLDRGTSGLVVFAKLPFMQYYLQIV---KPMSKLYFAV 161

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + +   I   + +K   G + +       +  + AI+++KV+   +++F  L+++
Sbjct: 162 VEGKMEGE-GRINLPISRKPQSGIERMV-----SEEGDRAITNYKVVKS-SERFSLLKVK 214

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  H+G PIVGD  Y +      +     +  LHA  +   HP   + +
Sbjct: 215 IETGRTHQIRVHLSHIGHPIVGDTLYGS------SDDYIKRQALHAYRLTFVHPLEEKSI 268

Query: 306 QITAPLPAHMVKTWDSL 322
            + +PLP  M      L
Sbjct: 269 SVYSPLPQDMQHLLKLL 285


>gi|251795436|ref|YP_003010167.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247543062|gb|ACT00081.1| pseudouridine synthase, RluA family [Paenibacillus sp. JDR-2]
          Length = 316

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 77/316 (24%), Positives = 131/316 (41%), Gaps = 28/316 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           V V  D     +    +     ++   L ++ L    + V+  R     ++  G  V I 
Sbjct: 15  VEVGADMAGKDVRTVLERKL-GVSRSLLSRLKLTEYGITVNGVRAYTTAKVTEGDSVAIR 73

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                          ++  ++       L   +++ED  + V NKPAGI V    G   +
Sbjct: 74  ---------------MEEEISEDILPQDLPLSIVFEDDYLLVVNKPAGIIVHPTKGHYTN 118

Query: 129 I--DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +G +  W V  +  + R  HRLD++TSG++V+A+     Q L+E  +   I KIY +
Sbjct: 119 TLANGIVHHWQVRGERVRFRPVHRLDEDTSGLVVIAKNPYIHQQLSEQLQAGTIMKIYCA 178

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLE 244
            V+G P      +   + +           V+        +++H+K    F       + 
Sbjct: 179 YVYGTPSPADGTVGAPIDRNPEDPH-----VRIVTPEGYPSVTHYKTAAVFGGGQASKVR 233

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++  TGRTHQ+RVH  H+GCP++GD  Y     K +       +  LHA  + L HP   
Sbjct: 234 LKLETGRTHQIRVHMKHIGCPLIGDGMYGLQTGKVDEWETAAGRQALHAETLGLTHPMTK 293

Query: 304 RL-QITAPLPAHMVKT 318
              + TA LP  +V+ 
Sbjct: 294 EWSEWTAALPPDLVQL 309


>gi|196036248|ref|ZP_03103647.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
 gi|195991223|gb|EDX55192.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
          Length = 297

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 134/315 (42%), Gaps = 33/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQAGEEIRVFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + V NK A +S       +    
Sbjct: 68  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHSSGSV 113

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 114 ANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HF+VID  A     + ++ 
Sbjct: 174 HGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVSLEL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP     + 
Sbjct: 228 DTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEKEMS 281

Query: 307 ITAPLPAHMVKTWDS 321
             A +P+ M +    
Sbjct: 282 FAAMIPSDMQEVLRQ 296


>gi|218902402|ref|YP_002450236.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|218537046|gb|ACK89444.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
          Length = 292

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 134/318 (42%), Gaps = 39/318 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQAGEEIRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPSGSV 108

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 109 A---NALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G    ++  I   + +KS    +         +    AI+HF+VI   A     + 
Sbjct: 166 ALVHGEMIEQEGTIDAPIGRKSDSIIERTVC-----EEGQRAITHFRVIAS-ANHKTHVS 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD  Y              +  LH+  +   HP    
Sbjct: 220 LELDTGRTHQIRVHMAHIGHPLLGDTLYGGKRDEV------KRQALHSTSLTFYHPILEK 273

Query: 304 RLQITAPLPAHMVKTWDS 321
            +  TA +P+ M +    
Sbjct: 274 EMSFTAMIPSDMQEVLRQ 291


>gi|257458325|ref|ZP_05623473.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
 gi|257444260|gb|EEV19355.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
          Length = 326

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 78/344 (22%), Positives = 143/344 (41%), Gaps = 48/344 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT +    V +    +RLD +  +  P++    L+  ++S  V ++ ++ K ++ +Q+G 
Sbjct: 1   MTEIFEFKVPDGTGKLRLDAFCSSVLPNMTRSRLKTGMQS--VELNGRQAKLSSSVQAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +++     + + +I E                +   +LYED+ +   NK  G+     +
Sbjct: 59  RIKLMWNNPSPDFLIPEH---------------IPLQILYEDNDVIAVNKRVGMVTHPAA 103

Query: 124 GIAYHIDGFLKSWVDSKG-----------------------QKPRLTHRLDQETSGILVV 160
           G          ++                             +  + HRLD++TSG+L+ 
Sbjct: 104 GNWTGTLVQALAYYRLHTSPIHDKFAGLLEAEQGRGNFEDLLRAGIVHRLDKDTSGVLIT 163

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR+ AA   L + F+MRR +K Y +++ G+P+ +   I   + +  H           + 
Sbjct: 164 ARSAAAEAFLKDEFKMRRTEKYYAAILNGVPEKRTGVIETSVFRDEH--SRIRFTASADL 221

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               YA S +KV+  + + +  +  +  TGRTHQ+R+HA  +GCPIVGD  Y        
Sbjct: 222 AKGKYARSRYKVLRVYGR-YALVLFKIDTGRTHQIRLHARFIGCPIVGDPLYGKKEAEWK 280

Query: 281 TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
                  + LHA  + +  P    +   TAPLP         L 
Sbjct: 281 PY----GMMLHAYRLCVALPSTREKTVFTAPLPRRFQTVLHLLR 320


>gi|49477132|ref|YP_035440.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|49328688|gb|AAT59334.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
          Length = 297

 Score =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 135/318 (42%), Gaps = 39/318 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI   
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 68  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPSGSV 113

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 114 A---NALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID  A     + 
Sbjct: 171 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVS 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 225 LELDTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 278

Query: 304 RLQITAPLPAHMVKTWDS 321
            +  TA +P+ M +    
Sbjct: 279 EMSFTAMIPSDMQEVLRQ 296


>gi|227875267|ref|ZP_03993409.1| possible pseudouridylate synthase [Mobiluncus mulieris ATCC 35243]
 gi|227844172|gb|EEJ54339.1| possible pseudouridylate synthase [Mobiluncus mulieris ATCC 35243]
          Length = 306

 Score =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 144/323 (44%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V      +R D         ++     +IL  G V + +  +K ++ +QSG+ + +
Sbjct: 3   RVLPVPEGLTGLRADVGLAKLL-GLSRAKAGEILAQGGVAMGETVLKKSDALQSGETLEV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
              I+   ++ +   +                 LLYED+ + V +KPAG++   G G   
Sbjct: 62  TAPIHPKVYVPEVTPVP-------------GMKLLYEDADLVVVDKPAGVAAHTGPGWDG 108

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L++           ++  + HRLD  TSG +VVA++  A   L  +FR  R++K
Sbjct: 109 PTVVGALRAAGVRISTSGPVEREGIVHRLDAGTSGAMVVAKSELAYGKLKNAFRYHRVEK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           IY ++  GI K     I   + +    G ++   V     G   A++H+   +       
Sbjct: 169 IYLAVARGILKPSLGTIDAPIGRAP--GREFKMAVVV---GGKPAVTHYDTAESLP-GAT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
              +Q  TGRTHQ+RVH   +G P++GD +Y A+ K      ++ + +LHA  +   HP 
Sbjct: 223 LARVQLETGRTHQIRVHFAAIGHPLLGDTEYGADAKQAVRLGLE-RQWLHASRLVFKHPR 281

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G  + + +PLP+ +      L 
Sbjct: 282 TGIEIAMDSPLPSDLQGVLAVLR 304


>gi|213420845|ref|ZP_03353911.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 278

 Score =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 66/276 (23%), Positives = 123/276 (44%), Gaps = 32/276 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
              V  ++   RLD+     +P  +   +++ + + +V V+ +   K   ++  G+ V I
Sbjct: 8   TATVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                            +    +   +  +   ++YED  I V NKP  + V  G+G   
Sbjct: 68  D---------------AEIDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPD 112

Query: 128 -HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   L  +       PR  + HRLD++T+G++VVA+T  A   L ES ++R I + Y 
Sbjct: 113 GTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172

Query: 185 SLVWGIPKNKK---ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           ++  G         E I+    K++H+    +            A++H+++++ F +   
Sbjct: 173 AVAIGHMTAGGTVNEPISRHPTKRTHMSVHPM---------GKPAVTHYRIMEHF-RVHT 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            L ++  TGRTHQ+RVH  H+  P+VGD  Y    +
Sbjct: 223 RLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPR 258


>gi|229490347|ref|ZP_04384188.1| pseudouridine synthase, RluA family [Rhodococcus erythropolis
           SK121]
 gi|229322637|gb|EEN88417.1| pseudouridine synthase, RluA family [Rhodococcus erythropolis
           SK121]
          Length = 308

 Score =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 78/328 (23%), Positives = 140/328 (42%), Gaps = 30/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  + MR+D         ++   +  +   G V VD   V  ++R+ +G 
Sbjct: 1   MRESRSMPVPDGLDAMRVDAGLARLL-GLSRTVVAALAEEGSVLVDGVAVGKSDRLTAGS 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGG 122
            + +               + +    LT  +  ++ + +LY D  +   +KP G++    
Sbjct: 60  WLEV--------------VLPEPPRPLTIEATPVEGMEILYADDDVVAVDKPVGVAAHAS 105

Query: 123 SG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ 
Sbjct: 106 VGWTGPTVIGGLAAAGFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTLLKRAFKQ 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I K Y +LV G P      I   + +  H G D+   V  +      +++H+  I+ F
Sbjct: 166 RTIDKRYHALVQGHPDPSSGTIDAPIGR--HHGNDWRFTVTAD---GKPSVTHYDTIEAF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q    L++   TGRTHQ+RVH   +  P  GD  Y A+ +      ++ + +LHA  + 
Sbjct: 221 -QAASLLDVHLETGRTHQIRVHFSALRHPCCGDLTYGADPRLAERLGLE-RQWLHAVSLG 278

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  GR ++I +  P  +    + L 
Sbjct: 279 FAHPADGRWVEIKSKYPKDLEHALEVLR 306


>gi|317124659|ref|YP_004098771.1| ribosomal large subunit pseudouridine synthase D [Intrasporangium
           calvum DSM 43043]
 gi|315588747|gb|ADU48044.1| ribosomal large subunit pseudouridine synthase D [Intrasporangium
           calvum DSM 43043]
          Length = 310

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 142/324 (43%), Gaps = 26/324 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT ++ V+V +     R+D      +  ++      +   G V VD K V  ++R+  G 
Sbjct: 1   MTELRTVLVPDGLAGERVDAGVARLF-GLSRTRAADLAGEGLVVVDGKVVGKSDRLAPGS 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ +     A    +   +++   V            ++++D  I V +KP G++     
Sbjct: 60  MLEVSLPGAAQGPAV---RVVAEPVP--------GMRIIHDDEDIVVVDKPVGVAAHPSV 108

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  +  RLD  TSG++VVA++  A   L ++FR R
Sbjct: 109 GWSGPDVVGGLAAAGYRISTSGAPERQGIVSRLDVGTSGLMVVAKSEYAYSRLKQAFRTR 168

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G+P      +   + +  H G D+   V +N      +++H++VI+ F 
Sbjct: 169 AVDKNYHALVQGLPDPLVGTVDAPIGR--HPGHDFKFAVMRN---GKPSVTHYEVIEAF- 222

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    L++   TGRTHQ+RVH   +  P  GD  Y A+          ++ +LHA  +  
Sbjct: 223 RHASLLDIHLETGRTHQIRVHMAAIKHPCCGDPLYGADPTL-ARKLGLDRQWLHAVGLGF 281

Query: 298 PHPEGG-RLQITAPLPAHMVKTWD 320
            HP  G  +   +  P  + +  D
Sbjct: 282 EHPGTGAYVHFESEYPEDLQRALD 305


>gi|325289223|ref|YP_004265404.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324964624|gb|ADY55403.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 303

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 73/307 (23%), Positives = 131/307 (42%), Gaps = 34/307 (11%)

Query: 24  WFKNHYPH---INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           + ++       ++   + ++    +++V+ + V  N R+Q+G  V I   ++  N+II E
Sbjct: 18  FLRDLLASKLLLSHSLVVRLKHQNKIQVNGQLVHTNYRLQAGDFVTINIDLSEENNIIPE 77

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVD 138
              LD               ++YED      NKPAG+S+      G     +     W  
Sbjct: 78  SIPLD---------------IVYEDEDFVAVNKPAGMSIHPSRLGGTGTLANAVTYHWQG 122

Query: 139 -SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +    R  +RLD++TSG++++ +++ A Q +    +  +I + Y +LV          
Sbjct: 123 LGRNILFRPINRLDKDTSGLVLIGKSQFAHQGIFNQLKQHKIDRRYIALVERALTRDHGH 182

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +        +            A +H++V+D +      L ++  TGRTHQ+RV
Sbjct: 183 IDQPIARPDANKRRRIV-----HPAGQAATTHYQVLDRYPD-HTLLSLKLETGRTHQIRV 236

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
           H  ++G P+ GD  Y       F SP+  +  LHA  +   HP  G  + +  PL   M 
Sbjct: 237 HLSYIGHPVSGDLLYG------FASPLIKRQALHADRIRFTHPRSGKEVILDIPLAQDMQ 290

Query: 317 KTWDSLG 323
              D LG
Sbjct: 291 TAVDYLG 297


>gi|294790528|ref|ZP_06755686.1| ribosomal large subunit pseudouridine synthase D [Scardovia
           inopinata F0304]
 gi|294458425|gb|EFG26778.1| ribosomal large subunit pseudouridine synthase D [Scardovia
           inopinata F0304]
          Length = 311

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 76/329 (23%), Positives = 141/329 (42%), Gaps = 33/329 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V    V  D   +R D         ++      ++  GQ+ +  +    + ++QSG 
Sbjct: 1   MNKVTM--VPEDLVGVRFDLAVSRMM-GLSRSKAANLIDQGQISLIGRCGLKSEKLQSGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +R+     +L    K  + +D  +            ++YED  + V +KP G++     
Sbjct: 58  SIRV-----SLTTSEKAPEPIDYDMG-----------IVYEDGDLVVVDKPVGMAAHQSV 101

Query: 124 G-IAYHIDGFLKSW-VDSKGQKPR----LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G LK+  V      P+    +  RLD  TSG+++V +++ A + +   F   
Sbjct: 102 GWTGSTVLGSLKARGVHITDYGPQGRQGIVSRLDVGTSGLMLVCKSQMAYKEMRRQFSQH 161

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y++L  G  K  K  +   + + S     +             AI+H+ VI+ F 
Sbjct: 162 EVKKTYYALAQGNLKEDKATVDAPIGRDSAADFRFTI-----TPAGKPAITHWDVIERFG 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q   ++ +   TGRTHQ+RVH   +G P+VGD  Y AN        + ++ +LH+  +D 
Sbjct: 217 Q-ATYISVNLETGRTHQIRVHMSSLGHPLVGDSMYGANPVLAEQLGL-SRQWLHSMKLDF 274

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
            HP     + + + LP  +    ++L  +
Sbjct: 275 RHPRTHCPVHLESTLPTDLATALETLRLR 303


>gi|325677946|ref|ZP_08157588.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
 gi|324110500|gb|EGC04674.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
          Length = 321

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 69/302 (22%), Positives = 137/302 (45%), Gaps = 23/302 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +  ++ + R+D++     P +    L K +R  +++++ KR + + R++ G +V+
Sbjct: 1   MREFTISKNDADQRMDKFLTKAVPALPKNLLYKYIRLKRIKLNGKRCEISTRLKDGDIVQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
           +           +++      +N  K  +     ++YED  + + NKP G+ V    SG 
Sbjct: 61  LYINDEF---FPEKRDAAHRFLNAPKDIE-----VVYEDDDVILCNKPCGLVVHEDESGE 112

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +  +   +  ++  KG+          P L +R+D+ T+GI++ A+   + + L +  + 
Sbjct: 113 SDTLIDRILHYLYDKGEYDPDSELSFTPALCNRIDRNTAGIVICAKNAESLRILNQKVKD 172

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R ++K Y  +  G+PK K   +  +  +        V V  +   G    I+ +KV++  
Sbjct: 173 RELEKKYLCVTVGVPKAKSAELKAYHRRNEQT--KTVKVADKPFDGCKTMITRYKVLEEN 230

Query: 237 AQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
            Q     LE+   TGRTHQ+R H  H+GCP++GD KY  N              L A  +
Sbjct: 231 KQSGLALLEVDLVTGRTHQIRAHLAHIGCPLLGDGKYGINRINR--EFGVKTQALCAYKL 288

Query: 296 DL 297
             
Sbjct: 289 TF 290


>gi|41407349|ref|NP_960185.1| hypothetical protein MAP1251 [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41395701|gb|AAS03568.1| hypothetical protein MAP_1251 [Mycobacterium avium subsp.
           paratuberculosis K-10]
          Length = 308

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 137/327 (41%), Gaps = 29/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  + + V      MR+D         ++      +   G V +D      ++R+  G 
Sbjct: 1   MTE-RSMPVPEGLAGMRVDAGLARLL-GLSRSAAAALAEDGGVELDGVPAGKSDRLTGGA 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          + E      +  +    D     +LY D  I   +KPA ++     
Sbjct: 59  WLHVR---------LPEAPAPPQNTPV----DIEGMTILYSDDDIVAVDKPAAVAAHASV 105

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R
Sbjct: 106 GWTGPTVLGGLAAAGYRITTSGVPERQGIVHRLDVGTSGVMVVALSERAYTLLKRAFKQR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G P      I   + +  H GG++   V    K   ++++H+  ++ F 
Sbjct: 166 TVDKRYHALVQGHPDPSSGTIDAPIGR--HRGGEWKFAVT---KDGRHSLTHYDTVEAFV 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                L++   TGRTHQ+RVH   +  P  GD  Y A+ K      +Q + +LHAR +  
Sbjct: 221 -AASLLDVHLETGRTHQIRVHFSALHHPCCGDLVYGADPKLAKKLGLQ-RQWLHARSLSF 278

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLG 323
            HP +G R++I +P P  +    D L 
Sbjct: 279 AHPADGRRMEIVSPYPPDLQHALDVLR 305


>gi|167041971|gb|ABZ06708.1| putative RNA pseudouridylate synthase [uncultured marine
           microorganism HF4000_141E02]
          Length = 320

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 85/325 (26%), Positives = 152/325 (46%), Gaps = 13/325 (4%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  +     V+V  D++ MRLD +       +    + +++R G+VR++ KR K  +R+ 
Sbjct: 1   MKDLGINNKVIVSRDDDGMRLDNYLIKIIKGMPKSRIYRMIRKGEVRINSKRAKPRSRVH 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
               VRIPP        + E K   SSV        + +I+++E+    + NKP+G++V 
Sbjct: 61  VNDTVRIPPYA------LNEPKTNVSSVRKD-DFRRINNIVIFENDSFLLVNKPSGLAVH 113

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSGI   +   L+S+ + + +   L HRLD++TSG L+V++ ++  + L E FR  ++Q
Sbjct: 114 GGSGIHLGLIELLRSFREQRNEHLELVHRLDKDTSGCLLVSKKKSKLRKLHEYFREGKVQ 173

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y  L+ G        I   L   S      + V    +     A + F +++ + +  
Sbjct: 174 KTYLGLMVGKFTQTVYEIDQPLKIISTPENGRLAV---PDDSGTKAKTKFFLMEKY-KNS 229

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
              +++P TG+THQ+R HA +M  P+  D +Y        +     +L+LHA  +  P  
Sbjct: 230 ALFKIEPITGKTHQIRAHAKYMKTPLAADQRYGIQPDQIVSEFGLTRLFLHAESITFPGL 289

Query: 301 EGGR--LQITAPLPAHMVKTWDSLG 323
                     + L   + +  + L 
Sbjct: 290 SSTENTFSFRSKLDTKLAEVLEKLR 314


>gi|166031887|ref|ZP_02234716.1| hypothetical protein DORFOR_01588 [Dorea formicigenerans ATCC
           27755]
 gi|166028340|gb|EDR47097.1| hypothetical protein DORFOR_01588 [Dorea formicigenerans ATCC
           27755]
          Length = 335

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 71/337 (21%), Positives = 145/337 (43%), Gaps = 29/337 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +++ +E   RLD++ K + P      + K+LR   + ++ K+     ++ +G  ++
Sbjct: 1   MKETIIKENESGQRLDKYLKKYLPQAPGSFIYKMLRKKNITLNGKKAAGQEKLNTGDSIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                  ++      K   ++     +       ++YED  I + NKPAG+  Q      
Sbjct: 61  FFLAEETID------KFTGNAAASESYPVKKDLEIIYEDDNILLINKPAGMLSQKAKKED 114

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +  ++  ++ S G           P + +RLD+ TSG++V  ++ A  Q + E+F+ R
Sbjct: 115 VSLVEYVIGYLLSNGSVTKEELLTFHPGICNRLDRNTSGMVVAGKSLAGLQIMGEAFKER 174

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  LV G  K     I  +L K        V + ++  +GA    + ++ +    
Sbjct: 175 TLAKYYLCLVKGCIKETS-HIRGYLKKDEKTN--KVMISRKMSEGAAAIETEYEPVAYQK 231

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMD 296
           +    L++   TGRTHQ+R H   +G P++GD+KY   ++   + +       LH+  + 
Sbjct: 232 E-LTLLKVHLITGRTHQIRAHLASIGHPLMGDYKYGNISWNHQYETYGVKTQMLHSYELH 290

Query: 297 LP-HPEGGRLQ------ITAPLPAHMVKTWDSLGFKY 326
            P  P    L+        A +P    +      +++
Sbjct: 291 FPQMP--KPLENLSKNVFQARVPGKFYRLIKETAWEH 325


>gi|196037436|ref|ZP_03104747.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
 gi|196031678|gb|EDX70274.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
          Length = 297

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 70/318 (22%), Positives = 137/318 (43%), Gaps = 39/318 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI   
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +   +  +               ++ +   ++YED  + V NK A +S         H  
Sbjct: 68  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSR---EHPS 110

Query: 131 GFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + + + S   K        +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 111 GSVANALLSHYDKQYLPSTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID  A     + 
Sbjct: 171 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVS 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 225 LELDTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 278

Query: 304 RLQITAPLPAHMVKTWDS 321
            +  TA +P+ M +    
Sbjct: 279 EMSFTAMIPSDMQEVLRQ 296


>gi|283458362|ref|YP_003362985.1| pseudouridylate synthase [Rothia mucilaginosa DY-18]
 gi|283134400|dbj|BAI65165.1| pseudouridylate synthase [Rothia mucilaginosa DY-18]
          Length = 328

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 132/304 (43%), Gaps = 35/304 (11%)

Query: 33  NFVNLQKILRSGQVRV--DKKRVK--FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
                   +  G V V  + K VK   + ++ +G  V +          I+ +K+     
Sbjct: 40  PRTRTSGWILDGHVTVTNNGKAVKIGKSYKLSAGDEVVVDASAPRDLADIRPEKV----- 94

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------- 140
                       +++ D  I V +KPAG++     G  +H    + + +           
Sbjct: 95  --------DGFRIVHLDEDIVVVDKPAGVAAHPSPG--WHGPTVISALMGEGISVATSGA 144

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            ++  + HRLD  TSG++VVAR+  A   L  +F+ R + K+Y +LV G+P   +  I  
Sbjct: 145 AERQGIVHRLDVGTSGLMVVARSERAYTELKRAFKERTVDKVYHTLVQGLPDPLRGTIDA 204

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H G ++   V ++      +I+H+ V++ F      +E+   TGRTHQ+RVH  
Sbjct: 205 PIGR--HPGNEWKFAVVED---GRNSITHYDVLEAFG-PASLVEVHLETGRTHQIRVHFS 258

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
            +  P  GD  Y A+ + +    +  + +LHA  +   HP  G R+  T+  P  +    
Sbjct: 259 ALRHPCCGDLTYGADPRFSAELGL-TRQWLHAHRLGFDHPGTGERVTFTSEYPLDLSYAL 317

Query: 320 DSLG 323
            +L 
Sbjct: 318 TALR 321


>gi|332652460|ref|ZP_08418205.1| pseudouridine synthase, RluA family [Ruminococcaceae bacterium D16]
 gi|332517606|gb|EGJ47209.1| pseudouridine synthase, RluA family [Ruminococcaceae bacterium D16]
          Length = 327

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 70/301 (23%), Positives = 129/301 (42%), Gaps = 23/301 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +  ++   RLDRW     P +     QK +R  +V+V+ K  K + R+Q G V++
Sbjct: 1   MKEFTIAKNDAGQRLDRWLAKTLPLLPAPLAQKYIRLKRVKVNGKGSKRDVRLQVGDVLQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---- 122
           +       +    E   L             K  +LYED  I + +K  G+ V       
Sbjct: 61  LYINDEFFDRPTPENAFLSLYQP--------KLNILYEDEHILLLDKRPGLVVHPDETER 112

Query: 123 -SGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            + +  HI  +L    +    K     P L +R+D+ T GI++ A+T  A + + +  + 
Sbjct: 113 VNTLLTHIQAYLYQKKEWSPYKENSFAPALCNRIDRNTGGIVIAAKTAEALRVMNQKIKD 172

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K Y   V G  + ++  +  ++ K        V+V  + + GA  AI+ +K +   
Sbjct: 173 RELSKFYLCAVLGRMEPREGKLEGFIWKDE--VKKQVYVRSRPQPGAKTAITLYKTL-AV 229

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +E    TGRTHQ+R      G P++GD KY +  +       ++   L++  ++
Sbjct: 230 QNGLSLVECDLITGRTHQIRAQFAAAGHPLLGDGKYGSERENR--KYGRHGQALYSYRLE 287

Query: 297 L 297
            
Sbjct: 288 F 288


>gi|11279841|pir||A81748 ribosomal large chain pseudouridine synthase D TC0029 [imported] -
           Chlamydia muridarum (strain Nigg)
          Length = 345

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 79/323 (24%), Positives = 142/323 (43%), Gaps = 32/323 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIP 68
            VV+      RLD+    H    +    Q+ +  G+VRV+ +   + +  +  G +V + 
Sbjct: 24  FVVDERLIG-RLDKGLVLHNNAYSRAFYQQQIDLGRVRVNGRVQTRASYLLSQGDLVDL- 81

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
                        ++++     +   + +    +YED+ I V NKP  + V    G    
Sbjct: 82  -------------ELVEEETPSSLTPENIPLDKVYEDNMILVINKPRNMVVHPAPGHVQG 128

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + + I   LK     +  +P + HRLD++TSG+L+  +TR A    +E F  +++
Sbjct: 129 TVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKAVYSELFSSKQM 188

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K+Y ++    P  K     +  + +  +    + V+ ++ +G   AI+H  V+    + 
Sbjct: 189 KKMYIAICINSPAQKH---IHTRIARHPVKRKEMTVLSKDTEGGKEAITHCHVLASNGR- 244

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + + P TGRTHQLRVH  H+G PI+GD  Y             +K  LHA  +   H
Sbjct: 245 LSVVALYPETGRTHQLRVHMKHLGTPILGDPVYG--VPSINFRYGLDKQQLHAYSLVFTH 302

Query: 300 PEG-GRLQITAPLPAHMVKTWDS 321
           PE   R+++   LP  M    + 
Sbjct: 303 PESAERVELVTKLPDDMTSLIEK 325


>gi|88607282|ref|YP_504969.1| ribosomal large subunit pseudouridine synthase A [Anaplasma
           phagocytophilum HZ]
 gi|88598345|gb|ABD43815.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Anaplasma phagocytophilum HZ]
          Length = 324

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 83/335 (24%), Positives = 137/335 (40%), Gaps = 36/335 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSG 62
           MT+V  ++VE+     RLD        +I+    Q I+  G V +    V  N+ +  +G
Sbjct: 1   MTHVHTILVEHYNAKKRLDVLISASL-NISRSKAQCIISDGGVTLLDTPVLNNSHLTNTG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V  +       +  I               +  +   ++YED  I V +K   I+V  G
Sbjct: 60  DVYTVTVPDTPQSTSI-------------DPNHDIPLHIIYEDEHIIVIDKAPNIAVHPG 106

Query: 123 SGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            G     D    + +   G          +P + HRLD++TSG++V+A+T  A   L+++
Sbjct: 107 HGTKN--DTLAHALLAHCGNALCAVGNSHRPGIIHRLDKDTSGLMVIAKTEKAYLVLSQA 164

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
              ++ +K Y +L+WG+P  K   I   L  K         +++       +A + + + 
Sbjct: 165 LEEKKFRKEYLALIWGVPTTKHCFIQTNLDVK----RSDKTMMEVTLSRGKHANTEYIIE 220

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-----NKL 288
             F           HTGRTHQ+RVH  H+G  +VGD KY  N K +    I       + 
Sbjct: 221 KTFGNVASLARCILHTGRTHQIRVHMSHIGHSVVGDQKYGKNNKKSLRCGIPEVRNFKRQ 280

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            LHA  +   HP  G  L   +     + +    L
Sbjct: 281 ALHACLLGFHHPCTGEYLCFNSNPAKDIQELISIL 315


>gi|308235820|ref|ZP_07666557.1| pseudouridine synthase, RluA family protein [Gardnerella vaginalis
           ATCC 14018]
 gi|311114402|ref|YP_003985623.1| ribosomal large subunit pseudouridine synthase D [Gardnerella
           vaginalis ATCC 14019]
 gi|310945896|gb|ADP38600.1| ribosomal large subunit pseudouridine synthase D [Gardnerella
           vaginalis ATCC 14019]
          Length = 310

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 75/331 (22%), Positives = 146/331 (44%), Gaps = 36/331 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ +++  V +     R D         ++  N   ++ SG+ ++  ++ + ++ +Q G 
Sbjct: 1   MSDIRF-TVTSQFAGCRFDVCLSKLM-GVSRANAISLIDSGKAKILDRKSQKSSTLQDGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ I            ++++ D     T  S      ++Y D  I V +KP G++     
Sbjct: 59  VIVIN-----------QEEVDDQKEKSTSKSTICNIPIVYNDEDIVVVDKPVGVAAHSAK 107

Query: 124 GIAYHIDG-FLKSWVDSKGQKPR----------LTHRLDQETSGILVVARTRAAAQHLTE 172
           G     DG  +   +++ G + +          +  RLD  TSG+++V +T  A + + +
Sbjct: 108 G----WDGPTVPECLEASGVEIKTTVCDESRKGIVSRLDVGTSGLMLVCKTDFAYEEMKK 163

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F    ++KIY +LV G  K  K  I   + +                K    AI+H+ V
Sbjct: 164 QFANHSVKKIYHALVQGNLKQNKATIDAPIGR-----AKVSDFRFTITKSGKPAITHWDV 218

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           I+ F +    +++   TGRTHQ+RVH   +G P+VGD  Y AN + +    + ++ +LHA
Sbjct: 219 IERF-KGATLVKVNLETGRTHQIRVHFSSIGHPVVGDPMYGANPQLSEKLGL-SRQWLHA 276

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +   HP  G  +++ +  P  +     ++
Sbjct: 277 MSLKFKHPRTGELIKVESKYPLDLQHALHAI 307


>gi|226307021|ref|YP_002766981.1| pseudouridine synthase RluD [Rhodococcus erythropolis PR4]
 gi|226186138|dbj|BAH34242.1| putative pseudouridine synthase RluD [Rhodococcus erythropolis PR4]
          Length = 308

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 78/328 (23%), Positives = 140/328 (42%), Gaps = 30/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +  + MR+D         ++   +  +   G V VD   V  ++R+ +G 
Sbjct: 1   MRESRSMPVPDGLDAMRVDAGLARLL-GLSRTVVATLAEEGSVLVDGVAVGKSDRLTAGS 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGG 122
            + +               + +    LT  +  ++ + +LY D  +   +KP G++    
Sbjct: 60  WLEV--------------VLPEPPRPLTIEATPVEGMEILYADDDVVAVDKPVGVAAHAS 105

Query: 123 SG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ 
Sbjct: 106 VGWTGPTVIGGLAAAGFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTLLKRAFKQ 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I K Y +LV G P      I   + +  H G D+   V  +      +++H+  I+ F
Sbjct: 166 RTIDKRYHALVQGHPDPSSGTIDAPIGR--HHGNDWRFTVTAD---GKPSVTHYDTIEAF 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q    L++   TGRTHQ+RVH   +  P  GD  Y A+ +      ++ + +LHA  + 
Sbjct: 221 -QAASLLDVHLETGRTHQIRVHFSALRHPCCGDLTYGADPRLAERLGLE-RQWLHAVSLG 278

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             HP  GR ++I +  P  +    + L 
Sbjct: 279 FAHPADGRWVEIKSKYPKDLEHALEVLR 306


>gi|38234158|ref|NP_939925.1| putative pseudouridine synthase [Corynebacterium diphtheriae NCTC
           13129]
 gi|38200420|emb|CAE50108.1| Putative pseudouridine synthase [Corynebacterium diphtheriae]
          Length = 308

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 131/324 (40%), Gaps = 31/324 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V      MR+D         I+      +  +G V VD   V  ++R+  GQ + +
Sbjct: 6   RSLPVPEGLAGMRVDAALSKLL-GISRTAAADLAIAGDVVVDGHCVGKSDRLSEGQWLDV 64

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLK-SILLYEDSKIYVFNKPAGISVQGGSGIA 126
                           L    +LT   + ++   +LY D  +   NKP G++     G  
Sbjct: 65  T---------------LPEVRDLTPREELIEGMDILYSDDDVIAVNKPVGVAAHPTLGWE 109

Query: 127 -YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + G L +           ++  +  RLD  TSG++VVA +      L  +F+ R + 
Sbjct: 110 GPTVIGGLAAAGFRISTSGPPERKGIVQRLDVGTSGVMVVAASERGYSVLKRAFKERTVT 169

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y SLV G        I   + +    G  +            +A++H++ I+ FA+  
Sbjct: 170 KTYHSLVQGHMDPLSGTIDAPIGRHPSAGWRFAVTT-----DGKHAVTHYETIEAFAE-A 223

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L +   TGRTHQ+RVH   +  P  GD  Y ++   +    + ++ +LHA  +   HP
Sbjct: 224 SLLRIHLETGRTHQIRVHMSALHHPCCGDPMYGSDPALSARLGL-DRQWLHAVSLGFHHP 282

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             GR ++I +P    +    D L 
Sbjct: 283 ADGRWVEIESPYSKDLQHALDVLR 306


>gi|255318859|ref|ZP_05360085.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           radioresistens SK82]
 gi|262378883|ref|ZP_06072040.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           radioresistens SH164]
 gi|255304115|gb|EET83306.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           radioresistens SK82]
 gi|262300168|gb|EEY88080.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           radioresistens SH164]
          Length = 350

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 71/323 (21%), Positives = 130/323 (40%), Gaps = 34/323 (10%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           +      R+D+     +   +   L++ ++ G + V+   VK   + +  +++ +   + 
Sbjct: 44  DESYLGQRIDQAAALVWNEFSREKLKQWIKDGHLLVNGNNVKPKYKCEGNELLTLEAELE 103

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHID 130
                  E   LD                          NK  G+ V    G+G    ++
Sbjct: 104 IQTASQPENIPLDIIYEDDDIIVI---------------NKTVGMVVHPGAGNGSGTLVN 148

Query: 131 GFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             L  +  S    +  L HR+D++TSG+LVVA+   A   L++    + + +IY  +V+G
Sbjct: 149 ALLYHYPKSNELARAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLAKKTVYRIYDLVVYG 208

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   I   + K+  +    + ++     G   A++H+ V + F + F  ++ Q  T
Sbjct: 209 NIVA-GGTIDEPI-KRHPVDRVKMAIL----PGGKEAVTHYNVKERF-KDFTRVQAQLET 261

Query: 250 GRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           GRTHQ+RVH  ++G  +VGD  Y         A+ +   T     +  LHA  + L HP 
Sbjct: 262 GRTHQIRVHFSYIGYGLVGDPVYMSRVRVPAGASEELADTLRSFKRQALHAAKLGLVHPR 321

Query: 302 GGR-LQITAPLPAHMVKTWDSLG 323
            G  +   AP P       + L 
Sbjct: 322 TGENMMFEAPWPEDFKHLIEVLR 344


>gi|313892058|ref|ZP_07825656.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
 gi|313119510|gb|EFR42704.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
          Length = 328

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 79/317 (24%), Positives = 143/317 (45%), Gaps = 16/317 (5%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E  +L ++     P  +   + K LR   +  + K+   N  I+SG V+ I      L 
Sbjct: 10  DEGQKLIKFLFKLLPGASKSLIYKSLRKKNILYNNKKANGNEIIKSGDVIEIWFSDETLE 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           +  K++      +     +   K I+LYE+  I V NKP G+  Q        ++ +L  
Sbjct: 70  NFSKKES--KEILKGNIENFSFKDIILYENEDIIVVNKPKGMLSQRDISRQKSLNDYLLE 127

Query: 136 WVDSK---GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           ++ +    G KP + +RLD+ TSG L+ A+T   A+ + E  +   I K Y  LV+G  K
Sbjct: 128 YIKNSNYSGFKPSICNRLDKNTSGTLICAKTFKIAREINELIKNHVINKKYLCLVFGDIK 187

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHT 249
           +    + ++L K   +  +   V  + ++G     +   VI           +LE+   T
Sbjct: 188 DDL-YLKDYLFKN--VENNKAIVSNEKKEGFLEIKTKVHVIKSFKLHEYPVTFLEVTLLT 244

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP--HPEGG--R 304
           G+ HQ+R H  ++G PI+GD KY  N     +  ++  +  LH+  ++ P  H       
Sbjct: 245 GKFHQIRAHLSYIGHPILGDRKYGNNESLEISKILEIGRQLLHSYSIEFPENHCLKELSG 304

Query: 305 LQITAPLPAHMVKTWDS 321
           ++I AP+P  ++   + 
Sbjct: 305 MKIKAPIPKDIMCILNK 321


>gi|152990499|ref|YP_001356221.1| ribosomal large subunit pseudouridine synthase D [Nitratiruptor sp.
           SB155-2]
 gi|151422360|dbj|BAF69864.1| ribosomal large subunit pseudouridine synthase D [Nitratiruptor sp.
           SB155-2]
          Length = 319

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 83/343 (24%), Positives = 151/343 (44%), Gaps = 46/343 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M  + +     + E  RLD+             ++++++ G VR++ K  K   ++++SG
Sbjct: 1   MEKITFT----NREKERLDKALAKKL-QKPRNQIEQLIKQGYVRINGKIEKKAGSKLKSG 55

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +V +               I +  V+  K   F    + YED  I V NKPAG+ V   
Sbjct: 56  DLVEVT--------------IPEPKVSQPKDVHFDVERI-YEDEDILVLNKPAGLVVHPA 100

Query: 123 SGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
             +    +  L  W+ +           ++  + HRLD+ETSG++V+A+     Q L++ 
Sbjct: 101 PSV---KEPTLVDWLKANDISLSTLSGEERHGIVHRLDKETSGLIVIAKNNETHQALSKQ 157

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF-KV 232
            + + + + Y ++V   P  K++ I    + ++      + VV    +G  YA S F K+
Sbjct: 158 LQDKSMGRYYLAIVE--PPLKEDLIIEKPIARNPKNRLKMGVV----EGGRYAKSAFVKL 211

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                 K+  +  +  TGRTHQ+RVH   +   I+GD  Y    K    S    +++LHA
Sbjct: 212 TTSKNNKYELIGAKLFTGRTHQIRVHLASINRHILGDSLYGFKSK----SVTIPRVFLHA 267

Query: 293 RYMDLPHP-EGGRLQITAPLPAHMVKTWDS-LGFKYDRNLYIK 333
             + L HP  G +++  AP+P  M+           D  +++ 
Sbjct: 268 YILYLKHPKSGEKMRFLAPVPEDMLDFLQKYFEENIDETIHVD 310


>gi|163841219|ref|YP_001625624.1| ribosomal large subunit pseudouridine synthase D [Renibacterium
           salmoninarum ATCC 33209]
 gi|162954695|gb|ABY24210.1| ribosomal large subunit pseudouridine synthase D [Renibacterium
           salmoninarum ATCC 33209]
          Length = 308

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 143/319 (44%), Gaps = 28/319 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++ + +R D         I+      +L  G V  + K +  + R+ +G  V +    
Sbjct: 10  VTDEFDGVRADAALAQLL-EISRSAAAVLLNGGHVSSEGKSLGKSARLFTGMSVLVSIPE 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
                 +  + + D ++ L   +               V +KP G++     G +   + 
Sbjct: 69  QRDPLAVVVEAVDDLNILLDDDA-------------FVVIDKPVGVAAHPSPGWVGPTVV 115

Query: 131 GFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           G L +           ++  + HRLD  TSG++VVA+T  A   L  +F+ R + K+Y++
Sbjct: 116 GALAAAGYRISTSGAAERAGIVHRLDVGTSGVMVVAKTEQAYTVLKRAFKERTVNKVYYA 175

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+P   +  +   + +  H G D+   V ++      +++H++V++ F  K   LE+
Sbjct: 176 VVQGLPDPLRGTVDAPIGR--HPGHDWRFAVIED---GRPSVTHYEVLEAFG-KASLLEV 229

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
              TGRTHQ+RVH   +  P VGD  Y A+ K      +  + +LHA+ +   HP  G  
Sbjct: 230 HLETGRTHQIRVHFSALNHPCVGDLTYGADPKLAAELGL-TRQWLHAKSLGFDHPVTGEW 288

Query: 305 LQITAPLPAHMVKTWDSLG 323
           +++++  PA +     +L 
Sbjct: 289 VEVSSEYPADLDYALQALR 307


>gi|307263793|ref|ZP_07545399.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
 gi|306870914|gb|EFN02652.1| Ribosomal large subunit pseudouridine synthase D [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
          Length = 319

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 68/304 (22%), Positives = 125/304 (41%), Gaps = 32/304 (10%)

Query: 4   MTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           MT    +   V  D    RLD+     +P  +   ++  + S  V+V+   V K   ++ 
Sbjct: 1   MTQQMTLTAEVTADLLGCRLDQALAQLFPDYSRSRIKVWIESDLVKVNGIVVNKAREKVF 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ V I   I                         +   ++YED  I V NKP  + V 
Sbjct: 61  GGEQVEIQAEIEEEIRF---------------EPQDIPLNIVYEDDDIIVINKPKDLVVH 105

Query: 121 GGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+G     +   L  +     + PR  + HRLD++T+G++VVA+   A  HL  + + R
Sbjct: 106 PGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRLDKDTTGLMVVAKNIPAQTHLVTALQKR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           RI + Y ++  G+   +   +   + +                     A++H+++++ F 
Sbjct: 166 RITREYEAVASGVM-TQGGKVDEPMARHPT-----KRTAMAVHPMGKPAVTHYRIMERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  L ++  TGRTHQ+RVH  H+  P++GD  Y    +       + +++        
Sbjct: 219 RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQLYGGRPRP--PKGGERRIFSGVTR--F 274

Query: 298 PHPE 301
           P P 
Sbjct: 275 PTPS 278


>gi|294628838|ref|ZP_06707398.1| RluA family RNA pseudouridine synthase [Streptomyces sp. e14]
 gi|292832171|gb|EFF90520.1| RluA family RNA pseudouridine synthase [Streptomyces sp. e14]
          Length = 314

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 76/327 (23%), Positives = 140/327 (42%), Gaps = 18/327 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R++
Sbjct: 1   MSTLPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVLVDGTAVGKSERVR 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   ++ E   L   + +    D +  I+       +     +G +V
Sbjct: 60  GGAWLEVEMPQAPAPVQVVAE---LVEGMEIVHDDDDVVVIVKPVGVAAHPSPGWSGPTV 116

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GG   A +             ++  + HRLD  TSG++VVA++  A   L   F+ R +
Sbjct: 117 IGGLAAAGYRIST-----SGAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQFKERTV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G P      I   + +  H   DY   V  +      +++H+ +I+ F + 
Sbjct: 172 DKRYHTLVQGHPDPTSGTIDAPIGR--HPNHDYKWAVTAD---GKPSVTHYDLIEAF-RA 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA  +   H
Sbjct: 226 ASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADPTLAKRLKL-TRQWLHAVRLGFEH 284

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFK 325
           P  G+ ++  +  P  + +  D +  +
Sbjct: 285 PGDGQWVEFASDYPEDLQQALDQVREE 311


>gi|217958782|ref|YP_002337330.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|217067935|gb|ACJ82185.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
          Length = 297

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 67/314 (21%), Positives = 136/314 (43%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 10  IDSAEEGTLVREFLKT--KGISKAALTDIKFHGGSIEVNGQHASVRHQLQAGEELRVFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHI 129
           +   +  +               ++ +   ++YED  + V NK A +S        A  +
Sbjct: 68  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPAGSV 113

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L S  D +       +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 114 ANALLSHYDKRHLTSTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HF+VID    K   + ++ 
Sbjct: 174 HGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDSVNHK-THVSLEL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  ++G P++GD+ Y              +  LH+  +   HP     + 
Sbjct: 228 DTGRTHQIRVHMAYIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEKEMS 281

Query: 307 ITAPLPAHMVKTWD 320
            T P+P+ M     
Sbjct: 282 FTTPIPSDMQAVLR 295


>gi|294497498|ref|YP_003561198.1| pseudouridine synthase, RluA family [Bacillus megaterium QM B1551]
 gi|294347435|gb|ADE67764.1| pseudouridine synthase, RluA family [Bacillus megaterium QM B1551]
          Length = 302

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 136/322 (42%), Gaps = 36/322 (11%)

Query: 4   MTYVQYV--VVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  V  +   V+N  E + +  + K H     +  +++   R G + V+ K       +Q
Sbjct: 1   MKQVFTLSWTVDNSFEGVAVREFLKEHDISKASLTDIK--FRGGAIEVNGKHATVRYILQ 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  +++                     + +     +   ++YED  I V NK   +   
Sbjct: 59  KGDEIKV--------------AFPPEKASESLLPRAIPLDIVYEDEYILVLNKQPNMPSI 104

Query: 121 GGS-GIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                + + +   +  + +         L +RLD++TSG+L+VA+ R      +++ +  
Sbjct: 105 PSREHLTWSLSNAVLYYYEENNINSTVHLVNRLDRDTSGLLIVAKHRHVHYLFSKAQKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I+++Y + V G    K E I   + +K     +   + ++  +   +AI+H+  +  ++
Sbjct: 165 EIKRVYRAFVHGKLVGK-ETIEAPIGRK-----ESSIIEREVREDGQFAITHYTALRQYS 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  + +   TGRTHQ+RVH  + G P++GD  Y        T+ + ++  LH+  +  
Sbjct: 219 S-FTEVALSLETGRTHQIRVHMAYKGYPLLGDTLYGG------TNHLISRQALHSYELTF 271

Query: 298 PHPE-GGRLQITAPLPAHMVKT 318
            HP     L  TAPLP  M K 
Sbjct: 272 FHPFLQKTLSFTAPLPPDMQKL 293


>gi|270284819|ref|ZP_06194213.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           muridarum Nigg]
 gi|270288848|ref|ZP_06195150.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           muridarum Weiss]
 gi|301336199|ref|ZP_07224401.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           muridarum MopnTet14]
          Length = 338

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 79/323 (24%), Positives = 142/323 (43%), Gaps = 32/323 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIP 68
            VV+      RLD+    H    +    Q+ +  G+VRV+ +   + +  +  G +V + 
Sbjct: 17  FVVDERLIG-RLDKGLVLHNNAYSRAFYQQQIDLGRVRVNGRVQTRASYLLSQGDLVDL- 74

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG---- 124
                        ++++     +   + +    +YED+ I V NKP  + V    G    
Sbjct: 75  -------------ELVEEETPSSLTPENIPLDKVYEDNMILVINKPRNMVVHPAPGHVQG 121

Query: 125 -----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                + + I   LK     +  +P + HRLD++TSG+L+  +TR A    +E F  +++
Sbjct: 122 TVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKAVYSELFSSKQM 181

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K+Y ++    P  K     +  + +  +    + V+ ++ +G   AI+H  V+    + 
Sbjct: 182 KKMYIAICINSPAQKH---IHTRIARHPVKRKEMTVLSKDTEGGKEAITHCHVLASNGR- 237

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + + P TGRTHQLRVH  H+G PI+GD  Y             +K  LHA  +   H
Sbjct: 238 LSVVALYPETGRTHQLRVHMKHLGTPILGDPVYG--VPSINFRYGLDKQQLHAYSLVFTH 295

Query: 300 PEG-GRLQITAPLPAHMVKTWDS 321
           PE   R+++   LP  M    + 
Sbjct: 296 PESAERVELVTKLPDDMTSLIEK 318


>gi|237785359|ref|YP_002906064.1| pseudouridylate synthase [Corynebacterium kroppenstedtii DSM 44385]
 gi|237758271|gb|ACR17521.1| pseudouridylate synthase [Corynebacterium kroppenstedtii DSM 44385]
          Length = 313

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 139/326 (42%), Gaps = 27/326 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V    + +R+D         ++   +  +  SG + +D      ++R+ +  
Sbjct: 1   MRDSRRMPVPVGLDGLRVDSGLSKLL-GLSRTVVADLASSGDILIDGVPASKSDRLTTDS 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         + + + I D      +  D     +LY DS + V +KP G++     
Sbjct: 60  WLDVT--------LPESRSIADEPAREVEGMD-----ILYSDSDVIVVDKPVGVAAHPTM 106

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     +   L++           ++  +  RLD  TSG+++VA +  A   L ++FR R
Sbjct: 107 GWDGPTVTSGLRAAGFRVSTSGPPERQGIVQRLDVGTSGVMIVAASERAYSLLKQAFRDR 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G P      I   + +  H G  +   V+ +      A++H+  ++ F 
Sbjct: 167 TVDKTYHALVQGHPDPTVGTIDAPIAR--HPGAGWKFAVRSD---GKRAVTHYSTMEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++   + +   TGRTHQ+RVH   +  P  GD  Y ++ K        ++ +LHA  +  
Sbjct: 221 REATLVSVHLETGRTHQIRVHFSALHHPCCGDPMYGSDPKLT-EHLGLSRQWLHAVSLGF 279

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLG 323
            HP+G  + + +P PA +     +L 
Sbjct: 280 THPDGHYMVVESPYPADLDHALTTLR 305


>gi|91227385|ref|ZP_01261774.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio alginolyticus
           12G01]
 gi|91188649|gb|EAS74939.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio alginolyticus
           12G01]
          Length = 268

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 86/279 (30%), Positives = 151/279 (54%), Gaps = 16/279 (5%)

Query: 47  RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
           RV+KKR+K   ++++  +VRIPP       + K+   +  S  L K ++ L++++++ED 
Sbjct: 2   RVNKKRIKAEYKLKARDLVRIPP-----VTVEKKDDDVAPSTKLNKVAE-LENMIIFEDD 55

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
            + + NKP+G +V GGSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A
Sbjct: 56  HMLILNKPSGTAVHGGSGLKFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSA 114

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
            +HL   FR + ++K Y +LV G  K+  + +   LLK        V+ + +       +
Sbjct: 115 LRHLQAQFREKTVKKFYLALVMGQWKSSCKVVNAPLLKNE------VNSIVRVNPNGKPS 168

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-IQ 285
            + FK+++ F Q    ++  P TGRTHQ+RVH  + G PI  D +Y       +T     
Sbjct: 169 ETRFKILEKFEQ-ATLIQASPITGRTHQIRVHTQYTGHPIAWDDRYGDRRFDAYTGQVGL 227

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           ++L+LHA  +   HP     ++I AP+   + K    L 
Sbjct: 228 DRLFLHAANIKFQHPSNDEWMEINAPMEPKLEKVLAGLR 266


>gi|227486639|ref|ZP_03916955.1| pseudouridylate synthase [Anaerococcus lactolyticus ATCC 51172]
 gi|227235351|gb|EEI85366.1| pseudouridylate synthase [Anaerococcus lactolyticus ATCC 51172]
          Length = 297

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 68/324 (20%), Positives = 140/324 (43%), Gaps = 37/324 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++ +D   +R+D++  +    I    ++  +++  ++V+ K++K + ++Q G  + I  
Sbjct: 2   ILIADDL--IRVDKYISDELDSIPREKIKDFIKASLIKVNDKKIKPSFKLQMGDEIFIDD 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
            +  +  I  E   LD               ++YE++   + NK   + V     I    
Sbjct: 60  SLFEVQEIKAEDIPLD---------------IVYENNDYAIINKQKNLIVHPAGAIVTGT 104

Query: 128 HIDGFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            ++  L  +            +P + HRLD++T+G++V+A+   + ++L   F  R+++K
Sbjct: 105 LVNALLYKYGYDGLSHIGGDDRPGIVHRLDKDTTGLMVIAKNNESYRYLKTLFETRQVRK 164

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V+G    K   I N++ +  H                  AIS ++V+      F 
Sbjct: 165 EYLAIVFGNFDEKCGRIENFMDRDPHNRRKMAVR-----PSGRRAISEYEVL-SETDGFS 218

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
            +++   TGRTHQ+RVH   +  P++GD  Y     K N   P+      H  ++     
Sbjct: 219 LVKVHIITGRTHQIRVHMTSINHPLLGDPVYGNFKHKFNLDHPLL-----HCAHLSFEDK 273

Query: 301 EGGRLQITAPLPAHMVKTWDSLGF 324
           +G  +     +P    K  + LG 
Sbjct: 274 DGNEMVFDKEVPEEFEKYKNILGL 297


>gi|293365515|ref|ZP_06612224.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           oralis ATCC 35037]
 gi|307703473|ref|ZP_07640415.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
 gi|291315883|gb|EFE56327.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           oralis ATCC 35037]
 gi|307622880|gb|EFO01875.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
          Length = 298

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 76/305 (24%), Positives = 134/305 (43%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L KI  R G + V+ +       +  G  V I          I  ++
Sbjct: 16  FLKKH--EVSKGLLAKIKFRGGAILVNGQAQNATYLLDIGDRVTID---------IPAEE 64

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
             +S   + +  D     +LYED    V NKP G++       +  I  F+K +    + 
Sbjct: 65  GFESLEAINRPLD-----ILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQEY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G      +  I
Sbjct: 120 ENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQRKSIEKRYFALVKGAGVLEPEGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  KG  YA + +KV+  +      ++++ HTGRTHQ+RVH
Sbjct: 180 IAPIARDVD-----SIITRRVAKGGKYAHTSYKVVASYGNIH-LVDIRLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
             H+G P++GD  Y  +           +  LH  Y+   HP   + LQ+ +PLP     
Sbjct: 234 FSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHYLSFYHPFLEQDLQLESPLPDDFSN 288

Query: 318 TWDSL 322
               L
Sbjct: 289 LITQL 293


>gi|257784642|ref|YP_003179859.1| pseudouridine synthase, RluA family [Atopobium parvulum DSM 20469]
 gi|257473149|gb|ACV51268.1| pseudouridine synthase, RluA family [Atopobium parvulum DSM 20469]
          Length = 336

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 140/333 (42%), Gaps = 38/333 (11%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQ 63
             +  ++V  + +++RLD +        +     K++  G+V ++       + ++  G 
Sbjct: 3   ERIVEILVGPEGDSVRLDAFLSAQDMLPSRSACVKLVEEGRVTINATLATSKSEKLMLGD 62

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                 +S   L + +  +   + +ED  + V +K  G+      
Sbjct: 63  RLLVSL------------PNAESQTGLLRPNPDIPLDIRFEDQYLIVLSKQIGLVCHPSP 110

Query: 124 GIAYHIDGFLKSWVDSKG-----------QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           G   H+D  L + + +              +P + HRLD +TSG+++  ++  A + L +
Sbjct: 111 G---HVDDTLANALVAHCGYEHLGMLQGEDRPGIVHRLDMDTSGLMLAVKSDEAQKALQD 167

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
             R+R + + Y  LV G   +    I   + + +    D + +   +  GA  AI+ F+ 
Sbjct: 168 LIRLRVLDRRYIVLVHGYVAHDSGTIETGIARST---RDRLKMTVSDAPGAREAITTFRT 224

Query: 233 IDCF-----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           ++ F        +  LE   +TGRTHQ+RVH  H+G P+VGD  Y    K    +   N+
Sbjct: 225 LERFEAGRKGDGYSLLECHLYTGRTHQIRVHMRHIGHPVVGDQLYGK--KDTSLNLGLNR 282

Query: 288 LYLHARYMDLPHPEGGRLQITAP-LPAHMVKTW 319
            +LH+  +   HP  G   I A  LP  + +  
Sbjct: 283 QFLHSWRVQFEHPFTGENIIVADTLPKDLQEAL 315


>gi|159038967|ref|YP_001538220.1| RluA family pseudouridine synthase [Salinispora arenicola CNS-205]
 gi|157917802|gb|ABV99229.1| pseudouridine synthase, RluA family [Salinispora arenicola CNS-205]
          Length = 314

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 133/323 (41%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  + MRLD+     +  ++  +   ++  G   VD      + ++++G  + +
Sbjct: 12  RSLPVPDGLDGMRLDQAVARLF-GLSRTSAAALVDEGAALVDGTVRVNSYKVRAGAWLEV 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                A                           ++Y D  I V NKP G++     G   
Sbjct: 71  TLPAPAAPPA-------------VVPQAVSGLRVVYADDDIVVVNKPVGVAAHPSPGWSG 117

Query: 127 YHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  + HRLD  T+GI+VVA++  A   L  +F+ R ++K
Sbjct: 118 PTVIGGLAAIGHRIATSGAAERQGVVHRLDVGTTGIMVVAKSEQAYTGLKRAFKYREVEK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G     +  +   + +  H    +  V      G   +I+H+  ++ F     
Sbjct: 178 RYHAVVQGHLDPLRGTVDAPIDRHPHHDYRWAVVS-----GGKPSITHYDTLEAFP-AAS 231

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++  TGRTHQ+RVH   +  P VGD  Y A+     +    ++ +LHAR +   HP 
Sbjct: 232 LVDVRLETGRTHQIRVHFSTLRHPCVGDLTYGADPTL-ASRLGLDRQWLHARELAFRHPR 290

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G  ++  +  P  + +    L 
Sbjct: 291 TGDEVRFVSSYPDDLDRALAILR 313


>gi|254361951|ref|ZP_04978082.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|153093498|gb|EDN74478.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
          Length = 266

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 66/280 (23%), Positives = 120/280 (42%), Gaps = 28/280 (10%)

Query: 4   MTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           MT  + +   +  D    RLD+     +P  +   ++  + S  V+V+   V K   ++ 
Sbjct: 1   MTQQKILTAEITADLLGARLDQALAQLFPDYSRSRIKVWIESDLVKVNGNIVNKAREKVF 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ V I   I                         +   ++YED  I V NKP  + V 
Sbjct: 61  GGETVEITAEIEEEIRF---------------EPQDIPLNIVYEDDDIIVINKPKDLVVH 105

Query: 121 GGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+G     +   L  +     + PR  + HRLD++T+G++VVA+   A  HL  + + R
Sbjct: 106 PGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRLDKDTTGLMVVAKNIPAQTHLVTALQKR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           RI + Y ++  GI   +   +   + +                     A++H+++++ F 
Sbjct: 166 RITREYEAIASGIM-TQGGKVDEPMARHPT-----KRTAMAVHPMGKPAVTHYRIMERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           + +  L ++  TGRTHQ+RVH  H+  P++GD  Y    +
Sbjct: 219 RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGDQLYGGRPR 258


>gi|288553393|ref|YP_003425328.1| hypothetical protein BpOF4_01845 [Bacillus pseudofirmus OF4]
 gi|288544553|gb|ADC48436.1| hypothetical protein BpOF4_01845 [Bacillus pseudofirmus OF4]
          Length = 322

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 143/313 (45%), Gaps = 36/313 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E + L  + ++    I+  +L  I  + G++ V++K V     I SG  V +        
Sbjct: 37  EGILLRTFLRDVI-GISKKSLADIKFKGGKILVNQKEVTVRTTIFSGDRVEVY------- 88

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHID 130
                  +     N +   + +   + YED  + V NKP G+            +A  + 
Sbjct: 89  -------VPPEPKNESLRPECIPLDIHYEDDHLLVINKPQGMPTIPSREHPSRTLANAVM 141

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G+ +S            +RLD++TSG+LVVA+   A   L++  R  ++++ Y +L  G 
Sbjct: 142 GYYES--HHIPFTFHAVNRLDRDTSGLLVVAKHGLAHDQLSKGQRAGKLKRYYLALAEGF 199

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            + ++  I   + ++     + +            AI+H+KVI+   Q +  +E+   TG
Sbjct: 200 VQPREGTIHAPIKRRPSSIIERMVAA-----DGQEAITHYKVIN-DNQAYSEVEINLETG 253

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  H+G P++GD  Y  + +      +  +  LH + ++L HP  G+ L  +A
Sbjct: 254 RTHQIRVHFAHLGHPLLGDDLYGGSIE------LLARQALHCQRVELIHPFTGKHLHFSA 307

Query: 310 PLPAHMVKTWDSL 322
           PLP  +++  D L
Sbjct: 308 PLPKDLIEVKDKL 320


>gi|260906535|ref|ZP_05914857.1| ribosomal large subunit pseudouridine synthase D [Brevibacterium
           linens BL2]
          Length = 307

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 69/324 (21%), Positives = 138/324 (42%), Gaps = 30/324 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + ++V    E  R+D         ++      I   G V++  + V  ++R+ +G+ + I
Sbjct: 4   RSILVPEGLEGQRVDSALSKLL-GLSRTAAADICAEGGVQLSGQVVAKSDRVSAGERLDI 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGI- 125
                         ++ +    L    D +  + +++++    V +KP G++     G  
Sbjct: 63  --------------EMPEPPRPLEVVPDPVPGMKVVHDEDSFVVVDKPVGVAAHPALGWK 108

Query: 126 AYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + G L +           ++  +  RLD  TSG++V+A++  A   L  +F+ R ++
Sbjct: 109 GRTVVGGLAAAGFRIATSGAPERQGIVQRLDVGTSGLMVIAKSEYAYSVLKRAFKERTVE 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++V G+P      I   + +     G Y         G   AI+H++V++   ++ 
Sbjct: 169 KTYHAVVQGLPDPVLGTIDAPIARNPRHDGLYAV-----HSGGKNAITHYEVLEAH-RRA 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E+   TGRTHQ+RVH   +  P VGD  Y A+        ++ + +LHA  +   HP
Sbjct: 223 SLVEVHLETGRTHQIRVHFSALKRPCVGDLPYGADPTLAKDLHLE-RQWLHAVKLGFHHP 281

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
           E    ++  +  P  +    D + 
Sbjct: 282 ESNEWVEFESGYPEDLQYAIDRIR 305


>gi|302335822|ref|YP_003801029.1| pseudouridine synthase, RluA family [Olsenella uli DSM 7084]
 gi|301319662|gb|ADK68149.1| pseudouridine synthase, RluA family [Olsenella uli DSM 7084]
          Length = 342

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 73/346 (21%), Positives = 140/346 (40%), Gaps = 39/346 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPV 70
           V  D + MRLD +        +     +++  G V ++       +  +  G  ++    
Sbjct: 10  VGPDADGMRLDAFLATVDGCPSRSACARLIGEGAVTINSTPATSKSECVCLGDRIQACV- 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                       +          +  ++  + +ED  + V +K AG+      G   H+D
Sbjct: 69  -----------PVAQGGPGALSPNPDIELDVRFEDEHLLVLSKQAGLVCHPSPG---HVD 114

Query: 131 GFLKSWV-----------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             L + +                +P + HRLD +TSG++V A++    + L +  R+R +
Sbjct: 115 DTLANALVAHCGYGHLGMLQGDDRPGIVHRLDMDTSGLMVAAKSDEVQRALQDLIRLRAL 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-- 237
            + Y  LV G        +   + + +    D + +   ++  A  AI+ F  ++ F   
Sbjct: 175 DRRYVVLVQGYVAPDAGTVTTGIARST---RDRLRMAVSDDPMAREAITTFATLERFEAS 231

Query: 238 ---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              + +  LE   +TGRTHQ+RVH  H+G  +VGD  Y     G+  +    + +LH+ +
Sbjct: 232 RSDEGYSLLECHLYTGRTHQIRVHMRHIGHQVVGDQLYG--RGGDRQNRGLRRQFLHSWH 289

Query: 295 MDLPHPEGG-RLQITAPLPAHMVKTWDSL-GFKYDRNLYIKRLYSQ 338
           +   HP  G  ++    LP  ++   +SL G    R    +R+  Q
Sbjct: 290 IRFDHPVTGATIERADALPDDLLGILESLKGSSMGRTEAGERICPQ 335


>gi|229090249|ref|ZP_04221495.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-42]
 gi|228693095|gb|EEL46810.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-42]
          Length = 292

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 67/318 (21%), Positives = 135/318 (42%), Gaps = 39/318 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI   
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPSGSV 108

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 109 A---NALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VI+  A     + 
Sbjct: 166 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVINS-ANHKTHVS 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 220 LELDTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 273

Query: 304 RLQITAPLPAHMVKTWDS 321
            +  TA +P+ M +    
Sbjct: 274 EMSFTAMIPSDMQEVLRQ 291


>gi|307719385|ref|YP_003874917.1| ribosomal large subunit pseudouridine synthase D [Spirochaeta
           thermophila DSM 6192]
 gi|306533110|gb|ADN02644.1| ribosomal large subunit pseudouridine synthase D [Spirochaeta
           thermophila DSM 6192]
          Length = 319

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 138/332 (41%), Gaps = 39/332 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V    + +RLD+        I    +++ +    + +D +  K + R+ +G  +    + 
Sbjct: 11  VPPHLDGLRLDQALAELL-GITRSQVKQRIAD--LALDGRPAKPSQRVHAGARIAGTLLP 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY---- 127
            A   +  E                +   +LYED    V +KP G+ V  G+G       
Sbjct: 68  EAPPDLTPEP---------------VPFTILYEDPHCLVIDKPQGLVVHPGAGNPTGTLV 112

Query: 128 ----HIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               H    L +        D +  +  + HRLD++TSG+LVVA+  A    L   F+ +
Sbjct: 113 HGLLHYSHELAARATSEELDDEERMRIGIVHRLDKDTSGVLVVAKDPATHHFLAAQFKEK 172

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +K+Y +++ G P  ++  I   L +       +  +   +     Y+ + ++++  F 
Sbjct: 173 ETKKLYLAVLKGTPPAREGDIEGHLARHPVHRKKFTLLSTPDR--GKYSHTRYRLLAAFG 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
               ++ + P TGRTHQLRVH   +GCPI+GD  Y A     F       L LHA  + +
Sbjct: 231 -THSFVALYPTTGRTHQLRVHTAALGCPILGDPLY-ARPDTRFPDAT---LMLHAYLLTI 285

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
             P  G L   APLP    +   +L    D +
Sbjct: 286 RIPGRGLLTFRAPLPRRFKQILRALARASDGD 317


>gi|317154635|ref|YP_004122683.1| RluA family pseudouridine synthase [Desulfovibrio aespoeensis
           Aspo-2]
 gi|316944886|gb|ADU63937.1| pseudouridine synthase, RluA family [Desulfovibrio aespoeensis
           Aspo-2]
          Length = 305

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 91/307 (29%), Positives = 140/307 (45%), Gaps = 27/307 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M   Q+V V   E   +L ++ +      +    +Q+ +R GQVRVDK R K  +RI++G
Sbjct: 1   MHSAQFVTVTPAESGQKLLQFLERRLDGAVPRTAIQRWIRKGQVRVDKGRSKPFDRIEAG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP                 +      +       +Y+D ++ V  KPAG++V GG
Sbjct: 61  QTVRIPPYEPG------------ETGGGKPAAPGGPLEFVYDDDRMLVIAKPAGLAVHGG 108

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            GI+  + G L +       KP L HRLD++TSG+L+ ART  A + L + F    I K+
Sbjct: 109 DGISDSVAGRLAAAFADADFKPTLAHRLDRDTSGLLLAARTYDALRDLNDRFAAGTIGKL 168

Query: 183 YWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V G  +      + + L K+   G + V  V+        A++    +    +K  
Sbjct: 169 YLTWVTGRWREPGTVLLEDQLEKRGAPGSEKVEPVRDGS--GKEALARVACLLA-GEKRS 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD----- 296
            L ++  TGRTHQ+RV     G P+ GD KY    +         +L+  A  +D     
Sbjct: 226 LLAVRLLTGRTHQIRVQLASRGHPVAGDGKYGPARQRTSL-----RLHCFALRLDGQTLT 280

Query: 297 LPHPEGG 303
           LP P  G
Sbjct: 281 LPPPWTG 287


>gi|222094929|ref|YP_002528989.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           Q1]
 gi|221238987|gb|ACM11697.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           Q1]
          Length = 297

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 68/314 (21%), Positives = 136/314 (43%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 10  IDSAEEGTLVREFLKT--KGISKAALTDIKFHGGSIEVNGQHASVRHQLQAGEELRVFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHI 129
           +   +  +               ++ +   ++YED  + V NK A +S        A  +
Sbjct: 68  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPAGSV 113

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L S  D +       +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 114 ANALLSHYDKRHLTSTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    K+  I   + +KS    +         +    A++HF+VID    K   + ++ 
Sbjct: 174 HGEMVEKEGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDSVNHK-THVSLEL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  ++G P++GD+ Y              +  LH+  +   HP     + 
Sbjct: 228 DTGRTHQIRVHMAYIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEKEMS 281

Query: 307 ITAPLPAHMVKTWD 320
            T P+P+ M     
Sbjct: 282 FTTPIPSDMQAILR 295


>gi|228926342|ref|ZP_04089415.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pondicheriensis BGSC 4BA1]
 gi|228833334|gb|EEM78898.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pondicheriensis BGSC 4BA1]
          Length = 292

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 133/315 (42%), Gaps = 33/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQAGEEIRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + V NK A +S            
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPSGSV 108

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HF+VID  A     + ++ 
Sbjct: 169 HGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVSLEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP     + 
Sbjct: 223 DTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWDS 321
             A +P+ M +    
Sbjct: 277 FAAMIPSDMQEVLRQ 291


>gi|296126237|ref|YP_003633489.1| pseudouridine synthase, RluA family [Brachyspira murdochii DSM
           12563]
 gi|296018053|gb|ADG71290.1| pseudouridine synthase, RluA family [Brachyspira murdochii DSM
           12563]
          Length = 307

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 142/320 (44%), Gaps = 35/320 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +Y ++E  +   RLD +      +I+   ++  L S  V+V+    K +  ++    + +
Sbjct: 10  KYFIIEEADAKKRLDVFISEKL-NISRSQVKNYLNS--VKVNGIEKKLSYALKINDKIEV 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
               +     I+  K           ++ +   ++YED  + V NKPAG+SV   +    
Sbjct: 67  DIKNSDKEIDIENPK-----------AENISLDIIYEDKYLLVINKPAGMSVHCSASEIT 115

Query: 126 AYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L +  D        +  + HRLD++TSGI+++ +       + E F+ R+I+K
Sbjct: 116 GTLVNALLYNIKDFDFIGNKSRAGIIHRLDKDTSGIMIIGKNADIVSSIQEQFKNRKIKK 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKF 240
           IY ++V G+ K       N+L     IG   V+  K   +     A++H KV+  F +  
Sbjct: 176 IYHAIVIGVLK------DNYLEINLPIGRHQVYRKKMTVREDGKKALTHIKVLKRF-KNH 228

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E+   TGRTHQ+RVH+ +   P+ GD  Y        +S     L L A+ ++  HP
Sbjct: 229 TLIEIDLKTGRTHQIRVHSSYKNFPVAGDKIYSK------SSNKYKSLMLVAKKIEFTHP 282

Query: 301 EGGR-LQITAPLPAHMVKTW 319
                L+     P++  +  
Sbjct: 283 ITNEVLEFEIDYPSYFYEFL 302


>gi|84495993|ref|ZP_00994847.1| putative ribosomal large subunit pseudouridine synthase [Janibacter
           sp. HTCC2649]
 gi|84382761|gb|EAP98642.1| putative ribosomal large subunit pseudouridine synthase [Janibacter
           sp. HTCC2649]
          Length = 321

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 72/330 (21%), Positives = 142/330 (43%), Gaps = 26/330 (7%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+ M+  + ++V    +  R+D      +  ++      +   G V V+   V  ++R+ 
Sbjct: 1   MANMSDSRTMLVPEGLQGERVDAAISRLF-GLSRTRAADLAADGGVAVNGASVGKSHRVH 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G ++ +    N  +  ++        +++    D +  +           +KP G++  
Sbjct: 60  GGDLLELTLPSNDASPTLEVIAEPVPGMSIIHDDDDIVVV-----------DKPVGVAAH 108

Query: 121 GGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G     + G L +           ++  +  RLD  TSG++VV ++      L  +F
Sbjct: 109 PSVGWTGPTVLGGLAAAGYRISTSGASERQGIVSRLDVGTSGLMVVCKSERGYSVLKRAF 168

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R ++K Y +LV G+P      I   + +  H G DY   V ++     +A++H+++I+
Sbjct: 169 KERTVEKTYHTLVQGLPDPLVGTIDAPIAR--HPGHDYKFAVMES---GKHAVTHYELIE 223

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F +    L+++  TGRTHQ+RVH   +  P VGD  Y A+        ++ + +LHA  
Sbjct: 224 AF-RYASLLDIRLETGRTHQIRVHFSALRHPCVGDLTYGADPTLAKKLGLE-RQWLHAVG 281

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +   HP  G  +   +  PA +    D L 
Sbjct: 282 LGFEHPGSGEWVTFESQYPADLQAALDRLA 311


>gi|225861064|ref|YP_002742573.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298230857|ref|ZP_06964538.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae str. Canada MDR_19F]
 gi|298255783|ref|ZP_06979369.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae str. Canada MDR_19A]
 gi|298502886|ref|YP_003724826.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus pneumoniae
           TCH8431/19A]
 gi|225728340|gb|ACO24191.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298238481|gb|ADI69612.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus pneumoniae
           TCH8431/19A]
 gi|327389344|gb|EGE87689.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA04375]
          Length = 298

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 139/322 (43%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNNQPQNATYLLDVGDYV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +  L   +LYED    V NKP G++       
Sbjct: 57  TIDIPAEKGFETLE--------------AIELPLDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +      +   + ++  KG  YA + +K++  +     
Sbjct: 163 YFALVKGDGHLEPEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++ HTGRTHQ+RVH  H+G P++GD  Y  +           +  LH  Y+   HP 
Sbjct: 217 LVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHYLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LEQDLQLESPLPDDFSNLITQL 293


>gi|254382579|ref|ZP_04997937.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           Mg1]
 gi|194341482|gb|EDX22448.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           Mg1]
          Length = 313

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 75/334 (22%), Positives = 136/334 (40%), Gaps = 28/334 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAIARMF-GFSRTKAAELAAAGKVSVDGSVVGKSERVH 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +         +    + ++         + +          I V  KP G++  
Sbjct: 60  GGAWLEV--------EMPAPPRPVELVAEPVPGMEIVHDD-----DDIVVVMKPVGVAAH 106

Query: 121 GGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G     + G L +           ++  + HRLD  TSG++ VA++  A   L   F
Sbjct: 107 PSPGWTGTTVIGGLAAAGYRISTSGASERQGVVHRLDVGTSGLMAVAKSERAYTSLKNQF 166

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R + K Y +LV G P      I   + +  H   DY   V Q+      +++H+ +I+
Sbjct: 167 RERVVDKRYHALVQGHPDPMSGTIDAPIGR--HPNADYKWAVTQD---GKASVTHYDLIE 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F +    L+++  TGRTHQ+RVH      P VGD  Y A+           + +LHA  
Sbjct: 222 AF-RAASLLDIKLETGRTHQIRVHMSAHRHPCVGDLTYGADP-TVAKRLGLTRQWLHAVR 279

Query: 295 MDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
           +   HP +G  ++  +  PA +    D +  + +
Sbjct: 280 LGFEHPADGSWVEFESTYPADLQHALDVIRAESE 313


>gi|315613225|ref|ZP_07888135.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus sanguinis
           ATCC 49296]
 gi|315314787|gb|EFU62829.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus sanguinis
           ATCC 49296]
          Length = 298

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 137/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNGQPQNATYLLDIGDRV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +      +LYED    V NKP G++       
Sbjct: 57  TIDIPAEEGFESLE--------------AIDRPLDVLYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQEYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQRKSIEKR 162

Query: 183 YWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +          + ++  KG  YA + +KV+  +     
Sbjct: 163 YFALVKGAGVLEPEGEIIAPIARDVD-----SIITRRVAKGGKYAHTSYKVVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++ HTGRTHQ+RVH  H+G P++GD  Y  +           +  LH  Y+   HP 
Sbjct: 217 LVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHYLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LEQDLQLESPLPDDFSNLITQL 293


>gi|220912349|ref|YP_002487658.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
 gi|219859227|gb|ACL39569.1| pseudouridine synthase, RluA family [Arthrobacter chlorophenolicus
           A6]
          Length = 308

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 135/323 (41%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + ++V  +    R D         I+      ++  G V    K +  + ++ +G  + +
Sbjct: 3   EQIIVTEEYGGTRADAGLAAIM-GISRSAAAALIAEGHVISRGKALGKSAKLAAGDTLEV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                     + E+ +    + L      +               KP G++     G + 
Sbjct: 62  TIPERRDPLEVVEEIVEGLKILLDDDDFVVVD-------------KPVGVAAHPSPGWVG 108

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L             ++  + HRLD  TSG++VVA++  A   L  +F+ R + K
Sbjct: 109 PTVVGGLAGAGYRISTSGSPERAGIVHRLDVGTSGVMVVAKSERAYTALKRAFKERTVDK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++V G+P      I   + +  H G D+   V +       +++H++V++ F  K  
Sbjct: 169 VYHAVVQGLPDPLTGTIDAPIGR--HPGHDWRFAVTEE---GRPSVTHYEVLEAFG-KAS 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+   TGRTHQ+RVH   +  P  GD  Y A+ +   T  +  + +LHAR +   HP 
Sbjct: 223 LVEVHLETGRTHQIRVHFSALRHPCAGDLTYGADPRLAATLGL-TRQWLHARELGFDHPV 281

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G R+++T+  P  +    D L 
Sbjct: 282 TGERVRVTSDYPQDLAFALDVLA 304


>gi|10129882|dbj|BAB13516.1| pseudouridine synthase homolog [Sinorhizobium meliloti]
          Length = 264

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 74/262 (28%), Positives = 126/262 (48%), Gaps = 29/262 (11%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG----- 141
           +     + +   +LYED+ + V  KPAG+ V  G+G      ++  +    DS       
Sbjct: 1   DPEPKGEAIPLDVLYEDADLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGGV 60

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR----IQKIYWSLVWGIPKNKKEC 197
           ++P + HRLD++TSG++VVA+  AA +HL++ F        +++ Y ++VWG P+  K  
Sbjct: 61  KRPGIVHRLDKDTSGVMVVAKNDAAHRHLSDQFADHGRNGPLERAYRAVVWGRPRQLKGK 120

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGR 251
           I   L +          V +++   A  AI+H++V++ + +K         +E    TGR
Sbjct: 121 IDAPLGRAG--DRTKRAVKREDSDDAREAITHYEVVERYHEKPDGTSLASTVECHLETGR 178

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NKLYLHARYMDLPHPEG 302
           THQ+RVH  H+G P++GD  Y A F+       +          +  LHA  +   HP  
Sbjct: 179 THQIRVHMAHIGHPLIGDPDYGAAFRTKANLLPEPARAAVNRFPRQALHAFMLQFEHPAT 238

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  +    P+PA M +   +L 
Sbjct: 239 GETMHFETPVPADMQELIAALR 260


>gi|270292781|ref|ZP_06198992.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M143]
 gi|270278760|gb|EFA24606.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M143]
          Length = 298

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 138/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFITDEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNDRPQNATYLLDIGDRV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          +K              +      +LYED    V NKP GI+       
Sbjct: 57  TIDIPAEEGFESLK--------------AIDRPLDILYEDDHFLVLNKPYGIASIPSVNH 102

Query: 126 AYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +   +G   Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKRGYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQRKSIEKR 162

Query: 183 YWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +          + ++  KG  YA + +KV+  +     
Sbjct: 163 YFALVKGAGVLEPEGEIIAPIARDVD-----SIITRRVAKGGKYAHTSYKVVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++ HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH   +   HP 
Sbjct: 217 LVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLED-----GIQRQALHCHSLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
            GR L++ +PLP         L
Sbjct: 272 LGRQLELESPLPDDFNNLIIQL 293


>gi|324325321|gb|ADY20581.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus thuringiensis serovar finitimus YBT-020]
          Length = 297

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 65/317 (20%), Positives = 135/317 (42%), Gaps = 39/317 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 10  IDSAEEGTLVREFLKT--KGISKAALTDIKFHGGSIEVNGQHASVRHQLQAGEELRVFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 68  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPAGSV 113

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 114 A---NALLSHYDKRHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID    K   + 
Sbjct: 171 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDSVNHK-THVS 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  ++G P++GD+ Y              +  LH+  +   HP    
Sbjct: 225 LELDTGRTHQIRVHMAYIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 278

Query: 304 RLQITAPLPAHMVKTWD 320
            +  T P+P+ M     
Sbjct: 279 EMSFTTPIPSDMQAILR 295


>gi|315604414|ref|ZP_07879480.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 180 str. F0310]
 gi|315314120|gb|EFU62171.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 180 str. F0310]
          Length = 310

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 134/327 (40%), Gaps = 32/327 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + + V +     R+D         ++     ++  +G V ++      + R+ +  
Sbjct: 1   MSSSRMLPVPDALVGERVDAALARML-GLSRSRCAELCAAGLVLINAVSADKSARLGADD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ +          I E +         K +      +LY+D  I V +KP G++   G 
Sbjct: 60  IIEVT---------IPEPE--------NKPAPVTDMEILYDDDDIVVVDKPVGVAAHTGP 102

Query: 124 G------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      +        +       ++  + HRLD  TSG ++VA++  A   +  +F+ R
Sbjct: 103 GWEGPTVLGNLEAAGYRITSHGPPERQGIVHRLDVGTSGAMMVAKSELAYSVMKRAFKER 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           RI KIY ++V G        I   + +  H   ++   V     G   A++H+  ++  A
Sbjct: 163 RIDKIYHAVVAGHLDPPSGTIDAPIGR--HPSREWRMAVID---GGKRAVTHYDTLELMA 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                 E+   TGRTHQ+RVH   +G P VGD  Y A+        +  + +LHA  +  
Sbjct: 218 -GAQLTEVHLETGRTHQIRVHMAAVGHPCVGDTFYGADPTQAQRLGLA-RQWLHAVRLGF 275

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLG 323
            HP  G  + +++P P  +    + L 
Sbjct: 276 AHPRTGMPMTVSSPYPRDLRDALEQLR 302


>gi|330997883|ref|ZP_08321717.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
 gi|329569487|gb|EGG51257.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
          Length = 313

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 76/303 (25%), Positives = 129/303 (42%), Gaps = 34/303 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIK 79
           LD +       I+    + IL    + V+KK V ++N  ++ G VVR+            
Sbjct: 26  LD-FIMESMNGISRNKAKDILTGHGITVNKKSVSQYNYELRPGMVVRV------------ 72

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                 S              ++YED  + V  K AGI         + I   L  +   
Sbjct: 73  ------SKHKRNNELKNKYVKIVYEDKDLIVIEKSAGILSMPAVAQQFSIKTVLDEYFTR 126

Query: 140 KGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +  K    + HRLD++TSG+++ A+     + L E ++     + Y ++V G  + +   
Sbjct: 127 RHFKCTAHVVHRLDRDTSGLMMYAKNIEVQRILEEHWQEIVTDRRYVAIVSGKMEKEGGT 186

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I++WL         YV      + G  YA++HF  +D   +++  +E++  TGR +Q+RV
Sbjct: 187 ISSWL----KDNKAYVTYSSPTDNGGKYAVTHFHTLDAR-ERYSLVELKLETGRKNQIRV 241

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +G P+VGD KY         S    +L LHA  ++  HP  G  ++   P P    
Sbjct: 242 HMQDIGHPVVGDSKYGNG------SDPIGRLGLHAYRLNFYHPITGEPMEFETPFPTLFT 295

Query: 317 KTW 319
           K +
Sbjct: 296 KLF 298


>gi|330723209|gb|AEC45579.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyorhinis MCLD]
          Length = 294

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 75/312 (24%), Positives = 138/312 (44%), Gaps = 40/312 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINAL 74
           +E  RLD + +     ++ V +Q+I+ + QV VD + V K N  ++ G  + +       
Sbjct: 6   DEQTRLDIFLRKKL-ELSRVFVQEIIANNQVWVDNQIVNKKNFILKQGSQIEVHYQEKEQ 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           N I K Q I              +  +++ED  + V +KP  + V    G   + +  + 
Sbjct: 65  NIIAKAQDI--------------ELKIVFEDENVIVVDKPTNMVVHPAPG--NYENTLVN 108

Query: 135 SWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + V    Q        +P + HRLD++TSG+++VA+       L +  + R+I++ Y+++
Sbjct: 109 ALVYKFAQLSNVNGSLRPGIVHRLDKDTSGLMLVAKNDKMHNFLAQQLKERKIKRKYYAI 168

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWL 243
           + G  +N+   I   + +        + V   N   +  AI+H  V   F  K   F ++
Sbjct: 169 IEGQLENQISHINLPIARDEK-NRKKMSVSHFN---SKEAITHVFVEKYFHYKKKVFSFV 224

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +  TGRTHQ+RVH  ++  P+ GD  Y              +L  HA  ++  + +G 
Sbjct: 225 RCELETGRTHQIRVHLAYIKHPVYGDPVYGKKVDD-----FNQRL--HAYEIEFINIDGK 277

Query: 304 RLQITAPLPAHM 315
            L+  + LP   
Sbjct: 278 TLKFNSKLPKEF 289


>gi|254775679|ref|ZP_05217195.1| hypothetical protein MaviaA2_13575 [Mycobacterium avium subsp.
           avium ATCC 25291]
          Length = 303

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 133/319 (41%), Gaps = 28/319 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V      MR+D         ++      +   G V +D      ++R+  G  + +    
Sbjct: 3   VPEGLAGMRVDAGLARLL-GLSRSAAAALAEDGGVELDGVPAGKSDRLTGGAWLHVR--- 58

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
                 + E      +  +    D     +LY D  I   +KPA ++     G     + 
Sbjct: 59  ------LPEAPAPPQNTPV----DIEGMTILYSDDDIVAVDKPAAVAAHASVGWTGPTVL 108

Query: 131 GFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R + K Y +
Sbjct: 109 GGLAAAGYRITTSGVPERQGIVHRLDVGTSGVMVVALSERAYTLLKRAFKQRTVDKRYHA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G P      I   + +  H GG++   V    K   ++++H+  ++ F      L++
Sbjct: 169 LVQGHPDPSSGTIDAPIGR--HRGGEWKFAVT---KDGRHSLTHYDTVEAFV-AASLLDV 222

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
              TGRTHQ+RVH   +  P  GD  Y A+ K      +Q + +LHAR +   HP +G R
Sbjct: 223 HLETGRTHQIRVHFSALHHPCCGDLVYGADPKLAKKLGLQ-RQWLHARSLSFAHPADGRR 281

Query: 305 LQITAPLPAHMVKTWDSLG 323
           ++I +P P  +    D L 
Sbjct: 282 MEIVSPYPPDLQHALDVLR 300


>gi|319949599|ref|ZP_08023642.1| pseudouridine synthase, RluA family protein [Dietzia cinnamea P4]
 gi|319436736|gb|EFV91813.1| pseudouridine synthase, RluA family protein [Dietzia cinnamea P4]
          Length = 308

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 75/327 (22%), Positives = 135/327 (41%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++   V +  + MR+D         I+   +  +   G+V +D + V  ++++    
Sbjct: 1   MGELRTFPVPDGLDGMRVDAGVSRLL-GISRTAVADLAGEGKVLLDGRTVGKSDKLTGMS 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +      +     E  ++   V            ++Y D+ I V +KP G++     
Sbjct: 60  WIEV-----EMPEPRAEPAVVAEPV--------AGMAVVYSDADIVVVDKPVGVAAHASV 106

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +FR R
Sbjct: 107 GWTGPTVIGGLAAAGYRISTSGPPERKGIVHRLDVGTSGLMVVAASERAYTLLKRAFRDR 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G P      I   + +  H   D+   V  +      +I+H+  ++   
Sbjct: 167 TVDKTYHALVQGHPDPLSGTIDAPIGR--HTSNDWRFAVISD---GKPSITHYDTLEAH- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q    +E++  TGRTHQ+RVH   +  P  GD  Y A+        ++ + +LHA  +  
Sbjct: 221 QAATLVEVKLETGRTHQIRVHFSALHHPCAGDLTYGADPVLARRLGLE-RQWLHAVGLGF 279

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLG 323
            HP  G R+   +  P  +    D L 
Sbjct: 280 EHPGTGARVDFESRYPDDLQHAIDVLR 306


>gi|229137994|ref|ZP_04266592.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST26]
 gi|229195503|ref|ZP_04322271.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           m1293]
 gi|228588043|gb|EEK46093.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           m1293]
 gi|228645339|gb|EEL01573.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST26]
          Length = 292

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 67/314 (21%), Positives = 136/314 (43%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 5   IDSAEEGTLVREFLKT--KGISKAALTDIKFHGGSIEVNGQHASVRHQLQAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHI 129
           +   +  +               ++ +   ++YED  + V NK A +S        A  +
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPAGSV 108

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L S  D +       +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKRHLTSTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HF+VID    K   + ++ 
Sbjct: 169 HGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDSVNHK-THVSLEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  ++G P++GD+ Y              +  LH+  +   HP     + 
Sbjct: 223 DTGRTHQIRVHMAYIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWD 320
            T P+P+ M     
Sbjct: 277 FTTPIPSDMQAVLR 290


>gi|121534815|ref|ZP_01666635.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
 gi|121306610|gb|EAX47532.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
          Length = 301

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 76/305 (24%), Positives = 133/305 (43%), Gaps = 37/305 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K+    I+   L+KI R GQV ++   VK F   + SG  + I    ++    +K   
Sbjct: 18  FLKSA--GISLTQLRKIKRQGQVLINGHPVKSFQTPVSSGDEISIDYGDDSCLTPMK--- 72

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKG 141
                         +   ++YED  + + NKPAG+ V   S          +  ++ SKG
Sbjct: 73  --------------MPLHIVYEDDFLLIVNKPAGLLVHPTSDPTEPTLAHGILYYLHSKG 118

Query: 142 Q--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                   HRLD+ TSG++ +A+       L+     + ++++Y ++V GIP +    I 
Sbjct: 119 ALGAFHPIHRLDRNTSGLVAIAKHPHIQHALS-GGGAKGLKRLYLAVVTGIPSSLMGRID 177

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + +  +     V            AI+ ++V+  F+     +E++  TGRTHQ+RVH 
Sbjct: 178 APIGRHPNSIIKRVVRS-----DGQPAITLYRVLSTFS-MASLVELELLTGRTHQIRVHL 231

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
            H+G P++GD  Y         + +  +  LHA  +   HP   + L +T+PLP  +   
Sbjct: 232 SHIGHPLLGDDLYGG------ATDLIRRQALHAASLSFRHPATDKVLTLTSPLPPDLADL 285

Query: 319 WDSLG 323
              L 
Sbjct: 286 IQLLR 290


>gi|325109066|ref|YP_004270134.1| pseudouridine synthase [Planctomyces brasiliensis DSM 5305]
 gi|324969334|gb|ADY60112.1| pseudouridine synthase, RluA family [Planctomyces brasiliensis DSM
           5305]
          Length = 410

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 70/334 (20%), Positives = 137/334 (41%), Gaps = 41/334 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + VE  +  +R D +      + +   +Q++   G + +  + V    R+  G  +++ 
Sbjct: 78  ELTVEPYQSGLRTDAFLVQQLRNYSLWKIQRLAHWGAITIRHQPVDLMKRLYPGDTIQVR 137

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAY 127
                          L          +     + YED+ +   NKP G+     G+  + 
Sbjct: 138 ---------------LVEPPETVYEPEPFPLEIEYEDAWMLAVNKPPGVIAHPTGNMQSG 182

Query: 128 HIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +  +L++  D++       KP + HRLD+ETSG++++A+T  A ++  ++F   R+ K 
Sbjct: 183 TLCNYLQAHFDTQSGIPGLLKPGIVHRLDRETSGVMLIAKTHRAHRNFVDAFEHSRVSKT 242

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L+ G    ++  I   + + + +    +   + + K    A +H++V+         
Sbjct: 243 YVALLEGDVAKEEGTIDLPIGQ-ATVDSKVLMSARGDAKNPKPAKTHWRVLKRLGS-HTL 300

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-----------------GNFTSPIQ 285
           +  +P TGR HQ+RVH   +G P+ GD  Y  + +                         
Sbjct: 301 VAAKPVTGRNHQIRVHFATIGHPLAGDEFYDRDGQFKAATRDSLEEGRRMTDTRCARTGL 360

Query: 286 NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
            +  LHA  +   HP  G  + I A LPA M+  
Sbjct: 361 TRHALHASTIQTAHPITGVWMTIQAGLPADMLAA 394


>gi|300780856|ref|ZP_07090710.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           genitalium ATCC 33030]
 gi|300532563|gb|EFK53624.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           genitalium ATCC 33030]
          Length = 307

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 70/327 (21%), Positives = 141/327 (43%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + +VV    ++MR+D      +  ++     +++ +G+V +D  RV  ++R+ +G 
Sbjct: 1   MSRYRSLVVPEGLDSMRVDAAVAKAF-GLSRTVAAELIEAGEVLIDGSRVTKSDRVSTGH 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +         + KE+ +   +V        +                P G++     
Sbjct: 60  SLEVTLPEPKQAPMPKEEIVEGLTVLYDDDDVIVVDK-------------PVGVAAHPTL 106

Query: 124 G-IAYHIDGFLKSWV-----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L++           ++  +  RLD  TSG++VVA +      L  +F+ R
Sbjct: 107 GWDGPTVVGGLQAMGYQLPDAGPPERKGIVQRLDVGTSGVMVVANSIPGYSVLKRAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y ++V G+P      I   + +    G  +            ++++H++V++ F 
Sbjct: 167 TVEKTYHAVVQGLPDPIVGTIDAPIGRHPSSGWKFAVTA-----DGRHSVTHYEVLEAF- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++   LE+   TGRTHQ+RVH   +G P VGD  Y ++        +  + +LHA  +  
Sbjct: 221 REASLLEVHLETGRTHQIRVHMSSVGHPCVGDPMYGSDPNLGKRLGLI-RQWLHATALGF 279

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDSLG 323
            HP  G  +++ +P P  +    D L 
Sbjct: 280 VHPGTGVWMEVESPYPPDLQHAVDVLR 306


>gi|154249509|ref|YP_001410334.1| RluA family pseudouridine synthase [Fervidobacterium nodosum
           Rt17-B1]
 gi|154153445|gb|ABS60677.1| pseudouridine synthase, RluA family [Fervidobacterium nodosum
           Rt17-B1]
          Length = 317

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 90/330 (27%), Positives = 154/330 (46%), Gaps = 31/330 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQ 63
           + V+   V       R+D++ +    ++    + K LR+G+V+++ K+VK  + ++  G 
Sbjct: 14  SNVKVWTVNESNYFSRVDKFLRKMLKNVPLSAIYKFLRTGKVKINGKKVKDPSTKLNIGD 73

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +  +  +L++  +E         L      +   ++YED  I   NKPAG+SV  G 
Sbjct: 74  VIEL--IEESLDNYSREY--------LELKPVKMDLDIIYEDELIIAINKPAGVSVHPGK 123

Query: 124 GI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +    I   L  +    G +P L HRLD+ETSG+L+VA+ R+ A+ L+E    R ++KI
Sbjct: 124 NVNKPSIIEGLIHYGKENGFEPFLVHRLDKETSGVLIVAKDRSVARELSEIISSRNVEKI 183

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFC 241
           Y +LV+G    +K  I   +      G D V  +          I +F+V ++  + +  
Sbjct: 184 YNALVFGKV--QKVTINTPI-----DGQDAVSHIIP--------IEYFRVKLNGISVELS 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--PIQNKLYLHARYMDLPH 299
           +LE++  TGR HQ+R H   + CPIVGD  Y         S      + +LH + M    
Sbjct: 229 FLEVEIETGRKHQIRKHLSSINCPIVGDKDYGNFRLNREFSKNFGLKRHFLHCKQMKFVF 288

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
             G    I A LP  +      L  +  ++
Sbjct: 289 -NGRNYNILAQLPKDLTTVIKYLNAESGKD 317


>gi|304373162|ref|YP_003856371.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyorhinis HUB-1]
 gi|304309353|gb|ADM21833.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyorhinis HUB-1]
          Length = 297

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 72/324 (22%), Positives = 142/324 (43%), Gaps = 44/324 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           M  ++ +     +E  RLD + +     ++ V +Q+I+ + QV VD + V K N  ++ G
Sbjct: 1   MKKMKLI----ADEQTRLDIFLRKKL-ELSRVFVQEIIANNQVWVDNQIVNKKNFILKQG 55

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +                 +   N+   +  ++  +++ED  + V +KP  + V   
Sbjct: 56  SQIEVHYQ--------------EKEQNINAKAQDIELKIVFEDENVIVVDKPTNMVVHPA 101

Query: 123 SGIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            G   + +  + + V    Q        +P + HRLD++TSG+++VA+       L +  
Sbjct: 102 PG--NYENTLVNALVYKFAQLSNVNGSLRPGIVHRLDKDTSGLMLVAKNDKMHNFLAQQL 159

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R+I++ Y++++ G  +N+   I   + +        + V   N   +  AI+H  V  
Sbjct: 160 KERKIKRKYYAIIEGQLENQISHINLPIARDEK-NRKKMSVSHFN---SKEAITHIFVEK 215

Query: 235 CFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
            F  K   F ++  +  TGRTHQ+RVH  ++  P+ GD  Y              +L  H
Sbjct: 216 YFHYKKKVFSFVRCELETGRTHQIRVHLAYIKHPVYGDPVYGKKVDD-----FNQRL--H 268

Query: 292 ARYMDLPHPEGGRLQITAPLPAHM 315
           A  ++  + +G  L+  + LP   
Sbjct: 269 AYEIEFINIDGKTLKFNSKLPKEF 292


>gi|227813199|ref|YP_002813208.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|227006370|gb|ACP16113.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
          Length = 239

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 113/247 (45%), Gaps = 18/247 (7%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKSWVDSKG 141
           +     L    + +   + YED+ + V NKP G+ V    G      ++G +    D  G
Sbjct: 3   IPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSG 62

Query: 142 ----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +P + HR+D++TSG+L+VA+   A + L      + + + Y ++V G+  + K  
Sbjct: 63  INGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGT 122

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +               ++   +A++HF+V++ F + F  +E +  TGRTHQ+RV
Sbjct: 123 IDAPIARD-----KKERQSMTVDENGKHAVTHFQVLERF-KDFTLVECRLETGRTHQIRV 176

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H  ++G P+ GD KY      +      N   LHA  +   HP  G  +Q  AP+P    
Sbjct: 177 HMKYIGYPLAGDPKYGPKKTLDM-----NGQALHAGILGFDHPRTGEYIQFEAPIPEVFE 231

Query: 317 KTWDSLG 323
              + L 
Sbjct: 232 DALNILR 238


>gi|163939103|ref|YP_001643987.1| RluA family pseudouridine synthase [Bacillus weihenstephanensis
           KBAB4]
 gi|163861300|gb|ABY42359.1| pseudouridine synthase, RluA family [Bacillus weihenstephanensis
           KBAB4]
          Length = 297

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 64/312 (20%), Positives = 133/312 (42%), Gaps = 39/312 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           EE   +  + K     I+   L  I  R G + V+ +     +++Q+G+ ++I   +   
Sbjct: 14  EEGTLVREFLKT--KGISKAALTDIKFRGGAIEVNGQHTSVRHKLQAGEELQIFFPVEER 71

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHI 129
           +  ++ + I                 ++YED  + V NK A +S           IA   
Sbjct: 72  SEGMEVEDI--------------PLCIVYEDDAVLVINKEANMSTIPSREHPSGSIA--- 114

Query: 130 DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L  +   +      +  RLD++TSG++++A+ R     L++  + + +++ Y ++V 
Sbjct: 115 NALLYHYDKQNLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKGVKRTYEAIVH 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G    +   I   + +K+    +         +    A++HF+V++  + K   + ++  
Sbjct: 175 GTILEEVGTIDAPIGRKADSIIERTVC-----EDGQRAVTHFRVMESSSDK-THVALELE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  ++G P++GD  Y           +  +  LH+  +   HP   + +  
Sbjct: 229 TGRTHQIRVHMAYIGHPLLGDDLYGGRRD------VIKRQALHSTSLTFYHPILEKGMTF 282

Query: 308 TAPLPAHMVKTW 319
           T  +P  M    
Sbjct: 283 TVSIPEDMQYAL 294


>gi|322375304|ref|ZP_08049817.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C300]
 gi|321279567|gb|EFX56607.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C300]
          Length = 298

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 138/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNDQPQNATYLLDIGDRV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +      +L+ED    V NKP G++       
Sbjct: 57  TIDIPAEEGFETLE--------------AIDRPLDILFEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQEYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQRKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +  +       + ++  KG  YA + +KV+  +     
Sbjct: 163 YFALVKGNGDLEPEGEIIAPIARDVN-----SIITRRVAKGGKYAHTSYKVVASYGDIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++ HTGRTHQ+RVH  H+G P++GD  Y  +           +  LH  ++   HP 
Sbjct: 217 LIDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHFLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             R L++ +PLP         L
Sbjct: 272 LERQLELESPLPDDFNNLITQL 293


>gi|297624276|ref|YP_003705710.1| pseudouridine synthase [Truepera radiovictrix DSM 17093]
 gi|297165456|gb|ADI15167.1| pseudouridine synthase, RluA family [Truepera radiovictrix DSM
           17093]
          Length = 312

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 80/331 (24%), Positives = 144/331 (43%), Gaps = 41/331 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           V V       RLD         ++    + ++  G V++D + V K + ++   ++V + 
Sbjct: 3   VRVFEAPAGERLDVAIAVAL-ELSRTYAKDLVLGGYVQLDGQPVAKASTKLSGRELVSV- 60

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                         +L     L    +     ++YED  +   +KP G++    + +   
Sbjct: 61  --------------VLPPPRPLRVEPENTPLDIIYEDDDLAAIDKPPGMTAHPTATVREG 106

Query: 129 I--DGFLKSW---------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
              +  L             + +  +P + HRLD+ETSG++VVA+  AA + L  +F+ R
Sbjct: 107 TVVNALLGRMALAKEKLFDPEDEDYRPGIVHRLDKETSGVMVVAKNDAAHRELASAFKKR 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +K Y ++  G  ++    +   + +  H G      +         A ++F+V+    
Sbjct: 167 LTEKEYIAIAVGTLEDDL-YMDGPIGRHPHHGRK----MTVGGNNPRSASTYFRVLAR-T 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++   +  +PHTGRTHQ+RVH  H+G PI+GD  Y         SP+  +  LHA+ + L
Sbjct: 221 REAVLVRAKPHTGRTHQIRVHLAHLGAPILGDSVYGK------PSPLIARHALHAQRLSL 274

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           PHP     +  +A +P  MV  W SLG  + 
Sbjct: 275 PHPRDHHAITFSAQVPLDMVSAWVSLGGTWP 305


>gi|291545793|emb|CBL18901.1| pseudouridine synthase, RluA family [Ruminococcus sp. SR1/5]
          Length = 298

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 70/321 (21%), Positives = 138/321 (42%), Gaps = 30/321 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSG 62
           M  +    +   +    +  + +      +   L  + R+ Q + ++ +       ++ G
Sbjct: 1   MERIITYTISTGDSGENVLGFLRK--KGFSKHILTTMKRAEQAILLNGQPAFGRTVLKEG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V+RI         ++ E+    S  ++      L   +LYED  I V NKPA + V   
Sbjct: 59  DVLRI---------LVPEEAGDGSESSIIPVP--LPLDILYEDEDILVLNKPADMPVHPS 107

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHR---LDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +G   +      +W   +  K  +      LD++T+G+LV+A+   +   L+   + R+I
Sbjct: 108 AGNYENTLANGVAWYYKQQGKAFVYRCINRLDRDTTGVLVLAKNPLSGALLSAQMKQRQI 167

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +L  GIP  +   I+  + +        V   + N +    A++H++ +   +  
Sbjct: 168 RRTYLALTDGIPPER-GTISAPVARMDAS----VITREVNFERGEAAVTHYERL-AVSNG 221

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +E+   TGRTHQ+RVH  ++GCP+ GD  Y   F          +  LH+  ++  H
Sbjct: 222 YALVELHLDTGRTHQIRVHMKYIGCPLPGDFLYHPVFDR------IGRQALHSFQLEFAH 275

Query: 300 PEGGR-LQITAPLPAHMVKTW 319
           P  G  +   AP+P    + +
Sbjct: 276 PITGEPMCFLAPVPEDFRRAF 296


>gi|323700246|ref|ZP_08112158.1| pseudouridine synthase, RluA family [Desulfovibrio sp. ND132]
 gi|323460178|gb|EGB16043.1| pseudouridine synthase, RluA family [Desulfovibrio desulfuricans
           ND132]
          Length = 305

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 88/334 (26%), Positives = 148/334 (44%), Gaps = 39/334 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M   Q VVV   E   +L ++ +      +    +QK +R+GQVRVDK R K  +R+++G
Sbjct: 1   MPETQSVVVSQAESGQKLLQFLERRLSGEVPRSAIQKWIRTGQVRVDKGRKKPFDRLEAG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VRIPP     +  + E   L                + YED+++    KPAG++  GG
Sbjct: 61  QTVRIPPYAPGQDKQVSEAGGL---------------AVAYEDAELLAVAKPAGLAAHGG 105

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            G+   +   L++   +    P L HRLD++TSG+L+ A++ A  + L + F    + K+
Sbjct: 106 DGVDDSVVARLRAMYRNADFMPTLAHRLDRDTSGLLLAAKSYAVLRELNDLFASNGVAKV 165

Query: 183 YWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V G         + + + K+   G + V            A++    +   ++   
Sbjct: 166 YLAWVDGRWDEPDGTLLEDVMEKRGAPGAERVR-----TGSGKTALARVTGL-VSSRDRS 219

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP 300
            + ++  TGRTHQ+RV     G  ++GD KY A + +G  +S    +L+  A        
Sbjct: 220 LVAVRLLTGRTHQIRVQLASRGHAVIGDRKYGAPSARGKGSSRGPMRLHCFALR------ 273

Query: 301 EGGRLQITAPLPA-------HMVKTWDSLGFKYD 327
             G   I+ P PA              +LG  +D
Sbjct: 274 -AGERTISLP-PAWSGGWAVDRDALQKALGLLFD 305


>gi|149194036|ref|ZP_01871134.1| Pseudouridine synthase, RluD [Caminibacter mediatlanticus TB-2]
 gi|149135989|gb|EDM24467.1| Pseudouridine synthase, RluD [Caminibacter mediatlanticus TB-2]
          Length = 308

 Score =  213 bits (542), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 134/323 (41%), Gaps = 49/323 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +Q  + +    N RLD++  N   +++   ++++++ G V+V++K + K   +++  + V
Sbjct: 1   MQTFIADK---NKRLDKFLANKL-NVSRNQIEQLIKKGYVKVNEKVITKSGYKLKENEKV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            + P+        K                     +LYED  + V NKP GI V      
Sbjct: 57  EVLPIKKEEKETKKAN---------------FDIPILYEDEDLLVINKPPGIVVHPAPS- 100

Query: 126 AYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             + +  L  W+  KG         ++  + HR+D+ETSG LV+A+     + L+   + 
Sbjct: 101 --YKEATLVDWLKQKGYSLSTIAGEERFGIVHRIDKETSGALVIAKNNKTHEFLSNQLKD 158

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y  L+   P  + +C+   + +          V     K    A + F  I   
Sbjct: 159 KSMGRYYLMLL-NEPLKEAKCVEEKIGRNPKNRLKMAIV-----KNGKEAKTLFVPI--- 209

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                    + +TGRTHQ+RVH   +G  I+GD  Y    +         ++ LHAR + 
Sbjct: 210 --FDNLTAAKLYTGRTHQIRVHLTKLGRYILGDTTYGKKDQN------IKRVMLHAREIY 261

Query: 297 LPHPEGGRLQITAPLPAHMVKTW 319
             HP G +L I APL        
Sbjct: 262 FTHPNGKKLSIIAPLFDDFKNLL 284


>gi|254420499|ref|ZP_05034223.1| RNA pseudouridine synthase family [Brevundimonas sp. BAL3]
 gi|196186676|gb|EDX81652.1| RNA pseudouridine synthase family [Brevundimonas sp. BAL3]
          Length = 241

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 79/228 (34%), Positives = 128/228 (56%), Gaps = 3/228 (1%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++S +++ED+ +  F+KP+G+S QGG   A+ +D  L ++  S G++P L HRLD++TSG
Sbjct: 17  VRSWVIHEDAHVIAFSKPSGLSSQGGRIQAHTLDDLLWAFARSNGKRPELVHRLDRDTSG 76

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++ A+T+ AA  L ++ +MRR +K Y +L+   P+     I   L ++      Y+ VV
Sbjct: 77  VILAAKTKPAAGFLGKALQMRRFRKQYLALLSAAPEPASGTIDAPLRREEIGRESYMRVV 136

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +  GA  + S ++ +    Q    +E++P TGR HQLRVH  H+G P++GD +Y    
Sbjct: 137 AFDAPGAQGSQSRYRTLAANDQGAV-VELEPLTGRMHQLRVHMAHLGRPLIGDVRYGGAL 195

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
                     +L LHA  +  PHPEGG   + AP PA       +LG 
Sbjct: 196 TTEVGP--APRLMLHALKLSFPHPEGGTTTVEAPPPADFAGLRSALGL 241


>gi|212639937|ref|YP_002316457.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
 gi|212561417|gb|ACJ34472.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
          Length = 292

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 66/314 (21%), Positives = 128/314 (40%), Gaps = 33/314 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V   ++ M +  + K    HI+   L  I  + G++ V+   V     +++G  V +  
Sbjct: 7   IVTQQQDGMLVREFLKQQ--HISKTALTDIKFQGGRIEVNDVPVTVRYVLKAGDEVCVS- 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-- 127
                                   ++ +   ++YED  + V NKP  +S        +  
Sbjct: 64  -------------FPPEQKGANMVAEPIPLAIVYEDDYVIVINKPPHMSTIPSREHPHGT 110

Query: 128 HIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +  L  +   + Q    +  RLD++TSG+++VA+ R     L+E  +  R+++ Y ++
Sbjct: 111 LANALLHHYEQQQLQTTVHVVTRLDRDTSGLVLVAKHRHVHHLLSEQQKQGRVKRRYEAV 170

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        I   + +K     +    +         A++H++V+    +    + +Q
Sbjct: 171 CHGYVIQLVGTIDAPIGRKGDSIIEREVRL-----DGQRAVTHYEVLQQKNE-MTHVSIQ 224

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  H+G P+VGD  Y             ++  LH+  +   HP   + +
Sbjct: 225 LETGRTHQIRVHFSHIGHPLVGDDLYGG------LREHIDRQALHSCELTFFHPFFEKTM 278

Query: 306 QITAPLPAHMVKTW 319
              APLP  + +  
Sbjct: 279 TFHAPLPDDIARLL 292


>gi|51893029|ref|YP_075720.1| 23S rRNA pseudouridine synthase [Symbiobacterium thermophilum IAM
           14863]
 gi|51856718|dbj|BAD40876.1| 23S rRNA pseudouridine synthase [Symbiobacterium thermophilum IAM
           14863]
          Length = 327

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 69/339 (20%), Positives = 142/339 (41%), Gaps = 51/339 (15%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV+     +RL ++  +    ++   +++   SG + VD +  + +  +  G+VV +  
Sbjct: 3   FVVDPSARGLRLSQYLFDRLK-LSRTVVRRAKTSGGILVDGRPARTSLVLAGGEVVEV-- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYH 128
                  + +E ++    + +          ++YED  + V +KPAG+ V      ++  
Sbjct: 60  ------RVAQEGRVEPEPIPIQ---------VVYEDPWLLVVDKPAGMVVHPVRDYVSGT 104

Query: 129 IDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +   +   G  P  R   R+D+ETSG+++ A+  A A  L      +++++ Y ++
Sbjct: 105 LANAVAHHLLRSGSDPVARPVQRIDRETSGLVLFAKDPAVAGLLARELERQKLERRYVAV 164

Query: 187 VWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEK--------------------GAN 224
           V G        +   + +     +  +     +  E+                       
Sbjct: 165 VEGAVAADAGTVDRPIRRVWGHPVAREVAEGPRTPEQERLLAEAAAQGRALREDWTAAGQ 224

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
            A++H++V+  +      LE++  TGRTHQ+RVH  ++G P++GD  Y        +  +
Sbjct: 225 PAVTHWRVLRRWP-AATMLELRLETGRTHQIRVHMAYLGHPLLGDELYGG------SRTL 277

Query: 285 QNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
             +  LHA  +   HP     ++ TAPLPA +      L
Sbjct: 278 IQRQALHAATLAFVHPVTREPVRFTAPLPADLEDLVARL 316


>gi|229132101|ref|ZP_04260962.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST196]
 gi|228651369|gb|EEL07343.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST196]
          Length = 292

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 64/312 (20%), Positives = 134/312 (42%), Gaps = 39/312 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           EE   +  + K     I+   L  I  R G + V+ +     +++Q+G+ ++I   +   
Sbjct: 9   EEGTLVREFLKT--KGISKAALTDIKFRGGAIEVNGQHTSVRHKLQAGEELQIFFPVEER 66

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHI 129
           +  ++ ++I                 ++YED  + V NK A +S           IA   
Sbjct: 67  SEGMEVEEI--------------PLCIVYEDDAVLVINKEANMSTIPSREHPSGSIA--- 109

Query: 130 DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L  +   +      +  RLD++TSG++++A+ R     L++  + + +++ Y ++V 
Sbjct: 110 NALLYHYDKQNLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKGVKRTYEAIVH 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G    +   I   + +K+    +         +    A++HF+V++  + K   + ++  
Sbjct: 170 GTILEEVGTIDAPIGRKADSIIERTVC-----EDGQRAVTHFRVMESSSDK-THVALELE 223

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  ++G P++GD  Y           +  +  LH+  +   HP   + +  
Sbjct: 224 TGRTHQIRVHMAYIGHPLLGDDLYGGRRD------VIKRQALHSTSLTFYHPILEKGMTF 277

Query: 308 TAPLPAHMVKTW 319
           T  +P  M    
Sbjct: 278 TVSIPEDMQYAL 289


>gi|206977693|ref|ZP_03238585.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
 gi|206744121|gb|EDZ55536.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
          Length = 292

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 67/314 (21%), Positives = 136/314 (43%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 5   IDSAEEGTLVREFLKT--KGISKAALTDIKFHGGSIEVNGQHASVRHQLQAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHI 129
           +   +  +               ++ +   ++YED  + V NK A +S        A  +
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPAGSV 108

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L S  D +       +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKRHLTSTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HF+VID    K   + ++ 
Sbjct: 169 HGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDSVNHK-THVSLEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  ++G P++GD+ Y              +  LH+  +   HP     + 
Sbjct: 223 DTGRTHQIRVHMAYIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWD 320
            T P+P+ M     
Sbjct: 277 FTTPIPSDMQAILR 290


>gi|108804319|ref|YP_644256.1| ribosomal large subunit pseudouridine synthase D [Rubrobacter
           xylanophilus DSM 9941]
 gi|108765562|gb|ABG04444.1| ribosomal large subunit pseudouridine synthase D [Rubrobacter
           xylanophilus DSM 9941]
          Length = 305

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 82/308 (26%), Positives = 141/308 (45%), Gaps = 43/308 (13%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
            I+    Q++L  G  RV  +    + R++ G+VV              E ++ +  +  
Sbjct: 26  GISRSRAQRLLAEGLARVGGEAAAPSLRVRGGEVV--------------EARLPEEGLE- 70

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-------QK 143
              ++ +   +L+ED  I V +KPAG+ V  G+G   +  G L + +  +G       ++
Sbjct: 71  ---AEEIPVPILFEDEHIAVVDKPAGMVVHPGAG---NRSGTLVNALLGRGIAGGEDPER 124

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD++TSG++VVA+   A   L E    RR++++Y +LV G        +     
Sbjct: 125 PGIVHRLDRDTSGLMVVAKGEPAYSRLVEMLAARRVRRVYRALVVGEGLPPSGTV----- 179

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
             S +G D  +           A++HF+V+   A     L ++  TGRTHQ+RVH   +G
Sbjct: 180 -DSPVGRDPENPALMAAGVGRPAVTHFEVLG-EAAGHTMLRVRLETGRTHQIRVHLSAIG 237

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            P+  D  Y     G        +L+LHA  +   HP  GR L   +P+P  + +    L
Sbjct: 238 YPVYADPLYGRAVPGR-------RLWLHAERLSFEHPAEGRPLDFFSPVPEELRRAAAEL 290

Query: 323 GFKYDRNL 330
             +++  L
Sbjct: 291 DARFEELL 298


>gi|331266315|ref|YP_004325945.1| 23S rRNA pseudouridine synthase [Streptococcus oralis Uo5]
 gi|326682987|emb|CBZ00604.1| 23S rRNA pseudouridine synthase [Streptococcus oralis Uo5]
          Length = 298

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 73/305 (23%), Positives = 131/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L KI  R G + V+ +       +  G  V I          ++   
Sbjct: 16  FLKKH--EVSKGLLAKIKFRGGAILVNGQPQNATYLLDIGDRVTIDIPAEEGFESLE--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
                      +      +LYED    V NKP G++       +  I  F+K +    + 
Sbjct: 71  -----------AIDRPLDILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQEY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G      +  I
Sbjct: 120 ENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQRKSIEKRYFALVKGAGVLEPEGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      +   + ++  KG  YA + +KV+  + +    ++++ HTGRTHQ+RVH
Sbjct: 180 IAPIARD-----EDSIITRRVAKGGKYAHTSYKVVVSY-RNIHLVDIRLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
             H+G P++GD  Y  +           +  LH  Y+   HP   + LQ+ +PLP     
Sbjct: 234 FSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHYLSFYHPFLEQDLQLESPLPDDFSN 288

Query: 318 TWDSL 322
               L
Sbjct: 289 LITQL 293


>gi|148994152|ref|ZP_01823467.1| phosphotransacetylase [Streptococcus pneumoniae SP9-BS68]
 gi|168488941|ref|ZP_02713140.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae SP195]
 gi|147927395|gb|EDK78425.1| phosphotransacetylase [Streptococcus pneumoniae SP9-BS68]
 gi|183572419|gb|EDT92947.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae SP195]
 gi|332073458|gb|EGI83937.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA17570]
          Length = 298

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 138/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNNQPQNATYLLDVGDYV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +  L   +LYED    V NKP G++       
Sbjct: 57  TIYIPAEEGFETLE--------------AIELPLDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +      +   + ++  KG  YA + +K++  +     
Sbjct: 163 YFALVKGDGHLEPEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +  HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH  Y+   HP 
Sbjct: 217 LVYIHLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLED-----GIQRQALHCHYLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LEQDLQLESPLPDDFSNLITQL 293


>gi|306829567|ref|ZP_07462757.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus mitis ATCC
           6249]
 gi|304428653|gb|EFM31743.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus mitis ATCC
           6249]
          Length = 298

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 137/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNDQPQNATYLLDIGDRV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +      +L+ED    V NKP G++       
Sbjct: 57  TIDIPAEEGFETLE--------------AIDRPLDILFEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQEYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQRKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +          + ++  KG  YA + +KV+  +     
Sbjct: 163 YFALVKGNGDLEPEGEIIAPIARDVD-----SIITRRVAKGGKYAHTSYKVVASYGDIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++ HTGRTHQ+RVH  H+G P++GD  Y  +           +  LH  ++   HP 
Sbjct: 217 LIDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHFLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             R L++ +PLP         L
Sbjct: 272 LERQLELESPLPDDFNNLITQL 293


>gi|89894036|ref|YP_517523.1| hypothetical protein DSY1290 [Desulfitobacterium hafniense Y51]
 gi|219668420|ref|YP_002458855.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
 gi|89333484|dbj|BAE83079.1| hypothetical protein [Desulfitobacterium hafniense Y51]
 gi|219538680|gb|ACL20419.1| pseudouridine synthase, RluA family [Desulfitobacterium hafniense
           DCB-2]
          Length = 302

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 75/297 (25%), Positives = 121/297 (40%), Gaps = 31/297 (10%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           H +   +Q + +  +V V+        R ++G+ + +      +N I  E          
Sbjct: 30  HFSRKLIQHLKQGERVWVNGAFTFLTTRGKAGETLSVQLQPPEINSIPGEN--------- 80

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQKP-RLT 147
                 L   +LYED      NKPAG  V            +  +  W+     +P R  
Sbjct: 81  ------LPLEILYEDDYFIAINKPAGQVVHPTPRYPRGTIGNAVVGYWLAKGEARPFRPI 134

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HR+D+ TSG++V+ + + A Q +       RI K Y  +V G     +  I   +     
Sbjct: 135 HRIDRNTSGVVVIGKNQFAHQQMAWQHAHGRIHKCYRGIVEGQVMEDQGTIKAPIALAPD 194

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  + +Q     + A++ +KV++ + Q    LE    TGRTHQ+RVH  H+G P++
Sbjct: 195 -----SFIQRQISPEGSPAVTLYKVLERY-QDASLLEFILETGRTHQIRVHCQHLGHPLL 248

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
           GD  Y  N          N+  LH+   +  HP  G L  I APLP  + +    L 
Sbjct: 249 GDDLYGGNLAR------INRQALHSSIYEFNHPLTGELTTIQAPLPEDLQRLLRELA 299


>gi|255655078|ref|ZP_05400487.1| putative pseudouridylate synthase [Clostridium difficile QCD-23m63]
 gi|296451065|ref|ZP_06892807.1| RluA family pseudouridine synthase [Clostridium difficile NAP08]
 gi|296880582|ref|ZP_06904544.1| RluA family pseudouridine synthase [Clostridium difficile NAP07]
 gi|296260072|gb|EFH06925.1| RluA family pseudouridine synthase [Clostridium difficile NAP08]
 gi|296428536|gb|EFH14421.1| RluA family pseudouridine synthase [Clostridium difficile NAP07]
          Length = 300

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 72/313 (23%), Positives = 134/313 (42%), Gaps = 32/313 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +EE M L     +   + +  +L K+ R   V V+    K + ++ SG ++ +       
Sbjct: 16  NEEEMTLKEVLLDKL-NFSVRSLSKMKREKSVLVNGVYKKPSLKVYSGDLIEVKINEEKA 74

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFL 133
           N                     L   ++Y+D  I + NK   + V    S     I   +
Sbjct: 75  N----------------FEPQDLNLQIIYDDFDIIMVNKLPFMVVHPTKSHYDKTIANGI 118

Query: 134 KSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             ++D++ +  K R  +RLD  TSG+++VA+   A   L+ +    +++K Y ++V GI 
Sbjct: 119 SYYIDNQKENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGII 178

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K  +  I   + + +      +      ++    +++H+KVI+   +    LE+   TGR
Sbjct: 179 KENEGTIDEPIYRPTEDSIKRII-----DERGQSSVTHYKVIERL-ENATVLEVSLETGR 232

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           THQ+RVH  H+G  I+GD  Y           + N+  LHA  ++   P    +L+  A 
Sbjct: 233 THQIRVHMAHIGHGIIGDELYGC-----VDEELINRQALHAYRLEFEQPRTKEKLKFKAD 287

Query: 311 LPAHMVKTWDSLG 323
           +P  + +    L 
Sbjct: 288 IPEDIKELISKLR 300


>gi|225568048|ref|ZP_03777073.1| hypothetical protein CLOHYLEM_04121 [Clostridium hylemonae DSM
           15053]
 gi|225163144|gb|EEG75763.1| hypothetical protein CLOHYLEM_04121 [Clostridium hylemonae DSM
           15053]
          Length = 341

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 77/348 (22%), Positives = 146/348 (41%), Gaps = 24/348 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++++ +E   RLD++ K +        L K+LR   + ++ +R   N ++ +G  VR
Sbjct: 1   MKIIIIKPNESEQRLDKFLKKYMNRAPGSFLYKMLRKKNITLNGRRAGGNEKLHTGDEVR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +     + + +  +       D     ++YEDS +   NKPAG+  Q      
Sbjct: 61  LFLSDETIEKFTGDDEPVAGAKGRNTTLD-----IIYEDSHVLFVNKPAGMLSQKAEKTD 115

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   + S++   GQ         +P + +RLD+ TSG++   +T A  Q     FR R
Sbjct: 116 ISLVEHIISYLLDSGQLTREELRTFRPSVCNRLDRNTSGLVAAGKTLAGLQMFGSLFRDR 175

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  +V G        I  +L+K        +    + EK A    + +  +  ++
Sbjct: 176 NLRKYYLCIVKGKVDKPS-HIKGYLIKNEQTNEVRIVTSGEAEKAA-PIETEYIPL-AYS 232

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYM 295
           ++   L +   TGRTHQ+R H  ++  P+ GD+KY                   LH+  +
Sbjct: 233 REHSLLRVHLITGRTHQIRAHLAYVSHPLCGDYKYGDRDVNERYRKKYGVTSQMLHSYEL 292

Query: 296 DLPHPEGG-----RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
            LP  EG           AP+PA   K      +++     ++ L+ +
Sbjct: 293 VLPVLEGEFAALSERTFRAPVPALFQKVIKETAWEHGTQEALEVLHWK 340


>gi|296129452|ref|YP_003636702.1| pseudouridine synthase, RluA family [Cellulomonas flavigena DSM
           20109]
 gi|296021267|gb|ADG74503.1| pseudouridine synthase, RluA family [Cellulomonas flavigena DSM
           20109]
          Length = 311

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 69/324 (21%), Positives = 135/324 (41%), Gaps = 15/324 (4%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + + V +     R+D         ++     ++   G VRVD + V  ++R+ +G 
Sbjct: 1   MSGTRALPVPDGLAGERVDAALARLL-GLSRTRAAELAAQGAVRVDGRAVGKSDRLVAGS 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +   +      +         + +    D L  +        +     +G +V G  
Sbjct: 60  FLEVDLSLPVPTAPVV-VPEPVPGMRIVHDDDDLVVVDKPVGVAAHPSPGWSGPTVVGAL 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             A +             ++  + HRLD  TSG++VVA++  A   L  +F+ R ++K+Y
Sbjct: 119 AAAGYRIST-----SGSAERQGVVHRLDAGTSGLMVVAKSEHAYTVLKRAFKERTVEKVY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L  G P      I   + +  H   D+   V  +      +++H++V++        +
Sbjct: 174 HALAQGHPSPTTGTIDAPIGR--HPSSDWKFAVVAD---GKPSVTHYEVLEMLP-GASLV 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E+   TGRTHQ+RVH   +   +VGD  Y A+        + ++ +LHA  +   HP  G
Sbjct: 228 EVHLETGRTHQIRVHFAALRHSLVGDLTYGADPALAARLGV-SRQWLHAVRLGFEHPATG 286

Query: 304 R-LQITAPLPAHMVKTWDSLGFKY 326
             L++ +  P  +V   ++L   Y
Sbjct: 287 EWLEVASDYPEDLVAALETLRGAY 310


>gi|293977792|ref|YP_003543222.1| pseudouridine synthase, RluA family [Candidatus Sulcia muelleri
           DMIN]
 gi|292667723|gb|ADE35358.1| pseudouridine synthase, RluA family [Candidatus Sulcia muelleri
           DMIN]
          Length = 314

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 86/318 (27%), Positives = 143/318 (44%), Gaps = 31/318 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D + K      N   +QKI+  G V V+   +K N  ++   V+ I       N I 
Sbjct: 14  IRIDTYIKFILHKKNRNFIQKIIEKGFVYVNNILIKKNYIVKINDVIEIFLPEGKKNII- 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKSW 136
                           + LK  + YED  + + NK +G+ V  G G      I+G    +
Sbjct: 73  ---------------PENLKINIFYEDEYVIIINKQSGLVVHPGKGNESMTLINGLHFYF 117

Query: 137 VDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +  K      P L HR+D+ TSG+++VA+ +   + +++ F +  I++ Y +LVWG  KN
Sbjct: 118 LKKKNIYNKIPILVHRIDKGTSGLILVAKDKNILEKISKQFYINHIKRKYITLVWGYIKN 177

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K  I    + +S     Y++V   N     ++I+H+KV++ F +    L+    TGRTH
Sbjct: 178 NKGTII-CNIGRSLKNRIYMNVF-PNGIYGKFSITHYKVLERF-KYVTLLKCTLETGRTH 234

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPEGGRLQ- 306
           Q+RVH  ++G PI+ D  Y  N        I+          LHA Y++  HP   +   
Sbjct: 235 QIRVHLKYIGHPILNDKDYGGNHTFKEKKNIKKLFINMKYQALHAYYIEYIHPIYRKKNY 294

Query: 307 ITAPLPAHMVKTWDSLGF 324
              P+P  +     +L  
Sbjct: 295 FICPIPDRIKFLIKNLRL 312


>gi|229056939|ref|ZP_04196335.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH603]
 gi|228720467|gb|EEL72040.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH603]
          Length = 292

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 62/309 (20%), Positives = 132/309 (42%), Gaps = 33/309 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           EE   +  + K     I+   L  I  R G + V+ +     +++Q+G+ ++I   +   
Sbjct: 9   EEGTLVREFLKT--KGISKAALTDIKFRGGAIEVNGQHTSVRHKLQAGEELQIFFPVEER 66

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGF 132
           +  ++ ++I                 ++YED  + V NK A +S             +  
Sbjct: 67  SEGMEVEEI--------------PLCIVYEDDAVLVINKEANMSTIPSREHPSGSIANAL 112

Query: 133 LKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L  +   +      +  RLD++TSG++++A+ R     L++  + + +++ Y ++V G  
Sbjct: 113 LYHYDKQNLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKGVKRTYEAIVHGTI 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             +   I   + +K+    +         +    A++HF+V++  + K   + ++  TGR
Sbjct: 173 LEEVGTIDAPIGRKADSIIERTVC-----EDGQRAVTHFRVMESSSDK-THVALELETGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P++GD  Y           +  +  LH+  +   HP   + +  T  
Sbjct: 227 THQIRVHMAYIGHPLIGDDLYGGRRD------VIKRQALHSTSLTFYHPILEKGMTFTVS 280

Query: 311 LPAHMVKTW 319
           +P  M    
Sbjct: 281 IPEDMQYAL 289


>gi|315186195|gb|EFU19957.1| pseudouridine synthase, RluA family [Spirochaeta thermophila DSM
           6578]
          Length = 319

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 81/332 (24%), Positives = 138/332 (41%), Gaps = 39/332 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V    + +RLD+        I    +++ +    + +D +  K + R+ +G  +    + 
Sbjct: 11  VPPHLDGLRLDQALAELL-GITRSQVKQRIAD--LALDGRPAKPSQRVHAGARIAGTLLP 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY---- 127
            A   +  E                +   +LYED    V +KP G+ V  G+G       
Sbjct: 68  EAPPDLTPEP---------------VPFTVLYEDPHCLVIDKPQGLVVHPGAGNPTGTLV 112

Query: 128 ----HIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               H    L +        D +  +  + HRLD++TSG+LVVA+  A    L   F+ +
Sbjct: 113 HGLLHYSHELATRASSDDLDDEERLRIGIVHRLDKDTSGVLVVAKDPATHHFLATQFKEK 172

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +K+Y +++ G P  ++  I   L +       +  + + +     Y+ + ++++  F 
Sbjct: 173 ETKKLYLAVLKGTPPAREGEIEGHLARDPVHRKKFTLLSRPDR--GKYSHTRYRLLAAFG 230

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
               ++ + P TGRTHQLRVH   +GCPI+GD  Y A     F       L LHA  + +
Sbjct: 231 -THSFVALYPTTGRTHQLRVHTAALGCPILGDPLY-ARPDPRFPDAT---LMLHAYLLTI 285

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
             P  G L   APLP        SL    D +
Sbjct: 286 RIPGRGLLTFRAPLPHRFKTVLRSLARASDGD 317


>gi|254821467|ref|ZP_05226468.1| hypothetical protein MintA_16155 [Mycobacterium intracellulare ATCC
           13950]
          Length = 308

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 141/328 (42%), Gaps = 31/328 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  + + V      MR+D         ++      +   G V +D  +   ++R+  G 
Sbjct: 1   MSD-RSMPVPEGLAGMRVDAGLARLL-GLSRSAAAALAEDGGVELDGVQAGKSDRLTGGA 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGG 122
            +++              ++ +    L      ++ + +LY D  I   +KPA ++    
Sbjct: 59  WLQV--------------RLPEPPAPLQNTPVDIEGMTILYSDDDIVAVDKPAAVAAHAS 104

Query: 123 SG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ 
Sbjct: 105 VGWSGPTVLGGLAAAGYRITTSGVPERQGIVHRLDVGTSGVMVVALSERAYTLLKRAFKQ 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K Y +LV G P      I   + +  H GG++   +    K   ++++H+  ++ F
Sbjct: 165 RTVDKRYHALVQGHPDPSSGTIDAPIGR--HRGGEWKFAIT---KDGRHSLTHYDTVEAF 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 L++   TGRTHQ+RVH   +  P  GD  Y A+ K      ++ + +LHAR + 
Sbjct: 220 V-AASLLDVHLETGRTHQIRVHFSALHHPCCGDLVYGADPKLAKRLGLE-RQWLHARSLS 277

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSLG 323
             HP +G R++I +P P  +    D L 
Sbjct: 278 FAHPADGRRMEIVSPYPPDLQHALDVLR 305


>gi|322376764|ref|ZP_08051257.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M334]
 gi|321282571|gb|EFX59578.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M334]
          Length = 298

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 141/322 (43%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNDQPQNATYLLDIGDRV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          +   + ++  +N           +LYED    V NKP G++       
Sbjct: 57  IINIPAEEGFETL---EAIERPLN-----------ILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    D + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQDYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIEKR 162

Query: 183 YWSLVWGIP-KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +      +   + ++  KG  YA + +K++  +     
Sbjct: 163 YFALVKGDGYLESEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++ HTGRTHQ+RVH  H+G P++GD  Y  +           +  LH  Y+   HP 
Sbjct: 217 LVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHYLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LEQDLQLESPLPDDFSNLIKQL 293


>gi|261414686|ref|YP_003248369.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261371142|gb|ACX73887.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 386

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 87/380 (22%), Positives = 155/380 (40%), Gaps = 62/380 (16%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            ++ +  NMRLDR+ +  +P  +      ++R  +VRV+    K N  +  G VV I   
Sbjct: 5   TIDRNFANMRLDRFLRKAFPEESLSVFFAVIRKKKVRVNGVVGKANQMLVEGDVVNIYEN 64

Query: 71  INALNHIIKEQKILDS-------------------------------------------- 86
             ++N   + ++  D                                             
Sbjct: 65  FKSVNESDERRETKDERNINGESLPLASAAEAAPATPSSGDTPQRPDAKSATGFAKNKST 124

Query: 87  ------SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVD 138
                       H    +  L+ +     + NKP+G++ Q GSG      +  +L  W  
Sbjct: 125 WGRHLTGAEKQAHWGAHELDLVVQTEDYVIVNKPSGLASQPGSGTRPGESLVEYLWEWGR 184

Query: 139 SKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           ++G   KP + HRLDQETSG+++ A      +  T   R   + K Y++LV G  K  + 
Sbjct: 185 NEGLDFKPTIAHRLDQETSGLIIAALHGDTLRDFTRMIREHVVDKFYFALVKGNLKKDRG 244

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I+  LL+     G  + +V Q+++ A  AI+H++V     + +  ++++  TGR HQ+R
Sbjct: 245 TISESLLRTDSAKGSKM-LVGQDDENAQKAITHYRV-KQHYEGYDLVKIKLETGRMHQIR 302

Query: 257 VHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
            H   +G P++GD +Y   A  +        N+L+LH+  ++    +G       PLP  
Sbjct: 303 AHFASIGHPLLGDTRYGDFALNREVKKLFGLNRLFLHSCRLEF-DWQGEHKVFDCPLPKE 361

Query: 315 MVKTWDSL---GFKYDRNLY 331
           +      L    F+   N +
Sbjct: 362 LRDVIKQLKPMRFERPENNF 381


>gi|332879235|ref|ZP_08446932.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
 gi|332682655|gb|EGJ55555.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
          Length = 320

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 76/303 (25%), Positives = 129/303 (42%), Gaps = 34/303 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIK 79
           LD +       I+    + IL    + VD+K V ++N  ++ G VVR+            
Sbjct: 33  LD-FIMESMKGISRNKAKDILTGHGITVDRKSVSQYNYELRPGMVVRV------------ 79

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                 S              ++YED  + V  K AGI         + I   L  +   
Sbjct: 80  ------SKHKRNNELKNKYVKIVYEDKDLIVIEKSAGILSMPAVTQQFSIKTVLDEYFTR 133

Query: 140 KGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +  K    + HRLD++TSG+++ A+     + L E ++     + Y ++V G  + +   
Sbjct: 134 RHFKCTAHVVHRLDRDTSGLMMYAKNIEVQRILEEHWQEIVTDRRYVAVVSGKMEKEGGT 193

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I++WL         YV      + G  YA++HF  +D   +++  +E++  TGR +Q+RV
Sbjct: 194 ISSWL----KDNKAYVTYSSPTDNGGKYAVTHFHTLDAR-ERYSLVELKLETGRKNQIRV 248

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +G P+VGD KY         S    +L LHA  ++  HP  G  ++   P P    
Sbjct: 249 HMQDIGHPVVGDSKYGNG------SDPIGRLGLHAYRLNFYHPITGEPMEFETPFPTLFT 302

Query: 317 KTW 319
           K +
Sbjct: 303 KLF 305


>gi|15900967|ref|NP_345571.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae TIGR4]
 gi|15903050|ref|NP_358600.1| 23S rRNA pseudouridine synthase [Streptococcus pneumoniae R6]
 gi|111657593|ref|ZP_01408329.1| hypothetical protein SpneT_02001203 [Streptococcus pneumoniae
           TIGR4]
 gi|116516162|ref|YP_816460.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae D39]
 gi|149006229|ref|ZP_01829941.1| phosphotransacetylase [Streptococcus pneumoniae SP18-BS74]
 gi|149012907|ref|ZP_01833820.1| phosphotransacetylase [Streptococcus pneumoniae SP19-BS75]
 gi|168483173|ref|ZP_02708125.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1873-00]
 gi|168491992|ref|ZP_02716135.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC0288-04]
 gi|168494532|ref|ZP_02718675.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC3059-06]
 gi|169832712|ref|YP_001694523.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae Hungary19A-6]
 gi|182684150|ref|YP_001835897.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CGSP14]
 gi|221231840|ref|YP_002510992.1| RNA pseudouridylate synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225854594|ref|YP_002736106.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae JJA]
 gi|303254191|ref|ZP_07340303.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           BS455]
 gi|303259761|ref|ZP_07345736.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP-BS293]
 gi|303262936|ref|ZP_07348871.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS292]
 gi|303264899|ref|ZP_07350815.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS397]
 gi|303266879|ref|ZP_07352757.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS457]
 gi|303268916|ref|ZP_07354701.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS458]
 gi|307127370|ref|YP_003879401.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 670-6B]
 gi|14972575|gb|AAK75211.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae TIGR4]
 gi|15458622|gb|AAK99810.1| 23S rRNA pseudouridine synthase [Streptococcus pneumoniae R6]
 gi|116076738|gb|ABJ54458.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae D39]
 gi|147762006|gb|EDK68968.1| phosphotransacetylase [Streptococcus pneumoniae SP18-BS74]
 gi|147763196|gb|EDK70136.1| phosphotransacetylase [Streptococcus pneumoniae SP19-BS75]
 gi|168995214|gb|ACA35826.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Hungary19A-6]
 gi|172043330|gb|EDT51376.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1873-00]
 gi|182629484|gb|ACB90432.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CGSP14]
 gi|183573763|gb|EDT94291.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC0288-04]
 gi|183575559|gb|EDT96087.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC3059-06]
 gi|220674300|emb|CAR68842.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           ATCC 700669]
 gi|225722385|gb|ACO18238.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae JJA]
 gi|301802010|emb|CBW34739.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           INV200]
 gi|302598862|gb|EFL65896.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           BS455]
 gi|302635913|gb|EFL66413.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS292]
 gi|302638966|gb|EFL69426.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP-BS293]
 gi|302641534|gb|EFL71896.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS458]
 gi|302643577|gb|EFL73846.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS457]
 gi|302645587|gb|EFL75818.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS397]
 gi|306484432|gb|ADM91301.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 670-6B]
 gi|332075053|gb|EGI85524.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA17545]
 gi|332201583|gb|EGJ15653.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA47368]
          Length = 298

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 138/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNNQPQNATYLLDVGDYV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +  L   +LYED    V NKP G++       
Sbjct: 57  TIDIPAEKGFETLE--------------AIELPLDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +      +   + ++  KG  YA + +K++  +     
Sbjct: 163 YFALVKGDGHLEPEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +  HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH  Y+   HP 
Sbjct: 217 LVYIHLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLED-----GIQRQALHCHYLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LEQDLQLESPLPDDFSNLITQL 293


>gi|145294446|ref|YP_001137267.1| hypothetical protein cgR_0401 [Corynebacterium glutamicum R]
 gi|140844366|dbj|BAF53365.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 294

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 83/309 (26%), Positives = 139/309 (44%), Gaps = 26/309 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           ++ V     + R+D++ +     ++   + + +R G +RV+ ++V  N R+Q G  +R+ 
Sbjct: 5   FIEVSAGHADRRIDKFLRAQLKGVSASLIFRQMRKGDIRVNGRKVDPNYRLQEGDRIRMW 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            +    +        L   V        +   +L+ED+++ V NKPAGI V GG+G    
Sbjct: 65  QMDLPAD--------LPPPVVDKHIFKAVADSVLFEDAELLVINKPAGIPVHGGTGHGGG 116

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--RIQKIYWSL 186
           +   L+     + +   L HRLD++TSG+L+V++T +  + L E  R R   I + Y   
Sbjct: 117 VIEALRQKFPQE-RDLELVHRLDRDTSGLLLVSKTTSVLRELQEILRDREEEIFRGYLLK 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   L                       A ++F+V+         ++ Q
Sbjct: 176 VEGAWPGDLRQIDVPL--------KRTETTVVPHSDGLRARTYFEVVKRLP-GATLVKAQ 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
             TGR HQ+RVHA + G PIVGD +Y +      T      ++LHA  + +P   G R +
Sbjct: 227 LATGRKHQIRVHAQYAGHPIVGDPRYGSRGGRAAT------MHLHAAELVVPRGAGKRQK 280

Query: 307 ITAPLPAHM 315
            TAPLP   
Sbjct: 281 FTAPLPKEW 289


>gi|301052847|ref|YP_003791058.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           anthracis CI]
 gi|300375016|gb|ADK03920.1| ribosomal large subunit pseudouridylate synthase D [Bacillus cereus
           biovar anthracis str. CI]
          Length = 297

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 69/318 (21%), Positives = 136/318 (42%), Gaps = 39/318 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI   
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +   +  +               ++ +   ++YED  + V NK A +S         H  
Sbjct: 68  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSR---EHPS 110

Query: 131 GFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + + + S   K        +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 111 GSVANALLSHYDKQYLPSTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID  A     + 
Sbjct: 171 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVS 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 225 LELDTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 278

Query: 304 RLQITAPLPAHMVKTWDS 321
            +   A +P+ M +    
Sbjct: 279 EMSFAAMIPSDMQEVLRQ 296


>gi|269795564|ref|YP_003315019.1| ribosomal large subunit pseudouridine synthase D [Sanguibacter
           keddieii DSM 10542]
 gi|269097749|gb|ACZ22185.1| ribosomal large subunit pseudouridine synthase D [Sanguibacter
           keddieii DSM 10542]
          Length = 311

 Score =  212 bits (540), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 72/330 (21%), Positives = 146/330 (44%), Gaps = 27/330 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  + + V +     R+D         ++     +I   G VR+D + +  ++R+    
Sbjct: 1   MT-TRTLPVPDGLAGERVDAALARML-GLSRTVAAQIASDGGVRLDGRALGKSDRLAPDS 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          + +       V + +    +K  ++Y+D  + V +KP G++     
Sbjct: 59  WIEVD---------VPDPSAPRGPVVVAEPVPGMK--IMYDDDDVVVIDKPVGVAAHPSV 107

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  + HRLD  TSG++VVA++  A   +  +F+ R
Sbjct: 108 GWTGPTVVGALIAAGYTIATSGAAERQGIVHRLDVGTSGLMVVAKSEHAYSVMKRAFKER 167

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K+Y +LV G P+     I   + +  H   DY   V  +      +++H++V++  +
Sbjct: 168 TVEKVYHALVQGHPEPTTGTIDAPIGR--HPNHDYKFGVVAD---GKPSVTHYEVLEMLS 222

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +E+   TGRTHQ+RVH   +  P VGD  Y A+ +      +  + +LHA+ +  
Sbjct: 223 -AASLVEVHLETGRTHQIRVHFSALRHPCVGDLTYGADPRLAEKVSL-TRQWLHAKRLGF 280

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            HP  G  +++ +  P  +    + +  +Y
Sbjct: 281 EHPSTGEWVEVVSEYPEDLAAALEVVRGEY 310


>gi|297199052|ref|ZP_06916449.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           sviceus ATCC 29083]
 gi|197715994|gb|EDY60028.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           sviceus ATCC 29083]
          Length = 314

 Score =  212 bits (540), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 77/322 (23%), Positives = 133/322 (41%), Gaps = 18/322 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  SG+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAASGKVTVDGSVVGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E       + +    D +  I+       +      G +V
Sbjct: 60  GGAWLEVEMPQAAAPVQIVAEPV---EGMEIVHDDDDVVVIVKPVGVAAHPSPGWTGTTV 116

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GG   A +             ++  + HRLD  TSG++VVA++  A   L   F+ R +
Sbjct: 117 IGGLAAAGYRIST-----SGAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKRQFKERTV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G P      I   + +  H   DY   V         +++H+ +I+ F + 
Sbjct: 172 DKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAE---GKPSVTHYDLIEAF-RA 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA  +   H
Sbjct: 226 ASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADPTLAKRLRL-TRQWLHAVRLGFEH 284

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  ++  +  P  + +  D
Sbjct: 285 PGDGEWVEFASDYPEDLQQALD 306


>gi|145343527|ref|XP_001416372.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144576597|gb|ABO94665.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 332

 Score =  212 bits (540), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 79/352 (22%), Positives = 137/352 (38%), Gaps = 77/352 (21%)

Query: 20  RLDRWFKNHYPHIN--FVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNH 76
           RLD +   + P  +     +   +++  V ++ K   K +  ++ G V+           
Sbjct: 2   RLDAYVAANVPDASASRGRVAAAIKARMVTLNGKTASKPSRALKPGDVI----------- 50

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
              E ++     +  K   ++K  +++ED  + V NK AG+     +G   H  G L + 
Sbjct: 51  ---EGELERERASEAKPEPWVKLDIVHEDESVLVVNKAAGMVTHPSAG---HESGTLVNA 104

Query: 137 VDSKG-----------------------------------QKPRLTHRLDQETSGILVVA 161
           V                                        +P + HRLD+ TSG++VVA
Sbjct: 105 VLGHCDLPELVVPTGNQALSDDDEDDEDAVDEDEGARDGMIRPGIVHRLDKGTSGVMVVA 164

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +  +A   L E F  R +++ Y +++ G+P   K  I   + +      D + +      
Sbjct: 165 KDASAHNSLCEQFAARVVRRKYVAILSGVPSPSKGRIEAPIGRDP---RDRLRMAVTQG- 220

Query: 222 GANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF---- 276
           G  +A S+++VI   A      +E +  TGRTHQ+RVHA H+G PI+GD  Y        
Sbjct: 221 GGRFAASNYEVIATLANGNASLVEWRLETGRTHQIRVHAKHIGHPILGDDTYGGGGGAAV 280

Query: 277 ------------KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
                       +        ++  LHAR +   HP+ G  L  +   P   
Sbjct: 281 SALSRYGVFDVKEAKALMSTIDRPMLHARTLGFTHPQSGEALDFSRDPPEDF 332


>gi|291563059|emb|CBL41875.1| pseudouridine synthase, RluA family [butyrate-producing bacterium
           SS3/4]
          Length = 334

 Score =  212 bits (539), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 71/323 (21%), Positives = 138/323 (42%), Gaps = 35/323 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQS 61
           M  V    ++  E    +  +  +     +   L   LR   G   ++ K V  N  +Q 
Sbjct: 28  MNIVLIYTIKEAESGRSIAAFLLD--SGYS-SRLVVHLRNTEGSFLLNGKTVFSNTVLQP 84

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              +R+          + E+K  D  V +      +   +++ED  + V +KPAG+ V  
Sbjct: 85  KDQLRVH---------VTEKKTSDQIVPVP-----MDLSVVFEDEHVLVIDKPAGMPVHP 130

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL---THRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             G   +      +W       P +    +RLD++TSG++++A+   ++  L+++ +   
Sbjct: 131 SQGHYENTLANGIAWYYRNEATPFVFRAVNRLDRDTSGLVLLAKNPYSSCVLSDAVKDHT 190

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y ++V G   +    I   + +K     + V     + +    A++H++       
Sbjct: 191 IHREYAAIVSGK-TDASGTIDLPIARKDGSTIERVC----DPERGETAVTHYRTFAYNKD 245

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
               ++ +   TGRTHQ+RVH   +G P+ GD  YC +++        ++  LH+ Y+  
Sbjct: 246 ADISFIRLLLETGRTHQIRVHMKAIGHPLPGDFLYCPDYR------FIDRQPLHSTYLRF 299

Query: 298 PHPEGGR-LQITAPLPAHMVKTW 319
            HP  G  L+ +A LP  M K +
Sbjct: 300 SHPVTGEKLEFSASLPEDMRKLF 322


>gi|306820474|ref|ZP_07454110.1| ribosomal large subunit pseudouridine synthase D [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304551549|gb|EFM39504.1| ribosomal large subunit pseudouridine synthase D [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 300

 Score =  212 bits (539), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 68/324 (20%), Positives = 137/324 (42%), Gaps = 37/324 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   ++ DE  +RLD +  +    ++   +Q ++ SG + ++  + K + ++++G  V +
Sbjct: 3   EIFTLQEDENLIRLDVYLGDKL-ELSRSKIQSLIESGNISLNGNKAKASVKLKTGDTVYV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ--GGSGI 125
                    I  +   LD               ++YED  + V NKP G+      G+  
Sbjct: 62  NYQEENKAEIKAQDIALD---------------IVYEDDDVLVVNKPRGMVTHVANGNHE 106

Query: 126 AYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              ++  L        + +   +  + HR+D++TSG+LVVA+   ++  LT   +   + 
Sbjct: 107 GTLVNALLYYLKDDISLQNGMYRAGIVHRIDKDTSGLLVVAKNDFSSTELTNQLKDHSMT 166

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           ++Y  +  G+  +++  I   + +       Y  +     +   YA +    ++ F +K+
Sbjct: 167 RVYTLICNGVI-DEETVIEQNIGRNPKDRMKYCVI-----EDGKYAHTTIIPLEIF-EKY 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            + +    TGRTHQ+RVH  H+  PIVGD  Y             +   LHA  +   HP
Sbjct: 220 TYAKAILKTGRTHQIRVHLRHINRPIVGDRLYSN------YKEKIDGQLLHAGTLGFLHP 273

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
           +  + L+ +   P    +    L 
Sbjct: 274 KTKKYLEFSVEEPEIFQRELKRLR 297


>gi|224372561|ref|YP_002606933.1| ribosomal large subunit pseudouridine synthase D [Nautilia
           profundicola AmH]
 gi|223588812|gb|ACM92548.1| ribosomal large subunit pseudouridine synthase D [Nautilia
           profundicola AmH]
          Length = 311

 Score =  212 bits (539), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 73/332 (21%), Positives = 140/332 (42%), Gaps = 46/332 (13%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINA 73
            ++N R+D++      +++   +++++++  V V+ K +K    ++Q+G  V +      
Sbjct: 7   SDKNERVDKFLSQKL-NVSRNQIEQLIKNSLVSVNSKTIKKGGVKLQAGDTVDV------ 59

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                   +I ++  +   +       +LYED  + V NKP GI V     +    +  L
Sbjct: 60  --------EIKEAESSKEDYEVNFDIPVLYEDEDVLVINKPPGIVVHPAPSV---KEATL 108

Query: 134 KSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             W+ +K  +           + HR+D+ETSG L++A+   A + L+   + + + + Y 
Sbjct: 109 VDWLKTKNYRLSTIAGEERFGIVHRIDKETSGALIIAKNNKAHEFLSAQLKDKTMGRYYI 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            L+   P  +  C+   + +         +V     K    A + F  +           
Sbjct: 169 MLL-NEPLKEAVCVDKPIARNPKNRLKMAYV-----KNGREAKTLFVPVYEN-----VAA 217

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGRTHQ+RVH   +G  I+GD  Y    +         ++ LHA+ +   HP G +
Sbjct: 218 AKLFTGRTHQIRVHLSTIGRYILGDTLYGKKEQK------LPRVMLHAKELYFIHPSGKK 271

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLY 336
           L I AP+     K     GF Y+    I  ++
Sbjct: 272 LSIIAPMFDDFKKNLPK-GFNYEETDTISDIF 302


>gi|302325509|gb|ADL24710.1| putative ribosomal large subunit pseudouridine synthase C
           [Fibrobacter succinogenes subsp. succinogenes S85]
          Length = 411

 Score =  212 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 87/380 (22%), Positives = 155/380 (40%), Gaps = 62/380 (16%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            ++ +  NMRLDR+ +  +P  +      ++R  +VRV+    K N  +  G VV I   
Sbjct: 30  TIDRNFANMRLDRFLRKAFPEESLSVFFAVIRKKKVRVNGVVGKANQMLVEGDVVNIYEN 89

Query: 71  INALNHIIKEQKILDS-------------------------------------------- 86
             ++N   + ++  D                                             
Sbjct: 90  FKSVNESDERRETKDERNINGESLPLASAAEAAPATPSSGDTPQRPDAKSATGFAKNKST 149

Query: 87  ------SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVD 138
                       H    +  L+ +     + NKP+G++ Q GSG      +  +L  W  
Sbjct: 150 WGRHLTGAEKQAHWGAHELDLVVQTEDYVIVNKPSGLASQPGSGTRPGESLVEYLWEWGR 209

Query: 139 SKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           ++G   KP + HRLDQETSG+++ A      +  T   R   + K Y++LV G  K  + 
Sbjct: 210 NEGLDFKPTIAHRLDQETSGLIIAALHGDTLRDFTRMIREHVVDKFYFALVKGNLKKDRG 269

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I+  LL+     G  + +V Q+++ A  AI+H++V     + +  ++++  TGR HQ+R
Sbjct: 270 TISESLLRTDSAKGSKM-LVGQDDENAQKAITHYRV-KQHYEGYDLVKIKLETGRMHQIR 327

Query: 257 VHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
            H   +G P++GD +Y   A  +        N+L+LH+  ++    +G       PLP  
Sbjct: 328 AHFASIGHPLLGDTRYGDFALNREVKKLFGLNRLFLHSCRLEF-DWQGEHKVFDCPLPKE 386

Query: 315 MVKTWDSL---GFKYDRNLY 331
           +      L    F+   N +
Sbjct: 387 LRDVIKQLKPMRFERPENNF 406


>gi|154498138|ref|ZP_02036516.1| hypothetical protein BACCAP_02119 [Bacteroides capillosus ATCC
           29799]
 gi|150273128|gb|EDN00285.1| hypothetical protein BACCAP_02119 [Bacteroides capillosus ATCC
           29799]
          Length = 321

 Score =  212 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 66/309 (21%), Positives = 123/309 (39%), Gaps = 22/309 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   ++ ++   RLDRW     P +     QK +R  +V+V+ K    + R+Q G  ++
Sbjct: 1   MKEFTIKKNDAGQRLDRWLGKTLPLLPAPLAQKYIRLKRVKVNGKGSARDYRLQEGDFLQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---- 122
           +       +    E   L             +  ++YED  + + +K  GI V       
Sbjct: 61  LYINDEFFDTPTLENAFLSVFKP--------RLNIVYEDENLLLVDKQPGIVVHPDETER 112

Query: 123 -SGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            + +  HI  +L    +    K     P L +R+D+ T GI++ A+     + + +  + 
Sbjct: 113 VNTLITHIQAYLYQKKEWSPYKENSFAPALCNRIDRNTGGIVIAAKNAETLRIMNQKIKD 172

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I K Y ++V G     +  +  +L+K        V V          A++ +K +   
Sbjct: 173 REIDKFYLAVVLGKMNPPEGRLEGFLVKDE--VKKQVTVYHHPVPDGRTALTVYKTLK-V 229

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +E +  TGRTHQ+R      G P++GD KY    + N      N   L++  + 
Sbjct: 230 GNGLSLVECELLTGRTHQIRAQFADAGHPLLGDGKYG-RERDNRRFGRTNGQALYSYKLT 288

Query: 297 LPHPEGGRL 305
              P    +
Sbjct: 289 FSFPTDAGI 297


>gi|260682684|ref|YP_003213969.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260686282|ref|YP_003217415.1| putative pseudouridylate synthase [Clostridium difficile R20291]
 gi|260208847|emb|CBA61782.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260212298|emb|CBE03063.1| putative pseudouridylate synthase [Clostridium difficile R20291]
          Length = 281

 Score =  212 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 71/309 (22%), Positives = 132/309 (42%), Gaps = 32/309 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           M L     +   + +  +L K+ +   V V+    K + ++ SG ++ +       N   
Sbjct: 1   MTLKEVLLDKL-NFSVRSLSKMKKEKSVLVNGVYKKPSLKVYSGDLIEVKIDEEKAN--- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWV 137
                             L   ++Y+D  I + NKP  + V    S     I   +  ++
Sbjct: 57  -------------FEPQDLNLQIIYDDFDIIMVNKPPFMVVHPTKSHYDKTIANGISYYI 103

Query: 138 DSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D++ +  K R  +RLD  TSG+++VA+   A   L+ +    +++K Y ++V GI K  +
Sbjct: 104 DNQKENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTAMSENKVEKKYITVVDGIIKENE 163

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   + + +      +      ++    +++H+KVI+   +    LE+   TGRTHQ+
Sbjct: 164 GTIDEPIYRPTEDSIKRII-----DERGQSSVTHYKVIERL-ENATVLEVSLETGRTHQI 217

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAH 314
           RVH  H+G  I+GD  Y           + N+  LHA  ++   P    +L+  A +P  
Sbjct: 218 RVHMAHIGHGIIGDELYGY-----VDEELINRQALHAYKLEFEQPRTKEKLKFKADIPED 272

Query: 315 MVKTWDSLG 323
           M +    L 
Sbjct: 273 MKELISKLR 281


>gi|302561137|ref|ZP_07313479.1| RluA family RNA pseudouridine synthase [Streptomyces griseoflavus
           Tu4000]
 gi|302478755|gb|EFL41848.1| RluA family RNA pseudouridine synthase [Streptomyces griseoflavus
           Tu4000]
          Length = 314

 Score =  212 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 135/327 (41%), Gaps = 18/327 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVTVDGSVVGKSERVS 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   I+ E       + +    D +  I+       +      G +V
Sbjct: 60  GGAWLEVEMPGAPAPVRIVAEPV---EGMEIVHDDDDVVVIVKPVGVAAHPSPGWTGPTV 116

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GG   A +             ++  + HRLD  TSG++VVA++  A   L   F+ R +
Sbjct: 117 IGGLAAAGYRIST-----SGAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQFKERTV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G P      I   + +  H   DY   V         +++H+ +I+ F + 
Sbjct: 172 DKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAE---GKPSVTHYDLIEAF-RA 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA  +   H
Sbjct: 226 ASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADPTLAKRLHL-TRQWLHAVRLGFEH 284

Query: 300 PEGGRL-QITAPLPAHMVKTWDSLGFK 325
           P  G+  + +   P  + K  D +  +
Sbjct: 285 PGDGQWAEFSCDYPEDLQKALDQVREE 311


>gi|229171950|ref|ZP_04299515.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           MM3]
 gi|228611293|gb|EEK68550.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           MM3]
          Length = 292

 Score =  212 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 67/317 (21%), Positives = 136/317 (42%), Gaps = 39/317 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I  R G + V+ +     +++Q+G+ +R+   
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFRGGAIEVNNQHASVRHQLQAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  + ++ I                 ++YED  + V NK A +S           +
Sbjct: 63  VEERSEGMIKEDI--------------PLCIVYEDDAVLVINKEANMSTIPSREHPAGSV 108

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 109 A---NALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+V+D    K   + 
Sbjct: 166 AIVHGEMIEREGTIDAPIGRKSDSIIERTVC-----ENGQRAVTHFRVMDSVNHK-THVS 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD  Y           +  +  LH+  +   HP    
Sbjct: 220 LELETGRTHQIRVHMAHIGHPLLGDDLYGGRRD------VIKRQALHSTSLTFYHPILEK 273

Query: 304 RLQITAPLPAHMVKTWD 320
            +  T  +P+ M +   
Sbjct: 274 EMSFTTTIPSDMEEVLR 290


>gi|228944912|ref|ZP_04107274.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar monterrey BGSC 4AJ1]
 gi|229120827|ref|ZP_04250069.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           95/8201]
 gi|228662487|gb|EEL18085.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           95/8201]
 gi|228814780|gb|EEM61039.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar monterrey BGSC 4AJ1]
          Length = 292

 Score =  212 bits (539), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 132/315 (41%), Gaps = 33/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI   
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + V NK A +S            
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPSGSV 108

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HF+VID  A     + ++ 
Sbjct: 169 HGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVSLEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP     + 
Sbjct: 223 DTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWDS 321
             A +P+ M +    
Sbjct: 277 FAAMIPSDMQEVLRQ 291


>gi|238810211|dbj|BAH70001.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 315

 Score =  212 bits (539), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 67/310 (21%), Positives = 136/310 (43%), Gaps = 41/310 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDK--KRVKFNNRIQSGQVVRIPPVINALNH 76
            R+D++       ++  ++++++  G V ++   +  K N  ++ GQ + I      +  
Sbjct: 18  ERIDKYI-GQNSELSRNDIKELIEQGAVYINDNVQVHKCNYIVREGQEITI------VKL 70

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
           + KE KI   ++ L          + YED  + + NKP+ + V    G      ++G L 
Sbjct: 71  LNKEIKIEPVNIPLD---------IKYEDDDLVIINKPSNLVVHPSPGHYNDTLVNGLLY 121

Query: 135 SWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            + ++        +P + HR+D++TSG+L++A+       LT+  +   I++ Y ++V G
Sbjct: 122 HFKNNLSNENGLLRPGIVHRIDKDTSGLLIIAKNNKMHNSLTDMLKRHEIERSYLAIVRG 181

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQ 246
           + +N    I   + + + +    + V     K    AI+   ++  F    +    +  +
Sbjct: 182 LIENPLTKINLPIARNT-VDRKMMSV----HKEGKEAITFVHLLKHFYLDKEPMSLVRCE 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
             TGRTHQ+RVH  ++  P+ GD  Y  +           +L  HA  +   HP     +
Sbjct: 237 LKTGRTHQIRVHLSYIKHPVYGDPTYGKSV-----DEFNQRL--HAYKLKFIHPLTKKEI 289

Query: 306 QITAPLPAHM 315
            + AP+P   
Sbjct: 290 CVYAPVPKEF 299


>gi|295702869|ref|YP_003595944.1| pseudouridine synthase [Bacillus megaterium DSM 319]
 gi|294800528|gb|ADF37594.1| pseudouridine synthase, RluA family [Bacillus megaterium DSM 319]
          Length = 302

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 136/322 (42%), Gaps = 36/322 (11%)

Query: 4   MTYVQYV--VVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  V  +   V++  E + +  + K H     +  +++   R G + V+ K       +Q
Sbjct: 1   MKQVFTLSWTVDHSFEGVAVREFLKEHDISKASLTDIK--FRGGAIEVNGKHATVRYILQ 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  +++                     + +     +   ++YED  I V NK   +   
Sbjct: 59  KGDEIKV--------------AFPPEKASESLLPKAIPLDIVYEDEYILVLNKQPNMPSI 104

Query: 121 GGS-GIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                + + +   +  + +         L +RLD++TSG+L+VA+ R      +++ +  
Sbjct: 105 PSREHLTWSLSNAVLYYYEKNNINSTVHLVNRLDRDTSGLLIVAKHRHVHYLFSKAQKEH 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I+++Y + V G    K E I   + +K     +   + ++  +   +AI+H+  +  ++
Sbjct: 165 EIKRVYRAFVHGKLVGK-ETIEAPIGRK-----ESSIIEREVREDGQFAITHYTALRQYS 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F  + +   TGRTHQ+RVH  + G P++GD  Y        T+ + ++  LH+  +  
Sbjct: 219 S-FTEVALSLETGRTHQIRVHMAYKGYPLLGDTLYGG------TNHLISRQALHSYELTF 271

Query: 298 PHPE-GGRLQITAPLPAHMVKT 318
            HP     L  TAPLP  M K 
Sbjct: 272 FHPFLQKTLSFTAPLPPDMQKL 293


>gi|227499268|ref|ZP_03929380.1| pseudouridylate synthase [Anaerococcus tetradius ATCC 35098]
 gi|227218677|gb|EEI83908.1| pseudouridylate synthase [Anaerococcus tetradius ATCC 35098]
          Length = 305

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 66/323 (20%), Positives = 137/323 (42%), Gaps = 38/323 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D++  +    I    ++  ++   ++V+ K VK + ++  G  + I   + A+  I 
Sbjct: 9   IRIDKFISDELEEIAREKIKDFIKDKLIKVNNKAVKPSFKLSEGDEIFIDDSLFAIAEIK 68

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E                +   ++YE+    V +K + + V     I       + + + 
Sbjct: 69  AEN---------------IDLKVVYENEDYAVIDKDSDLIVHPAGKIVTG--TLVNALLY 111

Query: 139 SKGQ----------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             G           +P + HRLD++T+G++++ +  A+ ++  + F  R++ K Y+++V+
Sbjct: 112 KYGYDGLSHIGGEDRPGIVHRLDKDTTGLILITKNNASYKYFKKMFETRKVDKYYYAIVF 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G    K   I  ++ +  +                  A+SH++V+      F  L ++  
Sbjct: 172 GNFDKKTGTIETFMDRDPNNRRKMAVR-----PAGRRAVSHYEVL-REVDGFSLLRIKIE 225

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT 308
           TGRTHQ+RVH  H+  P++GD  Y  N K  F     +   LH   +     +G  +   
Sbjct: 226 TGRTHQIRVHMTHINHPLLGDPVYG-NVKHKFN---LSHQLLHCGKIGFKDMDGSYVTYE 281

Query: 309 APLPAHMVKTWDSLGFKYDRNLY 331
           A      +K    LG   D++++
Sbjct: 282 ASPHEEFLKYQKILGLG-DKDVF 303


>gi|149182747|ref|ZP_01861212.1| hypothetical protein BSG1_15258 [Bacillus sp. SG-1]
 gi|148849561|gb|EDL63746.1| hypothetical protein BSG1_15258 [Bacillus sp. SG-1]
          Length = 294

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 73/317 (23%), Positives = 135/317 (42%), Gaps = 39/317 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++  DE  + +  +   H  HI+   L  I    G++ VD + V     +Q G  + +  
Sbjct: 9   IITKDESGVEIKTFLSEH--HISKRMLTDIKFAGGKISVDGQEVTVRYVLQEGNHLTVIF 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                +  +K + IL                ++YED  + V NKP+ +S         H 
Sbjct: 67  PPEPKSPTLKPEDIL--------------LHIIYEDKDLLVINKPSNMSTIPSR---EHP 109

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG L + V    ++        +  RLD++TSG++++A+ R     ++   + R I++ Y
Sbjct: 110 DGSLANAVYGYYRRREIDSAIHIVTRLDRDTSGLVLIAKHRHIHHLMSLQQKKREIKRSY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +   G+   ++  I   + +K     +   + ++       A++H+KVI  +   F  +
Sbjct: 170 EAFAEGLFSVREGKINEPIGRK-----ETSIIEREVRSDGKTAVTHYKVIGQYG-GFAHI 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +   TGRTHQ+RVH  + G P++GD  Y  + +        ++  LH   +   HP  G
Sbjct: 224 GLVLETGRTHQIRVHMSYKGHPLLGDSLYGGSREK------IDRQALHCHSLSFFHPTTG 277

Query: 304 R-LQITAPLPAHMVKTW 319
             L    PLP  M +  
Sbjct: 278 EPLHFHVPLPDDMDRLL 294


>gi|229101887|ref|ZP_04232601.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-28]
 gi|228681470|gb|EEL35633.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-28]
          Length = 292

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 66/313 (21%), Positives = 135/313 (43%), Gaps = 33/313 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQYASVRHQLQAGEQLRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHI 129
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPEGSV 108

Query: 130 DGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L S+ D +       +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSYYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HF+VI   +QK   + ++ 
Sbjct: 169 HGEMIKREGTIDAPIGRKSDSIIERTVC-----EDGQRAVTHFRVIHSSSQK-THVSLEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y              +  LH+  +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAHIGHPLLGDDLYGGRRDE------MKRQALHSTSLAFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTW 319
               +P+ M +  
Sbjct: 277 FATTIPSDMQQLL 289


>gi|161833681|ref|YP_001597877.1| ribosomal large subunit pseudouridine synthase D [Candidatus Sulcia
           muelleri GWSS]
 gi|152206171|gb|ABS30481.1| ribosomal large subunit pseudouridine synthase D [Candidatus Sulcia
           muelleri GWSS]
          Length = 337

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 86/318 (27%), Positives = 142/318 (44%), Gaps = 31/318 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D + K      N   +QKI+  G V V+   +K N  ++   V+ I       N I 
Sbjct: 37  IRIDTYLKFILHKKNRNFIQKIIEKGFVYVNNILIKKNYIVKINDVIEIFLPEGKKNII- 95

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKSW 136
                           + LK  + YED  + + NK +G+ V  G G      I+G    +
Sbjct: 96  ---------------PENLKINIFYEDEYVIIINKQSGLVVHPGKGNESMTLINGLHFYF 140

Query: 137 VDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +  K      P L HR+D+ TSG+++VA+ +   + + + F +  I++ Y +LVWG  KN
Sbjct: 141 LKKKNIYNKIPILVHRIDKGTSGLILVAKDKNILEKIYKQFYINHIKRKYITLVWGYIKN 200

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K  I    + +S     Y++V   N     ++I+H+KV++ F +    L+    TGRTH
Sbjct: 201 NKGTII-CNIGRSLKNRIYMNVF-PNGIYGKFSITHYKVLERF-KYVTLLKCTLETGRTH 257

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPEGGRLQ- 306
           Q+RVH  ++G PI+ D  Y  N        I+          LHA Y++  HP   +   
Sbjct: 258 QIRVHLKYIGHPILNDKDYGGNHTFKEKKNIKKLFINMKYQALHAYYIEYIHPIYRKKNY 317

Query: 307 ITAPLPAHMVKTWDSLGF 324
              P+P  +     +L  
Sbjct: 318 FICPIPDRIKFLIKNLRL 335


>gi|317055012|ref|YP_004103479.1| RluA family pseudouridine synthase [Ruminococcus albus 7]
 gi|315447281|gb|ADU20845.1| pseudouridine synthase, RluA family [Ruminococcus albus 7]
          Length = 321

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 66/302 (21%), Positives = 136/302 (45%), Gaps = 23/302 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +  ++   R+D++     P +    + K +R  +++++ KR + + ++  G  V+
Sbjct: 1   MREFSINKNDAGQRMDKFLTKAVPALPKNLMYKYIRLKRIKLNGKRCEISTKLSEGDSVQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
           +       +    E++  D +         ++  ++YED  I + +KP G+ V    SG 
Sbjct: 61  LYIN----DEFFPEKR--DEAHRFLNSPKDIE--IVYEDENIILCDKPCGLVVHEDESGE 112

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           A  +   +  ++  KG+          P L +R+D+ TSGI++ A+   + + L +  + 
Sbjct: 113 ADTLIDRVLHYLYDKGEYDPDTENSFTPALCNRIDRNTSGIVICAKNAESLRVLNQKVKD 172

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-DC 235
           R ++K+Y  +  GIP  K   +  +  +        V V  ++  G+   I+ +KV+ + 
Sbjct: 173 RELEKLYLCVTVGIPNKKSAELKAFHRRDEKT--KVVRVEDKSFPGSKTMITRYKVLAEN 230

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                  LE+   TGRTHQ+R H  H+G P++GD KY +N              L +  +
Sbjct: 231 KQSGLALLEVDLVTGRTHQIRAHLAHIGYPLLGDGKYGSNKINRAL--GVKTQALCSYKL 288

Query: 296 DL 297
             
Sbjct: 289 TF 290


>gi|94502329|ref|ZP_01308802.1| ribosomal large subunit pseudouridine synthase D [Candidatus Sulcia
           muelleri str. Hc (Homalodisca coagulata)]
 gi|94451116|gb|EAT14068.1| ribosomal large subunit pseudouridine synthase D [Candidatus Sulcia
           muelleri str. Hc (Homalodisca coagulata)]
          Length = 338

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 86/318 (27%), Positives = 142/318 (44%), Gaps = 31/318 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D + K      N   +QKI+  G V V+   +K N  ++   V+ I       N I 
Sbjct: 38  IRIDTYLKFILHKKNRNFIQKIIEKGFVYVNNILIKKNYIVKINDVIEIFLPEGKKNII- 96

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKSW 136
                           + LK  + YED  + + NK +G+ V  G G      I+G    +
Sbjct: 97  ---------------PENLKINIFYEDEYVIIINKQSGLVVHPGKGNESMTLINGLHFYF 141

Query: 137 VDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +  K      P L HR+D+ TSG+++VA+ +   + + + F +  I++ Y +LVWG  KN
Sbjct: 142 LKKKNIYNKIPILVHRIDKGTSGLILVAKDKNILEKIYKQFYINHIKRKYITLVWGYIKN 201

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K  I    + +S     Y++V   N     ++I+H+KV++ F +    L+    TGRTH
Sbjct: 202 NKGTII-CNIGRSLKNRIYMNVF-PNGIYGKFSITHYKVLERF-KYVTLLKCTLETGRTH 258

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPEGGRLQ- 306
           Q+RVH  ++G PI+ D  Y  N        I+          LHA Y++  HP   +   
Sbjct: 259 QIRVHLKYIGHPILNDKDYGGNHTFKEKKNIKKLFINMKYQALHAYYIEYIHPIYRKKNY 318

Query: 307 ITAPLPAHMVKTWDSLGF 324
              P+P  +     +L  
Sbjct: 319 FICPIPDRIKFLIKNLRL 336


>gi|302382659|ref|YP_003818482.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
 gi|302193287|gb|ADL00859.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
          Length = 248

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 83/242 (34%), Positives = 133/242 (54%), Gaps = 4/242 (1%)

Query: 84  LDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           L + V+LT+     ++S +++ED+ +  F KPAG+S QGG   A+ +D  L ++  S G+
Sbjct: 3   LRTPVSLTEDEIAAVRSWVIHEDASVIAFAKPAGLSSQGGRIQAHTLDDLLWAFARSNGK 62

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +P L HRLD++TSG+++ A+T+ AA  L ++ +  R+ K Y +LV   P+  +  I   L
Sbjct: 63  RPELVHRLDRDTSGVILAAKTKPAASFLGKAIQAHRLTKTYLALVSAAPEPPQGDINVPL 122

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           +++      Y+ V   + KGA  + S ++ +         +E+QP TGR HQLRVH  H+
Sbjct: 123 VRQEIGRESYMRVAAFDTKGAQGSRSRYRTLASSDDGA-LVELQPFTGRMHQLRVHMAHI 181

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G P++GD +Y         +    +L LHA  +  PHPEGG   +TA LP        SL
Sbjct: 182 GRPLIGDVRYGGALTAGGRA--APRLMLHAVSLTFPHPEGGERTVTAGLPEDFSALAASL 239

Query: 323 GF 324
             
Sbjct: 240 DL 241


>gi|218661228|ref|ZP_03517158.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli IE4771]
          Length = 260

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 70/258 (27%), Positives = 124/258 (48%), Gaps = 28/258 (10%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG-----QKPR 145
             + +   + +ED  I V +KPAG+ V  G G      ++  +    D+       ++P 
Sbjct: 3   QGEDIPLDIFHEDDDIIVISKPAGLVVHPGPGNWTGTLVNALIYHCGDTLSGIGGVRRPG 62

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRR----IQKIYWSLVWGIPKNKKECIANW 201
           + HRLD++T+G++VVA+   A +HL+  F        +++ Y ++VWG P++    +   
Sbjct: 63  IVHRLDKDTTGVMVVAKNDVAHRHLSLQFADHGRTMPLERAYQAIVWGRPRSLTGTVDAP 122

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQL 255
           L + +        V + +   A+ AI+H++VI+ F +          +E +  TGRTHQ+
Sbjct: 123 LGRATG-DRTRRAVKRPDSHDADEAITHYEVIERFHETPDATALAALVECRLETGRTHQI 181

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NKLYLHARYMDLPHPEGGR-L 305
           RVH  H+G P++GD  Y A F+       +         ++  LHA  +   HP  G  +
Sbjct: 182 RVHMAHIGHPLLGDTVYGAGFRTKANLLPEEIRKVVNGFDRQALHAFMLQFEHPRSGDLM 241

Query: 306 QITAPLPAHMVKTWDSLG 323
               PLP  MV+  ++L 
Sbjct: 242 HFEVPLPEDMVELVEALR 259


>gi|49184141|ref|YP_027393.1| pseudouridine synthetase [Bacillus anthracis str. Sterne]
 gi|167636101|ref|ZP_02394406.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|167641221|ref|ZP_02399475.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|170686706|ref|ZP_02877926.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|177654397|ref|ZP_02936294.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|227815949|ref|YP_002815958.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|229600901|ref|YP_002865732.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|254682628|ref|ZP_05146489.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. CNEVA-9066]
 gi|254725424|ref|ZP_05187206.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. A1055]
 gi|254734046|ref|ZP_05191760.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Western North America USA6153]
 gi|254740807|ref|ZP_05198496.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Kruger B]
 gi|254753650|ref|ZP_05205686.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Vollum]
 gi|254758747|ref|ZP_05210774.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Australia 94]
 gi|270000595|ref|YP_003329033.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. Ames]
 gi|291612207|ref|YP_003541021.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. 'Ames Ancestor']
 gi|49178068|gb|AAT53444.1| pseudouridine synthetase [Bacillus anthracis str. Sterne]
 gi|167510862|gb|EDR86254.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|167528455|gb|EDR91220.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|170669229|gb|EDT19972.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|172080681|gb|EDT65763.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|224552858|gb|ACN55068.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. 'Ames Ancestor']
 gi|227004816|gb|ACP14559.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|229265309|gb|ACQ46946.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|269850244|gb|ACZ49984.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. Ames]
          Length = 297

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 69/318 (21%), Positives = 136/318 (42%), Gaps = 39/318 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI   
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +   +  +               ++ +   ++YED  + V NK A +S         H  
Sbjct: 68  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSR---EHPS 110

Query: 131 GFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + + + S   K        +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 111 GSVANALLSHYDKQYLPSTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID  A     + 
Sbjct: 171 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVS 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 225 LELDTGRTHQIRVHLAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 278

Query: 304 RLQITAPLPAHMVKTWDS 321
            +   A +P+ M +    
Sbjct: 279 EMSFAAMIPSDMQEVLRQ 296


>gi|322387849|ref|ZP_08061457.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           infantis ATCC 700779]
 gi|321141351|gb|EFX36848.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           infantis ATCC 700779]
          Length = 299

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 71/305 (23%), Positives = 129/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L KI  R G +RV+         +  G  V I               
Sbjct: 16  FLKKH--EVSKGLLAKIKFRGGDIRVNGHPQNATYLLDIGDEVVI--------------D 59

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
           I       T  +      +L+ED    + NKP G++       +  I  F+K +    + 
Sbjct: 60  IPPEEGFETLEAIDYPLDILFEDDHFLIINKPFGVASIPSVNHSNTIANFIKGYYVKQNY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G      +  I
Sbjct: 120 ENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKAIEKRYYALVKGDGHLEPQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      +   + ++  KG  YA + ++++  +      ++++ HTGRTHQ+RVH
Sbjct: 180 IAPIARD-----EDSIITRRVAKGGKYAHTSYQIVASYGNIH-LVDIRLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH  Y+   HP     L++  PLP     
Sbjct: 234 FSHIGFPLLGDDLYGGSLE-----HGIQRQALHCHYLSFYHPFLEEQLELECPLPDDFDT 288

Query: 318 TWDSL 322
               L
Sbjct: 289 LITQL 293


>gi|158320206|ref|YP_001512713.1| RluA family pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158140405|gb|ABW18717.1| pseudouridine synthase, RluA family [Alkaliphilus oremlandii
           OhILAs]
          Length = 305

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 82/314 (26%), Positives = 147/314 (46%), Gaps = 32/314 (10%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           END+    L +  KN     +   L ++ R   + V+ + +K++  I +G  ++I  + +
Sbjct: 17  ENDDAGKELKKILKNKL-DFSSRLLARVKRGKTIFVNGEYLKYHETINAGDEIKI-VMED 74

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDG 131
             NH   +    ++               +YED  + + NK  GI      S   + I  
Sbjct: 75  EPNHFTLQDVPFEA---------------VYEDVDLILVNKEPGIVTHPTKSHPDWTIAN 119

Query: 132 FLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               ++ SKG   K R  +RLD +TSG+L++A+   A   L+E  +  RI+K Y + VWG
Sbjct: 120 GAALYLKSKGIDCKVRFVNRLDMDTSGLLIIAKNAYAHHVLSEQMQEDRIEKKYIAFVWG 179

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           + K  +  I   + + +      V      ++    +I+ FKV++ + +    +E++  T
Sbjct: 180 VIKEDEGRIEAPIYRTTMDSIKRVV-----DERGQESITEFKVLERY-KNATMVEVKLLT 233

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  H+G P++GD  Y         + + ++  LHA Y+    P   R +++ 
Sbjct: 234 GRTHQIRVHMEHLGHPLIGDTLYGKE-----DAELIDRQALHAEYLRFWQPRFKRAIEVK 288

Query: 309 APLPAHMVKTWDSL 322
           A LPA ++   D L
Sbjct: 289 ADLPADLLSLRDKL 302


>gi|311029802|ref|ZP_07707892.1| pseudouridine synthase, RluA family protein [Bacillus sp. m3-13]
          Length = 302

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 129/316 (40%), Gaps = 32/316 (10%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRI-PPV 70
           E  +E   L  + K     I+   L  I    G + V+   V     +  G  + +  P 
Sbjct: 11  EAQDEGKLLREFLKER--QISKAALIDIKFNGGALHVNGSAVTVRYILHEGDTIEVLFPK 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HI 129
                 ++ E+  LD               +++ED  + V NKPAG++        +  +
Sbjct: 69  EEPSEDLVAEEIPLD---------------IVFEDEYVLVVNKPAGMASIPSREHRHGTL 113

Query: 130 DGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              +  +   KG      +  RLD++TSG++++A+ R A    +   +   +++ Y +LV
Sbjct: 114 ANAVLGYYHLKGICATIHIVTRLDRDTSGLMLIAKHRHAHHLFSLQQKEFGVKRRYEALV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQ 246
            G         +      + IG     ++++  +     A++H++V+      +  + + 
Sbjct: 174 HGEMTGDAG--SACGKVDAPIGRKDSSIIEREVRSDGQRAVTHYEVL-RVGAGWSHVTLH 230

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  H+G P++GD  Y  +  G  +     +  LH+  +   HP   + +
Sbjct: 231 LETGRTHQIRVHMAHLGHPLLGDTLYGGSMFGGMS-----RQALHSCELRFFHPVEEQDM 285

Query: 306 QITAPLPAHMVKTWDS 321
                LP  M +  + 
Sbjct: 286 TFRCELPEDMKRVLEE 301


>gi|315648999|ref|ZP_07902093.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
 gi|315275680|gb|EFU39034.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
          Length = 358

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 86/345 (24%), Positives = 141/345 (40%), Gaps = 59/345 (17%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV   E+ M L +        ++   + ++ L    + ++  RV  + ++Q+G ++ I  
Sbjct: 11  VVSEREDGMLL-KTIMQKRMGVSRKLISRLKLTEQGIMLNGTRVYISAKVQTGDIIEIRM 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                + ++ +   LD               +LYED  + V NKPAGI V    G     
Sbjct: 70  EQERSDDMLPQPMELD---------------ILYEDGHLLVLNKPAGIIVHPTKGHYTDT 114

Query: 128 HIDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +G +  W++     + R  HRLDQETSG+LVVA+     QH++E      + K Y +L
Sbjct: 115 LANGVVHYWLEQGWNYRFRAVHRLDQETSGVLVVAKNPYVHQHVSEQMIAGTVDKRYIAL 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G P ++   I   + +        +        G   +++ +KV + F +    +E++
Sbjct: 175 VHGTPASRSGDIEGPIDRDPLEPHRRIV-----TPGGYPSLTRYKVCETF-KSASMVELK 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-------------------------- 280
             TGRTHQ+RVH L +GCP++GD  Y                                  
Sbjct: 229 LETGRTHQIRVHMLSIGCPLIGDRMYRHPVYDTRVQRNDQVQTIAPEAALNGVVPRTELE 288

Query: 281 ------TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
                       +  LHA  + L HP  GR +  +APLP  M   
Sbjct: 289 AASIQELDSSIGRQALHAASLTLVHPIEGRTMVFSAPLPEDMKSL 333


>gi|85859994|ref|YP_462196.1| ribosomal large subunit pseudouridine synthase D [Syntrophus
           aciditrophicus SB]
 gi|85723085|gb|ABC78028.1| ribosomal large subunit pseudouridine synthase D [Syntrophus
           aciditrophicus SB]
          Length = 324

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 80/297 (26%), Positives = 141/297 (47%), Gaps = 35/297 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHIIKEQK 82
           +    YP  +   ++K+LR G +R + K V   ++++ +G VV I               
Sbjct: 49  FLAEQYPDSSRTRIKKLLRHGNIRCNNKPVTLHSHKLSAGDVVEINTYGG---------- 98

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-- 140
                         L   +L+ED  +    KP GI+     G A       ++  +    
Sbjct: 99  --------IAAKAGLPFPVLFEDQHVIAVEKPVGIATFSADGSASVQWIVAQALKEHSRG 150

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                  HRLD+E SG+L+ A+++ A  H+ E +  +  +K Y++LV G P++    I +
Sbjct: 151 KIHAFAVHRLDKEVSGVLLFAKSKMAMDHIKEKW--KEAEKRYYALVEGKPESPDGTIES 208

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           WL++        VH  +++ K A ++++H+++I    Q +  L+++  TGR +Q+RVH  
Sbjct: 209 WLVEDH---AQKVHSTRESSK-AKFSVTHYRIIKQVNQ-YTLLDVKLQTGRKNQIRVHLS 263

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
            +GCPI GD KY A       +    ++ LHA Y+  PHP  G R+ I +P+P   +
Sbjct: 264 DIGCPIAGDRKYGA------AADFVRRIRLHAYYLSFPHPVTGERISIESPMPEGFL 314


>gi|229095789|ref|ZP_04226768.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-29]
 gi|228687622|gb|EEL41521.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-29]
          Length = 292

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 67/313 (21%), Positives = 135/313 (43%), Gaps = 33/313 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQYASVRHQLQAGEQLRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHI 129
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPEGSV 108

Query: 130 DGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L S+ D +       +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSYYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HF+VI   +QK   + ++ 
Sbjct: 169 HGEMIKREGTIDAPIGRKSDSIIERTVC-----EDGQRAVTHFRVIHSSSQK-THVSLEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  HMG P++GD  Y              +  LH+  +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAHMGHPLLGDDLYGGRRDE------MKRQALHSTSLAFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTW 319
               +P+ M +  
Sbjct: 277 FATTIPSDMQQLL 289


>gi|322391936|ref|ZP_08065400.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           peroris ATCC 700780]
 gi|321145162|gb|EFX40559.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           peroris ATCC 700780]
          Length = 299

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 70/305 (22%), Positives = 129/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L KI  R G +RV+ +       +  G  V I               
Sbjct: 16  FLKKH--EVSKGLLAKIKFRGGDIRVNGRPQNATYLLDVGDEVVI--------------D 59

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
           I       T  +      +L+ED    + NKP G++       +  I  F+K +    + 
Sbjct: 60  IPPEEGFETLEAIDYPLDILFEDDHFLIINKPFGVASIPSVNHSNTIANFIKGYYVKQNY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++L  G      +  I
Sbjct: 120 ENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKAIEKHYYALFKGDGHLEPQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      +   + ++  KG  YA + ++++  +      ++++ HTGRTHQ+RVH
Sbjct: 180 IAPIARD-----EDSIITRRVAKGGKYAHTSYQIVASYGNIH-LVDIRLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH  Y+   HP     L++  PLP     
Sbjct: 234 FSHIGFPLLGDDLYGGSLE-----HGIERQALHCHYLSFYHPFLEEQLELECPLPDDFDT 288

Query: 318 TWDSL 322
               L
Sbjct: 289 LITQL 293


>gi|302791942|ref|XP_002977737.1| hypothetical protein SELMODRAFT_107344 [Selaginella moellendorffii]
 gi|300154440|gb|EFJ21075.1| hypothetical protein SELMODRAFT_107344 [Selaginella moellendorffii]
          Length = 421

 Score =  211 bits (537), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 83/391 (21%), Positives = 138/391 (35%), Gaps = 93/391 (23%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            +  +  + R+D W     PH +   +Q  +R G   V+ K + K +  +  G  V    
Sbjct: 40  TIPEETVSTRIDVWLSGQLPHTSRARVQDSIRKGLALVNGKTITKPSFPVIGGDEVVCTL 99

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSG 124
              A                L    + ++  +++ED  + V NK A + V       G  
Sbjct: 100 CGAA---------------PLEATPERIQLDIVHEDDHVIVVNKAADMVVHPAPGHYGGT 144

Query: 125 IAY---HIDGF----------------------LKSWVDSKGQK---------------- 143
           +     H  G                       L    D   +K                
Sbjct: 145 LVNAILHHCGLPAVEVSLPVMMDEESDDDEGEELSENGDQDYEKDEVEVHKARGETPSRF 204

Query: 144 --------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                   P + HRLD+ TSG++VVA+   +   L+E F+ R++++ Y SL  G P    
Sbjct: 205 RGPRPVIRPGIVHRLDKGTSGLIVVAKDEQSQLSLSEQFKSRKVRRTYLSLTCGTPSTTS 264

Query: 196 ECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTH 253
             I   +L+               + + A +A S +KV+D  A      ++ +  TGRTH
Sbjct: 265 GRIEAEILRDPRDRKRMTTSDTVPSARNARFAASRYKVLDVLANGGVALVQWKLETGRTH 324

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------------------NKLYLHAR 293
           Q+RVHA +MG P++GD  Y        ++ +                      +  LHA 
Sbjct: 325 QIRVHARYMGFPLLGDDVYGGTVGKANSTLLSALCATKTNSRKKIHEFTSDIRRPCLHAY 384

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            +   HP   + +  T P P    + W  L 
Sbjct: 385 SLGFEHPATEKYVHFTCPPPEDFEEAWTRLR 415


>gi|319777728|ref|YP_004137379.1| pseudouridine synthase [Mycoplasma fermentans M64]
 gi|318038803|gb|ADV35002.1| Pseudouridine synthase [Mycoplasma fermentans M64]
          Length = 307

 Score =  211 bits (537), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 67/310 (21%), Positives = 136/310 (43%), Gaps = 41/310 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDK--KRVKFNNRIQSGQVVRIPPVINALNH 76
            R+D++       ++  ++++++  G V ++   +  K N  ++ GQ + I      +  
Sbjct: 10  ERIDKYI-GQNSELSRNDIKELIEQGAVYINDNVQVHKCNYIVREGQEITI------VKL 62

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
           + KE KI   ++ L          + YED  + + NKP+ + V    G      ++G L 
Sbjct: 63  LNKEIKIEPVNIPLD---------IKYEDDDLVIINKPSNLVVHPSPGHYNDTLVNGLLY 113

Query: 135 SWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            + ++        +P + HR+D++TSG+L++A+       LT+  +   I++ Y ++V G
Sbjct: 114 HFKNNLSNENGLLRPGIVHRIDKDTSGLLIIAKNNKMHNSLTDMLKRHEIERSYLAIVRG 173

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQ 246
           + +N    I   + + + +    + V     K    AI+   ++  F    +    +  +
Sbjct: 174 LIENPLTKINLPIARNT-VDRKMMSV----HKEGKEAITFVHLLKHFYLDKEPMSLVRCE 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
             TGRTHQ+RVH  ++  P+ GD  Y  +           +L  HA  +   HP     +
Sbjct: 229 LKTGRTHQIRVHLSYIKHPVYGDPTYGKSV-----DEFNQRL--HAYKLKFIHPLTKKEI 281

Query: 306 QITAPLPAHM 315
            + AP+P   
Sbjct: 282 CVYAPVPKEF 291


>gi|228932580|ref|ZP_04095460.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar andalousiensis BGSC 4AW1]
 gi|228827098|gb|EEM72852.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar andalousiensis BGSC 4AW1]
          Length = 292

 Score =  211 bits (537), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 133/316 (42%), Gaps = 33/316 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI   
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + V NK A +S            
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPSGSV 108

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HF+VID  A     + ++ 
Sbjct: 169 HGEMVEREGTIGAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVSLEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP     + 
Sbjct: 223 DTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWDSL 322
             A +P+ M +    +
Sbjct: 277 FAAMIPSDMQEVLRQI 292


>gi|225620833|ref|YP_002722091.1| Pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
 gi|225215653|gb|ACN84387.1| Pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
          Length = 329

 Score =  211 bits (537), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 139/320 (43%), Gaps = 34/320 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  ++  D+   RLD +      +I    ++  L S  + V+    K +  ++    + I
Sbjct: 31  KSFIITEDDIGKRLDTFISEKL-NITRSQVKNYLTS--IIVNDAEKKLSYSLKLNDNIII 87

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ--GGSGI 125
                  ++I KE+    + +      + +   +LYED  + V NKPAG+SV        
Sbjct: 88  D-----SDNIFKEKTDTANPI-----PENIDLDILYEDKYLLVINKPAGMSVHCSPSEMS 137

Query: 126 AYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D       ++  + HRLD++TSG++++ +       + E F+ R I+K
Sbjct: 138 GTLVNALLYKIKDFDFVGNKERAGIIHRLDKDTSGLMIIGKNANIVSSIQEQFKNRTIKK 197

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKF 240
           IY ++V G+ K       N++     IG  +V+  K   +     A++H KV+  F    
Sbjct: 198 IYHAIVVGVLK------DNYIEINLPIGRHHVYRKKMTVREDGKEALTHIKVLKRF-NSH 250

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E+   TGRTHQ+RVH+ + G P+ GD  Y  +F         + L L A+ ++  HP
Sbjct: 251 TLIEINLKTGRTHQIRVHSSYKGFPVAGDKIYSKSFSK------YSGLMLVAKKIEFMHP 304

Query: 301 EGGR-LQITAPLPAHMVKTW 319
                L      P +     
Sbjct: 305 ITKELLDFEIDYPDYFTNFL 324


>gi|296876557|ref|ZP_06900608.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus parasanguinis
           ATCC 15912]
 gi|296432550|gb|EFH18346.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus parasanguinis
           ATCC 15912]
          Length = 297

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 77/309 (24%), Positives = 132/309 (42%), Gaps = 33/309 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L KI  R GQ+ V+ +       +  G  + I          +K   
Sbjct: 16  FLKKH--EVSKGLLAKIKFRGGQILVNGRPENAIYLLDIGDRLVIDIPAEEGFETLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
                             +L+ED    V NKP GI+    +  +  +  F+K +   +G 
Sbjct: 71  -----------PMDRPLDILFEDDHFLVLNKPFGIASIPSAIHSNTLANFVKGYYVKQGY 119

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
             Q+  +  RLD++TSG+++ A+   A   L +  + + IQK Y++LV G  K +    I
Sbjct: 120 ENQQVHIVTRLDKDTSGVMLFAKHGYAHARLDKQLQSKSIQKRYYALVKGSGKLDPVGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      +   + ++  KG  YA + ++V+  F   +  +++Q HTGRTHQ+RVH
Sbjct: 180 IAPIARD-----EESIITRKVAKGGKYAHTSYQVVQSFGDIY-LVDIQLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   HP     L I +PLP     
Sbjct: 234 FSHIGFPLLGDDLYGGSLED-----GIERQALHCHRLSYYHPFLEEELVIESPLPPDFQA 288

Query: 318 TWDSLGFKY 326
               L   Y
Sbjct: 289 VLTQLQTSY 297


>gi|228996384|ref|ZP_04156026.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           Rock3-17]
 gi|228763347|gb|EEM12252.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           Rock3-17]
          Length = 286

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 135/316 (42%), Gaps = 39/316 (12%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
              E+ M +  + K     I+   L  I  + G + VD K     + +Q+ +V+++   +
Sbjct: 2   TEAEKGMLIREFLKT--KGISKAALTDIKFQGGAIEVDGKHATVRHVLQAEEVLQVFFPV 59

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIA 126
              +  +               ++ +   +LYED  + V NK   +S           +A
Sbjct: 60  EERSEGM--------------LAENIPLTVLYEDESVLVINKAPYMSTIPSREHPAGSVA 105

Query: 127 YHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +  L  +   +      +  RLD++TSG++++A+ R     L++  + +++++ Y +
Sbjct: 106 ---NALLYHYDRQNLASTVHIVTRLDRDTSGLMLIAKNRFIHHLLSKQHQQKKVKRTYEA 162

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G    +   I   + +K     + +       +    A++HF+V++ F  K   + +
Sbjct: 163 IVHGEWLEESGTIDAPIGRKGDSIIERMVC-----EDGQKAVTHFQVMERFPDK-TRVSL 216

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P++GD  Y  +           +  LH+  +   HP   + 
Sbjct: 217 QLETGRTHQIRVHMAYLGHPLLGDDLYGGSKSQ------MKRQALHSTSLTFYHPILEKQ 270

Query: 305 LQITAPLPAHMVKTWD 320
           ++  A +P  M +   
Sbjct: 271 MKFHADVPEDMKELLK 286


>gi|229820887|ref|YP_002882413.1| pseudouridine synthase, RluA family [Beutenbergia cavernae DSM
           12333]
 gi|229566800|gb|ACQ80651.1| pseudouridine synthase, RluA family [Beutenbergia cavernae DSM
           12333]
          Length = 309

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 69/327 (21%), Positives = 135/327 (41%), Gaps = 28/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   + + V +     R+D         ++      +  +G+V +D      ++R+ +G 
Sbjct: 1   MAERRSLPVPDGLAGERVDVGMARLL-GLSRSAAADLAAAGRVLLDGAAAGKSDRLAAGA 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +      L    +  +++   V            ++Y D  + V +KP G++     
Sbjct: 60  WLEV-----ELPEAAEPPQVVAEPVP--------GMRIVYSDDDVVVVDKPVGVAAHPSP 106

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  + HRLD  TSG++ VA++  A   L  +F+ R
Sbjct: 107 GWSGPTVIGALAAAGVRVSTSGAAERQGVVHRLDVGTSGLMAVAKSERAYSVLKRAFKER 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K+Y +LV G P      I   + +       +  V          +++H++ ++   
Sbjct: 167 TVTKVYHALVQGHPDPSAGTIDAPIGRHPRHDYKWAVVA-----DGKPSVTHYETLEAMP 221

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                LE+   TGRTHQ+RVH   +  P VGD  Y A+ +      +  + +LHA  +  
Sbjct: 222 -AASLLEVHLETGRTHQIRVHMAAVKHPCVGDVTYGADPRLAERLGL-TRQWLHAVRLGF 279

Query: 298 PHPEGGRL-QITAPLPAHMVKTWDSLG 323
            HP  G   ++T+  PA +  + ++L 
Sbjct: 280 EHPVTGEWTEVTSDYPADLAASLEALR 306


>gi|296501895|ref|YP_003663595.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
 gi|296322947|gb|ADH05875.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
          Length = 297

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 65/317 (20%), Positives = 134/317 (42%), Gaps = 39/317 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE   +  + K     I+   L  I    G + V+ +     +++++G+ +R+   
Sbjct: 10  IGPAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLRAGEELRVFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + + NK A +S           +
Sbjct: 68  VEERSEGM--------------MAEDIPLCIIYEDDAVLIINKEANMSTIPSREHPAGSV 113

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 114 A---NALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    + +       +    A++HFKVID    K   + 
Sbjct: 171 AIVHGKIVEREGMIDAPIGRKSDSIIERMVC-----EDGQRAVTHFKVIDSTYHK-THVA 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD  Y              +  LH++ +   HP    
Sbjct: 225 LELETGRTHQIRVHMAHIGHPLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEK 278

Query: 304 RLQITAPLPAHMVKTWD 320
            +  T  LP+ M +   
Sbjct: 279 EMSFTIKLPSDMQEVLR 295


>gi|228913878|ref|ZP_04077503.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pulsiensis BGSC 4CC1]
 gi|228845817|gb|EEM90843.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pulsiensis BGSC 4CC1]
          Length = 292

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 132/315 (41%), Gaps = 33/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI   
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + V NK A +S            
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPSGSV 108

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HF+VID  A     + ++ 
Sbjct: 169 HGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVSLEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP     + 
Sbjct: 223 DTGRTHQIRVHLAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWDS 321
             A +P+ M +    
Sbjct: 277 FAAMIPSDMQEVLRQ 291


>gi|297184482|gb|ADI20596.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium EBAC_27G05]
          Length = 311

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 69/327 (21%), Positives = 141/327 (43%), Gaps = 40/327 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ +D  N+RLD+     +   +   +Q+ + +G + ++ + ++  +++Q G  + + P+
Sbjct: 7   IISSDFHNIRLDQAATALFEDYSRSQIQRWIEAGNLLINGESLRPKDKVQEGDELSLDPI 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +                  ++  ++ +   + +E+ +  + NKP G+ +  G+G     +
Sbjct: 67  LEN---------------RVSWEAEDIPLNIHHEEDEFLIINKPYGLVMHPGAGC---NN 108

Query: 131 GFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + +           +  + HRLD++TSG+LV+A+T        E  + R I K Y 
Sbjct: 109 GTLANALAFHYPQLIQLPRCGIVHRLDKDTSGLLVIAKTEKFRNFFVEKLQNREIFKEYE 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G      + I ++ ++++        +  +       AISH  +I  F   +  + 
Sbjct: 169 ALVVG------QVIGSFSIEQAIERDPRNRIKMRTTDFGREAISHISLIK-FYNGYSHVA 221

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           ++  TGRTHQ+RVH  H   PI+GD  Y         +P +         +  LHA  + 
Sbjct: 222 IEIETGRTHQIRVHLSHHKLPIIGDRTYNPRNAIAKDTPKEILPIIQHFPRQALHASKIG 281

Query: 297 LP-HPEGGRLQITAPLPAHMVKTWDSL 322
                 G ++Q     P  M     +L
Sbjct: 282 FELMGTGQKIQFEQSPPEDMSTLISTL 308


>gi|1491643|emb|CAA61435.1| ORFA [Chloroflexus aurantiacus J-10-fl]
          Length = 253

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 81/248 (32%), Positives = 125/248 (50%), Gaps = 17/248 (6%)

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVD 138
           Q  +   +     ++ +   ++YED+ I V NKPAG+ V    G      ++  L  + D
Sbjct: 10  QLTIPPPIPTELVAEPIPLDVVYEDADIAVINKPAGMVVHPAPGHPRGTLVNALLARYPD 69

Query: 139 ---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                  +P + HRLD++TSG+LV+AR   A + L +  + RR++KIY +LV G P  + 
Sbjct: 70  LAIGGELRPGIVHRLDRDTSGLLVIARHDQAMRSLVDQQQARRMRKIYQALVIGRPP-ET 128

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   + +        + VV         A +H++++D F   +  LE+Q  TGRTHQ+
Sbjct: 129 GTIDAPIGRDPR-DRLRMAVV----PDGRPARTHYRLLDTFGD-YSLLEVQLETGRTHQI 182

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           RVH  H+G PIVGD  Y        +    ++ +LHA Y+ L HP  GR  + TAPLPA 
Sbjct: 183 RVHLRHLGYPIVGDPVYGPRR----SHLHLSRQFLHAAYLGLVHPRSGRWQEFTAPLPAD 238

Query: 315 MVKTWDSL 322
           +      L
Sbjct: 239 LQIVLRQL 246


>gi|56416692|ref|YP_153766.1| ribosomal large subunit pseudouridine synthase [Anaplasma marginale
           str. St. Maries]
 gi|222475057|ref|YP_002563472.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Florida]
 gi|255003036|ref|ZP_05278000.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Puerto Rico]
 gi|255004159|ref|ZP_05278960.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Virginia]
 gi|56387924|gb|AAV86511.1| ribosomal large subunit pseudouridine synthase [Anaplasma marginale
           str. St. Maries]
 gi|222419193|gb|ACM49216.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Florida]
          Length = 296

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 94/315 (29%), Positives = 155/315 (49%), Gaps = 21/315 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  +VE     +R+DR+ +   P +    ++++LR G++ ++  + K + R+ +G V+ I
Sbjct: 3   REYLVEGTCFEVRVDRYLRGLLPGVTQSFIERLLRRGEILLNNTKAKSSTRVSNGDVLSI 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                A    ++E++I   ++      D +   +LYED  I   NKPAG+SVQGGS +  
Sbjct: 63  KH---ADRIALREKEI--RALQHVPLLDLISGSILYEDKNIIAINKPAGVSVQGGSKVKV 117

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            ID  L       G+  R+ HRLD++TSG+LV+AR    A++L   FR RR++K Y ++ 
Sbjct: 118 SIDDVLDKI--KPGECCRIVHRLDKDTSGVLVLARNLDVARYLAREFRERRVKKEYIAVT 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+P+     ++  +  K         +          A + F V+         L ++P
Sbjct: 176 RGVPQPASGEVSTPIFYKVRSATGESMI-------EKEAKTFFSVMRILGDCAVVL-LRP 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGR HQLR+H   +GCPIVGD+KY               L+LHA  +      G  L I
Sbjct: 228 VTGRKHQLRIHMSQIGCPIVGDNKYHKCDLAEKEM-----LHLHASLLTFE-LMGRTLSI 281

Query: 308 TAPLPAHMVKTWDSL 322
            A +P +M +  + L
Sbjct: 282 AANVPRYMEEKINPL 296


>gi|167037131|ref|YP_001664709.1| RluA family pseudouridine synthase [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|320115551|ref|YP_004185710.1| RluA family pseudouridine synthase [Thermoanaerobacter brockii
           subsp. finnii Ako-1]
 gi|166855965|gb|ABY94373.1| pseudouridine synthase, RluA family [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|319928642|gb|ADV79327.1| pseudouridine synthase, RluA family [Thermoanaerobacter brockii
           subsp. finnii Ako-1]
          Length = 285

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 74/317 (23%), Positives = 140/317 (44%), Gaps = 38/317 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV  +E+ + L+ + +N       + + K    G++ V+  +      +Q G V+ +  
Sbjct: 3   LVVGENEKGVILENFLRNKGFSKRLIRIYKW--QGEILVNGIKSNVKRILQPGDVIDL-- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                  I+ E              + L   + YED +I + NKPA + V          
Sbjct: 59  -------ILPEND-------SNIAPEKLDLDICYEDEEILIVNKPANMVVHPTKRYQSGT 104

Query: 129 IDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +  +   KG K   R  +RLD+ TSG++V A+      +L      + + K+Y+++
Sbjct: 105 LANGVAWYFKEKGLKALIRPVNRLDRGTSGLVVFAKRPFMQYYLQII---KPMTKLYFAV 161

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + +   I   + +K   G + +       +  + AI+++KV+   +++F  L+++
Sbjct: 162 VEGKMEGE-GRIDLPISRKPQSGIERMV-----SEEGDRAITNYKVVKS-SKRFSLLKVK 214

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  H+G PIVGD  Y +      +     +  LHA  +   HP   + +
Sbjct: 215 IETGRTHQIRVHLSHIGHPIVGDTLYGS------SDDYIKRQALHAYRLTFVHPLEEKSI 268

Query: 306 QITAPLPAHMVKTWDSL 322
            + +PLP  +       
Sbjct: 269 SVYSPLPQDIQNLLKLF 285


>gi|308190331|ref|YP_003923262.1| pseudouridylate synthase [Mycoplasma fermentans JER]
 gi|307625073|gb|ADN69378.1| pseudouridylate synthase [Mycoplasma fermentans JER]
          Length = 307

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 65/310 (20%), Positives = 135/310 (43%), Gaps = 41/310 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDK--KRVKFNNRIQSGQVVRIPPVINALNH 76
            R+D++       ++  ++++++  G V ++   +  K N  ++ GQ + I         
Sbjct: 10  ERIDKYI-GQNSELSRNDIKELIEQGAVYINDNVQVHKCNYIVREGQEITI--------- 59

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLK 134
                K+LD  + +   +  +   + YED  + + NKP+ + V    G      ++G L 
Sbjct: 60  ----VKLLDKEIKIEPVN--IPLDIKYEDDDLVIINKPSNLVVHPSPGHYNDTLVNGLLY 113

Query: 135 SWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            + ++        +P + HR+D++TSG+L++A+       LT+  +   I++ Y ++V G
Sbjct: 114 HFKNNLSNENGLLRPGIVHRIDKDTSGLLIIAKNNKMHNSLTDMLKRHEIERSYLAIVRG 173

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQ 246
           + +N    I   + + + +    + V     K    AI+   ++  F    +    +  +
Sbjct: 174 LIENPLTKINLPIARNT-VDRKMMSV----HKEGKEAITFVHLLKHFYLDKEPMSLVRCE 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
             TGRTHQ+RVH  ++  P+ GD  Y  +           +L  HA  +   HP     +
Sbjct: 229 LKTGRTHQIRVHLSYIKHPVYGDPTYGKSV-----DEFNQRL--HAYKLKFIHPLTKKEI 281

Query: 306 QITAPLPAHM 315
            + AP+P   
Sbjct: 282 CVYAPVPKEF 291


>gi|229084299|ref|ZP_04216581.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-44]
 gi|228699010|gb|EEL51713.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-44]
          Length = 297

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 67/328 (20%), Positives = 138/328 (42%), Gaps = 39/328 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRI 59
           M L  +     +   E+ M +  + K     I+   L  I  + G + V+ K     + +
Sbjct: 1   MYLRRFALKWCITEAEKGMLIREFLKA--KGISKAALTDIKFQGGAIEVNGKHATVRHVL 58

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G+ +++   +   +  +               ++ +   ++YED  + V NK   +S 
Sbjct: 59  QAGEELQVFFPLEERSEGM--------------LAENIPLNVVYEDDSVLVMNKAPYMST 104

Query: 120 -----QGGSGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                     +A   +  L  +          +  RLD++TSG+++VA+ R     L++ 
Sbjct: 105 IPSREHPAGSVA---NALLYHYDKQHLASTVHIVTRLDRDTSGLMLVAKNRFIHHLLSKQ 161

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + +++Q+ Y ++V G    +   I   + +KS    +         +    A++HF+V+
Sbjct: 162 HQEKQVQRTYEAIVHGELVEESGTIDAPIGRKSDSIIERTVC-----EDGQKAVTHFQVL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F  K   + +Q  TGRTHQ+RVH  ++G P++GD  Y        ++    +  LH+ 
Sbjct: 217 ERFPDK-TRVSLQLETGRTHQIRVHMAYVGHPLLGDDLYGG------STSEMKRQALHST 269

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            +   HP   + +   A +P  M +   
Sbjct: 270 SLTFYHPILEKQMTFHADVPKDMKEVLK 297


>gi|307709450|ref|ZP_07645907.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
 gi|307619764|gb|EFN98883.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
          Length = 298

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 138/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNDQPQNATYLLDIGDRV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +      +LYED    V NKP G++       
Sbjct: 57  TIDIPAEEGFETLE--------------AIERPLDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +      +   + ++  KG  YA + +K++  +     
Sbjct: 163 YFALVKGDGHLEPEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++ HTGRTHQ+RVH  H+G P++GD  Y  +           +  LH  ++   HP 
Sbjct: 217 LVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHFLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LKQDLQLESPLPDDFSNLITQL 293


>gi|171920977|ref|ZP_02696366.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           13 str. ATCC 33698]
 gi|185179169|ref|ZP_02555823.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           5 str. ATCC 27817]
 gi|188024223|ref|ZP_02570294.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           7 str. ATCC 27819]
 gi|188518627|ref|ZP_02556991.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           11 str. ATCC 33695]
 gi|188524489|ref|ZP_02558401.2| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           12 str. ATCC 33696]
 gi|195867617|ref|ZP_03079619.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           9 str. ATCC 33175]
 gi|198273670|ref|ZP_03206205.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           4 str. ATCC 27816]
 gi|225550414|ref|ZP_03771363.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           2 str. ATCC 27814]
 gi|225551125|ref|ZP_03772071.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           8 str. ATCC 27618]
 gi|171903003|gb|EDT49292.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           13 str. ATCC 33698]
 gi|184208903|gb|EDU05946.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           5 str. ATCC 27817]
 gi|188018878|gb|EDU56918.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           7 str. ATCC 27819]
 gi|188997853|gb|EDU66950.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           11 str. ATCC 33695]
 gi|195659610|gb|EDX52990.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           12 str. ATCC 33696]
 gi|195660674|gb|EDX53929.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           9 str. ATCC 33175]
 gi|198249698|gb|EDY74479.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           4 str. ATCC 27816]
 gi|225378940|gb|EEH01305.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           8 str. ATCC 27618]
 gi|225379568|gb|EEH01930.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           2 str. ATCC 27814]
          Length = 299

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 78/311 (25%), Positives = 136/311 (43%), Gaps = 31/311 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
              R+D++        +  +++K+L    V V+   + K +  +Q    V I        
Sbjct: 9   SPKRIDKFLVE-VTDYSRTSIKKMLEQNLVLVNDNIITKQSYLLQKNDSVEIKN------ 61

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLK 134
               EQ ++DS   L   +  L+  +++ED  + V NKP+G+ V   S      +   LK
Sbjct: 62  ----EQCVIDSQKELLPFACPLE--IVFEDQDLLVINKPSGMLVHPTSFQEQNTLANALK 115

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            ++ +      +THRLD+ TSG++V+ + + A   L + F  + ++K Y+++V       
Sbjct: 116 HYLKTDDF--YITHRLDKNTSGLIVICKNQKALCCLQQQFMQKTVKKSYYAIVHNRFDMH 173

Query: 195 KECIANWLLKKSHIGG---DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                   +    IG    D + +   + K A  AIS  KVI+ + Q    +E+   TGR
Sbjct: 174 ----HLHFMINEPIGHSYQDKLRMKTGDAKNAKEAISIVKVIEQY-QNTALVEVSIITGR 228

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAP 310
           THQ+RVH  H+  PI  D  Y        T+P +   YLH+ Y+   HP    + +    
Sbjct: 229 THQIRVHMRHINHPIYNDPLYG---ISKHTTPYE--QYLHSFYISFIHPSTNEIVEFKTL 283

Query: 311 LPAHMVKTWDS 321
           +P   +     
Sbjct: 284 MPNEFINLIKE 294


>gi|301060346|ref|ZP_07201209.1| pseudouridine synthase, RluA family [delta proteobacterium NaphS2]
 gi|300445542|gb|EFK09444.1| pseudouridine synthase, RluA family [delta proteobacterium NaphS2]
          Length = 265

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 71/259 (27%), Positives = 113/259 (43%), Gaps = 20/259 (7%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSK 140
           ++          + +   + +ED+ I V  KP GI V  G G      + G LK   D  
Sbjct: 3   VIPKPATTRLVPEAVSFSVFFEDTWIIVLYKPPGIVVHPGPGHSSGTLVHGLLKHCTDLS 62

Query: 141 GQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           G     +P + HRLD++TSG+++VA+   A Q L   F+   + K Y +LV G+  ++  
Sbjct: 63  GIGGTLRPGIVHRLDKDTSGLMLVAKNDMAHQALARQFKDGTVHKEYVALVHGLLPSESG 122

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   + +   +    + + K    G   A++ +K I    + F  L +   TGRTHQ+R
Sbjct: 123 TIDLPICRH-PVRRKEMSIAKS---GGRNALTLWKKIAECEEGFSLLSITIKTGRTHQIR 178

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NKLYLHARYMDLPHPEGG-RLQ 306
           VH  H+G P+VGD  Y           ++          +  LHA  +   HPE    + 
Sbjct: 179 VHFAHLGHPLVGDTVYGHGPDTLKKRFLKSNPGLVTAVKRQMLHAARIGFLHPEEKTYMT 238

Query: 307 ITAPLPAHMVKTWDSLGFK 325
             APLP  M +   +L   
Sbjct: 239 FEAPLPEDMRQVLRALNLN 257


>gi|307706671|ref|ZP_07643477.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK321]
 gi|307617915|gb|EFN97076.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK321]
          Length = 298

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 139/322 (43%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G +V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNDQPQNATYLLDIGDLV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I   +      ++              +      +LYED    V NKP G++       
Sbjct: 57  IIDIPVEEGFETLE--------------AIERPLDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    D + Q+  +  RLD++TSG+++ A+   A   L +  + + IQK 
Sbjct: 103 SNTIANFIKGYYVKQDYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIQKR 162

Query: 183 YWSLVWGIP-KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +      +   + ++  KG  YA + +K++  +     
Sbjct: 163 YFALVKGDGYLESEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++ HTGRTHQ+RVH  H+G P++GD  Y  +           +  LH   +   HP 
Sbjct: 217 LVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHSLTFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LEQDLQLESPLPDDFSNLITQL 293


>gi|89055892|ref|YP_511343.1| ribosomal large subunit pseudouridine synthase D [Jannaschia sp.
           CCS1]
 gi|88865441|gb|ABD56318.1| ribosomal large subunit pseudouridine synthase D [Jannaschia sp.
           CCS1]
          Length = 310

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 71/317 (22%), Positives = 126/317 (39%), Gaps = 42/317 (13%)

Query: 32  INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I+   L +++ +G V ++ + V     R+  G  V I     A    + E   LD     
Sbjct: 7   ISRTRLARLIPAGAVAINGRVVTDPKARVAEGDGVEITVEDAAEVETVAEDIPLD----- 61

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKG-----QK 143
                     +++ED  + V NKPAG+ V    G      ++  L  +          ++
Sbjct: 62  ----------IVHEDDDLIVVNKPAGMVVHPAPGSPSGTLVNALLHHFGGKLSGVGGEKR 111

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D++TSG+LVVA++  A   L   F    +++ Y +L  G+P      +     
Sbjct: 112 PGIVHRIDKDTSGLLVVAKSDRAHHGLAAQFADHSMEREYLALCHGVPDGSDPRLRGVKG 171

Query: 204 KK---------SHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                      + +        +Q     G  +A++  +V++        +  +  TGRT
Sbjct: 172 VSFEGSTVKITTQLARHKTDRQRQAVLFSGGRHAVTRVRVLEAHG-PVALVSCRLETGRT 230

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------NKLYLHARYMDLPHPEGGR-L 305
           HQ+RVH  H+G  ++GD  Y    K +   P         +  LHA  +   HP     +
Sbjct: 231 HQIRVHMSHVGHALIGDQTYGGRRKISAKLPGAEAVNAFPRQALHAATLGFVHPVSQDVM 290

Query: 306 QITAPLPAHMVKTWDSL 322
           +  APL   +     +L
Sbjct: 291 RFDAPLAPDLRILLTAL 307


>gi|239931821|ref|ZP_04688774.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           ghanaensis ATCC 14672]
 gi|291440189|ref|ZP_06579579.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           ghanaensis ATCC 14672]
 gi|291343084|gb|EFE70040.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           ghanaensis ATCC 14672]
          Length = 314

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 74/327 (22%), Positives = 135/327 (41%), Gaps = 18/327 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVTVDGSVVGKSERVS 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   ++ E       + +    D +  I+       +      G +V
Sbjct: 60  GGAWLEVEMPQAPAPVQVVAEPV---EGMEIVHDDDDVVVIVKPVGVAAHPSPGWTGPTV 116

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GG   A +             ++  + HRLD  TSG++VVA++  A   L   F+ R +
Sbjct: 117 IGGLAAAGYRIST-----SGAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQFKERTV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G P      I   + +  H    +    +        +++H+ +I+ F + 
Sbjct: 172 DKRYHTLVQGHPDPTSGTIDAPIGRHPHHDYKWAVTAE-----GKPSVTHYDLIEAF-RA 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA  +   H
Sbjct: 226 ASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADPTLAKRLRL-TRQWLHAVRLGFEH 284

Query: 300 PEGGRL-QITAPLPAHMVKTWDSLGFK 325
           P  GR  + ++  P  + K  D +  +
Sbjct: 285 PGDGRWAEYSSDYPEDLQKALDQVREE 311


>gi|77919474|ref|YP_357289.1| pseudouridylate synthase, 23S RNA-specific [Pelobacter carbinolicus
           DSM 2380]
 gi|77545557|gb|ABA89119.1| pseudouridylate synthase, 23S RNA-specific [Pelobacter carbinolicus
           DSM 2380]
          Length = 301

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 85/309 (27%), Positives = 146/309 (47%), Gaps = 31/309 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +  P  +    +KI+  G V ++ +R++ ++          P   +A   + 
Sbjct: 1   MRLDQYLASAIPDFSRSFARKIIDLGGVHLNGRRMRRSS---------FPVPGHAAVEVY 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLK 134
            + + LD      +H       +L  D  + V NKP GI+ Q       G  Y     L 
Sbjct: 52  LDHRDLDIFALDDEH-------ILLRDRYLVVVNKPPGINSQPTPARYKGTLYEALLRLL 104

Query: 135 SWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
               +KG+KP L    RLD++TSG+++ +    A + L++ F  RR+QK Y +LV G  +
Sbjct: 105 DDPYNKGRKPSLGMVQRLDRDTSGVMIFSIHARAHKSLSDIFAARRVQKHYLALVAGCMQ 164

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +    + L ++        +++K   +G   A++ ++VI+ F      LE++  TGR+
Sbjct: 165 APQGEFRSLLARQH-----RTNLMKSVARGGKEAVTRYRVIEKFGD-AELLEVEIPTGRS 218

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           HQ+RVH    G P++GD +Y    +         +  LHAR ++L HP     L I APL
Sbjct: 219 HQIRVHFAEAGHPLLGDIRYGGPDRWRGVD--VPRQMLHARRLELLHPISKEPLNIEAPL 276

Query: 312 PAHMVKTWD 320
           P   +K  +
Sbjct: 277 PQDFLKLLE 285


>gi|153953520|ref|YP_001394285.1| RluD1 [Clostridium kluyveri DSM 555]
 gi|219854142|ref|YP_002471264.1| hypothetical protein CKR_0799 [Clostridium kluyveri NBRC 12016]
 gi|146346401|gb|EDK32937.1| RluD1 [Clostridium kluyveri DSM 555]
 gi|219567866|dbj|BAH05850.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 299

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 80/315 (25%), Positives = 141/315 (44%), Gaps = 30/315 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  E+ ++L  + K      +   ++    SG++ +D KRVK N+ ++SG V+    + 
Sbjct: 10  VKEQEQGLKLKEYLKK-IQRFSGRLIRGAALSGRIEIDNKRVKLNHVLKSGDVICFNLIK 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
               +I  E+               +   ++YED  I V NK  GI V          + 
Sbjct: 69  EESQNIGAEK---------------MDIEVVYEDRDIIVVNKKPGIVVHPTRSYPSGTLA 113

Query: 131 GFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             L  +    G+    RL  RLD +TSG+++VA+ + A   L+   +    +K Y +++ 
Sbjct: 114 NGLIYYFQKSGENCIVRLVSRLDMDTSGLIIVAKNQFAHMCLSRDMKSEDFEKSYIAVIH 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  K  +  I   + +    G D   +V   +K    +I+H+KVI+ F      L++   
Sbjct: 174 GKMKEGQGIIDLPIYR--PEGDDIRRIV---DKRGQRSITHYKVIEEFKHDQ-LLKLILK 227

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QI 307
           TGRTHQ+RVH  ++G P+ GD  Y       +     N+  LHA  +  PHP G ++ ++
Sbjct: 228 TGRTHQIRVHLSYLGHPLYGDTLYGIEGDNRY----INRQALHAYRLKFPHPRGNKILEL 283

Query: 308 TAPLPAHMVKTWDSL 322
              +P  +      +
Sbjct: 284 ETDIPEDISHLIKEI 298


>gi|254994901|ref|ZP_05277091.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Mississippi]
          Length = 296

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 94/315 (29%), Positives = 155/315 (49%), Gaps = 21/315 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  +VE     +R+DR+ +   P +    ++++LR G++ ++  + K + R+ +G V+ I
Sbjct: 3   REYLVEGTCFEVRVDRYLRGLLPGVTQSFIERLLRRGEILLNNTKAKSSTRVSNGDVLSI 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                A    ++E++I   ++      D +   +LYED  I   NKPAG+SVQGGS +  
Sbjct: 63  KH---ADRIALREKEI--HALQHVPLLDLISGSILYEDKNIIAINKPAGVSVQGGSKVKV 117

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            ID  L       G+  R+ HRLD++TSG+LV+AR    A++L   FR RR++K Y ++ 
Sbjct: 118 SIDDVLDKI--KPGECCRIVHRLDKDTSGVLVLARNLDVARYLAREFRERRVKKEYIAVT 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+P+     ++  +  K         +          A + F V+         L ++P
Sbjct: 176 RGVPQPASGEVSTPIFYKVRSATGESMI-------EKEAKTFFSVMRILGDCAVVL-LRP 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGR HQLR+H   +GCPIVGD+KY               L+LHA  +      G  L I
Sbjct: 228 VTGRKHQLRIHMSQIGCPIVGDNKYHKCDLAEKEM-----LHLHASLLTFE-LMGRTLSI 281

Query: 308 TAPLPAHMVKTWDSL 322
            A +P +M +  + L
Sbjct: 282 AANVPRYMEEKINPL 296


>gi|229114740|ref|ZP_04244154.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock1-3]
 gi|228668805|gb|EEL24233.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock1-3]
          Length = 292

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 68/313 (21%), Positives = 135/313 (43%), Gaps = 33/313 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + VD +     +++Q+G+ +R+   
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVDGQYASVRHQLQAGEQLRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHI 129
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPEGSV 108

Query: 130 DGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L S+ D +       +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSYYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HF+VI   +QK   + ++ 
Sbjct: 169 HGEMIKREGTIDAPIGRKSDSIIERTFC-----EDGQRAVTHFRVIHSSSQK-THVSLEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  HMG P++GD  Y              +  LH+  +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAHMGHPLLGDDLYGGRRDE------MKRQALHSTSLAFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTW 319
               +P+ M +  
Sbjct: 277 FATTIPSDMQQLL 289


>gi|134298263|ref|YP_001111759.1| RluA family pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134050963|gb|ABO48934.1| pseudouridine synthase, RluA family [Desulfotomaculum reducens
           MI-1]
          Length = 303

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 71/318 (22%), Positives = 130/318 (40%), Gaps = 32/318 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + VE  +    L  + K  +  I+   L+K+   G++  +  +V +   + +G  V +  
Sbjct: 10  LCVEASQNGKFLRDFLK--HKDISDRALKKLRNEGEILCNGAKVTWRTIVNTGDKVVLIY 67

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAY 127
            I   N  +                + L   ++ ED  I + NK  G+ V          
Sbjct: 68  PIPPRNQYLP--------------PEPLDLSIISEDEDIALVNKQPGMCVHPTLAYPSGT 113

Query: 128 HIDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +G +  W+++         +R+D+ TSG+++VA+   +AQ L    + +++ + Y +L
Sbjct: 114 LANGLVYHWLENNPAPTFHAVNRIDRNTSGLVLVAKNSYSAQKLFLQRKRKQLARSYVAL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    +   I   L K      +     +Q       A++ F+V+         + + 
Sbjct: 174 VHGKIVQRNGYIDLPLEK-----CEGKTTKRQISSTGQQALTRFEVLQYITD-CTLIRLM 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
           P TGRTHQ+RVH  H+G P+VGD  Y  +           +  LHA  +   HP  G  +
Sbjct: 228 PETGRTHQIRVHLSHLGHPLVGDTLYGGSIAQ------IGRHCLHADKISFLHPRTGHPM 281

Query: 306 QITAPLPAHMVKTWDSLG 323
               PL   M++    +G
Sbjct: 282 SFQIPLAEDMLQVITEMG 299


>gi|65318577|ref|ZP_00391536.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Bacillus
           anthracis str. A2012]
 gi|165872829|ref|ZP_02217455.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|170708875|ref|ZP_02899309.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|190569145|ref|ZP_03022043.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|164711406|gb|EDR16957.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|170126191|gb|EDS95084.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|190559728|gb|EDV13715.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
          Length = 292

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 69/318 (21%), Positives = 136/318 (42%), Gaps = 39/318 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI   
Sbjct: 5   IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +   +  +               ++ +   ++YED  + V NK A +S         H  
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSR---EHPS 105

Query: 131 GFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + + + S   K        +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 106 GSVANALLSHYDKQYLPSTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID  A     + 
Sbjct: 166 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVS 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 220 LELDTGRTHQIRVHLAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 273

Query: 304 RLQITAPLPAHMVKTWDS 321
            +   A +P+ M +    
Sbjct: 274 EMSFAAMIPSDMQEVLRQ 291


>gi|229166145|ref|ZP_04293906.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH621]
 gi|228617367|gb|EEK74431.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH621]
          Length = 292

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 62/309 (20%), Positives = 131/309 (42%), Gaps = 33/309 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           EE   +  + K     I+   L  I  R G + V+ +     +++Q+G+ ++I   +   
Sbjct: 9   EEGTLVREFLKT--KGISKAALTDIKFRGGAIEVNGQHTSVRHKLQAGEELQIFFPVEER 66

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGF 132
           +  ++ + I                 ++YED  + V NK A +S             +  
Sbjct: 67  SEGMEVEDI--------------PLCIVYEDDAVLVINKEANMSTIPSREHPSGSIANAL 112

Query: 133 LKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L  +   +      +  RLD++TSG++++A+ R     L++  + + +++ Y ++V G  
Sbjct: 113 LYHYDKQNLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKGVKRTYEAIVHGTI 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             +   I   + +K+    +         +    A++HF+V++  + K   + ++  TGR
Sbjct: 173 LEEVGTIDAQIGRKADSIIERTVC-----EDGQRAVTHFRVMESSSDK-THVALELETGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH  ++G P++GD  Y           +  +  LH+  +   HP   + +  T  
Sbjct: 227 THQIRVHMAYIGHPLLGDDLYGGRRD------VIKRQALHSTSLTFYHPILEKGMTFTVS 280

Query: 311 LPAHMVKTW 319
           +P  M    
Sbjct: 281 IPEDMQYAL 289


>gi|329940930|ref|ZP_08290210.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           griseoaurantiacus M045]
 gi|329300224|gb|EGG44122.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           griseoaurantiacus M045]
          Length = 314

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 73/327 (22%), Positives = 135/327 (41%), Gaps = 18/327 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V VD   V  + R+ 
Sbjct: 1   MSTLPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELASAGKVHVDGSAVGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   ++ E       + +    + +  ++       +      G +V
Sbjct: 60  GGAWLEVEMPQAAAPVRVVAEPV---EGMEIVYDDEDVVVVVKPVGVAAHPSPGWTGTTV 116

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GG   A +             ++  + HRLD  TSG++VVA++  A   L   F+ R +
Sbjct: 117 IGGLAAAGYRVST-----SGAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKRQFKERTV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G P      I   + +  H   DY   V         +++H+ +I+ F + 
Sbjct: 172 DKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAE---GKPSVTHYDLIEAF-RA 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA  +   H
Sbjct: 226 ASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADPTLAKRLRL-TRQWLHAVRLGFEH 284

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFK 325
           P  G  ++  +  P  + +  D +  +
Sbjct: 285 PGDGEWVEFASEYPEDLRQALDQVREE 311


>gi|86740132|ref|YP_480532.1| ribosomal large subunit pseudouridine synthase D [Frankia sp. CcI3]
 gi|86566994|gb|ABD10803.1| ribosomal large subunit pseudouridine synthase D [Frankia sp. CcI3]
          Length = 313

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 140/325 (43%), Gaps = 28/325 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++ + V +  + +RLD      +  ++      ++  GQ  +D K    ++R+  G  +
Sbjct: 7   DLRSLPVPDGLDGVRLDAAIARMF-GLSRTVAAALVDDGQASLDGKVRGRSDRVSGGAWL 65

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +             +          + +      +LY+D  I V +KP G++V    G 
Sbjct: 66  EV-------------RLPAPPRPVAVEPTPVEALGILYDDDDIIVVDKPVGVAVHPAPGF 112

Query: 125 IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               + G L +           ++  + HRLD  T+G++VVA++  A   L  +FR R +
Sbjct: 113 TGPTVIGALAAAGYRISTSGAAERQGVVHRLDVGTTGVMVVAKSERAYTLLKRAFRDRTV 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y ++V G P   +  +   + +     G +  V          +I+H+ + + F + 
Sbjct: 173 DKRYRAVVQGHPDPLRGTVDAPIDRHPRRPGLFAVVA-----DGKPSITHYDLQEAF-RA 226

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L ++  TGRTHQ+RVH   +  P VGD  Y A+        +  + +LHA  +   H
Sbjct: 227 ASLLSVRLETGRTHQIRVHMSALRHPCVGDLAYGADPTLAERLGL-TRQWLHAARLSFDH 285

Query: 300 P-EGGRLQITAPLPAHMVKTWDSLG 323
           P  GGR++ T+P PA + +  + L 
Sbjct: 286 PGHGGRVEFTSPDPADLAEAVERLR 310


>gi|193216796|ref|YP_002000038.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           arthritidis 158L3-1]
 gi|193002119|gb|ACF07334.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           arthritidis 158L3-1]
          Length = 298

 Score =  210 bits (535), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 64/309 (20%), Positives = 130/309 (42%), Gaps = 32/309 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            R+D++  N+   I   ++Q ++  G V V+  ++ K    +     + I  +++   +I
Sbjct: 10  ERIDKYIANN-SEITRNDIQALIVQGAVFVNSTKINKNKYIVHENDEIEIIKLLDKQQNI 68

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKS 135
                           +  L   ++YE     V NKP+G+ V    G      ++  +  
Sbjct: 69  ---------------EAQNLPLEIVYECDDYLVINKPSGLVVHPAPGHSSGTLVNSLMYH 113

Query: 136 WVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           + ++        +  + HR+D++TSG+L+VA+      +  +  +   I++ Y+++V G 
Sbjct: 114 FKNNLSDVNGLLRMGIVHRIDKDTSGLLLVAKNNETHNYFAKLLKNHEIKRTYYAIVDGH 173

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +N+   +   + +  +       V +QN K A  A+   K ++   Q    ++    TG
Sbjct: 174 IENRLINLDLPIGRDPN-NRQKFAVTEQNSKEAFTALEVIKYLNLAGQNKTLVKCNLKTG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQ+RVH  ++  P+ GD  Y              +L  HA+ +D     G  +   + 
Sbjct: 233 RTHQIRVHLAYIKHPVYGDPVYNKKVDD-----FNQRL--HAKELDFVDKSGKIMHFESE 285

Query: 311 LPAHMVKTW 319
           LP  M+   
Sbjct: 286 LPQIMLNEL 294


>gi|256827075|ref|YP_003151034.1| pseudouridine synthase, RluA family [Cryptobacterium curtum DSM
           15641]
 gi|256583218|gb|ACU94352.1| pseudouridine synthase, RluA family [Cryptobacterium curtum DSM
           15641]
          Length = 347

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 69/333 (20%), Positives = 133/333 (39%), Gaps = 33/333 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M     ++V   +  MRLD        + +     K + +G+V V+       + +  G 
Sbjct: 1   MASQFSLIVTQADAGMRLDSLLAVSGAYPSRSAAVKQIEAGKVLVNGLARSKRSIVAPGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +            + E+  L + + L    + +   + +ED  +   +K AG+ V    
Sbjct: 61  TI------------VYEEIPLATHIPL--RGEPIPLDVRFEDRWMMAISKQAGLCVHPAP 106

Query: 124 GIA--YHIDGFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G      ++  + ++            +P + HRLD +TSG+++ A+       L +  R
Sbjct: 107 GHEGGTLVNALIYAYGRDSLAHVQGDDRPGIVHRLDMDTSGLMMCAKDDTCGMALQDLVR 166

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             ++ + Y +LV G        I   + +   +G D + +       A  A++ F V++ 
Sbjct: 167 DHKVDRRYLTLVHGNIAFDTGQIDEPIGR---VGDDRLRMKISYRPTARNALTTFTVLER 223

Query: 236 FA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           F        +  LE + +TGRTHQ+RVH   +G   VGD  Y   +     +   ++ +L
Sbjct: 224 FEAGRADNGYTLLECRLYTGRTHQIRVHMEFIGHCCVGDPLY--RWGNEQVNLELSRQFL 281

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           H+  +   HP  G  + +   LP  +     SL
Sbjct: 282 HSYSLSFNHPMTGDDIALVDGLPPDLFGALRSL 314


>gi|322389492|ref|ZP_08063043.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 903]
 gi|321143767|gb|EFX39194.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 903]
          Length = 297

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 77/309 (24%), Positives = 131/309 (42%), Gaps = 33/309 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L KI  R GQ+ V+ +       +  G  + I          +K   
Sbjct: 16  FLKKH--EVSKGLLAKIKFRGGQILVNGRPENAIYLLDIGDRLVIDIPAEEGFETLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
                             +L+ED    V NKP GI+    +  +  +  F+K +   +G 
Sbjct: 71  -----------PMDRPLDILFEDDHFLVLNKPFGIASIPSAIHSNTLANFVKGYYVKQGY 119

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
             Q+  +  RLD++TSG+++ A+   A   L +  + + IQK Y++LV G  K +    I
Sbjct: 120 ENQQVHIVTRLDKDTSGVMLFAKHGYAHARLDKQLQSKTIQKRYYALVKGSGKLDPVGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      +   + ++  KG  YA + ++V+  F      +++Q HTGRTHQ+RVH
Sbjct: 180 IAPIARD-----EDSIITRKVAKGGKYAHTSYQVVQSFGDIH-LVDIQLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   HP     L I +PLP     
Sbjct: 234 FSHIGFPLLGDDLYGGSLED-----GIERQALHCHRLSYYHPFLEEELVIESPLPPDFQA 288

Query: 318 TWDSLGFKY 326
               L   Y
Sbjct: 289 VLTQLQTSY 297


>gi|148985070|ref|ZP_01818313.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP3-BS71]
 gi|148998365|ref|ZP_01825807.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP11-BS70]
 gi|149024900|ref|ZP_01836301.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP23-BS72]
 gi|225856742|ref|YP_002738253.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae P1031]
 gi|225858911|ref|YP_002740421.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 70585]
 gi|307067719|ref|YP_003876685.1| 23S RNA-specific pseudouridylate synthase [Streptococcus pneumoniae
           AP200]
 gi|147755762|gb|EDK62807.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP11-BS70]
 gi|147922768|gb|EDK73885.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP3-BS71]
 gi|147929523|gb|EDK80517.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP23-BS72]
 gi|225721947|gb|ACO17801.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 70585]
 gi|225724376|gb|ACO20228.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae P1031]
 gi|301800069|emb|CBW32664.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           OXC141]
 gi|306409256|gb|ADM84683.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           pneumoniae AP200]
 gi|332200523|gb|EGJ14595.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA41317]
          Length = 298

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 137/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNNQPQNATYLLDVGDYV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +      +LYED    V NKP G++       
Sbjct: 57  TIYIPAEEGFETLE--------------AIEHPLDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +      +   + ++  KG  YA + +K++  +     
Sbjct: 163 YFALVKGDGHLEPEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +  HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH  Y+   HP 
Sbjct: 217 LVYIHLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLED-----GIQRQALHCHYLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LEQDLQLESPLPDDFSNLITQL 293


>gi|229010596|ref|ZP_04167798.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           DSM 2048]
 gi|228750794|gb|EEM00618.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           DSM 2048]
          Length = 292

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 64/312 (20%), Positives = 133/312 (42%), Gaps = 39/312 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           EE   +  + K     I+   L  I  R G + V+ +     +++Q+G+ ++I   +   
Sbjct: 9   EEGTLVREFLKT--KGISKAALTDIKFRGGAIEVNGQHTSVRHKLQAGEELQIFFPVEER 66

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHI 129
           +  ++ + I                 ++YED  + V NK A +S           IA   
Sbjct: 67  SEGMEVEDI--------------PLCIVYEDDAVLVINKEANMSTIPSREHPSGSIA--- 109

Query: 130 DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L  +   +      +  RLD++TSG++++A+ R     L++  + + +++ Y ++V 
Sbjct: 110 NALLYHYDKQNLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKGVKRTYEAIVH 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G    +   I   + +K+    +         +    A++HF+V++  + K   + ++  
Sbjct: 170 GTILEEVGTIDAPIGRKADSIIERTVC-----EDGQRAVTHFRVMESSSDK-THVALELE 223

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  ++G P++GD  Y           +  +  LH+  +   HP   + +  
Sbjct: 224 TGRTHQIRVHMAYIGNPLLGDDLYGGRRD------VIKRQALHSTSLTFYHPILEKGMTF 277

Query: 308 TAPLPAHMVKTW 319
           T  +P  M    
Sbjct: 278 TVSIPEDMQYAL 289


>gi|229143914|ref|ZP_04272332.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST24]
 gi|228639575|gb|EEK95987.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST24]
          Length = 292

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 132/314 (42%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE   +  + K     I+   L  I    G + V+ +     +++++G+ +R+   
Sbjct: 5   IGPAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLRAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + + NK A +S            
Sbjct: 63  VEERSEGM--------------MAEDIPLCIIYEDDAVLIINKEANMSTIPSREHPAGSV 108

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    + +       +    A++HFKVID    K   + ++ 
Sbjct: 169 HGKIVEREGMIDAPIGRKSDSIIERMVC-----EDGQRAVTHFKVIDSTYHK-THVALEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y              +  LH++ +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAHIGHPLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWD 320
            T  LP+ M +   
Sbjct: 277 FTIKLPSDMQEVLR 290


>gi|168576177|ref|ZP_02722071.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae MLV-016]
 gi|194398218|ref|YP_002037729.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Streptococcus pneumoniae G54]
 gi|183577907|gb|EDT98435.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae MLV-016]
 gi|194357885|gb|ACF56333.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae G54]
          Length = 298

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 137/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNNQPQNATYLLDVGDYV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +      +LYED    V NKP G++       
Sbjct: 57  TIYIPAEEGFETLE--------------AIEHPLDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +      +   + ++  KG  YA + +K++  +     
Sbjct: 163 YFALVKGDGHLEPEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +  HTGRTHQ+RVH  ++G P++GD  Y  + +         +  LH  Y+   HP 
Sbjct: 217 LVYIHLHTGRTHQIRVHFSYIGFPLLGDDLYGGSLED-----GIQRQALHCHYLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LEQDLQLESPLPDDFSNLITQL 293


>gi|84500882|ref|ZP_00999117.1| putative Pseudouridine synthase, Rlu [Oceanicola batsensis
           HTCC2597]
 gi|84390949|gb|EAQ03367.1| putative Pseudouridine synthase, Rlu [Oceanicola batsensis
           HTCC2597]
          Length = 339

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 78/337 (23%), Positives = 130/337 (38%), Gaps = 50/337 (14%)

Query: 20  RLDRWFKNHYPH---INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           RLD+      P    ++   + +++  G V      V     R+  G V+ I        
Sbjct: 19  RLDKALARDVPEAAALSRTRIARLIAGGAVARAGAAVTDPKARVAEGDVIEIT------- 71

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL 133
                   L ++  +      +   ++YED+ + V +KP G+ V    G      ++  L
Sbjct: 72  --------LGAAAEVETRPQAIPLDVVYEDAALIVVDKPVGMVVHPAPGTPEGTLVNALL 123

Query: 134 KSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               DS       ++P + HR+D++TSG+LV A+T  A   L   F     ++ Y ++  
Sbjct: 124 HHCGDSLSGIGGERRPGIVHRIDKDTSGLLVAAKTDRAHHALAAQFERHSAERAYLAICH 183

Query: 189 GIPKN-------------KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           G+P               +   +     + +    D        E G  +A++  +V++ 
Sbjct: 184 GVPDAADPRLRGVRGASFEPGGVLKLTTQLARHRTDRQRQAVCFE-GGRHAVTRARVLEG 242

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NK 287
           F      LE +  TGRTHQ+RVH  H G  ++GD  Y    +                 +
Sbjct: 243 FG-GAALLECRLETGRTHQIRVHMAHAGHALIGDAVYGGRRRAGKAMGAAAAEALNGFPR 301

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             LHA  +   HPE GR L+  A LPA M      L 
Sbjct: 302 QALHAAVLGFAHPEDGRPLRFEADLPADMAGLLAVLR 338


>gi|260912047|ref|ZP_05918609.1| RluA family ribosomal large subunit pseudouridine synthase
           [Prevotella sp. oral taxon 472 str. F0295]
 gi|260633852|gb|EEX51980.1| RluA family ribosomal large subunit pseudouridine synthase
           [Prevotella sp. oral taxon 472 str. F0295]
          Length = 298

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 83/318 (26%), Positives = 136/318 (42%), Gaps = 37/318 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           Y +YVV E     M LD W  ++    +   L+ ILR   V VD K V  F+ R+Q G  
Sbjct: 14  YDRYVVAEES---MLLD-WLLHNVKGKSRNKLKDILRGHGVFVDGKCVTQFDYRLQPGMK 69

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V +                  S              ++YED  + V +K AG+       
Sbjct: 70  VTV------------------SRAKKAAPFKSRYIKIVYEDRYLIVVDKSAGVLSMAAGH 111

Query: 125 IAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            + ++   L ++ +  GQK    + HRLD+ETSG++V A+     Q L  ++      + 
Sbjct: 112 SSLNVKAILDTYFEKSGQKCRAHVVHRLDRETSGLMVYAKDMDTEQILEHNWHDIVYDRR 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G   ++   I++WL         Y+      + G  YA++HF V++        
Sbjct: 172 YVAVVSGEIVDEGGTISSWL----KDNNSYITYSSPVDNGGKYAVTHFHVLNRTT-THSL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGR +Q+RVH   +G P+ GD KY             ++L LHA  +   HP  
Sbjct: 227 VEYKLETGRKNQIRVHTADIGHPVCGDLKYGNG------DNPLDRLCLHAYMLCFYHPIT 280

Query: 303 -GRLQITAPLPAHMVKTW 319
             R++   P+P    + +
Sbjct: 281 RERMEFFTPIPQTFKQLF 298


>gi|253583482|ref|ZP_04860680.1| pseudouridylate synthase [Fusobacterium varium ATCC 27725]
 gi|251834054|gb|EES62617.1| pseudouridylate synthase [Fusobacterium varium ATCC 27725]
          Length = 290

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 93/309 (30%), Positives = 160/309 (51%), Gaps = 25/309 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V+ + E++RLD++ +  Y +I    + K +R+G+++V+ K+ K N R+Q    +++   
Sbjct: 4   IVDKEFEDVRLDKFLRKKYENIPLTEIFKGIRTGKIKVNGKKSKENYRLQLNDKIKVFFK 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                   KE+K+L+      +  + +K  ++YED  I +FNK   + +  GSG  + I 
Sbjct: 64  DGET----KEEKLLEIE---DREIEKIKKSIVYEDENILIFNKKNNMVMHKGSGYDFGIS 116

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             LK ++  K       +R+D+ TSG+++ A++  AA+ L E  R R I+K Y+ LV GI
Sbjct: 117 ELLKGYL--KNPNFNFVNRIDKATSGLIIGAKSLVAARELAEEIRNRNIEKKYYILVEGI 174

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            KN++  I ++L K      D V  V++ E+GA  +IS+FK I  + +    LE    +G
Sbjct: 175 IKNREFTIKSYLKKIE----DKVIEVEEFEEGAKESISYFK-IKKYGKDCTLLEGTLGSG 229

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLRV   +MG  I+GD KY    +          L+ H   +         ++I  P
Sbjct: 230 RTHQLRVQLANMGNAIIGDVKYGKGKEKMMY------LFSHYLKIKKY-----GIEIDLP 278

Query: 311 LPAHMVKTW 319
           +P   +K  
Sbjct: 279 IPEEYIKRL 287


>gi|66808785|ref|XP_638115.1| hypothetical protein DDB_G0285543 [Dictyostelium discoideum AX4]
 gi|60466557|gb|EAL64609.1| hypothetical protein DDB_G0285543 [Dictyostelium discoideum AX4]
          Length = 718

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 99/337 (29%), Positives = 156/337 (46%), Gaps = 56/337 (16%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V++ + ++KFN+++Q G  +  P  +     I   +     +    +    ++  +LY+D
Sbjct: 375 VQLKRHKLKFNDKVQVGSWIYFPAQVILDQQIADIKDPQKYARLSDQEIKEIRESVLYKD 434

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
             I V NKP G+SVQGG+G+  H+D  L      K + P+L HRLD+ TSGIL++ R++ 
Sbjct: 435 EHIIVLNKPQGLSVQGGTGLNKHLDMMLSHLRFEKDENPKLVHRLDRNTSGILILGRSKL 494

Query: 166 AAQHLTESFR-------------------------------------------------- 175
           AA  +T+ F                                                   
Sbjct: 495 AASAMTKKFELKLVKENKKDKDDNNNNKNNKNNNKNDSKRLFREKEVFNNNKNKDEENEN 554

Query: 176 -MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             + I+K YW+L+   P  K+  I   L K    G + V        GA  AI+ +KV++
Sbjct: 555 YSKGIKKTYWALLGSTPTPKEGRIRAPLKKVVVGGFEKVVPTLTTGDGAKIAITEYKVLE 614

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNFTS---PIQNKLYL 290
               K C++ + P TGRTHQLRVH    +  PI+GD KY      +      P  +KL+L
Sbjct: 615 SSLTKHCFISLWPETGRTHQLRVHCASVLNTPIIGDPKYGDKESDSNLKDLLPYPSKLHL 674

Query: 291 HARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKY 326
           HAR ++  HP    ++ I+APLP  +V+ W ++GF Y
Sbjct: 675 HARRIEFIHPFTNKKIDISAPLPRELVQNWKTMGFNY 711



 Score = 43.4 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 10/35 (28%), Positives = 17/35 (48%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV 46
           V  D E MR+D+W     P +    + + LR+  +
Sbjct: 226 VSKDMEGMRVDKWISTKLPVLPHSLICRWLRNKAI 260


>gi|47568408|ref|ZP_00239109.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus G9241]
 gi|47554956|gb|EAL13306.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus G9241]
          Length = 297

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 133/315 (42%), Gaps = 39/315 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 10  IDSAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQYASVRHQLQAGEELRVFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 68  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPAGSV 113

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 114 A---NALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFMHHLLSKQHQQKAVKRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID  A     + 
Sbjct: 171 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVS 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 225 LELDTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 278

Query: 304 RLQITAPLPAHMVKT 318
            +  T  +P  M   
Sbjct: 279 EMSFTTTIPNDMQAV 293


>gi|330839025|ref|YP_004413605.1| pseudouridine synthase, RluA family [Selenomonas sputigena ATCC
           35185]
 gi|329746789|gb|AEC00146.1| pseudouridine synthase, RluA family [Selenomonas sputigena ATCC
           35185]
          Length = 301

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 71/315 (22%), Positives = 126/315 (40%), Gaps = 38/315 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIP 68
           +VV      M L  + +      +    +K+ RSG   ++         RI+SG  +   
Sbjct: 6   LVVPEGLTCMALREFLQKEC-GFSTTLWKKLRRSGTFSLNGLPANAARIRIKSGDELCW- 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                  H+ +E +I    + L          +LYED+ + + NKPAG+ V    G   H
Sbjct: 64  -------HLAEESRIAPEDIPLE---------ILYEDAALLIVNKPAGMLVHPTGGEYRH 107

Query: 129 I--DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +  L  +    +       HRLD++TSG++++A+       L+       I++IY +
Sbjct: 108 TLANAVLFHYEAHGEKHAFHPVHRLDRQTSGLVLIAKEAHVQHLLSAHNA---IERIYLA 164

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           ++ G        I   + ++     + +            A++H+  +         L +
Sbjct: 165 VIEGKLPEPCGTIDAPIARRPGSIIERMV-----SPAGKCAVTHYATLAERG-GLSLLAL 218

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           +  TGRTHQ+RVH  H+  P++GD  Y              +  LHA  +   HP  G  
Sbjct: 219 RLATGRTHQIRVHLAHLAHPLLGDDLYGGRTDR------IARQALHAHRLRFRHPISGKE 272

Query: 305 LQITAPLPAHMVKTW 319
           + + AP PA M   +
Sbjct: 273 ITVHAPFPADMSAFF 287


>gi|319935496|ref|ZP_08009931.1| pseudouridine synthase [Coprobacillus sp. 29_1]
 gi|319809527|gb|EFW05944.1| pseudouridine synthase [Coprobacillus sp. 29_1]
          Length = 324

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 88/329 (26%), Positives = 146/329 (44%), Gaps = 34/329 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++++ +  N R+D++ K          + K+LR   V+V+  +VK N  +Q+  VV 
Sbjct: 1   MKKLIIDENHANQRIDKYLKKLLCQAPSQLIYKMLRKKDVKVNGVKVKENYILQNHDVVE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
           +    +      + Q I D  +            ++YED KI V  KPAG+ V    +  
Sbjct: 61  LFLYEDKFQEYTRAQTIFDLKIEFQ---------VIYEDDKILVVGKPAGLLVHEDINED 111

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +   + +++  KG+          P   HRLD+ TSGI++  +T  A Q L E  + 
Sbjct: 112 MNTLSNQVITYLYQKGEYDPQISLGFTPGPVHRLDRNTSGIVIFGKTMRALQDLNEMMKK 171

Query: 177 RR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           R  I+K Y ++  G   +    +  ++ K        V VV QN  GA    +  + I+ 
Sbjct: 172 RHCIEKTYLTICKGHMSSAD--LVGYMKKDGDQS--LVKVVTQNTPGALMMHTLVENIEY 227

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHAR 293
             Q F  L++Q  TGRTHQ+RVH   +G PI+GD KY      +           +LHA 
Sbjct: 228 H-QGFSLLKVQLVTGRTHQIRVHLASVGHPIIGDSKYGDFELNREMKKKYHLQHQFLHAY 286

Query: 294 YMDLPHPEG------GRLQITAPLPAHMV 316
            +    P G       ++ I  PLP ++ 
Sbjct: 287 TIKFVKPIGCLKYLQNQVMI-CPLPQNLQ 314


>gi|184201118|ref|YP_001855325.1| pseudouridine synthase RluD [Kocuria rhizophila DC2201]
 gi|183581348|dbj|BAG29819.1| pseudouridine synthase RluD [Kocuria rhizophila DC2201]
          Length = 325

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 139/321 (43%), Gaps = 28/321 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             V  +++ +RLD      +  ++     ++    +V      V  ++R+   +   +  
Sbjct: 20  FTVPPEQDGLRLDAAVAA-WTGLSRSAAAQLCAEQRVSHRGSPVAKSHRVAVSETYTVEV 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYH 128
            +    H I  Q + D               L++ +    V +KPAG++     G     
Sbjct: 79  PVPEDPHRIAPQHVPD-------------LRLVHVEPSYVVVDKPAGVAAHPSPGWKGPT 125

Query: 129 IDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           + G L             ++  + HRLD  TSG++VVAR   A   L  +F+ R + K+Y
Sbjct: 126 VVGALAGAGISVATSGAPERQGIVHRLDVGTSGLMVVAREEGAYSQLKRAFKERTVTKVY 185

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V GIP   K  I   + +  H G ++   V ++      +++H++V++ F +    +
Sbjct: 186 HAVVQGIPDPLKGTIDAPIGR--HPGHEWRFAVMED---GRNSVTHYEVLEAFGR-ASLV 239

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E+   TGRTHQ+RVH   +  P  GD  Y A+   +    +  + +LHA+ +    P  G
Sbjct: 240 EVHLETGRTHQIRVHFSALQYPCCGDLTYGADPALSAGLGL-TRQWLHAKRLGFTSPATG 298

Query: 304 R-LQITAPLPAHMVKTWDSLG 323
           + ++  +P P  +    ++L 
Sbjct: 299 QHVEYESPYPTDLAYAVETLR 319


>gi|302338972|ref|YP_003804178.1| pseudouridine synthase [Spirochaeta smaragdinae DSM 11293]
 gi|301636157|gb|ADK81584.1| pseudouridine synthase, RluA family [Spirochaeta smaragdinae DSM
           11293]
          Length = 319

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 129/321 (40%), Gaps = 36/321 (11%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +  +R+DR+            L++  R+ +  ++ K VK ++R+ +G  + +        
Sbjct: 19  DGGVRIDRYVSEVAGLFARSQLRQ--RNPRFFINGKVVKASSRVYTGDRIALMY------ 70

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFL 133
                    +     +  +  +   ++YED  + V +KP G+ V   +G      + G L
Sbjct: 71  ---------EDQPEPSFGAQAIDLSIIYEDEHVIVVDKPQGLVVHPAAGNWSGTLVQGLL 121

Query: 134 KSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               +          +P + HRLD++TSG+L+ A+     Q L E F  RR +K Y +LV
Sbjct: 122 YHCRELGERFGEDTVRPGIVHRLDKDTSGVLIAAKDPETRQFLAEQFANRRCKKRYIALV 181

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   N    + + +++       +   +     G   A++ +  +              
Sbjct: 182 KGDLSNATGRMESGIIRDPKNRKRFTWTMS----GGKPAVTEYTRL-RRGNDCSLAAFNL 236

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGRTHQ+RVH L +G P++GD  Y        T      L LH+  +++  P E    +
Sbjct: 237 LTGRTHQIRVHTLMLGHPVIGDPIYGRKN----TRFPDLGLMLHSMSLEILLPGEREPRR 292

Query: 307 ITAPLPAHMVKTWDSL-GFKY 326
             APLP           G  Y
Sbjct: 293 FIAPLPERFRAPLQQCWGLDY 313


>gi|254459281|ref|ZP_05072702.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacterales bacterium GD 1]
 gi|207083894|gb|EDZ61185.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacterales bacterium GD 1]
          Length = 325

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 149/330 (45%), Gaps = 41/330 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           M+ ++  V +N E   RLD +  +         +  +++   V VD+K V +   +++SG
Sbjct: 1   MSDIKSYVCDNPE---RLDIFLASEI-GQTRSQIASLIKHKCVFVDEKLVTRPGVKLKSG 56

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q +++           KE   LD   N+          +LYED  + V NKP+G++V   
Sbjct: 57  QNIKVEFPE------AKESPALDIDFNVE---------ILYEDDDVLVINKPSGVTVHPA 101

Query: 123 SGIAYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTES 173
             +    +  L  W+  KG +           + HRLD+ TSG +VVA+   A + L+E 
Sbjct: 102 PSV---KEATLVDWLKHKGIRLSNISGEERHGIVHRLDKGTSGTMVVAKNNEAHEFLSEQ 158

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + + + + Y +++    K++   I   + + +H   + + +   +   + YA + FKV+
Sbjct: 159 LQDKSMGRYYLAVLNPPLKDEITTIEQNIGRSAH---NRLKMTCTDAGKSKYAKTMFKVL 215

Query: 234 D-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                +K  ++  +  TGRTHQ+RVH   +   I+GDH Y  + K   +     ++ LHA
Sbjct: 216 SLSNDEKQQFVACKLFTGRTHQIRVHLESINRHIIGDHIYALSPKAEKSE----RILLHA 271

Query: 293 RYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
             +   HP    +L   APL   M    D 
Sbjct: 272 YMIYFVHPTSKEKLTFVAPLDETMKDYLDK 301


>gi|30019354|ref|NP_830985.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|229126613|ref|ZP_04255626.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-Cer4]
 gi|29894897|gb|AAP08186.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|228656850|gb|EEL12675.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-Cer4]
          Length = 292

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 132/314 (42%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   +E   +  + K     I+   L  I    G + V+ +     +++++G+ +R+   
Sbjct: 5   IGPAQEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLRAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + + NK A +S            
Sbjct: 63  VEERSEGM--------------MAEDIPLCIIYEDDAVLIINKEANMSTIPSREHPAGSV 108

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    + +       +    A++HFKVID    K   + ++ 
Sbjct: 169 HGKIVEREGMIDAPIGRKSDSIIERMVC-----EDGQRAVTHFKVIDSTYHK-THVALEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y              +  LH++ +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAHIGHPLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWD 320
            T  LP+ M +   
Sbjct: 277 FTIKLPSDMQEVLR 290


>gi|320536301|ref|ZP_08036344.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
 gi|320146861|gb|EFW38434.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
          Length = 320

 Score =  210 bits (534), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 80/339 (23%), Positives = 138/339 (40%), Gaps = 51/339 (15%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   ++VV E   E  RLD +      +I    L+  L+S    V+ K+ K +  ++   
Sbjct: 1   MQNKRFVVSEAYNEPRRLDVFCGAQM-NIPRSKLKAGLQSAA--VNGKQAKLSTLVRPND 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V I          I E+               +   +L+E+  +   NK  G+     S
Sbjct: 58  IVEIKWADPIPEVFIPEE---------------IPLSILFENEDVIAVNKQQGLVTHPAS 102

Query: 124 GIAYHIDGFLKSWVD-----------------------SKGQKPRLTHRLDQETSGILVV 160
           G   +  G L   +                            +  + HRLD++TSG+L+ 
Sbjct: 103 G---NWTGTLVQGLAYYRLHCSPIKDEFSEILQNTQSFQSCFRQGIVHRLDKDTSGVLIT 159

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R   A +     F+  +  KIY ++V G P+  K  I   + +       +      + 
Sbjct: 160 ERNTRAEEFFKAQFKQHKTTKIYLAVVQGCPRTLKGKIETSIYRDPKHRTKFAASSDLSV 219

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               YA + ++V+  F  K+  ++ +  TGRTHQ+R+HA  +GCPI+GD  Y        
Sbjct: 220 --GRYADTLYRVLKTFG-KYSIVQFKLGTGRTHQIRMHAAFIGCPILGDPLYGKKD---- 272

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
           +    + L LHA+++ +  P+G  ++ITAPLP       
Sbjct: 273 SRFSSSSLMLHAQHLKINLPDGNPIKITAPLPERFRSFL 311


>gi|328948139|ref|YP_004365476.1| pseudouridine synthase, RluA family [Treponema succinifaciens DSM
           2489]
 gi|328448463|gb|AEB14179.1| pseudouridine synthase, RluA family [Treponema succinifaciens DSM
           2489]
          Length = 326

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 78/334 (23%), Positives = 146/334 (43%), Gaps = 43/334 (12%)

Query: 12  VENDEEN-MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V    +  +RLD++  +    +N   L+  +    ++V+ K+ K + ++++  ++ I   
Sbjct: 8   VPPTYKGEIRLDKYIASLPNGMNRSKLKSGIV--CIQVNGKKQKISCQVKANDIIDIQWE 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
            N  ++I  E   LD+               +YED  + V NK  G+     +G      
Sbjct: 66  ENVPDNIEPENIPLDT---------------IYEDENVCVVNKKQGMVTHPAAGNWKGTL 110

Query: 129 IDGFLKSWVDSK--------------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           ++  L  W                   ++P + HRLD+ETSGI++ A+     + L+  F
Sbjct: 111 VNALLYHWGRESIPELKEGQVSKILSNRRPGIVHRLDKETSGIIITAKNHDTEEFLSAQF 170

Query: 175 RMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           R    I K Y ++  G P+++   I   +++       +  VV   E     A S+++ I
Sbjct: 171 RNHSSIVKEYIAICIGRPQHQHGIIQTNIIRDPKERKRFKAVVGTEE--GKPAESYYECI 228

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
            C+ + +  ++++ +TGRTHQ+RVH  ++ CPI+GD  Y    K       +  L L+AR
Sbjct: 229 SCYGE-YSLMKVRINTGRTHQIRVHMKYLNCPILGDGIYAHQDK----KFPKATLMLNAR 283

Query: 294 YMDLPHPEGGRLQ-ITAPLPAHMVKTWDSLGFKY 326
            + +  P    L    +P P   ++    L   Y
Sbjct: 284 LLKIKIPGKEELSIFKSPTPERFIEVMKVLKRDY 317


>gi|312867737|ref|ZP_07727943.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
 gi|311096800|gb|EFQ55038.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
          Length = 297

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 76/309 (24%), Positives = 132/309 (42%), Gaps = 33/309 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L KI  R GQ+ V+ +       +  G  + I          +K   
Sbjct: 16  FLKKH--EVSKGLLAKIKFRGGQILVNGRPENAIYLLDIGDRLVIDIPAEEGFETLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
                             +L+ED    + NKP GI+    +  +  +  F+K +   +G 
Sbjct: 71  -----------PMDRSLDILFEDDHFLILNKPFGIASIPSAIHSNTLANFVKGYYVKQGY 119

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
             Q+  +  RLD++TSG+++ A+   A   L +  + + IQK Y++LV G  K +    I
Sbjct: 120 ENQQVHIVTRLDKDTSGVMLFAKHGYAHARLDKQLQSKTIQKRYYALVKGSGKLDPVGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      +   + ++  KG  YA + ++V+  F   +  +++Q HTGRTHQ+RVH
Sbjct: 180 IAPIARD-----EDSIITRKVAKGGKYAHTSYQVVQSFGDIY-LVDIQLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   HP     L I +PLP     
Sbjct: 234 FSHIGFPLLGDDLYGGSLED-----GIERQALHCHRLSYYHPFLEEELVIESPLPPDFQA 288

Query: 318 TWDSLGFKY 326
               L   Y
Sbjct: 289 VLTQLQTSY 297


>gi|307704763|ref|ZP_07641659.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
 gi|307621672|gb|EFO00713.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
          Length = 298

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 140/323 (43%), Gaps = 37/323 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNDQPQNATYLLDIGDRV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +      +LYED    V NKP G++       
Sbjct: 57  IIDIPAEGGFETLE--------------AIERPLDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIEKR 162

Query: 183 YWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           Y++LV G    + + E IA     +  I      + ++  KG  YA + +K++  +    
Sbjct: 163 YFALVKGDGHLETEGEIIAPIARDEDSI------ITRRVAKGGKYAHTSYKIVASYGNIH 216

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             ++++ HTGRTHQ+RVH  H+G P++GD  Y  +           +  LH  Y+   HP
Sbjct: 217 -LVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHYLSFYHP 270

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
              + LQ+ +PLP         L
Sbjct: 271 FLEQDLQLESPLPDDFSNLITQL 293


>gi|168486485|ref|ZP_02710993.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1087-00]
 gi|183570531|gb|EDT91059.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1087-00]
          Length = 298

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 137/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNNQPQNATYLLDVGDYV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +      +LYED    V NKP G++       
Sbjct: 57  TIDIPAEEGFETLE--------------AIEHPLDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHTRLDKQLQKKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +      +   + ++  KG  YA + +K++  +     
Sbjct: 163 YFALVKGDGHLEPEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +  HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH  Y+   HP 
Sbjct: 217 LVYIHLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLED-----GIQRQALHCHYLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LEQDLQLESPLPDDFSNLITQL 293


>gi|157737249|ref|YP_001489932.1| ribosomal large subunit pseudouridine synthase D [Arcobacter
           butzleri RM4018]
 gi|157699103|gb|ABV67263.1| ribosomal large subunit pseudouridine synthase D [Arcobacter
           butzleri RM4018]
          Length = 328

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 81/325 (24%), Positives = 152/325 (46%), Gaps = 37/325 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
           ++V+E +    RLD++   +    +   ++++++   V+VD K   K   +++  Q V +
Sbjct: 5   FIVLETN----RLDKFLAQNI-DASRNQIEQLIKKEFVKVDGKITNKTGLKLKENQNVEV 59

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                 LN   K+++ L +S+      +  +  ++YED  I V NKP  ++V     +  
Sbjct: 60  FFPETQLNKR-KDEEFLKNSL------EDKEVEIIYEDDYILVLNKPYNLTVHDAPSV-- 110

Query: 128 HIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             D  L  W+  K          ++  + HRLD+ TSG++V+A+T  A  +L++    + 
Sbjct: 111 -KDATLVDWLKLKNISLSTISGEERHGIVHRLDKGTSGVMVIAKTNEAHLNLSKQLEDKS 169

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFA 237
           + + Y +++      K+  I    ++++      + +    E+   YA S F  I     
Sbjct: 170 MGRYYLAILD--LALKENVIIEKPIRRNPNNRLKMSI----EENGRYAKSAFSKIALSDN 223

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +KF  +  + +TGRTHQ+RVH   +   I+GD+ Y   FKG       N+  LHA Y+ L
Sbjct: 224 EKFELIACKLYTGRTHQIRVHLSSINRHILGDNLYG--FKGELNK--INRFLLHAYYLYL 279

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDS 321
            HP    ++   A LP  M    ++
Sbjct: 280 THPVTNKQMCFKANLPEDMKNFLNT 304


>gi|239623805|ref|ZP_04666836.1| pseudouridine synthase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521836|gb|EEQ61702.1| pseudouridine synthase [Clostridiales bacterium 1_7_47FAA]
          Length = 330

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 140/333 (42%), Gaps = 28/333 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V  +E   R+D+    +        L K++R   + ++ K+   +  ++ G  ++
Sbjct: 1   MQTLTVTPNEAGQRMDKLLAKYLDQAGKGFLYKMMRKKNITLNGKKCDGSEHLEEGDEIQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +     A   I K Q    +    T    + K  ++YED  I V NKP+G+  Q      
Sbjct: 61  LFM---ADETIEKFQAAPKAPARSTAGYGYKKLDIIYEDRHILVVNKPSGMLSQKAREGD 117

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             ++ ++ +++   G          KP + +RLD+ TSG++V  ++ A  Q +   F+ R
Sbjct: 118 MSLNEYILNYLIDSGGLPISQLRTFKPSICNRLDRNTSGLVVAGKSLAGLQVMNGVFKDR 177

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  LV G  K KK  IA +L K      + V +     + +   ++ +  +    
Sbjct: 178 SLHKYYQCLVAGQIKEKK-LIAGFLRKDE--AANTVTIYPLEVEDSVPIMTEYLPLAGNG 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNK-LYLHARYM 295
                L++   TGR+HQ+R H   +G PIVGD+KY   +           +   LH+  +
Sbjct: 235 -NHTLLQVTLITGRSHQIRAHLASIGHPIVGDYKYGRQDLNDAMKKKYGVRSQLLHSWRL 293

Query: 296 ----DLPHP----EGGRLQITAPLPAHMVKTWD 320
                LP P     G  +   A LP    +   
Sbjct: 294 VMPDKLPQPLDYLSGKEMV--AGLPDQFARVLK 324


>gi|149003786|ref|ZP_01828618.1| phosphotransacetylase [Streptococcus pneumoniae SP14-BS69]
 gi|237650771|ref|ZP_04525023.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae CCRI 1974]
 gi|237822358|ref|ZP_04598203.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae CCRI 1974M2]
 gi|147758232|gb|EDK65234.1| phosphotransacetylase [Streptococcus pneumoniae SP14-BS69]
 gi|301794215|emb|CBW36634.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           INV104]
 gi|332075432|gb|EGI85901.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA41301]
 gi|332202956|gb|EGJ17024.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA47901]
          Length = 298

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 137/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNNQPQNATYLLDVGDYV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +      +LYED    V NKP G++       
Sbjct: 57  TIDIPAEEGFETLE--------------AIEHPLDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +      +   + ++  KG  YA + +K++  +     
Sbjct: 163 YFALVKGDGHLEPEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +  HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH  Y+   HP 
Sbjct: 217 LVYIHLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLED-----GIQRQALHCHYLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LEQDLQLESPLPDDFSNLITQL 293


>gi|229177719|ref|ZP_04305094.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           172560W]
 gi|228605774|gb|EEK63220.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           172560W]
          Length = 292

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 64/313 (20%), Positives = 131/313 (41%), Gaps = 33/313 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE   +  + K     I+   L  I    G + V+ +     +++++G+ +R+   
Sbjct: 5   IGPAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLRAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + + NK A +S            
Sbjct: 63  VEERSEGM--------------MAEDIPLSIVYEDDAVLIINKEANMSTIPSREHPTRSV 108

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HFKVID    K   + ++ 
Sbjct: 169 HGKIVEREGMIDAPIGRKSDSIIERTVC-----EDGQRAVTHFKVIDSTYHK-THVALEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y              +  LH++ +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAHIGHPLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTW 319
            T  LP+ M +  
Sbjct: 277 FTIKLPSDMQEVL 289


>gi|288573309|ref|ZP_06391666.1| pseudouridine synthase, RluA family [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288569050|gb|EFC90607.1| pseudouridine synthase, RluA family [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 305

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 77/329 (23%), Positives = 134/329 (40%), Gaps = 31/329 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   VV   ++  RLD+  +  +P +    + K  R  QVR+D  R  F+ R+  GQ + 
Sbjct: 1   MDRFVVSRHDDGRRLDKVIRKKWPSLPLGAMMKAFRKKQVRIDGARASFDQRLVEGQEIL 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P           E    D     T        + +Y D  ++V +KPAG+  Q      
Sbjct: 61  VPW----------ESAPTDVGAKRTGGH----LVTVYRDESLWVVSKPAGLLSQPDKKGG 106

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +    ++++     +P+  +RLD+ TSGI+V+A T  + + L+  +R   ++K+Y +L
Sbjct: 107 DSVVT--RAFLPGSSFQPQAVNRLDRNTSGIMVLALTGESLRDLSSRWRDGEMEKVYLAL 164

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    ++  I   L K       +V      +     +++ ++ +           + 
Sbjct: 165 VVGDLP-EEGSIDAPLSKDGSSNKVFV------DSKGQSSLTLYRRLAS-GGGLSLCLVT 216

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG--- 303
             TGR+HQ+RVH  H+G P++GD KY              +  LHA  +  P   G    
Sbjct: 217 LITGRSHQIRVHMSHIGHPVLGDVKYGDRALNGVK--GAKRPMLHAFSVSFPDMSGDLSS 274

Query: 304 --RLQITAPLPAHMVKTWDSLGFKYDRNL 330
                   P+P  M       G   DR  
Sbjct: 275 LSSKTFRTPMPEDMADMCSKNGIVPDRAF 303


>gi|206896098|ref|YP_002247034.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Coprothermobacter proteolyticus DSM 5265]
 gi|206738715|gb|ACI17793.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Coprothermobacter proteolyticus DSM 5265]
          Length = 315

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 78/314 (24%), Positives = 137/314 (43%), Gaps = 37/314 (11%)

Query: 20  RLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNH 76
           RLD           I+   +Q  +++G VR +   V K + R++ G ++ I      L  
Sbjct: 18  RLDLALMEIIDDEGISRTWIQNNIKAGLVRCNGDVVTKPSLRVKKGDLLEI-----RLRS 72

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLK 134
            I E +  D           ++  ++Y D  + V +KP  + V     +       G LK
Sbjct: 73  RISELQPAD-----------VEYSVVYYDEHLAVIDKPPNLVVHPAPSVKGLTLCHGLLK 121

Query: 135 SWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            +         ++P + HRLD++TSG+++VA +      LT+    + + + Y   V+G+
Sbjct: 122 DFPQVKNVGSAERPGIVHRLDKDTSGLMLVALSEKGYAGLTKMISEKSVSRKYLVAVYGV 181

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N+   +   + +          V          A + F+ + C  +K   LE +  TG
Sbjct: 182 -ANRPFEVDAPIGRDPRNPTRMAVV-----PHGKNAYTRFRPVQCL-EKVSLLEAELFTG 234

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           RTHQ+RVH  H G  ++GD  Y        +  +  +++LH+ Y++L HP  G RL   +
Sbjct: 235 RTHQIRVHLSHAGFYVLGDPVYG----NVESRLLAPRVFLHSYYLELEHPITGERLFFVS 290

Query: 310 PLPAHMVKTWDSLG 323
           PLP  + + W  LG
Sbjct: 291 PLPEDLDECWHILG 304


>gi|254823760|ref|ZP_05228761.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
 gi|255521997|ref|ZP_05389234.1| ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes FSL J1-175]
 gi|293592981|gb|EFG00742.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
          Length = 296

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 145/319 (45%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE +E+ + L  + K+   HI+   L   K    G++ V+ K       +++G  VR+  
Sbjct: 7   VETEEDGLLLRTFLKS--KHISKQLLTAVKFGAEGKIEVNNKEQNVLYHVKAGDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTDLDIIFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 NGSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +   G+   +K  I   + +K     +   + +       YA ++++V+  + + F  +
Sbjct: 168 QAFTSGVLVEQKGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLARY-RAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
           + +    PLPA M +    
Sbjct: 276 KYMAFDLPLPADMEEIIQK 294


>gi|88607689|ref|YP_505141.1| ribosomal large subunit pseudouridine synthase C [Anaplasma
           phagocytophilum HZ]
 gi|88598752|gb|ABD44222.1| ribosomal large subunit pseudouridine synthase C [Anaplasma
           phagocytophilum HZ]
          Length = 297

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 87/304 (28%), Positives = 156/304 (51%), Gaps = 20/304 (6%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+ ++  P +    ++K+LR G++R++  +   ++R+Q G  V I  V    +   
Sbjct: 1   MRLDRYVRSILPGVPQALVEKLLRKGEIRLNSSKALASSRVQRGDTVSIRNVDKIASRSK 60

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + +++ D ++        +   ++Y+D  I   NKPAG++VQGG+ ++  +   L   + 
Sbjct: 61  EAKEVHDDALLR-----LVSDNIIYKDENIIAINKPAGVNVQGGTKVSISLSDLLNKIIP 115

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             G++  + HRLD++TSG+L++AR ++ A+ L+E  R RR++K Y ++  G+P   K  I
Sbjct: 116 --GEQLHIVHRLDRDTSGVLIIARGQSIARILSEELRFRRVRKEYIAVTKGVPAFSKGEI 173

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +  K   G     +          A + F V+   +++   + + P TGR HQLR+H
Sbjct: 174 TMPIYCKKQSGVGETLI-------PKEAKTVFSVLQS-SKRHAVMLLSPVTGRKHQLRIH 225

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                CPI+GD KY  + +        N L+LHA            + I AP+P +M+ T
Sbjct: 226 LSQFCCPIIGDTKYSKDTEVQ----QHNSLHLHAFRTSFQ-LFDREIVIKAPVPEYMIAT 280

Query: 319 WDSL 322
            + L
Sbjct: 281 INEL 284


>gi|52144130|ref|YP_082698.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
 gi|51977599|gb|AAU19149.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
          Length = 297

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 132/315 (41%), Gaps = 39/315 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q G+ +RI   
Sbjct: 10  IESAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLQVGEELRIFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 68  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPSGSV 113

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 114 A---NALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID  A     + 
Sbjct: 171 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVS 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 225 LELDTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 278

Query: 304 RLQITAPLPAHMVKT 318
            +  T  +P  M   
Sbjct: 279 EMSFTTTIPNDMQAV 293


>gi|228984376|ref|ZP_04144555.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar tochigiensis BGSC 4Y1]
 gi|228775345|gb|EEM23732.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar tochigiensis BGSC 4Y1]
          Length = 292

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 135/315 (42%), Gaps = 39/315 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ EE   +  + K     I+   L  I  + G + V+ +     +++Q+G+ +R+   
Sbjct: 5   IDSAEEGTLVREFLKT--KGISKAALTDIKFQGGAIEVNGQHASVRHQLQAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPAGSV 108

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 109 A---NALLTHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID  A     + 
Sbjct: 166 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVS 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 220 LELDTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 273

Query: 304 RLQITAPLPAHMVKT 318
            +  T  +P+ M   
Sbjct: 274 EMSFTTTIPSDMQAV 288


>gi|319646539|ref|ZP_08000768.1| YjbO protein [Bacillus sp. BT1B_CT2]
 gi|317391127|gb|EFV71925.1| YjbO protein [Bacillus sp. BT1B_CT2]
          Length = 296

 Score =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 132/319 (41%), Gaps = 39/319 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++  ++  + L  + +     I+   L  I    G + V+   V     +Q G  + I  
Sbjct: 9   IITEEDSGVLLKEYVQRL--GISKRMLTDIKFGGGDLLVNGGHVTVRYVLQKGDELVIQF 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               ++  ++ +++                 +L+ED  + V NK   IS         H 
Sbjct: 67  PPEKMSESLQPEEV--------------PLHILFEDDHVLVLNKQPCISSIPSR---EHP 109

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G L + +    Q+        L  RLD++TSG+++VA+ R A   L+   +   +++ Y
Sbjct: 110 SGSLANGLIHYYQRTGVHATVHLVSRLDRDTSGVMLVAKHRFAHSLLSGLQKKGAVKRQY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G+   ++  I   + +KS    +   +          A++HF V   F+     +
Sbjct: 170 RAVVHGLIAEEQGTIDAPIGRKSSSIIERAVI-----PDGQKAVTHFWVNRRFS-GMTDV 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
            ++  TGRTHQ+RVH  H+G P+ GD  Y        T    N+  LH+  +   HP   
Sbjct: 224 SIRLETGRTHQIRVHMSHIGYPLCGDTLYGG------TRGFINRQALHSERLTFFHPFTM 277

Query: 303 GRLQITAPLPAHMVKTWDS 321
             L   AP+P  M +  +S
Sbjct: 278 EELTFQAPVPNDMRQLIES 296


>gi|170756838|ref|YP_001782613.1| RluA family pseudouridine synthase [Clostridium botulinum B1 str.
           Okra]
 gi|169122050|gb|ACA45886.1| pseudouridine synthase, RluA family [Clostridium botulinum B1 str.
           Okra]
          Length = 300

 Score =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 147/323 (45%), Gaps = 28/323 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      VV+    N+ +  + +    +++   ++K +R G+V V+K++V   N++    
Sbjct: 1   MDNKLIFVVKKINHNIDIKDYLRE-IENLSGRFIRKAVRDGRVFVNKEKVIKKNKLSQDD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I    +   +I  E   ++               ++YED+ I V NK  GI V    
Sbjct: 60  LIEIYMQEDEHQNIEPEDMNIE---------------IVYEDNDIIVINKRPGIVVHPTK 104

Query: 124 GIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G     +   +       G+K   RL  RLD++TSG++++A+ + +   L         +
Sbjct: 105 GHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFR 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY ++V G  K K+  I   + K+     +   + +  ++    +I+ ++V++  ++  
Sbjct: 165 KIYIAVVHGSMKEKEGRINLPIYKEE----ESESIKRIVDERGQESITTYEVLEELSKG- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++  TGRTHQ+RVH  H+G P+ GD  Y    KG        +  LHA  ++ PHP
Sbjct: 220 SVVRLELETGRTHQIRVHMSHLGHPLYGDSLYG---KGEEEKEYIERQALHAYKLEFPHP 276

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
             G + ++   LP  +    + +
Sbjct: 277 RTGDILKLQCSLPDDIKNLIEKI 299


>gi|269114915|ref|YP_003302678.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hominis]
 gi|268322540|emb|CAX37275.1| Ribosomal large subunit pseudouridine synthaseD (RNA
           pseudouridylate synthase, RNA-uridine isomerase )
           [Mycoplasma hominis ATCC 23114]
          Length = 297

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 132/308 (42%), Gaps = 36/308 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           R+D++  N+   I+  ++++++ +G V V+  ++ K    ++ G  + I           
Sbjct: 11  RIDKYVANN-SEISRNDIKELIENGAVFVNSIKINKPKFVVKEGDEILI----------- 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +++LD  + +   +  L   ++YE     + NKP+G+ V    G  +H +  + + + 
Sbjct: 59  --ERLLDKQIKVEPQNIHLD--IVYECDDYLIINKPSGLVVHPAPG--HHDNTLVNALMY 112

Query: 139 SKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                           + HR+D++TSG+L++A+   A  +     +   I++ Y+++V G
Sbjct: 113 HFKNNLSDVNGLLRMGVVHRIDKDTSGLLLIAKNNKAHNYFASLLKTHEIKRSYYAIVEG 172

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N++  I   + + +        V + N K A   ++  K      + F  ++    T
Sbjct: 173 KIANEELHIELPIGRDTK-NRQKYAVSETNSKPAYTIVNVVKYFKMNNKDFSLVKCNLKT 231

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           GRTHQ+RVH  ++  P+ GD  Y              +L  HA  +D     G      A
Sbjct: 232 GRTHQIRVHLAYIKHPVYGDPIYGHKIDD-----FNQRL--HAFALDFVDLNGNNKHFEA 284

Query: 310 PLPAHMVK 317
            +P  M K
Sbjct: 285 EMPEIMKK 292


>gi|19551566|ref|NP_599568.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glutamicum ATCC 13032]
 gi|62389214|ref|YP_224616.1| ribosomal large subunit pseudouridine synthase C [Corynebacterium
           glutamicum ATCC 13032]
 gi|21323080|dbj|BAB97709.1| Pseudouridylate synthases, 23S RNA-specific [Corynebacterium
           glutamicum ATCC 13032]
 gi|41324547|emb|CAF18887.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE C [Corynebacterium
           glutamicum ATCC 13032]
          Length = 294

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 83/309 (26%), Positives = 137/309 (44%), Gaps = 26/309 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           ++ V     + R+D++ +     +    + + +R G +RV+ ++V  N R+Q G  +R+ 
Sbjct: 5   FIEVSAGHADRRIDKFLRAQLKGVPASLIFRQMRKGDIRVNGRKVDPNYRLQEGDRIRMW 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            +    +        L   V        +   +L+ED+++ V NKPAGI V GG+G    
Sbjct: 65  QMDLLAD--------LPPPVVDKHIFKAVADSVLFEDAELLVINKPAGIPVHGGTGHGGG 116

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--RIQKIYWSL 186
           +   L+     + +   L HRLD++TSG+L+V++T +  + L E  R R   I + Y   
Sbjct: 117 VIEALRQKFPQE-RDLELVHRLDRDTSGLLLVSKTTSVLRELQEILRDREEEIFRGYLLK 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        I   L                       A ++F+V+         ++ Q
Sbjct: 176 VEGAWPGDLRQIDVPL--------KRTETTVVPHSDGLRARTYFEVVKRLP-GATLVKAQ 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
             TGR HQ+RVHA + G PIVGD +Y +      T      ++LHA  +  P   G R +
Sbjct: 227 LATGRKHQIRVHAQYAGHPIVGDPRYGSRGGRAAT------MHLHAAELVAPRGAGKRQK 280

Query: 307 ITAPLPAHM 315
            TAPLP   
Sbjct: 281 FTAPLPKEW 289


>gi|148989142|ref|ZP_01820532.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP6-BS73]
 gi|147925365|gb|EDK76443.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP6-BS73]
          Length = 298

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 138/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNNQPQNATYLLDVGDYV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++  + L                +LYED    V NKP G++       
Sbjct: 57  TIDIPAEEGFETLEAIEHL--------------LDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +      +   + ++  KG  YA + +K++  +     
Sbjct: 163 YFALVKGDGHLEPEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +  HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH  Y+   HP 
Sbjct: 217 LVYIHLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLED-----GIQRQALHCHYLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LEQDLQLESPLPDDFSNLITQL 293


>gi|306825158|ref|ZP_07458500.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus sp. oral
           taxon 071 str. 73H25AP]
 gi|304432594|gb|EFM35568.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus sp. oral
           taxon 071 str. 73H25AP]
          Length = 298

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 136/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNDRPQNATYLLDIGDRV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +      +LYED    V NKP G++       
Sbjct: 57  TIDIPAEEGFESLE--------------AIDRPLDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQEYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQRKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G      +  I   + +          + ++  KG  YA + +KV+  +     
Sbjct: 163 YFALVKGNGDLEPEGEIIAPIARDVD-----SIITRRVAKGGKYAHTSYKVVASYGDIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++ HTGRTHQ+RVH  H+G P++GD  Y  +           +  LH  Y+   HP 
Sbjct: 217 LIDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHYLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+  PLP         L
Sbjct: 272 LEQDLQLENPLPDDFSNLITQL 293


>gi|206967561|ref|ZP_03228517.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
 gi|206736481|gb|EDZ53628.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
          Length = 297

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 131/314 (41%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE   +  + K     ++   L  I    G + V+ +     +++++G+ +R+   
Sbjct: 10  IGPAEEGTLVREFLKT--KGVSKAALTDIKFHGGAIEVNGQHASVRHQLRAGEELRVFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + + NK A +S            
Sbjct: 68  VEERSEGM--------------MAEDIPLSIVYEDDAVLIINKEANMSTIPSREHPTRSV 113

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 114 ANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HFKVID    K   + ++ 
Sbjct: 174 HGRIVEREGMIDAPIGRKSDSIIERTVC-----EDGQRAVTHFKVIDSTYHK-THVALEL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y              +  LH++ +   HP     + 
Sbjct: 228 ETGRTHQIRVHMAHIGHPLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEKEMS 281

Query: 307 ITAPLPAHMVKTWD 320
            T  LP+ M +   
Sbjct: 282 FTIKLPSDMQEVLR 295


>gi|307708761|ref|ZP_07645223.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus mitis NCTC 12261]
 gi|307615127|gb|EFN94338.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus mitis NCTC 12261]
          Length = 298

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 139/322 (43%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EVSKGLLAKIKFRGGAILVNDQPQNATYLLDIGDRV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +      +LYED    V NKP G++       
Sbjct: 57  AIDIPAEEGFETLE--------------AIERPLDILYEDDHFLVLNKPYGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +    + + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G     ++  I   + +      +   + ++  KG  YA + +K++  +     
Sbjct: 163 YFALVKGDGHLEQEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGNIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++ HTGRTHQ+RVH  H+G P++GD  Y  +           +  LH  Y+   HP 
Sbjct: 217 LVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHYLSFYHPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ +PLP         L
Sbjct: 272 LEQDLQLESPLPNDFSNLITQL 293


>gi|319950238|ref|ZP_08024165.1| pseudouridine synthase, RluA family protein [Dietzia cinnamea P4]
 gi|319436142|gb|EFV91335.1| pseudouridine synthase, RluA family protein [Dietzia cinnamea P4]
          Length = 297

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 81/291 (27%), Positives = 135/291 (46%), Gaps = 19/291 (6%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    L K+LR G++RV+ +R + N R+  G V+ +P +                +   T
Sbjct: 1   MPAGLLFKLLRQGRLRVNGRRAEQNYRLAEGDVIDLPAMQAGAPATT-------VTRPPT 53

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
              D +   +LYEDS + V +KPAG++V  GS +   +   L+ ++        L HRLD
Sbjct: 54  ALLDRMAKTVLYEDSNLLVVDKPAGVAVHRGSDMPAGVIETLR-FLCPDLPGLELGHRLD 112

Query: 152 QETSGILVVARTRAAAQHLTESFRMRR--IQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           ++TSG+LV+ +T    +HL E  R R   I++ Y ++V G        +   L ++    
Sbjct: 113 RDTSGVLVLTKTPPMLRHLHEMLRDREKEIERHYLAIVAGQWPANLGVLEAPLRRRD--- 169

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                     +     A +H +V          ++++  TGR HQ+RVH  H G PI GD
Sbjct: 170 -----ADVVVDPRGQRAETHVRVRRRVGDWATLVDVRLFTGRKHQIRVHLQHAGHPIAGD 224

Query: 270 HKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
            +Y    F     S   + L+LHA  M +P P+G  + ++AP+P    +  
Sbjct: 225 DRYGDPRFDSVVASRGGSGLHLHAARMVIPLPDGRDVVVSAPMPERWRRVL 275


>gi|237736831|ref|ZP_04567312.1| tRNA pseudouridine synthase A [Fusobacterium mortiferum ATCC 9817]
 gi|229420693|gb|EEO35740.1| tRNA pseudouridine synthase A [Fusobacterium mortiferum ATCC 9817]
          Length = 292

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 86/315 (27%), Positives = 160/315 (50%), Gaps = 23/315 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++Y+ ++ + E++RLD++ +   P +    + K +R G+++V+ K+ K N R+Q   VV+
Sbjct: 1   MEYL-IDKEYEDVRLDKFLRKKLPDMALTEIFKCIRVGKIKVNGKKSKENYRLQLNDVVK 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V+ +            +S    K    +K  ++YED ++ + NK A + +  GSG  
Sbjct: 60  LFFVVESKECDKNNNINKINSEKFEK----IKKYIVYEDDRVLILNKKANMVMHKGSGHE 115

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   LK ++++        +R+D+ TSG++V A++    + L+E  R R++ K Y+ L
Sbjct: 116 YGVSEILKEYLNNPNFN--FVNRIDKATSGLVVGAKSLVVTRELSEEIRERKVDKKYYIL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K ++  I ++L K      D V  ++Q E+GA  ++S FKV++ + +    LE  
Sbjct: 174 VEGKVKRREFQIKSYLKKLE----DKVVELEQYEEGAKESLSFFKVVE-YGKNCTLLEGT 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
             +GRTHQLRV    MG PI+GD KY    +          L+ H   ++        ++
Sbjct: 229 LGSGRTHQLRVQLASMGNPIIGDSKYGKGKEKMMY------LFSHYLKIEKY-----GIE 277

Query: 307 ITAPLPAHMVKTWDS 321
           I  P+P   ++    
Sbjct: 278 IDLPIPKEYIQRLSK 292


>gi|169629784|ref|YP_001703433.1| pseudouridine synthase RluD [Mycobacterium abscessus ATCC 19977]
 gi|169241751|emb|CAM62779.1| Probable pseudouridine synthase RluD [Mycobacterium abscessus]
          Length = 305

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 143/327 (43%), Gaps = 29/327 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  + + V +    MR+D         ++      +   G V +D   V  + ++ +G 
Sbjct: 1   MTS-RSLPVPDGLSGMRVDAGLARLL-GLSRTAAAALAEEGAVLLDGVAVTKSEKLTAGT 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          + E K      N  +  + +K  +LY D  +   +KPAG++     
Sbjct: 59  WLEVT---------LPEPKAPPE--NRVEVIEGMK--ILYADDDLVAVDKPAGVAAHASV 105

Query: 124 G-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R
Sbjct: 106 GWTGPTVLGGLAAAGFRMTTSGVPERKGIVHRLDVGTSGVMVVALSEKAYTELKRAFKYR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           R++K Y +LV G P      I   + +  H G D+   V ++     ++I+H+  ++ F 
Sbjct: 166 RVEKRYHALVQGHPDPSSGTIDAPIGR--HRGHDWKFAVVED---GRHSITHYDTLEAFV 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                L++   TGRTHQ+RVH   +  P  GD  Y A+        ++ + +LHA+ +  
Sbjct: 221 -AASLLDIHLETGRTHQIRVHFSAIKHPCCGDLTYGADPTLAAKLGLE-RQWLHAKSLAF 278

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLG 323
            HP  GR ++IT+  P  +    D L 
Sbjct: 279 AHPGDGRWIEITSEYPEDLAHALDVLR 305


>gi|308805484|ref|XP_003080054.1| ribosomal large subunit pseudouridine syn (ISS) [Ostreococcus
           tauri]
 gi|116058513|emb|CAL53702.1| ribosomal large subunit pseudouridine syn (ISS) [Ostreococcus
           tauri]
          Length = 422

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 82/378 (21%), Positives = 145/378 (38%), Gaps = 85/378 (22%)

Query: 15  DEENMRLDRWFKNHYPHIN--FVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVI 71
           D+ + RLD +  +     +     + + +++  V+V+ K  +   R ++ G +V      
Sbjct: 63  DDTSPRLDAYVASSVVDASASRARVARAIKASMVKVNGKTERKPARGVKPGDIVEGELEG 122

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY---- 127
              +  I E  I              +  ++YED  + V  KPAG+     +G A     
Sbjct: 123 ERRSEAIPEPSI--------------ELDIVYEDESVLVVCKPAGMVTHPSAGHARGTLV 168

Query: 128 -----HID--------GFLKSWV-----------------------------DSKGQKPR 145
                H D        G + + +                             D+   +P 
Sbjct: 169 NAVLGHCDLPELVVPTGRVSNRMNEDGDFDDDDGPSTSESDSDAESASDSDDDAGSIRPG 228

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+ TSG++VVA+  +A   L   F  R +++ Y +++ G+PK  K  I   + + 
Sbjct: 229 IVHRLDRGTSGVMVVAKDASAHNSLCNQFASRTVRRRYVAILSGVPKTSKGRIEAPVGRD 288

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                D + +      G  YA S+++VI    +     +E +  TGRTHQ+RVHA H+G 
Sbjct: 289 PK---DRLRMAVTPGSG-RYAASNYEVIATLASGNASLVEWRLETGRTHQIRVHAKHIGH 344

Query: 265 PIVGDHKYCANFKGNFTSPIQ----------------NKLYLHARYMDLPHPEGGR-LQI 307
           PI+GD  Y         +  +                ++  LHAR +   HP  G  +  
Sbjct: 345 PILGDEVYGGGGGAAVDALARRGVFDLKAAKALLSRIDRPMLHARTLGFTHPRTGEAMDF 404

Query: 308 TAPLPAHMVKTWDSLGFK 325
           +   P        +L  +
Sbjct: 405 SRDPPEDFDAFASALAER 422


>gi|228990288|ref|ZP_04150255.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           pseudomycoides DSM 12442]
 gi|228769455|gb|EEM18051.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           pseudomycoides DSM 12442]
          Length = 286

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 135/316 (42%), Gaps = 39/316 (12%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
              E+ M +  + K     I+   L  I  + G + VD K     + +Q+ +V+++   +
Sbjct: 2   TEAEKGMLIREFLKT--KGISKAALTDIKFQGGAIEVDGKHATVRHVLQAEEVLQVFFPV 59

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIA 126
              +  +               ++ +   +LYED  + V NK   +S           +A
Sbjct: 60  EERSEGM--------------LAENIPLTVLYEDESVMVINKEPYMSTIPSREHPAGSVA 105

Query: 127 YHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +  L  +   +      +  RLD++TSG++++A+ R     L++  + +++Q+ Y +
Sbjct: 106 ---NALLYHYDRQNLASTVHIVTRLDRDTSGLMLIAKNRFIHHLLSKQHQQKQVQRTYEA 162

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G    +   I   + +K     + +       +    A++HF+V++ F  K   + +
Sbjct: 163 IVHGELLEESGTIDAPIGRKGDSIIERMVC-----EDGQKAVTHFQVMERFPDK-TRVSL 216

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P++GD  Y  +           +  LH+  +   HP   + 
Sbjct: 217 QLETGRTHQIRVHMAYLGHPLLGDDLYGGSKSQ------MKRQALHSTSLTFYHPILEKQ 270

Query: 305 LQITAPLPAHMVKTWD 320
           ++  A +P  M +   
Sbjct: 271 MKFHADVPEDMKELLK 286


>gi|255527608|ref|ZP_05394471.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
 gi|255508709|gb|EET85086.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
          Length = 319

 Score =  209 bits (532), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 133/325 (40%), Gaps = 34/325 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ +     +    + K +R G V+V+ K+ K    +  G ++    
Sbjct: 3   IEIGPNEAGQRLDKFLRKWLKDMPLSAIYKSIRKGDVKVNGKKAKEKYALMEGDLIE-TR 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYH 128
            I +     K  +I +S +            + YED  + V  K  G+ V   G    + 
Sbjct: 62  DITSNQTKKKFNRIENSFLK-----------IAYEDENMVVIEKWPGVLVHSDGKKKEHT 110

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI++  +   A + L E  R ++I
Sbjct: 111 LTDYVLSYLYDKGDYTPENEVTFTPASCNRLDRNTSGIVIFGKNYEALKLLNEMIREKKI 170

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +L+ G  K+       ++ K      +   V  +  K       + K I      
Sbjct: 171 HKYYQALIKGRIKD--GLYKAYIHKNE--SENISQVYDEPRKDTKEISMNVKNIQSCG-T 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDL 297
           F  +E++  TGR+HQLR H  H+G PI+GD KY      +  F     N  +L+A  +  
Sbjct: 226 FSLVELELLTGRSHQLRAHLNHLGNPILGDTKYGTAKLNSFFFNKYGLNYQFLYAYKLIF 285

Query: 298 PHPEGGRL-----QITAPLPAHMVK 317
                  +      + + LP  + K
Sbjct: 286 RDCTEKFIYMQNKTVASGLPPVLKK 310


>gi|319938961|ref|ZP_08013325.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319812011|gb|EFW08277.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 296

 Score =  209 bits (532), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 71/323 (21%), Positives = 141/323 (43%), Gaps = 37/323 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K     I+   L KI    G ++V+ K+      +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKQ--EISKSLLAKIKFSGGDIQVNGKKQNAIYLLDIGDKV 56

Query: 66  RIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
            I  P     + +   +K LD               ++YED    + NKP+G++      
Sbjct: 57  VIDIPAEEGFSSLCAVEKELD---------------IVYEDKHFLILNKPSGVASIPSVN 101

Query: 125 IAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            +  +  F+K++      + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K
Sbjct: 102 HSNTMANFVKAYYIANHYENQQIHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKVIEK 161

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y++LV G  P   +  I   + ++     D   + +   K   YA + +KV+  +   +
Sbjct: 162 HYYALVKGSAPLKPEGDIIAPIARE-----DSSIITRCVAKNGKYAHTSYKVLAQYDDIY 216

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +++  HTGRTHQ+RVH  ++G P++GD  Y  +     T     +  LH   +   +P
Sbjct: 217 -LVDIHLHTGRTHQIRVHFSYIGFPLLGDDLYGGSMTDGIT-----RQALHCHSLRFYNP 270

Query: 301 EGGR-LQITAPLPAHMVKTWDSL 322
                +  ++PLP         L
Sbjct: 271 FHEEVVNKSSPLPEDFQTVIQKL 293


>gi|325661187|ref|ZP_08149814.1| hypothetical protein HMPREF0490_00547 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325472694|gb|EGC75905.1| hypothetical protein HMPREF0490_00547 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 323

 Score =  209 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 75/333 (22%), Positives = 138/333 (41%), Gaps = 29/333 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V  +E   RLD+    +          K++R   + ++ K+   N +++ G +V+
Sbjct: 1   MQEIKVTKNEAGQRLDKLLAKYLNEAPKSFFYKMMRKKNIVLNGKKATGNEKLEEGDIVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +         +  E     SSV + +    L   ++YED  + + NKP G+  Q      
Sbjct: 61  LF--------LADETIRKFSSVKIQRTKTNLS--VIYEDQDVVLINKPVGMLSQKAKESD 110

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   L S++   G+         +P + +RLD+ TSGI+V  ++    Q + E F+ R
Sbjct: 111 VSLVEHLISYLFDAGELSEETLKSFRPSICNRLDRNTSGIVVAGKSLPGLQKMGELFKER 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  LV G+ +  +  +  WL K        + + + ++       + +  +    
Sbjct: 171 TLHKYYRCLVQGVIREDQ-YLKGWLKKDEKTNKVQI-LDRPSDPSDQPIETEYHPLWTK- 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYM 295
           +    LE++  TG+THQ+R H    G P++GD+KY      +F           LHA  +
Sbjct: 228 EGVTLLEVRLITGKTHQIRAHLASEGHPLIGDYKYGDRKLNDFYQKKYGLKSQLLHAYRL 287

Query: 296 DLPHPEG-----GRLQITAPLPAHMVKTWDSLG 323
           + P  EG           A +P    K    L 
Sbjct: 288 EFPVMEGVCSQLSEKVFIADVPPLFAKICKELR 320


>gi|229028975|ref|ZP_04185074.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1271]
 gi|228732255|gb|EEL83138.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1271]
          Length = 292

 Score =  209 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 133/315 (42%), Gaps = 39/315 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+ EE   +  + K     I+   L  I    G + V+ +     +++Q+G  +R+   
Sbjct: 5   IESPEEGTLVREFLK--IKGISKAALTDIKFHGGAIEVNNQHASVRHQLQAGDELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPAGSV 108

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 109 A---NALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +K     + +       +    A++HF+V+D  A     + 
Sbjct: 166 AIVHGEMIEREGTIDAPIGRKPDSIIERIVC-----EDGQRAVTHFRVMDS-ANHKTHVS 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD  Y              +  LH+  +   HP    
Sbjct: 220 LELETGRTHQIRVHMAHIGHPLLGDTLYGGKRDE------MKRQALHSTSLTFYHPVLEK 273

Query: 304 RLQITAPLPAHMVKT 318
            +  T  +P+ M + 
Sbjct: 274 EMSFTTTIPSDMQEV 288


>gi|261408890|ref|YP_003245131.1| RluA family pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261285353|gb|ACX67324.1| pseudouridine synthase, RluA family [Paenibacillus sp. Y412MC10]
          Length = 354

 Score =  209 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 85/352 (24%), Positives = 142/352 (40%), Gaps = 56/352 (15%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRI 59
           MSL       VV + E+ M L    +     ++   L ++ L    + ++  RV  + ++
Sbjct: 1   MSLYYPPIRYVVPSHEDGMLLKTILQKRM-GVSRKLLSRLKLTEQGIMLNGTRVYISVKV 59

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G +V I       N ++ +                ++  +LYED  + V NKPAG+ V
Sbjct: 60  QAGDLVEIRMEQERSNDMLPQP---------------MELHILYEDEHLLVLNKPAGVIV 104

Query: 120 QGGSG--IAYHIDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               G       +G +  W +     + R  HRLDQETSG+LV+A+     QH++E    
Sbjct: 105 HPTHGHYTDTLANGVVHYWQEKGWNYRFRAVHRLDQETSGVLVIAKNAYIHQHVSEQMIA 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + K Y + V G P ++   I   + +        +            +++ ++V + +
Sbjct: 165 GTVDKRYVAFVHGRPSSQTGDIDGPIDRDPLEPHRRIV-----TPEGYPSLTRYRVCETY 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN----------------- 279
                 +E++  TGRTHQ+RVH L +GCP++GD  Y                        
Sbjct: 220 PS-ASLVELKLETGRTHQIRVHMLSIGCPLIGDQMYRHPVYSEQGLLPDAPERDEDSNGA 278

Query: 280 ------------FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
                             ++  LHA  + L HP EG  +  TAPLP  M   
Sbjct: 279 VGSLDPLAATIMRLDGYMDRQALHAASLTLMHPIEGKTMVFTAPLPEDMKSL 330


>gi|170759270|ref|YP_001788292.1| RluA family pseudouridine synthase [Clostridium botulinum A3 str.
           Loch Maree]
 gi|169406259|gb|ACA54670.1| pseudouridine synthase, RluA family [Clostridium botulinum A3 str.
           Loch Maree]
          Length = 300

 Score =  209 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 147/323 (45%), Gaps = 28/323 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      VV+    N+ +  + +    +++   ++K +R G+V V+K++V   N++    
Sbjct: 1   MDNKLIFVVKKINHNIDIKDYLRE-MENLSGRFIRKAVRDGRVFVNKEKVIKKNKLSQDD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I    +   +I  E   ++               ++YED+ I V NK  GI V    
Sbjct: 60  LIEIYMQEDEHQNIEPEDMNIE---------------IVYEDNDIIVINKRPGIVVHPTK 104

Query: 124 GIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G     +   +       G+K   RL  RLD++TSG++++A+ + +   L         +
Sbjct: 105 GHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFR 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY ++V G  K K+  I   + K+     +   + +  ++    +I+ ++V++  ++  
Sbjct: 165 KIYIAVVHGSMKEKEGRINLPIYKEE----ESESIKRIVDERGQESITTYEVLEELSKG- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++  TGRTHQ+RVH  H+G P+ GD  Y    KG        +  LHA  ++ PHP
Sbjct: 220 SVVRLELETGRTHQIRVHMSHLGHPLYGDSLYG---KGEEEKEYIERQALHAYKLEFPHP 276

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
             G + ++   LP  +    + +
Sbjct: 277 RTGDILKLQCSLPDDIKNLMEKI 299


>gi|226950404|ref|YP_002805495.1| pseudouridine synthase, RluA family [Clostridium botulinum A2 str.
           Kyoto]
 gi|226842595|gb|ACO85261.1| pseudouridine synthase, RluA family [Clostridium botulinum A2 str.
           Kyoto]
          Length = 300

 Score =  209 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 147/323 (45%), Gaps = 28/323 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      VV+    N+ +  + +    +++   ++K +R G+V V+K++V   +++    
Sbjct: 1   MDNKLIFVVKKINHNIDIKDYLRE-MENLSGRFIRKAVRDGRVFVNKEKVIKKHKLSQDD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I    +   +I  E   ++               ++YED+ I V NK  GI V    
Sbjct: 60  LIEIYMQEDEHQNIEPEDMNIE---------------IVYEDNDIIVINKRPGIVVHPTK 104

Query: 124 GIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G     +   +       G+K   RL  RLD++TSG++++A+ + +   L         +
Sbjct: 105 GHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFR 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY ++V G  K K+  I   + K+     +   + +  ++    +I+ ++V++  ++  
Sbjct: 165 KIYIAVVHGSMKEKEGRINLPIYKEE----ESESIKRIVDERGQESITTYEVLEELSKG- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++  TGRTHQ+RVH  H+G P+ GD  Y    KG        +  LHA  ++ PHP
Sbjct: 220 SVVRLELETGRTHQIRVHMSHLGHPLYGDSLYG---KGEEEKEYIERQALHAYKLEFPHP 276

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
             G + ++   LP  +    + +
Sbjct: 277 RTGDILKLQCSLPDDIKNLIEKI 299


>gi|52785027|ref|YP_090856.1| YjbO [Bacillus licheniformis ATCC 14580]
 gi|163119352|ref|YP_078456.2| pseudouridine synthase YjbO [Bacillus licheniformis ATCC 14580]
 gi|52347529|gb|AAU40163.1| YjbO [Bacillus licheniformis ATCC 14580]
 gi|145902858|gb|AAU22818.2| Pseudouridine synthase YjbO [Bacillus licheniformis ATCC 14580]
          Length = 291

 Score =  209 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 132/319 (41%), Gaps = 39/319 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++  ++  + L  + +     I+   L  I    G + V+   V     +Q G  + I  
Sbjct: 4   IITEEDSGVLLKEYVQRL--GISKRMLTDIKFGGGDLLVNGGHVTVRYVLQKGDELVIQF 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               ++  ++ +++                 +L+ED  + V NK   IS         H 
Sbjct: 62  PPEKMSESLQPEEV--------------PLHILFEDDHVLVLNKQPCISSIPSR---EHP 104

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G L + +    Q+        L  RLD++TSG+++VA+ R A   L+   +   +++ Y
Sbjct: 105 SGSLANGLIHYYQRTGVHATVHLVSRLDRDTSGVMLVAKHRFAHSLLSGLQKKGAVKRQY 164

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G+   ++  I   + +KS    +   +          A++HF V   F+     +
Sbjct: 165 RAVVHGLIAEEQGTIDAPIGRKSSSIIERAVI-----PDGQKAVTHFWVNRRFS-GMTDV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
            ++  TGRTHQ+RVH  H+G P+ GD  Y        T    N+  LH+  +   HP   
Sbjct: 219 SIRLETGRTHQIRVHMSHIGYPLCGDTLYGG------TRGFINRQALHSERLTFFHPFTM 272

Query: 303 GRLQITAPLPAHMVKTWDS 321
             L   AP+P  M +  +S
Sbjct: 273 EELTFQAPVPNDMRQLIES 291


>gi|229068860|ref|ZP_04202155.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           F65185]
 gi|228714278|gb|EEL66158.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           F65185]
          Length = 292

 Score =  209 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 130/314 (41%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE   +  + K     I+   L  I    G + V+ +     +++++G+ +R+   
Sbjct: 5   IGPAEEGTLVREFLKTKC--ISKAALTDIKFHGGAIEVNGQHASVRHQLRAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + + NK A +S            
Sbjct: 63  VEERSEGM--------------MAEDIPLSIVYEDDAVLIINKEANMSTIPSREHPTRSV 108

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HFKVID    K   + ++ 
Sbjct: 169 HGKIVEREGMIDAPIGRKSDSIIERTVC-----EDGQRAVTHFKVIDSTYHK-THVALEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y              +  LH++ +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAHIGHPLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWD 320
            T  LP  M +   
Sbjct: 277 FTIKLPNDMQEVLR 290


>gi|228951685|ref|ZP_04113787.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar kurstaki str. T03a001]
 gi|228807970|gb|EEM54487.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar kurstaki str. T03a001]
          Length = 292

 Score =  209 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 131/314 (41%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE   +  + K     I+   L  I    G + V+ +     +++++G+ +R+   
Sbjct: 5   IGPAEEGTLVREFLKTKC--ISKAALTDIKFHGGAIEVNGQHASVRHQLRAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + + NK A +S            
Sbjct: 63  VEERSEGM--------------MAEDIPLSIVYEDDAVLIINKEANMSTIPSREHPTRSV 108

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HFKVID    K   + ++ 
Sbjct: 169 HGKIVEREGMIDAPIGRKSDSIIERTVC-----EDGQRAVTHFKVIDSTYHK-THVALEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y              +  LH++ +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAHIGHPLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWD 320
            T  LP+ M +   
Sbjct: 277 FTIKLPSDMQEVLR 290


>gi|310821071|ref|YP_003953429.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309394143|gb|ADO71602.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 269

 Score =  209 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 80/290 (27%), Positives = 130/290 (44%), Gaps = 36/290 (12%)

Query: 47  RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
           R D + VK ++R++ G+++ +                +   V     ++ L   +L+ED 
Sbjct: 2   RADGRPVKASSRLRGGELLSLH---------------VPPPVAALPEAEELPLEVLHEDR 46

Query: 107 KIYVFNKPAGISVQGGSGIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVV 160
            + V NK AG+ V  G+G A    ++  L    D  G     +P + HRLD++T+G LVV
Sbjct: 47  DLVVVNKAAGMVVHPGAGHASGTLVNALLHRVKDLAGVGGELRPGIVHRLDKDTTGCLVV 106

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+   A   L ++F+ R ++K Y +LV G PK +      +       G   VH  +   
Sbjct: 107 AKNEQALVALQKAFKTRAVEKTYLALVHGHPKAEGRIETLY-------GRHPVHRQRFTG 159

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K    A++ F+  + F +    +E+   TGRTHQ+RVH    G P++ D  Y A  K 
Sbjct: 160 KVKEGKSAVTVFRTREFF-EGAALVEVDLLTGRTHQIRVHLSESGHPLLCDALYGAGRKA 218

Query: 279 NF----TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                       +  LHA  +   HP  G+ L++ APLP     +   L 
Sbjct: 219 KGQVAQAQERLGRQALHAWRLGFAHPRTGKALKLEAPLPEDFAASMKVLR 268


>gi|209554367|ref|YP_002284711.1| RluA [Ureaplasma urealyticum serovar 10 str. ATCC 33699]
 gi|209541868|gb|ACI60097.1| RluA [Ureaplasma urealyticum serovar 10 str. ATCC 33699]
          Length = 299

 Score =  209 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 75/311 (24%), Positives = 132/311 (42%), Gaps = 31/311 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
              R+D++        +  +++K+L    V V+   + K +  +Q    V I        
Sbjct: 9   SPKRIDKFLVE-VTDYSRTSIKKMLEQNLVLVNDNIITKQSYLLQKNDSVEIKN------ 61

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLK 134
               EQ ++DS   L   +  L+  +++ED  + V NKP+G+ V   S      +   LK
Sbjct: 62  ----EQCVIDSQKELLPFACPLE--IVFEDQDLLVINKPSGMLVHPTSFQEQNTLANALK 115

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            ++ +      +THRLD+ TSG++V+ + + A   L + F  + ++K Y+++V       
Sbjct: 116 HYLKTDDF--YITHRLDKNTSGLIVICKNQKALCCLQQQFMQKTVKKSYYAIVHNRFDMH 173

Query: 195 KECIANWLLKKSHIGG---DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                   +    IG    D + +   + K    AIS  KVI+ + Q    +E+   TGR
Sbjct: 174 ----HLHFMINEPIGHSYQDKLRMKTGDAKNVKEAISIVKVIEQY-QNTALVEVSIITGR 228

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAP 310
           THQ+RVH  H+  PI  D  Y  +             YLH+ Y+   HP    + +    
Sbjct: 229 THQIRVHMRHINHPIYNDPLYGISKHTTPYE-----QYLHSFYISFIHPSTNEIVEFKTL 283

Query: 311 LPAHMVKTWDS 321
           +P   +     
Sbjct: 284 MPNEFINLIKE 294


>gi|229154871|ref|ZP_04282985.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           ATCC 4342]
 gi|228628429|gb|EEK85142.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           ATCC 4342]
          Length = 292

 Score =  209 bits (531), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 133/315 (42%), Gaps = 39/315 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ EE   +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 5   IDSAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQYASVRHQLQAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + V NK A +S           +
Sbjct: 63  VEERSEGM--------------IAEDIPLCIVYEDDAVLVINKEANMSTIPSREHPAGSV 108

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 109 A---NALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HF+VID  A     + 
Sbjct: 166 AIVHGEMVEREGTIDAPIGRKSDSIIERTVC-----EEGQRAVTHFRVIDS-ANHKTHVS 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD+ Y              +  LH+  +   HP    
Sbjct: 220 LELDTGRTHQIRVHMAHIGHPLLGDNLYGGKRDE------MKRQALHSTSLTFYHPILEK 273

Query: 304 RLQITAPLPAHMVKT 318
            +  T  +P  M   
Sbjct: 274 EMSFTTTIPNDMQAV 288


>gi|18310186|ref|NP_562120.1| ribosomal large subunit pseudouridine synthase C [Clostridium
           perfringens str. 13]
 gi|110800940|ref|YP_695859.1| RluA family pseudouridine synthase [Clostridium perfringens ATCC
           13124]
 gi|169344395|ref|ZP_02865365.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
 gi|182626167|ref|ZP_02953926.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
 gi|18144865|dbj|BAB80910.1| ribosomal large subunit pseudouridine synthase C [Clostridium
           perfringens str. 13]
 gi|110675587|gb|ABG84574.1| pseudouridine synthase, RluA family [Clostridium perfringens ATCC
           13124]
 gi|169297468|gb|EDS79576.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
 gi|177908523|gb|EDT71051.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
          Length = 324

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 125/300 (41%), Gaps = 25/300 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ + +   +    + K LR G +RV+ K+ K    +  G V+ I  
Sbjct: 3   IEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLEGDVIEI-- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
                + + KE+K  +  +      D     ++YED  + +  K  G+ V       A  
Sbjct: 61  -RYLQSVVTKEKKKPNFQM-----VDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAPT 114

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI+   +     + L E  R R++
Sbjct: 115 LTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKV 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G  +        ++ K   +      V               KV+      
Sbjct: 175 KKYYCALVKGKIQP--GKYEAYISKDDELNKS--TVYDTERPDTKKIKMDVKVLQTNG-A 229

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F  LE++  TGR+HQLR H  H+G PIVGD KY  N   +F          +L+A  +  
Sbjct: 230 FSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSFFENKFGLTYQFLYAYKVTF 289


>gi|290893473|ref|ZP_06556457.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J2-071]
 gi|290556974|gb|EFD90504.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J2-071]
          Length = 296

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 142/319 (44%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE +E  + L  + K+   HI+   L   K    G++ V+ +       ++ G  VR+  
Sbjct: 7   VETEENGLLLRTFLKS--KHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKVGDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTDLDIVFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 SGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRCY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +   G+  +++  I   + +K     +   + +       YA ++++V++ +   F  +
Sbjct: 168 QAFTSGVLASQEGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLERYT-AFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TTLLKRQALHSCHLHLVHPVTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
             +    PLPA M +    
Sbjct: 276 EYMAFDLPLPADMEEIIQK 294


>gi|168217835|ref|ZP_02643460.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
 gi|182380127|gb|EDT77606.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
          Length = 324

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 125/300 (41%), Gaps = 25/300 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ + +   +    + K LR G +RV+ K+ K    +  G V+ I  
Sbjct: 3   IEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLEGDVIEI-- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
                + + KE+K  +  +      D     ++YED  + +  K  G+ V       A  
Sbjct: 61  -RYLQSVVTKEKKKPNFQM-----VDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAPT 114

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI+   +     + L E  R R++
Sbjct: 115 LTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKV 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G  +        ++ K   +      V               KV+      
Sbjct: 175 KKYYCALVKGKIQP--GKYEAYISKDDELNKS--TVYDTERPDTKKIKMDVKVLQTNG-A 229

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F  LE++  TGR+HQLR H  H+G PIVGD KY  N   +F          +L+A  +  
Sbjct: 230 FSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSFFENKFGLTYQFLYAYKVTF 289


>gi|256752736|ref|ZP_05493584.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           CCSD1]
 gi|256748374|gb|EEU61430.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           CCSD1]
          Length = 285

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 72/317 (22%), Positives = 140/317 (44%), Gaps = 38/317 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V  +E+ + L+ + +N       + + K    G++ V+  +      +Q G V+    
Sbjct: 3   LIVGENEKGVILENFLRNKGFSKRLIRIYKW--QGEILVNGVKENVQRILQPGDVI---- 56

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                        ++   V+     + +   + YED  + + +KPAG+ V          
Sbjct: 57  ------------DLILPEVDSDIAPEKMGLDIYYEDEDVLIVDKPAGVVVHPTKRYQSGT 104

Query: 129 IDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +  +   KG K   R  +RLD+ TSG++V A+      +L      + + K+Y+++
Sbjct: 105 LANGVAWYFKDKGIKALIRPVNRLDKGTSGLVVFAKRPFMQYYLQIV---KPMSKLYFAV 161

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + +   I   + +K   G + +       +  + AI+++KVI   +++F  L+++
Sbjct: 162 VEGKMEGE-GRIDLPISRKPQSGIERMV-----SEEGDRAITNYKVIKS-SERFSLLKVK 214

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  H+G PIVGD  Y +      +     +  LHA  +   HP   R +
Sbjct: 215 IETGRTHQIRVHLSHIGHPIVGDTLYGS------SDDYIKRQALHAYRLTFVHPLEERSI 268

Query: 306 QITAPLPAHMVKTWDSL 322
            + +PLP  +       
Sbjct: 269 SVYSPLPQDIQHLLKLF 285


>gi|229108765|ref|ZP_04238373.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock1-15]
 gi|229149508|ref|ZP_04277743.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           m1550]
 gi|228633981|gb|EEK90575.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           m1550]
 gi|228674704|gb|EEL29940.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock1-15]
          Length = 292

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 131/314 (41%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE   +  + K     I+   L  I    G + V+ +     +++++G+ +R+   
Sbjct: 5   IGPAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLRAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + + NK A +S            
Sbjct: 63  VEERSEGM--------------MAEDIPLCIIYEDDAVLIINKEANMSTIPSREHPAGSV 108

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HFKVID    K   + ++ 
Sbjct: 169 HGKIVEREGMIDAPIGRKSDSIIERTVC-----EDGQRAVTHFKVIDSTYHK-THVALEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y              +  LH++ +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAHIGHPLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWD 320
            T  LP+ M +   
Sbjct: 277 FTIKLPSDMQEVLR 290


>gi|197104730|ref|YP_002130107.1| ribosomal large subunit pseudouridine synthase D [Phenylobacterium
           zucineum HLK1]
 gi|196478150|gb|ACG77678.1| ribosomal large subunit pseudouridine synthase D [Phenylobacterium
           zucineum HLK1]
          Length = 243

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 81/244 (33%), Positives = 122/244 (50%), Gaps = 4/244 (1%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           K L      +     ++S++LYED+ I   NKPAG+S QGG G    +D  L ++     
Sbjct: 2   KPLKPIHLTSDEVALVRSLVLYEDADILALNKPAGLSSQGGRGQVNTLDELLWAFAKPGK 61

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIAN 200
            +PRL HRLD++TSG+++ A+T+ AA  L ++   R   K Y ++V  G P   K  I  
Sbjct: 62  ARPRLIHRLDRDTSGVILTAKTKPAAGFLGKALMKRAFSKTYLAIVTPGAPVPAKGVIDR 121

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L +       Y+ V + +   A  A S ++ +    +    +E+ P TGR HQLRVH  
Sbjct: 122 PLRRVEEGREAYMRVCEPDHPDAEAAASRYRTLK-EGEGAALVELSPETGRMHQLRVHLA 180

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
            +G PI GD +Y              +L LHAR +  PHP GG  ++ A  P+ M +   
Sbjct: 181 AVGRPIAGDARYGGAL--MVGGRPVPRLMLHARALAFPHPAGGTKRLEAEPPSDMAELIQ 238

Query: 321 SLGF 324
           +LG 
Sbjct: 239 ALGL 242


>gi|148380931|ref|YP_001255472.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 3502]
 gi|153932924|ref|YP_001385300.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           ATCC 19397]
 gi|153936215|ref|YP_001388708.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           Hall]
 gi|148290415|emb|CAL84542.1| putative ribosomal large subunit pseudouridine synthase
           [Clostridium botulinum A str. ATCC 3502]
 gi|152928968|gb|ABS34468.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 19397]
 gi|152932129|gb|ABS37628.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           Hall]
          Length = 300

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 72/303 (23%), Positives = 141/303 (46%), Gaps = 28/303 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + +    +++   ++K +R G+V V+K++V   +++    ++ I    +   +I  E   
Sbjct: 21  YLRE-MENLSGRFIRKAVRDGRVFVNKEKVIKKHKLSQDDLIEIYMQEDEHQNIEPEDMN 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQ 142
           ++               ++YED+ I V NK  GI V    G     +   +       G+
Sbjct: 80  IE---------------IVYEDNDIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGE 124

Query: 143 K--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           K   RL  RLD++TSG++++A+ + +   L       R +KIY ++V G  K K+  I  
Sbjct: 125 KSIVRLVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDRFRKIYIAVVHGSMKEKEGRINL 184

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + K+     +   + +  ++    +I+ ++V++  ++    + ++  TGRTHQ+RVH  
Sbjct: 185 PIYKEE----ESESIKRIVDERGQESITTYEVLEELSKG-SVVRLELETGRTHQIRVHMS 239

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           H+G P+ GD  Y    KG        +  LHA  ++ PHP  G  L++   LP  +    
Sbjct: 240 HLGHPLYGDSLYG---KGEEEKEYIERQALHAYKLEFPHPRTGDVLKLQCSLPDDIKNLI 296

Query: 320 DSL 322
           + +
Sbjct: 297 EKI 299


>gi|289578773|ref|YP_003477400.1| pseudouridine synthase [Thermoanaerobacter italicus Ab9]
 gi|289528486|gb|ADD02838.1| pseudouridine synthase, RluA family [Thermoanaerobacter italicus
           Ab9]
          Length = 285

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 74/317 (23%), Positives = 139/317 (43%), Gaps = 38/317 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V   +E+ + L+ + +N       + + K    G++ V+  +      +Q G V+ +  
Sbjct: 3   LVAGENEKGIILENFLRNKGFSKRLIRIYKW--QGEILVNGIKSNVKRILQPGDVIDL-- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                  I+ E              + L   + YED +I + NKPA + V    G     
Sbjct: 59  -------ILPEND-------SNIAPEKLDLDICYEDEEILIVNKPANMVVHPTKGYQSGT 104

Query: 129 IDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +  +   KG K   R  +RLD+ TSG++V A+      +L      + + K+Y+++
Sbjct: 105 LANGIAWYFKDKGLKALIRPVNRLDRGTSGLVVFAKLPFMQYYLQIV---KPMSKLYFAV 161

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + +   I   + +K   G + +       +    AI+++KV+   +++F  L+++
Sbjct: 162 VEGKMEGE-GRINLPISRKPQSGIERMV-----SEEGEIAITNYKVVKS-SERFSLLKVK 214

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  H+G PIVGD  Y +      +     +  LHA  +   HP   + +
Sbjct: 215 IETGRTHQIRVHLSHIGHPIVGDTLYGS------SDDYIKRQALHAYRLTFVHPLEEKSI 268

Query: 306 QITAPLPAHMVKTWDSL 322
            + +PLP  +       
Sbjct: 269 SVYSPLPQDIQHLLKLF 285


>gi|168205450|ref|ZP_02631455.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
 gi|170662972|gb|EDT15655.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
          Length = 324

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 125/300 (41%), Gaps = 25/300 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ + +   +    + K LR G +RV+ K+ K    +  G V+ I  
Sbjct: 3   IEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLEGDVIEI-- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
                + + KE+K  +  +      D     ++YED  + +  K  G+ V       A  
Sbjct: 61  -RYLQSVVTKEKKKPNFQM-----VDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAAT 114

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI+   +     + L E  R R++
Sbjct: 115 LTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKV 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G  +        ++ K   +      V               KV+      
Sbjct: 175 KKYYCALVKGKIQP--GKYEAYISKDDELNKS--TVYDTERPDTKKIKMDVKVLQTNG-A 229

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F  LE++  TGR+HQLR H  H+G PIVGD KY  N   +F          +L+A  +  
Sbjct: 230 FSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSFFENKFGLTYQFLYAYKVTF 289


>gi|226223587|ref|YP_002757694.1| ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes Clip81459]
 gi|225876049|emb|CAS04755.1| Putative ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes serotype 4b str. CLIP 80459]
          Length = 296

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 144/319 (45%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE +E+ + L  + K+   HI+   L   K    G++ V+ K       ++ G  VR+  
Sbjct: 7   VETEEDGLLLRTFLKS--KHISKQLLTAVKFGAEGKIEVNNKEQNVLYHVKVGDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTNLDIIFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 NGSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +   G+   +K  I   + +K     +   + +       YA ++++V+  + + F  +
Sbjct: 168 QAFTSGVLVEQKGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLARY-RAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
           + +    PLPA M +    
Sbjct: 276 KYMAFDLPLPADMEEIIQK 294


>gi|125974463|ref|YP_001038373.1| RluA family pseudouridine synthase [Clostridium thermocellum ATCC
           27405]
 gi|256005181|ref|ZP_05430149.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281418990|ref|ZP_06250008.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|125714688|gb|ABN53180.1| pseudouridine synthase, RluA family [Clostridium thermocellum ATCC
           27405]
 gi|255990835|gb|EEU00949.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281407447|gb|EFB37707.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|316941600|gb|ADU75634.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           1313]
          Length = 320

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 74/304 (24%), Positives = 132/304 (43%), Gaps = 25/304 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +  D+ N R+D+  +  +P +    L K  R   ++V+  RVK ++ ++    V 
Sbjct: 1   MRTITITEDKANKRIDKVLRETFPRLPNGALFKAFRKKDIKVNGVRVKEDHIVKLNDRVD 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-I 125
           I  +   L+ + K  ++   +             + YEDS + + NK  GI V       
Sbjct: 61  IYIIDEILDGVPKAGELNYETA----------FSVAYEDSNLLIVNKKQGIPVHPDRTQT 110

Query: 126 AYHIDGFLKSWVDSKGQ-------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              +  F+K ++  KG+        P L HRLD+ T G++++A+  +    + +  +   
Sbjct: 111 ENTLIDFVKEYLKLKGEFEENSGFTPSLCHRLDRNTGGLVMIAKNSSTLHMVLKKMKSGE 170

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--- 235
           I K Y  LV G  + K++ +  +L K        V +     K A   I+ +KV+     
Sbjct: 171 ISKYYQCLVKGKMEKKEDILKAYLEKDEK--KSRVFIKDTKSKNAVEIITGYKVLSYKEL 228

Query: 236 --FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
               +    LE+  +TGRTHQ+R H  H+G P+VGD KY  N            L+ +  
Sbjct: 229 PDIGEGISNLEVTLYTGRTHQIRAHLAHIGHPVVGDGKYGINTFNRLLGAKYQALWAYKL 288

Query: 294 YMDL 297
             D 
Sbjct: 289 KFDF 292


>gi|262198126|ref|YP_003269335.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262081473|gb|ACY17442.1| pseudouridine synthase, RluA family [Haliangium ochraceum DSM
           14365]
          Length = 369

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 86/337 (25%), Positives = 136/337 (40%), Gaps = 42/337 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+  VV+ D    RLD + K   P ++   LQ ++R     V  +++K +  + SG V+ 
Sbjct: 34  VRRFVVDEDSAGFRLDHYLKRQIPRLSRTKLQDVIRHQLEPVRGRQLKPSASVHSGDVIV 93

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +                        +        +LY D  + V +KPAG+ V   +   
Sbjct: 94  MSRRAR------------------PEPPCPRTIGVLYSDPHMLVIDKPAGLPVHASARFY 135

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           ++    +       GQ  ++ HRLD+ETSG LVVAR +  A  L  +F  +R  K Y +L
Sbjct: 136 FNTLTRVLGERFP-GQPMQICHRLDRETSGALVVARGKPEAARLKGAFADKRAHKTYLAL 194

Query: 187 VWGIPKNKKECIANWLLKKSHIGGD---------YVHVVKQNEKGANYAISHFKVIDCFA 237
           VWG P        +     + I             + +  +   GA  +++  +V++   
Sbjct: 195 VWGDPPWPDGAWDSAPEDDAIIDLPLGLVADESARIKIRMEVRAGALPSLTRVRVLERRG 254

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------------ANFKGNFTSPIQ 285
           +    +   P TGR HQ+R H    G PIVGD  Y                         
Sbjct: 255 R-AALVRCLPLTGRQHQIRAHLAACGHPIVGDKLYAHGDDVFAAYCDRGMTPELLERVRL 313

Query: 286 NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
            +  LHA  + LPHP EG +++  +PLPA M    D 
Sbjct: 314 PRQALHAAAIALPHPFEGRQVRAESPLPADMRAFLDR 350


>gi|171059556|ref|YP_001791905.1| RluA family pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170777001|gb|ACB35140.1| pseudouridine synthase, RluA family [Leptothrix cholodnii SP-6]
          Length = 369

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 71/320 (22%), Positives = 135/320 (42%), Gaps = 50/320 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVR 66
           +  VVE      RLD+W     P  +  +LQ ++  G VR  ++ ++ +++ + +GQ + 
Sbjct: 41  RLAVVEAAAHGERLDKWLVRIAPEFSRAHLQGLVEGGHVRCGEQVLRQSHKKVMAGQQIE 100

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +     A +   +              ++ +   +++ED+ + V +KPAG+ V   +G  
Sbjct: 101 VALWPTAQSTAFR--------------AEAMTLAVVHEDAHLLVIDKPAGLVVHPAAG-- 144

Query: 127 YHIDGFLKS------WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            H  G L +         +   +  + HRLD++TSG+++VA++  A   L  +   R ++
Sbjct: 145 -HWSGTLLNGLLAHHAAAAHLPRAGIVHRLDKDTSGLMLVAKSLQAHTALVRAIAARDVK 203

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID------ 234
           + Y +LV G   +  + I   L +   +    + +V         A +  + +       
Sbjct: 204 REYLALVHGAVMDGLQVIDAPLGRD-PVSRVRMAIVA----SGKPARTDVRRLAVAELPG 258

Query: 235 ----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
                        ++   +  Q HTGRTHQ+RVH    G P++ D  Y         +  
Sbjct: 259 DGVRQLPGATRAPRQVSAVHCQLHTGRTHQIRVHLASRGHPLLADAMYGG-----APAFG 313

Query: 285 QNKLYLHARYMDLPHPEGGR 304
             +  LHA  + L HP  GR
Sbjct: 314 LQRQALHAARLHLLHPIDGR 333


>gi|47093663|ref|ZP_00231418.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|47017959|gb|EAL08737.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|328466988|gb|EGF38091.1| ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes 1816]
          Length = 296

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 144/319 (45%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE +E+ + L  + K+   HI+   L   K    G++ V+ K       ++ G  VR+  
Sbjct: 7   VETEEDGLLLRTFLKS--KHISKQLLTAVKFGAEGKIEVNNKEQNVLYHVKVGDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTDLDIIFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 NGSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +   G+   +K  I   + +K     +   + +       YA ++++V+  + + F  +
Sbjct: 168 QAFTSGVLVEQKGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLARY-RAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
           + +    PLPA M +    
Sbjct: 276 KYMAFDLPLPADMEEIIQK 294


>gi|332366862|gb|EGJ44603.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1059]
          Length = 295

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 140/322 (43%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   I+   L KI    G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKRH--EISKGLLAKIKFSGGNILVNHQPQNAIYLLDIGDKV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          +K              +      ++YED    V +KPAG++       
Sbjct: 57  TIDIPSEKGFESLK--------------AVDKDLYVVYEDEHFLVLDKPAGVASIPSVNH 102

Query: 126 AYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +  F+K++   +G   Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 TNTMANFVKAYYIGQGYENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G     ++  I   + +          + ++  +   YA + +KVI+ F   + 
Sbjct: 163 YYALVRGTGDLEEQGEIIAPIGRNPE-----SIITRRVTEDGKYAHTSYKVIEQFGDVY- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++ HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH   +   +P 
Sbjct: 217 LVDIRLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLE-----HGIERQALHCHSLKFYNPF 271

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
            G  ++  +PLP    +  + L
Sbjct: 272 SGQEVERASPLPEDFKQVIEKL 293


>gi|110803565|ref|YP_698546.1| pseudouridylate synthase [Clostridium perfringens SM101]
 gi|110684066|gb|ABG87436.1| pseudouridine synthase, RluA family [Clostridium perfringens SM101]
          Length = 324

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 124/300 (41%), Gaps = 25/300 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ + +   +    + K LR G +RV+ K+ K    +  G V+ I  
Sbjct: 3   IEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLDGDVIEI-- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
                + + KE+K  +  +      D     ++YED  + +  K  G+ V       A  
Sbjct: 61  -RYLQSVVTKEKKKPNFQM-----VDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAPT 114

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI+   +     + L E  R R++
Sbjct: 115 LTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKV 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G  +        ++ K   +      V               KV+      
Sbjct: 175 NKYYCALVKGKIQP--GKYEAYISKDDELNKS--TVYDTERPDTKKIKMDVKVLQTNG-A 229

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F  LE++  TGR+HQLR H  H+G PIVGD KY  N   +F          +L+A  +  
Sbjct: 230 FSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSFFENKFGLTYQFLYAYKVTF 289


>gi|326391214|ref|ZP_08212757.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           JW 200]
 gi|325992718|gb|EGD51167.1| pseudouridine synthase, RluA family [Thermoanaerobacter ethanolicus
           JW 200]
          Length = 285

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 71/317 (22%), Positives = 140/317 (44%), Gaps = 38/317 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V  +E+ + L+ + +N       + + K    G++ V+  +      +Q G V+    
Sbjct: 3   LIVGENEKGVILENFLRNKGFSKRLIRIYKW--QGEILVNGVKENVQRILQPGDVI---- 56

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                        ++   V+     + +   + YED  + + +KPAG+ V          
Sbjct: 57  ------------DLILPEVDSDIAPEKMGLDIYYEDEDVLIVDKPAGVVVHPTKRYQSGT 104

Query: 129 IDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +  +   KG K   R  +RLD+ TSG++V A+      +L      + + K+Y+++
Sbjct: 105 LANGVAWYFKDKGIKALIRPVNRLDKGTSGLVVFAKRPFMQYYLQIV---KPMSKLYFAV 161

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + +   I   + +K   G + +       +  + AI+++KVI   +++F  L+++
Sbjct: 162 VEGKMEGE-GRIDLPISRKPQSGIERMV-----SEEGDRAITNYKVIKS-SERFSLLKVK 214

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  H+G PIVGD  Y +      +     +  LHA  +   HP   + +
Sbjct: 215 IETGRTHQIRVHLSHIGHPIVGDTLYGS------SDDYIKRQALHAYRLTFVHPLEEKSI 268

Query: 306 QITAPLPAHMVKTWDSL 322
            + +PLP  +       
Sbjct: 269 SVYSPLPQDIQHLLKLF 285


>gi|217964932|ref|YP_002350610.1| pseudouridine synthase, RluA family [Listeria monocytogenes HCC23]
 gi|217334202|gb|ACK39996.1| pseudouridine synthase, RluA family [Listeria monocytogenes HCC23]
 gi|307570509|emb|CAR83688.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes L99]
          Length = 296

 Score =  208 bits (530), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 141/319 (44%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE +E  + L  + K+   HI+   L   K    G++ V+ +       ++ G  VR+  
Sbjct: 7   VETEENGLLLRTFLKS--KHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKVGDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTDLDIVFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 SGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +   G+   ++  I   + +K     +   + +       YA ++++V++ +   F  +
Sbjct: 168 QAFTSGVLATQEGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLERYT-AFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TTLLKRQALHSCHLHLVHPVTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
             +    PLPA M +    
Sbjct: 276 EYMAFDLPLPADMEEIIQK 294


>gi|119713310|gb|ABL97374.1| putative ribosomal large subunit pseudouridine synthase D
           [uncultured marine bacterium EB80_02D08]
          Length = 310

 Score =  208 bits (530), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 74/324 (22%), Positives = 134/324 (41%), Gaps = 42/324 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V N+    RLD+     +   +   ++K +  G+V V+ +  +   ++     + + P  
Sbjct: 6   VPNNLALKRLDKAAAEMFTDYSRTQIKKWIEDGKVLVNGEISQPREKVHENDEIELNP-- 63

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +EQK+       +   + ++  + +E+    + NKPAG+ +  GSG     DG
Sbjct: 64  ------AEEQKV-------SWEPEDIQFEVHFENEDFIIINKPAGLIMHPGSGC---YDG 107

Query: 132 FLKSWVDSKGQKP------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L + +  K  +        + HRLD++TSGIL+VART +         + RR+ K Y S
Sbjct: 108 TLANGLIFKFPELVNIPRSGIVHRLDKDTSGILLVARTESFRNFFINEMQERRVIKKYSS 167

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           +V G               +  IG D  +  K    +    A++  K+ +     +  L+
Sbjct: 168 IVIGSTLGSFSI-------EDPIGRDKNNRTKMAIREDGKDALTFVKLKENIG-NYSVLD 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           ++  TGRTHQ+RVH      PI+GD  Y  +      S  +         +  LHA ++ 
Sbjct: 220 VRIETGRTHQIRVHLASKKLPIIGDKTYDPSRSIARGSSSELIDIVRSFPRQALHATHLS 279

Query: 297 LPHPEG-GRLQITAPLPAHMVKTW 319
               +   +     P+P  M +  
Sbjct: 280 FNDQKTDNQFSFDIPIPNDMEQLI 303


>gi|284037752|ref|YP_003387682.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283817045|gb|ADB38883.1| pseudouridine synthase, RluA family [Spirosoma linguale DSM 74]
          Length = 308

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 79/320 (24%), Positives = 136/320 (42%), Gaps = 46/320 (14%)

Query: 16  EENMRLD------------RWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSG 62
           +   R D             +     PH N  N++ +L + Q+ VD K   +FN+ ++ G
Sbjct: 11  QRGQRTDVILPVSEPAELMAFLIAQLPHKNRNNIKSLLSNKQILVDGKVFTQFNHPLKPG 70

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q V +                  ++    + S +    +LYED  + V NK AG+     
Sbjct: 71  QSVTV------------------AANRAPQTSQYRGLTILYEDQFLIVINKQAGLLSMAT 112

Query: 123 SGIAYHID-GFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +        G L  +   +  K    + HRLD+ETSG+++ A++    + + ES+     
Sbjct: 113 NKERDRTAYGILSEYTKKENPKNKIFIIHRLDRETSGVMMFAKSEKVQRLMQESWNATTK 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +LV GIP+  +  I ++L          +    QN      +I+++ V       
Sbjct: 173 ERTYVALVEGIPEPPQGTITSYL----RESKALIVYSSQNPDTGQLSITNYTVTKT-GNG 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  LE++  TGR +Q+RVH   +G P+ GD KY A       S    +L LHA  +   H
Sbjct: 228 YALLELELETGRKNQIRVHMQDIGHPVAGDEKYGAE------SDPIGRLGLHAEVLAFEH 281

Query: 300 PEGG-RLQITAPLPAHMVKT 318
           P  G  ++  AP+P   +  
Sbjct: 282 PITGVPMRFDAPIPKSFLAM 301


>gi|134301061|ref|YP_001114557.1| RluA family pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134053761|gb|ABO51732.1| pseudouridine synthase, RluA family [Desulfotomaculum reducens
           MI-1]
          Length = 320

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 72/313 (23%), Positives = 132/313 (42%), Gaps = 32/313 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  + E   ++ + KN     +   +QK+ R   + ++ K V    ++ +   + I  + 
Sbjct: 31  ISQEHEGFTVENYLKNIL-QYSGRKIQKLTRRKGILLNGKTVYLQKKLNAEDTLSILDLE 89

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHID 130
           +    +  E+  ++               +LYED  + V NKPA   V   G      + 
Sbjct: 90  DTNYGVQPEKGAIE---------------VLYEDDFLLVLNKPAHQLVHPTGQTTRGTMA 134

Query: 131 GFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +L  ++  +      R  HRLD+ETSG ++ A+   +   L +  + R +++ YW+LV 
Sbjct: 135 NYLAYYLKQRNVVSAIRPVHRLDRETSGCVIFAKDSRSQFILEQQLKERTLKRTYWALVK 194

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           GI       I   +     +            +    +I+H++ +  F +    L++   
Sbjct: 195 GIVHPPSGTIDAPIGPHPSLANRRAI-----NEHGEQSITHYQTLRSFPE-ISLLKLNLD 248

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH-PEGGRLQI 307
           TGRTHQ+R+H  H+G PI+GD  Y         SP  N+  LHA  +   H  E   + +
Sbjct: 249 TGRTHQIRLHLAHLGYPIIGDRMYGVR------SPWINRQALHAYDVSFRHLKENHEIAV 302

Query: 308 TAPLPAHMVKTWD 320
            APLP    +  +
Sbjct: 303 HAPLPTDFAQAIN 315


>gi|152974728|ref|YP_001374245.1| RluA family pseudouridine synthase [Bacillus cereus subsp.
           cytotoxis NVH 391-98]
 gi|152023480|gb|ABS21250.1| pseudouridine synthase, RluA family [Bacillus cytotoxicus NVH
           391-98]
          Length = 297

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 133/315 (42%), Gaps = 33/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE + +  + K     I+   L  I    G + V+ +     + +++G++++I   
Sbjct: 10  ITEAEEGVLIREFVKT--KGISKAALTDIKFHGGAIEVNGEEATVRHILKTGEILQIFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +  +KI                 ++YED  + V NK   +S            
Sbjct: 68  VEERSEGMVAEKI--------------PLSIVYEDDAVLVINKEPYMSTIPSREHPTGSI 113

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + +++++ Y ++V
Sbjct: 114 ANALLYHYDTQKLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKQVKRTYEAVV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   N+   I   + +KS    + +       +    A++HF+V   ++ K   + +Q 
Sbjct: 174 HGRMLNESGTIDAPIGRKSDSIIERMVR-----EDGQKAVTHFQVRKRYSNK-THVALQL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y           +  +  LH++ +   HP     + 
Sbjct: 228 DTGRTHQIRVHMAHIGHPLLGDDLYGGQLD------LIKRQALHSKSLTFYHPILEKEMS 281

Query: 307 ITAPLPAHMVKTWDS 321
            +A +P  M      
Sbjct: 282 FSADIPTDMHTVLAR 296


>gi|229189393|ref|ZP_04316412.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           ATCC 10876]
 gi|228594104|gb|EEK51904.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           ATCC 10876]
          Length = 292

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 131/314 (41%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE   +  + K     I+   L  I    G + V+ +     +++++G+ +R+   
Sbjct: 5   IGPAEEGTLVREFLKTKC--ISKAALTDIKFHGGAIEVNGQHASVRHQLRAGEKLRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + + NK A +S            
Sbjct: 63  VEERSEGM--------------MAEDIPLSIVYEDDAVLIINKEANMSTIPSREHPTRSV 108

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HFKVID    K   + ++ 
Sbjct: 169 HGKIVEREGMIDAPIGRKSDSIIERTVC-----EDGQRAVTHFKVIDSTYHK-THVALEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y              +  LH++ +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAHIGHPLLGDSLYGGGRDE------MKRQALHSKSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWD 320
            T  LP+ M +   
Sbjct: 277 FTIKLPSDMQEVLR 290


>gi|168209672|ref|ZP_02635297.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
 gi|168213116|ref|ZP_02638741.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE
           str. F4969]
 gi|170712270|gb|EDT24452.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
 gi|170715381|gb|EDT27563.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE
           str. F4969]
          Length = 324

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 125/300 (41%), Gaps = 25/300 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ + +   +    + K LR G +RV+ K+ K    +  G V+ I  
Sbjct: 3   IEIGTNEAGQRLDKFLRKYLKDVPLSAIFKALRKGDIRVNGKKQKEKYSLLDGDVIEI-- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
                + + KE+K  +  +      D     ++YED  + +  K  G+ V       A  
Sbjct: 61  -RYLQSVVTKEKKKPNFQM-----VDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAPT 114

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI+   +     + L E  R R++
Sbjct: 115 LTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERKV 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G  +        ++ K   +      V               KV+      
Sbjct: 175 KKYYCALVKGKIQP--GKYEAYISKDDELNKS--TVYDTERPDTKKIKMDVKVLQTNG-A 229

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F  LE++  TGR+HQLR H  H+G PIVGD KY  N   +F          +L+A  +  
Sbjct: 230 FSLLEIELITGRSHQLRAHLAHLGNPIVGDFKYGDNKMNSFFENKFGLTYQFLYAYKVTF 289


>gi|328946274|gb|EGG40418.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1087]
          Length = 297

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 138/322 (42%), Gaps = 33/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   I+   L KI    G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKRH--EISKSLLAKIKFSGGNILVNHQSQNAVYLLDIGDKV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          +K              +      ++YED    V +KPAG++       
Sbjct: 57  TIDIPSEKGFESLK--------------AVDKGLSVIYEDEHFLVLDKPAGVASIPSVNH 102

Query: 126 AYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  +  F+K++   +G   Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTMANFVKAYYIRQGYENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKR 162

Query: 183 YWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G     ++  I   + +        +      +    YA + +KVI+ F   + 
Sbjct: 163 YYALVRGSGLLEEQGEIIAPIGRNPE---SIITRRVTEDGDGKYAHTSYKVIERFGDVY- 218

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++  HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH   +   +P 
Sbjct: 219 LVDIHLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLEQ-----GIERQALHCHSLKFYNPF 273

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
            G  ++  +PLP    +  + L
Sbjct: 274 SGQEVERASPLPEDFKQVIEKL 295


>gi|308173127|ref|YP_003919832.1| pseudouridylate synthase [Bacillus amyloliquefaciens DSM 7]
 gi|307605991|emb|CBI42362.1| pseudouridylate synthase [Bacillus amyloliquefaciens DSM 7]
 gi|328554031|gb|AEB24523.1| pseudouridylate synthase [Bacillus amyloliquefaciens TA208]
 gi|328911188|gb|AEB62784.1| pseudouridylate synthase [Bacillus amyloliquefaciens LL3]
          Length = 297

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 68/314 (21%), Positives = 126/314 (40%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   E  M +  +       I+   L  I    G + V+ + V     + +G V++I   
Sbjct: 10  ISAPEAGMTVKEYTAQL--GISKRLLADIKFGGGDLLVNGEHVTVRTVLAAGDVLKI--- 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                      +     V+ T   + +   +LYED  + V NK   +S            
Sbjct: 65  -----------EFPKEHVSETLLPEPVPLDILYEDDHVLVVNKQPYVSSIPSREHPSESI 113

Query: 130 -DGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +G +  +  +  Q    L  RLD++TSG +++A+ R A   L+ + +   + + Y ++V
Sbjct: 114 ANGVISHYRKNGVQSTVHLVTRLDRDTSGAMLIAKHRLAHSLLSAAQKKGLVNRRYLAVV 173

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+   K+  +   + +K     + +            A++HF+  +          ++ 
Sbjct: 174 HGVILQKEGTVDAPIGRKPDSIIERMV-----TPEGQKAVTHFQ-AEKAGHASTLAALRL 227

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++G P+VGD  Y    +G        +  LH+  +   HP  G  L 
Sbjct: 228 ETGRTHQIRVHMSYLGHPLVGDTLYGGKNEG------IARQALHSELLSFVHPMTGETLV 281

Query: 307 ITAPLPAHMVKTWD 320
             AP+P  M    +
Sbjct: 282 FHAPVPDDMKTLIE 295


>gi|218234328|ref|YP_002365988.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
 gi|218162285|gb|ACK62277.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
          Length = 297

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 65/317 (20%), Positives = 133/317 (41%), Gaps = 39/317 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE   +  + K     I+   L  I    G + V+ +     +++++G+ +R+   
Sbjct: 10  IGPAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLRAGEELRVFFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + + NK A +S           +
Sbjct: 68  VEERSEGM--------------MAEDIPLCIIYEDDAVLIINKEANMSTIPSREHPAGSV 113

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 114 A---NALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS    +         +    A++HFKVID    K   + 
Sbjct: 171 AIVHGKIVEREGMIDAPIGRKSDSIIERTVC-----EDGQRAVTHFKVIDSTYHK-THVA 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G P++GD  Y              +  LH++ +   HP    
Sbjct: 225 LELETGRTHQIRVHMAHVGHPLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEK 278

Query: 304 RLQITAPLPAHMVKTWD 320
            +  T  LP+ M +   
Sbjct: 279 EMSFTIKLPSDMQEVLR 295


>gi|220931673|ref|YP_002508581.1| pseudouridine synthase, RluA family [Halothermothrix orenii H 168]
 gi|219992983|gb|ACL69586.1| pseudouridine synthase, RluA family [Halothermothrix orenii H 168]
          Length = 310

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 76/323 (23%), Positives = 136/323 (42%), Gaps = 32/323 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQ 63
             +    + ++E  + L  + KN    ++   ++K+ R  ++R++ + VKF   ++ SG 
Sbjct: 14  EEITSYRISDEEAGVTLYTFLKNRLK-MSRKFIRKMGREYRIRLNCRYVKFTEVKLNSGD 72

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++          +                    L   ++YED  + V NKPA + V    
Sbjct: 73  LIEFNLNFKEKTY---------------YDPAPLDLDIIYEDRHLLVINKPANMLVHPTP 117

Query: 124 GIAYHI--DGFLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +   +G L    +       R  HRLD+ T+G+L++A+ + A  ++T  F+   I 
Sbjct: 118 VEKSNTIVNGVLYHMRNQGNYNLVRPIHRLDRNTTGLLLIAKNQYAHNYITHQFQNNNIH 177

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y + V G  + KKE I   + K      D +   K +      A++H KV+       
Sbjct: 178 REYLAFVHGNVEFKKESINAPIGK----TRDSLIKRKVDHTLGKRAVTHIKVVK-PGGLI 232

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++  TGRTHQ+RVH  H+G P++GD  Y           +  +  LH+  +    P
Sbjct: 233 SLIRVKLETGRTHQIRVHLSHLGHPLLGDTLYGGE------DILIKRPALHSYKVTCCLP 286

Query: 301 -EGGRLQITAPLPAHMVKTWDSL 322
            +   +   APLP  M K    L
Sbjct: 287 FKHKEVTFKAPLPVDMEKLKKQL 309


>gi|46907201|ref|YP_013590.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|254852463|ref|ZP_05241811.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|254931351|ref|ZP_05264710.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|300764179|ref|ZP_07074174.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
 gi|46880468|gb|AAT03767.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Listeria monocytogenes serotype 4b str. F2365]
 gi|258605772|gb|EEW18380.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|293582902|gb|EFF94934.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|300515169|gb|EFK42221.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
 gi|332311376|gb|EGJ24471.1| Pseudouridylate synthase [Listeria monocytogenes str. Scott A]
          Length = 296

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 145/319 (45%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE +E+ + L  + K+   HI+   L   K    G++ V+ +       +++G  VR+  
Sbjct: 7   VETEEDGLLLRTFLKS--KHISKQLLTAVKFGAEGKIEVNNEEQNVLYHVKAGDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTDLDIIFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 NGSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +   G+   +K  I   + +K     +   + +       YA ++++V+  + + F  +
Sbjct: 168 QAFTSGVLVEQKGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLARY-RAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
           + +    PLPA M +    
Sbjct: 276 KYMAFDLPLPADMEEIIQK 294


>gi|307265946|ref|ZP_07547494.1| pseudouridine synthase, RluA family [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|306919010|gb|EFN49236.1| pseudouridine synthase, RluA family [Thermoanaerobacter wiegelii
           Rt8.B1]
          Length = 285

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/317 (22%), Positives = 140/317 (44%), Gaps = 38/317 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V  +E+ + L+ + +N       + + K    G++ V+  +      +Q G V+    
Sbjct: 3   LIVGENEKGVILENFLRNKGFSKRLIRIYKW--QGEILVNGVKENVQRILQPGDVI---- 56

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                        ++   V+     + +   + YED  + + +KPAG+ V          
Sbjct: 57  ------------DLILPEVDSDIAPEKMGLDIYYEDEDVLIVDKPAGVVVHPTKRYQSGT 104

Query: 129 IDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +  +   KG K   R  +RLD+ TSG++V A+      +L      + + K+Y+++
Sbjct: 105 LANGVAWYFKDKGIKALIRPVNRLDKGTSGLVVFAKRPFMQYYLQIV---KPMSKLYFAV 161

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + +   I   + +K   G + +       +  + AI+++KV+   +++F  L+++
Sbjct: 162 VEGKMEGE-GRIDLPISRKPQSGIERMV-----SEEGDRAITNYKVVKS-SERFSLLKVK 214

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  H+G PIVGD  Y +      +     +  LHA  +   HP   + +
Sbjct: 215 IETGRTHQIRVHLSHIGHPIVGDTLYGS------SDDYIKRQALHAYRLTFVHPLEEKSI 268

Query: 306 QITAPLPAHMVKTWDSL 322
            + +PLP  +       
Sbjct: 269 SVYSPLPQDIQHLLKLF 285


>gi|229016558|ref|ZP_04173498.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1273]
 gi|229022765|ref|ZP_04179289.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1272]
 gi|228738577|gb|EEL89049.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1272]
 gi|228744734|gb|EEL94796.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1273]
          Length = 292

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 63/312 (20%), Positives = 131/312 (41%), Gaps = 39/312 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   +  + K     I+   L  I    G + V+ +     +++Q+G+ +++       
Sbjct: 9   DEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHKLQAGEELQVFFPFEER 66

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHI 129
           +  ++ + I                 ++YED  + V NK A +S           +A   
Sbjct: 67  SEGMEVEDI--------------PLNIVYEDDAVLVVNKEAYMSTIPSREHPSGSVA--- 109

Query: 130 DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L  +   +      +  RLD++TSG++++A+ R     L++  + + +++ Y +LV 
Sbjct: 110 NALLYHYDKQNLASTVHIVTRLDRDTSGLMLIAKNRFVHNLLSKQHQQKGVKRTYEALVH 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+   +   I   + +K+    +         +    A++HFKV++  + K   + ++  
Sbjct: 170 GMILEEIGTIDAPIGRKADSIIERTVC-----EDGQRAVTHFKVMESSSNK-THVALELE 223

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQI 307
           TGRTHQ+RVH  H+G P++GD  Y           +  +  LH+  +   HP     +  
Sbjct: 224 TGRTHQIRVHMAHIGHPLLGDDLYGGRRD------VMKRQALHSTSLTFYHPILEKEMTF 277

Query: 308 TAPLPAHMVKTW 319
           T  +P  M    
Sbjct: 278 TVGIPDDMQSAL 289


>gi|289168022|ref|YP_003446291.1| 23S_rRNA pseudouridine synthase [Streptococcus mitis B6]
 gi|288907589|emb|CBJ22426.1| 23S rRNA pseudouridine synthase [Streptococcus mitis B6]
          Length = 298

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 71/305 (23%), Positives = 130/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L K+  R G + V+ +       +  G  V I          ++   
Sbjct: 16  FLKKH--EVSKGLLAKVKFRGGAILVNDQPQNATYLLDIGDRVAIDIPAEEGFETLE--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
                      +      +LYED    V NKP G++       +  I  F+K +    + 
Sbjct: 71  -----------AIERPLDILYEDDHFLVLNKPYGVASIPSVNHSNTIANFIKGYYVKQNY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G      +  I
Sbjct: 120 ENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLESEGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      +   + ++  KG  YA + +K++  +      ++++ HTGRTHQ+RVH
Sbjct: 180 IAPIARD-----EDSIITRRVAKGGKYAHTSYKIVASYGSIH-LVDIRLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
             H+G P++GD  Y  +           +  LH  Y+   HP   + LQ+ +PLP     
Sbjct: 234 FSHIGFPLLGDDLYGGSLDD-----GIQRQALHCHYLSFYHPFLEQDLQLESPLPDDFSN 288

Query: 318 TWDSL 322
               L
Sbjct: 289 LITQL 293


>gi|194015110|ref|ZP_03053727.1| pseudouridylate synthase [Bacillus pumilus ATCC 7061]
 gi|194014136|gb|EDW23701.1| pseudouridylate synthase [Bacillus pumilus ATCC 7061]
          Length = 288

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/313 (22%), Positives = 130/313 (41%), Gaps = 33/313 (10%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
              EE   L  +  +    I+   L  I    G + ++ + V    ++ +G  + I    
Sbjct: 2   TAKEEGQLLKDYLIDL--GISKRMLTDIKFDGGDLLINGEHVTVRYKLHNGDRLTILFPE 59

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
             ++  +K                 +   +L+ED  + V NK   I          H   
Sbjct: 60  EKVSEGLK--------------PAPIPLDILFEDDHVLVLNKKPYIPSIPSREHPEHSIA 105

Query: 130 DGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +G L  + +   +    L +RLD++TSG+++VA+ R A   L+++ +   +++ Y +   
Sbjct: 106 NGLLHHYAEQSVRLTVHLVNRLDRDTSGVMLVAKHRFAHSLLSKAQKSGAVKRTYRAFTH 165

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQP 247
           G+ + K   I   + +K     + +       +    A++HF V    A+     + +  
Sbjct: 166 GMIREKHGTIRAKIARKGDSIIERMV-----NETGQEAVTHFTVRAVDAELNMSDVRLTL 220

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGRTHQ+RVH  ++G P++GD  Y        T+   N+  LH+  +  PHP  G  + 
Sbjct: 221 ETGRTHQIRVHMQYLGYPLIGDTLYGG------TNERMNRQALHSETLVFPHPMTGEEMT 274

Query: 307 ITAPLPAHMVKTW 319
            +APLP  M    
Sbjct: 275 FSAPLPEDMKSLL 287


>gi|189466071|ref|ZP_03014856.1| hypothetical protein BACINT_02441 [Bacteroides intestinalis DSM
           17393]
 gi|189434335|gb|EDV03320.1| hypothetical protein BACINT_02441 [Bacteroides intestinalis DSM
           17393]
          Length = 303

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 73/309 (23%), Positives = 122/309 (39%), Gaps = 35/309 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     ++N  ++ G  V+I        
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDSVITTQYNFPLKPGMKVQISRDKGK-- 78

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----IAYHIDG 131
                           K        ++YED+ I V  K  G+            AYHI  
Sbjct: 79  ----------------KEFHNKLLKIVYEDAYIIVVEKMQGLLSVSSERQKERTAYHILN 122

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                 + +G    + HRLD++TSG+++ A+     + L +++      + Y ++V G  
Sbjct: 123 EYVQRSNGRGSNVYIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVAGEM 182

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           +    CI +WL  ++             + G   +I+H++ I   A  +  +E+   TGR
Sbjct: 183 EKNAGCIISWLTDRT-----LYVYSSPTDDGGQKSITHYRTIKR-ANGYSLVELNLETGR 236

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            +Q+RVH   +G PIVGD +Y              +L LHA  +   HP  G  +Q   P
Sbjct: 237 KNQIRVHMQDLGHPIVGDGRYGLEEVNP-----IGRLALHAFKLCFYHPVTGELMQFETP 291

Query: 311 LPAHMVKTW 319
            P    K +
Sbjct: 292 YPNDFKKLF 300


>gi|229078499|ref|ZP_04211059.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock4-2]
 gi|228704815|gb|EEL57241.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock4-2]
          Length = 292

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 131/314 (41%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE   +  + K     I+   L  I    G + V+ +     +++++G+ +R+   
Sbjct: 5   IGPAEEGTLVREFLKTKC--ISKAALTDIKFHGGAIEVNGQHASVRHQLRAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
           +   +  +               ++ +   ++YED  + + NK A +S            
Sbjct: 63  VEERSEGM--------------MAEDIPLSIVYEDDAVLIINKEANMSTIPSREHPTRSV 108

Query: 130 -DGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +KS    +         +    A++HFKVID    K   + ++ 
Sbjct: 169 HGKIVEREGMIDAPIGRKSDSIIERTVC-----EHGQRAVTHFKVIDSTYHK-THVALEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y              +  LH++ +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAHIGHPLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWD 320
            T  LP+ M +   
Sbjct: 277 FTIKLPSDMQEVLR 290


>gi|15605391|ref|NP_220177.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis D/UW-3/CX]
 gi|255349046|ref|ZP_05381053.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 70]
 gi|255503584|ref|ZP_05381974.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 70s]
 gi|255507264|ref|ZP_05382903.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis D(s)2923]
 gi|3329108|gb|AAC68253.1| Pseudouridine Synthase [Chlamydia trachomatis D/UW-3/CX]
          Length = 334

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 144/328 (43%), Gaps = 32/328 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQ 63
           T V   V++      RLD+   ++    +    Q+ +  G+VRV+ +   + ++ +  G 
Sbjct: 8   TAVFSFVIDEQLTG-RLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGD 66

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                 V   L    +   ++   + L K         +YED  + V NKP  + V    
Sbjct: 67  -----VVEVELIEEEEPSSLIPEDIPLDK---------VYEDDMMLVINKPRDMVVHPAP 112

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + + I   LK     +  +P + HRLD++TSG+L+  +TR A    +E F
Sbjct: 113 GHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKALYSELF 172

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             ++++K+Y ++    P  ++    +  + +  +    + V+  + +G   AI+H +V+ 
Sbjct: 173 ATKQVKKLYVAICINAPSQER---IHTRIARHPLKRKEMTVLSTHAEGGKEAITHCQVLA 229

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              +    + + P TGRTHQLRVH  H+G PI+GD  Y             +K  LHA  
Sbjct: 230 TNGR-LSVVALYPETGRTHQLRVHMKHLGTPILGDPVYG--IPSINFRYGLDKQQLHAYS 286

Query: 295 MDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           +   HPE   R+++   LP  M    + 
Sbjct: 287 LVFAHPESAERVKLVTKLPDDMTSLIEK 314


>gi|302389469|ref|YP_003825290.1| pseudouridine synthase, RluA family [Thermosediminibacter oceani
           DSM 16646]
 gi|302200097|gb|ADL07667.1| pseudouridine synthase, RluA family [Thermosediminibacter oceani
           DSM 16646]
          Length = 291

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 137/319 (42%), Gaps = 44/319 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV+   + + +  + K +    +   ++++   G++ ++      N RI    V+ +  
Sbjct: 3   FVVDETSQGLTVGEFLKAN--GFSSRTIRRLKLGGKILINGVPAYTNTRISCNDVIEV-- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  + ++  I+ S V +          +LYED  I V NK  G+ V      A+H 
Sbjct: 59  ------DLTEKSGIVPSPVPIN---------ILYEDDHIIVLNKQPGVVVHP---TAFHY 100

Query: 130 DGFLKS----WVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +  + +    +++ KG+K      +RLD++T+G+L++A ++     +    RM++    Y
Sbjct: 101 NDTIANGVIYYLNQKGKKGGFHPVNRLDRDTTGVLIIALSQHMHNLIQTHGRMKK---RY 157

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G+ K  +  I   + +      +   + +   +    AI+ FKV+          
Sbjct: 158 IAVVEGVVKENEGVIVEPIAR-----REGSLIERCVSEKGQKAITRFKVVKRLKDLTVL- 211

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +++P TGRTHQ+RVH    G P+ GD  Y              +  LH   M   +P  G
Sbjct: 212 DIEPVTGRTHQIRVHLSFKGHPVAGDTLYGGKNDR------IKRQALHCAEMTFFYPVTG 265

Query: 304 -RLQITAPLPAHMVKTWDS 321
             L   APLP  MV   +S
Sbjct: 266 TYLSFKAPLPEDMVNLINS 284


>gi|315281680|ref|ZP_07870254.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria marthii FSL S4-120]
 gi|313614674|gb|EFR88244.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria marthii FSL S4-120]
          Length = 296

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 71/320 (22%), Positives = 142/320 (44%), Gaps = 40/320 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            VE +E  + L  + K+   HI+   L   K    G++ V+ +       ++SG  VR+ 
Sbjct: 6   TVETEENGLLLRTFLKS--KHISKQLLTAVKFSADGKIEVNNEEQNVLYHVKSGDQVRLT 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                 N  +               ++  +  +++ED  + + NKPAG++        YH
Sbjct: 64  FPTEQQNERL--------------LAEHTELEIVFEDDFLLIINKPAGMASIPSQ---YH 106

Query: 129 IDGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ 
Sbjct: 107 PHGSVANFVKGHYETQGLTSAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQQGLLKRR 166

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +   G+   ++  I   + +K     +   + +       YA +++ V++ + + F  
Sbjct: 167 YQAFTGGVLAEQEGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYAVLERY-RAFDH 220

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP  
Sbjct: 221 VAIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TTLLQRQALHSCHLHLVHPLT 274

Query: 303 GR-LQITAPLPAHMVKTWDS 321
              +    PLPA M +    
Sbjct: 275 EEYMAFDLPLPADMEEIIQK 294


>gi|167039932|ref|YP_001662917.1| RluA family pseudouridine synthase [Thermoanaerobacter sp. X514]
 gi|300915271|ref|ZP_07132585.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X561]
 gi|307724743|ref|YP_003904494.1| RluA family pseudouridine synthase [Thermoanaerobacter sp. X513]
 gi|166854172|gb|ABY92581.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X514]
 gi|300888547|gb|EFK83695.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X561]
 gi|307581804|gb|ADN55203.1| pseudouridine synthase, RluA family [Thermoanaerobacter sp. X513]
          Length = 285

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 72/317 (22%), Positives = 140/317 (44%), Gaps = 38/317 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++V  +E+ + L+ + +N       + + K    G++ V+  +      +Q G V+ +  
Sbjct: 3   LIVGENEKGVILENFLRNKGFSKRLIRIYKW--QGEILVNGVKENVQRILQPGDVIDL-- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                  I+ E              + +   + YED +I + NKPA + V          
Sbjct: 59  -------ILPEND-------SNIAPEKMGLDIYYEDEEILIVNKPANMVVHPTKRYQSGT 104

Query: 129 IDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +  +   KG K   R  +RLD+ TSG++V A+      +L      + + K+Y+++
Sbjct: 105 LANGVAWYFKDKGIKALIRPVNRLDKGTSGLVVFAKRPFMQYYLQIL---KPMSKLYFAV 161

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + +   I   + +K   G + +       +  + AI+++KV+   +++F  L+++
Sbjct: 162 VEGKMEGE-GRIDLPISRKPQSGIERMV-----SEEGDRAITNYKVVKS-SKRFSLLKVK 214

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  H+G PIVGD  Y +      +     +  LHA  +   HP   + +
Sbjct: 215 IETGRTHQIRVHLSHIGHPIVGDTLYGS------SDDYIKRQALHAYRLTFVHPLEEKSI 268

Query: 306 QITAPLPAHMVKTWDSL 322
            + +PLP  +       
Sbjct: 269 SVYSPLPQDIQNLLKLF 285


>gi|313609638|gb|EFR85147.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes FSL F2-208]
          Length = 296

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 141/319 (44%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE +E  + L  + K+   HI+   L   K    G++ V+ +       ++ G  VR+  
Sbjct: 7   VETEENGLLLRTFLKS--KHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKVGDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTDLDIVFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 SGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +   G+   ++  I   + +K     +   + +       YA ++++V++ +   F  +
Sbjct: 168 QAFTSGVLAAQEGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLERYT-AFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TTLLKRQALHSCHLHLVHPVTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
             +    PLPA M +    
Sbjct: 276 EYMAFDLPLPADMEEIIQK 294


>gi|289525702|emb|CBJ15183.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis Sweden2]
 gi|296435271|gb|ADH17449.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis E/150]
 gi|296438990|gb|ADH21143.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis E/11023]
 gi|297748789|gb|ADI51335.1| Ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis D-EC]
 gi|297749669|gb|ADI52347.1| Ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis D-LC]
          Length = 335

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 144/328 (43%), Gaps = 32/328 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQ 63
           T V   V++      RLD+   ++    +    Q+ +  G+VRV+ +   + ++ +  G 
Sbjct: 9   TAVFSFVIDEQLTG-RLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGD 67

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                 V   L    +   ++   + L K         +YED  + V NKP  + V    
Sbjct: 68  -----VVEVELIEEEEPSSLIPEDIPLDK---------VYEDDMMLVINKPRDMVVHPAP 113

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + + I   LK     +  +P + HRLD++TSG+L+  +TR A    +E F
Sbjct: 114 GHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKALYSELF 173

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             ++++K+Y ++    P  ++    +  + +  +    + V+  + +G   AI+H +V+ 
Sbjct: 174 ATKQVKKLYVAICINAPSQER---IHTRIARHPLKRKEMTVLSTHAEGGKEAITHCQVLA 230

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              +    + + P TGRTHQLRVH  H+G PI+GD  Y             +K  LHA  
Sbjct: 231 TNGR-LSVVALYPETGRTHQLRVHMKHLGTPILGDPVYG--IPSINFRYGLDKQQLHAYS 287

Query: 295 MDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           +   HPE   R+++   LP  M    + 
Sbjct: 288 LVFAHPESAERVKLVTKLPDDMTSLIEK 315


>gi|13357873|ref|NP_078147.1| pseudouridine synthase (uracil hydrolase) [Ureaplasma parvum
           serovar 3 str. ATCC 700970]
 gi|11279832|pir||H82907 pseudouridine synthase (uracil hydrolase) UU313 [imported] -
           Ureaplasma urealyticum
 gi|6899289|gb|AAF30722.1|AE002128_10 pseudouridine synthase (uracil hydrolase) [Ureaplasma parvum
           serovar 3 str. ATCC 700970]
          Length = 299

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 69/310 (22%), Positives = 137/310 (44%), Gaps = 31/310 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            R+D++   +  + +   ++K+L    + V+   + K +  ++    ++I   +     I
Sbjct: 11  QRIDKFLVEN-TNYSRTLIKKMLDQNLILVNDNFISKASYLLKKNDYIQINNELP----I 65

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSW 136
           ++EQK L   V            +++ED  + + NKP+G+ V   S      +   LK +
Sbjct: 66  VQEQKKLLPFV--------YSLEIIFEDQDLLIVNKPSGMLVHPTSFHEQNTLANALKYY 117

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           + +      +THRLD+ TSG++++ + + A   L + F  + I+K Y+++V      +  
Sbjct: 118 LKTDNF--YITHRLDKNTSGLIIICKNQIALNSLQQQFMQKTIRKSYYAIVHNRFDMQ-- 173

Query: 197 CIANWLLKKSHIGG---DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                 +    IG    D + +   N K    AIS  KV++ + +    +E+   TGRTH
Sbjct: 174 --HLHFMINEPIGHSYQDKLRMKTGNSKNTKEAISIVKVLEQY-KNTALVEVSIITGRTH 230

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           Q+RVH  ++  P+  D  Y  +             YLH+ Y+   HP    +++    +P
Sbjct: 231 QIRVHMRYINHPVYNDPLYGISKHTTEYE-----QYLHSFYISFNHPSTNKKVEFKINMP 285

Query: 313 AHMVKTWDSL 322
              ++    L
Sbjct: 286 KEFMELIREL 295


>gi|167971859|ref|ZP_02554136.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 6 str. ATCC 27818]
 gi|168282520|ref|ZP_02690187.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 14 str. ATCC 33697]
 gi|168308674|ref|ZP_02691349.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 1 str. ATCC 27813]
 gi|170762382|ref|YP_001752395.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 3 str. ATCC 27815]
 gi|168827959|gb|ACA33221.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 3 str. ATCC 27815]
 gi|171902645|gb|EDT48934.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 1 str. ATCC 27813]
 gi|182675832|gb|EDT87737.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 14 str. ATCC 33697]
 gi|186700803|gb|EDU19085.1| pseudouridylate synthase, 23S RNA-specific [Ureaplasma parvum
           serovar 6 str. ATCC 27818]
          Length = 292

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 69/310 (22%), Positives = 137/310 (44%), Gaps = 31/310 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            R+D++   +  + +   ++K+L    + V+   + K +  ++    ++I   +     I
Sbjct: 4   QRIDKFLVEN-TNYSRTLIKKMLDQNLILVNDNFISKASYLLKKNDYIQINNELP----I 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSW 136
           ++EQK L   V            +++ED  + + NKP+G+ V   S      +   LK +
Sbjct: 59  VQEQKKLLPFV--------YSLEIIFEDQDLLIVNKPSGMLVHPTSFHEQNTLANALKYY 110

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           + +      +THRLD+ TSG++++ + + A   L + F  + I+K Y+++V      +  
Sbjct: 111 LKTDNF--YITHRLDKNTSGLIIICKNQIALNSLQQQFMQKTIRKSYYAIVHNRFDMQ-- 166

Query: 197 CIANWLLKKSHIGG---DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                 +    IG    D + +   N K    AIS  KV++ + +    +E+   TGRTH
Sbjct: 167 --HLHFMINEPIGHSYQDKLRMKTGNSKNTKEAISIVKVLEQY-KNTALVEVSIITGRTH 223

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           Q+RVH  ++  P+  D  Y  +             YLH+ Y+   HP    +++    +P
Sbjct: 224 QIRVHMRYINHPVYNDPLYGISKHTTEYE-----QYLHSFYISFNHPSTNKKVEFKINMP 278

Query: 313 AHMVKTWDSL 322
              ++    L
Sbjct: 279 KEFMELIREL 288


>gi|229004047|ref|ZP_04161850.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           Rock1-4]
 gi|228757200|gb|EEM06442.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           Rock1-4]
          Length = 286

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 135/316 (42%), Gaps = 39/316 (12%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
              E+ M +  + K     I+   L  I  + G + VD K     + +Q+ +V+++   +
Sbjct: 2   TEAEKEMLIREFLKT--KGISKAALTDIKFQGGAIEVDGKHATVRHVLQAEEVLQVFFPV 59

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIA 126
              +  +               ++ +   +LYED  + V NK   +S           +A
Sbjct: 60  EERSEGM--------------LAENIPLTVLYEDESVLVINKAPYMSTIPSREHPAGSVA 105

Query: 127 YHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +  L  +   +      +  RLD++TSG++++A+ R     L++  + +++++ Y +
Sbjct: 106 ---NALLYHYDRQNLASTVHIVTRLDRDTSGLMLIAKNRFIHHLLSKQHQQKKVKRTYEA 162

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G    +   I   + +K     + +       +    A++HF+V++ F  K   + +
Sbjct: 163 IVHGEWLEESGTIDAPIGRKGDSIIERMVC-----EDGQKAVTHFQVMERFPDK-TRVSL 216

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           Q  TGRTHQ+RVH  ++G P++GD  Y  +           +  LH+  +   HP   + 
Sbjct: 217 QLETGRTHQIRVHMAYLGHPLLGDDLYGGSKSQ------MKRQALHSTSLTFYHPILEKQ 270

Query: 305 LQITAPLPAHMVKTWD 320
           ++  A +P  M +   
Sbjct: 271 MKFHADVPEDMKELLK 286


>gi|47096256|ref|ZP_00233854.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|254898858|ref|ZP_05258782.1| hypothetical protein LmonJ_03555 [Listeria monocytogenes J0161]
 gi|254911653|ref|ZP_05261665.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes J2818]
 gi|254935979|ref|ZP_05267676.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|47015401|gb|EAL06336.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|258608567|gb|EEW21175.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|293589602|gb|EFF97936.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes J2818]
          Length = 296

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 144/319 (45%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE +EE + L  + K+   HI+   L   K    G++ V+ +       ++ G  VR+  
Sbjct: 7   VETEEEGLLLRTFLKS--KHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKVGDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTNLDIVFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 NGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            + + G+   +K  I   + +K     +   + +       YA ++++V+  + + F  +
Sbjct: 168 QAFISGVLVEQKGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLARY-RAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
             +    PLPA M +    
Sbjct: 276 EYMAFDLPLPADMEEIIQK 294


>gi|329850247|ref|ZP_08265092.1| RNA pseudouridylate synthase family protein [Asticcacaulis
           biprosthecum C19]
 gi|328840562|gb|EGF90133.1| RNA pseudouridylate synthase family protein [Asticcacaulis
           biprosthecum C19]
          Length = 267

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 75/220 (34%), Positives = 121/220 (55%), Gaps = 3/220 (1%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++KS+++YED+ I  FNKP+G+S QGG G  +++D  + ++  S G++P+L HRLD++TS
Sbjct: 42  WVKSMVIYEDADIMGFNKPSGLSSQGGRGDGHNLDDMMWAFAKSNGKRPKLVHRLDRDTS 101

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GIL+VA+T+ A   L ++   R   K Y ++V G     +  +   L ++      +  V
Sbjct: 102 GILLVAKTQPAVSFLGKAMIRRAFDKTYLAIVSGAELPDRFTVDAPLRREEVGREAWSRV 161

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              +   A  A + F+V+         ++  PHTGR HQ+RVH  H+G PI GD +Y   
Sbjct: 162 CAPDHPDALTAQTTFEVLKR-GDDAALIQCSPHTGRMHQIRVHLAHLGTPIAGDVRYGGA 220

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
              +       +L LHA  +  PHP GG   ++AP+P   
Sbjct: 221 L--SVGGRGVPRLMLHALSLTFPHPAGGDKTLSAPIPEDF 258


>gi|167758127|ref|ZP_02430254.1| hypothetical protein CLOSCI_00465 [Clostridium scindens ATCC 35704]
 gi|167664024|gb|EDS08154.1| hypothetical protein CLOSCI_00465 [Clostridium scindens ATCC 35704]
          Length = 333

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 76/336 (22%), Positives = 146/336 (43%), Gaps = 29/336 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +++  +E   RLD++ K +        L K+LR   + ++ K+   N ++  G  V+
Sbjct: 1   MKEIIISQNEAGQRLDKFLKKYLAKAPGSFLYKMLRKKNIVLNGKKATGNEKLGVGDSVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    + +        I +       +   +   +++ED+ +   NKPAG+  Q  +   
Sbjct: 61  LFLADDTIGKFAGLAPIKEE------YQVSVNLDIIHEDANVLFINKPAGMLSQKAAKDD 114

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   + +++ ++G          +P + +RLD+ TSG++V  +T    Q +   F+ R
Sbjct: 115 VSMVEHVIAYLLAEGSITQEELRTFRPSICNRLDRNTSGLIVAGKTLIGLQAMARLFKDR 174

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y   V G  + ++E I  +L K           V   E G     + +  I  + 
Sbjct: 175 TLKKYYLCFVKGGIR-RREHIYGYLAKNEKTNK-----VTIREAGDTPIETEYVPI-AYN 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNK-LYLHARYM 295
           Q+   L++   TGRTHQ+R H    G P++GD+KY  A +   F    Q +   LHA  M
Sbjct: 228 QEMTLLKVHLITGRTHQIRAHLASKGHPLLGDYKYGDAGWNRQFQERYQVRAQQLHAYQM 287

Query: 296 DLPHPEG-----GRLQITAPLPAHMVKTWDSLGFKY 326
            LP  E        +  TA +P    +      +++
Sbjct: 288 KLPWMEAPLDEISGMTFTAKVPPLFWRLIKETTWEH 323


>gi|154685597|ref|YP_001420758.1| YjbO [Bacillus amyloliquefaciens FZB42]
 gi|154351448|gb|ABS73527.1| YjbO [Bacillus amyloliquefaciens FZB42]
          Length = 297

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 65/281 (23%), Positives = 117/281 (41%), Gaps = 30/281 (10%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G + V+ + V     +  G V++I              +     V+ T   + +   +LY
Sbjct: 41  GDLLVNGEHVTVRAVLAEGDVLKI--------------EFPKEHVSETLVPEPVPLDILY 86

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQ-KPRLTHRLDQETSGILVV 160
           ED  + V NK   +S             +G +  +  S  Q    L  RLD++TSG +++
Sbjct: 87  EDDHVLVVNKQPYVSSIPSREHPSESIANGVISHYRKSGVQSTVHLVTRLDRDTSGAMLI 146

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ R +   L+ + +   + + Y ++V GI   K+  +   + +K     + +       
Sbjct: 147 AKHRLSHSLLSAAQKKGLVSRRYLAVVHGIMLQKEGTVDAPIGRKHDSIIERMV-----T 201

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A++HF+  +     F    ++  TGRTHQ+RVH  ++G P+VGD  Y    +G  
Sbjct: 202 PEGQRAVTHFQT-EKAGHAFTLAALRLETGRTHQIRVHMSYLGHPLVGDTLYGGKNEG-- 258

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
                 +  LH+  +   HP  G  L   AP+P  M    +
Sbjct: 259 ----IARQALHSERLSFVHPMTGETLVFHAPVPDDMKTLIE 295


>gi|311067653|ref|YP_003972576.1| pseudouridylate synthase [Bacillus atrophaeus 1942]
 gi|310868170|gb|ADP31645.1| pseudouridylate synthase [Bacillus atrophaeus 1942]
          Length = 298

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 59/285 (20%), Positives = 117/285 (41%), Gaps = 36/285 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G + ++   V     ++ G  +                +  +  V+ +   + +   +LY
Sbjct: 41  GDILINGGHVTVKYVLKLGDTLVF--------------EFPEEQVSESLFPEPVPLHVLY 86

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGI 157
           ED  + V NK   +S         H  G + + +    +K        L  RLD++TSG+
Sbjct: 87  EDDHVLVINKQPYVSSIPSR---EHPSGSIANGILGHYKKNGVRATVHLVTRLDRDTSGV 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R A   L+   +   +++ Y ++V G  +  +  +   + +K     + +    
Sbjct: 144 MLIAKHRFAHSILSTGQKNGLVKRRYLAVVHGSMEQAEGTVDAPIGRKPDSIIERMV--- 200

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
               G   A++HF+V +        + +Q  TGRTHQ+RVH  H+G P+ GD  Y    +
Sbjct: 201 --TPGGQRAVTHFQV-NKKTNGLTSVTLQLETGRTHQIRVHMSHLGHPLCGDTLYGGTRQ 257

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
                   ++  LH+  +   HP     +   AP+P  M +  + 
Sbjct: 258 K------ISRQALHSERLSFIHPLTDETMVFYAPVPQDMQQLIEE 296


>gi|21220553|ref|NP_626332.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           coelicolor A3(2)]
 gi|256788308|ref|ZP_05526739.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           lividans TK24]
 gi|289772202|ref|ZP_06531580.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           lividans TK24]
 gi|5689945|emb|CAB51982.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces coelicolor A3(2)]
 gi|289702401|gb|EFD69830.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           lividans TK24]
          Length = 314

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 134/322 (41%), Gaps = 18/322 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +  ++ + V +  E  R+D      +   +     ++  +G+V+VD   V  + R+ 
Sbjct: 1   MSTIPEIRTLPVPDGLEGERVDAAISRMF-GFSRTKAAELAAAGKVQVDGSVVGKSERVH 59

Query: 61  SGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            G  + +  P   A   ++ E       + +    + +  ++       +     +G +V
Sbjct: 60  GGAWLEVEMPQAPAPVQVVAEPV---EGMEIVHDDEDVVVVVKPVGVAAHPSPGWSGPTV 116

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            GG   A +             ++  + HRLD  TSG++ VA++  A   L   F+ R +
Sbjct: 117 IGGLAAAGYRVST-----SGAAERQGIVHRLDVGTSGLMAVAKSERAYTSLKRQFKERTV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G P      I   + +  H   DY   V         +++H+ +I+ F + 
Sbjct: 172 DKRYHTLVQGHPDPTSGTIDAPIGR--HPQHDYKWAVTAE---GKPSVTHYDLIEAF-RA 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L+++  TGRTHQ+RVH      P VGD  Y A+        +  + +LHA  +   H
Sbjct: 226 ASLLDVKLETGRTHQIRVHMAAHRHPCVGDLTYGADPTLAKRLRL-TRQWLHAVRLGFEH 284

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P  G  ++  +  P  + +  D
Sbjct: 285 PGTGDWVEYASEYPDDLQQALD 306


>gi|153940669|ref|YP_001392256.1| RluA family pseudouridine synthase [Clostridium botulinum F str.
           Langeland]
 gi|152936565|gb|ABS42063.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           Langeland]
 gi|295320251|gb|ADG00629.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           230613]
          Length = 300

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 73/323 (22%), Positives = 146/323 (45%), Gaps = 28/323 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      VV+    N+ +  + +    +++   ++K +R G+V V+K++V   +++    
Sbjct: 1   MDNKLIFVVKKINHNIDIKDYLRE-MENLSGRFIRKAVRDGRVFVNKEKVIKKHKLSQDD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I    +   +I  E   ++               ++YED+ I V NK  GI V    
Sbjct: 60  LIEIYMQEDEHQNIEPEDMNIE---------------IVYEDNDIIVINKRPGIVVHPTK 104

Query: 124 GIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G     +   +       G+K   RL  RLD++TSG++++A+ + +   L         +
Sbjct: 105 GHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFR 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY ++V G  K K+  I   +  +     +   + +  ++    +I+ ++V++  ++  
Sbjct: 165 KIYIAVVHGSMKEKEGRINLPIYNEE----ESESIKRIVDERGQESITTYEVLEELSKG- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++  TGRTHQ+RVH  H+G P+ GD  Y    KG        +  LHA  ++ PHP
Sbjct: 220 SVVRLELETGRTHQIRVHMSHLGHPLYGDSLYG---KGEEEKEYIERQALHAYKLEFPHP 276

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
             G + ++   LP  +    + +
Sbjct: 277 RTGDILKLQCSLPDDIKNLIEKI 299


>gi|255994448|ref|ZP_05427583.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Eubacterium saphenum ATCC 49989]
 gi|255993161|gb|EEU03250.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Eubacterium saphenum ATCC 49989]
          Length = 318

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 78/314 (24%), Positives = 144/314 (45%), Gaps = 34/314 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VVE++ EN  +    K  Y   +   L K+ +   +R++ K  K     ++G V+ +   
Sbjct: 24  VVEHNFENRSIKSIIKREYSISSR-FLSKLKQEDLIRLNGKPAKNWFTPKAGDVIEL--- 79

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                       ++    +       ++   +YED  + V +KPAGI V    G   +  
Sbjct: 80  ------------VMPKESSYFTPYSGIEINAVYEDEHLLVIDKPAGIVVHPTHGYEENTI 127

Query: 131 GF-LKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L  ++D+ G+  K R  +RLD +T+G+L++A+ +     +    +   ++K Y ++V
Sbjct: 128 AHALIHYMDTVGEEFKIRFINRLDMDTTGLLMIAKNQFIQNAVVSEMKRGNVEKRYLAVV 187

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQ 246
            G+P N++  I   +          V       +G   +I+ +KV+    +    +L+++
Sbjct: 188 HGLPCNREGIIDAPIKAVEGEPRRQVM------EGGKPSITEYKVVGVSDELNVSFLDVR 241

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL- 305
            HTGRTHQ+RVH  H+GCPI+GD  Y             ++  LH+RY+   HP   ++ 
Sbjct: 242 LHTGRTHQIRVHLKHIGCPILGDEFYGGKESA-------DRQLLHSRYLRFTHPVSKKIV 294

Query: 306 QITAPLPAHMVKTW 319
           ++TA LP  +    
Sbjct: 295 ELTANLPDDIASIL 308


>gi|324992871|gb|EGC24791.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK405]
 gi|325696535|gb|EGD38425.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK160]
 gi|327460322|gb|EGF06659.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1057]
          Length = 295

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 67/305 (21%), Positives = 130/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L KI    G + V+ +       +  G  V I          +K   
Sbjct: 16  FLKRH--EVSKSLLAKIKFSGGNILVNHQPQNAIYLLDIGDKVTIDIPSEKGFESLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
                      +      ++YED    V +KPAG++       +  +  F+K++      
Sbjct: 71  -----------AVDKDLSVVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G     ++  I
Sbjct: 120 ENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  +   YA + +KVI+     +  +++  HTGRTHQ+RVH
Sbjct: 180 IAPIGRNPE-----SIITRRVTEDGKYAHTSYKVIERIGDVY-LVDIHLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   +P  G  ++  +PLP    +
Sbjct: 234 FSHIGFPLLGDDLYGGSLE-----YGIERQALHCHSLKFYNPFSGQEVERASPLPEDFKQ 288

Query: 318 TWDSL 322
             + L
Sbjct: 289 VIEKL 293


>gi|315222714|ref|ZP_07864603.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
 gi|315188400|gb|EFU22126.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
          Length = 296

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 137/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   I+   L KI    G ++V+ K+      +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EISKSLLAKIKFSGGDIQVNGKKQNAIYLLDIGDKV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +               I       +  +      ++YED    + NKPAG++       
Sbjct: 57  AV--------------DIPAEEGFGSLQAVEKDLEIVYEDEHFLILNKPAGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  +  F+K++      + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTMANFVKAYYIANHYENQQIHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKVIEKH 162

Query: 183 YWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G  P   +  I   + ++         + +   K   YA + +KV+  +   + 
Sbjct: 163 YYALVKGSAPLKPEGDIIAPIAREGS-----SIITRCVAKNGKYAHTSYKVLAQYDDIY- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++  HTGRTHQ+RVH  ++G P++GD  Y  +     T     +  LH   +   +P 
Sbjct: 217 LVDIHLHTGRTHQIRVHFSYIGFPLLGDDLYGGSMTDGIT-----RQALHCHSLRFYNPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
               +  ++PLP         L
Sbjct: 272 HEEVVNKSSPLPEDFQTVIQKL 293


>gi|297180028|gb|ADI16253.1| pseudouridylate synthases, 23S RNA-specific [uncultured bacterium
           HF0010_16H03]
          Length = 309

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/317 (22%), Positives = 127/317 (40%), Gaps = 36/317 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
            N RLD+     +   +   ++K +  G++ V+    K  + +     + I P       
Sbjct: 10  ANQRLDKAATELFDEYSRTQIKKWILEGRILVNGDLSKPRDSVHENDEIEINPT------ 63

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLK 134
             KE+K+     N+   +        +E     + NKP G+ +  GSG       +G + 
Sbjct: 64  --KERKVSWEPQNINFET-------YHECEDFIIINKPPGLIMHPGSGCYDGTLANGLIN 114

Query: 135 SWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            + D +   +  + HRLD++TSG+L+VAR      +  +  + RR+ K Y ++V G    
Sbjct: 115 KYPDLENLPRCGIVHRLDKDTSGVLLVARNEGFRNYFIQLMQERRVTKKYTAIVVGSTLG 174

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                      +  IG D  +  K +       A++  K  +     +  L++   TGRT
Sbjct: 175 SFSI-------EDPIGRDKSNRTKMSVRPDGKEALTFVKTSERIG-NYSILDIAIETGRT 226

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG- 303
           HQ+RVH L    PI+ D  Y  +      S ++         +  LHAR +    P+   
Sbjct: 227 HQIRVHLLSKKLPIIADITYDPSRTIAKDSSLELIKLVRSFPRQALHARVLSFNCPKTQN 286

Query: 304 RLQITAPLPAHMVKTWD 320
            +    P+P+ +     
Sbjct: 287 EMTFEIPIPSDIQNLIK 303


>gi|327474483|gb|EGF19889.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK408]
          Length = 295

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 139/322 (43%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   I+   L KI    G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKRH--EISKGLLAKIKFSGGNILVNHQPQNAVYLLDIGDRV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          +K              +      ++YED    V +KPAG++       
Sbjct: 57  TIDIPSEKGFESLK--------------AVDKDLSVIYEDEHFLVLDKPAGVASIPSVNH 102

Query: 126 AYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  +  F+K++   +G   Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTMANFVKAYYIRQGYENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKR 162

Query: 183 YWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G     ++  I   + +          + +   K   YA + +KVI+ F   + 
Sbjct: 163 YYALVRGSGLLEEQGEIIAPIGRNPE-----SIITRLVTKDGKYAHTSYKVIERFGDVY- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++  HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH   +   +P 
Sbjct: 217 LVDIHLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLEC-----GIERQALHCHSLKFYNPF 271

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
            G  ++  +PLP    +  + L
Sbjct: 272 SGQEVERASPLPEDFKQVIEKL 293


>gi|295694723|ref|YP_003587961.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
 gi|295410325|gb|ADG04817.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
          Length = 322

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 140/327 (42%), Gaps = 30/327 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +   E   +L R+ + + P +    + K +R G+V+V++K+ K +  +  G  V++    
Sbjct: 6   ITRAENGKKLHRFLRQNLPGLPLSGVYKWIRVGRVKVNRKKGKPDLVLHEGDTVQLFVSD 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHID 130
                + +            +        +LYED  + V NKPAG+            + 
Sbjct: 66  EEYAALRRRGPKFQGVPRTFE--------ILYEDGDLLVVNKPAGLLTHPDRQEHRDTLI 117

Query: 131 GFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             + +++  KG+       P   +RLD+ TSGI+++ +   A + L ++ R RR+ K Y 
Sbjct: 118 NRVLAYLYDKGEWDGRAFAPAAANRLDRNTSGIVLIGKHAQALRELADALRGRRVDKRYL 177

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQKF 240
           +LV G  +     +   L++        +   K+   G       A + ++ +   A++ 
Sbjct: 178 ALVHGRIETP-GTLKQALIRDHENNRTRLAGEKRGRHGVAPETLEAETRYRPL-AVAERL 235

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L++   +GRTHQ+R H    G P+VGD KY                +LHA  + L   
Sbjct: 236 TLLDITLVSGRTHQIRAHLAAAGHPLVGDIKYGGKPLRGLRH-----QFLHAYALTL--- 287

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYD 327
             GR +  APLPA + K  +S G   D
Sbjct: 288 ADGR-RFVAPLPAELRKLLESYGLSTD 313


>gi|152993336|ref|YP_001359057.1| ribosomal large subunit pseudouridine synthase D [Sulfurovum sp.
           NBC37-1]
 gi|151425197|dbj|BAF72700.1| ribosomal large subunit pseudouridine synthase D [Sulfurovum sp.
           NBC37-1]
          Length = 317

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 76/337 (22%), Positives = 140/337 (41%), Gaps = 53/337 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           R+D+   +    ++   ++K+++ G V V+KK V K + ++  G  +             
Sbjct: 11  RIDKVLAHEL-DVSRNQVEKLVKDGLVSVNKKMVTKTSFKVVEGDEITYEFK-------- 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                   +             +LYED  + V NKP+G+ V     +    +  L  W+ 
Sbjct: 62  -------EAEKREPVEIDFDVEILYEDEYLMVVNKPSGLVVHPAPSV---KEPTLVDWLV 111

Query: 139 SKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            KG         ++  + HR+D+ET+G LV+A+     + L+E  + + + + Y +L+  
Sbjct: 112 KKGISLSTISGEERHGIVHRIDKETTGALVIAKDNKVHEMLSEQLQDKSMGRYYLALIDH 171

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             K     + +  + ++      + VV         A + FK +         +  +  T
Sbjct: 172 FLKED--VVVDKPIGRNPHNRLKMDVV----PHGKPAKTAFKKLLTSEYDVELIAAKLFT 225

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
           GRTHQ+RVH   +G  I+GD  Y    K +       ++YLHA  + L HP  G +++ T
Sbjct: 226 GRTHQIRVHLNTLGRHILGDDLYGFKSKRDK----IPRVYLHAYLLYLIHPVTGVKMEFT 281

Query: 309 APLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNI 345
           APL   M              LY+ + + Q +  + I
Sbjct: 282 APLFDDMK-------------LYLSKYFDQSDIDEKI 305


>gi|325689674|gb|EGD31678.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK115]
          Length = 295

 Score =  207 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 69/305 (22%), Positives = 131/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   I+   L KI    G + V+ +       +  G  V I          +K   
Sbjct: 16  FLKRH--EISKSLLAKIKFSGGNILVNHQPQNAIYLLDIGDKVTIDIPSEKGFESLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
                      +      ++YED    V +KPAG++       +  +  F+K++   +G 
Sbjct: 71  -----------AVDKDLSVIYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIGQGY 119

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
             Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G     ++  I
Sbjct: 120 ENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH
Sbjct: 180 IAPIGRNPE-----SIITRRVTEDGKYAHTSYKVIERFGDVY-LVDIHLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
             H+  P++GD  Y  + +         +  LH   +   +P  G  ++  +PLP    +
Sbjct: 234 FSHISFPLLGDDLYGGSLE-----HGIERQALHCHSLKFYNPFSGQEVERASPLPEDFKQ 288

Query: 318 TWDSL 322
             + L
Sbjct: 289 VIEKL 293


>gi|307297764|ref|ZP_07577570.1| pseudouridine synthase, RluA family [Thermotogales bacterium
           mesG1.Ag.4.2]
 gi|306917024|gb|EFN47406.1| pseudouridine synthase, RluA family [Thermotogales bacterium
           mesG1.Ag.4.2]
          Length = 312

 Score =  207 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 78/324 (24%), Positives = 144/324 (44%), Gaps = 32/324 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQS 61
           +++  +   V  +    RLDR  +     +   ++ K+LR G VRV+  +++  + +++ 
Sbjct: 16  VISIEKEFKVTKENFYERLDRVLRKELSDLKLSSIYKLLRRGNVRVNGNKIRDGSWKMEI 75

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  V++    +         K L+ S  LT     +   +L+ED  I   +KP+GISV  
Sbjct: 76  GDKVQVVFSGDPSKL-----KRLEESRELTPKH--IPLDILFEDDLIVAVDKPSGISVHP 128

Query: 122 GSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G GI    +   L ++ +SKG  PR  HRLD+ TSG+++ A++  AA+ L++ FR R ++
Sbjct: 129 GKGIQIITLVEGLMAYGNSKGFVPRPVHRLDKHTSGVILFAKSPEAARELSKLFRERGVE 188

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y++LV G P+ + + +                      +   +  S    ++      
Sbjct: 189 KGYFTLVKGFPEKRGKLV---------------------SQREKFVESLAFTVEKSYATT 227

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYMDLP 298
             L +   TG+ HQ+R      G P+VGD  Y      +         + +LH   +   
Sbjct: 228 SLLWIDLFTGKKHQIRRQLSEAGYPVVGDDVYGDRLFNRDFKKETGLRRYFLHCSRLSFA 287

Query: 299 HPEGGRLQITAPLPAHMVKTWDSL 322
             +G  ++I + LP  + +    L
Sbjct: 288 RNDGKEIEIISELPGDLKRVLGCL 311


>gi|118475501|ref|YP_892378.1| ribosomal pseudouridine synthase [Campylobacter fetus subsp. fetus
           82-40]
 gi|118414727|gb|ABK83147.1| ribosomal pseudouridine synthase [Campylobacter fetus subsp. fetus
           82-40]
          Length = 323

 Score =  207 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 72/330 (21%), Positives = 135/330 (40%), Gaps = 43/330 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHII 78
           RLD+   ++   I+   + ++++SG V V+    +K + ++     +             
Sbjct: 11  RLDQILASYLS-ISRNQISELIKSGNVYVNDNLMLKPSFKVLLNDKIGFN---------- 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
               +  +     +        +LYED  I V NKP+ ++V     +    +  L  W+ 
Sbjct: 60  ----LPKAKFENCEFKADFDVEILYEDDDILVLNKPSNLTVHPAPSV---KEATLVEWLK 112

Query: 139 SKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             G          +  + HRLD+ TSG++VVA+  A+   L      + + ++Y +L+  
Sbjct: 113 QNGYMLSTLNGDIRAGIVHRLDKGTSGVIVVAKNNASHSALAAQLSDKSMGRVYLALI-D 171

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                K  I   + +         + V  N + A  A ++             +  +  T
Sbjct: 172 FNLKDKLIIDRPIGRNPQ--NRLKNSVAANGRAAKSAFTNI----ICEDDLNLIAAKLFT 225

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
           GRTHQ+RVH   +   I+GD+ Y    K         ++ LHA  ++L HP  G ++Q  
Sbjct: 226 GRTHQIRVHLASINRHILGDNLYGFKSKNCK----IKRVMLHAYILNLTHPKSGEKMQFI 281

Query: 309 APLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           APLP      +D L  K D+ +  +++  +
Sbjct: 282 APLPTDF---YDILSKKIDKEILNEKIDPE 308


>gi|167957398|ref|ZP_02544472.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [candidate division TM7 single-cell isolate
           TM7c]
          Length = 379

 Score =  207 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 83/305 (27%), Positives = 129/305 (42%), Gaps = 37/305 (12%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           E+  +  RLD          +    QK++ +GQV VD K  K                  
Sbjct: 107 ESKSDKKRLDILLVEKVGKESRSTYQKMITAGQVLVDGKIAK---------------NAK 151

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHID 130
            L  I    KI       T     +K   +YED+ I V NKPAG+       IA  +   
Sbjct: 152 QLVGIESNVKIESKQQKFTP----IKYETIYEDNDIIVINKPAGMLTHAKGAIAEEFTAA 207

Query: 131 GFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             +K   + K    +P + HRLD+ TSG+L++ +   AA  + + F  R ++K Y+++V 
Sbjct: 208 DIVKPITNYKADTNRPGIIHRLDRNTSGVLLMVKNSDAASKIQKQFSQRTVKKTYYAIVC 267

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQP 247
           GIP   K  I   + +       +   V         A + ++V      +    +++QP
Sbjct: 268 GIPYQHKALIDLPIERNPSRPSTFRVGV-----NGKSAQTSYEVERSIIKKNISLIKLQP 322

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQLRVH  ++  PI+GD  Y              +++LHA  +++    G R   
Sbjct: 323 KTGRTHQLRVHMQYLNTPILGDLVYGGKPAE--------RMFLHAESLEVTLLSGERKVF 374

Query: 308 TAPLP 312
            APLP
Sbjct: 375 KAPLP 379


>gi|99034795|ref|ZP_01314715.1| hypothetical protein Wendoof_01000461 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 276

 Score =  207 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 78/288 (27%), Positives = 139/288 (48%), Gaps = 27/288 (9%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++++ QV++    +  N+ I       + P    + H+++     D S ++  + D +K 
Sbjct: 1   MIQNEQVKLLGTPIINNDYI-------VKPDEEYVVHLVQ----PDISTSIEPNYD-IKL 48

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++YED  I V +K +G++V  G+G   + D  L + +     +P + HRLD++TSG++V
Sbjct: 49  NIVYEDEDIIVLSKQSGLTVHPGAGT--NNDTLLNAVIAHLNVRPGIVHRLDKDTSGLMV 106

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+  AA   L+E    R+I++ Y ++VWG   +++  I   +  K     + + V K  
Sbjct: 107 IAKNEAAHSFLSELLSNRKIKREYLAVVWGTLSSQQGTIKTSIAPKRG-NKEMMCVTKI- 164

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---- 275
                 AI+H+ V     Q    ++    TGRTHQ+RVH  H+G  IVGD  Y  N    
Sbjct: 165 --TGKLAITHYLVQKVIGQ-VSLVKCTLETGRTHQIRVHMSHIGHSIVGDQVYGKNSSKS 221

Query: 276 ---FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
               K +      N+  LHA  + L HP+    ++  + LP  +    
Sbjct: 222 TKYAKNSSFIRNFNRQALHAYTLGLYHPKSKEYMEFVSDLPQDIKTLI 269


>gi|257439373|ref|ZP_05615128.1| ribosomal large subunit pseudouridine synthase C [Faecalibacterium
           prausnitzii A2-165]
 gi|257198248|gb|EEU96532.1| ribosomal large subunit pseudouridine synthase C [Faecalibacterium
           prausnitzii A2-165]
          Length = 316

 Score =  207 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 138/313 (44%), Gaps = 19/313 (6%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD +    +P +N   L K LR  +++++ K+   + R+ +G  +++      L+ 
Sbjct: 10  APTRLDNYLMQQFPALNPGRLNKALRENKIKLNGKKQPLSTRVMAGDEIKLFI----LDE 65

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK-- 134
           ++   K ++             + ++Y+  +I V NKPAG++V G           L   
Sbjct: 66  VLDADKRVEGPAWKNARG---PAQVIYDCPQILVVNKPAGLAVDGPEDDTLLNRALLYLN 122

Query: 135 ---SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
               + ++    P L HRLD  TSG++++A+T  A Q   E  + R ++K Y  + +G P
Sbjct: 123 QQGEYKENDLYTPALCHRLDTGTSGLVIIAKTPEAEQLFLEVIKNREVKKTYLCVTFGRP 182

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 +  +LLK +  G   V +V   + GA    + ++ +   + +   L+++  TGR
Sbjct: 183 TPPDGTLGGYLLKDADRG--IVKIVPDKQPGAKDVETQYETV-AVSGRLALLKVRLITGR 239

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM-DLPHPEGGRL---QI 307
           THQ+R H   +GCPI+GD KY  N            L      +     P+   L     
Sbjct: 240 THQIRAHMASIGCPILGDSKYGNNTANRELKLKYQALCAWELVLPRFASPDFADLSGKTF 299

Query: 308 TAPLPAHMVKTWD 320
            AP P +  +  D
Sbjct: 300 RAPKPWYYQQVLD 312


>gi|254520113|ref|ZP_05132169.1| ribosomal large subunit pseudouridine synthase C [Clostridium sp.
           7_2_43FAA]
 gi|226913862|gb|EEH99063.1| ribosomal large subunit pseudouridine synthase C [Clostridium sp.
           7_2_43FAA]
          Length = 323

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 72/300 (24%), Positives = 130/300 (43%), Gaps = 27/300 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ +     +    + K LR G V+V+ K+ K N  +Q   VV I  
Sbjct: 3   IEIGTNEAGQRLDKFLRKLLKDVPLSKIFKALRKGDVKVNGKKQKENYSLQIDDVVEIKY 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
           + +  N    E+K +  +    K        + YEDS + +  K   I V     G    
Sbjct: 63  IQS--NKEKPEEKFIKVNARGMK--------ITYEDSNMLIVEKWPNILVHPDEKGKEAS 112

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S+++ KG           P   +RLD+ TSGI++  +   A + + E  R  ++
Sbjct: 113 LTDYVLSYLNEKGDYLPENELTFTPAPCNRLDRNTSGIVIFGKNFEALRTMNEMIREGKV 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G  K+       ++ K        ++  K  +  +       K +      
Sbjct: 173 EKYYNTLVKGKIKD--GLYKGYIHKNEEANISRIYDEKITD--SKEIAMEVKTLKTNG-A 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           + +LE+   TGR+HQ+R H  H+G PI+GD+KY      +F       +  +L+A  +  
Sbjct: 228 YSFLEIDLITGRSHQIRAHLSHLGTPIIGDNKYGDRKLNSFFANKFGLDCQFLYAYKLIF 287


>gi|226315112|ref|YP_002775008.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226098062|dbj|BAH46504.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
          Length = 310

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 68/324 (20%), Positives = 143/324 (44%), Gaps = 20/324 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS   +++Y  V   +  M +++  +    +++   +Q++ RS  + +++K+     +++
Sbjct: 1   MSRKDWIEY-TVSEQDTGMNVEQIVRQKL-NVSGRMMQRLTRSKGILLNRKQPFLQRQVK 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  + +   +      +  Q   D+      ++      +LYED  + + NKPAG+ V 
Sbjct: 59  AGDTIAV--RVIERQEQVPRQPQHDTKPE-GPNTPMPSIDILYEDDHLLIANKPAGMMVH 115

Query: 121 GGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                   +   L + + ++G++      HRLD++TSG ++VA++    Q      R   
Sbjct: 116 PIKQETDTLVHALAAVLAARGEQTSVHPVHRLDKDTSGAILVAKSSYGHQLADRLLREGG 175

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y ++  G+       I   + + +        V     +  + AI+H++V    ++
Sbjct: 176 IHREYLAVASGVLSEGAGTIDAPIGRDARHPTKRRVV-----ESGDPAITHYEV-QQTSE 229

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +     +   TGRTHQ+RVH  H+G P+ GD  Y           +  +  LHA  +   
Sbjct: 230 EMTLARVWLETGRTHQIRVHFAHIGHPLAGDTMYGG------ARGLLRRQALHASKLSFL 283

Query: 299 HP-EGGRLQITAPLPAHMVKTWDS 321
           HP     + + AP+P+ M +   +
Sbjct: 284 HPLLEKEIVVEAPIPSDMKRLMQA 307


>gi|76789398|ref|YP_328484.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis A/HAR-13]
 gi|237805009|ref|YP_002889163.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis B/TZ1A828/OT]
 gi|255317785|ref|ZP_05359031.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 6276s]
 gi|76167928|gb|AAX50936.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis A/HAR-13]
 gi|231273309|emb|CAX10224.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis B/TZ1A828/OT]
 gi|296436198|gb|ADH18372.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis G/9768]
 gi|296437127|gb|ADH19297.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis G/11222]
 gi|296438058|gb|ADH20219.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis G/11074]
 gi|297140560|gb|ADH97318.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis G/9301]
          Length = 335

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 144/328 (43%), Gaps = 32/328 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQ 63
           T V   V++      RLD+   ++    +    Q+ +  G+VRV+ +   + ++ +  G 
Sbjct: 9   TAVFSFVIDEQLTG-RLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGD 67

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V     V   L    +   ++   + L K         +YED  I V NKP  + V    
Sbjct: 68  V-----VEVELIEEEEPSSLIPEDIPLDK---------VYEDDMILVINKPRDMVVHPAP 113

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + + I   LK     +  +P + HRLD++TSG+L+  +TR A    +E F
Sbjct: 114 GHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKALYSELF 173

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             ++++K+Y ++    P  +   + +  + +  +    + V+  + +G   AI+H  V+ 
Sbjct: 174 ATKQVKKLYVAICINAPSQE---LIHTRIARHPLKRKEMTVLSTHAEGGKEAITHCHVLA 230

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              +    + + P TGRTHQLRVH  H+G PI+GD  Y             +K  LHA  
Sbjct: 231 TNGR-LSVVALYPETGRTHQLRVHMKHLGTPILGDPVYG--IPSINFRYGLDKQQLHAYS 287

Query: 295 MDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           +   HPE   R+++   LP  M    + 
Sbjct: 288 LVFAHPESAERVKLVTKLPDDMTSLIEK 315


>gi|42520963|ref|NP_966878.1| ribosomal large subunit pseudouridine synthase D [Wolbachia
           endosymbiont of Drosophila melanogaster]
 gi|42410704|gb|AAS14812.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Drosophila melanogaster]
          Length = 276

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 78/288 (27%), Positives = 139/288 (48%), Gaps = 27/288 (9%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++++ QV++    +  N+ I       + P    + H+++     D S ++  + D +K 
Sbjct: 1   MIQNEQVKLLGTPIINNDYI-------VKPDEEYVVHLVQ----PDISTSIEPNYD-IKL 48

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++YED  I V +K +G++V  G+G   + D  L + +     +P + HRLD++TSG++V
Sbjct: 49  NIVYEDEDIIVLSKQSGLTVHPGAGT--NNDTLLNAVIAHLNVRPGIVHRLDKDTSGLMV 106

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+  AA   L+E    R+I++ Y ++VWG   +++  I   +  K     + + V K  
Sbjct: 107 IAKNEAAHSFLSELLSNRKIKREYLAVVWGTLSSQQGTIKTNIAPKRG-NKEMMCVTKI- 164

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---- 275
                 AI+H+ V     Q    ++    TGRTHQ+RVH  H+G  IVGD  Y  N    
Sbjct: 165 --TGKLAITHYLVQKVIGQ-VSLVKCTLETGRTHQIRVHMSHIGHSIVGDQVYGKNSSKS 221

Query: 276 ---FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
               K +      N+  LHA  + L HP+    ++  + LP  +    
Sbjct: 222 TKYAKNSSFIRNFNRQALHAYTLGLYHPKSKEYMEFVSDLPQDIKTLI 269


>gi|153823924|ref|ZP_01976591.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
 gi|126518556|gb|EAZ75779.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
          Length = 224

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 74/233 (31%), Positives = 134/233 (57%), Gaps = 12/233 (5%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            + T VQ++ ++ D    R+D + +N   +I    + +ILR G+VRV+KKRVK   ++++
Sbjct: 3   EIRTQVQFIDIDEDMAGQRIDNFLRNQLKNIPKSVVYRILRKGEVRVNKKRVKAEYKLEA 62

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VVR+PPV       +KE +    S  L+K ++ L+  ++YED  + + NKP+G +V G
Sbjct: 63  GDVVRVPPVTVE----VKENEPAPPSTKLSKVAE-LEHCIVYEDDHLLILNKPSGTAVHG 117

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           GSG+ +     L++ +  + +   L HR+D++TSGIL+VA+ R+A +HL   FR + +QK
Sbjct: 118 GSGLHFGAIEALRA-LRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            Y++LV G    + + +   LLK        V+ + +       + + F++++
Sbjct: 177 YYYALVMGHWDAECKVVNAPLLKNE------VNSIVRVNPNGKPSETRFRILE 223


>gi|330444047|ref|YP_004377033.1| RluA family pseudouridine synthase [Chlamydophila pecorum E58]
 gi|328807157|gb|AEB41330.1| pseudouridine synthase, RluA family [Chlamydophila pecorum E58]
          Length = 328

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 89/327 (27%), Positives = 136/327 (41%), Gaps = 36/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSG 62
           MT      V      MRLD++    YP  +    QK + +  V ++ +   K ++R+  G
Sbjct: 9   MTEALSFTVTEPTL-MRLDKYLAMMYPEYSRAFYQKHIVNHNVFINGEVQTKVSSRLSEG 67

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            VV I               I +         + +    +YEDS I V NKP  + V   
Sbjct: 68  DVVTIH--------------IQEKEELSELLPEEIPLHKVYEDSMIIVVNKPRDMVVHPS 113

Query: 123 SG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            G         + + I   LK     +  +P + HRLD++TSG+L+ A+T  A +   E 
Sbjct: 114 PGHHAGTIVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITAKTLKAKKIYGEL 173

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  + +QK Y ++  G P   +  I   L +      ++             A +H +V+
Sbjct: 174 FAKKLLQKRYLAVCVGKPLQTQ--IHTRLARHPQKRKEFTVSSV-----GKEATTHCQVL 226

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                K   + + P TGRTHQLRVH  H   PI+GD  Y ++          +K  LHA 
Sbjct: 227 AYNG-KLSLVLLSPETGRTHQLRVHMKHSHSPILGDPIYGSSSANRVY--GLDKQQLHAY 283

Query: 294 YMDLPHPEG-GRLQITAPLPAHMVKTW 319
            +D  HPE    L++TA LP  M    
Sbjct: 284 SLDFIHPETHQPLKLTAALPEDMKALI 310


>gi|149019517|ref|ZP_01834836.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP23-BS72]
 gi|147930892|gb|EDK81872.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP23-BS72]
          Length = 237

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 113/247 (45%), Gaps = 18/247 (7%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKSWVDSKG 141
           +     L   ++ L   ++Y+D  + V NKP G+ V   +G      ++  +    D  G
Sbjct: 1   MPEPEVLEYVAEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSG 60

Query: 142 Q----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +P + HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  
Sbjct: 61  INGVLRPGIVHRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGV 120

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +            K        A++ F V++ F   +  +E+Q  TGRTHQ+RV
Sbjct: 121 IEAPIGRSEKDRKKQAVTAK-----GKPAVTRFHVLERFGD-YSLVELQLETGRTHQIRV 174

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H  ++G  + GD  Y         +   +  +LHA+ +   HP  G+ L+  A +P    
Sbjct: 175 HMAYIGHSVAGDEVYGPR-----KTLKGHGQFLHAKTLGFTHPRTGKTLEFKADIPEIFK 229

Query: 317 KTWDSLG 323
           +T + L 
Sbjct: 230 ETLERLR 236


>gi|15827611|ref|NP_301874.1| pseudouridine synthase [Mycobacterium leprae TN]
 gi|221230088|ref|YP_002503504.1| putative pseudouridine synthase [Mycobacterium leprae Br4923]
 gi|4539134|emb|CAB39580.1| putative pseudouridine synthase [Mycobacterium leprae]
 gi|13093162|emb|CAC31581.1| putative pseudouridine synthase [Mycobacterium leprae]
 gi|219933195|emb|CAR71295.1| putative pseudouridine synthase [Mycobacterium leprae Br4923]
          Length = 308

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 141/329 (42%), Gaps = 29/329 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  + + +      MR+D         ++   +  +   G V +D  +   ++R+ SG 
Sbjct: 1   MTD-RSMPIPEGLAGMRVDAGLARLL-GLSRTAVAALAEDGGVELDGVQAGKSDRLTSGA 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +++         + +    L+++       D     +LY D  I   +KPA ++     
Sbjct: 59  WLQV--------RLCEAPAPLENT-----PVDIEDMTILYSDDDIVAVDKPAAVAAHASV 105

Query: 124 GIA-YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G A   + G L +           ++  + HRLD  TSG+++VA +  A   L  +F+ R
Sbjct: 106 GWAGPTVLGGLAAAGYRITTSGVPERQGIVHRLDVGTSGVMLVAISERAYTVLKRAFKCR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y +LV G P      I   + +  H G  +   V    K   ++I+H+  ++ F 
Sbjct: 166 TVDKRYHALVQGHPDPSSGTIDAPIGR--HRGHTWKFAVT---KDGRHSITHYDTLEAFV 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                L++   TGRTHQ+R H   +  P  GD  Y A+ K      ++ + +LHAR +  
Sbjct: 221 -AASLLDVHLETGRTHQIRAHFAELHRPCCGDLVYGADPKLAKRLGLE-RQWLHARSLSF 278

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            HP +G R++I +  P  +    D L  +
Sbjct: 279 AHPADGRRVEIVSSYPPDLQHALDVLRAE 307


>gi|294155914|ref|YP_003560298.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           crocodyli MP145]
 gi|291600512|gb|ADE20008.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           crocodyli MP145]
          Length = 312

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 139/311 (44%), Gaps = 43/311 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            R+D++  N+   I+  +++ ++    V V+   V +    ++ GQV+ +  +I+   HI
Sbjct: 10  ERIDKYISNN-SEISRNDIKALIEQKAVFVNDVVVNQPKFIVREGQVISVTKLIDKEIHI 68

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                           +  +   + YED  + V  KP+G+ V    G  +H +  + + +
Sbjct: 69  ---------------EAQDIDLDIAYEDEHLLVIKKPSGMVVHPAPG--HHENTLVNALL 111

Query: 138 DSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                         +P + HR+D++TSG+L+VA+T    Q L+E F  + I + Y+++  
Sbjct: 112 FHFKNNLSNENGLLRPGIVHRIDKDTSGLLIVAKTNEVHQLLSEGFSNKSINRKYFAICD 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEM 245
           G+ K+KK  +   + +        + V   N   + +AI++ +++  F    Q  C ++ 
Sbjct: 172 GVLKSKKMKLDLPIGRDVK-NRQQMSVTNSN---SKHAITNLEMLKSFYFDNQPKCLVKA 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
              TGRTHQ+RVH  ++  PI GD  Y              +L  HA  ++  HP    +
Sbjct: 228 TLETGRTHQIRVHCAYINNPIFGDSTYGKKVDD-----FNQRL--HAYRLEFVHPITNKK 280

Query: 305 LQITAPLPAHM 315
           + I +  P   
Sbjct: 281 IIIYSNPPKEF 291


>gi|324991124|gb|EGC23058.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK353]
          Length = 295

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 70/305 (22%), Positives = 132/305 (43%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   I+   L KI    G + V+ +       +  G  V I          +K   
Sbjct: 16  FLKRH--EISKGLLAKIKFSGGNILVNHQPQNAVYLLDIGDRVTIDIPSEKGFESLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
                      +      ++YED    V +KPAG++       +  +  F+K++   +G 
Sbjct: 71  -----------AVDKDLSVIYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRQGY 119

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
             Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G     ++  I
Sbjct: 120 ENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH
Sbjct: 180 IAPIGRNPE-----SIITRRVTEDGKYAHTSYKVIERFGDVY-LVDIHLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   +P  G  ++  +PLP    +
Sbjct: 234 FSHIGFPLLGDDLYGGSLE-----HGIERQALHCHSLKFYNPFSGQEVERASPLPEDFKQ 288

Query: 318 TWDSL 322
             + L
Sbjct: 289 VIEKL 293


>gi|187778438|ref|ZP_02994911.1| hypothetical protein CLOSPO_02032 [Clostridium sporogenes ATCC
           15579]
 gi|187772063|gb|EDU35865.1| hypothetical protein CLOSPO_02032 [Clostridium sporogenes ATCC
           15579]
          Length = 299

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 148/323 (45%), Gaps = 29/323 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      VV+    N+ +  + K    +++   ++K +R G++ V+ ++V   +++    
Sbjct: 1   MNNKLIFVVKEINHNIDIKDYLKE-IENLSGRFVRKAVRDGRIFVNGEKVIKKHKLSQDD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I    +   +I  E   ++               ++YEDS I V NK  GI V    
Sbjct: 60  LIEIYMQEDEHQNIEPEDINIE---------------IVYEDSDIIVINKKPGIVVHPTK 104

Query: 124 GIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             +   +   +      KG+K   RL +RLD++TSG+++VA+ + +   L         +
Sbjct: 105 SHSTGTLSNGILYHFKKKGEKSIVRLVNRLDRDTSGLVIVAKNQFSHMRLASDMSKDSFR 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY ++V G  K K+  I   + K+ +     +      ++    +I+ ++V++  ++  
Sbjct: 165 KIYIAVVHGSMKEKEGRINLPIYKEENESIKRIV-----DERGQESITTYEVLEELSKG- 218

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             ++++  TGRTHQ+RVH  H+G  + GD  Y     G        +  LHA  ++LPHP
Sbjct: 219 SVVKLELETGRTHQIRVHMSHLGHHLYGDSLYG---MGEEEKEYIERQALHAYKLELPHP 275

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
             G + ++   LP  + K  + +
Sbjct: 276 RTGNILKLQCSLPEDIKKLIEKI 298


>gi|297839485|ref|XP_002887624.1| T4O12.25 [Arabidopsis lyrata subsp. lyrata]
 gi|297333465|gb|EFH63883.1| T4O12.25 [Arabidopsis lyrata subsp. lyrata]
          Length = 930

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 80/360 (22%), Positives = 142/360 (39%), Gaps = 79/360 (21%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            V+  +  +RLD W  +    ++   +Q  +R G V V+ + V K ++ +++G  V    
Sbjct: 576 TVDALKGKIRLDSWISSRVNGVSRARVQSSIRLGLVTVNGRVVDKVSHNVKAGDEVNCT- 634

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                         +     L   ++ +   ++YED  + V NKPA + V    G     
Sbjct: 635 --------------ISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGT 680

Query: 128 HIDGFLKSW-------------------------------VDSKGQKPRLTHRLDQETSG 156
            ++G L                                    +   +P + HRLD+ T+G
Sbjct: 681 LVNGILHHCSLPCVSYSNAEDDDSDEETFSDDEEMTTSSSSYAASVRPGIVHRLDKGTTG 740

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LVVA+   +  HL E F++  I+++Y  +   I ++    I    +     GG      
Sbjct: 741 LLVVAKDEHSHAHLAEQFKLHTIERVYGRIEIPIGRDSSNRIRMAAIPGGLSGGR----- 795

Query: 217 KQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
                 A +A S +KVI+ FA      +E +  TGRTHQ+R HA +MG P++GD  Y   
Sbjct: 796 ------ARHAASRYKVIETFAGGGSALVEWRLETGRTHQIRAHAKYMGVPLLGDEVYGGT 849

Query: 275 -------------NFKGNFTSPIQNKL---YLHARYMDLPHPEGGRL-QITAPLPAHMVK 317
                                 + +++    LHA  +   HP  G + + + P P+ + +
Sbjct: 850 KSMALSLLQKRVSRSDQEEIVELISRMDRPCLHAIVLGFTHPCTGEIVKFSCPPPSDLAE 909


>gi|16803009|ref|NP_464494.1| hypothetical protein lmo0969 [Listeria monocytogenes EGD-e]
 gi|224502716|ref|ZP_03671023.1| hypothetical protein LmonFR_09374 [Listeria monocytogenes FSL
           R2-561]
 gi|254827914|ref|ZP_05232601.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL N3-165]
 gi|16410371|emb|CAC99047.1| lmo0969 [Listeria monocytogenes EGD-e]
 gi|258600295|gb|EEW13620.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL N3-165]
          Length = 296

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 144/319 (45%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE +E+ + L  + K+   HI+   L   K    G++ V+ +       ++ G  VR+  
Sbjct: 7   VETEEDGLLLRTFLKS--KHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKVGDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTNLDIVFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 NGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            + + G+   +K  I   + +K     +   + +       YA ++++V+  + + F  +
Sbjct: 168 QAFISGVLVEQKGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLARY-RAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
             +    PLPA M +    
Sbjct: 276 EYMAFDLPLPADMEEIIQK 294


>gi|319947093|ref|ZP_08021327.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
 gi|319747141|gb|EFV99400.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
          Length = 296

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 137/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L K+    GQ+ V+         +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--QVSKGLLAKVKFSGGQILVNGIEQNAIYLLDIGDKV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          ++              +      +LYED    V NKPAG++    S  
Sbjct: 57  TIDIPSEEGYEALE--------------AIDRDLEILYEDDHFLVLNKPAGVASIPSSLH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  I  F+K +      + Q   +  RLD++TSGI++ A+   A   L +  + + IQK 
Sbjct: 103 SNTIANFVKGYYVRNQYENQLVHIVTRLDKDTSGIMLFAKHGYAHARLDKQLQAKTIQKH 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G  +   K  I   + +      +   + ++  KG  YA + ++V+  F     
Sbjct: 163 YFALVKGKGELASKGDIIAPIARD-----EDSIITRKVAKGGKYAHTSYQVVQSFGDIH- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++Q HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH   +   HP 
Sbjct: 217 LVDIQLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLEDGIL-----RQALHCHSLAFYHPF 271

Query: 302 G-GRLQITAPLPAHMVKTWDSL 322
               L+I + LP    +    L
Sbjct: 272 WEEELRIESSLPDDFSQVLKQL 293


>gi|327462178|gb|EGF08505.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1]
          Length = 295

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 69/305 (22%), Positives = 131/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   I+   L KI    G + V+ +       +  G  V I          +K   
Sbjct: 16  FLKRH--EISKGLLAKIKFSGGNILVNHQPQNAVYLLDIGDRVTIDIPSEKGFESLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
                      +      ++YED    V +KPAG++       +  +  F+K++   +G 
Sbjct: 71  -----------AVDKDLSVIYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRQGY 119

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
             Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G     ++  I
Sbjct: 120 ENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  +   YA + +KVI+     +  +++  HTGRTHQ+RVH
Sbjct: 180 IAPIGRNPE-----SIITRRVTEDGKYAHTSYKVIERIGDVY-LVDIHLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   +P  G  ++  +PLP    +
Sbjct: 234 FSHIGFPLLGDDLYGGSLE-----YGIERQALHCHSLKFYNPFSGQEVERASPLPEDFKQ 288

Query: 318 TWDSL 322
             + L
Sbjct: 289 VIEKL 293


>gi|222054177|ref|YP_002536539.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
 gi|221563466|gb|ACM19438.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
          Length = 298

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 77/323 (23%), Positives = 143/323 (44%), Gaps = 40/323 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V  +   MRLD   +  +P ++   +++I+  G   +    V+  + +++ G ++ +   
Sbjct: 7   VSAELAGMRLDDGARQLFPELSKTQIRRIIDWGGCTISDALVRVASRQLREGDLISLG-- 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-----GI 125
                 +++ ++ ++ +        + K  LLYED      NK AG++ Q         +
Sbjct: 65  ------VMEPERCVEIT--------YGKGDLLYEDGGYLAINKAAGLNSQRTPYQLKGTV 110

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            Y +D +LKS      +  R+ HRLD+ TSG++   + + AA H++   +  +++K+YW+
Sbjct: 111 EYAVDCYLKSL--GSKEPARVIHRLDRGTSGVMFFPKHKKAATHISFLLKEGKVEKVYWA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV  +P+  +  +   + K +                   A + F+VI    +    +E 
Sbjct: 169 LVADVPEQDQWTVDAPIAKLNK-------FRYGVALPGREARTAFRVI-TAGKGATLIEA 220

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            P TGRTHQ+RVH  H G PI+GD  Y  +           ++ LH R M     EG  +
Sbjct: 221 HPFTGRTHQIRVHLAHNGLPIIGDATYGGDHA--------PRMMLHCRTMAFTSREGKEI 272

Query: 306 QITAPLPAHMVKTWDSLGFKYDR 328
             TAP      +     G + D+
Sbjct: 273 SATAPPDEAFRQVCRDFGIEIDQ 295


>gi|295688944|ref|YP_003592637.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
 gi|295430847|gb|ADG10019.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
          Length = 271

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 86/268 (32%), Positives = 133/268 (49%), Gaps = 11/268 (4%)

Query: 78  IKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           + + K ++  + LT       +S +LYED  I V +KPAG+S QGG   A+ +D  L ++
Sbjct: 12  VAKPKAVECPITLTPDEIATAQSWVLYEDEAIIVLDKPAGLSSQGGRIKAHTLDDLLWAF 71

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIPKNKK 195
                 +PRL HRLD++TSG+++ A+T+  A  L E+   +R +K Y ++V  G P+ K 
Sbjct: 72  AKPGKARPRLIHRLDRDTSGVILTAKTKPGAAFLGEAMMAKRFRKSYLAIVAPGAPEPKG 131

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I + L ++S     Y+ V   +   A  A S ++           +E+ P TGR HQL
Sbjct: 132 GMIDSPLRRESIGREAYMRVCAPDHPEAETARSRYRT-LAANATAALVELSPDTGRMHQL 190

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           RVH   +G P+ GD +Y              +L LHA  +  PHP GG  ++ APLP+  
Sbjct: 191 RVHMASIGRPLAGDSRYGGAL--MLGGVAVPRLMLHAAKLTFPHPLGGERKVMAPLPSDF 248

Query: 316 VKTWDSLGFKYDRNLYIKRLYSQDECKQ 343
           V    +L      +L I    + D   Q
Sbjct: 249 VAMLKAL------DLPIPEQPASDAVDQ 270


>gi|166154000|ref|YP_001654118.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 434/Bu]
 gi|166154875|ref|YP_001653130.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis L2b/UCH-1/proctitis]
 gi|301335199|ref|ZP_07223443.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis L2tet1]
 gi|165929988|emb|CAP03471.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 434/Bu]
 gi|165930863|emb|CAP06425.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis L2b/UCH-1/proctitis]
          Length = 335

 Score =  206 bits (525), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 144/328 (43%), Gaps = 32/328 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQ 63
           T V   V++      RLD+   ++    +    Q+ +  G+VRV+ +   + ++ +  G 
Sbjct: 9   TAVFSFVIDEQLTG-RLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGD 67

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V     V   L    +   ++   + L K         +YED  I V NKP  + V    
Sbjct: 68  V-----VEVELIEEEEPSSLIPEDIPLDK---------VYEDDMILVINKPRDMVVHPAP 113

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + + I   LK     +  +P + HRLD++TSG+L+  +TR A    +E F
Sbjct: 114 GHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKALYSELF 173

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             ++++K+Y ++    P  +   + +  + +  +    + V+  + +G   AI+H  V+ 
Sbjct: 174 ATKQVKKLYVAICINAPSQE---LIHTRITRHPLKRKEMTVLSTHAEGGKEAITHCHVLA 230

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              +    + + P TGRTHQLRVH  H+G PI+GD  Y             +K  LHA  
Sbjct: 231 TNGR-LSVVALYPETGRTHQLRVHMKHLGTPILGDPVYG--IPSINFRYGLDKQQLHAYS 287

Query: 295 MDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           +   HPE   R+++   LP  M    + 
Sbjct: 288 LVFAHPESAERVKLVTKLPDDMTSLIEK 315


>gi|291166075|gb|EFE28121.1| pseudouridine synthase, RluA family [Filifactor alocis ATCC 35896]
          Length = 298

 Score =  206 bits (525), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 141/315 (44%), Gaps = 36/315 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE +E    L +        I+   + ++     V V+      +  +  G+++ +    
Sbjct: 16  VEKEEV---LKKVLIEEM-GISLRMISELKSRRAVNVNGTLRFNHEPVHVGEIITVDLGE 71

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHID 130
           N   + ++E  +                 ++YED  I   NK   I V   G+ +   + 
Sbjct: 72  NRSEYGLEEGVV----------------DVIYEDEDIVAVNKSPFIVVHPTGTHLTGTLL 115

Query: 131 GFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +++SW    G  +K R   RLD++TSGIL++A+ R A   ++++ +   +QK Y +L+ 
Sbjct: 116 NYMESWFRQNGILEKVRFISRLDRDTSGILLIAKNRYAHHRMSQAHQDMMMQKTYVALIE 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  K ++  I   + ++ + G     +     +    AI+ +KV+    +KF  +E+ P 
Sbjct: 176 GKMKRQEGEINAPIGRRENDGIKREVM-----EDGQTAITKYKVLK-EGEKFSLVELTPV 229

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQLR H  ++G P++GD  Y  N +        N+  LH+  ++   P     + +
Sbjct: 230 TGRTHQLRCHMAYIGYPLIGDSLYGGNME------YMNRQALHSVTLEFFSPRKEEKIYL 283

Query: 308 TAPLPAHMVKTWDSL 322
            A LP  M +  + L
Sbjct: 284 KAELPQDMQELVNRL 298


>gi|229043051|ref|ZP_04190781.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH676]
 gi|228726292|gb|EEL77519.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH676]
          Length = 292

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 64/317 (20%), Positives = 134/317 (42%), Gaps = 39/317 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE   +  + K     I+   L  I    G + V+ +     +++++G+ +R+   
Sbjct: 5   IGPAEEGTLVRGFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLRAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGI 125
           +   +  +               ++ +   ++YED  + + NK A +S           +
Sbjct: 63  VEERSEGM--------------MAEDIPLCIIYEDDAVLIINKEANMSTIPSREHPAGSV 108

Query: 126 AYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           A   +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y 
Sbjct: 109 A---NALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYE 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G    ++  I   + +KS+   + +       +    A++HFKVID    K   + 
Sbjct: 166 AIVHGKIVEREGMIDAPIGRKSNSIIERMIC-----EDGQRAVTHFKVIDSTYHK-THVA 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G  ++GD  Y              +  LH++ +   HP    
Sbjct: 220 LELETGRTHQIRVHMAHIGHSLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEK 273

Query: 304 RLQITAPLPAHMVKTWD 320
            +  T  LP+ M +   
Sbjct: 274 EMSFTIKLPSDMQEVLR 290


>gi|15894548|ref|NP_347897.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|15024193|gb|AAK79237.1|AE007639_10 Pseudouridylate synthase family protein, yabo B.subtilis ortholog
           [Clostridium acetobutylicum ATCC 824]
 gi|325508681|gb|ADZ20317.1| Pseudouridylate synthase family protein [Clostridium acetobutylicum
           EA 2018]
          Length = 299

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 140/323 (43%), Gaps = 32/323 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +M      +VE   EN ++  + K  +   +   ++      ++ V+ K V+ + R+  G
Sbjct: 1   MMDNKLVYLVEKKYENFKIRDYLKQVH-GFSTRLIRGAAFGERLFVNGKTVRLSYRVLEG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +        ++  E+               +   ++YEDS I V NKPA + V   
Sbjct: 60  DKIEVDVNKPESQNVDPEK---------------MDLNIVYEDSDIIVLNKPANMIVHPT 104

Query: 123 SGIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               +  +   L  +   KG+    RL +RLD +TSG+++VA+ + +   L    ++   
Sbjct: 105 KNYQHGTLSNGLLYYFREKGENCIVRLVNRLDMDTSGLVLVAKNQFSHMALARDMKLDTF 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y ++V G   + K  I   + K+         + +  +     +I+HF+V++ + + 
Sbjct: 165 KKEYIAVVRGNLSSLKGTIDKPIYKEEEEP-----IRRTIDDRGQESITHFEVVERY-KN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +++   TGRTHQ+RVH   +G PI+GD  Y         S +  +  LHA  +  PH
Sbjct: 219 ADKVKLVLETGRTHQIRVHLSSIGNPIIGDSLYGEE------SELIKRQALHAFKLQFPH 272

Query: 300 PEGGRL-QITAPLPAHMVKTWDS 321
           P  GR+  I   LP  +      
Sbjct: 273 PRDGRIVNIEVKLPEDIENLISK 295


>gi|255691622|ref|ZP_05415297.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           finegoldii DSM 17565]
 gi|260622691|gb|EEX45562.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           finegoldii DSM 17565]
          Length = 306

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 76/308 (24%), Positives = 132/308 (42%), Gaps = 33/308 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  +Q G  V+I        
Sbjct: 24  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLQPGMKVQI-------- 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     S     K  +     ++YED+ I V  K  G+ SV             L 
Sbjct: 76  ----------SKEKGKKEFNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 125

Query: 135 SWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G+  +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 126 EYVQRSGRQFRVYIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSME 185

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                + ++L  ++     YV   +Q++ GA  +I+H++ I   A  +  +E+   TGR 
Sbjct: 186 KDYGTVESFLTDRTL----YVSSSQQDDGGA-LSITHYRTIKR-ANGYSLIELDLETGRK 239

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y      N       ++ LHA  +   HP  G  ++   P 
Sbjct: 240 NQIRVHMQDLGHPIIGDGRYGGENTPN----PIGRMALHAFKLCFYHPITGDLMEFETPY 295

Query: 312 PAHMVKTW 319
           PA   K +
Sbjct: 296 PADFKKLF 303


>gi|322807303|emb|CBZ04877.1| similar to ribosomal large subunit pseudouridine synthase D,
           CAC1266-type [Clostridium botulinum H04402 065]
          Length = 300

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 147/323 (45%), Gaps = 28/323 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      VV+    N+ +  + +    +++   ++K +R G+V V+K++V   +++    
Sbjct: 1   MDNKLIFVVKKINHNIDIKDYLRE-MENLSGRFIRKAVRDGRVFVNKEKVIKKHKLSQDD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I    +   +I  E   ++               ++YED+ I V NK  GI V    
Sbjct: 60  LIEIYMQEDEHQNIEPEDMNIE---------------IVYEDNDIIVINKRPGIVVHPTK 104

Query: 124 GIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G     +   +       G+K   RL  RLD++TSG++++A+ + +   L         +
Sbjct: 105 GHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFR 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY ++V G  K K+  I   + K+     +   + +  ++    +I+ ++V++  ++  
Sbjct: 165 KIYIAVVHGSMKEKEGRINLPIYKEE----ESESIKRIVDERGQESITTYEVLEELSKG- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++  TGRTHQ+RVH  H+G P+ GD  Y    KG        +  LHA  ++ PHP
Sbjct: 220 SVVRLELETGRTHQIRVHMSHLGHPLYGDSLYG---KGEEEKEYIERQALHAYKLEFPHP 276

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
             G + ++   LP  +    + +
Sbjct: 277 RTGDILKLQYSLPDDIKNLIEKI 299


>gi|224539550|ref|ZP_03680089.1| hypothetical protein BACCELL_04455 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224518831|gb|EEF87936.1| hypothetical protein BACCELL_04455 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 303

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 73/309 (23%), Positives = 126/309 (40%), Gaps = 35/309 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     ++N  ++ G  V+I        
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDSVITTQYNFPLKPGMKVQISRDKGKK- 79

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----IAYHIDG 131
                            H++ LK  ++YED+ I V  K  G+            AYHI  
Sbjct: 80  ---------------EFHNNLLK--IVYEDAYIIVVEKMQGLLSVSSERQKERTAYHILN 122

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                 + +G    + HRLD++TSG+++ A+     + L +++      + Y ++V G  
Sbjct: 123 EYVQRSNGRGSNVYIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVTGEM 182

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           +    C+ +WL  ++             + G   AI+H++ I   A  +  +E+   TGR
Sbjct: 183 EKNAGCVISWLTDRT-----LYVYSSPTDDGGQKAITHYRTIKR-ANGYSLVELDLETGR 236

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            +Q+RVH   +G PI+GD +Y              +L LHA  +   HP  G  ++   P
Sbjct: 237 KNQIRVHMQDLGHPIIGDGRYGIEDVNP-----IGRLALHAFKLCFYHPVTGELMKFETP 291

Query: 311 LPAHMVKTW 319
            P    K +
Sbjct: 292 YPNEFKKLF 300


>gi|331085058|ref|ZP_08334145.1| hypothetical protein HMPREF0987_00448 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330408758|gb|EGG88223.1| hypothetical protein HMPREF0987_00448 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 323

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 74/331 (22%), Positives = 137/331 (41%), Gaps = 29/331 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V  +E   RLD+    +          K++R   + ++ K+   N +++ G +V+
Sbjct: 1   MQEIKVTKNEAGQRLDKLLAKYLNEAPKSFFYKMMRKKNIVLNGKKATGNEKLEEGDIVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +         +  E     SSV + +    L   ++YED  + + NKP G+  Q      
Sbjct: 61  LF--------LADETIRKFSSVKIQRTKTNLS--VIYEDQDVVLINKPVGMLSQKAKESD 110

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   L S++   G+         +P + +RLD+ TSGI+V  ++    Q + E F+ R
Sbjct: 111 VSLVEHLISYLLDAGELSEETLKSFRPSICNRLDRNTSGIVVAGKSLPGLQKMGELFKER 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y  LV G+ +  +  +  WL K        + + + ++       + +  +    
Sbjct: 171 TLHKYYRCLVQGVIREDQ-YLKGWLKKDEKTNKVQI-LDRPSDPSDQPIETEYHPLWTK- 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYM 295
           +    LE++  TG+THQ+R H    G P++GD+KY      +F           LHA  +
Sbjct: 228 EGVTLLEVRLITGKTHQIRAHLASEGHPLIGDYKYGDRKLNDFYQKKYGLKSQLLHAYRL 287

Query: 296 DLPHPEG-----GRLQITAPLPAHMVKTWDS 321
           + P  EG           A +P    K    
Sbjct: 288 EFPVMEGVCSQLSEKVFIADVPPLFAKICKE 318


>gi|150390922|ref|YP_001320971.1| RluA family pseudouridine synthase [Alkaliphilus metalliredigens
           QYMF]
 gi|149950784|gb|ABR49312.1| pseudouridine synthase, RluA family [Alkaliphilus metalliredigens
           QYMF]
          Length = 308

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 72/315 (22%), Positives = 137/315 (43%), Gaps = 32/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE +++   L    KN    ++   L K+ +S ++ ++ +  K++  +  G  ++I    
Sbjct: 16  VEAEDDQQPLKETLKNRL-DLSSRLLTKLKKSKRILINGQYAKYHELLSEGDWIKIDMTE 74

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHID 130
            A     +E                +   ++YED  + V NK  GI      S     I 
Sbjct: 75  EASQFEPQE----------------IPFNVVYEDIDVIVINKEPGIVSHPTKSHPKDTIA 118

Query: 131 GFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              +++++ KG   + R  +RLD +TSG+LV+A+       +++  +   I K Y + V 
Sbjct: 119 NAAQNYLEKKGVACRIRFVNRLDMDTSGLLVIAKNPYTHHIMSQQMKANEITKKYVAFVK 178

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+    +  I   + + S      V   +        +++ F V++ +A     LE+   
Sbjct: 179 GVVVANEGEIDGAIYRSSDETIKRVVDDR-----GQQSLTKFTVLERYAD-ATMLEVSLL 232

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQI 307
           TGRTHQ+RVH   +G P++GDH Y         + +  +  LHA Y+    P    ++++
Sbjct: 233 TGRTHQIRVHMESIGHPMLGDHLYGY-----VDTELIRRQALHASYLSFLQPRYKEKIEV 287

Query: 308 TAPLPAHMVKTWDSL 322
            A LP  + +  + L
Sbjct: 288 RASLPKDLNELRNKL 302


>gi|237803088|ref|YP_002888282.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis B/Jali20/OT]
 gi|231274322|emb|CAX11117.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis B/Jali20/OT]
          Length = 335

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 144/328 (43%), Gaps = 32/328 (9%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQ 63
           T V   V++      RLD+   ++    +    Q+ +  G+VRV+ +   + ++ +  G 
Sbjct: 9   TAVFSFVIDEQLTG-RLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGD 67

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V     V   L    +   ++   + L K         +YED  I V NKP  + V    
Sbjct: 68  V-----VEVELIEEEEPSSLIPEDIPLDK---------VYEDDMILVINKPRDMVVHPAP 113

Query: 124 G---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G         + + I   LK     +  +P + HRLD++TSG+L+  +TR A    +E F
Sbjct: 114 GHTQGTVVHALLHEIGERLKQEFPEEPWRPGIVHRLDKDTSGLLITVKTRRAKALYSELF 173

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             ++++K+Y ++    P  +   + +  + +  +    + V+  + +G   AI+H  V+ 
Sbjct: 174 ATKQVKKLYVAICINAPSQE---LIHTRIARHPLKRKEMTVLSTHAEGGKEAITHCHVLA 230

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              +    + + P TGRTHQLRVH  H+G PI+GD  Y             +K  LHA  
Sbjct: 231 TNGR-LSVVALYPETGRTHQLRVHMKHLGTPILGDSVYG--IPSINFRYGLDKQQLHAYS 287

Query: 295 MDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           +   HPE   R+++   LP  M    + 
Sbjct: 288 LVFAHPESAERVKLVTKLPDDMTSLIEK 315


>gi|47459161|ref|YP_016023.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma mobile
           163K]
 gi|47458490|gb|AAT27812.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma mobile
           163K]
          Length = 298

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 67/313 (21%), Positives = 133/313 (42%), Gaps = 36/313 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           R+D++  N     +  ++Q+++   QV V+   V K + +I+    + I         +I
Sbjct: 13  RIDKFLANS-TDYSRNDIQQLIDEHQVYVNDILVRKASFKIKENDQIEIK------KQLI 65

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSW 136
           KE   +  ++NL          +++E+    + NK +G+ V    G      ++  L  +
Sbjct: 66  KETNAIAQNINLD---------IVFENEDFLIINKRSGMVVHPAPGNMQDTLVNALLFHF 116

Query: 137 VDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            ++        +P + HR+D++TSG+L+VA+T  A  +     +  +I++ Y +++ G  
Sbjct: 117 KNNLSNINGEIRPGIVHRIDKDTSGLLLVAKTNEAHNYFALLLKKHQIERKYQAIIVGKM 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            +    I   + + +      + V   N K A   I+  K     ++    ++ +  TGR
Sbjct: 177 DHTITNINLPIGRNTS-SRLKMEVTAHNSKEAFTKITSLK----ASETHSLIQCELKTGR 231

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           THQ+RVH  H+  PI GD+ Y              +L  HA  +   + +  +     PL
Sbjct: 232 THQIRVHLAHINKPIYGDNIYGKKVDD-----FNQRL--HAYELSFTYKDNKQYSFNVPL 284

Query: 312 PAHMVKTWDSLGF 324
           P  M +       
Sbjct: 285 PKEMQEDLIKFNL 297


>gi|167950143|ref|ZP_02537217.1| 23S rRNA pseudouridine synthase D [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 306

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 122/270 (45%), Gaps = 27/270 (10%)

Query: 1   MSLMTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR 58
           + +   ++ ++  V  ++   RLD+     +   +   LQ+ ++ G++ +D +  K   +
Sbjct: 6   IEMSEEIETLISEVALEQAGRRLDQVVAEQFAQFSRSRLQRWIKDGRLLLDGRPGKPKQK 65

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           ++ G+ + + P +                  +T     +   +L+ED  + V NKPAG+ 
Sbjct: 66  VRGGERLELVPQLEQ---------------EVTSRPQPIPLDILFEDESLLVVNKPAGLV 110

Query: 119 VQGGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFR 175
           V    G     +   L  +  +  Q PR  + HRLD+ETSG+LVVA+T  A   L    +
Sbjct: 111 VHPAVGNPDGTLVNALLHYFPAISQVPRGGIVHRLDKETSGLLVVAKTLQAQTALVAQLQ 170

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R +++ Y +   G+         +  + +  +    + VV         A++H++VI+ 
Sbjct: 171 ARSMKREYRAFAQGVMAA--GGKVDAPIGRHPVHRTRMAVVA----NGKPAVTHYRVIER 224

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           + +    L +Q  TGRTHQ+RVH   +  P
Sbjct: 225 Y-RFHTDLRIQLETGRTHQIRVHMAQIRFP 253


>gi|228957577|ref|ZP_04119329.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pakistani str. T13001]
 gi|228802169|gb|EEM49034.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pakistani str. T13001]
          Length = 292

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 129/314 (41%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE   +  + K     I+   L  I    G + V+ +     +++++ + +RI   
Sbjct: 5   IGPAEEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLRASEELRIFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYH 128
           +   +  +               ++ +   ++YED  + + NK A +S            
Sbjct: 63  VEERSEGM--------------MAEDIPLCIIYEDDAVLIINKEANMSTIPSREHPTGSV 108

Query: 129 IDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++  I   + +K     +         +    A++HFKVID    K   + ++ 
Sbjct: 169 HGKIVEREGMIDAPIGRKPDSIIERTVC-----EDGQRAVTHFKVIDSTYHK-THVALEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y              +  LH++ +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAHIGHPLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWD 320
            T  LP+ M +   
Sbjct: 277 FTIKLPSDMQEVLR 290


>gi|111221643|ref|YP_712437.1| pseudouridylate synthase [Frankia alni ACN14a]
 gi|111149175|emb|CAJ60858.1| Pseudouridylate synthase [Frankia alni ACN14a]
          Length = 325

 Score =  205 bits (523), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 72/326 (22%), Positives = 137/326 (42%), Gaps = 28/326 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  + +RLD      +  ++      ++  GQ  +D +    ++R+  G  + +
Sbjct: 21  RSLPVPDGLDGIRLDAAIARMF-GLSRTAAATLVDDGQASLDGRIRGRSDRVSGGAWLEV 79

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                        +          + +      +LY+D  I V +KP G++     G   
Sbjct: 80  -------------RLPAPPRPVTVEPTPVAGLGILYDDDDIVVVDKPPGVAAHPAPGFTG 126

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  + HRLD  TSG +VVA++  A   L  +FR R++ K
Sbjct: 127 PTVIGALAAAGYRISTSGAAERQGVVHRLDVGTSGAMVVAKSERAYTLLKRAFRERQVDK 186

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G P      +     +     G +  V          +++H+ +++ F +   
Sbjct: 187 RYRAVVQGHPDPLSGTVDAPTDRHPRRPGLFAVVA-----DGKPSVTHYDLVEAF-RSAS 240

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            L ++  TGRTHQ+RVH   +  P VGD  Y A+        +  + +LHA  +   HP 
Sbjct: 241 LLSIRLETGRTHQIRVHMSALRHPCVGDLAYGADPTLAERLGL-TRQWLHAARLSFDHPG 299

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKY 326
            GG ++ T+P PA + +  + L  + 
Sbjct: 300 HGGPVEFTSPDPADLAEAVERLREQA 325


>gi|291543834|emb|CBL16943.1| pseudouridine synthase, RluA family [Ruminococcus sp. 18P13]
          Length = 326

 Score =  205 bits (523), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 71/320 (22%), Positives = 141/320 (44%), Gaps = 29/320 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + ++ ++   RLD++     P +    + K +R+  ++ + KR   ++R++ G V+ 
Sbjct: 1   MRQITIQQNDAGQRLDKFLAKSMPALPKGLMCKFIRTKHIKRNGKRCAISDRLEPGDVLT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                +       +Q                K  ++YED+++ + NKP G+ V   +G  
Sbjct: 61  FFISDDFFPEHAPQQTPDFLKAP-------AKLDVVYEDTQVLILNKPVGLVVHADNGGT 113

Query: 127 YH--IDGFLKSWVD--------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               I   L              +   P L +RLD+ T G+++ A+T AA + + E  R 
Sbjct: 114 EDTLIHRVLHHLYQAGTYDPAGEQSFTPALCNRLDRNTGGLVIAAKTAAALRDVNELIRS 173

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R++ K Y  +   +P  +++ +  +   +    G+ V +     +G     + ++V+   
Sbjct: 174 RQLCKQYLCVTAALPPRQQDRVQAY--HRKQPAGNLVEIRDAPAEGFAPIDTEYRVL-AQ 230

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q    + +  HTGRTHQ+R H  H+G P++GD+KY +            +L+  A  + 
Sbjct: 231 EQGLSLVLVTLHTGRTHQIRAHLAHLGAPLLGDNKYGSVRANRRYRVFTQQLW--AWRLG 288

Query: 297 LPH------PEGGRLQITAP 310
            P       P  GR+ +TAP
Sbjct: 289 FPELDGALAPLSGRI-VTAP 307


>gi|293363941|ref|ZP_06610677.1| pseudouridine synthase, RluA family [Mycoplasma alligatoris A21JP2]
 gi|292552431|gb|EFF41205.1| pseudouridine synthase, RluA family [Mycoplasma alligatoris A21JP2]
          Length = 312

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 136/311 (43%), Gaps = 43/311 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            R+D++  N+   I+  +++ ++    V V+   V K    +  GQV+ I      L  I
Sbjct: 10  ERIDKYISNN-SEISRNDIKSLIEQKAVLVNDIVVNKPKFSVNEGQVITI------LKLI 62

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            KE KI   +++L          + YED  + V  KP+G+ V    G  +H +  + + +
Sbjct: 63  DKEIKIEAQNIDLD---------IAYEDEYLLVLKKPSGMVVHPAPG--HHENTLVNALL 111

Query: 138 DSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                         +P + HR+D++TSG+L++A+     + L E F  + I + Y ++  
Sbjct: 112 YHFKNNLSNENGLLRPGIVHRIDKDTSGLLLIAKNNEVHKILAEGFATKTINRKYVAICD 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEM 245
           GI K+ K  +   + +        + +   N   +  A++H +++  F    Q    ++ 
Sbjct: 172 GILKSPKLKLDLPIGRDIK-NRQLMAITNAN---SKSAVTHLELLKSFYYENQPKSLVKA 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
              TGRTHQ+RVH  ++  P+ GD  Y              +L  HA  ++  HP    +
Sbjct: 228 TLETGRTHQIRVHCAYIKNPVFGDPVYGRKVDD-----FNQRL--HAYKLEFNHPITNKK 280

Query: 305 LQITAPLPAHM 315
           + I +  PA  
Sbjct: 281 IVIYSAPPAEF 291


>gi|291459169|ref|ZP_06598559.1| pseudouridine synthase, RluA family [Oribacterium sp. oral taxon
           078 str. F0262]
 gi|291418423|gb|EFE92142.1| pseudouridine synthase, RluA family [Oribacterium sp. oral taxon
           078 str. F0262]
          Length = 352

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 74/342 (21%), Positives = 138/342 (40%), Gaps = 32/342 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +  +E   RLD+  + +        L K+LR   + ++ ++      ++ G +++
Sbjct: 1   MRELRIGENEAGQRLDKLLRKYLRRAENGFLYKMLRKKNITLNGRKASGKELLKEGDLLK 60

Query: 67  IPPVIN-------ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +             L  + +E+K  +         +   S ++YED  + +FNKPAG+  
Sbjct: 61  LFFSEESFQKLCAPLTPLPEEKKREEGRAKAEWEGEAFSSRIVYEDENLLLFNKPAGLLS 120

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHL 170
           Q        ++    S++  KG+         +P   +RLD+ T+G+L+  +T  A Q L
Sbjct: 121 QSDGSGLPSVNELCLSYLMEKGELGREQLASFRPGAANRLDRNTTGLLLFGKTLPALQEL 180

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
           +   + R I K Y ++V G    ++  I  +L K      + V + ++   GA    S +
Sbjct: 181 SFCLKKRTIGKYYLAVVRGH-TPERGRIEGFLRKDP--DKNRVFLQEEASGGAKEVQSEY 237

Query: 231 KVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPI 284
           + +          F  L +   +G+THQ+R H   +  PI+GD KY              
Sbjct: 238 RRLFAGESGEQISFSVLLVHLISGKTHQIRAHLASVSHPILGDPKYGDRDLNRLLQKRTG 297

Query: 285 QNKLYLHARYMDLP-HPEGGRL------QITAPLPAHMVKTW 319
                LHA  +  P  PE  RL         A  P   +   
Sbjct: 298 LRSQLLHACELHFPKLPEDSRLSYLSEKNFYASPPRSFLPFL 339


>gi|27804835|gb|AAO22876.1| AgmF [Myxococcus xanthus]
          Length = 264

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 70/274 (25%), Positives = 125/274 (45%), Gaps = 31/274 (11%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             +    R+D++    +P +    +  ++ +G V  D +  K   R++ G+++ +     
Sbjct: 12  PPEARGERVDQYLARAFPDLTRSRIHGLIEAGHVLADGQPAKPARRLRGGELLVLH---- 67

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHID 130
                      + + V     ++ L   LL+ED  + V +K AG+ V  G+G A    ++
Sbjct: 68  -----------IPAPVPAVPLAEELPLALLHEDRDLVVVDKAAGMVVHPGAGHASGTLVN 116

Query: 131 GFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             L    D  G     +P + HRLD++T+G LVVA+   A   L ++F+ R ++K Y +L
Sbjct: 117 ALLHRVKDLAGVGGELRPGIVHRLDKDTTGCLVVAKNEQALVALQKAFKTRAVEKTYLAL 176

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLE 244
           V G+P  +      +       G   +H  +     K    AI+ ++V++ F      +E
Sbjct: 177 VHGVPPAEGRIETLY-------GRHPIHRQRFTGKVKEGKNAITEYRVLETF-DGAALVE 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +   TGRTHQ+RVH    G P++ D  Y A  K 
Sbjct: 229 VDLLTGRTHQIRVHLSEAGHPLLCDALYGAGRKA 262


>gi|168179470|ref|ZP_02614134.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
 gi|182669738|gb|EDT81714.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
          Length = 300

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 148/323 (45%), Gaps = 28/323 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      VV+    N+ +  + +    +++   ++K +R G+V V++++V   +++    
Sbjct: 1   MDNKLIFVVKKINHNIDIKDYLRE-MENLSGRFIRKAVRDGRVFVNEEKVIKKHKLSQDD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I    +   +I  E   ++               ++YED+ I V NK  GI V    
Sbjct: 60  LIEIYMQEDEHQNIEPEDMNIE---------------IVYEDNDIIVINKRPGIVVHPTK 104

Query: 124 GIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G     +   +       G+K   RL  RLD++TSG++++A+ + +   L         +
Sbjct: 105 GHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFR 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY ++V G  K K++ I   + K+     +   + +  ++    +I+ +KV++  ++  
Sbjct: 165 KIYIAVVHGSMKEKEKRINLPIYKEE----ESESIKRIVDERGQESITTYKVLEELSKG- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++  TGRTHQ+RVH  H+G P+ GD  Y    KG        +  LHA  ++ PHP
Sbjct: 220 SVVRLELETGRTHQIRVHMSHLGHPLYGDSLYG---KGEEEKEYIERQALHAYKLEFPHP 276

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
             G + ++   LP  +    + +
Sbjct: 277 RTGDILKLQCSLPDDIKNLIEKI 299


>gi|58698738|ref|ZP_00373623.1| ribosomal large subunit pseudouridine synthase D [Wolbachia
           endosymbiont of Drosophila ananassae]
 gi|58534736|gb|EAL58850.1| ribosomal large subunit pseudouridine synthase D [Wolbachia
           endosymbiont of Drosophila ananassae]
          Length = 282

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 81/294 (27%), Positives = 143/294 (48%), Gaps = 33/294 (11%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++++GQV++    +  N+ I       + P    + H+++     D S ++  + D +K 
Sbjct: 1   MIQNGQVKLLGIPIINNDHI-------VKPGEEYIVHLVQ----PDISTSIEPNYD-IKL 48

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ------KPRLTHRLDQE 153
            ++YED  I V +K +G++V  G+G   + D  L + +   G+      +P + HRLD++
Sbjct: 49  DIVYEDEDIIVLSKQSGLTVHPGAGT--NNDTLLNAVIAHLGKIPYSHVRPGIVHRLDKD 106

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V+A+   A   L+E    R+I++ Y ++VWGI  +++  I   +  K     + +
Sbjct: 107 TSGLMVIAKNEEAHGFLSELLSNRKIKREYLAIVWGILSSQQGTIKTNIAPKRG-NKEMM 165

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            V K        AI+H+ V     Q    ++    TGRTHQ+RVH  H+G  IVGD  Y 
Sbjct: 166 CVTKI---TGKLAITHYLVQKVIGQ-VSLVKCTLETGRTHQIRVHMSHIGHSIVGDQVYG 221

Query: 274 AN-------FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
            N        K +      N+  LHA  + L HP+  G ++  + LP  +    
Sbjct: 222 KNSSKSTKYAKNSSFIRNFNRQALHAYTLGLYHPKSKGYMEFVSDLPQDIKTLI 275


>gi|225375309|ref|ZP_03752530.1| hypothetical protein ROSEINA2194_00934 [Roseburia inulinivorans DSM
           16841]
 gi|225212798|gb|EEG95152.1| hypothetical protein ROSEINA2194_00934 [Roseburia inulinivorans DSM
           16841]
          Length = 298

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 131/321 (40%), Gaps = 33/321 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           MT      +   +  + +  + K   + H   V L+KI  S  + ++ K    + R+  G
Sbjct: 1   MTRDLEYNITAQDNGVTISDYLKKQGFSHAVTVQLKKIPES--ILLNGKWEYMSTRLNDG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I       +  I               +  L   + YED  I V NKPA + +   
Sbjct: 59  DCLFIHFEETEGSENI--------------VATNLPLSICYEDEDILVVNKPADMPIHPS 104

Query: 123 -SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            +     +   +  +  ++G     R  +RLD++T+G+ ++A+   ++  L     +R I
Sbjct: 105 MNNYDNTLANAVCHYYQTQGIPYTFRCVNRLDRDTTGLTILAKHLISSAILNSEVSVRGI 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G     +  +   + +K     +    V   E     AI+H+K +      
Sbjct: 165 SREYLAIVKGF-TEDEGTVNAPIGRKEGSTIERQIDVLHGE----TAITHYKRLAYQ-DG 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + ++  TGRTHQ+RVH   +G P++GD  Y  +F         N+  LH+  +   H
Sbjct: 219 LSLISLKLETGRTHQIRVHMKSIGHPLIGDFLYNPDFTK------INRQALHSYRLRFTH 272

Query: 300 PEGGR-LQITAPLPAHMVKTW 319
           P   + L  TAPLP  M   +
Sbjct: 273 PVTKKPLVFTAPLPEDMQALF 293


>gi|291530201|emb|CBK95786.1| pseudouridine synthase, RluA family [Eubacterium siraeum 70/3]
          Length = 322

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 70/330 (21%), Positives = 135/330 (40%), Gaps = 31/330 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V  ++   R+DR+    +P +    + K+ R   ++++ K+ K +  I    +++
Sbjct: 1   MKEIKVTKNDSGQRIDRFLSKSFP-LGQGQICKLARKNCIKLNGKKCKPDTHIAENDIIK 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
           +      L    K              +   K  ++YED  I + +KP G+ V    SG 
Sbjct: 60  LFIPDEMLIPKAKSD-------PDDFTAVSDKIDIVYEDENILLVDKPVGMVVHEDESGD 112

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +  +   +KS++  KG+          P L +R+D+ T GI++ A+   + + L +  R 
Sbjct: 113 SDTLINRIKSYLYRKGEYHPENELSFAPALCNRIDRNTCGIVIAAKNAESLRILNQKIRD 172

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K+Y  +  G        +  +L K S    + V +  +  K      + +KVI   
Sbjct: 173 RELTKLYLCIACGKVTPDSATLTAYLEKNS--DTNTVKISDKKTKSNLTIKTKYKVIAYN 230

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    L++   TGRTHQ+R H  ++G  ++GD KY  N            L  +     
Sbjct: 231 GEN-SLLKVDLLTGRTHQIRAHLAYIGHALLGDGKYGNNKLNKKYGFKYQTLCSYELQFK 289

Query: 297 LP-------HPEGGRLQITAPLPAHMVKTW 319
                    + +G   +  AP     VK +
Sbjct: 290 FTTDAGCLSYLDGKCFKAKAP---DFVKMF 316


>gi|291518249|emb|CBK73470.1| pseudouridine synthase, RluA family [Butyrivibrio fibrisolvens
           16/4]
          Length = 295

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 66/305 (21%), Positives = 137/305 (44%), Gaps = 31/305 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M      ++  + +  ++D++ K   Y   N   ++K+     V +D + V  N ++ +G
Sbjct: 1   MNRTLTYIISTEYDGFQIDKFLKTQGYSSANITAIKKMP--NNVVIDGEWVHMNRKLSAG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           +++ +       +  I   K              +   ++YED  I V NKPAG+ +   
Sbjct: 59  ELLTVNISEEDSSEKIPAVK--------------MDLDIVYEDEDIIVINKPAGLPIHPS 104

Query: 123 -SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            +     +   L  + + +G+    R  +RLD+ TSG+ V+++   +A  L+   + R  
Sbjct: 105 LNHYEDSLANGLAYYYEQQGKPFIFRCANRLDKNTSGLTVISKHLVSANILSTMVKNREF 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y+++V G  +  +  I   + +      D +   + + +    A++H+KV+D     
Sbjct: 165 HREYYAIVRGTLEQPEGTIDAPIGRVD----DSIITRQVDFENGERAVTHYKVMD-EKNG 219

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + +   TGRTHQ+RVH  ++G P++GDH Y  +F+         +  LH+  ++  H
Sbjct: 220 HSLVSIHLETGRTHQIRVHFKYIGHPLIGDHLYNPDFE------YMQRQALHSHRIEFVH 273

Query: 300 PEGGR 304
           P   +
Sbjct: 274 PITKK 278


>gi|62184670|ref|YP_219455.1| putative pseudouridine synthase [Chlamydophila abortus S26/3]
 gi|62147737|emb|CAH63481.1| putative pseudouridine synthase [Chlamydophila abortus S26/3]
          Length = 325

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 85/327 (25%), Positives = 149/327 (45%), Gaps = 37/327 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRI 59
           M   T + ++V E + +  RLD++  +  P  +    Q+ +   +V ++++ + K + ++
Sbjct: 1   MQSNTPLFFIVNETNRD--RLDKFLVSQNPKYSRAFYQQHIVDQRVTINEQIQTKVSTQL 58

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  V I      +    +  ++L  ++ L K         +YED  I V NKP  + V
Sbjct: 59  VPGDTVSI-----TIEEKEEPSELLPEAIPLEK---------IYEDEMILVINKPRDMVV 104

Query: 120 QGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
               G         + + I   LK     +  +P + HRLD++TSG+L+ A+TR A    
Sbjct: 105 HPAPGHTRGTVVHALLHEIGERLKQEFPEEPWRPGIIHRLDKDTSGLLITAKTRQAKMIY 164

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
           +E F  ++++K Y ++  G P      + +  L + H     + V          AI+  
Sbjct: 165 SELFATKQLKKSYLAICVGKPSAS---VIHTKLARHHTKRKEMAV----SSTGKEAITRC 217

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           +V+     KF  + + P TGRTHQLRVH  H+  PI+GD  Y +      +    +K  L
Sbjct: 218 EVLAYNG-KFSLVLLHPETGRTHQLRVHMKHLSTPILGDPVYGS--ASANSCYGLDKQQL 274

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMV 316
           HA  ++  HP+  + L +T  LP  M 
Sbjct: 275 HAYSVNFIHPQTHKHLNLTTELPRDMK 301


>gi|322385565|ref|ZP_08059209.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           cristatus ATCC 51100]
 gi|321270303|gb|EFX53219.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           cristatus ATCC 51100]
          Length = 297

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 140/322 (43%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   I+   L K+    G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--EISKALLAKVKFAGGNILVNGQSQNAIYLLDIGDKV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +          ++              +      ++YED    V +KPAG++       
Sbjct: 57  TVDIPSEKGFESLE--------------AVDRDLSIVYEDEHFLVLDKPAGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  +  F+K++    D + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTMANFVKAYYIRQDYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKKMIEKR 162

Query: 183 YWSLVWGIPKNK-KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G  + K +  I   + +          + +   K   YA + +KV+  F   + 
Sbjct: 163 YYALVQGSGELKLEGDIIAPIGRDPD-----SIITRCVTKDGKYAHTSYKVVGQFGDIY- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++ HTGRTHQ+RVH  H+G P++GD  Y    +   T     +  LH   +   +P 
Sbjct: 217 LVDIRLHTGRTHQIRVHFAHLGFPLLGDDLYGGTLEAGIT-----RQALHCHSLSFYNPF 271

Query: 302 GGR-LQITAPLPAHMVKTWDSL 322
             + LQ+ + LP     T  SL
Sbjct: 272 LEKQLQLESQLPIDFQNTITSL 293


>gi|291557011|emb|CBL34128.1| pseudouridine synthase, RluA family [Eubacterium siraeum V10Sc8a]
          Length = 322

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 70/330 (21%), Positives = 136/330 (41%), Gaps = 31/330 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V  ++   R+DR+    +P +    + K+ R   ++++ K+ K +  I    +++
Sbjct: 1   MKEIKVTKNDSGQRIDRFLSKSFP-LGQGQICKLARKNCIKLNGKKCKPDTHIAENDIIK 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
           +      L    K              +   K  ++YED  I + +KP G+ V    SG 
Sbjct: 60  LFIPDEMLIPKAKSD-------PDDFTAVSDKIDIVYEDENILLVDKPVGMVVHEDESGD 112

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +  +   +KS++  KG+          P L +R+D+ T GI++ A+   + + L +  R 
Sbjct: 113 SDTLINRIKSYLYHKGEYRPENELSFAPALCNRIDRNTCGIVIAAKNAESLRILNQKIRD 172

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K+Y  +  G        +  +L K S    + V +  +  K      + +KVI   
Sbjct: 173 RELTKLYLCIACGKVTPDSATLTAYLEKNS--DTNTVKISDKKTKSNLTIKTKYKVIAYN 230

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    L++   TGRTHQ+R H  ++G  ++GD KY  N            L  +  +  
Sbjct: 231 GEN-SLLKVDLLTGRTHQIRAHLAYIGHALLGDGKYGNNKLNKKYGFKYQALCSYELHFK 289

Query: 297 LP-------HPEGGRLQITAPLPAHMVKTW 319
                    + +G   +  AP     VK +
Sbjct: 290 FTTDAGCLSYLDGKCFKAKAP---DFVKMF 316


>gi|89098123|ref|ZP_01171009.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Bacillus sp. NRRL B-14911]
 gi|89087286|gb|EAR66401.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Bacillus sp. NRRL B-14911]
          Length = 295

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 71/317 (22%), Positives = 128/317 (40%), Gaps = 39/317 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++  +    +  + K     I+   L  I    G++ V+         ++ G  + +   
Sbjct: 10  IDKQDSGQSIKDYLKQR--EISKAALTDIKFSGGKIEVNGNEENVRYMLKEGDCLSV--- 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                      +      +    ++ +   ++YED  + V NKPA +S         H  
Sbjct: 65  -----------RFPSEMPSPGMEAEDIPLAIVYEDPYVLVVNKPAAMSTIPSR---EHPR 110

Query: 131 GFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + +    +K        +  RLD++TSG+++VA+ R     ++   R  R+++ Y 
Sbjct: 111 GSLANALIGYYRKIDLASTVHIVTRLDRDTSGLVLVAKHRHVHHLMSTLQREGRVKRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +   G     +  I   + +K     D +   + N     YA +H+KV      +F + E
Sbjct: 171 AFAEGKLFPVEGSIEAPIARK----KDSIIEREVNFLEGQYACTHYKV--KGTGEFTYAE 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TGRTHQ+RVH  H+G P++GD  Y  N          ++  LH R +   HP   R
Sbjct: 225 LVLETGRTHQIRVHLSHLGHPLLGDGLYGGNKNQ------ISRQALHCRELRFFHPFLER 278

Query: 305 -LQITAPLPAHMVKTWD 320
            L  +A LP  M    +
Sbjct: 279 ELCFSAGLPDDMKALLE 295


>gi|254832286|ref|ZP_05236941.1| hypothetical protein Lmon1_13109 [Listeria monocytogenes 10403S]
 gi|284801300|ref|YP_003413165.1| hypothetical protein LM5578_1050 [Listeria monocytogenes 08-5578]
 gi|284994442|ref|YP_003416210.1| hypothetical protein LM5923_1004 [Listeria monocytogenes 08-5923]
 gi|284056862|gb|ADB67803.1| hypothetical protein LM5578_1050 [Listeria monocytogenes 08-5578]
 gi|284059909|gb|ADB70848.1| hypothetical protein LM5923_1004 [Listeria monocytogenes 08-5923]
          Length = 296

 Score =  205 bits (523), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 144/319 (45%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE +E+ + L  + K+   HI+   L   K    G++ V+ +       ++ G  VR+  
Sbjct: 7   VETEEDGLLLRTFLKS--KHISKQLLTAVKFGADGKIEVNSEEQNVLYHVKVGDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTNLDIVFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 NGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            + + G+   +K  I   + +K     +   + +       YA ++++V+  + + F  +
Sbjct: 168 QAFISGVLVEQKGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLARY-RAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
             +    PLPA M +    
Sbjct: 276 EYMAFDLPLPADMEEIIQK 294


>gi|154505454|ref|ZP_02042192.1| hypothetical protein RUMGNA_02983 [Ruminococcus gnavus ATCC 29149]
 gi|153794247|gb|EDN76667.1| hypothetical protein RUMGNA_02983 [Ruminococcus gnavus ATCC 29149]
          Length = 354

 Score =  205 bits (523), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 139/322 (43%), Gaps = 32/322 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M      ++ + +    +++  ++  Y   N  +L+K   S  V ++   V   + + SG
Sbjct: 60  MNRTITYLISDKDAGFTIEQNLRHRGYSAKNITHLKKTPES--VLLNGIWVHMTHHLTSG 117

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I              +I++   +           ++YED  I V +K AG+ +   
Sbjct: 118 DELVI--------------RIVEEQSSERVPPVEHPIHIVYEDEDILVIDKQAGMPIHPS 163

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRL---THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               Y+      +W   + +KP +    +RLD++TSG+ ++A+   +A  L+     R I
Sbjct: 164 LNNYYNSLANALAWYFEQQKKPFIFRCVNRLDRDTSGLTIIAKHVVSAAILSSMNARREI 223

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    +   I   L +K     +        EK    A+++++ ++     
Sbjct: 224 HREYRAIVRGHLTPESGVITAPLGRKDSSIIERTVDFDHGEK----AVTYYQFLE-EKNG 278

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + ++  TGRTHQ+R+H  ++G P+VGD+ Y  + +         +  LH+  +   H
Sbjct: 279 HSLVSLRLGTGRTHQIRIHMKYIGFPLVGDYLYNPDME------YITRQALHSYRLTFLH 332

Query: 300 PEGG-RLQITAPLPAHMVKTWD 320
           P  G ++  TAPLP  M K  +
Sbjct: 333 PITGQKMDFTAPLPDDMKKILN 354


>gi|153853078|ref|ZP_01994487.1| hypothetical protein DORLON_00472 [Dorea longicatena DSM 13814]
 gi|149753864|gb|EDM63795.1| hypothetical protein DORLON_00472 [Dorea longicatena DSM 13814]
          Length = 340

 Score =  205 bits (523), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 68/338 (20%), Positives = 142/338 (42%), Gaps = 26/338 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +++ ++E   RLD+  + +        + K+LR   + ++ K+   N  ++ G  V+
Sbjct: 1   MKELIIHDNEAGQRLDKLLRKYLSEAPGSFIYKMLRKKNIVLNGKKATGNEHLKKGDSVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    + +       K ++ S+      + +K  ++YED  +   NKP+G+  Q      
Sbjct: 61  LFLADDTIAKFQAAGKTVEESIK-----NTVKLDVIYEDQNVIFINKPSGMLSQKAKETD 115

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             +   + +++   GQ         +P + +RLD+ TSG++V  ++ A  Q + E F+ R
Sbjct: 116 VSVVENVTAYLLESGQLTRENLKTFRPSICNRLDRNTSGLIVAGKSLAGLQQMGELFKKR 175

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-DYVHVVKQNEKGANYAISHFKVIDCF 236
            ++K Y  +V G    +   I  +L+K                +       + +  I  +
Sbjct: 176 TLKKYYLCIVKGRI-TEPAHIRGYLVKDEKTNRVSLSKGGFSKDAKGLPIETEYVPI-AW 233

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARY 294
            ++   L++   TGRTHQ+R H    G P++GD+KY +    +            LHA  
Sbjct: 234 NEEMTLLKVHLITGRTHQIRAHLASTGHPLLGDYKYGSKKWNDRYKKEWKIEDQVLHAYQ 293

Query: 295 MDLPHPEGGRLQ------ITAPLPAHMVKTWDSLGFKY 326
           + +P      L+        A +P    K      +++
Sbjct: 294 LTMP-GMKKELENLSGKTFYAKVPEVFWKLIKETAWEH 330


>gi|328461874|gb|EGF34095.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus MTCC 5462]
          Length = 260

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 66/255 (25%), Positives = 115/255 (45%), Gaps = 37/255 (14%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           V V+ K VK N ++ +G VV +                +     L   ++ +   ++YED
Sbjct: 2   VTVNGKPVKANFKVTAGDVVTVT---------------IPEVKPLKAVAEPIPLEIVYED 46

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGI 157
            ++ V NKP G+ V    G   H DG L + +    +        +P + HR+D++TSG+
Sbjct: 47  DQVIVVNKPQGMVVHPAPG---HPDGTLVNGLLYHTKLPGINGVIRPGIVHRIDKDTSGL 103

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+T  A   L+   + +   + Y +LV G  K  +  I   L +          V  
Sbjct: 104 LMVAKTETAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRDRKRQAVVA- 162

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                  +A++HF+V++ F   +  ++    TGRTHQ+RVH  ++  P+ GD  Y     
Sbjct: 163 ----DGRHAVTHFQVLERFT-NYTLVKCILDTGRTHQIRVHMAYIHHPVAGDPLYGPK-- 215

Query: 278 GNFTSPIQNKLYLHA 292
               + + +  +LHA
Sbjct: 216 ---RTLLGDGQFLHA 227


>gi|257468012|ref|ZP_05632108.1| tRNA pseudouridine synthase A [Fusobacterium ulcerans ATCC 49185]
 gi|317062298|ref|ZP_07926783.1| rRNA pseudouridylate synthase C [Fusobacterium ulcerans ATCC 49185]
 gi|313687974|gb|EFS24809.1| rRNA pseudouridylate synthase C [Fusobacterium ulcerans ATCC 49185]
          Length = 290

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 89/309 (28%), Positives = 156/309 (50%), Gaps = 25/309 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V+ + E++RLD++ +  Y  I    + K +R+G+++V+ K+ K N R+Q    +++   
Sbjct: 4   IVDKEFEDVRLDKFLRKKYEDIPLTEIFKGIRTGKIKVNGKKSKENYRLQLNDEIKVFFK 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                   KE+K+L+      K  + +K  ++YE+  + +FNK   + +  GSG  + I 
Sbjct: 64  GGET----KEEKLLEVE---DKEIEKIKKSIVYENENVLIFNKKNNMVMHKGSGYDFGIS 116

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             LK ++  K       +R+D+ TSG+++ A++   A+ L E  R R I K Y+ LV G 
Sbjct: 117 ELLKGYL--KNPNFNFVNRIDKATSGLIIGAKSLVTARELAEEIRNRNIDKRYYILVEGK 174

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K+K+  I ++L K      D V  V++ E+GA  ++S FKV   + +    LE    +G
Sbjct: 175 VKDKEFTIKSYLKKIE----DKVIEVEKFEEGAKESLSFFKV-KKYGKDCTLLEGTLGSG 229

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLRV   +MG  I+GD KY    +          L+ H   ++        ++I  P
Sbjct: 230 RTHQLRVQLANMGNAIIGDTKYGKGKEKIMY------LFSHYLKINKY-----GIEIDLP 278

Query: 311 LPAHMVKTW 319
           +P   +K  
Sbjct: 279 IPDEYIKRL 287


>gi|229160262|ref|ZP_04288261.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           R309803]
 gi|228623223|gb|EEK80050.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           R309803]
          Length = 292

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 129/314 (41%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   EE + +  + K     I+   L  I    G + V+ +     +++Q+G+ +R+   
Sbjct: 5   IGPAEEGILVREFLKT--KEISKAALTDIKFHGGAIEVNGQHTSVRHQLQAGEELRVFFP 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYH 128
           +   +  +               ++ +   ++YED  + V NK A +S            
Sbjct: 63  VEERSEGM--------------IAEDIPLSIVYEDEAVLVINKEANMSTIPSREHPTGSV 108

Query: 129 IDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V
Sbjct: 109 ANALLSHYDKQHVASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVRRTYEAVV 168

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    +   I   + +KS    +         +    A++HF+VID    K   + ++ 
Sbjct: 169 HGEMIERAGTIDAPIGRKSDSIIERTVC-----ENGQRAVTHFRVIDSAYHK-THVSLEL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH  +MG P++GD  Y              +  LH+  +   HP     + 
Sbjct: 223 ETGRTHQIRVHMAYMGHPLLGDSLYGGRKDE------MKRQALHSTSLTFYHPILEKEMS 276

Query: 307 ITAPLPAHMVKTWD 320
            T  +P  M +   
Sbjct: 277 FTTTIPLDMKELLK 290


>gi|315636965|ref|ZP_07892189.1| RluA family ribosomal large subunit pseudouridine synthase
           [Arcobacter butzleri JV22]
 gi|315478795|gb|EFU69504.1| RluA family ribosomal large subunit pseudouridine synthase
           [Arcobacter butzleri JV22]
          Length = 328

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 151/325 (46%), Gaps = 37/325 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
           ++V+E +    RLD++   +    +   ++++++   V+VD K   K   +++  Q V +
Sbjct: 5   FIVLETN----RLDKFLAQNI-DASRNQIEQLIKKEFVKVDGKITNKTGLKLKENQNVEV 59

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                 LN   K+++ L +S+      +  +  ++YED  I V NKP  ++V     +  
Sbjct: 60  FFPEAQLNKR-KDEEFLKNSL------EDKEVEIIYEDDYILVLNKPYNLTVHDAPSV-- 110

Query: 128 HIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             D  L  W+  K          ++  + HRLD+ TSG++V+A+T  A  +L++    + 
Sbjct: 111 -KDATLVDWLKLKNISLSTISGEERHGIVHRLDKGTSGVMVIAKTNEAHLNLSKQLEDKS 169

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFA 237
           + + Y +++      K+  I    + ++      + +    E+   YA S F  I     
Sbjct: 170 MGRYYLAILD--LALKENVIIEKPIGRNPNNRLKMSI----EENGRYAKSAFSKIALSDN 223

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +KF  +  + +TGRTHQ+RVH   +   I+GD+ Y   FKG       N+  LHA Y+ L
Sbjct: 224 EKFELIACKLYTGRTHQIRVHLSSINRHILGDNLYG--FKGELNK--INRFLLHAYYLYL 279

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDS 321
            HP    ++   A LP  +    ++
Sbjct: 280 THPVTNKQMCFKANLPEDIKNFLNT 304


>gi|167750591|ref|ZP_02422718.1| hypothetical protein EUBSIR_01567 [Eubacterium siraeum DSM 15702]
 gi|167656517|gb|EDS00647.1| hypothetical protein EUBSIR_01567 [Eubacterium siraeum DSM 15702]
          Length = 322

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 70/330 (21%), Positives = 135/330 (40%), Gaps = 31/330 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V  ++   R+DR+    +P +    + K+ R   ++++ K+ K +  I    +++
Sbjct: 1   MKEIKVTKNDSGQRIDRFLSKSFP-LGQGQICKLARKNCIKLNGKKCKPDTHIAENDIIK 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
           +      L    K              +   K  ++YED  I + +KP G+ V    SG 
Sbjct: 60  LFIPDEMLIPKAKSD-------PDDFTAVSDKIDIVYEDENILLVDKPVGMVVHEDESGD 112

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           +  +   +KS++  KG+          P L +R+D+ T GI++ A+   + + L +  R 
Sbjct: 113 SDTLINRIKSYLYHKGEYRPENELSFAPALCNRIDRNTCGIVIAAKNAESLRILNQKIRD 172

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K+Y  +  G        +  +L K S    + V +  +  K      + +KVI   
Sbjct: 173 RELTKLYLCIACGKVTPDSATLTAYLEKNS--DTNTVKISDKKTKSNLTIKTKYKVIAYN 230

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    L++   TGRTHQ+R H  ++G  ++GD KY  N            L  +     
Sbjct: 231 GEN-SLLKVDLLTGRTHQIRAHLAYIGHALLGDGKYGNNKLNKKYGFKYQALCSYELQFK 289

Query: 297 LP-------HPEGGRLQITAPLPAHMVKTW 319
                    + +G   +  AP     VK +
Sbjct: 290 FTTDAGCLSYLDGKCFKAKAP---DFVKMF 316


>gi|237796432|ref|YP_002863984.1| pseudouridine synthase, RluA family [Clostridium botulinum Ba4 str.
           657]
 gi|229261661|gb|ACQ52694.1| pseudouridine synthase, RluA family [Clostridium botulinum Ba4 str.
           657]
          Length = 300

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 147/323 (45%), Gaps = 28/323 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      VV+    N+ +  + +     ++   ++K +R G+V V+K++V   +++    
Sbjct: 1   MDNKLIFVVKKINHNIDIKDYLRE-MESLSGRFIRKAVRDGRVFVNKEKVIKKHKLSQDD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I    +   +I  E   ++               ++YED+ I V NK  GI V    
Sbjct: 60  LIEIYMQEDEHQNIEPEDMNIE---------------IVYEDNDIIVINKRPGIVVHPTK 104

Query: 124 GIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G     +   +       G+K   RL  RLD++TSG++++A+ + +   L         +
Sbjct: 105 GHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFR 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY ++V G  K K++ I   + K+     +   + +  ++    +I+ +KV++  ++  
Sbjct: 165 KIYIAVVHGSMKEKEKRINLPIYKEE----ESESIKRIVDERGQESITTYKVLEELSKG- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++  TGRTHQ+RVH  H+G P+ GD  Y    KG        +  LHA  ++ PHP
Sbjct: 220 SVVRLELETGRTHQIRVHMSHLGHPLYGDSLYG---KGEEEKEYIERQALHAYKLEFPHP 276

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
             G + ++   LP  +    + +
Sbjct: 277 RTGDILKLQCSLPNDIKNLIEKI 299


>gi|332360478|gb|EGJ38289.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK355]
          Length = 295

 Score =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 72/305 (23%), Positives = 136/305 (44%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   I+   L KI    G + V+ +       +  G  V I          I  +K
Sbjct: 16  FLKRH--EISKGLLAKIKFSGGNILVNHQPQNAIYLLDIGDKVTID---------IPSEK 64

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
             +S + + K        ++YED    V +KPAG++       +  +  F+K++      
Sbjct: 65  GFESLMAVDKD-----LSVIYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G     ++  I
Sbjct: 120 ENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH
Sbjct: 180 IAPIGRNPE-----SIITRRVTEDGKYAHTSYKVIERFGDVY-LVDIHLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   +P  G  ++  +PLP    +
Sbjct: 234 FSHIGFPLLGDDLYGGSLE-----HGIERQALHCHSLKFYNPFSGQEVERASPLPEDFKQ 288

Query: 318 TWDSL 322
             + L
Sbjct: 289 VIEKL 293


>gi|157691873|ref|YP_001486335.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
 gi|157680631|gb|ABV61775.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
          Length = 288

 Score =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 70/313 (22%), Positives = 130/313 (41%), Gaps = 33/313 (10%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
              EE + L  +  +    I+   L  I    G + ++ + V    ++ +G  + I    
Sbjct: 2   TAKEEGLLLKDYLIDL--GISKRMLTDIKFDGGDLLINGEHVTVRYKLHNGDRLTILFPK 59

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
             ++  +K                 +   +L+ED  + V NK   I          H   
Sbjct: 60  EKVSEGLK--------------PAPIPLDILFEDEHVLVLNKRPYIPSIPSREHPEHSIA 105

Query: 130 DGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +G L  + +   +    L +RLD++TSG+++VA+ R A   L+++ +   +++ Y +   
Sbjct: 106 NGLLHHYAEQSVRLTVHLVNRLDRDTSGVMLVAKHRFAHSLLSKAQKSGAVKRTYRAFTH 165

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQP 247
           G+ K K   I   + +K     + +      +     A++HF V     +     + +  
Sbjct: 166 GMIKEKHGTIRAKIARKGDSIIERMV-----DDTGQEAVTHFTVRAVDTELNMSDVALAL 220

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGRTHQ+RVH  ++G P++GD  Y        T+   N+  LH+  +  PHP  G  + 
Sbjct: 221 ETGRTHQIRVHMQYLGYPLIGDTLYGG------TNERMNRQALHSETLVFPHPMTGEEMT 274

Query: 307 ITAPLPAHMVKTW 319
            +APLP  M    
Sbjct: 275 FSAPLPEDMKSLL 287


>gi|327470007|gb|EGF15471.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK330]
          Length = 295

 Score =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 69/305 (22%), Positives = 131/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   I+   L KI    G + V+ +       +  G  V I          +K   
Sbjct: 16  FLKRH--EISKGLLAKIKFSGGNILVNHQPQNAIYLLDIGDKVTIDIPSEKGFESLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
                      +      ++YED    V +KPAG++       +  +  F+K++      
Sbjct: 71  -----------AVDKDLSVVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G     ++  I
Sbjct: 120 ENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH
Sbjct: 180 IAPIGRNPE-----SIITRRVTEDGKYAHTSYKVIERFGDVY-LVDIHLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   +P  G  ++  +PLP    +
Sbjct: 234 FSHIGFPLLGDDLYGGSLE-----HGIERQALHCHSLKFYNPFSGQEVERASPLPEDFKQ 288

Query: 318 TWDSL 322
             + L
Sbjct: 289 VIEKL 293


>gi|118463205|ref|YP_882412.1| ribosomal large subunit pseudouridine synthase d [Mycobacterium
           avium 104]
 gi|118164492|gb|ABK65389.1| ribosomal large subunit pseudouridine synthase d [Mycobacterium
           avium 104]
          Length = 294

 Score =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 78/312 (25%), Positives = 132/312 (42%), Gaps = 28/312 (8%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D         ++      +   G V +D      ++R+  G  + +          +
Sbjct: 1   MRVDAGLARLL-GLSRSAAAALAEDGGVELDGVPAGKSDRLTGGAWLHVR---------L 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW- 136
            E      +  +    D     +LY D  I   +KPA ++     G     + G L +  
Sbjct: 51  PEAPAPPQNTPV----DIEGMTILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAAG 106

Query: 137 ----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                    ++  + HRLD  TSG++VVA +  A   L  +F+ R + K Y +LV G P 
Sbjct: 107 YRITTSGVPERQGIVHRLDVGTSGVMVVALSERAYTLLKRAFKQRTVDKRYHALVQGHPD 166

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I   + +  H GG++   V    K   ++++H+  ++ F      L++   TGRT
Sbjct: 167 PSSGTIDAPIGR--HRGGEWKFAVT---KDGRHSLTHYDTVEAFV-AASLLDVHLETGRT 220

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           HQ+RVH   +  P  GD  Y A+ K      +Q + +LHAR +   HP +G R++I +P 
Sbjct: 221 HQIRVHFSALHHPCCGDLVYGADPKLAKKLGLQ-RQWLHARSLSFAHPADGRRMEIVSPY 279

Query: 312 PAHMVKTWDSLG 323
           P  +    D L 
Sbjct: 280 PPDLQHALDVLR 291


>gi|149923941|ref|ZP_01912327.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
 gi|149815173|gb|EDM74722.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
          Length = 324

 Score =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 137/327 (41%), Gaps = 40/327 (12%)

Query: 9   YVVVENDEENMRLDRWF------KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
            +V+  D    RLD+           +  ++   L +   +G+VR+  ++VK + R+++ 
Sbjct: 4   TLVLGEDAIGQRLDKALVDAFARSEAHESLSRSQLARAFAAGEVRIAGRKVKASFRLEA- 62

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
                         +  E ++   +       + +   +++ED+ + V +KPAG+ V  G
Sbjct: 63  ------------AGVCVELRVPAPAPLAHARPEAIPLTVVHEDASLLVLDKPAGMVVHAG 110

Query: 123 SGIA---------YH---IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
            G           +H       L     +  ++P + HRLD++TSG++V AR   A   L
Sbjct: 111 PGHDSGTLVNAVLHHLQVHADALPVLPGNGPERPGVVHRLDKDTSGLIVFARGLRAQTVL 170

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            E FR   I + Y  +V G P  ++  +     +       +       ++G   A++  
Sbjct: 171 AEQFRDHSIDRAYLGVVLGRPSFERRRLETTHGRDPADRRRFA-----PDQGTRRAVTTM 225

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---K 287
           +V+               TGRTHQ+R+HA  +G PI  D  Y    K      + +   +
Sbjct: 226 EVLRPLGAHAALARFTLETGRTHQIRMHARMVGHPIFADPLYGRRPKHPALRRLADGLGR 285

Query: 288 LYLHARYMDLPHPEG-GRLQITAPLPA 313
             LHA  +   HP+G GRL + APLP 
Sbjct: 286 HALHAALLGFAHPDGSGRLVLEAPLPP 312


>gi|255029306|ref|ZP_05301257.1| hypothetical protein LmonL_09598 [Listeria monocytogenes LO28]
          Length = 245

 Score =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 119/264 (45%), Gaps = 28/264 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +++E      R+D+         +   +Q +L++G + V+ +  K N ++Q G  +  
Sbjct: 4   ETLIIEESHARERVDKVIAEMM-GKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHY 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                    ++ E   LD               + +ED  + V NKP G+ V   +G A 
Sbjct: 63  EVREPEELEVLAEDIPLD---------------IYFEDKDMLVVNKPEGMVVHPSAGHAS 107

Query: 127 -YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +   +
Sbjct: 108 GTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G   ++K  I   + + +      + VV+        A +HF+V++     + 
Sbjct: 168 EYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVLERLP-GYT 221

Query: 242 WLEMQPHTGRTHQLRVHALHMGCP 265
            +  +  TGRTHQ+RVH  ++G P
Sbjct: 222 LINCKLDTGRTHQIRVHLKYIGHP 245


>gi|183222495|ref|YP_001840491.1| pseudouridine synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Paris)']
 gi|189912533|ref|YP_001964088.1| 23S RNA-specific pseudouridylate synthase [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Ames)']
 gi|167777209|gb|ABZ95510.1| Pseudouridylate synthase, 23S RNA-specific [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Ames)']
 gi|167780917|gb|ABZ99215.1| Pseudouridine synthase (Uracil hydrolyase) [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 312

 Score =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 86/326 (26%), Positives = 146/326 (44%), Gaps = 44/326 (13%)

Query: 9   YVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDK---KRVKFN-NRIQSGQ 63
           +V V  D +  RLD + K++    ++   +QK + SG V  +K   + V  N  ++  G+
Sbjct: 4   FVTVSEDYDQSRLDVFLKDNAGDDLSRSTVQKWIDSGFVT-NKTKDQVVHKNGYKVALGE 62

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
              +  +    + +                   +   +LY++ +  V +K AGI+   G 
Sbjct: 63  EFVVDVIARPPSRL---------------EPIAMDIPVLYDEDEFMVIHKKAGIACHSGP 107

Query: 124 GIAY--HIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G L  + +  G    ++P + HRLD+ T G+L++A+T  A   L++ F+ R
Sbjct: 108 GDDSPSLVNGLLYQFKNLSGTGGERRPGIVHRLDKPTEGVLIIAKTDRAHAALSKLFQDR 167

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFK----V 232
            ++K Y++ V   P   +  I         IG   V  VK   +     AI+H+K    V
Sbjct: 168 LVEKTYYAWVLQAPVEAEGTI------NMPIGRHPVERVKMCVREDGRMAITHYKTEKIV 221

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                +KF  +++   TGRTHQ+RVH   +GCP+VGD  Y  + K       Q  L L A
Sbjct: 222 QTQTGRKFSLMKLGLETGRTHQIRVHMAKVGCPVVGDSLYSRSAK----DYTQYGLLLFA 277

Query: 293 RYMDLPHPE--GGRLQITAPLPAHMV 316
           + +D PHP     R+ +    P    
Sbjct: 278 KKLDFPHPFVPDKRIVVELDFPERFK 303


>gi|229824816|ref|ZP_04450885.1| hypothetical protein GCWU000182_00165 [Abiotrophia defectiva ATCC
           49176]
 gi|229790819|gb|EEP26933.1| hypothetical protein GCWU000182_00165 [Abiotrophia defectiva ATCC
           49176]
          Length = 353

 Score =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 75/347 (21%), Positives = 148/347 (42%), Gaps = 41/347 (11%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL- 74
           +   RLD++            + K+LR   + ++ K+   N  ++    V++      + 
Sbjct: 10  DAGGRLDKYLMKFLKDAPTSFIYKMLRKKNIVLNGKKAAGNELLKENDEVKLFLADETIV 69

Query: 75  --------------NHIIKEQKILDSSVNLTKHS-------DFLKSILLYEDSKIYVFNK 113
                          ++   +  ++S  + + +        +F +  ++YED  I + NK
Sbjct: 70  KFGGKVTLSQTADREYVATAEDSVESGSDDSLYDFLKSLKWEFDEPKVIYEDRDIIIVNK 129

Query: 114 PAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTR 164
           P  +  Q        ++ +L S++ + G          KP + +RLD+ TSGI++  +T 
Sbjct: 130 PVNVLSQIAKTGDVSMNEWLISYLINSGSLTAEDMLTVKPAVVNRLDRNTSGIILAGKTL 189

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
              + L++  + R++ K Y ++V G   N       +LLK      + V + K   +GA 
Sbjct: 190 TGLRFLSDIIKTRKLTKYYLTIVKGEIPNN-FTAEAYLLKND--NHNTVKIYKDKVEGAE 246

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSP 283
           Y  + ++V+         L+++  TG++HQ+R H   +G P++GD KY    +  N+   
Sbjct: 247 YIKTAYEVLQVK-DGHSLLKVELITGKSHQIRAHLSFLGYPVIGDGKYGLKSENTNYRRM 305

Query: 284 IQNKLYLHARYMDLPHPEGG-----RLQITAPLPAHMVKTWDSLGFK 325
             N  +LH+  +  P  EG          +A LP  + K  + LGF 
Sbjct: 306 GLNTQFLHSYEIKFPKFEGEFAYLSERSFSAKLPERLEKVANKLGFN 352


>gi|332360854|gb|EGJ38660.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK49]
          Length = 295

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 69/305 (22%), Positives = 131/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   I+   L KI    G + V+ +       +  G  V I          +K   
Sbjct: 16  FLKRH--EISKGLLAKIKFSGGNILVNHQPQNAIYLLDIGDKVTIDIPSEKGFESLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
                      +      ++YED    V +KPAG++       +  +  F+K++      
Sbjct: 71  -----------AVDKDLSVVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G     ++  I
Sbjct: 120 ENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH
Sbjct: 180 IAPIGRNPE-----SIITRRVTEDGKYAHTSYKVIERFGDVY-LVDIHLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   +P  G  ++  +PLP    +
Sbjct: 234 FSHIGFPLLGDDLYGGSLE-----HGIERQALHCHSLKFYNPFSGQEVERASPLPEDFKQ 288

Query: 318 TWDSL 322
             + L
Sbjct: 289 VIEKL 293


>gi|253682033|ref|ZP_04862830.1| pseudouridine synthase, RluA family [Clostridium botulinum D str.
           1873]
 gi|253561745|gb|EES91197.1| pseudouridine synthase, RluA family [Clostridium botulinum D str.
           1873]
          Length = 323

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 136/326 (41%), Gaps = 29/326 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ +     +    + K LR G +RV+ K+ K N  +Q   ++    
Sbjct: 3   IEIGPNESGQRLDKFCRKWLEDVPLGAIFKALRKGDIRVNGKKAKQNYFLQEEDIIE--- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
                 +I   ++         +  DF    + YED  I +  K  G+ V          
Sbjct: 60  ----TKYIETYKQNKKDIPKKFQEVDFSSIKISYEDENILIIEKWPGVLVHSDKKNGEPT 115

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSG+++  +     + L    R R+I
Sbjct: 116 LTDYVLSYLFQKGDYDPQKEVTFTPAPCNRLDRNTSGMVIFGKNFKTLKILNAMIRERKI 175

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G  K K+     ++LK        +H  K+ ++ +       KVID     
Sbjct: 176 KKYYNALVKG--KIKEGYYEAYILKDQVNNISEIH--KEEKQNSKRIAMEVKVIDTVG-T 230

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F +LE+   TGR+HQLR H  ++G PI+GD KY      +F       +  +L+A  +  
Sbjct: 231 FSFLELDLLTGRSHQLRAHLAYLGNPIIGDDKYGDKKLNSFFNNKYGLDFQFLYAYKLIF 290

Query: 298 PHPEGG--RLQ---ITAPLPAHMVKT 318
                    ++   IT  LP    K 
Sbjct: 291 KDCPNELAYMENKIITESLPPIFKKV 316


>gi|81429051|ref|YP_396051.1| pseudouridine synthase, 23S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610693|emb|CAI55744.1| Pseudouridine synthase, 23S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 306

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 63/321 (19%), Positives = 130/321 (40%), Gaps = 33/321 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN- 72
           D E   L  + + H   I+   L KI    GQ+ V+ +    N R+    VV +      
Sbjct: 9   DSEGCILRNFLRRH--EISRSQLSKIKFSGGQILVNGQEAHTNIRLVQNDVVTVYLAPEV 66

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDG 131
           A+ H+I  +                   + YED    + +KPA ++         + +  
Sbjct: 67  AVEHVIPVK---------------GDLKIAYEDDHFLIVDKPAFVASLPAPNHPNNTMAN 111

Query: 132 FLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           F+K ++    ++     +  RLD++TSG+++  +   A   L    + + +QK Y ++  
Sbjct: 112 FVKQYLIDEQAESLAVHVVTRLDRDTSGLMMFTKHGFAHSLLDRQLQSKELQKTYIAIAS 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  +       +  + +     +  ++ +   +G   +++ +            ++++  
Sbjct: 172 GDMRED--LPQHAWIDRPIKRSEEFYMRRVVGEGGKRSLTEYW-QAAHGDGATLVKLKLL 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH   +G  ++GD+ Y        ++ +  +  LH R +   HP   R + +
Sbjct: 229 TGRTHQIRVHFASLGHSLIGDNLYGE------SNDLLPRQALHCRQLTFYHPFEERTITV 282

Query: 308 TAPLPAHMVKTWDSLGFKYDR 328
            +P+PA          F +D 
Sbjct: 283 KSPVPADFSAVLAQRQFDFDE 303


>gi|304404981|ref|ZP_07386641.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
 gi|304345860|gb|EFM11694.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
          Length = 337

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 70/308 (22%), Positives = 130/308 (42%), Gaps = 41/308 (13%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHIIKEQK 82
           +            ++ IL  GQV V+ +     N  ++ G  V +               
Sbjct: 56  FLLTALSSTGRNAVKSILARGQVSVNGQATTAYNYPLKPGFTVTV--------------- 100

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
              S   + +    +  ++L+ED  I V  K AG+          + +  L ++      
Sbjct: 101 ---SKEKIEEAPPLIGLVILHEDDDIVVVQKDAGLLSISS--DKENKENELTAYRQLTAH 155

Query: 142 -------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                   +  + HRLD++TSG+++ A+T AA Q L  +++    ++ Y +LV G  +  
Sbjct: 156 VRVHNPRNRIFVVHRLDRDTSGVMMFAKTEAAQQQLQNNWQEVVKERSYIALVDGKVRKA 215

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I +WL + S +           E    +A++H+K +    Q +  LE+   TGR +Q
Sbjct: 216 EGTITSWLRESSTL----KMYSSFREGDGQHAVTHYKTLQTN-QHYSLLEVHLETGRKNQ 270

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +G PI GD KY +  +         +L LHAR +   HP  G  ++  + +P 
Sbjct: 271 IRVHMEDIGHPIAGDKKYGSRSRE------IGRLGLHARILSFLHPTTGELMRFESDIPK 324

Query: 314 HMVKTWDS 321
             ++ + +
Sbjct: 325 AFLRPFRT 332


>gi|303234008|ref|ZP_07320657.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
 gi|302494933|gb|EFL54690.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
          Length = 307

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 64/327 (19%), Positives = 133/327 (40%), Gaps = 35/327 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   ++++  +N RLD +  N    ++   +QK++   +V V+ K  K N ++     + 
Sbjct: 2   IYEFLIDDSNQNARLDVFLANVV-ELSRSEIQKLIDDKKVLVNGKIQKKNYKLNLNDKIT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +                     + T  +      ++YED  + + NK   + V     I 
Sbjct: 61  LDY----------------EKPDKTIKAQKQDLDIVYEDDYLAIINKDKDVIVHPTETIY 104

Query: 126 AYHIDGFL----KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           +  +  +L    K+  D  G  +  + HRLD++T+G++++A+       L E  +   I 
Sbjct: 105 SDTLVNYLMYNFKNLSDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEII 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y  +V G   ++   I  ++ +        +            +IS ++ +D     +
Sbjct: 165 KTYLCIVHGKI-DECGTIEEYMSRNPKDRKKMMV-----SDEGKLSISQYERLDYN-DDY 217

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +++Q  TGRTHQ+RVH  ++  PI+GD  Y    +      + +   LHA  +   HP
Sbjct: 218 SLVKVQIKTGRTHQIRVHMNYIHHPILGDKLYGLKKEKI----LFDSQVLHAYNLQFIHP 273

Query: 301 EG-GRLQITAPLPAHMVKTWDSLGFKY 326
           +   ++ +   L    +   +     Y
Sbjct: 274 QTHEKINVIGKLKPDFMTAIEKTKLDY 300


>gi|288923211|ref|ZP_06417353.1| pseudouridine synthase, RluA family [Frankia sp. EUN1f]
 gi|288345447|gb|EFC79834.1| pseudouridine synthase, RluA family [Frankia sp. EUN1f]
          Length = 313

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 77/325 (23%), Positives = 141/325 (43%), Gaps = 28/325 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T  + V V +  + MRLD      +  ++      ++  GQV VD +    ++R+  G  
Sbjct: 6   TDRRSVPVPDGLDGMRLDAALARMF-GLSRTAAVSVVDDGQVSVDGQVRGRSDRVAGGAW 64

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +     AL    +   +  + V            +L++D  I V +KP G++     G
Sbjct: 65  LEV-----ALPAPPRPVTVDATPVE--------GLGILHDDDDIVVVDKPVGVAAHPAPG 111

Query: 125 -IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                + G L +           ++  + HRLD  T+GI+VVA++  A   L  +FR R 
Sbjct: 112 FTGPTVIGALAAAGYRISTSGAAERQGVVHRLDVGTTGIMVVAKSERAYTLLKRAFRDRE 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K+Y ++V G P   +  +   + +     G +  V      G   +++H+   + F +
Sbjct: 172 VEKVYRAVVQGHPDPLRGTVDAPIDRHPRRPGLFAVVA-----GGKPSVTHYDTEEAF-R 225

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               L ++  TGRTHQ+RVH   +  P VGD  Y A+        ++ + +LHA  +   
Sbjct: 226 SASLLSVRLETGRTHQIRVHLSALRHPCVGDLAYGADPTLAQRLGLE-RQWLHAASLAFA 284

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSL 322
           HP  G  ++  +P P  + +    L
Sbjct: 285 HPSDGSWVRFVSPDPDDLAEALRRL 309


>gi|283853730|ref|ZP_06370958.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
 gi|283570880|gb|EFC18912.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
          Length = 333

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 87/316 (27%), Positives = 133/316 (42%), Gaps = 34/316 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           + T VQ   V   E   +L ++        +    LQK +R+GQVR+D KR K  +RI  
Sbjct: 1   MKTPVQTFTVSPAEAGQKLLQYLARRLGSGVPQAALQKFIRTGQVRLDGKRCKPFDRISE 60

Query: 62  GQVVRIPPVINALNHIIKEQKIL---------------DSSVNLTKHSDFLKSILLYEDS 106
           GQ+VR+PP            K                 + +         +   +L+ED 
Sbjct: 61  GQLVRVPPYETDAPGAPPPPKAETGTRGQALHLLRRGGEPARPGDGGRRDIVLDILHEDD 120

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           ++ V  KPAG+ V  GSG  + +   L          P   HRLD++T+G+L+VA+T   
Sbjct: 121 ELLVVVKPAGLPVHPGSGHPFALTTLLHERHADAPFAPTPAHRLDRDTTGLLLVAKTYRK 180

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKE----CIANWLLKKSHIGGDYVHVVKQNEKG 222
            + L E+      +K Y++ V G     +E     + + L K+   G   V    +  + 
Sbjct: 181 LRALHEAMVTGAARKDYFAWVRGRWLLGEEGEWLTLRDRLAKEGGPGRQRV----EASEA 236

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A+S  +++    Q    LE++  TGRT Q+R      G PIVGD KY          
Sbjct: 237 GKEAVSKVRLLAATPQ-ASLLEVRLETGRTQQIRAQLASRGYPIVGDAKYGGGVP----- 290

Query: 283 PIQNKLYLHARYMDLP 298
                L LHA  + LP
Sbjct: 291 ----PLLLHAWRVTLP 302


>gi|327489667|gb|EGF21458.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1058]
          Length = 295

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 140/322 (43%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   I+   L KI    G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKRH--EISKGLLAKIKFSGGNILVNHQPQNAIYLLDIGDKV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          +K              +      ++YED    V +KPAG++       
Sbjct: 57  SIDIPSEKGFESLK--------------AVDKDLYVVYEDEHFLVLDKPAGVASIPSVNH 102

Query: 126 AYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  +  F+K++   +G   Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTMANFVKAYYIRQGYENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G     ++  I   + +          + ++  +   YA + +K+I+ F   + 
Sbjct: 163 YYALVQGTGDLEEQGEIIAPIGRNPE-----SIITRRVTEDGKYAHTSYKIIEQFGDVY- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++  HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH   +   +P 
Sbjct: 217 LVDIHLHTGRTHQIRVHFSHIGFPLLGDELYGGSLE-----HGIERQALHCHSLKFYNPF 271

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
            G  ++  +PLP    +  + L
Sbjct: 272 SGQEVERASPLPEDFKQVIEKL 293


>gi|228906938|ref|ZP_04070805.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis IBL 200]
 gi|228852686|gb|EEM97473.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis IBL 200]
          Length = 292

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 62/310 (20%), Positives = 130/310 (41%), Gaps = 33/310 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           EE + +  + K     I+   L  I    G + V+ +     +R+++ + +RI   +   
Sbjct: 9   EEGILVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHRLRASEELRIFFPVEER 66

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGF 132
           +  +               ++ +   ++YED  + + +K A +S             +  
Sbjct: 67  SEGM--------------IAEDIPLCIVYEDDAVLIIDKEANMSTIPSREHPTGSVANAL 112

Query: 133 LKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V G  
Sbjct: 113 LSHYDKQYLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEM 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             ++  I   + +KS    +         +    A++HFKVI     K   + ++  TGR
Sbjct: 173 VEREGMIDAPIGRKSDSIIERTVC-----EDGQRAVTHFKVIGSTYHK-THVALELETGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
           THQ+RVH  H+G P++GD+ Y              +  LH++ +   HP     +  T  
Sbjct: 227 THQIRVHMAHIGHPLLGDNLYGGRRDE------MKRQALHSKSLTFYHPILEKEMSFTIK 280

Query: 311 LPAHMVKTWD 320
           +P+ M +   
Sbjct: 281 IPSDMQELLR 290


>gi|325687489|gb|EGD29510.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK72]
          Length = 295

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 130/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   I+   L KI    G + V+ +       +  G  V I          +K   
Sbjct: 16  FLKRH--EISKGLLAKIKFSGGNILVNHQPQNAIYLLDIGDKVTIDIPSEKGFESLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
                      +      ++YED    V +KPAG++       +  +  F+K++      
Sbjct: 71  -----------AVDKDLSVVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G     ++  I
Sbjct: 120 ENQQVHIVTRLDKDTSGLMLFAKHSYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH
Sbjct: 180 IAPIGRNPE-----SIITRRVTEDGKYAHTSYKVIERFGDVY-LVDIHLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   +P     ++  +PLP    +
Sbjct: 234 FSHIGFPLLGDDLYGGSLE-----HGIERQALHCHSLKFYNPFSSQEVERASPLPEDFKQ 288

Query: 318 TWDSL 322
             + L
Sbjct: 289 VIEKL 293


>gi|302380682|ref|ZP_07269147.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
 gi|302311625|gb|EFK93641.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
          Length = 307

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 64/327 (19%), Positives = 133/327 (40%), Gaps = 35/327 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   ++++  +N RLD +  N    ++   +QK++   +V V+ K  K N ++     + 
Sbjct: 2   IYEFLIDDSNQNARLDVFLANVV-ELSRSEIQKLIDDKKVLVNGKIQKKNYKLNLNDKIT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +                     + T  +      ++YED  + + NK   + V     I 
Sbjct: 61  LDY----------------EKPDKTIKAQKQDLDIVYEDDYLAIINKDKDVIVHPTETIY 104

Query: 126 AYHIDGFL----KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           +  +  +L    K+  D  G  +  + HRLD++T+G++++A+       L E  +   I 
Sbjct: 105 SDTLVNYLMYNFKNLSDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEII 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y  +V G   ++   I  ++ +        +            +IS ++ +D     +
Sbjct: 165 KTYLCIVHGKI-DECGTIEEYMSRNPKDRKKMMV-----SDEGKLSISQYERLDYN-DDY 217

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +++Q  TGRTHQ+RVH  ++  PI+GD  Y    +      + +   LHA  +   HP
Sbjct: 218 SLVKVQIKTGRTHQIRVHMNYIHHPILGDKLYGLKKEKI----LFDSQVLHAYNLQFIHP 273

Query: 301 EG-GRLQITAPLPAHMVKTWDSLGFKY 326
           +   ++ +   L    +   +     Y
Sbjct: 274 QTHEKINVIGKLKPDFMTAIEKTKLDY 300


>gi|282880676|ref|ZP_06289379.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
 gi|281305459|gb|EFA97516.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
          Length = 315

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 79/317 (24%), Positives = 134/317 (42%), Gaps = 36/317 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVR 66
           Q  VVE  +    L  W  NH  H++   L+  L    + V+ K++  F+  +  G  + 
Sbjct: 11  QCYVVEETD---TLLNWLLNHVTHLSKSKLKATLAGRGIIVNGKQITQFDYPVTPGTKIA 67

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I    +  N + K + +                 ++YED  + V  K AGI        +
Sbjct: 68  IS--KSKKNTLFKSKYV----------------KIVYEDRYLVVIEKQAGILSMAAGHAS 109

Query: 127 YHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            ++   L S+     QK    + HRLD++TSG+++ A+    AQ L   +      + Y 
Sbjct: 110 LNVKKVLDSYFKQSKQKCTAHVVHRLDRDTSGLMIYAKDIQTAQLLEHDWHHNVYDRRYV 169

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G  +  +  IANWL         Y+      + G  +A++HF  ++   +    +E
Sbjct: 170 AVVSGEMEQDEGTIANWL----KDNRAYITYSSPEDNGGKFAVTHFHTLNRTTE-HSLVE 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +  TGR +Q+RVH+  MG P+ GDHKY              +L LHA  +   HP   R
Sbjct: 225 YRLETGRKNQIRVHSADMGHPVCGDHKYGNG------DNPIGRLCLHAYVLCFYHPVTHR 278

Query: 305 -LQITAPLPAHMVKTWD 320
            ++   P+P      + 
Sbjct: 279 PMEFETPIPPAFAHLFK 295


>gi|160939065|ref|ZP_02086416.1| hypothetical protein CLOBOL_03959 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438028|gb|EDP15788.1| hypothetical protein CLOBOL_03959 [Clostridium bolteae ATCC
           BAA-613]
          Length = 366

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 81/351 (23%), Positives = 147/351 (41%), Gaps = 51/351 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + V  +E   RLD+    +        + K++R   + ++ K+   + R++ G  V+
Sbjct: 1   MQTLTVTQNEAGQRLDKLLTKYLNQAGKGFIYKMMRKKNITLNGKKCDGSERLEEGDQVK 60

Query: 67  IPPVINALNHI-------IKEQKILDSSVNLTKHSDFLKS-------------------I 100
           +      +           ++Q    SS   + H    K+                    
Sbjct: 61  LFLSDETIEKFSVPDMGGYEKQPGDQSSTGASSHEKREKARGKGGEHQGSRDREGGRRLD 120

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLD 151
           ++YED  I V NKP+G+  Q        ++ ++ +++   G+         KP + +RLD
Sbjct: 121 IVYEDQHILVVNKPSGMLSQKAKDSDMSLNEYILNYLIDSGKLPISQLRTFKPSICNRLD 180

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG++V  ++ A  Q + E F+ R I K Y  LV G  K K+  IA +L K      +
Sbjct: 181 RNTSGLVVAGKSLAGLQVMNEVFKDRSIHKYYQCLVAGEIKEKQ-LIAGFLKKDE--STN 237

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V +     + +   ++ +  +    + F  L++   TGR+HQ+R H   +G PIVGD+K
Sbjct: 238 TVSIFPLEVEDSVPIMTEYLPL-SGNKTFTLLQVTLITGRSHQIRAHLASIGHPIVGDYK 296

Query: 272 YCANFKGNFTSP--IQNKLYLHARYMDLP--------HPEGGRLQITAPLP 312
           Y +    +            LH+  + +P        H  G   + TA LP
Sbjct: 297 YGSRSLNDAVKKKYAVRSQLLHSWRLVMPETLPAPLKHLRGE--EFTARLP 345


>gi|326203527|ref|ZP_08193391.1| pseudouridine synthase, RluA family [Clostridium papyrosolvens DSM
           2782]
 gi|325986347|gb|EGD47179.1| pseudouridine synthase, RluA family [Clostridium papyrosolvens DSM
           2782]
          Length = 299

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 139/320 (43%), Gaps = 36/320 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V  +E    L ++   +   ++   ++K+    ++ V++   + N  ++    +++   
Sbjct: 6   TVSENEAGKTL-KYVLKNGLQLSERLIKKLKLQQKIYVNEHPERVNYVVKEEDKLKVILD 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +      I+ Q I                 ++YED  + V NK  GI V   S   YH D
Sbjct: 65  LEEECENIEPQDI--------------PLNIIYEDECMLVLNKQPGIVVHPTS---YHPD 107

Query: 131 GFLKS----WVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             + +    ++  KG  +K R   RLD+ETSGI++ A+ +   + L +       +K Y 
Sbjct: 108 NTIANGIVYYLKQKGVIKKVRPVSRLDRETSGIIIFAKNQFTQETLIQQMHANLFKKEYL 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWL 243
            +V GIP+  +  I   + +K         +++   +    +I+H+KV++ F       L
Sbjct: 168 GVVQGIPEKSEGTINLPIARKPG-----SIMLRHISEEGAPSITHYKVLNSFPLHNSALL 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
                TGRTHQ+RVH   MG PI GD  Y  N     T+   ++  LH+   ++ HP   
Sbjct: 223 GFNLETGRTHQIRVHCHAMGFPIYGDTLYSDN-----TNLFISRQALHSYRTEILHPVTR 277

Query: 303 GRLQITAPLPAHMVKTWDSL 322
             +  TA LP+ +    + L
Sbjct: 278 KEVIFTAELPSDIAGLLEIL 297


>gi|153951567|ref|YP_001397630.1| ribosomal large subunit pseudouridine synthase A [Campylobacter
           jejuni subsp. doylei 269.97]
 gi|152939013|gb|ABS43754.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacter jejuni subsp. doylei 269.97]
          Length = 322

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 138/321 (42%), Gaps = 39/321 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +Q  +V+ +    RLD +      + +   +  ++    V+V+ K   K + ++++G ++
Sbjct: 1   MQTFLVDKNS---RLDVFLAKKL-NQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDII 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I      L   IK Q  +D  ++           +LYED  + V NKP+ + V G S +
Sbjct: 57  SIT--SLKLYDEIKPQFEVDFDID-----------ILYEDEDLLVLNKPSNLVVHGASSV 103

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W+  K           +  L HRLD++TSG +++A+     Q L+E    
Sbjct: 104 ---KNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDTSGAILIAKNNFTHQKLSEQLAD 160

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + +IY +L+    K  K  +  +L++        + + K+N+   N   +   V+   
Sbjct: 161 KSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIAIDKENKFSKNAKSAFINVVKT- 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    +  +  TGRTHQ+R H   +   I+GD  Y    K         ++ LHA ++ 
Sbjct: 220 -ENLTLMAAKLFTGRTHQIRAHLASLNRHILGDSLYGYKGK------YDCRIMLHAYFLY 272

Query: 297 LPHPEGGR-LQITAPLPAHMV 316
             HP+    + + APL     
Sbjct: 273 FIHPKTKEQIFVKAPLMEDFK 293


>gi|168181665|ref|ZP_02616329.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
 gi|182675008|gb|EDT86969.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
          Length = 300

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 147/323 (45%), Gaps = 28/323 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      VV+    N+ +  + +     ++   ++K +R G+V V+K++V   +++    
Sbjct: 1   MDNKLIFVVKKINHNIDIKDYLRE-MESLSGRFIRKAVRDGRVFVNKEKVIKKHKLSQDD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I    +   +I  E   ++               ++YED+ I V NK  GI V    
Sbjct: 60  LIEIYMQEDEHQNIEPEDMNIE---------------IVYEDNDIIVINKRPGIVVHPTK 104

Query: 124 GIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G     +   +       G+K   RL  RLD++TSG++++A+ + +   L         +
Sbjct: 105 GHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKNQFSHMRLASDMSKDSFR 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY ++V G  K K++ I   + K+     +   + +  ++    +I+ +KV++  ++  
Sbjct: 165 KIYIAVVHGSMKEKEKRINLPIYKEE----ESESIKRIVDERGQESITTYKVLEELSKG- 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++  TGRTHQ+RVH  H+G P+ GD  Y    KG        +  LHA  ++ PHP
Sbjct: 220 SVVRLELETGRTHQIRVHMSHLGHPLYGDSLYG---KGEEEKEYVERQALHAYKLEFPHP 276

Query: 301 EGGRL-QITAPLPAHMVKTWDSL 322
             G + ++   LP  +    + +
Sbjct: 277 RTGDILKLQCSLPNDIKNLIEKI 299


>gi|86153072|ref|ZP_01071277.1| ribosomal pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|121612140|ref|YP_001000956.1| ribosomal large subunit pseudouridine synthase A [Campylobacter
           jejuni subsp. jejuni 81-176]
 gi|157415544|ref|YP_001482800.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|167005866|ref|ZP_02271624.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|85843957|gb|EAQ61167.1| ribosomal pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|87249616|gb|EAQ72575.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni 81-176]
 gi|157386508|gb|ABV52823.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|307748184|gb|ADN91454.1| Pseudouridine synthase [Campylobacter jejuni subsp. jejuni M1]
 gi|315932431|gb|EFV11374.1| pseudouridine synthase, RluA family protein [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 322

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 76/321 (23%), Positives = 140/321 (43%), Gaps = 39/321 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +Q  +V+ +    RLD +      + +   +  ++    V+V+ K   K + ++++G ++
Sbjct: 1   MQTFLVDENS---RLDVFLAKKL-NQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDII 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I      L + IK Q  +D  ++           +LYED  + V NKP+ + V G S +
Sbjct: 57  SI--ASLKLCNEIKPQFEVDFDID-----------VLYEDEDLLVLNKPSNLVVHGASSV 103

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W+  K           +  L HRLD++TSG +++A+     Q L+E    
Sbjct: 104 ---KNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDTSGAILIAKNNFTHQKLSEQLAD 160

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + +IY +L+    K  K  +  +L++        + + K+N K +  A S F  I   
Sbjct: 161 KSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIAIDKEN-KFSKNAKSAFINI-VK 218

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    +  +  TGRTHQ+R H   +   I+GD  Y    K         ++ LHA ++ 
Sbjct: 219 TENLTLMAAKLFTGRTHQIRAHLASLNRHILGDSLYGYKGK------YDCRIMLHAYFLY 272

Query: 297 LPHPEGGR-LQITAPLPAHMV 316
             HP+    + + APL     
Sbjct: 273 FIHPKTKEQIFVKAPLMEDFK 293


>gi|134299211|ref|YP_001112707.1| RluA family pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134051911|gb|ABO49882.1| pseudouridine synthase, RluA family [Desulfotomaculum reducens
           MI-1]
          Length = 303

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 139/316 (43%), Gaps = 33/316 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +++    +   ++R  +     ++   L++  R+  + +++  VK N  +++G+V+ +  
Sbjct: 12  LIIPQTMDGWTVERVLRREV-GVSRTLLRRAKRNRVILLNQLPVKTNVTVKTGEVLELWM 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAY 127
                     E +++   + L          +LYED+ +   NKP G+ V          
Sbjct: 71  GSQ-------ETQVVPERMELN---------ILYEDAHLLAVNKPPGMLVHPLTNETSGT 114

Query: 128 HIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +G L  W+      + R  HRLD+ TSGI+++AR     Q L    +  +  + Y +L
Sbjct: 115 LANGVLYHWLQQGTIDRFRPVHRLDRNTSGIVLIARNPYVQQQLQIQMKQGQFVRRYLAL 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + ++  I   +  +     +   + +        AISH++V+  F Q    + ++
Sbjct: 175 VKGKVQPEQGVIQAPIALE-----EGSFIKRMISPAGKEAISHYQVLRTFNQ-ASLVRVE 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
             TGRTHQ+RVH  HMG P++GD  Y  +           +  LH  Y+   HP  G R+
Sbjct: 229 LETGRTHQVRVHMAHMGHPLLGDSLYGGDTSN------IKRQALHCAYLAFNHPVQGSRI 282

Query: 306 QITAPLPAHMVKTWDS 321
           +I+  +   + +  + 
Sbjct: 283 KISCSVAGDIRQLMEE 298


>gi|154148379|ref|YP_001406840.1| RluA family pseudouridine synthase [Campylobacter hominis ATCC
           BAA-381]
 gi|153804388|gb|ABS51395.1| pseudouridine synthase, RluA family [Campylobacter hominis ATCC
           BAA-381]
          Length = 357

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 84/365 (23%), Positives = 155/365 (42%), Gaps = 51/365 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           ++   V+N   ++RLD +       I+   +  ++    + V+     K + ++++  +V
Sbjct: 11  LENFAVKNLSSSIRLDIFLTKILK-ISRNKILNLIEENHIFVNNSVQNKASFKLKNDDIV 69

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I   +   N  +K+    D               +LYED  + V NKP+G+ V     +
Sbjct: 70  GINFPLKKENENLKQNANFD-------------IEILYEDDDLLVLNKPSGVVVHPAKSV 116

Query: 126 AYHIDGFLKSWVDSK---------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W+  K          ++  + HRLD++TSG ++VA+T  A   L    + 
Sbjct: 117 ---KEPTLAEWLKQKKYMLSSINGDERAGIVHRLDKQTSGAILVAKTDFAHVKLAAQLKD 173

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS-------- 228
           + + +IY + +  +   +  C+  ++ +          VV  NE GA  A S        
Sbjct: 174 KSMGRIYLAFL-DLALKENVCVDRFIARN-PSNRLKKAVVPPNENGARSAKSAFLNIAND 231

Query: 229 ----HFKVID--CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
               +FK ++       F  +  +  TGRTHQ+RVH   +   I+GD  Y   FK +F  
Sbjct: 232 TILQNFKPLNFSQNQTNFNLIAAKLFTGRTHQIRVHLSSINRHIIGDFLYG--FKSDFDK 289

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK---YDRNLYIKRLYSQ 338
               +++LHA  +   HP   R + I+A +P+      +   FK   Y++ L    + + 
Sbjct: 290 --IKRIFLHAYLLYFTHPRTNRQILISAKIPSEFKNLIEKSDFKDEIYEKILPSNLISAF 347

Query: 339 DECKQ 343
           D+C Q
Sbjct: 348 DDCDQ 352


>gi|324994489|gb|EGC26402.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK678]
          Length = 295

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 69/305 (22%), Positives = 131/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   I+   L KI    G + V+ +       +  G  V I          +K   
Sbjct: 16  FLKRH--EISKGLLAKIKFSGGNILVNHQPQNAIYLLDIGDKVTIDIPSEKGFESLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
                      +      ++YED    V +KPAG++       +  +  F+K++      
Sbjct: 71  -----------AVDKDLSVVYEDKHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G     ++  I
Sbjct: 120 ENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  K   +A + +KVI+ F   +  +++  HTGRTHQ+RVH
Sbjct: 180 IAPIGRNPE-----SIITRRVTKDGKHAHTSYKVIERFGDVY-LVDIHLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   +P  G  ++  +PLP    +
Sbjct: 234 FSHIGFPLLGDDLYGGSLEC-----GIERQALHCHSLKFYNPFSGQEVERASPLPEDFKQ 288

Query: 318 TWDSL 322
             + L
Sbjct: 289 VIEKL 293


>gi|57238152|ref|YP_179402.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           jejuni RM1221]
 gi|57166956|gb|AAW35735.1| ribosomal large subunit pseudouridine synthases, RluD subfamily
           [Campylobacter jejuni RM1221]
 gi|315058713|gb|ADT73042.1| Ribosomal large subunit pseudouridine synthase D [Campylobacter
           jejuni subsp. jejuni S3]
          Length = 322

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 74/321 (23%), Positives = 140/321 (43%), Gaps = 39/321 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +Q  +V+ +    RLD +      + +   +  ++    V+V+ K   K + ++++G ++
Sbjct: 1   MQTFLVDENS---RLDVFLAKKL-NQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDII 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I      L + IK Q  +D  ++           +LYED  + V NKP+ + V G S +
Sbjct: 57  SI--ASLKLCNEIKPQFEVDFDID-----------VLYEDEDLLVLNKPSNLVVHGASSV 103

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W+  K           +  L HRLD++TSG +++A+     Q L+E    
Sbjct: 104 ---KNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDTSGSILIAKNNFTHQKLSEQLAD 160

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + +IY +L+    K  K  +  +L++        + + K+N+   N   +   V+   
Sbjct: 161 KSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIAIDKENKFSKNAKSAFINVVKT- 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    +  +  TGRTHQ+R H   +   I+GD  Y  N K         ++ LHA ++ 
Sbjct: 220 -ENLTLMAAKLFTGRTHQIRAHLASLNRHILGDGLYGYNGK------YDCRIMLHAYFLY 272

Query: 297 LPHPEGGR-LQITAPLPAHMV 316
             HP+    + + APL     
Sbjct: 273 FIHPKTKEQIFVKAPLMEDFK 293


>gi|226324582|ref|ZP_03800100.1| hypothetical protein COPCOM_02366 [Coprococcus comes ATCC 27758]
 gi|225207030|gb|EEG89384.1| hypothetical protein COPCOM_02366 [Coprococcus comes ATCC 27758]
          Length = 302

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 66/301 (21%), Positives = 128/301 (42%), Gaps = 36/301 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSG--QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           + K H    +   + + ++     +R++ + V     +  G  + I              
Sbjct: 29  FLKAH--GYSSSLI-RAIKEDTEGIRLNGEPVLARTLLTPGDQLAI-------------- 71

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           +I ++  +       L   ++YED  + V NKPAG+ +    G   +      +W   + 
Sbjct: 72  RITETKFSENIVPSDLPLSIVYEDPDLLVINKPAGMPIHPSQGNYDNTLANACAWYFKEK 131

Query: 142 QKPRLTHR---LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +P +      LD++T+G+L++AR   +A  L+     R I + Y +L  GI       I
Sbjct: 132 GEPFVYRCINRLDRDTTGLLIIARHLYSASLLSAMMARREIHREYLALATGIVPED-GII 190

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLR 256
              + +K     + +     + K   YA +H++ I        +  + ++  TGRTHQ+R
Sbjct: 191 TAPIARKEGSTIERM----VDFKHGEYACTHYRRISITNTDPVYSLVALKLDTGRTHQIR 246

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           VH  ++G P+ GD  Y  ++         ++  LH+ ++   HP  G  +  TAP+P  M
Sbjct: 247 VHMNYIGHPLPGDFLYNPDYS------HISRQALHSHHLRFRHPITGEEMHFTAPVPEDM 300

Query: 316 V 316
           +
Sbjct: 301 L 301


>gi|315302419|ref|ZP_07873284.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria ivanovii FSL F6-596]
 gi|313629211|gb|EFR97479.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria ivanovii FSL F6-596]
          Length = 296

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 71/317 (22%), Positives = 139/317 (43%), Gaps = 40/317 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE  E  + L  + +N   HI+   L   K    G++ V+        +++ G  V +  
Sbjct: 7   VEEKESGLLLRTFLRN--KHISKQLLTAVKYSDDGKIEVNGTEQNVLYQVEIGDEVCLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PREQQNERL--------------LAEYTALEIIFEDEFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G + ++V    +K        +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 SGSVANFVKGHYEKQGLTSAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQQGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +   G+  N+   I   + +K+        + +       YA ++++V+  + + F  +
Sbjct: 168 QAFTSGVLNNRIGSIEAPIGRKT-----VSIMERFVTPEGKYAKTNYEVLKRY-EAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TTLLKRQALHSCHLHLIHPLTE 275

Query: 304 R-LQITAPLPAHMVKTW 319
             L    PLP  M +  
Sbjct: 276 EYLTFDLPLPKDMEEII 292


>gi|283956675|ref|ZP_06374154.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 1336]
 gi|283791924|gb|EFC30714.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 1336]
          Length = 322

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 138/321 (42%), Gaps = 39/321 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +Q  +V+ +    RLD +      + +   +  ++    V+V+ K   K + ++++G ++
Sbjct: 1   MQTFLVDENS---RLDVFLAKKL-NQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDII 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I      L   IK Q  +D  ++           +LYED  + V NKP+ + V G S +
Sbjct: 57  SI--ASLKLYDEIKPQFEVDFDID-----------VLYEDEDLLVLNKPSNLVVHGASSV 103

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W+  K           +  L HRLD++TSG +++A+     Q L+E    
Sbjct: 104 ---KNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDTSGAILIAKNNFTHQRLSEQLAD 160

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + +IY +L+    K  K  +  +L++        + + K+N+   N   +   V+   
Sbjct: 161 KSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIAIDKENKFSKNAKSAFINVVKT- 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    +  +  TGRTHQ+R H   +   I+GD  Y    K         ++ LHA ++ 
Sbjct: 220 -ENLTLMAAKLFTGRTHQIRAHLASLNRHILGDSLYGYKGK------YDCRIMLHAYFLY 272

Query: 297 LPHPEGGR-LQITAPLPAHMV 316
             HP+    + + APL     
Sbjct: 273 FIHPKTKEQIFVKAPLMEDFK 293


>gi|169824298|ref|YP_001691909.1| putative ribosomal large subunit pseudouridine synthase [Finegoldia
           magna ATCC 29328]
 gi|167831103|dbj|BAG08019.1| putative ribosomal large subunit pseudouridine synthase [Finegoldia
           magna ATCC 29328]
          Length = 321

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 79/339 (23%), Positives = 148/339 (43%), Gaps = 36/339 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ ++N   N R+DR+     P ++  ++QK++R+ +++V+KKR + +  ++   VV 
Sbjct: 1   MRHINIDNSNSNQRVDRFLMKLMPKMSKNHIQKLIRTKKIKVNKKRTEPDYDLKIDDVVN 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I          + ++ I     N    +D     ++YED  + + NK  G+     +   
Sbjct: 61  IY---------LYDEVIEKYQDNKIYTADDFNLDIIYEDDDLILINKKTGVLSHAANPQD 111

Query: 127 Y--HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           Y  +I   + S++    Q          P L +RLD+ TSGI+V A+T  + ++  + F+
Sbjct: 112 YGKNIVDMMVSYLIKTNQFKPTQNSTFTPALVNRLDRNTSGIVVGAKTYDSLKYFNDLFK 171

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I KIY ++V G  K++   I   L K +      ++           +++    +  
Sbjct: 172 KHEITKIYETIVVGNLKDQ--TIDLALEKDNDKNKSVIN------SSGKKSMTKVWNVKN 223

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHAR 293
           F  K+  + +   TGRTHQ+R H  H+  PI+GD KY       +       N   LH+ 
Sbjct: 224 FG-KYSLVNVDLLTGRTHQIRAHLSHINHPIIGDIKYGNREVNKYFKNKYDLNFQLLHSY 282

Query: 294 YMDLPHPEGGR-----LQITAPLPAHMVKTWDSLGFKYD 327
            +  P   G       +   +       K  + L  KYD
Sbjct: 283 KLVFPEKMGKYQKYESMVFESKRDDLFEKILNDLESKYD 321


>gi|260887212|ref|ZP_05898475.1| ribosomal large subunit pseudouridine synthase D [Selenomonas
           sputigena ATCC 35185]
 gi|260863274|gb|EEX77774.1| ribosomal large subunit pseudouridine synthase D [Selenomonas
           sputigena ATCC 35185]
          Length = 287

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 68/304 (22%), Positives = 122/304 (40%), Gaps = 38/304 (12%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHIIK 79
           L  + +      +    +K+ RSG   ++         RI+SG  +          H+ +
Sbjct: 3   LREFLQKEC-GFSTTLWKKLRRSGTFSLNGLPANAARIRIKSGDELCW--------HLAE 53

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW- 136
           E +I    + L          +LYED+ + + NKPAG+ V    G   H   +  L  + 
Sbjct: 54  ESRIAPEDIPLE---------ILYEDAALLIVNKPAGMLVHPTGGEYRHTLANAVLFHYE 104

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +       HRLD++TSG++++A+       L+       I++IY +++ G       
Sbjct: 105 AHGEKHAFHPVHRLDRQTSGLVLIAKEAHVQHLLSAHNA---IERIYLAVIEGKLPEPCG 161

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   + ++     + +            A++H+  +         L ++  TGRTHQ+R
Sbjct: 162 TIDAPIARRPGSIIERMV-----SPAGKCAVTHYATLAERG-GLSLLALRLATGRTHQIR 215

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           VH  H+  P++GD  Y              +  LHA  +   HP  G  + + AP PA M
Sbjct: 216 VHLAHLAHPLLGDDLYGGRTDR------IARQALHAHRLRFRHPISGKEITVHAPFPADM 269

Query: 316 VKTW 319
              +
Sbjct: 270 SAFF 273


>gi|298710073|emb|CBJ31789.1| pseudouridine synthase [Ectocarpus siliculosus]
          Length = 541

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 83/339 (24%), Positives = 140/339 (41%), Gaps = 27/339 (7%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V   VV +++    +D       P  +    +K L +G V+VD ++VK   R++ G  
Sbjct: 130 NAVISTVVSDEDNKAPIDWVLSRRLPQHSRRFYRKALEAGDVKVDGRKVKRFIRVKRGAR 189

Query: 65  VRIPPVINALNHIIKE--QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + +                       NL       +  +++ED  ++V  KPAG+  Q  
Sbjct: 190 ISVDLGRQQQQQGASAVAAATTTPPPNLVFPQRLPRLRVVFEDDHLFVAMKPAGMICQPC 249

Query: 123 S---------GIAYHI--DGFLKSWVDSKGQKP-----RLTHRLDQETSGILVVARTRAA 166
           +         G+ YH+   G L+   D            +  RLD++TSGI+VVA+T AA
Sbjct: 250 AAAPRGTVLHGLMYHMVQSGQLEEGSDITAAAANTLSQGIVQRLDKQTSGIMVVAKTLAA 309

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           +  L+  FR  +++K Y ++  G P      +   L ++S      V   +     A  A
Sbjct: 310 SSKLSALFRKGKVKKQYLAVCHGDP-GFDSVVDAPLYRRSSGKVGAVEPWEAEAFRAKEA 368

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------FKGNF 280
            +  + +   A+          TGR HQ+RVH   +GCPIVGD +Y          K + 
Sbjct: 369 QTRVRNVAT-ARGLSLCRADILTGRMHQVRVHLKWIGCPIVGDREYGDPEANFRVSKRSA 427

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
                 +  LH+  ++  HP   + +   AP+P  M +T
Sbjct: 428 HRVEAQRPLLHSVSLEFIHPFTNKPMSFKAPMPPDMWET 466


>gi|331270027|ref|YP_004396519.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium botulinum BKT015925]
 gi|329126577|gb|AEB76522.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium botulinum BKT015925]
          Length = 302

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 78/332 (23%), Positives = 139/332 (41%), Gaps = 37/332 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     +  + VE  +E +RL  + KN     +    +K  R G+++V+ + V+ +  ++
Sbjct: 1   MESKDNIIKLKVEIQDEEIRLSHYLKNVAQCSSR-FTRKAAREGRIKVNGENVRLSYMLK 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  +V +         II E+  LD                        V NKP GI V 
Sbjct: 60  NDDIVELQINRKEEQDIIPEKMDLDIIYEDDDII---------------VVNKPKGIVVH 104

Query: 121 GGSGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                  H++G L + V       ++    RL +RLD +TSG++++A+   +   L+   
Sbjct: 105 PTK---RHLNGTLSNGVLYYFNDKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDM 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           +     K Y ++V G        I   + +        V      ++    +I+ FKV++
Sbjct: 162 QKDDFVKKYLAIVHGNLNEDSGVIDKPIYRVGEGTLKRVI-----DERGQRSITRFKVVE 216

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            + +    +E+   TGRTHQ+RVH   +G PI GD  Y             ++  LHA  
Sbjct: 217 QY-KNASLVELTLETGRTHQIRVHLSSIGYPIYGDSLYGEEEPQ-----YIDRQALHAYK 270

Query: 295 MDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
           + +PHP+ G++ ++ + LP  M      L  K
Sbjct: 271 LQIPHPKDGKILKLESDLPEDMKNLIRKLSEK 302


>gi|291483642|dbj|BAI84717.1| hypothetical protein BSNT_01943 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 299

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 63/284 (22%), Positives = 119/284 (41%), Gaps = 36/284 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G ++++ + V     ++ G ++ +              K  +  V+ T  ++ +   +LY
Sbjct: 41  GDLQINGEHVTVKYVLKEGDLLIV--------------KFPEEQVSETLLAEPIPLDILY 86

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGI 157
           ED  + V NK   +S         H  G + + +    QK        L  RLD++TSG+
Sbjct: 87  EDEHVLVINKQPYVSSIPSR---EHPSGSIANGIIDHYQKNGVRATVHLVTRLDRDTSGV 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA+ R A   L+ + +   +++ Y ++V G     +  +   + +          + +
Sbjct: 144 MLVAKHRFAHSILSSAQKNGLVKRRYAAVVHGRMAQMEGTVDAPIGRHPD-----SIIER 198

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A++HF V  C       + +Q  TGRTHQ+RVH  ++G P+ GD  Y    +
Sbjct: 199 TVTPDGQKAVTHFYV-TCANDDMTSVALQLETGRTHQIRVHMSYLGHPLCGDTLYGGTRQ 257

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
                    +  LH+ ++   HP   + +   APLP  M K   
Sbjct: 258 E------IGRQALHSEHLSFIHPLTQKNMTFHAPLPQDMRKLIK 295


>gi|257469932|ref|ZP_05634024.1| pseudouridine synthase, RluA family protein [Fusobacterium ulcerans
           ATCC 49185]
 gi|317064162|ref|ZP_07928647.1| RNA pseudouridylate synthase [Fusobacterium ulcerans ATCC 49185]
 gi|313689838|gb|EFS26673.1| RNA pseudouridylate synthase [Fusobacterium ulcerans ATCC 49185]
          Length = 294

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 140/317 (44%), Gaps = 38/317 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRI 67
           + V E +E    L  +     P  +  +++ +L   +V V +    ++N+ +  GQ V +
Sbjct: 11  FKVTEKNE----LMNFLIEKMPEKSRTSIKSLLTKRKVFVGNDVVSQYNHPLLPGQTVTV 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                 ++  +K                     ++YED  + V  K +GI          
Sbjct: 67  DWGKVTIDTTMKG------------------VSIIYEDDDVLVVEKESGILSIATDNERE 108

Query: 128 -HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                 LK ++ +K  K    + HRLD++TSGI++ A+T  A   L  ++     ++ Y 
Sbjct: 109 KTAYNMLKEYLKNKDPKNKIFVVHRLDRDTSGIMIFAKTEKAQDILQTTWNDSVKERTYV 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+   +K+ I ++L +       ++    QN K    AISH+KV+    + +  LE
Sbjct: 169 ALVEGVVYKEKDTIISYLQEN----KAFITYSSQNPKEGKKAISHYKVLK-KNKNYSLLE 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TGR +Q+RVH   +G  +VGD KY +           N+L LHA  +   HP   +
Sbjct: 224 VNIETGRKNQIRVHMQDLGHSVVGDKKYGSGKSP------INRLGLHANTIVFVHPITKK 277

Query: 305 -LQITAPLPAHMVKTWD 320
            L  ++ +PA   K ++
Sbjct: 278 VLHFSSKIPAVFTKIFN 294


>gi|317129591|ref|YP_004095873.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
 gi|315474539|gb|ADU31142.1| pseudouridine synthase, RluA family [Bacillus cellulosilyticus DSM
           2522]
          Length = 298

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 68/325 (20%), Positives = 132/325 (40%), Gaps = 33/325 (10%)

Query: 4   MTYVQ-YVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQS 61
           M  ++   V++N      L  + +     I+   L  I    GQ+ V+ K       ++ 
Sbjct: 1   MKSIRLQWVIDNAATGKLLRDYLREE-KQISRKALADIKFNGGQITVNGKEENVRYTLRL 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G V+ +      ++  IK  KI              K  +++ED  + + NKP  +    
Sbjct: 60  GDVIEVIFPKEKVSRSIKPYKI--------------KLHIIFEDEHVIIINKPPHLPTIP 105

Query: 122 GSGIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                   + G + ++    G         RLD++TSG+++VA+ R       +  +   
Sbjct: 106 TRNEGEPSLAGAILAYYIENGIPSTFHAVSRLDRDTSGLVMVAKHRYMHDLCVKLQKSYE 165

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I++ Y +LV GI  +    I   + +K+        + ++  +    AI+H++V+  ++ 
Sbjct: 166 IKRSYVALVEGILSDDYNTIDLPISRKTT-----SIIEREVNEFGKSAITHYEVLKRYS- 219

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               L++   TGRTHQ+RVH   +G P++GD  Y  + +        ++  LH+  +   
Sbjct: 220 GATLLQLTLETGRTHQIRVHMSAIGHPLLGDTLYGGDVR------YIDRQALHSHQLSFF 273

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSL 322
           HP   R      P+P  +       
Sbjct: 274 HPINKREYTFHCPIPDDIEDAMSKF 298


>gi|300871333|ref|YP_003786206.1| pseudouridylate synthase, 23S RNA-specific [Brachyspira pilosicoli
           95/1000]
 gi|300689034|gb|ADK31705.1| pseudouridylate synthase, 23S RNA-specific [Brachyspira pilosicoli
           95/1000]
          Length = 298

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 76/315 (24%), Positives = 137/315 (43%), Gaps = 34/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E  + N RLD +      +I+   ++  L S  + V+    K +  ++   +V I    
Sbjct: 6   IEEKDLNKRLDIFVSEKL-NISRSQVKNYLSS--ILVNGNIKKLSYSLKLNDIVEINIKT 62

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ--GGSGIAYHI 129
           +      +E+ IL  +++L          +LYED  + V NKP  +SV           +
Sbjct: 63  DDNE---EEEDILAENIDLD---------ILYEDEYLLVVNKPCNMSVHCSPSERHGTLV 110

Query: 130 DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +  L    D        +  + HRLD++TSGI++V +       + E F+ R I+KIY +
Sbjct: 111 NALLYHIKDFNFVGDKSRAGIIHRLDKDTSGIMIVGKNADIVSAIQEQFKNRTIKKIYHA 170

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+ +     I   + + S +    + V     +    A+S+ KV++ F +K   +E+
Sbjct: 171 IVIGVLRENFYEINLPIGRHS-VYRKKMTVR----EDGKKALSYIKVLNRF-KKHTLIEV 224

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
              TGRTHQ+RVH  + G P+ GD  Y  ++           L L A+ ++  HP  G  
Sbjct: 225 NIKTGRTHQIRVHCSYKGFPVAGDKIYSKSYSNYSN------LMLIAKQIEFTHPISGEI 278

Query: 305 LQITAPLPAHMVKTW 319
           ++       +     
Sbjct: 279 MKFEVDYTDYFRDFL 293


>gi|288928148|ref|ZP_06421995.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 317 str. F0108]
 gi|288330982|gb|EFC69566.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 317 str. F0108]
          Length = 300

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 79/309 (25%), Positives = 135/309 (43%), Gaps = 34/309 (11%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINAL 74
           EE+  LD W   +    +   L+ ILR   V V+ K V  F+ ++  G  V +     A 
Sbjct: 22  EESTLLD-WLLRNVKGKSRNKLKDILRGHGVCVNGKCVTQFDYQLVPGMKVTVSRTKKA- 79

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                          +   S ++K  ++YED  + V +K  G+        + ++   L 
Sbjct: 80  ---------------VPFKSRYIK--IVYEDRYLIVVDKSVGVLSMAAGHSSLNVKAILD 122

Query: 135 SWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           ++ ++ GQK    + HRLD+ETSG+LV A+     Q L  ++      + Y ++V G   
Sbjct: 123 TYFENSGQKCRAHVVHRLDRETSGLLVYAKDMETEQILEHNWHDMVYDRRYVAVVSGEIV 182

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           ++   I++WL   S     Y+      + G  YA++HF V+         +E +  TGR 
Sbjct: 183 DEGGTISSWLKDNS----SYITYSSPVDNGGKYAVTHFHVLKRTT-THSLVEYKLETGRK 237

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPL 311
           +Q+RVH+  +G P+ GD KY              +L LHA  +   HP    R++   P+
Sbjct: 238 NQIRVHSADIGHPVCGDLKYGNG------DNPIGRLCLHAYMLCFYHPATRERMEFNTPI 291

Query: 312 PAHMVKTWD 320
           P    + + 
Sbjct: 292 PQTFKQLFK 300


>gi|86149976|ref|ZP_01068204.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni CF93-6]
 gi|88596472|ref|ZP_01099709.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni 84-25]
 gi|218562892|ref|YP_002344671.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|85839422|gb|EAQ56683.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni CF93-6]
 gi|88191313|gb|EAQ95285.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni 84-25]
 gi|112360598|emb|CAL35395.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|284926505|gb|ADC28857.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni IA3902]
 gi|315927093|gb|EFV06444.1| pseudouridine synthase, RluA family protein [Campylobacter jejuni
           subsp. jejuni DFVF1099]
 gi|315928797|gb|EFV08067.1| pseudouridine synthase, RluA family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 322

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 139/321 (43%), Gaps = 39/321 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +Q  +V+ +    RLD +      + +   +  ++    V+V+ K   K + ++++G ++
Sbjct: 1   MQTFLVDENS---RLDVFLAKKL-NQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDII 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I      L + IK Q  +D  ++           +LYED  + V NKP+ + V G S +
Sbjct: 57  SI--ASLKLCNEIKPQFEVDFDID-----------VLYEDEDLLVLNKPSNLVVHGASSV 103

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W+  K           +  L HRLD++TSG +++A+     Q L+E    
Sbjct: 104 ---KNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDTSGAILIAKNNFTHQKLSEQLAD 160

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + +IY +L+    K  K  +  +L++        + + K+N+   N   +   V+   
Sbjct: 161 KSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIAIDKENKFSKNAKSAFINVVKT- 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    +  +  TGRTHQ+R H   +   I+GD  Y    K         ++ LHA ++ 
Sbjct: 220 -ENLTLMAAKLFTGRTHQIRAHLASLNRYILGDSLYGYKGK------YDCRIMLHAYFLY 272

Query: 297 LPHPEGGR-LQITAPLPAHMV 316
             HP+    + + APL     
Sbjct: 273 FIHPKTKEQIFVKAPLMEDFK 293


>gi|319956600|ref|YP_004167863.1| ribosomal large subunit pseudouridine synthase d [Nitratifractor
           salsuginis DSM 16511]
 gi|319419004|gb|ADV46114.1| ribosomal large subunit pseudouridine synthase D [Nitratifractor
           salsuginis DSM 16511]
          Length = 327

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 143/332 (43%), Gaps = 43/332 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           MS       +VV       RLD+         +   + +++ +G V V+     K + ++
Sbjct: 1   MSQGQKSGEIVVSE---GGRLDKVLSAAL-GASRNQVARLIEAGAVSVEGIPAEKASRKV 56

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G+ +                +IL++    +   +F    +LYED  + + NKPAG+ V
Sbjct: 57  EPGERI--------------AYRILEAPRRDSLPVEF-DVEVLYEDEYLMILNKPAGVVV 101

Query: 120 QGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHL 170
                +    +  L  W+  +G         ++  + HRLD+ETSG LV+A+T A  Q L
Sbjct: 102 HPAPSVR---EPTLVHWLVQRGISLSTLAGEERHGIVHRLDKETSGALVIAKTNAVHQAL 158

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
           +E  + R + + Y +L+   P  +   +   + +        + VV    +G   A + F
Sbjct: 159 SEELKSREMGRYYLALI-DHPLKEDLTVDAPIARN-PANRLKMAVV----EGGREARTDF 212

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
             +    +    +  + HTGRTHQ+RVH   +G  I+GD  Y              +++L
Sbjct: 213 LKLAEGEEGSELIAARLHTGRTHQIRVHLAKIGRHILGDELYGYRGAQGK----IPRVFL 268

Query: 291 HARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           HA  + L HP    RL+++AP+P  M +    
Sbjct: 269 HAARLYLTHPATHRRLEVSAPIPEDMREYLRK 300


>gi|283954844|ref|ZP_06372360.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacter jejuni subsp. jejuni 414]
 gi|283793684|gb|EFC32437.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacter jejuni subsp. jejuni 414]
          Length = 322

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 137/321 (42%), Gaps = 39/321 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +Q  +V+ +    RLD +      + +   +  ++    V+V+ K   K + ++++G VV
Sbjct: 1   MQTFLVDENS---RLDVFLAKKL-NQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDVV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I   +N  N +  + ++                 +LYED  + V NKP+ + V G S +
Sbjct: 57  FI-ASLNLCNEVKPQFEV------------DFDIDVLYEDEDLLVLNKPSNLVVHGASSV 103

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W+  K           +  L HRLD++TSG +++A+     Q L+E    
Sbjct: 104 ---KNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDTSGAILIAKNNFTHQKLSEQLAD 160

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + +IY +L+    K  K  +  +L++        + + ++N+   N   +   VI   
Sbjct: 161 KSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIAIDEENKFSKNAKSAFINVIKT- 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    +  +  TGRTHQ+R H   +   I+GD+ Y    K         ++ LHA ++ 
Sbjct: 220 -ENLTLMAAKLFTGRTHQIRAHLASLNRHILGDNLYGYKGK------YDCRIMLHAYFLY 272

Query: 297 LPHPEGGR-LQITAPLPAHMV 316
             HP     + + APL     
Sbjct: 273 FIHPRTKEQIFVKAPLMEDFK 293


>gi|325694474|gb|EGD36383.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK150]
          Length = 295

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 131/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L KI    G + V+ +       +  G  V I          +K   
Sbjct: 16  FLKRH--EVSKSLLAKIKFSGGNILVNHQPQNAIYLLDIGDKVTIDIPSEKGFESLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
                      +      ++YED    V +KPAG++       +  +  F+K++      
Sbjct: 71  -----------AVDKDLSVVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G     ++  I
Sbjct: 120 ENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH
Sbjct: 180 IAPIGRNPE-----SIITRRVTEDGKYAHTSYKVIERFGDVY-LVDIHLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   +P  G  ++  +PLP    +
Sbjct: 234 FSHIGFPLLGDDLYEGSLE-----HGIERQALHCHSLKFYNPFSGQEVERASPLPEDFKQ 288

Query: 318 TWDSL 322
             + L
Sbjct: 289 VIEKL 293


>gi|146318712|ref|YP_001198424.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           05ZYH33]
 gi|146320920|ref|YP_001200631.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           98HAH33]
 gi|253751821|ref|YP_003024962.1| RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|253753644|ref|YP_003026785.1| RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|253755475|ref|YP_003028615.1| RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|145689518|gb|ABP90024.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           05ZYH33]
 gi|145691726|gb|ABP92231.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           98HAH33]
 gi|251816110|emb|CAZ51733.1| putative RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|251817939|emb|CAZ55717.1| putative RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|251819890|emb|CAR45926.1| putative RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|292558391|gb|ADE31392.1| Pseudouridine synthase, RluD [Streptococcus suis GZ1]
 gi|319758173|gb|ADV70115.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           JS14]
          Length = 297

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 66/306 (21%), Positives = 128/306 (41%), Gaps = 34/306 (11%)

Query: 24  WFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           + K H   ++   L K ++   G + V+         +  G  V I              
Sbjct: 16  FLKKH--GVSKGLLAK-IKYTGGNIWVNDIEQNATYLLDIGDRVTI-------------D 59

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---D 138
              +  +  +    F    ++YED      NKP G +    +  +  I  F+K ++   +
Sbjct: 60  IPAEEDLTGSLKPIFFPLDIVYEDDHFLAINKPVGYASIPSALHSSTIANFVKGYLIEQN 119

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKEC 197
            + ++  +  RLD++TSG+++ A+   A   L +  + + I K Y++LV G  +  +   
Sbjct: 120 YENKQVHIVTRLDRDTSGVMLFAKHGYAHARLDKQLQAKLIHKRYYALVKGNGQLEETGD 179

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +      +   + +   K   YA + ++V+  +      +++Q HTGRTHQ+RV
Sbjct: 180 IIAPIGRP-----EDSIITRCVTKNGKYAHTSYRVVQSWGDIH-LVDIQLHTGRTHQIRV 233

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
           H  H+G P++GD  Y  + +         +  LH   +   +P    R+ + APLP    
Sbjct: 234 HFSHIGFPLLGDDMYGGSLEC-----GIERQALHCHNLAFDNPFSAERIDLEAPLPEDFQ 288

Query: 317 KTWDSL 322
              + L
Sbjct: 289 AVINQL 294


>gi|323351544|ref|ZP_08087198.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis VMC66]
 gi|322122030|gb|EFX93756.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis VMC66]
          Length = 295

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 138/322 (42%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   I+   L KI    G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKRH--EISKGLLAKIKFSGGNILVNHQPQNAIYLLDIGDKV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          +K              +      ++YED    V +KPAG++       
Sbjct: 57  TIDIPSEKGFESLK--------------AVDKDLSVVYEDEHFLVLDKPAGVASIPSVNH 102

Query: 126 AYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  +  F+K++      + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K 
Sbjct: 103 SNTMANFVKAYYIRHAYENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKR 162

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y++LV G     ++  I   + +          + ++  K    A + +K+I+ F   + 
Sbjct: 163 YYALVRGTGDLEEQGEIIAPIGRNPE-----SIITRRVTKDGKCAHTSYKIIEQFGDVY- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++  HTGRTHQ+RVH  H+G P++GD  Y  + +         +  LH   +   +P 
Sbjct: 217 LVDIHLHTGRTHQIRVHFSHIGFPLLGDDLYGGSLEC-----GIERQALHCHSLKFYNPF 271

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
            G  ++  +PLP    +  + L
Sbjct: 272 SGQEVERASPLPEDFKQVIEKL 293


>gi|308233940|ref|ZP_07664677.1| pseudouridine synthase, RluA family [Atopobium vaginae DSM 15829]
 gi|328943952|ref|ZP_08241417.1| ribosomal large subunit pseudouridine synthase D [Atopobium vaginae
           DSM 15829]
 gi|327491921|gb|EGF23695.1| ribosomal large subunit pseudouridine synthase D [Atopobium vaginae
           DSM 15829]
          Length = 338

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 76/340 (22%), Positives = 140/340 (41%), Gaps = 40/340 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRI 59
           MS  T++Q +V    +  MRLD +               ++   +V ++    +  + R+
Sbjct: 1   MS-ETHIQLLVTPQHDR-MRLDAFLSTCSELGARNACAHLIEQRKVEINDTLALSKSERV 58

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G  + +             Q+I ++S +    +  +   + YED  + V +K  G+  
Sbjct: 59  RMGDRICV------------AQQIDNTSSSHIMPNASIPLDIRYEDDYLLVISKQTGLVC 106

Query: 120 QGGSGIAYHIDGFLKSWV-----------DSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
               G   H+D  L + +                +P + HRLD +T+G++V A+     Q
Sbjct: 107 HPSPG---HVDDTLSNALVAHCGYEHLGLLQGDDRPGIVHRLDMDTTGLMVAAKDNTTQQ 163

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            L +  R+R   + Y  LV G     +  I   + +      + + +    +  +  AI+
Sbjct: 164 ALQDLIRLRVFDRRYIVLVQGYVTPDEGTITTGIARSKK---NRLKMCISKDPASREAIT 220

Query: 229 HFKVIDCFA-----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
            FK ++ F        +  LE   +TGRTHQ+RVH  ++G  +VGD  Y    KG+  + 
Sbjct: 221 TFKTLERFEAGSKDDGYSLLECHLYTGRTHQIRVHMRYVGHSVVGDPLYG--RKGDALNQ 278

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              + +LH+  M   HP     LQ    LP+ + +    L
Sbjct: 279 GLQRQFLHSWRMSFDHPITHEHLQFCDKLPSDLSEVLARL 318


>gi|321314893|ref|YP_004207180.1| pseudouridylate synthase [Bacillus subtilis BSn5]
 gi|320021167|gb|ADV96153.1| pseudouridylate synthase [Bacillus subtilis BSn5]
          Length = 299

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 67/317 (21%), Positives = 129/317 (40%), Gaps = 39/317 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           + + E+ M +  +       I+   L  I    G ++++ + V     ++ G ++ +   
Sbjct: 10  ITSAEDGMTVKEYASEL--GISKRLLTDIKFGGGDLQINGEHVTVKYVLKEGDLLIV--- 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                      K  +  V+ T  ++ +   +LYED  + V NK   +S         H  
Sbjct: 65  -----------KFPEEQVSETLLAEPVPLDILYEDEHVLVINKQPYVSSIPSR---EHPS 110

Query: 131 GFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + + +    Q         L  RLD++TSG+++VA+ R A   L+ + +   +++ Y 
Sbjct: 111 GSIANGIIDHYQTTGVRATVHLVTRLDRDTSGVMLVAKHRFAHSILSSAQKNGLVKRRYA 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G     +  +   + +          + +        A++HF V  C       + 
Sbjct: 171 AVVHGRMAQMEGTVDAPIGRHPD-----SIIERTVTPDGQKAVTHFYV-TCANDDMTSVT 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  ++G P+ GD  Y    +         +  LH+ ++   HP   +
Sbjct: 225 LQLETGRTHQIRVHMSYLGHPLCGDTLYGGTRQE------IGRQALHSEHLSFIHPLTQK 278

Query: 305 -LQITAPLPAHMVKTWD 320
            +   APLP  M K   
Sbjct: 279 NMTFHAPLPQDMRKLIK 295


>gi|153812383|ref|ZP_01965051.1| hypothetical protein RUMOBE_02782 [Ruminococcus obeum ATCC 29174]
 gi|149831545|gb|EDM86632.1| hypothetical protein RUMOBE_02782 [Ruminococcus obeum ATCC 29174]
          Length = 293

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 146/322 (45%), Gaps = 35/322 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ--VRVDKKRVKFNNRIQS 61
           M  +    +   +E M +  + +      +  ++   +++ +  + ++ ++      +  
Sbjct: 1   MERILNYTISAADEGMIVLDFLRKQ--GFSR-HILTAMKADREALSLNGQKAGGRTVLSC 57

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G   R+      L   +    IL + +N+          +LYED  I V NKPA + V  
Sbjct: 58  GDHFRV-----RLLETVPADGILPTPLNIP---------VLYEDEDILVVNKPADMPVHP 103

Query: 122 GSG-IAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             G     +   + +++++KG+    R  +RLD++TSG L++A+   +A  L+   R R+
Sbjct: 104 SLGNYTNTLANGVAAYLETKGESCPFRCINRLDRDTSGALILAKNALSAAILSVQMRNRQ 163

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y ++V GIP+ +   I+  + +      D V   + + +    AI+H+++++    
Sbjct: 164 ISRTYLAVVEGIPR-QSGTISAPISR----AADSVIERRIDFENGESAITHYQLLEVK-N 217

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               LE+   TGRTHQ+RVH  ++G P+  D+ Y   +      P+      H+  +   
Sbjct: 218 NHSLLEIHLETGRTHQIRVHMGYIGHPLPADYLYNPVYDTFKRQPL------HSLQLKFC 271

Query: 299 HPEGG-RLQITAPLPAHMVKTW 319
           HP  G  + + AP+P  M   +
Sbjct: 272 HPITGTPMCLMAPVPEDMSNAF 293


>gi|332702347|ref|ZP_08422435.1| pseudouridine synthase, RluA family [Desulfovibrio africanus str.
           Walvis Bay]
 gi|332552496|gb|EGJ49540.1| pseudouridine synthase, RluA family [Desulfovibrio africanus str.
           Walvis Bay]
          Length = 297

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 76/298 (25%), Positives = 130/298 (43%), Gaps = 23/298 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M  V ++ V   E   +L ++ +      +    + K LR+GQ+RVD +R K  +R+++G
Sbjct: 1   MPSVSHIEVTPAEAGHKLLQFLERRLGKGVPRALVMKWLRTGQLRVDGRRAKPFDRLEAG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q VR+PP          E  +      L          +++ED ++ V  KPAG++ Q G
Sbjct: 61  QTVRVPPY---------EAVVEPEGQPLRAR----PLTIIHEDDELLVIAKPAGLASQPG 107

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           SG+   +   LK+        P   HRLD +TSG+LV  +T  + + L + F    + K 
Sbjct: 108 SGLTDSVQTRLKALYAGADFMPSCAHRLDMDTSGLLVAGKTYQSVRRLGDLFASGGVDKT 167

Query: 183 YWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V G    + +  + + ++K              + +    A++  + +        
Sbjct: 168 YLAWVQGQWPEQGQILLRDHIIKDGRAHVRIGADNAPDGEQGKLALARVRPMARRPD-AT 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
            L ++  TGRTHQ+R+     G P++GD KY               L LHA  + LP 
Sbjct: 227 LLAVELLTGRTHQIRIQLASRGHPVLGDRKYGRRPHATH-------LLLHAWKLRLPD 277


>gi|169350066|ref|ZP_02867004.1| hypothetical protein CLOSPI_00806 [Clostridium spiroforme DSM 1552]
 gi|169293279|gb|EDS75412.1| hypothetical protein CLOSPI_00806 [Clostridium spiroforme DSM 1552]
          Length = 322

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 77/334 (23%), Positives = 142/334 (42%), Gaps = 31/334 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +  ++ N R+D++ K    +     + K+ R   ++V+ K+V     +++  VV 
Sbjct: 1   MKKIQITENDANQRIDKYIKKLLVNAPTNFIYKMFRKKDIKVNGKKVNEKYILKNNDVVE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          + E K  + +     ++      +LYED+ + +  KPAG+ V      +
Sbjct: 61  M---------FLYEDKFKEFTATKDIYNVKKTFKVLYEDNHVLIVYKPAGLLVHEDKNES 111

Query: 127 -YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +   + S++ +K +          P   HRLD+ TSGI++  +T  A Q L E  + 
Sbjct: 112 VNTLTNQVLSYLANKNELDLSRENTFMPGPVHRLDRNTSGIVIFGKTLGALQVLNEMIKQ 171

Query: 177 RR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           R  I+K Y ++  G   N+K  +  +++K        V +V ++  GA    +  K +  
Sbjct: 172 RHCIEKSYLTICKGKV-NQKRNLKGYIVKLDDQA--QVKLVSKDYPGALTMETIVKPVKY 228

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHAR 293
               +  +E+   TGR HQ+RVH   +  PI+GD KY       F       N   LHA 
Sbjct: 229 NND-YSKVEVTLVTGRMHQIRVHLSSIDHPIIGDRKYGDFELNKFVKKEFGLNHQLLHAY 287

Query: 294 YMDLPHPEG-----GRLQITAPLPAHMVKTWDSL 322
            +      G        +I  P+P    K  + L
Sbjct: 288 KIRFVKSFGILAYLQDKEIVCPVPKLFEKIENRL 321


>gi|116872369|ref|YP_849150.1| ribosomal large subunit pseudouridine synthase [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|116741247|emb|CAK20369.1| ribosomal large subunit pseudouridine synthase [Listeria welshimeri
           serovar 6b str. SLCC5334]
          Length = 296

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 69/319 (21%), Positives = 145/319 (45%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VEN+E+ + L  + ++   HI+   L   K    G++ V++       ++Q+G  VR+  
Sbjct: 7   VENEEDGLLLRTFLRS--KHISKQLLTAVKFSADGKIEVNRTEQNVLYQVQTGDNVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++ K  +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTKLEVIFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G + ++V    +         +  RLD++TSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 SGSVANFVKGHYEAQGLTSAIHIVTRLDRDTSGLMLIAKNRFAHARLSTFLQQGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L  G+ + +   I   + +K     +   + +       YA ++++V+  + + F  +
Sbjct: 168 QALTSGVLQEEAGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLKRY-RGFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TSMLQRQALHSCHLHLVHPVTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
             +     LP  + +    
Sbjct: 276 EYMAFDLALPDDLEEIIQK 294


>gi|260654228|ref|ZP_05859718.1| ribosomal large subunit pseudouridine synthase C [Jonquetella
           anthropi E3_33 E1]
 gi|260630861|gb|EEX49055.1| ribosomal large subunit pseudouridine synthase C [Jonquetella
           anthropi E3_33 E1]
          Length = 276

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 80/293 (27%), Positives = 118/293 (40%), Gaps = 28/293 (9%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           K  R G VR+D  R  F  ++ +GQ+V +P                              
Sbjct: 3   KFFRKGSVRLDGARADFRTKVAAGQMVFVPWEA--------------PDAQPEVQVRHRP 48

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY    + V NKPAG+  Q  +     +      +        +L HRLD+ TSG++
Sbjct: 49  LDVLYRSDSVLVINKPAGLLSQPDTKGEDSVATRALGYASDPAFGAQLVHRLDRNTSGVM 108

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A    A + L   F+ R   K Y +LV G        I   LLK        V V   
Sbjct: 109 ILALDGQALRSLMVCFKERTANKTYLALVSGQLPP-SGQIDAPLLKDP--DKKLVRVAS- 164

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFK 277
                  A++ F+ +    Q F   E++  TGRTHQ+RVH  H+G PI+GD KY   + K
Sbjct: 165 ---NGERAVTRFRRLATDGQ-FSLAEVEILTGRTHQIRVHMNHIGHPILGDAKYGDFSAK 220

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEG--GRL---QITAPLPAHMVKTWDSLGFK 325
                    +  LHA  + +  P+     +   +  APL A M      LGF+
Sbjct: 221 PQVRRLGIRRPMLHATCLVVNSPDDCLKEISGRRFDAPLAADMASVCQKLGFE 273


>gi|86160593|ref|YP_467378.1| pseudouridine synthase RluD [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85777104|gb|ABC83941.1| Pseudouridine synthase, RluD [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 318

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 77/337 (22%), Positives = 130/337 (38%), Gaps = 40/337 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+    V++  VE +    RLDR+ +     ++   +Q+++       D +R+K + R+ 
Sbjct: 1   MTQQVRVRF-TVEPNYAGWRLDRYLQEKIRRLSRERVQRLIAQRLETDDGRRLKPSTRVA 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G    +     A     +E                    ++++D  + V +KPAG+ V 
Sbjct: 60  PGLSFALLKDAEAEPDTPQE------------------FGVVHDDGALLVVDKPAGLPVH 101

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             +  A +    L        +K    HRLD+ETSG+L         + L   F   R+ 
Sbjct: 102 PTARYAANTFTSLAKLRYPD-RKVDPAHRLDRETSGLLACGTAPEVTKVLKRDFAHARVH 160

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---- 236
           K Y +L  G P      +   L   +  G   V V          + + F+V+       
Sbjct: 161 KTYLALALGAPAEDAFTVDAPL---ALTGASAVRVRMHVAAEGLPSQTAFEVLARRRAPD 217

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------------GNFTSPI 284
                 L  +P TGR HQ+R H  H G P+VGD  Y  + +             +     
Sbjct: 218 GAPVALLACRPRTGRQHQIRAHLAHAGLPMVGDKIYGPDEEIFDRFTRRAMTDADLALLR 277

Query: 285 QNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWD 320
             +  LHA  ++LPHP     +++ APLP  +   W+
Sbjct: 278 LPRHALHAWRLELPHPLTRAPVRLEAPLPPDLAAFWE 314


>gi|332361173|gb|EGJ38977.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1056]
          Length = 295

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 69/305 (22%), Positives = 131/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   I+   L KI    G + V+ +       +  G  V I          +K   
Sbjct: 16  FLKRH--EISKGLLAKIKFSGGNILVNHQPQNAIYLLDIGDKVTIDIPSEKGFESLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
                      +      ++YED    V +KPAG++       +  +  F+K++      
Sbjct: 71  -----------AVDKDLSVVYEDKHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G     ++  I
Sbjct: 120 ENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH
Sbjct: 180 IAPIGRNPE-----SIITRRVTEDGKYAHTSYKVIERFGDVY-LVDIHLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   +P  G  ++  +PLP    +
Sbjct: 234 FSHIGFPLLGDDLYGGSLE-----HGIERQALHCHSLKFYNPFSGQEVERASPLPEDFKQ 288

Query: 318 TWDSL 322
             + L
Sbjct: 289 VIEKL 293


>gi|254479301|ref|ZP_05092641.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
 gi|214034749|gb|EEB75483.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
          Length = 285

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 73/317 (23%), Positives = 146/317 (46%), Gaps = 38/317 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VVE   E + L+ + K        + + K    G++RV+ ++      ++ G V+ +  
Sbjct: 3   LVVEKSAEGLTLEGFLKRKGFSTRLIKMYKW--HGEMRVNGEKENVKRVLKEGDVIELSL 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
              + + + +E                +   + YED +I + +KPAG+ V          
Sbjct: 61  FDTSSDILPQE----------------MDLSICYEDDEILIVDKPAGMVVHPTRRYREGT 104

Query: 129 IDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +  + + KG K   R  +RLD+ TSGI++ A+      +L      + + K Y+++
Sbjct: 105 LANGVAYYFEKKGIKTLIRPVNRLDKGTSGIVIFAKEPFMQYYLQIV---KPMSKFYYAI 161

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + +   I   + +KS     ++ + ++  +  + AI+++K +    ++F  L+++
Sbjct: 162 VNGKLEGE-GIIDVPIKRKS-----FMTIEREVSEEGDRAITYYKSLKA-TEEFSLLKIK 214

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  ++G PIVGD  Y         +    +  LHA  +   HP   + +
Sbjct: 215 IATGRTHQIRVHLNYIGHPIVGDDLYGE------PTSYIERPALHAYRVTFFHPLKEKVI 268

Query: 306 QITAPLPAHMVKTWDSL 322
            + APLP  + + ++ L
Sbjct: 269 SVYAPLPEDIKRLFELL 285


>gi|148273032|ref|YP_001222593.1| putative pseudouridine synthase [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147830962|emb|CAN01907.1| putative pseudouridine synthase [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
          Length = 305

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 135/322 (41%), Gaps = 29/322 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  +  R+D          +     ++  +G V  D +    ++R+  G V+ +
Sbjct: 4   RTIPVPDGLDGQRVDAGLARLL-GFSRSFAAEVAEAGGVTQDGREAGKSDRLVGGSVLAV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                    I+    + D  +        +               KP G++     G   
Sbjct: 63  SWQPKQEPTIVP-LAVPDLGIVHDDDDIVVID-------------KPVGVAAHPSVGWTG 108

Query: 127 YHIDGFLKS---WVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +    + + G  ++  + HRLD  TSG++VVA+T  A   L   F  R ++K
Sbjct: 109 PTVLGALAAAGFRLSTSGAEERQGIVHRLDAGTSGLMVVAKTERAYTELKRQFHDREVEK 168

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++V G P      I   + +  H   D+   V  +      +++H++ ++ F ++  
Sbjct: 169 VYHAVVQGHPDPLAGTIDAPIGR--HPRSDWKFAVTAD---GKPSVTHYETLEAF-RRAA 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE+   TGRTHQ+RVH      P VGD  Y A+   +    + ++ +LHA  +++ HP 
Sbjct: 223 LLEVHLETGRTHQIRVHMAAQRHPCVGDAMYGADPTLSAQLDL-HRQWLHAMRLEITHPA 281

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
            G R   ++  PA +    D L
Sbjct: 282 TGDRASFSSSYPADLQHALDVL 303


>gi|323704717|ref|ZP_08116295.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323536179|gb|EGB25952.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 286

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 72/318 (22%), Positives = 135/318 (42%), Gaps = 44/318 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +VV  ++  + L  +        +   ++K    G++ V+ +    N  +  G  V +  
Sbjct: 3   IVVNKEDAYLTLKEFL--LNKGFSPTLIRKYKNRGKMLVNGEISIVNRIVFEGDTVEL-- 58

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                         L    N +   + +   + YED  I V NK AGI V   +G   H 
Sbjct: 59  --------------LLDDENTSVSPEKMDLHICYEDEDILVVNKDAGIVVHPTAG---HP 101

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG L + V    +K       R  +RLD++TSG+++ A+      +L     M++   +Y
Sbjct: 102 DGTLVNGVAWYYEKNNIKAPIRPVNRLDRDTSGLIIFAKNPFMQNYLQIVCPMKK---LY 158

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G    +   I   + +K     + +      +   + A++ F V+   ++K   +
Sbjct: 159 IAIVEGDMDGR-GTIDLPIKRKPGSTIERMV-----DDEGDTAVTDFYVLKR-SEKLSLV 211

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +++  TGRTHQ+RVH  H+G PI+GD  Y ++      +    +  LHA  +    P  G
Sbjct: 212 KLELKTGRTHQIRVHLSHIGHPIIGDTLYGSD------TSYIKRQALHAYRLTFRQPFIG 265

Query: 304 R-LQITAPLPAHMVKTWD 320
           + + + +P+P  M     
Sbjct: 266 KCISLYSPIPDDMKAVLK 283


>gi|210615096|ref|ZP_03290443.1| hypothetical protein CLONEX_02657 [Clostridium nexile DSM 1787]
 gi|210150445|gb|EEA81454.1| hypothetical protein CLONEX_02657 [Clostridium nexile DSM 1787]
          Length = 303

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 134/322 (41%), Gaps = 33/322 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M  +    +     N  L  + K      +   +  + R    + ++K   +  + + + 
Sbjct: 1   MKRIFSYTISAKYNNCTLISFLKE--SGYSSQVITHLKRTENGILLNKTWARVRDILHTD 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++ I               + + + +    +  L   ++YED  + V NKPA + +   
Sbjct: 59  DILTIT--------------LEEKTSSENIVASPLPLHIVYEDEDLMVINKPADMPIHPS 104

Query: 123 SG-IAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            G     +   +  +   KG+    R  +RLD++T+G+L++A+   +A  L++  + R+I
Sbjct: 105 QGNYDNTLANAVAYYYAQKGEPFTYRCINRLDRDTTGLLILAKHMYSASLLSDMVKNRKI 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++  G        I   + +      +     +Q     +YA +H+K + C+   
Sbjct: 165 HREYLAVAEGK-TPSSGIIDAPIGRVDGSTIERQVDYEQ----GDYACTHYKRL-CYKNG 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  + +   TGRTHQ+RVH  H+G P+ GD  Y  N+       +  +  LH+  +   H
Sbjct: 219 YSLVSLTLKTGRTHQIRVHMKHVGHPLPGDFLYNPNYH------VIKRQALHSHCLSFEH 272

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P     L  ++PLP  M   ++
Sbjct: 273 PITKEPLTFSSPLPDDMAIFFN 294


>gi|86150741|ref|ZP_01068957.1| RluA [Campylobacter jejuni subsp. jejuni 260.94]
 gi|205356297|ref|ZP_03223063.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|315124736|ref|YP_004066740.1| RluA [Campylobacter jejuni subsp. jejuni ICDCCJ07001]
 gi|85841911|gb|EAQ59157.1| RluA [Campylobacter jejuni subsp. jejuni 260.94]
 gi|205345902|gb|EDZ32539.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|315018458|gb|ADT66551.1| RluA [Campylobacter jejuni subsp. jejuni ICDCCJ07001]
          Length = 322

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 139/321 (43%), Gaps = 39/321 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +Q  +V+ +    RLD +      + +   +  ++    V+V+ K   K + ++++G ++
Sbjct: 1   MQTFLVDENS---RLDVFLAKKL-NQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDII 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I      L + IK Q  +D  ++           +LYED  + V NKP+ + V G S +
Sbjct: 57  SI--ASLKLCNEIKPQFEVDFDID-----------VLYEDEDLLVLNKPSNLVVHGASSV 103

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W+  K           +  L HRLD++TSG +++A+     Q L+E    
Sbjct: 104 ---KNATLVDWLIEKKYTLSNLGGEIRAGLVHRLDKDTSGSILIAKNNFTHQKLSEQLAD 160

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + +IY +L+    K  K  +  +L++        + + K+N+   N   +   V+   
Sbjct: 161 KSMGRIYLALIDLPLKEDKIIVEKFLMRSPSNAIKKIAIDKENKFSKNAKSAFINVVKT- 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    +  +  TGRTHQ+R H   +   I+GD  Y    K         ++ LHA ++ 
Sbjct: 220 -ENLTLMAAKLFTGRTHQIRAHLASLNRYILGDSLYGYKGK------YDCRIMLHAYFLY 272

Query: 297 LPHPEGGR-LQITAPLPAHMV 316
             HP+    + + APL     
Sbjct: 273 FIHPKTKEQIFVKAPLMEDFK 293


>gi|310659241|ref|YP_003936962.1| ribosomal large subunit pseudouridylate synthase d [Clostridium
           sticklandii DSM 519]
 gi|308826019|emb|CBH22057.1| ribosomal large subunit pseudouridylate synthase D [Clostridium
           sticklandii]
          Length = 301

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 77/299 (25%), Positives = 131/299 (43%), Gaps = 33/299 (11%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+   L  + +  Q+ V+KK  K +  +  G ++ +     A  +               
Sbjct: 32  ISLRLLYSLKKDKQIFVNKKFYKMHEIVNIGDIIEVNLPDEANEY--------------- 76

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVD-SKGQKPRLTH 148
             ++ +   LLYED+ + V  K   I V    G   +   +G +K + D S   K R  +
Sbjct: 77  -DAEDMDIKLLYEDADLMVIEKEPFIVVHPTKGHQRNTLANGLIKLFKDKSINSKIRFVN 135

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD++TSGIL+VA+       LT++  M  ++K Y+++V G        I   + K    
Sbjct: 136 RLDRDTSGILIVAKNSYCHSILTKNDAMHEMEKKYYAVVSGHLDKASGVIDLPIDKSE-- 193

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             D +  +  ++     A++ +KVID   +    LE+   TGRTHQ+RVH  H+G P++G
Sbjct: 194 --DGIRRIVSDK--GQRAVTRYKVIDKL-KYATLLEISLETGRTHQIRVHFSHIGHPLLG 248

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSLGFKY 326
           D  Y  +        + N+  LH   +    P    +  I + LP  M +  + L   Y
Sbjct: 249 DELYGGDMS------LLNRQALHCFELGFYSPRKSEITYIKSELPHDMRELVEKLSLAY 301


>gi|296272938|ref|YP_003655569.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
 gi|296097112|gb|ADG93062.1| pseudouridine synthase, RluA family [Arcobacter nitrofigilis DSM
           7299]
          Length = 320

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 73/327 (22%), Positives = 142/327 (43%), Gaps = 43/327 (13%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQV 64
           Y  ++V+E      RLD++        +   ++++++   V+VD K + K   +++  Q 
Sbjct: 2   YKNFIVLEES----RLDKFLSEKLGE-SRNQIEQLIKKEYVKVDDKIIAKTGYKLKENQE 56

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +            E   ++ S++     D     ++YED  I V NKP  + V   + 
Sbjct: 57  ILV------------ELPEVEESISFDVDFD---VEIIYEDEHILVINKPYNLVVHPAAS 101

Query: 125 IAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +    +  L  W+ +K          ++  + HRLD+ TSG++VVA+T  A   L++   
Sbjct: 102 V---KEPTLVDWLKTKDISLSTISGEERHGIVHRLDKGTSGVMVVAKTNEAHVALSKQLE 158

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            + + + Y +++  +P      I   + +           + +  K A  A +   + + 
Sbjct: 159 DKTMGRYYLAII-DLPLKDNIIIDKPIARNP--NNRLKMGIVEKGKNAKTAFAKIALSE- 214

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             +K+  +  +  TGRTHQ+RVH   +   I+GD+ Y   FKG       N+ YLHA  +
Sbjct: 215 -DEKYELICCKLFTGRTHQIRVHLNSINRHILGDNLYG--FKGELNK--INRFYLHAFNL 269

Query: 296 DLPHPEG-GRLQITAPLPAHMVKTWDS 321
            L HP    ++   A +   + K  + 
Sbjct: 270 YLIHPITNEKMDFKANITNDINKFLNE 296


>gi|222874381|gb|EEF11512.1| predicted protein [Populus trichocarpa]
          Length = 304

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 77/264 (29%), Positives = 132/264 (50%), Gaps = 18/264 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V  + +++     R+D +       +   ++ +ILRSG+VRV+K R+    R++ G +V
Sbjct: 56  QVSMIEIDDSAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLELGDLV 115

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           R+PP+  A            S              +++ED  + V +KPAG++V GGSG+
Sbjct: 116 RVPPIRVAQ----------PSEAAAQAPVPAAHFRIIFEDEHLLVIDKPAGVAVHGGSGV 165

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+ +   ++       +   L HRLD+ETSGIL++A+ R+A  +L E  R  ++ K Y++
Sbjct: 166 AFGVIEQMREARPQ-AKFLELVHRLDRETSGILMLAKKRSALVNLHEQIRENKMDKRYYA 224

Query: 186 LVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            V G   +       +   L K     G+    V+ +      + + F +ID + + +  
Sbjct: 225 CVHGEWASDWGRRRAVREPLHKYLTADGERRVRVQPD---GLASHTVFNLIDRWPE-YAL 280

Query: 243 LEMQPHTGRTHQLRVHALHMGCPI 266
           LE +  TGRTHQ+RVH  H+G PI
Sbjct: 281 LEAELKTGRTHQIRVHLQHLGLPI 304


>gi|45644651|gb|AAS73039.1| predicted pseudouridine synthase D, 23S rRNA-specific [uncultured
           marine gamma proteobacterium EBAC20E09]
          Length = 311

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 67/325 (20%), Positives = 128/325 (39%), Gaps = 36/325 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V  +   MRLD+     +   +   ++K +  G+V ++       + +  G  ++I P+
Sbjct: 6   TVSKEHSKMRLDKVSTIIFEDFSRTQIKKWILEGRVFLNDDIASPRDLVHEGDSIQIDPI 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYH 128
                  + E+  +D               ++YE+    + NK   + +  G+G      
Sbjct: 66  AEEKISWVPEEIDID---------------VIYENDDYLIINKQPNLIMHPGAGCSSGTL 110

Query: 129 IDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L  + + K   +  + HRLD++TSG+++VAR      +  +  + R + K+Y ++V
Sbjct: 111 ANALLHHYPELKNIARAGIVHRLDKDTSGVILVARNDKFRNYFVDLLQKREVTKLYSAIV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQ 246
            G        I         IG D  + VK + +     + +  K+ +     +  L++ 
Sbjct: 171 VG-------TIIGSFKVTDPIGRDKKNRVKMSIRSDGKESETFVKLKESLG-NYSLLDIS 222

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQN------KLYLHARYMDLP 298
             TGRTHQ+RVH      PI+GD+ Y    N     +S + +      +  LHA  +   
Sbjct: 223 IMTGRTHQIRVHLSSKKLPIIGDNTYNPAKNIAKGTSSKLIDIIKQFPRQALHAYQLSFK 282

Query: 299 HPEGGRL-QITAPLPAHMVKTWDSL 322
                        +P  M    D L
Sbjct: 283 DMHTDEFKTFNCDIPDDMKYLIDIL 307


>gi|329955144|ref|ZP_08296101.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
 gi|328526143|gb|EGF53162.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
          Length = 297

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 76/308 (24%), Positives = 125/308 (40%), Gaps = 34/308 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     ++N  ++ G  V+I        
Sbjct: 15  EPMELMEFLAAKMPDASRTKLKSLLSKRIVYVDSVITTQYNFPLKPGMKVQIS------- 67

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
              +E+   + S  L K        ++YED+ I V  K  G+ SV             L 
Sbjct: 68  ---REKGRKEFSNKLLK--------IVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 116

Query: 135 SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G   +  + HRLD++TSG+++ A+       L +++      + Y ++V G  +
Sbjct: 117 EYVQRSGRQHRVYIVHRLDRDTSGLMMFAKDEKTQNTLRDNWHDIVTDRRYVAVVAGEME 176

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           N    + +WL                 + G   AI+H++ I   A  F  +E+   TGR 
Sbjct: 177 NNAGMVRSWLT-----DRKLYVYSNPTDDGGKEAITHYRTIKR-ANGFSLVELNLETGRK 230

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y              +L LHA  +   HP  G  +Q   P 
Sbjct: 231 NQIRVHMQDLGHPIIGDGRYGLEEVNP-----IGRLALHAFKLCFYHPVTGELMQFETPY 285

Query: 312 PAHMVKTW 319
           P    K +
Sbjct: 286 PGDFKKLF 293


>gi|158316843|ref|YP_001509351.1| RluA family pseudouridine synthase [Frankia sp. EAN1pec]
 gi|158112248|gb|ABW14445.1| pseudouridine synthase, RluA family [Frankia sp. EAN1pec]
          Length = 313

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 75/331 (22%), Positives = 139/331 (41%), Gaps = 29/331 (8%)

Query: 1   MSL-MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS   T  + + V +  + +RLD      +  ++      ++  GQV VD +    ++R+
Sbjct: 1   MSTADTDRRSLPVPDGLDGIRLDAAIARMF-GLSRTAAATLVDDGQVSVDGQVRGRSDRV 59

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  + +     AL    +   +  + V            +L++D  I V +KP G++ 
Sbjct: 60  SGGAWLDV-----ALPAPPRPLTVEPTPVG--------GLRILHDDDDIVVVDKPVGVAA 106

Query: 120 QGGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
               G     + G L +           ++  + HRLD  T+G + VA++  A   L  +
Sbjct: 107 HPAPGFTGPTVIGALAAAGYRVSTSGSAERQGVVHRLDVGTTGAMAVAKSERAYTLLKRA 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           FR R ++K Y ++V G P   +  +   + +     G +  V          +++H+   
Sbjct: 167 FREREVEKEYRAVVQGHPDPLRGTVDAPIDRHPRRPGLFAVVA-----DGKPSVTHYDTE 221

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           + F +    L ++  TGRTHQ+RVH   +  P VGD  Y A+        +  + +LHA 
Sbjct: 222 EAF-RAASLLSVRLETGRTHQIRVHMAALRHPCVGDLAYGADPTLAQRLGL-TRQWLHAA 279

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            +   HP  G  ++ T+P P  + +    L 
Sbjct: 280 RLAFAHPADGTWVEFTSPDPDDLAEAVKRLR 310


>gi|311032387|ref|ZP_07710477.1| pseudouridine synthase, RluA family protein [Bacillus sp. m3-13]
          Length = 307

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 75/297 (25%), Positives = 131/297 (44%), Gaps = 34/297 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + K+    I   +L ++  S +V V+ +   + + ++ G  V +P +   +  I  E  I
Sbjct: 21  YLKDVI-GIPKGHLHELRMSKKVMVNGENPNWTHLLKEGDRVSVPILPEDITPIATEMDI 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-DGFLKSWVDSKGQ 142
                            ++YE   + V NK AG+     S   +      +  + ++ G 
Sbjct: 80  ----------------KIIYETEHLLVINKEAGMDTHPSSDQDFRSLSNGVAHYFNNNGI 123

Query: 143 --KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
             K R  HRLDQ+TSG ++ A+   +   L      R++++ Y +LV GI K  +  I  
Sbjct: 124 SSKVRHIHRLDQDTSGAILFAKHAISGAILDRMLEERKVKRTYLALVEGIVKTPEGTIDK 183

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHA 259
            + K  H          +       AI+H+KV+  +  ++   +E+   TGRTHQ+RVH 
Sbjct: 184 PIGKDRHHASRR-----RVSPNGQKAITHYKVVKTYPKEQLTLVELTLDTGRTHQIRVHM 238

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
             +G PI GD  Y +  K        ++  LHA  + +PHP  G +  + AP+P + 
Sbjct: 239 SSIGHPIYGDKLYGSKNK-------HHRHSLHAWKLTVPHPFNGEIVTVHAPVPRNF 288


>gi|15230381|ref|NP_188575.1| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|75274073|sp|Q9LT72|PUS4_ARATH RecName: Full=RNA pseudourine synthase 4, mitochondrial; AltName:
           Full=RNA pseudouridylate synthase 4; AltName:
           Full=RNA-uridine isomerase 4; Flags: Precursor
 gi|11994467|dbj|BAB02469.1| unnamed protein product [Arabidopsis thaliana]
 gi|110737723|dbj|BAF00800.1| hypothetical protein [Arabidopsis thaliana]
 gi|134031916|gb|ABO45695.1| At3g19440 [Arabidopsis thaliana]
 gi|332642719|gb|AEE76240.1| RNA pseudourine synthase 4 [Arabidopsis thaliana]
          Length = 477

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 110/375 (29%), Positives = 164/375 (43%), Gaps = 76/375 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVR------VDK--------KRVKFNNRIQSGQVVRIP 68
           RW     P +    +QK+ R  QVR      VD         KRV     +  G  + +P
Sbjct: 94  RWILRCRPDLPRTLVQKLFRLRQVRREMSMSVDGDELQRSQLKRVAAKESLNVGDRIYLP 153

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             ++         K  +S     +   F+ S++LY+D  I V NKP G++VQGGSGI   
Sbjct: 154 LSVDNDTPQTPPAKK-ESFQCSDEERKFVCSLVLYKDPAIIVLNKPHGLAVQGGSGIKTS 212

Query: 129 IDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI-------- 179
           ID    S +   K + PRL HRLD++ SG+LV+ART+ AA  L   FR +          
Sbjct: 213 IDELAASCLKFDKSESPRLVHRLDRDCSGLLVLARTQTAATVLHSIFREKTTGASAYGVK 272

Query: 180 ------QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG---ANYAISHF 230
                 ++ Y +LV G P  ++  I+  L K     G    +   +        +AI+ +
Sbjct: 273 KNVKSLKRKYMALVIGCPPRQRGQISAPLRKVVVDDGKSERITVNDNGELVSTQHAITEY 332

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCA--------------- 274
           +VI+     + WLE++P TGR HQLRVH    +G PIVGD+KY                 
Sbjct: 333 RVIESSPHGYTWLELRPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQAHKAREPFVSSENN 392

Query: 275 -----------NFKGNFTSPIQNKLYLHARYMDLPHPEG--GRLQ--------------I 307
                      +  G   S  Q  L+LH++ +DLP+      ++Q               
Sbjct: 393 PTKQSSSPFGLDLDGGDVSSKQPHLHLHSKQIDLPNISQLLEKMQVSSDSDISDLDSLKF 452

Query: 308 TAPLPAHMVKTWDSL 322
            APLP+HM  +++ L
Sbjct: 453 DAPLPSHMQLSFNLL 467


>gi|9971939|gb|AAG10501.1|AF279106_63 predicted ribosomal large subunit pseudouridine synthase D
           [uncultured marine gamma proteobacterium EBAC31A08]
          Length = 310

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 74/320 (23%), Positives = 134/320 (41%), Gaps = 42/320 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ND  +MRLD+     +   +   ++K +  G+V ++ +  +  +++     + + P  
Sbjct: 6   VPNDLSSMRLDKATAEMFTDYSRTQIKKWIEEGRVLINGEVSQPRDKVYENDQIELSPK- 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +EQK+       +  +  +   + +E+    + NKPAG+ +  GSG     DG
Sbjct: 65  -------EEQKV-------SWEAQDIDFEIHFENEDFIIINKPAGLIMHPGSGC---YDG 107

Query: 132 FLKSWVDSKGQKP------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            L + +  K  +        + HRLD++TSGIL+VAR  +         + RR+ K Y S
Sbjct: 108 TLANGLIYKFPELINIPRSGIVHRLDKDTSGILLVARNESFRNFFINEMQERRVVKKYTS 167

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           +V G               +  IG D  +  K    +    A++  K+ +     +  L+
Sbjct: 168 IVIGSTLGSFSI-------EEPIGRDKNNRTKMAIREDGKDALTFVKLKENIG-NYSVLD 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMD 296
           ++  TGRTHQ+RVH      PI+GD  Y  +      +P +         +  LHA ++ 
Sbjct: 220 IRIETGRTHQIRVHLSSKKLPIIGDKTYDPSRSIARDTPEELINIIRGFPRQALHATHLS 279

Query: 297 LPHPEGGRL-QITAPLPAHM 315
               +   +     P P  M
Sbjct: 280 FNDQKTNNIFSFDIPTPNDM 299


>gi|325289846|ref|YP_004266027.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324965247|gb|ADY56026.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 299

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 85/314 (27%), Positives = 133/314 (42%), Gaps = 38/314 (12%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             ++EN +L+   +  + H +   +QK+     V +D K    N R +SGQ + I     
Sbjct: 14  TENDENRKLEEILRRQF-HFSRKLIQKLKTGEHVWLDGKFSYLNIRGRSGQTLTIDFAEE 72

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
               +  E   LD               LL+ED  +   NKPAG  V   S    +  G 
Sbjct: 73  EDVSVSPEDADLD---------------LLFEDKILLAVNKPAGQVVHPTS---VYRSGT 114

Query: 133 LKSWVDSKGQKP------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           L + V    +K       R   R+D+ TSGI+++A+ R A Q L    +   + K Y  L
Sbjct: 115 LANAVTGYWKKNGLSLPFRPISRIDRNTSGIVMIAKNRYAHQQLAWMSQHHLVGKKYLGL 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K+    IA  L            +V++       +++ +KV++ +   +  LE  
Sbjct: 175 VHGHLKSSAGEIALPLRLAPD-----SRIVRETHPDGQQSLTLYKVLEEYP-YYSLLEFT 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+R H   +G  +VGD  Y         + +  +  LHA +    HP  G+ +
Sbjct: 229 LVTGRTHQIRAHCQAIGHSLVGDDLYGGQ------TELIARQALHAFHYSFIHPISGQPI 282

Query: 306 QITAPLPAHMVKTW 319
           +I APLPA M    
Sbjct: 283 KIEAPLPADMASLM 296


>gi|159487279|ref|XP_001701661.1| RNA pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158280880|gb|EDP06636.1| RNA pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 338

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 76/354 (21%), Positives = 129/354 (36%), Gaps = 76/354 (21%)

Query: 32  INFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           ++   +Q  + +G V V+ + V K   ++++G  V    +       I E   LD     
Sbjct: 1   VSRAKVQASIAAGLVAVNGRPVSKAGQQLRAGDTVTASLLPPPPMQAIPEPIPLD----- 55

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQ--GGSGIAYHIDGFLKSW------------ 136
                     + YED  + V NKPAG+ V    G      ++  L               
Sbjct: 56  ----------IKYEDEHLLVINKPAGMVVHVAPGHHTGTLVNALLHHCSLPALDLAPTEP 105

Query: 137 ---------------------------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
                                        S+  +P + HR+D+ TSG++VVA+T  A   
Sbjct: 106 GGDEEEEESAQLGSSRLLSSSSASSSSSGSRILRPGIVHRIDKGTSGLIVVAKTETALTR 165

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           L   F+ R + ++Y S+  G P ++   +   + +        +            A S 
Sbjct: 166 LQAQFKARTVDRLYLSMTVGCPSSRSGRVETNISRDPG-DRKRMAAAPYGGTRGRTAASS 224

Query: 230 FKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--- 285
           ++V++  A   C  ++ +  TGRTHQ+RVHA HMG P++ D  Y        ++  +   
Sbjct: 225 YQVLEPLAGGGCALVQWKLDTGRTHQIRVHAKHMGHPLLADDTYGGGGPAALSAVAKGGA 284

Query: 286 -------------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
                         +  LHA  +   HP  G RL    P P       + L  +
Sbjct: 285 RSVEEVKACLERLGRPALHALTLGFSHPVSGKRLSFEQPPPEDFASALEQLRGR 338


>gi|310829101|ref|YP_003961458.1| RluA family pseudouridine synthase [Eubacterium limosum KIST612]
 gi|308740835|gb|ADO38495.1| RluA family pseudouridine synthase [Eubacterium limosum KIST612]
          Length = 304

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 139/307 (45%), Gaps = 35/307 (11%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
             NHY + +   L+++ R G + ++ +     + +Q G  V I       +    E    
Sbjct: 27  LTNHYDYSSR-LLRQLKRDGSITLNGRDCWLTDPVQRGDQVVITFPEERFDIEAVEG--- 82

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-- 142
                           ++YED ++ V NK A            H    L + V    +  
Sbjct: 83  -------------PLDIVYEDDEVLVVNKDADCVTHPTKS---HQLDTLANHVAWYWEER 126

Query: 143 ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K R  +RLD++T+G++V+A+ +    ++    +   ++K Y + V  +P+ K+ CI
Sbjct: 127 GTPGKIRFVNRLDRDTTGLVVIAKNKYVHHYIQSRMKTDAVKKTYIAFVNNVPEEKEGCI 186

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + + S    + + +     +    +++HF+V++ + +    +E+   TGRTHQ+RVH
Sbjct: 187 RVPIGRPSEDSLERIVM-----EDGKESVTHFRVLESY-RNAAMVELVLETGRTHQIRVH 240

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
             ++GCPI+GD  Y  +   ++      +  LHA  ++L  P+ G L+++A L   +V  
Sbjct: 241 LKYIGCPIIGDSLYNHDGNPSY---GMARQALHAAKLNLTLPKSGELELSAGLTEDLVTL 297

Query: 319 WDSLGFK 325
            ++L  +
Sbjct: 298 QETLRKE 304


>gi|153003089|ref|YP_001377414.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152026662|gb|ABS24430.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 298

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 91/312 (29%), Positives = 144/312 (46%), Gaps = 29/312 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVRIP 68
           +VV + +   RLDR+       ++    ++ L SG V +D +R K + R+ Q+GQ V + 
Sbjct: 6   LVVASADGGERLDRFIAAR-GGVSRGAARRALDSGGVFLDGRRCKVSGRLLQAGQKVVVN 64

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                         + ++       S   ++ LLY D  +   +KPAG+  Q        
Sbjct: 65  --------------LEEAGRAAPARSALERARLLYADQDLVAVDKPAGVPSQP---TLTT 107

Query: 129 IDGFLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             G L   V D  G    L HRLD+ETSG+ V+ART AAA  L E+FR    +K Y +L 
Sbjct: 108 DRGTLPELVSDLLGAPVTLVHRLDRETSGVTVLARTAAAAAALAEAFRTGTPEKTYLALC 167

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
              P      I   L K     G     +++ +   + A + ++ +         +E +P
Sbjct: 168 ARPPAPPDGRIDAPLGKDPARAG-----LRRVDPRGDAAATRYRTL-RAGPLAALVEARP 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            TGRTHQ+RVH  H+G P++GD +Y    +         ++ LHAR +++ HP  G RL 
Sbjct: 222 ETGRTHQIRVHLAHLGAPLLGDPRYGGPRR--VGEVAIPRVMLHARRLEIDHPATGARLL 279

Query: 307 ITAPLPAHMVKT 318
           + AP+P  +   
Sbjct: 280 LEAPVPEDLRAA 291


>gi|27904851|ref|NP_777977.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
 gi|34395768|sp|Q89AD9|RLUD_BUCBP RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|27904249|gb|AAO27082.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
          Length = 317

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 71/318 (22%), Positives = 132/318 (41%), Gaps = 39/318 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD+   + +   +   L++ + S  V V+ + + + + ++    ++ I     A N   
Sbjct: 20  RLDQVLASLFKKHSRTILKRHILSKDVCVNGRILDQPDAKVLYKDIISINLKFKAKNDYQ 79

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   L+               ++YED  I V NK     V  G+G        L + + 
Sbjct: 80  AENIFLN---------------VIYEDDDILVINKQDNFVVHPGAG--NTSGTLLNALLH 122

Query: 139 SKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                    +  + HRLD++T+G++V+A+   +   L +  + +++ + Y ++V+G    
Sbjct: 123 RDSTFFNIPRAGIVHRLDKDTTGLMVIAKNNLSYMALIDQIKCKKVIREYQAIVYGK--- 179

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               I+   + KS I            K    AI+H++++  F      L++   TGRTH
Sbjct: 180 ---VISGGTIVKSIIRNPIKRTTMIVNKCGKRAITHYRILKRFTH-HTHLKIILETGRTH 235

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGGR- 304
           Q+R H L++  P+VGD  Y   FK      +          +  LHA  + L HP     
Sbjct: 236 QIRTHMLYINFPLVGDKTYGNKFKFYKNISLTLLEQVKKFPRQALHASRLCLYHPVTKHL 295

Query: 305 LQITAPLPAHMVKTWDSL 322
           ++  + LP  M+     L
Sbjct: 296 MEWNSTLPRDMLNLIALL 313


>gi|296332584|ref|ZP_06875045.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305673865|ref|YP_003865537.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
 gi|296150502|gb|EFG91390.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305412109|gb|ADM37228.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
          Length = 299

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 39/317 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   E  M L  +       I+   L  I    G + ++ + V     ++ G ++ +   
Sbjct: 10  ITCAENGMTLKEYAAEL--GISKRLLTDIKFGGGDLLINGEHVTVKYVLREGDLLVV--- 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                      K  +  V+ T   + +   +LYED  + V NK   +S         H  
Sbjct: 65  -----------KFPEEQVSETLLVEPVPLDILYEDEHVLVINKQPYVSSIPSR---EHPS 110

Query: 131 GFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G + + +    QK        L  RLD++TSG+++VA+ R A   L+ + +   +++ Y 
Sbjct: 111 GSIANGIIHHYQKNGVRATVHLVTRLDRDTSGVMLVAKHRFAHSILSSAQKNGLVKRRYA 170

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G     +  I   + +          + +        A++HF V  C       + 
Sbjct: 171 AVVHGRLTQAEGTIDAPIGRHPD-----SIIERTVTPDGQKAVTHFYV-TCANDDMTSVT 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  ++G P+ GD  Y    +         +  LH+  +   HP    
Sbjct: 225 LQLETGRTHQIRVHMSYLGHPLCGDTLYGGTRRE------IGRQALHSEQLSFIHPLTQE 278

Query: 304 RLQITAPLPAHMVKTWD 320
           ++   A LP  M +   
Sbjct: 279 KMTFHASLPQDMKELIK 295


>gi|297588316|ref|ZP_06946959.1| RluA family pseudouridine synthase [Finegoldia magna ATCC 53516]
 gi|297573689|gb|EFH92410.1| RluA family pseudouridine synthase [Finegoldia magna ATCC 53516]
          Length = 307

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 63/330 (19%), Positives = 133/330 (40%), Gaps = 41/330 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   ++++  +N RLD +  N    ++   +QK++   +V V++K  K N ++     ++
Sbjct: 2   MYEFLIDDSNQNTRLDVFLANEV-ELSRSEIQKLIDEKKVLVNEKTQKKNYKLNLNDKIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                          +  D ++   +H       ++YED  + + NK   + V     I 
Sbjct: 61  FDY------------EKPDKTIKPQQH----DLDIVYEDDYLAIINKDKNVIVHPTETI- 103

Query: 127 YHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 L +++ S  +            + HRLD++T+G++++A+       L E  +  
Sbjct: 104 --YSDTLVNYLMSNFENLSDVDGDYRRGIVHRLDKDTTGLIIIAKDNNTHLKLKEIIKNH 161

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I K Y  +V G   ++   I  ++ +        +            +IS+++ +D   
Sbjct: 162 EITKTYLCIVHGKI-DECGTIEEYMTRNPKDRKKMMI-----SDEGKLSISNYERLDYN- 214

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +++Q  TGRTHQ+RVH  ++  PI+GD  Y    +      + +   LHA  +  
Sbjct: 215 DDYSLVKVQIKTGRTHQIRVHMNYIHHPILGDKLYGLKKEKI----LFDSQVLHAYNLQF 270

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            HP+    + +   L    +         Y
Sbjct: 271 IHPQTHENINVIGNLKQDFITAIKKTNLDY 300


>gi|57167607|ref|ZP_00366747.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter coli RM2228]
 gi|305433113|ref|ZP_07402269.1| RluA family pseudouridine synthase [Campylobacter coli JV20]
 gi|57020729|gb|EAL57393.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter coli RM2228]
 gi|304443814|gb|EFM36471.1| RluA family pseudouridine synthase [Campylobacter coli JV20]
          Length = 321

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 135/326 (41%), Gaps = 40/326 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +Q  +V+      RLD +   +    +   +  ++    V V+ K   K + +++ G  +
Sbjct: 1   MQTFLVDE---PSRLDIFLAKNLQQ-SRNQIASMIEKNCVWVNDKIQNKNSFKLKVGDKL 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +         +++E K         K        +LYED  + V NKP+ + V G   +
Sbjct: 57  VLNLP------LVEEAKP--------KFDIDFDIEILYEDEDLLVLNKPSNLVVHGAKSV 102

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                  L  W+  K           +  L HRLD+ETSG +++A+     Q L+E    
Sbjct: 103 R---SATLVDWLIEKQYTLSTLGGEVRAGLVHRLDKETSGAILIAKNNFTHQKLSEQLSD 159

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + +IY +L+    K  K  I   L++ S      + V     KG+  A S F V    
Sbjct: 160 KTMGRIYLALIDLPLKEDKIIIDKALIRSSANAIKKI-VTNSFVKGSKEAKSAF-VNLAK 217

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           +++   +  +  TGRTHQ+R H   +   I+GD  Y    K       + ++ LHA ++ 
Sbjct: 218 SEEVSLIGAKLFTGRTHQIRAHLASINRHILGDELYGYRGK------YECRIMLHAYFLY 271

Query: 297 LPHPE-GGRLQITAPLPAHMVKTWDS 321
             HP  G ++ I APL     +  + 
Sbjct: 272 FIHPRNGEKIFIQAPLMDDFKQILEK 297


>gi|71651380|ref|XP_814369.1| pseudouridylate synthase-like protein [Trypanosoma cruzi strain CL
           Brener]
 gi|70879335|gb|EAN92518.1| pseudouridylate synthase-like protein, putative [Trypanosoma cruzi]
          Length = 448

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 88/350 (25%), Positives = 155/350 (44%), Gaps = 23/350 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV---RVDKKR--VKFNNRIQ 60
            VQY V+  D    R+D +   H+P  ++  ++ +++ G +   R + K+   +  +R++
Sbjct: 96  EVQYHVITQDWFGQRVDTFLTQHHPEWSYETMKTLVQQGHIYRYRKNGKKRFTRITDRLE 155

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLT------KHSDFLKSILLYEDSKIYVFNKP 114
             +++ +P  +     +     +L  S   T      +  +   +++L+++  + V NKP
Sbjct: 156 FDELLVVPTPVFYERQLAPPTGVLQESNKPTHFKLSSQVREMAHNMVLFKNEHVIVINKP 215

Query: 115 AGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            G+ +   S     +I   L +W  +   KP + H LD+ETSG +V+AR++ A + L   
Sbjct: 216 HGVPMMPTSDPQEMNIAAMLSAWKYTNSTKPIVCHNLDKETSGCVVLARSKNAHRMLARM 275

Query: 174 FRMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           F  R +   +YW    G P      I           GD +       K +   I+ F V
Sbjct: 276 FVKRVVPNSVYWGFCVGKPSVNFGRIRMHFEMTRGTKGDIIVARPSPTKTSKVGIAEFVV 335

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK-----GNFTSPIQN 286
                +   ++   P T R HQ R+ A H +  P++GD KY            F  P   
Sbjct: 336 NASALEFGSFISFYPLTTRRHQERIMAAHALRSPLLGDAKYGGESAFPSSMSLFWDPEDK 395

Query: 287 --KLYLHARYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
              L+LH R + LP+    G  + +TAPLP HM KT+  LG+  D +  +
Sbjct: 396 GLPLHLHHRKIQLPYKNSTGEFVCVTAPLPIHMEKTFKKLGWPCDVDDPL 445


>gi|228920025|ref|ZP_04083376.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar huazhongensis BGSC 4BD1]
 gi|228839650|gb|EEM84940.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar huazhongensis BGSC 4BD1]
          Length = 292

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 64/310 (20%), Positives = 129/310 (41%), Gaps = 33/310 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           EE   +  + K     I+   L  I    G + V+ +     +++++ + +RI   +   
Sbjct: 9   EEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLRASEELRIFFPVEER 66

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGF 132
           +  +               ++ +   ++YED  + + NK A +S             +  
Sbjct: 67  SEGM--------------MAEDIPLYIVYEDDAVLIINKEANMSTIPSREHPTGSVANAL 112

Query: 133 LKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V G  
Sbjct: 113 LSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGKI 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             ++  I   + +KS    +         +    A++HFKVID    K   + ++  TGR
Sbjct: 173 VEREGMIDALIGRKSDSIIERTVC-----EDGQRAVTHFKVIDSTYHK-THVALELETGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
           THQ+RVH  H+G P++GD  Y              +  LH++ +   HP     +  T  
Sbjct: 227 THQIRVHMAHIGHPLLGDSLYGGRRDE------MKRQALHSKSLTFYHPILEKEMSFTIK 280

Query: 311 LPAHMVKTWD 320
           LP+ M +   
Sbjct: 281 LPSDMQEVLR 290


>gi|319902371|ref|YP_004162099.1| pseudouridine synthase, RluA family [Bacteroides helcogenes P
           36-108]
 gi|319417402|gb|ADV44513.1| pseudouridine synthase, RluA family [Bacteroides helcogenes P
           36-108]
          Length = 309

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 76/308 (24%), Positives = 130/308 (42%), Gaps = 34/308 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     ++N  ++ G  V+I        
Sbjct: 21  EPMELMEFLTAKMPDASRTKLKSLLSKRIVYVDSVITTQYNFPLKPGMKVQIS------- 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
              +E+   + +  L K        ++YED+ I V  K  G+ SV             L 
Sbjct: 74  ---REKGRKEFNHKLIK--------IVYEDAYIIVIEKMQGLLSVNTERQKERTAYTILN 122

Query: 135 SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G   +    HRLD++TSG+++ A+       L +++      + Y ++V G  +
Sbjct: 123 EYVQRSGRQHRVYTVHRLDRDTSGLMMFAKDEKTQNTLRDNWHDIVFDRRYVAVVSGEME 182

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                +++WL  ++     YV+    N+ G   AI+H++ I   A  +  +E+   TGR 
Sbjct: 183 KNAGVVSSWLTDRTL----YVYSSPTND-GGKEAITHYRTIKR-ANGYSLMELNLETGRK 236

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y              +L LHA  +   HP  G  +    P 
Sbjct: 237 NQIRVHMQDLGHPIIGDGRYGLEDINP-----IGRLALHAFKLCFYHPVTGEKMSFETPY 291

Query: 312 PAHMVKTW 319
           PA   K +
Sbjct: 292 PADFKKLF 299


>gi|289434238|ref|YP_003464110.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
 gi|289170482|emb|CBH27022.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
          Length = 296

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 70/317 (22%), Positives = 138/317 (43%), Gaps = 40/317 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V  ++  + L  + ++   HI+   L   K    G++ V+         +Q+G  VR+  
Sbjct: 7   VNKEDSGLLLRTFLRS--KHISKQLLTAVKFSVDGKIEVNGTEQNVLYEVQTGDEVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTDLEIVFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 SGSVANFVKGHYEAQGLTSAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQQGLLKRSY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            + V G    +   I   + +K+        + +       YA ++++V+  + Q F  +
Sbjct: 168 QAFVSGELVKQVGSIEAPIGRKA-----VSIMERVVTPEGKYAKTNYQVLARY-QAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 ALQLETGRTHQIRVHLSYIGHPLIGDDMYGGD------TDLLKRQALHSCHLHLIHPLTE 275

Query: 304 R-LQITAPLPAHMVKTW 319
             L    PLP  M +  
Sbjct: 276 EYLAFDLPLPYDMEEII 292


>gi|228899885|ref|ZP_04064130.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis IBL 4222]
 gi|228964251|ref|ZP_04125371.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar sotto str. T04001]
 gi|228795446|gb|EEM42933.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar sotto str. T04001]
 gi|228859789|gb|EEN04204.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis IBL 4222]
          Length = 292

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 61/302 (20%), Positives = 127/302 (42%), Gaps = 33/302 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L  I    G + V+ +     +++++ + +RI   +   +  +    
Sbjct: 17  FLKT--KGISKAALTDIKFHGGAIEVNGQHASVRHQLRASEELRIFFPVEERSEGM---- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSW-VDS 139
                      ++ +   ++YED  + + NK A +S             +  L  +    
Sbjct: 71  ----------IAEDIPLCIVYEDDAVLIINKEANMSTIPSREHPTGSVANALLSHYDKQH 120

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                 +  RLD++TSG++++A+ R     L++  + + +++ Y ++V G    ++  I 
Sbjct: 121 LASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGMID 180

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + +KS    +         +    A++HFKVID    K   + ++  TGRTHQ+RVH 
Sbjct: 181 APIGRKSDSIIERTVC-----EDGQRAVTHFKVIDSTYHK-THVALELETGRTHQIRVHM 234

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKT 318
            H+G P++GD+ Y              +  LH++ +   HP     +  T  +P+ M + 
Sbjct: 235 AHIGHPLLGDNLYGGRRDE------MKRQALHSKSLTFYHPILEKEMSFTIKIPSDMQEL 288

Query: 319 WD 320
             
Sbjct: 289 LR 290


>gi|294806510|ref|ZP_06765351.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|294446373|gb|EFG14999.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
          Length = 281

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 75/301 (24%), Positives = 130/301 (43%), Gaps = 33/301 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +     P  +   L+ +L    V VD     +FN  +++G  V+I               
Sbjct: 6   FLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVKI--------------- 50

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKG 141
              S     K  +     ++YED+ I V  K  G+ SV             L  +V   G
Sbjct: 51  ---SKQKGKKEFNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSG 107

Query: 142 Q--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +  +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +   + + 
Sbjct: 108 RQFRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVEGSMEKDYDTVV 167

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WL  K+     YV   + ++ G+  +I+H+K I   A  +  LE+   TGR +Q+RVH 
Sbjct: 168 SWLTDKTL----YVSSSEYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRKNQIRVHM 221

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             +G PI+GD +Y      N       +L LHA  +   HP  G  ++   P PA   K 
Sbjct: 222 QDLGHPIIGDGRYGREDSPN----PIGRLALHAFKLCFYHPVTGDLMEFETPYPAEFKKL 277

Query: 319 W 319
           +
Sbjct: 278 F 278


>gi|255556673|ref|XP_002519370.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223541437|gb|EEF42987.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 399

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 75/300 (25%), Positives = 122/300 (40%), Gaps = 49/300 (16%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           VV      +RLD W  +    I+   +Q  ++SG V V+ + V K ++ ++ G  V    
Sbjct: 64  VVHAKSVKLRLDSWISSRISGISRARVQSSIKSGLVSVNGRVVDKVSHNVKFGDKVTCT- 122

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                         +     L    + +   ++YED  + V NKP  + V    G     
Sbjct: 123 --------------ISELQPLRAEPEDMPLDIVYEDEHLLVVNKPPHMVVHPAPGNPTGT 168

Query: 128 HIDGFLKSW-----------------------------VDSKGQKPRLTHRLDQETSGIL 158
            ++G L                                      +P + HRLD+ TSG+L
Sbjct: 169 LVNGILHHCNLPTVAISSQEVLSDAEDRSDDDERSYSSSCESSIRPGIVHRLDKGTSGLL 228

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA+   A  HL+E F+   IQ++Y SL  G+P      I   + +  +       +   
Sbjct: 229 VVAKDEHAHAHLSEQFKQHTIQRVYISLTSGVPSALTGRIDIPIGRDVNNRIRMTAIPGP 288

Query: 219 NEKG-ANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            ++G A +A S FKV++         +E +  TGRTHQ+R HA ++G P++GD  Y    
Sbjct: 289 IKQGRARHAASRFKVVETLAGGGSALVEWRLETGRTHQIRAHAKYIGIPLLGDEVYGGTR 348


>gi|223932325|ref|ZP_03624328.1| pseudouridine synthase, RluA family [Streptococcus suis 89/1591]
 gi|302023845|ref|ZP_07249056.1| RNA pseudouridylate synthase [Streptococcus suis 05HAS68]
 gi|330832880|ref|YP_004401705.1| RluA family pseudouridine synthase [Streptococcus suis ST3]
 gi|223899006|gb|EEF65364.1| pseudouridine synthase, RluA family [Streptococcus suis 89/1591]
 gi|329307103|gb|AEB81519.1| pseudouridine synthase, RluA family [Streptococcus suis ST3]
          Length = 297

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 66/306 (21%), Positives = 128/306 (41%), Gaps = 34/306 (11%)

Query: 24  WFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           + K H   ++   L K ++   G + V+         +  G  V I              
Sbjct: 16  FLKKH--GVSKGLLAK-IKYTGGNIWVNDIEQNATYLLDIGDRVTI-------------D 59

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---D 138
              +  +  +    F    ++YED      NKP G +    +  +  I  F+K ++   +
Sbjct: 60  IPAEEDLTGSLKPIFFPLDIVYEDDHFLSINKPVGYASIPSALHSSTIANFVKGYLIEQN 119

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKEC 197
            + ++  +  RLD++TSG+++ A+   A   L +  + + I K Y++LV G  +  +   
Sbjct: 120 YENKQVHIVTRLDRDTSGVMLFAKHGYAHARLDKQLQAKLIHKRYYALVKGNGQLEETGD 179

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +      +   + +   K   YA + ++V+  +      +++Q HTGRTHQ+RV
Sbjct: 180 IIAPIGRP-----EDSIITRCVTKNGKYAHTSYRVVQSWGDIH-LVDIQLHTGRTHQIRV 233

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
           H  H+G P++GD  Y  + +         +  LH   +   +P    R+ + APLP    
Sbjct: 234 HFSHIGFPLLGDDMYGGSLEC-----GIERQALHCHNLAFDNPFSAERIDLEAPLPEDFQ 288

Query: 317 KTWDSL 322
              + L
Sbjct: 289 AVINQL 294


>gi|237719529|ref|ZP_04550010.1| RNA pseudouridylate synthase [Bacteroides sp. 2_2_4]
 gi|229451389|gb|EEO57180.1| RNA pseudouridylate synthase [Bacteroides sp. 2_2_4]
          Length = 306

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 78/308 (25%), Positives = 133/308 (43%), Gaps = 33/308 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  +++G  V+I        
Sbjct: 24  EPMELMEFLATKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVQI-------- 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     S     K  +     ++YED+ I V  K  G+ SV             L 
Sbjct: 76  ----------SKQKGKKEFNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 125

Query: 135 SWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G+  +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 126 EYVQRSGRQFRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSME 185

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + +WL  K+     YV   + ++ G+  +I+H+K I   A  +  LE+   TGR 
Sbjct: 186 KDYDTVVSWLTDKTL----YVSSSEYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRK 239

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y      N       +L LHA  +   HP  G  ++   P 
Sbjct: 240 NQIRVHMQDLGHPIIGDGRYGREDAPN----PIGRLALHAFKLCFYHPVTGDLMEFETPY 295

Query: 312 PAHMVKTW 319
           PA   K +
Sbjct: 296 PAEFKKLF 303


>gi|108758129|ref|YP_629362.1| RNA pseudouridine synthase family protein [Myxococcus xanthus DK
           1622]
 gi|108462009|gb|ABF87194.1| RNA pseudouridine synthase family protein [Myxococcus xanthus DK
           1622]
          Length = 329

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 132/327 (40%), Gaps = 41/327 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VVE +    RLD +       +    LQ ++  G V  +++R+K +  +  G   RI   
Sbjct: 19  VVEPNYAGWRLDEYLGEKLRRMTRERLQGVILRG-VICEERRLKPSTPVYPGLAFRIRRR 77

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            +       E                    ++++D  + V +KPAG+ +   +   YH  
Sbjct: 78  ASEEPDTPTE------------------LPVVFQDDWLLVLDKPAGLPIHPTA--RYHKG 117

Query: 131 GFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             +    +  G++     HRLD+ETSG++V  RT  + + L   F  R + K Y +L  G
Sbjct: 118 TLVTLLRERFGERFAEPAHRLDRETSGLVVCGRTTESCRVLGRLFVSRDVHKEYLALCEG 177

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQ 246
            P      +   + + + +       V+ +      + + F+V+  F +    F  L   
Sbjct: 178 HPPEDTFTVDAPIAEGTELIR---IAVRIDPVEGKESRTRFQVLQRFTRDGAPFALLRCF 234

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANF------------KGNFTSPIQNKLYLHARY 294
           P TGR HQ+R+H  H G P+VGD  Y  +                +      +  LHA  
Sbjct: 235 PETGRQHQIRIHLCHAGFPLVGDKMYGPDPGYFDRFSKHCLEPEAWPRLRLPRQALHAAR 294

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWD 320
           +  PHP  G+ +   APLPA +    +
Sbjct: 295 IAFPHPGSGQAVAFEAPLPADLTDFIE 321


>gi|126727903|ref|ZP_01743731.1| putative Pseudouridine synthase, Rlu [Rhodobacterales bacterium
           HTCC2150]
 gi|126702844|gb|EBA01949.1| putative Pseudouridine synthase, Rlu [Rhodobacterales bacterium
           HTCC2150]
          Length = 308

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 125/316 (39%), Gaps = 47/316 (14%)

Query: 39  KILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           K+L  G +    + +     ++Q G    I                ++ SV +    + +
Sbjct: 2   KLLAEGAITFKGEVISDPRAKVQEGDEFTIT---------------VEQSVEVDVLPEDI 46

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKG-----QKPRLTHRL 150
              +L+ED  + V NKP G+ V    G      ++  L  +  +       ++P + HR+
Sbjct: 47  PLEILFEDDDLIVVNKPVGMVVHPAPGSPSGTLVNALLHHFGGNLSGIGGEKRPGIVHRI 106

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA----------N 200
           D++TSG+LVVA++ AA   L   F    + + Y ++ +G+P N    +           N
Sbjct: 107 DKDTSGVLVVAKSDAAHHGLAAQFEAHTVNRKYHAICYGVPDNADPRLKGVRGVSFEGSN 166

Query: 201 WLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLR 256
            +   + +        +Q+       +A++  +++  + +    C +E    TGRTHQ+R
Sbjct: 167 VVKINTQLARHRTDRQRQSVYFNQGRHAVTRARLVQRYGKPSVACLVECWLETGRTHQIR 226

Query: 257 VHALHMGCPIVGDHKYCANFK---------GNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
           VH  H G  ++GD  Y    K                  +  LHA  +   HP     L 
Sbjct: 227 VHMTHTGHSLIGDQTYGGRRKLSPKALSAAAIDAVAAFPRQALHAATLGFVHPITKEELS 286

Query: 307 ITAPLPAHMVKTWDSL 322
             APLP  M    D L
Sbjct: 287 FDAPLPNDMALLIDLL 302


>gi|304317468|ref|YP_003852613.1| pseudouridine synthase [Thermoanaerobacterium thermosaccharolyticum
           DSM 571]
 gi|302778970|gb|ADL69529.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 286

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 73/318 (22%), Positives = 140/318 (44%), Gaps = 44/318 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++   ++EN+ L     N     +   ++K   SG++ V+ +    N  I+ G ++ +  
Sbjct: 3   IIASKEDENLPLKEILINR--GFSSTLIRKYKHSGRILVNNEISIVNRIIKKGDIIELYL 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
             +                N++   + +   + YED  I V NK AG+ V   +G   H 
Sbjct: 61  DDD----------------NVSVKPEKMDLHICYEDDDILVVNKDAGVVVHPTAG---HP 101

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           DG L + V    +K       R  +RLD++TSG+++ A+      +L     M++    Y
Sbjct: 102 DGTLANGVAWYYEKNNINAPIRPVNRLDRDTSGLIIFAKNPFMQNYLQIVCPMKKF---Y 158

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G  +++   I   + +K     + +      +   + A++ F V+    +K   +
Sbjct: 159 IAIVRGDLEDR-GTIDLPIKRKPGSTIERMV-----DDDGDKAVTDFYVLKR-GEKLSLV 211

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +++  TGRTHQ+RVH  H+G PI+GD  Y ++      +    +  LHA  +    P  G
Sbjct: 212 KLELKTGRTHQIRVHLSHIGHPIIGDTLYGSD------TSYIKRQALHAYRITFRQPFIG 265

Query: 304 R-LQITAPLPAHMVKTWD 320
           + + I +P+P  M     
Sbjct: 266 KCISIYSPIPDDMKMVLK 283


>gi|260174510|ref|ZP_05760922.1| RNA pseudouridylate synthase [Bacteroides sp. D2]
          Length = 306

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 78/308 (25%), Positives = 133/308 (43%), Gaps = 33/308 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  +++G  V+I        
Sbjct: 24  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVQI-------- 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     S     K  +     ++YED+ I V  K  G+ SV             L 
Sbjct: 76  ----------SKQKGKKEFNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 125

Query: 135 SWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G+  +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 126 EYVQRSGRQFRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSME 185

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + +WL  K+     YV   + ++ G+  +I+H+K I   A  +  LE+   TGR 
Sbjct: 186 KDYDTVVSWLTDKTL----YVSSSEYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRK 239

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y      N       +L LHA  +   HP  G  ++   P 
Sbjct: 240 NQIRVHMQDLGHPIIGDGRYGREDAPN----PIGRLALHAFKLCFYHPVTGDLMEFETPY 295

Query: 312 PAHMVKTW 319
           PA   K +
Sbjct: 296 PAEFKKLF 303


>gi|28210692|ref|NP_781636.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           tetani E88]
 gi|28203130|gb|AAO35573.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           tetani E88]
          Length = 320

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 71/300 (23%), Positives = 128/300 (42%), Gaps = 27/300 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   R+D++ +     +    + K +R G V+++ K+VK    +  G +V I  
Sbjct: 3   IEIGANESGQRMDKFLRKMLTDVPLGAIYKSIRKGDVKINGKKVKEKYSLNLGDIVEI-- 60

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
                   IK      +     + ++ LK  + YED  + +  K  G+ V          
Sbjct: 61  ------RDIKTNAEKHNDFKAIEGANELK--VTYEDQNMIIVEKKPGVLVHSDKKNSDPT 112

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ T+GI++  +   + + L +  R R +
Sbjct: 113 LTDYVLSYLYDKGDYVPEEEITFTPASCNRLDRNTAGIIIFGKNYESLKDLNQMIRERHV 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G  K+        ++K       Y+H  K+ +K +       K I      
Sbjct: 173 DKYYQALVCGKIKD--GLYKAHIVKDEKSNKSYIH--KEPKKNSKEIEMEVKTIQTCG-T 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           +  LE+Q  TGR+HQ+R H   +G PIVGD KY +    +F       +  YL+A  +  
Sbjct: 228 YSLLEIQLITGRSHQIRAHLSSLGNPIVGDKKYGSKKLNSFFYNKYGVDYQYLYAYKLIF 287


>gi|160942600|ref|ZP_02089845.1| hypothetical protein FAEPRAM212_00074 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446079|gb|EDP23082.1| hypothetical protein FAEPRAM212_00074 [Faecalibacterium prausnitzii
           M21/2]
          Length = 316

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 139/313 (44%), Gaps = 19/313 (6%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD +    YP +    L K LR  +++++ K+   + R+ +G  +++      L+ 
Sbjct: 10  APARLDNYLTQQYPALTPGRLNKALRENKIKLNGKKQPLSTRVMAGDEIKLFI----LDD 65

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK-- 134
           ++   + ++        +    + ++Y+  +I + NKPAG++V G           L   
Sbjct: 66  VLDADRRVEGPAWKNART---PAQVVYDCPQILIVNKPAGVAVDGPEDDTLLNRALLYLN 122

Query: 135 ---SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
               + ++    P L HRLD  TSG++++A+T  A +    + + R +QK Y  + +G P
Sbjct: 123 KQGEYKENDLYTPALCHRLDTGTSGLVIIAKTPEAEELFLSAIKNREVQKTYLCVTFGRP 182

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 +  +LLK +  G   V +V+  + GA    + ++ I   + +   L++Q  TGR
Sbjct: 183 MPPDATLGGYLLKDADRG--IVKIVEDKQPGAKEVETRYETI-AVSGRLALLKVQLITGR 239

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM-DLPHPEGGRL---QI 307
           THQ+R H   +GCPI+GD KY  N            L      M     P+   L     
Sbjct: 240 THQIRAHMASIGCPILGDSKYGNNSANRELKLKYQALCAWELTMPRFTQPDFAFLSGKTF 299

Query: 308 TAPLPAHMVKTWD 320
            AP P +  +  D
Sbjct: 300 HAPKPWYYQQVLD 312


>gi|323453124|gb|EGB08996.1| hypothetical protein AURANDRAFT_25466 [Aureococcus anophagefferens]
          Length = 361

 Score =  202 bits (515), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 73/313 (23%), Positives = 128/313 (40%), Gaps = 30/313 (9%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD +    +P        + +  G VRV+                R    + A + +  
Sbjct: 56  RLDAFLAAQFPERTRREWAEAIGGGAVRVNGAVAT-----------RKSASVAAGDGVAA 104

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +    + + +    ++ L   +L +D+   V NK AG+      G          +    
Sbjct: 105 DAFAAEPAGDKPVEAEDLPLDVLVDDASFLVVNKAAGMVTHPAPGARRGTLANAVAHRCG 164

Query: 140 KG-------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW---- 188
            G        +P + HRLD+ TSG +VVAR   A + L   F+ R + K+Y +++     
Sbjct: 165 GGGVFAEATPRPGIVHRLDRYTSGAIVVARNARATRRLQAQFKARTVAKLYLAVLARPPP 224

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
             P    E + +  + +     + + VV     G   A+S  +V+    ++ C  ++   
Sbjct: 225 PPPDGADELVIDAPIGRHPARREKMAVV----PGGRPAVSRVRVLASDGRR-CVAQVAID 279

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL--YLHARYMDLPHPEGG-RL 305
           TGRTHQ+RVH  H+G P++GD  Y         +         LHA  +   HP+ G R+
Sbjct: 280 TGRTHQIRVHLAHVGSPVLGDPVYGDAQANARAAAAFAANRTLLHAWRLAFDHPDSGARV 339

Query: 306 QITAPLPAHMVKT 318
           ++TAP P  + + 
Sbjct: 340 EVTAPPPPDLARA 352


>gi|301168062|emb|CBW27648.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteriovorax marinus SJ]
          Length = 327

 Score =  202 bits (515), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 73/337 (21%), Positives = 135/337 (40%), Gaps = 45/337 (13%)

Query: 8   QYVVVENDEEN-MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            + + E D+ N  RLD++  +     +   ++ +   G++         N    + + + 
Sbjct: 11  TFTITEEDKANFKRLDQFLSHKLVDQSRSYIKMLFEKGEIS------SPN----AAKKIE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +    +    II               ++ +   + YED  + + NK AG+ V    G  
Sbjct: 61  LKKFPDVGTEIIVNIP---PPAPADAIAENIPLEIHYEDEDLIIVNKAAGMVVHPAPGNY 117

Query: 125 IAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               ++  L    D KG    ++P + HRLD+ TSGI+VVA+ +   + L + F    I 
Sbjct: 118 TGTLVNAILYHCKDIKGVGDQRRPGIVHRLDKGTSGIMVVAKNQKCHEGLVKLFSTHDIT 177

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y  +  G        + + + +           +    K   +A++H++V+  F  K 
Sbjct: 178 RRYECIAMGKSFPTGGKLESNIGRHPQNRLK----MSTESKAGKHALTHYRVLKQF-DKV 232

Query: 241 CWLEMQPHTGRTHQLRVHALHMGC-PIVGDHKYC-------------ANFKGNFTSPIQN 286
             +E++  TGRTHQ+RVH   +   PI+ D  Y              ++  G++  P   
Sbjct: 233 AHVELKLETGRTHQIRVHLSQLLHRPILCDPLYGNPKEHLQRIGPELSDIIGDYEHP--- 289

Query: 287 KLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
             +LHA+ +   HP     L  TAP P       + L
Sbjct: 290 --FLHAKELGFIHPITKKELHFTAPPPELFQNVLNHL 324


>gi|237714573|ref|ZP_04545054.1| RNA pseudouridylate synthase [Bacteroides sp. D1]
 gi|262406439|ref|ZP_06082988.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_22]
 gi|293373837|ref|ZP_06620181.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|298481084|ref|ZP_06999278.1| RNA pseudouridylate synthase [Bacteroides sp. D22]
 gi|229445342|gb|EEO51133.1| RNA pseudouridylate synthase [Bacteroides sp. D1]
 gi|262355142|gb|EEZ04233.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_22]
 gi|292631236|gb|EFF49870.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|295083972|emb|CBK65495.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens
           XB1A]
 gi|298272658|gb|EFI14225.1| RNA pseudouridylate synthase [Bacteroides sp. D22]
          Length = 306

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 78/308 (25%), Positives = 133/308 (43%), Gaps = 33/308 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  +++G  V+I        
Sbjct: 24  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVKI-------- 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     S     K  +     ++YED+ I V  K  G+ SV             L 
Sbjct: 76  ----------SKQKGKKEFNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 125

Query: 135 SWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G+  +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 126 EYVQRSGRQFRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVEGSME 185

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + +WL  K+     YV   + ++ G+  +I+H+K I   A  +  LE+   TGR 
Sbjct: 186 KDYDTVVSWLTDKTL----YVSSSEYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRK 239

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y      N       +L LHA  +   HP  G  ++   P 
Sbjct: 240 NQIRVHMQDLGHPIIGDGRYGREDSPN----PIGRLALHAFKLCFYHPVTGDLMEFETPY 295

Query: 312 PAHMVKTW 319
           PA   K +
Sbjct: 296 PAEFKKLF 303


>gi|220904744|ref|YP_002480056.1| pseudouridine synthase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|219869043|gb|ACL49378.1| pseudouridine synthase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 360

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 80/299 (26%), Positives = 139/299 (46%), Gaps = 14/299 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           +  +  VV+  E   +L ++ +    ++    L + +R+GQVR++  R K  +R+Q+G  
Sbjct: 17  SVTEIPVVQEPESGQKLLQFLQRRL-NLPQAMLHRWVRTGQVRINGSRCKPFSRVQTGDT 75

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK----SILLYEDSKIYVFNKPAGISVQ 120
           VR+PP    +           +S   +K            L+ +   ++ F+KPAG+ V 
Sbjct: 76  VRLPPFAMKMAAQCDSASPTPASKGKSKDDAPEDGPPLPPLVGKSGYLWAFDKPAGLPVH 135

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G+G    +   L          P   HRLD+ TSGI++VA + AA      + R   + 
Sbjct: 136 PGTGHEDSLTTRLSCHFAGVSFMPTPVHRLDRGTSGIILVAASYAALDETQRALRANAMH 195

Query: 181 KIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           K Y + V G   + + C + ++L K++  G + V  VK +   A  A+   + +   A +
Sbjct: 196 KEYVAWVAGRWPHTQTCLVRHFLRKEAVDGFERVRPVKADAPDAKEALCLVRAL-SIADR 254

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              ++++  TGRTHQ+RV    +G P++GD KY     G         LYLH+  + LP
Sbjct: 255 ASLVQVRLLTGRTHQIRVQLSSLGHPVLGDTKYGQTRAGVA-------LYLHSLRVILP 306


>gi|331269001|ref|YP_004395493.1| RluA family pseudouridine synthase [Clostridium botulinum
           BKT015925]
 gi|329125551|gb|AEB75496.1| pseudouridine synthase, RluA family [Clostridium botulinum
           BKT015925]
          Length = 323

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 135/326 (41%), Gaps = 29/326 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ +     +    + K LR G +RV+ K+ K N  +Q   ++    
Sbjct: 3   IEIGPNEAGQRLDKFCRKWLEDVPLGAIFKALRKGDIRVNGKKAKQNYFLQEEDIIE--- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                 +I   ++   +     +  DF    + YED  + +  K  G+ V          
Sbjct: 60  ----TKYIETYKQNKKNMPKKFQEVDFSSIKISYEDENMLIIEKWPGVLVHSDKKDGEPT 115

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSG+++  +     + L    R R+I
Sbjct: 116 LTDYVLSYLFQKGDYDPQKEVTFTPAPCNRLDRNTSGMVIFGKNFKTLKILNAMIRERKI 175

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G  K K+     ++ K        +H  K+ ++ +        VID     
Sbjct: 176 KKYYNALVKG--KIKEGYYEAYISKDQVNNISEIH--KEKKQNSKKIAMEVNVIDTVG-T 230

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F +LE+   TGR+HQLR H  ++G PI+GD KY      +F       +  +L+A  +  
Sbjct: 231 FSFLELDLLTGRSHQLRAHLAYLGNPIIGDDKYGDKKLNSFFNNKYGLDFQFLYAYKLIF 290

Query: 298 PHPEGG--RLQ---ITAPLPAHMVKT 318
                    ++   IT  LP    K 
Sbjct: 291 KDCPNELAYMENKIITESLPPIFKKV 316


>gi|160884288|ref|ZP_02065291.1| hypothetical protein BACOVA_02266 [Bacteroides ovatus ATCC 8483]
 gi|156110027|gb|EDO11772.1| hypothetical protein BACOVA_02266 [Bacteroides ovatus ATCC 8483]
          Length = 317

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 78/308 (25%), Positives = 133/308 (43%), Gaps = 33/308 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  +++G  V+I        
Sbjct: 35  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVQI-------- 86

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     S     K  +     ++YED+ I V  K  G+ SV             L 
Sbjct: 87  ----------SKQKGKKEFNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 136

Query: 135 SWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G+  +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 137 EYVQRSGRQFRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSME 196

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + +WL  K+     YV   + ++ G+  +I+H+K I   A  +  LE+   TGR 
Sbjct: 197 KDYDTVVSWLTDKTL----YVSSSEYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRK 250

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y      N       +L LHA  +   HP  G  ++   P 
Sbjct: 251 NQIRVHMQDLGHPIIGDGRYGREDAPN----PIGRLALHAFKLCFYHPVTGDLMEFETPY 306

Query: 312 PAHMVKTW 319
           PA   K +
Sbjct: 307 PAEFKKLF 314


>gi|299822427|ref|ZP_07054313.1| 23S rRNA pseudouridylate synthase RluD [Listeria grayi DSM 20601]
 gi|299815956|gb|EFI83194.1| 23S rRNA pseudouridylate synthase RluD [Listeria grayi DSM 20601]
          Length = 298

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 137/319 (42%), Gaps = 39/319 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKIL--RSGQVRVDKKRVKFNNRIQSGQVVRIP 68
               +EE + L  + K    HI+ + L  I     G++ V+        R++SG  V + 
Sbjct: 6   TATAEEEGLLLRTFLKR--KHISKLLLTAIKYHEGGRIAVNNATENVLYRVRSGDKVSVM 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                         + +   N    ++     + YED  + V NKPAG+         YH
Sbjct: 64  --------------LPEEKQNEQLIAEHTDLDIRYEDDFVIVLNKPAGMPSIPSQ---YH 106

Query: 129 IDGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             G + +++    Q+        +  RLD+ETSG++++A+TR A   L+   +   +++ 
Sbjct: 107 PTGSVANFIKGHYQEQNLTNAVHIVTRLDRETSGLMLIAKTRFAHARLSSFLQKGDLKRK 166

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L  G   NK   I   + + S I      + ++  +   YA ++++VI  +   F  
Sbjct: 167 YQALTMGDLANKAGYIEAPIGRDSDIS----IMARKVTETGKYAKTNYQVIASYPD-FEH 221

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +++Q  TGRTHQ+RVH  H+G  ++GD  Y         + +  +  LH+ ++   HP  
Sbjct: 222 VDIQLETGRTHQIRVHFSHIGHSLLGDDMYHGE------TSLIRRHALHSYHLHFIHPFT 275

Query: 303 GR-LQITAPLPAHMVKTWD 320
              L     LP  M +   
Sbjct: 276 EEYLSFECELPEDMEELLR 294


>gi|228938421|ref|ZP_04101031.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar berliner ATCC 10792]
 gi|228971300|ref|ZP_04131928.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar thuringiensis str. T01001]
 gi|228977911|ref|ZP_04138292.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis Bt407]
 gi|228781828|gb|EEM30025.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis Bt407]
 gi|228788450|gb|EEM36401.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar thuringiensis str. T01001]
 gi|228821283|gb|EEM67298.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar berliner ATCC 10792]
          Length = 292

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 61/310 (19%), Positives = 130/310 (41%), Gaps = 33/310 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           EE   +  + K     I+   L  I    G + V+ +     +++++G+ + +   +   
Sbjct: 9   EEGTLVREFLKT--KGISKAALTDIKFHGGAIEVNSQHASVRHQLRAGEELSVFFPVEER 66

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGF 132
           +  +               ++ +   ++YED  + + +K A +S             +  
Sbjct: 67  SEGM--------------MAEDIPLCIVYEDDAVLIIDKEANMSTIPSREHPTGSVANAI 112

Query: 133 LKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L  +          +  RLD++TSG++++A+ R     L++  + + +++ Y ++V G  
Sbjct: 113 LSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEM 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             ++  I   + +KS    +         +    A++HFKVID    K   + ++  TGR
Sbjct: 173 VEREGMIDAPIGRKSDSIIERTVC-----EDGQRAVTHFKVIDSTYDK-THVALELETGR 226

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
           THQ+RVH  H+G P++GD+ Y              +  LH++ +   HP     +  T  
Sbjct: 227 THQIRVHMAHIGHPLLGDNLYGGRRDE------MKRQALHSKSLTFYHPILEKEMSFTIK 280

Query: 311 LPAHMVKTWD 320
           +P+ M +   
Sbjct: 281 IPSDMQELLR 290


>gi|16800037|ref|NP_470305.1| hypothetical protein lin0968 [Listeria innocua Clip11262]
 gi|16413427|emb|CAC96199.1| lin0968 [Listeria innocua Clip11262]
          Length = 296

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 141/319 (44%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V+N+E+ + L  + K+   HI+   L   K    G++ V+ +       +++   VR+  
Sbjct: 7   VKNEEDGLLLRTFLKS--KHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKTDDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +           L +H+D     +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNDRL-----------LAEHTDL---EVVFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 TGSVANFVKGHYENQGLTSAIHIVTRLDRETSGLMLIAKNRYAHARLSSFLQQGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +   G  + +   I   + +K     D   + +       YA ++++V+  +   F  L
Sbjct: 168 QAFTSGTLEEEAGSIEAPIGRK-----DVSIMERFVTPEGKYAKTNYEVLMRY-NGFDHL 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +        +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------QELLKRQALHSCHLHLVHPVTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
             +    PLP  M +    
Sbjct: 276 EYMAFDLPLPEDMEQIIQK 294


>gi|220915339|ref|YP_002490643.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219953193|gb|ACL63577.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 301

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 85/316 (26%), Positives = 138/316 (43%), Gaps = 27/316 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRI 67
            ++V + +   R+DR+       I+    ++ + +G V VD +R K   R +  GQ V +
Sbjct: 5   TLLVPDADRYERIDRFIAAR-GGISRGLARRAIEAGGVFVDGRRCKVAGRTLTPGQQVVV 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                          + +        +   +  LLY D+ +   +KPAG+  Q       
Sbjct: 64  N--------------LEEGGRAAPALAALGRERLLYADADLCAVDKPAGVPAQPTLTTDR 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                L S +   G    L HRLD+ETSG+ V ARTR AA  L E+FR    +K Y +L 
Sbjct: 110 GALPELVSAL--LGAPVTLVHRLDRETSGVTVFARTRDAAAALAEAFRTGTPEKTYLALC 167

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
              P   +  +A  L K     G     +++ +   + A + ++ +   A     +E +P
Sbjct: 168 ARAPSPAEGRVALALGKDPARPG-----LRRVDPAGDPAATRYRTL-REAPGGALVEARP 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            TGRTHQ+RVH   +G P++GD +Y    +         ++ LHA  ++LPHP  G R+ 
Sbjct: 222 ETGRTHQIRVHLAALGAPLLGDARYGGPRR--VGEVAAPRVMLHATRLELPHPATGARMV 279

Query: 307 ITAPLPAHMVKTWDSL 322
             A  P        +L
Sbjct: 280 FEAEPPEDFRAVEAAL 295


>gi|167628351|ref|YP_001678850.1| pseudouridine synthase, rlua family [Heliobacterium modesticaldum
           Ice1]
 gi|167591091|gb|ABZ82839.1| pseudouridine synthase, rlua family [Heliobacterium modesticaldum
           Ice1]
          Length = 339

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 78/351 (22%), Positives = 145/351 (41%), Gaps = 46/351 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ +EE  R+    +      +   LQ + R+   R++ KR   + R++ G ++ +    
Sbjct: 12  VKPEEEGRRIGSILQFCL-GFSRRRLQILTRTDGFRLNGKRAHLDRRVKEGDLLEVCLHQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG---GSGIAYH 128
               ++                   ++  +LYED+ + + +KP GI V      +     
Sbjct: 71  EEEGNLAP---------------VAMELKVLYEDADLLILDKPPGIEVHPPEQRARFRPT 115

Query: 129 IDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +  +   KG K R+   HRLD++T+GI V A+   A Q L    R   +Q+ Y ++
Sbjct: 116 LAHGVAHYFAEKGIKARVRPLHRLDKDTTGICVFAKNAFAHQALDRQLRNGSLQRGYLAI 175

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--------IDCFA- 237
           + G+P      I   + +         H+ +        AI+ ++V        ++    
Sbjct: 176 LRGLPAELVGVIDAPIGRDPE-----HHMRRMVRDDGERAITRYRVTQVIEPSGLEMKGA 230

Query: 238 ----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                 +   E+   TGRTHQ+RVH  H+G P++GD  Y  +      SP  ++  LH+ 
Sbjct: 231 AESEGHWALAEVILETGRTHQIRVHFRHLGTPLLGDRLYGGD------SPRIDRQALHSA 284

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQ 343
           ++ L  P  G  +++TA LP  M +          +N   K    + E  +
Sbjct: 285 WVTLLQPRSGEAVKVTAELPEDMARLLGGKANDGSKNEDRKTEDGKTEDGK 335


>gi|298385355|ref|ZP_06994913.1| RNA pseudouridylate synthase [Bacteroides sp. 1_1_14]
 gi|298261496|gb|EFI04362.1| RNA pseudouridylate synthase [Bacteroides sp. 1_1_14]
          Length = 306

 Score =  202 bits (515), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 78/308 (25%), Positives = 130/308 (42%), Gaps = 33/308 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  +Q G  V+I        
Sbjct: 24  EPMELMEFLAAKMPDASRTKLKSLLSKRVVLVDNVITTQFNFPLQPGMKVQI-------- 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     S     K        ++YED+ I V  K  G+ SV             L 
Sbjct: 76  ----------SKEKGKKEFHNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 125

Query: 135 SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G   +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 126 EYVQRSGRQHRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVEGTME 185

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + +WL  K+     YV     ++ G+  +I+H+K I   A  +  LE+   TGR 
Sbjct: 186 KDYDTVVSWLTDKTL----YVSSSDYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRK 239

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH  ++G PI+GD +Y     G  +     +L LHA  +   HP  G  ++   P 
Sbjct: 240 NQIRVHMQNLGHPIIGDGRYG----GEESLNPIGRLALHAFKLCFYHPVTGDLMEFETPY 295

Query: 312 PAHMVKTW 319
           P    K +
Sbjct: 296 PGEFKKLF 303


>gi|299146120|ref|ZP_07039188.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_23]
 gi|298516611|gb|EFI40492.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_23]
          Length = 317

 Score =  202 bits (515), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 78/308 (25%), Positives = 133/308 (43%), Gaps = 33/308 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  +++G  V+I        
Sbjct: 35  EPMELMEFLATKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVQI-------- 86

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     S     K  +     ++YED+ I V  K  G+ SV             L 
Sbjct: 87  ----------SKQKGKKEFNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 136

Query: 135 SWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G+  +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 137 EYVQRSGRQFRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSME 196

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + +WL  K+     YV   + ++ G+  +I+H+K I   A  +  LE+   TGR 
Sbjct: 197 KDYDTVVSWLTDKTL----YVSSSEYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRK 250

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y      N       +L LHA  +   HP  G  ++   P 
Sbjct: 251 NQIRVHMQDLGHPIIGDGRYGREDAPN----PIGRLALHAFKLCFYHPVTGDLMEFETPY 306

Query: 312 PAHMVKTW 319
           PA   K +
Sbjct: 307 PAEFKKLF 314


>gi|304382476|ref|ZP_07364973.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
 gi|304336388|gb|EFM02627.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
          Length = 302

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 74/315 (23%), Positives = 125/315 (39%), Gaps = 36/315 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
             VE+D+    L  +   H    +   ++  L    V+V+ K +  ++  +  G  V + 
Sbjct: 16  FTVEHDD---TLLSFLLTHIGDKSRNKIKATLSGRGVKVNGKIITQYDFPLPVGTKVSVS 72

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
               +     K                     ++YED  + V  K  GI        A H
Sbjct: 73  RSKQSEPFKSK------------------YVKIVYEDRYLVVIEKNVGILSMAAGRRALH 114

Query: 129 IDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   L  +     Q  K  + HRLD+ETSG+++ A+     Q L   +      + Y ++
Sbjct: 115 VKAVLDDYFKMSRQRCKAHVVHRLDRETSGLMIYAKDMQTEQLLEHDWHRNVYDRRYMAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +  +  +ANWL         Y+      + G  YA++HF+ +         +E +
Sbjct: 175 VSGEMEEDEGTVANWL----KDNKAYITYASPVDNGGKYAVTHFRTLARTT-THSLVEFR 229

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
             TGR +Q+RVH   MG P+ GD KY             N+L LHA  +   HP    R+
Sbjct: 230 LETGRKNQIRVHTADMGHPVCGDTKYGNG------DNPCNRLCLHAYVLCFYHPVTHERM 283

Query: 306 QITAPLPAHMVKTWD 320
           +   P+PA   + ++
Sbjct: 284 EFQTPIPADFKRLFN 298


>gi|315922777|ref|ZP_07919017.1| RNA pseudouridylate synthase [Bacteroides sp. D2]
 gi|313696652|gb|EFS33487.1| RNA pseudouridylate synthase [Bacteroides sp. D2]
          Length = 317

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 78/308 (25%), Positives = 133/308 (43%), Gaps = 33/308 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  +++G  V+I        
Sbjct: 35  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVQI-------- 86

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     S     K  +     ++YED+ I V  K  G+ SV             L 
Sbjct: 87  ----------SKQKGKKEFNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 136

Query: 135 SWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G+  +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 137 EYVQRSGRQFRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSME 196

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + +WL  K+     YV   + ++ G+  +I+H+K I   A  +  LE+   TGR 
Sbjct: 197 KDYDTVVSWLTDKTL----YVSSSEYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRK 250

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y      N       +L LHA  +   HP  G  ++   P 
Sbjct: 251 NQIRVHMQDLGHPIIGDGRYGREDAPN----PIGRLALHAFKLCFYHPVTGDLMEFETPY 306

Query: 312 PAHMVKTW 319
           PA   K +
Sbjct: 307 PAEFKKLF 314


>gi|253584151|ref|ZP_04861349.1| pseudouridine synthase [Fusobacterium varium ATCC 27725]
 gi|251834723|gb|EES63286.1| pseudouridine synthase [Fusobacterium varium ATCC 27725]
          Length = 294

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 78/314 (24%), Positives = 138/314 (43%), Gaps = 37/314 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPV 70
           VE   E   L  +     P  +  +++ +L   +V V +    ++N+ +  GQ V +   
Sbjct: 13  VEEKNE---LMNFLIEKMPEKSRTSIKSLLTKRKVFVGNDVVSQYNHPLLPGQTVTVDWG 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HI 129
              +  ++K                     ++YED  I V  K  GI     +       
Sbjct: 70  KVTIETVMKG------------------VSVIYEDDDILVVEKENGILSIATNNEREKTA 111

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              LK ++ +K  K    + HRLD++TSGI++ A+T  A   L  ++     ++ Y +LV
Sbjct: 112 YNILKDYLKNKDPKNKIFVVHRLDRDTSGIMIFAKTEKAQDILQTTWNDSVKERTYIALV 171

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  + +K+ I ++L +       ++    QN K    AISH+KV+    + +  LE+  
Sbjct: 172 EGTVQKEKDTIISYLQEN----RAFITYSSQNPKDGKKAISHYKVLK-KNKNYSLLEVNI 226

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGR +Q+RVH   +G  +VGD KY +           N+L LHA  +   HP   + L 
Sbjct: 227 ETGRKNQIRVHMQDIGHSVVGDKKYGSGKSP------INRLGLHANTIVFVHPITKKVLH 280

Query: 307 ITAPLPAHMVKTWD 320
            ++ +P+   K ++
Sbjct: 281 FSSKIPSVFTKIFN 294


>gi|331090839|ref|ZP_08339685.1| hypothetical protein HMPREF9477_00328 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330399698|gb|EGG79360.1| hypothetical protein HMPREF9477_00328 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 294

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 133/322 (41%), Gaps = 33/322 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINF-VNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M  V    +  + EN  L  + K          +L++      + ++    +  + +   
Sbjct: 1   MRRVFTYRIPEEFENDTLLSFLKAECYSSPIITHLKR--TEKGLLLNGNWARVRDILHKN 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++ +               +L+++ +       L   ++YED  + V NKPA + +   
Sbjct: 59  DILTVT--------------LLETTSSDNIVPVSLPLDIVYEDEDLMVINKPANMPIHPS 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHR---LDQETSGILVVARTRAAAQHLTESFRMRRI 179
                +      ++  ++ + P +      LD++T+G+L++A+   +A  L++  + R I
Sbjct: 105 QNNYDNTLANAVAYYYAQKEVPFVYRCINRLDRDTTGLLILAKHMYSASLLSDMVKNRLI 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++  G   +    I   + +      D     + N    ++A +H+K +      
Sbjct: 165 HREYIAIADGYV-DDAGIIDAPIAR----TKDSTIEREVNFSEGDFARTHYKCLQRK-NG 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  + ++  TGRTHQ+RVH  ++G  ++GD  Y  ++          +  LH+  +   H
Sbjct: 219 YSLVSLKLETGRTHQIRVHMKYIGHALLGDFLYNPDY------TFIGRQALHSHRLTFMH 272

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P   + L  TAPLP  M K +D
Sbjct: 273 PITKQHLTFTAPLPYDMAKLFD 294


>gi|299143164|ref|ZP_07036244.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Peptoniphilus sp. oral taxon 386 str. F0131]
 gi|298517649|gb|EFI41388.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Peptoniphilus sp. oral taxon 386 str. F0131]
          Length = 293

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 70/305 (22%), Positives = 139/305 (45%), Gaps = 36/305 (11%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           + N+++  +   +   ++   ++  +    + ++ +++  N  ++    + +     +LN
Sbjct: 17  DGNIKIRDFLVQN--GLSSRFIRGSIEEENIYLNGEKIYRNELLRENDELFVKFSDESLN 74

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLK 134
             ++  K+                 ++YED  I V NKP  +        +   +  F+ 
Sbjct: 75  AKVQHGKL----------------DIIYEDDDIVVVNKPPYMVTHTAKDDVENTLLNFVA 118

Query: 135 SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            + +     +K R+ +RLD++TSGI++VA+   +   + E F    ++K Y ++V GI K
Sbjct: 119 GYFEDNKIRRKVRIVNRLDRDTSGIVIVAKNSFSHSSIQEQFGD-SVKKEYVAIVNGIIK 177

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           N    I   +     I  D +  +        Y+ + ++VI      F  ++++ +TGRT
Sbjct: 178 NDSGIIEKPI----DIAKDGIRRIV--SPDGKYSKTSYEVIKRN-DFFTLVKLRLYTGRT 230

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           HQ+RVH  HMG PI+GD  Y +      TS +  +  LH   M++ HP   + L+  AP+
Sbjct: 231 HQIRVHMSHMGTPILGDALYGS------TSNLILRQALHCYEMEIIHPRTKKLLKFIAPV 284

Query: 312 PAHMV 316
           P  M 
Sbjct: 285 PKDME 289


>gi|258648417|ref|ZP_05735886.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Prevotella tannerae ATCC 51259]
 gi|260851164|gb|EEX71033.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Prevotella tannerae ATCC 51259]
          Length = 294

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 77/302 (25%), Positives = 125/302 (41%), Gaps = 33/302 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        +   ++ IL  G ++VD+  VK F++ ++ G  V I               
Sbjct: 22  FLLEALGGTSRNRIKAILGGGGIKVDRAIVKQFDHPLRPGMQVEI--------------- 66

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
              S              L+YED  I V +K AGI    GS   + +   L  +     +
Sbjct: 67  ---SQSKPKSELKSSHLRLVYEDEFIVVIDKSAGILSMAGSPHIFSVKTILDDYFAKTHK 123

Query: 143 K--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           +    + HRLD+ETSG+LV A+T  A Q L  +++     + Y +++ G+ +     + N
Sbjct: 124 RCRAHVVHRLDRETSGLLVYAKTIEAEQILEHNWQRIVRDRRYVAVLSGVLETPSGTVRN 183

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           WL         YV      + G  +A++HF+ +   ++     E +  TGR +Q+RVHA 
Sbjct: 184 WL----KDNKAYVTYSSPTDNGGKFAVTHFRRLK-HSETHTLAEFKLETGRKNQIRVHAQ 238

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
            +G P+ GD KY              +L LHA  +D  HP  G  L    P P   +   
Sbjct: 239 DLGHPVCGDTKYGNG------DNPIGRLCLHAYRLDFYHPITGELLHFETPYPKPFLSVL 292

Query: 320 DS 321
             
Sbjct: 293 QK 294


>gi|300727932|ref|ZP_07061310.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bryantii B14]
 gi|299774774|gb|EFI71388.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bryantii B14]
          Length = 298

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 74/318 (23%), Positives = 128/318 (40%), Gaps = 39/318 (12%)

Query: 13  ENDEENMRLDR------WFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
            ND  +  +D+      W   +    +   ++  L++  +RV  K + KF+  ++ G  +
Sbjct: 10  SNDYAHYTVDKPALLLEWLLENVKGESKSKIKATLQNHGIRVGSKVITKFDYPLKPGMKI 69

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I           K  K                  ++YED  + V  K AGI        
Sbjct: 70  HISKNKRNNAFKSKWMK------------------IVYEDQYLVVIEKNAGILSMAAGHS 111

Query: 126 AYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           + +    L  + +   Q     + HRLD++TSG+++ A+ +     L E +      + Y
Sbjct: 112 SLNCKTVLDQYFNETRQHCQAHVVHRLDRDTSGLMIYAKDKKTELSLEEDWHNTVYDRRY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G  +  +  +ANWL         Y+      + G  YA++HF+V+D        +
Sbjct: 172 VAVVSGEMREDEGTVANWL----KDNRAYITFSSPVDNGGKYAVTHFRVLDRTP-NHSLV 226

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
           E +  TGR +Q+RVH   MG P+ GD KY              +L LHA  +   HP   
Sbjct: 227 EFKLETGRKNQIRVHTADMGHPVCGDIKYGNG------DNPLGRLCLHAYVLCFVHPVTH 280

Query: 303 GRLQITAPLPAHMVKTWD 320
            RL+   P+P +    + 
Sbjct: 281 KRLEFETPIPGNFRHLFK 298


>gi|288800870|ref|ZP_06406327.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 299 str. F0039]
 gi|288332331|gb|EFC70812.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 299 str. F0039]
          Length = 295

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 78/324 (24%), Positives = 129/324 (39%), Gaps = 37/324 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRI 59
           M    Y  YV  + D     L  W   +   ++   L+ IL    ++V+ K   K++  +
Sbjct: 5   MQKGDYDHYVTTDKD----TLLNWLLTNIKTMSRNKLKDILAGQGIKVNGKITTKYDYPL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  + I                  S              ++YED+ I V +K AGI  
Sbjct: 61  TPGMKISI------------------SKTKRNNLFKSKYVDIVYEDNHIIVVHKKAGILS 102

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 + ++   L  ++    QK    + HRLD+ETSG++V A+ +   +   E +   
Sbjct: 103 MPVGHGSLNVKTVLDDYLMRSKQKCNAHVVHRLDRETSGLMVYAKDKRVERLFEEDWHNI 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y ++V G  +  +  IANWL         +V      + G  YA++HF+V    A
Sbjct: 163 VYDRRYVAIVSGEVQENEGTIANWL----KDNKMFVTYSCPFDNGGKYAVTHFQVKKRTA 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +E +  TGR +Q+RVH+  +G P+ GD KY              +L LHA  +  
Sbjct: 219 -YHTLVEYKLETGRKNQIRVHSADIGHPVCGDTKYGNGDDP------IGRLCLHAYVLAF 271

Query: 298 PHPEG-GRLQITAPLPAHMVKTWD 320
            HP     L    P+P+   +   
Sbjct: 272 YHPITHKPLLFETPIPSDFKRIIK 295


>gi|225872530|ref|YP_002753985.1| pseudouridine synthase, RluA family [Acidobacterium capsulatum ATCC
           51196]
 gi|225792126|gb|ACO32216.1| pseudouridine synthase, RluA family [Acidobacterium capsulatum ATCC
           51196]
          Length = 301

 Score =  202 bits (514), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 127/319 (39%), Gaps = 29/319 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M    Y     + +      L     + YPH +    Q+ L  G++ ++    + +  + 
Sbjct: 1   MRNHGYAFTTTIGSKHHGQTLLFHLASLYPHSSAEVWQQRLSHGEITLNGITAQGSESVA 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +GQV+                         T+    L   +L+ED ++   NKP+G+   
Sbjct: 61  AGQVLVWNC------------------PPWTEPDAPLHFDVLFEDDELIAVNKPSGLPTL 102

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            GSG     +  L   V          HRL + TSGI++ ++T   A  L   +   ++Q
Sbjct: 103 PGSGFL---ENTLLRLVRRYAPHASPVHRLGRATSGIVLFSKTAQGAALLEAIWNTSKVQ 159

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y ++   + ++++  I   + +  H     +  V         + S  KV+       
Sbjct: 160 KVYRAVAVNVAEHEEYEIHTPIGRVPHP---RLGSVWAASSTGKPSWSSAKVLAR-GTTT 215

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQNKLYLHARYMDL 297
              E+  H+GR HQ+R+H   +G P+VGD  Y         +   P      LHA+++  
Sbjct: 216 TTFEVTLHSGRPHQIRIHLASVGHPLVGDGLYGPGGLPLADHPGLPGDGGYLLHAQFLAF 275

Query: 298 PHPEGG-RLQITAPLPAHM 315
            HP  G ++ + APLP+  
Sbjct: 276 LHPTSGSQISLEAPLPSEF 294


>gi|325473128|gb|EGC76324.1| ribosomal large subunit pseudouridine synthase [Treponema denticola
           F0402]
          Length = 338

 Score =  202 bits (514), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 75/332 (22%), Positives = 137/332 (41%), Gaps = 57/332 (17%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D +      +++   L+  L+S  + V+ ++ K +  +Q+G ++ +            
Sbjct: 26  RIDVYCTETLKNLSRSQLKTGLKS--LYVNSQKAKLSRNVQNGDLIEL------------ 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              + D+ +    H   L   ++YED  I V NK  G+      G   + DG L + ++ 
Sbjct: 72  ---VWDNPIPEYAHPQKLPLNIIYEDENIIVVNKERGMVTHPAGG---NWDGTLVNALNY 125

Query: 140 K--------------------------------GQKPRLTHRLDQETSGILVVARTRAAA 167
                                              +  + HRLD+ETSG+++ AR     
Sbjct: 126 YRLYDSRIKDEFAVELNKLLSGEVKNIEKLSLDPYRMGIVHRLDKETSGLIITARNLKTE 185

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           + L   F+ R ++K Y +++ G+P   K  I   + + S     +   V  +      A+
Sbjct: 186 KLLKSFFKKRAVKKYYLAVLDGVPPKNKGRIKTSVFRSSSDRKKFS--VSADLSKGKKAL 243

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           S +KV+     K   +  + +TGRTHQ+R+HA  MGCP+ GD  Y     G   + +   
Sbjct: 244 SAYKVLKSDG-KMSLVLFRIYTGRTHQIRLHAKFMGCPVAGDKVYGKKKTGLEKTGM--P 300

Query: 288 LYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
           L LHA  + +P     + +  AP+P    +  
Sbjct: 301 LMLHAYKLIIPDTVNSKKEFKAPIPNDFKQIL 332


>gi|317132480|ref|YP_004091794.1| pseudouridine synthase, RluA family [Ethanoligenens harbinense
           YUAN-3]
 gi|315470459|gb|ADU27063.1| pseudouridine synthase, RluA family [Ethanoligenens harbinense
           YUAN-3]
          Length = 334

 Score =  202 bits (514), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 128/302 (42%), Gaps = 28/302 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   V  ++  +R+D++     P +    L K +R  +++V   R   + R+  G  V 
Sbjct: 1   MKAFTVGPNDAGLRVDKFVAKVAPRLPQALLYKYIRLKRIKVGGGRAAISQRLAVGDRVE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
           +                       T      +  +LYED  I + +K  G+ V    SG 
Sbjct: 61  LYLNDEFFEEKAA-----------TFFDAPTEVDILYEDENILIADKKPGLVVHEDESGS 109

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           A  + G ++  +  +G+          P L +R+D+ T GI++ A+   A + L E  + 
Sbjct: 110 ADTLIGRIQHLLYDRGEYDPERENAFAPALCNRIDRNTGGIVLAAKNAPALRVLNEKIKA 169

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R ++K Y  +V G  + + + I  W +K        V V  +   G   A++ ++V+D  
Sbjct: 170 RELRKQYLCVVHGRMERRNDTITTWQVKDETE--KKVRVYDRPVPGGLTAVTRYRVLDEQ 227

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYM 295
                 LE+   TGRTHQ+R    H+G P++GD KY  N +     P   +   L+A  +
Sbjct: 228 -DTLSLLEVDLVTGRTHQIRATFAHIGHPLLGDGKYGDNARNR---PYGVRYQALYAYRV 283

Query: 296 DL 297
             
Sbjct: 284 TF 285


>gi|125718029|ref|YP_001035162.1| 23S rRNA pseudouridine synthase [Streptococcus sanguinis SK36]
 gi|125497946|gb|ABN44612.1| 23S rRNA pseudouridine synthase, putative [Streptococcus sanguinis
           SK36]
          Length = 295

 Score =  202 bits (514), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 131/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L KI    G + V+ +       +  G  V I          +K   
Sbjct: 16  FLKRH--EVSKGLLAKIKFSGGNILVNHQPQNAIYLLDIGDKVTIDIPSEKGFESLK--- 70

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
                      +      ++YED    V +KPAG++       +  +  F+K++      
Sbjct: 71  -----------AVDKDLSVVYEDEHFLVLDKPAGVASIPSVNHSNTMANFVKAYYIRHAY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
           + Q+  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G     ++  I
Sbjct: 120 ENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +          + ++  +   YA + +KVI+ F   +  +++  HTGRTHQ+RVH
Sbjct: 180 IAPIGRNPE-----SIITRRVTEDGKYAHTSYKVIERFGDVY-LVDIHLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
             H+G P++GD  Y  + +         +  LH   +   +P  G  ++  +PLP    +
Sbjct: 234 FSHIGFPLLGDDLYEGSLE-----HGIERQALHCHSLKFYNPFSGQEVERASPLPEDFKQ 288

Query: 318 TWDSL 322
             + L
Sbjct: 289 VIEKL 293


>gi|167768022|ref|ZP_02440075.1| hypothetical protein CLOSS21_02565 [Clostridium sp. SS2/1]
 gi|167710351|gb|EDS20930.1| hypothetical protein CLOSS21_02565 [Clostridium sp. SS2/1]
 gi|291561022|emb|CBL39822.1| pseudouridine synthase, RluA family [butyrate-producing bacterium
           SSC/2]
          Length = 323

 Score =  202 bits (514), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 78/331 (23%), Positives = 144/331 (43%), Gaps = 35/331 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +   EE  RLD+    +        + K+LR   ++++ K+   N ++  G  V 
Sbjct: 1   MRELNITTREEGQRLDKILSKYLNKAPKSFVYKMLRKKNIKLNGKKATGNEKLSQGDQVC 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I    + +N   +E K     + L          +LYED  + + NKP GI  Q      
Sbjct: 61  IYLAEDTINKFREEVKAGKQKIKLD---------VLYEDENVIMVNKPWGILSQKSKPED 111

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             I+  +  +  ++G          KP + +RLD+ T+GI++   +    Q + E  + R
Sbjct: 112 ISINDQIIPYAVNQGLISEKELQVVKPSICNRLDRNTTGIIICGISIEGLQTMAEMLKHR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  +V G  +  ++ ++ +L K        V V KQ   GA++  + ++ +    
Sbjct: 172 DMEKYYLCIVKGKIEGSQK-VSAYLKKDEKTN--KVKVSKQEIAGASHIETAYEPV-ISN 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYM 295
            +F  L+++  TG+THQ+R H   +G P++GD KY      +            LH   +
Sbjct: 228 DEFTLLKVELITGKTHQIRAHLASIGHPLIGDFKYGDKKINQEMKQRFGLKDQLLHCTEI 287

Query: 296 DLP-------HPEGGRLQITAPLPA--HMVK 317
             P       +  G ++Q  APLP    M+K
Sbjct: 288 VFPRDMKTCKNLSGKKIQ--APLPKRFDMIK 316


>gi|221309004|ref|ZP_03590851.1| hypothetical protein Bsubs1_06426 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221313329|ref|ZP_03595134.1| hypothetical protein BsubsN3_06352 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221318253|ref|ZP_03599547.1| hypothetical protein BsubsJ_06296 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221322526|ref|ZP_03603820.1| hypothetical protein BsubsS_06402 [Bacillus subtilis subsp.
           subtilis str. SMY]
          Length = 299

 Score =  202 bits (514), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 63/284 (22%), Positives = 118/284 (41%), Gaps = 36/284 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G ++++ + V     ++ G ++ +              K  +  V+ T  ++ +   +LY
Sbjct: 41  GDLQINGEHVTVKYVLKEGDLLIV--------------KFPEEQVSETLLAEPVPLDILY 86

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGI 157
           ED  + V NK   +S         H  G + + +    Q         L  RLD++TSGI
Sbjct: 87  EDEHVLVINKQPYVSSIPSR---EHPSGSIANGIIDHYQTTGVRATVHLVTRLDRDTSGI 143

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA+ R A   L+ + +   +++ Y ++V G     +  +   + +          + +
Sbjct: 144 MLVAKHRFAHSILSSAQKNGLVKRRYAAVVHGRMAQMEGTVDAPIGRHPD-----SIIER 198

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A++HF V  C       + +Q  TGRTHQ+RVH  ++G P+ GD  Y    +
Sbjct: 199 TVTPDGQKAVTHFYV-TCANDDMTSVALQLETGRTHQIRVHMSYLGHPLCGDTLYGGTRQ 257

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
                    +  LH+ ++   HP     ++  APLP  M K   
Sbjct: 258 E------IGRQALHSEHLSFIHPLTQENMRFHAPLPQDMSKLIK 295


>gi|331085858|ref|ZP_08334941.1| hypothetical protein HMPREF0987_01244 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406781|gb|EGG86286.1| hypothetical protein HMPREF0987_01244 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 298

 Score =  202 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 66/324 (20%), Positives = 131/324 (40%), Gaps = 35/324 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQS 61
           M       + ++   M +  + K      +   +  + R   G  R +    + +  +QS
Sbjct: 1   MKRTFTYPIHHEMAGMTIQSFLKQQ--QYSSQVITHLKRTPDGICR-NGVWARVHEVLQS 57

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G ++ I               I++ + +       L   ++YED  + V NKP+G+ +  
Sbjct: 58  GDLLTIS--------------IVEETSSEHIVPVPLPFPIVYEDEDLLVINKPSGMPIHP 103

Query: 122 GSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             G   +      ++  +    P   R  +RLD++T+G+L++A+   +A  L+     R 
Sbjct: 104 SQGNYENTLANAAAYYFASQNIPFTYRCINRLDRDTTGLLIIAKHMYSASLLSNMVARRE 163

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y +   G+ + +   I   + + +    +       +    +YA +HF  +     
Sbjct: 164 IHREYLAAATGLVE-ESGMIEAPIGRANGSTIER----CVDFAHGDYACTHFHRLAYQ-N 217

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  + ++  TGRTHQ+RVH  ++G P+ GD  Y             ++  LH+  +   
Sbjct: 218 GYSLVSLKLETGRTHQIRVHMKYIGHPLPGDFLYHPE------DHCIDRQALHSYRLSFI 271

Query: 299 HPEGGR-LQITAPLPAHMVKTWDS 321
           HP   + L  TAPLP  M   +  
Sbjct: 272 HPITKQSLTFTAPLPEDMQAIFQK 295


>gi|289674871|ref|ZP_06495761.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           FF5]
          Length = 256

 Score =  202 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 75/262 (28%), Positives = 125/262 (47%), Gaps = 21/262 (8%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSK 140
           I +        +  ++  ++YED +I V NKPAG+ V   +G A     +  L    D  
Sbjct: 3   IAEQEAQGEWVAQDIELDIIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDII 62

Query: 141 G-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +  + HRLD++T+G++VVA+T  A   L    + R + +IY  +V G+       I 
Sbjct: 63  NVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVV-TAGGKID 121

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + +        + V+    +G   A+SH++V++ F +    + ++  TGRTHQ+RVH 
Sbjct: 122 APIGRHGQQ-RQRMAVM----EGGKQAVSHYRVLERF-RSHTHVRVKLETGRTHQIRVHM 175

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAP 310
            H+  P+VGD  Y   F+    + +          +  LHAR+++L HP  G R+   +P
Sbjct: 176 AHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHARFLELDHPTTGKRMSWESP 235

Query: 311 LPAHMVKTWDSLGFKYDRNLYI 332
           LP   V     L  K DR  +I
Sbjct: 236 LPDDFVWLLSLL--KQDREAFI 255


>gi|293375853|ref|ZP_06622121.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|325844995|ref|ZP_08168320.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
 gi|292645532|gb|EFF63574.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|325488968|gb|EGC91358.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
          Length = 299

 Score =  202 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 69/313 (22%), Positives = 136/313 (43%), Gaps = 31/313 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +E  +    +  +   +  H+    + ++  S +V+++ +   FN  ++ G ++ IP   
Sbjct: 14  IEEKQAGQSIRDFLMTY--HLARKKIHELYMSKKVQLNAQIADFNKILEVGDILLIP--- 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHID 130
                       +  S  +      +   ++YED  + + NKPAG+ V          + 
Sbjct: 69  ------------VFESEGIDFKPQKMNLDIVYEDEHLLILNKPAGVMVHPDQKDGLNTLV 116

Query: 131 GFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             +  + + KG  ++ R  HR+D +TSG ++ A+   A   +      ++I++ Y +LV 
Sbjct: 117 NGVAYYYEQKGFNERIRYIHRIDTDTSGGIIFAKHFMAHSLMDYQLSEKQIRRWYLALVS 176

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  K +K  I   + K  H         ++  K  + A++ ++V   F + +  +E++  
Sbjct: 177 GNLKTRKGRIDAPIGKDRH-----HRARRRVAKNGDQAVTLYEVKKQF-KTYSLVELELK 230

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  H+G P++GD  Y     G        +  LH+  + + HP     L  
Sbjct: 231 TGRTHQIRVHMSHLGHPLLGDVLYG----GVAKVGKLKRQALHSAKIQMQHPMTKENLSF 286

Query: 308 TAPLPAHMVKTWD 320
           + P+P  M     
Sbjct: 287 SIPMPLDMQSLIK 299


>gi|29346052|ref|NP_809555.1| RNA pseudouridylate synthase [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|253568538|ref|ZP_04845949.1| RNA pseudouridylate synthase [Bacteroides sp. 1_1_6]
 gi|29337946|gb|AAO75749.1| RNA pseudouridylate synthase [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|251842611|gb|EES70691.1| RNA pseudouridylate synthase [Bacteroides sp. 1_1_6]
          Length = 306

 Score =  202 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 78/308 (25%), Positives = 129/308 (41%), Gaps = 33/308 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  +Q G  V+I        
Sbjct: 24  EPMELMEFLAAKMPDASRTKLKSLLSKRVVLVDNVITTQFNFPLQPGMKVQI-------- 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     S     K        ++YED+ I V  K  G+ SV             L 
Sbjct: 76  ----------SKEKGKKEFHNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 125

Query: 135 SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G   +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 126 EYVQRSGRQHRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVEGTME 185

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + +WL  K+     YV     ++ G+  +I+H+K I   A  +  LE+   TGR 
Sbjct: 186 KDYDTVVSWLTDKTL----YVSSSDYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRK 239

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y     G  +     +L LHA  +   HP  G  ++   P 
Sbjct: 240 NQIRVHMQDLGHPIIGDGRYG----GEESLNPIGRLALHAFKLCFYHPVTGDLMEFETPY 295

Query: 312 PAHMVKTW 319
           P    K +
Sbjct: 296 PGEFKKLF 303


>gi|313619655|gb|EFR91288.1| pseudouridine synthase YjbO [Listeria innocua FSL S4-378]
          Length = 296

 Score =  202 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 141/319 (44%), Gaps = 40/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V+N+E+ + L  + K+   HI+   L   K    G++ V+ +       +++   VR+  
Sbjct: 7   VKNEEDGLLLRTFLKS--KHISKQLLTAVKFGADGKIEVNNEEQNVLYHVKTDDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +           L +H+D     +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL-----------LAEHTDL---EVVFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 TGSVANFVKGHYENQGLTSAIHIVTRLDRETSGLMLIAKNRYAHARLSSFLQQGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +   G  + +   I   + +K     D   + +       YA ++++V+  +   F  L
Sbjct: 168 QAFTSGTLEEEAGSIEAPIGRK-----DVSIMERFVTPEGKYAKTNYEVLMRY-NGFDHL 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +        +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------QVLLKRQALHSCHLHLVHPVTE 275

Query: 304 R-LQITAPLPAHMVKTWDS 321
             +    PLP  M +    
Sbjct: 276 EYMAFDLPLPEDMEQIIQK 294


>gi|78355167|ref|YP_386616.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
 gi|78217572|gb|ABB36921.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 332

 Score =  202 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 86/316 (27%), Positives = 137/316 (43%), Gaps = 26/316 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           V+++ V   E   +L ++ +      +    L +I+R G+VRV+K R K  +R+  G VV
Sbjct: 9   VRHIEVTRAEAGQKLLQFLQRRLGSGVPQQFLMRIIRKGEVRVNKGRAKPYDRVSEGDVV 68

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           RIPPV  A           D++  +   S      ++     + V NKPAG+ VQ G+G 
Sbjct: 69  RIPPVRPAAEPSC------DAACAVPAVSASPLPQIIASGDGLLVINKPAGLPVQPGTGH 122

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-RRIQKIYW 184
              +   L +        P   HRLD+ TSG+L+   T  A + L + FR    + K Y 
Sbjct: 123 TDCVTARLAAHFAGADFMPAPAHRLDKNTSGLLLAGTTYTALRTLQDLFRNGHSLIKDYC 182

Query: 185 SLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQN-------EKGANYAISHFKVIDCF 236
           + V GI P+ +   + + L+K+   G + +H +                A+     +   
Sbjct: 183 AWVCGIWPEQEALTLTDVLVKEGTPGKEKIHALPAGSAQPHTAPPKGREALCQVVPLLRL 242

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 L ++  TGRTHQ+RV       P++GD KY A          +  + LHA  + 
Sbjct: 243 -DNATLLGIRLATGRTHQIRVQLASRNHPVIGDVKYGAPA-------CRAGMLLHAFRLV 294

Query: 297 LPHPEGGRLQITAPLP 312
           LP P G   +   P P
Sbjct: 295 LPAPFGR--EFFCPPP 308


>gi|325662008|ref|ZP_08150627.1| hypothetical protein HMPREF0490_01365 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471671|gb|EGC74890.1| hypothetical protein HMPREF0490_01365 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 298

 Score =  202 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 66/324 (20%), Positives = 131/324 (40%), Gaps = 35/324 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQS 61
           M       + ++   M +  + K      +   +  + R   G  R +    + +  +QS
Sbjct: 1   MKRTFTYPIHHEMAGMTIQSFLKQQ--QYSSQVITHLKRTPDGICR-NGVWARVHEVLQS 57

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G ++ I               I++ + +       L   ++YED  + V NKP+G+ +  
Sbjct: 58  GDLLTIS--------------IVEETSSEHIVPVPLPFPIVYEDEDLLVINKPSGMPIHP 103

Query: 122 GSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             G   +      ++  +    P   R  +RLD++T+G+L++A+   +A  L+     R 
Sbjct: 104 SQGNYENTLANAAAYYFASQNIPFTYRCINRLDRDTTGLLIIAKHMYSASLLSNMVARRE 163

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y +   G+ + +   I   + + +    +       +    +YA +HF  +     
Sbjct: 164 IHREYLAAATGLVE-ESGMIEAPIGRANGSTIER----CVDFAHGDYACTHFHRLAYQ-N 217

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  + ++  TGRTHQ+RVH  ++G P+ GD  Y             ++  LH+  +   
Sbjct: 218 GYSLVSLKLETGRTHQIRVHMKYIGHPLPGDFLYHPE------DHCIDRQALHSYRLSFI 271

Query: 299 HPEGGR-LQITAPLPAHMVKTWDS 321
           HP   + L  TAPLP  M   +  
Sbjct: 272 HPITKQSLTFTAPLPEDMQAIFQK 295


>gi|329923371|ref|ZP_08278854.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
 gi|328941362|gb|EGG37655.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
          Length = 353

 Score =  202 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 81/342 (23%), Positives = 136/342 (39%), Gaps = 57/342 (16%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV   E+ M L    +     ++   L ++ L    + ++  RV  + ++Q+G +V I  
Sbjct: 11  VVPTHEDGMLLKTILQKRM-GVSRKLLSRLKLTEQGIMLNGTRVYISVKVQAGDLVEIRM 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                N ++ +                ++  +LYED  + V NKPAG+ V    G     
Sbjct: 70  EQERSNDMLPQP---------------MELHILYEDEHLLVLNKPAGVIVHPTHGHYTDT 114

Query: 128 HIDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +G +  W +     + R  HRLDQETSG+LV+A+     QH++E      + K Y + 
Sbjct: 115 LANGVVHYWQEKGWNYRFRAVHRLDQETSGVLVIAKNAYIHQHVSEQMIAGTVDKRYVAF 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G P      I   + +        +            +++ ++V + +      +E++
Sbjct: 175 VHGRPSP-TGDIDGPIDRDPLEPHRRIV-----TPEGYPSLTRYRVCETYPS-ASLVELK 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------------------------- 279
             TGRTHQ+RVH L +GCP++GD  Y      +                           
Sbjct: 228 LETGRTHQIRVHMLSIGCPLIGDQMYRHPLYSDQGLLPDAPERDEDSNGAVGSLDPLAAT 287

Query: 280 --FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
                   ++  LHA  + L HP EG  +   APLP  M   
Sbjct: 288 IMRLDGYMDRQALHAASLTLMHPIEGKTMVFRAPLPEDMKSL 329


>gi|75759795|ref|ZP_00739872.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|218896239|ref|YP_002444650.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
 gi|74492695|gb|EAO55834.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|218543847|gb|ACK96241.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
          Length = 275

 Score =  202 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 60/296 (20%), Positives = 125/296 (42%), Gaps = 31/296 (10%)

Query: 30  PHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
             I+   L  I    G + V+ +     +++++ + +RI   +   +  +          
Sbjct: 4   KGISKAALTDIKFHGGAIEVNGQHASVRHQLRASEELRIFFPVEERSEGM---------- 53

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSW-VDSKGQKPR 145
                ++ +   ++YED  + + NK A +S             +  L  +          
Sbjct: 54  ----IAEDIPLCIVYEDDAVLIINKEANMSTIPSREHPTGSVANALLSHYDKQHLASTVH 109

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD++TSG++++A+ R     L++  + + +++ Y ++V G    ++  I   + +K
Sbjct: 110 IVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGMIDAPIGRK 169

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           S    +         +    A++HFKVID    K   + ++  TGRTHQ+RVH  H+G P
Sbjct: 170 SDSIIERTVC-----EDGQRAVTHFKVIDSTYHK-THVALELETGRTHQIRVHMAHIGHP 223

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWD 320
           ++GD+ Y              +  LH++ +   HP     +  T  +P+ M +   
Sbjct: 224 LLGDNLYGGRRDE------MKRQALHSKSLTFYHPILEKEMSFTIKIPSDMQELLR 273


>gi|260437125|ref|ZP_05790941.1| pseudouridine synthase, RluA family [Butyrivibrio crossotus DSM
           2876]
 gi|292810437|gb|EFF69642.1| pseudouridine synthase, RluA family [Butyrivibrio crossotus DSM
           2876]
          Length = 314

 Score =  202 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 70/327 (21%), Positives = 135/327 (41%), Gaps = 26/327 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++  +E   R D++      +     + K LR+  + ++ K+ K N  ++    VR
Sbjct: 1   MKEYIIGKNEAGQRFDKYIFKLLKNAGTGLIFKQLRNKNIVLNGKKAKGNEILKENDSVR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I    + +N          +   L       +  ++YED  I + +KP G+  Q  S   
Sbjct: 61  IFMSDDTINKF--------TGGPLHISKTGFRLDVIYEDDDILLASKPVGVLSQKSSDKD 112

Query: 127 YHIDGFLKSWVDSKG--------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             ++ +L  ++   G         KP   +RLD+ TSG+++  ++    Q ++E  + R 
Sbjct: 113 ISMNEYLIEYLTDNGFGKENLATFKPSFCNRLDRNTSGLMIAGKSLRGLQKMSEIIKDRS 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y ++V GI  +KK  I  +L K      + V +     K +    + ++ +     
Sbjct: 173 IHKFYLTIVKGIV-DKKSVIKGYLRKDEK--NNKVVIYDNPVKDSYEIHTEYEPLATK-D 228

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               L+++  TG+THQ+R H   +  P++GD KY            + K  LH+  +  P
Sbjct: 229 DMTLLKVRLITGKTHQIRAHLAGISHPVLGDFKYGDKVFNE--KYGEKKQLLHSYQVVFP 286

Query: 299 ----HPEGGRLQITAPLPAHMVKTWDS 321
                P+        P P +  K +  
Sbjct: 287 KLDDFPDISEKSFNTPYPVNFTKYFKE 313


>gi|255322530|ref|ZP_05363675.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           showae RM3277]
 gi|255300438|gb|EET79710.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           showae RM3277]
          Length = 354

 Score =  202 bits (513), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 71/333 (21%), Positives = 131/333 (39%), Gaps = 44/333 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           MT  +  +++  +   R D +      ++       +++SG V ++ K + K + ++  G
Sbjct: 17  MTEKEIKILDGAQA--RADAFLATEL-NVARNQALNLIKSGLVSLNGKPLNKPSVKLNLG 73

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++RI              K   S    TK     +  ++YED  + V NKPA + V   
Sbjct: 74  DILRI--------------KFEQSDPETTKFEAEFEVPIIYEDDDLLVLNKPANLVVHPA 119

Query: 123 SGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
             +    +  L  W+ +KG          +  + HRLD+ TSG +VVA+  AA   L+  
Sbjct: 120 PSV---KEPTLVDWLGAKGFLLSNLSGQSRAGIVHRLDKGTSGAIVVAKNNAAHAALSNQ 176

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI-----S 228
              + + +IY +L   +P  +   +   + +           +  + + A  A      S
Sbjct: 177 LSDKSMGRIYLALT-DLPLKQNCIVERAIGRNP--ANRLKKAIVSSGRAAKSAFANLLFS 233

Query: 229 HFK-VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            F   +         +  +  TGRTHQ+RVH   +   I+GD  Y    + +       +
Sbjct: 234 EFDGPVQSKNAGVNLIAAKLFTGRTHQIRVHLASLNRHILGDALYGFKSEKDK----IGR 289

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           + LHA  +   HP  G  +   AP+     +  
Sbjct: 290 VMLHAYGLYFTHPRSGEQMSFVAPIWDDFSEIL 322


>gi|297830600|ref|XP_002883182.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297329022|gb|EFH59441.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 477

 Score =  202 bits (513), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 110/375 (29%), Positives = 166/375 (44%), Gaps = 76/375 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVR------VDK--------KRVKFNNRIQSGQVVRIP 68
           RW     P +    +QK+ R  QVR      VD         KRV     +  G  + +P
Sbjct: 94  RWILRCRPDLPRTLVQKLFRLRQVRRQMSLSVDGHELQRSQLKRVAAKESLNVGDRIYLP 153

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             ++         K  +S     +   F+ S++LY+D  I V NKP G++VQGGSGI   
Sbjct: 154 LSVDNDTPPTPPAKK-ESFQCSEEERKFVCSLVLYKDPAIIVLNKPHGLAVQGGSGIKTS 212

Query: 129 IDGFLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--------- 178
           ID    + +   K + PRL HRLD++ SG+LV+ART+ AA  L   FR +          
Sbjct: 213 IDELAATCLTFDKSESPRLVHRLDRDCSGLLVLARTQTAATVLHSIFREKTCGASAYGVK 272

Query: 179 -----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG---ANYAISHF 230
                +++ Y +LV G P+ +K  I+  L K     G    +   +        +AI+ +
Sbjct: 273 KNIKSLKRKYMALVIGCPRRQKGQISAPLRKVVVDDGKSDRITVNDNGELVSTQHAITEY 332

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCA--------------- 274
           KVI+     + WLE++P TGR HQLRVH    +G PI+GD+KY                 
Sbjct: 333 KVIESSPHGYTWLELRPLTGRKHQLRVHCAEVLGTPILGDYKYGWQAHKAREPFVSSETT 392

Query: 275 -----------NFKGNFTSPIQNKLYLHARYMDLPHPEG--GRLQ--------------I 307
                      +  G   S  Q  L+LH++ +DLP+      ++Q               
Sbjct: 393 PTKPSSSPFGLDLDGGDVSSKQPHLHLHSKQIDLPNISQLLEKMQVSSDSDISDLDSLKF 452

Query: 308 TAPLPAHMVKTWDSL 322
            APLP+HM  +++ L
Sbjct: 453 DAPLPSHMQLSFNLL 467


>gi|262038157|ref|ZP_06011554.1| ribosomal large subunit pseudouridine synthase C [Leptotrichia
           goodfellowii F0264]
 gi|261747805|gb|EEY35247.1| ribosomal large subunit pseudouridine synthase C [Leptotrichia
           goodfellowii F0264]
          Length = 297

 Score =  202 bits (513), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 140/304 (46%), Gaps = 32/304 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +Y+ V+++ E MRLDR+ K  + + +   + + LR G V+++ K+ K N R+  G 
Sbjct: 1   METFEYI-VDSESEGMRLDRYLKKTFKNESLSKIFQALRKGDVKINGKKSKENYRLCLGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +          +  +K   +           K+++++E++  ++ NKP  + +  G+
Sbjct: 60  KITVKY--------LYSEKEEKTKKTFDFDEKKYKNMIIFENNDFFIINKPGNVPMHKGT 111

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G  + +    K   ++        +RLD ETSG+++  +     ++++E  R   +QK Y
Sbjct: 112 GHKHGLSEIFKKIYENDNIN--FANRLDYETSGLVIGCKNLKFLRYISEKIRNNEVQKKY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF------- 236
            + V G  +  K  I N+L     I  + V     ++K A  +I+ +K I+         
Sbjct: 170 VAAVDGEIEKDKFIIENYL----KITENGVIQSYVSDKDAKRSITKYKKINNRFFDKILN 225

Query: 237 ---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
               +K   L++   TGR HQ+RV    +G P++GD KY    +       +NKLYL   
Sbjct: 226 NIKKEKVTLLDIDLVTGRKHQIRVQLSSIGNPVIGDRKYGKKKE-------ENKLYLCCY 278

Query: 294 YMDL 297
            +  
Sbjct: 279 SVSF 282


>gi|169824338|ref|YP_001691949.1| pseudouridylate synthase [Finegoldia magna ATCC 29328]
 gi|167831143|dbj|BAG08059.1| pseudouridylate synthase [Finegoldia magna ATCC 29328]
          Length = 307

 Score =  202 bits (513), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 67/327 (20%), Positives = 136/327 (41%), Gaps = 35/327 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   ++++  +N RLD +  N    ++   +QK +   +V V+ K  K N ++ S   ++
Sbjct: 2   IYEFLIDDSNQNTRLDVFLANEV-ELSRSEIQKFIEDKKVLVNYKPQKKNYKLNSNDKIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
                          +  D ++   KH       ++YED  + + NK   + V     I 
Sbjct: 61  FDY------------EKEDKTIRAQKH----DLDVVYEDDYLAIINKDKDVIVHPTETIY 104

Query: 126 AYHIDGFL----KSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           +  +  +L    K+  D  G  +  + HRLD++T+G++++A+       L E  +   I 
Sbjct: 105 SDTLVNYLMYNFKNLSDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEII 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y  +V G   ++   I  ++ +        +            +IS ++ +D     +
Sbjct: 165 KTYLCIVHGKI-DESGTIKEYMTRNPKDRKKMMV-----SDEGKLSISQYERLDYN-DDY 217

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +++Q  TGRTHQ+RVH  ++  PI+GD  Y    +      + +   LHA  +   HP
Sbjct: 218 SLVKVQIKTGRTHQIRVHMNYIHHPILGDKLYGLKKEKI----LFDSQVLHAYNLQFIHP 273

Query: 301 EG-GRLQITAPLPAHMVKTWDSLGFKY 326
           +   ++ +   L    +   +     Y
Sbjct: 274 QTHEKINVIGKLKPDFMTAIEKTKLDY 300


>gi|241895991|ref|ZP_04783287.1| 23S rRNA pseudouridylate synthase RluD [Weissella paramesenteroides
           ATCC 33313]
 gi|241870722|gb|EER74473.1| 23S rRNA pseudouridylate synthase RluD [Weissella paramesenteroides
           ATCC 33313]
          Length = 305

 Score =  202 bits (513), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 65/313 (20%), Positives = 136/313 (43%), Gaps = 35/313 (11%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
             +  +R+  +       ++   +  I++   GQV ++ + V+  + ++ G +V +    
Sbjct: 9   QSDSTLRIKTFLAQR--GVSH-RMFAIIKRGGGQVLLNHRPVRTLDDVEPGDLVEVKMPA 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHID 130
              N I+               +  L   +LYED    V +K AG++   G       + 
Sbjct: 66  EKSNAIVA--------------ASDLPIKILYEDENWLVVDKVAGVTSVPGKADRETTMV 111

Query: 131 GFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             +K ++ S+G +   P +  RLD+ TSG+ ++A+ R A   L +  +   + K Y+++V
Sbjct: 112 NRVKGYLISEGAEDLVPHVVTRLDRFTSGVALLAKHRFAHGLLDKQLQTHTVDKRYYAIV 171

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            GI  +    I   + +  +       + ++       + + + V++    +   +++Q 
Sbjct: 172 DGIVPDDHGFIDAPIGRMDND-----FIRREVRADGRPSQTEYWVVNRMPNQ-TLVKVQL 225

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
           HTGRTHQ+RVH  ++G P++GD  Y              +  LHA +++   P    +  
Sbjct: 226 HTGRTHQIRVHFKYIGHPLIGDEIYGGPMDR-----GIERQALHAYWLEFYDPFSEIKRH 280

Query: 307 ITAPLPAHMVKTW 319
           I +PLP  + +  
Sbjct: 281 IQSPLPEDLKQIL 293


>gi|313902966|ref|ZP_07836361.1| pseudouridine synthase [Thermaerobacter subterraneus DSM 13965]
 gi|313466690|gb|EFR62209.1| pseudouridine synthase [Thermaerobacter subterraneus DSM 13965]
          Length = 386

 Score =  202 bits (513), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 83/371 (22%), Positives = 137/371 (36%), Gaps = 56/371 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR- 66
           +  VV   +E  RL R  +     +    + ++LR G++ V+ +RV  +  +++G VV  
Sbjct: 26  RRYVVTAADEGQRLHRLARRWLADVPLSAVFRMLRQGRITVNGRRVPRDTVLRAGDVVEA 85

Query: 67  -----------IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
                            +     +      S           +  ++YED  + V NKPA
Sbjct: 86  EVVDAPPHQAAPGAPPPSPAARPRSGPAGSSRAPRLPAPARHEPRVVYEDEHLLVVNKPA 145

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKG-----------QKPRLTHRLDQETSGILVVARTR 164
           G+   G  G     +  L  WV  +             +P   HRLD+ TSG++   +TR
Sbjct: 146 GLLTHGAGGFGAAREYTLLDWVRDELARRGTLPEGALYQPSPGHRLDRNTSGLVAFGKTR 205

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-- 222
             A  L +  R     K Y ++V G P   +  + + L +        V  V   +K   
Sbjct: 206 QGAARLADWMRSGAAVKEYLAIVRGRPP--EGVLQHQLQRDRQRRVTRVLPVSVAQKQPA 263

Query: 223 -------------------ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                              A  A  H  V+   ++ +    ++  TGRTHQ+R      G
Sbjct: 264 APVEIGEAGLEKAPGAAEQARSATLHLTVVGA-SRGYTLCRIRLLTGRTHQIRAQLAAAG 322

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
            P+ GD KY          P      LH   + LP    G +++ APLPA +++    LG
Sbjct: 323 HPLAGDRKYGGPRVEGLDRP-----ALHCHRLVLP----GGVELVAPLPADLMRLCRRLG 373

Query: 324 FKYDRNLYIKR 334
               +    +R
Sbjct: 374 LPVPQGAPGRR 384


>gi|329942341|ref|ZP_08291151.1| pseudouridine synthase, RluA family protein [Chlamydophila psittaci
           Cal10]
 gi|332286982|ref|YP_004421883.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           psittaci 6BC]
 gi|313847579|emb|CBY16567.1| putative pseudouridine synthase [Chlamydophila psittaci RD1]
 gi|325506899|gb|ADZ18537.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           psittaci 6BC]
 gi|328815251|gb|EGF85239.1| pseudouridine synthase, RluA family protein [Chlamydophila psittaci
           Cal10]
 gi|328914213|gb|AEB55046.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           psittaci 6BC]
          Length = 325

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 144/327 (44%), Gaps = 37/327 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRI 59
           M   T + ++V E + +  RLD++  +  P  +    Q+ +   +V ++++ + K + ++
Sbjct: 1   MKSNTPLLFIVNETNRD--RLDKFLVSQNPKYSRAFYQQHILDKRVTINEQIQTKVSTQL 58

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G +V I               I +         + +    +YED  I V NKP  + V
Sbjct: 59  APGDIVSIT--------------IEEKEELSELLPEAIPLEKIYEDEMILVINKPRDMVV 104

Query: 120 QGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
               G         + + I   LK     +  +P + HRLD++TSG+L+ A+TR A    
Sbjct: 105 HPAPGHTRGTVVHALLHEIGERLKQEFPEEPWRPGIIHRLDKDTSGLLITAKTRQAKMIY 164

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
           +E F  ++++K Y ++  G P      I +  L + H     + V          AI+  
Sbjct: 165 SELFATKQLKKSYLAICVGKPSAS---IIHTKLARHHTKRKEMAVSSI----GKEAITRC 217

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           +V+     K   + + P TGRTHQLRVH  H+  PI+GD  Y +      +    +K  L
Sbjct: 218 EVLAYNG-KLSLVLLYPETGRTHQLRVHMKHLSTPILGDPVYGS--ASANSCYGLDKQQL 274

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMV 316
           HA  ++  HP+  + L +T  LP  M 
Sbjct: 275 HAYSVNFIHPQTHKHLNLTTELPRDMK 301


>gi|15894302|ref|NP_347651.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|15023925|gb|AAK78991.1|AE007617_3 Pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|325508430|gb|ADZ20066.1| Pseudouridylate synthase [Clostridium acetobutylicum EA 2018]
          Length = 318

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 131/303 (43%), Gaps = 31/303 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIP 68
           +V+  +E   R+D++ +     +    + K  R G V ++  + K     ++ G V+ I 
Sbjct: 3   IVIGPNEAGQRVDKFIRKWLKDVPLSAIYKAFRKGDVIINGAKCKKEKYSLEEGDVLEIK 62

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAY 127
            + +      K+   ++++  +T           YED  + +  K  G+ V       + 
Sbjct: 63  YIRSDAKK--KKFTRIENNFKVT-----------YEDENMLLVEKWPGVLVHSDKEKTSP 109

Query: 128 HIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            +  ++ S++  KG           P   +RLD+ TSGI++  +   A + L E  R RR
Sbjct: 110 TLTDYVLSYLYDKGDYAPENEVTFTPSPCNRLDRNTSGIVIYGKNFEALKCLNEMIRERR 169

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I+K Y++LV G  K+       ++ K   +  +   ++     GA       K ++    
Sbjct: 170 IKKYYYALVKGKIKD--GIYEAYIKKD--VSSNKSEIINTPAPGAKQISMEIKCVETCG- 224

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMD 296
            F ++E++  TGR+HQLR H  H+G PI+GD KY      ++       N  +L+A  + 
Sbjct: 225 TFSFIEIELLTGRSHQLRAHLSHLGNPILGDPKYGIKDINSYFENKFGLNYQFLYAYKLI 284

Query: 297 LPH 299
              
Sbjct: 285 FKD 287


>gi|16078227|ref|NP_389044.1| pseudouridylate synthase [Bacillus subtilis subsp. subtilis str.
           168]
 gi|3915487|sp|O31613|YJBO_BACSU RecName: Full=Uncharacterized RNA pseudouridine synthase yjbO;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2633516|emb|CAB13019.1| pseudouridylate synthase [Bacillus subtilis subsp. subtilis str.
           168]
          Length = 283

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 63/284 (22%), Positives = 118/284 (41%), Gaps = 36/284 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G ++++ + V     ++ G ++ +              K  +  V+ T  ++ +   +LY
Sbjct: 25  GDLQINGEHVTVKYVLKEGDLLIV--------------KFPEEQVSETLLAEPVPLDILY 70

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGI 157
           ED  + V NK   +S         H  G + + +    Q         L  RLD++TSGI
Sbjct: 71  EDEHVLVINKQPYVSSIPSR---EHPSGSIANGIIDHYQTTGVRATVHLVTRLDRDTSGI 127

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA+ R A   L+ + +   +++ Y ++V G     +  +   + +          + +
Sbjct: 128 MLVAKHRFAHSILSSAQKNGLVKRRYAAVVHGRMAQMEGTVDAPIGRHPD-----SIIER 182

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A++HF V  C       + +Q  TGRTHQ+RVH  ++G P+ GD  Y    +
Sbjct: 183 TVTPDGQKAVTHFYV-TCANDDMTSVALQLETGRTHQIRVHMSYLGHPLCGDTLYGGTRQ 241

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
                    +  LH+ ++   HP     ++  APLP  M K   
Sbjct: 242 E------IGRQALHSEHLSFIHPLTQENMRFHAPLPQDMSKLIK 279


>gi|240047580|ref|YP_002960968.1| Pseudouridine synthase [Mycoplasma conjunctivae HRC/581]
 gi|239985152|emb|CAT05162.1| Pseudouridine synthase [Mycoplasma conjunctivae]
          Length = 306

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 77/311 (24%), Positives = 138/311 (44%), Gaps = 37/311 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
           E  R+D     H  +++    + ++ +  V+VD K V K N  ++ GQ + I        
Sbjct: 14  EKTRIDLVVAKHL-NVSRKISRYLIEANSVKVDNKVVNKVNFLLREGQFISILNNYQEPQ 72

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
             ++ QK+                 ++Y+D+ I V NKP  + V  G+G      ++G L
Sbjct: 73  LKVEAQKV--------------DFEIVYQDNDIIVINKPKNLVVHPGNGNWDKTLVNGLL 118

Query: 134 K----SWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                +  D  G+ +P + HRLD++TSG+L+VA+   A ++L +      I++ Y ++V 
Sbjct: 119 HEFATNLSDVNGEIRPGIVHRLDKDTSGLLLVAKNNQAHKYLAKQLENHEIERKYIAIVV 178

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEM 245
           G   + K  I   + + +      V     +   +  AI++ ++I+ F    + F  ++ 
Sbjct: 179 GKIPHTKMRINLPIGRDNQNRTKKV----VSSFNSKNAITNVELINTFVYKNEHFSIVKC 234

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              TGRTHQ+RVH  H+G PI GD  Y           +  +L  HA  +   H +G  +
Sbjct: 235 ILETGRTHQIRVHLSHIGYPIYGDPVYGKKIDD-----LGQRL--HAYEITFKHLDGRLM 287

Query: 306 QITAPLPAHMV 316
                +P    
Sbjct: 288 NFKTEMPDEFK 298


>gi|187779918|ref|ZP_02996391.1| hypothetical protein CLOSPO_03514 [Clostridium sporogenes ATCC
           15579]
 gi|187773543|gb|EDU37345.1| hypothetical protein CLOSPO_03514 [Clostridium sporogenes ATCC
           15579]
          Length = 317

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 128/300 (42%), Gaps = 30/300 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  +E   RLD++ +     +    + K +R G+++V+ K+ K  N ++ G +V    
Sbjct: 3   IVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGKKSKEKNFLEEGDIVESFN 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAY 127
           V +      K+   +D+++ +T           YED  + +  K  G+ V      G   
Sbjct: 63  VKSKGEK--KKFVRIDNNLKIT-----------YEDENMVLVEKWPGVLVHSDKKEGEPT 109

Query: 128 HIDGFLKSWVDSKGQKPRL--------THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             D  L    D     P L         +RLD+ TSGI++  +   + + L E  R R+I
Sbjct: 110 LTDYVLSYLYDKGDYTPELEVTFTPAPCNRLDRNTSGIVIFGKNYESLKTLNEMIRDRKI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y SLV G  K+       ++ K      +   +  + +          K I      
Sbjct: 170 EKYYSSLVKGRIKD--GIYEAYISKN--QDTNMSKIYNEPKPNTKKIAMEVKTIQTCGS- 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F ++E++  TGR+HQLR H  H+G PI+GD KY      +F       +  YL++  +  
Sbjct: 225 FSFIEIELLTGRSHQLRAHLSHLGNPIIGDSKYGDKKLNSFFHNKYGLSYQYLYSYKLIF 284


>gi|157150847|ref|YP_001450507.1| 23S rRNA pseudouridine synthase [Streptococcus gordonii str.
           Challis substr. CH1]
 gi|157075641|gb|ABV10324.1| 23S rRNA pseudouridine synthase [Streptococcus gordonii str.
           Challis substr. CH1]
          Length = 295

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 145/322 (45%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--DVSKGLLAKIKFRGGGILVNDEPQNAIYLLDIGDKV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          I +++  +S   ++K     K  +++ED    + +KPAG++       
Sbjct: 57  TID---------IPKEEGFESLEAISK-----KLEVVFEDDHFLILDKPAGVASIPSVNH 102

Query: 126 AYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  +  ++K++    G +    H   RLD++TSG+++ A+   A   L +  + R I+K 
Sbjct: 103 SNTMANYVKAYYIDSGYENHQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKRAIEKR 162

Query: 183 YWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y +LV G     K+  I   + +      +   + ++  KG  YA + +KVI+ F   + 
Sbjct: 163 YLALVKGDGLLEKEGEIILPIARD-----EDSIITRRVAKGGKYAHTSYKVIEQFGNIY- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            +++  HTGRTHQ+RVH  H+G P++GD  Y  +      +   ++  LH   +   +P 
Sbjct: 217 LVDIHLHTGRTHQIRVHFSHIGFPLLGDDLYGGSL-----TEGISRQALHCHTLKFYNPF 271

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
            G  +   +PLP        + 
Sbjct: 272 SGEEIGRASPLPTDFEHVIQTF 293


>gi|302380688|ref|ZP_07269153.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
 gi|302311631|gb|EFK93647.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
          Length = 321

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 77/339 (22%), Positives = 149/339 (43%), Gaps = 36/339 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ +++   N R+DR+     P ++  ++QK++R+ +++V+KKR + +  ++   VV 
Sbjct: 1   MRHINIDDSNSNQRVDRFLMKLMPKMSKNHIQKLIRTKKIKVNKKRTEPDYDLKIDDVVN 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I          + ++ I     N    +D     ++YED  + + NK  G+     +   
Sbjct: 61  IY---------LYDEVIEKYQDNKIYTADDFNLDIIYEDDDLILINKKTGVLSHAANPQD 111

Query: 127 Y--HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           Y  +I   + S++    Q          P L +RLD+ TSGI+V A+T  + ++  + F+
Sbjct: 112 YGKNIVDMMVSYLIKTNQFKPTQNSTFTPALVNRLDRNTSGIVVGAKTYDSLKYFNDLFK 171

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I KIY ++V G  K++   I   L K +      ++           +++    +  
Sbjct: 172 KHEITKIYETIVVGNLKDQ--TIDLALEKDNDKNKSVIN------SSGKKSMTKVWNVKN 223

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHAR 293
           F  K+  + +   TGRTHQ+R H  H+  PI+GD KY       +       N   LH+ 
Sbjct: 224 FG-KYSLVNVDLLTGRTHQIRAHLSHINHPIIGDIKYGNREVNKYFKNKYDLNFQLLHSY 282

Query: 294 YMDLP-----HPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            +  P     + +   +   +       K  + L  KYD
Sbjct: 283 KLVFPEKMEKYQKYESMVFESKRDDLFEKILNDLESKYD 321


>gi|115379077|ref|ZP_01466202.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|115363904|gb|EAU63014.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
          Length = 262

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 77/283 (27%), Positives = 126/283 (44%), Gaps = 36/283 (12%)

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
           K ++R++ G+++ +                +   V     ++ L   +L+ED  + V NK
Sbjct: 2   KASSRLRGGELLSLH---------------VPPPVAALPEAEELPLEVLHEDRDLVVVNK 46

Query: 114 PAGISVQGGSGIA--YHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAA 167
            AG+ V  G+G A    ++  L    D  G     +P + HRLD++T+G LVVA+   A 
Sbjct: 47  AAGMVVHPGAGHASGTLVNALLHRVKDLAGVGGELRPGIVHRLDKDTTGCLVVAKNEQAL 106

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANY 225
             L ++F+ R ++K Y +LV G PK +      +       G   VH  +     K    
Sbjct: 107 VALQKAFKTRAVEKTYLALVHGHPKAEGRIETLY-------GRHPVHRQRFTGKVKEGKS 159

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF----T 281
           A++ F+  + F +    +E+   TGRTHQ+RVH    G P++ D  Y A  K        
Sbjct: 160 AVTVFRTREFF-EGAALVEVDLLTGRTHQIRVHLSESGHPLLCDALYGAGRKAKGQVAQA 218

Query: 282 SPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                +  LHA  +   HP  G+ L++ APLP     +   L 
Sbjct: 219 QERLGRQALHAWRLGFAHPRTGKALKLEAPLPEDFAASMKVLR 261


>gi|313889046|ref|ZP_07822704.1| pseudouridine synthase, RluA family [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312844919|gb|EFR32322.1| pseudouridine synthase, RluA family [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 298

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 63/296 (21%), Positives = 133/296 (44%), Gaps = 35/296 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + K     ++   ++K ++SG + ++ +  + N  ++ G +V +       N  ++++ +
Sbjct: 27  FLKER--GVSSRLIRKSVKSGNIYLNSRVNRKNKFLKKGDLVSLRFEDEEPNGGVEQKDL 84

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG- 141
                            ++YED  + + NK   +        A   +  +L  + + +G 
Sbjct: 85  ----------------DIIYEDDDLVIVNKEPFMVTHTAKDDADGTLLNYLLGYFEEEGL 128

Query: 142 -QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            +K R  +RLD++TSG++V A+   A   ++  F+   ++K Y ++V G+ + K+  I  
Sbjct: 129 KRKVRFVNRLDRDTSGLVVAAKNSFAQDKISSDFKE-DVKKKYLAVVEGVFEEKEGLIDG 187

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +          V+ V         +++ ++V+D + +    + +  HTGRTHQ+RVH  
Sbjct: 188 PIATSEDGIRREVNYVI-----GKRSLTSYEVLDEY-KDMSLVLLTLHTGRTHQIRVHMA 241

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
           H+G PI+GD  Y         S + N+  LH+  +    P     +++ A LP   
Sbjct: 242 HIGHPILGDSLYGKK------SDLINRQALHSYSLKFKLPRNNKEIEVYAKLPKDF 291


>gi|315498200|ref|YP_004087004.1| pseudouridine synthase [Asticcacaulis excentricus CB 48]
 gi|315416212|gb|ADU12853.1| pseudouridine synthase [Asticcacaulis excentricus CB 48]
          Length = 286

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 85/254 (33%), Positives = 135/254 (53%), Gaps = 5/254 (1%)

Query: 73  ALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                 + QK +D  + L+ +   ++KS+L++ED  I  FNKP+ +S QGG G  +++D 
Sbjct: 35  RPVQTPRNQKAIDRPLKLSDEEVVWVKSMLIHEDGVIMGFNKPSNLSSQGGRGNFHNLDD 94

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L ++  S G KPRL HRLD++TSGI++ A+TR +A  +  +   R + K Y  +V    
Sbjct: 95  MLWAFARSNGNKPRLLHRLDRDTSGIILAAKTRTSAAFVGNAIAARDVHKAYVCIVANPH 154

Query: 192 KNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             K E + +  L++  IG + Y  +   +   A  A + ++V+         ++ +P TG
Sbjct: 155 NLKDEGVIDAPLRREEIGREAYSRICDPHHPDALTARTIYRVVSR-TDTSALVQCEPFTG 213

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           R HQ+RVH  H+GCPI GD +Y      +       +L LHAR +D PHP+GGR +  AP
Sbjct: 214 RMHQIRVHMAHLGCPIAGDVRYGGAL--SLDGLRVPRLMLHARAIDFPHPDGGRRRWEAP 271

Query: 311 LPAHMVKTWDSLGF 324
               +      LG 
Sbjct: 272 PSPDIQALCKGLGL 285


>gi|303228679|ref|ZP_07315504.1| putative Ribosomal large subunit pseudouridine synthase D
           [Veillonella atypica ACS-134-V-Col7a]
 gi|303230316|ref|ZP_07317081.1| putative Ribosomal large subunit pseudouridine synthase D
           [Veillonella atypica ACS-049-V-Sch6]
 gi|302515027|gb|EFL57004.1| putative Ribosomal large subunit pseudouridine synthase D
           [Veillonella atypica ACS-049-V-Sch6]
 gi|302516659|gb|EFL58576.1| putative Ribosomal large subunit pseudouridine synthase D
           [Veillonella atypica ACS-134-V-Col7a]
          Length = 295

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 77/322 (23%), Positives = 138/322 (42%), Gaps = 37/322 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M++  Y V   +E +  +  + K  +   +   +Q I R  +V+V+ +       ++ G 
Sbjct: 1   MSWRTYTV--KEEVDTTVSAYVKERFSLSSRN-VQMIFRKKRVKVNSRVAHSKRMLRKGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ I    +    +  E+  ++               +LYED    V  K   + V    
Sbjct: 58  VITIELPQDKDYGVEVEKGPIE---------------VLYEDEHTLVVYKSPFMLVHPAG 102

Query: 124 GIAYHI-DGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              YH     +  +   +G+  K R  HRLD++T+G+++  +TR A Q+ T+  +  RI 
Sbjct: 103 QTKYHTLSNLVAGYYAKRGEVHKIRPVHRLDRDTTGVIMFGKTREAEQYYTKQLQEGRIH 162

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFAQK 239
           ++Y  LV G        I +  +    IG D V    +  ++    A++ + VI+     
Sbjct: 163 RVYRGLVEGK-------ITSDGVVNEPIGVDPVFDNRRCVDEFGQDAVTEYHVIEYD-DV 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL-P 298
              LE    TGRTHQ+RVH  H+G PI+GD  Y    K         +  LHA  +   P
Sbjct: 215 QSLLEFTLLTGRTHQIRVHMAHIGHPIIGDAMYGMRKKP------YTRQALHAYSLTFIP 268

Query: 299 HPEGGRLQITAPLPAHMVKTWD 320
           + +   + + AP+P+ + +   
Sbjct: 269 YGQSELVTVIAPVPSDLGRELQ 290


>gi|223039842|ref|ZP_03610126.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Campylobacter rectus RM3267]
 gi|222878851|gb|EEF13948.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Campylobacter rectus RM3267]
          Length = 354

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 134/333 (40%), Gaps = 44/333 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           MT  +  + E+ +   R D +      ++       +++SG V ++ K + K + ++  G
Sbjct: 17  MTEKEIKICESAQA--RADAFLAAEL-NVARNQALNLIKSGLVSLNGKPLTKPSAKLNLG 73

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V+RI              K   S  N  K     +  ++YED  + V NKPA + V   
Sbjct: 74  DVLRI--------------KFEQSEQNAAKFEAEFEVPIIYEDEDLLVLNKPANLVVHPA 119

Query: 123 SGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
             +    +  L  W+ +KG          +  + HRLD+ TSG +VVA+  AA   L+  
Sbjct: 120 PSV---KEPTLVDWLGAKGFLLSNLSGQSRAGIVHRLDKGTSGAIVVAKNNAAHAALSSQ 176

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
              + + +IY +L   +P  +   +   + +           +  + + A  A ++    
Sbjct: 177 LSDKSMGRIYLALT-DLPLKQNCTVWRAIGRNP--ANRLKKAIVPDGRAAKSAFANLLFS 233

Query: 234 DCFAQKFC------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +              +  +  TGRTHQ+RVH   +   I+GD  Y    + +  +    +
Sbjct: 234 EFDGPAQSKNAGVNLIAAKLFTGRTHQIRVHLASLNRHILGDALYGFKSEKDKIA----R 289

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           + LHA  +   HP  GG++   AP+     +  
Sbjct: 290 VMLHAYGLYFTHPRTGGQMSFVAPIRDDFSEIL 322


>gi|148379407|ref|YP_001253948.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 3502]
 gi|153932742|ref|YP_001383785.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           ATCC 19397]
 gi|153936684|ref|YP_001387335.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           Hall]
 gi|148288891|emb|CAL82977.1| ribosomal large subunit pseudouridine synthase C [Clostridium
           botulinum A str. ATCC 3502]
 gi|152928786|gb|ABS34286.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 19397]
 gi|152932598|gb|ABS38097.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           Hall]
 gi|322805749|emb|CBZ03314.1| ribosomal large subunit pseudouridine synthase C [Clostridium
           botulinum H04402 065]
          Length = 317

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 130/300 (43%), Gaps = 30/300 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  +E   RLD++ +     +    + K +R G+++V+ ++ K  N ++ G +V    
Sbjct: 3   IVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKNFLEEGDIVESFN 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAY 127
           V +      K+   +D+++ +T           YED  + +  K  G+ V      G + 
Sbjct: 63  VKSKGEK--KKFVRIDNNLKIT-----------YEDENMVLVEKWPGVLVHSDKKEGEST 109

Query: 128 HIDGFLKSWVDSKGQKPRL--------THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             D  L    D     P L         +RLD+ TSGI++  +   A + L E  R R+I
Sbjct: 110 LTDYVLSYLYDKGDYTPELEVTFTPASCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRKI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y SLV G  K+       ++ K      +   +  + +        + K I      
Sbjct: 170 EKYYSSLVKGRIKD--GIYEAYISKNE--DTNMSKIYNEPKPNTKKIAMNVKTIQTCGS- 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F ++E++  TGR+HQLR H  H+G PI+GD KY      +F       +  YL++  +  
Sbjct: 225 FSFIEIELLTGRSHQLRAHLSHLGNPIIGDSKYGDKKLNSFFHNKYGLSYQYLYSYKLIF 284


>gi|297588274|ref|ZP_06946917.1| possible RluA protein [Finegoldia magna ATCC 53516]
 gi|297573647|gb|EFH92368.1| possible RluA protein [Finegoldia magna ATCC 53516]
          Length = 321

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 78/339 (23%), Positives = 148/339 (43%), Gaps = 36/339 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ ++N   N R+DR+     P ++  ++QK++R+ +V+V+KKR + +  ++   VV 
Sbjct: 1   MRHINIDNSNSNQRVDRFIMKLMPKMSKNHIQKLIRTKKVKVNKKRTEPDYNLKIDDVVN 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I          + ++ I     N    ++     ++YED  + + NK  G+     +   
Sbjct: 61  IY---------LYDEVIEKYQDNKVYTAEDFNLDIIYEDDDLILINKKTGVLSHAANPQD 111

Query: 127 Y--HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           Y  +I   + S++    Q          P L +RLD+ TSGI+V A+T  + ++  + F+
Sbjct: 112 YGKNIVDMMVSYLIKTNQFTPTQNSTFTPALVNRLDRNTSGIVVGAKTYDSLKYFNDLFK 171

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I KIY ++V G  K++   I   L K        ++           +++    +  
Sbjct: 172 KHEITKIYETIVVGNLKDQ--TIDLALEKDIDKNKSVIN------SSGKKSMTKVWNVKN 223

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHAR 293
           F  K+  + +   TGRTHQ+R H  H+  PI+GD KY       +       N   LH+ 
Sbjct: 224 FG-KYSLVNVDLLTGRTHQIRAHLSHINHPIIGDIKYGNRDVNKYFKNKYDLNFQLLHSY 282

Query: 294 YMDLP-----HPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            +  P     + +   +   +       K  + L  KYD
Sbjct: 283 KLIFPEKMEKYQKYESMVFESKRDDLFEKILNDLESKYD 321


>gi|225351455|ref|ZP_03742478.1| hypothetical protein BIFPSEUDO_03050 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225157799|gb|EEG71082.1| hypothetical protein BIFPSEUDO_03050 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 312

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 73/329 (22%), Positives = 133/329 (40%), Gaps = 35/329 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V   +     R D         I+     +++ SGQ RV  + +  ++ +QSG+ V  
Sbjct: 3   RLVPAPDALVGKRFDVAVAKML-GISRAKAAELIESGQARVLGRDISKSSTLQSGETV-- 59

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       E  I++        +  +   ++YED  + V +KP G++     G  +
Sbjct: 60  ------------EFDIVEERTEPEPIARDM--AVVYEDDDVIVVDKPVGVAAHASVG--W 103

Query: 128 HIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                L S +D            +  +  RLD  TSG+++V ++  A   +   F    +
Sbjct: 104 TGPTVLGSLLDRGVHITSYGAAGRQGIVSRLDVGTSGLMLVCKSDLAYVEMRRQFAEHEV 163

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G  K  K  I   + +                     AI+H+ V++ F + 
Sbjct: 164 VKTYHALVQGNLKENKATIEAPIGR-----AKVSDFRFCVTPAGKEAITHWDVMERFGE- 217

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + +   TGRTHQ+RVH   +G P+ GD  Y AN +      ++ + +LHA+ ++  H
Sbjct: 218 ATLVSVNLETGRTHQIRVHFSSIGHPLAGDAMYGANPQLGEALGLE-RQWLHAKQLEFRH 276

Query: 300 PEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
           P       + +  PA +    D +  ++D
Sbjct: 277 PRTHVWTTVKSHYPADLQHALDVMRGRHD 305


>gi|42526592|ref|NP_971690.1| ribosomal large subunit pseudouridine synthase D [Treponema
           denticola ATCC 35405]
 gi|41816785|gb|AAS11571.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Treponema denticola ATCC 35405]
          Length = 345

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 77/337 (22%), Positives = 137/337 (40%), Gaps = 60/337 (17%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D +      H++   L+  L+S  + V+ ++ K +  +Q+G ++ +            
Sbjct: 26  RIDVYCTETLKHLSRSQLKTGLKS--LYVNSQKAKLSRNVQNGDLIEL------------ 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD- 138
              + D+ +    H   L   ++YED  I V NK  G+      G   + DG L + ++ 
Sbjct: 72  ---VWDNPIPEYAHPQKLPLNIIYEDENIIVVNKERGMVTHPAGG---NWDGTLVNALNY 125

Query: 139 -------------------------------SKGQKPRLTHRLDQETSGILVVARTRAAA 167
                                           +  +  + HRLD+ETSG+++ AR     
Sbjct: 126 YRLYDSRIKDEFAVELNKLLSGEVKNIEKLSLEPYRMGIVHRLDKETSGLIITARNLKTE 185

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           + L   F+ R ++K Y +++ G+P   K  I   + + S     +   V  +      A+
Sbjct: 186 KLLKSFFKKRAVKKYYLAVLDGVPPKNKGRIKTSVFRSSSDRKKFS--VSADLSKGKKAL 243

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           S +KV+     K   +  + +TGRTHQ+R+HA  MGCP+ GD  Y     G        K
Sbjct: 244 SAYKVLKSDG-KMSLVLFRIYTGRTHQIRLHAKFMGCPVAGDKVYGKKKTGLEKKTGLAK 302

Query: 288 -----LYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
                L LHA  + +P     + +  AP+P    +  
Sbjct: 303 KTGMPLMLHAYKLIIPDTVNSKKEFKAPIPNDFKQIL 339


>gi|262282807|ref|ZP_06060574.1| 23S rRNA pseudouridine synthase [Streptococcus sp. 2_1_36FAA]
 gi|262261059|gb|EEY79758.1| 23S rRNA pseudouridine synthase [Streptococcus sp. 2_1_36FAA]
          Length = 295

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 145/322 (45%), Gaps = 35/322 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   ++   + K H   ++   L KI  R G + V+ +       +  G  V
Sbjct: 1   MRFEFIADEHVKVK--TFLKKH--DVSKGLLAKIKFRGGGILVNDEPQNAIYLLDIGDKV 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I          I +++  +S   ++K     K  +++ED    + +KPAG++       
Sbjct: 57  TID---------IPKEEGFESLEAISK-----KLEVVFEDDHFLILDKPAGVASIPSVNH 102

Query: 126 AYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  +  ++K++    G +    H   RLD++TSG+++ A+   A   L +  + R I+K 
Sbjct: 103 SNTMANYVKAYYIDSGYENHQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQKRAIEKR 162

Query: 183 YWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y +LV G     K+  I   + +      +   + ++  KG  YA + +KVI+ F   + 
Sbjct: 163 YLALVKGDGLLEKEGEIIAPIARD-----EDSIITRRVAKGGKYAHTSYKVIEQFGNIY- 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            +++  HTGRTHQ+RVH  H+G P++GD  Y  +      +   ++  LH   +   +P 
Sbjct: 217 LVDIHLHTGRTHQIRVHFSHIGFPLLGDDLYGGSL-----TEGISRQALHCHTLKFYNPF 271

Query: 301 EGGRLQITAPLPAHMVKTWDSL 322
            G  +   +PLP        + 
Sbjct: 272 SGEEIGRASPLPTDFEHVVQTF 293


>gi|326790893|ref|YP_004308714.1| pseudouridine synthase [Clostridium lentocellum DSM 5427]
 gi|326541657|gb|ADZ83516.1| pseudouridine synthase [Clostridium lentocellum DSM 5427]
          Length = 322

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 69/286 (24%), Positives = 129/286 (45%), Gaps = 28/286 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +   E N RLD++   +        + K +R+ +++ + K+ + N  +Q G  ++
Sbjct: 1   MRQITITPLEANQRLDKFLMKYLNECPKSFIYKGMRTKKIKYNGKKPQGNEILQEGDEIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I            E+++    ++            +YED  I + NKP G+  Q  +   
Sbjct: 61  IFFTEEQFKTFSSEKEVKKVPISFQT---------VYEDEHILIVNKPMGLLTQKDTATG 111

Query: 127 YHIDGFLKSWVD---------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           + +   + S++          SKG  P   +RLD+ T+GI++V +   A Q L E  + +
Sbjct: 112 HSLADEVLSYLKDNGSYDPKTSKGFTPAPCNRLDRNTAGIVLVGKHIPAVQVLGEMLQTK 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHI---GGDYVHVVKQNEKGANYAISHFKVID 234
           +I K Y S+V G         A  +LK  HI   G + V +  +  +GA    +    + 
Sbjct: 172 QISKYYMSIVLG------RVTAPMILKGYHIKQEGKNEVKITTEYVEGAKPVETRILPLK 225

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              + +  +E+Q  TG+THQ+R H   +G PI+GD KY    +  +
Sbjct: 226 TNGR-YTLVEVQLVTGKTHQIRAHLSKIGHPIIGDPKYGDPIENQY 270


>gi|115375226|ref|ZP_01462492.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|310818943|ref|YP_003951301.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115367788|gb|EAU66757.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|309392015|gb|ADO69474.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 345

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 75/327 (22%), Positives = 132/327 (40%), Gaps = 42/327 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VVE +    RLDR+       ++   +Q+I++ G V   ++R+K +  +  G    I   
Sbjct: 28  VVEPNYAGWRLDRYLGEKIRRLSRPRIQRIIQRGLVC--ERRLKPSTLVFPGLTFSIRRS 85

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           ++       E                    ++Y+D  + V +KPAG+ +   +   Y   
Sbjct: 86  LSTEPETPTE------------------LPIVYQDDWLLVLDKPAGLPIHPTA--RYQKG 125

Query: 131 GFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             +    +  G++     HRLD+ETSG++V  RT  A + L   F  R + K Y ++  G
Sbjct: 126 TLVSLLRERFGERFAEPAHRLDRETSGLVVCGRTTEACRVLGRLFLSRDVHKEYLAVCEG 185

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQ 246
            P      +   + + + +       V+ +      + + F+V+  F      F  L   
Sbjct: 186 HPPEDTFFVDAPIAEGTELIR---IAVRIDRAEGKESRTRFQVLQRFVRDGAPFALLRCY 242

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANF------------KGNFTSPIQNKLYLHARY 294
           P TGR HQ+R+H    G P+VGD  Y  +                +      +  LHA +
Sbjct: 243 PETGRQHQIRIHLHEAGFPLVGDKMYGPDPGYFDRFSKHCLEPEAWERLRLPRHALHAGH 302

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWD 320
           +  PHP   + +   +PLP  +V   D
Sbjct: 303 IAFPHPGTRQAVSFDSPLPGDLVDFMD 329


>gi|89898789|ref|YP_515899.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           felis Fe/C-56]
 gi|89332161|dbj|BAE81754.1| ribosomal large subunit pseudouridine synthase D [Chlamydophila
           felis Fe/C-56]
          Length = 330

 Score =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 89/356 (25%), Positives = 148/356 (41%), Gaps = 39/356 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRI 59
           M     + ++V E + +  RLD++  +  P  +    Q+ +   +V V+++   K   ++
Sbjct: 1   MKSKNTLLFIVNETNRD--RLDKFLVSQNPEYSRAFYQQHILDERVTVNEQVQTKVATQL 58

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  V I                           + +    +YED  I V NKP  + V
Sbjct: 59  VPGDSVSIIIEEKEELL--------------ELLPEAIPLDKVYEDEMILVINKPRDMVV 104

Query: 120 QGGSG---------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
               G         + + I   LK     +  +P + HRLD++TSG+L+ A+TR A    
Sbjct: 105 HPAPGHIRGTVVHALLHEIGERLKQEFPEEPWRPGIIHRLDKDTSGLLITAKTRQAKTIY 164

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
           +E F  ++++K Y ++  G P      + +  L + H     + V          AI+H 
Sbjct: 165 SELFATKQLKKSYLAICVGKPTA---TLIHTKLARHHSKRKEMAV----SLTGKEAITHC 217

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           +V+     K   + ++P TGRTHQLRVH  H+  PI+GD  Y +           +K  L
Sbjct: 218 EVLAYNG-KLSLVLLRPETGRTHQLRVHMKHLNTPILGDPVYGSPSIN--AGYGLDKQQL 274

Query: 291 HARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNI 345
           HA  +D  HP+   RL +T  LP  M      L   ++    I +   +   K NI
Sbjct: 275 HAYSLDFIHPQTHRRLNLTTELPCDMKILL--LKEFHNSKTVIDKQLFESIIKTNI 328


>gi|167747168|ref|ZP_02419295.1| hypothetical protein ANACAC_01882 [Anaerostipes caccae DSM 14662]
 gi|317473628|ref|ZP_07932917.1| RluA family pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
 gi|167654128|gb|EDR98257.1| hypothetical protein ANACAC_01882 [Anaerostipes caccae DSM 14662]
 gi|316898918|gb|EFV20943.1| RluA family pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 329

 Score =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 72/332 (21%), Positives = 140/332 (42%), Gaps = 29/332 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + + + EE  RLD+    +        L K+LR   ++++ K+   + +++SG VV 
Sbjct: 1   MKEIRISDREEEQRLDKLLAKYLNKAPKSFLYKMLRKKNIKLNGKKASGSEKLKSGDVVC 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +    +E +      +L+         ++Y+DS + + NKP G+  Q      
Sbjct: 61  VYMADATIASFREEPRAERRKADLS---------VIYQDSNVLIINKPYGMLSQKAKPSD 111

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             ++  +  +    G          +P + +RLD+ T+G+L+   +    Q + E  R R
Sbjct: 112 ISVNELIVPYCLEHGILKESDLELVRPSVCNRLDRNTTGLLIAGISLEGLQTMAEVLRDR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y+ +V G+  NKK  I+ ++ K        V   ++   G +   + ++ +    
Sbjct: 172 SVRKYYYCIVKGMV-NKKTRISGYICKDHREN--KVSFSERKISGGSRIETAYEPMAA-G 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYM 295
             F  L ++  TG+THQ+R H   MG P+ GD KY                   LH   +
Sbjct: 228 HGFTLLRVELITGKTHQIRAHLAGMGFPLAGDTKYGDRGVNLQMKQKFGVKHQLLHCGCL 287

Query: 296 DLP--HPEGGRL---QITAPLPAHMVKTWDSL 322
           + P      G L    + A  P   ++T + L
Sbjct: 288 EFPEGMKRCGELSGRTVAAEPPETFLRTANEL 319


>gi|289449856|ref|YP_003475266.1| putative ribosomal large subunit pseudouridine synthase D
           [Clostridiales genomosp. BVAB3 str. UPII9-5]
 gi|289184403|gb|ADC90828.1| putative ribosomal large subunit pseudouridine synthase D
           [Clostridiales genomosp. BVAB3 str. UPII9-5]
          Length = 319

 Score =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 74/318 (23%), Positives = 122/318 (38%), Gaps = 39/318 (12%)

Query: 19  MRLDRWFKNHYPHI----NFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINA 73
            RLD         +       ++ K L   +V + D    K   ++     V+I     A
Sbjct: 12  ERLDVTLTECLQELGHKLTRSDITKALNEKRVLLADGTFPKAGLKLTCPCHVKIELSEVA 71

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGF 132
           +                   ++ L   +++ED  + V NKP G+ V    G A   +   
Sbjct: 72  VPR---------------HEAEDLPLDIVFEDEYLLVVNKPRGLVVHPAPGHANGTLVNA 116

Query: 133 LKSWVDSKG-------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           L ++             +P + HR+D++TSG+LVVA+  +    L E   +  I ++Y +
Sbjct: 117 LLNYCGGNNLSDINGEFRPGIVHRIDKDTSGLLVVAKDNSIHNKLAELLSVHAINRVYQA 176

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V+G        I   + +           +K        A++HF V+      +  L +
Sbjct: 177 IVFGNFAETAGKIDAPIGRDPRNRQKMAVTLK-----GKPALTHFTVLASRP-GYSLLRL 230

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              TGRTHQ+RVH  ++G P+VGD  Y A  K            LHA  +   HP   R+
Sbjct: 231 NLETGRTHQIRVHLSYIGHPVVGDPLYAAGRKYA----DLGGQLLHAAELHFRHPITQRM 286

Query: 306 -QITAPLPAHMVKTWDSL 322
               APLP       +  
Sbjct: 287 IDCYAPLPEVFNTFLEQF 304


>gi|254517173|ref|ZP_05129231.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium NOR5-3]
 gi|219674678|gb|EED31046.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium NOR5-3]
          Length = 282

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 72/294 (24%), Positives = 125/294 (42%), Gaps = 33/294 (11%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           +D +  +  + +  G  + +   + +    +               +  L   +LYED +
Sbjct: 2   LDGRSARPRDAVHGGAQLSLSAELQSEVSWV---------------AQSLPLNILYEDEE 46

Query: 108 IYVFNKPAGISVQGGSGIAY--HIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTR 164
           + V +KPAG+ V  G+G  +   ++  L      +   +  + HRLD+ETSG+LVVA T 
Sbjct: 47  LLVIDKPAGLVVHPGAGNHHGTLVNALLSHRPALESVPRGGIVHRLDKETSGLLVVAGTL 106

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            A + L    + + +Q+ Y+++V G+P      I   + +        + VV        
Sbjct: 107 NAHRSLVAQLQKKDVQREYFAIVRGVPSG-GGRIETAIGRHPRQ-RTRMAVV---PNSGK 161

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-------- 276
            A++H+++   FAQ      +Q  TGRTHQ+RVH  H G P++GD  Y            
Sbjct: 162 PAVTHYRIAQRFAQYTALS-VQLETGRTHQIRVHMAHRGYPLLGDPVYGGRLQLPRACSE 220

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSLGFKYDRN 329
           +   T     +  LHAR +   HP  G L    +PL   +      L  +   +
Sbjct: 221 RLAETLRGFRRQALHARRLSFIHPGSGDLCSFESPLADDLQGLLQVLAEENPSD 274


>gi|167756776|ref|ZP_02428903.1| hypothetical protein CLORAM_02325 [Clostridium ramosum DSM 1402]
 gi|167702951|gb|EDS17530.1| hypothetical protein CLORAM_02325 [Clostridium ramosum DSM 1402]
          Length = 328

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 77/334 (23%), Positives = 144/334 (43%), Gaps = 31/334 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +  ++ N R+D++ K    +     + K+ R   ++V+ K+V     +     V 
Sbjct: 7   MKKLKITENDANQRIDKYLKKLLVNAPNNFIYKMFRKKDIKVNGKKVDEKYILSLDDEVE 66

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    +      + + I + +   +         +LYED  + +  KPAG+ V   +  +
Sbjct: 67  MFLYDDKFKEFTETKSIYEVNKTFS---------VLYEDKHVLIVFKPAGLLVHEDANES 117

Query: 127 -YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +   + S++ SK +          P   HRLD+ TSGI++  +T AA Q+L E  + 
Sbjct: 118 INTLTNQVLSYLASKNELDLSRENTFMPGPVHRLDRNTSGIVIFGKTLAALQNLNEMIKQ 177

Query: 177 RR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           R  I+K Y ++  G   N +  +  +++K  +     V +VK++  GA    +  + +  
Sbjct: 178 RHCIEKKYLTICRGQL-NHQRNLHGYMIKLENQA--QVKLVKKDYPGALTMETIVRPLKY 234

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHAR 293
               +  +E+   TGR HQ+RVH   +  PI+GD KY       +   +   N   LHA 
Sbjct: 235 NCD-YSLVEVTLITGRMHQIRVHLSSIEHPIIGDRKYGDFELNKYIKKTFGLNNQLLHAY 293

Query: 294 YMDLPHPEG-----GRLQITAPLPAHMVKTWDSL 322
            +      G        +I  P+PA   K   SL
Sbjct: 294 KIKFVKTFGVLNYLQDKEIICPVPALFEKIEKSL 327


>gi|310828937|ref|YP_003961294.1| pseudouridine synthase [Eubacterium limosum KIST612]
 gi|308740671|gb|ADO38331.1| pseudouridine synthase [Eubacterium limosum KIST612]
          Length = 321

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 144/326 (44%), Gaps = 16/326 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   ++ +  N RLDR+     P  +   LQK+LR  +++++  R +  + I SG  V+
Sbjct: 1   MKQYTIDENSGNQRLDRYLSKLMPLADRNFLQKMLRKKRIKLNGVRAEPKDMIHSGDTVQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +     ++K +    +L      +    +YED  + V NKPAG+  Q  S   
Sbjct: 61  VYFSEETIAGF--QEKKVQRHFDLKPEIKKIFEPPVYEDDHLLVVNKPAGLLSQADSSGN 118

Query: 127 YHIDGFLKSWV-----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             +    ++++     D+K  +  +++RLD+ TSGI+++ +     Q +  + R R+  K
Sbjct: 119 ISLIDAARTYLKKNATDTKAFEVVISNRLDRNTSGIILMPKDYPTLQTVNAAIRERQALK 178

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G+ K K   +  +L K +        +  Q+EKGA      +  +     KF 
Sbjct: 179 EYHTIVLGVLK-KPGTLTGFLTKDTIENKS--AIQSQSEKGAKEVRLDYCPL-MNNGKFT 234

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPH 299
            LE+  HTGR+HQ+R      G PI+GD+KY         S         LH+R+  +  
Sbjct: 235 LLEITLHTGRSHQIRSQLADYGFPIIGDYKYGDASINRHFSQKYGLKHHLLHSRHYAIKD 294

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFK 325
                   TAP P    +    L   
Sbjct: 295 L---EYDFTAPYPLLFKQLLKELNLD 317


>gi|170759830|ref|YP_001786858.1| RluA family pseudouridine synthase [Clostridium botulinum A3 str.
           Loch Maree]
 gi|169406819|gb|ACA55230.1| pseudouridine synthase, RluA family [Clostridium botulinum A3 str.
           Loch Maree]
          Length = 317

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 129/300 (43%), Gaps = 30/300 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  +E   RLD++ +     +    + K +R G+++V+ ++ K  N ++ G +V    
Sbjct: 3   IVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKNFLEEGDIVESFN 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAY 127
           V +      K+   +D+++ +T           YED  + +  K  G+ V      G   
Sbjct: 63  VKSKGEK--KKFVRIDNNLKIT-----------YEDENMVLVEKWPGVLVHSDKKEGEPT 109

Query: 128 HIDGFLKSWVDSKGQKPRL--------THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             D  L    D     P L         +RLD+ TSGI++  +   A + L E  R R+I
Sbjct: 110 LTDYVLSYLYDKGDYTPELEVTFTPAPCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRKI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y SLV G  K+       ++ K      +   +  + +        + K I      
Sbjct: 170 EKYYSSLVKGRIKD--GVYEAYISKNE--DTNMSKIYNEPKPNTKKIAMNVKTIQTCGS- 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F ++E++  TGR+HQLR H  H+G PI+GD KY      +F       +  YL++  +  
Sbjct: 225 FSFIEIELLTGRSHQLRAHLSHLGNPIIGDSKYGDKKLNSFFHNKYGLSYQYLYSYKLIF 284


>gi|168182364|ref|ZP_02617028.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
 gi|237794773|ref|YP_002862325.1| RluA family pseudouridine synthase [Clostridium botulinum Ba4 str.
           657]
 gi|182674479|gb|EDT86440.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
 gi|229262158|gb|ACQ53191.1| pseudouridine synthase, RluA family [Clostridium botulinum Ba4 str.
           657]
          Length = 317

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 129/300 (43%), Gaps = 30/300 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  +E   RLD++ +     +    + K +R G+++V+ ++ K  N ++ G +V    
Sbjct: 3   IVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKNFLEEGDIVESFN 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAY 127
           V +      K+   +D+++ +T           YED  + +  K  G+ V      G   
Sbjct: 63  VKSKGEK--KKFVRIDNNLKIT-----------YEDENMVLVEKWPGVLVHSDKKEGEPT 109

Query: 128 HIDGFLKSWVDSKGQKPRL--------THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             D  L    D     P L         +RLD+ TSGI++  +   A + L E  R R+I
Sbjct: 110 LTDYVLSYLYDKGDYTPELEVTFTPAPCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRKI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y SLV G  K+       ++ K      +   +  + +        + K I      
Sbjct: 170 EKYYSSLVKGRIKD--GVYEAYISKNE--DTNMSKIYNEPKPNTKKIAMNVKTIQTCGS- 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F ++E++  TGR+HQLR H  H+G PI+GD KY      +F       +  YL++  +  
Sbjct: 225 FSFIEIELLTGRSHQLRAHLSHLGNPIIGDSKYGDKKLNSFFHNKYGLSYQYLYSYKLIF 284


>gi|295698595|ref|YP_003603250.1| ribosomal large subunit pseudouridine synthase C [Candidatus Riesia
           pediculicola USDA]
 gi|291157274|gb|ADD79719.1| ribosomal large subunit pseudouridine synthase C [Candidatus Riesia
           pediculicola USDA]
          Length = 331

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 86/317 (27%), Positives = 159/317 (50%), Gaps = 17/317 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+ +    R+D +       +    + +++R G++RVD  +V  + R+Q   +++IP 
Sbjct: 17  IFVDENSLFQRIDNFLIKRLKRVPKRLIYRLIRIGKIRVDDSKVNPSYRVQKEDLIKIPI 76

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDF-LKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            ++            D S+++ + + + +K  +LYEDS+I V NKP+GI+V  GS  ++ 
Sbjct: 77  SLSYSQ---------DKSISIQRKNFYWIKKRILYEDSEILVLNKPSGIAVHSGSKFSFG 127

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           I   L+           L HR+D+ETSGIL++A++R   Q + + F  ++I K Y  LV 
Sbjct: 128 IIEILREVYFQSKY-LELIHRIDKETSGILLIAKSRNILQLIQKQFCSQKIFKKYIVLVH 186

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+  +K + I+ +L KK     +    +K+N      + + F++ + FA  F  +   P 
Sbjct: 187 GVWPSKIKRISCFLEKKISQKKEKKIEIKKN---GRMSETLFQIKERFAS-FTLMLATPI 242

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
           TGR HQ+R+H   +  PIV D +Y       N       +L+LH+  + + HP+    L 
Sbjct: 243 TGRKHQIRLHTKKINHPIVLDKRYGNRKLDRNLKESGLKRLFLHSSSITMNHPKKLINLT 302

Query: 307 ITAPLPAHMVKTWDSLG 323
             +P+  ++    + L 
Sbjct: 303 FVSPIDKNLNGCLNWLR 319


>gi|303234009|ref|ZP_07320658.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
 gi|302494934|gb|EFL54691.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
          Length = 321

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 78/339 (23%), Positives = 149/339 (43%), Gaps = 36/339 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++++ ++N   N R+DR+     P ++  ++QK++R+ +++V+KKR + +  ++   VV 
Sbjct: 1   MRHINIDNSNSNQRVDRFLMKLMPKMSKNHIQKLIRTKKIKVNKKRTEPDYDLKIDDVVN 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I          + ++ I     N    +D     ++YED+ + + NK  G+     +   
Sbjct: 61  IY---------LYDEVIEKYQDNKIYTADDFNLDIIYEDNDLILINKKTGVLSHAANPQD 111

Query: 127 Y--HIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           Y  +I   + S++    Q          P L +RLD+ TSGI+V A+T  + ++    F+
Sbjct: 112 YGENIVDMMVSYLIKTNQFKPTQNSTFTPALVNRLDRNTSGIVVGAKTYDSLKYFNGLFK 171

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I KIY ++V G  K++   I   L K +      ++           +++    +  
Sbjct: 172 KHEITKIYETIVVGNLKDQ--TIDFALEKDNDKNKSVIN------SSGKKSMTKVWNVKN 223

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHAR 293
           F  K+  + +   TGRTHQ+R H  H+  PI+GD KY       +       N   LH+ 
Sbjct: 224 FG-KYSLVNVDLLTGRTHQIRAHLSHINHPIIGDIKYGNREVNKYFKNKYDLNFQLLHSY 282

Query: 294 YMDLP-----HPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
            +  P     + +   +   +       K  + L  KYD
Sbjct: 283 KLVFPEKMEKYQKYESMVFESKRDDLFEKILNDLESKYD 321


>gi|153007158|ref|YP_001381483.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152030731|gb|ABS28499.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 350

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 71/327 (21%), Positives = 130/327 (39%), Gaps = 39/327 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             VE +    RLDR+ +     ++   +Q+++ +     D +R+K + R+ +G       
Sbjct: 38  FTVEPNYAGWRLDRYLQEKIRRLSRERVQRLIETRLEAEDGRRLKPSTRVVAG------- 90

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                  ++K+ +    +  +          ++++D  + V +KPAG+ V   +  + + 
Sbjct: 91  ---LAFALLKDAEPEPDTPQV--------FDVVHDDGALLVVDKPAGLPVHPTARYSANT 139

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L        +K    HRLD+ETSG+L           +   F   R++K Y ++  G
Sbjct: 140 FTSLARARFPD-RKVDPAHRLDRETSGLLACGSAPEWTSRMKRDFAQGRVKKTYLAIAEG 198

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----AQKFCWLEM 245
            P+     +   L   +  G   V V    + G   + + F+V+             L  
Sbjct: 199 APREDTFTVDAPL---ALTGASAVRVRMHVDAGGLASATDFEVLARRVLAGGVPVALLAC 255

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANF------------KGNFTSPIQNKLYLHAR 293
           +P TGR HQ+R H  H G P+VGD  Y  +               +       +  LHA 
Sbjct: 256 RPRTGRQHQIRAHLAHAGLPMVGDKIYGPDENIFDRFTRHALTDEDHARLRLPRHALHAW 315

Query: 294 YMDLPHPEG-GRLQITAPLPAHMVKTW 319
            ++LPHP     + + +PLP  +   W
Sbjct: 316 RLELPHPRTREPVGLESPLPPDLATFW 342


>gi|317476220|ref|ZP_07935471.1| RluA family pseudouridine synthase [Bacteroides eggerthii
           1_2_48FAA]
 gi|316907631|gb|EFV29334.1| RluA family pseudouridine synthase [Bacteroides eggerthii
           1_2_48FAA]
          Length = 303

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 76/308 (24%), Positives = 126/308 (40%), Gaps = 34/308 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     ++N  ++ G  V+I        
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKSLLSKRIVYVDSVITTQYNFPLKPGMKVQIS------- 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
              +E+   + S  L K        ++YED+ I V  K  G+ SV             L 
Sbjct: 74  ---REKGRKEFSNRLLK--------IVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 122

Query: 135 SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G   +  + HRLD++TSG+++ A+       L +++      + Y ++V G  +
Sbjct: 123 EYVQRSGRQHRVYIVHRLDRDTSGLMMFAKDEKTQNTLRDNWHNIVTDRRYVAVVAGEME 182

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           N    + +WL                 + G   A++H++ I   A  F  +E+   TGR 
Sbjct: 183 NNAGMVRSWLT-----DRKLYVYSSPTDDGGKEAVTHYRTIKR-ANGFSLVELVLETGRK 236

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y             N+L LHA  +   HP  G  +Q   P 
Sbjct: 237 NQIRVHMQDLGHPIIGDGRYGLEEVNP-----INRLALHAFKLCFHHPVTGELMQFETPY 291

Query: 312 PAHMVKTW 319
           P    K +
Sbjct: 292 PGEFKKLF 299


>gi|304438735|ref|ZP_07398663.1| RluA family pseudouridine synthase [Peptoniphilus duerdenii ATCC
           BAA-1640]
 gi|304372737|gb|EFM26315.1| RluA family pseudouridine synthase [Peptoniphilus duerdenii ATCC
           BAA-1640]
          Length = 292

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 77/312 (24%), Positives = 136/312 (43%), Gaps = 42/312 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           EE + +  + K    +++   +++ +R   + +++K  K N  +Q G VV I       N
Sbjct: 14  EEEISIKNFLKKL--NLSSRYIRRSIREEMIYINEKLNKRNVDLQPGDVVSIKIPDEEPN 71

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
            I                 +  K  +LYED  I   NK   + V     + +   G + +
Sbjct: 72  AI----------------PEDYKVEILYEDGDILAVNKEPFMIVHA---VDFKQTGTISN 112

Query: 136 WVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +V          +K RL +RLD++TSG++++A+   A   +    + R I K Y+++V G
Sbjct: 113 YVQCYFLKHDIHRKVRLINRLDRDTSGVILIAKNSNAHSTVARELQDRNILKKYYAIVEG 172

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           + +          + +  I      ++++      YA + ++ I         L +  HT
Sbjct: 173 VVEGSG-------IIEEPIDRGPDGILREVNPNGKYAKTSYEAILSK-NNMTLLRVVLHT 224

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
           GRTHQ+RVH  ++G PIVGD  Y         + + N+  LH+ Y  +  P  G  ++I 
Sbjct: 225 GRTHQIRVHLKYIGHPIVGDTLYGNE------TELINRQALHSYYTKIKSPRTGEEIEIE 278

Query: 309 APLPAHMVKTWD 320
           APLP  M    D
Sbjct: 279 APLPQDMKNLLD 290


>gi|197124689|ref|YP_002136640.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196174538|gb|ACG75511.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 323

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 74/328 (22%), Positives = 126/328 (38%), Gaps = 39/328 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             VE +    RLDR+ +     ++   +Q+++       D +R+K + R+  G    +  
Sbjct: 14  FTVEPNYAGWRLDRYLQEKIRRLSRERVQRLIEHRLETEDGRRLKPSTRVAPGLSFALLK 73

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
              A     +E                    ++++D  + V +KPAG+ V   +  A + 
Sbjct: 74  DAEAEPDTPQE------------------FAVVHDDGALLVVDKPAGLPVHPTARYAANT 115

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L      + +K    HRLD+ETSG+L    +    + L   F   R+ K Y +L  G
Sbjct: 116 FTSLAKLRFPE-RKVDPAHRLDRETSGLLACGTSPEVTKVLKRDFAHARVHKTYLALALG 174

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----AQKFCWLEM 245
            P      +   L   +  G   V V          + + F+V+             L  
Sbjct: 175 APVEDAFTVDAPL---ALTGASAVRVRMHVAAEGLPSQTAFEVLARRRAPDGAPVALLAC 231

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------------GNFTSPIQNKLYLHAR 293
           +P TGR HQ+R H  H G P+VGD  Y  + +             +       +  LHA 
Sbjct: 232 RPRTGRQHQIRAHLAHAGLPMVGDKIYGPDEEIFDRFTRRAMTDEDVALLRLPRHALHAW 291

Query: 294 YMDLPHPEG-GRLQITAPLPAHMVKTWD 320
            ++LPHP     +++  PLP  +   W+
Sbjct: 292 RLELPHPLTRAPVRLEVPLPPDLAAFWE 319


>gi|116515184|ref|YP_802813.1| RluD [Buchnera aphidicola str. Cc (Cinara cedri)]
 gi|116257038|gb|ABJ90720.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Cc (Cinara cedri)]
          Length = 321

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 83/344 (24%), Positives = 152/344 (44%), Gaps = 38/344 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRI 59
           MS +  + ++V +  E+++RLD+    H    +  +++K + SG ++V+     K   +I
Sbjct: 1   MSNLKKINFIVPKLKEKSIRLDKILVKHLNSFSRSSIKKWILSGFIKVNNITANKPKKKI 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
                + +     +    IK++ I                 +++EDS+I + NKP    V
Sbjct: 61  LFKDRISLIINKKSNFIKIKKENIF--------------LNIIFEDSEILIINKPTNFVV 106

Query: 120 QGGSGIA--YHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             G G      ++  +  + D+    +  + HRLD+ T+GILVVA+T +    L   F+ 
Sbjct: 107 HLGYGNTSGTLLNALIFHYPDNLLIPRAGIVHRLDRNTTGILVVAKTISTYYFLINLFKK 166

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R+I K Y  +V G  +   +      +K+       + V      G   AI+++ VI   
Sbjct: 167 RKIIKEYDVIVIGRIEVDGKIEK--PIKRDIYNRTKMTV----GIGGKQAITYYSVI-TI 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---------NK 287
            +   +L +Q  TGR HQ+RVH   +  P++GD  Y    K NF++  +         N+
Sbjct: 220 FKNHTYLRIQLKTGRMHQIRVHLSSIFHPVLGDKIYSKGIKSNFSNCSKKMKNFLSKFNR 279

Query: 288 LYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDRNL 330
             LHAR ++  HP+   +       P  M+   + L   Y  ++
Sbjct: 280 PALHARMLNFIHPKTNKKKNWIIYPPKDMLSLINVL---YSEDM 320


>gi|307720729|ref|YP_003891869.1| ribosomal large subunit pseudouridine synthase D [Sulfurimonas
           autotrophica DSM 16294]
 gi|306978822|gb|ADN08857.1| ribosomal large subunit pseudouridine synthase D [Sulfurimonas
           autotrophica DSM 16294]
          Length = 324

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 80/347 (23%), Positives = 150/347 (43%), Gaps = 45/347 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           M   Q  + +N E   RLD +  +         +  +++   V VD K+V +   ++++G
Sbjct: 1   MINTQEYICKNPE---RLDTFLTSQI-GQTRSQIAGLIKHECVFVDGKKVPRPGVKLKAG 56

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           QVV++           K++K LD + ++          +LYED  + V NKP+G++V   
Sbjct: 57  QVVKVEFPE------AKQEKALDVNFDVE---------ILYEDDDVLVINKPSGVTVHPA 101

Query: 123 SGIAYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTES 173
             +    +  L  W+  KG +           + HRLD+ TSG +VVA+   A + L++ 
Sbjct: 102 PSV---KEATLVDWLKHKGIRLSTISGEERHGIVHRLDKGTSGTMVVAKNNEAHEFLSKQ 158

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + + + + Y +++    K     + + + + SH        +    +   YA + FK +
Sbjct: 159 LQDKSMGRYYIAVIVPPLKEDITVVESNIGRSSHNRLK----MACGLEHGKYAKTMFKQL 214

Query: 234 DCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                +    +  +  TGRTHQ+RVH   M   I+GDH Y  + K   +     ++ LHA
Sbjct: 215 ALSEDEHTQLIACKLFTGRTHQIRVHLESMNRHILGDHIYGLSPKQENSE----RILLHA 270

Query: 293 RYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             +   HP    ++   A     M +T      K+D  +  + +  +
Sbjct: 271 YMIYFIHPTTKEKVTFKAEFDDIMRETIYK---KFDTEILNEVIEPE 314


>gi|329964802|ref|ZP_08301825.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
 gi|328524653|gb|EGF51716.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
          Length = 303

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 72/308 (23%), Positives = 124/308 (40%), Gaps = 34/308 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           + M L  +     P  +   L+ +L    V VD     ++N  ++ G  V+I        
Sbjct: 21  DPMELMEFLAAKMPDASRTKLKSLLSKRIVYVDSVITTQYNFPLKPGMKVQIS------- 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
              +E+   + +  L K        ++YED+ I V  K  G+ SV             L 
Sbjct: 74  ---REKGRKEFNHKLIK--------IVYEDAYIIVIEKMQGLLSVNTERQKERTAYTILN 122

Query: 135 SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G   +  + HRLD++TSG+++ A+       L + +      + Y ++V G  +
Sbjct: 123 EYVQRSGRQHRVYIVHRLDRDTSGLMMFAKDEKTQNTLRDHWHDIVFDRRYVAVVAGEME 182

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                +++WL                 + G   AI+H++ I   A  +  +E+   TGR 
Sbjct: 183 KNVGSVSSWLT-----DRKLYVYSSPIDDGGKEAITHYRTIKR-ANGYSLVELNLETGRK 236

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y              +L LHA  +   HP  G  +    P 
Sbjct: 237 NQIRVHMQDLGHPIIGDGRYGLEEVNP-----IGRLALHAFKLCFDHPVTGESMHFETPY 291

Query: 312 PAHMVKTW 319
           PA   K +
Sbjct: 292 PADFKKLF 299


>gi|153806600|ref|ZP_01959268.1| hypothetical protein BACCAC_00870 [Bacteroides caccae ATCC 43185]
 gi|149131277|gb|EDM22483.1| hypothetical protein BACCAC_00870 [Bacteroides caccae ATCC 43185]
          Length = 306

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 77/308 (25%), Positives = 133/308 (43%), Gaps = 33/308 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  ++ G  V+I        
Sbjct: 24  EPMELMEFLTAKMPDASRTKLKSLLSKRVVLVDNVITTQFNFPLKPGMKVQI-------- 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     S     K  +     ++YED+ I V  K  G+ SV             L 
Sbjct: 76  ----------SKDKGRKEFNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 125

Query: 135 SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G   +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 126 EYVQRSGRQHRVYIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSME 185

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + +WL  K+     YV     ++ G+  +I+H++ I   A  +  +E+   TGR 
Sbjct: 186 KDYDTVVSWLTDKTL----YVSSSGYDDGGSK-SITHYRTIKR-ANGYSLVELDLETGRK 239

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI GD +Y      N+++PI  +L LHA  +   HP  G  ++   P 
Sbjct: 240 NQIRVHMQDLGHPIAGDGRYGGE---NYSNPI-GRLALHAFKLCFYHPVTGDLMEFETPY 295

Query: 312 PAHMVKTW 319
           P    K +
Sbjct: 296 PGEFKKLF 303


>gi|15615410|ref|NP_243713.1| hypothetical protein BH2847 [Bacillus halodurans C-125]
 gi|10175468|dbj|BAB06566.1| BH2847 [Bacillus halodurans C-125]
          Length = 302

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 74/330 (22%), Positives = 141/330 (42%), Gaps = 39/330 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRI 59
           M     V++  V+   +   L  + +    H++  +L  I  + G + ++ + V     +
Sbjct: 1   MIRKAKVEW-TVDEQWDGELLRTFLREG-KHVSKRSLAAIKFKGGTILLNGEEVTVRETV 58

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
                V +              ++     + +  ++ +   ++YE+    V NKPAG+  
Sbjct: 59  HVNDQVTL--------------ELPHEYPSPSMIAEPVPFDVIYENDHYLVVNKPAGVPT 104

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTES 173
                   H  G L + + +  Q+          +RLD++TSG+L+VA+ + A   L++ 
Sbjct: 105 IPSR---DHPQGTLANGLLNYFQRQKMAATFHAVNRLDKDTSGLLIVAKHQLAHDQLSKQ 161

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R   I++ Y ++V G  + ++  I   + +K     +   + ++  +    AI+HFKVI
Sbjct: 162 QRQGNIKRTYMAIVQGEIEQQEGTITAPIARK-----EESLITREVREDGQLAITHFKVI 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D   Q    +++Q  TGRTHQ+RVH  ++G P+ GD  Y    KG        +  LH+ 
Sbjct: 217 DRLNQG-TIVQVQLETGRTHQIRVHFSYLGYPLFGDDLYGGERKG------IERQALHST 269

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            + +  P        T  LP  M +    L
Sbjct: 270 ELTIHCPFTEVEQTFTEGLPPDMKELIRHL 299


>gi|153938225|ref|YP_001390782.1| RluA family pseudouridine synthase [Clostridium botulinum F str.
           Langeland]
 gi|168180094|ref|ZP_02614758.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
 gi|170754896|ref|YP_001781073.1| RluA family pseudouridine synthase [Clostridium botulinum B1 str.
           Okra]
 gi|226948698|ref|YP_002803789.1| pseudouridine synthase, RluA family [Clostridium botulinum A2 str.
           Kyoto]
 gi|152934121|gb|ABS39619.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           Langeland]
 gi|169120108|gb|ACA43944.1| pseudouridine synthase, RluA family [Clostridium botulinum B1 str.
           Okra]
 gi|182668924|gb|EDT80900.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
 gi|226843753|gb|ACO86419.1| pseudouridine synthase, RluA family [Clostridium botulinum A2 str.
           Kyoto]
 gi|295318854|gb|ADF99231.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           230613]
          Length = 317

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 129/300 (43%), Gaps = 30/300 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V+  +E   RLD++ +     +    + K +R G+++V+ ++ K  N ++ G +V    
Sbjct: 3   IVIGANEAGQRLDKFCRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKNFLEEGDIVESFN 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAY 127
           V +      K+   +D+++ +T           YED  + +  K  G+ V      G   
Sbjct: 63  VKSKGEK--KKFVRIDNNLKIT-----------YEDENMVLVEKWPGVLVHSDKKEGEPT 109

Query: 128 HIDGFLKSWVDSKGQKPRL--------THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             D  L    D     P L         +RLD+ TSGI++  +   A + L E  R R+I
Sbjct: 110 LTDYVLSYLYDKGDYTPELEVTFTPASCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRKI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y SLV G  K+       ++ K      +   +  + +        + K I      
Sbjct: 170 EKYYSSLVKGRIKD--GVYEAYISKNE--DTNMSKIYNEPKPNTKKIAMNVKTIQTCGS- 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F ++E++  TGR+HQLR H  H+G PI+GD KY      +F       +  YL++  +  
Sbjct: 225 FSFIEIELLTGRSHQLRAHLNHLGNPIIGDSKYGDKKLNSFFHNKYGLSYQYLYSYKLIF 284


>gi|313634007|gb|EFS00696.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri FSL N1-067]
          Length = 296

 Score =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 74/317 (23%), Positives = 140/317 (44%), Gaps = 40/317 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V  ++  + L  + ++   HI+   L   K    G++ V+         +Q+G  VR+  
Sbjct: 7   VNKEDSGLLLRTFLRS--KHISKQLLTAVKFSVDGKIEVNGTEQNVLYEVQTGDEVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +           L +H+D     +++ED  + + NKPAGI+        YH 
Sbjct: 65  PTEQQNERL-----------LAEHTDL---EIVFEDEFLLIINKPAGIASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 SGSVANFVKGHYEAQGLTSAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQQGLLKRSY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            + V G    +   I   + +K+        + +       YA ++++V+  + Q F  +
Sbjct: 168 QAFVSGELAEQVGSIEAPIGRKA-----VSIMERVVTPEGKYAKTNYQVLARY-QAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP   
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TDLLKRQALHSCHLHLIHPLTE 275

Query: 304 R-LQITAPLPAHMVKTW 319
             L    PLP  M +  
Sbjct: 276 EYLAFDLPLPYDMEEII 292


>gi|229817354|ref|ZP_04447636.1| hypothetical protein BIFANG_02616 [Bifidobacterium angulatum DSM
           20098]
 gi|229785143|gb|EEP21257.1| hypothetical protein BIFANG_02616 [Bifidobacterium angulatum DSM
           20098]
          Length = 314

 Score =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 78/335 (23%), Positives = 140/335 (41%), Gaps = 36/335 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V   +     R D         ++      ++ +GQVRV  + +  +  +Q+G+
Sbjct: 1   MSRV--VPAPDALVGARFDVAVSKML-GVSRSKAATLIDTGQVRVLDREITKSTTLQAGE 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V I         +++E+K  +   N           ++YED  + V +KP G++     
Sbjct: 58  TVEI--------DLVEERKEPEPIAN--------DMAIVYEDDDVVVVDKPVGVAAHASV 101

Query: 124 GIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G  +     L S +D            +  +  RLD  TSG+++V ++  A   +   F 
Sbjct: 102 G--WTGPTVLGSLLDRGVHITAYGAAGRQGIVSRLDVGTSGLMLVCKSDLAYVEMRRQFA 159

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              + K Y +LV G  K  +  I   + +                     AI+H+ V++ 
Sbjct: 160 EHEVVKTYHALVQGNLKEDRATIEAPIGR-----AKVSDFRFCVTPAGKPAITHWDVMER 214

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F  +   +++   TGRTHQ+RVH   +G P+VGDH Y AN        I+ + +LHA  +
Sbjct: 215 FGSEATLVKVNLETGRTHQIRVHFSSIGHPLVGDHMYGANPVLAEDLNIE-RQWLHAMQL 273

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRN 329
           +  HP       +T+  PA +    D++  ++  N
Sbjct: 274 EFRHPRTHVWTTVTSSYPADLAHALDAMRARHADN 308


>gi|160901794|ref|YP_001567375.1| RluA family pseudouridine synthase [Petrotoga mobilis SJ95]
 gi|160359438|gb|ABX31052.1| pseudouridine synthase, RluA family [Petrotoga mobilis SJ95]
          Length = 303

 Score =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 84/326 (25%), Positives = 139/326 (42%), Gaps = 29/326 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVR 66
           +   V       RLD + + +YP I    +  ++R G V+V++KRVK N   ++ G  V+
Sbjct: 3   KETTVNEKNYYSRLDTFIRKNYPEIKLGAIYGLIRKGFVKVNEKRVKKNNYILEIGDNVK 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I    N L  + +           +  +  +   ++YED  + V NKPA +SV  GS   
Sbjct: 63  IILDENKLEELSR-------PTQPSLKARPVSFDIIYEDKDLLVINKPAKVSVHPGSKEE 115

Query: 127 Y-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              I   +  +   + + P L HRLD+ TSG++VVA+ +  A+ LT+  + R  +K Y +
Sbjct: 116 MATIIEGVMHYSRGEFE-PHLVHRLDKLTSGVMVVAKNKQTARELTQLIKSRETRKYYLT 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L+ G    K   +                V     K A    +  K  D F + +  +E+
Sbjct: 175 LLVGNLNKKSGEL----------------VSTVYGKTAQLKFNLKKKFDLFGELYSLVEI 218

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG 303
           + +TGR HQ+RV    +G PI GD  +    +           +++LHA  +   +    
Sbjct: 219 ELYTGRKHQIRVQFADLGFPIAGDDNHGDKKQNKLLRKNYGLKRIFLHASKISFDY-NNK 277

Query: 304 RLQITAPLPAHMVKTWDSLGFKYDRN 329
                APL   +    D L     RN
Sbjct: 278 HYDFYAPLSEDLQTVLDKLEKSPKRN 303


>gi|118444019|ref|YP_877712.1| ribosomal large subunit pseudouridine synthase C [Clostridium novyi
           NT]
 gi|118134475|gb|ABK61519.1| ribosomal large subunit pseudouridine synthase C, putative
           [Clostridium novyi NT]
          Length = 323

 Score =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 139/326 (42%), Gaps = 29/326 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ +     +    + K LR G +RV+ K+ K N  ++   VV    
Sbjct: 3   IEIGPNEAGQRLDKFCRKWLEDVPLGAIFKALRKGDIRVNGKKAKQNYFLEEEDVVE--- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                 +I   +K   +     +  +F    + YED  + +  K  G+ V          
Sbjct: 60  ----TKYIESYKKNKKNVPKKFQEVNFSSIKIAYEDENMLIIEKWPGVLVHSDKKDGDPT 115

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++ +KG+          P   +RLD+ TSG+++  +   + + L E  R R+I
Sbjct: 116 LTDYVLSYLFNKGEYIPENEVTFTPAPCNRLDRNTSGMVIFGKNFKSLKLLNEMIRERKI 175

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G  K ++     ++ K        +H+ K  +  +       KVID     
Sbjct: 176 SKYYNALVKG--KIREGRYEAYISKDQINNISEIHLNK--KPNSKKIAMEVKVIDTVG-T 230

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F +LE+   TGR+HQLR H   +G PI+GD KY      +F       +  +L+A  +  
Sbjct: 231 FSFLELDLITGRSHQLRAHLSFLGNPIIGDDKYGDRKLNSFFNNKYGLSFQFLYAYKLIF 290

Query: 298 PH-PEG-GRLQ---ITAPLPAHMVKT 318
              PE    ++   IT  LP    K 
Sbjct: 291 KDCPEELAYMENKIITQALPPIFKKV 316


>gi|154498381|ref|ZP_02036759.1| hypothetical protein BACCAP_02370 [Bacteroides capillosus ATCC
           29799]
 gi|150272449|gb|EDM99634.1| hypothetical protein BACCAP_02370 [Bacteroides capillosus ATCC
           29799]
          Length = 299

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 76/304 (25%), Positives = 132/304 (43%), Gaps = 35/304 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIK 79
           L  +        +   ++ +L   QV VD K V +F+  ++ G+VV I P          
Sbjct: 19  LLEFLLERVKGKSRNAVKHLLSGRQVAVDGKIVTRFDWPLEPGEVVTILPQGR------- 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                       +        +LY+D  +   +KPAG+   G  G        L +    
Sbjct: 72  ------------EEQTKAPFPILYQDRDLIAIDKPAGLLTVGHEGERQRTAYRLLADTLR 119

Query: 140 KG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            G   +K  + HRLD++TSG ++ AR     + L E +     ++IY ++  G P+ ++ 
Sbjct: 120 DGSREKKLFVVHRLDRDTSGAVLFARNEEMKRALQEDWDSLVKERIYLAVTVGAPEREEG 179

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + +WL + S      V        GA  A++ +KV+    + +  + +   TGR +Q+R
Sbjct: 180 VVRSWLRETST----RVVYSGGPGSGAKEAVTRYKVLARSGE-YALVRVALDTGRKNQIR 234

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           VH   +GCP+ GD KY         S   ++L LHA  + +  P  G  L +TAP+P   
Sbjct: 235 VHMADLGCPVAGDKKYGDG------SGPMDRLALHAVRLTITDPRTGAPLTVTAPVPKSF 288

Query: 316 VKTW 319
           ++ +
Sbjct: 289 LRLF 292


>gi|160935585|ref|ZP_02082960.1| hypothetical protein CLOBOL_00475 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441329|gb|EDP19039.1| hypothetical protein CLOBOL_00475 [Clostridium bolteae ATCC
           BAA-613]
          Length = 287

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 74/312 (23%), Positives = 139/312 (44%), Gaps = 38/312 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E+ + L ++ K      +     +I  +  + VD        R+++GQ V +        
Sbjct: 2   EDGIVLGQFLKA--KGFSHRLAVRIKAAQGLAVDGIAAYAGYRLKTGQTVEVT------- 52

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                  + +   +       L   ++YED  I V NK AG+ +    G   H D  L +
Sbjct: 53  -------LPEEEDSGNIVPVKLPLSIVYEDEDILVINKDAGVPIHPSQG---HYDNTLAN 102

Query: 136 ----WVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               +   KG+    R+ +RLD++T+G+LV+AR   +A  L+E    RRI++ Y ++V G
Sbjct: 103 AVSWYFHEKGEAFTYRVINRLDRDTTGLLVLARHMLSACILSEQMTGRRIRREYRAIVLG 162

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPH 248
               ++  + + + +      +     + + +    A++HF+ +    +K    + +   
Sbjct: 163 H-TPEEGTVDSPIARAEGSTIER----RVDHETGERAVTHFRTLLYNEEKDLSLVSLSLE 217

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+RVH   +G P+ GD  YC +++        ++  LH+  +   HP  G  ++ 
Sbjct: 218 TGRTHQIRVHMRSIGHPLPGDFLYCPDYR------YIDRQPLHSYLLRFEHPITGKEMEF 271

Query: 308 TAPLPAHMVKTW 319
           TA LP  M +  
Sbjct: 272 TAGLPEDMKQLL 283


>gi|317498384|ref|ZP_07956679.1| RluA family pseudouridine synthase [Lachnospiraceae bacterium
           5_1_63FAA]
 gi|316894278|gb|EFV16465.1| RluA family pseudouridine synthase [Lachnospiraceae bacterium
           5_1_63FAA]
          Length = 323

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 78/331 (23%), Positives = 145/331 (43%), Gaps = 35/331 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +   EE  RLD+    +        + K+LR   ++++ K+   N ++  G  V 
Sbjct: 1   MRELNITTREEGQRLDKILSKYLNKAPKSFVYKMLRKKNIKLNGKKATGNEKLSQGDQVC 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I    + +N   +E K     + L          +LYED  + + NKP GI  Q      
Sbjct: 61  IYLAEDTINKFREEVKAGKQKIKLD---------VLYEDENVIMVNKPWGILSQKSKPED 111

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             I+  +  +  ++G          KP + +RLD+ T+GI++   +    Q + E  + R
Sbjct: 112 ISINDQIIPYAVNQGLISEKELQVVKPSICNRLDRNTTGIIICGISIEGLQTMAEMLKHR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y  +V G  + + + ++ +L K        V V KQ   GA++  + ++ +    
Sbjct: 172 DMEKYYLCIVKGKLE-RTQKVSAYLKKDEKTN--KVKVSKQEIAGASHIETAYEPM-ISN 227

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF--KGNFTSPIQNKLYLHARYM 295
           ++F  L+++  TG+THQ+R H   +G P++GD KY      +            LH   +
Sbjct: 228 EEFTLLKVELITGKTHQIRAHLASIGHPLIGDFKYGDKKINQEMKQRFGLKDQLLHCTEV 287

Query: 296 DLP-------HPEGGRLQITAPLPA--HMVK 317
             P       +  G ++Q  APLP    M+K
Sbjct: 288 VFPRDMKTCRNLSGKKIQ--APLPKRFDMIK 316


>gi|315651236|ref|ZP_07904266.1| RluA family pseudouridine synthase [Eubacterium saburreum DSM 3986]
 gi|315486532|gb|EFU76884.1| RluA family pseudouridine synthase [Eubacterium saburreum DSM 3986]
          Length = 338

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 78/303 (25%), Positives = 135/303 (44%), Gaps = 14/303 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  ++V  +E   RLDR  +  + + +   + K+LR   + +D KR     R+++G  ++
Sbjct: 1   MVEIIVGENESGQRLDRVLEKIFVNADTGFIFKMLRKKNITLDDKRADGKERLKTGSSIK 60

Query: 67  IPPVINALNHIIKEQKILDSSV---NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +     +   + K+  +  S        K SD  KS ++YED    + NKPAG+  Q   
Sbjct: 61  MWFSDESFEKLTKKTCLAPSGKIKNKDNKVSDVFKSYIIYEDENTIIINKPAGLLSQKSQ 120

Query: 124 GIAYHIDGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                ++  L  ++          KP + +RLD+ TSG+LV  ++    +   E  + R 
Sbjct: 121 INDISVNDMLLEYLKFDENALHTFKPSICNRLDRNTSGLLVCGKSLEGLRVNNELIKTRA 180

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y ++V G   N+K  I+ WL K        +   K ++  A+Y  + +K I  F  
Sbjct: 181 VKKYYLAIVKGRV-NEKCAISGWLYKDEKTNKVSIKNNKFDK--ADYIETEYKPIGYF-D 236

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMD 296
               L ++  TG+THQ+R H   M  PI+GD KY       F           LH+  + 
Sbjct: 237 DITLLSVKLITGKTHQIRAHLASMAHPIIGDFKYGKRSVNEFYKKKYGIKWQLLHSYKLI 296

Query: 297 LPH 299
            P 
Sbjct: 297 YPD 299


>gi|114797784|ref|YP_761328.1| pseudouridine synthase family protein [Hyphomonas neptunium ATCC
           15444]
 gi|114737958|gb|ABI76083.1| pseudouridine synthase family protein [Hyphomonas neptunium ATCC
           15444]
          Length = 244

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 88/243 (36%), Positives = 137/243 (56%), Gaps = 8/243 (3%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           D      + +   +S+L++ED+ I  FNKP G++ QGGS +   +D  L ++  S G++P
Sbjct: 6   DIPALSPEAAALARSLLIHEDAAILGFNKPPGMASQGGSSVGQSLDDLLWAFAKSNGKRP 65

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLL 203
           RL HRLDQ TSG+++ ART+ AA  L+ +F  R  QK Y +LV G  P  +   I   L+
Sbjct: 66  RLVHRLDQGTSGVMLTARTQPAAAFLSAAFAGRDAQKTYLALVKGKLPPAEHGVIDASLV 125

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           K    G   + + K + KGA  A + + V+    +    +++ P TGR HQ+RVH + +G
Sbjct: 126 KVEEGGRPRMILAKPSRKGAQPARTGWAVLARN-EDHALMQLTPETGRMHQIRVHLMSLG 184

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
           CPI+GD  Y    +G  T+P   ++ LHA  +++PHPEGG L + AP+P       +  G
Sbjct: 185 CPILGDGLYG---EGQATAP---RVMLHAARLEVPHPEGGTLTLEAPVPEDFRAAAEKAG 238

Query: 324 FKY 326
            + 
Sbjct: 239 LQA 241


>gi|78044542|ref|YP_359965.1| ribosomal large subunit pseudouridine synthase A [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77996657|gb|ABB15556.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Carboxydothermus hydrogenoformans Z-2901]
          Length = 301

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 75/317 (23%), Positives = 131/317 (41%), Gaps = 36/317 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPV 70
           V  +     + ++ K+H   ++   L+K+     V  + + V  N+ +   G+VV     
Sbjct: 7   VNQEYIGKTVFQFLKSH--GLSKRQLRKLKLQNAVFFNNRPVPLNSHLTTPGEVV----- 59

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHI 129
                        L  ++     S      +LYED  + V +KPAG+      +  A  +
Sbjct: 60  -----------IKLPHTLPPAVQSQNAPVKVLYEDDYLIVIDKPAGVLAHPVKNHFAPSM 108

Query: 130 DGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                S+   KG   +     +RLD+ TSG +++A+    A+ L  S R R+I KIY +L
Sbjct: 109 QELTLSYYRDKGRIFEGFYPIYRLDRNTSGPMLIAKFSLIAEMLNNSLRKRQINKIYLAL 168

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           + G   +K   I   L        +   + +    G   A + ++ +  F      L+++
Sbjct: 169 IEGPLADKSGIINLPLG-----LLEGSIIKRAVVPGGQPACTKYQTVKAFP-THTLLKVE 222

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+R H   +G P+ GD  Y           +  +  LH  Y+  PHP   + +
Sbjct: 223 LLTGRTHQIRAHFAAIGHPLAGDDLYGGKMD------LIERQALHLYYISFPHPITKKTI 276

Query: 306 QITAPLPAHMVKTWDSL 322
            + APLP    +   +L
Sbjct: 277 SLYAPLPRDFKEALITL 293


>gi|163790745|ref|ZP_02185172.1| hypothetical protein CAT7_01150 [Carnobacterium sp. AT7]
 gi|159874046|gb|EDP68123.1| hypothetical protein CAT7_01150 [Carnobacterium sp. AT7]
          Length = 309

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 87/298 (29%), Positives = 138/298 (46%), Gaps = 33/298 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHIIKEQK 82
           +  +   H +  +++ IL  GQV VD+K  K  N  +  GQVV I     A+        
Sbjct: 36  FLLSVMTHTSRNSVKSILTRGQVTVDEKMTKKHNFPLLPGQVVAIQSNKAAI-------- 87

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKG 141
                    K +  +   +LYED  I V +K AG+                L ++V  + 
Sbjct: 88  ---------KETALIGMTILYEDDAIIVIDKEAGLLSIAAKFAQELTAHRQLINYVKQEN 138

Query: 142 Q--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           Q  +  + HRLD++TSG++V A+T    Q + E+++    ++IY +LV G+ +  +  I 
Sbjct: 139 QNNRIYVVHRLDRDTSGVMVFAKTEKIKQDMQENWKEIVKERIYTALVEGVVREDEGTIK 198

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            WL +   +    VH    +  G   AI+H+K I    + F  LE +  TGR +Q+RVH 
Sbjct: 199 TWLTESKAM---KVHSATYD-NGGKLAITHYKKI-RNNEDFTLLEARLETGRKNQIRVHM 253

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMV 316
             +G P+ GD KY A      TS    +L LHA  + L HP  G L +  + +P   +
Sbjct: 254 ETLGHPVAGDKKYGA------TSNPLKRLGLHATTLALIHPTTGELVRFHSKVPKAFL 305


>gi|226312125|ref|YP_002772019.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226095073|dbj|BAH43515.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
          Length = 302

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 77/303 (25%), Positives = 133/303 (43%), Gaps = 32/303 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
            +  +  +    +  + +  +V +D + V  +   ++GQ +R+                 
Sbjct: 28  LREEWK-LPRKQVHLLFQHKEVLLDGEPVAQHVVGKAGQEIRLRMCK------------- 73

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS---WVDSKG 141
             ++ L   S+     +LYED  + + NKP G+ +       +     L S   +     
Sbjct: 74  PEALGLDPASEA--PEILYEDDHLLIVNKPVGLLLHPTERYHHVTLDHLVSGHFFRTGLE 131

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            K R  HRLDQ+TSG+++ A+   A+  L E  R R I++ Y + V G    ++  I   
Sbjct: 132 AKVRHVHRLDQDTSGVVLYAKHPWASALLDEMLRERTIKRTYVAYVSGQMPKERGKINEP 191

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + K  + G        +     + AI+H++V + F Q    +E Q  TGRTHQ+RVH  H
Sbjct: 192 IGKDRNHGTRR-----RVTPNGDPAITHYQVKERF-QTATKVECQLETGRTHQIRVHFSH 245

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           +G P++GD  Y    +      +  +  LHA  +   HP GG  +++TAPLP  +     
Sbjct: 246 IGHPLLGDELYGGKRE------LIKRQALHAAVLKFEHPFGGEVIEVTAPLPLDLFHLEK 299

Query: 321 SLG 323
            L 
Sbjct: 300 KLR 302


>gi|162451431|ref|YP_001613798.1| pseudouridylate synthase/ribosomal large subunit pseudouridine
           synthase D [Sorangium cellulosum 'So ce 56']
 gi|161162013|emb|CAN93318.1| Pseudouridylate synthase/ribosomal large subunit pseudouridine
           synthase D [Sorangium cellulosum 'So ce 56']
          Length = 350

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 78/338 (23%), Positives = 141/338 (41%), Gaps = 41/338 (12%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V  + V  +   MRLDR+ +      +     +I+  G    + +R++ ++R++  Q 
Sbjct: 32  SVVTVLRVPPESAGMRLDRFVQTQLKRTSRTRAAEIVARGAYSPEARRLRGSDRVRPEQC 91

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +                        + +      +L+ED  +   +KPAG+ V   + 
Sbjct: 92  ILLW------------------REPWDEQAPDTPIPVLHEDDALLAIDKPAGLPVHPTA- 132

Query: 125 IAYHIDGFLKSWVDSK-GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKI 182
             YH    +K    ++ G++  L HRLD+ETSG+L++ RT  A + +   F  R  + K 
Sbjct: 133 -RYHKSTVIKMMEAARPGERLFLAHRLDRETSGVLLLCRTPEADRTVKAQFEERTGVVKR 191

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-----A 237
           Y ++ WG P+     +   L             V    +G   A +  +V+         
Sbjct: 192 YAAIAWGWPERDTFRVELPLELDDASRYKVKMRVAPPGRGLASA-TACEVLGRRADPLTG 250

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF------------KGNFTSPIQ 285
           +++  +     TGR HQ+RVH    G P+VGD  Y  +               +  +   
Sbjct: 251 RRYALVRCTLETGRQHQIRVHLAASGLPLVGDKLYGPDEGMFARGADGVLTDDDRRALEL 310

Query: 286 NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           ++  LHA  ++L HP  G R++I APL   +   WD+L
Sbjct: 311 DRHALHAALLELTHPMTGERVRIEAPLSDDLRTFWDAL 348


>gi|167762842|ref|ZP_02434969.1| hypothetical protein BACSTE_01200 [Bacteroides stercoris ATCC
           43183]
 gi|167699182|gb|EDS15761.1| hypothetical protein BACSTE_01200 [Bacteroides stercoris ATCC
           43183]
          Length = 302

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 74/308 (24%), Positives = 121/308 (39%), Gaps = 34/308 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     ++N  ++ G  V+I        
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKALLSKRVVYVDSVITTQYNFPLKPGMKVQI-------- 72

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     S     K  +     ++YED+ + V  K  G+ SV             L 
Sbjct: 73  ----------SREKGRKEFNNKLLKIVYEDAYLIVVEKMQGLLSVNTERQKERTAYTILN 122

Query: 135 SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G   +  + HRLD++TSG+L+ A+       L +++      + Y ++V G  +
Sbjct: 123 EYVQRSGRQHRVYIVHRLDRDTSGLLMFAKDEKTQNTLRDNWHNIVTDRRYVAVVAGEME 182

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           N    + +WL                 + G   AI+H++ I   A  F  +E+   TGR 
Sbjct: 183 NNAGMVRSWLT-----DRKLYVYSSPTDDGGKEAITHYRTIKR-ANGFSLVELMLETGRK 236

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y              +L LHA  +   HP  G  +Q   P 
Sbjct: 237 NQIRVHMQDLGHPIIGDGRYGLEEINP-----IGRLALHAFKLCFRHPVTGELMQFETPY 291

Query: 312 PAHMVKTW 319
           P    K +
Sbjct: 292 PGEFKKLF 299


>gi|296104263|ref|YP_003614409.1| 23S rRNA pseudouridine synthase D [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295058722|gb|ADF63460.1| 23S rRNA pseudouridine synthase D [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 282

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 75/298 (25%), Positives = 132/298 (44%), Gaps = 41/298 (13%)

Query: 47  RVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
            V+ K   K   ++  G+ V I   I                  +      +   ++YED
Sbjct: 2   LVNGKVWDKPKEKVLGGEAVAINAEIEE---------------EIRFEPQDIPLDIVYED 46

Query: 106 SKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVAR 162
             I V NKP  + V  G+G     +   L  +       PR  + HRLD++T+G++VVA+
Sbjct: 47  DDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAK 106

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQN 219
           T  A   L ES ++R I + Y ++  G         E I+    K++H+    +      
Sbjct: 107 TVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMSVHPM------ 160

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  Y    +  
Sbjct: 161 ---GKPAVTHYRIMEHF-RIHTRLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPP 216

Query: 280 FTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
             +  +        ++  LHA  + L HP  G +++  AP+P  MV+  D++   ++ 
Sbjct: 217 KGASDEFISVLRKFDRQALHATMLRLYHPVSGIQMEWHAPIPQDMVELIDAMRADFEE 274


>gi|302874505|ref|YP_003843138.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
 gi|307690886|ref|ZP_07633332.1| pseudouridine synthase, RluA family protein [Clostridium
           cellulovorans 743B]
 gi|302577362|gb|ADL51374.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
          Length = 321

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 125/300 (41%), Gaps = 27/300 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E+  R D++ +     +    L K  R G +RV+ K+VK N  +Q G VV    
Sbjct: 3   ITIGTNEQGQRTDKFVRKWLQDLPLSALYKAFRKGDIRVNGKKVKENYFLQEGDVVETSK 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
            + A        + +++          +   + +ED  I +  K  G+ V          
Sbjct: 63  YVQASPKKELNFQKIEN----------VHLKITFEDENILLVEKWPGVLVHADKKNGDPT 112

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI++  +T    + L E  R RRI
Sbjct: 113 LTDYVLSYLHDKGDYLPENEVTFTPASCNRLDRNTSGIVIFGKTFEGLKALNEMVRDRRI 172

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G  K+       ++ K        ++   +            K ++     
Sbjct: 173 QKYYMALVQGKLKD--GRYDAYISKDESQNLSKIY--NEGGADRKKISMEVKTLETVGS- 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           +  L+++  TGR+HQLR H  H+G PIVGD KY      +F       N  +L+A  +  
Sbjct: 228 YSLLDIELITGRSHQLRAHLSHLGNPIVGDSKYGDKKLNSFFNNKYGVNYQFLYAYKLIF 287


>gi|237734494|ref|ZP_04564975.1| pseudouridine synthase [Mollicutes bacterium D7]
 gi|229382314|gb|EEO32405.1| pseudouridine synthase [Coprobacillus sp. D7]
          Length = 328

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 76/334 (22%), Positives = 145/334 (43%), Gaps = 31/334 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +  ++ N R+D++ K    +     + K+ R   ++V+ K+V     +     V 
Sbjct: 7   MKKLKITENDANQRIDKYLKKLLVNAPNNFIYKMFRKKDIKVNGKKVDEKYILSLDDEVE 66

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    +      + + I + +   +         +LYED  + +  KPAG+ V   +  +
Sbjct: 67  MFLYDDKFKEFTETKSIYEVNRTFS---------VLYEDKHVLIVFKPAGLLVHEDANES 117

Query: 127 -YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +   + S++ SK +          P   HRLD+ TSGI++  +T AA Q+L E  + 
Sbjct: 118 INTLTNQVLSYLASKNELDLSRENTFMPGPVHRLDRNTSGIVIFGKTLAALQNLNEMIKQ 177

Query: 177 RR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           R  I+K Y ++  G   +++  +  +++K  +     V +VK++  GA    +  + +  
Sbjct: 178 RHCIEKKYLTICRGQLSHQRN-LHGYMVKLENQA--QVKLVKKDYPGALTMETIVRPLKY 234

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHAR 293
               +  +E+   TGR HQ+RVH   +  PI+GD KY       +   +   N   LHA 
Sbjct: 235 NCD-YSLVEVTLITGRMHQIRVHLSSIEHPIIGDRKYGDFELNKYIKKTFGLNNQLLHAY 293

Query: 294 YMDLPHPEG-----GRLQITAPLPAHMVKTWDSL 322
            +      G        +I  P+PA   K   SL
Sbjct: 294 KIKFVKTFGVLNYLQDKEIICPVPALFEKIEKSL 327


>gi|312870194|ref|ZP_07730326.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
 gi|311094285|gb|EFQ52597.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
          Length = 297

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 67/285 (23%), Positives = 119/285 (41%), Gaps = 30/285 (10%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           GQ+ ++ +     + +Q G    I               I     N           + Y
Sbjct: 37  GQMLINGEPKWAVDLVQPGDEYSI--------------VIPPEEANDHVDESTAPITIAY 82

Query: 104 EDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGIL 158
           ED    V NKPAG++      +  A  +   +K +   +  + ++TH   RLD++TSG++
Sbjct: 83  EDRDFLVLNKPAGVATVPAHNVPVADSLVNRVKYYYRERDYENQVTHVATRLDKDTSGLV 142

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V  + R A   L    +   ++K Y++LV G    +   I   + +          V ++
Sbjct: 143 VFPKHRFAHAVLDRQLKRHEVKKNYYALVSGHLHTQHGYIDAPIRRDPA-----SFVKRE 197

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  +++ + +    A++   + ++ HTGRTHQ+RVH   +G P+VGD  Y A    
Sbjct: 198 VAPDGKDSVTEYWLAQAQAER-SLVRIRLHTGRTHQIRVHFSFLGHPLVGDEMYGAP--- 253

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              SP+ ++  LH  +M    P   + + +TAPLPA         
Sbjct: 254 -AGSPLIDRQALHCYWMQFYSPFKEQFITVTAPLPADFAAAIKEF 297


>gi|259503014|ref|ZP_05745916.1| ribosomal large subunit pseudouridine synthase [Lactobacillus antri
           DSM 16041]
 gi|259169025|gb|EEW53520.1| ribosomal large subunit pseudouridine synthase [Lactobacillus antri
           DSM 16041]
          Length = 297

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 63/302 (20%), Positives = 121/302 (40%), Gaps = 31/302 (10%)

Query: 26  KNHYPHINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                 +    ++  +   GQ+ ++ +     +++Q G    I               + 
Sbjct: 18  ALKMSGVTSSLMKAAIYHGGQLLINGEPRWAADQVQPGDEYSI--------------VLP 63

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQ 142
               N           + YED    V NKPAG++      +  A  +   +K +   +G 
Sbjct: 64  PEQANDQVDESAAPIEIAYEDRDFLVLNKPAGVATVPAHNVPVADSLVNRVKRYYREQGY 123

Query: 143 KPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + R+TH   RLD++TSG++V  + R A   L    +   ++K Y++LV G   ++   I 
Sbjct: 124 ENRVTHVATRLDKDTSGLVVFPKHRFAHAVLDRQLKHHAVKKNYYALVNGRLGSQHVYID 183

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + +          V +        +++ +  ++    ++  + ++ HTGRTHQ+RVH 
Sbjct: 184 APIRRDPD-----SFVKRVVAPDGKPSVTEYW-LERSCTEWSLVRIRLHTGRTHQIRVHF 237

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             +G P+VGD  Y         S + ++  LH  ++    P   R + + APLP      
Sbjct: 238 SFLGHPLVGDRMYGP----AAGSSLIDRQALHCYWLQFYSPFKERLITVRAPLPGDFQMA 293

Query: 319 WD 320
             
Sbjct: 294 IK 295


>gi|326938929|gb|AEA14825.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar chinensis CT-43]
          Length = 275

 Score =  199 bits (507), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 58/296 (19%), Positives = 125/296 (42%), Gaps = 31/296 (10%)

Query: 30  PHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
             I+   L  I    G + V+ +     +++++G+ + +   +   +  +          
Sbjct: 4   KGISKAALTDIKFHGGAIEVNSQHASVRHQLRAGEELSVFFPVEERSEGM---------- 53

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSW-VDSKGQKPR 145
                ++ +   ++YED  + + +K A +S             +  L  +          
Sbjct: 54  ----MAEDIPLCIVYEDDAVLIIDKEANMSTIPSREHPTGSVANAILSHYDKQHLASTVH 109

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD++TSG++++A+ R     L++  + + +++ Y ++V G    ++  I   + +K
Sbjct: 110 IVTRLDRDTSGLMLIAKNRFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGMIDAPIGRK 169

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           S    +         +    A++HFKVID    K   + ++  TGRTHQ+RVH  H+G P
Sbjct: 170 SDSIIERTVC-----EDGQRAVTHFKVIDSTYDK-THVALELETGRTHQIRVHMAHIGHP 223

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWD 320
           ++GD+ Y              +  LH++ +   HP     +  T  +P+ M +   
Sbjct: 224 LLGDNLYGGRRDE------MKRQALHSKSLTFYHPILEKEMSFTIKIPSDMQELLR 273


>gi|197120627|ref|YP_002132578.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196170476|gb|ACG71449.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 302

 Score =  199 bits (507), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 85/316 (26%), Positives = 138/316 (43%), Gaps = 27/316 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRI 67
            ++V + +   R+DR+       I+    ++ + +G V VD +R K   R +  GQ V +
Sbjct: 5   TLLVPDADRYERIDRFIAAR-GGISRGLARRAIEAGGVFVDGRRCKVAGRTLTPGQQVVV 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                          + +        +   +  LLY D+ +   +KPAG+  Q       
Sbjct: 64  N--------------LEEGGRAAPALAALGRERLLYADADLCAVDKPAGVPAQPTLTTDR 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                L S +   G    L HRLD+ETSG+ V ARTR AA  L E+FR    +K Y +L 
Sbjct: 110 GALPELVSAL--LGAPVTLVHRLDRETSGVTVFARTRDAAAALAEAFRTGTPEKTYLALC 167

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
              P   +  +A  L K     G     +++ +   + A + ++ +   A     +E +P
Sbjct: 168 ARAPSPAEGRVALALGKDPARPG-----LRRVDPAGDPAATRYRTL-REAPGGARVEARP 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            TGRTHQ+RVH   +G P++GD +Y    +         ++ LHA  ++LPHP  G R+ 
Sbjct: 222 ETGRTHQIRVHLAALGAPLLGDARYGGPRR--VGEVAVPRVMLHATRLELPHPATGARMV 279

Query: 307 ITAPLPAHMVKTWDSL 322
             A  P        +L
Sbjct: 280 FEAEPPEDFRAIEAAL 295


>gi|315924025|ref|ZP_07920252.1| RluA protein [Pseudoramibacter alactolyticus ATCC 23263]
 gi|315622651|gb|EFV02605.1| RluA protein [Pseudoramibacter alactolyticus ATCC 23263]
          Length = 314

 Score =  199 bits (507), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 70/324 (21%), Positives = 129/324 (39%), Gaps = 13/324 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + + ++    R+DR+     P  +   L K+LR  ++++D  R    + +Q GQV+ 
Sbjct: 1   MIQLTISDNAAEQRMDRFLIKWLPQASKGFLMKMLRKKRIKLDGHRASPRDYLQKGQVLT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                       + Q       +L      L    LYED  +   NKP G+  Q      
Sbjct: 61  FYFSEETYRQF-RGQPAAPGEPSLPDSLKALMQPPLYEDDHLIAVNKPVGLLTQPDHTGT 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +     +   S    P   +RLD+ TSGI+++ +     + +  + R   I+K YW++
Sbjct: 120 PSLADLAGTLPHSGTFHPAPANRLDRNTSGIVLIPKDYPTQKQIAAAIRSHLIRKSYWAI 179

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    +   + + L K         ++V++   G   A   ++ + C       + ++
Sbjct: 180 VAGKI-TRGAKLHSRLTKNP-----RANIVQEETDGQREAWLRYQPL-CSGDAASLIAIE 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGGR 304
             +GR+HQ+RV    +G PI+GD KY +       + +   +   LHA    +P      
Sbjct: 233 LGSGRSHQIRVQLAGIGHPIIGDPKYGSRSHNREWAALYGLHHQLLHAHRYTIPELN--- 289

Query: 305 LQITAPLPAHMVKTWDSLGFKYDR 328
           + + AP P         L     R
Sbjct: 290 IDVVAPPPERFCAVAKHLRLALPR 313


>gi|218130909|ref|ZP_03459713.1| hypothetical protein BACEGG_02504 [Bacteroides eggerthii DSM 20697]
 gi|217987253|gb|EEC53584.1| hypothetical protein BACEGG_02504 [Bacteroides eggerthii DSM 20697]
          Length = 303

 Score =  199 bits (507), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 75/308 (24%), Positives = 126/308 (40%), Gaps = 34/308 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     ++N  ++ G  V+I        
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKSLLSKRIVYVDSVITTQYNFPLKPGMKVQIS------- 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
              +E+   + S  L K        ++YED+ I V  K  G+ SV             L 
Sbjct: 74  ---REKGRKEFSNRLLK--------IVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 122

Query: 135 SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G   +  + HRLD++TSG+++ A+       L +++      + Y ++V G  +
Sbjct: 123 EYVQRSGRQHRVYIVHRLDRDTSGLMMFAKDEKTQNTLRDNWHNIVTDRRYVAVVAGEME 182

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           N    + +WL                 + G   +++H++ I   A  F  +E+   TGR 
Sbjct: 183 NNAGMVRSWLT-----DRKLYVYSSPTDDGGKESVTHYRTIKR-ANGFSLVELVLETGRK 236

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y             N+L LHA  +   HP  G  +Q   P 
Sbjct: 237 NQIRVHMQDLGHPIIGDGRYGLEEVNP-----INRLALHAFKLCFHHPVTGELMQFETPY 291

Query: 312 PAHMVKTW 319
           P    K +
Sbjct: 292 PGEFKKLF 299


>gi|225019205|ref|ZP_03708397.1| hypothetical protein CLOSTMETH_03158 [Clostridium methylpentosum
           DSM 5476]
 gi|224948057|gb|EEG29266.1| hypothetical protein CLOSTMETH_03158 [Clostridium methylpentosum
           DSM 5476]
          Length = 322

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 67/302 (22%), Positives = 135/302 (44%), Gaps = 29/302 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  ++++++   RLD++       +    L K +R  +++++ KR   +  ++ G +V
Sbjct: 11  FMKSFLIDSNDAGQRLDKFVVKVTSGLPKGMLYKAVRKKRIKLNHKRCDCSAMLREGDLV 70

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG- 124
            +           +    L +  +L+         ++YEDS I + +KP G+ V      
Sbjct: 71  ELYLNDEFFPKQDETFSFLKAPASLS---------IVYEDSNILLVDKPVGLRVHSDRAA 121

Query: 125 IAYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +  +   ++ ++  K +          P L +R+D+ T GI++ A+   A + L E  +
Sbjct: 122 DSDSLVARIQHYLYQKQEYNPEKEHSFAPALCNRIDRNTQGIVIAAKNAPALRILNEKIK 181

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R ++K Y  +V GIP+ +   +  +  K S      V    Q+  G +  ++ + V+  
Sbjct: 182 QRELEKYYLCVVHGIPQPRHAVLTGYWSKDSRRNKALVRDTPQD--GFHEIVTEYTVL-R 238

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                  +E++ HTGR+HQ+R H  H+G P+VGD KY         S  Q    L A  +
Sbjct: 239 PGVHESLVEVRLHTGRSHQIRAHMAHIGHPLVGDAKYGG-------SGGQPHQLLCAYKL 291

Query: 296 DL 297
             
Sbjct: 292 RF 293


>gi|213691700|ref|YP_002322286.1| pseudouridine synthase, RluA family [Bifidobacterium longum subsp.
           infantis ATCC 15697]
 gi|213523161|gb|ACJ51908.1| pseudouridine synthase, RluA family [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 320

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 68/308 (22%), Positives = 121/308 (39%), Gaps = 34/308 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS M     V   +     R D         I+      ++ SGQ RV  + V  ++ +Q
Sbjct: 1   MSRM-----VPAPDALVGKRFDVAVAKML-GISRSKAADLVDSGQARVLGREVARSSTLQ 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ V            + E++     +            ++YED  + V +KP G++  
Sbjct: 55  AGETVEFD---------LAEEQAGPEPIAT-------DMAVVYEDDDVIVVDKPVGVAAH 98

Query: 121 GGSG------IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G      +    D  +         +  +  RLD  TSG+++V ++  A   +   F
Sbjct: 99  ASVGWTGPTVLGSLRDRGVHIASYGAAGREGIVSRLDVGTSGLMLVCKSDLAYTEMRRQF 158

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
               ++K Y +LV G  K  K  I   + +                     A++H+ V++
Sbjct: 159 AEHEVKKTYHALVQGGLKENKATIEAPIGR-----AKVSDFRFCVTPAGKPAVTHWDVLE 213

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F  +   + +   TGRTHQ+RVH   +G P+ GD  Y AN   +    + ++ +LHA  
Sbjct: 214 RFGHEATLVSVNLETGRTHQIRVHFSSIGHPLCGDPMYGANPVLSEALGL-DRQWLHAMK 272

Query: 295 MDLPHPEG 302
           ++  HP  
Sbjct: 273 LEFRHPRT 280


>gi|228990395|ref|ZP_04150360.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
 gi|228996496|ref|ZP_04156135.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|229004147|ref|ZP_04161948.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228757008|gb|EEM06252.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228763128|gb|EEM12036.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|228768921|gb|EEM17519.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
          Length = 307

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 130/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + +D   K  +  +    L ++     + V+ +R +++  +  G  +++ 
Sbjct: 11  EITVPAKWSGISIDSLLKEEW-GVPKKLLHQLRMEKGIIVNGERKRWSEPLAEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAY 127
             I     +  E               F    +++ED  + + NKPA +     S G   
Sbjct: 70  MFIQEEYGVQPE---------------FGDLEVIFEDDHVLIVNKPAHMDTHPSSKGGTG 114

Query: 128 HIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +   +  +G   K R  HRLD++T+G +V A+   A   +      R I++ Y +
Sbjct: 115 TLANLVAFHLQMQGVETKVRHIHRLDKDTTGGVVFAKHGIAGAIMDRLLMERNIKRTYLA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H        +K      + A++H++V   F  Q    + 
Sbjct: 175 LVEGKVKKKQGIIDAAIGRDRHHATRRRVSLK-----GDQAVTHYRVEKYFKHQDVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TG+THQ+RVH  H G P++GD  Y         S   +   LHA  +   HP    
Sbjct: 230 LQLETGKTHQIRVHMSHSGHPLIGDTLYGGQ------STYMSSQALHAMRIAFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            + +  PLP+++     S 
Sbjct: 284 EITVEVPLPSYLNNIMKSF 302


>gi|183602394|ref|ZP_02963760.1| hypothetical protein BIFLAC_05095 [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219683291|ref|YP_002469674.1| pseudouridine synthase RluD [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|241191252|ref|YP_002968646.1| hypothetical protein Balac_1228 [Bifidobacterium animalis subsp.
           lactis Bl-04]
 gi|241196658|ref|YP_002970213.1| hypothetical protein Balat_1228 [Bifidobacterium animalis subsp.
           lactis DSM 10140]
 gi|183218313|gb|EDT88958.1| hypothetical protein BIFLAC_05095 [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219620941|gb|ACL29098.1| pseudouridine synthase RluD [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|240249644|gb|ACS46584.1| hypothetical protein Balac_1228 [Bifidobacterium animalis subsp.
           lactis Bl-04]
 gi|240251212|gb|ACS48151.1| hypothetical protein Balat_1228 [Bifidobacterium animalis subsp.
           lactis DSM 10140]
 gi|289177367|gb|ADC84613.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           animalis subsp. lactis BB-12]
 gi|295794245|gb|ADG33780.1| hypothetical protein BalV_1192 [Bifidobacterium animalis subsp.
           lactis V9]
          Length = 317

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 71/344 (20%), Positives = 140/344 (40%), Gaps = 37/344 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ +  +   +     R D         I+     +++ +GQ RV  + +  +  +Q+G 
Sbjct: 1   MSTI--IPAPDALIGKRFDVAVAKMM-GISRAKATELIETGQARVIGRDIHKSATLQAGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V I          ++E++     V+        +  + YED  I V +KP G++     
Sbjct: 58  TVEID---------VREERREPEPVS-------NEMTIAYEDDDIVVVDKPVGVAAHASV 101

Query: 124 GIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G  +     L S +             +  +  RLD  TSG+++V ++  A + +   F 
Sbjct: 102 G--WTGPTVLGSLIQRGVHITSMGAAGRQGIVSRLDVGTSGLMLVCKSDLAYKEMRRQFS 159

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              ++K Y +LV G  K  K  I   + +                     A++H+ V++ 
Sbjct: 160 EHEVKKTYHALVQGNLKEDKATIEAPIGR-----AKVSDFRFTVTPAGKEAVTHWDVMER 214

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F +      +   TGRTHQ+RVH   +G P+VGD  Y AN + +    ++ + +LHA  +
Sbjct: 215 FGE-ATLASINLETGRTHQIRVHFSSIGHPLVGDPMYGANPRLSQALGLE-RQWLHAMEL 272

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           +  HP       +T+  P  +    ++   ++ +  + +   S+
Sbjct: 273 EFRHPRTHINTVVTSRYPTDLQHALETERERFAQREHQRLESSR 316


>gi|331088277|ref|ZP_08337196.1| hypothetical protein HMPREF1025_00779 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330408521|gb|EGG87987.1| hypothetical protein HMPREF1025_00779 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 245

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 61/265 (23%), Positives = 117/265 (44%), Gaps = 29/265 (10%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +Q+G ++ +              +I + + +    +  L   ++YED  I V NK AG+ 
Sbjct: 5   LQAGDILTV--------------RIQEETSSPNIPAVNLPIDIVYEDEDIIVINKAAGMP 50

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR---LDQETSGILVVARTRAAAQHLTESFR 175
           +        +       W   +  KP +      LD++TSG+ VVA+   ++  L+    
Sbjct: 51  IHPSLNNYRNSLANALMWYYEQQNKPFIFRCTNRLDRDTSGLTVVAKHMVSSNILSSMTA 110

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             +I++ Y ++V G     +  I   + +     G  +   K + +   +AI+H+  +  
Sbjct: 111 RHQIEREYLAIVRGHVTPFEGTINAPIGR----TGSSLIERKIDFENGEHAITHYHTV-F 165

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                  + +   TGRTHQ+RVH  H+G P++GD+ Y  + +      + ++  LH+  +
Sbjct: 166 EKNGLSLVSLILETGRTHQIRVHMKHLGFPLIGDYLYNPDME------LIDRQALHSHCL 219

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTW 319
              HP  GR +  TA LP  M + +
Sbjct: 220 RFLHPITGRQMTFTADLPEDMARLF 244


>gi|315639721|ref|ZP_07894860.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           italicus DSM 15952]
 gi|315484498|gb|EFU74955.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           italicus DSM 15952]
          Length = 298

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 71/307 (23%), Positives = 120/307 (39%), Gaps = 37/307 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L KI  + G + V+++       +Q G +V I               
Sbjct: 18  FLKEQ--GISRGLLAKIKFQGGAILVNQRVENVLYFLQEGDIVTI--------------V 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWV 137
             D   + T   D     +++ED  + + NKPA +            +A  + G+ K   
Sbjct: 62  TPDEKEHETLLVDNAPIEVVFEDDHLLIVNKPANVPSIPAQYHPNQTMANRVKGYYKR-K 120

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV--WGIPKNKK 195
           +   Q   +  RLD++T+G++V A+   A   L    R +   K Y +LV          
Sbjct: 121 NYPNQVVHIVTRLDRDTTGLMVFAKHGFAHAKLDVQLRDKSFTKKYQALVFDEANALENH 180

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   + +      D   + +Q      YA + +  ++   Q+   +++Q HTGRTHQ+
Sbjct: 181 AEIIAPIGRN-----DASLIQRQVVTDGRYAKTEYW-LEKKYQQIALVDIQLHTGRTHQI 234

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           RVH   +GCP++GD  Y              +  LH   +   HP  G  L    PLP  
Sbjct: 235 RVHFASIGCPLLGDDLYGGRLDLGIM-----RQALHCYELHFTHPFSGEALSFVQPLPED 289

Query: 315 MVKTWDS 321
           M +   +
Sbjct: 290 MARVIQA 296


>gi|283783562|ref|YP_003374316.1| pseudouridine synthase, RluA family [Gardnerella vaginalis 409-05]
 gi|283441085|gb|ADB13551.1| pseudouridine synthase, RluA family [Gardnerella vaginalis 409-05]
          Length = 321

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 63/329 (19%), Positives = 129/329 (39%), Gaps = 28/329 (8%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
            M+ + +  V +     R D         ++  +   ++   Q ++  ++ + ++ +Q G
Sbjct: 9   PMSDICFK-VTSQFSGCRFDVCLSKLM-GVSRASAISLIERNQAKILGRKSQKSSILQDG 66

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +    +A           +        S      ++Y D  + V +KP G++    
Sbjct: 67  DTIVVDQKESA-----------EQKEEQNNESSVCNIPIIYNDDDVVVIDKPVGVASHAA 115

Query: 123 SG-IAYHIDGFLKSWVDSKGQKPR------LTHRLDQETSGILVVARTRAAAQHLTESFR 175
            G     +   L++                +  RLD  TSG+++V +T  A + +   F 
Sbjct: 116 KGWSGPTVPECLEAVGIDIKTTLCDESRKGIVSRLDVGTSGLMLVCKTDFAYEVMKNQFA 175

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              ++K Y +LV G     K  I   + +                     A++H+ V++ 
Sbjct: 176 KHIVKKTYHALVQGDLAQDKATIDAPIGR-----AKVSDFRFTITSDGKPAVTHWDVLER 230

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           F+Q    + +   TGRTHQ+RVH   +G P+VGD  Y AN        +Q + +LH+  +
Sbjct: 231 FSQ-ATLVSVNLETGRTHQIRVHFSSIGHPLVGDSMYGANPVLAQKLGLQ-RQWLHSMEL 288

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              HP  G+ + + +  P  +    +++ 
Sbjct: 289 TFTHPRTGKSVTVKSHYPLDLQHALEAMR 317


>gi|150016268|ref|YP_001308522.1| RluA family pseudouridine synthase [Clostridium beijerinckii NCIMB
           8052]
 gi|149902733|gb|ABR33566.1| pseudouridine synthase, RluA family [Clostridium beijerinckii NCIMB
           8052]
          Length = 324

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 76/327 (23%), Positives = 137/327 (41%), Gaps = 35/327 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ +     +    + K LR   +RV+  +      +Q G VV I  
Sbjct: 3   IEIGPNEAGQRLDKFLRKLLKDVPLSAIFKALRKKDIRVNGTKQNEKYFLQEGDVVEIK- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-- 127
            I +     KE+ I           D  +  + YED  + V  K   + V   S  +   
Sbjct: 62  YIQSNKEDKKEKFI---------KVDPKRIKIAYEDENVVVIEKWPDVLVHSDSNNSEEP 112

Query: 128 HIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            +  ++ S+++ KG           P   +RLD+ TSG+++  +T    + + E+ R   
Sbjct: 113 TLTDYVLSYLNDKGDYIPENEITFTPAACNRLDRNTSGMVMFGKTFEGLKAINEAIREDE 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I+K Y++L  G  K +      ++LK        ++      K +        +++    
Sbjct: 173 IRKYYYALAKG--KIRAGLYEAYILKNPETNTSKIY--DTEVKNSKKISMEISIVESNG- 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMD 296
            +  LE+   TGR+HQ+R H  H+G PI+GD+KY      +F  +    N  YL+A  ++
Sbjct: 228 AYSLLEIHLITGRSHQIRAHLAHLGNPIIGDNKYGDKKLNSFFESKYGLNFQYLYAYKLN 287

Query: 297 LPHPEGGRLQ------ITAPLPAHMVK 317
                 G+L+      I + LP    K
Sbjct: 288 FR-KINGKLEYLKNKTIASALPPIFKK 313


>gi|295107941|emb|CBL21894.1| pseudouridine synthase, RluA family [Ruminococcus obeum A2-162]
          Length = 342

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 75/356 (21%), Positives = 139/356 (39%), Gaps = 49/356 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYP----HINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M     + V+       +++  +         I+    Q    S  +R +  + +  + +
Sbjct: 1   MEKYMTLTVDEHMAGQTVEKVLRTALKLTKKQISHAKFQ----SDGIRKNGIQCRTTDIV 56

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G+ + I            E    DS+  ++   D     +LYED  I   NKPAGI  
Sbjct: 57  QTGEQIMICI----------ETAKNDSNQLVSFCEDAHPLEILYEDEDILAVNKPAGILT 106

Query: 120 QG-GSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              G+  A  +   +  +   K    + R   RLD+ETSGI++ A+ + +AQ L      
Sbjct: 107 HPSGAHYADTLSNQVAGYFHKKKLSCRVRPIGRLDKETSGIVLFAKNQVSAQRLQTQRES 166

Query: 177 RRIQKIYWSLVWGIPKNKKE--------CIANWLLKKSHIGGDYVHVVKQNEKGANY--- 225
             + K Y ++V G   +            +   + K +        +       +     
Sbjct: 167 GILHKQYIAVVKGDFSDDTSASSDTAWHTVCFPIRKTADHPLRMEAITDFGSSFSPESAD 226

Query: 226 -------------AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                        A++H++V+   +  +  + ++  TGRTHQ+RVH   +G P++GD  Y
Sbjct: 227 FVAPLVDMATLLSAVTHYQVL-YSSPNWSVVTLKLDTGRTHQIRVHMKALGHPLLGDTLY 285

Query: 273 CANFKGNFTS--PIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
              F  +  S  P+ ++  LHA  +   HP     + + APLP      + ++ F 
Sbjct: 286 QKTFPADSVSEQPVFHRTALHAWKIQFRHPFNNAWISLEAPLPDDFCNCFQNINFS 341


>gi|270294141|ref|ZP_06200343.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|317478898|ref|ZP_07938046.1| RluA family pseudouridine synthase [Bacteroides sp. 4_1_36]
 gi|270275608|gb|EFA21468.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|316904932|gb|EFV26738.1| RluA family pseudouridine synthase [Bacteroides sp. 4_1_36]
          Length = 303

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 124/307 (40%), Gaps = 34/307 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    + VD     ++N  ++ G  V+I        
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKSLLSKRIIYVDSVITTQYNFPLKPGMKVQIS------- 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
              +E+   + +  L K        ++YED+ I V  K  G+ SV             L 
Sbjct: 74  ---REKGRKEFNHKLMK--------IVYEDAYIIVIEKMQGLLSVNTDRQKERTAYTILN 122

Query: 135 SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G   +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 123 EYVQRSGKQHRVHIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVVGEME 182

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                + +WL                 + G   +I+H++ I   A  +  +E+   TGR 
Sbjct: 183 KDAGTVVSWLT-----DRKLYVYSSPTDDGGQESITHYRTIKR-ANGYSLVELNLETGRK 236

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y              +L LHA  +   HP  G  ++   P 
Sbjct: 237 NQIRVHMQDLGHPIIGDGRYGLEDVNP-----IGRLALHAFKLCFYHPVTGELMRFETPY 291

Query: 312 PAHMVKT 318
           P    K 
Sbjct: 292 PGEFKKL 298


>gi|268607871|ref|ZP_06141602.1| pseudouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 315

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 65/324 (20%), Positives = 128/324 (39%), Gaps = 31/324 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V+ +++   R+D++     P +    + +++R   ++V+ KR + + ++ +  VV +  
Sbjct: 4   FVINDNDSGQRVDKFISKALPDLPKSMMYRLIRKKDIKVNGKRCEISTKLMTDDVVTVYV 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYH 128
                     +   L +   L           +YED  + + NKP G+     G      
Sbjct: 64  KQELSGTKQHDMSFLKADTALDT---------VYEDENVIIVNKPLGLDSHSNGEHNDDT 114

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +   +K ++ +K +          P L  RLD+ TSG++   +  AA + +  + R   +
Sbjct: 115 LINRIKLYLYNKNEYQPDEESSFAPALCSRLDRNTSGLVTAVKNAAALREINSAIRDGMV 174

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            KIY  +    P    + I  +  K+     + V +      G     + ++V+    + 
Sbjct: 175 HKIYLCITIAQPPKSADIITAYHKKED--SRNIVRISDHPLDGYKPIKTGYEVLKSH-KG 231

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +++   TGRTHQ+R H  H+G P++GD KY                 L A  ++   
Sbjct: 232 LSLVKVTLFTGRTHQIRAHLSHVGAPLLGDGKYGDTSVNKRYGVFY--QALCAYGLEFAL 289

Query: 300 PEG------GRLQITAPLPAHMVK 317
            E        +L I AP P    +
Sbjct: 290 SEDSPLAYLNKLDIHAPEP-DFAE 312


>gi|237744439|ref|ZP_04574920.1| tRNA pseudouridine synthase A [Fusobacterium sp. 7_1]
 gi|229431668|gb|EEO41880.1| tRNA pseudouridine synthase A [Fusobacterium sp. 7_1]
          Length = 292

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 84/309 (27%), Positives = 150/309 (48%), Gaps = 22/309 (7%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ D E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G ++ I   
Sbjct: 5   IIDEDYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDIIFIF-- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
              L    KEQ             + LK ++++E+  ++V NKP G  V  GSG    + 
Sbjct: 63  ---LPETFKEQNEEKFIEISQIRKEKLKQMIVFENDNLFVINKPLGDVVHKGSGHDISLL 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+ LV G 
Sbjct: 120 EEFRSYYSNNNIN--FVNRIDKLTSGLVIGAKNIKTAREIAKEIQTGNIVKKYYILVNGK 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +     + N+L K      + V V    ++G   +I++FK I  +  K+  LE +  TG
Sbjct: 178 IEKDNFILENYLKKDE----ERVIVSDIEKEGYKKSITYFKKIKEY-DKYTLLEAELKTG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLR    H+G  IVGD KY  N K +        L+ +   +DL +     L+I   
Sbjct: 233 RTHQLRAQLDHLGNNIVGDTKYGKNEKEDIMY-----LFSYYLKIDLYN-----LEIKLD 282

Query: 311 LPAHMVKTW 319
           +P      +
Sbjct: 283 MPVFFKTKF 291


>gi|168186684|ref|ZP_02621319.1| pseudouridine synthase, RluA family [Clostridium botulinum C str.
           Eklund]
 gi|169295320|gb|EDS77453.1| pseudouridine synthase, RluA family [Clostridium botulinum C str.
           Eklund]
          Length = 323

 Score =  199 bits (505), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 139/326 (42%), Gaps = 29/326 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ +     +    + K LR G +RV+ K+ K N  ++   VV    
Sbjct: 3   IEIGPNEAGQRLDKFCRKWLEDVPLGAIFKALRKGDIRVNGKKAKQNYFLEEEDVVE--- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                 +I   +K  ++     +  +F    + YED  + +  K  G+ V          
Sbjct: 60  ----TKYIESYKKNKNNVPKKFQEVNFSSIKIAYEDENMLIIEKWPGVLVHSDKKDGDPT 115

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++ +KG+          P   +RLD+ TSG+++  +   + + L E  R R+I
Sbjct: 116 LTDYVLSYLFNKGEYIPEKEVTFTPAPCNRLDRNTSGMVIFGKNFKSLKLLNEMIRERKI 175

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y +LV G  K K+     ++ K        +H+ K  +  +        VID     
Sbjct: 176 SKYYNALVKG--KIKEGRYEAYISKDQINNISEIHLDK--KPNSKKIAMEVSVIDTVG-T 230

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           F +LE+   TGR+HQLR H   +G PI+GD KY      +F       +  +L+A  +  
Sbjct: 231 FSFLELDLITGRSHQLRAHLSFLGNPIIGDDKYGDRKLNSFFNNKYGLSFQFLYAYKLIF 290

Query: 298 PH-PEG-GRLQ---ITAPLPAHMVKT 318
              PE    ++   IT  LP    K 
Sbjct: 291 KDCPEELAYMENKIITQALPPIFKKV 316


>gi|258647021|ref|ZP_05734490.1| ribosomal large subunit pseudouridine synthase D [Dialister invisus
           DSM 15470]
 gi|260404462|gb|EEW98009.1| ribosomal large subunit pseudouridine synthase D [Dialister invisus
           DSM 15470]
          Length = 562

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 71/298 (23%), Positives = 128/298 (42%), Gaps = 36/298 (12%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
           +   +    ++I  +G+V ++  R+      +  G  VR+    ++              
Sbjct: 23  HKGFSSALWKRIKWNGEVWLNGTRIHNAKTVLHEGDRVRLVWDESS-------------- 68

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQK--P 144
                    +   +LYED  + V NK  G+ +   + GI   +   +  +   KG+K   
Sbjct: 69  ---DIVPADIPLDILYEDDTLLVVNKGTGMIIHPTNAGIHDTLVNAVAGYFQKKGEKSGI 125

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              +RLD+ T+G++VVA++  A   LT S     I + Y ++  G    +   +   + +
Sbjct: 126 HPVYRLDRNTTGVVVVAKSAKAQYALTRSHD--LIHREYIAVAGGYIPGEFGIVDAPIGR 183

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           K     ++        K    A + + V+      +  L++   TGRTHQ+RVHA +MG 
Sbjct: 184 KEGSIIEWTVR-----KDGRPARTEYTVL-RHGDNYTVLKLHLLTGRTHQIRVHARYMGT 237

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           P++GD  Y  N        + ++  LHA  + L HPE G  ++ TAP+PA M    + 
Sbjct: 238 PLLGDDLYGGNHD------LISRQALHAHTVTLTHPETGEAMKFTAPVPADMEPFMNE 289


>gi|256027210|ref|ZP_05441044.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
 gi|289765187|ref|ZP_06524565.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
 gi|289716742|gb|EFD80754.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
          Length = 304

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 83/306 (27%), Positives = 149/306 (48%), Gaps = 22/306 (7%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ D E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G ++ I   
Sbjct: 5   IIDEDYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDIIFIF-- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
              L    KEQ             + LK ++++++  ++V NKP G  V  GSG    + 
Sbjct: 63  ---LPETFKEQNEEKFIELSQVRKEKLKQMIVFQNDNLFVINKPLGDVVHKGSGHDISLL 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+ LV G 
Sbjct: 120 EEFRSYYSNNNIN--FVNRIDKLTSGLVIGAKNIKTAREIAKEIQTGNIVKKYYILVNGK 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +     + N+L K      + V V    ++G   +I++FK I  +  K+  LE +  TG
Sbjct: 178 IEKDNFILENYLKKDE----ERVIVSDIEKEGYKKSITYFKKIKEY-DKYTLLEAELKTG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLR    H+G  IVGD KY  N K +        L+ +   +DL +     L+I   
Sbjct: 233 RTHQLRAQLNHLGNNIVGDTKYGKNEKEDIMY-----LFSYYLKIDLYN-----LEIKLE 282

Query: 311 LPAHMV 316
           +P    
Sbjct: 283 IPDLFK 288


>gi|261880461|ref|ZP_06006888.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bergensis DSM 17361]
 gi|270332800|gb|EFA43586.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bergensis DSM 17361]
          Length = 306

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 68/308 (22%), Positives = 125/308 (40%), Gaps = 33/308 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           EE+  LD    N     +   ++  L+   ++V+ K++  ++                  
Sbjct: 29  EESTLLDWLLANLNE--SRTKIKATLKGRGIKVNGKQITRHD-----------------F 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
            ++   KI  S              ++YED+ I V  K  GI        + ++   L  
Sbjct: 70  PLVPGMKIAVSKTKRNNTLKSRYVKIVYEDAYIIVVEKNVGILSMPAGHHSLNVKAVLDE 129

Query: 136 WVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +     Q  +  + HRLD++TSG+++ A+ +     L   ++     + Y ++V G+ + 
Sbjct: 130 YFHKTKQPCQAHVVHRLDRDTSGLMIYAKDKKTEFSLQADWKGTVYDRRYVAVVSGVMEQ 189

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            +  I +WL         Y       + G  YA++HF  +D   Q    +E +  TGR +
Sbjct: 190 DEGTIDSWL----KDNKSYFSYSSSTDNGGKYAVTHFYTLDRSPQ-HSLVEFKLDTGRKN 244

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           Q+RVHA  MG P+ GD KY              +L LHA  +   HP     ++  A +P
Sbjct: 245 QIRVHAADMGHPVCGDPKYGNGDDP------IGRLCLHAYVLCFYHPVTHEPMEFQARIP 298

Query: 313 AHMVKTWD 320
            + ++ + 
Sbjct: 299 QNFIQLFR 306


>gi|148262258|ref|YP_001228964.1| RluA family pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146395758|gb|ABQ24391.1| pseudouridine synthase, RluA family [Geobacter uraniireducens Rf4]
          Length = 296

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 149/327 (45%), Gaps = 40/327 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           +  VVV  D   MRLD   K  +P ++   +++I+  G   + +  V+  +  ++ G ++
Sbjct: 2   ILKVVVGADHAGMRLDDGAKELFPQLSKTQIRRIIDWGGCTICEALVRVASRPLREGDLI 61

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-- 123
            +         +++ ++ ++ S        + K  LL+ED+     NK AGI+ Q     
Sbjct: 62  ALG--------VMEPERCVEIS--------YRKEDLLFEDANYLAVNKAAGINSQRTPYQ 105

Query: 124 ---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               + Y ++ ++KS      +  R+ HRLD+ TSG++   + + AA H++   +  +++
Sbjct: 106 LKGTVEYAVETYMKSL--GSKEPARVIHRLDRGTSGVMFFPKDKRAATHISFLLKEGKVE 163

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+YW++V G+P  ++  +   + K +                   A + F+VI    +  
Sbjct: 164 KVYWAMVAGVPDEEQWTVDAPIAKLNK-------FRYGVALPGREARTAFRVI-AVGKGA 215

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             LE  P TGRTHQ+RVH +H   PI+GD  Y  +           ++ LH R M     
Sbjct: 216 TLLEALPFTGRTHQIRVHLVHSNLPIIGDTTYGGDTAA--------RMMLHCRSMAFTSR 267

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYD 327
           +G  +Q  APL    +K     G + +
Sbjct: 268 DGKPVQAIAPLDEGFLKACRDFGIETE 294


>gi|317486117|ref|ZP_07944964.1| RNA pseudouridylate synthase [Bilophila wadsworthia 3_1_6]
 gi|316922640|gb|EFV43879.1| RNA pseudouridylate synthase [Bilophila wadsworthia 3_1_6]
          Length = 308

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 137/318 (43%), Gaps = 19/318 (5%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V   E   +L ++    +       L + +R+GQVR++  R K  +R++    +R+
Sbjct: 3   EPLQVTAAEAGQKLLQFLSRRFEE-PQSVLHRWIRTGQVRINGGRAKPFDRVKLNDEIRV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PP   A     K +++  SS             ++ E + + VF KP+G+ V  G+G   
Sbjct: 62  PPFAGAGT---KAERVPASSGGKELPP------IVAETADVIVFCKPSGLPVHPGTGHTD 112

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE--SFRMRRIQKIYWS 185
            +   L++        P   HRLD++TSG+L+V +T AA + L++  +     + K Y +
Sbjct: 113 SLTTRLEAAFAGSPFIPAPVHRLDRDTSGLLLVGKTYAAVRRLSDALAAHDGSVAKDYLA 172

Query: 186 LVWGI-PKNKKECIANWLLKKSHIGGDYVHVV----KQNEKGANYAISHFKVIDCFAQKF 240
            V G  P ++ + + + L K++        VV    +        A    + +    +  
Sbjct: 173 WVQGECPWSRPKRLEDHLAKRTVGAQGREKVVAGKSRTGGPDEKPASLTVRSL-TVREGR 231

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++ HTGRTHQ+RV     G P+VGD KY     G+       +L +         P
Sbjct: 232 SLVLIRLHTGRTHQIRVQLSERGFPLVGDVKYGGPRCGDGLKLHAVRLRVGEETYTALPP 291

Query: 301 EGGRLQITAPLPAHMVKT 318
             G  ++ A LP      
Sbjct: 292 WAGPWRV-AHLPPEWEDV 308


>gi|294674059|ref|YP_003574675.1| RNA pseudouridine synthase family protein [Prevotella ruminicola
           23]
 gi|294471803|gb|ADE81192.1| RNA pseudouridine synthase family protein [Prevotella ruminicola
           23]
          Length = 277

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 69/292 (23%), Positives = 120/292 (41%), Gaps = 32/292 (10%)

Query: 33  NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +   ++  L+   ++V+ K V +F+ +++ G  V +                        
Sbjct: 14  SRSKIKATLQGRGIKVNGKTVSQFDFQLEPGMKVAVSKTKRNQQSFKSR----------- 62

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHR 149
                    ++YED  + V  K  GI        + ++   L  +     QK    + HR
Sbjct: 63  ------YVKIVYEDKWLIVIEKAEGILSMAAGHSSLNVKTVLDDYFKKSRQKCTAHVVHR 116

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG++V A+     Q L  ++      + Y ++  G  +N +  IANWL       
Sbjct: 117 LDRDTSGLMVYAKDMETEQILEHNWHDIVYDRRYVAVCSGEMENDEGTIANWL----KDN 172

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             YV      + G  YA++H+ V+D        +E +  TGR +Q+RVH+  MG P+ GD
Sbjct: 173 KAYVTYSSPTDNGGKYAVTHYHVLDRTTD-HSLVEFKLETGRKNQIRVHSADMGHPVCGD 231

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            KY             ++L LHA  +   HP  G  ++   P+P    K + 
Sbjct: 232 PKYGNGDDP------IHRLCLHAWLLCFHHPVTGEPMEFETPVPTAFKKLFK 277


>gi|225428918|ref|XP_002282614.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|296090438|emb|CBI40257.3| unnamed protein product [Vitis vinifera]
          Length = 476

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 106/384 (27%), Positives = 160/384 (41%), Gaps = 90/384 (23%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVR------------VDK-----KRVKFNNRIQSGQVV 65
           +W     P +    +QK+ R  QVR            V       KRV   + +  G  +
Sbjct: 97  KWVVRCCPQLPRSLVQKLFRLRQVRRESYNMITSDIGVQNQEHRLKRVAAKDLMNLGDQI 156

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +P  +        E    D  +N   + +      LY+D  I V NKP G+ VQGG GI
Sbjct: 157 LLPITVEEFPSEKHEYHCNDEEINFVHNLE------LYKDPAIIVVNKPPGLPVQGGIGI 210

Query: 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI----- 179
              +D    +++     + PRL HRLD+++SGIL++ RT+ +A  L   FR +       
Sbjct: 211 KRSLDELAATYLRYDCSEPPRLVHRLDRDSSGILIMGRTQTSATILHSIFREKTFGASNN 270

Query: 180 ---------QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAI 227
                    Q+ YW+LV G P+  +  I+  L K     G    +   +      + +AI
Sbjct: 271 DIDTKKRILQRRYWALVIGSPRRPRGLISAPLGKVVVDDGKSERITIVDNVQTMSSQHAI 330

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC------------A 274
           + ++VI      + WLE+ P TGR HQLRVH    +G PIVGD+KY             +
Sbjct: 331 TEYRVIKSSCHGYTWLELSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQAHRKWKQLFQS 390

Query: 275 NFKGNFTSPIQNK--------------------LYLHARYMDLPH--------------- 299
           N + N    + N+                    L+LH + M LP+               
Sbjct: 391 NIEKNLDENLSNRKTHPFGLDLESGSILDKQPHLHLHCKQMVLPNVSLALQNLQLSAECD 450

Query: 300 -PEGGRLQITAPLPAHMVKTWDSL 322
             E   L+  APLP+HM ++WD L
Sbjct: 451 LSELESLEFVAPLPSHMQRSWDIL 474


>gi|313682856|ref|YP_004060594.1| ribosomal large subunit pseudouridine synthase d [Sulfuricurvum
           kujiense DSM 16994]
 gi|313155716|gb|ADR34394.1| ribosomal large subunit pseudouridine synthase D [Sulfuricurvum
           kujiense DSM 16994]
          Length = 325

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 76/340 (22%), Positives = 140/340 (41%), Gaps = 43/340 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINAL 74
           +E +RLD +            + +++    V VD K   K   +++  Q V I       
Sbjct: 11  DEAVRLDVFLTQQL-GQTRNQITQLIEQNCVSVDGKETAKSGLKLKPSQTVIIRF----- 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                         +           +L+ED  I V NKP+ ++V     +    +  L 
Sbjct: 65  ----------PEQKSTPAQEIDFDVDILFEDDDILVINKPSSLTVHPAPSV---KEPTLV 111

Query: 135 SWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            W+  KG         ++  + HRLD+ TSG +V+A+   A + L+   + + + + Y +
Sbjct: 112 DWLKHKGIALSTLSGEERHGIVHRLDRGTSGAMVIAKNNEAHEALSLQLQDKTMGRYYLA 171

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           ++    K     I   + + +         + ++ K A  A +  K++    +    +  
Sbjct: 172 IITPAMKETITVIDRPIGRSA--NNRLKMAISESGKNAKTAFA--KLLPSHDETEELIAC 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
           + +TGRTHQ+RVH   +   I+GDH Y  + K +       ++ LHA  +   HP    R
Sbjct: 228 KLYTGRTHQIRVHLESISRHIIGDHLYGTSAKSDK----MERILLHAYNLYFTHPTTLKR 283

Query: 305 LQITAPL----PAHMVKTWDSLGF-KYDRNLYIKRLYSQD 339
           +  TAPL      ++ K +DS    +    L I+RL+S +
Sbjct: 284 VNFTAPLGDVMEDYLTKHFDSKELHELIDPLRIERLFSTE 323


>gi|210623700|ref|ZP_03293984.1| hypothetical protein CLOHIR_01934 [Clostridium hiranonis DSM 13275]
 gi|210153388|gb|EEA84394.1| hypothetical protein CLOHIR_01934 [Clostridium hiranonis DSM 13275]
          Length = 303

 Score =  199 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 73/331 (22%), Positives = 133/331 (40%), Gaps = 45/331 (13%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +LM+Y        +E+ + L     +     +  ++ K+ R   V V+ +  K    ++ 
Sbjct: 10  NLMSY------TAEEDGV-LKEILLDKL-GFSVRSISKMKRERTVNVNGEYRKPTLDVKK 61

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G ++ +    +  N                     L+  +LY+D  I + +KP  + V  
Sbjct: 62  GDLIEVEINEDMAN----------------FEPQNLEMGILYDDFDIIMVDKPPYMVVHP 105

Query: 122 GSGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                 H DG + + V        +  K R  +RLD  TSG+++VA+   A   L+    
Sbjct: 106 TKS---HFDGTVANGVTDFIIKKDEKVKVRFVNRLDMNTSGLVIVAKNAYAHHVLSTDMS 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              ++K Y ++V G+ K  K  I   + + +      V      ++    +I+H+ VI+ 
Sbjct: 163 ENLVEKKYIAVVKGVMKEDKGTIDAPIYRPTDDSIKRVV-----DERGQRSITHYSVIER 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                  +E++  TGRTHQ+RVH  H+G  I+GD  Y           +  +  LHA  +
Sbjct: 218 L-DDATVVELKLETGRTHQIRVHLAHLGYGIIGDELYGY-----VDENLIKRQALHAYSL 271

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
               P     L+  A +P  M +    L  +
Sbjct: 272 KFKQPRTREDLEFKAEIPDDMKELIKKLKME 302


>gi|323487164|ref|ZP_08092469.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323399516|gb|EGA91909.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 298

 Score =  199 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 67/310 (21%), Positives = 137/310 (44%), Gaps = 33/310 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ ++    ++ + +      +   L  + ++   + V  +       ++ G ++ +   
Sbjct: 9   IKENDCGKTIESYLRER--GYSRKILVHLRQTNLGITVAGELAYTTRVLKEGNILSV--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHI 129
              L+     ++I+   + L+         +LYED  + V NK AG+ V    G     +
Sbjct: 64  --RLSEETSSERIIPVPMELS---------VLYEDEDLMVINKAAGMPVHPSQGNFDNTL 112

Query: 130 DGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L  +   KG+    R  +RLD++T+G+L++A+   +   L+     + I++ Y ++V
Sbjct: 113 ANGLAWYFKEKGEAFVFRAVNRLDRDTTGLLLIAKNMLSGAILSSMVSEKTIRREYRAIV 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQ 246
            G+   ++ CI   + +     G  +      E+G  YA + ++ +     K C  L + 
Sbjct: 173 SGL-TEEEGCICRPIARAE---GSTIERCVDPERG-EYACTRYRRLGYDRDKDCSLLLIT 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  ++G P++GD  Y  +++         +  LH+  +   HP  G  +
Sbjct: 228 LDTGRTHQIRVHMKYIGHPLLGDFLYNPDYR------FIKRQSLHSCRLTFTHPLTGEAM 281

Query: 306 QITAPLPAHM 315
             TAPLP   
Sbjct: 282 DFTAPLPEDF 291


>gi|302670812|ref|YP_003830772.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
 gi|302395285|gb|ADL34190.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
          Length = 341

 Score =  199 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 67/341 (19%), Positives = 140/341 (41%), Gaps = 39/341 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +V+ N+E + RLD + K++ P+ +   + K+LR   + ++ K+     ++ S  V+ 
Sbjct: 1   MKEIVIGNNESDKRLDGFLKSYLPNASMGFIYKMLRKKNITLNGKKASGTEKLASNDVIC 60

Query: 67  IPPVINALNHII---------------KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           I      L                   +          ++ +    +  ++YE+  +   
Sbjct: 61  IFFADETLEKFRGISTDSTQSGNNSNSRSDIQDYCKREISSYKKIGELKVIYENKHVIFV 120

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWV---------DSKGQKPRLTHRLDQETSGILVVAR 162
           +KPAG+  Q        ++ +L  ++         + +  KP + +RLD+ TSG+++ A+
Sbjct: 121 DKPAGLLSQKSKDTDDSLNDWLIGYMLTNNLITPSELETYKPSICNRLDRNTSGLVICAK 180

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           +   A+ +    + R + K Y ++V G      E +  +L K       ++      +  
Sbjct: 181 SLLGARTMNNMLKDRTLHKYYRTIVTGQISESSE-LKGFLYKDEKKNKVFIKTSDPGDDR 239

Query: 223 ANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            +Y  + +K +  +       LE++  TG+ HQ+R H   +G PI+GD KY  +      
Sbjct: 240 YSYIETEYKPVRYYYDLDMTLLEVKLITGKPHQIRAHLQSIGHPIIGDVKYGGSPVKGLK 299

Query: 282 SPIQNKLYLHARYMDLP-------HPEGGRLQITAPLPAHM 315
                   LH+  + LP           G+ +  A LP   
Sbjct: 300 Y-----QLLHSYRLVLPKDLNDVFCDIAGK-EFIAELPDTF 334


>gi|220928045|ref|YP_002504954.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|219998373|gb|ACL74974.1| pseudouridine synthase, RluA family [Clostridium cellulolyticum
           H10]
          Length = 299

 Score =  199 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 143/320 (44%), Gaps = 36/320 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++  +E    L    KN    ++   ++K+    ++ V++   + N  +++   +++   
Sbjct: 6   IISENEARKTLKHVLKNGLK-LSERLIRKLKLQQKIYVNEHPERVNYIVKADDRLKVILD 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +      I+ Q I                 ++YED  + V NK +GI V   S   YH D
Sbjct: 65  LEEECEHIEPQDI--------------PLDVIYEDECMLVLNKQSGIVVHPTS---YHPD 107

Query: 131 GFLKS----WVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             + +    ++  KG  +K R   RLD+ETSGI++ A+ +   + L +       +K Y 
Sbjct: 108 NTIANGIVYYLKQKGVTKKVRPVSRLDRETSGIIIFAKNQFTQEMLIQQMHNNLFKKEYL 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWL 243
            +V GIP+N +  I   + +K         +++   +    +I+H+K++  F +     L
Sbjct: 168 GIVQGIPQNNEGTINLPIARKPG-----SIMLRHISEEGAPSITHYKILKTFPSHNSALL 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +  TGRTHQ+RVH   MG PI GD  Y  N     T+   ++  LH+   ++ HP   
Sbjct: 223 SFKLETGRTHQIRVHCKAMGFPIYGDTLYSDN-----TNLFISRQALHSYRTEIIHPVTL 277

Query: 304 R-LQITAPLPAHMVKTWDSL 322
           + +   A LP+ +    + L
Sbjct: 278 KGVIFKAELPSDISGLLEIL 297


>gi|284991670|ref|YP_003410224.1| RluA family pseudouridine synthase [Geodermatophilus obscurus DSM
           43160]
 gi|284064915|gb|ADB75853.1| pseudouridine synthase, RluA family [Geodermatophilus obscurus DSM
           43160]
          Length = 315

 Score =  198 bits (504), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 139/325 (42%), Gaps = 29/325 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  E  R+D+     +  ++      +  +G V VD +     +RI  G  + +
Sbjct: 12  RALPVPDGLEGQRVDQALSRLF-GLSRGAAADLADAGAVVVDGRVRGKGDRISGGSWLEV 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
                 L     E    +    LT   D    +         V +KP G++     G   
Sbjct: 71  -----ELPPPPGESAAPEPVPGLTVVHDDDDIV---------VVDKPVGVAAHPSPGWEG 116

Query: 127 YHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  + HRLD  T+G++VVA++  A   L  +F+ R ++K
Sbjct: 117 PTVVGGLAAAGYRVSTSGAAERQGVVHRLDAGTTGLMVVAKSERAYTALKAAFKQRTVEK 176

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G P   +  I   +    H   D+   V Q   G   +++H++V + F     
Sbjct: 177 GYAALVQGHPDPSRGTIDAPI--DRHPKHDWRFAVVQ---GGRPSVTHYEVAEAFP-AAS 230

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++  TGRTHQ+RVH   M  P VGD  Y A+        + ++ +LHA  + +PHP 
Sbjct: 231 LVDIRLETGRTHQIRVHFSAMRHPCVGDTTYGADPTLAARLGV-SRQWLHAARLGIPHPA 289

Query: 302 GGR-LQITAPLPAHMVKTWDSLGFK 325
            G  ++ T+P P  +    D L  +
Sbjct: 290 DGHWMEFTSPFPPDLAGALDILRAE 314


>gi|218263542|ref|ZP_03477623.1| hypothetical protein PRABACTJOHN_03310 [Parabacteroides johnsonii
           DSM 18315]
 gi|218222665|gb|EEC95315.1| hypothetical protein PRABACTJOHN_03310 [Parabacteroides johnsonii
           DSM 18315]
          Length = 306

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 121/316 (38%), Gaps = 38/316 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVR 66
           + V V+ +     L  +        +  +++ +L  GQ+ V+     +FN  +  G  V 
Sbjct: 19  RKVTVKEEN---TLLPFLFGLLNEQSKSSVKALLAHGQISVNGTVTSQFNTPLIPGDEVL 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I      +                    +     +++ED  + V NK  G+     + + 
Sbjct: 76  ISYERGKV------------------EFNNPLLTIVWEDDDLIVVNKKEGLLSVSSTRVK 117

Query: 127 YHIDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                 L S    K     K  + HRLD++TSG+++ A+     + L  ++      + Y
Sbjct: 118 ERTAFHLLSGYVKKTDPRNKIFVLHRLDRDTSGLMMFAKNLQVQKALQSNWNSAITARTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G P+   + I + L + +      + V    E     AI+ ++++      +  L
Sbjct: 178 VAVVEGRPEKDSDLIISNLTENTK-----MQVYVTTEGDGKEAITRYRLLHSNG-AYSLL 231

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E+   TGR +Q+R     +G  I GD+KY A            +L LHAR +D  HP  G
Sbjct: 232 ELDLETGRKNQIRAQMQSIGHSIAGDYKYGAETDPT------GRLMLHARRLDFIHPVTG 285

Query: 304 -RLQITAPLPAHMVKT 318
             +     +P      
Sbjct: 286 EEMHFETRIPDKFTSL 301


>gi|289422957|ref|ZP_06424779.1| ribosomal large subunit pseudouridine synthase D
           [Peptostreptococcus anaerobius 653-L]
 gi|289156637|gb|EFD05280.1| ribosomal large subunit pseudouridine synthase D
           [Peptostreptococcus anaerobius 653-L]
          Length = 307

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 71/300 (23%), Positives = 127/300 (42%), Gaps = 34/300 (11%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
             +  ++ ++ R   + V+ K  K    +  G ++ IP +    +               
Sbjct: 31  GFSARSISRLKREKNIYVNGKYTKPTLHVDKGDIIEIPIIEEGSD--------------- 75

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQ--KPRLT 147
                 L   +LYED  + V +KP  + V    S     +   L   +D +GQ  + R  
Sbjct: 76  -FEGQDLNVRVLYEDFDLVVVDKPPFMVVHPTKSHYQNTLANHLSYHLDQEGQDVRVRFV 134

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           +RLD  TSG+++VA+   A   L+     + ++K Y+++V G+P +K+  I   + +++ 
Sbjct: 135 NRLDMNTSGLVIVAKNAYAHHKLSSDMSDKLVEKEYYAIVNGVPDHKEATIDQPIYRETE 194

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                +      +     +I+H+ +I    DC       L +   TGRTHQ+RVH  ++G
Sbjct: 195 DSIKRIV-----DPRGQRSITHYSLIGSYKDCEGHLISLLRISLETGRTHQIRVHMDYIG 249

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
            PIV D  Y           +  +  LHAR +    P     +++ A LP  MV+  D  
Sbjct: 250 HPIVSDELYG-----QLQDNLIGRQALHARKLVFNQPRMKNEIELVADLPDDMVRLLDKC 304


>gi|71653582|ref|XP_815426.1| pseudouridylate synthase-like protein [Trypanosoma cruzi strain CL
           Brener]
 gi|70880480|gb|EAN93575.1| pseudouridylate synthase-like protein, putative [Trypanosoma cruzi]
          Length = 407

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 88/350 (25%), Positives = 155/350 (44%), Gaps = 23/350 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV---RVDKKR--VKFNNRIQ 60
            VQY V+  D    R+D +   H+P  ++  ++ +++ G +   R + K+   +  +R++
Sbjct: 55  EVQYHVITQDWFGQRVDTFLTQHHPEWSYETMKTLVQQGHIYRYRKNGKKRFTRITDRLE 114

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLT------KHSDFLKSILLYEDSKIYVFNKP 114
             +++ +P  +     +     +L  S   T      +  +   +++L+++  + V NKP
Sbjct: 115 FDELLVVPTPVFYERQLAPPTGVLQESKKPTHFKLSSQVREMAHNMVLFKNEHVIVINKP 174

Query: 115 AGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            G+ +   S     +I   L +W  +   KP + H LD+ETSG +V+AR++ A + L   
Sbjct: 175 HGVPMMPTSDPQEMNIAAMLSAWKYTNSTKPIVCHNLDKETSGCVVLARSKNAHRMLARM 234

Query: 174 FRMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
           F  R +   +YW    G P      I           GD +       K +   I+ F V
Sbjct: 235 FVKRVVPNSVYWGFCVGKPSVNFGRIRMHFEMTRGTKGDIIVARPSPTKTSKVGIAEFVV 294

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK-----GNFTSPIQN 286
                +   ++   P T R HQ R+ A H +  P++GD KY            F  P   
Sbjct: 295 NASALEFGSFISFYPLTTRRHQERIMAAHALRSPLLGDAKYGGESAFPSSMSLFWDPEDK 354

Query: 287 --KLYLHARYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
              L+LH R + LP+    G  + +TAPLP HM KT+  LG+  D +  +
Sbjct: 355 GLPLHLHHRKIQLPYKNSTGEFVCVTAPLPIHMEKTFKKLGWPCDVDDPL 404


>gi|289705615|ref|ZP_06502005.1| pseudouridine synthase, RluA family [Micrococcus luteus SK58]
 gi|289557665|gb|EFD50966.1| pseudouridine synthase, RluA family [Micrococcus luteus SK58]
          Length = 295

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 69/309 (22%), Positives = 133/309 (43%), Gaps = 33/309 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD------KKRVKFNNRIQ 60
            + + V   E   R+D    + +  +    L      G VR +       + +  + +  
Sbjct: 6   TERLEVTEAEAGRRVDAVLADAF-GVPRSLLADWFSRGLVRAESRSGRRDRVLAKSAKAV 64

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ + +    +     ++ +++   S             +LYED  +   +KP G++  
Sbjct: 65  AGETLAVDVPDDPDPLEVRAERVDALS-------------ILYEDEDLVAVDKPTGVAAH 111

Query: 121 GGSG-IAYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
              G +   + G L +           ++  + HRLD  T+G++VVA+T  A   + + F
Sbjct: 112 PSPGWVGPTVVGALAALGYHITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQF 171

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R R  +K+Y ++V GIP      +   + +  H G  +   V  +      +++H++ ++
Sbjct: 172 RERVPEKVYHAVVQGIPDPLSGTVDAPIGR--HPGHHWKFAVLDD---GRPSVTHYETLE 226

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            F +    LE+   TGRTHQ+RVH   +  P VGD  Y A+ +      +  + +LHA  
Sbjct: 227 VFGR-ATLLEVHLETGRTHQIRVHTSALRHPCVGDLTYGADPRMAAELGL-TRQWLHAHR 284

Query: 295 MDLPHPEGG 303
           +  PHP  G
Sbjct: 285 LAFPHPVTG 293


>gi|327538476|gb|EGF25140.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica WH47]
          Length = 321

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 73/333 (21%), Positives = 131/333 (39%), Gaps = 31/333 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIP 68
             V+   E  R+D          +    + ++  G V ++    K     ++ G +V + 
Sbjct: 8   TTVDETNEG-RVD-IIVRELSETSRSQARGMIDHGCVMINGSPCKSVGTTVKPGDLVAVR 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAY 127
              +      K Q             D     +++ED  I V NK AG ++V    G   
Sbjct: 66  YDKHQRYREKKRQ------------WDDRTFEIVFEDEHIIVVNKSAGTLTVPTDRGEPN 113

Query: 128 HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +  ++     K    + HRLD+ETSG+LV  +    A  L E F+ RR  +++ +
Sbjct: 114 SLVDRVSIYLSYSKSKKEAFVVHRLDRETSGLLVFGKHEPIADLLIEQFKDRRPTRVFHA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-------FAQ 238
           +V G     +    + L      G +      +  K  + AI+H+KV+           +
Sbjct: 174 IVAGNVAEDEGTFESHLA----TGSNLDRYETRPGKDTDQAITHYKVVRRLAERESSHGE 229

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +   +E Q  T + +Q+RV   + G P++GD +Y    +       + ++ LHA  +   
Sbjct: 230 ETTLIEAQLETSKRNQVRVQFANAGHPVLGDPRYKPK-EATHARWHRKRMALHASTLGFF 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           HP  G  +    PLP+ M K       + DR  
Sbjct: 289 HPVSGEPVNFDTPLPSAMEKFVAGARGRSDRKA 321


>gi|253579056|ref|ZP_04856327.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251849999|gb|EES77958.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 299

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 73/320 (22%), Positives = 140/320 (43%), Gaps = 31/320 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +   ++  +   + +  + K      +   L  +           +   N  I +G+
Sbjct: 1   MQRILKYIISENTTPVTILDFLKK--EGFSRHILSSM-----------KNTPNTIILNGE 47

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                 V+   +H+I      +S  N+ +    L   ++YED  I V NKPA + V   +
Sbjct: 48  RGFGRSVLKPQDHLIVTVPETESGENIIRTKMDLN--IIYEDEDILVINKPADMPVHPSA 105

Query: 124 G-IAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G     +   +  +   KG+    R  +RLD++T+G L++A+   +A  L+   + R+I 
Sbjct: 106 GNYENTLANGIAWYFAEKGEDFVYRCINRLDRDTTGALILAKNPLSAAILSVQMKKRQIL 165

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV G+       I   + +        V   + N      AI+H++ +    +++
Sbjct: 166 RTYLALVDGLLP-DSGTINAPIARMEGS----VITREVNFGTGESAITHYERLAA-GKEY 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
              E+   TGRTHQ+RVH  ++G P+ GD+ Y  +++        N+  LH+  ++  HP
Sbjct: 220 SLAELHLETGRTHQIRVHMKYIGHPLPGDYLYNPDYRR------INRQPLHSYQLEFTHP 273

Query: 301 EGGR-LQITAPLPAHMVKTW 319
             G+ +  TAPLP   +  +
Sbjct: 274 TTGKVMLFTAPLPIDFISAF 293


>gi|160889892|ref|ZP_02070895.1| hypothetical protein BACUNI_02323 [Bacteroides uniformis ATCC 8492]
 gi|156860884|gb|EDO54315.1| hypothetical protein BACUNI_02323 [Bacteroides uniformis ATCC 8492]
          Length = 303

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 124/307 (40%), Gaps = 34/307 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    + VD     ++N  ++ G  V+I        
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKSLLSKRIIYVDSVITTQYNFPLKPGMKVQIS------- 73

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
              +E+   + +  L K        ++YED+ I V  K  G+ SV             L 
Sbjct: 74  ---REKGRKEFNHKLMK--------IVYEDAYIIVIEKMQGLLSVNTDRQKERTAYTILN 122

Query: 135 SWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G   +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 123 EYVQRSGKQHRVHIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHGIVTDRRYVAVVVGEME 182

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                + +WL                 + G   +I+H++ I   A  +  +E+   TGR 
Sbjct: 183 KDAGTVVSWLT-----DRKLYVYSSPTDDGGQESITHYRTIKR-ANGYSLVELNLETGRK 236

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G PI+GD +Y              +L LHA  +   HP  G  ++   P 
Sbjct: 237 NQIRVHMQDLGHPIIGDGRYGLEDVNP-----IGRLALHAFKLCFYHPVTGELMRFETPY 291

Query: 312 PAHMVKT 318
           P    K 
Sbjct: 292 PGEFKKL 298


>gi|145595716|ref|YP_001160013.1| RluA family pseudouridine synthase [Salinispora tropica CNB-440]
 gi|145305053|gb|ABP55635.1| ribosomal large subunit pseudouridine synthase D [Salinispora
           tropica CNB-440]
          Length = 314

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 68/323 (21%), Positives = 130/323 (40%), Gaps = 28/323 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  + +RLD+     +  ++      ++ +G   VD      + +I++G  + +
Sbjct: 12  RSLPVPDGLDGLRLDQAVARLF-GLSRTTAAALVDAGAALVDGTVRANSYKIRAGSWLEV 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                A                           ++Y D  I V +KP G++     G   
Sbjct: 71  TLPAPAAPPA-------------VVPQAVSGLRVVYADDDIVVVDKPVGVAAHPSPGWTG 117

Query: 127 YHIDGFLKSWVDSK-----GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +           ++  + HRLD  T+GI+ VA++  A   L  +F+ R ++K
Sbjct: 118 PTVIGGLAAIGHRISTSGAAERQGVVHRLDVGTTGIMAVAKSEQAYTSLKRAFKYREVEK 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G     +  I   + +  H    +  V          +I+H+  ++ F     
Sbjct: 178 RYHAVVQGHLDPLRGTIDAPIDRHPHHDYRWAVVS-----DGKPSITHYDTLEAFP-AAS 231

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            ++++  TGRTHQ+RVH   +  P VGD  Y A+     T    ++ +LHAR +   HP 
Sbjct: 232 LVDVRLETGRTHQIRVHFSTLRHPCVGDLTYGADPTL-ATRLGLDRQWLHARELRFRHPR 290

Query: 302 GG-RLQITAPLPAHMVKTWDSLG 323
            G  +   +  P  + +    L 
Sbjct: 291 TGEEVCFVSDYPDDLDRALGILR 313


>gi|58697309|ref|ZP_00372669.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Drosophila simulans]
 gi|225630832|ref|YP_002727623.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia sp. wRi]
 gi|58536323|gb|EAL59813.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia endosymbiont of Drosophila simulans]
 gi|225592813|gb|ACN95832.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Wolbachia sp. wRi]
          Length = 276

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 77/275 (28%), Positives = 133/275 (48%), Gaps = 27/275 (9%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           I +   + + P    + H+++     D S ++  + D +K  ++YED  I V +K +G++
Sbjct: 8   IINNDHI-VKPGEEYIVHLVQ----PDISTSIEPNYD-IKLDIVYEDEDIIVLSKQSGLT 61

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           V  G+G   + D  L + +   G+      +P + HRLD++TSG++V+A+   A   L+E
Sbjct: 62  VHPGAGT--NNDTLLNAVIAHLGKIPYSHVRPGIVHRLDKDTSGLMVIAKNEEAHGFLSE 119

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
               R+I++ Y ++VWGI  +++  I   +  K     + + V K        AI+H+ V
Sbjct: 120 LLSNRKIKREYLAIVWGILSSQQGTIKTNIAPKRG-NKEMMCVTKI---TGKLAITHYLV 175

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------FKGNFTSPIQ 285
                Q    ++    TGRTHQ+RVH  H+G  IVGD  Y  N        K +      
Sbjct: 176 QKVIGQ-VSLVKCTLETGRTHQIRVHMSHIGHSIVGDQVYGKNSSKSTKYAKNSSFIRNF 234

Query: 286 NKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
           N+  LHA  + L HP+  G ++  + LP  +    
Sbjct: 235 NRQALHAYTLGLYHPKSKGYMEFVSDLPQDIKTLI 269


>gi|71894605|ref|YP_278713.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           synoviae 53]
 gi|71851393|gb|AAZ44002.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           synoviae 53]
          Length = 303

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 67/308 (21%), Positives = 134/308 (43%), Gaps = 39/308 (12%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPVINALNHII 78
           R+D++  ++   ++  ++Q++++S  V V+     K +  +   Q ++I  +++    I 
Sbjct: 11  RIDKYIASN-SSLSRADIQELIKSKAVFVNNGLVCKPSYIVHPPQEIKIIRLLDKTPKI- 68

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSW 136
                          +  +K  ++YED  + + +KP+G+ V        +   +G L  +
Sbjct: 69  --------------EAQNIKLDIIYEDDHLVIIDKPSGLIVHPSPTHYENTLANGLLYHF 114

Query: 137 VDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            ++        +P + HR+D++TSG+L+V +T A    L E F+   I++ Y ++     
Sbjct: 115 KNNLSDTNGLLRPGIVHRIDKDTSGLLIVTKTNAVHIKLAEMFKNHSIKRSYIAICDNFL 174

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPH 248
            +KK  I   +              K     A  AI++ ++I  F    Q    ++    
Sbjct: 175 TDKKLRINLPIGLDPKNPQKR----KVTNIKAKEAITNVELIKTFYHEKQPKSLVKCNLE 230

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  H+  PI GD+ Y              +L  HA  ++  HP   + +  
Sbjct: 231 TGRTHQIRVHLAHINNPIYGDNVYNKKIDD-----FNQRL--HAYKLEFFHPMLEKQMTF 283

Query: 308 TAPLPAHM 315
            + +P+  
Sbjct: 284 YSKVPSEF 291


>gi|254966988|gb|ACT97528.1| ribosomal large subunit pseudouridine synthase D [uncultured
           organism]
          Length = 274

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 110/256 (42%), Gaps = 22/256 (8%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-------VD 138
                +   + +   ++YED ++ V NK AG+ V  G+G  +       +W        D
Sbjct: 5   PRHETSIKPEEIAINVVYEDDQLMVVNKEAGMVVHPGAGNFHGTLIQAVAWHLRDMPEFD 64

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +   +  L HR+D++TSG+LVVA+T  A   L + F  +   + Y +LVWG     +  I
Sbjct: 65  ANDPEVGLVHRIDKDTSGLLVVAKTPTAKTALGKQFFNKTTHRSYHALVWGNIVEDEGRI 124

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +        + V   +      A++H+KV++ F      ++    TGRTHQ+R H
Sbjct: 125 EGNIGRDPK-NRLRMKVFDPDSGIGKTAVTHYKVLERFG-YTTLVQCVLETGRTHQIRAH 182

Query: 259 ALHMGCPIVGDHKYC------ANFKGNFTSPIQN------KLYLHARYMDLPHPEGG-RL 305
             H+G P+  D  Y            ++ + IQN      +  LHA+ +   HP    ++
Sbjct: 183 MKHIGHPLFMDETYGGTEILRGQRSSSYKAFIQNCFKLCPRQALHAKTLGFVHPTTKQQM 242

Query: 306 QITAPLPAHMVKTWDS 321
              +  P    +  + 
Sbjct: 243 DFDSEWPNDFRQLIEK 258


>gi|32472413|ref|NP_865407.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica SH 1]
 gi|32443649|emb|CAD73091.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica SH 1]
          Length = 321

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 73/333 (21%), Positives = 131/333 (39%), Gaps = 31/333 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIP 68
             V+   E  R+D          +    + ++  G V ++    K     ++ G +V + 
Sbjct: 8   TTVDETNEG-RVD-IIVRELSETSRSQARGMIDHGCVMINGSPCKSVGTTVKPGDLVAVR 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAY 127
              +      K Q             D     +++ED  I V NK AG ++V    G   
Sbjct: 66  YDKHQRYREKKRQ------------WDDRTFEIVFEDEHIIVVNKSAGTLTVPTDRGEPN 113

Query: 128 HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +  ++     K    + HRLD+ETSG+LV  +    A  L E F+ RR  +++ +
Sbjct: 114 SLVDRVSIYLSYSKSKKEAFVVHRLDRETSGLLVFGKHEPIADLLIEQFKDRRPTRVFHA 173

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-------FAQ 238
           +V G     +    + L      G +      +  K  + AI+H+KV+           +
Sbjct: 174 IVAGNVSEDEGTFESHLA----TGSNLDRYETRPGKDTDQAITHYKVVRRLAERESSHGE 229

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +   +E Q  T + +Q+RV   + G P++GD +Y    +       + ++ LHA  +   
Sbjct: 230 ETTLIEAQLETSKRNQVRVQFANAGHPVLGDPRYKPK-EATHARWHRKRMALHASTLGFF 288

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           HP  G  +    PLP+ M K       + DR  
Sbjct: 289 HPVSGEPVNFDTPLPSAMEKFVAGARGRSDRKA 321


>gi|291086839|ref|ZP_06344600.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium sp. M62/1]
 gi|291077108|gb|EFE14472.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium sp. M62/1]
          Length = 331

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 66/326 (20%), Positives = 134/326 (41%), Gaps = 36/326 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI--LRSGQVR-VDKK-RVKFNNR 58
            M       +   +    ++ +        +   L ++    +G     D +  V     
Sbjct: 17  PMKQTFTYHITRQDAGKSVEHYL--RCRGFSRRLLIRLRKTENGLCLGADGELPVYTTKL 74

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +  G ++ +              ++ D + +           ++YED  + V +KPAG+ 
Sbjct: 75  LAEGDLLTV--------------RLPDDAPSEHIVPVRQNFDIIYEDRDLMVIDKPAGMP 120

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           V    G  Y+      +W  S+  +P   R  +RLD++T+G+L++A+    A  L+E   
Sbjct: 121 VHPSQGNFYNTLANGIAWYFSERGEPFTFRAVNRLDRDTTGLLIIAKHGLCAALLSEMVA 180

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            + +++ Y ++  G   +++  I   + +      +       +E    YA +H++ +  
Sbjct: 181 RKEVRRQYLAIASGK-TDEEGTICAPIARADGSTIER----CVDETRGEYACTHYRRLVY 235

Query: 236 FAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
            ++  C  L +   TGRTHQ+RVH  H+G P++GD  Y  +++      +  +  LH+  
Sbjct: 236 SSENDCSLLLLTLDTGRTHQIRVHMKHIGHPLLGDFLYNPDYR------LFRRQSLHSFL 289

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTW 319
           +   HP  G  L  +APLP       
Sbjct: 290 LSFTHPLTGESLNFSAPLPPDFCSAL 315


>gi|24212923|ref|NP_710404.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
 gi|45656097|ref|YP_000183.1| hypothetical protein LIC10192 [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|24193592|gb|AAN47422.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
 gi|45599330|gb|AAS68820.1| conserved hypothetical protein [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 312

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 76/314 (24%), Positives = 137/314 (43%), Gaps = 38/314 (12%)

Query: 12  VENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVR-VDKKRV-KFNNRIQSGQVVRIP 68
           V  +    RLDR+ K      I+   +QK + +G V+  D K + K + ++++G+   + 
Sbjct: 9   VSEEFSGNRLDRFLKYSLGDEISRATIQKWIEAGYVQGQDGKILDKSSWKVKTGEKYLLS 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
                          +     L      ++  ++ E     + +KP+GI+   G G    
Sbjct: 69  ---------------IPPKPPLNLEPIPMELPVILERENFLIIHKPSGIASHSGPGDRSP 113

Query: 128 -HIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G +  + +        +P + HRLD+ T G++++A+   A   L+E FR R I+K 
Sbjct: 114 SLVNGLIYHFKELSKMGGEARPGIVHRLDKPTEGLILIAKNDRAHGKLSELFRKREIEKK 173

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID----CFAQ 238
           Y++ V G P  +   I   + +   +    + V          +I+H+KV+        +
Sbjct: 174 YYAWVQGHPPEESGTIDLPIARH-PVERLKMTV----SPKGRRSITHYKVLKYINSRSGR 228

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           KF ++E+   TGRTHQ+RVH  +  CP+VGD  Y       F S     L   + ++   
Sbjct: 229 KFSFIEVGLETGRTHQIRVHFQNQRCPVVGDLLYS-RAGSQFESYGLQLL---SYFLKFK 284

Query: 299 HPEGGRLQITAPLP 312
            P     +I A LP
Sbjct: 285 DPFTNE-KIEAILP 297


>gi|255994432|ref|ZP_05427567.1| pseudouridylate synthase [Eubacterium saphenum ATCC 49989]
 gi|255993145|gb|EEU03234.1| pseudouridylate synthase [Eubacterium saphenum ATCC 49989]
          Length = 331

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 73/338 (21%), Positives = 134/338 (39%), Gaps = 35/338 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V+      R D +       I+     K+   G V +D  ++  N+R+ +  ++ I  
Sbjct: 3   IKVDVGNNQRRADVYIAGALK-ISRAKAAKLCDVGSVTLDGIKISKNHRMNANDLLEISD 61

Query: 70  VINALNHIIKEQK---------------ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
              A  H  ++                   D+ +        LK  +LYED  I V +KP
Sbjct: 62  DREAGLHQSEQDSTGVHISSDDVEVIKVPEDNDLYNANEEGILKIGILYEDDYIIVVDKP 121

Query: 115 AGISVQ--GGSGIAYHIDGFLKSWVDSK------GQKPRLTHRLDQETSGILVVARTRAA 166
           AG+     G       +   +  + +          +P + HRLD+ T G++V+A+T  A
Sbjct: 122 AGLLTHAKGDKSCECTLSDKILEYTEGSLANGSGANRPGVVHRLDRGTCGVMVMAKTDTA 181

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
            +HLTE+F  + + K Y ++V+         I   + +          +          A
Sbjct: 182 LKHLTEAFEKQEVSKEYEAIVYDNIVRDSGVITAKIERN-----KKNRLKMSAGDEGREA 236

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
            + FKVI+ F  KF ++ +   +GRTHQ+RVH  ++  P++GD  Y              
Sbjct: 237 HTEFKVIERFG-KFTYVSLVIKSGRTHQIRVHMNYIHHPVLGDMLYGKRKDKFNLMWPML 295

Query: 287 KLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +    ++ +   HP    +++ TA +P    +    L 
Sbjct: 296 R----SKKIGFLHPITSEKMEFTAAMPYEFKRILRILR 329


>gi|304385186|ref|ZP_07367532.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici DSM 20284]
 gi|304329380|gb|EFL96600.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici DSM 20284]
          Length = 301

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 69/315 (21%), Positives = 132/315 (41%), Gaps = 33/315 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVI 71
            DE    L  +       I+   L+ I    G++ V+++  + N  + +G  V +  P  
Sbjct: 8   QDESPQHLRTFLTR--KRISRALLKSIKFNGGKILVNEQPKRTNEMVTAGDQVTVELPPE 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHID 130
               H+++ ++ +D               ++YED    V NKP  +  VQ        + 
Sbjct: 66  PGNPHVVRSRQPID---------------VIYEDQDYLVVNKPPFLPTVQSARNQTDTLV 110

Query: 131 GFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             +K++    D + Q   +  RLDQ+TSG+++ A+ R A   + +  R  R+QK Y ++ 
Sbjct: 111 NRVKNYYAERDYESQVVHVVTRLDQDTSGLVLFAKHRFAHTIMDQDLRQHRVQKYYLAMA 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        I   + +       ++     +      + + + V++  A     L++Q 
Sbjct: 171 TGRFAQSHGLIDAPIERDP---ASFIKRRVASAGNGKPSKTEYWVLEQTATD-SLLKVQL 226

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH-PEGGRLQ 306
           HTGRTHQ+RVH   +  P++GD  Y        +     +  LH   +   +   G ++ 
Sbjct: 227 HTGRTHQIRVHFSELHHPLIGDPLY-----NETSFRSLQRQALHCFSLKFENVFRGKKID 281

Query: 307 ITAPLPAHMVKTWDS 321
           + AP+P  M++ W  
Sbjct: 282 VQAPIPNDMLEYWKK 296


>gi|254303145|ref|ZP_04970503.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148323337|gb|EDK88587.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 289

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 82/300 (27%), Positives = 151/300 (50%), Gaps = 20/300 (6%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ + E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G +V I   
Sbjct: 5   IIDEEYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLILGDIVFIFLP 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            N   +   E+K ++ S    +  + LK ++++E+  ++V NK  G  V  GSG    + 
Sbjct: 65  ENFKEN--NEEKFIELS---QERKEKLKEMIVFENDSLFVINKLLGDVVHKGSGHDISLL 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+ LV G 
Sbjct: 120 EEFRSYYSNNNIN--FVNRIDKLTSGLVIGAKNIKTAREVAKEIQSGNIVKKYYILVNGK 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +     I N+L K      + V V    + G   +I++FK I  +  K+  LE +  TG
Sbjct: 178 IEKNDFIIENYLKKDE----EKVIVSDVEKDGYKKSITYFKKIKEY-NKYTLLEAELKTG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLR    H+G  IVGD KY  N K +        L+ +   +DL +     +++  P
Sbjct: 233 RTHQLRAQLNHIGNNIVGDTKYGKNEKEDLMY-----LFSYYLKIDLYNL---EIKLEIP 284


>gi|167771389|ref|ZP_02443442.1| hypothetical protein ANACOL_02755 [Anaerotruncus colihominis DSM
           17241]
 gi|167666029|gb|EDS10159.1| hypothetical protein ANACOL_02755 [Anaerotruncus colihominis DSM
           17241]
          Length = 292

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 69/316 (21%), Positives = 126/316 (39%), Gaps = 41/316 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKI--LRSGQVRVDKKRVKFNNRIQSGQVVRI 67
            V+  + +  +   + +      ++  ++ +     G + ++  R++  +R+ +G  + I
Sbjct: 8   FVIPPEYDGRKAIHFLRGP-AQCSYTLVRSLKTFEDG-ILLNGTRIRTIDRLHTGDCLSI 65

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                                  T     +   +LYEDS + V+NKPA ++     G+  
Sbjct: 66  TIC----------------DAPQTFEPCEIPVEILYEDSDVIVYNKPAAMACHPVRGLRQ 109

Query: 128 HIDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                + +     + +    RL  RLD++TSG +V+A+   AA  LT       ++K Y 
Sbjct: 110 GTLANVFARDCAANGESCACRLVGRLDRDTSGAVVIAKNARAAAVLT-----GHVEKQYI 164

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+P  K   I   + +        + V          A++ ++      + +  + 
Sbjct: 165 ALVTGMPNPKHGVIDAPIGQPDRKNPRRMIVA-----NGKPAVTEYET-QIRCEGYSVVH 218

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
               TGRTHQ+RVH   +GCP++GD  Y    +         +  LH       HP   R
Sbjct: 219 CVLRTGRTHQIRVHMASIGCPLLGDTLYGGETER------IERQALHCMQASFIHPVDKR 272

Query: 305 LQI-TAPLPAHMVKTW 319
           L I  AP+P  M K  
Sbjct: 273 LCIVHAPIPKDMQKLI 288


>gi|291320661|ref|YP_003515926.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           agalactiae]
 gi|290752997|emb|CBH40973.1| Ribosomal large subunit pseudouridine synthaseD [Mycoplasma
           agalactiae]
          Length = 305

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 58/310 (18%), Positives = 133/310 (42%), Gaps = 41/310 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR--VKFNNRIQSGQVVRIPPVINALNH 76
            R+D++  ++   I   + + ++    V VD K+   K N  ++ G V+ +  ++   ++
Sbjct: 10  ERIDKYISDN-SEITRNDAKALIEQEAVYVDDKKFVRKPNYMVREGMVITVLRLLEKESN 68

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLK 134
           I                +  +   + YED  + + NKP+G+ V    G       +  + 
Sbjct: 69  I---------------EAVDMPLDIRYEDEYLLILNKPSGLVVHPAPGHLNDTLVNALMY 113

Query: 135 SWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            + ++        +  + HR+D++TSG+L++A+       L +  +  +I++ Y ++  G
Sbjct: 114 HFKNNLSDTNGLLRLGIVHRIDKDTSGLLIIAKDNETHNELAKMLKNHQIKRTYLAICEG 173

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQ 246
           I  NK   I   + + +      + +     K    ++++  ++  F    + +  ++ +
Sbjct: 174 ILPNKVTKINLPIQRDTK-NRKLMSI----HKDGKSSVTYVHMLKSFYIDNKPYSLVKCE 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  ++  P+ GD  Y  +           +L  HA  +   HP   + +
Sbjct: 229 LETGRTHQIRVHLTYIKHPVYGDSIYGKSV-----DEFNQRL--HAYKLSFIHPVTNKLI 281

Query: 306 QITAPLPAHM 315
           ++ + +P   
Sbjct: 282 EVYSDIPKEF 291


>gi|282600817|ref|ZP_06257758.1| ribosomal large subunit pseudouridine synthase [Subdoligranulum
           variabile DSM 15176]
 gi|282571024|gb|EFB76559.1| ribosomal large subunit pseudouridine synthase [Subdoligranulum
           variabile DSM 15176]
          Length = 302

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 81/283 (28%), Positives = 139/283 (49%), Gaps = 26/283 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD++    YP +    L K LR  +++++ K+   + R+Q+G V+R+          
Sbjct: 11  PVRLDKYLMEQYPSLGLGRLNKALRENKIKLNGKKQPLSTRVQNGDVIRL---------F 61

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGFLKS 135
           +K++++ D  +          ++ +YED  I V NKPAGI V G     +   +   L +
Sbjct: 62  LKDEQLEDRPLP--------SAVFVYEDEDILVVNKPAGIEVDGPAADTLLKRVQTTLAA 113

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               K     L HRLD  TSG++++A+ +A    LT++ + R I+K Y  + +G P+   
Sbjct: 114 --AGKAGHAVLCHRLDTGTSGLVLLAKNQATELFLTQAIKARTIEKRYLCVTFGRPQPPA 171

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             + ++LLK +  G   V ++     GA   I+ ++ +   + +   LE++  TGRTHQ+
Sbjct: 172 ALMHDYLLKDAERG--VVKIITSPASGAKEVITGYETL-AVSGRLALLEVELVTGRTHQI 228

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           R H  H+GCPI+GD KY  N              L A  +  P
Sbjct: 229 RAHLAHIGCPILGDSKYGNNAANRELHF--KYQALCAWELRFP 269


>gi|164687176|ref|ZP_02211204.1| hypothetical protein CLOBAR_00817 [Clostridium bartlettii DSM
           16795]
 gi|164603600|gb|EDQ97065.1| hypothetical protein CLOBAR_00817 [Clostridium bartlettii DSM
           16795]
          Length = 326

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 70/313 (22%), Positives = 132/313 (42%), Gaps = 32/313 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           N+++++ L     +   + +     K+ R   V V+K   K + +++ G ++ +    + 
Sbjct: 41  NEDDDLTLREVLLDRL-NFSVRYASKLKRFKTVTVNKNFKKLDKKVKKGDLIEVEIKEDM 99

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGF 132
            N                  S  L   ++Y+D  + + +KP  + V    S     +   
Sbjct: 100 AN----------------FTSQDLNLNIIYDDFDLIMVDKPPFMVVHPTKSHFENTMANG 143

Query: 133 LKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           +  ++  KG+  K R  +RLD  TSG+++VA+   A   L+   +    +K Y ++V GI
Sbjct: 144 VTDYIIKKGEDVKIRFVNRLDMNTSGLVIVAKNPFAQHVLSSEMKDDDFEKKYITVVKGI 203

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +  +  I   + + +      V      ++    +I+H+KVI+        +E++  TG
Sbjct: 204 IEEDEGTINQPIYRPTDDSVKRVV-----DERGQESITHYKVIERLND-ATIVEVKLETG 257

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH  H+G PI+GD  Y           +  +  LHA  +    P     L+  A
Sbjct: 258 RTHQIRVHMEHIGHPIIGDELYG-----FVDENLIKRQALHAYSLKFRQPRTKELLEFKA 312

Query: 310 PLPAHMVKTWDSL 322
            +P  M      L
Sbjct: 313 DIPEDMKILIQKL 325


>gi|290979858|ref|XP_002672650.1| predicted protein [Naegleria gruberi]
 gi|284086228|gb|EFC39906.1| predicted protein [Naegleria gruberi]
          Length = 624

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 99/355 (27%), Positives = 159/355 (44%), Gaps = 54/355 (15%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQ 60
           SL      + V  + ++MRLD++       INF  +QKI R  Q+  +   VK N  R+ 
Sbjct: 271 SLKKKYVTLTVSQEHDDMRLDKFLTKTLA-INFGLIQKITRKKQLFKNGIAVKENNERVF 329

Query: 61  SGQVVRIPPV-----------------INALNHIIKEQKILDSSVNLT------------ 91
            G +++IP                       N   +E   +D    +             
Sbjct: 330 KGDIIKIPKDFIDSEKRQEIDEHITGKREQFNKAQRETDKIDRDDEMDTISSETLGNPIY 389

Query: 92  -------------KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-- 136
                        +  + ++S +L+++ +I   NKP GI VQGGS   +HID  L +   
Sbjct: 390 SKNGGKMKLELTQEQIEEIRSWILFKNDEIIALNKPYGICVQGGSNQTFHIDALLDALTG 449

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI--QKIYWSLVWGIPKNK 194
           +D    +P+L HRLD++T+G+L+VAR RA A  + +  +   +  +K YW++  G+P   
Sbjct: 450 LDGFNVRPKLVHRLDRDTTGVLIVARNRAGAIRMQQWLQESTVPLKKCYWAVTVGVPTPT 509

Query: 195 KECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
              I   + ++K   G + V  V      +  ++S +K ID    K  W+ + P TGR H
Sbjct: 510 TGRIKMVIDIQKDANGVEKVVPVDNKTDSSKISVSEYKTIDHMTDKLAWVALYPVTGRKH 569

Query: 254 QLRVHAL-HMGCPIVGDHKYCANFKGNFT----SPIQNKLYLHARYMDLPHPEGG 303
           QLRVH    +G PI+GD+KY      + T         +L+LH R M LP+    
Sbjct: 570 QLRVHCASALGAPILGDYKYGEGVPESLTHVVPDKSLKRLHLHHRAMKLPYLNSK 624


>gi|295091133|emb|CBK77240.1| pseudouridine synthase, RluA family [Clostridium cf.
           saccharolyticum K10]
          Length = 314

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 66/325 (20%), Positives = 134/325 (41%), Gaps = 36/325 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI--LRSGQVR-VDKK-RVKFNNRI 59
           M       +   +    ++ +        +   L ++    +G     D +  V     +
Sbjct: 1   MKQTFTYHITRQDAGKSVEHYL--RCRGFSRRLLIRLRKTENGLCLGADGELPVYTTKLL 58

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G ++ +              ++ D + +           ++YED  + V +KPAG+ V
Sbjct: 59  TEGDLLTV--------------RLPDDAPSEHIVPARQNFDIIYEDRDLMVIDKPAGMPV 104

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               G  Y+      +W  S+  +P   R  +RLD++T+G+L++A+    A  L+E    
Sbjct: 105 HPSQGNFYNTLANGIAWYFSERGEPFTFRAVNRLDRDTTGLLLIAKHGLCAALLSEMVAR 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + +++ Y ++  G   +++  I   + +      +       +E    YA +H++ +   
Sbjct: 165 KEVRRQYLAIASGK-TDEEGTICAPIARADGSTIER----CVDETRGEYACTHYRRLVYS 219

Query: 237 AQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           ++  C  L +   TGRTHQ+RVH  H+G P++GD  Y  +++      +  +  LH+  +
Sbjct: 220 SENDCSLLLLTLDTGRTHQIRVHMKHIGHPLLGDFLYNPDYR------LFRRQSLHSFLL 273

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTW 319
              HP  G  L  +APLP       
Sbjct: 274 SFTHPLTGESLNFSAPLPPDFCSAL 298


>gi|323692319|ref|ZP_08106558.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
 gi|323503644|gb|EGB19467.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
          Length = 298

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 67/310 (21%), Positives = 137/310 (44%), Gaps = 33/310 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ ++    ++ + +      +   L  + ++   + V  +       ++ G ++ +   
Sbjct: 9   IKENDCGKTIESYLRER--GYSRKILVHLRQTNLGITVAGELAYTTRVLKEGNILSV--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHI 129
              L+     ++I+   + L+         +LYED  + V NK AG+ V    G     +
Sbjct: 64  --RLSEETSSERIIPVPMELS---------VLYEDEDLMVINKAAGMPVHPSQGNFDNTL 112

Query: 130 DGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L  +   KG+    R  +RLD++T+G+L++A+   +   L+     + I++ Y ++V
Sbjct: 113 ANGLAWYFKEKGEAFVFRAVNRLDRDTTGLLLIAKNMLSGAILSSMVSEKTIRREYRAIV 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQ 246
            G+   ++ CI   + +     G  +      E+G  YA + ++ +     K C  L + 
Sbjct: 173 SGL-TEEEGCICRPIARAE---GSTIERCVDPERG-EYASTRYRRLGYDRDKDCSLLLIT 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  ++G P++GD  Y  +++         +  LH+  +   HP  G  +
Sbjct: 228 LDTGRTHQIRVHMKYIGHPLLGDFLYNPDYR------FIKRQSLHSCRLTFTHPLTGEAM 281

Query: 306 QITAPLPAHM 315
             TAPLP   
Sbjct: 282 DFTAPLPEDF 291


>gi|78100963|pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli
           Pseudouridine Synthase Rluc
 gi|78100964|pdb|1XPI|B Chain B, Crystal Structure Of The Catalytic Domain Of E. Coli
           Pseudouridine Synthase Rluc
          Length = 231

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 123/231 (53%), Gaps = 9/231 (3%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L  ++LYED  I V NKP+G +V GGSG+++ +   L++ +  + +   L HRLD++TSG
Sbjct: 3   LADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSG 61

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+VA+ R+A + L E  R + +QK Y +LV G  ++  + +   LLK     G+ +  V
Sbjct: 62  VLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRV 121

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-- 274
            Q       + + FKV + +A     +   P TGRTHQ+RVH  + G PI  D +Y    
Sbjct: 122 SQE---GKPSETRFKVEERYA-FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDRE 177

Query: 275 -NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            + +        N+L+LHA  +   HP  G  ++I AP+   + +    L 
Sbjct: 178 FDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKLR 228


>gi|260494008|ref|ZP_05814139.1| pseudouridylate synthase [Fusobacterium sp. 3_1_33]
 gi|260198154|gb|EEW95670.1| pseudouridylate synthase [Fusobacterium sp. 3_1_33]
          Length = 304

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 84/306 (27%), Positives = 150/306 (49%), Gaps = 22/306 (7%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ D E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G ++ I   
Sbjct: 5   IIDEDYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDIIFIF-- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
              L  I KE+             + LK ++++E+  ++V NKP G  V  GSG    + 
Sbjct: 63  ---LPEIFKEKNEEKFIEISQIRKEKLKQMIVFENDNLFVINKPLGDVVHKGSGHDISLL 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+ LV G 
Sbjct: 120 EEFRSYYSNNNIN--FVNRIDKLTSGLVIGAKNIKTAREVAKEIQAGNIVKKYYILVNGK 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +     + N+L K      + V V    ++G   +I++FK I  +  K+  LE +  TG
Sbjct: 178 IEKDNFILENYLKKDE----ERVIVSDIEKEGYKKSITYFKKIKEY-DKYTLLEAELKTG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLR    H+G  IVGD KY  N K +        L+ +   +DL +     L+I   
Sbjct: 233 RTHQLRAQLNHLGNNIVGDIKYGKNEKEDIMY-----LFSYYLKIDLYN-----LEIKLE 282

Query: 311 LPAHMV 316
           +P    
Sbjct: 283 IPDLFK 288


>gi|213023738|ref|ZP_03338185.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 282

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 74/297 (24%), Positives = 132/297 (44%), Gaps = 41/297 (13%)

Query: 47  RVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
            V+ +   K   ++  G+ V I   I+                 +   +  +   ++YED
Sbjct: 2   LVNGQLCDKPKEKVLGGERVAIDAEIDE---------------EIRFEAQDIPLDIVYED 46

Query: 106 SKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVAR 162
             I V NKP  + V  G+G     +   L  +       PR  + HRLD++T+G++VVA+
Sbjct: 47  DDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAK 106

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK---ECIANWLLKKSHIGGDYVHVVKQN 219
           T  A   L ES ++R I + Y ++  G         E I+    K++H+    +      
Sbjct: 107 TVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPISRHPTKRTHMSVHPM------ 160

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  Y    +  
Sbjct: 161 ---GKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPP 216

Query: 280 FTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
             +  +        ++  LHA  + L HP  G  ++  AP+P  MV   D++   ++
Sbjct: 217 KGASEEFISTLRKFDRQALHATMLRLYHPVSGIEMEWHAPIPQDMVDLIDAMRADFE 273


>gi|220919409|ref|YP_002494713.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219957263|gb|ACL67647.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 323

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 73/328 (22%), Positives = 125/328 (38%), Gaps = 39/328 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             VE +    RLDR+ +     ++   +Q+++       D +R+K + R+  G       
Sbjct: 14  FTVEPNYAGWRLDRYLQEKIRRLSRERVQRLIEHRLETEDGRRLKPSTRVAPG------- 66

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L+  + +    +               ++++D  + V +KPAG+ V   +  A + 
Sbjct: 67  ----LSFALLKDAEAEPDTPQAF-------AVVHDDGALLVVDKPAGLPVHPTARYAANT 115

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L        +K    HRLD+ETSG+L         + L   F   R+ K Y +L  G
Sbjct: 116 FTSLAKLRYPD-RKVDPAHRLDRETSGLLACGTAPEVTKVLKRDFAHARVHKTYLALALG 174

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----AQKFCWLEM 245
            P      +   L   +  G   V V          + + F+V+             L  
Sbjct: 175 APAEDAFTVDAPL---ALTGASAVRVRMHVAAAGLPSQTAFEVLARRRAPDGAPVALLAC 231

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------------GNFTSPIQNKLYLHAR 293
           +P TGR HQ+R H  H G P+VGD  Y  + +             +       +  LHA 
Sbjct: 232 RPRTGRQHQIRAHLAHAGLPMVGDKIYGPDEEIFDRFTRRAMTDEDVALLRLPRHALHAW 291

Query: 294 YMDLPHPEG-GRLQITAPLPAHMVKTWD 320
            ++LPHP     +++  PLP  +   W+
Sbjct: 292 RLELPHPLTRAPVRLEVPLPPDLAAFWE 319


>gi|332970065|gb|EGK09063.1| ribosomal large subunit pseudouridine synthase D [Desmospora sp.
           8437]
          Length = 300

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 128/287 (44%), Gaps = 31/287 (10%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +  +  V V+ + V   +R+++G  + +    +A + +                   L  
Sbjct: 38  LKEAEAVEVNGETVYLTSRVKAGDRIAVFLPGDAGDGV---------------KPQSLPL 82

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQETSG 156
            +++ED  + + +K  G+ V      +   +   L ++   +G+    R   RLD++TSG
Sbjct: 83  RVVHEDEDLIILDKQPGVVVHPTRNYSEGTLANGLAAYWQERGEFHLVRPVTRLDKDTSG 142

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V A+   A   L+     +R  + Y ++V G  + ++  +   + + S    +  H+ 
Sbjct: 143 LIVFAKHPHAHAVLSGQMERKRYLREYLAVVHGSLEMEEGRVEEPIARSS----ETPHLR 198

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             + +GA  A + ++V+  + +    + ++  TGRTHQ+RVH  H+G P+ GD  Y    
Sbjct: 199 TVSPEGA-PARTQYRVVRRWPE-ATLVRLRLETGRTHQIRVHMAHLGHPLYGDTLYGGRT 256

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
            G       ++  LHA  + L HP  G +    +PLP  +    +SL
Sbjct: 257 AG------IDRQALHAVRLSLIHPRDGKKRCWESPLPEDIHLLMESL 297


>gi|150010359|ref|YP_001305102.1| RNA pseudouridylate synthase [Parabacteroides distasonis ATCC 8503]
 gi|255012377|ref|ZP_05284503.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_7]
 gi|256839209|ref|ZP_05544719.1| RNA pseudouridylate synthase [Parabacteroides sp. D13]
 gi|149938783|gb|ABR45480.1| RNA pseudouridylate synthase [Parabacteroides distasonis ATCC 8503]
 gi|256740128|gb|EEU53452.1| RNA pseudouridylate synthase [Parabacteroides sp. D13]
          Length = 304

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 61/300 (20%), Positives = 119/300 (39%), Gaps = 35/300 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        +  +++ +L  GQ+ V+ K  + F+  +     V I      +        
Sbjct: 33  FLFELLKEQSRSSVKGLLSRGQISVNGKVTRQFDAPLNPNDTVGINYGRGKV-------- 84

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKG 141
                       +     +++ED  + V NK  G+       I        L  ++    
Sbjct: 85  ----------EFNNPLLRIVWEDDDLIVINKREGLLSVSTDRIKERTAYRILSDYLKECD 134

Query: 142 Q--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              K  + HRLD++TSGI++ A+ +   + L  ++     Q+ Y +++ G P+   + I 
Sbjct: 135 PRNKIFVLHRLDRDTSGIMMFAKNQKVKEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIV 194

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + L++  H     + V    +     AI+ ++++     ++  +E+   TGR +Q+R   
Sbjct: 195 SNLVENKH-----MQVYVTQDGDGKEAITRYRLLQTN-NRYSLVELDLETGRKNQIRAQM 248

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
             +G PI GD KY A            +L LHAR +   HP  G  ++    +P     T
Sbjct: 249 QSIGHPIAGDSKYGAETNPA------GRLMLHARRLCFIHPVTGEEMRFETRIPEKFTST 302


>gi|298507387|gb|ADI86110.1| RNA pseudouridine synthase, RluA family [Geobacter sulfurreducens
           KN400]
          Length = 296

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 129/319 (40%), Gaps = 36/319 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V  D+  +RLD      +P ++   ++ I+  G   V    V+  + R+Q+G  + +  +
Sbjct: 7   VGADQAGVRLDEGAARLFPQLSKTRIRTIIDWGGCAVGGTMVRVASRRLQAGDEIVLGVM 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                  I                      +L+ED+     NK +G++ Q          
Sbjct: 67  EPERYREIT----------------LAPEDILFEDAGYLAVNKASGLNCQRTPYQLKGTV 110

Query: 131 GF---LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L        +  R+ HRLD+ TSG+++   +R AA H++   +  R++K+YW+LV
Sbjct: 111 EYAVTLHFRACGSAEPARVIHRLDRGTSGVMIFPASRRAAAHISRELKEGRVEKVYWALV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+P      +   + K   +G     V          A++ F+V+         +E +P
Sbjct: 171 AGMPLADSWQVDAPVAK---VGTSRYGVAPV----GKAALTEFRVVAR-GNGATLVEARP 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH  H G  I+GD  Y              ++ LH R M     +G  +  
Sbjct: 223 RTGRTHQIRVHLAHGGLSIIGDTTYGG--------IAAPRMMLHCRTMTFRAEDGRPVSA 274

Query: 308 TAPLPAHMVKTWDSLGFKY 326
           TAP         +  G ++
Sbjct: 275 TAPPDREFTAACEQHGIQF 293


>gi|188589626|ref|YP_001921981.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str.
           Alaska E43]
 gi|251780373|ref|ZP_04823293.1| pseudouridine synthase, RluA family [Clostridium botulinum E1 str.
           'BoNT E Beluga']
 gi|188499907|gb|ACD53043.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str.
           Alaska E43]
 gi|243084688|gb|EES50578.1| pseudouridine synthase, RluA family [Clostridium botulinum E1 str.
           'BoNT E Beluga']
          Length = 322

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 72/308 (23%), Positives = 132/308 (42%), Gaps = 32/308 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ +     +    + K LR   +RV+ K+      ++ G +V I  
Sbjct: 3   IEIGANEAGQRLDKFLRKLLKDVPLSAIFKALRKKDIRVNGKKQSEKYFLEEGDIVEIKY 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYH 128
           +    ++  K++K +  + +  K +        YED  + V  K  GI V          
Sbjct: 63  IK---SNPEKKEKFIQVNFSGMKTA--------YEDENLLVVEKWPGILVHPDKDEKDPT 111

Query: 129 IDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSG+++  +T    + + E+ R  R+
Sbjct: 112 LTDYVLSYLKEKGSYVPENEITFTPAPCNRLDRNTSGLVMFGKTFEGLKSINETIREDRV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +K Y +LV G  ++       ++LK   ++I   Y   V  ++K A    +         
Sbjct: 172 RKYYVALVKGKVQD--GLHTGYILKNQDTNISKVYEKEVPDSKKIAMEVTT-----TQTN 224

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYM 295
             +  LE+   TGR+HQ+R H  H+G PI+GD KY      +F          YL+A  +
Sbjct: 225 GAYSLLEINLITGRSHQIRAHLAHLGSPIIGDDKYGDRKLNSFFKNKYGLEYQYLYAYKL 284

Query: 296 DLPHPEGG 303
                +G 
Sbjct: 285 VFKEMKGK 292


>gi|158426220|ref|YP_001527512.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
 gi|158333109|dbj|BAF90594.1| pseudouridine synthase [Azorhizobium caulinodans ORS 571]
          Length = 319

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 76/236 (32%), Positives = 112/236 (47%), Gaps = 6/236 (2%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
                 L + LL+ D  + V +KPAG+ V  G      +   L        + P L HRL
Sbjct: 76  EPPVSPLAARLLHRDGMVLVLDKPAGLPVHPGPKGGETLHDHLNGLRFGLPRAPELAHRL 135

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG LV+ R   A   L   F   +  K Y ++  G P  +   I   L K+S   G
Sbjct: 136 DKDTSGCLVLGRHGKALALLNRLFAEGQADKTYVAVTRGAPAEETGRIDQPLAKRSPHRG 195

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            ++  V +   G   A++ ++V+    +    + + P TGRTHQLR H  H+G PI+GD 
Sbjct: 196 WWMQAVPKGTPGGLEAVTDWRVLAR-TEGLAVMALSPVTGRTHQLRAHLSHIGFPILGDS 254

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            Y     G    P    L+LH+R + LP  + G  +   APLP HMV+T  +LG +
Sbjct: 255 IYG----GASRLPGGPMLHLHSRRIVLPVAKNGPAIDARAPLPPHMVETLTALGLE 306


>gi|83312904|ref|YP_423168.1| putative pseudouridine synthase in lpd 3'region [Magnetospirillum
           magneticum AMB-1]
 gi|82947745|dbj|BAE52609.1| Hypothetical pseudouridine synthase in lpd 3'region
           [Magnetospirillum magneticum AMB-1]
          Length = 229

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 76/234 (32%), Positives = 125/234 (53%), Gaps = 12/234 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            D + S +LY+D  + V +KPAG++V  G     H++ +L +      + P+L HRLD++
Sbjct: 3   PDEILSRVLYKDQDVIVLDKPAGLAVHAGPNSPDHLELYLGALAFGWAEMPKLAHRLDRD 62

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG L++ R   A + L + F  RR++K+YWS+  G P      +   LLK S  G  + 
Sbjct: 63  TSGCLILGRHAKAIKRLGKMFEHRRVEKVYWSVSHGSPAADSGTVDAPLLKVSARGQGWR 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             V   +     +I+ + V+   +    W+E +P TGRTHQ+R+HA ++GCP++GD  Y 
Sbjct: 123 IKV---DPAGQPSITDWSVLGR-SDGLSWIEWRPRTGRTHQIRIHAQYLGCPLLGDAYYG 178

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLP--HPEGGRLQITAPLPAHMVKTWDSLGFK 325
            + +         +L+L AR +  P   P    +++TAP P HMV+     G+ 
Sbjct: 179 PDPEPKV------RLHLLARAVAFPALAPSKDPVRVTAPPPEHMVEALRRCGWS 226


>gi|39998442|ref|NP_954393.1| RNA pseudouridine synthase family protein [Geobacter sulfurreducens
           PCA]
 gi|39985389|gb|AAR36743.1| RNA pseudouridine synthase family protein [Geobacter sulfurreducens
           PCA]
          Length = 296

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 128/319 (40%), Gaps = 36/319 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V  D+  +RLD      +P ++   ++ I+  G   V    V+  + R+Q+G  + +  +
Sbjct: 7   VGADQAGVRLDEGAARLFPQLSKTRIRTIIDWGGCAVGGTMVRVASRRLQAGDEIVLGVM 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                  I                      +L+ED      NK +G++ Q          
Sbjct: 67  EPERYREIT----------------LAPEDILFEDGGYLAVNKASGLNCQRTPYQLKGTV 110

Query: 131 GF---LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L        +  R+ HRLD+ TSG+++   +R AA H++   +  R++K+YW+LV
Sbjct: 111 EYAVTLHFRACGSAEPARVIHRLDRGTSGVMIFPASRRAAAHISRELKEGRVEKVYWALV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+P      +   + K   +G     V          A++ F+V+         +E +P
Sbjct: 171 AGMPLADSWQVDAPVAK---VGTSRYGVAPV----GKAALTEFRVVAR-GNGATLVEARP 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH  H G  I+GD  Y              ++ LH R M     +G  +  
Sbjct: 223 RTGRTHQIRVHLAHGGLSIIGDTTYGG--------IAAPRMMLHCRTMTFRAEDGRPVSA 274

Query: 308 TAPLPAHMVKTWDSLGFKY 326
           TAP         +  G ++
Sbjct: 275 TAPPDREFTAACEQHGIQF 293


>gi|261331103|emb|CBH14092.1| pseudouridylate synthase, putative [Trypanosoma brucei gambiense
           DAL972]
          Length = 406

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 87/349 (24%), Positives = 155/349 (44%), Gaps = 22/349 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV---RVDKKR--VKFNNRIQ 60
            +QY VV  +    R+D +   HYP  ++  ++++++ G +   R + K+   +  +R++
Sbjct: 55  DLQYHVVTQEWFGERVDSFLTCHYPQWDYETIKRLVQQGHIYRYRKNGKKKFTRLTDRLE 114

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKH-----SDFLKSILLYEDSKIYVFNKPA 115
             +++ +P        +     +L+ +            +   +++L+++  + V NKP 
Sbjct: 115 FDELLVVPTRAFWEKQLAPPSGVLEETDGPKFKLSATAREMAHNMVLFKNEHVIVINKPH 174

Query: 116 GISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G+ +          I   L +W  +   KP + H LD+ETSG +V+ARTR A + L   F
Sbjct: 175 GLPMMPTDDPQEMSIAAMLPAWKFTNVAKPVVCHNLDRETSGCVVLARTRNAHRMLGRMF 234

Query: 175 RMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             R +   +YWS   G P      +           GD +       K +  AI+ F V 
Sbjct: 235 VKRVVPNSVYWSFCVGKPTVNYGRVRMHFDITRGNKGDIIVARPSPTKTSKVAIAEFVVN 294

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK-----GNFTSPIQN- 286
               +   ++   P T R HQ R+ A H + CP++GD KY  +         F  P    
Sbjct: 295 ASALEFGSFISFYPLTTRRHQERIMAAHALRCPVLGDAKYGGDAAFPSSLSLFWDPENKG 354

Query: 287 -KLYLHARYMDLPHPE--GGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
             L+LH R + LP+    G  + +TAPLP  M KT+  LG+  + +  +
Sbjct: 355 LPLHLHHRKIQLPYKNTAGEFICVTAPLPTQMEKTFKKLGWPCEVDDPL 403


>gi|258646966|ref|ZP_05734435.1| ribosomal large subunit pseudouridine synthase C [Dialister invisus
           DSM 15470]
 gi|260404405|gb|EEW97952.1| ribosomal large subunit pseudouridine synthase C [Dialister invisus
           DSM 15470]
          Length = 305

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 74/301 (24%), Positives = 138/301 (45%), Gaps = 29/301 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +E      RLDR+      H     + K +R+ +++V+ K+     R+  G  V 
Sbjct: 1   MKEFRIEGRHAGKRLDRF-MEEIEHWPHGMVVKAVRTKKLKVNGKKEDGTYRLCEGDRV- 58

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-I 125
                  +++++ ++K  D +             ++YED  I + +K AG+     +G  
Sbjct: 59  -------VSYVLPKEKRRDFT-------------IVYEDEHILIADKKAGLLCMDSTGKT 98

Query: 126 AYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              + G +  ++  KG+    + HR+D  TSG++V+A+   +   L    + R ++K+Y 
Sbjct: 99  TRTLIGEVNEYLADKGEPSAYMVHRIDFNTSGLMVIAKDEESKGILDRMIKERELEKVYL 158

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +V G+PK K+  + ++L K S  G   V +    +KGA  A++ + ++    Q    LE
Sbjct: 159 CIVSGVPKKKEGHLIHYLFKDSKQG--KVFLSDVPQKGAKSAVTDYHIVKT-GQNLSLLE 215

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
               TGRTHQ+R    ++G P++GD KY +  K       +    LHA  +       G 
Sbjct: 216 CTLLTGRTHQIRSQMAYIGHPLIGDDKYGS--KEVNRRYGEKGQLLHAWKITFHLKGSGH 273

Query: 305 L 305
           L
Sbjct: 274 L 274


>gi|320457791|dbj|BAJ68412.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 317

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 65/299 (21%), Positives = 118/299 (39%), Gaps = 29/299 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V   +     R D         I+      ++ SGQ RV  + V  ++ +Q+G+ V    
Sbjct: 2   VPAPDALVGKRFDVAVAKML-GISRSKAADLVDSGQARVLGREVARSSTLQAGETVEFD- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                   + E++     +            ++YED  + V +KP G++     G     
Sbjct: 60  --------LAEEQAGPEPIAT-------DMAVVYEDDDVIVVDKPVGVAAHASVGWTGPT 104

Query: 125 -IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            +    D  +         +  +  RLD  TSG+++V ++  A   +   F    ++K Y
Sbjct: 105 VLGSLRDRGVHIASYGAAGREGIVSRLDVGTSGLMLVCKSDLAYTEMRRQFAEHEVKKTY 164

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G  K  K  I   + +                     A++H+ V++ F  +   +
Sbjct: 165 HALVQGGLKENKATIEAPIGR-----AKVSDFRFCVTPAGKPAVTHWDVLERFGHEATLV 219

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            +   TGRTHQ+RVH   +G P+ GD  Y AN   +    + ++ +LHA  ++  HP  
Sbjct: 220 SVNLETGRTHQIRVHFSSIGHPLCGDPMYGANPVLSEALGL-DRQWLHAMKLEFRHPRT 277


>gi|150402179|ref|YP_001329473.1| RluA family pseudouridine synthase [Methanococcus maripaludis C7]
 gi|150033209|gb|ABR65322.1| pseudouridine synthase, RluA family [Methanococcus maripaludis C7]
          Length = 298

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 71/327 (21%), Positives = 148/327 (45%), Gaps = 36/327 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     V  +VV++     +L    +N++  ++   ++K  +  ++ V+ K +   ++++
Sbjct: 1   MESQKNVLKLVVDSKIAGHKLIDVLRNNF-ELSNKMIKKFDKEKKIFVNSKNISLKSKLK 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
             + V +                +D  +N T   + L   ++YED  + + +KP  + V 
Sbjct: 60  ENETVSVE---------------IDCGIN-TIDPENLALNIIYEDDDLLIVDKPKNMVVH 103

Query: 121 GGSGIAYHIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               +              ++++  K R  +RLD +T+G+L++A+   + QHL +     
Sbjct: 104 PTKNVLSKTLANAVSNHQKINNQNYKIRFVNRLDMDTTGLLIIAKDPYSHQHLAKQMDEG 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            ++KIY ++V G    K+  I + + L    I  +  +V          + + +KVI+  
Sbjct: 164 ILEKIYIAVVNGHLDLKEGIIEDSIDLNDDGIKRELSNV-------GKISKTKYKVIEEL 216

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    LE+   TGRTHQ+RVH  ++G PI+GD  Y         S + N+  LH+  + 
Sbjct: 217 -KNASILEINLLTGRTHQIRVHLSNIGNPIIGDVLYGE------ISDLINRQALHSHILS 269

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWDSL 322
           + HP    +++ ++ LP  +    ++L
Sbjct: 270 IIHPITKEKMKFSSNLPKDIENLIENL 296


>gi|257462593|ref|ZP_05627003.1| tRNA pseudouridine synthase A [Fusobacterium sp. D12]
 gi|317060244|ref|ZP_07924729.1| ribosomal large subunit pseudouridine synthase C [Fusobacterium sp.
           D12]
 gi|313685920|gb|EFS22755.1| ribosomal large subunit pseudouridine synthase C [Fusobacterium sp.
           D12]
          Length = 290

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 80/315 (25%), Positives = 146/315 (46%), Gaps = 25/315 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   VE     +R+DR+ +  +P ++  ++ K LR+G+++V+ KRVK N R  S   ++
Sbjct: 1   MKEYQVEEKYIGVRVDRYLRKEFPDLSLGDIFKALRTGKIKVNGKRVKENYRFVSEDWIQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          I+EQK  +     ++    L+  + Y+D  I V+ K AG  +  GS   
Sbjct: 61  LYLE-------IEEQKKREFLTLSSEERAELEEGIFYQDQDILVYYKKAGELMHKGSSHD 113

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +    +++     +     +RLD+ETSG+++  +     + L E+ + R I K Y+ +
Sbjct: 114 YGLAEQFQAYFQ--NEDFHFVNRLDKETSGLVLGGKCLKIVRELAEAIKKRTIVKKYYII 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G P      + ++L K    G   V   +  ++      + F+V+    + +  LE  
Sbjct: 172 VEGNPPKNHFSLRSYLKK----GESRVLESQCAKEDYRECSASFQVLKRKKE-YSLLEAN 226

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
             TGRTHQLRV    MG PI+GD KY     G        ++YLH+  + +        +
Sbjct: 227 LETGRTHQLRVQLAGMGFPILGDGKYGKKKAG--------RMYLHSHLLKISAW---EQE 275

Query: 307 ITAPLPAHMVKTWDS 321
               +PA  +  ++ 
Sbjct: 276 WDTGIPAEFLWYFNK 290


>gi|157691654|ref|YP_001486116.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
 gi|157680412|gb|ABV61556.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
          Length = 302

 Score =  197 bits (500), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 139/327 (42%), Gaps = 32/327 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M +  +   + V+    +  L  + K      +   +   +   +VR+++K      ++ 
Sbjct: 1   MIIKGHTLSLKVDEQYHHTSLSHFLKTAVS-ASKPIIHFWMEHQKVRLNQKPAHHAAKVS 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + I       + +  E   L+               +L+ED  + +  KPAG    
Sbjct: 60  QGDQIIIDLFETEESDVTPEYGELE---------------VLFEDEHLLIVQKPAGRPTH 104

Query: 121 GG-SGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               G    +   +     + G+  + R  HRLDQ+TSG ++ A+ R A   L +    +
Sbjct: 105 PNEQGQTGTLANLVAFHFQANGEEKRVRHIHRLDQDTSGTVIFAKHRLAHAALDQMLSKK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I++ Y ++  G+ K KK  I   + +  H       V ++       A++HF+V+D   
Sbjct: 165 TIKRTYIAIAEGLFKKKKGTIDAAIGRDKHHA-----VRRRISPTGQKAVTHFQVMDVNK 219

Query: 238 Q-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           + +   +++Q  TGRTHQ+RVH   +G P+ GD  Y      +      N+  LHA+ +D
Sbjct: 220 RLQLTAVKLQLETGRTHQIRVHLSSLGHPLAGDTLY------DGVREYINRCALHAKQVD 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + HP  G  L I APLP  M +    +
Sbjct: 274 MKHPFTGEHLIIEAPLPPDMDQLMSQI 300


>gi|300854916|ref|YP_003779900.1| putative ribosomal large subunit pseudouridine synthase D
           [Clostridium ljungdahlii DSM 13528]
 gi|300435031|gb|ADK14798.1| predicted ribosomal large subunit pseudouridine synthase D
           [Clostridium ljungdahlii DSM 13528]
          Length = 319

 Score =  197 bits (500), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 66/300 (22%), Positives = 119/300 (39%), Gaps = 29/300 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ +     +    + + +R G ++V+ K+ K    +  G +V    
Sbjct: 3   LEIGKNEAGQRLDKFSRKWLRDVPLSGIYRAIRKGDIKVNGKKAKEKYFLLEGDIVN--- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                     E      + +  +  D     ++YED  + +  K  G+ V        A 
Sbjct: 60  ---------AEYITSKETKSKFERIDNAFLKIIYEDKNMLLVEKWPGVLVHSDKNSKDAT 110

Query: 128 HIDGFLKSWVDSKGQKPR--------LTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             D  L    D     P           +RLD+ TSGI++  +   + + L E  R R I
Sbjct: 111 LTDYVLSHLYDRGEFNPEEEVTFTPSPCNRLDRNTSGIVIYGKNYESLKLLNEMIRERSI 170

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G  K+       ++ K          V    EK +       K ++     
Sbjct: 171 KKYYIALVIGKIKD--GVYEGYIKKDRTNNKS--SVSNTPEKDSKKISMRVKNVNTCG-I 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           +  ++++  TGR+HQLR H  ++G  IVGD KY  +   +F       +  YL+A  ++ 
Sbjct: 226 YSLIQLELITGRSHQLRAHLAYLGNAIVGDSKYGVSNINSFFYNKYGLDYQYLYAYKLNF 285


>gi|118579004|ref|YP_900254.1| RluA family pseudouridine synthase [Pelobacter propionicus DSM
           2379]
 gi|118501714|gb|ABK98196.1| pseudouridine synthase, RluA family [Pelobacter propionicus DSM
           2379]
          Length = 306

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 71/320 (22%), Positives = 130/320 (40%), Gaps = 42/320 (13%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPP 69
            + ++    RLD         ++    ++I+  G   ++   V+  +R ++SG  + +  
Sbjct: 6   TINDEVSGRRLDEALSLLCDQVSKSEARRIIDRGGCNLNGSMVRVASRMVRSGDTIDVGV 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +       +                   +  LL+ED  +   NKPAG++ Q      Y +
Sbjct: 66  MEPGRFRDL----------------VLPQEALLHEDDDLIALNKPAGVNTQRTP---YQL 106

Query: 130 DGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            G L+ W           +  R+ HRLD+ TSG+++  + + AA  L++ F   +++K Y
Sbjct: 107 KGTLEYWASEYFRRQGNPEPARVIHRLDRGTSGVMLFPKHKRAAAWLSKRFHDGQVEKRY 166

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G P   +  +   + K +      V        G   A++ F+++   +  +  +
Sbjct: 167 LALVSGTPGQIEWRVDGPIGKIASARYGIVA-------GGRSALTEFRLL-AESCGYALV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E +P TGRTHQ+RVH    G PIVGD  Y              ++ LH   +      G 
Sbjct: 219 EAKPLTGRTHQIRVHLQSCGLPIVGDGTYGGEPAA--------RMMLHCASLRFADGGGR 270

Query: 304 RLQITAPLPAHMVKTWDSLG 323
            + + APL        +  G
Sbjct: 271 EIVVEAPLDRDFRGLMEERG 290


>gi|269956094|ref|YP_003325883.1| pseudouridine synthase, RluA family [Xylanimonas cellulosilytica
           DSM 15894]
 gi|269304775|gb|ACZ30325.1| pseudouridine synthase, RluA family [Xylanimonas cellulosilytica
           DSM 15894]
          Length = 310

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 67/327 (20%), Positives = 134/327 (40%), Gaps = 28/327 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V +     R+D          +     ++  +G V++D + V  ++R+ +G  + 
Sbjct: 3   LRTLPVPDGLAGERVDAALARML-GFSRTQAAELAAAGAVQLDGRAVGKSDRLTAGSWLE 61

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-I 125
           +     A    +  + +    V        +                P G++     G  
Sbjct: 62  VDLPDPAAPVEVTPEPVPGMGVVHEDDDVVVIDK-------------PVGVAAHPSPGWT 108

Query: 126 AYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + G L +           ++  + HRLD  TSG++VVA++ AA   L  +F+ R ++
Sbjct: 109 GPTVVGALAAAGYRVSTSGAAERQGIVHRLDVGTSGLMVVAKSEAAYTGLKRAFKERTVE 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y +L  G P+     I   + +  H   D+   V  +      +++H++V++      
Sbjct: 169 KVYHALAQGHPEPTVGTIDAPIGR--HPSNDWRFAVVAD---GKPSVTHYEVLEMLP-AA 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E+   TGRTHQ+RVH   +  P+VGD  Y A+     T     + +LHA  +   HP
Sbjct: 223 SLVEVHLETGRTHQIRVHFSAVRHPLVGDLTYGADPVL-ATHTGLTRQWLHAVRLGFEHP 281

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKY 326
             G  + + +  P  +    +++   Y
Sbjct: 282 LTGEWVSVESAYPDDLAAALETVRGAY 308


>gi|255555275|ref|XP_002518674.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223542055|gb|EEF43599.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 536

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 107/379 (28%), Positives = 168/379 (44%), Gaps = 86/379 (22%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRV------DK------KRVKFNNRIQSGQVVRIPPV 70
           +W     P +    +QK+ R  QV+       D       KRV   + +  G  + +P  
Sbjct: 163 KWVLRCCPELPRNLVQKLFRLRQVKRELLNVGDGEMEHKTKRVAAKDLMNVGDRIFLPIS 222

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           + AL    ++QK         K ++F++ + LY+D  I V NKP G+ VQGG GI    D
Sbjct: 223 VQAL--PFEKQKC----HCGEKEANFIRGLELYKDEAIIVVNKPPGMPVQGGIGIKSSFD 276

Query: 131 GFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI---------- 179
               S +     + PRL HRLD+++SGILV+ RT+ +   L   FR +            
Sbjct: 277 ELAASCLSYDYSEPPRLVHRLDRDSSGILVMGRTQTSTMVLHSVFREKTFAASNHDIGER 336

Query: 180 ----QKIYWSLVWGIPKNKKECIANWLLKKSHIGG--DYVHVVKQNEKGA-NYAISHFKV 232
               Q+ YW+LV G P+ +K  I+  L K     G  D + VV+  E  +  +A++ ++V
Sbjct: 337 RRILQRKYWALVIGSPRRQKGIISAPLGKVVVDDGKSDRITVVENAESTSFQHAVTQYRV 396

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKY------------------- 272
           ++  +  + WLE+ P TGR HQLRVH    +G PIVGD+KY                   
Sbjct: 397 MES-SHGYAWLELSPITGRKHQLRVHCAEVLGTPIVGDYKYGWQVHRKWKQLPFPNLEKI 455

Query: 273 -------------CANFKGNFTSPIQNKLYLHARYMDLPH----------------PEGG 303
                          + +    S    +L+LH + M LP                  +  
Sbjct: 456 SNENALCKKILPFGIDLESGSISEKHPRLHLHCKQMVLPDVSQALRGVQTSSNYDFSDLK 515

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++ APLP++M ++WD L
Sbjct: 516 SIELDAPLPSYMQRSWDIL 534


>gi|301308438|ref|ZP_07214392.1| RNA pseudouridylate synthase [Bacteroides sp. 20_3]
 gi|300833908|gb|EFK64524.1| RNA pseudouridylate synthase [Bacteroides sp. 20_3]
          Length = 304

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 62/300 (20%), Positives = 119/300 (39%), Gaps = 35/300 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        +  +++ +L  GQ+ V+ K  + F+  +     V I      +        
Sbjct: 33  FLFELLKEQSRSSVKGLLSRGQISVNGKVTRQFDAPLNPNDTVGINYGRGKV-------- 84

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKG 141
                       +     +++ED  + V NK  G+       I        L  +V    
Sbjct: 85  ----------EFNNPLLRIVWEDDDLIVINKREGLLSVSTDRIKERTAYRILSDYVKECD 134

Query: 142 Q--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              K  + HRLD++TSGI++ A+ +   + L  ++     Q+ Y +++ G P+   + I 
Sbjct: 135 PRNKIFVLHRLDRDTSGIMMFAKNQKVKEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIV 194

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + L++  H     + V    +     AI+ ++++     ++  +E+   TGR +Q+R   
Sbjct: 195 SNLVENKH-----MQVYVTQDGDGKEAITRYRLLQTN-NRYSLVELDLETGRKNQIRAQM 248

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
             +G PI GD KY A            +L LHAR +   HP  G  ++    +P     T
Sbjct: 249 QSIGHPIAGDSKYGAETNPA------GRLMLHARRLCFIHPVTGEEMRFETRIPEKFTST 302


>gi|187934776|ref|YP_001887060.1| pseudouridine synthase, RluA family [Clostridium botulinum B str.
           Eklund 17B]
 gi|187722929|gb|ACD24150.1| pseudouridine synthase, RluA family [Clostridium botulinum B str.
           Eklund 17B]
          Length = 322

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 72/308 (23%), Positives = 132/308 (42%), Gaps = 32/308 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  +E   RLD++ +     +    + K LR   +RV+ K+      ++ G +V I  
Sbjct: 3   IEIGANEAGQRLDKFLRKLLKDVPLSAIFKALRKKDIRVNGKKQSEKYFLEEGDIVEIKY 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYH 128
           +    ++  K++K +  + +  K +        YED  + V  K  GI V          
Sbjct: 63  IK---SNPEKKEKFIQVNFSGMKTA--------YEDENLLVVEKWPGILVHPDKDEKDPT 111

Query: 129 IDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSG+++  +T    + + E+ R  R+
Sbjct: 112 LTDYVLSYLKEKGSYVPENEITFTPAPCNRLDRNTSGLVMFGKTFEGLKSINETIREDRV 171

Query: 180 QKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +K Y +LV G  ++       ++LK   ++I   Y   V  ++K A    +         
Sbjct: 172 RKYYVALVKGKVQD--GLHTGYILKNQDTNISKVYEKEVPDSKKIAMEVTT-----TQTN 224

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYM 295
             +  LE+   TGR+HQ+R H  H+G PI+GD KY      +F          YL+A  +
Sbjct: 225 GAYSLLEINLITGRSHQIRAHLSHLGSPIIGDDKYGDRKLNSFFKNKYGLEYQYLYAYKL 284

Query: 296 DLPHPEGG 303
                +G 
Sbjct: 285 VFKEMKGK 292


>gi|238924045|ref|YP_002937561.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale ATCC 33656]
 gi|238875720|gb|ACR75427.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale ATCC 33656]
          Length = 324

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 72/334 (21%), Positives = 134/334 (40%), Gaps = 26/334 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++      +E   RLD++ K   P+ +   + K+LR   ++++ K+      +     ++
Sbjct: 1   MKEFKAGKNEAGQRLDKYLKKILPNASMGFIYKMLRKKNIKLNDKKASGTEIVSVDDKIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I    +        +  L                ++YED  I   NKP  +  Q      
Sbjct: 61  IFLSDDTFAKFSVNEDRLMKDFKALSALKPDGLGVVYEDDDILAANKPVNMLSQKSKETD 120

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
              +  L  ++  +G+         KP + +RLD+ TSG++++ ++    Q+L++  + R
Sbjct: 121 ISANERLIGYLIKEGKLDFDTYKSFKPSVCNRLDRNTSGLILMGKSLHGLQYLSQVLKAR 180

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +K Y +LV G        I  +L K   +    +     +++ +    + ++ +    
Sbjct: 181 TAEKYYMALVAGEVDEPM-TIEGFLTKDEAVNKVQITREPISDE-SLPIKTAYRPLKTID 238

Query: 238 -----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYL 290
                 K   LE+   TGR+HQ+R H   +G PI+GD KY       F     +     L
Sbjct: 239 MSASCHKATLLEVHLITGRSHQIRAHLSSIGHPIIGDIKYGDRRINAFYKENYHVTSQLL 298

Query: 291 HARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           HA ++ LP    GR  I A LP      W  +G 
Sbjct: 299 HAHHVILPD---GRY-IEAALPD----IWSRVGL 324


>gi|71744254|ref|XP_803639.1| pseudouridylate synthase [Trypanosoma brucei TREU927]
 gi|70830922|gb|EAN76427.1| pseudouridylate synthase, putative [Trypanosoma brucei]
          Length = 406

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 87/349 (24%), Positives = 155/349 (44%), Gaps = 22/349 (6%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV---RVDKKR--VKFNNRIQ 60
            +QY VV  +    R+D +   HYP  ++  ++++++ G +   R + K+   +  +R++
Sbjct: 55  DLQYHVVTQEWFGERVDSFLTCHYPQWDYETIKRLVQQGHIYRYRKNGKKKFTRLTDRLE 114

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKH-----SDFLKSILLYEDSKIYVFNKPA 115
             +++ +P        +     +L+ +            +   +++L+++  + V NKP 
Sbjct: 115 FDELLVVPTRAFWEKQLAPPSGVLEETDGPKFKLSATAREMAHNMVLFKNEHVIVINKPH 174

Query: 116 GISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           G+ +          I   L +W  +   KP + H LD+ETSG +V+ARTR A + L   F
Sbjct: 175 GLPMMPTDDPQEMSIAAMLPAWKFTNVAKPVVCHNLDRETSGCVVLARTRNAHRMLGRMF 234

Query: 175 RMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
             R +   +YWS   G P      +           GD +       K +  AI+ F V 
Sbjct: 235 VKRVVPNSVYWSFCVGKPTVNYGRVRMHFDITRGNKGDIIVARPSPTKTSKVAIAEFVVN 294

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK-----GNFTSPIQN- 286
               +   ++   P T R HQ R+ A H + CP++GD KY  +         F  P    
Sbjct: 295 ASALEFGSFISFYPLTTRRHQERIMAAHALRCPVLGDAKYGGDAAFPSSLSLFWDPENKG 354

Query: 287 -KLYLHARYMDLPHPE--GGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
             L+LH R + LP+    G  + +TAPLP  M KT+  LG+  + +  +
Sbjct: 355 LPLHLHHRKIQLPYKNTAGEFICVTAPLPTQMEKTFKKLGWPCEVDDPL 403


>gi|270291471|ref|ZP_06197693.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus
           acidilactici 7_4]
 gi|270280317|gb|EFA26153.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus
           acidilactici 7_4]
          Length = 301

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 68/315 (21%), Positives = 131/315 (41%), Gaps = 33/315 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVI 71
            DE    L  +       I+   L+ I    G++ V+++  + N  + +G  V +  P  
Sbjct: 8   QDESPQHLRTFLTR--KRISRALLKSIKFNGGKILVNEQPKRTNEMVTAGDQVTVELPPE 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHID 130
               H+++ ++ +D               ++YED    V NKP  +  VQ        + 
Sbjct: 66  PGNPHVVRSRQPID---------------VIYEDQDYLVVNKPPFLPTVQSARNQTDTLV 110

Query: 131 GFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             +K++    D + Q   +  RLDQ+TSG+++ A+ R A   + +  R  R+QK Y ++ 
Sbjct: 111 NRVKNYYAERDYESQVVHVVTRLDQDTSGLVLFAKRRFAHTIMDQDLRQHRVQKYYLAMA 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        I   + +       ++     +      + + + V++        L++Q 
Sbjct: 171 TGRFAQSHGLIDAPIERDP---ASFIKRRVASAGNGKPSKTEYWVLE-QTDTDSLLKVQL 226

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH-PEGGRLQ 306
           HTGRTHQ+RVH   +  P++GD  Y        +     +  LH   +   +   G ++ 
Sbjct: 227 HTGRTHQIRVHFSELHHPLIGDPLY-----NETSFRSLQRQALHCFSLKFENVFRGKKID 281

Query: 307 ITAPLPAHMVKTWDS 321
           + AP+P  M++ W  
Sbjct: 282 VQAPIPNDMLEYWKK 296


>gi|298374755|ref|ZP_06984713.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_19]
 gi|298269123|gb|EFI10778.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_19]
          Length = 304

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 61/300 (20%), Positives = 119/300 (39%), Gaps = 35/300 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        +  +++ +L  GQ+ V+ K  + F+  +     V I      +        
Sbjct: 33  FLFELLKEQSRSSVKGLLSRGQISVNGKVTRQFDAPLNPNDTVGINYGRGKV-------- 84

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKG 141
                       +     +++ED  + V NK  G+       I        L  ++    
Sbjct: 85  ----------EFNNPLLRIVWEDDDLIVINKREGLLSVSTDRIKERTAYRILSDYLKECD 134

Query: 142 Q--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              K  + HRLD++TSGI++ A+ +   + L  ++     Q+ Y +++ G P+   + I 
Sbjct: 135 PRNKIFVLHRLDRDTSGIMMFAKNQKVKEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIV 194

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + L++  H     + V    +     AI+ ++++     ++  +E+   TGR +Q+R   
Sbjct: 195 SNLVENKH-----MQVYVTQDGDGKEAITRYRLLQTN-NRYSLVELDLETGRKNQIRAQM 248

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
             +G PI GD KY A            +L LHAR +   HP  G  ++    +P     T
Sbjct: 249 QSIGHPIAGDSKYGAETNPA------GRLMLHARRLCFIHPVTGEEMRFETRIPEKFTST 302


>gi|153954106|ref|YP_001394871.1| RluD2 [Clostridium kluyveri DSM 555]
 gi|219854718|ref|YP_002471840.1| hypothetical protein CKR_1375 [Clostridium kluyveri NBRC 12016]
 gi|146346987|gb|EDK33523.1| RluD2 [Clostridium kluyveri DSM 555]
 gi|219568442|dbj|BAH06426.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 319

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 136/325 (41%), Gaps = 34/325 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V + ++E   RLD++ +     +    + K +R G ++V+ K+ K    +    +V    
Sbjct: 3   VEIGSNESGQRLDKFLRKWLRDVPISGIYKAIRKGDIKVNGKKTKEKYFLMDKDIVE--- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
                 +II + K  + +     +S+FLK  + YED  + +  K  G+ V          
Sbjct: 60  ----AQYIISKGKSFEFN---KVNSNFLK--ITYEDENMILVEKWPGVLVHSDKKTDDVT 110

Query: 129 IDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +  ++ S++  KG           P   +RLD+ TSGI++  +   + + L E  R R I
Sbjct: 111 LTDYVLSYLYDKGDFKPETEVTFTPSPCNRLDRNTSGIVIYGKNYESLKLLNEIIRERNI 170

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G  +  +     ++LK      +  +V    +K         KV+      
Sbjct: 171 RKYYQALVKG--RINEGIYEGYILKDRK--NNISNVYDSPKKNTKKISMDVKVLHTCG-T 225

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDL 297
           +   E++  TGR+HQLR H  H+G PI+GD KY  +   +F          YL+A  +  
Sbjct: 226 YSLAELELITGRSHQLRTHLAHLGNPIIGDTKYGISKINSFFYNKYGLTYQYLYAYKVIF 285

Query: 298 PHPEGG-----RLQITAPLPAHMVK 317
               G         I+  LP    K
Sbjct: 286 KDCNGKLSYMNNKTISEKLPPIFKK 310


>gi|281420178|ref|ZP_06251177.1| ribosomal large subunit pseudouridine synthase D [Prevotella copri
           DSM 18205]
 gi|281405673|gb|EFB36353.1| ribosomal large subunit pseudouridine synthase D [Prevotella copri
           DSM 18205]
          Length = 315

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 64/304 (21%), Positives = 124/304 (40%), Gaps = 32/304 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIK 79
           L  W   +    +   +++ L+   ++V+ K +  F+  ++ G  V +       +   K
Sbjct: 37  LLEWLMENVKGPSKTKVKQTLQGRGIKVNGKTITQFDYALKPGMKVSV-------SKTKK 89

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD- 138
            Q++  S              ++YED  + V  K  GI          ++   L  +   
Sbjct: 90  NQEVFKSR----------YLKIVYEDRYLIVVEKNIGILSMAAGHSTLNVKTVLDDYFHK 139

Query: 139 -SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +  +  + HRLD++TSG+++ A+ +     L + +      + Y +LV G  ++ +  
Sbjct: 140 TRQNCQAHVVHRLDRDTSGLMIYAKDKQTELALEDDWHHNVYDRRYVALVSGEMEDDEGT 199

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +ANWL         Y+      + G  YA++++  ++        +E +  TGR +Q+RV
Sbjct: 200 VANWL----KDNKAYITYSSDTDNGGKYAVTYYHTLERTT-AHSLVEFKLETGRKNQIRV 254

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
           H   MG P+ GD KY              +L LHA  +   HP     ++   P+PA   
Sbjct: 255 HTADMGHPVCGDIKYGNGDDP------CQRLCLHAYVLCFYHPVTHQPMEFETPIPAEFR 308

Query: 317 KTWD 320
           +   
Sbjct: 309 RALK 312


>gi|170781776|ref|YP_001710108.1| putative ribosomal large subunit pseudouridine synthase
           [Clavibacter michiganensis subsp. sepedonicus]
 gi|169156344|emb|CAQ01492.1| putative ribosomal large subunit pseudouridine synthase
           [Clavibacter michiganensis subsp. sepedonicus]
          Length = 342

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 134/322 (41%), Gaps = 29/322 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +  +  R+D          +     ++  +G V  D +    ++R+  G ++ +
Sbjct: 41  RTMPVPDGLDGQRVDVGLARLL-GFSRSFAAEVAEAGGVTQDGREAGKSDRLVGGSMLAV 99

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IA 126
                    ++    + D  +        +                P G++     G   
Sbjct: 100 SWQPRQEPSVVP-LAVPDLGIVHDDDDIVVVDK-------------PVGVAAHPSVGWTG 145

Query: 127 YHIDGFLKS---WVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + G L +    + + G  ++  + HRLD  TSG++VVA+T  A   L   F  R ++K
Sbjct: 146 PTVLGALAAAGFRLSTSGAEERQGIVHRLDAGTSGLMVVAKTERAYTELKRQFHDREVEK 205

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++V G P      I   + +  H   D+   V  +      +++H++ ++ F ++  
Sbjct: 206 VYHAVVQGHPDPLAGTIDAPIGR--HPRSDWKFAVTAD---GKPSVTHYETLEAF-RRAA 259

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE+   TGRTHQ+RVH      P VGD  Y A+   +    +Q + +LHA  +D+ HP 
Sbjct: 260 LLEVHLETGRTHQIRVHMAAQRHPCVGDAMYGADPTISAQLGLQ-RQWLHAMRLDITHPA 318

Query: 302 GG-RLQITAPLPAHMVKTWDSL 322
            G R   ++  PA +    D L
Sbjct: 319 TGDRASFSSTYPADLQHALDVL 340


>gi|189184769|ref|YP_001938554.1| ribosomal large subunit pseudouridine synthase C [Orientia
           tsutsugamushi str. Ikeda]
 gi|189181540|dbj|BAG41320.1| ribosomal large subunit pseudouridine synthase C [Orientia
           tsutsugamushi str. Ikeda]
          Length = 312

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 85/319 (26%), Positives = 150/319 (47%), Gaps = 19/319 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + + +     RLD++ K  Y H+    +++ +R G ++V+  + K   +++   V+ I  
Sbjct: 3   ITINDCLVTTRLDKFLKRKYSHLTQGVIERGIRKGHIKVNDAKSKAKLQVKDNDVLTIAD 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLY---EDSKIYVFNKPAGISVQGGSGIA 126
            +   ++    +       N+   +   K +  Y   E S   + NKPA +  QGGS I+
Sbjct: 63  YLTTCSNQKHIKLKKKVKDNVGVKALAHKIVNDYKIAETSDYIIINKPALLPTQGGSKIS 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +D  +K    S     +L HRLD+ETSG+L++A+    A  L+++F    I+K Y ++
Sbjct: 123 LSLDDAIKYLNKSFYYDFKLVHRLDRETSGLLIIAKNHKTAIKLSQAFLHHSIEKEYTAI 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEM 245
           + G+P      I   + K     GD +    + + G   +I+ ++V       +   +  
Sbjct: 183 LQGVPSQLSGEIITNITK----TGDRML---ETQNGGKVSITKYQVKAVSMNSQLSLVSF 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP-HPEGG 303
            P TGRTHQLRVHA  +G PI+GD KY  +N   N++  +      HA  + +P H  G 
Sbjct: 236 IPVTGRTHQLRVHAAKIGHPIIGDKKYNISNTYYNYSLKL------HAAKICIPKHMFGD 289

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +    APLP    +   + 
Sbjct: 290 QRIYYAPLPYQFQQVISTF 308


>gi|154245827|ref|YP_001416785.1| pseudouridine synthase [Xanthobacter autotrophicus Py2]
 gi|154159912|gb|ABS67128.1| pseudouridine synthase [Xanthobacter autotrophicus Py2]
          Length = 264

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 75/244 (30%), Positives = 112/244 (45%), Gaps = 6/244 (2%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
            + +           +LY D  + + +KP G+ V  G      +   L +      + P 
Sbjct: 6   PTASPRPPEPAPDLPVLYRDGMMLIIDKPHGLPVHAGPKGGETLADHLDALRFGLPRAPE 65

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD++TSG LV+ R   A   L + F    + K Y ++  G P      I   L K+
Sbjct: 66  LAHRLDKDTSGCLVLGRHAKALALLGKLFANGSVGKTYLAVTQGSPAEDAGRIDQPLAKR 125

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           S   G ++  V +   GA  AI+ ++V+   A  F  + + P TGRTHQLR H  ++G P
Sbjct: 126 SPHRGWWMQAVPKGTPGAQEAITDYRVLHR-AGGFAVMALSPVTGRTHQLRAHLSNLGHP 184

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           I GD  Y     G    P    L+LH+R + +P    G  +  +APLP H+ +T  SLG 
Sbjct: 185 IFGDAIYG----GASRLPGGPTLHLHSRRIVVPLKANGPAVAASAPLPPHICETLSSLGL 240

Query: 325 KYDR 328
             D 
Sbjct: 241 SPDE 244


>gi|294782109|ref|ZP_06747435.1| tRNA pseudouridine synthase A [Fusobacterium sp. 1_1_41FAA]
 gi|294480750|gb|EFG28525.1| tRNA pseudouridine synthase A [Fusobacterium sp. 1_1_41FAA]
          Length = 296

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 78/310 (25%), Positives = 151/310 (48%), Gaps = 23/310 (7%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
             +++ + E +R+DR+ + H  +I    + K+LR  +++V+ K+V  + R+  G ++ + 
Sbjct: 3   EFIIDEEYETVRIDRFLRKHLKNIALSEIYKMLRKAKIKVNNKKVSQDYRLILGDIIFVF 62

Query: 69  PVINALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                L    KE+   ++ + L +   + LKS++ YE+  +++ NK  G  +  GSG   
Sbjct: 63  -----LPENFKEKNEDETFIELNEIRKEKLKSMITYENENLFIINKNLGDVIHKGSGHDI 117

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +    +++      K    +R+D+ TSG+++ A+    A+ + +  ++  I K Y+ LV
Sbjct: 118 SLLEEFRAYY--SNNKVNFVNRIDKLTSGLVIGAKNIKTAREIAKEIQLGNITKKYYILV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G  + ++  + N+L K      + V V    ++    +I+H+K I+     +  LE + 
Sbjct: 176 YGKIEKEEFILENYLKKDE----EKVIVSDIEKEDYKKSITHYKRINGN-DDYTLLEAEL 230

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQLR    H+G  IVGD KY  N K          L+ +   +DL       L++
Sbjct: 231 KTGRTHQLRAQLNHIGHTIVGDTKYGKNIKEETMY-----LFSYYLKIDLYD-----LEL 280

Query: 308 TAPLPAHMVK 317
              +P    K
Sbjct: 281 EMGIPDFFFK 290


>gi|291528898|emb|CBK94484.1| Pseudouridylate synthases, 23S RNA-specific [Eubacterium rectale
           M104/1]
          Length = 324

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 76/333 (22%), Positives = 133/333 (39%), Gaps = 24/333 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++      +E   RLD++ K   P+ +   + K+LR   ++++ K+      +     ++
Sbjct: 1   MKEFKAGKNEAGQRLDKYLKKILPNASMGFIYKMLRKKNIKLNDKKASGTEIVSVDDKIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I    +        +  L                ++YED  I V NKP  +  Q      
Sbjct: 61  IFLSDDTFAKFSVNEDSLMKDFKALGALKPDGLGVVYEDDDILVANKPVNMLSQKSKETD 120

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
              +  L  ++  +G+         KP + +RLD+ TSG++++ ++    Q+L++  + R
Sbjct: 121 ISANERLIGYLIKEGKLDFDTYKSFKPSVCNRLDRNTSGLILMGKSLHGLQYLSQVLKDR 180

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFKVIDC 235
             +K Y +LV G        I  +L K   +    +    +         A    K+I+ 
Sbjct: 181 TAEKYYMALVAGEVDEPM-TIEGFLTKDEAVNKVQITKEPISDESLPIKTAYRPIKIIEM 239

Query: 236 FA--QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLH 291
                K   LE+   TGR+HQ+R H   +G PI+GD KY       F     +     LH
Sbjct: 240 SDSCHKATLLEVHLITGRSHQIRAHLSSIGHPIIGDMKYGDKRINAFYKENYHVTSQLLH 299

Query: 292 ARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           A ++ LP    GR  I A LP      W  +G 
Sbjct: 300 AHHVILPD---GRY-IEAALPD----IWSRVGL 324


>gi|257413757|ref|ZP_04744118.2| pseudouridine synthase, RluA family [Roseburia intestinalis L1-82]
 gi|257202334|gb|EEV00619.1| pseudouridine synthase, RluA family [Roseburia intestinalis L1-82]
          Length = 313

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 70/324 (21%), Positives = 129/324 (39%), Gaps = 39/324 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M       +E + +++ +  +     YP+  FV L+K   S  V ++        ++ +G
Sbjct: 17  MIRQFTYRIEPEYDSLTIREYLSLKGYPNAVFVQLKKTPES--VLLNGVWAYMRTKLSAG 74

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I              ++ +S+ +       +   + YED  I   NKPA + V   
Sbjct: 75  DELFI--------------RLEESTSSAHILPVSMPLSICYEDEDILAVNKPAQMPVHPS 120

Query: 123 SGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                H D  L + V             R  +RLD++T+G+ ++A+   ++  L+ +   
Sbjct: 121 ---LNHYDHTLANAVCGYYNDQEIPYTFRCVNRLDRDTTGLTLIAKHMLSSAILSTAAAR 177

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I + Y ++  G    +   I   + + +            + +    AI+H++ +   
Sbjct: 178 REISREYIAIASGK-TPESGTIDAPIGRVAGSTIKRQI----DFENGERAITHYRRLAYH 232

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 L +   TGRTHQ+RVH   +G P++GD  Y      N T     +  LH+  + 
Sbjct: 233 -DGLSLLSLHLETGRTHQIRVHLKSIGHPLIGDFLY------NPTDTTIKRQALHSYRLT 285

Query: 297 LPHPEGGR-LQITAPLPAHMVKTW 319
             HP  G    +TAPLP  M   +
Sbjct: 286 FSHPITGESFVLTAPLPDDMHCLF 309


>gi|291524781|emb|CBK90368.1| Pseudouridylate synthases, 23S RNA-specific [Eubacterium rectale
           DSM 17629]
          Length = 324

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 72/334 (21%), Positives = 134/334 (40%), Gaps = 26/334 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++      +E   RLD++ K   P+ +   + K+LR   ++++ K+      +     ++
Sbjct: 1   MKEFKAGKNEAGQRLDKYLKKILPNASMGFIYKMLRKKNIKLNDKKASGTEIVSVDDKIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I    +        +  L                ++YED  I   NKP  +  Q      
Sbjct: 61  IFLSDDTFAKFSVNEDSLMKDFKALGALKPDGLGVVYEDDDILAANKPVNMLSQKSKETD 120

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
              +  L  ++  +G+         KP + +RLD+ TSG++++ ++    Q+L++  + R
Sbjct: 121 ISANERLIGYLIKEGKLDFDTYKSFKPSVCNRLDRNTSGLILMGKSLHGLQYLSQVLKDR 180

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +K Y +LV G        I  +L K   +    +     +++ +    + ++ +    
Sbjct: 181 TAEKYYMALVAGEVDEPM-TIEGFLTKDEAVNKVQITKESISDE-SLPIKTAYRPLKTIE 238

Query: 238 -----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYL 290
                 K   LE+   TGR+HQ+R H   +G PI+GD KY       F     +     L
Sbjct: 239 MSASCHKATLLEVHLITGRSHQIRAHLSSIGHPIIGDMKYGDRRINAFYKENYHVTSQLL 298

Query: 291 HARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           HA ++ LP    GR  I A LP      W  +G 
Sbjct: 299 HAHHVILPD---GRY-IEAALPD----IWSRVGL 324


>gi|323345230|ref|ZP_08085453.1| ribosomal large subunit pseudouridine synthase D [Prevotella oralis
           ATCC 33269]
 gi|323093344|gb|EFZ35922.1| ribosomal large subunit pseudouridine synthase D [Prevotella oralis
           ATCC 33269]
          Length = 299

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 128/319 (40%), Gaps = 37/319 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           YV Y V   ++E   LD W        +   ++  L+   +RV+ K V  F+  +  G  
Sbjct: 14  YVHYTV---EQEASLLD-WLFATVKSASKSKVKATLKGRGIRVNGKTVTQFDFPLLPGMK 69

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V +                  S      +       ++YED  + V  K  GI    G  
Sbjct: 70  VSV------------------SKSKRNNNLQSKYVRIVYEDRFLVVVEKNIGILSMAGGH 111

Query: 125 IAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++   L  +     Q     + HRLD++TSG++V  +    AQ L   +      + 
Sbjct: 112 STLNVKNILDDYFSKGRQHCTAHVVHRLDRDTSGLMVYTKDTQTAQLLESDWHDIVYDRR 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G  ++ +  IANWL         Y+      + G  YA++HF  +   A  +  
Sbjct: 172 YVAVVSGEMEDDEGTIANWL----KDNKSYISYSSPVDNGGKYAVTHFHTLQRTAD-YSL 226

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGR +Q+RVH+  MG P+ GD KY             ++L LHA  +   HP  
Sbjct: 227 VEYKLETGRKNQIRVHSADMGHPVCGDIKYGNGDDP------LHRLCLHAYLLCFYHPVT 280

Query: 303 -GRLQITAPLPAHMVKTWD 320
             R++   P+P    K + 
Sbjct: 281 HERMEFYTPIPPAFKKLFK 299


>gi|149926150|ref|ZP_01914412.1| ribosomal large subunit pseudouridine synthase D [Limnobacter sp.
           MED105]
 gi|149824968|gb|EDM84180.1| ribosomal large subunit pseudouridine synthase D [Limnobacter sp.
           MED105]
          Length = 388

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 132/311 (42%), Gaps = 46/311 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPPV 70
           V  +    RLD+     +P  +   LQ  L+  +V V+     K N ++Q    + + P 
Sbjct: 22  VPMELGGSRLDKVIAELFPQYSRSRLQGWLKEERVLVNGVAAAKGNQKVQGMDRIELSPG 81

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +     +   Q ++   +NL          ++   ++  V NK AG+ V    G   H  
Sbjct: 82  V-----LAHMQALIPEDMNLD---------IVARTNEYTVVNKQAGLVVHPAPG---HWT 124

Query: 131 GFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + +           +  + HRLD +T+G++VVART+     L +  + R ++++Y 
Sbjct: 125 GTLMNGLYHLDPELIHVPRAGIVHRLDADTTGLMVVARTQETQVKLVQMLQARIVKRVYL 184

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVI---DCFAQKF 240
           ++VWG        I++ L   + +G D  + ++         A++HF  +   +      
Sbjct: 185 AMVWG-------RISSPLTVNNPLGRDPRNRLRMAVVDHGKPAVTHFTPVAFGELLEVPV 237

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-----------KLY 289
             +  +  TGRTHQ+RVHA H G  +V D  Y     G+ ++   +           +  
Sbjct: 238 TLMVCRLETGRTHQIRVHAQHAGFALVADPVYKIKGAGSHSALRLSSIELPNGEKFERQA 297

Query: 290 LHARYMDLPHP 300
           LHA ++  P P
Sbjct: 298 LHATHLSFPDP 308


>gi|255283977|ref|ZP_05348532.1| ribosomal large subunit pseudouridine synthase D [Bryantella
           formatexigens DSM 14469]
 gi|255265430|gb|EET58635.1| ribosomal large subunit pseudouridine synthase D [Bryantella
           formatexigens DSM 14469]
          Length = 313

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 67/337 (19%), Positives = 141/337 (41%), Gaps = 41/337 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINF---VNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  +    +E + E      + +      +     +L++    G +  +  R+  + R+ 
Sbjct: 5   MKRILNYQIEKEWEGESAAAFLRA--KGFSRHILTHLKQ--TEGGICRNGSRIWLSERLH 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G V+ +                L+   +       +K  ++YED  + V +KPA + V 
Sbjct: 61  FGDVLTVT--------------FLEERSSENIVPVPMKLDIVYEDEDLLVIDKPADMPVH 106

Query: 121 GG-SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                    +   L  + +S+G+    R   RLD++T+G+L+VA+   +   L E  + R
Sbjct: 107 PSIHNFDNTLANGLAYYYESRGEAFVYRCITRLDRDTTGLLLVAKNMLSGAFLAEMGKRR 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I + Y ++V G     +  +   + +      +       + +    A++H++ ++   
Sbjct: 167 EIHREYLAIVTGK-TEAEGTVDAPIARVEGSVLER----CVDFQRGERAVTHYRTLEYR- 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  + ++  TGRTHQ+RVH  ++G P+ GD  Y  +++      + +   LH+ Y+  
Sbjct: 221 DGYSLVRLKLETGRTHQIRVHMKYIGHPLTGDFLYNPDYR------LMDHQALHSHYLAF 274

Query: 298 PHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
            HP  G R++ T+  P      W+  G + D    +K
Sbjct: 275 RHPITGERMEFTSQPP--WQGLWE--GREEDGEETLK 307


>gi|116624899|ref|YP_827055.1| RluA family pseudouridine synthase [Candidatus Solibacter usitatus
           Ellin6076]
 gi|116228061|gb|ABJ86770.1| pseudouridine synthase, RluA family [Candidatus Solibacter usitatus
           Ellin6076]
          Length = 304

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 126/319 (39%), Gaps = 29/319 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M    Y    ++ +      L     + YPH      Q+ L +G+V ++      +  ++
Sbjct: 1   MLNRGYAYTTIISSKYPGQTLLSHLASLYPHSTSEAWQQNLNNGEVTLNGVAATGSESVR 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SGQ++                  ++  V            +L+ED  +   NKP+G+   
Sbjct: 61  SGQILIWN-----------RPPWIEPDVPKHFE-------VLFEDPHLLAVNKPSGLPTL 102

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G G     +  L   V          HRL + TSGI++ ART  AA +L  ++   +I+
Sbjct: 103 PGGGFL---ENTLLRLVQKHTPNANPVHRLGRATSGIVLFARTPQAASNLFANWNTPKIR 159

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY +L   I ++    I   +    H     +  V         + S  KVI       
Sbjct: 160 KIYRALAQNIAQHDAYEILTPIGLVPHP---RIGSVWAANPSGKPSKSLAKVISRSTSTT 216

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDL 297
            + E+  ++GR HQ+R+H   +G P+VGD  Y       +     P     +LHA+++  
Sbjct: 217 TF-EVSLNSGRPHQIRIHLASIGHPLVGDPLYGLTGQPLENLPGLPGDGGYFLHAQFLQF 275

Query: 298 PHPEGGR-LQITAPLPAHM 315
            HP  G  + + A LP+  
Sbjct: 276 QHPITGEQINLEAALPSGF 294


>gi|282890613|ref|ZP_06299136.1| hypothetical protein pah_c022o218 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281499610|gb|EFB41906.1| hypothetical protein pah_c022o218 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 295

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 76/316 (24%), Positives = 136/316 (43%), Gaps = 30/316 (9%)

Query: 12  VENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
           V + E  M L+ + K       +   L+  +     R++++  +  + R+ +G  +    
Sbjct: 6   VASAESGMTLNAFLKLKLGDAYSAKQLKHAIERNLCRINQRVERFASTRVANGDQIEWDN 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                             +  +    F    ++YED+ + V++KPAGI            
Sbjct: 66  DKLQF-------------LFASSQLKFEAKRIIYEDADLLVYDKPAGI---------NCD 103

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +   +  K    +L HRLD++T+GIL+ A+T A    +   F+  +++K Y+ +V G
Sbjct: 104 TSGIVRLIHQKDPSLKLVHRLDRDTTGILLFAKTDAVLHKMIRLFKTFKVKKTYYVIVDG 163

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               +K  I N L       G  V       KG  +A + ++  +   Q    ++  P T
Sbjct: 164 AISKEKGVIDNNLAPLHKYQGQTVWGQATGSKGV-HARTGWRK-EKKGQDCTLIQCYPVT 221

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
           G THQ+RVH   MG PI+GD++Y   F  ++     ++  LHA  +  PHP     +++ 
Sbjct: 222 GITHQIRVHMSEMGHPILGDYQYGRRFICSYQP---SRYLLHAYEITFPHPSSEKEIRLK 278

Query: 309 APLPAHMVKTWDSLGF 324
           APLP+   +  D L  
Sbjct: 279 APLPSDFKQALDHLRL 294


>gi|255070545|ref|XP_002507354.1| predicted protein [Micromonas sp. RCC299]
 gi|226522629|gb|ACO68612.1| predicted protein [Micromonas sp. RCC299]
          Length = 357

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 77/335 (22%), Positives = 132/335 (39%), Gaps = 49/335 (14%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD +  +    ++   + + ++SG V V+     K ++++  G  V    ++ +    +
Sbjct: 37  RLDAFLADQISGVSRSRIVESIKSGVVVVNGNVTTKPSHKLDIGDRVICGEIVASPPTEV 96

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKSW 136
                           + +   +++ED  + V NKP G+ V   +G A    ++  L   
Sbjct: 97  A--------------PENIPLDVVFEDDHLVVVNKPPGMVVHPSAGHAGGSLVNALLFHC 142

Query: 137 VDSKG-----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +               +  + HR+D+ TSG+LV+A+  AA   L   F  R +++ Y +
Sbjct: 143 NERSNRGDDASKMIDVPRLGVVHRIDKGTSGLLVMAKDAAAQAGLQTQFANRSVRRRYLA 202

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLE 244
           +V G P  +   I   + +      D + +          AIS+F V     +     +E
Sbjct: 203 IVLGTPARESGRIDAPIGRDP---ADRLKMAIVRGATGRQAISNFGVRARLVRGNASLVE 259

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA---------NFKGNFTSPIQN-------KL 288
            Q  TGRTHQ+RVHA  MG PIVGD  Y              G  ++           + 
Sbjct: 260 WQLETGRTHQIRVHAREMGHPIVGDEAYGGGGSAAAEFLRRDGAMSAAAAREIVAKCARP 319

Query: 289 YLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            LHAR +   HP  G  +      P   V  +  L
Sbjct: 320 MLHARSLGFRHPVTGEEISFAVEPPPDFVDAFTEL 354


>gi|149920990|ref|ZP_01909450.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
 gi|149818122|gb|EDM77578.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
          Length = 356

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 78/334 (23%), Positives = 132/334 (39%), Gaps = 41/334 (12%)

Query: 6   YVQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV--DKKRVKFNN-RIQS 61
           Y+++ + V    +  RLDR+    +  ++   + K+L +G VR     + +  N  R++ 
Sbjct: 28  YIEFELEVGPGSDGYRLDRFLSLRFVRMSRTRVHKLLAAGNVRCRSSGEVLTKNALRVRG 87

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           GQVV I         +I                  L   +++ED  + V +KP  + V  
Sbjct: 88  GQVVIIRRPAPEEPAVI------------------LDYGVVHEDPDVLVLDKPGNLPVHP 129

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            +    H    L            + HR+D+ETSG+++  R +A+   +  SF  R + K
Sbjct: 130 TARYHRHTLTALMRRRLGPKHGWEMAHRIDRETSGVIIFGRRKASGPKIKGSFFRREVHK 189

Query: 182 IYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI---DCF 236
            Y ++V G  +  +    I   L              +  ++G   A +  +V+   +  
Sbjct: 190 EYLAIVLGRLELPEGPRLIDMPLGSAVGSKIMIKMGPRPVDEGGLPAQTTIEVLAHGEHR 249

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-------------CANFKGNFTSP 283
            Q    +   P TGRTHQ+RVH   +G PI+GD  Y                        
Sbjct: 250 GQPITLVRCLPRTGRTHQIRVHLAEIGHPILGDKLYAAEEDEFLAVVEDGEPVAELEARL 309

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
              +  LHAR + LPHP  G  ++  AP P  + 
Sbjct: 310 GLWRQALHARALSLPHPTTGDGVRYVAPWPKELA 343


>gi|147771519|emb|CAN66750.1| hypothetical protein VITISV_034413 [Vitis vinifera]
          Length = 611

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 85/373 (22%), Positives = 151/373 (40%), Gaps = 65/373 (17%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF----NNRIQSGQVVRI 67
           V +D   +RLD W  +    I+   +Q  +RSG V V+ + V      + + + G+  +I
Sbjct: 199 VNSDSGKLRLDSWISSRIIGISRARVQSSIRSGLVSVNDRIVDKAMLVSRKFEVGEGKKI 258

Query: 68  PP-----VINALNHIIKEQKILDSSV----NLTKHSDFLKSILLYEDSKIYVFNKP---A 115
                      ++H+I+    ++ ++     L    + +   ++YED  + V   P   +
Sbjct: 259 EEKDPITYSEQVSHVIRAGDKVNCTISELQPLRAEPEDIPLDIVYEDEHV-VHPAPGNAS 317

Query: 116 GISVQGGSGIAYHI--------------DGFLKSWVD-----------SKGQKPRLTHRL 150
           G  V   +GI +H               D  L    +               +P + HRL
Sbjct: 318 GTLV---NGILHHCSLPTVALPNRDSEEDDILDDEFNSFAAGQNCGTCETNIRPGIVHRL 374

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSG+LVVA+   +  HL+E F++  I ++Y SL  G+P      +   + +  +   
Sbjct: 375 DKGTSGLLVVAKDEHSHAHLSEQFKLHSIHRVYISLTSGVPTPLSGRVEIPVGRDPNNRI 434

Query: 211 DYVHVVKQNEKG-ANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               V   +  G A +A S +KVI+   A     +E +  TGRTHQ+R HA ++G P++G
Sbjct: 435 RMTAVPGPSNSGQARHAASRYKVIEILAAGGSALVEWRLETGRTHQIRAHAKYLGIPLLG 494

Query: 269 DHKYCANFKGNFTSP-----------------IQNKLYLHARYMDLPHPEGGR-LQITAP 310
           D  Y        +                     ++  LHA  +   HP+ G+ +  +  
Sbjct: 495 DEVYGGTKNMALSLLRPRIPSSHHGQLAQLVSRLDRPCLHAVALGFNHPKTGKNVHFSCQ 554

Query: 311 LPAHMVKTWDSLG 323
            P    +    L 
Sbjct: 555 PPEDFAEILSWLR 567


>gi|258645458|ref|ZP_05732927.1| pseudouridine synthase, RluA family [Dialister invisus DSM 15470]
 gi|260402809|gb|EEW96356.1| pseudouridine synthase, RluA family [Dialister invisus DSM 15470]
          Length = 313

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 67/299 (22%), Positives = 122/299 (40%), Gaps = 13/299 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +   EE   L ++     P        K  R   +  + ++      ++    ++
Sbjct: 1   MKEFTITKAEEGQTLFKYLCKLLPQAPASLFHKSFRKKNITWNDEKCTGKEILREKDNIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I    +   H   E+K  D S    K +      ++YED  I + +KPAGI  Q  +   
Sbjct: 61  I-WFSDETFHTFSEKKNADPSQK--KSAFPFSRRIIYEDEHILIVDKPAGILTQSDNSNE 117

Query: 127 YHIDGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             ++  L  +         KP + +RLD+ TSGI++  +T    Q L E  + R + K Y
Sbjct: 118 LSLNDALLDYCHYNNHSTAKPSVCNRLDRNTSGIVLCGKTVKGLQMLNEIIKNRTLHKYY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI---DCFAQKF 240
             +V G    +++ +  +L+K      + V ++ + +  A    + +K I   +      
Sbjct: 178 RCIVLGE-TKEQDTLKGFLIKNE--SANQVTIITEQKDNAVPIETRYKRISTMERAGNIC 234

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLP 298
             LE++  TGR HQ+R H   +G PI+GD KY        +  +      L A  +  P
Sbjct: 235 SLLEVRLITGRPHQIRAHLTSIGHPILGDRKYRNKKSIEISKALHIPHQLLCACSITFP 293


>gi|78776982|ref|YP_393297.1| pseudouridine synthase, RluD [Sulfurimonas denitrificans DSM 1251]
 gi|78497522|gb|ABB44062.1| ribosomal large subunit pseudouridine synthase D [Sulfurimonas
           denitrificans DSM 1251]
          Length = 323

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 79/330 (23%), Positives = 141/330 (42%), Gaps = 43/330 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           M   Q  + E  E   RLD +  +     +   + ++++   V+VD K V +   +++  
Sbjct: 1   MNETQSYICETIE---RLDTFLTSIL-GQSRSQIAQLIKKELVQVDGKVVSRSGVKLKKN 56

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           QVV +              K   + +      DF    +LYED  I V NKP G++V   
Sbjct: 57  QVVLV--------------KFPPAEIKPALDIDF-DVEILYEDDDILVINKPTGLTVHPA 101

Query: 123 SGIAYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTES 173
             +    +  L  W+  KG +           + HRLD+ TSG +V+A+  +  + L++ 
Sbjct: 102 PSV---KEATLVDWLKHKGMRLSSLSGEERHGIVHRLDKGTSGAMVIAKNNSTHEFLSDQ 158

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + + + + Y +++    K++   +   + + SH       +     +   YA S FKV+
Sbjct: 159 LQDKSMGRYYLAVINPPLKDELTEVIFPIARSSHNRLKMAPL-----EHGKYAKSAFKVL 213

Query: 234 DCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                +    +  + +TGRTHQ+RVH   +   IVGDH Y  + K   +     ++ LHA
Sbjct: 214 AYSNDEANQLIACKLYTGRTHQIRVHLESLNRHIVGDHIYAQSPKQEKSE----RILLHA 269

Query: 293 RYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
             +   HP+   R+   A L   M +  D 
Sbjct: 270 YIIYFIHPKSKERVSFVASLDKGMQEYIDK 299


>gi|116329455|ref|YP_799175.1| pseudouridylate synthase, 23S RNA-specific [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
 gi|116122199|gb|ABJ80242.1| Pseudouridylate synthase, 23S RNA-specific [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
          Length = 312

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 72/313 (23%), Positives = 135/313 (43%), Gaps = 38/313 (12%)

Query: 12  VENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRV--KFNNRIQSGQVVRIP 68
           V  +    RLDR+ K  +   ++   +QK +  G VR   +++  K + ++++G+   + 
Sbjct: 9   VLEEFSGNRLDRFLKFSFGDEMSRATIQKWIECGYVRNQDRKICDKSSWKVKTGEQYFLS 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
                          +     L+     +   ++ E     + +KP GI+   G G    
Sbjct: 69  ---------------IPPRPPLSLEPIPMTLPVVLEREDYLIIHKPPGIASHSGPGDRSP 113

Query: 128 -HIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G L  + +        +P + HRLD+ T G++++A+   A   L+E FR R I+K 
Sbjct: 114 SLVNGLLHHFKELSKVGGEARPGIVHRLDKPTEGLMLIAKNDRAHGKLSELFRKREIEKK 173

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID----CFAQ 238
           Y++ + G    +   I   + +   I    + V          +++H+KV+        +
Sbjct: 174 YYAWIQGHLPAETGTIDLPIARH-PIERLKMTV----SPKGRKSVTHYKVLKYVNSRSGR 228

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           KF ++E+   TGRTHQ+R+H     CP+VGD  Y        +  +Q    L + Y+   
Sbjct: 229 KFSFVEVGLETGRTHQIRIHFQSQRCPVVGDLLYSRTGSQFESYGLQ----LLSYYLKFK 284

Query: 299 HPEGGRLQITAPL 311
            P  G + I A L
Sbjct: 285 DPFTGEM-IEATL 296


>gi|269140174|ref|YP_003296875.1| 23S rRNA pseudouridine synthase D [Edwardsiella tarda EIB202]
 gi|267985835|gb|ACY85664.1| 23S rRNA pseudouridine synthase D [Edwardsiella tarda EIB202]
 gi|304560007|gb|ADM42671.1| Ribosomal large subunit pseudouridine synthase D [Edwardsiella
           tarda FL6-60]
          Length = 280

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 74/287 (25%), Positives = 128/287 (44%), Gaps = 41/287 (14%)

Query: 49  DKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           +   + K   ++  G+ + I  +I   N    +   LD               ++YED  
Sbjct: 2   NGVIINKPKEKVLGGEHIAIDALIEEENRWEAQDIALD---------------IVYEDED 46

Query: 108 IYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTR 164
           I V NKP  + V  G+G     +   L  +       PR  + HRLD++T+G++VVA+T 
Sbjct: 47  ILVINKPRDLVVHPGAGNPDGTVLNALLHYYPQIADVPRAGIVHRLDKDTTGLMVVAKTV 106

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGDYVHVVKQNEK 221
            A   L ES ++R I + Y ++  G        +E IA    K++H+    +        
Sbjct: 107 PAQTRLVESLQLREITREYEAVAIGTMTAGGTVREPIARHPTKRTHMSVHPM-------- 158

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               A++H+++++ F +    L ++  TGRTHQ+RVH  H+  P+VGD  Y    +    
Sbjct: 159 -GKPAVTHYRIMEHF-RAHTRLRLRLETGRTHQIRVHMAHINHPLVGDPLYGGRPRPPRD 216

Query: 282 SPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           +  +        ++  LHA  + L HP  G  ++  AP+P  M +  
Sbjct: 217 ASPEFIRVLREFDRQALHATMLRLYHPISGIEMEWHAPIPEDMQRLI 263


>gi|296327421|ref|ZP_06869968.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
 gi|296155434|gb|EFG96204.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
          Length = 289

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 80/300 (26%), Positives = 150/300 (50%), Gaps = 20/300 (6%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ + E +R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G VV I   
Sbjct: 5   IIDEEYEKVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDVVFIFLP 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            N   +   E+K ++ S    +  + LK ++++E+  ++V NK  G  V  GSG    + 
Sbjct: 65  ENFKEN--NEEKFIELS---QERKEKLKEMIVFENENLFVINKLLGDVVHKGSGHDISLL 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+ LV G 
Sbjct: 120 EEFRSYYSNNNIN--FVNRIDKLTSGLVIGAKNIKTAREVAKEIQASNIIKRYYILVNGK 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +     + N+L K      + V V    ++G   +I++FK I     K+  LE +  TG
Sbjct: 178 IEKDNFILENYLKKDE----EKVIVSDIEKEGYKKSITYFKKIKEH-NKYTLLEAELKTG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLR    H+G  IVGD KY  + + +        L+ +   +DL +     +++  P
Sbjct: 233 RTHQLRAQLNHIGNNIVGDTKYGKDEREDMMY-----LFSYYLKIDLYNL---EIKLEIP 284


>gi|195978164|ref|YP_002123408.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
 gi|195974869|gb|ACG62395.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
          Length = 298

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 127/304 (41%), Gaps = 32/304 (10%)

Query: 25  FKNHYPHINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
            K H   ++   L KI  + G + V+         +  G VV I          I  ++ 
Sbjct: 17  LKEH--DVSKGLLAKIKYKGGNIWVNGVAQNAIYLLDIGDVVAID---------IPNEEP 65

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSK 140
            +    ++   D     ++YED    + NKPAG +    +  +  I  F+K++    D  
Sbjct: 66  FEQLTAISHDLD-----IVYEDEHFLILNKPAGYASIPSAIHSNTIANFIKAYYIKQDYP 120

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIA 199
            ++  +  RLD++TSG+++ A+   A   L +  + R I K Y++LV G  +   +  I 
Sbjct: 121 NKQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQQRAINKRYYALVCGQERLPDQGEII 180

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + +      D   + +       YA + +KVI  + +    ++++ HTGRTHQ+RVH 
Sbjct: 181 APIGR-----TDDSIITRTVTPKGKYAKTSYKVIARYPENVSLVDIRLHTGRTHQIRVHF 235

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
            H+G P++GD  Y        T     +  LH  ++   HP    R   T  L       
Sbjct: 236 AHLGFPLLGDDLYGGRLDLGMT-----RQALHCHHLSFTHPFTESRSDHTICLTDDFESV 290

Query: 319 WDSL 322
              L
Sbjct: 291 IIDL 294


>gi|87309950|ref|ZP_01092084.1| ribosomal large subunit pseudouridine synthase [Blastopirellula
           marina DSM 3645]
 gi|87287714|gb|EAQ79614.1| ribosomal large subunit pseudouridine synthase [Blastopirellula
           marina DSM 3645]
          Length = 281

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 76/295 (25%), Positives = 143/295 (48%), Gaps = 39/295 (13%)

Query: 47  RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
            +D +  K  +++ +G+ + + P+    +  I     LD               ++Y+D 
Sbjct: 2   TIDGEPCKPAHKLSAGEQLIVKPIAAYSDEQIGVNVHLD---------------IIYQDD 46

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGI 157
           +I V NKPAG+      G   H  G L   +  +           +P + HRLD++TSG+
Sbjct: 47  RIAVINKPAGMITHPAKG---HWKGTLTEGLKGQFPQLSTIGGPTRPGIVHRLDRDTSGV 103

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+A+  AA + L   F+ R  +K Y+++V G P   ++ I   +     I  + + + +
Sbjct: 104 IVIAKDDAAHEFLKTQFQDRLTEKEYFAMVIGAPDRDRDLINEPVGPHPKI-RERMAIRR 162

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF- 276
            +++G   A + ++V++ + Q F  ++  P TGRTHQ+RVH +H G P++ D  Y +   
Sbjct: 163 GDDEG-KDAQTFYEVLERY-QGFAAIKALPKTGRTHQIRVHLMHAGHPVLCDPLYGSRRF 220

Query: 277 -------KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
                    +  + + N+  LHA  + + HP+ G + +  APLPA + +T + L 
Sbjct: 221 LSLGELQHDDDRTVLLNRTALHAHRIAIAHPDDGEIREFIAPLPADLERTQNMLR 275


>gi|212640160|ref|YP_002316680.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
 gi|212561640|gb|ACJ34695.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
          Length = 315

 Score =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 72/287 (25%), Positives = 120/287 (41%), Gaps = 32/287 (11%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    L +   +  V ++     F+  I     +RI          IKE++I  +     
Sbjct: 45  VPKKMLHEWRMTKGVAINDNIAPFHTIISPNDRIRIR---------IKEEQIEPTPT--- 92

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQ--KPRLTH 148
               ++   +++ED  + V NK A + V     G    +   +      +G   K R  H
Sbjct: 93  ----YVPLHIVFEDDHVLVVNKRAHMDVHPTQPGQTNTLANAVAFHFQCEGIYSKVRHIH 148

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD++TSG+++ A+   A   L +    R I++ Y +LV G  K KK  I   + +  H 
Sbjct: 149 RLDRDTSGVILFAKHALAGAILDQYLAKRTIRRTYIALVHGYVKQKKGTIEAPIGRDRHH 208

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIV 267
                    +  K  + AI+H++ +    QK    + +   TGRTHQ+RVH  ++G P+V
Sbjct: 209 PTRR-----RVSKTGDTAITHYERLQYDKQKHVSLVRLTLDTGRTHQIRVHMSYIGHPLV 263

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
           GD  Y          P  ++  LHA  +   HP    L   + LP  
Sbjct: 264 GDTLYGGK-------PWIDRQALHAFSLSFLHPFTEELITCSALPDE 303


>gi|291532509|emb|CBL05622.1| pseudouridine synthase, RluA family [Megamonas hypermegale ART12/1]
          Length = 288

 Score =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 64/301 (21%), Positives = 131/301 (43%), Gaps = 37/301 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHIIKEQK 82
           + K H  +I+    +KI R  +  V+ ++V+     ++   ++     + +    I+   
Sbjct: 18  YLKRH-ENISSTLWKKIKRQDEFFVNGQKVRATQAIVKPNDIIEYNLPVTSKVEAIQ--- 73

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSK 140
                         +   +++ED    + +K AG+     +        +G +  +  + 
Sbjct: 74  --------------IPLNIVFEDDYFLIVDKIAGMLTHPLTFENTQTLANGVMYHFAKTN 119

Query: 141 GQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                   +RLD+ TSG++V A+       L  + +  + Q+ Y++LV G    K+  I 
Sbjct: 120 QNVGCHPLYRLDRNTSGLVVFAKMPQLQHQLANNHQ--KFQRYYYALVHGKLSQKQGQIN 177

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + +K     D + + + N++G  +AI+++ VI  F + +  +E+   TGRTHQ+RVH 
Sbjct: 178 APIGRK----KDSIILHEVNDEG-KHAITNYHVIKEF-ENYSLIELWLETGRTHQIRVHM 231

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKT 318
            ++G P++GD  Y           +  +  LHA  +   HP     + +++ LP  M K 
Sbjct: 232 SYLGHPLLGDDLYGGKLN------LIARHALHAYKLKFTHPFTHEEICLSSSLPDDMAKL 285

Query: 319 W 319
            
Sbjct: 286 I 286


>gi|282877802|ref|ZP_06286615.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
 gi|281300118|gb|EFA92474.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
          Length = 295

 Score =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 72/304 (23%), Positives = 131/304 (43%), Gaps = 33/304 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIK 79
           L  W  NH  +++   ++  L    + V+ K +  F+  +++G  + +            
Sbjct: 21  LLNWLLNHVTNLSKSKIKATLAGKGIIVNGKCITQFDYPLEAGMKIAVS----------- 69

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                 S  N+   + +LK  ++YED  + V  K  GI        + ++   L  +  +
Sbjct: 70  -----KSKKNINFKNRYLK--IVYEDRYLVVIEKHVGILSMAAGHSSLNVKRVLDDYFRN 122

Query: 140 KGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             QK    + HRLD+ETSG+++ A+  A  Q L  ++      + Y ++V G  ++ +  
Sbjct: 123 SKQKCTAHVVHRLDRETSGLMIYAKDMATEQELEHNWHDIVYDRRYVAVVSGEMEDDEGV 182

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I +WL         YV      + G  +AI+HF  +D   +    +E +  TGR +Q+RV
Sbjct: 183 ITSWL----KDNKAYVTYSSPVDNGGKFAITHFHTLDRTTE-HSLVEYRLETGRKNQIRV 237

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H+  +G P+ GD KY             ++L LHA  +   HP   R ++    +P    
Sbjct: 238 HSADIGHPVCGDFKYGNG------DNPLDRLCLHAYMLCFTHPVTRRPMEFETQIPPAFR 291

Query: 317 KTWD 320
           K + 
Sbjct: 292 KLFK 295


>gi|239826073|ref|YP_002948697.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239806366|gb|ACS23431.1| pseudouridine synthase, RluA family [Geobacillus sp. WCH70]
          Length = 304

 Score =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 70/310 (22%), Positives = 135/310 (43%), Gaps = 34/310 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ +  +   ++   K  +   +     ++     V+++ K V +   +Q    +++   
Sbjct: 12  IIPSFWKGRTIESLLKEVWC-ASKKLAHQLRMEKGVKLNGKEVSWQIPLQENDRLQLYLY 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HI 129
               + ++ E + L                +L+ED  + + NK AG+ +          +
Sbjct: 71  KPEASSLLPEYREL---------------SVLWEDEHLLIINKDAGMDIHPSEPSQTGTL 115

Query: 130 DGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              +  ++ S+G   K R  HRLD++TSG ++ A+   A   L      R+I++ Y +LV
Sbjct: 116 ANAVAFYLQSQGILTKVRHIHRLDRDTSGTILFAKHPLAGATLDRMLAKRQIKRTYVALV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQ 246
            GI KNK   I+  + +  H         + ++ GA  A++H++V+  F  Q+   +E+ 
Sbjct: 176 HGIMKNKSGTISAPIGRDRHHPTRR----RVSQTGAK-AVTHYRVLHTFPNQQLSLVELS 230

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL- 305
             TGRTHQ+RVH  ++G P+VGD  Y             ++  LHA  +   HP    + 
Sbjct: 231 LDTGRTHQIRVHMSYIGHPLVGDVLYGGE-------NTFHRQALHAAKLSFLHPFTNEMI 283

Query: 306 QITAPLPAHM 315
              AP+    
Sbjct: 284 SCIAPV-DDF 292


>gi|15608678|ref|NP_216056.1| hypothetical protein Rv1540 [Mycobacterium tuberculosis H37Rv]
 gi|15841007|ref|NP_336044.1| pseudouridine synthase, RluD-related protein [Mycobacterium
           tuberculosis CDC1551]
 gi|31792726|ref|NP_855219.1| hypothetical protein Mb1567 [Mycobacterium bovis AF2122/97]
 gi|121637461|ref|YP_977684.1| hypothetical protein BCG_1592 [Mycobacterium bovis BCG str. Pasteur
           1173P2]
 gi|148661336|ref|YP_001282859.1| pseudouridine synthase, RluD-related protein [Mycobacterium
           tuberculosis H37Ra]
 gi|148822764|ref|YP_001287518.1| pseudouridylate synthase [Mycobacterium tuberculosis F11]
 gi|224989936|ref|YP_002644623.1| hypothetical protein member of YabO/YceC/YfiL family [Mycobacterium
           bovis BCG str. Tokyo 172]
 gi|253799405|ref|YP_003032406.1| hypothetical protein TBMG_02437 [Mycobacterium tuberculosis KZN
           1435]
 gi|254231769|ref|ZP_04925096.1| conserved hypothetical protein member of yabO/yceC/yfiI family
           [Mycobacterium tuberculosis C]
 gi|254364412|ref|ZP_04980458.1| conserved hypothetical protein member of yabO/yceC/yfiI family
           [Mycobacterium tuberculosis str. Haarlem]
 gi|289442994|ref|ZP_06432738.1| pseudouridylate synthase [Mycobacterium tuberculosis T46]
 gi|289447151|ref|ZP_06436895.1| conserved hypothetical protein [Mycobacterium tuberculosis CPHL_A]
 gi|289554668|ref|ZP_06443878.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN 605]
 gi|289569575|ref|ZP_06449802.1| conserved hypothetical protein [Mycobacterium tuberculosis T17]
 gi|289574224|ref|ZP_06454451.1| pseudouridylate synthase [Mycobacterium tuberculosis K85]
 gi|289745296|ref|ZP_06504674.1| conserved hypothetical protein [Mycobacterium tuberculosis 02_1987]
 gi|289750107|ref|ZP_06509485.1| conserved hypothetical protein [Mycobacterium tuberculosis T92]
 gi|289753627|ref|ZP_06513005.1| conserved hypothetical protein [Mycobacterium tuberculosis EAS054]
 gi|289757656|ref|ZP_06517034.1| pseudouridylate synthase [Mycobacterium tuberculosis T85]
 gi|289761703|ref|ZP_06521081.1| conserved hypothetical protein member of yabO/yceC/yfiI family
           [Mycobacterium tuberculosis GM 1503]
 gi|307079554|ref|ZP_07488724.1| hypothetical protein TMKG_02048 [Mycobacterium tuberculosis
           SUMu011]
 gi|308369471|ref|ZP_07666738.1| hypothetical protein TMBG_00096 [Mycobacterium tuberculosis
           SUMu002]
 gi|308377761|ref|ZP_07668589.1| hypothetical protein TMIG_01808 [Mycobacterium tuberculosis
           SUMu009]
 gi|308378965|ref|ZP_07668871.1| hypothetical protein TMJG_02974 [Mycobacterium tuberculosis
           SUMu010]
 gi|308400685|ref|ZP_07669399.1| hypothetical protein TMLG_00526 [Mycobacterium tuberculosis
           SUMu012]
 gi|313658428|ref|ZP_07815308.1| hypothetical protein MtubKV_08412 [Mycobacterium tuberculosis KZN
           V2475]
 gi|61250913|sp|P0A5T2|Y1540_MYCTU RecName: Full=Uncharacterized RNA pseudouridine synthase
           Rv1540/MT1592; AltName: Full=RNA pseudouridylate
           synthase; AltName: Full=RNA-uridine isomerase
 gi|61250914|sp|P0A5T3|Y1567_MYCBO RecName: Full=Uncharacterized RNA pseudouridine synthase Mb1567;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|1403502|emb|CAA98322.1| CONSERVED HYPOTHETICAL PROTEIN MEMBER OF yabO/yceC/yfiI FAMILY
           [Mycobacterium tuberculosis H37Rv]
 gi|13881216|gb|AAK45858.1| pseudouridine synthase, RluD-related protein [Mycobacterium
           tuberculosis CDC1551]
 gi|31618316|emb|CAD96234.1| CONSERVED HYPOTHETICAL PROTEIN MEMBER OF yabO/yceC/yfiI FAMILY
           [Mycobacterium bovis AF2122/97]
 gi|121493108|emb|CAL71579.1| Conserved hypothetical protein member of yabO/yceC/yfiL family
           [Mycobacterium bovis BCG str. Pasteur 1173P2]
 gi|124600828|gb|EAY59838.1| conserved hypothetical protein member of yabO/yceC/yfiI family
           [Mycobacterium tuberculosis C]
 gi|134149926|gb|EBA41971.1| conserved hypothetical protein member of yabO/yceC/yfiI family
           [Mycobacterium tuberculosis str. Haarlem]
 gi|148505488|gb|ABQ73297.1| pseudouridine synthase, RluD-related protein [Mycobacterium
           tuberculosis H37Ra]
 gi|148721291|gb|ABR05916.1| pseudouridylate synthase [Mycobacterium tuberculosis F11]
 gi|224773049|dbj|BAH25855.1| hypothetical protein member of YabO/YceC/YfiL family [Mycobacterium
           bovis BCG str. Tokyo 172]
 gi|253320908|gb|ACT25511.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN
           1435]
 gi|289415913|gb|EFD13153.1| pseudouridylate synthase [Mycobacterium tuberculosis T46]
 gi|289420109|gb|EFD17310.1| conserved hypothetical protein [Mycobacterium tuberculosis CPHL_A]
 gi|289439300|gb|EFD21793.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN 605]
 gi|289538655|gb|EFD43233.1| pseudouridylate synthase [Mycobacterium tuberculosis K85]
 gi|289543329|gb|EFD46977.1| conserved hypothetical protein [Mycobacterium tuberculosis T17]
 gi|289685824|gb|EFD53312.1| conserved hypothetical protein [Mycobacterium tuberculosis 02_1987]
 gi|289690694|gb|EFD58123.1| conserved hypothetical protein [Mycobacterium tuberculosis T92]
 gi|289694214|gb|EFD61643.1| conserved hypothetical protein [Mycobacterium tuberculosis EAS054]
 gi|289709209|gb|EFD73225.1| conserved hypothetical protein member of yabO/yceC/yfiI family
           [Mycobacterium tuberculosis GM 1503]
 gi|289713220|gb|EFD77232.1| pseudouridylate synthase [Mycobacterium tuberculosis T85]
 gi|308327489|gb|EFP16340.1| hypothetical protein TMBG_00096 [Mycobacterium tuberculosis
           SUMu002]
 gi|308354710|gb|EFP43561.1| hypothetical protein TMIG_01808 [Mycobacterium tuberculosis
           SUMu009]
 gi|308358696|gb|EFP47547.1| hypothetical protein TMJG_02974 [Mycobacterium tuberculosis
           SUMu010]
 gi|308362576|gb|EFP51427.1| hypothetical protein TMKG_02048 [Mycobacterium tuberculosis
           SUMu011]
 gi|308366240|gb|EFP55091.1| hypothetical protein TMLG_00526 [Mycobacterium tuberculosis
           SUMu012]
 gi|323719988|gb|EGB29100.1| hypothetical protein TMMG_00801 [Mycobacterium tuberculosis
           CDC1551A]
 gi|326903170|gb|EGE50103.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           tuberculosis W-148]
 gi|328459155|gb|AEB04578.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN
           4207]
          Length = 308

 Score =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 75/326 (23%), Positives = 142/326 (43%), Gaps = 30/326 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +    MR+D         ++      +   G V ++      ++R+ SG ++++
Sbjct: 4   RSMPVPDGLAGMRVDTGLARLL-GLSRTAAAALAEEGAVELNGVPAGKSDRLVSGALLQV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG-I 125
                         ++ ++   L      ++ + +LY D  I   +KPA ++     G  
Sbjct: 63  --------------RLPEAPAPLQNTPIDIEGMTILYSDDDIVAVDKPAAVAAHASVGWT 108

Query: 126 AYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R + 
Sbjct: 109 GPTVLGGLAAAGYRITTSGVHERQGIVHRLDVGTSGVMVVAISERAYTVLKRAFKYRTVD 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G P      I   + +  H G ++   +    K   ++++H+  ++ F    
Sbjct: 169 KRYHALVQGHPDPSSGTIDAPIGR--HRGHEWKFAIT---KNGRHSLTHYDTLEAFV-AA 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L++   TGRTHQ+RVH   +  P  GD  Y A+ K      + ++ +LHAR +   HP
Sbjct: 223 SLLDVHLETGRTHQIRVHFAALHHPCCGDLVYGADPKLAKRLGL-DRQWLHARSLAFAHP 281

Query: 301 -EGGRLQITAPLPAHMVKTWDSLGFK 325
            +G R++I +P PA +      L  +
Sbjct: 282 ADGRRVEIVSPYPADLQHALKILRGE 307


>gi|313905836|ref|ZP_07839194.1| pseudouridine synthase, RluA family [Eubacterium cellulosolvens 6]
 gi|313469350|gb|EFR64694.1| pseudouridine synthase, RluA family [Eubacterium cellulosolvens 6]
          Length = 326

 Score =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 68/345 (19%), Positives = 135/345 (39%), Gaps = 49/345 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSG-QVRVDKKRVKFNNRIQSG 62
           M  +    +   +    +  + +      +   L  +      + V+        ++Q+G
Sbjct: 1   MERIFRYEITEQDAGKDIHEFLRG--KKYSRHILASMKPDKTAILVNGVHEFMCYKLQTG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V++               +++D   ++      +   ++YED  + + +KPAG ++   
Sbjct: 59  DVLQ--------------TRVVDPKSSVNIRPAPVPFSVIYEDEDVLIVDKPAGQAIHPA 104

Query: 123 -SGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S  A  +   L  +   KG     R  +RLD++T+G+L+VA+   +A  L +    R I
Sbjct: 105 ISHPADTLANGLAWYYQQKGIPFVVRCINRLDRDTTGLLIVAKNLVSACVLEQDLLARNI 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-- 237
            + Y ++  G    +   I   + +K     +       +E   + A++HF     +   
Sbjct: 165 HRTYLAIAEGELP-ESGTINLPIARKEGSLIER----CVDEDRGDRAVTHFFRKGYYPPA 219

Query: 238 ----------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
                             +  ++++  TGRTHQ+RVH  H G P++GD  Y  ++     
Sbjct: 220 TNASPESVSTGSVKNRNGYSLVQLKLETGRTHQIRVHLSHTGHPLLGDTLYHPDYLRTPE 279

Query: 282 SPI-----QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            PI      N+  LH+  ++  HP  G  +   AP+P  M K   
Sbjct: 280 DPIPEGLPINRQALHSWQLEFTHPITGEAMHFEAPIPEDMRKLLR 324


>gi|26553465|ref|NP_757399.1| pseudouridine synthase [Mycoplasma penetrans HF-2]
 gi|26453471|dbj|BAC43803.1| pseudouridine synthase [Mycoplasma penetrans HF-2]
          Length = 301

 Score =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 66/324 (20%), Positives = 133/324 (41%), Gaps = 35/324 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + ++ +EEN  L  +    +  ++   + K +++G ++V+ K+  +N ++Q    ++
Sbjct: 1   MIQIFIKKEEENQILKDFISKSFKELSLSKISKSIKNGDIKVNHKKTTWNYKLQENDSLQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I   +          K +   + L          ++YED  I V NKP G+  Q      
Sbjct: 61  IFLRL----------KPIKKELKLNFLEAKPILNVIYEDKNIIVVNKPRGLICQPDKNEK 110

Query: 127 -YHIDGFLKSWV----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++  +K ++    D    +  L HRLD+ T+G+ V A+ +     L   +    + K
Sbjct: 111 IDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQKTLTELNNLWNTEAVSK 170

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y  L +G  K K + + +++          +  + +  K     I+ ++VI+   +   
Sbjct: 171 YYLCLCYGKFKKKSDTLKDFIFLNEE---KQIMEIDRENKFNKEIITKYRVIE-QKKDMA 226

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE+Q  TG+ HQ+RVH   +G P++GD KY       F  P      L +  +     +
Sbjct: 227 LLEIQLLTGKKHQIRVHMASIGHPVLGDTKYNKKGNFGFQFP-----CLTSYKIKFNFDK 281

Query: 302 GGRLQITAPLPAHMVKTWDSLGFK 325
                       H +   + L  +
Sbjct: 282 N-----------HFLHYLNKLNLE 294


>gi|167968095|ref|ZP_02550372.1| pseudouridylate synthase [Mycobacterium tuberculosis H37Ra]
 gi|215445738|ref|ZP_03432490.1| pseudouridylate synthase [Mycobacterium tuberculosis T85]
 gi|260186491|ref|ZP_05763965.1| hypothetical protein MtubCP_10749 [Mycobacterium tuberculosis
           CPHL_A]
 gi|260204826|ref|ZP_05772317.1| hypothetical protein MtubK8_11038 [Mycobacterium tuberculosis K85]
 gi|294996507|ref|ZP_06802198.1| hypothetical protein Mtub2_18881 [Mycobacterium tuberculosis 210]
 gi|297731096|ref|ZP_06960214.1| hypothetical protein MtubKR_08397 [Mycobacterium tuberculosis KZN
           R506]
 gi|308370756|ref|ZP_07422607.2| hypothetical protein TMCG_02690 [Mycobacterium tuberculosis
           SUMu003]
 gi|308371993|ref|ZP_07426975.2| hypothetical protein TMDG_02186 [Mycobacterium tuberculosis
           SUMu004]
 gi|308373178|ref|ZP_07431294.2| hypothetical protein TMEG_01448 [Mycobacterium tuberculosis
           SUMu005]
 gi|308374339|ref|ZP_07435673.2| hypothetical protein TMFG_00637 [Mycobacterium tuberculosis
           SUMu006]
 gi|308375610|ref|ZP_07444499.2| hypothetical protein TMGG_00098 [Mycobacterium tuberculosis
           SUMu007]
 gi|308376755|ref|ZP_07439920.2| hypothetical protein TMHG_00734 [Mycobacterium tuberculosis
           SUMu008]
 gi|308330950|gb|EFP19801.1| hypothetical protein TMCG_02690 [Mycobacterium tuberculosis
           SUMu003]
 gi|308334771|gb|EFP23622.1| hypothetical protein TMDG_02186 [Mycobacterium tuberculosis
           SUMu004]
 gi|308338559|gb|EFP27410.1| hypothetical protein TMEG_01448 [Mycobacterium tuberculosis
           SUMu005]
 gi|308342261|gb|EFP31112.1| hypothetical protein TMFG_00637 [Mycobacterium tuberculosis
           SUMu006]
 gi|308345756|gb|EFP34607.1| hypothetical protein TMGG_00098 [Mycobacterium tuberculosis
           SUMu007]
 gi|308350056|gb|EFP38907.1| hypothetical protein TMHG_00734 [Mycobacterium tuberculosis
           SUMu008]
          Length = 303

 Score =  195 bits (497), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 75/322 (23%), Positives = 140/322 (43%), Gaps = 30/322 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +    MR+D         ++      +   G V ++      ++R+ SG ++++    
Sbjct: 3   VPDGLAGMRVDTGLARLL-GLSRTAAAALAEEGAVELNGVPAGKSDRLVSGALLQV---- 57

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG-IAYHI 129
                     ++ ++   L      ++ + +LY D  I   +KPA ++     G     +
Sbjct: 58  ----------RLPEAPAPLQNTPIDIEGMTILYSDDDIVAVDKPAAVAAHASVGWTGPTV 107

Query: 130 DGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R + K Y 
Sbjct: 108 LGGLAAAGYRITTSGVHERQGIVHRLDVGTSGVMVVAISERAYTVLKRAFKYRTVDKRYH 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G P      I   + +  H G ++   +    K   ++++H+  ++ F      L+
Sbjct: 168 ALVQGHPDPSSGTIDAPIGR--HRGHEWKFAIT---KNGRHSLTHYDTLEAFV-AASLLD 221

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
           +   TGRTHQ+RVH   +  P  GD  Y A+ K      + ++ +LHAR +   HP +G 
Sbjct: 222 VHLETGRTHQIRVHFAALHHPCCGDLVYGADPKLAKRLGL-DRQWLHARSLAFAHPADGR 280

Query: 304 RLQITAPLPAHMVKTWDSLGFK 325
           R++I +P PA +      L  +
Sbjct: 281 RVEIVSPYPADLQHALKILRGE 302


>gi|194015109|ref|ZP_03053726.1| YhcT [Bacillus pumilus ATCC 7061]
 gi|194014135|gb|EDW23700.1| YhcT [Bacillus pumilus ATCC 7061]
          Length = 302

 Score =  195 bits (497), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 139/327 (42%), Gaps = 32/327 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M +  +   + V+    +  L  + K      +   +   +   +VR+++K      ++ 
Sbjct: 1   MIIKGHTLSLKVDEQYHHTSLSHFLKTAVF-ASKPIIHFWMEHQKVRLNQKPAHHAAKVS 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + I       + +  E   L+               +L+ED  + +  KPAG    
Sbjct: 60  QGDQIIIDLFETEESDVTPEYGELE---------------VLFEDEHLLIVQKPAGRPTH 104

Query: 121 GG-SGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               G    +   +     + G+  + R  HRLDQ+TSG ++ A+ R A   L +    +
Sbjct: 105 PNEQGQTGTLANLVAFHFQANGEEKRVRHIHRLDQDTSGTVIFAKHRLAHAALDQMLSKK 164

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I++ Y ++  G+ K KK  I   + +  H       V ++       A++HF+V+D   
Sbjct: 165 TIKRTYIAIAEGLFKKKKGTIDAAIGRDKHHA-----VRRRISPNGQKAVTHFQVMDMNK 219

Query: 238 Q-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           + +   +++Q  TGRTHQ+RVH   +G P+ GD  Y      +      N+  LHA+ +D
Sbjct: 220 RLQLTAVKLQLETGRTHQIRVHLSSLGHPLAGDTLY------DGVRDYINRCALHAKQVD 273

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + HP  G  L I APLP  M +    +
Sbjct: 274 MKHPFTGEHLIIEAPLPPDMDQLMSQI 300


>gi|298525052|ref|ZP_07012461.1| conserved hypothetical protein [Mycobacterium tuberculosis
           94_M4241A]
 gi|298494846|gb|EFI30140.1| conserved hypothetical protein [Mycobacterium tuberculosis
           94_M4241A]
          Length = 308

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 75/326 (23%), Positives = 142/326 (43%), Gaps = 30/326 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V +    MR+D         ++      +   G V ++      ++R+ SG ++++
Sbjct: 4   RSMPVPDGLAGMRVDTGLARLL-GLSRTAAAALAEEGAVELNGVPAGKSDRLVSGALLQV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG-I 125
                         ++ ++   L      ++ + +LY D  I   +KPA ++     G  
Sbjct: 63  --------------RLPEAPAPLQNTPIDIEGMKILYSDDDIVAVDKPAAVAAHASVGWT 108

Query: 126 AYHIDGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              + G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R + 
Sbjct: 109 GPTVLGGLAAAGYRITTSGVHERQGIVHRLDVGTSGVMVVAISERAYTVLKRAFKYRTVD 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G P      I   + +  H G ++   +    K   ++++H+  ++ F    
Sbjct: 169 KRYHALVQGHPDPSSGTIDAPIGR--HRGHEWKFAIT---KNGRHSLTHYDTLEAFV-AA 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L++   TGRTHQ+RVH   +  P  GD  Y A+ K      + ++ +LHAR +   HP
Sbjct: 223 SLLDVHLETGRTHQIRVHFAALHHPCCGDLVYGADPKLAKRLGL-DRQWLHARSLAFAHP 281

Query: 301 -EGGRLQITAPLPAHMVKTWDSLGFK 325
            +G R++I +P PA +      L  +
Sbjct: 282 ADGRRVEIVSPYPADLQHALKILRGE 307


>gi|47779342|gb|AAT38571.1| predicted ribosomal large subunit pseudouridine synthase D
           [uncultured gamma proteobacterium eBACHOT4E07]
          Length = 311

 Score =  195 bits (496), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 68/324 (20%), Positives = 133/324 (41%), Gaps = 36/324 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  D    R D+     +   +   L+K +  G+V ++ +       + +   + + P+ 
Sbjct: 7   ITEDLSMERFDKACALIFNDYSRSQLKKWIIEGRVLLNNEIASPKEIVTTDDEISLNPIF 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHI 129
             +     E                +   +++ED    + NKP+ + +  GSG       
Sbjct: 67  KKIIQWEPEN---------------IDFEVVHEDENFLIINKPSKLVIHPGSGCDSGTLA 111

Query: 130 DGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +G L  + + +K  +  + HRLD++TSGIL+VART     +     + R+++KIY ++V 
Sbjct: 112 NGLLFKYPELNKMPRAGIVHRLDKDTSGILLVARTEKFRNYFVSLLQERKVKKIYKAVVV 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQP 247
           G        I         IG D  + +K + +     AIS  K+ +     +  +++  
Sbjct: 172 GK-------IIGSFQINEPIGRDKTNRIKMSIRSDGKEAISFVKLHESLG-NYSVVDVSI 223

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQN--KLYLHARYMDLPH 299
            TGRTHQ+RVH  +   PI+GD  Y +            T  I++  +  LH+  +    
Sbjct: 224 ETGRTHQIRVHLANKKLPIIGDKTYNSAGNIAKETSQELTESIRSFPRQALHSCNLSFKD 283

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
                 +   + LP  +    +++
Sbjct: 284 MSSDNIISFESDLPNDIKTLINTI 307


>gi|303252861|ref|ZP_07339020.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307247850|ref|ZP_07529886.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|302648291|gb|EFL78488.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306855652|gb|EFM87819.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
          Length = 247

 Score =  195 bits (496), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 60/250 (24%), Positives = 111/250 (44%), Gaps = 18/250 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELEILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPVHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ ++E F   +++K Y ++V G   +K E      +    I   +    
Sbjct: 61  VLLFALNSKMARLMSEQFEQHQLEKGYLAVVRGYLLDKGEIDYPLKVILDKIADKFSQ-- 118

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               K A  A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 ---PKEAQQAVTFYQNLASVEMLYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI 175

Query: 267 VGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD KY    +    +     ++L LH+ ++   HP+   +++I APL       + +  
Sbjct: 176 IGDTKYGDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLDKQWQNLFATFN 235

Query: 324 FKYDRNLYIK 333
           + +      +
Sbjct: 236 WNFPTFFQSE 245


>gi|215411202|ref|ZP_03420010.1| pseudouridylate synthase [Mycobacterium tuberculosis 94_M4241A]
          Length = 303

 Score =  195 bits (496), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 75/322 (23%), Positives = 140/322 (43%), Gaps = 30/322 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +    MR+D         ++      +   G V ++      ++R+ SG ++++    
Sbjct: 3   VPDGLAGMRVDTGLARLL-GLSRTAAAALAEEGAVELNGVPAGKSDRLVSGALLQV---- 57

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG-IAYHI 129
                     ++ ++   L      ++ + +LY D  I   +KPA ++     G     +
Sbjct: 58  ----------RLPEAPAPLQNTPIDIEGMKILYSDDDIVAVDKPAAVAAHASVGWTGPTV 107

Query: 130 DGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            G L +           ++  + HRLD  TSG++VVA +  A   L  +F+ R + K Y 
Sbjct: 108 LGGLAAAGYRITTSGVHERQGIVHRLDVGTSGVMVVAISERAYTVLKRAFKYRTVDKRYH 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G P      I   + +  H G ++   +    K   ++++H+  ++ F      L+
Sbjct: 168 ALVQGHPDPSSGTIDAPIGR--HRGHEWKFAIT---KNGRHSLTHYDTLEAFV-AASLLD 221

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
           +   TGRTHQ+RVH   +  P  GD  Y A+ K      + ++ +LHAR +   HP +G 
Sbjct: 222 VHLETGRTHQIRVHFAALHHPCCGDLVYGADPKLAKRLGL-DRQWLHARSLAFAHPADGR 280

Query: 304 RLQITAPLPAHMVKTWDSLGFK 325
           R++I +P PA +      L  +
Sbjct: 281 RVEIVSPYPADLQHALKILRGE 302


>gi|326504872|dbj|BAK06727.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 472

 Score =  195 bits (496), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 104/378 (27%), Positives = 161/378 (42%), Gaps = 83/378 (21%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDK-----------------KRVKFNNRIQSGQVV 65
           RW +   P +    +QK+ R  +V+ +                  +RV   + +  G  +
Sbjct: 95  RWVRRCCPDLPASLVQKLFRLRKVKKNAVTAETSSTHASAEQFRLRRVSAKDHLLPGDTL 154

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +P  I   +   K +K  + +       DFL+S+ +Y+D  I V NKP G+ VQGG GI
Sbjct: 155 FLPVNIQESSVAEKARKFDNRN-----EIDFLRSLEIYKDKAIIVVNKPPGMPVQGGVGI 209

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR------- 178
              ID     + ++    PRL HRLD++ SG+LV+ RT+ +A  L   FR +        
Sbjct: 210 KNSIDVLAPMFEENSSDAPRLVHRLDRDCSGVLVLGRTQLSASILHAIFREKTADALADG 269

Query: 179 ----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA---NYAISHFK 231
               +Q+ Y +LV G P++ K  ++  L K     G    +  +          A++ ++
Sbjct: 270 TQQVLQRKYVALVMGTPRHPKGLLSAPLAKVLLQDGKSERLTVRAGPNTTSVQDALTEYR 329

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNFT--------- 281
           VI+   Q F WLE+ P TGR HQLRVH    +G PIVGD+KY      ++T         
Sbjct: 330 VIESCPQGFTWLELFPLTGRKHQLRVHCAEVLGTPIVGDYKYGRQAHQDWTPLPVSQTVD 389

Query: 282 --------------------SPIQNKLYLHARYMDLPHPEG-----------------GR 304
                               +  Q +L+LH + M LP                      +
Sbjct: 390 KELLRKQRLPFGLVLGGGSIAEQQPQLHLHCKQMMLPDISAAVQGLQSEDADRDFSDLEK 449

Query: 305 LQITAPLPAHMVKTWDSL 322
           L   APLP HM  +W+ L
Sbjct: 450 LSFVAPLPLHMRLSWEVL 467


>gi|160946974|ref|ZP_02094177.1| hypothetical protein PEPMIC_00936 [Parvimonas micra ATCC 33270]
 gi|158447358|gb|EDP24353.1| hypothetical protein PEPMIC_00936 [Parvimonas micra ATCC 33270]
          Length = 318

 Score =  195 bits (496), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 81/325 (24%), Positives = 138/325 (42%), Gaps = 35/325 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + V N++   R+DR+ K +  + +   +QK LR+ +++V++K+V  N  +    V+ 
Sbjct: 1   MRDIEVNNNDSGQRIDRFLKKYLNNASTSMIQKFLRTKKIKVNRKKVDSNYILAENDVIN 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I      L  +I             K+S   K  ++YED  I V NKP  +     S   
Sbjct: 61  IFIYEEELEKLI--------VSKSKKYSYSKKLDIIYEDENIIVMNKPKNLLSHASSKED 112

Query: 127 YHID--GFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           Y  +   F+  ++  KG           P + +RLD+ TSG+++ A+   A + L    +
Sbjct: 113 YGNNLVDFMIGYLLEKGDYNPRAEKTFVPAIINRLDRNTSGLVIGAKNSKALRELNR-LK 171

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I+K Y ++V G  K K   I   L K        +       K    +I+   V + 
Sbjct: 172 ENSIEKYYKTIVSGKVK-KNFVINEKLEKDEEKNKSTI------SKNGKDSITEIYV-EK 223

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNK-LYLHAR 293
              +F  L+++  TGRTHQ+R H    G  I+GD KY  A     F      +  +LHA 
Sbjct: 224 NNDEFSLLKIKLITGRTHQIRSHLSSKGFYIIGDIKYGNAKVNKFFRDNFNLRSQFLHAE 283

Query: 294 YMDLPHPEG-----GRLQITAPLPA 313
            +   +  G        +  AP+  
Sbjct: 284 TIIFKNIVGDLSYLNNKEFFAPMDE 308


>gi|266623222|ref|ZP_06116157.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           hathewayi DSM 13479]
 gi|288865005|gb|EFC97303.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           hathewayi DSM 13479]
          Length = 311

 Score =  195 bits (495), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 69/337 (20%), Positives = 145/337 (43%), Gaps = 36/337 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSG 62
           M      +++  +     +++  ++    +   ++++ R+   +  +   +   +R+  G
Sbjct: 1   MKTTMTYLIQQHDTQKTAEQFLLSN--GYSAALIRRLRRTEHSILKNGSPIYTTHRLNEG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +          + E    ++ + +      +   + YED  + + NK AG+ +   
Sbjct: 59  DTLSVT---------LPEDHGSENILPIP-----MDLDICYEDRDLLIINKAAGVPIHPS 104

Query: 123 SG-IAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            G     +   +  ++  KG+    R  +RLD++T+G+L++AR   +A  L+E  R   I
Sbjct: 105 QGNHDNTLANGIAWYLGEKGETAAYRAINRLDRDTTGLLILARHALSACILSEMVRTHAI 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +   G+   +   I   + +    G   +      E+G + A +H++ +      
Sbjct: 165 RRCYLAAATGLVPPE-GVIDAPIAR---AGTSTIERCVDFERG-DSARTHYRTLCYNPDT 219

Query: 240 FC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            C  +E++  TGRTHQ+RVH  H+G P+ GD  Y  +++      +  +  LH+  +D  
Sbjct: 220 NCSLVELRLETGRTHQIRVHMKHIGHPLPGDFLYNPDYR------LIGRQALHSWQLDFI 273

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
           HP     L   APLP  M   +   G      LY +R
Sbjct: 274 HPIKKEPLHFEAPLPDDMRPLF---GMDLPLALYSQR 307


>gi|19704361|ref|NP_603923.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|19714613|gb|AAL95222.1| tRNA pseudouridine synthase A [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 289

 Score =  195 bits (495), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 80/300 (26%), Positives = 150/300 (50%), Gaps = 20/300 (6%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ + E +R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G VV I   
Sbjct: 5   IIDEEYEKVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDVVFIFLP 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            N   +   E+K ++ S    +  + LK ++++E+  ++V NK  G  V  GSG    + 
Sbjct: 65  ENFKEN--NEEKFIELS---QERKEKLKEMIVFENENLFVINKLLGDVVHKGSGHDISLL 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+ LV G 
Sbjct: 120 EEFRSYYSNNNIN--FVNRIDKLTSGLIIGAKNIKTAREVAKEIQADNIIKRYYILVNGK 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +     + N+L K      + V V    ++G   +I++FK I     K+  LE +  TG
Sbjct: 178 IEKDNFILENYLKKDE----EKVIVSDIEKEGYKKSITYFKKIKEH-NKYTLLEAELKTG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLR    H+G  IVGD KY  + + +        L+ +   +DL +     +++  P
Sbjct: 233 RTHQLRAQLNHIGNNIVGDTKYGKDEREDMMY-----LFSYYLKIDLYNL---EIKLEIP 284


>gi|154491501|ref|ZP_02031127.1| hypothetical protein PARMER_01111 [Parabacteroides merdae ATCC
           43184]
 gi|154088302|gb|EDN87347.1| hypothetical protein PARMER_01111 [Parabacteroides merdae ATCC
           43184]
          Length = 303

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 63/316 (19%), Positives = 121/316 (38%), Gaps = 38/316 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVR 66
           + V V+ +     L  +        +  +++ +L  GQ+ V+     +FN  +  G  V 
Sbjct: 19  RKVTVKEEN---TLLPFLFGLLNEQSKSSVKALLAHGQISVNGTVTSQFNTPLTPGNEVL 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           I      +                    +     +++ED  + V NK  G+     + + 
Sbjct: 76  ISYERGKV------------------EFNNPLLTIVWEDDDLIVVNKKEGLLSVSSTRVK 117

Query: 126 AYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                  L  +V       K  + HRLD++TSG+++ A+     + L  ++      + Y
Sbjct: 118 ERTALHLLSEYVKKTDPRNKIFVLHRLDRDTSGLMMFAKNLQVQKALQSNWNSAITARTY 177

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G P+   + I + L + +      + V    E     AI+ ++++      +  L
Sbjct: 178 VAVVEGRPEKDSDLIVSNLTENAK-----MQVYVTAEGDGKEAITRYRLLHSNG-AYSLL 231

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E+   TGR +Q+R     +G  I GD+KY A            +L LHAR ++  HP  G
Sbjct: 232 ELDLETGRKNQIRAQMQSIGHSIAGDYKYGAETDPT------GRLMLHARRLNFIHPVTG 285

Query: 304 -RLQITAPLPAHMVKT 318
             +     +P      
Sbjct: 286 EEMHFETRIPDKFTSL 301


>gi|313678812|ref|YP_004056552.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma bovis PG45]
 gi|312950691|gb|ADR25286.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma bovis PG45]
          Length = 305

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 59/310 (19%), Positives = 134/310 (43%), Gaps = 41/310 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR--VKFNNRIQSGQVVRIPPVINALNH 76
            R+D++  ++   I   + + ++    V +D K+   K N  ++ G V+ I  ++    +
Sbjct: 10  ERIDKYISDN-SEITRNDAKALIEQEAVYIDDKKFVRKPNYMVREGMVITILRLLEKETN 68

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLK 134
           I                +  +   + YED  + V NKP+G+ V    G       +  + 
Sbjct: 69  I---------------EAVNMPLDIRYEDDNLLVLNKPSGLVVHPAPGHLNDTLVNALMY 113

Query: 135 SWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            + ++        +  + HR+D++TSG+L++A+       L +  +  +I++ Y ++  G
Sbjct: 114 HFKNNLSDTNGLLRLGIVHRIDKDTSGLLIIAKDNETHNELAKMLKNHQIKRTYIAICKG 173

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQ 246
           I  NK   I   + + +      + +     K    ++++  ++  F    + +  ++ +
Sbjct: 174 ILPNKVTKINLPIQRDAK-NRKLMSI----HKDGKSSVTYVHLLKTFYIDNKPYSLVKCE 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  ++  P+ GD+ Y ++           +L  HA  +   HP   + +
Sbjct: 229 LETGRTHQIRVHLAYIKHPVYGDNIYGSHVDD-----FNQRL--HAYRLSFIHPISKKQV 281

Query: 306 QITAPLPAHM 315
            + + +P+  
Sbjct: 282 DVYSDIPSEF 291


>gi|308068083|ref|YP_003869688.1| Pseudouridylate synthase, 23S RNA-specific [Paenibacillus polymyxa
           E681]
 gi|305857362|gb|ADM69150.1| Pseudouridylate synthase, 23S RNA-specific [Paenibacillus polymyxa
           E681]
          Length = 337

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 133/319 (41%), Gaps = 37/319 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVR 66
           +  +V+   E   L  +   H   +   +++  L  GQV V+       N  ++ GQ V 
Sbjct: 51  KTYIVQEPAE---LLSFLVEHVTGMGRNSIKSALARGQVSVNGIPRTVHNFPLEQGQTVA 107

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--- 123
           +                  S   +T         +L+ED  I V +K AG+     +   
Sbjct: 108 L------------------SKEKVTPVVPLTGLRILHEDEAIIVIHKDAGLLSVASAQEQ 149

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            +  +         +    +  + HRLD++TSG+++ A++ A  Q + ++++    ++ Y
Sbjct: 150 EVTAYRQLTAHVRREHPYNRIFVLHRLDRDTSGVMMFAKSEAIQQEMQKAWKEVVYERTY 209

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G  K  +  I +WL                      +A++H+K++    + F  L
Sbjct: 210 IALVEGQVKKAEGTITSWL----KESKTLKMYSSPYPNDGQHAVTHYKLLQAN-RHFSLL 264

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E++  TGR +Q+RVH   +G PIVGD KY +  K         +L LHAR +   HP  G
Sbjct: 265 EVRLETGRKNQIRVHMEDIGHPIVGDKKYGSKSKS------IGRLGLHARLLSFIHPVTG 318

Query: 304 R-LQITAPLPAHMVKTWDS 321
             L+  + +P   +  +  
Sbjct: 319 VLLRFESDIPKTFLNPFRE 337


>gi|159906031|ref|YP_001549693.1| RluA family pseudouridine synthase [Methanococcus maripaludis C6]
 gi|159887524|gb|ABX02461.1| pseudouridine synthase, RluA family [Methanococcus maripaludis C6]
          Length = 297

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 68/327 (20%), Positives = 139/327 (42%), Gaps = 36/327 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     +  +  ++     +L    K+++  ++   ++K  +  ++ V+ K +   ++++
Sbjct: 1   MESQKKILKITADSKIAGNKLIDVLKDNF-ELSNKMIKKFDKEKKIFVNSKIISLKSKLK 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
             + V +                +D  +N     + L   ++YED  + + +KP  + V 
Sbjct: 60  ENETVSVE---------------IDCGIN-NIDPEELPLNVIYEDDDLLIVDKPKNMVVH 103

Query: 121 GGSGIAYHIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               +              ++++  K R   RLD +T+G+L++A+   + QHL +     
Sbjct: 104 PTKNVLSKTLANAISNHQKINNQNYKIRFVSRLDMDTTGLLIIAKNSYSHQHLAKQMDEG 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            ++KIY ++V G    K+  I + + L    I  +  +           + + +KVI+  
Sbjct: 164 ILEKIYVAVVNGRLDLKEGIIEDSIDLNDDGIKRELSN-------SGKISKTKYKVIEEL 216

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    LE+   TGRTHQ+RVH   +G  I+GD  Y        TS + ++  LH+  + 
Sbjct: 217 -KNASVLEINLLTGRTHQIRVHLSSLGNYILGDILYGK------TSKLIDRQALHSHILR 269

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWDSL 322
             HP    R + T+ LP  M     +L
Sbjct: 270 FIHPITKERKEFTSKLPDDMENLIKNL 296


>gi|182417587|ref|ZP_02948909.1| pseudouridine synthase, RluA family [Clostridium butyricum 5521]
 gi|237668273|ref|ZP_04528257.1| pseudouridine synthase, RluA family [Clostridium butyricum E4 str.
           BoNT E BL5262]
 gi|182378542|gb|EDT76071.1| pseudouridine synthase, RluA family [Clostridium butyricum 5521]
 gi|237656621|gb|EEP54177.1| pseudouridine synthase, RluA family [Clostridium butyricum E4 str.
           BoNT E BL5262]
          Length = 324

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 70/327 (21%), Positives = 137/327 (41%), Gaps = 35/327 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + + ++E   RLD++ +     +    + K LR   +RV+ K+      ++ G +V I  
Sbjct: 3   IEIGSNEAGQRLDKFLRKLLKDVPLSAIFKALRKKDIRVNGKKQNEKYFLEEGDIVEIKY 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
           + +      ++   +D            +  + +ED  + +  K  GI V   +      
Sbjct: 63  IQSKKEDKTQKFIKVDPK----------RMKICFEDENMVIVEKWPGILVHSDTNDNKEP 112

Query: 128 HIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            +  ++ S+++ KG           P   +RLD+ TSGI++  +T    + + E+ R   
Sbjct: 113 TLTDYVLSYLNDKGDYLPENEITFTPAACNRLDRNTSGIIMYGKTFEGLKCINEAIREDE 172

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y++L  G    K      +++K          V  +  K +        V++    
Sbjct: 173 VKKYYYTLAKGKV--KSGLYEGYIVKNPETN--ISTVYDKEVKNSKKIAMDVNVVETNG- 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMD 296
            + ++E+   TGR+HQ+R H  H+G PI+GD+KY      +F  +    N  YL+A  ++
Sbjct: 228 AYSFVEINLITGRSHQIRAHLAHVGNPIIGDNKYGDKKLNSFFESKYGLNYQYLYAYKLN 287

Query: 297 LPHPEGGRLQ------ITAPLPAHMVK 317
                 G+L+      I   LP    K
Sbjct: 288 FR-KIKGKLEYLDNKTIAVALPPLFKK 313


>gi|262382346|ref|ZP_06075483.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_33B]
 gi|262295224|gb|EEY83155.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_33B]
          Length = 304

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 60/297 (20%), Positives = 118/297 (39%), Gaps = 35/297 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        +  +++ +L  GQ+ V+ K  + F+  +     V I      +        
Sbjct: 33  FLFELLKEQSRSSVKGLLSRGQISVNGKVTRQFDAALNPNDTVGINYGRGKV-------- 84

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKG 141
                       +     +++ED  + V NK  G+       +        L  +V    
Sbjct: 85  ----------EFNNPLLRIVWEDDDLIVINKREGLLSVSTDRVKERTAYRLLSDYVKQSD 134

Query: 142 Q--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              K  + HRLD++TSGI++ A+ +   + L  ++     Q+ Y +++ G P+   + I 
Sbjct: 135 PRNKIFVLHRLDRDTSGIMMFAKNQGVKEQLQSNWSEMITQRTYVAVIEGRPEKDTDLIV 194

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + L++  +     + V    E     AI+ ++++      +  LE++  TGR +Q+R   
Sbjct: 195 SNLVENKN-----MQVYVTLEGDGKEAITRYRLLQTN-NSYSLLELELETGRKNQIRAQM 248

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
             +G P+ GD KY A            +L LHAR +   HP  G  ++    +P   
Sbjct: 249 QSIGHPVAGDTKYGAETNPA------GRLMLHARKLCFIHPVTGEEMRFETRIPEIF 299


>gi|256845300|ref|ZP_05550758.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_36A2]
 gi|256718859|gb|EEU32414.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_36A2]
          Length = 290

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 80/300 (26%), Positives = 146/300 (48%), Gaps = 20/300 (6%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ D E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G +V I   
Sbjct: 5   IIDEDYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDIVFIF-- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
              L    KE              + LK ++++E+  ++V NK  G  V  GSG    + 
Sbjct: 63  ---LPESFKENNEKKFIELNQVRKEKLKQMIVFENENLFVINKSLGDVVHKGSGHDISLL 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +S+  +        +R+D+ TSG+++ A+    A+ + +  +   I K Y+ LV G 
Sbjct: 120 EEFRSYYSNNNIN--FVNRIDRLTSGLVIGAKNIKTARDIAKEIQAGNIVKKYYILVNGK 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +     + N+L K      + V V    ++G   +I++FK I  +  ++  LE +  TG
Sbjct: 178 IEKDNFILENYLKKDE----EKVIVSDIEKEGYKKSITYFKKIKEY-DRYTLLEAELKTG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLR    H+G  IVGD KY  N K +        L+ +   +DL +     +++  P
Sbjct: 233 RTHQLRAQLNHIGNNIVGDTKYGRNEKEDIMY-----LFSYYLKIDLYNL---EIKLEIP 284


>gi|229541367|ref|ZP_04430427.1| pseudouridine synthase, RluA family [Bacillus coagulans 36D1]
 gi|229325787|gb|EEN91462.1| pseudouridine synthase, RluA family [Bacillus coagulans 36D1]
          Length = 290

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 67/310 (21%), Positives = 120/310 (38%), Gaps = 39/310 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +  DE +  L  + K    HI+   L  I  R G + V+ + V    R+Q G    I  
Sbjct: 7   TITEDEAHQELKEFLKAR--HISKRALADIKFRGGMILVNGREVTVRYRLQPGDAAAI-- 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                            + +     + +    +YED  + V +KPA ++         H 
Sbjct: 63  ------------VFPKETPSPNLTPENIPFGHVYEDESVLVADKPAFMNTIPSR---EHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              L + V    +K        +  RLD+ TSG++++A+ R      +   +   I + Y
Sbjct: 108 SASLANAVLGHYRKNGIESAVHVVTRLDRNTSGLVLIAKNRYIHHLCSLMQQKHVICRTY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L  G    K   I   + +K     +   + +       +A +H++V+  F   +  +
Sbjct: 168 EALAEGAFTEKSGTIEAPIGRK-----ETSIIERGVRDDGQFARTHYEVVRQFP-AYAHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++  TGRTHQ+RVH  ++G P++GD  Y  N           +  LH   +   HP  G
Sbjct: 222 RLRLDTGRTHQIRVHLSYIGHPLLGDSLYGGNTSR------FTRQALHCSELSFQHPVSG 275

Query: 304 -RLQITAPLP 312
             +   +  P
Sbjct: 276 KEMHFFSKPP 285


>gi|270290798|ref|ZP_06197022.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
 gi|270280858|gb|EFA26692.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
          Length = 304

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 73/314 (23%), Positives = 131/314 (41%), Gaps = 25/314 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT+  ++ ++       L    +  +  ++   +  +    +V V+++    +  +++G 
Sbjct: 1   MTWTYHIKLDQSYSPQTLRELLQKTWW-LSRKVVHFLRTERRVLVNQRYQPVSTVVRTGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ +    +  +  +       S              +L+E+  + V NKPAGI      
Sbjct: 60  LISLTFKESDFSTPLPPFDPDSSQ----------SPDVLFENDDLLVVNKPAGIKTHANQ 109

Query: 124 GIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                 +  FL+++   K       HRLDQ TSG L+VA+       L+     + IQ+ 
Sbjct: 110 PHELGSMINFLQAYFAKKDSNAYNVHRLDQWTSGALLVAKNPVVVPILSRQISQKLIQRT 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  +V G  K++   I   +    H           N  GA  A +H++V+  F ++   
Sbjct: 170 YLCVVEGHLKSRSGTITLPIGLDPHDQRKRQ----INGPGAQPATTHYQVVREFVER-SL 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L +Q  TGRTHQ+RVH   +G PIVGD  Y +   G         + LH+  +  P P  
Sbjct: 225 LRVQLATGRTHQIRVHLAALGHPIVGDPLYNSLADGA-------PMRLHSWQVKFPLPFS 277

Query: 303 G-RLQITAPLPAHM 315
                +TAP+P + 
Sbjct: 278 QSWQTVTAPVPNYF 291


>gi|261367348|ref|ZP_05980231.1| ribosomal large subunit pseudouridine synthase D [Subdoligranulum
           variabile DSM 15176]
 gi|282570108|gb|EFB75643.1| ribosomal large subunit pseudouridine synthase D [Subdoligranulum
           variabile DSM 15176]
          Length = 299

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 64/329 (19%), Positives = 136/329 (41%), Gaps = 43/329 (13%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRI 67
           + VV ++ E  RL  + +     +    ++ +  +GQ    D + +  + ++ +GQ +  
Sbjct: 4   HYVVPSEAEGQRLGLFLRTC--GVTAGLIKSVKHTGQGFFADGQALHTDQKVHAGQCITF 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIA 126
                           L      +     +   ++YED    V +KPAG++V    +   
Sbjct: 62  ---------------ALPPEPATSVIPQPIPLSIVYEDEFAAVLDKPAGLAVHPTLNYPD 106

Query: 127 YHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           + +      ++ S+G+    R  +R+D+ TSG+++ A+   AA  L       + +K Y 
Sbjct: 107 HTLANGWIYYLQSQGKNGVFRPVNRIDKNTSGLVLCAQNAFAAPLLA-----GQAKKCYL 161

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G        +   + ++         + +       Y+++ + V+   A+    + 
Sbjct: 162 AIVQGSLPLGPGRVEAPIGRRGD-----SIIGRCVTPEGKYSLTEYTVLAASAE-HSLVA 215

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             P TGRTHQ+RVH  ++G P+ GD  Y  N +         +  LH   +   HP   +
Sbjct: 216 CIPRTGRTHQIRVHMAYIGHPLAGDTLYGGNIRR------IGRHALHCAVLHFVHPVTRK 269

Query: 305 -LQITAPLPAHMVKTWDSL----GFKYDR 328
            ++++ P+P+ M     +     G+  D+
Sbjct: 270 PIRVSCPMPSDMEGLAQANYLLDGWSLDQ 298


>gi|237740738|ref|ZP_04571219.1| tRNA pseudouridine synthase A [Fusobacterium sp. 2_1_31]
 gi|229422755|gb|EEO37802.1| tRNA pseudouridine synthase A [Fusobacterium sp. 2_1_31]
          Length = 295

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 78/312 (25%), Positives = 154/312 (49%), Gaps = 24/312 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   +++ + E +R+DR+ + H  +I    + K+LR  +++V+ K+V  + R+  G ++ 
Sbjct: 1   MIEFIIDEEYETVRIDRFLRKHLKNIALSEIYKMLRKAKIKVNNKKVSQDYRLVLGDIIF 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +    +       E+K  ++ + L +   + LKS++ YE+  +++ NK  G  +  GSG 
Sbjct: 61  VFLPESF------EEKNEETFIELNEIRKEELKSMIAYENENLFIINKNLGDVIHKGSGH 114

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +    +S+      K    +R+D+ TSG+++ A+    A+ + +  ++  I K Y+ 
Sbjct: 115 DISLLEEFRSYY--SNNKINFVNRIDKLTSGLVIGAKNIKTAREIAKEIQLGNILKKYYI 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV+G  + ++  + N+L K      + V V    ++    +I+H+K I+     +  LE 
Sbjct: 173 LVYGKIEKEEFILENYLKKDE----EKVIVSDVEKEDYKKSITHYKRINGDND-YTLLEA 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +  TGRTHQLR    H+G  IVGD KY  N K +        L+ +   +DL       L
Sbjct: 228 ELKTGRTHQLRAQLNHLGHTIVGDTKYGKNIKEDIMY-----LFSYYLKIDLYD-----L 277

Query: 306 QITAPLPAHMVK 317
           ++   +P   +K
Sbjct: 278 ELELRIPNFFLK 289


>gi|116492157|ref|YP_803892.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
 gi|116102307|gb|ABJ67450.1| Pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
          Length = 296

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 66/273 (24%), Positives = 113/273 (41%), Gaps = 24/273 (8%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           +V V+ K V  N  +Q G ++ +    +  +  +       +             I+LYE
Sbjct: 41  RVLVNGKYVPVNTIVQGGDLIELNFESSDFDTPLPPFDPDFTQAP----------IILYE 90

Query: 105 DSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           +S + V NKP G+            +  FL+++      +    HRLDQ TSG L+VA+ 
Sbjct: 91  NSDLMVVNKPTGVKTHANQPHELGSMMNFLQAYFKDTENEAYNVHRLDQFTSGALLVAKN 150

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
                 L      + I + Y  +V G  +  K  I   +                N    
Sbjct: 151 PVVVPILNRQISTKVINRTYLCVVSGHLEQSKGTINVPIGFDPDDKRKRQI----NGLNP 206

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
             AI+H++V+  + +    +++   TGRTHQ+RVH  ++G PI+GD  Y           
Sbjct: 207 LSAITHYQVLAQY-ENSSLIQVDLETGRTHQIRVHLSYLGHPIIGDPLYN-------LDN 258

Query: 284 IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
            Q  + LH+  +  P P     +++TAP+P + 
Sbjct: 259 TQQPMLLHSWKIRFPLPFNLETIEVTAPIPDYF 291


>gi|225570461|ref|ZP_03779486.1| hypothetical protein CLOHYLEM_06562 [Clostridium hylemonae DSM
           15053]
 gi|225160658|gb|EEG73277.1| hypothetical protein CLOHYLEM_06562 [Clostridium hylemonae DSM
           15053]
          Length = 291

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 133/319 (41%), Gaps = 35/319 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQS 61
           M  +    +  + +   +  + K+     +   +  +     G  R      +  ++++ 
Sbjct: 1   MKRILDYCIPKEYDGTDILGFLKSR--GYSHTVITHLKHTPDGICR-GGAWARTCDKLRC 57

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + +               I +   +       L   ++YED  + V +KPAG+  Q 
Sbjct: 58  GDRLTVT--------------IEEKEGSAGIAPVSLPLHIIYEDEDLLVIDKPAGMPTQP 103

Query: 122 GSG-IAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             G     +   L  +   +G     R  +RLD+ TSG+L+VA+   +A  L    + RR
Sbjct: 104 SQGNHDNTLANALVCYYSRRGIPFTYRCINRLDKNTSGLLIVAKHMLSASILYAMIKERR 163

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y +L  G+    +  I   + ++S    +       +E    YA +H++ +D   +
Sbjct: 164 IHREYLALAEGL-TPSEGTITAPIARRSRSTIER----CVDETNGEYACTHYRRLDYR-K 217

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  L +   TGRTHQ+RVH  H+G P+ GD  Y  ++       I ++  LH+  +  P
Sbjct: 218 GYSLLSVTLDTGRTHQIRVHLKHIGHPLPGDFLYHPDY------TIISRQALHSCRLTFP 271

Query: 299 HPEGGR-LQITAPLPAHMV 316
           HP  GR +   +PLP  M 
Sbjct: 272 HPVTGRLMDFESPLPDDMR 290


>gi|302385721|ref|YP_003821543.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
 gi|302196349|gb|ADL03920.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
          Length = 307

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 133/319 (41%), Gaps = 33/319 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSG 62
           M       +    E M + ++  +     +   ++++  RS  + V  + V     ++ G
Sbjct: 1   MKLTMNYTITQTHEAMTVKQYLLDL--GYSQSLIRQLRSRSNGIVVGGEPVSSTRILKPG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +    +            +SS N+      +   + YED  I V NK AG+ +   
Sbjct: 59  DHLSVFICED------------ESSENIVPTP--MPLQIEYEDEHILVVNKEAGVPIHPS 104

Query: 123 SGIAYHID-GFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            G   H     +  +   +G+    R  +RLD++T+G+LV+A+   +A  L++  + R I
Sbjct: 105 QGNFDHTLANGMAYYFMKRGESFVYRAINRLDRDTTGLLVLAKNPLSACILSDMVQKREI 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-Q 238
           ++ Y ++  G P  +   I   + +   + G  +       +G   A +H+K +      
Sbjct: 165 RRRYLAITCGKPPLE-GTIDAPIAR---VDGSTIERCVDFIRGEK-ARTHYKRLYYDPVT 219

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               + +   TGRTHQ+RVH   +G P+ GD  Y  +++        ++  LH+  +D  
Sbjct: 220 GQSLVGLCLETGRTHQIRVHLKSIGYPLPGDFLYHPDYR------YISRQALHSFRLDFL 273

Query: 299 HPEGGR-LQITAPLPAHMV 316
           HP     L   APLP  M 
Sbjct: 274 HPIKKEPLSFEAPLPKDMQ 292


>gi|229084380|ref|ZP_04216660.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
 gi|228698920|gb|EEL51625.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
          Length = 307

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 129/323 (39%), Gaps = 32/323 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      M +D   K  +  I    L K+     + V+ +R  ++  +Q G  +++ 
Sbjct: 11  EITVPTKWSGMSIDSLLKEEW-GIPKKLLHKLRMEKGIIVNGERKVWSEMLQEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAY 127
                   +  E               +    +++ED  + + NKPA +     + G   
Sbjct: 70  MFAQEEYGVQPE---------------YGDLEVIFEDDHVLIVNKPAHMDTHPSNKGGTG 114

Query: 128 HIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +   +  +G   K R  HRLD++T+G +V A+   A   +      R I++ Y +
Sbjct: 115 TLANLVAFHLQMQGVETKVRHIHRLDKDTTGGVVFAKHGIAGVIMDRLLMERNIKRTYLA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLE 244
           LV G  + K+  I   + +  H         K      + A++H+K+   F  Q    + 
Sbjct: 175 LVEGKVRKKQGIIDEAIGRDRHHATRRRVSQK-----GDRAVTHYKIEKYFKKQDVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  H G P++GD  Y         +       LHA  +   HP    
Sbjct: 230 LQLETGRTHQIRVHMSHSGHPLIGDVLYGGQ------ATYMPYQALHAMRIHFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSLGFKY 326
            + + APLP ++    +S    +
Sbjct: 284 EITVEAPLPNNLNNIIESFKMSH 306


>gi|294785400|ref|ZP_06750688.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_27]
 gi|294487114|gb|EFG34476.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_27]
          Length = 290

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 79/300 (26%), Positives = 145/300 (48%), Gaps = 20/300 (6%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ D E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G +V I   
Sbjct: 5   IIDEDYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDIVFIF-- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
              L    KE              + LK ++++E+  ++V NK  G  V  GSG    + 
Sbjct: 63  ---LPESFKENNEKKFIELNQVRKEKLKQMIVFENENLFVINKSLGDVVHKGSGHDISLL 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +S+  +        +R+D+ TSG+++ A+     + + +  +   I K Y+ LV G 
Sbjct: 120 EEFRSYYSNNNIN--FVNRIDRLTSGLVIGAKNIKTTREIAKEIQQGNIIKKYFILVNGK 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +     + N+L K      + V V    ++G   +I++FK I  +  ++  LE +  TG
Sbjct: 178 IEKDNFILENYLKKDE----EKVIVSDIEKEGYKKSITYFKKIKEY-DRYTLLEAELKTG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLR    H+G  IVGD KY  N K +        L+ +   +DL +     +++  P
Sbjct: 233 RTHQLRAQLNHIGNNIVGDTKYGRNEKEDIMY-----LFSYYLKIDLYNL---EIKLEIP 284


>gi|251795307|ref|YP_003010038.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247542933|gb|ACS99951.1| pseudouridine synthase, RluA family [Paenibacillus sp. JDR-2]
          Length = 322

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 78/301 (25%), Positives = 131/301 (43%), Gaps = 38/301 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRI 67
           Y V E  E    L  +   H  +    +++ +L  GQV V+ +   K+N  +Q G+ V I
Sbjct: 27  YAVAEASE----LLAFLLAHL-NQGRNSVKSLLAHGQVYVNDRVETKYNYPLQPGETVVI 81

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIA 126
                     +                  +   +L+ED  + V +K AG+          
Sbjct: 82  RKEREKEKFPL------------------IGLTILHEDEHVIVASKEAGLLTIASDKETD 123

Query: 127 YHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                 L ++V     K R+   HRLD++TSG+L+ A++ A  Q L E ++    ++ Y 
Sbjct: 124 MTAYRQLMAYVRESDPKNRIFIVHRLDRDTSGVLMFAKSEAVQQKLQEEWQTIVKERSYV 183

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  K ++  I++WL                +     +A++H+K++    + F  +E
Sbjct: 184 ALVEGEVKRQEGTISSWL----KETKTLRMYSSPHPNDGQHAVTHYKLLQA-GKVFSLVE 238

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TGR +Q+RVH   +G PI GD KY +  K         +L LHAR +   HP  G+
Sbjct: 239 VHLETGRKNQIRVHMQDIGHPIAGDKKYGSTTKP------IGRLGLHARVLAFEHPVTGK 292

Query: 305 L 305
           L
Sbjct: 293 L 293


>gi|168703294|ref|ZP_02735571.1| RNA pseudouridylate synthase [Gemmata obscuriglobus UQM 2246]
          Length = 275

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 71/299 (23%), Positives = 131/299 (43%), Gaps = 36/299 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       +N   ++++LRSG+V V+   V + ++ ++    V           + +E  
Sbjct: 4   FLLAALAPMNRTRVKQLLRSGRVVVNGASVTRHDHTVRPADKV----------GVAREAP 53

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGFLKSWVDSK 140
               S +           +++ED+ + V +KP+G+         +               
Sbjct: 54  PAPPSAS--------GLEIVHEDAHLVVIDKPSGLLTVATESEKLDTAFVRLSDYLRARN 105

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
             +P + HRLD++TSG+L+ AR+      L  ++    + K Y ++V G P++ +  + N
Sbjct: 106 AGRPFVVHRLDRDTSGLLLFARSAEVRDQLQGNWEE--LTKTYLAVVEGRPESSEGGVEN 163

Query: 201 WLLKKSHIGGD-YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +L +    G D  V    +       A S + V       +  +E++  TGR HQ+RVH 
Sbjct: 164 YLTE----GRDLRVRASPRPGPDGKRAASRYTVRQTRG-GYSLVEVEIETGRKHQIRVHL 218

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVK 317
             +GCP+ GD  Y A      T+    +L LHA  +   HP    RL++ APLP+ + +
Sbjct: 219 AGLGCPVAGDKMYGA------TTDPVRRLGLHAWRLSFDHPFTLERLELEAPLPSALAR 271


>gi|312112210|ref|YP_003990526.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
 gi|311217311|gb|ADP75915.1| pseudouridine synthase, RluA family [Geobacillus sp. Y4.1MC1]
          Length = 309

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 63/298 (21%), Positives = 126/298 (42%), Gaps = 32/298 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            + +  +   ++   K  +   +     ++     ++++ K V +   ++    +++   
Sbjct: 12  TIPSFWQGQTIESLLKEVWCT-SKKFAHQLRMEKGIKLNGKEVSWQTTLRENDRLQLRLY 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HI 129
               + I+ E + +                +L+ED  + + NK AGI +          +
Sbjct: 71  HPEPSAILPEYREI---------------SVLWEDEHLLIINKEAGIDIHPSEPSQTGTL 115

Query: 130 DGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              +  ++ ++G   K R  HRLD++TSG ++ A+   A   L      R+I++ Y +LV
Sbjct: 116 ANAVAFYLQAQGILTKVRHIHRLDRDTSGTILFAKHPLAGATLDRMLEKRQIKRTYVALV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQ 246
            GI K+K   I+  + +  H          +  K    A++H++V+  F   +   +E+ 
Sbjct: 176 HGIVKHKSGTISAPIGRDRHHPTRR-----RVSKTGAKAVTHYRVLHTFLNDQASLVELS 230

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             TGRTHQ+RVH  ++G P+VGD  Y             ++  LHA  +   HP    
Sbjct: 231 LDTGRTHQIRVHMSYIGHPLVGDVLYGGE-------NTFHRQALHAVKLSFLHPFTKE 281


>gi|225868502|ref|YP_002744450.1| RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
 gi|225701778|emb|CAW99179.1| putative RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
          Length = 298

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 67/278 (24%), Positives = 121/278 (43%), Gaps = 29/278 (10%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L KI  + G + V+         +  G VV I          I  ++  +    
Sbjct: 21  DVSKGLLAKIKYKGGNIWVNGVAQNAIYLLDIGDVVAID---------IPNEESFEQLTA 71

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL 146
           ++   D     ++YED    + NKPAG +    +  +  I  F+K++    D   ++  +
Sbjct: 72  ISHDLD-----IVYEDEHFLILNKPAGYASIPSAIHSNTIANFIKAYYIKQDYPNKQVHI 126

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKK 205
             RLD++TSG+++ A+   A   L +  + R I K Y++LV G  +   +  I   + + 
Sbjct: 127 VTRLDRDTSGLMLFAKHGYAHARLDKQLQQRAINKRYYALVCGQERLPDQGEIIAPIGR- 185

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                D   + +       YA + +KVI  + +    ++++ HTGRTHQ+RVH  H+G P
Sbjct: 186 ----TDDSIITRTVTPKGKYAKTSYKVIARYPENVSLVDIRLHTGRTHQIRVHFAHLGFP 241

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++GD  Y        T     +  LH  ++   HP   
Sbjct: 242 LLGDDLYGGRLDLGMT-----RQALHCHHLSFTHPFTK 274


>gi|299137599|ref|ZP_07030780.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX8]
 gi|298600240|gb|EFI56397.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX8]
          Length = 298

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 124/319 (38%), Gaps = 29/319 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M    Y    ++ +      L     + YPH      Q+ L SG+V ++      +  + 
Sbjct: 1   MLNRGYAYTTIIGSKSRGQTLLSHLASLYPHSTLQAWQQNLDSGEVTLNGIIATGSESVT 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            GQ +                  +       +        +L +DS +   NKP+G+   
Sbjct: 61  LGQTL------------------VWERPPWIEPDSPQHFEVLLDDSHLLAVNKPSGLPTL 102

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G G    ++  L   V  +       HRL + T+GI++ A+T  AA  L+ ++   RIQ
Sbjct: 103 PGGGF---MENTLLRLVQKQNPNANPVHRLGRATTGIVLFAKTPQAASQLSANWNTSRIQ 159

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY +L  G+ +     I   +    H     +  V         + S  KVI       
Sbjct: 160 KIYRALAQGVAQQDAYEILTPIGLVPHP---LIGSVWAASPSGKPSKSLAKVISRTTSTT 216

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQNKLYLHARYMDL 297
            + E+  H+GR  Q+R+H   +G P+VGD  Y  N    +     P     +LHA+++  
Sbjct: 217 TF-EVSLHSGRPQQIRIHLASIGHPLVGDPLYGLNGQPLEDRPGLPGDGGYFLHAQFLRF 275

Query: 298 PHPEGGR-LQITAPLPAHM 315
            HP  G  + + A LP+  
Sbjct: 276 HHPITGEQITLEAALPSGF 294


>gi|220927804|ref|YP_002504713.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|219998132|gb|ACL74733.1| pseudouridine synthase, RluA family [Clostridium cellulolyticum
           H10]
          Length = 303

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 68/298 (22%), Positives = 126/298 (42%), Gaps = 24/298 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +  E + E  ++DR  ++ +P++    L K LR   ++V+  R+K +  +  G  + 
Sbjct: 1   MRSITAEENHEGKKIDRVVRDFFPNLASGMLYKALRKKDIKVNGVRIKEDYIVSFGDKID 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I  + + L                    D     ++Y+D  + + NK  GI V       
Sbjct: 61  IYIIDDYL-----------------IGRDDDGFSVVYDDDNLLIVNKETGIPVHPDKNQK 103

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 +       G    L HRLD+ TSG++++A+  A  + + E  + R IQK Y  +
Sbjct: 104 E--ATLIDKLQSIYGPNLALCHRLDRNTSGLVIIAKNPATLEVMLEKIKNREIQKYYTCI 161

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + K   + ++L K   +    V +  +  + +   I+ ++++         LE++
Sbjct: 162 VSGKMEKKNAELVDYLEKNEKLSR--VFINPEKTRNSVQIITRYRILASM-NSLNLLEVE 218

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             TGRTHQ+R H  + G PI+GD KY  N +    +       L A  +        R
Sbjct: 219 LVTGRTHQIRAHLAYYGHPIIGDGKYGKNAENKQYN--AKYQLLCASRLTFNFQSSAR 274


>gi|227488548|ref|ZP_03918864.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glucuronolyticum ATCC 51867]
 gi|227543153|ref|ZP_03973202.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glucuronolyticum ATCC 51866]
 gi|227091442|gb|EEI26754.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glucuronolyticum ATCC 51867]
 gi|227180962|gb|EEI61934.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glucuronolyticum ATCC 51866]
          Length = 306

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 135/323 (41%), Gaps = 22/323 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT V+ + +      +R D+        ++   + +I+    VR D   +  + R+  G 
Sbjct: 1   MT-VRRLPIPEGLGGLRADQGLSKLL-GLSRSAVAEIIADEGVRQDDMIISKSTRLTPGT 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG- 122
            V +         + + ++++   + +      +  +        +      G +V GG 
Sbjct: 59  WVDVRLPGPKKPLLPQAEEVV--GMKILHVDSDVVVVDKPVGVAAHPTVGWEGKTVLGGL 116

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             +GI     G          ++  + HRLD  TSG++V+AR+  A   L  +FR R + 
Sbjct: 117 AAAGIDVTTSG--------PPERKGIVHRLDVGTSGVMVIARSERAYTLLKRAFRERTVD 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++V G P   +  I   + +       +  V     +G   A++H++ ++ F ++ 
Sbjct: 169 KTYHAVVQGHPDPLEGTIEAPIGRHPKKSYKFAVV-----EGGKMAVTHYETLEAF-REA 222

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L++   TGRTHQ+RVH   +  P VGD  Y  + K      + N+ +LHA  +   HP
Sbjct: 223 SLLKVHLETGRTHQIRVHFSSLHHPCVGDPMYGCDPKLAKRLGL-NRQWLHAVSLGFDHP 281

Query: 301 EGGRLQITAPLPAHMVKTWDSLG 323
            G  L I +  P  +    + L 
Sbjct: 282 NGKHLVIESDYPEDLSHALEILR 304


>gi|225870507|ref|YP_002746454.1| RNA pseudouridylate synthase [Streptococcus equi subsp. equi 4047]
 gi|225699911|emb|CAW93829.1| putative RNA pseudouridylate synthase [Streptococcus equi subsp.
           equi 4047]
          Length = 300

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 71/298 (23%), Positives = 124/298 (41%), Gaps = 30/298 (10%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L KI  + G + V+         +  G VV I          I  ++  +    
Sbjct: 21  DVSKGLLAKIKYKGGNIWVNGVAQNAIYLLDIGDVVAID---------IPNEESFEQLTA 71

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL 146
           ++   D     ++YED    + NKPAG +    +  +  I  F+K++    D   ++  +
Sbjct: 72  ISHDLD-----IVYEDEHFLILNKPAGYASIPSAIHSNTIANFIKAYYIKQDYPNKQVHI 126

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKK 205
             RLD++TSG+++ A+   A   L +  + R I K Y++LV G  +   +  I   + + 
Sbjct: 127 VTRLDRDTSGLMLFAKHGYAHARLDKQLQQRAINKRYYALVCGQERLPDQGEIIAPIGR- 185

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                D   + +       YA + +KVI  + +    +++  HTGRTHQ+RVH  H+G P
Sbjct: 186 ----TDDSIITRTVTPKGKYAKTSYKVIARYPENVSLVDITLHTGRTHQIRVHFAHLGFP 241

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           ++GD  Y        T     +  LH  ++   HP    R   T  L          L
Sbjct: 242 LLGDDLYGGRLDLGMT-----RQALHCHHLSFTHPFTESRSDHTICLTDDFESVIIDL 294


>gi|304386318|ref|ZP_07368651.1| ribosomal large subunit pseudouridine synthase [Pediococcus
           acidilactici DSM 20284]
 gi|304327675|gb|EFL94902.1| ribosomal large subunit pseudouridine synthase [Pediococcus
           acidilactici DSM 20284]
          Length = 304

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 73/314 (23%), Positives = 131/314 (41%), Gaps = 25/314 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT+  ++ ++       L    +  +  ++   +  +    +V V+++    +  +++G 
Sbjct: 1   MTWTYHIKLDQSYSPQTLRELLQKTWW-LSRKVVHFLRTERRVLVNQRYQPVSTVVRTGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ +    +  +  +       S              +L+E+  + V NKPAGI      
Sbjct: 60  LISLTFKESDFSTPLPPFDPDSSQ----------SPDVLFENDDLLVVNKPAGIKTHANQ 109

Query: 124 GIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                 +  FL+++   K       HRLDQ TSG L+VA+       L+     + IQ+ 
Sbjct: 110 PHELGSMINFLQAYFAKKDSNAYNVHRLDQWTSGALLVAKNPVVVPILSRQISQKLIQRT 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  +V G  K++   I   +    H           N  GA  A +H++V+  F ++   
Sbjct: 170 YLCMVEGHLKSRSGTITLPIGLDPHDQRKRQ----INGPGAQPATTHYQVVREFVER-SL 224

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           L +Q  TGRTHQ+RVH   +G PIVGD  Y +   G         + LH+  +  P P  
Sbjct: 225 LRVQLATGRTHQIRVHLAALGHPIVGDPLYNSLADGA-------PMRLHSWQVKFPLPFS 277

Query: 303 G-RLQITAPLPAHM 315
                +TAP+P + 
Sbjct: 278 QSWQTVTAPVPNYF 291


>gi|328957863|ref|YP_004375249.1| uncharacterized RNA pseudouridine synthase YlyB [Carnobacterium sp.
           17-4]
 gi|328674187|gb|AEB30233.1| uncharacterized RNA pseudouridine synthase YlyB [Carnobacterium sp.
           17-4]
          Length = 302

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 85/298 (28%), Positives = 134/298 (44%), Gaps = 33/298 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHIIKEQK 82
           +  +   H +  +++ IL  GQV VD K +K  N+ +   QVV I     A+        
Sbjct: 29  FLLSIMSHTSRNSVKSILTRGQVTVDGKVIKKHNHPLLPNQVVAIQSNKAAI-------- 80

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKG 141
                    K +  +   +LYED  I V +K AG+                L ++V  + 
Sbjct: 81  ---------KETALVGMTILYEDDAIIVIDKEAGLLSIAAKFAQELTAHRQLINYVKQEN 131

Query: 142 --QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +  + HRLD++TSG++V A+T    Q + E+++    ++IY  LV GI    +  I 
Sbjct: 132 HNNRIYVVHRLDRDTSGVMVFAKTEQVKQEMQENWKDIVKERIYSVLVEGIVSEDEGSIK 191

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            WL +   +    VH    +  G   AI+H+K I     +F  LE +  TGR +Q+RVH 
Sbjct: 192 TWLTESKAM---KVHSATYD-NGGKLAITHYKKI-RNNDEFTLLEARLETGRKNQIRVHM 246

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMV 316
             +G P+ GD KY A      TS    +L LHA  + L HP    L +  + +P   +
Sbjct: 247 ETLGHPVAGDKKYGA------TSNPLKRLGLHATTLALIHPTSKELVRFHSKVPKVFL 298


>gi|320527002|ref|ZP_08028191.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
 gi|320132587|gb|EFW25128.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
          Length = 293

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 129/321 (40%), Gaps = 37/321 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +   +++ E+ + +           +   + +   SG + ++  + +    + +  
Sbjct: 1   MKIAKQKKIKSSEDGLLVKNILAKQM-GFSRREISRSHVSGSIYLNDVKCRLTQEVHTND 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V +            E+ IL+S           K I+LYED+ I V NKPAGI     +
Sbjct: 60  IVTVR----------TEEPILES-----------KPIILYEDTDIVVVNKPAGIPSHASA 98

Query: 124 -GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                 +   LK +        R   RLD+  SGI+V A+T+  A  L  +   + + K 
Sbjct: 99  EHFDDDMGSILKRYYQDDAFTVRTVGRLDKGVSGIVVYAKTKQMAALLASACEEQLLHKE 158

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G  + K   +   L K+  I G  V             I++++VI      F  
Sbjct: 159 YLAIVKGKFEEKWGKLIYTLGKEKGIRGRSVTA------DGQKCITNYEVI-TEGNFFSL 211

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +++   TGR HQ+R    + G P++GD  Y  +           +  LH   ++  HP+ 
Sbjct: 212 IKVHIETGRLHQIRAGMAYFGHPLIGDRLYGGSMHA------MKRPALHCWKVEFIHPKT 265

Query: 303 GR-LQITAPLPAHMVKTWDSL 322
            + + I   LP  M K  D L
Sbjct: 266 KKQISIECELPTDMQKVVDKL 286


>gi|229172031|ref|ZP_04299596.1| Pseudouridine synthase [Bacillus cereus MM3]
 gi|228611374|gb|EEK68631.1| Pseudouridine synthase [Bacillus cereus MM3]
          Length = 307

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 131/319 (41%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + +D   K  +  I    L ++     + V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EITVPAKWNGISIDSLLKIEW-EIPKKLLHQLRMEKGITVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E   LD               ++YED  + + NKP  +       G   
Sbjct: 70  MFMEEEYDVEPEYGELD---------------VVYEDDHVLIVNKPEKMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+ +KV   F  Q   ++ 
Sbjct: 175 LVEGKVKGKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITFYKVEKYFKNQNVTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    +        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYHGNPLVGDVLYGGQTQ------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P PA +  T    
Sbjct: 284 EIEVDVPFPAKLNDTMKEF 302


>gi|148285150|ref|YP_001249240.1| ribosomal large subunit pseudouridine synthase [Orientia
           tsutsugamushi str. Boryong]
 gi|146740589|emb|CAM81239.1| ribosomal large subunit pseudouridine synthase [Orientia
           tsutsugamushi str. Boryong]
          Length = 312

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 84/319 (26%), Positives = 151/319 (47%), Gaps = 19/319 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + + N     RLD++ K  Y H+    +++ +R G ++V+  + K   +++   ++ I  
Sbjct: 3   ITISNCLVTTRLDKFLKRKYSHLTQGVIERGIRKGHIKVNDAKSKAKLQVKDNDILTIAD 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLY---EDSKIYVFNKPAGISVQGGSGIA 126
            + + ++    +       N+   +   K +  Y   E S   + NKPA +  QGGS I+
Sbjct: 63  YLTSCSNQKHIKLKKKVKDNVGVKALAHKIVNNYKIAETSDYIIINKPALLPTQGGSKIS 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +D  +K    S     +L HRLD+ET+G+L++A+    A  L+++F    I+K Y ++
Sbjct: 123 LSLDDAIKYLNKSFYYDFKLVHRLDRETTGLLIIAKNHGTAIKLSQAFLHHSIEKEYIAI 182

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEM 245
           + G+P      I   + K     GD +    + + G   +I+ ++V       +   +  
Sbjct: 183 LQGVPSQLSGEIITNITK----TGDRMI---ETQNGGKVSITKYQVKAISINSQLSLVSF 235

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLP-HPEGG 303
            P TGRTHQLRVHA  +G PI+GD KY  +N   N++  +      HA  + +P H  G 
Sbjct: 236 IPVTGRTHQLRVHAAKIGYPIIGDKKYNISNTYYNYSLKL------HAAKICIPKHLFGN 289

Query: 304 RLQITAPLPAHMVKTWDSL 322
           +    APLP    +   + 
Sbjct: 290 QRIYYAPLPYQFQQVISTF 308


>gi|238916958|ref|YP_002930475.1| ribosomal large subunit pseudouridine synthase C [Eubacterium
           eligens ATCC 27750]
 gi|238872318|gb|ACR72028.1| ribosomal large subunit pseudouridine synthase C [Eubacterium
           eligens ATCC 27750]
          Length = 333

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 69/326 (21%), Positives = 143/326 (43%), Gaps = 22/326 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + ++      ++ R  + +  +     L K+LR   + ++  +   + +++ G +++
Sbjct: 1   MKEINIDEKLAGQKMMRCLERYLSNAPKSFLYKMLRKKNITLNNSKATGDEKLKCGDIIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKS-ILLYEDSKIYVFNKPAGISVQGGSGI 125
           I            +    + +VN   ++   +   ++YE+S +   NKP+G+  Q     
Sbjct: 61  IFFSDETFEKFSADN---NRTVNYDYYNRIYRPLDIIYENSDVIFINKPSGMLSQKAKPE 117

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +  +L + +  KG+         KP + +RLD+ TSGI+   +T    Q L+E+F+ 
Sbjct: 118 DVSLVEYLIAHLIHKGELNAGDLASFKPGICNRLDRNTSGIVAAGKTTKGLQQLSEAFKQ 177

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R + K Y  +V G   +K+  I  +L K +      V + +   K +    + +  + C 
Sbjct: 178 RTLGKYYLCIVKGNV-DKRALIKGYLYKDNKTN--KVTISRTETKDSLPIETEYIPV-CS 233

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNK-LYLHARY 294
                 L++   TGR+HQ+R H   +G P++GD+KY        F    + K   LH+  
Sbjct: 234 NGNVTLLKIHLLTGRSHQIRAHLASIGHPLIGDYKYGQKSVNDTFNRQYKVKDQMLHSYE 293

Query: 295 MDLPHPEGGRLQITAPLPAHMVKTWD 320
           +D+P  +   + I A +P        
Sbjct: 294 LDIPDMD---IHIYAVIPDSFKNVMK 316


>gi|303233294|ref|ZP_07319965.1| pseudouridine synthase, RluA family [Atopobium vaginae PB189-T1-4]
 gi|302480594|gb|EFL43683.1| pseudouridine synthase, RluA family [Atopobium vaginae PB189-T1-4]
          Length = 338

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 72/334 (21%), Positives = 127/334 (38%), Gaps = 39/334 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVR 66
           Q  +V    + MRLD +              K +  G V ++          ++ G  V 
Sbjct: 6   QTFLVSPQFDRMRLDSFLAAQTDMPARSACAKYIERGCVEINNTEALSKAEHVRLGDRVS 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I         +I     +   V              YED  + V +K  G+     SG  
Sbjct: 66  IVVETQQKPTVIMPNPQIPLDVR-------------YEDEYLLVISKQKGLVCHPSSG-- 110

Query: 127 YHIDGFLKSWV-----------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            HID  L + +                +P + HRLD +T+G++V A+     + L +  R
Sbjct: 111 -HIDDTLANALVAHCGFDHLGKLQGDDRPGIVHRLDMDTTGLMVAAKDNETQEQLQDLIR 169

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           +R   + Y +LV G     +  I   + +      + + +    +  +  AI+ FK +D 
Sbjct: 170 LRDFDRRYLALVQGYVSPDEGTITTGIARSKK---NRLKMCVSKDPLSRQAITTFKTLDR 226

Query: 236 -----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
                    +  LE   +TGRTHQ+RVH  + G  +VGD  Y     G   +    + +L
Sbjct: 227 FEASAHDDGYSLLECHLYTGRTHQIRVHMRYTGHCLVGDPLYGK--VGERINLHLKRQFL 284

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           H+ +++  HP     +++   LP+ +     +L 
Sbjct: 285 HSWHINFDHPITHEHIELFDTLPSDLYTALINLR 318


>gi|94992202|ref|YP_600301.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
 gi|94545710|gb|ABF35757.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
          Length = 223

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 107/233 (45%), Gaps = 18/233 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQ----KPRLTHRLDQE 153
            ++YED  + + NKP G+ V   +G      ++  +    D        +P + HR+D++
Sbjct: 2   DIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPGIVHRIDKD 61

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+L+VA+T AA Q L E  + ++  + Y ++V G   N +  I   + +         
Sbjct: 62  TSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEKDRKKQA 121

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              K        A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y 
Sbjct: 122 VTAK-----GKEAVTRFTVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYG 175

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
                   +   +  +LHA+ + L HP  G  +  T   P    K    L  K
Sbjct: 176 PR-----KTLSGHGQFLHAKTLGLTHPMTGKEMIFTVEAPEIFQKVLKLLRKK 223


>gi|144898737|emb|CAM75601.1| Pseudouridylate synthase [Magnetospirillum gryphiswaldense MSR-1]
          Length = 226

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 120/233 (51%), Gaps = 13/233 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            D +K+ +L++D  + V +KPAG++V  G     H++ +L +        PRL HRLD++
Sbjct: 3   EDEIKARILFKDQDVIVLDKPAGLAVHAGPNSPDHLELYLDALKFGWSMAPRLAHRLDRD 62

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG L++ R   + + L + F   R++K YW++V G P      I+  + K +  GG  +
Sbjct: 63  TSGCLLLGRHDKSIKRLGKMFMQGRVEKAYWTVVHGTPPEDTGEISAPIHKVTGKGGWRI 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +    +     A++ ++V+        W+E  P TGRTHQ+RVH  H+GCP+ GD  Y 
Sbjct: 123 II----DAAGQPAVTRWRVLGR-GDGLSWIECTPLTGRTHQIRVHMKHLGCPVRGDVYYG 177

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR--LQITAPLPAHMVKTWDSLGF 324
            + +          L+L +  + +P    G+  ++  AP P HMV+     G+
Sbjct: 178 PDPESELG------LHLQSHAIGVPPLSTGKDWIRAEAPPPPHMVQALFMCGW 224


>gi|116329941|ref|YP_799659.1| pseudouridylate synthase, 23S RNA-specific [Leptospira
           borgpetersenii serovar Hardjo-bovis JB197]
 gi|116123630|gb|ABJ74901.1| Pseudouridylate synthase, 23S RNA-specific [Leptospira
           borgpetersenii serovar Hardjo-bovis JB197]
          Length = 312

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 71/313 (22%), Positives = 133/313 (42%), Gaps = 38/313 (12%)

Query: 12  VENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRV--KFNNRIQSGQVVRIP 68
           V  +    RLDR+ K  +   ++   +QK +  G VR   +++  K + ++++G+   + 
Sbjct: 9   VLEEFSGNRLDRFLKFSFGDEMSRATIQKWIECGYVRNQDRKICDKSSWKVKTGEQYFLS 68

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
                          +     L      +   ++ E     + +KP GI+   G G    
Sbjct: 69  ---------------IPPRPPLNLEPIPMTLPVVLEREDYLIIHKPPGIASHSGPGDRSP 113

Query: 128 -HIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             ++G L  + +        +P + HRLD+ T G++++ +   A   L+E FR R I+K 
Sbjct: 114 SLVNGLLHHFKELSKVGGEARPGIVHRLDKPTEGLMLIPKNDRAHGKLSELFRKREIEKK 173

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID----CFAQ 238
           Y++ + G    +   I   + +   I    + V          +++H+KV+        +
Sbjct: 174 YYAWIQGHLPAETGTIDLPIARH-PIERLKMTV----SPKGRKSVTHYKVLKYVNSRSGR 228

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           KF ++E+   TGRTHQ+R+H     CP+VGD  Y        +  +Q    L + Y+   
Sbjct: 229 KFSFVEVGLETGRTHQIRIHFQSQRCPVVGDLLYSRTGSQFESYGLQ----LLSYYLKFK 284

Query: 299 HPEGGRLQITAPL 311
            P  G + I A L
Sbjct: 285 DPFTGEM-IEATL 296


>gi|95929488|ref|ZP_01312231.1| Pseudouridine synthase, RluD [Desulfuromonas acetoxidans DSM 684]
 gi|95134604|gb|EAT16260.1| Pseudouridine synthase, RluD [Desulfuromonas acetoxidans DSM 684]
          Length = 303

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 70/324 (21%), Positives = 133/324 (41%), Gaps = 33/324 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V++     RLD+W       ++   ++K++  G V V+ +RV K +  ++ G  + +   
Sbjct: 2   VDSPLVEKRLDQWLATTDRSLSRTVIRKVIDLGGVHVNGRRVRKCSQALKRGDKIELYRD 61

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-----GI 125
              L                       +  +L+ D  + V NKP+G+  Q         +
Sbjct: 62  QQPLTPF-----------------RLSEEDVLFRDDFLLVVNKPSGVESQPTPSRYKGTL 104

Query: 126 AYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              +  FLK  +      +  +  RLD+ETSG ++ +      + LTE+++  R++K+Y 
Sbjct: 105 YEALLVFLKDPYRPLDKPELGMVQRLDRETSGAMIFSIHSRCHKPLTEAWQSHRVRKVYH 164

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV     + +    + L +           +K   +G   A + ++V+   +  F  +E
Sbjct: 165 ALVRDPGLDDEGEFISLLARNRRTNR-----MKSVARGGKSAHTRYRVLKRLS-GFALVE 218

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGR HQ+RVH    G P++GD  Y           +  +  LH+  +   HP   +
Sbjct: 219 IQLLTGRMHQIRVHFSEAGAPLLGDKLYGGTCCLGGQEIL--RTMLHSFRLACDHPVDHK 276

Query: 305 -LQITAPLPAHMVKTWDSLGFKYD 327
            ++  AP P         L   +D
Sbjct: 277 VVEFEAPRPHDFDSLLTRLENNHD 300


>gi|225572464|ref|ZP_03781328.1| hypothetical protein RUMHYD_00761 [Blautia hydrogenotrophica DSM
           10507]
 gi|225040101|gb|EEG50347.1| hypothetical protein RUMHYD_00761 [Blautia hydrogenotrophica DSM
           10507]
          Length = 294

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 147/322 (45%), Gaps = 33/322 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSG 62
           M  + +  +   +E + +  + ++     +   L  + RS Q +  + +    +  +Q G
Sbjct: 1   MERIFHYTITKTQEGITIYDFLRSL--GYSRSLLLHLKRSPQGILRNGQNTFGSVLLQEG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I              +++++  +       ++  +LYED  I V NKPA   +   
Sbjct: 59  DCLDI--------------RLVENISSQNIPPTPMELKILYEDEDILVLNKPADTPIHPS 104

Query: 123 SG-IAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            G     +   +  +  S+G     R  +RLD++T+G L++A+   +A  L+ + + R I
Sbjct: 105 MGNYENTLANGVAHYYQSQGISFVYRCINRLDRDTTGALILAKHAYSAALLSAAMQRREI 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y +LV G+   +   I   + +K     +     + N +    A++ ++ +  F Q 
Sbjct: 165 HRTYLALVQGLCP-ECGVIDAPIARKDASVIER----EVNLRTGAPALTRYECL-AFHQG 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              ++++  TGRTHQ+RVH  ++G P++GD+ Y  ++          ++ LH+  +D  H
Sbjct: 219 LSLVQLRLETGRTHQIRVHMKYLGYPLLGDYLYNPDYSR------IGRVSLHSYQLDFCH 272

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P   + L +TAP+P   ++ W+
Sbjct: 273 PITDKPLCLTAPVPKDFLQAWE 294


>gi|190150190|ref|YP_001968715.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|307250101|ref|ZP_07532064.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|307261347|ref|ZP_07543022.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|307263527|ref|ZP_07545142.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|189915321|gb|ACE61573.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|306857898|gb|EFM89991.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306869078|gb|EFN00880.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|306871170|gb|EFN02899.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 247

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 60/250 (24%), Positives = 111/250 (44%), Gaps = 18/250 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELEILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ ++E F   +++K Y ++V G   +K E      +    I   +    
Sbjct: 61  VLLFALNSEMARLMSEQFEQHQLEKGYLAVVRGYLLDKGEIDYPLKVILDKIADKFSQ-- 118

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               K A  A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 ---PKEAQQAVTFYQNLASVEMLYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI 175

Query: 267 VGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD KY    +    +     ++L LH+ ++   HP+   +++I APL       + +  
Sbjct: 176 MGDTKYGDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLDKQWQNLFATFN 235

Query: 324 FKYDRNLYIK 333
           + +      +
Sbjct: 236 WNFPTFFQSE 245


>gi|46446340|ref|YP_007705.1| hypothetical protein pc0706 [Candidatus Protochlamydia amoebophila
           UWE25]
 gi|46399981|emb|CAF23430.1| conserved hypothetical protein [Candidatus Protochlamydia
           amoebophila UWE25]
          Length = 298

 Score =  194 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 76/315 (24%), Positives = 142/315 (45%), Gaps = 33/315 (10%)

Query: 11  VVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           VV N+E   +L  +      PH +   L++++     +V+ +  +  +  + +G  V + 
Sbjct: 8   VVSNEESGSKLVSFLSKQLSPHYSSRQLKRMIEQNDCQVNGRIERFASTFLGTGDRVSLN 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                                 T +    +S +LYED  +++++KPA +           
Sbjct: 68  LKNPQQ----------------TFNRQLEQSRILYEDEDLFIYDKPAEM---------NC 102

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +  + + +       +L HRLD++T+G+L +A+ +   + L   F+  ++ K Y ++V 
Sbjct: 103 DEQGIIALLRPSFPSIQLIHRLDRQTTGVLALAKNKTTFEALVNQFKQLKVSKSYRAIVD 162

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           GI  + K  I N+L KK    G  +     + +G  YA +++  ++   +K   +   P 
Sbjct: 163 GILTSSKGHIENYLGKKHVYQGQSIWGEVPSFQG-LYASTYWSCLE-IGKKASLVRCFPK 220

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           TGRTHQ+RVH   +G PI+GD++Y   F   +  P   +  LHA  M   HP    +L +
Sbjct: 221 TGRTHQIRVHLAGLGHPILGDYQYGKKFTCLYNPP---RYLLHAEEMGFIHPRTRQKLIV 277

Query: 308 TAPLPAHMVKTWDSL 322
            A LP   +  +  L
Sbjct: 278 QAILPEDFLGAYKKL 292


>gi|218201639|gb|EEC84066.1| hypothetical protein OsI_30347 [Oryza sativa Indica Group]
          Length = 465

 Score =  194 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 100/380 (26%), Positives = 162/380 (42%), Gaps = 87/380 (22%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVD-----------------KKRVKFNNRIQSGQVV 65
           +W +   P +    +QK+ R  +V+ +                  +RV   +++  G ++
Sbjct: 88  KWVRRCCPDLPTSLVQKLFRLRKVKKNVVTAEISSADASAEQHRLRRVSAKDQLMPGDIL 147

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +P         +KE  + + +      ++  FL+ + +Y+D  I V NKP G+ VQGG 
Sbjct: 148 FLPVN-------LKESSVAEKTKKFDNRNEINFLRGLEIYKDEAIIVVNKPPGMPVQGGV 200

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR----- 178
           GI   ID     + ++  + PRL HRLD++ SGILV+ R + +   L   FR +      
Sbjct: 201 GIKNSIDVLASMFEENSSEAPRLVHRLDRDCSGILVLGRNQLSTSMLHAIFREKTADALA 260

Query: 179 ------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA---NYAISH 229
                 +Q+ Y +LV G P++ K  ++  L K     G    +  +    A     A++ 
Sbjct: 261 DGTQHVLQRKYVALVIGTPRHPKGLLSAPLAKILLQDGKSERLTVRASSNAASVQDALTE 320

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK----------- 277
           ++VI+   Q + WLE+ P TGR HQLRVH    +G PIVGD+KY                
Sbjct: 321 YRVIESCPQGYTWLELFPRTGRKHQLRVHCAEVLGTPIVGDYKYGRQAHQKWMPLPLPRT 380

Query: 278 ------------------GNFTSPIQNKLYLHARYMDLPH--------------PEG--- 302
                             G   +  Q +L+LH + M LP               P+    
Sbjct: 381 IDEELLRKRKLPFGLVVGGGSIAEEQPQLHLHCKQMVLPDVSVALHRLQSSDVNPDFSDL 440

Query: 303 GRLQITAPLPAHMVKTWDSL 322
            +L   APLP HM  +W+ L
Sbjct: 441 EKLNFVAPLPLHMRLSWEIL 460


>gi|32033504|ref|ZP_00133831.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
 gi|126208338|ref|YP_001053563.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae L20]
 gi|126097130|gb|ABN73958.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
          Length = 247

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 60/250 (24%), Positives = 111/250 (44%), Gaps = 18/250 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELEILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ ++E F   +++K Y ++V G   +K E      +    I   +    
Sbjct: 61  VLLFALNSEMARLMSEQFEQHQLKKGYLAVVRGYLLDKGEIDYPLKVILDKIADKFSQ-- 118

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               K A  A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 ---PKEAQQAVTFYQNLASVEMLYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI 175

Query: 267 VGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD KY    +    +     ++L LH+ ++   HP+   +++I APL       + +  
Sbjct: 176 MGDTKYGDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLDKQWQNLFATFN 235

Query: 324 FKYDRNLYIK 333
           + +      +
Sbjct: 236 WNFPTFFQSE 245


>gi|229829105|ref|ZP_04455174.1| hypothetical protein GCWU000342_01190 [Shuttleworthia satelles DSM
           14600]
 gi|229792268|gb|EEP28382.1| hypothetical protein GCWU000342_01190 [Shuttleworthia satelles DSM
           14600]
          Length = 337

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 76/350 (21%), Positives = 146/350 (41%), Gaps = 35/350 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +  +E   RLD++   ++       L K+LR   + +++KR +    +  G  ++
Sbjct: 1   MREISITKEEAGQRLDKFLCKYFRAATTSFLYKMLRKKNIVLNQKRAEGRELLSEGDRIQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +         + +     D +    K  D+    ++YED  I   +KPAG   Q      
Sbjct: 61  VFFSDETFERM-RGGDHQDQAFFTLKEIDYRHVHVIYEDEDILALDKPAGCLSQRAGQKD 119

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             ++  + +++ +KG           P + +RLD+ TSG+++  +T    Q+L+E  R R
Sbjct: 120 ISLNEEMLAYLIAKGALTRESYFLFHPSVANRLDRNTSGLILAGKTLRGQQYLSEQLRDR 179

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCF 236
            + K+Y ++V G    + + +  +L K        V   K++  +GA    + ++ +D  
Sbjct: 180 SVIKLYHTIVRGRLTEELQ-LDGYLYKDVGRNQVLVSEKKEDLPEGAQEIHTAYRPLDHR 238

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARY 294
            +    LE+   TGR+HQ+R H   +G PI GD KY                   LH+  
Sbjct: 239 -KDLTLLEVHLMTGRSHQIRAHLASIGHPIAGDPKYGDFHWNQILRRKYGVRGQLLHSYS 297

Query: 295 MDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQN 344
           + LP       +I  P                +  +Y + L  QD C ++
Sbjct: 298 IKLPDGR----EIICP----------------EGEIYRRVLSGQDGCARD 327


>gi|313202664|ref|YP_004041321.1| pseudouridine synthase, rlua family [Paludibacter propionicigenes
           WB4]
 gi|312441980|gb|ADQ78336.1| pseudouridine synthase, RluA family [Paludibacter propionicigenes
           WB4]
          Length = 299

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 74/301 (24%), Positives = 133/301 (44%), Gaps = 33/301 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +  +    ++  +++ +L   QV V+ K   +FN  +Q   +V I               
Sbjct: 26  FLLSKMGGMSRNSVKSLLAHRQVMVNNKITTQFNLALQPEDLVVINNGRG---------- 75

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVD--S 139
               ++ L       K  +++ED  + V  K  G+  V  G+         LK+ V   S
Sbjct: 76  ----NIELNHP----KLKIIFEDEYLIVVEKKEGLLTVSTGNPDETTAFSILKNHVKKSS 127

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +  + HRLD+ETSG+++ A+ +     L E++     ++IY +LV G  + +++ I 
Sbjct: 128 PDNRIYVVHRLDRETSGVIMFAKNKEVQTILQENWHRIITRRIYVALVEGKVEKEQDTIV 187

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WLL+               + G   A++H++ +      +  LE++  TGR +Q+RVH 
Sbjct: 188 SWLLENEK---SLKIHSSATDNGGQQAVTHYRCV-RSNDNYSLLEIELETGRKNQIRVHM 243

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
             +G PIVGD KY AN          N+L LHAR +   HP     +     +P + +  
Sbjct: 244 QDIGHPIVGDKKYGANISP------INRLGLHARLLAFYHPVTTEVVSFETQVPRNFLNI 297

Query: 319 W 319
           +
Sbjct: 298 F 298


>gi|148377937|ref|YP_001256813.1| ribosomal large subunit pseudouridine synthaseD [Mycoplasma
           agalactiae PG2]
 gi|148291983|emb|CAL59375.1| Ribosomal large subunit pseudouridine synthaseD [Mycoplasma
           agalactiae PG2]
          Length = 305

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 57/310 (18%), Positives = 133/310 (42%), Gaps = 41/310 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR--VKFNNRIQSGQVVRIPPVINALNH 76
            R+D++  ++   I   + + ++    V VD ++   K N  ++ G V+ +  ++   ++
Sbjct: 10  ERIDKYISDN-SEITRNDAKALIEQEAVYVDDRKFVRKPNYMVREGMVITVLRLLEKESN 68

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLK 134
           I                +  +   + YED  + + NKP+G+ V    G       +  + 
Sbjct: 69  I---------------EAVDMPLDIRYEDEYLLILNKPSGLVVHPAPGHLNDTLVNALMY 113

Query: 135 SWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            + ++        +  + HR+D++TSG+L++A+       L +  +  +I++ Y ++  G
Sbjct: 114 HFKNNLSDANGLLRLGIVHRIDKDTSGLLIIAKDNETHNELAKMLKNHQIKRTYLAICEG 173

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQ 246
           I  NK   I   + + +      + +     K    ++++  ++  F    + +  ++ +
Sbjct: 174 ILPNKTTKINLPIQRDTK-NRKLMSI----HKDGKSSVTYVHMLKSFYIDNKPYSLVKCE 228

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH  ++  P+ GD  Y  +           +L  HA  +   HP   + +
Sbjct: 229 LETGRTHQIRVHLAYIKHPVYGDSIYGKSV-----DEFNQRL--HAYKLSFMHPVINKLI 281

Query: 306 QITAPLPAHM 315
           ++ + +P   
Sbjct: 282 EVYSDIPKEF 291


>gi|320161265|ref|YP_004174489.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
 gi|319995118|dbj|BAJ63889.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
          Length = 231

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 69/229 (30%), Positives = 114/229 (49%), Gaps = 14/229 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           KS++L++D  I V +KPAG+               ++  ++ K  K  + HRLD++TSGI
Sbjct: 10  KSMILFQDEWILVISKPAGLLSIRDGYNPNLP--TIQGVLEPKLGKLWMIHRLDKDTSGI 67

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+ART  A ++L   F  R+++KIY+++  G+P+  +  I + L     + GD  H   
Sbjct: 68  MVLARTSEAHKNLDRQFAERKVRKIYYAICVGVPEWDEILIQSPL----RVNGDRKHRTV 123

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY----- 272
            + +    A +H +VI  +   + W+E+ PH+G THQ+R H   +G P++GD  Y     
Sbjct: 124 VDFEHGKPAETHVRVISRYG-FYTWVEVHPHSGYTHQIRAHLSSIGYPLLGDSLYRIPPN 182

Query: 273 -CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
                      P   ++ LHA  +   HP  G  +  TAPLP       
Sbjct: 183 CAVIPPKAENLPAFPRVALHAYALTFSHPNSGEEITFTAPLPEDFSSLL 231


>gi|326203344|ref|ZP_08193209.1| pseudouridine synthase, RluA family [Clostridium papyrosolvens DSM
           2782]
 gi|325986602|gb|EGD47433.1| pseudouridine synthase, RluA family [Clostridium papyrosolvens DSM
           2782]
          Length = 303

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 70/298 (23%), Positives = 127/298 (42%), Gaps = 24/298 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +  E + E  ++DR  ++ +P++    L K LR   ++V+  R+K +  +  G  + 
Sbjct: 1   MRSITAEKNHEGKKIDRVVRDFFPNLASGMLYKALRKKDIKVNGIRIKEDYIVSCGDKID 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I  + + L     E                    ++Y+D  + + NK AGI V       
Sbjct: 61  IYIIDDYLLGRNDEG-----------------FSVVYDDDNLLIVNKEAGIPVHPDKNQK 103

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 +       G    L HRLD+ TSG+++VA+     + + +  + R IQK Y  +
Sbjct: 104 E--ATLIDKLQSIYGPNLALCHRLDRNTSGLVIVAKNNPTLEVMLDKIKDREIQKYYSCI 161

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  + KK  + ++L K   +    V +  +  + +   I+ ++V +        LE++
Sbjct: 162 VSGKMEKKKAELVDYLDKNEKLSR--VFITSEKTRNSVQIITRYRVTESL-NSLSMLEVE 218

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             TGRTHQ+R H  + G PI+GD KY  N +    +       L A  +        R
Sbjct: 219 LVTGRTHQIRAHLAYYGHPIIGDGKYGKNIENKQYN--AKYQLLCASRLTFDFQSSAR 274


>gi|31544701|ref|NP_853279.1| RNA pseudouridine synthase [Mycoplasma gallisepticum str. R(low)]
 gi|31541547|gb|AAP56847.1| RNA pseudouridine synthase [Mycoplasma gallisepticum str. R(low)]
 gi|284930765|gb|ADC30704.1| RNA pseudouridine synthase [Mycoplasma gallisepticum str. R(high)]
 gi|284931330|gb|ADC31268.1| RNA pseudouridine synthase [Mycoplasma gallisepticum str. F]
          Length = 330

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 69/302 (22%), Positives = 135/302 (44%), Gaps = 25/302 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +V+++ ++ +R+D++   +  +    N+ K++R   + V+ +R+ F+  ++    +  
Sbjct: 3   KTIVIKSVDDCIRIDKFLFKYLKNYTRTNIYKMIRKKDITVNNQRIDFDYILKVNDKITY 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
              +   +H  K  +   +   L          L+YED  + +F KP GI  Q     + 
Sbjct: 63  YDFLRT-DHKKKVPEFFKAKPELD---------LIYEDENLVIFEKPLGIPAQQTDEPSQ 112

Query: 127 -YHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             H+   L  ++    Q          P + +RLD  T+GI++ A+   A Q L +  + 
Sbjct: 113 YDHMQNRLVHYLVKSNQYDYLNNQAYLPSIVNRLDTYTTGIMLGAKNLKAQQALNQIIKN 172

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R ++K Y  LV G    KK  +  +L K        V + K+        I+ ++ +  F
Sbjct: 173 RDLKKFYHCLVHGEINPKKATLTAYLTKDP--NRSLVSIQKEKTNDNKIIITRYQTLYYF 230

Query: 237 -AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             Q +  L+++  TGRTHQ+R H   +  P+VGD+KY      N     +++L  H+  +
Sbjct: 231 KKQNYTLLDVELITGRTHQIRAHLASINHPVVGDYKYAKKQYQNNQGNFKHQLL-HSYKI 289

Query: 296 DL 297
             
Sbjct: 290 IF 291


>gi|165976282|ref|YP_001651875.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|165876383|gb|ABY69431.1| probable pseudouridine synthase Rlu family protein [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
          Length = 247

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 60/250 (24%), Positives = 111/250 (44%), Gaps = 18/250 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELEILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ ++E F   +++K Y ++V G   +K E      +    I   +    
Sbjct: 61  VLLFALNSEMARLMSEQFEQHQLEKGYLAVVRGYLLDKGEIDYPLKVILDKIADKFSQ-- 118

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               K A  A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 ---PKEAQQAVTFYQNLASVEMLYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI 175

Query: 267 VGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD KY    +    +     ++L LH+ ++   HP+   +++I APL       + +  
Sbjct: 176 MGDTKYGDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLDKQWQNLFTTFN 235

Query: 324 FKYDRNLYIK 333
           + +      +
Sbjct: 236 WNFPTFFQSE 245


>gi|227499592|ref|ZP_03929699.1| pseudouridylate synthase [Anaerococcus tetradius ATCC 35098]
 gi|227218351|gb|EEI83605.1| pseudouridylate synthase [Anaerococcus tetradius ATCC 35098]
          Length = 328

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 65/302 (21%), Positives = 123/302 (40%), Gaps = 28/302 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  +V+  ++   R DR+ + ++ +     +QK +R    +++ KR K ++ +  G  V+
Sbjct: 11  MIEIVINENDGGQRFDRFLRKYFENAPLSLIQKNIRKKNFKINDKRAKKDDFVYPGDSVK 70

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    +  +  +          NL          ++YED  I + +K  G+     S   
Sbjct: 71  MYINDSDYDKWLTRTDFKAQDFNLD---------IVYEDDNIIIMDKREGLLTHSSSRKD 121

Query: 127 YHI---DGFLKSWVDSKGQ-------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           Y     D  L     +K         KP + +RLD+ T+G+++ A+   A + L  + R 
Sbjct: 122 YGNNLVDNMLAYLYKTKSIDMTDKTFKPAVVNRLDRNTAGLVIGAKNAKALRSLNRAIRN 181

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + I K Y ++V G               ++ I  +      +  +     I+HF+ +D  
Sbjct: 182 KYIDKYYMTIVNGHIDKDFSI-------RTTIAKNENKNRIRKSEDGKEIITHFRPLDSN 234

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYM 295
            +KF  LE +  TG+THQ+R        PI+GD KY + N          +   L A  +
Sbjct: 235 -KKFTLLECKLETGKTHQIRFSLKENRTPIIGDRKYGSVNSNRKLEKFGIHNQVLLAYKL 293

Query: 296 DL 297
             
Sbjct: 294 SF 295


>gi|293401025|ref|ZP_06645170.1| pseudouridine synthase (uracil hydrolase) [Erysipelotrichaceae
           bacterium 5_2_54FAA]
 gi|291306051|gb|EFE47295.1| pseudouridine synthase (uracil hydrolase) [Erysipelotrichaceae
           bacterium 5_2_54FAA]
          Length = 314

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 64/301 (21%), Positives = 139/301 (46%), Gaps = 28/301 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +++ D+ N R+D++ +   P +    + K +R+ +++V++KR +   R+  G  V 
Sbjct: 1   MREFIIQEDDANQRVDKFLQKTLPALPKSLMYKYIRNKKIKVNRKRCEIAQRLLPGDHVL 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-I 125
                         ++  ++  + +      +  +LYED+ + +  KP+G+     S  I
Sbjct: 61  CFI----------AEEFFETGEDCSFLKVSSELDVLYEDANVILMKKPSGLLTHKDSNEI 110

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             ++      ++  KGQ          P L HRLD+ T GI++ A+T  A + +    R 
Sbjct: 111 QDNLADRFLHYLYKKGQYDPQTRQSFTPALCHRLDRNTEGIVIGAKTAEALRRMNAYIRE 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +++K Y  +V G+ + K   +  W  K +    + VH+    +K +    + ++ +   
Sbjct: 171 HKVEKHYVCIVEGVMEQKTGHVVLWHKKDAK--SNKVHLYAHEQKNSQRIETSYRTL-HQ 227

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +++ ++E+Q HTG++HQ+R    ++  P+ GD KY A          ++   L A  + 
Sbjct: 228 GKRYAYVEVQLHTGKSHQIRAVMAYLHHPLFGDVKYGAQKNQR-----KDFQALCAYKVH 282

Query: 297 L 297
            
Sbjct: 283 F 283


>gi|144227643|gb|AAZ44541.2| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae J]
          Length = 304

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 68/316 (21%), Positives = 130/316 (41%), Gaps = 35/316 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINA 73
           D+E++R+D        +++    Q ++   +V ++   V K N  +++GQ ++I      
Sbjct: 12  DQEDIRID-ILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKR 70

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYH 128
               ++  +I                 ++++D  + + NKP  + V  G G     +   
Sbjct: 71  PKPQLEPAEI--------------DFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNG 116

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +     S       +P + HRLD++T+G+L+VA+   A          R+I++ Y ++V 
Sbjct: 117 LISHFDSLEQLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVI 176

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEM 245
           G   +K   I   + +                  +  AI++ ++I  F+   Q F  ++ 
Sbjct: 177 GKVLHKFMKINLPIGRDLKNPLKKTISFF----NSKPAITNVELIKHFSYQNQDFSLVKC 232

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           Q  TGRTHQ+R+H  H+G PI GD  Y           +  +L  HA  +      G   
Sbjct: 233 QLETGRTHQIRLHLAHIGYPIYGDPIYGKKI-----DELGQRL--HAYKLVFKDLNGLSR 285

Query: 306 QITAPLPAHMVKTWDS 321
           +  A LP      ++ 
Sbjct: 286 EFEADLPEEFNIAFEQ 301


>gi|239623515|ref|ZP_04666546.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239521546|gb|EEQ61412.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 297

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 73/320 (22%), Positives = 141/320 (44%), Gaps = 34/320 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHIN-FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           ++Y + E       ++ + K+     +  + +      G + V  + V   +R+Q G+V+
Sbjct: 6   IEYTITEP-YTGCTVEEFLKSR--GYSHRLVVYLRNTEGSLTVKGQPVYTIHRLQPGEVL 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           ++               + + + + +     L   ++YED  I V NK AG+ +    G 
Sbjct: 63  KV--------------VLTEDNPSRSIVPVNLPLSIVYEDEDILVINKEAGVPIHPSQGH 108

Query: 126 AYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             +      +W  S+  +P   R  +RLD++T+G+L++AR   +A  L+     RRI++ 
Sbjct: 109 HDNTLANAVAWYYSQKGEPFTYRAINRLDRDTTGLLILARHMLSACVLSNDMLNRRIKRE 168

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFC 241
           Y ++V G  +     I   + +   + G  +      EKG   A +H++ I         
Sbjct: 169 YRAIVCGRTR-DMGTIDAPIAR---VEGSTIERQVDFEKG-ESACTHYRRIAYNEHLDLS 223

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +   TGRTHQ+RVH   +G P+ GD  Y  +++        ++  LH+  +   HP 
Sbjct: 224 CVSLWLETGRTHQIRVHMKSIGHPLPGDFLYHPDYR------YISRQPLHSCRLSFTHPV 277

Query: 302 GGR-LQITAPLPAHMVKTWD 320
            G  ++ TA LP  M +  +
Sbjct: 278 TGEPMEFTAGLPEDMRRLLE 297


>gi|256545099|ref|ZP_05472465.1| RNA pseudouridylate synthase [Anaerococcus vaginalis ATCC 51170]
 gi|256399140|gb|EEU12751.1| RNA pseudouridylate synthase [Anaerococcus vaginalis ATCC 51170]
          Length = 326

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 131/304 (43%), Gaps = 31/304 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   +  ++ N R DR+ + +  +     +QK +R    +++ KR K ++ +++G 
Sbjct: 8   MIEVK---INENDANQRFDRFLRKYLQNAPLSLIQKNIRKKNFKINDKRAKKDDFVKNGD 64

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ +          +++++   S  +L          ++YED  I + +K +G+     +
Sbjct: 65  IITMYIKDEDYKKWVRKKEFKASDFDLD---------IIYEDENIIIIDKKSGVLSHAAN 115

Query: 124 GIAYHID--GFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              Y  +    + S++    +        KP + +RLD+ T+G+++ A+   A + L ++
Sbjct: 116 KNDYGNNIVDQMTSYLYKTNKVNSRDLTFKPSIVNRLDRNTAGLIIGAKNAKALRSLNKA 175

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R  +I K Y ++V G      E         + I  +    + + ++     I+ F  +
Sbjct: 176 IRQGKINKYYLTIVEGEIHKDFEI-------DTRISKNENKNMVKEKEDGKRIITKFHPL 228

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           +     F  LE +  TG+THQ+R        PI+GD KY  +        + N   L A 
Sbjct: 229 ETK-NNFTLLECKLITGKTHQIRYSLNKNSTPIIGDRKYSKSSIDYKKINLNN-QALLAY 286

Query: 294 YMDL 297
            ++ 
Sbjct: 287 KLEF 290


>gi|312601410|gb|ADQ90665.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 168]
          Length = 304

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 130/316 (41%), Gaps = 35/316 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINA 73
           D+E++R+D        +++    Q ++   +V ++   V K N  +++GQ ++I      
Sbjct: 12  DQEDIRID-ILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKR 70

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYH 128
               ++  ++                 ++++D  + + NKP  + V  G G     +   
Sbjct: 71  PKPQLEPAEV--------------DFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNG 116

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +     S       +P + HRLD++T+G+L+VA+   A          R+I++ Y ++V 
Sbjct: 117 LISHFDSLEQLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVI 176

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEM 245
           G   +K   I   + +                  +  AI++ ++I  F+   Q F  ++ 
Sbjct: 177 GKVLHKFMKINLPIGRDLKNPLKKTISFF----NSKPAITNVELIKHFSYQNQDFSLVKC 232

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           Q  TGRTHQ+R+H  H+G PI GD  Y           +  +L  HA  +      G   
Sbjct: 233 QLETGRTHQIRLHLAHIGYPIYGDPIYGKKI-----DELGQRL--HAYKLVFKDLNGLSR 285

Query: 306 QITAPLPAHMVKTWDS 321
           +  A LP      ++ 
Sbjct: 286 EFEADLPEEFNIAFEQ 301


>gi|6942292|gb|AAF32394.1|AF224466_1 putative pseudouridylate synthase [Haemophilus ducreyi]
          Length = 250

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 61/272 (22%), Positives = 117/272 (43%), Gaps = 28/272 (10%)

Query: 4   MTYVQYVV--VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
           MT    +   +  D    RLD+     +P  +   ++  + +  V+V+   V +   ++ 
Sbjct: 1   MTQQMTLTAEISADLLGYRLDQALAQLFPDYSRSRIKVWIENDLVKVNGIIVNRARGKVF 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ + I   I                         +   +++ED  I + NKP  + V 
Sbjct: 61  GGEQIEIQAEIEEEIRF---------------EPQNIPLNIVHEDDDIIIINKPKNLVVH 105

Query: 121 GGSGIAY-HIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+G     +   L  +     + PR  + HRLD++T+G++VVA+   A  HL  + + R
Sbjct: 106 PGAGNPDGTVLNALLYYYPPIAEVPRAGIIHRLDKDTTGLMVVAKNIPAQTHLVTALQKR 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           RI + Y ++  GI   +   +   + +                     AI+H+++++ F 
Sbjct: 166 RITREYEAIASGIM-TQGGKVDEPMARHPT-----KRTAMAVHPMGKPAITHYRIMERF- 218

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           + +  L ++  TGRTHQ+RVH  H+  P++GD
Sbjct: 219 RNYTRLRLRLETGRTHQIRVHMAHIAHPLLGD 250


>gi|322435857|ref|YP_004218069.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX9]
 gi|321163584|gb|ADW69289.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX9]
          Length = 297

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 76/320 (23%), Positives = 129/320 (40%), Gaps = 29/320 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M    Y    ++ + +    L       YPH +    Q+ L +G+V +D      +  + 
Sbjct: 1   MLNRGYAYTTIIGSKQHGWTLLSHLAGLYPHSSAEAWQENLDNGEVTLDGITAAGSELLS 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SGQ++           + K    ++               +L++D  +   NKP+G+   
Sbjct: 61  SGQIL-----------VWKRPAWIEPDAPQHFE-------VLFDDLHLLAVNKPSGLPTL 102

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G G     +  L   V          HRL + T+GI++ A+T  AA  LT  +   R+Q
Sbjct: 103 PGGGFL---ENTLLRLVHRHSPSANPVHRLGRATTGIVMFAKTAQAAAGLTADWNTPRVQ 159

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY +L  G+ + +   I   +    H     +  V     G   + S  KVI   A   
Sbjct: 160 KIYRALAQGVARQEAYEILTPIGLVPHP---RLGSVWAASAGGKASKSSAKVISRTA-AT 215

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMDL 297
              E++  +GR HQ+R+H   +G P+VGD  Y +           P      LHA+++  
Sbjct: 216 TTFEVRLGSGRPHQIRIHLASIGHPLVGDPLYGSTGLPLDDLPGLPGDGGYLLHAQFLKF 275

Query: 298 PHPEGGR-LQITAPLPAHMV 316
            HP  G  +++ A LP+  +
Sbjct: 276 HHPVTGEQIELEAALPSGFL 295


>gi|108759583|ref|YP_629678.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108463463|gb|ABF88648.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 310

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 84/286 (29%), Positives = 131/286 (45%), Gaps = 24/286 (8%)

Query: 40  ILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           ++  G V V  KR +  N R+ +GQVV +         +++E         L++     +
Sbjct: 35  LVEVGAVYVAGKRSRDANARLTAGQVVTV---------VLEEG----GQSPLSEAPPAPE 81

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LYED+ +   +KPAG+S Q   G     D  +       G+   L HRLD+ETSG+ 
Sbjct: 82  LRVLYEDADVIAVDKPAGVSAQPTEGRV--GDSLVDLVGAKLGRPAGLVHRLDRETSGVT 139

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V  +T  A   L   FR  R +K Y +   G        +   L K     G +      
Sbjct: 140 VFGKTAEATSALAAEFREGRARKRYVAAT-GPGLPPSGTVDLPLSKDPSRPGRWRATRAA 198

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           N      A++ F  +      FC +E+ PHTGRTHQLR H   +G PI+GD +Y    + 
Sbjct: 199 N---GVPALTDFHTLSS-GPAFCVVELLPHTGRTHQLRAHLTALGAPILGDARYGGAARA 254

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                   +  LHA+ ++L HP  G+ L+I AP+P  +++ + + G
Sbjct: 255 EGVE--APRCLLHAQALELGHPRTGKLLRIEAPVPEDLMRFFLAAG 298


>gi|255009494|ref|ZP_05281620.1| putative RNA pseudouridylate synthase [Bacteroides fragilis 3_1_12]
          Length = 302

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 72/308 (23%), Positives = 128/308 (41%), Gaps = 33/308 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  +Q G  V I    N   
Sbjct: 20  EPMELMDFLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQPGMKVLISKDKNK-- 77

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLK 134
                           K        ++YED+ I V  K  G+   G            L 
Sbjct: 78  ----------------KEFRHPLLKIVYEDAYIIVVEKKEGLLSVGTDRQKERTAQHILS 121

Query: 135 SWV--DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V    +G +  + HRLD++TSG+++ A+     + L + +      + Y ++V G  +
Sbjct: 122 EYVGRSGRGNRIFVVHRLDRDTSGLMMFAKDEKTQRTLRDHWHDIVTDRRYVAVVTGEME 181

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + +WL  ++     YV     ++ G+  +I+H++ I   A  +  +E++  TGR 
Sbjct: 182 KDSDTVVSWLTDRTL----YVSSSSYDDGGSK-SITHYRTIKR-ANGYSLVELRLETGRK 235

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G P++GD +Y  +   N       +L LHA  +   HP   + ++   P 
Sbjct: 236 NQIRVHMQDLGHPLIGDGRYGIDGGPN----PLGRLALHAFKLCFYHPVTDQLMEFETPY 291

Query: 312 PAHMVKTW 319
           P    K +
Sbjct: 292 PPAFKKLF 299


>gi|222641041|gb|EEE69173.1| hypothetical protein OsJ_28343 [Oryza sativa Japonica Group]
          Length = 465

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 100/380 (26%), Positives = 162/380 (42%), Gaps = 87/380 (22%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVD-----------------KKRVKFNNRIQSGQVV 65
           +W +   P +    +QK+ R  +V+ +                  +RV   +++  G ++
Sbjct: 88  KWVRRCCPDLPTSLVQKLFRLRKVKKNVVTAEISSADASAEQHRLRRVSAKDQLMPGDIL 147

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +P         +KE  + + +      ++  FL+ + +Y+D  I V NKP G+ VQGG 
Sbjct: 148 FLPVN-------LKESSVAEKTKKFDNRNEINFLRGLEIYKDEAIIVVNKPPGMPVQGGV 200

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR----- 178
           GI   ID     + ++  + PRL HRLD++ SGILV+ R + +   L   FR +      
Sbjct: 201 GIKNSIDVLASMFEENSSEAPRLVHRLDRDCSGILVLGRNQLSTSMLHAIFREKTADALA 260

Query: 179 ------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA---NYAISH 229
                 +Q+ Y +LV G P++ K  ++  L K     G    +  +    A     A++ 
Sbjct: 261 DGTQHVLQRKYVALVIGTPRHPKGLLSAPLAKILLQDGKSERLTIRASSNAASVQDALTE 320

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK----------- 277
           ++VI+   Q + WLE+ P TGR HQLRVH    +G PIVGD+KY                
Sbjct: 321 YRVIESCPQGYTWLELFPRTGRKHQLRVHCAEVLGTPIVGDYKYGRQAHQKWMPLPLPRT 380

Query: 278 ------------------GNFTSPIQNKLYLHARYMDLPH--------------PEG--- 302
                             G   +  Q +L+LH + M LP               P+    
Sbjct: 381 IDEELLRKRKLPFGLVVGGGSIAEEQPQLHLHCKQMVLPDVSVALHRLQSSDVNPDFSDL 440

Query: 303 GRLQITAPLPAHMVKTWDSL 322
            +L   APLP HM  +W+ L
Sbjct: 441 EKLNFVAPLPLHMRLSWEIL 460


>gi|284048346|ref|YP_003398685.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
 gi|283952567|gb|ADB47370.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
          Length = 285

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 66/306 (21%), Positives = 117/306 (38%), Gaps = 39/306 (12%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RL  + ++    ++    +K+  +G ++V+ + ++ +  +Q G  V    +       
Sbjct: 11  PQRLKSFLRDQ--GLSGTYWKKLKAAGALQVNGEIIQRDLLLQPGDRVAWTFLPE----- 63

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                        T   +     +L E       +KPAG+                 +W 
Sbjct: 64  -----------PCTLEPEEAPLSILEETELYLAVDKPAGLVTHNAGKERTPALSRRVAWY 112

Query: 138 DSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                         RLD+ETSG+++ A+       L+      R++K Y +L  G  +  
Sbjct: 113 FQTHHISSAVHPVSRLDRETSGVVLFAKNACLHHMLSR----NRLEKTYLALTLGHWEQP 168

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              +   + ++         V +Q +     A + ++V+    +    +  Q  TGRTHQ
Sbjct: 169 AGILDWPIGRRPG-----SIVERQVDPDGQPARTRYQVLG-EKEGLSLVRFQLETGRTHQ 222

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVHA   G P++GD  Y        T     + YLHA  +    P  GR ++ITAPLP 
Sbjct: 223 IRVHAAAAGHPLLGDTLYG-------TPGAPGRHYLHAWKVAFREPFTGRPVEITAPLPP 275

Query: 314 HMVKTW 319
              K W
Sbjct: 276 DFRKVW 281


>gi|54020208|ref|YP_115967.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 232]
 gi|53987381|gb|AAV27582.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 232]
          Length = 304

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 69/316 (21%), Positives = 130/316 (41%), Gaps = 35/316 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINA 73
           D+E++R+D        +++    Q ++   +V ++   V K N  +++GQ +RI      
Sbjct: 12  DQEDIRID-ILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIRIFNDYKR 70

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYH 128
               ++  +I                 ++++D  + + NKP  + V  G G     +   
Sbjct: 71  PKPQLEPAEI--------------DFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNG 116

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +     S       +P + HRLD++T+G+L+VA+   A          R+I++ Y ++V 
Sbjct: 117 LISHFDSLEQLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVI 176

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEM 245
           G   +K   I   + +                  +  AI++ ++I  F+   Q F  ++ 
Sbjct: 177 GKVLHKFMKINLPIGRDLKNPLKKTISFF----NSKPAITNVELIKHFSYQNQDFSLVKC 232

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           Q  TGRTHQ+R+H  H+G PI GD  Y           +  +L  HA  +      G   
Sbjct: 233 QLETGRTHQIRLHLAHIGYPIYGDPIYGKKI-----DELGQRL--HAYKLVFKDLNGLSR 285

Query: 306 QITAPLPAHMVKTWDS 321
           +  A LP      ++ 
Sbjct: 286 EFQADLPEEFNIAFEQ 301


>gi|219870928|ref|YP_002475303.1| tRNA pseudouridine synthase C [Haemophilus parasuis SH0165]
 gi|219691132|gb|ACL32355.1| tRNA pseudouridine synthase C, pseudouridylate synthase, 23S
           RNA-specific [Haemophilus parasuis SH0165]
          Length = 242

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 111/243 (45%), Gaps = 18/243 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +K  ++Y+D ++   NKPAG+ V       +     +++  D  GQ   L HRLD+ TSG
Sbjct: 1   MKLEIIYQDDELIAINKPAGMLVHRSWLDKHETVFAMQTLRDQIGQHVFLIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ +++ F+  +IQK Y ++V G  + +        ++   I   +    
Sbjct: 61  VLLFALNSEMARTISQLFKQHQIQKSYLAVVRGYLQGEGRIDYPLKVQLDKIADKFSQ-- 118

Query: 217 KQNEKGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              EK A  AI+ ++ I               ++  +++ P TGR HQLR H  H+  PI
Sbjct: 119 ---EKEAQEAITDYRNIATVEMPYPAGKFATARYSLVQLYPKTGRKHQLRRHLKHLFHPI 175

Query: 267 VGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD  Y    +      +   ++L LH+  +   HP+    ++I APL       +   G
Sbjct: 176 MGDTNYGDLHQNRALTANTGCDRLMLHSNSLQFIHPKTLQTIEIKAPLDEQWKALFTQFG 235

Query: 324 FKY 326
           + +
Sbjct: 236 WNF 238


>gi|46202662|ref|ZP_00208608.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 227

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 113/231 (48%), Gaps = 10/231 (4%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L + +LY D  + + +KPAG+ V  G     H+  FL        Q P L HRLD+ETS
Sbjct: 4   DLVARVLYRDPAVLIIDKPAGLMVHAGPKGGEHLGLFLDQLRFGLAQSPELAHRLDRETS 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G LV+ RTR A   L + F      K YW++V G P+  +  I   L K+    G  + V
Sbjct: 64  GCLVLGRTRKALAGLGDLFAKGLADKTYWAVVVGKPREDQGVIDYALKKREKKFGWRMEV 123

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               ++    +++ ++++    +   WLE +P TGRTHQ+R H   +G P+VGD  Y   
Sbjct: 124 ----DRNGLASVTQWRLLGTDGR-LSWLECRPLTGRTHQIRAHCAAIGHPLVGDAIYGRG 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
                 +   ++L LH+R + LP   G   +   AP+P HM    +  G+ 
Sbjct: 179 T----GTLAGDRLMLHSRNIVLPFHAGKPPIAAKAPVPEHMRAVLEGCGWD 225


>gi|256846962|ref|ZP_05552408.1| pseudouridine synthase [Lactobacillus coleohominis 101-4-CHN]
 gi|256715626|gb|EEU30601.1| pseudouridine synthase [Lactobacillus coleohominis 101-4-CHN]
          Length = 295

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 68/289 (23%), Positives = 123/289 (42%), Gaps = 32/289 (11%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           I   G +++D +     +++  GQ+V I              ++ D + N    +     
Sbjct: 33  IFHGGSLQIDHQPAWAVDKVLPGQMVGI--------------ELPDETANPRITAFPGSF 78

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKSWV---DSKGQKPRLTHRLDQET 154
            + YED+   V NK AG++      +A    +   +K++        Q   +  RLD++T
Sbjct: 79  QIAYEDADFLVINKDAGVATVPAHNVAVQDSLVNRVKNYYLVHQYPNQVTHVATRLDKDT 138

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V  + R A   L    +  +++K Y ++V G   N    I   + +          
Sbjct: 139 SGLVVFPKHRFAHAVLDRQLKRHQVKKEYVAIVGGQLSNHHGYIYAPISRDPE-----SF 193

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V +Q       +I+ +   +   ++F  + ++ HTGRTHQ+RVH   +G P++GD  Y  
Sbjct: 194 VKRQVCDDGKESITEYWT-ERTVEQFSVVRIRLHTGRTHQIRVHFSFLGHPLIGDDMYGG 252

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
                 T    ++  LH RY+    P    +++  APLP  M K    L
Sbjct: 253 ------TGLFMSRQALHCRYISFYSPFKKQQIECQAPLPDDMNKLIAKL 295


>gi|206900407|ref|YP_002249968.1| ribosomal large subunit pseudouridine synthase C [Dictyoglomus
           thermophilum H-6-12]
 gi|206739510|gb|ACI18568.1| ribosomal large subunit pseudouridine synthase C [Dictyoglomus
           thermophilum H-6-12]
          Length = 226

 Score =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 77/233 (33%), Positives = 128/233 (54%), Gaps = 17/233 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTH 148
           +DFL   ++YED+ + V NKPAGI VQG    +  +    K+++  K +KP      + H
Sbjct: 2   ADFLNLEVIYEDNHLLVVNKPAGILVQGDITKSTTLLEISKAYIKEKYKKPGNVFLAIVH 61

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+  SG+++ AR   +A  L+E+FR R+++K Y +L  GI K KK  I+  LL    +
Sbjct: 62  RLDKPVSGVVIFARNSKSAGRLSEAFRERKVEKEYIALCKGIFKVKKGTISESLL---WV 118

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +    V Q++K +  AI+H++V++ F +    + + P TGR HQLR H  ++G PI+G
Sbjct: 119 EKERKARVSQDDK-SKNAITHYEVLEEF-KNLSLVRLIPETGRKHQLRAHLSYIGHPILG 176

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           D KY            +++++LH + M +PHP     ++  A +P    +   
Sbjct: 177 DEKYGGGRI------FKDRIFLHCKKMAVPHPVRKDIMEFEAKIPDFWSEFLK 223


>gi|300814457|ref|ZP_07094719.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
 gi|300511427|gb|EFK38665.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
          Length = 300

 Score =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 143/321 (44%), Gaps = 35/321 (10%)

Query: 1   MSLMTYVQYV--VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR 58
           M  +   +++  +V +++   R  ++ +     I+  ++++  R   + V+ KR   N  
Sbjct: 1   MEKLNPYEFLEFIVTDEKIKSR--KFLEKM--DISSRHIRRACRENSIYVNGKRTFENVE 56

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           ++ G  V I     +LN + + + I                 + YED  + + NK     
Sbjct: 57  VKKGDSVAIKFPDESLNALCQYKDI----------------DICYEDYDLLIVNKEYNCV 100

Query: 119 VQGGSGIA-YHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                  +   +  +L ++ +     +K R  +RLD++TSG+++VA+   A   + + F 
Sbjct: 101 THTAKDDSQDTLLNYLAAYFEKNNIKRKVRFVNRLDRDTSGLIIVAKNSYAHAKIMDEFS 160

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             ++ KIY ++  G  K K+  I    +KK  +  D +   + ++    YA + ++V+  
Sbjct: 161 NNQVDKIYLAICRGDFKEKQGEI----VKKISLCQDGIRR-EVDDDNGKYAKTKYQVLK- 214

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             +K   ++++  TGRTHQ+RVH   +G PI+GD  Y      N    + ++  LH+  +
Sbjct: 215 DNKKLALVKLKLFTGRTHQIRVHLKSIGHPIIGDKLYN---DSNEEQNLLDRQALHSYSL 271

Query: 296 DLPHPEGGRL-QITAPLPAHM 315
               P  G L   TA L   M
Sbjct: 272 SFKLPRTGELKTFTAKLSDDM 292


>gi|134045627|ref|YP_001097113.1| RluA family pseudouridine synthase [Methanococcus maripaludis C5]
 gi|132663252|gb|ABO34898.1| pseudouridine synthase, RluA family [Methanococcus maripaludis C5]
          Length = 298

 Score =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 67/327 (20%), Positives = 137/327 (41%), Gaps = 36/327 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     +  V +++     +L    K+ +  ++   ++K  +  ++ V+ K +   ++++
Sbjct: 1   MESQKKILKVTIDSKIAGNKLIDVLKDDF-ELSNKMIKKFDKEKKIFVNSKNISLKSKLK 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
             + V +                +D  +N     + L   ++YED  + + +KP  + V 
Sbjct: 60  ENETVSVE---------------IDCGIN-NIDPEKLLLCVIYEDDDLLIVDKPKNMVVH 103

Query: 121 GGSGIAYHIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               +              ++++  K R  +RLD +T+G+L++A+   + Q L +     
Sbjct: 104 PTKNVLSGTLANAISNHQKINNQNYKIRFVNRLDMDTTGLLIIAKNSYSHQQLAKQMDEG 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            ++KIY  +V G   +K+  I + + L    I  +              + + +KVI+ F
Sbjct: 164 ILEKIYIVVVNGHLDSKEGVIEDSIDLNDDGIKRELSTF-------GKISKTKYKVIEEF 216

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 LE++  TGRTHQ+RVH    G  I+GD  Y        T+ +  +  LH+  + 
Sbjct: 217 -NNVSVLEIKLLTGRTHQIRVHLSSFGNNIIGDTLYGK------TADLIERQALHSHILR 269

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDSL 322
             HP     ++I + LP  M     +L
Sbjct: 270 FIHPITKENMEIRSKLPDDMENLIKNL 296


>gi|218248702|ref|YP_002374073.1| RluA family pseudouridine synthase [Cyanothece sp. PCC 8801]
 gi|218169180|gb|ACK67917.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8801]
          Length = 306

 Score =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 74/314 (23%), Positives = 126/314 (40%), Gaps = 34/314 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M    ++    V   +  + +  ++   YPH +    Q+ + SGQ+ ++ +    +  +Q
Sbjct: 1   MLNQGWIYREQVNPSDAGLTILAYYTQRYPHSSQGQWQERIISGQILLNGQPTTPDTPLQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            GQ +                          +    L   +LYED  + V  KP+G+ V 
Sbjct: 61  PGQCLSYH------------------RPPWQEPDVPLAFEVLYEDVDVLVVAKPSGLPVL 102

Query: 121 GGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            G G   H   G LK       + P   HRL + TSG++++AR+  AA HL+   R  ++
Sbjct: 103 PGGGFLEHTLLGQLKRLYPQ--ETPTPIHRLGRGTSGLMLLARSPLAASHLSHQMRQGQM 160

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y +LV       +  I   + K  H    YV+    +     +A SH +V+    Q 
Sbjct: 161 TKVYHALVGAGDLPHQFSIHQPIGKIPHPVLGYVYGATPD---GLFAHSHCRVLQRSTQG 217

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFK-------GNFTSPIQNKLYL 290
              +E++  TGR HQ+R+H   +G P++GD  Y      +            P      L
Sbjct: 218 -TLVEVRIFTGRPHQIRIHLASVGYPLLGDPLYEVGGIPRTEPEIEVNKLPVPGDCGYLL 276

Query: 291 HARYMDLPHPEGGR 304
           H+  +   HP    
Sbjct: 277 HSHLLGFTHPRTHE 290


>gi|320102049|ref|YP_004177640.1| RluA family pseudouridine synthase [Isosphaera pallida ATCC 43644]
 gi|319749331|gb|ADV61091.1| pseudouridine synthase, RluA family [Isosphaera pallida ATCC 43644]
          Length = 337

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 71/317 (22%), Positives = 129/317 (40%), Gaps = 33/317 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD+     +  ++       + +G++ ++ +                    +    ++
Sbjct: 26  VRLDKLVAQRF-GLSRRAAGDAVLNGRIDLEGQLC------------------DEPGRLV 66

Query: 79  KEQKILDSSVNLTKHSDFL--KSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLK 134
             + +L  + N  K    +  K  +L+ED  + + NKPAG+                 LK
Sbjct: 67  PPESVLRFNPNRPKERKVVTAKLDILFEDRHLLIVNKPAGLLTLETEARETDTLRGRVLK 126

Query: 135 S--WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                        + HRLD+ETSG + +A T  A + L   FR   +++ Y ++V G   
Sbjct: 127 HQSLRRRGRPFVGIVHRLDRETSGAIALALTPEAMKPLQALFRSHAVERRYLAIVAGAVA 186

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                +   ++  S  G     + +  +  A  A++ F+V++ F      L  +  TGR 
Sbjct: 187 EDHGVVEAAIV--SRPGEVRRRLARPGDPDARDALTRFRVLERFGCDASLLACELETGRG 244

Query: 253 HQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
           HQ+RVH   +G P++GD  Y        F+G   + + ++  LHA  + L HP  GG + 
Sbjct: 245 HQIRVHLASIGHPVLGDRLYAPRKDKHAFQGGSGTILFDRQALHAETLGLVHPVAGGTVW 304

Query: 307 ITAPLPAHMVKTWDSLG 323
           + AP P    K    L 
Sbjct: 305 VEAPPPGDFRKLIARLR 321


>gi|218288262|ref|ZP_03492561.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|218241621|gb|EED08794.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
          Length = 303

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 149/325 (45%), Gaps = 33/325 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + + + ++   + +W +   P +    + K +R+G+V+V+ KR K + R+  G +V 
Sbjct: 1   MIEITIGSSDDGKPVHKWLRLLLPGLPLSGVYKSIRTGRVKVNGKRAKQDTRLHEGDIVH 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-I 125
           +         +          V+           +LYED +I   NKPAG+      G  
Sbjct: 61  LYFSDEDYASLHAHPVAKYQGVSRAID-------ILYEDDEIVAVNKPAGVLTHPADGEY 113

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +   ++++V  +G      +    HRLD+ TSG+++ A+T  AA+   ++F+   ++
Sbjct: 114 KTSLAAQVEAYVYDRGAREGAFRAAPVHRLDRNTSGVVIFAKTARAAKAWADAFQRGEVE 173

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++V G    +   +A  + ++        +V +  E     + + ++V+   ++  
Sbjct: 174 KEYLAIVEGAWSGR-GRVAVDVQREG-------NVTRVVEDSGKPSETAYEVVAS-SRGT 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++  TGRTHQ+RVH  ++G P++ D KY A      +       YLHA  +     
Sbjct: 225 SLVRLRLLTGRTHQIRVHMANLGHPLLADRKYGARPIRGES------FYLHAHRV----- 273

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFK 325
               + +TAPLP  M +   +LG+K
Sbjct: 274 RWNEVDVTAPLPDRMTEKLRTLGYK 298


>gi|306826329|ref|ZP_07459662.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|304431442|gb|EFM34425.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
          Length = 291

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 73/320 (22%), Positives = 135/320 (42%), Gaps = 32/320 (10%)

Query: 7   VQYV-VVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQV 64
           +Q++  +      M + ++ +     I    ++  LR    + ++ + V +N  ++SG +
Sbjct: 1   MQFIFTLPESLPQMTVKQFLEEQLL-IPR-KIRHFLRTKKNILINHEEVHWNEMVKSGDI 58

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
            ++            +++IL  + +L +         +Y+D  + V NKP G+   G   
Sbjct: 59  CQLTFDEEDY----PKKEILWGNPDLVQE--------VYQDQHLIVVNKPEGMKTHGNQP 106

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +   + ++V   GQ   + HRLD ETSG+++ A+       L      + I + YW
Sbjct: 107 NEIALLNHISAYV---GQTCYVVHRLDMETSGLVLFAKNPFILPILNRLLEKKEIAREYW 163

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G  ++K+    + + +  H     V     + K   +A +    +  F  K   + 
Sbjct: 164 ALVEGRVESKELVFRDKIGRDRHDRRKRV----VDPKNGQHAETQVSRLKQFPNKTSLVR 219

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
            +  TGRTHQ+R+H  H   PI+GD  Y +  K        ++L LHA  +   HP    
Sbjct: 220 CKLKTGRTHQIRIHLSHHKHPILGDPLYNSKSKT-------SRLMLHAFRLSFTHPLTLE 272

Query: 304 RLQITAPLPAHMVKTWDSLG 323
           +L  TA L     K     G
Sbjct: 273 KLSFTA-LSDTFEKELKKNG 291


>gi|282892129|ref|ZP_06300604.1| hypothetical protein pah_c207o069 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498024|gb|EFB40368.1| hypothetical protein pah_c207o069 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 283

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 80/304 (26%), Positives = 131/304 (43%), Gaps = 37/304 (12%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIK 79
           LD       P+ +   L++ L+  +V VD + VK  +  +++GQ + +            
Sbjct: 12  LD-ALAKLSPNSSKTTLREWLKHERVFVDDQIVKIASTPLEAGQTISLG----------- 59

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVD 138
                       + +   K  +LYED+ + V  KPAG+     +   A     FLK    
Sbjct: 60  -----------VRKARKEKVPILYEDAHLVVIEKPAGLLSVATNFDKAKTAHAFLKERYR 108

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  K  + HRLDQ+TSG+++ A T  A   L   F    I + Y ++V G    ++   
Sbjct: 109 PR--KVYVVHRLDQDTSGVMLFALTGEAFFGLKALFADHDIDREYTAVVHGKMTQQEGTW 166

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            ++L +       YV    Q+      AI+HFK ++     F  L ++  TG+ +Q+RVH
Sbjct: 167 QSYLYED----KAYVVHSTQDPDKGELAITHFKTVEARTH-FSLLNLKLETGKKNQIRVH 221

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVK 317
               G PIVGD KY     G   S I  +L LHA ++   HP     +   +P+P    +
Sbjct: 222 CEDHGFPIVGDKKYG----GEGESHITKRLCLHAHHLGFVHPIYKKEMSFDSPIPEKFYQ 277

Query: 318 TWDS 321
              +
Sbjct: 278 CLKT 281


>gi|325479239|gb|EGC82335.1| pseudouridine synthase, RluA family [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 303

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 69/314 (21%), Positives = 139/314 (44%), Gaps = 33/314 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D++  +    I    ++  ++  +++V+ K VK + ++  G  + I    ++L H+ 
Sbjct: 7   IRIDKFISDELEEIPREKIKDFIKDKKIKVNDKIVKPSFKLSEGDEIEID---DSLFHVP 63

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSW 136
                       T   + +   ++YE+    + +K + + V     I     ++G L  +
Sbjct: 64  ------------TIDPEAMDLKIVYENDDYAIIDKDSNVIVHPAGKIVTGTLVNGLLDRY 111

Query: 137 VD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                       +P + HRLD++T+G++ + +   + ++  + F  R++ KIY+++V+G 
Sbjct: 112 GYDGLSHIGGDDRPGIVHRLDKDTTGLIAITKNNTSYKYFKKMFETRKVDKIYYAIVFGT 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              K + I  ++ +  H                  AISH++V+      +  ++++  TG
Sbjct: 172 FDKKSDTIETFMDRDPHNRRKMAVTSS-----GRKAISHYEVV-AETNDYSLVKVKIVTG 225

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQ+RVH  H+  PI+GD  Y  N K NF     +   LH  Y+     EG  +   A 
Sbjct: 226 RTHQIRVHMTHLNHPILGDPVYG-NVKHNFN---LDHQLLHCAYIGFTDMEGKYVSYIAN 281

Query: 311 LPAHMVKTWDSLGF 324
                +K    LG 
Sbjct: 282 PHEDFLKYQKILGL 295


>gi|322411665|gb|EFY02573.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus dysgalactiae subsp. dysgalactiae
           ATCC 27957]
          Length = 300

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 68/277 (24%), Positives = 118/277 (42%), Gaps = 27/277 (9%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L KI  + G + V+         +  G VV I         I KE+        
Sbjct: 21  DVSRGLLAKIKYKGGNILVNGIEQNAIYLLDIGDVVTI--------DIPKEEPFEKL--- 69

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK---GQKPRL 146
               +      ++YED    V NKP G +    +  +  I  F+K++   K    Q+  +
Sbjct: 70  ---EAIPFDLDIVYEDDHFLVINKPVGFASIPSAIHSNTIANFIKAYYVEKSYPNQQVHI 126

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD++TSG+++ A+   A   L +  + R I+K Y++LV G      E      + +S
Sbjct: 127 VTRLDRDTSGLMLFAKHGYAHARLDKQLQTRAIEKRYFALVSGQGALPDEGDIVAPIGRS 186

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                   + +  +    YA + +KV+  + +    ++++ HTGRTHQ+RVH  H+G P+
Sbjct: 187 KDS----IITRAVDSMGKYAKTSYKVVARYPENVHLVDIKLHTGRTHQIRVHFAHLGFPL 242

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +GD  Y        T     +  LH  Y++   P   
Sbjct: 243 LGDDLYGGRLDLGIT-----RQALHCHYLNFKDPFTE 274


>gi|47566178|ref|ZP_00237206.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus G9241]
 gi|47556731|gb|EAL15062.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus G9241]
          Length = 307

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 130/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + +D   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EITVPAKWNGISIDSLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFMEEEYGVEPE---------------YGELHVVYEDDHVLIVNKPEKMDTHPSEKGGMG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHYQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYVA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEKYFKNQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNDTMKEF 302


>gi|45358573|ref|NP_988130.1| RluA family pseudouridine synthase [Methanococcus maripaludis S2]
 gi|44921331|emb|CAF30566.1| Pseudouridine synthase:Pseudouridine synthase, Rlu. Related protein
           [Methanococcus maripaludis S2]
          Length = 297

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 67/327 (20%), Positives = 141/327 (43%), Gaps = 36/327 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     +  + V++     +L    K+++  ++   ++K  +  ++ V+ K +   ++++
Sbjct: 1   MECQKKILNLTVDSKIAGNKLIDVLKDNF-ELSNKMIKKFDKENKIFVNSKNISLKSKLK 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
             + V +                +D  +N     + L   ++YED  + + +K   + V 
Sbjct: 60  ENETVSVE---------------IDYGIN-NITPENLTLNVIYEDDDLLIVDKSKNMVVH 103

Query: 121 GGSGIAYHIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               +              ++++  K R  +RLD +T+G+L+VA+   + Q L +     
Sbjct: 104 PTKNVLSGTLANAISNHQKINNQNYKIRFVNRLDMDTTGLLIVAKNSYSHQQLAKQMDEG 163

Query: 178 RIQKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            ++KIY ++V G    K+  I + + L ++ I  +  +           + + +KVI+  
Sbjct: 164 ILEKIYIAVVNGHLDLKEGIIEDSIDLNENGIKRELSNF-------GKISKTKYKVIEEL 216

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    LE+   TGRTHQ+RVH    G  I+GD  Y        TS + ++  LH+  + 
Sbjct: 217 -KNASVLEINLLTGRTHQIRVHLSSTGNYIIGDTLYGE------TSKLIDRQALHSHILR 269

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWDSL 322
             HP    +++I + LP  M     +L
Sbjct: 270 FIHPITKEKIEIISKLPDDMKNLIKNL 296


>gi|227891522|ref|ZP_04009327.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
 gi|227866669|gb|EEJ74090.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
          Length = 315

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 78/336 (23%), Positives = 136/336 (40%), Gaps = 28/336 (8%)

Query: 2   SLMTYVQYV-VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRI 59
            +M+  ++  +V  +   + L       +  +    +  + +R   V++D K    N  +
Sbjct: 3   EMMSKYKFERIVNAEFSGISLRALLSEKWL-LPRKFIHFLRIRE-NVKIDGKYYPMNTIV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q  Q + +          I E     ++ +        K  +++E+  + V NKP GI  
Sbjct: 61  QGNQKIEL----------IFEGDEFRTATSNYIVDKGRKIPIIFENDDLLVVNKPQGIKS 110

Query: 120 QGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                     +  ++  ++D++ + P + HRLD  TSG ++VA+       LT       
Sbjct: 111 HPNQPYETGTLMNYIAGYLDARDEHPYMVHRLDMLTSGAMIVAKNPVVVPILTRLISTHT 170

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I++ Y ++  GI   K+  I   + K  +         K +  GA  A +H++VI  F  
Sbjct: 171 IKRAYLAITEGIFDQKEGVIDLPIGKDENDKRKR----KVDGIGALPARTHYQVIKEFGN 226

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
                 ++  TGRTHQLRVH   MG PIVGD  Y    K       +  + LH     L 
Sbjct: 227 NSAVY-LRLETGRTHQLRVHLSAMGHPIVGDVLYNHVSK-------EKHMMLHGYKQKLT 278

Query: 299 HPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
            P   R L++ A +P +     + +      N Y K
Sbjct: 279 LPFSMRELELKADIPEYFANYEEKIKENKKLNFYKK 314


>gi|229154958|ref|ZP_04283072.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|228628516|gb|EEK85229.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
          Length = 307

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 129/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + +D   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EITVPAKWNGISIDSLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E               + +  ++YED  + + NKP  +           
Sbjct: 70  MFMEEEYGVEPE---------------YGELHVVYEDDHVLIVNKPEKMDTHPSEKGGMG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEKYFKNQNVTLVM 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNDTMKEF 302


>gi|294660309|ref|NP_852991.2| pseudouridine synthase [Mycoplasma gallisepticum str. R(low)]
 gi|284811965|gb|AAP56559.2| Pseudouridine synthase [Mycoplasma gallisepticum str. R(low)]
 gi|284930466|gb|ADC30405.1| Pseudouridine synthase [Mycoplasma gallisepticum str. R(high)]
          Length = 311

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 139/326 (42%), Gaps = 25/326 (7%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVR 66
           ++  V ND E +RLD +   +  +++      ++ +  V+V+KK V K N  ++ G VV 
Sbjct: 3   KHTFVNNDSEKIRLDIFLTYNL-NLSRNKTSFLILNDLVKVNKKLVNKNNFVLKVGDVVE 61

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    +  N +  E  IL  +  L          ++YED  + + NKP  +     +   
Sbjct: 62  LEYEESIFNKVSNE--ILPFNKKLD---------IVYEDDDLIIVNKPTNMLSHPTTH-- 108

Query: 127 YHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              D  L      +K QK  L HRLD++T+G++V  +   A + + E    R +++ Y +
Sbjct: 109 NEPDTLLNCLMYHNKKQKVYLAHRLDKDTTGLIVATKNFKALEKIQEQITKRIMKRYYLA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V       +  I   +    ++    +    +N K    AI+   V+D   +K+  ++ 
Sbjct: 169 IVHYPFNELRAVIDAPIG---YLKDHDLKFGVENTKNPKNAITKIYVLD-QNKKYALIKC 224

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           +  TGRTHQ+RVH   +   I+ D  Y    +         K +LHA  ++L HP     
Sbjct: 225 ELLTGRTHQIRVHMDFIKHNIINDPLYGVKGEQRTDY----KQFLHAYQLELTHPTTNVS 280

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNL 330
           L          +K    +    ++ L
Sbjct: 281 LFFEVKPDEVFMKKLFDVHLDLNQEL 306


>gi|225619476|ref|YP_002720733.1| ribosomal large subunit pseudouridine synthase C [Brachyspira
           hyodysenteriae WA1]
 gi|225214295|gb|ACN83029.1| ribosomal large subunit pseudouridine synthase C [Brachyspira
           hyodysenteriae WA1]
          Length = 345

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 71/338 (21%), Positives = 144/338 (42%), Gaps = 46/338 (13%)

Query: 5   TYVQYVVVEND-EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           + ++   +E D EEN R+D++  + + + +    Q ++  G V ++  +VK+   ++ G 
Sbjct: 19  SVIRKCRIEEDVEENTRIDKYMGDRFSYYSRNKWQDLIGQGLVLLNNSKVKYTRTVKKGD 78

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-G 122
            +    +      + K                     ++Y+D  + + NKPA + V   G
Sbjct: 79  EIAYHIIGMKEPEVDKN------------------VTIVYDDGDLIIANKPANLPVIPSG 120

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI--- 179
                 +   +K+ ++S      + +R+D+ETSG +V++R+  +A +       R++   
Sbjct: 121 KYYHNTLHTIVKNMLNSNIN---MLNRIDRETSGCVVLSRSSKSASNFCAMLAGRKVNGK 177

Query: 180 -------QKIYWSLVW-GIPKNKKECIANWLLKKSHI-GGDYVHVVKQNEKGANYAISHF 230
                  +K Y +++        K  +  ++L+  H     +  + K+N +G+ Y+ + F
Sbjct: 178 QYKRNSIKKTYIAVIENAKDIEDKFTVEGYMLESGHEYYRRFQTLHKENVEGSKYSKTSF 237

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ----- 285
           K I         +  + +TGR HQ+RVH    G  +VGD  Y       F   I+     
Sbjct: 238 KTIKRIGDYAVVM-ARLYTGRMHQIRVHLYSKGFFMVGDKIYGKYGPKVFDDFIEKGIIP 296

Query: 286 ----NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
               N+  LHA  +   HP     +++ APLP  + + 
Sbjct: 297 EGFFNRQALHAYSLKFNHPITDEIIKVKAPLPKDLKEL 334


>gi|15639330|ref|NP_218779.1| hypothetical protein TP0339 [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189025572|ref|YP_001933344.1| hypothetical protein TPASS_0339 [Treponema pallidum subsp. pallidum
           SS14]
 gi|3322614|gb|AAC65324.1| conserved hypothetical protein [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189018147|gb|ACD70765.1| hypothetical protein TPASS_0339 [Treponema pallidum subsp. pallidum
           SS14]
          Length = 331

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 137/331 (41%), Gaps = 52/331 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R D +   H        L++I+R+  + V+    KF+  +     V    V +    +I 
Sbjct: 28  RCDVFCAEHVFFCARSQLKRIVRA--LCVNGHTAKFSRPLHVRDRVSFEWVRSVPPALIP 85

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD- 138
           E                +   +L+E+  I   NK  G+ V  G+G   H  G L   +  
Sbjct: 86  EN---------------ISLSILFENEDIIAVNKAQGMIVHPGAG---HWTGTLVQALSF 127

Query: 139 ----------------SKGQ-------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                            KG        +  + HRLD++TSG+L+ +R   A + L  SF+
Sbjct: 128 YRVYRARFEDEFSRQFQKGFPDFFSTLRQGIVHRLDKDTSGVLLTSRNMHAHEALVRSFK 187

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R+++K+Y +L+ G+P      I   +++          V  ++     YA + +KV+  
Sbjct: 188 KRQVRKVYLALLQGVPARGVGVIETTIVRDRRRR--TRFVASEDFSKGKYARTRYKVMKI 245

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                 +++    TGRTHQ+RVHA ++GCP+VGD  Y +         I   L LHA  +
Sbjct: 246 CG-ACAFVQFLLDTGRTHQIRVHARYLGCPVVGDPLYGSRN----ICGIPTTLMLHAYAV 300

Query: 296 DLPHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
               P    R+ + AP+P   V+    L  +
Sbjct: 301 RFVLPRTKKRITLVAPIPLRFVRLIHRLSVR 331


>gi|167757067|ref|ZP_02429194.1| hypothetical protein CLORAM_02616 [Clostridium ramosum DSM 1402]
 gi|167703242|gb|EDS17821.1| hypothetical protein CLORAM_02616 [Clostridium ramosum DSM 1402]
          Length = 279

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 77/300 (25%), Positives = 135/300 (45%), Gaps = 43/300 (14%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
              H N  N++ +L+  QV V+ + + +F+  ++    + +    N  + +         
Sbjct: 16  LLNHYNKKNVKNLLKFKQVSVNGQVISQFDYSLKRDDEIVVDRNPNNNSSL--------- 66

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----IAYHIDG-FLKSWVDSKG 141
                         ++YED ++ V NKPAG+    G       AYH+ G +LKS   +K 
Sbjct: 67  -------------DIIYEDRELIVINKPAGLLSMAGGNEKEKTAYHLVGEYLKS--KNKN 111

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +  + HRLD+ETSG+L+ A+       L  ++     ++ Y +++ G  K K   I N 
Sbjct: 112 ARVFIVHRLDKETSGVLLFAKNEIIKNKLQNNWNDIVYKRGYLAIIEGKLKKKHGTIKNH 171

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L          +  +  N KG   AI+++KV+   ++    +E+   TGR +Q+RVH   
Sbjct: 172 L----DESKTQMVYIANNGKG-KLAITNYKVLK-ESRYNSLIEVFLETGRKNQIRVHMQS 225

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
           +G  IVGD KY A      T+    ++ LH+      HP+   R++  A +P    K + 
Sbjct: 226 LGHSIVGDKKYGA------TTNPIKRMGLHSHVFAFVHPDTKARMEFKAVVPEEFKKMFK 279


>gi|313147267|ref|ZP_07809460.1| RNA pseudouridylate synthase [Bacteroides fragilis 3_1_12]
 gi|313136034|gb|EFR53394.1| RNA pseudouridylate synthase [Bacteroides fragilis 3_1_12]
          Length = 305

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 72/308 (23%), Positives = 128/308 (41%), Gaps = 33/308 (10%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  +Q G  V I    N   
Sbjct: 23  EPMELMDFLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQPGMKVLISKDKNK-- 80

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLK 134
                           K        ++YED+ I V  K  G+   G            L 
Sbjct: 81  ----------------KEFRHPLLKIVYEDAYIIVVEKKEGLLSVGTDRQKERTAQHILS 124

Query: 135 SWV--DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V    +G +  + HRLD++TSG+++ A+     + L + +      + Y ++V G  +
Sbjct: 125 EYVGRSGRGNRIFVVHRLDRDTSGLMMFAKDEKTQRTLRDHWHDIVTDRRYVAVVTGEME 184

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + +WL  ++     YV     ++ G+  +I+H++ I   A  +  +E++  TGR 
Sbjct: 185 KDSDTVVSWLTDRTL----YVSSSSYDDGGSK-SITHYRTIKR-ANGYSLVELRLETGRK 238

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +Q+RVH   +G P++GD +Y  +   N       +L LHA  +   HP   + ++   P 
Sbjct: 239 NQIRVHMQDLGHPLIGDGRYGIDGGPN----PLGRLALHAFKLCFYHPVTDQLMEFETPY 294

Query: 312 PAHMVKTW 319
           P    K +
Sbjct: 295 PPAFKKLF 302


>gi|261418827|ref|YP_003252509.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|297531211|ref|YP_003672486.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|319765643|ref|YP_004131144.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
 gi|261375284|gb|ACX78027.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC61]
 gi|297254463|gb|ADI27909.1| pseudouridine synthase, RluA family [Geobacillus sp. C56-T3]
 gi|317110509|gb|ADU93001.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC52]
          Length = 299

 Score =  192 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 70/317 (22%), Positives = 132/317 (41%), Gaps = 36/317 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ +    + +++  K+ +   +     +      V+++ + V +   +     +++   
Sbjct: 12  IIPSWWSGLTIEQLLKDVWA-ASKKLAHRWRMEHGVKLNGQAVPWKTVLNERDRLQLYAY 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHI 129
               + I+ E + L                +L+ED  + V NK AGI +     G    +
Sbjct: 71  EPEPSFIVPEYREL---------------SILWEDDHLLVLNKEAGIDIHPSEPGQTGTL 115

Query: 130 DGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              +  ++ S+    K R  HRLD++TSG ++ A+   A   L      R I++ Y +LV
Sbjct: 116 ANAVAFYLQSQAILTKVRHIHRLDRDTSGAILFAKHPLAGATLDRMLAHRAIKRTYVALV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    K   I+  + +  H          +  K    A++H++VI  F      +E+  
Sbjct: 176 HGRLSPKSGTISAPIGRDRHHPTRR-----RVSKTGAKAVTHYRVIKTFPS-TSLVELSL 229

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH  H+G P+VGD  Y          P+ ++  LHA  +   HP      I
Sbjct: 230 ETGRTHQIRVHLAHLGHPLVGDVLYGGK-------PVFHRHALHAAKLTFRHPFTNEEVI 282

Query: 308 ----TAPLPAHMVKTWD 320
               T+  P  + + ++
Sbjct: 283 CLAPTSDFPTDLSRIYN 299


>gi|163852141|ref|YP_001640184.1| pseudouridine synthase [Methylobacterium extorquens PA1]
 gi|163663746|gb|ABY31113.1| pseudouridine synthase [Methylobacterium extorquens PA1]
          Length = 239

 Score =  192 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 79/239 (33%), Positives = 117/239 (48%), Gaps = 11/239 (4%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           SV+       +   LLY D+ + V +KPAG+ V  G      +   L +      ++P  
Sbjct: 6   SVSDRTVGPEIGPPLLYRDALMLVIDKPAGLPVHPGPKGGPTLTDHLDALRFGLPRRPEA 65

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
           THRLD++TSG LV+ R   A   L   F   ++ K YW+LV G P+  +  I   L K+S
Sbjct: 66  THRLDRDTSGCLVLGRHAKALARLNRLFADGKVDKTYWALVEGGPEAMEGRIDLPLAKRS 125

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               D      + +     +++ ++V+    +  CWLE++P TGRTHQLRVH   MG PI
Sbjct: 126 ---DDPRSWWMKTDPAGAPSLTFYRVLGR-TEGLCWLELKPVTGRTHQLRVHCAAMGWPI 181

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
            GD  Y    +          L LHAR + LP +P+   + + AP PAHM    ++ G 
Sbjct: 182 RGDAIYGGAGRDG------PGLQLHARGLSLPLYPKREAIAVEAPAPAHMRAGLEACGM 234


>gi|313894254|ref|ZP_07827819.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313441078|gb|EFR59505.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 288

 Score =  192 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 128/316 (40%), Gaps = 35/316 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M++  Y V E  E  + + ++ K  +   +  ++Q + R  +V+V+ +       ++ G 
Sbjct: 1   MSWKTYTVKEPTE--LTVSKYVKERFSLSSR-DIQMMFRKKRVKVNSRVAHSQRSLKKGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-G 122
           V+ +                L    +     +     +LYED+   V NK   + V   G
Sbjct: 58  VLTLE---------------LPQDKDYGVDVEKGPITVLYEDAHTLVINKDPFMLVHPAG 102

Query: 123 SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  +  ++  +   KG   K R  HRLD++TSG ++  +T+ A Q+ T+  +  RI 
Sbjct: 103 QTKSCTLSNYVAGYYAKKGVVHKVRPVHRLDRDTSGCILFGKTKEAQQYYTDELQAGRID 162

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           +IY  LV G   +    +   +          V      ++    A + + V+       
Sbjct: 163 RIYTGLVEGRIDSD-GVVDAPIGIDPVFDNRRVI-----DEFGQPAQTEYIVLSHDGD-H 215

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL-PH 299
             L  +  TGRTHQ+RVH  H+G PIVGD  Y    K         +  LHA  +   P+
Sbjct: 216 TLLRFRLLTGRTHQIRVHMEHIGHPIVGDAMYGTCNKP------YTRQCLHASELTFVPY 269

Query: 300 PEGGRLQITAPLPAHM 315
            +   + +T  +    
Sbjct: 270 GKDEAITVTCEVGEDF 285


>gi|306827367|ref|ZP_07460654.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus pyogenes ATCC
           10782]
 gi|304430514|gb|EFM33536.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus pyogenes ATCC
           10782]
          Length = 301

 Score =  192 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 63/277 (22%), Positives = 117/277 (42%), Gaps = 27/277 (9%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L KI  + G + V+         +Q G VV I          ++          
Sbjct: 21  DVSKGLLAKIKYKGGNILVNGIEQNAIYLLQVGDVVTIDIPNEEPFEKLE---------- 70

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL 146
               +      +++ED    V NKP G +    +  +  I  F+K++        Q+  +
Sbjct: 71  ----AIPFDLDIVHEDDHFLVINKPIGFASIPSAIHSNTIANFIKAYYVDNHYLDQQVHI 126

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD++TSG+++ A+   A   L +  + R ++K Y++LV G      E      + +S
Sbjct: 127 VTRLDRDTSGLMLFAKHGYAHARLDKQLQTRSVEKRYFALVSGNGTLPDEGDIIAPIGRS 186

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                   + +  +    YA + +KV+  +++    ++++ HTGRTHQ+RVH  H+G P+
Sbjct: 187 KDS----IITRAVDPMGKYAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGFPL 242

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +GD  Y        T     +  LH  Y++   P   
Sbjct: 243 LGDDLYGGRLDLGIT-----RQALHCHYLNFKDPFTE 274


>gi|257066092|ref|YP_003152348.1| pseudouridine synthase, RluA family [Anaerococcus prevotii DSM
           20548]
 gi|256797972|gb|ACV28627.1| pseudouridine synthase, RluA family [Anaerococcus prevotii DSM
           20548]
          Length = 305

 Score =  192 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 69/321 (21%), Positives = 141/321 (43%), Gaps = 34/321 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D++  +    I    ++  ++  +++V+   VK + ++  G  + I   +  +  + 
Sbjct: 9   IRIDKFISDELEEIPREKIKDFIKDKKIKVNNSFVKPSFKLSEGDEIEIDDSLFHVPELK 68

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSW 136
            E                ++  ++YE+    + +K + + V     I     ++G L  +
Sbjct: 69  AED---------------MELKIVYENDDYAIIDKDSNVIVHPAGKIITGTLVNGLLGRY 113

Query: 137 VD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                       +P + HRLD++T+G++ + +T  A ++  + F  R++ K Y+++V+G 
Sbjct: 114 GYDGLSHIGGDDRPGIVHRLDKDTTGLIAITKTNEAYKYFKKMFETRKVDKYYYAIVFGN 173

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              KK  I N++ +  H                  A+SH++VI    + F  + ++  TG
Sbjct: 174 FDKKKGTIDNFMDRDVHNRRKMAVR-----NTGRRAVSHYEVI-SEVEGFSLVRIKIETG 227

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQ+RVH  H+  PI+GD  Y  N K  F     +   LH   +   + EG  +   A 
Sbjct: 228 RTHQIRVHMTHINHPILGDPVYG-NVKHKFN---LDHQLLHCGKVGFKNMEGDYVTYEAI 283

Query: 311 LPAHMVKTWDSLGFKYDRNLY 331
                +K    LG   D++++
Sbjct: 284 PHEDFLKYQKILGLG-DKDVF 303


>gi|83312510|ref|YP_422774.1| putative pseudouridine synthase in lpd 3'region [Magnetospirillum
           magneticum AMB-1]
 gi|82947351|dbj|BAE52215.1| Hypothetical pseudouridine synthase in lpd 3'region
           [Magnetospirillum magneticum AMB-1]
          Length = 225

 Score =  192 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 73/233 (31%), Positives = 115/233 (49%), Gaps = 10/233 (4%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L + LLY D  + + +KPAG++V  G     H+  +L +      ++P L HRLD+ETS
Sbjct: 2   DLLARLLYRDPAVLIIDKPAGLAVHAGPKGGEHLMLYLDALSFGLKRRPELAHRLDRETS 61

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G LV+ RT  A   L E F      K YW++V G P+  +  I   L K+    G  + V
Sbjct: 62  GCLVLGRTSKALAGLGELFAKGLADKTYWAVVVGKPREDQGVIDYALKKREKKFGWRMEV 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               ++    +++ ++++    +   WLE +P TGRTHQ+R H   +G P+VGD  Y   
Sbjct: 122 ----DRTGLASVTQWRLLGSDGR-LSWLECRPLTGRTHQIRAHCAAIGHPLVGDSIYGRG 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
                 +   ++L LH+R + LP   G   +   AP+P HM+      G+   
Sbjct: 177 T----GTLAGDRLMLHSRRIVLPFHAGKPPIAAEAPVPEHMLSVLKGCGWSES 225


>gi|71910662|ref|YP_282212.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
 gi|71853444|gb|AAZ51467.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
          Length = 301

 Score =  192 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 63/278 (22%), Positives = 117/278 (42%), Gaps = 29/278 (10%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L KI  + G + V+         +Q G VV I          ++          
Sbjct: 21  DVSKGLLAKIKYKGGNILVNGIEQNAIYLLQVGDVVTIDIPNEEPFEKLE---------- 70

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL 146
               +      +++ED    V NKP G +    +  +  I  F+K++        Q+  +
Sbjct: 71  ----AIPFDLDIVHEDDHFLVINKPIGFASIPSAIHSNTIANFIKAYYVDNHYLDQQVHI 126

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKK 205
             RLD++TSG+++ A+   A   L +  + R I+K Y++LV G      +  I   + + 
Sbjct: 127 VTRLDRDTSGLMLFAKHGYAHARLDKQLQTRSIEKRYFALVSGNGMLPDEGDIIAPIGRS 186

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                    + +  +    YA + +KV+  +++    ++++ HTGRTHQ+RVH  H+G P
Sbjct: 187 -----KDSIITRAVDPMGKYAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGFP 241

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++GD  Y        T     +  LH  Y++   P   
Sbjct: 242 LLGDDLYGGRLDLGIT-----RQALHCHYLNFKDPFTE 274


>gi|254796544|ref|YP_003081380.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Neorickettsia risticii str. Illinois]
 gi|254589781|gb|ACT69143.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Neorickettsia risticii str. Illinois]
          Length = 315

 Score =  192 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 68/302 (22%), Positives = 136/302 (45%), Gaps = 32/302 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +V   +   RLD +   + P  +   ++  ++ G+V+ D K      R++  + V +   
Sbjct: 16  IVAECDVGNRLDVFLHRYLPFFSRTFIKHCIKGGRVKADGKI-----RLEPSKQVLLGEE 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HI 129
            + L+  ++++          +H+      + YED  + V +KPAG+ V  G G     +
Sbjct: 71  YHLLDLPLEQKP---------RHAFVQPLDVRYEDDSLLVIHKPAGLVVHPGIGNKEQTL 121

Query: 130 DGFLKSWVDSK------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              L+    ++        +P + HRLD++T+G L+VA+T  +   L+E  +   I++ Y
Sbjct: 122 VNILEHHYPTEQLSNLDSSRPGIVHRLDKDTAGFLIVAKTNPSHVRLSEMIKEGVIRREY 181

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCW 242
            +LV  +P + +  I     K    G   + + K +      A++++ V+     +K+  
Sbjct: 182 LALVHSVPASLRGEIK----KSIKRGQRKMMIGKCS---GKPALTYYNVLARTVDRKYSL 234

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +  +  +GRTHQ+R+H   +GCP+VGD  Y      +  +       L A  +   HP  
Sbjct: 235 VHCKLGSGRTHQIRLHMKSIGCPVVGDKLYGLKRDADLCAAHH---ALWAYSLQFRHPFT 291

Query: 303 GR 304
            +
Sbjct: 292 DK 293


>gi|228984465|ref|ZP_04144642.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
 gi|228775168|gb|EEM23557.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
          Length = 307

 Score =  192 bits (487), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 129/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + +D   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EITVPAKWNGISIDSLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E               + +  ++YED  + + NKP  +           
Sbjct: 70  MFMEEEYGVEPE---------------YGELHVVYEDDHVLIVNKPEKMDTHPSEKGGMG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEKYFKNQNVTLVM 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    +        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQTR------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNDTMKEF 302


>gi|261493572|ref|ZP_05990092.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261310754|gb|EEY11937.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 242

 Score =  192 bits (487), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 108/245 (44%), Gaps = 18/245 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MTLDILYQDDLLIAINKPAGMLVHRSWLDKHETVFAMQTLRDQIGQHVFPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ ++E F   ++QK Y ++V G  +   +      +    I   +    
Sbjct: 61  VLLFALNSETARVMSEQFEQHQVQKTYLAVVRGYLQGSAQIDYPLTVILDKIADKFSQ-- 118

Query: 217 KQNEKGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              EK A  AI+ +K          V      ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 ---EKEAQAAITDYKGLATVEMPYAVGKHQTARYSLVELSPKTGRKHQLRRHLKHLFHPI 175

Query: 267 VGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD KY    +    +      +L LHA  +   HP+   +++I APL     + +    
Sbjct: 176 MGDSKYGDLHQNRALAEKSGVSRLMLHAHKLQFQHPKNLQKIEIIAPLDEQWQRLFAFFD 235

Query: 324 FKYDR 328
           + + +
Sbjct: 236 WNFTQ 240


>gi|15675107|ref|NP_269281.1| hypothetical protein SPy_1127 [Streptococcus pyogenes M1 GAS]
 gi|13622265|gb|AAK34002.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS]
          Length = 301

 Score =  192 bits (487), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 63/278 (22%), Positives = 117/278 (42%), Gaps = 29/278 (10%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L KI  + G + V+         +Q G VV I          ++          
Sbjct: 21  DVSKGLLAKIKYKGGNILVNGIEQNAIYLLQVGDVVTIDIPNEEPFEKLE---------- 70

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL 146
               +      +++ED    V NKP G +    +  +  I  F+K++        Q+  +
Sbjct: 71  ----AIPFDLDIVHEDDHFLVINKPIGFASIPSAIHSNTIANFIKAYYVDNHYLDQQVHI 126

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKK 205
             RLD++TSG+++ A+   A   L +  + R I+K Y++LV G      +  I   + + 
Sbjct: 127 VTRLDRDTSGLMLFAKHGYAHARLDKQLQTRSIEKRYFALVSGNGMLPDEGDIIAPIGRS 186

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                    + +  +    YA + +KV+  +++    ++++ HTGRTHQ+RVH  H+G P
Sbjct: 187 -----KDSIITRAVDPMGKYAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGFP 241

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++GD  Y        T     +  LH  Y++   P   
Sbjct: 242 LLGDDLYGGRLDLGIT-----RQALHCHYLNFKDPFTE 274


>gi|237735862|ref|ZP_04566343.1| RNA pseudouridylate synthase [Mollicutes bacterium D7]
 gi|229381607|gb|EEO31698.1| RNA pseudouridylate synthase [Coprobacillus sp. D7]
          Length = 294

 Score =  192 bits (487), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 77/300 (25%), Positives = 135/300 (45%), Gaps = 43/300 (14%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
              H N  N++ +L+  QV V+ + + +F+  ++    + +    N  + +         
Sbjct: 31  LLNHYNKKNVKNLLKFKQVSVNGQVISQFDYSLKRDDEIVVDRNPNNNSSL--------- 81

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----IAYHIDG-FLKSWVDSKG 141
                         ++YED ++ V NKPAG+    G       AYH+ G +LKS   +K 
Sbjct: 82  -------------DIIYEDRELIVINKPAGLLSMAGGNEKEKTAYHLVGEYLKS--KNKN 126

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +  + HRLD+ETSG+L+ A+       L  ++     ++ Y +++ G  K K   I N 
Sbjct: 127 ARVFIVHRLDKETSGVLLFAKNEIIKNKLQNNWNDIVYKRGYLAIIEGKLKKKHGTIKNH 186

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L          +  +  N KG   AI+++KV+   ++    +E+   TGR +Q+RVH   
Sbjct: 187 L----DESKTQMVYIANNGKG-KLAITNYKVLK-ESRYNSLIEVFLETGRKNQIRVHMQS 240

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
           +G  IVGD KY A      T+    ++ LH+      HP+   R++  A +P    K + 
Sbjct: 241 LGHSIVGDKKYGA------TTNPIKRMGLHSHVFAFVHPDTKARMEFKAVVPEEFKKMFK 294


>gi|20808199|ref|NP_623370.1| pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter
           tengcongensis MB4]
 gi|20516793|gb|AAM24974.1| Pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter
           tengcongensis MB4]
          Length = 268

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 67/291 (23%), Positives = 135/291 (46%), Gaps = 38/291 (13%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
            + K    G++RV+ ++      ++ G V+ +     + + + +E               
Sbjct: 12  KMYKW--HGEMRVNGEKENVKRVLKEGDVIELSLFDTSSDILPQE--------------- 54

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQK--PRLTHRLDQ 152
            +   + YED +I + +KPAG+ V          +   +  + + KG K   R  +RLD+
Sbjct: 55  -MDLSICYEDDEILIVDKPAGMVVHPTRRYREGTLANGVAYYFEKKGIKTLIRPVNRLDK 113

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++ A+      +L      + + K Y+++V G  + +   I   + +KS     +
Sbjct: 114 GTSGIVIFAKEPFMQYYLQIV---KPMSKFYYAIVNGKLEGE-GIIDVPIKRKS-----F 164

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + + ++  +  + AI+++K +    ++F  L+++  TGRTHQ+RVH  ++G PIVGD  Y
Sbjct: 165 MTIEREVSEEGDRAITYYKSLKA-TEEFSLLKIKIATGRTHQIRVHLNYIGHPIVGDDLY 223

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                    +    +  LHA  +   HP   + + + APLP  + + ++ L
Sbjct: 224 GE------PTSYIERPALHAYRVTFFHPLKEKVISVYAPLPEDIKRLFELL 268


>gi|237741960|ref|ZP_04572441.1| tRNA pseudouridine synthase A [Fusobacterium sp. 4_1_13]
 gi|229429608|gb|EEO39820.1| tRNA pseudouridine synthase A [Fusobacterium sp. 4_1_13]
          Length = 290

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 78/300 (26%), Positives = 144/300 (48%), Gaps = 20/300 (6%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +++ D E++R+DR+ + H  +IN   + K+LR G+++V+ K++  + R+  G +V I   
Sbjct: 5   IIDEDYESVRVDRFLRKHLKNINLSEIYKMLRKGKIKVNNKKISQDYRLVLGDIVFIF-- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
              L    KE              + LK ++++E+  ++V NK  G  V  GSG    + 
Sbjct: 63  ---LPESFKENNEKKFIELNQVRKEKLKQMIVFENENLFVINKSLGDVVHKGSGHDISLL 119

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              +S+  +        +R+D+ TSG+++ A+     + + +  +   I K Y+ LV G 
Sbjct: 120 EEFRSYYSNNNIN--FVNRIDRLTSGLVIGAKNIKTTREIAKEIQQGNIIKKYFILVNGK 177

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +     + N+L K      + V V    ++    +I++FK I  +  ++  LE +  TG
Sbjct: 178 IEKDNFILENYLKKDE----EKVIVSDIEKERYKKSITYFKKIKEY-DRYTLLEAELKTG 232

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQLR    H+G  IVGD KY  N K +        L+ +   +DL +     +++  P
Sbjct: 233 RTHQLRAQLNHIGNNIVGDTKYGRNEKEDIMY-----LFSYYLKIDLYNL---EIKLEIP 284


>gi|167563550|ref|ZP_02356466.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           oklahomensis EO147]
          Length = 247

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 82/231 (35%), Positives = 119/231 (51%), Gaps = 14/231 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  I   NKPAG++V GGSG+A+ +   ++       +   L HRLD+ETSGIL++
Sbjct: 15  ILFEDDAIIALNKPAGVAVHGGSGVAFGVIEQMRHAR-PHAKFLELVHRLDRETSGILML 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVK 217
           A+ R+A   L E  R  R+ K Y++ V G           +   L K S   G+    V+
Sbjct: 74  AKKRSALVGLHEQIRENRMDKRYFACVHGEWAPDWGRRRAVKAPLFKYSTPDGERRVRVQ 133

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---- 273
           ++      + + F ++DC+   +  LE +  TGRTHQ+RVH  H+G PIVGD KY     
Sbjct: 134 ED---GLPSHTVFNLVDCWPD-YALLEAELKTGRTHQIRVHLAHLGLPIVGDAKYGDFAL 189

Query: 274 -ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                     P   +++LHA  + L HP  G  LQ  APLPA   +  D L
Sbjct: 190 NKALARANAVPSLKRMFLHAHRLRLAHPLTGEPLQFDAPLPAECRQFLDQL 240


>gi|238018437|ref|ZP_04598863.1| hypothetical protein VEIDISOL_00263 [Veillonella dispar ATCC 17748]
 gi|237864908|gb|EEP66198.1| hypothetical protein VEIDISOL_00263 [Veillonella dispar ATCC 17748]
          Length = 289

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 130/316 (41%), Gaps = 35/316 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M++  Y V E  E  + + ++ K  +   +  ++Q + R  +V+V+ +       ++ G 
Sbjct: 1   MSWKTYTVKEPTE--LTVSKYVKERFSLSSR-DIQMMFRKKRVKVNSRVAHSQRSLKKGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-G 122
           V+ +                L    +     +     +LYED+   V +K   + V   G
Sbjct: 58  VLTLE---------------LPQDKDYGVDVEKGPITVLYEDAHTLVVDKAPFMLVHPAG 102

Query: 123 SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  +  ++  +   KG   K R  HRLD++TSG ++  +T+ A Q+ T+  +  RI 
Sbjct: 103 QTKSGTLSNYVAGYYAKKGVVHKVRPVHRLDRDTSGCILFGKTKEAQQYYTDELQAGRID 162

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           +IY  LV G   N    +   +          V      ++    A + + V+    +  
Sbjct: 163 RIYTGLVEGRI-NSDGVVDAPIGVDPVFDNRRVI-----DEFGQPAQTEYTVLGHEGE-H 215

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL-PH 299
             L+ +  TGRTHQ+RVH  H+G PIVGD  Y    K         +  LHA  +   P+
Sbjct: 216 TLLKFKLLTGRTHQIRVHMEHIGHPIVGDAMYGTRNKP------YTRQCLHASELTFVPY 269

Query: 300 PEGGRLQITAPLPAHM 315
            +   + +T  +    
Sbjct: 270 GKDEAMTVTCEVGDDF 285


>gi|118581355|ref|YP_902605.1| RluA family pseudouridine synthase [Pelobacter propionicus DSM
           2379]
 gi|118504065|gb|ABL00548.1| pseudouridine synthase, RluA family [Pelobacter propionicus DSM
           2379]
          Length = 310

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 75/340 (22%), Positives = 138/340 (40%), Gaps = 45/340 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +    +   +   RL+ + +   P  +F   +K++RSG V+V+      ++ +     V 
Sbjct: 1   MLTYTITPHDHCRRLESYLRLLLPQASFAYPRKLIRSGAVKVNAAPATADSLLTIDDRVT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    +    I  E+  LD               +LYED +I + NKP+G+++   +   
Sbjct: 61  LKESTSLTALISTERPGLD---------------ILYEDDQIAIVNKPSGLAMHRTAEQE 105

Query: 127 YHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            ++     +++  +G   K    +RLD+ TSG +++A++  AA       +   + K+Y 
Sbjct: 106 TNLVEQGTAFMAWRGTPCKLYPVNRLDRGTSGAVILAKSSTAAGIFGRQVKETGLDKLYL 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G P      I   L                         + ++++      F  LE
Sbjct: 166 ALVAGRPDGA-GVIDAPL-------------------DGKECRTDYRLL-AQGCGFSLLE 204

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           + P +GR HQ+R H   +G PI+GD +Y                 LH+    L  P+G R
Sbjct: 205 LLPFSGRMHQIRRHLEMIGHPILGDQRYSGRVVEELA-----GFALHSFRTGLTMPDGRR 259

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNLYIKRL--YSQDECK 342
           L + APL   ++      G + D  L + +    S+DE  
Sbjct: 260 LVVCAPLTDELLALCQQGGIESDSLLPLLKRVALSRDEAG 299


>gi|307245726|ref|ZP_07527812.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307254697|ref|ZP_07536525.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307256915|ref|ZP_07538693.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|307259139|ref|ZP_07540869.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306853428|gb|EFM85647.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306862370|gb|EFM94336.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306864649|gb|EFM96554.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306866806|gb|EFM98664.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 244

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 110/244 (45%), Gaps = 18/244 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELEILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPVHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ ++E F   +++K Y ++V G   +K E      +    I   +    
Sbjct: 61  VLLFALNSKMARLMSEQFEQHQLEKGYLAVVRGYLLDKGEIDYPLKVILDKIADKFSQ-- 118

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               K A  A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 ---PKEAQQAVTFYQNLASVEMPYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI 175

Query: 267 VGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD KY    +    +     ++L LH+ ++   HP+   +++I APL       + +  
Sbjct: 176 MGDTKYGDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLDEQWQNVFLTFN 235

Query: 324 FKYD 327
           + + 
Sbjct: 236 WNFP 239


>gi|295114100|emb|CBL32737.1| pseudouridine synthase, RluA family [Enterococcus sp. 7L76]
          Length = 283

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 127/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETATFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVFPTIHL---GEATRVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|284931618|gb|ADC31556.1| Pseudouridine synthase [Mycoplasma gallisepticum str. F]
          Length = 311

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 75/326 (23%), Positives = 139/326 (42%), Gaps = 25/326 (7%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVR 66
           ++  V ND E +RLD +   +  +++      ++ +  V+V+KK V K N  ++ G VV 
Sbjct: 3   KHTFVNNDSEKIRLDIFLTYNL-NLSRNKTSFLILNDLVKVNKKLVNKNNFVLKVGDVVE 61

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    +  N +  E  IL  +  L          ++YED  + + NKP  +     +   
Sbjct: 62  LEYEESIFNKVSNE--ILPFNKKLD---------IVYEDDDLIIVNKPTNMLSHPTTH-- 108

Query: 127 YHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              D  L      +K QK  L HRLD++T+G++V  +   + + + E    R +++ Y +
Sbjct: 109 NEPDTLLNCLMYYNKKQKVYLAHRLDKDTTGLIVATKNFKSLEKIQEQITKRIMKRYYLA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V       +  I   +    ++    +    +N K    AI+   V+D   +K+  ++ 
Sbjct: 169 IVHYPFNELRAVIDAPIG---YLKDHDLKFGVENTKNPKNAITKIYVLD-QNKKYALIKC 224

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           +  TGRTHQ+RVH   +   I+ D  Y    +         K +LHA  ++L HP     
Sbjct: 225 ELLTGRTHQIRVHMDFIKHNIINDPLYGVKGEQRTDY----KQFLHAYQLELTHPTTNVP 280

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNL 330
           L          +K    +    ++ L
Sbjct: 281 LFFEVKPDEVFMKKLFDVHLDLNQEL 306


>gi|144575467|gb|AAZ53825.2| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 7448]
          Length = 304

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 68/316 (21%), Positives = 129/316 (40%), Gaps = 35/316 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINA 73
           D+E++R+D        +++    Q ++   +V ++   V K N  +++GQ ++I      
Sbjct: 12  DQEDIRID-ILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKR 70

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYH 128
               ++  +I                 ++++D  + + NKP  + V  G G     +   
Sbjct: 71  PKPQLEPAEI--------------DFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNG 116

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +     S       +P + HRLD++T+G+L+VA+   A          R+I++ Y ++V 
Sbjct: 117 LISHFDSLEQLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVI 176

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEM 245
           G   +K   I   + +                  +  AI++ ++I  F    Q F  ++ 
Sbjct: 177 GKVLHKFMKINLPIGRDLKNPLKKTISFF----NSKPAITNVELIKHFNYQNQDFSLVKC 232

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           Q  TGRTHQ+R+H  H+G PI GD  Y           +  +L  HA  +      G   
Sbjct: 233 QLETGRTHQIRLHLAHIGYPIYGDPIYGKKI-----DELGQRL--HAYKLVFKDLNGLSR 285

Query: 306 QITAPLPAHMVKTWDS 321
           +  A LP      ++ 
Sbjct: 286 EFQADLPEEFNIAFEQ 301


>gi|189463385|ref|ZP_03012170.1| hypothetical protein BACCOP_04104 [Bacteroides coprocola DSM 17136]
 gi|189429814|gb|EDU98798.1| hypothetical protein BACCOP_04104 [Bacteroides coprocola DSM 17136]
          Length = 307

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 118/303 (38%), Gaps = 39/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       I+   ++ +L +  V VD      +N  ++ G  V+I    N          
Sbjct: 34  FLMKKMAGISRTRVKALLTNRVVLVDNNIQTLYNYPLKPGMKVQISREKNK--------- 84

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV----QGGSGIAYHI-DGFLKSWV 137
                             +LYED+ + V  K  G+            A HI + ++K   
Sbjct: 85  ---------HEFRHPMLKILYEDAYLIVVEKKEGLLSVATDHQKEKTAQHILNEYVKR-- 133

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +  +  + HRLD+ETSGI++ A+       L +++      + Y S+V G  +  +  
Sbjct: 134 QHRNNRVFVVHRLDRETSGIMMYAKDEKTQHTLRDNWHDIVRDRRYVSIVMGDMEKDQGT 193

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + +WL                 + G  Y+++H++ I   A  +  +E+Q  TGR +Q+RV
Sbjct: 194 VESWLT-----DRKLYVSSSPVDDGGKYSVTHYRTIKR-ANGYSLVELQLETGRKNQIRV 247

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +G P+VGD +Y              +L LHA  +   HP  G  ++   P P    
Sbjct: 248 HMQSLGHPVVGDERYGCEVNP------LGRLALHAFKLCFYHPVTGELMEFETPYPTPFK 301

Query: 317 KTW 319
              
Sbjct: 302 NLM 304


>gi|310640867|ref|YP_003945625.1| pseudouridine synthase, rlua family protein [Paenibacillus polymyxa
           SC2]
 gi|309245817|gb|ADO55384.1| pseudouridine synthase, RluA family protein [Paenibacillus polymyxa
           SC2]
          Length = 293

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 74/326 (22%), Positives = 131/326 (40%), Gaps = 38/326 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRI 59
           M       Y+V E  E    L  +   H   +   +++  L  GQV V+       N  +
Sbjct: 1   MDKAPAKTYIVQEPAE----LLSFLVEHVTGMGRNSIKSALARGQVSVNGIPRTVHNFPL 56

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + GQ V +                  S   +          +L+ED  I V +K AG+  
Sbjct: 57  EQGQTVAL------------------SKEKVAPVVPLTGLRILHEDEAIIVIHKDAGLLS 98

Query: 120 QGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +    +  +         +    +  + HRLD++TSG+++ A++ A  Q + ++++ 
Sbjct: 99  VASAQEQEVTAYRQLTAHVRREHPYNRIFVLHRLDRDTSGVMMFAKSEAIQQEMQQAWKE 158

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
              ++ Y +LV G  K +   I +WL                      +A++H+K +   
Sbjct: 159 VVYERTYIALVEGQVKKETGTITSWL----KESKTLKMYSSPYPNDGQHAVTHYKRLQAN 214

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + F  LE++  TGR +Q+RVH   +G PIVGD KY +  K         +L LHA+ + 
Sbjct: 215 -RHFSLLEVRLETGRKNQIRVHMEDIGHPIVGDKKYGSKSKS------IGRLGLHAKVLS 267

Query: 297 LPHPEGGR-LQITAPLPAHMVKTWDS 321
             HP  G  L+  +  P   +  +  
Sbjct: 268 FIHPLTGVLLRFESDTPKTFLNPFRE 293


>gi|19746076|ref|NP_607212.1| hypothetical protein spyM18_1088 [Streptococcus pyogenes MGAS8232]
 gi|21910322|ref|NP_664590.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28895899|ref|NP_802249.1| hypothetical protein SPs0987 [Streptococcus pyogenes SSI-1]
 gi|50914193|ref|YP_060165.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|71903490|ref|YP_280293.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94988598|ref|YP_596699.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|94990474|ref|YP_598574.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94994396|ref|YP_602494.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|139473780|ref|YP_001128496.1| RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo]
 gi|209559410|ref|YP_002285882.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pyogenes NZ131]
 gi|251782299|ref|YP_002996601.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|19748247|gb|AAL97711.1| conserved hypothetical protein [Streptococcus pyogenes MGAS8232]
 gi|21904518|gb|AAM79393.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28811149|dbj|BAC64082.1| conserved hypothetical protein [Streptococcus pyogenes SSI-1]
 gi|50903267|gb|AAT86982.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|71802585|gb|AAX71938.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94542106|gb|ABF32155.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|94543982|gb|ABF34030.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94547904|gb|ABF37950.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|134272027|emb|CAM30266.1| putative RNA pseudouridylate synthase [Streptococcus pyogenes str.
           Manfredo]
 gi|209540611|gb|ACI61187.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pyogenes NZ131]
 gi|242390928|dbj|BAH81387.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
          Length = 301

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 64/277 (23%), Positives = 117/277 (42%), Gaps = 27/277 (9%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L KI  + G + V+         +Q G VV I          ++          
Sbjct: 21  DVSKGLLAKIKYKGGNILVNGIEQNAIYLLQVGDVVTIDIPNEEPFEKLE---------- 70

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL 146
               +      +++ED    V NKP G +    +  +  I  F+K++        Q+  +
Sbjct: 71  ----AIPFDLDIVHEDDHFLVINKPIGFASIPSAIHSNTIANFIKAYYVDNHYLDQQVHI 126

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD++TSG+++ A+   A   L +  + R I+K Y++LV G      E      + +S
Sbjct: 127 VTRLDRDTSGLMLFAKHGYAHARLDKQLQTRSIEKRYFALVSGNGTLPDEGDIIAPIGRS 186

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                   + +  +    YA + +KV+  +++    ++++ HTGRTHQ+RVH  H+G P+
Sbjct: 187 KDS----IITRAVDPMGKYAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGFPL 242

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +GD  Y        T     +  LH  Y++   P   
Sbjct: 243 LGDDLYGGRLDLGIT-----RQALHCHYLNFKDPFTE 274


>gi|242280705|ref|YP_002992834.1| pseudouridine synthase [Desulfovibrio salexigens DSM 2638]
 gi|242123599|gb|ACS81295.1| pseudouridine synthase [Desulfovibrio salexigens DSM 2638]
          Length = 292

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 119/270 (44%), Gaps = 22/270 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++V V   E   +L R+ +      +    + + +R G VRVDK R K  + ++ GQ VR
Sbjct: 4   EFVQVTKAEAGQKLVRFLERRVDGAVPRSAIMRWIRKGNVRVDKGRCKPFDLVKEGQTVR 63

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IPP                 +    +H    +  ++YED       KPAG+  QGG+G  
Sbjct: 64  IPPY---------------KAEETAQHKKLPELPIIYEDDNYLAVCKPAGLPTQGGTGHD 108

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIYWS 185
             +   L S       KP   HRLD++TSG+++  ++    + L++ F       K Y +
Sbjct: 109 DSVADRLLSMFADAHYKPAPAHRLDRDTSGVILAGKSHQGQKDLSDFFAEHGEGGKFYLA 168

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G    +     +  ++KS   G    VV  + K A+ ++    +     +K   L +
Sbjct: 169 EVEGRWPEEDWVELHDKMEKSGSKG-REKVVVGSGKDASSSVCPVTI----GEKSSLLIV 223

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           + HTGRTHQ+RV     G PI GD KY   
Sbjct: 224 KLHTGRTHQIRVQLSSRGFPIAGDVKYGGQ 253


>gi|313888154|ref|ZP_07821828.1| putative rRNA pseudouridylate synthase C [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312845844|gb|EFR33231.1| putative rRNA pseudouridylate synthase C [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 329

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 76/305 (24%), Positives = 130/305 (42%), Gaps = 31/305 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ ++V  ++E  RLDR+ K ++       + K LR   + V+ K+ K  + +  G  ++
Sbjct: 1   MREIIVNKNDEGRRLDRFLKIYFEKAPLSFIYKNLRKKNIVVNGKKAKPEDILGEGDEIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          + E+ I     ++ K  +     +LYED  I +  KP  +     S   
Sbjct: 61  L---------FLAEETIEKFKKDIKKSKNSKLPDILYEDEDIILVKKPINMLTHNDS--K 109

Query: 127 YHIDGFLKSWVD------------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            + D  L   VD             K  +P   +RLD+ TSGIL+ A+   + Q L ++ 
Sbjct: 110 AYQDNALDRMVDYLIAQGDYNPRLEKSFRPAFVNRLDRNTSGILIGAKNLKSLQDLNDAI 169

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R I+K+Y +LV G      +   N  LKK+        + K + +    AI+ F V+ 
Sbjct: 170 KKREIKKLYLTLVAGRVTKDFDVDIN--LKKTGNN----VMKKSSREEGKRAITEFNVLK 223

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHAR 293
              + +  L +   TGRTHQ+R      G  IVGD KY  +     F     +  +LH  
Sbjct: 224 SN-KDYSLLSVNLITGRTHQIRASLKEEGLAIVGDRKYGEDRVNKIFRESGLDSQFLHNY 282

Query: 294 YMDLP 298
            +   
Sbjct: 283 AIVFE 287


>gi|295401808|ref|ZP_06811773.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294976175|gb|EFG51788.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 305

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 66/299 (22%), Positives = 127/299 (42%), Gaps = 32/299 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V+ +  E   ++   K  +   +     ++     ++++ K   +   ++    +++   
Sbjct: 13  VIPSFWEGRTIESLLKEVWC-ASKKLAHQLRMEKGIKLNGKEASWQTPLKEKDRLQLHLY 71

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HI 129
               + II E + L                +L+ED  + + NK AGI +          +
Sbjct: 72  KPEPSIIIPEYREL---------------SVLWEDEHLLIINKGAGIDIHPSEPSQTGTL 116

Query: 130 DGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              +  ++ ++G   K R  HRLD++TSG ++ A+   A   L      R+I++ Y +LV
Sbjct: 117 ANAVAFYLQAQGILTKVRHIHRLDRDTSGTILFAKHPLAGATLDRMLEKRQIKRTYVALV 176

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQ 246
            GI K+K   I+  + +  H          +  K    A++H++V+  F   +   +E+ 
Sbjct: 177 HGIVKHKSGTISAPIGRDRHHPTRR-----RVSKTGAKAVTHYRVLHTFPDEQTSLVELS 231

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
             TGRTHQ+RVH  ++G P+VGD  Y             ++  LHA  +   HP    +
Sbjct: 232 LDTGRTHQIRVHMSYIGHPLVGDVLYGGK-------DTFHRQALHAVKLSFLHPFTNEM 283


>gi|169335579|ref|ZP_02862772.1| hypothetical protein ANASTE_01994 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258317|gb|EDS72283.1| hypothetical protein ANASTE_01994 [Anaerofustis stercorihominis DSM
           17244]
          Length = 307

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 141/324 (43%), Gaps = 25/324 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +++  +  +MRLDR+       ++   +QK+LR   ++V+ K+ + + R +    V+
Sbjct: 1   MREIIITEEFMDMRLDRFISK-VTTLSKGEIQKLLRKKYIKVNGKKQEGSYRTEKLDKVQ 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                                 NL    +     ++YED  I + +KP+GI  Q      
Sbjct: 60  FFLSDEVFKQD-----------NLHSKLNTNNLNIIYEDKNIILIDKPSGILSQADGSSK 108

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             I   L S+++SK     +  RLD  TSGI++  + R A   L E  + + I K Y +L
Sbjct: 109 EDIVSNLISYLNSKST--GIVTRLDLNTSGIVLAGKNRRALMLLNEMSKNKLIDKRYLTL 166

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +++  + ++ +K +      +   K +    ++ +S   +I    +    LE++
Sbjct: 167 VRGDF-DREGKVTHYGIKDNKENKLILGNKKVD---GSFEVSAEFIIKKRYKYHTLLEVR 222

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPE---- 301
             TG+THQ+R     MG P+VGD KY  + + GN      N+ +LH   + L + E    
Sbjct: 223 LITGKTHQIRSQLDKMGFPVVGDRKYNKSKQCGNKDDFKINRQFLHCYKLTLKYSEKYKE 282

Query: 302 --GGRLQITAPLPAHMVKTWDSLG 323
                    + LP  +      LG
Sbjct: 283 IVTEDKTFYSDLPKDLKNVLKELG 306


>gi|303239847|ref|ZP_07326370.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
 gi|302592557|gb|EFL62282.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
          Length = 337

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 74/355 (20%), Positives = 139/355 (39%), Gaps = 66/355 (18%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
             +N++    + ++       I+   ++K+    ++  +K+ V  N  ++SG V+ +   
Sbjct: 6   TADNNDNGKAV-KYILKSKLDISERLIKKLKYQSKILCNKQPVFVNAVVKSGDVIEVEIE 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            +     +  Q               L   ++YED  + V NK   I V        H D
Sbjct: 65  YDEELEGLVPQD--------------LPIDIIYEDDCLIVINKAPDIVVHP---TCSHPD 107

Query: 131 GFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + V    QK       R   RLD+ TSGI++ A+   + + L      +   K Y 
Sbjct: 108 GTLANAVAYHLQKSGVAKKIRPVIRLDRNTSGIIIFAKNSFSQESLIRQMNTKTFVKEYI 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            +V+GI KN +  I   + +K     +   +++      + +++HF+ ++        L+
Sbjct: 168 GIVYGILKNTRGTIDLPIERK-----EGSIMLRHVSLSGDRSVTHFETLEVL-NNTSLLK 221

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYC------------------------------- 273
            +  TGRTHQ+RVH   +G P++GD  Y                                
Sbjct: 222 FRLETGRTHQIRVHCQAIGHPLIGDTLYPFLDISQTPELMSRTDGDDIYYEIGNSISSNE 281

Query: 274 ----ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                N + +    I  +  LH+  ++  HP   + LQ+ AP+P  +  + + L 
Sbjct: 282 NSITQNLEFHPELNIIERQALHSYKVEFIHPLTKKNLQLVAPIPKDINNSLEILR 336


>gi|78221275|ref|YP_383022.1| pseudouridine synthase, RluD [Geobacter metallireducens GS-15]
 gi|78192530|gb|ABB30297.1| Pseudouridine synthase, RluD [Geobacter metallireducens GS-15]
          Length = 295

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 78/316 (24%), Positives = 131/316 (41%), Gaps = 38/316 (12%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVIN 72
             E  MRLD      +P ++   ++KI+  G   V    V+  +R +++G+ + +  +  
Sbjct: 9   EGEAGMRLDDGAVRLFPQLSKTRVRKIIDWGGCAVAGAMVRVASRTLRAGEEIVLGVMEP 68

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----SGIAYH 128
                +                 + +  LL+E+      NK AG++ Q       G   H
Sbjct: 69  ERYQELA----------------YTRDDLLFENDDYLAVNKAAGLNCQRTPYQLKGTVEH 112

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                   + S+ +  R+ HRLD+ TSG+++  +T+ AA H++   +  R++K+YW+LV 
Sbjct: 113 AVTLYLRTLGSQ-EPARVIHRLDRGTSGVMIFPKTKRAAAHISAQLKEGRVEKVYWALVT 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
             P + +  +   + K   +G     V          A++ F VI         +E +P 
Sbjct: 172 AEPASDQWEVNAPIAK---VGSARYGVATP----GREALTRFAVIARGTCGV-LVEARPL 223

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT 308
           TGRTHQ+RVH  H G PIVGD  Y              ++ LH R M     +   +   
Sbjct: 224 TGRTHQIRVHLAHCGLPIVGDPTYGGEKA--------PRMMLHCRAMSFTAADRRPITAE 275

Query: 309 APLPAHMVKTWDSLGF 324
           APL         S G 
Sbjct: 276 APLDDPFRDACASRGI 291


>gi|225028084|ref|ZP_03717276.1| hypothetical protein EUBHAL_02354 [Eubacterium hallii DSM 3353]
 gi|224954554|gb|EEG35763.1| hypothetical protein EUBHAL_02354 [Eubacterium hallii DSM 3353]
          Length = 422

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 88/396 (22%), Positives = 154/396 (38%), Gaps = 63/396 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +   EE  R D++   + P  +   L K+LR   ++++ K+ +   ++ +G +++
Sbjct: 1   MKEITITKREEGQRFDKFLIKYLPGASSGFLHKMLRKKNIKLNGKKAEGREKLTAGDLIQ 60

Query: 67  IPPVINALNHIIKEQKILDSS--------------------------------------- 87
           I      L      Q   D S                                       
Sbjct: 61  IFFSDETLEKFQNPQSGRDDSYEADSSMENHKSDRGFGQSGRNRQPDREQAKVYTKDRAG 120

Query: 88  -----VNLTKHSDFLK--SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--- 137
                  LTK    L+    +LY    I VF+KPAG+  Q        ++ +L  +    
Sbjct: 121 NGGQERKLTKEERELRKQVRVLYSSEDILVFHKPAGMLSQRAKASDDSLNDYLIDYCIQT 180

Query: 138 ------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                 +  G +P + +RLD+ TSGI++   +    Q L    R R + K Y  LV G  
Sbjct: 181 GIISKEELAGFRPSIANRLDRNTSGIVLAGISIKGLQRLASMLRERTLGKYYLCLVEGKV 240

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K     IA +L K+     + V + K+  +GA+Y  + +KV+     K   L+++  TG+
Sbjct: 241 KEDA-RIAGYLTKEEK--NNKVSLHKEKAEGASYIETEYKVLKS-TDKASLLKIRLITGK 296

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGG--RLQI 307
           +HQ+R H   +G P+ GD+KY      N        N   LH+  + +P   G    L I
Sbjct: 297 SHQIRGHLASVGHPVFGDYKYGNRDFNNQIKWKDGVNYQLLHSYELVVPEGTGELFGLHI 356

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQ 343
             P+P    K     G +     Y     +++   +
Sbjct: 357 IDPVPEVFHKVQTRWGLEVPELSYENEAKNRETDNK 392


>gi|329122013|ref|ZP_08250622.1| RluA family pseudouridine synthase [Dialister micraerophilus DSM
           19965]
 gi|327467065|gb|EGF12577.1| RluA family pseudouridine synthase [Dialister micraerophilus DSM
           19965]
          Length = 290

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 66/314 (21%), Positives = 134/314 (42%), Gaps = 37/314 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V    +   + ++ K +   ++    +KI  +G V ++  ++   N  +     V     
Sbjct: 7   VPEKWDGCSIKKFIKGYC-GLSTNLWKKIKWNGSVILNGVQIYNANIVVHVNDKVVCEWS 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHI 129
                   +E  I+ S + L          ++YED+ + + +K A + +   S      +
Sbjct: 66  --------EETDIIPSCIPL---------KIIYEDNTLLIIDKDADMIIHPTSKTETNTL 108

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              +  +     Q       +RLD+ T+G++VVA++      L++      I++ Y ++V
Sbjct: 109 VNAISGYYKKNNQMSGIHPIYRLDRNTTGLIVVAKSAKLQYELSK--EHGTIKREYLAVV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  KNK+  I   + +K     ++             A + +KVI+        L+++ 
Sbjct: 167 EGRFKNKEGSIIYPIGRKEGSIIEWKVR-----DDGKEARTDYKVIEEKPS-CTLLKLRL 220

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
           +TGRTHQ+RVH   +G P+VGD  Y  N           +  LH+ ++   HP+ G  ++
Sbjct: 221 YTGRTHQIRVHMSFLGHPLVGDDLYGGNCSK------LKRQALHSHHISFIHPDTGECME 274

Query: 307 ITAPLPAHMVKTWD 320
             +P+P  M + ++
Sbjct: 275 FKSPMPYDMYEFFE 288


>gi|270293436|ref|ZP_06199644.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M143]
 gi|270278098|gb|EFA23947.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M143]
          Length = 291

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 70/303 (23%), Positives = 125/303 (41%), Gaps = 30/303 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
              +      M +  + +     I    ++  LR    + ++ K V +N  ++ G + ++
Sbjct: 4   TFTLPESLPQMTVKHFLEEQLL-IPR-KIRHFLRIKKNILINHKEVHWNEMVKPGDICQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       +++IL  + +L +         +Y+D  + + NKP G+   G      
Sbjct: 62  TFDEEDY----PKKEILWGNPDLVQE--------IYQDQHLIIVNKPEGMKTHGNQPDEI 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   GQ   + HRLD ETSG+++ A+       L      + I + YW+LV
Sbjct: 110 ALLNHVSAYV---GQTCYVVHRLDMETSGLVLFAKNPFILPILNRLLEKKEIAREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +K+    + + +  H     V     + K   YA +  + +  F  K   +  + 
Sbjct: 167 EGQVGSKELIFRDKIGRDRHDRRKRV----VDAKSGQYAETQVRRLKQFLNKTSLVRCKL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H   PI+GD  Y +  K         +L LHA  +   HP    +L 
Sbjct: 223 KTGRTHQIRVHLSHHKHPILGDPLYNSRSKA-------GRLMLHAFRLSFTHPLTLEKLS 275

Query: 307 ITA 309
            TA
Sbjct: 276 FTA 278


>gi|148825977|ref|YP_001290730.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittEE]
 gi|148716137|gb|ABQ98347.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittEE]
          Length = 239

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 111/238 (46%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLIAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q  
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQEN 119

Query: 221 KGANYAISHF---KVID-------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG+  AI+ +   K+++           ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KGSQEAITDYGGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y    +     +    ++L+LH+  +   HP     + ITA L     K  +  G++
Sbjct: 180 QYGDLHQNRALISHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWQKLINQFGWE 237


>gi|257061765|ref|YP_003139653.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8802]
 gi|256591931|gb|ACV02818.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 8802]
          Length = 306

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 73/314 (23%), Positives = 126/314 (40%), Gaps = 34/314 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M    ++    V   +  + +  ++   YPH +    Q+ + SGQ+ ++ +    +  +Q
Sbjct: 1   MLNQGWIYREQVNPSDAGLTILAYYTQRYPHSSQGQWQERIISGQILLNGQPTTPDTPLQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            GQ +                          +    L   +LYED  + V  KP+G+ V 
Sbjct: 61  PGQCLSYH------------------RPPWQEPDVPLAFEVLYEDVDVLVVAKPSGLPVL 102

Query: 121 GGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            G G   H   G LK       + P   HRL + TSG++++AR+  AA HL++  R  ++
Sbjct: 103 PGGGFLEHTLLGQLKRLYPQ--ETPTPIHRLGRGTSGLMLLARSPLAASHLSKQMRQGQM 160

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y +LV       +  I   + K  H    YV+    +     +A S  +V+    Q 
Sbjct: 161 TKVYHALVGAGDLPHQFSIHQPIGKIPHPVLGYVYGATPD---GLFAHSDCRVLQRSTQG 217

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFK-------GNFTSPIQNKLYL 290
              +E++  TGR HQ+R+H   +G P++GD  Y      +            P      L
Sbjct: 218 -TLVEVRIFTGRPHQIRIHLASVGYPLLGDPLYEVGGIPRTAPKIEVNKLPVPGDCGYLL 276

Query: 291 HARYMDLPHPEGGR 304
           H+  +   HP    
Sbjct: 277 HSHLLGFTHPRTHE 290


>gi|325270275|ref|ZP_08136882.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           multiformis DSM 16608]
 gi|324987576|gb|EGC19552.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           multiformis DSM 16608]
          Length = 296

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 125/304 (41%), Gaps = 34/304 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIK 79
           L  W   +    +   ++  L++  ++V+ K V  F++ +Q+G  V +            
Sbjct: 23  LLEWLLANLKE-SRSKVKATLQNRGIKVNGKCVTQFDHPLQAGDKVSV------------ 69

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                 S              ++YED  + V  K  GI        + ++   L  +   
Sbjct: 70  ------SKSKKNDQFRSRYVKIIYEDRFLVVVEKNTGILSMAAGHASLNVKTVLDDYFRM 123

Query: 140 KGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             QK    + HRLD++TSG+++ A+     Q L   +      + Y ++V G  + ++  
Sbjct: 124 TRQKCTAHVVHRLDRDTSGLMIYAKDMQTEQLLERDWHNIVYDRRYIAVVSGEMEQEEGT 183

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +ANWL         YV      + G  YA++HF+V+D        +E +  TGR +Q+RV
Sbjct: 184 VANWL----KDNKAYVTYSSPVDNGGKYAVTHFRVLDRTV-AHSLVEYRLETGRKNQIRV 238

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
           H+  MG P+ GD KY             ++L LHA  +   HP    R++   P+P    
Sbjct: 239 HSADMGHPVCGDVKYGNGDDP------LHRLCLHAYVLCFYHPVNHQRMEFETPVPTAFR 292

Query: 317 KTWD 320
             + 
Sbjct: 293 HLFK 296


>gi|293364538|ref|ZP_06611261.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           oralis ATCC 35037]
 gi|291316950|gb|EFE57380.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           oralis ATCC 35037]
          Length = 291

 Score =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 128/303 (42%), Gaps = 30/303 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
              +      M + ++ +     I    ++  LR    + ++ K V +N  ++ G + ++
Sbjct: 4   TFTLPESLPQMTVKQFLEEQLL-IPR-KIRHFLRIKKNILINHKEVHWNEMVKPGDICQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                        ++IL  + +L +         +Y+D  + + NKP G+   G      
Sbjct: 62  TFDEEDY----PPKEILWGNSDLVQE--------VYQDQHLIIVNKPEGMKTHGNQPGEI 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   GQ   + HRLD ETSG+++ A+       L      + I + YW+L+
Sbjct: 110 ALLNHVSAYV---GQTCYVVHRLDMETSGLVLFAKNPFILPILNRLLEKKEIARDYWALI 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  ++K+    + + +  H     +     + K   YA +H   +  F  K   +  + 
Sbjct: 167 EGRVESKELVFRDKIGRDRHDRRKRI----VDAKNGQYAETHISRLKQFPNKTTLVRCKL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+R+H  H   PI+GD  Y ++ K        ++L LHA  +   HP    +L 
Sbjct: 223 KTGRTHQIRIHLSHHKHPILGDPLYNSSSK-------VSRLMLHAFRLSFTHPLTLEQLS 275

Query: 307 ITA 309
            TA
Sbjct: 276 FTA 278


>gi|86156624|ref|YP_463409.1| pseudouridine synthase RluD [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85773135|gb|ABC79972.1| Pseudouridine synthase, RluD [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 299

 Score =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 85/316 (26%), Positives = 139/316 (43%), Gaps = 27/316 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRI 67
            ++V + +   R+DR+       I+    ++ + +G V VD +R K   R +  GQ V +
Sbjct: 5   TLLVPDVDRYERIDRFIAAR-GGISRGLARRAIEAGGVFVDGRRCKVAGRTLTPGQQVVV 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                          + +     +  +   +  LLY D+ +   +KPAG+  Q       
Sbjct: 64  N--------------LEEGGRAASAPAALGRERLLYADADLCAVDKPAGVPAQPTLTTDR 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                L S +   G    L HRLD+ETSG+ V ARTR AA  L E+FR    +K Y +L 
Sbjct: 110 GALPELVSAL--LGAPVTLVHRLDRETSGVTVFARTREAAAALAEAFRTGAPEKTYLALC 167

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
              P   +  +A  L K     G     +++ +   + A + ++ +   A     +E +P
Sbjct: 168 ARAPSPAEGRVALALGKDPARPG-----LRRVDPAGDPAATRYRTL-REAPGGAQVEARP 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            TGRTHQ+RVH   +G P++GD +Y    +         ++ LHA  ++LPHP  G R+ 
Sbjct: 222 ETGRTHQIRVHLAALGAPLLGDARYGGPRR--VGEVAVPRVMLHAARLELPHPVTGVRMV 279

Query: 307 ITAPLPAHMVKTWDSL 322
             A  P        +L
Sbjct: 280 FEAEPPDDFRAVEAAL 295


>gi|257066386|ref|YP_003152642.1| pseudouridine synthase, RluA family [Anaerococcus prevotii DSM
           20548]
 gi|256798266|gb|ACV28921.1| pseudouridine synthase, RluA family [Anaerococcus prevotii DSM
           20548]
          Length = 318

 Score =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 64/307 (20%), Positives = 126/307 (41%), Gaps = 28/307 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ V +  ++ N R DR+ + ++ +     +QK +R    +++ KR K ++ +    +V+
Sbjct: 1   MKEVRISENDGNQRFDRFLRKYFENAPLSVIQKNIRKKNFKINDKRAKKDDFVYPNDIVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +       +  I           +          ++YED+ I + +K +G+     S   
Sbjct: 61  MYIKDEDYDKWI---------TKIDYKPSDFDLDIVYEDNNIIIMDKKSGLLTHSSSKKD 111

Query: 127 YHI---DGFLKSWVDSKG-------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           Y     D  L     +K         KP + +RLD+ T+G+++ A+   + + L ++ R 
Sbjct: 112 YGNNLVDNMLHYLYKTKSFDMSDRTFKPAVVNRLDRNTAGLVIGAKNAESLRSLNKAIRE 171

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
            +I K Y ++V G  + +           +HI  +         +      ++FK ++  
Sbjct: 172 NKIDKFYLTIVKGYVEKEFSI-------DTHISKNDNRNRVSKSRNGKRIKTNFKPLETN 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYM 295
            +KF  LE +  TG+THQ+R        PI+GD KY              N   L A  +
Sbjct: 225 -KKFSLLECELITGKTHQIRFSLKENSTPIIGDRKYGDRNTNQKLRKFGINNQILLAYKI 283

Query: 296 DLPHPEG 302
              + EG
Sbjct: 284 RFSNIEG 290


>gi|149183528|ref|ZP_01861954.1| ribosomal large subunit pseudouridylate synthase D [Bacillus sp.
           SG-1]
 gi|148848774|gb|EDL62998.1| ribosomal large subunit pseudouridylate synthase D [Bacillus sp.
           SG-1]
          Length = 334

 Score =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 67/309 (21%), Positives = 123/309 (39%), Gaps = 37/309 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
                        + ++     + +D + + +   ++ G  +           I  E   
Sbjct: 53  ALMRDIWQAPKKTVHQLRMDKAIILDGQPLNWTTPLKKGDKLHFSLTEKEYGVIPAE--- 109

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFLKSWVDSKG 141
                        +   +LYED+ + + NKPAG++    +       +   +   +  KG
Sbjct: 110 -------------MPLHILYEDAHMMIVNKPAGMNTHPNNPSLEKDTLANAVAWHLQQKG 156

Query: 142 QKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +K   +  HRLD++T+G +V A+       L      R+I++ YW++V G+  NKK  I 
Sbjct: 157 EKVDVQHIHRLDKDTTGAVVFAKHALVKGILDRLLAERKIKRTYWAIVHGLITNKKGTIT 216

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVH 258
             + +  H          +       A +HF++++    +    +++   TGRTHQ+RVH
Sbjct: 217 KAIGRDRHHNTRR-----RVSPSGQPATTHFQLLEQNKPKNLSLVQLVLDTGRTHQIRVH 271

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPL---PAH 314
              +G P+ GD  Y          PI ++  LHA+Y++  HP    RL   AP    P  
Sbjct: 272 MSSIGHPLAGDTLYGGK-------PIVSRQALHAKYIEFDHPLTEERLAFEAPFLDEPPL 324

Query: 315 MVKTWDSLG 323
               +   G
Sbjct: 325 FSAFFKKEG 333


>gi|148543809|ref|YP_001271179.1| RluA family pseudouridine synthase [Lactobacillus reuteri DSM
           20016]
 gi|184153213|ref|YP_001841554.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227365096|ref|ZP_03849120.1| RluA family pseudouridine synthase [Lactobacillus reuteri MM2-3]
 gi|325681570|ref|ZP_08161092.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           reuteri MM4-1A]
 gi|148530843|gb|ABQ82842.1| pseudouridine synthase, RluA family [Lactobacillus reuteri DSM
           20016]
 gi|183224557|dbj|BAG25074.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227069874|gb|EEI08273.1| RluA family pseudouridine synthase [Lactobacillus reuteri MM2-3]
 gi|324979111|gb|EGC16056.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           reuteri MM4-1A]
          Length = 301

 Score =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 59/246 (23%), Positives = 111/246 (45%), Gaps = 18/246 (7%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSK 140
           +   + N           ++YED    + NKPAG++      +  A  +   +K +   +
Sbjct: 62  LPPETANDNVDVSEAPIDIIYEDQDFLIMNKPAGVATVPAHNVPVADSLVNRVKGYYKRQ 121

Query: 141 GQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             + ++TH   RLD++TSG++V  + R A   L E  +   ++K Y +L+ G    +   
Sbjct: 122 NYENQVTHVATRLDRDTSGLVVFPKHRFAHAVLDEQLKKHLVKKNYLALIKGKVPAEHGY 181

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +  +       V +   K    +++ +   +C  Q    ++++ HTGRTHQ+RV
Sbjct: 182 IDAPIQRDPN-----SFVKRMVGKEGKASVTEYWRQECNVQ-ASLIKIRLHTGRTHQIRV 235

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +G P++GD  Y         S +  +  LH  ++    P  G+ + ++APLP+   
Sbjct: 236 HFASLGFPLIGDKMYGEE------SGLIARQALHCYWLSFYSPFKGKNITVSAPLPSDFK 289

Query: 317 KTWDSL 322
              D L
Sbjct: 290 NAKDDL 295


>gi|297170431|gb|ADI21463.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0070_10G19]
          Length = 312

 Score =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 66/327 (20%), Positives = 130/327 (39%), Gaps = 37/327 (11%)

Query: 10  VVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
             V+      RLD     +     +   ++  +  G V+++ +  K  +++ SG  +   
Sbjct: 6   FFVDETMHGTRLDIAITKYLGRKYSRNQIKNFILGGCVQINDENCKPKDKLVSGDEIEFN 65

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                 +  + E+               +   ++ E +   +  K   + +  G+G    
Sbjct: 66  FNDYHDSSWMPEK---------------IDFNVIDETNDYIIVEKSPNLIMHPGAGNEQG 110

Query: 127 YHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +G L  + + +K  +  + HRLD++TSG+LVVA+T     H+   F+ R ++K Y++
Sbjct: 111 TLANGLLFRFPELAKLPRCGIVHRLDKDTSGLLVVAKTNEFRNHIVSEFQNRNVKKYYYA 170

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLE 244
           L+ G        I   ++    I  D  + ++   ++    A S  K I+ F   +  +E
Sbjct: 171 LIKGN-------ILGQIIINEPILRDKSNRIRMTVDQAGREATSIVKNIETF-DFYSLVE 222

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--------KLYLHARYMD 296
           ++  TGRTHQ+RVH      PI+GD  Y    +                 +  LHA  + 
Sbjct: 223 VEILTGRTHQIRVHMDFNKTPIIGDKIYGHRNQLAKNLSKGKIDAIQQFPRQALHACKLS 282

Query: 297 L-PHPEGGRLQITAPLPAHMVKTWDSL 322
             P      +   + LP  + +  + L
Sbjct: 283 FAPKINSEYVSYQSELPKDIQELVNVL 309


>gi|291059729|gb|ADD72464.1| ribosomal large subunit pseudouridine synthase D [Treponema
           pallidum subsp. pallidum str. Chicago]
          Length = 336

 Score =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 137/331 (41%), Gaps = 52/331 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R D +   H        L++I+R+  + V+    KF+  +     V    V +    +I 
Sbjct: 33  RCDVFCAEHVFFCARSQLKRIVRA--LCVNGHTAKFSRPLHVRDRVSFEWVRSVPPALIP 90

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD- 138
           E                +   +L+E+  I   NK  G+ V  G+G   H  G L   +  
Sbjct: 91  EN---------------ISLSILFENEDIIAVNKAQGMIVHPGAG---HWTGTLVQALSF 132

Query: 139 ----------------SKGQ-------KPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                            KG        +  + HRLD++TSG+L+ +R   A + L  SF+
Sbjct: 133 YRVYRARFEDEFSRQFQKGFPDFFSTLRQGIVHRLDKDTSGVLLTSRNMHAHEALVRSFK 192

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R+++K+Y +L+ G+P      I   +++          V  ++     YA + +KV+  
Sbjct: 193 KRQVRKVYLALLQGVPARGVGVIETTIVRDRRRR--TRFVASEDFSKGKYARTRYKVMKI 250

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                 +++    TGRTHQ+RVHA ++GCP+VGD  Y +         I   L LHA  +
Sbjct: 251 CG-ACAFVQFLLDTGRTHQIRVHARYLGCPVVGDPLYGSRN----ICGIPTTLMLHAYAV 305

Query: 296 DLPHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
               P    R+ + AP+P   V+    L  +
Sbjct: 306 RFVLPRTKKRITLVAPIPLRFVRLIHRLSVR 336


>gi|32491284|ref|NP_871538.1| hypothetical protein WGLp535 [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|25166491|dbj|BAC24681.1| rluD [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 314

 Score =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 72/320 (22%), Positives = 144/320 (45%), Gaps = 37/320 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINA 73
            +   RLD+     +P  +   ++K + + QV+V+    +     I+ G+ ++I   I+ 
Sbjct: 14  SQNGKRLDKSIAEIFPEYSRNKIKKFIINNQVKVNDICIINPKKNIKGGECIKIK--ISK 71

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
            N++I +++                  L+YED  I V NK   + V    G   H +  L
Sbjct: 72  KNNLISKKRKT--------------YKLIYEDDDILVINKYKDVIVHP--GCDKHENTLL 115

Query: 134 K----SWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                ++ DSK   +  + HRLD++T+G++++AR   + + L +  ++R I + Y +++ 
Sbjct: 116 HDILFNYPDSKNLYRAGIVHRLDKDTTGLMLIARNSFSQKKLIKLLKLRLINREYRAVLL 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        ++  +++ S      + V          +I+H+K+I  F   F ++++   
Sbjct: 176 GKIICD-GTVSAPIIRNSK-NRTRMKVHI----SGKESITHYKIIKNFND-FSYVKINLE 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-----NKLYLHARYMDLPHPEGG 303
           +GRTHQ+R+H  ++  P++GD  Y         +  +     ++  LHAR +   HP   
Sbjct: 229 SGRTHQIRLHMSYINHPVLGDFVYGNKKNKYIKTLYKSIFNISRHALHARKIKFIHPINN 288

Query: 304 RLQIT-APLPAHMVKTWDSL 322
            L +    LP  M     +L
Sbjct: 289 CLMVHKIDLPDDMKILLKNL 308


>gi|226491450|ref|NP_001140404.1| hypothetical protein LOC100272459 [Zea mays]
 gi|194699356|gb|ACF83762.1| unknown [Zea mays]
          Length = 419

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 72/310 (23%), Positives = 121/310 (39%), Gaps = 62/310 (20%)

Query: 12  VENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           V   E   R+D W         ++   +Q  +R+G V V+ + V K ++ ++ G +V   
Sbjct: 63  VPVGEGRSRVDAWISARLGGGGVSRARVQASIRAGLVAVNGRPVSKVSHTVKGGDLVSCT 122

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-- 126
                          +     L   ++ +   ++YED  + V NKPA + V    G A  
Sbjct: 123 ---------------VSELQPLRAEAEDIPLDIVYEDDHVLVVNKPAHMVVHPAPGNAKG 167

Query: 127 YHIDGFLKSW-----------------------------------------VDSKGQKPR 145
             ++  L                                            V +   +P 
Sbjct: 168 TLVNAILHHCKISTFTCLARSSAGDECPDSTDEDTDVFHVDQFAAEDVSSEVRNALVRPG 227

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+ TSG+LVVA+   +   L E F++  I+++Y SL  G P      I   + + 
Sbjct: 228 IVHRLDKGTSGLLVVAKDEHSHARLAEQFKLHTIRRVYISLTCGAPNPNSGRIEASIARD 287

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGC 264
            +       +     + A  A S +KV + FA      +E +  TGRTHQ+R HA ++G 
Sbjct: 288 PNNRIRMTAIAGSGHRYARNAASRYKVREVFAGGGSALVEWRLETGRTHQIRAHAKYIGI 347

Query: 265 PIVGDHKYCA 274
           P++GD  Y  
Sbjct: 348 PLLGDETYGG 357


>gi|312904302|ref|ZP_07763464.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
 gi|310632398|gb|EFQ15681.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
          Length = 283

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 73/312 (23%), Positives = 128/312 (41%), Gaps = 37/312 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M L      + V+   EN     W       H              V+++ +   F+  +
Sbjct: 1   MRLPENFSTMTVKELLENE----WLVPRKVRHFLRTR-------KNVKINGETAAFHFPV 49

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI  
Sbjct: 50  QAGDCVTLTF---------EETDYVFPTIHL---GEATRVKVLYEDEHLMIVNKPYGIKT 97

Query: 120 QGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               S     +   + +++  K Q P + HRLD+ETSG +V A+       L      ++
Sbjct: 98  HPNQSQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQ 157

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   + 
Sbjct: 158 IYRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSN 213

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L 
Sbjct: 214 NQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLL 266

Query: 299 HPEGGR-LQITA 309
           HP   + + +TA
Sbjct: 267 HPFTKKQIVVTA 278


>gi|256854461|ref|ZP_05559825.1| pseudouridine synthase [Enterococcus faecalis T8]
 gi|256710021|gb|EEU25065.1| pseudouridine synthase [Enterococcus faecalis T8]
          Length = 288

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 72/312 (23%), Positives = 127/312 (40%), Gaps = 37/312 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M L      + V+   EN     W       H              V+++ +   F+  +
Sbjct: 6   MRLPENFSTMTVKELLENE----WLVPRKVRHFLRTR-------KNVKINGETAAFHFPV 54

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI  
Sbjct: 55  QAGDCVTLTF---------EETDYVFPTIHL---GEATRVKVLYEDEHLMIVNKPYGIKT 102

Query: 120 QGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                     +   + +++  K Q P + HRLD+ETSG +V A+       L      ++
Sbjct: 103 HPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQ 162

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   + 
Sbjct: 163 IYRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSN 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L 
Sbjct: 219 NQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLL 271

Query: 299 HPEGGR-LQITA 309
           HP   + + +TA
Sbjct: 272 HPFTKKQIVVTA 283


>gi|229546507|ref|ZP_04435232.1| pseudouridylate synthase RluD [Enterococcus faecalis TX1322]
 gi|257089108|ref|ZP_05583469.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|229308407|gb|EEN74394.1| pseudouridylate synthase RluD [Enterococcus faecalis TX1322]
 gi|256997920|gb|EEU84440.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|323479863|gb|ADX79302.1| pseudouridine synthase, RluA family protein [Enterococcus faecalis
           62]
          Length = 287

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 72/312 (23%), Positives = 127/312 (40%), Gaps = 37/312 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M L      + V+   EN     W       H              V+++ +   F+  +
Sbjct: 5   MRLPENFSTMTVKELLENE----WLVPRKVRHFLRTR-------KNVKINGETAAFHFPV 53

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI  
Sbjct: 54  QAGDCVTLTF---------EETDYVFPTIHL---GEATRVKVLYEDEHLMIVNKPYGIKT 101

Query: 120 QGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                     +   + +++  K Q P + HRLD+ETSG +V A+       L      ++
Sbjct: 102 HPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQ 161

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   + 
Sbjct: 162 IYRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSN 217

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L 
Sbjct: 218 NQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLL 270

Query: 299 HPEGGR-LQITA 309
           HP   + + +TA
Sbjct: 271 HPFTKKQIVVTA 282


>gi|189467632|ref|ZP_03016417.1| hypothetical protein BACINT_04022 [Bacteroides intestinalis DSM
           17393]
 gi|189435896|gb|EDV04881.1| hypothetical protein BACINT_04022 [Bacteroides intestinalis DSM
           17393]
          Length = 510

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 71/239 (29%), Positives = 114/239 (47%), Gaps = 18/239 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ +       + K  ++YED  + V NKP+G+    G G    +
Sbjct: 278 CEPILQHMLQGLEVEENPMLQLPEQGYGKLKIVYEDKWLLVVNKPSGMLSVPGKGEKESV 337

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               +     +   P + HRLD  TSG+L+VA+ +   QHL   F+   I+K+Y +L+ G
Sbjct: 338 YSLARQLY-PEADGPMIVHRLDMATSGLLIVAKNKKVHQHLQAQFKNHTIRKMYIALLDG 396

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I    +  I   +          V  ++        AI+H++V++    K   +   PHT
Sbjct: 397 IIPQDEGTIELPICPDPLDRPRQVVDMEY----GKPAITHYQVLERR-DKCTRIAFHPHT 451

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           GRTHQLRVHA H   + CPI+GD  Y    K         +LYLHA  ++  HP  GR+
Sbjct: 452 GRTHQLRVHAAHPSGLHCPIIGDELYGRKDK---------RLYLHAESIEFTHPADGRI 501


>gi|212702057|ref|ZP_03310185.1| hypothetical protein DESPIG_00059 [Desulfovibrio piger ATCC 29098]
 gi|212674572|gb|EEB35055.1| hypothetical protein DESPIG_00059 [Desulfovibrio piger ATCC 29098]
          Length = 335

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 86/309 (27%), Positives = 144/309 (46%), Gaps = 17/309 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M        V+V+  E   +L ++ +     +    L + +R+GQVR++  R K    + 
Sbjct: 2   MGEAPDPNTVIVDPREGGQKLLQFLQRRL-DLPPSLLHRWIRTGQVRINGGRAKPFGLVA 60

Query: 61  SGQVVRIPPVINALNHIIKE---QKILDSSVNLTKHSDFLKS--ILLYEDSKIYVFNKPA 115
           +G  VR+PP    ++   K    Q   +        +  L      L +D  ++VF KPA
Sbjct: 61  AGDSVRLPPFALGMSRRSKATGGQASPEQGHEPRPRAQALPPAPRPLQKDGDLWVFCKPA 120

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G+    G+G    +   L +       KP   HRLD++TSGIL+VA + A  + +T + R
Sbjct: 121 GLPTHPGTGHEDSLSSRLAAGAGDAPFKPTPVHRLDKDTSGILLVAASFAVLREMTTALR 180

Query: 176 MRRIQKIYWSLVWGIPKNKKECI-ANWLLKK--SHIGGDYVHVVKQN--EKGANYAISHF 230
            RR++K Y + V G+  +    +  +WL K+  +  G + +HV +    +KG   A+   
Sbjct: 181 ERRMKKEYLAWVEGLWPHSGVRLFRHWLRKEAGTGNGREQMHVRQTGAPDKGETEALLLV 240

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           + +     +   L ++  TGRTHQ+R     +G PI GD KY A  + + T      +YL
Sbjct: 241 RPV-RVEDRRSLLLVRLLTGRTHQIRAQLSSLGHPIEGDVKYGARGRASGT-----PMYL 294

Query: 291 HARYMDLPH 299
           HA  + LP 
Sbjct: 295 HAMRVILPD 303


>gi|303251277|ref|ZP_07337455.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307252489|ref|ZP_07534385.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|302649819|gb|EFL79997.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306860081|gb|EFM92098.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 247

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 110/244 (45%), Gaps = 18/244 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELEILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPVHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ ++E F   +++K Y ++V G   +K E      +    I   +    
Sbjct: 61  VLLFALNSKMARLMSEQFEQHQLEKGYLAVVRGYLLDKGEIDYQLKVILDKIADKFSQ-- 118

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               K A  A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 ---PKEAQQAVTFYQNLASVEMPYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI 175

Query: 267 VGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD KY    +    +     ++L LH+ ++   HP+   +++I APL       + +  
Sbjct: 176 MGDTKYGDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLDEQWQNVFLTFN 235

Query: 324 FKYD 327
           + + 
Sbjct: 236 WNFP 239


>gi|203283948|ref|YP_002221688.1| ribosomal large subunit pseudouridine synthase D [Borrelia duttonii
           Ly]
 gi|201083391|gb|ACH92982.1| ribosomal large subunit pseudouridine synthase D [Borrelia duttonii
           Ly]
          Length = 326

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 75/328 (22%), Positives = 135/328 (41%), Gaps = 34/328 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK---RVKFNNRIQSGQVVRIPPVINALN 75
            RLD +   H    N   ++K       + +      +K +  +     +          
Sbjct: 15  QRLDIYLSEHLCLFNRSQIKKR-ELKAFKFNDGYFSAIKLSKPVFINDRI---------- 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLK 134
            +I+  + +D    L   +  L   +LYED  + V  KP GI    G S +   +  FL 
Sbjct: 64  -LIEFNESIDLGEYLVPLN--LPINILYEDINVIVIEKPQGILSHPGISNLENTVVNFLL 120

Query: 135 SWV-------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             +            +P + HRLD+ETSG+++ A+       L E F+ R ++K+Y ++V
Sbjct: 121 HHISNLRYKFQENKIRPGIVHRLDKETSGVMICAKNLETLNFLFEQFKNRSVKKVYIAIV 180

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  K     I  ++ +  +    +      ++     A++ +KV+    + +  + +QP
Sbjct: 181 KGNFKVDSGIIDTFIDRDRYDRKKF----TVHKNSGKRALTEYKVLISM-KNYSLVVLQP 235

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQLRVH  ++  PI+GD  Y       F       L LH+  +++   EG   + 
Sbjct: 236 KTGRTHQLRVHMKYLNHPILGDDIYS-RLDQEFKEIS---LMLHSFKLEISIKEGFLKKF 291

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            + LP   +    +       +L +K L
Sbjct: 292 ISVLPKRFIDFLSNFYDDATLDLLVKDL 319


>gi|222153007|ref|YP_002562184.1| RNA pseudouridylate synthase [Streptococcus uberis 0140J]
 gi|222113820|emb|CAR41903.1| putative RNA pseudouridylate synthase [Streptococcus uberis 0140J]
          Length = 301

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 68/324 (20%), Positives = 126/324 (38%), Gaps = 50/324 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRS---------------GQVRVDKKRVKFNNRIQSGQ 63
           MR D +  +         ++ +L+S               G + V+ +       +  G 
Sbjct: 1   MRFD-FIADK-----RSKVKTLLKSHDVSKGLLAKVKYKGGNILVNGQEQNAIYLVDVGD 54

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VV I              ++    +    H       ++YED    V NKP G +    +
Sbjct: 55  VVTIHI----------PDELPFEKLEAVPH----PLDIVYEDDHFLVLNKPVGYASIPSA 100

Query: 124 GIAYHIDGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             +  I  F+K++   +     +  +  RLD++TSG+++ A+   A   L +  + R I+
Sbjct: 101 IHSNTIANFIKAYYFEQNYPNKQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQKRSIE 160

Query: 181 KIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           K Y++LV G  +      I   + +          + +  +    YA + ++V+  FA+ 
Sbjct: 161 KRYFALVSGNGQLPDFGEIVEPIGRS-----KDSIITRTVDPMGKYAKTTYEVVARFAEN 215

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              ++++ HTGRTHQ+RVH  H+G P++GD  Y              +  LH  ++   +
Sbjct: 216 VHLVDIKLHTGRTHQIRVHFSHIGFPLLGDDLYGGRM-----DLGIERQALHCHFLSFFN 270

Query: 300 PEGGRLQI-TAPLPAHMVKTWDSL 322
           P      I T  L          L
Sbjct: 271 PFTENESIHTINLTEDFENVIIDL 294


>gi|292669466|ref|ZP_06602892.1| ribosomal large subunit pseudouridine synthase D [Selenomonas noxia
           ATCC 43541]
 gi|292648919|gb|EFF66891.1| ribosomal large subunit pseudouridine synthase D [Selenomonas noxia
           ATCC 43541]
          Length = 290

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 130/327 (39%), Gaps = 44/327 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           MT +   + E  E   R   +       I+    ++I  SG   V+   V      +++G
Sbjct: 1   MTEILVTLPEGTECPAR--AYLMREC-GISSGLWKRIKHSGTFAVNGMPVIAARTVLRAG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +V     +  ++ +I EQ               L   ++YED+ + V +K AG  V   
Sbjct: 58  DMVS--YELPVISSVIPEQ---------------LPLTVVYEDADLLVIDKSAGQLVHPT 100

Query: 123 S-----GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +      +A  + G   +     G  P   HRLD+ T+G+L++A+       +       
Sbjct: 101 TKEAHGTVANAVLGLYAARRAPLGFHP--CHRLDRNTTGLLLIAKHPEVQYQIARQD--- 155

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + + Y +L+ G+   +K CI   + +          +++        A +H++  +   
Sbjct: 156 TLTREYLALIKGMLSPEKGCIDAPIARALP-----SIILRHVAPDGKPARTHYQT-EQTD 209

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                L +   TGRTHQ+RVH  H+G P++GD  Y  N           +  LH+  + L
Sbjct: 210 GTHTLLRLHLETGRTHQIRVHLAHLGHPLLGDDLYGGNADE------IKRHALHSARLTL 263

Query: 298 PHPEGGRL-QITAPLPAHMVKTWDSLG 323
            HP   ++    +PLP  M +    L 
Sbjct: 264 SHPRTQKMLVFESPLPPDMARIAKQLR 290


>gi|322391241|ref|ZP_08064713.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           peroris ATCC 700780]
 gi|321145994|gb|EFX41383.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           peroris ATCC 700780]
          Length = 291

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 75/317 (23%), Positives = 132/317 (41%), Gaps = 31/317 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
              + +    M +  + +     I    ++  LR    + V+++ V ++  I++G   ++
Sbjct: 4   TFTIPDALPEMTVKFFLEEQLL-IPR-KIRHFLRVKKNILVNQEEVHWHQTIKAGDECQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             + +  ++ +KE  I      L K         +Y+D  + V NKP G+   G      
Sbjct: 62  --IFDEEDYPVKE--ITPGDPKLVKE--------IYQDQHLIVVNKPEGMKTHGNQPDEI 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   GQ   + HRLD+ETSG+++ A+       L      + I + YW+LV
Sbjct: 110 ALLNHVSAYV---GQTCYVIHRLDKETSGLVLFAKNPFILPILNRLLEKKEISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  + K+    + L +  H     +     + K    A +    +  F  K   +  + 
Sbjct: 167 DGKIEAKELIFRDKLGRNRHDRRKRI----VDPKNGQCAETQVTRLKQFQNKTSLVRCKL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G PI+GD  Y  + K        ++L LHA  +   HP    +L 
Sbjct: 223 KTGRTHQIRVHLSHHGHPILGDPLYNPHSKT-------SRLMLHAFKLSFIHPLTLKKLS 275

Query: 307 ITAPLPAHMVKTWDSLG 323
            TA L     +     G
Sbjct: 276 FTA-LSDTFERELKQNG 291


>gi|327441282|dbj|BAK17647.1| pseudouridylate synthase, 23S RNA-specific [Solibacillus silvestris
           StLB046]
          Length = 294

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 60/283 (21%), Positives = 115/283 (40%), Gaps = 30/283 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
              G + V+ +     +R+  G  V I   +   +  +                   +  
Sbjct: 37  FDGGAILVNGEERNVRHRLAEGDDVTIIFPVEEASEGL--------------IPVQGELA 82

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGI 157
           ++YED  + + +KPA +S         +    L      + Q     H   RLD++TSG+
Sbjct: 83  VVYEDEAVLLVDKPAFMSSIPSREHPNNTLANLVYGYFEQQQHASTVHIVTRLDRDTSGL 142

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+ R     ++E  +  +I + Y ++  GI    ++ I   + +K     D   + +
Sbjct: 143 MLIAKHRHIHHLMSEQQKKGQIHREYEAVAEGIIVQDQQSIIAPIGRK-----DTSIIER 197

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +      +A +   V+         + ++ HTGRTHQ+RVH  ++G P+VGD  Y     
Sbjct: 198 EVRPDGQFAHTDVTVLTRK-NNMTHIRLKLHTGRTHQIRVHMAYIGHPLVGDELYGG--- 253

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
              T    ++  LH RY++  HP    R+   + LP  +    
Sbjct: 254 ---THTFIDRQALHCRYIEFEHPLTKERVHFESKLPEEISTLI 293


>gi|315638897|ref|ZP_07894069.1| RluA family pseudouridine synthase [Campylobacter upsaliensis JV21]
 gi|315481115|gb|EFU71747.1| RluA family pseudouridine synthase [Campylobacter upsaliensis JV21]
          Length = 325

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 76/345 (22%), Positives = 143/345 (41%), Gaps = 38/345 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +Q  +V+ +    RLD        + +   +  ++ +  V ++ K   K + ++++G ++
Sbjct: 1   MQTFLVDEEA---RLDVKLAKIL-NQSRSQVSLLIENNAVLINDKIQNKNSFKLKNGDII 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +              K L      T++    +  +L+ED  + V NKP  + V G S +
Sbjct: 57  TL--------------KTLPQKELKTQYEVNFEVDVLFEDEDVLVLNKPQNLVVHGASSV 102

Query: 126 --AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             A  ID  L             +  L HRLD+ETSG +++A+   + Q L+E  + + +
Sbjct: 103 KEATLIDWLLAKKYALSNLAGELRAGLVHRLDKETSGAIIIAKNNFSHQRLSEQLQDKSL 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAISHFKVIDCF 236
            +IY +L+    K  K  I   L + +      + + ++N   +  A  A S F  +   
Sbjct: 163 GRIYLALIDLPLKEDKIIINKALTRSTQNRIKKIAIERENYSPKIKAKEAKSAFINL-AL 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           A+    +  +  +GRTHQ+R H   +   I+GD  Y              ++ LHA ++ 
Sbjct: 222 AKDVNLIAAKLFSGRTHQIRAHLASINRHILGDTLYGYKGNE------ICRVMLHAYFVY 275

Query: 297 LPHPEGGRLQI-TAPLPAHMVKTWDS--LGFKYDRNLYIKRLYSQ 338
             HP    L    APL     +  +   L  + D  + +K L  +
Sbjct: 276 FKHPRTKELVFVKAPLMEDFKEILEKKLLIGEDDETISLKHLLGE 320


>gi|300215051|gb|ADJ79467.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 311

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 79/334 (23%), Positives = 134/334 (40%), Gaps = 28/334 (8%)

Query: 4   MTYVQYV-VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQS 61
           M+  ++   V  +   + L       +  +    +  + +R   V++D K    N  +Q 
Sbjct: 1   MSKYKFERTVNAEFSGISLRALLSEKWL-LPRKFIHFLRIRE-NVKIDGKYYPMNTIVQG 58

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            Q + +          I E     ++ +        K  +++E+  + V NKP GI    
Sbjct: 59  NQKIEL----------IFEGDEFRTATSNYIVDKGRKIPIIFENEDLLVVNKPQGIKSHP 108

Query: 122 GSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                   +  ++  ++D+K + P + HRLD  TSG ++VA+       LT       I+
Sbjct: 109 NQPYETGTLMNYIAGYLDAKDEHPYMVHRLDMLTSGAMIVAKNPVVVPILTCLISTHTIK 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++  GI   K+  I   + K  +         K +  GA  A +H++VI  F    
Sbjct: 169 RDYLAITEGIFDQKEGVIDLPIGKDENDKRKR----KVDGIGALPARTHYQVIKEFGNNS 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
               ++  TGRTHQLRVH   MG PIVGD  Y    K       +  + LH     L  P
Sbjct: 225 AVY-LRLETGRTHQLRVHLSAMGHPIVGDVLYNHVSK-------EKHMMLHGYKQKLTLP 276

Query: 301 EGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
              R L++ A +P +     + +      N Y K
Sbjct: 277 FSMRELELKADIPEYFANYEEKIKENKKLNFYKK 310


>gi|256371990|ref|YP_003109814.1| pseudouridine synthase, RluA family [Acidimicrobium ferrooxidans
           DSM 10331]
 gi|256008574|gb|ACU54141.1| pseudouridine synthase, RluA family [Acidimicrobium ferrooxidans
           DSM 10331]
          Length = 309

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 130/319 (40%), Gaps = 41/319 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIP 68
           + +       RLDR        I     Q+++  G V VD +   + + R+++G+++   
Sbjct: 6   LTIGASLAGERLDRAVA-IAGGIERAFAQQLVDDGGVLVDGRVEQRRSRRLRAGELLE-- 62

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                                    +     ++ YED  + V +KPAG+ V         
Sbjct: 63  ---------------ATWPDPAAPPAPEGAPVVCYEDDDVAVIDKPAGLIVHRTHLRDVR 107

Query: 129 I---DGFLKSW-----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               D  L+ W     +     +  L HRLD+ TSG++V+A +  A + L  +     ++
Sbjct: 108 PSVADWALERWPSLRALPGDPLRRGLVHRLDRGTSGLMVIALSAGAYESLRRAVHDHEVE 167

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y +LV G+P      I   L +      D   V   +  G   A +  +V+       
Sbjct: 168 RRYRALVVGVPPQAA-RIEAPLGRDL---RDLSRVAVVS--GGRDARTQLRVV-WHGPDT 220

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E+   TGRTHQ+RVH   +G PIVGD  Y   + G        + +LHA  +   HP
Sbjct: 221 SLVELTLETGRTHQIRVHLSAIGHPIVGDEVYGVPYGG------LERPFLHATALAFEHP 274

Query: 301 EG-GRLQITAPLPAHMVKT 318
              GR+++TA LP  + + 
Sbjct: 275 TRPGRVEVTAELPEDLGEL 293


>gi|150399091|ref|YP_001322858.1| RluA family pseudouridine synthase [Methanococcus vannielii SB]
 gi|150011794|gb|ABR54246.1| pseudouridine synthase, RluA family [Methanococcus vannielii SB]
          Length = 297

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 62/317 (19%), Positives = 129/317 (40%), Gaps = 36/317 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           VE      +L  +    +  ++   ++K  +  ++ V+ K +   +++   +VV +    
Sbjct: 11  VEKKNAGKKLSDFLSEDF-ELSNKMIKKYDKEKKIFVNSKNISLKSKLVENEVVYVNIDA 69

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                I +E                +   ++YED  + + +KP  + V     +      
Sbjct: 70  GNNTIIAEE----------------IPISVIYEDEYVMIIDKPKNMVVHETKNVVSGTLS 113

Query: 132 FL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                +  V+++  K R  +RLD +T+GIL+VA+   +   +++       +K Y  +V 
Sbjct: 114 NAISNRQKVNNQNYKIRFVNRLDMDTTGILIVAKNPYSHYLISKQMDEGIFEKKYICVVN 173

Query: 189 GIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           G  + K   I+N L L +  I  +  +           + + + VI+   +    LE++ 
Sbjct: 174 GHLRLKSGIISNPLDLGEDGIKRELKN-------TGKESKTKYTVIEEL-KNASLLEIEL 225

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TG+THQ+RVH   +G  I+GD  Y         S + ++  LH+  +   HP     + 
Sbjct: 226 FTGKTHQIRVHLSSIGNFIIGDELYGEK------SDLIDRQALHSSSLKFIHPITKENMH 279

Query: 307 ITAPLPAHMVKTWDSLG 323
             + +P  +    + L 
Sbjct: 280 FKSEIPKDIKNLVERLR 296


>gi|315611921|ref|ZP_07886839.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis ATCC 49296]
 gi|315315910|gb|EFU63944.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis ATCC 49296]
          Length = 291

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 128/303 (42%), Gaps = 30/303 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
              +      M + ++ +     I    ++  LR    + ++ K V +N  ++ G + ++
Sbjct: 4   TFTLPESLPQMTVKQFLEEQLL-IPR-KIRHFLRIKKNILINHKEVHWNEMVKPGDICQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                        ++IL  + +L +         +Y+D  + + NKP G+   G      
Sbjct: 62  TFDEEDY----PPKEILWGNSDLVQE--------VYQDQHLIIVNKPEGMKTHGNQPGEI 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   GQ   + HRLD ETSG+++ A+       L      + I + YW+L+
Sbjct: 110 ALLNHVSAYV---GQTCYVVHRLDMETSGLVLFAKNPFILPILNRLLEKKEIAREYWALI 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  ++K+    + + +  H     +     + K   YA +H   +  F  +   +  + 
Sbjct: 167 EGRVESKELVFRDKIGRDRHDRRKRI----VDAKHGQYAETHVSRLKQFPNQTTLVRCKL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+R+H  H   PI+GD  Y ++ K        ++L LHA  +   HP    +L 
Sbjct: 223 KTGRTHQIRIHLSHHNHPILGDPLYNSSSK-------VSRLMLHAFRLSFTHPLTLEQLS 275

Query: 307 ITA 309
            TA
Sbjct: 276 FTA 278


>gi|262195124|ref|YP_003266333.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262078471|gb|ACY14440.1| pseudouridine synthase, RluA family [Haliangium ochraceum DSM
           14365]
          Length = 345

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 83/333 (24%), Positives = 141/333 (42%), Gaps = 42/333 (12%)

Query: 22  DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           D+    H+P  +   +  +   G+VRV+ ++VK    + +G  + +  +  A   ++   
Sbjct: 28  DKLVGEHFPAASRRRVTALFADGRVRVNGRKVKKGAIVPAGAEIALTRLPVADEELVP-- 85

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGFLKSW--- 136
                     + +  L   LLYED  I V +KPAG+              +  +  +   
Sbjct: 86  ----------QANHELVLDLLYEDDAIAVVSKPAGLPSHPLRAGERDTLANALVAHYPEC 135

Query: 137 --VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN- 193
             + +  ++  L HRLD +TSG+LV ART+ A   L  +F    ++K Y +L +G P + 
Sbjct: 136 AAIGADPREAGLAHRLDIDTSGVLVAARTQKAWHALRAAFGSGAVEKHYLALTFGAPSSG 195

Query: 194 -------KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                  ++   A+ + +     G      +     A  A + ++ I+      C L  +
Sbjct: 196 EMDVALVQRGRRAHPVFRDD--AGFGGFGGRGERGDALPARTTWR-IERRFGPACLLLCR 252

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCA-----------NFKGNFTSPIQNKLYLHARYM 295
            HTGR HQ+RVH    G PI+GD  Y             +       P   + +LHA  +
Sbjct: 253 AHTGRMHQIRVHLALAGAPIIGDSLYAPAPETLSAAEREDLAALSEHPEATRHFLHASAV 312

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +PHPE GR L+I APLP    +    L  ++ 
Sbjct: 313 TIPHPETGRALRIEAPLPEGRAQFLAELSRRWP 345


>gi|295110320|emb|CBL24273.1| pseudouridine synthase, RluA family [Ruminococcus obeum A2-162]
          Length = 293

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 69/321 (21%), Positives = 141/321 (43%), Gaps = 33/321 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSG 62
           M  + +  +  +E+   +  + +      +   L  +    + +  + +R+    ++ +G
Sbjct: 1   MNRIFHYQITENEQGTTVLDFLRK--KGFSRHILSSMKADKEALTRNGQRIGGREQLLAG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
              R+      L   +    I+  S+ L+         +LYED  I V NKPA + V   
Sbjct: 59  DHFRV-----RLLETVDSDGIVPVSMPLS---------ILYEDEDILVINKPADMPVHPS 104

Query: 123 SG-IAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            G     +   + +++D+K +    R  +RLD++TSG L++A+   +A  L+   R R+I
Sbjct: 105 IGNYTNTLANGVAAYLDAKDEHSPFRCINRLDRDTSGALILAKNAFSAAVLSTQMRNRQI 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y ++V GI       I+  + +      D V     +      A++H++ ++   + 
Sbjct: 165 RRTYLAVVEGI-TPPNGTISAPISRVD----DSVIERHVDFLRGEPAVTHYERLEVKNE- 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              LE+   TGRTHQ+RVH  ++G P+  D+ Y   +          +  LH+  ++  H
Sbjct: 219 HSLLEIHLETGRTHQIRVHMGYIGHPLPADYLYHPVYD------CFKRQPLHSLQLEFRH 272

Query: 300 PEGGR-LQITAPLPAHMVKTW 319
           P   + + + AP+   M   +
Sbjct: 273 PVTDKPMCLLAPVSEDMCNAF 293


>gi|282883125|ref|ZP_06291724.1| pseudouridine synthase, RluA family [Peptoniphilus lacrimalis
           315-B]
 gi|281296937|gb|EFA89434.1| pseudouridine synthase, RluA family [Peptoniphilus lacrimalis
           315-B]
          Length = 300

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 142/321 (44%), Gaps = 35/321 (10%)

Query: 1   MSLMTYVQYV--VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR 58
           M  +   +++  +V +++   R  ++ +     I+  ++++  R   + V+ KR   N  
Sbjct: 1   MEKLNPYEFLEFIVTDEKIKSR--KFLEKM--DISSRHIRRACRENSIYVNGKRTFENVE 56

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           ++ G  V I     +LN + + + I                 + YED  + + NK     
Sbjct: 57  VKKGDSVAIRFPDESLNALCQYKDI----------------DICYEDYDLLIVNKEYNCV 100

Query: 119 VQGGSGIA-YHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                  +   +  +L  + +     +K R  +RLD++TSG+++VA+   A   + + F 
Sbjct: 101 THTAKDDSKDTLLNYLAGYFEKNNIKRKVRFVNRLDRDTSGLIIVAKNSYAHAKIMDEFS 160

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             ++ KIY ++  G  K K+  I    +KK  +  D +   + ++    YA + ++V+  
Sbjct: 161 NNQVDKIYLAICRGDFKEKQGEI----VKKISLCQDGIRR-EVDDDNGKYAKTKYQVLK- 214

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             +K   ++++  TGRTHQ+RVH   +G PI+GD  Y      N    + N+  LH+  +
Sbjct: 215 DNKKLALVKLKLFTGRTHQIRVHLKSIGHPIIGDKLYN---DSNEEQNLMNRQALHSYSL 271

Query: 296 DLPHPEGGRL-QITAPLPAHM 315
               P  G L   TA L   M
Sbjct: 272 SFKLPRTGELKTFTAKLSDDM 292


>gi|315283354|ref|ZP_07871565.1| ribosomal large subunit pseudouridine synthase D [Listeria marthii
           FSL S4-120]
 gi|313613002|gb|EFR86933.1| ribosomal large subunit pseudouridine synthase D [Listeria marthii
           FSL S4-120]
          Length = 289

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 81/319 (25%), Positives = 135/319 (42%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           MT+V  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  G
Sbjct: 1   MTHV-TLPILEDWEGLSLTTILQEKF-HLGKKARHEIRMSQDVLLNNKPLEDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P              IL   + +  +       ++YED  + V NKP G+     
Sbjct: 59  ASLSLPI-------------ILHEKIPVYAY----DLEIIYEDDFLLVVNKPVGMKTHPN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++  GQ+      HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYERDTCANAVQYYLEKTGQEANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            + Y + V G      + I   + +  H G        Q       A++H KV++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDNEK 216

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L 
Sbjct: 217 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|307277035|ref|ZP_07558141.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|307289950|ref|ZP_07569879.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|306499016|gb|EFM68505.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|306506279|gb|EFM75443.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|315030583|gb|EFT42515.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4000]
 gi|315159704|gb|EFU03721.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0312]
 gi|315161994|gb|EFU06011.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0645]
 gi|315578744|gb|EFU90935.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0630]
          Length = 283

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 127/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVFPTIHL---GEATRVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|254881959|ref|ZP_05254669.1| RNA pseudouridylate synthase [Bacteroides sp. 4_3_47FAA]
 gi|294775568|ref|ZP_06741078.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|319641038|ref|ZP_07995742.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_40A]
 gi|254834752|gb|EET15061.1| RNA pseudouridylate synthase [Bacteroides sp. 4_3_47FAA]
 gi|294450618|gb|EFG19108.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|317387282|gb|EFV68157.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_40A]
          Length = 308

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 66/303 (21%), Positives = 119/303 (39%), Gaps = 34/303 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       I+   ++ +L +  + VD     ++N  ++ G  V+I               
Sbjct: 34  FLMRKMAGISRSKVKALLANRVILVDNVITTQYNFALKPGMKVQI--------------- 78

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDS-- 139
              S V   +        L+YED+ I V  K  G+                L  +V    
Sbjct: 79  ---SKVKNNREFKHPMLKLVYEDAYILVVEKKEGLLSVSTEHQKERTAQHILNEYVKRSH 135

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +  +  + HRLD+ETSG+++ A+       L +++      + Y S+V G  +     + 
Sbjct: 136 RFNRVFVVHRLDRETSGLMMYAKDEKTQNTLRDNWHDIVTDRRYVSIVSGDMEKDYGTVE 195

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WL  +      YV+    +     +A++H+K I   A  +  +E+   TGR +Q+RVH 
Sbjct: 196 SWLTDRKL----YVYSSPVDNGEGKFAVTHYKTIKR-ANGYSLVELDLETGRKNQIRVHM 250

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           L +G P+VGD +Y +            +L LHA  +   HP     ++   P P      
Sbjct: 251 LDLGHPVVGDRRYGSECDP------LGRLALHAFKLCFYHPVTKELMEFETPYPTAFKGL 304

Query: 319 WDS 321
              
Sbjct: 305 MQK 307


>gi|150005860|ref|YP_001300604.1| putative RNA pseudouridylate synthase [Bacteroides vulgatus ATCC
           8482]
 gi|149934284|gb|ABR40982.1| putative RNA pseudouridylate synthase [Bacteroides vulgatus ATCC
           8482]
          Length = 308

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 66/303 (21%), Positives = 118/303 (38%), Gaps = 34/303 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       I+   ++ +L +  + VD     ++N  ++ G  V+I               
Sbjct: 34  FLMRKMAGISRSKVKALLANRVILVDNVITTQYNFALKPGMKVQI--------------- 78

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDS-- 139
              S V   +        L+YED+ I V  K  G+                L  +V    
Sbjct: 79  ---SKVKNNREFKHPMLKLVYEDAYILVVEKKEGLLSVSTEHQKERTAQHILNEYVKRSH 135

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +  +  + HRLD+ETSG+++ A+       L +++      + Y S+V G  +     + 
Sbjct: 136 RFNRVFVVHRLDRETSGLMMYAKDEKTQNTLRDNWHDIVTDRRYVSIVSGDMEKDYGTVE 195

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WL  +      YV     +     +A++H+K I   A  +  +E+   TGR +Q+RVH 
Sbjct: 196 SWLTDRKL----YVSSSPVDNGEGKFAVTHYKTIKR-ANGYSLVELDLETGRKNQIRVHM 250

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           L +G P+VGD +Y +            +L LHA  +   HP     ++   P P      
Sbjct: 251 LDLGHPVVGDRRYGSECDP------LGRLALHAFKLCFYHPVTKELMEFETPYPTAFKGL 304

Query: 319 WDS 321
              
Sbjct: 305 MQK 307


>gi|281423241|ref|ZP_06254154.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           F0302]
 gi|299140516|ref|ZP_07033654.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           C735]
 gi|281402577|gb|EFB33408.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           F0302]
 gi|298577482|gb|EFI49350.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           C735]
          Length = 299

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 124/304 (40%), Gaps = 32/304 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIK 79
           L  W   +   ++   +++ L+   +RV  K V  F+  +  G  +       AL+   +
Sbjct: 24  LLEWLLENVKGLSRSKIKQTLQGRGIRVGSKVVTQFDYPVSVGTKI-------ALSKTKR 76

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              I  S              ++YED  + V  K  GI        + ++   L  +   
Sbjct: 77  NNDIFKSR----------YVKIVYEDRHLVVVEKNIGILSMAAGHSSLNVKAVLDDYFKK 126

Query: 140 KGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             QK    + HRLD+ETSG+++ A+ +     L   +      + Y ++V G  + ++  
Sbjct: 127 SRQKCMAHVVHRLDRETSGLMLYAKDKETELLLERDWHHIVFDRRYVAVVSGEMEQREGT 186

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           IANWL         Y+      + G  YA++HF V++     +  +E +  TGR +Q+RV
Sbjct: 187 IANWL----KDNKAYITYSSPVDNGGKYAVTHFHVLNRN-DNYSLVEYKLETGRKNQIRV 241

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
           H+  MG P+ GD KY              +L LHA  +   HP     +    P+PA   
Sbjct: 242 HSADMGHPVCGDTKYGNGDDP------IGRLCLHAYVLCFYHPITHVPMTFETPIPASFH 295

Query: 317 KTWD 320
           K   
Sbjct: 296 KIIK 299


>gi|118476866|ref|YP_894017.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|196046511|ref|ZP_03113736.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|225863254|ref|YP_002748632.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|229183584|ref|ZP_04310807.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|118416091|gb|ABK84510.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|196022695|gb|EDX61377.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|225789436|gb|ACO29653.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|228599827|gb|EEK57424.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
          Length = 307

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 131/319 (41%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EMTVPAKWNGISIESLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E   LD               ++YED  + + NKP  +       G   
Sbjct: 70  MFMEEEYDVEPEYGELD---------------VVYEDDHVLIVNKPEKMDTHPAEKGGMG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      KG   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV + F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATKRRVSPK-----GDQAITYYKVEEYFKKQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNDTMKEF 302


>gi|315453493|ref|YP_004073763.1| putative ribosomal pseudouridine synthase [Helicobacter felis ATCC
           49179]
 gi|315132545|emb|CBY83173.1| putative ribosomal pseudouridine synthase [Helicobacter felis ATCC
           49179]
          Length = 321

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 73/312 (23%), Positives = 122/312 (39%), Gaps = 36/312 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD+       +I+   +   +++G V +D K   K    ++ G  V +           
Sbjct: 11  RLDQLLAQEL-NISRSQVLGCIKAGLVSMDGKICQKGGVEVKPGSYVCVQ---------- 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                   +  +T     L    LYED  + V NKP  ++V     +    +  +   V 
Sbjct: 60  -----EPPTAEITPLPTTLNIECLYEDEDLLVINKPPHLAVHPAPSLKE--ESLVDYLVA 112

Query: 139 SKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
              Q        +  + HRLD+ETSG LV+A+  A   HL+   + R++ + Y +L+ G 
Sbjct: 113 KGYQLSNLNGTSRCGIVHRLDKETSGALVIAKNNACHAHLSAQLQSRQMGRYYVALIQGH 172

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +     +   L +         ++     KG   + + F  +     K   +  + ++G
Sbjct: 173 LREPLF-VECHLGRHPKNRLKRANLDALKVKGGKPSKTFFVPL-FDGLKCQLVGARLYSG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITA 309
           RTHQ+R H   +G PI+GD  Y A            +  LHA  + L HP  G      A
Sbjct: 231 RTHQVRAHLESLGRPILGDRLYGAKEGSA------KRTMLHAYILYLIHPRTGHQHLFKA 284

Query: 310 PLPAHMVKTWDS 321
            L   MV+   S
Sbjct: 285 ELLKDMVECAQS 296


>gi|71893806|ref|YP_279252.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae J]
          Length = 289

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 67/312 (21%), Positives = 126/312 (40%), Gaps = 35/312 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MR+D        +++    Q ++   +V ++   V K N  +++GQ ++I          
Sbjct: 1   MRID-ILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKRPKPQ 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGF 132
           ++  +I                 ++++D  + + NKP  + V  G G     +   +   
Sbjct: 60  LEPAEI--------------DFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISH 105

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             S       +P + HRLD++T+G+L+VA+   A          R+I++ Y ++V G   
Sbjct: 106 FDSLEQLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVL 165

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHT 249
           +K   I   + +                  +  AI++ ++I  F+   Q F  ++ Q  T
Sbjct: 166 HKFMKINLPIGRDLKNPLKKTISFF----NSKPAITNVELIKHFSYQNQDFSLVKCQLET 221

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           GRTHQ+R+H  H+G PI GD  Y           +  +L  HA  +      G   +  A
Sbjct: 222 GRTHQIRLHLAHIGYPIYGDPIYGKKI-----DELGQRL--HAYKLVFKDLNGLSREFEA 274

Query: 310 PLPAHMVKTWDS 321
            LP      ++ 
Sbjct: 275 DLPEEFNIAFEQ 286


>gi|237752376|ref|ZP_04582856.1| ribosomal large subunit pseudouridine synthase A [Helicobacter
           winghamensis ATCC BAA-430]
 gi|229375865|gb|EEO25956.1| ribosomal large subunit pseudouridine synthase A [Helicobacter
           winghamensis ATCC BAA-430]
          Length = 353

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 139/338 (41%), Gaps = 47/338 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVV 65
           +    + +  + +R D +      +++   +Q ++    + ++ K +K     + +   +
Sbjct: 12  LNTFAITDKNQGIRADIFLSKTL-NLSRSKVQNLISKQAILLNSKPLKKYGTILNANDTL 70

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           ++     A               + ++H   L   ++YEDS + + NKPA + V      
Sbjct: 71  KLISQAKAKQD------------SNSQHLQDLNIPIIYEDSDLLILNKPANLIVH--RID 116

Query: 126 AYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                  L  ++  KG          +  + HRLD+ TSG +V+A+  A   HL+   + 
Sbjct: 117 ENDTQFTLVDYLKQKGFALSNLGDSYRLGIVHRLDKNTSGAIVIAKNNATHAHLSMQIKS 176

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF------ 230
           +++ + Y  ++    KN +  +   +++       Y  +   N   A  A + F      
Sbjct: 177 KQMGRYYLCIINQPLKNPQ-TVEIPIMRHPKQRLKY--ITTTNNVNAKTAKTAFFMIPTL 233

Query: 231 ------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
                 K  +   +    +  +  TGRTHQ+RVH   +   I+GD  Y   +KGN+T   
Sbjct: 234 LDSNFLKTENPKKEIPTLIGAKLFTGRTHQIRVHLNSINRHILGDGFYG--YKGNYT--- 288

Query: 285 QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
             ++ LHA ++ L HP+  + L+  AP+P  M     +
Sbjct: 289 -GRILLHAHFLHLIHPKTQKLLEFHAPIPDDMQNFIKT 325


>gi|33152257|ref|NP_873610.1| tRNA pseudouridine synthase C [Haemophilus ducreyi 35000HP]
 gi|34582379|sp|P59840|TRUC_HAEDU RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|33148479|gb|AAP95999.1| probable pseudouridine synthase Rlu family protein [Haemophilus
           ducreyi 35000HP]
          Length = 243

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 107/248 (43%), Gaps = 18/248 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY D ++   NKPAG+ V             +++  D   Q     HRLD+ TSG
Sbjct: 1   MELDILYRDDELIAINKPAGMLVHRSWLDKAETLFAMQTLRDQINQHVFPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ ++E F   +++K Y ++V G    K E      +    I   +    
Sbjct: 61  VLLFALNSEMARLMSEQFEQHKVEKEYLAIVRGYIAEKGEIDYPLKVILDKIADKFSQ-- 118

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               K A  A++ ++ +               ++  + + P TGR HQLR H  H+  PI
Sbjct: 119 ---PKAAQQAVTFYQNLAKVEMPYSTGKYATTRYSLVALSPKTGRKHQLRRHMKHLFHPI 175

Query: 267 VGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD KY    +    +     N+L LHAR +   HP+   ++ I+A L       ++  G
Sbjct: 176 MGDTKYGDLHQNRRLTEKTGCNRLMLHARLLHFTHPKTLQKITISALLDQQWQMLFNQFG 235

Query: 324 FKYDRNLY 331
           + +    Y
Sbjct: 236 WHFTDFFY 243


>gi|294794409|ref|ZP_06759545.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Veillonella sp. 3_1_44]
 gi|294454739|gb|EFG23112.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Veillonella sp. 3_1_44]
          Length = 301

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 76/317 (23%), Positives = 133/317 (41%), Gaps = 37/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M++  Y V E  E  + + ++ K  +   +  ++Q + R  +V+V+ +       ++ G 
Sbjct: 13  MSWKTYTVKEPTE--LTVSKYVKERFSLSSR-DIQMMFRKKRVKVNSRVAHSQRALKKGD 69

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-G 122
           V+ +                L    +     +     +LYED+   V NK   + V   G
Sbjct: 70  VLTLE---------------LPQDKDYGVDVEKGPITVLYEDAHTLVVNKAPFMLVHPAG 114

Query: 123 SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  +  ++  +   KG   K R  HRLD+ETSG ++  +T+ A Q+ T+  +  RI 
Sbjct: 115 QTKSCTLSNYIAGYYAKKGVVHKVRPVHRLDRETSGCILFGKTKEAQQYYTDELQAGRID 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQK 239
           +IY  LV G        I    +    IG D V   ++  ++    A + + V+      
Sbjct: 175 RIYTGLVEGH-------IDADGMVDEPIGVDPVFDNRRVIDEFGQPAQTEYTVLGYEGDN 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL-P 298
              L  +  TGRTHQ+RVH  H+G PI+GD  Y    K         +  LHA  +   P
Sbjct: 228 -TLLRFKLLTGRTHQIRVHMEHIGHPIIGDAMYGTRNKP------YTRQCLHASELTFVP 280

Query: 299 HPEGGRLQITAPLPAHM 315
           + +   + IT  +  + 
Sbjct: 281 YGKDEAITITCEVGDNF 297


>gi|225028953|ref|ZP_03718145.1| hypothetical protein EUBHAL_03243 [Eubacterium hallii DSM 3353]
 gi|224953728|gb|EEG34937.1| hypothetical protein EUBHAL_03243 [Eubacterium hallii DSM 3353]
          Length = 306

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 70/283 (24%), Positives = 133/283 (46%), Gaps = 27/283 (9%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           + ++ KRV    R + GQ++++       +   K+ KI  + +NL          +LYED
Sbjct: 43  ILLNGKRVTVRARGKEGQLLKVM----LEDSQEKQNKIASTKMNLH---------ILYED 89

Query: 106 SKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGIL 158
             +   +KPAGI      G ++  +   ++++ +++G++        L  RLD+ETSGIL
Sbjct: 90  EDLIFVDKPAGIVSHPSKGHLSDSMINGVQAYFENEGREKNERSNIHLIGRLDKETSGIL 149

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            +A+    A+ + +  +   + K Y++LV G P  +          +    GD + +   
Sbjct: 150 GIAKNSVTAERMIKQRQRGILIKEYYALVKGNPPEEGILEIPMEEMRDARDGDKLKMKVG 209

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             + A  A + F+V+  F +KF  + +   TGRTHQ+R H   +GCP++GD  Y    + 
Sbjct: 210 KSENAKTAKTFFQVVKRF-EKFSLVSLVIETGRTHQIRFHMASIGCPLLGDSFYGDGPE- 267

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
                  ++  LHA+ +   HP   + ++I + +P  +     
Sbjct: 268 ----LGISRTALHAQQLTFTHPFCEKVMRIESEMPKDLSFLLR 306


>gi|256761450|ref|ZP_05502030.1| pseudouridine synthase [Enterococcus faecalis T3]
 gi|256682701|gb|EEU22396.1| pseudouridine synthase [Enterococcus faecalis T3]
          Length = 287

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 127/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 5   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +V+L    +  +  +LYED  + + NKP GI   
Sbjct: 55  AGDCVTLTF---------EETDYVRPTVHL---GEATRVKVLYEDEHLMIVNKPYGIKTH 102

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 103 PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 163 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQTLSNN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 219 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 271

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 272 PFTKKQIVVTA 282


>gi|227528997|ref|ZP_03959046.1| RluA family pseudouridine synthase [Lactobacillus vaginalis ATCC
           49540]
 gi|227351009|gb|EEJ41300.1| RluA family pseudouridine synthase [Lactobacillus vaginalis ATCC
           49540]
          Length = 294

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 59/304 (19%), Positives = 137/304 (45%), Gaps = 34/304 (11%)

Query: 26  KNHYPHINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
              +  ++   ++  +   G+++++ +     + +  G            + I+  +K  
Sbjct: 18  ALKHEGVSASLIKVAVYHGGKMQINGEDRWTVDLVNPGD---------YFSLILPSEKPN 68

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQ 142
           D+ + +      L   ++YED    + NKPAG++      +  A  +   ++++ + +G 
Sbjct: 69  DNVIPIN-----LPIQIIYEDRDFLILNKPAGVATVPAHHVTVADSLVNRVRNYYERQGY 123

Query: 143 KPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +  + H   RLD++TSG++V  + R A   + +  +  +++K Y+++V G  K     I 
Sbjct: 124 ENLVIHVATRLDKDTSGLVVFPKHRFAHAVMDQQLKKHQVKKNYYAVVGGQIKAPHGYID 183

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + +          V +        +++ +  ++  + +   L ++ HTGRTHQ+RVH 
Sbjct: 184 APIDRDPE-----KFVSRTVISTGKPSVTEYW-LEKSSVQMSLLRIRLHTGRTHQIRVHF 237

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
            ++G P++GD  Y           I ++  LH  +M    P   + +++ AP+P  M+  
Sbjct: 238 QYLGHPLIGDEMYGGKQ-------IISRQALHCYWMKFYSPFKQQWIEVHAPVPEDMLNL 290

Query: 319 WDSL 322
            +S+
Sbjct: 291 INSI 294


>gi|313636721|gb|EFS02383.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri FSL S4-171]
          Length = 294

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 134/319 (42%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT++   ++E D E + L    +  + H+      +I  S  V ++ K    +N  +  G
Sbjct: 6   MTHITLPIIE-DWEGLTLSTILQEKF-HLGKKARHEIRMSHDVLLNNKPFDDWNTPLFVG 63

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P              IL   +++ ++       ++YED  + V NKP G+     
Sbjct: 64  ASLSLPV-------------ILHEKIDVYEY----DLEVIYEDDFLLVVNKPVGMKTHPN 106

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++   Q       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 107 DSYETDTCANAVQYYLEQTNQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 166

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            + Y + V G      + I   + +  H G        Q       A++H  V++   + 
Sbjct: 167 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHITVLENDTEK 221

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L 
Sbjct: 222 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLN 274

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 275 HPFKGKEMNFSAPAGDDWV 293


>gi|254445726|ref|ZP_05059202.1| pseudouridine synthase, RluA family [Verrucomicrobiae bacterium
           DG1235]
 gi|198260034|gb|EDY84342.1| pseudouridine synthase, RluA family [Verrucomicrobiae bacterium
           DG1235]
          Length = 324

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 81/329 (24%), Positives = 139/329 (42%), Gaps = 37/329 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPV 70
           +  D E  RLD+  K H+  + +   +  + +G+V +D   V      + +G  + +   
Sbjct: 16  IGADLEGARLDKTVKQHF-QLPWAKARAWIDTGKVFIDGNCVSDQAFAVAAGSRIELRMS 74

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYH 128
                    E KI D++             ++Y D  I V NK AG+       S     
Sbjct: 75  QPKKR---PEPKIPDAA-------------IVYFDEHIVVVNKAAGLMTVPHPESDETET 118

Query: 129 IDGFLKSWVDSKGQK-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           +D  +  ++  +            + HR+D++TSG++V ART  A + L+E FR   I++
Sbjct: 119 LDRLVNDYLRIRDPDAKTNRASLGVVHRIDKDTSGLVVFARTFLAKRALSEQFRAHSIER 178

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIG----GDYVHVVKQNEKGANYAISHFKVIDCFA 237
            Y ++V G  K +   I   L++++  G            + E+    AI+H  V++  A
Sbjct: 179 RYLAIVHGELKAQS--IRTHLVRETGDGLRGSAPKGATNSEGEELGRLAITHVDVVERLA 236

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +  +  TGRTHQ+R+H   +G PIVG+  Y   F+G       N+  LHA  +  
Sbjct: 237 -GATLVSCRIETGRTHQIRIHLSEIGHPIVGEKVYIRGFEGELIP--ANRAMLHAAELGF 293

Query: 298 PHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            HP  G  +           + + SL  K
Sbjct: 294 IHPGSGEAVSWQEEASKDFQRIYKSLRLK 322


>gi|315924134|ref|ZP_07920360.1| ribosomal large subunit pseudouridine synthase D [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315622536|gb|EFV02491.1| ribosomal large subunit pseudouridine synthase D [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 287

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 74/305 (24%), Positives = 133/305 (43%), Gaps = 29/305 (9%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           R +       +   L++I+R G++ ++ K     + +  G  + +     +++       
Sbjct: 4   RVYLQKIQGYSSRILRRIIRDGRLMINGKDRWLVDDVHRGDTIEVMLPRESVDVRPVRGI 63

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG-FLKSWVDSKG 141
           +                 ++YED +I   NK AG+             G  +  + +S G
Sbjct: 64  V----------------DIIYEDDEILAVNKDAGLVTHPTKSHQLDTLGNLVAGYFESTG 107

Query: 142 Q--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           Q  K R   RLD +TSG++V+A+ +    +L     + + +K Y + V G P+     I 
Sbjct: 108 QYAKVRFVTRLDSDTSGVIVIAKNKYIHHYLQSHQLIPKPEKRYLAFVNGCPEEMVGTID 167

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVH 258
             + +      D +H     E     +I+H++V++ F  QK   + ++  TGRTHQ+RVH
Sbjct: 168 LPIGR----AEDGIHRCVMPE--GKPSITHYRVVETFPEQKASAIALRLETGRTHQIRVH 221

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
              +GCPI+GD  Y     G +      +  LHAR + L  P+ G+  + APL + +V  
Sbjct: 222 LATIGCPIIGDSLYNTTADGAY---GIRRTALHARSIALSLPKTGQHILYAPLKSDLVNL 278

Query: 319 WDSLG 323
              L 
Sbjct: 279 QHQLR 283


>gi|302871790|ref|YP_003840426.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302574649|gb|ADL42440.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 293

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 73/264 (27%), Positives = 132/264 (50%), Gaps = 15/264 (5%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSV---NLTKHSDFLKSILLYEDSKIYVFNKP 114
           R+++   +R  P I + N   +E  I++ ++               +LYED+     NKP
Sbjct: 33  RLKAHGQIRFIPPIYSTNQYPEENAIIEVNLISSKSNIVPVEGSIDILYEDNFFLFVNKP 92

Query: 115 AGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           +G+      G  +  I  +++ +++SK     + +RLD+ETSGI+V A+       ++  
Sbjct: 93  SGLPSHPSKGHYSDTIANYVEYYLNSKNLTSHIINRLDKETSGIVVFAKNSYFHSIVSRE 152

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  R+++K Y ++V G    K   I   + K+S  G     + ++  +  ++A ++++VI
Sbjct: 153 FEKRQVEKTYIAIVHGRLTKKSGLIEKPI-KRSQDG-----IKREIHQDGSFASTYYEVI 206

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           DCF + F  L+++P TGRTHQLRVH   +G PIVGD+ Y      N        L+ ++ 
Sbjct: 207 DCF-ENFTLLKLKPITGRTHQLRVHLSSIGHPIVGDYIYGEQKTQNTPLL----LHAYSI 261

Query: 294 YMDLPHPEGGRLQITAPLPAHMVK 317
             +    +     IT+PLP +  +
Sbjct: 262 RFNFKLIDNKIYNITSPLPHYFYE 285


>gi|94992422|ref|YP_600521.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
 gi|94545930|gb|ABF35977.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
          Length = 275

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 61/265 (23%), Positives = 112/265 (42%), Gaps = 26/265 (9%)

Query: 42  RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
           + G + V+         +Q G VV I          ++              +      +
Sbjct: 7   KGGNILVNGIEQNAIYLLQVGDVVTIDIPNEEPFEKLE--------------AIPFDLDI 52

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGIL 158
           ++ED    V NKP G +    +  +  I  F+K++        Q+  +  RLD++TSG++
Sbjct: 53  VHEDDHFLVINKPIGFASIPSAIHSNTIANFIKAYYVDNHYLDQQVHIVTRLDRDTSGLM 112

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A+   A   L +  + R I+K Y++LV G      E      + +S        + + 
Sbjct: 113 LFAKHGYAHARLDKQLQTRSIEKRYFALVSGNGTLPDEGDIIAPIGRSKDS----IITRA 168

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +    YA + +KV+  +++    ++++ HTGRTHQ+RVH  H+G P++GD  Y      
Sbjct: 169 VDPMGKYAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGFPLLGDDLYGGRLDL 228

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
             T     +  LH  Y++   P   
Sbjct: 229 GIT-----RQALHCHYLNFKDPFTE 248


>gi|312900272|ref|ZP_07759584.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
 gi|311292633|gb|EFQ71189.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
          Length = 283

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 127/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVCPTIHL---GEATRVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|282849742|ref|ZP_06259126.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
 gi|282580679|gb|EFB86078.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
          Length = 289

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 134/313 (42%), Gaps = 37/313 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M++  Y V E  E  + + ++ K  +   +  ++Q + R  +V+V+ +       ++ G 
Sbjct: 1   MSWKTYTVKEPTE--LTVSKYVKERFSLSSR-DIQMMFRKKRVKVNSRVAHSQRVLKKGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-G 122
           V+ +    +    +  EQ  +                +LYED+   V NK   + V   G
Sbjct: 58  VLTLELPQDKDYGVDVEQGPI---------------TVLYEDAHTLVVNKAPFMLVHPAG 102

Query: 123 SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  +  ++  +   K    K R  HRLD++TSG ++  +T+ A Q+ T+  +  RI 
Sbjct: 103 QTKSCTLSNYVAGYYAKKNVVHKVRPVHRLDRDTSGCILFGKTKEAQQYYTDELQAGRID 162

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQK 239
           +IY  LV G        I    +  + IG D V   ++  ++    A + + V+      
Sbjct: 163 RIYTGLVEG-------RIDADGMVDAPIGVDPVFDNRRVIDEFGQPAQTEYTVLGYEGDN 215

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL-P 298
              L  +  TGRTHQ+RVH  H+G PIVGD  Y    K         +  LHA  +   P
Sbjct: 216 -TLLRFKLLTGRTHQIRVHMEHIGHPIVGDAMYGTRKKS------YTRQCLHASELTFVP 268

Query: 299 HPEGGRLQITAPL 311
           + +   + IT  +
Sbjct: 269 YGKDEAITITCEV 281


>gi|313632225|gb|EFR99288.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri FSL N1-067]
          Length = 289

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 134/319 (42%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT++   ++E D E + L    +  + H+      +I  S  V ++ K    +N  +  G
Sbjct: 1   MTHITLPIIE-DWEGLTLSTILQEKF-HLGKKARHEIRMSHDVLLNNKPFDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P              IL   +++ ++       ++YED  + V NKP G+     
Sbjct: 59  ASLSLPV-------------ILHEKIDVYEY----DLEVIYEDDFLLVVNKPVGMKTHPN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++   Q       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEQTNQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            + Y + V G      + I   + +  H G        Q       A++H  V++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHITVLENDTEK 216

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L 
Sbjct: 217 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|196040729|ref|ZP_03108028.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
 gi|228932672|ref|ZP_04095546.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|229090345|ref|ZP_04221588.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|196028519|gb|EDX67127.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
 gi|228692928|gb|EEL46646.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|228826990|gb|EEM72750.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 307

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 131/319 (41%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EMTVPAKWNGISIESLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E   LD               ++YED  + + NKP  +       G   
Sbjct: 70  MFMEEEYDVEPEYGELD---------------VVYEDDHVLIVNKPEKMDTHPAEKGGMG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      KG   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV + F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEEYFKKQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDIPFPTKLNDTMKEF 302


>gi|331701048|ref|YP_004398007.1| RluA family pseudouridine synthase [Lactobacillus buchneri NRRL
           B-30929]
 gi|329128391|gb|AEB72944.1| pseudouridine synthase, RluA family [Lactobacillus buchneri NRRL
           B-30929]
          Length = 296

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 69/311 (22%), Positives = 127/311 (40%), Gaps = 33/311 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +  +++  +  ++   I    L+KI    G+  V+ +    N  +Q+G  V++      
Sbjct: 10  GQAPIKVRTFIMSY--GITRTLLKKIKYHGGKTLVNGEASLVNRMLQTGDTVKV------ 61

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                    +     N       +   +++ED    V NKP G++          +   +
Sbjct: 62  --------VLPPEPENDHVGVSNVPIEIVHEDPNFLVVNKPYGVASVPAHNHVDSLVNRV 113

Query: 134 KSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           K +   +G   QK  +  RLD++TSG+++ A+   A   L +  + R IQK Y ++V G 
Sbjct: 114 KGYYQRQGYANQKIHIVTRLDKDTSGLVIFAKHHFAHSVLDKQLKDRTIQKTYLAIVAGR 173

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                  I   + +      D   V +Q       +++    +   A++   L+++ HTG
Sbjct: 174 ISMPHFEIYLPIGR-----ADDSFVKRQVVDSGKMSVTEAWTVRRLAKQ-TLLKVRLHTG 227

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           RTHQ+RVH   +G P++GD  Y ++           +  LH   +    P  GR L   A
Sbjct: 228 RTHQIRVHMAAIGHPLIGDWLYNSDDHS------MTRQALHCAELTFYDPFAGRLLHCEA 281

Query: 310 PLPAHMVKTWD 320
            LP  M    +
Sbjct: 282 RLPEDMQSYIN 292


>gi|317502895|ref|ZP_07960993.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           salivae DSM 15606]
 gi|315666001|gb|EFV05570.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           salivae DSM 15606]
          Length = 300

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 129/316 (40%), Gaps = 35/316 (11%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
           ++VV  D    +L  W   +   ++   +++ L+   ++V+ K + KF+  +  G  + +
Sbjct: 15  HLVVNRD---GKLLEWLLENVKGLSKSKIKQTLQGRGIKVESKVITKFDYPVSPGMKISV 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                  +   +   I  S              ++YED  + V  K  GI          
Sbjct: 72  -------SRTKRNNDIFKSR----------YVKIVYEDRYLVVVEKNIGILSMAAGHSTL 114

Query: 128 HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           ++   L  +     QK    + HRLD++TSG+++ A+ +     L + +      + Y +
Sbjct: 115 NVKTILDDYFKKSRQKCTAHVVHRLDRDTSGLMIYAKDKQTEMLLEQDWHHIVYDRRYVA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+ +  +  IANWL         Y+      + G  YA++HF V+      +  +E 
Sbjct: 175 VVSGVIEAPEGTIANWL----KDNKAYITYSSPVDNGGKYAVTHFHVLG-QNNDYSLVEY 229

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
           +  TGR +Q+RVH+  MG P+ GD KY              +L LHA  +   HP     
Sbjct: 230 KLETGRKNQIRVHSADMGHPVCGDIKYGNGDDP------IGRLCLHAYVLCFYHPITHAP 283

Query: 305 LQITAPLPAHMVKTWD 320
           +    P+P    K   
Sbjct: 284 MTFETPIPTSFRKLIK 299


>gi|300862110|ref|ZP_07108190.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|300848635|gb|EFK76392.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|315031415|gb|EFT43347.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0017]
 gi|315144507|gb|EFT88523.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2141]
          Length = 283

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETNTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  N AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGNSAITHVQVVQVLSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|171912659|ref|ZP_02928129.1| hypothetical protein VspiD_15805 [Verrucomicrobium spinosum DSM
           4136]
          Length = 596

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 76/311 (24%), Positives = 127/311 (40%), Gaps = 28/311 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVR 66
           + + V ++++   L       +P I+    Q+    G+   +  +R+  +  + +G    
Sbjct: 305 RPLNVPSEQDGKPLLEVVIALFPQIDAEEWQRRCEEGRFTRESGERLTASTVLAAGD--- 361

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                          + +       +        +L+ED  I V +KPA + +       
Sbjct: 362 ---------------RCVQHFPAAAEPPVNADLKVLHEDEAIVVLDKPAPLPMHPAGRFN 406

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            +   ++ S V +  Q+PRL HRLD  T+G++V ARTR  A  L + F+   I+K Y   
Sbjct: 407 RNTAQYILSQVYAP-QRPRLVHRLDANTTGLVVCARTRHFANLLQKQFKDFSIEKGYVVR 465

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G P+  +  +   +  +    G Y      +E+    A + F V+         LE +
Sbjct: 466 VLGHPEADQFMVDAPISAEPGHLGSYA----VDEEMGQSARTDFVVLSRDGDGTSLLEAR 521

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
           P TGRT+Q+R+H  H+G  IVGD  Y                  + LHA  +   HP  G
Sbjct: 522 PLTGRTNQIRLHLAHLGHNIVGDPTYLQGGGLGDTQTLELGSPPMCLHAWKLGFKHPLTG 581

Query: 303 GRLQITAPLPA 313
            RL    PLP 
Sbjct: 582 ERLAFETPLPD 592


>gi|219128013|ref|XP_002184218.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217404449|gb|EEC44396.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 325

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 69/316 (21%), Positives = 128/316 (40%), Gaps = 34/316 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRV---DKKRV---KFNNRIQSGQVVRIPPVIN 72
            R+D       P ++      ++ + +V +   +       + + +++ GQ + I     
Sbjct: 1   KRIDAVLAALEPEMSRSFCGNLVANKRVSIIQENGDNCLVDRKSFKVEPGQQLIISLPRE 60

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAY 127
                I  Q               L   +++ED  + V NK A + V   +G     +  
Sbjct: 61  EGASEIIAQD--------------LPLDIIFEDEHMIVINKAANMVVHPAAGNWDGTVVN 106

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  +L +  +S   +P + HRLD+ T+G+LVVA+T      L+  F  R+++K Y ++ 
Sbjct: 107 ALAYYLANRSESISFRPGIVHRLDKGTTGVLVVAKTSQTLATLSNFFAARQVKKTYMAIT 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK---GANYAISHFKVIDCFAQKFCWLE 244
            G P      + +  + +  +    + VV    +       A+S+   +  F  K   ++
Sbjct: 167 VGNPGKH--VVIDKPIGRHPLHRQRMRVVPDPHQKNSTGRRALSYVDTL-AFDGKLSLVQ 223

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEG 302
           ++  TGRTHQ+RVH      PI GD  Y         S      +  LHA  +++ HP  
Sbjct: 224 VRIETGRTHQIRVHLQDRHTPIYGDDIYGLADWNKKLSKTHRIVRPLLHAYKLEINHPVT 283

Query: 303 GR-LQITAPLPAHMVK 317
           G  +   A L   M +
Sbjct: 284 GEPMVFKASLADDMKR 299


>gi|220908619|ref|YP_002483930.1| RluA family pseudouridine synthase [Cyanothece sp. PCC 7425]
 gi|219865230|gb|ACL45569.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7425]
          Length = 303

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 127/326 (38%), Gaps = 35/326 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M    +V    V+     + L  ++   Y H +    Q  +  GQ+ ++ +      R+Q
Sbjct: 1   MGNQGWVYRDQVDRRHAGLTLLDYYSQRYRHTSSAEWQTRIELGQIHLNGQPAPPTTRLQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +GQ +                          +    LK   +Y D+ + + +KPAG+ V 
Sbjct: 61  AGQQLTYH------------------RPPWPEPEVPLKFETIYSDADLLIISKPAGLPVL 102

Query: 121 GGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            G G   H    L        Q+ P   HRL + TSG++++A +  A   L++  R + I
Sbjct: 103 PGGGFLEH--TLLWQLQQQYPQETPVPIHRLGRGTSGLMILAISGLAKSALSQQMRDQHI 160

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +LV G     +  I   + K  H    YV+          +A S  +V+     +
Sbjct: 161 RKTYRALVGGGEMPDRFTIDYPIGKIPHPELGYVY---GATPTGRFAHSECQVLKRTPDR 217

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---------CANFKGNFTSPIQNKLYL 290
              L +   TGR HQ+R+H    G P++GD  Y          A        P     +L
Sbjct: 218 -TLLAVTILTGRPHQIRIHLAAAGYPLLGDPLYINGGIPRSFGATPTDKVAVPGDCGYHL 276

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHM 315
           HA ++   HP  G  L+  +P P  +
Sbjct: 277 HAHHLAFAHPRTGEPLEFISPPPREL 302


>gi|322514573|ref|ZP_08067606.1| tRNA pseudouridine synthase C [Actinobacillus ureae ATCC 25976]
 gi|322119512|gb|EFX91599.1| tRNA pseudouridine synthase C [Actinobacillus ureae ATCC 25976]
          Length = 250

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 60/251 (23%), Positives = 109/251 (43%), Gaps = 18/251 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY D ++   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELEILYRDDELIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ ++E F   +++K Y ++V G   +K E      +    I   +    
Sbjct: 61  VLLFALNSEMARLMSEQFEQHQMEKGYLAVVRGYLLDKGEIDYPLKVILDKIADKFSQ-- 118

Query: 217 KQNEKGANYAISH----------FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               K A  A++           +        ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 ---PKEAQQAVTFSQNLASVEMPYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI 175

Query: 267 VGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD KY    +    +     ++L LH+ ++   HP+   +++I APL       + +  
Sbjct: 176 MGDTKYGDLHQNRTLTEKTGCDRLMLHSHFLKFTHPKTAQKIEIFAPLDEQWQNLFITFN 235

Query: 324 FKYDRNLYIKR 334
           + +       +
Sbjct: 236 WNFPNFFQSDK 246


>gi|256957449|ref|ZP_05561620.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|257080924|ref|ZP_05575285.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257083608|ref|ZP_05577969.1| pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256947945|gb|EEU64577.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256988954|gb|EEU76256.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|256991638|gb|EEU78940.1| pseudouridine synthase [Enterococcus faecalis Fly1]
          Length = 287

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 127/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 5   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI   
Sbjct: 55  AGDCVTLTF---------EETDYVRPTIHL---GEATRVKVLYEDEHLMIVNKPYGIKTH 102

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 103 PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 163 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQALSNN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 219 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 271

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 272 PFTKKQIVVTA 282


>gi|49477179|ref|YP_035519.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|49328735|gb|AAT59381.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
          Length = 307

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 131/319 (41%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N R++ G  +++ 
Sbjct: 11  EMTVPAKWNGISIESLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNERLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E               + +  ++YED  + + NKP  +           
Sbjct: 70  MFMEEEYDVEPE---------------YGELHVVYEDDHVLIVNKPEKMDTHPSEKGGMG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV + F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEEYFKKQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGGTK------YMSRQALHAMTINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNDTMKEF 302


>gi|88608012|ref|YP_506045.1| ribosomal large subunit pseudouridine synthase A [Neorickettsia
           sennetsu str. Miyayama]
 gi|88600181|gb|ABD45649.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Neorickettsia sennetsu str. Miyayama]
          Length = 330

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 130/303 (42%), Gaps = 34/303 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPP 69
           +V   +   RLD +     P  +   ++  ++  ++  + K +++ + R+  G+   +  
Sbjct: 5   IVAECDAGNRLDVFLHRCLPFFSRSFIKHCIKGSRIESEGKIQLEPSRRVVVGEEYHLFD 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
           +                     +H+      + YED  + V  KPAG+ V  G G     
Sbjct: 65  LPLERK---------------PRHAFVQPLDVRYEDDCLLVIYKPAGLVVHPGIGNREQT 109

Query: 129 IDGFLKSWVDSK------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +   L+    ++        +P + HRLD++T+G L+VA+T  A   L++  +   I++ 
Sbjct: 110 LVNILEHHYPTEKLSSLDSSRPGIVHRLDKDTAGFLIVAKTNPAHLSLSQMIKEGVIRRE 169

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFC 241
           Y +LV  +P +    I   + +    G   + + + +      A++++ VI     +K  
Sbjct: 170 YLALVHSVPASLSGEIKKPIKR----GQRKMMIGRCS---GKPALTYYGVIARTVDRKCS 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  +GRTHQ+R+H   +GCP+VGD  Y  N   +  +P      L A  +   HP 
Sbjct: 223 LVHCRLGSGRTHQIRLHMKSIGCPVVGDKLYGLNRDADLCAPHH---ALWAYSLQFRHPF 279

Query: 302 GGR 304
             +
Sbjct: 280 TRK 282


>gi|255973763|ref|ZP_05424349.1| pseudouridine synthase [Enterococcus faecalis T2]
 gi|255966635|gb|EET97257.1| pseudouridine synthase [Enterococcus faecalis T2]
          Length = 287

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 127/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 5   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI   
Sbjct: 55  AGDCVTLTF---------EETDYVRPTIHL---GETTRVKVLYEDEHLMIVNKPYGIKTH 102

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 103 PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 163 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQALSNN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 219 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 271

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 272 PFTKKQIVVTA 282


>gi|253565801|ref|ZP_04843256.1| RNA pseudouridylate synthase [Bacteroides sp. 3_2_5]
 gi|265764176|ref|ZP_06092744.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_16]
 gi|251946080|gb|EES86487.1| RNA pseudouridylate synthase [Bacteroides sp. 3_2_5]
 gi|263256784|gb|EEZ28130.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_16]
 gi|301163522|emb|CBW23073.1| putative RNA pseudouridylate synthase [Bacteroides fragilis 638R]
          Length = 307

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 69/301 (22%), Positives = 124/301 (41%), Gaps = 33/301 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +     P  +   L+ +L    V VD     +FN  +Q G  V I    N          
Sbjct: 32  FLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQPGMKVLISKDKNK--------- 82

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWV--DS 139
                    K        ++YED+ I V  K  G+   G            L  +V    
Sbjct: 83  ---------KEFRHPLLKIVYEDAYIIVVEKKEGLLSVGTERQKERTAQHILSEYVGRSG 133

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +  + HRLD++TSG+++ A+       L + +      + Y ++V G  +   + + 
Sbjct: 134 RGNRIYVVHRLDRDTSGLMMFAKDEKTQYTLRDHWHDIVTDRRYVAVVTGEMEKDSDTVV 193

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WL  ++     YV     ++ G+  +I+H++ I   A  +  +E++  TGR +Q+RVH 
Sbjct: 194 SWLTDRTL----YVSSSSYDDGGSK-SITHYRTIKR-ANGYSLVELRLETGRKNQIRVHM 247

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             +G P++GD +Y  +   N       +L LHA  +   HP   + ++   P P    K 
Sbjct: 248 QDLGHPLIGDGRYGIDGGPN----PLGRLALHAFKLCFYHPVTDQLMEFETPYPPTFKKL 303

Query: 319 W 319
           +
Sbjct: 304 F 304


>gi|289435585|ref|YP_003465457.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
 gi|289171829|emb|CBH28375.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
          Length = 289

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 134/319 (42%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT++   ++E D E + L    +  + H+      +I  S  V ++ K    +N  +  G
Sbjct: 1   MTHITLPIIE-DWEGLTLSTILQEKF-HLGKKARHEIRMSHDVLLNNKPFDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P              IL   +++ ++       ++YED  + V NKP G+     
Sbjct: 59  ASLSLPV-------------ILHEKIDVYEY----DLEVIYEDDFLLVVNKPVGMKTHPN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++   Q       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEQTNQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            + Y + V G      + I   + +  H G        Q       A++H  V++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVTVLENDTEK 216

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L 
Sbjct: 217 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|56419100|ref|YP_146418.1| ribosomal large subunit pseudouridine synthase [Geobacillus
           kaustophilus HTA426]
 gi|56378942|dbj|BAD74850.1| ribosomal large subunit pseudouridine synthase [Geobacillus
           kaustophilus HTA426]
          Length = 299

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 70/314 (22%), Positives = 129/314 (41%), Gaps = 36/314 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ +    + +++  K+ +   +     +      V+++ + V +   +     +++   
Sbjct: 12  IIPSWWSGLTIEQLLKDVWA-ASKKLAHRWRMEHGVKLNGQAVPWKTVLNERDRLQLYAY 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHI 129
               + I+ E + L                +L+ED  + V NK AGI +     G    +
Sbjct: 71  EPEPSFIVPEYREL---------------SILWEDDHLLVLNKEAGIDIHPSEPGQTGTL 115

Query: 130 DGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              +  ++ S+    K R  HRLD++TSG ++ A+   A   L      R I++ Y +LV
Sbjct: 116 ANAVAFYLQSQAILTKVRHIHRLDRDTSGAILFAKHPLAGATLDRMLAHRAIKRTYVALV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    K   I   + +  H          +  K    A++H++VI  F      +E+  
Sbjct: 176 HGRLSPKSGTIFAPIGRDRHHPTRR-----RVSKTGAKAVTHYRVIKTFPS-TSLVELSL 229

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH  H+G P+VGD  Y          P+ ++  LHA  +   HP      I
Sbjct: 230 ETGRTHQIRVHLAHLGHPLVGDVLYGGK-------PVFHRHALHAAKLTFRHPFTNEEVI 282

Query: 308 ----TAPLPAHMVK 317
               T+  P  + +
Sbjct: 283 CLAPTSDFPTDLSR 296


>gi|228926422|ref|ZP_04089494.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229120931|ref|ZP_04250173.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|228662591|gb|EEL18189.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|228833246|gb|EEM78811.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 307

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 131/319 (41%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EMTVPAKWNGISIESLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E   LD               ++YED  + + NKP  +       G   
Sbjct: 70  MFMEEEYDVEPEYGELD---------------VVYEDDHVLIVNKPEKMDTHPAEKGGMG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      KG   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV + F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEEYFKKQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNDTMKEF 302


>gi|325570826|ref|ZP_08146509.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           casseliflavus ATCC 12755]
 gi|325156336|gb|EGC68518.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           casseliflavus ATCC 12755]
          Length = 305

 Score =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 69/306 (22%), Positives = 124/306 (40%), Gaps = 33/306 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L KI  + G++ V+         +     V I               
Sbjct: 23  FLKEQ--GVSKGLLAKIKFQGGKIFVNDHEQNVLFSLAQNDRVTI--------------V 66

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKG 141
           I     + T  +D     ++YED+ + + NKPAGIS           +   +K++  ++ 
Sbjct: 67  IPPEGEHETMLADPTPIEIVYEDAHLLIVNKPAGISSIPAQYHPTGTMANRVKAYYQAQH 126

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R +++ K Y +LV G        +
Sbjct: 127 YEDQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDSQLRKKQVVKKYQALVAG----DLSAL 182

Query: 199 ANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +        I  D   ++K+   +    A + +  +         +++Q HTGRTHQ+RV
Sbjct: 183 SAHSEIDLPIARDLTSLLKRKVSEEGKEARTEYW-LKQRNSDCALVDVQLHTGRTHQIRV 241

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GCP++GD  Y         +    +  LH   +   HP     L    PLPA M 
Sbjct: 242 HFSAIGCPLLGDEMYGGPM-----AFGIRRQALHCCQLQFQHPFTNEPLAFELPLPADMA 296

Query: 317 KTWDSL 322
               ++
Sbjct: 297 AVCSAI 302


>gi|60682049|ref|YP_212193.1| putative RNA pseudouridylate synthase [Bacteroides fragilis NCTC
           9343]
 gi|60493483|emb|CAH08269.1| putative RNA pseudouridylate synthase [Bacteroides fragilis NCTC
           9343]
          Length = 305

 Score =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 69/301 (22%), Positives = 124/301 (41%), Gaps = 33/301 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +     P  +   L+ +L    V VD     +FN  +Q G  V I    N          
Sbjct: 30  FLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQPGMKVLISKDKNK--------- 80

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWV--DS 139
                    K        ++YED+ I V  K  G+   G            L  +V    
Sbjct: 81  ---------KEFRHPLLKIVYEDAYIIVVEKKEGLLSVGTERQKERTAQHILSEYVGRSG 131

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +  + HRLD++TSG+++ A+       L + +      + Y ++V G  +   + + 
Sbjct: 132 RGNRIYVVHRLDRDTSGLMMFAKDEKTQYTLRDHWHDIVTDRRYVAVVTGEMEKDSDTVV 191

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WL  ++     YV     ++ G+  +I+H++ I   A  +  +E++  TGR +Q+RVH 
Sbjct: 192 SWLTDRTL----YVSSSSYDDGGSK-SITHYRTIKR-ANGYSLVELRLETGRKNQIRVHM 245

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             +G P++GD +Y  +   N       +L LHA  +   HP   + ++   P P    K 
Sbjct: 246 QDLGHPLIGDGRYGIDGGPN----PLGRLALHAFKLCFYHPVTDQLMEFETPYPPTFKKL 301

Query: 319 W 319
           +
Sbjct: 302 F 302


>gi|228944990|ref|ZP_04107351.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|228814659|gb|EEM60919.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
          Length = 307

 Score =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 131/319 (41%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  +    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EMTVPAKWNGISIESLLKIEW-EVPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVR 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E   LD               ++YED  + + NKP  +       G   
Sbjct: 70  MFMEEEYDVEPEYGELD---------------VVYEDDHVLIVNKPEKMDTHPAEKGGMG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      KG   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV + F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEEYFKKQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNDTMKEF 302


>gi|257867857|ref|ZP_05647510.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC30]
 gi|257874186|ref|ZP_05653839.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC10]
 gi|257801940|gb|EEV30843.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC30]
 gi|257808350|gb|EEV37172.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC10]
          Length = 299

 Score =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 70/306 (22%), Positives = 124/306 (40%), Gaps = 33/306 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L KI  + G++ V+         +     V I               
Sbjct: 17  FLKEQ--GVSKGLLAKIKFQGGKIFVNDHEQNVLFSLAQNDRVTI--------------V 60

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKG 141
           I     + T  +D     ++YED+ + V NKPAGIS           +   +K++  ++ 
Sbjct: 61  IPPEGEHETMLADPTPIEIVYEDAHLLVVNKPAGISSIPAQYHPTGTMANRVKAYYQAQH 120

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R +++ K Y +LV G        +
Sbjct: 121 YEDQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDSQLRKKQVVKKYQALVAGELPA----L 176

Query: 199 ANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +     +  I  D   ++K+        A + +  +         +++Q HTGRTHQ+RV
Sbjct: 177 SAHGEIELPIARDLTSLLKRKVSDEGKEARTEYW-LKQRNSDCALVDIQLHTGRTHQIRV 235

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GCP++GD  Y         +    +  LH   +   HP     L    PLPA M 
Sbjct: 236 HFSAIGCPLLGDEMYGGTM-----ALGIKRQALHCCQLQFQHPFTNEPLAFELPLPADMA 290

Query: 317 KTWDSL 322
               ++
Sbjct: 291 AVCSAI 296


>gi|198274965|ref|ZP_03207497.1| hypothetical protein BACPLE_01124 [Bacteroides plebeius DSM 17135]
 gi|198272412|gb|EDY96681.1| hypothetical protein BACPLE_01124 [Bacteroides plebeius DSM 17135]
          Length = 308

 Score =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 65/301 (21%), Positives = 117/301 (38%), Gaps = 35/301 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       I+   ++ +L +  V V +  + ++N  ++ G  V++    N          
Sbjct: 35  FLMKKMDGISRTRVKALLANRVVLVDNNIQTQYNFPLKPGMKVQVSREKNK--------- 85

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDS-- 139
                             +LYED+ + V  K  G+                L  +V    
Sbjct: 86  ---------HEFRHPMLKILYEDAYLIVVEKKEGLLSVATDHQKERTAQHILNEYVKRTH 136

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +  +  + HRLD+ETSGI++ A+       L +++      + Y S+V G  +  +  + 
Sbjct: 137 RNNRIFVVHRLDRETSGIMMYAKDEKTQHTLRDNWHDIVYDRRYVSIVMGDMEKDQGTVR 196

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WL                 + G   +I+H++ I   A  +  +E+Q  TGR +Q+RVH 
Sbjct: 197 SWLT-----DRKLYVSSSPVDDGGKLSITHYRTIKR-ANGYSLMELQLETGRKNQIRVHM 250

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
             +G P+VGD +Y              +L LHA  +   HP  G R++   P PA     
Sbjct: 251 QSLGHPVVGDARYGCETDP------LGRLALHAFKLCFYHPLTGERMEFETPYPAPFKNL 304

Query: 319 W 319
            
Sbjct: 305 M 305


>gi|196035329|ref|ZP_03102734.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
 gi|195992006|gb|EDX55969.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
          Length = 307

 Score =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 131/319 (41%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EMTVPAKWNGISIESLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVR 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E   LD               ++YED  + + NKP  +       G   
Sbjct: 70  MFMEEEYDVEPEYGELD---------------VVYEDDHVLIVNKPEKMDTHPAEKGGMG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      KG   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV + F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEEYFKKQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNDTMKEF 302


>gi|322378277|ref|ZP_08052759.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M334]
 gi|321280779|gb|EFX57797.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M334]
          Length = 291

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 71/317 (22%), Positives = 126/317 (39%), Gaps = 31/317 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
              +      M + +  +     I    ++  LR    + ++++ V +N  +  G V ++
Sbjct: 4   TFTLPASLSQMTVKQLLEEQLL-IPR-KIRHFLRIKKHILINQREVHWNETVNPGDVCQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       E++I   + +L +         +Y+D  + + NKP G+   G      
Sbjct: 62  TFDEEDY----PEKEIPWGNPDLVQE--------VYQDQHLIIVNKPEGMKTHGNQPNEI 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   GQ   + HRLD ETSG+++ A+       L      + I + YW+LV
Sbjct: 110 ALLNHVSAYV---GQTCYVVHRLDMETSGLVLFAKNPFILPILNRLLEKKEISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    K+    + + +  H     +     + K   YA +H   +  F  K   +  + 
Sbjct: 167 DGNTNKKELVFKDKIGRDRHDRRKRI----VDTKNGQYAETHVSRLKQFPNKTSLVRCKL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H   PI+GD  Y +  K        ++L LHA  +   HP    +L 
Sbjct: 223 KTGRTHQIRVHLSHHNFPILGDPLYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLS 275

Query: 307 ITAPLPAHMVKTWDSLG 323
             A L     +     G
Sbjct: 276 FNA-LSDTFERELKKNG 291


>gi|319897067|ref|YP_004135262.1| tRNA pseudouridine synthase [Haemophilus influenzae F3031]
 gi|317432571|emb|CBY80931.1| tRNA pseudouridine synthase [Haemophilus influenzae F3031]
          Length = 239

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 108/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|148826937|ref|YP_001291690.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittGG]
 gi|148718179|gb|ABQ99306.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittGG]
          Length = 239

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 108/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|257418294|ref|ZP_05595288.1| pseudouridine synthase [Enterococcus faecalis T11]
 gi|257160122|gb|EEU90082.1| pseudouridine synthase [Enterococcus faecalis T11]
          Length = 287

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 5   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 55  AGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 102

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 103 PNQPQETNTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 163 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQALSNN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 219 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 271

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 272 PFTKKQIVVTA 282


>gi|209965860|ref|YP_002298775.1| RNA pseudouridine synthase, putative [Rhodospirillum centenum SW]
 gi|209959326|gb|ACI99962.1| RNA pseudouridine synthase, putative [Rhodospirillum centenum SW]
          Length = 239

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 74/240 (30%), Positives = 120/240 (50%), Gaps = 16/240 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF---LKSWVDSKGQKPRLTHRL 150
            + +++ LLY D  + + +KPAGI+V GG G  +  D      +       + P L HRL
Sbjct: 3   PEEIQARLLYRDGLMLILDKPAGIAVHGGPGSRHGADNLERYFEHLRFGLPRPPALAHRL 62

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG LV+ R   A + L   F+  RI K YW++V G P+     I   LLK++    
Sbjct: 63  DRDTSGCLVLGRHPKALRKLGLLFQDGRIGKTYWAVVRGGPEGDAGTIDKALLKRTDARR 122

Query: 211 DYVHVV-KQNEKGANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            +  +        A  A++ ++V+   +        WLE+ P TGRTHQ+R H   MGCP
Sbjct: 123 GWKMIALPPGTPEAQEAVTDWRVMGRGSLPKIGDLAWLELHPRTGRTHQIRAHCAAMGCP 182

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           ++GD  Y   ++          L+LH+R + +P       + +TAP+P H+ +   + G+
Sbjct: 183 VLGDPVYGGRYEAE-------PLHLHSRAISVPVYATKPAVAVTAPVPPHLREALAACGW 235


>gi|49184224|ref|YP_027476.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|65318659|ref|ZP_00391618.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Bacillus
           anthracis str. A2012]
 gi|165870408|ref|ZP_02215063.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|167634370|ref|ZP_02392691.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|167639342|ref|ZP_02397614.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|170686762|ref|ZP_02877982.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|170706270|ref|ZP_02896731.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|177651449|ref|ZP_02934238.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|190568721|ref|ZP_03021625.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|218902499|ref|YP_002450333.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|227815867|ref|YP_002815876.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|228913961|ref|ZP_04077585.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|229604571|ref|YP_002865810.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|254682548|ref|ZP_05146409.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. CNEVA-9066]
 gi|254726210|ref|ZP_05187992.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. A1055]
 gi|254733966|ref|ZP_05191680.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Western North America USA6153]
 gi|254740346|ref|ZP_05198037.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Kruger B]
 gi|254753734|ref|ZP_05205769.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Vollum]
 gi|254758830|ref|ZP_05210857.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Australia 94]
 gi|270000596|ref|YP_003329034.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. Ames]
 gi|291612209|ref|YP_003541023.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. 'Ames Ancestor']
 gi|49178151|gb|AAT53527.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|164713903|gb|EDR19425.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|167512781|gb|EDR88155.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|167530258|gb|EDR92984.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|170128804|gb|EDS97670.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|170669285|gb|EDT20028.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|172082727|gb|EDT67790.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|190560137|gb|EDV14118.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|218535216|gb|ACK87614.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|224552848|gb|ACN55061.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. 'Ames Ancestor']
 gi|227003057|gb|ACP12800.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|228845683|gb|EEM90710.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|229268979|gb|ACQ50616.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|269850296|gb|ACZ49998.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. Ames]
          Length = 307

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 132/319 (41%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EMTVPAKWNGISIESLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E   LD               ++YED  + + NKP  +       G   
Sbjct: 70  MFMEEEYDVEPEYGELD---------------VVYEDDHVLIVNKPEKMDTHPAEKGGMG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      KG   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV + F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEEYFKKQNVTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDIPFPTKLNDTMKEF 302


>gi|291542721|emb|CBL15831.1| pseudouridine synthase, RluA family [Ruminococcus bromii L2-63]
          Length = 291

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 134/322 (41%), Gaps = 40/322 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSG 62
           M+   Y  V ++ +NM   R+ ++    ++   + ++ R    + +D K ++  + +QSG
Sbjct: 1   MSDRLYFPVPDECDNMLAQRFLRDKC-GLSARIITRLKREKDGILMDGKILRTIDCVQSG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + V I               I D    +      L   + YED    V NKP  + V   
Sbjct: 60  KTVSI--------------AIPDEKCEIEPTKGTLD--IRYEDEHFLVVNKPHSMPVHPV 103

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRL---THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                     + S+  S+  KP +    +RLD++TSG++++A+ R  A          + 
Sbjct: 104 KQHQSDTLANIVSYYCSQNGKPFVFRAINRLDKDTSGLVLIAKNRFTANA-----VKNKT 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y++L  G      E     ++ K     D   +V+        A++H+K +    + 
Sbjct: 159 HKVYYALCEG------EINIEGIVDKPMDLRDDSKMVRIVRDDGMKAVTHYKPL-VATKD 211

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           F  LE+   TGRTHQ+R H  ++G P++GD  Y             ++  LH   ++  H
Sbjct: 212 FTLLELWLETGRTHQIRCHMAYLGHPLMGDDLYGGKLDK------ISRQALHCARLEFYH 265

Query: 300 PEGGR-LQITAPLPAHMVKTWD 320
           P     + +TA +P  M    +
Sbjct: 266 PIKNEYITVTAEIPEDMQSVIN 287


>gi|332638678|ref|ZP_08417541.1| ribosomal large subunit pseudouridine synthase D [Weissella cibaria
           KACC 11862]
          Length = 303

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 68/324 (20%), Positives = 130/324 (40%), Gaps = 33/324 (10%)

Query: 12  VENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   +E +++  +       H  F  +++    G V +  K+V+  + ++ G  V I   
Sbjct: 7   INQGDETLKIKTFLAQRGVSHRMFSIVKR--GGGAVLLAGKQVRTVDEVKPGDKVTIVMP 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHI 129
               N ++                  L   +LYED    V  K AG++   G       +
Sbjct: 65  PEESNDVVA--------------MSDLPITVLYEDENWLVVEKEAGVTSVPGKADRETTM 110

Query: 130 DGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
              +K ++   G +   P +  RLD+ TSG+ ++A+ R A   L +  +   + K Y+++
Sbjct: 111 VNRVKGYLARSGAEDLVPHVVTRLDRFTSGVALLAKHRFAHGLLDKQLQTHSVDKRYYAI 170

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +    I   + +          + ++  +    + + + V+  F  +   + +Q
Sbjct: 171 VDGDLPDDYGFIDAPIGRMDDD-----FIRREVREDGRPSQTEYWVVKRFGNQ-TLVRVQ 224

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
            HTGRTHQ+RVH  ++G P++GD  Y        T     +  LHA ++    P      
Sbjct: 225 LHTGRTHQIRVHFKYLGHPLIGDEIYGGPMDRGIT-----RQALHAYWLRFYDPFAQVER 279

Query: 306 QITAPLPAHMVKTWDSLGFKYDRN 329
              + LP  +V   D    + D N
Sbjct: 280 TTQSALPQDIVAVLDGYQVEPDEN 303


>gi|53713831|ref|YP_099823.1| RNA pseudouridylate synthase [Bacteroides fragilis YCH46]
 gi|52216696|dbj|BAD49289.1| RNA pseudouridylate synthase [Bacteroides fragilis YCH46]
          Length = 307

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 69/301 (22%), Positives = 124/301 (41%), Gaps = 33/301 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +     P  +   L+ +L    V VD     +FN  +Q G  V I    N          
Sbjct: 32  FLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQPGMKVLISKDKNK--------- 82

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWV--DS 139
                    K        ++YED+ I V  K  G+   G            L  +V    
Sbjct: 83  ---------KEFRHPLLKIVYEDAYIIVVEKKEGLLSVGTERQKERTAQHILSEYVGRSG 133

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +  + HRLD++TSG+++ A+       L + +      + Y ++V G  +   + + 
Sbjct: 134 RGNRIYVVHRLDRDTSGLMMFAKDEKTQYTLRDHWHDIVTDRRYVAVVTGEIEKDSDTVV 193

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WL  ++     YV     ++ G+  +I+H++ I   A  +  +E++  TGR +Q+RVH 
Sbjct: 194 SWLTDRTL----YVSSSSYDDGGSK-SITHYRTIKR-ANGYSLVELRLETGRKNQIRVHM 247

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             +G P++GD +Y  +   N       +L LHA  +   HP   + ++   P P    K 
Sbjct: 248 QDLGHPLIGDGRYGIDGGPN----PLGRLALHAFKLCFYHPVTDQLMEFETPYPPTFKKL 303

Query: 319 W 319
           +
Sbjct: 304 F 304


>gi|288962105|ref|YP_003452400.1| ribosomal large subunit pseudouridine synthase C [Azospirillum sp.
           B510]
 gi|288914371|dbj|BAI75856.1| ribosomal large subunit pseudouridine synthase C [Azospirillum sp.
           B510]
          Length = 257

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 70/255 (27%), Positives = 121/255 (47%), Gaps = 9/255 (3%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I DS  + +  +  L++ +L+ D   +V +KPAG++V     I  H++ +L    ++ G+
Sbjct: 2   IPDSPPSASLSAGQLRARVLHRDELCFVIDKPAGLAVHKAGRITDHLELYLPHLAEADGE 61

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P+L HRLD++T+G L++ RT  A +   + F    ++K YW++  G+P+     I   L
Sbjct: 62  PPKLAHRLDRDTAGCLILGRTPWALKRFGQMFAAGHVEKTYWAVADGVPEAGSGVIDLPL 121

Query: 203 LKK----SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           LK+    S  G          +     A++ ++V+   A   CWLE++P TGRTHQ+RVH
Sbjct: 122 LKRIEPKSPSGAGRSSWTILPDPAGQPAVTEYRVLGTAADGRCWLELRPRTGRTHQIRVH 181

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
              +GCP+VG+  Y    +      +  +    A  M   H     +        HM   
Sbjct: 182 CAAIGCPLVGEPFYGPERRPPGALHLLAR--SVAFRMAFEHAAVSAVAPAP---EHMRDA 236

Query: 319 WDSLGFKYDRNLYIK 333
             + G++      I 
Sbjct: 237 LAACGWREREGAAIP 251


>gi|315173986|gb|EFU18003.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1346]
          Length = 283

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 127/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVRPTIHL---GEATRVKVLYEDDHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|307269713|ref|ZP_07551043.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|306513823|gb|EFM82425.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|315034494|gb|EFT46426.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0027]
 gi|315147005|gb|EFT91021.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4244]
 gi|329576828|gb|EGG58313.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1467]
          Length = 283

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 127/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVRPTIHL---GEATRVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|254294411|ref|YP_003060434.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254042942|gb|ACT59737.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
          Length = 272

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 75/237 (31%), Positives = 114/237 (48%), Gaps = 5/237 (2%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               D++  +LL ED  I  FNKP+G++ Q  S      D  L+ +V   G++PR+ HRL
Sbjct: 28  HADRDYMDELLLGEDDSILAFNKPSGLACQTRSPADRTFDALLQVYVKRNGKRPRMLHRL 87

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSH-I 208
           D  TSG+++ ART+ A     ++F  R   K Y ++V G   +  +  I   L +     
Sbjct: 88  DMLTSGVIIAARTKPATSFFQQTFERREAYKSYLAIVRGPAFEKSEGVIDAHLQRYQKEP 147

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +     + +GA  A + + V+         L + P TGRTHQLRVH  H G PI+ 
Sbjct: 148 NLALMRPCDVDGEGAQDARTRYLVLSSQNDYHFLL-LTPETGRTHQLRVHLEHFGRPILA 206

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           D  Y  +       P   +L LHA  +  PHP+GG + I A +P  M +   +L  +
Sbjct: 207 DPYYGTDALEGSYQPA--RLMLHAYRLLTPHPDGGEIDIIADVPDDMKECLTALSLE 261


>gi|119952824|ref|YP_945033.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           turicatae 91E135]
 gi|119861595|gb|AAX17363.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           turicatae 91E135]
          Length = 326

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 77/333 (23%), Positives = 133/333 (39%), Gaps = 39/333 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK--RVKFNNRIQSGQVV 65
           +  +V  D    RLD +            ++K         D     +K +  +     +
Sbjct: 6   KEFIVRKDS--QRLDIYLSEDLCLFTRSQIKKREVKAFKYHDGVFVAIKLSRPVFVDDKI 63

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--- 122
            I                 + ++        L   +LYED  + V +KP GI    G   
Sbjct: 64  LIEFNE-------------EINLREYVRPLNLPISILYEDINVIVVDKPQGILSHPGISN 110

Query: 123 ------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                 + + YHI G L+        +P + HRLD+ETSG+++ A+       L+  F+ 
Sbjct: 111 LENTIVNFLLYHISG-LRDSFQEDKLRPGIVHRLDKETSGVMICAKNLKTLNFLSRQFKE 169

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R ++K+Y ++V G  K     I  ++ +  H    +      +E     A++ ++V+   
Sbjct: 170 RFVKKVYIAVVKGNFKIDSGIIETFIDRDRHDRKRF----SVHENRGKRALTEYRVLASI 225

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  + ++P TGRTHQLRVH  H+  PI+GD  Y A     F       L LHA  ++
Sbjct: 226 G-NYSLVALKPKTGRTHQLRVHMKHLNHPILGDSIY-ARLDKEFKEMS---LMLHAFKLE 280

Query: 297 LPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           +   EG   +  +  P    +  + L   YD+ 
Sbjct: 281 INIKEGSLKKFISVFP---QRFINFLSIFYDKE 310


>gi|28211672|ref|NP_782616.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           tetani E88]
 gi|28204114|gb|AAO36553.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           tetani E88]
          Length = 226

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 110/235 (46%), Gaps = 14/235 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQE 153
           ++  ++YED  I V NK  GI V    S     +   +  + + KG+    RL  RLD++
Sbjct: 1   MELDIVYEDEDILVINKNPGIVVHPTKSHPRGTLSNGILYYFEDKGENCIVRLVSRLDRD 60

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++++A+ + A   L         +K Y +++ G    K+  I   + +        V
Sbjct: 61  TSGLIIIAKNQFAHMALARDMNKDTFKKFYLAIIHGKLTKKEGTIDLPIYRPEDSSLKRV 120

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              K        +I+H+KV++ F +    +E    TGRTHQ+RVH  H+G PI+GD  Y 
Sbjct: 121 VDQK-----GQRSITHYKVVEEF-KDASLVEFLLETGRTHQIRVHVEHLGHPIIGDSLYG 174

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYD 327
                 +     N+  LHA  +  PHP  G + +++  +P+ +  + +    + +
Sbjct: 175 NEDDTMY----INRQALHAYKLVFPHPRTGEILELSCDIPSDIKDSMEIFKKREN 225


>gi|218530900|ref|YP_002421716.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
 gi|218523203|gb|ACK83788.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
          Length = 239

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 118/240 (49%), Gaps = 11/240 (4%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           +SV+       +   LLY D+ + V +KPAG+ V  G      +   L +      ++P 
Sbjct: 5   ASVSDRTVGPEIGPPLLYRDALMLVIDKPAGLPVHPGPKGGPTLTDHLDALRFGLPRRPE 64

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD++TSG LV+ R   A   L   F   R+ K YW+LV G P+  +  I   L K+
Sbjct: 65  AAHRLDRDTSGCLVLGRHAKALARLNRLFADGRVDKTYWALVEGGPEAMEGRIDLPLAKR 124

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           S    D      + +     +++ ++V+   ++   WLE++P TGRTHQLRVH   MG P
Sbjct: 125 S---DDPRSWWMKTDPAGAPSLTLYRVLG-QSEGLSWLELKPVTGRTHQLRVHCAAMGWP 180

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
           I GD  Y +  +          L LHAR + LP +P+   + + AP PAHM    D+ G 
Sbjct: 181 IRGDAIYGSAGRDG------PGLQLHARGLSLPLYPKREAIAVEAPAPAHMRAGLDACGM 234


>gi|298375940|ref|ZP_06985896.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_19]
 gi|298266977|gb|EFI08634.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_19]
          Length = 545

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 77/247 (31%), Positives = 121/247 (48%), Gaps = 20/247 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L+H+++  ++ ++ +    H +  K  +LYED  + V NKP G+    G G A  +
Sbjct: 311 CEPILHHMLQGLRVDENPLLADSHRET-KLDILYEDDYLLVINKPEGMLSVPGKGDADSV 369

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L      +   P + HRLD  TSG+L+ A+T+ A Q+L   F+ R IQK Y +L+ G
Sbjct: 370 YQRLSILY-PEATGPIIVHRLDMATSGLLLAAKTKEAHQNLQAQFKNRTIQKRYIALLEG 428

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I   L          +     +E+    A++H++V++  + K   +   P T
Sbjct: 429 EVPQDEGEIRLPLCPDPLDRPRQI----VSEEFGKPALTHYRVLERTSGK-TLIAFYPQT 483

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVHA H   + CPI+GD  Y    +         +LYLHA Y+   HP    R+
Sbjct: 484 GRTHQLRVHAAHPQGLHCPILGDELYGRKAE---------RLYLHAEYLAFTHPITSERI 534

Query: 306 QITAPLP 312
           +I A +P
Sbjct: 535 EIRAKIP 541


>gi|57505439|ref|ZP_00371367.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter upsaliensis RM3195]
 gi|57016264|gb|EAL53050.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter upsaliensis RM3195]
          Length = 325

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 75/345 (21%), Positives = 142/345 (41%), Gaps = 38/345 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +Q  +V+ +    RLD        + +   +  ++ +  V ++ K   K + ++++G ++
Sbjct: 1   MQTFLVDKEA---RLDVKLAKIL-NQSRSQVSLLIENNAVLINDKIQNKNSFKLKNGDII 56

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +              K L       ++    +  +L+ED  + V NKP  + V G S +
Sbjct: 57  TL--------------KTLPQKELKAQYEVNFEVDVLFEDEDVLVLNKPQNLVVHGASSV 102

Query: 126 --AYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             A  ID  L             +  L HRLD+ETSG +++A+   + Q L+E  + + +
Sbjct: 103 KEATLIDWLLAKKYALSNLAGDLRAGLVHRLDKETSGAIIIAKNNFSHQRLSEQLQNKSL 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN---EKGANYAISHFKVIDCF 236
            +IY +L+    K  K  I   L + +      + + ++N   +  A  A S F  +   
Sbjct: 163 GRIYLALIDLPLKEDKIIINKALTRSTQNRIKKIAIERENYNPKIKAKEAKSAFINL-AL 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           A+    +  +  +GRTHQ+R H   +   I+GD  Y              ++ LHA ++ 
Sbjct: 222 AKDVNLIAAKLFSGRTHQIRAHLASINRHILGDTLYGYKGNE------ICRVMLHAYFVY 275

Query: 297 LPHPEGGRLQI-TAPLPAHMVKTWDS--LGFKYDRNLYIKRLYSQ 338
             HP    L    APL     +  +   L  + D  + +K L  +
Sbjct: 276 FKHPRTKELVFVKAPLMEDFKEILEKKLLIGEDDETISLKHLLGE 320


>gi|56698216|ref|YP_168588.1| ribosomal large subunit pseudouridine synthase A [Ruegeria pomeroyi
           DSS-3]
 gi|56679953|gb|AAV96619.1| ribosomal large subunit pseudouridine synthase A [Ruegeria pomeroyi
           DSS-3]
          Length = 215

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 108/226 (47%), Gaps = 13/226 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++   +       +L+ED+++ V NKPAG+    G G   H+   L S V +      L 
Sbjct: 1   MSDDYNPPQDPLDVLHEDAELIVLNKPAGLLSVPGRG--AHLADCLLSRVQAAFPGALLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG++V A+T  A ++L   F  R+ +K Y + +WG  + K   +   L+    
Sbjct: 59  HRLDRDTSGVMVFAQTPHAQRNLGRQFEERKTRKTYVARLWGRLEPKTGTVDLPLIVD-W 117

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  V     +    A++ ++V+         + + P TGR+HQLRVH   +G PI+
Sbjct: 118 PNRPRQMVC---HETGKPAVTDWRVLRYEGD-TTRVRLLPRTGRSHQLRVHCQALGHPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           GD  Y       F      +L LH+  + L HPE GR +   AP P
Sbjct: 174 GDPFYATGAAQAFP-----RLMLHSEELRLKHPESGRSMTFRAPAP 214


>gi|307284559|ref|ZP_07564721.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
 gi|306503236|gb|EFM72490.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
          Length = 283

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 127/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVRPTIHL---GETTRVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|303237284|ref|ZP_07323854.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
 gi|302482671|gb|EFL45696.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
          Length = 299

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 76/310 (24%), Positives = 129/310 (41%), Gaps = 34/310 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINAL 74
           +EN  L  W   +    +   ++  L++  + V+KK V  FN  + +G  + +       
Sbjct: 19  QENALLLEWLLANVKQ-SKSKIKATLQNRGIMVNKKIVTQFNYELHAGDKISV------- 70

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                      S+             LLYED  I V  K  GI        + ++   L 
Sbjct: 71  -----------STSKKNDQFQSRYVKLLYEDRYIVVIEKAQGILSMEAGHASLNVKKVLD 119

Query: 135 SWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +     QK    + HRLD++TSG+++ A+   A Q L   +      + Y +++ GI +
Sbjct: 120 DYFKKSKQKCTAHVVHRLDRDTSGLMIYAKDMQAEQILEHEWHNIVYDRRYVAVLSGIME 179

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           +    I+NWL         YV      + G  YA++HF V+   +     +E +  TGR 
Sbjct: 180 DDSGTISNWL----KDNKAYVTYSSPFDNGGKYAVTHFSVLKR-SNSHSLVEFKLDTGRK 234

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPL 311
           +Q+RVHA  M  P+ GD+KY              +L LHA  +   HP     ++ +  +
Sbjct: 235 NQIRVHAADMNHPVCGDNKYGNGDDP------LRRLCLHAYMLCFYHPITRQPMEFSTYI 288

Query: 312 PAHMVKTWDS 321
           PA   + ++S
Sbjct: 289 PAGFKRLFES 298


>gi|227509498|ref|ZP_03939547.1| pseudouridylate synthase RluD [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
 gi|227191041|gb|EEI71108.1| pseudouridylate synthase RluD [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
          Length = 302

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 77/312 (24%), Positives = 134/312 (42%), Gaps = 25/312 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           ++    V    +   L R+  +HY  +    +  +    ++ V+ + +  N  +     +
Sbjct: 5   WLFKTTVPQTMDGKPL-RYLLHHYWLLPKHLVFSLRSDERILVNNRYLPVNFPVHFHDHI 63

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SG 124
            +  + +   H    Q + DS+  L          +LYED+ + V NK  G        G
Sbjct: 64  SLTFIPSDFQHPFP-QVLPDSAATL---------KILYEDANLIVINKRRGNKTHPNQPG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                   L +++ +KG  P + HRLDQETSG ++ A+  A    L      + I++ Y 
Sbjct: 114 EVGATINHLAAYLKTKGMLPYMVHRLDQETSGAILFAKNPAVVPTLVAKIAAKNIKRTYL 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           + V G   + +  I   +    +     +       K    +++H+ V+      +  L 
Sbjct: 174 AWVVGTDIDSQGIIDFPIGLDPNDKRKRMIDGSHPAK----SLTHYTVLQ-KEDGYSLLA 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH   +G P+VGD  Y  + K  F       L LH+  + +P P   +
Sbjct: 229 VQLETGRTHQIRVHLAAIGHPLVGDPLYNPDDKHPF-------LLLHSWKLKIPLPFSEQ 281

Query: 305 -LQITAPLPAHM 315
            ++ITAPLPAH 
Sbjct: 282 VIEITAPLPAHF 293


>gi|194467694|ref|ZP_03073681.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
 gi|194454730|gb|EDX43627.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
          Length = 301

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 61/299 (20%), Positives = 125/299 (41%), Gaps = 33/299 (11%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L+  +   G+++++       + +     V +               +   + N
Sbjct: 23  GVSSSLLKVAIYHGGKMQINGVDKWAVDTVNYHDKVTL--------------ILPPETAN 68

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQKPRLT 147
                      ++YED    + NKPAG++      +  A  +   +K +   +  + ++T
Sbjct: 69  DNVDVSEAPIDIIYEDQDFLIMNKPAGVATVPAHNVPVADSLVNRVKGYYKRQDYENQVT 128

Query: 148 H---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           H   RLD++TSG++V  + R A   L E  +   ++K Y +L+ G    +   I   + +
Sbjct: 129 HVATRLDRDTSGLVVFPKHRFAHAVLDEQLKKHLVKKNYLALIKGKVPVEHGYIDAPIQR 188

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             +       V +   K    +++ +   +C  Q    ++++ HTGRTHQ+RVH   +G 
Sbjct: 189 DPN-----SFVKRMVGKEGKASVTEYWCQECNVQ-ASLIKIRLHTGRTHQIRVHFASLGF 242

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           P++GD  Y    +      +  +  LH  ++    P  G  + ++APLP+      D L
Sbjct: 243 PLIGDKMYGEESR------LIARQALHCYWLSFYSPFKGENITVSAPLPSDFKNAKDDL 295


>gi|331004271|ref|ZP_08327749.1| hypothetical protein HMPREF0491_02611 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330411436|gb|EGG90848.1| hypothetical protein HMPREF0491_02611 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 338

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 72/303 (23%), Positives = 137/303 (45%), Gaps = 14/303 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  ++V  +E+  RL+R  +  + + N   + K+LR   + ++ K+     R+ +G  ++
Sbjct: 1   MIEIIVGKNEDGQRLERVLEKIFVNANAGFIFKMLRKKNITLNDKKADGKERLVAGSSIK 60

Query: 67  IPPVINALNHI---IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +     +   +     E   + ++    K+ +   S ++YED    + NKP GI  Q  +
Sbjct: 61  LWFSDESFEKLSGKKVENTKVKNNCTDKKNVEKFNSYIVYEDDNTIILNKPEGILSQKSN 120

Query: 124 GIAYHIDGFLKSWVD-----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                I+  L  ++D         KP + +RLD+ T+G+LV  ++    +   E  + + 
Sbjct: 121 IKDASINDMLLEYLDFDDSVLNTFKPSICNRLDRNTTGLLVCGKSLEGLRVNNELIKTKA 180

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y +LV G  K K   I+ WL K      + V +  +  + A++  + ++V+D F  
Sbjct: 181 VDKFYLALVKGYIKEKC-LISGWLYKDE--SSNKVIIKNKAFEAADFIQTEYEVLDYFEN 237

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSP-IQNKLYLHARYMD 296
               L ++  TG+THQ+R H   +  PI+GD KY      G F          LH+  + 
Sbjct: 238 N-TLLLVKLITGKTHQIRAHLSSISHPIIGDFKYGDKAVNGEFKKRYGIKSQLLHSYRLV 296

Query: 297 LPH 299
            P 
Sbjct: 297 YPD 299


>gi|301311874|ref|ZP_07217796.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           20_3]
 gi|300829976|gb|EFK60624.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           20_3]
          Length = 546

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 76/247 (30%), Positives = 119/247 (48%), Gaps = 20/247 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L+H+++  ++ ++ +    H +  K  +LYED  + + NKPAG+    G G A  +
Sbjct: 312 CEPILHHMLQGLRVDENPLLADSHQET-KLDILYEDDYLLIVNKPAGMLSVPGKGDADSV 370

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L          P + HRLD  TSG+L+ A+T+ A Q+L   F+ R IQK Y +L+ G
Sbjct: 371 YHRLHILY-PDATGPIIVHRLDMATSGLLLAAKTKEAHQNLQAQFKNRTIQKRYIALLEG 429

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I   L          +     +E+    A + ++V++  + K   +   P T
Sbjct: 430 EVPQDEGEIRLPLCPDPLDRPRQI----VSEEFGKPAFTRYRVLERTSGK-TLIAFYPQT 484

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVHA H   + CPI+GD  Y    +         +LYLHA Y+   HP    R+
Sbjct: 485 GRTHQLRVHAAHPLGLHCPILGDELYGRKAE---------RLYLHAEYLAFTHPITFERI 535

Query: 306 QITAPLP 312
           +I A +P
Sbjct: 536 EIRAKIP 542


>gi|327534269|gb|AEA93103.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis OG1RF]
          Length = 283

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETNTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|255971139|ref|ZP_05421725.1| pseudouridine synthase [Enterococcus faecalis T1]
 gi|255962157|gb|EET94633.1| pseudouridine synthase [Enterococcus faecalis T1]
          Length = 287

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 71/311 (22%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 5   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++     +  +  +LYED  + + NKP GI   
Sbjct: 55  AGDCVTLTF---------EETDYVRPTIHF---GEATRVKVLYEDEHLMIVNKPYGIKTH 102

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 103 PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 163 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQALSNN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 219 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 271

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 272 PFTKKQIVVTA 282


>gi|52144044|ref|YP_082785.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           E33L]
 gi|51977513|gb|AAU19063.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           E33L]
          Length = 307

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 131/319 (41%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EMTVPAKWNGISIESLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E               + +  ++YED  + + NKP  +           
Sbjct: 70  MFMEEEYDVEPE---------------YGELHVVYEDDHVLIVNKPEKMDTHPSEKGGMG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV + F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEEYFKKQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGGTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T  + 
Sbjct: 284 EIEVDVPFPTKLNDTMKAF 302


>gi|268315647|ref|YP_003289366.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
 gi|262333181|gb|ACY46978.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
          Length = 235

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 61/227 (26%), Positives = 109/227 (48%), Gaps = 12/227 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LYED  +   +KP G++       +      L     ++G++  + HRLD+E SG
Sbjct: 1   MELPILYEDDDLLAVHKPEGLAAIPERDPSRPSARRL--LEAARGERLWVVHRLDKEASG 58

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ AR   A +++   F  R+++K+Y +LV G  +  +  I   +             +
Sbjct: 59  VLLFARNAEAHRYMNTLFEQRQVRKVYRALVHGRLEPGQGQIRAPIRMYG------SGRM 112

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             + +    + + ++V++   + +  +E  P TGR HQ+RVH  H+G PIVGD +Y    
Sbjct: 113 GVDPERGKPSETRYRVLEYLDEAYSLIEALPLTGRRHQIRVHCYHIGHPIVGDPRYGDRS 172

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
                     +L LHA  +   HP G  L+I AP+P    +  D+L 
Sbjct: 173 VQQRY----PRLMLHALSIRFRHPNGQELEIVAPVPESFQQVLDALR 215


>gi|153810915|ref|ZP_01963583.1| hypothetical protein RUMOBE_01301 [Ruminococcus obeum ATCC 29174]
 gi|149832803|gb|EDM87886.1| hypothetical protein RUMOBE_01301 [Ruminococcus obeum ATCC 29174]
          Length = 334

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 74/340 (21%), Positives = 139/340 (40%), Gaps = 42/340 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHY----PHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M     + V    + M +++   ++       ++        R   +  +K + +   ++
Sbjct: 1   MKKYLTITVREQMQGMTVEKVLYDYLELTKKQVSRAK----FRPDGICKNKVQCRVTEKV 56

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G  + I            E   + S+  +       +  +LYED  I   NKPAG+  
Sbjct: 57  SMGDEICICL----------ETDEIQSAQLVLAKIQGERLCILYEDEDILAVNKPAGVLT 106

Query: 120 QG-GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRM 176
              G   +  +   + ++   +     +    RLD+ETSGI++ A+ + AAQ L E    
Sbjct: 107 HPAGMHYSDSLANQVAAYFQERNLSVCIRPIGRLDKETSGIVLFAKNQVAAQRLQEQRET 166

Query: 177 RRIQKIYWSLVWGIPKNKKECI---ANWLLKKSHIGGDYVHVVKQNEKGANY-------- 225
             ++K Y +LV G     ++ I    ++ +KK       +  VK++    N         
Sbjct: 167 GVLEKQYLALVDGNLPKDQDDIWHTIDFPIKKIGNHPLRMEAVKKSSSAENEKYIAHQLT 226

Query: 226 -------AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A++H+ V+     K+  ++++  TGRTHQ+RVH   +G P++GD  Y  +   
Sbjct: 227 DYINCFQAVTHYHVL-YSTDKWSAIKLKLDTGRTHQIRVHMQAIGHPLLGDSIYNTSTMN 285

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
                I  +  LHA  + L  P  GR +++  P+P    K
Sbjct: 286 REQCTIY-RAALHAWKVRLRQPFNGRKIELEVPVPEDFKK 324


>gi|313115842|ref|ZP_07801276.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310621840|gb|EFQ05361.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 298

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 76/304 (25%), Positives = 136/304 (44%), Gaps = 19/304 (6%)

Query: 26  KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILD 85
              YP +N   L K LR  +++++ K+   + R+ +G  +++      L+ ++   + +D
Sbjct: 1   MQQYPALNPGRLNKALRENKIKLNGKKQPLSTRVMAGDEIKLFI----LDEVLDADRRVD 56

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK-----SWVDSK 140
                        + ++Y+  +I + NKPAG++V G           L       + ++ 
Sbjct: 57  GPAWKNARG---PAQVVYDCPQIVIVNKPAGLAVDGPEDDTLLNRTLLYLNQQGEYKEND 113

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P L HRLD  TSG+++VA+T  A +    + + R ++K Y  + +G P      +  
Sbjct: 114 LYTPALCHRLDTGTSGLVIVAKTPEAEELFLAAIKNREVKKTYLCVTFGRPMPPDATLGG 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           +LLK +  G   V +V++ + GA    + ++ I   + +   L++Q  TGRTHQ+R H  
Sbjct: 174 YLLKDADRG--IVKIVEEKQPGAKEVETRYETI-AVSGRLALLKVQLITGRTHQIRAHMA 230

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM-DLPHPEGGRL---QITAPLPAHMV 316
            +GCPI+GD KY  N            L      M     P+   L      AP P +  
Sbjct: 231 SIGCPILGDSKYGNNTANRELKLKYQALCAWELTMPRFTQPDFEFLSGKTFRAPKPWYYS 290

Query: 317 KTWD 320
           +  D
Sbjct: 291 QVLD 294


>gi|319776302|ref|YP_004138790.1| tRNA pseudouridine synthase [Haemophilus influenzae F3047]
 gi|317450893|emb|CBY87118.1| tRNA pseudouridine synthase [Haemophilus influenzae F3047]
          Length = 239

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 108/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|329123449|ref|ZP_08252013.1| tRNA pseudouridine synthase C [Haemophilus aegyptius ATCC 11116]
 gi|327471031|gb|EGF16486.1| tRNA pseudouridine synthase C [Haemophilus aegyptius ATCC 11116]
          Length = 239

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 108/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|138894182|ref|YP_001124635.1| ribosomal large subunit pseudouridine synthase D [Geobacillus
           thermodenitrificans NG80-2]
 gi|196250721|ref|ZP_03149409.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
 gi|134265695|gb|ABO65890.1| Ribosomal large subunit pseudouridine synthase D [Geobacillus
           thermodenitrificans NG80-2]
 gi|196209800|gb|EDY04571.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
          Length = 299

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 67/304 (22%), Positives = 126/304 (41%), Gaps = 33/304 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ +    + +++  K  +   +     +      V+++ + V +   ++    +++   
Sbjct: 12  IIPSLWSGLTIEQLLKEVWA-ASKKLAHRWRMEQGVKLNGQAVSWQTTLRERDRLQLYAY 70

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HI 129
               + II E + L                +L+ED  + + NK AGI +          +
Sbjct: 71  EPEPSLIIPEYREL---------------SVLWEDEHLLILNKEAGIDIHPSEPEQTGTL 115

Query: 130 DGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              +  ++ S+    K R  HRLD++TSG ++ A+   A   L      R I++ Y +LV
Sbjct: 116 ANAVAFYLQSQAILTKVRHIHRLDRDTSGTILFAKHPLAGATLDRMLAHRTIKRTYVALV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    K   I+  + +  H          +  K    A++H++V++ F      +E+  
Sbjct: 176 HGRLSPKSGTISAPIGRDRHHPTRR-----RVSKTGARAVTHYRVLETFPS-ASLVELNL 229

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H+G P+VGD  Y          P  ++  LHA  +   HP     + 
Sbjct: 230 DTGRTHQIRVHLAHLGHPLVGDMLYGGQ-------PTFHRHALHAVKLTFRHPFTNEEIV 282

Query: 307 ITAP 310
             AP
Sbjct: 283 CLAP 286


>gi|229844088|ref|ZP_04464229.1| tRNA pseudouridine synthase C [Haemophilus influenzae 6P18H1]
 gi|229813082|gb|EEP48770.1| tRNA pseudouridine synthase C [Haemophilus influenzae 6P18H1]
          Length = 239

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 63/238 (26%), Positives = 109/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K +      ++   I   +     Q  
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLTVVRGYLQGKAQIDYPLKIQLDKIADKF----SQEN 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG+  AI+ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KGSQEAITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y    +     +    ++L+LH+  +   HP     + ITA L     K  +  G++
Sbjct: 180 QYGDLHQNRALISHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWKKLINQFGWE 237


>gi|227872635|ref|ZP_03990967.1| RluA protein [Oribacterium sinus F0268]
 gi|227841522|gb|EEJ51820.1| RluA protein [Oribacterium sinus F0268]
          Length = 340

 Score =  189 bits (479), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 75/339 (22%), Positives = 146/339 (43%), Gaps = 28/339 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +++  +E+  +L +  + ++       L K+LR   + ++ K+      ++ G  V+
Sbjct: 1   MREILISQNEKEQKLLKLLQKYFKGQADSFLYKMLRKKNILLNGKKADGKEILRLGDTVQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +     +L  +I+E++  +  +   K  +F    +LYED    +FNKP G+  +     +
Sbjct: 61  LYFSEESLGKLIQERESGEKELWTQKWQNF----ILYEDKHCILFNKPVGLLSENDGSSS 116

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           + ++  L S++ +KG+         +P + +RLD+ TSGI++  ++    Q   +  +  
Sbjct: 117 FSVNSLLLSYMRTKGELSKEQEKSFRPGIANRLDRNTSGIIIFGKSLGGLQAFAKLLQSH 176

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y++LV+G  + K     ++L K          +  +  K    A      ++   
Sbjct: 177 DLEKKYYALVYGDFQ-KTGMQEHFLEKDKGQNK---ALESERGKRVKSAFEKLACVESSV 232

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG---NFTSPIQNKLYLHARY 294
                L +Q  TG+THQ+R     +  PIVGD KY    K      T P+  +L  HA  
Sbjct: 233 GSLSLLSVQIFTGKTHQIRTQLSLLSHPIVGDDKYGDTRKNARLRKTLPLSYQLL-HAYS 291

Query: 295 MDLP-HPEG------GRLQITAPLPAHMVKTWDSLGFKY 326
           +  P  PE             APLP    +   S     
Sbjct: 292 LRFPKLPESSVLFSLSEKCFFAPLPKEYFEILKSFHLDA 330


>gi|257415249|ref|ZP_05592243.1| pseudouridine synthase [Enterococcus faecalis AR01/DG]
 gi|257157077|gb|EEU87037.1| pseudouridine synthase [Enterococcus faecalis ARO1/DG]
          Length = 287

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 71/311 (22%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 5   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI   
Sbjct: 55  AGDCVTLTF---------EETDYVRPTIHL---GEATRVTVLYEDEHLMIVNKPYGIKTH 102

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 103 PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++  G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 163 YRQYQAIAAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSNN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 219 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 271

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 272 PFTKKQIVVTA 282


>gi|331265601|ref|YP_004325231.1| 23S rRNA pseudouridine synthase [Streptococcus oralis Uo5]
 gi|326682273|emb|CBY99890.1| 23S rRNA pseudouridine synthase [Streptococcus oralis Uo5]
          Length = 291

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 130/303 (42%), Gaps = 30/303 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
              +      M + ++ +     I    ++  LR    + ++ K+V +N  ++ G + ++
Sbjct: 4   TFTLPESLPQMTVKQFLEEQLL-IPR-KIRHFLRIKKNILMNHKQVHWNEMVKPGDICQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       +++IL  + +L +         +Y+D  + + NKP G+   G      
Sbjct: 62  TFDEEDY----PKKEILWGNPDLVQE--------IYQDQHLIIVNKPEGMKTHGNQPGEI 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   GQ   + HRLD ETSG+++ A+       L      + I + YW+L+
Sbjct: 110 ALLNHVSAYV---GQTCYVVHRLDMETSGLVLFAKNPFILPILNRLLEKKEIAREYWALI 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  ++K+    + + +  H     +     + K   YA +H   +  F  +   +  + 
Sbjct: 167 EGRVESKELVFRDKIGRDRHDRRKRI----VDAKHGQYAETHVSRLKQFPNQTTLVRCKL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+R+H  H   PI+GD  Y ++ K        ++L LHA  +   HP    +L 
Sbjct: 223 KTGRTHQIRIHLSHHNHPILGDPLYNSSSK-------VSRLMLHAFRLSFTHPLTLEQLS 275

Query: 307 ITA 309
            TA
Sbjct: 276 FTA 278


>gi|227554793|ref|ZP_03984840.1| pseudouridylate synthase RluD [Enterococcus faecalis HH22]
 gi|257077553|ref|ZP_05571914.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|294780463|ref|ZP_06745828.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|227176092|gb|EEI57064.1| pseudouridylate synthase RluD [Enterococcus faecalis HH22]
 gi|256985583|gb|EEU72885.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|294452462|gb|EFG20899.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
          Length = 287

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 5   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 55  AGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 102

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 103 PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 163 YRQYQAIVAGHFSQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQALSNN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 219 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 271

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 272 PFTKKQIVVTA 282


>gi|289167119|ref|YP_003445386.1| 23S_rRNA pseudouridine synthase [Streptococcus mitis B6]
 gi|288906684|emb|CBJ21518.1| 23S rRNA pseudouridine synthase [Streptococcus mitis B6]
          Length = 291

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 69/280 (24%), Positives = 119/280 (42%), Gaps = 29/280 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ + +N  +  G V ++            E++I   + NL
Sbjct: 26  IPR-KIRHFLRIKKHILINQREIHWNETVNPGDVCQLTFDEEDY----PEKEIPWGNPNL 80

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +         +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 81  IQE--------VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYV---GQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      ++I + YW+LV G   +K+    + + +  H   
Sbjct: 130 DMETSGLILFAKNPFILPILNRLLEKKKISREYWALVDGNINSKELVFRDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             V     + K    A +H   +  F  K   +  +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 190 KRV----VDTKNGQSAETHISRLKQFPNKTSLVRCKLKTGRTHQIRVHLSHHNFPILGDP 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
            Y  N          ++L LHA  +   HP    +L  TA
Sbjct: 246 LYNNNSTT-------SRLMLHAFRLSFTHPLTLEKLNFTA 278


>gi|217966766|ref|YP_002352272.1| pseudouridine synthase [Dictyoglomus turgidum DSM 6724]
 gi|217335865|gb|ACK41658.1| pseudouridine synthase [Dictyoglomus turgidum DSM 6724]
          Length = 226

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 120/233 (51%), Gaps = 17/233 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTH 148
           +D L+  ++YED+ + V NKPAG+ VQG    +  +    K+++  K QK       + H
Sbjct: 2   ADLLRPEIIYEDNHLLVVNKPAGVLVQGDITKSTTLLEISKAYIKEKYQKAGNVFLAIVH 61

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+  SG+++ AR   +A  L+E+FR R+++K Y ++  GI K KK  I   L      
Sbjct: 62  RLDKPVSGVVIFARNSKSAGRLSEAFRERKVEKEYLAICEGIFKIKKGTINESLFWDERE 121

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +     N+  +  AI+H++V++ F +    + + P TGR HQLR H  ++G PI+G
Sbjct: 122 RKAKIS----NKAESRVAITHYEVLEEF-KNLSLVRLIPETGRKHQLRAHLSYIGHPILG 176

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           D KY            ++K++LH R M +PHP     ++    +P    +   
Sbjct: 177 DEKYGG------VRIFKDKIFLHCRRMRIPHPVKKEIMEFKTEVPNFWSEFLK 223


>gi|145641594|ref|ZP_01797171.1| tRNA pseudouridine synthase C [Haemophilus influenzae R3021]
 gi|145273641|gb|EDK13510.1| tRNA pseudouridine synthase C [Haemophilus influenzae 22.4-21]
          Length = 239

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 109/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDAFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|322418067|ref|YP_004197290.1| RluA family pseudouridine synthase [Geobacter sp. M18]
 gi|320124454|gb|ADW12014.1| pseudouridine synthase, RluA family [Geobacter sp. M18]
          Length = 300

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 140/311 (45%), Gaps = 36/311 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           ++ ++  +RLD   K  +  ++   +++++  G   +++  V+  + +++ G  V +   
Sbjct: 7   IDAEQSGLRLDDAAKALFSQLSKGEIRRVIDWGGCNINQVLVRVASRQVKEGDEVALG-- 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 +++ ++ +D          + K+ LLYED       K AG++ Q          
Sbjct: 65  ------VMEAERCIDL--------VYQKNELLYEDKDFLAVYKAAGVNSQRTPYQLKGTV 110

Query: 131 GF-LKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            + ++ ++ S G +   R+ HRLD+ TSG++   + + AA  ++   +  ++QK YW+LV
Sbjct: 111 EYAVECYMKSIGLRDPSRVVHRLDRGTSGVMFFPKHKQAATLISNLLKEGKVQKTYWALV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G P  +   +   L     +G     V  +       A + F V+    +    +E +P
Sbjct: 171 SGSPDQQGWKVDAPL---DRVGKFRYGVSLR----GKPARTVFSVLG-EGKGVTVIEAKP 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH  H G PI+GD  Y             +++ LH R M    P G  ++ 
Sbjct: 223 LTGRTHQIRVHLAHSGFPIIGDESYGGIPA--------SRMMLHCRAMRFTGPRGKIIEA 274

Query: 308 TAPLPAHMVKT 318
            APL A   + 
Sbjct: 275 VAPLDAEFREA 285


>gi|307566026|ref|ZP_07628484.1| pseudouridine synthase, RluA family [Prevotella amnii CRIS 21A-A]
 gi|307345214|gb|EFN90593.1| pseudouridine synthase, RluA family [Prevotella amnii CRIS 21A-A]
          Length = 297

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 69/292 (23%), Positives = 116/292 (39%), Gaps = 33/292 (11%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
               ++  L+   ++V+ K V  ++ ++++G  + I                  S     
Sbjct: 35  TKTKIKSTLKHRGIKVNGKIVTQYDYQLKAGDKISI------------------SKSKKN 76

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHR 149
                    L+YED  + V  K  GI        + ++   L  +     Q     + HR
Sbjct: 77  DQFKSRYVKLVYEDKYLVVIEKNVGILSMAAGHSSLNVKSVLDDYFQKSKQHCRAHVVHR 136

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG++V A+     Q L   +      + Y +++ G    ++  +ANWL       
Sbjct: 137 LDRDTSGLMVYAKDMQTEQLLEHDWHNIVYDRRYVAVLSGELMQQQGTVANWL----KDN 192

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             YV      + G  YA++HF  ID  A  +  +E +  TGR +Q+RVHA  MG P+ GD
Sbjct: 193 KSYVTYSSAVDNGGKYAVTHFFTIDTTAS-YSLVEFKLETGRKNQIRVHAADMGYPVCGD 251

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWD 320
            KY              +L LHA  +   HP    R++   P+P        
Sbjct: 252 TKYGNGDDP------IGRLCLHAFMLCFYHPVTHERMEFETPIPPLFRHLLK 297


>gi|288960501|ref|YP_003450841.1| ribosomal large subunit pseudouridine synthase D [Azospirillum sp.
           B510]
 gi|288912809|dbj|BAI74297.1| ribosomal large subunit pseudouridine synthase D [Azospirillum sp.
           B510]
          Length = 226

 Score =  189 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 116/233 (49%), Gaps = 13/233 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
              ++  +LY D  + + +KPAG+ V  G     +++    +      + P L HRLD++
Sbjct: 3   PAQIQDRILYRDGLMLILDKPAGLPVHAGPAGGPNLERHFDALRFGFPKPPSLAHRLDRD 62

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG L++ R   A + +   F+  ++ K YW++V G P      I   L K S+  G + 
Sbjct: 63  TSGCLILGRHAKALRKIGILFQNGKVDKTYWAVVAGGPPQDSGRIELPLAKISNKTGGWR 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            V          A++ + V+   A    WLE+ PHTGRTHQ+RVH   +GCP++GD +Y 
Sbjct: 123 IV---GSPDGQSAVTDY-VVRGQADGLTWLELTPHTGRTHQIRVHCASIGCPLIGDPQYG 178

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGFK 325
                    P    L+LH+R + LP +P+   +   AP+P HM    ++ GF 
Sbjct: 179 G--------PEGKPLHLHSRAISLPLYPKRDPVGAVAPVPPHMRAALEACGFS 223


>gi|315304428|ref|ZP_07874717.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria ivanovii FSL F6-596]
 gi|313627200|gb|EFR96044.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria ivanovii FSL F6-596]
          Length = 289

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 134/319 (42%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT++   ++E D E + L    +  + H+      +I  S  V ++ K    +N  +  G
Sbjct: 1   MTHITLPIIE-DWEGLTLSTILQEKF-HLGKKARHEIRMSHDVLLNNKPFDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P              IL   +++ ++       ++YED  + V NKP G+     
Sbjct: 59  ASLSLPV-------------ILHEKIDVYEY----DLEVIYEDDFLLVVNKPVGMKTHPN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++   Q       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEQTNQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            + Y + V G      + I   + +  H G        Q       A++H  V++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHITVLENDTEK 216

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L 
Sbjct: 217 NTSIVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|227517641|ref|ZP_03947690.1| pseudouridylate synthase RluD [Enterococcus faecalis TX0104]
 gi|227074898|gb|EEI12861.1| pseudouridylate synthase RluD [Enterococcus faecalis TX0104]
          Length = 287

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 72/312 (23%), Positives = 126/312 (40%), Gaps = 37/312 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M L      + V+   EN     W       H              V+++ +   F+  +
Sbjct: 5   MRLPENFSTMTVKELLENE----WLVPRKVRHFLRTR-------KNVKINGETTAFHFPV 53

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI  
Sbjct: 54  QAGDCVTLTF---------EETDYVRPTIHL---GEATRVKVLYEDEHLMIVNKPYGIKT 101

Query: 120 QGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                     +   + +++  K Q P + HRLD+ETSG +V A+       L      ++
Sbjct: 102 HPNQPQETNTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQ 161

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y ++  G    K++ I   + +  H         + + +  + AI+H KV+   + 
Sbjct: 162 IYRQYQAIAAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVKVVKALSN 217

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L 
Sbjct: 218 NQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLL 270

Query: 299 HPEGGR-LQITA 309
           HP   + + +TA
Sbjct: 271 HPFTKKQIVVTA 282


>gi|332828459|gb|EGK01164.1| hypothetical protein HMPREF9455_00204 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 316

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 71/305 (23%), Positives = 138/305 (45%), Gaps = 35/305 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIK 79
           L  +  +     +   ++ +L   Q++V+ K V  F++ +++G  V +     +      
Sbjct: 22  LLEFLIDQQVRKSRNAIKSLLAHKQIKVNGKLVTQFDHELKAGDKVSVMKFDQSR----- 76

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVD 138
                       K        +++ED +I V +K AG +SV         + G L  +V 
Sbjct: 77  ------------KEKKLKGLKIVFEDDEIIVIDKEAGFLSVSTDKEKLRTVYGALNEYVK 124

Query: 139 SKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            K +    +  + HRLD+E SG++V AR     +   +++     + IY ++V G P+ +
Sbjct: 125 KKSRNKTDRVFVLHRLDREASGLMVFARNAELQEIFQKNWNNLVKEYIYTAVVDGRPEQE 184

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  + +WL +      +YV +    + G   +++H+KVI    + +  L+    T R +Q
Sbjct: 185 EGTVISWLTEN----KNYVMMSSPYDNGGLKSVTHYKVIKSTGR-YSLLDFDLETKRKNQ 239

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           LR+    +G  +VGD KY A      ++    ++ LH R + L HP  G  L+  +P+P 
Sbjct: 240 LRIQMQTIGHSVVGDKKYGA------SNNPIKRIALHVRELVLKHPVTGEVLEFKSPVPK 293

Query: 314 HMVKT 318
            M++ 
Sbjct: 294 AMLQL 298


>gi|295702688|ref|YP_003595763.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           megaterium DSM 319]
 gi|294800347|gb|ADF37413.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           megaterium DSM 319]
          Length = 303

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 122/305 (40%), Gaps = 32/305 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  ++    ++ + K  +  I    L +      V ++ + + + N ++    + +P   
Sbjct: 12  IAKNDAGQTIEDYLKTKWR-IPKKMLHQFRMKKNVLINGEPLPWRNTLKEHDKMSLPFFE 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
              N I      ++               +L+ED  + + NKP  +     S      + 
Sbjct: 71  AEPNEITPYNVDIE---------------ILFEDEHVLIVNKPINLDTHPSSEQDQKTLL 115

Query: 131 GFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             + ++    G K  PR  HRLD +TSG ++  +   A+    +    R+I + Y ++V 
Sbjct: 116 NAVAAYFQKIGLKTKPRHVHRLDSDTSGAILFTKHFVASSVFDQLLAERKINRTYIAIVQ 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQP 247
           GI K +   I   + +  H          +  +    A + ++V+    A+    +E+  
Sbjct: 176 GIIKKEDGIINEPIGRDRHHATRR-----RVSRTGQAAKTRYRVLKRNTAKNETLIELSL 230

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H+G P++GD  Y            + +  LHA  +   HP    R+ 
Sbjct: 231 ETGRTHQIRVHMSHIGYPLLGDTLYGGKRLK------EQQQALHAIKLSFLHPFTHQRVS 284

Query: 307 ITAPL 311
             APL
Sbjct: 285 AVAPL 289


>gi|229548625|ref|ZP_04437350.1| pseudouridylate synthase RluD [Enterococcus faecalis ATCC 29200]
 gi|257420942|ref|ZP_05597932.1| pseudouridine synthase [Enterococcus faecalis X98]
 gi|229306256|gb|EEN72252.1| pseudouridylate synthase RluD [Enterococcus faecalis ATCC 29200]
 gi|257162766|gb|EEU92726.1| pseudouridine synthase [Enterococcus faecalis X98]
          Length = 287

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 5   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 55  AGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 102

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 103 PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 163 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQTLSNN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 219 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 271

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 272 PFTKKQIVVTA 282


>gi|288905218|ref|YP_003430440.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
 gi|306831289|ref|ZP_07464449.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus gallolyticus
           subsp. gallolyticus TX20005]
 gi|325978193|ref|YP_004287909.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|288731944|emb|CBI13509.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus gallolyticus UCN34]
 gi|304426525|gb|EFM29637.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus gallolyticus
           subsp. gallolyticus TX20005]
 gi|325178121|emb|CBZ48165.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 296

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 69/305 (22%), Positives = 123/305 (40%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L K+  + G + V+         +  G VV I              +
Sbjct: 16  FLKGH--DVSKGLLAKVKFKGGNIWVNGVEQNAIYLLNVGDVVTI--------------E 59

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D   + T         + YED    + NKP G +       +  I  F+K +   +  
Sbjct: 60  IPDEEEHETLVPVKHDLNIAYEDEHFLIINKPHGYASIPSVLHSNTIANFVKHYYLEQNY 119

Query: 143 ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
              +  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G  +   K  I
Sbjct: 120 PNKQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQNKTIEKRYYALVSGKGELADKGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      D   + +       YA + ++V+  F +    ++++ HTGRTHQ+RVH
Sbjct: 180 IAPIARS-----DDSIITRCVHPSGKYAHTSYEVVARFGE-VALVDIRLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
             H+G P++GD  Y  +     T     +  LH  Y+   +P     +  T  L      
Sbjct: 234 FSHIGFPLLGDDMYGGSMDYGIT-----RQALHCHYLRFVNPYTNEEIIQTTNLTDDFDS 288

Query: 318 TWDSL 322
               L
Sbjct: 289 VIMEL 293


>gi|313885034|ref|ZP_07818786.1| pseudouridine synthase, RluA family [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312619725|gb|EFR31162.1| pseudouridine synthase, RluA family [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 296

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 62/312 (19%), Positives = 129/312 (41%), Gaps = 33/312 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++   +  + +     I    L  +  R G + ++ + V     ++ G  +++       
Sbjct: 10  DQPQLVRNFLQEQ--GIPRKFLSAVKYRGGSILLNGQAVTVRASLRPGDRLKVQAAPELG 67

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFL 133
           +  +               +  L   ++YED    V NKP               +   +
Sbjct: 68  HETVP--------------ASQLPIEIVYEDPDCLVVNKPINTVSIPSQKHPDSSMANRI 113

Query: 134 KSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           K +   +G   Q   +  RLD++TSG++++A+ R A  +  +  R + I+K Y+++  GI
Sbjct: 114 KGYYQQQGYSDQVIHIVTRLDRDTSGLMLIAKHRLAHAYFDQQIRNKTIKKYYYAISEGI 173

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              ++  I   + +          + ++ +     A++ F V D + +    L++Q  TG
Sbjct: 174 DWPREGLIDAPIGRHPD-----SIIQRRVDVSGRPALTRFWVQDKYPE-ATLLKLQLLTG 227

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           RTHQ+RVH  H+G P+VGD  Y  +++         +  LH   ++   P    ++ +  
Sbjct: 228 RTHQIRVHLAHLGGPLVGDTLYGGSYQDQ-----IQRQALHCGQLEFKQPFSHEQIILKQ 282

Query: 310 PLPAHMVKTWDS 321
            LPA M    ++
Sbjct: 283 ALPADMQAWLEA 294


>gi|171779340|ref|ZP_02920304.1| hypothetical protein STRINF_01185 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281957|gb|EDT47388.1| hypothetical protein STRINF_01185 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 296

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 124/305 (40%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L K+  + G + V+         +  G VV I              +
Sbjct: 16  FLKGH--DVSKGLLAKVKFKGGNIWVNGVEQNAIYLLDVGDVVTI--------------E 59

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D   + T         + YED    +FNKP G +       +  I  F+K +   +  
Sbjct: 60  IPDEQEHETLIPVKHDLDIAYEDDHFLIFNKPHGYASIPSVLHSNTIANFVKYYYMEQNY 119

Query: 143 ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
              +  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G  +   +  I
Sbjct: 120 PNKQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQSKTIEKRYYALVSGQGELEDEGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      +   + ++      YA + ++V++ F      ++++ HTGRTHQ+RVH
Sbjct: 180 IAPIARD-----EDSIITRRVHPSGKYAHTSYRVVERFGD-VALVDIRLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
             H+G P++GD  Y        T     +  LH  Y+    P     +  +A L      
Sbjct: 234 FAHIGFPLLGDDLYGGCMDLGIT-----RQALHCHYLRFVDPYTNKEIIQSANLTDDFDS 288

Query: 318 TWDSL 322
               L
Sbjct: 289 VIMKL 293


>gi|256964482|ref|ZP_05568653.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|256954978|gb|EEU71610.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
          Length = 287

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 5   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 55  AGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 102

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 103 PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 163 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSNN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 219 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 271

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 272 PFTKKQIVVTA 282


>gi|332312732|gb|EGJ25827.1| Ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes str. Scott A]
          Length = 291

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 132/320 (41%), Gaps = 37/320 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQS 61
            MT+V  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  
Sbjct: 2   TMTHV-TLPILEDWEGLSLTTILQEKF-HLGKKARHEIRMSQNVLLNNKPLDDWNTPLFV 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + +P  ++    + +                     ++YED  + V NKP  +    
Sbjct: 60  GASLSLPVFLHDKIPVYE-----------------YDLEIIYEDDFLLVVNKPVDMKTHP 102

Query: 122 -GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             S         ++ +++  GQ       HRLDQ TSG+++ A+ + A   L+     R 
Sbjct: 103 NDSYETDTCANAVQYYLEKTGQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRA 162

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y + V G      + I   + +  H G        Q       A++H KV++   +
Sbjct: 163 IHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDNE 217

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L
Sbjct: 218 KNTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHL 270

Query: 298 PHP-EGGRLQITAPLPAHMV 316
            HP +G  +  +AP     V
Sbjct: 271 NHPFKGKEMNFSAPAGDDWV 290


>gi|294792627|ref|ZP_06757774.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Veillonella sp. 6_1_27]
 gi|294456526|gb|EFG24889.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Veillonella sp. 6_1_27]
          Length = 300

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 74/317 (23%), Positives = 134/317 (42%), Gaps = 37/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M++  Y V E  E  + + ++ K  +   +  ++Q + R  +V+V+ +       ++ G 
Sbjct: 13  MSWKTYTVKEPTE--LTVSKYVKERFSLSSR-DIQMMFRKKRVKVNSRVAHSQRALKKGD 69

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-G 122
           V+ +                L    +     +     +LYED+   V NK   + V   G
Sbjct: 70  VLTLE---------------LPQDKDYGVDVEKGPITVLYEDAHTLVVNKDPFMLVHPAG 114

Query: 123 SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  +  ++  +   K    K R  HRLD++TSG ++  +T+ A Q+ T+  +  RI 
Sbjct: 115 QTKSCTLSNYVAGYYAKKNVVHKVRPVHRLDRDTSGCILFGKTKEAQQYYTDELQAGRID 174

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQK 239
           +IY  LV G        I    +  + IG D V   ++  ++    A + + V++     
Sbjct: 175 RIYTGLVEG-------RIDADGMVDAPIGVDPVFDNRRVIDEFGQPAQTEYIVLNHEGDN 227

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL-P 298
              L  +  TGRTHQ+RVH  H+G PIVGD  Y    K         +  LHA  +   P
Sbjct: 228 -TLLRFKLLTGRTHQIRVHMEHIGHPIVGDAMYGTRNKP------YTRQCLHASELTFVP 280

Query: 299 HPEGGRLQITAPLPAHM 315
           + +   + +T  +  + 
Sbjct: 281 YGKDEAITVTCEVGDNF 297


>gi|315166865|gb|EFU10882.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1341]
 gi|315575307|gb|EFU87498.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309B]
 gi|315581474|gb|EFU93665.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309A]
          Length = 283

 Score =  188 bits (478), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFSQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|257876751|ref|ZP_05656404.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC20]
 gi|257810917|gb|EEV39737.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC20]
          Length = 299

 Score =  188 bits (478), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 71/306 (23%), Positives = 125/306 (40%), Gaps = 33/306 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L KI  + G++ V+         +     V I               
Sbjct: 17  FLKEQ--GVSKGLLAKIKFQGGKIFVNDHEQNVLFSLAQNDRVTI--------------V 60

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKG 141
           I     + T  +D     ++YED+ + V NKPAGIS           +   +K++  ++ 
Sbjct: 61  IPPEGEHETMLADPTPIEIVYEDAHLLVVNKPAGISSIPAQYHPTGTMANRVKAYYQAQH 120

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R +++ K Y +LV G        +
Sbjct: 121 YEDQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDSQLRKKQVVKKYQALVAGELPA----L 176

Query: 199 ANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +     +  I  D   ++K+        A + +  +      F  +++Q HTGRTHQ+RV
Sbjct: 177 SAHGEIELPIARDLTSLLKRKVSDEGKEARTEYW-LKQRNSDFALVDIQLHTGRTHQIRV 235

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GCP++GD  Y         +    +  LH   +   HP     L    PLPA M 
Sbjct: 236 HFSAIGCPLLGDEMYGGTM-----ALGIKRQALHCCQLQFQHPFTNEPLAFKLPLPADMA 290

Query: 317 KTWDSL 322
               ++
Sbjct: 291 AVCSAM 296


>gi|72080790|ref|YP_287848.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 7448]
          Length = 289

 Score =  188 bits (478), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 67/312 (21%), Positives = 125/312 (40%), Gaps = 35/312 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MR+D        +++    Q ++   +V ++   V K N  +++GQ ++I          
Sbjct: 1   MRID-ILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKRPKPQ 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGF 132
           ++  +I                 ++++D  + + NKP  + V  G G     +   +   
Sbjct: 60  LEPAEI--------------DFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISH 105

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             S       +P + HRLD++T+G+L+VA+   A          R+I++ Y ++V G   
Sbjct: 106 FDSLEQLDHIRPGIVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVL 165

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHT 249
           +K   I   + +                  +  AI++ ++I  F    Q F  ++ Q  T
Sbjct: 166 HKFMKINLPIGRDLKNPLKKTISFF----NSKPAITNVELIKHFNYQNQDFSLVKCQLET 221

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           GRTHQ+R+H  H+G PI GD  Y           +  +L  HA  +      G   +  A
Sbjct: 222 GRTHQIRLHLAHIGYPIYGDPIYGKKI-----DELGQRL--HAYKLVFKDLNGLSREFQA 274

Query: 310 PLPAHMVKTWDS 321
            LP      ++ 
Sbjct: 275 DLPEEFNIAFEQ 286


>gi|257086040|ref|ZP_05580401.1| pseudouridine synthase [Enterococcus faecalis D6]
 gi|256994070|gb|EEU81372.1| pseudouridine synthase [Enterococcus faecalis D6]
          Length = 287

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 5   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 55  AGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 102

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 103 PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 163 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQALSNN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 219 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 271

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 272 PFTKKQIVVTA 282


>gi|307707719|ref|ZP_07644198.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus mitis NCTC 12261]
 gi|307616217|gb|EFN95411.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus mitis NCTC 12261]
          Length = 291

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 71/317 (22%), Positives = 128/317 (40%), Gaps = 31/317 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
              + +    M + +  +     I    ++  LR    + ++++ V++N  +  G + ++
Sbjct: 4   TFTLPDSLPQMTVKQLLEEQLL-IPR-KIRHFLRIKKHILINQREVRWNEMVNPGDICQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       E++I   + NL +         +Y+D  + + NKP G+   G      
Sbjct: 62  TFDKEDY----PEKEIPWGNPNLVQE--------VYQDQHLIIVNKPEGMKTHGNQPNEI 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   GQ   + HRLD ETSG+++ A+       L      + I + YW+ V
Sbjct: 110 ALLNHVSAYV---GQTCYVVHRLDMETSGLVLFAKNPFILPILNRLLEKKEISREYWAQV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +K+    + + +  H     +     + K   YA +H   +  F  K   +  + 
Sbjct: 167 DGHINSKELVFKDKIGRDRHDRRKRI----VDTKNGQYAETHVSRLKQFPNKTSLVRCKL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H   PI+GD  Y +  K        ++L LHA  +   HP    +L 
Sbjct: 223 KTGRTHQIRVHLSHHNFPILGDPLYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLS 275

Query: 307 ITAPLPAHMVKTWDSLG 323
            T  L     K     G
Sbjct: 276 FTT-LSDTFEKELKKNG 291


>gi|257869733|ref|ZP_05649386.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           gallinarum EG2]
 gi|257803897|gb|EEV32719.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           gallinarum EG2]
          Length = 299

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 74/310 (23%), Positives = 129/310 (41%), Gaps = 33/310 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             +E  +L  + K     I+   L KI  + G++ V+ +R      +     V I     
Sbjct: 8   ERQEPQQLKYFLKEQ--GISKGLLAKIKFQGGKIFVNDQRQNVLYSLVQNDTVTI----- 60

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDG 131
                     I D   + T   D     ++YED  + + NKPAGI+           +  
Sbjct: 61  ---------VIPDEGEHETVLLDETPIEIVYEDQHLLIVNKPAGIASIPAQYHPNGTMAN 111

Query: 132 FLKSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +K++   +G + ++ H   RLD++TSG+++ A+   A   L    R +++ K Y ++V 
Sbjct: 112 RVKAYYKQQGYQDQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDVQLRQKQLIKKYQAIVA 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQP 247
           G  +     +A+       I  D   ++K+        A + +  +    Q+   + +  
Sbjct: 172 GQIQE----LASHGEITYPIARDLSSLLKRKTSLEGKSARTEYW-LTKKDQQVAVVTILL 226

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
           HTGRTHQ+RVH   + CP++GD  Y             ++  LH   +   HP  G+ L 
Sbjct: 227 HTGRTHQIRVHFAAIHCPLLGDELYGG-----AMDLGIDRQALHCCELAFTHPFSGKSLH 281

Query: 307 ITAPLPAHMV 316
             A LPA M 
Sbjct: 282 FKADLPADMA 291


>gi|256617567|ref|ZP_05474413.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256597094|gb|EEU16270.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
          Length = 287

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 5   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +V+L    +  +  +LYED  + + NKP GI   
Sbjct: 55  AGDCVTLTF---------EETDYVRPTVHL---GEATRVKVLYEDEHLMIVNKPYGIKTH 102

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V  +       L      ++I
Sbjct: 103 PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFTKNPFVLPILGRLLETKQI 162

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 163 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQTLSNN 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 219 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 271

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 272 PFTKKQIVVTA 282


>gi|167854653|ref|ZP_02477433.1| tRNA pseudouridine synthase C [Haemophilus parasuis 29755]
 gi|167854190|gb|EDS25424.1| tRNA pseudouridine synthase C [Haemophilus parasuis 29755]
          Length = 242

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 59/243 (24%), Positives = 109/243 (44%), Gaps = 18/243 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +K  ++Y+D ++   NKPAG+ V       +     +++  +   Q     HRLD+ TSG
Sbjct: 1   MKLEIIYQDDELIAINKPAGMLVHRSWLDKHETVFAMQTLRNQIRQHVFPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ +++ F   +IQK Y ++V G  + +        ++   I   +    
Sbjct: 61  VLLFALNSEMARTMSQLFEQHQIQKSYLAVVRGYLQGEGRIDYPLKVQLDKIADKFSQ-- 118

Query: 217 KQNEKGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              EK A  AI+ ++ I    +          ++  +++ P TGR HQLR H  H+  PI
Sbjct: 119 ---EKEAQEAITDYRNIATAERPYPAGKFATARYSLVQLYPKTGRKHQLRRHLKHLFHPI 175

Query: 267 VGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD  Y    +      +   ++L LH+  +   HP+    ++I APL       +   G
Sbjct: 176 MGDTNYGDLHQNRVLTANTGCDRLMLHSNSLQFIHPKTLQTIEIKAPLDEQWKALFTQFG 235

Query: 324 FKY 326
           + +
Sbjct: 236 WNF 238


>gi|315156668|gb|EFU00685.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0043]
          Length = 283

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQTLSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|312874750|ref|ZP_07734769.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
 gi|311089495|gb|EFQ47920.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
          Length = 302

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 70/296 (23%), Positives = 118/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 34  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGNEKPNATLK-------------- 79

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 80  FSNLPIAIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITR 139

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 140 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 198

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 199 PVKRYIM------EGGKESVTKYRVIKQVA-GASLVELQLLTGRTHQIRVHMQYLGHPLF 251

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y             ++  LH   +    P E  R+++    PA MV+ W  L
Sbjct: 252 GDHLYGVEDD-------FHRQALHCFLLAFDDPLEHKRIEVQIADPADMVQLWQKL 300


>gi|116617792|ref|YP_818163.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
 gi|116096639|gb|ABJ61790.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
          Length = 299

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 66/286 (23%), Positives = 124/286 (43%), Gaps = 34/286 (11%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G + V++K V  ++ +++G +V I       N ++                D+    +++
Sbjct: 37  GAILVNEKPVYTSDYLKNGDIVTIVMPTEKSNDLV--------------VPDYKPLDIIF 82

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHID-----GFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           E+    V +KP GI+   G     H       G L++ + +    P +  RLD++TSGI+
Sbjct: 83  ENEHWLVVDKPYGITTVPGHADRLHTLVNQVKGHLET-IKADDLVPHVVTRLDRDTSGIV 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+ R A   L +  +   ++K Y +   GI  +    I   + +   + GD++    +
Sbjct: 142 LLAKHRFAHAVLDQQLQDHTVEKFYLAYPSGILADDHGDINAPIGR---MDGDFIKREVR 198

Query: 219 NEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           ++     + + + V   +    Q    +++Q HTGRTHQ+RVH  ++G P+VGD  Y   
Sbjct: 199 DD--GKPSRTEYWVERRYEDDEQNMTRVKVQLHTGRTHQIRVHFANIGHPLVGDTLYGGP 256

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWD 320
                      +  LHA +M    P      +   PLP  +    D
Sbjct: 257 AWHGL-----QRQALHAYHMKFYDPFIEEYREFNTPLPDDLKTLRD 297


>gi|229029062|ref|ZP_04185161.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|228732342|gb|EEL83225.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 307

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 128/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + +D   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EITVPAKWNGISIDSLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFVEEEYDVEPE---------------YGELHVVYEDDHVLIVNKPEKMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  +   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKGKQGTVDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEKYFKKQNVTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K            LHA  +   HP    
Sbjct: 230 LQLETGRTHQIRVHMSYHGNPLVGDVLYGGQTK------HMTGQALHAMKIHFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNNTMKEF 302


>gi|313891609|ref|ZP_07825216.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
 gi|313119887|gb|EFR43072.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
          Length = 290

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 133/314 (42%), Gaps = 37/314 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70
           V    +   + ++ K +   ++    +KI  +G V ++  ++   N  +     V     
Sbjct: 7   VSEKWDGCSIKKFVKGYC-GLSTNLWKKIKWNGSVILNGVQIYNANIVVHVNDKVVCEWS 65

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHI 129
                   +E  I+ S + L          ++YED+ + + +K   + +   S      +
Sbjct: 66  --------EETDIIPSCIPL---------KIIYEDNTLLIIDKDEDMIIHPTSKTETNTL 108

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              +  +     Q       +RLD+ T+G++VVA++      L++      I++ Y ++V
Sbjct: 109 VNAISGYYKKNNQMSGIHPIYRLDRNTTGLIVVAKSAKLQYELSK--EHGTIKREYLAVV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  KNK+  I   + +K     ++             A + +KVI+        L+++ 
Sbjct: 167 EGRFKNKEGSIIYPIGRKEGSIIEWKVR-----DDGKEARTDYKVIEEKPS-CTLLKLRL 220

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
           +TGRTHQ+RVH   +G P++GD  Y  N           +  LH+ ++   HP+ G  ++
Sbjct: 221 YTGRTHQIRVHMSFLGHPLIGDDLYGGNCSK------LKRQALHSHHISFIHPDTGECME 274

Query: 307 ITAPLPAHMVKTWD 320
             +P+P  M + ++
Sbjct: 275 FKSPMPDDMYEFFE 288


>gi|259501034|ref|ZP_05743936.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
 gi|302190517|ref|ZP_07266771.1| pseudouridine synthase, RluA family protein [Lactobacillus iners
           AB-1]
 gi|259167728|gb|EEW52223.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
          Length = 300

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 70/296 (23%), Positives = 118/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 32  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGNEKPNATLK-------------- 77

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 78  FSNLPITIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALIKIKPHIITR 137

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 138 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 196

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 197 PVKRYIM------EGGKESVTKYRVIKQIA-GASLVELQLLTGRTHQIRVHMQYLGHPLF 249

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y             ++  LH   +    P E  R+++    PA MV+ W  L
Sbjct: 250 GDHLYGVEDD-------FHRQALHCFLLAFDDPLEHKRIEVQIADPADMVQLWQKL 298


>gi|258511340|ref|YP_003184774.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478066|gb|ACV58385.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 303

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 74/325 (22%), Positives = 143/325 (44%), Gaps = 33/325 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  +++   ++   + +W +   P +    + K +R+G+V+V+ KR K + R+  G +V 
Sbjct: 1   MIEIIIGPSDDGKPVHKWLRLLLPGLPLSGVYKSIRTGRVKVNGKRAKQDTRLHEGDIVH 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-I 125
           +         +          V+           +LYED +I   NKP G+      G  
Sbjct: 61  LYFSDEDYASLHAHPVAKYQGVSRAID-------ILYEDDEIVAVNKPVGVLTHPADGEY 113

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +   ++++V  +G      +    HRLD+ TSG++V A+T  AA+   ++F    ++
Sbjct: 114 KTSLAAQVEAYVYDRGAREGAFRAAPVHRLDRNTSGVVVFAKTARAAKAWADAFHRGEVE 173

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y ++V G    +     +             +V +  +     + + ++V+   ++  
Sbjct: 174 KEYLAIVEGEWSGRGRVAVD--------VRREGNVTRVVDDSGKPSETAYEVVAS-SRGT 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + +   TGRTHQ+RVH  H+G P++ D KY A      +       YLHA  +     
Sbjct: 225 SLVRLHLLTGRTHQIRVHMAHLGHPLLADRKYGARPIRGES------FYLHAHRV----- 273

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFK 325
              ++ +TAPLP  M +   +LG+K
Sbjct: 274 RWNQVHVTAPLPDRMTEKLRTLGYK 298


>gi|312874385|ref|ZP_07734416.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
 gi|311090151|gb|EFQ48564.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
          Length = 307

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 70/296 (23%), Positives = 118/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 39  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGKEKPNATLK-------------- 84

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 85  FSNLPIAIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITR 144

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 145 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 204 PVKRYIM------EGGKESVTKYRVIKQVA-GASLVELQLLTGRTHQIRVHMQYLGHPLF 256

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y             ++  LH   +    P E  R+++    PA MV+ W  L
Sbjct: 257 GDHLYGVEDD-------FHRQALHCFLLAFDDPLEHKRIEVQIADPADMVQLWQKL 305


>gi|288926989|ref|ZP_06420884.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           D17]
 gi|315608748|ref|ZP_07883726.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
 gi|288336235|gb|EFC74621.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           D17]
 gi|315249598|gb|EFU29609.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
          Length = 294

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 74/318 (23%), Positives = 133/318 (41%), Gaps = 39/318 (12%)

Query: 13  ENDEENMRLDR------WFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVV 65
            ND ++ R+D       W   +    +   ++  L+   ++V+ K   +F+  ++ G  +
Sbjct: 6   PNDYDHYRVDEKAPLLEWLLANVKGESRSKIKATLKGRGIKVNGKQTTRFDYPLEPGMKI 65

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +    N  N   + + +                 L+YED  I V  K  GI        
Sbjct: 66  SVS--RNKRNDTFRSRYV----------------RLVYEDRHIVVLEKAVGILSMAAGHS 107

Query: 126 AYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           + ++   L  +     QK    + HRLD++TSG+++ A+++   Q L   +      + Y
Sbjct: 108 SLNVKKVLDDYFKKTRQKCTAHVVHRLDRDTSGLMIYAKSKEIEQMLEHDWHHVVYDRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G   + +  IANWL         YV      + G  YA++HF V+         +
Sbjct: 168 VAVVSGEVYDDEGTIANWL----KDNKAYVTYSSPVDNGGKYAVTHFHVLRRTTD-HSLV 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG- 302
           E +  TGR +Q+RVH+  MG P+ GD KY             ++L LHA  +   HP   
Sbjct: 223 EYRLETGRKNQIRVHSADMGHPVCGDIKYGNGDDP------LHRLCLHAYVLCFYHPVTH 276

Query: 303 GRLQITAPLPAHMVKTWD 320
            R++   P+P+  +  + 
Sbjct: 277 ERMEFDTPVPSAFLSLFK 294


>gi|218283674|ref|ZP_03489635.1| hypothetical protein EUBIFOR_02229 [Eubacterium biforme DSM 3989]
 gi|218215663|gb|EEC89201.1| hypothetical protein EUBIFOR_02229 [Eubacterium biforme DSM 3989]
          Length = 295

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 68/301 (22%), Positives = 134/301 (44%), Gaps = 26/301 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + +  ++ N RLD++    +P +    + K +R+ +++V++KR  F+ +IQ    + 
Sbjct: 1   MKEIKINQNDANQRLDKFLMKTFPKLGKSMMYKAIRNKKIKVNRKRCTFDQKIQENDSIL 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    + L     E   + S           K  ++YED  I + NKP G+  Q      
Sbjct: 61  LFLPPDVLEEKKVETNYISS-----------KLDVIYEDENILIVNKPYGLLSQSDQSQN 109

Query: 127 YHI-DGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                  +++++  K +          P + HRLD+ T+G+++ A+   A + + E+   
Sbjct: 110 QDCLVNRVQAYLMEKNEYDPNKEHSFAPSICHRLDRNTTGLVIAAKNANALRKVNEAIAN 169

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R IQK+Y + V G  + K   +  ++ K++ I      V  +  +G   A+    V +  
Sbjct: 170 RTIQKMYRAHVVGTFEQKDFTMCYYIRKENTIAK----VSDKKLEGYQKALMDVHV-ERD 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
             +     +  HTGR HQ+R    H+  P++GD KY  + K      +  +L  H   + 
Sbjct: 225 DGENSICTITLHTGRFHQIRALMGHIQHPLLGDVKYGYHGKKRPIELMAYRLEFHEVDLP 284

Query: 297 L 297
           L
Sbjct: 285 L 285


>gi|237709871|ref|ZP_04540352.1| RNA pseudouridylate synthase [Bacteroides sp. 9_1_42FAA]
 gi|229455964|gb|EEO61685.1| RNA pseudouridylate synthase [Bacteroides sp. 9_1_42FAA]
          Length = 308

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 62/303 (20%), Positives = 117/303 (38%), Gaps = 34/303 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       I+   ++ +L +  + VD     ++N  ++ G  V++               
Sbjct: 34  FLMRKMAGISRSKVKALLANRVILVDNVITTQYNFALKPGMKVQM--------------- 78

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDS-- 139
              S     +        L+YED+ I V  K  G+                L  +V    
Sbjct: 79  ---SKAKNNREFKHPMLKLVYEDAYILVVEKKEGLLSVSTERQKERTAQHILNEYVKRSH 135

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +  +  + HRLD+ETSG+++ A+       L +++      + Y S+V G  +     + 
Sbjct: 136 RFNRVFVVHRLDRETSGLMMYAKDEKTQNTLRDNWHDIVTDRRYVSIVSGNMEKDYGTVE 195

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WL  +      YV     ++    +A++H+K I   A  +  +E+   TGR +Q+RVH 
Sbjct: 196 SWLTDRKL----YVSSSPVDDGEGKFAVTHYKTIKR-ANGYSLVELDLETGRKNQIRVHM 250

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             +G P++GD +Y +            +L LHA  +   HP     ++   P P      
Sbjct: 251 SDLGHPVIGDRRYGSECDP------LGRLALHAFKLCFYHPVTRELMEFETPYPTAFKGL 304

Query: 319 WDS 321
              
Sbjct: 305 MQK 307


>gi|284802691|ref|YP_003414556.1| hypothetical protein LM5578_2447 [Listeria monocytogenes 08-5578]
 gi|284995833|ref|YP_003417601.1| hypothetical protein LM5923_2398 [Listeria monocytogenes 08-5923]
 gi|284058253|gb|ADB69194.1| hypothetical protein LM5578_2447 [Listeria monocytogenes 08-5578]
 gi|284061300|gb|ADB72239.1| hypothetical protein LM5923_2398 [Listeria monocytogenes 08-5923]
          Length = 291

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 132/319 (41%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT+V  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  G
Sbjct: 3   MTHV-TLPILEDWEGLSLTTILQEKF-HLGKKARHEIRMSQNVLLNNKPLDDWNTPLFVG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P  ++    + +                     ++YED  + V NKP  +     
Sbjct: 61  ASLSLPIFLHDKIPVYE-----------------YDLEIIYEDDFLLVVNKPVDMKTHPN 103

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++  GQ       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 104 DSYETDTCANAVQYYLEKTGQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 163

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            + Y + V G      + I   + +  H G        Q       A++H KV++   + 
Sbjct: 164 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDNEK 218

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L 
Sbjct: 219 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLN 271

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 272 HPFKGKEMNFSAPAGDDWV 290


>gi|315025718|gb|EFT37650.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2137]
          Length = 283

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|307272491|ref|ZP_07553744.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|306510776|gb|EFM79793.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
          Length = 283

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|260593255|ref|ZP_05858713.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           veroralis F0319]
 gi|260534812|gb|EEX17429.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           veroralis F0319]
          Length = 296

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 77/307 (25%), Positives = 132/307 (42%), Gaps = 40/307 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIK 79
           L  W   +    +   ++  L++  ++V+ K V  F+  +++G  V              
Sbjct: 23  LLEWLLANLSE-SKSKVKATLQNRGIKVNSKCVTQFDYPLRAGDKV-------------- 67

Query: 80  EQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                  SV+ +K +D  +S    ++YED  + V  K  GI        A ++   L  +
Sbjct: 68  -------SVSKSKKNDLFRSRYVKIVYEDRFLVVIEKNIGILSMAAGHSALNVKAVLDDY 120

Query: 137 VDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                QK    + HRLD++TSG+++ A+     Q L   +      + Y ++V G  +N 
Sbjct: 121 FHKSRQKCTAHVVHRLDRDTSGLMIYAKDMQTEQLLERDWHNIVYDRRYVAVVSGEMEND 180

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  IANWL         YV      + G  YA++HF V+D   +    +E +  TGR +Q
Sbjct: 181 EGTIANWL----KDNKAYVTYSSPVDNGGKYAVTHFHVLDRTVR-HSLVEYRLETGRKNQ 235

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
           +RVH+  MG P+ GD KY             ++L LHA  +   HP    R++   P+P 
Sbjct: 236 IRVHSADMGHPVCGDVKYGNGDDP------LHRLCLHAYVLCFYHPVTHQRMEFETPIPM 289

Query: 314 HMVKTWD 320
           +    + 
Sbjct: 290 NFRHLFK 296


>gi|227877169|ref|ZP_03995243.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus crispatus
           JV-V01]
 gi|227863223|gb|EEJ70668.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus crispatus
           JV-V01]
          Length = 304

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 128/328 (39%), Gaps = 35/328 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  MT +  ++V+  +         KN + H    N +     G + V+ KR   +  ++
Sbjct: 1   MKKMTSLFKLIVQERDPKKLGPFLLKNGFSHQALNNAKH--HHGMILVNHKRRYTSFNLR 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V         N  +K                     ++ E+    V NKPAG+   
Sbjct: 59  AGDEVIFISGEEKKNDFLK--------------PSNNPVSIVLENKNYLVVNKPAGVLSI 104

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                    +   L  +   KGQK   P +  RLD++TSG+++V +   +    ++  + 
Sbjct: 105 PSRYEDDDAVVNRLLGYFAQKGQKNLKPHVITRLDRDTSGLVLVGKNAISHARFSKIGKE 164

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + ++K + ++V G     +       L    IG     V +        A + ++V+D  
Sbjct: 165 KFVKKYH-AIVHGNFAPNELT----GLIDQPIGKKGSGVKRAVVADGKDAQTAYRVLDQV 219

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +E++  TGRTHQ+RVH  ++G P+ GD  Y             ++  L+  Y++
Sbjct: 220 T-GASLVELRLLTGRTHQIRVHMAYLGHPLYGDPLYG-------IQDGFSRQALNCFYLN 271

Query: 297 LPHPEGGRLQITAPL--PAHMVKTWDSL 322
            P P   +   T  L  P  M + W  L
Sbjct: 272 FPDPFSQQKCKTIELNDPKDMQELWQKL 299


>gi|329920350|ref|ZP_08277082.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
 gi|328936026|gb|EGG32479.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
          Length = 307

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 117/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 39  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGNEKPNATLK-------------- 84

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 85  FSNLPITIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALIKIKPHIITR 144

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 145 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 204 PVKRYIM------EGGKESVTKYRVIKQVA-GASLVELQLFTGRTHQIRVHMQYLGHPLF 256

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y              +  LH   +    P E  R+++    PA M++ W  L
Sbjct: 257 GDHLYGVEDD-------FPRQALHCFLLAFDDPLEHKRIEVQIADPADMLQLWQKL 305


>gi|47096862|ref|ZP_00234442.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|254899054|ref|ZP_05258978.1| hypothetical protein LmonJ_04559 [Listeria monocytogenes J0161]
 gi|254912805|ref|ZP_05262817.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes J2818]
 gi|254937132|ref|ZP_05268829.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|47014781|gb|EAL05734.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|258609734|gb|EEW22342.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|293590800|gb|EFF99134.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes J2818]
          Length = 289

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 132/319 (41%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT+V  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  G
Sbjct: 1   MTHV-TLPILEDWEGLSLTTILQEKF-HLGKKARHEIRMSQNVLLNNKPLDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P  ++    + +                     ++YED  + V NKP  +     
Sbjct: 59  ASLSLPIFLHDKIPVYE-----------------YDLEIIYEDDFLLVVNKPVDMKTHPN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++  GQ       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEKTGQDTNALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            + Y + V G      + I   + +  H G        Q       A++H KV++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDNEK 216

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L 
Sbjct: 217 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|298292787|ref|YP_003694726.1| pseudouridine synthase [Starkeya novella DSM 506]
 gi|296929298|gb|ADH90107.1| pseudouridine synthase [Starkeya novella DSM 506]
          Length = 250

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 74/230 (32%), Positives = 113/230 (49%), Gaps = 9/230 (3%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            + + +L+ D  + V +KPAG++V  G      +   L +        P L HRLD++TS
Sbjct: 10  DIAARVLHRDGMMLVIDKPAGLAVHKGPKGGETLADHLDALRFGLPNAPELAHRLDKDTS 69

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G LV+ R R A   L ++F    + K Y ++V G+P   +  I   L K+S   G ++ V
Sbjct: 70  GCLVLGRHRKALADLGKAFADGTVGKTYMAVVRGVPAEPRGRIELKLSKRSPTRGWWMAV 129

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               +     AIS ++ I         + + P TGRTHQLRVH   +G PI+GD  Y   
Sbjct: 130 ----DPNGQEAISEWETIAAGEGLAVLV-LSPLTGRTHQLRVHMNAIGHPILGDSIYG-- 182

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
             G    P    L+LH+R + +P  +G  + + APLP H+  T +  GF 
Sbjct: 183 --GASRLPGGPILHLHSRRVVIPQRKGEAIDVRAPLPPHIRATIERAGFD 230


>gi|16804283|ref|NP_465768.1| hypothetical protein lmo2244 [Listeria monocytogenes EGD-e]
 gi|224498988|ref|ZP_03667337.1| hypothetical protein LmonF1_04513 [Listeria monocytogenes Finland
           1988]
 gi|224500956|ref|ZP_03669263.1| hypothetical protein LmonFR_00305 [Listeria monocytogenes FSL
           R2-561]
 gi|254826867|ref|ZP_05231554.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL N3-165]
 gi|254831319|ref|ZP_05235974.1| hypothetical protein Lmon1_08172 [Listeria monocytogenes 10403S]
 gi|16411714|emb|CAD00322.1| lmo2244 [Listeria monocytogenes EGD-e]
 gi|258599247|gb|EEW12572.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL N3-165]
          Length = 289

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 132/319 (41%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT+V  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  G
Sbjct: 1   MTHV-TLPILEDWEGLSLTTILQEKF-HLGKKARHEIRMSQNVLLNNKPLDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P  ++    + +                     ++YED  + V NKP  +     
Sbjct: 59  ASLSLPIFLHDKIPVYE-----------------YDLEIIYEDDFLLVVNKPVDMKTHPN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++  GQ       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEKTGQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            + Y + V G      + I   + +  H G        Q       A++H KV++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDNEK 216

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L 
Sbjct: 217 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|301052930|ref|YP_003791141.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           anthracis CI]
 gi|300375099|gb|ADK04003.1| ribosomal large subunit pseudouridylate synthase D [Bacillus cereus
           biovar anthracis str. CI]
          Length = 307

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 130/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EMTVPARWNGISIESLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E   LD               ++YED  + + NKP  +       G   
Sbjct: 70  MFMEEEYDVEPEYGELD---------------VVYEDDHVLIVNKPEKMDTHPAEKGGMG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      KG   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEGYFKKQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNDTMKEF 302


>gi|49259509|pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of
           Pseudouridine Synthase Rluc From Escherichia Coli
 gi|49259510|pdb|1V9K|B Chain B, The Crystal Structure Of The Catalytic Domain Of
           Pseudouridine Synthase Rluc From Escherichia Coli
          Length = 228

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 73/227 (32%), Positives = 118/227 (51%), Gaps = 9/227 (3%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            ++ YED  I V NKP+G +V GGSG+++ +   L++ +  + +   L HRLD++TSG+L
Sbjct: 2   DVIXYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVL 60

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+ R+A + L E  R +  QK Y +LV G  ++  + +   LLK     G+ +  V Q
Sbjct: 61  LVAKKRSALRSLHEQLREKGXQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQ 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---N 275
                  + + FKV + +A     +   P TGRTHQ+RVH  + G PI  D +Y     +
Sbjct: 121 E---GKPSETRFKVEERYA-FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFD 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDS 321
            +        N+L+LHA  +   HP  G + +I AP    + +    
Sbjct: 177 RQLTEAGTGLNRLFLHAAALKFTHPGTGEVXRIEAPXDEGLKRCLQK 223


>gi|312953063|ref|ZP_07771913.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|310628972|gb|EFQ12255.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|315154025|gb|EFT98041.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0031]
          Length = 283

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNHPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQTLSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|146074929|ref|XP_001462641.1| pseudouridylate synthase-like protein [Leishmania infantum]
 gi|134066719|emb|CAM65179.1| pseudouridylate synthase-like protein [Leishmania infantum JPCM5]
 gi|322496043|emb|CBZ31115.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 413

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 89/358 (24%), Positives = 157/358 (43%), Gaps = 30/358 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV---RVDKKR--VKFNNRI 59
             +QY VV  D    R+D +   H+P  ++  ++++++ G +   R + K+   +  +R+
Sbjct: 53  NELQYHVVTQDWFGQRVDDFVMQHHPEWDYETVKRLVQQGHIYRYRKNGKKRYTRLTDRL 112

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNL-------------TKHSDFLKSILLYEDS 106
           +  ++V +P        +     +   S +               K  +  + ++L+++ 
Sbjct: 113 EFDELVVVPTASFWERQLAPPSGVELQSSSTSQQQERRQKFHLSAKTREMAQEMVLFKNE 172

Query: 107 KIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
            + V NKP+G+ +      +A +I   L +W  +  QKP + H LD ETSG +V+AR+  
Sbjct: 173 HVIVINKPSGVPIMPTHDPLAMNITDLLPAWRYTNTQKPVICHNLDTETSGCVVLARSAN 232

Query: 166 AAQHLTESFRMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           A + L   F  R +   +YW    G P      I      +   GGD +         + 
Sbjct: 233 AHRMLGRMFVKRVVPNSVYWGFAVGKPPVNFGRIRMHFEIQKGQGGDVIVARPTPTADSK 292

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK-----G 278
             I+ F V     +   ++   P T R HQ R+ A H +  P++GD KY           
Sbjct: 293 VGIAEFVVNASALEFGSFISFYPLTTRRHQERIMAAHALRAPLLGDAKYGGESAFPHSLS 352

Query: 279 NFTSPIQN--KLYLHARYMDLPHPE--GGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            F  P +    L+LH R + LP+    G  + +TAPLP HM KT+  LG+  D +  +
Sbjct: 353 LFWDPARKDVPLHLHHRKIQLPYKNGAGEFVCVTAPLPPHMEKTFKRLGWPVDADDPL 410


>gi|160943193|ref|ZP_02090429.1| hypothetical protein FAEPRAM212_00679 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445432|gb|EDP22435.1| hypothetical protein FAEPRAM212_00679 [Faecalibacterium prausnitzii
           M21/2]
          Length = 329

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 63/300 (21%), Positives = 121/300 (40%), Gaps = 17/300 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++      +++ +RL R+ ++         L K  R+ +V+V+ K+     R+Q+G ++ 
Sbjct: 1   MKQFTATANDDGVRLSRFVQSVTRDFPTSLLYKSFRNKRVKVNGKKAAPEYRLQAGDLIE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +            E           K  +  K  ++YED  + V  KP  +         
Sbjct: 61  LYINDEF---FPPEGAKPVQKAAPKKQPNQPKVTVIYEDENLAVLYKPTHLLCHSDRTGD 117

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            ++      ++  KG+         KP + +RLD+ T G+++ A+  AA + + E  R  
Sbjct: 118 ANLVDAFTQYLTQKGEYDPHGENRFKPGICNRLDRGTEGLVIAAKNYAALRDMNEIIRTD 177

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y+++  GIP  +      W           +H  +  ++     I+   V+   A
Sbjct: 178 LLKKEYYTITVGIP--QSGRFTAWWEHDEKNNKVSIHAHQSQDERRKQIITDVDVL-RTA 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F   ++   TGRTHQ+R H  ++G P++GD KY        T        L A  +  
Sbjct: 235 GPFALCKIGLVTGRTHQIRAHLAYLGKPVLGDIKYGNRKMNERT--GTKTQALCAVRISF 292


>gi|309803082|ref|ZP_07697181.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           11V1-d]
 gi|308164863|gb|EFO67111.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           11V1-d]
          Length = 307

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 117/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 39  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGNEKPNETLK-------------- 84

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 85  FSNLPITIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALLNIKPHIITR 144

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 145 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 204 PIKRYIM------EGGKDSVTKYRVIKQVA-GASLVELQLLTGRTHQIRVHMQYLGHPLF 256

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y              +  LH   +    P E  R+++    PA M++ W  L
Sbjct: 257 GDHLYGVEDD-------FPRQALHCFLLAFDDPLEHKRIEVQIADPADMLQLWQKL 305


>gi|227545484|ref|ZP_03975533.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus reuteri
           CF48-3A]
 gi|300908150|ref|ZP_07125618.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus reuteri
           SD2112]
 gi|227184534|gb|EEI64605.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus reuteri
           CF48-3A]
 gi|300894715|gb|EFK88069.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus reuteri
           SD2112]
          Length = 301

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 62/299 (20%), Positives = 123/299 (41%), Gaps = 33/299 (11%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L+  +   G+++++       + +     V +               +   + N
Sbjct: 23  GVSSSLLKVAIYHGGKMQINGVDKWAVDTVNYHDKVTL--------------ILPPETAN 68

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQKPRLT 147
                      ++YED    + NKPAG++      +  A  +   +K +   +  + ++T
Sbjct: 69  DNVDISEAPIDIIYEDQDFLIMNKPAGVATVPAHNVPVADSLVNRVKGYYKRQNYENQVT 128

Query: 148 H---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           H   RLD++TSG++V  + R A   L E  +   ++K Y +L+ G    +   I   + +
Sbjct: 129 HVATRLDRDTSGLVVFPKHRFAHAVLDEQLKKHLVKKNYLALIKGKVPAEHGYIDAPIQR 188

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                     V +   K    +++ +   +C  Q    ++++ HTGRTHQ+RVH   +G 
Sbjct: 189 DPS-----SFVKRMVGKEGKASVTEYWRQECNVQ-ASLIKIRLHTGRTHQIRVHFASLGF 242

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           P++GD  Y         S +  +  LH  ++    P  G  + + APLP+      D L
Sbjct: 243 PLIGDKMYGEE------SGLIARQALHCYWLSFYSPFKGENITVLAPLPSDFKNAKDDL 295


>gi|309808775|ref|ZP_07702661.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           01V1-a]
 gi|308168011|gb|EFO70143.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           01V1-a]
          Length = 302

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 70/296 (23%), Positives = 118/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 34  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGKEKPNATLK-------------- 79

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 80  FSNLPIAIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITR 139

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 140 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 198

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 199 PVKRYIM------EGGKESVTKYRVIKQVA-GASLVELQLLTGRTHQIRVHMQYLGHPLF 251

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y             ++  LH   +    P E  R+++    PA MV+ W  L
Sbjct: 252 GDHLYGVEDD-------FHRQALHCFLLAFDDPLEHKRIEVQIADPADMVQLWQKL 300


>gi|269798694|ref|YP_003312594.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269095323|gb|ACZ25314.1| pseudouridine synthase, RluA family [Veillonella parvula DSM 2008]
          Length = 288

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 76/317 (23%), Positives = 134/317 (42%), Gaps = 37/317 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M++  Y V E  E  + + ++ K  +   +  ++Q + R  +V+V+ +       ++ G 
Sbjct: 1   MSWKTYTVKEPTE--LTVSKYVKERFSLSSR-DIQMMFRKKRVKVNSRVAHSQRALKKGD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-G 122
           V+ +                L    +     +     +LYED+   V NK   + V   G
Sbjct: 58  VLTLE---------------LPQDKDYGVDVEKGPITVLYEDAHTLVVNKDPFMLVHPAG 102

Query: 123 SGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +  +  ++  +   K    K R  HRLD++TSG ++  +T+ A Q+ T+  +  RI 
Sbjct: 103 QTKSCTLSNYVAGYYAKKNVVHKVRPVHRLDRDTSGCILFGKTKEAQQYYTDELQAGRID 162

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQK 239
           +IY  LV G        I    +  + IG D V   ++  ++    A + + V+D     
Sbjct: 163 RIYTGLVEG-------RIDANGMVDAPIGVDPVFDNRRVIDELGQPAQTEYIVLDHEGDN 215

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL-P 298
              L  +  TGRTHQ+RVH  H+G PIVGD  Y    K         +  LHA  +   P
Sbjct: 216 -TLLRFKLLTGRTHQIRVHMEHIGHPIVGDAMYGTRNKPYI------RQCLHASELTFVP 268

Query: 299 HPEGGRLQITAPLPAHM 315
           + +   + IT  +  + 
Sbjct: 269 YGKDEAITITCEVGDNF 285


>gi|227509368|ref|ZP_03939417.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
 gi|227191080|gb|EEI71147.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
          Length = 297

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 69/297 (23%), Positives = 118/297 (39%), Gaps = 32/297 (10%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            I    L+KI    GQ  V+ +    N ++ +  VV +               +     N
Sbjct: 24  GITRTLLKKIKYHGGQTLVNGEPSLVNRKLITNDVVTV--------------VLPPEPEN 69

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSK---GQKPR 145
               +  L   +++ED    V NK AG++       A   +   +K +        QK  
Sbjct: 70  DNVPASDLPIQIVFEDEHFLVVNKSAGVASVPAHNRANDSLVNRVKGYYQRNHYANQKIH 129

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD++TSG+++ A+   A   L +  +  +I+K Y ++V G+       I   + + 
Sbjct: 130 IVTRLDKDTSGLVIFAKHHFAHSVLDKQLKDHQIKKTYLAIVEGVFSTTHFEIYLPIKRA 189

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +        V +Q       +++         ++   L++Q HTGRTHQ+RVH   +G P
Sbjct: 190 AG-----SLVKRQVGFPGKMSVTEAWTKQRL-RQHTLLKLQIHTGRTHQIRVHMTAIGHP 243

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           +VGD  Y    K         +  LH   +   +P  G  +   APLP  M     S
Sbjct: 244 LVGDWLYNPEDKS------FPRQALHCAGLRFFNPFAGHFVDCRAPLPDDMKTYLAS 294


>gi|295105227|emb|CBL02771.1| Pseudouridylate synthases, 23S RNA-specific [Faecalibacterium
           prausnitzii SL3/3]
          Length = 329

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 63/300 (21%), Positives = 121/300 (40%), Gaps = 17/300 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++      +++ +RL R+ ++         L K  R+ +V+V+ K+     R+Q+G ++ 
Sbjct: 1   MKQFTATANDDGVRLSRFVQSVTRDFPTSLLYKSFRNKRVKVNGKKAAPEYRLQAGDLIE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +            E           K  +  K  ++YED  + V  KP  +         
Sbjct: 61  LYINDEF---FPPEGAKPVQKAAPKKQPNQPKVTVIYEDENLAVLYKPTHLLCHSDRTGD 117

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            ++      ++  KG+         KP + +RLD+ T G+++ A+  AA + + E  R  
Sbjct: 118 ANLVDAFTQYLTQKGEYDPHGENRFKPGICNRLDRGTEGLVIAAKNYAALRDMNEIIRTD 177

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y+++  GIP  +      W           +H  +  ++     I+   V+   A
Sbjct: 178 LLKKEYYTITVGIP--QSGRFTAWWEHDEKNNKVNIHAHQSQDERRKQIITDVDVL-RTA 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F   ++   TGRTHQ+R H  ++G P++GD KY        T        L A  +  
Sbjct: 235 GPFALCKIGLVTGRTHQIRAHLAYLGKPVLGDIKYGNRKMNERT--GTKTQALCAVRISF 292


>gi|251783426|ref|YP_002997731.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|242392058|dbj|BAH82517.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
          Length = 341

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 80/299 (26%), Positives = 123/299 (41%), Gaps = 37/299 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVR 66
           Q + V+   E    D+        I    ++  LR    V V+   + + + + SG  V 
Sbjct: 58  QTLTVKELLE----DKLL------IPR-KIRHFLRTKKNVLVNGSAITWQSAVNSGDQVE 106

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +            E+   D  + + + +   K   LYED  + + NKP G+      G  
Sbjct: 107 LFFD---------EEDYPDKPIMMGQAN---KVDCLYEDDHLIIVNKPEGMKTH---GNE 151

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 L       G+   + HRLD ETSG++V A+T      L      R I + YW+L
Sbjct: 152 PTELALLNHVSAYTGRTCYVVHRLDMETSGVIVFAKTPFILPILNRLLEKREISRDYWAL 211

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +K+      + +  H     V  VKQ +K    A++  K++  F Q    +  +
Sbjct: 212 VHGTLSSKEVSYREPIGRHRHDRRKRVVDVKQGQK----AVTDVKLLKSFKQNVSLINCR 267

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
             TGRTHQ+RVH  H G  ++GD  Y    KG    P   +L LHA  + L HP    +
Sbjct: 268 LQTGRTHQIRVHLSHHGHALLGDPLYS---KGKAECP---RLMLHAHQLRLRHPLTQEM 320


>gi|325297415|ref|YP_004257332.1| pseudouridine synthase, RluA family [Bacteroides salanitronis DSM
           18170]
 gi|324316968|gb|ADY34859.1| pseudouridine synthase, RluA family [Bacteroides salanitronis DSM
           18170]
          Length = 307

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 121/319 (37%), Gaps = 39/319 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           Y  Y V E  E    L  +       I+   ++ +L +  V VD      +N  +Q G  
Sbjct: 20  YTTYRVSEPGE----LMEFLMKKMAGISRTRVKALLTNRVVLVDNTIQTLYNYPLQPGMC 75

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-S 123
           V+I                         H   LK  +LYED+ I V  K  G+       
Sbjct: 76  VQISR----------------EKHKHEFHHPMLK--ILYEDAYIIVVEKKEGLLSVATER 117

Query: 124 GIAYHIDGFLKSWVDS--KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                    L  +V    KG +  + HRLD+ETSGI++ A+       L +++      +
Sbjct: 118 QKERTAQHILNEYVKRIHKGNRIYVVHRLDRETSGIMMYAKDEKTQHTLRDNWHDLVRDR 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G  +  +  + +WL                 + G  Y+++H+  I   A  F 
Sbjct: 178 RYVTIVQGEMEQDEGTVCSWLT-----DRKLYVSSSPTDDGGKYSVTHYHTIKR-ANGFS 231

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE+Q  TGR +Q+RVH   +G P+VGD +Y              +L LHA  +   HP 
Sbjct: 232 LLELQLETGRKNQIRVHMQSLGHPVVGDERYGCEMNP------LGRLALHAFKLCFYHPV 285

Query: 302 GGR-LQITAPLPAHMVKTW 319
               ++   P P       
Sbjct: 286 THEWMEFETPYPTPFKTLM 304


>gi|16801409|ref|NP_471677.1| hypothetical protein lin2346 [Listeria innocua Clip11262]
 gi|16414869|emb|CAC97573.1| lin2346 [Listeria innocua Clip11262]
 gi|313617601|gb|EFR89910.1| ribosomal large subunit pseudouridine synthase D [Listeria innocua
           FSL S4-378]
          Length = 289

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 136/319 (42%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT++  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  G
Sbjct: 1   MTHL-TLPILEDWEGLTLTAILQEKF-HLGKKARHEIRMSQDVLLNNKPLDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P              IL   + + ++       ++YED  + V NKP G+     
Sbjct: 59  ASLSLPI-------------ILHDKIPVYEY----DLEIIYEDDFLLVVNKPVGMKTHAN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++  GQ+      HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEKTGQEANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y + V G      + I   + +  H G        Q       A++H KV++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDNEN 216

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y  + +        N++ LHA  + L 
Sbjct: 217 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGGSSRA-------NRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|307702537|ref|ZP_07639490.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
 gi|307623883|gb|EFO02867.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
          Length = 278

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 67/289 (23%), Positives = 125/289 (43%), Gaps = 30/289 (10%)

Query: 23  RWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           ++ +     I    ++  LR    + ++ K V +N  ++ G + ++             +
Sbjct: 5   QFLEEQLL-IPR-KIRHFLRIKKNILINHKEVHWNEMVKPGDICQLTFDEEDY----PPK 58

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           +IL  + +L +         +Y+D  + + NKP G+   G       +   + ++V   G
Sbjct: 59  EILWGNSDLVQE--------VYQDQHLIIVNKPEGMKTHGNQPGEIALLNHVSAYV---G 107

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           Q   + HRLD ETSG+++ A+       L      + I + YW+L+ G  ++K+    + 
Sbjct: 108 QTCYVVHRLDMETSGLVLFAKNPFILPILNRLLEKKEIARDYWALIEGRVESKELVFRDK 167

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +  H     +     + K   YA +H   +  F  K   +  +  TGRTHQ+R+H  H
Sbjct: 168 IGRDRHDRRKRI----VDAKNGQYAETHISRLKQFPNKTTLVRCKLKTGRTHQIRIHLSH 223

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
              PI+GD  Y ++ K        ++L LHA  +   HP    +L  TA
Sbjct: 224 HKHPILGDPLYNSSSK-------VSRLMLHAFRLSFTHPLTLEQLSFTA 265


>gi|255994608|ref|ZP_05427743.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saphenum ATCC 49989]
 gi|255993321|gb|EEU03410.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saphenum ATCC 49989]
          Length = 322

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 65/281 (23%), Positives = 121/281 (43%), Gaps = 29/281 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             +  ++   RLDR+FK +Y + +   + K++R   V+V+ K+ K N  + +G  V I  
Sbjct: 4   FTITENDAGQRLDRFFKKYYCNASLAYIYKLIRK-DVKVNGKKCKQNFLLNAGDAVHIYI 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YH 128
             +    +I + K +    +           +++ED  + V  K AG+   G S      
Sbjct: 63  SDDEHKRMILKDKGVQIKPSF---------KIIFEDDNLLVVYKRAGLLTHGSSTEKKRT 113

Query: 129 IDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +   +K+++  KG+             ++RLD+ T G++ +A+  A+ + L  +F+  RI
Sbjct: 114 LLNEVKTYLIQKGEYDPGFEKTFSLATSNRLDRNTEGLIAIAKNAASQRELNAAFKEGRI 173

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCF-- 236
           ++ Y + V G  +     I   L K +     +              AI+    I     
Sbjct: 174 ERYYVAEVVGEVRGD-VTIDYPLYKSAKNNTVFADKDGSVPPDVTKEAITKVHPIRVNRI 232

Query: 237 -----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                   +  + ++  TGRTHQ+RVH   +G P+V D KY
Sbjct: 233 DKNGSEFTYTVVRVKLLTGRTHQIRVHLAAIGHPLVNDRKY 273


>gi|15594364|ref|NP_212152.1| hypothetical protein BB0018 [Borrelia burgdorferi B31]
 gi|2687903|gb|AAC66413.1| conserved hypothetical protein [Borrelia burgdorferi B31]
          Length = 336

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 74/342 (21%), Positives = 152/342 (44%), Gaps = 32/342 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +   V+ +   +RLD +   ++       +++       + + K +K        
Sbjct: 11  MIRVKREFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK-------- 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++   +   + I+ E     S ++  + S+ +   ++YEDS + V NKP GI    G
Sbjct: 61  --IKLSKPVFKDDEILIEFDEESSQIDCLRPSN-IPIAIIYEDSNVIVLNKPQGILSHPG 117

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                    + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + 
Sbjct: 118 ISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQ 176

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ +R  K+Y ++V G   +    I +++ +  H    +     +       A++ ++++
Sbjct: 177 FKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLL 232

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F + +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+ 
Sbjct: 233 LNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLKKIT---LMLHSY 287

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            +++   +    +  +  P   V    +     + NL I  L
Sbjct: 288 KLEIDVGKNSFKKFISEFPKRFVIFLSNFYKSDELNLIIDNL 329


>gi|315149417|gb|EFT93433.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0012]
          Length = 283

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 71/311 (22%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVRPTIHL---GEATRVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++  G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIAAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVQALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|23098677|ref|NP_692143.1| pseudouridine synthase [Oceanobacillus iheyensis HTE831]
 gi|22776904|dbj|BAC13178.1| pseudouridine synthase [Oceanobacillus iheyensis HTE831]
          Length = 322

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 61/316 (19%), Positives = 129/316 (40%), Gaps = 31/316 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRS-GQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++ +E+ M +  +      H +   L  + +    ++V+        +++   ++ +   
Sbjct: 30  IKKNEQGMLIKTYL-QQIHHFSRRLLISLKKVPSSIQVNGTSQWVTYKLKREDILTV--- 85

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                       + D   +     + L   ++YED+   V NKPAG +        ++  
Sbjct: 86  -----------ALPDEKPSDAITPEKLPLDIIYEDAYCLVVNKPAGQACLPSMNHRHNTL 134

Query: 131 GFLKSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               ++   K   P   H   RLD  TSG+++VA+ +      +   +   I ++Y ++V
Sbjct: 135 ANGLTYYYQKNSIPSTVHIVTRLDVNTSGLVLVAKNQYVHSLFSRMQQEGNINRVYEAIV 194

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        +   + +K     +       + +   YA ++++V+   +    W+E++ 
Sbjct: 195 HGEVSPTSGIVDAPIARKEGSIIER----TVDMRNGKYAKTNYRVLYADS-IASWVEIKL 249

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+RVH  ++G  + GD+ Y        +  I  +  LH + + + HP   + +Q
Sbjct: 250 ETGRTHQIRVHFQYLGHSLYGDNLYGG------SKDIMLRQALHCKQITMMHPIKNQPIQ 303

Query: 307 ITAPLPAHMVKTWDSL 322
           + A LP  M      L
Sbjct: 304 LEASLPEDMGILLKRL 319


>gi|224532575|ref|ZP_03673198.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi WI91-23]
 gi|224512518|gb|EEF82896.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi WI91-23]
          Length = 326

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 75/342 (21%), Positives = 153/342 (44%), Gaps = 32/342 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +   V+ +   +RLD +   ++       +++       + + K +K        
Sbjct: 1   MIRVKREFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK-------- 50

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++   +   + I+ E     S ++  + S+ +   ++YEDS + V NKP GI    G
Sbjct: 51  --IKLSKPVFKDDEILIEFDEESSQIDCLRPSN-IPIAIIYEDSNVIVLNKPQGILSHPG 107

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                    + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + 
Sbjct: 108 ISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ +RI K+Y ++V G   +    I +++ +  H    +     +       A++ ++++
Sbjct: 167 FKDKRINKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLL 222

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F + +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+ 
Sbjct: 223 LNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLEKIT---LMLHSY 277

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            +++   +    +  +  P   V    +     + NL I  L
Sbjct: 278 KLEIDVGKNSFKKFISEFPKRFVIFLSNFYKSDELNLIIDNL 319


>gi|188582089|ref|YP_001925534.1| pseudouridine synthase [Methylobacterium populi BJ001]
 gi|179345587|gb|ACB80999.1| pseudouridine synthase [Methylobacterium populi BJ001]
          Length = 249

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 113/239 (47%), Gaps = 11/239 (4%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           SV        +   +LY D+ + V +KPAG+ V  G      +   L +      ++P  
Sbjct: 6   SVPDRTVGPDIGLPILYRDALMLVIDKPAGLPVHPGPKGGPTLTDHLDALRFGLPRRPEA 65

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG LV+ R   A   L   F   +  K YW+LV G P   +  I   L K+S
Sbjct: 66  AHRLDRDTSGCLVLGRHARALARLNRLFADGKADKTYWALVEGGPDEAEGRIDLPLAKRS 125

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               D      + +     +++ ++V+   A    WLE++P TGRTHQLRVH   MG PI
Sbjct: 126 ---DDPRSWWMKTDPAGAPSLTLYRVLGR-ADGLSWLELKPVTGRTHQLRVHCAAMGWPI 181

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
            GD  Y +  +          L LHAR + LP +P+   +++ AP P HM    ++ G 
Sbjct: 182 RGDAIYGSAGRAG------PGLQLHARALSLPLYPKRDAIRVEAPAPMHMRAGLEACGM 234


>gi|331702478|ref|YP_004399437.1| RluA family pseudouridine synthase [Lactobacillus buchneri NRRL
           B-30929]
 gi|329129821|gb|AEB74374.1| pseudouridine synthase, RluA family [Lactobacillus buchneri NRRL
           B-30929]
          Length = 304

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 72/324 (22%), Positives = 128/324 (39%), Gaps = 28/324 (8%)

Query: 4   MTYVQY---VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  +Q+     V        L +   ++Y  +    +  I  + +V VD      N  ++
Sbjct: 1   MKDIQWCFNETVPEAMNGRPL-KALLSNYWQLPKHLVYSIRHAERVLVDGHYQPVNFPVK 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V++  V                              +LYED  + V +K  G    
Sbjct: 60  AGSQVQLTFVPADFARPFPN----------VTADSAATVAILYEDQNLVVMDKRRGDKTH 109

Query: 121 GG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               G        L +++ ++   P + HRLDQETSG ++  +       L  +   ++I
Sbjct: 110 PNQPGEVGATINHLAAYLATEKTVPYMIHRLDQETSGAIIFGKNPVVVPILVANIANKQI 169

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y + V G     +  I   + +            K N   A  A++ ++V+   +  
Sbjct: 170 KRTYLAWVEGTDLPDEGTINLPIGRDPDDKRKR----KINGPHAAPALTRYRVLRKQS-G 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  +++   TGRTHQ+RVH   +G P+VGD  Y ++    F       L LH+  +DL  
Sbjct: 225 YALVQISLETGRTHQIRVHFAALGHPLVGDPLYNSSNGSPF-------LMLHSWKVDLLM 277

Query: 300 PEGGRLQ-ITAPLPAHMVKTWDSL 322
           P   + + I AP+P H +K    L
Sbjct: 278 PFTKQRKLIEAPIPDHFIKFEQEL 301


>gi|260914145|ref|ZP_05920618.1| tRNA pseudouridine synthase C [Pasteurella dagmatis ATCC 43325]
 gi|260631778|gb|EEX49956.1| tRNA pseudouridine synthase C [Pasteurella dagmatis ATCC 43325]
          Length = 241

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 108/242 (44%), Gaps = 17/242 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELEILYQDDYLVAVNKPAGMLVHRSWLDMHETQFVMQTLRDQIGQHVYPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A +   A  L   F  ++++K Y ++V G    K+       +K   +   +V   
Sbjct: 61  VLLFALSSEVANLLCLQFEDKQVEKSYLAIVRGYLTGKERIDYPLKVKLDKVADKFV--- 117

Query: 217 KQNEKGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            Q +K    A++ ++          V      ++  + + P TGR HQLR H  H+  PI
Sbjct: 118 -QEDKAPQDAVTDYQGLLTVEMPYSVKKYNTTRYSLVRLLPQTGRKHQLRRHMKHIFHPI 176

Query: 267 VGDHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
           +GD +Y    +    +      +L LHA  +   HP     +++TA L A  +K  +  G
Sbjct: 177 LGDTQYGDLHQNRAFTEYTEVKRLMLHAETLVFIHPIIREPIKLTAELDADWLKVLEIFG 236

Query: 324 FK 325
           + 
Sbjct: 237 WS 238


>gi|167816774|ref|ZP_02448454.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           pseudomallei 91]
          Length = 248

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 80/234 (34%), Positives = 122/234 (52%), Gaps = 14/234 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +L+ED  I V NKPAG++V GGSG+A+ +   ++       +   L HRLD+ETSGI
Sbjct: 13  EFEILFEDDAIIVLNKPAGVAVHGGSGVAFGVIEQMRHAR-PHAKFLELAHRLDRETSGI 71

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGDYVH 214
           L++A+ R+A   L E  R  R+ K Y++ V G       ++  +   L K +   G+   
Sbjct: 72  LMLAKKRSALVGLHEQIRENRMDKRYFACVHGDWAADWGRRRVVKAPLFKYATPDGERRV 131

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC- 273
            V+++      + + F ++D +   +  +E +  TGRTHQ+RVH  H+G PIVGD KY  
Sbjct: 132 RVQED---GLPSHTVFNLVDRWPD-YALVEAELKTGRTHQIRVHLAHLGLPIVGDAKYGD 187

Query: 274 ----ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                        P   +++LHA  + L HP  G  LQ  APLPA   +  D L
Sbjct: 188 FALNKALARANAVPSIKRMFLHAHRLRLAHPLTGEPLQFDAPLPAECRQFIDQL 241


>gi|215403396|ref|ZP_03415577.1| pseudouridylate synthase [Mycobacterium tuberculosis 02_1987]
 gi|215426884|ref|ZP_03424803.1| pseudouridylate synthase [Mycobacterium tuberculosis T92]
 gi|215430434|ref|ZP_03428353.1| pseudouridylate synthase [Mycobacterium tuberculosis EAS054]
 gi|218753261|ref|ZP_03532057.1| pseudouridylate synthase [Mycobacterium tuberculosis GM 1503]
 gi|219557451|ref|ZP_03536527.1| pseudouridylate synthase [Mycobacterium tuberculosis T17]
 gi|254550560|ref|ZP_05141007.1| hypothetical protein Mtube_08877 [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260200601|ref|ZP_05768092.1| hypothetical protein MtubT4_10875 [Mycobacterium tuberculosis T46]
 gi|297634109|ref|ZP_06951889.1| hypothetical protein MtubK4_08307 [Mycobacterium tuberculosis KZN
           4207]
          Length = 294

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 74/315 (23%), Positives = 138/315 (43%), Gaps = 30/315 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D         ++      +   G V ++      ++R+ SG ++++           
Sbjct: 1   MRVDTGLARLL-GLSRTAAAALAEEGAVELNGVPAGKSDRLVSGALLQV----------- 48

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW 136
              ++ ++   L      ++ + +LY D  I   +KPA ++     G     + G L + 
Sbjct: 49  ---RLPEAPAPLQNTPIDIEGMTILYSDDDIVAVDKPAAVAAHASVGWTGPTVLGGLAAA 105

Query: 137 -----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                     ++  + HRLD  TSG++VVA +  A   L  +F+ R + K Y +LV G P
Sbjct: 106 GYRITTSGVHERQGIVHRLDVGTSGVMVVAISERAYTVLKRAFKYRTVDKRYHALVQGHP 165

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   + +  H G ++   +    K   ++++H+  ++ F      L++   TGR
Sbjct: 166 DPSSGTIDAPIGR--HRGHEWKFAIT---KNGRHSLTHYDTLEAFV-AASLLDVHLETGR 219

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH   +  P  GD  Y A+ K      + ++ +LHAR +   HP +G R++I +P
Sbjct: 220 THQIRVHFAALHHPCCGDLVYGADPKLAKRLGL-DRQWLHARSLAFAHPADGRRVEIVSP 278

Query: 311 LPAHMVKTWDSLGFK 325
            PA +      L  +
Sbjct: 279 YPADLQHALKILRGE 293


>gi|46908477|ref|YP_014866.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|47093359|ref|ZP_00231127.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|226224852|ref|YP_002758959.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes Clip81459]
 gi|254825192|ref|ZP_05230193.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
 gi|254931643|ref|ZP_05265002.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|254992053|ref|ZP_05274243.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J2-064]
 gi|46881748|gb|AAT05043.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Listeria monocytogenes serotype 4b str. F2365]
 gi|47018278|gb|EAL09043.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|225877314|emb|CAS06028.1| Putative ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes serotype 4b str. CLIP 80459]
 gi|293583198|gb|EFF95230.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|293594437|gb|EFG02198.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
 gi|328465825|gb|EGF37013.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes 1816]
 gi|328472136|gb|EGF43011.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes 220]
          Length = 289

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 132/319 (41%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT+V  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  G
Sbjct: 1   MTHV-TLPILEDWEGLSLTTILQEKF-HLGKKARHEIRMSQNVLLNNKPLDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P  ++    + +                     ++YED  + V NKP  +     
Sbjct: 59  ASLSLPVFLHDKIPVYE-----------------YDLEIIYEDDFLLVVNKPVDMKTHPN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++  GQ       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEKTGQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            + Y + V G      + I   + +  H G        Q       A++H KV++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDNEK 216

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L 
Sbjct: 217 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|269791933|ref|YP_003316837.1| pseudouridine synthase [Thermanaerovibrio acidaminovorans DSM 6589]
 gi|269099568|gb|ACZ18555.1| pseudouridine synthase [Thermanaerovibrio acidaminovorans DSM 6589]
          Length = 302

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 90/322 (27%), Positives = 138/322 (42%), Gaps = 28/322 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +  D+E  RLDR  +  +P +N       +R GQVR+D +RV  + R+  GQ + 
Sbjct: 1   MRTYRIPPDQEGRRLDRLIREWWPEVNMGLRMGAIRRGQVRLDGRRVPCSQRLLEGQELT 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P          +E +   S          L   +++ D ++ V NKPAG   Q G G  
Sbjct: 61  VPWD--------QEPRRSGSGTPCPAEGRELPRWVIHWDRRLLVANKPAGWICQPGGGRG 112

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   +   +    + P  +HRLD  T+G+++V    A  + L   FR   I+K+YW+L
Sbjct: 113 TSLPEEVWRLL-GVDRGPVPSHRLDVNTTGVVLVPLDGALGRELHRLFREGTIRKLYWAL 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G    +   +   L K                     A S  + +      F  +E++
Sbjct: 172 VRGTCVGEA-LVDLPLSKDGRGN-------VTPSPSGQPARSVVRPLAVRG-GFSLVEVE 222

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
             TGR HQ RVH  H+G PI+GD +Y   F+G        +  LHAR + LP  E  G L
Sbjct: 223 LLTGRQHQARVHLAHLGLPILGDVRYGVRFRGV------GRTMLHARRVLLPFGESLGDL 276

Query: 306 ---QITAPLPAHMVKTWDSLGF 324
                 APL   M +    LG 
Sbjct: 277 AGAAFEAPLYPDMAEAARRLGL 298


>gi|299143272|ref|ZP_07036352.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           386 str. F0131]
 gi|298517757|gb|EFI41496.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           386 str. F0131]
          Length = 329

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 71/309 (22%), Positives = 129/309 (41%), Gaps = 25/309 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + V  ++E  R+DR+ K ++       + K LR   ++++ K+ +  + +  G  ++
Sbjct: 1   MIEIFVNENDEGQRIDRFLKKYFEKATLSFIYKNLRKKNIKLNDKKAEPEDLLSKGDCIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           +      +    +E              +     +++ED  I + NKPAGI     S   
Sbjct: 61  LYLSDETIEKFKREP---------INFKNNKFPKIIFEDENIILMNKPAGILSHNDSKDF 111

Query: 126 AYHIDGFLKSWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             ++   +  ++         +    +P + +RLD+ TSGIL+ A+     + L    + 
Sbjct: 112 KKNMVDMMIDYLIARQEYNPRNENSFRPAICNRLDRNTSGILIGAKKSGVLRSLNYEIKK 171

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I K Y +LV G  K ++    ++L K      + V V+K+N  GA  +I+ FK I   
Sbjct: 172 NNIDKFYLALVSGEAK-EQFSDRSYLSKDG--DRNKVTVLKKNSIGAKESITEFKRI-AM 227

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARY 294
              +  L++   TGRTHQ+R        PIVGD KY  +               +LH   
Sbjct: 228 QNDYSLLKVNLITGRTHQIRTVLSSKKLPIVGDVKYGDSSVNRLFKNKYKYESQFLHNYS 287

Query: 295 MDLPHPEGG 303
           +     EG 
Sbjct: 288 IHFNKIEGE 296


>gi|218249610|ref|YP_002374552.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi ZS7]
 gi|226321152|ref|ZP_03796693.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 29805]
 gi|218164798|gb|ACK74859.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi ZS7]
 gi|226233444|gb|EEH32184.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 29805]
          Length = 326

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/342 (21%), Positives = 153/342 (44%), Gaps = 32/342 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +   V+ +   +RLD +   ++       +++       + + K +K        
Sbjct: 1   MIRVKREFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK-------- 50

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++   +   + I+ E     S ++  + S+ +   ++YEDS + V NKP GI    G
Sbjct: 51  --IKLSKPVFKDDEILIEFDEESSQIDCLRPSN-IPIAIIYEDSNVIVLNKPQGILSHPG 107

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                    + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + 
Sbjct: 108 ISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ +RI K+Y ++V G   +    I +++ +  H    +     +       A++ ++++
Sbjct: 167 FKDKRINKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLL 222

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F + +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+ 
Sbjct: 223 LNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLKKIT---LMLHSY 277

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            +++   +    +  +  P   V    +     + NL I  L
Sbjct: 278 KLEIDVGKNSFKKFISEFPKRFVIFLSNFYKSDELNLIIDNL 319


>gi|144897601|emb|CAM74465.1| Pseudouridylate synthase [Magnetospirillum gryphiswaldense MSR-1]
          Length = 230

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 119/233 (51%), Gaps = 11/233 (4%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
            D L + +LY D+ + + +KPAG++V  G    ++H+   L+       + P L HRLD+
Sbjct: 3   PDELLARVLYRDAMVLIIDKPAGLAVHAGARDGSHHLMDLLEPLRFGLPRNPELAHRLDR 62

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG LV+ R R A   L E F     QK YW++V G P  +   I   L K     G  
Sbjct: 63  DTSGCLVLGRHRKALARLGEIFAGSEAQKTYWAVVVGKPPAESGIIDKRLKKLERRHGWR 122

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + V    +     A++ ++V+    +   W+E +P TGRTHQ+RVH   +GCPIVGD  Y
Sbjct: 123 MVV----DDKGQDAVTEYRVLGGNGR-LSWIEAKPRTGRTHQIRVHLAAIGCPIVGDSTY 177

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPH-PEGGRLQITAPLPAHMVKTWDSLGF 324
                      +   L+LHAR + LP+ P+   +   AP+PAHM+      G+
Sbjct: 178 GRGT----ADLVSPHLHLHARSITLPYNPKKSPITAQAPVPAHMIDALIQCGW 226


>gi|212693126|ref|ZP_03301254.1| hypothetical protein BACDOR_02633 [Bacteroides dorei DSM 17855]
 gi|237725459|ref|ZP_04555940.1| RNA pseudouridylate synthase [Bacteroides sp. D4]
 gi|265753523|ref|ZP_06088878.1| conserved hypothetical protein [Bacteroides sp. 3_1_33FAA]
 gi|212664231|gb|EEB24803.1| hypothetical protein BACDOR_02633 [Bacteroides dorei DSM 17855]
 gi|229436146|gb|EEO46223.1| RNA pseudouridylate synthase [Bacteroides dorei 5_1_36/D4]
 gi|263235237|gb|EEZ20761.1| conserved hypothetical protein [Bacteroides sp. 3_1_33FAA]
          Length = 308

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 62/303 (20%), Positives = 117/303 (38%), Gaps = 34/303 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       I+   ++ +L +  + VD     ++N  ++ G  V++               
Sbjct: 34  FLMRKMAGISRSKVKALLANRVILVDNVITTQYNFALKPGMKVQM--------------- 78

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDS-- 139
              S     +        L+YED+ I V  K  G+                L  +V    
Sbjct: 79  ---SKAKNNREFKHPMLKLVYEDAYILVVEKKEGLLSVSTERQKERTAQHILNEYVKRSH 135

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +  +  + HRLD+ETSG+++ A+       L +++      + Y S+V G  +     + 
Sbjct: 136 RFNRVFVVHRLDRETSGLMMYAKDEKTQNTLRDNWHDIVTDRRYVSIVSGDMEKDYGTVE 195

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WL  +      YV     ++    +A++H+K I   A  +  +E+   TGR +Q+RVH 
Sbjct: 196 SWLTDRKL----YVSSSPVDDGEGKFAVTHYKTIKR-ANGYSLVELDLETGRKNQIRVHM 250

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             +G P++GD +Y +            +L LHA  +   HP     ++   P P      
Sbjct: 251 SDLGHPVIGDRRYGSECDP------LGRLALHAFKLCFYHPVTRELMEFETPYPTAFKGL 304

Query: 319 WDS 321
              
Sbjct: 305 MQK 307


>gi|257081816|ref|ZP_05576177.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis E1Sol]
 gi|256989846|gb|EEU77148.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis E1Sol]
          Length = 297

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/309 (24%), Positives = 135/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L K+  + G+++V+         +Q+G VV++               
Sbjct: 18  FLKEQ--GVSKGLLAKVKFQGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLS 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   +   +A + + +    AQ    + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAA-VRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGEMDQ-----GIGRQALHCMELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKSVDDTL 297


>gi|145629453|ref|ZP_01785251.1| tRNA pseudouridine synthase C [Haemophilus influenzae 22.1-21]
 gi|144978296|gb|EDJ88060.1| tRNA pseudouridine synthase C [Haemophilus influenzae 22.1-21]
 gi|309750918|gb|ADO80902.1| tRNA U65 pseudouridine synthase [Haemophilus influenzae R2866]
          Length = 239

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 107/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y    +    +      +L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALTFHLGFSRLFLHSNSLSFIHPIKKEQITITAGLDEQWQQLMNQFGWE 237


>gi|295397129|ref|ZP_06807237.1| ribosomal large subunit pseudouridine synthase D [Aerococcus
           viridans ATCC 11563]
 gi|294974627|gb|EFG50346.1| ribosomal large subunit pseudouridine synthase D [Aerococcus
           viridans ATCC 11563]
          Length = 294

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 63/304 (20%), Positives = 122/304 (40%), Gaps = 34/304 (11%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K  +  I+   L +I    GQ+ V+ +     +++  G  V +         II+   
Sbjct: 17  FLK--HKGISRRLLSRIKFHGGQILVNGQEENVRHQLTVGDKVTVILPNEGKQEIIE--- 71

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKG 141
                      +  L   +L+ED      NKPAG +           +   LK++   + 
Sbjct: 72  -----------AIHLPIDILFEDDHYIAVNKPAGYTSIPSQYNPQGSMANILKAYYQRQD 120

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KKEC 197
              ++ H   RLD++TSG+++ A+   A   + +  + + I+K Y ++      +     
Sbjct: 121 YDNQVIHVVTRLDRDTSGVMLFAKHAFAHGLIDQQMQQKGIEKTYLAISDKRVSDFNHGF 180

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I + + +          + ++  +    A++ + + +         ++Q HTGRTHQ+RV
Sbjct: 181 IDDPIARSP-----RSIIERRVHESGQSALTEYWLAEQVG-ALKVYKVQLHTGRTHQIRV 234

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMV 316
           H    G P++GD  Y              +  LH R +   H   G + +I APLP  + 
Sbjct: 235 HFAFNGAPLIGDDLYGGQM-----DHGIQRQALHCRSLKFKHQFTGEMIEIQAPLPEDIS 289

Query: 317 KTWD 320
             +D
Sbjct: 290 ACFD 293


>gi|184155038|ref|YP_001843378.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
 gi|227514836|ref|ZP_03944885.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus fermentum
           ATCC 14931]
 gi|260663582|ref|ZP_05864471.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
 gi|183226382|dbj|BAG26898.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
 gi|227086826|gb|EEI22138.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus fermentum
           ATCC 14931]
 gi|260551808|gb|EEX24923.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
 gi|299783021|gb|ADJ41019.1| Pseudouridine synthase [Lactobacillus fermentum CECT 5716]
          Length = 296

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 66/314 (21%), Positives = 125/314 (39%), Gaps = 36/314 (11%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            E+  RL   F++    +    L+  +   GQ+R++ +     ++++ G VV +      
Sbjct: 9   GEQPRRLRSVFRSF--GVTNSLLKVAIFHGGQMRINDRVAWAIDQVEPGDVVYL------ 60

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDG 131
                    + +   N T         + YED    V NK AG++      +A    +  
Sbjct: 61  --------VVPNEPANPTITVSDQTFEIAYEDEDFLVINKEAGVATVPAHHVAVQDSLVN 112

Query: 132 FLKSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +K +   +    ++TH   RLD++TSG++V  + R A   L    + R+++K Y ++V 
Sbjct: 113 RVKGYYQRQNYPNQVTHVATRLDKDTSGLVVFPKHRFAHAVLDRQLKARQVKKEYLAMVQ 172

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        I   + +          V +        + + +   +        + ++ H
Sbjct: 173 GRLTVSHGYIDAPIRRDPD-----SFVKRLVAPDGKASATEYWC-ERVTDTTSLVRVRLH 226

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH   +G P++GD  Y   F          +  LH + +    P   + + +
Sbjct: 227 TGRTHQIRVHFSFLGHPLLGDDMYGTGF-------GMPRQALHCQRVSFYSPFKQKVISV 279

Query: 308 TAPLPAHMVKTWDS 321
            APLP    +  D 
Sbjct: 280 AAPLPTDFQRAEDE 293


>gi|293374677|ref|ZP_06620987.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|292646694|gb|EFF64694.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
          Length = 297

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 72/324 (22%), Positives = 136/324 (41%), Gaps = 42/324 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKIL-----RSGQVRVDKKRVKFNNR 58
           M+      ++  ++   L  + K     I+    +K +     R G + V+ +       
Sbjct: 1   MSLTLTYEIKAADDQTLLLNFLKKQ--DIS----KKAIVATKHRGGNMEVNGEHQNVRYL 54

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           ++ G V+ I                 + S  LT +   +   ++YED  + V NKPAGI 
Sbjct: 55  LKEGDVLVITFPEE------------ERSTGLTPYE--MPLDVVYEDEYLLVINKPAGIP 100

Query: 119 VQGG-SGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                      +   L  + +           +RLD++TSG+L+VA+ R     LT+   
Sbjct: 101 TIPSLRHPEKTLANALIHYYNEHEIASTIHFVNRLDRDTSGLLMVAKYRHIHHLLTKDV- 159

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            ++I++ Y++LV G+ +     +   + ++S   G+    V+ +      +I+H++V++ 
Sbjct: 160 -KQIKRKYYTLVKGVMEKNSGTVHAPIARESE--GNVRRCVRADGDD---SITHYQVLEV 213

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           + +K   +E +  TGRTHQ+RVH  ++G P+VGD  Y       F   ++    LH+  +
Sbjct: 214 W-EKLTLVECELETGRTHQIRVHMNYLGHPLVGDTLY-----DEFALELEEGHLLHSYEL 267

Query: 296 DLPHPEGGRLQ-ITAPLPAHMVKT 318
              HP           LP      
Sbjct: 268 SFTHPITKERHLFQTDLPKRFKAL 291


>gi|325841309|ref|ZP_08167410.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
 gi|325489990|gb|EGC92337.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
          Length = 297

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 72/324 (22%), Positives = 136/324 (41%), Gaps = 42/324 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKIL-----RSGQVRVDKKRVKFNNR 58
           M+      ++  ++   L  + K     I+    +K +     R G + V+ +       
Sbjct: 1   MSLTLTYEIKAADDQTLLLNFLKKQ--DIS----KKAIVATKHRGGNMEVNGEHQNVRYL 54

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           ++ G V+ I                 + S  LT +   +   ++YED  + V NKPAGI 
Sbjct: 55  LKEGDVLVITFPEE------------ERSTGLTPYE--MPLDVVYEDEYLLVINKPAGIP 100

Query: 119 VQGG-SGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                      +   L  + +           +RLD++TSG+L+VA+ R     LT+   
Sbjct: 101 TIPSLRHPEKTLANALIHYYNEHEIASTIHFVNRLDRDTSGLLMVAKYRHIHHLLTKDV- 159

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            ++I++ Y++LV G+ +     +   + ++S   G+    V+ +      +I+H++V++ 
Sbjct: 160 -KQIKRKYYTLVKGVMEKNSGTVHAPIARESE--GNVRRCVRADGDD---SITHYQVLEV 213

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           + +K   +E +  TGRTHQ+RVH  ++G P+VGD  Y       F   ++    LH+  +
Sbjct: 214 W-EKSTLVECELETGRTHQIRVHMNYLGHPLVGDTLY-----DEFALELEEGHLLHSYEL 267

Query: 296 DLPHPEGGRLQ-ITAPLPAHMVKT 318
              HP           LP      
Sbjct: 268 SFTHPITKERHLFQTDLPKRFKAL 291


>gi|25011211|ref|NP_735606.1| hypothetical protein gbs1160 [Streptococcus agalactiae NEM316]
 gi|76787983|ref|YP_329799.1| ribosomal large subunit pseudouridine synthase A [Streptococcus
           agalactiae A909]
 gi|77405506|ref|ZP_00782598.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
 gi|77408702|ref|ZP_00785434.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
 gi|77410529|ref|ZP_00786890.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77413047|ref|ZP_00789249.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
 gi|23095635|emb|CAD46819.1| unknown [Streptococcus agalactiae NEM316]
 gi|76563040|gb|ABA45624.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus agalactiae A909]
 gi|77160945|gb|EAO72054.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
 gi|77163477|gb|EAO74427.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77172677|gb|EAO75814.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
 gi|77175903|gb|EAO78680.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
 gi|319745122|gb|EFV97447.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus agalactiae
           ATCC 13813]
          Length = 294

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 68/298 (22%), Positives = 122/298 (40%), Gaps = 31/298 (10%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L KI  R G++ V+ +       ++ G VV I               I D   +
Sbjct: 21  DVSRGLLAKIKYRGGKIFVNGEEQNAIFLLEIGDVVTI--------------DIPDEPSH 66

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL 146
            T         ++YED    + NKP G +    S  +  I  F+K +    +   Q+  +
Sbjct: 67  ETLEPVPHDLDIVYEDDHFLILNKPFGFASIPSSIHSNTIANFIKHYYVSNNYANQQVHI 126

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKK 205
             RLD++TSG+++ A+   A   L +  + + I+K Y++LV G         I   + + 
Sbjct: 127 VTRLDRDTSGLMLFAKHGYAHARLDKQLQAKAIEKRYYALVSGSGDLADSGDIIAPIARD 186

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                    + ++  +   YA + ++V+  +      ++++ HTGRTHQ+RVH  H+G P
Sbjct: 187 VD-----SIITRRVHESGKYAHTSYQVVARYGD-VRLVDIKLHTGRTHQIRVHFAHIGFP 240

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
           ++GD  Y             N+  LH   +    P  G++   T  L          L
Sbjct: 241 LLGDDLYGGRM-----DLGINRQALHCHSLSFYDPFMGKINKQTLDLTDDFDSVIMEL 293


>gi|298252641|ref|ZP_06976435.1| pseudouridylate synthase, 23S RNA-specific [Gardnerella vaginalis
           5-1]
 gi|297533005|gb|EFH71889.1| pseudouridylate synthase, 23S RNA-specific [Gardnerella vaginalis
           5-1]
          Length = 288

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 121/301 (40%), Gaps = 26/301 (8%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
            ++  +   ++   Q ++  ++ + ++ +Q G  + +    +A           +     
Sbjct: 2   GVSRASAISLIERNQAKILGRKSQKSSILQDGDTIVVDQKESA-----------EQKEEQ 50

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPR---- 145
              S      ++Y D  + V +KP G++     G     +   L++              
Sbjct: 51  NNESSVCNIPIIYNDDDVVVIDKPVGVASHAAKGWSGPTVPECLEAVGIDIKTTLCDESR 110

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             +  RLD  TSG+++V +T  A + +   F    ++K Y +LV G     K  I   + 
Sbjct: 111 KGIVSRLDVGTSGLMLVCKTDFAYEVMKNQFAKHIVKKTYHALVQGDLAQDKATIDAPIG 170

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +                     A++H+ V++ F+Q    + +   TGRTHQ+RVH   +G
Sbjct: 171 R-----AKVSDFRFTITSDGKPAVTHWDVLERFSQ-ATLVSVNLETGRTHQIRVHFSSIG 224

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            P+VGD  Y AN        +Q + +LH+  +   HP  G+ + + +  P  +    +++
Sbjct: 225 HPLVGDSMYGANPVLAQKLGLQ-RQWLHSMELTFTHPRTGKSVTVKSHYPLDLQHALEAM 283

Query: 323 G 323
            
Sbjct: 284 R 284


>gi|22537251|ref|NP_688102.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           agalactiae 2603V/R]
 gi|22534119|gb|AAM99974.1|AE014242_3 ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 2603V/R]
          Length = 294

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 68/298 (22%), Positives = 122/298 (40%), Gaps = 31/298 (10%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L KI  R G++ V+ +       ++ G VV I               I D   +
Sbjct: 21  DVSRGLLAKIKYRGGKIFVNGEEQNAIFLLEIGDVVTI--------------DIPDEPSH 66

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL 146
            T         ++YED    + NKP G +    S  +  I  F+K +    +   Q+  +
Sbjct: 67  ETLEPVPHDLDIIYEDDHFLILNKPFGFASIPSSIHSNTIANFIKHYYVSNNYANQQVHI 126

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKK 205
             RLD++TSG+++ A+   A   L +  + + I+K Y++LV G         I   + + 
Sbjct: 127 VTRLDRDTSGLMLFAKHGYAHARLDKQLQAKAIEKRYYALVSGSGDLADSGDIIAPIARD 186

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                    + ++  +   YA + ++V+  +      ++++ HTGRTHQ+RVH  H+G P
Sbjct: 187 VD-----SIITRRVHESGKYAHTSYQVVARYGD-VRLVDIKLHTGRTHQIRVHFAHIGFP 240

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSL 322
           ++GD  Y             N+  LH   +    P  G++   T  L          L
Sbjct: 241 LLGDDLYGGRM-----DLGINRQALHCHSLSFYDPFMGKINKQTLDLTDDFDSVIMEL 293


>gi|322376158|ref|ZP_08050666.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C300]
 gi|321278840|gb|EFX55885.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C300]
          Length = 291

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 127/303 (41%), Gaps = 30/303 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
              +      M + ++ +     I    ++  LR    + ++ + V +N  ++ G + ++
Sbjct: 4   TFTLPESLPQMTVKQFLEEQLL-IPR-KIRHFLRIKKNILMNHEEVHWNEMVKPGDICQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                        ++IL  + +L +         +Y+D  + + NKP G+   G      
Sbjct: 62  TFDEEDY----PSKEILWGNPDLVQE--------VYQDQHLIIVNKPEGMKTHGNQPGEI 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   GQ   + HRLD ETSG+++ A+       L      + I + YW+L+
Sbjct: 110 ALLNHVSAYV---GQTCYVVHRLDMETSGLVLFAKNPFILPILNRLLEKKEIARDYWALI 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  ++K+    + + +  H     +     + K   YA +H   +  F  K   +  + 
Sbjct: 167 EGRVESKELVFRDKIGRDRHDRRKRI----VDTKNGQYAETHISRLKQFPNKTTLVRCKL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+R+H  H   PI+GD  Y +  K        ++L LHA  +   HP    +L 
Sbjct: 223 KTGRTHQIRIHLSHHKHPILGDPLYNSRSK-------VSRLMLHAFRLSFTHPLTLEQLS 275

Query: 307 ITA 309
            TA
Sbjct: 276 FTA 278


>gi|315173724|gb|EFU17741.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1346]
          Length = 297

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/309 (24%), Positives = 134/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L K+    G+++V+         +Q+G VV++               
Sbjct: 18  FLKEQ--GVSKGLLAKVKFEGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   +   +A + + +    AQ    + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAA-VRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGEMDQ-----GIERQALHCMELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKSVDDTL 297


>gi|258406577|ref|YP_003199319.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
 gi|257798804|gb|ACV69741.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
          Length = 299

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 85/309 (27%), Positives = 135/309 (43%), Gaps = 19/309 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M+  Q++ +  +E N ++    +N     +    L K +R+GQVRVDKKR K  +R+Q G
Sbjct: 1   MSPPQFLEITPEEANSKVLSVLQNRLDGQVPRSALMKWIRTGQVRVDKKRTKPFDRVQPG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q++R+PP                 S +       LK   + E   + V  KPAG+ VQ G
Sbjct: 61  QILRLPPQATL------------KSASSPGPPPALKLERIAETETLLVLAKPAGLPVQPG 108

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           S     +   L          P+  HRLD++TSGI++VA+     Q + ++++   +QK 
Sbjct: 109 SKHGASLVRELAKAYPETPWPPQPVHRLDKDTSGIILVAKRADVFQIIQQAWQRGEVQKD 168

Query: 183 YWS-LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + L  G             ++  H             +G   AI H + +   +    
Sbjct: 169 YLAWLAPGDDVGPGWHTWRDRIEICHTDRGEKMCCT---EGGKEAILHLRPLRRNSLGEI 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-YLHARYMDLPHP 300
            + +Q  TGR HQ+RV + + G P+VGD KY    +         +L Y  A +  LP P
Sbjct: 226 LVAIQLETGRKHQIRVQSANRGLPVVGDRKYGQTSQKTGLMLHAWRLGYSEALWTHLP-P 284

Query: 301 EGGRLQITA 309
             G   +TA
Sbjct: 285 WHGEYAVTA 293


>gi|312872564|ref|ZP_07732632.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
 gi|311091926|gb|EFQ50302.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
          Length = 300

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 117/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 32  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGNEKPNATLK-------------- 77

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 78  FSNLPITIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALLNIKPHIITR 137

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 138 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 196

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 197 PIKRYIM------EGGKDSVTKYRVIKQVA-GASLVELQLLTGRTHQIRVHMQYLGHPLF 249

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y              +  LH   +    P E  R+++    PA M++ W  L
Sbjct: 250 GDHLYGVEDD-------FPRQALHCFLLAFDDPLEHKRIEVQIADPADMLQLWQKL 298


>gi|282600856|ref|ZP_05979923.2| pseudouridine synthase, RluA family [Subdoligranulum variabile DSM
           15176]
 gi|282571159|gb|EFB76694.1| pseudouridine synthase, RluA family [Subdoligranulum variabile DSM
           15176]
          Length = 320

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 63/300 (21%), Positives = 120/300 (40%), Gaps = 23/300 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++     ++E  +RL R+ ++    +    + K  R+ +++V+ KR + + R+ +G V+ 
Sbjct: 1   MKSFTAGSNENGVRLSRFVESVTQQLPRSMMYKAFRNKRIKVNGKRAEPDTRLCTGDVIE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +                   +             ++YED    V  KPA +         
Sbjct: 61  MYINDEFFPAHT-------GTSKPKPPRRQPPVTIVYEDENFAVLYKPAHLLCHRDRTGD 113

Query: 127 YHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            ++     +++++KG+          P L +RLD+ T G+++ A+T  A + L E  R  
Sbjct: 114 PNLVDAFAAYLEAKGEYNPHAEQRFAPALCNRLDRGTEGLVLAAKTYQALRDLNEIIRTD 173

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y ++  G P         WL          +H   +  +G    I+   VI   +
Sbjct: 174 LMKKEYLTITVGAPPA--GRHIAWLQHSEKNNKVRIHA--RQSEGYKQIITDVTVI-RQS 228

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F    +   TGRTHQ+R H  ++G P++GD KY        T        L A+ +  
Sbjct: 229 GPFALCRIGLITGRTHQIRAHLSYLGHPVLGDIKYGNRKMNERT--GLKTQALCAQRLTF 286


>gi|285808641|gb|ADC36159.1| RluA family pseudouridine synthase [uncultured bacterium 162]
          Length = 326

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 126/319 (39%), Gaps = 29/319 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M    Y    ++ + +    L     + Y H      Q+ L +G+V VD      +  + 
Sbjct: 29  MLNRGYAYTTIISSKDRGRTLLSHLASLYTHSTAQAWQQNLDNGEVTVDGVTANGSESLA 88

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SGQ +                  + +     +        +L++D  +   NKP+G+   
Sbjct: 89  SGQTL------------------VWNRPPWVEPDAPQHFEMLFDDPYLLAVNKPSGLPTL 130

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            G G    ++  L   V ++       HRL + TSGI++ A+T  AA  L  ++   RIQ
Sbjct: 131 PGGGF---MENTLLRLVQNQCPSANPVHRLGRGTSGIVLFAKTPKAAAELCANWNTPRIQ 187

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y ++  G+ ++    I   +    H     +  V         + S  KVI   A+  
Sbjct: 188 KVYRAVAQGVAEHDAYEILTPIGLVPHP---LIGSVWGASPDGKPSKSVAKVISR-AEST 243

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDL 297
              E+   +GR HQ+R+H   +G P+VGD  Y       +     P      LHA+ +  
Sbjct: 244 TTFEVSLQSGRPHQIRIHLASIGYPLVGDPLYGLGGQPLENLPGLPGDGGYLLHAQLLKF 303

Query: 298 PHP-EGGRLQITAPLPAHM 315
            HP  G R+++ A LP   
Sbjct: 304 QHPISGERIELEAALPLGF 322


>gi|254455655|ref|ZP_05069084.1| pseudouridylate synthase [Candidatus Pelagibacter sp. HTCC7211]
 gi|207082657|gb|EDZ60083.1| pseudouridylate synthase [Candidatus Pelagibacter sp. HTCC7211]
          Length = 325

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 77/340 (22%), Positives = 143/340 (42%), Gaps = 40/340 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSG 62
           M      +VE  E N+R+D         I+   ++ ++   +++++ K  +  + ++ +G
Sbjct: 1   MEKNINFIVEESENNLRVDVIINKREQLISRTRIKNLILKNKLKLNNKIVISPSKKVVTG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +                +      +      K  ++YED  + V NKPAGI +  G
Sbjct: 61  DKLSLN---------------IPEPEEASLKPYKFKLDIIYEDEDLLVINKPAGIIMHPG 105

Query: 123 SG-IAYHIDGFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +G     I   L ++            +P + HR+D+ TSG++VVA+     + L++ F 
Sbjct: 106 AGNYDKTIVNALMNYDKDSLSNIGDELRPGIVHRIDKNTSGLVVVAKNNETHESLSKQFS 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              I ++Y  L+WG  +     I  ++ + S      + V +        AI+++K I  
Sbjct: 166 DHSITRVYQLLIWGKLRPSSGKIDTFITRSSK-NRQLMEVSRSK---GKRAITNYKTIKI 221

Query: 236 FAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI------- 284
           F          +E +  TGRTHQ+RVH  +MG  IVGD KY   +K      +       
Sbjct: 222 FESNKTPTLSLIECKLETGRTHQIRVHMTYMGNSIVGDDKYKKKYKKLKNVDVGLENLIS 281

Query: 285 -QNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
              + +LHA+ +   HP+    +  ++ LP  +      L
Sbjct: 282 KLKRQFLHAKTLGFVHPKTDKEMIFSSNLPKELNNLLKML 321


>gi|312870695|ref|ZP_07730803.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
 gi|311093806|gb|EFQ52142.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
          Length = 307

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 117/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 39  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGKEKPNATLK-------------- 84

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 85  FSNLPIAIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALIKIKPHIITR 144

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 145 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 203

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 204 PIKRYIM------EGGKNSVTKYRVIKQVA-GASLVELQLLTGRTHQIRVHMQYLGHPLF 256

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y              +  LH   +    P E  R+++    PA M++ W  L
Sbjct: 257 GDHLYGVEDD-------FPRQALHCFLLAFDDPLEHKRIEVQIADPADMLQLWQKL 305


>gi|225552312|ref|ZP_03773252.1| ribosomal large subunit pseudouridine synthase D [Borrelia sp. SV1]
 gi|225371310|gb|EEH00740.1| ribosomal large subunit pseudouridine synthase D [Borrelia sp. SV1]
          Length = 326

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/337 (22%), Positives = 151/337 (44%), Gaps = 32/337 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V+ +   +RLD +   ++       +++       + + K +K          +++
Sbjct: 6   REFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK----------IKL 53

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----- 122
              +   + I+ E     S V+  + S+ +  +++YEDS + V NKP GI    G     
Sbjct: 54  SKPVFKDDEILIEFDEESSQVDCLRPSN-IPIVIIYEDSNVIVLNKPQGILSHPGISHWD 112

Query: 123 ----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + F+ +R
Sbjct: 113 DTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFKDKR 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             K+Y ++V G   +    I +++ +  H    +     +       A++ ++++  F +
Sbjct: 172 TNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLLLNFGE 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+  +++ 
Sbjct: 228 -YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLKKIT---LMLHSYKLEID 282

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
             +    +  +  P   V    +     + NL I  L
Sbjct: 283 VGKNSFKKFISEFPKRFVIFLSNFYKSDELNLIIDNL 319


>gi|309810028|ref|ZP_07703875.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
 gi|308169668|gb|EFO71714.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
          Length = 302

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 117/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 34  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGKEKPNATLK-------------- 79

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 80  FSNLPIAIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALIKIKPHIITR 139

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 140 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 198

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 199 PIKRYIM------EGGKNSVTKYRVIKQVA-GASLVELQLLTGRTHQIRVHMQYLGHPLF 251

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y              +  LH   +    P E  R+++    PA M++ W  L
Sbjct: 252 GDHLYGVEDD-------FPRQALHCFLLAFDDPLEHKRIEVQIADPADMLQLWQKL 300


>gi|116515147|ref|YP_802776.1| RluC [Buchnera aphidicola str. Cc (Cinara cedri)]
 gi|116257001|gb|ABJ90683.1| ribosomal large subunit pseudouridine synthase C [Buchnera
           aphidicola str. Cc (Cinara cedri)]
          Length = 317

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 85/304 (27%), Positives = 149/304 (49%), Gaps = 15/304 (4%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D +    +  +    + + LR G+++++KK+V    +++    +           I 
Sbjct: 20  QRIDNFLFKTFKKLPKSMIYRSLRIGKIKINKKKVHPYYKLKINDNITFF-------SIN 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E K    +++ +    F+K+ +L+ED+ + +FNKP G +V GGSGI+Y +    +  + 
Sbjct: 73  IETKKKKINLSKSIIQLFIKN-ILFEDNDLIIFNKPYGFAVHGGSGISYGVIEIFRK-IR 130

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           S  +   L HR+D+ETSGIL++++ R+  + +  + R ++I K Y +++ G    K + +
Sbjct: 131 SDLKFLELVHRIDKETSGILILSKKRSILKKMHINLREKKIYKEYLAILHGYWSKKNKIV 190

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              LLKK +I       V    K    A ++F+ I  +      +++ P TGRTHQ+RVH
Sbjct: 191 KLPLLKKKNIKQKKKVCV---HKEGKLAQTNFE-IKKYLNNKTLVKIIPITGRTHQIRVH 246

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQN-KLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
               G PIV D++Y    K       +N +L LHA  +   HP       ITAPL     
Sbjct: 247 TAQFGHPIVFDNRYGKIEKKKKKIIKKNSRLLLHAFKVSFLHPRNNENFSITAPLDKKFQ 306

Query: 317 KTWD 320
               
Sbjct: 307 NCLK 310


>gi|170741578|ref|YP_001770233.1| pseudouridine synthase [Methylobacterium sp. 4-46]
 gi|168195852|gb|ACA17799.1| pseudouridine synthase [Methylobacterium sp. 4-46]
          Length = 228

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 112/231 (48%), Gaps = 9/231 (3%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           + + S +LY D+ + V +KPAG+ V  G      +   L +      ++P   HRLD++T
Sbjct: 4   EDIVSRVLYRDALVLVIDKPAGLPVHPGPKGGETLVQHLDALRFGLPRRPEAAHRLDRDT 63

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L + R   A   L + F     +K YW+LV G P  ++  I   L ++S    D   
Sbjct: 64  SGCLALGRHAKALARLGQLFAQGHARKTYWALVDGAPAAEEGEIDLALARRSE---DPRS 120

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              + +   + A++ +++     +   WLE++P TGRTHQLRVH   MG PI GD  Y A
Sbjct: 121 WWMRADPAGDPALTRWRLRGRSPEGGAWLELEPVTGRTHQLRVHCAAMGWPIRGDAVYGA 180

Query: 275 NFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
             +          L LHAR + LP +P    +   AP+P HM     + GF
Sbjct: 181 APRR-----GGPGLQLHARSLSLPLYPRKPPVTAEAPVPPHMRAGLAACGF 226


>gi|256544688|ref|ZP_05472060.1| RluA family pseudouridine synthase [Anaerococcus vaginalis ATCC
           51170]
 gi|256399577|gb|EEU13182.1| RluA family pseudouridine synthase [Anaerococcus vaginalis ATCC
           51170]
          Length = 299

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 65/314 (20%), Positives = 137/314 (43%), Gaps = 33/314 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D++  + +  I    ++  ++  +++++ K++K + ++     + I       + + 
Sbjct: 9   IRIDKYLSDLFEEIPREKVKDFIKDEKIKINNKKIKPSYKLLLEDEIEIS------DKLF 62

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWV 137
           +++KI    +NL          +LYE+    + +K   + V   GS ++  +   L  + 
Sbjct: 63  EKEKIEAEKMNL---------KILYENEDYAIIDKDENVIVHPAGSIVSGTLVNGLLDYF 113

Query: 138 DSKG-------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                       +P + HRLD++T+G++V+A+  ++ ++L   F  R+I K Y ++  GI
Sbjct: 114 GYDNLSHIGGDDRPGIVHRLDKDTTGLMVIAKNNSSYKYLKNLFETRKIDKEYLAICNGI 173

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            + K   I  ++ +  +                  AIS ++VI      +  ++++  TG
Sbjct: 174 FQKKSGTIHTFMDRDPNNRRKMAV-----TNSGRDAISKYEVI-SENNGYSLVKIKILTG 227

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQ+RVH  ++  P++GD  Y  N K  F     +   LH   +      G   +  A 
Sbjct: 228 RTHQIRVHMTYINHPLLGDPVYG-NVKHKFN---LDHQLLHCHKLGFTDKNGIYKEFCAD 283

Query: 311 LPAHMVKTWDSLGF 324
                 K    LG 
Sbjct: 284 CHEDFKKYQKILGL 297


>gi|167720581|ref|ZP_02403817.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei DM98]
          Length = 247

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 80/234 (34%), Positives = 122/234 (52%), Gaps = 14/234 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +L+ED  I V NKPAG++V GGSG+A+ +   ++       +   L HRLD+ETSGI
Sbjct: 12  EFEILFEDDAIIVLNKPAGVAVHGGSGVAFGVIEQMRHAR-PHAKFLELAHRLDRETSGI 70

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK---NKKECIANWLLKKSHIGGDYVH 214
           L++A+ R+A   L E  R  R+ K Y++ V G       ++  +   L K +   G+   
Sbjct: 71  LMLAKKRSALVGLHEQIRENRMDKRYFACVHGDWAADWGRRRVVKAPLFKYATPDGERRV 130

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC- 273
            V+++      + + F ++D +   +  +E +  TGRTHQ+RVH  H+G PIVGD KY  
Sbjct: 131 RVQED---GLPSHTVFNLVDRWPD-YALVEAELKTGRTHQIRVHLAHLGLPIVGDAKYGD 186

Query: 274 ----ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                        P   +++LHA  + L HP  G  LQ  APLPA   +  D L
Sbjct: 187 FALNKALARANAVPSIKRMFLHAHRLRLAHPLTGEPLQFDAPLPAECRQFIDQL 240


>gi|291520763|emb|CBK79056.1| pseudouridine synthase, RluA family [Coprococcus catus GD/7]
          Length = 310

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 58/319 (18%), Positives = 126/319 (39%), Gaps = 36/319 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +E + + + ++ +   +   ++   L+ +  R   + ++ +RV     + +G  +    
Sbjct: 7   TIEPEADGLSVNAY-ARNIAGLSRAFLRSVKFRENGILINGQRVTTRGVLHAGDSLVFNM 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYH 128
             +    ++  +                   +++E+  I + NKPA + +    G  +  
Sbjct: 66  PNDRTQKVVPAE---------------GPVSIVFENEDIVLVNKPARLVIHPCHGHYSDT 110

Query: 129 IDGFLKSWVDSKGQKPRLT--HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +  +L  +     ++P L    RLD++TSG++++A+ + AAQ L        + ++Y +L
Sbjct: 111 LLSYLAWYYRLLPEQPLLCPIGRLDKDTSGLILIAKNKYAAQQLERQRANHTLSRVYLAL 170

Query: 187 VWGIPKN--KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQKFC 241
             G   N  K   I   + K       Y     Q       + + ++V+         F 
Sbjct: 171 AEGHWTNQSKSGLIDRPIEKVPECFNRY-----QVADTGRPSRTEYEVLSEFTYEETPFS 225

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + ++  TGRTHQ+RVH   +  P++GD  Y       F     ++  LH+  +    P 
Sbjct: 226 LVRLKLQTGRTHQIRVHMASLSHPLLGDSIYGHEGFLGF-----DRAALHSFEITCQLPG 280

Query: 302 GGRL-QITAPLPAHMVKTW 319
              L   ++ +P    K  
Sbjct: 281 HQDLAVFSSEMPEDFQKMI 299


>gi|325913175|ref|ZP_08175545.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
 gi|325477596|gb|EGC80738.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
          Length = 309

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 117/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 41  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGKEKPNATLK-------------- 86

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 87  FSNLPIAIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITR 146

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 147 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 205

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 206 PIKRYIM------EGGKNSVTKYRVIKQVA-GASLVELQLLTGRTHQIRVHMQYLGHPLF 258

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y              +  LH   +    P E  R+++    PA M++ W  L
Sbjct: 259 GDHLYGVEDD-------FPRQALHCFLLAFDDPLEHKRIEVQIADPADMLQLWQKL 307


>gi|159900009|ref|YP_001546256.1| pseudouridine synthase [Herpetosiphon aurantiacus ATCC 23779]
 gi|159893048|gb|ABX06128.1| pseudouridine synthase [Herpetosiphon aurantiacus ATCC 23779]
          Length = 560

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 74/224 (33%), Positives = 110/224 (49%), Gaps = 12/224 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D +I V NKP G++     G     D         + +   +  RLD++TSG+++ 
Sbjct: 5   ILYRDEQILVINKPTGVATHAPQGDLALTDVERALRAQLQLEYLAIHQRLDRDTSGVMLF 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A   AA  +L  +F    I+K Y +LV+G+P   +  I   L   +  G   + V   ++
Sbjct: 65  ALDPAANANLATAFAEHTIEKTYQALVYGVPIQTQGVIDAAL---APAGDGMIQVASAHD 121

Query: 221 KGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           + A  AI+H++V+     Q+F  LE+QP TGRTHQLRVH   +G PIVGD  Y       
Sbjct: 122 RRAQSAITHYRVLVSSPDQRFSLLELQPKTGRTHQLRVHCECLGHPIVGDPLY------- 174

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +    +L LHA  +   HP   + L I AP PA   +    L
Sbjct: 175 DVARAAPRLMLHASELRFTHPLTQQPLHIQAPTPALFTRVAQGL 218


>gi|154173855|ref|YP_001407891.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           curvus 525.92]
 gi|112803415|gb|EAU00759.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           curvus 525.92]
          Length = 323

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 76/340 (22%), Positives = 139/340 (40%), Gaps = 54/340 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD    +    I+      ++++  V V+ K   K + ++     + +          +
Sbjct: 11  RLDVALASELK-ISRNQATNLIKNALVSVNSKPALKPSMQLNQNDEICVKF-------AL 62

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            ++K  D   N           ++YED  I V NKP  I V     +    +  L  W++
Sbjct: 63  PKEKTNDYEANFEIP-------VIYEDEDILVLNKPPQIVVHQAPSV---KEATLVEWLN 112

Query: 139 SKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            KG          +  + HRLD+ TSG +VVA+  AA   L+     + + +IY +L   
Sbjct: 113 QKGFMLSNLNGDLRAGIVHRLDKGTSGAIVVAKNNAAHAALSAQLNDKSMGRIYLALTD- 171

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               K+ECI +  + +S      + +V        +A S F  +     +   +  +  T
Sbjct: 172 -LPLKQECIIDKPIGRSPSNRLKMGIVT----NGRHAKSAFLNL-VQTDEVNLIAAKLFT 225

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+R H   +   I+GD+ Y    + +       ++ LHA  +   HP  G  ++  
Sbjct: 226 GRTHQIRAHLASINRHILGDNLYGFKSENDK----IKRVMLHAYMLYFFHPRSGEKVEFI 281

Query: 309 APLPAHMVKTWDSLGFKYDRNLYI---KRLYSQDECKQNI 345
           A       +TWD     +++ +Y    K L+ +  C +++
Sbjct: 282 A-------QTWD----DFNQIVYKKISKELFDEKICPKSL 310


>gi|325911465|ref|ZP_08173877.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
 gi|325476815|gb|EGC79969.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
          Length = 309

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 117/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 41  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGKEKPNATLK-------------- 86

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 87  FSNLPIAIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALIKIKPHIITR 146

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 147 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 205

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 206 PIKRYIM------EGGKNSVTKYRVIKQVA-GASLVELQLLTGRTHQIRVHMQYLGHPLF 258

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y              +  LH   +    P E  R+++    PA M++ W  L
Sbjct: 259 GDHLYGVEDD-------FPRQALHCFLLAFDDPLEHKRIEVQIADPADMLQLWQKL 307


>gi|195941758|ref|ZP_03087140.1| hypothetical protein Bbur8_02614 [Borrelia burgdorferi 80a]
          Length = 336

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 73/342 (21%), Positives = 153/342 (44%), Gaps = 32/342 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +   V+ +   +RLD +   ++       +++       + + K +K        
Sbjct: 11  MIRVKREFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK-------- 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++   +   + I+ E     S ++  + S+ +   ++YEDS + V NKP GI    G
Sbjct: 61  --IKLSKPVFKDDEILIEFDEESSQIDCLRPSN-IPIAIIYEDSNVIVLNKPQGILSHPG 117

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                    + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + 
Sbjct: 118 ISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQ 176

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ +R  K+Y ++V G   +    I +++ +  H    +     +       A++ ++++
Sbjct: 177 FKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLL 232

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F + +  L ++P TGRTHQLRVH  ++  PI+GD  Y        +S  +  L LH+ 
Sbjct: 233 LNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYGRVD----SSLKKITLMLHSY 287

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            +++   +    +  +  P   +    +     + NL I  L
Sbjct: 288 KLEIDVGKNSFKKFISEFPKRFIIFLSNFYKSDELNLIIDNL 329


>gi|145636146|ref|ZP_01791816.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittHH]
 gi|145270668|gb|EDK10601.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittHH]
          Length = 239

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 108/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWHQLMNQFGWE 237


>gi|284048156|ref|YP_003398495.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
 gi|283952377|gb|ADB47180.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
          Length = 294

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 69/294 (23%), Positives = 125/294 (42%), Gaps = 36/294 (12%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
           H++    +KI  +G + V+   V   ++R+++G  +       A    +           
Sbjct: 25  HLSEKLWRKIKWNGTITVNGSPVSSPSHRLEAGDRLVFRWEEKAAVIPVH---------- 74

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKP--RL 146
                  L   LLYED  + V +KPAG+ +    SG    +   +  +    GQ      
Sbjct: 75  -------LPLSLLYEDEDLLVVDKPAGMLIHPTWSGARDTLVQAVGGYFRRTGQHCGIHP 127

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            +RLD++T+G+L+VA++  A   LT      +I + Y ++  G     +  I + + + +
Sbjct: 128 LYRLDRDTTGVLMVAKSAFAKHALTRDHS--QIYREYLAVCEGRWGIPQGRIEHPIGRVA 185

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                +             A++ +++++   Q++  L++   TGRTHQ+RVH  H G P+
Sbjct: 186 EGVDRWTVR-----PDGRPAVTEYRILE-ENQEWTVLKIHLLTGRTHQIRVHFAHEGHPL 239

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           VGD  Y              +  LHA  +   HP  G  + +TAP+P  M    
Sbjct: 240 VGDPLYGTK------DGRIARQALHAWTVRFRHPRTGEEILLTAPMPGDMEGLL 287


>gi|309807023|ref|ZP_07701005.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
 gi|308166643|gb|EFO68840.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
          Length = 302

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 117/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 34  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGKEKPNATLK-------------- 79

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 80  FSNLPIAIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITR 139

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 140 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 198

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 199 PIKRYIM------EGGKDSVTKYRVIKQVA-GASLVELQLFTGRTHQIRVHMQYLGHPLF 251

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y              +  LH   +    P E  R+++    PA M++ W  L
Sbjct: 252 GDHLYGVEDD-------FPRQALHCFLLAFDDPLEHKRIEVQIADPADMLQLWQKL 300


>gi|216264271|ref|ZP_03436263.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 156a]
 gi|215980744|gb|EEC21551.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 156a]
          Length = 326

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/342 (21%), Positives = 153/342 (44%), Gaps = 32/342 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +   V+ +   +RLD +   ++       +++       + + K +K        
Sbjct: 1   MIRVKREFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK-------- 50

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++   +   + I+ E     S ++  + S+ +   ++YEDS + V NKP GI    G
Sbjct: 51  --IKLSKPVFKDDEILIEFDEESSQIDCLRPSN-IPIAIIYEDSNVIVLNKPQGILSHPG 107

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                    + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + 
Sbjct: 108 ISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ +RI K+Y ++V G   +    I +++ +  H    +     +       A++ ++++
Sbjct: 167 FKDKRINKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLL 222

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F + +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+ 
Sbjct: 223 LNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLKKIT---LMLHSY 277

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            +++   +    +  +  P   V    +     + NL I  L
Sbjct: 278 KLEIDVGKNSFRKFISEFPKRFVIFLSNFYKSDELNLIIDNL 319


>gi|307289628|ref|ZP_07569572.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|306499442|gb|EFM68815.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|315164544|gb|EFU08561.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1302]
          Length = 283

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +     +LYED  + + NKP GI   
Sbjct: 51  AGDYVTLTF---------EETDYVRPTIHL---GEATHVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L H
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLH 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|226322067|ref|ZP_03797592.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi Bol26]
 gi|3915840|sp|P70870|RLUD_BORBU RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|226232657|gb|EEH31411.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi Bol26]
          Length = 326

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 74/342 (21%), Positives = 152/342 (44%), Gaps = 32/342 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +   V+ +   +RLD +   ++       +++       + + K +K        
Sbjct: 1   MIRVKREFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK-------- 50

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++   +   + I+ E     S ++  + S+ +   ++YEDS + V NKP GI    G
Sbjct: 51  --IKLSKPVFKDDEILIEFDEESSQIDCLRPSN-IPIAIIYEDSNVIVLNKPQGILSHPG 107

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                    + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + 
Sbjct: 108 ISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ +R  K+Y ++V G   +    I +++ +  H    +     +       A++ ++++
Sbjct: 167 FKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLL 222

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F + +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+ 
Sbjct: 223 LNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLKKIT---LMLHSY 277

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            +++   +    +  +  P   V    +     + NL I  L
Sbjct: 278 KLEIDVGKNSFKKFISEFPKRFVIFLSNFYKSDELNLIIDNL 319


>gi|269123695|ref|YP_003306272.1| pseudouridine synthase [Streptobacillus moniliformis DSM 12112]
 gi|268315021|gb|ACZ01395.1| pseudouridine synthase [Streptobacillus moniliformis DSM 12112]
          Length = 280

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 72/291 (24%), Positives = 133/291 (45%), Gaps = 24/291 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   +V+ D  N+RLD++ + +    +   +  ++R G V+V+ K+ K N R+     + 
Sbjct: 2   INKYLVDKDHVNIRLDKFMRKYSKEESLSIIFSLIRKGFVKVNGKKSKENYRLLLNDEIF 61

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            P     +     E++I+D         D  K+++++ED  +++ NKP  + +  G    
Sbjct: 62  FPDAAKIVMDKKIEKEIIDI--------DLFKNMIVFEDEDVFIINKPNNMPMHKGDKHK 113

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           + +    K++ +         +RLD ET G+++  +     + + E  R ++I K Y + 
Sbjct: 114 FGLSETAKAYYN--NPNVNFANRLDLETEGLVIGCKNLQILRKVNEEIRNKKIIKRYIAK 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V        E    +  KK  I  D V V     K    A ++FKVI+        L+++
Sbjct: 172 VEQKKLQLDE--EFFSDKKIKIFEDRVRV----SKDGLEAKTYFKVIE-VKDFKVLLDIE 224

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             TGR HQ+RVH   +G PI+GD KY    K       ++++YL   Y+  
Sbjct: 225 LITGRKHQIRVHLSDIGHPIIGDSKYGNYQK-------KDRMYLKCYYIKF 268


>gi|23006096|ref|ZP_00048580.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 279

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 68/262 (25%), Positives = 121/262 (46%), Gaps = 38/262 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RLDR     +  ++   LQ ++R G VR D   ++    ++ +G  + +          
Sbjct: 10  ERLDRALARAFEDLSRARLQALVRDGLVRCDGAVLRDPARKVGAGCRLDLS--------- 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                 + + +      + L   +++ED  + V +KPAG+ V   +G   H DG L + +
Sbjct: 61  ------VPAPLPAEPMGEALPLTVVHEDEDLIVIDKPAGLVVHPAAG---HEDGTLVNRL 111

Query: 138 DSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR----RIQKIY 183
            +            ++P + HRLD++TSG+LVVA+   A Q L+  F        +++ Y
Sbjct: 112 IAHCGASLSGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQFADHGRNGALERAY 171

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--IDCFAQKFC 241
            +LVW +P+ +   I   L +  H   + + VV++ E     AI+H++V  +        
Sbjct: 172 LALVWNVPEPRHGTIRANLARSRH-NREKIAVVREGE--GREAITHYRVEALPGADGVTA 228

Query: 242 WLEMQPHTGRTHQLRVHALHMG 263
            L  +  TGRTHQ+RVH  + G
Sbjct: 229 LLRCRLETGRTHQIRVHLRNRG 250


>gi|227512235|ref|ZP_03942284.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus buchneri ATCC
           11577]
 gi|227524034|ref|ZP_03954083.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus hilgardii
           ATCC 8290]
 gi|227084629|gb|EEI19941.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus buchneri ATCC
           11577]
 gi|227088773|gb|EEI24085.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus hilgardii
           ATCC 8290]
          Length = 297

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 71/297 (23%), Positives = 117/297 (39%), Gaps = 32/297 (10%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            I    L+KI    GQ  V+ +    N ++ +  VV +               +     N
Sbjct: 24  GITRTLLKKIKYHGGQTLVNGEPSLVNRKLITNDVVTV--------------VLPPEPEN 69

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSK---GQKPR 145
               +  L   +++ED    V NK +GI+       A   +   +K +        QK  
Sbjct: 70  DNVPASDLPIQIVFEDEHFLVVNKLSGIASVPAHNRANDSLVNRVKGYYQRNHYANQKIH 129

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           +  RLD++TSG+++ A+   A   L +  +  +I+K Y ++V G        I   + + 
Sbjct: 130 IVTRLDKDTSGLVIFAKHHFAHSVLDKQLKDHQIKKTYLAIVEGTFSTTHFEIYLPIKR- 188

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                D   V +Q       +I+         ++   L++Q HTGRTHQ+RVH   +G P
Sbjct: 189 ----ADGSLVKRQVGFPGKMSITEAWTKQRL-RQHTLLKLQIHTGRTHQIRVHMTAIGHP 243

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           +VGD  Y    K         +  LH   +   +P  G  +   APLP  M     S
Sbjct: 244 LVGDWLYNPEDKS------FPRQALHCAGLRFFNPFAGHFVDCRAPLPDDMKTYLAS 294


>gi|300871600|ref|YP_003786473.1| ribosomal large subunit pseudouridine synthase C [Brachyspira
           pilosicoli 95/1000]
 gi|300689301|gb|ADK31972.1| ribosomal large subunit pseudouridine synthase C [Brachyspira
           pilosicoli 95/1000]
          Length = 330

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 65/328 (19%), Positives = 133/328 (40%), Gaps = 36/328 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +E D E+MRLD++  N + + +    Q ++  G V V+ +++K+   I  G  + 
Sbjct: 21  IRKCRIEEDIESMRLDKYMGNRFSYYSRNKWQDLIGEGLVLVNGEKIKYTRTISKGDEIS 80

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                     + K+ +                  ++Y+D  + + NKPA + V       
Sbjct: 81  YYFKDMKEPEVNKDIE------------------IIYDDGDLIIVNKPANLPVIPSG--K 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES---FRMRRIQKIY 183
           Y+ +       +  G    + +R+D+ETSG ++++R    A              I+K Y
Sbjct: 121 YYYNTLHTIMQERLGCHLNMINRIDRETSGCVILSRGSLVASKFCAMLANKNNNNIKKTY 180

Query: 184 WSLVW-GIPKNKKECIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            ++V           +  ++ +    +   Y  + K+N + + Y+ + FK +        
Sbjct: 181 IAIVENAKDIEDSFTVEGYMQEVGDKLYRRYQILHKENVEDSKYSKTKFKTVKKIGDYAI 240

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---------KLYLHA 292
             +++ +TGR HQ+RVH       +VGD  Y       F S I+          +  LH+
Sbjct: 241 L-KIRLYTGRMHQIRVHLHSKNLYMVGDKIYGKYGPKVFNSFIEKSIIPEGFFYRQALHS 299

Query: 293 RYMDLPHPEG-GRLQITAPLPAHMVKTW 319
             ++  HP    R+++ A +P  +    
Sbjct: 300 YMLEFNHPITNERIKVKAKIPKDLKDFI 327


>gi|224534885|ref|ZP_03675454.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           spielmanii A14S]
 gi|224513825|gb|EEF84150.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           spielmanii A14S]
          Length = 328

 Score =  187 bits (474), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 79/339 (23%), Positives = 150/339 (44%), Gaps = 34/339 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V+ +   +RLD +  N+        +++       + + K  K          +++
Sbjct: 6   KEFTVKENA--LRLDLYLSNNLEGFTRSQIKRRNVEAFKKNNGKFFK----------IKL 53

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----- 122
              +   + ++ E     S ++  + S+ +   ++YED  I V NKP GI    G     
Sbjct: 54  SKPVFKDDEMLIEFDEESSQIDCLRPSN-IPIAIIYEDPNIIVLNKPQGILSHPGISHWD 112

Query: 123 ----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               + + YHI G LK   + +  +P + HRLD++TSG+L+ A+  +  + L + F+ +R
Sbjct: 113 DTVVNFLLYHIKG-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFKDKR 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K+Y ++V G   +    I +++  +         V K        A++ +K++  F  
Sbjct: 172 INKVYIAIVKGNFNSFIGSIESFI-DRDKYNRKKFSVSKDK---GKKALTEYKLLLNFG- 226

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  L ++P TGRTHQLRVH  ++  PI+GD  Y        +S  +  L LH+  +++ 
Sbjct: 227 GYSLLALKPKTGRTHQLRVHMKYLNFPILGDDVYGRVD----SSFKKITLMLHSYKLEID 282

Query: 299 HPEGGR--LQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
              G +   +  +  P   V    +     + NL I  L
Sbjct: 283 VGNGSKSFRKFISEFPKRFVIFLSNFYKSDELNLIIDNL 321


>gi|92118358|ref|YP_578087.1| pseudouridine synthase, RluD [Nitrobacter hamburgensis X14]
 gi|91801252|gb|ABE63627.1| ribosomal large subunit pseudouridine synthase D [Nitrobacter
           hamburgensis X14]
          Length = 264

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 64/260 (24%), Positives = 111/260 (42%), Gaps = 37/260 (14%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-- 141
           +  +++     + +   ++YED  + V NKP G+ V   +G   H  G L + + +    
Sbjct: 1   MPPAISAEPKGEAIALDIVYEDDDLIVVNKPKGLVVHPAAG---HEAGTLVNALIAHCGG 57

Query: 142 --------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR----RIQKIYWSLVWG 189
                    +P + HRLD++T+G++V A+  AA + L+  F        +++ Y +  WG
Sbjct: 58  SLSGIGGVCRPGIVHRLDKDTTGLMVAAKNDAAHKSLSAQFADHGRTGALRRGYLAFAWG 117

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-----FCWLE 244
           +P      +   +  +     + + V          AI+H++V   F  +        L 
Sbjct: 118 LPNRPHGTVDAPI-DRHPYAREKMAVRA----SGREAITHWEVRKAFNGRDGKPVAALLA 172

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---------GNFTSPIQNKLYLHARYM 295
            Q  TGRTHQ+RVH  H G P++GD  Y  +FK                  +  LHA  +
Sbjct: 173 CQLETGRTHQIRVHLAHAGHPLMGDGVYGPHFKTKANQLGPSARTALDALGRQALHAYLL 232

Query: 296 DLPHPEGGRL-QITAPLPAH 314
            + HP  G + +  A LP  
Sbjct: 233 AIEHPRTGEILRWEAALPED 252


>gi|312149435|gb|ADQ29506.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi N40]
          Length = 326

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 74/342 (21%), Positives = 153/342 (44%), Gaps = 32/342 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +   V+ +   +RLD +   ++       +++       + + K +K        
Sbjct: 1   MIRVKREFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK-------- 50

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++   +   + I+ E     S ++  + S+ +   ++YEDS + V NKP GI    G
Sbjct: 51  --IKLSKPVFKDDEILIEFDEESSQIDCLRPSN-IPIAIIYEDSNVIVLNKPQGILSHPG 107

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                    + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + 
Sbjct: 108 ISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ +RI K+Y ++V G   +    I +++ +  H    +     +       A++ ++++
Sbjct: 167 FKDKRINKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLL 222

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F + +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+ 
Sbjct: 223 LNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLKKIT---LMLHSY 277

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            +++   +    +  +  P   +    +     + NL I  L
Sbjct: 278 KLEIDVGKNSFKKFISEFPKRFIIFLSNFYKSDELNLIIDNL 319


>gi|229195588|ref|ZP_04322354.1| Pseudouridine synthase [Bacillus cereus m1293]
 gi|228587837|gb|EEK45889.1| Pseudouridine synthase [Bacillus cereus m1293]
          Length = 307

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 129/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EMTVPAKWNGISIESLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E               + +  ++YED  + + NKP  +           
Sbjct: 70  MFMEEEYDVEPE---------------YGELHVVYEDDHVLIVNKPEKMDTHPSEKGGMG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEKYFRKQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGGTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNDTMKEF 302


>gi|315170755|gb|EFU14772.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1342]
          Length = 274

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 117/268 (43%), Gaps = 25/268 (9%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
             V+++ +   F+  +Q+G  V +           +E   +  +++L    +     +LY
Sbjct: 25  KNVKINGETAAFHFPVQAGDCVTLTF---------EETDYVRPTIHL---GEATHVKVLY 72

Query: 104 EDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           ED  + + NKP GI            +   + +++  K Q P + HRLD+ETSG +V A+
Sbjct: 73  EDEHLMIVNKPYGIKTHPNQPQETNTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAK 132

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      ++I + Y ++V G    K++ I   + +  H         + + + 
Sbjct: 133 NPFVLPILGRLLETKQIYRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQK 188

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
            + AI+H +V+   +     +     TGRTHQ+RVH    G PI+GD  Y    +     
Sbjct: 189 GDSAITHVQVVQALSNNQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA--- 245

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITA 309
               +L LHA  + L HP   + + +TA
Sbjct: 246 ----RLMLHASQLHLLHPFTKKQIVVTA 269


>gi|229549211|ref|ZP_04437936.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis ATCC
           29200]
 gi|255971927|ref|ZP_05422513.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T1]
 gi|256957901|ref|ZP_05562072.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis DS5]
 gi|257416850|ref|ZP_05593844.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis AR01/DG]
 gi|257420067|ref|ZP_05597061.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T11]
 gi|300861004|ref|ZP_07107091.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|229305448|gb|EEN71444.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis ATCC
           29200]
 gi|255962945|gb|EET95421.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T1]
 gi|256948397|gb|EEU65029.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis DS5]
 gi|257158678|gb|EEU88638.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis ARO1/DG]
 gi|257161895|gb|EEU91855.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T11]
 gi|300850043|gb|EFK77793.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|315035177|gb|EFT47109.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0027]
 gi|315148637|gb|EFT92653.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4244]
 gi|315159322|gb|EFU03339.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0312]
 gi|315168785|gb|EFU12802.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1341]
 gi|315573843|gb|EFU86034.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309B]
 gi|315580414|gb|EFU92605.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309A]
 gi|323481597|gb|ADX81036.1| pseudouridine synthase, RluA family protein [Enterococcus faecalis
           62]
 gi|327535892|gb|AEA94726.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           OG1RF]
          Length = 297

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 75/309 (24%), Positives = 135/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L K+  + G+++V+         +Q+G VV++               
Sbjct: 18  FLKEQ--GVSKGLLAKVKFQGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLS 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   +   +A + + +    AQ    + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAA-VRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGKMDQ-----GIERQALHCMELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKSVDDTL 297


>gi|227512368|ref|ZP_03942417.1| pseudouridylate synthase RluD [Lactobacillus buchneri ATCC 11577]
 gi|227084341|gb|EEI19653.1| pseudouridylate synthase RluD [Lactobacillus buchneri ATCC 11577]
          Length = 302

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 78/312 (25%), Positives = 134/312 (42%), Gaps = 25/312 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           ++    V    +   L R+  +HY  +    +  +    +V V+ + +  N  +     +
Sbjct: 5   WLFKTTVPQTMDGKPL-RYLLHHYWLLPKHLVFSLRSDERVLVNNRYLPVNFPVHFHDHI 63

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SG 124
            +  + +   H    Q + DS+  L          +LYED+ + V NK  G        G
Sbjct: 64  SLTFIPSDFQHPFP-QVLPDSAATL---------KILYEDANLIVINKRRGNKTHPNQPG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                   L +++ +K   P + HRLDQETSG ++ A+  A    L      + I++ Y 
Sbjct: 114 EVGATINHLAAYLKTKEALPYMVHRLDQETSGAILFAKNPAVVPTLVAKIATKNIKRTYL 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           + V G   + +  I   +    +     +       K    +I+H+ V+      +  L 
Sbjct: 174 AWVVGTDIDSQGIIDFPIGLDPNDKRKRMIDGNHPAK----SITHYTVLQ-KEDGYSLLA 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH   +G P+VGD  Y  + K  F       L LH+  +++P P   +
Sbjct: 229 VQLETGRTHQIRVHLTAIGHPLVGDPLYNPDDKHPF-------LLLHSWKLNIPLPFSEQ 281

Query: 305 -LQITAPLPAHM 315
            ++ITAPLPAH 
Sbjct: 282 VIEITAPLPAHF 293


>gi|154331307|ref|XP_001561472.1| pseudouridylate synthase-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
 gi|134058789|emb|CAM36459.1| pseudouridylate synthase-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 413

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 88/358 (24%), Positives = 158/358 (44%), Gaps = 30/358 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV---RVDKKR--VKFNNRI 59
             +QY VV  D    R+D +   H+P  ++  ++++++ G +   R + KR   +  +R+
Sbjct: 53  NELQYHVVTQDWFGQRVDDFITQHHPEWDYETVKRLVQQGHIYRYRRNGKRRYTRLTDRL 112

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLT-------------KHSDFLKSILLYEDS 106
           +  ++V +P        +     +   S++ +             K  +  + ++L+++ 
Sbjct: 113 EFDELVVVPTASFWGRQLAPPSGVELQSLSTSQQRERRQKFHLSAKAREMAQEMVLFKNE 172

Query: 107 KIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
            + V NKP+G+ +      +A +I   L +W  +  Q P + H LD ETSG +++AR+  
Sbjct: 173 HVVVINKPSGVPIMPTHDPLAMNITDLLPAWRYTNTQMPIVCHNLDAETSGCVLLARSAN 232

Query: 166 AAQHLTESFRMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           A + L   F  R +   +YW    G P      I      +   GGD +         + 
Sbjct: 233 AHRMLGRMFVKRVVPNSVYWGFAVGKPPVNFGRIRMHFEIQKGQGGDVIVARPAPTANSK 292

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK-----G 278
             I+ F V     +   ++   P T R HQ R+ A H +  P++GD KY           
Sbjct: 293 VGIAEFVVNASALEFGSFISFYPLTTRRHQERIMAAHALRAPLLGDAKYGGESAFPHSLS 352

Query: 279 NFTSPIQN--KLYLHARYMDLPHPE--GGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            F  P +    L+LH R + LP+    G  + +TAPLP HM KT+  LG+  D +  +
Sbjct: 353 LFWDPARKDVPLHLHHRKIQLPYKNGAGAFVCVTAPLPQHMEKTFKRLGWPVDADDPL 410


>gi|172058049|ref|YP_001814509.1| RluA family pseudouridine synthase [Exiguobacterium sibiricum
           255-15]
 gi|171990570|gb|ACB61492.1| pseudouridine synthase, RluA family [Exiguobacterium sibiricum
           255-15]
          Length = 293

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 66/311 (21%), Positives = 128/311 (41%), Gaps = 36/311 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V + E+   +  +      HI+   L  I   G +  +++ V  N  + +G  + +    
Sbjct: 9   VTSIEDGWSVGHFCTTRL-HISRKMLVSIKHHGDILRNEQHVNVNEPVHAGDRIHV---- 63

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHID 130
                     +  +       H+   +  +L+ED  + + NKP G++           + 
Sbjct: 64  ----------RFPEEQPAQDMHATSGELDILFEDDWLLIVNKPPGMASIPSRLHPERSLS 113

Query: 131 GFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            F+  +           + +RLD++TSG++V A+   A   L++  +   + + Y +L+ 
Sbjct: 114 NFVLGYYRQHQIPYAIHIVNRLDRDTSGLVVFAKHSLAHHQLSKMQQNGLLDRRYVALIE 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF---KVIDCFAQKFCWLEM 245
           G    +   I   + +  H   + +       +    AI+H    + I  F+++   L +
Sbjct: 174 GTIPAQ--TIDLPIGQTDHSFMERMVR-----EDGQQAITHILTSEPITAFSRELSRLTI 226

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +  TGRTHQ+RVH   +G P+VGD  Y         +P+  +  LH+     PHP  G  
Sbjct: 227 KLETGRTHQIRVHLAALGHPLVGDTMYKG-------TPLIARQALHSASATFPHPGTGEV 279

Query: 305 LQITAPLPAHM 315
           +   APLP  +
Sbjct: 280 MTFVAPLPDDL 290


>gi|322388362|ref|ZP_08061965.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           infantis ATCC 700779]
 gi|321140675|gb|EFX36177.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           infantis ATCC 700779]
          Length = 291

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 72/317 (22%), Positives = 128/317 (40%), Gaps = 31/317 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
              + +    M +  + +     I    ++  LR    + ++++ V ++  +++G   ++
Sbjct: 4   TFTIPDSLPEMTVKHFLEEQLL-IPR-KIRHFLRIKKHILINQEEVHWHQTVKTGDECQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                        +KIL  +  L +         +Y+D  + + NKP G+   G      
Sbjct: 62  IFDEEDY----PTKKILWGNPKLVEE--------VYQDQHLIIVNKPEGMKTHGNQPDEI 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   GQ   + HRLD ETSG+++ A+       L      + I + YW+LV
Sbjct: 110 ALLNHVSAYV---GQTCYVVHRLDMETSGLVLFAKNPFILPILNRLLEKKEISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    K     + + +  H     +     ++K   YA +H   +  F  K   +  + 
Sbjct: 167 DGRLGAKDLIYRDKIGRNRHDRRKRI----VDQKNGQYAETHVTRLKQFQNKTSLVRCRL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G PI+GD  Y  + K         +L LHA  +   HP    +L 
Sbjct: 223 KTGRTHQIRVHLSHHGHPILGDPLYNPHSKN-------KRLMLHAFKLSFIHPLTLNKLS 275

Query: 307 ITAPLPAHMVKTWDSLG 323
            TA L     +     G
Sbjct: 276 FTA-LSDTFERELKQNG 291


>gi|312865090|ref|ZP_07725318.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
 gi|311099201|gb|EFQ57417.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
          Length = 303

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 65/302 (21%), Positives = 124/302 (41%), Gaps = 33/302 (10%)

Query: 24  WFKNHYPHINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   I+   L K+  + G + V+   V     +  G  V I              +
Sbjct: 16  FLKGH--DISKGLLAKVKYQGGHIWVNGIEVNAIYLLAPGDRVSI--------------E 59

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS--- 139
           I     + +         ++ ED    V NKPAG            +  F+K++ +    
Sbjct: 60  IPAEVGSPSLLPIQHPLDIVAEDEHFLVINKPAGYPSIPSILHDESMANFVKAYYEEQTY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KKECI 198
           + Q+  +  RLD++TSG+++ A+   A   + ++ + + I+K Y++LV G         I
Sbjct: 120 ENQQIHIVTRLDKDTSGLMLFAKHGYAHSRMDKALQAKTIEKRYYALVSGHKDLLDAGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +++        + ++      YA + ++V+  F      ++++ HTGRTHQ+RVH
Sbjct: 180 IAPIAREAE-----SIITRRVHPSGKYAHTSYRVLKRFG-PVKLVDIRLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAPLPAHMVK 317
             H+G P++GD  Y  +           +  LH   +    P  G+ ++  APL      
Sbjct: 234 FSHIGQPLLGDDLYGGSM-----DFGIKRQALHCHSLKFRDPFTGQERVHEAPLTDDFEN 288

Query: 318 TW 319
             
Sbjct: 289 VI 290


>gi|197119918|ref|YP_002140345.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
 gi|197089278|gb|ACH40549.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
          Length = 297

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 125/311 (40%), Gaps = 36/311 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           V+ +    RLD   K  +P  +   +++I+  G   + +  V+  +R ++ G+ + +  +
Sbjct: 7   VDAELAGTRLDDAAKTLFPQYSKGEIRRIIDWGGCYLSQTLVRVASRTVKEGEEIALGIM 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                                    + K  LLYED       K AG + Q          
Sbjct: 67  ----------------EAERCIELAYKKEELLYEDKDFLAVYKAAGFNSQRTPYQLKGTV 110

Query: 131 GF-LKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            + ++ ++ S G +   R+ HRLD+ TSG++   + + AA  ++   +  ++QK YW+LV
Sbjct: 111 EYAVECYMKSIGLRDPSRVVHRLDRGTSGVMFFPKHKQAATLISNLLKDGKVQKTYWALV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G P  +   +   L K S                   A + F+V+         +E +P
Sbjct: 171 AGSPDQQSWKVDAPLGKVSK-------FKYGVALNGKPARTLFRVVG-EGAGVTAVEAKP 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH  H G PI+GD  Y              ++ LH R M      G  ++ 
Sbjct: 223 LTGRTHQIRVHLAHSGFPIIGDETYGGIPAA--------RMMLHCRGMRFTGARGKVIEA 274

Query: 308 TAPLPAHMVKT 318
            AP+ A     
Sbjct: 275 FAPIDADFRAA 285


>gi|322412796|gb|EFY03704.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus dysgalactiae subsp. dysgalactiae ATCC
           27957]
          Length = 303

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 80/299 (26%), Positives = 123/299 (41%), Gaps = 37/299 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVR 66
           Q + V+   E    D+        I    ++  LR    V V+   + + + + SG  V 
Sbjct: 20  QTLTVKELLE----DKLL------IPR-KIRHFLRTKKNVLVNGSAITWQSAVNSGDQVE 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +            E+   D  + + + +   K   LYED  + + NKP G+      G  
Sbjct: 69  LFFD---------EEDYPDKPIMMGQAN---KVDCLYEDDHLIIVNKPEGMKTH---GNE 113

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 L       G+   + HRLD ETSG++V A+T      L      R I + YW+L
Sbjct: 114 PTELALLNHVSAYTGRTCYVVHRLDMETSGVIVFAKTPFILPILNRLLEKREISRDYWAL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +K+      + +  H     V  VKQ +K    AI+  K++  F Q    +  +
Sbjct: 174 VHGTLSSKEVGYREPIGRHRHDRRKRVVDVKQGQK----AITDVKLLKSFKQNVSLINCR 229

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
             TGRTHQ+RVH  + G  ++GD  Y    KG    P   +L LHA  + L HP    +
Sbjct: 230 LQTGRTHQIRVHLSYHGHALLGDPLYS---KGKAECP---RLMLHAHQLWLRHPLTQEM 282


>gi|225549251|ref|ZP_03770224.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 94a]
 gi|225370109|gb|EEG99549.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 94a]
          Length = 326

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 74/342 (21%), Positives = 152/342 (44%), Gaps = 32/342 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +   V+ +   +RLD +   ++       +++       + + K +K        
Sbjct: 1   MIRVKREFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK-------- 50

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++   +   + I+ E     S ++  + S+ +   ++YEDS + V NKP GI    G
Sbjct: 51  --IKLSKPVFKDDEILIEFDEEGSQIDCLRPSN-IPIAIIYEDSNVIVLNKPQGILSHPG 107

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                    + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + 
Sbjct: 108 ISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ +R  K+Y ++V G   +    I +++ +  H    +     +       A++ ++++
Sbjct: 167 FKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLL 222

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F + +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+ 
Sbjct: 223 LNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLKKIT---LMLHSY 277

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            +++   +    +  +  P   V    +     + NL I  L
Sbjct: 278 KLEIDVGKNSFKKFISEFPKRFVIFLSNFYKSDELNLIIDNL 319


>gi|203287491|ref|YP_002222506.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           recurrentis A1]
 gi|201084711|gb|ACH94285.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           recurrentis A1]
          Length = 326

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 75/328 (22%), Positives = 135/328 (41%), Gaps = 34/328 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK---RVKFNNRIQSGQVVRIPPVINALN 75
            RLD +   H    N   ++K       + +      +K +  +     +          
Sbjct: 15  QRLDIYLSEHLCLFNRSQIKKR-ELKAFKFNDGYFSAIKLSKPVFINDRI---------- 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLK 134
            +I+  + +D    L   +  L   +LYED  + V  KP GI    G S +   +  FL 
Sbjct: 64  -LIEFNESIDLGEYLVPLN--LPINILYEDINVIVIEKPQGILSHLGISNLENTVVNFLL 120

Query: 135 SWV-------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
             +            +P + HRLD+ETSG+++ A+       L E F+ R ++K+Y ++V
Sbjct: 121 HHISNLRYKFQENKIRPGIVHRLDKETSGVMICAKNLETLNFLFEQFKNRSVKKVYIAIV 180

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  K     I  ++ +  +    +      ++     A++ +KV+    + +  + +QP
Sbjct: 181 KGNFKVDSGIIDTFIDRDRYDRKKF----TVHKNSGKRALTEYKVLISM-KNYSLVVLQP 235

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQLRVH  ++  PI+GD  Y       F       L LH+  +++   EG   + 
Sbjct: 236 KTGRTHQLRVHMKYLNHPILGDDIYS-RLDQEFKEIS---LMLHSFKLEISIKEGFLKKF 291

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            + LP   +    +       +L +K L
Sbjct: 292 ISVLPKRFIDFLSNFYDDATLDLLVKDL 319


>gi|185178732|ref|ZP_02554745.2| pseudouridine synthase [Ureaplasma urealyticum serovar 5 str. ATCC
           27817]
 gi|188024269|ref|ZP_02569983.2| pseudouridine synthase [Ureaplasma urealyticum serovar 7 str. ATCC
           27819]
 gi|188518686|ref|ZP_02557148.2| pseudouridine synthase [Ureaplasma urealyticum serovar 11 str. ATCC
           33695]
 gi|209554557|ref|YP_002284535.1| pseudouridine synthase [Ureaplasma urealyticum serovar 10 str. ATCC
           33699]
 gi|225551323|ref|ZP_03772269.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           8 str. ATCC 27618]
 gi|184209334|gb|EDU06377.1| pseudouridine synthase [Ureaplasma urealyticum serovar 5 str. ATCC
           27817]
 gi|188018935|gb|EDU56975.1| pseudouridine synthase [Ureaplasma urealyticum serovar 7 str. ATCC
           27819]
 gi|188997684|gb|EDU66781.1| pseudouridine synthase [Ureaplasma urealyticum serovar 11 str. ATCC
           33695]
 gi|209542058|gb|ACI60287.1| pseudouridine synthase [Ureaplasma urealyticum serovar 10 str. ATCC
           33699]
 gi|225379138|gb|EEH01503.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           8 str. ATCC 27618]
          Length = 315

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 67/279 (24%), Positives = 134/279 (48%), Gaps = 30/279 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + ++ ++ N RLDR+   ++P+++ + + K++R+  ++V+ K+ + N  ++   VV 
Sbjct: 3   LKEIKIKINDANQRLDRFLLKNFPNLSRIAIYKLIRTKDIKVNHKKAEHNYLLKENDVVS 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I            ++  L+  ++L       +  ++YEDS I V +KP G+ V       
Sbjct: 63  IY----------AKENFLEKKIDLDFAKAKDELEIIYEDSNILVVHKPIGLIVH---EDD 109

Query: 127 YHIDGFLKSWV-------------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            H +  L++ +             D     P L HRLD  TSG++V A+T  A + + E 
Sbjct: 110 NHKNDTLQNRIKKYLVKKNEYHPFDESAFVPSLCHRLDLNTSGLIVAAKTANALRIIAEM 169

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+   + ++Y  L +       + + N++ K      + + V     K    AI+ ++ I
Sbjct: 170 FKNNDVNRVYKCLTYNRLPKNNDIVYNYMYK---ANDNTMIVQNFKTKVNKTAITKYQYI 226

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             + +K+   +++  TGRTHQ+R     +  PIVG+ KY
Sbjct: 227 GNY-KKYFVYDIELLTGRTHQIRAVLNFLHAPIVGEQKY 264


>gi|261337488|ref|ZP_05965372.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           gallicum DSM 20093]
 gi|270277883|gb|EFA23737.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           gallicum DSM 20093]
          Length = 313

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 73/336 (21%), Positives = 126/336 (37%), Gaps = 39/336 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS     + +   +     R D         ++     +++ SG  RV  + V     + 
Sbjct: 1   MST----RLLPAPDMLIGKRFDVALAK-MTGLSRAKAAELVASGSARVLGRDVDKAAVLL 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G ++ I                 +               ++YED  + V +KP G++  
Sbjct: 56  EGDMIEID----------------EHDPEPVAEPIATDMAIVYEDDDVVVVDKPVGVAAH 99

Query: 121 GGSGIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTE 172
              G  +     L S +D            +  +  RLD  TSG+++V ++  A + +  
Sbjct: 100 ASVG--WTGPTVLGSLLDRGVHITSYGAAGRQGIVSRLDVGTSGLMLVCKSELAYKEMRR 157

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F    + K Y +LV G  +  K  I   + +                     AI+H+ V
Sbjct: 158 QFSEHEVVKTYEALVQGNLQEDKATIDAPIGR-----AKVSDFRFCITPAGKPAITHWDV 212

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++ F +      +   TGRTHQ+RVH   +G P+VGD  Y AN K      +Q + +LHA
Sbjct: 213 LERFGE-ATLARINLETGRTHQIRVHFSSIGHPLVGDPMYGANPKLAQECGLQ-RQWLHA 270

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
             +D  HP       +T+ LP  +    D +  + D
Sbjct: 271 MQLDFRHPRTHVWTTVTSTLPPDLSHALDVMAQRRD 306


>gi|227554161|ref|ZP_03984208.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis HH22]
 gi|227176703|gb|EEI57675.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis HH22]
          Length = 297

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 75/309 (24%), Positives = 135/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L K+  + G+++V+         +Q+G VV++               
Sbjct: 18  FLKEQ--GVSKGLLAKVKFQGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIP---TQYHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLS 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   +   +A + + +    AQ    + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAA-VRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGKMDQ-----GIERQALHCMELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKSVDDTL 297


>gi|255657995|ref|ZP_05403404.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
 gi|260850197|gb|EEX70204.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
          Length = 296

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 70/320 (21%), Positives = 126/320 (39%), Gaps = 37/320 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSG 62
           MT ++ V +     +M +  +   H   I+    ++I  SG  RV           +++G
Sbjct: 1   MTQIR-VELPEALTSMPVKAFLTQH-EGISSTQWKRIKHSGTFRVGGILCNAARTEVRTG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++    V  +                     + L   + YED  + + NKPAG  V   
Sbjct: 59  DIITFDIVRPS-----------------DIEPEDLPLDIRYEDDYLLIVNKPAGQLVHPT 101

Query: 123 SGIAYHIDG-FLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLT-ESFRMRR 178
           +  A+   G  +  W  + G+       HRLD+ TSG++++A+       LT      + 
Sbjct: 102 TKEAHGTLGNAVLYWYKAHGEHHAYHPVHRLDRNTSGLVLIAKVPQVQYKLTPRHGEGKL 161

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             + Y +L+ G     +  I   + +          ++++       A +H+  +     
Sbjct: 162 FHREYLALIEGELTPPEGLIDAPIARALP-----SIILRKVSPDGQTARTHYDTVQTDG- 215

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           K   + +   TGRTHQ+RVH  H+G P++GD  Y  N           +  LHA  +   
Sbjct: 216 KLSLIHLVLDTGRTHQIRVHLAHLGHPLLGDDLYGGNLAR------IKRQALHAARLHFR 269

Query: 299 HPEGG-RLQITAPLPAHMVK 317
           HP  G  + +  PLP+ M +
Sbjct: 270 HPMTGAEIDVQVPLPSDMAQ 289


>gi|306833402|ref|ZP_07466529.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus bovis ATCC
           700338]
 gi|304424172|gb|EFM27311.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus bovis ATCC
           700338]
          Length = 296

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 122/305 (40%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L K+  + G + V+         +  G VV I              +
Sbjct: 16  FLKGH--DVSKGLLAKVKFKGGNIWVNGVEQNAIYLLNVGDVVTI--------------E 59

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D   + T         + YED    + NK  G +       +  I  F+K +   +  
Sbjct: 60  IPDEEEHETLVPVKHDLNIAYEDEHFLIINKSYGYASIPSVLHSNTIANFVKYYYLEQNY 119

Query: 143 ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
              +  +  RLD++TSG+++ A+   A   L +  + + I+K Y++LV G  +   K  I
Sbjct: 120 PNKQVHIVTRLDKDTSGLMLFAKHGYAHARLDKQLQNKTIEKRYYALVSGKGELADKGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      D   + +       YA + ++V+  F +    ++++ HTGRTHQ+RVH
Sbjct: 180 IAPIARS-----DDSIITRCVHPSGKYAHTSYEVVARFGE-VALVDIRLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
             H+G P++GD  Y  +     T     +  LH  Y+   +P     +  T  L      
Sbjct: 234 FSHIGFPLLGDDMYGGSMDYGIT-----RQALHCHYLRFVNPYTNEEIIQTTNLTDDFDS 288

Query: 318 TWDSL 322
               L
Sbjct: 289 VIMEL 293


>gi|297568139|ref|YP_003689483.1| pseudouridine synthase, RluA family [Desulfurivibrio alkaliphilus
           AHT2]
 gi|296924054|gb|ADH84864.1| pseudouridine synthase, RluA family [Desulfurivibrio alkaliphilus
           AHT2]
          Length = 334

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 77/330 (23%), Positives = 131/330 (39%), Gaps = 43/330 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V VE  +    +  +    + ++     Q+ L  G++RV+ + V     + +   V    
Sbjct: 17  VRVEAGQAGGTVLDFVAGRFTYLTREQWQQELVDGRLRVNGEPVPPERLLAAADRVSY-- 74

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                               L +        ++YED  + V NKPA +    G     H 
Sbjct: 75  ----------------RGRELAEPPVASHFSVVYEDDDLLVVNKPAPLPCHPGGRYFRH- 117

Query: 130 DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L   +  +    KP L +RLD+ETSG++VVA+ RAAA+     ++ ++++K Y  LV
Sbjct: 118 --TLWRLLQERCGVPKPLLVNRLDRETSGLVVVAKKRAAARDCARQWQEQQVEKRYLVLV 175

Query: 188 WGIPKNKKECIANWLLKKS----HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            G      + +A +L             +    +    GA    + F+++         L
Sbjct: 176 EGEFPLGAQAVAGFLAPDPASLVRKKSRFFPADQAAPAGAVSCATAFRLLALQG-GISLL 234

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-------------YL 290
           E +P TGR HQ+R     +G P+VGD  Y  + +  F   + ++L              L
Sbjct: 235 EARPLTGRCHQIRATLCSLGFPVVGDKIYGLD-EELFLRFLADRLSSDDRRRLRLPRQAL 293

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           H+  + + HP   R L+ T PLP  M    
Sbjct: 294 HSAGLKMRHPADHRPLEFTCPLPPEMAGLL 323


>gi|254853367|ref|ZP_05242715.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|300763946|ref|ZP_07073942.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
 gi|258606732|gb|EEW19340.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|300515287|gb|EFK42338.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
          Length = 289

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 131/319 (41%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT+V  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  G
Sbjct: 1   MTHV-TLPILEDWEGLSLTTILQEKF-HLGKKARHEIRMSQNVLLNNKPLDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P  ++    + +                     ++YED  + V NKP  +     
Sbjct: 59  ASLSLPVFLHDKIPVYE-----------------YDLEIIYEDDFLLVVNKPVDMKTHPN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++  GQ       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEKTGQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            + Y + V G      + I   + +  H G        Q       A++H KV++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDNEK 216

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y          P  N++ LHA  + L 
Sbjct: 217 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------FPRANRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|256959811|ref|ZP_05563982.1| pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256950307|gb|EEU66939.1| pseudouridine synthase [Enterococcus faecalis Merz96]
          Length = 287

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 71/312 (22%), Positives = 126/312 (40%), Gaps = 37/312 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M L      + V+   EN     W       H              V+++ +   F+  +
Sbjct: 5   MRLPENFSTMTVKELLENE----WLVPRKVRHFLRTR-------KNVKINGETAAFHFPV 53

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q+G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI  
Sbjct: 54  QAGDCVTLTF---------EETDYVRPTIHL---GEATRVKVLYEDEHLMIVNKPYGIKT 101

Query: 120 QGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                     +   + +++  K Q P + HRLD+ETSG +V A+       L      ++
Sbjct: 102 HPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQ 161

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   + 
Sbjct: 162 IYRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSN 217

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L 
Sbjct: 218 NQTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLL 270

Query: 299 HPEGGR-LQITA 309
            P   + + +TA
Sbjct: 271 QPFTKKQIVVTA 282


>gi|223889096|ref|ZP_03623685.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 64b]
 gi|223885345|gb|EEF56446.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 64b]
          Length = 322

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 73/342 (21%), Positives = 152/342 (44%), Gaps = 32/342 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +   V+ +   +RLD +   ++       +++       + + K +K        
Sbjct: 1   MIRVKREFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK-------- 50

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++   +   + I+ E     S ++  + S+ +   ++YEDS + V NKP GI    G
Sbjct: 51  --IKLSKPVFKDDEILIEFDEESSQIDCLRPSN-IPIAIIYEDSNVIVLNKPQGILSHPG 107

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                    + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + 
Sbjct: 108 ISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ +R  K+Y ++V G   +    I +++ +  H    +     +       A++ ++++
Sbjct: 167 FKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLL 222

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F + +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+ 
Sbjct: 223 LNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLKKIT---LMLHSY 277

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            +++   +    +  +  P   +    +     + NL I  L
Sbjct: 278 KLEIDVGKNSFKKFISEFPKRFIIFLSNFYKSDELNLIIDNL 319


>gi|288802331|ref|ZP_06407771.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           melaninogenica D18]
 gi|288335298|gb|EFC73733.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           melaninogenica D18]
          Length = 296

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 76/307 (24%), Positives = 132/307 (42%), Gaps = 40/307 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIK 79
           L  W   +    +   ++  L++  ++V+ K V  F++ +++G  +              
Sbjct: 23  LLEWLLANLNE-SKSKVKATLQNRGIKVNGKCVTQFDHPLKAGDKI-------------- 67

Query: 80  EQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                  SV+ +K +D  +S    ++YED  + V  K  GI        + ++   L  +
Sbjct: 68  -------SVSKSKKNDLFRSRYVKIVYEDRFLVVIEKNIGILSMAAGHSSLNVKTVLDDY 120

Query: 137 VDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                QK    + HRLD++TSG+++ A+     Q L   +      + Y ++V G  ++ 
Sbjct: 121 FRKTKQKCTAHVVHRLDRDTSGLMIYAKDIQTEQLLEHDWHNIVYDRRYVAVVSGEMEHD 180

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  IANWL         YV      + G  YA++HF V+D        +E Q  TGR +Q
Sbjct: 181 EGTIANWL----KDNKSYVTYSSPVDNGGKYAVTHFHVLDRTV-AHSLVEYQLETGRKNQ 235

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
           +RVH+  MG P+ GD KY             ++L LHA  +   HP    R++   P+PA
Sbjct: 236 IRVHSADMGHPVCGDIKYGNGDDP------LHRLCLHAYVLCFHHPVTHQRMEFETPIPA 289

Query: 314 HMVKTWD 320
                + 
Sbjct: 290 VFRHLFK 296


>gi|171920745|ref|ZP_02695367.2| pseudouridine synthase [Ureaplasma urealyticum serovar 13 str. ATCC
           33698]
 gi|188524118|ref|ZP_02557392.2| pseudouridine synthase [Ureaplasma urealyticum serovar 12 str. ATCC
           33696]
 gi|195867425|ref|ZP_03079429.1| pseudouridine synthase [Ureaplasma urealyticum serovar 9 str. ATCC
           33175]
 gi|198273522|ref|ZP_03206058.1| pseudouridine synthase [Ureaplasma urealyticum serovar 4 str. ATCC
           27816]
 gi|225550899|ref|ZP_03771848.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           2 str. ATCC 27814]
 gi|171903495|gb|EDT49784.1| pseudouridine synthase [Ureaplasma urealyticum serovar 13 str. ATCC
           33698]
 gi|195659776|gb|EDX53156.1| pseudouridine synthase [Ureaplasma urealyticum serovar 12 str. ATCC
           33696]
 gi|195660901|gb|EDX54154.1| pseudouridine synthase [Ureaplasma urealyticum serovar 9 str. ATCC
           33175]
 gi|198250042|gb|EDY74822.1| pseudouridine synthase [Ureaplasma urealyticum serovar 4 str. ATCC
           27816]
 gi|225380053|gb|EEH02415.1| pseudouridine synthase, RluA family [Ureaplasma urealyticum serovar
           2 str. ATCC 27814]
          Length = 315

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 67/279 (24%), Positives = 134/279 (48%), Gaps = 30/279 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + ++ ++ N RLDR+   ++P+++ + + K++R+  ++V+ K+ + N  ++   VV 
Sbjct: 3   LKEIKIKINDANQRLDRFLLKNFPNLSRIAIYKLIRTKDIKVNHKKAEHNYLLKENDVVS 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I            ++  L+  ++L       +  ++YEDS I V +KP G+ V       
Sbjct: 63  IY----------AKENFLEKKIDLDFAKAKDELEIIYEDSNILVVHKPIGLIVH---EDD 109

Query: 127 YHIDGFLKSWV-------------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
            H +  L++ +             D     P L HRLD  TSG++V A+T  A + + E 
Sbjct: 110 NHKNDTLQNRIKKYLVKKNEYHPFDESAFVPSLCHRLDLNTSGLIVAAKTANALRIIAEM 169

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+   + ++Y  L +       + + N++ K      + + V     K    AI+ ++ I
Sbjct: 170 FKNNDVNRVYKCLTYNRLPKNNDIVYNYMYK---ANDNTMIVQNFKTKVNKTAITKYQYI 226

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             + +K+   +++  TGRTHQ+R     +  PIVG+ KY
Sbjct: 227 GNY-KKYFVYDIELLTGRTHQIRAVLNFLHAPIVGEQKY 264


>gi|260583056|ref|ZP_05850838.1| tRNA pseudouridine synthase C [Haemophilus influenzae NT127]
 gi|260093907|gb|EEW77813.1| tRNA pseudouridine synthase C [Haemophilus influenzae NT127]
          Length = 222

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 106/228 (46%), Gaps = 14/228 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKG 278
           K    A++ ++ +         +++ PHTGR HQLR H  H+  PI+GD +Y      + 
Sbjct: 120 KEPQEAVTDYEGLK-------IVKLIPHTGRKHQLRRHMKHIFHPILGDTQYGDLHQNRA 172

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
             +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 173 LMSHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 220


>gi|327312402|ref|YP_004327839.1| RluA family pseudouridine synthase [Prevotella denticola F0289]
 gi|326945177|gb|AEA21062.1| pseudouridine synthase, RluA family [Prevotella denticola F0289]
          Length = 319

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 70/304 (23%), Positives = 121/304 (39%), Gaps = 34/304 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHIIK 79
           L  W   +    +   ++  L++  +RV+   V   +R +++G  V +            
Sbjct: 46  LLEWLLANLKE-SKSKVKATLQNRGIRVNGSCVTQFDRQLKAGDKVSV------------ 92

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                 S              ++YED  + V  K  GI        + ++   L  +   
Sbjct: 93  ------SKSKKNGQFRSRYVKIVYEDRFLVVVEKNIGILSMAAGHASLNVKSILDDYFYK 146

Query: 140 KGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             QK    + HRLD++TSG+++ A+     Q     +      + Y  +V G  +  +  
Sbjct: 147 TRQKCTAHVVHRLDRDTSGLMIYAKDMQTEQLFEHDWHNIVYDRRYVGVVSGEMEQDEGT 206

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +ANWL         YV      + G  YA++HF V+D     +  +E +  TGR +Q+RV
Sbjct: 207 VANWL----KDNKAYVTYSSPVDNGGKYAVTHFYVLDRTV-AYSLVEYRLETGRKNQIRV 261

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
           H+  MG P+ GD KY             ++L LHA  +   HP    R++   P+PA   
Sbjct: 262 HSADMGHPVCGDVKYGNGDDP------LHRLCLHAYVLCFHHPVTHQRMEFETPVPATFR 315

Query: 317 KTWD 320
             + 
Sbjct: 316 HLFK 319


>gi|257421756|ref|ZP_05598746.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis X98]
 gi|257163580|gb|EEU93540.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis X98]
 gi|315155543|gb|EFT99559.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0043]
          Length = 297

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 75/309 (24%), Positives = 135/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L K+  + G+++V+         +Q+G VV++               
Sbjct: 18  FLKEQ--GVSKGLLAKVKFQGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   +   +A + + +    AQ    + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAA-VRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGEMDQ-----GIERQALHCMELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKNVDDTL 297


>gi|260580730|ref|ZP_05848556.1| tRNA pseudouridine synthase C [Haemophilus influenzae RdAW]
 gi|260092547|gb|EEW76484.1| tRNA pseudouridine synthase C [Haemophilus influenzae RdAW]
          Length = 239

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 108/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDGFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHVFHPILGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|182680419|ref|YP_001834565.1| pseudouridine synthase [Beijerinckia indica subsp. indica ATCC
           9039]
 gi|182636302|gb|ACB97076.1| pseudouridine synthase [Beijerinckia indica subsp. indica ATCC
           9039]
          Length = 234

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 77/233 (33%), Positives = 119/233 (51%), Gaps = 11/233 (4%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L++ LLY D  + V +KPAGI V  G     +++ F         ++P L HRLD++TS
Sbjct: 5   DLQARLLYRDGMMLVLDKPAGIPVHKGPKGGDNLEAFFDDLRFGLPRRPALAHRLDRDTS 64

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G LV+ R   A + L   F+  +I K YWS+V G P   +  I   L ++    G ++ V
Sbjct: 65  GCLVLGRHHKALEKLGLLFKQGKIAKTYWSVVLGGPTEDEGLIDLPLGRRDAERGWWMKV 124

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               +     A + + V+   A   C L ++P TGRTHQLRVH    G PI+GD  Y   
Sbjct: 125 ----DPEGAPAQTRWTVLARSAD-HCLLALKPLTGRTHQLRVHCAAQGFPILGDPVYGPA 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
                 +     L+LHAR +++P  +    +++ AP+PAHM     +LG++ +
Sbjct: 180 DHKGGET-----LHLHARAIEIPLYKNKEAIKVEAPVPAHMRPALMALGWREE 227


>gi|28849821|gb|AAN64577.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gordonii]
          Length = 290

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 123/303 (40%), Gaps = 35/303 (11%)

Query: 25  FKNHYPHI---NFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K             ++  LR    V V+ + + + ++IQ+G ++ +             
Sbjct: 16  IKELLEDYFLIPR-KIRHFLRTKKHVLVNDQTINWQSKIQAGDLLSLTFDEEDY----PA 70

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           + IL     L +         LY+D  + + NKP G+           +   + ++V   
Sbjct: 71  KAILMGKPELVQE--------LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV--- 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G+   + HRLD+ETSG ++ A+       L      + IQ+ YW+LV G    K     +
Sbjct: 120 GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLENKDIQREYWALVDGKFIEKSRIYKD 179

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + K   YA +H   +  F QK   ++ Q  TGRTHQ+RVH  
Sbjct: 180 KIGRDRHNRRKRL----VDNKHGQYAETHVTRLKSFGQK-TLVKCQLKTGRTHQIRVHLS 234

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
           H G P+VGD  Y    +G        +L LHA  +   HP    ++ + AP      +  
Sbjct: 235 HHGFPLVGDPLYHPQPQG--------RLMLHAYRLSFVHPFTLEKISLEAP-SKSFEEGL 285

Query: 320 DSL 322
           + L
Sbjct: 286 EKL 288


>gi|257438386|ref|ZP_05614141.1| pseudouridine synthase, RluA family [Faecalibacterium prausnitzii
           A2-165]
 gi|257199217|gb|EEU97501.1| pseudouridine synthase, RluA family [Faecalibacterium prausnitzii
           A2-165]
          Length = 365

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 73/332 (21%), Positives = 144/332 (43%), Gaps = 24/332 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++      ++E +RL R+ ++    +    L K  R+ +V+V+ K+    +R+++G ++ 
Sbjct: 30  MKQFTATANDEGVRLSRFVQSVTRDLPTSLLYKSFRNKRVKVNGKKGAPEDRLKAGDLIE 89

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +   IN      +  K         K  +  K  ++YED  I V  KP  +         
Sbjct: 90  L--YINDEFFPPEGAKPAARKPAPKKQQNQPKVTVIYEDENIAVLYKPTHLLCHSDRTGD 147

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            ++      ++  KG+         KP + +RLD+ T G+++ A++ AA + + E  R  
Sbjct: 148 ANLVDAFTQYLAQKGEYDAGGENRFKPGICNRLDRGTEGLVIAAKSYAALRDMNEIIRTD 207

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y+++  GIP  +      W           +H  +  ++     I+   V+   A
Sbjct: 208 LLKKEYYTITVGIP--QSGRFTAWWEHDEKNNKVSIHAHQSQDERRKQIITDVDVL-RTA 264

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-YLHARYMD 296
             F   ++   TGRTHQ+R H  ++G P++GD KY        T      L  +   ++D
Sbjct: 265 GPFALCKIGLVTGRTHQIRAHLAYLGKPVLGDIKYGNRKMNERTGTRTQALCAVRISFLD 324

Query: 297 LP------HPEGGRLQITAPLPAHMVKTWDSL 322
           +P      +  G  +++  P    +VK +D+L
Sbjct: 325 IPEENSLRYLSGKVIKLKDP---QIVKQFDAL 353


>gi|206977555|ref|ZP_03238449.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
 gi|217958867|ref|YP_002337415.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|222095026|ref|YP_002529086.1| ribosomal large subunit pseudouridine synthase d [Bacillus cereus
           Q1]
 gi|229138078|ref|ZP_04266676.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|206744273|gb|EDZ55686.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
 gi|217063723|gb|ACJ77973.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|221239084|gb|ACM11794.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           Q1]
 gi|228645423|gb|EEL01657.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
          Length = 307

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 129/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EMTVPAKWNGISIESLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E               + +  ++YED  + + NKP  +           
Sbjct: 70  MFMEEEYGVEPE---------------YGELHVVYEDDHVLIVNKPEKMDTHPSEKGGMG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEKYFRKQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGGTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNDTMKEF 302


>gi|224024089|ref|ZP_03642455.1| hypothetical protein BACCOPRO_00808 [Bacteroides coprophilus DSM
           18228]
 gi|224017311|gb|EEF75323.1| hypothetical protein BACCOPRO_00808 [Bacteroides coprophilus DSM
           18228]
          Length = 307

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 64/301 (21%), Positives = 116/301 (38%), Gaps = 35/301 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       ++   ++ +L +  V V+   + ++N  +  G  V+I    N          
Sbjct: 34  FLMKKMAGVSRTRVKALLSNRVVLVNNNIQTQYNFPLTPGMKVQISKDRNK--------- 84

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWV--DS 139
                             +LYED+ + V  K  G+                L  +V    
Sbjct: 85  ---------HEFRHPMLKILYEDAYLIVVEKKEGLLSVATEKQKERTAQHILNEYVKRQH 135

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +  +  + HRLD+ETSGI++ A+       L +++      + Y ++V G  +  +  + 
Sbjct: 136 RNNRVFVVHRLDRETSGIMMYAKDEKTQHTLRDNWHDIVYDRRYVTIVTGDMEKDQGKVE 195

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WL                 + G  ++++H+  I   A  F  +E+Q  TGR +Q+RVH 
Sbjct: 196 SWLT-----DRKLYVSSSPVDDGGKFSVTHYHTIKR-ANGFSLVELQLETGRKNQIRVHM 249

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
             +G P+VGD +Y              +L LHA  +   HP  G R++   P PA     
Sbjct: 250 QTLGHPVVGDERYGCEVNP------LGRLALHAFKLCFYHPVTGERMEFETPYPAPFKTL 303

Query: 319 W 319
            
Sbjct: 304 M 304


>gi|312900037|ref|ZP_07759354.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
 gi|311292794|gb|EFQ71350.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
          Length = 297

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 74/309 (23%), Positives = 134/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L K+  + G+++V+         +Q+G VV++               
Sbjct: 18  FLKEQ--GVSKGLLAKVKFQGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLS 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   +   +A + +  +     K   + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETGQFASTEYW-LAKRGAKAAAVRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGKMDQ-----GIERQALHCMELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKSVDDTL 297


>gi|227519595|ref|ZP_03949644.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           TX0104]
 gi|229544944|ref|ZP_04433669.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           TX1322]
 gi|256763299|ref|ZP_05503879.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T3]
 gi|256853972|ref|ZP_05559337.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T8]
 gi|257079838|ref|ZP_05574199.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis JH1]
 gi|257090805|ref|ZP_05585166.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis CH188]
 gi|294779490|ref|ZP_06744886.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|307270621|ref|ZP_07551912.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|307287513|ref|ZP_07567556.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|307290324|ref|ZP_07570239.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|312902437|ref|ZP_07761643.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
 gi|227072945|gb|EEI10908.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           TX0104]
 gi|229309836|gb|EEN75823.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           TX1322]
 gi|256684550|gb|EEU24245.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T3]
 gi|256710915|gb|EEU25958.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T8]
 gi|256987868|gb|EEU75170.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis JH1]
 gi|256999617|gb|EEU86137.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis CH188]
 gi|294453447|gb|EFG21853.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|306498517|gb|EFM68019.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|306501251|gb|EFM70554.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|306512931|gb|EFM81572.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|310634107|gb|EFQ17390.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
 gi|315030281|gb|EFT42213.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4000]
 gi|315164911|gb|EFU08928.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1302]
 gi|315170401|gb|EFU14418.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1342]
 gi|315579152|gb|EFU91343.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0630]
          Length = 297

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 75/309 (24%), Positives = 135/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L K+  + G+++V+         +Q+G VV++               
Sbjct: 18  FLKEQ--GVSKGLLAKVKFQGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   +   +A + + +    AQ    + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAA-VRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGKMDQ-----GIERQALHCMELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKSVDDTL 297


>gi|291545303|emb|CBL18411.1| pseudouridine synthase, RluA family [Ruminococcus sp. SR1/5]
          Length = 380

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 79/384 (20%), Positives = 137/384 (35%), Gaps = 70/384 (18%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNL-QKILRSGQVRVDKKRVKFNNRIQSG 62
           M     + +        + R+ +     +    + Q   R G +R + ++ +       G
Sbjct: 1   MNRYLTIYIPKTAVPAPVSRFLRTQ-AGLTKKQISQAKFRPGGIRKNGQQCRVTETAYPG 59

Query: 63  QVVRIPPVINALNHIIKEQ---KILDSSVNLTKHSDFL---------------------- 97
             + +    + ++    E     +  S+ N    +D +                      
Sbjct: 60  DQIIVCLEADDVDSAQLESSSFTVYSSNHNFQFSADAISYSDSAASEFAGSDVNSHNYHS 119

Query: 98  ---------KSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQ--KPR 145
                    +  ++YED  I   NKPAGI     GS  +  +   + S+  SKG+  K R
Sbjct: 120 PATTSQFLPELAIIYEDQDILAINKPAGIVTHPSGSHYSDSLANQVASYFRSKGEPTKVR 179

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE----CIANW 201
              RLD+ETSGIL+ AR + AA  L         +K Y + V G     ++     I+  
Sbjct: 180 SIGRLDKETSGILLFARNQTAAARLQNQREEGISEKTYLAAVSGFMPVDEDGAFHRISVP 239

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF----CWLEMQPHTGRTHQLRV 257
           L          V        G+ +A + + V+             + ++  TGRTHQ+RV
Sbjct: 240 LAPDPDNRLKMVVSTDGTLPGSKHAETLYSVLKSTGPDAAAPASLVMLRLKTGRTHQIRV 299

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG--------------- 302
           H   +G P++GD  YC +   N  S    +  LHA  +    P                 
Sbjct: 300 HMASLGHPLLGDSLYCLSDISNPFS----RAALHAWKLKFQLPFSIDESASDTQASMHHD 355

Query: 303 ----GRLQITAPLPAHMVKTWDSL 322
                 + + APLP    K ++++
Sbjct: 356 KNAKKEISLEAPLPEDFKKFYETI 379


>gi|256616825|ref|ZP_05473671.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis ATCC 4200]
 gi|256963780|ref|ZP_05567951.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis HIP11704]
 gi|257084358|ref|ZP_05578719.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis Fly1]
 gi|257087643|ref|ZP_05582004.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis D6]
 gi|307271727|ref|ZP_07552998.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|307276911|ref|ZP_07558021.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|256596352|gb|EEU15528.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis ATCC 4200]
 gi|256954276|gb|EEU70908.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis HIP11704]
 gi|256992388|gb|EEU79690.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis Fly1]
 gi|256995673|gb|EEU82975.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis D6]
 gi|295113627|emb|CBL32264.1| pseudouridine synthase, RluA family [Enterococcus sp. 7L76]
 gi|306506334|gb|EFM75494.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|306511605|gb|EFM80604.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|315025558|gb|EFT37490.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2137]
 gi|315032794|gb|EFT44726.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0017]
 gi|315143807|gb|EFT87823.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2141]
 gi|315162164|gb|EFU06181.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0645]
          Length = 297

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 75/309 (24%), Positives = 135/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L K+  + G+++V+         +Q+G VV++               
Sbjct: 18  FLKEQ--GVSKGLLAKVKFQGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   +   +A + + +    AQ    + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAA-VRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGEMDQ-----GIERQALHCMELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKSVDDTL 297


>gi|313607319|gb|EFR83739.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL F2-208]
          Length = 289

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 131/319 (41%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT+V  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  G
Sbjct: 1   MTHV-TLPILEDWEGLSLTTILQEKF-HLGKKARHEIRMSQNVLLNNKPLDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P                   ++    +      ++YED  + V NKP  +     
Sbjct: 59  ASLSLPVF-----------------LHDKIPTYEYDLEIIYEDDFLLVVNKPVDMKTHAN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++  GQ       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEKTGQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            + Y + V G      + I   + +  H G        Q       A++H KV++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDNEK 216

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L 
Sbjct: 217 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPSANRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|332298019|ref|YP_004439941.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332181122|gb|AEE16810.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 336

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 70/337 (20%), Positives = 133/337 (39%), Gaps = 24/337 (7%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           +     D+   RLD+  +   P+     +   +R   VRV+ K+     R+  G ++ I 
Sbjct: 5   HFTAGPDDARRRLDKIIRKFLPNAPLSAIYSYIRKSLVRVNGKKTDAAARVNEGDLIDI- 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
              + L      +   +     ++ + F     ++ +  + V NKP  I VQG  G    
Sbjct: 64  --ADFLLQPQPAELPSEPEPARSRPAAFPALDDVFCNDFLRVINKPYDIPVQGCRGARVS 121

Query: 129 IDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           I   +++      +      KP   HRLD++T+G+LV +R    A+  + + R   +QK 
Sbjct: 122 IADIVQAEYAETARASSLSFKPGPLHRLDRKTTGLLVCSRNLEGARWFSAAVRDHLLQKR 181

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV---VKQNEKGANYAISHFKVIDC---F 236
           Y ++V G  + ++  I    +++   G          +        A +    +      
Sbjct: 182 YAAIVQGCLETER--IWTDKIERETEGLHRFRRSLACRSGGSEGKTADTRAVPLAHGSYE 239

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            +    +     +GRTHQ+R+H    G P++GD  Y         S     +YLHA  + 
Sbjct: 240 GEPVTLVLFSIGSGRTHQIRLHGGAHGFPLLGDTAYGGRPISEAQS-----IYLHAWQLG 294

Query: 297 L--PHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLY 331
           +  P+P      + AP+  +  K       ++D + Y
Sbjct: 295 IPEPNPVSLPPLLCAPISTNFQKMLKKCLLEWDYSAY 331


>gi|157164896|ref|YP_001467348.1| P-protein [Campylobacter concisus 13826]
 gi|112801995|gb|EAT99339.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Campylobacter concisus 13826]
          Length = 323

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 70/330 (21%), Positives = 124/330 (37%), Gaps = 43/330 (13%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD         I+      +++   V V+ K V K +  +     + +           
Sbjct: 11  RLDVVVAKEL-QISRNQALNLIKDSLVSVNLKPVSKPSFLLSENDEICVNFAPKKEVQ-- 67

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                        ++       ++YED  + V NKP  I V     +    +  L  W++
Sbjct: 68  ------------NEYEVNFDIPIIYEDDDLIVLNKPPQIVVHQAPSV---KEATLVEWLN 112

Query: 139 SKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            KG          +  + HRLD+ TSG +VVA+   A   L+E    + + +IY +L   
Sbjct: 113 KKGFMLSNLNGDVRAGIVHRLDKGTSGAIVVAKNNFAHAKLSEQLSDKSMGRIYLALT-D 171

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +P  +   I   + +  +       V       A +A S F  +         +  +  T
Sbjct: 172 LPLKEDIIIDKPIGRNPNNRLKKAIVA-----DAKFAKSAFVNLLSEG-GVNLIAAKLFT 225

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
           GRTHQ+RVH   +   I+GD  Y    +G+  S    ++ LHA  +   HP  G R++ T
Sbjct: 226 GRTHQIRVHLASINRHILGDDLYGFKSQGDKIS----RVMLHAYMLYFIHPRTGKRVEFT 281

Query: 309 APLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           A       +       K  + ++ +++   
Sbjct: 282 AKTYDDFNQIIYK---KIPKEIFDEKICPT 308


>gi|293384999|ref|ZP_06630833.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis R712]
 gi|293389269|ref|ZP_06633731.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis S613]
 gi|312905988|ref|ZP_07765001.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|312909334|ref|ZP_07768190.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
 gi|291077677|gb|EFE15041.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis R712]
 gi|291081433|gb|EFE18396.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis S613]
 gi|310627983|gb|EFQ11266.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|311290358|gb|EFQ68914.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
          Length = 283

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 71/311 (22%), Positives = 126/311 (40%), Gaps = 35/311 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L      + V+   EN  L         H              V+++ +   F+  +Q
Sbjct: 1   MRLPENFSTMTVKELLENEWL---VPRKVRHFLRTR-------KNVKINGETAAFHFPVQ 50

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  V +           +E   +  +++L    +  +  +LYED  + + NKP GI   
Sbjct: 51  AGDCVTLTF---------EETDYVRPTIHL---GEATRVKVLYEDEHLMIVNKPYGIKTH 98

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   + +++  K Q P + HRLD+ETSG +V A+       L      ++I
Sbjct: 99  PNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNPFVLPILGRLLETKQI 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y ++V G    K++ I   + +  H         + + +  + AI+H +V+   +  
Sbjct: 159 YRQYQAIVAGHFNQKEQTINQPIGRDRHD----RRKRRIDPQKGDSAITHVQVVKALSNN 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +     TGRTHQ+RVH    G PI+GD  Y    +         +L LHA  + L  
Sbjct: 215 QTAVTCVLETGRTHQIRVHLASEGHPIIGDPLYNPKSQAA-------RLMLHASQLHLLQ 267

Query: 300 PEGGR-LQITA 309
           P   + + +TA
Sbjct: 268 PFTKKQIVVTA 278


>gi|324325409|gb|ADY20669.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar finitimus YBT-020]
          Length = 307

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 69/319 (21%), Positives = 128/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EITVPAKWNGISIESLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E               + +  ++YED  + + NKP  +           
Sbjct: 70  MFMEEEYGVEPE---------------YGELHVVYEDDHVLIVNKPEKMDTHPAEKGGMG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEKYFRKQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGGTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +       
Sbjct: 284 EIEVDVPFPTKLNDKMKEF 302


>gi|223937244|ref|ZP_03629150.1| pseudouridine synthase, RluA family [bacterium Ellin514]
 gi|223894029|gb|EEF60484.1| pseudouridine synthase, RluA family [bacterium Ellin514]
          Length = 599

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 85/307 (27%), Positives = 126/307 (41%), Gaps = 28/307 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPV 70
           V    + M L  +     PHI   + + +   G  V  D   V   + + +G        
Sbjct: 309 VPQHCDGMSLFDFLHTILPHIPRADWEGLAAQGLLVTDDHLPVTGKHIVSAG-------- 360

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                     ++IL    NLT+        +L+ED  + V NKPA + +  G     +  
Sbjct: 361 ----------KRILQKMPNLTEPEVNGDIQILHEDEALIVLNKPAPLPMHAGGRFNRNTL 410

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            ++   V    QKPR  HRLD  TSG+++V RTR  A HL   F    + K Y   V G 
Sbjct: 411 EYILHQV-YHPQKPRAAHRLDANTSGVVLVTRTRHFASHLQPQFAHGEVGKFYLVKVQGT 469

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           PK         +  +    G      + + +    + + F+V+   A     LE +P TG
Sbjct: 470 PKEDSFSCNAPISAEPSEAGAR----EVDFEEGLPSRTEFRVLQRNADGTTLLEARPLTG 525

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ---NKLYLHARYMDLPHP-EGGRLQ 306
           RT+Q+RVH   MG P+ GD  Y    K   T  ++     L LHA  +   HP    R++
Sbjct: 526 RTNQIRVHLWQMGLPVCGDPVYLPGNKLGETQTLRVEDAPLCLHAWRVTFLHPLHRQRME 585

Query: 307 ITAPLPA 313
            TAP P 
Sbjct: 586 FTAPKPE 592


>gi|24214190|ref|NP_711671.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
 gi|24195091|gb|AAN48689.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
          Length = 365

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 76/375 (20%), Positives = 139/375 (37%), Gaps = 84/375 (22%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             +   ++  +E   RLD +    + + +    QK +  G++ +  K VK    ++ G +
Sbjct: 12  EELFQFLISKEESGTRLDHFLSKKFTYHSRTTWQKEITEGRILISSKTVKPGVSLKEGDL 71

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +   P       I KE+  + +              +LYED      +KP  + +     
Sbjct: 72  ISYHP-------IQKEEPPVRNDYK-----------ILYEDEFFVAVDKPGDLPIHPA-- 111

Query: 125 IAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +  G L +++   G  +     HRLD+ETSG+++ A+    A  L++SF +  IQK 
Sbjct: 112 -GIYRKGNLLTFLKESGKFKDLFTVHRLDRETSGVILFAKNSEIASILSKSFSLGNIQKY 170

Query: 183 YWSLVWGIPKNKK---ECIANWL---LKKSH-----------IGGDYVHVVKQNEKGANY 225
           Y + V G    +K     +   L   ++K                 Y+      EK    
Sbjct: 171 YITKVHGNFPKRKSAYGILKPDLSSKIRKKRTFVPLKFNFLKRNKKYLFENSLIEKQEEI 230

Query: 226 AISHFKVIDCF--------------------------------AQKFCWLEMQPHTGRTH 253
           ++++F+ I+                                     + +L  +P TGR H
Sbjct: 231 SLTYFQKIEYDKGRESKFKFSKIEFQFKNVNNEKIKSVFLDQEKDCYSFLLCKPITGRMH 290

Query: 254 QLRVHALHMGCPIVGDHKYCANFK-----------GNFTSPIQNKLYLHARYMDLPHPEG 302
           Q+R     +G P+ GD  Y  + K              T     +  LH+  + L HP  
Sbjct: 291 QIRATLFSLGFPLFGDKLYGKDEKVFLEFIEGKNPDLTTRLGMKRQALHSYAVCLNHPVT 350

Query: 303 -GRLQITAPLPAHMV 316
             +++ITAP+P   +
Sbjct: 351 NQKMKITAPIPEDFL 365


>gi|221217384|ref|ZP_03588855.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 72a]
 gi|225549717|ref|ZP_03770682.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 118a]
 gi|221192662|gb|EEE18878.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 72a]
 gi|225369677|gb|EEG99125.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 118a]
          Length = 326

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 73/342 (21%), Positives = 152/342 (44%), Gaps = 32/342 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +   V+ +   +RLD +   ++       +++       + + K +K        
Sbjct: 1   MIRVKREFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK-------- 50

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++   +   + I+ E     S ++  + S+ +   ++YEDS + V NKP GI    G
Sbjct: 51  --IKLSKPVFKDDEILIEFDEEGSQIDCLRPSN-IPIAIIYEDSNVIVLNKPQGILSHPG 107

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                    + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + 
Sbjct: 108 ISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ +R  K+Y ++V G   +    I +++ +  H    +     +       A++ ++++
Sbjct: 167 FKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLL 222

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F + +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+ 
Sbjct: 223 LNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLKKIT---LMLHSY 277

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            +++   +    +  +  P   +    +     + NL I  L
Sbjct: 278 KLEIDVGKNSFKKFISEFPKRFIIFLSNFYKSDELNLIIDNL 319


>gi|23012044|ref|ZP_00052228.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 238

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 78/246 (31%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
             D++   T   + +   LLY D+ + V +KPAG+ V  G      +   L S      +
Sbjct: 3   PPDTAPKRTVDPE-IGLSLLYRDALMLVIDKPAGLPVHPGPKGGPTLTDHLDSLRFGLPR 61

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +P   HRLD++TSG LV+ R   A   L   F   ++ K YW+LV G P   +  I   L
Sbjct: 62  RPEAAHRLDRDTSGCLVLGRHAKALARLNRLFADSKVDKSYWALVEGGPSETEGRIDLPL 121

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            ++S    D      + +     +++ ++V+    +   WLE++P TGRTHQLRVH   M
Sbjct: 122 ARRS---DDPRSWWMKTDPAGAPSLTLYRVLGR-TEGLSWLELKPVTGRTHQLRVHCAAM 177

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDS 321
           G PI GD  Y    +          L LHAR + LP +P+   + + AP PAHM     +
Sbjct: 178 GWPIRGDAIYGQADRQG------PGLQLHARSLSLPLYPKRDAIAVEAPAPAHMQAGLVA 231

Query: 322 LGFKYD 327
            G + D
Sbjct: 232 CGMRAD 237


>gi|28493478|ref|NP_787639.1| pseudouridylate synthase-like protein [Tropheryma whipplei str.
           Twist]
 gi|28476520|gb|AAO44608.1| pseudouridylate synthase-like protein [Tropheryma whipplei str.
           Twist]
          Length = 303

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 136/313 (43%), Gaps = 29/313 (9%)

Query: 32  INFVNLQKILRSGQVR---VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           ++   + + +  G++    V  KR+  ++ + SG    +        H   E      SV
Sbjct: 1   MSRSCVARAISLGEITRQNVSDKRLTKSD-LASG----VYVWNRHALHTSGEDSAAPDSV 55

Query: 89  NLTKHSDF----------LKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWV 137
           + +   D               ++Y D  ++V +KPAG++     G     + G L   +
Sbjct: 56  HFSSTLDSCCLDPCASTRDLLRVIYSDDDLFVIDKPAGVAAHASPGWCGPTVTGCLSGLL 115

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + G + R  + HRLD  TSG++V+A++  A  +L  +FR R I K Y +LV G P    
Sbjct: 116 AACGPQDRQGIVHRLDANTSGLMVLAKSDLAYHNLKAAFRDRAIHKRYKALVQGYPDPSS 175

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   + +      D   +    +     A++ +   + +   F  L + P TGRTHQ+
Sbjct: 176 GVINAPIGRDLKH-RDRFCI----DYSGRDAVTQYSTEEVYP-GFTLLSVAPKTGRTHQI 229

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           RVH   +  P+VGD KY A+   +    +  + +LHA ++   HP  G  ++  + +   
Sbjct: 230 RVHFSALRHPLVGDVKYGADPVFSQKVNL-KRQWLHAYHLSFTHPVSGVFVEFESRIHED 288

Query: 315 MVKTWDSLGFKYD 327
           + ++   L   YD
Sbjct: 289 LQESLRILSKIYD 301


>gi|307705695|ref|ZP_07642541.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
 gi|307620709|gb|EFN99799.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
          Length = 278

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 72/294 (24%), Positives = 122/294 (41%), Gaps = 30/294 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++            E++I   + NL
Sbjct: 13  IPR-KIRHFLRIKKHILINQREVHWNEMVNPGDVCQLTFDEEDY----PEKEIPWGNPNL 67

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +         +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 68  IQE--------VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G   +K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNISSKELVFKDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             V     + K   YA +H   +  F  K   +  +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRV----VDTKNGQYAETHVSRLKQFPNKTSLVRCKLKTGRTHQIRVHLSHHNLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
            Y +  K        ++L LHA  +   HP    +L   A L     +     G
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLSFNA-LSDTFERELKKNG 278


>gi|227522610|ref|ZP_03952659.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
 gi|227090190|gb|EEI25502.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
          Length = 302

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 78/312 (25%), Positives = 134/312 (42%), Gaps = 25/312 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           ++    V    +   L R+  +HY  +    +  +    +V V+ + +  N  +     +
Sbjct: 5   WLFKTTVPQTMDGKPL-RYLLHHYWLLPKHLVFSLRSDERVLVNNRYLPVNFPVHFHDHI 63

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SG 124
            +  + +   H    Q + DS+  L          +LYED+ + V NK  G        G
Sbjct: 64  SLTFIPSDFQHPFP-QVLPDSAATL---------KILYEDANLIVINKRRGNKTHPNQPG 113

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                   L +++ +K   P + HRLDQETSG ++ A+  A    L      + I++ Y 
Sbjct: 114 EIGATINHLAAYLKTKEALPYMVHRLDQETSGAILFAKNPAVVPTLVAKIATKNIKRTYL 173

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           + V G   + +  I   +    +     +       K    +I+H+ V+      +  L 
Sbjct: 174 AWVVGTDIDSQGIIDFPIGLDPNDKRKRMIDGNHPAK----SITHYTVLQ-KEDGYSLLA 228

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH   +G P+VGD  Y  + K  F       L LH+  +++P P   +
Sbjct: 229 VQLETGRTHQIRVHLTAIGHPLVGDPLYNPDDKHPF-------LLLHSWKLNIPLPFSEQ 281

Query: 305 -LQITAPLPAHM 315
            ++ITAPLPAH 
Sbjct: 282 VIEITAPLPAHF 293


>gi|307709867|ref|ZP_07646315.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
 gi|307619357|gb|EFN98485.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
          Length = 278

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 70/280 (25%), Positives = 119/280 (42%), Gaps = 29/280 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++            E++I   + NL
Sbjct: 13  IPR-KIRHFLRIKKHILINQREVHWNETVNPGDVCQLTFDEEDY----PEKEIPWGNPNL 67

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +         +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 68  IQE--------VYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G   +K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNISSKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F  K   +  +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRI----VDAKHGQYAETHVNRLKQFPNKTSLVRCKLKTGRTHQIRVHLSHHNFPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
            Y +  K        ++L LHA  +   HP    RL   A
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLERLSFNA 265


>gi|301170223|emb|CBW29827.1| tRNA pseudouridine synthase [Haemophilus influenzae 10810]
          Length = 239

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 108/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAITDYEGLKIVEMPYPAGRYQTVRYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y    +     +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALISHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWHQLMNQFGWE 237


>gi|225019500|ref|ZP_03708692.1| hypothetical protein CLOSTMETH_03453 [Clostridium methylpentosum
           DSM 5476]
 gi|224947721|gb|EEG28930.1| hypothetical protein CLOSTMETH_03453 [Clostridium methylpentosum
           DSM 5476]
          Length = 299

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 74/302 (24%), Positives = 131/302 (43%), Gaps = 42/302 (13%)

Query: 34  FVNLQ---KILRS-----GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILD 85
              LQ   +I+R      G + +D    +  +  +SGQ +R+         +++  +   
Sbjct: 20  RRELQLSTRIIRQLKRIPGGITLDGMPARVTDSARSGQELRL---------LLQTGEASS 70

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-- 143
            S+            + YED  + + NKPAG  V    G   H +  L ++   +  +  
Sbjct: 71  QSIRPVPG----PFDIAYEDDDLLLVNKPAGTPVHPSPG---HYEDSLANYSAWQYAQRR 123

Query: 144 ----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                R  +RLD+ TSG+L VA+   A   L++       ++IY+++V G P      I 
Sbjct: 124 EQLVFRPVNRLDRGTSGLLCVAKNAHAQARLSQQLHTGAFERIYYAVVCGAPSPAAGTID 183

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + +            + + +GA  A++H++ +      +  L+++  TGRTHQ+RVH 
Sbjct: 184 LPIGRTPGSVLKR----RVDPQGAR-AVTHYETV-RVNGAYTLLKIRLETGRTHQIRVHF 237

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
            H+GCP+ GD  Y    +            LH+  + L HP  G  ++ + PLPA+M   
Sbjct: 238 AHLGCPLFGDFLYGTERRDVVEGH-----ALHSGEIRLLHPISGEEIRCSVPLPAYMENL 292

Query: 319 WD 320
            D
Sbjct: 293 MD 294


>gi|149007842|ref|ZP_01831438.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP18-BS74]
 gi|298229086|ref|ZP_06962767.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae str. Canada MDR_19F]
 gi|298254837|ref|ZP_06978423.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae str. Canada MDR_19A]
 gi|298501509|ref|YP_003723449.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|147760692|gb|EDK67665.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP18-BS74]
 gi|298237104|gb|ADI68235.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
          Length = 291

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 68/280 (24%), Positives = 115/280 (41%), Gaps = 29/280 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D S   
Sbjct: 26  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYSQKT 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 73  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 130 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 190 KRI----VDAKNGQYAETYVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNFPILGDP 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
            Y +N K        ++L LHA  +   HP    +L  TA
Sbjct: 246 LYNSNSKT-------SRLMLHAFRLSFTHPLTLEKLNFTA 278


>gi|255014662|ref|ZP_05286788.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_1_7]
          Length = 549

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 117/242 (48%), Gaps = 20/242 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               LNH+++  ++ ++ +    H +  K  +LYED  + + NKPAG+    G G A  +
Sbjct: 312 CEPILNHMLQGLQVDENPLLADSHRET-KLDILYEDDYLLIVNKPAGMLSVPGKGDADSV 370

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+         P + HRLD  TSG+L+ A+T+ A Q+L   F+ R IQK Y +L+ G
Sbjct: 371 YHRLRILY-PDATGPIIVHRLDMATSGLLLAAKTKEAHQNLQAQFKNRTIQKRYIALLEG 429

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I   L          +     +E+    A + ++V++  + K   +   P T
Sbjct: 430 EVPQDEGEIRLPLCPDPLDRPRQI----VSEEFGKPAFTRYRVLERTSGK-TLIAFYPQT 484

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVHA H   + CPI+GD  Y    +         +LYLHA Y+   HP    R+
Sbjct: 485 GRTHQLRVHAAHPLGLHCPILGDELYGRKAE---------RLYLHAEYLAFTHPITSERI 535

Query: 306 QI 307
           +I
Sbjct: 536 EI 537


>gi|256961078|ref|ZP_05565249.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis Merz96]
 gi|293384024|ref|ZP_06629918.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis R712]
 gi|293386837|ref|ZP_06631407.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis S613]
 gi|312908026|ref|ZP_07767009.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|312978446|ref|ZP_07790184.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
 gi|256951574|gb|EEU68206.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis Merz96]
 gi|291078504|gb|EFE15868.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis R712]
 gi|291083671|gb|EFE20634.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis S613]
 gi|310626117|gb|EFQ09400.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|311288595|gb|EFQ67151.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
          Length = 297

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 75/309 (24%), Positives = 135/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L K+  + G+++V+         +Q+G VV++               
Sbjct: 18  FLKEQ--GVSKGLLAKVKFQGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   +   +A + + +    AQ    + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAA-VRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGKMDQ-----GIERQALHCIELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKSVDDTL 297


>gi|312147848|gb|ADQ30507.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi JD1]
          Length = 326

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 73/342 (21%), Positives = 151/342 (44%), Gaps = 32/342 (9%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +   V+ +   +RLD +   ++       +++       + + K +K        
Sbjct: 1   MIRVKREFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK-------- 50

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++   +   + I+ E     S ++  + S+ +   ++YED  + V NKP GI    G
Sbjct: 51  --IKLSKPVFKDDEILIEFDEESSQIDCLRPSN-IPIAIIYEDFNVIVLNKPQGILSHPG 107

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                    + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + 
Sbjct: 108 ISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ +R  K+Y ++V G   +    I +++ +  H    +     +       A++ ++++
Sbjct: 167 FKDKRTNKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLL 222

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F + +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+ 
Sbjct: 223 LNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLKKIT---LMLHSY 277

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
            +++   +    +  +  P   V    +     + NL I  L
Sbjct: 278 KLEIDVGKNSFKKFISEFPKRFVIFLSNFYKSDELNLIIDNL 319


>gi|28572410|ref|NP_789190.1| pseudouridine synthase [Tropheryma whipplei TW08/27]
 gi|28410541|emb|CAD66927.1| putative pseudouridine synthase [Tropheryma whipplei TW08/27]
          Length = 303

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 136/313 (43%), Gaps = 29/313 (9%)

Query: 32  INFVNLQKILRSGQVR---VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           ++   + + +  G++    V  KR+  ++ + SG    +        H   E      SV
Sbjct: 1   MSRSCVARAISLGEITRQNVSDKRLTKSD-LASG----VYVWNRHALHTSGEDSAAPDSV 55

Query: 89  NLTKHSDF----------LKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWV 137
           + +   D               ++Y D  ++V +KPAG++     G     + G L   +
Sbjct: 56  HFSSTLDSCCLDPCASTRDLLRVIYSDDDLFVIDKPAGVAAHASPGWCGPTVTGCLSGLL 115

Query: 138 DSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + G + R  + HRLD  TSG++V+A++  A  +L  +FR R I K Y +LV G P    
Sbjct: 116 AACGPQDRQGVVHRLDANTSGLMVLAKSDLAYHNLKAAFRDRAIHKRYKALVQGYPDPSS 175

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   + +      D   +    +     A++ +   + +   F  L + P TGRTHQ+
Sbjct: 176 GVINAPIGRDLKH-RDRFCI----DYSGRDAVTQYSTEEVYP-GFTLLSVAPKTGRTHQI 229

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           RVH   +  P+VGD KY A+   +    +  + +LHA ++   HP  G  ++  + +   
Sbjct: 230 RVHFSALRHPLVGDVKYGADPVFSQKVNL-KRQWLHAYHLSFTHPVSGVFVEFESRIHED 288

Query: 315 MVKTWDSLGFKYD 327
           + ++   L   YD
Sbjct: 289 LQESLRILSKIYD 301


>gi|115374968|ref|ZP_01462239.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|115367995|gb|EAU66959.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
          Length = 272

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 83/289 (28%), Positives = 123/289 (42%), Gaps = 31/289 (10%)

Query: 47  RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
           RV+ + VK    + +GQ + +         +                      ++L+ED+
Sbjct: 2   RVNGRAVKKGLLVSAGQHILVEWEEETREAV---------------PDTGFPLVVLHEDA 46

Query: 107 KIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILV 159
            + V +KPAG        G    +   L +      Q      +  L HRLD ETSG+L+
Sbjct: 47  ALVVVDKPAGRPSHPLKPGETGTVANALIARYPECAQASEDAREGGLCHRLDIETSGVLL 106

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            ARTR A Q L  +F  R + K Y +LV G   ++ E      L+      D V      
Sbjct: 107 AARTREAWQRLRTAFSGREVDKHYVALVTGPLADEGEI--EIPLRHHPRHPDRVEPALPG 164

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E+GA  A S F+V       F  +E++  TG  HQ+R H   +G P+VGD  Y       
Sbjct: 165 EEGAREAHSLFQVQARSGD-FSLVEVRILTGVLHQVRAHLAGIGAPLVGDSLYGGR---- 219

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
              P  ++ +LHAR +   HPE G RLQ+ +PLP  + +     G   D
Sbjct: 220 -EEPGLSRFFLHARALGFTHPETGQRLQVESPLPQELAEVLRHHGLSAD 267


>gi|309973117|gb|ADO96318.1| tRNA U65 pseudouridine synthase [Haemophilus influenzae R2846]
          Length = 239

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 109/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDAFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K +      ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLTVVRGYLQGKAQIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|290893595|ref|ZP_06556577.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J2-071]
 gi|290556797|gb|EFD90329.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J2-071]
          Length = 289

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 131/319 (41%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT+V  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  G
Sbjct: 1   MTHV-TLPILEDWEGLSLTTILQEKF-HLGKKARHEIRMSQNVLLNNKPLDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P                   ++    +      ++YED  + V NKP  +     
Sbjct: 59  ASLSLPVF-----------------LHDKIPTYEYDLEIIYEDDFLLVVNKPVDMKTHAN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++  GQ       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEKTGQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y + V G      + I   + +  H G        Q       A++H KV++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDNEN 216

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L 
Sbjct: 217 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|116873677|ref|YP_850458.1| ribosomal large subunit pseudouridine synthase D [Listeria
           welshimeri serovar 6b str. SLCC5334]
 gi|116742555|emb|CAK21679.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria welshimeri serovar 6b str. SLCC5334]
          Length = 289

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 135/319 (42%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT++  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  G
Sbjct: 1   MTHL-TLPILEDWEGLTLTTILQEKF-HLGKKARHEIRMSHDVLLNNKPLDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P              IL   + + ++       ++YED  + V NKP G+     
Sbjct: 59  ASLSLPI-------------ILHDKIPVYEY----DLEIIYEDDFLLVVNKPVGMKTHPN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++   Q+      HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEKTDQEANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            + Y + V G      + I   + +  H G        Q       A++H KV++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDTEN 216

Query: 240 -FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y  + +        N++ LHA  + L 
Sbjct: 217 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGGSNRA-------NRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|325852028|ref|ZP_08171111.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
 gi|325484584|gb|EGC87500.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
          Length = 319

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 70/304 (23%), Positives = 121/304 (39%), Gaps = 34/304 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHIIK 79
           L  W   +    +   ++  L++  +RV+   V   +R +++G  V +            
Sbjct: 46  LLEWLLTNLKE-SKSKVKATLQNRGIRVNGSCVTQFDRQLKAGDKVSV------------ 92

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                 S              ++YED  + V  K  GI        + ++   L  +   
Sbjct: 93  ------SKSKKNGQFRSRYVKIVYEDRFLVVVEKNIGILSMAAGHASLNVKSILDDYFYK 146

Query: 140 KGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             QK    + HRLD++TSG+++ A+     Q     +      + Y  +V G  +  +  
Sbjct: 147 TRQKCTAHVVHRLDRDTSGLMIYAKDMQTEQLFEHDWHNIVYDRRYVGVVSGEMEQDEGT 206

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +ANWL         YV      + G  YA++HF V+D     +  +E +  TGR +Q+RV
Sbjct: 207 VANWL----KDNKAYVTYSSPVDNGGKYAVTHFHVLDRTV-AYSLVEYRLETGRKNQIRV 261

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
           H+  MG P+ GD KY             ++L LHA  +   HP    R++   P+PA   
Sbjct: 262 HSADMGHPVCGDVKYGNGDDP------LHRLCLHAYVLCFHHPVTHQRMEFETPVPAIFR 315

Query: 317 KTWD 320
             + 
Sbjct: 316 HLFK 319


>gi|282859371|ref|ZP_06268479.1| pseudouridine synthase, RluA family [Prevotella bivia JCVIHMP010]
 gi|282587856|gb|EFB93053.1| pseudouridine synthase, RluA family [Prevotella bivia JCVIHMP010]
          Length = 297

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 120/304 (39%), Gaps = 34/304 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIK 79
           L  W   +        ++  L++  ++V+ K V  F+++++ G  + I            
Sbjct: 24  LLAWLLANVGE-TKSKVKATLKNRGIKVNGKIVTQFDHQLKIGDKIAI------------ 70

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                 S              L+YED  + V  K  GI   G    + ++   L  +   
Sbjct: 71  ------SKSKKNDQFKSRYVKLVYEDKYLVVVEKNVGILSMGAGHASLNVKKVLDDYFHK 124

Query: 140 KGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             Q     + HRLD++TSG+++ A+     Q L   +      + Y +++ G   + +  
Sbjct: 125 TKQNCTAHVVHRLDRDTSGLMIYAKDMQTEQLLEHDWHNIVYDRRYIAVLSGEMADDEGT 184

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           IANWL         Y+      + G  YA++HF  ID        +E +  TGR +Q+RV
Sbjct: 185 IANWL----KDNKSYITYSSPVDNGGKYAVTHFFTIDR-TVNHSLVEFKLETGRKNQIRV 239

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
           HA  MG P+ GD KY              +L LHA  +   HP    R++   P+P    
Sbjct: 240 HAADMGHPVCGDIKYGNGDDP------IGRLCLHAFLLCFYHPVTHERMEFETPVPPMFR 293

Query: 317 KTWD 320
             + 
Sbjct: 294 HLFK 297


>gi|161507179|ref|YP_001577133.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DPC 4571]
 gi|160348168|gb|ABX26842.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DPC 4571]
          Length = 298

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 67/329 (20%), Positives = 127/329 (38%), Gaps = 43/329 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRS----GQVRVDKKRVKFNNRI 59
           MT +  +VV+  +   +L  +   +    +    Q ++++    G + V+ KR   +  +
Sbjct: 1   MTSLFKLVVQEKD-PKKLGSFLLKN--GFSH---QALIKARHHHGMILVNHKRRYLSFHL 54

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            +G  V         N  +K                      ++E     V NKPAG+  
Sbjct: 55  SAGDEVIFVSGEEKKNQFLK--------------PSNNPVDPVFETKNYIVLNKPAGVLS 100

Query: 120 QGGSGIAYH-IDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                     +   L  +    + K  KP +  RLD++TSG+++V +   A    ++  +
Sbjct: 101 IPSRYEDNDAVVNRLMGYFLQQNKKDLKPHVITRLDRDTSGLVLVGKNAIAHARFSKIGK 160

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              ++K + ++V G     +       +    IG +   V +        A + ++V+  
Sbjct: 161 DNFVKKYH-AIVHGNFAEDELT----GIIDEPIGKEGDGVKRAVVANGKKAQTRYRVLKQ 215

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             +    +E++  TGRTHQ+RVH  ++G P+ GD  Y  N          ++  L+  Y+
Sbjct: 216 V-EGASLVELRLLTGRTHQIRVHMAYLGHPLFGDPLYGINDN-------FSRQALNCFYL 267

Query: 296 DLPHPEGGR--LQITAPLPAHMVKTWDSL 322
             P P       +I    P  M K W  L
Sbjct: 268 AFPDPFDNERKQEIQIKDPEDMSKLWQKL 296


>gi|254510505|ref|ZP_05122572.1| ribosomal large subunit pseudouridine synthase A [Rhodobacteraceae
           bacterium KLH11]
 gi|221534216|gb|EEE37204.1| ribosomal large subunit pseudouridine synthase A [Rhodobacteraceae
           bacterium KLH11]
          Length = 215

 Score =  185 bits (471), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 69/224 (30%), Positives = 110/224 (49%), Gaps = 13/224 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++ T         +L+ED+++ V NKPAG+    G G   H+   L + V +   +  L 
Sbjct: 1   MSDTYDPPNTPLDVLFEDTQLIVVNKPAGLLSVPGRG--EHLADCLLTRVQAAFPQALLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG++V A+T  A +HL   F  R+ +K Y + VWG  + K   +   L+    
Sbjct: 59  HRLDRDTSGVMVFAQTPHAQRHLGLQFENRQTRKTYIARVWGRVEAKTGTVDLPLIVD-W 117

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  V     +    AI+ ++V+    +    + + P TGR+HQLRVH   +G PI+
Sbjct: 118 PNRPRQMVC---HETGKSAITDWRVVKYEGE-TTRIRLFPKTGRSHQLRVHMQALGSPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
           GD  Y       F      +L LH+  + L +PEGG  ++  AP
Sbjct: 174 GDPFYAEGPARAFP-----RLMLHSEELRLKNPEGGVSMKFRAP 212


>gi|152974818|ref|YP_001374335.1| RluA family pseudouridine synthase [Bacillus cereus subsp.
           cytotoxis NVH 391-98]
 gi|152023570|gb|ABS21340.1| pseudouridine synthase, RluA family [Bacillus cytotoxicus NVH
           391-98]
          Length = 307

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 128/320 (40%), Gaps = 32/320 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V +    + +  +       +    L ++     V V+ ++ +++  ++ G  +++ 
Sbjct: 11  EITVPSKWNGISI-EFLLREIWCVPKKILHQLRMGKSVIVNNEQKRWSELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             I     +I E               F +  +++ED  + + NKP  +           
Sbjct: 70  MFIPEEYGVIPE---------------FGELDVVFEDDHVLIVNKPEQMDTHPSEKNGTG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   + +    R I++ Y +
Sbjct: 115 TLANLIAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRLAGAIMDQLLMERNIKRTYMA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLE 244
           LV G  K +K  I   + +  H         K      + A++H+ V + F  Q    + 
Sbjct: 175 LVEGKMKKRKGTIDAAIGRDRHHATRRRVSPK-----GDRAVTHYTVEEYFKRQDTTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P++GD  Y  N          ++  LHA  +   HP    
Sbjct: 230 VQLETGRTHQIRVHMSYNGHPLLGDVLYGGNV------TYMSRQALHAMQIAFLHPITRE 283

Query: 304 RLQITAPLPAHMVKTWDSLG 323
            + +  P P  + K   S  
Sbjct: 284 EIIVDIPAPEKIDKLMQSFR 303


>gi|77412972|ref|ZP_00789175.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
 gi|77160984|gb|EAO72092.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
          Length = 342

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 63/291 (21%), Positives = 108/291 (37%), Gaps = 33/291 (11%)

Query: 25  FKNHYPHI---NFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K             ++  LR    V ++ + + +   +Q    + +             
Sbjct: 64  VKELLEDYFLIPR-KIRHFLRVKKHVLINNEFINWQTVVQENDTITLIFDDE-------- 114

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
               D                LYED  + + NKP G+   G      +    L       
Sbjct: 115 ----DYPTKKIPLGRAELIDCLYEDEHLIIVNKPEGMKTHGNQP---NEIALLNHVSAYS 167

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           GQ   + HRLD ETSG ++ A+       + +    + I + YW+LV G    K + + +
Sbjct: 168 GQTCYVVHRLDMETSGAVLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRD 227

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + K   +A++   V+    Q    ++ +  TGRTHQ+RVH  
Sbjct: 228 KIGRNRHDRRKRII----DSKNGQHAMTIIDVLKYI-QNSSLIKCRLETGRTHQIRVHLS 282

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           H G P++GD  Y  +           +L LHA  + L HP     + + AP
Sbjct: 283 HHGHPLIGDPLYNPSSNNE-------RLMLHAHRLTLSHPLTCETISVEAP 326


>gi|322487770|emb|CBZ23011.1| pseudouridylate synthase-like protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 414

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 89/358 (24%), Positives = 157/358 (43%), Gaps = 31/358 (8%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV---RVDKKR--VKFNNRIQ 60
            +QY VV  D    R+D +   H+P  ++  ++++++ G +   R + K+   +  +R++
Sbjct: 54  ELQYHVVTQDWFGQRVDDFVTQHHPEWDYETVKRLVQQGHIYRYRKNGKKRYTRLTDRLE 113

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNL--------------TKHSDFLKSILLYEDS 106
             ++V +P        +     +   S +                K  +  + ++L+++ 
Sbjct: 114 FDELVVVPTASFWERQLAPPSGVELQSSSTSQRQQERRQTFHLSAKAREMAQEMVLFKNE 173

Query: 107 KIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
            + V NKP+G+ +      +A +I   L +W  +  QKP + H LD ETSG +V+AR+  
Sbjct: 174 HVVVINKPSGVPIMPTHDPLAMNITDLLPAWRYTNTQKPIICHNLDTETSGCVVLARSSN 233

Query: 166 AAQHLTESFRMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
           A + L   F  R +   +YW    G P      I      +   GGD +         + 
Sbjct: 234 AHRMLGRMFVKRVVPNSVYWGFAVGKPPVNFGRIRMHFEVQKGQGGDVIVARPTPTADSK 293

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK-----G 278
             I+ F V     +   ++   P T R HQ R+ A H +  P++GD KY           
Sbjct: 294 VGIAEFVVNASALEFGSFISFYPLTTRRHQERIMAAHALRAPLLGDAKYGGESAFPHSLS 353

Query: 279 NFTSPIQN--KLYLHARYMDLPHPE--GGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            F  P +    L+LH R + LP+    G  + +TAPLP HM KT+  LG+  D +  +
Sbjct: 354 LFWDPARKDVPLHLHHRKIQLPYKNGAGEFVCVTAPLPPHMEKTFKRLGWPVDADDPL 411


>gi|51598281|ref|YP_072469.1| hypothetical protein BG0018 [Borrelia garinii PBi]
 gi|51572852|gb|AAU06877.1| conserved hypothetical protein [Borrelia garinii PBi]
          Length = 327

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 75/338 (22%), Positives = 140/338 (41%), Gaps = 33/338 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK--RVKFNNRIQSGQVV 65
           +   V+ +   +RLD +  N+        +++       + + K   +K +  +     +
Sbjct: 6   KEFTVKENA--LRLDLYLSNNLEVFTRSQIKRRNVEAFKKSNGKFFNIKLSKPVLKNDEI 63

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SG 124
            I            E    +SS       + +   ++YEDS I V NKP GI    G S 
Sbjct: 64  LI------------EFDEEESSQIDYLRPNNIPITIIYEDSNIIVLNKPQGILSHPGISH 111

Query: 125 IAYHIDGFLKSWV-------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               +  FL   +       + +  +P + HRLD++TSG+L+ A+       L + F+ +
Sbjct: 112 WDDTVVNFLLYHIKRLKINFNEEKVRPGIVHRLDKDTSGVLICAKNINTLSFLAQQFKDK 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           R  K+Y ++V G   +    I +++  +         V K        A++ ++++  F 
Sbjct: 172 RTNKVYIAIVKGNFNSFSGSIESFI-DRDKYNRKKFSVSKDR---GKKALTEYRLLLNF- 226

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  L ++P TGRTHQLRVH  ++  PI+GD  Y        T+     L LH+  +++
Sbjct: 227 RGYSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYGRVDSSFKTAT----LMLHSYKLEV 282

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
              +    +  +  P   V    +     + NL I  L
Sbjct: 283 DVGKNSFKKFISEFPKRFVIFLSNFYKSDELNLIIDNL 320


>gi|45658116|ref|YP_002202.1| ribosomal large subunit pseudouridine synthase C [Leptospira
           interrogans serovar Copenhageni str. Fiocruz L1-130]
 gi|45601358|gb|AAS70839.1| ribosomal large subunit pseudouridine synthase C [Leptospira
           interrogans serovar Copenhageni str. Fiocruz L1-130]
          Length = 394

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 76/375 (20%), Positives = 139/375 (37%), Gaps = 84/375 (22%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             +   ++  +E   RLD +    + + +    QK +  G++ +  K VK    ++ G +
Sbjct: 41  EELFQFLISKEESGTRLDHFLSKKFTYHSRTTWQKEITEGRILISSKTVKPGVSLKEGDL 100

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +   P       I KE+  + +              +LYED      +KP  + +     
Sbjct: 101 ISYHP-------IQKEEPPVRNDYK-----------ILYEDEFFVAVDKPGDLPIHPA-- 140

Query: 125 IAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +  G L +++   G  +     HRLD+ETSG+++ A+    A  L++SF +  IQK 
Sbjct: 141 -GIYRKGNLLTFLKESGKFKDLFTVHRLDRETSGVILFAKNSEIASILSKSFSLGNIQKY 199

Query: 183 YWSLVWGIPKNKK---ECIANWL---LKKSH-----------IGGDYVHVVKQNEKGANY 225
           Y + V G    +K     +   L   ++K                 Y+      EK    
Sbjct: 200 YITKVHGNFPKRKSAYGILKPDLSSKIRKKRTFVPLKFNFLKRNKKYLFENSLIEKQEEI 259

Query: 226 AISHFKVIDCF--------------------------------AQKFCWLEMQPHTGRTH 253
           ++++F+ I+                                     + +L  +P TGR H
Sbjct: 260 SLTYFQKIEYDKGRESKFKFSKIEFQFKNVNNEKIKSVFLDQEKDCYSFLLCKPITGRMH 319

Query: 254 QLRVHALHMGCPIVGDHKYCANFK-----------GNFTSPIQNKLYLHARYMDLPHPEG 302
           Q+R     +G P+ GD  Y  + K              T     +  LH+  + L HP  
Sbjct: 320 QIRATLFSLGFPLFGDKLYGKDEKVFLEFIEGKNPDLTTRLGMKRQALHSYAVCLNHPVT 379

Query: 303 -GRLQITAPLPAHMV 316
             +++ITAP+P   +
Sbjct: 380 NQKMKITAPIPEDFL 394


>gi|315149952|gb|EFT93968.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0012]
          Length = 297

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 74/309 (23%), Positives = 134/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L K+  + G+++V+         +Q+G VV++               
Sbjct: 18  FLKEQ--GVSKGLLAKVKFQGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   +   +A + +  +     K   + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETGQFASTEYW-LAKRGAKAAAVRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGEMDQ-----GIERQALHCMELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKSVDDTL 297


>gi|312953695|ref|ZP_07772531.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|310628369|gb|EFQ11652.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|315151826|gb|EFT95842.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0031]
          Length = 297

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 75/309 (24%), Positives = 135/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L K+  + G+++V+         +Q+G VV++               
Sbjct: 18  FLKEQ--GVSKGLLAKVKFQGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKLTKIYYALVGGAIEQLS 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   +   +A + + +    AQ    + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAA-VRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGKMDQ-----GIERQALHCMELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKSVDDTL 297


>gi|257465425|ref|ZP_05629796.1| tRNA pseudouridine synthase C [Actinobacillus minor 202]
 gi|257451085|gb|EEV25128.1| tRNA pseudouridine synthase C [Actinobacillus minor 202]
          Length = 242

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 60/243 (24%), Positives = 105/243 (43%), Gaps = 18/243 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   NKPAG+ V             +++  D  GQ     HRLD+ TSG
Sbjct: 1   MLLDILYQDDDLIAINKPAGMLVHRSWLDKAETVFVMQTLRDQIGQHVFPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ + E F   +++K Y ++V G  + K        +    +   +    
Sbjct: 61  VLLFALNSDMARTMCELFENHQVKKGYLAVVRGYLEGKARVDYPLKVILDKVADKFSQ-- 118

Query: 217 KQNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              EK    AI+ ++ +               ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 ---EKEPQEAITDYQGLATVEMPYPAGKFQTARYSLVELSPQTGRKHQLRRHLKHLFHPI 175

Query: 267 VGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD KY    +    +      +L LH+ +M   HP+   +++I APL     + +    
Sbjct: 176 MGDTKYGDLHQNRTLAEQSGVERLMLHSHFMQFQHPKTLQKIEIKAPLDQQWRQLFTFFN 235

Query: 324 FKY 326
           + +
Sbjct: 236 WNF 238


>gi|71083779|ref|YP_266499.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter ubique HTCC1062]
 gi|91763185|ref|ZP_01265149.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter ubique HTCC1002]
 gi|71062892|gb|AAZ21895.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter ubique HTCC1062]
 gi|91717598|gb|EAS84249.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter ubique HTCC1002]
          Length = 304

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 85/316 (26%), Positives = 153/316 (48%), Gaps = 20/316 (6%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V++   +MR+DRW +N+  +     ++K L+SG+V+++ K++K ++++++G  + +    
Sbjct: 7   VDSTFNDMRIDRWIRNNLGNYPQGLIEKSLKSGKVKINNKKIKSSHKVKTGDTIDLFNFD 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                + K  K + S   + ++ +     ++  +    V NK +GISVQGG+    ++  
Sbjct: 67  FKETIVQKTIKFVPSEEVIKENEEL----IIDNNDDFIVLNKSSGISVQGGTKSKKNLVD 122

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                   +  KP   HRLD++TSG+ ++A+ R +AQ LT  FR+R++ K Y ++  G  
Sbjct: 123 IFARSEIFQDTKPFSVHRLDKDTSGVFIMAKHRQSAQLLTSLFRLRKVHKTYLAICHGEL 182

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           +       + L +  +   D   V K        A + +KV+D  +     +EM+P TGR
Sbjct: 183 QKDSGEWNDDLTRYDN---DREVVEK--------ARTLYKVLDKNS-ICSLVEMKPITGR 230

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
            HQLR     +GCPI GD KY      N    I   L LH+  +        +   TA L
Sbjct: 231 KHQLRKQLYAVGCPIYGDQKY---KFSNTDKAINKNLMLHSYQIKF-MINDKKYTYTALL 286

Query: 312 PAHMVKTWDSLGFKYD 327
           P +  K   +   ++ 
Sbjct: 287 PDYFKKLLKTKRLRFP 302


>gi|56807621|ref|ZP_00365521.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Streptococcus
           pyogenes M49 591]
          Length = 218

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 103/229 (44%), Gaps = 18/229 (7%)

Query: 104 EDSKIYVFNKPAGISVQG--GSGIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGI 157
           ED  + + NKP G+ V    G      ++  +    D        +P + HR+D++TSG+
Sbjct: 1   EDDTLAIINKPQGMVVHPSVGHPSGTMVNALMYHIKDLSSINGVVRPGIVHRIDKDTSGL 60

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VA+T AA Q L E  + ++  + Y ++V G   N +  I   + +            K
Sbjct: 61  LMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEKDRKKQAVTAK 120

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A++ F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y     
Sbjct: 121 -----GKEAVTRFTVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGDPLYGPR-- 172

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
               +   +  +LHA+ + L HP  G  +  T   P    K    L  K
Sbjct: 173 ---KTLSGHGQFLHAKTLGLTHPMTGKEMIFTVEAPEIFQKVLKLLRKK 218


>gi|302346727|ref|YP_003815025.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
 gi|302151131|gb|ADK97392.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
          Length = 296

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 75/307 (24%), Positives = 131/307 (42%), Gaps = 40/307 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIK 79
           L  W   +    +   ++  L++  ++V+ K V  F++ +++G  +              
Sbjct: 23  LLEWLLANLNE-SKSKVKATLQNRGIKVNGKCVTQFDHPLKAGDKI-------------- 67

Query: 80  EQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                  SV+ +K +D  +S    ++YED  + V  K  GI        + ++   L  +
Sbjct: 68  -------SVSKSKKNDLFRSRYVKIVYEDRFLVVIEKNIGILSMAAGHSSLNVKTVLDDY 120

Query: 137 VDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                QK    + HRLD++TSG+++ A+     Q L   +      + Y ++V G  ++ 
Sbjct: 121 FRKTKQKCTAHVVHRLDRDTSGLMIYAKDIQTEQLLEHDWHNIVYDRRYVAVVSGEMEHD 180

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  IANWL         YV      + G  YA++HF V+D        +E Q  TGR +Q
Sbjct: 181 EGTIANWL----KDNKSYVTYSSPVDNGGKYAVTHFHVLDRTV-AHSLVEYQLETGRKNQ 235

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
           +RVH+  MG P+ GD KY             ++L LHA  +   HP    R++   P+P 
Sbjct: 236 IRVHSADMGHPVCGDIKYGNGDDP------LHRLCLHAYVLCFHHPVTHQRMEFETPVPQ 289

Query: 314 HMVKTWD 320
                + 
Sbjct: 290 VFRHLFK 296


>gi|256848967|ref|ZP_05554401.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus MV-1A-US]
 gi|295692522|ref|YP_003601132.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|312977754|ref|ZP_07789501.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus CTV-05]
 gi|256714506|gb|EEU29493.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus MV-1A-US]
 gi|295030628|emb|CBL50107.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|310895493|gb|EFQ44560.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus CTV-05]
          Length = 301

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 70/325 (21%), Positives = 127/325 (39%), Gaps = 35/325 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT +  ++V+  +         KN + H    N +     G + V+ KR   +  +++G 
Sbjct: 1   MTSLFKLIVQERDPKKLGPFLLKNGFSHQALNNAKH--HHGMILVNHKRRYTSFNLRAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V         N  +K                     ++ E+    V NKPAG+      
Sbjct: 59  EVIFISGEEKKNDFLK--------------PSNNPVSIVLENKNYLVVNKPAGVLSIPSR 104

Query: 124 G-IAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                 +   L  +   KGQK   P +  RLD++TSG+++V +   +    ++  + + +
Sbjct: 105 YEDDDAVVNRLLGYFAQKGQKNLKPHVITRLDRDTSGLVLVGKNAISHARFSKIGKEKFV 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K + ++V G     +       L    IG     V +        A + ++V+D     
Sbjct: 165 KKYH-AIVHGNFAPNELT----GLIDQPIGKKGSGVKRAVVADGKDAQTAYRVLDQVT-G 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E++  TGRTHQ+RVH  ++G P+ GD  Y             ++  L+  Y++ P 
Sbjct: 219 ASLVELRLLTGRTHQIRVHMAYLGHPLYGDPLYG-------IQDGFSRQALNCFYLNFPD 271

Query: 300 PEGGRLQITAPL--PAHMVKTWDSL 322
           P   +   T  L  P  M + W  L
Sbjct: 272 PFSQQKCKTIELNDPKDMQELWQKL 296


>gi|217963594|ref|YP_002349272.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes HCC23]
 gi|217332864|gb|ACK38658.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes HCC23]
 gi|307571830|emb|CAR85009.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes L99]
          Length = 289

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 131/319 (41%), Gaps = 37/319 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT+V  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  G
Sbjct: 1   MTHV-TLPILEDWEGLSLTTILQEKF-HLGKKARHEIRMSQNVLLNNKPLDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P                   ++    +      ++YED  + V NKP  +     
Sbjct: 59  ASLSLPVF-----------------LHDKIPTYEYDLEIIYEDDFLLVVNKPVDMKTHAN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++  GQ       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEKTGQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ- 238
            + Y + V G      + I   + +  H G        Q       A++H KV++   + 
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDNEK 216

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L 
Sbjct: 217 NTSLVECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLN 269

Query: 299 HP-EGGRLQITAPLPAHMV 316
           HP +G  +  +AP     V
Sbjct: 270 HPFKGKEMNFSAPAGDDWV 288


>gi|328957083|ref|YP_004374469.1| pseudouridylate synthase [Carnobacterium sp. 17-4]
 gi|328673407|gb|AEB29453.1| pseudouridylate synthase [Carnobacterium sp. 17-4]
          Length = 303

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 63/303 (20%), Positives = 124/303 (40%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L KI    G++ V++  V     ++   +V++               
Sbjct: 18  FLKT--KGISRSLLAKIKFHGGKIEVNETEVTVRYLLKDKDIVQVT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
           I D + + T     +   ++YED    V NKP G++         H +G + + V     
Sbjct: 62  IPDEAPHETTVPINIPIDIVYEDDHYLVVNKPYGVASVPSQ---VHPEGTMANRVKGYYV 118

Query: 142 ------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 Q   +  RLD++T+G+++ A+   A   +    R + I K Y +L+ G     +
Sbjct: 119 RQNYADQVIHIVTRLDRDTTGLMLFAKHGYAHALMDAKLRAKEITKKYTALISGQLDKAE 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
               +  + ++        + ++  +    A++ + +   F Q    +++Q HTGRTHQ+
Sbjct: 179 HGFIDAPIARTTDS----IITRRAHESGKEALTEYWIKGSFPQ-ATLVDIQLHTGRTHQI 233

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAH 314
           RVH  H+G P++GD  Y              +  LH R ++  HP    ++ +    P  
Sbjct: 234 RVHFTHIGHPLMGDDLYGGEKNN-----WITRQALHCRELNFSHPFTNEQINLELGYPED 288

Query: 315 MVK 317
           + +
Sbjct: 289 ITQ 291


>gi|222153833|ref|YP_002563010.1| RNA pseudouridylate synthase [Streptococcus uberis 0140J]
 gi|222114646|emb|CAR43689.1| RNA pseudouridylate synthase [Streptococcus uberis 0140J]
          Length = 294

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 69/287 (24%), Positives = 118/287 (41%), Gaps = 29/287 (10%)

Query: 25  FKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I    ++  LR    + ++ + V + N++Q+G  + +                
Sbjct: 25  LLEKHLLIPR-KIRHFLRIKKHILINHQMVNWQNQVQTGDHITLIFDEE----------- 72

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
            D    +    D      LY+D  + V NKP G+           +   + ++V   G+ 
Sbjct: 73  -DYPSKVIAFGDPKLVDCLYQDEHLIVVNKPEGMKSHANQPDELALLNHVSAYV---GKT 128

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLD+ETSG ++ A+       +      R I + YW+ V G  K KK  I   + 
Sbjct: 129 CYIIHRLDKETSGTILFAKNPFILPIMNRMLENRDISRTYWAFVSGTIKEKKLTIQKPIG 188

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +  H     V  +KQ +K    AI+  K +   +  F  +E    TGRTHQ+RVH   +G
Sbjct: 189 RHRHDRRKRVVDMKQGQK----AITIVKKLKNDSSSFTLVECHLKTGRTHQIRVHMDAIG 244

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
            P+ GD  Y  +           +L LHA+ ++  HP     +++ A
Sbjct: 245 HPLKGDPLYAPHLP-------YERLMLHAQQLEFTHPLNLETIRVKA 284


>gi|304437126|ref|ZP_07397088.1| ribosomal large subunit pseudouridine synthase D [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369885|gb|EFM23548.1| ribosomal large subunit pseudouridine synthase D [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 294

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 62/295 (21%), Positives = 120/295 (40%), Gaps = 37/295 (12%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
           H   I+    ++I   G   ++    V     ++ G  +                   D 
Sbjct: 22  HVHGISGSLWRRIKHHGAFTLNGIPAVAARTMLKDGDWI-----------------AYDL 64

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKP- 144
            +  +   + L   ++YED  + V +KPAG  V   +   +  I   ++ +  + G    
Sbjct: 65  PIVSSVIPESLPLSIIYEDDDLLVLDKPAGQLVHPTTKETHGTIANAVRGYYAACGVHLD 124

Query: 145 -RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD+ TSG+L++A+       + +      +++ Y +L+ G     + CI   + 
Sbjct: 125 FHPCHRLDRNTSGLLLIAKHPEVQYQIAQQ---NTLKREYLALIAGSLTPPEGCIDVPIA 181

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +          +++        A +H+  +    + +  L +Q  TGRTHQ+RVH  H+G
Sbjct: 182 RALP-----SIILRCVSTEGKSACTHYVTVQTDGR-YSLLRLQLDTGRTHQIRVHLAHLG 235

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVK 317
            P++GD  Y              +  LH+ ++ L HP   ++  ++A LPA M +
Sbjct: 236 HPLLGDDLYGGTRAE------IARHALHSAHLTLVHPRTKKMLALSALLPADMAR 284


>gi|145634988|ref|ZP_01790695.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittAA]
 gi|145267854|gb|EDK07851.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittAA]
          Length = 239

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 106/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP G+ V       +     +++  D  GQ     H LD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPDGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHCLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWHQLINQFGWE 237


>gi|229078576|ref|ZP_04211134.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|228704720|gb|EEL57148.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
          Length = 307

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 130/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            ++V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EIIVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                   +  E               + +  ++YED  + V NKP  +       G   
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLVVNKPEQMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGKIDAAIGRDRHHATRRRISSK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P ++ K     
Sbjct: 284 AIEVDVPFPTNLNKKIKEF 302


>gi|224532212|ref|ZP_03672844.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia valaisiana VS116]
 gi|224511677|gb|EEF82083.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia valaisiana VS116]
          Length = 326

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 74/337 (21%), Positives = 151/337 (44%), Gaps = 32/337 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V+ +   +RLD +  ++   +    +++       + + K +K          +++
Sbjct: 6   REFTVKENA--LRLDLYLSSNLEVLTRSQIKRRNVEAFKKSNGKFLK----------IKL 53

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----- 122
              +   + I+ E     S ++  + ++ +   ++YEDS I V NKP GI    G     
Sbjct: 54  SKPVFKDDEILIEFDEEISQIDCLRPNN-IPIAIIYEDSNIIVLNKPQGILSHPGISHWD 112

Query: 123 ----SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + FR +R
Sbjct: 113 DTVVNFLLYHIKS-LKIDFNGEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFRDKR 171

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             K+Y ++V G   +    I +++ +  H    +     +       +++ ++++  F  
Sbjct: 172 TNKVYIAIVKGNFNSFSGSIESFIDRDKHNRKKFAVSKDR----GKKSLTEYRLLLNFG- 226

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+  +++ 
Sbjct: 227 GYSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLKKIT---LMLHSYKLEID 282

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
             +    +  +  P   V  + +     + NL I  L
Sbjct: 283 VGKNSFEKFISEFPKRFVNFFGNFYKSDELNLIIDNL 319


>gi|71908482|ref|YP_286069.1| tRNA pseudouridine synthase C [Dechloromonas aromatica RCB]
 gi|71848103|gb|AAZ47599.1| tRNA pseudouridine synthase C [Dechloromonas aromatica RCB]
          Length = 242

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 105/240 (43%), Gaps = 17/240 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +LY D  + V +KP+G+ V       +     ++   D  GQ+    HRLD+ TSG+
Sbjct: 4   ELPILYRDEHVVVIDKPSGLLVHRSEIDRHETRFAIQILRDQIGQRVWPAHRLDRGTSGV 63

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+     A A  L + F    ++K YW++V G P      I + L ++      Y    +
Sbjct: 64  LLFGLNPAMASQLGKQFEQGTVEKAYWAVVRGYPPA-SGSIDHPLTRQRDP---YEFKGE 119

Query: 218 QNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           Q    A  A++HF+ +             + ++  LE++P TGR HQ+R H  H+  PI+
Sbjct: 120 QCSTEAQPALTHFRKLAEIELPVEVDRYPSSRYALLELEPITGRRHQIRRHLKHLAHPII 179

Query: 268 GDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
           GD  Y       + +     ++L L    +   HP  G RL I  P+      T    G+
Sbjct: 180 GDATYGKGRHNRYFAEQLGCHRLLLACIRLSFNHPVTGLRLDIKTPVSGEFAATLARFGW 239


>gi|307128211|ref|YP_003880242.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 670-6B]
 gi|306485273|gb|ADM92142.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 670-6B]
          Length = 278

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 68/280 (24%), Positives = 114/280 (40%), Gaps = 29/280 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D     
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYPQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNFPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
            Y +N K        ++L LHA  +   HP    +L  TA
Sbjct: 233 LYNSNSKT-------SRLMLHAFRLSFTHPLTLEKLNFTA 265


>gi|169349798|ref|ZP_02866736.1| hypothetical protein CLOSPI_00536 [Clostridium spiroforme DSM 1552]
 gi|169293366|gb|EDS75499.1| hypothetical protein CLOSPI_00536 [Clostridium spiroforme DSM 1552]
          Length = 278

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 76/299 (25%), Positives = 135/299 (45%), Gaps = 43/299 (14%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
              + N  N++ +L+   V V++  + +F+  ++ G VV +              K  D+
Sbjct: 16  LLNYYNKKNVKNLLKYKLVMVNENVISQFDFPLKIGDVVIVN-------------KKEDN 62

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----IAYHIDG-FLKSWVDSKG 141
             NL          ++YED ++ V NKP+G+    G       AYH+ G +LK+   +K 
Sbjct: 63  KHNLE---------IIYEDKELIVINKPSGLLSISGGNEKEKTAYHLVGEYLKN--KNKK 111

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            K  + HRLD++TSG+L+ A+       L  ++     ++ Y +++ G  K K   I N+
Sbjct: 112 AKVFVIHRLDKDTSGVLMFAKNEEIKNKLQNNWNKIVYKRGYLAIIEGRLKEKSGTIKNY 171

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L +          V   N K    AI++++V+    +    +E+   TGR +Q+RVH   
Sbjct: 172 LDES-----KTQMVYITNNKKGKLAITNYRVLK-ETKYNSLVEIFLDTGRKNQIRVHMQS 225

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
           +G  I+GD KY A      T+    ++ LH+      HP+   ++   A  P    K +
Sbjct: 226 LGHSIIGDKKYGA------TTNPIKRMALHSHVFAFVHPDTKKKMIFEAKYPEEFKKIF 278


>gi|157878817|ref|XP_001687420.1| pseudouridylate synthase-like protein [Leishmania major strain
           Friedlin]
 gi|321438079|emb|CBZ11831.1| pseudouridylate synthase-like protein [Leishmania major strain
           Friedlin]
          Length = 413

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 87/358 (24%), Positives = 155/358 (43%), Gaps = 30/358 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV---RVDKKR--VKFNNRI 59
             +QY VV  D    R+D +   H+P  ++  ++++++ G +   R + K+   +  +R+
Sbjct: 53  NELQYHVVTQDWFGQRVDDFVTQHHPEWDYETVKRLVQQGHIYRYRKNGKKRYTRLTDRL 112

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNL-------------TKHSDFLKSILLYEDS 106
           +  ++V +P        +     +   S +               K  +  + ++L+++ 
Sbjct: 113 EFDELVVVPTASFWERQLAPPSGVELQSSSTSQQQERRQKFHLSAKTREMAQEMVLFKNE 172

Query: 107 KIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
            + V NKP+G+ +      +A +I   L +W  +  Q P + H LD ETSG +V+AR+  
Sbjct: 173 HVIVINKPSGVPIMPTHDPLAMNITDLLPAWRYTNTQTPVICHNLDTETSGCVVLARSAN 232

Query: 166 AAQHLTESFRMRRI-QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
             + L   F  R +   +YW    G P      I      +   GGD +         + 
Sbjct: 233 THRMLGRMFVKRVVPNSVYWGFAVGKPPVNFGRIRMHFEVQKGQGGDVIVARPTPTADSK 292

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK-----G 278
             I+ F V     +   ++   P T R HQ R+ A H +  P++GD KY           
Sbjct: 293 VGIAEFVVNASALEFGSFISFYPLTTRRHQERIMAAHALRAPLLGDAKYGGESAFPHSLS 352

Query: 279 NFTSPIQN--KLYLHARYMDLPHPE--GGRLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            F  P +    L+LH R + LP+    G  + +TAPLP HM KT+  LG+  D +  +
Sbjct: 353 LFWDPARKDVPLHLHHRKIQLPYKNGAGEFVCVTAPLPPHMEKTFKRLGWPVDADDPL 410


>gi|150008790|ref|YP_001303533.1| ribosomal large subunit pseudouridine synthase A [Parabacteroides
           distasonis ATCC 8503]
 gi|149937214|gb|ABR43911.1| ribosomal large subunit pseudouridine synthase A [Parabacteroides
           distasonis ATCC 8503]
          Length = 549

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 77/254 (30%), Positives = 121/254 (47%), Gaps = 27/254 (10%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L+H+++  ++ ++ +    H +  K  +LYED  + V NKP G+    G G A  +
Sbjct: 312 CEPILHHMLQGLRVDENPLLADSHRET-KLDILYEDDYLLVINKPEGMLSVPGKGDADSV 370

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L      +   P + HRLD  TSG+L+ A+T+ A Q+L   F+ R IQK Y +L+ G
Sbjct: 371 YQRLSILY-PEATGPIIVHRLDMATSGLLLAAKTKEAHQNLQAQFKNRTIQKRYIALLEG 429

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I   L          +     +E+    A++H++V++  + K   +   P T
Sbjct: 430 EVPQDEGEIRLPLCPDPLDRPRQI----VSEEFGKPALTHYRVLERTSGK-TLIAFYPQT 484

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVHA H   + CPI+GD  Y    +         +LYLHA Y+   HP    R+
Sbjct: 485 GRTHQLRVHAAHPLGLHCPILGDELYGRKAE---------RLYLHAEYLAFTHPITSERI 535

Query: 306 QIT-------APLP 312
           +I         P+P
Sbjct: 536 EIQKSPAFPRCPMP 549


>gi|125718992|ref|YP_001036125.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK36]
 gi|125498909|gb|ABN45575.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Streptococcus sanguinis SK36]
          Length = 299

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 73/316 (23%), Positives = 128/316 (40%), Gaps = 33/316 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   ++SG  + +
Sbjct: 12  TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLAINWQTVVKSGDDICL 69

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+          
Sbjct: 70  IFDEEDY----PQKTILFGNGELVEE--------LYQDQHLIIVNKPEGMKTHANEPTEL 117

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+LV
Sbjct: 118 ALLNHVSAYV---GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLEKREISREYWALV 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +KK    + + +  H     +     + +   YA +H   +  F Q    ++ Q 
Sbjct: 175 QGKFPSKKLIYKDKIGRDRHDRRKRL----VDPRKGLYAETHVTRVKQFGQ-AALVKCQL 229

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G P++GD  Y    KG        +L LHA  +   HP    ++ 
Sbjct: 230 KTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG--------RLMLHAHRLIFTHPFTLEKIT 281

Query: 307 ITAPLPAHMVKTWDSL 322
           + A    +  K   SL
Sbjct: 282 VEA-CSDNFEKVLSSL 296


>gi|270293651|ref|ZP_06199853.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|270275118|gb|EFA20978.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 511

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 68/238 (28%), Positives = 111/238 (46%), Gaps = 17/238 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ +            ++YED  + V NKPAG+    G   A  +
Sbjct: 278 CEPILQHMLQGLQVEENPMLKRMQVPSQNLEIVYEDPWLSVINKPAGMLSVPGKEDAVSV 337

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++     +   P   HRLD  TSG++++A+T+   Q+L   F+ R ++K Y +L+ G
Sbjct: 338 YSLMREQY-PEADGPLTVHRLDMATSGLMLIAKTKRVHQNLQAQFKNRLVRKRYVALLEG 396

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I    K  +   L        D    +   E G   AI+ ++V++    K   +   P T
Sbjct: 397 IVPKDKGTVDLPLCLNPL---DRPRQMVHTEHG-KPAITDYQVLERLDGKRTRIAFYPRT 452

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GRTHQLR+HA H   + CPI+GD  Y             ++LYLHA Y++  HP  G 
Sbjct: 453 GRTHQLRIHAAHPLGLHCPIIGDELYGEK---------ADRLYLHAEYLEFTHPITGE 501


>gi|90962428|ref|YP_536344.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|90821622|gb|ABE00261.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
          Length = 304

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 73/317 (23%), Positives = 128/317 (40%), Gaps = 28/317 (8%)

Query: 4   MTYVQYV-VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQS 61
           M+  ++   V  +   + L       +  +    +  + +R   V++D K    N  +Q 
Sbjct: 1   MSKYKFERTVNAEFSGISLRALLSEKWL-LPRKFIHFLRIRE-NVKIDGKYYPMNTIVQG 58

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            Q + +          I E     ++ +        K  +++E+  + V NKP GI    
Sbjct: 59  NQKIEL----------IFEGDEFRTATSNYIVDKGRKIPIIFENDDLLVVNKPQGIKSHP 108

Query: 122 GSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                   +  ++  ++D++ + P + HRLD  TSG ++VA+       LT       I+
Sbjct: 109 NQPYETGTLVNYIAGYLDARDEHPYMVHRLDMLTSGAMIVAKNPVVVPILTRLISTHTIK 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++  GI   K+  I   + K  +         K +  GA  A + ++VI  F    
Sbjct: 169 RDYLAITEGIFDQKEGVIDLPIGKDENDKRKR----KVDGIGALPARTRYQVIKEFENNS 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
               ++  TGRTHQLRVH   MG PIVGD  Y    +       +  + LH     L  P
Sbjct: 225 VVY-LRLETGRTHQLRVHLSAMGHPIVGDVLYNHVSE-------EKHMMLHGYKQKLTLP 276

Query: 301 EGGR-LQITAPLPAHMV 316
              R L++ A +P +  
Sbjct: 277 FSMRELELKADIPEYFA 293


>gi|227484931|ref|ZP_03915247.1| possible RluA protein [Anaerococcus lactolyticus ATCC 51172]
 gi|227237086|gb|EEI87101.1| possible RluA protein [Anaerococcus lactolyticus ATCC 51172]
          Length = 328

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 64/304 (21%), Positives = 125/304 (41%), Gaps = 29/304 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  +V+  ++ N R DR+ + ++ +     + K +R    +++ KR K N+ +  G +++
Sbjct: 1   MIEIVISKNQANQRFDRFLRKYFENAPLSVISKNIRKKNFKINDKRAKNNDFVNEGDIIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          + +        +L          ++YED  I + +K  G      S   
Sbjct: 61  MYITDENYKKWLTKTDFKPVDFDLD---------IIYEDDNILIMDKKCGELTHAASNKD 111

Query: 127 YHIDGF--LKSWVDSKG--------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           Y  +    + S++   G         KP + +RLD+ T+G+++ A+     + L ++ R 
Sbjct: 112 YGNNLVDKMNSYLYKTGSFDMSDRTFKPAVVNRLDRNTAGLIIGAKNSETLRILNDAIRE 171

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I K Y ++V G  KN  +         ++I  +      +  +     +++FK ++  
Sbjct: 172 NSIDKYYLTIVVGKVKNNFKI-------DTYISKNENKNKVKKCEEGKNILTYFKPLETN 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARY 294
             KF  LE +  TGRTHQ+R      G PI+GD KY               N   L +  
Sbjct: 225 G-KFSLLECKLITGRTHQIRYSLKENGTPIIGDRKYGIKSINEEIRNKFGINNQVLLSYK 283

Query: 295 MDLP 298
           +  P
Sbjct: 284 LVFP 287


>gi|320546661|ref|ZP_08040973.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equinus ATCC 9812]
 gi|320448716|gb|EFW89447.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equinus ATCC 9812]
          Length = 296

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 67/305 (21%), Positives = 122/305 (40%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K H   ++   L K+  + G + V+         +  G VV I              +
Sbjct: 16  FLKGH--DVSKGLLAKVKFKGGNIWVNGVEQNAIYLLDEGDVVTI--------------E 59

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D   + T         + YED    + NKP G +       +  I  F+K++   +  
Sbjct: 60  IPDEQEHETLIPVKHDLNIAYEDEHFLILNKPYGYASIPSILHSNTIANFVKNYYLEQNY 119

Query: 143 ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
              +  +  RLD+ TSG+++ A+   A   L +  + + I+K Y++LV G      +  I
Sbjct: 120 PNKQVHIVTRLDKNTSGLMLFAKHGYAHARLDKQLQNKTIEKRYYALVSGQGDLADEGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      +   + ++      YA + +KV++ F      ++++ HTGRTHQ+RVH
Sbjct: 180 IAPIARD-----EDSIITRRVHPSGKYAHTSYKVVEKFGD-VALVDIRLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
             H+G P++GD  Y        T     +  LH  Y+   +P     +  +  L      
Sbjct: 234 FSHIGFPLLGDDLYGGRMDLGIT-----RQALHCHYLRFVNPYTNEEIIQSTNLTDDFDS 288

Query: 318 TWDSL 322
               L
Sbjct: 289 VIIEL 293


>gi|227432332|ref|ZP_03914325.1| 23S rRNA pseudouridylate synthase RluD [Leuconostoc mesenteroides
           subsp. cremoris ATCC 19254]
 gi|227351938|gb|EEJ42171.1| 23S rRNA pseudouridylate synthase RluD [Leuconostoc mesenteroides
           subsp. cremoris ATCC 19254]
          Length = 299

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 65/286 (22%), Positives = 123/286 (43%), Gaps = 34/286 (11%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G + V+++ V  ++ +++G +V I       N ++                D+    +++
Sbjct: 37  GAILVNERTVYTSDYLKNGDIVTIVMPTEKSNDLV--------------VPDYKPLDIIF 82

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHID-----GFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           E+    V +KP GI+   G     H       G L++ + +    P +  RLD++TSGI+
Sbjct: 83  ENEHWLVVDKPYGITTVPGHADRLHTLVNQVKGHLET-IKADDLVPHVVTRLDRDTSGIV 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+ R A   L +  +   ++K Y +   GI       I   + +   + GD++    +
Sbjct: 142 LLAKHRFAHAVLDQQLQDHTVEKFYLAYPSGILAYDHGDINAPIGR---MDGDFIKREVR 198

Query: 219 NEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           ++     + + + V   +    Q    +++Q HTGRTHQ+RVH  ++G P+VGD  Y   
Sbjct: 199 DD--GKPSRTEYWVERRYEDDEQNMTRVKVQLHTGRTHQIRVHFANIGHPLVGDTLYGGP 256

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWD 320
                      +  LHA +M    P      +   PLP  +    D
Sbjct: 257 AWHGL-----QRQALHAYHMKFYDPFIEEYREFNTPLPDDLKTLRD 297


>gi|229166225|ref|ZP_04293984.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228617170|gb|EEK74236.1| Pseudouridine synthase [Bacillus cereus AH621]
          Length = 307

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 66/319 (20%), Positives = 127/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  +    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EITVPATWNGISIESLLKMEW-EVPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E               + +  +++ED  + + NK   +           
Sbjct: 70  MFMEEEYGVEPE---------------YGELNVVFEDDHVLIINKQGQMDTHPSEKNGTG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYMA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEKYFKKQNATLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y         +   +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQ------TTYMSGQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            + +  P P ++  T    
Sbjct: 284 EIVVDVPFPTNLNDTMKKF 302


>gi|311063909|ref|YP_003970634.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           bifidum PRL2010]
 gi|310866228|gb|ADP35597.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           bifidum PRL2010]
          Length = 313

 Score =  185 bits (469), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 126/326 (38%), Gaps = 31/326 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V   +     R D         I+      ++ SGQ RV  + +  +  +  G+ V  
Sbjct: 3   RLVPAPDALVGSRFDVAVSKML-GISRAKAADLIESGQARVLNRAIAKSGTLLYGETVEF 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                     I E++     V        L   ++YED  + V +KP G++    +G   
Sbjct: 62  D---------IAEERHEPEPV-------CLDMAIVYEDDDVVVVDKPVGVAAHASAGWTG 105

Query: 128 HID--GFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                  LK  V         +  +  RLD  TSG+++V ++  A + +   F    + K
Sbjct: 106 PTVLGSLLKRGVRITSYGAPGRQGIVSRLDVGTSGLMLVCKSELAYKEMRRQFSEHEVVK 165

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G  K  K  I   + +                     A++H+ V+D F +   
Sbjct: 166 TYHAMVQGNLKEDKATIEAPIGR-----AKVSDFRFCVTPSGKPAVTHWDVLDRFGE-AT 219

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +   TGRTHQ+RVH   +G P+VGD  Y AN          ++ +LHA  ++  HP 
Sbjct: 220 LVSVNLETGRTHQIRVHFSSIGHPLVGDPMYGANPVL-AGELGLDRQWLHAMKLEFRHPR 278

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFKY 326
                 + +  PA +    + +  ++
Sbjct: 279 THLWTSVESHYPADLAHALELMRARH 304


>gi|160888881|ref|ZP_02069884.1| hypothetical protein BACUNI_01301 [Bacteroides uniformis ATCC 8492]
 gi|156861780|gb|EDO55211.1| hypothetical protein BACUNI_01301 [Bacteroides uniformis ATCC 8492]
          Length = 511

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 68/238 (28%), Positives = 111/238 (46%), Gaps = 17/238 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ +            ++YED  + V NKPAG+    G   A  +
Sbjct: 278 CEPILQHMLQGLQVEENPMLKRMQVPSQNLEIVYEDPWLSVINKPAGMLSVPGKEDAVSV 337

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++     +   P   HRLD  TSG++++A+T+   Q+L   F+ R ++K Y +L+ G
Sbjct: 338 YSLMREQY-PEADGPLTVHRLDMATSGLMLIAKTKRVHQNLQAQFKNRLVRKRYVALLEG 396

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I    K  +   L        D    +   E G   AI+ ++V++    K   +   P T
Sbjct: 397 IVPKDKGTVDLPLCLNPL---DRPRQMVHTEHG-KPAITDYQVLERLDGKRTRIAFYPRT 452

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GRTHQLR+HA H   + CPI+GD  Y             ++LYLHA Y++  HP  G 
Sbjct: 453 GRTHQLRIHAAHPLGLHCPIIGDELYGEK---------ADRLYLHAEYLEFTHPITGE 501


>gi|240949614|ref|ZP_04753949.1| tRNA pseudouridine synthase C [Actinobacillus minor NM305]
 gi|240295872|gb|EER46548.1| tRNA pseudouridine synthase C [Actinobacillus minor NM305]
          Length = 242

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 61/243 (25%), Positives = 106/243 (43%), Gaps = 18/243 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   NKPAG+ V             +++  D  GQ     HRLD+ TSG
Sbjct: 1   MMLEILYQDEDLIAINKPAGMLVHRSWLDKAETVFVMQTLRDQIGQHVFPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ + E F   +++K Y ++V G  + K        +    +   +    
Sbjct: 61  VLLFALNSDMARTMCELFENHQVKKGYLAIVRGYLEGKARVDYPLKVILDKVADRFSQ-- 118

Query: 217 KQNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              EK    AI+ ++ +               ++  +E+QP TGR HQLR H  H+  PI
Sbjct: 119 ---EKEPQEAITDYQGLATVEMPYPAGKFQTARYSLVELQPQTGRKHQLRRHLKHLFHPI 175

Query: 267 VGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD KY    +    +      +L LH+ +M   HP+   +++I APL     + +    
Sbjct: 176 MGDTKYGDLHQNRTLAEQSGVERLMLHSHFMQFQHPKTLQKIEIKAPLDQQWRQLFTFFN 235

Query: 324 FKY 326
           + +
Sbjct: 236 WNF 238


>gi|238019027|ref|ZP_04599453.1| hypothetical protein VEIDISOL_00889 [Veillonella dispar ATCC 17748]
 gi|237864511|gb|EEP65801.1| hypothetical protein VEIDISOL_00889 [Veillonella dispar ATCC 17748]
          Length = 322

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 76/330 (23%), Positives = 135/330 (40%), Gaps = 44/330 (13%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M   T +  ++V+++     ++   K    HI+    +++  +G + V+ +   +N  + 
Sbjct: 24  MKTATIID-LIVDSNVHTQSMNHIIKQQ--HISQRMRRRLRNNGIITVNDEPASWNTLVH 80

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +         +  EQ+   S ++L          ++YED  I V NK AGI + 
Sbjct: 81  GGDHLVM--------KLTPEQEFSLSPMDLD---------IVYEDEYILVINKEAGILMH 123

Query: 121 GGSGIAYHI--DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             S +  H   +G L  +  + +       HRLD++TSGI+++A+T        +  +  
Sbjct: 124 PTSTVRDHTLANGVLHYYQQTNQHYDFHPVHRLDKDTSGIVIIAKTSVVQHAFDK--KRT 181

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              K Y ++V G        +   + +K    G  +     NE     A +   VI+   
Sbjct: 182 HFHKNYDAIVEGQLPTNHISVQWPIGRKP---GSIIERCCTNE--GKPAHTDITVIESNT 236

Query: 238 -------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
                  Q F  ++   HTGRTHQ+RVH   +G P+ GD  Y  +           +  L
Sbjct: 237 IVKNKIEQCFTHVQCLLHTGRTHQIRVHLSQLGYPLAGDDLYGGHLD------YIGRQAL 290

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           HA  +   HP     L+I A +P+ M    
Sbjct: 291 HASRISFYHPMTDEWLEIQASIPSDMESLL 320


>gi|163939199|ref|YP_001644083.1| RluA family pseudouridine synthase [Bacillus weihenstephanensis
           KBAB4]
 gi|163861396|gb|ABY42455.1| pseudouridine synthase, RluA family [Bacillus weihenstephanensis
           KBAB4]
          Length = 307

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 66/319 (20%), Positives = 127/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  +    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EITVPATWNGISIESLLKMEW-EVPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E               + +  +++ED  + + NK   +           
Sbjct: 70  MFMEEEYGVEPE---------------YGELNVVFEDDHVLIVNKQGQMDTHPSEKNGTG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEKYFKKQNATLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y         +   +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQ------TTYMSGQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            + +  P P ++  T    
Sbjct: 284 EIVVDVPFPTNLNDTMKKF 302


>gi|306830219|ref|ZP_07463402.1| ribosomal large subunit pseudouridine synthase [Streptococcus mitis
           ATCC 6249]
 gi|304427586|gb|EFM30683.1| ribosomal large subunit pseudouridine synthase [Streptococcus mitis
           ATCC 6249]
          Length = 278

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 70/303 (23%), Positives = 123/303 (40%), Gaps = 31/303 (10%)

Query: 23  RWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           ++ +     I    ++  LR    + ++ + V +N  ++SG + ++             +
Sbjct: 5   QFLEEQLL-IPR-KIRHFLRIKKNILINHEEVHWNEMVKSGDICQLTFDEEDY----PPK 58

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           +IL    +L +         +Y+D  + V NKP G+   G       +   + S+V   G
Sbjct: 59  EILWGKPDLVQE--------VYQDQYLIVVNKPEGMKTHGNQPDEIALLNHVSSYV---G 107

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               + HRLD ETSG+++ A+       L      + I + YW+LV G   +K+    + 
Sbjct: 108 HTCYVVHRLDMETSGLVLFAKNPFILPILNRLLEKKEIAREYWALVEGQVGSKELIFRDK 167

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +  H     V     + K   +A +    +  F  K   +  +  TGRTHQ+RVH  H
Sbjct: 168 IGRDRHDRRKRV----VDPKNGQHAETQVSRLKQFPNKTSLVRCKLKTGRTHQIRVHLSH 223

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWD 320
              PI+GD  Y +  K        ++L LHA  +   HP    +   TA L     +   
Sbjct: 224 HKHPILGDPLYNSQSKT-------SRLMLHAFRLSFTHPLTLEKFSFTA-LSDTFERELK 275

Query: 321 SLG 323
             G
Sbjct: 276 KNG 278


>gi|322386603|ref|ZP_08060228.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           cristatus ATCC 51100]
 gi|321269276|gb|EFX52211.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           cristatus ATCC 51100]
          Length = 296

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 70/304 (23%), Positives = 122/304 (40%), Gaps = 32/304 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + +      M +    +     I    ++  LR    + V+ + + +   ++ G  +++
Sbjct: 4   TITIPASLPPMTVKELLEEQLL-IPR-KIRHFLRTKKHILVNGESIHWQTLVKPGDSIQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       E+++     +L +         LY+D  + + NKP G+   G      
Sbjct: 62  TFDKEDY----PEKELPAGHPHLVEE--------LYQDEHLIIVNKPNGMKSHGNEPTEV 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + S+V   GQ   + HRLD+ETSG ++ A+       L      + I + YW+L 
Sbjct: 110 ALLNHVSSYV---GQTCYVVHRLDKETSGAILFAKNPFVLPILNRLLENKEISREYWALA 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +K     + + +  H     +     + K   YA +H   +  F      ++ Q 
Sbjct: 167 QGKFHSKTIVYKDKIGRDRHDRRKRL----VDPKKGLYAETHVTRLKDFG-NTTLVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G PIVGD  Y    +G        +L LHA  + L HP     + 
Sbjct: 222 KTGRTHQIRVHLAHHGHPIVGDPLYHPQPQG--------RLMLHAHRLTLTHPFTLETIS 273

Query: 307 ITAP 310
           + AP
Sbjct: 274 VEAP 277


>gi|90962453|ref|YP_536369.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|301299242|ref|ZP_07205529.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|90821647|gb|ABE00286.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|300853202|gb|EFK80799.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 296

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 127/315 (40%), Gaps = 34/315 (10%)

Query: 14  NDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             +E M L ++ KN    H    +L+K   +G+V VD K+   +  +  G++  I P   
Sbjct: 8   ESDEKMTLKKFLKNKGVSHRTLSSLKK--GNGKVLVDGKKRSLSIEVGKGKITLILPPEK 65

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDG 131
           +  ++   ++ LD               ++YEDS   V +KP  +S   G S     +  
Sbjct: 66  SDENVKMSKEPLD---------------IIYEDSNWLVVDKPPLLSSVPGPSNRTDTLVN 110

Query: 132 FLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +K  +  +  K   P +  RLD++TSG+++VA+ R A   + +      I K Y ++V 
Sbjct: 111 RVKFHLWQQKSKDLVPHVITRLDRDTSGLVLVAKHRFAQGLINKQVEEHSIDKKYLAVVE 170

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           GI   K   I   L  + +  G  V            A + + V +    K   +E + H
Sbjct: 171 GIITEKHGIIDKPLGPRENGIGQMV------TDTGKIAKTEYWVREYLGDKATLVECKLH 224

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-I 307
           TGRTHQ+R H   +   +VGD  Y              +  LHA  +    P     +  
Sbjct: 225 TGRTHQIRAHFSSINHALVGDELYGGRLDWGLE-----RQALHAYQLAYVDPFTQEEKLF 279

Query: 308 TAPLPAHMVKTWDSL 322
            + +P  +      L
Sbjct: 280 KSEMPKDLENLIVRL 294


>gi|229132186|ref|ZP_04261043.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
 gi|228651234|gb|EEL07212.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
          Length = 307

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 66/319 (20%), Positives = 127/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  +    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EITVPATWNGISIESLLKMEW-EVPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E               + +  +++ED  + + NK   +           
Sbjct: 70  MFMEEEYGVEPE---------------YGELNVVFEDDHVLIVNKQGQMDTHPSEKNGTG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDKAITYYKVEKYFKKQNATLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y         +   +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQ------TTYMSGQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            + +  P P ++  T    
Sbjct: 284 EIVVDVPFPTNLNDTMKKF 302


>gi|170751707|ref|YP_001757967.1| pseudouridine synthase [Methylobacterium radiotolerans JCM 2831]
 gi|170658229|gb|ACB27284.1| pseudouridine synthase [Methylobacterium radiotolerans JCM 2831]
          Length = 224

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 71/228 (31%), Positives = 118/228 (51%), Gaps = 12/228 (5%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            + + LLY D+ + V +KPAG+ V  G      +   L +      ++P   HRLD++TS
Sbjct: 6   DIGARLLYRDALLLVIDKPAGLPVHPGPRGGETLTDHLDALRFGLPRRPEAAHRLDRDTS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L + R   A   L + F    ++K YW++V G P  ++  I   L ++S    D    
Sbjct: 66  GCLALGRHAKALARLGKLFSGSAVEKTYWAIVAGGPAGEEGSIDLPLARRS---DDPRSW 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             + +   + +++H++V+   A    WLE++P TGRTHQLRVH    G PI+GD  Y   
Sbjct: 123 WMKADPAGDPSLTHWRVLGR-AGGRTWLELKPVTGRTHQLRVHCAASGWPILGDAVYGGA 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSL 322
            +G+        L+LHAR + +P +P+   + +TAP P H+ +   ++
Sbjct: 182 PRGSA-------LHLHARALSIPLYPKRDAIAVTAPPPPHIAEAVAAM 222


>gi|254361102|ref|ZP_04977247.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261495410|ref|ZP_05991858.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|153092588|gb|EDN73643.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261308915|gb|EEY10170.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
          Length = 242

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 63/245 (25%), Positives = 107/245 (43%), Gaps = 18/245 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D+ +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MTLDILYQDNSLIAINKPAGVLVHRSWLDKHETVFAMQTLRDQIGQHVFPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A+ ++E F    +QK Y ++V G  +   +      +    I   +    
Sbjct: 61  VLLFALNSETARIMSEQFEQHLVQKTYLAVVRGYLQGSAQIDYPLKVILDKIADKFSQ-- 118

Query: 217 KQNEKGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              EK A  AI+ +K          V      ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 ---EKEAQAAITDYKGLATVEMPYPVGKHQTSRYSLVELSPKTGRKHQLRRHLKHLFHPI 175

Query: 267 VGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD KY    +          ++L LHA  +   HP+   +++I A L     + +    
Sbjct: 176 MGDSKYGDLHQNRALVEKSGVSRLMLHAHKLQFQHPKNLQKIEIIASLDEQWQRLFAFFD 235

Query: 324 FKYDR 328
           + + +
Sbjct: 236 WNFTQ 240


>gi|255974981|ref|ZP_05425567.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T2]
 gi|307285489|ref|ZP_07565628.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
 gi|255967853|gb|EET98475.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T2]
 gi|306502713|gb|EFM71978.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
          Length = 297

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 73/309 (23%), Positives = 133/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       ++   L K+  + G+++V+         +Q+G VV++               
Sbjct: 18  FLNEQ--GVSKGLLAKVKFQGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLS 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   +   +A + +  +     K   + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETGQFASTEYW-LAKRGAKAAAVRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGKMDQ-----GIERQALHCMELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKSVDDTL 297


>gi|228938507|ref|ZP_04101115.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228971386|ref|ZP_04132012.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228977999|ref|ZP_04138378.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228781660|gb|EEM29859.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228788253|gb|EEM36206.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228821105|gb|EEM67122.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|326939015|gb|AEA14911.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar chinensis CT-43]
          Length = 307

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 126/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EITVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                   +  E               + +  ++YED  + + NKP  +           
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEKMDTHPAEKGGTG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLEAKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      N AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKGKQGTIDAAIGRDRHHATRRRISPK-----GNQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P  +       
Sbjct: 284 AIEVDVPFPTKLDNKIREF 302


>gi|329117419|ref|ZP_08246136.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
 gi|326907824|gb|EGE54738.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
          Length = 297

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 66/298 (22%), Positives = 121/298 (40%), Gaps = 30/298 (10%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L K+  R G++ V+++       +    +V I               I D    
Sbjct: 21  DVSKGLLAKVKYRGGKILVNEQEQNATYLLDINDIVTIH--------------IPDELPF 66

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL 146
               +      ++YED    V NKP G +    +  +  I  F+K++    D   ++  +
Sbjct: 67  EKLEAVSHPLDIVYEDEHFLVINKPFGFASIPSAIHSNTIANFIKAYYIEKDYPNKQVHI 126

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKK 205
             RLD++TSG+++ A+   A   L +  + R I K Y++LV G  +      I   + + 
Sbjct: 127 VTRLDRDTSGLMLFAKHGYAHARLDKQLQARSIDKHYYALVSGPGQLPDSGEIIAPIGRS 186

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                    + +  +    YA + ++V+  FA+    ++++ HTGRTHQ+RVH  H+G P
Sbjct: 187 -----KDSIITRAVDPMGKYAKTTYQVVGRFAENVHLVDIKLHTGRTHQIRVHFSHIGFP 241

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA-PLPAHMVKTWDSL 322
           ++GD  Y        T     +  LH   ++   P   +    A  L          L
Sbjct: 242 LLGDDLYGGRIDLGIT-----RQALHCHSLNFYDPFTEKESKHAIDLTDDFENVIIDL 294


>gi|229010681|ref|ZP_04167879.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
 gi|228750575|gb|EEM00403.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
          Length = 307

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 66/319 (20%), Positives = 127/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  +    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EITVPATWNGISIESLLKVEW-EVPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E               + +  +++ED  + + NK   +           
Sbjct: 70  MFMEEEYGVEPE---------------YGELNVVFEDDHVLIVNKQGQMDTHPSEKNGTG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYMA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEKYFKKQNATLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y         +   +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQ------TTYMSGQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            + +  P P ++  T    
Sbjct: 284 EIVVDVPFPTNLNDTMKKF 302


>gi|146296964|ref|YP_001180735.1| RluA family pseudouridine synthase [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145410540|gb|ABP67544.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 292

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 80/273 (29%), Positives = 134/273 (49%), Gaps = 21/273 (7%)

Query: 58  RIQ-SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK--SILLYEDSKIYVFNKP 114
           +++ +GQ+  IPP+ +   H   E  I     ++  +   +K    +L+ED      NKP
Sbjct: 33  KLKSNGQIRFIPPIFSINQHPTVESIIELELKDVYSNIVPIKGSIDILFEDQFFLFVNKP 92

Query: 115 AGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           +GI      G  +  +   ++ +++S+G    + +RLD++TSGI+V A+       ++  
Sbjct: 93  SGIPSHPSKGHYFDTLANNVEWYLNSQGVTSHIINRLDKDTSGIVVFAKNSYFHSIVSSE 152

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  R I+K Y ++V GI   K   I   + + +        + ++  +  +YAI++++V+
Sbjct: 153 FEKRTIEKTYIAVVDGILTKKSGFIEKPISRSND------GIKREINEDGDYAITYYEVV 206

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D     +  L+++P TGRTHQLRVH   +G PIVGD  Y      NF       L LHA 
Sbjct: 207 DYK-NNYSILKLKPITGRTHQLRVHLASIGYPIVGDVLYGTGKNKNFP------LLLHAY 259

Query: 294 YMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
            M        R   ITAPLP +  +    LGF+
Sbjct: 260 SMKFDFKLIERQYNITAPLPPYFSEF---LGFE 289


>gi|189424176|ref|YP_001951353.1| pseudouridine synthase [Geobacter lovleyi SZ]
 gi|189420435|gb|ACD94833.1| pseudouridine synthase, RluA family [Geobacter lovleyi SZ]
          Length = 300

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 70/331 (21%), Positives = 140/331 (42%), Gaps = 46/331 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +    +  D+   RL+ W +   P       +K+++SG   ++  +   +  + +G ++ 
Sbjct: 1   MLTYTITADDHCRRLESWLQRLLPTALPAYCRKLIKSGACTLNGTKSSPDTLLSAGAIIS 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      L  + +    +D               LL++D ++   NKPAG+++   + + 
Sbjct: 61  LKESGQVLELLNRPLPPID---------------LLWQDDRLLAINKPAGLAMHPAAEVD 105

Query: 127 YHIDGFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            ++     +W++ K   P      +RLD+ TSG++++A + + A  L    +   + KIY
Sbjct: 106 ENLADIASAWLEKKANYPVRAYPVNRLDRGTSGVVLLATSSSNAGILGRQVKEEGLDKIY 165

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V G+ +   E I+  L                       +IS ++ +    +   +L
Sbjct: 166 LTVVEGMLEGIGE-ISQPL-------------------DGKESISRYRSL-SVGESCSFL 204

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++P TGRTHQ+R H   +G P++GD +Y A             + LH+    L HP   
Sbjct: 205 LVEPVTGRTHQIRRHLSAIGHPVLGDKRYDAQPLATLP-----GIALHSFRTRLQHPTPE 259

Query: 304 -RLQITAPLPAHMVKT-WDSLGFKYDRNLYI 332
            RL + APLP  + +   +  G      L +
Sbjct: 260 TRLTLCAPLPTALRELIIERCGIDEKELLDL 290


>gi|225861831|ref|YP_002743340.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|225728075|gb|ACO23926.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|327389005|gb|EGE87352.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA04375]
          Length = 278

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 68/280 (24%), Positives = 115/280 (41%), Gaps = 29/280 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D S   
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYSQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETYVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNFPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
            Y +N K        ++L LHA  +   HP    +L  TA
Sbjct: 233 LYNSNSKT-------SRLMLHAFRLSFTHPLTLEKLNFTA 265


>gi|23098304|ref|NP_691770.1| hypothetical protein OB0849 [Oceanobacillus iheyensis HTE831]
 gi|22776530|dbj|BAC12805.1| hypothetical conserved protein [Oceanobacillus iheyensis HTE831]
          Length = 303

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 73/297 (24%), Positives = 129/297 (43%), Gaps = 32/297 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +      + +  +++ IL  GQV VD     K N  +  G  VRI     A+   +    
Sbjct: 29  FLLKVMDNRSRNSVKSILTRGQVSVDDHIETKHNFMLNKGSTVRILKNKAAIQQDV---- 84

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-DGFLKSWVDSK- 140
                        F+   ++YED  I V  K +G+          H     L  +V  + 
Sbjct: 85  -------------FVGMSIMYEDDDIIVIEKESGLLSIATEKERKHTALHQLMHYVKQQH 131

Query: 141 -GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +  + HRLD++TSG+++ A+     + L  +++    ++ Y +LV G    +K  I 
Sbjct: 132 PANRVYVVHRLDKDTSGVMMFAKNERVKRKLQNNWKDIVKERTYVALVEGQVAKEKGYIV 191

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WL K+S     Y   VK +      A + ++V+     ++  LE+Q  TGR +Q+RVH 
Sbjct: 192 SWL-KESATRKMYSSRVKND---GQRAATRYRVLQTN-NRYSLLELQLETGRKNQIRVHM 246

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHM 315
             +G P+VGD +Y +  +      +  +L LHA+ +   HP   +L    + +P   
Sbjct: 247 EELGHPVVGDKRYGSKGRS-----VIGRLGLHAKILSFYHPVTNKLMLFRSDVPNAF 298


>gi|301299198|ref|ZP_07205485.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300853158|gb|EFK80755.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 304

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 73/317 (23%), Positives = 129/317 (40%), Gaps = 28/317 (8%)

Query: 4   MTYVQYV-VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQS 61
           M+  ++  +V  +   + L       +  +    +  + +R   V++D K    N  +Q 
Sbjct: 1   MSKYKFERIVNAEFSGISLRALLSEKWL-LPRKFIHFLRIRE-NVKIDGKYYPMNTIVQG 58

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
            Q + +          I E     ++ +        K  +++E+  + V NKP GI    
Sbjct: 59  NQKIEL----------IFEGDEFRTATSNYIVDKGRKIPIIFENDDLLVVNKPQGIKSHP 108

Query: 122 GSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                   +  ++  ++D++ + P + HRLD  TSG ++VA+       LT       I+
Sbjct: 109 NQPYETGTLMNYIAGYLDARDEHPYMVHRLDMLTSGAMIVAKNPVVVPILTRLISTHTIK 168

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y ++  GI   K+  I   + K  +         K +  GA  A + ++VI  F    
Sbjct: 169 RDYLAITEGIFDQKEGVIDLPIGKDENDKRKR----KVDGIGALPARTRYQVIKEFENNS 224

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
               ++  TGRTHQLRVH   MG PIVGD  Y    +       +  + LH     L  P
Sbjct: 225 VVY-LRLETGRTHQLRVHLSAMGHPIVGDVLYNHVSE-------EKHMMLHGYKQKLTLP 276

Query: 301 EGGR-LQITAPLPAHMV 316
              R L++ A +P +  
Sbjct: 277 FSMRELELKADIPEYFA 293


>gi|257126587|ref|YP_003164701.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
 gi|257050526|gb|ACV39710.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
          Length = 314

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 130/307 (42%), Gaps = 26/307 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + VVV+++ E MRLDR+ + ++       +   +R+G V+V+ K+ K N R+     + I
Sbjct: 4   KEVVVDSEMEGMRLDRYLRKNFKDEPLSRIFGAIRAGDVKVNGKKSKENYRLALNDTIVI 63

Query: 68  PPVINALNHIIK--EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
             + +      K  E+  L          +  K ++++E+   ++ NK   I +  G+G 
Sbjct: 64  KNLFSENFDNKKSFEKNNLKKIQIQKSDLEKYKKMIIFENEDFFIVNKSEKIPMHKGTGH 123

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            Y +    K     K +     +RLD ETSG+++  +     +++++  R   IQK Y++
Sbjct: 124 KYGLAEVFKEIF--KNENINFANRLDFETSGLVIGCKNLKFLRYISQKIRDNEIQKKYFA 181

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK-------------- 231
           +V  I  N +  I       +      +       K +  +I++FK              
Sbjct: 182 IVHNIKNNIESKIFKIENYLTTTENKVIVSENPISKDSKKSITNFKKILISELKNTKKIL 241

Query: 232 -VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
            +++   +    L++   TGR HQ+R    H   PIVGD KY             NK +L
Sbjct: 242 DLLEKNNKNVFLLDVDLVTGRKHQIRAQLAHQKIPIVGDKKYG-------IQDGSNKFFL 294

Query: 291 HARYMDL 297
              ++  
Sbjct: 295 CCYFLSF 301


>gi|307710900|ref|ZP_07647326.1| RNA pseudouridylate synthase family protein [Streptococcus mitis
           SK321]
 gi|307617256|gb|EFN96430.1| RNA pseudouridylate synthase family protein [Streptococcus mitis
           SK321]
          Length = 278

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 67/279 (24%), Positives = 119/279 (42%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V++N  +  G + ++            E++I   + NL
Sbjct: 13  IPR-KIRHFLRIKKHILINQREVRWNEVVNPGDICQLTFDKEDY----PEKEIPWGNPNL 67

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +         +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 68  VQE--------VYQDQHLVIVNKPEGMKTHGNQPNETALLNHVSAYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+ V G   +K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWAQVDGYINSKEIVFKDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F  K   +  +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRI----VDTKNGQYAETHVSRLKQFPNKTSLVRCKLKTGRTHQIRVHLSHHDLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    +L  T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFT 264


>gi|91223469|ref|ZP_01258734.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           12G01]
 gi|91191555|gb|EAS77819.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           12G01]
          Length = 256

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 64/252 (25%), Positives = 108/252 (42%), Gaps = 17/252 (6%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
            LT+ S+ ++  ++Y+D      NKPAG+ V       +     +++  D  GQ     H
Sbjct: 5   ELTRSSEPVELEIVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLH 64

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG+LV A +   A  +   F   +++K Y ++V G  + +        ++   I
Sbjct: 65  RLDRPTSGVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVELDKI 124

Query: 209 GGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVH 258
              +       EK A  A++ +K +               ++C +EM+P TGR HQLR H
Sbjct: 125 ADKFASQ----EKEAQEAVTEYKPLAKVEVPYSTGKFPTTRYCLVEMKPKTGRKHQLRRH 180

Query: 259 ALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
             H+  PIVGD  +          T    ++L LHA  +   HP     + +TA L    
Sbjct: 181 MAHLRHPIVGDTTHGDGKHNKLYRTEFESHRLLLHASELRFVHPFTDQEIVMTANLDETW 240

Query: 316 VKTWDSLGFKYD 327
            + +    +   
Sbjct: 241 QQLFTRFEWDES 252


>gi|229101991|ref|ZP_04232704.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
 gi|228681378|gb|EEL35542.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
          Length = 307

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 130/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  +    L ++     V V+ ++ ++N  ++ G   ++ 
Sbjct: 11  EITVPAKWNGISIESLLKVEW-ELPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKFQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFMEEEYGVEPE---------------YGELHVVYEDDHVLIVNKPEKMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K KK  I   + +  H         K +E     AI+++KV   F      ++ 
Sbjct: 175 LVEGKVKKKKGTIEAAIGRDRHHATRRRVSPKGDE-----AITYYKVEKYFKKHNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  H G P+VGD  Y         +   +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQ------TTYMSGQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            ++I  P PA +  T    
Sbjct: 284 EIEIDVPFPAKLNNTMKEF 302


>gi|313622709|gb|EFR93062.1| ribosomal large subunit pseudouridine synthase D [Listeria innocua
           FSL J1-023]
          Length = 288

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 76/309 (24%), Positives = 129/309 (41%), Gaps = 36/309 (11%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72
            D E + L    +  + H+      +I  S  V ++ K +  +N  +  G  + +P    
Sbjct: 9   EDWEGLTLTAILQEKF-HLGKKARHEIRMSQDVLLNNKPLDDWNTPLFVGASLSLPI--- 64

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDG 131
                     IL   + + ++       ++YED  + V NKP G+      S        
Sbjct: 65  ----------ILHDKIPVYEY----DLEIIYEDDFLLVVNKPVGMKTHANDSYETDTCAN 110

Query: 132 FLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            ++ +++  GQ+      HRLDQ TSG+++ A+ + A   L+     R I + Y + V G
Sbjct: 111 AVQYYLEKTGQEANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPH 248
                 + I   + +  H G        Q       A++H KV++   +     +E Q  
Sbjct: 171 TWGLVMQKINKPIGEDRHHGSRR-----QISPYGQPAVTHVKVLENDNENNTSLVECQIE 225

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
           TGRTHQ+RVH   +G PI+GD  Y  + +        N++ LHA  + L HP  G  +  
Sbjct: 226 TGRTHQIRVHLSGIGHPIIGDTLYGGSSRA-------NRIMLHAEKLHLNHPFIGKEMNF 278

Query: 308 TAPLPAHMV 316
           +AP     V
Sbjct: 279 SAPAGDDWV 287


>gi|77409155|ref|ZP_00785868.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
 gi|77172239|gb|EAO75395.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
          Length = 342

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 108/291 (37%), Gaps = 33/291 (11%)

Query: 25  FKNHYPHI---NFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K             ++  LR    V ++ + + +   +Q    + +             
Sbjct: 64  VKELLEDYFLIPR-KIRHFLRVKKHVLINNEFINWQTVVQENDTITLIFDDE-------- 114

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
               D                LYED  + + NKP G+   G      +    L       
Sbjct: 115 ----DYPTKKIPLGRAELIDCLYEDEHLIIVNKPEGMKTHGNQP---NEIALLNHVSAYS 167

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           GQ   + HRLD ETSG ++ A+       + +    + I + YW+LV G    K + + +
Sbjct: 168 GQTCYVVHRLDMETSGAVLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRD 227

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + K   +A++   V+    Q    ++ +  TGRTHQ+R+H  
Sbjct: 228 KIGRNRHDRRKRII----DSKNGQHAMTIIDVLKYI-QNSSLIKCRLETGRTHQIRIHLS 282

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           H G P++GD  Y  +           +L LHA  + L HP     + + AP
Sbjct: 283 HHGHPLIGDPLYNPSSNNE-------RLMLHAHRLTLSHPLTCETISVEAP 326


>gi|157149723|ref|YP_001451260.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gordonii str. Challis substr. CH1]
 gi|157074517|gb|ABV09200.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gordonii str. Challis substr. CH1]
          Length = 290

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 124/303 (40%), Gaps = 35/303 (11%)

Query: 25  FKNHYPHI---NFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K             ++  LR    V V+ + + + ++IQ+G ++ +             
Sbjct: 16  IKELLEDYFLIPR-KIRHFLRTKKHVLVNDQTINWQSKIQAGDLLSLTFDEEDY----PA 70

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           + IL     L +         LY+D  + + NKP G+           +   + ++V   
Sbjct: 71  KAILMGQPELVQE--------LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV--- 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G+   + HRLD+ETSG ++ A+       L      + IQ+ YW+LV G    K     +
Sbjct: 120 GETCYVVHRLDKETSGTVLFAKNPFVLPILNRLLENKDIQREYWALVDGKFIEKSRIYKD 179

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + K   YA +H   +  F QK   ++ Q  TGRTHQ+RVH  
Sbjct: 180 KIGRDRHDRRKRL----VDNKHGQYAETHVTRLKSFGQK-TLVKCQLKTGRTHQIRVHLS 234

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
           H G P+VGD  Y  + +G        +L LHA  +   HP    ++ + AP      +  
Sbjct: 235 HHGFPLVGDPLYHPHPQG--------RLMLHAHRLSFVHPFTLEKISLEAP-SKSFEEGL 285

Query: 320 DSL 322
           + L
Sbjct: 286 EKL 288


>gi|116629980|ref|YP_815152.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           ATCC 33323]
 gi|238853582|ref|ZP_04643952.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           202-4]
 gi|282851411|ref|ZP_06260776.1| pseudouridine synthase, RluA family [Lactobacillus gasseri 224-1]
 gi|311110388|ref|ZP_07711785.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           gasseri MV-22]
 gi|116095562|gb|ABJ60714.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           ATCC 33323]
 gi|238833800|gb|EEQ26067.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           202-4]
 gi|282557379|gb|EFB62976.1| pseudouridine synthase, RluA family [Lactobacillus gasseri 224-1]
 gi|311065542|gb|EFQ45882.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           gasseri MV-22]
          Length = 299

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 66/284 (23%), Positives = 112/284 (39%), Gaps = 32/284 (11%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G + V+  R   +  +  G  V         N  +K                  +  +++
Sbjct: 38  GMILVNHHRRYTSYLLHPGDEVIFILGEEKKNQWLK--------------PSTNQLNIVF 83

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQK---PRLTHRLDQETSGILV 159
           E     V NK AG+            +   L  +    GQK   P +  RLD++TSG+++
Sbjct: 84  EQHDYLVVNKEAGVLSIPSRYEDNDAVVNRLIYYFQKNGQKDLKPHVITRLDRDTSGLVL 143

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           V +   A    +E  +   I+K + ++V G    ++E         + IG     V +  
Sbjct: 144 VGKNAVAHARFSEMGKDCFIKKYH-AIVHGNFSKEQET----GTIDAPIGKLDAGVKRGI 198

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 +I+ ++V++        +E+Q  TGRTHQ+RVH  ++G P+ GD  Y    K N
Sbjct: 199 VANGQRSITKYRVLEQV-NGASLVELQLLTGRTHQIRVHMQYLGHPLYGDPLYG--IKDN 255

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           F      +  L+  Y+    P    + +IT   P  M   W SL
Sbjct: 256 F-----KRQALNCFYLKFDDPFSELKQEITISEPVDMKCLWQSL 294


>gi|310287036|ref|YP_003938294.1| Ribosomal large subunit pseudouridine synthase [Bifidobacterium
           bifidum S17]
 gi|291045148|dbj|BAI82361.1| pseudouridine synthase [Bifidobacterium bifidum]
 gi|309250972|gb|ADO52720.1| Ribosomal large subunit pseudouridine synthase [Bifidobacterium
           bifidum S17]
          Length = 313

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 126/326 (38%), Gaps = 31/326 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V   +     R D         I+      ++ SGQ RV  + +  +  +  G+ V  
Sbjct: 3   RLVPAPDALVGSRFDVAVSKML-GISRAKAADLIESGQARVLDRAIAKSGTLLYGETVEF 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                     I E++     V        L   ++YED  + V +KP G++    +G   
Sbjct: 62  D---------IAEERHEPEPV-------CLDMAIVYEDDDVVVVDKPVGVAAHASAGWTG 105

Query: 128 HID--GFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                  LK  V         +  +  RLD  TSG+++V ++  A + +   F    + K
Sbjct: 106 PTVLGSLLKRGVRITSYGAPGRQGIVSRLDVGTSGLMLVCKSELAYKEMRRQFSEHEVVK 165

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G  K  K  I   + +                     A++H+ V+D F +   
Sbjct: 166 TYHAMVQGNLKEDKATIEAPIGR-----AKVSDFRFCVTPSGKPAVTHWDVLDRFGE-AT 219

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +   TGRTHQ+RVH   +G P+VGD  Y AN          ++ +LHA  ++  HP 
Sbjct: 220 LVSVNLETGRTHQIRVHFSSIGHPLVGDPMYGANPVL-AGELGLDRQWLHAMKLEFRHPR 278

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFKY 326
                 + +  PA +    + +  ++
Sbjct: 279 THLWTSVESHYPADLAHALELMRARH 304


>gi|13357670|ref|NP_077944.1| pseudouridine synthase (uracil hydrolase) [Ureaplasma parvum
           serovar 3 str. ATCC 700970]
 gi|170762339|ref|YP_001752196.1| pseudouridine synthase [Ureaplasma parvum serovar 3 str. ATCC
           27815]
 gi|171920337|ref|ZP_02691044.2| pseudouridine synthase [Ureaplasma parvum serovar 1 str. ATCC
           27813]
 gi|183508769|ref|ZP_02689887.2| pseudouridine synthase [Ureaplasma parvum serovar 14 str. ATCC
           33697]
 gi|186701771|ref|ZP_02553233.2| pseudouridine synthase [Ureaplasma parvum serovar 6 str. ATCC
           27818]
 gi|11357016|pir||C82933 pseudouridine synthase (uracil hydrolase) UU113 [imported] -
           Ureaplasma urealyticum
 gi|6899069|gb|AAF30519.1|AE002111_8 pseudouridine synthase (uracil hydrolase) [Ureaplasma parvum
           serovar 3 str. ATCC 700970]
 gi|168827916|gb|ACA33178.1| pseudouridine synthase [Ureaplasma parvum serovar 3 str. ATCC
           27815]
 gi|171902761|gb|EDT49050.1| pseudouridine synthase [Ureaplasma parvum serovar 1 str. ATCC
           27813]
 gi|182675707|gb|EDT87612.1| pseudouridine synthase [Ureaplasma parvum serovar 14 str. ATCC
           33697]
 gi|186701046|gb|EDU19328.1| pseudouridine synthase [Ureaplasma parvum serovar 6 str. ATCC
           27818]
          Length = 315

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 73/276 (26%), Positives = 136/276 (49%), Gaps = 24/276 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ + ++ ++ N RLDR+   ++P+++ + + KI+R+  V+V+ K+V  N  ++   VV 
Sbjct: 3   LKEIKIKINDANQRLDRFLLKNFPNLSRIAVYKIIRTKDVKVNHKKVDHNYLLKENDVVS 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I            ++  L+  V+L+  +   +  ++YED  I V +KP G+ V   +   
Sbjct: 63  IY----------AKENFLEKKVDLSFANAKDELDIIYEDKNILVVHKPIGLIVHEDNRYK 112

Query: 127 Y-HIDGFLKSWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +   +K ++         D     P L HRLD  TSG++V A+T  A + +TE F+ 
Sbjct: 113 NDTLQNRIKKYLVKKDEYHPFDESAFVPSLCHRLDLNTSGLIVAAKTANALRVITEMFKN 172

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + +IY  L +       + I N++ K      + + V     K    AI+ +  ID +
Sbjct: 173 NDVIRIYKCLTYNQLPKNNDVIYNFMYK---ADDNTMIVQNFKTKFNKTAITKYTYIDKY 229

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +K+   +++  TGRTHQ+R     +  PIVG+ KY
Sbjct: 230 -KKYFIYDIELLTGRTHQIRAVLNFLHAPIVGEQKY 264


>gi|1665844|emb|CAA70352.1| yfiI [Borrelia burgdorferi]
          Length = 309

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 70/320 (21%), Positives = 146/320 (45%), Gaps = 32/320 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           ++   +   V+ +   +RLD +   ++       +++       + + K +K        
Sbjct: 1   MIRVKREFTVKENA--LRLDLYLSGNFEVFTRSQIKRRNVEAFKKSNGKFLK-------- 50

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++   +   + I+ E     S ++  + S+ +   ++YEDS + V NKP GI    G
Sbjct: 51  --IKLSKPVFKDDEILIEFDEESSQIDCLRPSN-IPIAIIYEDSNVIVLNKPQGILSHPG 107

Query: 123 ---------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                    + + YHI   LK   + +  +P + HRLD++TSG+L+ A+  +  + L + 
Sbjct: 108 ISHWDDTVVNFLLYHIKS-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQ 166

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ +RI K+Y ++V G   +    I +++ +  H    +     +       A++ ++++
Sbjct: 167 FKDKRINKVYIAIVKGNFNSFFGSIESFIDRDKHNRKKFSVSKDR----GKKALTEYRLL 222

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             F + +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+        L LH+ 
Sbjct: 223 LNFGE-YSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSLEKIT---LMLHSY 277

Query: 294 YMDLPHPEGGRLQITAPLPA 313
            +++   +    +  +  P 
Sbjct: 278 KLEIDVGKNSFKKFISEFPK 297


>gi|298530696|ref|ZP_07018098.1| pseudouridine synthase [Desulfonatronospira thiodismutans ASO3-1]
 gi|298510070|gb|EFI33974.1| pseudouridine synthase [Desulfonatronospira thiodismutans ASO3-1]
          Length = 318

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 75/302 (24%), Positives = 126/302 (41%), Gaps = 35/302 (11%)

Query: 1   MSLMTY--VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNN 57
           M  M     Q  +V + E   +L  + K           L +++R+GQVRV+ KR K  +
Sbjct: 1   MQDMQKQTAQQCLVSSTESGQKLFSYLKRRLGREFPGSGLMRLIRTGQVRVNSKRKKPYD 60

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           R+ +G  VRIPP                            +  +++E+    V +KPAG+
Sbjct: 61  RVYAGDTVRIPPHFPETGD---------------DPQRAGELQIVFENPDFTVLDKPAGV 105

Query: 118 SVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            V  G S    ++   L+         P L HRLD+ETSG+L+ A+  A  + +   +  
Sbjct: 106 PVHSGTSARRDNMVLRLRKHYAGADFSPALVHRLDKETSGLLLAAKNYAWLRRIQAMWNK 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             ++K Y + V G   ++   + + L+K             Q       A+S  + I   
Sbjct: 166 NLVEKTYLAWVHGSWPSRWVNLEHRLIK--------TFEKMQPSPEGRPALSRVRSIAS- 216

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           ++    ++++  TGRTHQ+R      G P++GD KY  +            +YLHA  + 
Sbjct: 217 SRDKTLVQIRIITGRTHQIRTQLSLSGHPVIGDGKYGKDSGYAE-------MYLHAYMLA 269

Query: 297 LP 298
            P
Sbjct: 270 WP 271


>gi|228964349|ref|ZP_04125466.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228795333|gb|EEM42823.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
          Length = 307

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 68/319 (21%), Positives = 126/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + +      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EITIPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                   +  E               + +  ++YED  + + NKP  +           
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAEKGGNR 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P  +       
Sbjct: 284 AIEVDVPFPTKLNNKIKEF 302


>gi|294497315|ref|YP_003561015.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           megaterium QM B1551]
 gi|294347252|gb|ADE67581.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           megaterium QM B1551]
          Length = 303

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 61/295 (20%), Positives = 118/295 (40%), Gaps = 31/295 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  ++    ++ + K  +  I    L +   +  V ++ + + + N ++    + +P   
Sbjct: 12  IAKNDAGQTIEDYLKTKWR-IPKKTLHQFRMNKNVLINGEPLPWRNTLKEHDKMSLPFFE 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
              N I      ++               +L+ED  + + NKP  +     S      + 
Sbjct: 71  AEPNEITPYNVDIE---------------ILFEDEHVLIVNKPINLDTHPSSEQDQKTLL 115

Query: 131 GFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             + ++    G K  PR  HRLD +TSG ++  +   A+    +    R+I + Y +LV 
Sbjct: 116 NAVAAYFQKIGLKTKPRHVHRLDSDTSGAILFTKHFVASSVFDQLLAERKINRTYIALVQ 175

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQP 247
           GI K +   I   + +  H          +  +    A + ++V+    A+    +E+  
Sbjct: 176 GIIKKEDGIINEPIGRDRHHATRR-----RVSRTGQAAKTRYRVLKRNTAKNETLIELSL 230

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            TGRTHQ+RVH  H+G P++GD  Y            + +  LHA  +   HP  
Sbjct: 231 ETGRTHQIRVHMSHIGYPLLGDTLYGGKRLK------EQQQALHAIKLSFIHPFT 279


>gi|317479385|ref|ZP_07938519.1| RNA pseudouridylate synthase [Bacteroides sp. 4_1_36]
 gi|316904459|gb|EFV26279.1| RNA pseudouridylate synthase [Bacteroides sp. 4_1_36]
          Length = 511

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 68/238 (28%), Positives = 111/238 (46%), Gaps = 17/238 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ +            ++YED  + V NKPAG+    G   A  +
Sbjct: 278 CEPILQHMLQGLQVEENPMLKRMQVPSKNLEIVYEDPWLSVINKPAGMLSVPGKEDAVSV 337

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++     +   P   HRLD  TSG++++A+T+   Q+L   F+ R ++K Y +L+ G
Sbjct: 338 YSLMREQY-PEADSPLTVHRLDMATSGLMLIAKTKRVHQNLQAQFKNRLVRKRYVALLEG 396

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I    K  +   L        D    +   E G   AI+ ++V++    K   +   P T
Sbjct: 397 IVPKDKGTVDLPLCLNPL---DRPRQMVHTEHG-KPAITDYQVLERLDGKRTRIVFYPRT 452

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GRTHQLR+HA H   + CPI+GD  Y             ++LYLHA Y++  HP  G 
Sbjct: 453 GRTHQLRIHAAHPLGLHCPIIGDELYGEK---------ADRLYLHAEYLEFTHPITGE 501


>gi|94987157|ref|YP_595090.1| pseudouridylate synthases, 23S RNA-specific [Lawsonia
           intracellularis PHE/MN1-00]
 gi|94731406|emb|CAJ54769.1| Pseudouridylate synthases, 23S RNA-specific [Lawsonia
           intracellularis PHE/MN1-00]
          Length = 321

 Score =  184 bits (468), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 79/308 (25%), Positives = 135/308 (43%), Gaps = 20/308 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M +   +Q ++V ++E   +L ++       +    L + +R+GQ R++ KRV     + 
Sbjct: 1   MYIELIMQPIIVSSNEAGQKLFQFLTRRL-TVPKSILHRWIRTGQTRINGKRVTPFTIVN 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD----FLKSILLYEDSKIYVFNKPAG 116
               +RIPP             ++ +  +++  S      L  ++ +      +F KPAG
Sbjct: 60  FKDKIRIPPFAYEYKKKDLTTSLIHNQYDISPISSHTTSPLPPVIAHSPE-FIIFYKPAG 118

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           ++V GG+G    +   L          P   HRLD++TSG+L+VA+T  + ++ +E F  
Sbjct: 119 LAVHGGTGQTDSLAHRLSQHYAHSTFMPTPVHRLDKDTSGLLLVAKTYNSLRYFSELFAS 178

Query: 177 RRIQKI--YWSLVWGI-PKNKKECIANWLLKKSHIG---GDYVHVVKQNEKGANYAISHF 230
              Q    Y + V GI P  +  C+ + L KK           +  K  +  A  A    
Sbjct: 179 HSTQLTKEYLAWVVGICPWTQPICLEDILTKKQKQDNYSRLNSYQNKLQQTSAQKASLTV 238

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           + I  +  K   L ++ HTGRTHQ+R+     G PI+GD KY    + +        L L
Sbjct: 239 RCIKQYKDK-SLLLIKLHTGRTHQIRIQLSIHGFPIIGDKKYGNTIRSHN-------LKL 290

Query: 291 HARYMDLP 298
           HA  +  P
Sbjct: 291 HAFRLSFP 298


>gi|42780479|ref|NP_977726.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 10987]
 gi|42736398|gb|AAS40334.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus ATCC 10987]
          Length = 307

 Score =  184 bits (468), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 129/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++  + +++ 
Sbjct: 11  EITVPAKWNGISIESLLKIEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKEDEKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E   LD               ++YED  + + NKP  +           
Sbjct: 70  MFMEEEYGVEPEYGELD---------------VVYEDDHVLIVNKPEKMDTHPAEKGGMG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEKYFKKQNVTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        ++  LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDILYGGGTK------YMSRQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNDTMKEF 302


>gi|229177799|ref|ZP_04305172.1| Pseudouridine synthase [Bacillus cereus 172560W]
 gi|228605590|gb|EEK63038.1| Pseudouridine synthase [Bacillus cereus 172560W]
          Length = 307

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 130/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            ++V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EIIVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                   +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGKIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P ++ K     
Sbjct: 284 AIEVDVPFPTNLNKKIKEF 302


>gi|317012555|gb|ADU83163.1| hypothetical protein HPLT_03755 [Helicobacter pylori Lithuania75]
          Length = 327

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 69/331 (20%), Positives = 138/331 (41%), Gaps = 35/331 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHI 77
            R+D +       I+   +  +++ G V   KK VK     ++ G  + +          
Sbjct: 12  KRIDEFLAKEL-QISKNQVLNLIKEGLVFCQKKGVKKGGLALKEGDEITL---------- 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                    +    K    L+  +++ED  + V NKP  + V     +    +  L  W+
Sbjct: 61  ----LTPQITPKPLKRGLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSV---KEPTLVDWL 113

Query: 138 DSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +SK  +           + HRLD++TSG +V+A+      HL+E  + + + + Y +L+ 
Sbjct: 114 ESKNYELSNLGLKERYGIVHRLDKDTSGGIVIAKNNFTHAHLSEQLKTKTMGRYYIALLS 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
              K +K  +  +L +  +     + +    ++ + Y+ S F  +         +  +  
Sbjct: 174 TPLKEEKMSVECYLTRNPNNRLKMIALKATKKEKSRYSKSEFTSLLTSQNNLNLIGAKLF 233

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+R H  ++   I+GD+ Y  N +  F   I  ++ LHA  ++  HP    +L+ 
Sbjct: 234 TGRTHQIRAHLEYLNRHIIGDNLYGLN-QALFKEEI--RIMLHAYLIEFKHPRSEQKLRF 290

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             PL   M++    +   +D+    + L  +
Sbjct: 291 KVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|323128176|gb|ADX25473.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus dysgalactiae subsp. equisimilis ATCC
           12394]
          Length = 303

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 80/299 (26%), Positives = 123/299 (41%), Gaps = 37/299 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVR 66
           Q + V+   E    D+        I    ++  LR    V V+   + + + + SG  V 
Sbjct: 20  QTLTVKELLE----DKLL------IPR-KIRHFLRTKKNVLVNGSAITWQSAVNSGDQVE 68

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +            E+   D  + + + +   K   LYED  + + NKP G+      G  
Sbjct: 69  LFFD---------EEDYPDKPIMMGQAN---KVDCLYEDDHLIIVNKPEGMKTH---GNE 113

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 L       G+   + HRLD ETSG++V A+T      L      R I + YW+L
Sbjct: 114 PTELALLNHVSAYTGRTCYVVHRLDMETSGVIVFAKTPFILPILNRLLEKREISRDYWTL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G   +K+      + +  H     V  VKQ +K    A++  K++  F Q    +  +
Sbjct: 174 VHGTLSSKEVSYREPIGRHRHDRRKRVVDVKQGQK----AVTDVKLLKSFKQNVSLINCR 229

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
             TGRTHQ+RVH  H G  ++GD  Y    KG    P   +L LHA  + L HP    +
Sbjct: 230 LQTGRTHQIRVHLSHHGHALLGDPLYS---KGKAECP---RLMLHAHQLRLRHPLTQEM 282


>gi|238927181|ref|ZP_04658941.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
 gi|238884963|gb|EEQ48601.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
          Length = 294

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 62/295 (21%), Positives = 120/295 (40%), Gaps = 37/295 (12%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
           H   I+    ++I   G   ++    V     ++ G  +                   D 
Sbjct: 22  HVHGISGSLWRRIKHHGAFTLNGIPAVAARTMLKDGDWI-----------------AYDL 64

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKP- 144
            +  +   + L   ++YED  + V +KPAG  V   +   +  I   ++ +  + G    
Sbjct: 65  PIVSSVIPESLPLSIIYEDDDLLVLDKPAGQLVHPTTKETHGTIANAVRGYYAACGVHLD 124

Query: 145 -RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD+ TSG+L++A+       + +      +++ Y +L+ G     + CI   + 
Sbjct: 125 FHPCHRLDRNTSGLLLIAKHPEVQYQIAQQ---NTLRREYLALIAGSLTPPEGCIDVPIA 181

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +          +++        A +H+  +    + +  L +Q  TGRTHQ+RVH  H+G
Sbjct: 182 RALP-----SIILRCVSTEGKSACTHYVTVQTDGR-YSLLRLQLDTGRTHQIRVHLAHLG 235

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVK 317
            P++GD  Y              +  LH+ ++ L HP   ++  ++A LPA M +
Sbjct: 236 HPLLGDDLYGGTRAE------IARHALHSAHLTLVHPRTKKMLALSALLPADMAR 284


>gi|283780201|ref|YP_003370956.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
 gi|283438654|gb|ADB17096.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
          Length = 313

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 74/318 (23%), Positives = 134/318 (42%), Gaps = 25/318 (7%)

Query: 10  VVVENDEENM-RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
           V+ E++   + RLD          +   ++ +L    V+++          +     + I
Sbjct: 9   VITESNLAELHRLDLAV-KQLSGFSREQVRGLLDHQCVKLNGAVTDEPGQPLSVDDRIEI 67

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
               +   H  K            K    L   ++YED  + V  KPA +          
Sbjct: 68  AFDPHHRYHPKK------------KIRGGLGFGIVYEDRHLIVVEKPAALLTVPTPKNDR 115

Query: 128 -HIDGFLKSWVD--SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   + ++V   S+G+     HRLD+  SG+L+  +T   AQ L + F M + ++ Y 
Sbjct: 116 GTLLERVANYVKIVSRGKGAFQVHRLDRGVSGLLIFGKTTELAQMLRDQFAMHKPEREYV 175

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G     +  I ++L        D       +E    +A++H++VI+  A     ++
Sbjct: 176 AIVRGKLDKPEGMIESFLA----TDRDLNRYSTDDESIGQHAVTHYRVIEELA-GASVVQ 230

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TGR +Q+RVH    G P++GD +Y A+   + T     ++ LHAR + L HP  G 
Sbjct: 231 VWLETGRRNQIRVHFAEAGHPLIGDQRYRADEAAD-TRWTHARIALHARLLGLSHPMTGE 289

Query: 305 -LQITAPLPAHMVKTWDS 321
            L+  +PLP  M     +
Sbjct: 290 PLRFESPLPHEMKNFIRA 307


>gi|59711220|ref|YP_203996.1| tRNA pseudouridine synthase C [Vibrio fischeri ES114]
 gi|59479321|gb|AAW85108.1| tRNA pseudouridine synthase [Vibrio fischeri ES114]
          Length = 259

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 66/260 (25%), Positives = 108/260 (41%), Gaps = 17/260 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E+    +   L + ++ ++  ++Y D  +   NKPAG+ V       +     +++  D 
Sbjct: 4   EEMTAVNDELLEEQAEPIELEIVYRDEHLIAINKPAGMLVHRSWLDKHETVFAMQTLRDQ 63

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            GQ     HRLD+ TSGIL  A +   A  ++  F  R I+K Y ++V G  +       
Sbjct: 64  IGQHVFPLHRLDRPTSGILFFALSSEIAAQVSPLFASREIKKTYHAIVRGWIEEANTLDY 123

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
               +   I           E  A  AI+ +K +               ++C +E++PHT
Sbjct: 124 PLKKELDKIADKKASQ----EVEAKEAITEYKPLAKVELPYSTGKFPTTRYCLMELKPHT 179

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQ 306
           GR HQLR H  H+  PIVGD  +             +  +L LHA  ++  HP  G  + 
Sbjct: 180 GRKHQLRRHMAHLRHPIVGDTSHGDGKHNRLFKEKLDSHRLLLHASELNFTHPITGEDIV 239

Query: 307 ITAPLPAHMVKTWDSLGFKY 326
           I A       K +   G+ +
Sbjct: 240 IKADFDETWKKLFTEFGWDF 259


>gi|306821486|ref|ZP_07455089.1| RluA family pseudouridine synthase [Eubacterium yurii subsp.
           margaretiae ATCC 43715]
 gi|304550501|gb|EFM38489.1| RluA family pseudouridine synthase [Eubacterium yurii subsp.
           margaretiae ATCC 43715]
          Length = 300

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/290 (24%), Positives = 131/290 (45%), Gaps = 37/290 (12%)

Query: 41  LRSGQ--VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           ++ G+  + ++  ++  N+ I    V+++       ++I +E+                 
Sbjct: 40  IKKGKYVISINDGKIPKNHIISEKDVIKVVMHDEKSDYISQEK----------------N 83

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---KPRLTHRLDQETS 155
             +L+ED  I +F+KPAGI          +       W+  K     K R   RLD +TS
Sbjct: 84  LDILFEDEDIIIFDKPAGIVSHPTKSHLENTMLNYAQWIFEKKNIESKVRFISRLDMDTS 143

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSHIGGDYV 213
           GI+ +A+   +   L++ F   +IQK Y ++V G     +    IA  + K      D +
Sbjct: 144 GIITIAKNAFSHYALSQGFLSDKIQKRYTAIVSGDTSILSDSGTIAEKIEKSE----DGI 199

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             +  +E     AI+H+K++    +K+  LE+   TGRTHQ+RVH  H+G PI+GD  Y 
Sbjct: 200 KRIITDE--GQEAITHYKIVKR-GEKYSVLELLLETGRTHQIRVHLSHLGLPIIGDELYG 256

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
            +        + ++  LH   +++  P    ++ +T+P P  M    D +
Sbjct: 257 GDMS------VMSRQALHCHSLEIISPRSMEKISVTSPYPKDMQDIMDEI 300


>gi|227893162|ref|ZP_04010967.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus ultunensis
           DSM 16047]
 gi|227865028|gb|EEJ72449.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus ultunensis
           DSM 16047]
          Length = 310

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 70/330 (21%), Positives = 139/330 (42%), Gaps = 43/330 (13%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRS----GQVRVDKKRVKFNNR 58
           +MT +  ++V+  +   +L  +   +    +    Q ++++    G + V+ KR   + R
Sbjct: 9   IMTSLFKLIVQERD-PKKLGSFLLKN--GFSH---QALIKARYHHGMILVNHKRRYLSFR 62

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +++G  V             K+ + L  S N  K         + E     V +KPAG+ 
Sbjct: 63  LRTGDEVIFISGEE------KKNEFLKPSSNPVKP--------VLETKNYIVLDKPAGVL 108

Query: 119 VQGGSGIAYH-IDGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                      I   L  +   K     KP +  RLD++TSG+++V +   A    ++  
Sbjct: 109 SIPSRYEDNDAIVNRLMGYFAKKNMSNLKPHVITRLDRDTSGLVLVGKNAIAHARFSKIG 168

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + + ++K + ++V G     K       +  + IG     V +   +G   A + ++V+ 
Sbjct: 169 KEKFVKKYH-AIVHGNFSEDKLT----GVIDAPIGKKGSGVKRAVVEGGKKAQTKYRVLK 223

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
             +     +E++  TGRTHQ+RVH  ++G P+ GDH Y             ++  L+  Y
Sbjct: 224 QVS-GASLVELRLLTGRTHQIRVHMAYLGHPLYGDHLYGIEDD-------FSRQALNCFY 275

Query: 295 MDLPHP-EGGRL-QITAPLPAHMVKTWDSL 322
           +  P P +  ++ +I+   P  M + W  +
Sbjct: 276 LSFPDPFDNEKIKEISIEEPTDMNELWQKM 305


>gi|12045061|ref|NP_072871.1| RluA family pseudouridine synthase [Mycoplasma genitalium G37]
 gi|255660210|ref|ZP_05405619.1| RluA family pseudouridine synthase [Mycoplasma genitalium G37]
 gi|1351510|sp|P47451|Y209_MYCGE RecName: Full=Uncharacterized RNA pseudouridine synthase MG209;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|3844807|gb|AAC71427.1| pseudouridine synthase, RluA family [Mycoplasma genitalium G37]
 gi|166079007|gb|ABY79625.1| pseudouridine synthase, RluA family [synthetic Mycoplasma
           genitalium JCVI-1.0]
          Length = 308

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 126/302 (41%), Gaps = 24/302 (7%)

Query: 34  FVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
            V + K++ +GQ++V++K   K +  +    V+++       +  I            + 
Sbjct: 25  RVKVVKLIMNGQIKVNEKLTFKNSLIVAKDDVIKVEIHDETTSDFIT-----------SV 73

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLD 151
               LK  +L+ED  + V NKP+G+     +         L + +    + P  L HRLD
Sbjct: 74  EPYNLKLEVLFEDKDLMVINKPSGLLTHPTT--FNEKASLLAACIFHNNKNPVYLVHRLD 131

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG +VV + +A+  +L    + R +++ Y +LV          I   L +   +  +
Sbjct: 132 RDTSGAIVVCKNQASLLNLQNQLQNRTLKRYYVALVHFPFNALTGSINAPLAR---VNNN 188

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V         A  AI+ FKVI+   +K   + ++  TGRTHQ+RVH   +  P+  D  
Sbjct: 189 KVMFKIAQTAKAKQAITKFKVIN-QNEKAALISLELLTGRTHQIRVHLKFIQHPVYNDPL 247

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
           Y    +   +       +LHA  +   HP     +   APL         SL       L
Sbjct: 248 YGIKSEKKDSY----GQFLHANRICFIHPTLNKPMDFHAPLEPKFSTKLKSLNLSLTDPL 303

Query: 331 YI 332
           ++
Sbjct: 304 HV 305


>gi|197334594|ref|YP_002155370.1| tRNA pseudouridine synthase C [Vibrio fischeri MJ11]
 gi|197316084|gb|ACH65531.1| tRNA pseudouridine synthase C [Vibrio fischeri MJ11]
          Length = 259

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 66/260 (25%), Positives = 107/260 (41%), Gaps = 17/260 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E+    +   L +  + ++  ++Y D  +   NKPAG+ V       +     +++  D 
Sbjct: 4   EEITAVNDELLEEQVEPIELEIVYRDEHLIAINKPAGMLVHRSWLDKHETVFAMQTLRDQ 63

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            GQ     HRLD+ TSGIL  A +   A  ++  F  R I+K Y ++V G  +       
Sbjct: 64  IGQHVFPLHRLDRPTSGILFFALSSEIAAQVSPLFASREIKKTYHAIVRGWIEEADTLDY 123

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
               +   I           E  A  AI+ +K +               ++C +E++PHT
Sbjct: 124 PLKKELDKIADKKASQ----EVEAKEAITEYKPLAKVELPYSTGKFPTTRYCLMELKPHT 179

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQ 306
           GR HQLR H  H+  PIVGD  +             +  +L LHA  ++  HP  G  + 
Sbjct: 180 GRKHQLRRHMAHLRHPIVGDTSHGDGKHNRLFKEKLDSHRLLLHASELNFTHPITGENIV 239

Query: 307 ITAPLPAHMVKTWDSLGFKY 326
           I A       K +   G+ +
Sbjct: 240 IKADFDETWKKLFTEFGWDF 259


>gi|15903866|ref|NP_359416.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae R6]
 gi|116515727|ref|YP_817230.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae D39]
 gi|15459512|gb|AAL00627.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae R6]
 gi|116076303|gb|ABJ54023.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae D39]
          Length = 291

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 68/279 (24%), Positives = 114/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V++N  +  G V ++                 D     
Sbjct: 26  IPR-KIRHFLRIKKHILINQEEVRWNEIVNPGDVCQLTFDEE------------DYPQKT 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 73  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 130 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD 
Sbjct: 190 KRI----VDAKNGKYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDP 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    RL  T
Sbjct: 246 LYNSKSKT-------SRLMLHAFRLSFTHPLTLERLTFT 277


>gi|262283613|ref|ZP_06061378.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           2_1_36FAA]
 gi|262260670|gb|EEY79371.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           2_1_36FAA]
          Length = 290

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/303 (23%), Positives = 122/303 (40%), Gaps = 35/303 (11%)

Query: 25  FKNHYPHI---NFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K             ++  LR    V V+ + + + ++IQ+G ++ +             
Sbjct: 16  IKELLEDYFLIPR-KIRHFLRTKKHVLVNNQTINWQSKIQAGDLLSLTFDEEDY----PA 70

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           + IL     L +         LY+D  + + NKP G+           +   + ++V   
Sbjct: 71  KDILMGHPELVQE--------LYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV--- 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G+   + HRLD+ETSG ++ A+       L      + IQ+ YW+LV G    K     +
Sbjct: 120 GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLENKDIQREYWALVDGKFPVKNRVFKD 179

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + K   YA +H   +  F QK   ++ Q  TGRTHQ+RVH  
Sbjct: 180 KIGRDRHDRRKRL----VDSKHGQYAETHVTRLKSFGQK-TLIKCQLKTGRTHQIRVHLS 234

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
             G P+VGD  Y    +G        +L LHA  +   HP    ++ + AP      +  
Sbjct: 235 RHGFPLVGDPLYHPQPQG--------RLMLHAHRLSFVHPFTLEKISLEAP-SKSFEEGL 285

Query: 320 DSL 322
           + L
Sbjct: 286 EKL 288


>gi|322420987|ref|YP_004200210.1| RluA family pseudouridine synthase [Geobacter sp. M18]
 gi|320127374|gb|ADW14934.1| pseudouridine synthase, RluA family [Geobacter sp. M18]
          Length = 303

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/316 (22%), Positives = 128/316 (40%), Gaps = 45/316 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +   +   R+D + +N  P   F  L+K++ SG ++++   V+    ++    V I    
Sbjct: 6   IAAQDHLRRVDSFLRNLLPSAQFSYLKKLINSGHLKINGSAVEPGQILRFADQVTIKESS 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
                + +          LT   D     +L+ED+ I   NKPAG++V          + 
Sbjct: 66  KTAALLAR----------LTPEMD-----ILFEDTWIVCLNKPAGLAVHRTEDPDEITLV 110

Query: 131 GFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              ++ +  +    K R  +RLD+ TSG +++A++  AA    +  +   + K+Y ++V 
Sbjct: 111 DLAEALLKKRDGAGKLRPVNRLDKGTSGAIILAKSAVAAGMFGKMVQEEGLGKLYLAMVE 170

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  + K+  I   L                       + + +  +         L + P 
Sbjct: 171 GKLQ-KQGTIDAPL-------------------DGKESQTSYLRL-FQGGGVALLAVYPL 209

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGR HQ+R H   +G P++GD +Y       FT        LH+    L HP  G  L I
Sbjct: 210 TGRMHQIRQHFRMIGHPVLGDKRYGGRGLSGFTGH-----ALHSFRTTLVHPATGEDLDI 264

Query: 308 TAPLPAHMVKTWDSLG 323
            APLP  +++     G
Sbjct: 265 PAPLPEQLLRLATRCG 280


>gi|34556591|ref|NP_906406.1| putative ribosomal pseudouridine synthase [Wolinella succinogenes
           DSM 1740]
 gi|34482305|emb|CAE09306.1| PUTATIVE RIBOSOMAL PSEUDOURIDINE SYNTHASE [Wolinella succinogenes]
          Length = 320

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 71/331 (21%), Positives = 138/331 (41%), Gaps = 50/331 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD+         +   ++ ++R G V VD ++  K   +++ G+ + +         ++
Sbjct: 14  RLDQALAKLLGE-SRNQVEALVRGGNVWVDGEKSSKGGVKLKGGERIEVEIP------LL 66

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   ++            +  +L+E+    V NKP+G  V G   +    +  L  W+ 
Sbjct: 67  RENPAMEVE---------FEVEILHEEEHFIVLNKPSGAVVHGAPSV---KEATLVDWLK 114

Query: 139 SKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            KG         ++  + HRLD+ETSG +V+A++  A + L+   + + + + Y +++  
Sbjct: 115 KKGISLSTLNGEERHGIVHRLDKETSGAIVIAKSNEAHRRLSLQLQEKSMGRYYLAII-D 173

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF-KVIDCFAQKFCWLEMQPH 248
            P  + + +  +L +  H       V         YA S F K+ +        +  +  
Sbjct: 174 HPLKEDQRVECYLGRHPHHRLKIAKVPV-----GRYAKSAFVKLEESIDGSKELIAAKLF 228

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+R H   +G  I+ D  Y       +    + +++LHA  +   HP  G  +  
Sbjct: 229 TGRTHQIRAHLELLGRHILHDELYG------YRGTSEGRIFLHAYGLYFDHPMTGESMFF 282

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
            APL   M+           +N   +RL+  
Sbjct: 283 KAPLFEDMIGYLQ-------QNFPSERLHET 306


>gi|257896942|ref|ZP_05676595.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium Com12]
 gi|293379115|ref|ZP_06625266.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
 gi|257833507|gb|EEV59928.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium Com12]
 gi|292642256|gb|EFF60415.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
          Length = 299

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/306 (23%), Positives = 123/306 (40%), Gaps = 33/306 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L KI  + GQ++V+ +       +     V I               
Sbjct: 18  FLKE--KGISKGLLAKIKFQGGQIKVNDQVENVLFSLAKDDKVTI--------------V 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG 141
           I     + T   D     ++YED  + V NKPAG+S           +   +K++   +G
Sbjct: 62  IPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQYHPNGTMANRVKAYYKKQG 121

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G+  N    +
Sbjct: 122 YENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDTQLREKKFVKKYQALVSGMLSN----L 177

Query: 199 ANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +        I  DY  ++K+        A + +++     +    +++Q HTGRTHQ+RV
Sbjct: 178 SAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYRIEKRLTEIA-LVDIQLHTGRTHQIRV 236

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GC ++GD  Y              +  LH   +   HP     L+   PL A M 
Sbjct: 237 HFSAIGCALLGDDMYSGRM-----DLGIKRQALHCYDLRFYHPFTEELLEFKQPLAADME 291

Query: 317 KTWDSL 322
                 
Sbjct: 292 AVVRRF 297


>gi|260574483|ref|ZP_05842487.1| pseudouridine synthase [Rhodobacter sp. SW2]
 gi|259023379|gb|EEW26671.1| pseudouridine synthase [Rhodobacter sp. SW2]
          Length = 215

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 65/226 (28%), Positives = 108/226 (47%), Gaps = 13/226 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++ T     +   +LY D ++ V +KPAG+    G G        L + + +   +  L 
Sbjct: 1   MSYTYTPPDVPLEILYHDDQVLVVSKPAGLLSVPGKGAD--KADCLITRLQAVFPEVLLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD +TSG++V A  +AA   L + F  R+ +K+Y + + G+ + ++  +   L+    
Sbjct: 59  HRLDTDTSGVMVFAMNKAAQGALGQQFEKRQTKKVYIARLDGLLEPREGRVDLPLIVD-W 117

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                 HV   N      A + ++V+  + +    + + P TGR+HQLRVH   +G PI+
Sbjct: 118 PNRPRQHV---NHDTGRPAQTDWRVVK-YGKAETRVRLMPLTGRSHQLRVHMAALGHPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           GD  Y +            +L LHA  +   HPE G+ L  TAP P
Sbjct: 174 GDALYASGAACEHP-----RLMLHAESLRFRHPETGKSLTFTAPCP 214


>gi|206967734|ref|ZP_03228690.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
 gi|206736654|gb|EDZ53801.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
          Length = 307

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 130/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            ++V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EIIVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                   +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGKIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFRKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P ++ K     
Sbjct: 284 AIEVDVPFPTNLNKKIKEF 302


>gi|111114840|ref|YP_709458.1| hypothetical protein BAPKO_0017 [Borrelia afzelii PKo]
 gi|216263838|ref|ZP_03435832.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia afzelii ACA-1]
 gi|110890114|gb|ABH01282.1| conserved hypothetical protein [Borrelia afzelii PKo]
 gi|215979882|gb|EEC20704.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia afzelii ACA-1]
          Length = 326

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 80/339 (23%), Positives = 145/339 (42%), Gaps = 36/339 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK--RVKFNNRIQSGQVV 65
           +   V+ +   +RLD +  N+        ++K       + + +  ++K +  +     +
Sbjct: 6   KEFTVKENA--LRLDLYLSNNLEFFTRSQIKKRNVEAFKKSNGEFFKIKLSKPVFKDDEM 63

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--- 122
            I                 +SS       + +   ++YEDS I V NKP GI    G   
Sbjct: 64  LIEFDE-------------ESSQIDYLRPNNISIDIIYEDSNIIVLNKPQGILSHPGISH 110

Query: 123 ------SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                 + + YHI G LK   + +  +P + HRLD++TSG+L+ A+  +  + L + F+ 
Sbjct: 111 WDNTVVNFLLYHIKG-LKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTVRFLAQQFKD 169

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           RR  K+Y ++V G   +    I +++  +         V K        A++ +K++  F
Sbjct: 170 RRTNKVYIAIVKGNFNSFFGSIESFI-DRDKYNRKKFSVSKDR---GKKALTEYKLLLNF 225

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  L ++P TGRTHQLRVH  ++  PI+GD  Y     G+F       L LH+  ++
Sbjct: 226 G-GYSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDGSFKKIT---LMLHSYKLE 280

Query: 297 LPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
           +   +    +  +  P   V    +     + NL I  L
Sbjct: 281 IDVGKNSFKKFISEFPKRFVIFLSNFYKSDELNLIIDNL 319


>gi|68250034|ref|YP_249146.1| tRNA pseudouridine synthase C [Haemophilus influenzae 86-028NP]
 gi|145632796|ref|ZP_01788529.1| tRNA pseudouridine synthase C [Haemophilus influenzae 3655]
 gi|229846708|ref|ZP_04466815.1| tRNA pseudouridine synthase C [Haemophilus influenzae 7P49H1]
 gi|68058233|gb|AAX88486.1| tRNA pseudouridine synthase C [Haemophilus influenzae 86-028NP]
 gi|144986452|gb|EDJ93018.1| tRNA pseudouridine synthase C [Haemophilus influenzae 3655]
 gi|229810197|gb|EEP45916.1| tRNA pseudouridine synthase C [Haemophilus influenzae 7P49H1]
          Length = 239

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 107/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP G+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPDGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQEAVTDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSNSLSFIHPITKEQITITAGLDEQWHQLINQFGWE 237


>gi|261838022|gb|ACX97788.1| pseudouridine synthase D [Helicobacter pylori 51]
          Length = 327

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 68/331 (20%), Positives = 136/331 (41%), Gaps = 35/331 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHI 77
            R+D +       I+   +  +++ G V   KK VK     ++ G  + +     A   +
Sbjct: 12  KRIDEFLAKEL-QISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPKIAPKPL 70

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            KE                L+  +++ED  + V NKP  + V     +    +  L  W+
Sbjct: 71  KKELD--------------LEIEVIFEDKDLLVLNKPPNLVVHKAPSV---KEPTLVDWL 113

Query: 138 DSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           + K  +           + HRLD++TSG +V+A+      HL+E  + + + + Y +L+ 
Sbjct: 114 EFKNYELSNLGLKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKTKTMGRYYIALLS 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
              K +K  +  +L +  +     + +    ++ + Y+ S F  +         +  +  
Sbjct: 174 TPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTSQNHLNLIGAKLF 233

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++  HP    +L+ 
Sbjct: 234 TGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRF 290

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             PL   M++        +D+    + L  +
Sbjct: 291 KVPLLKDMLEYLKKF---FDKENLDEVLDEE 318


>gi|89070986|ref|ZP_01158209.1| ribosomal large subunit pseudouridine synthase A [Oceanicola
           granulosus HTCC2516]
 gi|89043449|gb|EAR49664.1| ribosomal large subunit pseudouridine synthase A [Oceanicola
           granulosus HTCC2516]
          Length = 215

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 64/226 (28%), Positives = 110/226 (48%), Gaps = 13/226 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++       +   +L+ED ++ + +KPAG+    G G   H+   L + V +      L 
Sbjct: 1   MSSDYDPPDVPLAVLHEDHEVVLVDKPAGLLSVPGKG--EHLADCLLARVQAAFPTALLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG+++ A T  A +HL   F  R+ +K Y + V G   +K   +   L+    
Sbjct: 59  HRLDRDTSGVMIFALTPHAQRHLGLQFEKRQTRKTYVARVAGRIADKTGTVDLPLIVDWP 118

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                +     + +    A++ ++V+   +     + + P TGR+HQLRVH L +G PI+
Sbjct: 119 NRPKQM----VDHENGKPAVTDWRVV-RASDAETRVRLFPKTGRSHQLRVHMLALGHPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           GD  Y              ++ LH+  +   HP+GGR ++ITAP P
Sbjct: 174 GDPFYAEGPARAHP-----RMMLHSETLQFRHPDGGRGMRITAPAP 214


>gi|227522958|ref|ZP_03953007.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus hilgardii
           ATCC 8290]
 gi|227089776|gb|EEI25088.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus hilgardii
           ATCC 8290]
          Length = 299

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 70/313 (22%), Positives = 130/313 (41%), Gaps = 35/313 (11%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
              E   L ++   H   I+   + K ++ SGQV ++ +      ++  G  V +     
Sbjct: 16  QSNEPKTLKKFLNTH--GISH-RMYKNIKTSGQVLINSRSSDSQTKLADGDQVTV----- 67

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDG 131
                I   +  D +V +++        ++YED    V +KPAG++V  G       +  
Sbjct: 68  -----ILPDEAGDPNVAVSEQ----PIKVVYEDDNWLVVDKPAGLTVVPGPANRDDTLVN 118

Query: 132 FLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +K ++   G     P +  RLD+ TSG++++A+ R A     E    +++ K Y ++V 
Sbjct: 119 RVKGYLVRAGATDMVPHIITRLDRFTSGLVLIAKHRLANSLANELLAAKQLHKRYLAVVS 178

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+       I   + K  +  G  +           ++ + + V          +E+  H
Sbjct: 179 GVGLPDHGRIQKPIAKDPNGYGQII------SDDGRFSDTEYWVRQRLNDDM-LVEVALH 231

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+RVH   +G P++GD  Y         +   ++  LHA  +    P     +++
Sbjct: 232 TGRTHQIRVHFASIGHPLLGDQLYHGPM-----NMGIDRQALHAVMLGFNDPFSQSEIKL 286

Query: 308 TAPLPAHMVKTWD 320
            +PLP  M    D
Sbjct: 287 KSPLPKDMSSILD 299


>gi|312622364|ref|YP_004023977.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202831|gb|ADQ46158.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 293

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/262 (27%), Positives = 130/262 (49%), Gaps = 15/262 (5%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK---HSDFLKSILLYEDSKIYVFNKP 114
           R+++   +R  P I +++   +E  +++  +  +K           +LYED+     NKP
Sbjct: 33  RLKAHGQIRFIPPIYSVHQYPQENAVIEVDLIFSKSNIVPVEGSIDILYEDNFFLFVNKP 92

Query: 115 AGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           +G+      G  +  I  +++ +++SK     + +RLD++TSGI+V A+       ++  
Sbjct: 93  SGLPSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRLDKDTSGIVVFAKNSYFHSIVSYE 152

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  RR+ K Y ++V GI   K   I   + K+S  G     + ++  +  ++A ++++VI
Sbjct: 153 FEKRRVDKTYIAIVHGILTKKSGLIEKPI-KRSDDG-----IKREIHQDGSFAFTYYEVI 206

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D F + F  L+++P TGRTHQLRVH   +G PIVGD  Y      N        L+ ++ 
Sbjct: 207 DTF-ENFSVLKLKPITGRTHQLRVHLSSIGHPIVGDCIYGKEKTQNTPLL----LHAYSI 261

Query: 294 YMDLPHPEGGRLQITAPLPAHM 315
             +          IT+PLP + 
Sbjct: 262 RFNFKLISNKAYDITSPLPHYF 283


>gi|228907022|ref|ZP_04070887.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228852613|gb|EEM97402.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
          Length = 307

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 68/319 (21%), Positives = 125/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EITVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                   +  E               + +  ++YED  + + NKP  +           
Sbjct: 70  MFAEEEYGVNPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAEKGGNG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G    K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVNKKQGTIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P  +       
Sbjct: 284 AIEVDVPFPTKLNNKIKEF 302


>gi|329577387|gb|EGG58842.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1467]
          Length = 297

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 76/309 (24%), Positives = 135/309 (43%), Gaps = 39/309 (12%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     ++   L K+  + G+++V+         +Q+G VV++               
Sbjct: 18  FLKEQ--GVSKGLLAKVKFQGGKIQVNGTVQNAIYPLQTGDVVKMT-------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D + + T  +D     +++ED    V NKPAGI+        YH  G + + V    +
Sbjct: 62  IPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQ---YHPSGTMANRVKGYYK 118

Query: 143 K-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +         +  RLD++TSG+++ A+   A   + +  R +++ KIY++LV G  +   
Sbjct: 119 RQNYVNQVIHVVTRLDRDTSGLMLFAKHGFAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           E      L +  IG D   ++K+   + AN   + + +    AQ    + +Q HTGRTHQ
Sbjct: 179 E----HQLIEKPIGRDLSSLLKRQVIETANCFSTEYWLAKRGAQAAA-VRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +RVH   +GC ++GD  Y              +  LH   +   HP     + + +PL  
Sbjct: 234 IRVHFEAIGCSLLGDEMYHGKMDQ-----GIERQALHCMELIFTHPFTKETVHLISPLAE 288

Query: 314 HMVKTWDSL 322
            M    D+L
Sbjct: 289 DMKSVDDTL 297


>gi|257899597|ref|ZP_05679250.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium Com15]
 gi|293571564|ref|ZP_06682586.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E980]
 gi|257837509|gb|EEV62583.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium Com15]
 gi|291608370|gb|EFF37670.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E980]
          Length = 299

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/306 (23%), Positives = 122/306 (39%), Gaps = 33/306 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L KI  + GQ++V+ +       +     V I               
Sbjct: 18  FLKE--KGISKGLLAKIKFQGGQIKVNDQVENVLFSLAKDDKVTI--------------V 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG 141
           I     + T   D     ++YED  + V NKPAG+S           +   +K++   +G
Sbjct: 62  IPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQYHPNGTMANRVKAYYKKQG 121

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G+  N    +
Sbjct: 122 YENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDTQLREKKFVKKYQALVSGMLSN----L 177

Query: 199 ANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +        I  DY  ++K+        A + + +     +    +++Q HTGRTHQ+RV
Sbjct: 178 SAHGHIDLPIARDYSSLLKRMVSNEGRSAQTEYWIEKRLTEIA-LVDIQLHTGRTHQIRV 236

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GC ++GD  Y              +  LH   +   HP     L+   PL A M 
Sbjct: 237 HFSAIGCALLGDDMYSGRM-----DLGIKRQALHCYDLRFYHPFTEELLEFKQPLAADME 291

Query: 317 KTWDSL 322
                 
Sbjct: 292 AVVRRF 297


>gi|254779279|ref|YP_003057384.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
 gi|254001190|emb|CAX29153.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
          Length = 327

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 70/339 (20%), Positives = 141/339 (41%), Gaps = 33/339 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +       R+D +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIAPTNH-KRIDEFLAKEL-QISKNQVLNLIKEGLVFCQKKEVKKGGLALKKGDAI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +              KI+   +   K    L+  +++ED  + V NKP  + V     +
Sbjct: 59  TLLT-----------PKIVPKPL---KKGLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      HL+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGLKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMMALKAAKKEKSRYSKSEFSSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N      S  + ++ LHA  ++
Sbjct: 222 PNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALSKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
             HP    +L+   PL   M++    +  K + +  +  
Sbjct: 279 FKHPRSEQKLRFKVPLLKDMLEYLKKVFNKENLDEVLDE 317


>gi|81428927|ref|YP_395927.1| pseudouridylate synthase, 23S rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610569|emb|CAI55620.1| Pseudouridylate synthase, 23S rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 300

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 126/322 (39%), Gaps = 36/322 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSG 62
           M  +++ V     + M+  ++   +   I+     KI   G  VR++ +     +++Q+G
Sbjct: 1   MMEIKWQVATQQSQTMK--QFLLKN--GISQRLYAKIKSQGLPVRLNNRLSSPADQVQNG 56

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V +       +  +                  +   +LYED    V NKPAG++   G
Sbjct: 57  DQVSLTLPAELADETVA--------------VSGVPIKVLYEDDYWLVVNKPAGLATIPG 102

Query: 123 S-GIAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                  +   +K +    G     P +  RLD +TSGI++ A+ + A   L       +
Sbjct: 103 PTNTTDTLLNRIKGYWQQNGATDLVPHIITRLDFDTSGIVLAAKHQVAQSLLQPQIEQHQ 162

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           +QK Y ++V G    +   I   + +        V            A + +  +    +
Sbjct: 163 LQKFYLAVVAGTGLPEFGTIKAPIGRVGVEPRRRVIA------DGQSAWTDYWRL-AQDE 215

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +   L++Q HTGRTHQ+RVH   +  P+VGD  Y             ++  LHA  +   
Sbjct: 216 RLTVLKVQIHTGRTHQIRVHLSDLDHPLVGDQLYEGPLGW-----GIDRQALHAYQLTFN 270

Query: 299 HPEG-GRLQITAPLPAHMVKTW 319
            P    + Q TAP+PA +    
Sbjct: 271 DPFSQQKRQFTAPIPADIQAIL 292


>gi|319940421|ref|ZP_08014771.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319810477|gb|EFW06819.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 286

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 71/303 (23%), Positives = 120/303 (39%), Gaps = 32/303 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + +      M +    + H+  I    ++  LR    V V+++ + + +RI     + +
Sbjct: 4   TITIPQGLPEMTVKELLEEHFL-IPR-KVRHFLRIKKHVLVNQQPINWQSRIHPADAIVL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       E+ IL    NL +         LY+D  I + NKP GI          
Sbjct: 62  IFDEEDY----PEKSILMGKANLVEE--------LYQDEHIIIVNKPEGIKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G    + HRLD+ETSG ++ A+       L      + I + YW+LV
Sbjct: 110 ALLNHVYAYV---GNTCYVVHRLDKETSGAVLFAKNPFILPILNRLLENKEISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+   K++   + + +  H     +     + K   YA +    +         ++ Q 
Sbjct: 167 QGVFPKKRQIYTDKIGRDRHDRRKRL----VDNKNGQYAETQVTKLKEIGNN-TLIKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G PIVGD  Y              +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGHPIVGDPLYNPQKA--------KRLMLHAHRLTFTHPFTLEKIS 273

Query: 307 ITA 309
           + A
Sbjct: 274 VEA 276


>gi|300871781|ref|YP_003786654.1| pseudouridine synthase [Brachyspira pilosicoli 95/1000]
 gi|300689482|gb|ADK32153.1| pseudouridine synthase [Brachyspira pilosicoli 95/1000]
          Length = 238

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 77/221 (34%), Positives = 114/221 (51%), Gaps = 10/221 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQETS 155
           LLYED+ I V  KP  I  Q  +         +K ++  K  K       L HRLD+  S
Sbjct: 13  LLYEDNHIIVAVKPPNIPTQADNTGDTSFFENIKDYIKLKYNKQGNVFLGLVHRLDRPVS 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  L+E+ R R  QK Y+ +V GI   K+  + N+L+KK++  G+   V
Sbjct: 73  GVMVFAKTSKAASRLSEAIRNRNFQKTYYCVVKGILLEKENTLENYLIKKTNKLGNIAMV 132

Query: 216 VKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V +N K A  AI H+KV+ +   +    L+++  TGR HQ+RV   ++G  I GD KY +
Sbjct: 133 VFENTKNAKKAILHYKVLKEDNIKNLSLLKIELETGRFHQIRVQLSNLGHAIYGDRKYGS 192

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAH 314
             K +        L L A+ +  PHP     + I A LP +
Sbjct: 193 YIKYDRDDV---PLALFAKSIKFPHPTKNEEIFIEANLPDY 230


>gi|330814173|ref|YP_004358412.1| crcB-like protein [Candidatus Pelagibacter sp. IMCC9063]
 gi|327487268|gb|AEA81673.1| crcB-like protein [Candidatus Pelagibacter sp. IMCC9063]
          Length = 297

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 84/318 (26%), Positives = 149/318 (46%), Gaps = 24/318 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M + +   ++ +  N R+D+W K +        ++K+LRSG+++V+ K+VK + ++Q   
Sbjct: 1   MKFNEKFTIDENYANTRIDKWLKLNTQKFPQSFVEKLLRSGKIKVNNKKVKSSYKLQLED 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +           KE +    S N+ ++ + +++ +++E+    + NKP+GISVQ G+
Sbjct: 61  EIFLQFSYEEK----KENEKFSYSANIKEYKE-IRNNIIFENHDYLILNKPSGISVQSGT 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               ++   L  +  S+ +K  L HR+D+ETSGI+V A  R  AQ L+E FR + ++K Y
Sbjct: 116 KSPKNLIDILNKF--SEDKKFYLVHRIDKETSGIIVFACNRLFAQTLSEQFRNKEVKKSY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++++G     +  + +          D V  VK   K    A + F V+    + F ++
Sbjct: 174 LAILYGSIPRNEGTLDH----------DLVFKVKNQMKTFK-AETDFSVL-SKNKDFSYV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E  P TGR HQ+R     +  PIVGD KY      N        L LH+  +     +G 
Sbjct: 222 EATPITGRKHQIRQQFFKVNHPIVGDGKYEIPHYVNKDKF----LMLHSYKITFYD-KGK 276

Query: 304 RLQITAPLPAHMVKTWDS 321
                   P         
Sbjct: 277 EKTFKVEPPKEFKNFLKK 294


>gi|24379482|ref|NP_721437.1| putative pseudouridylate synthase [Streptococcus mutans UA159]
 gi|24377420|gb|AAN58743.1|AE014943_6 putative pseudouridylate synthase [Streptococcus mutans UA159]
          Length = 296

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 69/305 (22%), Positives = 129/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K+H   I+   L KI  + GQ+ V+ +       +  G  V I         II +++
Sbjct: 16  FLKSH--DISKTLLAKIKFKGGQILVNDQEENAIYLLDIGDRVTI---------IIPDEE 64

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
            L++   +          ++YED    + +KPAG +          I  F+K +    D 
Sbjct: 65  ALETLQPIKHD-----LNIVYEDEHFLILDKPAGYASIPSILHTNTIANFVKYYYLKKDY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
             ++  +  RLD++TSG++++A+   A   L +  + + I+K Y++LV G  +   +  I
Sbjct: 120 PNKQIHIVTRLDKDTSGLMLLAKHGYAHARLDKQLQKKTIKKRYYALVSGQGQLPDQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      +   + +       YA + +KV+  +      +++Q HTGRTHQ+RVH
Sbjct: 180 IAPIARP-----EDSIITRCVHPSGKYAHTSYKVLARYGDIA-LVDIQLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVK 317
             H+G P++GD  Y              +  LH  ++    P      Q  + L   +  
Sbjct: 234 FAHIGFPLLGDDLYGGEMG-----YGLKRQALHCHFLSFVDPFSKEHKQYNSSLTEDLDS 288

Query: 318 TWDSL 322
               L
Sbjct: 289 VIIDL 293


>gi|291457515|ref|ZP_06596905.1| RNA pseudouridine synthase, RluA family [Bifidobacterium breve DSM
           20213]
 gi|291381350|gb|EFE88868.1| RNA pseudouridine synthase, RluA family [Bifidobacterium breve DSM
           20213]
          Length = 314

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 69/332 (20%), Positives = 129/332 (38%), Gaps = 23/332 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS M     V   +     R D         I+      ++ SGQ RV  + V  ++ + 
Sbjct: 1   MSRM-----VPAPDALIGKRFDVAVAKML-GISRSKAADLIDSGQARVLGREVARSSSLM 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G+ V    V N +     E + + + + +    D +  +        +     +G +V 
Sbjct: 55  AGETVEFDLVENHV-----EPEPIANDMAVVYEDDDVVVVDKPVGVAAHASVGWSGPTVL 109

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G        D  ++        +  +  RLD  TSG+++V ++  A   +   F    ++
Sbjct: 110 GS-----LRDRGVRITSYGAAGREGIVSRLDVGTSGLMLVCKSELAYTEMRRQFAEHEVK 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +LV G  K  K  I   + +                     AI+H+ V++ F  + 
Sbjct: 165 KTYHALVQGGLKEDKATIEAPIGR-----AKVSDFRFCITPAGKPAITHWDVLERFDHEA 219

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + +   TGRTHQ+RVH   +G P+ GD  Y AN   +    + ++ +LHA  ++  HP
Sbjct: 220 TLVSVNLETGRTHQIRVHFSSIGHPLCGDPMYGANPVLSEALGL-DRQWLHAMKLEFRHP 278

Query: 301 EGG-RLQITAPLPAHMVKTWDSLGFKYDRNLY 331
                  + +  PA +    D +  ++   + 
Sbjct: 279 RTRVWTTVESHYPADLAAALDVMRARHTEPVE 310


>gi|227552604|ref|ZP_03982653.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecium
           TX1330]
 gi|227178230|gb|EEI59202.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecium
           TX1330]
          Length = 307

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/306 (23%), Positives = 123/306 (40%), Gaps = 33/306 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L KI  + GQ++V+ +       +     V I               
Sbjct: 26  FLKE--KGISKGLLAKIKFQGGQIKVNDQVENVLFSLAKDDKVTI--------------V 69

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG 141
           I     + T   D     ++YED  + V NKPAG+S           +   +K++   +G
Sbjct: 70  IPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQYHPNGTMANRVKAYYKKQG 129

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G+  N    +
Sbjct: 130 YENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDTQLREKKFVKKYQALVSGMLSN----L 185

Query: 199 ANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +        I  DY  ++K+        A + +++     +    +++Q HTGRTHQ+RV
Sbjct: 186 SAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYRIEKRLTEIA-LVDIQLHTGRTHQIRV 244

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GC ++GD  Y              +  LH   +   HP     L+   PL A M 
Sbjct: 245 HFSAIGCALLGDDMYSGRM-----DLGIKRQALHCYDLRFYHPFTEELLEFKQPLAADME 299

Query: 317 KTWDSL 322
                 
Sbjct: 300 AVVRRF 305


>gi|199599112|ref|ZP_03212517.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|199590005|gb|EDY98106.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
          Length = 300

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 64/308 (20%), Positives = 120/308 (38%), Gaps = 35/308 (11%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K      +   L+K+  + G + V+K++      +++G  + +              +
Sbjct: 17  FLKQQ--GFSRAQLKKLRYQGGFIFVNKRQQHTAYPLRNGDRILV--------------Q 60

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---D 138
                   +      +  + YED    V NKPAG++     G     +   +K+++    
Sbjct: 61  TAPEQAAASVVPYEHEFPICYEDDDYLVVNKPAGVASIPAVGRRNDSMANMVKAYLIKTH 120

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKEC 197
           ++ Q   +  RLD++TSG++V A+   A   L          K Y +LV      +    
Sbjct: 121 AESQAVHVVTRLDRDTSGLMVFAKHSLAHSLLDRQLHSENFLKQYLALVTSKSLLSAHGW 180

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   +   +   G Y+  V    +    +++ ++ +   +     L +  HTGRTHQ+RV
Sbjct: 181 IILPIGVST---GFYMRRVVI--ETGKPSVTEYQTLAQNSDAAAVL-VTLHTGRTHQIRV 234

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +G P+ GD  Y              +  LH  ++    P   + + + APLP  M 
Sbjct: 235 HFAAIGHPLFGDDLYNRQADD------FKRQALHCAHLRFWQPLQKKWVDLHAPLPTDMA 288

Query: 317 KTWDSLGF 324
           K  D L  
Sbjct: 289 KLSDHLNL 296


>gi|222823615|ref|YP_002575189.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           lari RM2100]
 gi|222538837|gb|ACM63938.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           lari RM2100]
          Length = 320

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 71/314 (22%), Positives = 124/314 (39%), Gaps = 36/314 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            RLD +  +     +   + K+++   + +++K   K + +I+    + I         +
Sbjct: 10  ERLDIFLSDILKQ-SRSQVAKLIKENCIYINEKIENKSSKKIKQKDEISIFLP------L 62

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           IKE K          ++      +LYED  + V NK   I V G S +    +  L  W+
Sbjct: 63  IKEAK--------ESYTPEFDIEILYEDDDVLVLNKAPNIVVHGASSV---KEATLVDWL 111

Query: 138 DSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             KG          +  L HRLD+ TSG +++A+   A Q L      + + + Y +L  
Sbjct: 112 LHKGYTLSNLNGEHRAGLVHRLDKGTSGAIIIAKNNQAHQFLANQLLDKSMGRFYLALSE 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
              KN K      +++  +     +    +N   A  A + F  +   A+    +  + +
Sbjct: 172 LPLKNDKMSNEKAIMRCPNNRLKKITTNTKN-PLAKNAKTDFINLLS-AKNCSLIAAKLY 229

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI- 307
           TGRTHQ+R H       I+GD  Y    K  +     N++ LHA  +   HP    L   
Sbjct: 230 TGRTHQIRTHLADFNRYILGDELYGYKGKIKY-----NRVMLHAYLIYFIHPRTKELMFI 284

Query: 308 TAPLPAHMVKTWDS 321
            AP+     +    
Sbjct: 285 KAPMFDDFYQILKE 298


>gi|257885366|ref|ZP_05665019.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,501]
 gi|257821222|gb|EEV48352.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,501]
          Length = 299

 Score =  184 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 71/306 (23%), Positives = 121/306 (39%), Gaps = 33/306 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L KI  + GQ++V+ +       +     V I               
Sbjct: 18  FLKE--KGISKGLLAKIKFQGGQIKVNDQVENVLFSLAKDDKVTI--------------V 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG 141
           I     + T   D     ++YED  + V NKPAG+S           +   +K++   +G
Sbjct: 62  IPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQYHPNGTMANRVKAYYKKQG 121

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G   +    +
Sbjct: 122 YENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQLREKKFVKKYQALVSGRLSD----L 177

Query: 199 ANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +        I  DY  ++K+        A + + +     +    +++Q HTGRTHQ+RV
Sbjct: 178 SAHGRIDLPIARDYSSLLKRMVSDEGRSAQTEYWIEKRLTEIA-LVDIQLHTGRTHQIRV 236

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GC ++GD  Y              +  LH   +   HP     L+   PL A M 
Sbjct: 237 HFSTIGCALLGDDMYGGRM-----DLGIKRQALHCYDLRFYHPFTEELLEFKQPLAADME 291

Query: 317 KTWDSL 322
                 
Sbjct: 292 AVVRRF 297


>gi|224538849|ref|ZP_03679388.1| hypothetical protein BACCELL_03745 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224519524|gb|EEF88629.1| hypothetical protein BACCELL_03745 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 510

 Score =  184 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 71/243 (29%), Positives = 115/243 (47%), Gaps = 19/243 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++  + +         K  ++YED  + + NKPAG+    G      I
Sbjct: 278 CEPILRHMLQGLEVEANPMQQEAERGNEKLNIVYEDQWLLIINKPAGMLSVPGKERQTSI 337

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               +     + + P + HRLD  TSG+L++A+ +   QHL   F+ R I+K Y +L+ G
Sbjct: 338 YDLAREAY-PEAEGPMIVHRLDMATSGLLIIAKDKKTHQHLQAQFKNRSIRKKYIALLDG 396

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I    +  I   L          +     + +    AI++++V++    K+  +   PHT
Sbjct: 397 IVPEDEGTIELSLCPNPLDRPRQM----VDTQYGKPAITYYQVLER-TDKYTRIAFYPHT 451

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVHA H   + CPI+GD  Y    K         +LYLHA  ++  HP  G+ +
Sbjct: 452 GRTHQLRVHAAHPSGLHCPIIGDELYGKKDK---------RLYLHAESIEFTHPVNGQSM 502

Query: 306 QIT 308
            IT
Sbjct: 503 CIT 505


>gi|160890006|ref|ZP_02071009.1| hypothetical protein BACUNI_02440 [Bacteroides uniformis ATCC 8492]
 gi|270294676|ref|ZP_06200878.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|156860394|gb|EDO53825.1| hypothetical protein BACUNI_02440 [Bacteroides uniformis ATCC 8492]
 gi|270276143|gb|EFA22003.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 223

 Score =  184 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 69/219 (31%), Positives = 112/219 (51%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKQYLKEKYSKPGNVFIGVAHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E F+   ++K YW++V  +P+ ++  + N+L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFKNSEVKKTYWAVVKNLPREEEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   G+  AI H+++I   +Q +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVPGSKKAILHYRLIGR-SQNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                 S     + LHARY+   HP     +++ AP+P 
Sbjct: 180 RSNPDGS-----ICLHARYIRFVHPVSKELIEVEAPVPP 213


>gi|262047145|ref|ZP_06020104.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus MV-3A-US]
 gi|293380273|ref|ZP_06626351.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
 gi|260572722|gb|EEX29283.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus MV-3A-US]
 gi|290923182|gb|EFE00107.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
          Length = 301

 Score =  184 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 70/325 (21%), Positives = 126/325 (38%), Gaps = 35/325 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT +  ++V+  +         KN + H    N +     G + V+ KR   +  +++G 
Sbjct: 1   MTSLFKLIVQERDPKKLGPFLLKNGFSHQALNNAKH--HHGMILVNHKRRYTSFNLRAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V         N  +K                     ++ E+    V NKPAG+      
Sbjct: 59  EVIFISGEEKKNDFLK--------------PSNNPVSIVLENKNYLVVNKPAGVLSIPSR 104

Query: 124 G-IAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                 +   L  +   KGQK   P +  RLD+ TSG+++V +   +    ++  + + +
Sbjct: 105 YEDDDAVVNRLLGYFAQKGQKNLKPHVITRLDRYTSGLVLVGKNAISHARFSKIGKEKFV 164

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K + ++V G     +       L    IG     V +        A + ++V+D     
Sbjct: 165 KKYH-AIVHGNFAPNELT----GLIDQPIGKKGSGVKRAVVADGKDAQTAYRVLDQVT-G 218

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E++  TGRTHQ+RVH  ++G P+ GD  Y             ++  L+  Y++ P 
Sbjct: 219 ASLVELRLLTGRTHQIRVHMAYLGHPLYGDPLYG-------IQDGFSRQALNCFYLNFPD 271

Query: 300 PEGGRLQITAPL--PAHMVKTWDSL 322
           P   +   T  L  P  M + W  L
Sbjct: 272 PFSQQKCKTIELNDPKDMQELWQKL 296


>gi|322831582|ref|YP_004211609.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321166783|gb|ADW72482.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 259

 Score =  184 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 66/257 (25%), Positives = 115/257 (44%), Gaps = 18/257 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHLIAVNKPAGMLVHRSWLDRHETVFVMQTLRDQIGQHVFTVHRLDKPTSGVLLL 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++ K+Y ++V G              +   I   +       +
Sbjct: 64  ALSSDVARLLSQQFENNQMSKVYHAVVRGYVPQDGTLDYALTEELDKIADKFAS----PD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++V+               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHYRVVAQVEMPVAVGRYDTARYSLVELKPETGRKHQLRRHMSHLRHPIIGDS 179

Query: 271 KYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +      +G       + L LHA +M LPHP  G  L I A             G++  
Sbjct: 180 AHGDLKQNRGMTQHFGCSGLMLHASHMQLPHPVTGEPLSIQARWDHRWQNVVTQFGWQ-G 238

Query: 328 RNLYIKRLYSQDECKQN 344
           +   ++R+   + C+Q+
Sbjct: 239 KIPELERVEFAETCRQD 255


>gi|307637434|gb|ADN79884.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 908]
 gi|325996024|gb|ADZ51429.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 2018]
 gi|325997619|gb|ADZ49827.1| Ribosomal large subunit pseudouridylate synthase D [Helicobacter
           pylori 2017]
          Length = 327

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 68/331 (20%), Positives = 137/331 (41%), Gaps = 35/331 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHI 77
            R+D +       I+   +  +++ G V   KK VK     ++ G  + +     A   +
Sbjct: 12  KRIDEFLAKEL-QISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPKIAPKPL 70

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            KE                L+  +++ED  + V NKP  + V     +    +  L  W+
Sbjct: 71  KKELD--------------LEIEVIFEDEDLLVLNKPPNLVVHKAPSV---KEPTLVDWL 113

Query: 138 DSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            S+  +           + HRLD++TSG +V+A+       L+E  + + + + Y +L+ 
Sbjct: 114 KSQNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVCLSEQLKTKTMGRYYIALLS 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
              K +K  +  +L +  +     + +    ++ + Y+ S F  +         +  +  
Sbjct: 174 TPLKEEKMSVECYLTRNPNNRLKMIALKAAQKEKSRYSKSEFISLLTSQNGMDLIGAKLF 233

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+R H  ++   I+GD+ Y  N      S  + ++ LHA  ++  HP    +L+ 
Sbjct: 234 TGRTHQIRAHLEYLNRHIIGDNLYGLN---GALSKEEIRIMLHAYLIEFKHPRSEQKLRF 290

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             PL   M++    +   +D+    + L  +
Sbjct: 291 KVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|253702213|ref|YP_003023402.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251777063|gb|ACT19644.1| pseudouridine synthase, RluA family [Geobacter sp. M21]
          Length = 297

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 125/311 (40%), Gaps = 36/311 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           V+ +    RLD   K  +P  +   +++I+  G   + +  V+  +R ++ G+ + +  +
Sbjct: 7   VDAELAGTRLDDAAKTLFPQYSKGEIRRIIDWGGCYLSQTLVRVASRTVKEGEEIALGIM 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                                    + K  LLYED       K AG + Q          
Sbjct: 67  ----------------EAERCIELVYKKEELLYEDKDFLAVYKAAGFNSQRTPYQLKGTV 110

Query: 131 GF-LKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            + ++ ++ S G +   R+ HRLD+ TSG++   + + AA  ++   +  ++QK YW+LV
Sbjct: 111 EYAVECYMKSIGLRDPSRVVHRLDRGTSGVMFFPKHKQAATLISNLLKDGKVQKTYWALV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G P  +   +   L K S                   A + F+V+         +E +P
Sbjct: 171 SGSPDQQSWKVEAPLGKVSK-------FKYGVALNGKPARTLFRVVG-EGAGVTAVEAKP 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGRTHQ+RVH  + G PI+GD  Y              ++ LH R M     +G  ++ 
Sbjct: 223 LTGRTHQIRVHLAYSGFPIIGDETYGGIPAA--------RMMLHCRGMRFTGAKGKVIEA 274

Query: 308 TAPLPAHMVKT 318
            AP  A     
Sbjct: 275 FAPADADFRAA 285


>gi|325300058|ref|YP_004259975.1| pseudouridine synthase [Bacteroides salanitronis DSM 18170]
 gi|324319611|gb|ADY37502.1| pseudouridine synthase [Bacteroides salanitronis DSM 18170]
          Length = 224

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 70/230 (30%), Positives = 117/230 (50%), Gaps = 15/230 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   LK ++     KP      +THRLD+  S
Sbjct: 3   IVYEDNHIIIVNKTASEIVQGDKTGDTPLSEMLKQYIKEAYAKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L + FR   ++K YW++V   P  ++  + ++L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNDMFRNGEVRKTYWAIVKQCPPAEEGELVHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K +  A+ H+K+ID  ++ +  +E+   TGR HQ+R      GCPI GD KY   
Sbjct: 122 -DREVKDSKKAVLHYKLIDR-SENYYLVEVDLKTGRHHQIRCQLAKAGCPIKGDLKYGFP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA-HMVKTWDSLG 323
                 S     + LHAR +   HP   + +++TAPLP  ++ K + ++G
Sbjct: 180 RSNPDGS-----ICLHARTVSFIHPVSKKLIEVTAPLPEGNLWKAFQTIG 224


>gi|262277120|ref|ZP_06054913.1| ribosomal large subunit pseudouridine synthase C [alpha
           proteobacterium HIMB114]
 gi|262224223|gb|EEY74682.1| ribosomal large subunit pseudouridine synthase C [alpha
           proteobacterium HIMB114]
          Length = 288

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 79/320 (24%), Positives = 142/320 (44%), Gaps = 33/320 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   ++  V+  D E  R+DR+ K  +P+I     +K LR   + V+ K+VK   +++  
Sbjct: 1   MKKPLKSFVINKDFEGSRVDRFLKKQFPNIPQSLFEKNLRKKNITVNNKKVKNLFKLEIN 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +V I   +   N I K+++I +         + LK   ++E     V NKP G + Q G
Sbjct: 61  DIVNIFTELKIENKINKKKQIFN-----INDYNELKKNFVFECEDYCVLNKPYGYASQDG 115

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           S +   +   L S   +      + HRLD++TSG++++A+ R  A+  +E F+ R ++K 
Sbjct: 116 SKVKLSVIDILNSTKKNYY----IVHRLDKDTSGLMLLAKNRFYAKKFSEMFKSREVKKK 171

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  ++ G  K  K  I +    K  + G  +            +  +F+VI      F +
Sbjct: 172 YLVIINGKIKKNKGEIHS----KEKVNGKEI-----------ESKLYFEVI-SKKNNFSY 215

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           LE+   TGR HQ+R     +G P+VGD KY              +L L +  ++  +   
Sbjct: 216 LEIDLITGRKHQIRKQFSDIGHPVVGDLKYGDKKNNT-------QLCLLSYEIEFEY-NN 267

Query: 303 GRLQITAPLPAHMVKTWDSL 322
              +  A +P +     +  
Sbjct: 268 KIKKYKATIPDNFKTCLEKF 287


>gi|317481349|ref|ZP_07940417.1| RNA pseudouridylate synthase [Bacteroides sp. 4_1_36]
 gi|316902445|gb|EFV24331.1| RNA pseudouridylate synthase [Bacteroides sp. 4_1_36]
          Length = 223

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 69/219 (31%), Positives = 112/219 (51%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKQYLKEKYSKPGNVFIGVAHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E F+   ++K YW++V  +P+ ++  + N+L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFKNSEVKKTYWAVVKNLPREEEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   G+  AI H+++I   +Q +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVPGSKKAILHYRLIGR-SQNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                 S     + LHARY+   HP     +++ AP+P 
Sbjct: 180 RSNPDGS-----ICLHARYIRFVHPVSKEPIEVEAPVPP 213


>gi|120601247|ref|YP_965647.1| pseudouridine synthase [Desulfovibrio vulgaris DP4]
 gi|120561476|gb|ABM27220.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           vulgaris DP4]
          Length = 390

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 129/319 (40%), Gaps = 41/319 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +VV  +E   +L ++    +  +    L + +RSGQVR +  R K  +R++ G  VR+
Sbjct: 4   QAIVVTREEAGQKLLQFLARRFA-LPQAMLHRWIRSGQVRRNGGRCKPFDRLEMGDEVRV 62

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLK----------------------------- 98
           PP   +++       +  SS  +    D                                
Sbjct: 63  PPFAASMSERADVGPVSASSDAVRNVPDAAASRPAPSRHDRDGHDAMQPSRQRRPKADTS 122

Query: 99  -------SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                    ++ E   +++F+KPAG++V  G+G    +   L          P   HRLD
Sbjct: 123 LQPARPLPPVVAETPDLFIFDKPAGLAVHPGTGHTDSLTTRLAQHFAKAPFMPTPAHRLD 182

Query: 152 QETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           ++TSG+L+VAR+ A  + L E+F     + K Y + V G  +       +  L K     
Sbjct: 183 RDTSGLLLVARSYAMLRTLHEAFASHDALVKEYLAWVAGCWQPAAPVTLHDRLSKGAEAS 242

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  V   +E GA  A +   ++    Q    L +  HTGRTHQ+RV     G P++GD 
Sbjct: 243 GFERVASDDE-GAEAACTVRCLL--REQHRSLLLVTLHTGRTHQIRVQLSRRGHPLLGDR 299

Query: 271 KYCANFKGNFTSPIQNKLY 289
           KY    +         +L 
Sbjct: 300 KYGGPPRMGGFLLHAVRLC 318


>gi|328948648|ref|YP_004365985.1| pseudouridine synthase, RluA family [Treponema succinifaciens DSM
           2489]
 gi|328448972|gb|AEB14688.1| pseudouridine synthase, RluA family [Treponema succinifaciens DSM
           2489]
          Length = 317

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 72/314 (22%), Positives = 143/314 (45%), Gaps = 33/314 (10%)

Query: 17  ENMRLDRWFKNHYPHI-----NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           E   L+ + +   P +     +   +++++ SG V ++ ++ +  + +I SG  +++   
Sbjct: 10  EKKTLNEFLRQKIPELLEGEISNSKIRRLIVSGAVYINSRQCRIPSFKINSGTAIKV--- 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHI 129
                 +I ++K            +  ++ +L+ED  +   NKP  +   Q  +G   + 
Sbjct: 67  ------LIDKEKFFFEKQPEDADFELTENDVLFEDEYLIAINKPPFLPTEQTITGQRKNA 120

Query: 130 DGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                 ++  K           + HRLD+ETSGIL+  ++R+  + ++E F+ R I+KIY
Sbjct: 121 HDCTVKYLWQKNSSLRNPPYVGIMHRLDRETSGILLFTKSRSVNKDISEMFKTRGIKKIY 180

Query: 184 WSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
            ++  G  P+ K+  + N++ + S         +    +G  +  + FK+I      F  
Sbjct: 181 RAVCTGKLPEQKEFTVENFIARISPKSSACKMGIVPESRGGLFTKTDFKII-SEKNGFIQ 239

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           ++ Q HTGRTHQ+RV    M  PI GD  Y             +++ LHAR ++  HP  
Sbjct: 240 IDCQLHTGRTHQIRVQLSSMNLPIAGDELYGGIK--------SDRIKLHARKIEFVHPVS 291

Query: 303 -GRLQITAPLPAHM 315
             ++ I + +P + 
Sbjct: 292 KEKITIESEIPKNF 305


>gi|309806639|ref|ZP_07700635.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
 gi|309810106|ref|ZP_07703952.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
 gi|312870915|ref|ZP_07731020.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
 gi|315653177|ref|ZP_07906102.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
 gi|308166944|gb|EFO69127.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
 gi|308169605|gb|EFO71652.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
 gi|311093605|gb|EFQ51944.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
 gi|315489542|gb|EFU79179.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
          Length = 292

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 74/303 (24%), Positives = 128/303 (42%), Gaps = 34/303 (11%)

Query: 3   LMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQ 60
           +M  Y+ Y+ +  +E N  +D+  +N    I     +  LR    + V+ K +  N ++ 
Sbjct: 9   IMNQYIYYLTISQNENNQNIDQIMRNLL--IPR-KWRHFLRIEKNILVNNKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V NKPAG    
Sbjct: 66  TNDLITI-----KLNHVESLQQKYPASGNMPN--------IIYENDDVLVINKPAGQKTH 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 113 PN---LYETDTALNDCASYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           + Y++ +      +    I   +          +            AI+H++V+   A K
Sbjct: 170 RSYFAWIDATNDISDNGTINLPIGDDPLDMRKRMVRT-----DGLKAITHYQVVKKTANK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++         KL L A  +    
Sbjct: 225 I-LVKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQAG------EKLQLTAYKLVFQK 277

Query: 300 PEG 302
           P  
Sbjct: 278 PFS 280


>gi|257888167|ref|ZP_05667820.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,141,733]
 gi|257824221|gb|EEV51153.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,141,733]
          Length = 299

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 72/306 (23%), Positives = 122/306 (39%), Gaps = 33/306 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L KI  + GQ++V+ +       +     V I               
Sbjct: 18  FLKE--KGISKGLLAKIKFQGGQIKVNDQVENVLFSLAKDDKVTI--------------V 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG 141
           I     + T   D     ++YED  + V NKPAG+S           +   +K++   +G
Sbjct: 62  IPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQYHPNGTMANRVKAYYKKQG 121

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G+  N    +
Sbjct: 122 YENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDTQLREKKFVKKYQALVSGMLSN----L 177

Query: 199 ANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +        I  DY  ++K+        A + + +     +    +++Q HTGRTHQ+RV
Sbjct: 178 SAHSHIDLPIARDYSSLLKRMVSDEGRSAQTEYWIEKRLTEIA-LVDIQLHTGRTHQIRV 236

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GC ++GD  Y              +  LH   +   HP     L+   PL A M 
Sbjct: 237 HFSAIGCALLGDDMYSGRM-----DLGIKRQALHCYDLRFYHPFTEELLEFKQPLAADME 291

Query: 317 KTWDSL 322
                 
Sbjct: 292 AVVRRF 297


>gi|229068942|ref|ZP_04202236.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|228714226|gb|EEL66107.1| Pseudouridine synthase [Bacillus cereus F65185]
          Length = 307

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 129/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            ++V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EIIVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                   +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGKIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P  + K     
Sbjct: 284 AIEVDVPFPTKLNKKIKEF 302


>gi|281599417|gb|ADA72401.1| Ribosomal large subunit pseudouridine synthase A [Shigella flexneri
           2002017]
          Length = 238

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 74/251 (29%), Positives = 117/251 (46%), Gaps = 20/251 (7%)

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P  +  N  + E K+   + N  +       ++LY+D  I V NKP+G+    G  +  
Sbjct: 5   CPAFDRCNASVTEPKMGMENYNPPQEPWL---VILYQDDHIMVVNKPSGLLSVPGR-LEE 60

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           H D  + + +     +    HRLD  TSG++VVA T+AA + L   FR R  +K Y + V
Sbjct: 61  HKDSVM-TRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARV 119

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEM 245
           WG P   +  +   L+       D+ +  KQ    +    A + ++V++  A     + +
Sbjct: 120 WGHPSPAEGLVDLPLI------CDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVL 173

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGR 304
           +P TGR+HQLRVH L +G PI+GD  Y +            +L LHA  + + HP  G  
Sbjct: 174 KPITGRSHQLRVHMLALGHPILGDRFYASPEARAMA----PRLLLHAEMLTITHPAYGNS 229

Query: 305 LQITAPLPAHM 315
           +   A  PA  
Sbjct: 230 MTFKA--PADF 238


>gi|261209248|ref|ZP_05923640.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium TC 6]
 gi|289565997|ref|ZP_06446435.1| pseudouridylate synthase, 23S RNA-specific [Enterococcus faecium
           D344SRF]
 gi|294616199|ref|ZP_06695996.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1636]
 gi|260076794|gb|EEW64529.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium TC 6]
 gi|289162195|gb|EFD10057.1| pseudouridylate synthase, 23S RNA-specific [Enterococcus faecium
           D344SRF]
 gi|291590954|gb|EFF22666.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1636]
          Length = 299

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 121/302 (40%), Gaps = 33/302 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L KI  + GQ++V+ +       +     V I               
Sbjct: 18  FLKE--KGISKGLLAKIKFQGGQIKVNDQVENVLFSLAKDDKVTI--------------V 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG 141
           I     + T   D     ++YED  + V NKPAG+S           +   +K++   +G
Sbjct: 62  IPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQYHPNGTMANRVKAYYKKQG 121

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G   +    +
Sbjct: 122 YENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQLREKKFVKKYQALVSGRLSD----L 177

Query: 199 ANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +        I  DY  ++K+        A + + +     +    +++Q HTGRTHQ+RV
Sbjct: 178 SAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYWIEKRLTEIA-LVDIQLHTGRTHQIRV 236

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GC ++GD  Y              +  LH   +   HP     L+   PL A M 
Sbjct: 237 HFSAIGCALLGDDMYGGRM-----DLGIKRQALHCYDLRFYHPFTEELLEFKQPLAADME 291

Query: 317 KT 318
             
Sbjct: 292 AV 293


>gi|317014156|gb|ADU81592.1| hypothetical protein HPGAM_03855 [Helicobacter pylori Gambia94/24]
          Length = 327

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 70/331 (21%), Positives = 138/331 (41%), Gaps = 35/331 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHI 77
            RLD +       I+   +  +++ G V   KK VK     ++ G  + +     A   +
Sbjct: 12  KRLDEFLAKELR-ISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPKIAPKPL 70

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            KE                L+  +++ED  + V NKP  + V     +    +  L  W+
Sbjct: 71  KKELD--------------LEIEVIFEDEDLLVLNKPPNLVVHKAPSV---KEPTLVDWL 113

Query: 138 DSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            S+  +           + HRLD++TSG +V+A+      HL+E  + + + + Y +L+ 
Sbjct: 114 KSQNYELSNLGLKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLS 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
              K +K  +  +L +  +     + +    ++ + Y+ S F  +         +  +  
Sbjct: 174 TPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFISLLTSQNGMDLIGAKLF 233

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+R H  ++   I+GD+ Y  N      S  + ++ LHA  ++  HP    +L+ 
Sbjct: 234 TGRTHQIRAHLEYLNRHIIGDNLYGLN---GALSKEEIRIMLHAYLIEFKHPRSEQKLRF 290

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             PL   M++    +   +D+    + L  +
Sbjct: 291 KVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|257880319|ref|ZP_05659972.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,230,933]
 gi|257882173|ref|ZP_05661826.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,502]
 gi|257890978|ref|ZP_05670631.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,410]
 gi|257894233|ref|ZP_05673886.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,408]
 gi|258614733|ref|ZP_05712503.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Enterococcus faecium DO]
 gi|260562377|ref|ZP_05832891.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium C68]
 gi|293553066|ref|ZP_06673708.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1039]
 gi|293559437|ref|ZP_06675975.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1162]
 gi|293568340|ref|ZP_06679663.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1071]
 gi|294621976|ref|ZP_06701121.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium U0317]
 gi|257814547|gb|EEV43305.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,230,933]
 gi|257817831|gb|EEV45159.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,502]
 gi|257827338|gb|EEV53964.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,410]
 gi|257830612|gb|EEV57219.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,408]
 gi|260073301|gb|EEW61642.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium C68]
 gi|291588949|gb|EFF20774.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1071]
 gi|291598455|gb|EFF29527.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium U0317]
 gi|291602775|gb|EFF32985.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1039]
 gi|291606592|gb|EFF35988.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1162]
          Length = 299

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 71/306 (23%), Positives = 121/306 (39%), Gaps = 33/306 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L KI  + GQ++V+ +       +     V I               
Sbjct: 18  FLKE--KGISKGLLAKIKFQGGQIKVNDQVENVLFSLAKDDKVTI--------------V 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG 141
           I     + T   D     ++YED  + V NKPAG+S           +   +K++   +G
Sbjct: 62  IPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQYHPNGTMANRVKAYYKKQG 121

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G   +    +
Sbjct: 122 YENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQLREKKFVKKYQALVSGRLSD----L 177

Query: 199 ANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +        I  DY  ++K+        A + + +     +    +++Q HTGRTHQ+RV
Sbjct: 178 SAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYWIEKRLTEIA-LVDIQLHTGRTHQIRV 236

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GC ++GD  Y              +  LH   +   HP     L+   PL A M 
Sbjct: 237 HFSAIGCALLGDDMYGGRM-----DLGIKRQALHCYDLRFYHPFTEELLEFKQPLAADME 291

Query: 317 KTWDSL 322
                 
Sbjct: 292 AVVRRF 297


>gi|294618813|ref|ZP_06698339.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1679]
 gi|291594936|gb|EFF26287.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1679]
          Length = 299

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 72/306 (23%), Positives = 121/306 (39%), Gaps = 33/306 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L KI  + GQ++V+ +       +     V I               
Sbjct: 18  FLKE--KGISKGLLAKIKFQGGQIKVNDQVENVLFSLAKDDKVTI--------------V 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG 141
           I     + T   D     ++YED  + V NKPAG+S           +   +K++   KG
Sbjct: 62  IPAEGEHETVLLDETSIDIVYEDEHVLVVNKPAGVSSIPAQYHPNGTMANRVKAYYKKKG 121

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G   +    +
Sbjct: 122 YENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQLREKKFVKKYQALVSGRLSD----L 177

Query: 199 ANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +        I  DY  ++K+        A + + +     +    +++Q HTGRTHQ+RV
Sbjct: 178 SAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYWIEKRLTEIA-LVDIQLHTGRTHQIRV 236

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GC ++GD  Y              +  LH   +   HP     L+   PL A M 
Sbjct: 237 HFSAIGCALLGDDMYGGRM-----DLGIKRQALHCYDLRFYHPFTEELLEFKQPLAADME 291

Query: 317 KTWDSL 322
                 
Sbjct: 292 AVVRRF 297


>gi|329919667|ref|ZP_08276645.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
 gi|328937319|gb|EGG33743.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
          Length = 292

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 74/303 (24%), Positives = 130/303 (42%), Gaps = 34/303 (11%)

Query: 3   LMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQ 60
           +M  Y+ Y+ +  +E N  +D+  +N    I     +  LR    + V+ K +  N ++ 
Sbjct: 9   IMNQYIYYLTISQNENNQNVDQIMRNLL--IPR-KWRHFLRIEKNILVNDKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V NKPAG    
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENDDVLVINKPAGQKTH 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L    +  G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 113 PN---LYETDTALNDCANYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           + Y++ +      +    I   +          +       +    AI+H++V+   A K
Sbjct: 170 RSYFAWIEATNDISDNGTINLPIGDDPLDMRKRMVR-----EDGLKAITHYQVVKKTANK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++         KL L A  +    
Sbjct: 225 I-LVKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQAG------EKLQLTAYKLVFQK 277

Query: 300 PEG 302
           P  
Sbjct: 278 PFS 280


>gi|312872184|ref|ZP_07732257.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
 gi|311092268|gb|EFQ50639.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
          Length = 292

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 74/303 (24%), Positives = 128/303 (42%), Gaps = 34/303 (11%)

Query: 3   LMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQ 60
           +M  Y+ Y+ +  +E N  +D+  +N    I     +  LR    + V+ K +  N ++ 
Sbjct: 9   IMNQYIYYLTISQNENNQNVDQIMRNLL--IPR-KWRHFLRIEKNILVNNKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V NKPAG    
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENDDVLVINKPAGQKTH 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 113 PN---LYETDTALNDCASYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLY 169

Query: 181 KIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           + Y++ +      +    I   +          +            AI+H++V+   A K
Sbjct: 170 RSYFAWIEATNDISDNGTINLPIGDDPLDMRKRMVRA-----DGLKAITHYQVVKKTANK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++         KL L A  +    
Sbjct: 225 I-LVKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQAG------EKLQLTAYKLVFQK 277

Query: 300 PEG 302
           P  
Sbjct: 278 PFS 280


>gi|228951772|ref|ZP_04113871.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228807894|gb|EEM54414.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
          Length = 307

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 129/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            ++V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EIIVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                   +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAERGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGKIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P  + K     
Sbjct: 284 AIEVDVPFPTKLNKKIKEF 302


>gi|319946086|ref|ZP_08020334.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
 gi|319747732|gb|EFV99977.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
          Length = 278

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 71/269 (26%), Positives = 119/269 (44%), Gaps = 29/269 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              V+V+ + V + + +Q+G  + +           +E+ +L    +L +         L
Sbjct: 24  KKHVQVNGETVHWQSMLQAGDQLTLTFDPEDY----EEKDLLAGDASLVET--------L 71

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + + NKP G+           +   + ++V   G+   + HRLD+ETSG LV A+
Sbjct: 72  YEDEHLIIVNKPEGMKTHANQPDEIALLNHVSTYV---GKTCYVVHRLDKETSGALVFAK 128

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      ++IQ+ YW+L+ G    K+    + L +  H     +     + + 
Sbjct: 129 NPFVLPVLNRLLEDKKIQRDYWALILGSLPKKQLVYKDKLGRDRHDRRKRI----VDPRK 184

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             YA +H  ++  F ++   +  Q  TGRTHQ+RVH  H G PIVGD  Y          
Sbjct: 185 GLYAETHVTILKTF-KRTSLVNCQLQTGRTHQIRVHLSHHGHPIVGDPLYNPERA----- 238

Query: 283 PIQNKLYLHARYMDLPHPEG-GRLQITAP 310
               +L LHA  + L HP    ++Q+ AP
Sbjct: 239 ---PRLMLHAHRLRLSHPFTLEKIQVEAP 264


>gi|229057021|ref|ZP_04196415.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228720298|gb|EEL71874.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 307

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 65/319 (20%), Positives = 126/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  +    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EITVPATWNGISIESLLKVEW-ELPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +     +  E               + +  +++ED  + + NK   +           
Sbjct: 70  MFMEEEYGVEPE---------------YGELNVVFEDDHVLIVNKQGQMDTHPSEKNGTG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYMA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV    K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEAKVKKKQGTIDAAIGRDRHHATRRRVSPK-----GDQAITYYKVEKYFKKQNATLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y         +   +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQ------TTYMSGQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            + +  P P ++  T    
Sbjct: 284 EIVVDVPFPTNLNDTMKKF 302


>gi|295426413|ref|ZP_06819063.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           amylolyticus DSM 11664]
 gi|295063781|gb|EFG54739.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           amylolyticus DSM 11664]
          Length = 294

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 65/296 (21%), Positives = 119/296 (40%), Gaps = 40/296 (13%)

Query: 38  QKILRS----GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
           Q ++++    G V V+ KR   +  +++G  V   P     NH ++  +           
Sbjct: 28  QALIKARHHGGLVLVNHKRRYNSFHLRAGDEVIFIPGHEKENHWLRPSEE---------- 77

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK----GQKPRLTHR 149
                  ++ E     + NK AG+                      K    G KP +  R
Sbjct: 78  ----PIKIVKETPNYLIVNKEAGVLSIPSRYEDSDALVNRAMCYFEKQNEAGLKPHVVTR 133

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSH 207
           LD++TSG++++ +   A    ++  +   ++K + ++V G       K  I         
Sbjct: 134 LDRDTSGLVLIGKNSVAHARFSKMDKENFVKKYH-AIVAGNFSSNELKGLIDQP------ 186

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           IG +   V +Q       A + ++V+         +E++  TGRTHQ+RVH  ++G P++
Sbjct: 187 IGKEGSGVKRQVMSTGQKAQTEYQVL-AQKNNASLVELRLLTGRTHQIRVHMAYIGHPLL 245

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GD  Y         S I  +  L+  Y+    P +  +++     PA M K W+SL
Sbjct: 246 GDKLYGG-------SNIFFRQALNCFYLAFTDPFDQEQVEEKISDPADMQKLWNSL 294


>gi|293394695|ref|ZP_06638987.1| tRNA pseudouridine synthase C [Serratia odorifera DSM 4582]
 gi|291422821|gb|EFE96058.1| tRNA pseudouridine synthase C [Serratia odorifera DSM 4582]
          Length = 257

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 107/237 (45%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDQYLVAVNKPAGWLVHRSWLDSRETVFVMQTVRDQIGQHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  L++ F   ++QK Y ++V G              ++  I   +     + +
Sbjct: 64  ALSSEVAHLLSQQFEQHQVQKTYHAVVRGFVTQGARLDYPLTQERDKIADKFA----EQD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +             + ++  +E+QP TGR HQLR H  H+  PI+GD 
Sbjct: 120 KEPQPAVTHYRPLAQVEMPVAIGRYDSARYSLMELQPETGRKHQLRRHMTHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           K+      +G       ++L LHA ++   HP  G+ L I+A       +     G+
Sbjct: 180 KHGDLRQNRGMAQHFGSSRLMLHASHLQFTHPVTGQPLCISARWDDTWQRVMSQFGW 236


>gi|56551401|ref|YP_162240.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis ZM4]
 gi|59802982|sp|O66114|Y505_ZYMMO RecName: Full=Uncharacterized RNA pseudouridine synthase ZMO0505;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|56542975|gb|AAV89129.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis ZM4]
          Length = 219

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 119/231 (51%), Gaps = 14/231 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
             L   +L+ D++  + +KPAG+ V      +  ++ +L S      + P + HRLD++T
Sbjct: 2   PILAKRVLFIDAEAMIIDKPAGLPVTSVRDGSLSLENYLASLCFGFKRWPSIVHRLDRDT 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L++AR     + L+E+F   +++K YW+++ G+P+  +  I   LLK S     +  
Sbjct: 62  SGCLLLARNPKMHRRLSEAFSQGQVKKCYWAILEGVPEKNEGIIDLPLLKISSPKSGWRI 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC 273
           V          A++H++++    +    +  +P TGRTHQLRVHA   +G PIVGD  Y 
Sbjct: 122 VADDK---GKRAVTHWEIL-AKNKGRSLVAFRPETGRTHQLRVHAATGLGLPIVGDPFYG 177

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           ++   N      +++ LHA  +++   E   +   APLP    K +  LGF
Sbjct: 178 SHKDEN-----ISRMMLHAHSLEIARLEKKPITAEAPLP----KAFTDLGF 219


>gi|149011862|ref|ZP_01833010.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP19-BS75]
 gi|194398411|ref|YP_002038593.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Streptococcus pneumoniae G54]
 gi|237650123|ref|ZP_04524375.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae CCRI 1974]
 gi|237821869|ref|ZP_04597714.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae CCRI 1974M2]
 gi|147763817|gb|EDK70750.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP19-BS75]
 gi|194358078|gb|ACF56526.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae G54]
          Length = 291

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 67/279 (24%), Positives = 113/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D S   
Sbjct: 26  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYSQKT 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 73  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 130 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 190 KRI----VDAKNGQYAETHVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDP 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    +L  T
Sbjct: 246 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFT 277


>gi|170766087|ref|ZP_02900898.1| tRNA pseudouridine synthase C [Escherichia albertii TW07627]
 gi|170125233|gb|EDS94164.1| tRNA pseudouridine synthase C [Escherichia albertii TW07627]
          Length = 260

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 66/259 (25%), Positives = 112/259 (43%), Gaps = 22/259 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    + E     + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKCYHAIVRGWLMEEAELDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK-- 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++  
Sbjct: 180 KHGDLRQNRSAAEHFGLQRLMLHASKLSLTHPFTGEPLTIHAGLDNTWMQALSQFGWRGL 239

Query: 326 YDRNLYIKRLYSQDECKQN 344
              N   +R+   +   Q+
Sbjct: 240 LPEN---ERVEFSESSGQD 255


>gi|222529402|ref|YP_002573284.1| RluA family pseudouridine synthase [Caldicellulosiruptor bescii DSM
           6725]
 gi|222456249|gb|ACM60511.1| pseudouridine synthase, RluA family [Caldicellulosiruptor bescii
           DSM 6725]
          Length = 293

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 72/262 (27%), Positives = 131/262 (50%), Gaps = 15/262 (5%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK---HSDFLKSILLYEDSKIYVFNKP 114
           R+++   +R  P I +++   +E  +++  +  +K           +LYED+     NKP
Sbjct: 33  RLKALGQIRFIPPIYSVHQYPQENAVIEVDLIFSKSNIVPVEGSIDILYEDNFFLFVNKP 92

Query: 115 AGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           +G+      G  +  I  +++ +++SK     + +RLD++TSGI+V A+       ++  
Sbjct: 93  SGLPSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRLDKDTSGIVVFAKNSYFHSIVSYE 152

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  RR+ K Y ++V GI   K   I   + K+S  G     + ++  +  ++A ++++VI
Sbjct: 153 FEKRRVDKTYIAIVHGILTKKSGLIEKPI-KRSDDG-----IKREIHQDGSFASTYYEVI 206

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D F + F  L+++P TGRTHQLRVH   +G PIVGD+ Y      N        L+ ++ 
Sbjct: 207 DSF-ENFSVLKLKPITGRTHQLRVHLSSIGHPIVGDYIYGEEKTQNTPLL----LHAYSI 261

Query: 294 YMDLPHPEGGRLQITAPLPAHM 315
             +          IT+PLP + 
Sbjct: 262 SFNFKLINNKVYDITSPLPHYF 283


>gi|262383706|ref|ZP_06076842.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_1_33B]
 gi|262294604|gb|EEY82536.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_1_33B]
          Length = 549

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 116/242 (47%), Gaps = 20/242 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L+H+++  ++ ++ +    H +  K  +LYED  + V NKP G+    G G A  +
Sbjct: 312 CEPILHHMLQGLRVDENPLLADSHRET-KLDILYEDDYLLVINKPEGMLSVPGKGDADSV 370

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L      +   P + HRLD  TSG+L+ A+T+ A Q+L   F+ R IQK Y +L+ G
Sbjct: 371 YQRLSILY-PEATGPIIVHRLDMATSGLLLAAKTKEAHQNLQAQFKNRTIQKRYIALLEG 429

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I   L          +     +E+    A + ++V++  + K   +   P T
Sbjct: 430 EVPQDEGEIRLPLCPDPLDRPRQI----VSEEFGKPAFTRYRVLERTSGK-TLIAFYPQT 484

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVHA H   + CPI+GD  Y    +         +LYLHA Y+   HP    R+
Sbjct: 485 GRTHQLRVHAAHPLGLHCPILGDELYGRKAE---------RLYLHAEYLAFTHPITSERI 535

Query: 306 QI 307
           +I
Sbjct: 536 EI 537


>gi|268319849|ref|YP_003293505.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
 gi|262398224|emb|CAX67238.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
          Length = 299

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 65/286 (22%), Positives = 115/286 (40%), Gaps = 36/286 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G V V+  R   +  + +G  V         N  +K                  K  +++
Sbjct: 38  GMVLVNHHRRYTSYLLHAGDEVIFILGEEKENKWLK--------------PSSKKLNIVF 83

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQ---KPRLTHRLDQETSGILV 159
           E     V NK AGI            +   L  +   + Q   KP +  RLD++TSG+++
Sbjct: 84  EQKDYLVINKDAGILSIPSRYEDNDAVVNRLLHYFQQQKQTDLKPHVITRLDRDTSGLVL 143

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN--KKECIANWLLKKSHIGGDYVHVVK 217
           V +   A    ++  +   I+K + ++V G  +   ++  I   + K          V +
Sbjct: 144 VGKNAVAHARFSKMEKNEFIKKYH-AIVHGNFEEAQRQGTIDAPIGKIDT------GVKR 196

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   +++ ++V+D   +    +E+Q  TGRTHQ+RVH  ++G P+ GD  Y    K
Sbjct: 197 GVVNNGQRSVTKYRVLDQV-KGASLIELQLLTGRTHQIRVHMQYLGHPLFGDPLYG--IK 253

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            NF      +  L+  Y++   P    R +I    P  M + W +L
Sbjct: 254 DNF-----KRQALNCFYLEFDDPFSEKRQKIEIADPIDMKRLWKNL 294


>gi|228920104|ref|ZP_04083453.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228839560|gb|EEM84852.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 307

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 128/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EITVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                   +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   + R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETRVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGKIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P PA +       
Sbjct: 284 AIEVDVPFPAKLNNKIKEF 302


>gi|15672346|ref|NP_266520.1| pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
 gi|12723234|gb|AAK04462.1|AE006273_8 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 293

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 60/303 (19%), Positives = 119/303 (39%), Gaps = 34/303 (11%)

Query: 25  FKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
              H   I+   L K+    G++ V+ +      R++   +V +               +
Sbjct: 18  LSRH--GISRRLLTKVKFDGGKITVNGQEKNAIYRLEKDDLVTVT--------------V 61

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVD 138
            D   N     D     +L+ED    V  KPAG             ++  + G++    +
Sbjct: 62  PDEPDNEKLIPDDFPLNVLFEDDHYLVVEKPAGKPSITGSLHPTGAMSNAVKGYISQ-KN 120

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              Q   +  RLD++TSG++ +A+ R A   + +      ++K Y+++V          I
Sbjct: 121 YANQTVHIITRLDRDTSGLMFLAKHRYAHALMNQHKFRDTMEKRYFAIVNDQDLPDSGRI 180

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + ++       +    + ++ A  A++ + V +        L++  HTGRTHQ+RVH
Sbjct: 181 DLPIGRRD---DSIIQRQVRFDEKAKDALTSYVVAERKND-LALLDIILHTGRTHQIRVH 236

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVK 317
             H+G P++GD  Y  N        + ++  LH  ++   +P    +  +   +P  M  
Sbjct: 237 FSHLGYPLIGDDLYGGNHD------LISRQALHCHHLQFLNPFTDEMVHVELDMPEDMKN 290

Query: 318 TWD 320
              
Sbjct: 291 LLK 293


>gi|332365407|gb|EGJ43168.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK355]
          Length = 277

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 68/290 (23%), Positives = 118/290 (40%), Gaps = 34/290 (11%)

Query: 25  FKNHYPH---INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K        I    ++  LR    V V+   + + + +++G  + +         I  E
Sbjct: 3   IKELLEEQFLIPR-KIRHFLRTKKHVSVNGLAINWQSLVKAGDEICL---------IFDE 52

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +     ++ L    +      LY+D  + + NKP G+           +   + ++V   
Sbjct: 53  EDYPQKTILL---GNGELVEELYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV--- 106

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G+   + HRLD+ETSG+++ A+       L      R I + YW+LV G    K     +
Sbjct: 107 GETCYVVHRLDKETSGVVLFAKNPFVLPILNRLLEKREISRQYWALVQGKFPAKNLIYKD 166

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + +   YA +H   +  F Q    ++ Q  TGRTHQ+RVH  
Sbjct: 167 KIGRDRHDRRKRL----VDPRKGLYAETHVTRLKQFGQ-ATLVQCQLKTGRTHQIRVHLA 221

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           H G P+VGD  Y    +G        +L LHA  +   HP    ++ + A
Sbjct: 222 HHGHPLVGDPLYHPQPQG--------RLMLHAHRLTFTHPFTLEKITVEA 263


>gi|229160344|ref|ZP_04288342.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228623068|gb|EEK79896.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 307

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 131/319 (41%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++ G  +++ 
Sbjct: 11  EMTVPATWNGISIESLLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNEPLKEGDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E               + +  +++ED  + + NKP  +       G   
Sbjct: 70  MFMEEEYGVDPE---------------YGELHVIFEDDHVLIVNKPEQMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K +E     AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDE-----AITYYKVEKYFKKQDITFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  + G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSYNGNPLVGDVLYGGQTK------YMSAQALHAMRINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            +++  P P  +  T    
Sbjct: 284 EIEVDVPFPTKLNNTMKEF 302


>gi|315653906|ref|ZP_07906822.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
 gi|315488602|gb|EFU78248.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
          Length = 300

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 68/296 (22%), Positives = 116/296 (39%), Gaps = 36/296 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 32  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGKEKPNATLK-------------- 77

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 78  FSNLPIAIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITR 137

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 138 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 196

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 197 PIKRYIM------EGGKNSVTKYRVIKQVA-GASLVELQLLTGRTHQIRVHMQYLGHPLF 249

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           GDH Y              +  LH   +    P E  R+++     A M++ W  L
Sbjct: 250 GDHLYGVEDD-------FPRQALHCFLLAFDDPLEHKRIEVQIADSADMLQLWQKL 298


>gi|257466757|ref|ZP_05631068.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315917906|ref|ZP_07914146.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
 gi|313691781|gb|EFS28616.1| tRNA pseudouridine synthase A [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 291

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 79/315 (25%), Positives = 151/315 (47%), Gaps = 27/315 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   VE     +R+DR+ +  +P+++  ++ K LR+G+++V+ K+VK N R      ++
Sbjct: 1   MKEYRVEEKYIGVRIDRYLRKEFPNLSLGDIFKTLRTGKIKVNGKKVKENYRFLEEDRIQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                   N++  E+K   + ++L+ +    L+  + Y+D+ I VF K AG  +  GS  
Sbjct: 61  --------NYLQVEEKEKMTFIHLSQEEKKRLEDGIFYQDTDILVFYKKAGELMHKGSSH 112

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            Y +    +++     +     +RLD+ETSG+++  +     + L E+ + R I K Y+ 
Sbjct: 113 DYGLAEQFQAYFQ--NEDFHFVNRLDKETSGLVLGGKCLKIVRELAEAIKKRTIIKKYYI 170

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           ++ GIP+     +  +L K    G + V   K  ++      + F VI    +++  LE 
Sbjct: 171 IIEGIPEKNHFSLKTYLKK----GENKVLESKTAKEEYKECSASFSVI-RKNKEYSLLEA 225

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              TGRTHQLRV    +G PI+GD KY              ++YLH+  + +   E    
Sbjct: 226 VLETGRTHQLRVQLAGIGFPILGDIKYGKKRA--------KRMYLHSHLLKISDWEK--- 274

Query: 306 QITAPLPAHMVKTWD 320
           +    +P   +  ++
Sbjct: 275 EWDTGIPTEFLSYFN 289


>gi|227891498|ref|ZP_04009303.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
 gi|227866645|gb|EEJ74066.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
          Length = 296

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 74/312 (23%), Positives = 126/312 (40%), Gaps = 34/312 (10%)

Query: 14  NDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             +E M L ++ KN    H    +L+K   +G+V VD K+   +  +  G++  I P   
Sbjct: 8   ESDEKMTLKKFLKNKGVSHRTLSSLKK--GNGKVLVDGKKRSLSIEVGKGKITLILP--- 62

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDG 131
                    +  D +V ++K        ++YEDS   V +KP  +S   G S     +  
Sbjct: 63  --------PEKSDENVKISKE----PLDIIYEDSNWLVVDKPPLLSSVPGPSNRTDTLVN 110

Query: 132 FLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +K  +  +  K   P +  RLD++TSG+++VA+ R A   + +      I K Y ++V 
Sbjct: 111 RVKFHLWQQKSKDLVPHVITRLDRDTSGLVLVAKHRFAQGLINKQVEEHSIDKRYLAVVE 170

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           GI   K   I   L  + +  G  V            A + + V +    K   +E + H
Sbjct: 171 GIIAEKHGIIDKPLGPRENGIGQMV------TDTGKIAKTEYWVREYLGDKATLVECKLH 224

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-I 307
           TGRTHQ+R H   +   ++GD  Y              +  LHA  +    P     +  
Sbjct: 225 TGRTHQIRAHFSSINHALIGDKLYGGRLDWGLE-----RQALHAYQLAYVDPFTQEEKLF 279

Query: 308 TAPLPAHMVKTW 319
            + +P  +    
Sbjct: 280 KSKMPKDLENLI 291


>gi|163814113|ref|ZP_02205505.1| hypothetical protein COPEUT_00266 [Coprococcus eutactus ATCC 27759]
 gi|158450562|gb|EDP27557.1| hypothetical protein COPEUT_00266 [Coprococcus eutactus ATCC 27759]
          Length = 334

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 72/314 (22%), Positives = 141/314 (44%), Gaps = 23/314 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +V+  +E   RL++    +        + +++R   ++++  +   N  +  G V++
Sbjct: 1   MREIVISKNEAGQRLNKLVMKYLNKAPSSFVYRMIRKKNIKLNGGKAVGNEIVYVGDVIQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +    + ++    +     +S +  K     K  ++Y D  + + NKP G+  Q  S   
Sbjct: 61  LYLADDTIDSFRDDNIQTAASGSQKK----FKPEIIYHDHNVLIVNKPVGVLSQKASKDD 116

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           Y I+  +  ++   G          KP + +RLD+ TSG+++   +    Q L+   R R
Sbjct: 117 YSINESVLDYLLDNGYITSEQLRTYKPSICNRLDRNTSGLVLCGVSLMGNQELSRIIRER 176

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSH----IGGDYVHVVKQN-EKGANYAI-SHFK 231
            I K Y+++V G  K+ ++ +  +L+K       I  D V  +KQ+  K     I + F+
Sbjct: 177 NIDKYYYTIVKGHIKSVQD-VTAYLVKDEKKNTVIVRDGVDEIKQDSGKNEFEKIHTIFE 235

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNK-LY 289
            +     K+  ++++  TG+THQ+R    HMG PIVGD KY        F    + +   
Sbjct: 236 PVRSNG-KYTEVKVKLITGKTHQIRAQLSHMGYPIVGDQKYGDRETNIYFRQTYKLRNQL 294

Query: 290 LHARYMDLPHPEGG 303
           LH   +   +  GG
Sbjct: 295 LHCGEVKFTNVTGG 308


>gi|312135211|ref|YP_004002549.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           owensensis OL]
 gi|311775262|gb|ADQ04749.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           owensensis OL]
          Length = 293

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 70/262 (26%), Positives = 130/262 (49%), Gaps = 15/262 (5%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSV---NLTKHSDFLKSILLYEDSKIYVFNKP 114
           R+++   +R  P I +++   +E  +++  +               +LYED+     NKP
Sbjct: 33  RLKAHGQIRFIPPIYSIHQYPQENAVIEVDLISSKSNIVPVEGSIDILYEDNFFLFVNKP 92

Query: 115 AGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           +G+      G  +  I  +++ +++SK     + +RLD+ETSGI+V A+       ++  
Sbjct: 93  SGLPSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRLDKETSGIVVFAKNSYFHSIVSRE 152

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  R+++K Y ++V G    K   I   + K+S  G     + ++  +  ++A ++++VI
Sbjct: 153 FEKRQVEKTYIAIVHGKLTKKSGLIEKPI-KRSQDG-----IKREIHQDGSFASTYYEVI 206

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D F + F  L+++P TGRTHQLRVH   +G PIVGD+ Y      N        L+ ++ 
Sbjct: 207 DSF-ENFSVLKLKPITGRTHQLRVHLSSIGHPIVGDYIYGQQKTQNTPLL----LHAYSI 261

Query: 294 YMDLPHPEGGRLQITAPLPAHM 315
             +    +     IT+PLP + 
Sbjct: 262 RFNFKLIDNKIYNITSPLPHYF 283


>gi|256842723|ref|ZP_05548211.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus 125-2-CHN]
 gi|256614143|gb|EEU19344.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus 125-2-CHN]
          Length = 301

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 74/327 (22%), Positives = 128/327 (39%), Gaps = 39/327 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT +  ++V+  +         KN + H    N +     G + V+ KR   +  +++G 
Sbjct: 1   MTSLFKLIVQERDPKKLGPFLLKNGFSHQALNNAKH--HHGMILVNHKRRYTSFNLRAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V         N  +K                     ++ E+    V NKPAG+      
Sbjct: 59  EVIFISGEEKKNDFLK--------------PSNNPVSIVLENKNYLVVNKPAGVLSIPSR 104

Query: 124 G-IAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                 +   L  +   KGQK   P +  RLD+ TSG+++V +   +    ++  + + +
Sbjct: 105 YEDDDAVVNRLLGYFAQKGQKNLKPHVITRLDRYTSGLVLVGKNAISHARFSKIGKEKFV 164

Query: 180 QKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +K + ++V G   P      I   + KK   G      V  + K A  A   ++V+D   
Sbjct: 165 KKYH-AIVHGNFAPNELTGLIDQPIGKK---GSGVKRAVVADGKDAQTA---YRVLDQVT 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +E+   TGRTHQ+RVH  ++G P+ GD  Y             ++  L+  Y++ 
Sbjct: 218 -GASLVELCLLTGRTHQIRVHMAYLGHPLYGDPLYG-------IQDGFSRQALNCFYLNF 269

Query: 298 PHPEGGRLQITAPL--PAHMVKTWDSL 322
           P P   +   T  L  P  M + W  L
Sbjct: 270 PDPFSQQKCKTIELNDPKDMQELWQKL 296


>gi|150006268|ref|YP_001301012.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           vulgatus ATCC 8482]
 gi|294776519|ref|ZP_06741993.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|149934692|gb|ABR41390.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           vulgatus ATCC 8482]
 gi|294449648|gb|EFG18174.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
          Length = 540

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 115/241 (47%), Gaps = 19/241 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ + L KH   +   ++YED+ + V NKPAG+    G G    +
Sbjct: 309 CGPILGHMLQGLEVEENPL-LKKHYHEMPLEIVYEDNYLVVINKPAGMLSVPGKGEIDSV 367

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K         P + HRLD  TSG+L++A+ +   QHL   F+ R I+K Y +L+ G
Sbjct: 368 YQHIKILY-PDATGPLIVHRLDMATSGVLLIAKNKEVHQHLQAQFKNRMIKKRYIALLDG 426

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              +K+  I   L +   +      V   + +    AI+ ++V++   +    +   P T
Sbjct: 427 KISSKEGTIILPL-RMDPLDRPRQVV---DHEHGKTAITQYQVLNEQ-EGNTLIAFYPLT 481

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           GRTHQLRVHA H   + CPI GD  Y             ++LYLHA  ++  HP    + 
Sbjct: 482 GRTHQLRVHAAHPEGLHCPIRGDELYGQK---------ADRLYLHAESLEFVHPVTKEII 532

Query: 307 I 307
            
Sbjct: 533 F 533


>gi|332523959|ref|ZP_08400211.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
 gi|332315223|gb|EGJ28208.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 275

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 106/268 (39%), Gaps = 27/268 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              V V+++ V + + +  G  + +    +            D         +      L
Sbjct: 24  KKHVLVNQQLVTWQDLVTKGDEISLNFDSD------------DYPQKRIPFGNPDLVECL 71

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+DS + V NK  G+      G   +    L       GQ   + HRLD ETSG ++ A+
Sbjct: 72  YQDSHLIVVNKSEGMKTH---GNEPNELALLNHVSAFVGQTCYIIHRLDMETSGAIIFAK 128

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  +      R I + YW+L+ GI +NK   +   + +  H     V     + K 
Sbjct: 129 NPFILPIMNRLLENREIGRNYWALIDGIIENKDTTLRFPIGRHRHDRRKRV----VDLKN 184

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              AI+H K +  +  KF  ++    TGRTHQ+RVH  H+G PI+GD  Y          
Sbjct: 185 GQKAITHVKRLKAYRPKFSLVDCSLKTGRTHQIRVHLSHIGHPIIGDPLY-------HQQ 237

Query: 283 PIQNKLYLHARYMDLPHPEG-GRLQITA 309
               +L LHA  +   HP     + I A
Sbjct: 238 TTSQRLMLHAHQLYFKHPLTLETIVIDA 265


>gi|218896324|ref|YP_002444735.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
 gi|228899971|ref|ZP_04064209.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|218541071|gb|ACK93465.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
 gi|228859657|gb|EEN04079.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
          Length = 307

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 68/319 (21%), Positives = 125/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EITVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                   +  E               + +  ++YED  + + NK   +           
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKLEQMDTHPAEKGGNG 114

Query: 129 IDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               L ++   +     K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGTIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P  +       
Sbjct: 284 AIEVDVPFPTKLNNKIKEF 302


>gi|332969275|gb|EGK08302.1| RluA family pseudouridine synthase [Desmospora sp. 8437]
          Length = 308

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 74/321 (23%), Positives = 140/321 (43%), Gaps = 35/321 (10%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            +  +  N  ++   K     ++   + ++ RS  +R++++       ++ G  +++   
Sbjct: 10  TITGEWHNRTVEEVLKGPLL-LSNRMINRLTRSRGIRLNRQMPFLKRVVKEGDRLQVAVR 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHI 129
                 +  E   L+                 YED    V NKPAGI+V     G    +
Sbjct: 69  PRERADLEPEPFPLEVP---------------YEDEDWMVVNKPAGINVHPVRPGETGTL 113

Query: 130 DGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              +  W   +G   K R  HRLD+ TSG+LVVA++  A Q +    R RR++++Y++ +
Sbjct: 114 AHGIVHWWKEQGWEGKVRPVHRLDRHTSGLLVVAKSAYAHQLMDRELRERRLKRVYYAFL 173

Query: 188 WGIP---KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            G        +  I   + +          + ++     + A++H++V+         ++
Sbjct: 174 EGSLTQAPAAEGTIDAAIDRDPDHP-----LRRRVSPAGDPAVTHYRVLARNND-ATLVQ 227

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
           ++  TGRTHQ+RVH  H+G P+ GD  Y +      TSP+  +  LHA  +   HP +G 
Sbjct: 228 VELETGRTHQIRVHFSHLGFPLFGDGLYGS------TSPLIRRQALHACEVGFHHPLQGE 281

Query: 304 RLQITAPLPAHMVKTWDSLGF 324
            + + +PLP  + +    L  
Sbjct: 282 PVTVHSPLPKDLTRLAKELKL 302


>gi|258511645|ref|YP_003185079.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478371|gb|ACV58690.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 333

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 63/344 (18%), Positives = 121/344 (35%), Gaps = 28/344 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +D    RL          ++   L++I+++G   V+ + V  +  +Q G  V      
Sbjct: 2   VPSDLAGRRLSAVLSGRL-GMSRRMLRRIIQAGGFYVNGEPVYLSVTVQDGDRVTWERPE 60

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
             +    +                 +   + YED  + V NKPAG+            + 
Sbjct: 61  EEVAVEPEN----------------IPLEICYEDDDVIVVNKPAGMLTHPSPHERRGSLL 104

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                ++  +G  P   HRLD+ TSG +++A+   A   L  + R   + + Y ++V+  
Sbjct: 105 AAAAHYLRDRGGVPHAVHRLDKYTSGAVLIAKHAHAHHQLDRALRQGLVDRRYVAIVYAP 164

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              +      ++   +         +       + A++H   +   A     + +   TG
Sbjct: 165 EGCETGRWLTFVDGLAPNPHRPSRRIVVPPDRGDRAVTHALPL-VQAGPLALVALVLETG 223

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLPHPEG 302
           RTHQ+R      G P+VGD  Y               F      +  LHA  +  P  E 
Sbjct: 224 RTHQIRAQMAFHGMPLVGDRDYTYALANRRDPLGQASFYEKAFGRQALHAYALSWPRVED 283

Query: 303 GRL-QITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNI 345
             + ++ A +   M + W ++  + D   +       +     I
Sbjct: 284 RAMCKVRARVADDMRELWQTVAGRDDIEAWCDEAQDVEPPGDPI 327


>gi|315037877|ref|YP_004031445.1| Pseudouridine synthase [Lactobacillus amylovorus GRL 1112]
 gi|312276010|gb|ADQ58650.1| Pseudouridine synthase [Lactobacillus amylovorus GRL 1112]
          Length = 301

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 70/326 (21%), Positives = 127/326 (38%), Gaps = 37/326 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSG 62
           MT +  ++V+  +   +L  +        +   L+     +G + V+ KR   + R+++ 
Sbjct: 1   MTSLFKLIVQERD-PKKLGSFLLK--KGFSHQALKHARYNNGLILVNHKRRYTSFRLKTN 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V         N  +K                      + E     + +KPAG+     
Sbjct: 58  DEVIFVTGEEKKNDFLK--------------PSNNPVEPVLETKNYIILSKPAGVLSIPS 103

Query: 123 SG-IAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                  I   L  +   +G+K   P +  RLD++TSG+++V +   A    ++  + R 
Sbjct: 104 RYEDDDAIVNRLMCYFIKEGKKDLKPHVITRLDRDTSGLVLVGKNAVAHARFSKIGKERF 163

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I+K + ++V G  +N +       L    IG     V +        A + +KV+   + 
Sbjct: 164 IKKYH-AIVHGNFENDELT----GLVDEPIGKIDSGVKRGVIPDGKSAQTEYKVLKQVS- 217

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E++  TGRTHQ+RVH  ++G P+ GD  Y             ++  L+  Y+  P
Sbjct: 218 GASLVELRLLTGRTHQIRVHMAYLGHPLYGDQLYGIKDP-------FSRQALNCFYLSFP 270

Query: 299 HPEGGR--LQITAPLPAHMVKTWDSL 322
            P        +  P PA M K W  L
Sbjct: 271 DPFNSEKNKTVEIPDPADMQKLWQGL 296


>gi|194434667|ref|ZP_03066921.1| tRNA pseudouridine synthase C [Shigella dysenteriae 1012]
 gi|194417064|gb|EDX33179.1| tRNA pseudouridine synthase C [Shigella dysenteriae 1012]
 gi|332089085|gb|EGI94195.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           155-74]
          Length = 260

 Score =  183 bits (464), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQYVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|270291159|ref|ZP_06197382.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
 gi|270280555|gb|EFA26390.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
          Length = 292

 Score =  183 bits (464), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 86/298 (28%), Positives = 138/298 (46%), Gaps = 30/298 (10%)

Query: 35  VNLQKILRSGQVRVDKKRVKFNNRI-----QSGQVVRIPPVINALNHIIKEQKI-----L 84
            NL++I+ + +V    +R+  + R+     Q+G++V       AL   +   +       
Sbjct: 7   NNLEEIISAQKVL---QRLGASQRLMQKIRQAGRLVDENERTVALKDKLMPFEPFWIELP 63

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKG-- 141
           D   +           ++YED    V NKPAG+ +V G S     +   +K    + G  
Sbjct: 64  DEDSDPAVPVSDQPLDVIYEDDNWLVVNKPAGLTAVPGPSNRTDTLVNRVKGHWQANGAV 123

Query: 142 -QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P L  RLD+ TSGI +VAR + A   L+E  R R+I+K Y +LV G+   +K     
Sbjct: 124 NLVPHLITRLDRFTSGITLVARHQVANSLLSEQVRHRKIKKTYLALVDGVVSAEKGTFNQ 183

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L     +  D +H  ++ ++G   A + FKV+  FA +   +++   TGRTHQ+RVH  
Sbjct: 184 PLG----LAADGIH--REVQEGGQSATTSFKVVQRFANQ-TLVQVHLKTGRTHQIRVHFA 236

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVK 317
           + G P+VGD  Y              +  LHA+ +    P    +L+ TAPLPA +  
Sbjct: 237 NAGHPLVGDQLYGGPMDR-----GIERQALHAQSIRFFDPFTNQKLEFTAPLPADLQA 289


>gi|312870084|ref|ZP_07730220.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
 gi|311094387|gb|EFQ52695.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
          Length = 289

 Score =  183 bits (464), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 73/307 (23%), Positives = 132/307 (42%), Gaps = 35/307 (11%)

Query: 15  DEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +E +++ ++ ++    H  F  ++K    GQ  VD + V+   +I   Q + I      
Sbjct: 9   GQEPVKIKKFLQSLGMGHRLFNEIKK--GQGQFLVDHRVVRPTTQILPNQPLTI------ 60

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGF 132
                   ++   + + T         + YED    V +KPAG+S   G   +   I   
Sbjct: 61  --------QVAPETADPTVAVSHEPLKVAYEDDNWLVVDKPAGVSSIPGPTTSNGTILNR 112

Query: 133 LKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +K +++ +G    +P L  RLD+ TSG+L+VA+   A+  +++  +  R+ K Y ++V G
Sbjct: 113 VKGYLEEQGSEDLRPHLITRLDRFTSGLLLVAKHHVASSMISQQVQQHRMLKEYTAVVSG 172

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              +    I   + ++         V +        A++ + V +     +  L +Q HT
Sbjct: 173 RFADDHGVIDQPIARREGQ------VARVIAPDGQRAVTEYWV-EDQGVDWARLRLQLHT 225

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH    G P++GDH Y  +          +   LHA  +    P   + L  T
Sbjct: 226 GRTHQIRVHMASAGHPLIGDHLYGGDMTRA------DHQLLHASKISFLDPFSQKQLTFT 279

Query: 309 APLPAHM 315
           + LP   
Sbjct: 280 SSLPEEF 286


>gi|269966247|ref|ZP_06180336.1| tRNA pseudouridine synthase C [Vibrio alginolyticus 40B]
 gi|269829162|gb|EEZ83407.1| tRNA pseudouridine synthase C [Vibrio alginolyticus 40B]
          Length = 256

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 62/252 (24%), Positives = 107/252 (42%), Gaps = 17/252 (6%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
            + + S+ ++  ++Y+D      NKPAG+ V       +     +++  D  GQ     H
Sbjct: 5   KIARSSEPVELEIVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLH 64

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG+LV A +   A  +   F   +++K Y ++V G  + +        ++   I
Sbjct: 65  RLDRPTSGVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVELDKI 124

Query: 209 GGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVH 258
              +       EK A  A++ +K +               ++C +EM+P TGR HQLR H
Sbjct: 125 ADKFASQ----EKEAQEAVTEYKPLAKVEVPYSTGKFPTTRYCLVEMKPKTGRKHQLRRH 180

Query: 259 ALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
             H+  PIVGD  +          T    ++L LHA  +   HP     + +TA L    
Sbjct: 181 MAHLRHPIVGDTTHGDGKHNKLYRTEFDSHRLLLHASELRFVHPFTDQEIVMTANLDETW 240

Query: 316 VKTWDSLGFKYD 327
            + +    +   
Sbjct: 241 QQLFTRFEWDES 252


>gi|221232733|ref|YP_002511887.1| RNA pseudouridylate synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225855502|ref|YP_002737014.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae JJA]
 gi|220675195|emb|CAR69781.1| RNA pseudouridylate synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225723486|gb|ACO19339.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae JJA]
          Length = 278

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 68/279 (24%), Positives = 114/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V++N  +  G V ++                 D     
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVRWNEIVNPGDVCQLTFDEE------------DYPQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD 
Sbjct: 177 KRI----VDAKNGKYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    RL  T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLERLTFT 264


>gi|251798409|ref|YP_003013140.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247546035|gb|ACT03054.1| pseudouridine synthase, RluA family [Paenibacillus sp. JDR-2]
          Length = 332

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 71/231 (30%), Positives = 108/231 (46%), Gaps = 16/231 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGI 157
           +LYED    V NKPAG+ V    SG    +D     W+  +G     R  HRLD +TSG 
Sbjct: 114 VLYEDDFSLVLNKPAGMPVHESHSGQTGTLDEAAARWLLEQGDPLPVRHIHRLDDDTSGP 173

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ ++   A   L E+ R +RI + Y ++V G  K     +   + K  H          
Sbjct: 174 VLYSKNDLAQWVLDEAMREKRIDRRYLAVVQGKVKKSSGTVNAPIGKDRHHSSRR----- 228

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +   G + AI+H++ I  F+     + +Q  TGRTHQ+RVH  H+G P++GD  Y  + +
Sbjct: 229 RVTPGGDLAITHYETIRAFSD-ATLVRLQLETGRTHQIRVHMSHLGHPLLGDKLYGGDTR 287

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYD 327
                 +     LH   +  PHP  G L +  A  P  +V   D LG + +
Sbjct: 288 ------LLQHQALHGERLLFPHPWTGELVEAAAAKPEWLVNLLDKLGGRTN 332


>gi|299783552|gb|ADJ41550.1| Pseudouridine synthase [Lactobacillus fermentum CECT 5716]
          Length = 329

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 61/285 (21%), Positives = 116/285 (40%), Gaps = 32/285 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           +G+ +VD +RV+   +I   Q + +       +  +   +                  ++
Sbjct: 71  AGEFQVDHRRVRPTTKILPNQPLTLTVQPEPGDATVATSEE--------------PLTIV 116

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---DSKGQKPRLTHRLDQETSGIL 158
           YED    V NKP G++   G  +    I   +K ++   D+   +P L  RLD++T+G+L
Sbjct: 117 YEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLVAKDAPDLRPHLITRLDRDTAGLL 176

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+   A+  ++       +QK Y ++V G    +   I         I      + ++
Sbjct: 177 LVAKHNVASSMISPQVEGHTMQKEYRAIVAGTFAKEHGIIDAP------IARIKGQIERE 230

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A + +   +     +  + ++ H+GRTHQ+RVH   +G P++GDH Y  +   
Sbjct: 231 VNPAGQPAKTEYWAEESRGD-WTLVRLRLHSGRTHQIRVHMASVGHPLLGDHLYGGDLSX 289

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                  +   L+A ++    P     L     +P      WD L
Sbjct: 290 T------DHQALYASHLAFTDPFTQTNLAFEVEMPVAFKTLWDGL 328


>gi|187917901|ref|YP_001883464.1| ribosomal large subunit pseudouridine synthase D [Borrelia hermsii
           DAH]
 gi|119860749|gb|AAX16544.1| ribosomal large subunit pseudouridine synthase D [Borrelia hermsii
           DAH]
          Length = 326

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 75/338 (22%), Positives = 133/338 (39%), Gaps = 40/338 (11%)

Query: 4   MTYVQ-YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR---VKFNNRI 59
           M  +Q   +V  D    RLD +   +        ++K       + +      +K +  +
Sbjct: 1   MKKLQKEFIVRKDS--QRLDIYLSENLCFFTRSQIKKR-EVKAFKYNDGVFVSIKLSKPV 57

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
                + I                 + ++        L   +LYED  + V +KP GI  
Sbjct: 58  FVDDRILIEFNE-------------EVNLKEYVAPLNLPISILYEDINVIVVDKPQGILS 104

Query: 120 QGG-SGIAY-------HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
             G S +         H    L+        +P + HRLD+ETSG+++ A+       L+
Sbjct: 105 HPGISNLDNTVVNFLLHHISSLRDSFQEDKIRPGIVHRLDKETSGVMICAKNLTTLNFLS 164

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           + F+ R ++K+Y ++V G  K     I  ++ +  +    +     +       A++ +K
Sbjct: 165 KQFKERFVKKVYVAVVKGNFKIDSGIIETFIDRDRYDRKRFSVYANR----GKRALTEYK 220

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V+      +  + ++P TGRTHQLRVH  H+  PI+GD  Y       F       L LH
Sbjct: 221 VLANMG-NYSLVALKPKTGRTHQLRVHMKHLNHPILGDSIY-TRLDKVFKEMS---LMLH 275

Query: 292 ARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           A  +++   EG   +  +  P    +  D L   YD+ 
Sbjct: 276 AFKLEINIEEGSLKKFISAFP---QRFIDFLSIFYDKE 310


>gi|84683903|ref|ZP_01011805.1| ribosomal large subunit pseudouridine synthase A [Maritimibacter
           alkaliphilus HTCC2654]
 gi|84667656|gb|EAQ14124.1| ribosomal large subunit pseudouridine synthase A [Rhodobacterales
           bacterium HTCC2654]
          Length = 215

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 66/213 (30%), Positives = 105/213 (49%), Gaps = 13/213 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D +I V NKP+G+    G G   H+   L + + +   +  L HRLD++TSG++V 
Sbjct: 14  IIHMDHEILVVNKPSGLLSVPGKG--EHLADCLIARLQTAFPEVLLVHRLDRDTSGVMVF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A T  A +HL   F  R+++K Y + VWG  +     +   L+          HV   + 
Sbjct: 72  ALTPHAQRHLGLQFEKRQVKKTYVARVWGDVQEDTGTVDLPLIVD-WPNRPRQHV---DF 127

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    A++ +KV+         + + P TGR+HQLRVH L +G PI GD  Y      +F
Sbjct: 128 EKGKPAVTDWKVLKREG-ATTRMRLFPQTGRSHQLRVHMLELGHPICGDPFYAEGPARDF 186

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                 +L LHA  +   HP+GG+ +   A  P
Sbjct: 187 P-----RLMLHAESLRFRHPDGGKGMNFRAKAP 214


>gi|254557025|ref|YP_003063442.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254045952|gb|ACT62745.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 300

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 62/319 (19%), Positives = 125/319 (39%), Gaps = 33/319 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   M++      H   +    L+K+    G + VD++ V   + +  G+ V
Sbjct: 1   MRFTWINHETTPMKVKTLLAQH--GVTRSLLKKVKFHGGAILVDERPVLAIHMLTGGETV 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +       N  +                  L   +LYED    + NKPAG++      +
Sbjct: 59  TMVTPAEIGNDHL--------------GVSTLPIDILYEDRDYLIVNKPAGVASVPAHAL 104

Query: 126 -AYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
               +   +K +  +      + H   RLD++TSGI++ A+   A   +    +   ++K
Sbjct: 105 PDNTLANRVKGYYQAAHYDNEVVHITTRLDRDTSGIVLFAKHHFAHSIIDHQLKAHAMRK 164

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++V G        +   + + +        + +        +++ + V+        
Sbjct: 165 MYLAVVSGELTTDHGWLDAPIGRAAD-----SFIKRTTRPDGKPSLTEYWVVKRLC-NMT 218

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            + ++ HTGRTHQ+RVH    G P++GD  Y          P   +  LH   ++   P 
Sbjct: 219 VVRVRLHTGRTHQIRVHFAASGHPLIGDALYGGP-----RDPWIQRQALHCMRLEFDDPF 273

Query: 301 EGGRLQITAPLPAHMVKTW 319
               L   APLPA + +  
Sbjct: 274 ISQTLTTFAPLPADLNRLI 292


>gi|326803815|ref|YP_004321633.1| pseudouridine synthase, RluA family [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326651014|gb|AEA01197.1| pseudouridine synthase, RluA family [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 300

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 69/304 (22%), Positives = 120/304 (39%), Gaps = 37/304 (12%)

Query: 24  WFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           + +     ++   L K ++   G + V+ KRV     +  G  V I          I   
Sbjct: 17  FLRQ--KGVSRRQLAK-IKYHGGTIIVNNKRVGSKYFLSLGDQVTIIYPAEGSQDQI--- 70

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSK 140
                       +      +LYED    + NKPAG +         Y +  F+K++   K
Sbjct: 71  -----------MAVDFPLDILYEDRDYLIVNKPAGYTSIPSQFKDEYSMANFVKAYFVRK 119

Query: 141 GQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKE 196
             + ++ H   RLD+ TSG ++ A+ + A   + +  +   I K Y +     I  ++  
Sbjct: 120 NYENQVIHVVTRLDRFTSGAMIFAKHKYAHSQIDQLMQSGGINKQYLAFTHSAIGSDQHG 179

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   + +K     +   + +       +A + + + D  A  +    +Q HTGRTHQ+R
Sbjct: 180 LIEAPIGRK-----EGSIIERCIRADGQHAKTEYWLEDSQAGLY-RYRVQLHTGRTHQIR 233

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           VH  ++G P+ GD  Y  + +   +        LH + +    P     L I APL    
Sbjct: 234 VHFAYLGAPLCGDDLYGGSQEAGLS-----GQALHCQRLAFKQPLTQEDLVIEAPLSQDF 288

Query: 316 VKTW 319
            KTW
Sbjct: 289 -KTW 291


>gi|332883200|gb|EGK03483.1| hypothetical protein HMPREF9456_01550 [Dysgonomonas mossii DSM
           22836]
          Length = 225

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 76/228 (33%), Positives = 116/228 (50%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I + NK     VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VLYEDNHIIIINKTVSEIVQGDKTGDKPLSEIVKEYLKEKYNKPGNVFCGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ A+T  A   L E F+ ++I K YW++V  +PK  +  + N+L++       Y + 
Sbjct: 63  GIVIFAKTSKALSRLNEMFKNKQIDKTYWAIVKNMPKEPEGTLRNYLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V   +  +  AI H+K+I   + ++  LE+   TGR HQ+RV    MGCPI GD KY  +
Sbjct: 123 V--EKPNSKLAILHYKLIAR-SDRYNLLEVGLETGRHHQIRVQLSKMGCPIKGDLKYGFD 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     + LHAR +   HP     +++TAPLP      W +L
Sbjct: 180 -----RSNPDGGISLHARKVSFLHPVSKELIEVTAPLPKD--TLWQAL 220


>gi|281490911|ref|YP_003352891.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
 gi|281374669|gb|ADA64189.1| Ribosomal large subunit pseudouridine synthase D, RluA family
           [Lactococcus lactis subsp. lactis KF147]
          Length = 293

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 61/303 (20%), Positives = 119/303 (39%), Gaps = 34/303 (11%)

Query: 25  FKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
              H   I+   L K+    G++ V+ +      R++   +V +               +
Sbjct: 18  LSRH--GISRRLLTKVKFDGGKITVNGQEKNAIYRLEKDDLVTVT--------------V 61

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVD 138
            D   N     D     +L+ED    V  KPAG             ++  + G++    +
Sbjct: 62  PDEPDNEKLIPDDFPLNVLFEDDHYLVVEKPAGKPSITGSLHPTGAMSNAVKGYISQ-KN 120

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              Q   +  RLD++TSGI+ +A+ R A   + +      ++K Y+++V          I
Sbjct: 121 YANQTVHIITRLDRDTSGIMFLAKHRYAHALMNQHKFRDTMEKRYFAIVNDQDLPDSGRI 180

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + ++       +    + ++ A  A++ + V +        L++  HTGRTHQ+RVH
Sbjct: 181 DLPIGRRD---DSIIQRQVRFDEKAKDALTSYVVAERKND-LALLDIILHTGRTHQIRVH 236

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVK 317
             H+G P++GD  Y  N        + ++  LH  ++   +P    +  +   +P  M  
Sbjct: 237 FSHLGYPLIGDDLYGGNHD------LISRQALHCHHLQFLNPFTDEMVHVELDMPEDMKN 290

Query: 318 TWD 320
              
Sbjct: 291 LLK 293


>gi|242310704|ref|ZP_04809859.1| ribosomal large subunit pseudouridine synthase [Helicobacter
           pullorum MIT 98-5489]
 gi|239523102|gb|EEQ62968.1| ribosomal large subunit pseudouridine synthase [Helicobacter
           pullorum MIT 98-5489]
          Length = 322

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 137/319 (42%), Gaps = 39/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPV 70
           V + E  MRLD +      +++   + K+L + Q+ +++ +   N   ++    + I P 
Sbjct: 2   VTSQESGMRLDIFLATKL-NLSRNKINKMLHNKQITLNQIQASKNGIILKEQDQIHIFPS 60

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +                +   K +  +   +LYED  + V NKP  + V   +       
Sbjct: 61  L----------------LETAKPTPKIHIPILYEDEDLLVLNKPINLVVHKTNQEDTQY- 103

Query: 131 GFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             L  W+  +  K           + HRLD+ TSG +V+A+   + Q L++  + + + +
Sbjct: 104 -TLHEWLKEQNFKLSNLGDSYREGIIHRLDKTTSGAIVIAKNNHSHQILSQQLKTKEMGR 162

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y   V   P  +   I + L++       Y+   KQ     +   + FK+ID    K  
Sbjct: 163 YYLC-VINQPLKQDIIIDSPLIRHPKNRLKYITTSKQTPDSKDAKTAFFKIID--NGKTE 219

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  +GRTHQ+R H   +   I+GD  Y  N++GN+T     ++ LH+  + L HP 
Sbjct: 220 LIGAKLFSGRTHQIRAHLSKINRHILGDFFY--NYEGNYT----QRILLHSSLLYLKHPT 273

Query: 302 GGR-LQITAPLPAHMVKTW 319
             + L+I APL   M+   
Sbjct: 274 TQKPLKIYAPLFEDMLLFL 292


>gi|218678850|ref|ZP_03526747.1| RNA-pseudouridine synthase protein, ribosomal large subunit C
           [Rhizobium etli CIAT 894]
          Length = 174

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 91/174 (52%), Positives = 122/174 (70%), Gaps = 2/174 (1%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1   MAGIEHIKVEPDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            VR+PP+   ++  +K   I    +  +   + L  ++L+ED K+ V NKP GI+VQGGS
Sbjct: 61  TVRVPPL--DVDAKVKSGPIAGRDLKHSSDFELLSRMVLHEDDKVIVLNKPPGIAVQGGS 118

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +FR R
Sbjct: 119 GVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAFRER 172


>gi|319641478|ref|ZP_07996168.1| pseudouridine synthase [Bacteroides sp. 3_1_40A]
 gi|317386879|gb|EFV67768.1| pseudouridine synthase [Bacteroides sp. 3_1_40A]
          Length = 540

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 115/241 (47%), Gaps = 19/241 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ + L KH   +   ++YED+ + V NKPAG+    G G    +
Sbjct: 309 CGPILGHMLQGLEVEENPL-LKKHYHEMPLEIVYEDNYLVVINKPAGMLSVPGKGEIDSV 367

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K         P + HRLD  TSG+L++A+ +   QHL   F+ R I+K Y +L+ G
Sbjct: 368 YQHIKILYPDTT-GPLIVHRLDMATSGVLLIAKNKEVHQHLQAQFKNRMIKKRYIALLDG 426

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              +K+  I   L +   +      V   + +    AI+ ++V++   +    +   P T
Sbjct: 427 KISSKEGTIILPL-RMDPLDRPRQVV---DHEHGKTAITQYQVLNEQ-EGNTLIAFYPLT 481

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           GRTHQLRVHA H   + CPI GD  Y             ++LYLHA  ++  HP    + 
Sbjct: 482 GRTHQLRVHAAHPEGLHCPIRGDELYGQK---------ADRLYLHAESLEFVHPVTKEII 532

Query: 307 I 307
            
Sbjct: 533 F 533


>gi|212696916|ref|ZP_03305044.1| hypothetical protein ANHYDRO_01479 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676206|gb|EEB35813.1| hypothetical protein ANHYDRO_01479 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 299

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 65/314 (20%), Positives = 134/314 (42%), Gaps = 33/314 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  + +  I    ++  ++  +++V+ K++K + ++     + I   +     I 
Sbjct: 9   IRLDKYLSDIFEEIPREKIKDFIKEKKIKVNNKKIKPSYKLILEDEIEISDDLFERAKIE 68

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSW 136
            E+               +   ++YE+    + +K   + V     I     ++G L  +
Sbjct: 69  AEK---------------MDLKIVYENKDYAIIDKDENVIVHPAGSIVSGTLVNGLLYHF 113

Query: 137 VDSK------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             +         +P + HRLD++T+G++V+A++ ++ + L   F  R+I K Y ++  GI
Sbjct: 114 GYNNLSHIGGDDRPGIVHRLDKDTTGLMVIAKSNSSYKFLKNLFETRKIDKEYLAICNGI 173

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K K   I  ++ +  +                  AIS ++V+      +  ++++  TG
Sbjct: 174 FKKKSGEIHTFMDRDPNNRRKMAVR-----NSGRDAISKYEVL-SENDGYSLVKIKILTG 227

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RTHQ+RVH  H+  P++GD  Y  N K  F     +   LH   +     +G   +  A 
Sbjct: 228 RTHQIRVHMTHINHPLLGDPVYG-NVKHKFN---LDHQLLHCHKLGFTDKDGVYREFEAD 283

Query: 311 LPAHMVKTWDSLGF 324
           +     K    LG 
Sbjct: 284 VHEDFKKYQKVLGL 297


>gi|15806687|ref|NP_295407.1| pseudouridine synthase [Deinococcus radiodurans R1]
 gi|6459452|gb|AAF11241.1|AE002010_4 pseudouridine synthase, putative [Deinococcus radiodurans R1]
          Length = 321

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 66/297 (22%), Positives = 117/297 (39%), Gaps = 27/297 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             R+  +    + H +       L +G+V VD   V+ +  ++ GQ++            
Sbjct: 40  GQRVLDFLAQEFRHSDRATWAARLAAGEVTVDGLTVRGDETLRPGQML------------ 87

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                 +       +    L   ++YED+ +   +KP+G+    G G   H    L   V
Sbjct: 88  ------VWQRPPWAEPDAPLHFDVIYEDADLLAVSKPSGLPTMPGGGFLEH---TLLHQV 138

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +       HRL + TSG+++ + T  A   L + +R  R+QK+Y +L  G+ +  +  
Sbjct: 139 RGRWPDASPLHRLGRGTSGLVLFSLTSQAGAALLKDWRAGRVQKVYRALSAGVAEQDEYD 198

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   +     +    +  V         A S  +V++   +     E++  TGR HQ+R+
Sbjct: 199 ITVPIG---PVAHPRLGQVFAASTAGKTAHSRARVLERR-EDTTLFEVEIFTGRPHQIRI 254

Query: 258 HALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           H   +G P+  D  Y           P      LHA  +   HP  G  L ++AP P
Sbjct: 255 HLASLGLPLAVDPLYVSGGLPRPDALPGDLGYALHASTLTFQHPAHGAALTLSAPAP 311


>gi|314937995|ref|ZP_07845306.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|314941579|ref|ZP_07848463.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|314948435|ref|ZP_07851823.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
 gi|314991305|ref|ZP_07856784.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|314995356|ref|ZP_07860462.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313590449|gb|EFR69294.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313594078|gb|EFR72923.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|313599599|gb|EFR78442.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|313642670|gb|EFS07250.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|313645160|gb|EFS09740.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
          Length = 307

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 71/306 (23%), Positives = 121/306 (39%), Gaps = 33/306 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L KI  + GQ++V+ +       +     V I               
Sbjct: 26  FLKE--KGISKGLLAKIKFQGGQIKVNDQVENVLFSLAKDDKVTI--------------V 69

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG 141
           I     + T   D     ++YED  + V NKPAG+S           +   +K++   +G
Sbjct: 70  IPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQYHPNGTMANRVKAYYKKQG 129

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G   +    +
Sbjct: 130 YENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQLREKKFVKKYQALVSGRLSD----L 185

Query: 199 ANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +        I  DY  ++K+        A + + +     +    +++Q HTGRTHQ+RV
Sbjct: 186 SAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYWIEKRLTEIA-LVDIQLHTGRTHQIRV 244

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GC ++GD  Y              +  LH   +   HP     L+   PL A M 
Sbjct: 245 HFSAIGCALLGDDMYGGRM-----DLGIKRQALHCYDLRFYHPFTEELLEFKQPLAADME 299

Query: 317 KTWDSL 322
                 
Sbjct: 300 AVVRRF 305


>gi|308184530|ref|YP_003928663.1| hypothetical protein HPSJM_03780 [Helicobacter pylori SJM180]
 gi|308060450|gb|ADO02346.1| hypothetical protein HPSJM_03780 [Helicobacter pylori SJM180]
          Length = 327

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 128/314 (40%), Gaps = 32/314 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI-QSGQVVRIPPVINALNHI 77
            R+D +       I+   +  +++ G V   KK VK    + + G  + +         +
Sbjct: 12  KRIDEFLAKEL-QISKNQVLNLIKEGLVFCQKKEVKKGGLVLKEGDEITLLTPKITPKPL 70

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            KE                L+  +++ED  + V NKP  + V     +    +  L  W+
Sbjct: 71  KKELD--------------LEIEVIFEDEDLLVLNKPPNLVVHKAPSV---KEPTLVDWL 113

Query: 138 DSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            S+  +           + HRLD++TSG +V+A+       L+E  + + + + Y +L+ 
Sbjct: 114 KSQNYELSNLGLKERYGIVHRLDKDTSGGIVIAKNNFTHVCLSEQLKTKTMGRYYIALLS 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
              K +K  +  +L +  +     + +    ++ + Y+ S F  +         +  +  
Sbjct: 174 TPLKEEKMSVECYLTRNPNNRLKMIALKVAQKEKSRYSKSEFTSLLASQNGMDLIGAKLF 233

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++  HP    +L+ 
Sbjct: 234 TGRTHQIRAHLEYLNRHIIGDNLYGLN---EALPKEEIRIMLHAYLIEFKHPRSEQKLRF 290

Query: 308 TAPLPAHMVKTWDS 321
             PL   M++    
Sbjct: 291 KVPLLKDMLEYLKK 304


>gi|82778170|ref|YP_404519.1| tRNA pseudouridine synthase C [Shigella dysenteriae Sd197]
 gi|309786089|ref|ZP_07680718.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
 gi|81242318|gb|ABB63028.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
 gi|308926200|gb|EFP71678.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
          Length = 260

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 105/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +             + ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPSTRYGLVELEPKTGRKHQLRRHLAHLCHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLKRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|77406648|ref|ZP_00783692.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
 gi|77411850|ref|ZP_00788184.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77162127|gb|EAO73104.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77174748|gb|EAO77573.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
          Length = 325

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 109/291 (37%), Gaps = 33/291 (11%)

Query: 25  FKNHYPHI---NFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K             ++  LR    V ++ + + +   +Q    + +             
Sbjct: 47  VKELLEDYFLIPR-KIRHFLRVKKHVLINNEFINWQTVVQENDTITLIFDDE-------- 97

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
               D                LYED  + + NKP G+   G      +    L       
Sbjct: 98  ----DYPTKKIPLGRAELIDCLYEDEHLIIVNKPEGMKTHGNQP---NEIALLNHVSAYS 150

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           GQ   + HRLD ETSG ++ A+       + +    + I + YW+LV G    K + + +
Sbjct: 151 GQTCYVVHRLDMETSGAVLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRD 210

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + K   +A++   V+  + Q    ++ +  TGRTHQ+R+H  
Sbjct: 211 KIGRNRHDRRKRII----DSKNGQHAMTIIDVLK-YTQNSSLIKCRLETGRTHQIRIHLS 265

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           H G P++GD  Y  +           +L LHA  + L HP     + + AP
Sbjct: 266 HHGHPLIGDPLYNPSSNNE-------RLMLHAHRLTLSHPLTCETISVEAP 309


>gi|314951376|ref|ZP_07854428.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|313596434|gb|EFR75279.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
          Length = 307

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 71/306 (23%), Positives = 121/306 (39%), Gaps = 33/306 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K     I+   L KI  + GQ++V+ +       +     V I               
Sbjct: 26  FLKE--KGISKGLLAKIKFQGGQIKVNDQVENVLFSLAKDDKVTI--------------V 69

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG 141
           I     + T   D     ++YED  + V NKPAG+S           +   +K++   +G
Sbjct: 70  IPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGVSSIPAQYHPNGTMANRVKAYYKKQG 129

Query: 142 QKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++ H   RLD++TSG+++ A+   A   L    R ++  K Y +LV G   +    +
Sbjct: 130 YENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQLREKKFVKKYQALVSGRLSD----L 185

Query: 199 ANWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +        I  DY  ++K+        A + + +     +    +++Q HTGRTHQ+RV
Sbjct: 186 SAHGHIDLPIARDYSSLLKRMVSDEGRSAQTEYWIEKRLTEIA-LVDIQLHTGRTHQIRV 244

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +GC ++GD  Y              +  LH   +   HP     L+   PL A M 
Sbjct: 245 HFSAIGCALLGDDMYGGGM-----DLGIKRQALHCYDLRFYHPFTEELLEFKQPLAADME 299

Query: 317 KTWDSL 322
                 
Sbjct: 300 AVVRRF 305


>gi|332999543|gb|EGK19128.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           VA-6]
          Length = 260

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|218290916|ref|ZP_03494973.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|218239081|gb|EED06284.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
          Length = 333

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 62/344 (18%), Positives = 121/344 (35%), Gaps = 28/344 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V +D    RL          ++   L++I+++G   ++ + V  +  +Q G  V      
Sbjct: 2   VPSDLAGRRLSAVLSGRL-GMSRRMLRRIIQAGGFYLNGEPVYLSVTVQDGDRVTWERPE 60

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
             +                    + +   + YED  + V NKPAG+            + 
Sbjct: 61  EEVAV----------------EPEDIPLEICYEDDDVIVVNKPAGMLTHPSPHERRGSLL 104

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                ++  +G  P   HRLD+ TSG +++A+   A   L  + R   + + Y ++V+  
Sbjct: 105 AAAAHYLRDRGGVPHAVHRLDKYTSGAVLIAKHAHAHHQLDRALRQGLVDRRYVAIVYAP 164

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              +      ++   +         +       + A++H   +   A     + +   TG
Sbjct: 165 EGCETGRWLTFVDGLAPNPHRPSRRIVVPPDRGDRAVTHALPL-VQAGPLALVALVLETG 223

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLPHPEG 302
           RTHQ+R      G P+VGD  Y               F      +  LHA  +  P  E 
Sbjct: 224 RTHQIRAQMAFHGMPLVGDRDYTYALANRRDPLGQASFYEKAFGRQALHAYALSWPRVED 283

Query: 303 GRL-QITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNI 345
             +  + A +   M + W ++  + D   +  +    +     I
Sbjct: 284 RAMCTVRARVADDMRELWQTVAGRDDIEAWCDQAQDVEPPGDPI 327


>gi|28378819|ref|NP_785711.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|300768863|ref|ZP_07078757.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308181018|ref|YP_003925146.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28271656|emb|CAD64562.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|300493596|gb|EFK28770.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308046509|gb|ADN99052.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 300

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 62/319 (19%), Positives = 126/319 (39%), Gaps = 33/319 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           +++  + ++   M++      H   +    L+K+    G + VD++ V   + +  G+ V
Sbjct: 1   MRFTWINHETTPMKVKTLLAQH--GVTRSLLKKVKFHGGAILVDERPVLAIHMLTGGETV 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +       N  +                  L   +LYED    + NKPAG++      +
Sbjct: 59  TMVTPAEIGNDHL--------------GVSTLPIDILYEDRDYLIVNKPAGVASVPAHAL 104

Query: 126 -AYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
               +   +K +  +      + H   RLD++TSGI++ A+   A   +    +   ++K
Sbjct: 105 PDNTLANRVKGYYQAAHYDNEVVHITTRLDRDTSGIVLFAKHHFAHSIIDHQLKAHAMRK 164

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y ++V G        +   + + +        + +        +++ + V+    +   
Sbjct: 165 MYLAVVSGELTTDHGWLDAPIGRAAD-----SFIKRTTRPDGKPSLTEYWVVKRL-RNMT 218

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            + ++ HTGRTHQ+RVH    G P++GD  Y          P   +  LH   ++   P 
Sbjct: 219 VVRVRLHTGRTHQIRVHFAASGHPLIGDALYGGP-----RDPWIQRQALHCMQLEFDDPF 273

Query: 301 EGGRLQITAPLPAHMVKTW 319
               L   APLPA + +  
Sbjct: 274 ISQTLTTFAPLPADLNRLI 292


>gi|332524051|ref|ZP_08400303.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
 gi|332315315|gb|EGJ28300.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 284

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 66/300 (22%), Positives = 122/300 (40%), Gaps = 34/300 (11%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L K+  + G++ V+         +  G  V I               I D    
Sbjct: 9   DVSRGLLAKVKYKGGRIEVNGIERNAIYLLDIGDEVSIT--------------IPDELPF 54

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL 146
               +      ++YED    V NKP G +    +  +  I  F+K +    D   ++  +
Sbjct: 55  EKLEAISHPLDIVYEDDHFLVINKPVGYASIPSAIHSNTIANFIKGYYVDQDYPNKQVHI 114

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKK 205
             RLD++TSG+++ A+   A   L +  + R I+K Y++LV G  +   +  I   + + 
Sbjct: 115 VTRLDRDTSGLMLFAKHGYAHARLDKQLQARAIEKRYFALVCGEGQLPDQGEIVAPIGRS 174

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                    + +  +    YA + ++V+  +A+    ++++ HTGRTHQ+RVH  H+G P
Sbjct: 175 -----KDSIITRTVDPMGKYARTTYQVVGRYAENVHLVDIKLHTGRTHQIRVHFSHIGFP 229

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAPLPAHMVKTWDSL 322
           ++GD  Y        T     +  LH  +++  +P      R  I   L          L
Sbjct: 230 LLGDDLYGGRLDLGIT-----RQALHCHFLNFHNPFTENPSRHTIN--LTDDFENVIIDL 282


>gi|313899281|ref|ZP_07832797.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
 gi|312955961|gb|EFR37613.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
          Length = 317

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 61/301 (20%), Positives = 141/301 (46%), Gaps = 29/301 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++  ++ + R+D++ +     +    + K +R+ +++V++KR + + R+Q G  ++
Sbjct: 1   MKEFIINENDADQRVDKFIQKTMKTMPKSLMYKYIRNKKIKVNRKRCEISQRLQVGDTMQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
                         ++  + +   +         ++YED  + + NKP G+      S +
Sbjct: 61  CYI----------PEEFYEVATMRSFLQVPNALDVVYEDDAVLLMNKPKGLRAHSDTSEV 110

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             ++   L  ++  K +          P L HR+D+ T G+++ A+T AA + + E   +
Sbjct: 111 QDNLADRLLHYLYCKKEYDPTTEQSFTPALCHRIDRNTQGLVIAAKTAAALRCMNEKIAL 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R+++K Y  +V G  K K++ I  +  K      +   V+ +  +G     + ++V+   
Sbjct: 171 RQVEKKYLCIVQGKLKKKQDHIVLYHRKNEQNTAE---VIDREREGYTRMETGYRVLQ-E 226

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           A+++  +E++ H+G++HQ+R     +G P++GD KY A      T        L A ++ 
Sbjct: 227 AERYSLVEVELHSGKSHQIRALMSWLGHPLLGDVKYGARKTKEKTY-----QALCAYHVA 281

Query: 297 L 297
            
Sbjct: 282 F 282


>gi|253578463|ref|ZP_04855735.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850781|gb|EES78739.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 349

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 70/341 (20%), Positives = 134/341 (39%), Gaps = 29/341 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNL-QKILRSGQVRVDKKRVKFNNRIQSG 62
           M       ++     ++++ + K +   +    + Q   R   +  +  R +    I  G
Sbjct: 1   MERYLEFRIDEQTTELKMEAFLKKN-AGLTKRQISQAKFRPDGITRNGVRCRVTETIYPG 59

Query: 63  QVVRIP--------PVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVF 111
            V+R+           +   N  I+ + + D   +  + +         +LYED+ I   
Sbjct: 60  DVIRVCLEEAGTASAHLENYNDGIRSKDLSDFHSNRASASISETSFSLNILYEDTDILAV 119

Query: 112 NKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQ 168
           +KPAG+     G      +   +  +   K ++  +    RLDQETSGI+V A+ + AA 
Sbjct: 120 DKPAGMVTHPTGMHYTDSLSNLVAGYFREKNEQVCVRPVGRLDQETSGIVVFAKNQVAAS 179

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKE----CIANWLLKKSHIGGDYVHVVKQNEKGA- 223
            L       +I K Y + V G            +   L++              +   + 
Sbjct: 180 RLQSVKSPCKIHKQYLAAVSGTLPVDMPGVWHTLDLPLMQDPENHLKMKTAADLSLHSSA 239

Query: 224 -----NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A++H+  +   +Q +  + ++  TGRTHQ+RVH    G P++GD  Y ++ K 
Sbjct: 240 LSGKIKTAVTHYHTLFS-SQDWSLITLKLDTGRTHQIRVHMASTGHPLLGDTLYHSDDKI 298

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKT 318
           +  +   ++  LHA  +   HP    +  + APLP    + 
Sbjct: 299 SSCASF-SRAALHAWKVSFQHPFRDEMLLLEAPLPFDFREL 338


>gi|229095877|ref|ZP_04226855.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|229114830|ref|ZP_04244243.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228668522|gb|EEL23951.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228687501|gb|EEL41401.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
          Length = 307

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 128/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  +    L ++     V V+ ++ ++N  ++ G   ++ 
Sbjct: 11  EITVPAKWNGISIESLLKVEW-ELPKKLLHQLRMEKGVTVNGEQRRWNELLKEGDKFQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
             +     +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFMEEEYGVEPE---------------YGELHVVYEDDHVLIVNKPEKMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K KK  I   + +  H         K +E     AI+++KV   F      ++ 
Sbjct: 175 LVEGKVKKKKGTIDAAIGRDRHHATRRRVSPKGDE-----AITYYKVEKYFKKHNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           +Q  TGRTHQ+RVH  H G P+VGD  Y         +   +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQ------TTYMSGQALHAMKINFLHPITKE 283

Query: 304 RLQITAPLPAHMVKTWDSL 322
            ++I  P P  +       
Sbjct: 284 EIEIDVPFPTKLNNIMKEF 302


>gi|323339639|ref|ZP_08079911.1| RluA family pseudouridine synthase [Lactobacillus ruminis ATCC
           25644]
 gi|323092935|gb|EFZ35535.1| RluA family pseudouridine synthase [Lactobacillus ruminis ATCC
           25644]
          Length = 304

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 67/307 (21%), Positives = 121/307 (39%), Gaps = 33/307 (10%)

Query: 23  RWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           R   NH   ++   L K+ R  G VR+++++   +  +     V +          +   
Sbjct: 20  RILTNH--GVSHRMLAKLKRGQGNVRLNEEKTVLSALVGQNDKVTL----------VLPP 67

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV--- 137
           +  D  + ++      +  ++YED    + +KPAGIS   G    +  +   +K ++   
Sbjct: 68  EKDDERILVSHE----RIKVVYEDENWLLLDKPAGISSVPGPSNDHDTMMNRVKGYLIDQ 123

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            S+   P    RLD+ TSG+++ A+   A   +++  +   ++K Y ++  G  K     
Sbjct: 124 KSENLVPHAVTRLDRFTSGLMLCAKHGFAQGLISKQVQEHSMEKRYLAVCSGFVKKDHGI 183

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   L K+ +     V            A++ + V + F  +   +E   HTGRTHQ+R 
Sbjct: 184 IDLPLKKEDNGFRRIVSC------DGQNAVTEYWVRERFGNEATLVECVLHTGRTHQIRA 237

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
           H  H   P++ D  Y              +  LHA  +    P    RL+   PL   M 
Sbjct: 238 HFAHFAHPLISDELYGGKKND-----ACKRQALHACCLAFDDPFSCKRLKFELPLENDME 292

Query: 317 KTWDSLG 323
                L 
Sbjct: 293 HLLGELR 299


>gi|227550294|ref|ZP_03980343.1| pseudouridylate synthase RluD [Enterococcus faecium TX1330]
 gi|227180554|gb|EEI61526.1| pseudouridylate synthase RluD [Enterococcus faecium TX1330]
          Length = 299

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 65/265 (24%), Positives = 110/265 (41%), Gaps = 28/265 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R   V ++++   F++ ++    + +       N+               +  D     
Sbjct: 50  IRK-NVWINQQPALFHHEVKGNDQITLLFEETDYNY------------QEVQLGDAKHIR 96

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+                L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 97  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKKQRPYVVHRLDKETSGAVL 156

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+       L      + I + Y ++VWG     +  I N + +  H     V     +
Sbjct: 157 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGKIAKDR-TITNKIGRDRHDRRKRV----VD 211

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +K    A++H  V D        +     TGRTHQ+RVH  H+G PIVGD  Y       
Sbjct: 212 DKNGQNALTHVTV-DKVLSGKTQVYCVLETGRTHQIRVHLAHIGHPIVGDPLYQNRPAE- 269

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR 304
                  +L LHA  + + HP    
Sbjct: 270 -------RLMLHALELHMIHPFTQE 287


>gi|224282575|ref|ZP_03645897.1| hypothetical protein BbifN4_01992 [Bifidobacterium bifidum NCIMB
           41171]
 gi|313139732|ref|ZP_07801925.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
           41171]
 gi|313132242|gb|EFR49859.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
           41171]
          Length = 313

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 125/326 (38%), Gaps = 31/326 (9%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V   +     R D         I+      ++ SGQ RV  + +  +  +  G+ V  
Sbjct: 3   RLVPAPDALVGSRFDVAVSKML-GISRAKAADLIESGQARVLDRAIAKSGTLLYGETVEF 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                     I E++     V        L   + YED  + V +KP G++    +G   
Sbjct: 62  D---------IAEERHEPEPV-------CLDMAIAYEDDDVVVVDKPVGVAAHASAGWTG 105

Query: 128 HID--GFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                  LK  V         +  +  RLD  TSG+++V ++  A + +   F    + K
Sbjct: 106 PTVLGSLLKRGVRITSYGAPGRQGIVSRLDVGTSGLMLVCKSELAYKEMRRQFSEHEVVK 165

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G  K  K  I   + +                     A++H+ V+D F +   
Sbjct: 166 TYHAMVQGNLKEDKATIEAPIGR-----AKVSDFRFCVTPSGKPAVTHWDVLDRFGE-AT 219

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            + +   TGRTHQ+RVH   +G P+VGD  Y AN          ++ +LHA  ++  HP 
Sbjct: 220 LVSVNLETGRTHQIRVHFSSIGHPLVGDPMYGANPVL-AGELGLDRQWLHAMKLEFRHPR 278

Query: 302 GG-RLQITAPLPAHMVKTWDSLGFKY 326
                 + +  PA +    + +  ++
Sbjct: 279 THLWTSVESHYPADLAHALELMRARH 304


>gi|146296753|ref|YP_001180524.1| pseudouridine synthase [Caldicellulosiruptor saccharolyticus DSM
           8903]
 gi|145410329|gb|ABP67333.1| pseudouridine synthase [Caldicellulosiruptor saccharolyticus DSM
           8903]
          Length = 311

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 70/289 (24%), Positives = 131/289 (45%), Gaps = 24/289 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            +++E +   M+L++  K  YP I    + K+LR G++RV+ +  +    +Q G ++   
Sbjct: 4   EMLIEKNFAGMKLEKAIKKKYPTIPMSVIFKLLRKGRIRVNFEVAQKGQILQFGDLISFD 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                    I+E+ +    V ++K         +YED  I V +KP GI     +   Y 
Sbjct: 64  ---------IEEKYLDQKKVEISK---------VYEDDNIIVIDKPYGIPSHPDTNNEYS 105

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  +++    S  Q P L HRLD+ TSG++++A+ R     + +    R I+K Y  +  
Sbjct: 106 VVNWIEDNY-SGNQLPALCHRLDRNTSGLMIIAKNRQVLNEMLKYMSRRAIKKKYLCITK 164

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
            +   K   + ++L K S      V++     +G +  ++ +K+I         ++++  
Sbjct: 165 KVDLPKSGVLVHYLKKDSK--KSKVYISDLPAEGYSEIVTRYKII-RGKDDLLLVDVEIE 221

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           TG+THQ+R    H+G  I+GD KY         +       L A Y+  
Sbjct: 222 TGKTHQIRSQLAHVGLCILGDSKYGDWALNKKYNASI--QCLCAYYLKF 268


>gi|254517296|ref|ZP_05129353.1| tRNA pseudouridine synthase C [gamma proteobacterium NOR5-3]
 gi|219674134|gb|EED30503.1| tRNA pseudouridine synthase C [gamma proteobacterium NOR5-3]
          Length = 248

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 103/241 (42%), Gaps = 17/241 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  ++Y+D  + V +KP G+ V       +     L+   D  GQ     HRLD+ TSG+
Sbjct: 5   KLDVIYQDRDLVVIDKPPGLLVHRSKIDRHETQFALQMLRDQLGQHVFPVHRLDKPTSGL 64

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A +   A  L+E F  R + K Y ++V G      E       K   I         
Sbjct: 65  LIFALSSEVATLLSEQFENRAVAKRYLAVVRGYCPQGGEIDHALTEKHDRIVDKRARA-- 122

Query: 218 QNEKGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             +K    A++H++ +               ++  +E++P TGR HQLR H  H+G PI+
Sbjct: 123 --DKAPQEALTHYRTLAQVEWPEAVDRYPQARYSLVELRPQTGRKHQLRRHMKHIGHPII 180

Query: 268 GDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           GD  +       F        +L L    ++  HP  G+ LQ++AP      +  D+  +
Sbjct: 181 GDATHGKGVHNRFFARRFDCGRLLLACTGLEFDHPVTGQPLQLSAPPGDAFDRVIDAFAW 240

Query: 325 K 325
           +
Sbjct: 241 R 241


>gi|259502474|ref|ZP_05745376.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           antri DSM 16041]
 gi|259169617|gb|EEW54112.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           antri DSM 16041]
          Length = 289

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 69/280 (24%), Positives = 117/280 (41%), Gaps = 32/280 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
            GQ  VD + V+   +I   Q + I              K+     + T         ++
Sbjct: 36  QGQFLVDHRVVRPTTQILPNQPLTI--------------KVAPEPADPTVAVSHEPLKVV 81

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHRLDQETSGIL 158
           YED    V +KPAG++   G  I    +   +K  ++ +G    +P L  RLD+ TSG+L
Sbjct: 82  YEDDSWLVIDKPAGVTSVPGPSITNGTVLNRVKGHLEKQGSEDLRPHLITRLDRFTSGLL 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+   A+  +++  +  R+ K Y ++V G   +    I   ++++       +     
Sbjct: 142 LVAKHHVASSMISQQVQQHRMLKEYTAVVSGRFADGHGIIDQPIVRREGQAARIIA---- 197

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A++ + V D          +Q HTGRTHQ+RVH    G P++GDH Y  +   
Sbjct: 198 --PDGQQAVTEYWVEDQEPDWARL-RLQLHTGRTHQIRVHLASKGHPLIGDHLYGGDLTR 254

Query: 279 NFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVK 317
                  +   LHA  +    P    +L  T+PLP    +
Sbjct: 255 A------DHQLLHASRLAFLDPFSREQLTFTSPLPEEFNE 288


>gi|218678880|ref|ZP_03526777.1| pseudouridine synthase, RluA family protein [Rhizobium etli CIAT
           894]
          Length = 231

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 28/231 (12%)

Query: 120 QGGSG--IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
             G+G      ++  +    D+       ++P + HRLD++T+G++VVA+   A +HL+ 
Sbjct: 1   HPGAGNWTGTLVNALIYHCGDTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSL 60

Query: 173 SFRMRR----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            F        +++ Y ++VWG P+     I   L + +        V + +   A+ AI+
Sbjct: 61  QFADHGRTMPLERAYQAVVWGRPRALTGTIDAPLGRATG-DRTRRAVKRPDSHDADEAIT 119

Query: 229 HFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
           H++VI+ F +K         +E    TGRTHQ+RVH  H+G P++GD  Y A FK     
Sbjct: 120 HYEVIERFQEKPDATALASLVECHLETGRTHQIRVHMAHIGHPLLGDTVYGAGFKTKANR 179

Query: 283 PIQN---------KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
             ++         +  LHA  +   HP  G  +    PLP  MV+  ++L 
Sbjct: 180 LPEDIRKVVNGFGRQALHAFMLQFEHPRTGEIMHFEVPLPDDMVELVEALR 230


>gi|212691882|ref|ZP_03300010.1| hypothetical protein BACDOR_01377 [Bacteroides dorei DSM 17855]
 gi|237724767|ref|ZP_04555248.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D4]
 gi|265756237|ref|ZP_06090566.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_33FAA]
 gi|212665554|gb|EEB26126.1| hypothetical protein BACDOR_01377 [Bacteroides dorei DSM 17855]
 gi|229436962|gb|EEO47039.1| ribosomal large subunit pseudouridine synthase A [Bacteroides dorei
           5_1_36/D4]
 gi|263233828|gb|EEZ19437.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_33FAA]
          Length = 540

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 118/241 (48%), Gaps = 19/241 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ + L KH   +   ++YED+ + V NKPAG+    G G    +
Sbjct: 309 CEPILKHMLQGLEVEENPL-LKKHYHEIPLEIVYEDNYLVVVNKPAGMLSVPGKGEIDSV 367

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K+        P + HRLD  TSG+L++A+ +   QHL   F+ R I+K Y +L+ G
Sbjct: 368 YQHIKTLY-PDATGPLIVHRLDMATSGVLLIAKNKKVHQHLQAQFKNRMIKKRYIALLDG 426

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              +K+  I   L + + +      V   + +    AI+ ++V++   +    +   P T
Sbjct: 427 KIPSKEGTITLPL-RMNPLDRPRQIV---DHEHGKTAITLYRVLNEQ-EGRTLIAFYPLT 481

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           GRTHQLRVHA H   + CPI GD  Y             ++LYLHA  ++  HP   ++ 
Sbjct: 482 GRTHQLRVHAAHPEGLHCPIRGDELYGRK---------ADRLYLHAESLEFVHPITKKII 532

Query: 307 I 307
            
Sbjct: 533 F 533


>gi|207092511|ref|ZP_03240298.1| hypothetical protein HpylHP_06295 [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 327

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 68/330 (20%), Positives = 137/330 (41%), Gaps = 34/330 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHI 77
            R+D +       I+   +  +++ G V   KK VK     ++ G  + +     A   +
Sbjct: 12  KRIDEFLAKEL-QISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPKIAPKPL 70

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            ++                L+  +++ED  + V NKP  + V     +    +  L  W+
Sbjct: 71  KRDLD--------------LEIEVIFEDEDLLVLNKPPNLVVHKAPSV---KEPTLVDWL 113

Query: 138 DSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            SK  +           + HRLD++TSG +V+A+      HL+E  + + + + Y +L+ 
Sbjct: 114 KSKNYELSNLGLKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLS 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
              K +K  +  +L +  +     + +    ++ + Y+ S F  +         +  +  
Sbjct: 174 TPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLF 233

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++  HP    +L+ 
Sbjct: 234 TGRTHQIRAHLEYLNRHIIGDNLYGLN---GALPKEEIRIMLHAYLIEFKHPRSEQKLRF 290

Query: 308 TAPLPAHMVKTWDSLGFKY--DRNLYIKRL 335
             PL   M++    +  K   D  L  +++
Sbjct: 291 KVPLLKDMLEYLKKVFNKENLDEILDEEKI 320


>gi|329957415|ref|ZP_08297890.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
 gi|328522292|gb|EGF49401.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
          Length = 223

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 69/218 (31%), Positives = 113/218 (51%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKLYLKEKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E F+   ++K YW++V   P+ ++  + N+L++       Y + 
Sbjct: 63  GLVIFAKTSKALTRLNEMFKNSEVKKTYWAVVKNQPREQEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   +Q +C LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVPNSKKAILHYRLI-AKSQNYCLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                 S     + LHAR++   HP     +++ AP+P
Sbjct: 180 RSNPDGS-----ICLHARFVRFVHPVSKELIEVEAPVP 212


>gi|313113934|ref|ZP_07799491.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310623729|gb|EFQ07127.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 335

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 72/332 (21%), Positives = 139/332 (41%), Gaps = 25/332 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++      +++ +RL R+ ++         L K  R+ +V+V+ K+     RIQ+G ++ 
Sbjct: 1   MKQYTATANDDGVRLSRFVQSVTRDFPTSLLYKSFRNKRVKVNGKKAVPEYRIQAGDLIE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +            E           K  +  K  ++YED  I V  KP  +         
Sbjct: 61  LYINDEF---FPPEGAKTVQKAAPKKKQNQPKVNVIYEDENIAVLYKPTHLLCHSDRTGD 117

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            ++      ++  KG+         KP + +RLD+ T G+++ A++  A + + E  R  
Sbjct: 118 ANLVDAFTQYLAEKGEYDPHGENRFKPGICNRLDRGTEGLVIAAKSYTALRDMNEIIRTD 177

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y+++  GIP  +      W           +H  +  ++     I+   V+   A
Sbjct: 178 LLKKEYYTITVGIP--QSGRFTAWWEHDEKNNKVSIHAHQSQDERRKQIITDVDVL-RTA 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL-YLHARYMD 296
             F   ++   TGRTHQ+R H  ++G P++GD KY        T      L  +   ++D
Sbjct: 235 GPFALCKIGLVTGRTHQIRAHLAYLGRPVLGDIKYGNRKMNERTGTKTQALCAVRVTFLD 294

Query: 297 LP-----HPEGGR-LQITAPLPAHMVKTWDSL 322
           +P     H   G+ +++  P    +VK +D+L
Sbjct: 295 IPEENTLHYLSGKVVKLKDP---QIVKQFDAL 323


>gi|240139473|ref|YP_002963948.1| pseudouridine synthase [Methylobacterium extorquens AM1]
 gi|240009445|gb|ACS40671.1| pseudouridine synthase [Methylobacterium extorquens AM1]
          Length = 213

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 71/218 (32%), Positives = 107/218 (49%), Gaps = 11/218 (5%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + V +KPAG+ V  G      +   L +      ++P   HRLD++TSG LV+ R   A 
Sbjct: 1   MLVIDKPAGLPVHPGPKGGPTLTDHLDALRFGLPRRPEAAHRLDRDTSGCLVLGRHAKAL 60

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             L   F   ++ K YW+LV G P+  +  I   L K+S    D      + +     ++
Sbjct: 61  ARLNRLFADGKVDKTYWALVEGGPEAMEGRIDLPLAKRS---DDPRSWWMKTDPAGAPSL 117

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           + ++V+   ++   WLE++P TGRTHQLRVH   MG PI GD  Y    +          
Sbjct: 118 TLYRVLGR-SECLSWLELKPVTGRTHQLRVHCAAMGWPIRGDAIYGGAGRDG------PG 170

Query: 288 LYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
           L LHAR + LP +P+   + + AP PAHM    ++ G 
Sbjct: 171 LQLHARGLSLPLYPKREAIAVEAPAPAHMRAGLEACGM 208


>gi|228957662|ref|ZP_04119409.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|228802004|gb|EEM48874.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
          Length = 307

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 127/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EITVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                   +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGKIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P  +       
Sbjct: 284 AIEVDVPFPTKLNNKIKEF 302


>gi|229189473|ref|ZP_04316490.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|228594064|gb|EEK51866.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
          Length = 307

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 128/319 (40%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            ++V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EIIVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                   +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGKIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P  +       
Sbjct: 284 AIEVDVPFPTKLNNKIKEF 302


>gi|192359752|ref|YP_001982432.1| RNA pseudouridine synthase family protein [Cellvibrio japonicus
           Ueda107]
 gi|190685917|gb|ACE83595.1| RNA pseudouridine synthase family protein [Cellvibrio japonicus
           Ueda107]
          Length = 254

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 107/238 (44%), Gaps = 19/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP G+ V       +     L+   D  G++    HRLD+ TSG L+ 
Sbjct: 7   ILYQDEHLLAVNKPTGLLVHRSPIDRHETRFALQLVRDQIGRRVYPVHRLDKPTSGALLF 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A T   A+ L + F   +++K Y ++V G+ + +   I + L ++     D      + +
Sbjct: 67  ALTPDIARQLGQQFEQHQVRKTYVAVVRGLCEGE-GVIDHPLREEIDACAD-----MRTD 120

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K +  AI+H+K +             + ++  +   P TGR HQ+R H  H+  PI+GD 
Sbjct: 121 KSSQPAITHYKHLASVELPYCVDKYPSSRYSLVRCHPLTGRKHQIRRHLKHINHPIIGDA 180

Query: 271 KYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+             +  +L L A  +   HP+    +Q+TAPL     +     G++
Sbjct: 181 KHGKGRHNRLFQQQLDCHRLLLAATELCFTHPQTQESIQLTAPLEQDFYQLLQRFGWE 238


>gi|293449117|ref|ZP_06663538.1| tRNA pseudouridine synthase C [Escherichia coli B088]
 gi|291322207|gb|EFE61636.1| tRNA pseudouridine synthase C [Escherichia coli B088]
          Length = 260

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 105/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG+  A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGSQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|317493195|ref|ZP_07951618.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918855|gb|EFV40191.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 256

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 105/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHLVALNKPAGWLVHRSWLDRHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+E F  R + K Y ++V G  + +         +   I   +       +
Sbjct: 64  ALSSEVARMLSEQFEQREMNKTYHAVVRGYLEGEAVIDYALTPELDKIADKF----SSPD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQTAVTHYRSLATVEMPVAVGKYQTARYSLIELKPETGRKHQLRRHMAHLRHPIIGDT 179

Query: 271 KYCANFKGNFTS--PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+    +    S     + L LHA  + L HP  G  L + A L     +     G++
Sbjct: 180 KHGDLRQNRAMSQHFACSGLMLHASELCLEHPITGEPLFLQAGLDDRWQRMMAHFGWE 237


>gi|229043131|ref|ZP_04190856.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|228726190|gb|EEL77422.1| Pseudouridine synthase [Bacillus cereus AH676]
          Length = 307

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 125/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EITVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                   +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGSIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q    + 
Sbjct: 175 LVEGKVKKKQGKIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTLVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  +   HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKIHFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P  +       
Sbjct: 284 AIEVDVPFPTKLNNKIKEF 302


>gi|163745453|ref|ZP_02152813.1| ribosomal large subunit pseudouridine synthase A [Oceanibulbus
           indolifex HEL-45]
 gi|161382271|gb|EDQ06680.1| ribosomal large subunit pseudouridine synthase A [Oceanibulbus
           indolifex HEL-45]
          Length = 215

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 67/226 (29%), Positives = 113/226 (50%), Gaps = 15/226 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++   +      ++L+ED+++ + +KPAG+    G G   H+   L + V +   +  L 
Sbjct: 1   MDSEYNPPQEPLVILHEDAEVLLVDKPAGLLSVPGKG--EHLADCLIARVQAVFPEALLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG+++ A T  A +HL   F  R  +K Y + VWG+P+ K   I   L+    
Sbjct: 59  HRLDRDTSGVMIFAMTAHAQRHLGLQFEKRMTRKTYVARVWGVPEEKSGSIDLPLIVD-W 117

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  V     +    A + +KVI    +    + + P TGR+HQLRVH L +G PI+
Sbjct: 118 PNRPLQMVC---HETGKPAQTDWKVIKTDGE-TSRVRLFPKTGRSHQLRVHMLALGHPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
           GD  Y      ++      +L LH+  +   HP+GG   ++++ AP
Sbjct: 174 GDPFYATGPARDYP-----RLMLHSEELRFNHPQGGASTKVRVKAP 214


>gi|157157184|ref|YP_001464113.1| tRNA pseudouridine synthase C [Escherichia coli E24377A]
 gi|191168568|ref|ZP_03030353.1| tRNA pseudouridine synthase C [Escherichia coli B7A]
 gi|193065141|ref|ZP_03046215.1| tRNA pseudouridine synthase C [Escherichia coli E22]
 gi|193071106|ref|ZP_03052031.1| tRNA pseudouridine synthase C [Escherichia coli E110019]
 gi|194426330|ref|ZP_03058885.1| tRNA pseudouridine synthase C [Escherichia coli B171]
 gi|209920242|ref|YP_002294326.1| tRNA pseudouridine synthase C [Escherichia coli SE11]
 gi|218555342|ref|YP_002388255.1| tRNA pseudouridine synthase C [Escherichia coli IAI1]
 gi|218696390|ref|YP_002404057.1| tRNA pseudouridine synthase C [Escherichia coli 55989]
 gi|256019422|ref|ZP_05433287.1| tRNA pseudouridine synthase C [Shigella sp. D9]
 gi|260845437|ref|YP_003223215.1| tRNA pseudouridine synthase [Escherichia coli O103:H2 str. 12009]
 gi|260856901|ref|YP_003230792.1| tRNA pseudouridine synthase [Escherichia coli O26:H11 str. 11368]
 gi|260869469|ref|YP_003235871.1| tRNA pseudouridine synthase [Escherichia coli O111:H- str. 11128]
 gi|300815791|ref|ZP_07096015.1| tRNA pseudouridine synthase [Escherichia coli MS 107-1]
 gi|300820579|ref|ZP_07100730.1| tRNA pseudouridine synthase [Escherichia coli MS 119-7]
 gi|300906681|ref|ZP_07124370.1| tRNA pseudouridine synthase [Escherichia coli MS 84-1]
 gi|300923234|ref|ZP_07139288.1| tRNA pseudouridine synthase [Escherichia coli MS 182-1]
 gi|301304561|ref|ZP_07210671.1| tRNA pseudouridine synthase [Escherichia coli MS 124-1]
 gi|301325733|ref|ZP_07219190.1| tRNA pseudouridine synthase [Escherichia coli MS 78-1]
 gi|307312780|ref|ZP_07592410.1| pseudouridine synthase [Escherichia coli W]
 gi|309795259|ref|ZP_07689678.1| tRNA pseudouridine synthase [Escherichia coli MS 145-7]
 gi|331669526|ref|ZP_08370372.1| tRNA pseudouridine synthase C [Escherichia coli TA271]
 gi|331678771|ref|ZP_08379445.1| tRNA pseudouridine synthase C [Escherichia coli H591]
 gi|332280540|ref|ZP_08392953.1| tRNA pseudouridine synthase C [Shigella sp. D9]
 gi|157079214|gb|ABV18922.1| tRNA pseudouridine synthase C [Escherichia coli E24377A]
 gi|190901415|gb|EDV61179.1| tRNA pseudouridine synthase C [Escherichia coli B7A]
 gi|192927272|gb|EDV81892.1| tRNA pseudouridine synthase C [Escherichia coli E22]
 gi|192955567|gb|EDV86045.1| tRNA pseudouridine synthase C [Escherichia coli E110019]
 gi|194415638|gb|EDX31905.1| tRNA pseudouridine synthase C [Escherichia coli B171]
 gi|209913501|dbj|BAG78575.1| putative pseudouridine synthase [Escherichia coli SE11]
 gi|218353122|emb|CAU98959.1| tRNA pseudouridine synthase [Escherichia coli 55989]
 gi|218362110|emb|CAQ99719.1| tRNA pseudouridine synthase [Escherichia coli IAI1]
 gi|257755550|dbj|BAI27052.1| tRNA pseudouridine synthase [Escherichia coli O26:H11 str. 11368]
 gi|257760584|dbj|BAI32081.1| tRNA pseudouridine synthase [Escherichia coli O103:H2 str. 12009]
 gi|257765825|dbj|BAI37320.1| tRNA pseudouridine synthase [Escherichia coli O111:H- str. 11128]
 gi|300401582|gb|EFJ85120.1| tRNA pseudouridine synthase [Escherichia coli MS 84-1]
 gi|300420473|gb|EFK03784.1| tRNA pseudouridine synthase [Escherichia coli MS 182-1]
 gi|300526843|gb|EFK47912.1| tRNA pseudouridine synthase [Escherichia coli MS 119-7]
 gi|300531720|gb|EFK52782.1| tRNA pseudouridine synthase [Escherichia coli MS 107-1]
 gi|300840165|gb|EFK67925.1| tRNA pseudouridine synthase [Escherichia coli MS 124-1]
 gi|300847483|gb|EFK75243.1| tRNA pseudouridine synthase [Escherichia coli MS 78-1]
 gi|306907215|gb|EFN37721.1| pseudouridine synthase [Escherichia coli W]
 gi|308121230|gb|EFO58492.1| tRNA pseudouridine synthase [Escherichia coli MS 145-7]
 gi|315062072|gb|ADT76399.1| tRNA pseudouridine synthase [Escherichia coli W]
 gi|315256652|gb|EFU36620.1| tRNA pseudouridine synthase [Escherichia coli MS 85-1]
 gi|320202437|gb|EFW77007.1| tRNA pseudouridine synthase C [Escherichia coli EC4100B]
 gi|323154837|gb|EFZ41030.1| RNA pseudouridylate synthase family protein [Escherichia coli
           EPECa14]
 gi|323159892|gb|EFZ45862.1| RNA pseudouridylate synthase family protein [Escherichia coli
           E128010]
 gi|323180223|gb|EFZ65775.1| RNA pseudouridylate synthase family protein [Escherichia coli 1180]
 gi|323183332|gb|EFZ68729.1| RNA pseudouridylate synthase family protein [Escherichia coli 1357]
 gi|323377345|gb|ADX49613.1| pseudouridine synthase [Escherichia coli KO11]
 gi|323946486|gb|EGB42512.1| RNA pseudouridylate synthase [Escherichia coli H120]
 gi|324016355|gb|EGB85574.1| tRNA pseudouridine synthase [Escherichia coli MS 117-3]
 gi|331063194|gb|EGI35107.1| tRNA pseudouridine synthase C [Escherichia coli TA271]
 gi|331073601|gb|EGI44922.1| tRNA pseudouridine synthase C [Escherichia coli H591]
 gi|332102892|gb|EGJ06238.1| tRNA pseudouridine synthase C [Shigella sp. D9]
          Length = 260

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 105/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG+  A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGSQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|237708087|ref|ZP_04538568.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           9_1_42FAA]
 gi|229457915|gb|EEO63636.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           9_1_42FAA]
          Length = 540

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 118/241 (48%), Gaps = 19/241 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ + L KH   +   ++YED+ + V NKPAG+    G G    +
Sbjct: 309 CEPILKHMLQGLEVEENPL-LKKHYHEIPLEIVYEDNYLVVVNKPAGMLSVPGKGEIDSV 367

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K+        P + HRLD  TSG+L++A+ +   QHL   F+ R I+K Y +L+ G
Sbjct: 368 YQHIKTLY-PDATGPLIVHRLDMATSGVLLIAKNKKVHQHLQAQFKNRMIKKRYIALLDG 426

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              +K+  I   L + + +      V   + +    AI+ ++V++   +    +   P T
Sbjct: 427 KIPSKEGTITLPL-RMNPLDRPRQIV---DHEHGKTAITLYRVLNEQ-EGRTLIAFYPLT 481

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           GRTHQLRVHA H   + CPI GD  Y             ++LYLHA  ++  HP   ++ 
Sbjct: 482 GRTHQLRVHAAHPEGLHCPIRGDELYGRK---------ADRLYLHAESLEFVHPITKKII 532

Query: 307 I 307
            
Sbjct: 533 F 533


>gi|259909472|ref|YP_002649828.1| tRNA pseudouridine synthase C [Erwinia pyrifoliae Ep1/96]
 gi|224965094|emb|CAX56626.1| tRNA pseudouridine synthase C [Erwinia pyrifoliae Ep1/96]
 gi|283479545|emb|CAY75461.1| tRNA pseudouridine synthase C [Erwinia pyrifoliae DSM 12163]
          Length = 265

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 111/240 (46%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G+ V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDRWLVAVNKPSGMLVHRSWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++QK Y ++V G  +           ++  I   +     Q E
Sbjct: 64  ALSSEVARLLSQQFEQHQLQKTYHAVVRGWLEGADTLDYPLTEEQDKIADKF----SQPE 119

Query: 221 KGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++          V      ++  +EM P +GR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHWRGVATAELPVPVGRYQTSRYSLVEMLPESGRKHQLRRHMTHLRHPIIGDS 179

Query: 271 KYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +      +    +   N+L LHA  ++L HP     L + A L A   K  + LG++ +
Sbjct: 180 AHGDLKQNRSAAANFGMNRLMLHASELNLTHPVTAEPLMLRAGLDAVWQKVINQLGWQAN 239


>gi|317970429|ref|ZP_07971819.1| putative pseudouridylate synthase [Synechococcus sp. CB0205]
          Length = 207

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 71/218 (32%), Positives = 111/218 (50%), Gaps = 17/218 (7%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           F    L+YED  + V  KP+G+  Q G G        L + V S+  + RL HRLD++TS
Sbjct: 2   FDPLWLVYEDPALLVLEKPSGLLSQPGLGPELSDS--LITAVQSEWPEARLVHRLDRDTS 59

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++VVAR+    + L+E+F  RR++K Y + V G+P  ++  I + + K+ H    Y   
Sbjct: 60  GLIVVARSALVHRTLSEAFAERRVEKRYVADVSGVPDGEEGWIDHPIAKRQHRPPLY--- 116

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               +       +H++ +         L +QP TGR+HQLRVH   +G PI+GD  Y   
Sbjct: 117 --GVDPAGKPCRTHWR-LSAQHSSCSRLALQPLTGRSHQLRVHLQALGHPILGDPLYGER 173

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                      +L+LHA  ++  HP  GR +   +P+P
Sbjct: 174 SAA--------RLHLHACCLEFSHPSDGRWMHFDSPVP 203


>gi|227509897|ref|ZP_03939946.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
 gi|227190617|gb|EEI70684.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
          Length = 299

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 70/313 (22%), Positives = 129/313 (41%), Gaps = 35/313 (11%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
              E   L ++   H   I+   + K ++ SGQV ++ +      ++  G  V +     
Sbjct: 16  QSNEPKTLKKFLNTH--GISH-RMYKNIKTSGQVLINSRSSDSQTKLADGDQVTV----- 67

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDG 131
                I   +  D +V +++        ++YED    V +KPAG++V  G       +  
Sbjct: 68  -----ILPDEAGDPNVAVSEQ----PIKVVYEDDNWLVVDKPAGLTVVPGPANRDDTLVN 118

Query: 132 FLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +K ++   G     P +  RLD+ TSG++++A+ R A     E    +++ K Y ++V 
Sbjct: 119 RVKGYLVRAGVTDLVPHIITRLDRFTSGLVLIAKHRLANSLANELLAAKQLHKRYLAVVS 178

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        I   + K  +  G  +           ++ + + V          +E+  H
Sbjct: 179 GGGLPDHGRIQKPIAKDPNGYGQII------SDDGRFSDTEYWVRQRLNDDM-LVEVALH 231

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+RVH   +G P++GD  Y         +   ++  LHA  +    P     +++
Sbjct: 232 TGRTHQIRVHFASIGHPLLGDQLYHGPM-----NMGIDRQALHAVMLGFNDPFSQSEIKL 286

Query: 308 TAPLPAHMVKTWD 320
            +PLP  M    D
Sbjct: 287 KSPLPKDMSSILD 299


>gi|290580515|ref|YP_003484907.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
 gi|254997414|dbj|BAH88015.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
          Length = 296

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 69/305 (22%), Positives = 130/305 (42%), Gaps = 33/305 (10%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K+H   I+ + L KI  + GQ+ V+ +       +  G  V I         II +++
Sbjct: 16  FLKSH--DISKILLAKIKFKGGQILVNDQEENAIYLLDIGDRVTI---------IIPDEE 64

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DS 139
            L++   +          ++YED    + +KPAG +          I  F+K +    D 
Sbjct: 65  ALETLQPIKHD-----LNIVYEDEHFLILDKPAGYASIPSILHTNTIANFVKYYYLKKDY 119

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECI 198
             ++  +  RLD++TSG++++A+   A   L +  + + I+K Y++LV G  +   +  I
Sbjct: 120 PNKQIHIVTRLDKDTSGLMLLAKHGYAHARLDKQLQKKTIKKRYYALVSGQGQLPDQGEI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      +   + +       YA + +KV+  +      +++Q HTGRTHQ+RVH
Sbjct: 180 IAPIARP-----EDSIITRCVHPSGKYAHTSYKVLARYGDIA-LVDIQLHTGRTHQIRVH 233

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVK 317
             H+G P++GD  Y              +  LH  ++    P      Q  + L   +  
Sbjct: 234 FAHIGFPLLGDDLYGGEMG-----YGLKRQALHCHFLSFVDPFSKEHKQYNSSLTEDLDS 288

Query: 318 TWDSL 322
               L
Sbjct: 289 VIIDL 293


>gi|309799108|ref|ZP_07693361.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus infantis SK1302]
 gi|308117343|gb|EFO54766.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus infantis SK1302]
          Length = 291

 Score =  182 bits (462), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 72/303 (23%), Positives = 131/303 (43%), Gaps = 30/303 (9%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
             V+ +    M +  + +     I    ++  LR    + ++++ V ++  ++SG   ++
Sbjct: 4   TFVIPDSLPEMTVKVFLEEQLL-IPK-KIRHFLRIKKHILINQEEVHWHQTVKSGDECQL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             + +  ++  KE  I+  + NL +         +Y+D  + + NKP  +   G      
Sbjct: 62  --IFDEEDYPTKE--IVWGNPNLVQE--------VYQDQHLIIVNKPEDMKTHGNQPEEI 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   GQ   + HRLD+ETSG+++ A+       L      + I + YW+LV
Sbjct: 110 TLLNHVSAYV---GQTCYVVHRLDKETSGLILFAKNPFILPILNRLLEKKEISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +K+    + + +  H     V     + K   YA +H   +  F  K   +  + 
Sbjct: 167 EGKVGSKELIFRDKIGRDRHDRRKRV----VDFKNGQYAETHVTRLKQFQNKTSLVRCRL 222

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G  I+GD  Y  + K         +L LHA  +   HP    +L 
Sbjct: 223 KTGRTHQIRVHLSHHGHSILGDPLYNPHSKT-------KRLMLHAFKLSFVHPLTLNKLS 275

Query: 307 ITA 309
            TA
Sbjct: 276 FTA 278


>gi|304385442|ref|ZP_07367787.1| RluA family pseudouridine synthase [Pediococcus acidilactici DSM
           20284]
 gi|304328649|gb|EFL95870.1| RluA family pseudouridine synthase [Pediococcus acidilactici DSM
           20284]
          Length = 292

 Score =  182 bits (462), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 81/301 (26%), Positives = 135/301 (44%), Gaps = 34/301 (11%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +  +      +   +QKI + G+ V  +++ V   +++   +   +              
Sbjct: 17  KVLQRL--GASQRLMQKIRQDGRLVDENERTVALKDKVMPFEPFWV-------------- 60

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSK 140
           ++ D   +           ++YED    V NKPAG+ +V G S     +   +K    + 
Sbjct: 61  ELPDEDSDPAVPVSDQPLDVIYEDDNWLVVNKPAGLTAVPGPSNRTDTLVNRIKGHWQAN 120

Query: 141 G---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           G     P L  RLD+ TSGI +VAR + A   L+E  R R+I+K Y +LV G+   +K  
Sbjct: 121 GAVNLVPHLITRLDRFTSGITLVARHQVANSLLSEQVRHRKIKKTYLALVDGVVSAEKGT 180

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               L     +  D +H  ++ ++G   A + FKV+  FA +   +++   TGRTHQ+RV
Sbjct: 181 FNQPLG----LAADGIH--REVQEGGQSATTSFKVVQRFANQ-TLVQVHLKTGRTHQIRV 233

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
           H  + G P+VGD  Y              +  LHA+ +    P    +L+ TAPLPA + 
Sbjct: 234 HFANAGHPLVGDQLYGGPMDR-----GIERQALHAQSIRFFDPFTNQKLEFTAPLPADLQ 288

Query: 317 K 317
            
Sbjct: 289 A 289


>gi|325688842|gb|EGD30850.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK115]
          Length = 291

 Score =  182 bits (462), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 73/316 (23%), Positives = 126/316 (39%), Gaps = 33/316 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   ++ G  + +
Sbjct: 4   TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLAINWQTVVKPGDDICL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+          
Sbjct: 62  IFDEEDY----PQKTILFGNGELVEE--------LYQDQHLIIVNKPEGMKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+LV
Sbjct: 110 ALLNHVSAYV---GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLEKREISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +KK    + + +  H     +       +   YA +H   I  F Q    ++ Q 
Sbjct: 167 QGKFPSKKLIYKDKIGRDRHDRRKRL----VEPQKGLYAETHVTRIKQFGQ-AALVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G P++GD  Y    KG        +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG--------RLMLHAHRLTFTHPFTLEKIT 273

Query: 307 ITAPLPAHMVKTWDSL 322
           + A    +  K   SL
Sbjct: 274 VEAR-SDNFEKVLRSL 288


>gi|322378406|ref|ZP_08052860.1| RNA pseudouridine synthase [Helicobacter suis HS1]
 gi|322380087|ref|ZP_08054343.1| pseudouridine synthase [Helicobacter suis HS5]
 gi|321147494|gb|EFX42138.1| pseudouridine synthase [Helicobacter suis HS5]
 gi|321149162|gb|EFX43608.1| RNA pseudouridine synthase [Helicobacter suis HS1]
          Length = 342

 Score =  182 bits (462), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 80/357 (22%), Positives = 147/357 (41%), Gaps = 46/357 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           M  ++       EE  RLD +       +    + + ++S +V+V+ K + K   +++ G
Sbjct: 9   MVQIERTFTAMQEE--RLDTFLTKSL-GVAKNQILQCIKSSRVQVNDKTILKGGLKLKIG 65

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V + P    L                      LK  +LYED  I V NKP  +++   
Sbjct: 66  DEVVLKPSQAPLE---------------VYKPTDLKIEILYEDEDILVLNKPPYLAMHPA 110

Query: 123 SGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
             +    +  L  ++ +KG          +  + HRLD+ TSG +V+A+  A   +L   
Sbjct: 111 ISL---HEPTLVDYLQAKGVTLSTLSGESRCGIVHRLDKNTSGAVVIAKNNATHANLATQ 167

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--VVKQNEKGANYAISHFK 231
            ++R + + Y +L+   P  K   +   L +         +   ++QN  G  Y+ + F 
Sbjct: 168 LQIREMGRYYLALIT-EPLKKPMRVECHLGRHPKNRLKMTNLDTLRQNINGGRYSKTDFI 226

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
            +   A+    +  + ++GRTHQ+R H   +G  I+GD  Y            + ++ LH
Sbjct: 227 PLLSNARGIQLIAAKLYSGRTHQVRAHLESLGRHILGDSLYGKK------DNYKGRILLH 280

Query: 292 ARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL--GFKYD---RNLYIKRLYSQDECK 342
           A  + + HP    +L   A +   MV+  +    G  +D   R  YI  L++   C+
Sbjct: 281 AYLLYMTHPTSQEKLLFKAQILEDMVECLEKEFQGVAWDGLIRENYILDLFNTTVCE 337


>gi|290967748|ref|ZP_06559303.1| pseudouridine synthase, RluA family [Megasphaera genomosp. type_1
           str. 28L]
 gi|290782264|gb|EFD94837.1| pseudouridine synthase, RluA family [Megasphaera genomosp. type_1
           str. 28L]
          Length = 301

 Score =  182 bits (462), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 64/299 (21%), Positives = 120/299 (40%), Gaps = 34/299 (11%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
            ++    ++I  SG    + + +   N + +G  + I   +         Q      +  
Sbjct: 23  GVSATLRRRIKHSGTCTCNGQVIGLQNFVHTGDTICISLPVR--------QAFAPEPLAF 74

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKP--RLT 147
           T+         +YED  + V NKPAG+ +   +G     +   +  +  +  Q       
Sbjct: 75  TR---------VYEDRHLLVINKPAGLLMHPTAGQRSGTLANAVSYYYITSNQHCAYHPV 125

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+ ++A+     Q L +    R  +++Y +L  G        + + + +   
Sbjct: 126 HRLDKNTSGLCMIAKNPYV-QSLFDHAPNRYYKRLYLALSTGYFPTPTATVHSPVGR--- 181

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              +   + +        A + F  +   A  +  L++  HTGRTHQ+RVH  ++G P++
Sbjct: 182 --AENSIIKRCVCLDGQKAHTDFVRLAA-ADTYSLLQVSLHTGRTHQIRVHCSYLGFPLL 238

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
           GD  Y        T  + ++  LHA  M   HP     +++ A  PA M       G+ 
Sbjct: 239 GDDLYGG------THELLSRQALHAYAMLFIHPITHKEIRLFALPPADMQALITEAGWD 291


>gi|148989706|ref|ZP_01821015.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP6-BS73]
 gi|147924822|gb|EDK75905.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP6-BS73]
          Length = 291

 Score =  182 bits (462), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 69/279 (24%), Positives = 114/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D S   
Sbjct: 26  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYSQKT 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 73  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 130 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD 
Sbjct: 190 KRI----VDAKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDP 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    RL  T
Sbjct: 246 LYNSKSKT-------SRLMLHAFRLSFTHPLTLERLTFT 277


>gi|257452878|ref|ZP_05618177.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
 gi|317059420|ref|ZP_07923905.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
 gi|313685096|gb|EFS21931.1| tRNA pseudouridine synthase A [Fusobacterium sp. 3_1_5R]
          Length = 291

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 77/315 (24%), Positives = 149/315 (47%), Gaps = 27/315 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   VE     +R+DR+ +  +P ++  ++ K LR+G+++V+ K+VK N R      ++
Sbjct: 1   MKEYQVEEKYVGVRIDRYLRKEFPDLSLGDIFKTLRTGKIKVNGKKVKENYRFLEEDRIQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                   N++  E+K   + ++L+ +    L+  + Y+D+ I VF K AG  +  GS  
Sbjct: 61  --------NYLQVEEKEKMTFIHLSQEEKKRLEDGIFYQDTDILVFYKKAGELMHKGSSH 112

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            Y +    +++     +     +RLD+ETSG+++  +     + L E+ + R I K Y+ 
Sbjct: 113 DYGLAEQFQAYFQ--NEDFHFVNRLDKETSGLVLGGKCLKIVRELAEAIKKRTIIKKYYI 170

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           ++ G P+     +  +L K    G + V   +  ++      + F VI    +++  LE 
Sbjct: 171 IIEGSPEKNHFSLKTYLKK----GENKVLESQTAKEEYKECSASFSVI-RKNKEYSLLEA 225

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              TGRTHQLRV    +G PI+GD KY              ++YLH+  + +   E    
Sbjct: 226 VLETGRTHQLRVQLAGIGFPILGDIKYGKKRA--------KRMYLHSHLLKISDWEK--- 274

Query: 306 QITAPLPAHMVKTWD 320
           +    +P   +  ++
Sbjct: 275 EWDTGIPTEFLSYFN 289


>gi|258507862|ref|YP_003170613.1| pseudouridine synthase [Lactobacillus rhamnosus GG]
 gi|257147789|emb|CAR86762.1| Pseudouridine synthase [Lactobacillus rhamnosus GG]
 gi|259649190|dbj|BAI41352.1| pseudouridylate synthase [Lactobacillus rhamnosus GG]
          Length = 300

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 61/306 (19%), Positives = 119/306 (38%), Gaps = 35/306 (11%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K      +   L+K+  + G + V+K++      +++G  + +              +
Sbjct: 17  FLKQQ--GFSRAQLKKLRYQGGFIFVNKRQRHTAYPLRNGDRILV--------------Q 60

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---D 138
                   +      +  + YED    V NKPAG++     G     +   +K+++    
Sbjct: 61  TAPEQAAASVVPYEHEFPICYEDDDYLVVNKPAGVASIPAVGRRNDSMANMVKAYLIKTH 120

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKEC 197
           ++ Q   +  RLD++TSG++V A+   A   L          K Y +LV      +    
Sbjct: 121 AESQAVHVVTRLDRDTSGLMVFAKHSLAHSLLDRQLHSENFLKQYLALVTSKSLLSAHGW 180

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   +   +       ++ +   +    +++ ++ +   +     L +  HTGRTHQ+RV
Sbjct: 181 IVLPIGVSTG-----FYMRRVVSETGKPSVTEYQTLAQNSHAAAVL-VTLHTGRTHQIRV 234

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +G P+ GD  Y              +  LH  ++    P   + + + APLP  M 
Sbjct: 235 HFAAIGHPLFGDDLYNRQADD------FKRQALHCAHLRFWQPLQKKWVDLHAPLPTDMA 288

Query: 317 KTWDSL 322
           K  D L
Sbjct: 289 KLSDHL 294


>gi|324119833|gb|EGC13712.1| RNA pseudouridylate synthase [Escherichia coli E1167]
          Length = 260

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 63/238 (26%), Positives = 105/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +V      +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFVR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHACLDDTWMQALSQFGWR 237


>gi|149919776|ref|ZP_01908253.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
 gi|149819383|gb|EDM78814.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
          Length = 322

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 77/333 (23%), Positives = 132/333 (39%), Gaps = 35/333 (10%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQS 61
           + +  +  VV+ DE+   L    +     +++   + ++R+G+V+VD + R     R+++
Sbjct: 1   MASEQRRGVVDEDEDGATLAAVVRGLMDGLSWNKSRDLVRTGRVQVDGQMRFDPAERLRA 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G +V + P     +     +  L    +                       KPAG+    
Sbjct: 61  GALVEVNPTGRRRSAPPLPEDRLVFVDSEVVVVR-----------------KPAGLLSVP 103

Query: 122 GSGIAYHIDGFLKS----WVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
                   D  ++       + +G       +  +  RLD++TSG+LV ARTR A + L 
Sbjct: 104 -WDDRDDRDTLIERTRITLREREGTRSGERDRLGVVQRLDKDTSGLLVFARTRRARKALE 162

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             FR   I + Y +LV G    K     ++L+     G       K   K A  AI+  +
Sbjct: 163 AQFRAHTIFRRYVALVHG--AAKAGVHESYLIADRGDGLRGSWRGKSPPKAAKKAITKVR 220

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V +        +  Q  TGR HQ+R+H    G P+VG+  Y   ++G        +  LH
Sbjct: 221 VEEKL-DGATLISCQLETGRQHQIRIHLAEAGHPLVGEPVYGRGYRGR--RLPAPRPMLH 277

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           A  +   HP G R ++  AP P       + L 
Sbjct: 278 AASLGFRHPVGDRPVRFEAPPPDDFCAALEQLR 310


>gi|1568620|gb|AAB09035.1| orfEU5; uncharacterized orf upstream of txpA similar to H.
           influenzae HI0412 [Bartonella bacilliformis]
          Length = 221

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 104/195 (53%), Positives = 134/195 (68%), Gaps = 3/195 (1%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           +++M  ++   VE DE  MRLDRWFK HYP + F  LQKILRSGQVRVD  RVK N R+ 
Sbjct: 30  VTVMVNIKIKNVEEDENGMRLDRWFKVHYPGLGFGYLQKILRSGQVRVDGGRVKANMRLV 89

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +GQ +R+P         I    I    ++     D LK +LLYED KI+VFNKPAG++VQ
Sbjct: 90  TGQSIRVPSFFIESKRNIS---ITSKVISQQDDGDLLKKMLLYEDPKIFVFNKPAGLAVQ 146

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           GGSG+  H+DG L++W + KG+KPRL HRLD+ETSG+LVVAR+  AAQ LT +FR R ++
Sbjct: 147 GGSGLTRHVDGMLEAWRNKKGEKPRLVHRLDRETSGLLVVARSXXAAQALTAAFRTREMK 206

Query: 181 KIYWSLVWGIPKNKK 195
           KIYW+LV   P  K+
Sbjct: 207 KIYWALVRRXPXKKQ 221


>gi|182684947|ref|YP_001836694.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CGSP14]
 gi|303253824|ref|ZP_07339955.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS455]
 gi|303260789|ref|ZP_07346745.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP-BS293]
 gi|303263120|ref|ZP_07349049.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS292]
 gi|303265168|ref|ZP_07351080.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS397]
 gi|303267680|ref|ZP_07353509.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS457]
 gi|303270027|ref|ZP_07355752.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS458]
 gi|182630281|gb|ACB91229.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CGSP14]
 gi|302599211|gb|EFL66226.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS455]
 gi|302635742|gb|EFL66248.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS292]
 gi|302638071|gb|EFL68550.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP-BS293]
 gi|302640439|gb|EFL70861.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS458]
 gi|302642786|gb|EFL73104.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS457]
 gi|302645249|gb|EFL75484.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS397]
          Length = 291

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 69/294 (23%), Positives = 116/294 (39%), Gaps = 30/294 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D S   
Sbjct: 26  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYSQKT 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 73  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 130 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 190 KRI----VDAKNGQYAETYVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDP 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
            Y +  K        ++L LHA  +   HP    +L  T  L     K     G
Sbjct: 246 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFTT-LSNTFEKELKKNG 291


>gi|2995386|emb|CAA63803.1| hypothetical protein [Zymomonas mobilis subsp. mobilis ATCC 29191]
          Length = 219

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 119/231 (51%), Gaps = 14/231 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
             L   +L+ D++  + +KPAG+ V      +  ++ +L S      + P + HRLD++T
Sbjct: 2   PILAERVLFIDAEAMIIDKPAGLPVTSVRDGSLSLENYLASLCFGFKRWPSIVHRLDRDT 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L++AR     + L+E+F   +++K YW+++ G+P+  +  I   LLK S     +  
Sbjct: 62  SGCLLLARNPKMHRRLSEAFSQGQVKKCYWAILEGVPEKNEGTIDLPLLKISSPKSGWRI 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC 273
           V          A++H++++    +    +  +P TGRTHQLRVHA   +G PIVGD  Y 
Sbjct: 122 VADDK---GKRAVTHWEIL-AKNKGRSLVAFRPETGRTHQLRVHAATGLGLPIVGDPFYS 177

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           ++   N      +++ LHA  +++   E   +   APLP    K +  LGF
Sbjct: 178 SHKDEN-----ISRMMLHAHSLEIARLEKKPIAAEAPLP----KAFTDLGF 219


>gi|333001149|gb|EGK20719.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-272]
 gi|333015787|gb|EGK35124.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-227]
          Length = 260

 Score =  182 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVLMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|148985947|ref|ZP_01819000.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP3-BS71]
 gi|168492590|ref|ZP_02716733.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC0288-04]
 gi|147921920|gb|EDK73045.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP3-BS71]
 gi|183573261|gb|EDT93789.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC0288-04]
          Length = 291

 Score =  182 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 68/279 (24%), Positives = 113/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D     
Sbjct: 26  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYPQKT 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 73  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 130 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD 
Sbjct: 190 KRI----VDAKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDP 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    RL  T
Sbjct: 246 LYNSKSKT-------SRLMLHAFRLSFTHPLTLERLTFT 277


>gi|241761046|ref|ZP_04759135.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis ATCC
           10988]
 gi|260752988|ref|YP_003225881.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis NCIMB
           11163]
 gi|241374665|gb|EER64126.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis ATCC
           10988]
 gi|258552351|gb|ACV75297.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis NCIMB
           11163]
          Length = 219

 Score =  182 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 119/231 (51%), Gaps = 14/231 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
             L   +L+ D++  + +KPAG+ V      +  ++ +L S      + P + HRLD++T
Sbjct: 2   PILAKRVLFIDAEAMIIDKPAGLPVTSVRDGSLSLENYLASLCFGFKRWPSIVHRLDRDT 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L++AR     + L+E+F   +++K YW+++ G+P+  +  I   LLK S     +  
Sbjct: 62  SGCLLLARNPKMHRRLSEAFSQGQVKKCYWAILEGVPEKNEGIIDLPLLKISSPKSGWRI 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC 273
           V          A++H++++    +    +  +P TGRTHQLRVHA   +G PIVGD  Y 
Sbjct: 122 VADDK---GKRAVTHWEIL-AKNKGRSLVAFRPETGRTHQLRVHAATGLGLPIVGDPFYG 177

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           ++   N      +++ LHA  +++   E   +   APLP    K +  LGF
Sbjct: 178 SHKDEN-----ISRMMLHAHSLEIARLEKKPIAAEAPLP----KAFTDLGF 219


>gi|293379048|ref|ZP_06625201.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
 gi|292642327|gb|EFF60484.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
          Length = 285

 Score =  182 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 65/265 (24%), Positives = 112/265 (42%), Gaps = 28/265 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R   V ++++   F++ ++    + +              ++ D +    +  D     
Sbjct: 36  IRK-NVWINQQPALFHHEVKGNDQITLLF------------EVTDYNYQEVQLGDAKHIR 82

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+                L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKKQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+       L      + I + Y ++VWG     +  I N + +  H     V     +
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGKIAKDR-TITNKIGRDRHDRRKRV----VD 197

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +K    A++H  V D        +     TGRTHQ+RVH  H+G PIVGD  Y       
Sbjct: 198 DKNGQNALTHVTV-DKVLSGKTQVYCVLETGRTHQIRVHLAHIGHPIVGDPLYQNRPAE- 255

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR 304
                  +L LHA  + + HP    
Sbjct: 256 -------RLMLHALELHMIHPFTQE 273


>gi|124006880|ref|ZP_01691710.1| ribosomal large subunit pseudouridine synthase D [Microscilla
           marina ATCC 23134]
 gi|123987561|gb|EAY27270.1| ribosomal large subunit pseudouridine synthase D [Microscilla
           marina ATCC 23134]
          Length = 297

 Score =  182 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 79/334 (23%), Positives = 136/334 (40%), Gaps = 50/334 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M  ++   V ++    RL  +    +  + +   ++K ++ G VR++    +    +Q G
Sbjct: 1   MFLLKTHTVPHNAPAARLSDYACGIFEQLPSRKGVKKAIKKGAVRLNGMPAETGRWVQPG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++ +                +D      K  +F    ++YED    V NKPAG+ V G 
Sbjct: 61  DIITL----------------VDLEETPPKQYEF-TLEVVYEDDHFAVINKPAGVKVSGN 103

Query: 123 --SGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               I   + G LK+       K  +  HRLD  TSG+L+VA+T  A  HL +    + I
Sbjct: 104 QYRTIVNMLPGNLKASPLPDALKWAKPVHRLDVPTSGLLMVAKTTQAHIHLGQQLEQKTI 163

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-- 237
           +K Y ++V G P  +   I   +                       A S F+V+      
Sbjct: 164 KKAYHAIVKGTPAAR-GHIRTPI-------------------NGQSAHSEFEVLQTVPSL 203

Query: 238 --QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             +    + + PHTGRTHQLRVH   +G PI GD  Y         + +   L+L A  +
Sbjct: 204 RNETLSLVRLSPHTGRTHQLRVHLASLGHPITGDTTY----DEAGNTMLHKGLFLAATSL 259

Query: 296 DLPHPE-GGRLQITAPLPAHMVKTWDSLGFKYDR 328
            L HP     ++++  +P       +    ++++
Sbjct: 260 QLQHPTLTQTIEVSIDIPHKFASLLEREARRWEK 293


>gi|317050965|ref|YP_004112081.1| pseudouridine synthase [Desulfurispirillum indicum S5]
 gi|316946049|gb|ADU65525.1| pseudouridine synthase [Desulfurispirillum indicum S5]
          Length = 273

 Score =  182 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 67/244 (27%), Positives = 110/244 (45%), Gaps = 17/244 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           + +  +++Y D  +   +KPAG+ V   S   +     ++   D  GQ     HRLD+ T
Sbjct: 7   EPMPLVIVYRDDHLIAIHKPAGLLVHRSSIDRHETRFAMQLLRDQIGQPVYPVHRLDKPT 66

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+ A     A+ L   F    + K Y ++V G+P  +   I + L ++ +   D   
Sbjct: 67  SGVLLFALNPEVARLLGALFVSAAVAKTYLAVVRGVPP-RSGIIDSPLREERNRYDDQRT 125

Query: 215 VVKQNEKGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            +   EK    A++ F+          V      ++  +E+QP TGR HQ+R H  H+  
Sbjct: 126 AL---EKAPQSAVTRFQTRATVELPFAVGPYPTSRYALVEVQPQTGRRHQIRRHFKHLCH 182

Query: 265 PIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           P++GD KY       F        +L L A  + L HP  G  L IT+PL  +  +   +
Sbjct: 183 PLIGDTKYGEGRHNRFFRDHFGCQRLLLAAVELQLNHPVNGMPLVITSPLEENFRELVTA 242

Query: 322 LGFK 325
           LG+ 
Sbjct: 243 LGWD 246


>gi|320530955|ref|ZP_08031988.1| pseudouridine synthase, RluA family [Selenomonas artemidis F0399]
 gi|320136820|gb|EFW28769.1| pseudouridine synthase, RluA family [Selenomonas artemidis F0399]
          Length = 297

 Score =  182 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 64/324 (19%), Positives = 126/324 (38%), Gaps = 39/324 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSG 62
           MT +   +   +E   +   +       ++    ++I  SG    +    +     ++ G
Sbjct: 1   MTEIHISLPPGEEMPAK--AYLTKKC-GVSGGLWKRIKHSGTFSHNGVPAIAARTAVRDG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V+                      +  +   + L   + YED  + + +KPAG+ V   
Sbjct: 58  DVLS-----------------YALPIVSSVVPEDLPLAIAYEDDDLLIIDKPAGMLVHPT 100

Query: 123 S-GIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +      I   ++    S+G        HRLD+ T+G+L++A+      + T+      +
Sbjct: 101 TQETRGTIANAVRGLYASRGDTLDFHPCHRLDRNTTGLLLIAKRPEVQYYFTKHLDA--V 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +L+ G      + I   + +          ++++       A +H+   +    +
Sbjct: 159 RRAYLALIEGRLTPASDIIDAPIARALP-----SIILRRVAPDGKPARTHYTT-ERTTGR 212

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  L +   TGRTHQ+RVH  H+G P++GD  Y  N           +  LHA  + L  
Sbjct: 213 YSLLRLTLETGRTHQIRVHLAHLGHPLLGDDLYGCNTDE------IARHALHAARLSLRL 266

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  G  L + +PLP  M +   +L
Sbjct: 267 PRTGELLTVESPLPEDMARIAGTL 290


>gi|256841173|ref|ZP_05546680.1| ribosomal large subunit pseudouridine synthase A [Parabacteroides
           sp. D13]
 gi|256737016|gb|EEU50343.1| ribosomal large subunit pseudouridine synthase A [Parabacteroides
           sp. D13]
          Length = 548

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 115/242 (47%), Gaps = 20/242 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L+H+++  ++ ++ +    H +  K  +LYED  + V NKP G+    G G    +
Sbjct: 311 CEPILHHMLQGLRVDENPLLADSHRET-KLDILYEDDYLLVINKPEGMLSVPGKGDVDSV 369

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L      +   P + HRLD  TSG+L+ A+T+ A Q+L   F+ R IQK Y +L+ G
Sbjct: 370 YQRLSILY-PEATGPIIVHRLDMATSGLLLAAKTKEAHQNLQAQFKNRTIQKRYIALLEG 428

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I   L          +     +E+    A + ++V++  + K   +   P T
Sbjct: 429 EVPQDEGEIRLPLCPDPLDRPQQI----VSEEFGKPAFTRYRVLERTSGK-TLIAFYPQT 483

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVHA H   + CPI+GD  Y    +         +LYLHA Y+   HP    R+
Sbjct: 484 GRTHQLRVHAAHPLGLHCPILGDELYGRKAE---------RLYLHAEYLAFTHPITSERI 534

Query: 306 QI 307
           +I
Sbjct: 535 EI 536


>gi|254229488|ref|ZP_04922902.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262393515|ref|YP_003285369.1| tRNA pseudouridine synthase C [Vibrio sp. Ex25]
 gi|151937953|gb|EDN56797.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262337109|gb|ACY50904.1| tRNA pseudouridine synthase C [Vibrio sp. Ex25]
          Length = 256

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/252 (24%), Positives = 108/252 (42%), Gaps = 17/252 (6%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
            + + S+ ++  ++Y+D      NKPAG+ V       +     +++  D  GQ     H
Sbjct: 5   EIARSSEPVELEIVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLH 64

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG+LV A +   A  +   F   +++K Y ++V G  + +        ++   I
Sbjct: 65  RLDRPTSGVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVELDKI 124

Query: 209 GGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVH 258
              +       EK A  A++ +K +               ++C +EM+P TGR HQLR H
Sbjct: 125 ADKFASQ----EKEAQEAVTEYKPLAKVEVPYSTGKFPTTRYCLVEMKPKTGRKHQLRRH 180

Query: 259 ALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             H+  PIVGD  +          T    ++L LHA  +   HP   + + +TA L    
Sbjct: 181 MAHLRHPIVGDTTHGDGKHNKLYRTEFDSHRLLLHASELRFVHPFTDQDIVMTANLDETW 240

Query: 316 VKTWDSLGFKYD 327
            + +    +   
Sbjct: 241 QQLFTRFEWDES 252


>gi|325913377|ref|ZP_08175744.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
 gi|325477303|gb|EGC80448.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
          Length = 292

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 128/303 (42%), Gaps = 34/303 (11%)

Query: 3   LMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQ 60
           +M  Y+ Y+ +  +E N  +D+  +N    I     +  LR    + V+ K +  N ++ 
Sbjct: 9   IMNQYIYYLTISQNENNQNVDQIMRNLL--IPR-KWRHFLRIEKNILVNDKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V NKPAG    
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENDDVLVINKPAGQKTH 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L    +  G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 113 PN---LYETDTALNDCANYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           + Y++ +      +    I   +          +            AI+H++V+     K
Sbjct: 170 RSYFAWIDATNDISDNGTINLPIGDDPLDMRKRMVRT-----DGLKAITHYQVVKKIGSK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++         KL L A  +    
Sbjct: 225 I-LVKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQAG------EKLQLTAYKLVFQK 277

Query: 300 PEG 302
           P  
Sbjct: 278 PFS 280


>gi|291529049|emb|CBK94635.1| pseudouridine synthase, RluA family [Eubacterium rectale M104/1]
          Length = 295

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 61/314 (19%), Positives = 126/314 (40%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +  ++    ++ + K H Y H   V L++      +  +      N R+    ++ +   
Sbjct: 9   INENDTGKTVEGFLKEHGYTHQVLVRLKQ--TDHGILRNGIWAYTNERLCKDDLITV--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                      +I+++  +       L   + YED  I V NKP  +     +G   +  
Sbjct: 64  -----------QIVENECSDNISPVNLPLDIAYEDDDIIVINKPFDMPAHPSAGNHDNTL 112

Query: 131 GFLKSWVDSKGQKPRLTHR---LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                +      KP +      LD++T+G+ +VA+   A   L  +   R I + Y+++ 
Sbjct: 113 ANALMYYYGSQNKPFVYRCINRLDRDTTGLTIVAKHALAGGILGNAVAKRAIHRTYYAVC 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQ 246
            G        I+  + +K     +       + K   YA++ F  I          ++++
Sbjct: 173 SGC-TPACMRISAPIARKDASTIER----CVDFKRGEYAVTDFIRIKYNPDNNLSLVKLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
             TGRTHQ+RVH  ++G P++GD  Y  ++         ++  LH+  +   HP  G ++
Sbjct: 228 LLTGRTHQIRVHMKYIGFPLIGDFLYNPDY------TYISRQALHSGRLVFTHPVTGQKM 281

Query: 306 QITAPLPAHMVKTW 319
            + + +P+ M   +
Sbjct: 282 NLISDIPSDMKSLF 295


>gi|116491175|ref|YP_810719.1| pseudouridylate synthase, 23S RNA-specific [Oenococcus oeni PSU-1]
 gi|290890691|ref|ZP_06553761.1| hypothetical protein AWRIB429_1151 [Oenococcus oeni AWRIB429]
 gi|116091900|gb|ABJ57054.1| Pseudouridylate synthase, 23S RNA-specific [Oenococcus oeni PSU-1]
 gi|290479666|gb|EFD88320.1| hypothetical protein AWRIB429_1151 [Oenococcus oeni AWRIB429]
          Length = 299

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 140/316 (44%), Gaps = 35/316 (11%)

Query: 13  ENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
             + E +RL  + K     H  F  ++     G++ V+ + V  N+ +++G+ + I    
Sbjct: 9   TKEPEKVRL--FLKARGVSHRMFSQIKHF--GGKIVVEGREVFTNDYVKNGEKITIF--- 61

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHID 130
                +  E++ ++   + T         +++ED    + +KPA ++   G       + 
Sbjct: 62  -----MPPERENVELDADFTD-----PLKVVFEDKNFLIVDKPAFVTTVPGHADRKTTLV 111

Query: 131 GFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSL 186
             +K+ +  +      P +  RLD++TSG++++A+ + A   L ++      I+K Y +L
Sbjct: 112 NMIKAHLIQEKADSLVPHVVTRLDRDTSGLVLLAKHKFAHALLNDALMEHHDIEKFYVAL 171

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +     I   + +   I GD++   +Q  +    +++ + V   F   F  L +Q
Sbjct: 172 VSGNFQEDHGMIDEPIGR---IEGDFIR--RQVRQDGKRSVTEYWVEKRF-DNFTQLRIQ 225

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
            HTGRTHQ+RVH    G P++GD  Y         S + ++  LHA  M    P   +  
Sbjct: 226 LHTGRTHQIRVHMAWAGHPLIGDVLYGGPH-----SKLISRQALHASEMIFFDPFANKNQ 280

Query: 306 QITAPLPAHMVKTWDS 321
              A LP  + +  ++
Sbjct: 281 HFNAGLPDDIQRIIEA 296


>gi|308273177|emb|CBX29780.1| hypothetical protein N47_F14750 [uncultured Desulfobacterium sp.]
          Length = 271

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 67/254 (26%), Positives = 114/254 (44%), Gaps = 21/254 (8%)

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLK 134
            ++    ++ S + +          +LYED  I V +K +G+     +  A       L 
Sbjct: 19  KMLPGNNMIKSKIKIRTKHVPAGLRILYEDRDIIVIDKSSGLLSVEANYEAENTAHNLLT 78

Query: 135 SWVDSKGQKPRL----THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           ++V     K R+     HRLD+ETSG+L+ A++    +     ++   ++K Y +LV+G 
Sbjct: 79  NYVRKGNPKARINLFVVHRLDRETSGVLIFAKSLEIREKFAAQWKN--VEKKYIALVYGN 136

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              K   I ++L +    G +Y     +N      AI+ +KVI   ++ +  LE+   TG
Sbjct: 137 LTKKSGIIESYLAE----GDNYKVQSVKNPIEGKLAITKYKVIK-ESKNYSLLEIDLLTG 191

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           + +Q+R H    G PIVGD KY  N KG        +L LHA  +   HP     +   A
Sbjct: 192 KKNQIRAHLSENGHPIVGDTKYRENTKG--------RLALHAFSIKFKHPFNNEEMMFEA 243

Query: 310 PLPAHMVKTWDSLG 323
            +P + +  +   G
Sbjct: 244 KIPEYFLTYFKLNG 257


>gi|293412139|ref|ZP_06654862.1| conserved hypothetical protein [Escherichia coli B354]
 gi|291468910|gb|EFF11401.1| conserved hypothetical protein [Escherichia coli B354]
          Length = 260

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRMLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|227889588|ref|ZP_04007393.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
 gi|227849890|gb|EEJ59976.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
          Length = 299

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 66/286 (23%), Positives = 115/286 (40%), Gaps = 36/286 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G V V+  R   +  + +G  V         N  +K                  K  +++
Sbjct: 38  GMVLVNHHRRYTSYLLHAGDEVIFILGEEKENKWLK--------------PSSKKLNIVF 83

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQ---KPRLTHRLDQETSGILV 159
           E     V NK AGI            +   L  +   + Q   KP +  RLD++TSG+++
Sbjct: 84  EQKDYLVINKDAGILSIPSRYEDNDAVVNRLLHYFQQQKQTDLKPHVITRLDRDTSGLVL 143

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN--KKECIANWLLKKSHIGGDYVHVVK 217
           V R   A    ++  +   I+K + ++V G  +   ++  I   + K          V +
Sbjct: 144 VGRNAVAHARFSKMEKNEFIKKYH-AIVHGNFEEAQRQGTIDAPIGKIDT------GVKR 196

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   +++ ++V+D   +    +E+Q  TGRTHQ+RVH  ++G P+ GD  Y    K
Sbjct: 197 GIVNNGQRSVTKYRVLDQV-KGASLIELQLLTGRTHQIRVHMQYLGHPLFGDPLYG--IK 253

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            NF      +  L+  Y++   P    R +I    P  M + W +L
Sbjct: 254 DNF-----KRQALNCFYLEFDDPFSEKRQKIEIADPIDMKRLWKNL 294


>gi|169833510|ref|YP_001695365.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae Hungary19A-6]
 gi|168996012|gb|ACA36624.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Hungary19A-6]
          Length = 278

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 67/279 (24%), Positives = 113/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D S   
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYSQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETHVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    +L  T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFT 264


>gi|320182406|gb|EFW57303.1| tRNA pseudouridine synthase C [Shigella boydii ATCC 9905]
          Length = 260

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWFMEEAVLDYPLVEELDKIADKFAC----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|238924179|ref|YP_002937695.1| pseudouridine synthase [Eubacterium rectale ATCC 33656]
 gi|238875854|gb|ACR75561.1| pseudouridine synthase [Eubacterium rectale ATCC 33656]
          Length = 295

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 61/314 (19%), Positives = 126/314 (40%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +  ++    ++ + K H Y H   V L++      +  +      N R+    ++ +   
Sbjct: 9   INENDTGKTVEGFLKEHGYTHQVLVRLKQ--TDHGILRNGIWAYTNERLCKDDLITV--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                      +I+++  +       L   + YED  I V NKP  +     +G   +  
Sbjct: 64  -----------QIVENECSDNIAPVNLPLDIAYEDDDIIVINKPFDMPAHPSAGNHDNTL 112

Query: 131 GFLKSWVDSKGQKPRLTHR---LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                +      KP +      LD++T+G+ +VA+   A   L  +   R I + Y+++ 
Sbjct: 113 ANALMYYYGSQNKPFVYRCINRLDRDTTGLTIVAKHALAGGILGNAVAKRAIHRTYYAVC 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQ 246
            G        I+  + +K     +       + K   YA++ F  I          ++++
Sbjct: 173 SGC-TPACMRISAPIARKDASTIER----CVDFKRGEYAVTDFIRIKYNPDNNLSLVKLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
             TGRTHQ+RVH  ++G P++GD  Y  ++         ++  LH+  +   HP  G ++
Sbjct: 228 LLTGRTHQIRVHMKYIGFPLIGDFLYNPDY------TYISRQALHSGRLVFTHPVTGQKM 281

Query: 306 QITAPLPAHMVKTW 319
            + + +P+ M   +
Sbjct: 282 NLISDIPSDMKSLF 295


>gi|294101380|ref|YP_003553238.1| pseudouridine synthase, RluA family [Aminobacterium colombiense DSM
           12261]
 gi|293616360|gb|ADE56514.1| pseudouridine synthase, RluA family [Aminobacterium colombiense DSM
           12261]
          Length = 314

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 144/331 (43%), Gaps = 32/331 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+Y     V       RLD+  +  +P++    + + +R G VRVD ++   + R++ GQ
Sbjct: 1   MSY--TFKVSEHHAGRRLDKVIRTLWPNLPLGAMMRGIRKGLVRVDGRKTSCSVRLEDGQ 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +P          +E ++++ SV   +        ++Y+D  I V NK AG+ +Q   
Sbjct: 59  SVYVPW---------EEPELIEKSVKTKRTG---ALSIVYKDHYIMVLNKEAGLIIQPDQ 106

Query: 124 GIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +   +   V+ +G  +    HRLD+ T+G++VVA    + + L  +FR   + K 
Sbjct: 107 SGEESLIERVWLEVEPEGDFRACAVHRLDRNTTGLVVVALHGQSLRELQRAFRDNDVDKT 166

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y   V G     +  I   L K      D  H +         A +H++ I     +   
Sbjct: 167 YLVAVRGQ-TPLEGDITAPLQK------DRDHNIVTASPDGLPAHTHYEKI-AGDDECSL 218

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL---YLHARYMDL-- 297
           L++   TGR+HQ+RVH    G P++GD KY  +F  N     + +L    LHA  +    
Sbjct: 219 LKVSLLTGRSHQIRVHLAISGYPVIGDVKYG-DFALNKQWYHRIRLDHPLLHAWKISFRR 277

Query: 298 -PHPEG--GRLQITAPLPAHMVKTWDSLGFK 325
              P     R + +AP     +K   + G++
Sbjct: 278 LNPPLSYIERREFSAPPDRLFLKFLRTKGWQ 308


>gi|331664352|ref|ZP_08365258.1| tRNA pseudouridine synthase C [Escherichia coli TA143]
 gi|331058283|gb|EGI30264.1| tRNA pseudouridine synthase C [Escherichia coli TA143]
          Length = 260

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFAQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|325695366|gb|EGD37266.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK150]
          Length = 291

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 124/303 (40%), Gaps = 32/303 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   ++ G  +R+
Sbjct: 4   TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLSINWQTVVKPGDDIRL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+          
Sbjct: 62  IFDEEDY----PQKTILFGNGELVEE--------LYQDQHLIIVNKPEGMKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+LV
Sbjct: 110 ALLNHVSAYV---GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLEKREISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +KK    + + +  H     +     + +   YA +H   +  F Q    ++ Q 
Sbjct: 167 QGKFPSKKLIYKDKIGRDRHDRRKRL----VDPRKGLYAETHVTRVKQFGQ-AALVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G P++GD  Y    +G        +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGHPLIGDPLYHPQPQG--------RLMLHAHRLTFTHPFTLEKIT 273

Query: 307 ITA 309
           + A
Sbjct: 274 VEA 276


>gi|320194932|gb|EFW69561.1| tRNA pseudouridine synthase C [Escherichia coli WV_060327]
          Length = 260

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMLVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|67924151|ref|ZP_00517595.1| Pseudouridine synthase, RluD [Crocosphaera watsonii WH 8501]
 gi|67854003|gb|EAM49318.1| Pseudouridine synthase, RluD [Crocosphaera watsonii WH 8501]
          Length = 302

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 81/315 (25%), Positives = 131/315 (41%), Gaps = 41/315 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILR---SGQVRVDKKRVKFNNRIQSGQVVRIP 68
           ++ +   + L  ++  HY H    N Q+ L    SGQV VD++ V     +++GQ +   
Sbjct: 11  IKQNHAGLTLIEYYTKHYHH---SNYQQWLERIISGQVLVDEQTVDPQTVLKTGQRLSYH 67

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                                  +    L   ++YED  + + NKP+G+ V  G G   H
Sbjct: 68  ------------------RPPWQEPEVPLSFEIIYEDDNLLIVNKPSGLPVLPGGGFLEH 109

Query: 129 IDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               L        Q +P   HRL + TSG++++ ++  A  HLT+  R ++I K+Y  L+
Sbjct: 110 --TLLWQLKKQYPQNEPIPIHRLGRGTSGLMLMGKSAIARSHLTQQMREQKISKVYQGLI 167

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                  K  I + + K       Y++  K +     YA S  +V+  +  K   LE+  
Sbjct: 168 GKNNLPDKFSIDHPIGKIPDPVLGYIYGAKVD---GKYAYSECRVLGRYVDK-TLLEVTI 223

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTS-------PIQNKLYLHARYMDLP 298
            TGR HQ+R+H   +G P++GD  Y      K  F         P     +LHA  +   
Sbjct: 224 LTGRPHQIRIHLATIGYPLLGDPLYVVGGIPKTGFKEDNDTINVPGDCGYFLHAYQLSFV 283

Query: 299 HPEGGR-LQITAPLP 312
           HP   + L  T   P
Sbjct: 284 HPVTNQCLTFTCERP 298


>gi|324992609|gb|EGC24530.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK405]
 gi|327460012|gb|EGF06351.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1]
 gi|327472158|gb|EGF17595.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK408]
 gi|327488602|gb|EGF20402.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1058]
          Length = 291

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 121/303 (39%), Gaps = 32/303 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   ++ G  + +
Sbjct: 4   TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLAINWQTVVKPGDDICL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+          
Sbjct: 62  IFDEEDY----PQKTILFGNGELVEE--------LYQDQHLIIVNKPEGMKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+LV
Sbjct: 110 ALLNHVSAYV---GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLEKREISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    K     + + +  H     +     + +   YA +H   +  F Q    ++ Q 
Sbjct: 167 QGKFPAKNLIYKDKIGRDRHDRRKRL----VDPRKGLYAETHVTRLKQFGQSA-LVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G P+VGD  Y    +G        +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGHPLVGDPLYHPQPQG--------RLMLHAHRLTFTHPFTLEKIT 273

Query: 307 ITA 309
           + A
Sbjct: 274 VEA 276


>gi|259501425|ref|ZP_05744327.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
 gi|302190854|ref|ZP_07267108.1| hypothetical protein LineA_02435 [Lactobacillus iners AB-1]
 gi|259167174|gb|EEW51669.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
          Length = 283

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 73/299 (24%), Positives = 126/299 (42%), Gaps = 33/299 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQV 64
           Y+ Y+ +  +E N  +D+  +N    I     +  LR    + V+ K +  N ++ +  +
Sbjct: 4   YIYYLTISQNENNQNIDQIMRNLL--IPR-KWRHFLRIEKNILVNNKYLPLNFKVHTNDL 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I      LNH+   Q+   +S N+          ++YE+  I V +KPAG        
Sbjct: 61  ITI-----KLNHVESLQQKYPASGNMPN--------IIYENDDILVIDKPAGQKTHPN-- 105

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + + Y+
Sbjct: 106 -LYETDTALNDCTSYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLSRSYF 164

Query: 185 SLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           + +      +    I   +          +            AI+H++V+   A K   +
Sbjct: 165 AWIDATNDISDNGTINLPIGDDPLDMRKRMVRT-----DGLKAITHYQVVKKTANKI-LV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           ++Q  TGRTHQ+RVH   +G PI+GD  Y +N++         KL L A  +    P  
Sbjct: 219 KLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQAG------EKLQLTAYKLVFQKPFS 271


>gi|16130698|ref|NP_417271.1| tRNA U65 pseudouridine synthase [Escherichia coli str. K-12 substr.
           MG1655]
 gi|24114075|ref|NP_708585.1| tRNA pseudouridine synthase C [Shigella flexneri 2a str. 301]
 gi|30064136|ref|NP_838307.1| tRNA pseudouridine synthase C [Shigella flexneri 2a str. 2457T]
 gi|74313363|ref|YP_311782.1| tRNA pseudouridine synthase C [Shigella sonnei Ss046]
 gi|89109577|ref|AP_003357.1| tRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           W3110]
 gi|157162245|ref|YP_001459563.1| tRNA pseudouridine synthase C [Escherichia coli HS]
 gi|170018963|ref|YP_001723917.1| tRNA pseudouridine synthase C [Escherichia coli ATCC 8739]
 gi|170082362|ref|YP_001731682.1| tRNA U65 pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170682843|ref|YP_001744955.1| tRNA pseudouridine synthase C [Escherichia coli SMS-3-5]
 gi|187734142|ref|YP_001881468.1| tRNA pseudouridine synthase C [Shigella boydii CDC 3083-94]
 gi|188493340|ref|ZP_03000610.1| tRNA pseudouridine synthase C [Escherichia coli 53638]
 gi|194439667|ref|ZP_03071738.1| tRNA pseudouridine synthase C [Escherichia coli 101-1]
 gi|215488108|ref|YP_002330539.1| tRNA pseudouridine synthase C [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218690914|ref|YP_002399126.1| tRNA pseudouridine synthase C [Escherichia coli ED1a]
 gi|218706287|ref|YP_002413806.1| tRNA pseudouridine synthase C [Escherichia coli UMN026]
 gi|238901929|ref|YP_002927725.1| tRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|253772358|ref|YP_003035189.1| tRNA pseudouridine synthase C [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254037844|ref|ZP_04871902.1| tRNA pseudouridine synthase C [Escherichia sp. 1_1_43]
 gi|254162717|ref|YP_003045825.1| tRNA pseudouridine synthase C [Escherichia coli B str. REL606]
 gi|256024706|ref|ZP_05438571.1| tRNA pseudouridine synthase C [Escherichia sp. 4_1_40B]
 gi|291284120|ref|YP_003500938.1| tRNA pseudouridine synthase C [Escherichia coli O55:H7 str. CB9615]
 gi|293406283|ref|ZP_06650209.1| tRNA pseudouridine synthase C [Escherichia coli FVEC1412]
 gi|293416038|ref|ZP_06658678.1| tRNA pseudouridine synthase C [Escherichia coli B185]
 gi|297517184|ref|ZP_06935570.1| tRNA pseudouridine synthase C [Escherichia coli OP50]
 gi|298382019|ref|ZP_06991616.1| tRNA pseudouridine synthase C [Escherichia coli FVEC1302]
 gi|300898152|ref|ZP_07116515.1| tRNA pseudouridine synthase [Escherichia coli MS 198-1]
 gi|300920353|ref|ZP_07136791.1| tRNA pseudouridine synthase [Escherichia coli MS 115-1]
 gi|300931251|ref|ZP_07146591.1| tRNA pseudouridine synthase [Escherichia coli MS 187-1]
 gi|300936292|ref|ZP_07151224.1| tRNA pseudouridine synthase [Escherichia coli MS 21-1]
 gi|300950522|ref|ZP_07164431.1| tRNA pseudouridine synthase [Escherichia coli MS 116-1]
 gi|300958108|ref|ZP_07170267.1| tRNA pseudouridine synthase [Escherichia coli MS 175-1]
 gi|301026250|ref|ZP_07189710.1| tRNA pseudouridine synthase [Escherichia coli MS 196-1]
 gi|301027548|ref|ZP_07190883.1| tRNA pseudouridine synthase [Escherichia coli MS 69-1]
 gi|301645242|ref|ZP_07245195.1| tRNA pseudouridine synthase [Escherichia coli MS 146-1]
 gi|307139477|ref|ZP_07498833.1| tRNA pseudouridine synthase C [Escherichia coli H736]
 gi|312964939|ref|ZP_07779179.1| RNA pseudouridylate synthase family protein [Escherichia coli
           2362-75]
 gi|312972991|ref|ZP_07787164.1| RNA pseudouridylate synthase family protein [Escherichia coli
           1827-70]
 gi|331643478|ref|ZP_08344609.1| tRNA pseudouridine synthase C [Escherichia coli H736]
 gi|331654276|ref|ZP_08355276.1| tRNA pseudouridine synthase C [Escherichia coli M718]
 gi|331674285|ref|ZP_08375045.1| tRNA pseudouridine synthase C [Escherichia coli TA280]
 gi|92090982|sp|P0AA42|TRUC_SHIFL RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|108936020|sp|P0AA41|TRUC_ECOLI RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|882686|gb|AAB40441.1| corresponds to hypothetical protein from E. carotovora PIR
           Accession Number S45108; 2 ORFs in E. coli; ORF_f260
           [Escherichia coli str. K-12 substr. MG1655]
 gi|1789155|gb|AAC75833.1| tRNA U65 pseudouridine synthase [Escherichia coli str. K-12 substr.
           MG1655]
 gi|24053203|gb|AAN44292.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
 gi|30042392|gb|AAP18117.1| hypothetical protein S2998 [Shigella flexneri 2a str. 2457T]
 gi|73856840|gb|AAZ89547.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|85675610|dbj|BAE76863.1| tRNA pseudouridine synthase [Escherichia coli str. K12 substr.
           W3110]
 gi|157067925|gb|ABV07180.1| tRNA pseudouridine synthase C [Escherichia coli HS]
 gi|169753891|gb|ACA76590.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|169890197|gb|ACB03904.1| tRNA U65 pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170520561|gb|ACB18739.1| tRNA pseudouridine synthase C [Escherichia coli SMS-3-5]
 gi|187431134|gb|ACD10408.1| tRNA pseudouridine synthase C [Shigella boydii CDC 3083-94]
 gi|188488539|gb|EDU63642.1| tRNA pseudouridine synthase C [Escherichia coli 53638]
 gi|194421414|gb|EDX37430.1| tRNA pseudouridine synthase C [Escherichia coli 101-1]
 gi|209761378|gb|ACI79001.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|209761384|gb|ACI79004.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|215266180|emb|CAS10606.1| tRNA pseudouridine synthase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218428478|emb|CAR09404.2| tRNA pseudouridine synthase [Escherichia coli ED1a]
 gi|218433384|emb|CAR14286.1| tRNA pseudouridine synthase [Escherichia coli UMN026]
 gi|226839468|gb|EEH71489.1| tRNA pseudouridine synthase C [Escherichia sp. 1_1_43]
 gi|238863710|gb|ACR65708.1| tRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|242378338|emb|CAQ33115.1| tRNA pseudouridine 65 synthase [Escherichia coli BL21(DE3)]
 gi|253323402|gb|ACT28004.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253974618|gb|ACT40289.1| tRNA pseudouridine synthase [Escherichia coli B str. REL606]
 gi|253978783|gb|ACT44453.1| tRNA pseudouridine synthase [Escherichia coli BL21(DE3)]
 gi|260448158|gb|ACX38580.1| pseudouridine synthase [Escherichia coli DH1]
 gi|281602151|gb|ADA75135.1| tRNA pseudouridine synthase C [Shigella flexneri 2002017]
 gi|284922729|emb|CBG35817.1| tRNA pseudouridine synthase C [Escherichia coli 042]
 gi|290763993|gb|ADD57954.1| tRNA pseudouridine synthase C [Escherichia coli O55:H7 str. CB9615]
 gi|291426289|gb|EFE99321.1| tRNA pseudouridine synthase C [Escherichia coli FVEC1412]
 gi|291432227|gb|EFF05209.1| tRNA pseudouridine synthase C [Escherichia coli B185]
 gi|298277159|gb|EFI18675.1| tRNA pseudouridine synthase C [Escherichia coli FVEC1302]
 gi|299879762|gb|EFI87973.1| tRNA pseudouridine synthase [Escherichia coli MS 196-1]
 gi|300315205|gb|EFJ64989.1| tRNA pseudouridine synthase [Escherichia coli MS 175-1]
 gi|300358142|gb|EFJ74012.1| tRNA pseudouridine synthase [Escherichia coli MS 198-1]
 gi|300394909|gb|EFJ78447.1| tRNA pseudouridine synthase [Escherichia coli MS 69-1]
 gi|300412678|gb|EFJ95988.1| tRNA pseudouridine synthase [Escherichia coli MS 115-1]
 gi|300450155|gb|EFK13775.1| tRNA pseudouridine synthase [Escherichia coli MS 116-1]
 gi|300458544|gb|EFK22037.1| tRNA pseudouridine synthase [Escherichia coli MS 21-1]
 gi|300460905|gb|EFK24398.1| tRNA pseudouridine synthase [Escherichia coli MS 187-1]
 gi|301076512|gb|EFK91318.1| tRNA pseudouridine synthase [Escherichia coli MS 146-1]
 gi|309703149|emb|CBJ02483.1| tRNA pseudouridine synthase C [Escherichia coli ETEC H10407]
 gi|310332933|gb|EFQ00147.1| RNA pseudouridylate synthase family protein [Escherichia coli
           1827-70]
 gi|312290495|gb|EFR18375.1| RNA pseudouridylate synthase family protein [Escherichia coli
           2362-75]
 gi|313647852|gb|EFS12298.1| RNA pseudouridylate synthase family protein [Shigella flexneri 2a
           str. 2457T]
 gi|315137398|dbj|BAJ44557.1| tRNA pseudouridine synthase C [Escherichia coli DH1]
 gi|315615179|gb|EFU95816.1| RNA pseudouridylate synthase family protein [Escherichia coli 3431]
 gi|320173224|gb|EFW48434.1| tRNA pseudouridine synthase C [Shigella dysenteriae CDC 74-1112]
 gi|320640440|gb|EFX09979.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. G5101]
 gi|320645686|gb|EFX14671.1| tRNA pseudouridine synthase C [Escherichia coli O157:H- str.
           493-89]
 gi|320650986|gb|EFX19426.1| tRNA pseudouridine synthase C [Escherichia coli O157:H- str. H
           2687]
 gi|320656482|gb|EFX24378.1| tRNA pseudouridine synthase C [Escherichia coli O55:H7 str. 3256-97
           TW 07815]
 gi|320662378|gb|EFX29775.1| tRNA pseudouridine synthase C [Escherichia coli O55:H7 str. USDA
           5905]
 gi|320667076|gb|EFX34039.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323167869|gb|EFZ53560.1| RNA pseudouridylate synthase family protein [Shigella sonnei 53G]
 gi|323172906|gb|EFZ58537.1| RNA pseudouridylate synthase family protein [Escherichia coli
           LT-68]
 gi|323188791|gb|EFZ74076.1| RNA pseudouridylate synthase family protein [Escherichia coli
           RN587/1]
 gi|323935847|gb|EGB32150.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323941527|gb|EGB37709.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323960691|gb|EGB56315.1| RNA pseudouridylate synthase [Escherichia coli H489]
 gi|323971607|gb|EGB66838.1| RNA pseudouridylate synthase [Escherichia coli TA007]
 gi|324005662|gb|EGB74881.1| tRNA pseudouridine synthase [Escherichia coli MS 57-2]
 gi|331036949|gb|EGI09173.1| tRNA pseudouridine synthase C [Escherichia coli H736]
 gi|331047658|gb|EGI19735.1| tRNA pseudouridine synthase C [Escherichia coli M718]
 gi|331068379|gb|EGI39774.1| tRNA pseudouridine synthase C [Escherichia coli TA280]
 gi|332087547|gb|EGI92675.1| RNA pseudouridylate synthase family protein [Shigella boydii
           5216-82]
 gi|332344684|gb|AEE58018.1| conserved hypothetical protein [Escherichia coli UMNK88]
 gi|332753644|gb|EGJ84023.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-671]
 gi|332754556|gb|EGJ84922.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           2747-71]
 gi|332765743|gb|EGJ95956.1| tRNA pseudouridine 65 synthase [Shigella flexneri 2930-71]
 gi|333015363|gb|EGK34703.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-304]
          Length = 260

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|325911610|ref|ZP_08174018.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
 gi|325476596|gb|EGC79754.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
          Length = 292

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 129/303 (42%), Gaps = 34/303 (11%)

Query: 3   LMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQ 60
           +M  Y+ Y+ +  +E N  +D+  +N    I     +  LR    + V+ K +  N ++ 
Sbjct: 9   IMNQYIYYLTISQNENNQNVDQIMRNLL--IPR-KWRHFLRIEKNILVNDKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE++ + V NKPAG    
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENADVLVINKPAGQKTH 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L    +  G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 113 PN---LYETDTALNDCANYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           + Y++ +      +    I   +          +            AI+H++V+     K
Sbjct: 170 RSYFAWIEATNDISDNGTINLPIGDDPLDMRKRMVRA-----DGLKAITHYQVVKKIGSK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++         KL L A  +    
Sbjct: 225 I-LVKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQAG------EKLQLTAYKLVFQK 277

Query: 300 PEG 302
           P  
Sbjct: 278 PFS 280


>gi|297622146|ref|YP_003710283.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
 gi|297377447|gb|ADI39277.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
          Length = 284

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 75/307 (24%), Positives = 136/307 (44%), Gaps = 39/307 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINAL 74
           +++  L    +  YP  +   L+ +L+  +++VD +  K     ++ GQ++ +       
Sbjct: 6   DQDQPLLEALRLLYPDSSKTTLRSLLKEERIKVDGQTCKLGTLSLKKGQILEV------- 58

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
              +K+Q ++   V            +LY+D  + V  KP+G+         +  +  L 
Sbjct: 59  ---VKKQNVIAEGVK-----------ILYQDPHLAVVFKPSGLLSVA---TDFEKNLTLH 101

Query: 135 SWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             +    Q     + HRLDQ+TSG++V A  +     L   F    I++ Y ++V G   
Sbjct: 102 KILKEHFQPKTVEVVHRLDQDTSGVIVFALDKQTCLKLKILFEKHEIERCYTAIVEGKLT 161

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +     ++L    H   +YV     N +    AI+H+ V++ +++KF  L ++  TG+ 
Sbjct: 162 PRSGSWRSYL----HEDENYVVHSTDNARKGKLAITHY-VVEGYSKKFTRLRLKLETGKK 216

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPL 311
           +Q+RVH    G PI GD KY A      +S    +L LHA ++   HP    ++Q T   
Sbjct: 217 NQIRVHCSDAGHPIAGDTKYGA------SSNPGKRLMLHADHLGFIHPVKRKKMQFTIDP 270

Query: 312 PAHMVKT 318
           P    K 
Sbjct: 271 PESFDKV 277


>gi|46581593|ref|YP_012401.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           vulgaris str. Hildenborough]
 gi|46451016|gb|AAS97661.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           vulgaris str. Hildenborough]
 gi|311235236|gb|ADP88090.1| pseudouridine synthase [Desulfovibrio vulgaris RCH1]
          Length = 390

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 129/319 (40%), Gaps = 41/319 (12%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           Q +VV  +E   +L ++    +  +    L + +RSGQVR +  R K  +R++ G  VR+
Sbjct: 4   QAIVVTREEAGQKLLQFLARRFA-LPQAMLHRWIRSGQVRRNGGRCKPFDRLEMGDEVRV 62

Query: 68  PPVINALNHIIKEQKILDSS------------------------------------VNLT 91
           PP   +++       +  +S                                     + +
Sbjct: 63  PPFAASMSERADVGPVSANSDAVRNVPDAAAPRPAPSRHDRDGHDAMQPSRQRRPKADTS 122

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                    ++ E   +++F+KPAG++V  G+G    +   L          P   HRLD
Sbjct: 123 LQPARPLPPVVAETPDLFIFDKPAGLAVHPGTGHTDSLTTRLAQHFAKAPFMPTPAHRLD 182

Query: 152 QETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           ++TSG+L+VAR+ A  + L E+F     + K Y + V G  +       +  L K     
Sbjct: 183 RDTSGLLLVARSYAMLRTLHEAFASHDALVKEYLAWVAGCWQPAAPVTLHDRLSKGAEAS 242

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  V   +E GA  A +   ++    Q    L +  HTGRTHQ+RV     G P++GD 
Sbjct: 243 GFERVASDDE-GAEAACTVRCLL--REQHRSLLLVTLHTGRTHQIRVQLSRRGHPLLGDR 299

Query: 271 KYCANFKGNFTSPIQNKLY 289
           KY    +         +L 
Sbjct: 300 KYGGPPRMGGFLLHAVRLC 318


>gi|161504785|ref|YP_001571897.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160866132|gb|ABX22755.1| hypothetical protein SARI_02909 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 219

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 71/226 (31%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQDPWLVILYQDEHIMVVNKPSGLLSVPGR-LEAHKDSIM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  I   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYIARVWGHPTPAEGLIDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + + V+D  A     + +QP TGR+HQLRVH   +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYNVVDFAADNTARVALQPITGRSHQLRVHMQALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            Y +         +  +L+LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPE----ALSLAPRLHLHAEMLTITHPTYGTSMTFKA--PADF 219


>gi|219684788|ref|ZP_03539730.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia garinii PBr]
 gi|219685395|ref|ZP_03540214.1| ribosomal large subunit pseudouridine synthase D [Borrelia garinii
           Far04]
 gi|219671733|gb|EED28788.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia garinii PBr]
 gi|219673168|gb|EED30188.1| ribosomal large subunit pseudouridine synthase D [Borrelia garinii
           Far04]
          Length = 326

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 70/339 (20%), Positives = 138/339 (40%), Gaps = 34/339 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK--RVKFNNRIQSGQVV 65
           +   V+ +   +RLD +  N+        +++       + + K  ++K +  +     +
Sbjct: 6   KEFTVKENA--LRLDLYLSNNLEVFTRSQIKRRNVEAFKKSNGKFFKIKLSKPVFKNDEM 63

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SG 124
            I     +                     + +   ++YEDS I V NKP GI    G S 
Sbjct: 64  LIEFDEESNQIDC-------------LRPNNIPIAIIYEDSNIIVLNKPQGILSHPGISH 110

Query: 125 IAYHIDGFLKSWV-------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               +  FL   +       + +  +P + HRLD++TSG+L+ A+       L + F+ +
Sbjct: 111 WDDTVVNFLLYHIKRLKINFNEEKVRPGIVHRLDKDTSGVLICAKNINTLSFLAQQFKDK 170

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +  K+Y ++V G   +    I +++  +         V K        A++ ++++  F 
Sbjct: 171 KTNKVYIAIVKGNFNSFSGSIESFI-DRDKYNRKKFSVSKDR---GKKALTEYRLLLNFG 226

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  L ++P TGRTHQLRVH  ++  PI+GD  Y      +F +     L LH+  +++
Sbjct: 227 -GYSLLALKPKTGRTHQLRVHMKYLNFPILGDEVYG-RVDSSFKTVT---LMLHSYKLEV 281

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLY 336
              +    +  +  P   +    +     + NL I  L 
Sbjct: 282 DVGKNSFKKFISEFPKRFIIFLSNFYKSDELNLIIDNLI 320


>gi|153006285|ref|YP_001380610.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152029858|gb|ABS27626.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 295

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 128/320 (40%), Gaps = 34/320 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V  +    RLDRW       I     + ++ +G+ R+  K      R+  G+ V +
Sbjct: 3   EILEVPREAAGERLDRWLAGALA-IPLDRARALVEAGRARIRGKTCAIQRRLFGGERVEV 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                            +      + +      +LY+D    V +KPAG++V+  S  A 
Sbjct: 62  -----------------ERPAPRAERASGPALTVLYDDPDCLVVSKPAGLAVEPSSPGAP 104

Query: 128 HIDGFLKSW--VDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              G        D  G+  P L HRLD++T+G L++AR   A   L  +F  R ++K Y 
Sbjct: 105 SAVGAASRIGTFDVDGRAAPGLPHRLDRDTTGALLLARHDRALAALRAAFEGRAVEKEYL 164

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            L  G P ++   +     + +     +             A   F V +        L 
Sbjct: 165 VLAAGAPPDR-GALDTPYGRSAADPRRFTTRA----PSPRRARLTFAV-ERRLTGAALLR 218

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
           +   TGRTHQ+RV     G P++GD  Y         S    +  LHA  +  P P +G 
Sbjct: 219 VVLDTGRTHQIRVQLAEAGFPVLGDAVYG------VASEAIARQALHAERLAFPRPSDGA 272

Query: 304 RLQITAPLPAHMVKTWDSLG 323
           R+++ APLP  + +  ++L 
Sbjct: 273 RVEVRAPLPEDLARAIEALA 292


>gi|116334072|ref|YP_795599.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
 gi|116099419|gb|ABJ64568.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
          Length = 299

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 66/296 (22%), Positives = 120/296 (40%), Gaps = 33/296 (11%)

Query: 31  HINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +    L+++    G V +D + V+       GQVV +              ++     N
Sbjct: 24  GVTRTFLKQVKFHGGVVTLDGQPVRVIAMATPGQVVGL--------------QLPPEPDN 69

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-----GIAYHIDGFLKSWVDSKGQKP 144
                 F    +LYED    V NKPAG++           +A  + G L + + +     
Sbjct: 70  PHVTPSFAPLDILYEDEHFLVVNKPAGMASVPSHLYSEDTLANRVKGHLLT-IQAPSTVT 128

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            +  RLD++TSG+++ A+   A   L +  ++++I K Y ++  G      + +   + +
Sbjct: 129 HIVTRLDRDTSGVVLFAKHHFAHSVLDKQLKLKQIDKRYVAVASGRMMPAHQQLTGPIGR 188

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           ++        + +        A +   V    +     L ++ HTGRTHQ+RVH  + G 
Sbjct: 189 EAG-----SFIKRTVRPDGRAAETEVWV-RATSATASLLAVKLHTGRTHQIRVHCANAGH 242

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           P++GD  Y        T+P   +  LH   +    P  G+ +   APLP  M +  
Sbjct: 243 PLLGDWLYG-----RPTNPWIQRQALHCARVQFFQPFAGKWVTCYAPLPDDMARVI 293


>gi|30019444|ref|NP_831075.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|229126707|ref|ZP_04255719.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|229143996|ref|ZP_04272412.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|29894988|gb|AAP08276.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|228639393|gb|EEK95807.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|228656647|gb|EEL12473.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
          Length = 307

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 126/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EITVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                   +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGSIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGKIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  +   HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKIHFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P  +       
Sbjct: 284 AIEVDVPFPTKLNNKIKEF 302


>gi|39998250|ref|NP_954201.1| RNA pseudouridine synthase family protein [Geobacter sulfurreducens
           PCA]
 gi|39985196|gb|AAR36551.1| RNA pseudouridine synthase family protein [Geobacter sulfurreducens
           PCA]
 gi|307635144|gb|ADI85911.2| tRNA pseudouridine-65 synthase [Geobacter sulfurreducens KN400]
          Length = 250

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 107/237 (45%), Gaps = 18/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  +   +KPAG+ V       +     L+   D  G++    HRLD+ TSG+LV 
Sbjct: 3   ILFRDQYLVAVHKPAGLLVHRSPIDRHETRFALQEVRDLLGRRVYPVHRLDKPTSGVLVF 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A   A A+ L ++F   R+ K Y ++  GI   +   I + L ++     D +   K + 
Sbjct: 63  ALDPATARSLGDAFAGGRVNKTYLAVTRGIVPPE-GIIDHSLSEEP----DRLDGAKSSP 117

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++ F+ +             + ++   E+ PHTGR HQLR H  H+  PI+GD 
Sbjct: 118 AAPQPAVTVFRRLAEAELPVVTGRYASSRYSLAELTPHTGRRHQLRRHMKHIFHPIIGDT 177

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            Y       F        +L LHA  + LPHP  G  L I AP    + +  D LG+
Sbjct: 178 TYGEGRHNRFFREEFGCGRLLLHAAELSLPHPASGETLTIAAPPDRELARLLDRLGW 234


>gi|253988118|ref|YP_003039474.1| tRNA pseudouridine synthase C [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253779568|emb|CAQ82729.1| tRNA pseudouridine synthase C [Photorhabdus asymbiotica]
          Length = 256

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 67/238 (28%), Positives = 108/238 (45%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   VLYQDDHIVAVNKPAGWLVHRSWLARHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++QK Y ++V G            + +   I   +      ++
Sbjct: 64  ALSSDIARQLSQQFEHHQLQKTYHAVVRGYVLESDVIDYALVEELDKIADKFA----DSD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KGA  +I++++ +               +F  LE+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGAQPSITYYRPLAKVECPVEIGRYPTSRFSLLELTPKTGRKHQLRRHMAHIRHPIIGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +      +G       N+L LHA ++ L HP  G  L +TA   A         G++
Sbjct: 180 THGDLRQNRGISAHYQTNRLMLHASHLKLDHPVTGEQLSLTAKWDASWQHLIQQFGWQ 237


>gi|323466963|gb|ADX70650.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 321

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 69/331 (20%), Positives = 129/331 (38%), Gaps = 43/331 (12%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRS----GQVRVDKKRVKFNN 57
            +MT +  +VV+  +   +L  +   +    +    Q ++++    G + V+ KR   + 
Sbjct: 22  RIMTSLFKLVVQEKD-PKKLGSFLLKN--GFSH---QALIKARHHHGMILVNHKRRYLSF 75

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
            + +G  V         N  +K       S N             +E     V NKPAG+
Sbjct: 76  HLSAGDEVIFVSGEEKKNQFLK------PSNNPVDPG--------FETKNYIVLNKPAGV 121

Query: 118 SVQGGSGIAYH-IDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                       +   L  +    + K  KP +  RLD++TSG+++V +   A    ++ 
Sbjct: 122 LSIPSRYEDNDAVVNRLMGYFLQQNKKDLKPHVITRLDRDTSGLVLVGKNAIAHARFSKI 181

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            +   ++K + ++V G     +       +    IG +   V +        A + ++V+
Sbjct: 182 GKDNFVKKYH-AIVHGNFAEDELT----GIIDEPIGKEGDGVKRAVVANGKKAQTRYRVL 236

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
               +    +E++  TGRTHQ+RVH  ++G P+ GD  Y  N          ++  L+  
Sbjct: 237 KQV-EGASLVELRLLTGRTHQIRVHMAYLGYPLFGDPLYGINDN-------FSRQALNCF 288

Query: 294 YMDLPHPEGGR--LQITAPLPAHMVKTWDSL 322
           Y+  P P       +I    P  M K W  L
Sbjct: 289 YLAFPDPFDNERKQEIQIKDPEDMSKLWQKL 319


>gi|260584109|ref|ZP_05851857.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Granulicatella elegans ATCC 700633]
 gi|260158735|gb|EEW93803.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Granulicatella elegans ATCC 700633]
          Length = 296

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 66/305 (21%), Positives = 133/305 (43%), Gaps = 35/305 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + +     I    L  + R+G++ V+ +       +  G V+ +               I
Sbjct: 18  FLQE--KGITKTFLAHVKRNGKLLVNGREEIVLKTLVPGDVLTM--------------VI 61

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVD 138
                + T     +   +L+ED  + + NKP G +           +A  + G+L++   
Sbjct: 62  PPEGEHETVVPSHIPLDILFEDDYLLIVNKPQGTASIPSQLHPDQSMANRVKGYLQT-TR 120

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           ++     +  RLD++T+G+++ A+ R     + ++ R + IQK Y ++V      K++ +
Sbjct: 121 TQDCVTHVVTRLDRDTTGVMMFAKHRVVHAWMDQALRNKTIQKTYHAIV-----TKQDVL 175

Query: 199 ANWLLKKSHIGG-DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               L  + IG  D   + +        +++ +  ++   Q    ++++ HTGRTHQ+RV
Sbjct: 176 KEHDLIDAPIGRTDDSIINRCVRPDGKPSLTEYW-LEETYQHSQLVKIRLHTGRTHQIRV 234

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           H   +GCP++GD  Y     G    P+  +  LH   +D  HP  G ++ + A LP  M 
Sbjct: 235 HFSWLGCPLLGDDLYG----GEKIEPLM-RQALHCSQLDFVHPMTGEKMCVKALLPKDMA 289

Query: 317 KTWDS 321
           +  + 
Sbjct: 290 EWIEK 294


>gi|229551713|ref|ZP_04440438.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus rhamnosus
           LMS2-1]
 gi|258539108|ref|YP_003173607.1| pseudouridine synthase [Lactobacillus rhamnosus Lc 705]
 gi|229314918|gb|EEN80891.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus rhamnosus
           LMS2-1]
 gi|257150784|emb|CAR89756.1| Pseudouridine synthase [Lactobacillus rhamnosus Lc 705]
          Length = 300

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 61/306 (19%), Positives = 119/306 (38%), Gaps = 35/306 (11%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K      +   L+K+  + G + V+K++      +++G  + +              +
Sbjct: 17  FLKQQ--GFSRAQLKKLRYQGGFIFVNKRQRHTAYPLRNGDRILV--------------Q 60

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---D 138
                   +      +  + YED    V NKPAG++     G     +   +K+++    
Sbjct: 61  TAPEQAAASVVPYEHEFPICYEDDDYLVVNKPAGVASIPAVGRRNDSMANMVKAYLIKTH 120

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKEC 197
           ++ Q   +  RLD++TSG++V A+   A   L          K Y +LV      +    
Sbjct: 121 AESQAVHVVTRLDRDTSGLMVFAKHSLAHSLLDRQLHSENFLKQYLALVTSKSLLSAHGW 180

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   +   +       ++ +   +    +++ ++ +   +     L +  HTGRTHQ+RV
Sbjct: 181 IILPIGVSTG-----FYMRRVVSETGKPSVTEYQTLAQNSHAAAVL-VTLHTGRTHQIRV 234

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +G P+ GD  Y              +  LH  ++    P   + + + APLP  M 
Sbjct: 235 HFAAIGHPLFGDDLYNRQADD------FKRQALHCAHLRFWQPLQKQWVDLHAPLPTDMA 288

Query: 317 KTWDSL 322
           K  D L
Sbjct: 289 KLSDHL 294


>gi|323966769|gb|EGB62200.1| RNA pseudouridylate synthase [Escherichia coli M863]
 gi|323978598|gb|EGB73680.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
 gi|327251531|gb|EGE63217.1| RNA pseudouridylate synthase family protein [Escherichia coli
           STEC_7v]
          Length = 260

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|291524908|emb|CBK90495.1| pseudouridine synthase, RluA family [Eubacterium rectale DSM 17629]
          Length = 295

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 61/314 (19%), Positives = 126/314 (40%), Gaps = 33/314 (10%)

Query: 12  VENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +  ++    ++ + K H Y H   V L++      +  +      N R+    ++ +   
Sbjct: 9   INENDTGKTVEGFLKEHGYTHQVLVRLKQ--TDHGILRNGIWAYTNERLCKDDLITV--- 63

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                      +I+++  +       L   + YED  I V NKP  +     +G   +  
Sbjct: 64  -----------QIVENECSDNIAPVNLPLDIAYEDDDIIVINKPFDMPAHPSAGNHDNTL 112

Query: 131 GFLKSWVDSKGQKPRLTHR---LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                +      KP +      LD++T+G+ +VA+   A   L  +   R I + Y+++ 
Sbjct: 113 ANALMYYYGSQNKPFVYRCINRLDRDTTGLTIVAKHALAGGILGNAVAKRAIHRTYYAVC 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQ 246
            G        I+  + +K     +       + K   YA++ F  I          ++++
Sbjct: 173 SGC-TPACMRISAPIARKDASTIER----CVDFKRGEYAVTDFIRIKYNPDNNLSLVKLR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
             TGRTHQ+RVH  ++G P++GD  Y  ++         ++  LH+  +   HP  G ++
Sbjct: 228 LLTGRTHQIRVHMKYIGFPLIGDFLYNPDY------TYISRQALHSGRLVFTHPVTGQKM 281

Query: 306 QITAPLPAHMVKTW 319
            + + +P+ M   +
Sbjct: 282 DLISDIPSDMKSLF 295


>gi|217032147|ref|ZP_03437646.1| hypothetical protein HPB128_186g13 [Helicobacter pylori B128]
 gi|298736447|ref|YP_003728973.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori B8]
 gi|216946137|gb|EEC24746.1| hypothetical protein HPB128_186g13 [Helicobacter pylori B128]
 gi|298355637|emb|CBI66509.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori B8]
          Length = 327

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 71/343 (20%), Positives = 141/343 (41%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDAI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +         + KE                L+  +++ED  + V NKP  + V     +
Sbjct: 59  TLLTPQITPKPLKKELD--------------LEIEVIFEDEDLLVLNKPPNLVVHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W+ SK  +           + HRLD++TSG +V+A+      HL+E  + 
Sbjct: 105 ---KEPTLVDWLKSKNYELSNLGLKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFISLLAS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNGMDLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L+   PL   M++    +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLRFKVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|227535627|ref|ZP_03965676.1| pseudouridine synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|239631158|ref|ZP_04674189.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|227186757|gb|EEI66824.1| pseudouridine synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|239525623|gb|EEQ64624.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
          Length = 300

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 66/309 (21%), Positives = 124/309 (40%), Gaps = 35/309 (11%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K      +   L+K+  + G V V+K++      ++SG  + +               
Sbjct: 17  FLKQQ--GFSRAQLKKLRYQGGFVFVNKRQRHTAYPVRSGDRILVQTAPEH-----AADS 69

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWV---D 138
           ++  S +L          + YED    + NKPAG++     G   + +   +K+++    
Sbjct: 70  VVPYSHDLA---------ISYEDDDYLIVNKPAGVASIPAVGRQNNSMANMVKAYLIKTK 120

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKEC 197
           ++ Q   +  RLD++TSG++V A+   A   L +    +   K Y ++V    P      
Sbjct: 121 AESQAVHVVTRLDRDTSGLMVFAKHGLAHSLLDQQLHSQDFVKQYVAIVTAQTPLATHGW 180

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   +        D  ++ +        +++ ++ +D        L +  HTGRTHQ+RV
Sbjct: 181 IVLPIGVS-----DGFYMRRVVTDTGKASVTEYRTLDQNTAGAMML-VTLHTGRTHQIRV 234

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +G  + GD  Y  +  G       N+  LH  ++    P   + + + APLPA M 
Sbjct: 235 HFAAIGHALYGDGLYSPDTHG------FNRQALHCAHLRFWQPLKHKLIDLHAPLPADMA 288

Query: 317 KTWDSLGFK 325
                L   
Sbjct: 289 TLAAKLKLS 297


>gi|110806543|ref|YP_690063.1| tRNA pseudouridine synthase C [Shigella flexneri 5 str. 8401]
 gi|110616091|gb|ABF04758.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
          Length = 260

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----KD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|224542059|ref|ZP_03682598.1| hypothetical protein CATMIT_01233 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524992|gb|EEF94097.1| hypothetical protein CATMIT_01233 [Catenibacterium mitsuokai DSM
           15897]
          Length = 276

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 69/290 (23%), Positives = 123/290 (42%), Gaps = 42/290 (14%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
             + + +L+   V+V+ +   ++   +  G  V +    N                    
Sbjct: 22  RNDCKNLLKYKSVQVNGEVQTYHAFELHPGDEVEVGKKTN-------------------- 61

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-KSWVDSKGQKPRLTHRLD 151
               L   LLYED  + V NKP+G+  +      Y    ++   +   K Q+  L HRLD
Sbjct: 62  ----LPFELLYEDDDMIVINKPSGLVSEETRNNKYQTAFYMVMEYCRKKRQQCYLVHRLD 117

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q+TSG+L+  + +   Q LT ++      + Y +++ G  + K   I N L++   +   
Sbjct: 118 QDTSGVLMFVKNKKLYQELTHNWNKYVKTRGYVAILEGQCR-KSGTIKNHLVEDKQLK-- 174

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                 +  K    AI+H+K ++  ++ +  +E+   TGR +Q+RVH   +  PI+GD K
Sbjct: 175 -----MRIAKEGQLAITHYKPLE-VSKDYTMMEVFLDTGRKNQIRVHMASLNHPIIGDRK 228

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           Y A            +L LHA      HP   + +   APLP+   + + 
Sbjct: 229 YGACTNP------LKRLGLHAHEFAFTHPFTHKTMTFKAPLPSSFKQMFK 272


>gi|296501973|ref|YP_003663673.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
 gi|296323025|gb|ADH05953.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
          Length = 307

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 126/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EITVPAKWTGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                   +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGSIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K K+  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKQGKIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  +   HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKIHFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P  +       
Sbjct: 284 AIEVDVPFPTKLNNKIKEF 302


>gi|15803313|ref|NP_289346.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 EDL933]
 gi|15832905|ref|NP_311678.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. Sakai]
 gi|168751005|ref|ZP_02776027.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4113]
 gi|168758485|ref|ZP_02783492.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4401]
 gi|168764507|ref|ZP_02789514.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4501]
 gi|168766761|ref|ZP_02791768.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4486]
 gi|168777585|ref|ZP_02802592.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4196]
 gi|168778782|ref|ZP_02803789.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4076]
 gi|168788052|ref|ZP_02813059.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. EC869]
 gi|168802525|ref|ZP_02827532.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. EC508]
 gi|195936394|ref|ZP_03081776.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4024]
 gi|208807818|ref|ZP_03250155.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4206]
 gi|208813945|ref|ZP_03255274.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4045]
 gi|208821365|ref|ZP_03261685.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4042]
 gi|209397015|ref|YP_002272257.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4115]
 gi|217327006|ref|ZP_03443089.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           TW14588]
 gi|254794732|ref|YP_003079569.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           TW14359]
 gi|261226091|ref|ZP_05940372.1| tRNA U65 pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261256654|ref|ZP_05949187.1| tRNA U65 pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK966]
 gi|34582446|sp|Q8X6T6|TRUC_ECO57 RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|12517267|gb|AAG57905.1|AE005507_6 hypothetical protein Z4107 [Escherichia coli O157:H7 str. EDL933]
 gi|13363123|dbj|BAB37074.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|187767213|gb|EDU31057.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4196]
 gi|188014875|gb|EDU52997.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4113]
 gi|189003616|gb|EDU72602.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4076]
 gi|189354717|gb|EDU73136.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4401]
 gi|189363807|gb|EDU82226.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4486]
 gi|189365505|gb|EDU83921.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4501]
 gi|189372179|gb|EDU90595.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. EC869]
 gi|189375502|gb|EDU93918.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. EC508]
 gi|208727619|gb|EDZ77220.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735222|gb|EDZ83909.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4045]
 gi|208741488|gb|EDZ89170.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4042]
 gi|209158415|gb|ACI35848.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4115]
 gi|209761380|gb|ACI79002.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|209761382|gb|ACI79003.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|209761386|gb|ACI79005.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|217319373|gb|EEC27798.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           TW14588]
 gi|254594132|gb|ACT73493.1| tRNA U65 pseudouridine synthase [Escherichia coli O157:H7 str.
           TW14359]
 gi|320189127|gb|EFW63786.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC1212]
 gi|326339134|gb|EGD62949.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. 1044]
 gi|326342983|gb|EGD66751.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. 1125]
          Length = 260

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|332883134|gb|EGK03417.1| hypothetical protein HMPREF9456_01484 [Dysgonomonas mossii DSM
           22836]
          Length = 313

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 69/310 (22%), Positives = 131/310 (42%), Gaps = 34/310 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           ++ D+    LD +        +   ++ +L   Q++V+ K +  F+  +++   V +   
Sbjct: 13  IKVDQPTQLLD-FLVQKEVRKSRNAVKSLLAHKQIKVNGKLITQFDFELKAKDKVSVMKY 71

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHI 129
             +                  K        +++ED  + V  K AG +SV      +  +
Sbjct: 72  DQSR-----------------KEKRLKGLKIVFEDDDLLVIEKEAGFLSVATDKEKSRTV 114

Query: 130 DGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L  +V  K +K R+   HRLD+E SG+++ A+         +++     +  Y ++V
Sbjct: 115 YNSLNEYVKKKDKKARVYVLHRLDREVSGLMIFAKDMELQDIFQKNWDNLVPKYSYMAIV 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G P  K   + +WL +      ++V +    + G   +++H+K        +  L+   
Sbjct: 175 EGRPNPKNGTVTSWLTEN----KNFVMMSSLIDNGGLKSVTHYKTQKSKG-GYSLLDFDL 229

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            T R +Q+RVH   +G PIVGD KY A      ++    ++ LHA  + L HP  G  L+
Sbjct: 230 ETRRKNQVRVHMQQIGHPIVGDKKYGA------SNNPIKRIALHAGGLILKHPRTGELLE 283

Query: 307 ITAPLPAHMV 316
             A +P  M 
Sbjct: 284 FKAGIPKAMQ 293


>gi|326405945|gb|ADZ63016.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis CV56]
          Length = 293

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 60/297 (20%), Positives = 119/297 (40%), Gaps = 32/297 (10%)

Query: 31  HINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            I+   L K+    G++ V+ +      R++   +V +               + D   N
Sbjct: 22  GISRRLLTKVKFDGGKITVNGQEKNAIYRLEKDDLVTVT--------------VPDEPDN 67

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKP 144
                D     +L+ED    V  KPAG             ++  + G++    +   Q  
Sbjct: 68  EKLIPDDFPLNVLFEDDHYLVVEKPAGKPSITGSLHPTGAMSNAVKGYISQ-KNYANQTV 126

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            +  RLD++TSGI+ +A+ R A   + +      ++K Y+++V          I   + +
Sbjct: 127 HIITRLDRDTSGIMFLAKHRYAHALMNQHKFRDTMEKRYFAIVNDQDLPDSGRIDLPIGR 186

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +       +    + ++ A  A++ + V +        L++  HTGRTHQ+RVH  H+G 
Sbjct: 187 RD---DSIIQRQVRFDEKAKDALTSYVVAERKND-LALLDIILHTGRTHQIRVHFSHLGY 242

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWD 320
           P++GD  Y  N        + ++  LH+ ++   +P    +  +   +P  M     
Sbjct: 243 PLIGDDLYGGNHD------LISRQALHSHHLQFLNPFTDEMVHVELDMPEDMKNLLK 293


>gi|332071723|gb|EGI82215.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA17545]
          Length = 286

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 65/267 (24%), Positives = 109/267 (40%), Gaps = 27/267 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              + ++++ V++N  +  G V ++                 D         +      +
Sbjct: 24  KKHILINQEEVRWNEIVNPGDVCQLTFDEE------------DYPQKTIPWGNPDLVQEV 71

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A+
Sbjct: 72  YQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFAK 128

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      + I + YW+LV G    K+    + + +  H     +     + K 
Sbjct: 129 NPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRI----VDAKN 184

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD  Y +  K     
Sbjct: 185 GKYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDPLYNSKSKT---- 240

Query: 283 PIQNKLYLHARYMDLPHPEG-GRLQIT 308
              ++L LHA  +   HP    RL  T
Sbjct: 241 ---SRLMLHAFRLSFTHPLTLERLTFT 264


>gi|217974069|ref|YP_002358820.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499204|gb|ACK47397.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 287

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 68/259 (26%), Positives = 107/259 (41%), Gaps = 17/259 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            +  L++S      +   +  +LYED  + V +KPAG+ V             ++   D 
Sbjct: 11  PENALNASQEDDSEAQAPEIEILYEDDHLVVIHKPAGLLVHRSYLARRERFFAMQLTRDL 70

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G      HRLD+ TSG+L+ A++   A  L E F    I+K Y +LV G   ++   + 
Sbjct: 71  VGCHVFPVHRLDRPTSGVLLFAKSSEVANALCEQFASHTIEKQYLALVRGNM-HESGILD 129

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
             L  +    GD         K A  A++ ++ +               +F  + + P T
Sbjct: 130 YALKVELDELGDKNA---DPNKAAQEAVTAYEPLLNTEIPYPSGRYPTSRFALVRLSPKT 186

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQ 306
           GR HQLR H  H+  PIVGD  +    +  F       N+L+L A+ +   HP    RL 
Sbjct: 187 GRKHQLRRHMAHLRHPIVGDTTHGDGKQNAFFREHFGINRLWLIAKKLSFTHPVTQVRLS 246

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I   L       +  LG+ 
Sbjct: 247 IETELEPEWETVFAELGWD 265


>gi|295884073|gb|ADG57579.1| RluD [Streptococcus sanguinis]
 gi|332363746|gb|EGJ41526.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK49]
          Length = 291

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 71/303 (23%), Positives = 122/303 (40%), Gaps = 32/303 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   +  G  V +
Sbjct: 4   TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLAINWQTVVNPGDDVCL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+          
Sbjct: 62  IFDEEDY----PQKTILFGNGELVEE--------LYQDQHLIIVNKPEGMKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+LV
Sbjct: 110 ALLNHVSTYV---GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLEKREISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +KK    + + +  H     +     + +   YA +H   +  F Q    ++ Q 
Sbjct: 167 QGKFPSKKLIYKDKIGRDRHDRRKRL----VDPRKGLYAETHVTRLKQFGQ-AALVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G P++GD  Y    KG        +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG--------RLMLHAHRLTFTHPFTLEKIT 273

Query: 307 ITA 309
           I A
Sbjct: 274 IEA 276


>gi|163801775|ref|ZP_02195672.1| pseudouridine synthase Rlu family protein [Vibrio sp. AND4]
 gi|159174283|gb|EDP59087.1| pseudouridine synthase Rlu family protein [Vibrio sp. AND4]
          Length = 255

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 64/258 (24%), Positives = 110/258 (42%), Gaps = 19/258 (7%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
             +  ++ +   ++Y+D      NKPAG+ V       +     +++  D  GQ     H
Sbjct: 5   ETSPSTEPVVLEIIYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLH 64

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG+LV A +   A  +   F   +++K Y ++V G  + +        ++   I
Sbjct: 65  RLDRPTSGVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGLLDYALKVELDKI 124

Query: 209 GGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVH 258
              +       EK A  A++ +K +               ++C +EM P TGR HQLR H
Sbjct: 125 ADKFASQ----EKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMNPKTGRKHQLRRH 180

Query: 259 ALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
             H+  PIVGD  +          T    ++L LHA  +   HP       T  + A + 
Sbjct: 181 MAHLRHPIVGDTTHGDGKHNKLYRTEFDSHRLLLHASELRFVHPFTDE---TIVMRADID 237

Query: 317 KTWDSLGFKYDRNLYIKR 334
           +TW  L  ++D +  + +
Sbjct: 238 ETWQQLFTRFDWDESLIQ 255


>gi|325578324|ref|ZP_08148459.1| tRNA pseudouridine synthase C [Haemophilus parainfluenzae ATCC
           33392]
 gi|325160060|gb|EGC72189.1| tRNA pseudouridine synthase C [Haemophilus parainfluenzae ATCC
           33392]
          Length = 238

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEYLVAVNKPAGMLVHRSWLDTHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  + + F  + +QK Y ++V G  + K +      ++   I   +     Q +
Sbjct: 64  ALNSEIANLMCQQFEQKTVQKSYLAIVRGYLQGKGQIDYPLKIQLDKIADKFA----QED 119

Query: 221 KGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++          V      ++  +++ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQEAVTDYEGLNIVEMPYAVGRYQTTRYSLVKLIPQTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNFTSP--IQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLGFK 325
           +Y    +    +      +L+LHA  +   HP    + +I A L    +K  +   + 
Sbjct: 180 QYGDLHQNRALTEHSGCQRLFLHADTLIFEHPIHSTKFEIKANLDEQWMKVMELFNWS 237


>gi|83855236|ref|ZP_00948766.1| ribosomal large subunit pseudouridine synthase A [Sulfitobacter sp.
           NAS-14.1]
 gi|83941758|ref|ZP_00954220.1| ribosomal large subunit pseudouridine synthase A [Sulfitobacter sp.
           EE-36]
 gi|83843079|gb|EAP82246.1| ribosomal large subunit pseudouridine synthase A [Sulfitobacter sp.
           NAS-14.1]
 gi|83847578|gb|EAP85453.1| ribosomal large subunit pseudouridine synthase A [Sulfitobacter sp.
           EE-36]
          Length = 215

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/226 (28%), Positives = 107/226 (47%), Gaps = 15/226 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +    +      ++L+ED+++ + +KPAG+    G G   H+   L + V        L 
Sbjct: 1   METEYNPPQDPLVVLHEDAEVLLVDKPAGLLSVPGKGP--HLADCLIARVQDAFPDALLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG+++ A T  A +HL   F  R  +K Y + VWG+P+ K   I   L+    
Sbjct: 59  HRLDRDTSGVMIFALTPHAQRHLGLQFEKRMTRKTYVARVWGVPQEKTGTIDLPLIVD-W 117

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  V     +    A + ++V+         + + P TGR+HQLRVH L +G PI+
Sbjct: 118 PNRPRQMVC---HETGKPAQTDWRVLKDEGD-TARVRLSPKTGRSHQLRVHMLSLGHPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
           GD  Y       +      +L LH+  +   HP+GG   +++  AP
Sbjct: 174 GDPFYATGPALAYP-----RLMLHSEELRFNHPQGGHSTKIRAKAP 214


>gi|327463496|gb|EGF09815.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1057]
          Length = 299

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 123/303 (40%), Gaps = 32/303 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   ++ G  + +
Sbjct: 12  TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLAINWQTVVKPGDDICL 69

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+       I  
Sbjct: 70  IFDEEDY----PQKTILIGNGKLVEE--------LYQDQHLIIVNKPEGMKTHANEPIEL 117

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+L+
Sbjct: 118 ALLNHVSAYV---GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLEKREISREYWALI 174

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +KK    + + +  H     +     + +   YA +H   +    Q    ++ Q 
Sbjct: 175 QGKFPSKKLIYKDKIGRDRHDRRKRL----VDPRKGLYAETHVTRLKQLGQ-AALVKCQL 229

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G P++GD  Y    KG        +L LHA  +   HP    ++ 
Sbjct: 230 KTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG--------RLMLHAHRLTFTHPFTLEKIT 281

Query: 307 ITA 309
           + A
Sbjct: 282 VEA 284


>gi|324995861|gb|EGC27772.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK678]
          Length = 291

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 123/303 (40%), Gaps = 32/303 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   ++SG  + +
Sbjct: 4   TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKNHVSVNGLAINWQTVVKSGDDICL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+          
Sbjct: 62  IFDEEDY----PQKTILFGNGELVEE--------LYQDQHLIIVNKPEGMKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+LV
Sbjct: 110 ALLNHVSAYV---GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLEKREISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +KK    + + +  H     +     + +   YA +H   +    Q    ++ Q 
Sbjct: 167 QGKFPSKKLIYKDKIGRDRHDRRKRL----VDPRKGLYAETHVTRLKQLGQ-AALVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G P++GD  Y    KG        +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG--------RLMLHAHRLTFTHPFTLEKIT 273

Query: 307 ITA 309
           + A
Sbjct: 274 VEA 276


>gi|303228397|ref|ZP_07315230.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302516899|gb|EFL58808.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 306

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 69/337 (20%), Positives = 134/337 (39%), Gaps = 51/337 (15%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M   T +  ++V+ +     ++   K    HI+    +++   G + ++ +   ++  + 
Sbjct: 1   MKTATIID-LIVDANVHTQSMNHIIKQQ--HISQRMRRRLKNDGIITINGQPATWDTLVH 57

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  +        L  +  EQ+   + +NL          ++YED  I   NK AG+ + 
Sbjct: 58  GGDHL--------LMKLAPEQEFSRTPMNLE---------IVYEDDYILAVNKAAGVLMH 100

Query: 121 GGSGI--AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             S +      +G L  + +  +       HRLD++TSGI+++A+T        +     
Sbjct: 101 PTSTVRDGTLANGVLYYYDETEQAHDFHPVHRLDKDTSGIVIIAKTSIVQHAFDKQRT-- 158

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF- 236
           + +K+Y ++V G   ++   I   + +K+        + +        A +   V+    
Sbjct: 159 KFKKVYDAIVEGTMPSQSLTIKWPIGRKAG-----SIIERCCTSIGKPARTDVTVLARHI 213

Query: 237 -------------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
                         Q    ++   HTGRTHQ+RVH  H+G P+ GD  Y  +        
Sbjct: 214 VSQPVQMNKNLSTQQVLTHVQCVLHTGRTHQIRVHLSHLGYPLAGDDLYGGHLD------ 267

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
              +  LHA Y+   HP     +++ AP+P  M    
Sbjct: 268 HIRRQALHAGYLAFTHPMTQEYIELRAPMPTDMKDLL 304


>gi|328907008|gb|EGG26774.1| pseudouridine synthase, RluA family [Propionibacterium sp. P08]
          Length = 227

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 59/228 (25%), Positives = 103/228 (45%), Gaps = 14/228 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSG------IAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            ++++DS I V +KPAG++     G      + +              ++  +  RLD  
Sbjct: 2   RIVHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTSGLLERQGIVQRLDVG 61

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++VVA++  A   L ++FR R + K+Y +LV G P      I   + +         
Sbjct: 62  TSGLMVVAKSEHAYTLLKQAFRDRAVDKVYLALVQGHPDPFAGTIDAPIGRDHRHDWKMA 121

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            V      G  ++++H++ ++ F +    L++   TGRTHQ+RVH   +  P  GD  Y 
Sbjct: 122 IV-----DGGRHSVTHYETVEAF-RHATLLKVHLETGRTHQIRVHMAAVKHPCCGDPLYG 175

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            +        ++ + +LHA  +   HP  G  +   A LPA +    D
Sbjct: 176 CDPALAKELGLE-RQWLHAAELSFAHPGSGEWVTFHADLPADLQHALD 222


>gi|158334165|ref|YP_001515337.1| RluA family pseudouridine synthase [Acaryochloris marina MBIC11017]
 gi|158304406|gb|ABW26023.1| pseudouridine synthase, RluA family [Acaryochloris marina
           MBIC11017]
          Length = 306

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 74/312 (23%), Positives = 134/312 (42%), Gaps = 40/312 (12%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             + L  ++   Y H +    Q  + +GQV +D ++   +  ++ GQ           N 
Sbjct: 16  AGLTLLEFYAQRYRHSSGTEWQVRIETGQVTIDGRQATPDTVLKQGQ-----------NL 64

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                   + +V LT         +LYED+ +   +KP+G+ V  G G   H    L   
Sbjct: 65  AYHRPPWQEPTVPLTFD-------VLYEDADVLAIHKPSGLQVLPGGGFLEH---TLLHQ 114

Query: 137 VDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG----I 190
           V  +  +  P   HRL + TSG++++AR++ A   L++  R R+IQK+Y +L+       
Sbjct: 115 VQQRFPQGTPFPIHRLGRGTSGVVLMARSQQARAALSQQMRNRQIQKVYRALIGPEQTTH 174

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P  ++  I   + K  +    Y++      + A+ A +   ++    +    L +   TG
Sbjct: 175 PLEEQFEITQAIGKVPYPELGYIYAATPKGRPAHSACT---ILQRRPE-ATLLAVTITTG 230

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------PIQNKLYLHARYMDLPHPEG 302
           R HQ+R+H   +G P++GD  Y A  +    S        P     +LHA  +   HP  
Sbjct: 231 RPHQIRIHLATIGYPLLGDPLYVAGGQPQSISSEERSQPVPGDCGYWLHAFSLQFIHPTS 290

Query: 303 -GRLQITAPLPA 313
             R+++ +  P 
Sbjct: 291 QERVKVVSEPPQ 302


>gi|332828139|gb|EGK00855.1| hypothetical protein HMPREF9455_02820 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 225

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 72/228 (31%), Positives = 112/228 (49%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I + NK     VQG       +   +K ++  K  KP      +THRLD+ TS
Sbjct: 3   VLYEDNHIIIVNKTVSEIVQGDKTGDKPLSEIVKEYLKEKYNKPGNVFCGVTHRLDRPTS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V ++T  A   L + F+ + I K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GIVVFSKTSKALPRLNDMFKNKEISKTYWAVVKNAPKQPEGTLKHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               +  +  AI H+K+I   + K+  LE+   TGR HQ+R     +G PI GD KY A 
Sbjct: 122 -DTEKPNSKLAILHYKLIAR-SDKYSLLEIDLETGRHHQIRCQLAKIGSPIKGDLKYGAE 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     + LHAR +   HP     +++TAP+P      W +L
Sbjct: 180 -----RSNPDGGISLHARKISFIHPVSKELIEVTAPVPED--NLWQAL 220


>gi|315651177|ref|ZP_07904208.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saburreum DSM 3986]
 gi|315486575|gb|EFU76926.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saburreum DSM 3986]
          Length = 298

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 135/322 (41%), Gaps = 32/322 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M      +++ D ++  +  + K+        N+ K+ +    + ++      N +    
Sbjct: 1   MERQILYIIDKDYKS--ISDFLKS--KGYTASNIAKLKKYENGILLNGIWAYMNQKPARF 56

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +              ++ + + +       +K  + YED  I V NKP+ + +   
Sbjct: 57  DRLLV--------------RVCEYNNSENILPVCIKLDIKYEDDDIVVVNKPSDMPIHPS 102

Query: 123 -SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            +     +   L  +   K    R  +RLD++T+G+ VVA+   +A  L  S + R I++
Sbjct: 103 LNNYDNSMANALMYYYRDKNFVFRCINRLDRDTTGLTVVAKHFLSAGILNTSMQRREIKR 162

Query: 182 IYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           IY ++V           I   + ++     D   + ++     + AI+H+K++    +  
Sbjct: 163 IYNAIVEDDGSLTDSGSIDAPISRE-----DNTLIKRRVSANGHRAITHYKILKRM-RGA 216

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E+   TGRTHQ+RVH  H+G P+VGD+ Y   +          +  LH++ +DL  P
Sbjct: 217 SLIELGLETGRTHQIRVHMSHIGHPLVGDYLYNEKYYDKDNV----RPLLHSKSLDLLQP 272

Query: 301 -EGGRLQITAPLPAHMVKTWDS 321
             G RL +   LP    +  D 
Sbjct: 273 LTGKRLHLECELPTDFTERIDR 294


>gi|169335105|ref|ZP_02862298.1| hypothetical protein ANASTE_01512 [Anaerofustis stercorihominis DSM
           17244]
 gi|169257843|gb|EDS71809.1| hypothetical protein ANASTE_01512 [Anaerofustis stercorihominis DSM
           17244]
          Length = 305

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 71/303 (23%), Positives = 126/303 (41%), Gaps = 32/303 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + +N Y + +      I+R G++ ++ K   F + ++   ++++   +   +    + KI
Sbjct: 28  FLENEYDYSSRTFRY-IIREGRLLINDKDAMFVDILKEEDIIKVSFPVEEADAPSTDMKI 86

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ--GGSGIAYHIDGFLKSW-VDSK 140
                +                    V NK  G+ V       +    +     W ++ K
Sbjct: 87  DIIYEDDDI----------------AVINKKPGMVVHVTKSHPLDTLQNAIYHKWEIEKK 130

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
             K R  +RLD +TSGI+V+A+ +     +       +I K Y  +V GI   K+  I  
Sbjct: 131 HFKTRFVNRLDMDTSGIVVIAKNKYVHHFIQNQSINNQIDKKYVLIVDGIMDQKEGYINA 190

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +  K   G     +V ++       I+ +KVI+ F +    +E +  TGRTHQLRVH  
Sbjct: 191 PI--KRAEGHPLRRIVAED---GKECITKYKVIEEF-KNHSLVEAKLITGRTHQLRVHFS 244

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           ++G PI+GD  Y  N      S + +   LHA+ +   HP G + +   A L        
Sbjct: 245 YVGHPILGDSLYNEN-----KSELISHQALHAKSISFVHPRGNKPMTFEAELFDDFKDVL 299

Query: 320 DSL 322
           + L
Sbjct: 300 EIL 302


>gi|15611749|ref|NP_223400.1| hypothetical protein jhp0682 [Helicobacter pylori J99]
 gi|11136015|sp|Q9ZL98|Y745_HELPJ RecName: Full=Uncharacterized RNA pseudouridine synthase jhp_0682;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|4155249|gb|AAD06270.1| putative [Helicobacter pylori J99]
          Length = 327

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 67/331 (20%), Positives = 136/331 (41%), Gaps = 35/331 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHI 77
            R+D +       I+   +  +++ G V   KK VK     ++ G  + +         +
Sbjct: 12  KRIDEFLAKEL-QISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDAITLLTPKIVPKPL 70

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            KE                L+  +++ED  + V NKP  + V     +    +  L  W+
Sbjct: 71  KKELD--------------LEIEVIFEDEDLLVLNKPPNLVVHKAPSV---KEPTLVDWL 113

Query: 138 DSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            S+  +           + HRLD++TSG +V+A+       L+E  + + + + Y +L+ 
Sbjct: 114 KSQNYELSNLGLKERYGIVHRLDKDTSGGIVIAKNNFTHVCLSEQLKTKMMGRYYIALLS 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
              K +K  +  +L +  +     + +    ++ + Y+ S F  +         +  +  
Sbjct: 174 TPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTSQNGMDLIGAKLF 233

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+R H  ++   I+GD+ Y  N      S  + ++ LHA  ++  HP    +L+ 
Sbjct: 234 TGRTHQIRAHLEYLNRHIIGDNLYGLN---GVLSKEEIRIMLHAYLIEFKHPRSEQKLRF 290

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             PL   M++    +   +D+    + L  +
Sbjct: 291 KVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|332199087|gb|EGJ13167.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA41317]
          Length = 278

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 66/279 (23%), Positives = 112/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D     
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYPQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    +L  T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFT 264


>gi|220924284|ref|YP_002499586.1| pseudouridine synthase [Methylobacterium nodulans ORS 2060]
 gi|219948891|gb|ACL59283.1| pseudouridine synthase [Methylobacterium nodulans ORS 2060]
          Length = 228

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 71/231 (30%), Positives = 113/231 (48%), Gaps = 9/231 (3%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           + + S +LY D+ + V +KPAG+ V  G      +   L +      ++P   HRLD++T
Sbjct: 4   EDIVSRVLYRDALVLVIDKPAGLPVHPGPRGGETLVQHLDALRFGLPRRPEAAHRLDRDT 63

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L + R   A   L   F    ++K YW+LV G+P  ++  I   L ++S    D   
Sbjct: 64  SGCLALGRHAKALARLGGLFAGCEVRKTYWALVEGMPAAEEGAIDLPLARRS---DDPRS 120

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              + +   + A++ +++         WLE++P TGRTHQLRVH   MG PI GD  Y  
Sbjct: 121 WWMKPDPAGDPALTRWRLRGRGPDGSAWLELEPVTGRTHQLRVHCAAMGWPIRGDAIYGV 180

Query: 275 NFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGF 324
             +          L LHAR + LP +P+   + + AP+P H+     + G+
Sbjct: 181 APRQ-----GGPGLQLHARALTLPLYPKKPAIAVAAPVPPHIRPGLSACGW 226


>gi|15901834|ref|NP_346438.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae TIGR4]
 gi|148992153|ref|ZP_01821927.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP9-BS68]
 gi|14973521|gb|AAK76078.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae TIGR4]
 gi|147929202|gb|EDK80213.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP9-BS68]
          Length = 291

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 66/279 (23%), Positives = 112/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +   +  G V ++                 D S   
Sbjct: 26  IPR-KIRHFLRIKKHILINQEEVHWKEIVNPGDVCQLTFDEE------------DYSQKT 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 73  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 130 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 190 KRI----VDAKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNLPILGDP 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    +L  T
Sbjct: 246 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFT 277


>gi|224418218|ref|ZP_03656224.1| ribosomal large subunit pseudouridine synthase A [Helicobacter
           canadensis MIT 98-5491]
          Length = 340

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 132/319 (41%), Gaps = 39/319 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPV 70
           V+ +E  MRLD++       ++   + KI++  Q+ ++   ++ N   +     + +   
Sbjct: 15  VQQEETKMRLDKFLTQKL-GLSRNQISKIIQEKQITLNGVFIQKNGTSLNFNDQIILT-- 71

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                        L +    +K  + L   +LYED  + + NKP  + V           
Sbjct: 72  -------------LPNKQEKSK-PNHLNIPILYEDEDLLILNKPINLIVHQTHQDDSQY- 116

Query: 131 GFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             L+ W+              +  + HRLD+ TSG +V+A+   A + L++  + + + +
Sbjct: 117 -TLQDWLQENNFSLSNLGDSYRQGIIHRLDKTTSGAIVIAKNNYAHEILSQQLKSKEMGR 175

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y   V   P  +   I   L++       Y+   K          + FK+I     K  
Sbjct: 176 YYVC-VIDSPLKQNILIDAPLIRHPKNRLKYIPTTKDTPLSKEAKTAFFKII--NNDKIE 232

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +  +  +GRTHQ+R H   +   I+GD  Y   +KGN+T+    ++ LH+  + L HP 
Sbjct: 233 LIGAKLFSGRTHQIRAHLSKIQRHILGDVFYG--YKGNYTA----RILLHSHLVYLTHPT 286

Query: 302 GG-RLQITAPLPAHMVKTW 319
              RL+I APL   M+   
Sbjct: 287 TKQRLEIYAPLWEDMLLFL 305


>gi|91212158|ref|YP_542144.1| tRNA pseudouridine synthase C [Escherichia coli UTI89]
 gi|117625019|ref|YP_854007.1| tRNA pseudouridine synthase C [Escherichia coli APEC O1]
 gi|218559779|ref|YP_002392692.1| tRNA pseudouridine synthase C [Escherichia coli S88]
 gi|237706579|ref|ZP_04537060.1| tRNA pseudouridine synthase C [Escherichia sp. 3_2_53FAA]
 gi|331684413|ref|ZP_08385005.1| tRNA pseudouridine synthase C [Escherichia coli H299]
 gi|91073732|gb|ABE08613.1| hypothetical protein UTI89_C3161 [Escherichia coli UTI89]
 gi|115514143|gb|ABJ02218.1| tRNA pseudouridine synthase [Escherichia coli APEC O1]
 gi|218366548|emb|CAR04301.1| tRNA pseudouridine synthase [Escherichia coli S88]
 gi|226899619|gb|EEH85878.1| tRNA pseudouridine synthase C [Escherichia sp. 3_2_53FAA]
 gi|294489605|gb|ADE88361.1| tRNA pseudouridine synthase C [Escherichia coli IHE3034]
 gi|307625640|gb|ADN69944.1| tRNA pseudouridine synthase C [Escherichia coli UM146]
 gi|315289310|gb|EFU48705.1| tRNA pseudouridine synthase [Escherichia coli MS 110-3]
 gi|323950992|gb|EGB46868.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323957197|gb|EGB52921.1| RNA pseudouridylate synthase [Escherichia coli H263]
 gi|331078028|gb|EGI49234.1| tRNA pseudouridine synthase C [Escherichia coli H299]
          Length = 260

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDLIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|119385528|ref|YP_916584.1| pseudouridylate synthase [Paracoccus denitrificans PD1222]
 gi|119375295|gb|ABL70888.1| ribosomal large subunit pseudouridine synthase A [Paracoccus
           denitrificans PD1222]
          Length = 215

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 66/216 (30%), Positives = 98/216 (45%), Gaps = 13/216 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +++ D +I V  KPAG+    G G        L   +        L HRLD +TSG+
Sbjct: 11  QPRVIHADHEILVVEKPAGLLSVPGRG--EDRADCLIERLRGAFPTVLLVHRLDMDTSGV 68

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V   T  A +HL+  F  RR +K Y + +WG  + K   +   L+             K
Sbjct: 69  MVFGLTPHAQRHLSRQFEDRRTKKTYVARLWGRLEPKTGMVDLPLIVD----WPNRPRQK 124

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +      A + ++V+         + + P TGR+HQLRVH   +G PI+GD  Y A   
Sbjct: 125 VDHAEGRPAQTEWRVVKA-TDAETRVRLMPITGRSHQLRVHMAQLGHPILGDPLYAAGAA 183

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
            +F      +L LHA  +   HPE G +Q  TAP P
Sbjct: 184 ADFP-----RLMLHAESLRFKHPETGVMQSFTAPAP 214


>gi|312875041|ref|ZP_07735059.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
 gi|311089436|gb|EFQ47862.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
          Length = 283

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 72/299 (24%), Positives = 126/299 (42%), Gaps = 33/299 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQV 64
           Y+ Y+ +  +E N  +D+  +N    I     +  LR    + V+ K +  N ++ +  +
Sbjct: 4   YIYYLTISQNENNQNVDQIMRNLL--IPR-KWRHFLRIEKNILVNDKYLPLNFKVHTNDL 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + I      LNH+   Q+   +S N+          ++YE+  + V +KPAG        
Sbjct: 61  ITI-----KLNHVESLQQQYPASGNMPN--------IIYENDDVLVIDKPAGQKTHPN-- 105

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + + Y+
Sbjct: 106 -LYETDTALNDCASYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLSRSYF 164

Query: 185 SLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
           + +      +    I   +          +            AI+H++V+   A K   +
Sbjct: 165 AWIEATNDISDNGTINLPIGDDPLDMRKRMVRT-----DGLKAITHYQVVKKTANKI-LV 218

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           ++Q  TGRTHQ+RVH   +G PI+GD  Y +N++         KL L A  +    P  
Sbjct: 219 KLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQAG------EKLQLTAYKLVFQKPFS 271


>gi|291535995|emb|CBL09107.1| pseudouridine synthase, RluA family [Roseburia intestinalis M50/1]
          Length = 247

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 60/271 (22%), Positives = 109/271 (40%), Gaps = 36/271 (13%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
             ++ +G  + I              ++ +S+ +       +   + YED  I   NKPA
Sbjct: 2   RTKLSAGDELFI--------------RLEESTSSAHILPVSMPLSICYEDEDILAVNKPA 47

Query: 116 GISVQGGSGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
            + V        H D  L + V             R  +RLD++T+G+ ++A+   ++  
Sbjct: 48  QMPVHPS---LNHYDHTLANAVCGYYNDQEIPYTFRCVNRLDRDTTGLTLIAKHMLSSAI 104

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           L+ +   R I + Y ++  G    +   I   + + +    +       + +    AI+H
Sbjct: 105 LSTAAARREISREYIAIASGK-TPESGTIDAPIGRVAGSTIERQI----DFENGERAITH 159

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           ++ +         L +   TGRTHQ+RVH   +G P++GD  Y      N T     +  
Sbjct: 160 YRRLAYH-DGLSLLSLHLETGRTHQIRVHLKSIGHPLIGDFLY------NPTDTTIKRQA 212

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           LH+  +   HP  G    +TAPLP  M   +
Sbjct: 213 LHSYRLTFSHPITGESFVLTAPLPDDMHCLF 243


>gi|156975510|ref|YP_001446417.1| tRNA pseudouridine synthase C [Vibrio harveyi ATCC BAA-1116]
 gi|156527104|gb|ABU72190.1| hypothetical protein VIBHAR_03241 [Vibrio harveyi ATCC BAA-1116]
          Length = 255

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 64/258 (24%), Positives = 111/258 (43%), Gaps = 19/258 (7%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           S   ++   D +   ++Y+D      NKPAG+ V       +     +++  D  GQ   
Sbjct: 2   SEQEISPSVDPVVLEIVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVF 61

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD+ TSG+LV A +   A  +   F   +++K Y ++V G  + +        ++ 
Sbjct: 62  PLHRLDRPTSGVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVEL 121

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQL 255
             I   +       EK A  A++ +K +               ++C +EM+P TGR HQL
Sbjct: 122 DKIADKFASQ----EKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQL 177

Query: 256 RVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           R H  H+  PIVGD  +          T    ++L LHA  +   HP    ++ + A + 
Sbjct: 178 RRHMAHLRHPIVGDTTHGDGKHNKLYRTEFDSHRLLLHASELRFVHPFTDEKIVMKANID 237

Query: 313 AHMVKTWDSLGFKYDRNL 330
               + +    F++D +L
Sbjct: 238 ETWQQLFTR--FEWDESL 253


>gi|291538489|emb|CBL11600.1| pseudouridine synthase, RluA family [Roseburia intestinalis XB6B4]
          Length = 247

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 60/271 (22%), Positives = 109/271 (40%), Gaps = 36/271 (13%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
             ++ +G  + I              ++ +S+ +       +   + YED  I   NKPA
Sbjct: 2   RTKLSAGDELFI--------------RLEESTSSAHILPVSMPLSICYEDEDILAVNKPA 47

Query: 116 GISVQGGSGIAYHIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
            + V        H D  L + V             R  +RLD++T+G+ ++A+   ++  
Sbjct: 48  QMPVHPS---LNHYDHTLANAVCGYYNDQEIPYTFRCVNRLDRDTTGLTLIAKHMLSSAI 104

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           L+ +   R I + Y ++  G    +   I   + + +    +       + +    AI+H
Sbjct: 105 LSTAAARREISREYIAIASGK-TPESGTIDAPIGRVAGSTIERQI----DFENGERAITH 159

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           ++ +         L +   TGRTHQ+RVH   +G P++GD  Y      N T     +  
Sbjct: 160 YRRLAYH-DGLSLLSLHLETGRTHQIRVHLKSIGHPLIGDFLY------NPTDTTIKRQA 212

Query: 290 LHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           LH+  +   HP  G    +TAPLP  M   +
Sbjct: 213 LHSYRLTFSHPITGESFVLTAPLPDDMHCLF 243


>gi|189468453|ref|ZP_03017238.1| hypothetical protein BACINT_04850 [Bacteroides intestinalis DSM
           17393]
 gi|189436717|gb|EDV05702.1| hypothetical protein BACINT_04850 [Bacteroides intestinalis DSM
           17393]
          Length = 223

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 70/228 (30%), Positives = 109/228 (47%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSEIVKQYLKEKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E F+   ++K YW++V   PK  +  + N+L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFKTSEVKKTYWAIVKNAPKEPEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   +  +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPKSKKAILHYRLIG-KSDNYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYG-- 177

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
                 S     + LHAR +   HP    + ++ AP+P      W   
Sbjct: 178 ---FARSNPDGSICLHARRISFVHPVSKEMIEVEAPVPP--TNLWQGF 220


>gi|330718647|ref|ZP_08313247.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc fallax KCTC
           3537]
          Length = 301

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 63/285 (22%), Positives = 124/285 (43%), Gaps = 35/285 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G + V++K V  ++ ++ G  V I   +   N ++                D+    +++
Sbjct: 37  GAILVNEKPVYTSDFLKQGDSVTIIMPVEESNDLV--------------VPDYRPMDIIF 82

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHID-----GFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           E+    + NKP G++   G     H       G L+  ++++   P +  RLD++TSG++
Sbjct: 83  ENEHWLIVNKPFGVTTVPGHADRLHTLVNQVKGHLEE-IEAEDLVPHVVTRLDRDTSGLV 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+ R A   L +  +   ++K Y +   GI +     I   + +   + GD++   ++
Sbjct: 142 LLAKHRFAHAVLDDQLQRHEVEKFYVAYPSGILEQNHGEINAPIGR---MDGDFIK--RE 196

Query: 219 NEKGANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             +    +++ + V D            +++Q HTGRTHQ+RVH  ++G P+VGD  Y  
Sbjct: 197 VREDGKPSLTEYWVEDVIGADTPHPMTRVKVQLHTGRTHQIRVHFSNIGHPLVGDDLYGG 256

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKT 318
               N       +  LHA +M    P   +  +    LP  +   
Sbjct: 257 PLVHN-----IQRQALHAYHMRFYDPFVEQYREFETGLPDDLTAL 296


>gi|257889020|ref|ZP_05668673.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257897615|ref|ZP_05677268.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|293571088|ref|ZP_06682128.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E980]
 gi|257825083|gb|EEV52006.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257834180|gb|EEV60601.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|291608818|gb|EFF38100.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E980]
          Length = 285

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/265 (24%), Positives = 111/265 (41%), Gaps = 28/265 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R   V ++++   F++ ++    + +              +  D +    +  D     
Sbjct: 36  IRK-NVWINQQPALFHHEVKGNDQITLLF------------EETDYNYQEVQLGDAKHIR 82

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+                L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKKQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+       L      + I + Y ++VWG     +  I N + +  H     V     +
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGKIAKDR-TITNKIGRDRHDRRKRV----VD 197

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +K    A++H  V D        +     TGRTHQ+RVH  H+G PIVGD  Y       
Sbjct: 198 DKNGQNALTHVTV-DKVLSGKTQVYCVLETGRTHQIRVHLAHIGHPIVGDPLYQNRPAE- 255

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR 304
                  +L LHA  + + HP    
Sbjct: 256 -------RLMLHALELHMIHPFTQE 273


>gi|313890421|ref|ZP_07824052.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
 gi|313121264|gb|EFR44372.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
          Length = 296

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 67/280 (23%), Positives = 113/280 (40%), Gaps = 29/280 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V + + +  G  + +    +            D     
Sbjct: 34  IPR-KIRHFLRTKKHLLINQQLVTWQDLVTKGDEISLSFDSD------------DYPQKR 80

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      LY+DS + V NKP G+      G   +    L       GQ   + HRL
Sbjct: 81  IPFGNPELVECLYQDSHLIVVNKPEGMKTH---GNEPNELALLNHVSAFVGQTCYIIHRL 137

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG ++ A+       +      R I + YW+L+ G+ +NK   I   + +  H   
Sbjct: 138 DMETSGAIIFAKNPFILPIMNRLLEDREIGRNYWALIDGVIENKDTAIQFPIGRHRHDRR 197

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             V     + K    AI+  K +  + Q+   ++    TGRTHQ+RVH  ++G PI+GD 
Sbjct: 198 KRV----VDLKHGQKAITQVKCLKRYRQQLSLVDCSLKTGRTHQIRVHLSYIGHPIIGDP 253

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
            YC             +L LHA  +   HP     +++ A
Sbjct: 254 LYCQRTTT-------QRLMLHAHQLYFKHPLTLETIRVDA 286


>gi|225859768|ref|YP_002741278.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 70585]
 gi|225720831|gb|ACO16685.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 70585]
          Length = 278

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 69/279 (24%), Positives = 114/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D S   
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYSQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    RL  T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLERLTFT 264


>gi|257900349|ref|ZP_05680002.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|257838261|gb|EEV63335.1| pseudouridine synthase [Enterococcus faecium Com15]
          Length = 285

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/265 (24%), Positives = 111/265 (41%), Gaps = 28/265 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R   V ++++   F++ ++    + +              +  D +    +  D     
Sbjct: 36  IRK-NVWINQQPALFHHEVKGNDQITLLF------------EETDYNYQEVQLGDAKHIR 82

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+                L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKKQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+       L      + I + Y ++VWG     +  I N + +  H     V     +
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGEIAKDR-TITNKIGRDRHDRRKRV----VD 197

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +K    A++H  V D        +     TGRTHQ+RVH  H+G PIVGD  Y       
Sbjct: 198 DKNGQNALTHVTV-DKVLSGKTQVYCVLETGRTHQIRVHLAHIGHPIVGDPLYQNRPAE- 255

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR 304
                  +L LHA  + + HP    
Sbjct: 256 -------RLMLHALELHMIHPFTQE 273


>gi|222034482|emb|CAP77224.1| tRNA pseudouridine synthase C [Escherichia coli LF82]
 gi|312947318|gb|ADR28145.1| tRNA pseudouridine synthase C [Escherichia coli O83:H1 str. NRG
           857C]
          Length = 260

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMSVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLAIHAGLDDTWMQALSQFGWR 237


>gi|118587355|ref|ZP_01544781.1| pseudouridine synthase [Oenococcus oeni ATCC BAA-1163]
 gi|118432179|gb|EAV38919.1| pseudouridine synthase [Oenococcus oeni ATCC BAA-1163]
          Length = 301

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 70/316 (22%), Positives = 140/316 (44%), Gaps = 35/316 (11%)

Query: 13  ENDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
             + E +RL  + K     H  F  ++     G++ V+ + V  N+ +++G+ + I    
Sbjct: 11  TKEPEKVRL--FLKARGVSHRMFSQIKHF--GGKIVVEGREVFTNDYVKNGEKITIF--- 63

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHID 130
                +  E++ ++   + T         +++ED    + +KPA ++   G       + 
Sbjct: 64  -----MPPERENVELDADFTD-----PLKVVFEDKNFLIVDKPAFVTTVPGHADRKTTLV 113

Query: 131 GFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSL 186
             +K+ +  +      P +  RLD++TSG++++A+ + A   L ++      I+K Y +L
Sbjct: 114 NMIKAHLIQEKADSLVPHVVTRLDRDTSGLVLLAKHKFAHALLNDALMEHHDIEKFYVAL 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  +     I   + +   I GD++   +Q  +    +++ +  I+     F  L +Q
Sbjct: 174 VSGNFQEDHGMIDEPIGR---IEGDFIR--RQVRQDGKRSVTEYW-IEKRFDNFTQLRIQ 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
            HTGRTHQ+RVH    G P++GD  Y         S + ++  LHA  M    P   +  
Sbjct: 228 LHTGRTHQIRVHMAWAGHPLIGDVLYGGPH-----SKLISRQALHASEMIFFDPFANKNQ 282

Query: 306 QITAPLPAHMVKTWDS 321
              A LP  + +  ++
Sbjct: 283 HFNAGLPDDIQRIIEA 298


>gi|37524666|ref|NP_928010.1| tRNA pseudouridine synthase C [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36784091|emb|CAE12960.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 256

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 107/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   VLYQDDHIVAVNKPAGWLVHRSWLARHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++QK Y ++V G            + +   I   +     + +
Sbjct: 64  ALSSDVARQLSQQFEHHQLQKTYHAVVRGYVLESAIIDYALVEELDKIADKFA----EGD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A   +++++ +               +F  LE+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KEAQSCVTYYRPLATVECPVEIGRYPTSRFSLLELTPKTGRKHQLRRHMAHIRHPIIGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +      +G       ++L LHA Y++L HP  G  L +TA   A         G++
Sbjct: 180 THGDLRQNRGVAVHYQTSRLMLHASYLELDHPVTGEKLSLTAKWDASWQHLIQQFGWQ 237


>gi|116494411|ref|YP_806145.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
 gi|116104561|gb|ABJ69703.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
          Length = 300

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 66/309 (21%), Positives = 124/309 (40%), Gaps = 35/309 (11%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K      +   L+K+  + G V V+K++      ++SG  + +               
Sbjct: 17  FLKQQ--GFSRAQLKKLRYQGGFVFVNKRQRHTAYLVRSGDRILVQTAPEH-----AADS 69

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWV---D 138
           ++  S +L          + YED    + NKPAG++     G   + +   +K+++    
Sbjct: 70  VVPYSHDLA---------ISYEDDDYLIVNKPAGVASIPAVGRQNNSMANMVKAYLIKTK 120

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKEC 197
           ++ Q   +  RLD++TSG++V A+   A   L +    +   K Y ++V    P      
Sbjct: 121 AESQAVHVVTRLDRDTSGLMVFAKHGLAHSLLDQQLHSQDFVKQYVAIVTAQTPLATHGW 180

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   +        D  ++ +        +++ ++ +D        L +  HTGRTHQ+RV
Sbjct: 181 IVLPIGVS-----DGFYMRRVVTDTGKASVTEYRTLDENTAGAMML-VTLHTGRTHQIRV 234

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +G  + GD  Y  +  G       N+  LH  ++    P   + + + APLPA M 
Sbjct: 235 HFAAIGHALYGDGLYSPDTHG------FNRQALHCAHLRFWQPLKHKLIDLHAPLPADMA 288

Query: 317 KTWDSLGFK 325
                L   
Sbjct: 289 TLAAKLKLS 297


>gi|115372352|ref|ZP_01459661.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|310819495|ref|YP_003951853.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115370565|gb|EAU69491.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|309392567|gb|ADO70026.1| Pseudouridine synthase, RluA family [Stigmatella aurantiaca
           DW4/3-1]
          Length = 324

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 126/285 (44%), Gaps = 24/285 (8%)

Query: 39  KILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +++ +G V V  +R +    R+++GQVV +         +++E         L   +   
Sbjct: 34  QLVEAGAVYVGGRRCREGGLRLRAGQVVAV---------VLEEG----GRSPLEALAPPP 80

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +L+ED  +   +KP GI+ Q   G A      +    +  GQ   L HRLD+ETSG+
Sbjct: 81  ALGVLFEDEALIAVDKPVGITAQPTEGRA--GGSLVDLVSERLGQLAGLVHRLDRETSGV 138

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
            V  +T  A   L   FR  R +K Y +   G        +   L +     G +     
Sbjct: 139 TVFGKTPQATTALAAEFREGRARKRYVAAT-GPGLPASGTVDLPLSRDPARPGRWRASRA 197

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            N      A++ F+ +      FC +E+ P TGRTHQLR H   +G PI+GD +Y     
Sbjct: 198 AN---GVPALTDFRTL-YSGADFCLVELLPQTGRTHQLRAHLTALGAPILGDSRYGGAAT 253

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
               S    +  LHA+ ++L HP  G  L+I APLP  +   + +
Sbjct: 254 AGGLS--AGRCLLHAQGLELAHPLTGAALRIEAPLPGDLRCFFTA 296


>gi|191637795|ref|YP_001986961.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|301065920|ref|YP_003787943.1| 23S RNA-specific pseudouridylate synthase [Lactobacillus casei str.
           Zhang]
 gi|190712097|emb|CAQ66103.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|300438327|gb|ADK18093.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           str. Zhang]
 gi|327381861|gb|AEA53337.1| Uncharacterized RNA pseudouridine synthase yhcT [Lactobacillus
           casei LC2W]
 gi|327385023|gb|AEA56497.1| Uncharacterized RNA pseudouridine synthase yhcT [Lactobacillus
           casei BD-II]
          Length = 300

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 66/309 (21%), Positives = 124/309 (40%), Gaps = 35/309 (11%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K      +   L+K+  + G V V+K++      ++SG  + +               
Sbjct: 17  FLKQQ--GFSRAQLKKLRYQGGFVFVNKRQRHTAYPVRSGDRILVQTAPEH-----AADS 69

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWV---D 138
           ++  S +L          + YED    + NKPAG++     G   + +   +K+++    
Sbjct: 70  VVPYSHDLA---------ISYEDDDYLIVNKPAGVASIPAVGRQNNSMANMVKAYLIKTK 120

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKEC 197
           ++ Q   +  RLD++TSG++V A+   A   L +    +   K Y ++V    P      
Sbjct: 121 AESQAVHVVTRLDRDTSGLMVFAKHGLAHSLLDQQLHSQDFVKQYVAIVTAQTPLATHGW 180

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   +        D  ++ +        +++ ++ +D        L +  HTGRTHQ+RV
Sbjct: 181 IVLPIGVS-----DGFYMRRVVTDTGKASVTEYRTLDQNKAGAMML-VTLHTGRTHQIRV 234

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H   +G  + GD  Y  +  G       N+  LH  ++    P   + + + APLPA M 
Sbjct: 235 HFAAIGHALYGDGLYSPDTHG------FNRQALHCAHLRFWQPLKHKLIDLHAPLPADMA 288

Query: 317 KTWDSLGFK 325
                L   
Sbjct: 289 TLAAKLKLS 297


>gi|172079581|ref|ZP_02709037.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1873-00]
 gi|172042644|gb|EDT50690.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1873-00]
 gi|301802690|emb|CBW35457.1| RNA pseudouridylate synthase [Streptococcus pneumoniae INV200]
 gi|332199159|gb|EGJ13238.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA47368]
          Length = 278

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 66/279 (23%), Positives = 113/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D S   
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYSQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETYVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    +L  T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFT 264


>gi|229016637|ref|ZP_04173574.1| Pseudouridine synthase [Bacillus cereus AH1273]
 gi|229022852|ref|ZP_04179372.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228738387|gb|EEL88863.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228744627|gb|EEL94692.1| Pseudouridine synthase [Bacillus cereus AH1273]
          Length = 307

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/297 (21%), Positives = 120/297 (40%), Gaps = 31/297 (10%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
            +    L ++     + V+ ++ +++  ++ G  +++   +     +             
Sbjct: 32  EVPKKLLHQLRMEKGITVNGEQRRWDELLKEGDKLQVHMFMEEEYGV------------- 78

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW---VDSKGQKPRLT 147
                + +  ++YED  + + NKP  +               L ++   +     K R  
Sbjct: 79  --DPQYGELDVVYEDDHVLIVNKPEQMDTHPSEKNGTGTLANLVAFHFQMQGLETKVRHI 136

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++T+G +V A+ R A   +      R+I++ Y +LV G  K K+  I   + +  H
Sbjct: 137 HRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQGTIDAAIGRDRH 196

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                    K      + AI+++KV   F  Q    + +Q  TGRTHQ+RVH  + G P+
Sbjct: 197 HATRRRVSPK-----GDQAITYYKVEKYFNKQNATLVTLQLETGRTHQIRVHMSYNGNPL 251

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           VGD  Y    K        +   LHA  ++  HP     + +  P PA +  T    
Sbjct: 252 VGDVLYGGQTK------YMSHQALHAMKINFLHPITKEEIMVDVPFPAKLNNTMKKF 302


>gi|312866863|ref|ZP_07727076.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
 gi|311097646|gb|EFQ55877.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
          Length = 287

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 68/291 (23%), Positives = 117/291 (40%), Gaps = 34/291 (11%)

Query: 25  FKNHYPHI---NFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K             ++  LR    V V+ + + + + +Q G  +++  + +A ++  KE
Sbjct: 16  VKELLEDYFLIPR-KIRHFLRTKKHVLVNGETINWQSPVQKGDQIQL--IFDADDYPEKE 72

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
               D S+             LY+D  + + NKP G+           +   + S+V   
Sbjct: 73  LPAGDPSL----------VEELYQDEHVIIVNKPEGMKTHANEPTEISLLNHVSSYV--- 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G    + HRLD+ETSG ++ A+       L      + IQ+ YW+L+ G    K     +
Sbjct: 120 GSTCYVVHRLDKETSGAILFAKNPFILPILNRILEDKNIQREYWALIQGSLAQKTIVYKD 179

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + +   YA +    +    +    ++ Q  TGRTHQ+RVH  
Sbjct: 180 KIGRDRHDRRKRL----VDPRKGQYAETQVTQLKKIGRN-SLVKCQLKTGRTHQIRVHLS 234

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           H G PIVGD  Y              +L LHA  +   +P     +Q+ AP
Sbjct: 235 HHGHPIVGDPLYNPARGE--------RLMLHAHRLTFTNPLTLETIQVEAP 277


>gi|163790580|ref|ZP_02185009.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Carnobacterium sp. AT7]
 gi|159874183|gb|EDP68258.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Carnobacterium sp. AT7]
          Length = 310

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 64/295 (21%), Positives = 126/295 (42%), Gaps = 32/295 (10%)

Query: 30  PHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
             I+   L KI    G++ V++  V     +++   V+I               I D + 
Sbjct: 31  KGISRSLLAKIKFHGGKIEVNEIEVTVRYLLKNKDTVQIT--------------IPDEAP 76

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGIS-----VQGGSGIAYHIDGFLKSWVDSKGQK 143
           + T     +   ++YED    V NKP G++     V     +A  + G+     +   Q 
Sbjct: 77  HETTIPIDIPIDIVYEDEHYLVVNKPFGVASVPSQVHPEGTMANRVKGYYVRQ-NYDDQV 135

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             +  RLD++T+G+++ A+   A   + E  R + I K Y +L+ G     +    +  +
Sbjct: 136 IHIVTRLDRDTTGLMLFAKHGYAHALMDEKLRAKEITKKYTALISGQFNESEHGFIDAPI 195

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            ++        + ++  +    A++ + + + F Q    +++Q HTGRTHQ+RVH  H+G
Sbjct: 196 ARTTDS----IITRRAHESGKEALTEYWIKEAFPQ-ATLVDIQLHTGRTHQIRVHFAHIG 250

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVK 317
            P++GD  Y         +    +  LH R ++  HP    ++ +    P  + +
Sbjct: 251 HPLMGDDLYGGK-----KNEWIVRQALHCRELNFKHPFTDKKINLKLDYPEDITQ 300


>gi|325697307|gb|EGD39193.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK160]
          Length = 298

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 67/280 (23%), Positives = 116/280 (41%), Gaps = 31/280 (11%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    V V+   + +   ++ G  + +         I  E+     ++ L
Sbjct: 34  IPR-KIRHFLRTKKHVSVNGLAINWQTVVKPGDDICL---------IFDEEDYPQKTILL 83

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      LY+D  + + NKP G+           +   + ++V   G+   + HRL
Sbjct: 84  ---GNGELVEELYQDQHLIIVNKPEGMKTHANEPTELALLNHVSAYV---GETCYVVHRL 137

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ETSG ++ A+       L      R I + YW+LV G   +KK    + + +  H   
Sbjct: 138 DKETSGAVLFAKNPFVLPILNRLLEKREISRQYWALVQGKFPSKKLIYKDKIGRDRHDRR 197

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + +   +A +H   +  F Q    ++ Q  TGRTHQ+RVH  H G P+VGD 
Sbjct: 198 KRL----VDPRKGLFAETHVTRLKQFGQ-AGLVKCQLKTGRTHQIRVHLAHHGHPLVGDP 252

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
            Y    +G        +L LHA  +   HP    ++ + A
Sbjct: 253 LYHPQPQG--------RLMLHAHRLTFTHPFTLEKITVEA 284


>gi|167761861|ref|ZP_02433988.1| hypothetical protein BACSTE_00204 [Bacteroides stercoris ATCC
           43183]
 gi|167700231|gb|EDS16810.1| hypothetical protein BACSTE_00204 [Bacteroides stercoris ATCC
           43183]
          Length = 517

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 71/244 (29%), Positives = 111/244 (45%), Gaps = 21/244 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ +     S      ++YED  + V NKPAG+    G      +
Sbjct: 285 CEPILGHMLQGLEVDENPILKELQSGKKTLDIIYEDEWLAVVNKPAGMLSVPGKEDVVSV 344

Query: 130 DGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              ++  + D+ G  P + HRLD  TSG+LVVA+T+   Q+L   F+ R I K Y +L+ 
Sbjct: 345 YSMMRERYPDADG--PLIVHRLDMATSGLLVVAKTKQVHQNLQAQFKNRSIGKRYIALLQ 402

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        +   L          +            A++ F+V++        +   P 
Sbjct: 403 GSVSQDAGTVELPLCPNPLDRPRQMVHTGY----GKPAVTDFEVLERK-DNRTRIAFYPR 457

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           TGRTHQLRVHA H   + CPI+GD  Y    +         +LYLHA  ++  HP  G R
Sbjct: 458 TGRTHQLRVHAAHPLGLHCPIIGDELYGRKAE---------RLYLHAEMLEFTHPVTGKR 508

Query: 305 LQIT 308
           + IT
Sbjct: 509 ISIT 512


>gi|290579729|ref|YP_003484121.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
 gi|254996628|dbj|BAH87229.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
          Length = 288

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 61/281 (21%), Positives = 106/281 (37%), Gaps = 30/281 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    V V+ + V + + ++ G ++++                 D  +  
Sbjct: 26  IPR-KIRHFLRIKKNVTVNSQAVNWQSLVRRGDIIQLNF------------DNTDYPIKK 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      LY+D  + + NK  G+          +    L       GQ   + HRL
Sbjct: 73  IPMGNKALIDCLYQDEHLIIVNKIEGMKTHAN---DPNEIALLNHASAYVGQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D +TSG ++ A+       L      + I++ YW+L  G    +       + +  H   
Sbjct: 130 DMKTSGTVMFAKNPFILPILNRLLENKSIKREYWALAQGQFSERAIIYREPIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             V     + K    AI+   ++  F      ++ Q  TGRTHQ+RVH  +    IVGD 
Sbjct: 190 KRV----VDHKHGQTAITQVSLLKHFPNNTSLIKCQLQTGRTHQIRVHLAYHDHAIVGDP 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
            Y     G        +L LHA  +   HP    ++++ AP
Sbjct: 246 LYSQQTAG--------RLMLHAHQLTFTHPLTLEKIKVEAP 278


>gi|110677435|ref|YP_680442.1| ribosomal large subunit pseudouridine synthase A [Roseobacter
           denitrificans OCh 114]
 gi|109453551|gb|ABG29756.1| ribosomal large subunit pseudouridine synthase A [Roseobacter
           denitrificans OCh 114]
          Length = 215

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 111/226 (49%), Gaps = 15/226 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++ T         +L+ED+++ + +KPAG+    G G   H+   L + V +      L 
Sbjct: 1   MDETYAPPQTPLTVLHEDAEVLLVDKPAGLLSVPGKGP--HLADCLLARVQAMFADALLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG+++ A T  A +HL   F  R  +K Y + VWG+P +K   +   L+    
Sbjct: 59  HRLDRDTSGVMIFALTPHAQRHLGLQFEKRMTRKTYVARVWGVPCDKTGTVDLPLIVD-W 117

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  V     +    A + ++V+    Q    + + PHTGR+HQLRVH   +G PI+
Sbjct: 118 PNRPRQMVC---HETGKPAQTEWRVLKDDGQ-TARMRLHPHTGRSHQLRVHMRALGHPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
           GD  Y      ++      +L LH+  +   HP+GGR   ++ TAP
Sbjct: 174 GDPFYATGPARDYP-----RLMLHSEELRFKHPQGGRSMKVRATAP 214


>gi|167761774|ref|ZP_02433901.1| hypothetical protein BACSTE_00112 [Bacteroides stercoris ATCC
           43183]
 gi|167700410|gb|EDS16989.1| hypothetical protein BACSTE_00112 [Bacteroides stercoris ATCC
           43183]
          Length = 223

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 71/219 (32%), Positives = 113/219 (51%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKLYLKEKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E FR   ++K YW++V   P+  +  + N+L++       Y + 
Sbjct: 63  GLVVFAKTSKALARLNEMFRNSEVKKTYWAVVKNRPRESEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   +Q +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVPNSKKAILHYRLIAR-SQNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                 S     + LHAR++   HP   + +++ AP+PA
Sbjct: 180 RSNPDGS-----ICLHARFVRFVHPVSKKLIEVEAPVPA 213


>gi|313889381|ref|ZP_07823029.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
 gi|313122213|gb|EFR45304.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
          Length = 296

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 66/298 (22%), Positives = 127/298 (42%), Gaps = 30/298 (10%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L K+  + G++ V+         +  G +V I          I  ++  +    
Sbjct: 21  DVSKGLLAKVKYKGGRIAVNGIERNAIYLLDIGDIVSIT---------IPNERPFEKLEA 71

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL 146
           ++   D     ++YED    V NKP G +    +  +  I  F+K +    D   ++  +
Sbjct: 72  ISHPLD-----IVYEDDHFLVINKPVGYASIPSAIHSNTIANFIKGYYVEQDYPNKQVHI 126

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKK 205
             RLD++TSG+++ A+   A   L +  + R I+K Y++LV G  +   +  I   + + 
Sbjct: 127 VTRLDRDTSGLMLFAKHGYAHARLDKQLQARAIEKRYFALVSGDGQLPDQGEIIAPIGRS 186

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                    + +  +    YA + ++V+  +A+    ++++ HTGRTHQ+RVH  H+G P
Sbjct: 187 -----KDSIITRTVDPMGKYARTSYQVVGRYAENVHLVDIKLHTGRTHQIRVHFSHIGFP 241

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           ++GD  Y        T     +  LH  ++   +P    + Q T  L          L
Sbjct: 242 LLGDDLYGGRLDLGIT-----RQALHCHFLSFHNPFTENVSQHTIHLTDDFENVIIDL 294


>gi|309805370|ref|ZP_07699419.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
 gi|308165297|gb|EFO67531.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
          Length = 292

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 72/303 (23%), Positives = 127/303 (41%), Gaps = 34/303 (11%)

Query: 3   LMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQ 60
           +M  Y+ Y+ +  +E N  +D+  +N    I     +  LR    + V+ K +  N ++ 
Sbjct: 9   IMNQYIYYLTISQNENNQNVDQIMRNLL--IPR-KWRHFLRIEKNILVNDKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V +KPAG    
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENDDVLVIDKPAGQKTH 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 113 PN---LYETDTALNDCASYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           + Y++ +      +    I   +          +            AI+H++V+     K
Sbjct: 170 RSYFAWIEATNDISDNGTINLPIGDDPLDMRKRMVRA-----DGLKAITHYQVVKKIGSK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++         KL L A  +    
Sbjct: 225 I-LVKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQAG------EKLQLTAYKLVFQK 277

Query: 300 PEG 302
           P  
Sbjct: 278 PFS 280


>gi|225857586|ref|YP_002739097.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae P1031]
 gi|225726338|gb|ACO22190.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae P1031]
 gi|301800771|emb|CBW33421.1| RNA pseudouridylate synthase [Streptococcus pneumoniae OXC141]
          Length = 278

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 68/279 (24%), Positives = 113/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D     
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYPQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    RL  T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLERLTFT 264


>gi|148998774|ref|ZP_01826211.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP11-BS70]
 gi|168576962|ref|ZP_02722796.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae MLV-016]
 gi|307068624|ref|YP_003877590.1| 23S RNA-specific pseudouridylate synthase [Streptococcus pneumoniae
           AP200]
 gi|147755335|gb|EDK62385.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP11-BS70]
 gi|183577335|gb|EDT97863.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae MLV-016]
 gi|306410161|gb|ADM85588.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           pneumoniae AP200]
          Length = 291

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/279 (23%), Positives = 112/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +   +  G V ++                 D S   
Sbjct: 26  IPR-KIRHFLRIKKHILINQEEVHWKEIVNPGDVCQLTFDEE------------DYSQKT 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 73  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 130 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 190 KRI----VDAKNGQYAETYVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDP 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    +L  T
Sbjct: 246 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFT 277


>gi|314938511|ref|ZP_07845796.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|314942472|ref|ZP_07849312.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|314949504|ref|ZP_07852839.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
 gi|314952915|ref|ZP_07855882.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|314992184|ref|ZP_07857627.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|314995258|ref|ZP_07860370.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313590514|gb|EFR69359.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313593242|gb|EFR72087.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|313594987|gb|EFR73832.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|313598780|gb|EFR77625.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|313642139|gb|EFS06719.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|313644118|gb|EFS08698.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
          Length = 299

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 64/265 (24%), Positives = 110/265 (41%), Gaps = 28/265 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R   V ++++   F++ ++    + +       N+               +  D     
Sbjct: 50  IRK-NVWINQQPALFHHEVKGNDQITLLFEETDYNYQE------------VQLGDAKHIR 96

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+                L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 97  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVL 156

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+       L      + I + Y ++VWG        I N + +  H     V     +
Sbjct: 157 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGEIAKDM-TITNKIGRDRHDRRKRV----VD 211

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +K    A++H  V    +++         TGRTHQ+RVH  H G PIVGD  Y       
Sbjct: 212 DKNGQSALTHVTVNKVLSEQTQVY-CVLETGRTHQIRVHLAHKGHPIVGDPLY------- 263

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR 304
             +    +L LHA  + + HP    
Sbjct: 264 -QNRTAERLMLHALELHMIHPFTQE 287


>gi|183603679|ref|ZP_02718812.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC3059-06]
 gi|183575456|gb|EDT95984.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC3059-06]
          Length = 278

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 65/279 (23%), Positives = 112/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D     
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYPQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETYVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    +L  T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFT 264


>gi|323350661|ref|ZP_08086322.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis VMC66]
 gi|322123081|gb|EFX94772.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis VMC66]
          Length = 291

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 122/303 (40%), Gaps = 32/303 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   ++ G  + +
Sbjct: 4   TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLAINWQTVVKPGDDICL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+          
Sbjct: 62  IFDEEDY----PQKTILFGNGELVEE--------LYQDQHLIIVNKPEGMKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+LV
Sbjct: 110 ALLNHVSAYV---GETCYVVHRLDKETSGAILFAKNPFVLPILNRLLEKREISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +KK    + + +  H     +       +   YA +H   +  F Q    ++ Q 
Sbjct: 167 QGKFPSKKLIYKDKIGRDRHDRRKRL----VEPQKGLYAETHVTRVKQFGQ-AALVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G P++GD  Y    KG        +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG--------RLMLHAHRLTFTHPFTLEKIT 273

Query: 307 ITA 309
           + A
Sbjct: 274 VEA 276


>gi|269960587|ref|ZP_06174959.1| tRNA pseudouridine synthase C [Vibrio harveyi 1DA3]
 gi|269834664|gb|EEZ88751.1| tRNA pseudouridine synthase C [Vibrio harveyi 1DA3]
          Length = 255

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 60/255 (23%), Positives = 104/255 (40%), Gaps = 17/255 (6%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           S    +   + +   ++Y+D      NKPAG+ V       +     +++  D  GQ   
Sbjct: 2   SEQETSPSVEPVVLEIVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVF 61

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD+ TSG+LV A +   A  +   F   +++K Y ++V G  + +        ++ 
Sbjct: 62  PLHRLDRPTSGVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVEL 121

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQL 255
             I   +       EK A  A++ +K +               ++C +EM+P TGR HQL
Sbjct: 122 DKIADKFASQ----EKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQL 177

Query: 256 RVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           R H  H+  PIVGD  +          T    ++L LHA  +   HP     + + A + 
Sbjct: 178 RRHMAHLRHPIVGDTTHGDGKHNKLYRTEFDSHRLLLHASELRFVHPFTDEEIVMKANID 237

Query: 313 AHMVKTWDSLGFKYD 327
               + +    +   
Sbjct: 238 ETWQQLFARFEWDAS 252


>gi|15645364|ref|NP_207538.1| hypothetical protein HP0745 [Helicobacter pylori 26695]
 gi|3915378|sp|O25441|Y745_HELPY RecName: Full=Uncharacterized RNA pseudouridine synthase HP_0745;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2313872|gb|AAD07795.1| conserved hypothetical protein [Helicobacter pylori 26695]
          Length = 327

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 70/343 (20%), Positives = 141/343 (41%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +         + KE                L+  +++ED  + V NKP  + V     +
Sbjct: 59  TLLTPKITPKPLKKELD--------------LEIEVIFEDEDLLVLNKPPNLVVHKALSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      HL+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGLKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAVKKEKSRYSKSEFISLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---GALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L+   PL   M++    +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLRFKVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|319650250|ref|ZP_08004396.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317398081|gb|EFV78773.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 265

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 62/273 (22%), Positives = 115/273 (42%), Gaps = 32/273 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           + QV  +     + N +Q+G  ++                      +L     +    +L
Sbjct: 4   NKQVVTNDAPANWTNPLQAGDKLKFHFFREE---------------DLGLIPSYYDIEVL 48

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW---VDSKGQKPRLTHRLDQETSGILV 159
           +ED  + V NKPAG+     S    +      ++   +  + +  +  HRLD++T+G ++
Sbjct: 49  FEDDHLLVLNKPAGMDTHPNSPEQNNTLANAAAFHMQMQGEYRSIKHIHRLDRDTTGAIL 108

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+   A   L +    R I++ Y +LV G     +  I+  + +  H          + 
Sbjct: 109 FAKHALAGAILDKKLEERTIKRTYLALVHGRISKIRGTISEPIGRDRHHPARR-----RV 163

Query: 220 EKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             G   A++++++I+ F   K   ++ +  TGRTHQ+RVH  H+G P+ GD  Y      
Sbjct: 164 SPGGQPAVTNYELIEYFPNLKLSLIKCRLDTGRTHQIRVHLSHIGHPLAGDILYGGK--- 220

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
               P   +  LHA  +++PHP     +   AP
Sbjct: 221 ----PAFPRQALHAVKLEIPHPFLEETIVCHAP 249


>gi|312127537|ref|YP_003992411.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311777556|gb|ADQ07042.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           hydrothermalis 108]
          Length = 293

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 71/262 (27%), Positives = 128/262 (48%), Gaps = 15/262 (5%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSV---NLTKHSDFLKSILLYEDSKIYVFNKP 114
           R+++   +R  P I +++   +E  +++  +               +LYED+     NKP
Sbjct: 33  RLKAHGQIRFIPPIYSIHQYPQENAVIEVDLISYKSNIVPVEGSIDILYEDNFFLFVNKP 92

Query: 115 AGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           +G+      G  +  I  +++ +++SK     + +RLD+ETSGI+V A+       ++  
Sbjct: 93  SGLPSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRLDKETSGIVVFAKNSYFHSIVSYE 152

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  RR+ K Y ++V G    K   I   + K+S  G     + ++  +  ++A ++++VI
Sbjct: 153 FEKRRVDKTYIAIVHGRLTKKSGLIEKPI-KRSDDG-----IKREIHQDGSFASTYYEVI 206

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D F + F  L+++P TGRTHQLRVH   +G PIVGD+ Y      N        L+ ++ 
Sbjct: 207 DTF-ENFSVLKLKPITGRTHQLRVHLSSIGHPIVGDYIYGEEKTQNTPLL----LHAYSI 261

Query: 294 YMDLPHPEGGRLQITAPLPAHM 315
             +          IT+PLP + 
Sbjct: 262 RFNFKLINNKVYDITSPLPHYF 283


>gi|253701860|ref|YP_003023049.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251776710|gb|ACT19291.1| pseudouridine synthase, RluA family [Geobacter sp. M21]
          Length = 302

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 71/311 (22%), Positives = 126/311 (40%), Gaps = 45/311 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++  +   R+D + +N  P   F  L+K++ SG V+V+   V+    ++    V +    
Sbjct: 6   IDAKDHCRRMDSFMRNLLPTAQFSYLKKLISSGHVKVNGSSVEAAQLLKYADQVTLKESS 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
                + +    LD               +L+EDS I   NK  G+SV         ++ 
Sbjct: 66  KTAAFLARLTPELD---------------ILFEDSWIISLNKAPGLSVHRTEDPDEVNLV 110

Query: 131 GFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              ++ +  +    + R  +RLD+ TSG +++A++  AA    +  +   + K+Y +LV 
Sbjct: 111 DLAETLLQKRDGVGRLRPVNRLDKGTSGAIILAKSAVAAGMFGKMVQEEGLGKLYLALVE 170

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  + K+  I   L                       + + +  +         L + P 
Sbjct: 171 GKLQ-KQGVIDAPL-------------------DGKESQTSYLRL-FHGGGVSLLAVYPI 209

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
           TGR HQ+R H   +G PI+GD +Y       FT        LH+    L HP  G  + I
Sbjct: 210 TGRMHQIRQHFKMIGHPILGDKRYGGRALTGFTGH-----ALHSFKTTLVHPATGEEVNI 264

Query: 308 TAPLPAHMVKT 318
            APLP  +++ 
Sbjct: 265 PAPLPEQLMRL 275


>gi|205372953|ref|ZP_03225761.1| pseudouridine synthetase [Bacillus coahuilensis m4-4]
          Length = 238

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 106/233 (45%), Gaps = 22/233 (9%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------PRL 146
             + +   ++YED  + V NKPA ++         H  G L + +    +K        +
Sbjct: 15  KPENIPLTIVYEDEHVLVVNKPARMNTIPSK---EHPTGSLANALLFYYEKIGLPSTVHI 71

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD++TSG++++A+ +     L+   + +++ + Y +L  G  K     I   + +K 
Sbjct: 72  VTRLDRDTSGLVLIAKHQFVHGKLSLLQQQKKVNREYEALSEGTFKEPYGKIELPIGRK- 130

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               D   + ++      YA ++++V+  F QKF  ++++  TGRTHQ+RVH  H+G P+
Sbjct: 131 ----DTSIIEREVRHDGKYACTYYRVLQNF-QKFSHVKLKLETGRTHQIRVHLSHIGHPL 185

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKT 318
           VGD  Y    K         +  LH   +   HP     L +   LP  + K 
Sbjct: 186 VGDTLYGGGTKW------LKRQALHCSSLSFFHPFLKEELHLKCQLPKDIEKL 232


>gi|150002980|ref|YP_001297724.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           vulgatus ATCC 8482]
 gi|254883622|ref|ZP_05256332.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           4_3_47FAA]
 gi|294775614|ref|ZP_06741123.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|319642310|ref|ZP_07996968.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_40A]
 gi|149931404|gb|ABR38102.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           vulgatus ATCC 8482]
 gi|254836415|gb|EET16724.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           4_3_47FAA]
 gi|294450556|gb|EFG19047.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|317386033|gb|EFV66954.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_40A]
          Length = 223

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 77/234 (32%), Positives = 117/234 (50%), Gaps = 18/234 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
           I++YED+ I V NK +   VQG       +   +K ++  K  KP      +THRLD+  
Sbjct: 2   IVVYEDNHIIVVNKTSSEIVQGDKTGDTPLSEMVKQYLKEKYNKPGNVFIGVTHRLDRPV 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V A+T  A   L E FR   ++K YW++V   PK  +  + ++L++       Y +
Sbjct: 62  SGLVVFAKTSKALPRLNEMFRNGEVKKTYWAIVKECPKETEGELVHYLVRNEKQNKSYAY 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              +  K +  A+ H+K+I   +Q +  LE+   TGR HQ+R     MGCPI GD KY  
Sbjct: 122 --DKEVKNSKKAVLHYKLIG-HSQNYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGF 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYD 327
                  S     + LHAR +   HP    + Q+TAP+P      W+  GF+ D
Sbjct: 179 PRSNPDGS-----ICLHARTVQFVHPVSKEMIQLTAPVPEG--NLWN--GFEMD 223


>gi|323488794|ref|ZP_08094034.1| putative RNA pseudouridine synthase yjbO [Planococcus donghaensis
           MPA1U2]
 gi|323397492|gb|EGA90298.1| putative RNA pseudouridine synthase yjbO [Planococcus donghaensis
           MPA1U2]
          Length = 291

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 64/284 (22%), Positives = 122/284 (42%), Gaps = 38/284 (13%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVR-IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           GQ+ V+ + V   + ++ G  V  I P       ++ E   L+               ++
Sbjct: 38  GQILVNGQEVTVRHVLEKGDAVTVIFPNEEHGKGLLAEDGDLE---------------IV 82

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSG 156
           YED  + +  KP    +Q       H  G L + V              +  RLD++TSG
Sbjct: 83  YEDEVLLIVEKP---PLQNTIPSREHPFGSLANIVAKHFNDHGIPSTLHIATRLDRDTSG 139

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++ +A+ R     +++  + +++++ Y +LV G     +  I   + +K     +   + 
Sbjct: 140 LVCIAKNRHIHHMISQQQQEKKMKRRYEALVHGQIDKTEFTITAPIGRK-----NTSIIE 194

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           ++  +   +A +  +V++   Q +  + +Q +TGRTHQ+RVH  H+G P+VGD  Y    
Sbjct: 195 REVREDGQFAETEVRVLENL-QGYAHVSLQLNTGRTHQIRVHLAHIGHPLVGDDLYGGKR 253

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
                  + N+  LH   ++L HP  G+ L   + L   M    
Sbjct: 254 D------LVNRQALHCTELELIHPVSGKPLFFHSALNDDMQSLL 291


>gi|117924690|ref|YP_865307.1| pseudouridine synthase [Magnetococcus sp. MC-1]
 gi|117608446|gb|ABK43901.1| pseudouridine synthase [Magnetococcus sp. MC-1]
          Length = 255

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 80/238 (33%), Positives = 121/238 (50%), Gaps = 9/238 (3%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           T  ++ L+S LLY D  + + NKPAGI V  G G   +++           + P L HRL
Sbjct: 5   TITANDLESRLLYRDGLLLIINKPAGIPVHAGPGGGANLEALFGGLRFGLPKAPALAHRL 64

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG LV+ R   A   L + F   ++QK YW++V G P   +  +   L K S    
Sbjct: 65  DRDTSGCLVLGRHAKALSKLGKLFSQGKVQKTYWAVVQGGPPQAQGSMDFPLYKISTAQQ 124

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  VV  + +    +++ ++V+   A    WLE+ P TGRTHQ+RVH  H+G PI GD 
Sbjct: 125 GWRMVV--DPEQGKSSLTLYRVLGRSA-THSWLELTPKTGRTHQIRVHCAHVGLPIEGDL 181

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
           +Y A       S  Q  L+LHAR + LP       + ++AP P  M    +  G++ +
Sbjct: 182 QYGA-----APSEPQLTLHLHARQIILPISASKAPINVSAPPPRAMRGLLEQCGYRAE 234


>gi|329955390|ref|ZP_08296298.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
 gi|328525793|gb|EGF52817.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
          Length = 600

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 70/239 (29%), Positives = 114/239 (47%), Gaps = 20/239 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ +     S+  +  ++YED  + V NKPAG+    G   A  +
Sbjct: 368 CEPILRHMLQGLEVDENPMLKELQSNKKELEIIYEDEWLAVVNKPAGMLSVPGKEDAASV 427

Query: 130 DGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              ++  + D+ G  P + HRLD  TSG+LVVA+T+   Q+L   F+ R IQK Y +L+ 
Sbjct: 428 YSVVRERYPDADG--PLIVHRLDMATSGLLVVAKTKQVHQNLQAQFKNRSIQKRYIALLQ 485

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+       +   L          +     + +    A++ F+V+         +   P 
Sbjct: 486 GMVSQDTGTVELPLCPNPLDRPRQM----VHAEYGKPAVTDFEVLKR-GDNRTRIAFYPR 540

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           TGRTHQLRVHA H   + CPI+GD  Y    +         +LYLHA  ++  HP  G+
Sbjct: 541 TGRTHQLRVHAAHPLGLHCPIIGDELYGKKAE---------RLYLHAETLEFTHPITGK 590


>gi|261342219|ref|ZP_05970077.1| tRNA pseudouridine synthase [Enterobacter cancerogenus ATCC 35316]
 gi|288315555|gb|EFC54493.1| tRNA pseudouridine synthase [Enterobacter cancerogenus ATCC 35316]
          Length = 261

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 108/242 (44%), Gaps = 17/242 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG
Sbjct: 1   MTLEILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++  +  A + L++ F   ++QK Y ++V G    +   +   L+++     D     
Sbjct: 61  VLLMGLSSEAGRLLSQQFEQHQMQKRYHAIVRG-WLTESGTLDYPLVEELDKIADKFAR- 118

Query: 217 KQNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             ++KG   A++ ++ +               ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 --DDKGPQPAVTDYRAMATTEMPVATSKFPTTRYSLVELLPKTGRKHQLRRHLAHLRHPI 176

Query: 267 VGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD K+      +        ++L LHA  + L HP  G  L I A L    ++     G
Sbjct: 177 IGDSKHGDLRQNRSAAEHFGCHRLMLHASELSLTHPFTGEPLSIRAGLDDVWMQALSQFG 236

Query: 324 FK 325
           ++
Sbjct: 237 WR 238


>gi|183603400|ref|ZP_02712152.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1087-00]
 gi|183569583|gb|EDT90111.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1087-00]
          Length = 278

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 67/279 (24%), Positives = 113/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D S   
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYSQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNLPILGDT 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    +L  T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFT 264


>gi|110642932|ref|YP_670662.1| tRNA pseudouridine synthase C [Escherichia coli 536]
 gi|191171222|ref|ZP_03032772.1| tRNA pseudouridine synthase C [Escherichia coli F11]
 gi|227888331|ref|ZP_04006136.1| TruC protein [Escherichia coli 83972]
 gi|300976014|ref|ZP_07173255.1| tRNA pseudouridine synthase [Escherichia coli MS 45-1]
 gi|300976318|ref|ZP_07173382.1| tRNA pseudouridine synthase [Escherichia coli MS 200-1]
 gi|301049449|ref|ZP_07196408.1| tRNA pseudouridine synthase [Escherichia coli MS 185-1]
 gi|331648518|ref|ZP_08349606.1| tRNA pseudouridine synthase C [Escherichia coli M605]
 gi|331658904|ref|ZP_08359846.1| tRNA pseudouridine synthase C [Escherichia coli TA206]
 gi|110344524|gb|ABG70761.1| hypothetical protein YqcB (putative RNA pseudouridylate synthase)
           [Escherichia coli 536]
 gi|190908522|gb|EDV68111.1| tRNA pseudouridine synthase C [Escherichia coli F11]
 gi|227834600|gb|EEJ45066.1| TruC protein [Escherichia coli 83972]
 gi|281179792|dbj|BAI56122.1| putative pseudouridine synthase [Escherichia coli SE15]
 gi|300298765|gb|EFJ55150.1| tRNA pseudouridine synthase [Escherichia coli MS 185-1]
 gi|300308560|gb|EFJ63080.1| tRNA pseudouridine synthase [Escherichia coli MS 200-1]
 gi|300410152|gb|EFJ93690.1| tRNA pseudouridine synthase [Escherichia coli MS 45-1]
 gi|307554763|gb|ADN47538.1| tRNA pseudouridine synthase C [Escherichia coli ABU 83972]
 gi|315293748|gb|EFU53100.1| tRNA pseudouridine synthase [Escherichia coli MS 153-1]
 gi|315298808|gb|EFU58062.1| tRNA pseudouridine synthase [Escherichia coli MS 16-3]
 gi|324015525|gb|EGB84744.1| tRNA pseudouridine synthase [Escherichia coli MS 60-1]
 gi|331042265|gb|EGI14407.1| tRNA pseudouridine synthase C [Escherichia coli M605]
 gi|331053486|gb|EGI25515.1| tRNA pseudouridine synthase C [Escherichia coli TA206]
          Length = 260

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLAIHAGLDDTWMQALSQFGWR 237


>gi|184156035|ref|YP_001844375.1| pseudouridylate synthase [Lactobacillus fermentum IFO 3956]
 gi|183227379|dbj|BAG27895.1| pseudouridylate synthase [Lactobacillus fermentum IFO 3956]
          Length = 294

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 61/285 (21%), Positives = 116/285 (40%), Gaps = 32/285 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           +G+ +VD +RV+   +I   Q + +       +  +   +                  ++
Sbjct: 36  AGEFQVDHRRVRPTTKILPNQPLTLTVQPEPGDATVATSEE--------------PLTIV 81

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---DSKGQKPRLTHRLDQETSGIL 158
           YED    V NKP G++   G  +    I   +K ++   D+   +P L  RLD++T+G+L
Sbjct: 82  YEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLVAKDAPDLRPHLITRLDRDTAGLL 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+   A+  ++       +QK Y ++V G        I         I      + ++
Sbjct: 142 LVAKHNVASSMISPQVEGHTMQKEYRAIVAGTFATDHGFIDAP------IARIKGQIERE 195

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A + +   +     +  + ++ H+GRTHQ+RVH   +G P++GDH Y  +   
Sbjct: 196 VNPAGQPAKTEYWAEESRGD-WTLVRLRLHSGRTHQIRVHMASVGHPLLGDHLYGGDLS- 253

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                + +   L+A ++    P     L     +P      WD L
Sbjct: 254 -----MTDHQALYASHLAFTDPFTQTNLAFEVEMPVAFKTLWDGL 293


>gi|170727628|ref|YP_001761654.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169812975|gb|ACA87559.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 285

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 67/262 (25%), Positives = 114/262 (43%), Gaps = 19/262 (7%)

Query: 81  QKILDSSVNLTKHSD--FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            K +++ VN  +  D    +  +L+ED  I V +KPAG+ V             ++   D
Sbjct: 17  NKEIEAGVNEAELHDETAPEIEILFEDDDIVVIHKPAGLLVHRSYLARRERFFAMQMTRD 76

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             G      HRLD+ TSGIL+ A++   A +L E F  + ++K Y ++V G         
Sbjct: 77  KVGCHVFPVHRLDRPTSGILLFAKSSEMANNLCEQFSAKTVEKQYLAIVRGNMHEADTLD 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPH 248
               ++    G   V       K A  A++ ++ +               ++  +++ PH
Sbjct: 137 YALKVELDDHGDKDV----DPNKAAQEAVTSYQPLLNTEIPFPSGRYATSRYAMVKLIPH 192

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPE-GGRL 305
           TGR HQLR H  H+  PIVGD  +    +  F       N+L+L A+ +   HP  G R+
Sbjct: 193 TGRKHQLRRHMAHLRHPIVGDTTHGDGKQNKFFREHFAINRLWLIAKSLAFDHPRSGERI 252

Query: 306 QITAPLPAHMVKTWDSLGFKYD 327
            I   L    +  +++ G+  +
Sbjct: 253 TIETELEKEWLTLFEAFGWDDE 274


>gi|194439387|ref|ZP_03071464.1| pseudouridine synthase, RluA family [Escherichia coli 101-1]
 gi|194421646|gb|EDX37656.1| pseudouridine synthase, RluA family [Escherichia coli 101-1]
 gi|323970730|gb|EGB65984.1| RNA pseudouridylate synthase [Escherichia coli TA007]
          Length = 230

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 69/227 (30%), Positives = 107/227 (47%), Gaps = 17/227 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMV 316
            Y +            +L LHA  + + HP  G  +   A  PA   
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADFE 220


>gi|95931222|ref|ZP_01313943.1| pseudouridine synthase [Desulfuromonas acetoxidans DSM 684]
 gi|95132741|gb|EAT14419.1| pseudouridine synthase [Desulfuromonas acetoxidans DSM 684]
          Length = 295

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 137/325 (42%), Gaps = 42/325 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             VE +E  +    + + H    +   L+++L+ G+V+  +  V   ++++ G V+ +P 
Sbjct: 4   FTVEANEIPLSPLAFLQRHISAASKSYLRQLLKKGKVKGPRGVVSEQDQLKLGDVLILPD 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                       ++ +      + S   +  +LYE  +I + +KP+G+++    G   H 
Sbjct: 64  S----------GRLSELLAATAQPSLEQQLFILYESREILIVDKPSGLAIHSSEG---HQ 110

Query: 130 DGFLKSWVDS------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           D  L + VD          +    HRLD ETSG ++  + + A   L + F    ++K Y
Sbjct: 111 DRNLAALVDELIRSRGDAYQVAPIHRLDLETSGPVLFGKGKKACSELGKLFMCHEVEKSY 170

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G                   G   +     ++     A + F+ +D   Q    L
Sbjct: 171 LALVAGK----------------TPGRGLIQSEVPSKGKTKEAQTAFQALDRNEQ-ASLL 213

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++  +TGR HQ+R     +G P+ GD +Y              +L+LH   +    P  G
Sbjct: 214 KVTLYTGRQHQIRRQLAELGHPLFGDRRYRGQQPDALP-----RLFLHCCQLAFIDPFSG 268

Query: 304 -RLQITAPLPAHMVKTWDSLGFKYD 327
             ++I +PLPA + +  D++G +Y 
Sbjct: 269 APVEINSPLPADLSQFLDTVGLRYP 293


>gi|42518750|ref|NP_964680.1| hypothetical protein LJ0825 [Lactobacillus johnsonii NCC 533]
 gi|41583036|gb|AAS08646.1| hypothetical protein LJ_0825 [Lactobacillus johnsonii NCC 533]
          Length = 299

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 65/286 (22%), Positives = 115/286 (40%), Gaps = 36/286 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G V V+  R   +  + +G  V         N  +K                  K  +++
Sbjct: 38  GMVLVNHHRRYTSYLLHAGDEVIFILGEEKENKWLK--------------PSSKKLNIVF 83

Query: 104 EDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQ---KPRLTHRLDQETSGILV 159
           E     V NK AGI         +  +   L  +   + Q   KP +  RLD++TSG+++
Sbjct: 84  EQKDYLVINKDAGILSIPSRYEDSDAVVNRLLHYFQQQKQTDLKPHVITRLDRDTSGLVL 143

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN--KKECIANWLLKKSHIGGDYVHVVK 217
           V +   A    ++  +   I+K + ++V G  +   ++  I   + K          V +
Sbjct: 144 VGKNAVAHARFSKMEKNEFIKKYH-AIVHGNFEEAQRQGTIDAPIGKID------AGVKR 196

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   +++ ++V+D   +    +E+Q  TGRTHQ+RVH  ++G P+ GD  Y    K
Sbjct: 197 GVVNNGQRSVTKYRVLDQV-KGASLIELQLLTGRTHQIRVHMQYLGHPLFGDPLYG--IK 253

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            NF      +  L+  Y++   P    R +I    P  M   W +L
Sbjct: 254 DNF-----KRQALNCFYLEFDDPFSEKRQKIEIADPIDMEILWKNL 294


>gi|289450514|ref|YP_003475442.1| putative rRNA pseudouridylate synthase C [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
 gi|289185061|gb|ADC91486.1| putative rRNA pseudouridylate synthase C [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
          Length = 327

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 144/326 (44%), Gaps = 29/326 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++ N++   ++ R     YP +     QK LR+  + +D KR+K +   ++GQ +R
Sbjct: 1   MREFIINNEQSGKKVVRILTTLYPTVPAYIFQKALRNKDLMLDGKRLKNDVTAEAGQTLR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I          +K++ +  +S N  + +      ++YED  I + NKP G++V  G    
Sbjct: 61  IY---------VKDEVLAQASDNTDRKNQLPSYTVVYEDKNIILINKPQGLTVHPGKNTP 111

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            H     K   D   +   L HRLD+ T G+++VA+ +     + E+   +++ K Y  L
Sbjct: 112 PHSTLIEKLRADYNDENLTLCHRLDRNTGGLVLVAKNKVTLGKINEALAEQQVIKRYRCL 171

Query: 187 VWGIPK-NKKECIANW-------LLKKSHIGGDYVHVVKQNEKGANYAISHFKVID---- 234
           V GIP   +   I++           +     D V +  + +       + ++V+     
Sbjct: 172 VRGIPDIGRDVYISDGDSMHELNAFWEKPANSDEVFIHDEQQADDLPICTRYRVLHIFTA 231

Query: 235 --CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                +    LE++  TGRTHQ+R H  H+G PI+GD KY    +  F S  +NK   H 
Sbjct: 232 LAADGEPISELEVELVTGRTHQIRAHLAHIGHPILGDGKYG---RNEFNSQFKNK---HG 285

Query: 293 RYMDLPHPEGGRLQITAPLPAHMVKT 318
             ++        L     LPA + + 
Sbjct: 286 GKLNKQQLFATTLMFGNDLPAGLTEL 311


>gi|152978874|ref|YP_001344503.1| tRNA pseudouridine synthase C [Actinobacillus succinogenes 130Z]
 gi|150840597|gb|ABR74568.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 238

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 100/240 (41%), Gaps = 17/240 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D  I   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L
Sbjct: 2   LDILYQDEFIVAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A     A  L   F  + ++K Y ++V G    +        +++  I   +     Q
Sbjct: 62  LFALHSDIANLLCRQFEGKTVRKSYLAVVRGYLSGEARIDYALKIRRDKIADKF----SQ 117

Query: 219 NEKGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             K A  A++ +           V      ++  + + PHTGR HQLR H  H+  PI+G
Sbjct: 118 ENKEAQAAVTDYTGLQTAEMPWAVGKYQTCRYSLVRLMPHTGRKHQLRRHMKHIFHPILG 177

Query: 269 DHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           D +Y    +    +     ++L LHA  +   HP    RL + A      +K     G+ 
Sbjct: 178 DTQYGDLHQNRALAEQTQVSRLMLHAEKLAFNHPVNQTRLVLQAGFDEQWLKLLRMFGWN 237


>gi|295097354|emb|CBK86444.1| tRNA pseudouridine synthase C [Enterobacter cloacae subsp. cloacae
           NCTC 9394]
          Length = 261

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 103/241 (42%), Gaps = 17/241 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG
Sbjct: 1   MTLEILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++  +  A + L++ F   ++QK Y ++V G   +        + +   I   +    
Sbjct: 61  VLLMGLSSEAGRLLSQQFEQHQMQKRYHAIVRGWLTDSATLDYPLVEELDKIADKFAR-- 118

Query: 217 KQNEKGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              +KG   A++ ++                 ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 --EDKGPQPAVTDYRGMATTELPVATSKFPTTRYSLVELLPKTGRKHQLRRHLAHLRHPI 176

Query: 267 VGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD K+      +        N+L LHA  + L HP  G  L I A L    ++     G
Sbjct: 177 IGDSKHGDLRQNRSAAEHFGCNRLMLHASELRLTHPFTGEPLTIRAGLDEVWMQALSQFG 236

Query: 324 F 324
           +
Sbjct: 237 W 237


>gi|24380298|ref|NP_722253.1| putative pseudouridylate synthase [Streptococcus mutans UA159]
 gi|24378312|gb|AAN59559.1|AE015019_4 putative pseudouridylate synthase [Streptococcus mutans UA159]
          Length = 288

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 61/281 (21%), Positives = 109/281 (38%), Gaps = 30/281 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    V V+ + V + + ++ G ++++                 D  +  
Sbjct: 26  IPR-KIRHFLRIKKNVTVNSQAVNWQSLVRRGDIIQLNF------------DNTDYPIKK 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      LY+D  + + NK  G+           +   + ++V   GQ   + HRL
Sbjct: 73  IPMGNKTLIDCLYQDEHLIIVNKIEGMKTHANDPNEIALLNHVSAYV---GQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D +TSG ++ A+       L      + I++ YW+L  G            + +  H   
Sbjct: 130 DMKTSGTVMFAKNPFILPILNRLLENKSIKREYWALAQGQFSEHAIIYREPIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             V     + K    AI+   ++  F+     ++ Q  TGRTHQ+RVH  +    IVGD 
Sbjct: 190 KRV----VDHKHGQTAITQVSLLKHFSNNTSLIKCQLQTGRTHQIRVHLAYHDHAIVGDP 245

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
            Y     G        +L LHA  +   HP    ++++ AP
Sbjct: 246 LYSQQTAG--------RLMLHAHQLTFTHPLTLEKIKVEAP 278


>gi|290473651|ref|YP_003466523.1| pseudouridine synthase [Xenorhabdus bovienii SS-2004]
 gi|289172956|emb|CBJ79727.1| pseudouridine synthase [Xenorhabdus bovienii SS-2004]
          Length = 250

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 66/240 (27%), Positives = 105/240 (43%), Gaps = 17/240 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y+D  I   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L
Sbjct: 2   LDIIYQDDHIVAVNKPAGWLVHRSWLARHETVFVMQTLRDQIGQHVFPVHRLDKPTSGVL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A +   A+ L++ F    IQK Y ++V G  +         + +   I   +      
Sbjct: 62  LMALSSEVARTLSQQFECHHIQKTYHAIVRGYVEGDGIIDYALMEELDKIADKFA----D 117

Query: 219 NEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            ++ A  AI+H++ +               +F  LE+ P TGR HQLR H  H+  PI+G
Sbjct: 118 TDREAQSAITHYRSLAKVECPVEIGRYPTSRFSLLELMPKTGRKHQLRRHMSHLRHPIIG 177

Query: 269 DHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           D  +      +G        +L LHA  + L HP  G  L +TA   A      +  G++
Sbjct: 178 DTTHGDLRQNRGVVKYYQTGRLMLHASQLQLAHPVTGEDLLLTARWEASWQHLLEQFGWQ 237


>gi|217324150|ref|ZP_03440234.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           TW14588]
 gi|217320371|gb|EEC28795.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           TW14588]
          Length = 279

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 68/221 (30%), Positives = 106/221 (47%), Gaps = 15/221 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFRERVPKKQYVTRVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            Y +            +L LHA  + + HP  G  +   AP
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|300174185|ref|YP_003773351.1| ribosomal large subunit pseudouridine synthase A [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299888564|emb|CBL92532.1| Ribosomal large subunit pseudouridine synthase A [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 306

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 68/329 (20%), Positives = 123/329 (37%), Gaps = 43/329 (13%)

Query: 5   TYVQYVVVENDEENMRLDRWFKN-HYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           T+V    + N      + +  K    P      ++  LR      V+   V  +  +Q  
Sbjct: 4   TWVHQFTITNQNAGQSVKQTLKMWLLPQ----RIRGALRIKKNYLVNGNEVPTSYELQVN 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +            +Q+   +S +    +   +  +++E     V NKPAG+ +   
Sbjct: 60  DKLTLRF----------DQEDFRTSESHYPPNGMQRVGIVFESEDFVVVNKPAGMKMHP- 108

Query: 123 SGIAYHIDGFLKSWVDSKGQ-----------KPRLTHRLDQETSGILVVARTRAAAQHLT 171
                  +  L +++ +              +P + HRLD+ETSG ++VA+       L 
Sbjct: 109 --HTLTENDTLLNYLAADFSERHLVSAGVVARPYMVHRLDRETSGAVIVAKNPVVVPILN 166

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
                + I++ Y + V G        I   +          +     N      AI+H+ 
Sbjct: 167 RMLADKDIKRTYLAWVNGKMTGNSGTINAPIGVDLDDDRKRM----VNGIDEQLAITHWT 222

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
            I    QK   L +Q  TGR HQ+RVH   +G PI+GD  Y +            ++ LH
Sbjct: 223 QIHMVFQK-TLLRVQLETGRMHQIRVHLAAIGHPIIGDSLYGSAMGTV-------RMMLH 274

Query: 292 ARYMDLPHPEGGRLQ-ITAPLPAHMVKTW 319
           A  ++L  P  G  + ++ P+P    +  
Sbjct: 275 ATSIELTIPFSGDTKMVSVPVPPDFPRQL 303


>gi|2828514|sp|P44197|TRUC_HAEIN RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
          Length = 239

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 106/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDGFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +++ PHTGR H LR H  H+  PI GD 
Sbjct: 120 KEPQEAITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHXLRXHMKHVFHPIXGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           +Y      +   +    ++L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 180 QYGDLHQNRALMSHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQWQQLMNQFGWE 237


>gi|332637468|ref|ZP_08416331.1| pseudouridylate synthase [Weissella cibaria KACC 11862]
          Length = 298

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 64/294 (21%), Positives = 122/294 (41%), Gaps = 25/294 (8%)

Query: 31  HINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +    ++   R G+ + ++      + R++ G V+ +   + A   +     + D+S  
Sbjct: 27  QVPR-RIRGNFRMGRRILLNGVYQPTSTRLKPGDVLDMT-WLPADFEVADSHYVPDASQP 84

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           L          +L+E+  + V NK  G+       G    +  F ++++  +G+   + H
Sbjct: 85  LD---------VLFENDDLIVVNKRKGVKTHPNSPGEDGTMMNFAQAYLAEQGKSAYMVH 135

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD +T+G L++A+       L +  R + I++ Y + V G        I   +      
Sbjct: 136 RLDGDTTGALIIAKNPYVVPMLNQMLRDKTIKRTYLAWVCGNITATSGTIDAPIGDNPVD 195

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                     N   A  A++++  +    Q    + +   TGRTHQ+R+H  H+G P+VG
Sbjct: 196 SRTR----TVNGPNARPAVTYWHKVHTVYQN-TLVRLALATGRTHQIRLHMKHLGYPLVG 250

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDS 321
           D  Y  +      S   + L LHA  + LP P    ++ + APLP    +    
Sbjct: 251 DPLYNPD------SNYSDGLLLHAAAIQLPIPFTNDVKSVGAPLPPTFPRNLRK 298


>gi|76800233|ref|ZP_00781992.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
 gi|76584552|gb|EAO61413.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
          Length = 267

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 65/279 (23%), Positives = 118/279 (42%), Gaps = 30/279 (10%)

Query: 31  HINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            ++   L KI  R G++ V+ +       ++ G VV I               I D   +
Sbjct: 12  DVSRGLLAKIKYRGGKIFVNGEEQNAIFLLEIGDVVTI--------------DIPDEPSH 57

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRL 146
            T         ++YED    + NKP G +    S  +  I  F+K +    +   Q+  +
Sbjct: 58  ETLEPVPHDLDIVYEDDHFLILNKPFGFASIPSSIHSNTIANFIKHYYVSNNYANQQVHI 117

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKK 205
             RLD++TSG+++ A+   A   L +  + + I+K Y++LV G         I   + + 
Sbjct: 118 VTRLDRDTSGLMLFAKHGYAHARLDKQLQAKAIEKRYYALVSGSGDLADSGDIIAPIARD 177

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                    + ++  +   YA + ++V+  +      ++++ HTGRTHQ+RVH  H+G P
Sbjct: 178 VD-----SIITRRVHESGKYAHTSYQVVARYGD-VRLVDIKLHTGRTHQIRVHFAHIGFP 231

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++GD  Y             N+  LH  +     P  G+
Sbjct: 232 LLGDDLYGGRM-----DLGINRQALHWXFFVFLRPFYGK 265


>gi|260432354|ref|ZP_05786325.1| ribosomal large subunit pseudouridine synthase A [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260416182|gb|EEX09441.1| ribosomal large subunit pseudouridine synthase A [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 215

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 64/223 (28%), Positives = 108/223 (48%), Gaps = 13/223 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++ T +       +L+ED+++ V NKPAG+    G G   H+   L + V +   +  L 
Sbjct: 1   MSDTYNPPRTPLDVLHEDAQVIVVNKPAGLLSVPGRG--AHLADCLLTRVQAAFPQALLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG+++ A+T  A ++L + F  R  +K Y + VWG  + K   +   L+    
Sbjct: 59  HRLDRDTSGVMIFAQTPHAQKYLGQQFENRLARKTYVARVWGRVEPKTGTVDLPLIVD-W 117

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  V          A++ ++V+         + + P TGR+HQLRVH   +G PI+
Sbjct: 118 PNRPRQMVCHD---TGKPAVTDWRVV-RHEGDTTRVRLFPKTGRSHQLRVHMQALGHPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           GD  Y      +F      +L LH+  + + HPE G  ++  A
Sbjct: 174 GDPFYAEGPARDFP-----RLMLHSEELRIKHPEDGVSMKFRA 211


>gi|257463597|ref|ZP_05627988.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
 gi|317061151|ref|ZP_07925636.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
 gi|313686827|gb|EFS23662.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
          Length = 289

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 73/320 (22%), Positives = 133/320 (41%), Gaps = 38/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   +VE + +   +  + K      +   L+K+    ++ ++ K++K   +        
Sbjct: 1   MHKYIVEPEYDGYEIGEYLKET-KGYSGRGLRKL----EIYLNGKKIKNTAK-------- 47

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
               +  LN I+    I++           +   ++YED  + V NK A +     +   
Sbjct: 48  ---KVRKLNRIL----IVEKEKKTGIRPMEIPLDIVYEDENLLVLNKQANLVTHPTTKKV 100

Query: 125 IAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            A   +G +  ++ + G+   PR  +RLD  T+G+++V +   +  +L E      ++K 
Sbjct: 101 DATLANGVVAYFLKTTGKTMVPRFYNRLDMNTTGLIIVTKNAYSQAYLQEKT---EVRKS 157

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFC 241
           Y ++V G+ +  +  I   + K   +G D   V    EKG   A +  KV+  F Q    
Sbjct: 158 YQTIVKGMVEQDEFYITRPIGK---VGEDLRRVELPVEKGGQEAKTFVKVLKRFPQKNRT 214

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            LE+   TGRTHQ+R H    G PIVGD  Y        +     +  LHA  +   +P+
Sbjct: 215 LLEVTLFTGRTHQIRAHLSLEGYPIVGDDLYGG------SEETIKRQLLHAYRLCFQNPK 268

Query: 302 G-GRLQITAPLPAHMVKTWD 320
                +I   LP  M    +
Sbjct: 269 NAEEQEIVIDLPQDMKDYLN 288


>gi|157962710|ref|YP_001502744.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157847710|gb|ABV88209.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 284

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 71/279 (25%), Positives = 120/279 (43%), Gaps = 23/279 (8%)

Query: 63  QVVRIPPVINALNHIIKEQKI-LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              + P     L+  + EQ +  D    +  H +     +L+ED  I V +KPAG+ V  
Sbjct: 3   DNTKNPSQSEQLDESLLEQDLCQDEEQEIAPHIE-----VLFEDDDIVVIHKPAGLLVHR 57

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                      ++   D  G      HRLD+ TSGIL+ A++   A  L E F    + K
Sbjct: 58  SYLARRERFFAMQLTRDLVGCHVFPVHRLDRPTSGILLFAKSSEMANVLCEQFAAHTVDK 117

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-------- 233
            Y ++V G   ++   +   L ++    GD         K A  A++ +K +        
Sbjct: 118 EYLAIVRGNM-HEAGTLDYALKEELDELGDK---DVDPNKAAQDAVTSYKPLLNSEIPFS 173

Query: 234 --DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLY 289
                  ++  +++ PHTGR HQLR H  H+  PI+GD  +    +  F  +    N+L+
Sbjct: 174 SGRYATSRYALVQLSPHTGRKHQLRRHMAHLRHPILGDTTHGDGKQNKFFRSHFGINRLW 233

Query: 290 LHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLGFKYD 327
           L A+ +   HP  G R+ +   L A  +  ++ LG+  +
Sbjct: 234 LIAKKLSFNHPRSGERMSVETELEAEWLSLFEGLGWHEE 272


>gi|26249194|ref|NP_755234.1| tRNA pseudouridine synthase C [Escherichia coli CFT073]
 gi|34582426|sp|Q8FEF9|TRUC_ECOL6 RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|26109601|gb|AAN81804.1|AE016765_206 Hypothetical protein yqcB [Escherichia coli CFT073]
          Length = 260

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 103/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +         +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLAEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLAIHAGLDDTWMQALSQFGWR 237


>gi|327467897|gb|EGF13387.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK330]
          Length = 291

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 121/303 (39%), Gaps = 32/303 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   ++ G  + +
Sbjct: 4   TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLAINWQTVVKPGDDICL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+          
Sbjct: 62  IFDEEDY----PQKTILFGNGELVEE--------LYQDQHLIIVNKPEGMKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+LV
Sbjct: 110 ALLNHVSAYV---GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLEKREISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    K     + + +  H     +     + +   YA +H   +  F Q    ++ Q 
Sbjct: 167 QGKLPAKNLIYKDKIGRDRHDRRKRL----VDPRKGLYAETHVTRLKQFGQ-AALVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G P+VGD  Y    KG        +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLGHHGHPLVGDPLYHPQPKG--------RLMLHAHRLTFTHPFTLEKIT 273

Query: 307 ITA 309
           + A
Sbjct: 274 VEA 276


>gi|312793590|ref|YP_004026513.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312180730|gb|ADQ40900.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 293

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 70/262 (26%), Positives = 130/262 (49%), Gaps = 15/262 (5%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKP 114
           R++    +R  P I +++   +E  +++  +  +K +         +LYED+     NKP
Sbjct: 33  RLKVHGQIRFIPPIYSVHQYPQENAVIEVDLISSKSNIAPVEGNIDILYEDNFFLFVNKP 92

Query: 115 AGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           +G+      G  +  I  +++ +++SK     + +RLD++TSGI+V A+       ++  
Sbjct: 93  SGLPSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRLDKDTSGIVVFAKNSYFHSIVSHE 152

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  R+++K Y ++V G    K   I   + K+S  G     + ++  +  ++A ++++VI
Sbjct: 153 FEKRQVEKTYIAIVHGRLAKKSGLIEKPI-KRSDDG-----IKREIHQDGSFASTYYEVI 206

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D F + F  L+++P TGRTHQLRVH   +G PIVGD  Y      N        L+ ++ 
Sbjct: 207 DSF-ENFSLLKLKPITGRTHQLRVHLSSIGYPIVGDCIYGKERTQNTPLL----LHAYSI 261

Query: 294 YMDLPHPEGGRLQITAPLPAHM 315
                  +     IT+PLP + 
Sbjct: 262 RFTFKLIDNKVYDITSPLPHYF 283


>gi|206577943|ref|YP_002236857.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae 342]
 gi|288933804|ref|YP_003437863.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|290511116|ref|ZP_06550485.1| tRNA pseudouridine synthase C [Klebsiella sp. 1_1_55]
 gi|206567001|gb|ACI08777.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae 342]
 gi|288888533|gb|ADC56851.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|289776109|gb|EFD84108.1| tRNA pseudouridine synthase C [Klebsiella sp. 1_1_55]
          Length = 264

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 63/257 (24%), Positives = 113/257 (43%), Gaps = 18/257 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDDWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G   ++       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMDEALLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KDPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPILGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           K+      +        ++L LHA  + L HP  G  L + A      ++     G++  
Sbjct: 180 KHGDLRQNRSAAEHFGCHRLMLHASELSLTHPFTGEPLTLRAGFDEVWMRALSQFGWRGL 239

Query: 328 RNLYIKRLYSQDECKQN 344
             L  +R+   D+C Q+
Sbjct: 240 LPLN-ERVEFADDCGQD 255


>gi|125625156|ref|YP_001033639.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|124493964|emb|CAL98959.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|300071964|gb|ADJ61364.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris NZ9000]
          Length = 290

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 122/307 (39%), Gaps = 34/307 (11%)

Query: 23  RWFKNHYPH---INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           +   +       +       +       V+ + +  N  + +G  V +       +++  
Sbjct: 14  QVLSDLLEKTWLVPRKQRHFLRTKKHSLVNDQIIDENQLLHAGDKVTLIFDKEDFSNLS- 72

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                       K      + +LYED  + V NKP G+   G +     +   + + ++ 
Sbjct: 73  -----------LKFGSASLADILYEDEHLIVVNKPEGMKTHGNTADEIALQNHVAAAIN- 120

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             Q   + HRLDQ TSG ++ A+ +     L + F   +I + Y +LV G    +   I 
Sbjct: 121 --QNVFVVHRLDQATSGAVLFAKNQFVLPILGKMFEENKIHREYLALVAGHFLEETFTIN 178

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + +  H     +       K    AI+H ++I  F  K   ++    TGRTHQ+RVH 
Sbjct: 179 QAIGQNRHEKNKRII-----SKHGQKAITHVQLIQNFTDK-SLVKCILDTGRTHQIRVHL 232

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             +G PI+GD  Y             ++L LHA  + +PHP   + L I+AP P+     
Sbjct: 233 SSLGHPIIGDALYGQKST--------SRLMLHAESIIIPHPFTNQLLNISAPSPS-FSNI 283

Query: 319 WDSLGFK 325
            + +  K
Sbjct: 284 LNKIKKK 290


>gi|295100993|emb|CBK98538.1| Pseudouridylate synthases, 23S RNA-specific [Faecalibacterium
           prausnitzii L2-6]
          Length = 303

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 65/333 (19%), Positives = 121/333 (36%), Gaps = 54/333 (16%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           Y  V  + + M L  + +      +     K   SG    D   V  N R+++GQV+   
Sbjct: 4   YFKVPPEADGMLLRGFLRRCSVSTDLSRAVKFRGSGF-FADGVPVLANRRVEAGQVISFE 62

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIA 126
                          L          D +   ++YED+   V  KP  ++V       + 
Sbjct: 63  ---------------LPPEGEGVAPQDDIPVDVVYEDAFALVVEKPPHLAVHPTLNYPLD 107

Query: 127 YHIDGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +G+   +    +    R  +R+D++TSG+++ A+   AA  L +     R++K+Y++
Sbjct: 108 TLANGYAAWALRQGRSPVFRPVNRIDKDTSGLVLAAQNGYAAPLLAQ-----RVEKLYYA 162

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  G        I   + ++         + +        + + + ++            
Sbjct: 163 VAEGELPLGPGVIDAPIGRQGE-----SIIGRCVTPDGKPSRTEYTIL-RAENGLSLAAC 216

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL------PH 299
            P TGRTHQ+RVH   +G P+ GD  Y  +           +  LH            P 
Sbjct: 217 VPVTGRTHQIRVHFASIGHPLAGDDLYGGSRAR------IGRQALHCAKQTFWVPRCEPM 270

Query: 300 PEGGRLQ------------ITAPLPAHMVKTWD 320
           P+G R++            + +PLP  M   +D
Sbjct: 271 PDGIRIEVPVDETTLRPVTVESPLPEDMAALFD 303


>gi|82545090|ref|YP_409037.1| tRNA pseudouridine synthase C [Shigella boydii Sb227]
 gi|81246501|gb|ABB67209.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|332091999|gb|EGI97077.1| RNA pseudouridylate synthase family protein [Shigella boydii
           3594-74]
          Length = 260

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  +  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVSVNKPSGWLVHRSWLDRDEKVVVMQTVRNQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|301794949|emb|CBW37412.1| RNA pseudouridylate synthase [Streptococcus pneumoniae INV104]
          Length = 278

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 65/279 (23%), Positives = 112/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D     
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYPQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQYLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETYVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    +L  T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFT 264


>gi|296122965|ref|YP_003630743.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
 gi|296015305|gb|ADG68544.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
          Length = 246

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 70/234 (29%), Positives = 112/234 (47%), Gaps = 17/234 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+   V  KPAG+   G      ++       +  + QKP      L HRLD+  S
Sbjct: 6   ILFEDNHCLVVEKPAGVLTMGDETGDENMVQLAMDDLKIRHQKPGNVYVGLVHRLDRPVS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A+T  AA  L+  FR R  +K+Y ++V G        I +WL+K      ++  V
Sbjct: 66  GVLLLAKTSKAASRLSAQFREREPEKVYLAIVEGQLNPAAGEIVDWLIKD--QERNHTRV 123

Query: 216 VKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                 GA  A   ++ ++           +E+QP TGR+HQ+RV   H G  I+GD +Y
Sbjct: 124 TSPQTPGAKQAKLRYRQLETLVTPEGIRTLVEVQPMTGRSHQIRVQLAHAGASILGDLRY 183

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +       +P+   + LHAR +   HP   + L I APLP+      + L ++
Sbjct: 184 GSK------TPLGKMIALHARSLTFEHPVQKQPLTIYAPLPSDWKPFMNPLLWE 231


>gi|326692754|ref|ZP_08229759.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc argentinum
           KCTC 3773]
          Length = 300

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 60/282 (21%), Positives = 115/282 (40%), Gaps = 33/282 (11%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G +  + + V  ++ +  G  V I       N ++                D+    +++
Sbjct: 37  GAILKNGQPVYTSDYLDDGDEVTIVMPTEKSNDLV--------------VPDYKPLNIIF 82

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHI-DGFLKSWVDSKGQK---PRLTHRLDQETSGILV 159
           E+    V +KP G++   G     H     +K  ++    +   P +  RLD++TSGI++
Sbjct: 83  ENEHWLVVDKPYGVTTVPGHADRLHTLVNQVKGHLEETNAEDLVPHVVTRLDRDTSGIVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ R A   L +  +   ++K Y +   GI       I   + +   + GD++    ++
Sbjct: 143 LAKHRFAHAVLDQQLQEHTVEKFYLAYTSGILPEDHGDINAPIGR---VEGDFIKREVRD 199

Query: 220 EKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +     + + + V   + +        + +Q HTGRTHQ+RVH  ++G P+VGD  Y   
Sbjct: 200 D--GKPSRTEYWVERRYDEDGDNPMTRVRVQLHTGRTHQIRVHFQNIGHPLVGDDLYGGP 257

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
                      +  LHA +M    P  G   +    LP  + 
Sbjct: 258 LWHGLE-----RQALHAYHMKFYDPFIGDYREFNTKLPEDLK 294


>gi|319900985|ref|YP_004160713.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           helcogenes P 36-108]
 gi|319416016|gb|ADV43127.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           helcogenes P 36-108]
          Length = 223

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 67/219 (30%), Positives = 111/219 (50%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKQYLKEKYDKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E F+   ++K YW++V   P  ++  + N++++       Y + 
Sbjct: 63  GLVVFAKTGKALSRLNEMFKNSEVKKTYWAVVKNQPPEEEGELVNYMVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   G+  AI H+++I   +Q +  LE+   TGR HQ+R     +GCPI GD KY   
Sbjct: 122 -DKERPGSKRAILHYRLIG-KSQNYYLLEIDLKTGRHHQIRCQLAKIGCPIKGDLKYGFP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                 S     + LHAR++   HP     +++ AP+P+
Sbjct: 180 RSNPDGS-----ICLHARFIRFVHPVSKETIEVEAPIPS 213


>gi|294678837|ref|YP_003579452.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           capsulatus SB 1003]
 gi|294477657|gb|ADE87045.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           capsulatus SB 1003]
          Length = 217

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 68/220 (30%), Positives = 102/220 (46%), Gaps = 12/220 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                  +L+ D +I V +K +G+    G G   H    L   +     +  L HRLD +
Sbjct: 8   PPSEPPRILHADHEILVVDKQSGLLSVPGKG--DHKADCLIERLKGAFPQVLLVHRLDGD 65

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V A T  A +HL   F  R+ +K Y + +WG  + K   +   L           
Sbjct: 66  TSGVMVFALTAHAQRHLGLQFETRQTKKHYLARLWGHLEPKAGRVDLPLCVD-WPNRPKQ 124

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           HV   + +    A + +KV+         + + P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 125 HV---DPENGKPAQTDWKVLRHDPDGTTRVRLTPLTGRSHQLRVHMLELGHPILGDPFYA 181

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                +F      +L LHA  + L HP+GG+ +  TAP P
Sbjct: 182 EGPARDFP-----RLMLHAESLRLRHPDGGQYMTFTAPCP 216


>gi|257886368|ref|ZP_05666021.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257822224|gb|EEV49354.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
          Length = 285

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 64/265 (24%), Positives = 111/265 (41%), Gaps = 28/265 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R   V ++++   F++ ++    + +              +  D +    +  D     
Sbjct: 36  IRK-NVWINQQPALFHHEVKGNDQITLLF------------EETDYNYQEVQLGDAAHIR 82

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+                L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+       L      + I + Y ++VWG        I N + +  H     V     +
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGEIAKDM-TITNKIGRDRHDRRKRV----VD 197

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +K    A++H  V    +++         TGRTHQ+RVH  H G PIVGD  Y       
Sbjct: 198 DKNGQSALTHVTVNKVLSEQTQVY-CVLETGRTHQIRVHLAHKGHPIVGDPLY------- 249

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR 304
             +    +L LHA  + + HP    
Sbjct: 250 -QNRTAERLMLHALELHMIHPFTQE 273


>gi|269121328|ref|YP_003309505.1| pseudouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268615206|gb|ACZ09574.1| pseudouridine synthase, RluA family [Sebaldella termitidis ATCC
           33386]
          Length = 285

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 79/285 (27%), Positives = 133/285 (46%), Gaps = 21/285 (7%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           + + E +RLDR+ +          + + +R G+V+++ K+ K N R+  G V+ I  +  
Sbjct: 6   DENMEGVRLDRFLRKKLKDTALNTIFEYIRKGKVKINGKKKKENYRLVLGDVIEIKSLEE 65

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           +      E        +L    D    ++ +ED    + NKP G++V  G+G  Y +   
Sbjct: 66  S------ENTEKKHYSSLRIDKDRYMKMVFFEDDDCLIINKPGGVAVHKGTGNQYGLAEV 119

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            KS    K +     +R+D+ET G+L+ A+     ++LTE  R   ++K Y ++V GI  
Sbjct: 120 YKSIY--KNENLNFANRIDKETKGLLLGAKNLKFLRYLTEKIRNNELEKRYIAVVSGIIT 177

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +  I N+L  K +       VV  +++    A + FK I     K+  LE++  TGR 
Sbjct: 178 EDEFTIDNFLETKEN------KVVVSDKENGKAAKAVFKKIKTIKNKYTVLEVELITGRK 231

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           HQ+RV    MG PI GD KY +          + +L L A Y+  
Sbjct: 232 HQIRVQLADMGFPIAGDKKYGSR-------NTRGELMLLAYYLKF 269


>gi|56964283|ref|YP_176014.1| ribosomal large subunit pseudouridine synthase D [Bacillus clausii
           KSM-K16]
 gi|56910526|dbj|BAD65053.1| ribosomal large subunit pseudouridine synthase D [Bacillus clausii
           KSM-K16]
          Length = 301

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 68/308 (22%), Positives = 130/308 (42%), Gaps = 32/308 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           +++  + L  + +     ++   L  +  + G +RV++      + +++G +V +     
Sbjct: 11  DEDAPLLLRTFLREK-KQVSKRLLAAVKFKGGLLRVNEMEATVRHVVKTGDLVTM----- 64

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHID 130
                     +   S +L+   + L   + YED  + V +KP  ++             +
Sbjct: 65  ---------VLPPESPSLSLQPEQLLFGIPYEDEHLLVADKPGHMATIPSRDRPGGSLAN 115

Query: 131 GFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           G L  +     Q      +RLD+ TSG+L+VA+ R A   L+   +   +++ Y +LV G
Sbjct: 116 GVLHYYKQQHLQATFHAVNRLDRGTSGLLIVAKHRYAHDLLSRLQQQGGVKRCYKALVTG 175

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +   K   I   + +K         + ++   G   AI+H+KV +  ++    + +Q  T
Sbjct: 176 VLSEKAGIINAPIDRKPG-----SIIEREVGPGGKSAITHYKV-EAESKTHSLVSLQLET 229

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GRTHQ+RVH  ++G P+VGD  Y  + +            LH   + L HP     L + 
Sbjct: 230 GRTHQIRVHFAYIGHPLVGDGLYGDHGEALAH------QALHCDRVALTHPFTDEVLYVE 283

Query: 309 APLPAHMV 316
             LP    
Sbjct: 284 KSLPKEWR 291


>gi|295101803|emb|CBK99348.1| Pseudouridylate synthases, 23S RNA-specific [Faecalibacterium
           prausnitzii L2-6]
          Length = 334

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 62/300 (20%), Positives = 121/300 (40%), Gaps = 17/300 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++      ++E +RL R+ ++         L K  R+ +++V+ K+    +R+++G ++ 
Sbjct: 1   MKQYTATANDEGVRLSRFVQSVTRDFPTSLLYKSFRNKRIKVNGKKGVPEDRLKAGDLIE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +            E           K  +  K  ++YED  I V  KP  +         
Sbjct: 61  LYINDEF---FPPEGAKPTRKPAPKKQQNQPKVTVIYEDENIAVLYKPTHLLCHSDRTGD 117

Query: 127 YHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            ++      ++  KG+         KP + +RLD+ T G+++ A++  A + + E  R  
Sbjct: 118 ANLVDAFTQYLAQKGEYDPQGENRFKPGICNRLDRGTEGLVIAAKSYTALRDMNEIIRTD 177

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y+++  GIP  +      W           +H  +  ++     I+   V+   A
Sbjct: 178 LLKKEYYTITVGIP--QSGRFTAWWEHDEKNNKVSIHAHQSQDERRKQIITDVDVL-RTA 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             F    +   TGRTHQ+R H  ++G P++GD KY        T        L A  +  
Sbjct: 235 GPFALCRIGLITGRTHQIRAHLAYLGKPVLGDIKYGNRKMNERT--GTRTQALCAVRISF 292


>gi|224535322|ref|ZP_03675861.1| hypothetical protein BACCELL_00184 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224523048|gb|EEF92153.1| hypothetical protein BACCELL_00184 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 223

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 70/228 (30%), Positives = 110/228 (48%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKQYLKEKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E F+   ++K YW++V   PK  +  + N+L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFKTSEVRKTYWAIVKNAPKEPEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   +  +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVPKSKKAILHYRLIG-KSDNYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYG-- 177

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
                 S     + LHAR++   HP    + ++ AP+P      W   
Sbjct: 178 ---FARSNPDGSICLHARHISFVHPVSKEMIEVEAPVPP--TNLWQGF 220


>gi|312873566|ref|ZP_07733613.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
 gi|311090819|gb|EFQ49216.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
          Length = 292

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 72/303 (23%), Positives = 127/303 (41%), Gaps = 34/303 (11%)

Query: 3   LMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQ 60
           +M  Y+ Y+ +  +E N  +D+  +N    I     +  LR    + V+ K +  N ++ 
Sbjct: 9   IMNQYIYYLTISQNENNQNVDQIMRNLL--IPR-KWRHFLRIEKNILVNDKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE+  + V +KPAG    
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENDDVLVIDKPAGQKTH 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 113 PN---LYETDTALNDCTSYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           + Y++ +      +    I   +          +            AI+H++V+     K
Sbjct: 170 RSYFAWIDATNDISDNGTINLPIGDDPLDMRKRMVRT-----DGLKAITHYQVVKKIGSK 224

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +++Q  TGRTHQ+RVH   +G PI+GD  Y +N++         KL L A  +    
Sbjct: 225 I-LVKLQLETGRTHQIRVHLAAIGHPIIGDPLYNSNYQAG------EKLQLTAYKLVFQK 277

Query: 300 PEG 302
           P  
Sbjct: 278 PFS 280


>gi|298482488|ref|ZP_07000674.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. D22]
 gi|298271467|gb|EFI13042.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. D22]
          Length = 224

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 112/232 (48%), Gaps = 16/232 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQ        +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQADKTGDTPLSETVKQYLKEKYQKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTSKALTRLNEMFRTSEVKKTYWAVVKNAPKEPEGELVHFLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   ++ +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVPNSKKAILHYRLIG-HSENYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
                 S     + LHAR +   HP     +++ APLP      W     ++
Sbjct: 180 RSNPDGS-----ICLHARRVRFIHPVSKELIELEAPLPEG--NLWKGFTIEF 224


>gi|296446414|ref|ZP_06888358.1| pseudouridine synthase [Methylosinus trichosporium OB3b]
 gi|296256049|gb|EFH03132.1| pseudouridine synthase [Methylosinus trichosporium OB3b]
          Length = 229

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 81/237 (34%), Positives = 121/237 (51%), Gaps = 14/237 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           + S LLY D  + V +KPAG+ V  G     +++    +      + P L HRLD++TSG
Sbjct: 1   MLSRLLYRDGLMLVVDKPAGLPVHRGPRGGDNLEDHFDALRFGLPRPPALAHRLDRDTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R R A + L + FR  RI+K YW++V G P +    I   L +     G ++   
Sbjct: 61  CLVLGRHRKALERLGKLFRDGRIEKTYWAVVEGAPADDAGEIDMALGRLDSTRGWWMR-- 118

Query: 217 KQNEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +     A +H++ +    D   +   +LE++P TGRTHQLRVH   MG PI+GD  Y
Sbjct: 119 --PDPLGLPAQTHWRALARGQDTEGRDIAFLELKPRTGRTHQLRVHMQAMGWPILGDPVY 176

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
               +          L+LHAR + +P  +G   + +TAP+P HM  T D+LG    R
Sbjct: 177 GHGKREGAP-----PLHLHARAIVVPIRDGHESVAVTAPVPPHMRGTLDTLGCDETR 228


>gi|226501200|ref|NP_001151637.1| LOC100285271 [Zea mays]
 gi|195648278|gb|ACG43607.1| RNA binding protein [Zea mays]
          Length = 439

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 92/312 (29%), Positives = 146/312 (46%), Gaps = 51/312 (16%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDK-----------------KRVKFNNRIQSGQVV 65
           RW ++  PH+    +QK+ R  +V+ +                  +RV   + +  G ++
Sbjct: 85  RWVRHCCPHVPASLVQKLFRLRKVKKNLVTADTSSTDSITLQLRLRRVSAKDELVPGDIL 144

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +P  I   +   K +K  + +       DFL+ + +Y+D  I V NKP G+ VQGG GI
Sbjct: 145 FLPVNIQESSVTEKTKKFGNKN-----EIDFLRDLEIYKDRAIIVLNKPPGMPVQGGVGI 199

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR------- 178
              ID     + +   + PRL HRLD++ SG+LV+ RT+ +A  +   FR +        
Sbjct: 200 KNSIDILAPMFENGSSEVPRLVHRLDRDCSGVLVLGRTQFSASLMHAIFREKTADALGDG 259

Query: 179 ----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFK 231
               +Q+ Y +LV G P++ K  ++  L K     G    +      N      A++ ++
Sbjct: 260 TQQVLQRKYVALVIGRPRHPKGLLSAPLAKVVLQDGRSERLTVCAGSNTASVQDALTEYR 319

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           VI+ F Q + WLE+ P TGR HQLRVH    +G PIVGD+KY              +   
Sbjct: 320 VIESFPQGYTWLELFPRTGRKHQLRVHCAEVLGTPIVGDYKYG-------------RQA- 365

Query: 291 HARYMDLPHPEG 302
           H  +M LP P+ 
Sbjct: 366 HQNWMPLPMPQT 377


>gi|22538202|ref|NP_689053.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           agalactiae 2603V/R]
 gi|22535113|gb|AAN00926.1|AE014285_8 ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 2603V/R]
          Length = 294

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 63/291 (21%), Positives = 108/291 (37%), Gaps = 33/291 (11%)

Query: 25  FKNHYPHI---NFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K             ++  LR    V ++ + + +   +Q    + +             
Sbjct: 16  VKELLEDYFLIPR-KIRHFLRVKKHVLINNEFINWQTVVQENDTITLIFDDE-------- 66

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
               D                LYED  + + NKP G+   G      +    L       
Sbjct: 67  ----DYPTKKIPLGRAELIDCLYEDEHLIIVNKPEGMKTHGNQP---NEIALLNHVSAYS 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           GQ   + HRLD ETSG ++ A+       + +    + I + YW+LV G    K + + +
Sbjct: 120 GQTCYVVHRLDMETSGAVLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRD 179

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + K   +A++   V+    Q    ++ +  TGRTHQ+RVH  
Sbjct: 180 KIGRNRHDRRKRII----DSKNGQHAMTIIDVLKYI-QNSSLIKCRLETGRTHQIRVHLS 234

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           H G P++GD  Y  +           +L LHA  + L HP     + + AP
Sbjct: 235 HHGHPLIGDPLYNPSSNNE-------RLMLHAHRLTLSHPLTCETISVEAP 278


>gi|282881245|ref|ZP_06289932.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
 gi|281305049|gb|EFA97122.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
          Length = 566

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 69/223 (30%), Positives = 105/223 (47%), Gaps = 19/223 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + V +KPAGI    G      +   L+S + S  +     HRLD  TSG+L++
Sbjct: 353 VVYEDDALIVVDKPAGILSVPGRSQRPSVYSILRSQMPSSVE-LFSVHRLDMATSGLLIL 411

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+     +HL   FR   IQK Y +++ G    ++  +   L        D    V   E
Sbjct: 412 AKNSVVYRHLQRQFRTHHIQKEYIAILEGALSQREGVVTLPL---RPDPFDRPRQVVDWE 468

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFK 277
            G   A++ ++V++       W+ + P TGRTHQLR+H  H   + CPI+GD  Y  +  
Sbjct: 469 HGKK-AVTSYRVLNVR-HGKTWVALFPETGRTHQLRMHCAHAEGLNCPILGDPLYGHH-- 524

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
                   N+LYLHA  +   HP  G+ L + A  PA     +
Sbjct: 525 -------ANRLYLHATSITFEHPISGQLLTLHAQPPADFQDVF 560


>gi|260662712|ref|ZP_05863606.1| pseudouridylate synthase [Lactobacillus fermentum 28-3-CHN]
 gi|260552793|gb|EEX25792.1| pseudouridylate synthase [Lactobacillus fermentum 28-3-CHN]
          Length = 294

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 61/285 (21%), Positives = 117/285 (41%), Gaps = 32/285 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           +G+ +VD +RV+   +I   Q + +       +  +   +                  ++
Sbjct: 36  AGEFQVDHRRVRPTTKILPNQPLTLTVQPEPGDATVATSEE--------------PLTIV 81

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---DSKGQKPRLTHRLDQETSGIL 158
           YED    V NKP G++   G  +    I   +K ++   D+   +P L  RLD++T+G+L
Sbjct: 82  YEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLVAKDAPDLRPHLITRLDRDTAGLL 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+   A+  ++       +QK Y ++V G    +   I         I      + ++
Sbjct: 142 LVAKHNVASSMISPQVEGHTMQKEYRAIVAGTFAKEHGIIDAP------IARIKGQIERE 195

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A + +   +     +  + ++ H+GRTHQ+RVH   +G P++GDH Y  +   
Sbjct: 196 VNPAGQPAKTEYWAEESRGD-WTLVRLRLHSGRTHQIRVHMASVGHPLLGDHLYGGDLS- 253

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                + +   L+A ++    P     L     +P      WD L
Sbjct: 254 -----MTDHQALYASHLAFTDPFTQTNLAFDVEMPVAFKTLWDGL 293


>gi|306812329|ref|ZP_07446527.1| tRNA pseudouridine synthase C [Escherichia coli NC101]
 gi|305854367|gb|EFM54805.1| tRNA pseudouridine synthase C [Escherichia coli NC101]
          Length = 260

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----KD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFSLQRLMLHASQLSLTHPFTGEPLAIHAGLDDTWMQALSQFGWR 237


>gi|304409553|ref|ZP_07391173.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307303911|ref|ZP_07583664.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304352071|gb|EFM16469.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306912809|gb|EFN43232.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 287

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 67/259 (25%), Positives = 105/259 (40%), Gaps = 17/259 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            +  L++S          +  +LYED  +   +KPAG+ V             ++   D 
Sbjct: 11  PENALNASQEDDSEEQAPEIEILYEDDHLVAIHKPAGLLVHRSYLARRERFFAMQLTRDL 70

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G      HRLD+ TSG+L+ A++   A  L E F    I+K Y +LV G   ++   + 
Sbjct: 71  VGCHVFPVHRLDRPTSGVLLFAKSSEVANALCEQFASHTIEKQYLALVRGNM-HESGILD 129

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
             L  +    GD         K A  A++ ++ +               +F  + + P T
Sbjct: 130 YALKVELDELGDKNA---DPNKAAQEAVTAYEPLLNTEIPYPSGRYPTSRFALVRLSPKT 186

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQ 306
           GR HQLR H  H+  PIVGD  +    +  F       N+L+L A+ +   HP    RL 
Sbjct: 187 GRKHQLRRHMAHLRHPIVGDTTHGDGKQNAFFREHFGINRLWLIAKKLSFTHPVTQVRLS 246

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I   L       +  LG+ 
Sbjct: 247 IETELEPEWETVFAELGWD 265


>gi|255659830|ref|ZP_05405239.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
 gi|260847905|gb|EEX67912.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
          Length = 302

 Score =  179 bits (455), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 125/314 (39%), Gaps = 37/314 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPP 69
            V+   +   L +  +     ++    + I  +G V V+ K+      R+ +G  + +  
Sbjct: 6   TVDAAHDGRELRQLVRAPL-GLSAKLWKHIKWNGTVLVNGKKNGDARLRVHTGDELTLLW 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YH 128
              +    +                  L   +LYED    V NKPA + V      A   
Sbjct: 65  QEVSSVVPV-----------------DLPLDILYEDETFLVVNKPADMIVHPTHRAARDT 107

Query: 129 IDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   +  + + +G+       +RLD++T+GI+++A++      +T+     +I + Y +L
Sbjct: 108 LVHAVAGYFERRGEAAGIHPLYRLDRDTTGIVILAKSARIQHAMTK--HHGQIYREYLAL 165

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G        I   + +       +             A++ ++ I  +   +  L++ 
Sbjct: 166 AQGHLDCLSGRIDMPIGRDITRANHWQVRA-----DGRRALTEYETIASWP-AYSLLKIH 219

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
             TGRTHQ+RVH   +G P++GD  Y      + +     +  LHA  +   HP+ G  +
Sbjct: 220 LLTGRTHQIRVHFAALGHPLLGDTAY------DGSCDTIPRQALHAWRVHFFHPDTGKEI 273

Query: 306 QITAPLPAHMVKTW 319
           +I AP+P  M +  
Sbjct: 274 RIEAPIPEDMCRLI 287


>gi|125623253|ref|YP_001031736.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|124492061|emb|CAL96989.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|300070003|gb|ADJ59403.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris NZ9000]
          Length = 293

 Score =  179 bits (455), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 64/297 (21%), Positives = 119/297 (40%), Gaps = 32/297 (10%)

Query: 31  HINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            I+   L K+    GQ+ V+        R++ G +V I               + D   N
Sbjct: 22  GISRRLLTKVKFDGGQIMVNGIEKTAIYRLEKGDLVTIT--------------VPDEPDN 67

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKP 144
                D +   +L+ED    V  KPAG +           ++  + G++ S  +   Q  
Sbjct: 68  EKLIPDDVPLNVLFEDDHYLVVEKPAGKASITGSLHPTGAMSNAVKGYI-SRKNYPNQTV 126

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            +  RLD++TSGI+ +A+ R A   + +      ++K Y++++          I   + +
Sbjct: 127 HIITRLDRDTSGIMFLAKHRYAHALMVQHKFRDTLEKRYYAIINDGDLPDSGQIDLPIGR 186

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +     +      +  K    A++ + V +        L++  HTGRTHQ+RVH  H+G 
Sbjct: 187 RDDSIIERQVRFDEKSKN---ALTSYVVTERKND-LALLDIILHTGRTHQIRVHFSHLGY 242

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWD 320
           P+VGD  Y  N        + ++  LH  ++   +P    +  +   +P  M     
Sbjct: 243 PLVGDDLYGGNHD------LISRQALHCHHLQFLNPFTDEMVHVELDMPDDMKNLLK 293


>gi|111657101|ref|ZP_01407890.1| hypothetical protein SpneT_02001674 [Streptococcus pneumoniae
           TIGR4]
 gi|183603313|ref|ZP_02714103.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae SP195]
 gi|183571639|gb|EDT92167.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae SP195]
 gi|332071803|gb|EGI82293.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA17570]
          Length = 278

 Score =  179 bits (455), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 66/279 (23%), Positives = 112/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +   +  G V ++                 D S   
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWKEIVNPGDVCQLTFDEE------------DYSQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLSHHNLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    +L  T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFT 264


>gi|89056515|ref|YP_511966.1| ribosomal large subunit pseudouridine synthase A [Jannaschia sp.
           CCS1]
 gi|88866064|gb|ABD56941.1| ribosomal large subunit pseudouridine synthase A [Jannaschia sp.
           CCS1]
          Length = 217

 Score =  179 bits (455), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 72/227 (31%), Positives = 105/227 (46%), Gaps = 13/227 (5%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           SV+           +++ED  + + NKPAG+    G G   H+   L + +     +  L
Sbjct: 2   SVDFVYAPPTDPLDIIHEDHDLLLVNKPAGLLSVPGKG--EHLSDCLIARLKIAFPEVLL 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD +TSG++V ART  A +HL   F  R  +K Y + VWG   +K   I   L+   
Sbjct: 60  VHRLDMDTSGVMVFARTPHAQRHLGLQFEKRHTKKAYVARVWGEVTDKDGHIDLPLIVD- 118

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                  HV   N +    A + ++ I         + + P TGR+HQLRVH L +G PI
Sbjct: 119 WPNRPLQHV---NHETGKPAQTDWRRI-RVEDGTTRMRLFPKTGRSHQLRVHMLAIGHPI 174

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +GD  Y       F      +L LHA  + L HP+GG  +   A +P
Sbjct: 175 LGDPFYATGPALAFP-----RLMLHAESLKLRHPDGGIGMTFRARVP 216


>gi|212690568|ref|ZP_03298696.1| hypothetical protein BACDOR_00054 [Bacteroides dorei DSM 17855]
 gi|237709607|ref|ZP_04540088.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           9_1_42FAA]
 gi|237725250|ref|ZP_04555731.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D4]
 gi|265754237|ref|ZP_06089426.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_33FAA]
 gi|212666917|gb|EEB27489.1| hypothetical protein BACDOR_00054 [Bacteroides dorei DSM 17855]
 gi|229436516|gb|EEO46593.1| ribosomal large subunit pseudouridine synthase D [Bacteroides dorei
           5_1_36/D4]
 gi|229456243|gb|EEO61964.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           9_1_42FAA]
 gi|263234946|gb|EEZ20501.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_1_33FAA]
          Length = 223

 Score =  179 bits (455), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 75/233 (32%), Positives = 117/233 (50%), Gaps = 18/233 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK +   VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VVYEDNHIVVVNKTSSEIVQGDKTGDTPLSEMVKQYLKEKYNKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E FR   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVVFAKTSKALPRLNEMFRNGEVKKTYWAIVKECPKETEGELVHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K +  A+ H+K+I   +Q +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVKNSKKAVLHYKLIG-HSQNYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYD 327
                 S     + LHAR +   HP    + ++TAP+P      W+  GF+ D
Sbjct: 180 RSNPDGS-----ICLHARTVQFVHPVSKEMIRLTAPVPEG--NLWN--GFEID 223


>gi|126657910|ref|ZP_01729063.1| probable pseudouridine synthase [Cyanothece sp. CCY0110]
 gi|126620850|gb|EAZ91566.1| probable pseudouridine synthase [Cyanothece sp. CCY0110]
          Length = 299

 Score =  179 bits (455), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 74/309 (23%), Positives = 129/309 (41%), Gaps = 34/309 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           ++    ++     + +  ++  +Y H +     + + SGQV ++KK V     +Q GQ  
Sbjct: 5   WIYREQIKPKNAGLTVLEYYTQNYHHSSSQQWLERIISGQVLLNKKVVTPETILQIGQ-- 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                ++      KE  +             L   ++YED  + V NKP+G+ V  G G 
Sbjct: 63  ----WLSYHRTPWKEPDVP------------LNFDIIYEDDDLLVINKPSGLPVLPGGGF 106

Query: 126 AYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             H    L        + K    HRL + TSG++V+ ++  A   LT+  R  +I K+Y 
Sbjct: 107 LEH--TLLWQLKKQYPKDKVFPIHRLGRGTSGLMVMGKSAIARSQLTQQMREHKITKVYR 164

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L+          I + + K S     Y++  K +     YA S   +++ ++ K   +E
Sbjct: 165 TLIGNNNLPDHFNIDHPIGKISDPVLGYIYGAKAD---GKYAYSECHILERYSDK-TLVE 220

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTS-------PIQNKLYLHARYM 295
           +   TGR HQ+R+H   +G P++GD  Y      K  F         P     +LHA  +
Sbjct: 221 VTILTGRPHQIRIHLATIGYPLLGDPLYTIGGIPKTGFEEQNDTINVPGDCGYFLHAYQL 280

Query: 296 DLPHPEGGR 304
              HP   +
Sbjct: 281 SFVHPITNQ 289


>gi|262068065|ref|ZP_06027677.1| tRNA pseudouridine synthase A [Fusobacterium periodonticum ATCC
           33693]
 gi|291378151|gb|EFE85669.1| tRNA pseudouridine synthase A [Fusobacterium periodonticum ATCC
           33693]
          Length = 295

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 83/317 (26%), Positives = 157/317 (49%), Gaps = 24/317 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   +++ + E +R+DR+ + H  +I    + K+LR  +V+V+ K+V  + R+  G +V 
Sbjct: 1   MIEFIIDEEYETVRIDRFLRKHLKNIALSEVYKMLRKAKVKVNNKKVSQDYRLVLGDIVF 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +    +       E+K  + S+ L +   + LK +++YED  +++ NK  G  +  GSG 
Sbjct: 61  VFLPESF------EEKNEEKSIELNEVRKEKLKFMIVYEDENLFIINKNLGDVIHKGSGH 114

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              +    +S+      K    +R+D+ TSG+++ A+    A+ + +  ++  I K Y+ 
Sbjct: 115 DVSLLEEFRSYY--SNNKINFVNRIDKLTSGLVIGAKNIKTAREIAKEIQLGNISKKYYI 172

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV+G  + +K  + N+L K      + V V    ++    +I+++K I+     +  LE 
Sbjct: 173 LVYGKIEKEKFVLENYLKKDE----EKVIVSDIEKEDYKKSITYYKRINGN-DDYTLLEA 227

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +  TGRTHQLR    H+G  IVGD KY  N K +        L+ +   +DL +     L
Sbjct: 228 ELKTGRTHQLRAQLNHLGHTIVGDTKYGKNIKEDIMY-----LFSYYLKIDLYN-----L 277

Query: 306 QITAPLPAHMVKTWDSL 322
           ++   +P   +K  D L
Sbjct: 278 ELELGIPNFFLKKCDML 294


>gi|160933803|ref|ZP_02081191.1| hypothetical protein CLOLEP_02664 [Clostridium leptum DSM 753]
 gi|156867680|gb|EDO61052.1| hypothetical protein CLOLEP_02664 [Clostridium leptum DSM 753]
          Length = 298

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 62/323 (19%), Positives = 125/323 (38%), Gaps = 47/323 (14%)

Query: 10  VVVENDEENMRLDRWFKNHYPHIN---FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
             V  +    ++  + +     ++       +K+     +  + K V             
Sbjct: 6   FTVPPEYSGAQVKTFLRRGC-GVSAKLLSQCKKM--QNGILKNGKPV------------- 49

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                          ++     + +   + L   +L+ED  + + NKP  + V    G  
Sbjct: 50  ---WAADTAAAGDTVRLTLPQEHNSMAPEALPVSVLWEDDALLILNKPPLMPVHPCPGHD 106

Query: 127 Y-HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              +  F+  +   KG+  + R  +RLD++TSG+++ A+    A  L +      + K Y
Sbjct: 107 RGTVCNFVSYYQKRKGEDWRFRPLNRLDKDTSGLVIGAKDSYTASALND------VGKTY 160

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQKF 240
           +++  G    +        LK+ H       + ++  +G   A++H+K +       + +
Sbjct: 161 FAVCQGSLPGEGVIDTPIRLKEGH------SIQREAGEGGKPAVTHWKSLAQGAAAGKSY 214

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             L +   TGRTHQ+RVH   +G P+ GD  Y        +  + ++  LH   ++L HP
Sbjct: 215 TLLALTLETGRTHQIRVHLSSIGHPLAGDDFYGG------SRELISRQALHCGLVELTHP 268

Query: 301 EG-GRLQITAPLPAHMVKTWDSL 322
               R+ + AP P    K  + L
Sbjct: 269 FFLSRICVKAPFPNDFKKILEFL 291


>gi|301162138|emb|CBW21683.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis 638R]
          Length = 539

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 72/243 (29%), Positives = 111/243 (45%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  +       S  +   +L+ED  + V +KP G+    G      I
Sbjct: 308 CEPILRHMLQGLDVEPAPSERYSLSQNMPE-ILFEDQWLLVLHKPEGVLSVPGKSEEQSI 366

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++    +   P + HRLD  TSG+L+ A+T+   +HL   F  R I+K Y +L+ G
Sbjct: 367 YSLLRARY-PEATGPLVVHRLDMATSGLLLAAKTQEVHRHLQAQFENRSIKKRYIALLDG 425

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I   ++  I   +          +     NE+    AI+ ++V+D        +   P T
Sbjct: 426 ILPEEEGVIDLPICPDYLDRPRQM----VNEELGKTAITRYRVMDRK-NGQTRIAFFPLT 480

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
           GRTHQLRVHA H   + CPIVGD  Y    +         +LYLHA Y++  HP  G R+
Sbjct: 481 GRTHQLRVHAAHPLGLNCPIVGDELYGRKAE---------RLYLHAEYLEFIHPVSGQRM 531

Query: 306 QIT 308
            I 
Sbjct: 532 VIE 534


>gi|218701508|ref|YP_002409137.1| tRNA pseudouridine synthase C [Escherichia coli IAI39]
 gi|218371494|emb|CAR19332.1| tRNA pseudouridine synthase [Escherichia coli IAI39]
          Length = 260

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 103/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D   Q     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIDQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|218547690|ref|YP_002381481.1| tRNA pseudouridine synthase C [Escherichia fergusonii ATCC 35469]
 gi|218355231|emb|CAQ87838.1| tRNA pseudouridine synthase [Escherichia fergusonii ATCC 35469]
 gi|325496166|gb|EGC94025.1| tRNA pseudouridine synthase C [Escherichia fergusonii ECD227]
          Length = 260

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 103/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   Y       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKYAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTQYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGELLTIHAGLDDIWMQALSQFGWR 237


>gi|159029331|emb|CAO90197.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 302

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 129/320 (40%), Gaps = 29/320 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+   ++    +  ++  + L  ++   YPH +       + S  + V+ +    +  ++
Sbjct: 1   MANQGWIYRDKISKNQAGLSLLAYYTGKYPHSSPEEWLDRILSAAILVNGRPAYPDTVLE 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            GQ +                         T+    L   +LYED+++ V  KP+G+ V 
Sbjct: 61  IGQQLTYQ------------------RPPWTEPDVPLFFEVLYEDTEVLVVAKPSGLPVL 102

Query: 121 GGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            G G   H    L   V        P   HRL + TSGI+++A+++ A   L++  R  +
Sbjct: 103 AGGGFLEH---TLIHLVHQHYADVTPYPIHRLGRGTSGIVLMAKSKPARSKLSQQMREGK 159

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I KIY +LV          I   + K +H    YV+    +      A S  +V+     
Sbjct: 160 ITKIYRALVGQGDIPDNFTINQAIGKIAHPILGYVYGALTD---GLSARSEGRVLKKHLD 216

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDL 297
               LE++  TGR HQ+R+H    G P++GD  Y           P     YLHA  +  
Sbjct: 217 S-TLLEVEIFTGRPHQIRIHLAFFGHPLIGDPLYSVGGLPRPDAVPGDCGYYLHANQILF 275

Query: 298 PHPEGG-RLQITAPLPAHMV 316
            HP  G R+ I  P P  +V
Sbjct: 276 NHPSTGERISICCPAPPELV 295


>gi|160915826|ref|ZP_02078034.1| hypothetical protein EUBDOL_01842 [Eubacterium dolichum DSM 3991]
 gi|158432302|gb|EDP10591.1| hypothetical protein EUBDOL_01842 [Eubacterium dolichum DSM 3991]
          Length = 313

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 55/301 (18%), Positives = 135/301 (44%), Gaps = 29/301 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +V+  ++ + R+D++     P +    + K +R+ +++V++KR + + R+Q G  ++
Sbjct: 1   MREIVIGKNDCDQRVDKFLSKALPTLPKSLMYKAIRNKKIKVNRKRCEISQRLQEGDTMQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--G 124
           +             ++   + ++        +  ++YED  + + NK  G+        G
Sbjct: 61  LFL----------AEEFFMTQIDTAFLKVPSELDIVYEDENLLIVNKAKGLLAHRDQKVG 110

Query: 125 IAYHIDGFLKSWVDSKGQKPR--------LTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +D  L      K   PR        L HR+D+ T G+++ A+  A+ + +    + 
Sbjct: 111 QDNLMDRILHYLYIHKEYDPRMENSFVPALCHRIDRNTQGLVIAAKNAASLRAMNAHIKQ 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R+++K Y  +  G+   ++E +   LL       +  H++   ++G      ++++ +  
Sbjct: 171 RKVRKKYVCIAQGVFDKRQEHV---LLYHCKTKDNVAHILPYPKEGYKPIEINYQIKEQK 227

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            Q +  +E++  +G++HQ+R    ++  P+ GD KY A          ++   L A  ++
Sbjct: 228 KQ-YALVEVELLSGKSHQIRAMLAYLSHPLYGDVKYGAKHTA-----AKHYQMLCAYRIE 281

Query: 297 L 297
            
Sbjct: 282 F 282


>gi|126173680|ref|YP_001049829.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125996885|gb|ABN60960.1| tRNA pseudouridine synthase C [Shewanella baltica OS155]
          Length = 287

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 67/259 (25%), Positives = 105/259 (40%), Gaps = 17/259 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            +  L++S          +  +LYED  +   +KPAG+ V             ++   D 
Sbjct: 11  PENALNASQEDDSEEQAPEIEILYEDEHLVAIHKPAGLLVHRSYLARRERFFAMQLTRDL 70

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G      HRLD+ TSG+L+ A++   A  L E F    I+K Y +LV G   ++   + 
Sbjct: 71  VGCHVFPVHRLDRPTSGVLLFAKSSEVANALCEQFASHTIEKQYLALVRGNM-HESGILD 129

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
             L  +    GD         K A  A++ ++ +               +F  + + P T
Sbjct: 130 YALKVELDELGDKNA---DPNKAAQEAVTAYEPLLNTEIPYPSGRYPTSRFALVRLSPKT 186

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQ 306
           GR HQLR H  H+  PIVGD  +    +  F       N+L+L A+ +   HP    RL 
Sbjct: 187 GRKHQLRRHMAHLRHPIVGDTTHGDGKQNAFFREHFGINRLWLIAKKLSFTHPVTQVRLS 246

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I   L       +  LG+ 
Sbjct: 247 IETELEPEWETVFAELGWD 265


>gi|317009246|gb|ADU79826.1| pseudouridine synthase D [Helicobacter pylori India7]
          Length = 327

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 71/343 (20%), Positives = 139/343 (40%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLNLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                   +    K    L+  +++ED  + V NKP  + V     +
Sbjct: 59  TL--------------LTPQITPKPLKKGLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++SK  +           + HRLD+ETSG +V+A+      HL+E  + 
Sbjct: 105 ---KEPTLVDWLESKNYELSNLGLKERYGIVHRLDKETSGGIVIAKNNFTHVHLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMMALKAAKKEKSRYSKSAFISLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L    PL   M++        +D+    + L  +
Sbjct: 279 FKHPRSEQKLHFKVPLLKDMLEYLKK---NFDKENLDEVLDGE 318


>gi|328474367|gb|EGF45172.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus 10329]
          Length = 255

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 64/258 (24%), Positives = 108/258 (41%), Gaps = 19/258 (7%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           S    ++    ++  ++Y+D      NKPAG+ V       Y     +++  D  GQ   
Sbjct: 2   SEQETSQTVAPVELEIVYQDEYFVAVNKPAGMLVHRSWLDKYETQFVMQTLRDQIGQHVF 61

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD+ TSG+LV A +   A  +   F   +++K Y ++V G  + +        ++ 
Sbjct: 62  PLHRLDRPTSGVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVEL 121

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQL 255
             I   +       EK A  A++ +K +               ++C +EM+P TGR HQL
Sbjct: 122 DKIADKFASQ----EKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQL 177

Query: 256 RVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           R H  H+  PIVGD  +               ++L LHA  +   HP     L + A + 
Sbjct: 178 RRHMAHLRHPIVGDTSHGDGKHNKLFRNEFDSHRLLLHASELRFVHPFTNEELVMKASID 237

Query: 313 AHMVKTWDSLGFKYDRNL 330
               + +    F++D  L
Sbjct: 238 DTWQQLFTR--FEWDEEL 253


>gi|332095345|gb|EGJ00368.1| RNA pseudouridylate synthase family protein [Shigella boydii
           5216-82]
          Length = 219

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPSYGNSMTFKA--PADF 219


>gi|86159798|ref|YP_466583.1| pseudouridine synthase RluD [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85776309|gb|ABC83146.1| Pseudouridine synthase, RluD [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 300

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 126/321 (39%), Gaps = 34/321 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M      + + V  +    RLDRW             + ++ +G+VR+  K    + ++ 
Sbjct: 1   MGTPAAPELLRVPREAAGARLDRWLAAAL-GATAERARWLVETGRVRIRGKTCSPHRKLF 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G+ V +                 +        +      +LY+D+   V  KP G++V+
Sbjct: 60  GGEEVAV-----------------ERPAPRAAEASGPALAVLYDDADCLVVAKPPGLAVE 102

Query: 121 GGSGIAYHIDGFLKSW--VDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            G+                D  G+  P L HRLD++TSG L++AR   A   L  +F   
Sbjct: 103 AGAPGGASAVAAASRLGAFDVDGRAAPGLAHRLDRDTSGALLLARHDRALAALRAAFEAG 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            I+K Y +LV G P  +   +     +       +             A   +KV +   
Sbjct: 163 AIEKEYLALVAGAPPPE-GRLDTPYGRDPEDPRRFTTRF----PSPRRARLSWKV-ERPL 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    L ++  TGRTHQ+RV     G P++GD  Y    +         +  LHA  +  
Sbjct: 217 RGAALLRVRLETGRTHQIRVQLAEAGFPVLGDAVYGVRGEA------IARQALHAERLAF 270

Query: 298 PHP-EGGRLQITAPLPAHMVK 317
           P P +G R+++ AP+P  + +
Sbjct: 271 PRPSDGARVEVRAPVPEDLER 291


>gi|312171317|emb|CBX79576.1| tRNA pseudouridine synthase C [Erwinia amylovora ATCC BAA-2158]
          Length = 255

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 111/240 (46%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G+ V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDRWLVAVNKPSGMLVHRSWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  L++ F   ++QK Y ++V G  +           ++  I   +     Q E
Sbjct: 64  ALSSEVAHLLSQQFEQHQLQKTYHAVVRGWLEGADTLDYPLTEERDKIADKF----SQPE 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +EMQP +GR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHWRGVATAELAVPIGRYETSRYSLVEMQPESGRKHQLRRHMTHLRHPIIGDS 179

Query: 271 KYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
            +      +    +   N+L LHA  ++L HP   G L + A L A   K  +  G++ +
Sbjct: 180 AHGDLKQNRSAAANFGINRLMLHASELNLTHPVTAGPLILRAGLDAVWQKVINQFGWQAE 239


>gi|227515440|ref|ZP_03945489.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus fermentum
           ATCC 14931]
 gi|227086199|gb|EEI21511.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus fermentum
           ATCC 14931]
          Length = 294

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 61/285 (21%), Positives = 117/285 (41%), Gaps = 32/285 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           +G+ +VD +RV+   +I   Q + +       +  +   +                  ++
Sbjct: 36  AGEFQVDHRRVRPTTKILPNQPLTLTVQPEPGDATVATSEE--------------PLTIV 81

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---DSKGQKPRLTHRLDQETSGIL 158
           YED    V NKP G++   G  +    I   +K ++   D+   +P L  RLD++T+G+L
Sbjct: 82  YEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLVAKDAPDLRPHLITRLDRDTAGLL 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+   A+  ++       +QK Y ++V G    +   I         I      + ++
Sbjct: 142 LVAKHNVASSMISPQVEGHTMQKEYRAIVAGTFAKEHGIIDTP------IARIKGQIERE 195

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A + +   +     +  + ++ H+GRTHQ+RVH   +G P++GDH Y  +   
Sbjct: 196 VNPAGQPAKTEYWAEESRGD-WTLVRLRLHSGRTHQIRVHMASVGHPLLGDHLYGGDLS- 253

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                + +   L+A ++    P     L     +P      WD L
Sbjct: 254 -----VTDHQALYASHLAFTDPFTQTNLAFDVEMPVAFKTLWDGL 293


>gi|109947248|ref|YP_664476.1| pseudouridine synthase [Helicobacter acinonychis str. Sheeba]
 gi|109714469|emb|CAJ99477.1| pseudouridine synthase [Helicobacter acinonychis str. Sheeba]
          Length = 326

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 68/332 (20%), Positives = 137/332 (41%), Gaps = 39/332 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHI 77
            R+D +       I+      +++ G V   KK VK     ++ G  + +     A   +
Sbjct: 12  KRIDEFLAKEL-QISKNQALSLIKEGLVFCQKKEVKKGGLALKEGDEIALLTPKIAPKPL 70

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +E                L+  +++ED  + V NKP  + V     +    +  L  W+
Sbjct: 71  KRELD--------------LEIEVIFEDDDLLVLNKPPNLVVHKAPSV---KEPTLVDWL 113

Query: 138 DSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           ++K  +           + HRLD++TSG +V+A+      +L+E  + + + + Y +L+ 
Sbjct: 114 EAKNYQLSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVYLSEQLKTKTMGRYYIALLS 173

Query: 189 GIP--KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                K +K  +  +L +  +     + + K+    + Y+ S F  +         +  +
Sbjct: 174 TPLSRKEEKISVECYLTRNPNNRLKMMAIKKEK---SRYSKSEFTSLLTSQNNLNLIGAK 230

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
            +TGRTHQ+RVH  ++   I+GD+ Y  N         + ++ LHA  ++  HP+   +L
Sbjct: 231 LYTGRTHQIRVHLEYLNRHIIGDNLYGLN---EALPKEEIRIMLHAYLIEFKHPKSEQKL 287

Query: 306 QITAPLPAHMVKTWDSL--GFKYDRNLYIKRL 335
               PL   M++           D  L  +++
Sbjct: 288 CFKVPLLKDMLEYLKKFFDKENLDEILDEEKI 319


>gi|323143516|ref|ZP_08078196.1| pseudouridine synthase A [Succinatimonas hippei YIT 12066]
 gi|322416710|gb|EFY07364.1| pseudouridine synthase A [Succinatimonas hippei YIT 12066]
          Length = 242

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 72/226 (31%), Positives = 109/226 (48%), Gaps = 13/226 (5%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           +     F    +LYED  I V NKP+G+    G  +  H D  L S + S        HR
Sbjct: 6   VYNPPLFPFLDVLYEDDDIMVVNKPSGLLSVPGR-LKEHHDSIL-SRIKSSYPDAFAVHR 63

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG+LVV   + A  +L + F  R ++KIY ++V GI + K   ++  L+    + 
Sbjct: 64  LDMGTSGVLVVGLNKNAVSNLGKQFMGREVKKIYIAIVDGIIE-KSGSVSLPLI----LD 118

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +     K + +    A++ ++ + C   K   + + P TGR+HQLRVH   +G PI+GD
Sbjct: 119 INNRPYQKVDFEVGKPALTFYEPL-CHDGKTTLVRLFPLTGRSHQLRVHLKEIGHPILGD 177

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAH 314
           H Y      + +      LYLHA  +   HP  G R++  AP P  
Sbjct: 178 HLYAPPEIRDASPH----LYLHAGCLSFCHPVSGNRMEFCAPPPFD 219


>gi|322390416|ref|ZP_08063937.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           parasanguinis ATCC 903]
 gi|321142874|gb|EFX38331.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           parasanguinis ATCC 903]
          Length = 287

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 67/291 (23%), Positives = 117/291 (40%), Gaps = 34/291 (11%)

Query: 25  FKNHYPHI---NFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K             ++  LR    V V+ + + + + +Q G  +++  + +A ++  KE
Sbjct: 16  VKELLEDYFLIPR-KIRHFLRTKKHVLVNGETINWQSPVQKGDQIQL--IFDADDYPEKE 72

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
               D S+             LY+D  + + NKP G+           +   + S+V   
Sbjct: 73  LPAGDPSL----------VEELYQDEHVIIVNKPEGMKTHANEPTEIALLNHVSSYV--- 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G    + HRLD+ETSG ++ A+       L      + IQ+ YW+L+ G    +     +
Sbjct: 120 GSTCYVVHRLDKETSGAILFAKNPFILPILNRILEDKNIQREYWALIQGSLAQRTIVYKD 179

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + +   YA +    +    +    ++ Q  TGRTHQ+RVH  
Sbjct: 180 KIGRDRHDRRKRL----VDPRKGQYAETQVTQLKKIGRN-SLVKCQLKTGRTHQIRVHLS 234

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           H G PIVGD  Y              +L LHA  +   +P     +Q+ AP
Sbjct: 235 HHGHPIVGDPLYNPARGE--------RLMLHAHRLTFTNPLTLETIQVEAP 277


>gi|237653878|ref|YP_002890192.1| transaldolase [Thauera sp. MZ1T]
 gi|237625125|gb|ACR01815.1| transaldolase [Thauera sp. MZ1T]
          Length = 648

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 63/255 (24%), Positives = 106/255 (41%), Gaps = 31/255 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  +   +KP+G+ V      A+     ++   D  G++    HRLD+ TSG+L+ 
Sbjct: 4   ILYRDDWLVAIHKPSGLLVHRSPIAAHEERFAVQLLRDQLGRRVYPAHRLDRGTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--------------- 205
           A  R  A+ L + F  + + K Y ++V G P      I + L+++               
Sbjct: 64  ALDREVARTLAQRFEAQAVDKRYLAVVRGHPPEH-GVIEHALVRRLDAVEVRSGKGAGAR 122

Query: 206 --SHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTH 253
                  D     +  E  A  A + F+ +             + ++  +E+ P TGR H
Sbjct: 123 DALPEDVDDSDSPEAAEPVAQPARTRFRRLATVELPHAVDRYPSSRYALVELLPETGRRH 182

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGGR-LQITAP 310
           QLR H  H+  PI+GD  Y           +   ++L L    + L HP   R L+I AP
Sbjct: 183 QLRRHLKHIAHPIIGDATYGKGRHNRLFQALFGSHRLLLACTRLALAHPVTERPLEIVAP 242

Query: 311 LPAHMVKTWDSLGFK 325
           +         +LG++
Sbjct: 243 VAEDFAAVLAALGWQ 257


>gi|42519556|ref|NP_965486.1| hypothetical protein LJ1679 [Lactobacillus johnsonii NCC 533]
 gi|41583845|gb|AAS09452.1| hypothetical protein LJ_1679 [Lactobacillus johnsonii NCC 533]
          Length = 282

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 74/302 (24%), Positives = 124/302 (41%), Gaps = 34/302 (11%)

Query: 4   MTYVQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQS 61
           MT  QY ++  +    M +D+  +     I     +  LR   ++ V+ K +  N  ++ 
Sbjct: 1   MTIYQYSLIYPDYLMPMSVDKLMRKLL--IPR-KWRHFLRSEKKILVNGKYLPLNFLVKP 57

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + I      L+HI  +Q+   +S  L K        ++YED+ I V NKPAG     
Sbjct: 58  GDKIEIQ-----LDHIESDQQPYPASGKLPK--------VVYEDNDILVINKPAGQKTHP 104

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                   D  L       G  P + HRLD  TSG+L+VA+  A    L      + + +
Sbjct: 105 N---LNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLLVAKNPAVVPILNRQLTDKTLHR 161

Query: 182 IYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y + +   P+      I   +    H     +       +    A++H++VI     + 
Sbjct: 162 EYLAWISNSPQIKNTGIIDLPIGHDPHDQRKRMVR-----QDGQKAVTHYEVIKRDKDRI 216

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +++   TGRTHQ+RVH   +G PI+GD  Y + ++         +L L A  +    P
Sbjct: 217 -LVKLTLETGRTHQIRVHLAALGAPIIGDPLYNSAYQDG------EQLQLTAFQLTFRKP 269

Query: 301 EG 302
             
Sbjct: 270 FS 271


>gi|152999968|ref|YP_001365649.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|160874589|ref|YP_001553905.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|151364586|gb|ABS07586.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|160860111|gb|ABX48645.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315266830|gb|ADT93683.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 287

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 70/277 (25%), Positives = 111/277 (40%), Gaps = 18/277 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            +  L++S          +  +LYED  +   +KPAG+ V             ++   D 
Sbjct: 11  PENALNASQEDDSEEQAPEIEILYEDEHLVAIHKPAGLLVHRSYLARRERFFAMQLTRDL 70

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G      HRLD+ TSG+L+ A++   A  L E F    I+K Y +LV G   ++   + 
Sbjct: 71  VGCHVFPVHRLDRPTSGVLLFAKSSEVANALCEQFASHTIEKQYLALVRGNM-HESGILD 129

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
             L  +    GD         K A  A++ ++ +               +F  + + P T
Sbjct: 130 YALKVELDELGDKNA---DPNKAAQEAVTAYEPLLNTEIPYPSGRYPTSRFALVRLSPKT 186

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQ 306
           GR HQLR H  H+  PIVGD  +    +  F       N+L+L A+ +   HP    RL 
Sbjct: 187 GRKHQLRRHMAHLRHPIVGDTTHGDGKQNAFFREHFGINRLWLIAKKLSFTHPVTQVRLS 246

Query: 307 ITAPLPAHMVKTWDSLGFKYDR-NLYIKRLYSQDECK 342
           I   L       +  LG+     +   + L + DE  
Sbjct: 247 IETELEPQWETVFAELGWDEATLSQQAELLIATDEIP 283


>gi|312875913|ref|ZP_07735903.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311797394|gb|EFR13733.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 293

 Score =  179 bits (454), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 70/262 (26%), Positives = 130/262 (49%), Gaps = 15/262 (5%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKP 114
           R++    +R  P I +++   +E  +++  +  +K +         +LYED+     NKP
Sbjct: 33  RLKVHGQIRFIPPIYSVHQYPQENAVIEVDLISSKSNIAPVEGNIDILYEDNFFLFVNKP 92

Query: 115 AGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           +G+      G  +  I  +++ +++SK     + +RLD++TSGI+V A+       ++  
Sbjct: 93  SGLPSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRLDKDTSGIVVFAKNSYFHSIVSHE 152

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  R+++K Y ++V G    K   I   + K+S  G     + ++  +  ++A ++++VI
Sbjct: 153 FEKRQVEKTYIAIVHGRLTKKSGLIEKPI-KRSDDG-----IKREIHQDGSFASTYYEVI 206

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           D F + F  L+++P TGRTHQLRVH   +G PIVGD  Y      N        L+ ++ 
Sbjct: 207 DSF-ENFSLLKLKPITGRTHQLRVHLSSIGYPIVGDCIYGKERTQNTPLL----LHAYSI 261

Query: 294 YMDLPHPEGGRLQITAPLPAHM 315
                  +     IT+PLP + 
Sbjct: 262 RFTFKLIDNKVYYITSPLPHYF 283


>gi|325686709|gb|EGD28735.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK72]
          Length = 291

 Score =  179 bits (454), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 73/316 (23%), Positives = 125/316 (39%), Gaps = 33/316 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   +  G  + +
Sbjct: 4   TLTIPDGLPTMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLAINWQTVVNPGDDICL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+          
Sbjct: 62  IFDEEDY----PQKTILFGNGELVEE--------LYQDQHLIIVNKPEGMKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+LV
Sbjct: 110 ALLNHVSAYV---GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLEKREISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    KK    + + +  H     +     + +   YA +H   I  F Q    ++ Q 
Sbjct: 167 QGKFPAKKLIYKDKIGRDRHDRRKRL----VDPRKGLYAETHVNRIKQFGQ-ASLVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G P++GD  Y    KG        +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGRPLIGDPLYHPQPKG--------RLMLHAHRLTFTHPFTLEKIT 273

Query: 307 ITAPLPAHMVKTWDSL 322
           + A    +  K   SL
Sbjct: 274 VEAR-SDNFEKVLSSL 288


>gi|308048661|ref|YP_003912227.1| tRNA pseudouridine synthase C [Ferrimonas balearica DSM 9799]
 gi|307630851|gb|ADN75153.1| tRNA pseudouridine synthase C [Ferrimonas balearica DSM 9799]
          Length = 247

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 59/247 (23%), Positives = 105/247 (42%), Gaps = 17/247 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   +KP+G+ V       +     ++   D+ G      HRLD+ TSG+L+ 
Sbjct: 4   ILYQDDHLVAVHKPSGLLVHRSWLDRHETQFAMQMTRDAVGCHVFPVHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            ++   A+ ++E      I K Y +LV G      E      ++   I       +   +
Sbjct: 64  TKSAETARIMSEKMAAHDIDKHYLALVRGYVHEAGELDYALKVELDDIADK----MADKD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  + ++P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KAPQEAVTRYRPLAQVELPFAVGRYPTSRYSLMALEPLTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +       F        +L+L A+ +   HP  G  L I APL    +  +++ G+   
Sbjct: 180 THGDGRHNKFYRDHFGVQRLWLIAKGLGFAHPVSGEPLWIEAPLEQEWLTLFETFGWSTA 239

Query: 328 RNLYIKR 334
           +  Y+ R
Sbjct: 240 QQDYLIR 246


>gi|69244119|ref|ZP_00602655.1| Pseudouridine synthase, RluD [Enterococcus faecium DO]
 gi|257880479|ref|ZP_05660132.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257883291|ref|ZP_05662944.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257894567|ref|ZP_05674220.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|258614127|ref|ZP_05711897.1| RNA pseudouridylate synthase [Enterococcus faecium DO]
 gi|260562478|ref|ZP_05832988.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|293559878|ref|ZP_06676390.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1162]
 gi|293568196|ref|ZP_06679530.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1071]
 gi|294617460|ref|ZP_06697092.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1679]
 gi|294620663|ref|ZP_06699873.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium U0317]
 gi|68196576|gb|EAN11002.1| Pseudouridine synthase, RluD [Enterococcus faecium DO]
 gi|257814707|gb|EEV43465.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257818949|gb|EEV46277.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257830946|gb|EEV57553.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|260073163|gb|EEW61508.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|291589096|gb|EFF20910.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1071]
 gi|291596267|gb|EFF27528.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1679]
 gi|291599760|gb|EFF30767.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium U0317]
 gi|291606150|gb|EFF35572.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1162]
          Length = 285

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 64/265 (24%), Positives = 111/265 (41%), Gaps = 28/265 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R   V ++++   F++ ++    + +              +  D +    +  D     
Sbjct: 36  IRK-NVWINQQPALFHHEVKGNDQITLLF------------EETDYNYQEVQLGDAKHIR 82

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+                L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+       L      + I + Y ++VWG        I N + +  H     V     +
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGEIAKDM-TITNKIGRDRHDRRKRV----VD 197

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +K    A++H  V    +++         TGRTHQ+RVH  H G PIVGD  Y       
Sbjct: 198 DKNGQSALTHVTVNKVLSEQTQVY-CVLETGRTHQIRVHLAHKGHPIVGDPLY------- 249

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR 304
             +    +L LHA  + + HP    
Sbjct: 250 -QNRTAERLMLHALELHMIHPFTQE 273


>gi|257891490|ref|ZP_05671143.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|257827850|gb|EEV54476.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
          Length = 285

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 64/265 (24%), Positives = 111/265 (41%), Gaps = 28/265 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R   V ++++   F++ ++    + +              +  D +    +  D     
Sbjct: 36  IRK-NVWINQQPALFHHEVKGNDQITLLF------------EETDYNYQEVQLGDAKHIR 82

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LYED  + + +KPAG+                L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLYEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+       L      + I + Y ++VWG        I N + +  H     V     +
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGEIDKDM-TITNKIGRDRHDRRKRV----VD 197

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +K    A++H  V    +++         TGRTHQ+RVH  H G PIVGD  Y       
Sbjct: 198 DKNGQSALTHVTVNKVLSEQTQVY-CVLETGRTHQIRVHLAHKGHPIVGDPLY------- 249

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR 304
             +    +L LHA  + + HP    
Sbjct: 250 -QNRTAERLMLHALELHMIHPFTQE 273


>gi|218129090|ref|ZP_03457894.1| hypothetical protein BACEGG_00664 [Bacteroides eggerthii DSM 20697]
 gi|317474871|ref|ZP_07934141.1| RNA pseudouridylate synthase [Bacteroides eggerthii 1_2_48FAA]
 gi|217988725|gb|EEC55044.1| hypothetical protein BACEGG_00664 [Bacteroides eggerthii DSM 20697]
 gi|316909009|gb|EFV30693.1| RNA pseudouridylate synthase [Bacteroides eggerthii 1_2_48FAA]
          Length = 223

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 68/218 (31%), Positives = 110/218 (50%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDTPLSETVKLYLKEKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L + F+   ++K YW++V   P   +  + N+L++       Y + 
Sbjct: 63  GLVVFAKTSKALTRLNDMFKNGEVKKTYWAVVKNQPHEPEGELVNYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   +Q +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVPNSKKAILHYRLI-AKSQNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                 S     + LHAR++   HP     +++ AP+P
Sbjct: 180 RSNPDGS-----ICLHARFVRFIHPVSKELIEVEAPVP 212


>gi|149915492|ref|ZP_01904019.1| DNA mismatch repair protein [Roseobacter sp. AzwK-3b]
 gi|149810781|gb|EDM70622.1| DNA mismatch repair protein [Roseobacter sp. AzwK-3b]
          Length = 215

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 68/220 (30%), Positives = 110/220 (50%), Gaps = 13/220 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
              +   +L+ED +I V NKPAG+    G G   H+   L + V        L HRLD++
Sbjct: 7   PPQVPLEVLHEDHEILVVNKPAGLLSVPGKGP--HLADCLIARVQEAFPNALLVHRLDRD 64

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V A +  A +HL   F  R+++K Y + VWG+ + K   +   L+    +     
Sbjct: 65  TSGVMVFALSPHAQRHLGLQFEKRQMKKTYVARVWGMLEPKTGTVDLPLI----VDWPNR 120

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + K   +    A++ ++V+    +    + + P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 121 PLQKVCHETGKPALTDWRVL-RHVKGETRVRLAPKTGRSHQLRVHMLALGHPILGDPLYA 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +    +       +L LH+  + L HP+GG  L+  A  P
Sbjct: 180 SGAAADHP-----RLMLHSEELRLRHPDGGMGLRFRAKTP 214


>gi|114562440|ref|YP_749953.1| pseudouridylate synthase [Shewanella frigidimarina NCIMB 400]
 gi|114333733|gb|ABI71115.1| tRNA pseudouridine synthase C [Shewanella frigidimarina NCIMB 400]
          Length = 293

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 66/267 (24%), Positives = 117/267 (43%), Gaps = 19/267 (7%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +  I E    D+ ++   H   +   +L+ED  +   +KPAG+ V             ++
Sbjct: 23  SEYIDENATADTELDDDLHPPHID--ILFEDEHLVAIHKPAGLLVHRSYLARRERFFAMQ 80

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
              D  G      HRLD+ TSG+L+ A++   A+ L E F    I+K Y ++V G   ++
Sbjct: 81  MTRDLVGCHVFPVHRLDRPTSGVLLFAKSSEVARALCEQFADHSIKKHYLAIVRGNM-HE 139

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLE 244
              +   L ++    GD         K A  A++ ++ +               ++  ++
Sbjct: 140 SGTLDYALKQEFDDLGDKH---VDQNKAAQDAVTDYQPLLNTEIPFSSGRYPTSRYGLVK 196

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG 302
           + PHTGR HQLR H  H+  PIVGD  +    +  F       N+L+L A+ +   HP  
Sbjct: 197 LSPHTGRKHQLRRHMAHLRHPIVGDTTHGDGKQNKFFREHFTINRLWLIAKSLQFVHPVT 256

Query: 303 GR-LQITAPLPAHMVKTWDSLGFKYDR 328
            + + I   L A  +  +++ G+  D+
Sbjct: 257 QQSMHIETELEAEWLTVFNAFGWDDDQ 283


>gi|224370646|ref|YP_002604810.1| TruC [Desulfobacterium autotrophicum HRM2]
 gi|223693363|gb|ACN16646.1| TruC [Desulfobacterium autotrophicum HRM2]
          Length = 260

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 72/247 (29%), Positives = 107/247 (43%), Gaps = 11/247 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           TK S      +LY+D  +   NKP G+ V   +   +     L+   D         HRL
Sbjct: 5   TKASAPGTLEILYQDEDLVAVNKPPGLLVHRTALATHETRFALQMVRDQTQGHVFPVHRL 64

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL--LKKSHI 208
           D+ T G+L+ AR R  A  ++  F+  +IQK Y ++V G  K +   I + L  +K    
Sbjct: 65  DRPTQGVLLFARNRNMATRMSHLFQTGKIQKTYLAVVRGHVKER-GTIVHPLKNIKHPQD 123

Query: 209 GGDYVHVVKQNEKGANYA-----ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                H +K ++   +YA        F V      ++C + + P TGR HQLR H  H+ 
Sbjct: 124 NKRINHSLKIDDAVTDYACLASVELPFYVDRYPTTRYCLVALIPKTGRRHQLRRHMKHIS 183

Query: 264 CPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            PIVGD  Y  +    F +   N   L L AR +   HP+ G  + ITAPL     +   
Sbjct: 184 HPIVGDTVYGKSSHNRFFATHLNCTGLLLAARELCFVHPDTGIFITITAPLDKRFQEVIS 243

Query: 321 SLGFKYD 327
              +   
Sbjct: 244 KFSWDEP 250


>gi|332365269|gb|EGJ43032.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1059]
          Length = 291

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 121/303 (39%), Gaps = 32/303 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   +  G  V +
Sbjct: 4   TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLAINWQTVVNPGDDVCL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+          
Sbjct: 62  IFDEEDY----PQKTILFGNGELVEE--------LYQDQHLIIVNKPEGMKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+LV
Sbjct: 110 ALLNHVSAYV---GETCYVVHRLDKETSGAILFAKNPFVLPILNRLLEKREISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +KK    + + +  H     +       +   YA +H   +  F Q    ++ Q 
Sbjct: 167 QGKFPSKKLIYKDKIGRDRHDRRKRL----VEPQKGLYAETHVTRLKQFGQ-AALVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G P++GD  Y    +G        +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGHPLIGDPLYHPQPQG--------RLMLHAHLLTFTHPFTLEKIT 273

Query: 307 ITA 309
           + A
Sbjct: 274 VEA 276


>gi|332668407|ref|YP_004451195.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
 gi|332337221|gb|AEE54322.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
          Length = 243

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 65/242 (26%), Positives = 103/242 (42%), Gaps = 25/242 (10%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ D  I V  KP+G+            +  L   ++++  +  + HR+D+ETSGI
Sbjct: 5   PLKIIHVDEHIIVCEKPSGLLSIPDRFDQEKPN--LYHLLEAQYGQVWIVHRIDRETSGI 62

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV AR   A + L + F  R ++KIY +LV G P      I   +     I G  +   K
Sbjct: 63  LVFARNEDAHRALNQQFLDRSVEKIYLALVEGRPMPPTGEINKAIAPHPSIAGKMITSGK 122

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF- 276
                   A++ +KV+D + + +  +E    TGRTHQ+RVH   +G P+  D  Y     
Sbjct: 123 -----GKSALTLYKVVDTY-KAYALVEADIKTGRTHQIRVHFASIGHPLAVDPVYGKRAA 176

Query: 277 ---------------KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
                            +    + ++L LHA  + L HP  G R+  T  LP        
Sbjct: 177 FFLSEIKTHRFNLKKDQDEEQALVSRLTLHAHKLTLDHPATGERMAFTCELPKDFRALLS 236

Query: 321 SL 322
            L
Sbjct: 237 QL 238


>gi|76786717|ref|YP_330596.1| ribosomal large subunit pseudouridine synthase A [Streptococcus
           agalactiae A909]
 gi|76561774|gb|ABA44358.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus agalactiae A909]
          Length = 294

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 109/291 (37%), Gaps = 33/291 (11%)

Query: 25  FKNHYPHI---NFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K             ++  LR    V ++ + + +   +Q    + +             
Sbjct: 16  VKELLEDYFLIPR-KIRHFLRVKKHVLINNEFINWQTVVQENDTITLIFDDE-------- 66

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
               D                LYED  + + NKP G+   G      +    L       
Sbjct: 67  ----DYPTKKIPLGRAELIDCLYEDEHLIIVNKPEGMKTHGNQP---NEIALLNHVSAYS 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           GQ   + HRLD ETSG ++ A+       + +    + I + YW+LV G    K + + +
Sbjct: 120 GQTCYVVHRLDMETSGAVLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRD 179

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + K   +A++   V+  + Q    ++ +  TGRTHQ+R+H  
Sbjct: 180 KIGRNRHDRRKRII----DSKNGQHAMTIIDVLK-YTQNSSLIKCRLETGRTHQIRIHLS 234

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           H G P++GD  Y  +           +L LHA  + L HP     + + AP
Sbjct: 235 HHGHPLIGDPLYNPSSNNE-------RLMLHAHRLTLSHPLTCETISVEAP 278


>gi|254507454|ref|ZP_05119589.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 16]
 gi|219549710|gb|EED26700.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 16]
          Length = 254

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 109/228 (47%), Gaps = 12/228 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED  I V NKP+G+    G  +  H D      V +     ++ HRLD +TSG++
Sbjct: 23  VDIVFEDEHILVANKPSGLLSVPGR-LEEHYDSLWSRLV-AIYPDIQVVHRLDMDTSGLM 80

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+ + A + L + F+ R   K+Y++ VWG P N    I   L+           V   
Sbjct: 81  LLAKHKEAERSLKKQFQYRLTHKVYYARVWGHPTNDNGEIDLPLICD-WPNRPRQIVCFD 139

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + K +    + ++V+    ++   + + P TGR+HQLRVH   +G PIVGD  Y      
Sbjct: 140 DGKPSK---TLYQVVKR-EERTSIVRLLPITGRSHQLRVHMQALGHPIVGDEFYSEGEAF 195

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
            F+    ++L LHA  +   HP    LQ  A +P       +++ F Y
Sbjct: 196 EFS----DRLELHAAELSFYHPHSEALQ-CAFVPCDFYLEAEAMIFNY 238


>gi|261338949|ref|ZP_05966807.1| hypothetical protein ENTCAN_05150 [Enterobacter cancerogenus ATCC
           35316]
 gi|288318776|gb|EFC57714.1| pseudouridine synthase A [Enterobacter cancerogenus ATCC 35316]
          Length = 219

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 66/227 (29%), Positives = 107/227 (47%), Gaps = 15/227 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +           ++LY+D  I V NKP+G+    G  +  H D  + + +     +    
Sbjct: 3   MEPYNPPTDPWLVILYQDEHIMVVNKPSGLLSVPGR-LDEHKDSVM-TRIQRDYPQAESV 60

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA  + A + L   FR R  +K Y + VWG P   +  +   L+    
Sbjct: 61  HRLDMATSGVIVVALNKDAERELKRQFREREPKKQYVARVWGHPAQAEGLVDLPLI---- 116

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G P
Sbjct: 117 --CDWPNRPKQKVCYETGKAAQTEYEVLEYAADNTARVLLKPITGRSHQLRVHMLAIGHP 174

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           I+GD  Y           +  +L LHA+ + + HP  G  +   AP+
Sbjct: 175 ILGDRFYAPPD----ALALAPRLQLHAQTLTITHPAFGNSMTFKAPV 217


>gi|108563155|ref|YP_627471.1| hypothetical protein HPAG1_0730 [Helicobacter pylori HPAG1]
 gi|107836928|gb|ABF84797.1| pseudouridine synthase D [Helicobacter pylori HPAG1]
          Length = 327

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 127/314 (40%), Gaps = 32/314 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHI 77
            R+D +       I+   +  +++ G V   KK VK     ++ G  + +          
Sbjct: 12  KRIDEFLAKEL-QISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITL---------- 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                    +    K    L+  +++ED  + V NKP  + V     +    +  L  W+
Sbjct: 61  ----LTPQITPKPLKKGLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSV---KEPTLVDWL 113

Query: 138 DSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           + K  +           + HRLD++TSG +V+A+      HL+E  + + + + Y +L+ 
Sbjct: 114 EFKNYELSNLGLKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLS 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
              K +K  +  +L +  +     + +    ++   Y+ S F  +         +  +  
Sbjct: 174 TPLKEEKMSVECYLARNPNNRLKMIALKAAKKEKIRYSKSEFTSLLTSQNGMDLIGAKLF 233

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++  HP    +L+ 
Sbjct: 234 TGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRF 290

Query: 308 TAPLPAHMVKTWDS 321
             PL   M++    
Sbjct: 291 KVPLLKDMLEYLKK 304


>gi|299783639|gb|ADJ41637.1| Pseudouridine synthase [Lactobacillus fermentum CECT 5716]
          Length = 295

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 68/293 (23%), Positives = 112/293 (38%), Gaps = 33/293 (11%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                 H      Q       V V+      +  + +G V+ +    +            
Sbjct: 31  LPKRLVHYLRSRRQ-------VLVNGSYRPVSKTVAAGDVITLNFSGDEFR--------- 74

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQK 143
             + + +   D     +LYE+  + V +KPAGI      +G    +   + ++++     
Sbjct: 75  --TPDSSYLPDPGPLTVLYENRDLLVVDKPAGIKSHPNQAGEVGTLMNRVAAYLEGTNDA 132

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLDQETSG ++VA+       L +      I + Y +LV G+P   +      L 
Sbjct: 133 AYMVHRLDQETSGAMIVAKNPVVVPILDQLISTGEIHRDYLALVAGVPNPARGIWDLPLG 192

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +            K   K A  A +H++ +     +   + +   TGRTHQLRVH    G
Sbjct: 193 QDPTDVRKR----KVFGKNAQPARTHYRTLAVNGDQA-LVVLNLETGRTHQLRVHLAAAG 247

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           CPIVGD  Y         +    ++YLH    +L  P    R +I A +P   
Sbjct: 248 CPIVGDPLYG--------TVAAPRMYLHGVAQELVLPFSLKRERIVAKIPDDF 292


>gi|126726068|ref|ZP_01741910.1| pseudouridine synthase [Rhodobacterales bacterium HTCC2150]
 gi|126705272|gb|EBA04363.1| pseudouridine synthase [Rhodobacterales bacterium HTCC2150]
          Length = 218

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 116/230 (50%), Gaps = 15/230 (6%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D +      +D L  +++++D ++ + +KPAG+    G G   H+   L + V +    
Sbjct: 2   IDPTAAYNPPNDPL--VIIHDDHEVLLVDKPAGLLSVPGKG--EHLADCLLTRVQAAFPM 57

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD++TSG++V A TR A +HL   F  R+ +K Y + V+G+P  K   +   L+
Sbjct: 58  ALLVHRLDRDTSGVMVFALTRNAQRHLGLQFEKRQTKKTYVADVYGVPSEKSGTVDLPLI 117

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                      + K   +    A + +KV+         + + P TGR+HQLRVH L +G
Sbjct: 118 VD----WPNRPLQKVCHETGKAAQTDWKVMRTKG-NVTRVRLMPLTGRSHQLRVHMLAIG 172

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            PI+GD  Y    +         ++ LH++ +   HP+GG+ ++ TA LP
Sbjct: 173 HPIMGDPFYATEPEMAAP-----RMMLHSQTLAFRHPDGGKGVRYTAKLP 217


>gi|332762292|gb|EGJ92559.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           2747-71]
 gi|332768845|gb|EGJ99024.1| 23S rRNA/tRNA pseudouridine synthase [Shigella flexneri 2930-71]
          Length = 219

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCFETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|296875626|ref|ZP_06899697.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           parasanguinis ATCC 15912]
 gi|296433423|gb|EFH19199.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           parasanguinis ATCC 15912]
          Length = 274

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 66/291 (22%), Positives = 115/291 (39%), Gaps = 34/291 (11%)

Query: 25  FKNHYPHI---NFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K             ++  LR    V V+ + + + + +Q G  +++    +       E
Sbjct: 3   VKELLEDYFLIPR-KIRHFLRTKKHVLVNGETINWQSPVQKGDQIQLIFDADDY----PE 57

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +++     NL +         LY+D  + + NKP G+           +   + S+V   
Sbjct: 58  KELPAGDPNLVEE--------LYQDEHVIIVNKPEGMKTHANEPTEIALLNHVSSYV--- 106

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G    + HRLD+ETSG ++ A+       L      + IQ+ YW+L+ G    K     +
Sbjct: 107 GSTCYVVHRLDKETSGAILFAKNPFILPILNRILEDKNIQREYWALIQGSLAQKTIVYKD 166

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + +   YA +    +    +    ++ Q  TGRTHQ+RVH  
Sbjct: 167 KIGRDRHDRRKRL----VDPRKGQYAETQVTQLKKIGRN-SLVKCQLKTGRTHQIRVHLS 221

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           H G PIVGD  Y              +L LHA  +   +P     +Q+ AP
Sbjct: 222 HHGHPIVGDPLYNPARGE--------RLMLHAHRLTFTNPLTLETIQVEAP 264


>gi|332199442|gb|EGJ13518.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA47901]
          Length = 278

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 64/279 (22%), Positives = 111/279 (39%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +   +  G V ++                 D     
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWKEIVNPGDVCQLTFDEE------------DYPQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA ++   +  F+ K      +  TGRTHQ+RVH  H   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETYVSRLKQFSNKTSLARCKLKTGRTHQIRVHLSHHNLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    +L  T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLEKLTFT 264


>gi|310766621|gb|ADP11571.1| tRNA pseudouridine synthase C [Erwinia sp. Ejp617]
          Length = 265

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 110/240 (45%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G+ V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDRWLVAVNKPSGMLVHRSWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++QK Y ++V G  +           ++  I   +     Q E
Sbjct: 64  ALSSEVARLLSQQFEQHQLQKTYHAVVRGWLEGADTLDYPLTEEQDKIADKF----SQPE 119

Query: 221 KGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++          V      ++  +EM P +GR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHWRGVATAELPVPVGRYQTSRYSLVEMLPESGRKHQLRRHMTHLRHPIIGDS 179

Query: 271 KYC--ANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLGFKYD 327
            +      +    +   N+L LHA  ++L HP     L + A L A   K  +  G++ +
Sbjct: 180 AHGDLKQNRSAAANFGMNRLMLHASELNLTHPVIAEPLMLRAGLDAVWQKVINQFGWQAN 239


>gi|91792903|ref|YP_562554.1| pseudouridylate synthase [Shewanella denitrificans OS217]
 gi|91714905|gb|ABE54831.1| tRNA pseudouridine synthase C [Shewanella denitrificans OS217]
          Length = 298

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 64/258 (24%), Positives = 109/258 (42%), Gaps = 17/258 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E    D  V         +  +LY+D  I   +KPAG+ V             ++   D 
Sbjct: 33  ESAGADIEVTDDMDEPAPELTILYQDDDIVAIHKPAGLLVHRSYLARKERFFAMQLTRDL 92

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G      HRLD+ TSG+L+ A++   A++L E F   +I+K Y +LV G          
Sbjct: 93  IGCHVFPVHRLDRPTSGVLLFAKSSEVARNLCEQFAEHKIKKDYLALVRGNMHEAGLLDY 152

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
              ++   +   +       +K A  A + ++ +               +F  +++ PHT
Sbjct: 153 PLRVELDDVADKHAKA----DKPAQEAQTSYQPLLNSEIPFSSGRYPTSRFALIKLSPHT 208

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR-LQ 306
           GR HQLR H  H+  PI+GD  +    +  F+      N+L+L A+ +   HP  G+ + 
Sbjct: 209 GRKHQLRRHMAHLRHPILGDTTHGDGKQNKFSREHFGVNRLWLIAKRLSFTHPVTGKPMT 268

Query: 307 ITAPLPAHMVKTWDSLGF 324
           I   +    + T+  LG+
Sbjct: 269 IETQIEQQWLATFALLGW 286


>gi|84515048|ref|ZP_01002411.1| ribosomal large subunit pseudouridine synthase A [Loktanella
           vestfoldensis SKA53]
 gi|84511207|gb|EAQ07661.1| ribosomal large subunit pseudouridine synthase A [Loktanella
           vestfoldensis SKA53]
          Length = 214

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 62/220 (28%), Positives = 105/220 (47%), Gaps = 13/220 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                 ++L+ D ++ + +KP+G+    G G        L + V        L HRLD++
Sbjct: 6   PPQDPLVILHHDHQVLLVDKPSGLLSVPGKGEDLT--DCLIARVQRIFPDALLVHRLDRD 63

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++ A T  A +HL   F  R+ +K Y + VWG   +K   +   L+         +
Sbjct: 64  TSGVMIFAMTPHAQRHLGLQFENRQTKKTYVARVWGEMADKTGTVDLPLIVDWPNRPLQM 123

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                + +    A++ ++V+         + + P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 124 ----VDHENGRAAVTDWRVV-RVGGGETRVRLMPKTGRSHQLRVHMLALGHPILGDPFYA 178

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                +       +L LH+  +   HP+GG+ ++ITAP P
Sbjct: 179 TGPARDHP-----RLMLHSETLQFRHPDGGQGIRITAPCP 213


>gi|191167762|ref|ZP_03029569.1| pseudouridine synthase, RluA family [Escherichia coli B7A]
 gi|190902188|gb|EDV61930.1| pseudouridine synthase, RluA family [Escherichia coli B7A]
          Length = 219

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLSLGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|331702115|ref|YP_004399074.1| RluA family pseudouridine synthase [Lactobacillus buchneri NRRL
           B-30929]
 gi|329129458|gb|AEB74011.1| pseudouridine synthase, RluA family [Lactobacillus buchneri NRRL
           B-30929]
          Length = 292

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 69/316 (21%), Positives = 128/316 (40%), Gaps = 37/316 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRS--GQVRVDKKRVKFNNRIQSGQVVRIP 68
            V +++    L ++       I+   + K  ++  GQ RV  ++V     +++G  V + 
Sbjct: 6   TVTDND-PQSLKKFLNT--KGISH-RMYKSAKTDGGQFRVGGRKVDATVVLRAGDQVTVD 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAY 127
               A           D +V +++        ++YED    + +KPAG++V  G      
Sbjct: 62  FPAEAS----------DPNVAVSRQ----PISVIYEDDNWLIVDKPAGLTVVPGPANRDD 107

Query: 128 HIDGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            +   +K  +   G +   P +  RLD+ TSG++++A+ R A     E    + + K Y 
Sbjct: 108 TLVNRVKGHLVENGAEDLVPHIITRLDRFTSGLVLIAKHRLANSLANEMLAAKTLHKQYQ 167

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++V G+   K   I   + K     G  +            A + + V D   +    ++
Sbjct: 168 AVVAGVGLQKHGFIDRPIAKDPTGYGQRITA------DGKPAQTEYWV-DQAYEDRTLVD 220

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +  HTGRTHQ+RVH   +  P++GD  Y    +         +  LHA  ++   P   R
Sbjct: 221 VVLHTGRTHQIRVHFASIDHPLLGDALYHGPME-----LGIGRQALHATQLNFEDPFSNR 275

Query: 305 -LQITAPLPAHMVKTW 319
            L   + LP  +    
Sbjct: 276 ALSFKSQLPQDISALL 291


>gi|331661428|ref|ZP_08362352.1| pseudouridine synthase A [Escherichia coli TA143]
 gi|331061343|gb|EGI33306.1| pseudouridine synthase A [Escherichia coli TA143]
          Length = 219

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 108/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R+ +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFRERKPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|209694302|ref|YP_002262230.1| tRNA pseudouridine synthase C [Aliivibrio salmonicida LFI1238]
 gi|208008253|emb|CAQ78398.1| tRNA pseudouridine synthase C [Aliivibrio salmonicida LFI1238]
          Length = 263

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 110/250 (44%), Gaps = 17/250 (6%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +    ++  ++Y D  +   NKPAG+ V       +     +++  D  GQ     HRL
Sbjct: 17  EEKPKPIELEIVYRDDDLIAINKPAGMLVHRSWLDKHETVFAMQTLRDQIGQHVFPLHRL 76

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSGIL  A + A A   +  F  R I+K Y ++V G    ++  I ++ LK+     
Sbjct: 77  DRPTSGILFFALSSAVAAQFSPLFASREIKKTYHAIVRGWI--EEGDILDYPLKEQLDKI 134

Query: 211 DYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHAL 260
                 K  E  A  AI+ +K +               ++C +E++PHTGR HQLR H  
Sbjct: 135 ADKKASKDVE--AKEAITEYKPLANVELPYSTGKFPTSRYCLMELKPHTGRKHQLRRHMA 192

Query: 261 HMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
           H+  PIVGD  +  +        +   ++L LHA  +   HP   + + I A +     K
Sbjct: 193 HLRHPIVGDTTHGDSKHNRLFQNNLDSHRLLLHASELSFIHPSTNKHVVIKASVGEKWNK 252

Query: 318 TWDSLGFKYD 327
                G++ +
Sbjct: 253 LMADFGWEIE 262


>gi|315641865|ref|ZP_07896857.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           italicus DSM 15952]
 gi|315482433|gb|EFU72973.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           italicus DSM 15952]
          Length = 316

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 67/272 (24%), Positives = 114/272 (41%), Gaps = 29/272 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R   V V+ +   F+  +++G  + +    +            D S          +  
Sbjct: 62  IRK-NVWVNDQLALFHQEVRAGDRITLRLEAD------------DYSYQPVALGQASRVS 108

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + + NKPAGI            +   +K+++  K Q+  + HRLD+ETSG+++
Sbjct: 109 VLFEDEHLLLVNKPAGIKTHPNQPNEDDTLLNDIKAYLAPKQQQAYVVHRLDKETSGVIL 168

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+       L      ++I + Y ++V G        I   + +  H     V     +
Sbjct: 169 FAKNPLVLPILGRLLEQKKIYRTYQAIVTGKLTKNC-TIRKKIGRDRHDRRKRVI----D 223

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           E+    A++H +VI   +Q    +  Q  TGRTHQ+RVH   +G PI+GD  Y       
Sbjct: 224 ERHGQQAVTHVQVIQVHSQ-TTNITCQLETGRTHQIRVHLASIGHPIIGDSLYQTKPAE- 281

Query: 280 FTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
                  +L+LHA  M   HP     + I  P
Sbjct: 282 -------RLFLHAYQMHFIHPFTQQEMTIATP 306


>gi|294792069|ref|ZP_06757217.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           6_1_27]
 gi|294457299|gb|EFG25661.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           6_1_27]
          Length = 321

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 74/353 (20%), Positives = 134/353 (37%), Gaps = 66/353 (18%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M   T +  ++V++D     ++   K    HI+    +++   G + ++ K   +N  I 
Sbjct: 1   MKTATIID-LIVDSDVHTQSINHIIKQQ--HISQRMRRRLRSDGIITINGKPATWNTLIH 57

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +         +  EQ+   S + L          ++YED  I V NK AGI + 
Sbjct: 58  GGDHLIM--------KLTPEQEFSLSPMELD---------IIYEDEYILVINKAAGILMH 100

Query: 121 GGSGIAYHI--DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             S +  H   +G L  + ++ +       HRLD++TSGI+++A+T        +     
Sbjct: 101 PTSTVRDHTLANGVLHYYQETNQHYDFHPVHRLDKDTSGIVIIAKTSVVQHAFDKKHTY- 159

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF- 236
              K Y ++V G   +    I   + +K    G  +     ++     A +   VI    
Sbjct: 160 -FYKSYDAIVEGHLPSVPISINWPIGRKP---GSIIERCCTDQ--GKPARTDITVISKNT 213

Query: 237 ----------------------------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                                          F  ++   HTGRTHQ+RVH   +G P+ G
Sbjct: 214 SKINYSKNNSDNLINNSNICPTDNSLIDHNHFTHVQCLLHTGRTHQIRVHLSQLGYPLAG 273

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           D  Y  + +         +  LHA ++   HP     +++ A +P  M    +
Sbjct: 274 DDLYGGHLE------FIQRQALHASHVSFYHPITNEWIELHAEMPEDMNVLLN 320


>gi|333010548|gb|EGK29981.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           VA-6]
          Length = 219

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 106/226 (46%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A       ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARAVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|126730410|ref|ZP_01746221.1| ribosomal large subunit pseudouridine synthase A [Sagittula
           stellata E-37]
 gi|126709143|gb|EBA08198.1| ribosomal large subunit pseudouridine synthase A [Sagittula
           stellata E-37]
          Length = 214

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 70/220 (31%), Positives = 105/220 (47%), Gaps = 13/220 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                 ++L+EDS + V +KPAG+    G G A  +   L S +++     RL HRLD++
Sbjct: 6   PPSGDIVVLHEDSDLLVVDKPAGLLSVPGKGAA--LADCLLSRLEAAFPTVRLVHRLDRD 63

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V   T  A +HL   F  R+ +K Y + V G    K   +   L+          
Sbjct: 64  TSGVMVFGLTAHAQRHLGAQFEARKTKKTYVARVAGRLAPKSGEVDLPLIVD-WPNRPRQ 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            V   N      A++ +KV+   +     + + PHTGR+HQLRVH L +G PI+GD  Y 
Sbjct: 123 MVCHDN---GKPALTGWKVMKA-SDAESRVRLFPHTGRSHQLRVHMLALGHPILGDELYA 178

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                 +      ++ LHA  + L HPE GR +    P P
Sbjct: 179 PETAAQYP-----RMMLHAEELRLSHPESGRGMSFRQPAP 213


>gi|159045646|ref|YP_001534440.1| ribosomal large subunit pseudouridine synthase A [Dinoroseobacter
           shibae DFL 12]
 gi|157913406|gb|ABV94839.1| ribosomal large subunit pseudouridine synthase A [Dinoroseobacter
           shibae DFL 12]
          Length = 219

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 105/230 (45%), Gaps = 13/230 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +      T         L++ED+ + +  KP+G+    G G    +   L S V      
Sbjct: 1   MPPIPPDTYAPPQEPLRLVHEDAHLLLVEKPSGLLSVPGRGPE--LADCLLSRVQGAFPD 58

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD++TSG++V A T  A +HL   F  R+I+K Y + VWG        +   L+
Sbjct: 59  ALLVHRLDRDTSGLMVFALTAHAQRHLGLQFEKRQIKKSYVARVWGQVAEATGTVDLPLI 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
               +      + K + +    A++ ++V+   ++    + + P TGR+HQLRVH   +G
Sbjct: 119 ----VDWPNRPLQKVDPETGKAAVTDWRVLKR-SEAETRVRLFPKTGRSHQLRVHMQALG 173

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            PI+GD  Y       F      +L LH+  + L HP+GG  +   +  P
Sbjct: 174 HPILGDPFYAEGAARAFP-----RLMLHSESLRLRHPDGGVGMTFRSKPP 218


>gi|325474713|gb|EGC77899.1| RNA pseudouridylate synthase [Treponema denticola F0402]
          Length = 244

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 80/240 (33%), Positives = 123/240 (51%), Gaps = 22/240 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGI 157
           +LYED  I + NK A + V        A  +D  L+     KG+ K    HRLD+ETSG+
Sbjct: 8   ILYEDKDILIVNKSADLLVGADRWDSEAPRLDKILEELYKDKGERKIYPVHRLDKETSGL 67

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A    A + L + F+ R+I+KIY ++  GIP+ +       L     I GD +H   
Sbjct: 68  IIYALNAEAHKILNDDFQNRKIEKIYHAVSAGIPQEENFKTEAKL----RIDGDKLHRTV 123

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---- 273
            +EK    +++ F ++  F++ FC LE +P TGRTHQ+R H  H+G PI+ D+ Y     
Sbjct: 124 IDEKKGKESLTEFSLLKKFSR-FCLLEARPITGRTHQIRAHLKHLGLPILCDNLYGNGEP 182

Query: 274 -------ANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
                   N++GN     PI ++L LHA  +   HP    +++I+A  P  M    + LG
Sbjct: 183 VYISALKKNWRGNKYEERPIISRLALHAHSLKFFHPISKEKIEISASCPKDMAGLINQLG 242


>gi|94986325|ref|YP_605689.1| pseudouridine synthase, RluD [Deinococcus geothermalis DSM 11300]
 gi|94556606|gb|ABF46520.1| Pseudouridine synthase, RluD [Deinococcus geothermalis DSM 11300]
          Length = 301

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 76/305 (24%), Positives = 120/305 (39%), Gaps = 29/305 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            + L  +   HY H +  + Q  L  G+V +D         ++ GQV+            
Sbjct: 19  GLTLLAYLTRHYLHSSESDWQARLERGEVCLDGLPAYGPETLRPGQVLEWH--------- 69

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                         +    L   ++Y D+ +    KP+G+    G G   H    L + V
Sbjct: 70  ---------RPPWEEEDAPLDFAVVYRDAALLAVAKPSGLPTLPGGGFLKH---TLLAQV 117

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +   + R  HRL + TSG+++ ART  A   L  ++R+R +QK Y +L  G P  ++  
Sbjct: 118 RTDFPEARPLHRLGRGTSGLVLFARTHEAGAILARAWRVRAVQKRYRALAVGTPLQEEYA 177

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   +    H     V       K A+       V++  A       +  HTGR HQ+R+
Sbjct: 178 ITTPIGPVPHPRLGSVFAASAAGKAASSLA---HVLERRA-ATALFAVDIHTGRPHQIRI 233

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHP-EGGRLQITAPLPA 313
           H   +G P+VGD  Y +        P         LHA  +   HP  G RL + AP P 
Sbjct: 234 HLAAIGHPLVGDPLYASGGLPRADLPGLPGDLGYLLHAERLTFLHPLTGERLSLKAPPPP 293

Query: 314 HMVKT 318
            + + 
Sbjct: 294 ELRRA 298


>gi|126736207|ref|ZP_01751950.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           CCS2]
 gi|126714373|gb|EBA11241.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           CCS2]
          Length = 214

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 62/223 (27%), Positives = 108/223 (48%), Gaps = 13/223 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             +      ++L++D ++ + +KP+G+    G G   H+   L + V +      L HRL
Sbjct: 3   DYNPPQDPLVILHDDHQVLLVDKPSGLLSVPGKG--EHLADCLLARVQAAFPMALLVHRL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+++ A T  A +HL   F  R+ +K Y + VWG    K   +   L+       
Sbjct: 61  DRDTSGVMIFALTPHAQRHLGLQFEKRQTKKTYVARVWGEMTEKTGTVDLPLIVDWPNRP 120

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + +    A++ ++V+         + + P TGR+HQLRVH L +G PI+GD 
Sbjct: 121 RQM----VDHENGKQAVTDWRVV-RAKDGETRVRLMPRTGRSHQLRVHMLALGHPILGDP 175

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            Y      +       +L LH+  +   HP+GG+ ++ITA  P
Sbjct: 176 FYAEGKARDHP-----RLMLHSETLQFRHPDGGQGIRITAKCP 213


>gi|295696332|ref|YP_003589570.1| pseudouridine synthase [Bacillus tusciae DSM 2912]
 gi|295411934|gb|ADG06426.1| pseudouridine synthase [Bacillus tusciae DSM 2912]
          Length = 356

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 69/339 (20%), Positives = 120/339 (35%), Gaps = 54/339 (15%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             V   +   ++    L+   +     ++   ++++ R  ++ V+ +       ++ G  
Sbjct: 28  PQVFRYIAGAEDRGKTLEEILRR--GGLSGRRIRRLAREKKILVNGRVSFLAKPMKPGDR 85

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ---G 121
           V              E  + +               +LYED  + V +KPAG+ V     
Sbjct: 86  V--------------EADLREIGRKAGTTESNPSIPILYEDDWVLVIDKPAGLVVHAPAP 131

Query: 122 GSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                      L   + S+G        P L HRLD++T G+L+ A++      L  + R
Sbjct: 132 ARRTGRPGTTSLADILHSRGAAANPPWVPHLVHRLDRDTGGVLLAAKSAHIHARLDRALR 191

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF----- 230
              I +IY  +  G      E I   +       G      +  + GA  A++       
Sbjct: 192 EGGIHRIYSVVAEGNAMEIPERIELPVAPDPGRPG-RFRPAEPGDAGAKPAVTRVCGRRF 250

Query: 231 ---------------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                          +          +L++   TGRTHQ+RVH   +G PI+GD  Y + 
Sbjct: 251 IPLPAPAAPRGSPLDEPRWSALSGVTFLDVSLETGRTHQIRVHLSALGHPILGDRWYGSR 310

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                       L L AR +  PHP  G  +++ AP P 
Sbjct: 311 HPNL-------PLMLFARSLTFPHPADGHSVEVAAPFPE 342


>gi|253563535|ref|ZP_04840992.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_2_5]
 gi|265762620|ref|ZP_06091188.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_1_16]
 gi|251947311|gb|EES87593.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_2_5]
 gi|263255228|gb|EEZ26574.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_1_16]
          Length = 539

 Score =  179 bits (453), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 72/243 (29%), Positives = 111/243 (45%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  +       S  +   +L+ED  + V +KP G+    G      I
Sbjct: 308 CEPILRHMLQGLNVEPAPSERYSLSQNMPE-ILFEDQWLLVLHKPEGVLSVPGKSEEQSI 366

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++    +   P + HRLD  TSG+L+ A+T+   +HL   F  R I+K Y +L+ G
Sbjct: 367 YSLLRARY-PEATGPLVVHRLDMATSGLLLAAKTQEVHRHLQAQFENRSIKKRYIALLDG 425

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I   ++  I   +          +     NE+    AI+ ++V+D        +   P T
Sbjct: 426 ILPEEEGVIDLPICPDYLDRPRQM----VNEELGKTAITRYRVMDRK-NGQTRIAFFPLT 480

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
           GRTHQLRVHA H   + CPIVGD  Y    +         +LYLHA Y++  HP  G R+
Sbjct: 481 GRTHQLRVHAAHPLGLNCPIVGDELYGRKAE---------RLYLHAEYLEFIHPVSGQRM 531

Query: 306 QIT 308
            I 
Sbjct: 532 VIE 534


>gi|15602344|ref|NP_245416.1| tRNA pseudouridine synthase C [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|34582475|sp|Q9CNF3|TRUC_PASMU RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|12720737|gb|AAK02563.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 243

 Score =  179 bits (453), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 59/244 (24%), Positives = 103/244 (42%), Gaps = 17/244 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MTLEILYQDPYLIAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVYPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A +   A  L   F  +++QK Y ++V G    +        ++   I   +    
Sbjct: 61  VLLFALSSEVANLLCLQFENKQVQKSYLAIVRGYLVGEGRIDYPLKVQLDKIADKFA--- 117

Query: 217 KQNEKGANYAISH----------FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            Q++K    A++           + V      ++  + + PHTGR HQLR H  H+  PI
Sbjct: 118 -QDDKAPQEAVTDYLGLAKVEMPYCVKKYPTTRYSLVRLIPHTGRKHQLRRHMKHLFHPI 176

Query: 267 VGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           +GD +Y    +     T     +L LHA  +   HP    ++ I A +    +   +   
Sbjct: 177 LGDTQYGDLHQNRALTTHTGVQRLMLHAERLIFTHPITQQQITICAGVDQQWLDLINIFD 236

Query: 324 FKYD 327
           +  +
Sbjct: 237 WDLN 240


>gi|157148329|ref|YP_001455648.1| tRNA pseudouridine synthase C [Citrobacter koseri ATCC BAA-895]
 gi|157085534|gb|ABV15212.1| hypothetical protein CKO_04146 [Citrobacter koseri ATCC BAA-895]
          Length = 260

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 66/261 (25%), Positives = 112/261 (42%), Gaps = 21/261 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G   ++       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMDEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK-- 325
           K+      +         +L LHA  + L HP  G  L + A L    ++     G++  
Sbjct: 180 KHGDLRQNRSAAEHFGCQRLMLHASQLTLTHPFTGEPLILRAGLDDVWMQALSQFGWRGL 239

Query: 326 --YDRNLYIKRLYSQDECKQN 344
              +  +    L  QDE  Q 
Sbjct: 240 LPENERVEFNALSRQDENNQA 260


>gi|167757078|ref|ZP_02429205.1| hypothetical protein CLORAM_02627 [Clostridium ramosum DSM 1402]
 gi|167703253|gb|EDS17832.1| hypothetical protein CLORAM_02627 [Clostridium ramosum DSM 1402]
          Length = 278

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 62/300 (20%), Positives = 124/300 (41%), Gaps = 41/300 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIP 68
            ++   E  M L  +       ++   + K+++  G++ V+ +R      ++ G VV + 
Sbjct: 3   FIIAMKESGMLLREFLSQQ--ELSKKAV-KLIKMHGKILVNGQRQTVRYCLRYGDVVELL 59

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AY 127
                                 T     L   + YED    V +KPAG+           
Sbjct: 60  WPEEVS----------------TMEPYPLALKICYEDENFLVIDKPAGLPSIPTKRYPRN 103

Query: 128 HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +  +  S+G K    L +RLD++T G+L++A+   A   L+     ++++++Y  
Sbjct: 104 TLANAVVYYYQSQGIKATVHLVNRLDKDTQGLLLIAKNSYAHYLLSRDI--KQVRRVYHC 161

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+    +  I   ++K        +H          +A++H++ ++  A +   +E 
Sbjct: 162 VVEGVLTG-QGTITAPIIKDKKSVKRLIH------PAGKFAVTHYRGLEVSANQ-SKIEC 213

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              TGRTHQ+RVH   +  P+VGD  Y + ++ ++        YL +  +    P   RL
Sbjct: 214 ILETGRTHQIRVHLSSINHPLVGDTLYDSIYQESY--------YLDSIALSFIDPFTQRL 265


>gi|16128052|ref|NP_414600.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           MG1655]
 gi|30061623|ref|NP_835794.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella flexneri 2a str.
           2457T]
 gi|74310675|ref|YP_309094.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella sonnei Ss046]
 gi|82542662|ref|YP_406609.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella boydii Sb227]
 gi|82775462|ref|YP_401809.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella dysenteriae Sd197]
 gi|89106942|ref|AP_000722.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           W3110]
 gi|110640270|ref|YP_667998.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli 536]
 gi|110804122|ref|YP_687642.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella flexneri 5 str.
           8401]
 gi|157159461|ref|YP_001461228.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli E24377A]
 gi|157159527|ref|YP_001456845.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli HS]
 gi|170021586|ref|YP_001726540.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli ATCC 8739]
 gi|170079719|ref|YP_001729039.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170679993|ref|YP_001742177.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli SMS-3-5]
 gi|188492494|ref|ZP_02999764.1| pseudouridine synthase, RluA family [Escherichia coli 53638]
 gi|191174210|ref|ZP_03035721.1| pseudouridine synthase, RluA family [Escherichia coli F11]
 gi|193065885|ref|ZP_03046946.1| pseudouridine synthase, RluA family [Escherichia coli E22]
 gi|193070842|ref|ZP_03051775.1| pseudouridine synthase, RluA family [Escherichia coli E110019]
 gi|194429362|ref|ZP_03061887.1| pseudouridine synthase, RluA family [Escherichia coli B171]
 gi|209917249|ref|YP_002291333.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli SE11]
 gi|218547506|ref|YP_002381297.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia fergusonii ATCC
           35469]
 gi|218552641|ref|YP_002385554.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli IAI1]
 gi|218687934|ref|YP_002396146.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli ED1a]
 gi|218693528|ref|YP_002401195.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli 55989]
 gi|218698480|ref|YP_002406109.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli IAI39]
 gi|218703318|ref|YP_002410837.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli UMN026]
 gi|238899461|ref|YP_002925257.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli BW2952]
 gi|253774912|ref|YP_003037743.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254037473|ref|ZP_04871550.1| pseudouridine synthase for 23S rRNA and tRNA [Escherichia sp.
           1_1_43]
 gi|254160181|ref|YP_003043289.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B str.
           REL606]
 gi|256020104|ref|ZP_05433969.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella sp. D9]
 gi|256025373|ref|ZP_05439238.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia sp. 4_1_40B]
 gi|260842293|ref|YP_003220071.1| pseudouridine synthase [Escherichia coli O103:H2 str. 12009]
 gi|293403132|ref|ZP_06647229.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           FVEC1412]
 gi|293408151|ref|ZP_06651991.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B354]
 gi|293476720|ref|ZP_06665128.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           B088]
 gi|297517418|ref|ZP_06935804.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli OP50]
 gi|298378660|ref|ZP_06988544.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           FVEC1302]
 gi|300816093|ref|ZP_07096316.1| pseudouridine synthase A [Escherichia coli MS 107-1]
 gi|300821939|ref|ZP_07102083.1| pseudouridine synthase A [Escherichia coli MS 119-7]
 gi|300900916|ref|ZP_07119052.1| pseudouridine synthase A [Escherichia coli MS 198-1]
 gi|300905460|ref|ZP_07123226.1| pseudouridine synthase A [Escherichia coli MS 84-1]
 gi|300919609|ref|ZP_07136101.1| pseudouridine synthase A [Escherichia coli MS 115-1]
 gi|300923165|ref|ZP_07139223.1| pseudouridine synthase A [Escherichia coli MS 182-1]
 gi|300939473|ref|ZP_07154135.1| pseudouridine synthase A [Escherichia coli MS 21-1]
 gi|300948662|ref|ZP_07162745.1| pseudouridine synthase A [Escherichia coli MS 116-1]
 gi|300956988|ref|ZP_07169239.1| pseudouridine synthase A [Escherichia coli MS 175-1]
 gi|300984199|ref|ZP_07176927.1| pseudouridine synthase A [Escherichia coli MS 200-1]
 gi|301024876|ref|ZP_07188512.1| pseudouridine synthase A [Escherichia coli MS 196-1]
 gi|301026173|ref|ZP_07189644.1| pseudouridine synthase A [Escherichia coli MS 69-1]
 gi|301305052|ref|ZP_07211153.1| pseudouridine synthase A [Escherichia coli MS 124-1]
 gi|301330173|ref|ZP_07222835.1| pseudouridine synthase A [Escherichia coli MS 78-1]
 gi|301648375|ref|ZP_07248112.1| pseudouridine synthase A [Escherichia coli MS 146-1]
 gi|306815344|ref|ZP_07449493.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli NC101]
 gi|307136660|ref|ZP_07496016.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli H736]
 gi|307311490|ref|ZP_07591132.1| pseudouridine synthase [Escherichia coli W]
 gi|309796045|ref|ZP_07690457.1| pseudouridine synthase A [Escherichia coli MS 145-7]
 gi|312970151|ref|ZP_07784333.1| RNA pseudouridylate synthase family protein [Escherichia coli
           1827-70]
 gi|331640509|ref|ZP_08341657.1| pseudouridine synthase A [Escherichia coli H736]
 gi|331650951|ref|ZP_08351979.1| pseudouridine synthase A [Escherichia coli M718]
 gi|331666293|ref|ZP_08367174.1| pseudouridine synthase A [Escherichia coli TA271]
 gi|331680629|ref|ZP_08381288.1| pseudouridine synthase A [Escherichia coli H591]
 gi|332281257|ref|ZP_08393670.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella sp. D9]
 gi|76363883|sp|P0AA37|RLUA_ECOLI RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|92090791|sp|P0AA38|RLUA_SHIFL RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|1786244|gb|AAC73169.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           MG1655]
 gi|30039865|gb|AAP15599.1| hypothetical protein S0055 [Shigella flexneri 2a str. 2457T]
 gi|73854152|gb|AAZ86859.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|81239610|gb|ABB60320.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
 gi|81244073|gb|ABB64781.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|85674306|dbj|BAE76039.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K12 substr.
           W3110]
 gi|110341862|gb|ABG68099.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           536]
 gi|110613670|gb|ABF02337.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|157065207|gb|ABV04462.1| pseudouridine synthase, RluA family [Escherichia coli HS]
 gi|157081491|gb|ABV21199.1| pseudouridine synthase, RluA family [Escherichia coli E24377A]
 gi|169756514|gb|ACA79213.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|169887554|gb|ACB01261.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170517711|gb|ACB15889.1| pseudouridine synthase, RluA family [Escherichia coli SMS-3-5]
 gi|188487693|gb|EDU62796.1| pseudouridine synthase, RluA family [Escherichia coli 53638]
 gi|190905495|gb|EDV65123.1| pseudouridine synthase, RluA family [Escherichia coli F11]
 gi|192926472|gb|EDV81105.1| pseudouridine synthase, RluA family [Escherichia coli E22]
 gi|192955872|gb|EDV86342.1| pseudouridine synthase, RluA family [Escherichia coli E110019]
 gi|194412582|gb|EDX28879.1| pseudouridine synthase, RluA family [Escherichia coli B171]
 gi|209910508|dbj|BAG75582.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           SE11]
 gi|218350260|emb|CAU95943.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli 55989]
 gi|218355047|emb|CAQ87653.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia fergusonii ATCC 35469]
 gi|218359409|emb|CAQ96948.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli IAI1]
 gi|218368466|emb|CAR16202.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli IAI39]
 gi|218425498|emb|CAR06280.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli ED1a]
 gi|218430415|emb|CAR11282.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli UMN026]
 gi|226840579|gb|EEH72581.1| pseudouridine synthase for 23S rRNA and tRNA [Escherichia sp.
           1_1_43]
 gi|238863331|gb|ACR65329.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli BW2952]
 gi|242375895|emb|CAQ30576.1| 23S rRNA and tRNA pseudouridine synthase [Escherichia coli
           BL21(DE3)]
 gi|253325956|gb|ACT30558.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253972082|gb|ACT37753.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli B str. REL606]
 gi|253976291|gb|ACT41961.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli BL21(DE3)]
 gi|257757440|dbj|BAI28937.1| pseudouridine synthase [Escherichia coli O103:H2 str. 12009]
 gi|281177273|dbj|BAI53603.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           SE15]
 gi|284919840|emb|CBG32895.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           042]
 gi|291321173|gb|EFE60615.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           B088]
 gi|291430047|gb|EFF03061.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           FVEC1412]
 gi|291472402|gb|EFF14884.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B354]
 gi|298280994|gb|EFI22495.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           FVEC1302]
 gi|299880242|gb|EFI88453.1| pseudouridine synthase A [Escherichia coli MS 196-1]
 gi|300306729|gb|EFJ61249.1| pseudouridine synthase A [Escherichia coli MS 200-1]
 gi|300316231|gb|EFJ66015.1| pseudouridine synthase A [Escherichia coli MS 175-1]
 gi|300355628|gb|EFJ71498.1| pseudouridine synthase A [Escherichia coli MS 198-1]
 gi|300395642|gb|EFJ79180.1| pseudouridine synthase A [Escherichia coli MS 69-1]
 gi|300402676|gb|EFJ86214.1| pseudouridine synthase A [Escherichia coli MS 84-1]
 gi|300413355|gb|EFJ96665.1| pseudouridine synthase A [Escherichia coli MS 115-1]
 gi|300420558|gb|EFK03869.1| pseudouridine synthase A [Escherichia coli MS 182-1]
 gi|300451839|gb|EFK15459.1| pseudouridine synthase A [Escherichia coli MS 116-1]
 gi|300455694|gb|EFK19187.1| pseudouridine synthase A [Escherichia coli MS 21-1]
 gi|300525539|gb|EFK46608.1| pseudouridine synthase A [Escherichia coli MS 119-7]
 gi|300531300|gb|EFK52362.1| pseudouridine synthase A [Escherichia coli MS 107-1]
 gi|300839659|gb|EFK67419.1| pseudouridine synthase A [Escherichia coli MS 124-1]
 gi|300843813|gb|EFK71573.1| pseudouridine synthase A [Escherichia coli MS 78-1]
 gi|301073563|gb|EFK88369.1| pseudouridine synthase A [Escherichia coli MS 146-1]
 gi|305851006|gb|EFM51461.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli NC101]
 gi|306908469|gb|EFN38967.1| pseudouridine synthase [Escherichia coli W]
 gi|308120287|gb|EFO57549.1| pseudouridine synthase A [Escherichia coli MS 145-7]
 gi|309700270|emb|CBI99558.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           ETEC H10407]
 gi|310337649|gb|EFQ02760.1| RNA pseudouridylate synthase family protein [Escherichia coli
           1827-70]
 gi|313646565|gb|EFS11026.1| RNA pseudouridylate synthase family protein [Shigella flexneri 2a
           str. 2457T]
 gi|315059282|gb|ADT73609.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli W]
 gi|315255668|gb|EFU35636.1| pseudouridine synthase A [Escherichia coli MS 85-1]
 gi|315616165|gb|EFU96784.1| RNA pseudouridylate synthase family protein [Escherichia coli 3431]
 gi|320179617|gb|EFW54566.1| Ribosomal large subunit pseudouridine synthase A [Shigella boydii
           ATCC 9905]
 gi|320200424|gb|EFW75010.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           EC4100B]
 gi|323160072|gb|EFZ46034.1| RNA pseudouridylate synthase family protein [Escherichia coli
           E128010]
 gi|323166108|gb|EFZ51887.1| RNA pseudouridylate synthase family protein [Shigella sonnei 53G]
 gi|323380161|gb|ADX52429.1| pseudouridine synthase [Escherichia coli KO11]
 gi|323935111|gb|EGB31478.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323939843|gb|EGB36044.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323945687|gb|EGB41735.1| RNA pseudouridylate synthase [Escherichia coli H120]
 gi|323960005|gb|EGB55651.1| RNA pseudouridylate synthase [Escherichia coli H489]
 gi|323964843|gb|EGB60310.1| RNA pseudouridylate synthase [Escherichia coli M863]
 gi|323975775|gb|EGB70871.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
 gi|324008404|gb|EGB77623.1| pseudouridine synthase A [Escherichia coli MS 57-2]
 gi|324012314|gb|EGB81533.1| pseudouridine synthase A [Escherichia coli MS 60-1]
 gi|324017675|gb|EGB86894.1| pseudouridine synthase A [Escherichia coli MS 117-3]
 gi|324112541|gb|EGC06518.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
 gi|325495982|gb|EGC93841.1| pseudouridine synthase [Escherichia fergusonii ECD227]
 gi|327255037|gb|EGE66640.1| RNA pseudouridylate synthase family protein [Escherichia coli
           STEC_7v]
 gi|330909906|gb|EGH38416.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           AA86]
 gi|331040255|gb|EGI12462.1| pseudouridine synthase A [Escherichia coli H736]
 gi|331051405|gb|EGI23454.1| pseudouridine synthase A [Escherichia coli M718]
 gi|331066504|gb|EGI38381.1| pseudouridine synthase A [Escherichia coli TA271]
 gi|331072092|gb|EGI43428.1| pseudouridine synthase A [Escherichia coli H591]
 gi|332098910|gb|EGJ03861.1| RNA pseudouridylate synthase family protein [Shigella boydii
           3594-74]
 gi|332103609|gb|EGJ06955.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella sp. D9]
 gi|332341388|gb|AEE54722.1| pseudouridine synthase RluA [Escherichia coli UMNK88]
 gi|332762617|gb|EGJ92882.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           4343-70]
 gi|332764899|gb|EGJ95127.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-671]
 gi|333009190|gb|EGK28646.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-218]
 gi|333011440|gb|EGK30854.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-272]
 gi|333021679|gb|EGK40928.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-227]
 gi|333022430|gb|EGK41668.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-304]
          Length = 219

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|296125314|ref|YP_003632566.1| pseudouridine synthase [Brachyspira murdochii DSM 12563]
 gi|296017130|gb|ADG70367.1| pseudouridine synthase [Brachyspira murdochii DSM 12563]
          Length = 336

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 67/336 (19%), Positives = 137/336 (40%), Gaps = 39/336 (11%)

Query: 5   TYVQYVVVEND-EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           + ++   +E + ++++RLD++  + + + +    Q ++  G V ++ K+VK+   I  G 
Sbjct: 19  SVIRKCRIEENIDDSIRLDKYMGDRFSYYSRNKWQDLIGQGLVLLNGKKVKYTRTINKGD 78

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +    +      + K                     ++Y+D  + + NKPA + V    
Sbjct: 79  EIEYHIIGMKEPEVDKN------------------VTIIYDDGDLIIANKPANLPVIPSG 120

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-----R 178
              Y+ +               + +R+D+ETSG +V++R    A         R     +
Sbjct: 121 --KYYHNTLHTIVKQMLNCNINMLNRIDRETSGCVVMSRGHETASKFCAMIARRKNTKKK 178

Query: 179 IQKIYWSLVW-GIPKNKKECIANWLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCF 236
           I+K Y ++V           +  ++L+  H     +  + K+N +G+ Y+ + FK I   
Sbjct: 179 IKKTYIAVVENAKNIEDNFIVEGYMLESGHEYYRRFQTLHKENIEGSKYSKTAFKTIKRL 238

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---------K 287
              +  +  + +TGR HQ+RVH       +VGD  Y       F   I+          +
Sbjct: 239 GD-YAIVMARLYTGRMHQIRVHLYSKNLYMVGDKIYGKYGPKVFDDFIEKNIIPEGFFHR 297

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             LHA  ++  HP   + ++I APL   + +    +
Sbjct: 298 QALHAYSLEFNHPINDKLIKIKAPLAKDLKEFIKKI 333


>gi|331004377|ref|ZP_08327850.1| hypothetical protein HMPREF0491_02712 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330411107|gb|EGG90526.1| hypothetical protein HMPREF0491_02712 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 299

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 63/299 (21%), Positives = 130/299 (43%), Gaps = 28/299 (9%)

Query: 24  WFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K+     +  N+  + +    + ++      N + +    + +       +  I    
Sbjct: 19  FLKS--KGYSSSNIIGLKKYENGIMLNGVWAYMNQKPELNDRLLVRVCEYKKSENI---- 72

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKG 141
                         +K  + YED  I V NKP  + +    +     +   L  +   K 
Sbjct: 73  ----------VPVDIKLDIKYEDEDIVVINKPGDMPIHPSLNNYENSLANALMHYYKDKN 122

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
              R  +RLD++T+G+ +VA+   +A  L  + + R+I+++Y ++V    +  KE I + 
Sbjct: 123 FVFRCINRLDKDTTGLTIVAKHFLSAGILNIAMQKRQIKRVYNAIVKDEGRLAKEGIIDL 182

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            + + +       + ++  +    A+++FK+I  F + +  +E++  TGRTHQ+RVH  H
Sbjct: 183 PIAREND----TLIKRKVSEDGQRAVTYFKMIKRFGE-YSLIELRLETGRTHQIRVHMSH 237

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           +G P+ GD+ Y  +  G        +  LH++ +D  HP  G R+ +   LP    +  
Sbjct: 238 IGAPLAGDYLYNESEYGKRNI----RPLLHSKSLDFIHPVTGERIYLECDLPLDFKEKI 292


>gi|25012059|ref|NP_736454.1| hypothetical protein gbs2021 [Streptococcus agalactiae NEM316]
 gi|24413602|emb|CAD47680.1| Unknown [Streptococcus agalactiae NEM316]
          Length = 270

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 60/269 (22%), Positives = 103/269 (38%), Gaps = 28/269 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              V ++ + + +   +Q    + +                 D                L
Sbjct: 13  KKHVLINNEFINWQTVVQENDTITLIFDDE------------DYPTKKIPLGRAELIDCL 60

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + + NKP G+   G      +    L       GQ   + HRLD ETSG ++ A+
Sbjct: 61  YEDEHLIIVNKPEGMKTHGNQP---NEIALLNHVSAYSGQTCYVVHRLDMETSGAVLFAK 117

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  + +    + I + YW+LV G    K + + + + +  H     +     + K 
Sbjct: 118 NPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRDKIGRNRHDRRKRII----DSKN 173

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             +A++   V+    Q    ++ +  TGRTHQ+RVH  H G P++GD  Y  +       
Sbjct: 174 GQHAMTIIDVLKYI-QNSSLIKCRLETGRTHQIRVHLSHHGHPLIGDPLYNPSSNNE--- 229

Query: 283 PIQNKLYLHARYMDLPHPEG-GRLQITAP 310
               +L LHA  + L HP     + + AP
Sbjct: 230 ----RLMLHAHRLTLSHPLTCETISVEAP 254


>gi|260853270|ref|YP_003227161.1| pseudouridine synthase [Escherichia coli O26:H11 str. 11368]
 gi|260866210|ref|YP_003232612.1| pseudouridine synthase [Escherichia coli O111:H- str. 11128]
 gi|257751919|dbj|BAI23421.1| pseudouridine synthase [Escherichia coli O26:H11 str. 11368]
 gi|257762566|dbj|BAI34061.1| pseudouridine synthase [Escherichia coli O111:H- str. 11128]
 gi|323157880|gb|EFZ43983.1| RNA pseudouridylate synthase family protein [Escherichia coli
           EPECa14]
 gi|323176365|gb|EFZ61957.1| RNA pseudouridylate synthase family protein [Escherichia coli 1180]
 gi|324118408|gb|EGC12302.1| RNA pseudouridylate synthase [Escherichia coli E1167]
          Length = 219

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYVADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|307151795|ref|YP_003887179.1| pseudouridine synthase [Cyanothece sp. PCC 7822]
 gi|306982023|gb|ADN13904.1| pseudouridine synthase [Cyanothece sp. PCC 7822]
          Length = 562

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 72/220 (32%), Positives = 104/220 (47%), Gaps = 21/220 (9%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS--WVDSKGQKPRLTHRLDQETSG 156
             ++YED  +   NKP G+    G G ++  D  +     + + G +  + HRLDQ+TSG
Sbjct: 355 LPIIYEDEYLIAINKPEGLLSVPGRG-SHQYDSVISRITHLLADGDQCMVVHRLDQDTSG 413

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           IL++AR R    HL + FR R+I K+Y +LV G    +K  I   L    +         
Sbjct: 414 ILLLARHRQIYNHLAQQFRQRKIHKVYHALVKGGVSAQKGTINLPLWGDPNTRP----RQ 469

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL---HMGCPIVGDHKYC 273
           K +      +I+HF+VI   A+ F  LE  P TGRTHQ+RVH      +G PI+GD  Y 
Sbjct: 470 KVDFCYGKESITHFQVI-AVAENFTRLEFIPVTGRTHQIRVHCADQNGLGTPIIGDRLYG 528

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
                        +L+LHA  +   HP       L +  P
Sbjct: 529 HESATT-------RLHLHAYSLSFVHPTTEEKVYLTVETP 561


>gi|300361258|ref|ZP_07057435.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus gasseri
           JV-V03]
 gi|300353877|gb|EFJ69748.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus gasseri
           JV-V03]
          Length = 299

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 66/284 (23%), Positives = 111/284 (39%), Gaps = 32/284 (11%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G + V+  R   +  + SG  V         N  +K                  +  ++ 
Sbjct: 38  GMILVNHHRRYTSYLLHSGDEVIFILGEEKKNQWLK--------------PSTNQLNIVL 83

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQK---PRLTHRLDQETSGILV 159
           E     V NK AG+            +   L  +    GQK   P +  RLD++TSG+++
Sbjct: 84  EQHDYLVINKEAGVLSIPSRYEDNDAVVNRLLYYFQKNGQKDLKPHVITRLDRDTSGLVL 143

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           V +   A    +E  +   I+K + ++V G    ++E      +  + IG     V +  
Sbjct: 144 VGKNAVAHARFSEMGKDCFIKKYH-AIVHGNFSKEQEI----GIIDAPIGKLDASVKRGI 198

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 +I+ ++V+D        +E+Q  TGRTHQ+RVH  ++  P+ GD  Y    K N
Sbjct: 199 VANGQRSITKYRVLDQV-NGASLVELQLLTGRTHQIRVHMQYLDHPLFGDPLYG--IKDN 255

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           F      +  L+  Y+    P   R  ++T   P  M   W  L
Sbjct: 256 F-----KRQALNCFYLKFDDPFSERKQEVTISEPVDMKCLWQRL 294


>gi|215485220|ref|YP_002327651.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O127:H6
           str. E2348/69]
 gi|312966179|ref|ZP_07780405.1| RNA pseudouridylate synthase family protein [Escherichia coli
           2362-75]
 gi|215263292|emb|CAS07607.1| pseudouridine synthase for 23S rRNA (position 746) and tRNAphe
           (position 32) [Escherichia coli O127:H6 str. E2348/69]
 gi|312289422|gb|EFR17316.1| RNA pseudouridylate synthase family protein [Escherichia coli
           2362-75]
          Length = 219

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  I+LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQDPWLIVLYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|157376301|ref|YP_001474901.1| pseudouridylate synthase [Shewanella sediminis HAW-EB3]
 gi|157318675|gb|ABV37773.1| pseudouridylate synthase [Shewanella sediminis HAW-EB3]
          Length = 278

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 64/278 (23%), Positives = 113/278 (40%), Gaps = 19/278 (6%)

Query: 74  LNHIIKEQKILDSS--VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              + K+  I +S   V         +  +L+ED  +   +KPAG+ V            
Sbjct: 3   EETVEKDPDIAESPEMVEDAVEESAPEIEILFEDDDVVAIHKPAGLLVHRSYLARRERFF 62

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            ++   D  G      HRLD+ TSG+L+ A++   A  L E F  + + K Y ++V G  
Sbjct: 63  AMQLTRDKVGCHVFPVHRLDRPTSGVLLFAKSSEMANKLCEQFEAKTVDKHYLAIVRGNM 122

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFC 241
                      ++    G   V       K A  A++ ++ +               ++ 
Sbjct: 123 HEADTLDYALKVELDDHGDKDV----DPNKAAQDAVTSYQPLLNTEIPFPSGRYATSRYA 178

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPH 299
            +++ PHTGR HQLR H  H+  PIVGD  +    +  F       N+L+L A+++   H
Sbjct: 179 LVKLTPHTGRKHQLRRHMAHLRHPIVGDTTHGDGKQNKFFREHFSMNRLWLIAKHLSFDH 238

Query: 300 PE-GGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLY 336
           P  G R+ I   L       +++ G+  ++    +  +
Sbjct: 239 PRSGERITIETELEEQWFTLFEAFGWDEEKLATDRSYF 276


>gi|303230703|ref|ZP_07317450.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514463|gb|EFL56458.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 306

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/337 (20%), Positives = 134/337 (39%), Gaps = 51/337 (15%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M   T +  ++V+ +     ++   K    HI+    +++   G + ++ +   ++  + 
Sbjct: 1   MKTATIID-LIVDANIHTQSMNHIIKQQ--HISQRMRRRLKNDGIITINGQPATWDTLVH 57

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  +        L  +  EQ+   + ++L          ++YED  I   NK A + + 
Sbjct: 58  GGDHL--------LMKLAPEQEFSRTQMDLE---------IVYEDEYILAINKAASVLMH 100

Query: 121 GGSGI--AYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             S +      +G L  + +  +       HRLD++TSGI+++A+T        +     
Sbjct: 101 PTSTVRDGTLANGVLYYYDETEQAHDFHPVHRLDKDTSGIVIIAKTSVVQHAFDKQRT-- 158

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF- 236
           + QK+Y ++V G   ++   I   + +K+        + +        A +   V+    
Sbjct: 159 KFQKVYDAIVEGTMPSQSLTIKWPIGRKAG-----SIIERCCTSIGKPARTDVTVLARHI 213

Query: 237 -------------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
                         Q    ++   HTGRTHQ+RVH  H+G P+VGD  Y  +        
Sbjct: 214 VSQPVQMDKNLSTQQILTHVQCVLHTGRTHQIRVHLSHLGFPLVGDDLYGGHLD------ 267

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
              +  LHA Y+   HP     +++ APLP  M    
Sbjct: 268 YIRRQALHAGYLAFTHPMTQEYVELRAPLPTDMKDLL 304


>gi|261344742|ref|ZP_05972386.1| hypothetical protein PROVRUST_06000 [Providencia rustigianii DSM
           4541]
 gi|282567184|gb|EFB72719.1| tRNA pseudouridine synthase C [Providencia rustigianii DSM 4541]
          Length = 252

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 103/237 (43%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V      +      +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IIYQDEFVVAVNKPAGMLVHRSWLDSKETVFVMQTLRDQIGQHVYPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L E F   +++K Y ++V G   + +      L +   I   +       E
Sbjct: 64  ALSSEVARLLAEQFEQHKMEKTYHAVVRGYVTDAQRLDYPLLEELDKIADKHAS----KE 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                 ++H++ +               +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 PKLQDCVTHYRPLVTAECPVAIGRYETSRFSLVELKPETGRKHQLRRHMSHLRHPILGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           K+      +G       ++L LHA  +   HP     + + A   A  +   +  G+
Sbjct: 180 KHGDLRQNRGVVEHFGVSRLMLHASQLVFIHPITEEQISLVASWDAQWLSLIEQFGW 236


>gi|163734280|ref|ZP_02141720.1| ribosomal large subunit pseudouridine synthase A [Roseobacter
           litoralis Och 149]
 gi|161392288|gb|EDQ16617.1| ribosomal large subunit pseudouridine synthase A [Roseobacter
           litoralis Och 149]
          Length = 215

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/226 (29%), Positives = 111/226 (49%), Gaps = 15/226 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++ T         +L+ED+++ + +KPAG+    G G   H+   L + V +      L 
Sbjct: 1   MDETYAPPQTPLTVLHEDAEVLLVDKPAGLLSVPGKGP--HLADCLLARVQAMFADALLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG+++ A T  A +HL   F  R  +K Y + +WG+P  K   +   L+    
Sbjct: 59  HRLDRDTSGVMIFALTPHAQRHLGLQFEKRMTRKTYVARIWGVPLEKTGTVDLPLIVD-W 117

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  V     +    A + ++V+    Q    + + P+TGR+HQLRVH L +G PI+
Sbjct: 118 PNRPRQMVC---HETGKSAQTEWRVLKDDGQ-TARVRLHPYTGRSHQLRVHMLALGHPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
           GD  Y      ++      +L LH+  +   HP+GGR   ++ TAP
Sbjct: 174 GDPFYATGPARDYP-----RLMLHSEELRFKHPQGGRSMKVRATAP 214


>gi|227512831|ref|ZP_03942880.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus buchneri ATCC
           11577]
 gi|227083831|gb|EEI19143.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus buchneri ATCC
           11577]
          Length = 299

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 69/310 (22%), Positives = 129/310 (41%), Gaps = 35/310 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   L ++   H   I+   + K ++ SGQV ++ +      ++  G  V +     A  
Sbjct: 19  EPKTLKKFLNTH--GISH-RMYKNIKTSGQVLINSRSSDSQTKLADGDQVTVILHDEAG- 74

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLK 134
                    D +V +++        ++YED    V +KPAG++V  G       +   +K
Sbjct: 75  ---------DPNVAVSEQ----PIKVVYEDDNWLVVDKPAGLTVVPGPANRDDTLVNRVK 121

Query: 135 SWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            ++   G     P +  RLD+ TSG++++A+ R A     E    +++ K Y ++V G+ 
Sbjct: 122 GYLVRAGATDLVPHIITRLDRFTSGLVLIAKHRLANSLANELLAAKQLHKRYLAVVSGVG 181

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   + K  +  G  +           ++ + + V          +E+  HTGR
Sbjct: 182 LPDHGRIQKPIAKDPNGYGQII------SDDGRFSDTEYWVRQRLNDDM-LVEVALHTGR 234

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
           THQ+RVH   +G P++GD  Y         +   ++  LHA  +    P     +++ +P
Sbjct: 235 THQIRVHFASIGHPLLGDQLYHGPM-----NMGIDRQALHAVMLGFNDPFSQSEIKLKSP 289

Query: 311 LPAHMVKTWD 320
           LP  +    D
Sbjct: 290 LPKDISLILD 299


>gi|216263435|ref|ZP_03435430.1| RNA pseudouridine synthase family protein [Borrelia afzelii ACA-1]
 gi|215980279|gb|EEC21100.1| RNA pseudouridine synthase family protein [Borrelia afzelii ACA-1]
          Length = 315

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 133/319 (41%), Gaps = 22/319 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L  YV ++ +  ++   RLD        +++   + K +R G +R++  +  F+ R+ 
Sbjct: 1   MRLDKYV-FLEILANDNGKRLDSILIKIL-NLSKARIIKHIRKGDIRLNGIKSHFSYRVC 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   +    ++      ++           ++  ++YEDS + V +K  GI V 
Sbjct: 59  KGDKIYLYKSLAQGLNL-----TMNECYKSNIDFQCIRERIIYEDSDLLVLDKQRGILVH 113

Query: 121 GGSGIAYHIDG--FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           GG      +     LK  + S   KP   HRLD+ TSGI+V A+    A+ L+ +F    
Sbjct: 114 GGRNSLDFLVNAYLLKEELRSLSFKPAAVHRLDRNTSGIIVFAKNINTARKLSTAFSSGS 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y++++ G  K       N L +   +   +V     + K    AI+    I   ++
Sbjct: 174 ITKKYFAILLGEVK-STVVYKNHLFRNKRLKKTFV----LDGKDFINAITKVNPILS-SK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +    E+   TG THQ+R        P++ D KY   F+       ++  +LHA  +   
Sbjct: 228 RATLAEIVIETGFTHQIRAQCSFNNHPLINDKKYHDKFE-------KSNYFLHAFLVKFN 280

Query: 299 HPEGGRLQITAPLPAHMVK 317
                + +  A      +K
Sbjct: 281 EAFFKKNEFYAKPSLEFLK 299


>gi|78224034|ref|YP_385781.1| pseudouridine synthase, RluD [Geobacter metallireducens GS-15]
 gi|78195289|gb|ABB33056.1| Pseudouridine synthase, RluD [Geobacter metallireducens GS-15]
          Length = 296

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 66/323 (20%), Positives = 123/323 (38%), Gaps = 44/323 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +    +   +    ++ + +N  P      L K+ R G + V+   V  +  + +G  + 
Sbjct: 1   MLTFTITESDHCRGVESFLRNLLPGAPLAYLGKLTRGGHLTVNGLPVTPDTLLVTGDTMA 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +         +  ++  LD               +L+ED +I V NKP G+ V   +   
Sbjct: 61  LKESGRTRELLAAKRPSLD---------------ILFEDDRIVVVNKPPGLPVHRTAEDE 105

Query: 127 YHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +    + ++  +G   K R  +RLD+ TSG  ++A++  +A       +   + K+Y 
Sbjct: 106 QTLVDVAERFLAQRGTPAKLRPVNRLDRGTSGATILAKSATSAGMFGRFVKETGLGKLYL 165

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           ++  G    +   I   L                       A + ++ +    +    L 
Sbjct: 166 AVADGKLPAE-GTIDTPL-------------------EGKEAQTQYRTL-FQGKSAALLL 204

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGG 303
           + P TGRTHQ+R H    G P+ GD +Y       +         LHA  +   HP  G 
Sbjct: 205 VTPITGRTHQIRKHLALTGHPVRGDRRYRGAPLAAYPGH-----CLHAFLVSFRHPVSGE 259

Query: 304 RLQITAPLPAHMVKTWDSLGFKY 326
            + I APLPA +++    L   +
Sbjct: 260 EIVIHAPLPAALLEEVRLLSGDF 282


>gi|325479486|gb|EGC82582.1| pseudouridine synthase, RluA family [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 318

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 58/279 (20%), Positives = 116/279 (41%), Gaps = 27/279 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  + +  ++ N R DR+ + ++ +     +QK +R    +++ KR K ++ + +   V+
Sbjct: 1   MIEIEISENDGNQRFDRFLRKYFENAPLSVIQKNIRKKNFKINDKRAKKDDFVYANDKVK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +          + +        +L          ++YED  I + +K  G+     S   
Sbjct: 61  MYIKDEDYKRWLTKTDFKPQDFDLN---------IIYEDRNIIIMDKDRGVLTHSSSKKD 111

Query: 127 YHI---DGFLKSWVDSKG-------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           Y     D  L     +K         KP + +RLD+ T+G+++ A+   + + L ++ R 
Sbjct: 112 YGNNLVDNMLSYLYKTKSFDMSDKTFKPAVVNRLDRNTAGLVIGAKNAKSLRALNKAIRD 171

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I K Y ++V G    +           ++I  +      +     +   + F+ I+  
Sbjct: 172 NLIDKYYLTIVKGNIAKEFTI-------DTNIKKNENKNKIKRATEGSRIRTFFRPIESN 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             KF  LE +  TG+THQ+R      G PI+GD KY + 
Sbjct: 225 G-KFTLLECKLDTGKTHQIRFSLRENGTPIIGDRKYGSK 262


>gi|323171216|gb|EFZ56864.1| RNA pseudouridylate synthase family protein [Escherichia coli
           LT-68]
          Length = 219

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMAL----RLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|91209118|ref|YP_539104.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli UTI89]
 gi|117622346|ref|YP_851259.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli APEC O1]
 gi|218556997|ref|YP_002389910.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli S88]
 gi|237704202|ref|ZP_04534683.1| ribosomal large subunit pseudouridine synthase A [Escherichia sp.
           3_2_53FAA]
 gi|91070692|gb|ABE05573.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           UTI89]
 gi|115511470|gb|ABI99544.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           APEC O1]
 gi|218363766|emb|CAR01427.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli S88]
 gi|222031890|emb|CAP74628.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           LF82]
 gi|226902114|gb|EEH88373.1| ribosomal large subunit pseudouridine synthase A [Escherichia sp.
           3_2_53FAA]
 gi|294491670|gb|ADE90426.1| pseudouridine synthase, RluA family [Escherichia coli IHE3034]
 gi|307629632|gb|ADN73936.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli UM146]
 gi|312944664|gb|ADR25491.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O83:H1
           str. NRG 857C]
 gi|315285114|gb|EFU44559.1| pseudouridine synthase A [Escherichia coli MS 110-3]
 gi|323950944|gb|EGB46821.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323955254|gb|EGB51027.1| RNA pseudouridylate synthase [Escherichia coli H263]
          Length = 219

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQDPWLVVLYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|227515296|ref|ZP_03945345.1| pseudouridylate synthase RluD [Lactobacillus fermentum ATCC 14931]
 gi|227086356|gb|EEI21668.1| pseudouridylate synthase RluD [Lactobacillus fermentum ATCC 14931]
          Length = 296

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 110/293 (37%), Gaps = 33/293 (11%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                 H      Q       V V+      +  + +G V+ +    +            
Sbjct: 32  LPKRLVHYLRSRRQ-------VLVNGSYRPVSKTVAAGDVITLNFSGDEFR--------- 75

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQK 143
             + + +   D     +LYE+  + V +KPAGI      +G    +   + ++++     
Sbjct: 76  --TPDSSYLPDPGPLTVLYENRDLLVVDKPAGIKSHPNQAGEVGTLMNRVAAYLEGTNDA 133

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLD+ETSG ++VA+       L        I + Y +LV G+P   +      L 
Sbjct: 134 AYMVHRLDKETSGAMIVAKNPVVVPILDRLISTGEIHRDYLALVAGVPNPARGIWDLPLG 193

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +            K   K A  A +H++ +         + +   TGRTHQLRVH    G
Sbjct: 194 QDPTDVRKR----KVFGKNAQPARTHYRTL-AVNDDRALVVLNLETGRTHQLRVHLAAAG 248

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           CPIVGD  Y         +    ++YLH    +L  P    R +I A +P   
Sbjct: 249 CPIVGDPLYG--------TVAAPRMYLHGVAQELVLPFSLKRERIVAKIPDDF 293


>gi|309787283|ref|ZP_07681895.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
 gi|308924861|gb|EFP70356.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
 gi|323181753|gb|EFZ67166.1| RNA pseudouridylate synthase family protein [Escherichia coli 1357]
          Length = 217

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 6   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 63

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 64  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 117

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 118 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 177

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 178 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 217


>gi|311746883|ref|ZP_07720668.1| RNA pseudouridine synthase family protein [Algoriphagus sp. PR1]
 gi|126578569|gb|EAZ82733.1| RNA pseudouridine synthase family protein [Algoriphagus sp. PR1]
          Length = 237

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 75/245 (30%), Positives = 106/245 (43%), Gaps = 27/245 (11%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +L+ED  I   NKPAG+ V   S  A      L+   D  G      HRLD+ TSG
Sbjct: 1   MELPILFEDDSIIAINKPAGLLVHRTSIAAQETVFALQILRDQIGMHVHPVHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           IL+ A+      HL   F  R+I+K Y ++V GIP+ KK  I + L K    G       
Sbjct: 61  ILLFAKKEEILPHLKNLFSERQIKKNYLTIVRGIPEQKKALIDHPL-KSERSGR------ 113

Query: 217 KQNEKGANYAISHFKVI-----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                    A + +KVI                ++  L + P TGRTHQ+R H  H+   
Sbjct: 114 ------LQEAQTWYKVISETEIPFDTTGRYPTSRYSLLSVNPETGRTHQIRRHLAHIRHY 167

Query: 266 IVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           I+GD K+  N +  F         L LHA  +   HP     ++I+ P+P H      SL
Sbjct: 168 IIGDKKHGDNKQNIFFQNQFGLENLLLHAIRLSFNHPITEETIEISCPVPEHFQSILKSL 227

Query: 323 GFKYD 327
             +  
Sbjct: 228 NLQEP 232


>gi|332288146|ref|YP_004418998.1| tRNA pseudouridine synthase C [Gallibacterium anatis UMN179]
 gi|330431042|gb|AEC16101.1| tRNA pseudouridine synthase C [Gallibacterium anatis UMN179]
          Length = 242

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 105/237 (44%), Gaps = 17/237 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SD     +LY+D  +   NKPAG+ V       +  +  ++   D  GQ     HRLD+ 
Sbjct: 2   SDQQALPILYQDQALIAVNKPAGMLVHRSWLDKHETEFVMQKLRDQIGQYVFPIHRLDRP 61

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+L+ A +   A  +   F  +++QK Y ++V G    ++        K   I   + 
Sbjct: 62  TSGVLLFALSSEIANAVCRQFEQKQVQKQYLAVVRGYLTGQERIDYPLKPKWDKIADKF- 120

Query: 214 HVVKQNEKGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
               Q +K    A++ ++          V      ++  + + P TGR HQLR H  H+ 
Sbjct: 121 ---SQQDKTPQEAVTDYQGLATLEIPVAVGRYATSRYSLVRLTPQTGRKHQLRRHLKHIF 177

Query: 264 CPIVGDHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
            PI+GD +Y    +    S     N+L LHA  ++L HP   + L+I APL     K
Sbjct: 178 HPIIGDTQYGDLHQNRAFSAYFSVNRLMLHAESLELLHPTTQQVLRICAPLDPSFAK 234


>gi|292487216|ref|YP_003530088.1| tRNA pseudouridine synthase C [Erwinia amylovora CFBP1430]
 gi|292900409|ref|YP_003539778.1| tRNA pseudouridylate synthase C [Erwinia amylovora ATCC 49946]
 gi|291200257|emb|CBJ47385.1| tRNA pseudouridylate synthase C [Erwinia amylovora ATCC 49946]
 gi|291552635|emb|CBA19680.1| tRNA pseudouridine synthase C [Erwinia amylovora CFBP1430]
          Length = 255

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 111/240 (46%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G+ V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDRWLVAVNKPSGMLVHRSWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  L++ F   ++QK Y ++V G  +           ++  I   +     Q E
Sbjct: 64  ALSSEVAHLLSQQFERHQLQKTYHAVVRGWLEGADTLDYPLTEERDKIADKF----SQPE 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +EMQP +GR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHWRGVATAELAVPIGRYETSRYSLVEMQPESGRKHQLRRHMTHLRHPIIGDS 179

Query: 271 KYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
            +      +    +   N+L LHA  ++L HP   G L + A L A   K  +  G++ +
Sbjct: 180 AHGDLKQNRSAAANFGINRLMLHASELNLTHPVTAGPLILRAGLDAVWQKVINQFGWQAE 239


>gi|198276202|ref|ZP_03208733.1| hypothetical protein BACPLE_02391 [Bacteroides plebeius DSM 17135]
 gi|198271014|gb|EDY95284.1| hypothetical protein BACPLE_02391 [Bacteroides plebeius DSM 17135]
          Length = 223

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 72/231 (31%), Positives = 113/231 (48%), Gaps = 16/231 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQGDKTGDIPLSETVKQYLKEKYAKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E FR   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFRNGEVKKTYWAIVKQQPKETEGELVHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K +  A+ ++++I   ++ +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVKNSKKAVLNYRLIGR-SENYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGFP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
                 S     + LHAR +   HP     + + APLPA     W+  G +
Sbjct: 180 RSNPDGS-----ICLHARRVRFIHPVSKEPIDLVAPLPAG--NLWNGFGME 223


>gi|42526895|ref|NP_971993.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
 gi|41817210|gb|AAS11904.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
          Length = 305

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 73/329 (22%), Positives = 124/329 (37%), Gaps = 41/329 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    + Y  +  D+   RLDR  +     +    +   +R G++RV+ K+       Q
Sbjct: 1   MSKENKIFY--IGEDDSGRRLDRVIRKFLGKMPLSGVYSAIRRGKIRVNGKKENGAYLTQ 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   +  L     E +          +    K  +L +   +   NK +G  V 
Sbjct: 59  KGDEISMDLSLFGLTAPASEDQT---------NYSISKPDVLLKTDDLLFINKRSGELVH 109

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G   +   +  +  S   S   K    HRLD++TSGIL  +++   AQ  + + +  +I 
Sbjct: 110 GEKSLCEAVLKYFPSKEKSLSFKVGALHRLDKDTSGILAFSQSLKGAQGFSRALQEGKIG 169

Query: 181 KIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFA 237
           K Y  +  G P     K  I                            +   +++D    
Sbjct: 170 KFYIGITEGRPSLSEFKSIID-----------------------GKECLCLIRILDFSKE 206

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK--LYLHARYM 295
           +    +     TGR HQ+R+     G P++ D KY +  K  F+  +  K   +LHA  +
Sbjct: 207 ENLSLVLFNLITGRKHQIRIQCSQFGTPLLNDKKYGSKQKKAFSEDLSKKTTYFLHAYKL 266

Query: 296 DLPHPEGGRL--QITAPLPAHMVKTWDSL 322
               P    L  +ITAPLP +  +   SL
Sbjct: 267 IFSEPFLDDLPKEITAPLPENFKRAVKSL 295


>gi|332753507|gb|EGJ83887.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           4343-70]
 gi|333000233|gb|EGK19816.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-218]
          Length = 260

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR +  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRYLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWR 237


>gi|293391529|ref|ZP_06635863.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952063|gb|EFE02182.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 219

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/214 (31%), Positives = 106/214 (49%), Gaps = 11/214 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             L+Y D  I V NKP+G+    G+   Y+      S V  K       HRLD  TSGIL
Sbjct: 14  LDLVYRDDYIAVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPAHRLDMATSGIL 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A +++A + L   FR R  +K Y +LVWG  + ++  +   L+       +     K 
Sbjct: 72  LFALSKSADRELKRQFREREPKKYYQALVWGHLEQEQGVVELPLICD----WENRPRQKI 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             +    A++ ++V+         +++ P TGR+HQLR+H L +G PI+GD  Y A+ + 
Sbjct: 128 CFERGKRAVTFYEVLQRHPNNTTRIKLTPITGRSHQLRLHMLALGHPILGDKFY-AHPQA 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
              SP   +L LHA  + + HP  G  ++ T P+
Sbjct: 187 KALSP---RLCLHAESLQIRHPITGETMEFTTPV 217


>gi|170768656|ref|ZP_02903109.1| pseudouridine synthase, RluA family [Escherichia albertii TW07627]
 gi|170122760|gb|EDS91691.1| pseudouridine synthase, RluA family [Escherichia albertii TW07627]
          Length = 219

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVVLYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA Q L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAEQELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|325956350|ref|YP_004291762.1| Pseudouridine synthase [Lactobacillus acidophilus 30SC]
 gi|325332915|gb|ADZ06823.1| Pseudouridine synthase [Lactobacillus acidophilus 30SC]
          Length = 301

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/326 (20%), Positives = 122/326 (37%), Gaps = 37/326 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSG 62
           MT +  ++V+  +   +L  +        +   L+     +G + V+ KR   + R+++ 
Sbjct: 1   MTSLFKLIVQERD-PKKLGSFLLK--KGFSHQALKHARYNNGLILVNHKRRYTSFRLKTN 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V         N  +K                      + E     + NKP G+     
Sbjct: 58  DEVIFVTGEEKKNDFLK--------------PSNNPVEPVLETKNYIILNKPVGVLSIPS 103

Query: 123 SGIAYH-IDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                  I   L  +   KG    KP +  RLD++TSG+++V +   A    ++  + R 
Sbjct: 104 RYEDNDAIVNRLMGYFTRKGAKDLKPHVITRLDRDTSGLVLVGKNAVAHARFSKMGKERF 163

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I+K + ++V G  ++ +       L    IG     V +        A + +KV+     
Sbjct: 164 IKKYH-AIVHGNFESTELT----GLIDEPIGKIDSGVKRGVIPDGKSAQTEYKVLKQVP- 217

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E++  TGRTHQ+RVH  ++G P+ GD  Y             ++  L+  Y+  P
Sbjct: 218 GASLVELRLLTGRTHQIRVHMAYLGHPLYGDQLYGVKDS-------FSRQALNCFYLSFP 270

Query: 299 HPEGGR--LQITAPLPAHMVKTWDSL 322
            P        +    P+ M   W  L
Sbjct: 271 DPVNSEKDKTVEISDPSDMQNLWQKL 296


>gi|88704640|ref|ZP_01102353.1| tRNA pseudouridine synthase C [Congregibacter litoralis KT71]
 gi|88700961|gb|EAQ98067.1| tRNA pseudouridine synthase C [Congregibacter litoralis KT71]
          Length = 255

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 99/245 (40%), Gaps = 17/245 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           H D  +  ++Y DS + V NKP G+ V             L+   D  GQ     HRLD+
Sbjct: 2   HPDAERLEIIYRDSDLVVINKPPGLLVHRSKIDRQETRFALQLLRDQIGQHVFPVHRLDK 61

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+LV A     A+ L + F  R + K Y ++V G              K+  I    
Sbjct: 62  PTSGLLVFALNPEMAKRLADQFARREVSKQYLAVVRGYAPGHGTIDHALTEKRDPIADKR 121

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHM 262
            +      K    A++H++ +               ++  +E++PHTGR HQLR H  H+
Sbjct: 122 AN----TSKAPQEALTHYRRLAQIEWPVAVDRYPQARYSLVELRPHTGRKHQLRRHMKHI 177

Query: 263 GCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPH-PEGGRLQITAPLPAHMVKTW 319
           G PI+GD  +       F +   N  +L L    +   H   GG L + A          
Sbjct: 178 GHPIIGDANHGKGVHNRFFAETLNCPRLLLACTGLSFDHRASGGSLSLRARPGVAFEGLL 237

Query: 320 DSLGF 324
            + G+
Sbjct: 238 ATFGW 242


>gi|329667702|gb|AEB93650.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus johnsonii
           DPC 6026]
          Length = 299

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 65/286 (22%), Positives = 115/286 (40%), Gaps = 36/286 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G V V+  R   +  + +G  V         N  +K                  K  +++
Sbjct: 38  GMVLVNHHRRYTSYLLHAGDEVIFILGEEKENKWLK--------------PSSKKLNIVF 83

Query: 104 EDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQ---KPRLTHRLDQETSGILV 159
           E     V NK AGI         +  +   L  +   + Q   KP +  RLD++TSG+++
Sbjct: 84  EQKDYLVINKDAGILSIPSRYEDSDAVVNRLLHYFQQQKQTDLKPHVITRLDRDTSGLVL 143

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN--KKECIANWLLKKSHIGGDYVHVVK 217
           V +   A    ++  +   I+K + ++V G  +   ++  I   + K          V +
Sbjct: 144 VGKNAVAHARFSKMEKNEFIKKYH-AIVHGNFEEAQRQGTIDAPIGKIDT------GVKR 196

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   +++ ++V+D   +    +E+Q  TGRTHQ+RVH  ++G P+ GD  Y    K
Sbjct: 197 GVVNNGQRSVTKYRVLDQV-KGASLIELQLLTGRTHQIRVHMQYLGHPLFGDPLYG--IK 253

Query: 278 GNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
            NF      +  L+  Y++   P    R +I    P  M   W +L
Sbjct: 254 DNF-----KRQALNCFYLEFDDPFLEKRQKIEIADPIDMEILWKNL 294


>gi|237735851|ref|ZP_04566332.1| pseudouridine synthase [Mollicutes bacterium D7]
 gi|229381596|gb|EEO31687.1| pseudouridine synthase [Coprobacillus sp. D7]
          Length = 278

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 63/300 (21%), Positives = 124/300 (41%), Gaps = 41/300 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIP 68
            +V   E  M L  +       ++   + K+++  G++ V+ +R      ++ G VV + 
Sbjct: 3   FIVAMKESGMLLREFLSQQ--ELSKKAV-KLIKMHGKILVNGQRQTVRYCLRYGDVVELL 59

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AY 127
                                 T     L   + YED    V +KPAG+           
Sbjct: 60  WPEEVS----------------TMEPYPLALKISYEDENFLVIDKPAGLPSIPTKRYPRN 103

Query: 128 HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +  +  S+G K    L +RLD++T G+L++A+   A   L+     ++++++Y  
Sbjct: 104 TLANAVVYYYQSQGIKATVHLVNRLDKDTQGLLLIAKNSYAHYLLSRDI--KQVRRVYHC 161

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G+    +  I   ++K        +H          +A++H++ ++  A +   +E 
Sbjct: 162 VVEGVLTG-QGTITAPIIKDKKSVKRLIH------PAGKFAVTHYRGLEVSANQ-SKIEC 213

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              TGRTHQ+RVH   +  P+VGD  Y + ++ ++        YL +  +    P   RL
Sbjct: 214 ILETGRTHQIRVHLSSINHPLVGDTLYDSIYQESY--------YLDSIALSFIDPFTQRL 265


>gi|324989625|gb|EGC21569.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK353]
          Length = 291

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 72/316 (22%), Positives = 126/316 (39%), Gaps = 33/316 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   ++ G  + +
Sbjct: 4   TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLAINWQTVVKPGDDICL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+          
Sbjct: 62  IFDEEDY----PQKTILIGNGKLVEE--------LYQDQHLIIVNKPEGMKTHANEPREL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+LV
Sbjct: 110 ALLNHVSAYV---GETCYVVHRLDKETSGAILFAKNSFVLPILNRLLEKREISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +KK    + + +  H     +       +   YA +H   +  F Q    ++ Q 
Sbjct: 167 QGKFPSKKLIYKDKIGRDRHDRRKRL----VEPQKGLYAETHVTRVKQFGQ-AALVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G P++GD  Y    KG        +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGHPLIGDPLYHPQPKG--------RLMLHAHRLTFTHPFTLEKIT 273

Query: 307 ITAPLPAHMVKTWDSL 322
           + A    +  K   SL
Sbjct: 274 VEAR-SDNFEKVLSSL 288


>gi|226357282|ref|YP_002787022.1| RNA pseudouridine synthase [Deinococcus deserti VCD115]
 gi|226319272|gb|ACO47268.1| putative RNA pseudouridine synthase [Deinococcus deserti VCD115]
          Length = 298

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 75/302 (24%), Positives = 127/302 (42%), Gaps = 30/302 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    Y H         L  G+V+VD   V+ + R+++GQ +           +   
Sbjct: 21  LD-FLSTRYRHSAPEVWAARLAQGEVQVDGLTVQGHERLRAGQTL-----------VWHR 68

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
               + SV L          +L+ED+ +   +KP+G+    G G   H    L + V ++
Sbjct: 69  PPWQEESVPLHFE-------VLHEDASLLAVHKPSGLPTLPGGGFLEH---TLLTVVRAQ 118

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                  HRL + TSG+++ ART AA   L  ++R + ++K+Y +L  G+    +  I  
Sbjct: 119 FPGASPLHRLGRGTSGVVLFARTGAAGSALARAWREQDVRKMYRALASGVATQDETEITV 178

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +    H     V            + S  +V++  +      ++Q  TGR HQ+R+H  
Sbjct: 179 SIGPVPHPRLGEVFAAC---PTGKPSRSVARVVERCS-GTTLFDVQIFTGRPHQIRIHLA 234

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
            +G P+VGD  Y          P         LHA  +   HP  G+ + +TAP P+ + 
Sbjct: 235 SIGQPLVGDPLYGPGGHPLPDLPGLPGDLGYLLHAHTLSFTHPVSGQVITVTAPAPSALE 294

Query: 317 KT 318
            T
Sbjct: 295 PT 296


>gi|15674094|ref|NP_268269.1| pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
 gi|12725167|gb|AAK06210.1|AE006439_7 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 288

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 113/268 (42%), Gaps = 30/268 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
                V+ K +  N  + +G  + +       +++              K      + +L
Sbjct: 37  KKHCLVNNKLINENQLVHAGDKITLIFDNEDFSNLS------------LKFGSANLADIL 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + V NKP G+   G +     +   + + ++   Q+  + HRLDQ TSG ++ A+
Sbjct: 85  YEDEHLIVVNKPEGMKTHGNTADELALQNHVAAAIN---QEVFVVHRLDQATSGAVLFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            +     L + F   +I + Y +LV G     +  I   + +  H     +   K     
Sbjct: 142 NQFVLPILGKMFEENKIHREYLALVKGHFSENQFTIDRAIGQNRHDKNKRILSAK----- 196

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++H ++I  F  K   ++    TGRTHQ+RVH   +  PI+GD  Y          
Sbjct: 197 GQKAVTHVEIIKKFTDK-TLVKCTLDTGRTHQIRVHLSSLNHPIIGDALYGQKS------ 249

Query: 283 PIQNKLYLHARYMDLPHP-EGGRLQITA 309
             Q ++ LHA  + +PHP E   L+I+A
Sbjct: 250 --QERMMLHAGKIIIPHPFENKILEISA 275


>gi|328946974|ref|YP_004364311.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
 gi|328447298|gb|AEB13014.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
          Length = 248

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 112/244 (45%), Gaps = 24/244 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y D +I V NK +G+ V      A      L    + +       HR+D++TSGI++ 
Sbjct: 9   VIYSDDEIVVLNKKSGLLVAADRYDAEAP--RLDLLAEKEFGSLFAVHRIDKDTSGIVIY 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T  A ++++  F  R ++K Y  LV G P      +   LL      GD  H    N+
Sbjct: 67  AKTPEAHRNISIQFTERTVKKTYHCLVNGHPAWDNFTVDLPLL----PDGDDRHRTVINK 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K    ++++ +V+      + W++  P TGRTHQ+R H    G PIV D  Y  N K   
Sbjct: 123 KFGKPSVTYLEVVGHCG-PYSWIKAFPKTGRTHQIRAHLQSTGFPIVCDPLYSGNQKPVR 181

Query: 281 TS--------------PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG-- 323
            S              P+ N+L LHA  +++ HP+ G  +  TAP P  M    + L   
Sbjct: 182 LSDIKRKWNGDVYEERPLLNRLALHAYSIEIAHPKTGEQIIFTAPYPKDMDAVRNQLAKI 241

Query: 324 FKYD 327
           FK D
Sbjct: 242 FKID 245


>gi|116334307|ref|YP_795834.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
 gi|116099654|gb|ABJ64803.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
          Length = 294

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/310 (22%), Positives = 120/310 (38%), Gaps = 34/310 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L R+  N    I+      + + G +RV+ +       +  G  V +             
Sbjct: 14  LKRFLTNQ--GISHRVFSDLKQQGTIRVNGQVTTPAVTLAVGDHVAVTF----------P 61

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDS 139
            +  D +V ++         +L+E+    V +KPAG++V  G       +   +K + ++
Sbjct: 62  PETADEAVAVSHE----PITVLFENRDWLVVDKPAGLNVVPGPANRTDTLVNRIKGYWEA 117

Query: 140 KGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +  +   P +  RLD+ TSG++ VAR R A    ++     +I K Y ++V G  +    
Sbjct: 118 EHAENLVPHILTRLDRFTSGVVWVARHRLANSLASQLQAAHQIDKRYLAVVSGRLEADHA 177

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   L        D     +        A + + V   FA     + ++ HTGRTHQ+R
Sbjct: 178 VIDAPL------ASDPTGYNQMVSPTGKPARTEYWVQQRFA-TATVVAVKLHTGRTHQIR 230

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
            H   +G P++GD  Y     G       N+  L A  +    P      Q T+ LPA  
Sbjct: 231 AHFASLGHPLLGDALYDGPVTG------INRQALQALSLTFKDPFTDEQRQFTSELPADW 284

Query: 316 VKTWDSLGFK 325
                 L  +
Sbjct: 285 QTLIHQLSEE 294


>gi|187731746|ref|YP_001878869.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella boydii CDC
           3083-94]
 gi|187428738|gb|ACD08012.1| pseudouridine synthase, RluA family [Shigella boydii CDC 3083-94]
          Length = 219

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPFPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|116627150|ref|YP_819769.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus LMD-9]
 gi|116100427|gb|ABJ65573.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           thermophilus LMD-9]
          Length = 290

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/279 (24%), Positives = 105/279 (37%), Gaps = 31/279 (11%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    V ++ + + + + ++ G  + +                 D     
Sbjct: 26  IPR-KIRHFLRTKKHVLINGETINWQSPVKEGDRISLTF------------DTEDYPNKT 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               D      LYEDS I V NKP G+   G           L       GQ   + HRL
Sbjct: 73  IPMGDANLVKPLYEDSHIIVVNKPEGMKTHGNKPTE---IALLNHVSAYCGQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG ++ A+       L      + IQ+ YW+L  G  + KK    + + +  H   
Sbjct: 130 DMETSGAVLFAKNPFILPILNRLLEDKMIQRQYWALTEGKFQTKKTVYKDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             V V  +  + A   ++  K  +        +  Q  TGRTHQ+RVH  H G  I+GD 
Sbjct: 190 KRV-VDPRKGQSAYTTVTRLKTFE----GASLVNCQLKTGRTHQIRVHLSHHGHAILGDP 244

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y             ++L LHA  +   HP    ++ + 
Sbjct: 245 LYSHQP--------SSRLMLHAHSLSFTHPLTLEKVTVK 275


>gi|160885619|ref|ZP_02066622.1| hypothetical protein BACOVA_03622 [Bacteroides ovatus ATCC 8483]
 gi|237715236|ref|ZP_04545717.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D1]
 gi|237719607|ref|ZP_04550088.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_2_4]
 gi|260172064|ref|ZP_05758476.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D2]
 gi|262405080|ref|ZP_06081630.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_22]
 gi|293371645|ref|ZP_06618056.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|294643576|ref|ZP_06721380.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|294808675|ref|ZP_06767409.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|299147480|ref|ZP_07040545.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 3_1_23]
 gi|315920374|ref|ZP_07916614.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D2]
 gi|156109241|gb|EDO10986.1| hypothetical protein BACOVA_03622 [Bacteroides ovatus ATCC 8483]
 gi|229444545|gb|EEO50336.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D1]
 gi|229450876|gb|EEO56667.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_2_4]
 gi|262355955|gb|EEZ05045.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_22]
 gi|292633342|gb|EFF51912.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|292641071|gb|EFF59285.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|294444114|gb|EFG12847.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|295088159|emb|CBK69682.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           xylanisolvens XB1A]
 gi|298514758|gb|EFI38642.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 3_1_23]
 gi|313694249|gb|EFS31084.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           D2]
          Length = 223

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 68/219 (31%), Positives = 109/219 (49%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQ        +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQADKTGDTPLSETVKQYLKEKYQKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR   ++K YW++V   P+  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTSKALTRLNEMFRTSEVKKTYWAVVKNAPQEPEGELVHFLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   ++ +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVPNSKKAILHYRLIG-HSENYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                 S     + LHAR +   HP     +++ APLP 
Sbjct: 180 RSNPDGS-----ICLHARRVRFIHPVSKELIELEAPLPE 213


>gi|312277628|gb|ADQ62285.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 290

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/279 (24%), Positives = 105/279 (37%), Gaps = 31/279 (11%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    V ++ + + + + ++ G  + +                 D     
Sbjct: 26  IPR-KIRHFLRTKKHVLINGETINWQSPVKEGDRISLTF------------DTEDYPNKT 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               D      LYEDS I V NKP G+   G           L       GQ   + HRL
Sbjct: 73  IPMGDANLVKPLYEDSHIIVVNKPEGMKTHGNKPTE---IALLNHVSAYCGQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG ++ A+       L      + IQ+ YW+L  G  + KK    + + +  H   
Sbjct: 130 DMETSGAVLFAKNPFILPILNRLLEDKMIQRQYWALTEGKFQTKKTVYKDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             V V  +  + A   ++  K  +        +  Q  TGRTHQ+RVH  H G  I+GD 
Sbjct: 190 KRV-VDPRKGQSAYTTVTRLKTFE----GASLVNCQLKTGRTHQIRVHLSHHGHAILGDP 244

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y             ++L LHA  +   HP    ++ + 
Sbjct: 245 LYSHQPA--------SRLMLHAHSLSFTHPLTLEKVTVK 275


>gi|296101220|ref|YP_003611366.1| pseudouridine synthase, RluA family [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295055679|gb|ADF60417.1| pseudouridine synthase, RluA family [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 219

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 66/227 (29%), Positives = 106/227 (46%), Gaps = 15/227 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +           ++LY+D  I V NKP+G+    G  +  H D  + + +     +    
Sbjct: 3   MQPYNPPQDPWLVILYQDEHIMVVNKPSGLLSVPGR-LDEHKDSVM-TRIQRDYPQAESV 60

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA  +AA + L   FR R  +K Y + VWG P   +  +   L+    
Sbjct: 61  HRLDMATSGVIVVALNKAAERELKRQFREREPKKQYVARVWGHPAQTEGLVDLPLI---- 116

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V++        + ++P TGR+HQLRVH L +G P
Sbjct: 117 --CDWPNRPKQKVCYETGKAAQTEYEVLEYAPDNTARVLLKPITGRSHQLRVHMLALGHP 174

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           I+GD  Y              +L LHA+ + + HP  G  +   AP+
Sbjct: 175 ILGDRFYAPPE----ALASAPRLQLHAQTLTITHPAFGNAMTFKAPV 217


>gi|170717564|ref|YP_001784651.1| tRNA pseudouridine synthase C [Haemophilus somnus 2336]
 gi|168825693|gb|ACA31064.1| pseudouridine synthase [Haemophilus somnus 2336]
          Length = 240

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 58/244 (23%), Positives = 106/244 (43%), Gaps = 18/244 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           S+ ++  +LY+D  + V NKPAG+ V       +     +++  D  GQ     HRLD+ 
Sbjct: 2   SEPIELDILYQDEFLVVVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVFPIHRLDRP 61

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+L+ A     A  L   F +++++K Y ++V G   + +       ++   I   + 
Sbjct: 62  TSGVLLFALNAGIANLLCSQFELKQVKKSYLAIVRGYLSDAQRIDYPLKVQLDKIADKFS 121

Query: 214 HVVKQNEKGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                 ++    AI+ +  +             + ++  + + P+TGR HQLR H  H+ 
Sbjct: 122 R-----KEELQDAITDYYGLKTVEMPYGVGRYSSSRYSLVRLMPYTGRKHQLRRHLKHIF 176

Query: 264 CPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            PI+GD +Y    +    S     ++L LHA  +   HP     ++I A L       + 
Sbjct: 177 HPILGDTQYGDLHQNRAFSQNLGVSRLMLHAEKLCFQHPVTNETIEIVADLDEQWKLLFK 236

Query: 321 SLGF 324
              +
Sbjct: 237 IFNW 240


>gi|319746042|gb|EFV98321.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           agalactiae ATCC 13813]
          Length = 294

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 108/291 (37%), Gaps = 33/291 (11%)

Query: 25  FKNHYPHI---NFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
            K             ++  LR    V ++ + + +   +Q    + +             
Sbjct: 16  VKELLEDYFLIPR-KIRHFLRVKKHVLINNEFINWQTVVQENDTITLIFDDE-------- 66

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
               D                LYED  + + NKP G+   G      +    L       
Sbjct: 67  ----DYPTKKIPLGRAELIDCLYEDEHLIIVNKPEGMKTHGNQP---NEIALLNHVSAYS 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           GQ   + HRLD ETSG ++ A+       + +    + I + YW+LV G    K + + +
Sbjct: 120 GQTCYVVHRLDMETSGAVLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRD 179

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +  H     +     + K   +A++   V+    Q    ++ +  TGRTHQ+R+H  
Sbjct: 180 KIGRNRHDRRKRII----DSKNGQHAMTIIDVLKYI-QNSSLIKCRLETGRTHQIRIHLS 234

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           H G P++GD  Y  +           +L LHA  + L HP     + + AP
Sbjct: 235 HHGHPLIGDPLYNPSSNNE-------RLMLHAHRLTLSHPLTCEIISVEAP 278


>gi|53712433|ref|YP_098425.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           fragilis YCH46]
 gi|52215298|dbj|BAD47891.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           fragilis YCH46]
          Length = 539

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 72/243 (29%), Positives = 111/243 (45%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  +       S  +   +L+ED  + V +KP G+    G      I
Sbjct: 308 CEPILRHMLQGLNVEPAPTERYSLSQNMPE-ILFEDQWLLVLHKPEGVLSVPGKSEEQSI 366

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++    +   P + HRLD  TSG+L+ A+T+   +HL   F  R I+K Y +L+ G
Sbjct: 367 YSLLRARY-PEATGPLVVHRLDMATSGLLLAAKTQEVHRHLQAQFENRSIKKRYIALLDG 425

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I   ++  I   +          +     NE+    AI+ ++V+D        +   P T
Sbjct: 426 ILPEEEGVIDLPICPDYLDRPRQM----VNEELGKTAITRYQVMDRK-NGQTRIAFFPLT 480

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
           GRTHQLRVHA H   + CPIVGD  Y    +         +LYLHA Y++  HP  G R+
Sbjct: 481 GRTHQLRVHAAHPLGLNCPIVGDELYGRKAE---------RLYLHAEYLEFIHPVSGQRM 531

Query: 306 QIT 308
            I 
Sbjct: 532 VIE 534


>gi|325684453|gb|EGD26617.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp. lactis
           DSM 20072]
          Length = 302

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 66/327 (20%), Positives = 129/327 (39%), Gaps = 42/327 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQV 64
            V  ++V  ++    L  +        +   +      G +  V+  R   + R++ G V
Sbjct: 2   QVYKMIVAKNDPGQ-LSHFLLK--KGFSRRAVNNCKNHGGMMLVNHHRRNGSYRLKEGDV 58

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V          H +  Q+ ++  + +++    L   ++ E +   V NKPAG+       
Sbjct: 59  V----------HFLMGQEPVNPWLKVSR----LPLDIVEETADYLVINKPAGLLSIPSGF 104

Query: 125 IAYHID-GFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            A       + ++ + +G      KP +  RLDQ+TSG++++ +   A    ++  +   
Sbjct: 105 HAEDAVINRVLAYFEKQGVNPAYVKPHIVTRLDQDTSGLVLLGKNAIAHDRFSKLGKDAF 164

Query: 179 IQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           I+K + ++V G          I   L +          V ++       A++ ++V+D  
Sbjct: 165 IKKYH-AIVHGNFAEGDLSGLIDKPLARVGD------TVKREVNPKGQRALTEYRVLDQV 217

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +E++  TGRTHQ+R+H   +G  + GD  Y A            +  L+  Y+ 
Sbjct: 218 P-GASLVELRLLTGRTHQIRIHMASIGHVLYGDDLYGAR-------DAFARQALNCFYLS 269

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSL 322
             +P  G   +I  P P  M   W  L
Sbjct: 270 FTNPFSGEEREIEIPDPGDMQGLWRQL 296


>gi|320535819|ref|ZP_08035900.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
 gi|320147367|gb|EFW38902.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
          Length = 248

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 72/248 (29%), Positives = 108/248 (43%), Gaps = 21/248 (8%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           K  +     L+Y+D  I   NK AGISV     +     +D  L+     K +K    HR
Sbjct: 2   KKPEKHPFTLVYQDEDIIAVNKSAGISVTADRWNPDEQRLDILLQQSPALKDKKFFTVHR 61

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D++TSG+++ A    + + L ESF  R +QK Y  L+  IP      +   L       
Sbjct: 62  IDKDTSGLILYALNEESHKKLNESFMRRNVQKTYHCLIADIPYENSFSVDLKL----KSD 117

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           GD  H    ++K    A++HF+V+    + F  LE +P +GRTHQ+R H    G PI+ D
Sbjct: 118 GDEKHRTIIDKKNGKEALTHFEVLKPLGR-FTLLEAKPVSGRTHQIRAHLAAAGLPILCD 176

Query: 270 HKYCA-------------NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             Y                 +     P+ ++L LHA  ++  HP  G  L  TA      
Sbjct: 177 SLYGNAKPLFLSELKKNWRGEKAQEQPLISRLALHAYKLEFEHPRTGTLLSFTAEYARDF 236

Query: 316 VKTWDSLG 323
               + LG
Sbjct: 237 KTALNQLG 244


>gi|254555966|ref|YP_003062383.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254044893|gb|ACT61686.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 293

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 76/306 (24%), Positives = 125/306 (40%), Gaps = 41/306 (13%)

Query: 23  RWFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQSGQV--VRIPPVINALNHII 78
           R+   H   I+   + K ++  +G   V+ +       I  G +  +++P        ++
Sbjct: 16  RFLTTH--AISMRTI-KAIKHGTGAFLVNNQVQTGVITIHDGDIAGIQLPDEAPDTAVVV 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWV 137
            EQ I                 + YED+   V NKPAG+ SV G S     +   +K ++
Sbjct: 73  SEQPI----------------QIEYEDANWLVLNKPAGLTSVPGPSNRTDTLVNRIKGYL 116

Query: 138 ---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               +  Q+P L  RLD++TSG+++VA+ R A   LTE     ++ K Y + + G     
Sbjct: 117 IASHASNQRPHLITRLDRDTSGLVLVAKHRVAQGMLTEPRIAAQLVKTYQAWIEGTITPA 176

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTH 253
              I   + + +      V            AI+ ++V  D        L ++  TGRTH
Sbjct: 177 SGTIDRPIGRVADSPRRVVTT------AGQRAITTYQVEADQLQHNVSRLRLELVTGRTH 230

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Q+RVH   +G P++GD  Y  N           +  LHA  +    P   + L   A LP
Sbjct: 231 QIRVHLTALGHPLLGDTLYGGNLAW------IQRQALHAASLQFFDPFSEQTLHFEAALP 284

Query: 313 AHMVKT 318
           A +   
Sbjct: 285 ADLQAL 290


>gi|26245982|ref|NP_752021.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli CFT073]
 gi|227885043|ref|ZP_04002848.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli 83972]
 gi|300981032|ref|ZP_07175309.1| pseudouridine synthase A [Escherichia coli MS 45-1]
 gi|301048442|ref|ZP_07195469.1| pseudouridine synthase A [Escherichia coli MS 185-1]
 gi|331661098|ref|ZP_08362030.1| pseudouridine synthase A [Escherichia coli TA206]
 gi|331681442|ref|ZP_08382079.1| pseudouridine synthase A [Escherichia coli H299]
 gi|34395780|sp|Q8FL93|RLUA_ECOL6 RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|26106379|gb|AAN78565.1|AE016755_65 Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           CFT073]
 gi|227837872|gb|EEJ48338.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli 83972]
 gi|300299735|gb|EFJ56120.1| pseudouridine synthase A [Escherichia coli MS 185-1]
 gi|300409068|gb|EFJ92606.1| pseudouridine synthase A [Escherichia coli MS 45-1]
 gi|307551903|gb|ADN44678.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           ABU 83972]
 gi|315293367|gb|EFU52719.1| pseudouridine synthase A [Escherichia coli MS 153-1]
 gi|315298424|gb|EFU57679.1| pseudouridine synthase A [Escherichia coli MS 16-3]
 gi|331052140|gb|EGI24179.1| pseudouridine synthase A [Escherichia coli TA206]
 gi|331081663|gb|EGI52824.1| pseudouridine synthase A [Escherichia coli H299]
          Length = 219

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVVLYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|320109289|ref|YP_004184879.1| RluA family pseudouridine synthase [Terriglobus saanensis SP1PR4]
 gi|319927810|gb|ADV84885.1| pseudouridine synthase, RluA family [Terriglobus saanensis SP1PR4]
          Length = 298

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 120/319 (37%), Gaps = 29/319 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M    Y    ++   +    L     + YPH +    Q+ L +G+V V+      +  + 
Sbjct: 1   MLNRGYAYTTIIGGKDHGQTLLSHLASLYPHSSPQAWQQNLNNGEVTVNGVIATGSEALT 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SGQ++                  ++               +L +D  +   NKP      
Sbjct: 61  SGQMLVWN-----------RPPWIEPDAPQHFE-------VLLDDPHLLAVNKP---GGL 99

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                   ++  L   V  +       HRL + T+GI++ A+T  AA +LT  +   RI+
Sbjct: 100 PTLPGGGFMENTLLRLVQKQSPDANPVHRLGRATTGIVLFAKTPQAASNLTADWNTSRIE 159

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           KIY +L  GI       I   +    H     +  V         + S  KVI       
Sbjct: 160 KIYRALAQGIADRDAYEILTPIGLVPHP---RIGSVWAANPDGKPSKSLAKVISRTTDAT 216

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMDL 297
            + E+   +GR HQ+R+H   +G P+VGD  Y       +     P     +LHA+++  
Sbjct: 217 TF-EVSLGSGRPHQIRIHLASIGHPLVGDPLYGPTGQPLEDLPGLPGDGGYFLHAQFLKF 275

Query: 298 PHP-EGGRLQITAPLPAHM 315
            HP  G R+ + A LP+  
Sbjct: 276 HHPITGERIHLEAALPSGF 294


>gi|296104461|ref|YP_003614607.1| tRNA pseudouridine synthase C [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295058920|gb|ADF63658.1| tRNA pseudouridine synthase C [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 261

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 103/241 (42%), Gaps = 17/241 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG
Sbjct: 1   MTLEILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++  +  A + L + F   +IQK Y ++V G            + +   I   +    
Sbjct: 61  VLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLTEAATLDYPLVEELDKIADKFAR-- 118

Query: 217 KQNEKGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             ++KG   A++ ++                 ++  +E+ P TGR HQLR H  H+  PI
Sbjct: 119 --DDKGPQPAVTEYRGMATTEMPVATSKFPTTRYSLVELLPKTGRKHQLRRHLKHLRHPI 176

Query: 267 VGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD K+      +        ++L LHA  + L HP  G+ L I A L    ++     G
Sbjct: 177 IGDSKHGDLRQNRSAAEHFGCDRLMLHASELSLTHPFTGKPLTIHAGLDDVWMQALSQFG 236

Query: 324 F 324
           +
Sbjct: 237 W 237


>gi|223986739|ref|ZP_03636725.1| hypothetical protein HOLDEFILI_04048 [Holdemania filiformis DSM
           12042]
 gi|223961305|gb|EEF65831.1| hypothetical protein HOLDEFILI_04048 [Holdemania filiformis DSM
           12042]
          Length = 295

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 64/303 (21%), Positives = 121/303 (39%), Gaps = 35/303 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  + E   +           +     K+    ++ ++ + V+ + +++ G  + +    
Sbjct: 14  VSAEAEGQTIAELLAPW--GCSKAARYKLEIEQKITLNGQPVRQSAKVKVGDELALKVFQ 71

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHID 130
              +  +                  +   +LYED  I   +KPAG+ V   + G    + 
Sbjct: 72  QEESDFVPW---------------AIPVRILYEDELILAVSKPAGMIVHPDNKGKTGTLA 116

Query: 131 GFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             + ++    GQ    R  HRLD+ TSGI++ ++       L ++   ++I + Y ++V 
Sbjct: 117 NAVAAYYLRTGQHCTVRPIHRLDEGTSGIVLFSKCPFFQPKLDQALAQKQIARTYLAVVS 176

Query: 189 GIPKNKKE-CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQ 246
           G+ K K    +   + +  H    Y             A++H +V+ C   +K   +  Q
Sbjct: 177 GVMKPKDRLTLDKPIGRDRHNAKAYRI-----SPTGKPAVTHVEVLRCRQKEKQTLVRCQ 231

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGRTHQ+RVH   +  P+V D  Y          P+Q ++ LHA          GR +
Sbjct: 232 LETGRTHQIRVHLASIQRPVVNDPLYNPR-------PVQGRMKLHAWKCAWTDLVSGRQV 284

Query: 306 QIT 308
           +IT
Sbjct: 285 EIT 287


>gi|71904404|ref|YP_281207.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94991334|ref|YP_599434.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94995246|ref|YP_603344.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|209560185|ref|YP_002286657.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
 gi|71803499|gb|AAX72852.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94544842|gb|ABF34890.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94548754|gb|ABF38800.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|209541386|gb|ACI61962.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
          Length = 333

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 69/289 (23%), Positives = 106/289 (36%), Gaps = 28/289 (9%)

Query: 23  RWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +        I    ++  LR    V ++   V + + ++ G  V++              
Sbjct: 55  KALLEEQLLIPR-KIRHFLRTKKHVLINGHPVNWQSCVKYGDQVKLFFDHE--------- 104

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
              D    +       K   LYED  I + NKP G+      G        L       G
Sbjct: 105 ---DYPEKIIVMGQAEKVTCLYEDEHIIIVNKPEGMKTH---GNDPTELALLNHVSAYTG 158

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           Q   + HRLD+ETSG ++ A+T      L      R I + Y +LV G   + +    + 
Sbjct: 159 QTCYVVHRLDKETSGAILFAKTPFILPILNRLLEKRDIHREYLALVHGSLDSPRVTYHHP 218

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +  H     V     +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H
Sbjct: 219 IGRHRHDRRKRV----VDPINGKKAITEVTLVKNFHKTASLLNCQLQTGRTHQIRVHLAH 274

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
            G  + GD  Y    K         +L LHA  + L HP     + + A
Sbjct: 275 QGHVLFGDPLYSNGKKD------CARLMLHAYQLRLKHPLTQEDICVQA 317


>gi|55820309|ref|YP_138751.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMG 18311]
 gi|55822199|ref|YP_140640.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus CNRZ1066]
 gi|55736294|gb|AAV59936.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus LMG 18311]
 gi|55738184|gb|AAV61825.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus CNRZ1066]
          Length = 290

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 66/279 (23%), Positives = 105/279 (37%), Gaps = 31/279 (11%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    V ++ + + + + ++ G  + +                 D     
Sbjct: 26  IPR-KIRHFLRTKKHVLINGETINWQSPVKEGDRISLTF------------DTEDYPNKT 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               D      LYEDS + V NKP G+   G           L       GQ   + HRL
Sbjct: 73  IPMGDANLVKPLYEDSHLIVVNKPEGMKTHGNKPTE---IALLNHVSAYCGQTCYVVHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG ++ A+       L      + IQ+ YW+L  G  + KK    + + +  H   
Sbjct: 130 DMETSGAVLFAKNPFILPILNRLLEDKMIQRQYWALTEGKFQTKKTVYKDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             V V  +  + A   ++  K  +        +  Q  TGRTHQ+RVH  H G  I+GD 
Sbjct: 190 KRV-VDPRKGQSAYTTVTRLKTFE----GASLVNCQLKTGRTHQIRVHLSHHGHAILGDP 244

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y             ++L LHA  +   HP    ++ + 
Sbjct: 245 LYSHQPA--------SRLMLHAHSLSFTHPLTLEKVTVK 275


>gi|324111198|gb|EGC05181.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
          Length = 260

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 103/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G    +       + +   I   Y       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKYAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTQYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  + L HP  G  L I A +    ++     G++
Sbjct: 180 KHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGELLTIHAGMDDIWMQALSQFGWR 237


>gi|301156232|emb|CBW15703.1| tRNA pseudouridine synthase [Haemophilus parainfluenzae T3T1]
          Length = 238

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 101/238 (42%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEYLVAVNKPAGMLVHRSWLDTHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  + + F  + +QK Y ++V G  + +        ++   I   +     Q +
Sbjct: 64  ALNSEIANLMCQQFEQKTVQKSYLAIVRGYLQGEGRIDYPLKIQLDKIADKFA----QED 119

Query: 221 KGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++          V      ++  +++ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQEAVTDYEGLNIVEMPYAVGRYQTTRYSLVKLIPQTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           +Y    +    +      +L+LHA  +   HP    +++I A L            + 
Sbjct: 180 QYGDLHQNRALTEYSGCQRLFLHADTLIFEHPIHLIKIEIKAGLDEQWEHVMKLFNWS 237


>gi|111115650|ref|YP_710268.1| hypothetical protein BAPKO_0868 [Borrelia afzelii PKo]
 gi|110890924|gb|ABH02092.1| hypothetical protein BAPKO_0868 [Borrelia afzelii PKo]
          Length = 315

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 132/319 (41%), Gaps = 22/319 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L  YV ++ +  ++   RLD        +++   + K +R G +R++  +  F+ R+ 
Sbjct: 1   MRLDKYV-FLEILANDNGKRLDSILIKIL-NLSKARIIKHIRKGDIRLNGIKSHFSYRVC 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   +    ++      ++           ++  ++YEDS + V +K  GI V 
Sbjct: 59  KGDKIYLYKSLAQGLNL-----TMNECYKSNIDFQCIRERIIYEDSDLLVLDKQRGILVH 113

Query: 121 GGSGIAYHIDG--FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           GG      +     LK  + S   KP   HRLD+ TSGI+V A+    A+ L+ +     
Sbjct: 114 GGRNSLDFLVNAYLLKEELRSLSFKPAAVHRLDRNTSGIIVFAKNINTARKLSTALSSGS 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y++++ G  K       N L +   +   +V     + K    AI+    I   ++
Sbjct: 174 ITKKYFAILLGEVK-STVVYKNHLFRNKRLKKTFV----LDGKDFINAITKVNPILS-SK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +    E+   TG THQ+R        P++ D KY   F+       ++  +LHA  +   
Sbjct: 228 RATLAEIVIETGFTHQIRAQCSFNNHPLINDKKYHDKFE-------KSNYFLHAFLVKFN 280

Query: 299 HPEGGRLQITAPLPAHMVK 317
                + +  A      +K
Sbjct: 281 EAFFKKNEFYAKPSLEFLK 299


>gi|237800319|ref|ZP_04588780.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. oryzae str. 1_6]
 gi|331023176|gb|EGI03233.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. oryzae str. 1_6]
          Length = 211

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 65/214 (30%), Positives = 104/214 (48%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIYQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDPDTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++++KV++  A   C +E+ P TGR+HQLRVH L +G P++GD  Y  +    
Sbjct: 122 HEAGKHALTYWKVLERHAS-HCRVELTPVTGRSHQLRVHMLSIGHPLLGDGLYAHSE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G R+    P+P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGSGERMTFECPVP 210


>gi|237755669|ref|ZP_04584280.1| ribosomal large subunit pseudouridine synthase protein
           [Sulfurihydrogenibium yellowstonense SS-5]
 gi|237692181|gb|EEP61178.1| ribosomal large subunit pseudouridine synthase protein
           [Sulfurihydrogenibium yellowstonense SS-5]
          Length = 270

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 72/301 (23%), Positives = 117/301 (38%), Gaps = 51/301 (16%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       I+    + I+ S  V V+ KRV   ++ ++ G VV I               
Sbjct: 16  FIAESLK-ISKNQAKDIIDSRNVIVNNKRVWIASHNLKPGDVVEI--------------- 59

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                    +        +LYED  I   +KP  I     S  A   +  L+  + +   
Sbjct: 60  --------VQSEPKNDLKILYEDDYIIAIDKPPTIVSDKESSSA---EDLLRKKLKNDKI 108

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           K    HRLD+ETSG+L+ A+     +   E +  + + KIY ++       K   I + +
Sbjct: 109 KA--IHRLDKETSGVLLFAKDYKIFEKFKEIWEDKNVLKIYLAISHNEANFKDFTINHDI 166

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                                  AI+H KV+      F + +++  TGR HQ+R H   +
Sbjct: 167 -------------------EGKQAITHLKVL-SKGNGFTYFQVRIETGRKHQIRKHLASI 206

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
             PIVGD  Y      N       +  LH+  + LPHP    +++ITAP+P+      + 
Sbjct: 207 RHPIVGDKIYGIKKFENNLVKRVTRQMLHSHKLVLPHPYLNKKIEITAPIPSDFKNVLNY 266

Query: 322 L 322
           L
Sbjct: 267 L 267


>gi|153840388|ref|ZP_01993055.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|260361363|ref|ZP_05774428.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus K5030]
 gi|260876822|ref|ZP_05889177.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus AN-5034]
 gi|260895884|ref|ZP_05904380.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus Peru-466]
 gi|260900382|ref|ZP_05908777.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus AQ4037]
 gi|149745949|gb|EDM57079.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|308089361|gb|EFO39056.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus Peru-466]
 gi|308091361|gb|EFO41056.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus AN-5034]
 gi|308108565|gb|EFO46105.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus AQ4037]
 gi|308113659|gb|EFO51199.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus K5030]
          Length = 255

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 63/258 (24%), Positives = 108/258 (41%), Gaps = 19/258 (7%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           S    ++    ++  ++Y+D      NKPAG+ V       +     +++  D  GQ   
Sbjct: 2   SEQETSQTVAPVELEIVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVF 61

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD+ TSG+LV A +   A  +   F   +++K Y ++V G  + +        ++ 
Sbjct: 62  PLHRLDRPTSGVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVEL 121

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQL 255
             I   +       EK A  A++ +K +               ++C +EM+P TGR HQL
Sbjct: 122 DKIADKFASQ----EKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQL 177

Query: 256 RVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           R H  H+  PIVGD  +               ++L LHA  +   HP     L + A + 
Sbjct: 178 RRHMAHLRHPIVGDTSHGDGKHNKLFRNEFDSHRLLLHASELRFVHPFTNEELVMKASID 237

Query: 313 AHMVKTWDSLGFKYDRNL 330
               + +    F++D  L
Sbjct: 238 DTWQQLFTR--FEWDEEL 253


>gi|237739111|ref|ZP_04569592.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           2_1_31]
 gi|229423711|gb|EEO38758.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           2_1_31]
          Length = 292

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 69/324 (21%), Positives = 135/324 (41%), Gaps = 38/324 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   ++  +VE++ +   +  + K    + +       LR+ ++ ++ KR          
Sbjct: 1   MRNRMKKYIVEHEFDGYEIGTYLKETKGYSSRG-----LRNLEIYLNGKR---------- 45

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +      I  LN I+    I++   +    +  +   + YED  + + NK   I V   
Sbjct: 46  -IKNNAKKIKKLNRIV----IIEKEKSTGIKAMDIPIDIAYEDENLLIVNKEPYIIVHPT 100

Query: 123 -SGIAYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              +   +   + ++ +    K   PR  +RLD  TSG++++A+       L +      
Sbjct: 101 QKKVDKTLANAVVNYFEKTLGKTLVPRFYNRLDMNTSGLIIIAKNAYTQAFLQDKT---E 157

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-A 237
           ++K Y  +V GI +     I   + K   IG D   +    E G   A +H KV++    
Sbjct: 158 VKKTYKVIVSGIIEEDDFFIELPIGK---IGDDLRRIELSEENGGKSAKTHIKVLERNRE 214

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +   +LE + +TGRTHQ+R H   +G P+VGD  Y  +        +  +  LHA  ++ 
Sbjct: 215 KNITFLEARLYTGRTHQIRAHLSLIGHPLVGDELYGGDMN------LAKRQMLHAYKLEF 268

Query: 298 PHPEG-GRLQITAPLPAHMVKTWD 320
            +P+    L++   +P  M +   
Sbjct: 269 QNPKTLENLKVEIEIPLDMKELLK 292


>gi|300724802|ref|YP_003714127.1| pseudouridine synthase [Xenorhabdus nematophila ATCC 19061]
 gi|297631344|emb|CBJ92039.1| pseudouridine synthase [Xenorhabdus nematophila ATCC 19061]
          Length = 250

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 65/240 (27%), Positives = 105/240 (43%), Gaps = 17/240 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y+D  I   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L
Sbjct: 2   LDIIYQDEHIVAVNKPAGWLVHRSWLARHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A +   A+ L++ F    IQK Y ++V G  +         + +   I   +      
Sbjct: 62  LMALSSEVARTLSQQFEFHDIQKTYHAVVRGYVEGDDIIDYALMEQLDKIADKFA----D 117

Query: 219 NEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            ++ A  AI+H++ +               +F  LE+ P TGR HQLR H  H+  PI+G
Sbjct: 118 TDREAQSAITHYRPLAKVECPVEIGRYSTSRFSLLELMPKTGRKHQLRRHMAHIRHPIIG 177

Query: 269 DHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           D  +    +           +L LHA ++ L HP  G  L +TA         ++  G+K
Sbjct: 178 DTTHGDLRQNRGVDKYYQTGRLMLHASHLQLKHPVTGDDLILTARWDTSWQHLFEQFGWK 237


>gi|293417934|ref|ZP_06660556.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B185]
 gi|291430652|gb|EFF03650.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B185]
          Length = 219

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/221 (30%), Positives = 105/221 (47%), Gaps = 15/221 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVVLYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++        + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYATDNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            Y +            +L LHA  + + HP  G  +   AP
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKAP 216


>gi|42528076|ref|NP_973174.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
 gi|41819121|gb|AAS13093.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
          Length = 244

 Score =  177 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 77/239 (32%), Positives = 118/239 (49%), Gaps = 22/239 (9%)

Query: 101 LLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGI 157
           +LYED  I + NK AG+ V        A  +D  L+     KG+ K    HRLD+ETSG+
Sbjct: 8   ILYEDKDILIVNKNAGLLVGADRWDSEAPRLDKILEELYKDKGERKIYPVHRLDKETSGL 67

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A    A + L + F+ R+I+KIY ++  GIP+ +       L     I GD +H   
Sbjct: 68  IIYALNAEAHKTLNDDFQNRKIEKIYHAVSAGIPQEENFKAEEKL----RIDGDKLHRTV 123

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--- 274
            +EK    +++ F ++  F++ FC LE +P TGRTHQ+R H  H+G PI+ D+ Y     
Sbjct: 124 IDEKKGKESLTEFSLLKRFSR-FCLLEARPITGRTHQIRAHLKHLGLPILCDNLYGNGEP 182

Query: 275 ----------NFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
                             PI ++L LHA  +   HP    +++I+A  P  M    + L
Sbjct: 183 VYISALKKNWRGDKYEERPIISRLALHAHSLKFFHPISKEKIEISADYPKDMAGLINQL 241


>gi|116328674|ref|YP_798394.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116121418|gb|ABJ79461.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
          Length = 377

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 75/384 (19%), Positives = 134/384 (34%), Gaps = 99/384 (25%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  D+  +RLD +    + + +    QK +  G++ V  K+VK    ++ G  V   P
Sbjct: 14  IFISKDDVGIRLDHFLSKKFTYHSRNVWQKEINEGRISVLGKKVKSGILLREGDTVVYQP 73

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +      + K+ K                  +LYED      +KP  + V          
Sbjct: 74  IERKEPPVRKDYK------------------ILYEDEFFVAVDKPGDLPVHPAGKYR--- 112

Query: 130 DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            G L + +   G  +     HRLD+ETSG+++ A+   AA  L+  F   +IQK Y + V
Sbjct: 113 KGNLLTLLKESGKFENLFTVHRLDRETSGVVLFAKDSKAASLLSGLFSSGKIQKYYITKV 172

Query: 188 WGIPKNK-------KECIANWLLKKSHIGGDYVHVVKQNEK---------GANYAISHFK 231
           +G    +       K  +++ + KK        + +K+N+K            + ++ F+
Sbjct: 173 YGDFPRRKIAYGVLKPDVSSIIRKKRKFFLLKSNFLKRNKKYFLENSFSPEEEFCLTAFR 232

Query: 232 VIDCF------------------------------------------------AQKFCWL 243
            I+ +                                                 + + ++
Sbjct: 233 KIESYFIKTQFQEIESDVGELKVRSRKKKLNFESLQTQNEKNEEPKVRSIYPKHEFYSFV 292

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----------ANFKGNFTSPIQNKLYLHA 292
             +P TGR HQ+R     +G PI GD  Y                         +  LHA
Sbjct: 293 LCKPITGRMHQIRAVLYGLGFPIWGDKLYGKDEEVFLEFIEGKNPDLTERLGMERQALHA 352

Query: 293 RYMDLPHPEGGR-LQITAPLPAHM 315
             +   HP   R ++I A +P   
Sbjct: 353 YAIRFNHPITNRKMKIVASVPKDF 376


>gi|256847721|ref|ZP_05553166.1| pseudouridylate synthase [Lactobacillus coleohominis 101-4-CHN]
 gi|256715410|gb|EEU30386.1| pseudouridylate synthase [Lactobacillus coleohominis 101-4-CHN]
          Length = 297

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 69/287 (24%), Positives = 120/287 (41%), Gaps = 32/287 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
            GQ  VD + V+   ++   Q + I              ++   + + T  S      ++
Sbjct: 36  DGQFLVDHRHVRPTTQVLPNQTLTI--------------QVDAETPDPTVQSSSQPLTIV 81

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSK---GQKPRLTHRLDQETSGIL 158
           YED+   V NKP GI+   G       I   +K +++      Q+P L  RLD+ TSG+L
Sbjct: 82  YEDANWLVINKPTGIASIPGPTEDNGTILNRVKGYLEKNEDPNQRPHLITRLDKYTSGLL 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA+ R A+  +++      +QK Y ++V G    +   I   + + +      +     
Sbjct: 142 LVAKHRVASSMISQQVEKHTMQKRYLAVVAGKLTKQHGVIDQPIKRVAGQTARII----- 196

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +     A + +       + +  +++Q H+GRTHQ+RVH   +G P+VGDH Y    + 
Sbjct: 197 -DPAGQPARTEYWC-QQTNEDYSLVQLQLHSGRTHQIRVHMSFIGHPLVGDHLYGGPLE- 253

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
                I +   LHA  +    P    +LQ  AP+          L  
Sbjct: 254 -----IAHHQVLHASTLSFRDPFTEQQLQFQAPMSKAQQALLKQLKL 295


>gi|255505626|ref|ZP_05347239.3| ribosomal large subunit pseudouridine synthase, RluD family
           [Bryantella formatexigens DSM 14469]
 gi|255266705|gb|EET59910.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Bryantella formatexigens DSM 14469]
          Length = 342

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 69/330 (20%), Positives = 138/330 (41%), Gaps = 53/330 (16%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++   +    +  + K+H   ++   ++ +  R   + V+ +RV+    ++   ++ +  
Sbjct: 26  IITPADAGSTVGDFLKHHMK-LSAAQIRSLKFRESGICVNGERVRVTQVLREHDLLELRF 84

Query: 70  VINA--LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-A 126
                 ++H+I E+  L                +LYED  +    K AG+ +    G  +
Sbjct: 85  GDEPCRMSHLIPEKHPL---------------HILYEDEDLICVWKEAGMVLHPAHGHYS 129

Query: 127 YHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +  +L+ ++  KG  ++ R   RLD++TSGI+V AR R AA  L +  +  R QK Y 
Sbjct: 130 DSLANYLQGYLAGKGGQEQVRGIGRLDKDTSGIVVFARNRIAAARLWQQRQSGRFQKEYV 189

Query: 185 SLVWGIPKNK----KECIANWLLKKSHIGGDYVHVV--KQNEKGANYAISHFKVIDCF-- 236
           +L  G+  ++    ++ I   + K +    + + +V  +       +A++H++ I     
Sbjct: 190 ALCEGVFPDEAYEREQTIDAPIQKVTGE-KNKMCIVQERCCPAAGCFAVTHYRAISEKES 248

Query: 237 ----------------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                            ++   + +   TGRTHQ+RVH  ++G P+VGD  Y     G  
Sbjct: 249 CFHEAMRLLSAGDLPGPEQASLVRLHLETGRTHQIRVHMAYIGHPLVGDAVYGRGIAGQT 308

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
            + +       A    L  P  G   +  P
Sbjct: 309 CAKL------CAWRARLVQPFTGETILLCP 332


>gi|282881599|ref|ZP_06290268.1| RNA pseudouridine synthase [Prevotella timonensis CRIS 5C-B1]
 gi|281304585|gb|EFA96676.1| RNA pseudouridine synthase [Prevotella timonensis CRIS 5C-B1]
          Length = 226

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 72/228 (31%), Positives = 108/228 (47%), Gaps = 15/228 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSG 156
           LYED+ I + +K +G  VQG       +   +K ++  K QKP      + HRLD+   G
Sbjct: 4   LYEDNHIIIVSKRSGEIVQGDKTGDLPLSETVKQYIKEKYQKPGNVFLGVVHRLDRPVWG 63

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V A+T  A   L + FR   + K YW++    P   +  + +WL++       Y H  
Sbjct: 64  LVVFAKTSKALTRLNKMFREGEVHKTYWAITKEAPPAAEGVLTDWLVRNERQNKSYAH-- 121

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            Q    A  A+  +KVI   +  +  LE+Q  TGR HQ+R    +MGCPI GD KY A  
Sbjct: 122 SQETPNAKKAVLKYKVI-AHSDHYHLLEVQLMTGRHHQIRCQLANMGCPIKGDLKYGAKR 180

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                S     + L AR +   HP     + + APLP    + W++L 
Sbjct: 181 SNPDGS-----ICLLARSIAFVHPVSKENIVVEAPLPPQ-DRLWEALA 222


>gi|261207216|ref|ZP_05921905.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289566649|ref|ZP_06447067.1| pseudouridine synthase [Enterococcus faecium D344SRF]
 gi|293557194|ref|ZP_06675744.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1039]
 gi|294614335|ref|ZP_06694252.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1636]
 gi|260078844|gb|EEW66546.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289161549|gb|EFD09431.1| pseudouridine synthase [Enterococcus faecium D344SRF]
 gi|291592807|gb|EFF24399.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1636]
 gi|291600646|gb|EFF30948.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1039]
          Length = 285

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 63/265 (23%), Positives = 111/265 (41%), Gaps = 28/265 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R   V ++++   F++ ++    + +              +  D +    +  D     
Sbjct: 36  IRK-NVWINQQPALFHHEVKGNDQITLLF------------EETDYNYQEVQLGDAAHIR 82

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + + +KPAG+                L +++D+K Q+P + HRLD+ETSG ++
Sbjct: 83  VLHEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+       L      + I + Y ++VWG        I N + +  H     V     +
Sbjct: 143 FAKNPFVLPILGRMLEQKMIYRRYQAIVWGEIAKDM-TITNKIGRDRHDRRKRV----VD 197

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +K    A++H  V    +++         TGRTHQ+RVH  H G PIVGD  Y       
Sbjct: 198 DKNGQSALTHVTVNKVLSEQTQVY-CVLETGRTHQIRVHLAHKGHPIVGDPLY------- 249

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR 304
             +    +L LHA  + + HP    
Sbjct: 250 -QNRTAERLMLHALELHMIHPFTQE 273


>gi|332673452|gb|AEE70269.1| RluA family ribosomal large subunit pseudouridine synthase
           [Helicobacter pylori 83]
          Length = 327

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 68/343 (19%), Positives = 141/343 (41%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLYLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                   +    K    L+  +++ED  + V NKP  + +     +
Sbjct: 59  TL--------------LTPKITPKPLKRGLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      HL+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEETRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L+   PL   M++ +  +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLRFKVPLLKDMLEYFKKV---FDKENLDEVLDEE 318


>gi|320528517|ref|ZP_08029674.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
 gi|320131103|gb|EFW23676.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
          Length = 287

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 60/309 (19%), Positives = 127/309 (41%), Gaps = 34/309 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           + + +  + +     +     +   + +    + Q+ +++K VK N  + +G V+ I  +
Sbjct: 9   ITDKQNGLTVKAVLSSL--GFSRHEILRFKFSAYQMYLNEKPVKVNRVVHTGDVLVIQEL 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHI 129
                          +    T H   ++  +LYED  + V  KPAG+        +   +
Sbjct: 67  ---------------NIETYTLHPSTVRPDILYEDEDVVVVCKPAGMPSHPSHHHLTDDM 111

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+ +   +    R   RLD++ SGI++ A+ + +A  L    +   +QK Y+++V G
Sbjct: 112 GTLLRDYYQDEHFVIRPIGRLDKDVSGIMIYAKNQLSAARLAAQRKDGILQKHYYAIVEG 171

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             ++K   I + + +   +   +        +G    ++ ++VI  + Q  C + +   T
Sbjct: 172 QLEDKDTLIFSLIKEDGQMAQSF-------NQGGKQCVTEYEVIKHY-QTECLIRVYLKT 223

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
           GRTHQ+R     +G P+ GD  Y  +           +  LH   ++   P    ++ + 
Sbjct: 224 GRTHQIRAGFAGIGHPLCGDTLYGGSIHW------IKRPALHCARIEFLQPFTKEKMILE 277

Query: 309 APLPAHMVK 317
             LP  M +
Sbjct: 278 KSLPEDMKR 286


>gi|209883418|ref|YP_002287275.1| pseudouridine synthase, RluD [Oligotropha carboxidovorans OM5]
 gi|209871614|gb|ACI91410.1| pseudouridine synthase, RluD [Oligotropha carboxidovorans OM5]
          Length = 244

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 72/237 (30%), Positives = 117/237 (49%), Gaps = 11/237 (4%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
               +  +++ +L+ D  + V +KPAGI+V  G     +++    +      + P L HR
Sbjct: 4   PQPTAQEMQARVLHRDGLMLVIDKPAGIAVHRGPKGGPNLEASFDALRYGLPRPPVLAHR 63

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG LV+ R R A   L   F+  +I K YW++V G P   +  I   L + +   
Sbjct: 64  LDRDTSGCLVLGRHRKATASLGLLFKHGKIGKTYWAVVEGGPAEDEGEIDIPLGRLNAER 123

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           G +     + +     + S + V+        WL ++P TGRTHQLRVH   MG PIVGD
Sbjct: 124 GWWQ----KPDPNGLPSKSRWSVLGRN-NGLSWLALEPLTGRTHQLRVHCAAMGFPIVGD 178

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           + Y      N     +  L+LHAR + +P       +++ AP+PAH+ +   + G+ 
Sbjct: 179 NIYG-----NGPRFGEPSLHLHAREIVVPLSRNKPPVRVIAPVPAHLQERLQACGWN 230


>gi|294054887|ref|YP_003548545.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
 gi|293614220|gb|ADE54375.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
          Length = 335

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 83/332 (25%), Positives = 135/332 (40%), Gaps = 40/332 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           W    YP      L++    G+V +D + + K + R++                + K Q+
Sbjct: 13  WLAKQYPDSPKKRLKEWFAQGRVTLDGEVITKPHLRLED---------PGKRLSMGKPQQ 63

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKG 141
           + +            +  LLY D+ + + NK  G+      G         L+S+   KG
Sbjct: 64  VPNVVFKRLPIRIHAQVNLLYIDNSLAIVNKGPGLLSVPLPGKNQPSALKILESYFKGKG 123

Query: 142 -------------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                          P   HRLDQ TSG+L  A T  A +HL +  R     + Y +L  
Sbjct: 124 ASELERNRVDRATLTPLPVHRLDQYTSGLLCFAMTPQAREHLVKQVRDHSFIREYMALAD 183

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--------QKF 240
           G    ++    +W   K    G    V  +  +GA  AISH++VID  +        Q  
Sbjct: 184 GWVDPRRGTWRSWF--KLDKEGMQQAVFDEPTEGATEAISHYEVIDSISWPTRDGKKQTV 241

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP-----IQNKLYLHARYM 295
             L+++  TG  HQLR+H+   GCP++GD  Y  +FK    +         +  LHA ++
Sbjct: 242 SRLKLRLETGLKHQLRIHSARAGCPLLGDRHYNPDFKKAAEANTGQPYGCKRQALHASHI 301

Query: 296 DLPHPEGGRL-QITAPLPAHMVKTWDSLGFKY 326
              HPE G+  + ++  P  +V+  + L  K 
Sbjct: 302 GFVHPETGKTKRFSSKFPRDLVELEERLREKA 333


>gi|260450733|gb|ACX41155.1| pseudouridine synthase [Escherichia coli DH1]
 gi|315134754|dbj|BAJ41913.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           DH1]
          Length = 219

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKICYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|312962216|ref|ZP_07776708.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens WH6]
 gi|311283553|gb|EFQ62142.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens WH6]
          Length = 211

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 67/213 (31%), Positives = 101/213 (47%), Gaps = 11/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V NKP  +    G       D  +    ++   + R+ HRLD ETSGI+++
Sbjct: 8   ILYQDDAVLVVNKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIILL 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR     + L+  F  R  +K Y +L WG P      I   L           HVV  + 
Sbjct: 67  ARDADTHRELSRQFHDRETEKAYTALAWGQPALDSGSIDLPLRYDPPT--KPRHVV--DH 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +   +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y        
Sbjct: 123 EFGKHALTFWKVLERCGD-WCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHEQALAA 181

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                 +L LHA  +   HP  G RL+   P P
Sbjct: 182 W----PRLCLHASMLSFTHPQSGERLRFECPAP 210


>gi|283835440|ref|ZP_06355181.1| tRNA pseudouridine synthase [Citrobacter youngae ATCC 29220]
 gi|291068616|gb|EFE06725.1| tRNA pseudouridine synthase [Citrobacter youngae ATCC 29220]
          Length = 260

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 66/257 (25%), Positives = 110/257 (42%), Gaps = 21/257 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +IQK Y ++V G   +        + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEHHQIQKRYHAIVRGWLMDDAVLDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELDPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK-- 325
           K+      +         +L LHA  ++L HP  G  L I A L    ++     G++  
Sbjct: 180 KHGDLRQNRSAAEHFGCQRLMLHASQLELIHPFTGEPLVIRAGLDDVWMQALSQFGWRGL 239

Query: 326 --YDRNLYIKRLYSQDE 340
              +  +    L  QDE
Sbjct: 240 LPENERVEFSGLSGQDE 256


>gi|332360116|gb|EGJ37930.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1056]
          Length = 290

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 121/303 (39%), Gaps = 32/303 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   +  G  + +
Sbjct: 4   TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLAINWQTVVNPGDDICL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  +  L +         LY+D  + + NKP G+          
Sbjct: 62  IFDEEDY----PQKTILFGNGELVEE--------LYQDQHLIIVNKPEGMKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + YW+LV
Sbjct: 110 ALLNHVSAYV---GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLEKREISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +KK    + + +  H     +     + +   YA +H   +  F Q    ++ Q 
Sbjct: 167 QGKFPSKKLIYKDKIGRDRHDRRKRL----VDPRKGLYAETHVNRLKQFGQ-ASLVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G  +VGD  Y    +G        +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGHQLVGDPLYHPQPQG--------RLMLHAHRLTFTHPFTLEKIT 273

Query: 307 ITA 309
           + A
Sbjct: 274 VEA 276


>gi|325846774|ref|ZP_08169689.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481532|gb|EGC84573.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 318

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 68/304 (22%), Positives = 131/304 (43%), Gaps = 31/304 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   +  ++ N R DR+ + ++ +     +QK +R    +++ KR K ++ ++   
Sbjct: 1   MIEVK---INENDSNQRFDRFLRKYFKNAPLSIIQKNIRKKNFKINDKRAKKDDLVKKDD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V++       +  +++     S  NL          ++YED  I + +K +G+     S
Sbjct: 58  IVKMYIKDEDYHKWVRKDDFKASDFNLD---------IIYEDENIIIIDKKSGVLSHAAS 108

Query: 124 GIAYHID--GFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              Y  +    + S++    +        +P + +RLD+ T+G+++ A+   A + L E+
Sbjct: 109 SSDYGKNLVDQMTSYLYKTNKVNSRDLTFRPSIVNRLDRNTAGLIIGAKNTKALRALNEA 168

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R  +I K Y +LV G  K          +  ++I       + +  KG    I+ F  +
Sbjct: 169 IRQGKIYKYYLTLVEGEIKKD-------FIVDTNISKYENKNMVKGNKGGKRIITKFYPL 221

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           +     F  LE +  TG+THQ+R        PI+GD KY    K N+     N   L A 
Sbjct: 222 ESK-NNFTLLECELITGKTHQIRYSLHKNSTPIIGDRKYS-KSKINYKKINLNSQALLAY 279

Query: 294 YMDL 297
            +  
Sbjct: 280 KLVF 283


>gi|208434657|ref|YP_002266323.1| pseudo uridine synthase D [Helicobacter pylori G27]
 gi|208432586|gb|ACI27457.1| pseudo uridine synthase D [Helicobacter pylori G27]
          Length = 333

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 69/349 (19%), Positives = 141/349 (40%), Gaps = 36/349 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-I 59
           M    ++Q V +       R+D +       I+   +  +++ G V   KK VK     +
Sbjct: 1   MQKRVWMQKVFIALTNH-KRIDEFLTKEL-QISKNQVLNLIKEGLVFCQKKEVKKGGLAL 58

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + G  + +                   +    K    L+  +++ED  + V NKP  + V
Sbjct: 59  KEGDEITL--------------LTPKITQKPLKRGLDLEIEVIFEDEDLLVLNKPPNLVV 104

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHL 170
                +    +  L  W++ K  +           + HRLD++TSG +V+A+      HL
Sbjct: 105 HKAPSV---KEPTLVDWLEFKNYELSNLGLKERYGIVHRLDKDTSGGIVIAKNNFTHVHL 161

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
           +E  + + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F
Sbjct: 162 SEQLKTKTMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKIIALKAAKKEKSRYSKSEF 221

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
             +         +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ L
Sbjct: 222 ISLLTSQNNLNLIGAKLFTGRTHQIRAHLEYLNRHIMGDNLYGLN---QALPKEEIRIML 278

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           HA  ++  HP    +L+   PL   M++    +   +D+    + L  +
Sbjct: 279 HAYLIEFKHPRSEQKLRFKVPLLKDMLEYLKKV---FDKENLDEVLDEE 324


>gi|206579088|ref|YP_002240476.1| pseudouridine synthase, RluA family [Klebsiella pneumoniae 342]
 gi|290512597|ref|ZP_06551963.1| ribosomal large subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
 gi|206568146|gb|ACI09922.1| pseudouridine synthase, RluA family [Klebsiella pneumoniae 342]
 gi|289774938|gb|EFD82940.1| ribosomal large subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
          Length = 219

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 108/228 (47%), Gaps = 15/228 (6%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           ++           ++LY+D  I V NKP+G+    G  +  H D  + + +     +   
Sbjct: 2   AMENYNPPQDPWLVILYQDEHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDFPQAES 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  TSG++VVA  +AA + L   FR R  +K Y + VWG P+  +  +   L+   
Sbjct: 60  VHRLDMATSGVIVVALNKAAERELKRQFREREPKKQYVARVWGHPQPAEGLVDLPLI--- 116

Query: 207 HIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               D+ +  KQ    +    A + ++V++        + ++P TGR+HQLRVH L +G 
Sbjct: 117 ---CDWPNRPKQKVCYETGKAAQTEYEVLEYAEDNTARVRLKPITGRSHQLRVHMLALGH 173

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
           PI+GD  Y           +  +L LHA  + + HP  G  +   AP+
Sbjct: 174 PILGDRFY----ATPEALAMAPRLLLHAETLTITHPAYGNAMTFRAPV 217


>gi|255007945|ref|ZP_05280071.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           fragilis 3_1_12]
 gi|313145657|ref|ZP_07807850.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           fragilis 3_1_12]
 gi|313134424|gb|EFR51784.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           fragilis 3_1_12]
          Length = 539

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 68/243 (27%), Positives = 106/243 (43%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +    +  T  +   +  +L+ED  + V +KP G+    G       
Sbjct: 308 CGPILRHMLQGLDVEPDPLA-TAPAPPKEIEILFEDEWLLVIHKPEGLLSVPGKSEELSA 366

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++    +   P + HRLD  TSG+L+VA+T+   QHL   F    I+K Y +L+ G
Sbjct: 367 YSLLRARY-PEATGPMIVHRLDMATSGLLLVAKTKEVHQHLQAQFESHSIKKQYTALLEG 425

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I    +  I   +              K + +    A++ + VID        +   P T
Sbjct: 426 ILPTDEGTIDLPICPDLLDRP----RQKADRESGKKAVTRYCVIDRK-NGRTRIAFFPQT 480

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
           GRTHQLRVH+ H   + CPI GD  Y    +         +LYLHA  ++  HP  G R+
Sbjct: 481 GRTHQLRVHSAHPSGLNCPIAGDELYGKRAE---------RLYLHAERLEFTHPVSGQRI 531

Query: 306 QIT 308
            I 
Sbjct: 532 YIE 534


>gi|251792621|ref|YP_003007347.1| tRNA pseudouridine synthase C [Aggregatibacter aphrophilus NJ8700]
 gi|247534014|gb|ACS97260.1| tRNA pseudouridine synthase C [Aggregatibacter aphrophilus NJ8700]
          Length = 236

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 99/237 (41%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDDVLVAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQLVYPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  L + F  ++ +K Y ++V G      E      ++   I   +     Q +
Sbjct: 64  ALNSEIANLLCQQFEQKQTEKQYLAVVRGYVTGHGEIDYPLKIQLDKIADKF----SQQD 119

Query: 221 KGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  + + P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQSAVTFYEGLQTVEMPYGVGCYATSRYSLVRLVPKTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
           +Y    +    +     ++L LHA  +   HP     + I A L A       +  +
Sbjct: 180 QYGDLHQNRALTEHTGCSRLMLHAEKLTFVHPLTQLPITIQAGLDAQWRNLMQTFQW 236


>gi|239632089|ref|ZP_04675120.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|239526554|gb|EEQ65555.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
          Length = 277

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 107/283 (37%), Gaps = 32/283 (11%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I      ++  +  + V+     FN ++Q   V+ +                 D    L 
Sbjct: 24  IPRKRQHQLRVAKTILVNGHYRNFNEKVQPSDVITMTY---------------DEPTPLA 68

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
              +     + YED  + + +KPAG+       G    +     +++        +THRL
Sbjct: 69  YVPETPALTIHYEDDDLLIVDKPAGMKTHPNLPGETGTLMNQAAAYLAP--FPALITHRL 126

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+LV+A+       +     ++ + + Y +LV          I   +        
Sbjct: 127 DMATSGLLVIAKNPLTQAIINRQLALKTMHRDYIALVPQGIAA-SGTITAPIGHDPDDQR 185

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +            AI+HF+ I   +     + ++  TGRTHQ+RVH   +G PI+GD 
Sbjct: 186 KRMIR-----PDGASAITHFRRIAKTSTTAT-VALRLETGRTHQIRVHLASIGYPILGDP 239

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y  +           ++YLHA  +    P     L +T+PLP
Sbjct: 240 LYAPD------QTTYQRMYLHAFQVRFTKPLSDTTLTVTSPLP 276


>gi|237729755|ref|ZP_04560236.1| tRNA pseudouridine synthase C [Citrobacter sp. 30_2]
 gi|226908361|gb|EEH94279.1| tRNA pseudouridine synthase C [Citrobacter sp. 30_2]
          Length = 260

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 65/257 (25%), Positives = 111/257 (43%), Gaps = 21/257 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V             +++  D  G+     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGRHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L++ F   +IQK Y ++V G   +        + +   I   +      ++
Sbjct: 64  GLSSEAGRLLSQQFEHHQIQKRYHAIVRGWLMDDAVLDYPLVEELDKIADKFAR----DD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELDPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK-- 325
           K+      +         +L LHA  + L HP  G  L I A L    ++     G++  
Sbjct: 180 KHGDLRQNRSAAEHFGCQRLMLHASQLALTHPFTGEPLVIRAGLDDVWMQALSQFGWRGL 239

Query: 326 --YDRNLYIKRLYSQDE 340
              +  +    L  QDE
Sbjct: 240 LPENERVEFSGLSGQDE 256


>gi|332071869|gb|EGI82358.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA41301]
          Length = 278

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 67/279 (24%), Positives = 112/279 (40%), Gaps = 29/279 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++++ V +N  +  G V ++                 D     
Sbjct: 13  IPR-KIRHFLRIKKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYPQKT 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               +      +Y+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 60  IPWGNPDLVQEVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRL 116

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++ A+       L      + I + YW+LV G    K+    + + +  H   
Sbjct: 117 DMETSGLVLFAKNPFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRR 176

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +     + K   YA +H   +  F+ K      +  TGRTHQ+RVH LH   PI+GD 
Sbjct: 177 KRI----VDAKNGQYAETHVSRLKQFSNKTSLAHCKLKTGRTHQIRVHLLHHNLPILGDP 232

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
            Y +  K        ++L LHA  +   HP    R   T
Sbjct: 233 LYNSKSKT-------SRLMLHAFRLSFTHPLTLERPTFT 264


>gi|255692700|ref|ZP_05416375.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides finegoldii DSM 17565]
 gi|260621534|gb|EEX44405.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides finegoldii DSM 17565]
          Length = 229

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 112/237 (47%), Gaps = 16/237 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQ        +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQADKTGDTPLSETVKQYLKEKYQKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR   ++K YW++V   P+  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTGKALTRLNEMFRTSEVKKTYWAVVKNAPQEPEGELVHFLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+++I   ++ +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVPNSKKAILHYRLIG-HSENYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLY 331
                 S     + LHAR +   HP     +++ APLP      W     +     Y
Sbjct: 180 RSNPDGS-----ICLHARRVRFIHPVSKELIELEAPLPEG--NLWKGFTIEDTEKTY 229


>gi|224534166|ref|ZP_03674746.1| RNA pseudouridine synthase family protein [Borrelia spielmanii
           A14S]
 gi|224514591|gb|EEF84905.1| RNA pseudouridine synthase family protein [Borrelia spielmanii
           A14S]
          Length = 315

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 137/319 (42%), Gaps = 22/319 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L  Y+ ++ +  ++   RLD        +++   + K +R G +R++  +  F+ R+ 
Sbjct: 1   MRLDKYI-FLEILANDNGKRLDSILIKIL-NLSKARIIKHIRKGDIRLNGIKPHFSYRVC 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   +    ++      ++          +++  ++YEDS + V NK  GI V 
Sbjct: 59  KGDKIYLYKSLAQGLNL-----TINECYKSDLDFQYIRERIIYEDSDLLVLNKQRGILVH 113

Query: 121 GGSG-IAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           G    + + ++ +L    + S   KP   HRLD+ TSGI+V A+    A+ L+  F    
Sbjct: 114 GDRNSLDFLVNAYLSREDLRSLSFKPSAVHRLDRNTSGIIVFAKNIDTARKLSILFSRGF 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y+++++G  K       N L +   +   +V       K    AI+    I   ++
Sbjct: 174 VTKKYFAILFGEVK-STVVYENHLFRNKRLRKTFV----LEGKDFINAITKVNPILS-SK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +   +E+   TG THQ+R        P++ D KYC  FK       ++  +LHA  +   
Sbjct: 228 RATLVEIIIKTGFTHQIRAQCSFNNHPLINDKKYCDKFK-------KSNYFLHAFLVKFN 280

Query: 299 HPEGGRLQITAPLPAHMVK 317
                + +  A      +K
Sbjct: 281 EAFFKKNEFYAKPSLEFLK 299


>gi|309776002|ref|ZP_07670994.1| ribosomal large subunit pseudouridine synthase C
           [Erysipelotrichaceae bacterium 3_1_53]
 gi|308916284|gb|EFP62032.1| ribosomal large subunit pseudouridine synthase C
           [Erysipelotrichaceae bacterium 3_1_53]
          Length = 323

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 58/306 (18%), Positives = 137/306 (44%), Gaps = 28/306 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +  ++ + R+D++ +     +    + K +R+ +++V++KR + + R+  G  ++
Sbjct: 1   MKEFYIGENDADQRVDKFIQKTMKTMPKSLMYKYIRNKKIKVNRKRCEISQRLALGDTMQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
                         ++  ++              ++YED  I + NKP G+      S +
Sbjct: 61  CYI----------AEEFYETQSMRQFLQVPSTLDIVYEDEHILLINKPKGLRAHSDTSEV 110

Query: 126 AYHIDGFLKSWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             ++   L  ++           +   P L HR+D+ T G+++ A+T AA + + E    
Sbjct: 111 QDNLADRLLHYLYESQEYDPAHEQSFTPALCHRIDRNTQGLVIAAKTAAALRCMNEKIAA 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R ++K Y  ++ G  + +++ I  +  KK     +   V++  ++G     + ++V+   
Sbjct: 171 REVEKKYLCIIQGGLRKQQDHIVLYHRKKEQ--DNIAEVIEHEQEGYARMETSYRVLQDK 228

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
              +  +E++ H+G++HQ+R     +G P++GD KY A+         +    L A Y+ 
Sbjct: 229 GS-YSLVEVELHSGKSHQIRALMSWLGHPLLGDVKYGADKTAQ-----KQYQALCAYYVA 282

Query: 297 LPHPEG 302
               +G
Sbjct: 283 FHFHDG 288


>gi|308062067|gb|ADO03955.1| hypothetical protein HPCU_03975 [Helicobacter pylori Cuz20]
          Length = 327

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 66/331 (19%), Positives = 136/331 (41%), Gaps = 35/331 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHI 77
            RLD +       I+   +  +++ G V   KK VK     ++ G  + +          
Sbjct: 12  KRLDEFLAKEL-QISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEITL---------- 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                    +    K    L+  +++ED  + V NKP  + +     +    +  L  W+
Sbjct: 61  ----LTPKITPKPLKRGLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSV---KEPTLVDWL 113

Query: 138 DSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           + K  +           + HRLD++TSG +V+A+      HL+E  + + + + Y +L+ 
Sbjct: 114 EFKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHAHLSEQLKTKMMGRYYIALLS 173

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
              K +K  +  +L +  +     + +    ++ + Y+ S F  +         +  +  
Sbjct: 174 TPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLF 233

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++  HP    +L+ 
Sbjct: 234 TGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIEFKHPRSEQKLRF 290

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             PL   M++ +  +   +D+    + L  +
Sbjct: 291 KVPLLKDMLEYFKKV---FDKENLDEVLDEE 318


>gi|254487090|ref|ZP_05100295.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           GAI101]
 gi|214043959|gb|EEB84597.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           GAI101]
          Length = 215

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 63/226 (27%), Positives = 106/226 (46%), Gaps = 15/226 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +           ++L+ED+++ + +KPAG+    G G   H+   L + V +      L 
Sbjct: 1   METEYSPPQDPLVILHEDAEVLLVDKPAGLLSVPGKGP--HLADCLIARVQAVFPDALLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG+++ A T  A +HL   F  R  +K Y + VWG+P      I   L+    
Sbjct: 59  HRLDRDTSGVMIFALTPYAQRHLGLQFEKRMTRKTYVARVWGVPTENSGTIDLPLIVD-W 117

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  V     +    A + ++++         + + P TGR+HQLRVH L +G PI+
Sbjct: 118 PNRPLQMVC---HETGKSAQTDWRLLKNEGD-TARVRLSPKTGRSHQLRVHMLSLGHPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
           GD  Y      N+      ++ LH+  +   HP+GG   +++  AP
Sbjct: 174 GDPFYATGPALNYP-----RMMLHSEELRFNHPQGGHSTKVRSKAP 214


>gi|85711787|ref|ZP_01042843.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
 gi|85694402|gb|EAQ32344.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
          Length = 218

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 65/215 (30%), Positives = 106/215 (49%), Gaps = 16/215 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D+ + V +KPAG+    G  + +     + + +       +L HRLD  TSG++V 
Sbjct: 16  IIHRDNALVVVDKPAGLLSVPGKLLEHRDS--VYTRLARIFPDIKLVHRLDMATSGVMVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +AA  HL+  F+ R  +K Y + VWG       CI   L        D+ +  KQ  
Sbjct: 74  ALGKAAQSHLSRQFQQRTPKKTYLAKVWGALPADNGCIDLPL------SCDWPNRPKQQV 127

Query: 221 K--GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  + + ++V+   AQ  C +++ P+TGR+HQLRVH L + CPI+GD  Y  +   
Sbjct: 128 DFFNGKPSQTFYRVLKRQAQG-CTVKLSPYTGRSHQLRVHMLALNCPILGDKFYAHSAAF 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                   +L LHA  + + HP+  + L  T+P P
Sbjct: 187 EAAE----RLLLHAFELRITHPQTEQTLTFTSPCP 217


>gi|270264826|ref|ZP_06193090.1| tRNA pseudouridine synthase C [Serratia odorifera 4Rx13]
 gi|270041124|gb|EFA14224.1| tRNA pseudouridine synthase C [Serratia odorifera 4Rx13]
          Length = 257

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 107/237 (45%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHLVAVNKPSGWLVHRSWLDRHETRFMMQTVRDQIGQHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++QK Y ++V G  +           +   I   +  V    +
Sbjct: 64  ALSSEVARLLSQQFEQHQVQKTYHAVVRGYVQEGATLDYPLTEELDKIADKHTAV----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +             + ++  +E++P  GR HQLR H +H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRPLAQVEMPVAIGRYDSARYSLMELKPENGRKHQLRRHMVHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           K+      +G        +L LHA ++ L HP  G  L I+A             G+
Sbjct: 180 KHGDLRQNRGMAQHFGCPRLMLHASHLQLNHPVTGEPLPISARWDEPWQGVMSQFGW 236


>gi|320332730|ref|YP_004169441.1| RluA family pseudouridine synthase [Deinococcus maricopensis DSM
           21211]
 gi|319754019|gb|ADV65776.1| pseudouridine synthase, RluA family [Deinococcus maricopensis DSM
           21211]
          Length = 318

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 126/304 (41%), Gaps = 29/304 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              R   +  + Y H +  + ++ +  G+V +D   +  +  +Q+GQV+           
Sbjct: 36  HGQRSLWYLVSKYRHSSAQDWRERVARGEVTLDGAPIDGHEILQAGQVL----------- 84

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                  + +     + +      + Y D  +    KP+G+    G G     +  L S 
Sbjct: 85  -------VWNRPPWDEEATPRTFDIAYLDDALLAVIKPSGLPTMHGGGFL---ENTLLSL 134

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           V ++  +    HRL + TSG+++ ART AAA  L+E++RM  ++K Y +L  G+    + 
Sbjct: 135 VRAQHPEATPLHRLGRATSGLVLFARTHAAASRLSEAWRMHHVEKRYRALASGVLAQDRV 194

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   +    H     VH V         + S   V++   +    L++   TGR HQ+R
Sbjct: 195 TIEAPIGPVPHPRLGTVHGV---SATGKASRSVACVLERR-EDATLLQVDIFTGRPHQIR 250

Query: 257 VHALHMGCPIVGDHKYCANFK---GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           +H   +G P+VGD  Y    +    N   P      LHA  +   HP  G  L + AP P
Sbjct: 251 IHTAFLGHPLVGDPLYGPGGQPKADNPGLPGDGGYLLHAERLAFTHPVTGAPLDVYAPAP 310

Query: 313 AHMV 316
             + 
Sbjct: 311 PALR 314


>gi|315222228|ref|ZP_07864135.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
 gi|315188731|gb|EFU22439.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
          Length = 286

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 68/302 (22%), Positives = 121/302 (40%), Gaps = 32/302 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + +      M +    + H+  I    ++  LR    V V++  + + +++    V+ +
Sbjct: 4   TITIPQGLPEMTVKELLEEHFL-IPR-KIRHFLRIKKHVLVNQHPINWQSQVHPADVITL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                       ++ IL  + +L +         LY+D  I + NKP G+          
Sbjct: 62  IFDEEDY----PQKSILMGNASLVEE--------LYQDEHITIVNKPEGMKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G    + HRLD+ETSG ++ A+       L      + I + YW+LV
Sbjct: 110 ALLNHVSAYV---GNTCYVVHRLDKETSGAVLFAKNPFILPILNRLLENKEISREYWALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    K++   + + +  H     +     + K   YA +H   +  F  K   +  Q 
Sbjct: 167 QGAFPQKRQIYTDKIGRDRHDRRKRL----VDNKNGQYAETHISKLKEFENK-TLVSCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G PI+GD  Y              +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGYPIIGDPLYNPQKA--------KRLMLHAHRLTFTHPFTLEKIS 273

Query: 307 IT 308
           + 
Sbjct: 274 VE 275


>gi|329961725|ref|ZP_08299756.1| RNA pseudouridine synthase [Bacteroides fluxus YIT 12057]
 gi|328531466|gb|EGF58306.1| RNA pseudouridine synthase [Bacteroides fluxus YIT 12057]
          Length = 223

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 66/219 (30%), Positives = 110/219 (50%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + +K A   VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIIVSKTASEIVQGDKTGDTPLSETVKQYLKEKYNKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E F+   ++K YW++V   P  ++  + +++++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFKDGEVKKTYWAVVKNRPPEEEGELVHYMVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   G+  AI H+++I   +Q +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKERPGSKKAILHYRLIG-KSQNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKYGFP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPA 313
                 S     + LHAR++   HP    +  + AP+P+
Sbjct: 180 RSNPDGS-----ICLHARFIRFVHPVSKEMVAVEAPVPS 213


>gi|308182904|ref|YP_003927031.1| hypothetical protein HPPC_03775 [Helicobacter pylori PeCan4]
 gi|308065089|gb|ADO06981.1| hypothetical protein HPPC_03775 [Helicobacter pylori PeCan4]
          Length = 327

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 69/343 (20%), Positives = 141/343 (41%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                   +    K    L+  +++ED  + V NKP  + +     +
Sbjct: 59  TL--------------LTPKITPKPLKRGLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      HL+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+RVH  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRVHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L    PL   M++ +  +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLCFKVPLLKDMLEYFKKV---FDKENLDEVLDEE 318


>gi|304399240|ref|ZP_07381107.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304353294|gb|EFM17674.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 259

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 65/259 (25%), Positives = 110/259 (42%), Gaps = 18/259 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRHETVFVMQTVRDQIGQHVFTAHRLDKPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +    + L+  F   ++QK Y ++V G        I   L+++     D         
Sbjct: 64  GLSSEVGRLLSLQFEQHQMQKTYHAVVRG-WLESSGTIDYPLVEELDKIADKHAT---EA 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           + A  A++ ++ +               ++  +EM P TGR HQLR H  H+  PI+GD 
Sbjct: 120 RTAQPAVTDYQSLATVEMPVGIGRYPTSRYSLVEMAPKTGRKHQLRRHMSHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +      +G       N+L LHA  + L HP  G  L I A L        +  G++ D
Sbjct: 180 AHGDLRQNRGAAEHFGANRLMLHASSLALTHPVTGEPLLIRAGLDGVWQNLMNQFGWQ-D 238

Query: 328 RNLYIKRLYSQDECKQNIL 346
           +   + R+       Q+ +
Sbjct: 239 QIPEVPRVEFNAAPGQDSV 257


>gi|260662398|ref|ZP_05863293.1| pseudouridylate synthase [Lactobacillus fermentum 28-3-CHN]
 gi|260553089|gb|EEX26032.1| pseudouridylate synthase [Lactobacillus fermentum 28-3-CHN]
          Length = 294

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 68/293 (23%), Positives = 110/293 (37%), Gaps = 33/293 (11%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                 H      Q       V V+      +  + +G V+ +    +            
Sbjct: 30  LPKRLVHYLRSRRQ-------VLVNGSYRPVSKTVAAGDVITLNFSGDEFR--------- 73

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQK 143
             + + +   D     +LYE+  + V +KPAGI      +G    +   + ++++     
Sbjct: 74  --TPDSSYLPDPGPLTVLYENRDLLVVDKPAGIKSHPNQAGEVGTLMNRVAAYLEGTNDA 131

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLDQETSG ++VA+       L        I + Y +LV G+P   +      L 
Sbjct: 132 AYMVHRLDQETSGAMIVAKNPVVVPILDRLISTGEIHRDYLALVAGVPNPARGIWDLPLG 191

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +            K   K A  A +H++ +         + +   TGRTHQLRVH    G
Sbjct: 192 QDPTDVRKR----KVFGKNAQPARTHYRTL-AVNDDRALVVLNLETGRTHQLRVHLAAAG 246

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           CPIVGD  Y         +    ++YLH    +L  P    R +I A +P   
Sbjct: 247 CPIVGDPLYG--------TVAAPRMYLHGVAQELVLPFSLKRERIVAKIPDDF 291


>gi|300908288|ref|ZP_07125753.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
 gi|300894535|gb|EFK87892.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
          Length = 325

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 66/291 (22%), Positives = 125/291 (42%), Gaps = 32/291 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
            G+  VD ++V+   +I   Q + I       +  ++              S      ++
Sbjct: 61  EGEFLVDHRKVRPTTQILPNQPLTIKAQPELADDTVE--------------SSNEPLNVV 106

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---DSKGQKPRLTHRLDQETSGIL 158
           YED    V +KPAG++   G  +    +   +K ++   +S   +P L  RLD+ T G+L
Sbjct: 107 YEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIANNSADLRPHLITRLDRFTGGLL 166

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+   A+  +++  +  ++ K Y +LV G   ++   I         IG       + 
Sbjct: 167 LIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHGEI------NKPIGRKDGQAARV 220

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            ++    A++ + V +    K+  + ++ HTGRTHQ+RVH   +G  ++GDH Y  +   
Sbjct: 221 IDENGQRALTEYWVEER-GAKWTRVRVRLHTGRTHQIRVHFAAIGHSLIGDHLYGGDTSK 279

Query: 279 NFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDR 328
                  +   LHA  +    P    ++  T+ LPA   +      FK +R
Sbjct: 280 ------YDHQLLHASKISFNDPFTLKQMTFTSELPAAFFELVPKCQFKLER 324


>gi|294793936|ref|ZP_06759073.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           3_1_44]
 gi|294455506|gb|EFG23878.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           3_1_44]
          Length = 321

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 74/353 (20%), Positives = 133/353 (37%), Gaps = 66/353 (18%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M   T +  ++V++      ++   K    HI+    +++   G + V+ K   +N  I 
Sbjct: 1   MKTATIID-LIVDSGVHTQSINHVIKQQ--HISQRMRRRLRNEGIITVNGKFATWNTLIH 57

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +         +  EQ+   S ++L          ++YED  I V NK AGI + 
Sbjct: 58  GGDHLVM--------KLTPEQEFSLSPMSLD---------IIYEDEYILVINKAAGILMH 100

Query: 121 GGSGIAYHI--DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             S +  H   +G L  + ++ +       HRLD+ TSGI+++A+T        +     
Sbjct: 101 PTSTVRNHTLANGVLHYYQETNQHYDFHPVHRLDKNTSGIVIIAKTSVVQHAFDKKHTH- 159

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              KIY ++V G   + +  I   + +K         + +        A +   V+    
Sbjct: 160 -FYKIYDAIVEGHLPSVRISINWPIGRKPD-----SIIERCCTDQGKPARTDITVVSKNT 213

Query: 238 -----------------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                                          F  ++   HTGRTHQ+RVH   +G P+ G
Sbjct: 214 SKFNYSKNNSDDMINNSNICPADNSIIVYNHFTHVQCLLHTGRTHQIRVHLSQLGYPLAG 273

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           D  Y  + +         +  LHA ++   HP     L++ A +P  M    +
Sbjct: 274 DDLYGGHLE------FIQRQALHASHVSFYHPITNEWLELHAEMPEDMNVLLN 320


>gi|293401387|ref|ZP_06645530.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305025|gb|EFE46271.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 293

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 71/323 (21%), Positives = 133/323 (41%), Gaps = 34/323 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M +      + +++++++  +D   ++   H +      + ++ Q+ ++    K N  I 
Sbjct: 1   MKITMKYHSIQIQSEQDSD-IDTLLQDL--HQSKKARYLLYQNKQLYLNGNLCKQNQSIT 57

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
               V+I      L+ I                 DF +  + YED  +   NKP+ + V 
Sbjct: 58  KNDEVQIHLPDETLSSI---------------PPDFTELSICYEDELLLAVNKPSHLLVH 102

Query: 121 G-GSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             G   ++ +   ++ +   +G     R  HRLD+ETSGI++  +       L    + +
Sbjct: 103 SDGVDTSHTLCNRVQGYYLMQGITAPVRPLHRLDKETSGIVLFCKIPFFQPLLDHMMKEK 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +IQ+ Y ++V G    KK+ I   + +  H        V    K A   I+    +    
Sbjct: 163 QIQREYEAIVEGSIHQKKQTITYPIARDRHDARK--MRVSATGKHAKTTIT----LQKNY 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             + W+  +  TGRTHQ+RVH   +  P++ D  Y         S   ++L LHA  + L
Sbjct: 217 GAYSWIHARLFTGRTHQIRVHLAALKHPLLSDSLYGT------PSDKIHRLALHASLLTL 270

Query: 298 PHPEG-GRLQITAPLPAHMVKTW 319
            HP    ++Q+T  +P  M    
Sbjct: 271 QHPFTNKKIQVTCEMPLDMKDLL 293


>gi|153809024|ref|ZP_01961692.1| hypothetical protein BACCAC_03328 [Bacteroides caccae ATCC 43185]
 gi|149128357|gb|EDM19576.1| hypothetical protein BACCAC_03328 [Bacteroides caccae ATCC 43185]
          Length = 223

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 67/219 (30%), Positives = 108/219 (49%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQ        +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQADKTGDTPLSETVKQYLKEKYQKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTSKALTRLNEMFRAGEVKKTYWAVVKNAPKESEGELVHFLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  A+  +++I   ++ +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVPNSKKAVLDYRLIGR-SENYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                 S     + LHAR +   HP     +++ APLP 
Sbjct: 180 RSNPDGS-----ICLHARRVRFVHPVSKELIELKAPLPE 213


>gi|60680595|ref|YP_210739.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis NCTC 9343]
 gi|60492029|emb|CAH06791.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis NCTC 9343]
          Length = 539

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 71/243 (29%), Positives = 110/243 (45%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  +       S  +   +L+ED  + V +KP G+    G      I
Sbjct: 308 CEPILRHMLQGLDVEPAPSERYSLSQNMPE-ILFEDQWLLVLHKPEGVLSVPGKSEEQSI 366

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++    +   P + HRLD  TSG+L+ A+ +   +HL   F  R I+K Y +L+ G
Sbjct: 367 YSLLRARY-PEATGPLVVHRLDMATSGLLLAAKAQEVHRHLQAQFENRSIKKRYIALLDG 425

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I   ++  I   +          +     NE+    AI+ ++V+D        +   P T
Sbjct: 426 ILPEEEGVIDLPICPDYLDRPRQM----VNEELGKTAITRYRVMDRK-NGQTRIAFFPLT 480

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
           GRTHQLRVHA H   + CPIVGD  Y    +         +LYLHA Y++  HP  G R+
Sbjct: 481 GRTHQLRVHAAHPLGLNCPIVGDELYGRKAE---------RLYLHAEYLEFIHPVSGQRM 531

Query: 306 QIT 308
            I 
Sbjct: 532 VIE 534


>gi|295098569|emb|CBK87659.1| ribosomal large subunit pseudouridine synthase A [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 210

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 67/216 (31%), Positives = 106/216 (49%), Gaps = 15/216 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD  TSG++
Sbjct: 5   LVILYQDEHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 62

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  +AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 63  VVALNKAAERELKRQFREREPKKQYVARVWGHPAQAEGLVDLPLI------CDWPNRPKQ 116

Query: 219 NE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               +    A + ++V++        + ++P TGR+HQLRVH L MG PI+GD  Y    
Sbjct: 117 KVCYETGKAAQTEYEVLEYAPDNTARVLLKPITGRSHQLRVHMLAMGHPILGDRFYAPPE 176

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
                  +  +L LHA+ + + HP  G  +   AP+
Sbjct: 177 ----ALALAPRLQLHAQTLTITHPAFGNAMTFKAPV 208


>gi|228476465|ref|ZP_04061155.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Streptococcus salivarius SK126]
 gi|228251886|gb|EEK10932.1| ribosomal large subunit pseudouridine synthase, RluD   family
           [Streptococcus salivarius SK126]
          Length = 289

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 60/268 (22%), Positives = 101/268 (37%), Gaps = 29/268 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              V ++ + + + + ++ G  + +                 D    +    +      L
Sbjct: 37  KKHVLINGEAINWQSPVEKGDKINLTF------------DTEDYPEKIIPMGNASLVEPL 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + V NKP G+      G        L       GQ   + HRLD ETSG ++ A+
Sbjct: 85  YEDQHLIVVNKPEGMKTH---GNEPTEIALLNHVSAYCGQTCYVVHRLDMETSGAVLFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      ++IQ+ YW+L  G  + K+    + + +  H     V     + + 
Sbjct: 142 NPFILPILNRLLEDKKIQRQYWALAEGKFQTKETVYKDKIGRDRHDRRKRV----VDPRK 197

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A +    +  F +    +  Q  TGRTHQ+RVH  H G  I+GD  Y          
Sbjct: 198 GQVAYTTITRLKAF-KGASLVNCQLKTGRTHQIRVHLAHHGHAILGDPLYSHRPA----- 251

Query: 283 PIQNKLYLHARYMDLPHPEG-GRLQITA 309
              ++L LHA  +   HP    ++ + A
Sbjct: 252 ---SRLMLHAHTLSFTHPLTLDKITVKA 276


>gi|170018031|ref|YP_001728950.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
 gi|169804888|gb|ACA83506.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
          Length = 306

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 75/330 (22%), Positives = 130/330 (39%), Gaps = 37/330 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKN-HYPHINFVNLQKILR-SGQVRVDKKRVKFNNR 58
           M+   Y   +   ++     +     +   P      ++  LR    VR++      N +
Sbjct: 1   MTTWHYQMTITPNSEHIGQSIKAVLIHWLIPQ----RIRGALRLKQHVRINGLYRPTNYQ 56

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +Q+   + +          + +Q    +  +    ++     +++E+  + V NKPAG+ 
Sbjct: 57  LQANDQLSL----------VFDQADFRTGESQYPANNSHALDIIFENDDLVVVNKPAGMK 106

Query: 119 VQG-GSGIAYHIDGFLKS-------WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           +          +  FL +       +      KP + HR+D+ETSG ++VA+       L
Sbjct: 107 MHPHSPSETDTLLNFLAANFSKRHLYSAGAIAKPYMVHRIDRETSGAVIVAKNPVVVPIL 166

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
               + + IQ+ Y + V GI       I   + +   I   +   V  N   A +A +H+
Sbjct: 167 NRMLKEKVIQRTYLAWVQGILLKNSGTIDRPIGRD--ISKPFQRQV--NGVQAQHAKTHW 222

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
             I    Q    L +Q  TGR HQ+RVH   +  PIVGD  Y            Q ++ L
Sbjct: 223 FKIHTVFQN-TLLRLQLDTGRMHQIRVHLASINHPIVGDSLYGQRLN-------QQRMML 274

Query: 291 HARYMDLPHPEGGRLQ-ITAPLPAHMVKTW 319
           HA  + LP P  G  + IT  LP+   K  
Sbjct: 275 HAMSLTLPLPFDGPKRIITTSLPSDFPKQL 304


>gi|320182959|gb|EFW57827.1| Ribosomal large subunit pseudouridine synthase A [Shigella flexneri
           CDC 796-83]
          Length = 206

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 69/219 (31%), Positives = 107/219 (48%), Gaps = 17/219 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD  TSG++V
Sbjct: 2   VILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVIV 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ 
Sbjct: 60  VALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQK 113

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y +   
Sbjct: 114 VCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEA 173

Query: 278 GNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
                    +L LHA  + + HP  G  +   A  PA  
Sbjct: 174 RAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 206


>gi|29349180|ref|NP_812683.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|253571343|ref|ZP_04848750.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           1_1_6]
 gi|29341088|gb|AAO78877.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|251839296|gb|EES67380.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           1_1_6]
          Length = 223

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 70/229 (30%), Positives = 114/229 (49%), Gaps = 15/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQ        +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQADKTGDTPLSETVKQYLKEKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR   ++K YW++V   PK  +  + ++L +       + + 
Sbjct: 63  GLVIFAKTSKALTRLNEMFRTSEVKKTYWAVVKNAPKEPEGELVHYLARNEKQNKSFAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI ++++I   ++ +  LE+   TGR HQ+R     MGCPI GD KY A 
Sbjct: 122 -DKEVPNSKKAILNYRLIG-HSENYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGAP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA-HMVKTWDSL 322
                 S     + LHAR +   HP     +++ APLP  ++ K ++ L
Sbjct: 180 RSNPDGS-----ICLHARKVRFIHPVSKELIELEAPLPEGNLWKGFELL 223


>gi|94989396|ref|YP_597497.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|94993288|ref|YP_601387.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
 gi|94542904|gb|ABF32953.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|94546796|gb|ABF36843.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
          Length = 333

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 69/289 (23%), Positives = 106/289 (36%), Gaps = 28/289 (9%)

Query: 23  RWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +        I    ++  LR    V ++   V + + ++ G  V++              
Sbjct: 55  KALLEEQLLIPR-KIRHFLRTKKHVLINGHPVNWQSCVKYGDQVKLFFDHE--------- 104

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
              D    +       K   LYED  I + NKP G+      G        L       G
Sbjct: 105 ---DYPEKIIVMGQAEKVTCLYEDEHIIIVNKPEGMKTH---GNDPTELALLNHVSAYTG 158

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           Q   + HRLD+ETSG ++ A+T      L      R I + Y +LV G   + +    + 
Sbjct: 159 QTCYVVHRLDKETSGAILFAKTPFILPILNRLLEKRDIHREYLALVHGSLDSPRVTYHHP 218

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +  H     V     +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H
Sbjct: 219 IGRHRHDRRKRV----VDPINGKKAITEVTLVKNFHKTASLLNCQLQTGRTHQIRVHLAH 274

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
            G  + GD  Y    K         +L LHA  + L HP     + + A
Sbjct: 275 QGHVLFGDPLYSNGKKD------CARLMLHAYQLRLKHPLTREDICVQA 317


>gi|294635111|ref|ZP_06713622.1| tRNA pseudouridine synthase [Edwardsiella tarda ATCC 23685]
 gi|291091488|gb|EFE24049.1| tRNA pseudouridine synthase [Edwardsiella tarda ATCC 23685]
          Length = 264

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 65/257 (25%), Positives = 109/257 (42%), Gaps = 18/257 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG  V             +++  D  G+     HRLD+ TSG+L++
Sbjct: 3   IIYQDEHLVAINKPAGWLVHRSWLDRKEKVVVMQTVRDQLGRHVYTVHRLDRPTSGVLLM 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +   A+ L + F   +I K+Y ++V G  + +         +   I   +    +  E
Sbjct: 63  GLSSEVARALAQQFEQHQIHKVYHAVVRGYLQGEALLDYPLTPELDKIADRF----RSAE 118

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +G   A +H++ +               +F  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 119 RGPQPAQTHYRGVATAEVPLAIGRYPTARFSLVELTPQTGRKHQLRRHMAHLRHPIIGDT 178

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +      +G         L LHA  + L HP  G  L + A L          LG++ D
Sbjct: 179 AHGDLRQNRGVAAHFGTAGLMLHASELQLTHPVTGEALCLRAGLDGRWQTLMAGLGWQ-D 237

Query: 328 RNLYIKRLYSQDECKQN 344
               + R+    +C Q+
Sbjct: 238 YLPELDRVEFTPDCPQD 254


>gi|71278616|ref|YP_271168.1| ribosomal large subunit pseudouridine synthase A [Colwellia
           psychrerythraea 34H]
 gi|71144356|gb|AAZ24829.1| ribosomal large subunit pseudouridine synthase A [Colwellia
           psychrerythraea 34H]
          Length = 227

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 64/225 (28%), Positives = 103/225 (45%), Gaps = 15/225 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   ++Y+D  I V NK +GI    G    +     L++ V        + HRLD 
Sbjct: 11  PPMSPYLDIIYQDDDIVVLNKASGILSVPGRLPEHQ--DCLQNRVQRVLPTATIVHRLDM 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI+++A  + A   ++  F  R+ QK Y + VWG+ +  +  +   L+         
Sbjct: 69  ATSGIMIMALNKPAHVAISRQFEQRKTQKSYLARVWGLVELNEGSVDLPLISDWPNRPK- 127

Query: 213 VHVVKQNEKGANYAISHFKVIDCF----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               K + +    +++H++V+        Q    LE+ P TGR+HQLRVH L +G PI+G
Sbjct: 128 ---QKVDHENGKKSLTHYRVLSHNDSIDEQANTLLELTPITGRSHQLRVHMLALGHPILG 184

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           D  Y           ++N+L LHA  + L HP   + +   AP P
Sbjct: 185 DRLYAPEE----ALTMRNRLQLHALKLSLFHPRTEQAITFDAPCP 225


>gi|282878833|ref|ZP_06287600.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
 gi|281299041|gb|EFA91443.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
          Length = 516

 Score =  177 bits (449), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 105/234 (44%), Gaps = 19/234 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+        ++ ++  ++YED  + V NKPAG+    G      +   L+  +      
Sbjct: 292 LEVDDEYPDDAEPMQLQMVYEDDDLVVVNKPAGLLSVPGRSSRPSVLTILQEMMPQD-MP 350

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD  TSG+L+VA+      HL   F+   IQK Y +++ G        I N  L
Sbjct: 351 LHAVHRLDMATSGLLIVAKNMKVYHHLQAQFKAHTIQKEYIAVLDGKVTQTDGSI-NLPL 409

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +   +      V + +      AI+ ++V+    Q    L + P TGRTHQLR+H  H  
Sbjct: 410 RPDLLDRPRQMVDRVH---GKSAITFYRVLSVH-QGKTMLALSPMTGRTHQLRMHCAHQE 465

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
            + CPI+GD  Y             ++LYLHA  +   HP  G+ + + AP+P 
Sbjct: 466 GLNCPILGDELYGHQ---------ADRLYLHAASITFIHPTSGKHMTLKAPIPD 510


>gi|320172856|gb|EFW48088.1| Ribosomal large subunit pseudouridine synthase A [Shigella
           dysenteriae CDC 74-1112]
          Length = 219

 Score =  177 bits (449), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 105/226 (46%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++        + ++P TGR+HQLRVH L  G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAPDNTARVVLKPITGRSHQLRVHMLAQGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|297621148|ref|YP_003709285.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
 gi|297376449|gb|ADI38279.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
          Length = 287

 Score =  177 bits (449), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 76/309 (24%), Positives = 144/309 (46%), Gaps = 35/309 (11%)

Query: 16  EENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINA 73
           E  ++L  +         +   +++ + +  V V+    +F + ++  G +V     +  
Sbjct: 8   ESGIKLVDFIHQKLQGKHSLRKIKRAIENNHVCVNGAVERFYSFQLSKGDLVEFDDSVLE 67

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
            +               ++     +  +L+ED  + ++NKP+G+          + D F 
Sbjct: 68  KSE--------------SEKPVPERDAILFEDDHLLIYNKPSGM----------NSDEF- 102

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              +        L HRLD+ET+G ++ A+       + E F+ ++I K Y ++V G+P  
Sbjct: 103 --GLGKFFPSFPLIHRLDKETTGCIMFAKYPKVKNRMIELFKGKKISKHYLAVVDGVPNK 160

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           ++    +++ + S   G  +     + K   +A + + +I+   ++   L+MQP TGRTH
Sbjct: 161 REGVEESFIGQISSNPGS-IKWGNVSPKQGQHAKTQW-MIEKRGKEAALLKMQPITGRTH 218

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
           QLRVHA  MG PI+GD +YC +FK ++     ++  LHA  +  PHP     L+I AP+P
Sbjct: 219 QLRVHAAQMGHPILGDFRYCRHFKCSYQP---SRTLLHAYTLHFPHPILDAYLKIKAPIP 275

Query: 313 AHMVKTWDS 321
           A M +    
Sbjct: 276 ADMKQAIRQ 284


>gi|325282268|ref|YP_004254809.1| pseudouridine synthase, RluA family [Deinococcus proteolyticus MRP]
 gi|324314077|gb|ADY25192.1| pseudouridine synthase, RluA family [Deinococcus proteolyticus MRP]
          Length = 305

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 67/307 (21%), Positives = 121/307 (39%), Gaps = 27/307 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V      + +  ++   YPH +       L +G+V ++      +  ++ G         
Sbjct: 17  VRPQAAGLSVLDYYARFYPHSDRQTWGARLAAGEVELNGHPAAGSESLRPGD-------- 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                     ++        + +  L   +LYED+ I   +KP+G+      G   H   
Sbjct: 69  ----------RLAWHRPPWAEEAVPLHFSVLYEDAHILAVHKPSGLPTLPAGGFLDH--- 115

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L + +  +       HRL + TSG+++ + T AA   LT  +R  RI K Y +L  G+ 
Sbjct: 116 TLLALLRRQWPAATPLHRLGRGTSGLVLCSLTPAAGSRLTADWREGRIHKRYRALSAGVA 175

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             +K  I   +    H     ++           + S  +V++         ++   TGR
Sbjct: 176 AQEKYDITAPIGLVDHPRLGQIYAAT---PAGKPSRSRAQVLERR-DGSTLFQVDIETGR 231

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHPEGGR-LQITA 309
            HQ+R+H    G P++GD  Y    +    + P      LHA  ++  HP GG  L ++A
Sbjct: 232 PHQIRIHLASAGLPLLGDPLYLPGGQARPDALPGDLGYLLHAERLEFRHPAGGEHLSLSA 291

Query: 310 PLPAHMV 316
           P+P  + 
Sbjct: 292 PVPPELR 298


>gi|218129851|ref|ZP_03458655.1| hypothetical protein BACEGG_01432 [Bacteroides eggerthii DSM 20697]
 gi|217987961|gb|EEC54286.1| hypothetical protein BACEGG_01432 [Bacteroides eggerthii DSM 20697]
          Length = 518

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 111/242 (45%), Gaps = 19/242 (7%)

Query: 70  VINALNHIIKEQKILDSSV-NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
               L H++K  ++ ++ +      S   +   +YED  + V NKPAG+    G   A  
Sbjct: 285 CEPILKHMLKGLEVDENPMQKALLQSAAQELETVYEDEWLLVVNKPAGMLSVPGKEEAVS 344

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +   ++     +   P + HRLD  TSG+LV+A+T+   Q+L   FR R + K Y +L+ 
Sbjct: 345 VYSVMRGRY-PEADGPLIVHRLDMATSGLLVIAKTKQVHQNLQAQFRDRSVSKRYIALLQ 403

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           GI       +   L        D    +   E G   A++ F+V++        +   P 
Sbjct: 404 GIVSPDTGTVELPLCLNPL---DRPRQMVHTEHG-KPAVTDFEVLERK-DNHTRIAFYPR 458

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           TGRTHQLRVHA H   + CPI+GD  Y    +         +LYLHA  ++  HP  G+ 
Sbjct: 459 TGRTHQLRVHAAHPLGLHCPIIGDELYGKKAE---------RLYLHAEALEFTHPITGKR 509

Query: 306 QI 307
            I
Sbjct: 510 VI 511


>gi|224025955|ref|ZP_03644321.1| hypothetical protein BACCOPRO_02702 [Bacteroides coprophilus DSM
           18228]
 gi|224019191|gb|EEF77189.1| hypothetical protein BACCOPRO_02702 [Bacteroides coprophilus DSM
           18228]
          Length = 223

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 70/219 (31%), Positives = 109/219 (49%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIVVNKTASEIVQGDKTGDTPLSETVKQYLKEKYAKPGNVFLGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E FR   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNEMFRNGEVKKTYWAIVKNCPKEPEAELTHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K +  A+ H+++I   +  +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVKDSKKAVLHYRLIG-HSVNYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                 S     + LHAR +   HP     + +TAP+P 
Sbjct: 180 RSNPDGS-----ICLHARRVRFVHPVSKELIDLTAPVPE 213


>gi|254466034|ref|ZP_05079445.1| ribosomal large subunit pseudouridine synthase A [Rhodobacterales
           bacterium Y4I]
 gi|206686942|gb|EDZ47424.1| ribosomal large subunit pseudouridine synthase A [Rhodobacterales
           bacterium Y4I]
          Length = 217

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 59/218 (27%), Positives = 102/218 (46%), Gaps = 12/218 (5%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +V+           +L+ D+++   NKPAG+    G G   H+   L + V +   +  L
Sbjct: 2   AVSSEYTPPQDPLDILHHDAELLAVNKPAGLLSVPGRG--EHLADCLIARVQAVFPEALL 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG++V   T  A +HL+  F  R  +K Y + V G  + +   +   L+   
Sbjct: 60  VHRLDRDTSGVMVFGLTPHAQRHLSMQFEKRTAKKAYVARVEGQLEPRSGTVDLPLIVDW 119

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                 +       +    A++ ++V+ C       + + P TGR+HQLRVH L +G PI
Sbjct: 120 PNRPKQMVC----HETGKPAVTDWRVMKC-EDGATRVRLTPKTGRSHQLRVHMLSLGHPI 174

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +GD  Y +    +       +L LH+  + + HP+ G 
Sbjct: 175 LGDPLYASGAALDHP-----RLMLHSEELRIKHPDSGE 207


>gi|116492962|ref|YP_804697.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
 gi|116103112|gb|ABJ68255.1| Pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
          Length = 253

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 59/247 (23%), Positives = 111/247 (44%), Gaps = 14/247 (5%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVD 138
           E  +     N       +   + YED+   + NKP  +  VQ  +     +   +K++  
Sbjct: 9   EVTLPPEPSNPHVGLSDVPIDVRYEDADYLIVNKPPFLPTVQSAANQKDTLVNRVKNYYV 68

Query: 139 SKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               + R+ H   RLDQ+TSG+++ A+ R A   + +  R R+I K+Y ++V G   N+ 
Sbjct: 69  KNNYESRVVHVVTRLDQDTSGLVIFAKHRFAHTVMDQDLRQRKINKMYLTIVEGTFTNQH 128

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   + +       ++  +         +++ + V D F + F  L+++ H+GRTHQ+
Sbjct: 129 GIIETPIQRDP---DSFIKRMVAPMGEGKPSLTEYWVEDTF-KNFTLLKVKLHSGRTHQI 184

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAH 314
           RVH   +G P+VGD  Y         + I  +  LH   +   +    ++  I   +P  
Sbjct: 185 RVHFSSIGHPLVGDELYGG-----MANDILQRQALHCFSLTFKNVFTEKMIDIKTSIPDD 239

Query: 315 MVKTWDS 321
           M++ W+ 
Sbjct: 240 MLEYWNK 246


>gi|90407469|ref|ZP_01215652.1| pseudouridine synthase Rlu family protein [Psychromonas sp. CNPT3]
 gi|90311390|gb|EAS39492.1| pseudouridine synthase Rlu family protein [Psychromonas sp. CNPT3]
          Length = 253

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 114/253 (45%), Gaps = 18/253 (7%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
            S+   + +  +   +LY+D  +   NKP G+ V       +  +  ++   D  G    
Sbjct: 5   PSLETNETAIPIPLEILYQDEAVVAINKPPGLLVHRSWLDPHATEFAIQKLRDQIGVHVY 64

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD+ TSG+L+    +   + +   F  ++I+K Y ++V G      E I ++ LKK
Sbjct: 65  PAHRLDRPTSGVLLFLLDKNYLKPVMAQFAEQKIEKRYLAIVRGHI---GEGIIDYALKK 121

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQL 255
                 + HV++  E  A  A++H++          V      ++  +E+ P TGR HQL
Sbjct: 122 KLDKIAHKHVLR--EPEAQSAVTHYRNMAHCEVDIGVRPYPTSRYSLVELSPKTGRRHQL 179

Query: 256 RVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           R H  H+  PI+GD  +           +   ++L LHA  +   HP  G +++I APL 
Sbjct: 180 RRHMKHVFHPIIGDTTHGDGKHNQMFRDNFEVSRLLLHAASLTFEHPVSGDKIEIKAPLD 239

Query: 313 AHMVKTWDSLGFK 325
                  ++LG K
Sbjct: 240 NDFKTLLETLGLK 252


>gi|330891514|gb|EGH24175.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. mori str. 301020]
          Length = 211

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 66/214 (30%), Positives = 102/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIYQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDPPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEGGKHALTFWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL    P P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|229591788|ref|YP_002873907.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens SBW25]
 gi|229363654|emb|CAY50999.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens SBW25]
          Length = 211

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 67/213 (31%), Positives = 103/213 (48%), Gaps = 11/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + V NKP  +    G       D  +    ++   + R+ HRLD ETSGI+++
Sbjct: 8   ILYQDAAVLVVNKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIILL 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR     + L+  F  R  +K Y +L WG P+     I   L           HVV  + 
Sbjct: 67  ARDADTHRELSRQFHDRETEKAYTALAWGQPELDSGSIDLPLRYDPPT--KPRHVV--DH 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +   +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y        
Sbjct: 123 EFGKHALTFWKVLERCGD-WCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHEQALAA 181

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                 +L LHA  +   HP  G RL+   P P
Sbjct: 182 W----PRLCLHASMLSFTHPQSGERLRFECPAP 210


>gi|184156168|ref|YP_001844508.1| pseudouridylate synthase [Lactobacillus fermentum IFO 3956]
 gi|183227512|dbj|BAG28028.1| pseudouridylate synthase [Lactobacillus fermentum IFO 3956]
          Length = 294

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 68/293 (23%), Positives = 110/293 (37%), Gaps = 33/293 (11%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                 H      Q       V V+      +  + +G V+ +    +            
Sbjct: 30  LPKRLVHYLRSRRQ-------VLVNGSYRPVSKTVAAGDVITLNFSGDEFR--------- 73

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQK 143
             + + +   D     +LYE+  + V +KPAGI      +G    +   + ++++     
Sbjct: 74  --TPDSSYLPDPGPLTVLYENRDLLVVDKPAGIKSHPNQAGEVGTLMNRVAAYLEGTNDA 131

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLDQETSG ++VA+       L        I + Y +LV G+P   +      L 
Sbjct: 132 AYMVHRLDQETSGAMIVAKNPVVVPILDRLISTGEIHRDYLALVAGVPNPARGIWDLPLG 191

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +            K   K A  A +H++ +         + +   TGRTHQLRVH    G
Sbjct: 192 QDPTDVRKR----KVFGKNAQPARTHYRTL-AVNDDRALVVLNLETGRTHQLRVHLAAAG 246

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           CPIVGD  Y         +    ++YLH    +L  P    R +I A +P   
Sbjct: 247 CPIVGDPLYG--------TVAAPRMYLHGVAQELVLPFSLKRERIVAKIPDDF 291


>gi|260599139|ref|YP_003211710.1| tRNA pseudouridine synthase C [Cronobacter turicensis z3032]
 gi|260218316|emb|CBA33307.1| tRNA pseudouridine synthase C [Cronobacter turicensis z3032]
          Length = 262

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 104/242 (42%), Gaps = 17/242 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG
Sbjct: 1   MSLEILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++  +  A + L + F   +IQK Y ++V G   +        + +   I   +    
Sbjct: 61  VLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLTDSAVLDYPLVEELDKIADKFSRQ- 119

Query: 217 KQNEKGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              +K    A++H++ +    Q          ++  +EM P TGR HQLR H  H+  PI
Sbjct: 120 ---DKEPQPAVTHYRGLATTTQPVAVGRYESVRYSLVEMLPQTGRKHQLRRHMAHLRHPI 176

Query: 267 VGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           +GD K+      +        ++L LHA  + L HP  G  L I A L     +     G
Sbjct: 177 IGDSKHGDLRQNRAAAEHFGCHRLMLHASELTLTHPFTGAPLTIRAGLDDVWRQALAHFG 236

Query: 324 FK 325
           ++
Sbjct: 237 WQ 238


>gi|127513571|ref|YP_001094768.1| pseudouridylate synthase [Shewanella loihica PV-4]
 gi|126638866|gb|ABO24509.1| tRNA pseudouridine synthase C [Shewanella loihica PV-4]
          Length = 273

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 112/247 (45%), Gaps = 18/247 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  +   +KPAG+ V             ++   D  G      HRLD+ TSG+L+ 
Sbjct: 25  ILYEDDDLVAIHKPAGLLVHRSYLARREKYFAMQMTRDLVGCHVFPVHRLDRPTSGVLLF 84

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++   A  L E F  + +QK Y +LV G   ++   +   L ++    GD         
Sbjct: 85  AKSSEMANQLCEQFASKSVQKHYVALVRGNM-HEPGLLDYPLKQELDELGDK---NVDPN 140

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A + +  +             + ++  +++ PHTGR HQLR H  H+  PI+GD 
Sbjct: 141 KAAQEAQTSYHPLLNCEIPYPSGRYASSRYALVQLTPHTGRKHQLRRHMAHLRHPIIGDT 200

Query: 271 KYCANFKGNFTSP--IQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLGFKYD 327
            +    +  F       N+L+L A+ ++  HP  G R+ +   L A  +  ++ LG+  D
Sbjct: 201 THGDGKQNRFMREHSGINRLWLIAKKLEFNHPRSGERIAVETELEAEWLSLFELLGWD-D 259

Query: 328 RNLYIKR 334
           + L  ++
Sbjct: 260 QQLSGEQ 266


>gi|146293584|ref|YP_001184008.1| pseudouridylate synthase [Shewanella putrefaciens CN-32]
 gi|145565274|gb|ABP76209.1| Pseudouridylate synthase [Shewanella putrefaciens CN-32]
 gi|319426883|gb|ADV54957.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 223

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 66/222 (29%), Positives = 107/222 (48%), Gaps = 9/222 (4%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        + Y+D  + + NKP+G+      GIA H      + +     +  L HRLD
Sbjct: 7   QPPAIPWLDIRYKDRDLIIINKPSGLLSNP--GIAAHTYDCALTRLQRLYPETILVHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V AR + A  HL   F+ R+ +K+Y + V G+  N++  I   +         
Sbjct: 65  CATSGIMVFARNKKAESHLKTQFQDRQSKKVYIAEVMGLIANEQGIINLSIAPNCEHP-P 123

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y   ++  E G   A++H++V++   +    +E+ P TGRTHQLRVH L +G PI+GD  
Sbjct: 124 YQKALQAGEAGGKSALTHYRVLERR-KNSTLVELTPETGRTHQLRVHMLALGHPILGDEF 182

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y            + +L LHA+ +   HP  G+ +   +  P
Sbjct: 183 YG----DAAVINAKPRLCLHAQSLRFSHPYSGKPMSFHSKHP 220


>gi|152979640|ref|YP_001345269.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150841363|gb|ABR75334.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 219

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 64/225 (28%), Positives = 100/225 (44%), Gaps = 13/225 (5%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                    +++ D+ I V NKP+G+    G+   Y+      S V  K       HRLD
Sbjct: 7   HPPKTPYLDIIHHDNHILVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPAHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI++ A ++ A   L   FR R+ +K Y ++VWG PK     +   L+       +
Sbjct: 65  MATSGIILFAMSKLADSELKRQFRERQTEKFYQAVVWGHPKQDSGTVNLPLICD----WE 120

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                + +      A++ F+V++        L++ P TGR+HQLR+H L +G PI+GD  
Sbjct: 121 NRPRQRIDFNAGKSAVTKFEVLERLPNNSTRLKLTPITGRSHQLRLHMLALGHPILGDKF 180

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           Y              +LYLHA  + + HP  G  +      PA  
Sbjct: 181 YAHPQAKAMA----PRLYLHAESLTITHPVTGEAMTFRC--PADF 219


>gi|152968638|ref|YP_001333747.1| 23S rRNA/tRNA pseudouridine synthase A [Klebsiella pneumoniae
           subsp. pneumoniae MGH 78578]
 gi|238893033|ref|YP_002917767.1| 23S rRNA/tRNA pseudouridine synthase A [Klebsiella pneumoniae
           NTUH-K2044]
 gi|262044907|ref|ZP_06017949.1| pseudouridine synthase A [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|330009270|ref|ZP_08306486.1| pseudouridine synthase A [Klebsiella sp. MS 92-3]
 gi|150953487|gb|ABR75517.1| 23S rRNA pseudouridylate 746 synthase [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238545349|dbj|BAH61700.1| 23S rRNA pseudouridylate 746 synthase [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|259037634|gb|EEW38863.1| pseudouridine synthase A [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|328534847|gb|EGF61389.1| pseudouridine synthase A [Klebsiella sp. MS 92-3]
          Length = 219

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 65/228 (28%), Positives = 107/228 (46%), Gaps = 15/228 (6%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           ++           ++LY+D  I V NKP+G+    G  +  H D  + + +     +   
Sbjct: 2   AMENYNPPQDPWLVILYQDEHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDFPQAES 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  TSG++VVA  +AA + L   FR R  +K Y + VWG P+  +  +   L+   
Sbjct: 60  VHRLDMATSGVIVVALNKAAERELKRQFREREPKKQYVARVWGHPQPAEGLVDLPLI--- 116

Query: 207 HIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               D+ +   Q    +    A + ++V++        + ++P TGR+HQLRVH L +G 
Sbjct: 117 ---CDWPNRPMQKVCYETGKAAQTEYEVLEYAEDNTARVRLKPITGRSHQLRVHMLALGH 173

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
           PI+GD  Y           +  +L LHA  + + HP  G  +   AP+
Sbjct: 174 PILGDRFY----ATPEALAMAPRLLLHAETLTITHPAYGNAMTFRAPI 217


>gi|323495104|ref|ZP_08100191.1| tRNA pseudouridine synthase C [Vibrio brasiliensis LMG 20546]
 gi|323310655|gb|EGA63832.1| tRNA pseudouridine synthase C [Vibrio brasiliensis LMG 20546]
          Length = 240

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 98/241 (40%), Gaps = 17/241 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G             ++   I   +       E
Sbjct: 64  ALSSEVASQVMPMFANHEMEKTYHAIVRGWILESGRLDYPLKVELDKIADKHASQ----E 119

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ ++ +               ++C +EM+P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQEAITDYQPLAQVEIPHSTGRFPTTRYCLMEMKPLTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNFTSPI--QNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
            +           +   ++L LHA  +   HP     + I A L     K  +   +   
Sbjct: 180 THGDGKHNKLFREVYDSHRLLLHASSLKFVHPFTQQEIIIEAGLDETWQKLCEEFAWSTP 239

Query: 328 R 328
           +
Sbjct: 240 K 240


>gi|283782368|ref|YP_003373123.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
 gi|283440821|gb|ADB19263.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
          Length = 603

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 79/316 (25%), Positives = 138/316 (43%), Gaps = 34/316 (10%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVR 66
           + + V  + +   +  +     PH+      +I   G++R  D + +   + +++G  V 
Sbjct: 305 RPLRVPQEYDGKPVIEFLAGILPHVPRDEWAQIAGEGRLRTSDHQPMVLESLVKAGDRV- 363

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGI 125
                     +  +   ++  VN+          ++YED  I V +KPA + +   G   
Sbjct: 364 ----------LHHQPATIEPDVNVD-------IRVVYEDEAIAVVHKPAPLPLHASGRFH 406

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
              ++  L+   D   QKPR  HRLD  TSG+++ ARTR  A+ L + F   +++K Y +
Sbjct: 407 RNTLEWILREIYDP--QKPRPVHRLDANTSGLVLFARTRHFAKLLQQQFTQGKVEKFYLA 464

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC----FAQKFC 241
           LV G P   +      +  ++ + G        +E+    A + F+V+        +   
Sbjct: 465 LVSGHPVEDRFVSTAPISAEAGVFGSR----SVDEEAGLPAETRFEVLARTTTADGKPVA 520

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI---QNKLYLHARYMDLP 298
            +  QP TGRT+Q+RVH   +G PI+G+  Y A+ K   T         L L A  +   
Sbjct: 521 LVRCQPITGRTNQIRVHLWQLGHPIMGEQSYLADQKHGTTQTHTVDDPPLCLLAHQLSFQ 580

Query: 299 HPEG-GRLQITAPLPA 313
           HP    R+  T+ LPA
Sbjct: 581 HPVSRERMTFTSQLPA 596


>gi|332535815|ref|ZP_08411548.1| tRNA pseudouridine synthase C [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332034793|gb|EGI71331.1| tRNA pseudouridine synthase C [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 254

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 98/256 (38%), Gaps = 17/256 (6%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
                 ++ +  +LY+D      NKP+G+ V       +     ++   D  GQ     H
Sbjct: 3   ERPAPIEYGELTILYQDENYVAINKPSGLLVHRSFLDKHETQFAMQMLRDQLGQHVFPVH 62

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG+L+ A +  AA+ + + F    I K Y +LV G              +   I
Sbjct: 63  RLDRPTSGVLLFALSSEAARDMNQLFIEGTIAKRYLALVRGFAPESVFLDKPLKEELDKI 122

Query: 209 GGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVH 258
              +       +K    A + F  +               ++  +E  P TGR HQ+R H
Sbjct: 123 ADKFADQ----DKAPQEAQTQFNCLHQAALPIPIGKYPTVRYSLVECFPKTGRKHQIRRH 178

Query: 259 ALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             H+  PI+GD  +  N    F        +L L A  +   HP     + I APL   M
Sbjct: 179 LKHLSLPIIGDVNHGDNQHNQFFREHFELRRLMLFATELSFVHPYSNESITIKAPLGEDM 238

Query: 316 VKTWDSLGFKYDRNLY 331
           ++    LG+      Y
Sbjct: 239 LEICKQLGWPEQEKDY 254


>gi|152971656|ref|YP_001336765.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238896253|ref|YP_002920989.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae NTUH-K2044]
 gi|262041533|ref|ZP_06014730.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|330012185|ref|ZP_08307318.1| RNA pseudouridine synthase [Klebsiella sp. MS 92-3]
 gi|150956505|gb|ABR78535.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae MGH
           78578]
 gi|238548571|dbj|BAH64922.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae
           NTUH-K2044]
 gi|259041094|gb|EEW42168.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|328533887|gb|EGF60555.1| RNA pseudouridine synthase [Klebsiella sp. MS 92-3]
          Length = 264

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/257 (24%), Positives = 112/257 (43%), Gaps = 18/257 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDDWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +I+K Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIRKRYHAIVRGWLMEEALLDYPLVEELDRIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTSRYGLVELEPKTGRKHQLRRHLAHLRHPILGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           K+      +        ++L LHA  + L HP  G  L + A      ++     G++  
Sbjct: 180 KHGDLRQNRSAAEHFGCHRLMLHASELSLTHPFTGEPLTLRAGFDDVWMRALSQFGWRGL 239

Query: 328 RNLYIKRLYSQDECKQN 344
             L  +R+   D+  Q+
Sbjct: 240 LPLN-ERVEFADDSGQD 255


>gi|148982218|ref|ZP_01816647.1| tRNA pseudouridine synthase C [Vibrionales bacterium SWAT-3]
 gi|145960609|gb|EDK25961.1| tRNA pseudouridine synthase C [Vibrionales bacterium SWAT-3]
          Length = 249

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 63/243 (25%), Positives = 105/243 (43%), Gaps = 19/243 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IIYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    +QK Y ++V G  +          ++   I   +     + +
Sbjct: 64  ALSSEVASEVMPMFANHEMQKTYHAIVRGWIEEGDTLDYALKVELDKIADKFA----KED 119

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EM P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQEAVTAYEPLAKVEVPYSTGRFPTSRYCLVEMLPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNFTSPIQN--KLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
            +             +  +L LHA  +   HP     L + A L    ++ +++  F++D
Sbjct: 180 SHGDGKHNRLFRENLDSHRLLLHASELRFIHPFTKEELVMKASLDETWLQLFET--FEWD 237

Query: 328 RNL 330
            NL
Sbjct: 238 TNL 240


>gi|291086115|ref|ZP_06354861.2| pseudouridine synthase A [Citrobacter youngae ATCC 29220]
 gi|291069419|gb|EFE07528.1| pseudouridine synthase A [Citrobacter youngae ATCC 29220]
          Length = 219

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 108/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDEHIMVVNKPSGLLSVPGR-LDEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPAPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y           +  +L LHA  + + HPE G  +     +PA  
Sbjct: 180 FYAPPE----ALAMAPRLLLHAEMLTITHPEYGNSMTFK--VPADF 219


>gi|258647905|ref|ZP_05735374.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella tannerae ATCC 51259]
 gi|260851740|gb|EEX71609.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella tannerae ATCC 51259]
          Length = 245

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 72/236 (30%), Positives = 112/236 (47%), Gaps = 15/236 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-----HRLDQETS 155
           +LYED+ I + NK AG  +QG       +   +K+++  K  KP        HRLD+  S
Sbjct: 9   ILYEDNHIIIVNKQAGEIIQGDKTGDRTVADEIKAYLKEKYNKPGAVFLGIPHRLDRPVS 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+ + ART  A   L E FR   I+K Y ++V   P+     + +WL +       Y H 
Sbjct: 69  GVSIFARTSKALARLNEMFRKGEIEKTYQAIVIHEPQIASGTLVHWLTRNEKQNKAYAH- 127

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K  +K A  AI  +KV +  + ++  + +Q  TGR HQ+R     +GCPI GD KY A 
Sbjct: 128 -KAPQKNAKKAILDYKV-EAKSDRYWLINVQLQTGRHHQIRCQLAAIGCPIKGDLKYGAP 185

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAPLPAH-MVKTWDSLGFKYDRN 329
                 S     + LHAR +   HP   ++    AP P+  +   +  L  + +++
Sbjct: 186 RSNADGS-----ICLHARSIRFEHPVSHKIIFAEAPYPSFPLWNVFQKLCNESEQS 236


>gi|145638949|ref|ZP_01794557.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittII]
 gi|145271921|gb|EDK11830.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittII]
          Length = 232

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 101/230 (43%), Gaps = 17/230 (7%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
              NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ A +   A 
Sbjct: 5   VAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALSSEIAN 64

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            + E F  + +QK Y ++V G  + K+       ++   I   +     Q +K    A++
Sbjct: 65  LMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQEDKEPQEAVT 120

Query: 229 HFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            ++ +               ++  +++ PHTGR HQLR H  H+  PI+GD +Y    + 
Sbjct: 121 DYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPILGDTQYGDLHQN 180

Query: 279 NFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
              +      +L+LH+  +   HP     + ITA L     +  +  G++
Sbjct: 181 RALTFHLGFSRLFLHSNSLSFIHPIKKEQITITAGLDEQWQQLMNQFGWE 230


>gi|294673069|ref|YP_003573685.1| RNA pseudouridine synthase family protein [Prevotella ruminicola
           23]
 gi|294472960|gb|ADE82349.1| RNA pseudouridine synthase family protein [Prevotella ruminicola
           23]
          Length = 223

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 69/227 (30%), Positives = 106/227 (46%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK +G  VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHIIIVNKQSGEIVQGDKTGDRPLSELVKDYIKEKYAKPGAVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ART  A   L + F   ++ K YW++V   PK  +  + NWL++       Y + 
Sbjct: 63  GLVVFARTSKALTRLNKMFAEGQVHKTYWAIVKNRPKALEGTLENWLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    A  A+  ++VI      +  LE+   TGR HQ+R     MGCPI GD KY A 
Sbjct: 122 -DKERPNAKKALLKYRVIG-QTDNYTVLEVNLMTGRHHQIRCQLAAMGCPIKGDLKYGAP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
                 S     + L +R ++  HP     + + APLP      W +
Sbjct: 180 RSNPDGS-----ISLMSRRVEFVHPVSKETIIVEAPLPND--PLWQA 219


>gi|156932726|ref|YP_001436642.1| tRNA pseudouridine synthase C [Cronobacter sakazakii ATCC BAA-894]
 gi|156530980|gb|ABU75806.1| hypothetical protein ESA_00515 [Cronobacter sakazakii ATCC BAA-894]
          Length = 265

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 104/242 (42%), Gaps = 17/242 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG
Sbjct: 1   MSLEILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++  +  A + L + F   +IQK Y ++V G   +        + +   I   +    
Sbjct: 61  VLLMGLSSEAGRRLAQQFEQHQIQKRYHAIVRGWLTDSAVLDYPLVEELDKIADKFSRQ- 119

Query: 217 KQNEKGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              +K    A++H++ +   +Q          ++  +EM P TGR HQLR H  H+  PI
Sbjct: 120 ---DKEPQPAVTHYRGLATTSQPVAVGRYDSVRYSLVEMLPQTGRKHQLRRHMAHLRHPI 176

Query: 267 VGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           +GD K+      +        N+L LHA  + L HP  G    I A L     +     G
Sbjct: 177 IGDSKHGDLRQNRAAAEHFGCNRLMLHASELTLTHPFTGAPFTIRAGLDDVWRQALAHFG 236

Query: 324 FK 325
           ++
Sbjct: 237 WQ 238


>gi|323190261|gb|EFZ75537.1| RNA pseudouridylate synthase family protein [Escherichia coli
           RN587/1]
          Length = 219

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 106/226 (46%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQDPWLVILYHDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|304407496|ref|ZP_07389148.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
 gi|304343447|gb|EFM09289.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
          Length = 308

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 64/267 (23%), Positives = 117/267 (43%), Gaps = 19/267 (7%)

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q G+ + +     A    + +  +   +             +LYED  I V +KPAG+ V
Sbjct: 49  QDGERIALDAFPPAD---LDKDPLYRLASEGEAGKAIAACRVLYEDDSILVMHKPAGVPV 105

Query: 120 QGGS-GIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                G    +D      +  KG     R  HRLDQETSG ++ ++   A   L E+ R 
Sbjct: 106 HPSRPGERGTLDEAAARHMLKKGDPLPVRHIHRLDQETSGPVLYSKNDLAQLRLDEAMRQ 165

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + I+++Y + V G     +  I   + +  H       +        ++A++ ++ ++ +
Sbjct: 166 KTIERVYLAFVQGKISKPRGVIDAPIGRDRHQPARRRVIA-----NGDHAVTRYETMERY 220

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           + K   + ++  TGRTHQ+RVH  H+G P++GD  Y  +      + +     LH   + 
Sbjct: 221 S-KATLVRIRLETGRTHQIRVHMSHLGHPLIGDSLYGGD------TALLKHQALHGEMLV 273

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSL 322
             HP  G  +++ +PLP    +   +L
Sbjct: 274 FHHPLSGAPVKVFSPLPDWYAQLKQTL 300


>gi|311280961|ref|YP_003943192.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308750156|gb|ADO49908.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 219

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 68/227 (29%), Positives = 108/227 (47%), Gaps = 15/227 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++          ++LY+D  I V NKP+G+    G  +  H D  + + V     +    
Sbjct: 3   MDAYNPPQDPWLVVLYQDKHIMVVNKPSGLLSVPGR-LEEHKDSIM-TRVQRDFPQAESV 60

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG P  ++  +   L+    
Sbjct: 61  HRLDMATSGVIVVALTKAAERELKRQFREREPKKQYLARVWGHPHPEEGLVDLPLI---- 116

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V++        + ++P TGR+HQLRVH   +G P
Sbjct: 117 --CDWPNRPKQKVCFETGKAAQTEYQVLEYSDDNTARVLLKPITGRSHQLRVHMQALGHP 174

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
           I+GD  Y         S    +L LHA  + + HP  G  +   AP+
Sbjct: 175 ILGDRFYATPEALAMAS----RLLLHAETLTITHPAYGNSMTFKAPV 217


>gi|298486181|ref|ZP_07004244.1| Ribosomal large subunit pseudouridine synthase A [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|298159188|gb|EFI00246.1| Ribosomal large subunit pseudouridine synthase A [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
          Length = 211

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 66/214 (30%), Positives = 102/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIYQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDPDTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HQGGKHALTFWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL    P P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|254497897|ref|ZP_05110662.1| ribosomal large subunit (23S rRNA) pseudouridine synthase C
           [Legionella drancourtii LLAP12]
 gi|254352895|gb|EET11665.1| ribosomal large subunit (23S rRNA) pseudouridine synthase C
           [Legionella drancourtii LLAP12]
          Length = 263

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 83/269 (30%), Positives = 129/269 (47%), Gaps = 17/269 (6%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           + +G V+RIPP+  +    +     L         +  LK  +++ED+   V NKP+GI+
Sbjct: 1   MHAGDVIRIPPIRTSEAKEVFVGDAL---------AKRLKDCIIFEDACFLVINKPSGIA 51

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           V GGSG++  +   L+           L HRLD+ETSG L++A+ R+  + +      R 
Sbjct: 52  VHGGSGLSLGVIEALRKTRQDLAY-LELIHRLDKETSGCLLLAKKRSTLRAMHALLEARE 110

Query: 179 IQKIYWSLVWGIPKNKKE-CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +QK YW+L+    + KK+  +   L K     G+ V  V         + + FK+++ + 
Sbjct: 111 VQKTYWALLTHRWEGKKQVTVHAALEKNILKSGERVVSVNDE---GKASETTFKLLENY- 166

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMD 296
           Q+ CW+E  P TGRTHQ+RVH+ H+G  IVGD KY A             +LYLHAR + 
Sbjct: 167 QQACWVEASPKTGRTHQIRVHSAHLGHVIVGDEKYGALAGEVEGIDNRHRRLYLHARSIQ 226

Query: 297 LPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                G +    A        T   L  +
Sbjct: 227 FE-LNGTKHCFQANADDIFSNTLKQLRAR 254


>gi|281492772|ref|YP_003354752.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
 gi|281376424|gb|ADA65910.1| Ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
          Length = 288

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 67/268 (25%), Positives = 116/268 (43%), Gaps = 30/268 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
                V+ K +  N  + +G  + +       +++     +   SVNL        + +L
Sbjct: 37  KKHCLVNNKLINENQLVHAGDKITLIFDNEDFSNL----SLKFGSVNL--------ADIL 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + V NKP G+   G +     +   + + ++   Q+  + HRLD  TSG ++ A+
Sbjct: 85  YEDEHLIVVNKPEGMKTHGNTADELALQNHVAAAIN---QEVFVVHRLDHATSGAVLFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            +     L + F   +I + Y +LV G     +  I   + +  H     +   K     
Sbjct: 142 NQFVLPILGKMFEENKIHREYLALVKGHFSENQFTIDRAIGQNRHDKNKRILSAK----- 196

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++H ++I  F  K   ++    TGRTHQ+RVH   +  PI+GD  Y          
Sbjct: 197 GQKAVTHVEIIKKFTDK-TLVKCTLDTGRTHQIRVHLSSLNHPIIGDALYGQKS------ 249

Query: 283 PIQNKLYLHARYMDLPHP-EGGRLQITA 309
             Q ++ LHA  + +PHP E   L+I+A
Sbjct: 250 --QERMMLHADKIIIPHPFENKILEISA 275


>gi|119471760|ref|ZP_01614120.1| tRNA pseudouridine synthase C [Alteromonadales bacterium TW-7]
 gi|119445383|gb|EAW26671.1| tRNA pseudouridine synthase C [Alteromonadales bacterium TW-7]
          Length = 254

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/252 (24%), Positives = 102/252 (40%), Gaps = 17/252 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
            +++ +  +LY+D      NKP+G+ V       +     ++   D  GQ     HRLD+
Sbjct: 7   PTEYGELDILYQDENFVAINKPSGLLVHRSFLDKHETQFAMQMLRDQLGQHVFPVHRLDR 66

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+L+ A +  AA+ + + F    I K Y +LV G   +          +   I   +
Sbjct: 67  PTSGVLLFALSSEAARDMNQLFIEGTIAKRYLALVRGFAPDSVFLDKPLKEELDKIADKF 126

Query: 213 VHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                   K    A + F  +               ++  +E  P TGR HQ+R H  H+
Sbjct: 127 ADQ----NKAPQEAQTQFNCLYQAALPIPIGKYPTVRYSLVECFPKTGRKHQIRRHLKHL 182

Query: 263 GCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
             PI+GD  +  N    F        +L L A  +   HP   + + I APL   M++  
Sbjct: 183 SLPIIGDVNHGDNQHNQFFRDHFELRRLMLFATELSFVHPYTYKAITIKAPLGNDMLQIC 242

Query: 320 DSLGFKYDRNLY 331
           + LG+  +   Y
Sbjct: 243 EQLGWPNEEKDY 254


>gi|300767769|ref|ZP_07077679.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|300494754|gb|EFK29912.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 293

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 74/306 (24%), Positives = 124/306 (40%), Gaps = 41/306 (13%)

Query: 23  RWFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQSGQV--VRIPPVINALNHII 78
           R+   H   I+   + K ++  +G   V+ +       I  G +  +++P        ++
Sbjct: 16  RFLTTH--AISMRTI-KAIKHGTGAFLVNNQVQTGVITIHDGDIAGIQLPDEAPDTAVVV 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWV 137
            EQ I                 + YED+   V NK AG+ SV G S     +   +K ++
Sbjct: 73  SEQPI----------------QIEYEDANWLVLNKSAGLTSVPGPSNRTDTLVNRIKGYL 116

Query: 138 ---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               +  Q+P L  RLD++TSG+++VA+ R A   LTE     ++ K Y + + G     
Sbjct: 117 IASHASNQRPHLVTRLDRDTSGLVLVAKHRVAQGMLTEPRIAAQLVKTYQAWIEGTITPA 176

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTH 253
              I   + + +      V            AI+ ++V  D        L ++  TGRTH
Sbjct: 177 SGTIDRPIGRVADSPRRVVTT------AGQRAITTYQVEADQLQHNVSRLRLELVTGRTH 230

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
           Q+RVH   +G P++GD  Y  N           +  LHA  +    P   ++    A LP
Sbjct: 231 QIRVHLTALGHPLLGDALYGGNLAW------IQRQALHAASLQFFDPFSEQILHFEAALP 284

Query: 313 AHMVKT 318
           A +   
Sbjct: 285 ADLQAL 290


>gi|28899096|ref|NP_798701.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus RIMD
           2210633]
 gi|34582398|sp|Q87MD4|TRUC_VIBPA RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|28807320|dbj|BAC60585.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           RIMD 2210633]
          Length = 246

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 105/248 (42%), Gaps = 19/248 (7%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            ++  ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TS
Sbjct: 3   PVELEIVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LV A +   A  +   F   +++K Y ++V G  + +        ++   I   +   
Sbjct: 63  GVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVELDKIADKFASQ 122

Query: 216 VKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
               EK A  A++ +K +               ++C +EM+P TGR HQLR H  H+  P
Sbjct: 123 ----EKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHP 178

Query: 266 IVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           IVGD  +               ++L LHA  +   HP     L + A +     + +   
Sbjct: 179 IVGDTSHGDGKHNKLFRNEFDSHRLLLHASELRFVHPFTNEELVMKASIDDTWQQLFTR- 237

Query: 323 GFKYDRNL 330
            F++D  L
Sbjct: 238 -FEWDEEL 244


>gi|331645166|ref|ZP_08346277.1| pseudouridine synthase A [Escherichia coli M605]
 gi|331045923|gb|EGI18042.1| pseudouridine synthase A [Escherichia coli M605]
          Length = 219

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGYPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|308063469|gb|ADO05356.1| hypothetical protein HPSAT_03065 [Helicobacter pylori Sat464]
          Length = 327

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 68/343 (19%), Positives = 141/343 (41%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLYLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                   +    K    L+  +++ED  + V NKP  + +     +
Sbjct: 59  TL--------------LTPKITPKPLKRGLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      HL+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKTAKKEKSRYSKSEFTSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L+   PL   M++ +  +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLRFKVPLLKDMLEYFKKV---FDKENLDEVLDEE 318


>gi|50915102|ref|YP_061074.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|56808190|ref|ZP_00365968.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Streptococcus
           pyogenes M49 591]
 gi|306826523|ref|ZP_07459832.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes ATCC 10782]
 gi|50904176|gb|AAT87891.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|304431250|gb|EFM34250.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes ATCC 10782]
          Length = 303

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 69/289 (23%), Positives = 106/289 (36%), Gaps = 28/289 (9%)

Query: 23  RWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +        I    ++  LR    V ++   V + + ++ G  V++              
Sbjct: 25  KALLEEQLLIPR-KIRHFLRTKKHVLINGHPVNWQSCVKYGDQVKLFFDHE--------- 74

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
              D    +       K   LYED  I + NKP G+      G        L       G
Sbjct: 75  ---DYPEKIIVMGQAEKVTCLYEDEHIIIVNKPEGMKTH---GNDPTELALLNHVSAYTG 128

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           Q   + HRLD+ETSG ++ A+T      L      R I + Y +LV G   + +    + 
Sbjct: 129 QTCYVVHRLDKETSGAILFAKTPFILPILNRLLEKRDIHREYLALVHGSLDSPRVTYHHP 188

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +  H     V     +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H
Sbjct: 189 IGRHRHDRRKRV----VDPINGKKAITEVTLVKNFHKTASLLNCQLQTGRTHQIRVHLAH 244

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
            G  + GD  Y    K         +L LHA  + L HP     + + A
Sbjct: 245 QGHVLFGDPLYSNGKKD------CARLMLHAYQLRLKHPLTQEDICVQA 287


>gi|71737110|ref|YP_273849.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|71557663|gb|AAZ36874.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. phaseolicola 1448A]
          Length = 237

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 66/214 (30%), Positives = 102/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 33  RIIYQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGFPEARIVHRLDWETSGIIL 91

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 92  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 147

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 148 HEGGKHALTFWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 203

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL    P P
Sbjct: 204 -ALAAYPRLCLHASMLSFTHPGTGERLTFECPAP 236


>gi|313123295|ref|YP_004033554.1| pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
 gi|312279858|gb|ADQ60577.1| Pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
          Length = 297

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 128/323 (39%), Gaps = 42/323 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQVVRIP 68
           ++V  ++    L  +        +   +      G +  V+  R   + R++ G VV   
Sbjct: 1   MIVAKNDPGQ-LSHFLLK--KGFSRRAVNNCKNHGGMMLVNHHRRNGSYRLKEGDVV--- 54

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                  H +  Q+ ++  + +++    L   ++ E +   V NKPAG+        A  
Sbjct: 55  -------HFLMGQEPVNPWLKVSR----LPLDIVEETADYLVINKPAGLLSIPSGFHAED 103

Query: 129 ID-GFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                + ++ + +G      KP +  RLDQ+TSG++++ +   A    ++  +   I+K 
Sbjct: 104 AVINRVLAYFEKQGVNPAYVKPHIVTRLDQDTSGLVLLGKNAIAHDRFSKLGKDAFIKKY 163

Query: 183 YWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + ++V G          I   L +          V ++       A++ ++V+D      
Sbjct: 164 H-AIVHGNFAEGDLSGLIDKPLARVGD------TVKREVNPKGQRALTEYRVLDQVP-GA 215

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E++  TGRTHQ+R+H   +G  + GD  Y A            +  L+  Y+   +P
Sbjct: 216 SLVELRLLTGRTHQIRIHMASIGHVLYGDDLYGAR-------DAFARQALNCFYLSFTNP 268

Query: 301 -EGGRLQITAPLPAHMVKTWDSL 322
             G   +I  P P  M   W  L
Sbjct: 269 FSGEEREIEIPDPGDMQGLWRQL 291


>gi|218442079|ref|YP_002380408.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
 gi|218174807|gb|ACK73540.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7424]
          Length = 308

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 82/322 (25%), Positives = 128/322 (39%), Gaps = 35/322 (10%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           ++    V   +  + +  ++   YPH       + + SGQV +D      + R+ +GQ  
Sbjct: 10  WIYREQVNPSDAGLTVLDYYSQKYPHSTPCQWFERITSGQVLLDGHSCNPHTRLITGQ-- 67

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                           K+        + S  L   LLY DS + V  KPAG+ +  G G 
Sbjct: 68  ----------------KLAYHRPPWEEPSAPLNFDLLYSDSDVLVVAKPAGLPILPGGGF 111

Query: 126 AYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             H   G LK         P   HRL + TSG++++AR+  A   L+E  R R+I KIY 
Sbjct: 112 VEHTLLGQLKQHYPED--TPFPIHRLGRGTSGLVLLARSSFARGFLSEQMRSRQISKIYR 169

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L+          I   + K  H    Y+     N K    A+S  +V+   ++    +E
Sbjct: 170 ALIPKSDLTDHFTINQPIGKIPHPVLGYIFGATPNGKD---ALSECRVLKRTSE-TTLVE 225

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY---------CANFKGNFTSPIQNKLYLHARYM 295
           ++  TGR HQ+R+H   +G P++GD  Y                   P     YLHA  +
Sbjct: 226 VKILTGRPHQIRIHLAAIGYPLIGDPLYTMGGIPKIQTPITPEKLPVPGDCGYYLHAYQL 285

Query: 296 DLPHPEGG-RLQITAPLPAHMV 316
               P     L +T P P  + 
Sbjct: 286 TFNLPHRESPLTVTCPPPRELE 307


>gi|104773696|ref|YP_618676.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103422777|emb|CAI97416.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|325125343|gb|ADY84673.1| Ribosomal large subunit pseudouridine synthase [Lactobacillus
           delbrueckii subsp. bulgaricus 2038]
          Length = 302

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 65/327 (19%), Positives = 129/327 (39%), Gaps = 42/327 (12%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQV 64
            V  ++V  ++    L  +        +   +      G +  V+  R   + R++ G V
Sbjct: 2   QVYKMIVAKNDPGQ-LSHFLLK--KGFSRRAVNNCKNHGGMMLVNHHRRNGSYRLKEGDV 58

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V          H +  Q+ ++  + +++        ++ E +   V NKPAG+       
Sbjct: 59  V----------HFLMGQEPVNPWLKVSRR----PLDIVEETADYLVINKPAGLLSIPSGF 104

Query: 125 IAYHID-GFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            A       + ++ + +G      KP +  RLDQ+TSG++++ +   A    ++  +   
Sbjct: 105 HAEDAVINRVLAYFEKQGVNPAYVKPHIVTRLDQDTSGLVLLGKNAIAHDRFSKLGKDAF 164

Query: 179 IQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           I+K + ++V G          I   L +          V ++       A++ ++V++  
Sbjct: 165 IKKYH-AIVHGNFAEGDLSGLIDKPLARVGD------TVKREVNPKGQRALTEYRVLNQV 217

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +E++  TGRTHQ+R+H   +G  + GD  Y A            +  L+  Y+ 
Sbjct: 218 P-GASLVELRLLTGRTHQIRIHMASIGHVLYGDDLYGAR-------DAFARQALNCFYLA 269

Query: 297 LPHP-EGGRLQITAPLPAHMVKTWDSL 322
            P+P  G   +I  P P  M   W  L
Sbjct: 270 FPNPFSGEEREIEIPDPGDMQGLWRQL 296


>gi|308187954|ref|YP_003932085.1| tRNA pseudouridine synthase C [Pantoea vagans C9-1]
 gi|308058464|gb|ADO10636.1| tRNA pseudouridine synthase C [Pantoea vagans C9-1]
          Length = 259

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 65/257 (25%), Positives = 109/257 (42%), Gaps = 18/257 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEWLVAVNKPSGWLVHRSWLDRHETVFVMQTVRDQIGQHVFTAHRLDKPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +    + L+  F   ++QK Y ++V G        +   L+++     D         
Sbjct: 64  GLSSEVGRLLSLQFEQHQMQKTYHAVVRG-WLESSGTLDYPLVEELDKIADRHAT---EA 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           + A  A++ ++ +               ++  +EM P TGR HQLR H  H+  PI+GD 
Sbjct: 120 RTAQPAVTDYQSLATVEMPVGIGRYPTSRYSLVEMAPKTGRKHQLRRHMSHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +      +G       N+L LHA  + L HP  G  L I A L        +  G++ D
Sbjct: 180 AHGDLRQNRGAAEHFGANRLMLHASSLALTHPVTGEPLLIRAGLDGVWQNLMNQFGWQ-D 238

Query: 328 RNLYIKRLYSQDECKQN 344
           R   + R+       Q+
Sbjct: 239 RIPEVPRVEFNAAPGQD 255


>gi|169825961|ref|YP_001696119.1| putative RNA pseudouridine synthase yhcT [Lysinibacillus sphaericus
           C3-41]
 gi|168990449|gb|ACA37989.1| Hypothetical RNA pseudouridine synthase yhcT [Lysinibacillus
           sphaericus C3-41]
          Length = 287

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 63/298 (21%), Positives = 129/298 (43%), Gaps = 32/298 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINA 73
           +E+N+ ++   +NH+  +    + ++  +  + + + + V++N  +Q G +V+    I A
Sbjct: 7   NEDNLTIEELLRNHWR-LGKKLVHELRMAKAITLENDELVQWNTPLQVGTIVKFTFPIPA 65

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDG 131
            ++               K +      ++YED    + +KP G++         H  ++ 
Sbjct: 66  SSY---------------KRTPVCAIDIVYEDDHCLIVSKPKGMATHPNDDRDTHTCMNH 110

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +    +  G      HRLD+ T G+L+VA+   A          + I + Y + V G  
Sbjct: 111 VMAHIQEQGGIYAEHVHRLDKGTQGLLLVAKHPLAKSIFDRMIEEKSIIRTYAAEVQGNI 170

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           ++    I+  + K  H     V       +   +A++H++V+  + +  C + +   TGR
Sbjct: 171 RSSSGTISESIGKDRHHASRRVV-----SQTGQHAVTHYEVVSRY-KNSCVVHLILETGR 224

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQIT 308
           THQ+RVH  ++G PI+GD  Y A    +    +      HA  ++  HP    R+ + 
Sbjct: 225 THQIRVHLAYIGHPIIGDTMYGARETASGDYEL------HAIQLEFDHPFLNKRITVK 276


>gi|296111875|ref|YP_003622257.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
 gi|295833407|gb|ADG41288.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
          Length = 300

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/282 (21%), Positives = 118/282 (41%), Gaps = 33/282 (11%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G +  + K+V  ++ +  G  V I     A N ++                D+    +++
Sbjct: 37  GAILKNDKQVYTSDYLDDGDQVTIIMPTEASNDLV--------------VPDYKPLDIIF 82

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHI-DGFLKSWVDSKGQK---PRLTHRLDQETSGILV 159
           E+    V +KP GI+   G     H     +K  ++    +   P +  RLD++TSGI++
Sbjct: 83  ENEHWLVVDKPYGITTVPGHADRLHTLVNQVKGHLEETHAEDLVPHVVTRLDRDTSGIVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ R A   + +  +   ++K Y +   GI  +    I   + +   + GD++    ++
Sbjct: 143 LAKHRFAHAVMDQQLQEHTVEKFYLAYTSGILPDDHGDIQAPIGR---VDGDFIKREVRD 199

Query: 220 EKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +     + + + V   + +        +++Q HTGRTHQ+RVH  ++G P+VGD  Y   
Sbjct: 200 D--GKPSRTEYWVERRYDENGQQPMTRVKVQLHTGRTHQIRVHFQNIGHPLVGDDLYGGP 257

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
                      +  LHA +M    P      +    LP  + 
Sbjct: 258 LW-----YGLKRQALHAYHMRFYDPFIESYREFNTKLPEDLK 294


>gi|257870826|ref|ZP_05650479.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257804990|gb|EEV33812.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 283

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 72/299 (24%), Positives = 121/299 (40%), Gaps = 45/299 (15%)

Query: 31  HINFVNLQKILRS---------------GQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
                 ++++L                   VRV+ +   F+  +  G  + +        
Sbjct: 10  DHPRTTIRELLEQEWLVPRKVRHLLRTRKNVRVNGETALFHQEVAGGDQLTL-------- 61

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLK 134
            +++E    D +       +  K  +L+ED  + V NKPAGI            +   L 
Sbjct: 62  -LLEE---ADYTYQPVISGNKEKITVLFEDEHLIVVNKPAGIKTHPNQPNETDTLMNDLA 117

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           +++  +  +P + HRLD+ETSG+++ A+       L      ++I + Y + VWG   ++
Sbjct: 118 AYLSPET-RPYVVHRLDKETSGVILFAKNPLVLPILGRMLESKQIYRRYQATVWGQL-DQ 175

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I   + +  H     V     + +    A++H ++    AQ          TGRTHQ
Sbjct: 176 NQTIRKKIGRDRHDRRKRV----IDPRNGLSAVTHVEIAARNAQTTSIY-CVLDTGRTHQ 230

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +RVH   +G PIVGD  Y              +L LHA  + L HP     LQI A LP
Sbjct: 231 IRVHLASIGHPIVGDPLYQKKTAA--------RLELHAYELYLTHPFSQESLQIKA-LP 280


>gi|209523615|ref|ZP_03272169.1| pseudouridine synthase, RluA family [Arthrospira maxima CS-328]
 gi|209496020|gb|EDZ96321.1| pseudouridine synthase, RluA family [Arthrospira maxima CS-328]
          Length = 309

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 80/315 (25%), Positives = 125/315 (39%), Gaps = 35/315 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+     + +  ++   Y H +       +   Q+ +D K       +Q+GQ +      
Sbjct: 12  VDRLSAGLTVLDYYSKRYTHSSRNEWCDRINKQQIWLDGKPATAEIELQAGQQLAYH--- 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                              ++    L   ++YED+ I V  KP+G+ V  G G   H   
Sbjct: 69  ---------------RPPWSEPDVPLSFQVIYEDADILVVAKPSGLPVIPGGGFLEH--T 111

Query: 132 FLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            L+       Q  P   HRL + TSG++++AR+     HLT+  R R+I K+Y +L  G 
Sbjct: 112 LLRQLQREYPQDTPIPIHRLGRGTSGLVLLARSTLGRSHLTQQMRHRQITKVYLALAEGC 171

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                  I   + K  H    Y++      +    A SH +VI     K   +++   TG
Sbjct: 172 SPRDYFSINCAIGKIPHPIIGYIY---GATETGLSAESHCQVIKRDTDKM-IVQVTILTG 227

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---------KLYLHARYMDLPHPE 301
           R HQ+R+H    G P+VGD  Y    K     P  N           YLHA  +   HP+
Sbjct: 228 RPHQIRIHLAAAGFPLVGDPLYTIGGKPRIPDPTSNHHSTFPGDCGYYLHAYSLSFQHPQ 287

Query: 302 GG-RLQITAPLPAHM 315
            G  L +TA  P  +
Sbjct: 288 TGANLHLTATPPQEL 302


>gi|116495207|ref|YP_806941.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
 gi|116105357|gb|ABJ70499.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
          Length = 276

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 107/283 (37%), Gaps = 32/283 (11%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I      ++  +  + V+     FN ++Q   V+ +                 D    L 
Sbjct: 23  IPRKRQHQLRVAKTILVNGHYRNFNEKVQPSDVITMTY---------------DEPTPLA 67

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
              +     + YED  + + +KPAG+       G    +     +++        +THRL
Sbjct: 68  YVPETPALTIHYEDDDLLIVDKPAGMKTHPNLPGETGTLMNQAAAYLAP--FPALITHRL 125

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+LV+A+       +     ++ + + Y +LV          I   +        
Sbjct: 126 DMATSGLLVIAKNPLTQAIINRQLALKTMHRDYIALVPQGIAA-SGTITAPIGHDPDDQR 184

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +            AI+HF+ I   +     + ++  TGRTHQ+RVH   +G PI+GD 
Sbjct: 185 KRMIR-----PDGASAITHFRRIAETSTTAT-VALRLETGRTHQIRVHLASIGYPILGDP 238

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y  +           ++YLHA  +    P     L +T+PLP
Sbjct: 239 LYAPD------QTTYQRMYLHAFQVRFTKPLSDTTLTVTSPLP 275


>gi|330502180|ref|YP_004379049.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           mendocina NK-01]
 gi|328916466|gb|AEB57297.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           mendocina NK-01]
          Length = 211

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 66/216 (30%), Positives = 107/216 (49%), Gaps = 11/216 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +L++D+ + V NKP  +    G       D  +    ++   + R+ HRLD ETSGI
Sbjct: 5   QIEILHQDTALLVINKPTLLLSVPGRADDN-KDCLVTRLQENGYPEARIVHRLDWETSGI 63

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+AR   + + L+  F  R  +K Y +L WG P+     I   L         +V    
Sbjct: 64  IVLARDADSHRELSRQFHDRETEKAYTALCWGQPQADSGSIDLPLRYDPPTKPRHV---- 119

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +   +A++H++VI+     +C +E+ P TGR+HQLRVH L +G P++GD  Y     
Sbjct: 120 VDHELGKHALTHWRVIERCGD-WCRVELTPITGRSHQLRVHMLSIGHPLLGDRLYAHEQ- 177

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                   ++L LHA  + L HP  G R++   P P
Sbjct: 178 ---ALAAFDRLCLHASMLALTHPQTGERMRFECPAP 210


>gi|317475813|ref|ZP_07935070.1| RNA pseudouridylate synthase [Bacteroides eggerthii 1_2_48FAA]
 gi|316907973|gb|EFV29670.1| RNA pseudouridylate synthase [Bacteroides eggerthii 1_2_48FAA]
          Length = 518

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 71/239 (29%), Positives = 110/239 (46%), Gaps = 19/239 (7%)

Query: 70  VINALNHIIKEQKILDSSV-NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
               L H++K  ++ ++ +      S   +   +YED  + V NKPAG+    G   A  
Sbjct: 285 CEPILKHMLKGLEVDENPMQKALLQSAAQELETVYEDEWLLVVNKPAGMLSVPGKEEAVS 344

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +   ++     +   P + HRLD  TSG+LV+A+T+   Q+L   FR R + K Y +L+ 
Sbjct: 345 VYSVMRRRY-PEADGPLIVHRLDMATSGLLVIAKTKQVHQNLQAQFRDRSVSKRYIALLQ 403

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           GI       +   L        D    +   E G   A++ F+V++        +   P 
Sbjct: 404 GIVSPDTGTVELPLCLNPL---DRPRQMVHTEHG-KSAVTDFEVLERK-DNHTRIAFYPR 458

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           TGRTHQLRVHA H   + CPI+GD  Y    +         +LYLHA  ++  HP  G+
Sbjct: 459 TGRTHQLRVHAAHPLGLHCPIIGDELYGKKAE---------RLYLHAEALEFTHPITGK 508


>gi|325106618|ref|YP_004267686.1| pseudouridine synthase [Planctomyces brasiliensis DSM 5305]
 gi|324966886|gb|ADY57664.1| pseudouridine synthase [Planctomyces brasiliensis DSM 5305]
          Length = 296

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 67/246 (27%), Positives = 111/246 (45%), Gaps = 12/246 (4%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
               L    +     ++ ED  +   NKPAG+  QG     + +  ++K+++  K +KP 
Sbjct: 46  EPTPLPSAEEAASLEVICEDGPVVAVNKPAGMLSQGSPQGVFCLPDYVKAYLKHKYEKPG 105

Query: 146 -----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                + HRLD+  +G++V +R    A  L E FR R +QK+Y +L+  +P   +  + +
Sbjct: 106 NVYLGVVHRLDRPVTGVVVFSRNSKGAARLAEQFREREVQKVYLALLENVPDQPEGTLKD 165

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           ++ K          +     + A  A   ++V+     K+  +E+ P TGR HQ+R+   
Sbjct: 166 FIRKVPEQAR--AVIEPGETQEAKAAELSYRVLASDG-KYALVEVLPKTGRMHQIRIQFA 222

Query: 261 HMGCPIVGDHKYCANFK---GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
             GCPIVGD  Y A         T     ++ LHA  + + HP     L I AP PA   
Sbjct: 223 SRGCPIVGDQLYGAKKTIDLKPLTDDYTQRIALHAWKLTIKHPVRYDDLTIQAPPPADWP 282

Query: 317 KTWDSL 322
           +    L
Sbjct: 283 EVAHRL 288


>gi|227534773|ref|ZP_03964822.1| pseudouridine synthase, 23S-rRNA-specific [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
 gi|227187529|gb|EEI67596.1| pseudouridine synthase, 23S-rRNA-specific [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
          Length = 277

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 107/283 (37%), Gaps = 32/283 (11%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I      ++  +  + V+     FN ++Q   V+ +                 D    L 
Sbjct: 24  IPRKRQHQLRVAKTILVNGHYRNFNEKVQPSDVITMTY---------------DEPTPLA 68

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
              +     + YED  + + +KPAG+       G    +     +++        +THRL
Sbjct: 69  YVPETPALTIHYEDDDLLIVDKPAGMKTHPNLPGETGTLMNQAAAYLAP--FPALITHRL 126

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+LV+A+       +     ++ + + Y +LV          I   +        
Sbjct: 127 DMATSGLLVIAKNPLTQAIINRQLALKTMHRDYIALVPQGIAA-SGTITAPIGHDPDDQR 185

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +            AI+HF+ I   +     + ++  TGRTHQ+RVH   +G PI+GD 
Sbjct: 186 KRMIR-----PDGASAITHFRRIAETSTTAT-VALRLETGRTHQIRVHLASIGYPILGDP 239

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y  +           ++YLHA  +    P     L +T+PLP
Sbjct: 240 LYAPD------QTTYQRMYLHAFQVRFTKPLSDTTLTVTSPLP 276


>gi|194466992|ref|ZP_03072979.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
 gi|194454028|gb|EDX42925.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
          Length = 290

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 66/281 (23%), Positives = 127/281 (45%), Gaps = 32/281 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
            G+  VD ++V+   +I   Q + I            + ++ D +V ++  S      ++
Sbjct: 36  EGEFLVDHRKVRPTTQILPNQPLTIR----------AQPELADDTVEISNES----LNVV 81

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---DSKGQKPRLTHRLDQETSGIL 158
           YED    V +KPAG++   G  +    +   +K ++   +S   +P L  RLD+ T G+L
Sbjct: 82  YEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIANNSADLRPHLITRLDRFTGGLL 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+   A+  +++  +  ++ K Y +LV G   ++   I         IG       + 
Sbjct: 142 LIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHGEI------NKPIGRKDGQAARV 195

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            ++    A++ + V +    K+  + ++ HTGRTHQ+RVH   +G P++GDH Y  +   
Sbjct: 196 IDENGQRALTEYWVEER-GAKWTRVRVRLHTGRTHQIRVHFAAIGHPLIGDHLYGGDTSK 254

Query: 279 NFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKT 318
                  +   LHA  +    P    ++  T+ LPA   + 
Sbjct: 255 ------YDHQLLHASKISFNDPFTLKQMTFTSELPAAFFEL 289


>gi|332160586|ref|YP_004297163.1| tRNA pseudouridine synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|318606936|emb|CBY28434.1| tRNA pseudouridine synthase C; tRNA Psi65 [Yersinia enterocolitica
           subsp. palearctica Y11]
 gi|325664816|gb|ADZ41460.1| tRNA pseudouridine synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859592|emb|CBX69932.1| tRNA pseudouridine synthase C [Yersinia enterocolitica W22703]
          Length = 257

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 103/237 (43%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +       +
Sbjct: 64  ALSSDVARALSLQFEQHQIQKTYHAVVRGYVLEDGTIDYEMTEELDKIADKFAR----PD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    +++H++ +               +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYQALAQVEVPIAIGRYDTSRFSLMELKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            +      +G       ++L LHA ++ L HP  G  L +TA       +     G+
Sbjct: 180 AHGDLRQNRGVAEHFDCSRLMLHASHLHLNHPVTGESLSLTARWDESWQQLMSHFGW 236


>gi|253827544|ref|ZP_04870429.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           canadensis MIT 98-5491]
 gi|313141752|ref|ZP_07803945.1| ribosomal large subunit pseudouridine synthase [Helicobacter
           canadensis MIT 98-5491]
 gi|253510950|gb|EES89609.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           canadensis MIT 98-5491]
 gi|313130783|gb|EFR48400.1| ribosomal large subunit pseudouridine synthase [Helicobacter
           canadensis MIT 98-5491]
          Length = 319

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 70/312 (22%), Positives = 129/312 (41%), Gaps = 39/312 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++   + KI++  Q+ ++   ++ N   +     + +          
Sbjct: 1   MRLDKFLTQKL-GLSRNQISKIIQEKQITLNGVFIQKNGTSLNFNDQIILT--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                 L +    +K  + L   +LYED  + + NKP  + V             L+ W+
Sbjct: 51  ------LPNKQEKSK-PNHLNIPILYEDEDLLILNKPINLIVHQTHQDDSQY--TLQDWL 101

Query: 138 DSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                         +  + HRLD+ TSG +V+A+   A + L++  + + + + Y   V 
Sbjct: 102 QENNFSLSNLGDSYRQGIIHRLDKTTSGAIVIAKNNYAHEILSQQLKSKEMGRYYVC-VI 160

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
             P  +   I   L++       Y+   K +   +  A + F  I     K   +  +  
Sbjct: 161 DSPLKQNILIDAPLIRHPKNRLKYIPTTK-DTPLSKEAKTAFFKI-INNDKIELIGAKLF 218

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           +GRTHQ+R H   +   I+GD  Y   +KGN+T+    ++ LH+  + L HP    RL+I
Sbjct: 219 SGRTHQIRAHLSKIQRHILGDVFYG--YKGNYTA----RILLHSHLVYLTHPTTKQRLEI 272

Query: 308 TAPLPAHMVKTW 319
            APL   M+   
Sbjct: 273 YAPLWEDMLLFL 284


>gi|330985554|gb|EGH83657.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. lachrymans str. M301315]
          Length = 211

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 66/214 (30%), Positives = 102/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIYQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSPDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEGGKHALTLWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL    P P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|308179960|ref|YP_003924088.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|308045451|gb|ADN97994.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 293

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 76/306 (24%), Positives = 124/306 (40%), Gaps = 41/306 (13%)

Query: 23  RWFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQSGQV--VRIPPVINALNHII 78
           R+   H   I+   + K ++  +G   V+ +       I  G +  +++P         +
Sbjct: 16  RFLTTH--AISMRTI-KAIKHGTGAFLVNNQVQTGVITIHDGDIAGIQLPDEAPDTAVAV 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWV 137
            EQ I                 + YED+   V NKPAG+ SV G S     +   +K ++
Sbjct: 73  SEQPI----------------QIEYEDANWLVLNKPAGLTSVPGPSNRTDTLVNRIKGYL 116

Query: 138 ---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               +  Q+P L  RLD++TSG+++VA+ R A   LTE     ++ K Y + + G     
Sbjct: 117 IASHASNQRPHLITRLDRDTSGLVLVAKHRVAQGMLTEPRIAAQLVKTYQAWIEGTITPA 176

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTH 253
              I   + + +      V            AI+ ++V  D        L ++  TGRTH
Sbjct: 177 SGTIDRPIGRVADSPRRVVTT------AGQRAITTYQVEADQLQHNVSRLRLELVTGRTH 230

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Q+RVH   +G P++GD  Y  N           +  LHA  +    P   + L   A LP
Sbjct: 231 QIRVHLTTLGHPLLGDALYGGNLAW------IQRQALHAASLQFFDPFSEQTLHFEAALP 284

Query: 313 AHMVKT 318
           A +   
Sbjct: 285 ADLQAL 290


>gi|301066771|ref|YP_003788794.1| 23S RNA-specific pseudouridylate synthase [Lactobacillus casei str.
           Zhang]
 gi|300439178|gb|ADK18944.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           str. Zhang]
          Length = 276

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 107/283 (37%), Gaps = 32/283 (11%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I      ++  +  + V+     FN ++Q   V+ +                 D    L 
Sbjct: 23  IPRKRQHQLRVAKTILVNGHYRNFNEKVQPSDVITMTY---------------DEPTPLA 67

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
              +     + YED  + + +KPAG+       G    +     +++        +THRL
Sbjct: 68  YVPETPALTIHYEDDDLLIVDKPAGMKTHPNLPGETGTLMNQAAAYLAP--FPALITHRL 125

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+LV+A+       +     ++ + + Y +LV          I   +        
Sbjct: 126 DMATSGLLVIAKNPLTQAIINRQLALKTMHRDYIALVPQGIAA-SGTITAPIGHDPDDQR 184

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +            AI+HF+ I   +     + ++  TGRTHQ+RVH   +G PI+GD 
Sbjct: 185 KRMIR-----PDGASAITHFRRIAETSTTAT-VALRLETGRTHQIRVHLASIGYPILGDP 238

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y  +           ++YLHA  +    P     L +T+PLP
Sbjct: 239 LYAPD------QTTYQRMYLHAFQVRFTKPLSDTTLTVTSPLP 275


>gi|198275973|ref|ZP_03208504.1| hypothetical protein BACPLE_02156 [Bacteroides plebeius DSM 17135]
 gi|198271602|gb|EDY95872.1| hypothetical protein BACPLE_02156 [Bacteroides plebeius DSM 17135]
          Length = 539

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 68/238 (28%), Positives = 104/238 (43%), Gaps = 19/238 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++    +  + +    H       +LYED  + V +KPAG+    G      I
Sbjct: 308 CEPILKHMLVGLDVEPNPLEEDVHRQTA-LEILYEDEWLLVVHKPAGMLSVPGKNDLDSI 366

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L +    K   P + HRLD  TSG+L+ A+T+   + L   F  R IQK Y +L+ G
Sbjct: 367 LQRLHNLY-PKATGPLIVHRLDMATSGLLLAAKTKEVHKELQALFETRLIQKRYTALLEG 425

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +  +  I   +     +      V +   +    A++ ++V++        +   PHT
Sbjct: 426 ELETDEGIIDLPICPN-PMDRPRQMVSR---EYGKRAVTSYRVLERKG-GSTRVTFYPHT 480

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GRTHQLRVHA H   +  PIVGD  Y             ++LYLHA  ++  HP  G 
Sbjct: 481 GRTHQLRVHAAHPEGLNHPIVGDDLYGQP---------SDRLYLHAASLEFVHPVTGE 529


>gi|191638717|ref|YP_001987883.1| Pseudouridine synthase, 23S-rRNA-specific [Lactobacillus casei
           BL23]
 gi|190713019|emb|CAQ67025.1| Pseudouridine synthase, 23S-rRNA-specific [Lactobacillus casei
           BL23]
 gi|327382758|gb|AEA54234.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus casei LC2W]
 gi|327385945|gb|AEA57419.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus casei BD-II]
          Length = 277

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 107/283 (37%), Gaps = 32/283 (11%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I      ++  +  + V+     FN ++Q   V+ +                 D    L 
Sbjct: 24  IPRKRQHQLRVAKTILVNGHYRNFNEKVQPSDVITMTY---------------DEPTPLA 68

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
              +     + YED  + + +KPAG+       G    +     +++        +THRL
Sbjct: 69  YVPETPALTIHYEDDDLLIVDKPAGMKTHPNLPGETGTLMNQAAAYLAP--FPALITHRL 126

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+LV+A+       +     ++ + + Y +LV          I   +        
Sbjct: 127 DMATSGLLVIAKNPLTQAIINRQLALKTMHRDYIALVPQGIAA-SGTITAPIGHDPDDQR 185

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +            AI+HF+ I   +     + ++  TGRTHQ+RVH   +G PI+GD 
Sbjct: 186 KRMIR-----PDGASAITHFRRIAETSTTAT-VALRLETGRTHQIRVHLASIGYPILGDP 239

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y  +           ++YLHA  +    P     L +T+PLP
Sbjct: 240 LYAPD------QTTYQRMYLHAFQVRFTKPLSDTTLTVTSPLP 276


>gi|168242726|ref|ZP_02667658.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|194451570|ref|YP_002046934.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194409874|gb|ACF70093.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|205338110|gb|EDZ24874.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
          Length = 260

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 105/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +       +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLMIQAGLDETWMQALTQFGWR 237


>gi|269798210|ref|YP_003312110.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269094839|gb|ACZ24830.1| pseudouridine synthase, RluA family [Veillonella parvula DSM 2008]
          Length = 324

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 75/356 (21%), Positives = 132/356 (37%), Gaps = 69/356 (19%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M   T +  ++V++D     ++   K    HI+    +++     + V+ K   +N  + 
Sbjct: 1   MKTATIID-LIVDSDVHTQSINHIIKQQ--HISQRMRRRLRSDSIITVNGKPATWNTLVH 57

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +         +  EQ+   S + L          ++YED  I V NK AGI + 
Sbjct: 58  GGDHLIM--------KLTPEQEFSLSPMELD---------IIYEDEYILVINKAAGILMH 100

Query: 121 GGSGIAYHI--DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             S I  H   +G L  + ++ +       HRLD++TSGI+++A+T        +     
Sbjct: 101 PTSTIRDHTLANGVLHYYQETNQHYDFHPVHRLDKDTSGIVIIAKTSVVQHAFDKKHTH- 159

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              K Y ++V G   +    I   + +K     +    V+        A +   +I    
Sbjct: 160 -FYKSYDAIVEGHLPSVPISINWPIGRKPGSIIERCCTVQ-----GKPARTDITIISKNT 213

Query: 238 QK--------------------------------FCWLEMQPHTGRTHQLRVHALHMGCP 265
            K                                F  ++   HTGRTHQ+RVH   +G P
Sbjct: 214 SKISSGKINSDDVITLNNNSNICSTDSSLTSYSQFTHVKCLLHTGRTHQIRVHLSQLGYP 273

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           + GD  Y  + +         +  LHA  +   HP     L++ A +P  M    +
Sbjct: 274 LAGDDLYGGHLES------IQRQALHAARVSFYHPITNEWLELHAEMPEDMKVLLN 323


>gi|310817246|ref|YP_003965210.1| ribosomal large subunit pseudouridine synthase A
           [Ketogulonicigenium vulgare Y25]
 gi|308755981|gb|ADO43910.1| ribosomal large subunit pseudouridine synthase A
           [Ketogulonicigenium vulgare Y25]
          Length = 215

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 69/220 (31%), Positives = 106/220 (48%), Gaps = 13/220 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                 ++L++D +I V +KP+G+    G G   H+   L + V        L HRLD++
Sbjct: 7   PPQDPLVILHQDHEIVVVDKPSGLLSVPGKG--EHLADCLIARVQRVFPTALLVHRLDRD 64

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V A T  A +HL   F  R+ +KIY + VWG     +  I   L+         +
Sbjct: 65  TSGVMVFALTPHAQRHLGLQFENRQTKKIYIARVWGEVAAPEGHIDLPLIVDWPNRPLQM 124

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                + +    A + +K +         + + P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 125 ----VDHENGRPAQTDWKRV-RTGGGESRMRLMPKTGRSHQLRVHMLEIGHPILGDPFYA 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                +F      +L LH+  + L HP+GGR L+ TA  P
Sbjct: 180 TGPARDFP-----RLMLHSETLQLRHPDGGRTLRFTAKAP 214


>gi|294783884|ref|ZP_06749206.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           1_1_41FAA]
 gi|294479696|gb|EFG27475.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           1_1_41FAA]
          Length = 288

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 134/320 (41%), Gaps = 38/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +VE++ +   +  + K    + +       LR+ ++ ++ KR           +  
Sbjct: 1   MKKYIVEHEFDGYEIGTYLKETKGYSSRG-----LRNLEIYLNGKR-----------IKN 44

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
               I  LN I+    I++   +    +  +   + YED  + + NK   I V      +
Sbjct: 45  NAKKIKKLNRIV----IIEKEKSTGIKAMDIPIDIAYEDENLLIVNKEPYIIVHPTQKKV 100

Query: 126 AYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +   + ++ +    K   PR  +RLD  TSG++++A+       L +      ++K 
Sbjct: 101 DKTLANAVVNYFEKTLGKTLVPRFYNRLDMNTSGLIIIAKNAYTQAFLQDKT---EVKKT 157

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFC 241
           Y  +V GI +     I   + K   +G D   +    E G   A +H KV++    +   
Sbjct: 158 YKVIVSGIIEEDDFFIELPIGK---VGDDLRRIELSEENGGKSAKTHIKVLERNREKNIT 214

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +LE + +TGRTHQ+R H   +G P+VGD  Y  +        +  +  LHA  ++  +P+
Sbjct: 215 FLEARLYTGRTHQIRAHLSLIGHPLVGDELYGGDMN------LAKRQMLHAYKLEFQNPK 268

Query: 302 G-GRLQITAPLPAHMVKTWD 320
               L++   +P  M +   
Sbjct: 269 TLENLKVEIEIPVDMKELLK 288


>gi|291276623|ref|YP_003516395.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
 gi|290963817|emb|CBG39653.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
          Length = 322

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 63/330 (19%), Positives = 132/330 (40%), Gaps = 40/330 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSG 62
           M   + +         R+D +  +   H+    + +++++  V ++        + ++ G
Sbjct: 1   MQEQEIITTTPH---KRIDTFLCSFL-HLPKNQILQLIKNSLVLLNGSPCAKGGKELKIG 56

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I              KIL+S  +L   +       +YED  + + NKP+ + +   
Sbjct: 57  DRINI-------LAPTSRPKILESKTSLEIDT-------IYEDDHLLILNKPSDLVIHPA 102

Query: 123 SGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
                     L  W+ +KG         ++  + HRLD++T+G + +A+   A   L   
Sbjct: 103 PS---QKAETLLDWLKAKGYTLSTISGEERCGIVHRLDKDTTGAIAIAKNNLAHNSLANQ 159

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            + R + + Y +++   P  +   I   + +          +       A  + S F  +
Sbjct: 160 LQTRTMGRYYLAII-DQPIKEALSIHCHMGRNPKNRLKMCKLDPLVFPQARESKSLFLPL 218

Query: 234 D-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                  +  + ++  TGRTHQ+RVH   +   I+GD  Y   ++GNF+     ++ LHA
Sbjct: 219 FLSHNHSYQLVAIKLFTGRTHQIRVHLESISRHILGDGLYG--YRGNFS----KRIMLHA 272

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
             + L HP   + +   AP+   M++  + 
Sbjct: 273 FLLYLIHPSTQKNMLFRAPVFQDMLEFLEK 302


>gi|300812735|ref|ZP_07093142.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
 gi|300496275|gb|EFK31390.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
          Length = 297

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 66/323 (20%), Positives = 129/323 (39%), Gaps = 42/323 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQVVRIP 68
           ++V  ++    L  +        +   +      G +  V+  R   + R++ G VV   
Sbjct: 1   MIVAKNDPGQ-LSHFLLK--KGFSRRAVNNCKNHGGMMSVNHHRRNGSYRLKEGDVV--- 54

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                  H +  Q+ ++  + +++        ++ E +   V NKPAG+        A  
Sbjct: 55  -------HFLMGQEPVNPWLKVSRR----PLDIVEETADYLVINKPAGLLSIPSGFHAED 103

Query: 129 ID-GFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                + ++ + +G      KP +  RLDQ+TSG++++ +   A    ++  +   I+K 
Sbjct: 104 AVINRVLAYFEKQGVNPAYVKPHIVTRLDQDTSGLVLLGKNAIAHDRFSKLGKDDFIKKY 163

Query: 183 YWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + ++V G          I   L +          V ++       A++ ++V+D      
Sbjct: 164 H-AIVHGNFAEGDLSGLIDKPLARVGD------TVKREVNPKGQRALTEYRVLDQVP-GA 215

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E++  TGRTHQ+R+H   +G  + GD  Y A            +  L+  Y+  P+P
Sbjct: 216 SLIELRLLTGRTHQIRIHMASIGHVLYGDDLYGAR-------DAFARQALNCFYLAFPNP 268

Query: 301 EGG-RLQITAPLPAHMVKTWDSL 322
            GG   +I  P P  M   W  L
Sbjct: 269 FGGEEREIEIPDPGDMQGLWRQL 291


>gi|298208702|ref|YP_003716881.1| ribosomal large subunit pseudouridine synthase D [Croceibacter
           atlanticus HTCC2559]
 gi|83848627|gb|EAP86496.1| ribosomal large subunit pseudouridine synthase D [Croceibacter
           atlanticus HTCC2559]
          Length = 232

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 68/235 (28%), Positives = 109/235 (46%), Gaps = 16/235 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTH 148
           SD     ++YED+ + V NK AG  VQG       +   +KS++  K  KP      + H
Sbjct: 5   SDKNNLQVIYEDNHLIVVNKRAGDIVQGDKTGDKPLSDVVKSYIKEKYNKPGDVYLGVVH 64

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ T+G+++ ++T  A   L + F      K YW++V   P  +K+ + ++L +    
Sbjct: 65  RLDRPTTGVVLFSKTSKALSRLNKMFANHETSKTYWAVVKNNPPKEKDRLVHYLKRNPKQ 124

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              Y H  K     +  AI  + ++      +  LE+   TGR HQ+R     + CPI G
Sbjct: 125 NKSYAH--KHEVPDSKKAILDY-ILKFRLNNYNLLEVNLLTGRHHQIRSQLSSIECPIKG 181

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           D KY A+      S     ++LHAR++ + HP     +   APLP      W + 
Sbjct: 182 DLKYGADRSNPDGS-----IHLHARFLTIQHPVKKEPITFKAPLPED--AIWKAC 229


>gi|329961970|ref|ZP_08299981.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
 gi|328530618|gb|EGF57476.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
          Length = 541

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 63/238 (26%), Positives = 110/238 (46%), Gaps = 18/238 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ +  +      +  +++ED  + V NKPAG+    G   A  +
Sbjct: 309 CEPILRHMLQGLEVEENPMLRSMRFIPKELEIIFEDRWLAVINKPAGMLSVPGKEEAISV 368

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++       + P + HRLD  TSG+L++A+T+   ++L   F+ R ++K Y +L+ G
Sbjct: 369 YSLMRQRY-PDAEGPMIVHRLDMATSGLLIIAKTKQVHRNLQAQFKERTVRKRYIALLDG 427

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I       I   L          +     N +    AI+ F+V++        + + PHT
Sbjct: 428 IVPQNTGTIELPLCPNLLDRPRQM----VNTEHGKVAITDFEVLERKG-NITRISLYPHT 482

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GRTHQLR+H  H   + CPI+GD  Y             ++L LHA  ++  HP  G 
Sbjct: 483 GRTHQLRIHTAHPLGLHCPIIGDELYGKK---------ADRLCLHAETIEFIHPISGE 531


>gi|315633348|ref|ZP_07888639.1| pseudouridine synthase A [Aggregatibacter segnis ATCC 33393]
 gi|315477848|gb|EFU68589.1| pseudouridine synthase A [Aggregatibacter segnis ATCC 33393]
          Length = 219

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 69/220 (31%), Positives = 104/220 (47%), Gaps = 11/220 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   L+Y D  I V NKP+G+    G+   Y+      S V  K       HRLD 
Sbjct: 8   PPQEPWLDLVYRDDYIAVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPAHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGIL+ A ++AA + L   FR R  +K Y +LVWG  +     +   L+       + 
Sbjct: 66  ATSGILLFALSKAADRELKRQFREREPKKYYQALVWGHVEQDHGVVELPLICD----WEN 121

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               K   +    A++ + V+  +      +++ P TGR+HQLR+H L +G PI+GD  Y
Sbjct: 122 RPRQKICFERGKRAVTFYDVLQRYPNNTTRIKLTPITGRSHQLRLHMLALGHPILGDKFY 181

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
            A+ +    SP   +L LHA  + + HP  G  +  TAP+
Sbjct: 182 -AHPQAKALSP---RLCLHAESLQIQHPITGETMGFTAPV 217


>gi|52425127|ref|YP_088264.1| tRNA pseudouridine synthase C [Mannheimia succiniciproducens
           MBEL55E]
 gi|52307179|gb|AAU37679.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 236

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG+ V       +     +++  D  G+     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEHIVAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGRLVYPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  L + F  ++++K Y ++V G     +       ++   I   +     Q +
Sbjct: 64  ALSSETANLLCQQFETKQVEKSYLAVVRGYLTGSERIDYPLKIQLDKIADKFA----QED 119

Query: 221 KGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +    +          ++  + + PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTDYEGLKTVEKPYATPRYATSRYALVRLVPHTGRKHQLRRHMKHIFHPILGDT 179

Query: 271 KYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF 324
           +Y    +    +     ++L LHA  +   HP    R +ITA L     K      +
Sbjct: 180 QYGDLHQNRTLTEHTEVSRLMLHAEKLSFIHPIKRQRTEITAGLDEQWKKLMALFEW 236


>gi|300215069|gb|ADJ79485.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 296

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 72/315 (22%), Positives = 125/315 (39%), Gaps = 34/315 (10%)

Query: 14  NDEENMRLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             ++ M L ++ KN    H    +L+K   +G+V VD K+      +  G++  I P   
Sbjct: 8   ESDKKMTLKKFLKNKGVSHRTLSSLKK--GNGKVLVDGKKKSLFIEVGKGKITLILPPEK 65

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDG 131
           +  ++   ++ LD               ++YEDS   V +KP  +S   G S     +  
Sbjct: 66  SDENVKMSKEPLD---------------IIYEDSNWLVVDKPPLLSSVPGPSNRTDTLVN 110

Query: 132 FLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +K  +  +  K   P +  RLD++TSG+++VA+ R A   + +      I K Y +++ 
Sbjct: 111 RVKFHLWQQKSKDLVPHVITRLDRDTSGLVLVAKHRFAQGLINKQVEEHSIDKRYLAVIE 170

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           GI   K   I   L  + +  G  V            A + + V +    K   +E + H
Sbjct: 171 GIITEKHGIIDKPLGPRENGIGQMV------TDTGKIAKTEYWVREYLGDKATLVECKLH 224

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-I 307
           TGRTHQ+R H   +   +VGD  Y              +  LHA  +          +  
Sbjct: 225 TGRTHQIRAHFSSINHALVGDELYGGRLDWGLE-----RQALHAYQLAYVDLFTQEEKLF 279

Query: 308 TAPLPAHMVKTWDSL 322
            + +P  +      L
Sbjct: 280 KSEMPKDLENLIVRL 294


>gi|157372031|ref|YP_001480020.1| tRNA pseudouridine synthase C [Serratia proteamaculans 568]
 gi|157323795|gb|ABV42892.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 256

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 62/257 (24%), Positives = 111/257 (43%), Gaps = 18/257 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHLVAVNKPSGWLVHRSWLDRHETRFVMQTVRDQIGQHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++QK Y ++V G              +   I   +       +
Sbjct: 64  ALSSEVARLLSQQFEQHQMQKTYHAVVRGYVLEGATIDYPLTEELDKIADKFAS----KD 119

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +             + ++  +E++P  GR HQLR H +H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRPLARVEMPVAIGRYESARYSLVELKPENGRKHQLRRHMVHIRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           K+      +G        +L LHA ++ L HP  G  L ++A             G+  +
Sbjct: 180 KHGDLNQNRGMAQHFGCPRLMLHASHLQLNHPVTGEPLHLSARWDEPWQGVMSQFGWTEN 239

Query: 328 RNLYIKRLYSQDECKQN 344
               + R+       Q+
Sbjct: 240 LP-ELARVEFPPASGQD 255


>gi|261839435|gb|ACX99200.1| hypothetical protein HPKB_0602 [Helicobacter pylori 52]
          Length = 327

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 68/343 (19%), Positives = 140/343 (40%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +         + +E                L+  +++ED  + V NKP  + +     +
Sbjct: 59  TLLTPKITPKPLKRELD--------------LEIGVIFEDEDLLVLNKPPNLVIHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      HL+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNHLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L    PL   M++    +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLCFKVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|229513013|ref|ZP_04402479.1| tRNA pseudouridine synthase C [Vibrio cholerae TMA 21]
 gi|229349906|gb|EEO14860.1| tRNA pseudouridine synthase C [Vibrio cholerae TMA 21]
          Length = 245

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 98/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAVTAYRPLAKAELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 239


>gi|114048209|ref|YP_738759.1| tRNA pseudouridine synthase C [Shewanella sp. MR-7]
 gi|113889651|gb|ABI43702.1| tRNA pseudouridine synthase C [Shewanella sp. MR-7]
          Length = 284

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/259 (23%), Positives = 105/259 (40%), Gaps = 17/259 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            +   + S +  +     +  +LY+D  +   +KPAG+ V             ++   D 
Sbjct: 11  PEDKYNPSESDEQSEPAPELRVLYQDEHLVAIHKPAGLLVHRSYLARRERFFAMQLTRDL 70

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G      HRLD+ TSG+L+ A++   A  L E F    I+K Y +LV G          
Sbjct: 71  VGCHVFPVHRLDRPTSGVLLFAKSSEVANALCEQFANHSIEKQYLALVRGNMHESGILDY 130

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
              ++   +   + +     +K A  A++ ++ +               +F  +++ P T
Sbjct: 131 ALKVELDEVADKFANQ----DKAAQDAVTQYEPLLNTEIPYPSGRYATSRFALVKLSPKT 186

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQ 306
           GR HQLR H  H+  PI+GD  +    +  F       N+L+L A+ +   HP    RL 
Sbjct: 187 GRKHQLRRHMAHLRHPIIGDTTHGDGKQNAFFRAHFDINRLWLIAKKLTFTHPVTLERLS 246

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I   L       +  LG+ 
Sbjct: 247 IETELEPEWETVFAGLGWD 265


>gi|218439930|ref|YP_002378259.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
 gi|218172658|gb|ACK71391.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
          Length = 548

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 70/235 (29%), Positives = 105/235 (44%), Gaps = 19/235 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW--VDSKG 141
           L       +H+      ++YED  + + NKP G+    G   +   D  +     +   G
Sbjct: 326 LPEKKTTFRHTIKEPLPIVYEDDYLIIINKPEGLLSVPGRS-SDRYDSVISRLNHLLPDG 384

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
              R  HRLD +TSG+L++AR      HL + FR R+I+KIY +LV G     +  I   
Sbjct: 385 HLLRSVHRLDLDTSGLLLLARNDQIYNHLAQQFRDRKIEKIYQALVQGRVSQPQGTIKLP 444

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL- 260
           L         +  +   +      +I+ F+VI  F   F  +E  P TGRTHQ+RVH   
Sbjct: 445 LWGDPR----FRPLQTVDFIRGKESITQFRVI-AFEDNFTRVEFMPITGRTHQIRVHCAD 499

Query: 261 --HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              +G PI+GD  Y              +L+LHA+ +   HP   + L + AP P
Sbjct: 500 QLGLGTPIIGDRLYGKGDD-------LTRLHLHAQKLRFLHPITKQFLSVNAPPP 547


>gi|317182056|dbj|BAJ59840.1| hypothetical protein HPF57_0766 [Helicobacter pylori F57]
          Length = 327

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 71/343 (20%), Positives = 143/343 (41%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +              KI+   +   K    L+  +++ED  + V NKP  + +     +
Sbjct: 59  TLLT-----------PKIVPKPL---KRGLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      HL+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  H+   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRAHLEHLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L+   PL   M++    +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLRFKVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|224825896|ref|ZP_03699000.1| pseudouridine synthase [Lutiella nitroferrum 2002]
 gi|224602120|gb|EEG08299.1| pseudouridine synthase [Lutiella nitroferrum 2002]
          Length = 253

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 107/240 (44%), Gaps = 17/240 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY D ++   +KP+G+ V       +     ++   D  GQ+    HRLD+ TSG+L
Sbjct: 2   LPILYRDERLIAIHKPSGLLVHRTVLDRHETRFAIQLLRDQIGQRVYPVHRLDKGTSGVL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A  R   + ++  F  +++ K Y ++V G P +++  I + L ++     D   V ++
Sbjct: 62  LFALDRDMGREMSWQFERQQVDKRYLAVVRGWP-DEQGEIEHALTRRP---DDLEWVGEK 117

Query: 219 NEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +     A++ F+ +               ++  +E+ P TGR HQLR H  H+  PI+G
Sbjct: 118 VDTAPQAALTRFRRLATVELPYAVDKYPHSRYALVELTPETGRRHQLRRHLKHIAHPIIG 177

Query: 269 DHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           D  Y           +    +L L    M   HP  G  + +TAPL         +LG++
Sbjct: 178 DATYGKGRHNRLFGELFGSQRLLLACMEMRFAHPVSGETVTLTAPLADDFAGVVRALGWE 237


>gi|188527412|ref|YP_001910099.1| hypothetical protein HPSH_03105 [Helicobacter pylori Shi470]
 gi|188143652|gb|ACD48069.1| hypothetical protein HPSH_03105 [Helicobacter pylori Shi470]
          Length = 327

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 67/343 (19%), Positives = 140/343 (40%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q + +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKIFIALTDH-KRLDEFLAKEL-QISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                   +    K    L+  +++ED  + V NKP  + +     +
Sbjct: 59  TL--------------LTPKITPKPLKRGLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      HL+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L+   PL   M++    +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLRFKVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|90421737|ref|YP_530107.1| pseudouridine synthase [Rhodopseudomonas palustris BisB18]
 gi|90103751|gb|ABD85788.1| pseudouridine synthase [Rhodopseudomonas palustris BisB18]
          Length = 240

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 72/243 (29%), Positives = 115/243 (47%), Gaps = 11/243 (4%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
            + +      ++ + + +LY D  + V +KPAG+ V  G     +++   +       + 
Sbjct: 6   PEPTAMPELTAEEILARVLYRDGLMLVIDKPAGLPVHRGPKGGANLESSFEFLRYGLPRP 65

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P L HRLD++TSG LV+ R R A   L   F+  RI K YW++V G P   +  I   + 
Sbjct: 66  PVLAHRLDRDTSGCLVLGRHRKATASLGLLFKHGRISKTYWAVVEGGPIEDEGTIELPIG 125

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           + +   G +  +    +     A + ++V+        WL +QP TGRTHQLRVH+  MG
Sbjct: 126 RLNAERGWWQKI----DPEGQPATTKWRVLGR-GDGLTWLALQPVTGRTHQLRVHSAAMG 180

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            PIVGD+ Y      N     +  L+LHA  + +P       + +TAP P H+       
Sbjct: 181 WPIVGDNIYG-----NGPRFGEPTLHLHASEIVIPISRNKPPIVVTAPAPVHLHARLRGC 235

Query: 323 GFK 325
           G+ 
Sbjct: 236 GWN 238


>gi|120598338|ref|YP_962912.1| pseudouridylate synthase [Shewanella sp. W3-18-1]
 gi|120558431|gb|ABM24358.1| Pseudouridylate synthase [Shewanella sp. W3-18-1]
          Length = 223

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 68/222 (30%), Positives = 108/222 (48%), Gaps = 9/222 (4%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        + Y+D  + + NKP+G+      GIA H      + +     +  L HRLD
Sbjct: 7   QPPAIPWLDIRYKDRDLIIINKPSGLLSNP--GIAAHTYDCALTRLQRLYPETILVHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V AR + A  HL   F+ R+ +K+Y + V G+  N++  I   +         
Sbjct: 65  CATSGIMVFARNKKAESHLKTQFQDRQSKKVYIAEVMGLITNEQGIINLSIAPNCEHP-P 123

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y   ++  E G   A++HF+V++   +    +E+ P TGRTHQLRVH L +G PI+GD  
Sbjct: 124 YQKALQAGEAGGKSALTHFRVLERR-KNSTLVELTPETGRTHQLRVHMLALGHPILGDEF 182

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y      N     + +L LHA+ +   HP  G+ +   +  P
Sbjct: 183 YGDPAVINA----KPRLCLHAQSLRFSHPYSGKPMSFHSKHP 220


>gi|191638831|ref|YP_001987997.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|190713133|emb|CAQ67139.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|327382880|gb|AEA54356.1| hypothetical protein LC2W_2024 [Lactobacillus casei LC2W]
 gi|327386064|gb|AEA57538.1| hypothetical protein LCBD_2042 [Lactobacillus casei BD-II]
          Length = 287

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 127/303 (41%), Gaps = 42/303 (13%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           RW       ++    +K+L    + VD +    N  +++GQ++R                
Sbjct: 17  RWLAEQ--GVSHRLFKKMLVDHLIWVDGQ-ASDNGPVEAGQIIRF--------------- 58

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWV---D 138
             +   + T   +F    ++YED+   + +KPAG++   G           +  ++    
Sbjct: 59  --EIPTSKTLTPEFAPLEVIYEDANWLIVSKPAGLTSVPGPHTPNSSLLNRIAGYLVEQK 116

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +P +  RLD++T G+++ A+   A     +    R + K Y ++V G   + K  I
Sbjct: 117 IDAPQPAIMTRLDRDTVGLVLAAKHPYAQGRF-DQAHQRTLTKHYLAVVSGKLPSPKGEI 175

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L     +  D +H +   +     A++ ++V+         +++Q  TGRTHQ+RVH
Sbjct: 176 DAPL----KLAADGIHRIVAAD--GQTAVTKYRVLKEKTN--TLVDVQLLTGRTHQIRVH 227

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL--PAHMV 316
              +G P++GDH Y    + +   P      L A  ++   P  G+ QITA L  PA   
Sbjct: 228 FASLGHPLIGDHLYG---QPDARIPY---QALQATRLNFTDPFSGK-QITAELAVPALFN 280

Query: 317 KTW 319
           +  
Sbjct: 281 QLL 283


>gi|332686243|ref|YP_004456017.1| ribosomal large subunit pseudouridine synthase D [Melissococcus
           plutonius ATCC 35311]
 gi|332370252|dbj|BAK21208.1| similar to ribosomal large subunit pseudouridine synthase D
           [Melissococcus plutonius ATCC 35311]
          Length = 298

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 70/303 (23%), Positives = 128/303 (42%), Gaps = 40/303 (13%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + +     I+   L KI  + G+++V+ +       +     +++               
Sbjct: 18  FLREL--GISKRLLAKIKFQGGKIKVNHQIQNVLFYLTKNDQLQV--------------V 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
           I + + + T   D     +++ED    V NKP  I         YH +G + + V +   
Sbjct: 62  IPNEAEHETMLLDTTPIDIIFEDEHYLVVNKPVNIPSIPAQ---YHPNGTMANRVKAYYK 118

Query: 142 ------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 Q   +  RLD++T+G+++ A+   A   L +  R +R+ KIY +LV G   N  
Sbjct: 119 EKNYANQVVHIVTRLDRDTTGLMLFAKHGFAHALLDQELRNKRVVKIYQALVGGNIAN-- 176

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             + +       IG D+  ++K+        AI+ + + + +   F  + +Q HTGRTHQ
Sbjct: 177 --LDSHGRIDLPIGRDHSSLMKRQVISTGQQAITEYWIEEKYTD-FAAVRIQLHTGRTHQ 233

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPA 313
           +RVH   +GCP++GD  Y    +         +  LH   +   HP     +++  PLP 
Sbjct: 234 IRVHFSAIGCPLMGDELYGREKQR------IKRQALHCSCLYFKHPFTKQEIELKLPLPL 287

Query: 314 HMV 316
            M 
Sbjct: 288 DMK 290


>gi|297379941|gb|ADI34828.1| pseudouridine synthase, RluA family [Helicobacter pylori v225d]
          Length = 327

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 68/343 (19%), Positives = 141/343 (41%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                   +    K    L+  +++ED  + V NKP  + +     +
Sbjct: 59  TL--------------LTPKITPKPLKRGLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      HL+E  + 
Sbjct: 105 ---KEPTLVDWLELKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L+   PL   M++ +  +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLRFKVPLLKDMLEYFKKV---FDKENLDEVLDEE 318


>gi|261405374|ref|YP_003241615.1| RluA family pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261281837|gb|ACX63808.1| pseudouridine synthase, RluA family [Paenibacillus sp. Y412MC10]
          Length = 302

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 111/234 (47%), Gaps = 17/234 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-DGFLKSWVDSKGQK--PRLTHR 149
              + +  +LYED    V NKPAG++V   +       +  + ++ +++G     R  HR
Sbjct: 76  EPRWQELQVLYEDDFCLVVNKPAGLAVHPDNESRETTLNHVVAAYYEAEGIHAAVRHIHR 135

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++T+G ++ A+   A   L E+ R ++I ++Y ++V G    + + I   + K     
Sbjct: 136 LDKDTTGPVLYAKNEYAQLKLDEAMREKKIVRMYAAIVQGRVSQELKRIDLPIGKDR--- 192

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             Y    ++       AI+H    + +  K   L ++  TGRTHQ+RVH  HMG P++GD
Sbjct: 193 --YHASRRRVSLTGQAAITHILSAEAYP-KASLLHIRLETGRTHQIRVHLSHMGHPLLGD 249

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y     G F      +  LH   +   HP  G  +++ AP P  M++  + +
Sbjct: 250 VLYGG--PGTFA-----RQALHGERLLFHHPFTGESIEVPAPWPQDMMELRERI 296


>gi|329667795|gb|AEB93743.1| hypothetical protein LJP_1421 [Lactobacillus johnsonii DPC 6026]
          Length = 282

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 72/302 (23%), Positives = 123/302 (40%), Gaps = 34/302 (11%)

Query: 4   MTYVQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQS 61
           MT  QY +   +    + +D+  +     I     +  LR   ++ ++ K +  N  ++ 
Sbjct: 1   MTIYQYSITYPDHLTPISVDKLMRKLL--IPR-KWRHFLRSEKKILINGKYLPLNFLVKH 57

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + I      L+HI  +Q+   +S  L K        ++YED+ I V NKPAG     
Sbjct: 58  GDKIEIQ-----LDHIESDQQPYPASGKLPK--------VVYEDNDILVINKPAGQKTHP 104

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                   D  L       G  P + HRLD  TSG+L+VA+  A    L      + + +
Sbjct: 105 N---LNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLLVAKNPAVVPILNRQLTDKTLHR 161

Query: 182 IYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y + +   P+      I   +    H     +       +    A++H++VI     + 
Sbjct: 162 EYLAWISNSPQIKNTGIIDLPIGHDPHDQRKRMVR-----QDGQKAVTHYEVIKRDKDRI 216

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +++   TGRTHQ+RVH   +G PI+GD  Y + ++         +L L A  +    P
Sbjct: 217 -LVKLTLETGRTHQIRVHLAALGAPIIGDPLYNSAYQDG------EQLQLTAFQLTFRKP 269

Query: 301 EG 302
             
Sbjct: 270 FS 271


>gi|161506492|ref|YP_001573604.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160867839|gb|ABX24462.1| hypothetical protein SARI_04699 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 260

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 105/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDAWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        L ++  I   +       +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDALLDYPLLEERDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLIIQAGLDETWMQALTQFGWR 237


>gi|117921265|ref|YP_870457.1| tRNA pseudouridine synthase C [Shewanella sp. ANA-3]
 gi|117613597|gb|ABK49051.1| tRNA pseudouridine synthase C [Shewanella sp. ANA-3]
          Length = 284

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 61/259 (23%), Positives = 106/259 (40%), Gaps = 17/259 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            +   + + +  +     +  +LY+D  +   +KPAG+ V             ++   D 
Sbjct: 11  PEDKFNPTESDEQSEPAPELRVLYQDEHLVAIHKPAGLLVHRSYLARRERFFAMQLTRDL 70

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G      HRLD+ TSG+L+ A++   A  L E F    I+K Y +LV G          
Sbjct: 71  VGCHVFPVHRLDRPTSGVLLFAKSSEVANALCEQFANHSIEKQYLALVRGNMHESGVLDY 130

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
              ++   +   + +     +K A  A++ ++ +               +F  +++ P T
Sbjct: 131 ALKVELDEVADKFANQ----DKAAQDAVTQYEPLLNTEIPYPSGRYATSRFALVKLSPKT 186

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQ 306
           GR HQLR H  H+  PI+GD  +    +  F  T    N+L+L A+ +   HP    RL 
Sbjct: 187 GRKHQLRRHMAHLRHPIIGDTTHGDGKQNAFFRTHFDINRLWLIAKKLTFTHPVTQARLS 246

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I   L       +  LG+ 
Sbjct: 247 IETELEPEWETVFSGLGWD 265


>gi|327183169|gb|AEA31616.1| Pseudouridine synthase [Lactobacillus amylovorus GRL 1118]
          Length = 301

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 67/326 (20%), Positives = 122/326 (37%), Gaps = 37/326 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSG 62
           MT +  ++V+  +   +L  +        +   L+     +G + V+ KR   +  +++ 
Sbjct: 1   MTSLFKLIVQERD-PKKLGSFLLK--KGFSHQALKHARYNNGLILVNHKRRYTSFHLKTN 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V         N  +K                      + E     + NKPAG+     
Sbjct: 58  DEVIFVTGEEKKNDFLK--------------PSNNPVEPVLETKNYIILNKPAGVLSIPS 103

Query: 123 SGIAYH-IDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                  I   L  +   KG    KP +  RLD++TSG+++V +   A    ++  + R 
Sbjct: 104 RYEDNDAIVNRLMGYFTRKGAKDLKPHVITRLDRDTSGLVLVGKNAVAHARFSKIGKERF 163

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I+K + ++V G  ++ +       L    IG     V +        A + +KV+     
Sbjct: 164 IKKYH-AIVHGNFESTELT----GLIDEPIGKIDSGVKRGVIPDGKSAQTEYKVLKQVP- 217

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E++  TGRTHQ+RVH  ++G P+ GD  Y             ++  L+  Y+  P
Sbjct: 218 GASLVELRLLTGRTHQIRVHMAYLGHPLYGDQLYGVKDS-------FSRQALNCFYLSFP 270

Query: 299 HPEGGR--LQITAPLPAHMVKTWDSL 322
            P        +    P+ M   W  L
Sbjct: 271 DPVNSEKDKTVEISDPSDMQNLWQKL 296


>gi|70731732|ref|YP_261474.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens Pf-5]
 gi|68346031|gb|AAY93637.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens Pf-5]
          Length = 211

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 65/213 (30%), Positives = 103/213 (48%), Gaps = 11/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D+ + V NKP  +    G       D  +    ++   + R+ HRLD ETSGI+++
Sbjct: 8   ILHQDAAVLVVNKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIILL 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR     + L+  F  R  +K Y +L WG P+     I   L           HVV  + 
Sbjct: 67  ARDADTHRELSRQFHDRETEKAYTALCWGQPELDSGSIDLPLRYDPPT--KPRHVV--DH 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +   +A++ ++V++     +C +E+ P TGR+HQLRVH L +G P++GD  Y        
Sbjct: 123 EFGKHALTFWRVLERCGD-WCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPQALAA 181

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                 +L LHA  +   HP  G RL+   P P
Sbjct: 182 W----PRLCLHASMLSFTHPQTGERLRFECPAP 210


>gi|15799742|ref|NP_285754.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H7
           EDL933]
 gi|15829316|ref|NP_308089.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H7
           str. Sakai]
 gi|168751433|ref|ZP_02776455.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4113]
 gi|168755664|ref|ZP_02780671.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4401]
 gi|168764065|ref|ZP_02789072.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4501]
 gi|168771280|ref|ZP_02796287.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4486]
 gi|168781941|ref|ZP_02806948.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4076]
 gi|168789583|ref|ZP_02814590.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC869]
 gi|168801483|ref|ZP_02826490.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC508]
 gi|195939274|ref|ZP_03084656.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H7
           str. EC4024]
 gi|208813925|ref|ZP_03255254.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4045]
 gi|208819721|ref|ZP_03260041.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4042]
 gi|209396031|ref|YP_002268666.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4115]
 gi|254791196|ref|YP_003076033.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H7
           str. TW14359]
 gi|261226817|ref|ZP_05941098.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. FRIK2000]
 gi|261255220|ref|ZP_05947753.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. FRIK966]
 gi|291280883|ref|YP_003497701.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O55:H7 str. CB9615]
 gi|34395800|sp|Q8XA10|RLUA_ECO57 RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|12512752|gb|AAG54362.1|AE005182_11 orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]
 gi|13359518|dbj|BAB33485.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|188014525|gb|EDU52647.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4113]
 gi|189000435|gb|EDU69421.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4076]
 gi|189357052|gb|EDU75471.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4401]
 gi|189359892|gb|EDU78311.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4486]
 gi|189365889|gb|EDU84305.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4501]
 gi|189370824|gb|EDU89240.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC869]
 gi|189376359|gb|EDU94775.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC508]
 gi|208735202|gb|EDZ83889.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4045]
 gi|208739844|gb|EDZ87526.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4042]
 gi|209157431|gb|ACI34864.1| pseudouridine synthase, RluA family [Escherichia coli O157:H7 str.
           EC4115]
 gi|209746854|gb|ACI71734.1| hypothetical protein ECs0062 [Escherichia coli]
 gi|209746856|gb|ACI71735.1| hypothetical protein ECs0062 [Escherichia coli]
 gi|209746858|gb|ACI71736.1| hypothetical protein ECs0062 [Escherichia coli]
 gi|209746860|gb|ACI71737.1| hypothetical protein ECs0062 [Escherichia coli]
 gi|209746862|gb|ACI71738.1| hypothetical protein ECs0062 [Escherichia coli]
 gi|254590596|gb|ACT69957.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. TW14359]
 gi|290760756|gb|ADD54717.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O55:H7 str. CB9615]
 gi|320190420|gb|EFW65070.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC1212]
 gi|320642099|gb|EFX11450.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H7
           str. G5101]
 gi|320647462|gb|EFX16257.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H-
           str. 493-89]
 gi|320652796|gb|EFX21034.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H-
           str. H 2687]
 gi|320658185|gb|EFX25914.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O55:H7
           str. 3256-97 TW 07815]
 gi|320663494|gb|EFX30778.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O55:H7
           str. USDA 5905]
 gi|320668806|gb|EFX35601.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O157:H7
           str. LSU-61]
 gi|326345223|gb|EGD68966.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. 1125]
 gi|326346924|gb|EGD70658.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. 1044]
          Length = 219

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFRERVPKKQYVTRVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|320327741|gb|EFW83749.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330877702|gb|EGH11851.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|331012591|gb|EGH92647.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 211

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 66/214 (30%), Positives = 102/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIYQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEGGKHALTFWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL    P P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|297184316|gb|ADI20433.1| pseudouridylate synthases, 23S RNA-specific [uncultured alpha
           proteobacterium EB080_L43F08]
          Length = 217

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 65/225 (28%), Positives = 109/225 (48%), Gaps = 12/225 (5%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
                       +LY D  + V NKP+G+    G  + +H    L+  V  +     L H
Sbjct: 3   PFVYEPPKTPLDILYIDEDVLVVNKPSGLLTVPGKELKHHDS--LELRVKIEYPNSFLVH 60

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD +TSG+++ A +++  + L   F  R ++K+Y + V+G  K     I   L+    +
Sbjct: 61  RLDMDTSGVIIFALSKSTQRSLNLQFEKRIVKKLYEARVFGNIKEDNGFIDLPLI----V 116

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 + K + K    A++H++V+D        + + P TGRTHQLRVH + +G  I+G
Sbjct: 117 DWPNRPLQKIDAKEGKSALTHWQVLDREGD-VTRVALMPETGRTHQLRVHMMSLGHTILG 175

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
           D  Y    + N  + +Q    LHA+ + + HP+ G ++   APLP
Sbjct: 176 DRFYGNVAEINLANELQ----LHAKDLMIIHPKNGKKITFKAPLP 216


>gi|146312885|ref|YP_001177959.1| tRNA pseudouridine synthase C [Enterobacter sp. 638]
 gi|145319761|gb|ABP61908.1| Pseudouridylate synthase [Enterobacter sp. 638]
          Length = 261

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 104/241 (43%), Gaps = 17/241 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  I   NKP+G  V             +++  D  GQ     HRLD+ TSG
Sbjct: 1   MTIEILYQDEWIVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTVHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++  +  A + L++ F   +IQK Y ++V G   ++       + +   I   +    
Sbjct: 61  VLLMGLSSEAGRLLSQQFEQHQIQKRYHAIVRGWLMDEATLDYPLVEELDKIADKFAR-- 118

Query: 217 KQNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI
Sbjct: 119 --ENKDPQPAVTDYRGLATVEMPVATGKFPTTRYGLVELEPKTGRKHQLRRHLSHLRHPI 176

Query: 267 VGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD K+      +        ++L LHA  + L HP  G  L I A L    ++     G
Sbjct: 177 IGDSKHGDLRQNRSAAEHFGCDRLMLHASQLSLTHPFTGEPLVIRAGLDDVWMQALSQFG 236

Query: 324 F 324
           +
Sbjct: 237 W 237


>gi|229525503|ref|ZP_04414908.1| tRNA pseudouridine synthase C [Vibrio cholerae bv. albensis VL426]
 gi|229339084|gb|EEO04101.1| tRNA pseudouridine synthase C [Vibrio cholerae bv. albensis VL426]
          Length = 245

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 99/241 (41%), Gaps = 17/241 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASDVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAVTAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDDVWQGLLSEFGWQES 239

Query: 328 R 328
           R
Sbjct: 240 R 240


>gi|227874477|ref|ZP_03992652.1| pseudouridylate synthase [Oribacterium sinus F0268]
 gi|227839666|gb|EEJ50121.1| pseudouridylate synthase [Oribacterium sinus F0268]
          Length = 335

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 70/351 (19%), Positives = 132/351 (37%), Gaps = 57/351 (16%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-----LRSGQ----VRVDKK 51
           MS+ T +    V  D  N  ++ +            L  +         +    +  + +
Sbjct: 1   MSIPT-LFTYTVPRDFANTTIEAFLLEQ--GYTKTLLSALKRVHFFEEKKEHYGIEKNGQ 57

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
                + +  G  + +   +   N        LD               ++YED  I + 
Sbjct: 58  WAFTVDLLAEGDCLSVYLPMEEENSAPPYDFPLD---------------IVYEDRDILLL 102

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWV--------DSKGQKPRLTHRLDQETSGILVVART 163
           +KPA +      G   H +  L   +         +        HRLD +TSG++++A+ 
Sbjct: 103 DKPARLPCHPSPG---HFEKTLAGAIVFYQMQNSSASSFVCHFIHRLDLDTSGLILLAKN 159

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY----------- 212
           R AA  L +  +  RIQ+ Y +   G P+     I  +   +     ++           
Sbjct: 160 RLAASVLNKDMKEGRIQRSYLAFCQGNPEFSLGEIQGFTRLEEKKKKEFNYAFAISAPIA 219

Query: 213 -----VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                  +   N +    A+S+F V++ F +  +  L++Q  TGRTHQ+RVH  ++ CP+
Sbjct: 220 RVEEEKMLRTVNFQKGQEALSYFNVLNYFPEKNYSLLQLQLATGRTHQIRVHLSYLSCPL 279

Query: 267 VGDHKYCANFKGNFTSPI-QNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           +GD  Y    +  F+  I  ++  LH+  +   HP    ++     LP  +
Sbjct: 280 LGDSLYGNGEESVFSQNIGLSRQALHSYSISFTHPIRKEKMFFQRELPPDL 330


>gi|116495316|ref|YP_807050.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
 gi|239629769|ref|ZP_04672800.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|301066888|ref|YP_003788911.1| 23S RNA-specific pseudouridylate synthase [Lactobacillus casei str.
           Zhang]
 gi|116105466|gb|ABJ70608.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           casei ATCC 334]
 gi|239527381|gb|EEQ66382.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|300439295|gb|ADK19061.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           str. Zhang]
          Length = 293

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 65/294 (22%), Positives = 123/294 (41%), Gaps = 40/294 (13%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           RW       ++    +K+L    + VD +    N  +++GQ++R                
Sbjct: 17  RWLAEQ--GVSHRLFKKMLADHLIWVDGQ-ASGNGPVEAGQIIRF--------------- 58

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWV---D 138
             +   + T   +F    ++YED+   + +KPAG++   G           +  ++    
Sbjct: 59  --EIPTSKTLTPEFAPLEVIYEDANWLIVSKPAGLTSVPGPHTPNSSLLNRIAGYLVEQK 116

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +P +  RLD++T G+++ A+   A     +    R + K Y ++V G   + K  I
Sbjct: 117 IDAPQPAIMTRLDRDTVGLVLAAKHPYAQGRF-DQAHQRTLTKHYLAVVSGKLPSPKGEI 175

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L     +  D +H +   +     A++ ++V+         +++Q  TGRTHQ+RVH
Sbjct: 176 DAPL----KLAADGIHRIVAAD--GQTALTKYRVLKEKTN--TLVDVQLLTGRTHQIRVH 227

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
              +G P++GDH Y    + +   P      L A  +    P   + +ITA LP
Sbjct: 228 FASLGHPLIGDHLYG---QPDARIPY---QALQATRLKFTDPFSEK-RITAELP 274


>gi|218263602|ref|ZP_03477676.1| hypothetical protein PRABACTJOHN_03365 [Parabacteroides johnsonii
           DSM 18315]
 gi|218222612|gb|EEC95262.1| hypothetical protein PRABACTJOHN_03365 [Parabacteroides johnsonii
           DSM 18315]
          Length = 551

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 67/249 (26%), Positives = 110/249 (44%), Gaps = 25/249 (10%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   + ++ +    H D  +  ++YED  + V NKPAG+    G      +
Sbjct: 309 CGPILKHMLQGLDVEENPLETDVHRDA-ELEIVYEDESLLVVNKPAGMLSVPGKSDVDSV 367

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++         P + HRLD  TSG+++VA+T+   Q+L   F+ R + K Y + + G
Sbjct: 368 YQRVRRMYPG-ATGPMVVHRLDMATSGLMLVAKTKEVHQNLQAQFKNRTVCKRYVAWLDG 426

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------FCWL 243
           I + K+  +   L          V  V         A++ ++V+     K         +
Sbjct: 427 IVEEKEGHLELPLRPDPEDRPRQVVDVVH----GKPAVTDYRVLRYGGCKGGLRTTPTVV 482

Query: 244 EMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
              P TGRTHQLRVH+ H   +  PIVGD  Y             ++LYLHA Y+   HP
Sbjct: 483 SFVPKTGRTHQLRVHSAHPLGLNAPIVGDELYGKK---------ADRLYLHAEYLGFTHP 533

Query: 301 EGG-RLQIT 308
             G  +++ 
Sbjct: 534 VSGVYMEVE 542


>gi|254285561|ref|ZP_04960525.1| pseudouridine synthase Rlu family protein [Vibrio cholerae
           AM-19226]
 gi|150424423|gb|EDN16360.1| pseudouridine synthase Rlu family protein [Vibrio cholerae
           AM-19226]
          Length = 245

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 98/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAVTAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 239


>gi|227534246|ref|ZP_03964295.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
 gi|227188136|gb|EEI68203.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
          Length = 315

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 65/294 (22%), Positives = 123/294 (41%), Gaps = 40/294 (13%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           RW       ++    +K+L    + VD +    N  +++GQ++R                
Sbjct: 39  RWLAEQ--GVSHRLFKKMLADHLIWVDGQ-ASGNGPVEAGQIIRF--------------- 80

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWV---D 138
             +   + T   +F    ++YED+   + +KPAG++   G           +  ++    
Sbjct: 81  --EIPTSKTLTPEFAPLEVIYEDANWLIVSKPAGLTSVPGPHTPNSSLLNRIAGYLVEQK 138

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +P +  RLD++T G+++ A+   A     +    R + K Y ++V G   + K  I
Sbjct: 139 IDAPQPAIMTRLDRDTVGLVLAAKHPYAQGRF-DQAHQRTLTKHYLAVVSGKLPSPKGEI 197

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L     +  D +H +   +     A++ ++V+         +++Q  TGRTHQ+RVH
Sbjct: 198 DAPL----KLAADGIHRIVAAD--GQTALTKYRVLKEKTN--TLVDVQLLTGRTHQIRVH 249

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
              +G P++GDH Y    + +   P      L A  +    P   + +ITA LP
Sbjct: 250 FASLGHPLIGDHLYG---QPDARIPY---QALQATRLKFTDPFSEK-RITAELP 296


>gi|251790751|ref|YP_003005472.1| tRNA pseudouridine synthase C [Dickeya zeae Ech1591]
 gi|247539372|gb|ACT07993.1| pseudouridine synthase [Dickeya zeae Ech1591]
          Length = 260

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 64/258 (24%), Positives = 104/258 (40%), Gaps = 17/258 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHLIAVNKPAGWLVHRSWLDRKEKVVVMQTVRDQIGQHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L + F   R++K Y ++V G              +   I   +       +
Sbjct: 64  ALSADVARLLAQQFEQHRMEKTYHAVVRGYVMEDGVIDYALTEELDRIADKFA----DPD 119

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A+SH++V+               ++  LE+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVSHYRVLARAEMPVAIGRYDTARYSLLELSPKTGRKHQLRRHMAHLRHPIIGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +      +G        +L LHA  + L HP     L I A             G++  
Sbjct: 180 THGDLRQNRGMAAYFGCARLMLHASRLSLTHPVTDEPLVIQARWDESWQGVMTQFGWQGS 239

Query: 328 RNLYIKRLYSQDECKQNI 345
                +  + Q   + N+
Sbjct: 240 LADIERVEFPQVSGQDNL 257


>gi|71911569|ref|YP_283119.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
 gi|71854351|gb|AAZ52374.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
          Length = 333

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 69/289 (23%), Positives = 106/289 (36%), Gaps = 28/289 (9%)

Query: 23  RWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +        I    ++  LR    V ++   V + + ++ G  V++              
Sbjct: 55  KALLEEQLLIPR-KIRHFLRTKKHVLINGHSVNWQSCVKYGDQVKLFFDHE--------- 104

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
              D    +       K   LYED  I + NKP G+      G        L       G
Sbjct: 105 ---DYPEKIIVMGQAEKVTCLYEDEHIIIVNKPEGMKTH---GNDPTELALLNHVSAYTG 158

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           Q   + HRLD+ETSG ++ A+T      L      R I + Y +LV G   + +    + 
Sbjct: 159 QTCYVVHRLDKETSGAILFAKTPFILPILNRLLEKRDIHREYLALVHGSLDSPRVTYHHP 218

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +  H     V     +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H
Sbjct: 219 IGRHRHDRRKRV----VDPINGKKAITEVTLVKNFHKTASLLTCQLQTGRTHQIRVHLAH 274

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
            G  + GD  Y    K         +L LHA  + L HP     + + A
Sbjct: 275 QGHVLFGDPLYSNGKKD------CARLMLHAYQLRLKHPLTQEDICVQA 317


>gi|257866939|ref|ZP_05646592.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257873272|ref|ZP_05652925.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257800995|gb|EEV29925.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257807436|gb|EEV36258.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
          Length = 284

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 65/262 (24%), Positives = 110/262 (41%), Gaps = 27/262 (10%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
             V V+++   F+  ++ G  + +         II++       + L       K  +L+
Sbjct: 38  KNVTVNQQPAMFHQEVRGGDQITL---------IIEDSDYSYQPIQL---GQADKVDVLF 85

Query: 104 EDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           ED  + V NKPAG+       + A  +     +++  K Q+P + HRLD+ETSG+++ A+
Sbjct: 86  EDEHLLVLNKPAGVKTHPNQPLEADTLLNDAAAYLAPKQQQPYVVHRLDKETSGVVLFAK 145

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      ++I + Y + VWG     +  IA  + +  H     +     + + 
Sbjct: 146 NPLVLPILGRMLENKQIFRRYQATVWGKLTQDQ-TIAKKIGRDRHDRRKRI----IDPRN 200

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++H   I    QK   +     TGRTHQ+RVH   +G P+VGD  Y          
Sbjct: 201 GQSAVTHV-TIAHTQQKTTDVYCVLDTGRTHQIRVHLASIGHPVVGDPLYQNKPA----- 254

Query: 283 PIQNKLYLHARYMDLPHPEGGR 304
               +L LH   + L HP    
Sbjct: 255 ---PRLLLHGYELHLEHPFTKE 273


>gi|312864071|ref|ZP_07724307.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
 gi|322517537|ref|ZP_08070406.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           vestibularis ATCC 49124]
 gi|311100484|gb|EFQ58691.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
 gi|322123797|gb|EFX95371.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           vestibularis ATCC 49124]
          Length = 289

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 60/268 (22%), Positives = 102/268 (38%), Gaps = 29/268 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              V ++ + + + + ++ G  + +                 D         D      L
Sbjct: 37  KKHVLINGETINWQSPVKEGDRISLTF------------DTEDYPNKTIPMGDANLVEPL 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YEDS + V NKP G+   G       +   + ++     Q   + HRLD ETSG ++ A+
Sbjct: 85  YEDSHLIVVNKPEGMKTHGNEPTEIALLNHVSAYCR---QTCYVVHRLDMETSGAVIFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      + IQ+ YW+L  G  + K+    + + +  H     V     + + 
Sbjct: 142 NPFILPILNRLLEDKMIQRQYWALTEGKFQTKETVYNDKIGRDRHDRRKRV----VDPRK 197

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A +    +  F +    +  Q  TGRTHQ+RVH  H G  I+GD  Y          
Sbjct: 198 GQVAYTTVTRLKAF-KGASLVNCQLKTGRTHQIRVHLAHHGHAILGDPLYSHRPA----- 251

Query: 283 PIQNKLYLHARYMDLPHPEG-GRLQITA 309
              ++L LHA  +   HP    ++ + A
Sbjct: 252 ---SRLMLHAHTLSFTHPLTLEKVTVKA 276


>gi|315634350|ref|ZP_07889637.1| tRNA pseudouridine synthase C [Aggregatibacter segnis ATCC 33393]
 gi|315476940|gb|EFU67685.1| tRNA pseudouridine synthase C [Aggregatibacter segnis ATCC 33393]
          Length = 237

 Score =  176 bits (446), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 99/241 (41%), Gaps = 17/241 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY+D  I   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MRLEILYQDEHIVAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQLVYPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A  L   F  ++ +K Y ++V G    + +      ++   I   +    
Sbjct: 61  VLLFALNSETANLLCHQFEQKQTEKEYLAVVRGYVTGQGKIDYPLKVQLDKIADKFA--- 117

Query: 217 KQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            Q +K    A++ +  +               ++  + + P TGR HQLR H  H+  PI
Sbjct: 118 -QQDKEPQSAVTFYDGLKTVEMPYGVGRYATSRYSLVRLIPKTGRKHQLRRHMKHIFHPI 176

Query: 267 VGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD +Y    +    +     ++L LHA  +   HP   + + + A L            
Sbjct: 177 LGDTQYGDLHQNRALTEHTGCSRLMLHAEKLTFVHPLTQQSITLQAGLDEKWQNLMQIFQ 236

Query: 324 F 324
           +
Sbjct: 237 W 237


>gi|257877015|ref|ZP_05656668.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|257811181|gb|EEV40001.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
          Length = 284

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 66/262 (25%), Positives = 110/262 (41%), Gaps = 27/262 (10%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
             V V+++   F+  ++ G  + +         II++       + L       K  +L+
Sbjct: 38  KNVTVNQQPAMFHQEVRGGDQITL---------IIEDSDYSYQPIQL---GQADKVDVLF 85

Query: 104 EDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           ED  + V NKPAG+       + A  +     +++  K Q+P + HRLD+ETSG+++ A+
Sbjct: 86  EDEHLLVLNKPAGVKTHPNQPLEADTLLNDAAAYLAPKQQQPYVVHRLDKETSGVVLFAK 145

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      ++I + Y + VWG     +  IA  + +  H     +     + + 
Sbjct: 146 NPLVLPILGRMLENKQIFRRYQATVWGKLTQDQ-TIAKKIGRDRHDRRKRI----IDPRN 200

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              AI+H   I    QK   +     TGRTHQ+RVH   +G P+VGD  Y          
Sbjct: 201 GQSAITHV-TIAHTQQKTTDVYCVLDTGRTHQIRVHLASIGHPVVGDPLYQNKPA----- 254

Query: 283 PIQNKLYLHARYMDLPHPEGGR 304
               +L LH   + L HP    
Sbjct: 255 ---PRLLLHGYELHLEHPFTKE 273


>gi|15890930|ref|NP_356602.1| ribosomal large subunit pseudouridine synthase A [Agrobacterium
           tumefaciens str. C58]
 gi|15159240|gb|AAK89387.1| ribosomal large subunit pseudouridine synthase A [Agrobacterium
           tumefaciens str. C58]
          Length = 222

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 102/229 (44%), Gaps = 10/229 (4%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L  S  +          +++ D  + V +KP+G+    G   A      L + V  +  K
Sbjct: 3   LKLSNPIYNPPLDPWLTIVHRDDDLLVLDKPSGLLSVPGRDPALSDS--LMTRVQKQFPK 60

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + +RLD++TSGI++++  R A   +   F  R  +K Y ++VWG    ++  +   L 
Sbjct: 61  ALMINRLDKDTSGIVLMSLNRKAHAAIAAQFEKRETRKSYVAIVWGTVAGEEGEVDLPLA 120

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
               I  D     + + +    A S ++V++        L + P TGRTHQLRVH   +G
Sbjct: 121 ----IDPDNKPRHRVDHENGKPAQSLWRVLERLPLPATRLALTPLTGRTHQLRVHMKALG 176

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
            PI+GD  Y              +L LHA+ +   HP+G  +  T P P
Sbjct: 177 HPILGDEFY----AEGEALTAAPRLMLHAQEVGFRHPDGRDVTYTVPCP 221


>gi|327395022|dbj|BAK12444.1| tRNA pseudouridine synthase C TruC [Pantoea ananatis AJ13355]
          Length = 259

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 60/239 (25%), Positives = 106/239 (44%), Gaps = 17/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ +   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDAWLVAVNKPAGWLVHRSWLDRHETQFVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +    + L++ F   +++K Y ++V G  + +       + +   I   +V     + 
Sbjct: 64  GLSSEVGRLLSQQFEHHQMEKTYHAVVRGWLEGRDRLDYPLVEELDKIADKFVS----DP 119

Query: 221 KGANYAISHF----------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +    A++ +           V      ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 RAPQPAVTDYASLATVEMPVAVSRYPTARYSLIELKPKTGRKHQLRRHMSHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            +      +G       N+L LHA  + L HP  G  L I A L     +  D  G++ 
Sbjct: 180 AHGDLRQNRGAAAHFGANRLMLHASSLSLSHPVTGEPLVIRAGLDLVWQRVMDQFGWQA 238


>gi|220918618|ref|YP_002493922.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219956472|gb|ACL66856.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 287

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 70/316 (22%), Positives = 121/316 (38%), Gaps = 36/316 (11%)

Query: 13  ENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
             +    RLDRW                ++ +G+VR+  K    + ++  G+ V +    
Sbjct: 2   PREAAGARLDRWLAGAIGATAERTRW--LVETGRVRIRGKTCSPHRKLFGGEEVAV---- 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                        +        +      +LY+D+   V  KP G++V+  +        
Sbjct: 56  -------------ERPAPRAAEASGPALAVLYDDADCLVVAKPPGLAVEASAPGGASAVA 102

Query: 132 FLKSW--VDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                   D  G+  P L HRLD++TSG L++AR   A   L  +F    ++K Y +LV 
Sbjct: 103 AASRLGSFDVDGRAVPGLPHRLDRDTSGALLLARHDRALAALRAAFEAGAVEKEYLALVG 162

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G P  ++  +     +       +          A  A   + V +   +    L ++  
Sbjct: 163 GAPP-REGRLDTPYGRDPADPRRFTTRF----PSARRARLSWTV-ERALRGAALLRVRLE 216

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
           TGRTHQ+RV     G P++GD  Y              +  LHA  +  P P +G  +++
Sbjct: 217 TGRTHQIRVQLAEAGFPVLGDAAYGVRADA------IARQALHAARLAFPRPSDGAPVEV 270

Query: 308 TAPLPAHMVKTWDSLG 323
            APLP  + +   +L 
Sbjct: 271 RAPLPEDLERAIAALA 286


>gi|153216000|ref|ZP_01950222.1| tRNA pseudouridine synthase C [Vibrio cholerae 1587]
 gi|124114513|gb|EAY33333.1| tRNA pseudouridine synthase C [Vibrio cholerae 1587]
          Length = 244

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 98/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAVTAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 239


>gi|289627475|ref|ZP_06460429.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aesculi str. NCPPB3681]
 gi|289646428|ref|ZP_06477771.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aesculi str. 2250]
 gi|330868108|gb|EGH02817.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aesculi str. 0893_23]
          Length = 211

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 66/214 (30%), Positives = 102/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIYQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HQGGKHALTFWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL    P P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|282881959|ref|ZP_06290604.1| RluA family pseudouridine synthase [Peptoniphilus lacrimalis 315-B]
 gi|281298234|gb|EFA90685.1| RluA family pseudouridine synthase [Peptoniphilus lacrimalis 315-B]
          Length = 316

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 64/303 (21%), Positives = 124/303 (40%), Gaps = 37/303 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ V++  ++ + RLDR+ K ++       + K LR   ++VD K+    + I+ GQ + 
Sbjct: 1   MRKVIIGPNDSDQRLDRFLKKYFEKAPLSFIYKNLRKKNIKVDGKKASPEDLIKEGQEIS 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +    K+         L ++S      +LYED  I +  KP  +         
Sbjct: 61  LFISDETIEKYKKD--------KLARNSQKFP-QILYEDDNICLMKKPLNMLTHNDKN-- 109

Query: 127 YHIDGFLKSWVD------------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           ++ D  +  ++D                +P + +RLD+ TSGIL+ A+     + + ++ 
Sbjct: 110 FYQDNMVDRFIDYLIFKEEYSPREENTFRPSICNRLDRNTSGILLGAKNAETLREINKAI 169

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R + K Y ++V G  +   E      +K      + +    Q       +++ F  + 
Sbjct: 170 KERLVDKFYLTIVKGKVQKPFEI----NIKLEKTDKNIMRKSSQ----GKDSLTKFFPLI 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              + +  L+++  TGRTHQ+R      G  I+GD KY       F S       LH   
Sbjct: 222 SNGE-YSLLKVKLITGRTHQIRASLKEKGLYILGDRKYGTGKDKEFNS-----QALHNYL 275

Query: 295 MDL 297
           +  
Sbjct: 276 IKF 278


>gi|323498626|ref|ZP_08103618.1| tRNA pseudouridine synthase C [Vibrio sinaloensis DSM 21326]
 gi|323316324|gb|EGA69343.1| tRNA pseudouridine synthase C [Vibrio sinaloensis DSM 21326]
          Length = 241

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 57/243 (23%), Positives = 102/243 (41%), Gaps = 17/243 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++++D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L
Sbjct: 2   LDIIFQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A +   A  +   F    ++K Y ++V G  +          ++   I   +      
Sbjct: 62  IFALSSEVASQVMPMFANHEMEKTYHAIVRGWIEESGRLDYALKVELDKIADKHASQ--- 118

Query: 219 NEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A++ ++ +               ++C +EM+P TGR HQLR H  H+  PIVG
Sbjct: 119 -DKEAQEAVTDYRPLAKAEVPHSTGKFPTTRYCLMEMKPLTGRKHQLRRHMAHLRHPIVG 177

Query: 269 DHKYCANFKGNFTSPI--QNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           D  +           +   ++L LHA  +   HP  G +L I A + +   +  +   ++
Sbjct: 178 DTTHGDGKHNKLFRDVYESHRLLLHASSLSFIHPFSGEKLVIKAAVDSTWQRLCEEFDWQ 237

Query: 326 YDR 328
              
Sbjct: 238 MPE 240


>gi|259046558|ref|ZP_05736959.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           adiacens ATCC 49175]
 gi|259036723|gb|EEW37978.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           adiacens ATCC 49175]
          Length = 284

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 64/304 (21%), Positives = 124/304 (40%), Gaps = 33/304 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + +     I+   L  +  +G++ ++ +       +Q G V+ +               I
Sbjct: 5   FLQEI--GISRTFLAHVKSNGELLINGRHEIVLKTLQPGDVLTM--------------VI 48

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQ 142
             S  + T     +   +LYED  + + NKP G +         + +   +K +   +G 
Sbjct: 49  PPSGEHETVIPSEVPIDILYEDEYLLIINKPVGTASIPSKLHPDHSMANRVKGYYKRRGY 108

Query: 143 KPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             ++TH   RLD++T+G+++ A+ R     + ++ R + IQK Y +LV          + 
Sbjct: 109 ADQITHVVTRLDRDTTGVMMFAKHRVVHAWMDQALREKTIQKKYLALVH-----DTSTLE 163

Query: 200 NWLLKKSHIGGDYVHVV-KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                 + IG     ++ +   +    +++ +   +        +E+  HTGRTHQ+RVH
Sbjct: 164 AHGFIDAPIGRHEGSIINRCVSEDGKPSLTEYWKKETLV-GAELVEILLHTGRTHQIRVH 222

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
              +G P+V D  Y             ++  LH   +   HP     L I APLP  M +
Sbjct: 223 FSWIGAPLVADDLYGG-----VKDEFLDRQALHCHSLTFIHPMTKKELIIEAPLPKDMSQ 277

Query: 318 TWDS 321
             ++
Sbjct: 278 WIEA 281


>gi|219685683|ref|ZP_03540497.1| RNA pseudouridine synthase family protein [Borrelia garinii Far04]
 gi|219672799|gb|EED29824.1| RNA pseudouridine synthase family protein [Borrelia garinii Far04]
          Length = 315

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 73/335 (21%), Positives = 138/335 (41%), Gaps = 22/335 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L  Y+  + V +++   RLD        + +   + K +R G +R++  +  F+ R+ 
Sbjct: 1   MRLDKYI-LLEVLDNDNGKRLDSILIKIL-NFSKARIIKHIRKGDIRLNGLKPSFSYRVC 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   +    H+      +            ++  ++YEDS + V +K  GI V 
Sbjct: 59  KGDKIYLYKSLVQNLHLA-----MGECYKSNIDFQCIRKRIIYEDSDLLVMDKQRGILVH 113

Query: 121 GGSGIAYHIDG--FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           GG      +     L+  + S   KP   HRLD+ TSGI++ A+    A+ L+ +F    
Sbjct: 114 GGKNSLDFLVNSYLLREDLRSLSFKPSAVHRLDRNTSGIIIFAKNINVARKLSAAFSSGS 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y++++ G  K       N L +   +   +V      +K +  AI+    I   ++
Sbjct: 174 VTKKYFAILLGEVK-STVIYKNHLFRNQRLKKTFV----LEDKDSINAITKVNPILS-SK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +    E+   TG THQ+R        P++ D KY   FK +         +LHA  +   
Sbjct: 228 RATLAEIVIETGFTHQIRSQCSFNEHPLINDKKYYNKFKKSD-------YFLHAFLVKFN 280

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
                + +  A      +K    +   Y+ + ++K
Sbjct: 281 ETFFKKNEFYAKPSLEFLKQVKDIFGVYEFSEFLK 315


>gi|116330669|ref|YP_800387.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116124358|gb|ABJ75629.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 377

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 75/384 (19%), Positives = 134/384 (34%), Gaps = 99/384 (25%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +  D+  +RLD +    + + +    QK +  G++ V  K+VK    ++ G  V   P
Sbjct: 14  IFISKDDVGIRLDHFLSKKFTYHSRNVWQKEINEGRISVLGKKVKSGILLREGDTVVYQP 73

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           +      + K+ K                  +LYED      +KP  + V          
Sbjct: 74  IERKEPPVRKDYK------------------ILYEDEFFVAVDKPGDLPVHPAGKYR--- 112

Query: 130 DGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            G L + +   G  +     HRLD+ETSG+++ A+   AA  L+  F  R+IQK Y + V
Sbjct: 113 KGNLLTLLKESGKFENLFTVHRLDRETSGVVLFAKDSKAASLLSGLFSSRKIQKYYITKV 172

Query: 188 WGIPKNK-------KECIANWLLKKSHIGGDYVHVVKQNEK---------GANYAISHFK 231
           +G    +       K  +++ + KK        + +K+N+K            + ++ F+
Sbjct: 173 YGDFPRRKIAYGVLKPDVSSIIRKKRKFFLLKSNFLKRNKKYFLENSFSPEEEFCLTAFR 232

Query: 232 VIDCF------------------------------------------------AQKFCWL 243
            I+ +                                                 + + ++
Sbjct: 233 KIESYFIKTQFQEIESDVGELKVRSRKKKLNFESLQTQNEKNEEPKVRSIYPKHEFYSFV 292

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----------ANFKGNFTSPIQNKLYLHA 292
             +P TGR HQ+R     +  PI GD  Y                         +  LHA
Sbjct: 293 LCKPITGRMHQIRAVLYGLDFPIWGDKLYGKDEEVFLEFIEGKNPDLTERLGMERQALHA 352

Query: 293 RYMDLPHPEGGR-LQITAPLPAHM 315
             +   HP   R ++I A +P   
Sbjct: 353 YAIRFNHPITNRKMKIVASVPKDF 376


>gi|238751458|ref|ZP_04612950.1| tRNA pseudouridine synthase C [Yersinia rohdei ATCC 43380]
 gi|238710325|gb|EEQ02551.1| tRNA pseudouridine synthase C [Yersinia rohdei ATCC 43380]
          Length = 257

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 103/237 (43%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +       +
Sbjct: 64  ALSSEVARALSLQFEQHQIQKTYHAVVRGYVLEADTIDYEMTEELDKIADKFAR----PD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    +++H+K +               +F  LE++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYKPLAKVEVPVAIGRYDTARFSLLELKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            +      +G       ++L LHA ++ L HP  G  L +TA       +     G+
Sbjct: 180 AHGDLRQNRGVGQHFDCSRLMLHASHLQLNHPVTGEPLSLTARWDESWQQLMSHFGW 236


>gi|262039482|ref|ZP_06012784.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           goodfellowii F0264]
 gi|261746463|gb|EEY34000.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           goodfellowii F0264]
          Length = 293

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 64/319 (20%), Positives = 129/319 (40%), Gaps = 38/319 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +E   + M++ ++ +    +         LR+ +V ++ K+V+   ++ S   +R
Sbjct: 1   MKKFKLEKQYQRMKISQYLREVQNYSGRS-----LRNVEVFLNGKQVRTTKKLPSSGTLR 55

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
           +                ++           L   ++YED  + V NK   +         
Sbjct: 56  V----------------IEKEKGTDIKPIKLDLDIVYEDDDLLVVNKEPFLLTHPTQKKA 99

Query: 126 AYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            + +   +  +   K +K   PR  +RLD  TSG++++A+   A   L         +K 
Sbjct: 100 DFTLANGIVYYFKEKYEKETVPRFYNRLDMNTSGLIIIAKNSFAQAFLQNFS---NFEKK 156

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFC 241
           Y ++V GI +  +E +    + +     + +      ++   YA +  K +  + +    
Sbjct: 157 YLAIVDGIMETDEEIVIEKPIYRDGDKLERII-----DERGQYAKTIVKPLKKYPEKNVT 211

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
             E +  TGRTHQ+RVH   +G  IVGD  Y    KG+       + +LHA  +   HP 
Sbjct: 212 LAECELFTGRTHQIRVHLKSVGHTIVGDELYG---KGSDEKRGIKRQFLHAYKVKFTHPV 268

Query: 301 EGGRLQITAPLPAHMVKTW 319
           +   +++  PL   M +  
Sbjct: 269 KKEEIELEIPLFNDMKEFL 287


>gi|113460997|ref|YP_719064.1| tRNA pseudouridine synthase C [Haemophilus somnus 129PT]
 gi|112823040|gb|ABI25129.1| tRNA pseudouridine synthase C [Haemophilus somnus 129PT]
          Length = 234

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 102/238 (42%), Gaps = 18/238 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +LY+D  + V NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+
Sbjct: 2   DILYQDEFLVVVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLL 61

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A     A  L   F +++++K Y ++V G   + +       ++   I   +       
Sbjct: 62  FALNAGIANLLCSQFELKQVKKSYLAIVRGYLSDAQRIDYPLKVQLDKIADKFSR----- 116

Query: 220 EKGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           ++    AI+ +  +             + ++  + + PHTGR HQLR H  H+  PI+GD
Sbjct: 117 KEELQDAITDYYGLKTVEMPYGVGRYSSSRYSLVRLMPHTGRKHQLRRHLKHIFHPILGD 176

Query: 270 HKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            +Y    +    S     ++L LHA  +   HP     ++I A L       +    +
Sbjct: 177 TQYGDLHQNRAFSQNLGVSRLMLHAEKLCFQHPVTNETIEIVADLDEQWKLLFKIFNW 234


>gi|332686149|ref|YP_004455923.1| ribosomal large subunit pseudouridine synthase D [Melissococcus
           plutonius ATCC 35311]
 gi|332370158|dbj|BAK21114.1| similar to ribosomal large subunit pseudouridine synthase D
           [Melissococcus plutonius ATCC 35311]
          Length = 290

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 63/266 (23%), Positives = 108/266 (40%), Gaps = 24/266 (9%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R   V ++ + V F+  + +   + +              +  D  +      +     
Sbjct: 36  IRK-NVLLNNQPVLFHQTVSANDQITLKF------------EKEDYQIPTIHAGNSKLVH 82

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +L+ED  + + NKP G+            +   L +++  K Q P + HRLD+ETSG ++
Sbjct: 83  VLFEDEHLIIINKPVGMKTHPNQPDENDTLLNHLTAYLKPKQQIPYVVHRLDKETSGAIL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+       L      ++I + Y ++V GI       I   + +  H     +     +
Sbjct: 143 FAKNPFVLPILGRMLEKKQIYRCYQAIVDGIVLKNTWTITKKIGRDRHDRRKRI----ID 198

Query: 220 EKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            K    AI+H +      Q     L  +  TGRTHQ+RVH  + G PI+GD  Y  N  G
Sbjct: 199 SKHGMIAITHIQKAFTLTQENKTALLCRLETGRTHQIRVHLANAGFPIIGDPLYNTNKTG 258

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR 304
           N       +L LHA  + + HP   +
Sbjct: 259 N-----NKRLMLHAYELHIKHPFSKQ 279


>gi|219684906|ref|ZP_03539847.1| RNA pseudouridine synthase family protein [Borrelia garinii PBr]
 gi|219671644|gb|EED28700.1| RNA pseudouridine synthase family protein [Borrelia garinii PBr]
          Length = 315

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 73/335 (21%), Positives = 138/335 (41%), Gaps = 22/335 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L  Y+  + V +++   RLD        + +   + K +R G +R++  +  F+ R+ 
Sbjct: 1   MRLDKYI-LLEVLDNDNGKRLDSILIKIL-NFSKARIIKHIRKGDIRLNGLKPSFSYRVC 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   +    H+      +            ++  ++YEDS + V +K  GI V 
Sbjct: 59  KGDKIYLYKSLVQNLHLA-----MGECYKSNIDFQCIRKRIIYEDSDLLVMDKQRGILVH 113

Query: 121 GGSGIAYHIDG--FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           GG      +     L+  + S   KP   HRLD+ TSGI++ A+    A+ L+ +F    
Sbjct: 114 GGKNSLDFLVNSYLLREDLRSLSFKPSAVHRLDRNTSGIIIFAKNINVARKLSAAFSSGS 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y++++ G   N      N L +   +   +V      +K +  AI+    I   ++
Sbjct: 174 VTKKYFAILLGEV-NSTVIYKNHLFRNQRLKKTFV----LEDKDSINAITKVNPILS-SK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +    E+   TG THQ+R        P++ D KY   FK +         +LHA  ++  
Sbjct: 228 RATLAEIVIETGFTHQIRSQCSFNEHPLINDKKYYNKFKKSD-------YFLHAFLVEFN 280

Query: 299 HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
                + +  A      +K    +   Y+ + + K
Sbjct: 281 EAFFKKNEFYAKPSLEFLKQVKDIFGVYEFSEFFK 315


>gi|167032335|ref|YP_001667566.1| pseudouridine synthase [Pseudomonas putida GB-1]
 gi|166858823|gb|ABY97230.1| pseudouridine synthase [Pseudomonas putida GB-1]
          Length = 211

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 65/215 (30%), Positives = 102/215 (47%), Gaps = 11/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L+ED+ I V NKP  +    G     + D  +    ++      + HRLD ETSGI+
Sbjct: 6   VQILFEDAAILVINKPTLLLSVPGRA-EDNKDCLITRLQENGYPDALIVHRLDWETSGII 64

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR   + + L+  F  R  +K Y +L WG P      I   L           HVV  
Sbjct: 65  LLARDADSHRELSRQFHDRETEKSYTALCWGQPALDSGSIDLPLRYDPPT--KPRHVV-- 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +   +A++ +++++     +C +E+ P TGR+HQLRVH L +G P++GD  Y      
Sbjct: 121 DHEQGKHALTFWRIVERCGD-YCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY----AN 175

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                   +L LHA  +   HP  G RL+   P P
Sbjct: 176 PEALAAHERLCLHASMLSFTHPVSGERLKFECPAP 210


>gi|261868111|ref|YP_003256033.1| tRNA pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413443|gb|ACX82814.1| tRNA pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 237

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 100/241 (41%), Gaps = 17/241 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   NKPAG+ V       +     ++   D  GQ     HRLD+ TSG
Sbjct: 1   MNLAILYQDDVLVAVNKPAGMLVHRSWLDRHETQFVMQILRDQIGQLVYPFHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A  +   F  ++ +K Y ++V G    + E      ++   I   +    
Sbjct: 61  VLLFALNSETANLVCHQFEQKQTEKQYLAVVRGYVTGQGEIDYPLKVQLDKIADKFA--- 117

Query: 217 KQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            Q +K    A++ +  +             A ++  + + P TGR HQLR H  H+  PI
Sbjct: 118 -QQDKAPQSAVTFYDGLKTVEMPYGVGRYAASRYSLVRLTPKTGRKHQLRRHMKHIFHPI 176

Query: 267 VGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD +Y    +    +     ++L LHA  +   HP  G+ + I A L         +  
Sbjct: 177 LGDTQYGDLHQNRALTEHIGCSRLMLHAEKLTFVHPLTGQPITIEAGLDEQWKHLMRTFQ 236

Query: 324 F 324
           +
Sbjct: 237 W 237


>gi|330811143|ref|YP_004355605.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327379251|gb|AEA70601.1| Ribosomal large subunit pseudouridine synthase A [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 211

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 63/214 (29%), Positives = 102/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++++D  + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIHQDDAVLVVDKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P+     I   L           HVV  +
Sbjct: 66  LARDPDTHRELSRQFHDRETEKAYTALCWGQPELDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ ++V++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEHGKHALTFWRVLERCGD-WCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPQALA 180

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL+   P P
Sbjct: 181 AW----PRLCLHASMLSFTHPQSGERLRFECPAP 210


>gi|153802299|ref|ZP_01956885.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-3]
 gi|124122181|gb|EAY40924.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-3]
          Length = 245

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 99/240 (41%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  ++          +   I   +       +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEDTNVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAVTAYRPLAKVELPISTGKFATTRYCLMEMQPRTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 239


>gi|320583405|gb|EFW97618.1| DRAP deaminase, putative [Pichia angusta DL-1]
          Length = 569

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 56/254 (22%), Positives = 107/254 (42%), Gaps = 25/254 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +  + +        +  L  G+V +++K    +  +++G ++              E
Sbjct: 92  LDVF-AHEFRLHPKSYYRNALEKGRVTINEKVANIDTILKNGDLISHRMHR-------HE 143

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    V            +++ED ++ V +KP+GI V       ++   F+       
Sbjct: 144 PPVTSRPVK-----------IVHEDDELVVIDKPSGIPVHPTGRYRHNTVTFI--LEREM 190

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G K    +RLD+ TSG++ + +T A A+ + +  R R + K Y + V G    ++E +  
Sbjct: 191 GIKAHPCNRLDRLTSGLMFLGKTAAGAEKMVKQMREREVSKEYIAKVVGEFPAQREIVCE 250

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             L+        +     + +    A + FK +         +  +P TGRTHQ+RVH  
Sbjct: 251 EPLR---TVDPRIAFNIVDRENGKEAKTVFKRLSYDG-VTSLVICKPLTGRTHQIRVHLQ 306

Query: 261 HMGCPIVGDHKYCA 274
           ++G PIV D  Y +
Sbjct: 307 YLGHPIVNDPLYSS 320


>gi|332308153|ref|YP_004436004.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332175482|gb|AEE24736.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 218

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 57/213 (26%), Positives = 108/213 (50%), Gaps = 12/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D  + V NKP+G+    G  + +     L+  V       ++ HRLD  TSG+LV+
Sbjct: 16  IVFKDEHLLVLNKPSGLLTVPGKALEH--KDSLELRVQRVYPTAKIVHRLDMATSGLLVM 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +   + L++ F +R+ +K Y + V+G    ++  +   L+         +   ++  
Sbjct: 74  ALDKDTHRQLSKQFELRQTRKTYIARVYGEVSGERGSVDLPLICDWPNRPKQMVCQQR-- 131

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                +++H++V++        +E+ P TGR+HQLRVH L +G PI+GD  Y  +     
Sbjct: 132 --GKPSLTHWRVLERN-DNSTRMELTPVTGRSHQLRVHMLSLGHPILGDRLYAHSD---- 184

Query: 281 TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
              +  +L LHA+ +   HP     L+++AP+P
Sbjct: 185 ALTMAQRLQLHAQTLGFTHPVTELPLELSAPVP 217


>gi|332098238|gb|EGJ03211.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           155-74]
          Length = 217

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 106/226 (46%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NK +G+    G  +  H D  + + +     +    HRLD 
Sbjct: 6   PPQEPWLVILYQDDHIMVVNKRSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 63

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 64  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 117

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 118 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 177

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +            +L LHA  + + HP  G  +   A  PA  
Sbjct: 178 FYASPEARAMA----PRLLLHAEMLTITHPAYGNSMTFKA--PADF 217


>gi|83647350|ref|YP_435785.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83635393|gb|ABC31360.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 224

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 71/220 (32%), Positives = 107/220 (48%), Gaps = 18/220 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  I V NKP+GI    G G   H+   + S V  K     + HRLD  TSG+LV+A
Sbjct: 18  LYEDKDIIVVNKPSGILTSPGRG--AHLYDSVWSRVKEKHPLSHVVHRLDLATSGVLVLA 75

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE- 220
             R A + L   F  R ++K Y + VWG+ K  +  +   L+       D+ +  KQ   
Sbjct: 76  LRRKAEKELKRQFMQREVRKTYVAKVWGVIKEDQGEVDLPLI------CDWPNRPKQKVC 129

Query: 221 -KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +    A++ ++V+    +    +E+ P TGR+HQLRVH L +G PI+GD  Y +     
Sbjct: 130 FEHGKPAVTGYRVLAR-EENATLVELYPITGRSHQLRVHMLSLGHPILGDRFYASPEALA 188

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
            +     +L LHA+ +   HP  G  +      PA   ++
Sbjct: 189 ASE----RLLLHAQSLSFKHPYSGEDMTFHT--PADFAQS 222


>gi|50555826|ref|XP_505321.1| YALI0F12199p [Yarrowia lipolytica]
 gi|49651191|emb|CAG78128.1| YALI0F12199p [Yarrowia lipolytica]
          Length = 605

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 59/265 (22%), Positives = 108/265 (40%), Gaps = 31/265 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
             LD +  N +   +    +  + +GQV ++ K  + ++ +++G  ++            
Sbjct: 109 QLLDIF-ANEFRDRDESYYRWAIENGQVLLNGKVAQVDSVVRNGDAIQHRSHK------- 160

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  + D  ++           +++ED  + V +KP+G+ V       Y  +  +     
Sbjct: 161 HEPPVTDQEID-----------IVHEDDDLVVIDKPSGMPVHPAG--RYRFNTAVNILKH 207

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKEC 197
             G      +RLD+ TSG++ +A+   +A       R R++QK Y + V G  P  +   
Sbjct: 208 VNGLHVHPCNRLDRLTSGLMFMAKNPKSADKFGAQLRDRQVQKQYVARVVGKFPDGEISV 267

Query: 198 IANWLLKKSHIGGDYV--------HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             N       IG + V        H    +      A + FK I    +    +  +P+T
Sbjct: 268 DENLCTLDPKIGFNIVTTKVDRDHHRALMDRATEREAKTVFKRISYDGE-TSIVLCKPYT 326

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCA 274
           GRTHQ+RVH   +G PI  D  Y +
Sbjct: 327 GRTHQIRVHLQFLGHPIANDPLYSS 351


>gi|212636284|ref|YP_002312809.1| pseudouridylate synthase [Shewanella piezotolerans WP3]
 gi|212557768|gb|ACJ30222.1| Pseudouridylate synthase [Shewanella piezotolerans WP3]
          Length = 278

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 99/240 (41%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  +   +KPAG+ V             ++   D  G      HRLD+ TSGIL+ 
Sbjct: 29  ILFEDDDVVAIHKPAGLLVHRSYLARRERFFAMQLTRDKVGCHVFPVHRLDRPTSGILLF 88

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++   A  L E F    I K Y ++V G              +   +    V       
Sbjct: 89  AKSSEMANALCEQFAAHSIDKEYLAIVRGNMHEAATLDYALKEELDDVADKDV----DPN 144

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ +K +               ++  + + PHTGR HQLR H  H+  PI+GD 
Sbjct: 145 KAAQDAITSYKPLLNSEIPYASGRYATSRYALVHLSPHTGRKHQLRRHMAHLRHPILGDT 204

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            +    +  F       N+L+L A+ +   HP  G R+ +   L    +  +D LG+  D
Sbjct: 205 THGDGKQNKFFREHFGINRLWLIAKKLSFNHPRTGERVAVETELEQEWITLFDELGWDDD 264


>gi|323492963|ref|ZP_08098101.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           brasiliensis LMG 20546]
 gi|323312794|gb|EGA65920.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           brasiliensis LMG 20546]
          Length = 245

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 65/228 (28%), Positives = 112/228 (49%), Gaps = 12/228 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y+D +I   NKP+G+    G  +  H D      V++     ++ HRLD +TSG++
Sbjct: 14  VDIIYQDEQILAVNKPSGLLSVPGR-LEEHYDSMWSRLVET-YPDIQVVHRLDMDTSGLM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A+++ A + L + F+ R   K+Y++ VWG P+  +  +   L+           V  +
Sbjct: 72  VLAKSKQAERSLKKQFQYRLTHKVYYARVWGHPQQDEGEVDLPLICD-WPNRPRQKVCFE 130

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      + + ++V+    +K   + + P TGR+HQLRVH   +G PIVGD  Y      
Sbjct: 131 H---GKPSQTRYQVVKR-EEKTSIVRLLPITGRSHQLRVHMQALGHPIVGDEFYSEGEAF 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
            F+     +L LHA  +   HP+   LQ T  +P       +S+ F Y
Sbjct: 187 EFSE----RLELHAAELSFYHPDSELLQ-TIFVPCDFYLEAESVIFNY 229


>gi|15640904|ref|NP_230535.1| tRNA pseudouridine synthase C [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121588124|ref|ZP_01677871.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 2740-80]
 gi|147674217|ref|YP_001216366.1| tRNA pseudouridine synthase C [Vibrio cholerae O395]
 gi|227081064|ref|YP_002809615.1| pseudouridine synthase Rlu family protein [Vibrio cholerae M66-2]
 gi|229505507|ref|ZP_04395017.1| tRNA pseudouridine synthase C [Vibrio cholerae BX 330286]
 gi|229510823|ref|ZP_04400302.1| tRNA pseudouridine synthase C [Vibrio cholerae B33]
 gi|229517944|ref|ZP_04407388.1| tRNA pseudouridine synthase C [Vibrio cholerae RC9]
 gi|229608526|ref|YP_002879174.1| tRNA pseudouridine synthase C [Vibrio cholerae MJ-1236]
 gi|254848023|ref|ZP_05237373.1| tRNA pseudouridine synthase C [Vibrio cholerae MO10]
 gi|298498990|ref|ZP_07008797.1| tRNA pseudouridine synthase C [Vibrio cholerae MAK 757]
 gi|34582485|sp|Q9KTL4|TRUC_VIBCH RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|9655343|gb|AAF94050.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O1
           biovar El Tor str. N16961]
 gi|121547615|gb|EAX57714.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 2740-80]
 gi|146316100|gb|ABQ20639.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O395]
 gi|227008952|gb|ACP05164.1| pseudouridine synthase Rlu family protein [Vibrio cholerae M66-2]
 gi|227012708|gb|ACP08918.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O395]
 gi|229344659|gb|EEO09633.1| tRNA pseudouridine synthase C [Vibrio cholerae RC9]
 gi|229350788|gb|EEO15729.1| tRNA pseudouridine synthase C [Vibrio cholerae B33]
 gi|229357730|gb|EEO22647.1| tRNA pseudouridine synthase C [Vibrio cholerae BX 330286]
 gi|229371181|gb|ACQ61604.1| tRNA pseudouridine synthase C [Vibrio cholerae MJ-1236]
 gi|254843728|gb|EET22142.1| tRNA pseudouridine synthase C [Vibrio cholerae MO10]
 gi|297543323|gb|EFH79373.1| tRNA pseudouridine synthase C [Vibrio cholerae MAK 757]
          Length = 244

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 98/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAVTAYRPLAKVELPIATGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 239


>gi|188996912|ref|YP_001931163.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188931979|gb|ACD66609.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 270

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 72/304 (23%), Positives = 117/304 (38%), Gaps = 51/304 (16%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       I+    + I+ S  V V+ KRV   ++ ++ G VV I       +       
Sbjct: 16  FIAESLK-ISKNQAKDIIDSRNVIVNNKRVWIASHNLKPGDVVEIVQSELKND------- 67

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             +LYED  I   +KP  I     S  A   +  L+  + +   
Sbjct: 68  ----------------LKILYEDDYIIAIDKPPTIVSDKESSSA---EDILRKKLKNDKI 108

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           K    HRLD+ETSG+L+ A+     +   E +  + + KIY ++       K   I   +
Sbjct: 109 KA--IHRLDKETSGVLLFAKDYKIFEKFKEIWEDKNVLKIYLAISHNEANFKDFTINQDI 166

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                                  AI+H KV++     F + +++  TGR HQ+R H   +
Sbjct: 167 -------------------DGKQAITHLKVLN-KGNGFTYFQVRIETGRKHQIRKHLASI 206

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
             PIVGD  Y      N       +  LH+  + L HP    +++ITAPLP+      + 
Sbjct: 207 RHPIVGDKIYSIKKFENNLVKRVTRQMLHSYKLVLTHPYLNKKIEITAPLPSDFKNVLNY 266

Query: 322 LGFK 325
           L  +
Sbjct: 267 LNER 270


>gi|121728338|ref|ZP_01681368.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V52]
 gi|121629393|gb|EAX61823.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V52]
          Length = 244

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 98/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAVTAYRPLAKVELPIATGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDRVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 239


>gi|312879313|ref|ZP_07739113.1| pseudouridine synthase, RluA family [Aminomonas paucivorans DSM
           12260]
 gi|310782604|gb|EFQ23002.1| pseudouridine synthase, RluA family [Aminomonas paucivorans DSM
           12260]
          Length = 308

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 84/326 (25%), Positives = 134/326 (41%), Gaps = 26/326 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +  D+   R+DR  K  +P +      K LR G VR++ ++V  + R ++GQV+R
Sbjct: 1   MEEHRLGADQAGRRIDRILKEGWPDVPLGARMKALRIGLVRLEGRKVSCDERAEAGQVLR 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P          +  +     V            +L+    + V +KPAG   Q      
Sbjct: 61  VPW--------AEAPRWGVPLVTPAPEGRDDPPWVLFRGRNLLVADKPAGWLTQPDRPGG 112

Query: 127 YHIDGFLKSW--VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   +     V     +P   HRLD+ TSG++++  T    + L +  R RR++K YW
Sbjct: 113 DSLVTRVWELEGVGEGSFRPAAAHRLDRNTSGVVLLPLTAPLLRLLADLLRRRRLRKTYW 172

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +LV G+P      I   L K               +   + A++ ++++    +    LE
Sbjct: 173 ALVAGVPPA-TGEITRSLRKLEEENR------VVEDPRGDQALTRYRLLGTDGE-ASLLE 224

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGG 303
           +   TGR HQ R H    G PI+GD KY      +          LHAR + LP  P   
Sbjct: 225 LDLVTGRPHQARAHLAFSGFPILGDRKYAPPVPASAAPRPL----LHAREVVLPEDPALE 280

Query: 304 RLQ---ITAPLPAHMVKTWDSLGFKY 326
            L     TAPLP  M       G +Y
Sbjct: 281 DLAGRGFTAPLPEDMAGVLRRRGIRY 306


>gi|116511223|ref|YP_808439.1| pseudouridylate synthase, 23S RNA-specific [Lactococcus lactis
           subsp. cremoris SK11]
 gi|116106877|gb|ABJ72017.1| Pseudouridylate synthase, 23S RNA-specific [Lactococcus lactis
           subsp. cremoris SK11]
          Length = 293

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 62/297 (20%), Positives = 118/297 (39%), Gaps = 32/297 (10%)

Query: 31  HINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            I+   L K+    G++ V+         ++ G +V I               + D   N
Sbjct: 22  GISRRLLTKVKFDGGKIMVNGIEKTAIYHLEKGDLVTIT--------------VPDEPDN 67

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKP 144
                D +   +L+ED    V  KPAG +           ++  + G++ S  +   Q  
Sbjct: 68  EKLIPDDVPLNVLFEDDHYLVVEKPAGKASITGSLHPTGAMSNAVKGYI-SRKNYPNQTV 126

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            +  RLD++TSGI+ +A+ R A   + +      ++K Y++++          I   + +
Sbjct: 127 HIITRLDRDTSGIMFLAKHRYAHALMVQHKFRETLEKRYYAIINDGDLPDSGQIDLPIGR 186

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +     +      +  K    A++ + V +        L++  HTGRTHQ+RVH  H+G 
Sbjct: 187 RDDSIIERQVRFDEKSKN---ALTSYVVTERKND-LALLDIILHTGRTHQIRVHFSHLGY 242

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWD 320
           P+VGD  Y  N        + ++  LH  ++   +P    +  +   +P  M     
Sbjct: 243 PLVGDDLYGENHD------LISRQALHCHHLQFLNPFTDEMVHVELDMPDDMKNLLK 293


>gi|168698081|ref|ZP_02730358.1| ribosomal large subunit pseudouridine synthase D [Gemmata
           obscuriglobus UQM 2246]
          Length = 324

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 76/335 (22%), Positives = 130/335 (38%), Gaps = 43/335 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIP 68
             V   E    L +  +      ++ +++K++ + +V+V         R ++  +VV + 
Sbjct: 8   FTVTPQEVGFTLAKVLRARLGGPSWTDVRKLIAARRVKVGDSVCSDEARRLKEDEVVVL- 66

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGG---- 122
                          L+    L + +   + ++ + D  + V  KPAG++          
Sbjct: 67  ---------------LEHPKPLPRAAHPERLVVRHLDEHVVVVEKPAGVNTVRHPAELEW 111

Query: 123 SGIAYHIDGFLKSWVD-----------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           S     +D  L+                   + R+ HRLD+ETSG++V AR+  A + L 
Sbjct: 112 SEERRELDPTLQDLTQWAVGRQLNRDARDLPRLRIVHRLDKETSGLVVFARSALAERELG 171

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             FR   + + Y ++V GI   +   I + L+     G      +         A++H  
Sbjct: 172 MQFRKHTVVRRYLTVVPGILGTQ--TIKSNLVPDRGDGRRGSTKLPGV---GKEAVTHVT 226

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLY 289
             +     +  L  +  TGRTHQ+R+H    G P+ GD  YC    G          +L 
Sbjct: 227 PEERLP-GYTLLSCRLETGRTHQIRIHLSEAGHPVCGDKVYCKKANGEVFDDRSGAPRLA 285

Query: 290 LHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
           LHA  +   HP   G L  T PLP  + K  D L 
Sbjct: 286 LHATELGFEHPATSGHLHWTMPLPLDLAKFADRLR 320


>gi|114769616|ref|ZP_01447226.1| ribosomal large subunit pseudouridine synthase A [alpha
           proteobacterium HTCC2255]
 gi|114549321|gb|EAU52203.1| ribosomal large subunit pseudouridine synthase A [alpha
           proteobacterium HTCC2255]
          Length = 217

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 65/225 (28%), Positives = 109/225 (48%), Gaps = 12/225 (5%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
                       +LY D  + V NKP+G+    G  + +H    L+  V  +     L H
Sbjct: 3   PFVYEPPKTPLDILYIDEDVLVVNKPSGLLTVPGKELKHHDS--LELRVKIEYPNSFLVH 60

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD +TSG+++ A +++  + L   F  R ++K+Y + V+G  K     I   L+    +
Sbjct: 61  RLDMDTSGVIIFAFSKSTQRSLNLQFEKRIVKKLYEARVFGNIKEDNGFIDLPLI----V 116

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 + K + K    A++H++V+D        + + P TGRTHQLRVH + +G  I+G
Sbjct: 117 DWPNRPLQKIDAKEGKSALTHWQVLDREGD-VTRVALMPETGRTHQLRVHMMSLGHTILG 175

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
           D  Y    + N  + +Q    LHA+ + + HP+ G ++   APLP
Sbjct: 176 DRFYGNVAEINLANELQ----LHAKDLMIIHPKNGKKITFKAPLP 216


>gi|327483626|gb|AEA78033.1| tRNA pseudouridine synthase C tRNA Psi65 [Vibrio cholerae
           LMA3894-4]
          Length = 244

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 98/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASDVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAVTAYRPLAKVELPIATGKFNTTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 239


>gi|224024462|ref|ZP_03642828.1| hypothetical protein BACCOPRO_01187 [Bacteroides coprophilus DSM
           18228]
 gi|224017684|gb|EEF75696.1| hypothetical protein BACCOPRO_01187 [Bacteroides coprophilus DSM
           18228]
          Length = 547

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 74/250 (29%), Positives = 110/250 (44%), Gaps = 22/250 (8%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I      L H++   ++  + +   +H D     ++YED  I V NKPAG+    G    
Sbjct: 313 IGKCAPILKHMLIGLEVDPNPLVENRHHDT-PLEIIYEDPWIVVVNKPAGMLSVPGKNGL 371

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L+         P L HRLD +TSG+L+ A+ +   Q L   F  R+I+K Y +L
Sbjct: 372 DSVLQRLQELYPESD-SPLLVHRLDMDTSGLLLAAKDKNIHQCLQALFETRQIRKRYTAL 430

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           + G P+  +  I   L              + N +    A++ F+V +        +   
Sbjct: 431 LQGNPRQDEGTIDLPLC----PDFSDRPRQQVNWELGKKAVTRFRVEERSG-GTTRVSFW 485

Query: 247 PHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           P TGRTHQLRVHA H   +  PI+GD  Y             ++LYLHA  ++  HP  G
Sbjct: 486 PLTGRTHQLRVHAAHPEGLDSPILGDPLYGNQ---------ADRLYLHAAELEFTHPVTG 536

Query: 304 ---RLQITAP 310
              RL   AP
Sbjct: 537 ETIRLCKEAP 546


>gi|197248998|ref|YP_002147874.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197212701|gb|ACH50098.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
          Length = 260

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 105/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +       +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLIIQAGLDETWMQALTQFGWR 237


>gi|300928645|ref|ZP_07144164.1| pseudouridine synthase A [Escherichia coli MS 187-1]
 gi|300463314|gb|EFK26807.1| pseudouridine synthase A [Escherichia coli MS 187-1]
          Length = 219

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
                F       +  +L LHA  + + HP  G  +   A  PA  
Sbjct: 180 F----FASPEARAMAPRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|260773303|ref|ZP_05882219.1| tRNA pseudouridine synthase C [Vibrio metschnikovii CIP 69.14]
 gi|260612442|gb|EEX37645.1| tRNA pseudouridine synthase C [Vibrio metschnikovii CIP 69.14]
          Length = 246

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 99/241 (41%), Gaps = 17/241 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IIYQDPYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  L   F  ++++K Y ++V G  +           +   I   +     Q +
Sbjct: 64  ALSSEVASILMPMFASQQMEKTYHAVVRGWIEQAGVLDYPLKQELDKIADKFA----QQD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    AI+ ++ +               ++  +E++P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEPQSAITAYQPLANVEVPFSTGKFATTRYSLMELKPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   ++  + A       + + +  +   
Sbjct: 180 THGDGKHNRLYREQYQVQRLMLHASQLSFIHPYTEQMVTLNAGFDDDWQRLFSAFSWPDP 239

Query: 328 R 328
           +
Sbjct: 240 Q 240


>gi|254303628|ref|ZP_04970986.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148323820|gb|EDK89070.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 288

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 70/320 (21%), Positives = 135/320 (42%), Gaps = 38/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +VE++ +   +  + K    + +       LR+ ++ ++ KR           +  
Sbjct: 1   MKKYIVEHEYDGYEIGTYLKETKGYSSRG-----LRNLEIYLNGKR-----------IKN 44

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
               I  LN I+    I++   +    +  +   + YED  + + NK   I V      +
Sbjct: 45  NAKKIKKLNRIV----IIEKEKSTGIKAMDIPIDIAYEDENLLIVNKEPYIIVHPTQKKV 100

Query: 126 AYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +   + ++ +    K   PR  +RLD  TSG++++A+       L +      ++K 
Sbjct: 101 DKTLANAVVNYFEKTLGKTLVPRFYNRLDMNTSGLIIIAKNSYTQAFLQDKT---EVKKT 157

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFC 241
           Y  +V GI +     I   + K   IG D   +    E G   A +H KV++  + +   
Sbjct: 158 YKVIVSGIIEEDDFFIEKPIGK---IGDDLRRIELSEENGGKSAKTHIKVLERNYEKNIT 214

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +LE + +TGRTHQ+R H   +G  +VGD  Y  N +      +  +  LHA  ++  +P+
Sbjct: 215 FLEARLYTGRTHQIRAHLSLIGHSLVGDELYGGNME------LAKRQMLHAYKLEFQNPK 268

Query: 302 G-GRLQITAPLPAHMVKTWD 320
               L+I   +P  M +   
Sbjct: 269 TLENLKIEIDIPIDMKEVLK 288


>gi|87119949|ref|ZP_01075845.1| pseudouridine synthase Rlu family protein [Marinomonas sp. MED121]
 gi|86164651|gb|EAQ65920.1| pseudouridine synthase Rlu family protein [Marinomonas sp. MED121]
          Length = 244

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 105/235 (44%), Gaps = 17/235 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V NKP+G+ V      +   D  ++       +     HRLD+ TSG LV+
Sbjct: 8   ILYQDDYLVVINKPSGLLVHRTQLASQETDAVVQRLNAQLNKWVYPVHRLDRGTSGALVL 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A+ L E F   +++K Y  LV G     +  I   L K +   G     ++  E
Sbjct: 68  AFDANTAKLLAEQFSQSQVEKYYLCLVRGH-TESRGTIDYPLAKLNENKGKSRFKIEGTE 126

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H+K I+              + C +E++   GR HQ+R H  H+  P++GD 
Sbjct: 127 K---EAVTHYKKIEGFVLNQAVSKYDTTRCCLVEVKTEQGRKHQIRRHFKHIRFPLIGDT 183

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           +Y             ++ +L LHA+ +   HP  G +L   A LP    +T D L
Sbjct: 184 RYGCRHHNKLFRRLGLEQRLMLHAKTLAFKHPVTGHQLDCKASLPDGFKQTLDYL 238


>gi|116513066|ref|YP_811973.1| pseudouridylate synthase, 23S RNA-specific [Lactococcus lactis
           subsp. cremoris SK11]
 gi|116108720|gb|ABJ73860.1| Pseudouridylate synthase, 23S RNA-specific [Lactococcus lactis
           subsp. cremoris SK11]
          Length = 290

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 68/307 (22%), Positives = 121/307 (39%), Gaps = 34/307 (11%)

Query: 23  RWFKNHYPH---INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           +   +       +       +       V+ + +  N  + +G  V +       +++  
Sbjct: 14  QVLSDLLEKTWLVPRKQRHFLRMKKHALVNDQIIDENQLLHAGDKVTLIFDKEDFSNLS- 72

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                       K      + +LYED  + V NKP G+   G +     +   +++ ++ 
Sbjct: 73  -----------LKFGSASLADILYEDEHLIVVNKPEGMKTHGNTADEIALQNHVEAAIN- 120

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             Q   + HRLDQ TSG ++ A+ +     L + F   +I + Y +LV G    +   I 
Sbjct: 121 --QNVFVVHRLDQATSGAVLFAKNQFVLPILGKMFEENKIHREYLALVAGHFLEETFTIN 178

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + +  H     +       K    AI+H ++I  F  K   ++    TGRTHQ+RVH 
Sbjct: 179 QAIGQNRHEKNKRII-----SKHGQKAITHVQLIQNFTDK-SLVKCILDTGRTHQIRVHL 232

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             +  PI+GD  Y              +L LHA  + +PHP   + L I+AP P+     
Sbjct: 233 SSLAHPIIGDALYGQKSTL--------RLMLHAESIIIPHPFTNQLLNISAPSPS-FSNI 283

Query: 319 WDSLGFK 325
            + +  K
Sbjct: 284 LNKIKKK 290


>gi|317180509|dbj|BAJ58295.1| hypothetical protein HPF32_0713 [Helicobacter pylori F32]
          Length = 327

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 67/343 (19%), Positives = 139/343 (40%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                   +    K    L+  +++ED  + V NKP  + +     +
Sbjct: 59  TL--------------LTPKITPKPLKRGLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      +L+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVYLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L    PL   M++    +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLCFKVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|304396538|ref|ZP_07378419.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304356047|gb|EFM20413.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 217

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 105/229 (45%), Gaps = 13/229 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D+ I V NKP+G+    G  +  H D  + + +     +    
Sbjct: 1   MEPYNPPREPWLHILYQDAHIMVVNKPSGLLSVPGR-LDEHKDSVM-TRIQRDFPQAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R   K Y + +WG P+ ++  +   L+    
Sbjct: 59  HRLDMATSGVMVVALTKAAERELKRQFREREPSKTYVACIWGHPEKEEGLVDLPLICD-W 117

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  V  +N      A + ++V++  A     + ++P TGR+HQLRVH L +G PI+
Sbjct: 118 PNRPKQMVCFEN---GKAAQTEYQVLEYRADNSTRISLKPITGRSHQLRVHMLALGHPIL 174

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           GD+ Y              +L LHA  + + HP  G  +      PA  
Sbjct: 175 GDNFYAHPEAKAMA----PRLLLHAESLTITHPAFGNAMTFRQ--PADF 217


>gi|258624386|ref|ZP_05719334.1| tRNA pseudouridine synthase C [Vibrio mimicus VM603]
 gi|258583348|gb|EEW08149.1| tRNA pseudouridine synthase C [Vibrio mimicus VM603]
          Length = 244

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 97/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEADVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAITAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFVHPYTQQPLVIRAGLDEVWQGLLSEFGWQEP 239


>gi|218710322|ref|YP_002417943.1| tRNA pseudouridine synthase C [Vibrio splendidus LGP32]
 gi|218323341|emb|CAV19518.1| tRNA pseudouridine synthase C [Vibrio splendidus LGP32]
          Length = 252

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 63/251 (25%), Positives = 106/251 (42%), Gaps = 19/251 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 7   IIYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    +QK Y ++V G  +          ++   I   +     + +
Sbjct: 67  ALSSEVASEVMPMFANHEMQKTYHAIVRGWIEEGDTLDYALKVELDKIADKFA----KED 122

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++C +EM P TGR HQLR H  H+  PIVGD 
Sbjct: 123 KEPQEAVTVYEPLAKVEVPYSTGRFPTSRYCLVEMMPKTGRKHQLRRHMAHLRHPIVGDT 182

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
            +               ++L LHA  +   HP     L + A L    ++ +++  F++D
Sbjct: 183 SHGDGKHNRLFRDDLDSHRLLLHASELSFIHPFTKEELVMKANLDETWLRLFET--FEWD 240

Query: 328 RNLYIKRLYSQ 338
            NL   +  S 
Sbjct: 241 ANLIGAKACSS 251


>gi|311029948|ref|ZP_07708038.1| pseudouridylate synthase [Bacillus sp. m3-13]
          Length = 204

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 89/210 (42%), Gaps = 21/210 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT    + ++  ++N R+D+         +   +Q+ ++ GQ+ V+ ++ K N +   G 
Sbjct: 1   MTETMTIQIDESQKNDRIDKVLSTQNEEWSRSQVQQWIKEGQILVNGEKTKPNYKCSVGD 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  NITVT---------------IPEPEALDVVPEEMDLDIYYEDADVIVVNKPRGMVVHPAV 105

Query: 124 G--IAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++G +    D  G     +P + HR+D++TSG+L+VA+   A + L      +
Sbjct: 106 GHVTGTLVNGLMAHCNDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDFAHEKLVNQLVAK 165

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
            + + Y ++V G+  +    +   + +   
Sbjct: 166 TVTRKYQAIVHGVIAHDVGTVDAPIGRDKK 195


>gi|328724994|ref|XP_001952731.2| PREDICTED: hypothetical protein LOC100168337, partial
           [Acyrthosiphon pisum]
          Length = 1131

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 50/229 (21%), Positives = 99/229 (43%), Gaps = 26/229 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           ++ +   +E  +R+D+   +  P  +   +Q  ++ G V V+ K +K N + +   V+  
Sbjct: 477 EFKIETENEIGVRIDKLLPDLNPDWSRNQIQDWIKLGLVEVNGKVIKANYKTKLNDVI-- 534

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--I 125
                A   +I+E  I+         ++ L   + YED  + V  KP G+ V    G   
Sbjct: 535 ----VATEKVIEEVDIV---------AEDLGIEVYYEDKDVAVVYKPKGMVVHPAPGHYT 581

Query: 126 AYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
              ++G +    D  G     +P + HR+D++TSG+L++A+   A + L E    + + +
Sbjct: 582 GTLVNGLMYVIKDLSGINGEIRPGIVHRIDKDTSGLLMIAKNDIAHRGLVEQLVDKTVTR 641

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            Y +LV G   ++   I   + +      +   V          A++HF
Sbjct: 642 EYTALVHGNIPHEFGTIEAPIGRNPKERQEMAIV-----DDGKEAVTHF 685


>gi|237736082|ref|ZP_04566563.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           mortiferum ATCC 9817]
 gi|229421793|gb|EEO36840.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           mortiferum ATCC 9817]
          Length = 289

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 75/320 (23%), Positives = 132/320 (41%), Gaps = 38/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++E + +   +  + K    +         LR+ ++ ++ KRVK N++        
Sbjct: 2   MKKYIIEPEYDGYEIGTYLKETKGYSGRG-----LRNLEIYLNGKRVKNNSK-------- 48

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
               +  LN +   +K  ++ +        +   + YED  + + NK   I V       
Sbjct: 49  ---KVRKLNRLHIREKEKETGIK----PMDIPIKIAYEDKNLLLINKDPYIIVHPTQKKV 101

Query: 125 IAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +G +  ++ + G    PR  +RLD  TSGI++V +   A  +L E      + K 
Sbjct: 102 DKTLANGVVNYFLKTTGKVMVPRFYNRLDMNTSGIIIVTKNAYAQSYLQE---KGIVNKF 158

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFC 241
           Y ++V GI +  +  I   + K   IG +   V  Q E G   A +  KV+  F +    
Sbjct: 159 YQAIVLGIVEKDEFLIDRPIGK---IGDELRRVELQPEDGGQIAQTKVKVLKRFQEKNLT 215

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E +  TGRTHQ+R H    G P++GD  Y             ++  LH+   +    E
Sbjct: 216 LIEAELLTGRTHQIRAHMALEGYPLLGDELYGG------ADNRADRQMLHSYKTEFSDVE 269

Query: 302 GGRLQ-ITAPLPAHMVKTWD 320
            G L+ I   LP  M K  +
Sbjct: 270 TGDLKSIEVELPEDMKKLLE 289


>gi|148653020|ref|YP_001280113.1| pseudouridine synthase [Psychrobacter sp. PRwf-1]
 gi|148572104|gb|ABQ94163.1| tRNA pseudouridine synthase C [Psychrobacter sp. PRwf-1]
          Length = 256

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 105/241 (43%), Gaps = 18/241 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  ++YED  +   NK AG+ V             ++   D+ G      HRLD+ TSG+
Sbjct: 14  KIDIIYEDEHLVAINKEAGLLVHRSWLDKGETRFAMQLTRDAVGCHVFPVHRLDRPTSGV 73

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A++ A A+ LTE+F  R++ K Y ++V G    +         K   I   + ++  
Sbjct: 74  LLFAKSAAVARSLTEAFTERKVTKRYLAVVRGFMTEQGSVDYALSFKPDAIADKFANL-- 131

Query: 218 QNEKGANYAISHFKVI-----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             +K A  A++H++ +                ++  + + P TGR HQLR H  H+   I
Sbjct: 132 --DKPAQEAVTHWQSLAQIELPFAVSKKHDTSRYSLMRLIPETGRKHQLRRHMRHLFHHI 189

Query: 267 VGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD  Y       F     +  ++ LHA+ + L HP  G  L + A       +  ++  
Sbjct: 190 IGDTSYGDGRHNKFFRTQYDCTRMLLHAQTLSLTHPVTGEPLMLEAGFDDQWTRILEAFS 249

Query: 324 F 324
           +
Sbjct: 250 W 250


>gi|195977301|ref|YP_002122545.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
 gi|195974006|gb|ACG61532.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
          Length = 297

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 111/269 (41%), Gaps = 29/269 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              V V+ + + + + ++ G  +++            ++   D  + + K +       L
Sbjct: 45  KKHVWVNDELINWQSPVKQGDHIKLQFD---------QEDYPDKGILMGKPA---LVDCL 92

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP G+      G        L       G+   + HRLD ETSG ++ A+
Sbjct: 93  YQDEHLIIVNKPEGMKTH---GNEPTELALLNHVSAYTGKTCYVVHRLDMETSGAILFAK 149

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      R I++ YW+L+ G  + +     + + +  H     V     + K 
Sbjct: 150 NPFILPILNRLLERRDIKRDYWALIEGQLEQQTVTYRDPIGRHRHDRRKRV----VDSKH 205

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              AI+H  ++  F Q  C +  +  TGRTHQ+RVH  H   P++GD  Y          
Sbjct: 206 GQEAITHLALLQAFDQ-TCLVNCRLETGRTHQIRVHLAHHKHPLIGDPLYSRQKAE---- 260

Query: 283 PIQNKLYLHARYMDLPHPEGGRL-QITAP 310
               +L LHA  + L HP    + ++TAP
Sbjct: 261 ----RLMLHAHQLTLRHPLTQEMIRVTAP 285


>gi|315645744|ref|ZP_07898868.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
 gi|315279222|gb|EFU42532.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
          Length = 300

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 108/230 (46%), Gaps = 17/230 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-DGFLKSWVDSKGQK--PRLTHR 149
              + +  +L+ED    V NKPAG++V           +  + ++ +++G     R  HR
Sbjct: 76  KPRWQELHVLHEDEFCLVVNKPAGMAVHPDQESEETTLNHVVAAYYEAEGIHTAVRHIHR 135

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++T+G ++ A+   A   L E+ R ++I +IY ++V G    + + I   + K     
Sbjct: 136 LDKDTTGPVLYAKNEYAQLKLDEAMREKKIVRIYAAIVQGRVGQELKVIDLPIGKDR--- 192

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             Y    ++       AI+H    + + +    L +   TGRTHQ+RVH  HMG P++GD
Sbjct: 193 --YHSSRRRVSLTGQAAITHILSSEVYPR-ASLLNISLETGRTHQIRVHLSHMGHPLLGD 249

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKT 318
             Y           + ++  LH   +   HP  G R+++ AP P  M++ 
Sbjct: 250 SLYGGPA-------LFSRQALHGERLLFHHPLTGERVEVQAPWPQDMMEL 292


>gi|157147524|ref|YP_001454843.1| 23S rRNA/tRNA pseudouridine synthase A [Citrobacter koseri ATCC
           BAA-895]
 gi|157084729|gb|ABV14407.1| hypothetical protein CKO_03324 [Citrobacter koseri ATCC BAA-895]
          Length = 219

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 70/222 (31%), Positives = 108/222 (48%), Gaps = 15/222 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  I+LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLIILYQDEHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPAPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V+D  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTGYEVVDFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
            Y +         +  +L LHA  + + HP  G  +   AP+
Sbjct: 180 FYASPE----ALAMAPRLLLHAETLTITHPAYGNSMTFKAPV 217


>gi|271499489|ref|YP_003332514.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270343044|gb|ACZ75809.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 261

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 101/238 (42%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IVYQDEHLIAVNKPSGWLVHRSWLDRKEKVVVMQTVRDQIGQHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L + F   +++K+Y ++V G   +          +   I   Y       +
Sbjct: 64  ALSSDVARLLAQQFEQHQMEKMYHAVVRGYVMDDGVIDYALTEELDRIADKYA----DPD 119

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A+SH++V+               ++  LE+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVSHYRVLAHAELPVAIGRYDTARYSLLELTPKTGRKHQLRRHMAHLRHPIIGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +      +G        +L LHA  + L HP     L ITA             G++
Sbjct: 180 THGDLRQNRGMAAHFGCARLMLHASQLSLIHPVTNEPLVITARWDEAWQGVMTQFGWQ 237


>gi|149196356|ref|ZP_01873411.1| ribosomal large subunit pseudouridine synthase C [Lentisphaera
           araneosa HTCC2155]
 gi|149140617|gb|EDM29015.1| ribosomal large subunit pseudouridine synthase C [Lentisphaera
           araneosa HTCC2155]
          Length = 328

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 70/336 (20%), Positives = 135/336 (40%), Gaps = 41/336 (12%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQ 60
            ++  V+  +    E +  LD +    + + +  + Q+ L  G  +++ K+V  +N  ++
Sbjct: 14  EMLRVVRKKITPETEGHGVLD-FLCTKFTYRSREDWQEALLDGSSQINGKQVEDYNAILK 72

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G V+ +              KI +  ++           ++YED  I +  K   + V 
Sbjct: 73  AGDVISLDVT-----------KIPEPDIDRDFK-------VVYEDDDILMVEKTGDLPVH 114

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                       L   +  +     + +RLD+ETSG++++AR   AA  L + F  R++ 
Sbjct: 115 PAGSF---FKNTLWYMLVKQFGNVHIMNRLDRETSGLVLIARHHKAASVLGKQFERRQVG 171

Query: 181 KIYWSLVWGIPKNKKECIANW--LLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCF 236
           K Y  LV G+    +     +      S I   +     ++ +  G + A + F V+   
Sbjct: 172 KEYDVLVEGLVSWDQYDALGYMGPAVSSKIRKKFSFTEAEDWQDYGKHSARTEFSVL-RR 230

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------------GNFTSPI 284
           + +   L  + HTGRTHQ+R   L +G P+VGD  Y  + +             ++    
Sbjct: 231 SHELSHLHCRLHTGRTHQIRATLLSLGFPLVGDKIYGLDEQFFLSFIDGALTEQDYQKMR 290

Query: 285 QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
             +  LH   M   HP  G  +   + LP  + +  
Sbjct: 291 LRRQALHCSLMSFTHPMSGEDVVFESSLPKELAELI 326


>gi|298386878|ref|ZP_06996433.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 1_1_14]
 gi|298260552|gb|EFI03421.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 1_1_14]
          Length = 223

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 69/229 (30%), Positives = 113/229 (49%), Gaps = 15/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQ        +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQADKTGDTPLSETVKQYLKEKYHKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR   ++K YW++V   PK  +  + ++L +       + + 
Sbjct: 63  GLVIFAKTSKALTRLNEMFRTSEVKKTYWAVVKNAPKEPEGELVHYLARNEKQNKSFAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI ++++I   ++ +  LE+   TGR HQ+R     MGCPI GD KY A 
Sbjct: 122 -DKEVPNSKKAILNYRLIG-HSENYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGAP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA-HMVKTWDSL 322
                 S     + LHAR +   HP     +++ APLP  ++ K ++ L
Sbjct: 180 RSNPDGS-----ICLHARKVRFIHPVSKELIELEAPLPEGNLWKGFELL 223


>gi|326560902|gb|EGE11267.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 7169]
 gi|326566534|gb|EGE16680.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 12P80B1]
 gi|326569801|gb|EGE19851.1| tRNA pseudouridine synthase C [Moraxella catarrhalis BC8]
          Length = 254

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 99/239 (41%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + + NKPA + V       +     +++  +   Q     HRLD+ TSG+LV 
Sbjct: 15  ILYQDACMVIINKPANMLVHRSWLDKHETCFVVQTLRNQINQHVYPVHRLDRPTSGVLVF 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  L + F    IQK Y ++V GI       I   L  +     D         
Sbjct: 75  ALDSQTAGLLAKQFENHHIQKSYLAVVRGIIGT--GRIDYALKPRLDKIADKF---SNPN 129

Query: 221 KGANYAISHFKVIDCFAQ-----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           K +  AI+ ++V+    Q           ++  + + P TGR HQLR H  H+  PIVGD
Sbjct: 130 KASKSAITDYQVLATTQQPFISCRCFDSSRYSLVRLTPITGRKHQLRRHMKHIFHPIVGD 189

Query: 270 HKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
             Y    +           +L LHA  +   HP    + +I APL     +   + G+ 
Sbjct: 190 TTYGDKVQNRAVLAHIGVKRLLLHAHQLQFCHPLYDEMIRIVAPLDTAFCQVMTAFGWS 248


>gi|261253959|ref|ZP_05946532.1| ribosomal large subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
 gi|260937350|gb|EEX93339.1| ribosomal large subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
          Length = 245

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 111/234 (47%), Gaps = 12/234 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   +++ED  I V NKP+G+    G  +A H D      V+S     ++ HRLD 
Sbjct: 8   PPRDPWVDIVFEDQHILVANKPSGLLSVPGR-LAEHYDSMWSRLVES-YPDIQVVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+++ A+ + A + L + F+ R   K+Y++ VWG P+ +   +   L+         
Sbjct: 66  DTSGLMLFAKHKEAERSLKKQFQYRLTHKVYYARVWGHPEQQSGQVDLPLIAD-WPNRPK 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             V  Q+      + + ++V+    +K   + + P TGR+HQLRVH   +G PIVGD  Y
Sbjct: 125 QKVCYQD---GKPSQTLYQVVK-QEEKTAIVRLLPITGRSHQLRVHMQALGHPIVGDEFY 180

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                  F+     +L LHA  +   HP+   LQ T  +P       DS+ F Y
Sbjct: 181 SEGEAFEFSV----RLELHAAELSFYHPDSELLQ-TIFVPCDFYLEADSVIFNY 229


>gi|313893624|ref|ZP_07827192.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313441768|gb|EFR60192.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 322

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 75/355 (21%), Positives = 133/355 (37%), Gaps = 68/355 (19%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M   T +  ++V++D     ++   K    HI+    +++   G + V+ +   +N  + 
Sbjct: 1   MKTATIID-LIVDSDVHTQSMNHIIKQQ--HISQRMRRRLRNEGIITVNDEPATWNTLVH 57

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +         +  EQ+   S ++L          ++YED  I V NK AG+ + 
Sbjct: 58  GGDHLVM--------KLTPEQEFSLSPMDLD---------IVYEDEHILVINKAAGVLMH 100

Query: 121 GGSGIAYHI--DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             S +  H   +G L  + ++ +       HRLD++TSGI+++A+T        +     
Sbjct: 101 PTSTVRDHTLANGVLYYYQETHQHYDFHPVHRLDKDTSGIVIIAKTSVVQHAFDKKHTH- 159

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI---- 233
              K Y ++V G        I   + +K    G  +     NE     A +   VI    
Sbjct: 160 -FYKTYDAIVEGKLPAVPLTINWPIGRKP---GSIIERCCTNE--GKPARTDITVISHNS 213

Query: 234 ---------------------------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                                      +     F  ++   HTGRTHQ+RVH   +G P+
Sbjct: 214 INSSNTIVYGSPISDSNTIIGSNNMADENCETHFTHVQCLLHTGRTHQIRVHVSQLGYPL 273

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
            GD  Y  +           +  LHA  +   HP     L+++A +P  M     
Sbjct: 274 AGDDLYGGHLD------YIQRQALHAARVSFHHPMTNEWLELSADMPQDMKDLIQ 322


>gi|148549194|ref|YP_001269296.1| pseudouridine synthase [Pseudomonas putida F1]
 gi|148513252|gb|ABQ80112.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           putida F1]
          Length = 211

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 65/215 (30%), Positives = 102/215 (47%), Gaps = 11/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L+ED+ I V NKP  +    G     + D  +    ++      + HRLD ETSGI+
Sbjct: 6   VQILFEDAAILVINKPTLLLSVPGRA-EDNKDCLITRLQENGYPDALIVHRLDWETSGII 64

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR   + + L+  F  R  +K Y +L WG P      I   L           HVV  
Sbjct: 65  LLARDADSHRELSRQFHDRETEKAYTALCWGQPALDSGSIDLPLRYDPPT--KPRHVV-- 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +   +A++ +++++     +C +E+ P TGR+HQLRVH L +G P++GD  Y      
Sbjct: 121 DHEQGKHALTFWRIVERCGD-YCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY----AN 175

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                   +L LHA  +   HP  G RL+   P P
Sbjct: 176 PQALAAHERLCLHASMLSFTHPVSGQRLKFECPAP 210


>gi|162448280|ref|YP_001610647.1| ribosomal large subunit pseudouridine synthase D [Sorangium
           cellulosum 'So ce 56']
 gi|161158862|emb|CAN90167.1| ribosomal large subunit pseudouridine synthase D [Sorangium
           cellulosum 'So ce 56']
          Length = 356

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 70/317 (22%), Positives = 132/317 (41%), Gaps = 40/317 (12%)

Query: 27  NHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILD 85
                +++ + ++++ +G+V V          R+  G+++ I         + + +    
Sbjct: 52  RALAEVSWSDARRLIETGKVLVGSAVATSARRRVLGGELIEIRLHAPRPETVRRRK---- 107

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG---------GSGIAYHIDGFLKSW 136
                         +++Y D+ + V NKPAG+S             + +   +   L   
Sbjct: 108 ----------LEGELVVYADASVVVVNKPAGVSTIPYGDEAPAEQAATLDALVREVLARR 157

Query: 137 VDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              +G+ P  +  RLD+ TSG+LV ART AA +HL +  R+R + + Y +L  G     +
Sbjct: 158 DRLRGRAPLGVVQRLDKGTSGLLVFARTLAAKKHLAQQLRVRAMHRQYLALAHGAVP--R 215

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--------CFAQKFCWLEMQP 247
               ++L++    G       +   +    A++H + I+          A     +  + 
Sbjct: 216 GTYRSYLVEDRGDG--LRGSARDGRREGQLAVTHVEPIEVLRGPQEGAGAGGVTLVACRL 273

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+R+H    G P+VG+  Y  +++G  T     +L LHA  +   HP   R ++
Sbjct: 274 ETGRTHQIRIHLAEAGHPLVGETVYVRDYRG--TKVPAARLMLHAAELGFDHPADDRPMR 331

Query: 307 ITAPLPAHMVKTWDSLG 323
             AP P       + L 
Sbjct: 332 FQAPPPPDFDDVLERLR 348


>gi|156935424|ref|YP_001439340.1| 23S rRNA/tRNA pseudouridine synthase A [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156533678|gb|ABU78504.1| hypothetical protein ESA_03282 [Cronobacter sakazakii ATCC BAA-894]
          Length = 218

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 111/231 (48%), Gaps = 17/231 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++          ++LY+D  I V NKP+G+    G  +  H D  + + +     K    
Sbjct: 2   LDAYNPPQDPWLLILYQDEHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDFPKAESV 59

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++ VA T+AA + L   FR R  +K Y + VWG P+N +  +   L+    
Sbjct: 60  HRLDMATSGVIAVALTKAAERELKRQFREREPKKHYVARVWGHPENAQGVVDLPLI---- 115

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V++        + ++P TGR+HQLRVH + +G P
Sbjct: 116 --CDWPNRPKQKVCYETGKAAQTEYEVLEYADDNTARVLLRPITGRSHQLRVHMMALGHP 173

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           I+GD  Y A       +P   +L LHA  + + HP  G  +   A  PA  
Sbjct: 174 ILGDKFY-ATPDAFARAP---RLLLHAEQLTITHPAYGTPMTFRA--PADF 218


>gi|99079913|ref|YP_612067.1| ribosomal large subunit pseudouridine synthase A [Ruegeria sp.
           TM1040]
 gi|99036193|gb|ABF62805.1| ribosomal large subunit pseudouridine synthase A [Ruegeria sp.
           TM1040]
          Length = 217

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 64/227 (28%), Positives = 108/227 (47%), Gaps = 15/227 (6%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +V+           +L+ D+++ V NKPAG+    G G   H+   L + + +   +  L
Sbjct: 2   TVSSEYCPPSDPLDILHHDAQLLVVNKPAGLLSVPGKG--AHLADCLIARIQAAFPEALL 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG++V A T  A +HL   F  R  +K Y + + G  + +   +   L+   
Sbjct: 60  VHRLDRDTSGVMVFAMTPHAQRHLGLQFEKRMTKKAYVARLTGRLEPRSGTVDLPLIVD- 118

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                   + K   +    A + +KVI  + +    + + P TGR+HQLRVH   +G PI
Sbjct: 119 ---WPNRPLQKVCHETGKPAHTDWKVI-SYGENETRVRLSPKTGRSHQLRVHMQSLGHPI 174

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
           +GD  Y +            ++ LH+  + L HPEGG   + ++ AP
Sbjct: 175 LGDPLYASGAALEHP-----RMMLHSEELRLKHPEGGASQKFRVKAP 216


>gi|119775332|ref|YP_928072.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119767832|gb|ABM00403.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
          Length = 224

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 63/224 (28%), Positives = 99/224 (44%), Gaps = 10/224 (4%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        + Y D  + + NKP+G+      G+A H      + +     +  L HRLD
Sbjct: 7   RPPAVPWLDIRYIDRDLIIINKPSGLLSNP--GMAAHTHDSAITRLCRLYPEAILVHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V AR++ A  +L   F+ R  +K Y + V GI +  +  I   L K       
Sbjct: 65  CATSGIMVFARSKKAESNLKTQFQNRDTEKRYLAQVAGIIEQDEGTIDLPLGKD----RS 120

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                K +      A++H++V+    +    + ++P TGRTHQLRVH L +G PI+GD  
Sbjct: 121 NPPWQKVDMAEGRPAVTHYRVLARR-ENSTLVALEPETGRTHQLRVHMLSLGHPILGDDF 179

Query: 272 YCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y     F          +L LHA  +   HP   + +   +  P
Sbjct: 180 YGRTQEFGQGTVEEASPRLCLHAERLSFKHPWSNKPMTFVSRAP 223


>gi|300813392|ref|ZP_07093743.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
 gi|300512535|gb|EFK39684.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
          Length = 316

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 62/303 (20%), Positives = 123/303 (40%), Gaps = 37/303 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ V++  ++ + RLDR+ K ++       + K LR   ++VD K+    + I+ GQ + 
Sbjct: 1   MRKVIIGPNDSDQRLDRFLKKYFEKAPLSFIYKNLRKKNIKVDGKKASPEDLIKEGQEIS 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      +    K+         L ++S      +LYED  I +  KP  +         
Sbjct: 61  LFISDETIEKYKKD--------KLARNSQKFP-QILYEDDNICLMKKPLNMLTHNDKN-- 109

Query: 127 YHIDGFLKSWVD------------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           ++ D  +  ++D                +P + +RLD+ TSGIL+ A+     + + ++ 
Sbjct: 110 FYQDNMVDRFIDYLIFKEEYSPREENTFRPSICNRLDRNTSGILLGAKNAETLREINKAI 169

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + R + K Y ++V G  +   E      +K      + +            +++ F  + 
Sbjct: 170 KERLVDKFYLTIVKGKVQKPFEI----NIKLEKTDKNIMRKSCV----GKDSLTKFFPLI 221

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              + +  ++++  TGRTHQ+R      G  I+GD KY       F S       LH   
Sbjct: 222 SNGE-YSLIKVKLITGRTHQIRASLKEKGLYILGDRKYGKGKDKEFNS-----QALHNYL 275

Query: 295 MDL 297
           +  
Sbjct: 276 IKF 278


>gi|313896082|ref|ZP_07829636.1| pseudouridine synthase, RluA family [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312975507|gb|EFR40968.1| pseudouridine synthase, RluA family [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 297

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 61/319 (19%), Positives = 126/319 (39%), Gaps = 39/319 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSG 62
           MT +   +   +E   +   +       ++    ++I  SG    +    +     ++ G
Sbjct: 1   MTEIHISLPPGEEMPAK--AYLTKKC-GVSGGLWKRIKHSGTFSHNGVPAIAARTAVRDG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++                      +  +   + L   + YED  + + +KPAG+ V   
Sbjct: 58  DMLS-----------------YALPIVSSVVPEDLPLAIAYEDDDLLIIDKPAGMLVHPT 100

Query: 123 S-GIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
           +      I   ++    S+G        HRLD+ T+G+L++A+      + T+      +
Sbjct: 101 TQETRGTIANAVRGLYASRGDTLDFHPCHRLDRNTTGLLLIAKCPEVQYYFTKHRDA--V 158

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y +L+ G      + I   + +          ++++       A +H++ +    + 
Sbjct: 159 RREYLALIEGRLTPASDIIDAPIARALP-----SIILRRVAPEGKPARTHYETVASDGR- 212

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  L +   TGRTHQ+RVH  H+G P++GD  Y  N           +  LHA ++ L  
Sbjct: 213 YSLLRLTLETGRTHQIRVHLAHLGHPLLGDDLYGGNTDE------IARHALHAAWLSLRL 266

Query: 300 PEGGR-LQITAPLPAHMVK 317
           P  G  L + +PLP  + +
Sbjct: 267 PHTGELLTVASPLPKDIAR 285


>gi|113970985|ref|YP_734778.1| tRNA pseudouridine synthase C [Shewanella sp. MR-4]
 gi|113885669|gb|ABI39721.1| tRNA pseudouridine synthase C [Shewanella sp. MR-4]
          Length = 284

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 61/259 (23%), Positives = 105/259 (40%), Gaps = 17/259 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            +   + S +  +     +  +LY+D  +   +KPAG+ V             ++   D 
Sbjct: 11  PEDKYNPSESDEQSELAPELRVLYQDEHLVAIHKPAGLLVHRSYLARRERFFAMQLTRDL 70

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G      HRLD+ TSG+L+ A++   A  L E F    I+K Y +LV G          
Sbjct: 71  VGCHVFPVHRLDRPTSGVLLFAKSSEVANALCEQFANHSIEKQYLALVRGNMHESGILDY 130

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
              ++   +   + +     +K A  A++ ++ +               +F  +++ P T
Sbjct: 131 ALKVELDEVADKFANQ----DKAAQDAVTQYEPLLNTEIPYPSGRYATSRFALVKLSPKT 186

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQ 306
           GR HQLR H  H+  PI+GD  +    +  F       N+L+L A+ +   HP    RL 
Sbjct: 187 GRKHQLRRHMAHLRHPIIGDTTHGDGKQNAFFRAHFDINRLWLIAKKLTFTHPVTLERLS 246

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I   L       +  LG+ 
Sbjct: 247 IETELEPEWETVFAGLGWD 265


>gi|307129814|ref|YP_003881830.1| tRNA pseudouridine synthase [Dickeya dadantii 3937]
 gi|306527343|gb|ADM97273.1| tRNA pseudouridine synthase [Dickeya dadantii 3937]
          Length = 261

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 99/238 (41%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IVYQDEHLIAVNKPAGWLVHRSWLDRKEKVVVMQTVRDQIGQHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L + F   +++K Y ++V G              +   I   +       +
Sbjct: 64  ALSPEVARLLAQQFEQHQMEKTYHAVVRGYVMEDGVIDYALTEELDRIADKFA----DPD 119

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A+SH++V+               ++  L++ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVSHYRVLARAEMPVAIGRYDTARYSLLQLNPKTGRKHQLRRHMAHLRHPIIGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +      +G        +L LHA  + L HP     L I+A             G++
Sbjct: 180 THGDLRQNRGMAAHFDCARLMLHASCLSLTHPVTNEPLAISARWDEPWQGVMTKFGWQ 237


>gi|302880095|ref|YP_003848659.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
 gi|302582884|gb|ADL56895.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
          Length = 203

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 62/202 (30%), Positives = 91/202 (45%), Gaps = 14/202 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY D  + V NKPAG+    G G        L S V  K     + HRLD  TSG+LV A
Sbjct: 5   LYRDDWLLVVNKPAGLLSVPGRG--EDKQDCLSSRVQEKFPDALIVHRLDMATSGLLVFA 62

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R     + L+  F  R + K Y ++V G  +  +  I   +        +   + K +E 
Sbjct: 63  RGIEMQRQLSAMFHNREVSKRYVAIVAGKLQPDEGEINLSIGAD----WNERPLRKIDEA 118

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               +++ ++V+   A     +E++P TGRTHQLRVH   +G PI+GD  Y         
Sbjct: 119 TGKPSLTRYRVLSREAD-TTRVELEPVTGRTHQLRVHMRAIGHPILGDALYGEVASA--- 174

Query: 282 SPIQNKLYLHARYMDLPHPEGG 303
                +L LHA+ +   HP   
Sbjct: 175 ----PRLLLHAQSLSFVHPVSK 192


>gi|116513692|ref|YP_812598.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|116093007|gb|ABJ58160.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
          Length = 297

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 64/323 (19%), Positives = 128/323 (39%), Gaps = 42/323 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQVVRIP 68
           ++V  ++    L  +        +   +      G +  V+  R   + R++ G VV   
Sbjct: 1   MIVAKNDPGQ-LSHFLLK--KGFSRRAVNNCKNHGGMMLVNHHRRNGSYRLKEGDVV--- 54

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                  H +  Q+ ++  + +++        ++ E +   V NKPAG+        A  
Sbjct: 55  -------HFLMGQEPVNPWLKVSRR----PLDIVEETADYLVINKPAGLLSIPSGFHAED 103

Query: 129 ID-GFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                + ++ + +G      KP +  RLDQ+TSG++++ +   A    ++  +   I+K 
Sbjct: 104 AVINRVLAYFEKQGVNPAYVKPHIVTRLDQDTSGLVLLGKNAIAHDRFSKLGKDAFIKKY 163

Query: 183 YWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + ++V G          I   L +          V ++       A++ ++V++      
Sbjct: 164 H-AIVHGNFAEGDLSGLIDKPLARVGD------TVKREVNPKGQRALTEYRVLNQVP-GA 215

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E++  TGRTHQ+R+H   +G  + GD  Y A            +  L+  Y+  P+P
Sbjct: 216 SLVELRLLTGRTHQIRIHMASIGHVLYGDDLYGAR-------DAFARQALNCFYLAFPNP 268

Query: 301 -EGGRLQITAPLPAHMVKTWDSL 322
             G   +I  P P  M   W  L
Sbjct: 269 FSGEEREIEIPDPGDMQGLWRQL 291


>gi|288937176|ref|YP_003441235.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|288891885|gb|ADC60203.1| pseudouridine synthase [Klebsiella variicola At-22]
          Length = 219

 Score =  175 bits (444), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/228 (29%), Positives = 108/228 (47%), Gaps = 15/228 (6%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           ++           ++LY+D  I V NKP+G+    G  +  H D  + + +     +   
Sbjct: 2   AMENYNPPQDPWLVILYQDKHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDLPQAES 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  TSG++VVA  +AA + L   FR R  +K Y + VWG P+  +  +   L+   
Sbjct: 60  VHRLDMATSGVIVVALNKAAERELKRQFREREPKKQYVARVWGHPQPAEGLVDLPLI--- 116

Query: 207 HIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               D+ +  KQ    +    A + ++V++        + ++P TGR+HQLRVH L +G 
Sbjct: 117 ---CDWPNRPKQKVCYETGKAAQTEYEVLEYAEDNTARVRLKPITGRSHQLRVHMLALGH 173

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPL 311
           PI+GD  Y           I  +L LHA  + + HP  G  +   AP+
Sbjct: 174 PILGDRFY----ATPEALAIAPRLLLHAETLTITHPAYGNAMTFRAPV 217


>gi|320538536|ref|ZP_08038397.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
 gi|320144643|gb|EFW36398.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
          Length = 228

 Score =  175 bits (444), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 72/229 (31%), Positives = 116/229 (50%), Gaps = 22/229 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +L+E+  +++ NKPAGISVQGG+GI+  I   L+    +   K    HRLD+ETSG+
Sbjct: 8   EIPVLFENDSLFIINKPAGISVQGGAGISNCIIDILERQCAA---KLFPVHRLDKETSGV 64

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A+T  AA   ++  + + I K Y ++ +  P  ++  I   L +             
Sbjct: 65  LLIAKTSQAAAEYSKILQAKTIVKEYRAVCFYAPPKQRGSIRTPLRENG----------- 113

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--AN 275
                   A++ ++V+    +   +L +  HTGR HQ+R+H   +GCPI+ D KY     
Sbjct: 114 ----TEKTAVTDYRVLK-KTENHSYLSLALHTGRKHQIRIHLASLGCPIILDDKYGDFKQ 168

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
            K    +    K+ L A  + LP  +G   QI APLPAHM +  + L  
Sbjct: 169 NKALQKAFGIKKMQLSAYSLTLP-LDGKSRQIIAPLPAHMTEALEKLEL 216


>gi|323496130|ref|ZP_08101190.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           sinaloensis DSM 21326]
 gi|323318874|gb|EGA71825.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           sinaloensis DSM 21326]
          Length = 245

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 107/228 (46%), Gaps = 12/228 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED  I V NKP+G+    G  +A H D      V +     ++ HRLD +TSG++
Sbjct: 14  VDIVFEDEHILVANKPSGLLSVPGR-LAEHHDSLWSRLVAA-YPDIQVVHRLDMDTSGLM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+ + A + L + F+ R   K+Y++ VWG P   +  +   L+           V   
Sbjct: 72  LLAKHKEAERSLKKQFQYRLTHKVYYARVWGHPAQPQGEVDLPLICD-WPNRPRQKVCFV 130

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      + + ++V     +    + + P TGR+HQLRVH   +G PIVGD  Y      
Sbjct: 131 D---GKPSTTLYQVAKR-EEHTSIVRLLPITGRSHQLRVHMQMLGHPIVGDEFYSEGEAF 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
            F+    ++L LHA  +   HP    LQ +  +P       +++ F Y
Sbjct: 187 EFS----DRLALHAAELSFYHPASEVLQ-SVFVPCDFYLEAEAMIFNY 229


>gi|146319641|ref|YP_001199353.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           05ZYH33]
 gi|146321839|ref|YP_001201550.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           98HAH33]
 gi|253752639|ref|YP_003025780.1| RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|253754465|ref|YP_003027606.1| RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|253756398|ref|YP_003029538.1| RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|145690447|gb|ABP90953.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           05ZYH33]
 gi|145692645|gb|ABP93150.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           98HAH33]
 gi|251816928|emb|CAZ52577.1| RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|251818862|emb|CAZ56705.1| RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|251820711|emb|CAR47473.1| RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|292559258|gb|ADE32259.1| Pseudouridylate synthase [Streptococcus suis GZ1]
 gi|319759055|gb|ADV70997.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           JS14]
          Length = 288

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/268 (22%), Positives = 108/268 (40%), Gaps = 29/268 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
             QVRV+ + + +   I +G ++ +            E+ I     +L +         L
Sbjct: 37  KKQVRVNGELINWQCPITAGDLLELTFDQEDY----PEKSIPLGQADLVEE--------L 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG ++ A+
Sbjct: 85  YQDEHLIIVNKPEGMKTHGNDPTEIALLNHVSAYV---GQTCYVVHRLDMETSGAILFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      + I + Y +L  G  K     I + + +  H     V     + + 
Sbjct: 142 NPFILPILNRLLEDKVIYRDYLALCQGQLKMTDWTITDKIGRDRHDRRKRV----VDNRK 197

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++  +++    +    +  +  TGRTHQ+RVH  H G  ++GD  Y          
Sbjct: 198 GQTALTQVRLLKTLGKN-SLVSCRLQTGRTHQIRVHLAHHGHALIGDPLYSRVAP----- 251

Query: 283 PIQNKLYLHARYMDLPHPEG-GRLQITA 309
               +L LHA+ + L HP     + + A
Sbjct: 252 ---PRLMLHAQKLSLTHPLTLEEISVEA 276


>gi|77457919|ref|YP_347424.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens Pf0-1]
 gi|77381922|gb|ABA73435.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           fluorescens Pf0-1]
          Length = 211

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/215 (29%), Positives = 103/215 (47%), Gaps = 11/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++++D+ + V NKP  +    G       D  +    ++   + R+ HRLD ETSGI+
Sbjct: 6   VQIIHQDAAVLVVNKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGII 64

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR     + L+  F  R  +K Y +L WG P+     I   L           HVV  
Sbjct: 65  LLARDADTHRELSRQFHDRETEKAYTALCWGQPELDSGSIDLPLRYDPPT--KPRHVV-- 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +   +A++ ++V++     +C +E+ P TGR+HQLRVH L +G P++GD  Y      
Sbjct: 121 DHELGKHALTFWRVLERC-DDWCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHEQAL 179

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                   +L LHA  +   HP  G RL+   P P
Sbjct: 180 AAW----PRLCLHASMLSFTHPQSGERLRFECPAP 210


>gi|188534848|ref|YP_001908645.1| tRNA pseudouridine synthase C [Erwinia tasmaniensis Et1/99]
 gi|188029890|emb|CAO97774.1| tRNA pseudouridine synthase C [Erwinia tasmaniensis Et1/99]
          Length = 255

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 107/240 (44%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G+ V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDRWLVAVNKPSGMLVHRSWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F + ++QK Y ++V G     +        +   I   +     Q E
Sbjct: 64  ALSSDVARLLSQQFELHQLQKTYHAVVRGWLAGAETLDYPLTEELDKIADKF----SQPE 119

Query: 221 KGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++          V      ++  +EM P +GR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHWRGIATAELPVPVGRYETSRYSLVEMLPESGRKHQLRRHMTHLRHPIIGDS 179

Query: 271 KYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
            +      +    +   ++L LHA  + L HP     L + A L     K  +  G++  
Sbjct: 180 AHGDLKQNRSAAANFGMDRLMLHASELSLTHPVTSEPLILRAGLDEVWQKIINQFGWRAS 239


>gi|168230365|ref|ZP_02655423.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|194471112|ref|ZP_03077096.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194457476|gb|EDX46315.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|205334924|gb|EDZ21688.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
          Length = 219

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDEHIMVVNKPSGLLSVPGR-LEAHKDSIM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            Y +         +  +L LHA  + + HP  G  +     +PA  
Sbjct: 180 FYASPE----ALSLAPRLQLHAEMLTITHPTYGTSMTFK--VPADF 219


>gi|197123853|ref|YP_002135804.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196173702|gb|ACG74675.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 287

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 70/315 (22%), Positives = 120/315 (38%), Gaps = 38/315 (12%)

Query: 13  ENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
             +    RLDRW                ++ +G+VR+  K    + ++  G+ V      
Sbjct: 2   PREAAGARLDRWLAGAIGATAERTRW--LVETGRVRIRGKTCSPHRKLFGGEEV------ 53

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                       L+        +      +LY+D+   V  KP G++V+  +        
Sbjct: 54  -----------ALERPAPRAAEASGPALAVLYDDADCLVVAKPPGLAVEASAPGGASAVA 102

Query: 132 FLKSW----VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                    VD +   P L HRLD++TSG L++AR   A   L  +F    ++K Y +LV
Sbjct: 103 AASRLGAFDVDGRAM-PGLPHRLDRDTSGALLLARHDRALAALRAAFEAGAVEKEYLALV 161

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G P  +   +     +       +          A  A   + V +   +    L ++ 
Sbjct: 162 AGAPPPE-GRLDTPYGRDPADPRRFTTRF----PSARRARLSWTV-ERALRGAALLRVRL 215

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGRTHQ+RV     G P++GD  Y    +         +  LHA  +  P P +G  ++
Sbjct: 216 ETGRTHQIRVQLAEAGFPVLGDAVYGVRAEA------IARQALHAARLAFPRPSDGAPVE 269

Query: 307 ITAPLPAHMVKTWDS 321
           + APLP  + +   +
Sbjct: 270 VRAPLPEDLERAIAA 284


>gi|123443491|ref|YP_001007464.1| tRNA pseudouridine synthase C [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090452|emb|CAL13320.1| Conserved hypothetical protein [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 257

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 103/237 (43%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +       +
Sbjct: 64  ALSSDVARALSLQFEQHQIQKTYHAVVRGYVLEDGTIDYEMTEELDKIADKFAR----PD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    +++H++ +               +F  ++++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYQALAQVEVPIAIGRYDTSRFSLMQLKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            +      +G       ++L LHA ++ L HP  G  L +TA       +     G+
Sbjct: 180 AHGDLRQNRGVAEHFDCSRLMLHASHLHLNHPVTGESLSLTARWDESWQQLMSHFGW 236


>gi|2501677|sp|Q47417|TRUC_PECCC RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|496598|emb|CAA55982.1| unnamed protein product [Pectobacterium carotovorum]
          Length = 376

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 106/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 118 IIYQDEHLVAVNKPSGWLVHRSWLDRKEKVVVMQTVRDQIGQHVYTVHRLDRPTSGVLLL 177

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++QK Y ++V G   +          +   I   + +     +
Sbjct: 178 ALSSEVARALSQQFESHQMQKTYHAVVRGYVLDDGVIDYALTEELDKIADKFTN----PD 233

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 234 KAPQPAVTHYRSLAQAEMPVAIGRYPTARYSLMELKPQTGRKHQLRRHMSHIHHPIIGDT 293

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +    + +G  +     +L LHA  + L HP  G+ L + A   A         G+K
Sbjct: 294 AHGDLRHNRGMESHFSCGRLMLHASELQLNHPVSGQPLTLQARWDAPWQGVVTQFGWK 351


>gi|317178897|dbj|BAJ56685.1| hypothetical protein HPF30_0588 [Helicobacter pylori F30]
          Length = 327

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 68/343 (19%), Positives = 140/343 (40%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +     A   +              K    L+  +++ED  + V NKP  + +     +
Sbjct: 59  TLLTPKIAPKPL--------------KRGFDLEIGVIFEDEDLLVLNKPPNLVIHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      +L+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVYLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L    PL   M++    +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLHFKVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|229530008|ref|ZP_04419398.1| tRNA pseudouridine synthase C [Vibrio cholerae 12129(1)]
 gi|229333782|gb|EEN99268.1| tRNA pseudouridine synthase C [Vibrio cholerae 12129(1)]
          Length = 244

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 98/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASDVMPMFANHEMEKTYHAIVRGWIEEADVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAVTAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 239


>gi|217033764|ref|ZP_03439190.1| hypothetical protein HP9810_7g45 [Helicobacter pylori 98-10]
 gi|216943813|gb|EEC23253.1| hypothetical protein HP9810_7g45 [Helicobacter pylori 98-10]
          Length = 327

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/343 (19%), Positives = 140/343 (40%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                   +    K    L+  +++ED  + V NKP  + +     +
Sbjct: 59  TL--------------LTPKITPKPLKRGLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      +L+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVYLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L+   PL   M++    +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLRFKVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|225378039|ref|ZP_03755260.1| hypothetical protein ROSEINA2194_03699 [Roseburia inulinivorans DSM
           16841]
 gi|225210040|gb|EEG92394.1| hypothetical protein ROSEINA2194_03699 [Roseburia inulinivorans DSM
           16841]
          Length = 294

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 71/294 (24%), Positives = 131/294 (44%), Gaps = 20/294 (6%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +LR   + ++ ++     ++ +G +V++            + +     + L K  D  + 
Sbjct: 1   MLRKKNITLNDRKADGTEKLNAGDLVKLFLSDETFEKFSGKDETNSGYMKL-KSIDSGRL 59

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRL 150
            ++YED  + + NKP+G+  Q         + ++ S++  KG          KP + +RL
Sbjct: 60  QVVYEDDDVIIINKPSGMLSQKAVPEDISANEYILSYLIRKGALSEEQFKTFKPSICNRL 119

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSG+L+  +T    Q + E+ + R +QK Y  +V G  + +K  +  +L K      
Sbjct: 120 DRNTSGLLIAGKTLKGLQTMAEALKKRTVQKYYRCIVKGELR-EKTHLKGYLSKDEQNNK 178

Query: 211 DYVHVVKQNEKGAN--YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             V    + E+ A+     + ++ +   +  +  LE+   TGR+HQ+R H   +G PIVG
Sbjct: 179 VKVVSHIRPEEKADYLPIETEYRPV-AVSNGYTELEVHLITGRSHQIRAHLASIGHPIVG 237

Query: 269 DHKYCA-NFKGNFTSPIQNK-LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           D KY        F   +  +   LHA  + L   E GR ++ AP        WD
Sbjct: 238 DGKYGDLRTNERFRKEVHVRSQLLHAYRIVL---EDGR-EVIAPSGREFEDAWD 287


>gi|153830556|ref|ZP_01983223.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 623-39]
 gi|148873954|gb|EDL72089.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 623-39]
          Length = 244

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 99/240 (41%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  ++          +   I   +       +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEDTNVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAVTAYRPLAKVELPISTGKFATTRYCLIEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 239


>gi|197117385|ref|YP_002137812.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
 gi|197086745|gb|ACH38016.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
          Length = 302

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 69/311 (22%), Positives = 124/311 (39%), Gaps = 45/311 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++  +   R+D + +N  P   F  L+K++ SG V+V+   V+    ++    V +    
Sbjct: 6   IDAKDHCRRMDSFMRNLLPTAQFSYLKKLISSGHVKVNGSPVEAAQLLRFADQVTLKESS 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
                + +    LD               +L+EDS I   NK  G+SV         ++ 
Sbjct: 66  KTAAFLARLTPELD---------------ILFEDSWIISLNKAPGLSVHRTEDPDEVNLV 110

Query: 131 GFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              ++ +  +    + R  +RLD+ TSG +++A++  AA    +  +   + K+Y +LV 
Sbjct: 111 DLAEALLQKRDGVGRLRPVNRLDKGTSGAIILAKSAVAAGMFGKMVQEEGLGKLYLALVE 170

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  + K+  I   L                       + + +  +         L + P 
Sbjct: 171 GKLQ-KQGVIDAPL-------------------DGKESQTSYLRL-FHGGGVSLLAVYPI 209

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           TGR HQ+R H   +G PI+GD +Y       FT        LH+    L HP     + I
Sbjct: 210 TGRMHQIRQHFKMIGHPILGDKRYGGRALTGFTGH-----ALHSFKTTLVHPATREEVNI 264

Query: 308 TAPLPAHMVKT 318
            APL   +++ 
Sbjct: 265 PAPLSEQLMRL 275


>gi|322373824|ref|ZP_08048359.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C150]
 gi|321277196|gb|EFX54266.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C150]
          Length = 290

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/268 (22%), Positives = 106/268 (39%), Gaps = 29/268 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              V ++ + + + + ++ G  + +            ++ IL    +L +         L
Sbjct: 37  KKHVLINGETINWQSPVEKGDKISLTFDTEDY----PDKTILMGEASLVEP--------L 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + V NKP G+   G       +   + ++ D   Q   + HRLD ETSG ++ A+
Sbjct: 85  YEDQHLIVVNKPEGMKTHGNEPTEIALLNHVSAYCD---QTCYVVHRLDMETSGAVLFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      + IQ+ YW+L  G  + K+    + + +  H     V     + + 
Sbjct: 142 NPFILPILNRLLEDKLIQRQYWALAEGRFQTKETVYKDKIGRDRHDRRKRV----VDPRK 197

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A +    +  F      +  Q  TGRTHQ+RVH  H G  I+GD  Y          
Sbjct: 198 GQRAYTTVTRLKTF-NGASLVNCQLKTGRTHQIRVHLAHHGHAILGDPLYSHRHA----- 251

Query: 283 PIQNKLYLHARYMDLPHPEG-GRLQITA 309
              ++L LHA  +   HP    ++ + A
Sbjct: 252 ---SRLMLHAHSLSFTHPLTLEKITVQA 276


>gi|268319938|ref|YP_003293594.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
 gi|262398313|emb|CAX67327.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
          Length = 282

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 65/261 (24%), Positives = 109/261 (41%), Gaps = 29/261 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
             ++ V+ K +  N  ++ G  + I      L+HI  +Q+   +S  L K        ++
Sbjct: 39  EKKILVNGKYLPLNFLVKPGDKIEIQ-----LDHIESDQQTYPASGKLPK--------VV 85

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED+ I V NKPAG             D  L       G  P + HRLD  TSG+L+VA+
Sbjct: 86  YEDNDILVINKPAGQKTHPN---LNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLLVAK 142

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEK 221
             A    L      + + + Y + +   P+      I   +    H     +       +
Sbjct: 143 NPAVVPILNRQLTDKTLHREYLAWISNSPQIKNTGIIDLPIGHDPHDQRKRMVR-----Q 197

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               A++H++VI     +   +++   TGRTHQ+RVH   +G PI+GD  Y ++++    
Sbjct: 198 DGQKAVTHYEVIKRDKDRI-LVKLTLETGRTHQIRVHLAALGAPIIGDPLYNSDYQDG-- 254

Query: 282 SPIQNKLYLHARYMDLPHPEG 302
                +L L A  +    P  
Sbjct: 255 ----EQLQLTAFQLTFRKPFS 271


>gi|320353226|ref|YP_004194565.1| RluA family pseudouridine synthase [Desulfobulbus propionicus DSM
           2032]
 gi|320121728|gb|ADW17274.1| pseudouridine synthase, RluA family [Desulfobulbus propionicus DSM
           2032]
          Length = 292

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 71/306 (23%), Positives = 124/306 (40%), Gaps = 37/306 (12%)

Query: 24  WFKNHYPH-INFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
                  +  +   ++++L+   +RV ++      + + +G V+ +              
Sbjct: 12  VLAALLANGYSRTKVKQLLKYRALRVGEQLPAHPEHPLAAGDVLVVT------------- 58

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSW 136
                     ++       ++YED +I V +KP G+       +    + Y +   L   
Sbjct: 59  ---SEKEGGVRYPPCPGITIVYEDKEILVVDKPPGLLTIASASEKTKTMFYKLTACLGER 115

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            D K ++  + HRLDQ  SG+LV A+T  A   L +S+   + QK + ++V G P     
Sbjct: 116 PDGK-ERVFIVHRLDQGASGLLVFAKTEQAKHALQQSWP--QAQKRFRAIVEGTPCPPSG 172

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I + LL +S I    V+  K        A + ++VI      +  +E+ P T R +QLR
Sbjct: 173 TIKS-LLCESKI--HRVYSDKTGSGAGKPAETRYQVIHTAGD-YALVELIPVTARKNQLR 228

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           VH    G P+ GD KY A            +L L A ++   HP  G  ++ +  LPA  
Sbjct: 229 VHLAEQGHPVAGDKKYGAKTDP------IKRLALQASFLSFAHPISGAPMEFSLELPAKF 282

Query: 316 VKTWDS 321
                 
Sbjct: 283 KTLLKE 288


>gi|259417867|ref|ZP_05741786.1| ribosomal large subunit pseudouridine synthase A [Silicibacter sp.
           TrichCH4B]
 gi|259346773|gb|EEW58587.1| ribosomal large subunit pseudouridine synthase A [Silicibacter sp.
           TrichCH4B]
          Length = 217

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 68/227 (29%), Positives = 109/227 (48%), Gaps = 15/227 (6%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +V+           +L+ D++I V NKPAG+    G G   H+   L S + +   +  L
Sbjct: 2   TVSSEYCPPSDPLDILHHDAQILVVNKPAGLLSVPGKG--EHLSDCLISRIQAAFPEALL 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG++V A T  A +HL   F  R  +K Y + + G  + +   +   L+   
Sbjct: 60  VHRLDRDTSGVMVFAMTAHAQRHLGLQFEKRMTKKTYVARLTGKLEPRSGAVDLPLIVD- 118

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                   V K   +    A + +KVI    +    + +QP TGR+HQLRVH   +G PI
Sbjct: 119 WPNRPLQKVCK---ETGKPAYTDWKVI-SHGEDETRVRLQPKTGRSHQLRVHMQSLGHPI 174

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
           +GD  Y +    ++      ++ LH+  + L HPEGG   + +  AP
Sbjct: 175 LGDPLYASGAARDYP-----RMMLHSEELRLKHPEGGASQKFRAKAP 216


>gi|255012061|ref|ZP_05284187.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis 3_1_12]
 gi|313149904|ref|ZP_07812097.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis 3_1_12]
 gi|313138671|gb|EFR56031.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis 3_1_12]
          Length = 224

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 73/233 (31%), Positives = 114/233 (48%), Gaps = 18/233 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VVYEDNHIIVVNKTASEIVQGDKTGDTPLSETVKQYLKDKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E F+   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTSKALSRLNEMFKNSEVRKTYWAVVKNCPKQPEGELIHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI  +K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVPNSKKAILSYKLIGR-SDNYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
                 S     + LHARY+   HP     +++ AP+P      W   GF+ D
Sbjct: 180 RSNPDGS-----ICLHARYVRFVHPVSKELIELDAPVPD--SNLWH--GFEID 223


>gi|114764218|ref|ZP_01443456.1| ribosomal large subunit pseudouridine synthase A [Pelagibaca
           bermudensis HTCC2601]
 gi|114543370|gb|EAU46386.1| ribosomal large subunit pseudouridine synthase A [Roseovarius sp.
           HTCC2601]
          Length = 215

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 66/220 (30%), Positives = 106/220 (48%), Gaps = 15/220 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
               +  +L+EDS + V +KPAG+    G G    +   L + ++      RL HRLD++
Sbjct: 7   PPEGEIPILHEDSDLLVVDKPAGLLSVPGKGPE--LADCLIARLERAFPTVRLVHRLDRD 64

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V A T  A +HL + F  R+ +K Y + V G  + K   +   L+    +     
Sbjct: 65  TSGVMVFALTAHAQRHLGQQFETRKTRKTYIARVAGRLEPKTGSVDLPLI----VDWPNR 120

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + K   +    A++ +KV    +     + + P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 121 PLQKVCHETGKPALTEYKVTKA-SDAESRVRLHPLTGRSHQLRVHMLALGHPIIGDPLYA 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
                 +      ++ LHA  + L HPE G   + +  AP
Sbjct: 180 PETAAEYP-----RMMLHAEELRLHHPESGIGVKFRAKAP 214


>gi|262193432|ref|YP_003264641.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262076779|gb|ACY12748.1| pseudouridine synthase, RluA family [Haliangium ochraceum DSM
           14365]
          Length = 304

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/321 (20%), Positives = 138/321 (42%), Gaps = 34/321 (10%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72
           + +    L  + +     + +   ++++ +G+V +D  R      R+++GQ V +     
Sbjct: 3   DADAGKALAGFVRERLS-LPWSRARQLVGTGKVFIDGSRCTDAGQRLRAGQEVGLHMSAP 61

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG------GSGIA 126
                                +   +  + YED+ + V +KP  +S         G+ + 
Sbjct: 62  R------------------PQTRGARVRIAYEDAHVVVIDKPVDVSSVPYERRETGTAMD 103

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
              + + K   D+      + HR+D+ TSG+L  A+T+ A   L   FR   +++ Y  +
Sbjct: 104 LLREAWRKLRPDAGRTPLHVVHRIDKATSGLLAFAKTKRAELGLAAQFRQHTLERAYLCV 163

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G  + ++  I + L++     GD +    +       A++H +V++  A+     +++
Sbjct: 164 AHGAVRAQR--IESRLVRDR---GDGLRGSTRAPNQGKRAVTHVEVLEELAR-ASLCQVR 217

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHP-EGGR 304
             TG+THQ+R+H    G P+VG+  Y  + +    + I   +L LHA  +   HP  G R
Sbjct: 218 LETGKTHQIRIHLAERGHPLVGERVYKRDAEFRGHTLIDAPRLMLHAATLGFAHPITGER 277

Query: 305 LQITAPLPAHMVKTWDSLGFK 325
           + + +PLP +       L  +
Sbjct: 278 VFVESPLPENFAAVLARLRAE 298


>gi|315586586|gb|ADU40967.1| RluA family ribosomal large subunit pseudouridine synthase
           [Helicobacter pylori 35A]
          Length = 327

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 68/343 (19%), Positives = 141/343 (41%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +     A   +              K    L+  +++ED  + V NKP  + +     +
Sbjct: 59  TLLTPKIAPKPL--------------KRGLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      +L+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVYLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIVLKAAKKEKSRYSKSEFTSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L+   PL   M++    +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLRFKVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|210134948|ref|YP_002301387.1| pseudouridine synthase D [Helicobacter pylori P12]
 gi|210132916|gb|ACJ07907.1| pseudouridine synthase D [Helicobacter pylori P12]
          Length = 327

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/343 (19%), Positives = 137/343 (39%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLSKEL-QISKNQVLHLIKEGLVFCQKKEVKKGGLALKEGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                   +    K    L+  +++ED  + V NKP  + V     +
Sbjct: 59  TL--------------LTPQITPKPLKRGLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG + +A+       L+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGLKERYGIVHRLDKDTSGGIAIAKNNFTHVCLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFISLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNNLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L    PL   M++    +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLHFKVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|325106295|ref|YP_004275949.1| ribosomal large subunit pseudouridine synthase D [Pedobacter
           saltans DSM 12145]
 gi|324975143|gb|ADY54127.1| ribosomal large subunit pseudouridine synthase D [Pedobacter
           saltans DSM 12145]
          Length = 235

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 68/223 (30%), Positives = 106/223 (47%), Gaps = 14/223 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQ 152
              +LYED+ +    K AG  VQ        +D  +KS++  K +KP      + HRLD+
Sbjct: 10  DKDILYEDNHLIAIYKKAGWIVQVDDTGDLSLDEMVKSYIAEKYKKPNGAFLGVVHRLDR 69

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
             SG+++ A+T  A   + + F+ R + K YW++V   P      + +WL+K      + 
Sbjct: 70  PVSGVILFAKTSKALDRVNKMFKEREMHKTYWAVVKNKPSKMSGNLVHWLVKNPR--KNI 127

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                Q       A  +FKVI      +  +E+ P TGR HQ+RV    +G PIVGD+KY
Sbjct: 128 TTAYNQEVPNGQRAELNFKVIGHI-DGYYVIEVDPITGRPHQIRVQMASLGSPIVGDNKY 186

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAH 314
                    S     + LHA+ ++  HP +  ++ I APLP  
Sbjct: 187 GYPRGSRTKS-----ISLHAKRLEFIHPVKKEKIVIEAPLPKD 224


>gi|256851497|ref|ZP_05556886.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii 27-2-CHN]
 gi|260660920|ref|ZP_05861835.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii 115-3-CHN]
 gi|282931931|ref|ZP_06337399.1| pseudouridine synthase YjbO [Lactobacillus jensenii 208-1]
 gi|297206310|ref|ZP_06923705.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii JV-V16]
 gi|256616559|gb|EEU21747.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii 27-2-CHN]
 gi|260548642|gb|EEX24617.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii 115-3-CHN]
 gi|281303947|gb|EFA96081.1| pseudouridine synthase YjbO [Lactobacillus jensenii 208-1]
 gi|297149436|gb|EFH29734.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii JV-V16]
          Length = 297

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/330 (19%), Positives = 131/330 (39%), Gaps = 44/330 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSG 62
           M   +++V  ++E+  RL  +       ++   +     +G  + V+ +R   N  ++ G
Sbjct: 1   MKIFKFIV--SEEDPKRLGPFLSK--KKLSKQAIVNAKHNGGMLLVNHRRRFTNFTLKVG 56

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V        +N+ +K              +      ++ E     V NKPA +     
Sbjct: 57  DEVLFVMGKEKVNNFLK--------------ASNKSVKIVLETDNYLVINKPAAVLSIPS 102

Query: 123 SG-IAYHIDGFLKSWVDSK------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                  +   +  +   K        KP +  RLD++TSG+++V +   A    +E  +
Sbjct: 103 RYEDKDAVVNRVMGYFAKKKSSEQAFLKPHIVTRLDRDTSGLVLVGKNAVAHSKFSELKK 162

Query: 176 MRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
              +++ + ++V G    +++K  I   + K       YV            +++ ++V+
Sbjct: 163 DVFVKEYH-AIVHGNFNSEHQKGLITAPIGKIDDSVKRYV------TPNGQKSVTQYEVL 215

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                    ++++  TGRTHQ+RVH  H+G P+ GD  Y +    NFT     +  L+  
Sbjct: 216 -AQKDDASLVKLRLFTGRTHQIRVHMAHIGHPLFGDKLYGS--VDNFT-----RQALNCS 267

Query: 294 YMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           ++  P P    ++ +    P  M   W +L
Sbjct: 268 HLSFPDPFTDEKVTVEIDDPEDMAHLWQNL 297


>gi|332289163|ref|YP_004420015.1| 23S rRNA/tRNA pseudouridine synthase A [Gallibacterium anatis
           UMN179]
 gi|330432059|gb|AEC17118.1| 23S rRNA/tRNA pseudouridine synthase A [Gallibacterium anatis
           UMN179]
          Length = 217

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 104/229 (45%), Gaps = 13/229 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           + L  ++      +LY+D+ I V NK +G+    G+   Y       + V +K       
Sbjct: 1   MALIAYNPPQGLNILYQDNYIAVVNKQSGLLSVPGNQPQYQDSAT--TRVANKFGFTEPA 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSGIL+ A ++AA + L   FR R  +K Y ++VWG  +     +   L+    
Sbjct: 59  HRLDMATSGILLFALSKAAEKELKRQFREREPKKHYQAIVWGHLEQDNGIVDLPLICD-- 116

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              +     + +      A + ++V+  +      +++ P TGR+HQLR+H L +G PI+
Sbjct: 117 --WENRPRQRIDFLVGKKAQTQYQVLARYPNNTTRVKLTPITGRSHQLRLHMLALGHPIL 174

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           GD  Y           +  +LYLHA  + + HP    R+  T   P   
Sbjct: 175 GDKFYSPP----AVRAMAPRLYLHAESLTITHPITQERMTFTC--PPDF 217


>gi|146310269|ref|YP_001175343.1| 23S rRNA/tRNA pseudouridine synthase A [Enterobacter sp. 638]
 gi|145317145|gb|ABP59292.1| ribosomal large subunit pseudouridine synthase A [Enterobacter sp.
           638]
          Length = 217

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 107/231 (46%), Gaps = 17/231 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +           ++LY+D  I V NKP+G+    G  +  H D  + + V     +    
Sbjct: 1   METYNPPMEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRVQRDYPQAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  +K Y + +WG P+  +  +   L+    
Sbjct: 59  HRLDMATSGVIVVALTKAAERELKRQFRDREPKKQYIARIWGHPEKAEGLVDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V++        + ++P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCFETGKAAQTEYEVLEYAPDNTARILLKPITGRSHQLRVHMLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           I+GD  Y           +  +L LHA  + + HP  G  +      PA  
Sbjct: 173 ILGDRFY----ATPEALAMAPRLQLHAEMLTITHPAFGTSMTFKT--PADF 217


>gi|319425744|gb|ADV53818.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 280

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 69/259 (26%), Positives = 104/259 (40%), Gaps = 17/259 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
               LD  V            +L+ED  I   +KPAG+ V             ++   D 
Sbjct: 11  PDDELDHVVLDNTDEQAPDIRILFEDEHIVAIHKPAGLLVHRSYLARRERFFAMQLTRDL 70

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G      HRLD+ TSG+L+ A++   A  L E F    I+K Y +LV G   ++   + 
Sbjct: 71  VGCHVFPVHRLDRPTSGVLLFAKSSEVANALCEQFAEHSIEKQYLALVRGNM-HESGILD 129

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
             L  +    GD        +K A  A++ FK +               +F  +++ P T
Sbjct: 130 YPLKVELDELGDKHARQ---DKTAQDAVTAFKPLLNTEIPYPSGRYPTSRFALVQLTPKT 186

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQ 306
           GR HQLR H  H+  PI+GD  +    +  F       N+L+L A+ +   HP    RL 
Sbjct: 187 GRKHQLRRHMAHLRHPILGDTTHGDGKQNTFFREHFGINRLWLIAKKLTFTHPVTQTRLS 246

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I   L       +  LG+ 
Sbjct: 247 IETELEQQWETVFTGLGWD 265


>gi|326571595|gb|EGE21610.1| tRNA pseudouridine synthase C [Moraxella catarrhalis BC7]
          Length = 258

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 99/239 (41%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + + NKPA + V       +     +++  +   Q     HRLD+ TSG+LV 
Sbjct: 19  ILYQDACMVIINKPANMLVHRSWLDKHETCFVMQTLRNQINQHVYPVHRLDRPTSGVLVF 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  L + F    IQK Y ++V GI       I   L  +     D         
Sbjct: 79  ALDSQTAGLLAKQFENHHIQKSYLAVVRGIIGT--GRIDYALKPRLDKIADKF---SNPN 133

Query: 221 KGANYAISHFKVIDCFAQ-----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           K +  AI+ ++V+    Q           ++  + + P TGR HQLR H  H+  PIVGD
Sbjct: 134 KASKSAITDYQVLATTQQPFISCRRFDSSRYSLVCLTPITGRKHQLRRHMKHIFHPIVGD 193

Query: 270 HKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
             Y    +           +L LHA  +   HP    + +I APL     +   + G+ 
Sbjct: 194 TTYGDKVQNRAVLAHIGVKRLLLHAHQLQFCHPLYDEMIRIVAPLDTAFCQVMTAFGWS 252


>gi|294643719|ref|ZP_06721519.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|292640957|gb|EFF59175.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
          Length = 279

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 71/283 (25%), Positives = 123/283 (43%), Gaps = 32/283 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALN 75
           E M L  +     P  +   L+ +L    V VD     +FN  +++G  V+I        
Sbjct: 24  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVKI-------- 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
                     S     K  +     ++YED+ I V  K  G+ SV             L 
Sbjct: 76  ----------SKQKGKKEFNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILN 125

Query: 135 SWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +V   G+  +  + HRLD++TSG+++ A+     + L +++      + Y ++V G  +
Sbjct: 126 EYVQRSGRQFRVFIVHRLDRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVEGSME 185

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + +WL  K+     YV   + ++ G+  +I+H+K I   A  +  LE+   TGR 
Sbjct: 186 KDYDTVVSWLTDKTL----YVSSSEYDDGGSK-SITHYKTIKR-ANGYSLLELDLETGRK 239

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           +Q+RVH   +G PI+GD +Y      N       +L LHA  +
Sbjct: 240 NQIRVHMQDLGHPIIGDGRYGREDSPN----PIGRLALHAFKL 278


>gi|269138083|ref|YP_003294783.1| tRNA pseudouridine synthase C [Edwardsiella tarda EIB202]
 gi|267983743|gb|ACY83572.1| tRNA pseudouridine synthase C [Edwardsiella tarda EIB202]
 gi|304558127|gb|ADM40791.1| tRNA pseudouridine synthase C [Edwardsiella tarda FL6-60]
          Length = 276

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/257 (24%), Positives = 109/257 (42%), Gaps = 18/257 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG  V             +++  D  G+     HRLD+ TSG+L++
Sbjct: 14  IIYQDEHLVAINKPAGWLVHRSWLDRKEKVVVMQTVRDMLGRHVYTVHRLDRPTSGVLLL 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +   A+ L + F   +I K+Y ++V G  + +         +   I   +    +  +
Sbjct: 74  GLSSEVARALAQQFEQHQIHKVYHAVVRGYLQGEALLDYPLTPELDKIADRF----RSPD 129

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +    A +H++ +               +F  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 130 RAPQPAQTHYRGLATAEVPLAIGRYPTSRFSLVELMPQTGRKHQLRRHMAHLRHPIIGDT 189

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +      +G         L LHA  + L HP  G  L + A L     +  D LG++  
Sbjct: 190 AHGDLRQNRGVAAHFGTPGLMLHASELRLTHPVSGEALCLRAGLDLRWQELMDGLGWQA- 248

Query: 328 RNLYIKRLYSQDECKQN 344
               + R+    +C Q+
Sbjct: 249 YLPELDRVEFMPDCPQD 265


>gi|222056620|ref|YP_002538982.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
 gi|221565909|gb|ACM21881.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
          Length = 296

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/319 (21%), Positives = 126/319 (39%), Gaps = 46/319 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V   +   +L+ +     P  +   ++K+  S  VRV+    + ++ +    V+ I    
Sbjct: 6   VSAADHCRQLEGFLHVILPDASPSYVRKLASSVHVRVNDHPAESSSVLCLEDVITIKESG 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID- 130
                +   +  L+               +L+ED+ I VFNKP G+ +   + +      
Sbjct: 66  KTKALLRSVRPDLE---------------ILFEDTWIVVFNKPPGLPMHRAAEVDDVNLV 110

Query: 131 ---GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                L +  D    K R  +RLD+ TSG +++A++  AA       +   + K+Y ++V
Sbjct: 111 DVGSRLLNRRDGGNGKLRPVNRLDRGTSGAVILAKSSTAAGMFGRQLKEDGLDKLYLAIV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  + +   I   L                   G   A + +K +     +   + + P
Sbjct: 171 DGRLQGE-GTITVPL-------------------GGKEAETRYKTL-FNGLRHALVAVYP 209

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGR HQ+R+H   +G PI GD +Y  +              LH+    + HP  G  ++
Sbjct: 210 ITGRMHQIRLHFKSIGHPICGDVRYGGSILNELRGH-----ALHSFRSSIIHPATGESVK 264

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           + APLP   ++   S+  +
Sbjct: 265 VFAPLPEDFLQVVKSIAGE 283


>gi|161615893|ref|YP_001589858.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|168261891|ref|ZP_02683864.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|197262707|ref|ZP_03162781.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|198243086|ref|YP_002216938.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|204928136|ref|ZP_03219336.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205353907|ref|YP_002227708.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207858230|ref|YP_002244881.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|161365257|gb|ABX69025.1| hypothetical protein SPAB_03686 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|197240962|gb|EDY23582.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|197937602|gb|ACH74935.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|204322458|gb|EDZ07655.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205273688|emb|CAR38681.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205349202|gb|EDZ35833.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|206710033|emb|CAR34388.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|322614227|gb|EFY11159.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322620959|gb|EFY17817.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322624022|gb|EFY20856.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322628239|gb|EFY25028.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322633358|gb|EFY30100.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322636065|gb|EFY32773.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322639401|gb|EFY36089.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322643737|gb|EFY40288.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322648849|gb|EFY45296.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322655158|gb|EFY51468.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322658011|gb|EFY54279.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322664112|gb|EFY60311.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322667081|gb|EFY63253.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322673129|gb|EFY69236.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322677880|gb|EFY73943.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322681054|gb|EFY77087.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322685651|gb|EFY81645.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|323194790|gb|EFZ79977.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323196541|gb|EFZ81689.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323205046|gb|EFZ90029.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323207753|gb|EFZ92699.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323212695|gb|EFZ97512.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323214822|gb|EFZ99570.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323222551|gb|EGA06916.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323226431|gb|EGA10639.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323230690|gb|EGA14808.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323234959|gb|EGA19045.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323238998|gb|EGA23048.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323244644|gb|EGA28650.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323247260|gb|EGA31226.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323251792|gb|EGA35657.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323257479|gb|EGA41169.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323263264|gb|EGA46801.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323267516|gb|EGA51000.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323272705|gb|EGA56111.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
 gi|326624702|gb|EGE31047.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
 gi|326629020|gb|EGE35363.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
          Length = 260

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +       +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLMIQAGLDETWMQALTQFGWR 237


>gi|118588379|ref|ZP_01545788.1| pseudouridine synthase [Stappia aggregata IAM 12614]
 gi|118439085|gb|EAV45717.1| pseudouridine synthase [Stappia aggregata IAM 12614]
          Length = 223

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/213 (30%), Positives = 102/213 (47%), Gaps = 12/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  + V +KP+G+    G   A      ++S    +    R+ HRLD +TSGI+V+
Sbjct: 21  VLHADDDLLVVDKPSGLLSVPGK--AAEHADCIESRAQERYADARIVHRLDMDTSGIMVL 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR  AA +HL   F  R+  K Y + +WG P   +  +   L+         +       
Sbjct: 79  ARNPAAHRHLGLQFERRKTLKTYIADIWGSPSEDEGEVDLPLICDWPNRPKQMVSF---- 134

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    A++ ++V++        + + PHTGR+HQLRVH L +G PI GD  Y        
Sbjct: 135 EFGKPALTRWQVLERK-DTTSRVRLFPHTGRSHQLRVHMLALGHPIAGDRFY----AQGA 189

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                 +L LHA  ++L HP  GGR+   + +P
Sbjct: 190 ALTASPRLALHAETLELHHPAHGGRICFRSEVP 222


>gi|168236011|ref|ZP_02661069.1| tRNA pseudouridine synthase C (tRNA-uridine isomerase C)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
 gi|194734776|ref|YP_002115916.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|194710278|gb|ACF89499.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197290820|gb|EDY30174.1| tRNA pseudouridine synthase C (tRNA-uridine isomerase C)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
          Length = 260

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDQWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +       +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLMIQAGLDETWMQALTQFGWR 237


>gi|32266282|ref|NP_860314.1| ribosomal pseudouridine synthase [Helicobacter hepaticus ATCC
           51449]
 gi|32262332|gb|AAP77380.1| ribosomal pseudouridine synthase [Helicobacter hepaticus ATCC
           51449]
          Length = 351

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/331 (19%), Positives = 139/331 (41%), Gaps = 26/331 (7%)

Query: 7   VQYVVVEN---DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG 62
           ++ ++V N   +   +RLD +        +   +  I+++ QV ++     K    +++ 
Sbjct: 1   MKEIIVSNFDLNNGKLRLDSYLSIQL-QSSKNQIHHIIKNKQVWLNGILCLKNGTLLKAK 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +++                L SS  ++   +     ++Y+D  + + NKP  + +   
Sbjct: 60  DCIQV-------QSPCANNTPLSSSYTISADDERFSIDIVYQDEDVLIINKPPHLVIHHA 112

Query: 123 SGI------AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             +       +        +  S  ++  + HRLD++TSG L +A++  A   LT+  + 
Sbjct: 113 PSVKEPTLVDWLKLNAHILYTLSGEERYGIIHRLDKQTSGALAIAKSNLAYTTLTKELKS 172

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN----EKGANYAISHF-K 231
           R++ + Y +++   P    + +  ++ +  H       +  ++     KG   + S F K
Sbjct: 173 RQMGRYYLAII-DTPLKDNQQVQCFMGRNPHNRLKMSKIHIRSNSPIPKGVRDSKSSFIK 231

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           +       F  + ++ HTGRTHQ+R H   +   I+GD  Y    +   T   Q+++ LH
Sbjct: 232 IATSDNGAFELIAIKLHTGRTHQIRAHLESLSRHILGDTLYGYKPQAK-THYYQDRILLH 290

Query: 292 ARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           A  +   HP+  +     AP+   M+K   +
Sbjct: 291 AYILYFIHPKTQQNCTFKAPILPDMLKFLQT 321


>gi|326692367|ref|ZP_08229372.1| pseudouridylate synthase [Leuconostoc argentinum KCTC 3773]
          Length = 305

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/300 (22%), Positives = 123/300 (41%), Gaps = 38/300 (12%)

Query: 36  NLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
            L+  LR  Q + V+ + V  N   Q+G  + +  + +A +    E     ++       
Sbjct: 31  RLRGALRQKQHIHVNGQAVATNYVFQAGDQLAL--IFDAADFRTSESHYTPNAQETLP-- 86

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-----------K 143
                 +++E+    V +KPAG+ +      A +    L +++ +  Q           +
Sbjct: 87  ------IIFENDDFVVVDKPAGMKMHP---HAPNEADTLLNYLAADFQARHLMSAGQPAR 137

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D++TSG ++VA+       L      + I++ Y + V G        I   + 
Sbjct: 138 PYMVHRIDRDTSGAVIVAKNPVVVPILNRLLAQKAIKRTYLAWVQGAVAESAGEITTPIG 197

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                    V     N   A  A +H+  +    Q    L +Q  TGR HQ+RVH   +G
Sbjct: 198 VDPQDERRRVI----NGLAAQSARTHWARMHTVYQN-SLLRVQLDTGRMHQIRVHLASIG 252

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
            PI+GD  Y     G        ++ LHA  + +P P +GG + I+  +P+   +   ++
Sbjct: 253 HPIIGDPLYHPEQPGT-------RMMLHAATLIVPLPFDGGTVTISGAIPSDFPRQLRTI 305


>gi|218232731|ref|YP_002366075.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
 gi|229108847|ref|ZP_04238452.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
 gi|229149592|ref|ZP_04277824.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|218160688|gb|ACK60680.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
 gi|228633938|gb|EEK90535.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|228674616|gb|EEL29855.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
          Length = 307

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 127/319 (39%), Gaps = 32/319 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V      + ++   K  +  I    L ++     V V+ ++ ++N  ++    +++ 
Sbjct: 11  EITVPAKWNGISIESVLKVEW-EIPKKLLHQLRMEKGVTVNGEQRRWNELLKENDKLQVH 69

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAY 127
                   +  E               + +  ++YED  + + NKP  +       G   
Sbjct: 70  MFAEEEYGVDPE---------------YGELHVVYEDDHVLIVNKPEQMDTHPAEKGGTG 114

Query: 128 HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +   +      +G   K R  HRLD++T+G +V A+ R A   +      R+I++ Y +
Sbjct: 115 TLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGSIMDRLLMERKIKRTYAA 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLE 244
           LV G  K KK  I   + +  H         K      + AI+++KV   F  Q   ++ 
Sbjct: 175 LVEGKVKKKKGKIDAAIGRDRHHATRRRISPK-----GDQAITYYKVEKYFKKQNTTFVT 229

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  H G P+VGD  Y    K        +   LHA  ++  HP    
Sbjct: 230 LQLETGRTHQIRVHMSHNGNPLVGDVLYGGQTK------YMSSQALHAMKINFLHPITKE 283

Query: 305 -LQITAPLPAHMVKTWDSL 322
            +++  P P  +       
Sbjct: 284 AIEVDVPFPTKLNNKIKEF 302


>gi|317496022|ref|ZP_07954384.1| RluA family pseudouridine synthase [Gemella moribillum M424]
 gi|316913926|gb|EFV35410.1| RluA family pseudouridine synthase [Gemella moribillum M424]
          Length = 294

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 60/312 (19%), Positives = 128/312 (41%), Gaps = 42/312 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILR---SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           L  +   +  +I+   L + ++    G ++V+ K       +++G  V I       +  
Sbjct: 16  LREFLLEN--NISRKTLTR-IKFDNDGSIKVNDKEENVRYILKNGDKVTITLPSEKFSEH 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSW 136
           +   + ++ +++           ++YED    V NKPA +            +   + ++
Sbjct: 73  V---RFIEGNLD-----------IIYEDEYFLVVNKPANLPSIPSRNEGDASLLEIVNTY 118

Query: 137 VDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                    P +  RLD+ T+G++++A+ R       ++     I K Y +L  G   ++
Sbjct: 119 FHDNNYVTIPHIVTRLDKNTTGLVLIAKHRHIHALFGKTD----INKFYLALTKGKVADQ 174

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTH 253
              I   + +++        + +   +  +YA +   ++  + +     ++++  TGRTH
Sbjct: 175 --VIEANIKREAD-----SIITRCVAEDGDYAKTQIWLVKYYEKNDVSLVKLKLFTGRTH 227

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           Q+RVH  H+G P++GD  Y  N        +  +  LH   +   HP     L + APL 
Sbjct: 228 QIRVHMSHLGHPLLGDELYGGNKD------LIARQALHCHNLQFKHPITQKELSLEAPLA 281

Query: 313 AHMVKTWDSLGF 324
             +    DS+G 
Sbjct: 282 GDIKNITDSIGI 293


>gi|256830871|ref|YP_003159599.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256580047|gb|ACU91183.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 306

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 82/295 (27%), Positives = 130/295 (44%), Gaps = 33/295 (11%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T VQ V V  +E   +L  + +     +      +++R+GQVR+D +R K  +R+ +GQ 
Sbjct: 6   TSVQLVEVGREENGRKLVSFLEARLGTLPTGLFMRLVRTGQVRIDGRRCKPFDRVLTGQT 65

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+PP       + +++K L          D      ++E+ ++ V +K AG+ V GG+G
Sbjct: 66  VRVPP-----VTVQRKEKSL---------RDLPGLRGVFENDEMLVIDKLAGLPVHGGTG 111

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
               +   LK+    +   P   HRLD++TSG+L+ A+T    + +  S+    + K Y 
Sbjct: 112 WTDSVHDRLKACFAGQAFVPIPVHRLDRDTSGLLLCAKTHDFLRAMHASWP--TLTKGYL 169

Query: 185 SLVWGIPKNKK-ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             V G         + + L K     G+ V            A+SH   +   A K   L
Sbjct: 170 CWVEGAWAAAGWRTVVSELAKAQTGSGEQVV-----SGQGKRAVSHVHPVLVTAGK-SLL 223

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +   TGRTHQ+RVH    G  IVGD +Y               L LHA  +  P
Sbjct: 224 LVVLGTGRTHQIRVHLADCGHAIVGDPRYGQG----------GGLLLHAAALSWP 268


>gi|212710403|ref|ZP_03318531.1| hypothetical protein PROVALCAL_01464 [Providencia alcalifaciens DSM
           30120]
 gi|212686985|gb|EEB46513.1| hypothetical protein PROVALCAL_01464 [Providencia alcalifaciens DSM
           30120]
          Length = 252

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/237 (25%), Positives = 102/237 (43%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V      +      +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IIYQDEYVVAVNKPAGMLVHRSWLDSKETVFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L E F   R++K+Y ++V G   +        L +   I           E
Sbjct: 64  ALSSDVARLLAEQFEQHRMEKVYHAIVRGYVMDGDRLDYPLLEELDKIADKNAT----KE 119

Query: 221 KGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                 ++H+K +               +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 PRLQECVTHYKPLATVECSVAIGRYDTARFSLVELKPETGRKHQLRRHMSHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           K+      +G       ++L LHA  +   HP     + + A   A  +   +  G+
Sbjct: 180 KHGDLRQNRGVAEHFSVSRLMLHASQLIFIHPITEEKIPLVASWDAQWLSLIEQFGW 236


>gi|293390024|ref|ZP_06634358.1| tRNA pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290950558|gb|EFE00677.1| tRNA pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 237

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 100/241 (41%), Gaps = 17/241 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   NKPAG+ V       +     ++   D  GQ     HRLD+ TSG
Sbjct: 1   MNLAILYQDDVLVAVNKPAGMLVHRSWLDRHETQFVMQILRDQIGQLVYPIHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     A  +   F  ++ +K Y ++V G    + E      ++   I   +    
Sbjct: 61  VLLFALNSETANLVCHQFEQKQTEKQYLAVVRGYVTGQGEIDYPLKVQLDKIADKFA--- 117

Query: 217 KQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            Q +K    A++ +  +             A ++  + + P TGR HQLR H  H+  PI
Sbjct: 118 -QQDKAPQSAVTFYDGLKTVEMPYGVGRYAASRYSLVRLTPKTGRKHQLRRHMKHIFHPI 176

Query: 267 VGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD +Y    +    +     ++L LHA  +   HP  G+ + I A L         +  
Sbjct: 177 LGDMQYGDLHQNRALTEHIGCSRLMLHAEKLTFVHPLTGQPITIEAGLDEQWKHLMRTFQ 236

Query: 324 F 324
           +
Sbjct: 237 W 237


>gi|326407645|gb|ADZ64716.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis CV56]
          Length = 288

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 113/268 (42%), Gaps = 30/268 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
                V+ K +  N  + +G  + +       +++              K      + +L
Sbjct: 37  KKNCIVNNKLINENQLVHAGDKITLIFDNEDFSNLS------------LKFGSANLADIL 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + V NKP G+   G +     +   + + ++   Q+  + HRLDQ TSG ++ A+
Sbjct: 85  YEDEHLIVVNKPEGMKAHGNTADELALQNHVAAAIN---QEVFVVHRLDQATSGAVLFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            +     L + F   +I + Y +LV G     +  I   + +  H     +   K     
Sbjct: 142 NQFVLPILGKMFEGNKIHREYLALVKGHFPENQFTIDRAIGQNRHDKNKRILSAK----- 196

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++H ++I  F  K   ++    TGRTHQ+RVH   +  PI+GD  Y          
Sbjct: 197 GQKAVTHVEIIKKFTDK-TLVKCTLDTGRTHQIRVHLSSLNHPIIGDALYGQK------- 248

Query: 283 PIQNKLYLHARYMDLPHP-EGGRLQITA 309
             Q ++ LHA  + +PHP E   L+I+A
Sbjct: 249 -TQERMMLHADKIIIPHPFENKILEISA 275


>gi|86147828|ref|ZP_01066134.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp.
           MED222]
 gi|85834355|gb|EAQ52507.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp.
           MED222]
          Length = 244

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/216 (29%), Positives = 107/216 (49%), Gaps = 12/216 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D  I V NKPAG+    G  +  H D      V  +  + ++ HRLD  TSG+++
Sbjct: 15  DIIYQDDDILVVNKPAGLLSVPGR-LPEHYDSMWSRLV-VEFPEIQVVHRLDMSTSGLML 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A +HL + F+ R   K+Y++ VWG  ++K   I   L+           V   +
Sbjct: 73  LAKHKQAERHLKKQFQYRLTHKLYYARVWGSMEDKAGLIDLPLICD-WTNRPRQKVCFDD 131

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 + + + V++    +   L++ P TGR+HQLRVH + +G PIVGD  Y      N
Sbjct: 132 ---GKPSQTRY-VVEQQEPQTTLLKLLPITGRSHQLRVHCMELGNPIVGDEFYATPDAFN 187

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           ++    ++L LHA  +   HP   +L   A +P   
Sbjct: 188 YS----DRLALHACELSFYHPANNQL-FKAFVPCDF 218


>gi|308185634|ref|YP_003929765.1| ribosomal large subunit pseudouridine synthase A [Pantoea vagans
           C9-1]
 gi|308056144|gb|ADO08316.1| ribosomal large subunit pseudouridine synthase A [Pantoea vagans
           C9-1]
          Length = 217

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 105/229 (45%), Gaps = 13/229 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D+ I V NKP+G+    G  +  H D  + + +     +    
Sbjct: 1   MEPYNPPREPWLHILYQDAHIMVVNKPSGLLSVPGR-LDEHKDSVM-TRIQRDFPQAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R   K Y + +WG P+ ++  +   L+    
Sbjct: 59  HRLDMATSGVMVVALTKAAERELKRQFREREPSKTYVACIWGHPEKEEGLVDLPLICDWP 118

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                +       +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+
Sbjct: 119 NRPKQMVCF----ETGKAAQTEYQVLEYRADNSARVSLKPITGRSHQLRVHMLALGHPIL 174

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
           GD+ Y         +    +L LHA  + + HP  G  +      PA  
Sbjct: 175 GDNFYAHPEAKAMAA----RLLLHAESLTITHPAFGNAMTFRQ--PADF 217


>gi|296123212|ref|YP_003630990.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
 gi|296015552|gb|ADG68791.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
          Length = 623

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 77/309 (24%), Positives = 131/309 (42%), Gaps = 26/309 (8%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVR 66
           + + V      + +  + +   PH+     +     G++  +    ++ +  +Q GQ + 
Sbjct: 329 RPLQVSQKHAGLTVREFLQQVLPHLEASLWESAESEGRLLSETFAPMRLDETVQPGQRI- 387

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                     I +    L+ +VN            LYED  I V NKPA + V       
Sbjct: 388 ----------IHRLPGTLEPAVN-------ADIRWLYEDESIVVINKPAPLPVHASGRFH 430

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            +   +L + +    Q PR  HRLD  T+G+LV++RTR  A  L   F  R ++K+Y + 
Sbjct: 431 RNTLQYLLAQI-YDPQSPRAAHRLDAMTTGVLVLSRTRHMAGRLQPQFSRREVEKVYLAR 489

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G P  +       +   + + G        +E G   A + F+++         LE++
Sbjct: 490 VQGEPAEESFECHAPMTDVAGVMGSR----DIDESGGVEASTLFRLVQRLEDGTSLLEVR 545

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL-HARYMDLPHPEGG-R 304
           P TGRT+Q+RVH  H+G PI+GD  Y  + +         ++   HA  +   HP     
Sbjct: 546 PITGRTNQIRVHLWHLGLPILGDPLYLPSGELATEPKDSEQVMCLHAWRICFQHPVDRTT 605

Query: 305 LQITAPLPA 313
           ++  AP PA
Sbjct: 606 MEFMAPPPA 614


>gi|284050466|ref|ZP_06380676.1| pseudouridine synthase, RluA family protein [Arthrospira platensis
           str. Paraca]
 gi|291570540|dbj|BAI92812.1| probable pseudouridine synthase [Arthrospira platensis NIES-39]
          Length = 309

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 131/326 (40%), Gaps = 35/326 (10%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M    ++    V+     + +  ++   Y H +       + + Q+ +D K    +  +Q
Sbjct: 1   MLNSGWIYREQVDRLSAGLTVLDYYSKRYTHSSRNEWCDRINNQQIWLDGKPATADIELQ 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +GQ +                          +    L   ++YED+ I V  KP+G+ V 
Sbjct: 61  AGQQLAYH------------------RPPWNEPDVPLSFQVIYEDADILVVAKPSGLPVI 102

Query: 121 GGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            G G   H    L+       Q  P   HRL + TSG++++AR+     +LT+  R R+I
Sbjct: 103 PGGGFLEH--TLLRQLQRKYPQDTPIPIHRLGRGTSGLVLLARSTVGRSYLTKQMRQRQI 160

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K+Y +L  G        I   + K  H    Y++      +    A S+ +VI   + K
Sbjct: 161 TKVYLALAEGCSPRDYFSINCAIGKIPHPIIGYIY---GATETGLSAESNCQVIRRDSDK 217

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---------KLYL 290
              +++   TGR HQ+R+H    G P+VGD  Y    K   T P  N           YL
Sbjct: 218 M-IVQVTILTGRPHQIRIHLAAAGFPLVGDPLYTIGGKPRITDPTSNHHSTFPGDCGYYL 276

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHM 315
           HA  +   HP+ G  L +TA  P  +
Sbjct: 277 HAYSLSFQHPQTGANLHLTATPPQEL 302


>gi|327438734|dbj|BAK15099.1| pseudouridylate synthase [Solibacillus silvestris StLB046]
          Length = 277

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 62/287 (21%), Positives = 115/287 (40%), Gaps = 30/287 (10%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E    ++   ++ +  +    + ++  +  V +D + + +    + G  +     I A N
Sbjct: 8   ENGQTVEDLLRDKWR-LGKKLVHELRMAKAVTIDGEPIMWKEPFEKGTKIEFAFDIPASN 66

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFL 133
           +                 +D     + YED    + +KP G++            ++  +
Sbjct: 67  YT---------------PTDSCDVKIRYEDEHCLIVSKPKGMATHPNEPTDNDTCMNHVM 111

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +  +D+ G      HRLDQ T+G+L+VA+   A          + I + Y + V G  + 
Sbjct: 112 RYIMDNGGHYAEHVHRLDQGTNGLLLVAKHPVAKSIFDRMIEEKTIVRTYAAEVQGNLRT 171

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               I   + K  H     V           +A++H++V++ + +  C + +   TGRTH
Sbjct: 172 DSGTINAGIGKDRHHNTRRVV-----SPTGQHAVTHYEVVNRY-KGTCVVHVVLETGRTH 225

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           Q+RVH  H+G PIVGD  Y A    +          LHA  +   HP
Sbjct: 226 QIRVHMAHLGHPIVGDTMYGARETASGD------YALHAIQLAFMHP 266


>gi|329928505|ref|ZP_08282373.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
 gi|328937764|gb|EGG34172.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
          Length = 302

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 110/234 (47%), Gaps = 17/234 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-DGFLKSWVDSKGQK--PRLTHR 149
              + +  +LYED    V NKPAG++V   +       +  + ++ +++G     R  HR
Sbjct: 76  EPRWQELQVLYEDDFCLVVNKPAGMAVHPDNESRETTLNHVVAAYYEAEGVHAAVRHIHR 135

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++T+G ++ A+   A   L E+ R ++I ++Y ++V G    + + I   + K     
Sbjct: 136 LDKDTTGPVLYAKNEYAQLKLDEAMREKKIVRMYAAIVQGRVSQELKRIDLPIGKDR--- 192

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             Y    ++       AI+H    + +  K   L ++  TGRTHQ+RVH  HMG P++GD
Sbjct: 193 --YHASRRRVSLTGQAAITHILSAEAYP-KASLLHIRLETGRTHQIRVHLSHMGHPLLGD 249

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y     G F      +  LH   +   HP  G  + + AP P  M++  + +
Sbjct: 250 VLYGG--PGTFA-----RQALHGERLLFHHPFTGESIDVPAPWPQDMMELRERI 296


>gi|283783845|ref|YP_003363710.1| ribosomal large subunit pseudouridine synthase A [Citrobacter
           rodentium ICC168]
 gi|282947299|emb|CBG86844.1| ribosomal large subunit pseudouridine synthase A [Citrobacter
           rodentium ICC168]
          Length = 219

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 69/220 (31%), Positives = 108/220 (49%), Gaps = 17/220 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD  TSG++
Sbjct: 14  LVVLYQDEHIMVVNKPSGLLSVPGR-LEEHKDSIM-TRIQRDYPQAESVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+ +  KQ
Sbjct: 72  VVALTKAAERELKRQFREREPKKQYVARVWGHPVPAEGVVDLPLI------CDWPNRPKQ 125

Query: 219 NE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y +  
Sbjct: 126 KVCYETGKAAQTGYEVVEYAADNTARVVLKPTTGRSHQLRVHMLALGHPILGDRFYASPE 185

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
                  +  +L LHA  + + HP  G  +   A  PA  
Sbjct: 186 ----ALAMAPRLLLHAEMLTITHPAYGNSMTFKA--PADF 219


>gi|146306264|ref|YP_001186729.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           mendocina ymp]
 gi|145574465|gb|ABP83997.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           mendocina ymp]
          Length = 211

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/216 (31%), Positives = 106/216 (49%), Gaps = 11/216 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +L++D+ + V NKP  +    G       D  +    ++   + R+ HRLD ETSGI
Sbjct: 5   QIEILHQDAALLVINKPTLLLSVPGRADDN-KDCLVTRLQENGYPEARIVHRLDWETSGI 63

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+AR   + + L+  F  R  +K Y +L WG P+     I   L         +V    
Sbjct: 64  IVLARDADSHRELSRQFHDRETEKAYTALCWGQPEADSGSIDLPLRYDPPTKPRHV---- 119

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +   +A++H++VI+     +C +E+ P TGR+HQLRVH L +G P++GD  Y     
Sbjct: 120 VDHELGKHALTHWRVIERCGD-WCRVELTPITGRSHQLRVHMLSIGHPLLGDRLYAHEQ- 177

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                    +L LHA  + L HP  G RL+   P P
Sbjct: 178 ---ALAAHERLCLHASMLALTHPQSGERLRFECPAP 210


>gi|38492837|pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic
           Module
          Length = 252

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 105/248 (42%), Gaps = 19/248 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPR--LTHR 149
               +   ++YED  I V NKP  + V  G+G     +   L  +       PR  + HR
Sbjct: 4   EPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHR 63

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++T+G+ VVA+T  A   L ES + R I + Y ++  G        +   + +     
Sbjct: 64  LDKDTTGLXVVAKTVPAQTRLVESLQRREITREYEAVAIGH-XTAGGTVDEPISRHPT-- 120

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                           A++H+++ + F +    L ++  TGRTHQ+RVH  H+  P+VGD
Sbjct: 121 ---KRTHXAVHPXGKPAVTHYRIXEHF-RVHTRLRLRLETGRTHQIRVHXAHITHPLVGD 176

Query: 270 HKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
             Y    +    +           ++  LHA  + L HP  G   +  AP+P   V+  +
Sbjct: 177 PVYGGRPRPPKGASEAFISTLRKFDRQALHATXLRLYHPISGIEXEWHAPIPQDXVELIE 236

Query: 321 SLGFKYDR 328
                ++ 
Sbjct: 237 VXRADFEE 244


>gi|302671097|ref|YP_003831057.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
 gi|302395570|gb|ADL34475.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
          Length = 328

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 60/284 (21%), Positives = 119/284 (41%), Gaps = 34/284 (11%)

Query: 60  QSGQVVRIPPVINALNHIIKEQKIL----DSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           +  ++ RI PV    +    ++ I+    D+              + YED  + + NKP 
Sbjct: 52  RPDEINRIVPVRLIDSLFPGDELIVRVYEDNDNAGDIVPADGPLDIAYEDEDLIIVNKPG 111

Query: 116 GISVQGG-SGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTE 172
            + V    +     +  +L  +    GQ+   R   RLD+ETSG+++ A+ R AA  + +
Sbjct: 112 EMVVHPSYAHYKDSLSNYLLGYFIRSGQRHVIRTVGRLDRETSGLVIFAKNRHAAALMAQ 171

Query: 173 SFRMRRIQKI-----------------YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
             +    ++                  Y +L  G+     + I   + ++         +
Sbjct: 172 QIKTNDDKENAQDSLGDEPDNMSRRKEYLALCSGVFDKTHDTIDAPIRRRPDE-----RM 226

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +++       A++H++V+  +   +  + ++  TGRTHQ+RVH  ++G P++GD+ Y   
Sbjct: 227 IREVHPEGKRAVTHYEVVHQY-DDYALVRLRLDTGRTHQIRVHMAYIGHPLLGDNFYGKE 285

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
              +       +  LHA Y++   P  G  + I A +P  M K 
Sbjct: 286 IPDDH---GMTRAALHAGYIEFMQPITGEKIVINARMPEDMQKL 326


>gi|146281802|ref|YP_001171955.1| pseudouridine synthase RluA [Pseudomonas stutzeri A1501]
 gi|145570007|gb|ABP79113.1| pseudouridine synthase RluA [Pseudomonas stutzeri A1501]
          Length = 244

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/213 (29%), Positives = 105/213 (49%), Gaps = 11/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D+ + V +KP  +    G     + D  +    ++   + R+ HRLD ETSG++V+
Sbjct: 41  IVHQDAALLVIDKPTLLLSVPGRA-EDNRDCLVTRLQENGYPEARIVHRLDWETSGLIVL 99

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR   + + L+  F  R  +K Y +L WG P      I   L           HVV  + 
Sbjct: 100 ARDADSHRELSRQFHDRETEKAYTALCWGQPDADSGSIDLPLRYDPPT--KPRHVV--DP 155

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +   +A++ ++V++        +E+ P TGR+HQLRVH L +G P++GD  Y        
Sbjct: 156 ELGKHALTFWRVLERCGD-HSRVELTPITGRSHQLRVHMLSIGHPLLGDRLYAHEQALRA 214

Query: 281 TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                 +L LHA  + L HP+ G RL+  +P P
Sbjct: 215 ----HERLCLHASMLTLTHPQTGARLRFESPAP 243


>gi|120599561|ref|YP_964135.1| pseudouridylate synthase [Shewanella sp. W3-18-1]
 gi|120559654|gb|ABM25581.1| tRNA pseudouridine synthase C [Shewanella sp. W3-18-1]
          Length = 280

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 69/259 (26%), Positives = 104/259 (40%), Gaps = 17/259 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
               LD  V            +L+ED  I   +KPAG+ V             ++   D 
Sbjct: 11  PDDELDHVVLDNTDEQAPDIRILFEDEHIVAIHKPAGLLVHRSYLARRERFFAMQLTRDL 70

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G      HRLD+ TSG+L+ A++   A  L E F    I+K Y +LV G   ++   + 
Sbjct: 71  VGCHVFPVHRLDRPTSGVLLFAKSSEVANALCEQFAEHSIEKQYLALVRGNM-HESGILD 129

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
             L  +    GD        +K A  A++ FK +               +F  +++ P T
Sbjct: 130 YPLKVELDELGDKHARQ---DKAAQDAVTAFKPLLNAEIPYPSGRYPTSRFALVQLTPKT 186

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQ 306
           GR HQLR H  H+  PI+GD  +    +  F       N+L+L A+ +   HP    RL 
Sbjct: 187 GRKHQLRRHMAHLRHPILGDTTHGDGKQNTFFREHFGINRLWLIAKKLTFTHPVTQSRLS 246

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I   L       +  LG+ 
Sbjct: 247 IETELEQQWETVFTGLGWD 265


>gi|58039270|ref|YP_191234.1| ribosomal large subunit pseudouridine synthase A [Gluconobacter
           oxydans 621H]
 gi|58001684|gb|AAW60578.1| Ribosomal large subunit pseudouridine synthase A [Gluconobacter
           oxydans 621H]
          Length = 265

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 71/258 (27%), Positives = 117/258 (45%), Gaps = 12/258 (4%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
             +    + ++          T     +   +L E  +  +  KPAG++V  G      +
Sbjct: 17  NAHKPRRLPQQAASPTPEGPRTPFHPGMDIPVLLETPRFLILYKPAGLAVHPGPSTQDSV 76

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +  L          P L HRLD +TSG L+VAR + A     ++F+ R+  K+YW++V G
Sbjct: 77  ETRLLPHPRGG---PWLAHRLDADTSGCLLVARRKTALIEAQKAFQERQAHKLYWAVVVG 133

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   I   LL++S   G  + V    +   + A + ++V+   ++  CW+E++  T
Sbjct: 134 DLPQDSGEIDAPLLRQSDASGWRMVV----DAKGDEARTRWRVLGR-SKGLCWVELELLT 188

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           GRTHQ R+H   +G PI+GD  Y          P    L+L AR ++L  P    L   A
Sbjct: 189 GRTHQARIHCAELGTPILGDPVYGMPAPDGSALPG---LHLLARSLELSLP-SDTLSAQA 244

Query: 310 PLPAHMVKTWDSLGFKYD 327
           P P  M  +  ++GF+ D
Sbjct: 245 PPPEFMAASLRAMGFESD 262


>gi|229523315|ref|ZP_04412722.1| tRNA pseudouridine synthase C [Vibrio cholerae TM 11079-80]
 gi|229339678|gb|EEO04693.1| tRNA pseudouridine synthase C [Vibrio cholerae TM 11079-80]
          Length = 244

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 98/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASDVMPMFANHEMEKTYHAIVRGWIEEADVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAVTAYRPLAKVELPISTGKFATTRYCLIEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 239


>gi|300725911|ref|ZP_07059373.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella bryantii B14]
 gi|299776762|gb|EFI73310.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella bryantii B14]
          Length = 224

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 71/232 (30%), Positives = 113/232 (48%), Gaps = 16/232 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + +K +G  VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHIIIVSKKSGEIVQGDKTGDEPLSEIVKKYIKEKYHKPGNVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L + FR   + K YW++   +PKN +  + NW+ +       YV+ 
Sbjct: 63  GLVVFAKTSKALSRLNQMFRDSNVHKTYWAITKNVPKNPEGTLINWITRNEKQNKSYVY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  A+  +K+I      +  LE+   TGR HQ+R    HMGCPI GD KY A 
Sbjct: 122 -DKEVPHSKKAVLSYKLIG-HTDNYSLLEIHLMTGRHHQIRCQLAHMGCPIKGDLKYGAP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
                 S     + L +R+++  HP     ++ TAPLP      W S+  K+
Sbjct: 180 RSNPDGS-----ISLLSRFVEFVHPVSKETIKATAPLPDD--NLWQSIAPKH 224


>gi|296120899|ref|YP_003628677.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
 gi|296013239|gb|ADG66478.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
          Length = 269

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 76/249 (30%), Positives = 119/249 (47%), Gaps = 24/249 (9%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----L 146
           + +  L+  +L ED  +    KPAG+  QG       ++ ++K+W+  K  KP      +
Sbjct: 13  EPAWSLEPQILLEDGPLLAIWKPAGLLTQGVPQGLPTLENWVKNWIREKYAKPGNVYLGI 72

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+  SG+++ AR   AA  L E FR RR++K Y ++V G+P      + N+LLK  
Sbjct: 73  PHRLDRPVSGVMLFARNSKAAARLAEVFRDRRVKKTYTAVVEGMPPQTTGRLTNYLLKDP 132

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                   +V +   G+  AI  ++++   A     LE++  TGR HQ+RV    MGCP+
Sbjct: 133 QAAHS--QIVAEGTPGSKSAILDYRLLGTVA-GRSLLEIELQTGRMHQIRVQMAAMGCPV 189

Query: 267 VGDHKYCANFKGNFTS---------------PIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           VGD +Y     G+ T+                   ++ LHA  + +PHP     + I AP
Sbjct: 190 VGDQEYQTPQAGDTTTRTVEEQSTTNLTTQPRGSERIALHASQIIVPHPIRFDEVTIHAP 249

Query: 311 LPAHMVKTW 319
            PA     W
Sbjct: 250 FPAEWASYW 258


>gi|189461733|ref|ZP_03010518.1| hypothetical protein BACCOP_02399 [Bacteroides coprocola DSM 17136]
 gi|189431493|gb|EDV00478.1| hypothetical protein BACCOP_02399 [Bacteroides coprocola DSM 17136]
          Length = 224

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 70/234 (29%), Positives = 116/234 (49%), Gaps = 18/234 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + NK A   VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHIIIVNKTASEIVQGDKTGDIPLSETVKQYLKEKYSKPGNVFLGVAHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L + FR   ++K YW++V   P  ++  + ++L++       Y + 
Sbjct: 63  GLVVFAKTSKALARLNDMFRNSEVKKTYWAIVKQCPPAEEGELVHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  K +  A+ ++++I   +Q +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 122 -DKEVKNSKKAVLNYRLIG-HSQNYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGFP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
                 S     + LHAR +   HP     + ITAP+P+     W+  GF+ ++
Sbjct: 180 RSNPDGS-----ICLHARRVRFIHPVSKEPIDITAPVPSG--NLWN--GFEMNK 224


>gi|326577536|gb|EGE27413.1| tRNA pseudouridine synthase C [Moraxella catarrhalis O35E]
          Length = 258

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 99/239 (41%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + + NKPA + V       +     +++  +   Q     HRLD+ TSG+LV 
Sbjct: 19  ILYQDACMVIINKPANMLVHRSWLDKHETCFVVQTLRNQINQHVYPVHRLDRPTSGVLVF 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  L + F    IQK Y ++V GI       I   L  +     D         
Sbjct: 79  ALDSQTAGLLAKQFENHHIQKSYLAVVRGIIGT--GRIDYALKPRLDKIADKF---SNPN 133

Query: 221 KGANYAISHFKVIDCFAQ-----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           K +  AI+ ++V+    Q           ++  + + P TGR HQLR H  H+  PIVGD
Sbjct: 134 KASKSAITDYQVLATTQQPFISCRRFDSSRYSLVCLTPITGRKHQLRRHMKHIFHPIVGD 193

Query: 270 HKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
             Y    +           +L LHA  +   HP    + +I APL     +   + G+ 
Sbjct: 194 TTYGDKVQNRAVLAHIGVKRLLLHAHQLQFCHPLYDEMIRIVAPLDTAFCQVMTAFGWS 252


>gi|326571287|gb|EGE21309.1| tRNA pseudouridine synthase C [Moraxella catarrhalis BC1]
          Length = 254

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 99/239 (41%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + + NKPA + V       +     +++  +   Q     HRLD+ TSG+LV 
Sbjct: 15  ILYQDACMVIINKPANMLVHRSWLDKHETCFVMQTLRNQINQHVYPVHRLDRPTSGVLVF 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  L + F    IQK Y ++V GI       I   L  +     D         
Sbjct: 75  ALDSQTAGLLAKQFENHHIQKSYLAVVRGIIGT--GRIDYALKPRLDKIADKF---SNPN 129

Query: 221 KGANYAISHFKVIDCFAQ-----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           K +  AI+ ++V+    Q           ++  + + P TGR HQLR H  H+  PIVGD
Sbjct: 130 KASKSAITDYQVLATTQQPFISCRRFDSSRYSLVCLTPITGRKHQLRRHMKHIFHPIVGD 189

Query: 270 HKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
             Y    +           +L LHA  +   HP    + +I APL     +   + G+ 
Sbjct: 190 TTYGDKVQNRAVLAHIGVKRLLLHAHQLQFCHPLYDEMIRIVAPLDTAFCQVMTAFGWS 248


>gi|237809106|ref|YP_002893546.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
 gi|237501367|gb|ACQ93960.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
          Length = 220

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/224 (27%), Positives = 103/224 (45%), Gaps = 12/224 (5%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           +          +LYED  I V NKP+G+    G  + +     +   V  +  +    HR
Sbjct: 5   VYNPPMEPYLDILYEDEHIIVMNKPSGLLSVPGKALEH--ADSIAWRVRQRCPEAGSVHR 62

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++++A+   A   L + F+ R+ +K Y++ VWG     +  I   L       
Sbjct: 63  LDMSTSGVILMAKYSKATGILGKQFQERKTEKFYYAWVWGQVAGTEGMIDLPLCVD---- 118

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +   +   N +    A +H++ +   A +   +++ P+TGR+HQLRVH   +G PI+GD
Sbjct: 119 WENRPLQHVNYEHGRPAQTHWQRVRVEADR-TLMKLTPYTGRSHQLRVHMKELGHPILGD 177

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           H Y      +    +Q    LHA  +   HP  G  ++  AP P
Sbjct: 178 HLYAPKEVQDLVPHLQ----LHAAMLSFYHPVTGEQMRFEAPAP 217


>gi|163751074|ref|ZP_02158305.1| tRNA pseudouridine synthase C [Shewanella benthica KT99]
 gi|161329235|gb|EDQ00234.1| tRNA pseudouridine synthase C [Shewanella benthica KT99]
          Length = 284

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 105/239 (43%), Gaps = 17/239 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ED  I   +KPAG+ V             ++   D  G      HRLD+ TSG+L+ A
Sbjct: 39  LFEDDDIVAIHKPAGLLVHRSYLARRERFFAMQLTRDKVGCHVFPVHRLDRPTSGVLLFA 98

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           ++   A  L E F  + I+K Y ++V G             ++   +G   V      +K
Sbjct: 99  KSSEMANTLCEQFADKTIEKHYLAIVRGNMHEAATLDYPLKVELDDLGDKNVAA----DK 154

Query: 222 GANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            A  A++ ++ +             + ++  +++ PHTGR HQLR H  H+  PI+GD  
Sbjct: 155 PAQDAMTSYQPLLNTEIPFSSGRYASSRYALVKLTPHTGRKHQLRRHMAHLRHPILGDTT 214

Query: 272 YCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
           +    +  F       N+L+L A+ +   HP  G R+ I A L    +  +  LG+  +
Sbjct: 215 HGDGKQNKFFREHFSVNRLWLIAKQLTFNHPRTGERMVIEAELEHQWLDLFKGLGWDEE 273


>gi|116332841|ref|YP_794368.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
 gi|116098188|gb|ABJ63337.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
          Length = 295

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/277 (22%), Positives = 105/277 (37%), Gaps = 27/277 (9%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           +V V+      N  + SG  V++  +                              +LYE
Sbjct: 40  RVLVNGAYRSMNQLVYSGDTVQLTFLPTDFKEPFPN----------VDPDSAATVAVLYE 89

Query: 105 DSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
            + + V NK  G        G        + +++      P +  RLDQET+G L++ +T
Sbjct: 90  SADLLVINKTRGSKTHPNQPGERGTTLNHVAAYLGPDQPGPYILSRLDQETTGALLMTKT 149

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
            A    +      +++Q+ Y + V G          + + +              N   A
Sbjct: 150 PAVVPIMVRHIADKQVQRTYLAWVHGRLTGD-GVFTDPIGRDPLDKRKRQ----VNGDHA 204

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
             A++H+ V +   Q    ++++  TGRTHQLRVH    G P++GD  Y        T+ 
Sbjct: 205 QPAVTHYHVCEYREQ-ATLIQLRLETGRTHQLRVHLAAAGHPLIGDPLYG-------TAT 256

Query: 284 IQNKLYLHARYMDLPHPEG---GRLQITAPLPAHMVK 317
             N+L LH   +  P P         +TAP+PA   +
Sbjct: 257 DTNRLRLHCWQLTFPQPFTVNDAHTTVTAPVPADFDQ 293


>gi|23464749|ref|NP_695352.1| hypothetical protein BL0123 [Bifidobacterium longum NCC2705]
 gi|227546864|ref|ZP_03976913.1| possible pseudouridylate synthase [Bifidobacterium longum subsp.
           infantis ATCC 55813]
 gi|317481580|ref|ZP_07940616.1| RluA family pseudouridine synthase [Bifidobacterium sp.
           12_1_47BFAA]
 gi|23325319|gb|AAN23988.1| widely conserved hypothetical protein in the Rlu family of
           pseudouridine synthases [Bifidobacterium longum NCC2705]
 gi|227212826|gb|EEI80707.1| possible pseudouridylate synthase [Bifidobacterium longum subsp.
           infantis ATCC 55813]
 gi|316916940|gb|EFV38326.1| RluA family pseudouridine synthase [Bifidobacterium sp.
           12_1_47BFAA]
          Length = 320

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 63/299 (21%), Positives = 116/299 (38%), Gaps = 19/299 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ +  V   +     R D         I+      ++ SGQ RV  + V  ++ +Q+G+
Sbjct: 1   MSRI--VPAPDALVGKRFDVAVAKML-GISRSKAADLVDSGQARVLGREVARSSTLQAGE 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V        L     E + + + + +    D +  +        +      G +V G  
Sbjct: 58  TVEFD-----LAEEQAEPEPIATDMAVVYEDDDVVVVDKPVGVAAHASVGWTGPTVLGS- 111

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                 D  +         +  +  RLD  TSG+++V ++  A   +   F    ++K Y
Sbjct: 112 ----LRDRGVHITSYGAAGREGIVSRLDVGTSGLMLVCKSDLAYTEMRRQFAEHEVKKTY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G  K  K  I   + +                     A++H+ V++ F  +   +
Sbjct: 168 HALVQGGLKENKATIEAPIGR-----AKVSDFRFCVTPAGKPAVTHWDVLERFGHEATLV 222

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            +   TGRTHQ+RVH   +G P+ GD  Y AN   +    + ++ +LHA  ++  HP  
Sbjct: 223 SVNLETGRTHQIRVHFSSIGHPLCGDPMYGANPVLSEALGL-DRQWLHAMKLEFRHPRT 280


>gi|21911297|ref|NP_665565.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|21905511|gb|AAM80368.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
          Length = 282

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 69/289 (23%), Positives = 106/289 (36%), Gaps = 28/289 (9%)

Query: 23  RWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +        I    ++  LR    V ++   V + + ++ G  V++              
Sbjct: 4   KALLEEQLLIPR-KIRHFLRTKKHVLINGHPVNWQSCVKYGDQVKLFFDHE--------- 53

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
              D    +       K   LYED  I + NKP G+      G        L       G
Sbjct: 54  ---DYPEKIIVMGQAEKVTCLYEDEHIIIVNKPEGMKTH---GNDPTELALLNHVSAYTG 107

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           Q   + HRLD+ETSG ++ A+T      L      R I + Y +LV G   + +    + 
Sbjct: 108 QTCYVVHRLDKETSGAILFAKTPFILPILNRLLEKRDIHREYLALVHGSLDSPRVTYHHP 167

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +  H     V     +      AI+   ++  F +    L  Q  TGRTHQ+RVH  H
Sbjct: 168 IGRHRHDRRKRV----VDPINGKKAITEVTLVKNFHKTASLLNCQLQTGRTHQIRVHLAH 223

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
            G  + GD  Y    K         +L LHA  + L HP     + + A
Sbjct: 224 QGHVLFGDPLYSNGKKD------CARLMLHAYQLRLKHPLTQEDICVQA 266


>gi|315127084|ref|YP_004069087.1| tRNA pseudouridine synthase C [Pseudoalteromonas sp. SM9913]
 gi|315015598|gb|ADT68936.1| tRNA pseudouridine synthase C [Pseudoalteromonas sp. SM9913]
          Length = 254

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 99/256 (38%), Gaps = 17/256 (6%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
              +  ++ +  +LY+D      +KP+G+ V       +     ++   D  GQ     H
Sbjct: 3   ERPEPIEYGELSILYQDENYVAIDKPSGLLVHRSFLDKHETQFAMQMLRDQIGQHVFPVH 62

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG+L+ A +  AA+ + + F    I K Y +LV G              +   I
Sbjct: 63  RLDRPTSGVLLFALSSEAARDMNQLFIEGTITKRYLALVRGFAPESVFLDKPLKEELDKI 122

Query: 209 GGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVH 258
              +       +K A  A + F  +               ++  +E  P TGR HQ+R H
Sbjct: 123 ADKFADQ----DKAAQEAQTQFNCLHQAALPIPIGKYPTVRYSLVECFPKTGRKHQIRRH 178

Query: 259 ALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
             H+  PI+GD  +  N    F        +L L A  +   HP     + I APL   M
Sbjct: 179 LKHLSLPIIGDVNHGDNQHNQFFREHFSLRRLMLFASELSFVHPYNNEPITIKAPLGDAM 238

Query: 316 VKTWDSLGFKYDRNLY 331
           +     LG+      Y
Sbjct: 239 LNICKQLGWPEQEEDY 254


>gi|294054947|ref|YP_003548605.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
 gi|293614280|gb|ADE54435.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
          Length = 227

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 65/240 (27%), Positives = 104/240 (43%), Gaps = 25/240 (10%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   L+Y+D+ + + +KP+G+ V      A + +  ++   D  GQ+    HRLD+ TSG
Sbjct: 1   MPLNLIYQDTDLVIIDKPSGLLVHRSKLDAQNTEFAVQQLRDQIGQEVFPCHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV A  RA  + + + F   R+ K Y ++V G P N    I   L ++           
Sbjct: 61  LLVFALNRATLRTVAQQFAEGRVWKSYLAIVRGWP-NADGIIDYPLRQEEPPHK------ 113

Query: 217 KQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                    A +H+  + C             +   LE+QP +GRTHQLR H  H+  PI
Sbjct: 114 ------IQEAQTHYTTLKCSELPVPVGRYATARVALLELQPQSGRTHQLRRHLAHIRHPI 167

Query: 267 VGDHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           +GD ++    +  F       N+L L A  +    P G    I APL     +  + L  
Sbjct: 168 LGDTRHGDGAQNRFMRETAKCNRLLLRATQLRFTLPNGVEQHIEAPLEEDFEEARNRLRL 227


>gi|200387471|ref|ZP_03214083.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|199604569|gb|EDZ03114.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
          Length = 219

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDEHIMVVNKPSGLLSVPGR-LEAHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +         +  +L LHA  + + HP  G  +     +PA  
Sbjct: 180 FYASPE----ALSLAPRLQLHAEMLTITHPAYGNSMTFK--VPADF 219


>gi|329117142|ref|ZP_08245859.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
 gi|326907547|gb|EGE54461.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
          Length = 300

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 65/275 (23%), Positives = 108/275 (39%), Gaps = 28/275 (10%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++ + + + + ++ G ++ +    +            D     
Sbjct: 38  IPR-KIRHFLRTKKNLLINNESINWQSPVKKGDLITLDFDPD------------DYPEKS 84

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               D      L+ED  I V NKP G+           +   + ++     Q   + HRL
Sbjct: 85  ILLGDATLVDCLFEDENIIVVNKPEGMKTHANQPEELALLNHVSAFCQ---QTCYVVHRL 141

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG +V A+       L +    R I + YW+LV G    K     + + +  H   
Sbjct: 142 DMETSGAIVFAKNPFILPILNQLLEKREIHRDYWALVGGQIPQKSLVYKDKIGRHRHDRR 201

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             V     + K    AI++   +  +      +  Q  TGRTHQ+RVH  + G PI+GD 
Sbjct: 202 KRV----VDPKNGQTAITNLTRLKVYPSNRSLVNCQLETGRTHQIRVHLSYHGFPIIGDP 257

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            Y        + P + +L LHA  + L HP    L
Sbjct: 258 LY-------QSHPNKERLMLHAHQLQLVHPLTLEL 285


>gi|268608720|ref|ZP_06142447.1| hypothetical protein RflaF_04377 [Ruminococcus flavefaciens FD-1]
          Length = 446

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 124/322 (38%), Gaps = 44/322 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M  ++  V    +  + L  +       ++   L K+ R  G +  D K V+  + +  G
Sbjct: 1   MKELKLTV--ETDAPVTLQNFLIGE-KGVSKRLLTKLKRIDGGITRDGKTVRSIDTVNKG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V+ +    ++                  + +  L    +YE   + VFNKP+G+ V   
Sbjct: 58  DVIVLRFGDDS----------------FLEPNPDLDVPAVYESDGVIVFNKPSGMPVHPS 101

Query: 123 SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                H    L +   +       R  +RLD++TSG+ VVA+          +    R +
Sbjct: 102 ---IKHQGDTLGNKFAAMFPDLTFRAVNRLDRDTSGLCVVAKNAL-----AANALQGRCE 153

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K+Y++ V G    +   I   + ++         +++   +    A++H++ I    + +
Sbjct: 154 KVYYAAVTGEIP-ETGTIDAPIARERE-----SIIIRCVREDGQRAVTHYRRIAYNGR-Y 206

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
              E+   TGRTHQ+RVH  ++G P+ GD  Y              +  LH   M    P
Sbjct: 207 SLAEIHLETGRTHQIRVHFSYIGHPLAGDDLYGGTRCD------IGRQALHCGQMSFTDP 260

Query: 301 EGG-RLQITAPLPAHMVKTWDS 321
             G  + + A LP  +     S
Sbjct: 261 VTGEEVTVRAELPDDIKAIIKS 282


>gi|169349788|ref|ZP_02866726.1| hypothetical protein CLOSPI_00526 [Clostridium spiroforme DSM 1552]
 gi|169293356|gb|EDS75489.1| hypothetical protein CLOSPI_00526 [Clostridium spiroforme DSM 1552]
          Length = 275

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/302 (20%), Positives = 123/302 (40%), Gaps = 39/302 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   ++  +++ + L  +      +++   ++ I  +G + V+        R++   V+ 
Sbjct: 1   MNKFIIGIEDDEVLLKDFLFKQ--NLSKKAIKAIKMNGDILVNGNHQTVRYRLKKNDVIE 58

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +            E                    ++YED    + +KPAGI         
Sbjct: 59  LIWPDEISTMEPYE----------------YSLKIIYEDENYLIIDKPAGIPCMPTKRYP 102

Query: 127 Y-HIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              I   +  +      K    L +RLD++T G++++A+ R A   L++    ++++++Y
Sbjct: 103 NKTIANAIIYYFQMCNLKATVHLVNRLDKDTQGLMLIAKNRQAHYLLSKDI--KQVKRVY 160

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
             LV GI K +   I   ++K      D   V +  +     AI+ ++ +  F  K   +
Sbjct: 161 HCLVEGILKGE-GIIDKPIIK------DKNSVKRLIDASGKKAITVYRSLKIFDNK-SLI 212

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E    TGRTHQ+RVH   +G P+VGD  Y +     +        YL + Y++   P   
Sbjct: 213 ECDLKTGRTHQIRVHLSSIGHPLVGDGLYGSMETKTY--------YLDSVYLEFVSPFTN 264

Query: 304 RL 305
           +L
Sbjct: 265 KL 266


>gi|320325275|gb|EFW81342.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. glycinea str. B076]
          Length = 211

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 65/214 (30%), Positives = 101/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIYQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L  G P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCCGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEGGKHALTFWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL    P P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|225869691|ref|YP_002745638.1| RNA pseudouridylate synthase [Streptococcus equi subsp. equi 4047]
 gi|225699095|emb|CAW92255.1| RNA pseudouridylate synthase [Streptococcus equi subsp. equi 4047]
          Length = 301

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 110/269 (40%), Gaps = 29/269 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              V V+ + + + + ++ G  +++            ++   D  + + K         L
Sbjct: 49  KKHVWVNDELINWQSPVKQGDHIKLQFD---------QEDYPDKGILMGKPG---LVDCL 96

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP G+      G        L       G+   + HRLD ETSG ++ A+
Sbjct: 97  YQDEHLIIVNKPEGMKTH---GNEPTELALLNHVSAYTGKTCYVVHRLDMETSGAILFAK 153

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      R I++ YW+L+ G  + +     + + +  H     V     + K 
Sbjct: 154 NPFILPILNRLLEHRDIKRDYWALIEGQLEQQTVTYRDPIGRHRHDRRKRV----VDSKH 209

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              AI+H  ++  F Q  C +  +  TGRTHQ+RVH  H   P++GD  Y          
Sbjct: 210 GQEAITHLALLQAFDQ-TCLVNCRLETGRTHQIRVHLAHHKHPLIGDPLYSRQKAE---- 264

Query: 283 PIQNKLYLHARYMDLPHPEGGRL-QITAP 310
               +L LHA  + L HP    + ++TAP
Sbjct: 265 ----RLMLHAHQLTLRHPLAQEMIRVTAP 289


>gi|75674513|ref|YP_316934.1| pseudouridine synthase [Nitrobacter winogradskyi Nb-255]
 gi|74419383|gb|ABA03582.1| pseudouridine synthase [Nitrobacter winogradskyi Nb-255]
          Length = 264

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 73/268 (27%), Positives = 124/268 (46%), Gaps = 22/268 (8%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + + +I  +        + +++ +L+ D  + V +KPAGI+V  G     +++    +  
Sbjct: 1   MPQPEIKRTVDTAQPTPEEIQARVLHRDGLMLVIDKPAGIAVHRGPKGGANLEASFDALR 60

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               + P L HRLD++TSG LV+ R R A   L   F+  +I K YW++V G P   +  
Sbjct: 61  FGLPRPPVLAHRLDRDTSGCLVLGRHRKATASLGLLFKHGKISKTYWAVVEGGPSEDEGA 120

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF----------CWLEMQP 247
           I   L + +   G +     + +     + + +KV+   +              WL ++P
Sbjct: 121 IDIPLGRLNEERGWWQ----KPDPNGLPSTTKWKVLGRSSPDTSTVSGAGVQLTWLSLEP 176

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYC-------ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            TGRTHQLRVH   MG PIVGD+ Y        +  +       +  L+LHAR + +P  
Sbjct: 177 LTGRTHQLRVHCAAMGWPIVGDNIYGTQASLRRSRNEQYVPRLDEPGLHLHARQIAIPLS 236

Query: 301 EGG-RLQITAPLPAHMVKTWDSLGFKYD 327
                + +TAP PAH+     + G+  +
Sbjct: 237 RNKPPVVVTAPAPAHLHARLRACGWNAE 264


>gi|329121404|ref|ZP_08250029.1| pseudouridylate synthase [Dialister micraerophilus DSM 19965]
 gi|327469694|gb|EGF15161.1| pseudouridylate synthase [Dialister micraerophilus DSM 19965]
          Length = 303

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 60/295 (20%), Positives = 125/295 (42%), Gaps = 27/295 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNH--YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           ++   +  D+   RLD + K     PH   + ++ + +  +++V+ K+   N ++++G +
Sbjct: 1   MKEYKITPDKNGKRLDNYIKEKEKIPHF--IFIKSL-KKNKIKVNGKKESGNYKLKTGDI 57

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +         ++I  + K     ++ +         + YED  I +  K AGI     + 
Sbjct: 58  IT--------SYIENKNKNEKEKIHFS---------INYEDENIIIVEKEAGILCNDTTN 100

Query: 125 IAY--HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  D   +   +    +    HR+D  T+G+++ A+   A   L  + + R I+K 
Sbjct: 101 KEEKTLHDEINEYLKEKNEPEAYPVHRIDLNTTGLVIFAKNMHARAILDRAIKERNIKKY 160

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  +  G  K K   + + L K +    + V++ ++  KG+  A  ++K +         
Sbjct: 161 YLCVTTGTMKKKSGKLEHQLFKDAK--NNKVYIYEKPCKGSKTATMNYKCLKT-ENGLSL 217

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+R    ++G PI+GD KY            +  L  +   ++ 
Sbjct: 218 VECELITGRTHQIRSQLSYIGYPILGDDKYGNKTINKTYKERKQLLCAYKIKINF 272


>gi|189461580|ref|ZP_03010365.1| hypothetical protein BACCOP_02239 [Bacteroides coprocola DSM 17136]
 gi|189431690|gb|EDV00675.1| hypothetical protein BACCOP_02239 [Bacteroides coprocola DSM 17136]
          Length = 549

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 74/250 (29%), Positives = 108/250 (43%), Gaps = 22/250 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++   ++  + +    H D  K  ++YED  + V NKPAG+    G      +
Sbjct: 315 CEPILKHMLVGLQVEKNPLAENIHQDT-KPEIVYEDDWLVVVNKPAGMLSVPGKEALNSV 373

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             FL      +   P L HRLD  TSG+L+ A+ +   Q L   F  R I+K Y +++  
Sbjct: 374 YQFLHERY-PEATGPMLVHRLDMATSGLLLAAKDKDTHQKLQALFCGREIKKRYTAVLSS 432

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I    +  I+  L    H     +   +        AI+ +KV++    K   +   P T
Sbjct: 433 IVNADEGTISLPLCLNFHDRPRQMVSFEY----GKPAITRYKVLERKNGK-TLIAFYPLT 487

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVHA H   + CPIVGD  Y             ++LYLHA  +   HP  G  +
Sbjct: 488 GRTHQLRVHAAHPQGLACPIVGDELYGKR---------ADRLYLHAAELSFIHPVNGEDI 538

Query: 306 QITAPLPAHM 315
            I     A  
Sbjct: 539 TICCE--ADF 546


>gi|326799702|ref|YP_004317521.1| pseudouridine synthase [Sphingobacterium sp. 21]
 gi|326550466|gb|ADZ78851.1| pseudouridine synthase [Sphingobacterium sp. 21]
          Length = 235

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 71/233 (30%), Positives = 113/233 (48%), Gaps = 15/233 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQ 152
            S +LYED+ +   NK AG  VQ        +D  +K ++  K  KP      + HRLD+
Sbjct: 10  DSDILYEDNHLIAVNKRAGDIVQVDDTGDEPLDEKVKQYLAKKYNKPNGAFLGVVHRLDR 69

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
             SG+++ A+T  A   + + F+ R + K YW++V   P      + +WL+K S  G + 
Sbjct: 70  PVSGVILFAKTSKALDRINKMFKSREMHKTYWAVVRNRPAQTAGTLVHWLVKNS--GKNV 127

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                   KG+  A  H+K+I      +  +E+ P TGR HQ+RV    + CPIVGD+KY
Sbjct: 128 TKAYDHEVKGSLRAELHYKLIGEL-NGYYLVEVNPVTGRPHQIRVQLASLNCPIVGDNKY 186

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAH-MVKTWDSLG 323
                      ++  + LHAR +   HP +   ++I A LP     + ++  G
Sbjct: 187 GYPRGS-----LKKSICLHARKLVFEHPVKKEEVKIFASLPRDGFWERFEVFG 234


>gi|104780626|ref|YP_607124.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           entomophila L48]
 gi|95109613|emb|CAK14314.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           entomophila L48]
          Length = 211

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 65/213 (30%), Positives = 102/213 (47%), Gaps = 11/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED+ I V NKP  +    G     + D  +    ++      + HRLD ETSGI+++
Sbjct: 8   ILHEDAAILVINKPTLLLSVPGRA-EDNKDCLITRLQENGYPDALIVHRLDWETSGIILL 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR   + + L+  F  R  +K Y +L WG P      I   L           HVV  + 
Sbjct: 67  ARDADSHRELSRQFHDRETEKAYTALCWGQPALDSGSIDLPLRYDPPT--KPRHVV--DH 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +   +A++ +++++     +C +E+ P TGR+HQLRVH L +G P++GD  Y        
Sbjct: 123 EQGKHALTFWRIVERCGD-YCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY----ANPE 177

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                 +L LHA  +   HP  G RL+   P P
Sbjct: 178 ALAAHERLCLHASMLSFTHPVSGERLKFECPAP 210


>gi|317177424|dbj|BAJ55213.1| hypothetical protein HPF16_0616 [Helicobacter pylori F16]
          Length = 327

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 67/343 (19%), Positives = 140/343 (40%), Gaps = 36/343 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           +Q V +   +   RLD +       I+   +  +++ G V   KK VK     ++ G  +
Sbjct: 1   MQKVFIALTDH-KRLDEFLAKEL-QISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEI 58

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                   +    K    L+  +++ED  + V NKP  + +     +
Sbjct: 59  TL--------------LTPKITPKPLKRGLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSV 104

Query: 126 AYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
               +  L  W++ K  +           + HRLD++TSG +V+A+      +L+E  + 
Sbjct: 105 ---KEPTLVDWLEFKNYELSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVYLSEQLKT 161

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + + + Y +L+    K +K  +  +L +  +     + +    ++ + Y+ S F  +   
Sbjct: 162 KMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAKKEKSRYSKSEFTSLLTS 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 +  +  TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++
Sbjct: 222 QNHLNLIGAKLFTGRTHQIRAHLEYLNRHIIGDNLYGLN---QALPKEEIRIMLHAYLIE 278

Query: 297 LPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
             HP    +L+   PL   M++    +   +D+    + L  +
Sbjct: 279 FKHPRSEQKLRFKVPLLKDMLEYLKKV---FDKENLDEVLDEE 318


>gi|328944704|gb|EGG38865.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1087]
          Length = 290

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 121/303 (39%), Gaps = 32/303 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRI 67
            + + +    M +    +  +  I    ++  LR    V V+   + +   IQ G  + +
Sbjct: 4   TLTIPDGLPAMTVKELLEEQFL-IPR-KIRHFLRTKKHVSVNGLSINWQTVIQPGDDICL 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                    I  E+     ++ L    +      LY+D  + + NKP G+          
Sbjct: 62  ---------IFDEEDYPQKTILL---GNGELVEELYQDQHLIIVNKPEGMKTHANEPTEL 109

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   + ++V   G+   + HRLD+ETSG ++ A+       L      R I + Y +LV
Sbjct: 110 ALLNHVSAYV---GETCYVVHRLDKETSGAVLFAKNPFVLPILNRLLEKREISREYCALV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G   +KK    + + +  H     +     + +   YA +H   +  F Q    ++ Q 
Sbjct: 167 QGKFPSKKLIYKDKIGRDRHDRRKRL----VDPRKGLYAETHVTRVKQFGQ-ASLVKCQL 221

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQ 306
            TGRTHQ+RVH  H G  +VGD  Y    +G        +L LHA  +   HP    ++ 
Sbjct: 222 KTGRTHQIRVHLAHHGHQLVGDPLYHPQPQG--------RLMLHAHRLTFTHPFTLEKIT 273

Query: 307 ITA 309
           + A
Sbjct: 274 VEA 276


>gi|254509017|ref|ZP_05121122.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus 16]
 gi|219548052|gb|EED25072.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus 16]
          Length = 240

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 98/238 (41%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IIYQDDYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +          ++   I   +       +
Sbjct: 64  ALSSEVASQVMPMFANHEMEKTYHAIVRGWIEESGRLDYALKVELDKIADKHASQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ +  +               ++C +EM+P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQEAITDYWPLAKVEVPHSTGKFPTTRYCLMEMKPLTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNFTSPI--QNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
            +           +   ++L LHA  ++  HP    +L I A +            ++
Sbjct: 180 THGDGKHNKLFRDVYDSHRLLLHASSLEFVHPFTNEKLLIKASVDETWQALCQEFDWQ 237


>gi|322834449|ref|YP_004214476.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321169650|gb|ADW75349.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 239

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 105/234 (44%), Gaps = 16/234 (6%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I E        N    +D     ++++D  I V NKP+G+    G  +A H D  + + +
Sbjct: 14  IPEPSKTRPLENYNPPTDPW-LQVIFQDEHIMVVNKPSGLLSVPGK-LAEHQDSLM-TRI 70

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +  +    HRLD  TSG++VVA T+ A + L   FR R  +K+Y + VWG  +     
Sbjct: 71  QQEFPEAESVHRLDMSTSGVIVVALTKDAERELKRQFRERETKKVYIARVWGRVEEDYGI 130

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   L+             K   +    A++ ++V+         ++++P TGR+HQLRV
Sbjct: 131 IDLPLICDYPNRPK----QKVCHETGKKALTQYEVMSWDDDGTTRVKLRPITGRSHQLRV 186

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           H L +G PI+GD  Y              +L LHA+ +   HP        APL
Sbjct: 187 HLLALGHPILGDKFYAHPQ----ALAAAGRLQLHAQELSFYHPITD-----APL 231


>gi|323343472|ref|ZP_08083699.1| ribosomal large subunit pseudouridine synthase A [Prevotella oralis
           ATCC 33269]
 gi|323095291|gb|EFZ37865.1| ribosomal large subunit pseudouridine synthase A [Prevotella oralis
           ATCC 33269]
          Length = 573

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 111/231 (48%), Gaps = 21/231 (9%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +++ T  +      ++YED  I V NKPAG+    G   A  +   ++         P +
Sbjct: 354 ALSPTNATSVPDIPIVYEDEAIVVINKPAGMLSVPGKACALSVYDLMRMRYPDS-NSPLI 412

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP---KNKKECIANWLL 203
            HRLD  TSG+L++A+T+ A + L   F    I+K Y +++ G+P   +     I +  L
Sbjct: 413 VHRLDMATSGLLIIAKTKNAHRILQRQFAEHTIRKQYIAVLDGVPDSCRWPSAGIISLPL 472

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V   + +    A++ +K++    ++   + + PHTGRTHQLR+H  H  
Sbjct: 473 RPDLADRPRQLV---DFEHGKEAVTEYKILRTAGEE-TRIALFPHTGRTHQLRIHCAHPY 528

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            + CPI GD+ Y              +LYLHA  M+  HP  GR ++++A 
Sbjct: 529 GLNCPIKGDNLYGTR---------SQRLYLHAESMEFIHPVSGRCIKLSAE 570


>gi|256370634|ref|YP_003108459.1| putative RNA pseudouridine synthase fragment [Candidatus Sulcia
           muelleri SMDSEM]
 gi|256009426|gb|ACU52786.1| putative RNA pseudouridine synthase fragment [Candidatus Sulcia
           muelleri SMDSEM]
          Length = 246

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 111/238 (46%), Gaps = 21/238 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +K  LLYED  I + NK +G+ V  G+G     ++  +  + K+        P L HR+D
Sbjct: 1   MKLHLLYEDEYILIINKKSGLVVHPGNGNKSMTLSNGLHFYFKNKKIMNDNYPFLGHRID 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG+++V+++      +++ F   +I++ Y +LVWGI   K+  I   + +       
Sbjct: 61  KGTSGLILVSKSEKILNKISKQFWFNKIKRKYITLVWGIFFKKEGTIICNIGRCLK--NK 118

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V  N      AI+H+KV++ F + F  L+    TGRTHQ+RVH  ++G PI  D  
Sbjct: 119 THMNVFPNGCLGKQAITHYKVLETF-KYFSLLKCSLETGRTHQIRVHLKYIGHPIFNDKN 177

Query: 272 YCANFKGNFTSPIQNK------------LYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
           Y  + K       + +              LHA Y++  HP       + +P+P    
Sbjct: 178 YGEDKKYKNFLSFKERIFLEKCFKTLKSQALHAYYLEFKHPIYLKNKYLISPIPDKFK 235


>gi|170017524|ref|YP_001728443.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
 gi|169804381|gb|ACA82999.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
          Length = 300

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 59/282 (20%), Positives = 116/282 (41%), Gaps = 33/282 (11%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G +  + ++V  ++ +  G  V I       N ++                D+    +++
Sbjct: 37  GAILKNGQQVYTSDYLDHGDQVTIVMPTEKGNDLV--------------VPDYRPLDIIF 82

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHI-DGFLKSWVDSKGQK---PRLTHRLDQETSGILV 159
           E+    V +KP G++   G     H     +K  ++    +   P +  RLD++TSGI++
Sbjct: 83  ENEHWLVVDKPYGVTTVPGHADRLHTLVNQVKGHLEEINAEDLVPHVVTRLDRDTSGIVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ R A   L +  +   ++K Y +   GI       I   + +   + GD++    ++
Sbjct: 143 LAKHRFAHAVLDQQLQDHTVEKFYLAYPSGILTEDHGDINAPIGR---VEGDFIKREVRD 199

Query: 220 EKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +     + + + V   + +        +++Q HTGRTHQ+RVH  ++G P+VGD  Y   
Sbjct: 200 D--GKPSRTEYWVERRYDENGEQPMTRVKVQLHTGRTHQIRVHFKNIGHPLVGDDLYGGP 257

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMV 316
                      +  LHA +M    P      +    LP  + 
Sbjct: 258 LWHGL-----KRQALHAYHMRFYDPFIEDYREFNTKLPEDLK 294


>gi|296112643|ref|YP_003626581.1| tRNA pseudouridine synthase C [Moraxella catarrhalis RH4]
 gi|295920337|gb|ADG60688.1| tRNA pseudouridine synthase C [Moraxella catarrhalis RH4]
 gi|326563862|gb|EGE14113.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 46P47B1]
 gi|326566871|gb|EGE17010.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 103P14B1]
 gi|326576787|gb|EGE26694.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 101P30B1]
          Length = 254

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 99/239 (41%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + + NKPA + V       +     +++  +   Q     HRLD+ TSG+LV 
Sbjct: 15  ILYQDACMVIINKPANMLVHRSWLDKHETCFVVQTLRNQINQHVYPVHRLDRPTSGVLVF 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  L + F    IQK Y ++V GI       I   L  +     D         
Sbjct: 75  ALDSQTAGLLAKQFENHHIQKSYLAVVRGIIGT--GRIDYALKPRLDKIADKF---SNPN 129

Query: 221 KGANYAISHFKVIDCFAQ-----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           K +  AI+ ++V+    Q           ++  + + P TGR HQLR H  H+  PIVGD
Sbjct: 130 KASKSAITDYQVLATTQQPFISCRRFDSSRYSLVCLTPITGRKHQLRRHMKHIFHPIVGD 189

Query: 270 HKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
             Y    +           +L LHA  +   HP    + +I APL     +   + G+ 
Sbjct: 190 TTYGDKVQNRAVLAHIGVKRLLLHAHQLQFCHPLYDEMIRIVAPLDTAFCQVMTAFGWS 248


>gi|86146894|ref|ZP_01065213.1| pseudouridine synthase Rlu family protein [Vibrio sp. MED222]
 gi|85835346|gb|EAQ53485.1| pseudouridine synthase Rlu family protein [Vibrio sp. MED222]
          Length = 249

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 104/243 (42%), Gaps = 19/243 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IIYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    +QK Y ++V G  +          ++   I   +     + +
Sbjct: 64  ALSSEVASEVMPMFANHEMQKTYHAIVRGWIEEGDTLDYALKVELDKIADKFA----KED 119

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++C +EM P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEPQEAVTVYEPLAKVEVPYSTGRFPTSRYCLVEMMPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
            +               ++L LHA  +   HP     L + A L    ++ +++  F++D
Sbjct: 180 SHGDGKHNRLFRDDLDSHRLLLHASELRFIHPFTKEELVMKANLDETWLRLFET--FEWD 237

Query: 328 RNL 330
            NL
Sbjct: 238 ANL 240


>gi|218289812|ref|ZP_03494012.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
 gi|218240103|gb|EED07288.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
          Length = 314

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 65/309 (21%), Positives = 127/309 (41%), Gaps = 30/309 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           W      H+   +++ +LR G +RV            +   + I    +   H+  ++ +
Sbjct: 26  WLSQAL-HVPQAHVRHLLRHGAIRVRG---------CAPDHLEIC---DRPAHVWIDEDL 72

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ- 142
               +  T         +LY D  + V +KP  + V      A  +D  ++  ++ +G  
Sbjct: 73  RPVEMAPTSLP---TVRVLYSDPSLMVVDKPENLLVHSDGSDAPTLDACVQRLLNEEGAG 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +    HRLD+ T+G ++ A+     + +       R+++ Y ++  G  + +   ++  +
Sbjct: 130 RAYHVHRLDRGTTGCVLYAKHGLMLRAMDAELAAGRVRRTYLAIACGS-RIRPGVMSAPI 188

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHA 259
            +  H+ G Y             A +H +V+D      +++  + ++  TGR HQ+RVH 
Sbjct: 189 GRDRHVSGRYRVSW-----TGKAARTHVEVLDEADQGGERWTLVRLRLETGRRHQIRVHL 243

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             MG P+VGD  Y              ++ LHA  +   HP  G  + + APLP    K 
Sbjct: 244 SAMGAPVVGDALYGGTPHSALQP---GQIALHAARLQFRHPYAGEDVDVRAPLPPAWAKL 300

Query: 319 WDSLGFKYD 327
              +G  +D
Sbjct: 301 AADVGLSFD 309


>gi|146292442|ref|YP_001182866.1| pseudouridylate synthase [Shewanella putrefaciens CN-32]
 gi|145564132|gb|ABP75067.1| tRNA pseudouridine synthase C [Shewanella putrefaciens CN-32]
          Length = 275

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 69/259 (26%), Positives = 104/259 (40%), Gaps = 17/259 (6%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
               LD  V            +L+ED  I   +KPAG+ V             ++   D 
Sbjct: 6   PDDELDHVVLDNTDEQAPDIRILFEDEHIVAIHKPAGLLVHRSYLARRERFFAMQLTRDL 65

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G      HRLD+ TSG+L+ A++   A  L E F    I+K Y +LV G   ++   + 
Sbjct: 66  VGCHVFPVHRLDRPTSGVLLFAKSSEVANALCEQFAEHSIEKQYLALVRGNM-HESGILD 124

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHT 249
             L  +    GD        +K A  A++ FK +               +F  +++ P T
Sbjct: 125 YPLKVELDELGDKHARQ---DKAAQDAVTAFKPLLNAEIPYPSGRYPTSRFALVQLTPKT 181

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQ 306
           GR HQLR H  H+  PI+GD  +    +  F       N+L+L A+ +   HP    RL 
Sbjct: 182 GRKHQLRRHMAHLRHPILGDTTHGDGKQNTFFREHFGINRLWLIAKKLTFTHPVTQSRLS 241

Query: 307 ITAPLPAHMVKTWDSLGFK 325
           I   L       +  LG+ 
Sbjct: 242 IETELEQQWETVFTGLGWD 260


>gi|16759090|ref|NP_454707.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|29140640|ref|NP_803982.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|213027943|ref|ZP_03342390.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
 gi|213161694|ref|ZP_03347404.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213427538|ref|ZP_03360288.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
 gi|213580242|ref|ZP_03362068.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213646894|ref|ZP_03376947.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213853061|ref|ZP_03382593.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|289826179|ref|ZP_06545291.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|34395804|sp|Q8Z9J5|RLUA_SALTI RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|25514250|pir||AC0514 pseudouridylate synthase (EC 4.2.1.70) - Salmonella enterica subsp.
           enterica serovar Typhi (strain CT18)
 gi|16501380|emb|CAD01251.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Typhi]
 gi|29136264|gb|AAO67831.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Typhi str. Ty2]
          Length = 219

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDEHIMVVNKPSGLLSVPGR-LEAHKDSIM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDQ 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +         +  +L LHA  + + HP  G  +     +PA  
Sbjct: 180 FYASPE----ALSLAPRLQLHAEMLTITHPAYGNSMTFK--VPADF 219


>gi|319938146|ref|ZP_08012544.1| pseudouridine synthase [Coprobacillus sp. 29_1]
 gi|319806667|gb|EFW03316.1| pseudouridine synthase [Coprobacillus sp. 29_1]
          Length = 279

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 77/309 (24%), Positives = 124/309 (40%), Gaps = 39/309 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINAL 74
           E  M L ++           +++ +L+   V VD      +   +Q GQ V I    N  
Sbjct: 6   EVPMPLMQFLLEKTSQK-RNDIKNLLKYQNVWVDGHIETHYAYDLQVGQTVEIQAKKN-- 62

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFL 133
                                 +  ++LYED +I V +KP G+   Q           ++
Sbjct: 63  ---------------------DMPFVILYEDKEIIVIDKPCGLLSEQTAKENEKTAYQYV 101

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K ++  K +   L HRLDQ TSGIL+  + +     LT+++      + Y ++V G  K 
Sbjct: 102 KQYLYKKKENIFLVHRLDQYTSGILMFVKNKKLYDILTQNWNKYVKTRGYIAIVEGQMKK 161

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K  I N+L +          V    ++    AI+H+K I    +++  LE+   TGR +
Sbjct: 162 TKGTIENYLAESKTQN-----VYITTKEQGKKAITHYKQIQSN-KRYSMLEVYLDTGRKN 215

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           Q+RVH   +   IVGD KY A       S    +L LHA      HP     ++  +  P
Sbjct: 216 QIRVHLSSLHHSIVGDSKYGAQ------SNPLKRLGLHAHEFMFVHPLTHKEMRFVSKTP 269

Query: 313 AHMVKTWDS 321
               K +  
Sbjct: 270 ESFEKLFKK 278


>gi|16763485|ref|NP_459100.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|161612432|ref|YP_001586397.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167550721|ref|ZP_02344478.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|168234851|ref|ZP_02659909.1| pseudouridine synthase, RluA family protein [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. SL480]
 gi|168243497|ref|ZP_02668429.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|168262227|ref|ZP_02684200.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|168464361|ref|ZP_02698264.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|168820922|ref|ZP_02832922.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|194448284|ref|YP_002044064.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194737390|ref|YP_002113113.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197250796|ref|YP_002145080.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197265379|ref|ZP_03165453.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|204927079|ref|ZP_03218281.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|238911153|ref|ZP_04654990.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|34395809|sp|Q8ZRV9|RLUA_SALTY RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|16418593|gb|AAL19059.1| 23S rRNA pseudouridylate 746 synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|161361796|gb|ABX65564.1| hypothetical protein SPAB_00121 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194406588|gb|ACF66807.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194712892|gb|ACF92113.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|195632683|gb|EDX51137.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|197214499|gb|ACH51896.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197243634|gb|EDY26254.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197291993|gb|EDY31343.1| pseudouridine synthase, RluA family protein [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. SL480]
 gi|204323744|gb|EDZ08939.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|205324422|gb|EDZ12261.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|205337540|gb|EDZ24304.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|205342421|gb|EDZ29185.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|205348767|gb|EDZ35398.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|261245328|emb|CBG23116.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           D23580]
 gi|267991767|gb|ACY86652.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301156724|emb|CBW16198.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           SL1344]
 gi|312911065|dbj|BAJ35039.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320084333|emb|CBY94126.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           2007-60-3289-1]
 gi|321222334|gb|EFX47406.1| Ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|323128413|gb|ADX15843.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|332987047|gb|AEF06030.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 219

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDEHIMVVNKPSGLLSVPGR-LEAHKDSIM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y +         +  +L LHA  + + HP  G  +     +PA  
Sbjct: 180 FYASPE----ALSLAPRLQLHAEMLTITHPAYGNSMTFK--VPADF 219


>gi|261252272|ref|ZP_05944845.1| tRNA pseudouridine synthase C [Vibrio orientalis CIP 102891]
 gi|260935663|gb|EEX91652.1| tRNA pseudouridine synthase C [Vibrio orientalis CIP 102891]
          Length = 240

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 99/241 (41%), Gaps = 17/241 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IVFQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +          ++   I   +       E
Sbjct: 64  ALSSEVASQVMPMFANHEMEKTYHAIVRGWIEESGRLDYALKVELDKIADKHASQ----E 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ +  +               ++C +EM+P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQEAITDYWPLAKVEVPHSTGKFPTTRYCLMEMKPLTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNFTSPI--QNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
            +           +   ++L LHA  ++  HP    +L I A +     K      ++  
Sbjct: 180 THGDGKHNKLYREVYDSHRLLLHASSLEFVHPFTNEKLLIKAGIDETWQKLCAEFDWQVP 239

Query: 328 R 328
            
Sbjct: 240 E 240


>gi|251793535|ref|YP_003008264.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           aphrophilus NJ8700]
 gi|247534931|gb|ACS98177.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           aphrophilus NJ8700]
          Length = 219

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 68/218 (31%), Positives = 101/218 (46%), Gaps = 11/218 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   L+Y D  I V NKP+G+    G+   Y+      S V  K       HRLD 
Sbjct: 8   PPQEPWLDLVYRDDYIAVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPAHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGIL+ A ++AA + L   FR R  +K Y +LVWG  +     +   L+       + 
Sbjct: 66  ATSGILLFALSKAADRELKRQFREREPKKYYQALVWGHVEQDHGVVELPLICD----WEN 121

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               K        A++ + V+  +      +++ P TGR+HQLR+H L +G PI+GD  Y
Sbjct: 122 RPRQKICFAQGKRAVTFYDVLQRYPNNTTRVKLTPITGRSHQLRLHMLALGHPILGDKFY 181

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
            A+ +    SP   +L LHA  + + HP  G  +  TA
Sbjct: 182 -AHPQAKAMSP---RLCLHAESLQIQHPISGEIMTFTA 215


>gi|19746943|ref|NP_608079.1| hypothetical protein spyM18_2124 [Streptococcus pyogenes MGAS8232]
 gi|28896670|ref|NP_803020.1| hypothetical protein SPs1758 [Streptococcus pyogenes SSI-1]
 gi|19749193|gb|AAL98578.1| conserved hypothetical protein [Streptococcus pyogenes MGAS8232]
 gi|28811924|dbj|BAC64853.1| conserved hypothetical protein [Streptococcus pyogenes SSI-1]
          Length = 272

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 100/268 (37%), Gaps = 26/268 (9%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              V ++   V + + ++ G  V++                 D    +       K   L
Sbjct: 14  KKHVLINGHPVNWQSCVKYGDQVKLFFDHE------------DYPEKIIVMGQAEKVTCL 61

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  I + NKP G+      G        L       GQ   + HRLD+ETSG ++ A+
Sbjct: 62  YEDEHIIIVNKPEGMKTH---GNDPTELALLNHVSAYTGQTCYVVHRLDKETSGAILFAK 118

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           T      L      R I + Y +LV G   + +    + + +  H     V     +   
Sbjct: 119 TPFILPILNRLLEKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRV----VDPIN 174

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              AI+   ++  F +    L  Q  TGRTHQ+RVH  H G  + GD  Y    K     
Sbjct: 175 GKKAITEVTLVKNFHKTASLLNCQLQTGRTHQIRVHLAHQGHVLFGDPLYSNGKKD---- 230

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITA 309
               +L LHA  + L HP     + + A
Sbjct: 231 --CARLMLHAYQLRLKHPLTQEDICVQA 256


>gi|113971474|ref|YP_735267.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           MR-4]
 gi|113886158|gb|ABI40210.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           MR-4]
          Length = 225

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/215 (29%), Positives = 108/215 (50%), Gaps = 12/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D  I V NKP+G+    G   A++    + + V ++    ++ HRLD  TSG++
Sbjct: 14  LDVLYQDKDIIVVNKPSGLLSVPGRDPAHYDS--VYARVKAEHPHCQIVHRLDMATSGVM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  R+A + L   F  R   K Y + V G  KN    +   L+             K 
Sbjct: 72  VVALIRSAERELKRQFHDRETSKTYLARVAGHIKNDTGSVDYPLICDWPNRPK----QKV 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    +++HF+V+   A++   ++++P TGR+HQLRVH + +G PI+GD  Y      
Sbjct: 128 DHEIGKPSLTHFEVLSR-AKRSTLVKLKPITGRSHQLRVHMMALGHPILGDGFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +    +  +L LHA  + + HP  G  +  +A +P
Sbjct: 187 S----LAPRLLLHAAELTIKHPYTGESMTFSADVP 217


>gi|225551707|ref|ZP_03772651.1| RNA pseudouridine synthase family protein [Borrelia sp. SV1]
 gi|225371734|gb|EEH01160.1| RNA pseudouridine synthase family protein [Borrelia sp. SV1]
          Length = 313

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 72/316 (22%), Positives = 133/316 (42%), Gaps = 21/316 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    ++ V  ++   RLD        + +   + K +R G +R++  +  F+ R+  G 
Sbjct: 1   MDKYIFLEVIANDNGKRLDSILIKIL-NFSKARIIKHIRKGDIRLNGLKSHFSCRVCKGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +   +    ++       D          +++  ++YEDS + V +K  GI V GG 
Sbjct: 60  KIYLYKSLAQNLNL-----TTDECFKSNIDFQYIRKRIIYEDSDLLVLDKQKGILVHGGK 114

Query: 124 G-IAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + +  + +L S  + S   KP   HRLD+ TSGI++ A+    A+ L+E+F    I K
Sbjct: 115 NSLDFLANAYLLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTARKLSEAFSGGSIIK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++++ G  K       N L +   +   +V      +K    AI+    I    ++  
Sbjct: 175 KYFAILLGEVK-SSVVYKNHLFRNKRLRKTFV----LEDKNFVNAITKVNPILSC-KRAT 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+   TG THQ+R        P++ D KYC  FK +         +LHA  +      
Sbjct: 229 LVEIVIETGFTHQIRSQCSFNNHPLINDKKYCDKFKKSD-------YFLHAFLVKFNGTF 281

Query: 302 GGRLQITAPLPAHMVK 317
             + +  +      +K
Sbjct: 282 FKKNEFCSKPSLEFLK 297


>gi|282850437|ref|ZP_06259816.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
 gi|282579930|gb|EFB85334.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
          Length = 321

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 74/353 (20%), Positives = 130/353 (36%), Gaps = 66/353 (18%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M   T +  ++V+ D     ++   K    HI+    +++   G + V+ K   +N  + 
Sbjct: 1   MKTATIID-LIVDFDVHTQSINHIIKQQ--HISHRMRRRLRSDGIITVNGKPATWNTLVH 57

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +         +  EQ+   S + L          ++YED  I V NK A I + 
Sbjct: 58  GGDHLIM--------KLTPEQEFSLSPMELD---------IIYEDEYILVINKAANILMH 100

Query: 121 GGSGIAYHI--DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             S +  H   +G L  + ++ +       HRLD++TSGI+++A+T        +     
Sbjct: 101 PTSTVRDHTLANGVLHYYQETNQYYDFHPVHRLDKDTSGIVIIAKTSVVQHAFDKKHTH- 159

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF- 236
              KIY ++V G   +    I   + +K    G  +      +     A +   V+    
Sbjct: 160 -FYKIYDAIVEGHLPSVPISINWPIGRKP---GSIIERCCTGQ--GKPARTDITVVSKNI 213

Query: 237 ----------------------------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                                          F  ++   HTGRTHQ+RVH   +G P+ G
Sbjct: 214 SKINYSKNISDDMINNSNICPADNSLIAYNHFTHVQCLLHTGRTHQIRVHLSQLGYPLAG 273

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           D  Y  + +         +  LHA  +   HP     L++ A +P  M     
Sbjct: 274 DDLYGGHLES------IQRQALHAARVSFYHPITNEWLELHAEMPEDMNVLLK 320


>gi|139474518|ref|YP_001129234.1| RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo]
 gi|134272765|emb|CAM31038.1| RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo]
          Length = 272

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 100/268 (37%), Gaps = 26/268 (9%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              V ++   V + + ++ G  V++                 D    +       K   L
Sbjct: 14  KKHVLINGHPVNWQSCVKYGDQVKLFFDHE------------DYPEKIIVMGQAEKVTCL 61

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  I + NKP G+      G        L       GQ   + HRLD+ETSG ++ A+
Sbjct: 62  YEDEHIIIVNKPEGMKTH---GNDPTELALLNHVSAYTGQTCYVVHRLDKETSGAILFAK 118

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           T      L      R I + Y +LV G   + +    + + +  H     V     +   
Sbjct: 119 TPFILPILNRLLEKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRV----VDPIN 174

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              AI+   ++  F +    L  Q  TGRTHQ+RVH  H G  + GD  Y    K     
Sbjct: 175 GKKAITEVTLVKNFHKTASLLNCQLQTGRTHQIRVHLAHQGHVLFGDPLYSNEKKD---- 230

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITA 309
               +L LHA  + L HP     + + A
Sbjct: 231 --CARLMLHAYQLRLKHPLTQEDICVQA 256


>gi|28377784|ref|NP_784676.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|28270617|emb|CAD63523.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
          Length = 293

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 75/306 (24%), Positives = 123/306 (40%), Gaps = 41/306 (13%)

Query: 23  RWFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQSGQV--VRIPPVINALNHII 78
           R+   H   I+   + K ++  +G   V+ +       I  G +  +++P         +
Sbjct: 16  RFLTTH--AISMRTI-KAIKHGTGAFLVNNQVQTGVITIHDGDIAGIQLPDEAPDTAVAV 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWV 137
            EQ I                 + YED+   V NK AG+ SV G S     +   +K ++
Sbjct: 73  SEQPI----------------QIEYEDANWLVLNKTAGLTSVPGPSNRTDTLVNRIKGYL 116

Query: 138 ---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               +  Q+P L  RLD++TSG+++VA+ R A   LTE     ++ K Y + + G     
Sbjct: 117 MASHASNQRPHLITRLDRDTSGLVLVAKHRVAQGMLTEPRIAAQLVKTYQAWIEGTITPA 176

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTH 253
              I   + + +      V            AI+ ++V  D        L ++  TGRTH
Sbjct: 177 SGTIDRPIGRVADSPRRVVTT------AGQRAITTYQVEADQLQHNVSRLRLELVTGRTH 230

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Q+RVH   +G P++GD  Y  N           +  LHA  +    P   + L   A LP
Sbjct: 231 QIRVHLTTLGHPLLGDALYGGNLGW------IQRQALHAASLQFFDPFSEQTLHFEAALP 284

Query: 313 AHMVKT 318
           A +   
Sbjct: 285 ADLQAL 290


>gi|223933756|ref|ZP_03625728.1| pseudouridine synthase [Streptococcus suis 89/1591]
 gi|223897560|gb|EEF63949.1| pseudouridine synthase [Streptococcus suis 89/1591]
          Length = 291

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 59/268 (22%), Positives = 108/268 (40%), Gaps = 29/268 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              VRV+ + + + + I +G ++ +            E+ I     +L +         L
Sbjct: 37  KKHVRVNGELINWQSPITAGDLLELTFDQEDY----PEKSIPLGQADLVEE--------L 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG ++ A+
Sbjct: 85  YQDEHLIIVNKPEGMKTHGNEPTEIALLNHVSAYV---GQTCYVVHRLDMETSGAILFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      + I + Y +L  G  K     I + + +  H     +     + + 
Sbjct: 142 NPFILPILNRLLEDKVIYRDYLALCQGQLKETDWTITDKIGRDRHDRRKRM----VDNRK 197

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++  +++    +    +  +  TGRTHQ+RVH  H G  ++GD  Y          
Sbjct: 198 GQAALTQVRLLKPLGKN-SLVSCRLQTGRTHQIRVHLAHHGHALIGDPLYS--------R 248

Query: 283 PIQNKLYLHARYMDLPHPEG-GRLQITA 309
               +L LHA+ + L HP     + + A
Sbjct: 249 VAAPRLMLHAQKLSLTHPLTLEEISVEA 276


>gi|198244685|ref|YP_002214048.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|205351435|ref|YP_002225236.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|207855608|ref|YP_002242259.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|197939201|gb|ACH76534.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|205271216|emb|CAR36004.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Gallinarum str. 287/91]
 gi|206707411|emb|CAR31684.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Enteritidis str.
           P125109]
 gi|326621792|gb|EGE28137.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|326626458|gb|EGE32801.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 219

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDEHIMVVNKPSGLLSVPGR-LEAHKDSIM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            Y +         +  +L LHA  + + HP  G  +     +PA  
Sbjct: 180 FYASPE----ALSLAPRLQLHAEMLTITHPAYGTNMTFK--VPADF 219


>gi|168820315|ref|ZP_02832315.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|205342862|gb|EDZ29626.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|320087390|emb|CBY97155.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Weltevreden str. 2007-60-3289-1]
          Length = 260

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +       +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPRTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLIIQAGLDETWMQALTQFGWR 237


>gi|62178660|ref|YP_215077.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|194443178|ref|YP_002039326.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|224581938|ref|YP_002635736.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|62126293|gb|AAX63996.1| 23S rRNA pseudouridylate 746 synthase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|194401841|gb|ACF62063.1| pseudouridine synthase, RluA family [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|224466465|gb|ACN44295.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Paratyphi C strain
           RKS4594]
 gi|322615916|gb|EFY12833.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322620701|gb|EFY17561.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322623948|gb|EFY20785.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322627396|gb|EFY24187.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322630703|gb|EFY27467.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322638077|gb|EFY34778.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322640563|gb|EFY37214.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322647703|gb|EFY44188.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322648053|gb|EFY44520.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322656915|gb|EFY53201.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322657374|gb|EFY53646.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322663694|gb|EFY59894.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322666527|gb|EFY62705.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322672314|gb|EFY68426.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322676374|gb|EFY72445.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322679533|gb|EFY75578.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322686138|gb|EFY82122.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|322713113|gb|EFZ04684.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323194982|gb|EFZ80168.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323200109|gb|EFZ85196.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323201070|gb|EFZ86139.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323209467|gb|EFZ94400.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323212281|gb|EFZ97105.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323216586|gb|EGA01312.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323222475|gb|EGA06845.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323225786|gb|EGA10006.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323228673|gb|EGA12802.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323236713|gb|EGA20789.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323239786|gb|EGA23833.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323242166|gb|EGA26195.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323249409|gb|EGA33325.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323252256|gb|EGA36107.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323256653|gb|EGA40383.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323261313|gb|EGA44900.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323265507|gb|EGA49003.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323271705|gb|EGA55123.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
          Length = 219

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 107/226 (47%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDEHIMVVNKPSGLLSVPGR-LEAHKDSIM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            Y +         +  +L LHA  + + HP  G  +     +PA  
Sbjct: 180 FYASPE----ALSLAPRLQLHAEMLTITHPAYGTSMTFK--VPADF 219


>gi|16766270|ref|NP_461885.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|167550169|ref|ZP_02343926.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|167993457|ref|ZP_02574551.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|34582459|sp|Q8ZMD5|TRUC_SALTY RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|16421515|gb|AAL21844.1| putative synthase [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
 gi|205324883|gb|EDZ12722.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205328453|gb|EDZ15217.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|261248101|emb|CBG25936.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. D23580]
 gi|267995101|gb|ACY89986.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301159525|emb|CBW19044.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. SL1344]
 gi|312913986|dbj|BAJ37960.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|321225646|gb|EFX50700.1| tRNA pseudouridine synthase C ; tRNA Psi65 [Salmonella enterica
           subsp. enterica serovar Typhimurium str. TN061786]
 gi|323131322|gb|ADX18752.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|332989835|gb|AEF08818.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 260

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +       +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLIIQAGLDETWMQALTQFGWR 237


>gi|258621635|ref|ZP_05716667.1| tRNA pseudouridine synthase C [Vibrio mimicus VM573]
 gi|258586107|gb|EEW10824.1| tRNA pseudouridine synthase C [Vibrio mimicus VM573]
          Length = 244

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 98/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F   +++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASEVMPMFANHKMEKTYHAIVRGWIEEADVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAITAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L     +      ++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFVHPYTQQPLVIRAGLDEVWQRLLGEFDWQEP 239


>gi|325287572|ref|YP_004263362.1| pseudouridine synthase [Cellulophaga lytica DSM 7489]
 gi|324323026|gb|ADY30491.1| pseudouridine synthase [Cellulophaga lytica DSM 7489]
          Length = 232

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 72/228 (31%), Positives = 110/228 (48%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I   NK  G  VQG       +   +K+++  K  KP      + HRLD+ T+
Sbjct: 14  VLYEDNHIIAINKRVGDIVQGDKTGDAPLSDIVKAYIKEKYNKPGNVYLGVAHRLDRPTT 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  A   L + F  +  +K YW++V   PK   E + ++L + +     Y ++
Sbjct: 74  GIVVFAKTSKALPRLNKLFAEKDAKKTYWAVVKQQPKKNNETLVHYLKRNTKQNKSYANI 133

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI  + ++      +  LE+   TGR HQ+R     +GCPI GD KY  N
Sbjct: 134 --KEVPDSKKAILDYTILKKL-DNYYLLEINLQTGRHHQIRSQLSGIGCPIKGDLKYGFN 190

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     ++LHAR +   HP     L+ITAPLP      WD+ 
Sbjct: 191 -----RSNTDGGIHLHARKLSFIHPVKKEPLEITAPLPKD--PIWDAC 231


>gi|62181474|ref|YP_217891.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|168231056|ref|ZP_02656114.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|168463884|ref|ZP_02697801.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|194443144|ref|YP_002042215.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194468534|ref|ZP_03074518.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|200386574|ref|ZP_03213186.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|224584754|ref|YP_002638552.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|238909744|ref|ZP_04653581.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|62129107|gb|AAX66810.1| putative synthase [Salmonella enterica subsp. enterica serovar
           Choleraesuis str. SC-B67]
 gi|194401807|gb|ACF62029.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194454898|gb|EDX43737.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|195633159|gb|EDX51573.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|199603672|gb|EDZ02217.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|205334611|gb|EDZ21375.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|224469281|gb|ACN47111.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|322715958|gb|EFZ07529.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
          Length = 260

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +       +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLIIQAGLDETWMQALTQFGWR 237


>gi|325124374|gb|ADY83897.1| 23S rRNA pseudouridylate synthase [Acinetobacter calcoaceticus
           PHEA-2]
          Length = 233

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 56/183 (30%), Positives = 102/183 (55%), Gaps = 9/183 (4%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V +  V+  +   R+D +  +    +    + +++R GQVRV+KKR+K   +++ G  +R
Sbjct: 10  VTWFEVDEHQAGQRIDNFLFSRLKGVPKSRIYRLIREGQVRVNKKRIKAETKLEVGDQIR 69

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P       I  EQK   ++      +  L S ++YED  + V NKP+GI+V GGSG+A
Sbjct: 70  VAP-------IRYEQKDETAAPVSDSVAQSLLSRVVYEDEGLLVINKPSGIAVHGGSGVA 122

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           Y +   L++    K     L HR+D++TSG++++++ R+  + L +  R  +I+K Y ++
Sbjct: 123 YGLIEALRAATGKKY--LELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAI 180

Query: 187 VWG 189
           V G
Sbjct: 181 VKG 183


>gi|326575127|gb|EGE25055.1| tRNA pseudouridine synthase C [Moraxella catarrhalis CO72]
          Length = 258

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 99/239 (41%), Gaps = 19/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ + + NKPA + V       +     +++  +   Q     HRLD+ TSG+LV 
Sbjct: 19  ILYQDACMVIINKPANMLVHRSWLDKHETCFVVQTLRNQINQHVYPVHRLDRPTSGVLVF 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A  L + F    IQK Y ++V GI       I   L  +     D         
Sbjct: 79  ALDSQTAGLLAKQFEDHHIQKSYLAVVRGII--GAGRIDYALKPRLDKIADKF---SNPN 133

Query: 221 KGANYAISHFKVIDCFAQ-----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           K +  AI+ ++V+    Q           ++  + + P TGR HQLR H  H+  PIVGD
Sbjct: 134 KASKSAITDYQVLATTQQPFISCRRFDSSRYSLVRLTPITGRKHQLRRHMKHIFHPIVGD 193

Query: 270 HKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
             Y    +           +L LHA  +   HP    + +I APL     +   + G+ 
Sbjct: 194 TTYGDKVQNRAVLAHIGVKRLLLHAHQLQFCHPLYDEMIRIVAPLDTAFCQVMTAFGWS 252


>gi|203284710|ref|YP_002222450.1| RNA pseudouridylate synthase family protein [Borrelia duttonii Ly]
 gi|203284715|ref|YP_002222455.1| RNA pseudouridylate synthase family protein [Borrelia duttonii Ly]
 gi|201084153|gb|ACH93744.1| RNA pseudouridylate synthase family protein [Borrelia duttonii Ly]
 gi|201084158|gb|ACH93749.1| RNA pseudouridylate synthase family protein [Borrelia duttonii Ly]
          Length = 324

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 74/328 (22%), Positives = 145/328 (44%), Gaps = 23/328 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V N+++  RLD         +    + K +R+G +R++  +V F+ R+     + +  
Sbjct: 15  INVLNNDDGKRLDVVLIKFLK-LPKSKVIKHIRNGDIRLNNLKVSFSQRVLKDDKIYLYK 73

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +    ++     ++ +  ++ +    ++S L+YED  + V NK  G+ V    G  Y +
Sbjct: 74  PLVQGLNL--NGVVIKNKTDILR---DVESRLVYEDKDLLVINKRKGVLVH---GDGYSL 125

Query: 130 DGFLKSWV-----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           D  + +++      S   KP   HRLD+ TSG++V A+   +A+ L+++F    + K Y 
Sbjct: 126 DVLVNAYLLDENLASLSFKPSAVHRLDRNTSGLIVFAKNIYSARILSKAFSSGIVTKRYL 185

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L+ G  + K     N+L +   +   +V     +      AI+  K +   ++     E
Sbjct: 186 ALLDGEIR-KSLTYKNFLYRDKIVKKTFVMDNLNSNINKFNAITIVKPL-LVSKFATLAE 243

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TG THQ+R         ++ D KY   FK       +N  +LH+  ++  H    R
Sbjct: 244 VSIKTGFTHQIRAQCAFNNHALIDDKKYNPKFK-------KNNYFLHSFLINFNHSFFLR 296

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            +      +  VK  +S+   YD   +I
Sbjct: 297 NEFFVEPSSDFVKRINSIFGVYDFKEFI 324


>gi|312131061|ref|YP_003998401.1| ribosomal large subunit pseudouridine synthase d [Leadbetterella
           byssophila DSM 17132]
 gi|311907607|gb|ADQ18048.1| ribosomal large subunit pseudouridine synthase D [Leadbetterella
           byssophila DSM 17132]
          Length = 240

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 74/243 (30%), Positives = 115/243 (47%), Gaps = 17/243 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQ 152
              ++YED+ + V NK AG+ V   S     ++ ++K ++  K  KP        HRLD+
Sbjct: 3   PFHVIYEDNHLIVVNKAAGVLVHSDSTGDKTLEDYVKEYIKDKYNKPGEVFLGTVHRLDR 62

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
             SG+++ ART  A   + E F+ R+IQK YW++    P+ K   + +WL K S      
Sbjct: 63  PVSGVVIFARTSKALTRMNELFKKRQIQKTYWAITMRKPEKKSGRLTHWLRKDSVQN--K 120

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               +   +GA  A   ++ +     K   +E+ P TGR HQ+RV    MG PI GD KY
Sbjct: 121 TEAFESEVEGAQRADLDYRYVGTL-NKHHLIEVNPITGRPHQIRVQLASMGTPIKGDVKY 179

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLY 331
            +       S     ++LHAR +   HP     L I AP+P +    W+    + D+  Y
Sbjct: 180 GSPKGNADGS-----IFLHARRVYFIHPVKKEPLVIKAPVPPN--AFWEEF-LELDKEEY 231

Query: 332 IKR 334
            + 
Sbjct: 232 KED 234


>gi|51599066|ref|YP_073254.1| hypothetical protein BG0840 [Borrelia garinii PBi]
 gi|51573637|gb|AAU07662.1| conserved hypothetical protein [Borrelia garinii PBi]
          Length = 315

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 132/319 (41%), Gaps = 22/319 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L  Y+ ++ V  ++   RLD        + + V + K +R G +R++  +  F+ R+ 
Sbjct: 1   MRLDKYI-FLEVLANDNGKRLDSILIKIL-NFSKVRIIKHIRKGDIRLNGLKPHFSYRVC 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   +    ++      +            ++  ++YEDS + V +K  GI V 
Sbjct: 59  KGDKIYLYKSLVQSLNLA-----MGECYKSNIDFQCIRKRIIYEDSDLLVMDKQRGILVH 113

Query: 121 GGSGIAYHIDG--FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           GG      +     L+  + S   KP   HRLD+ TSGI++ A+   AA+ L+ +F    
Sbjct: 114 GGKNSLDFLVNSYLLREDLRSLSFKPSAVHRLDRNTSGIIIFAKNINAARKLSTAFSSGS 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y++++ G  K       N L +   +   +V      +K    AI+    I   ++
Sbjct: 174 VTKKYFAILLGEVK-STVLYKNHLFRNQRLKKTFV----LEDKDFINAITKVNPILS-SK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +    E+   TG THQ+R        P++ D KY   FK +         +LHA  +   
Sbjct: 228 RATLAEIVIETGFTHQIRSQCSFNDHPLINDKKYHDKFKKSD-------YFLHAFLVKFN 280

Query: 299 HPEGGRLQITAPLPAHMVK 317
                + +  A      +K
Sbjct: 281 EAFFKKNEFYAKPSLEFLK 299


>gi|300173026|ref|YP_003772192.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299887405|emb|CBL91373.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 300

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 119/283 (42%), Gaps = 35/283 (12%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G +  + K+V  ++ +  G  V I       N ++               +D+    +++
Sbjct: 37  GAILKNDKQVYTSDYLDDGDQVTIIMPTEKSNDLV--------------VADYNPLTIIF 82

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHI-DGFLKSWVDSKGQK---PRLTHRLDQETSGILV 159
           E+    V +KP G++   G     H     +K  ++    +   P +  RLD++TSGI++
Sbjct: 83  ENEHWLVVDKPYGLTTVPGHADRLHTLVNQVKGHLEEINAEDLVPHVVTRLDRDTSGIVL 142

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ R A   + +  +   ++K Y + V GI       I   + +   +  D++    ++
Sbjct: 143 LAKHRFAHAVMDQQLQEHTVEKFYVAYVSGILSEDHGDIHAPIGR---MDDDFIKREVRD 199

Query: 220 EKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +     + + + V   +          +++Q HTGRTHQ+RVH  ++G P+VGD+ Y   
Sbjct: 200 D--GKPSRTEYWVERRYDDGGVQPMTRVKVQLHTGRTHQIRVHFQNIGHPLVGDNLYGGP 257

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPAHMV 316
                      +  LHA +M    P  E  R +    LP  + 
Sbjct: 258 RW-----YGLKRQALHAYHMKFYDPFIEADR-EFNTTLPEDLK 294


>gi|311278253|ref|YP_003940484.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308747448|gb|ADO47200.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 260

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 103/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IVYQDQWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F   +I K Y ++V G    +       + +   I   +       +
Sbjct: 64  GLSSEAGRLLAQQFEQHQIHKRYHAIVRGWLSEEGILDYPLVEELDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           KG   A++H++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELDPKTGRKHQLRRHLKHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +        ++L LHA  + L HP  G  L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSAAEHFGCDRLMLHASELRLTHPFTGEPLVIRAGLDEVWMQALSHFGWR 237


>gi|261866897|ref|YP_003254819.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412229|gb|ACX81600.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 219

 Score =  174 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 66/217 (30%), Positives = 104/217 (47%), Gaps = 11/217 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   L+Y D  I V NKP+G+    G+   Y+      S V  K       HRLD 
Sbjct: 8   PPQEPWLDLVYRDDYIAVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPAHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGIL+ A +++A + L   FR R  +K Y +LVWG  + ++  +   L+       + 
Sbjct: 66  ATSGILLFALSKSADRELKRQFREREPKKYYQALVWGYLEQEQGMVELPLICD----WEN 121

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               K   +    A++ + V+  +      +++ P TGR+HQLR+H L +G PI+GD  Y
Sbjct: 122 RPRQKICFERGKRAVTFYDVLQRYPNNTTRIKLTPITGRSHQLRLHMLALGHPILGDKFY 181

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
            A+ +    SP   +L LHA  + + HP  G  ++ T
Sbjct: 182 -AHPQAKALSP---RLCLHAESLQIRHPITGETMEFT 214


>gi|227432728|ref|ZP_03914698.1| pseudouridylate synthase RluD [Leuconostoc mesenteroides subsp.
           cremoris ATCC 19254]
 gi|227351520|gb|EEJ41776.1| pseudouridylate synthase RluD [Leuconostoc mesenteroides subsp.
           cremoris ATCC 19254]
          Length = 297

 Score =  174 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 66/326 (20%), Positives = 132/326 (40%), Gaps = 38/326 (11%)

Query: 4   MTYVQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQS 61
           M   QY  ++ +      +       Y  +    ++  LR      V+   V  N ++++
Sbjct: 1   MKKWQYNFIITSQNSGQTVKELLIKWY--VPQ-RIRGALRIKKHFSVNNIIVPTNYKLRT 57

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  +++    +             +S +    +      +++E+  + V +KPAG+ +  
Sbjct: 58  GDQLQLNFDADDFR----------TSESNYLPNHQKSVNIIFENKDLVVIDKPAGMKMHP 107

Query: 122 GSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            S         L +++  +  +      P + HR+D+ TSG+++VA+       L     
Sbjct: 108 HSPTET---DTLLNYLAGEFIQRKVSDQPYMVHRIDRATSGLVIVAKNPVVVPILDRILA 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            ++I + Y + V G+ ++    IA  +   +            + K A  A++H+  +  
Sbjct: 165 DKQIVRTYVTWVSGVVQDNHGTIAKPIGIDARDDRKRA----VDGKEAQVAMTHWWRMHT 220

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                  L +Q  TGR HQ+RVH   +G PIVGD  Y   + G        ++ LH+  +
Sbjct: 221 -EFCSSLLRVQLSTGRMHQIRVHLASIGHPIVGDELYGGVYNG--------RMLLHSATI 271

Query: 296 DLPHPEGGRLQ-ITAPLPAHMVKTWD 320
            +P P    ++ IT PLP+   +   
Sbjct: 272 KIPLPFDEGVRMITGPLPSDFPRQLR 297


>gi|148544733|ref|YP_001272103.1| RluA family pseudouridine synthase [Lactobacillus reuteri DSM
           20016]
 gi|184154085|ref|YP_001842426.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|148531767|gb|ABQ83766.1| pseudouridine synthase, RluA family [Lactobacillus reuteri DSM
           20016]
 gi|183225429|dbj|BAG25946.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
          Length = 290

 Score =  174 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 63/281 (22%), Positives = 121/281 (43%), Gaps = 32/281 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
            G+  VD ++V+   +I   Q + I       +  ++              S      ++
Sbjct: 36  EGEFLVDHRKVRPTTQILPNQPLTIKAQPELADDTVE--------------SSNEPLNVV 81

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---DSKGQKPRLTHRLDQETSGIL 158
           YED    V +KPAG++   G  +    +   +K ++   +S   +P L  RLD+ T G+L
Sbjct: 82  YEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIANNSADLRPHLITRLDRFTGGLL 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+   A+  +++  +  ++ K Y +LV G   ++   I         IG       + 
Sbjct: 142 LIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHGEI------NKPIGRKDGQAARV 195

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            ++    A++ + V +    K+  + ++ HTGRTHQ+RVH   +G  ++GDH Y  +   
Sbjct: 196 IDENGQRALTEYWVEER-GAKWTRVRVRLHTGRTHQIRVHFAAIGHSLIGDHLYGGDTSK 254

Query: 279 NFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKT 318
                  +   LHA  +    P    ++  T+ LPA   + 
Sbjct: 255 ------YDHQLLHASKISFNDPFTLKQMTFTSELPAAFFEL 289


>gi|296111299|ref|YP_003621681.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
 gi|295832831|gb|ADG40712.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
          Length = 306

 Score =  174 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 66/297 (22%), Positives = 118/297 (39%), Gaps = 38/297 (12%)

Query: 36  NLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
            ++  LR     RV+ + V  +  +Q   ++ +    +             + V+    +
Sbjct: 32  RVRGALRIKKNYRVNGQEVPTSYNLQVNDILSLIFDESDFR----------TGVSHYAPN 81

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-----------K 143
                 +++E+  + V NKPAG+ +      +   D  L ++V +              K
Sbjct: 82  SEKVVDIVFENDDLVVVNKPAGMKMHP---HSETEDDTLLNYVAANFLARSVLSAGVPAK 138

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HR+D+ETSG +++A+       L      + IQ+ Y + V G    K   I   + 
Sbjct: 139 PYMVHRIDRETSGAVIIAKNPVVVPILNRLLFEKNIQRTYLAWVDGNMSAKAGVIDAPIG 198

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                    +     +   A  A +H+  +    Q    L +Q  TGR HQ+RVH   MG
Sbjct: 199 IDPQNNRKRL----VDGIDAQSAKTHWTRVHVVYQ-HTLLRLQLDTGRMHQIRVHLASMG 253

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
            PIVGD  Y +         I  ++ LHA  + +P P   + + I+ P+P    +  
Sbjct: 254 HPIVGDSLYASKV-------ITTRMLLHAVSVVIPLPFKNKTVVISCPVPNDFPRQL 303


>gi|291618642|ref|YP_003521384.1| TruC [Pantoea ananatis LMG 20103]
 gi|291153672|gb|ADD78256.1| TruC [Pantoea ananatis LMG 20103]
          Length = 259

 Score =  174 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 59/239 (24%), Positives = 106/239 (44%), Gaps = 17/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ +   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDAWLVAVNKPAGWLVHRSWLDRHETQFVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +    + L++ F   +++K Y ++V G  + +       + +   I   +V     + 
Sbjct: 64  GLSSEVGRLLSQQFEHHQMEKTYHAVVRGWLEGRDRLDYPLVEELDKIADKFVS----DP 119

Query: 221 KGANYAISHF----------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +    A++ +           V      ++  +E++P +GR HQLR H  H+  PI+GD 
Sbjct: 120 RAPQPAVTDYASLATVEMPVAVSRYPTARYSLIELKPKSGRKHQLRRHMSHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            +      +G       N+L LHA  + L HP  G  L I A L     +  D  G++ 
Sbjct: 180 AHGDLRQNRGAAAHFGANRLMLHASSLSLSHPVTGEPLVIRAGLDLVWQRVMDQFGWQA 238


>gi|296533864|ref|ZP_06896396.1| ribosomal large subunit pseudouridine synthase C [Roseomonas
           cervicalis ATCC 49957]
 gi|296265811|gb|EFH11904.1| ribosomal large subunit pseudouridine synthase C [Roseomonas
           cervicalis ATCC 49957]
          Length = 236

 Score =  174 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 70/228 (30%), Positives = 104/228 (45%), Gaps = 14/228 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +L +   + V +KPAG+ V  G      ++  L +    K   P+  HRLD +T+G 
Sbjct: 20  PLKILLQTEAVLVIDKPAGLPVHRGPRGGASLEDHLPALAQGKRHWPQPAHRLDTDTAGC 79

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV+ RT+ A   L   F   R +K YW++V G P  +   I   L K S     +     
Sbjct: 80  LVLGRTKPALAALGRLFAEGRARKTYWAVVRGGPAAQSGRIDLPLRKTSSAATGWRM--- 136

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +       A++ ++V         WLE++P TGRTHQLRVH    G PI+GD  Y     
Sbjct: 137 EAHPDGQPALTRWRVRGR-GPGLAWLELRPETGRTHQLRVHCASQGWPILGDPFYGTKAP 195

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           G         L+L AR ++L  P    L  TAP+P  +   + + G+ 
Sbjct: 196 GG--------LHLLARAIEL--PLDPPLSATAPVPPALRDAFAACGWS 233


>gi|170720467|ref|YP_001748155.1| pseudouridine synthase [Pseudomonas putida W619]
 gi|169758470|gb|ACA71786.1| pseudouridine synthase [Pseudomonas putida W619]
          Length = 211

 Score =  174 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 65/215 (30%), Positives = 100/215 (46%), Gaps = 11/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L+ED+ I V NKP  +    G       D  +    ++      + HRLD ETSGI+
Sbjct: 6   VQILHEDAAILVVNKPTLLLSVPGRADDN-KDCLITRLQENGYPDALIVHRLDWETSGII 64

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR   + + L+  F  R  +K Y +L WG P      I   L           HVV  
Sbjct: 65  LLARDADSHRELSRQFHDRETEKAYTALCWGQPALDSGSIDLPLRYDPPT--KPRHVV-- 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +   +A++ +++++      C +E+ P TGR+HQLRVH L +G P++GD  Y      
Sbjct: 121 DHEQGKHALTFWRILERCGD-HCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY----AN 175

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                   +L LHA  +   HP  G RL+   P P
Sbjct: 176 PEALAAHERLCLHAAMLSFTHPVSGERLKFECPAP 210


>gi|229823324|ref|ZP_04449393.1| hypothetical protein GCWU000282_00622 [Catonella morbi ATCC 51271]
 gi|229787099|gb|EEP23213.1| hypothetical protein GCWU000282_00622 [Catonella morbi ATCC 51271]
          Length = 300

 Score =  174 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/316 (19%), Positives = 126/316 (39%), Gaps = 37/316 (11%)

Query: 14  NDEENMRLDRWFKNHYPHINF---VNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
             E  +R+  + K+    I      +++     G + ++ + V    ++++G ++ +   
Sbjct: 9   EGEHPVRIKDYLKHL--GIPRKFVSHVK--FEGGNILLNGQEVNVLAKLEAGDILTL--- 61

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-I 129
                         D   + T     +   ++YED  + + NKP  +       I    +
Sbjct: 62  -----------VAADEGSHETVPPSHVPIQVIYEDRDLLIVNKPTDVVSIPSKRIPDSAM 110

Query: 130 DGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
              +K +   +    Q   +  RLD++T+G++++A+ R A   L +  +  +++K Y ++
Sbjct: 111 ANRVKGYYQRQDYADQVIHIVTRLDRQTTGLMLIAKHRLAHAMLDKQVQGGQVEKYYLAI 170

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                      I   + +      +   + ++  +    A++ + +   FA     L+++
Sbjct: 171 STKADWPDHGVIDRPIAR-----TEDSIITRRVHESGQRAVTEYWLKHRFADS-SLLKLR 224

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
            HTGRTHQ+RVH    G  +VGD  Y              +  LH   + L  P  G RL
Sbjct: 225 LHTGRTHQIRVHMQDAGGVLVGDDLYGGPH-----LEAIRRQALHCGELRLTQPFTGQRL 279

Query: 306 QITAPLPAHMVKTWDS 321
            ++APLP  M      
Sbjct: 280 VLSAPLPEDMAAWLAK 295


>gi|50291713|ref|XP_448289.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49527601|emb|CAG61250.1| unnamed protein product [Candida glabrata]
          Length = 457

 Score =  174 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/272 (22%), Positives = 114/272 (41%), Gaps = 26/272 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +  N +        +K +  G V ++ K     + I++G ++              E
Sbjct: 133 LDVF-TNEFRDRPAEYYKKTIERGAVLLNDKPATLESIIKNGDLITHKVHR-------HE 184

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED+ I V NKP+GI V       Y  +   K+    +
Sbjct: 185 PPVTSRPIE-----------IVFEDNDILVINKPSGIPVHPTG--RYRFNTITKALEKER 231

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A  + +  + R ++K Y + V G    +   + +
Sbjct: 232 GYVVHPCNRLDRMTSGLMFLAKTSKGADKIGDQLKAREVEKEYLAKVVGEFP-EGTTVVD 290

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             LK          V ++ +  A +A + F +V     ++   ++ +P TGR+HQ+RVH 
Sbjct: 291 KPLKLLEPRLTLNVVCEETDPDAKHARTIFERVSVSKDKQTSIVKCKPLTGRSHQIRVHL 350

Query: 260 LHMGCPIVGDHKYCANF---KGNFTSPIQNKL 288
            H+G PI  D  Y +      G     +  +L
Sbjct: 351 QHLGHPIANDPIYSSPEVWGDGKDYDEVIKRL 382


>gi|255017039|ref|ZP_05289165.1| hypothetical protein LmonF_03093 [Listeria monocytogenes FSL
           F2-515]
          Length = 201

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 57/207 (27%), Positives = 96/207 (46%), Gaps = 16/207 (7%)

Query: 122 GSGIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G      ++  L    D  G     +P + HR+D++TSG+L+VA+   A + L +  + +
Sbjct: 2   GHASGTLVNALLFHCDDLSGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDK 61

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              + Y +LV G   ++K  I   + + +      + VV+        A +HF+V++   
Sbjct: 62  TSDREYIALVHGDIVHQKGTIEAPIGR-AKEDRQKMAVVR----DGKEARTHFEVLERLP 116

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +  +  TGRTHQ+RVH  ++G P+ GD KY         +   N  +LHA  +  
Sbjct: 117 -GYTLINCKLDTGRTHQIRVHLKYIGHPLAGDPKYGPK-----NTIKGNGQFLHAAKLGF 170

Query: 298 PHPEG-GRLQITAPLPAHMVKTWDSLG 323
            HP    R+   APLP+   K   SL 
Sbjct: 171 DHPTTNERMTFEAPLPSSFEKALKSLR 197


>gi|317010964|gb|ADU84711.1| pseudouridine synthase [Helicobacter pylori SouthAfrica7]
          Length = 326

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 140/333 (42%), Gaps = 40/333 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHI 77
            R+D +       I+      +++ G V   KK VK     ++ G  + +  +      +
Sbjct: 12  KRIDEFLAKEL-QISKNQALSLIKEGLVLCQKKEVKKGGLALKEGDAIALLTLKITPKPL 70

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            KE                L+  +++ED  + V NKP  + V     +    +  L  W+
Sbjct: 71  KKELD--------------LEIGVIFEDDDLLVLNKPPNLIVHKAPSV---KEPTLVDWL 113

Query: 138 DSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +SK  +           + HRLD++TSG +V+A+      HL+E  + + + + Y +L+ 
Sbjct: 114 ESKNYQLSNLGSKERYGIVHRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLS 173

Query: 189 GIP--KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                K +K  +  +L +  +     + +  +NEKG  Y+ S F  +         +  +
Sbjct: 174 TPLSRKGEKVSVECYLTRNPNNRLKMMAI--KNEKG-RYSKSEFTSLLTSQNNLNLIGAK 230

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
            +TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++  HP    +L
Sbjct: 231 LYTGRTHQIRTHLEYLNRHIIGDNLYGLN---EALPKEEIRIMLHAYLIEFKHPRSEQKL 287

Query: 306 QITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           +   PL   M++    +   +D+    + L  +
Sbjct: 288 RFKVPLLKDMLEYLKKI---FDKENLDEVLDEE 317


>gi|291326503|ref|ZP_06124794.2| pseudouridine synthase A [Providencia rettgeri DSM 1131]
 gi|291313961|gb|EFE54414.1| pseudouridine synthase A [Providencia rettgeri DSM 1131]
          Length = 217

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 107/231 (46%), Gaps = 18/231 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +   + +      +LY+D  I V NKP+G+    G    +H    + S V          
Sbjct: 2   MEPYQPAVEPWLHILYQDDHIIVVNKPSGLLSVPGKAPEHHDS--IMSRVQRDFPAAESV 59

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA  + A + L   FR R  +K Y + VWG  + ++  +   L+    
Sbjct: 60  HRLDMATSGVMVVALHKKAERELKRQFREREPKKFYIARVWGHLEKEEGLVDLPLI---- 115

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V+    Q    +++ P TGR+HQLRVH L +G P
Sbjct: 116 --CDWPNRPKQKVCFETGKSAQTEYQVLQYEEQ-ATRVKLSPITGRSHQLRVHMLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           I+GD  Y      +    +  +L LHA+ + + HPE G  +  T   P   
Sbjct: 173 ILGDRFY----AQDEAKALATRLQLHAQELYITHPEYGTSMHFTC--PPDF 217


>gi|154495180|ref|ZP_02034185.1| hypothetical protein PARMER_04229 [Parabacteroides merdae ATCC
           43184]
 gi|154085730|gb|EDN84775.1| hypothetical protein PARMER_04229 [Parabacteroides merdae ATCC
           43184]
          Length = 544

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 67/243 (27%), Positives = 113/243 (46%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   + ++ +    H D  +  ++YED  + V NKPAG+    G      +
Sbjct: 309 CGPILKHMLQGLHVEENPLETDMHRDT-ELEIMYEDEWLSVVNKPAGMLSVPGKSDIDSV 367

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G ++     +   P + HRLD  TSG++++A+T+   Q+L   F+ R + K Y + + G
Sbjct: 368 YGRVRRMY-PEATGPMIVHRLDMATSGLILIAKTKEVHQNLQAQFKNRTVCKRYVAWLDG 426

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I + K+  I   L +          V   +      A++ + V+   +    ++   P T
Sbjct: 427 IVEKKEGHIELPL-RPDPEDRPRQVV---DAVHGKPAVTDYTVLHYDS-GRTFISFIPKT 481

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
           GRTHQLRVH+ H   +  PIVGD  Y             ++LYLHA Y+   HP  G  +
Sbjct: 482 GRTHQLRVHSAHPLGLNAPIVGDELYGRK---------ADRLYLHAEYLGFIHPVSGVYM 532

Query: 306 QIT 308
           +I 
Sbjct: 533 EIE 535


>gi|299535937|ref|ZP_07049256.1| putative RNA pseudouridine synthase yjbO [Lysinibacillus fusiformis
           ZC1]
 gi|298728542|gb|EFI69098.1| putative RNA pseudouridine synthase yjbO [Lysinibacillus fusiformis
           ZC1]
          Length = 311

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 66/317 (20%), Positives = 119/317 (37%), Gaps = 43/317 (13%)

Query: 23  RWFKNHYPHINFVNLQKI-----------LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++       +    LQ+               G + V+       + +Q G  V++    
Sbjct: 17  QFEAKKNGQLLREALQEWRISKRALTAIKFDGGMLTVNDVERNVRHILQVGDCVKVTFPP 76

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHID 130
              +  +                +     ++YED  I V NKPA  S           I 
Sbjct: 77  EEKSEGLA--------------IEHGDLTIVYEDDAILVLNKPAHQSTIPSREHPTNSIA 122

Query: 131 GFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             +  +   +G      +  RLD++TSG+L +A+          + R R I + Y ++V 
Sbjct: 123 NLVCGYFQKQGLASTAHIVTRLDRDTSGLLCIAKHAHIHHLTGLAQRKREISRQYEAIVH 182

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEM 245
           G  +   + I   + +K     +   + ++  +   YA +  KV+  F+   +    + +
Sbjct: 183 GHIEQNFQSIIAPIGRK-----EGSIIEREVREDGQYAHTDVKVLKRFSLGAEPMTHVRL 237

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           Q HTGRTHQ+RVH  H+G P+VGD  Y  +          ++  LH   + + HP     
Sbjct: 238 QLHTGRTHQIRVHMSHLGHPLVGDDLYGGSRLQ------IDRQALHCVSLSMEHPLTSVP 291

Query: 305 LQITAPLPAHMVKTWDS 321
           L  T+ L   M +    
Sbjct: 292 LHFTSMLNEDMQRLLKE 308


>gi|238787243|ref|ZP_04631042.1| tRNA pseudouridine synthase C [Yersinia frederiksenii ATCC 33641]
 gi|238724505|gb|EEQ16146.1| tRNA pseudouridine synthase C [Yersinia frederiksenii ATCC 33641]
          Length = 257

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 103/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +       +
Sbjct: 64  ALSSDVARALSLQFEQHQIQKTYHAVVRGYVLAGDTIDYEMTEELDKIADKFSR----PD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    +++H++ +               +F  LE+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYQPLAKVEVPVAIGRYDTARFSLLELLPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +      +G       ++L LHA ++ L HP  G  L +TA       +     G++
Sbjct: 180 AHGDLRQNRGVAQHFGCSRLMLHASHLQLNHPVTGEPLILTARWDESWQQLMSHFGWQ 237


>gi|260914556|ref|ZP_05921024.1| pseudouridine synthase A [Pasteurella dagmatis ATCC 43325]
 gi|260631347|gb|EEX49530.1| pseudouridine synthase A [Pasteurella dagmatis ATCC 43325]
          Length = 228

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 65/230 (28%), Positives = 110/230 (47%), Gaps = 11/230 (4%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            +K ++ ++ +          +++ D    V NKP+G+    G+   Y+      S V  
Sbjct: 4   NKKEINMALIIYNPPTEPYLDIVHYDDHFVVVNKPSGLLSVPGNQPQYYDSAM--SRVKE 61

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           K       HRLD  TSG+++ A ++AA + L   FR R  +K Y +LVWG  +  +  I 
Sbjct: 62  KYGFCEPAHRLDMSTSGLILFALSKAADRELKRQFREREPKKHYQALVWGHLEEDQGKIN 121

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L+       +     K   +    A++ ++V++ +      +++ P TGR+HQLR+H 
Sbjct: 122 LPLICD----WENRPRQKICFERGKSAVTLYEVLERYPNNTTRVKLTPITGRSHQLRLHM 177

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
           L +G PI+GD  Y A+ +    SP   +L LHA  ++  HP    RL  T
Sbjct: 178 LALGHPILGDKFY-AHPQAKALSP---RLCLHAESLEFSHPITQERLVFT 223


>gi|312869346|ref|ZP_07729511.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
 gi|311095141|gb|EFQ53420.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
          Length = 309

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 66/300 (22%), Positives = 118/300 (39%), Gaps = 31/300 (10%)

Query: 22  DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           D+W       +    +  + R   V ++ +    N  + +G  V +    +         
Sbjct: 28  DQWL------LPNRYVHFLRRRHHVLLNGRYAYMNTAVAAGDRVTLAFNGDEFRT----- 76

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSK 140
                + N  + +   +  +L+E+  + V NKP G        G    +   +  ++ +K
Sbjct: 77  ----PAANDYRPTCEPQVRVLFENRDLVVVNKPQGQKSHPNYHGETGTLMNDVAGYLTAK 132

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                + HRLDQETSG +++A+       L       +I + Y ++V G    +      
Sbjct: 133 DCGAFMVHRLDQETSGAMIIAKNPVVVPVLNRLISSGQIHRRYLAVVAGNLTGR-GKFTE 191

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K       Y        + A  A ++++V+         + +Q  TGRTHQLRVH  
Sbjct: 192 PLGKDPRDVRKY----CVAGENAKPAQTNYQVLASR-HNRTLVLLQLATGRTHQLRVHLA 246

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
           + G PI+GD  Y  +           ++ LH    +L  P    R+Q+TAPLP++     
Sbjct: 247 YHGHPIIGDPLYGRD--------GSPRMLLHGATQELVLPFSFKRIQVTAPLPSYFTDYL 298


>gi|53715401|ref|YP_101393.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis YCH46]
 gi|60683368|ref|YP_213512.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis NCTC 9343]
 gi|253567423|ref|ZP_04844871.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_2_5]
 gi|52218266|dbj|BAD50859.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           fragilis YCH46]
 gi|60494802|emb|CAH09608.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis NCTC 9343]
 gi|251943805|gb|EES84344.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           3_2_5]
 gi|301164854|emb|CBW24414.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteroides fragilis 638R]
          Length = 221

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 68/219 (31%), Positives = 110/219 (50%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VIYEDNHIIVVNKTASEIVQGDKTGDTPLSETVKQYLKDKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E F+   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTSKALSRLNEMFKNSEVKKTYWAIVKNCPKQPEGELVHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI ++K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVPNSKKAILNYKLIG-HSDHYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGS- 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                 S     + LHAR++   HP     +++ AP+P 
Sbjct: 179 ----ARSNPDGSICLHARHVRFVHPVSKELIELDAPVPD 213


>gi|148977837|ref|ZP_01814392.1| ribosomal large subunit pseudouridine synthase A [Vibrionales
           bacterium SWAT-3]
 gi|145962906|gb|EDK28177.1| ribosomal large subunit pseudouridine synthase A [Vibrionales
           bacterium SWAT-3]
          Length = 244

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 65/218 (29%), Positives = 110/218 (50%), Gaps = 16/218 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D  I V NKPAG+    G  +  H D      V+      ++ HRLD  TSG+++
Sbjct: 15  DIVYQDDDILVVNKPAGLLSVPGR-LPEHHDSMWSRLVEEFA-DIQVVHRLDMSTSGLML 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A +HL + F+ R   K+Y++ VWG  ++K+  I   L+       D+ +  KQ 
Sbjct: 73  LAKHKQAERHLKKQFQYRLTHKLYYARVWGAVEHKEGLIDLPLI------CDWPNRPKQK 126

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              +    + + + V++    +   L++ P TGR+HQLRVH + +G PIVGD  Y     
Sbjct: 127 VCFEDGKSSQTRY-VVEQQEPQTTLLKLLPITGRSHQLRVHCMEIGAPIVGDEFYATPEA 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
             ++    ++L LHA  +   HP   +L   A +P   
Sbjct: 186 FEYS----DRLALHACELSFYHPANNQL-FKAFVPCDF 218


>gi|312865419|ref|ZP_07725646.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
 gi|311098937|gb|EFQ57154.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
          Length = 287

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 63/271 (23%), Positives = 111/271 (40%), Gaps = 32/271 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              + V+ + + + +++++G ++++       +    ++KIL    NL           L
Sbjct: 37  KKHLLVNNQAINWQSQVRAGDLIQLIFD----DENYPKKKILLGQANLVDC--------L 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + + NKP G+           +   + ++V   G    + HRLD+ETSG+++ A+
Sbjct: 85  YEDQHLIIVNKPEGMKTHANQPDEIALLNHVSAYV---GDTCYVVHRLDKETSGLVLFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      ++I + YW+L  G    K     + + +  H     +   K     
Sbjct: 142 NPFVLPILNRLLEDKQISRQYWALAQGRLAQKVITYRDKIGRDRHDRRKRLVTNK----- 196

Query: 223 ANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              AI+H + +  F         ++ Q  TGRTHQ+RVH  H G  I+GD  Y       
Sbjct: 197 GQEAITHIRRLKEFNGSKGPCTLVDCQLETGRTHQIRVHLAHHGHAIIGDPLYSKIPA-- 254

Query: 280 FTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
                  +L LHA  +   HP     + I A
Sbjct: 255 ------KRLMLHAHKLSFVHPFTREEITIQA 279


>gi|16761743|ref|NP_457360.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|29143227|ref|NP_806569.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|213162034|ref|ZP_03347744.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
 gi|213424905|ref|ZP_03357655.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213622998|ref|ZP_03375781.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
 gi|213648743|ref|ZP_03378796.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
 gi|289829830|ref|ZP_06547345.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|34582455|sp|Q8Z439|TRUC_SALTI RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|25322427|pir||AG0861 probable RNA pseudouridylate synthase yqcB [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16504044|emb|CAD06078.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhi]
 gi|29138860|gb|AAO70429.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
          Length = 260

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +       +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLIDDAVLDYPLVEERDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLIIQAGLDETWMQVLTQFGWR 237


>gi|91792374|ref|YP_562025.1| pseudouridine synthase [Shewanella denitrificans OS217]
 gi|91714376|gb|ABE54302.1| pseudouridine synthase [Shewanella denitrificans OS217]
          Length = 229

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 66/222 (29%), Positives = 101/222 (45%), Gaps = 11/222 (4%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +LYED  I   +KP+G+    G          +   +       RL HRLD 
Sbjct: 16  PPCLAQIQILYEDEAILAIDKPSGLLSLSGKNPLN--LDSVHYRLVQDFADARLLHRLDF 73

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++VAR +     LT+ F+ R + K Y +L+ G        I   + K + +    
Sbjct: 74  GTSGIILVARNKHINGLLTQQFQNRSVTKTYQALLMGKLSTDSGVIDAPIAKDAAL---- 129

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              +K  E     A++ +KV+    Q     ++  P TGRTHQLR+H+ H+G PI+G   
Sbjct: 130 FPRLKICELEGKSAMTEYKVLSYCEQTDLSRVQFTPITGRTHQLRLHSQHLGHPILGCDL 189

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y     G       +++ LHA+ +   HP  GG +QI  P P
Sbjct: 190 YGGIVDGREPV---SRMMLHAQSLAFTHPLTGGDMQINCPCP 228


>gi|330973896|gb|EGH73962.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aceris str. M302273PT]
          Length = 211

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 64/214 (29%), Positives = 102/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++++D+ + V +KPA +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIHQDAAVLVIDKPALLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEGGKHALTFWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G R+      P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERMTFECAAP 210


>gi|213583042|ref|ZP_03364868.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 259

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 3   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +       +
Sbjct: 63  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLIDDAVLDYPLVEERDKIADKFAR----ED 118

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 119 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 178

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 179 KHGDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLIIQAGLDETWMQVLTQFGWR 236


>gi|84394418|ref|ZP_00993135.1| pseudouridine synthase Rlu family protein [Vibrio splendidus 12B01]
 gi|84374951|gb|EAP91881.1| pseudouridine synthase Rlu family protein [Vibrio splendidus 12B01]
          Length = 249

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 99/240 (41%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IIYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    +QK Y ++V G  +          ++   I   +     + +
Sbjct: 64  ALSSEVASQVMPMFANHEMQKTYHAIVRGWIEEGDTLDYALKVELDKIADKFA----KED 119

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++C +EM P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEPQEAVTVYEPLAKVEVPYSTGRFPTSRYCLVEMMPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
            +               ++L LHA  +   HP     L + A L    ++ +++  +   
Sbjct: 180 SHGDGKHNRLFRDDLDSHRLLLHASELRFIHPFTKKELVMKASLDETWLRLFETFEWDTS 239


>gi|227363858|ref|ZP_03847963.1| RluA family pseudouridine synthase [Lactobacillus reuteri MM2-3]
 gi|325683068|ref|ZP_08162584.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
 gi|227071085|gb|EEI09403.1| RluA family pseudouridine synthase [Lactobacillus reuteri MM2-3]
 gi|324977418|gb|EGC14369.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
          Length = 297

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 63/281 (22%), Positives = 121/281 (43%), Gaps = 32/281 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
            G+  VD ++V+   +I   Q + I       +  ++              S      ++
Sbjct: 43  EGEFLVDHRKVRPTTQILPNQPLTIKAQPELADDTVE--------------SSNEPLNVV 88

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---DSKGQKPRLTHRLDQETSGIL 158
           YED    V +KPAG++   G  +    +   +K ++   +S   +P L  RLD+ T G+L
Sbjct: 89  YEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIANNSADLRPHLITRLDRFTGGLL 148

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+   A+  +++  +  ++ K Y +LV G   ++   I         IG       + 
Sbjct: 149 LIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHGEI------NKPIGRKDGQAARV 202

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            ++    A++ + V +    K+  + ++ HTGRTHQ+RVH   +G  ++GDH Y  +   
Sbjct: 203 IDENGQRALTEYWVEER-GAKWTRVRVRLHTGRTHQIRVHFAAIGHSLIGDHLYGGDTSK 261

Query: 279 NFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKT 318
                  +   LHA  +    P    ++  T+ LPA   + 
Sbjct: 262 ------YDHQLLHASKISFNDPFTLKQMTFTSELPAAFFEL 296


>gi|114046948|ref|YP_737498.1| pseudouridylate synthase [Shewanella sp. MR-7]
 gi|113888390|gb|ABI42441.1| Pseudouridylate synthase [Shewanella sp. MR-7]
          Length = 223

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 63/211 (29%), Positives = 98/211 (46%), Gaps = 9/211 (4%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP+G+    G   A H      + +        L HRLD  TSGI+V AR
Sbjct: 18  YQDRDLIIINKPSGLLSNPGR--AAHTFDCALTRLQRLYPDTILVHRLDCATSGIMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            + A   L   F+ R+ +K+Y + V G+       I   +         Y         G
Sbjct: 76  NKKAESQLKTQFQDRQNEKVYVAEVMGLIAKDAGIIDLAIAPDPEHP-PYQKTQTAGTAG 134

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
           A  A++H++V++   +    +E+ P TGRTHQLRVH L +G PI+GD  Y  +       
Sbjct: 135 AKSALTHYRVLERR-ENSTLVELTPQTGRTHQLRVHMLALGHPILGDEFYGDDE----VI 189

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             + +L LHA+ +   HP  G+ +   +  P
Sbjct: 190 KARPRLCLHAQSLRFTHPYSGKAMHFYSKHP 220


>gi|332520567|ref|ZP_08397029.1| pseudouridine synthase [Lacinutrix algicola 5H-3-7-4]
 gi|332043920|gb|EGI80115.1| pseudouridine synthase [Lacinutrix algicola 5H-3-7-4]
          Length = 236

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 73/218 (33%), Positives = 105/218 (48%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK AG  VQG       +   +K ++  K  KP        HRLD+ T+
Sbjct: 17  VIYEDNHIIVVNKRAGDIVQGDKTGDKPLSDVVKEYLAEKYNKPGNVYLGTVHRLDRPTT 76

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ ++T  A   L + F  + I K YW+LV   PK +K+ + +WL K         H+
Sbjct: 77  GLVIFSKTSKALPRLNKLFVSKDISKTYWALVKNKPKKEKDTLIHWLKKNPKNNKSRAHI 136

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI H+K I      +  LE+   TGR HQ+R     +G PI GD KY  +
Sbjct: 137 --KEVPDSKKAILHYKTIKVL-DNYILLEVNLETGRHHQIRAQLSSIGSPIKGDLKYGFD 193

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                 S     + LHAR +   HP     L ITAPLP
Sbjct: 194 RSNKDAS-----ISLHARNIKFIHPVSKIELDITAPLP 226


>gi|254225113|ref|ZP_04918727.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V51]
 gi|125622500|gb|EAZ50820.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V51]
          Length = 245

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 98/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASDVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAMTAYRPLAKVELPISTGKFTTTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDDVWQGLLSEFGWQES 239


>gi|117919878|ref|YP_869070.1| pseudouridine synthase [Shewanella sp. ANA-3]
 gi|117612210|gb|ABK47664.1| pseudouridine synthase [Shewanella sp. ANA-3]
          Length = 223

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 63/211 (29%), Positives = 97/211 (45%), Gaps = 9/211 (4%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP+G+    G   A H      + +        L HRLD  TSGI+V AR
Sbjct: 18  YQDRDLIIINKPSGLLSNPGR--AAHTFDCALTRLQRLYPDTILVHRLDCATSGIMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            + A   L   F+ R+ +K+Y + V G        I   +         Y         G
Sbjct: 76  NKKAESQLKTQFQDRQNEKVYIAEVMGGIAKDAGIIDLAIAPDPEHP-PYQKTQTPGTAG 134

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
           A  A++H++V++   +    +E+ P TGRTHQLRVH L +G PI+GD  Y  +       
Sbjct: 135 AKSALTHYRVLERR-ENSTLVELTPQTGRTHQLRVHMLALGHPILGDEFYGDDE----VI 189

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             + +L LHA+ +   HP  G+ +   +  P
Sbjct: 190 KARPRLCLHAQSLRFTHPYSGKAMHFYSKHP 220


>gi|265768298|ref|ZP_06095557.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_16]
 gi|263252233|gb|EEZ23781.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_16]
          Length = 221

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 68/219 (31%), Positives = 110/219 (50%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK A   VQG       +   +K ++  K QKP      +THRLD+  S
Sbjct: 3   VIYEDNHIIVVNKTASEIVQGDKTGDTPLSETVKQYLKDKYQKPGNVFIGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E F+   ++K YW++V   PK  +  + ++L++       Y + 
Sbjct: 63  GLVIFAKTSKALSRLNEMFKNSEVKKTYWAIVKNCPKQSEGELVHYLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +    +  AI ++K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DKEVPNSKKAILNYKLIG-HSDHYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGS- 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                 S     + LHAR++   HP     +++ AP+P 
Sbjct: 179 ----ARSNPDGSICLHARHVRFVHPVSKELIELDAPVPD 213


>gi|306832623|ref|ZP_07465762.1| ribosomal large subunit pseudouridine synthase [Streptococcus bovis
           ATCC 700338]
 gi|304425231|gb|EFM28358.1| ribosomal large subunit pseudouridine synthase [Streptococcus bovis
           ATCC 700338]
          Length = 286

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 58/280 (20%), Positives = 107/280 (38%), Gaps = 31/280 (11%)

Query: 32  INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           I    ++  LR    + ++ + + + + +++G  + +    +            D     
Sbjct: 26  IPR-KIRHFLRTKKHLLINGEMINWQSLVKTGDTIHLIFDDD------------DYPQKE 72

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
                      LY+D  + + NKP G+   G       +   + ++V   GQ   + HRL
Sbjct: 73  IPFGQAELVDCLYQDEHLIIVNKPEGMKTHGNEPNEITLLNHVSAYV---GQTCYVIHRL 129

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG ++ A+       L      + I + YW+LV G  + K +   + + +  H   
Sbjct: 130 DMETSGAVMFAKNPFVLPILNRLLENKDIAREYWALVQGKFEPKHQVFQDKIGRDRHDRR 189

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             V     + K    A++    +  F      ++ +  TGRTHQ+RVH       I+GD 
Sbjct: 190 KRVI----DRKNGQTALTIVDRLKVFPNG-TLVKCRLKTGRTHQIRVHLSAHNHAIIGDP 244

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
            Y              +L LHA  +   HP    ++ + A
Sbjct: 245 LYSKIPA--------KRLMLHAHKLSFTHPFTLEKISVEA 276


>gi|262065871|ref|ZP_06025483.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           periodonticum ATCC 33693]
 gi|291380458|gb|EFE87976.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           periodonticum ATCC 33693]
          Length = 288

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 133/320 (41%), Gaps = 38/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +VE++ +   +  + K    + +       LR+ ++ ++ KR           +  
Sbjct: 1   MKKYIVEHEFDGYEIGTYLKETKGYSSRG-----LRNLEIYLNGKR-----------IKN 44

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
               I  LN I+    I++   +    +  +   + YED  + + NK   I V      +
Sbjct: 45  NAKKIKKLNRIV----IIEKEKSTGIKAMDIPIDIAYEDENLLIVNKEPYIIVHPTQKKV 100

Query: 126 AYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +   + ++ +    K   PR  +RLD  TSG++++A+       L +      ++K 
Sbjct: 101 DKTLANAVVNYFEKTLGKTLVPRFYNRLDMNTSGLIIIAKNAYTQAFLQDKT---EVKKT 157

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFC 241
           Y  +  GI +     I   + K   IG D   +    E G   A +H KV++    +   
Sbjct: 158 YKVIAGGIIEKDDFFIELPIGK---IGDDLRRIELSEENGGKSAKTHIKVLERNREKNIT 214

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +LE + +TGRTHQ+R H   +G P+VGD  Y  +        +  +  LHA  ++  +P+
Sbjct: 215 FLEARLYTGRTHQIRAHLSLIGHPLVGDELYGGDIN------LAKRQMLHAYKLEFQNPK 268

Query: 302 G-GRLQITAPLPAHMVKTWD 320
               L++   +P  M +   
Sbjct: 269 TLDDLKVEIEIPLDMKELLK 288


>gi|227889491|ref|ZP_04007296.1| pseudouridylate synthase RluD [Lactobacillus johnsonii ATCC 33200]
 gi|227849969|gb|EEJ60055.1| pseudouridylate synthase RluD [Lactobacillus johnsonii ATCC 33200]
          Length = 266

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 65/261 (24%), Positives = 109/261 (41%), Gaps = 29/261 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
             ++ V+ K +  N  ++ G  + I      L+HI  +Q+   +S  L K        ++
Sbjct: 23  EKKILVNGKYLPLNFLVKPGDKIEIQ-----LDHIESDQQPYPASGKLPK--------VV 69

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED+ I V NKP G             D  L       G  P + HRLD  TSG+L+VA+
Sbjct: 70  YEDNDILVINKPTGQKTHPN---LNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLLVAK 126

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIANWLLKKSHIGGDYVHVVKQNEK 221
             A    L      + + + Y + +   P+ K    I   +    H     +       +
Sbjct: 127 NPAVVPILNRQLTDKTLHREYLAWISNSPQIKYTGIIDLPIGHDPHDQRKRMVR-----Q 181

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               A++H++VI     +   +++   TGRTHQ+RVH   +G PI+GD  Y ++++    
Sbjct: 182 DGQKAVTHYEVIKRDKDRI-LVKLTLETGRTHQIRVHLAALGAPIIGDPLYNSDYQDG-- 238

Query: 282 SPIQNKLYLHARYMDLPHPEG 302
                +L L A  +    P  
Sbjct: 239 ----EQLQLTAFQLTFRKPFS 255


>gi|119026149|ref|YP_909994.1| hypothetical protein BAD_1131 [Bifidobacterium adolescentis ATCC
           15703]
 gi|154488937|ref|ZP_02029786.1| hypothetical protein BIFADO_02246 [Bifidobacterium adolescentis
           L2-32]
 gi|118765733|dbj|BAF39912.1| hypothetical protein [Bifidobacterium adolescentis ATCC 15703]
 gi|154083074|gb|EDN82119.1| hypothetical protein BIFADO_02246 [Bifidobacterium adolescentis
           L2-32]
          Length = 309

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 68/325 (20%), Positives = 127/325 (39%), Gaps = 20/325 (6%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V   +     R D         I+      ++ SGQ RV  + +  ++ +Q+G+ V  
Sbjct: 3   RLVPAPDALVGKRFDVAVAKML-GISRAKAADLIESGQARVLGRDISKSSTLQAGETVEF 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             V         E + +   + +    D +  +        +      G +V G      
Sbjct: 62  DIVEERS-----EPEPIAHDMAVVYEDDDVVVVDKPVGVAAHASVGWTGPTVLGS----- 111

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            ID  +         +  +  RLD  TSG+++V ++  A   +   F    + K Y +LV
Sbjct: 112 LIDRGVHITSYGAAGRQGIVSRLDVGTSGLMLVCKSDLAYVEMRRQFAEHEVVKTYHALV 171

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  K  K  I   + +                     AI+H+ V++ F +    + +  
Sbjct: 172 QGNLKEDKATIEAPIGR-----AKVSDFRFCVTPAGKEAITHWDVMERFGE-ATLVSVNL 225

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            TGRTHQ+RVH   +G P+ GD  Y AN + +    ++ + +LHA  ++  HP       
Sbjct: 226 ETGRTHQIRVHFSSIGHPLAGDAMYGANPQLSEALGLE-RQWLHAMQLEFRHPRTHVWTT 284

Query: 307 ITAPLPAHMVKTWDSLGFKY-DRNL 330
           + +  PA +    D +  ++ D++L
Sbjct: 285 VKSHYPADLQHALDVMRARHADQSL 309


>gi|183597604|ref|ZP_02959097.1| hypothetical protein PROSTU_00890 [Providencia stuartii ATCC 25827]
 gi|188023103|gb|EDU61143.1| hypothetical protein PROSTU_00890 [Providencia stuartii ATCC 25827]
          Length = 252

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 106/239 (44%), Gaps = 17/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V      +      +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IIYQDEYMVAVNKPAGMLVHRSWLDSKETVFVMQTLRDQIGQFVYPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L   F   +I+KIY ++V G  +  +      L +   I   +       E
Sbjct: 64  ALSSDVARQLAAQFESHQIEKIYHAVVRGYVEAPQTIDYPLLEQLDKIADKHATR----E 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                 ++H + I               +F  LE++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 PALQECVTHCQPIAQVECSVAIGRYPTSRFSLLELKPETGRKHQLRRHMSHIRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKY 326
           K+      +G       ++L LHA  + L HP  G R+ + A      +   +  G+++
Sbjct: 180 KHGDLRQNRGVSQHFAVSRLMLHASQLVLDHPISGERISLIAQWDESWLSLVNQFGWQH 238


>gi|325273101|ref|ZP_08139401.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas sp.
           TJI-51]
 gi|324101761|gb|EGB99307.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas sp.
           TJI-51]
          Length = 211

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 65/213 (30%), Positives = 99/213 (46%), Gaps = 11/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED+ I V NKP  +    G       D  +     +      + HRLD ETSGI+++
Sbjct: 8   ILHEDAAILVINKPTLLLSVPGRADDN-KDCLITRLQQNGYPDALIVHRLDWETSGIILL 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR   + + L+  F  R  +K Y +L WG P      I   L           HVV  + 
Sbjct: 67  ARDADSHRELSRQFHDRETEKAYTALCWGQPALDSGSIDLPLRYDPPT--KPRHVV--DH 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +   +A++ +++++      C +E+ P TGR+HQLRVH L +G P++GD  Y        
Sbjct: 123 EQGKHALTFWRIVERCGD-HCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY----ANPQ 177

Query: 281 TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                 +L LHA  +   HP  G RL+   P P
Sbjct: 178 ALAAHERLCLHASMLSFTHPVSGQRLKFECPAP 210


>gi|253687331|ref|YP_003016521.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251753909|gb|ACT11985.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 266

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 107/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 9   IIYQDEHLVAVNKPSGWLVHRSWLDRKEKVVVMQTVRDQIGQHVYTVHRLDRPTSGVLLL 68

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++QK+Y ++V G   +          +   I   + +     +
Sbjct: 69  ALSSEVARALSQQFESHQMQKMYHAVVRGYVLDDGVIDYALTEELDKIADKFTN----PD 124

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 125 KAPQPAVTHYRSLAQVEMPVAIGRYPTARYSLMELKPQTGRKHQLRRHMSHLRHPIIGDT 184

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +    + +G  T     +L LHA  + L HP  G+ L + A   A         G++
Sbjct: 185 AHGDLRHNRGMETHFSCGRLMLHASELQLNHPVSGQPLTLQARWDAPWQGVMTQFGWQ 242


>gi|74316676|ref|YP_314416.1| ribosomal large subunit pseudouridine synthase A [Thiobacillus
           denitrificans ATCC 25259]
 gi|74056171|gb|AAZ96611.1| ribosomal large subunit pseudouridine synthase A [Thiobacillus
           denitrificans ATCC 25259]
          Length = 211

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 63/215 (29%), Positives = 100/215 (46%), Gaps = 14/215 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY D  + VF+KP+G+    G G        L +   +      + HRLD  TSG++V+A
Sbjct: 6   LYADDCLLVFDKPSGLLAVPGRGPD--KQDCLAARAQACYPDALVVHRLDMATSGLMVMA 63

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE---CIANWLLKKSHIGGDYVHVVKQ 218
           R   A + L+ +F  R ++K Y ++V G P   +     I   L+         +    +
Sbjct: 64  RGTYAQRALSRAFAAREVEKRYVAVVAGHPAAPQGAWGTIDLPLVVDWPNRPLRIVDAVR 123

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  +++ ++V+         +E++P TGR+HQLRVH   +G PI+GD  Y      
Sbjct: 124 ----GKPSVTRWRVLGPAGADGTRVELEPVTGRSHQLRVHLREIGHPILGDALYAPPAVQ 179

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              S    +L LHAR + L HP  G  ++  AP P
Sbjct: 180 AQAS----RLLLHARSLGLAHPATGEWMRFEAPQP 210


>gi|83648421|ref|YP_436856.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83636464|gb|ABC32431.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 248

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 108/242 (44%), Gaps = 18/242 (7%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +   +LY+D  +   +KP+G+ V       +     ++   D  G++    HRLD+ TS
Sbjct: 1   MIPLSILYQDEWLVAIDKPSGLLVHRSEIDRHETLFAIQLLRDQIGRRVYPLHRLDKPTS 60

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+ A     A+   ES+    + K Y ++V G+P  ++  I   L +     GD    
Sbjct: 61  GVLMFALDSDTAKKCGESWETG-VDKAYLAIVRGVPA-EEGVIDKPLKEPWDRLGDR--- 115

Query: 216 VKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
               +K    A++H++ +               ++  L+++P TGR HQ+R H   +  P
Sbjct: 116 NVSKDKPEQPAVTHYQRLAECELPYAVDRYPTSRYALLKVRPQTGRRHQIRRHFKSLSHP 175

Query: 266 IVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           ++GD  Y       F        +L LHA  M LPHP  G  L + AP+   M +  ++L
Sbjct: 176 LIGDTSYGKGVHNRFFAEQFGVQRLLLHAAEMRLPHPCSGETLTVCAPVTGEMRRLLETL 235

Query: 323 GF 324
            +
Sbjct: 236 DW 237


>gi|56414914|ref|YP_151989.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197363842|ref|YP_002143479.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|56129171|gb|AAV78677.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197095319|emb|CAR60877.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
          Length = 260

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDRWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +  A + L + F    I+K Y ++V G   +        + ++  I   +       +
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAR----ED 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +         +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 180 KHGDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLIIQAGLDETWMQALTQFGWR 237


>gi|330995758|ref|ZP_08319655.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
 gi|329574488|gb|EGG56053.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
          Length = 522

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 73/247 (29%), Positives = 116/247 (46%), Gaps = 20/247 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  ++   +KH D  +  L+YED  +   NKPAG+    G G A  +
Sbjct: 291 CEPILGHMLQGLDVEPNAHESSKHLDH-EPELVYEDEWMVAVNKPAGMLSVPGKGDAPSV 349

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             + ++    +   P L HRLD +TSG+L++A+     + L + F  R I+K Y +L+ G
Sbjct: 350 WSWARAHF-PEATGPLLVHRLDMDTSGVLLIAKDPETHRQLQQLFETRHIKKRYVALLDG 408

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              + +  I   L        D       +      A++ F+V+   +     +   P T
Sbjct: 409 TVTDDEGFIRLPLCPNP----DDRPRQMVSTAHGKAAVTRFEVLSR-SCGQTRVAFYPLT 463

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVHA H   +  PIVGD+ Y             ++L+LHA  +   H + GR +
Sbjct: 464 GRTHQLRVHAAHPEGLDTPIVGDNLYGRR---------ASRLFLHAETVAFRHFKTGRWV 514

Query: 306 QITAPLP 312
            ITAP P
Sbjct: 515 SITAPAP 521


>gi|254557295|ref|YP_003063712.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254046222|gb|ACT63015.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 300

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 69/317 (21%), Positives = 127/317 (40%), Gaps = 27/317 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRS-GQVRVDKKRVKFNNRIQSG 62
           MT+   + + +      +    +     I    +Q  LR   +++++         + +G
Sbjct: 1   MTWTYQLTIPSSLNQQSIRACLRTWL--IPK-RIQGQLRQTRRIQLNGAPTSIAQLVNTG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +  + +             +  +    +    + +LY++S + V +KPAG+     
Sbjct: 58  DRLTLTFIPSDFR----------TPTSNYIAAATAPATILYQNSDLLVVDKPAGVKSHPN 107

Query: 123 -SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             G    I   L + +    Q P + HRLDQ TSG ++VA        L      ++I++
Sbjct: 108 QPGETGSILNDLAATLQPTQQVPYMVHRLDQMTSGAMLVALNPVVVPILDRLISDKQIRR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++ V G            +   +            N   A  A++ ++V    A +  
Sbjct: 168 TYYAWVRGHFATPTGHFTAPIGHDATDKRKR----WVNTADAQPALTDYEVCATTAHQ-S 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            +++  HTGRTHQLRVH      PI+GD  Y +  +         +L LHA+ +DL  P 
Sbjct: 223 LVKLTLHTGRTHQLRVHLAASDHPIIGDPLYDSQAESA------PRLMLHAQLLDLQLPF 276

Query: 301 EGGRLQITAPLPAHMVK 317
              R+ + APLP+   K
Sbjct: 277 STTRVTVPAPLPSLFEK 293


>gi|227499062|ref|ZP_03929199.1| pseudouridine synthase [Acidaminococcus sp. D21]
 gi|226904511|gb|EEH90429.1| pseudouridine synthase [Acidaminococcus sp. D21]
          Length = 296

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 66/311 (21%), Positives = 122/311 (39%), Gaps = 40/311 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +  ++V  ++  + L  +       ++    + + ++  + V+     ++  + +   V 
Sbjct: 1   MNQLLVPKNQSGIHLKTFLMQW--GLSASYWKALKKARALFVNGLVTVWDIPLSANDRVS 58

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            P +    + + +E                    +LYED  +   +K  G+ V       
Sbjct: 59  FPFLPEETDLVPEEG----------------PLTILYEDEVLLAVHKEQGLLVHNSGLTQ 102

Query: 127 YHIDGF-LKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                  +  +    G K       RLD+ETSGI++ A+  A    LT++   +    +Y
Sbjct: 103 ESSLSRRVLFYYREHGIKAALHPVSRLDRETSGIVLFAKNAALHHMLTKAPMKK----LY 158

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L  G  +     IA  + +K     D   + +        A + ++V+   A K   +
Sbjct: 159 LALSHGPWEKFSGVIAQPIARK-----DGSLIERCVAPQGKPARTRYRVLWQDAAK-SVV 212

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
               +TGRTHQ+RVHA  MG P++GD  Y A               LHA  +   HP  G
Sbjct: 213 AFHLYTGRTHQIRVHAAFMGHPLLGDTLYGAKGSQKAH-------ALHAMRLQFRHPLSG 265

Query: 304 R-LQITAP-LP 312
           + ++IT P LP
Sbjct: 266 KDVKITDPSLP 276


>gi|218132473|ref|ZP_03461277.1| hypothetical protein BACPEC_00332 [Bacteroides pectinophilus ATCC
           43243]
 gi|217992583|gb|EEC58585.1| hypothetical protein BACPEC_00332 [Bacteroides pectinophilus ATCC
           43243]
          Length = 229

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 47/235 (20%), Positives = 98/235 (41%), Gaps = 29/235 (12%)

Query: 10  VVVENDEENMRLDRWFK---NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           + V+  +   R+DR+          ++   LQK+++ G V V+   +K N +++   ++ 
Sbjct: 6   INVDELDAGSRIDRYMAQEREELSDLSRSYLQKLIQDGNVLVNGCNIKANYKLKKADIID 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           I         I  E   LD               +LYED  I V NKP G+ V   +G  
Sbjct: 66  ITLPDIKEPQIEAENIPLD---------------ILYEDEDIIVINKPKGMVVHPAAGHY 110

Query: 126 -AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++  +    D+        +P + HR+D  T+G+LV  +   A   ++    +  I
Sbjct: 111 SGTLVNALMYHCRDNLSGINGVMRPGIVHRIDMNTTGVLVACKNDFAHNAISAQLSVHSI 170

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            + Y ++V+     +   +   + + SH     + + + N      A++H+++++
Sbjct: 171 TRKYEAIVYNRFNEESGTVDAPIGR-SHNDRKKMAIDRDN---GRRAVTHYRLLE 221


>gi|312622224|ref|YP_004023837.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202691|gb|ADQ46018.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
          Length = 312

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 67/289 (23%), Positives = 125/289 (43%), Gaps = 23/289 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV+ +   +++++  K  YP I    + K+LR G++ V     +    ++ G  V    
Sbjct: 5   FVVDKELAGVKVEKAIKKKYPTIPMSVIFKMLRRGEIIVSFLPAQKGQVLRFGDTVSFEI 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H  K+++IL                 +YED  I V +KP GI     S   Y +
Sbjct: 65  EDRFLEH--KKEEILK----------------VYEDDNIVVIDKPYGIPSHPDSNNEYSV 106

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             +++    +K + P+L HRLD+ T+G++++A+ R     + +    R I K Y  +   
Sbjct: 107 VSWIEDNYSNKEELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRAIIKKYLCITKK 166

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               +   + ++L K S     Y+    Q+  G +  ++ +K++         ++++  T
Sbjct: 167 ADLPESGVLVHYLKKDSKKSKVYISDFPQD--GYSEVVTAYKIV-RQKDDLQLVDVEIKT 223

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           G+THQ+R    H+G  I+GD KY             +   L A Y+   
Sbjct: 224 GKTHQIRAQLAHIGLCILGDSKYGDWKLNKKYK--ADMQALCAYYLKFE 270


>gi|238763986|ref|ZP_04624942.1| tRNA pseudouridine synthase C [Yersinia kristensenii ATCC 33638]
 gi|238697803|gb|EEP90564.1| tRNA pseudouridine synthase C [Yersinia kristensenii ATCC 33638]
          Length = 257

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 103/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +       +
Sbjct: 64  ALSSDVARALSLQFEQHQIQKTYHAVVRGYVLEDGTIDYEMTEELDKIADKFSR----PD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    +++H+  +               +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYHALAQVEVPIAIGRYDTARFSLMELKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +      +G       ++L LHA +++L HP  G  L +TA       +      ++
Sbjct: 180 THGDLRQNRGIAEHFDCSRLMLHASHLNLNHPVTGEPLSLTARWDDSWQQLMSHFRWQ 237


>gi|332978702|gb|EGK15396.1| tRNA pseudouridine synthase C [Psychrobacter sp. 1501(2011)]
          Length = 261

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 102/241 (42%), Gaps = 18/241 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  ++YED  +   NK AG+ V             ++   D+ G      HRLD+ TSG+
Sbjct: 19  QIDIIYEDEHLVAINKEAGLLVHRSWLDKGETRFAMQLTRDAVGCHVVPVHRLDRPTSGV 78

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A+  A A+ LTE+F  R++ K Y ++V G    +         K   I   + ++  
Sbjct: 79  LLFAKNSAVARSLTEAFTERKVAKQYLAVVRGFMSEEGTVDYALSFKPDAIADKFANL-- 136

Query: 218 QNEKGANYAISHFKVI-----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              K A  A++H++ +                ++  + + P TGR HQLR H  H+   I
Sbjct: 137 --NKPAQEAVTHWQSLAQIELPFAVSKKHGTSRYSLMRLIPETGRKHQLRRHMRHLFHHI 194

Query: 267 VGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD  Y       F     +  ++ LHA+ + L HP  G  L + A       +  +   
Sbjct: 195 IGDTSYGDGRHNKFFRTQYDCTRMLLHAQTLALSHPVTGEPLMLEAGFDDQWTRILEEFS 254

Query: 324 F 324
           +
Sbjct: 255 W 255


>gi|149907559|ref|ZP_01896306.1| Pseudouridylate synthase [Moritella sp. PE36]
 gi|149809229|gb|EDM69158.1| Pseudouridylate synthase [Moritella sp. PE36]
          Length = 251

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 60/247 (24%), Positives = 106/247 (42%), Gaps = 18/247 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D  +   +KPAG+ V      ++     ++   D  GQ     HRLD+ TSG+L
Sbjct: 2   LDILYQDEYLVAIDKPAGLLVHRSWLDSHETQFAMQMVRDQIGQHVYTVHRLDRPTSGVL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A +   A+ ++E F+   + K Y ++V G             ++   I          
Sbjct: 62  LFALSSEVARQMSEIFQAHALTKRYLAVVRGWINEAGTLDYALKVELDKIADKQATQ--- 118

Query: 219 NEKGANYAISHFKVID-----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +K A  A++H+K +                ++C +E++P TGR HQLR H  H+  PIV
Sbjct: 119 -DKEAQEAVTHYKPLHQVEIPYPISKNHPTSRYCLMELEPQTGRKHQLRRHMKHLFHPIV 177

Query: 268 GDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           GD  +       F        +L L A+ +   HP   + + I A +   ++  ++  G+
Sbjct: 178 GDTTHGDGRHNVFYREHFELPRLLLIAKSLSFIHPVTAQPVHIEAAVGDEVLGLFEQFGW 237

Query: 325 KYDRNLY 331
               + Y
Sbjct: 238 PAQESDY 244


>gi|229553304|ref|ZP_04442029.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus rhamnosus
           LMS2-1]
 gi|258540084|ref|YP_003174583.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
 gi|229313390|gb|EEN79363.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus rhamnosus
           LMS2-1]
 gi|257151760|emb|CAR90732.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
          Length = 289

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 69/302 (22%), Positives = 124/302 (41%), Gaps = 40/302 (13%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           RW       ++    +K+L +  + +D  R   N  IQ+GQ VR                
Sbjct: 17  RWLAKQ--GVSHRLFKKMLANHLLWLDGHR-TGNTAIQAGQTVRF--------------- 58

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKG 141
                  +T   +     +LYED    + NKPA ++   G    +H     +  ++  + 
Sbjct: 59  --AIPTTMTVTPEKASLDVLYEDQNWLIINKPAHLTSVPGPHDPHHSLLNRIVWYLQQQK 116

Query: 142 ---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +P +  RLD++T G+++ A+   A     ++     ++K Y ++V G   +  E I
Sbjct: 117 VTEPQPAIITRLDRDTVGLVLAAKHPYAQGRFDQAHHA-TLKKEYLAVVAGHLSHATETI 175

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +     +G D +H +    +    AI+ ++V+         +E+Q  TGRTHQ+RVH
Sbjct: 176 EAPIG----LGPDGIHRMV--TENGQSAITKYQVLKEAVN--TLVEVQLLTGRTHQIRVH 227

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
              +G P++GD  Y         SP+ +   L A  +    P    R+Q   P+P   + 
Sbjct: 228 FASLGHPLIGDSLYGQ------ASPLIDHQALQATRLSFVDPFSEKRIQADLPIPDDFMN 281

Query: 318 TW 319
             
Sbjct: 282 LL 283


>gi|84394045|ref|ZP_00992782.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           12B01]
 gi|84375331|gb|EAP92241.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           12B01]
          Length = 244

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 63/216 (29%), Positives = 106/216 (49%), Gaps = 12/216 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D  I V NKPAG+    G  +  H D      V    +  ++ HRLD  TSG+++
Sbjct: 15  DIVYQDDDILVVNKPAGLLSVPGR-LPEHYDSMWSRLVVEFAE-IQVVHRLDMSTSGLML 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A +HL + F+ R   K+Y++ VWG  +  +  I   L+           V  ++
Sbjct: 73  LAKHKQAERHLKKQFQYRLTHKLYYARVWGSVEEAEGLIDLPLICD-WPNRPRQKVCFED 131

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 + + + V++    +   L++ P TGR+HQLRVH + +G PIVGD  Y      N
Sbjct: 132 ---GKPSQTRY-VVERQEAQTALLKLLPITGRSHQLRVHCMELGNPIVGDEFYATPDAFN 187

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           ++    ++L LHA  +   HP   +L   A +P   
Sbjct: 188 YS----DRLALHACELSFYHPANNQL-FKAFVPCEF 218


>gi|238760461|ref|ZP_04621598.1| tRNA pseudouridine synthase C [Yersinia aldovae ATCC 35236]
 gi|238701303|gb|EEP93883.1| tRNA pseudouridine synthase C [Yersinia aldovae ATCC 35236]
          Length = 257

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 65/257 (25%), Positives = 107/257 (41%), Gaps = 18/257 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I           +
Sbjct: 64  ALSSEVARTLSLQFEQHQIQKTYHAVVRGYVLESGTVDYAMAEELDKIADKRARQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    +++H++ +               ++  + ++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYQPVAQVEVPLAIGRYETARYSLVALKPETGRKHQLRRHMAHIRHPIIGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +      +G        +L LHA ++ L HP  G  L +TA   A         G+   
Sbjct: 180 AHGDLRQNRGVAEHFACPRLMLHASHLQLNHPVTGEALLLTARWDASWQGLMSHFGWSGI 239

Query: 328 RNLYIKRLYSQDECKQN 344
               ++R+   D   Q+
Sbjct: 240 APD-VERVEFSDTADQD 255


>gi|288924796|ref|ZP_06418733.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella buccae D17]
 gi|315607815|ref|ZP_07882808.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
 gi|288338583|gb|EFC76932.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella buccae D17]
 gi|315250284|gb|EFU30280.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
          Length = 223

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 107/228 (46%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           L+YED+ + +  K +G  VQG       +   +K ++  K QKP      + HRLD+  S
Sbjct: 3   LVYEDNHLIIVFKESGEIVQGDKTGDEPLSEAVKRYIKEKYQKPGNVFIGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L   FR   + K YW++V   P +++  + NW+++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNMMFRNGDVHKTYWAIVKDAPMHEEGTLENWIVRNEQQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +  A+  + VI   ++ +C LE+   TGR HQ+R    H+GCPI GD KY   
Sbjct: 122 -DHEVPNSKKAVLKYHVISR-SEHYCLLEVNLLTGRHHQIRCQLAHIGCPIKGDLKYGFP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     + L +R ++  HP     +   +PLPA     W + 
Sbjct: 180 -----RSNPDGGISLLSRRVEFVHPVSKETISAVSPLPAD--ALWKAF 220


>gi|260774106|ref|ZP_05883021.1| pseudouridylate synthase LSU rRNA-specific [Vibrio metschnikovii
           CIP 69.14]
 gi|260611067|gb|EEX36271.1| pseudouridylate synthase LSU rRNA-specific [Vibrio metschnikovii
           CIP 69.14]
          Length = 557

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 73/250 (29%), Positives = 109/250 (43%), Gaps = 22/250 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++K   + D+ + L   ++  +  ++Y+D  I V NKPA      G  I   +
Sbjct: 326 CQPILAHMLKGMPLEDNPL-LVNPAEGKQIEIVYQDEAIVVINKPAEFLSVPGVNIKDSV 384

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L       G+ P + HRLD  TSG+LV A TR A + L + F  R+I K Y +L+ G
Sbjct: 385 FTRLAEQF-PDGEGPFVLHRLDMSTSGLLVFALTRRANKSLQKQFITRQIDKQYVALLAG 443

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             ++    I   L        D     K   +    A + ++ +    Q    + + PHT
Sbjct: 444 ELEHDGGDITLPLAAD----RDDRPRQKVCLETGKSAQTRWEKV-AIEQGQTRVNLYPHT 498

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH  H   +G PIVGD  Y              +L LHA+ +   HP    ++
Sbjct: 499 GRTHQLRVHCAHPDGLGFPIVGDDLYG---------QAAERLCLHAQKLSFYHPYHHQKM 549

Query: 306 QITAPLPAHM 315
                +PA  
Sbjct: 550 TFE--VPADF 557


>gi|257470632|ref|ZP_05634722.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
 gi|317064838|ref|ZP_07929323.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
 gi|313690514|gb|EFS27349.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
          Length = 296

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 72/320 (22%), Positives = 129/320 (40%), Gaps = 38/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++E + +   +  + K    +         LR+ ++ ++ KRVK N++        
Sbjct: 1   MKKFIIEPEYDGYEIGTYLKETKGYSGRG-----LRNIEIYLNGKRVKNNSK-------- 47

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
               +  LN ++ ++K  ++ +        +   + YED  + + +K   I V       
Sbjct: 48  ---KVRKLNRLLIKEKDKETGI----IPMEIPIKVAYEDKNVLLIDKEPYIIVHPTQKKV 100

Query: 125 IAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +G +  ++ + G    PR  +RLD  TSG+++VA+   A   L E      + K 
Sbjct: 101 DKTLANGVVNYFLKTTGKIMVPRFYNRLDMNTSGLIIVAKNSFAQSFLQE---KGIVNKF 157

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G  +  +  I   + K   IG D        E G   A +  KVI  F +    
Sbjct: 158 YKAIVKGTVEKDEFLIDRPIGK---IGDDLRRREISVEDGGQEAQTKIKVIKRF-KDLTL 213

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+R H    G P++GD  Y    K         +  LH+        E 
Sbjct: 214 IEAELLTGRTHQIRAHMALEGYPLLGDELYGGEDKRA------KRQMLHSYKTQFSDVET 267

Query: 303 GRL-QITAPLPAHMVKTWDS 321
           G+L  +   +P  M K    
Sbjct: 268 GQLKTVEIDIPDDMKKILRE 287


>gi|281426229|ref|ZP_06257142.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella oris F0302]
 gi|281399643|gb|EFB30474.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella oris F0302]
          Length = 221

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 65/227 (28%), Positives = 110/227 (48%), Gaps = 15/227 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + +  K +G  VQG       +   +K ++  K QKP      + HRLD+  S
Sbjct: 3   IVYEDNHLIIVYKHSGEIVQGDKTGDVPLSEDVKCYLKEKYQKPGNVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L + FR   + K YW++   +P   +  + +WL++       Y + 
Sbjct: 63  GLVVFAKTSKALTRLNKMFRDGEVHKTYWAITKNLPPQSEGTLTDWLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +  AI  +++I   +  +C LE+   TGR HQ+R    HMGCPI GD KY A 
Sbjct: 122 -DHEVPHSKKAILKYRLIG-QSDHYCLLEVNLMTGRHHQIRCQLAHMGCPIKGDLKYGAQ 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH-MVKTWD 320
                 S     + L A +++  HP   + + + +PLP   + + W+
Sbjct: 180 RSNPDGS-----ICLLAHHVEFVHPVSKQLISLDSPLPEDKLWQVWE 221


>gi|297172088|gb|ADI23070.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0770_07M15]
          Length = 277

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 96/246 (39%), Gaps = 19/246 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  + V NKPAG+      G                 Q   L +RLD+ETSG++ V
Sbjct: 35  ILHEDDDLLVINKPAGLVCHPTKGDERSSLAGRLRLYRGAEQSAHLINRLDRETSGVVCV 94

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  AA+ L   +  R + K YW++V G     +  I   L          V V     
Sbjct: 95  GKTDEAARELRRLWESREVDKYYWAIVHGHVPESEGTIDAPLGSDD---ASEVVVKDCVR 151

Query: 221 KGANYAISHFKV---IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF- 276
              + + + +      +   +KF WL + P TGR HQ+R+H  H+G  IVGD  Y  +  
Sbjct: 152 DDGHPSQTRYWTQWKFERDDEKFTWLRVAPVTGRKHQIRIHLQHLGHAIVGDKLYGLDES 211

Query: 277 -----------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                        ++   +  K  LHA  +   H      +  A      V   +++   
Sbjct: 212 WYLKFVKDELTDSDWQKLVLKKQALHAHTLRF-HWRARDWEFVAEPADEFVDFIETVSES 270

Query: 326 YDRNLY 331
            +   +
Sbjct: 271 EEEIYF 276


>gi|317046871|ref|YP_004114519.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316948488|gb|ADU67963.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 217

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 70/218 (32%), Positives = 105/218 (48%), Gaps = 17/218 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD  TSG++VV
Sbjct: 14  ILYQDDHIMVVNKPSGLLSVPGR-LDEHKDSVM-TRIQRDYPQAESVHRLDMATSGVIVV 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A T+AA + L   FR R   K Y + VWG P  ++  I   L+       D+ +  KQ  
Sbjct: 72  ALTKAAERELKRQFREREPAKQYVARVWGHPAEEQGLIDLPLI------CDWPNRPKQKV 125

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A + ++V+   A     + ++P TGR+HQLRVH L +G PI+GD  Y +    
Sbjct: 126 CFDSGKPAQTEYQVLAYDADNSARVLLKPITGRSHQLRVHLLALGHPILGDRFYASPE-- 183

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                +  +L LHA  + + HP  G R+      PA  
Sbjct: 184 --ALAMAPRLLLHAESLTITHPAFGNRMTFRQ--PADF 217


>gi|113969719|ref|YP_733512.1| pseudouridylate synthase [Shewanella sp. MR-4]
 gi|113884403|gb|ABI38455.1| Pseudouridylate synthase [Shewanella sp. MR-4]
          Length = 223

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 63/211 (29%), Positives = 97/211 (45%), Gaps = 9/211 (4%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP+G+    G   A H      + +        L HRLD  TSGI+V AR
Sbjct: 18  YQDRDLIIINKPSGLLSNPGR--AAHTFDCALTRLQRLYPDTILVHRLDCATSGIMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            + A   L   F+ R+ +K+Y + V G+       I   +         Y         G
Sbjct: 76  NKKAESQLKTQFQDRQNEKVYVAEVMGVIAKDAGIIDLAIAPDPEHP-PYQKTQMPGTAG 134

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
           A  A +H++V++   +    +E+ P TGRTHQLRVH L +G PI+GD  Y  +       
Sbjct: 135 AKSAQTHYRVLERR-ENSTLVELTPQTGRTHQLRVHMLALGHPILGDEFYGDDE----VI 189

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             + +L LHA+ +   HP  G+ +   +  P
Sbjct: 190 KARPRLCLHAQSLRFTHPYSGKAMHFYSKHP 220


>gi|15595160|ref|NP_212949.1| hypothetical protein BB0815 [Borrelia burgdorferi B31]
 gi|2688762|gb|AAC67167.1| conserved hypothetical protein [Borrelia burgdorferi B31]
          Length = 297

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 76/317 (23%), Positives = 142/317 (44%), Gaps = 22/317 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L  Y+ ++ V  ++   RLD        + +  ++ K +R G +R++  +  F+ R+ 
Sbjct: 1   MRLDKYI-FLEVLANDNGKRLDSILIKIL-NFSKASIIKHIRKGDIRLNGLKSHFSCRVC 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   + A N  +   K   S+++      +++  ++YEDS + V +K  GI V 
Sbjct: 59  KGDKIYLYKSL-AQNLNLTTDKCFKSNIDF----QYIRKRIIYEDSDLLVLDKQKGILVH 113

Query: 121 GGSG-IAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           GG   + + ++ +L S  + S   KP   HRLD+ TSGI++ A+    A+ L+E+F    
Sbjct: 114 GGKNSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTARKLSEAFSGGS 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y++++ G  K+      N L +   +   +V      +K    AI+    I    +
Sbjct: 174 IIKKYFAILLGEVKSP-VVYKNHLFRNKRLRKTFV----LEDKNFVNAITKVNPILSC-K 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +   +E+   TG THQ+R        P++ D KYC  FK +         +LHA  +   
Sbjct: 228 RATLVEIVIETGFTHQIRSQCSFNNHPLINDKKYCNKFKKSD-------YFLHAFLVKFN 280

Query: 299 HPEGGRLQITAPLPAHM 315
                + +  +      
Sbjct: 281 GTFFKKNEFCSKPSLDF 297


>gi|15603701|ref|NP_246775.1| hypothetical protein PM1836 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|34395822|sp|Q9CK02|RLUA_PASMU RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|12722261|gb|AAK03920.1| RsuA [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 219

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 59/219 (26%), Positives = 97/219 (44%), Gaps = 11/219 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   +++ D    V NKP+G+    G+   Y+      S V  K       HRLD 
Sbjct: 8   PPTDPYLDIVHYDDHFVVINKPSGLLSVPGNQPQYYDSAM--SRVKEKYGFCEPAHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+++ A ++ A + L   FR R  +K Y +LVWG  +  +  +   L+       + 
Sbjct: 66  STSGLILFALSKVADRELKRQFREREPKKHYQALVWGHLEEDQGEVNLPLICD----WEN 121

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               K   +    A++ ++V+  +      +++ P TGR+HQLR+H L +G PI+GD  Y
Sbjct: 122 RPRQKICFERGKPALTLYEVLARYPNNTTRVKLTPITGRSHQLRLHMLALGHPILGDKFY 181

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
                      +  +L LHA  +   HP     L  +AP
Sbjct: 182 APPQAKA----LSPRLCLHAEQLAFRHPITQEWLSFSAP 216


>gi|89095308|ref|ZP_01168227.1| putative pseudouridine synthase Rlu family protein [Oceanospirillum
           sp. MED92]
 gi|89080427|gb|EAR59680.1| putative pseudouridine synthase Rlu family protein [Oceanospirillum
           sp. MED92]
          Length = 250

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 59/244 (24%), Positives = 105/244 (43%), Gaps = 22/244 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +  +L+ED  +   NKP+G+ V           ++   LK +   +G  P   HRLD+ T
Sbjct: 3   ELDILFEDDHLIAINKPSGLLVHPSWVAPRGTPNLASMLKVYF--EGGSPYTIHRLDRPT 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++  +++  AQ +   F  R + K Y  +  G              +   I   + +
Sbjct: 61  SGVILFGKSKEVAQKMNLIFAERDVSKTYLCMCRGYTPEADTIDYALKEQLDKIADKHAN 120

Query: 215 VVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                +K A  A+SH++ +               ++  +E++P TGR HQ+R H  H+  
Sbjct: 121 Q----DKEAQEAVSHYRRLGTVELDIPIGRYDKSRYSLVEVKPETGRKHQIRRHMKHIFH 176

Query: 265 PIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           PI GD K+  N        +    +L L A  +   HP     + ITAP+ ++  + +  
Sbjct: 177 PIAGDTKHGDNKHNKMLKQNFDLQRLMLMATNIQFTHPITQEFMDITAPVDSYCDELFAG 236

Query: 322 LGFK 325
            G+K
Sbjct: 237 FGWK 240


>gi|119476781|ref|ZP_01617091.1| tRNA pseudouridine synthase C [marine gamma proteobacterium
           HTCC2143]
 gi|119450037|gb|EAW31273.1| tRNA pseudouridine synthase C [marine gamma proteobacterium
           HTCC2143]
          Length = 243

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 109/245 (44%), Gaps = 19/245 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              ++Y D  +   NKP+G+ V   +   +     L+   D  GQ     HRLD+ TSG+
Sbjct: 4   PLSIIYRDDYLVAINKPSGLLVHRSNIDRHETQFALQLLRDQLGQHVYPVHRLDKPTSGL 63

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK-SHIGGDYVHVV 216
           L+ A +   A+ ++  F  + I+K Y +LV G    ++  I + L ++   + G      
Sbjct: 64  LLFALSSDVAKTVSLEFSNQTIKKKYLALVRG-WCAEQGTIDHALKEQFDKMSGKPKKQA 122

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            Q    A  A++HF  +             + ++  +E +P TGR HQ+R H  H+  PI
Sbjct: 123 IQ----AKDAVTHFTRLAKVELPFAVDRYPSSRYSLVEARPVTGRKHQIRRHFKHISHPI 178

Query: 267 VGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD K+  +    F  +    ++L L    M L HP  G  + + A L        D LG
Sbjct: 179 IGDAKHGKSSHNGFFQSQFNCHRLMLACTEMTLTHPTTGDMMTLRASLDNTFSDVIDKLG 238

Query: 324 FKYDR 328
           +K  +
Sbjct: 239 WKLPQ 243


>gi|115376841|ref|ZP_01464064.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|115366144|gb|EAU65156.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
          Length = 240

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 72/239 (30%), Positives = 114/239 (47%), Gaps = 13/239 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG----QKPRL 146
           T   +     +L++D  + + +KP G+ V+ G G A  +   L +           +P +
Sbjct: 5   TAAVEGPGLPVLHDDPDMVIVDKPVGLVVEPGGG-APSVVELLAAQRPPFDVEGVARPGV 63

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ETSG L+ ART AAA  L ++F+ +R+ K YW+LV G    + E +     +  
Sbjct: 64  VHRLDRETSGCLMFARTDAAAAALDQAFQQKRVDKRYWTLVLGE-TPEHERLEGPYGRDP 122

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                +   V    K A  A   F+V +   +    LE++  TGRTHQ+RV     G P+
Sbjct: 123 QDPRKFTTRV----KSARRAALSFEVRERL-RGATLLEVRLETGRTHQIRVQLSEAGFPV 177

Query: 267 VGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
           +GD  Y     + +  +    +  LHA  + +PHP  G L ++ APLP    K   +L 
Sbjct: 178 LGDSVYGPSEARAHPVAQALGRQALHALRLAVPHPSTGALVRVEAPLPEDFQKALAALR 236


>gi|307154171|ref|YP_003889555.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7822]
 gi|306984399|gb|ADN16280.1| pseudouridine synthase, RluA family [Cyanothece sp. PCC 7822]
          Length = 302

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 123/319 (38%), Gaps = 37/319 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           ++    V   E  + L  ++   Y H       + ++SGQ+ +D         +Q GQ +
Sbjct: 5   WIYEEQVSKTEAGLTLIEYYTQKYSHSGPSEWLERIQSGQILIDGCSQDPQTLLQPGQKL 64

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                                     +    L   + YED ++ V  KP+ + V  G G 
Sbjct: 65  TYH------------------RPPWEEPEVPLSFEVFYEDDEVLVVAKPSLLPVLPGGGF 106

Query: 126 AYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             H    L S +  +  +  P   HRL + TSG++++AR+  A  +LTE  R  ++ KIY
Sbjct: 107 LEH---TLLSLLQQQYPQRTPIPVHRLGRGTSGLVLLARSPHARANLTEQMRSHQVGKIY 163

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV          I + + K  H    YV     +      A S   V+         +
Sbjct: 164 RALVGSGNIPDHFVITHPIGKIPHPVLGYVFGATAD---GMKAYSECHVLKRNP-TTTLV 219

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFK-------GNFTSPIQNKLYLHARY 294
           E++  TGR HQ+R+H    G P++GD  Y      +            P     +LHA  
Sbjct: 220 EVKILTGRPHQIRIHLAVAGYPLIGDPLYQIGGVPRIPEPIAGEKLPVPGDGGYHLHAYG 279

Query: 295 MDLPHPEGGR-LQITAPLP 312
           +   HP  G+ +++  P P
Sbjct: 280 LSFFHPVTGKLIELICPPP 298


>gi|262165137|ref|ZP_06032874.1| tRNA pseudouridine synthase C [Vibrio mimicus VM223]
 gi|262024853|gb|EEY43521.1| tRNA pseudouridine synthase C [Vibrio mimicus VM223]
          Length = 244

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 98/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  ++          +   I   +       +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEDADVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAITAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L     +      ++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLMLHASELRFVHPYTQQPLAIRAGLDEVWQRLLGEFDWQEP 239


>gi|218262785|ref|ZP_03477143.1| hypothetical protein PRABACTJOHN_02822 [Parabacteroides johnsonii
           DSM 18315]
 gi|218223136|gb|EEC95786.1| hypothetical protein PRABACTJOHN_02822 [Parabacteroides johnsonii
           DSM 18315]
          Length = 223

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 72/228 (31%), Positives = 111/228 (48%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I   NK     VQG       +   LK+W+  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIAVNKTCREIVQGDKTGDTPLSDMLKAWLKEKYCKPGNVFVGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR+  ++K YW++V   P +++  + NWL++       Y + 
Sbjct: 63  GVVLFAKTSKALARLNEMFRVGEVKKTYWAIVKNCPPSEEGELVNWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  AI  +KVI   ++ +  L +   TGR HQ+R     MGCPI GD KY   
Sbjct: 123 TER--PNAKKAILRYKVIAR-SENYYLLAVDLKTGRHHQIRCQLAKMGCPIKGDLKYGFP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     + LH+R  +  HP   + + I AP+P      W +L
Sbjct: 180 -----RSNPDGGISLHSRSAEFIHPVSKQPVSIVAPVPVD--SLWKAL 220


>gi|28379165|ref|NP_786057.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|308181361|ref|YP_003925489.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28272003|emb|CAD64908.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|308046852|gb|ADN99395.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 300

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 69/317 (21%), Positives = 127/317 (40%), Gaps = 27/317 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRS-GQVRVDKKRVKFNNRIQSG 62
           MT+   + + +      +    +     I    +Q  LR   +++++         + +G
Sbjct: 1   MTWTYQLTIPSSLNQQSIRACLRTWL--IPK-RIQGQLRQTRRIQLNGAPTSIAQLVNTG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +  + +             +  +    +    + +LY++S + V +KPAG+     
Sbjct: 58  DRLTLTFIPSDFR----------TPTSNYIAAATAPATILYQNSDLLVVDKPAGVKSHPN 107

Query: 123 -SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             G    I   L + +    Q P + HRLDQ TSG ++VA        L      ++I++
Sbjct: 108 QPGETGSILNDLAATLQPTQQVPYMVHRLDQMTSGAMLVALNPVVVPILDRLISDKQIRR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++ V G            +   +            N   A  A++ ++V    A +  
Sbjct: 168 TYYAWVRGHFATPTGHFTAPIGHDATDKRKR----WVNTADAQPALTDYEVCATTAHQ-S 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            +++  HTGRTHQLRVH      PI+GD  Y +  +         +L LHA+ +DL  P 
Sbjct: 223 LVKLTLHTGRTHQLRVHLAASDHPIIGDPLYDSQAESA------PRLMLHAQLLDLQLPF 276

Query: 301 EGGRLQITAPLPAHMVK 317
              R+ + APLP+   K
Sbjct: 277 STTRVTVPAPLPSLFEK 293


>gi|254578372|ref|XP_002495172.1| ZYRO0B05082p [Zygosaccharomyces rouxii]
 gi|238938062|emb|CAR26239.1| ZYRO0B05082p [Zygosaccharomyces rouxii]
          Length = 611

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 101/236 (42%), Gaps = 22/236 (9%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +K +  G V ++ +     + I++G  +R             E  +    +         
Sbjct: 143 RKTIAGGSVYLNDEPANLESIIRNGDCIRHKIHR-------HEPPVTSRPIK-------- 187

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              ++YED  + V +KP+GI V       Y  +   K      G+     +RLD+ TSG+
Sbjct: 188 ---VVYEDENLLVIDKPSGIPVHPTG--RYRFNTITKILEKKLGRTVHPCNRLDRLTSGL 242

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           + +A+T   A  + +  + R + K Y + V G     +  + N L K          V  
Sbjct: 243 MFMAKTPKGADEMADQLKAREVTKEYVARVVGEFPVGEVVVDNPL-KSLEPKLGLNVVCG 301

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +E+GA +A + F+ +    +    ++ +P TGRTHQ+RVH  ++G PI  D  Y 
Sbjct: 302 MDEEGAKHAKTVFRRVSYDGE-TSIVKCKPLTGRTHQIRVHLQYLGHPIANDPIYS 356


>gi|126327383|ref|XP_001372198.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4, [Monodelphis domestica]
          Length = 364

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 148/328 (45%), Gaps = 46/328 (14%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           Q++     +R +K+  K   +      V   PV   ++ +I+  K L  +V+    S  L
Sbjct: 44  QRLAEK--LRTEKQEQKAKEK-----EVPRDPVQRRVHELIRYTKQLQ-NVHPNVLSKAL 95

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQE 153
           K  +L++D  + V NKP G+ V GG G+   I   L    K     K +   L HRLD+E
Sbjct: 96  KRGILHQDKDLIVINKPYGLPVHGGPGVKSCITDILPILAKMLFGHKAEPLHLCHRLDKE 155

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G++++AR +  A  + E F+ R++ K YW++  G+P      I   +++K   G    
Sbjct: 156 TTGVMILARDKEMAHQVQELFKTRQVTKKYWAICVGVPMPSAGMIDIPIIEKEVQGQQQH 215

Query: 214 H---------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           H               V  +  + A+ A++ ++V+         LE+QP TG  HQLRVH
Sbjct: 216 HKMTLAPNYRLENGKTVKVRPNRHAHIAVTQYRVLSS-TLTCALLELQPVTGVKHQLRVH 274

Query: 259 ALH-MGCPIVGDHKYC------------ANFKGNFTSPIQNK---LYLHARYMDLPH--P 300
               +GCP++GDHKY                K       + +   L+LHA+ + LP   P
Sbjct: 275 LAFGLGCPVLGDHKYSDWNKLAPQKLSVGILKKLGLEQAKTRYLPLHLHAQQLTLPPLGP 334

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           E   L +   LP + + +   LG +   
Sbjct: 335 ESEELNLVCKLPRYFLHSLLRLGLEIPE 362


>gi|116750307|ref|YP_846994.1| RluA family pseudouridine synthase [Syntrophobacter fumaroxidans
           MPOB]
 gi|116699371|gb|ABK18559.1| pseudouridine synthase, RluA family [Syntrophobacter fumaroxidans
           MPOB]
          Length = 300

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 68/311 (21%), Positives = 117/311 (37%), Gaps = 33/311 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPP 69
           ++     + +  +    Y H +       L +G+V +D +R + +  ++ GQ +  R PP
Sbjct: 13  IDARGAGLTVREYLAAAYRHSSEAEWMARLENGEVCLDGRRARGSVVLKPGQWLAWRRPP 72

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                                 +    L   +L+ D  +    KP G+      G     
Sbjct: 73  W--------------------EEPDVPLAYAVLHADEDLLAVAKPRGLPTVPAGGFL--- 109

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           D  L + V     +    HRL + TSGI+++ART  A   L  + R   + + Y +L  G
Sbjct: 110 DNTLLALVRRACPEATPVHRLGRGTSGIVLLARTARARSVLAAALRRNEVTRTYRALAGG 169

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +P      + + +    H     VH           A+S  +V++        + ++  T
Sbjct: 170 VPGRDAFTVGSPIGPVPHPLLGSVHAAN---PSGRPALSLVEVLERRT-GCSVVGVRIKT 225

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN---FKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GR HQ+R+H    G P+VGD  Y       +G    P      LHA  + L HP  G   
Sbjct: 226 GRPHQIRIHLACAGHPLVGDPLYAPGGMIVEGGCALPGDPGYLLHAESLRLLHPATGEPF 285

Query: 306 QITAPLPAHMV 316
           ++    P  + 
Sbjct: 286 ELWCRPPPELR 296


>gi|227326531|ref|ZP_03830555.1| tRNA pseudouridine synthase C [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 262

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 106/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHLVAVNKPSGWLVHRSWLDRKEKVVVMQTVRDQIGQHVYTVHRLDRPTSGVLLL 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++QK Y ++V G   +          +   I   + +     +
Sbjct: 64  ALSSEVARALSQQFESHQMQKTYHAVVRGYVLDDGVIDYALTEELDKIADKFTN----PD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHYRSLAQAEMPVAIGRYPTARYSLMELKPQTGRKHQLRRHMTHIHHPIIGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +    + +G  +     +L LHA  + L HP  G+ L + A   A         G+K
Sbjct: 180 AHGDLRHNRGMESYFSCGRLMLHASELQLNHPVSGQPLTLQARWDAPWQGVMTQFGWK 237


>gi|313891370|ref|ZP_07824986.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
 gi|313120145|gb|EFR43321.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
          Length = 303

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 61/295 (20%), Positives = 125/295 (42%), Gaps = 27/295 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNH--YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           ++   + +D+   RLD + K     PH   + ++ + +  +++V+ K+   N ++++G +
Sbjct: 1   MREYKITSDKNGKRLDNYIKEKEKIPHF--IFIKSL-KKNKIKVNGKKESGNYKLKTGDI 57

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V         ++I  + K     ++ +         + YED  I +  K AGI     + 
Sbjct: 58  VT--------SYIENKNKNEKEKIHFS---------INYEDENIIIAEKEAGILCNDTTN 100

Query: 125 IAY--HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  D   +        +    HR+D  T+G+++ A+   A   L  + + R I+K 
Sbjct: 101 KEEKTLHDEINEYLKGKNEPEAYPVHRIDLNTTGLVIFAKNMHARAILDRAIKERNIKKY 160

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y  +  G  K K   + + L K +    + V++ ++  KG+  A  ++K +         
Sbjct: 161 YLCVTTGTMKKKSGKLEHQLFKDAK--NNKVYIYEKPCKGSKTATMNYKCLKT-ENGLSL 217

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +E +  TGRTHQ+R    ++G PI+GD KY            +  L  +   ++ 
Sbjct: 218 VECELITGRTHQIRSQLSYIGYPILGDDKYGNKTINKTYKERKQLLCAYKIKINF 272


>gi|299537608|ref|ZP_07050901.1| putative RNA pseudouridine synthase yhcT [Lysinibacillus fusiformis
           ZC1]
 gi|298726977|gb|EFI67559.1| putative RNA pseudouridine synthase yhcT [Lysinibacillus fusiformis
           ZC1]
          Length = 279

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 57/254 (22%), Positives = 107/254 (42%), Gaps = 29/254 (11%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKI 108
           + + +++N  +Q+G V++    +   ++               K +      ++YED   
Sbjct: 41  NDELIQWNTPLQTGTVIKFTFPVPTSSY---------------KPTPVCAIDVVYEDDHC 85

Query: 109 YVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
            + +KP G++         H  ++  +    +  G      HRLD+ T G+L+VA+   A
Sbjct: 86  LIVSKPKGMATHPNDARDTHTCMNHIMAHIKEQGGIYAEHVHRLDKGTQGLLLVAKHPLA 145

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
                     + I + Y + V G  +     IA  + K  H     V       K   +A
Sbjct: 146 KSIFDRMIEEKTIIRTYAAEVQGNLRTSSGTIAEPIGKDRHHATRRVV-----SKTGQHA 200

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++H++V+  + +  C + +   TGRTHQ+RVH  ++G PI+GD  Y A    +    +  
Sbjct: 201 VTHYEVVARY-KNSCVVHLILETGRTHQIRVHLAYIGHPIIGDTMYGARETVSDDYEL-- 257

Query: 287 KLYLHARYMDLPHP 300
               HA  ++  HP
Sbjct: 258 ----HAIQLEFDHP 267


>gi|218249746|ref|YP_002375313.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           ZS7]
 gi|218164934|gb|ACK74995.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           ZS7]
          Length = 315

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 140/319 (43%), Gaps = 22/319 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L  Y+ ++ V  ++   RLD        + +  ++ K +R G +R++  +  F+ R+ 
Sbjct: 1   MRLDKYI-FLEVLANDNGKRLDSILIKIL-NFSKASIIKHIRKGDIRLNGLKSHFSCRVC 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   ++   ++      +D          +++  ++YEDS + V +K  GI V 
Sbjct: 59  KGDKIYLYKSLSQNLNL-----TMDECFKSNIDFQYIRKRIIYEDSDLLVLDKQKGILVH 113

Query: 121 GGSG-IAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           GG   + + ++ +L S  + S   KP   HRLD+ TSGI++ A+    A+ L+ +F    
Sbjct: 114 GGKNSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTARKLSAAFSGGS 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y++++ G  K+      N L +   +   +V      +K    AI+    I    +
Sbjct: 174 IIKKYFAILLGEVKSP-VVYKNHLFRNKRLRKTFV----LEDKNFVNAITKVNPILSC-K 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +   +E+   TG THQ+R        P++ D KYC  FK +         +LHA  +   
Sbjct: 228 RATLVEIVIETGFTHQIRSQCSFNNHPLINDKKYCNKFKKSD-------YFLHAFLVKFN 280

Query: 299 HPEGGRLQITAPLPAHMVK 317
                + +  +      +K
Sbjct: 281 GTFFKKNEFCSKPSLEFLK 299


>gi|239620840|ref|ZP_04663871.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|322689550|ref|YP_004209284.1| hypothetical protein BLIF_1367 [Bifidobacterium longum subsp.
           infantis 157F]
 gi|322691511|ref|YP_004221081.1| hypothetical protein BLLJ_1322 [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|239516416|gb|EEQ56283.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|320456367|dbj|BAJ66989.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|320460886|dbj|BAJ71506.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           infantis 157F]
          Length = 309

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 61/285 (21%), Positives = 111/285 (38%), Gaps = 17/285 (5%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             R D         I+      ++ SGQ RV  + V  ++ +Q+G+ V        L   
Sbjct: 2   GKRFDVAVAKML-GISRSKAADLVDSGQARVLGREVARSSTLQAGETVEFD-----LAEE 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E + + + + +    D +  +        +      G +V G        D  +    
Sbjct: 56  QAEPEPIATDMAVVYEDDDVVVVDKPVGVAAHASVGWTGPTVLGS-----LRDRGVHITS 110

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +  +  RLD  TSG+++V ++  A   +   F    ++K Y +LV G  K  K  
Sbjct: 111 YGAAGREGIVSRLDVGTSGLMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQGGLKENKAT 170

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +                     A++H+ V++ F  +   + +   TGRTHQ+RV
Sbjct: 171 IEAPIGR-----AKVSDFRFCVTPAGKPAVTHWDVLERFGHEATLVSVNLETGRTHQIRV 225

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           H   +G P+ GD  Y AN   +    + ++ +LHA  ++  HP  
Sbjct: 226 HFSSIGHPLCGDPMYGANPVLSEALGL-DRQWLHAMKLEFRHPRT 269


>gi|327480038|gb|AEA83348.1| pseudouridine synthase RluA [Pseudomonas stutzeri DSM 4166]
          Length = 211

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 62/213 (29%), Positives = 104/213 (48%), Gaps = 11/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D+ + V NKP  +    G     + D  +    ++   + R+ HRLD ETSG++V+
Sbjct: 8   IIHQDAALLVINKPTLLLSVPGRA-EDNRDCLVTRLQENGYPEARIVHRLDWETSGLIVL 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR     + L+  F  R  +K Y +L WG P+     I   L         +V     + 
Sbjct: 67  ARDADTHRELSRQFHDRETEKAYTALCWGQPEQDSGSIDLPLRYDPPTKPRHV----VDH 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +   +A++ ++V++     +  +E+ P TGR+HQLRVH L +G P++GD  Y      + 
Sbjct: 123 ELGKHALTFWRVLERCGD-YSRVELTPITGRSHQLRVHMLSIGHPLLGDRLYAHEQALHA 181

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                 +L LHA  + L HP  G RL+   P P
Sbjct: 182 ----HERLCLHASMLTLTHPQTGERLRFECPAP 210


>gi|203288242|ref|YP_002223257.1| RNA pseudouridylate synthase family protein [Borrelia recurrentis
           A1]
 gi|201085462|gb|ACH95036.1| RNA pseudouridylate synthase family protein [Borrelia recurrentis
           A1]
          Length = 324

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 74/328 (22%), Positives = 145/328 (44%), Gaps = 23/328 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V N+++  RLD         +    + K +R+G +R++  +V F+ R+     + +  
Sbjct: 15  INVLNNDDGKRLDVVLIKFLK-LPKSKVIKHIRNGDIRLNSLKVSFSQRVLKDDKIYLYK 73

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +    ++     ++ +  ++ +    ++S L+YED  + V NK  G+ V    G  Y +
Sbjct: 74  PLVQGLNL--NGVVIKNKTDILR---DVESRLVYEDKDLLVINKRKGVLVH---GDGYSL 125

Query: 130 DGFLKSWV-----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           D  + +++      S   KP   HRLD+ TSG++V A+   +A+ L+++F    + K Y 
Sbjct: 126 DVLVNAYLLDENLASLSFKPSAVHRLDRNTSGLIVFAKNIYSARILSKAFSSGIVTKRYL 185

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +L+ G  + K     N+L +   +   +V     +      AI+  K +   ++     E
Sbjct: 186 ALLDGEIR-KSLTYKNFLYRDKIVKKTFVMDNLNSNINKFNAITIVKPL-LVSKFATLAE 243

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +   TG THQ+R         ++ D KY   FK       +N  +LH+  ++  H    R
Sbjct: 244 VSIKTGFTHQIRAQCAFNNHALIDDKKYNPKFK-------KNNYFLHSFLINFNHSFFLR 296

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNLYI 332
            +      +  VK  +S+   YD   +I
Sbjct: 297 NEFFVEPSSDFVKRINSIFGVYDFKEFI 324


>gi|114046333|ref|YP_736883.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           MR-7]
 gi|113887775|gb|ABI41826.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           MR-7]
          Length = 225

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 64/215 (29%), Positives = 107/215 (49%), Gaps = 12/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D  I V NKP+G+    G   A++    + + V ++    ++ HRLD  TSG++
Sbjct: 14  LDVLYQDKDIIVVNKPSGLLSVPGRDPAHYDS--VYARVKAEHPHCQIVHRLDMATSGVM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  R+A + L   F  R   K Y + V G  KN    +   L+             K 
Sbjct: 72  VVALIRSAERELKRQFHDRETSKTYLARVAGHIKNDTGSVDYPLICDWPNRPK----QKV 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    +++HF+V+   A++   ++++P TGR+HQLRVH + +G PI+GD  Y      
Sbjct: 128 DHEIGKPSLTHFEVLSR-AKRSTLVKLKPITGRSHQLRVHMMALGHPILGDGFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +    +  +L LHA  + + HP  G  +  +A  P
Sbjct: 187 S----LAPRLLLHAAELTIKHPYTGESMTFSADAP 217


>gi|160916027|ref|ZP_02078235.1| hypothetical protein EUBDOL_02055 [Eubacterium dolichum DSM 3991]
 gi|158432503|gb|EDP10792.1| hypothetical protein EUBDOL_02055 [Eubacterium dolichum DSM 3991]
          Length = 317

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 70/303 (23%), Positives = 121/303 (39%), Gaps = 31/303 (10%)

Query: 36  NLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
            +QK L  GQ ++V+++ +  N  +Q   ++RI P                  +      
Sbjct: 41  KMQKQLYQGQRIQVNQQTILHNTPLQRKDLIRIQPFPQY-------------DLEKHLIP 87

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSW--VDSKGQKPRLTHRLD 151
            F    +LYED    +  KP+ + V   G+     +   +K +  +       R  HRLD
Sbjct: 88  CFDPLSILYEDDLFLIVYKPSFMLVHSDGNETETTLYDIVKGYYLLQGLDIPVRAIHRLD 147

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG ++  +       L    + ++I + Y +L   +  N    I   + +  H    
Sbjct: 148 KETSGAVIFCKIPLLQPLLDYMLQEKQIDRQYLALCAKVL-NDDLTIDKQIGRDRHNAKK 206

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                    K    A +   VI  + Q +  +  + + GRTHQ+RVH   +  P++ D  
Sbjct: 207 MRI-----SKQGKSAKTDVHVIAQY-QDYTLIACKLYQGRTHQIRVHLASITHPLLHDTL 260

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNL 330
           Y    K        N+  LHA  + L HP   + + I  PLP  M K  + +    DR++
Sbjct: 261 YGNYDKR------INRCALHAYRIQLCHPFTQQNITIECPLPTDMKKLVEPINLCNDRSI 314

Query: 331 YIK 333
           + K
Sbjct: 315 FKK 317


>gi|71280071|ref|YP_267294.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
 gi|71145811|gb|AAZ26284.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
          Length = 567

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 108/239 (45%), Gaps = 19/239 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +  L H+++  ++ D +  L   ++ +   ++++D  + V NKPAG+    G  I   +
Sbjct: 336 CLPILGHMLEGMEV-DKNPLLINPAEGIDLEIVFQDEHVVVVNKPAGLLSVPGKSIKDSV 394

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K+          + HRLD  TSG+L++A    A +HL + F  + I K Y + + G
Sbjct: 395 YTRIKTQFPQASGGL-IVHRLDMATSGLLMLALNERAHKHLQQQFMNKEINKRYVATIEG 453

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +     I   L +          V  ++     YA +H+++I+          + P T
Sbjct: 454 KLEKTSGEICLPL-RGDFDDRPKQMVCHEH---GKYAETHWQLIEEVDNTSKLF-LYPIT 508

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           GRTHQLR+H  H   +  PI+GD  Y  +          ++L+LHA+ +   HP    L
Sbjct: 509 GRTHQLRMHCAHPDGLNLPIIGDSLYGHS---------ADRLHLHAQRLSFTHPITKEL 558


>gi|154494935|ref|ZP_02033940.1| hypothetical protein PARMER_03979 [Parabacteroides merdae ATCC
           43184]
 gi|154085485|gb|EDN84530.1| hypothetical protein PARMER_03979 [Parabacteroides merdae ATCC
           43184]
          Length = 225

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 72/228 (31%), Positives = 111/228 (48%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I   NK     VQG       +   LK+W+  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIAVNKTCREIVQGDKTGDTPLSDMLKAWLKEKYCKPGNVFVGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR+  ++K YW++V   P  ++  + NWL++       Y + 
Sbjct: 63  GVVLFAKTSKALARLNEMFRVGEVKKTYWAIVKNCPPAEEGELVNWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  A+ H+KVI   +  +  L +   TGR HQ+R     MGCPI GD KY   
Sbjct: 123 TERT--NAKKAVLHYKVIAR-SDNYYLLAIDLKTGRHHQIRCQLAKMGCPIKGDLKYGFP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     + LH+R  +  HP   + + I AP+PA     W ++
Sbjct: 180 -----RSNPDGGISLHSRSAEFIHPVSKQPVSIVAPVPAD--SLWKAM 220


>gi|37680745|ref|NP_935354.1| tRNA pseudouridine synthase C [Vibrio vulnificus YJ016]
 gi|320155588|ref|YP_004187967.1| tRNA pseudouridine synthase C/tRNA Psi65 [Vibrio vulnificus
           MO6-24/O]
 gi|37199494|dbj|BAC95325.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
 gi|319930900|gb|ADV85764.1| tRNA pseudouridine synthase C tRNA Psi65 [Vibrio vulnificus
           MO6-24/O]
          Length = 245

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 97/237 (40%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F  + + K Y ++V G  + + E      ++   I   +       E
Sbjct: 64  ALSSEVASQVMPMFAGQEMSKTYHAIVRGWIEEEGELDYALKVELDKIADKFASQ----E 119

Query: 221 KGANYAISHFKVIDCFAQKFC----------WLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ +K +      +            +E++P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQDAITLYKPLAKVEVPYSTGKFPTTRYGLMELKPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
            +                +L LHA  +   HP     + I A +     + ++   +
Sbjct: 180 THGDGKHNKLFREEFEAPRLLLHASELRFVHPYTQQEVVIRAEVDKVWQQLFERFEW 236


>gi|332880233|ref|ZP_08447912.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
 gi|332681822|gb|EGJ54740.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
          Length = 224

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 67/220 (30%), Positives = 110/220 (50%), Gaps = 14/220 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
            ++YED+ + + NK +   VQG       +   +K ++  K  KP      + HRLD+  
Sbjct: 2   DVVYEDNHLIIVNKSSSEIVQGDKTGDKPLAEMVKEYIKQKYHKPGNVFLGVVHRLDRPV 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V ART  A   L E FR + + K YW++V   P  ++  + +WL++       Y +
Sbjct: 62  SGLVVFARTSKALARLNEMFRTKEVHKTYWAIVGNCPPTEEGELVHWLVRNEKQNKSYAY 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             +++E  A  AI  +++I   ++++  LE+   TGR HQ+R     MGCPI GD KY +
Sbjct: 122 DKEKSE--AKKAILDYRLIGR-SERYFLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGS 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPA 313
                  S     + LHAR +   HP     + + AP+P 
Sbjct: 179 PRSNPDGS-----ICLHARRVRFVHPVSKQEIDVEAPVPE 213


>gi|313886583|ref|ZP_07820296.1| pseudouridine synthase, RluA family [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|332300873|ref|YP_004442794.1| pseudouridine synthase [Porphyromonas asaccharolytica DSM 20707]
 gi|312923939|gb|EFR34735.1| pseudouridine synthase, RluA family [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|332177936|gb|AEE13626.1| pseudouridine synthase [Porphyromonas asaccharolytica DSM 20707]
          Length = 228

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 68/225 (30%), Positives = 104/225 (46%), Gaps = 14/225 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
                +LYED+ + + NKPAG+ VQG S     +   ++ ++  K  KP      +THR+
Sbjct: 1   MPDLQILYEDNHLLIVNKPAGMLVQGDSTGDTPLSELVERYLIDKYDKPGRAFVGVTHRI 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSG ++ A+T  A   L   F+ R I K+Y ++V G    K     + L +      
Sbjct: 61  DRPTSGAVLFAKTSKALARLNAMFQRREIHKVYHAVVCGAFPQKAGEAKDLLYRNRKQNK 120

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            Y  VV +    A  A   ++ +     ++  L +  HTGR HQ+R    HMG PI GD 
Sbjct: 121 SY--VVTEAHAEAKRAWLTYERL-AVGDRYSLLAVTLHTGRHHQIRTQLSHMGFPIKGDL 177

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAH 314
           KY A             + LHAR +   HP    ++++ AP P  
Sbjct: 178 KYGAPRSNK-----DGGISLHARILSFEHPVTHEQIEVVAPYPED 217


>gi|261822605|ref|YP_003260711.1| tRNA pseudouridine synthase C [Pectobacterium wasabiae WPP163]
 gi|261606618|gb|ACX89104.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
          Length = 261

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 107/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHLVAVNKPSGWLVHRSWLDRKEKVVVMQTVRDQIGQHVYTVHRLDRPTSGVLLL 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++QK+Y ++V G   +          +   I   + +     +
Sbjct: 64  ALSSEVARALSQQFESHQMQKMYHAVVRGYVLDDGVIDYALTEELDKIADKFAN----PD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHYRALAQVEMPVAIGRYPTARYSLMELKPQTGRKHQLRRHMSHLHHPIIGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +    + +G  T     +L LHA  + L HP  G+ L + A   A         G++
Sbjct: 180 AHGDLRHNRGMETHFSCGRLMLHASELQLNHPVSGQPLTLQARWDAPWQGVMRQFGWQ 237


>gi|325678153|ref|ZP_08157783.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
 gi|324110158|gb|EGC04344.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
          Length = 276

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 71/301 (23%), Positives = 119/301 (39%), Gaps = 41/301 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+ + V   E  + L    +     ++   L K+   G + +D   V+    + +GQ V+
Sbjct: 6   VRTLTVTEKENGLTLKDMLRGR--GVSRRLLTKLKLCGGITLDGDAVRVTVTVCTGQKVQ 63

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +     +      E                LK  +LYEDS + VF+KPA + V       
Sbjct: 64  LCEPEQSCPDPNPE----------------LKVPVLYEDSDVIVFDKPANMPVHES---I 104

Query: 127 YHIDGFLKSWVDS--KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            H    L +      KG   R  +RLD++T+G + VA+TR AA  L        I K+Y 
Sbjct: 105 NHRGDTLANAFAQRCKGMTFRAVNRLDRDTAGCVCVAKTRFAANALQ-----GSISKVYM 159

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            L+    K     +   + ++         +++       +A + ++V +        ++
Sbjct: 160 GLIPPT-KLSGGRVCAPIARERE-----SVILRCVRADGKFAATCWQVTERR-DDCALVK 212

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
               TGRTHQ+RVH  H+G P++GD  Y  +              L    +    PE GR
Sbjct: 213 FILETGRTHQIRVHMAHIGLPLIGDELYGGDCTKR------KGQALMCGEITFVSPENGR 266

Query: 305 L 305
           L
Sbjct: 267 L 267


>gi|304383656|ref|ZP_07366115.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           marshii DSM 16973]
 gi|304335180|gb|EFM01451.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           marshii DSM 16973]
          Length = 534

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 66/224 (29%), Positives = 108/224 (48%), Gaps = 17/224 (7%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           ++  VN  +         ++ED  + V  KPAG+    G      + G ++S        
Sbjct: 315 IEVEVNPLEEPSKQTLEWVFEDEHLTVVCKPAGMLSVPGRSPKESVVGIVQSQCGGNA-D 373

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD +TSG+LV+A+++AA +HL E FR + ++K Y +++ G     KE      L
Sbjct: 374 VLPVHRLDMQTSGLLVIAKSKAAHKHLQEQFRKQEVKKRYVAVLDGEWNGTKEGRIELPL 433

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +   +      V   + K    A++ +KV++   +    + + P TGRTHQLR+H  H  
Sbjct: 434 RPDPLDRPRQLV---DSKRGKRALTLYKVLET-GRGHTRIALYPKTGRTHQLRIHCAHMA 489

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +G PIVGD  Y  +          ++LYLHA  ++  HP  G+
Sbjct: 490 GLGIPIVGDELYGRH---------SDRLYLHAECIEFQHPATGK 524


>gi|126649461|ref|ZP_01721702.1| ribosomal large subunit pseudouridine synthase [Bacillus sp.
           B14905]
 gi|126593786|gb|EAZ87709.1| ribosomal large subunit pseudouridine synthase [Bacillus sp.
           B14905]
          Length = 279

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 63/298 (21%), Positives = 128/298 (42%), Gaps = 32/298 (10%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINA 73
           +E+++ ++   +NH+  +    + ++  +  + + + + V++N  +Q G +V+    I A
Sbjct: 7   NEDHLTIEELLRNHWR-LGKKLVHELRMAKAITLENDELVQWNTPLQVGTIVKFTFPIPA 65

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDG 131
            ++               K +      ++YED    + +KP G++         H  ++ 
Sbjct: 66  SSY---------------KPTPVCAIDIVYEDDHCLIVSKPKGMATHPNDDRDTHTCMNH 110

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +       G      HRLD+ T G+L+VA+   A          + I + Y + V G  
Sbjct: 111 VIAHIQQQGGMYAEHVHRLDKGTQGLLLVAKHPLAKSIFDRMIEEKSIIRTYAAEVQGNI 170

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           ++    I+  + K  H     V       K   +A++H++V+  + +  C + +   TGR
Sbjct: 171 RSSSGTISESIGKDRHHASRRVV-----SKTGQHAVTHYEVVSRY-KNSCVVHLILETGR 224

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQIT 308
           THQ+RVH  ++G PI+GD  Y A    +    +      HA  ++  HP    R+ + 
Sbjct: 225 THQIRVHLAYIGHPIIGDTMYGARETVSDDYEL------HAIQLEFDHPFLNKRITVK 276


>gi|317049313|ref|YP_004116961.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316950930|gb|ADU70405.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 259

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 65/257 (25%), Positives = 114/257 (44%), Gaps = 18/257 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEWLVAVNKPAGWLVHRSWLDRKEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +    + L + F   +I+K Y +++ G    +   +   L+++     D         
Sbjct: 64  GLSSEVGRLLAQQFEQHQIRKTYHAVLRG-WLMESGTLDYPLVEELDKIADKFAT---EP 119

Query: 221 KGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +G   A++ F+++               ++  +EMQP TGR HQLR H  H+  PI+GD 
Sbjct: 120 RGPQPAVTDFQMLAHTEMPVAIGRYATARYSLVEMQPRTGRKHQLRRHMAHLRHPIIGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +      +G   +   ++L LHA  + L HP  G  L I A L     +     G+++ 
Sbjct: 180 THGDLRQNRGAAANFGLDRLMLHASALSLNHPVTGEPLVIRAGLDTVWQQMLHQFGWQH- 238

Query: 328 RNLYIKRLYSQDECKQN 344
           +   + R+   DE  Q+
Sbjct: 239 QIPDVPRVEFVDEAVQD 255


>gi|260891446|ref|ZP_05902709.1| pseudouridylate synthase [Leptotrichia hofstadii F0254]
 gi|260858829|gb|EEX73329.1| pseudouridylate synthase [Leptotrichia hofstadii F0254]
          Length = 328

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 66/325 (20%), Positives = 138/325 (42%), Gaps = 38/325 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  +   + VVV ++ E MRLDR+ + ++       +   +RSG V+++ K+ K N R+ 
Sbjct: 1   MRKILGKKEVVVHSEMEGMRLDRYLRKNFKDEPLSRIFGAIRSGDVKINGKKSKENYRLL 60

Query: 61  SGQVVRI----PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
               + I          +  I+   KI +  + L K  +  K ++++E+   ++ NK   
Sbjct: 61  LNDKITIRNLSTGNTEKIGEIVNTYKIKELKI-LEKDLEKYKKMVIFENDDFFIVNKKEK 119

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           + +  G+G  Y +    K    S        +RLD ETSG+++  +T    +++++  R 
Sbjct: 120 VPMHKGTGHKYGLAEVFKKIYKSDNIN--FANRLDFETSGLVIGCKTLKFLRYISQKIRD 177

Query: 177 RRIQKIYWSLVW-------GIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAI 227
             + K Y+++V           + +K  + ++ ++      +   +V +N   + +  +I
Sbjct: 178 NEVHKKYFAVVHNKNIIRRNKLEREKFNLEDFKIENYLTTLENKVIVSENPVSRESKKSI 237

Query: 228 SHFKVI---------------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           ++FK +               +   +    L+++  TGR HQ+R    H    IVGD KY
Sbjct: 238 TYFKHVNFNKLKKSKEILKLFEKNNKNILLLDVELITGRKHQIRAQLAHESLFIVGDKKY 297

Query: 273 CANFKGNFTSPIQNKLYLHARYMDL 297
                        ++ +L    +  
Sbjct: 298 G-------IKDGSDRFFLCCYSISF 315


>gi|199598482|ref|ZP_03211900.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|258508901|ref|YP_003171652.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus GG]
 gi|199590666|gb|EDY98754.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|257148828|emb|CAR87801.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus GG]
 gi|259650194|dbj|BAI42356.1| pseudouridylate synthase [Lactobacillus rhamnosus GG]
          Length = 285

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 68/304 (22%), Positives = 125/304 (41%), Gaps = 40/304 (13%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           RW       ++    +K+L +  + +D  R   N  IQ+GQ VR                
Sbjct: 17  RWLAKQ--GVSHRLFKKMLANHLLWLDGHR-TGNTAIQAGQTVRF--------------- 58

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKG 141
                  +T   +     +LYED    + NKPA ++   G    +H     +  ++  + 
Sbjct: 59  --AIPTTMTVTPEKASLDVLYEDQNWLIINKPAHLTSVPGPHDPHHSLLNRIVWYLQQQK 116

Query: 142 ---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +P +  RLD++T G+++ A+   A     ++     ++K Y ++V G   +    I
Sbjct: 117 ITEPQPAIITRLDRDTVGLVLAAKHPYAQGRFDQAHHA-TLKKEYLAVVAGHLSHATGTI 175

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +     +G D +H +    +    AI+ ++V+         +++Q  TGRTHQ+RVH
Sbjct: 176 EAPIG----LGPDGIHRMV--TENGQSAITKYQVLKEAVN--TLVDVQLLTGRTHQIRVH 227

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
              +G P++GD  Y         SP+ +   L A ++    P    R+Q   P+P   V 
Sbjct: 228 FASLGHPLIGDSLYGQ------ASPLIDHQALQATHLSFVDPFSEKRIQADLPIPDDFVN 281

Query: 318 TWDS 321
             + 
Sbjct: 282 LLNQ 285


>gi|291615429|ref|YP_003525586.1| pseudouridine synthase [Sideroxydans lithotrophicus ES-1]
 gi|291585541|gb|ADE13199.1| pseudouridine synthase [Sideroxydans lithotrophicus ES-1]
          Length = 208

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 56/213 (26%), Positives = 95/213 (44%), Gaps = 15/213 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+Y+D  + + NKPAG+    G G        L + +  +     + HRLD  TSG++V 
Sbjct: 9   LIYQDDYLLLVNKPAGLLAVPGRGAD--KQDCLSARLQLQFPDALVVHRLDMATSGLMVF 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR       L+  FR R + K Y ++V G  + +   +   +            + K + 
Sbjct: 67  ARGARMQSRLSNMFRDREVGKRYVAVVAGRLEPETGEVDLPIAAD----WPKRPLRKIDS 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    +++ +++++        +E++P TGRTHQLRVH   +G PI+GD  Y        
Sbjct: 123 ELGKPSLTRYRLLELDVS-ASRVELEPFTGRTHQLRVHMAAIGHPILGDALYGDESSA-- 179

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                 +L LHA ++   HP     L   +  P
Sbjct: 180 -----PRLLLHASWLSFAHPFSSEPLNFVSAAP 207


>gi|227544440|ref|ZP_03974489.1| RluA family pseudouridine synthase [Lactobacillus reuteri CF48-3A]
 gi|227185580|gb|EEI65651.1| RluA family pseudouridine synthase [Lactobacillus reuteri CF48-3A]
          Length = 314

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 63/276 (22%), Positives = 120/276 (43%), Gaps = 32/276 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
            G+  VD ++V+   +I   Q + I       +  ++              S      ++
Sbjct: 65  EGEFLVDHRKVRPTTQILPNQPLTIKAQPELADDTVE--------------SSNEPLNVV 110

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---DSKGQKPRLTHRLDQETSGIL 158
           YED    V +KPAG++   G  +    +   +K ++   +S   +P L  RLD+ T G+L
Sbjct: 111 YEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIANNSADLRPHLITRLDRFTGGLL 170

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+   A+  +++  +  ++ K Y +LV G   ++   I         IG       + 
Sbjct: 171 LIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHGEI------NKPIGRKDGQAARV 224

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            ++    A++ + V +    K+  + ++ HTGRTHQ+RVH   +G  ++GDH Y  +   
Sbjct: 225 IDENGQRALTEYWVEER-GAKWTRVRVRLHTGRTHQIRVHFAAIGHSLIGDHLYGGDTSK 283

Query: 279 NFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
                  +   LHA  +    P    ++  T+ LPA
Sbjct: 284 ------YDHQLLHASKISFNDPFTLKQMTFTSELPA 313


>gi|238796600|ref|ZP_04640107.1| tRNA pseudouridine synthase C [Yersinia mollaretii ATCC 43969]
 gi|238719578|gb|EEQ11387.1| tRNA pseudouridine synthase C [Yersinia mollaretii ATCC 43969]
          Length = 257

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 100/238 (42%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+      ++QK Y ++V G              +   I   +       +
Sbjct: 64  ALSSDVARALSLQLEQHQMQKTYHAVVRGYVLEGGTVDYEMTEELDKIADKFSR----PD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    +++H+  +               +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYLPLAQVEVPVAIGRYETARFSLVELKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +      +G       ++L LHA ++ L HP  G  L +TA             G+ 
Sbjct: 180 THGDLRQNRGIAQHFDCSRLMLHASHLALNHPVTGEALSLTARWDESWQGLMSHFGWS 237


>gi|330878293|gb|EGH12442.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
 gi|330967569|gb|EGH67829.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 211

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 64/214 (29%), Positives = 101/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++++D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIHQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEAGKHALTFWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL    P P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|262172099|ref|ZP_06039777.1| tRNA pseudouridine synthase C [Vibrio mimicus MB-451]
 gi|261893175|gb|EEY39161.1| tRNA pseudouridine synthase C [Vibrio mimicus MB-451]
          Length = 244

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 97/240 (40%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEADVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQSAITAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +                +L LHA  +   HP   + L I A L           G++  
Sbjct: 180 THGDGVHNRLFREHFSAQRLILHASELRFVHPYTQQPLVIRAGLDEVWQGLLSEFGWQEP 239


>gi|86139411|ref|ZP_01057980.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           MED193]
 gi|85823914|gb|EAQ44120.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           MED193]
          Length = 217

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 62/227 (27%), Positives = 107/227 (47%), Gaps = 15/227 (6%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +V+           +L+ D++I V NKPAG+    G G   H+   L S V +   +  L
Sbjct: 2   AVSSDYTPPQDPLEILHHDAQILVVNKPAGLLSVPGRG--EHLADCLLSRVQTAFPEALL 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG++V   T  A +HL+  F  R  +K+Y + + G  + +   +   L+   
Sbjct: 60  VHRLDRDTSGVMVFGVTPHAQRHLSMQFEKRTTRKVYVARLAGHLEPRAGEVDLPLIVD- 118

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                   V          A++ F+V+  + +    + + P TGRTHQLRVH + +G  I
Sbjct: 119 WPNRPRQMVCHDT---GKPALTDFRVVK-YGEGETRVRLTPKTGRTHQLRVHMMALGHAI 174

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
           +GD  Y       ++     ++ LH+  + + HP+ G     ++ AP
Sbjct: 175 LGDPLYATGEDREYS-----RMMLHSEELRIKHPDTGESIKFRVKAP 216


>gi|27365203|ref|NP_760731.1| tRNA pseudouridine synthase C [Vibrio vulnificus CMCP6]
 gi|34582413|sp|Q8DBG5|TRUC_VIBVU RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|27361350|gb|AAO10258.1| tRNA pseudouridine synthase C [Vibrio vulnificus CMCP6]
          Length = 245

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 97/237 (40%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F  + + K Y ++V G  + + E      ++   I   +       E
Sbjct: 64  ALSSEVASQVMPMFAGQEMSKTYHAIVRGWIEEEGELDYALKVELDKIADKFASQ----E 119

Query: 221 KGANYAISHFKVIDCFAQKFC----------WLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ +K +      +            +E++P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KEAQDAITLYKPLAKVEVPYSTSKFPTTRYGLMELKPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
            +                +L LHA  +   HP     + I A +     + ++   +
Sbjct: 180 THGDGKHNKLFREEFDAPRLLLHASELRFVHPYTQQEVVIRAEVDKVWQQLFERFEW 236


>gi|260591041|ref|ZP_05856499.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella veroralis F0319]
 gi|260536906|gb|EEX19523.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella veroralis F0319]
          Length = 223

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 107/229 (46%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ + +  K AG  VQG       +   +K W+  K QKP      + HRLD+  S
Sbjct: 3   VLYEDNHVIIVYKEAGEIVQGDKSGDIPLSEIVKQWLKEKYQKPGNVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L   FR   + K YW++V   P   +  + +WL++       Y + 
Sbjct: 63  GLVIFAKTSKALTRLNNMFRNGEVHKTYWAIVTRPPFEPEATLTDWLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +  +I H+KVI+     +  LE+   TGR HQ+R    +M CPI GD KY A 
Sbjct: 122 -NHQVPTSKKSILHYKVIN-QTDHYTLLEVNLMTGRHHQIRCQLSNMDCPIKGDLKYGAP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 S     + L +  ++  HP     +++ +PLP      W ++G
Sbjct: 180 -----RSNPDGGICLLSHRVEFIHPVSKELIKVESPLPND--NLWQAIG 221


>gi|257093948|ref|YP_003167589.1| pseudouridine synthase [Candidatus Accumulibacter phosphatis clade
           IIA str. UW-1]
 gi|257046472|gb|ACV35660.1| pseudouridine synthase [Candidatus Accumulibacter phosphatis clade
           IIA str. UW-1]
          Length = 230

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 66/214 (30%), Positives = 96/214 (44%), Gaps = 10/214 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y D+ + + NKPAG+    G G        L   V ++     + HRLD  TSG+LV+
Sbjct: 24  VVYSDAALLLVNKPAGLLSVPGRGED--KQDCLARRVQAEYPDALIVHRLDMATSGLLVL 81

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +A  + L+  F  R++ K Y ++V G+P      I   L              K + 
Sbjct: 82  ARGKAMQRRLSTQFANRQVDKRYVAVVNGLPPLASGEIDLPLAAD----WPNRPRQKVDR 137

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                + + ++V+          L + P TGRTHQLRVH L +G PIVGD  Y     G 
Sbjct: 138 LAGKPSRTRYQVLSHDPFANTTRLALWPDTGRTHQLRVHLLAIGHPIVGDGLY--AEAGG 195

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                  +L LHA  +   HPE  R +    P P
Sbjct: 196 AACGADARLLLHAESLAFAHPETARPMAFCCPAP 229


>gi|196231266|ref|ZP_03130125.1| pseudouridine synthase, RluA family [Chthoniobacter flavus
           Ellin428]
 gi|196224602|gb|EDY19113.1| pseudouridine synthase, RluA family [Chthoniobacter flavus
           Ellin428]
          Length = 289

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 67/304 (22%), Positives = 126/304 (41%), Gaps = 34/304 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIK 79
           L  +   ++P      ++  L+   V V+ + V  FN+ ++ G +V I     A+   + 
Sbjct: 13  LLSYLFANWPTAKKKQVRTWLKHQAVVVNGRVVTQFNHPLKPGDIVAIRSDRFAVPGTVV 72

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLK 134
              I                 + +ED+ + V +KP  +            + + +  +L+
Sbjct: 73  GDDI----------------RICFEDAALLVIDKPPDLLTIASEAEQEKTVYFQLTEYLR 116

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++  + HRLD+ETSGI+V A+T  A   L   +   + +K Y +++ G   N 
Sbjct: 117 GNDVHSRERVWIVHRLDRETSGIMVFAKTPQAKGLLQTGWD--KAEKRYQAVIEGSLPND 174

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K    ++L +       +  +         +A++H++V+    +    +E+   TGR HQ
Sbjct: 175 KGTFRSYLDETDP----FRVISVPRTPTTRHAVTHYRVLKR-GKGRTLVELTLETGRRHQ 229

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
           +RVH    GCPIVGD KY A      T+P +         + L    G   +  + LP  
Sbjct: 230 IRVHLADAGCPIVGDKKYGAK-----TNPAKRLGLHSWSLLLLHPISGEEHRFESELPTD 284

Query: 315 MVKT 318
           + + 
Sbjct: 285 LARL 288


>gi|83951260|ref|ZP_00959993.1| ribosomal large subunit pseudouridine synthase A [Roseovarius
           nubinhibens ISM]
 gi|83839159|gb|EAP78455.1| ribosomal large subunit pseudouridine synthase A [Roseovarius
           nubinhibens ISM]
          Length = 222

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 106/221 (47%), Gaps = 13/221 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   +++ED ++ V NKP+G+    G G   H+   L + +++      L HRLD+
Sbjct: 13  DPPQDPLEVIHEDHEMLVVNKPSGLLSVPGKG--EHLADCLLARIEAAYPTALLVHRLDR 70

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG++V A T  A +H+++ F  R  +K Y + V G  + K   +   L+    +    
Sbjct: 71  DTSGVMVFALTPHAQRHMSKQFEKRIPKKTYVARVEGHLEPKTGVVDLPLI----VDWPN 126

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             + K   +    A++ ++V+         + + P TGR+HQLRVH L +G  I+GD  Y
Sbjct: 127 RPLQKVCHETGRAALTEYRVLKAR-DGESRVRLSPKTGRSHQLRVHMLALGHVILGDPLY 185

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                         +L LH+  + + HP+GG+ +Q  A  P
Sbjct: 186 ATGAAAEHP-----RLMLHSEELRIRHPDGGQGMQFRAKAP 221


>gi|295136359|ref|YP_003587035.1| RNA pseudouridylate synthase [Zunongwangia profunda SM-A87]
 gi|294984374|gb|ADF54839.1| RNA pseudouridylate synthase [Zunongwangia profunda SM-A87]
          Length = 288

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 83/325 (25%), Positives = 136/325 (41%), Gaps = 46/325 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHIN-FVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M   +  +V    E +RL  +  + +  I     ++K ++  Q+ VD +  +  + I  G
Sbjct: 1   MKIKEIHIVPQLSEKIRLQEYAASIFTSITTRSAVKKAIKKQQILVDGEIGQTGDWILEG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q +        L    K+QK+ +           L+  ++YED  I V NKPAG     G
Sbjct: 61  QQIE-------LLQPQKQQKVFE-----------LRLEVIYEDDHIAVINKPAGYPT-SG 101

Query: 123 SGIAYHIDGFLKSWVDSKGQK----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           +      +    +   SK       P+  HRLD  TSGIL+ A+T  A   L   F+ + 
Sbjct: 102 NYHKTIKNALPFNLQASKEIDKLEIPQPAHRLDNPTSGILLCAKTNKALIELNRQFQDKE 161

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           IQK Y ++V G    +++   + +                 EK A  A+     I   + 
Sbjct: 162 IQKTYIAIVEGCFPEEQQIFNDEI----------------EEKQATTAVKLLGTIMFKSA 205

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           K   LE +P TGRTHQ+R+H    G PI+G++ Y +        P +  L+L +  ++  
Sbjct: 206 KLSLLEAKPLTGRTHQIRIHLAKNGFPILGENLYGSP-----AIPFKKGLFLTSIAVNFK 260

Query: 299 HPEG-GRLQITAPLPAHMVKTWDSL 322
           HP G  +       P    +  D+L
Sbjct: 261 HPTGSAQQYFKIDFPKKFKRFTDNL 285


>gi|282877384|ref|ZP_06286207.1| RNA pseudouridine synthase [Prevotella buccalis ATCC 35310]
 gi|281300436|gb|EFA92782.1| RNA pseudouridine synthase [Prevotella buccalis ATCC 35310]
          Length = 227

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 67/228 (29%), Positives = 110/228 (48%), Gaps = 15/228 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSG 156
           LYED+ I + +K +G  VQG       +   +K ++  K  KP      + HRLD+   G
Sbjct: 4   LYEDNHIIIVSKRSGEIVQGDKTGDEPLSETVKQYIKEKYHKPGNVFLGVVHRLDRPVWG 63

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V A+T  A   L + F+  ++ K YW++    P  ++  + +WL++       Y H  
Sbjct: 64  LVVFAKTSKALTRLNKMFKEGQVHKTYWAITKNAPPAEEGVLTDWLVRNERQNKSYAHP- 122

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            Q    A  A+  ++VI   + ++  +E+   TGR HQ+R    +MGC I GD KY A+ 
Sbjct: 123 -QEVPNAKKAVLKYRVI-AHSDRYHLIEVNLLTGRHHQIRCQLANMGCAIKGDLKYGASR 180

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                S     + L AR +   HP     + + APLP +  K W++L 
Sbjct: 181 SNPDGS-----ISLLARRIMFVHPVSKENIVVEAPLPPN-DKLWEALA 222


>gi|160887288|ref|ZP_02068291.1| hypothetical protein BACOVA_05306 [Bacteroides ovatus ATCC 8483]
 gi|156107699|gb|EDO09444.1| hypothetical protein BACOVA_05306 [Bacteroides ovatus ATCC 8483]
          Length = 564

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 118/246 (47%), Gaps = 25/246 (10%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L+H+++  ++ ++ +  + H D  +  ++YED  + V NKPAG+    G       
Sbjct: 320 CEPILHHMLQGLEVDENPLLNSIHEDE-ELEIVYEDEWLVVVNKPAGMLSVPGKEEDRDS 378

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                         P + HRLD  TSG+L+VA+T+   QHL   F  R I+K Y +++ G
Sbjct: 379 VYHRLKKKYPDATGPMIVHRLDMATSGLLLVAKTKEVHQHLQAQFASRSIKKRYVAVLDG 438

Query: 190 I-------PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           +       P  +   I   L     +      V +++      AI+ +++I C ++K   
Sbjct: 439 VTVEKTALPPGRTGRIELPLCLN-PLDRPRQIVSREH---GKEAITEYRII-CESEKHTR 493

Query: 243 LEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +   P TGRTHQLRVHA H   +GCPI+GD  Y             ++LYLHA Y++  H
Sbjct: 494 IAFYPLTGRTHQLRVHAAHPEGLGCPILGDELYGKK---------ADRLYLHAEYIEFRH 544

Query: 300 PEGGRL 305
           P  G++
Sbjct: 545 PISGKI 550


>gi|225867747|ref|YP_002743695.1| RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
 gi|225701023|emb|CAW97796.1| RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
          Length = 289

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 110/269 (40%), Gaps = 29/269 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              V V+ + + + + ++ G  +++            ++   D  + + K         L
Sbjct: 37  KKHVWVNDELINWQSPVKQGDHIKLRFD---------QEDYPDKGILMGKPG---LVDCL 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP G+      G        L       G+   + HRLD ETSG ++ A+
Sbjct: 85  YQDEHLIIANKPEGMKTH---GNEPTELALLNHVSAYTGKTCYVVHRLDMETSGAILFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      R I++ YW+L+ G  + +     + + +  H     V     + K 
Sbjct: 142 NPFILPILNRLLERRDIKRDYWALIEGQLEQQTVTYRDPIGRHRHDRRKRV----VDSKH 197

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              AI+H  ++  F Q  C +  +  TGRTHQ+RVH  H   P++GD  Y          
Sbjct: 198 GQEAITHLALLQAFDQ-TCLVNCRLETGRTHQIRVHLAHHKHPLIGDPLYSRQKAE---- 252

Query: 283 PIQNKLYLHARYMDLPHPEGGRL-QITAP 310
               +L LHA  + L HP    + ++TAP
Sbjct: 253 ----RLMLHAHQLTLRHPLTQEMIRVTAP 277


>gi|15675829|ref|NP_270003.1| hypothetical protein SPy_2063 [Streptococcus pyogenes M1 GAS]
 gi|13623058|gb|AAK34724.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS]
          Length = 272

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 100/268 (37%), Gaps = 26/268 (9%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              V ++   V + + ++ G  V++                 D    +       K   L
Sbjct: 14  KKHVLINGHSVNWQSCVKYGDQVKLFFDHE------------DYPEKIIVMGQAEKVTCL 61

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  I + NKP G+      G        L       GQ   + HRLD+ETSG ++ A+
Sbjct: 62  YEDEHIIIVNKPEGMKTH---GNDPTELALLNHVSAYTGQTCYVVHRLDKETSGAILFAK 118

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           T      L      R I + Y +LV G   + +    + + +  H     V     +   
Sbjct: 119 TPFILPILNRLLEKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRV----VDPIN 174

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              AI+   ++  F +    L  Q  TGRTHQ+RVH  H G  + GD  Y    K     
Sbjct: 175 GKKAITEVTLVKNFHKTASLLTCQLQTGRTHQIRVHLAHQGHVLFGDPLYSNGKKD---- 230

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITA 309
               +L LHA  + L HP     + + A
Sbjct: 231 --CARLMLHAYQLRLKHPLTQEDICVQA 256


>gi|238784871|ref|ZP_04628871.1| tRNA pseudouridine synthase C [Yersinia bercovieri ATCC 43970]
 gi|238714188|gb|EEQ06200.1| tRNA pseudouridine synthase C [Yersinia bercovieri ATCC 43970]
          Length = 257

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 102/238 (42%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +       +
Sbjct: 64  ALSSDVARALSLQFEQHQIQKTYHAVVRGYVLEGGTVDYEMTEELDKIADKFSR----PD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    +++H + +               +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHHQPLAQVEMPVAIGRYDTARFSLMELKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +      +G       ++L LHA +++L HP  G  L +TA             G+ 
Sbjct: 180 THGDLRQNRGVAQHFDCSRLMLHASHLELNHPVTGEALSLTARWDESWQGLMSHFGWS 237


>gi|268590539|ref|ZP_06124760.1| tRNA pseudouridine synthase [Providencia rettgeri DSM 1131]
 gi|291313926|gb|EFE54379.1| tRNA pseudouridine synthase [Providencia rettgeri DSM 1131]
          Length = 252

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y D  +   NKPAG+ V      +      +++  D  GQ     HRLD+ TSGIL+ 
Sbjct: 4   IIYHDEYMVAVNKPAGMLVHRSWLDSKETVFVMQTLRDQIGQYVYPIHRLDRPTSGILLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +++K+Y ++V G    ++      L +   I   +       E
Sbjct: 64  ALSSDVARLLSAQFENHQLEKVYHAVVRGYLTEEQTIDYPLLEELDKIADKHASR----E 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                 ++H K I               +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 PVLQECVTHCKPIATVECAIAIGRYETSRFSLVELKPETGRKHQLRRHMSHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           K+      +G  T    ++L LHA  ++L HP     + + A      +   +  G+ 
Sbjct: 180 KHGDLRQNRGVNTHFSVSRLMLHASLLNLNHPITKENISLVATWDTQWLSLIEQFGWS 237


>gi|213421914|ref|ZP_03354980.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 216

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 67/221 (30%), Positives = 105/221 (47%), Gaps = 15/221 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDEHIMVVNKPSGLLSVPGR-LEAHKDSIM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDQ 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAP 310
            Y +         +  +L LHA  + + HP  G  +    P
Sbjct: 180 FYASPE----ALSLAPRLQLHAEMLTITHPAYGNSMTFKVP 216


>gi|329296365|ref|ZP_08253701.1| tRNA pseudouridine synthase C [Plautia stali symbiont]
          Length = 259

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 59/257 (22%), Positives = 106/257 (41%), Gaps = 17/257 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ +   NKPAG  V             +++  D  GQ     H LD+ TSG+L++
Sbjct: 4   IIYQDAWLVAVNKPAGWLVHRSWLDRKEKVVVMQTVRDQIGQHVFTAHCLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +    + L + F   +IQK Y ++V G            + +   I   +V       
Sbjct: 64  GLSSEIGRLLAQQFEQHQIQKTYHAVVRGWLDGSATLDYPLVEELDKIADKFVT----EP 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +    A++ ++ +             + ++  +E+ PHTGR HQLR H  H+  PI+GD 
Sbjct: 120 RAPQPAVTDYRALAQAELPVAIGKYSSARYTLVELSPHTGRKHQLRRHMAHLRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +      +G       ++L LHA  + L HP  G  L I A L     +     G++  
Sbjct: 180 SHGDLRQNRGAAAHFGMDRLMLHASALTLTHPVTGEPLVIRAGLDRVWQQMLHPFGWQQQ 239

Query: 328 RNLYIKRLYSQDECKQN 344
                +  ++ +  +  
Sbjct: 240 LPDVPRVEFAAEAVQDK 256


>gi|288799919|ref|ZP_06405378.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella sp. oral taxon 299 str. F0039]
 gi|288333167|gb|EFC71646.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella sp. oral taxon 299 str. F0039]
          Length = 222

 Score =  172 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 68/228 (29%), Positives = 111/228 (48%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I + +K +G  VQG       +   +K+++  K  KP      + HRLD+  S
Sbjct: 3   VLYEDNHIIIVHKNSGEIVQGDKTGDTPLSDIVKAYIKEKYAKPGNVFVGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  A   L   F    + K YW++    PK ++  + NWL++       Y + 
Sbjct: 63  GIVVFAKTSKALSRLNTMFSKGEVHKTYWAITANTPKEEQGTLVNWLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             + +  +  AI ++++I   ++++  LE+   TGR HQ+R    HMGC I GD KY A 
Sbjct: 122 -DEEKPNSKKAILNYQLI-SKSERYALLEVALLTGRHHQIRCQLAHMGCVIKGDLKYGAP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     + L AR ++  HP     + + APLP      W ++
Sbjct: 180 RSNPDAS-----ISLLARRIEFIHPVSKEAIVVEAPLPDD--NLWRAI 220


>gi|322373374|ref|ZP_08047910.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus sp. C150]
 gi|321278416|gb|EFX55485.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus sp. C150]
          Length = 298

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 68/314 (21%), Positives = 127/314 (40%), Gaps = 33/314 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           R+  + K H   ++   L KI    G + V+ +       +  G VV I           
Sbjct: 12  RVKTFLKEH--DVSKGLLAKIKFEGGHIWVNGEEQFATYPVHEGDVVAI----------- 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV- 137
              +I D + + T         ++YED    V NKP G +          +  F+K    
Sbjct: 59  ---EIPDEAPHDTLTPIPFDLDIVYEDDNFLVVNKPYGYASIPSVNHDNTMANFVKYHFV 115

Query: 138 --DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NK 194
             +   Q+  +  RLD++TSG+++ A+   A   + +  + + I+K Y++LV G  K  +
Sbjct: 116 SNNYPNQRVHIVTRLDKDTSGLMLFAKHGYAHARMDKQLQQKSIKKHYYALVEGDTKLEE 175

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I   + +          + ++  K   YA + ++++  + +    +++  HTGRTHQ
Sbjct: 176 QGEIIAPIARDVD-----SIITRRVHKSGKYAHTSYRLVGDYGR-VKLVDINLHTGRTHQ 229

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
           +RVH  H+G P++GD  Y  +           +  LH   +   +P     +   + L  
Sbjct: 230 IRVHFAHLGLPLLGDDLYGGSL-----DYGIERQALHCHRLAFVNPFTKKEMVFASSLTD 284

Query: 314 HMVKTWDSLGFKYD 327
                   L  K D
Sbjct: 285 DFETVIMDLQTKKD 298


>gi|238854907|ref|ZP_04645237.1| pseudouridine synthase, RluA family [Lactobacillus jensenii 269-3]
 gi|313472401|ref|ZP_07812893.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 1153]
 gi|238832697|gb|EEQ25004.1| pseudouridine synthase, RluA family [Lactobacillus jensenii 269-3]
 gi|239529732|gb|EEQ68733.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 1153]
          Length = 297

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 62/330 (18%), Positives = 122/330 (36%), Gaps = 44/330 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSG 62
           M   +Y+V E D    RL  +       ++   +     +G  + V+ +R   N  +++G
Sbjct: 1   MKIFKYIVTEKD--PKRLGLFLSK--KKLSKQVIVNAKHNGGMLLVNHRRRFTNFMLKNG 56

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V        +N  +K                     ++ E     V NKPA +     
Sbjct: 57  DEVLFVMGKEKVNEFLK--------------PSNKPIEIVLETDNYLVINKPANVLSIPS 102

Query: 123 SG-IAYHIDGFLKSWVDSK------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                  +   +  +   K        KP +  RLD++TSG+++V +   A    +E  +
Sbjct: 103 RYEDGDAVVNRVMGYFSKKKSSEQAFLKPHIVTRLDRDTSGLVLVGKNAVAHSKFSELKK 162

Query: 176 MRRIQKIYWSLVWGI--PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
              +++ + ++V     P+ +   I   + K       YV            +++ ++V+
Sbjct: 163 DVFVKEYH-AIVHSNFNPEEQAGLIDAPIGKIDDSVKRYVI------PNGQKSLTQYEVL 215

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
               +    ++++  TGRTHQ+RVH  H+G P+ GD  Y  +           +  L+  
Sbjct: 216 -AQKEGASLVKLRLFTGRTHQIRVHMAHIGHPLFGDKLYGIDDN-------FARQALNCS 267

Query: 294 YMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           ++  P P       +    P  M   W +L
Sbjct: 268 HLSFPDPFTNEEKIVEVSDPQDMTDLWRNL 297


>gi|288802466|ref|ZP_06407905.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella melaninogenica D18]
 gi|302346484|ref|YP_003814782.1| RNA pseudouridine synthase [Prevotella melaninogenica ATCC 25845]
 gi|288334994|gb|EFC73430.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella melaninogenica D18]
 gi|302151026|gb|ADK97287.1| RNA pseudouridine synthase [Prevotella melaninogenica ATCC 25845]
          Length = 223

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 69/229 (30%), Positives = 111/229 (48%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I +  K AG  VQG       +   +K W+  K QKP      + HRLD+  +
Sbjct: 3   VLYEDNHIIIVYKEAGEIVQGDKTGDEPLSEIVKQWIKEKYQKPGNVFLGVVHRLDRPVA 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L + FR   + K YW++V   P   +  + +WL++       Y + 
Sbjct: 63  GLVVFAKTSKALTRLNDMFRNGEVHKTYWAIVTRPPFETEATLTDWLVRNERQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +  +I H+KVI+  ++++  LE+   TGR HQ+R    +M CPI GD KY A 
Sbjct: 122 -NHQVPTSKKSILHYKVIN-QSERYTLLEINLMTGRHHQIRCQLSNMDCPIKGDLKYGAP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
                 S     + L +  ++  HP    ++ I +PLP      W ++G
Sbjct: 180 RSNPDGS-----ICLLSHRVEFIHPVSKEKICIESPLPKD--NLWQAIG 221


>gi|224531710|ref|ZP_03672342.1| RNA pseudouridine synthase family protein [Borrelia valaisiana
           VS116]
 gi|224511175|gb|EEF81581.1| RNA pseudouridine synthase family protein [Borrelia valaisiana
           VS116]
          Length = 315

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 71/278 (25%), Positives = 127/278 (45%), Gaps = 15/278 (5%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L  Y+ ++ V  ++   RLD        +++ V + K +R G +R++  +  F+ R+ 
Sbjct: 1   MRLDKYI-FLEVFANDNGKRLDSILIKIL-NLSKVRIIKHIRKGDIRLNGLKSHFSCRVC 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   +    ++      +D           +   ++YEDS + V +K  GI V 
Sbjct: 59  KGDKIYLYKSLAQSLNL-----TMDEYYKSNIDFQCIPKRIIYEDSDLLVVDKQRGILVH 113

Query: 121 GGSG-IAYHIDGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           GG   + + ++ +L    + S   KP   HRLD+ TSGI++ A+   AA+ L+ +F    
Sbjct: 114 GGRNSLDFLVNAYLLGENLRSLSFKPSAVHRLDRNTSGIIIFAKNVNAARRLSVAFSSGA 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y++++ G  K       N L +   +   +V    +N+K  N AI+    I   ++
Sbjct: 174 ITKKYFAILLGEVK-STVVYENHLFRDKRLRKTFVL---ENKKFIN-AITKVNPILS-SK 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K    E+   TG THQ+R        P++ D KY   F
Sbjct: 228 KATLAEIVIETGFTHQIRAQCSFNNHPLINDKKYYDKF 265


>gi|282859628|ref|ZP_06268730.1| RNA pseudouridine synthase [Prevotella bivia JCVIHMP010]
 gi|282587546|gb|EFB92749.1| RNA pseudouridine synthase [Prevotella bivia JCVIHMP010]
          Length = 233

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 68/228 (29%), Positives = 112/228 (49%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + +  K AG  VQG       +   +K W+  K QKP      + HRLD+  +
Sbjct: 3   VVYEDNHLIIVYKEAGEIVQGDKSGDEPLSEMVKRWIKEKYQKPGNVFLGVVHRLDRPVA 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ ART  A   L E FR   I K YW++V   P   +  + +WL++ +     Y + 
Sbjct: 63  GLVIFARTSKALTRLNEMFRNGDIHKTYWAIVQQPPIESENTLTDWLVRNTQQNKSYAYN 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +      A  +I H+K I    +++  LE+   TGR HQ+R    ++GCPI GD KY A 
Sbjct: 123 M--PAPMAKKSILHYKTISS-TERYTLLEVNLMTGRHHQIRCQLANIGCPIKGDLKYGA- 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
                 S     + L +  ++  HP    ++++ +PLP  M   W ++
Sbjct: 179 ----ARSNPDGSICLLSHKVEFVHPVSKKKIKVVSPLP--MDNLWQAI 220


>gi|127513457|ref|YP_001094654.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126638752|gb|ABO24395.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 578

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 64/224 (28%), Positives = 102/224 (45%), Gaps = 18/224 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           LD +  L   ++     ++Y+D  I V NKPA      G  +   +   ++     K   
Sbjct: 360 LDDNPLLNNPAEGKDLSIIYQDEAIAVVNKPAEFLSVPGKHVTDSVYSRMRQAF-PKATG 418

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG++V+A +  A   L + F  R ++K Y + V G  + ++  I   L 
Sbjct: 419 PLIVHRLDMSTSGLMVIALSSEANTALVQQFIGRTVEKRYLARVAGEVQGEEGEITLPL- 477

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V  ++     +A + + ++    +    L + P TGRTHQLRVH  H  
Sbjct: 478 RVDLDDRPRQLVCFEH---GKHAHT-YWLVKSRGEGTTLLSLFPKTGRTHQLRVHCAHQD 533

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +G PI+GD  Y A           N+L+LHA+Y+   HP  G 
Sbjct: 534 GLGMPIIGDDLYGAK---------ANRLHLHAQYLAFNHPISGE 568


>gi|294139995|ref|YP_003555973.1| tRNA pseudouridine synthase C [Shewanella violacea DSS12]
 gi|293326464|dbj|BAJ01195.1| tRNA pseudouridine synthase C [Shewanella violacea DSS12]
          Length = 292

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 103/239 (43%), Gaps = 17/239 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ED  I   +KPAG+ V             ++   D  G      HRLD+ TSG+L+ A
Sbjct: 47  LFEDDDIVAIHKPAGLLVHRSYLARRERFFAMQLTRDKVGCHVFPVHRLDRPTSGVLLFA 106

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           ++   A  L   F  + I+K Y ++V G             ++   +G   V+     +K
Sbjct: 107 KSCEMANALCVQFADKTIEKHYLAIVRGNMHEAATLDYPLKVELDDLGDKDVNQ----DK 162

Query: 222 GANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            A  A++ ++ +             + ++  +++ PHTGR HQLR H  H+  PI+GD  
Sbjct: 163 PAQDAVTSYQPLLNTEIPFTSGRYASSRYALVKLSPHTGRKHQLRRHMAHLRHPILGDTT 222

Query: 272 YCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
           +    +  F       N+L+L A+ +   HP  G R+ I   L       +  LG+  +
Sbjct: 223 HGDGKQNKFFREHFSVNRLWLIAKQLTFNHPRTGERMIIETELEQQWFDLFKGLGWDEE 281


>gi|288928581|ref|ZP_06422428.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella sp. oral taxon 317 str. F0108]
 gi|288331415|gb|EFC69999.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella sp. oral taxon 317 str. F0108]
          Length = 221

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 71/230 (30%), Positives = 107/230 (46%), Gaps = 16/230 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
           I +YED+ I + +K +G  VQ        +   +KS++  K  KP      + HRLD+  
Sbjct: 2   IPVYEDNHIIIVSKHSGEIVQSDKTGDVPLVDIVKSYLKEKYAKPGNVFLGVVHRLDRPV 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G++  A+T  A   +   FR   ++K YW++V   P+N+   + +WL +       Y H
Sbjct: 62  WGLVAFAKTSKALSRMNALFRTGDVEKTYWAIVQSPPENETGELVHWLTRNEKQNKSYAH 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                  GA  AI  +KVI   ++ +  LE+Q  TGR HQ+R     MGCPI GD KY A
Sbjct: 122 --NHEVAGAKKAILSYKVIGR-SENYTLLEVQLMTGRHHQIRCQLAAMGCPIKGDLKYGA 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                  S     + L +R +   HP     + + APLP      W + G
Sbjct: 179 RRSNADGS-----ISLLSRKISFVHPVSKETICVEAPLPDD--NLWHAFG 221


>gi|255530619|ref|YP_003090991.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
 gi|255343603|gb|ACU02929.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
          Length = 228

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 66/232 (28%), Positives = 107/232 (46%), Gaps = 15/232 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQ 152
              +LYED+ +    K AG  VQ        +D  +K ++  K  KP      + HRLD+
Sbjct: 5   DKDVLYEDNHLIAVCKKAGDIVQIDETGDEPLDEQVKKYLAIKYNKPNSAFLGVVHRLDR 64

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
             SG+++ A+T  A + +   F+ R ++K YW++V   P      + +WL+K      + 
Sbjct: 65  PVSGVILFAKTSKALERMNAIFKNREVKKTYWAIVRKKPVKTSGTLIHWLIKNPQ--KNV 122

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V    +   G+      +++I      +  +E+ P TGR+HQ+RV    MGCPIVGD+KY
Sbjct: 123 VTAYAEEVPGSQRCELSYRLIGTLNDYY-LIEVDPLTGRSHQIRVQLSTMGCPIVGDNKY 181

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH-MVKTWDSL 322
                    S     + LHAR +   HP     + I A LP     + ++  
Sbjct: 182 GYPRGSRKGS-----ICLHARRLQFIHPVKKEPVNIFAELPVDGFWEKFEGF 228


>gi|116617201|ref|YP_817572.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
 gi|116096048|gb|ABJ61199.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
          Length = 297

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 67/326 (20%), Positives = 131/326 (40%), Gaps = 38/326 (11%)

Query: 4   MTYVQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQS 61
           M   QY  ++ +      +       Y  +    ++  LR      V+   V  N  +++
Sbjct: 1   MKKWQYNFIITSQNSGQTVKELLIKWY--VPQ-RIRGALRIKKHFSVNNIIVPTNYELRT 57

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  +++    +             +S +    +      +++E+  + V +KPAG+ +  
Sbjct: 58  GDQLQLNFDADDFR----------TSESNYLPNHQKSVNIIFENKDLVVIDKPAGMKMHP 107

Query: 122 GSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            S         L +++  +  +      P + HR+D+ TSG+++VA+       L     
Sbjct: 108 HSPTET---DTLLNYLAGEFIQRKVSDQPYMVHRIDRATSGLVIVAKNPVVVPILDRMLA 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            +RI + Y + V G+ ++    IA  +   +            + K A  A++H+  +  
Sbjct: 165 DKRIVRTYVTWVSGVVQDNHGTIAKPIGIDARDDRKRA----VDGKEAQVAMTHWWRMHT 220

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                  L +Q  TGR HQ+RVH   +G PIVGD  Y   + G        ++ LH+  +
Sbjct: 221 V-FCSSLLRVQLSTGRMHQIRVHLASIGHPIVGDELYGGVYNG--------RMLLHSATI 271

Query: 296 DLPHPEGGRLQ-ITAPLPAHMVKTWD 320
            +P P    ++ IT PLP+   +   
Sbjct: 272 KIPLPFDEGVRMITGPLPSDFPRQLR 297


>gi|22127019|ref|NP_670442.1| tRNA pseudouridine synthase C [Yersinia pestis KIM 10]
 gi|45442581|ref|NP_994120.1| tRNA pseudouridine synthase C [Yersinia pestis biovar Microtus str.
           91001]
 gi|51597324|ref|YP_071515.1| tRNA pseudouridine synthase C [Yersinia pseudotuberculosis IP
           32953]
 gi|108806509|ref|YP_650425.1| tRNA pseudouridine synthase C [Yersinia pestis Antiqua]
 gi|108813124|ref|YP_648891.1| tRNA pseudouridine synthase C [Yersinia pestis Nepal516]
 gi|145598957|ref|YP_001163033.1| tRNA pseudouridine synthase C [Yersinia pestis Pestoides F]
 gi|149366961|ref|ZP_01888994.1| tRNA pseudouridine synthase C [Yersinia pestis CA88-4125]
 gi|153949809|ref|YP_001399991.1| tRNA pseudouridine synthase C [Yersinia pseudotuberculosis IP
           31758]
 gi|162421605|ref|YP_001607777.1| tRNA pseudouridine synthase C [Yersinia pestis Angola]
 gi|165927134|ref|ZP_02222966.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           F1991016]
 gi|165939825|ref|ZP_02228365.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           IP275]
 gi|166011912|ref|ZP_02232810.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166211483|ref|ZP_02237518.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167399889|ref|ZP_02305407.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167419839|ref|ZP_02311592.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           MG05-1020]
 gi|167425312|ref|ZP_02317065.1| tRNA pseudouridine synthase [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|167468860|ref|ZP_02333564.1| tRNA pseudouridine synthase [Yersinia pestis FV-1]
 gi|170023309|ref|YP_001719814.1| tRNA pseudouridine synthase C [Yersinia pseudotuberculosis YPIII]
 gi|186896429|ref|YP_001873541.1| tRNA pseudouridine synthase C [Yersinia pseudotuberculosis PB1/+]
 gi|218928206|ref|YP_002346081.1| tRNA pseudouridine synthase C [Yersinia pestis CO92]
 gi|229837745|ref|ZP_04457905.1| tRNA U65 pseudouridine synthase [Yersinia pestis Pestoides A]
 gi|229840967|ref|ZP_04461126.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229843068|ref|ZP_04463218.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229903567|ref|ZP_04518680.1| tRNA U65 pseudouridine synthase [Yersinia pestis Nepal516]
 gi|270487346|ref|ZP_06204420.1| tRNA pseudouridine synthase C [Yersinia pestis KIM D27]
 gi|294503055|ref|YP_003567117.1| hypothetical protein YPZ3_0945 [Yersinia pestis Z176003]
 gi|34582458|sp|Q8ZH72|TRUC_YERPE RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|21960067|gb|AAM86693.1|AE013915_2 hypothetical protein y3143 [Yersinia pestis KIM 10]
 gi|45437446|gb|AAS62997.1| Pseudouridylate synthases, 23S RNA-specific [Yersinia pestis biovar
           Microtus str. 91001]
 gi|51590606|emb|CAH22247.1| conserved hypothetical protein [Yersinia pseudotuberculosis IP
           32953]
 gi|108776772|gb|ABG19291.1| tRNA pseudouridine synthase C [Yersinia pestis Nepal516]
 gi|108778422|gb|ABG12480.1| tRNA pseudouridine synthase C [Yersinia pestis Antiqua]
 gi|115346817|emb|CAL19703.1| Conserved hypothetical protein [Yersinia pestis CO92]
 gi|145210653|gb|ABP40060.1| tRNA pseudouridine synthase C [Yersinia pestis Pestoides F]
 gi|149290575|gb|EDM40651.1| tRNA pseudouridine synthase C [Yersinia pestis CA88-4125]
 gi|152961304|gb|ABS48765.1| tRNA pseudouridine synthase [Yersinia pseudotuberculosis IP 31758]
 gi|162354420|gb|ABX88368.1| tRNA pseudouridine synthase [Yersinia pestis Angola]
 gi|165912228|gb|EDR30865.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           IP275]
 gi|165921030|gb|EDR38254.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           F1991016]
 gi|165989178|gb|EDR41479.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166207254|gb|EDR51734.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166962580|gb|EDR58601.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           MG05-1020]
 gi|167050597|gb|EDR62005.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167055712|gb|EDR65496.1| tRNA pseudouridine synthase [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|169749843|gb|ACA67361.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186699455|gb|ACC90084.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
 gi|229679337|gb|EEO75440.1| tRNA U65 pseudouridine synthase [Yersinia pestis Nepal516]
 gi|229689944|gb|EEO82003.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229697333|gb|EEO87380.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229704122|gb|EEO91134.1| tRNA U65 pseudouridine synthase [Yersinia pestis Pestoides A]
 gi|262361091|gb|ACY57812.1| hypothetical protein YPD4_0903 [Yersinia pestis D106004]
 gi|262365333|gb|ACY61890.1| hypothetical protein YPD8_1205 [Yersinia pestis D182038]
 gi|270335850|gb|EFA46627.1| tRNA pseudouridine synthase C [Yersinia pestis KIM D27]
 gi|294353514|gb|ADE63855.1| hypothetical protein YPZ3_0945 [Yersinia pestis Z176003]
 gi|320014170|gb|ADV97741.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 257

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 102/238 (42%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHIVAVNKPAGWLVHRSWLDRNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +     +++
Sbjct: 64  ALSSDVARMLSLQFEQHQIQKTYHAVVRGYVLEGGTVDYAMAEELDKIADKFA----KSD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    ++SH++ +               ++  + ++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVSHYEALAQVEVPLAIGRYETARYSLVALKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +      +G       ++L LHA ++ L HP  G  L +TA             G+ 
Sbjct: 180 THGDLRQNRGVAQHFGCSRLMLHASHLHLNHPVTGEALTLTARWDEPWQGLMSQFGWS 237


>gi|296454474|ref|YP_003661617.1| RluA family pseudouridine synthase [Bifidobacterium longum subsp.
           longum JDM301]
 gi|296183905|gb|ADH00787.1| pseudouridine synthase, RluA family [Bifidobacterium longum subsp.
           longum JDM301]
          Length = 317

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 61/293 (20%), Positives = 112/293 (38%), Gaps = 17/293 (5%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V   +     R D         I+      ++ SGQ RV  + V  ++ +Q+G+ V    
Sbjct: 2   VPAPDALVGKRFDVAVAKML-GISRSKAADLVDSGQARVLGREVARSSTLQAGETVEFD- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L       + + + + +    D +  +        +      G +V G        
Sbjct: 60  ----LAEEQAGPEPIATDMAVVYEDDDVVVVDKPVGVAAHASVGWTGPTVLGS-----LR 110

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           D  +         +  +  RLD  TSG+++V ++  A   +   F    ++K Y +LV G
Sbjct: 111 DRGVHIASYGAAGREGIVSRLDVGTSGLMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQG 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             K  K  I   + +                     A++H+ V++ F  +   + +   T
Sbjct: 171 GLKENKATIEAPIGR-----AKVSDFRFCVTPAGKPAVTHWDVLERFGHEATLVSVNLET 225

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           GRTHQ+RVH   +G P+ GD  Y AN   +    + ++ +LHA  ++  HP  
Sbjct: 226 GRTHQIRVHFSSIGHPLCGDPMYGANPVLSEALGL-DRQWLHAMKLEFRHPRT 277


>gi|149190306|ref|ZP_01868580.1| ribosomal large subunit pseudouridine synthase A [Vibrio shilonii
           AK1]
 gi|148835913|gb|EDL52876.1| ribosomal large subunit pseudouridine synthase A [Vibrio shilonii
           AK1]
          Length = 245

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 64/221 (28%), Positives = 110/221 (49%), Gaps = 12/221 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ED  I   NKP+G+    G  +  H D      V+    + ++ HRLD  TSG++++A
Sbjct: 17  VFEDEHILAVNKPSGLLSVPGKALE-HYDSMWSRLVEV-YPEIQVVHRLDMSTSGLMLLA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           + + A + L + F+ R   K+Y++ VWG P   +  I   L+           V  ++  
Sbjct: 75  KNKEAERSLKKQFQYRLTHKVYYARVWGTPDESEGLIDLPLICD-WPNRPRQKVCYEH-- 131

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               + ++++V+    Q+   + + P TGR+HQLRVH L +G PIVGD  Y      +F+
Sbjct: 132 -GKPSQTYYQVVK-QEQQTSIVRLFPITGRSHQLRVHLLELGHPIVGDEFYAHEEAMSFS 189

Query: 282 SPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
               ++L LHA  +   HPE  +LQ +  +P    +  + L
Sbjct: 190 ----DRLELHAAELCFYHPETEKLQ-SIFVPCDFHQVSEPL 225


>gi|258510958|ref|YP_003184392.1| pseudouridine synthase [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
 gi|257477684|gb|ACV58003.1| pseudouridine synthase [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
          Length = 314

 Score =  172 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 66/309 (21%), Positives = 129/309 (41%), Gaps = 30/309 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           W      H+   +++ +LR G VRV       ++       +   P    ++  ++   +
Sbjct: 26  WLSQAL-HVPQAHVRHLLRHGAVRVRGN--TPSHL-----EIWDRPTQVWIDEDLRPVDL 77

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ- 142
             +S+            +LY D  + V +KP  + V      A  +D  ++  ++ +G  
Sbjct: 78  ASASLP--------PVRVLYNDPSLLVVDKPENLLVHRDGSDAPTLDACVQRLLNEEGAG 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +    HRLD+ T+G ++ A+     + +       R+++ Y ++  G  + +   ++  +
Sbjct: 130 RAYHVHRLDRGTTGCVLYAKHGLMLRAMDAELAAGRVRRTYLAIASGT-RIRPGVMSAPI 188

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHA 259
            +  H+ G Y     +  +    A +H +V+D   Q    +  + ++  TGR HQ+RVH 
Sbjct: 189 GRDRHVSGRY-----RVSRTGKVARTHVEVLDEADQGGARWTLVRLRLETGRRHQIRVHL 243

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             MG P+VGD  Y              ++ LHA  +   HP  G  +++ APLP    K 
Sbjct: 244 SAMGAPVVGDTLYGGTPHPALAP---GQIALHAARLQFCHPYAGEDVEVRAPLPRAWEKL 300

Query: 319 WDSLGFKYD 327
              +G   D
Sbjct: 301 AADVGLSLD 309


>gi|51246876|ref|YP_066760.1| pseudouridine synthase [Desulfotalea psychrophila LSv54]
 gi|50877913|emb|CAG37753.1| related to pseudouridine synthase [Desulfotalea psychrophila LSv54]
          Length = 235

 Score =  172 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 64/255 (25%), Positives = 112/255 (43%), Gaps = 26/255 (10%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-----GSGIAYH 128
           ++++IKEQ+        +K        +L+ED  I V  KP G+   G          Y 
Sbjct: 1   MDNMIKEQRP-------SKKHQPRGLPILHEDKDIIVVVKPTGLLTIGTDREKSRTAHYL 53

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           ++ +++        +  + HRLDQ+TSG+L+ A++  A + L + +     +K Y ++V 
Sbjct: 54  LNDYVRKGNPKSSNRVYVVHRLDQDTSGLLIFAKSEEAKKFLQKDWEN--TEKHYLAIVC 111

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  K K+  I+++L +       Y      +      + + +KVI    ++   +++   
Sbjct: 112 GKLKEKEGTISSYLTEN----KAYKVYSTPDSTKGKLSKTAYKVIK-EGKEVSLIDIHLL 166

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGR HQ+RVH    G P+ GD KY     G        +L LHAR +   HP   + +  
Sbjct: 167 TGRKHQIRVHFAENGHPVAGDKKYGTGTSG------LKRLALHARSISFTHPYSHKIMTF 220

Query: 308 TAPLPAHMVKTWDSL 322
              LP    +    L
Sbjct: 221 DTGLPEDFTRLLRKL 235


>gi|255263975|ref|ZP_05343317.1| ribosomal large subunit pseudouridine synthase A [Thalassiobium sp.
           R2A62]
 gi|255106310|gb|EET48984.1| ribosomal large subunit pseudouridine synthase A [Thalassiobium sp.
           R2A62]
          Length = 215

 Score =  172 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 62/226 (27%), Positives = 112/226 (49%), Gaps = 13/226 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++   +      ++L+ED ++ + +KP G+    G G   H+   L + + +      L 
Sbjct: 1   MSSDYNPPHDPLVILHEDHEVILVDKPEGLLSVPGKG--EHLADCLLTRLQAAFPTALLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG+++ A TR A +HL   F  R  +K Y + VWG  + K+  +   ++    
Sbjct: 59  HRLDRDTSGVMIFAATRHAQRHLGLQFEKRHTKKTYVARVWGDLQPKEGTVDQPII---- 114

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +  +     K   +    A + ++V+         + + P TGR+HQLR+H LH+G PI+
Sbjct: 115 VDWENRPRQKICAETGRAAQTDWRVV-RGDGAETRVRLMPKTGRSHQLRLHMLHLGHPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           GD  Y      +       ++ LH+  +   HP+GG+ ++ITA  P
Sbjct: 174 GDPFYATGAALDHP-----RMMLHSETLQFRHPDGGQGMRITAKAP 214


>gi|300768616|ref|ZP_07078515.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|300493923|gb|EFK29092.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 300

 Score =  172 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 68/313 (21%), Positives = 126/313 (40%), Gaps = 27/313 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRS-GQVRVDKKRVKFNNRIQSG 62
           MT+   + + +      +    +     I    +Q  LR   +++++         + +G
Sbjct: 1   MTWTYQLTIPSSLNQQSIRACLRTWL--IPK-RIQGQLRQTRRIQLNGAPTSIAQLVNTG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + +  + +             +  +    +    + +LY++S + V +KPAG+     
Sbjct: 58  DCLTLTFIPSDFR----------TPTSNYIAAATAPATILYQNSDLLVVDKPAGVKSHPN 107

Query: 123 -SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             G    I   L + +    Q P + HRLDQ TSG ++VA        L      ++I++
Sbjct: 108 QPGETGSILNDLAATLQPTQQVPYMVHRLDQMTSGAMLVALNPVVVPILDRLISDKQIRR 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++ V G            +   +            N   A  A++ ++V    A +  
Sbjct: 168 TYYAWVRGHFTTPTGHFTAPIGHDATDKRKR----WVNTADAQPALTDYEVCATTAHQ-S 222

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
            +++  HTGRTHQLRVH      PI+GD  Y +  +         +L LHA+ +DL  P 
Sbjct: 223 LVKLTLHTGRTHQLRVHLAASDHPIIGDPLYDSQAESA------PRLMLHAQLLDLQLPF 276

Query: 301 EGGRLQITAPLPA 313
              R+ + APLP+
Sbjct: 277 STTRVTVPAPLPS 289


>gi|318040274|ref|ZP_07972230.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           CB0101]
          Length = 234

 Score =  172 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 63/224 (28%), Positives = 103/224 (45%), Gaps = 10/224 (4%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                    + ++++   + V NKP G+  Q   G+   +   L S V  +  + +L HR
Sbjct: 14  PVIREGLDPAWIVHQAPDLLVLNKPHGLLCQP--GLGPELADSLISRVQQRWPQAQLVHR 71

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG+++VA      + L+  F  R++QK Y + V G+P      I   + K  H  
Sbjct: 72  LDRDTSGLILVALASELHRELSRMFAERQVQKRYVADVHGVPDQPHGLIEWPIAKLQHRP 131

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             Y       +       + ++++    +    LE+QP TGR+HQLRVH   +G PI+GD
Sbjct: 132 PLY-----GVDPAGKACSTRWRLLQAHGR-CSRLELQPLTGRSHQLRVHLQAIGHPILGD 185

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             Y          P+ ++L+LHA  +   HP     L   AP P
Sbjct: 186 PLYGP-LASALDDPLGSRLHLHAAALHWLHPGSSESLAFDAPPP 228


>gi|255068551|ref|ZP_05320406.1| tRNA pseudouridine synthase C [Neisseria sicca ATCC 29256]
 gi|255047187|gb|EET42651.1| tRNA pseudouridine synthase C [Neisseria sicca ATCC 29256]
          Length = 261

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 65/225 (28%), Positives = 97/225 (43%), Gaps = 20/225 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY DS+    NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L
Sbjct: 28  LDILYRDSRTIAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVYPAHRLDRPTSGVL 87

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A    AA+ LT+ F  +  +K YW++V G   +          +   I         Q
Sbjct: 88  LFALDPEAARLLTQQFEQKTTRKTYWAIVRGYLPDDGLIDYPLKYQPDKIAES------Q 141

Query: 219 NEKGANYAISHFKVIDC-----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            E     A + ++ +                ++ W E+ PHTGR HQLR H  H+  PIV
Sbjct: 142 TEATLQEAQTRYRRLARTELPFQSAARYPTSRYSWAELIPHTGRKHQLRRHMKHIFHPIV 201

Query: 268 GDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITA 309
           GD  Y    + + T+      +L LHAR +     E G  L + A
Sbjct: 202 GDTNYGDLRQNHATAAHLGPTRLMLHARSLSFQSIENGETLTVCA 246


>gi|227114681|ref|ZP_03828337.1| tRNA pseudouridine synthase C [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 261

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 107/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHLVAVNKPSGWLVHRSWLDRKEKVVVMQTVRDQIGQHVYTVHRLDRPTSGVLLL 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++QK+Y ++V G   +          +   I   + +     +
Sbjct: 64  ALSSEVARALSQQFESHQMQKMYHAVVRGYVLDDGVIDYALTEELDKIADKFTN----PD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHYRSLAQVEMPVAIGRYPTARYSLMELKPQTGRKHQLRRHMSHIHHPIIGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +    + +G  +     +L LHA  + L HP  G+ L + A   A         G++
Sbjct: 180 AHGDLRHNRGMESHFSCGRLMLHASELQLNHPVSGQPLTLQARWDAPWQGVMTQFGWQ 237


>gi|224436616|ref|ZP_03657625.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
          Length = 359

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 66/335 (19%), Positives = 138/335 (41%), Gaps = 29/335 (8%)

Query: 5   TYVQYVVVEN---DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQ 60
           + +Q  +V     +   +RLD +       ++   +Q+++++  + ++    VK    ++
Sbjct: 4   SQIQKFIVTELDLNNGKLRLDSFLTLKL-QMSKNQIQQLIQANNITLNALPCVKNGTLLK 62

Query: 61  SGQVVRIP-PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
               + I  P  ++L+   +       S +L    + L   +LYED  I + NKP  + +
Sbjct: 63  LNDEIHITFPKPDSLDSNTQN-----ISPSLQNLYENLSIDILYEDDDILIINKPPHLVI 117

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPR---------LTHRLDQETSGILVVARTRAAAQHL 170
                +    D  L  W+                 + HRLD++TSG+L +A++  A + L
Sbjct: 118 HDAPSV---KDLTLTQWLKLHAHTLHTLSGRERYGIIHRLDKQTSGVLCIAKSLLAYEIL 174

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKEC---IANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
               + R++ + Y +++    K   +    +      +  +   ++   +   KG   + 
Sbjct: 175 PNQLKSRQMGRYYLAIIDTPLKQNLQVQCFMGRCPTNRLKMSKIHIDENENPPKGVRDSK 234

Query: 228 SHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           S F  +          + ++ HTGRTHQ+R H   +   I+GD  Y        +   + 
Sbjct: 235 SSFVKLATSNDGLLELIAIKLHTGRTHQIRTHLESLSRHILGDSLYGYKPSAK-SFFYEG 293

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           ++ LHA  + L HP+ G+     AP+   M++   
Sbjct: 294 RILLHAYILYLAHPKNGQNHTFKAPILLDMLEFIQ 328


>gi|163789051|ref|ZP_02183495.1| putative ribosomal large subunit pseudouridine synthase
           [Flavobacteriales bacterium ALC-1]
 gi|159875715|gb|EDP69775.1| putative ribosomal large subunit pseudouridine synthase
           [Flavobacteriales bacterium ALC-1]
          Length = 232

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 73/228 (32%), Positives = 108/228 (47%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I V NK AG  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 13  VLYEDNHIIVANKRAGDIVQGDKTGDKPLSEVVKEYIKDKYNKPGNVYLGVVHRLDRPTT 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ ++T  A   L + F  ++ +K YW+LV   P    + + +WL K           
Sbjct: 73  GIVLFSKTSKALPRLNKLFAEKKAKKTYWALVKNQPPKTNDTLTHWLKKNPKNNKS--TA 130

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  +G+  AI H+K+I      F  LE+   TGR HQ+R     +GCPI GD KY  N
Sbjct: 131 YHKEVEGSKKAILHYKIIKTL-DNFYLLEIDLETGRHHQIRTQLASIGCPIKGDLKYGFN 189

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     + LHA+ +   HP     + ITA LP      W++ 
Sbjct: 190 RSNKDAS-----ISLHAKTLRFVHPIKKEDIVITASLPND--PLWNAC 230


>gi|319935762|ref|ZP_08010192.1| hypothetical protein HMPREF9488_01023 [Coprobacillus sp. 29_1]
 gi|319809311|gb|EFW05752.1| hypothetical protein HMPREF9488_01023 [Coprobacillus sp. 29_1]
          Length = 277

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 60/307 (19%), Positives = 128/307 (41%), Gaps = 45/307 (14%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           Y + ++V  +   +R+D +   H  HI+   L+ I + G + V+ +       +  G  V
Sbjct: 2   YKRELIVTKENHQLRIDDFAYQH--HISRKALKVIKQCGDILVNGEHQTVRYVLNEGDYV 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-----VQ 120
            +       N II E                +   ++YED  + + +KP G++       
Sbjct: 60  -VFIYPPEDNQIIPEN---------------VPLYIVYEDDFLLIVDKPKGMACFPTRSH 103

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +A  +  +  S            +RLD++T+G++++A+ R     + ++ +   I 
Sbjct: 104 PCQTLANALSYYYHSI--ELDSTVHFVNRLDKDTAGLMMIAKYREIHDMMCQNIQH--IY 159

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           + Y + V G    ++  I   + K    G +   ++ +N K +    ++++ ++ ++   
Sbjct: 160 RRYQAHVEGQV--EQGVIDLPIHKD---GQNMRRIIDENGKDSR---TYYRCLE-YSDGI 210

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +E    TGRTHQ+RVH   +G P++GD  Y     G F           +  +   HP
Sbjct: 211 SRVECILETGRTHQIRVHMAAIGHPLIGDLLYGGKP-GTFDL--------ESIMIAFVHP 261

Query: 301 EGGRLQI 307
              ++++
Sbjct: 262 ITKQIKV 268


>gi|212715527|ref|ZP_03323655.1| hypothetical protein BIFCAT_00425 [Bifidobacterium catenulatum DSM
           16992]
 gi|212660894|gb|EEB21469.1| hypothetical protein BIFCAT_00425 [Bifidobacterium catenulatum DSM
           16992]
          Length = 312

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 65/321 (20%), Positives = 125/321 (38%), Gaps = 19/321 (5%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V   +     R D         I+     +++  GQ RV  + +  ++ +QSG+ V  
Sbjct: 3   RLVPAPDALVGKRFDVAVAKML-GISRAKAAELIEGGQARVLGRDISKSSTLQSGETVEF 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             V         E + +   + +    D +  +        +      G +V G      
Sbjct: 62  DIVEERT-----EPEPIAHDMAVVYEDDDVVVVDKPVGVAAHASVGWTGPTVLGS----- 111

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +D  +         +  +  RLD  TSG+++V ++  A   +   F    + K Y +LV
Sbjct: 112 LLDRGVHITSYGAAGRQGIVSRLDVGTSGLMLVCKSDLAYVEMRRQFAEHEVVKTYHALV 171

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  +  K  I   + +                     A++H+ V++ F +    + +  
Sbjct: 172 QGNLRENKATIEAPIGR-----AKVSDFRFCVTPAGKEAVTHWDVMERFGE-ATLVSVNL 225

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            TGRTHQ+RVH   +G P+ GD  Y AN + + T  ++ + +LHA  ++  HP       
Sbjct: 226 ETGRTHQIRVHFSSIGHPLAGDAMYGANPQLSETLGLE-RQWLHAMQLEFRHPRTRVWTT 284

Query: 307 ITAPLPAHMVKTWDSLGFKYD 327
           + +  PA +    D +  ++D
Sbjct: 285 VKSHYPADLQHALDVMHGRHD 305


>gi|296127625|ref|YP_003634877.1| pseudouridine synthase [Brachyspira murdochii DSM 12563]
 gi|296019441|gb|ADG72678.1| pseudouridine synthase [Brachyspira murdochii DSM 12563]
          Length = 237

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 74/220 (33%), Positives = 114/220 (51%), Gaps = 10/220 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQETSG 156
           +YED+ I V  KP  I VQG           +K ++  K  K       L HRLD+  SG
Sbjct: 14  IYEDNHIIVAVKPPNIPVQGDITGDLSFFDNIKDYIKIKYNKKGNVFLGLVHRLDRPVSG 73

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I+V A+T  AA  L+E+ R R+ +K Y+++V GI  +K+  + N+L+KK++  G+   VV
Sbjct: 74  IMVFAKTSKAASRLSEAIRDRKFEKTYYAVVNGILLDKEGMLENYLIKKTNKLGNIAQVV 133

Query: 217 KQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +N K A  A   ++VI +   +    L+++  TGR HQ+RV   ++G  I GD KY   
Sbjct: 134 FENTKNAKIAKLKYEVIKEDLIKNLSLLKIELETGRFHQIRVQLSNIGHTIYGDRKYGNY 193

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
            K +  +     L L A+ +  PHP     +   A LP +
Sbjct: 194 IKYDRDNV---PLALFAKSLRFPHPTKDEYIYAEADLPNY 230


>gi|260596481|ref|YP_003209052.1| 23S rRNA/tRNA pseudouridine synthase A [Cronobacter turicensis
           z3032]
 gi|260215658|emb|CBA27961.1| Ribosomal large subunit pseudouridine synthase A [Cronobacter
           turicensis z3032]
          Length = 217

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 68/231 (29%), Positives = 109/231 (47%), Gaps = 17/231 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++          ++LY+D  I V NKP+G+    G  +  H D  + + +          
Sbjct: 1   MDAYNPPQDPWLLILYQDEHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDFPNAESA 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++ VA T+AA + L   FR R  +K Y + VWG P+  +  +   L+    
Sbjct: 59  HRLDMATSGVIAVALTKAAERELKRQFREREPKKHYVARVWGHPEKAQGVVDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + + V++        + ++P TGR+HQLRVH + +G P
Sbjct: 115 --CDWPNRPKQKVCYETGKAAQTEYDVLEYADDNTARVLLRPITGRSHQLRVHMMALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           I+GD  Y A  +    +P   +L LHA  + + HP  G  +   A  PA  
Sbjct: 173 ILGDKFY-ATPEALARAP---RLLLHAEQLTITHPAYGTPMTFRA--PADF 217


>gi|219872253|ref|YP_002476628.1| pseudouridylate synthase, 23S RNA-specific [Haemophilus parasuis
           SH0165]
 gi|219692457|gb|ACL33680.1| pseudouridylate synthase, 23S RNA-specific [Haemophilus parasuis
           SH0165]
          Length = 236

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 107/231 (46%), Gaps = 14/231 (6%)

Query: 84  LDSSVNLTKHSDFLKSIL--LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           + +++ L +++  ++  L  +Y D+ I V NKP+G+    G+   Y     ++  V  K 
Sbjct: 11  IKNTMALIEYNPPVEPWLDEVYRDNHILVINKPSGLLSIPGNRPEYQDSAMVR--VQQKY 68

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIA 199
                 HRLD  TSGIL+ A ++ A + L   FR R  +K Y +LVWG    K       
Sbjct: 69  GFTEPAHRLDMATSGILLFALSKQAEKELKRQFREREPKKHYQALVWGKLGEKVGDTGTM 128

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           N+ L           +  +       A++ ++V+  +      +++ P+TGR+HQLRVH 
Sbjct: 129 NFPLICDWENRPRQKICYER---GKQAVTFYEVLAHYPNNTTRVKLTPYTGRSHQLRVHC 185

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           L +G PIVGD  Y           +  +L LHA  + + HP     +   A
Sbjct: 186 LALGHPIVGDKFY----ANPLAKSLSPRLCLHAEALTITHPVTQELMTFEA 232


>gi|254475763|ref|ZP_05089149.1| ribosomal large subunit pseudouridine synthase A [Ruegeria sp. R11]
 gi|214030006|gb|EEB70841.1| ribosomal large subunit pseudouridine synthase A [Ruegeria sp. R11]
          Length = 217

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 62/227 (27%), Positives = 105/227 (46%), Gaps = 13/227 (5%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +++   +       +LY D++I V NKP G+    G G   H+   L S V +   +  L
Sbjct: 2   TLSSEYNPPQDPLDILYHDAEIVVVNKPHGLLSVPGRG--EHLADCLISRVQAVFPEALL 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG+++   T  A +HL+  F  R  +K Y + V G  + +   +   L+   
Sbjct: 60  VHRLDRDTSGVMIFGMTAHAQRHLSMQFEKRTTKKAYVARVHGRLEPRSGTVDLPLIVD- 118

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                   V     +    A++ ++V   + +    + + P TGR+HQLRVH L +G  I
Sbjct: 119 WPNRPRQMVC---HETGKPAVTDWRVTK-YEEAATRVRLTPKTGRSHQLRVHMLALGHVI 174

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +GD  Y      N       +L LH+  + + HP+ G  ++  A  P
Sbjct: 175 LGDPIYAEGPARN-----HERLMLHSEELRVKHPDSGESMKFRAKAP 216


>gi|77360895|ref|YP_340470.1| tRNA pseudouridine synthase C [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875806|emb|CAI87027.1| tRNA pseudouridine synthase C [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 254

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 61/256 (23%), Positives = 98/256 (38%), Gaps = 17/256 (6%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
                 ++ +  +LY+D      +KP+G+ V       +     ++   D  GQ     H
Sbjct: 3   ERPIPIEYGELTILYQDENYVAIDKPSGLLVHRSFLDKHETQFAMQMLRDQLGQHVFPVH 62

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG+L+ A +  AA+ + + F    I K Y +LV G              +   I
Sbjct: 63  RLDRPTSGVLLFALSSEAARDMNQLFIEGTISKRYLALVRGFAPESVFLDKPLKEELDKI 122

Query: 209 GGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVH 258
              +       +K    A + F  +               ++  +E  P TGR HQ+R H
Sbjct: 123 ADKFADQ----DKAPQEAQTQFNCLHQAALPIPIGKYPTVRYSLVECFPKTGRKHQIRRH 178

Query: 259 ALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             H+  PI+GD  +  N    F        +L L A  +   HP     + I APL   M
Sbjct: 179 LKHLSLPIIGDVNHGDNQHNQFFREHFELRRLMLFATELSFVHPYSNESITIKAPLGDAM 238

Query: 316 VKTWDSLGFKYDRNLY 331
           +     LG+  +   Y
Sbjct: 239 LSICKQLGWPDEEKDY 254


>gi|323448015|gb|EGB03919.1| hypothetical protein AURANDRAFT_33292 [Aureococcus anophagefferens]
          Length = 259

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 59/225 (26%), Positives = 101/225 (44%), Gaps = 9/225 (4%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++ED ++ V +K +G+    G G  +  D  +     ++G    L HRLD++TSG++V
Sbjct: 37  RVVFEDDEVIVCDKGSGLLAVPGRG-DHKQDSLITRLRATRGASTTLAHRLDRDTSGLVV 95

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+T+ A + L+ +F  R ++K Y   V G P+     +   + K     G     V   
Sbjct: 96  AAKTKRALRSLSMAFEAREVEKSYVGAVLGWPEATFGTVDEPIGKVKTDAGHNRVAVVAE 155

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
             G   + +++ +++        L +QP TGR+ QLRVH   +G P++GD  +       
Sbjct: 156 ADGGRRSRTNWALLEKRDDGSSLLSLQPVTGRSQQLRVHCALIGLPLLGDALHGTEEAAG 215

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP----AHMVKTWD 320
                  +L LHA  + L  P  G +   A  P    A      D
Sbjct: 216 RA----PRLCLHAARLSLDLPTAGPMTFEAEAPFAASADYASLLD 256


>gi|260912603|ref|ZP_05919132.1| ribosomal large subunit pseudouridine synthase [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260633281|gb|EEX51442.1| ribosomal large subunit pseudouridine synthase [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 229

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 70/230 (30%), Positives = 107/230 (46%), Gaps = 16/230 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
           I +YED+ I + +K +G  VQ        +   +K+++  K  KP      + HRLD+  
Sbjct: 10  IPVYEDNHIIIVSKHSGEIVQSDKTGDVPLVDIVKNYLKEKYAKPGNVFLGVVHRLDRPV 69

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G++  A+T  A   +   FR   ++K YW++V   P+N+   + +WL +       Y H
Sbjct: 70  WGLVAFAKTSKALSRMNALFRTGDVEKTYWAIVQSPPENESGELVHWLTRNEKQNKSYAH 129

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                  GA  AI  +KVI   ++ +  LE+Q  TGR HQ+R     MGCPI GD KY A
Sbjct: 130 --NHEVAGAKKAILSYKVIG-QSENYTLLEVQLMTGRHHQIRCQLAAMGCPIKGDLKYGA 186

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                  S     + L +R +   HP     + + APLP      W + G
Sbjct: 187 KRSNPDGS-----ISLLSRKISFVHPVSKETICVEAPLPDD--NLWHAFG 229


>gi|87198472|ref|YP_495729.1| pseudouridylate synthase [Novosphingobium aromaticivorans DSM
           12444]
 gi|87134153|gb|ABD24895.1| Pseudouridylate synthase [Novosphingobium aromaticivorans DSM
           12444]
          Length = 222

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 105/231 (45%), Gaps = 16/231 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +   +L+ED +  V +KPAG+ +         ++  L +      ++P   HRLD++TS
Sbjct: 1   MIDFSILFEDGEALVIDKPAGLPLDRPRAGGDSLENHLDALRFGFQREPFPVHRLDRDTS 60

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L++AR   A +  + +F  R ++K+Y  +V G    +K  I   L K S     +  +
Sbjct: 61  GCLLLARNPKALKRFSAAFEAREVEKVYLGIVAGEVTGEKGTIDLALSKVSSAEKGWRMI 120

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKYCA 274
                +    A++H++V+         +E +P TGRTHQ+R+H    +G  +VGD  Y  
Sbjct: 121 ---PARKGKPALTHWRVVARKP-GLTLVEFRPETGRTHQIRIHALAGLGHALVGDPVYGD 176

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                       +  LHA  + +P      +   APLP       D+ GF+
Sbjct: 177 GKGAW-------RTMLHASDLVVPRAGKAPIVAHAPLPLDF----DAFGFE 216


>gi|260776531|ref|ZP_05885426.1| tRNA pseudouridine synthase C [Vibrio coralliilyticus ATCC BAA-450]
 gi|260607754|gb|EEX34019.1| tRNA pseudouridine synthase C [Vibrio coralliilyticus ATCC BAA-450]
          Length = 241

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 99/243 (40%), Gaps = 17/243 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++++D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L
Sbjct: 3   LDIVFQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVL 62

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A +   A  +   F    + K Y ++V G  +          ++   I   +      
Sbjct: 63  IFALSSDVASQVMPMFANHEMVKTYHAIVRGWIEEAGRLDYALKVELDKIADKHASQ--- 119

Query: 219 NEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            EK A  AI+ +  +               ++C +E++P TGR HQLR H  H+  PIVG
Sbjct: 120 -EKEAQEAITDYHTLAKAEIPYSTGKFPTTRYCLMELKPLTGRKHQLRRHMAHLRHPIVG 178

Query: 269 DHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           D  +           +   ++L LHA  ++  HP   + + I A +     K  D   ++
Sbjct: 179 DTTHGDGKHNKLFREVYDSHRLLLHASSLEFVHPFTNQTVLIKAKVDDTWQKICDEFAWQ 238

Query: 326 YDR 328
              
Sbjct: 239 MPE 241


>gi|227484916|ref|ZP_03915232.1| possible pseudouridylate synthase [Anaerococcus lactolyticus ATCC
           51172]
 gi|227237071|gb|EEI87086.1| possible pseudouridylate synthase [Anaerococcus lactolyticus ATCC
           51172]
          Length = 313

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 76/312 (24%), Positives = 128/312 (41%), Gaps = 42/312 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M Y+++     +   + L ++ K     I+    Q +L  G + V+   V  N  +  G 
Sbjct: 34  MNYIKF----ENFRKITLKKFLKE--KSISIRAYQDLLNEG-ILVNDSSVHNNINLGKGD 86

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V+I      L++   E ++                 ++YED  I V NKP+G++V   S
Sbjct: 87  IVKIKIDSEDLDYAPIEGEL----------------NIVYEDENIIVVNKPSGLTV--NS 128

Query: 124 GIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                +   L  +      K   RL +RLD  TSG+++VA+ R A  +  +     +  K
Sbjct: 129 KNQLSLANLLAYYFQKNDIKSKIRLINRLDMNTSGLMMVAKNRYAQAYYQKQIEENKTHK 188

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y + V G          N L K +    +     + +EKG   AI++FK +      + 
Sbjct: 189 KYLAYVAGALN------INELFKINLEYDEISKTYRNSEKG-RLAITYFKTL-SCDDDYS 240

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E    TG+THQ+R     MG PI+GD  Y + +         ++  LH+ Y+      
Sbjct: 241 LIECDIKTGKTHQIRASLRSMGHPIIGDKLYGSAYN-------FDRFLLHSFYLSFKEFV 293

Query: 302 GGRLQITAPLPA 313
           G    I   LP 
Sbjct: 294 GQESIILENLPE 305


>gi|153003163|ref|YP_001377488.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152026736|gb|ABS24504.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 311

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 70/315 (22%), Positives = 122/315 (38%), Gaps = 31/315 (9%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR   +    +   ++++    G+VRV  +R + ++  + G +V +            
Sbjct: 14  RLDRALADAL-GLGRASVKRAFLLGEVRVRGRRARASDPAEPGALVELD----------- 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGFLKSWV 137
               ++      +        +L E  ++ V +KPAG++V            +  +  + 
Sbjct: 62  ----VEEPAGAPEPEPEAPLAVLVETPRLVVVDKPAGVAVHPLAPGEGGTLANAVVARFP 117

Query: 138 DSKGQKPRL-----THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +  G  P         RLD ETSG +  AR   A Q L      R ++KIY +LV G   
Sbjct: 118 ECAGASPEPREGGAVQRLDLETSGCVTFARDPEAWQELHARLSAREVEKIYLALVAGRMA 177

Query: 193 NKKECIANWLLKKSH----IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
                      +          +    ++        A +H+ V   F +    L ++  
Sbjct: 178 TVGVSSVPLAQRGGRAIPVPDPETEERLRAKGLRPRPAETHWDVARRF-ETHTLLRVRIV 236

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT 308
           TG  HQ+R H  H+G P+ GD  Y  +       P   + +LHA  + L  P+G R++  
Sbjct: 237 TGVMHQIRAHLAHLGHPVAGDALYGGD---AAALPGLRRQFLHATRLALEGPDGERVEAE 293

Query: 309 APLPAHMVKTWDSLG 323
           +PLP  +      LG
Sbjct: 294 SPLPPELEAVLARLG 308


>gi|166364334|ref|YP_001656607.1| pseudouridine synthase [Microcystis aeruginosa NIES-843]
 gi|166086707|dbj|BAG01415.1| pseudouridine synthase [Microcystis aeruginosa NIES-843]
          Length = 299

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 74/309 (23%), Positives = 124/309 (40%), Gaps = 29/309 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  ++  + L  ++   Y H +       + S  + V+ +    +  ++ GQ +      
Sbjct: 12  ISKNQAGLSLLAYYTGKYCHSSPEEWLDRILSAAILVNGRPACPDTVLEIGQQLTYQ--- 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                              T+    L   +LYED+++ V  KP+G+ V  G G   H   
Sbjct: 69  ---------------RPPWTEPEVPLFFEVLYEDAEVLVVAKPSGLPVLAGGGFLEH--- 110

Query: 132 FLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            L   V     +  P   HRL + TSGI+++A+++ A   L++  R  +I KIY +LV  
Sbjct: 111 TLIHLVHQHYAEVTPYPIHRLGRGTSGIVLMAKSKPARAKLSQQMREGKITKIYRALVGQ 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   I   + K +H    +V+    +      A S  +V+         LE++  T
Sbjct: 171 GDIPDNFTINQAIGKIAHPILGHVYGALTD---GLSARSDGRVLKKHPDS-TLLEVRIFT 226

Query: 250 GRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           GR HQ+R+H    G P++GD  Y           P     YLHA  +   HP  G R+ I
Sbjct: 227 GRPHQIRIHLAFFGYPLIGDPLYGLGGLPRPDAVPGDCGYYLHANQIVFNHPSTGERISI 286

Query: 308 TAPLPAHMV 316
               P  +V
Sbjct: 287 CCQAPPELV 295


>gi|149279581|ref|ZP_01885710.1| ribosomal large subunit pseudouridine synthase D [Pedobacter sp.
           BAL39]
 gi|149229617|gb|EDM35007.1| ribosomal large subunit pseudouridine synthase D [Pedobacter sp.
           BAL39]
          Length = 228

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 65/228 (28%), Positives = 107/228 (46%), Gaps = 15/228 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQET 154
            +LYED+ +    K AG  VQ        +D  +K ++     KP      + HRLD+  
Sbjct: 7   DILYEDNHLIAICKRAGDIVQVDETGDEPLDEQVKKYLAKTYNKPNSAFLGVVHRLDRPV 66

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+T  A + +   F+ R ++K YW++V   P      + +WL+K      + V 
Sbjct: 67  SGVILFAKTSKALERMNAVFKNREVKKTYWAIVRNKPAKPSGTLVHWLVKNPQ--KNVVT 124

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             +    G+  A   +++I      +  +E+ P TGR+HQ+RV    +GCPIVGD+KY  
Sbjct: 125 PHQSEVPGSQRAELSYRLIGEL-NGYYLIEVDPLTGRSHQIRVQLSTLGCPIVGDNKYGY 183

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH-MVKTWD 320
                  S     + LHAR +   HP     + I A LP     + ++
Sbjct: 184 PRGSRKGS-----ICLHARRLQFVHPVKKEPVNIFAKLPVDGFWEKFE 226


>gi|238792761|ref|ZP_04636392.1| tRNA pseudouridine synthase C [Yersinia intermedia ATCC 29909]
 gi|238727869|gb|EEQ19392.1| tRNA pseudouridine synthase C [Yersinia intermedia ATCC 29909]
          Length = 257

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 100/237 (42%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I   NKPAG  V      +      +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L+  F   +IQK Y ++V G              +   I   +     + +
Sbjct: 64  ALSSDVARALSAQFEQHQIQKTYHAVVRGYVLEGGTVDYAMSEELDKIADKH----SKQD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    +++H++ +               +F  LE++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPSVTHYQPLAQVEVPIAIGRYDTARFSLLELKPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            +      +G        +L LHA ++ L HP  G  L  T              G+
Sbjct: 180 AHGDLRQNRGIAQHFGCPRLMLHASHLQLNHPVTGEVLSFTVRWDESWQGLMSHFGW 236


>gi|145628404|ref|ZP_01784205.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae 22.1-21]
 gi|144980179|gb|EDJ89838.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae 22.1-21]
          Length = 219

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 108/229 (47%), Gaps = 16/229 (6%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            +++ +  L  + D     ++Y+D+ + V NKP+G+    G+   Y+      S V  K 
Sbjct: 2   ALIEYNPPLEPYLD-----IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKF 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGI+V A ++AA + L   FR R  +K Y ++VWG  +N    +   
Sbjct: 55  GFCEPAHRLDMATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLP 114

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           ++       +     + +      A++ F+V+         +++ P TGR+HQLR+H L 
Sbjct: 115 MICD----WENRPRQRLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLA 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +G PI+GD  Y           I ++L LHA  + + HP  G  +   A
Sbjct: 171 LGHPILGDKFYSHPQAKA----ISSRLCLHAEELTITHPITGETMTFNA 215


>gi|299142856|ref|ZP_07035984.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella oris C735]
 gi|298575724|gb|EFI47602.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella oris C735]
          Length = 221

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 110/229 (48%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + +  K +G  VQG       +   +K ++  K QKP      + HRLD+  +
Sbjct: 3   IVYEDNHLIIVYKHSGEIVQGDKTGDVPLSEDVKCYLKEKYQKPGNVFLGVVHRLDRPVT 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L + FR   + K YW++   +P   +  +++WL++       Y + 
Sbjct: 63  GLVVFAKTSKALTRLNKMFRDGEVHKTYWAITKNLPPQPEGTLSHWLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +  AI  +++I   +  +C LE+   TGR HQ+R    HMGCPI GD KY A 
Sbjct: 122 -DHEVPHSKKAILKYRLIG-QSDHYCLLEVNLMTGRHHQIRCQLAHMGCPIKGDLKYGAQ 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 S     + L A +++  HP   + + + +PLP    K W   G
Sbjct: 180 RSNPDGS-----ICLLAHHVEFVHPVSKQLISLDSPLPED--KLWQVWG 221


>gi|313500106|gb|ADR61472.1| Pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 211

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 64/215 (29%), Positives = 100/215 (46%), Gaps = 11/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L+ D+ I V NKP  +    G     + D  +    ++      + HRLD ETSGI+
Sbjct: 6   VQILFVDAAILVINKPTLLLSVPGRA-EDNKDCLITRLQENGYPDALIVHRLDWETSGII 64

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR   + + L+  F  R  +K Y +L WG P      I   L           HVV  
Sbjct: 65  LLARDADSHRELSRQFHDRETEKAYTALCWGQPALDSGSIDLPLRYDPPT--KPRHVV-- 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +   +A++ +++++      C +E+ P TGR+HQLRVH L +G P++GD  Y      
Sbjct: 121 DHEQGKHALTFWRIVERCGD-HCRVELTPITGRSHQLRVHMLSIGHPLLGDRLY----AN 175

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                   +L LHA  +   HP  G RL+   P P
Sbjct: 176 PQALAAHERLCLHASMLSFTHPVSGQRLKFECPAP 210


>gi|306830382|ref|ZP_07463552.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325977346|ref|YP_004287062.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|304427407|gb|EFM30509.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325177274|emb|CBZ47318.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 286

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 59/289 (20%), Positives = 111/289 (38%), Gaps = 32/289 (11%)

Query: 23  RWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +  + H   I    ++  LR    +R++ + + + + +++G  + +    +         
Sbjct: 18  KLLEEHLL-IPR-KIRHFLRTKKHLRINGEMINWQSLVKTGDTIHLIFDDD--------- 66

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
              D                LY+D  + + NKP G+   G       +   + ++V   G
Sbjct: 67  ---DYPQKEIPFGQAELVDCLYQDEHLIIVNKPEGMKTHGNEPNEIALLNHVSAYV---G 120

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           Q   + HRLD ETSG ++ A+       +      + I + YW+LV G  + K +   + 
Sbjct: 121 QTCYVIHRLDMETSGAVMFAKNPFVLPIINRLLENKDIAREYWALVQGKFEPKHQVFQDK 180

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +  H     V     + K    A++    +  F      ++ +  TGRTHQ+RVH   
Sbjct: 181 IGRDRHDRRKRV----VDRKNGQTALTIVDRLKVFPNG-TLVKCRLKTGRTHQIRVHLSA 235

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
               I+GD  Y              +L LHA  +   HP    ++ + A
Sbjct: 236 HNHAIIGDPLYSKIPA--------KRLMLHAHKLSFTHPFTLEKISVEA 276


>gi|330996580|ref|ZP_08320462.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
 gi|329573136|gb|EGG54755.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
          Length = 224

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 68/220 (30%), Positives = 109/220 (49%), Gaps = 14/220 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
            ++YED+ + + +K +   VQG       +   +K ++  K  KP      + HRLD+  
Sbjct: 2   DVVYEDNHLIIVDKSSSEIVQGDKTGDKPLAEMVKEYIKQKYHKPGNVFLGVVHRLDRPV 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V ART  A   L E FR + + K YW++V   P  ++  + +WL++       Y +
Sbjct: 62  SGLVVFARTGKALARLNEMFRTKEVHKTYWAIVGNCPPAEEGELVHWLVRNEKQNKSYAY 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              + + GA  AI  +K+I   ++++  LE+   TGR HQ+R     MGCPI GD KY A
Sbjct: 122 --DKEKPGAKKAILDYKLIGR-SERYFLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKYGA 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPA 313
                  S     + LHAR +   HP     + + AP+P 
Sbjct: 179 PRSNPDGS-----ICLHARRVRFVHPVSKQEIDVEAPVPE 213


>gi|255015082|ref|ZP_05287208.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_7]
 gi|256840691|ref|ZP_05546199.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           sp. D13]
 gi|256737963|gb|EEU51289.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           sp. D13]
          Length = 224

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 70/228 (30%), Positives = 109/228 (47%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I   +K     VQG       +   LK+W+  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIAVDKTCREIVQGDKTGDKPLSEMLKAWLKEKYCKPGNVFVGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR+  ++K YW++V   P   +  + +WL++       Y + 
Sbjct: 63  GVVIFAKTSKALSRLNEMFRVGEVRKTYWAIVKNRPPQDEGELVDWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  AI  +K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY  +
Sbjct: 123 TER--PNAKKAILRYKLI-AHSDNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKYGFD 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                       + LHAR  +  HP     ++I AP+P      W +L
Sbjct: 180 RSNK-----DGGISLHARSAEFIHPVSKENVRIVAPVPDD--NLWKAL 220


>gi|313624349|gb|EFR94381.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria innocua FSL J1-023]
          Length = 208

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 54/221 (24%), Positives = 100/221 (45%), Gaps = 22/221 (9%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGILVVA 161
           + + NKPAG++        YH  G + ++V    +         +  RLD+ETSG++++A
Sbjct: 1   LLIINKPAGMASIPSQ---YHPTGSVANFVKGHYENQGLTSAIHIVTRLDRETSGLMLIA 57

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           + R A   L+   +   +++ Y +   G  +     I   + +K     D   + +    
Sbjct: 58  KNRYAHARLSSFLQQGLLKRRYQAFTSGTLEEAAGSIEAPIGRK-----DVSIMERFVTP 112

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
              YA ++++V+  +   F  L +Q  TGRTHQ+RVH  ++G P++GD  Y  +      
Sbjct: 113 EGKYAKTNYEVLMRY-NGFDHLAIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------ 165

Query: 282 SPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
             +  +  LH+ ++ L HP     +    PLP  M +    
Sbjct: 166 QELLKRQALHSCHLHLVHPVTEEYMAFDLPLPEDMEQIIQK 206


>gi|237750038|ref|ZP_04580518.1| pseudouridine synthase D [Helicobacter bilis ATCC 43879]
 gi|229374449|gb|EEO24840.1| pseudouridine synthase D [Helicobacter bilis ATCC 43879]
          Length = 326

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 69/335 (20%), Positives = 137/335 (40%), Gaps = 34/335 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD   +     I+     + + S  V++++K  K +  ++ G  + I  + N      
Sbjct: 12  MRLDNALQEILK-ISRSQASQWIESNLVKMNEKNTKKSQILKKGACIEIYTIKNTSK--- 67

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +N  +    L   +++E+S   + NKP  + V     +    +  L  ++ 
Sbjct: 68  --------VINTDELIQGLDIEVIHENSDYLILNKPRNLVVHHAPSV---KEVTLTDYLS 116

Query: 139 SKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +K  +           + HRLD++TSG ++VA+  A+     E  + R + +IY   V  
Sbjct: 117 AKNYELSTINGEMRFGIVHRLDKDTSGAILVAKNNASHLRFAEMLQNRTMGRIYIC-VIN 175

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK-VIDCFAQKFCWLEMQPH 248
                   +  ++ +  +       + K+    A  + S F+ +++     F  + ++  
Sbjct: 176 KALQHNTFVECYMGRNPNNRLKMAKLDKEKYPFARDSKSEFRKIMESKNGVFELIGVRLF 235

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT 308
           +GRTHQ+RVH   +   I GD  Y      N  S  + K+ LHA+ +     +G     +
Sbjct: 236 SGRTHQIRVHLSTLQRYIYGDMLYSPE---NLKSTYKTKMLLHAQLLYF---DGN--VFS 287

Query: 309 APLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQ 343
           A +P  ++K  +     Y+  L       QDE ++
Sbjct: 288 AKIPKDLLKFLNENFINYESKLEAFLSQWQDELRK 322


>gi|148264981|ref|YP_001231687.1| RluA family pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146398481|gb|ABQ27114.1| pseudouridine synthase, RluA family [Geobacter uraniireducens Rf4]
          Length = 296

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 70/321 (21%), Positives = 124/321 (38%), Gaps = 47/321 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +   +   +++ + +N  P  +   L+K+L +G + V+         ++ G  V +    
Sbjct: 6   ISETDHCRQVESFLQNLLPSASHSYLRKLLTAGHLAVNGTPGVSGTILRLGDTVTLKESS 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID- 130
                + K +  LD               +L+ED  I +FNK  G+ +   + +      
Sbjct: 66  KTSAFLRKARPELD---------------ILHEDQWIMIFNKAPGLPMHHAAEVDERNLV 110

Query: 131 ---GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                L +  D    K R  +RLD+ TSG +++A++  AA           + K+Y +LV
Sbjct: 111 DLGTKLLAGRDGGSVKLRPVNRLDRGTSGAVILAKSSMAAAMFGRLIMDEGLGKLYLALV 170

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G        I+  L                       A + ++V+   +    ++ + P
Sbjct: 171 EGELAED-GVISVPL-------------------EGKEAETRYRVLFHRSD-CTFVAVYP 209

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGR HQ+R H   +G PI GD +Y       F         LH+    + HP  G  LQ
Sbjct: 210 VTGRMHQIRQHFKFIGHPIRGDRRYGGQPLPGFAGN-----ALHSFRTSIVHPATGETLQ 264

Query: 307 ITAPLPAHMVKTWDSL-GFKY 326
           + APL    +    +L G +Y
Sbjct: 265 VFAPLSKEFLTLLKNLSGERY 285


>gi|162533083|ref|YP_001621407.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213969739|ref|ZP_03397874.1| Pseudouridine synthase [Pseudomonas syringae pv. tomato T1]
 gi|301382971|ref|ZP_07231389.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato Max13]
 gi|302063259|ref|ZP_07254800.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato K40]
 gi|302131645|ref|ZP_07257635.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato NCPPB 1108]
 gi|118201621|gb|ABK79684.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213925547|gb|EEB59107.1| Pseudouridine synthase [Pseudomonas syringae pv. tomato T1]
 gi|331019062|gb|EGH99118.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. lachrymans str. M302278PT]
          Length = 211

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 64/214 (29%), Positives = 100/214 (46%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++++D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIHQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ +KV++      C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEAGKHALTFWKVVERH-DSHCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL    P P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERLTFECPAP 210


>gi|323140403|ref|ZP_08075332.1| pseudouridine synthase, RluA family [Phascolarctobacterium sp. YIT
           12067]
 gi|322415088|gb|EFY05878.1| pseudouridine synthase, RluA family [Phascolarctobacterium sp. YIT
           12067]
          Length = 217

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 60/226 (26%), Positives = 107/226 (47%), Gaps = 20/226 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQET 154
            S+L YED  + + +KPAG+ V    S     +  ++K++ ++ G         RLD+ T
Sbjct: 7   PSMLAYEDDFLLIIDKPAGMLVHPTVSERGTTLYDYVKAYYEATGINAVIHPVSRLDRNT 66

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A+       L++     +++K Y +L  G  +  +  I   + +K    G  + 
Sbjct: 67  SGLVIFAKEPIVQHWLSQQ----QVEKEYLALACGRFETSEGIIEAPIARKE---GSIIE 119

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                 +G  YA + ++V+  ++     L+++  TGRTHQ+RVH   +G P+V D+ Y  
Sbjct: 120 RCVDYTRG-KYAKTAYEVLASYS-NHTLLKVRLFTGRTHQIRVHLASIGHPLVNDNLYG- 176

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
                 T   Q +  LHA  +   HP     L+IT  LP  ++K  
Sbjct: 177 ------TPGPQARHALHAYRLAFKHPVSDVFLEITRSLPNDLLKLL 216


>gi|16329580|ref|NP_440308.1| hypothetical protein slr1592 [Synechocystis sp. PCC 6803]
 gi|3915463|sp|P72970|Y1592_SYNY3 RecName: Full=Uncharacterized RNA pseudouridine synthase slr1592;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|1652063|dbj|BAA16988.1| slr1592 [Synechocystis sp. PCC 6803]
          Length = 291

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 70/300 (23%), Positives = 124/300 (41%), Gaps = 30/300 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD ++   Y H      Q+ +  GQ+ VD K V     +Q+GQ +               
Sbjct: 2   LD-FYSQRYLHSERQAWQERIEQGQIEVDGKTVDPTYPLQAGQTLTYWRS---------- 50

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                      +    L+  +L+ D  ++  +KP+G+ V  G    YH    L+      
Sbjct: 51  --------PWVEPEVPLQLSVLHRDEDLWAIDKPSGLPVLPGGDFVYH--TVLEQLKIQY 100

Query: 141 GQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            Q+     HRL   TSG+L++ R+    + L+  FR    +KIY +++      +K    
Sbjct: 101 PQESLFPLHRLGTGTSGLLLLGRSTLGRRELSRQFREHICRKIYRTVIGPCDLPEKFECH 160

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + K  +    Y++    +      A S+ +++    +K  WLE++  TGR HQ+R+H 
Sbjct: 161 QAIGKIPYPQLGYIYAASSH---GKPAQSYGRILARSPEK-TWLEVEIRTGRPHQIRIHL 216

Query: 260 LHMGCPIVGDHKYCAN---FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             +G P++GD  Y             P      LH+  +   H    + +++TAPLP  +
Sbjct: 217 ASLGYPLLGDRLYGPGGVPINCRTARPSDGGYTLHSYQLGFLHLHTQQAIKLTAPLPPEL 276


>gi|330833599|ref|YP_004402424.1| pseudouridine synthase [Streptococcus suis ST3]
 gi|329307822|gb|AEB82238.1| pseudouridine synthase [Streptococcus suis ST3]
          Length = 289

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 59/268 (22%), Positives = 109/268 (40%), Gaps = 29/268 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              VRV+ + + + + I +G ++ +            E+ I     NL +         L
Sbjct: 37  KKHVRVNGELINWQSPIAAGDLLELTFDQEDY----PEKSIPLGQANLVEE--------L 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG ++ A+
Sbjct: 85  YQDEHLIIVNKPEGMKTHGNDPTEIALLNHVSAYV---GQTCYVVHRLDMETSGAILFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      + I + Y +L  G  +     I + + +  H     V     + + 
Sbjct: 142 NPFILPILNRLLEDKVIYRDYLALCQGQLRKTDWTITDKIGRDRHDRRKRV----VDNRK 197

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++  +++   ++    +  +  TGRTHQ+RVH  H    ++GD  Y          
Sbjct: 198 GQVALTQVRLLKTLSKN-SLVTCRLQTGRTHQIRVHLAHHDHALIGDPLYS--------Q 248

Query: 283 PIQNKLYLHARYMDLPHPEG-GRLQITA 309
               +L LHA+ + L HP     +++ A
Sbjct: 249 VAAPRLMLHAQKLSLTHPLTLEEIRVEA 276


>gi|66044855|ref|YP_234696.1| pseudouridine synthase [Pseudomonas syringae pv. syringae B728a]
 gi|63255562|gb|AAY36658.1| Pseudouridine synthase [Pseudomonas syringae pv. syringae B728a]
          Length = 211

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 63/214 (29%), Positives = 101/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++++D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIHQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEGGKHALTFWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G R+      P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERMTFECAAP 210


>gi|88857814|ref|ZP_01132456.1| tRNA pseudouridine synthase C [Pseudoalteromonas tunicata D2]
 gi|88819431|gb|EAR29244.1| tRNA pseudouridine synthase C [Pseudoalteromonas tunicata D2]
          Length = 244

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 59/244 (24%), Positives = 100/244 (40%), Gaps = 17/244 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D      +KP+G+ V       +     ++   D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILFQDEHFVAIDKPSGLLVHRSFLDKHETQFAMQMLRDQLGQHVFPVHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +  AA+ + E F   R+ K Y +LV G   + +        +   I   Y        
Sbjct: 64  ALSSDAARKMNEQFSDHRVTKRYLALVRGFAPDYRLLDRPLKEELDKIADKYADQ----N 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A + F+ +               ++  +E  P TGR HQ+R H   +  PI+GD 
Sbjct: 120 KAPQAAQTEFRCLQQVTLPIALGKYPTIRYSLVECFPKTGRKHQIRRHLNFLSHPIIGDV 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
            +  N   +F      + +L L A+ +   HP  G ++ I APL    +  ++   +   
Sbjct: 180 NHGDNQHNHFFWQHFERQRLMLFAQRLTFMHPYSGQKIIIEAPLGESTLALFNQFSWPDK 239

Query: 328 RNLY 331
              Y
Sbjct: 240 EAAY 243


>gi|238754814|ref|ZP_04616165.1| tRNA pseudouridine synthase C [Yersinia ruckeri ATCC 29473]
 gi|238706974|gb|EEP99340.1| tRNA pseudouridine synthase C [Yersinia ruckeri ATCC 29473]
          Length = 257

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 101/237 (42%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D   Q     HRLD+ TSG+L++
Sbjct: 4   ILYQDEHMVAVNKPAGWLVHRSWLDRNETVFVMQTVRDQIDQHVYTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F    ++K+Y ++V G              +   I   +       +
Sbjct: 64  ALSSDVARLLSQQFEQHEVRKVYHAVVRGYVLEDDTLDYALTEELDKIADKFSSQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPKSAVTHYRAMAQAEMPVAIGRYETARYSLMELTPETGRKHQLRRHMAHIRHPIIGDS 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            +      +G       ++L LHA ++ L HP  G  L ++A           S G+
Sbjct: 180 THGDLRQNRGVAQHFDCSRLMLHASHLSLNHPVTGEPLNLSARWDCSWQGIMSSFGW 236


>gi|325577153|ref|ZP_08147637.1| pseudouridine synthase A [Haemophilus parainfluenzae ATCC 33392]
 gi|325160735|gb|EGC72856.1| pseudouridine synthase A [Haemophilus parainfluenzae ATCC 33392]
          Length = 219

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/214 (28%), Positives = 100/214 (46%), Gaps = 13/214 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y+D+ I V NKP+G+    G+   Y+      S V  K       HRLD  TSGI+
Sbjct: 14  LDIIYQDNHICVVNKPSGLLSVPGNQPEYYDSAM--SRVKEKFGFCEPAHRLDMATSGII 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK-SHIGGDYVHVVK 217
           + A ++AA + L   FR R  +K Y +LVWG  +     I   ++    +     +  V 
Sbjct: 72  LFALSKAADKELKRQFREREPKKYYQALVWGHLEQDSGEINLPMICDWENRPRQRIDFVF 131

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A++ ++V++        +++ P TGR+HQLR+H L +G PI+GD  Y     
Sbjct: 132 -----GKRAVTFYEVLERLPTNCTRVKLTPITGRSHQLRLHTLALGHPILGDKFYSHPQA 186

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
              +     +L LHA  + + HP  G  +   A 
Sbjct: 187 KAMS----PRLCLHAEELTITHPITGEKMTFRAE 216


>gi|84500695|ref|ZP_00998944.1| ribosomal large subunit pseudouridine synthase A [Oceanicola
           batsensis HTCC2597]
 gi|84391648|gb|EAQ03980.1| ribosomal large subunit pseudouridine synthase A [Oceanicola
           batsensis HTCC2597]
          Length = 215

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/221 (28%), Positives = 102/221 (46%), Gaps = 13/221 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   +++ED ++ + +KPAG+    G G   H+   L + V +      L HRLD+
Sbjct: 6   DPPDTPLSVIHEDQELLLVDKPAGLLSVPGKG--EHLADCLLTRVQAAFPTALLVHRLDR 63

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG++V A T  A +HL   F  RR +K Y + V G  + +   +   L    ++    
Sbjct: 64  DTSGVMVFALTHHAQRHLGLQFEHRRTRKTYVARVHGHLEPRSGTVDLPL----NVDWPN 119

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                 + +    A + +KV          + + P TGR+HQLRVH L +G PI+GD  Y
Sbjct: 120 RPRQMVDHENGRAARTDWKV-QRHGDGETRVRLMPRTGRSHQLRVHMLALGHPILGDPFY 178

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                 +       +L LH+  + L HP+GG+ +   A  P
Sbjct: 179 AEGAARDHP-----RLMLHSEELRLLHPDGGKGMSFRAKAP 214


>gi|126139263|ref|XP_001386154.1| DRAP deaminase [Scheffersomyces stipitis CBS 6054]
 gi|126093436|gb|ABN68125.1| DRAP deaminase [Scheffersomyces stipitis CBS 6054]
          Length = 585

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 59/257 (22%), Positives = 110/257 (42%), Gaps = 26/257 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +  + +   +    +K + +GQV ++KK    ++ +++G ++             +E
Sbjct: 108 LDIFV-DEFRDRSAEYYKKAIDAGQVTLNKKPANLDSIVRNGDLISHRTYRKEPPVSSRE 166

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            K                  ++YED  +   +KP+GI V       Y  +   K +    
Sbjct: 167 IK------------------IVYEDDDLIAIDKPSGIPVHPTG--RYRYNTITKIFQHEM 206

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G+     +RLD+ TSG++ + +T   A  L +  R R ++K Y + V G    ++  +  
Sbjct: 207 GKVVHPCNRLDRLTSGLMFLGKTAKGADKLVKQIRERSVRKEYIARVKGEFPLEEVEVDQ 266

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHA 259
            +   +H  G    + + + K    A + FK +    +     ++  P TGRTHQ+RVH 
Sbjct: 267 PMRTIAHKLG----LNRIDLKEGKDAKTAFKRVSYDPEHDTSIVKCIPLTGRTHQIRVHL 322

Query: 260 LHMGCPIVGDHKYCANF 276
            ++G PI  D  Y   F
Sbjct: 323 QYLGHPIANDPIYSNKF 339


>gi|332533880|ref|ZP_08409735.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332036688|gb|EGI73152.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 551

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 105/243 (43%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++K   + D+ + LT  +      ++Y+D  + V NKPA      G  I   +
Sbjct: 320 CQPILGHMLKGLDVEDNPL-LTNPAQGKDLSIVYKDDDLLVVNKPAEFLSVPGVNIDDSV 378

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K+    +   P + HRLD  TSG+L++A  +   + L + F  R I K Y +LV G
Sbjct: 379 YMRIKTQF-PEASGPLIVHRLDMSTSGLLMIALNKRVHKALQKQFIERTIDKRYVALVNG 437

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   I   L+         +            +++ ++V++        L++ P T
Sbjct: 438 NVAEDSGVIDLPLVLDFDDKPRQMVCYTH----GKPSLTTWQVLERN-NNITRLQLYPKT 492

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVH  H   +  PI+GD  Y             ++L+LHA Y+   HP    RL
Sbjct: 493 GRTHQLRVHCAHSLGLNMPIIGDTHYGQK---------ADRLHLHAEYLAFTHPITLKRL 543

Query: 306 QIT 308
           +  
Sbjct: 544 EFE 546


>gi|126207799|ref|YP_001053024.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae L20]
 gi|126096591|gb|ABN73419.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
          Length = 237

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 66/211 (31%), Positives = 101/211 (47%), Gaps = 12/211 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+      + V  K       HRLD  TSGIL+ A
Sbjct: 32  VYRDNHILVINKPSGLLSVPGNRPEYYDSAM--TRVQQKYGFTEPAHRLDMATSGILLFA 89

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWLLKKSHIGGDYVHVVKQN 219
            ++AA + L   FR R  +K Y +L+WG    K       N+ L           +  + 
Sbjct: 90  LSKAAEKELKRQFRDREPKKHYIALLWGKLGEKVGDTGEMNFPLICDWENRPRQKICYER 149

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y +    +
Sbjct: 150 ---GKKAITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGDKFYASPLAKS 206

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
               +  +L LHA  + + HP  G  +  TA
Sbjct: 207 ----LSPRLCLHAESLSITHPITGEAMTFTA 233


>gi|171742473|ref|ZP_02918280.1| hypothetical protein BIFDEN_01585 [Bifidobacterium dentium ATCC
           27678]
 gi|283456441|ref|YP_003361005.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           dentium Bd1]
 gi|306822383|ref|ZP_07455762.1| RluA family RNA pseudouridine synthase [Bifidobacterium dentium
           ATCC 27679]
 gi|309802127|ref|ZP_07696236.1| pseudouridine synthase, RluA family [Bifidobacterium dentium
           JCVIHMP022]
 gi|171278087|gb|EDT45748.1| hypothetical protein BIFDEN_01585 [Bifidobacterium dentium ATCC
           27678]
 gi|283103075|gb|ADB10181.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           dentium Bd1]
 gi|304554381|gb|EFM42289.1| RluA family RNA pseudouridine synthase [Bifidobacterium dentium
           ATCC 27679]
 gi|308221207|gb|EFO77510.1| pseudouridine synthase, RluA family [Bifidobacterium dentium
           JCVIHMP022]
          Length = 312

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/320 (20%), Positives = 124/320 (38%), Gaps = 19/320 (5%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V   +     R D         I+      ++ +GQ RV  + +  ++ +Q+G+ V  
Sbjct: 3   RLVPAPDALVGKRFDVAVAKML-GISRAKAADLIETGQARVLGRDIAKSSSLQAGETVEF 61

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             V         E + +   + +    D +  +        +      G +V G      
Sbjct: 62  DIVEERS-----EPEPIAHDMAVVYEDDDVVVVDKPVGVAAHASVGWTGPTVLGS----- 111

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +D  ++        +  +  RLD  TSG+++V ++  A   +   F    + K Y +LV
Sbjct: 112 LLDRGVRITSYGAAGRQGIVSRLDVGTSGLMLVCKSELAYVEMRRQFAEHEVVKTYHALV 171

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  K  K  I   + +                     AI+H+ V++ F +    + +  
Sbjct: 172 QGNLKEDKATIEAPIGR-----AKVSDFRFCVTPAGKEAITHWDVMERFGE-ATLVSVNL 225

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            TGRTHQ+RVH   +G P+VGD  Y AN + +    ++ + +LHA  ++  HP       
Sbjct: 226 ETGRTHQIRVHFSSIGHPLVGDPMYGANPQLSEALGLE-RQWLHAMQLEFRHPRTHVWTT 284

Query: 307 ITAPLPAHMVKTWDSLGFKY 326
           + +  P  +    D +  ++
Sbjct: 285 VRSHYPVDLQHALDVMRNRH 304


>gi|228477070|ref|ZP_04061708.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Streptococcus salivarius SK126]
 gi|228251089|gb|EEK10260.1| ribosomal large subunit pseudouridine synthase, RluD   family
           [Streptococcus salivarius SK126]
          Length = 298

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 70/314 (22%), Positives = 128/314 (40%), Gaps = 33/314 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           R+  + K H   I+   L KI    G + V+ +       +  G VV I           
Sbjct: 12  RVKTFLKEH--DISKGLLAKIKFEGGHIWVNGEEQFATYPVHEGDVVAI----------- 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV- 137
              +I D + + T         ++YED    V NKP G +          +  F+K    
Sbjct: 59  ---EIPDEAPHETLKPIPFDLDIVYEDDNFLVINKPYGYASIPSVNHDNTMANFVKHHFV 115

Query: 138 --DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NK 194
             +   Q+  +  RLD++TSG+++ A+   A   + +  + + I+K Y++LV G  K  +
Sbjct: 116 SNNYPNQRVHIVTRLDKDTSGLMLFAKHGYAHARMDKQLQQKSIKKHYYALVEGDTKLEE 175

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I   + +          + ++  K   YA + ++++  + +    +++  HTGRTHQ
Sbjct: 176 QGEIIAPIARDVD-----SIITRRVHKSGKYAHTSYRLVADYGR-VKLVDINLHTGRTHQ 229

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA-PLPA 313
           +RVH  H+G P++GD  Y  +           +  LH   +    P   +  + A  L  
Sbjct: 230 IRVHFAHLGLPLLGDDLYGGSL-----DYGIKRQALHCHRLAFIDPFTKKEMVHASSLTD 284

Query: 314 HMVKTWDSLGFKYD 327
                  +L  K D
Sbjct: 285 DFETVIMNLQTKKD 298


>gi|323343983|ref|ZP_08084209.1| ribosomal large subunit pseudouridine synthase [Prevotella oralis
           ATCC 33269]
 gi|323094712|gb|EFZ37287.1| ribosomal large subunit pseudouridine synthase [Prevotella oralis
           ATCC 33269]
          Length = 233

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 65/229 (28%), Positives = 109/229 (47%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I + +K +G  VQG       +   +K ++  K  KP      + HRLD+  +
Sbjct: 3   VLYEDNHIIIVSKRSGEIVQGDKTGDVPLSETVKQYIKDKYAKPGNVFIGVVHRLDRPVA 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  A   L   FR   + K YW++    P+  +  + +WL++       Y + 
Sbjct: 63  GIVVFAKTSKALSRLNSMFRDGEVHKTYWAITKNCPQQTEGTLTDWLVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +  A+  + +I   ++++  +E+Q  TGR HQ+R     +GCPI GD KY A 
Sbjct: 122 -DHEVPNSKKAVLKYDIIG-KSERYTLIEVQLMTGRHHQIRCQLARIGCPIKGDLKYGAP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 S     + L AR ++  HP   + + +TAPLP      W ++ 
Sbjct: 180 RSNTDGS-----ISLLARGVEFVHPVSKKTISVTAPLPDD--NLWQAIA 221


>gi|221640995|ref|YP_002527257.1| Ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides KD131]
 gi|221161776|gb|ACM02756.1| Ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides KD131]
          Length = 224

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 65/220 (29%), Positives = 106/220 (48%), Gaps = 13/220 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
              +   L++ D++I V +KPAG+    G G        L   +     +  L HRLD++
Sbjct: 16  PPDVPLSLIHHDAQIVVVDKPAGLLSVPGKGED--KADCLIERLRGVFPEILLVHRLDRD 73

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V A T+AA   L + F  R+ +KIY + V G  + ++  +   L           
Sbjct: 74  TSGVMVFALTKAAQGALGQQFEKRQTKKIYVARVAGRLEPREGRVDLPLCVD-WPNRPKQ 132

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           HV   + +    A + ++V+    ++   + + P TGR+HQLRVH    G PI+GD  Y 
Sbjct: 133 HV---DHENGRPAQTDWRVVKYLPKE-TRVRLMPVTGRSHQLRVHMAETGHPILGDALYS 188

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                +F      +L LHA  + + HP+ G+ L  +AP P
Sbjct: 189 EGAARDFP-----RLMLHAESLRVRHPDTGKSLTYSAPCP 223


>gi|262275057|ref|ZP_06052868.1| ribosomal large subunit pseudouridine synthase A [Grimontia
           hollisae CIP 101886]
 gi|262221620|gb|EEY72934.1| ribosomal large subunit pseudouridine synthase A [Grimontia
           hollisae CIP 101886]
          Length = 240

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 65/215 (30%), Positives = 107/215 (49%), Gaps = 16/215 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y+D  I   NKP+G+    G   A++   +  S + ++     L HRLD  TSG++
Sbjct: 14  LDVIYQDDDIIAINKPSGLLTNPGRDPAHYDSAW--SRIKAEYPDAELVHRLDMSTSGLI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+ + A +HL   FR R   K+Y++ VWG  + +K  +   L+       D+ +  KQ
Sbjct: 72  VFAKHKEAERHLKAQFRERVTHKLYYARVWGHVEQEKGRVDLPLI------CDWPNRPKQ 125

Query: 219 NE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               +    +++ ++VI    +K   + + P TGR+HQLRVH L +  PIVGD  Y    
Sbjct: 126 KVCFENGKPSVTDYEVIKR-EKKTTLVRLLPITGRSHQLRVHMLALDHPIVGDEFYAPPQ 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
              ++     +L LHA  +   HP  G  + + AP
Sbjct: 185 AQKYS----PRLQLHAGELCFLHPGSGDPMHLAAP 215


>gi|146320632|ref|YP_001200343.1| YlyB [Streptococcus suis 98HAH33]
 gi|145691438|gb|ABP91943.1| YlyB [Streptococcus suis 98HAH33]
          Length = 243

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 44/230 (19%), Positives = 94/230 (40%), Gaps = 27/230 (11%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RLD+   +    ++     + +++GQV V+ +  K    +Q G V+            
Sbjct: 9   GIRLDKALSD-LTDLSRSVANEQIKAGQVLVNGQPKKAKYSVQVGDVLTYQ--------- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKS 135
                 +     +   ++ +   ++++D  + V NKP G+ V   +G      ++  L  
Sbjct: 59  ------IPEVEEIDYVAEDIPLEIVFQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALLYH 112

Query: 136 WVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HR+D++TSG+L++A+   A   L    + ++  + YW++V G  
Sbjct: 113 VKDLSGINGVLRPGIVHRIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIVHGNL 172

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            N +  I   + +            K        A++ F+V++ F     
Sbjct: 173 PNDRGVIEAPIGRSEKDRKKQAVTAK-----GKEAVTRFQVLERFGDYTW 217


>gi|148827905|ref|YP_001292658.1| hypothetical protein CGSHiGG_07040 [Haemophilus influenzae PittGG]
 gi|148719147|gb|ABR00275.1| hypothetical protein CGSHiGG_07040 [Haemophilus influenzae PittGG]
          Length = 219

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 107/229 (46%), Gaps = 16/229 (6%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            +++ +  L  + D     ++Y+D+ + V NKP+G+    G+   Y+      S V  K 
Sbjct: 2   ALIEYNPPLEPYLD-----IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKF 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGI+V A ++AA + L   FR R  +K Y ++VWG  +N    I   
Sbjct: 55  GFCEPAHRLDMATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEINLP 114

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           ++       +     + +      A++ F+V+         +++ P TGR+HQLR+H L 
Sbjct: 115 MICD----WENRPRQRLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLA 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +G PI+GD  Y        +     +L LHA  + + HP  G  +   A
Sbjct: 171 LGHPILGDKFYSHPQAKVMS----PRLCLHAEELTITHPITGETMTFNA 215


>gi|311748343|ref|ZP_07722128.1| ribosomal large subunit pseudouridine synthase C [Algoriphagus sp.
           PR1]
 gi|126576852|gb|EAZ81100.1| ribosomal large subunit pseudouridine synthase C [Algoriphagus sp.
           PR1]
          Length = 237

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 70/240 (29%), Positives = 110/240 (45%), Gaps = 25/240 (10%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
             + ++L+E++   V NKP  +S       A +I    K++        +L HRLD+ETS
Sbjct: 5   DFQKLILFENADYLVINKPPYLSSLDDRHEAQNILDLAKAYT----PDAQLCHRLDKETS 60

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G LV+A+   A +HL   F  R++ KIY ++V GI   + E +   L+  +         
Sbjct: 61  GCLVIAKNPEAYRHLAIQFENRKVDKIYHAVVEGIQDYQNELVDRNLIATNK-------G 113

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V +  KG   A ++F+ +  +A     +E +P TGR HQ+RVH  ++  PI GD  Y  N
Sbjct: 114 VAKVSKGGKSAQTYFQTLKTYA-AHTLVECKPVTGRLHQIRVHLAYLKSPICGDTLYGGN 172

Query: 276 F-------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                         K     PI  ++ LHA  +     +G +LQ+ AP P         L
Sbjct: 173 ILYLSSLKRRFNLKKDTEELPIMQRVSLHAFSIGFEGLDGTKLQLNAPYPKDFQVLVKQL 232


>gi|218708391|ref|YP_002416012.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           LGP32]
 gi|218321410|emb|CAV17360.1| Ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           LGP32]
          Length = 244

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/218 (28%), Positives = 107/218 (49%), Gaps = 16/218 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D  I V NKPAG+    G  +  H D      V  +  + ++ HRLD  TSG+++
Sbjct: 15  DIVYQDDDILVVNKPAGLLSVPGR-LPEHYDSMWSRLV-VEFPEIQVVHRLDMSTSGLML 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A +HL + F+ R   K+Y++ VWG     +  I   L+       D+ +  +Q 
Sbjct: 73  LAKHKQAERHLKKQFQYRLTHKLYYARVWGSVGEAEGLIDLPLI------CDWPNRPRQK 126

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   + + + +++    +   L++ P TGR+HQLRVH + +G PIVGD  Y     
Sbjct: 127 VCFNEGKPSQTRY-IVEQQEPQTTLLKLLPITGRSHQLRVHCMELGNPIVGDEFYATPDA 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
            N++    ++L LHA  +   HP   +    A +P   
Sbjct: 186 FNYS----DRLALHACELSFYHPANNQF-FKAFVPCDF 218


>gi|145518940|ref|XP_001445342.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|31746352|emb|CAD97486.1| pseudouridine synthase [Paramecium tetraurelia]
 gi|124412786|emb|CAK77945.1| unnamed protein product [Paramecium tetraurelia]
          Length = 350

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 80/346 (23%), Positives = 149/346 (43%), Gaps = 46/346 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFV--NLQKILRSGQVRVDKKRVKFNN-RIQSGQVVR 66
           V V N     R+D++       +N     +QK++R+G++ V+ K++K +   ++ G VV 
Sbjct: 16  VPVFNSHSGTRIDKFL---IADLNRSWNEVQKLIRNGEINVNNKKIKDHQFLLKEGDVVT 72

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                   + + K+       V  T+  + LK ++LYE+ +I + NK  G + QGG+   
Sbjct: 73  YW------DKLKKQADTQLRPVPNTQAYEELKKMILYENDQIIILNKKHGYASQGGANPN 126

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWS 185
           Y+I   L  +  +      + HRLDQ TSG+L++A+ +  A  ++   + +  I K Y +
Sbjct: 127 YNIPEILNLYFKNFY----IIHRLDQLTSGLLIIAKNKDIATEISTIIQEKAFITKKYIA 182

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVID---CFAQKFC 241
           +V G  K +K  I   LL  ++      +  +Q  +G    A + ++VI+      + + 
Sbjct: 183 VVQGQIKVQKGLIDRPLLFNTNNQKQTCYNEEQLLEGKYLPARTSYEVIEEYQYQDEMYS 242

Query: 242 WLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNFTS------PIQNKLYLHARY 294
            L++Q   GR HQ+R H    +  PI+ D KY   F                 + L A+ 
Sbjct: 243 ILDLQIFEGRKHQIRAHLSQVLNTPILFDQKYGFQFTKTNRDLQTSIFGEDQGIMLQAKR 302

Query: 295 MDLPHP------------------EGGRLQITAPLPAHMVKTWDSL 322
           +   +                   + G+L+I A         +  +
Sbjct: 303 IVFQNFPVDINESFYQNSNGTIIQKNGKLEIEATFSTEFESLFQKI 348


>gi|50119965|ref|YP_049132.1| tRNA pseudouridine synthase C [Pectobacterium atrosepticum
           SCRI1043]
 gi|49610491|emb|CAG73936.1| putative RNA pseudouridylate synthase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 261

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 107/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP+G  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   IIYQDEHLVAVNKPSGWLVHRSWLDRKEKIVVMQTVRDQIGQHVYTVHRLDRPTSGVLLL 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F   ++QK+Y ++V G   +          +   I   + +     +
Sbjct: 64  ALSSEVARALSQQFESHQMQKMYHAVVRGYVLDDGVIDYALTEELDKIADKFAN----PD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H++ +               ++  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHYRSLAQAEMPVAIGRYPTARYSLMELKPQTGRKHQLRRHMSHLHHPIIGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +    + +G  T     +L LHA  + L HP  G+ L + A   +         G++
Sbjct: 180 AHGDLRHNRGMETHFSCGRLMLHASELQLNHPVSGQPLTLQARWDSPWQGVVRQFGWQ 237


>gi|225619888|ref|YP_002721145.1| pseudouridine synthase [Brachyspira hyodysenteriae WA1]
 gi|225214707|gb|ACN83441.1| pseudouridine synthase [Brachyspira hyodysenteriae WA1]
          Length = 241

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 73/220 (33%), Positives = 112/220 (50%), Gaps = 10/220 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQETSG 156
           +YED+ I V  KP  I  QG           +K ++  K  K       L HRLD+  SG
Sbjct: 18  IYEDNHIIVAVKPPNIPTQGDITGDVSFFENIKDYIKIKYNKKGNVFLGLVHRLDRPVSG 77

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I+V A+T  AA  L+E+ R R+ +K Y+++V GI   K+  + N+L+KK++  G+   VV
Sbjct: 78  IIVFAKTSKAASRLSEAIRDRKFEKTYYAVVNGILLEKEAKLENYLIKKTNKLGNIAQVV 137

Query: 217 KQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +N K A  A   + VI +   +    L ++  TGR HQ+RV   ++G  I GD KY + 
Sbjct: 138 FENTKNAKIAKLKYNVIKEDVIKNLSLLRIELETGRFHQIRVQLANIGHVIYGDRKYGSY 197

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAH 314
            K +        L L A+ +  PHP     + + A LP++
Sbjct: 198 IKYDRNDV---PLALFAKSLRFPHPTRDEEIYVEADLPSY 234


>gi|148825512|ref|YP_001290265.1| hypothetical protein CGSHiEE_02065 [Haemophilus influenzae PittEE]
 gi|229847517|ref|ZP_04467612.1| hypothetical protein CGSHi7P49H1_02889 [Haemophilus influenzae
           7P49H1]
 gi|148715672|gb|ABQ97882.1| hypothetical protein CGSHiEE_02065 [Haemophilus influenzae PittEE]
 gi|229809580|gb|EEP45308.1| hypothetical protein CGSHi7P49H1_02889 [Haemophilus influenzae
           7P49H1]
 gi|309972649|gb|ADO95850.1| Pseudouridine synthase A [Haemophilus influenzae R2846]
          Length = 219

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 107/229 (46%), Gaps = 16/229 (6%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            +++ +  L  + D     ++Y+D+ + V NKP+G+    G+   Y+      S V  K 
Sbjct: 2   ALIEYNPPLEPYLD-----IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKF 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGI+V A ++AA + L   FR R  +K Y ++VWG  +N    +   
Sbjct: 55  GFCEPAHRLDMATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLP 114

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           ++       +     + +      A++ F+V+         +++ P TGR+HQLR+H L 
Sbjct: 115 MICD----WENRPRQRLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLA 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +G PI+GD  Y        +     +L LHA  + + HP  G  +   A
Sbjct: 171 LGHPILGDKFYSHPQAKAMS----PRLCLHAEELTITHPITGETMTFNA 215


>gi|172038568|ref|YP_001805069.1| pseudouridine synthase [Cyanothece sp. ATCC 51142]
 gi|171700022|gb|ACB53003.1| probable pseudouridine synthase [Cyanothece sp. ATCC 51142]
          Length = 304

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 78/323 (24%), Positives = 132/323 (40%), Gaps = 37/323 (11%)

Query: 1   MSLMT--YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR 58
           M  M   ++    ++     + +  ++  +Y H +     + +   QV +D + V     
Sbjct: 1   MKNMNNGWIYREQIKQKNAGLTVLEYYTQNYHHSSSQQWLERILWAQVLLDNQVVTPETI 60

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +Q+GQ +           +                   L   L+YED  I V NKP+G+ 
Sbjct: 61  LQTGQWLSYHRPPWKEADVP------------------LDFDLIYEDHHILVINKPSGLP 102

Query: 119 VQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           V  G G   H   G LK       +K    HRL + TSG++++ +T  A  HLT   R  
Sbjct: 103 VLPGGGFLEHTLLGQLKKQYPK--EKVFPIHRLGRGTSGLMLMGKTAIARSHLTRQMREH 160

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +++K+Y +L+          I + + K S     Y++  K + K    A S  ++I+ ++
Sbjct: 161 KMRKVYRTLIGENNLPDYFNIEHPIGKISDPVLGYIYGAKADGKD---AYSQCQIIERYS 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTS-------PIQNKL 288
            K   +E+   TGR HQ+R+H   +G P++GD  Y      K  F         P     
Sbjct: 218 DK-TLVEVTILTGRPHQIRIHLATIGYPLLGDPLYVVGGIPKTGFKEQKETVNVPGDCGY 276

Query: 289 YLHARYMDLPHPEGGR-LQITAP 310
           +LHA  +   HP   + L  T  
Sbjct: 277 FLHAYQLSFVHPATHQCLTFTCE 299


>gi|319897782|ref|YP_004135979.1| ribosomal large subunit pseudouridine synthase a [Haemophilus
           influenzae F3031]
 gi|317433288|emb|CBY81663.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae F3031]
          Length = 219

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/219 (28%), Positives = 101/219 (46%), Gaps = 11/219 (5%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K        ++Y+D+ + V NKP+G+    G+   Y+      S V  K       HRLD
Sbjct: 7   KPPLEPYLDIIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKFGFCEPAHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V A ++AA + L   FR R  +K Y ++VWG  +     +   ++       +
Sbjct: 65  MATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLEKDYGEVNFPMICD----WE 120

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                + +      A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD  
Sbjct: 121 NRPRQRLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGDKF 180

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           Y        +S    +L LHA  + + HP  G  +   A
Sbjct: 181 YSHPQAKAMSS----RLCLHAEELTITHPITGETMTFNA 215


>gi|90580793|ref|ZP_01236596.1| putative ribosomal large subunit pseudouridine synthase A [Vibrio
           angustum S14]
 gi|90438061|gb|EAS63249.1| putative ribosomal large subunit pseudouridine synthase A [Vibrio
           angustum S14]
          Length = 233

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 66/210 (31%), Positives = 98/210 (46%), Gaps = 12/210 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ DS I   NKPAGI    G    +H   F  + V  K    ++ HRLD  TSG++V+A
Sbjct: 20  LFLDSDIIAVNKPAGILSNPGRAPEHHDSIF--ARVLEKYPNSQIVHRLDMGTSGLIVLA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
             + A  HL   FR R  QK+Y++ VWG  +     +   L+           V   +  
Sbjct: 78  LNKKAECHLKAQFRERETQKVYYARVWGHIEQDTGTVDLPLICD-WPNRPRQKVCFDD-- 134

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               +I+H++V+    +K   + + P TGR+HQLRVH   +G PI+GD  Y         
Sbjct: 135 -GKPSITHYEVLSRD-EKTTLVRLLPVTGRSHQLRVHMQALGHPILGDKFY----ANEEA 188

Query: 282 SPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
                +L LHA  +   HP   + + + AP
Sbjct: 189 MAASPRLLLHAAELTFTHPGSDQPMHLFAP 218


>gi|90411938|ref|ZP_01219946.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium profundum 3TCK]
 gi|90327196|gb|EAS43568.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium profundum 3TCK]
          Length = 239

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 69/248 (27%), Positives = 116/248 (46%), Gaps = 20/248 (8%)

Query: 88  VNLTKHSDFLK-SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
            +L  H        +L+ D  I + NKP+G+    G    ++    + S V     +  +
Sbjct: 5   PHLDYHPPTDPWLDILHHDEDIIMLNKPSGLLSNPGRNPEHYDS--VYSRVLRDYPEAHI 62

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  TSG++++A  + A +HL   FR R  QK+Y++ +WG P      +   L+   
Sbjct: 63  VHRLDMSTSGLIMLAVNKDAERHLHAQFRERATQKVYYARIWGHPDQDTGTVDLPLI--- 119

Query: 207 HIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               D+ +  KQ    +    +++H++V+   AQ    + + P TGR+HQLRVH   +G 
Sbjct: 120 ---CDWPNRPKQKVCYEDGKPSVTHYEVVAREAQ-TTLVRLHPITGRSHQLRVHMQALGH 175

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL---PAHMVKTWD 320
           PI+GD  Y  +        I ++L+LHA  +   HP     +   AP    P   +KT +
Sbjct: 176 PIIGDEFYANDEANA----IADRLHLHAAEIAFTHPGTKDPIHFFAPCELFPDVPMKTIE 231

Query: 321 SLGFKYDR 328
            L    ++
Sbjct: 232 FLSADQEK 239


>gi|169826808|ref|YP_001696966.1| putative RNA pseudouridine synthase yjbO [Lysinibacillus sphaericus
           C3-41]
 gi|168991296|gb|ACA38836.1| Hypothetical RNA pseudouridine synthase yjbO [Lysinibacillus
           sphaericus C3-41]
          Length = 293

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/311 (20%), Positives = 113/311 (36%), Gaps = 39/311 (12%)

Query: 23  RWFKNHYPHINFV-NLQKILR--SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           +  +               ++   G + V+         +Q    V +       +  + 
Sbjct: 7   QLLREALQEWRISKRALTAIKFNGGLLTVNGIERNVRYALQVDDCVEVTFPPEEKSEGL- 65

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLK 134
                         S+     ++YED  I V NKPA  S         + IA  + G+ +
Sbjct: 66  -------------TSEHGDLAIVYEDDTILVLNKPANQSTIPSREHPTNSIANLVCGYFE 112

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                      +  RLD++TSG+L +A+          + R   I + Y ++V G     
Sbjct: 113 Q--QGLASTAHIITRLDRDTSGLLCIAKHAHIHHLTGLAQRNGEISRKYEAIVHGHVHQD 170

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGR 251
            + I   + +K     +   + ++  +   YA +   VI  F   A+    + +  HTGR
Sbjct: 171 SQSIVAPIGRK-----ETSIIEREVREDGQYAHTDVTVIQRFYLGAEPMTHIGLTLHTGR 225

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           THQ+RVH   +G P+VGD  Y        +    ++  LH   +++ HP     LQ T+ 
Sbjct: 226 THQIRVHMSSLGHPLVGDELYGG------SRLHMDRQALHCVSLNMTHPLTSEHLQFTSM 279

Query: 311 LPAHMVKTWDS 321
           L   M      
Sbjct: 280 LNEDMQNLLKE 290


>gi|168705355|ref|ZP_02737632.1| pseudouridine synthase [Gemmata obscuriglobus UQM 2246]
          Length = 238

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 73/231 (31%), Positives = 112/231 (48%), Gaps = 12/231 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLT 147
            S  L   +LYED  + V NKPA +  Q   G+    +  +++++  K  KP      + 
Sbjct: 3   DSAALPLAVLYEDHHLVVVNKPAPLLTQAPPGVPNL-EERVRAYIKDKYAKPAGVYLGVP 61

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+  SG++  AR   AAQ +   F  R ++K+YW+LV G+ +       +++ K  +
Sbjct: 62  HRLDRPVSGVVCFARNTKAAQRVHSQFEHRSVRKVYWALVEGVVEPDAGVWDDYIRKVEN 121

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                     + E GA  A   F+V++ FA     +E+ P TGR HQLRV +   G P++
Sbjct: 122 EAR--AARGHEGEPGAKLATLEFRVLERFA-AHTRIELHPLTGRMHQLRVQSAWRGHPVI 178

Query: 268 GDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           GD  Y +   F      P    + LHAR +   HP     L I AP+PA+ 
Sbjct: 179 GDSLYGSVRPFGPPAELPRDRVIALHARRLTFEHPFTKQELVIEAPVPAYW 229


>gi|325856422|ref|ZP_08172138.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
 gi|325483606|gb|EGC86578.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
          Length = 255

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 109/229 (47%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I +  K AG  VQG       +   ++ W+  K QKP      + HRLD+  S
Sbjct: 33  VLYEDNHIIIVYKEAGEIVQGDKSGDEPLSETVRRWIKEKYQKPGNVFLGIVHRLDRPVS 92

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L   FR   + K YW++V   P   +  + +WL++       Y + 
Sbjct: 93  GLVIFAKTSKALARLNNMFRNGEVHKTYWAIVTRPPFEPEATLTDWLVRNERQNKSYAY- 151

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +  +I H+K+I+  + ++  LE+   TGR HQ+R    +M CPI GD KY A 
Sbjct: 152 -NHQVPTSKKSILHYKIINR-SDRYTLLEINLMTGRHHQIRCQLSNMDCPIKGDLKYGAP 209

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 S     + L +  ++  HP     ++I +PLP      W ++G
Sbjct: 210 RSNPDGS-----ISLLSHRVEFVHPVSKENIRIESPLPDD--TLWHAIG 251


>gi|260171398|ref|ZP_05757810.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D2]
 gi|315919711|ref|ZP_07915951.1| conserved hypothetical protein [Bacteroides sp. D2]
 gi|313693586|gb|EFS30421.1| conserved hypothetical protein [Bacteroides sp. D2]
          Length = 561

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 72/247 (29%), Positives = 117/247 (47%), Gaps = 25/247 (10%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  K+ ++ +  + H D  +  ++YED  + V NKPAG+    G       
Sbjct: 320 CEPILQHMLQGLKVDENPLLNSIHEDE-ELEIVYEDEWLVVVNKPAGMLSVPGKEEDRDS 378

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                         P + HRLD  TSG+L+VA+T+   QHL   F  R I+K Y +++ G
Sbjct: 379 VYHRLKKKYPDATGPMIVHRLDMATSGLLLVAKTKEVHQHLQAQFASRSIKKRYVAVLDG 438

Query: 190 IPKNKKECIANW--------LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
                ++ +            L  + +      V +++      AI+ +++I C ++K  
Sbjct: 439 ATATVEKTVPLPGKAGRIELPLCLNPLDRPRQIVSREH---GKEAITEYRII-CESEKHT 494

Query: 242 WLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +   P TGRTHQLRVHA H   +GCPI+GD  Y             ++LYLHA Y++  
Sbjct: 495 RIAFYPLTGRTHQLRVHAAHPEGLGCPILGDELYGKK---------ADRLYLHAEYIEFR 545

Query: 299 HPEGGRL 305
           HP  G++
Sbjct: 546 HPISGKI 552


>gi|145633817|ref|ZP_01789540.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae 3655]
 gi|144985320|gb|EDJ92155.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae 3655]
          Length = 219

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 107/229 (46%), Gaps = 16/229 (6%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            +++ +  L  + D     ++Y+D+ + V NKP+G+    G+   Y+      + V  K 
Sbjct: 2   ALIEYNPPLEPYLD-----IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--ARVKEKF 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGI+V A ++AA + L   FR R  +K Y ++VWG  +     +   
Sbjct: 55  GFCEPAHRLDMATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLEKDYGEVNLP 114

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           ++       +     + +      A++ F+V+   +     +++ P TGR+HQLR+H L 
Sbjct: 115 MICD----WENRPRQRLDFVLGKRAVTKFEVLARLSNNSTRVKLTPVTGRSHQLRLHMLA 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +G PI+GD  Y        +     +L LHA  + + HP  G  +   A
Sbjct: 171 LGHPILGDKFYSHPQAKAMS----PRLCLHAEELTITHPITGETMTFNA 215


>gi|56461324|ref|YP_156605.1| pseudouridylate synthase Rlu family protein [Idiomarina loihiensis
           L2TR]
 gi|56180334|gb|AAV83056.1| Predicted pseudouridylate synthase, Rlu family [Idiomarina
           loihiensis L2TR]
          Length = 218

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 65/214 (30%), Positives = 111/214 (51%), Gaps = 16/214 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YEDS++ V +K +G+    G    +     + + V     + R+ HRLD  TSG+L++
Sbjct: 16  VIYEDSQLLVVDKQSGLLSVPGKRPEH--KDSVYTRVQRVHPEIRVVHRLDMATSGVLLL 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T+AA  HL   F+ R  +K Y + VWG P   +  I   L        D+ +  +Q+ 
Sbjct: 74  AKTKAAQSHLNRQFQNRTTRKRYIAQVWGKPPALQGEIELPL------SCDWPNRPRQHM 127

Query: 221 K--GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  + + ++V   F +    +E+ PHTGR+HQLRVH   +GCPI+GD  Y  +   
Sbjct: 128 DFFTGKPSTTLYRV-TAFDKGCSRVELTPHTGRSHQLRVHMQAIGCPILGDKFYAHSDAF 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
                   +L LHA Y+ + HP+  + ++ ++P+
Sbjct: 187 AAAE----RLLLHAEYLGVTHPQTEQLIEFSSPV 216


>gi|260427871|ref|ZP_05781850.1| ribosomal large subunit pseudouridine synthase A [Citreicella sp.
           SE45]
 gi|260422363|gb|EEX15614.1| ribosomal large subunit pseudouridine synthase A [Citreicella sp.
           SE45]
          Length = 215

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 65/226 (28%), Positives = 107/226 (47%), Gaps = 13/226 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++ T         +L+ D+ + V +KPAG+    G G A  +   L + +++     RL 
Sbjct: 1   MSDTYDPPKGDIPILHADTDLLVVDKPAGLLSVPGKGEA--LADCLITRLEAAFPTVRLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG++V   T  A +HL   F  R+ +K Y + V G  + K   +   L+    
Sbjct: 59  HRLDRDTSGVMVFGLTAHAQRHLGMQFETRKTRKTYVARVAGRLEPKTGTVDLPLIVD-- 116

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  + K   +    A++ +KV    +     + + P TGR+HQLRVH L +G PI+
Sbjct: 117 --WPNRPLQKVCHETGKPALTDYKVTKS-SDTESRVRLHPLTGRSHQLRVHMLALGHPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           GD  Y  +    +      ++ LHA  + L HPE G  ++  A  P
Sbjct: 174 GDPLYAPDTASQYP-----RMMLHAEELRLHHPESGIGVKFRAKTP 214


>gi|254455970|ref|ZP_05069399.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter sp. HTCC7211]
 gi|207082972|gb|EDZ60398.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter sp. HTCC7211]
          Length = 292

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 83/309 (26%), Positives = 153/309 (49%), Gaps = 20/309 (6%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+DRW +     I    ++K  RSG+++++KK++K + ++++  V+     ++    II
Sbjct: 1   MRIDRWTRLKIGKIPQGLIEKYFRSGKIKINKKKIKSSTKVKTNDVIS-FFNLDFKEQII 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +++   + S  + K ++     ++  +    V NK +GISVQGG+    ++         
Sbjct: 60  QKKIKFEPSKEIIKSNED---QIIDNNENFIVLNKSSGISVQGGTKSKKNLVDIFAKSEI 116

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +G KP   HRLD++TSG+ ++A+TR +AQ LT  FR+R++ K Y ++  G         
Sbjct: 117 FQGTKPYSVHRLDKDTSGVFIMAKTRQSAQLLTSLFRLRKVHKTYLAICHGELNKDSGEW 176

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L++     G+   + K        A + ++V+D  ++    +E++P TGR HQLR  
Sbjct: 177 NDDLIRYD---GEKKIIEK--------AKTIYRVLDKNSE-ASLVELKPITGRKHQLRKQ 224

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
              +G PI GD KY      N +  +   L LH+  +     +  +   TA LP +  K 
Sbjct: 225 LYALGQPIFGDIKY---KLSNSSRGLNKNLMLHSYQIKFI-IDDVKHTYTALLPDYFRKL 280

Query: 319 WDSLGFKYD 327
             +   K+ 
Sbjct: 281 LKTKRLKFP 289


>gi|223889337|ref|ZP_03623924.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           64b]
 gi|224532458|ref|ZP_03673084.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           WI91-23]
 gi|226321280|ref|ZP_03796808.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           Bol26]
 gi|223885258|gb|EEF56361.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           64b]
 gi|224512630|gb|EEF83005.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           WI91-23]
 gi|226233312|gb|EEH32063.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           Bol26]
          Length = 313

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 137/316 (43%), Gaps = 21/316 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    ++ V  ++   RLD        + +  ++ K +R G +R++  +  F+ R+  G 
Sbjct: 1   MDKYIFLEVLANDNGKRLDSILIKIL-NFSKASIIKHIRKGDIRLNGLKSHFSCRVCKGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +   ++   ++      +D          +++  ++YEDS + V +K  GI V GG 
Sbjct: 60  KIYLYKSLSQNLNL-----TMDECFKSNIDFQYIRKRIIYEDSDLLVLDKQKGILVHGGK 114

Query: 124 G-IAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + + ++ +L S  + S   KP   HRLD+ TSGI++ A+    A+ L+ +F    I K
Sbjct: 115 NSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTARKLSAAFSGGSIIK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++++ G  K+      N L +   +   +V      +K    AI+    I    ++  
Sbjct: 175 KYFAILLGEVKSP-VVYKNHLFRNKRLRKTFV----LEDKNFVNAITKVNPILSC-KRAT 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+   TG THQ+R        P++ D KYC  FK +         +LHA  +      
Sbjct: 229 LVEIVIETGFTHQIRSQCSFNNHPLINDKKYCNKFKKSD-------YFLHAFLVKFNGTF 281

Query: 302 GGRLQITAPLPAHMVK 317
             + +  +      +K
Sbjct: 282 FKKNEFCSKPSLEFLK 297


>gi|312884948|ref|ZP_07744638.1| tRNA pseudouridine synthase C [Vibrio caribbenthicus ATCC BAA-2122]
 gi|309367425|gb|EFP94987.1| tRNA pseudouridine synthase C [Vibrio caribbenthicus ATCC BAA-2122]
          Length = 241

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 100/242 (41%), Gaps = 17/242 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D      NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   IVFQDDYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDKPTSGVLIF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    + K Y ++V G  +          ++   I   +  +    +
Sbjct: 64  ALSSEIASSVMPMFANHEMNKTYHAIVRGWIEQAGVLDYPLKVELDKIADKHATL----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ ++ I               ++C +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KEAQDAITDYQPIAKTELPIAMGKFPTTRYCMMELKPRTGRKHQLRRHMAHLRHPIIGDT 179

Query: 271 KYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +             +  +L LHA  +   HP  G  + I A L     +  +   +   
Sbjct: 180 SHGDGKHNKLFRHELDSHRLLLHASSLSFIHPFTGESVVINAGLDETWARLAEVFDWLLP 239

Query: 328 RN 329
           +N
Sbjct: 240 QN 241


>gi|225549410|ref|ZP_03770382.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           94a]
 gi|225370038|gb|EEG99479.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           94a]
          Length = 315

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 138/319 (43%), Gaps = 22/319 (6%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M L  Y+ ++ V  ++   RLD        + +  ++ K +R G +R++  +  F+ R+ 
Sbjct: 1   MRLDKYI-FLEVLANDNGKRLDSILIKIL-NFSKASIIKHIRKGDIRLNGLKSHFSCRVC 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   +    ++      +D          +++  ++YEDS + V +K  GI V 
Sbjct: 59  KGDKIYLYKSLAQNLNL-----TMDECFKSNIDFKYIRKRIIYEDSDLLVLDKQKGILVH 113

Query: 121 GGSG-IAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           GG   + + ++ +L S  + S   KP   HRLD+ TSGI++ A+    ++ L+ +F    
Sbjct: 114 GGKNSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTSRKLSAAFSGGS 173

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y++++ G  K+      N L +   +   +V       K    AI+    I    +
Sbjct: 174 IIKKYFAILLGEVKSP-VVYKNHLFRNKRLRKTFV----LEGKNFVNAITKVNPILSC-K 227

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +   +E+   TG THQ+R        P++ D KYC  FK +         +LHA  +   
Sbjct: 228 RATLVEIVIETGFTHQIRSQCSFNNHPLINDKKYCNKFKKSD-------YFLHAFLVKFN 280

Query: 299 HPEGGRLQITAPLPAHMVK 317
                + +  +      +K
Sbjct: 281 GTFFKKNEFCSKPSLEFLK 299


>gi|229829217|ref|ZP_04455286.1| hypothetical protein GCWU000342_01304 [Shuttleworthia satelles DSM
           14600]
 gi|229792380|gb|EEP28494.1| hypothetical protein GCWU000342_01304 [Shuttleworthia satelles DSM
           14600]
          Length = 341

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 125/324 (38%), Gaps = 52/324 (16%)

Query: 24  WFKNHYPHINFVNLQKILRSGQ--VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           W +          +   LRSG+   RV+ K+               P +   L    + Q
Sbjct: 43  WLRGKMR-FPRS-IVAALRSGEQDYRVNGKK---------------PVLWQPLPAGSRIQ 85

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            IL+   +       L   ++YED  I + +KPAG+          H    L + V    
Sbjct: 86  IILEDRKSSPFAPVNLPLNIIYEDEDILLIDKPAGMPSHPS---MNHQKDTLANAVLYYY 142

Query: 142 QK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           QK       R+ +RLD +TSG++ V++   AA  + +    R+I + Y  +V G      
Sbjct: 143 QKQGIPFVFRIANRLDMDTSGLVAVSKNSLAAARVKQMIDKRQIHREYLCIVEGSFSADS 202

Query: 196 ECIANWLLKKS--------------HIGGDYVHV--VKQNEKGANYAISHFKVIDCFAQK 239
                  +K                 I      V   + N      A++ F+++     K
Sbjct: 203 SLAKRDFVKMRYDADGQMIGGRIWAPISRREGSVLERRVNASDGQTALTDFEIVQ-EGAK 261

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +  L +   TGRTHQ+RVH  ++G P+  D+ Y   ++        ++  LH+  +  PH
Sbjct: 262 YSLLRVWLGTGRTHQIRVHMNYLGHPLPADYLYHPVYQD------ISRQPLHSAKLRFPH 315

Query: 300 PEGGR-LQITAPLPAHMVKTWDSL 322
           P  GR +   + LPA M    D+ 
Sbjct: 316 PVSGRQMCFESRLPADMRHLLDNF 339


>gi|303277917|ref|XP_003058252.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226460909|gb|EEH58203.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 508

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 68/297 (22%), Positives = 120/297 (40%), Gaps = 32/297 (10%)

Query: 59  IQSGQVVR----IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
           +++G   R    I     A     +         +    +     +++YED      +KP
Sbjct: 208 VRAGDDARASEVIAAASKASGAGKRANSKKSKKASKRPGAGAAPLVVVYEDDHFAAVSKP 267

Query: 115 AGISVQGGSG--IAYHIDGFLKSWVDSKGQKP----------RLTHRLDQETSGILVVAR 162
           AGI      G  +       +   +D+ G +            + HRLD+ T+G++V+A+
Sbjct: 268 AGILTHPTGGASVDKRSVTLVDLALDAFGDEHVSALNGADARGIVHRLDKPTTGVMVIAK 327

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           T  A   L  ++  R++QK YW++V G+P  ++         +     D++  V      
Sbjct: 328 TDVAHALLVTAWYQRKVQKTYWAIVEGVPGRRRPKRRGDAEGEDAETEDHLFGVVDAPAD 387

Query: 223 ANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHA-LHMGCPIVGDHKYCANFKG 278
              A S +KV++ F         +E+ PHTGR HQ+R H    +G P+VGD  Y      
Sbjct: 388 GRPAKSDWKVLEIFNLPDATCSLVEVTPHTGRKHQVRSHMGAILGAPLVGDPLYRRGKPA 447

Query: 279 NFTSPIQNK-----------LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              +                ++LHA  + L HP  G  + ++AP+P    +   +L 
Sbjct: 448 ATPAAAAAALTADGAKPGSVMFLHATSLRLEHPVTGEPMTLSAPVPDAFEELLGALR 504


>gi|86134338|ref|ZP_01052920.1| RNA pseudouridylate synthase [Polaribacter sp. MED152]
 gi|85821201|gb|EAQ42348.1| RNA pseudouridylate synthase [Polaribacter sp. MED152]
          Length = 228

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 110/226 (48%), Gaps = 14/226 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLT 147
           HS+     +L+ED+ I + NK +G   QG       +   +K ++  K  K       + 
Sbjct: 2   HSNKQNLQVLFEDNHIIIVNKRSGDITQGDKTGDKPLSDVVKEYIKEKYNKAGNVFLGVV 61

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+++ ART  A + L +  R + I K YW++V   PK +K  + N+L K   
Sbjct: 62  HRLDRPTSGVIIFARTSKALERLNKMLRDKEIHKTYWAVVKNHPKKEKATLINYLRKNPK 121

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  V ++  +G+  AI H+  +      +  LE+   TGR HQ+R    ++G PI 
Sbjct: 122 NNKS--SVFQKEIEGSKKAILHYSTLKKL-DNYSLLEIDLETGRHHQIRAQLSNIGFPIK 178

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
           GD KY  N      S     ++LHAR ++  HP    ++ + AP P
Sbjct: 179 GDLKYGFNRSNKDGS-----IHLHARKIEFIHPVAKEKITVIAPTP 219


>gi|320547814|ref|ZP_08042098.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           equinus ATCC 9812]
 gi|320447574|gb|EFW88333.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           equinus ATCC 9812]
          Length = 286

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 54/268 (20%), Positives = 103/268 (38%), Gaps = 29/268 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              + ++ + + + + +++G  +++    +            D                L
Sbjct: 37  KKHLLINGEMINWQSLVKTGDTIQLIFDDD------------DYPQKEIPFGQAELVDCL 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + + NKP G+   G       +   + ++V   G+   + HRLD ETSG ++ A+
Sbjct: 85  YEDEHLIIVNKPEGMKTHGNEPNEIALLNHVSAYV---GKTCYVIHRLDMETSGAVMFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      + I + YW+L  G  + K +   + + +  H     V     + K 
Sbjct: 142 NPFVLPILNRLLENKDISREYWALAQGKFEPKHQVFQDKIGRDRHDRRKRV----VDRKN 197

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++    +  F +    ++ +  TGRTHQ+RVH       I+GD  Y          
Sbjct: 198 GQTALTIVDRLKTFKKG-TLVKCRLKTGRTHQIRVHLSAHNHAIIGDPLYSKIPA----- 251

Query: 283 PIQNKLYLHARYMDLPHPEG-GRLQITA 309
               +L LHA  +   HP    ++ + A
Sbjct: 252 ---KRLMLHAHKLSFTHPFTLEKISVEA 276


>gi|88858181|ref|ZP_01132823.1| Pseudouridylate synthase, 23S RNA-specific [Pseudoalteromonas
           tunicata D2]
 gi|88819798|gb|EAR29611.1| Pseudouridylate synthase, 23S RNA-specific [Pseudoalteromonas
           tunicata D2]
          Length = 217

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 68/213 (31%), Positives = 101/213 (47%), Gaps = 13/213 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  I V +K +G+    G   A H      + +     +  L HRLD  TSGI+V 
Sbjct: 16  IVHVDKDIIVIDKQSGLLSNPGR--AAHTFDCALTRLQQAYPETLLVHRLDCATSGIMVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR++ A  HL   F+ R+ +K+Y + V G        I   L+             ++  
Sbjct: 74  ARSKKAESHLKTQFQDRQNKKVYIAEVAGHLAEPNGTILALLMADKENP-----PYQKVS 128

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                AISH+KV++        +E+   TGRTHQLRVH LH+G PI+GD  Y      N 
Sbjct: 129 PLGKSAISHYKVLEQRPDS-SLVELTLETGRTHQLRVHMLHLGHPILGDDFYGDEAIVNA 187

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
               + +L LHA  + + HP  G+ L  T+P P
Sbjct: 188 ----RPRLCLHATELSIIHPYSGKTLSFTSPHP 216


>gi|228470977|ref|ZP_04055822.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas uenonis 60-3]
 gi|228307374|gb|EEK16388.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas uenonis 60-3]
          Length = 228

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 69/225 (30%), Positives = 103/225 (45%), Gaps = 14/225 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
                +LYED+ + + NKPAG+ VQG S     +   ++ ++  K  KP      +THR+
Sbjct: 1   MPDLQILYEDNHLLIVNKPAGMLVQGDSTGDTPLSELVERYLIDKYDKPGRAFVGVTHRI 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSG ++ A+T  A   L   F+ R I K+Y ++V G    K     N L +      
Sbjct: 61  DRPTSGAVLFAKTSKALARLNAMFQRREIHKVYHAVVCGAFPQKAGEAKNLLYRNRKQNK 120

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            Y  VV +    A  A   ++ +     ++  L +  HTGR HQ+R    HMG PI GD 
Sbjct: 121 SY--VVTEPHAEAKRAWLTYERL-SVGDRYSLLAVTLHTGRHHQIRTQLSHMGYPIKGDL 177

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           KY A             + LHAR +   HP     +++ AP P  
Sbjct: 178 KYGAPRSNK-----DGGISLHARILSFEHPVTHEHVEVVAPYPED 217


>gi|260664193|ref|ZP_05865046.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii SJ-7A-US]
 gi|260562079|gb|EEX28048.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii SJ-7A-US]
          Length = 297

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 62/330 (18%), Positives = 121/330 (36%), Gaps = 44/330 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSG 62
           M   +Y+V E D    RL  +       ++   +     +G  + V+ +R   N  +++G
Sbjct: 1   MKIFKYIVTEKD--PKRLGLFLSK--KKLSKQVIVNAKHNGGMLLVNHRRRFTNFMLKNG 56

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V        +N  +K                     ++ E     V NKPA +     
Sbjct: 57  DEVLFVMGKEKVNEFLK--------------PSNKPIEIVLETDNYLVINKPANVLSIPS 102

Query: 123 SG-IAYHIDGFLKSWVDSK------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                  +   +  +   K        KP +  RLD++TSG+++V +   A    +E  +
Sbjct: 103 RYEDGDAVVNRVMGYFSKKKSSEQAFLKPHIVTRLDRDTSGLVLVGKNAVAHSKFSELKK 162

Query: 176 MRRIQKIYWSLVWGI--PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
              +++ + ++V     P+ +   I   + K       YV             ++ ++V+
Sbjct: 163 DVFVKEYH-AIVHSNFNPEEQAGLIDAPIGKIDDSVKRYVI------PNGQKFLTQYEVL 215

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
               +    ++++  TGRTHQ+RVH  H+G P+ GD  Y  +           +  L+  
Sbjct: 216 -AQKEGASLVKLRLFTGRTHQIRVHMAHIGHPLFGDKLYGIDDN-------FARQALNCS 267

Query: 294 YMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           ++  P P       +    P  M   W +L
Sbjct: 268 HLSFPDPFTNEEKIVEVSDPQDMTDLWRNL 297


>gi|332716762|ref|YP_004444228.1| ribosomal large subunit pseudouridine synthase A [Agrobacterium sp.
           H13-3]
 gi|325063447|gb|ADY67137.1| ribosomal large subunit pseudouridine synthase A [Agrobacterium sp.
           H13-3]
          Length = 222

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 102/228 (44%), Gaps = 10/228 (4%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           + S  +          +++ D  + V +KP+G+    G   A      L + V  +  K 
Sbjct: 4   ELSNPVYNPPLEPWLTIVHRDDDLLVLDKPSGLLSVPGRDPALSDS--LLTRVQKQFPKA 61

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + +RLD++TSGI++++  R A   +   F  R+ +K Y ++VWG  + ++  +   L  
Sbjct: 62  LMINRLDKDTSGIVLMSLNRKAHATVAAQFENRQTRKSYVAVVWGEVEGEEGKVDLPLA- 120

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              I  +     + +      A S ++V++        L + P TGRTHQLRVH   +G 
Sbjct: 121 ---IDPENKPRHRVDHDHGKPAQSLWRVLERLPLPATRLALAPLTGRTHQLRVHMKALGH 177

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           PI+GD  Y              +L LHA  +   HP+G  +  T P P
Sbjct: 178 PILGDEFY----AEGEALAAAPRLMLHAEAVGFRHPDGRDVTYTVPCP 221


>gi|224533460|ref|ZP_03674053.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           CA-11.2a]
 gi|224513422|gb|EEF83780.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           CA-11.2a]
          Length = 313

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 135/316 (42%), Gaps = 21/316 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    ++ V  ++   RLD        + +  ++ K +R G +R++  +  F+ R+  G 
Sbjct: 1   MDKYIFLEVLANDNGKRLDSILIKIL-NFSKASIIKHIRKGDIRLNGLKSHFSCRVCKGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +   +    ++      +D          +++  ++YEDS + V +K  GI V GG 
Sbjct: 60  KIYLYKSLAQNLNL-----TMDECFKSNIDFKYIRKRIIYEDSDLLVLDKQKGILVHGGK 114

Query: 124 G-IAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + + ++ +L S  + S   KP   HRLD+ TSGI++ A+    A+ L+ +F    I K
Sbjct: 115 NSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTARKLSAAFSGGSIIK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++++ G  K+      N L +   +   +V       K    AI+    I    ++  
Sbjct: 175 KYFAILLGEVKSP-VVYKNHLFRNKRLRKTFV----LEGKNFVNAITKVNPILSC-KRAT 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+   TG THQ+R        P++ D KYC  FK +         +LHA  +      
Sbjct: 229 LVEIVIETGFTHQIRSQCSFNNHPLINDKKYCNKFKKSD-------YFLHAFLVKFNGTF 281

Query: 302 GGRLQITAPLPAHMVK 317
             + +  +      +K
Sbjct: 282 FKKNEFCSKPSLEFLK 297


>gi|307249532|ref|ZP_07531519.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
 gi|306858387|gb|EFM90456.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
          Length = 237

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 66/211 (31%), Positives = 101/211 (47%), Gaps = 12/211 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+      + V  K       HRLD  TSGIL+ A
Sbjct: 32  VYRDNHILVINKPSGLLSVPGNRPEYYDSAM--TRVQQKYGFTEPAHRLDMATSGILLFA 89

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWLLKKSHIGGDYVHVVKQN 219
            ++AA + L   FR R  +K Y +L+WG    K       N+ L           +  + 
Sbjct: 90  LSKAAEKELKRQFRDREPKKHYIALLWGKLGEKVGDTGEMNFPLICDWENRPRQKICYER 149

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y +    +
Sbjct: 150 ---GKKAITHYEVLAHLPNNATRVKLTPITGRSHQLRVHSLALGHPILGDKFYASPLAKS 206

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
               +  +L LHA  + + HP  G  +  TA
Sbjct: 207 ----LSPRLCLHAESLSITHPITGEAMTFTA 233


>gi|307262909|ref|ZP_07544533.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 13
           str. N273]
 gi|306871814|gb|EFN03534.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 13
           str. N273]
          Length = 237

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 66/211 (31%), Positives = 101/211 (47%), Gaps = 12/211 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+      + V  K       HRLD  TSGIL+ A
Sbjct: 32  VYRDNHILVINKPSGLLSVPGNRPEYYDSAM--TRVQQKYGFTEPAHRLDMATSGILLFA 89

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWLLKKSHIGGDYVHVVKQN 219
            ++AA + L   FR R  +K Y +L+WG    K       N+ L           +  + 
Sbjct: 90  LSKAAEKELKRQFRDREPKKHYIALLWGKLGEKVGDTGEMNFPLICDWENRPRQKICYER 149

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y +    +
Sbjct: 150 ---GKKAITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGDKFYASPLAKS 206

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
               +  +L LHA  + + HP  G  +  TA
Sbjct: 207 ----LSPRLCLHAESLSITHPITGEAMTFTA 233


>gi|325954258|ref|YP_004237918.1| pseudouridine synthase [Weeksella virosa DSM 16922]
 gi|323436876|gb|ADX67340.1| pseudouridine synthase [Weeksella virosa DSM 16922]
          Length = 227

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 113/237 (47%), Gaps = 17/237 (7%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
            +   +L+ED+ + + NK  G   QG +     +   LK+++  +  KP      L HRL
Sbjct: 1   MVNPDILFEDNHLLIINKKPGELAQGDNTGDIPLVDSLKAYIKERDHKPGNVFLGLVHRL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSGI++ A+T  A   + ++F+ R + K+Y +L+ G P  + + + ++L K      
Sbjct: 61  DRPTSGIIMFAKTSKALARMNDAFQKREVTKVYRALIQGKPPKEHDRLTHYLRKNQK--N 118

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +   V  Q    A  AI  +  +          ++Q  TGR+HQ+R     +GCPI GD 
Sbjct: 119 NKTTVFSQPTNNAKEAILEYYWVGSLDSYEVL-DVQLFTGRSHQIRAQLSFIGCPIKGDL 177

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDS-LGFK 325
           KY A       S     + LHAR +   HP     + I AP P  +   W++ LGF+
Sbjct: 178 KYGAKRSNPDGS-----ISLHARKLIFTHPVSKEEITIIAPPPKDV--LWEASLGFE 227


>gi|297243790|ref|ZP_06927720.1| pseudouridylate synthase, 23S RNA-specific [Gardnerella vaginalis
           AMD]
 gi|296888211|gb|EFH26953.1| pseudouridylate synthase, 23S RNA-specific [Gardnerella vaginalis
           AMD]
          Length = 288

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 58/301 (19%), Positives = 119/301 (39%), Gaps = 26/301 (8%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
            ++  N   ++   Q ++  ++ + ++ +Q G  + +    +A     +  K    ++ +
Sbjct: 2   GVSRANAISLIERNQAKILGRKSQKSSILQDGDTIVVDQKESAERKEERNNKSSVCNIPI 61

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPR---- 145
               D +  I           +KP G++     G     +   L++              
Sbjct: 62  IYDDDDVVVI-----------DKPVGVASHAAKGWSGPTVPECLEAAGIDIKTTLCDESR 110

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             +  RLD  TSG++++ +T  A + +   F    ++K Y +LV G     K  I   + 
Sbjct: 111 KGIVSRLDVGTSGLMIICKTDFAYEVMKNQFAKHIVKKTYHALVQGDLAQDKATIDAPIG 170

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +                     A++H+ V++ F Q      +   TGRTHQ+RVH   +G
Sbjct: 171 R-----AKVSDFRFTITSDGKPAVTHWDVLERFGQ-ATLASVNLETGRTHQIRVHFSSIG 224

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            P+VGD  Y AN        +Q + +LH+  +   HP  G+ + + +  P  +    +++
Sbjct: 225 HPLVGDSMYGANPVLAQKLGLQ-RQWLHSMELTFTHPRTGKSVTVKSHYPLDLQHALEAM 283

Query: 323 G 323
            
Sbjct: 284 R 284


>gi|322516374|ref|ZP_08069299.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           vestibularis ATCC 49124]
 gi|322125107|gb|EFX96500.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           vestibularis ATCC 49124]
          Length = 298

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 70/314 (22%), Positives = 128/314 (40%), Gaps = 33/314 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           R+  + K H   I+   L KI    G + V+ +       +  G VV I           
Sbjct: 12  RVKTFLKEH--DISKGLLAKIKFEGGHIWVNGEEQFATYPVHEGDVVAI----------- 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV- 137
              +I D + + T         ++YED    V NKP G +          +  F+K    
Sbjct: 59  ---EIPDEAPHETLKPIPFNLDIVYEDDNFLVINKPYGYASIPSVNHDNTMANFVKYHFV 115

Query: 138 --DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NK 194
             +   Q+  +  RLD++TSG+++ A+   A   + +  + + I+K Y++LV G  K  +
Sbjct: 116 SNNYPNQRVHIVTRLDKDTSGLMLFAKHGYAHARMDKQLQQKSIKKHYYALVEGDTKLEQ 175

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I   + +          + ++  K   YA + ++++  + +    +++  HTGRTHQ
Sbjct: 176 QGEIIAPIARDVD-----SIITRRVHKSGKYAHTSYRLVGDYGR-VKLVDINLHTGRTHQ 229

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA-PLPA 313
           +RVH  H+G P++GD  Y  +           +  LH   +    P   +  + A  L  
Sbjct: 230 IRVHFAHLGLPLLGDDLYGGSL-----DYGIKRQALHCHRLAFIDPFTKKEMVHASSLTD 284

Query: 314 HMVKTWDSLGFKYD 327
                  +L  K D
Sbjct: 285 DFETVIMNLQTKKD 298


>gi|217974669|ref|YP_002359420.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499804|gb|ACK47997.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 225

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 66/217 (30%), Positives = 110/217 (50%), Gaps = 16/217 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D  I V NKP+G+    G   A++    + + V ++    ++ HRLD  TSG++
Sbjct: 14  LDILYQDKDIIVINKPSGLLSVPGRSPAHYDS--VYARVKAEHPHSQIVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  R+A + L   F  R   K Y++ V G  KN    +   L+       D+ +  KQ
Sbjct: 72  VVALIRSAERELKRQFHDRETSKTYFARVAGHVKNDTGSVDYPLI------CDWPNRPKQ 125

Query: 219 NEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                    +++H++VI   A++   +++ P TGR+HQLRVH + +G PI+GD  Y    
Sbjct: 126 KVDHLVGKPSLTHYQVISR-AKRSTLVKLTPITGRSHQLRVHMMALGHPILGDGFYADPL 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
             +    +  +L LHA  + + HP  G  +  +A +P
Sbjct: 185 AKS----LAPRLLLHAAELTIKHPYTGVSMTFSAEVP 217


>gi|294675292|ref|YP_003575908.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           ruminicola 23]
 gi|294472360|gb|ADE81749.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           ruminicola 23]
          Length = 459

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 70/221 (31%), Positives = 101/221 (45%), Gaps = 30/221 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I    KP+G+    G    Y     + +W   +     L HRLD  TSGI++V
Sbjct: 250 IVYEDEAIAAVYKPSGMLSVPGKTDDYS----VATWAKERWAASMLPHRLDLMTSGIMLV 305

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
           A+T  A  HL   F  R I+K Y ++V G  +     I   L        D ++   Q  
Sbjct: 306 AKTPEAYHHLQNQFAARTIKKKYLAVVEGEIQQPHGVIDLPL------SSDPMNRPCQIV 359

Query: 219 NEKGANYAISHFKVIDCF-----AQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDH 270
           + +    AI+ ++V+D        +    L + PHTGRTHQLR+H  H   +GCPI+GD 
Sbjct: 360 DYEHGKRAITEYRVLDRQQSPTTHRPVTLLALYPHTGRTHQLRMHCAHQEGLGCPILGDE 419

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
            Y             ++LYL A  +   HP  G RL +  P
Sbjct: 420 LYGHK---------ADRLYLQAESIAFEHPTTGKRLHLFCP 451


>gi|217976505|ref|YP_002360652.1| pseudouridine synthase [Methylocella silvestris BL2]
 gi|217501881|gb|ACK49290.1| pseudouridine synthase [Methylocella silvestris BL2]
          Length = 234

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 67/242 (27%), Positives = 113/242 (46%), Gaps = 15/242 (6%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D + +    ++ L + LLY D  + V +KPAG++V  G     +++           + 
Sbjct: 1   MDEAPSPLSEAE-LNARLLYRDGLMLVIDKPAGVAVHRGPKGGANLEAAFHWLRFGLPRS 59

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P L HRLD++TSG LV+ R   A + L   F+  +I K Y S+V G P  ++  I   L 
Sbjct: 60  PALAHRLDRDTSGCLVLGRHHKALEKLGLLFKQGKIGKTYVSIVNGRPGAEEGLIDLPLG 119

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           ++    G ++ V    +     + + ++++         L + P TGRTHQLRVH   MG
Sbjct: 120 RRDETRGWWMKV----DPAGQSSQTRWRIL-AKGPAHTLLALTPLTGRTHQLRVHCAAMG 174

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSL 322
             I+GD  Y               L LHA+ +++P +     +++ AP+P       +S 
Sbjct: 175 FSILGDPIYG--------EGGAIPLQLHAQKIEIPLYKNKDAVRVEAPIPESFRAALESC 226

Query: 323 GF 324
           G 
Sbjct: 227 GM 228


>gi|317503596|ref|ZP_07961617.1| ribosomal large subunit pseudouridine synthase [Prevotella salivae
           DSM 15606]
 gi|315665288|gb|EFV04934.1| ribosomal large subunit pseudouridine synthase [Prevotella salivae
           DSM 15606]
          Length = 221

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 69/228 (30%), Positives = 107/228 (46%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  K +G  VQG       +   +K ++  K QKP      + HRLD+  S
Sbjct: 3   VVYEDNHLIVVYKASGEIVQGDKTGDEPLSDTVKRYLKEKYQKPGNVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L + FR   + K YW+L    P   +  + NWL++       YV+ 
Sbjct: 63  GLVVFAKTSKALTRLNKMFREGEVHKTYWALTKNNPSQPEATLTNWLVRNEKQNKSYVY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +  AI  ++VI   ++ +  LE+   TGR HQ+R     MGCPI GD KY A 
Sbjct: 122 -DHEVPRSKKAILSYRVIGR-SEHYSLLEVNLMTGRHHQIRSQLAAMGCPIKGDLKYGAQ 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     + L +R+++  HP     + + +PLP      W S 
Sbjct: 180 RSNPDGS-----ISLLSRHVEFVHPVSKTLISLDSPLPDD--ALWHSF 220


>gi|222529546|ref|YP_002573428.1| pseudouridine synthase [Caldicellulosiruptor bescii DSM 6725]
 gi|222456393|gb|ACM60655.1| pseudouridine synthase [Caldicellulosiruptor bescii DSM 6725]
          Length = 311

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 68/289 (23%), Positives = 124/289 (42%), Gaps = 24/289 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV+ +   +++++  K  YP I    + K+LR G++ V     +    ++ G  V    
Sbjct: 5   FVVDKELAGLKVEKAIKKKYPTIPMSLIFKMLRRGEIIVSFLPAQKGEVLRFGDTVSFEI 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H               K  + LK   +YED  I V +KP GI     S   Y +
Sbjct: 65  EDRFLEH---------------KKVEILK---VYEDDNIVVIDKPYGIPSHPDSNNEYSV 106

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             ++++   SK + P+L HRLD+ T+G++++A+ R     + +    R I K Y  +   
Sbjct: 107 VSWIENNY-SKNELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRAIIKKYLCITKK 165

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               +   + ++L K S     Y+    Q+  G +  ++ +K++         ++++  T
Sbjct: 166 ADLPESGVLVHYLKKDSKKSKVYISDFPQD--GYSEVVTAYKIV-RQKDDLQLVDVEIKT 222

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           G+THQ+R    H+G  I+GD KY             +   L A Y+   
Sbjct: 223 GKTHQIRAQLAHIGLCILGDSKYGDWKLNKKYK--ADMQALCAYYLKFE 269


>gi|302871648|ref|YP_003840284.1| pseudouridine synthase [Caldicellulosiruptor obsidiansis OB47]
 gi|302574507|gb|ADL42298.1| pseudouridine synthase [Caldicellulosiruptor obsidiansis OB47]
          Length = 311

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 68/289 (23%), Positives = 123/289 (42%), Gaps = 24/289 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV+ +   +++++  K  YP I    + K+LR G++ V     +    ++ G  V    
Sbjct: 5   FVVDKELAGVKVEKAIKKKYPTIPMSVIFKMLRKGEIIVSFLPAQKGQVLRFGDTVSFEI 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H               K  + +K   +YED  I V +KP GI     S   Y +
Sbjct: 65  EDRFLEH---------------KKVEIIK---VYEDDNIVVIDKPYGIPSHPDSNNEYSV 106

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             +++    SKG+ P+L HRLD+ T+G++++A+ R     + +    R I K Y  +   
Sbjct: 107 VSWIEDNY-SKGELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRTIIKKYLCITKK 165

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               +   + ++L K S     Y+    Q+  G    ++ +K++         ++++  T
Sbjct: 166 ADLPESGVLVHYLKKDSKKSKVYISDFPQD--GYLEVVTAYKIV-RQKDDLQLVDVEIKT 222

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           G+THQ+R    H+G  I+GD KY             +   L A Y+   
Sbjct: 223 GKTHQIRAQLAHVGLCILGDSKYGDWELNKKYK--ADMQALCAYYLKFE 269


>gi|268679279|ref|YP_003303710.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
 gi|268617310|gb|ACZ11675.1| pseudouridine synthase, RluA family [Sulfurospirillum deleyianum
           DSM 6946]
          Length = 326

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 64/311 (20%), Positives = 116/311 (37%), Gaps = 36/311 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD         +    ++K+++   V VD              V+     +      +
Sbjct: 9   KRLDVAMSEILA-LPRNQVEKLIKKSGVYVD-------------DVLTHKCSLKLQESSV 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                +++  + + +       +LYED  I V NKP  ++V G   +    +  L  W+ 
Sbjct: 55  VRYDFIEAEASKSAYEIDFDVPVLYEDEDILVINKPPFLTVHGAPSV---KEPTLVDWLQ 111

Query: 139 SKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            +G         ++  + HR+D+ETSG LV+A+   A   L      + + + Y +++  
Sbjct: 112 HRGISLSTISGEERHGIVHRIDKETSGALVIAKNNEAHVKLASQLEDKSMGRYYLAII-D 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +P  +   +   + +           V++  + A  A    K       K   +  +  T
Sbjct: 171 LPLKENVVVDLPIGRNP--NHRLKMAVQREGRSAKSAFC--KCSLSHDGKKELIAAKLFT 226

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QIT 308
           GRTHQ+RVH   +   I+GD  Y              ++ LHA  + L HP    +  I 
Sbjct: 227 GRTHQIRVHLSALSRHILGDSLYGFKSHNG----TIPRVMLHAYILYLKHPRSQEMLYIH 282

Query: 309 APLPAHMVKTW 319
           APL        
Sbjct: 283 APLWDDFDDYL 293


>gi|16272559|ref|NP_438775.1| hypothetical protein HI0617 [Haemophilus influenzae Rd KW20]
 gi|145631647|ref|ZP_01787411.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae R3021]
 gi|260581431|ref|ZP_05849244.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae RdAW]
 gi|260583228|ref|ZP_05851006.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae NT127]
 gi|1175490|sp|P44782|RLUA_HAEIN RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|1573611|gb|AAC22276.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|144982726|gb|EDJ90258.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae R3021]
 gi|260091925|gb|EEW75875.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae RdAW]
 gi|260093730|gb|EEW77640.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae NT127]
 gi|301169333|emb|CBW28932.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Haemophilus influenzae 10810]
          Length = 219

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 107/229 (46%), Gaps = 16/229 (6%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            +++ +  L  + D     ++Y+D+ + V NKP+G+    G+   Y+      S V  K 
Sbjct: 2   ALIEYNPPLEPYLD-----IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKF 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGI+V A ++AA + L   FR R  +K Y ++VWG  +N    +   
Sbjct: 55  GFCEPAHRLDMATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLP 114

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           ++       +     + +      A++ F+V+         +++ P TGR+HQLR+H L 
Sbjct: 115 MICD----WENRPRQRLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLA 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +G PI+GD  Y        +     +L LHA  + + HP  G  +   A
Sbjct: 171 LGHPILGDKFYSHPQAKVMS----PRLCLHAEELTITHPITGETMTFNA 215


>gi|19703986|ref|NP_603548.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
 gi|296327555|ref|ZP_06870101.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
 gi|19714169|gb|AAL94847.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
 gi|296155381|gb|EFG96152.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
          Length = 288

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 134/320 (41%), Gaps = 38/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +VE++ +   +  + K    + +       LR+ ++ ++ KR           +  
Sbjct: 1   MKKYIVEHEYDGYEIGTYLKETKGYSSRG-----LRNLEIYLNGKR-----------IKN 44

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
               I  LN I+    +++   +    +  +   + YED  + + NK   I V      +
Sbjct: 45  NAKKIKKLNRIV----VIEKEKSTGIKAMDIPIDIAYEDENLLIVNKEPYIIVHPTQKKV 100

Query: 126 AYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +   + ++ +    K   PR  +RLD  TSG++++A+       L +      ++K 
Sbjct: 101 DKTLANAVVNYFEKTLGKTLVPRFYNRLDMNTSGLIIIAKNAYTQAFLQDKT---EVKKT 157

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFC 241
           Y  +  GI +     I   + K   +G D   +    E G   A +H KV++  + +   
Sbjct: 158 YKVIASGIIEKDDFFIKIPIGK---VGDDLRRIELSEENGGKSAKTHIKVLEKNYEKNIT 214

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +LE + +TGRTHQ+R H   +G  +VGD  Y  + K      +  +  LHA  ++  +P+
Sbjct: 215 FLEARLYTGRTHQIRAHLSLIGHSLVGDELYGGDMK------LAKRQMLHAYKLEFQNPK 268

Query: 302 G-GRLQITAPLPAHMVKTWD 320
               L+I   +P  M +   
Sbjct: 269 TLENLKIEIDIPVDMKEVLK 288


>gi|319775341|ref|YP_004137829.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae F3047]
 gi|317449932|emb|CBY86144.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae F3047]
          Length = 219

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 108/229 (47%), Gaps = 16/229 (6%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            +++ +  L  + D     ++Y+D+ + V NKP+G+    G+   Y+    + S V  K 
Sbjct: 2   ALIEYNPPLEPYLD-----IIYQDNHLCVVNKPSGLLSVPGNQPQYYDS--VMSRVKEKF 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGI+V A ++AA + L   FR R  +K Y ++VWG  +N    +   
Sbjct: 55  GFCEPAHRLDMATSGIIVFALSKAADRELKRQFREREPEKHYQAIVWGHLENDYGEVNLP 114

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           ++       +     + +      A++ F+V+         +++ P TGR+HQLR+H L 
Sbjct: 115 MICD----WENRPRQRLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLA 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +G PI+GD  Y        +     +L LHA  + + HP  G  +   A
Sbjct: 171 LGHPILGDKFYSHPQAKAMS----PRLCLHAEELTITHPITGETMTFNA 215


>gi|332828687|gb|EGK01379.1| hypothetical protein HMPREF9455_02212 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 242

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 51/227 (22%), Positives = 103/227 (45%), Gaps = 23/227 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V +  +  +R+D++   H   ++   +Q+   +  + V+   VK N +I+   V+ +  
Sbjct: 32  FVADKGQGMIRIDKYLAMHIVGVSRNRIQQAAEANCILVNDNPVKSNYKIKPLDVISV-- 89

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----SGI 125
               +N   +E +I+   + L          ++YED  + V NKP G+ V  G     G 
Sbjct: 90  ---VMNRPPRELEIIPEDIPLD---------VVYEDDDLMVINKPPGLVVHPGFGNYQGT 137

Query: 126 AYHIDGFLKS---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             +   +L       D+K  +  + HR+D++TSG++VVA+   A  HL+  F  +  ++ 
Sbjct: 138 LVNAVAYLLKDTPEYDAKDPRLGIVHRIDKDTSGLIVVAKNAYAKAHLSAQFFNKTTKRQ 197

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           Y +LVWG  +  +  I   + +        +  V ++ +    A++H
Sbjct: 198 YVALVWGAIEEDEGRIEGNIGRDLK--DRMLMTVFKDGEHGKSAVTH 242


>gi|237744692|ref|ZP_04575173.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           7_1]
 gi|229431921|gb|EEO42133.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           7_1]
          Length = 288

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 132/320 (41%), Gaps = 38/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   VE++ +   +  + K    + +       LR+ ++ ++ KR           +  
Sbjct: 1   MKKYTVEHEYDGYEIGTYLKEIKGYSSRG-----LRNLEIYLNGKR-----------IKN 44

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
               I  LN I+    I++   +    +  +   + YED  + + NK   I V       
Sbjct: 45  NAKKIKKLNRIV----IIEKEKSTGIKAMDIPIDIAYEDENLLIVNKEPYIIVHPTQKKV 100

Query: 125 IAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +  +  +  + G+K  PR  +RLD  TSG++++A+       L +      ++K 
Sbjct: 101 DKTLANAVVNYFEKTLGKKLVPRFYNRLDMNTSGLIIIAKNAYTQAFLQDKT---EVKKT 157

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFC 241
           Y  +  GI +     I   + K   +G D   +    + G   A +H KV++  + +   
Sbjct: 158 YKVIASGIIEKDDFFIEIPIGK---VGDDLRRIELSEKDGGKSAKTHIKVLERNYEKNIT 214

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +LE + +TGRTHQ+R H   +G  +VGD  Y  +        +  +  LHA  ++  +P+
Sbjct: 215 FLEARLYTGRTHQIRAHLSLIGHSLVGDELYGGDMN------LAKRQMLHAYKLEFQNPK 268

Query: 302 G-GRLQITAPLPAHMVKTWD 320
               L+I   +P  M +   
Sbjct: 269 TLENLKIEIDIPIDMKEVLK 288


>gi|89893256|ref|YP_516743.1| hypothetical protein DSY0510 [Desulfitobacterium hafniense Y51]
 gi|89332704|dbj|BAE82299.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 241

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 67/228 (29%), Positives = 109/228 (47%), Gaps = 9/228 (3%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-- 145
           +      +     ++YED+ + V +KP  I  Q  S     I   LK  +  +  KP   
Sbjct: 1   MRFEGVGELFTIPIVYEDNHLLVVDKPPNILSQKDSTGDMDILTLLKQDIKIRYNKPGNV 60

Query: 146 ---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD+   G++V A+T  +A  L+E  R R   K Y +L+ G P  +K  + ++L
Sbjct: 61  YLGLVHRLDRPVGGVMVFAKTSKSAARLSEQIRNREFTKTYLALIQGQPAKQKNTLIHYL 120

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           +K      + V  VK+  KGA  AI  ++V+   +     +++   TGR HQ+RV   H+
Sbjct: 121 VKDEK--SNKVSAVKKGAKGAKEAILDYEVVHSQSD-LSLVKVNLRTGRPHQIRVQFAHL 177

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           G P+ GD+KY    K + TS  +  L L +  +   HP   G++   +
Sbjct: 178 GHPLYGDYKYGKIVKTSKTSLTKPHLGLWSYEISCLHPISKGQIHFKS 225


>gi|307245129|ref|ZP_07527222.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|307247308|ref|ZP_07529356.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|307251849|ref|ZP_07533750.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|307254085|ref|ZP_07535932.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
 gi|307258540|ref|ZP_07540277.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 11
           str. 56153]
 gi|307260783|ref|ZP_07542470.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 12
           str. 1096]
 gi|306854018|gb|EFM86230.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|306856152|gb|EFM88307.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|306860541|gb|EFM92553.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|306863010|gb|EFM94957.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
 gi|306867444|gb|EFM99295.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 11
           str. 56153]
 gi|306869509|gb|EFN01299.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 12
           str. 1096]
          Length = 248

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 69/228 (30%), Positives = 109/228 (47%), Gaps = 14/228 (6%)

Query: 87  SVNLTKHSDFLKSIL--LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           ++ L ++   L+  L  +Y D+ I V NKP+G+    G+   Y+      + V  K    
Sbjct: 26  NMALIEYHPPLEPFLTEVYRDNHILVINKPSGLLSVPGNRPEYYDSAM--TRVQQKYGFT 83

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWL 202
              HRLD  TSGIL+ A ++AA + L   FR R  +K Y +L+WG    K       N+ 
Sbjct: 84  EPAHRLDMATSGILLFALSKAAEKELKRQFRDREPKKHYIALLWGKLGEKVGDTGEMNFP 143

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L           +  +       AI+H++V+         +++ P TGR+HQLRVH+L +
Sbjct: 144 LICDWENRPRQKICYER---GKKAITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLAL 200

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           G PI+GD  Y +    +    +  +L LHA  + + HP  G  +  TA
Sbjct: 201 GHPILGDKFYASPLAKS----LSPRLCLHAESLSITHPITGEAMTFTA 244


>gi|296102445|ref|YP_003612591.1| pseudouridylate synthase [Enterobacter cloacae subsp. cloacae ATCC
           13047]
 gi|295056904|gb|ADF61642.1| pseudouridylate synthase [Enterobacter cloacae subsp. cloacae ATCC
           13047]
          Length = 228

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 106/228 (46%), Gaps = 17/228 (7%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            I+DS +    H D     +L++D  + + NKP+G+    G          +   +    
Sbjct: 3   AIIDSFIAPPCHDDI---EILWQDEHLLLINKPSGLLSLSGKNPQN--LDSVHYRLVQSF 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +     L + F  R ++K+Y +L+ G  +N +  I   
Sbjct: 58  PGCTLVHRLDFGTSGLMVIARNKPINAALCQQFSQRSVEKVYSALLCGHLENNEGIIDAP 117

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF----CWLEMQPHTGRTHQLRV 257
           + K   +    + +   N      A S ++V++   Q        +E+ P TGRTHQLR+
Sbjct: 118 IAKDPAL-FPLMSICAVN---GKPARSRYRVVERLYQNAAMPLTRVELTPETGRTHQLRI 173

Query: 258 HALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           H   +G PI+G   Y    + G+ T+P   +L LHA  ++  HP  G 
Sbjct: 174 HCQLLGHPILGCDLYGGRTWPGSGTTP---RLMLHASQLNFIHPVSGE 218


>gi|87123579|ref|ZP_01079430.1| probable pseudouridine synthase [Synechococcus sp. RS9917]
 gi|86169299|gb|EAQ70555.1| probable pseudouridine synthase [Synechococcus sp. RS9917]
          Length = 314

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 72/316 (22%), Positives = 133/316 (42%), Gaps = 35/316 (11%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
             +    L  W  + Y H +    ++ L+SG++ ++ + ++ +  + +G  +R       
Sbjct: 3   AGQSGQLLSAWLADRYRHSSAATWRQRLQSGELGLNGRLLQGDVVVAAGDRIRW------ 56

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG-- 131
                  Q+       + +H        L++D  + V NKP+G+ V    G   H     
Sbjct: 57  -------QRPPWVEPAIPEHWQT-----LHDDGDVLVINKPSGLPVMPAGGFLVHTLSHQ 104

Query: 132 -FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-------IQKIY 183
             L S    +   P+  HRL + TSG+LV AR   +   L+   R           +K+Y
Sbjct: 105 LVLWSREQGEPLAPKPVHRLGRFTSGLLVCARRPESRAWLSRLLRDSTADGAASACRKVY 164

Query: 184 WSLVWGIPKN----KKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            +L   +P +    +   +   + +  H   G+       +   A  + S F +++   +
Sbjct: 165 RALTEPLPPDWPLGESREVTVAIGRHPHPLLGEIWCAADPSVATALPSRSSFTLLERRPE 224

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDL 297
             C +E+   +GR HQ+R+HA   G P++GD  Y       + + P +   +LHA  + L
Sbjct: 225 S-CLVEVVIASGRPHQIRIHAATAGAPLLGDPLYLPGGGASDQSLPGEGGYHLHAHRLQL 283

Query: 298 PHPEGGRLQITAPLPA 313
             P+GG L + APLP 
Sbjct: 284 ASPDGGLLDLEAPLPE 299


>gi|238786690|ref|ZP_04630491.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           frederiksenii ATCC 33641]
 gi|238725058|gb|EEQ16697.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           frederiksenii ATCC 33641]
          Length = 217

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 101/228 (44%), Gaps = 15/228 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G   A      + + + +        
Sbjct: 1   MEPYNPPRDPWLHILYQDEHIMVVNKPSGLLSVPGR--APENKDSVMTRIQADFPHAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG     +  I   L+    
Sbjct: 59  HRLDMATSGVIVVALTKAAERELKRQFREREPKKSYVARVWGHLAQDEGLIDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    + + + V+         +++ P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCYETGKSSQTEYLVLSRDTDGSTRVKLSPITGRSHQLRVHMLAIGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           I+GD  Y         S    +L LHA+ + + HPE G  +      P
Sbjct: 173 ILGDRFYAHPEAKAMAS----RLQLHAQELCITHPEFGTVMHFKCEAP 216


>gi|109900130|ref|YP_663385.1| pseudouridylate synthase [Pseudoalteromonas atlantica T6c]
 gi|109702411|gb|ABG42331.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           atlantica T6c]
          Length = 218

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 57/213 (26%), Positives = 105/213 (49%), Gaps = 12/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++D  + V NKP+G+    G  + +     L+  V       R+ HRLD  TSG+LV+
Sbjct: 16  IVFKDEYVLVLNKPSGLLTVPGKALEH--KDSLELRVQRVYPTARIVHRLDMATSGLLVM 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +   + L++ F +R+ +K Y + V+G    ++  +   L+         +   ++  
Sbjct: 74  ALDKDTHRQLSKQFELRQTRKTYIARVFGQVNGERGSVDLPLMCDWPNRPKQMVCQQR-- 131

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                +++H+++++        +E+ P TGR+HQLRVH L +G PI+GD  Y        
Sbjct: 132 --GKPSLTHWRILERN-DHTTRMELTPVTGRSHQLRVHMLSLGHPILGDRLYAHFD---- 184

Query: 281 TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
              + N+L LHA+ +   HP     +   AP+P
Sbjct: 185 ALAMANRLQLHAQTLGFTHPATNASVDFHAPVP 217


>gi|157961293|ref|YP_001501327.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157846293|gb|ABV86792.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 217

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 67/219 (30%), Positives = 100/219 (45%), Gaps = 13/219 (5%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K        + Y D  I V NKP+G+      GIA +      + +  + +   L HRLD
Sbjct: 7   KPPSIPWLDIRYLDRDIIVINKPSGLLSNP--GIAEYTHDCALTRLQQRFKDCILVHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V AR + A  +L   F+ R+ QK Y + V GI K +   I   +         
Sbjct: 65  CATSGIMVFARNKKAESNLKTQFQDRQTQKTYIAEVDGIFKLQSGVIELSIAADKLNPPK 124

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +       +    AI+H+KV+         +E++P TGRTHQLRVH L +G PI+GD  
Sbjct: 125 QMV-----SELGKAAITHYKVLQQKPHS-TLVELKPVTGRTHQLRVHMLAIGHPILGDDF 178

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           Y +            +L LHA+ +   HP  G+ +   +
Sbjct: 179 YGSEQ----VMSAAKRLQLHAQSLSFTHPYSGKAMHFNS 213


>gi|329768061|ref|ZP_08259571.1| hypothetical protein HMPREF0428_01268 [Gemella haemolysans M341]
 gi|328838329|gb|EGF87939.1| hypothetical protein HMPREF0428_01268 [Gemella haemolysans M341]
          Length = 293

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 60/325 (18%), Positives = 127/325 (39%), Gaps = 43/325 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR---SGQVRVDKKRVKFNNRIQ 60
           MT +    V  +E+ +R   +   +  +I+   L + ++    G ++V+ K       ++
Sbjct: 1   MTNIILKYVVKNEQVLR--EFLLEN--NISRKTLTR-IKFDNDGSIKVNSKEENVRYILK 55

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G +V I       +  +   + +D  ++           ++YED    V NK   +   
Sbjct: 56  EGDIVEITLPSENYSEFV---RFIDKPID-----------IVYEDDYFLVVNKEINLPSI 101

Query: 121 GGSG-IAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                    +   +  +   K     P +  RLD+ TSG++++A+ R      +      
Sbjct: 102 PSRNAEDESLLERVNYYFREKNINSIPHIVTRLDKNTSGLVLIAKHRHIHALFSNM---- 157

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF- 236
            I K Y +L+ G  K+    +   + + S        + ++  +G  YA + +       
Sbjct: 158 EIDKYYTALINGKIKDH-GILEAPIRRVSS-----SIIEREVGEGGEYAKTEYWSEKHNI 211

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 + ++ +TG+THQ+RVH  ++G P++GD  Y  +        + ++  LH   + 
Sbjct: 212 KNDINVIRLKLYTGKTHQIRVHMKYLGYPLLGDELYGGDIS------LISRQALHCSNLA 265

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWD 320
             HP    ++ +   LP  M     
Sbjct: 266 FIHPISREKVNVCTNLPDDMSNIIK 290


>gi|56412366|ref|YP_149441.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197361303|ref|YP_002140938.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|56126623|gb|AAV76129.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Paratyphi A str. ATCC
           9150]
 gi|197092778|emb|CAR58203.1| ribosomal large subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Paratyphi A str.
           AKU_12601]
          Length = 219

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 67/226 (29%), Positives = 106/226 (46%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDEHIMVVNKPSGLLSVPGR-LEAHKDSIM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VW  P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWRHPSPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + + V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            Y +         +  +L LHA  + + HP  G  +     +PA  
Sbjct: 180 FYASPE----ALSLAPRLQLHAEMLTITHPAYGTSMTFK--VPADF 219


>gi|329122662|ref|ZP_08251241.1| pseudouridine synthase A [Haemophilus aegyptius ATCC 11116]
 gi|327472676|gb|EGF18105.1| pseudouridine synthase A [Haemophilus aegyptius ATCC 11116]
          Length = 219

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 108/229 (47%), Gaps = 16/229 (6%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            +++ +  L  + D     ++Y+D+ + V NKP+G+    G+   Y+    + S V  K 
Sbjct: 2   ALIEYNPPLEPYLD-----IIYQDNHLCVVNKPSGLLSVPGNQPQYYDS--VMSRVKEKF 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGI+V A ++AA + L   FR R  +K Y ++VWG  +N    +   
Sbjct: 55  GFCEPAHRLDMATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLP 114

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           ++       +     + +      A++ F+V+         +++ P TGR+HQLR+H L 
Sbjct: 115 MICD----WENRPRQRLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLA 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +G PI+GD  Y        +     +L LHA  + + HP  G  +   A
Sbjct: 171 LGHPILGDKFYSHPQAKAMS----PRLCLHAEELTITHPITGETMTFNA 215


>gi|259502332|ref|ZP_05745234.1| ribosomal large subunit pseudouridine synthase [Lactobacillus antri
           DSM 16041]
 gi|259169712|gb|EEW54207.1| ribosomal large subunit pseudouridine synthase [Lactobacillus antri
           DSM 16041]
          Length = 309

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 64/282 (22%), Positives = 109/282 (38%), Gaps = 23/282 (8%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
            V ++ +    N  +  G  V +    +   +          S  +T         +L+E
Sbjct: 45  HVLLNGRYAYMNTAVAPGDRVMMAFNGDEFRNPTANDYCPTPSPAVT---------VLFE 95

Query: 105 DSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           +  + V NKP G        G    +   +  ++        + HRLDQETSG ++VA+ 
Sbjct: 96  NRDLVVVNKPQGQKSHPNYHGETGTLLNDVAGYLAGSDCGAFMVHRLDQETSGAMIVAKN 155

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
                 L       +I + Y ++V G    +       + K       Y        + A
Sbjct: 156 PVVVPVLNRLISSGQIHRRYLAVVAGRLTGR-GRFTEAIGKDPQDVRKYQ----VGGEHA 210

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
             A ++++V+     +   + +Q  TGRTHQ+RVH  H G PI+GD  Y  +        
Sbjct: 211 KPAQTNYQVLANQGDR-TLVLLQLATGRTHQIRVHLAHSGHPIIGDPLYSRDNFSRML-- 267

Query: 284 IQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
               L+  A+ + LP     R+Q+TAPLP +        G +
Sbjct: 268 ----LHGAAQELVLPFSF-KRIQVTAPLPTYFTDYLVKYGLE 304


>gi|298376445|ref|ZP_06986400.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 3_1_19]
 gi|298266323|gb|EFI07981.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 3_1_19]
          Length = 224

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 70/228 (30%), Positives = 109/228 (47%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I   +K     VQG       +   LK+W+  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIAVDKTCREIVQGDKTGDKPLSEMLKAWLKKKYCKPGNVFVGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR+  ++K YW++V   P   +  + +WL++       Y + 
Sbjct: 63  GVVIFAKTSKALSRLNEMFRVGEVRKTYWAIVKNRPPQDEGELVDWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  AI  +K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY  +
Sbjct: 123 TER--PNAKKAILRYKLI-AHSDHYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKYGFD 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                       + LHAR  +  HP     ++I AP+P      W +L
Sbjct: 180 RSNK-----DGGISLHARSAEFIHPVSKENVRIVAPVPDD--NLWKAL 220


>gi|188532876|ref|YP_001906673.1| 23S rRNA/tRNA pseudouridine synthase A [Erwinia tasmaniensis
           Et1/99]
 gi|188027918|emb|CAO95775.1| Ribosomal large subunit pseudouridine synthase A [Erwinia
           tasmaniensis Et1/99]
          Length = 217

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 70/226 (30%), Positives = 106/226 (46%), Gaps = 15/226 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G  +A + D  + + V          
Sbjct: 1   MEPYNPPQEPWLHVLYQDEHIIVVNKPSGLLSVPGR-LAEYKDSVM-TRVQRDYPAAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  QK Y + VWG PK     +   L+    
Sbjct: 59  HRLDMATSGVMVVALTKAAERELKRQFREREPQKTYVARVWGHPKPAIGLVDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ         A + ++V+D  +     + ++P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCFDSGKSAQTEYQVLDYASDNSARVLLKPITGRSHQLRVHMLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
           I+GD+ Y  +           +L LHA  + + HP+ G  +    P
Sbjct: 173 ILGDNFYAHDEARAMA----PRLQLHAESLCISHPQYGTPMTFRQP 214


>gi|330900138|gb|EGH31557.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. japonica str. M301072PT]
          Length = 211

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 63/214 (29%), Positives = 100/214 (46%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++++D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIHQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++      C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEGGKHALTFWKVVERH-DTHCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G R+      P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERMTFECAAP 210


>gi|238752280|ref|ZP_04613760.1| Ribosomal large subunit pseudouridine synthase A [Yersinia rohdei
           ATCC 43380]
 gi|238709548|gb|EEQ01786.1| Ribosomal large subunit pseudouridine synthase A [Yersinia rohdei
           ATCC 43380]
          Length = 218

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 68/231 (29%), Positives = 103/231 (44%), Gaps = 17/231 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G   A      + + + +        
Sbjct: 2   MEPYNPPRTPWLNILYQDEHIMVVNKPSGLLSVPGR--APENKDSIMTRILADFPTAESV 59

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG     +  I   L+    
Sbjct: 60  HRLDMATSGVMVVALTKAAERELKRQFREREPKKSYVARVWGHLAQDEGLIDLPLI---- 115

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    + + ++V+   A     +++ P TGR+HQLRVH L +G P
Sbjct: 116 --CDWPNRPKQKVCYETGKSSQTEYQVLSRDADGSTRVQLSPITGRSHQLRVHMLSIGHP 173

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           I+GD  Y         S    +L LHA+ + + HPE G  L       A  
Sbjct: 174 ILGDGFYAPPEAKAMAS----RLQLHAQELYITHPELGTALHFKCE--ADF 218


>gi|68249316|ref|YP_248428.1| pseudouridylate synthase [Haemophilus influenzae 86-028NP]
 gi|68057515|gb|AAX87768.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae 86-028NP]
          Length = 219

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 106/229 (46%), Gaps = 16/229 (6%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            +++ +  L  + D     ++Y+D+ + V NKP+G+    G+   Y+      S V  K 
Sbjct: 2   ALIEYNPPLEPYLD-----IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKF 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGI+V A ++AA + L   FR R  +K Y ++VWG  +     +   
Sbjct: 55  GFCEPAHRLDMATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLEKDYGEVNLP 114

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           ++       +     + +      A++ F+V+         +++ P TGR+HQLR+H L 
Sbjct: 115 MICD----WENRPRQRLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLA 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +G PI+GD  Y        +     +L LHA  + + HP  G  +   A
Sbjct: 171 LGHPILGDKFYSHPQAKAMS----PRLCLHAEELTITHPITGETMTFNA 215


>gi|46445765|ref|YP_007130.1| putative ribosomal large subunit pseudouridine synthase
           (pseudouridylate synthase), rluA [Candidatus
           Protochlamydia amoebophila UWE25]
 gi|46399406|emb|CAF22855.1| putative ribosomal large subunit pseudouridine synthase
           (pseudouridylate synthase), rluA [Candidatus
           Protochlamydia amoebophila UWE25]
          Length = 243

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 70/274 (25%), Positives = 122/274 (44%), Gaps = 37/274 (13%)

Query: 49  DKKRVKFNNR-IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           D   VK N+  +  GQV+ +           + +KI+ S +            +LYED+ 
Sbjct: 2   DGIVVKNNHFEVLEGQVISLN----------QRKKIVGSGI-----------QILYEDAD 40

Query: 108 IYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           + +  KP+G+     +          LK+    K +K  + HRLDQ+TSG++V A     
Sbjct: 41  LAIIYKPSGLLSVATAFEKGETTHALLKAHY--KPRKVFVVHRLDQDTSGVMVFAFNEKT 98

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
              L + F +  I + Y ++V G   +      ++L + S     Y     ++E     A
Sbjct: 99  CNGLKDLFEVHDISRSYTAIVEGQLLSPSGTWKSYLYEDSQ----YFVHETEDETYGRLA 154

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           I+H++ +    +K+  +E+   TGR +Q+RVH    G P+VGD KY A+           
Sbjct: 155 ITHYRTLKTL-KKYSLVELTLETGRKNQIRVHCQSAGHPVVGDKKYGAHTNP------LK 207

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           +L LHA  +   HP   + ++I +P+P    +  
Sbjct: 208 RLCLHAHLLAFKHPISRKIIRIESPIPEEFYRLI 241


>gi|125972800|ref|YP_001036710.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           thermocellum ATCC 27405]
 gi|256004990|ref|ZP_05429962.1| pseudouridine synthase [Clostridium thermocellum DSM 2360]
 gi|281416999|ref|ZP_06248019.1| pseudouridine synthase [Clostridium thermocellum JW20]
 gi|125713025|gb|ABN51517.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           thermocellum ATCC 27405]
 gi|255991059|gb|EEU01169.1| pseudouridine synthase [Clostridium thermocellum DSM 2360]
 gi|281408401|gb|EFB38659.1| pseudouridine synthase [Clostridium thermocellum JW20]
 gi|316940963|gb|ADU74997.1| pseudouridine synthase [Clostridium thermocellum DSM 1313]
          Length = 231

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 61/220 (27%), Positives = 103/220 (46%), Gaps = 14/220 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
            +++ED+ + V  KP  I  Q        +   LK  +  +  KP      L HRLD+  
Sbjct: 10  DIIFEDNHLLVVKKPVNIPTQKDKSNDSDMLTLLKEDIKKRYNKPGNVYLGLVHRLDRPV 69

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G++V A+T  AA  L++  R R+ +K+Y ++V GI    +  + N+LLK +    + V 
Sbjct: 70  GGVMVFAKTSKAASRLSDQVRTRQFKKVYLAVVHGILDKLEGRLENYLLKDTR--NNTVS 127

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VVK++  G   A+  +KV +     F  +++  HTGR HQ+RV   ++G P+ GD KY  
Sbjct: 128 VVKEDTPGGKLAVLDYKV-EGIYNGFSLVKVSLHTGRPHQIRVQLANIGHPLYGDQKYGH 186

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPA 313
                       ++ L +  +   HP     +  +   P 
Sbjct: 187 GVNKP-----GQQIALWSSEIAFVHPVLKQEMIFSCEPPE 221


>gi|330942690|gb|EGH45243.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. pisi str. 1704B]
          Length = 211

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 63/214 (29%), Positives = 100/214 (46%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++++D+   V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIHQDAAALVIDKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEGGKHALTFWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G R+      P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERMTFECAAP 210


>gi|117919251|ref|YP_868443.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           ANA-3]
 gi|117611583|gb|ABK47037.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           ANA-3]
          Length = 225

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 63/212 (29%), Positives = 106/212 (50%), Gaps = 12/212 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D  I V NKP+G+    G   A++    + + V ++    ++ HRLD  TSG++
Sbjct: 14  LDVLYQDKDIIVVNKPSGLLSVPGRDPAHYDS--VYARVKAEHPHCQIVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  R+A + L   F  R   K Y + V G  KN    +   L+             K 
Sbjct: 72  VVALIRSAERELKRQFHDRETSKTYLARVAGHVKNTTGSVDYPLICDWPNRPK----QKV 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    +++HF+V+   A++   ++++P TGR+HQLRVH + +G PI+GD  Y      
Sbjct: 128 DHEIGKPSLTHFEVLSR-AKRSTLVKLKPITGRSHQLRVHMMALGHPILGDGFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +    +  +L LHA  + + HP  G  +  +A
Sbjct: 187 S----LAPRLLLHAAELTIKHPYTGESMTFSA 214


>gi|257452370|ref|ZP_05617669.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|257465837|ref|ZP_05630148.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|315916994|ref|ZP_07913234.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|317058913|ref|ZP_07923398.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|313684589|gb|EFS21424.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|313690869|gb|EFS27704.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
          Length = 289

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 130/320 (40%), Gaps = 38/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +   +VE + +   +  + K      +   L+K+    ++ ++ K++K   +        
Sbjct: 1   MHKYIVEPEYDGYEIGEYLKES-KGYSGRGLRKL----EIYLNGKKIKNTAK-------- 47

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
               +  LN +     I++           +   ++YED  + + NK A +     +   
Sbjct: 48  ---KVRKLNRVF----IVEKEKETGIRPMDIPLEIVYEDENLLILNKQANLVTHPTTKKV 100

Query: 125 IAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            A   +G +  ++ + G+   PR  +RLD  T+G+++V +   +  +L E      ++K 
Sbjct: 101 DATLANGVVAYFLKTTGKTMVPRFYNRLDMNTTGLIIVTKNAYSQAYLQEKT---EVRKS 157

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFC 241
           Y ++V GI +  +  I   + K   +G D   +     +G   A +  KV+  F  +   
Sbjct: 158 YQTIVKGIVEQDEFYITKPIGK---VGEDLRRIELAVSEGGQEAKTFVKVLKRFPERNRT 214

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L++   TGRTHQ+R H    G PIVGD  Y              +  LHA  +   +P+
Sbjct: 215 LLDVTLFTGRTHQIRAHLSLEGYPIVGDDLYGG------ADDRIKRQLLHAYRLTFQNPK 268

Query: 302 GGR-LQITAPLPAHMVKTWD 320
            G   +I   L   M    +
Sbjct: 269 NGEQQEIMIDLAKDMQDYLN 288


>gi|237807273|ref|YP_002891713.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
 gi|237499534|gb|ACQ92127.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
          Length = 242

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 101/243 (41%), Gaps = 18/243 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +K  +LY+D  +   NKPAG+ V             ++   D  GQ     HRLD+ TSG
Sbjct: 1   MKLEILYQDEHLVAINKPAGLLVHRSWLDKGETQFAMQMTRDQIGQHVYTVHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           IL+ A     A+ LT++F   R+QK Y +LV G    +K        +   I   +    
Sbjct: 61  ILLFALDPDTARLLTDAFAGHRMQKEYLALVRGWAPLQKFLDYPLKEELDRIADKFADQ- 119

Query: 217 KQNEKGANYAISHFKVIDC-----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              +K A  A +H + +              + ++  +++ P TGR HQLR H  H+  P
Sbjct: 120 ---DKPAQPAKTHIRCLGRVELPFAVSPRHPSSRYSLVKLLPLTGRKHQLRRHLAHLRHP 176

Query: 266 IVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           IVGD  +       F       ++L LH   +   HP     L I A L     +   + 
Sbjct: 177 IVGDTSHGDGRHNRFFRDQFSCDRLMLHHHQLSFRHPHSNELLTIRASLDERWQQQLQAF 236

Query: 323 GFK 325
            ++
Sbjct: 237 NWQ 239


>gi|261364336|ref|ZP_05977219.1| tRNA pseudouridine synthase [Neisseria mucosa ATCC 25996]
 gi|288567596|gb|EFC89156.1| tRNA pseudouridine synthase [Neisseria mucosa ATCC 25996]
          Length = 235

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 65/223 (29%), Positives = 97/223 (43%), Gaps = 20/223 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY DS+    NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYRDSRTIAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVYPAHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    AA+ LT+ F  +  +K YW++V G   +          +   I         Q E
Sbjct: 64  ALDPEAARLLTQQFEQKTTRKTYWAIVRGYLPDDGLIDYPLKYQPDKIAES------QTE 117

Query: 221 KGANYAISHFKVIDC-----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                A + ++ +                ++ W E+ PHTGR HQLR H  H+  PIVGD
Sbjct: 118 ATLQEAQTQYRCLARTELPFQSAARYPTSRYSWAELIPHTGRKHQLRRHMKHIFHPIVGD 177

Query: 270 HKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITA 309
             Y    + + T+      +L LHAR +     E G  L + A
Sbjct: 178 TNYGDLRQNHATAAHLGTTRLMLHARSISFQSIENGETLTVCA 220


>gi|116628160|ref|YP_820779.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus LMD-9]
 gi|116101437|gb|ABJ66583.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           thermophilus LMD-9]
          Length = 298

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 69/314 (21%), Positives = 126/314 (40%), Gaps = 33/314 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           R+  + K H   I+   L KI    G + V+ +       +  G VV I           
Sbjct: 12  RVKTFLKEH--DISKGLLAKIKFEGGHIWVNGEEQFATYPVHEGDVVAI----------- 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV- 137
              +I D + + T         ++YED    V NKP G +          +  F+K    
Sbjct: 59  ---EIPDEAPHETLKPIPFDLDIVYEDDNFLVINKPYGYASIPSVNHDNTMANFVKHHFV 115

Query: 138 --DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NK 194
             +   Q+  +  RLD++TSG+++ A+   A   + +  + + I+K Y++LV G  K  +
Sbjct: 116 SNNYPNQRVHIVTRLDKDTSGLMLFAKHGYAHARMDKQLQQKSIKKHYYALVEGETKLEQ 175

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I   + +          + ++  K   YA + ++++  + +    +++  HTGRTHQ
Sbjct: 176 EGEIIAPIARDVD-----SIITRRVHKSGKYAHTSYRLVGDYGR-VKLVDINLHTGRTHQ 229

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
           +RVH  H+G P++GD  Y  +           +  LH   +    P     +   + L  
Sbjct: 230 IRVHFAHLGLPLLGDDLYGGSL-----DYGIERQALHCHRLAFVDPFTKKEMVHESSLTD 284

Query: 314 HMVKTWDSLGFKYD 327
                   L  K D
Sbjct: 285 DFETVIMDLKTKKD 298


>gi|157962835|ref|YP_001502869.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157847835|gb|ABV88334.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 572

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 71/243 (29%), Positives = 113/243 (46%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L+H++   + +D +  LT  ++     ++Y+D  + V NKPA      G  +   +
Sbjct: 337 CQPILSHMLAGIE-MDENPLLTNPAEGKSLEIIYQDEVMAVVNKPAEFLSVPGKNVTDSV 395

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K+        P + HRLD  TSG++V+A TR A + L + F  R ++K Y + V G
Sbjct: 396 YARMKAQFPQ-ATGPLIVHRLDMSTSGLMVIALTRDANKSLAQQFIARTVEKRYLAQVPG 454

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +   +K  I   L  +  I      +V        +A++H++V    +     L + PHT
Sbjct: 455 VVLGEKGEICLPL--RGDIDDRPRQLVCYEH--GKHALTHWQV-KSRSNDATMLYLYPHT 509

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVH  H   +  PI+GD  Y             N+L+LHA+ + L HP    RL
Sbjct: 510 GRTHQLRVHCAHHEGLHLPIIGDDLYGKK---------ANRLHLHAQRLVLNHPVSRERL 560

Query: 306 QIT 308
              
Sbjct: 561 TFE 563


>gi|27375585|ref|NP_767114.1| hypothetical protein blr0474 [Bradyrhizobium japonicum USDA 110]
 gi|27348722|dbj|BAC45739.1| blr0474 [Bradyrhizobium japonicum USDA 110]
          Length = 218

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 72/225 (32%), Positives = 113/225 (50%), Gaps = 11/225 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ D  + V +KPAG+ V  G     +++    +      + P L HRLD++TSG L++ 
Sbjct: 2   LHRDGLMLVIDKPAGLPVHRGPKGGANLEASFDALRFGLPRPPVLAHRLDKDTSGCLILG 61

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R R A   L   F+  +I K YW++V G P   +  I   L + +   G +     + + 
Sbjct: 62  RHRKATASLGLLFKHGKIGKTYWTVVEGGPAEDEGTIDMPLGRLNAERGWWQ----KPDP 117

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+++KV+      F WL M+P TGRTHQLRVH+   G PI GD+ Y      N  
Sbjct: 118 EGQKAITNWKVMGR-GDGFTWLAMEPVTGRTHQLRVHSAATGWPIFGDNIYG-----NGP 171

Query: 282 SPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
              + KL+LH+R + +P       +++ AP P HM +   + G+ 
Sbjct: 172 RFGEPKLHLHSREIVVPISRNKEPVRVVAPAPPHMHEKLRACGWN 216


>gi|167625019|ref|YP_001675313.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167355041|gb|ABZ77654.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 572

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 72/243 (29%), Positives = 115/243 (47%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L+H++ E   +D +  L+  ++     +LY+D  + V NKPA      G  +   +
Sbjct: 337 CQPILSHML-EGVEMDPNPLLSNPAEGKSIEVLYQDEAMAVINKPAEFLSVPGKNVTDSV 395

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +KS        P + HRLD  TSG++V+A TR A + L + F  R ++K Y + V G
Sbjct: 396 YARMKSMFPQ-ATGPLIVHRLDMSTSGLMVIALTRDANKSLAQQFIARTVEKRYVAQVAG 454

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           + + ++  I+  L +          V     K   +A + ++V    ++K   L + PHT
Sbjct: 455 VVQGEQGEISLPL-RVDLDDRPRQLVCY---KHGKHAHTLWQV-KSRSEKHTMLYLYPHT 509

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVH  H   +  PI+GD  Y +           N+L+LHA+ + L HP    RL
Sbjct: 510 GRTHQLRVHCAHHDGLHLPIIGDDLYGSK---------ANRLHLHAQKLVLNHPVSKERL 560

Query: 306 QIT 308
              
Sbjct: 561 TFE 563


>gi|294785258|ref|ZP_06750546.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_27]
 gi|294486972|gb|EFG34334.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_27]
          Length = 288

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 134/320 (41%), Gaps = 38/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +VE++ +   +  + K    + +       LR+ ++ ++ KR           +  
Sbjct: 1   MKKYIVEHEYDGYEIGTYLKETKGYSSRG-----LRNLEIYLNGKR-----------IKN 44

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
               I  LN I+    I++   +    +  +   + YED  + + NK   I V      +
Sbjct: 45  NAKKIKKLNRIV----IIEKEKSTGIKAIDIPIDIAYEDENLLIVNKEPYIIVHPTQKKV 100

Query: 126 AYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +   + ++ +    K   PR  +RLD  TSG++++A+       L +      ++K 
Sbjct: 101 DKTLANAIVNYFEKTLGKTLVPRFYNRLDMNTSGLIIIAKNAYTQAFLQDKT---EVKKT 157

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFC 241
           Y  +  GI +     I   + K   +G D   +    + G   A +H KV++  + +   
Sbjct: 158 YKVIASGIIEKDDFFIELPIGK---VGDDLRRIELSEKDGGKSAKTHIKVLERNYEKNIT 214

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +LE + +TGRTHQ+R H   +G  +VGD  Y  + K      +  +  LHA  ++  +P+
Sbjct: 215 FLEARLYTGRTHQIRAHLSLIGHSLVGDELYGGDMK------LAKRQMLHAYKLEFQNPK 268

Query: 302 G-GRLQITAPLPAHMVKTWD 320
               L+I   +P  M +   
Sbjct: 269 TLENLKIEIDIPIDMKEILK 288


>gi|289671918|ref|ZP_06492808.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. syringae FF5]
 gi|330975239|gb|EGH75305.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. aptata str. DSM 50252]
          Length = 211

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 63/214 (29%), Positives = 100/214 (46%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++++D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIHQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++      C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEGGKHALTFWKVVERH-DAHCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G R+      P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERMTFECAAP 210


>gi|55821440|ref|YP_139882.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMG 18311]
 gi|55823366|ref|YP_141807.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus CNRZ1066]
 gi|55737425|gb|AAV61067.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus LMG 18311]
 gi|55739351|gb|AAV62992.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus CNRZ1066]
 gi|312278771|gb|ADQ63428.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 298

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 69/314 (21%), Positives = 126/314 (40%), Gaps = 33/314 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           R+  + K H   I+   L KI    G + V+ +       +  G VV I           
Sbjct: 12  RVKTFLKEH--DISKGLLAKIKFEGGHIWVNGEEQFATYPVHEGDVVAI----------- 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV- 137
              +I D + + T         ++YED    V NKP G +          +  F+K    
Sbjct: 59  ---EIPDEAPHETLKPIPFDLDIVYEDDNFLVINKPYGYASIPSVNHDNTMANFVKHHFV 115

Query: 138 --DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NK 194
             +   Q+  +  RLD++TSG+++ A+   A   + +  + + I+K Y++LV G  K  +
Sbjct: 116 SNNYPNQRVHIVTRLDKDTSGLMLFAKHGYAHARMDKQLQQKSIKKHYYALVEGETKLEQ 175

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I   + +          + ++  K   YA + ++++  + +    +++  HTGRTHQ
Sbjct: 176 QGEIIAPIARDVD-----SIITRRVHKSGKYAHTSYRLVGDYGR-VKLVDINLHTGRTHQ 229

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
           +RVH  H+G P++GD  Y  +           +  LH   +    P     +   + L  
Sbjct: 230 IRVHFAHLGLPLLGDDLYGGSL-----DYGIERQALHCHRLAFVDPFTKKEMVHESSLTD 284

Query: 314 HMVKTWDSLGFKYD 327
                   L  K D
Sbjct: 285 DFETVIMDLKTKKD 298


>gi|320590514|gb|EFX02957.1| drap deaminase [Grosmannia clavigera kw1407]
          Length = 528

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 59/266 (22%), Positives = 110/266 (41%), Gaps = 32/266 (12%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           +        +  L +G V V+++ V  ++ +++G+ +              E  +    +
Sbjct: 82  FRDRPLAYYRAALEAGTVTVNQQTVGPDHVLRNGERISHRTHR-------HEPPVTAEPI 134

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
                      ++++ED  + V NKPAG+ V       Y+    +       G  P   +
Sbjct: 135 -----------VVIHEDDDMVVINKPAGVPVHPAGRYQYNSVVEMLKAQREPGFMPYPCN 183

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSH 207
           RLD+ TSGI+ +A++ AAA+ L+   + R ++K Y + V G  P  ++ C    L     
Sbjct: 184 RLDRLTSGIMFLAKSPAAAKRLSLQIQARAVRKEYLARVVGRFPDGQQVCDQPILQISPK 243

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCF-------AQKFCWLEMQPHTGRTHQLRVHAL 260
           +G + V            A + F+ +  +       ++ +  +   P TGRTHQ+RVH  
Sbjct: 244 LGLNRVRA------NGRSARTVFQRLAYYEGSAGGRSEGYSVVRCLPVTGRTHQIRVHLQ 297

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++G PI  D  Y       F     +
Sbjct: 298 YLGHPIENDPIYANQRVWGFELGAGD 323


>gi|162447506|ref|YP_001620638.1| pseudouridylate synthase, 23S RNA-specific [Acholeplasma laidlawii
           PG-8A]
 gi|161985613|gb|ABX81262.1| pseudouridylate synthase, 23S RNA-specific [Acholeplasma laidlawii
           PG-8A]
          Length = 277

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 69/308 (22%), Positives = 127/308 (41%), Gaps = 41/308 (13%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS +T      +E+    + +  + + +  ++    + K   +    V+ K V    R++
Sbjct: 1   MSTLT----FNIEDKYVGITIREYLQTY--NVGKPVIYKYSSNHLFEVNFKAVNSEYRLK 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G V+ I      +N I                 + ++  ++YED  I + NKP  + V 
Sbjct: 55  KGDVLNIHLEPYVMNDI-----------------EDVELDIIYEDDDIVIVNKPFNVIVH 97

Query: 121 GGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                  H+   +       G        HR+D+ET+GI+V A+   A  +L+  F  R+
Sbjct: 98  DDGASEDHLTRRVNMHFQYHGYHHQVLPAHRIDKETTGIVVFAKHFIALAYLSNLFESRQ 157

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y  +V    K+K   I + L+K S +                 AI+H++++   A 
Sbjct: 158 VVKNYICVVENKVKDKTGSIESKLIKDSKLQK------MVVSPHGKLAITHYELLGYEAT 211

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +   L++Q  TGRTHQ+R H   +  P+VGD  Y  +          ++L LH   +  P
Sbjct: 212 R-SRLKVQIETGRTHQIRAHMASINHPVVGDILYGVS---------SSRLLLHFSEISFP 261

Query: 299 HPEGGRLQ 306
                +++
Sbjct: 262 MIRTKKVE 269


>gi|46143820|ref|ZP_00133946.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
 gi|165975772|ref|YP_001651365.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|303249525|ref|ZP_07335732.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|303252557|ref|ZP_07338720.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|165875873|gb|ABY68921.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|302648525|gb|EFL78718.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|302651599|gb|EFL81748.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
          Length = 222

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 66/211 (31%), Positives = 101/211 (47%), Gaps = 12/211 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+      + V  K       HRLD  TSGIL+ A
Sbjct: 17  VYRDNHILVINKPSGLLSVPGNRPEYYDSAM--TRVQQKYGFTEPAHRLDMATSGILLFA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWLLKKSHIGGDYVHVVKQN 219
            ++AA + L   FR R  +K Y +L+WG    K       N+ L           +  + 
Sbjct: 75  LSKAAEKELKRQFRDREPKKHYIALLWGKLGEKVGDTGEMNFPLICDWENRPRQKICYER 134

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y +    +
Sbjct: 135 ---GKKAITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGDKFYASPLAKS 191

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
               +  +L LHA  + + HP  G  +  TA
Sbjct: 192 ----LSPRLCLHAESLSITHPITGEAMTFTA 218


>gi|221217613|ref|ZP_03589082.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           72a]
 gi|225550261|ref|ZP_03771220.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           118a]
 gi|221192559|gb|EEE18777.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           72a]
 gi|225369129|gb|EEG98583.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           118a]
          Length = 313

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 134/316 (42%), Gaps = 21/316 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    ++ V  ++   RLD        + +   + K +R G +R++  +  F+ R+  G 
Sbjct: 1   MDKYIFLEVLANDNGKRLDSILIKIL-NFSKAIIIKHIRKGDIRLNGLKSHFSCRVCKGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +   +    ++      +D          +++  ++YEDS + V +K  GI V GG 
Sbjct: 60  KIYLYKSLAQNLNL-----TMDECFKSNIDFKYIRKRIIYEDSDLLVLDKQKGILVHGGK 114

Query: 124 G-IAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + + ++ +L S  + S   KP   HRLD+ TSGI++ A+    A+ L+ +F    I K
Sbjct: 115 NSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTARKLSAAFSGGSIIK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++++ G  K+      N L +   +   +V       K    AI+    I    ++  
Sbjct: 175 KYFAILLGEVKSP-VVYKNHLFRNKRLRKTFV----LEGKNFVNAITKVNPILSC-KRAT 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+   TG THQ+R        P++ D KYC  FK +         +LHA  +      
Sbjct: 229 LVEIVIETGFTHQIRSQCSFNNHPLINDKKYCNKFKKSD-------YFLHAFLVKFNGTF 281

Query: 302 GGRLQITAPLPAHMVK 317
             + +  +      +K
Sbjct: 282 FKKNEFCSKPSLEFLK 297


>gi|300361154|ref|ZP_07057331.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           gasseri JV-V03]
 gi|300353773|gb|EFJ69644.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           gasseri JV-V03]
          Length = 285

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 65/301 (21%), Positives = 120/301 (39%), Gaps = 28/301 (9%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNR 58
           M  MT Y  ++    +   + +D   +     I     +  LR   Q+ ++   +  N  
Sbjct: 1   MEKMTSYHYFLTYPANLGPISVDELMRKLL--IPR-KWRHFLRTENQILINGHYLPLNFL 57

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +++G  + I      L+H+  EQ+   +S +L +        ++YEDS I + +KPAG  
Sbjct: 58  VKAGDKIDIY-----LDHVESEQQTYTASGSLPE--------VVYEDSDILIIDKPAGQK 104

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                      D  L       G  P + HRLD  T+G+L+VA+  A    L      + 
Sbjct: 105 THPN---LNEKDTALNDCATYLGYSPFIVHRLDMLTNGLLLVAKNPAVVPILNRQLTNKT 161

Query: 179 IQKIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           + + Y + V    +  +   I+  +    +     +            AI+H++++    
Sbjct: 162 LHREYLAWVSKSNQLKQSGTISLPIGHDPNDQRKRMVR-----PDGQKAITHYEIVKECE 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            K   +++   TGRTHQ+RVH   +  PI+GD  Y  N++   +  +        R    
Sbjct: 217 NKA-LVKLTLETGRTHQIRVHLAALNAPIIGDPLYNPNYQKGESLQLTAYQLTFMRPFKF 275

Query: 298 P 298
            
Sbjct: 276 E 276


>gi|226945565|ref|YP_002800638.1| Pseudouridylate synthase RluA [Azotobacter vinelandii DJ]
 gi|226720492|gb|ACO79663.1| Pseudouridylate synthase RluA [Azotobacter vinelandii DJ]
          Length = 211

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 66/213 (30%), Positives = 105/213 (49%), Gaps = 11/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  + V NKP  +    G     + D  +    ++   + R+ HRLD ETSG++V+
Sbjct: 8   IVHRDDALLVVNKPTLLLSVPGRA-EDNRDCLVTRLQENGYPEARIVHRLDWETSGLIVL 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR   + + L+  F  R  +K Y +L WG P+     I   L           HVV Q +
Sbjct: 67  ARDADSHRELSRQFHDRETEKAYTALCWGEPEADSGRIELPLRYDPPT--KPRHVVDQQQ 124

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               +A++ ++V++   + F  +E+ P TGR+HQLRVH L +G P++GD  Y        
Sbjct: 125 --GRHALTFWRVLERCGR-FSRIELTPITGRSHQLRVHMLAIGHPLLGDRLYAHGEALAA 181

Query: 281 TSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
                 +L LHA  + L HP  G RL+  +P P
Sbjct: 182 AE----RLCLHASLLVLGHPRSGERLRFESPAP 210


>gi|195941975|ref|ZP_03087357.1| hypothetical protein Bbur8_03759 [Borrelia burgdorferi 80a]
 gi|216264763|ref|ZP_03436755.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           156a]
 gi|226320862|ref|ZP_03796414.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           29805]
 gi|215981236|gb|EEC22043.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           156a]
 gi|226233728|gb|EEH32457.1| RNA pseudouridine synthase family protein [Borrelia burgdorferi
           29805]
          Length = 313

 Score =  170 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 135/316 (42%), Gaps = 21/316 (6%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M    ++ V  ++   RLD        + +   + K +R G +R++  +  F+ R+  G 
Sbjct: 1   MDKYIFLEVLANDNGKRLDSILIKIL-NFSKAIIIKHIRKGDIRLNGLKSHFSCRVCKGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +   +    ++      +D          +++  ++YEDS + V +K  GI V GG 
Sbjct: 60  KIYLYKSLAQNLNL-----TMDECFKSNIDFKYIRKRIIYEDSDLLVLDKQKGILVHGGK 114

Query: 124 G-IAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             + + ++ +L S  + S   KP   HRLD+ TSGI++ A+    A+ L+ +F    I K
Sbjct: 115 NSLDFLVNSYLLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTARKLSAAFSGGSIIK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y++++ G  K+      N L +   +   +V      +K    AI+    I    ++  
Sbjct: 175 KYFAILLGEVKSP-VVYKNHLFRNKRLRKTFV----LEDKNFVNAITKVNPILSC-KRAT 228

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E+   TG THQ+R        P++ D KYC  FK +         +LHA  +      
Sbjct: 229 LVEIVIETGFTHQIRSQCSFNNHPLINDKKYCNKFKKSD-------YFLHAFLVKFNGTF 281

Query: 302 GGRLQITAPLPAHMVK 317
             + +  +      +K
Sbjct: 282 FKKNEFCSKPSLEFLK 297


>gi|145300070|ref|YP_001142911.1| tRNA pseudouridine synthase C [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142852842|gb|ABO91163.1| tRNA pseudouridine synthase C [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 246

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 110/250 (44%), Gaps = 19/250 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETS 155
           +K  LLY+D  +   NKP+G+ V             ++   D  G +     HRLD+ TS
Sbjct: 1   MKLTLLYQDDWLVAVNKPSGLLVHRSWLDKAETRFAMQMTRDLIGGRHVYPVHRLDRPTS 60

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+ A   A A+ LTE+F  R++ K Y +LV G    ++  I   L +           
Sbjct: 61  GVLLFALDPAVARILTEAFAARQVHKEYLALVRG-WAPEQGVIDYPLKE---QLDKIADA 116

Query: 216 VKQNEKGANYAISHFKVI-----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +   ++ A  A++ F+ +                ++  +++ P TGR HQLR H  H+  
Sbjct: 117 MSNPDRPAQEAVTAFRCLHQVELPHAVSKKHPTSRYSLVKLFPKTGRKHQLRRHMEHLFH 176

Query: 265 PIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           PIVGD  +       F        +L L AR +   HP     ++I APL   +++ +  
Sbjct: 177 PIVGDTTHGDGRHNRFFREHFGCERLLLVARTLSFEHPILKVPMRIQAPLGLDLLQLFAE 236

Query: 322 LGFKYDRNLY 331
           LG+    + Y
Sbjct: 237 LGWPGSESDY 246


>gi|256845446|ref|ZP_05550904.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_36A2]
 gi|256719005|gb|EEU32560.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_36A2]
          Length = 288

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 134/320 (41%), Gaps = 38/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  +VE++ +   +  + K    + +       LR+ ++ ++ KR           +  
Sbjct: 1   MKKYIVEHEYDGYEIGTYLKETKGYSSRG-----LRNLEIYLNGKR-----------IKN 44

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
               I  LN I+    I++   +    +  +   + YED  + + NK   I V      +
Sbjct: 45  NAKKIKKLNRIV----IIEKEKSTGIKAIDIPIDIAYEDENLLIVNKEPYIIVHPTQKKV 100

Query: 126 AYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +   + ++ +    K   PR  +RLD  TSG++++A+       L +      ++K 
Sbjct: 101 DKTLANAIVNYFEKTLGKTLVPRFYNRLDMNTSGLIIIAKNAYTQAFLQDKT---EVKKT 157

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFC 241
           Y  +  GI +     I   + K   +G D   +    + G   A +H KV++  + +   
Sbjct: 158 YKVIASGIIEKDDFFIELPIGK---VGDDLKRIELSEKDGGKSAKTHIKVLERNYEKNIT 214

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +LE + +TGRTHQ+R H   +G  +VGD  Y  + K      +  +  LHA  ++  +P+
Sbjct: 215 FLEARLYTGRTHQIRAHLSLIGHSLVGDELYGGDMK------LAKRQMLHAYKLEFQNPK 268

Query: 302 G-GRLQITAPLPAHMVKTWD 320
               L+I   +P  M +   
Sbjct: 269 TLENLKIEIDIPIDMKEILK 288


>gi|77462043|ref|YP_351547.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides 2.4.1]
 gi|126460932|ref|YP_001042046.1| pseudouridine synthase [Rhodobacter sphaeroides ATCC 17029]
 gi|332559970|ref|ZP_08414292.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides WS8N]
 gi|77386461|gb|ABA77646.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides 2.4.1]
 gi|126102596|gb|ABN75274.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides ATCC 17029]
 gi|332277682|gb|EGJ22997.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides WS8N]
          Length = 215

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 65/220 (29%), Positives = 106/220 (48%), Gaps = 13/220 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
              +   L++ D++I V +KPAG+    G G        L   +     +  L HRLD++
Sbjct: 7   PPDVPLSLIHHDAQIVVVDKPAGLLSVPGKGED--KADCLIERLRGVFPEILLVHRLDRD 64

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V A T+AA   L + F  R+ +KIY + V G  + ++  +   L           
Sbjct: 65  TSGVMVFALTKAAQGALGQQFEKRQTKKIYVARVAGRLEPREGRVDLPLCVD-WPNRPKQ 123

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           HV   + +    A + ++V+    ++   + + P TGR+HQLRVH    G PI+GD  Y 
Sbjct: 124 HV---DPENGRPAQTDWRVVKYLPKE-TRVRLMPVTGRSHQLRVHMAETGHPILGDALYA 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                +F      +L LHA  + + HP+ G+ L  +AP P
Sbjct: 180 EGAARDFP-----RLMLHAESLRVRHPDTGKSLTYSAPCP 214


>gi|34762661|ref|ZP_00143653.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
 gi|27887682|gb|EAA24759.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
          Length = 292

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 67/324 (20%), Positives = 135/324 (41%), Gaps = 38/324 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   ++  +VE++ +   +  + K    + +       LR+ ++ ++ KR          
Sbjct: 1   MRKKMKKYIVEHEYDGYEIGTYLKETKGYSSRG-----LRNLEIYLNGKR---------- 45

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +      I  LN I+    I++   +    +  +   + YED  + + NK   I V   
Sbjct: 46  -IKNNAKKIKKLNRIV----IIEKEKSTGIKAIDIPIDIAYEDENLLIVNKEPYIIVHPT 100

Query: 123 -SGIAYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              +   +   + ++ +    K   PR  +RLD  TSG++++A+       L +      
Sbjct: 101 QKKVDKTLANAIVNYFEKTLGKTLVPRFYNRLDMNTSGLIIIAKNAYTQAFLQDKT---E 157

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FA 237
           ++K Y  +  GI +     I   + K   +G D   +    + G   A +H KV++  + 
Sbjct: 158 VKKTYKVIASGIIEKDDFFIELPIGK---VGDDLRRIELSEKDGGKSAKTHIKVLERNYE 214

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +   +LE + +TGRTHQ+R H   +G  +VGD  Y  + K      +  +  LHA  ++ 
Sbjct: 215 KNITFLEARLYTGRTHQIRAHLSLIGHSLVGDELYGGDMK------LAKRQMLHAYKLEF 268

Query: 298 PHPEG-GRLQITAPLPAHMVKTWD 320
            +P+    L+I   +P  M +   
Sbjct: 269 QNPKTLENLKIEIDIPIDMKEILK 292


>gi|315180900|gb|ADT87814.1| pseudouridine synthase Rlu family protein [Vibrio furnissii NCTC
           11218]
          Length = 243

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 104/241 (43%), Gaps = 21/241 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ I   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IIYQDAYIVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A ++   F    ++K Y ++V G  +     + ++ LK+            + +
Sbjct: 64  ALSSEIAANMMPMFANHEMEKTYHAIVRGWIEA--GDVLDYPLKEEL--DKIADKFAKQD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++C +EM+P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KAPQDAVTAYQPLAQVEVPHSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            +           +   ++L LHA  +   HP     L + A        TW  L   +D
Sbjct: 180 THGDGKHNRLYREVYDAHRLMLHASELRFVHPYTEQELVLRA----GFDATWQRLFALFD 235

Query: 328 R 328
            
Sbjct: 236 W 236


>gi|301155357|emb|CBW14823.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Haemophilus parainfluenzae T3T1]
          Length = 219

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 62/214 (28%), Positives = 101/214 (47%), Gaps = 13/214 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y+D+ I V NKP+G+    G+   Y+      S V  K       HRLD  TSGI+
Sbjct: 14  LDIIYQDNHICVVNKPSGLLSVPGNQPEYYDSAM--SRVKEKFGFCEPAHRLDMATSGII 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK-SHIGGDYVHVVK 217
           + A ++AA + L   FR R  +K Y +LVWG  +     I   ++    +     +  V 
Sbjct: 72  LFALSKAADKELKRQFREREPKKYYQALVWGHLEQDSGEINLPMICDWENRPRQRIDFVF 131

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A++ ++V++        +++ P TGR+HQLR+H L +G PI+GD  Y     
Sbjct: 132 -----GKRAVTFYEVLERLPTNCTRVKLTPITGRSHQLRLHTLALGHPILGDKFYSHPQA 186

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            + +     +L LHA  + + HP  G  +   A 
Sbjct: 187 KSMS----PRLCLHAEELTIMHPITGEKMTFRAE 216


>gi|307256344|ref|ZP_07538127.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 10
           str. D13039]
 gi|306865170|gb|EFM97070.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 10
           str. D13039]
          Length = 226

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 69/228 (30%), Positives = 109/228 (47%), Gaps = 14/228 (6%)

Query: 87  SVNLTKHSDFLKSIL--LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           ++ L ++   L+  L  +Y D+ I V NKP+G+    G+   Y+      + V  K    
Sbjct: 4   NMALIEYHPPLEPFLTEVYRDNHILVINKPSGLLSVPGNRPEYYDSAM--TRVQQKYGFT 61

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWL 202
              HRLD  TSGIL+ A ++AA + L   FR R  +K Y +L+WG    K       N+ 
Sbjct: 62  EPAHRLDMATSGILLFALSKAAEKELKRQFRDREPKKHYIALLWGKLGEKVGDTGEMNFP 121

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L           +  +       AI+H++V+         +++ P TGR+HQLRVH+L +
Sbjct: 122 LICDWENRPRQKICYER---GKKAITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLAL 178

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           G PI+GD  Y +    +    +  +L LHA  + + HP  G  +  TA
Sbjct: 179 GHPILGDKFYASPLAKS----LSPRLCLHAESLSITHPITGEAMTFTA 222


>gi|241760654|ref|ZP_04758746.1| tRNA pseudouridine synthase C [Neisseria flavescens SK114]
 gi|241318835|gb|EER55361.1| tRNA pseudouridine synthase C [Neisseria flavescens SK114]
          Length = 264

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 64/235 (27%), Positives = 100/235 (42%), Gaps = 21/235 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ DS+    NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L
Sbjct: 28  LDIIHRDSRTIAVNKPAGMLVHRSWLDKHETRFAVQTLRDQIGQHVYPVHRLDRPTSGVL 87

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A    AA+ LT+ F  + I+K YW++V G   +              I         Q
Sbjct: 88  LFALDTEAARLLTQQFENKTIEKTYWAIVRGYLPSDGLIDYALKYMPDKIAE------AQ 141

Query: 219 NEKGANYAISHFKV-----------IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            E     A + ++            +     ++ W E+ P+TGR HQLR H  H+  PIV
Sbjct: 142 TEATLQEAQTAYRCLAQTELPFQSALRYPTSRYSWAELTPYTGRKHQLRRHMKHIFHPIV 201

Query: 268 GDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           GD  Y    + +  +      +L LHAR +     E G R+ + AP      + W
Sbjct: 202 GDTNYGDLRQNHAVAEHIGTQRLMLHARSLSFQSIEDGSRITVNAPTDNDW-RLW 255


>gi|291616241|ref|YP_003518983.1| RluA [Pantoea ananatis LMG 20103]
 gi|291151271|gb|ADD75855.1| RluA [Pantoea ananatis LMG 20103]
          Length = 217

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 68/218 (31%), Positives = 104/218 (47%), Gaps = 17/218 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ I V NKP+G+    G  +  H D  + + +     +    HRLD  TSG++VV
Sbjct: 14  ILYQDAHIMVVNKPSGLLSVPGR-LDEHKDSVM-TRIQRDYPEAESVHRLDMATSGVIVV 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A T+AA + L   FR R   K Y + VWG P  +K  +   L+       D+ +  KQ  
Sbjct: 72  ALTKAAERELKRQFREREPAKTYVARVWGHPAQEKGMVDLPLI------CDWPNRPKQKV 125

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A + ++V++        + ++P TGR+HQLRVH L +G PI+GD  Y      
Sbjct: 126 CFDTGKSAQTDYQVVEYGEDNSARVALKPITGRSHQLRVHMLALGHPILGDGFYAHPEAK 185

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                  ++L LHA  + + HP  G  +      PA  
Sbjct: 186 AMA----DRLLLHAESLTITHPAFGNAMTFRQ--PADF 217


>gi|238755741|ref|ZP_04617074.1| Ribosomal large subunit pseudouridine synthase A [Yersinia ruckeri
           ATCC 29473]
 gi|238706033|gb|EEP98417.1| Ribosomal large subunit pseudouridine synthase A [Yersinia ruckeri
           ATCC 29473]
          Length = 217

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 105/231 (45%), Gaps = 17/231 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G   A      + + + +        
Sbjct: 1   MEAYNPPRDPWLHILYQDLHIMVVNKPSGLLSVPGR--APENKDSIMTRIQADFPTAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG  +  +  I   L+    
Sbjct: 59  HRLDMATSGVMVVALTKAAERELKRQFREREPKKSYIARVWGHLEQDEGLIDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V+   A     +++ P TGR+HQLRVH L MG P
Sbjct: 115 --CDWPNRPKQKVCYETGKSAQTEYQVLCRDADGSTRVKLSPITGRSHQLRVHMLAMGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           I+GD  Y         S    +L LHA+ + + HPE G  +   +   A  
Sbjct: 173 ILGDGFYAHPEAKAMAS----RLQLHAQELCITHPEFGTPMHFRSE--ADF 217


>gi|224543798|ref|ZP_03684337.1| hypothetical protein CATMIT_03019 [Catenibacterium mitsuokai DSM
           15897]
 gi|224523289|gb|EEF92394.1| hypothetical protein CATMIT_03019 [Catenibacterium mitsuokai DSM
           15897]
          Length = 282

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 61/301 (20%), Positives = 121/301 (40%), Gaps = 41/301 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +    ++    +MRLD +F  +   I+   ++     G++ V+ ++     +   G  V 
Sbjct: 2   ILQFEIDAQHVDMRLDEFF--YLHGISKKLVKDSRNHGEILVNGEKRYLCYKTVEGDSVA 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I       N I                   +   ++YED  + + +K   ++        
Sbjct: 60  IVFPKETSNVI----------------PVDIPLKVVYEDDYLMIIDKQPNLACIPVKKYL 103

Query: 127 YHIDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
               G    +   V+       L +RLD+ETSG++++A++R      +     ++++++Y
Sbjct: 104 TESLGNAIMYYYKVNHIESAIHLVNRLDKETSGLMMIAKSRYVHDAFSHDI--KQVKRVY 161

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G P   +  +   +      G        +  +G   AI+H++ I    + +  +
Sbjct: 162 HALVKGNP--GQGTVNAPIDHAEGHGTKR-----EVREGGKEAITHYRTIKTTGE-YSLV 213

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E +  TGRTHQ+RVH  ++GCP+VGD  Y                YL +  +   HP   
Sbjct: 214 ECKLETGRTHQIRVHMAYLGCPLVGDPLYGEG----------EGFYLDSVEIAFRHPITQ 263

Query: 304 R 304
           +
Sbjct: 264 Q 264


>gi|22127552|ref|NP_670975.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           KIM 10]
 gi|45443414|ref|NP_994953.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Microtus str. 91001]
 gi|51594989|ref|YP_069180.1| 23S rRNA pseudouridylate 746 synthase [Yersinia pseudotuberculosis
           IP 32953]
 gi|108810081|ref|YP_653997.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Antiqua]
 gi|108810536|ref|YP_646303.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|145600392|ref|YP_001164468.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Pestoides F]
 gi|150260466|ref|ZP_01917194.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           CA88-4125]
 gi|153948334|ref|YP_001402394.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           pseudotuberculosis IP 31758]
 gi|162419457|ref|YP_001605342.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Angola]
 gi|165928068|ref|ZP_02223900.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165937798|ref|ZP_02226359.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166008924|ref|ZP_02229822.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166211832|ref|ZP_02237867.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167401530|ref|ZP_02307024.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167421997|ref|ZP_02313750.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167426100|ref|ZP_02317853.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|167467289|ref|ZP_02331993.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           FV-1]
 gi|170025783|ref|YP_001722288.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186893990|ref|YP_001871102.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
 gi|218927695|ref|YP_002345570.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           CO92]
 gi|229836920|ref|ZP_04457085.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Pestoides A]
 gi|229840385|ref|ZP_04460544.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229842465|ref|ZP_04462620.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229900724|ref|ZP_04515848.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|270487905|ref|ZP_06204979.1| pseudouridine synthase A [Yersinia pestis KIM D27]
 gi|294502592|ref|YP_003566654.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Z176003]
 gi|34395807|sp|Q8ZIK1|RLUA_YERPE RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|21960656|gb|AAM87226.1|AE013971_2 hypothetical protein y3678 [Yersinia pestis KIM 10]
 gi|45438283|gb|AAS63830.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Microtus str. 91001]
 gi|51588271|emb|CAH19878.1| 23S rRNA pseudouridylate 746 synthase [Yersinia pseudotuberculosis
           IP 32953]
 gi|108774184|gb|ABG16703.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|108781994|gb|ABG16052.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Antiqua]
 gi|115346306|emb|CAL19177.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           CO92]
 gi|145212088|gb|ABP41495.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Pestoides F]
 gi|149289874|gb|EDM39951.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           CA88-4125]
 gi|152959829|gb|ABS47290.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           pseudotuberculosis IP 31758]
 gi|162352272|gb|ABX86220.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Angola]
 gi|165914210|gb|EDR32826.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|165919929|gb|EDR37230.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165992263|gb|EDR44564.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166206578|gb|EDR51058.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166960134|gb|EDR56155.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167048912|gb|EDR60320.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167055023|gb|EDR64823.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|169752317|gb|ACA69835.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186697016|gb|ACC87645.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
 gi|229682063|gb|EEO78155.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|229690775|gb|EEO82829.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229696751|gb|EEO86798.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229705863|gb|EEO91872.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Pestoides A]
 gi|262360622|gb|ACY57343.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           D106004]
 gi|262364568|gb|ACY61125.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           D182038]
 gi|270336409|gb|EFA47186.1| pseudouridine synthase A [Yersinia pestis KIM D27]
 gi|294353051|gb|ADE63392.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Z176003]
 gi|320016868|gb|ADW00440.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Medievalis str. Harbin 35]
          Length = 206

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 70/214 (32%), Positives = 101/214 (47%), Gaps = 15/214 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           I+LY+D  I V NKP+G+    G   A      + + V +        HRLD  TSG++V
Sbjct: 2   IVLYQDKHIMVVNKPSGLLSVPGR--APENKDSVMTRVQNDFPTAESVHRLDMATSGVIV 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ 
Sbjct: 60  VALTKAAERELKRQFREREPKKTYIARVWGHLAQDEGLIDLPLI------CDWPNRPKQK 113

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              +    A + ++VI         +++ P TGR+HQLRVH L MG PI+GD  Y     
Sbjct: 114 VCYETGKSAQTEYQVISRDDDGSTRVKLSPITGRSHQLRVHMLAMGHPILGDGFYAHPEA 173

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
               S    +L LHA+ + + HPE G  +     
Sbjct: 174 KAMAS----RLQLHAQQLCITHPEFGTPMHFKCE 203


>gi|312884626|ref|ZP_07744329.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           caribbenthicus ATCC BAA-2122]
 gi|309367718|gb|EFP95267.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           caribbenthicus ATCC BAA-2122]
          Length = 256

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 62/226 (27%), Positives = 108/226 (47%), Gaps = 15/226 (6%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
            +   ++           ++YED  I   NK  G+    G  + +H    + + +  +  
Sbjct: 9   PIVIPMHRYTPPTDPWLNVIYEDDAILAVNKQPGLLSVPGRKVEHHDS--IYTRLVERWP 66

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           + ++ HRLD +TSG++V+A+ + A + L + F+ R   K+Y++ VWG     +  I   L
Sbjct: 67  EVQVIHRLDMDTSGLMVLAKNKPAERALKKQFQYRLTHKVYYARVWGNVAADEGTIDAPL 126

Query: 203 LKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           +       D+ +  KQ    +    + +HF+V+   +Q    + + P TGR+HQLRVH  
Sbjct: 127 I------CDWPNRPKQKVCYETGKSSQTHFQVVKRESQ-TTIVRLLPITGRSHQLRVHMQ 179

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
            MG PI+GD  Y +      +S    +L LHA  +   HP+   LQ
Sbjct: 180 LMGHPILGDEFYASPQAFALSS----RLDLHAAELSFYHPDSQLLQ 221


>gi|303237207|ref|ZP_07323777.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
 gi|302482594|gb|EFL45619.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
          Length = 221

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 75/229 (32%), Positives = 112/229 (48%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I +  K +G  VQG       +   +K+W+  K  KP      + HRLD+  S
Sbjct: 3   VLYEDNHIIIVYKESGEIVQGDKTGDKPLSETVKAWLKEKYAKPGNVFVGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  A   L E FR   ++K YW++V   P+  +  I N+LL+       Y + 
Sbjct: 63  GIVVFAKTSKALSRLNEMFRKGEVKKTYWAMVQNSPQKLEGTIENYLLRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +  +KGA  AI  +K I    +++  LE+   TGR HQ+R    +MGC I GD KY A 
Sbjct: 122 -EYEKKGAKKAILKYKTIG-QTERYTLLEVNLMTGRHHQIRCQLANMGCVIKGDLKYGAK 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 S     L  H+  ++  HP   + + + +PLP      WDS  
Sbjct: 180 RSNPDGSIS---LLSHS--VEFIHPVSKQPISVVSPLPQE--AVWDSFR 221


>gi|91204218|emb|CAJ71871.1| similar to pseudouridine synthase C [Candidatus Kuenenia
           stuttgartiensis]
          Length = 274

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 65/318 (20%), Positives = 127/318 (39%), Gaps = 48/318 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           +   +V + +  + L  +  N    ++    +++L    V V++KRV   + +++ G  +
Sbjct: 1   MHKFIVTHRDSELTLLHFIANKLS-LSNKKAKQLLDDRLVFVNRKRVWIASYQLKPGDSI 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                       T   +     +L+ D    + +KP GI   G + I
Sbjct: 60  EVLSGK-------------------THQPEKKTYDILFNDDCYVIVSKPPGIVTNGQNSI 100

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                  L++  +    + +  HRLD++TSG L+ A+   A + + + F+   IQKIY  
Sbjct: 101 ERD----LRTQFNRD--RIQAVHRLDKDTSGALIFAKNENAFEEMKKVFKKHDIQKIYRV 154

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G        I + +                   G   A++H  ++    +   +LE+
Sbjct: 155 IVTGKICEPAFTINSPV-------------------GGQTAVTHITLLK-KGKNTSYLEV 194

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
              TGR HQ+R+H   +G P++G+ +Y      N       +  LHA  +   HP     
Sbjct: 195 ATETGRRHQIRIHLASIGHPVIGETEYARKEIENILHREAKRQMLHAHRISFVHPYTKKE 254

Query: 305 LQITAPLPAHMVKTWDSL 322
           + +TAP+    ++    L
Sbjct: 255 ISVTAPISHDFIQCLRLL 272


>gi|330952657|gb|EGH52917.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae Cit 7]
          Length = 211

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 64/214 (29%), Positives = 101/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++++D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIHQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEGGKHALTFWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL      P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERLTFECTAP 210


>gi|303238761|ref|ZP_07325293.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
 gi|302593640|gb|EFL63356.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
          Length = 233

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 75/241 (31%), Positives = 117/241 (48%), Gaps = 19/241 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LT 147
               +K  +LYED+ + V  KP  I VQ  S     +   LK  +  +  KP      L 
Sbjct: 3   PGKNMKIKILYEDNHLLVVEKPVNIPVQQDSTNDVDMLTLLKEDIKVRYNKPGNVYLGLV 62

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+   G +V A+T  AA  L++  R R + K Y+++V G  ++K+  + N+LLK   
Sbjct: 63  HRLDRPVGGAMVFAKTSKAASRLSDQVRTRGLNKTYYAVVHGKFEDKQGRLENYLLKDEK 122

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                V VV     GA  AI  +KVID F + +  +++  HTGR+HQ+RV   ++G P+ 
Sbjct: 123 TN--MVSVVSPEVAGAKQAILDYKVIDVF-KDYTLIKVDLHTGRSHQIRVQFSNIGHPLY 179

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWD---SLG 323
           GD +Y  +      + +  ++ L +  + L HP     L      P   V+ W+    LG
Sbjct: 180 GDQRYGKSV-----NKVGQQIALWSCGIALKHPTTEEELDFKCNPPD--VEPWNWFKYLG 232

Query: 324 F 324
           F
Sbjct: 233 F 233


>gi|88801297|ref|ZP_01116825.1| ribosomal large subunit pseudouridine synthase D [Polaribacter
           irgensii 23-P]
 gi|88781955|gb|EAR13132.1| ribosomal large subunit pseudouridine synthase D [Polaribacter
           irgensii 23-P]
          Length = 228

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 75/229 (32%), Positives = 112/229 (48%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ I + NK AG   QG       +   +K ++  K  KP        HRLD+ TS
Sbjct: 10  VLFEDNHIIIINKRAGDITQGDKTGDKPLSDVIKEYIKEKYNKPGEVFIGTVHRLDRPTS 69

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ ART  A   L +  R + I K YW+LV   P    + I N+L K +    +   V
Sbjct: 70  GIVIFARTSKALTRLNKMLRDKVIDKTYWALVKNAPIKATDTITNFLKKDTK--KNKSFV 127

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+  +G   A+ H+K++    + +C LE+   TGR HQ+R    H+G  I GD KY A+
Sbjct: 128 YKKEIEGCKKAVLHYKILQKL-ESYCLLEIDLETGRHHQIRTQLSHIGSVIKGDLKYGAS 186

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
                 S     + LHAR +   HP     + ITAP P  ++  W++  
Sbjct: 187 RSNKDGS-----ISLHARKIKFTHPVSKEEIAITAPTPKDII--WNACR 228


>gi|126172980|ref|YP_001049129.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|153002090|ref|YP_001367771.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|307304720|ref|ZP_07584470.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|125996185|gb|ABN60260.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           baltica OS155]
 gi|151366708|gb|ABS09708.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|306912122|gb|EFN42546.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 225

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 66/217 (30%), Positives = 110/217 (50%), Gaps = 16/217 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D  I V NKP+G+    G   A++    + + V ++    ++ HRLD  TSG++
Sbjct: 14  LDILYQDKDIIVINKPSGLLSVPGRDPAHYDS--VYARVKAEHPHSQIVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  R+A + L   F  R   K Y++ V G  KN    +   L+       D+ +  KQ
Sbjct: 72  VVALIRSAERELKRQFHDRETSKTYFARVAGHVKNDTGSVDYPLI------CDWPNRPKQ 125

Query: 219 NEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                    +++H++VI   A++   +++ P TGR+HQLRVH + +G PI+GD  Y    
Sbjct: 126 KVDHLVGKPSLTHYQVISR-AKRSTLVKLTPITGRSHQLRVHMMALGHPILGDGFYADPL 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
             +    +  +L LHA  + + HP  G  +  +A +P
Sbjct: 185 AKS----LAPRLLLHAAELTIKHPYTGVSMTFSAEVP 217


>gi|89095078|ref|ZP_01168005.1| Pseudouridine synthase [Oceanospirillum sp. MED92]
 gi|89080639|gb|EAR59884.1| Pseudouridine synthase [Oceanospirillum sp. MED92]
          Length = 210

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 68/215 (31%), Positives = 105/215 (48%), Gaps = 12/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y D  I V NKP  +    G G        L   V +     R+ HRLD  TSGI+
Sbjct: 6   VEIIYADEHIVVANKPWDMLSVPGKG--EDKQDCLWRRVQTSYPTARIVHRLDYATSGII 63

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A T  A + L+ SF+ R  QK Y +++ G PK     +   L        +   +   
Sbjct: 64  ILALTLDAQRALSRSFQERETQKRYQAIIAGRPKEDSGSVDLPL----RCDWENRPLQIV 119

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    A++H+ +ID   +    + + P TGR+HQLRVH   MG PI+GD  Y +  + 
Sbjct: 120 DHEQGKSALTHW-LIDEVTELGSRVLLTPVTGRSHQLRVHMQAMGHPIIGDRFYASEEQV 178

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             +     +L LHA ++ LPHPE G+ ++  AP P
Sbjct: 179 AASE----RLLLHAEFLKLPHPESGKMMEFNAPCP 209


>gi|237742173|ref|ZP_04572654.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           4_1_13]
 gi|229429821|gb|EEO40033.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           4_1_13]
          Length = 292

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 67/324 (20%), Positives = 135/324 (41%), Gaps = 38/324 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   ++  +VE++ +   +  + K    + +       LR+ ++ ++ KR          
Sbjct: 1   MRKKMKKYIVEHEYDGYEIGTYLKETKGYSSRG-----LRNLEIYLNGKR---------- 45

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +      I  LN I+    I++   +    +  +   + YED  + + NK   I V   
Sbjct: 46  -IKNNAKKIKKLNRIV----IIEKEKSTGIKAIDIPIDIAYEDENLLIVNKEPYIIVHPT 100

Query: 123 -SGIAYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
              +   +   + ++ +    K   PR  +RLD  TSG++++A+       L +      
Sbjct: 101 QKKVDKTLANAIVNYFEKTLGKTLVPRFYNRLDMNTSGLIIIAKNAYTQAFLQDKT---E 157

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FA 237
           ++K Y  +  GI +     I   + K   +G D   +    + G   A +H KV++  + 
Sbjct: 158 VKKTYKVIASGIIEKDDFFIELPIGK---VGDDLKRIELSEKDGGKSAKTHIKVLERNYE 214

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +   +LE + +TGRTHQ+R H   +G  +VGD  Y  + K      +  +  LHA  ++ 
Sbjct: 215 KNITFLEARLYTGRTHQIRAHLSLIGHSLVGDELYGGDMK------LAKRQMLHAYKLEF 268

Query: 298 PHPEG-GRLQITAPLPAHMVKTWD 320
            +P+    L+I   +P  M +   
Sbjct: 269 QNPKTLENLKIEIDIPIDMKEILK 292


>gi|330962664|gb|EGH62924.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. maculicola str. ES4326]
          Length = 211

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 65/214 (30%), Positives = 102/214 (47%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++++D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETS I++
Sbjct: 7   RIIHQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGFPEARIVHRLDWETSAIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +G  +A++ +KVI+     +C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEGGKHALTFWKVIERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPE--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  ++  HP  G RL    P P
Sbjct: 178 -ALAAYPRLCLHASMLNFTHPGTGERLTFECPAP 210


>gi|332292825|ref|YP_004431434.1| pseudouridine synthase [Krokinobacter diaphorus 4H-3-7-5]
 gi|332170911|gb|AEE20166.1| pseudouridine synthase [Krokinobacter diaphorus 4H-3-7-5]
          Length = 232

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 72/219 (32%), Positives = 105/219 (47%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I V NK +G  VQG       +   +K ++  K  KP      + HRLD+ TS
Sbjct: 13  VIYEDNHIIVINKRSGDIVQGDKTGDAPLSEVVKKYIAIKYDKPGAVYLGVVHRLDRPTS 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V ART  A   L ++F  R  QK YW+LV   P  +   + ++L +       Y H 
Sbjct: 73  GIVVFARTSKALPRLNKAFAERETQKTYWALVKNPPPAESGTLIHYLKRNPKQNKSYAH- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K     +  AI  ++VI    + F  LE+  HTGR HQ+R     +G PI GD KY  +
Sbjct: 132 -KHEVPDSKKAILDYRVIKKL-KTFFLLEIDLHTGRHHQIRAQLTAIGSPIKGDLKYGFD 189

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
                 S     + L +R + L HP +   +  TA +P 
Sbjct: 190 RSNPDGS-----ISLLSRKLTLTHPVKKEEMTFTAEVPE 223


>gi|323494676|ref|ZP_08099779.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           brasiliensis LMG 20546]
 gi|323311109|gb|EGA64270.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           brasiliensis LMG 20546]
          Length = 559

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 111/245 (45%), Gaps = 20/245 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  K+ D+ +     ++  +  +L+ED  + V NKP+G+    G  I    
Sbjct: 328 CQPILGHMLQGLKVDDNPLE-ENWAEDKELEILFEDDALVVVNKPSGLLSVPGKTITDSA 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+       + P + HRLD  TSG+LV A T+ A + L + F  R ++K Y +L+ G
Sbjct: 387 YTRLQQRY-PDVEGPFVIHRLDMATSGLLVFALTKRANKSLQKQFISRSVEKRYVALLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             + +   I   + +   +      V  ++      A ++++ I     +     + P T
Sbjct: 446 EVEQQNGQIKLPM-RGDPVDRPRQLVCFEH---GKPAETYWEKISTINGRSKLY-LYPKT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH  H   +  P+VGD  Y             ++L+LHA  ++  HP    RL
Sbjct: 501 GRTHQLRVHCAHHLGLDLPMVGDGLYGEK---------ADRLHLHAERLEFEHPYSKERL 551

Query: 306 QITAP 310
             +A 
Sbjct: 552 TFSAE 556


>gi|256420248|ref|YP_003120901.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
 gi|256035156|gb|ACU58700.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
          Length = 247

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 108/251 (43%), Gaps = 23/251 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +  I++ E +   + NKPAG+          +    L+  +     +    HRLD++TSG
Sbjct: 3   INDIIIKETADFVILNKPAGMLTIPDRHD--NQLDSLQGLLKKHYGEIFTVHRLDKDTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++ A+   A ++ ++ F  R ++K Y  LV G    +   +   +++   I G  V   
Sbjct: 61  VILFAKNEVAHKYYSQLFEGRNVKKFYKGLVNGQLHPETGSVDEAIMEHPTIKGRMVTNR 120

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-- 274
           K        A + ++V++ F   +  +++Q HTGRTHQ+RVH  H+G PI  D  Y    
Sbjct: 121 K-----GKNAQTDYQVLEAFGL-YSLVQLQIHTGRTHQIRVHMKHLGHPIAVDELYGTAA 174

Query: 275 -------------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
                          +     P+ ++L LHA  +     +G    I APLP  +      
Sbjct: 175 PVYLSAIKKNYKLGKRVEEERPLLSRLGLHAWQLQFKDQQGEENVIEAPLPKDIQAVVTQ 234

Query: 322 LGFKYDRNLYI 332
           L     R+  +
Sbjct: 235 LRKNSGRSTEL 245


>gi|332880211|ref|ZP_08447892.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
 gi|332681860|gb|EGJ54776.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
          Length = 544

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 71/247 (28%), Positives = 115/247 (46%), Gaps = 20/247 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  ++   +KH    +  L+YED  +   NKPAG+    G G A  +
Sbjct: 313 CEPILGHMLQGLDVEPNAHENSKHLKH-EPELVYEDEWMAAVNKPAGMLSVPGKGDALSV 371

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             + ++    +   P L HRLD +TSG+L++A+     + L + F  R I+K Y +L+ G
Sbjct: 372 WSWARAHF-PEATGPLLVHRLDMDTSGVLLIAKDPETHRQLQQLFETRHIKKRYIALLDG 430

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              + +  I   L    +     +            A++ F+V+   +     +   P T
Sbjct: 431 TVTDDEGFIRLPLCPNPNDRPRQMVSTAY----GKAAVTRFEVLSR-SHGQTRVAFYPFT 485

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVHA H   +  PIVGD+ Y             ++L+LHA  +   H + GR +
Sbjct: 486 GRTHQLRVHAAHPEGLDTPIVGDNLYGRR---------ASRLFLHAETVTFRHFKTGRWV 536

Query: 306 QITAPLP 312
            ITAP P
Sbjct: 537 SITAPAP 543


>gi|330830764|ref|YP_004393716.1| Pseudouridine synthase [Aeromonas veronii B565]
 gi|328805900|gb|AEB51099.1| Pseudouridine synthase [Aeromonas veronii B565]
          Length = 257

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 68/256 (26%), Positives = 110/256 (42%), Gaps = 19/256 (7%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHR 149
           T+    LK  LLY+D  +   NKP+G+ V             ++   D  G +     HR
Sbjct: 6   TREESDLKLTLLYQDEWLVAVNKPSGLLVHRSWLDKGETRFAMQMTRDLIGGRYVYPVHR 65

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ TSG+L+ A     A+ LTE+F  R++ K Y +LV G    ++  I   L +     
Sbjct: 66  LDRPTSGVLLFALDPVIARALTEAFTQRQVHKEYLALVRG-WAPEQGVIDYPLKE---QL 121

Query: 210 GDYVHVVKQNEKGANYAISHFKVI-----------DCFAQKFCWLEMQPHTGRTHQLRVH 258
                 +   ++ A  A++ F+ +                ++  + + P TGR HQLR H
Sbjct: 122 DKIADAMSNPDRPAQDAVTTFRRLHQVELPHAVSKKHPTSRYSLVRLFPKTGRKHQLRRH 181

Query: 259 ALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
             H+  PIVGD  +       F        +L L AR +   HP     ++I APL   +
Sbjct: 182 MDHLFHPIVGDTTHGDGRHNRFFREHFGCERLLLVARTLSFTHPVLKVPMRIQAPLGQDV 241

Query: 316 VKTWDSLGFKYDRNLY 331
           ++ +  LG+    + Y
Sbjct: 242 LRLFAELGWPASESDY 257


>gi|325969898|ref|YP_004246089.1| pseudouridine synthase [Spirochaeta sp. Buddy]
 gi|324025136|gb|ADY11895.1| pseudouridine synthase [Spirochaeta sp. Buddy]
          Length = 229

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 109/233 (46%), Gaps = 16/233 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRL 150
            +K  +LYED+ + + NK  G  VQG       +   +K ++     K       + HRL
Sbjct: 2   DIKDRILYEDNHLIIINKLCGELVQGDVTGDETLADLVKEYLRVNYNKQGNVFLGIPHRL 61

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSGI+V A+T  A   L E F+   ++K YW++V  +P   +  + +++++ +    
Sbjct: 62  DRPTSGIVVYAKTEKALIRLNELFKGSAMKKTYWAIVDHMPNQTEGTLVHYIVRDTKTNK 121

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                +   +KG   A   +K+I   ++ +  LE+  HTGR HQ+R     +G  I GD 
Sbjct: 122 S--VALSVEKKGGKLAKLDYKLISA-SKNYFLLEVNLHTGRHHQIRAQFAAIGLHIKGDL 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           KY A       S     + LHAR +   HP     + +TAP P      W++ 
Sbjct: 179 KYGA-----ARSNPDGGICLHARSISFTHPVKKEQITLTAPPPDD--ALWNAF 224


>gi|292489389|ref|YP_003532276.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           CFBP1430]
 gi|292898392|ref|YP_003537761.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           ATCC 49946]
 gi|291198240|emb|CBJ45346.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           ATCC 49946]
 gi|291554823|emb|CBA22677.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           CFBP1430]
 gi|312173554|emb|CBX81808.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           ATCC BAA-2158]
          Length = 217

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 67/202 (33%), Positives = 103/202 (50%), Gaps = 14/202 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G  +A + D  + + V          HRLD  TSG++VV
Sbjct: 14  VLYQDEHIIVVNKPSGLLSVPGR-LAEYKDSVM-TRVQRDYPAAESVHRLDMATSGVMVV 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A T+AA + L   FR R  QK Y + VWG P+ +   +   L+       D+ +  KQ  
Sbjct: 72  ALTKAAERELKRQFREREPQKTYVARVWGHPQPESGSVDLPLI------CDWPNRPKQKV 125

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             +    A + ++V+D  +     + ++P TGR+HQLRVH L +G PI+GD+ Y  +   
Sbjct: 126 CFETGKSAQTEYQVLDYASDHSARVRLKPVTGRSHQLRVHMLALGHPILGDNFYAHDEAR 185

Query: 279 NFTSPIQNKLYLHARYMDLPHP 300
                   +L LHA  + + HP
Sbjct: 186 AMA----PRLQLHAESLSITHP 203


>gi|54307622|ref|YP_128642.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium profundum SS9]
 gi|46912045|emb|CAG18840.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium profundum SS9]
          Length = 239

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 65/227 (28%), Positives = 107/227 (47%), Gaps = 17/227 (7%)

Query: 88  VNLTKHSDFLK-SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
            +L  H        +L  D  I + NKP+G+    G    ++    + S V     +  +
Sbjct: 5   PHLDYHPPTDPWLDILQHDEDIIMLNKPSGLLSNPGRNPEHYDS--VYSRVLRDYPEAHI 62

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  TSG++++A  + A +HL   FR R  QK+Y++ +WG P      +   L+   
Sbjct: 63  VHRLDMSTSGLIMLAVNKDAERHLHAQFRERATQKVYYARIWGHPDQDTGTVDLPLI--- 119

Query: 207 HIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               D+ +  KQ    +    +++H++V+   AQ    + + P TGR+HQLRVH   +G 
Sbjct: 120 ---CDWPNRPKQKVCYEDGKPSVTHYEVVAREAQ-TTLVRLHPITGRSHQLRVHMQALGH 175

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           PI+GD  Y  +        I ++L+LHA  +   HP     +   AP
Sbjct: 176 PIIGDEFYANDEANA----IADRLHLHAAEIAFTHPGTKEPIHFFAP 218


>gi|327392692|dbj|BAK10114.1| ribosomal large subunit pseudouridine synthase A RluA [Pantoea
           ananatis AJ13355]
          Length = 217

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 68/218 (31%), Positives = 104/218 (47%), Gaps = 17/218 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D+ I V NKP+G+    G  +  H D  + + +     +    HRLD  TSG++VV
Sbjct: 14  ILYQDAHIMVVNKPSGLLSVPGR-LDEHKDSVM-TRIQRDYPEAESVHRLDMATSGVIVV 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A T+AA + L   FR R   K Y + VWG P  +K  +   L+       D+ +  KQ  
Sbjct: 72  ALTKAAERELKRQFREREPAKTYVARVWGHPAQEKGMVDLPLI------CDWPNRPKQKV 125

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A + ++V++        + ++P TGR+HQLRVH L +G PI+GD  Y      
Sbjct: 126 CFDTGKSAQTDYQVVEYGDDNSARVALKPITGRSHQLRVHMLALGHPILGDGFYAHPEAK 185

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                  ++L LHA  + + HP  G  +      PA  
Sbjct: 186 AMA----DRLLLHAESLTITHPAFGNAMTFRQ--PADF 217


>gi|319638811|ref|ZP_07993569.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317399715|gb|EFV80378.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 238

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 100/238 (42%), Gaps = 20/238 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ DS+    NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L
Sbjct: 2   LDIIHRDSRTIAVNKPAGMLVHRSWLDKHETRFAVQTLRDQIGQHVYPVHRLDRPTSGVL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A    AA+ LT+ F  + I+K YW++V G   +              I         Q
Sbjct: 62  LFALDTEAARLLTQQFENKTIEKTYWAIVRGHLPSDGLIDYALKYMPDKIAE------AQ 115

Query: 219 NEKGANYAISHFKV-----------IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            E     A + ++            +     ++ W E+ PHTGR HQLR H  H+  PIV
Sbjct: 116 TEATLQEAQTAYRCLAQTELPFQSALRYPTSRYSWAELTPHTGRKHQLRRHMKHIFHPIV 175

Query: 268 GDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           GD  Y    + +  +      +L LHAR +     E G R+ + AP+        +  
Sbjct: 176 GDTNYGDLRQNHAVAEHVGTQRLMLHARSLSFQSIEDGSRMTVQAPIDNDWRLWLEKF 233


>gi|312863550|ref|ZP_07723788.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
 gi|311101086|gb|EFQ59291.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
          Length = 298

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 70/314 (22%), Positives = 127/314 (40%), Gaps = 33/314 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           R+  + K H   I+   L KI    G + V+ +       +  G VV I           
Sbjct: 12  RVKTFLKEH--DISKGLLAKIKFEGGHIWVNGEEQFATYPVHEGDVVAI----------- 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV- 137
              +I D   + T         ++YED    V NKP G +          +  F+K    
Sbjct: 59  ---EIPDEVPHETLKPIPFDLDIVYEDDNFLVINKPYGYASIPSVNHDNTMANFVKYHFV 115

Query: 138 --DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NK 194
             +   Q+  +  RLD++TSG+++ A+   A   + +  + + I+K Y++LV G  K  +
Sbjct: 116 SNNYPNQRVHIVTRLDKDTSGLMLFAKHGYAHARMDKQLQQKSIKKHYYALVEGDTKLEQ 175

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I   + +          + ++  K   YA + ++++  + +    +++  HTGRTHQ
Sbjct: 176 QGEIIAPIARDVD-----SIITRRVHKSGKYAHTSYRLVGDYGR-VKLVDINLHTGRTHQ 229

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA-PLPA 313
           +RVH  H+G P++GD  Y  +           +  LH   +    P   +  + A  L  
Sbjct: 230 IRVHFAHLGLPLLGDDLYGGSL-----DYGIKRQALHCHRLAFIDPFTKKEMVHASSLTD 284

Query: 314 HMVKTWDSLGFKYD 327
                  +L  K D
Sbjct: 285 DFETVIMNLQTKKD 298


>gi|313113493|ref|ZP_07799082.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310624220|gb|EFQ07586.1| pseudouridine synthase, RluA family [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 349

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 66/335 (19%), Positives = 120/335 (35%), Gaps = 57/335 (17%)

Query: 9   YVVVEND---EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +  V +    +  + L  + +      +     K   SG    D + V  N R+  GQ V
Sbjct: 45  FFTVPDTPQTQNGVLLRNFLRQCAVSTDLARAVKFRGSGF-FADGEPVLANRRVYPGQTV 103

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                             L            +   ++YED+   V  KP  ++V      
Sbjct: 104 SFE---------------LPPEGEGVAPQPEIPVNVVYEDAFAVVLEKPPHLAVHPTLNY 148

Query: 126 AY-HIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            Y  +     +W   +G  P  R  +R+D++TSG+++ A+   AA  L      R ++K+
Sbjct: 149 PYDTLANGYAAWAAQQGISPVFRPVNRIDKDTSGLVLAAKHAYAAPLLA-----RNVEKL 203

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y+++V G        I   + +++        + +        + + + ++         
Sbjct: 204 YYAVVEGELPLGPGVIDAPIGRQAE-----SIIGRCVTPDGKPSRTEYTILKA-ENGLSL 257

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-- 300
               P TGRTHQ+RVH   +G P+ GD  Y  + +         +  LH        P  
Sbjct: 258 AACVPVTGRTHQIRVHFASIGHPLAGDDLYGGSRER------IGRQALHCARQSFRVPVY 311

Query: 301 ---EGG-RLQ------------ITAPLPAHMVKTW 319
              EGG R++              +PLP  M + +
Sbjct: 312 TLVEGGIRVECPANGNNWKTAAAESPLPQDMKQLF 346


>gi|145635746|ref|ZP_01791440.1| hypothetical protein CGSHiAA_07285 [Haemophilus influenzae PittAA]
 gi|145267010|gb|EDK07020.1| hypothetical protein CGSHiAA_07285 [Haemophilus influenzae PittAA]
          Length = 219

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 109/229 (47%), Gaps = 16/229 (6%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            +++ +  L  + D     ++Y+D+ + V NKP+G+    G+   Y+    + S V  K 
Sbjct: 2   ALIEYNPPLEPYLD-----IIYQDNHLCVVNKPSGLLSVPGNQPQYYDS--VMSRVKEKF 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGI+V A ++AA + L   FR R  +K Y ++VWG  +N    +   
Sbjct: 55  GFCEPAHRLDMATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVKLP 114

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           ++       +     + +      A++ F+V+         +++ P TGR+HQLR+H L 
Sbjct: 115 MICD----WENRPRQRLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLA 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +G PI+GD  Y        T  +  +L LHA  + + HP  G  +   A
Sbjct: 171 LGHPILGDKFYSHPQ----TKVMSPRLCLHAEELTITHPITGETMTFNA 215


>gi|304410623|ref|ZP_07392241.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|304351107|gb|EFM15507.1| pseudouridine synthase [Shewanella baltica OS183]
          Length = 225

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 67/217 (30%), Positives = 110/217 (50%), Gaps = 16/217 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D  I V NKP+G+    G   A++    + + V ++    ++ HRLD  TSG++
Sbjct: 14  LDILYQDKDIIVINKPSGLLSVPGRSPAHYDS--VYARVKAEHPHSQIVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  R+A + L   F  R   K Y++ V G  KN    +   L+       D+ +  KQ
Sbjct: 72  VVALIRSAERELKRQFHDRETSKTYFARVAGHVKNDTGSVDYPLI------CDWPNRPKQ 125

Query: 219 NEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                    +++H+KVI   A++   +++ P TGR+HQLRVH + +G PI+GD  Y    
Sbjct: 126 KVDHLVGKQSLTHYKVISR-AKRSTLVKLTPITGRSHQLRVHMMALGHPILGDGFYADPL 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
             +    +  +L LHA  + + HP  G  +  +A +P
Sbjct: 185 AKS----LAPRLLLHAAELTIKHPYTGVSMTFSAEVP 217


>gi|323342987|ref|ZP_08083218.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322463051|gb|EFY08246.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 291

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 132/320 (41%), Gaps = 45/320 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M ++  + VE+++E   L  +  +     +   ++ +L+   + +D +    F++ I +G
Sbjct: 1   MKHI--LKVEHNDE---LLNYLLSQDLPYSRSKIKSLLKHECISIDNEVTTQFDDLITAG 55

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q + I       +  ++                     +LYED  I V +KP  +     
Sbjct: 56  QTITIVSHNQQRDTPLQ---------------------ILYEDKDILVVDKPYKLLTVSN 94

Query: 123 SGIAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                     L S          +  + HRLDQ+TSG+L+ A++    +   + +     
Sbjct: 95  RKEEELTAFRLASDYVKKQDSKNRIFVVHRLDQDTSGVLMFAKSEYVKRLYQDKWSELVD 154

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +++Y ++V G+    K+ I ++L                +      AI++++VI      
Sbjct: 155 ERLYVAIVEGVVPKDKDVIRSFL-------RQNKTTHMYSTSSGQEAITNYEVIKRTENN 207

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
               ++Q  TGR +Q+RVH   +G PI+GD KY      +  +    +L LHA  + + +
Sbjct: 208 TIL-KIQIDTGRKNQIRVHMNDIGHPIIGDKKY------DAKTNPLKRLGLHAYRLRVMN 260

Query: 300 PEGGR-LQITAPLPAHMVKT 318
           P+  + +   +PLP    K 
Sbjct: 261 PKTKKMMTFVSPLPPKFKKL 280


>gi|260777893|ref|ZP_05886786.1| pseudouridylate synthase LSU rRNA-specific [Vibrio coralliilyticus
           ATCC BAA-450]
 gi|260605906|gb|EEX32191.1| pseudouridylate synthase LSU rRNA-specific [Vibrio coralliilyticus
           ATCC BAA-450]
          Length = 559

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 63/245 (25%), Positives = 110/245 (44%), Gaps = 20/245 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   + D+ +     ++  +  +L+ED  + V NKP+G+    G  I    
Sbjct: 328 CFPILGHMLEGMAVDDNPLE-ENWAEDKELEILFEDEAMVVVNKPSGLLSVPGKTIKDSA 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+       + P + HRLD  TSG+LV A T+ A + L + F  R +QK Y +L+ G
Sbjct: 387 YTRLQQRY-PDVEGPFVIHRLDMATSGLLVFALTKRANKSLQKQFISRSVQKRYVALLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   I   + +          V  ++      A +++++I+    +     + P T
Sbjct: 446 EVNQTSGQIELPM-RGDPDDRPRQLVCFEH---GKPAETYWELIESRDGRSKLY-LYPKT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVH  H   +  P+VGD  Y             ++L+LHA+ +++ HP   + +
Sbjct: 501 GRTHQLRVHCAHRLGLNLPMVGDGLYGQR---------SDRLHLHAQRLEIEHPYSKQPM 551

Query: 306 QITAP 310
              A 
Sbjct: 552 TFEAE 556


>gi|78776810|ref|YP_393125.1| pseudouridine synthase [Sulfurimonas denitrificans DSM 1251]
 gi|78497350|gb|ABB43890.1| tRNA pseudouridine synthase C [Sulfurimonas denitrificans DSM 1251]
          Length = 241

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 104/238 (43%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G+ V       +  +  +++  +  G+     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEHLVAINKPSGLLVHRSPIDRHETEFAIQTLRNQLGRFVYPIHRLDKPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + +A+ + E F     +K Y ++V G      E      +K   I          ++
Sbjct: 64  ALDKESAKIMGEKFMAHEAKKSYIAVVRGYTLQSGEIDYALSIKFDKIADK----DSSSD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H+K +               ++  +++ P TGR HQLR H  H+   I+GD 
Sbjct: 120 KEPQEALTHYKRLATVELDFEVGKYDKTRYSLVKLNPLTGRKHQLRRHMKHISHHILGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
           KY               +++ LHA  +++ HP     L I APL    ++ +   G+ 
Sbjct: 180 KYGRGEHNKLIRQEFGCHRMLLHAIALEISHPYTKELLYIKAPLDVTFIEMFSFFGWD 237


>gi|317493312|ref|ZP_07951734.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918705|gb|EFV40042.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 248

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 113/242 (46%), Gaps = 17/242 (7%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSI--LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
           +N +     +   ++ L ++   L+    +LY+D  I V NKP+G+    G     H D 
Sbjct: 16  INSVASGGDLALPAIKLGEYFPALEPWLHVLYQDDHIIVVNKPSGLLSVPGKA-EEHKDS 74

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            + + V          HRLD  TSG++ VA T+AA + L   FR R  +K Y + VWG  
Sbjct: 75  VM-TRVQVDFPIAESVHRLDMATSGVIAVALTKAAERELKRQFREREPKKSYIARVWGHM 133

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           ++ +  I   L+       D+ +  KQ    +    A + ++V+   A     +++ P T
Sbjct: 134 EHDEGLIDLPLI------CDWPNRPKQKVCFEHGKSAQTQYQVLSRDADGSTRVKLTPIT 187

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
           GR+HQLRVH L +G PI+GD  Y         S    +L LHA+ + + HPE G  +   
Sbjct: 188 GRSHQLRVHMLALGHPILGDKFYAHPEAKAMAS----RLQLHAQELQITHPEFGTPMHFR 243

Query: 309 AP 310
             
Sbjct: 244 CE 245


>gi|262381293|ref|ZP_06074431.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_33B]
 gi|301309765|ref|ZP_07215704.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 20_3]
 gi|262296470|gb|EEY84400.1| ribosomal large subunit pseudouridine synthase D [Bacteroides sp.
           2_1_33B]
 gi|300831339|gb|EFK61970.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroides sp. 20_3]
          Length = 224

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 70/228 (30%), Positives = 108/228 (47%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I   +K     VQG       +   LK W+  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIAVDKTCREIVQGDKTGDKPLSEMLKVWLKEKYCKPGNVFVGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR+  ++K YW++V   P   +  + +WL++       Y + 
Sbjct: 63  GVVIFAKTSKALSRLNEMFRVGEVRKTYWAIVKSRPPQDEGELVDWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  AI  +K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY  +
Sbjct: 123 TER--PNAKKAILRYKLI-AHSDNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKYGFD 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                       + LHAR  +  HP     ++I AP+P      W +L
Sbjct: 180 RSNK-----DGGISLHARSAEFIHPVSKENVRIVAPVPDD--NLWKAL 220


>gi|167622731|ref|YP_001673025.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167352753|gb|ABZ75366.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 225

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 62/213 (29%), Positives = 104/213 (48%), Gaps = 12/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  I V NKP+G+    G   A+    +  + V ++    ++ HRLD  TSG++VV
Sbjct: 16  ILHQDKDIMVVNKPSGLLSVPGRDPAHADSTY--NRVLAEFPHAKIVHRLDMATSGVIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R+A   L   FR R  +K Y++ V G  K     +   L+             K + 
Sbjct: 74  ALLRSAESELKRQFRDRETEKTYYARVAGHVKETHGTVNLPLICDWPNRPK----QKVDH 129

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K    + +H++VI    ++   +++ P TGR+HQLRVH + +G PI+GD+ Y        
Sbjct: 130 KIGKPSQTHYEVISR-GKRSTLVKLTPITGRSHQLRVHMMALGHPILGDNFYADPLAKR- 187

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              +  +L LHA+ + + HP    R+  +   P
Sbjct: 188 ---LAPRLLLHAQSLTITHPYTKERMTFSCDAP 217


>gi|254507230|ref|ZP_05119367.1| pseudouridylate synthase, 23S RNA-specific [Vibrio parahaemolyticus
           16]
 gi|219549940|gb|EED26928.1| pseudouridylate synthase, 23S RNA-specific [Vibrio parahaemolyticus
           16]
          Length = 559

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 119/245 (48%), Gaps = 22/245 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  +I D+ +  +  ++  +  ++YED  + + NKP+G+    G  I    
Sbjct: 328 CQPILGHMLEGMRIDDNPLEKS-WAEDKELEIVYEDDAMVIVNKPSGLLSVPGKTITDSA 386

Query: 130 DGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              L K + D++G  P + HRLD  TSGILV A TR A ++L + F  R +QK Y + + 
Sbjct: 387 YTRLQKRYPDAEG--PFVIHRLDMATSGILVFALTRRANKNLQKQFISRSVQKRYIAQIE 444

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  + +   I N  ++          V  ++      A +++++I+    +     M P 
Sbjct: 445 GEVQVQNGTI-NLPMRGDPDDRPRQLVCYEH---GKPAETYWELIETSNGQSKLY-MHPK 499

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGR 304
           TGRTHQLRVH  H   +  PIVGD  Y             ++L+LHA+ ++L HP     
Sbjct: 500 TGRTHQLRVHCAHHLGLNMPIVGDALYGTK---------SDRLHLHAQRLELHHPYNHEP 550

Query: 305 LQITA 309
           +  +A
Sbjct: 551 MTFSA 555


>gi|238797483|ref|ZP_04640981.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           mollaretii ATCC 43969]
 gi|238718624|gb|EEQ10442.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           mollaretii ATCC 43969]
          Length = 217

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 67/226 (29%), Positives = 101/226 (44%), Gaps = 15/226 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G   A      + + + +        
Sbjct: 1   MEPYNPPRDPWLHILYQDEHIMVVNKPSGLLSVPGR--APENKDSIMTRIQADYPTAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG+++VA T+AA + L   FR R  +K Y + VWG     +  I   L+    
Sbjct: 59  HRLDMATSGVIIVALTKAAERELKRQFREREPKKSYIARVWGHLTQDEGLIDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + + V+   A     +++ P TGR+HQLRVH L MG P
Sbjct: 115 --CDWPNRPKQKVCYETGKSAQTEYHVLSRDADGSTRVKLSPITGRSHQLRVHMLAMGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           I+GD  Y         S    +L LHA+ + + HPE G  +     
Sbjct: 173 ILGDGFYAHPEAKAMAS----RLQLHAQELCITHPEFGTVMHFKCE 214


>gi|150008130|ref|YP_001302873.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           distasonis ATCC 8503]
 gi|149936554|gb|ABR43251.1| ribosomal large subunit pseudouridine synthase D [Parabacteroides
           distasonis ATCC 8503]
          Length = 224

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 70/228 (30%), Positives = 108/228 (47%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I   +K     VQG       +   LK W+  K  KP      +THRLD+  S
Sbjct: 3   VIYEDNHIIAVDKTCREIVQGDKTGDKPLSEMLKVWLKEKYCKPGNVFVGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR+  ++K YW++V   P   +  + +WL++       Y + 
Sbjct: 63  GVVIFAKTSKALSRLNEMFRVGEVRKTYWAIVKNRPPQDEGELVDWLVRNEKQNKSYAYD 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            ++    A  AI  +K+I   +  +  LE+   TGR HQ+R     MGCPI GD KY  +
Sbjct: 123 TER--PNAKKAILRYKLI-AHSDNYYLLEIDLKTGRHHQIRCQLAKMGCPIKGDLKYGFD 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                       + LHAR  +  HP     ++I AP+P      W +L
Sbjct: 180 RSNK-----DGGISLHARSAEFIHPVSKENVRIVAPVPDD--NLWKAL 220


>gi|190149589|ref|YP_001968114.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|189914720|gb|ACE60972.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
          Length = 226

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 66/211 (31%), Positives = 101/211 (47%), Gaps = 12/211 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+      + V  K       HRLD  TSGIL+ A
Sbjct: 21  VYRDNHILVINKPSGLLSVPGNRPEYYDSAM--TRVQQKYGFTEPAHRLDMATSGILLFA 78

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWLLKKSHIGGDYVHVVKQN 219
            ++AA + L   FR R  +K Y +L+WG    K       N+ L           +  + 
Sbjct: 79  LSKAAEKELKRQFRDREPKKHYIALLWGKLGEKVGDTGEMNFPLICDWENRPRQKICYER 138

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y +    +
Sbjct: 139 ---GKKAITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGDKFYASPLAKS 195

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
               +  +L LHA  + + HP  G  +  TA
Sbjct: 196 ----LSPRLCLHAESLSITHPITGEAMTFTA 222


>gi|37681108|ref|NP_935717.1| pseudouridylate synthase [Vibrio vulnificus YJ016]
 gi|37199858|dbj|BAC95688.1| pseudouridylate synthase [Vibrio vulnificus YJ016]
          Length = 250

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 59/210 (28%), Positives = 97/210 (46%), Gaps = 14/210 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I   NKP+G+    G    +H    + S +  +  + ++ HRLD  TSG++V 
Sbjct: 16  IIFEDDHILAVNKPSGLLSVPGRLPEHHDS--MWSRLQEQYPEIQVVHRLDMSTSGLMVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ + A   L + F+ R   KIY++ VWG  +     I   L+           + K   
Sbjct: 74  AKNKRAEAALKKQFQYRLTHKIYYARVWGHVETDSGMIDLPLICD----WPNRPMQKVCH 129

Query: 221 KGANYAISHFKV----IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +    + + F+V    +     +   + + P TGR+HQLRVH   +G PIVGD  Y    
Sbjct: 130 EHGKPSQTEFQVAKREVHANGAQTTIMRLLPVTGRSHQLRVHMQALGHPIVGDEFYAQGD 189

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
              F+     +L LHA  +   HP+   L+
Sbjct: 190 AFTFSE----RLELHAAELSFYHPKSHWLR 215


>gi|268316750|ref|YP_003290469.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
 gi|262334284|gb|ACY48081.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
          Length = 242

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 67/232 (28%), Positives = 112/232 (48%), Gaps = 17/232 (7%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHR 149
           +  +  +LY D+ + V NKP+G+  QG    A  +    K+ +  +  KP      L HR
Sbjct: 3   EVAELPVLYLDNHLLVINKPSGLRSQGDRSGAPTVLSLGKALIKERFNKPGNVYLGLVHR 62

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD   SG++V+ART  AA  L + FR R ++K+Y +LV G  +       +++       
Sbjct: 63  LDAPVSGVMVLARTSKAAARLMQQFRERTVEKVYLALVEGELEG-SGTWEDFIA----PA 117

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            D++ +V ++      A+ H++ +         + + P TGR HQ+RV     G PI+GD
Sbjct: 118 RDHMRLVPEDHPFGKRAVLHWQALMTR-NGLTLMRLVPETGRKHQIRVQLAFRGYPILGD 176

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWD 320
            +Y A            ++ LHA  + L HP    R+Q TAP+P+   + + 
Sbjct: 177 RRYRARRW-----LAPGQMALHAWKLALTHPTRRERMQWTAPVPSFWDEAFR 223


>gi|313677829|ref|YP_004055825.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
 gi|312944527|gb|ADR23717.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
          Length = 300

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 72/313 (23%), Positives = 131/313 (41%), Gaps = 37/313 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
           V++ D E   L +     YP+     L++++  GQ+R++   +  FN+ ++ G  ++I  
Sbjct: 16  VIQEDTE---LLKHLTTTYPNKKKALLKQVMGGGQIRINGDVITQFNHPLKKGDEIQINW 72

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYH 128
                                +K     K  ++YED  +    K AG+           +
Sbjct: 73  ------------------AKPSKKVKLQKLNIIYEDQHLIAIEKEAGLLSVASLKEKTKN 114

Query: 129 IDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
               LK  +++     K  + HRL++E SG+L+ A+++   + L   +    I + Y ++
Sbjct: 115 AVQILKEHMEAIDPRNKVYIIHRLEREASGVLLFAKSKEVQEQLQNHWEDYIIDRKYVAV 174

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G  K     + N+L    H        +    + A  AI+HFK++   +  +  LE +
Sbjct: 175 VEGKIKESSHTLRNYLRSNKHN----QVFIVNTAENATEAITHFKLLK-QSNAYSMLEFK 229

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TG  +Q+RV   H G P+ GD KY A            ++ LHA  ++L HP  G  L
Sbjct: 230 LETGFKNQIRVQMAHFGFPVTGDKKYTAKKNP------LARVALHANLIELKHPISGEHL 283

Query: 306 QITAPLPAHMVKT 318
           +     P++    
Sbjct: 284 KFELVPPSNFRNL 296


>gi|145640057|ref|ZP_01795653.1| hypothetical protein CGSHiII_01454 [Haemophilus influenzae PittII]
 gi|145270841|gb|EDK10762.1| hypothetical protein CGSHiII_01454 [Haemophilus influenzae PittII]
 gi|309751619|gb|ADO81603.1| Pseudouridine synthase A [Haemophilus influenzae R2866]
          Length = 219

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 106/229 (46%), Gaps = 16/229 (6%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            +++ +  L  + D     ++Y+D+ + V NKP+G+    G+   Y+      S V  K 
Sbjct: 2   ALIEYNPPLEPYLD-----IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKF 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGI+V A ++AA + L   FR R  +K Y ++VWG  +N    +   
Sbjct: 55  GFCEPAHRLDMATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLP 114

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           ++       +     + +      A++ F+V+         +++ P TGR+HQLR+H L 
Sbjct: 115 MICD----WENRPRQRLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLA 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
            G PI+GD  Y        +     +L LHA  + + HP  G  +   A
Sbjct: 171 SGHPILGDKFYSHPQAKAMS----PRLCLHAEELTITHPITGETMTFNA 215


>gi|310777837|ref|YP_003966170.1| pseudouridine synthase, RluA family [Ilyobacter polytropus DSM
           2926]
 gi|309747160|gb|ADO81822.1| pseudouridine synthase, RluA family [Ilyobacter polytropus DSM
           2926]
          Length = 287

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 137/319 (42%), Gaps = 39/319 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++E    N ++ ++ +    +         LR+ +  +D KRVK   +++      
Sbjct: 1   MKKFIIEPQYSNYKISQYLREVKGYSGRS-----LRNIECYLDGKRVKTTKKLR------ 49

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
                  LN ++ ++K   + +   K    +   ++YED+ + + +K   I V      +
Sbjct: 50  ------KLNRLVVKEKDKGTDMKPIK----MDLNIVYEDNNLILIDKEPYIIVHPTQKKV 99

Query: 126 AYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +   +  ++  K  K   PR  +RLD  T+GI+VVA+       L        ++K 
Sbjct: 100 DKTLAHGIIHYIHEKTGKILAPRFYNRLDMNTTGIIVVAKNAYTQAFLQYKA---EVKKY 156

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FC 241
           Y ++V GI +  +  I   L K+   G +    V   EKG   A +  KVI  + +K   
Sbjct: 157 YQAIVKGIIEEDEIMIEKPLGKE---GDELRRKVMPVEKGGQDAKTFVKVIKRYPEKDLS 213

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E++  TGRTHQ+R H   +G P++GD  Y A            +  LH+  ++  +P+
Sbjct: 214 LVELELFTGRTHQIRAHMESLGHPVLGDELYGAKDDRA------RRQMLHSYKLEFTNPD 267

Query: 302 GGRLQ-ITAPLPAHMVKTW 319
               + +   LP  M +  
Sbjct: 268 NLHQETVEIELPEDMKEVL 286


>gi|330445141|ref|ZP_08308793.1| tRNA pseudouridine 65 synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328489332|dbj|GAA03290.1| tRNA pseudouridine 65 synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 245

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 59/244 (24%), Positives = 99/244 (40%), Gaps = 17/244 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY D  +   NKPAG+ V      ++     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELEILYRDEYLIAVNKPAGMLVHRSWLDSHETVFVMQTLRDQIGQHVFPLHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+   +   A  +   F  R + K Y ++V G  K          ++   I        
Sbjct: 61  VLLFGLSSEIAAEMMPMFAGRDMHKTYHAVVRGWIKEAAVLDYPLKVELDKIADKNAS-- 118

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              EK A  A++ ++ +               ++C +EM+P TGR HQLR H  H+   I
Sbjct: 119 --EEKEAQPAVTAYEPLATVETDIAVGRYSTSRYCLVEMKPETGRKHQLRRHMHHLSHHI 176

Query: 267 VGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD  +             +  +L LHA  +   HP  G  + I A +     +   +  
Sbjct: 177 IGDVNHGDGRHNRMFREHYDCHRLMLHASRLQFAHPITGEPIDIRADIDETWQRVMSAFN 236

Query: 324 FKYD 327
           +  D
Sbjct: 237 WSSD 240


>gi|256026481|ref|ZP_05440315.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
          Length = 288

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 132/320 (41%), Gaps = 38/320 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   VE++ +   +  + K    + +       LR+ ++ ++ KR           +  
Sbjct: 1   MKKYTVEHEYDGYEIGTYLKEIKGYSSRG-----LRNLEIYLNGKR-----------IKN 44

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGI 125
               I  LN I+    I++   +    +  +   + YED  + + NK   I V      +
Sbjct: 45  NAKKIKKLNRIV----IIEKEKSTGIKAMDIPIDIAYEDENLLIVNKEPYIIVHPTQKKV 100

Query: 126 AYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +   + ++ +    K   PR  +RLD  TSG++++A+       L +      ++K 
Sbjct: 101 DKTLANAIVNYFEKTLGKTLVPRFYNRLDMNTSGLIIIAKNAYTQAFLQDKT---EVKKT 157

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFC 241
           Y  +  GI +     I   + K   +G +   +    + G   A +H KV++  + +   
Sbjct: 158 YKVIASGIIEKDDFFIEIPIGK---VGDNLRRIELSEKDGGKSAKTHIKVLERNYEKNIT 214

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +LE + +TGRTHQ+R H   +G  +VGD  Y  N        +  +  LHA  ++  +P+
Sbjct: 215 FLEARLYTGRTHQIRAHLSLIGHSLVGDELYGGNMN------LAKRQMLHAYKLEFQNPK 268

Query: 302 G-GRLQITAPLPAHMVKTWD 320
               L+I   +P  M +   
Sbjct: 269 TLENLKIEIDIPIDMKEVLK 288


>gi|153008381|ref|YP_001369596.1| pseudouridine synthase [Ochrobactrum anthropi ATCC 49188]
 gi|151560269|gb|ABS13767.1| pseudouridine synthase [Ochrobactrum anthropi ATCC 49188]
          Length = 222

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 105/230 (45%), Gaps = 11/230 (4%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +L +   +          +L+ D+   V +KP+G+    G   A      L + V  +  
Sbjct: 3   VLSAVTPVYHPPLEPYLSILHRDAGFLVLDKPSGLLSVPGRHPALSDS--LATRVQEQFP 60

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           + ++ +RLD++TSG+++++  R A   +   F  R  QK Y ++VWG+ ++ +  I   L
Sbjct: 61  QAQMINRLDKDTSGLVLMSLNRKAHAAIASQFEARTTQKSYVAVVWGLVEDDEGLIDLPL 120

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                I  D     + + +    A + ++V+D   +    L + P TGRTHQLRVH   +
Sbjct: 121 A----IDPDNKPRHRVDRENGKPAQTRWRVLDRD-ENTTRLRLHPLTGRTHQLRVHMKAL 175

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           G  I+GD  Y           +     LHA  +   HP+G  +  TAP P
Sbjct: 176 GHVILGDEFYAEGEALAAADRLL----LHAEELSFQHPDGRSVTFTAPCP 221


>gi|220929832|ref|YP_002506741.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|220000160|gb|ACL76761.1| pseudouridine synthase [Clostridium cellulolyticum H10]
          Length = 223

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 72/230 (31%), Positives = 113/230 (49%), Gaps = 16/230 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQE 153
             ++YED+ + V  KP  I VQ  +     +   LK ++  K  KP      L HRLD+ 
Sbjct: 3   PKIVYEDNHLLVVEKPVNIPVQADNSKDIDMLTLLKQYLKEKYNKPGEVYLGLVHRLDRP 62

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
             G++V A+T   A  L++  R R  +K Y ++V G+P+ +K+ + N+LLK S    + V
Sbjct: 63  VGGVMVFAKTSKCASRLSDQIRTRTFKKTYLAIVRGVPQKQKDELRNFLLKDS--SENMV 120

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           HVVK+  + A  AI  ++V+    +    L++Q HTGR HQ+RV   H G P+ GD +Y 
Sbjct: 121 HVVKEGTRDAKEAILDYEVLKSNGE-LSLLQIQLHTGRPHQIRVQLSHSGYPLYGDQRYG 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
                 + +    ++ L A  + L HP     +      P    K W  L
Sbjct: 180 -----IYVNKPGQQIALWASSLTLEHPTKKEEMTFGCGTPE--KKPWTEL 222


>gi|50285951|ref|XP_445404.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49524708|emb|CAG58310.1| unnamed protein product [Candida glabrata]
          Length = 584

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 57/256 (22%), Positives = 99/256 (38%), Gaps = 28/256 (10%)

Query: 21  LDRW---FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +D +   F++  P        K +  G V V+ K       +++G+++            
Sbjct: 104 IDIFTQEFRDQEPDHYR----KTIAKGAVSVNGKPANLETILRNGEMITHKMHR------ 153

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E  +    +            +++E+  I V +KP GI V       Y  +   K   
Sbjct: 154 -HEPPVTSRPIK-----------IVFENDDILVIDKPGGIPVHPTG--RYRYNTITKILE 199

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +     +RLD+ TSG++ +A+T   A  + +  + R + K Y + V G     +  
Sbjct: 200 KQMKRSVHPCNRLDRLTSGLMFLAKTPEGADQMADQMKTREVTKEYIARVVGEFPTGEIT 259

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   L          +     NE  A  A + F+ I    Q    ++ +P TGRTHQ+RV
Sbjct: 260 VEKPLKSYDPKVSLNIICDDTNEDDAKPAKTVFQRISFDGQ-TSIVKCKPLTGRTHQIRV 318

Query: 258 HALHMGCPIVGDHKYC 273
           H   +G PI  D  Y 
Sbjct: 319 HLQFLGHPIANDPIYS 334


>gi|326388573|ref|ZP_08210166.1| pseudouridylate synthase [Novosphingobium nitrogenifigens DSM
           19370]
 gi|326206824|gb|EGD57648.1| pseudouridylate synthase [Novosphingobium nitrogenifigens DSM
           19370]
          Length = 219

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 67/228 (29%), Positives = 108/228 (47%), Gaps = 16/228 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +L+ED +  V +KPAG+ +         +D  L        ++P   HRLD++TSG 
Sbjct: 3   ELSILFEDGEALVIDKPAGLPLDRPRAGGISLDDRLDELRLGFQRRPAPVHRLDRDTSGC 62

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++AR   A +    +F  R++ KIY  +V G  +  K  I+  L K S     +  +  
Sbjct: 63  LLLARNPKALKRFAAAFEARKVIKIYLGVVAGPVEGDKGTISLSLSKISSEKNGWRMI-- 120

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANF 276
              +    A++H++V+         +E +P TGRTHQ+RVHA   +G  ++GD  Y    
Sbjct: 121 -PARQGKAAVTHWRVLARK-DGLTLVEFRPETGRTHQIRVHAASGLGHALLGDPVYGKAV 178

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
            G        +  LHA  + +P      ++  APLPA  V    +LGF
Sbjct: 179 AGT-------RTMLHAAQLVIPREGKDTIEAEAPLPADFV----ALGF 215


>gi|288904349|ref|YP_003429570.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus gallolyticus UCN34]
 gi|288731074|emb|CBI12620.1| putative ribosomal large subunit pseudouridine synthase, RluD
           subfamily [Streptococcus gallolyticus UCN34]
          Length = 286

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 59/289 (20%), Positives = 110/289 (38%), Gaps = 32/289 (11%)

Query: 23  RWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +  + H   I    ++  LR    +R++ + + + + +++G  + +    +         
Sbjct: 18  KLLEEHLL-IPR-KIRHFLRTKKHLRINGEMINWQSLVKTGDTIHLIFDDD--------- 66

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
              D                LY+D  + + NKP G+   G       +   + ++V   G
Sbjct: 67  ---DYPQKEIPFGQAELVDCLYQDEHLIIVNKPEGMKTHGNEPNEIALLNHVSAYV---G 120

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           Q   + HRLD ETSG  + A+       +      + I + YW+LV G  + K +   + 
Sbjct: 121 QTCYVIHRLDMETSGAAMFAKNPFVLPIINRLLENKDIAREYWALVQGKFEPKHQVFQDK 180

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +  H     V     + K    A++    +  F      ++ +  TGRTHQ+RVH   
Sbjct: 181 IGRDRHDRRKRV----VDRKNGQTALTIVDRLKVFPNG-TLVKCRLKTGRTHQIRVHLSA 235

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
               I+GD  Y              +L LHA  +   HP    ++ + A
Sbjct: 236 HNHAIIGDPLYSKIPA--------KRLMLHAHKLSFTHPFTLEKISVEA 276


>gi|260767269|ref|ZP_05876210.1| tRNA pseudouridine synthase C [Vibrio furnissii CIP 102972]
 gi|260617777|gb|EEX42955.1| tRNA pseudouridine synthase C [Vibrio furnissii CIP 102972]
          Length = 243

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 103/237 (43%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ I   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IIYQDAYIVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A ++   F    ++K Y ++V G    +   + ++ LK+            + +
Sbjct: 64  ALSSEIAANMMPMFANHEMEKTYHAIVRGWI--EVGDVLDYPLKEEL--DKIADKFAKQD 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++ ++ +               ++C +EM+P TGR HQLR H  H+  PIVGD 
Sbjct: 120 KAPQDAVTAYQPLAKVEVPHSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIVGDT 179

Query: 271 KYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
            +           +   ++L LHA  +   HP     L + A   A   + +    +
Sbjct: 180 THGDGKHNRLYREVYDAHRLMLHASELRFVHPYTEQELVLRAGFDATWQRLFALFDW 236


>gi|167854620|ref|ZP_02477401.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           parasuis 29755]
 gi|167854375|gb|EDS25608.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           parasuis 29755]
          Length = 222

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 62/211 (29%), Positives = 95/211 (45%), Gaps = 12/211 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y     ++  V  K       HRLD  TSGIL+ A
Sbjct: 17  VYCDNHILVINKPSGLLSVPGNRPEYQDSAMVR--VQQKYGFTEPAHRLDMATSGILLFA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHVVKQN 219
            ++ A + L   FR R  +K Y +LVWG    K       N+ L           +  + 
Sbjct: 75  LSKQAEKELKRQFREREPKKHYQALVWGKLGEKVGDTGTMNFPLICDWENRPRQKICYER 134

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 A++ ++++  +      + + P+TGR+HQLRVH L +G PIVGD  Y       
Sbjct: 135 ---GKQAVTFYEILAHYPNNTTRVTLTPYTGRSHQLRVHCLALGHPIVGDKFY----ANP 187

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
               +  +L LHA  + + HP     +   A
Sbjct: 188 LAKSLSPRLCLHAEALTITHPVTQELMTFEA 218


>gi|78221490|ref|YP_383237.1| tRNA pseudouridine synthase C [Geobacter metallireducens GS-15]
 gi|78192745|gb|ABB30512.1| tRNA pseudouridine synthase C [Geobacter metallireducens GS-15]
          Length = 270

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 100/237 (42%), Gaps = 16/237 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  +   +KP G+ V       +     L+   D  G++    HRLD+ TSG+L+ 
Sbjct: 3   ILYRDEHLVAVHKPLGLLVHRSPIDRHETRFALQEVRDLLGRRVYPVHRLDKPTSGVLLF 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A   A A+ L  +F    + K Y ++V G    ++  I + L ++              E
Sbjct: 63  ALDPAFARGLVGAFASGSVTKTYLAVVRGTMP-EEGVIDHPLAEEP--DRFEQGRGNAGE 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +    A++ ++ +               ++  + + P TGR HQLR H  H+  PIVGD 
Sbjct: 120 RAPQSAVTGYRRLADVELPVAVGRYPTSRYSLVSLSPRTGRRHQLRRHLKHLFHPIVGDT 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
           KY       F     +  ++ LHA  + +PHP  G  L + AP+           G+
Sbjct: 180 KYGEGRHNRFFREELLTVRMLLHAVELTVPHPATGAPLTVCAPVEGAFAALLARFGW 236


>gi|310643591|ref|YP_003948349.1| pseudouridine synthase, rlua family [Paenibacillus polymyxa SC2]
 gi|309248541|gb|ADO58108.1| Pseudouridine synthase, RluA family [Paenibacillus polymyxa SC2]
          Length = 303

 Score =  169 bits (428), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 96/248 (38%), Gaps = 20/248 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF---LKSWVDSK 140
           L   V+L     +    +LYED    V +KPAG++V    G+          + S+ +  
Sbjct: 67  LFPVVDLGVIPRWYDLKILYEDDFCLVVHKPAGMAVHPDGGVKDSPLTLDHAVASYYEIN 126

Query: 141 GQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                 R  HRLD +T+G ++ A+   A   L E  R + I + Y +LV G        +
Sbjct: 127 DIHTAVRHVHRLDVDTTGPVLYAKNEFALLKLDEQMRAKDIGRRYVALVRGKVPPSLRTL 186

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQL 255
              + K  H         ++       A++H +V + +         + +   TGRTHQ+
Sbjct: 187 DWPIGKDRH-----HKQRRRVSPTGQKAVTHVEVGEVWGSGPSAVSLVYLTLETGRTHQI 241

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           RVH  H G P++GD  Y              +  LH   +   HP  G  + +    P  
Sbjct: 242 RVHLSHAGYPLLGDVLYGGRAVD------FGRQALHGERLTFCHPLSGETITVEDAWPDD 295

Query: 315 MVKTWDSL 322
             K    L
Sbjct: 296 FQKLHKQL 303


>gi|53804068|ref|YP_114042.1| ribosomal large subunit pseudouridine synthase A [Methylococcus
           capsulatus str. Bath]
 gi|53757829|gb|AAU92120.1| ribosomal large subunit pseudouridine synthase A [Methylococcus
           capsulatus str. Bath]
          Length = 212

 Score =  169 bits (428), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 60/215 (27%), Positives = 106/215 (49%), Gaps = 10/215 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D+ + V +KP+G+    G G        L + V ++     + HRLD  TSG++V+
Sbjct: 4   VVHTDAALLVLSKPSGLLAVPGRGQD--KQDCLSARVRARYPDALVVHRLDMATSGLMVM 61

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV--KQ 218
           AR  A  + L++SF  R + K Y +LV G+ +   E    W      +  D+ +    K 
Sbjct: 62  ARGIAVQRILSQSFARREVLKRYEALVHGVLETPPETENGWSSIDLPLLSDWPNRPLQKV 121

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      +++ ++++         +E++P TGR+HQLRVH   +G P++GD  Y      
Sbjct: 122 DPLHGKPSLTRWRILG-HEDGATRVELEPVTGRSHQLRVHLAALGYPVLGDPLYGHEVAK 180

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +       +L LHAR +   HP  G  L+  +P+P
Sbjct: 181 SRA----GRLLLHARTLGFFHPVSGEWLEFESPVP 211


>gi|109898644|ref|YP_661899.1| pseudouridine synthase [Pseudoalteromonas atlantica T6c]
 gi|109700925|gb|ABG40845.1| pseudouridine synthase [Pseudoalteromonas atlantica T6c]
          Length = 567

 Score =  169 bits (428), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 123/250 (49%), Gaps = 24/250 (9%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I      LNH++ E   ++ +  L   +D  +  ++Y+D ++ + NKPA +    G  I+
Sbjct: 331 IGKCQPILNHML-EGLTVEENQLLKNAADGEQIEIIYQDDEMLIINKPAQLLSVPGKHIS 389

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   +K+ +        + HRLD  TSG++V+A + AA + L + F  R++ K Y +L
Sbjct: 390 DSVYTRIKAMLPHATGSL-IVHRLDMSTSGLMVIALSTAAHKVLQKQFISRQVSKRYMAL 448

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQ-KFCWL 243
           + GI  ++   I   L       GD+    +Q   EK    A + ++VI+   + +   +
Sbjct: 449 IDGIVTDENGVITLPL------AGDFYDRPRQCVCEKTGKPAHTTWQVIERRHKTQQTKV 502

Query: 244 EMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            + P TGRTHQLRVH  H   +  PIVGD  Y    +         +L+LHA+Y+ L HP
Sbjct: 503 YLHPRTGRTHQLRVHCAHERGLNMPIVGDDLYGTQAR---------RLHLHAQYLGLFHP 553

Query: 301 EGGR-LQITA 309
              + L+ + 
Sbjct: 554 VSNQWLEFSC 563


>gi|254449436|ref|ZP_05062873.1| ribosomal large subunit pseudouridine synthase A [Octadecabacter
           antarcticus 238]
 gi|198263842|gb|EDY88112.1| ribosomal large subunit pseudouridine synthase A [Octadecabacter
           antarcticus 238]
          Length = 215

 Score =  169 bits (428), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 66/220 (30%), Positives = 109/220 (49%), Gaps = 13/220 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                  +++ D +I + NKP+G+    G G   H+   L + V     +  L HRLD++
Sbjct: 7   PPDDPLDVIHADHEILIVNKPSGLLSVPGKGP--HLADCLIARVQVAFPQALLIHRLDRD 64

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V A TR A +H+   F  R  +K Y + VWG+   KK  +   L+    +  +  
Sbjct: 65  TSGVMVFALTRHAQRHIGLQFEKRMTKKTYVARVWGMLDPKKGTVDLPLI----VDWENR 120

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + K   +    A + ++V+   A++   + + P TGR+HQLRVH L +G PI+GD  Y 
Sbjct: 121 PLQKVCHETGKSAQTDWRVLRNDARE-SRVRLMPKTGRSHQLRVHMLSLGHPILGDPFYA 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                 +      +L LH+  + L HP+GG  ++  A  P
Sbjct: 180 QGEAREYE-----RLMLHSEELRLRHPDGGEGVKFRAKAP 214


>gi|229845572|ref|ZP_04465699.1| hypothetical protein CGSHi6P18H1_05160 [Haemophilus influenzae
           6P18H1]
 gi|229811507|gb|EEP47209.1| hypothetical protein CGSHi6P18H1_05160 [Haemophilus influenzae
           6P18H1]
          Length = 219

 Score =  169 bits (428), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 111/231 (48%), Gaps = 20/231 (8%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            +++ +  L  + D     ++Y+D+ + V NKP+G+    G+   Y+      S V  K 
Sbjct: 2   ALIEYNPPLEPYLD-----IIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKF 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGI+V A ++AA + L   FR R  +K Y ++VWG  +N    +   
Sbjct: 55  GFCEPAHRLDMATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLP 114

Query: 202 LLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           ++       D+ +  +Q  +      A++ F+V+         +++ P TGR+HQLR+H 
Sbjct: 115 MI------CDWENRPRQCLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHM 168

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           L +G PI+GD  Y        +S    +L LHA  + + HP  G  +   A
Sbjct: 169 LALGNPILGDKFYSHPQAKAMSS----RLCLHAEELTITHPITGETMTFNA 215


>gi|78484624|ref|YP_390549.1| pseudouridine synthase [Thiomicrospira crunogena XCL-2]
 gi|78362910|gb|ABB40875.1| tRNA pseudouridine synthase C [Thiomicrospira crunogena XCL-2]
          Length = 252

 Score =  169 bits (428), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 69/245 (28%), Positives = 111/245 (45%), Gaps = 17/245 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   +KPAG+ V       +     ++   D   QK    HRLD+ TSG+L+ 
Sbjct: 12  ILYQDDSLVAVHKPAGLLVHRSPIDRHETQFAVQMTRDQINQKVYPLHRLDKATSGLLLF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A     A+ + + F    IQK Y ++  G    +   I + L  K    GD      Q  
Sbjct: 72  ALDSNTARLMGQQFEEHTIQKHYLAICRG-WTAEHGEIDHALKHKLDKLGDRHA---QTN 127

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A+++F+ +             +Q++  +++ P TGR HQLR H  H+  PI+GD 
Sbjct: 128 KPPQEALTNFERLATTDVMHKIGKFDSQRYSLVKLMPKTGRKHQLRRHLNHISHPIIGDV 187

Query: 271 KYCANFKGNFTSP--IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
           KY      +F +    Q++LYL A  +   HP+   R+ + APL     K    L ++ +
Sbjct: 188 KYGDRHHNHFFNTWLGQHRLYLAATSLTFNHPQTNARMTLNAPLELSYQKATQHLNWQEE 247

Query: 328 RNLYI 332
              YI
Sbjct: 248 TATYI 252


>gi|309778338|ref|ZP_07673264.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Erysipelotrichaceae bacterium 3_1_53]
 gi|308913904|gb|EFP59718.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Erysipelotrichaceae bacterium 3_1_53]
          Length = 293

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 67/280 (23%), Positives = 109/280 (38%), Gaps = 32/280 (11%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           +V ++ + +  N+ +     +RI                       T    +    +LYE
Sbjct: 42  RVFLNNRHISRNHTLHEKDTIRISLQAE----------------EDTVKPWYKHVEILYE 85

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQK--PRLTHRLDQETSGILVVA 161
           D    + NKPA + V      + H     +K+   ++G     R  HRLD ETSG+L+  
Sbjct: 86  DDLFCIVNKPANLLVHSDGVESEHTVCNMVKAHYLTEGSNACVRPLHRLDYETSGVLIFC 145

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L E  + ++I + Y +   G    K   I   + +  H          +   
Sbjct: 146 KLPFFQPMLDEMLKSKQIYREYEAFAVGRFTQKHYTITRGIARDRHDARR-----MRVSD 200

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               A +   V   F+  F W+  + HTGRTHQ+RVH + +  P++ D  Y         
Sbjct: 201 NGKEARTDVFVKQSFSD-FTWIRCRLHTGRTHQIRVHLVSLQHPLLSDSLYGKR------ 253

Query: 282 SPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            P   +L LHA  + +PHP     L I  PLP  M +  +
Sbjct: 254 DPRCARLALHAARVHIPHPLSHTTLNIECPLPEDMKRLLE 293


>gi|289764495|ref|ZP_06523873.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
 gi|289716050|gb|EFD80062.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
          Length = 292

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 66/321 (20%), Positives = 132/321 (41%), Gaps = 38/321 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++   VE++ +   +  + K    + +       LR+ ++ ++ KR           + 
Sbjct: 4   KMKKYTVEHEYDGYEIGTYLKEIKGYSSRG-----LRNLEIYLNGKR-----------IK 47

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SG 124
                I  LN I+    I++   +    +  +   + YED  + + NK   I V      
Sbjct: 48  NNAKKIKKLNRIV----IIEKEKSTGIKAMDIPIDIAYEDENLLIVNKEPYIIVHPTQKK 103

Query: 125 IAYHIDGFLKSWVD---SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           +   +   + ++ +    K   PR  +RLD  TSG++++A+       L +      ++K
Sbjct: 104 VDKTLANAIVNYFEKTLGKTLVPRFYNRLDMNTSGLIIIAKNAYTQAFLQDKT---EVKK 160

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKF 240
            Y  +  GI +     I   + K   +G +   +    + G   A +H KV++  + +  
Sbjct: 161 TYKVIASGIIEKDDFFIEIPIGK---VGDNLRRIELSEKDGGKSAKTHIKVLERNYEKNI 217

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            +LE + +TGRTHQ+R H   +G  +VGD  Y  N        +  +  LHA  ++  +P
Sbjct: 218 TFLEARLYTGRTHQIRAHLSLIGHSLVGDELYGGNMN------LAKRQMLHAYKLEFQNP 271

Query: 301 EG-GRLQITAPLPAHMVKTWD 320
           +    L+I   +P  M +   
Sbjct: 272 KTLENLKIEIDIPIDMKEVLK 292


>gi|119774268|ref|YP_927008.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119766768|gb|ABL99338.1| tRNA pseudouridine synthase C [Shewanella amazonensis SB2B]
          Length = 258

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 65/240 (27%), Positives = 106/240 (44%), Gaps = 17/240 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  +   +KPAG+ V             ++   D  G      HRLD+ TSG+L+ 
Sbjct: 12  ILYEDEAMVAIHKPAGLLVHRTYLARKEHWFAMQLTRDLVGCHVFPVHRLDRPTSGVLLF 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++   A  L   F    I+K Y +LV G   +    + ++ LK+     +        +
Sbjct: 72  AKSSEVANSLCGQFASHSIRKHYLALVRGNMFDAG--VLDYALKEEL--DELADKDVDPD 127

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K A  AI+ ++ +             + +F  + +QP TGR HQLR H  H+  PIVGD 
Sbjct: 128 KPAQEAITAYRPLLNSEIPYSSGRYPSSRFALMHLQPQTGRKHQLRRHMAHLRHPIVGDT 187

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYD 327
            +    +  F       N+L+L A+ ++L HP  G  + I   L    +  +  LG+  +
Sbjct: 188 THGDGKQNRFFREHFGVNRLWLIAKRLELTHPLTGAPIAIETELEPEWLDVFSGLGWDEE 247


>gi|149187993|ref|ZP_01866288.1| tRNA pseudouridine synthase C [Vibrio shilonii AK1]
 gi|148837981|gb|EDL54923.1| tRNA pseudouridine synthase C [Vibrio shilonii AK1]
          Length = 258

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 58/245 (23%), Positives = 96/245 (39%), Gaps = 17/245 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                  ++Y+D  +   NKPAG+ V             +++  D  GQ     HRLD+ 
Sbjct: 8   PAVEPLEIVYQDQYLVAVNKPAGMLVHRSWLDKNETRFVMQTLRDQIGQHVFPLHRLDRP 67

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+L+ A +   A      F    I+K Y ++V G             ++   I   + 
Sbjct: 68  TSGVLLFALSSEIASQAMPMFAEHNIEKTYHAIVRGWITEGDVLDYPLKVELDKIADKFA 127

Query: 214 HVVKQNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                 +K A  A++ ++ +               ++C +EM+P TGR HQLR H  H+ 
Sbjct: 128 SQ----DKEAQPAVTAYQPLASVEVPYTTGRFPTSRYCLVEMKPKTGRKHQLRRHMHHLS 183

Query: 264 CPIVGDHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            PI+GD  +               ++L LHA  +   HP       I+A   A      D
Sbjct: 184 HPIIGDTSHGDGKHNRLFREHYDSHRLLLHASELKFVHPITEQETTISANFDAVWQTLID 243

Query: 321 SLGFK 325
           +  ++
Sbjct: 244 AFDWQ 248


>gi|197286175|ref|YP_002152047.1| ribosomal large subunit pseudouridine synthase A [Proteus mirabilis
           HI4320]
 gi|194683662|emb|CAR44607.1| ribosomal large subunit pseudouridine synthase A [Proteus mirabilis
           HI4320]
          Length = 216

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 109/235 (46%), Gaps = 22/235 (9%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           + +          +LY+D  I V NKP+G+    G  + +H    + S + +        
Sbjct: 1   MEVYNPPTDPWLHVLYQDEHIIVVNKPSGLLSVPGKALEHHDS--IMSRIKADFPDAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA  +AA + L   FR R  +K Y + VWG  +  +  +   L+    
Sbjct: 59  HRLDMATSGVMVVALNKAAERELKRQFREREPKKTYIARVWGKLEKPQGLVDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V++ + +    +++ P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCYETGKSAQTFYEVLE-YEENATRVKLSPITGRSHQLRVHMLALGHP 171

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           I+GD  Y           +  +L LHA+ + + HP        +P+  H     D
Sbjct: 172 ILGDRFYAHPQ----ARALAPRLQLHAQELFITHPA-----FHSPI--HFECLAD 215


>gi|87308280|ref|ZP_01090421.1| pseudouridine synthase RluA [Blastopirellula marina DSM 3645]
 gi|87288837|gb|EAQ80730.1| pseudouridine synthase RluA [Blastopirellula marina DSM 3645]
          Length = 210

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 66/213 (30%), Positives = 102/213 (47%), Gaps = 12/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  + V +KP+G+    G G   +    L   V       R  HRLD++TSG++V+
Sbjct: 8   VLHQDEHLIVLDKPSGLLSVPGRGADKYDS--LAVQVADDFPGARNVHRLDRDTSGVIVM 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A   AA + L+  F  R   K Y ++  G+   +   I   L K      D+      + 
Sbjct: 66  ACDAAAHRELSRQFEQRETDKRYIAIAAGVVIEEAGKIELPLRKD----FDHPPRHMVDV 121

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    A+SH++V   +A       + P TGR+HQLRVH   +G PI+GD  Y        
Sbjct: 122 QLGKLALSHWQVEARYADSTRLS-LIPQTGRSHQLRVHLQAIGHPILGDPLYAP----AE 176

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           T    N+L LHA  +++ HP  G R++  AP P
Sbjct: 177 TQAAANRLMLHAIELEITHPASGERIRFVAPAP 209


>gi|85704028|ref|ZP_01035131.1| ribosomal large subunit pseudouridine synthase A [Roseovarius sp.
           217]
 gi|85671348|gb|EAQ26206.1| ribosomal large subunit pseudouridine synthase A [Roseovarius sp.
           217]
          Length = 214

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 64/223 (28%), Positives = 107/223 (47%), Gaps = 13/223 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
                     +L++D +I V NKPAG+    G G   H+   L + V        L HRL
Sbjct: 3   DYDPPTDPLEVLHDDHEIVVVNKPAGLLSVPGKG--EHLADCLMARVKDVFPTALLVHRL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+++ A T  A +HL   F  R+++K Y + VWG  + +   +   L+    +  
Sbjct: 61  DRDTSGVMIFALTPHAQRHLGLQFEKRQVRKTYVARVWGRLEPQVGVVDLPLI----VDW 116

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               + K   +    A++ ++V+         + + P TGR+HQLRVH L +G  I+GD 
Sbjct: 117 PNRPLQKVCHETGRAALTDWRVL-RAGDDETRVRLSPKTGRSHQLRVHMLALGHVILGDP 175

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            Y      ++      +L LH+  + L HP+GG  ++  A +P
Sbjct: 176 LYAQGAARDYP-----RLMLHSEELRLRHPDGGAGVKFRAAVP 213


>gi|89097691|ref|ZP_01170579.1| ribosomal large subunit pseudouridine synthase [Bacillus sp. NRRL
           B-14911]
 gi|89087550|gb|EAR66663.1| ribosomal large subunit pseudouridine synthase [Bacillus sp. NRRL
           B-14911]
          Length = 285

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 64/298 (21%), Positives = 120/298 (40%), Gaps = 33/298 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           M L+   ++ +       +  +     + VD                  P   + L    
Sbjct: 1   MTLEELLRSRWK-APKKQIHLMRMEKSILVDGSA---------------PAWTSPLIEGS 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS--- 135
           +    L +  +      + +  +LYED  + + NKPAG+       +         +   
Sbjct: 45  RLGLKLFAEEDFGVKPAYHEIDVLYEDDHMLILNKPAGMDTHPNEPMQEDTLANAAAFHL 104

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               + ++ +  HRLD++T+G ++ A+   A   L +  + R+I++ Y ++  G+ K KK
Sbjct: 105 LAKGEYRQVKHIHRLDKDTTGAVLFAKHALAGGMLDQLLKERKIKRTYIAMADGVIKQKK 164

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
             I   + +  H          +   G   A++H++V   F + +   +  +  TGRTHQ
Sbjct: 165 GVIRKPIGRDRHHPTRR-----RVSPGGQDAVTHYEVAAIFPREQQTLVSCRLETGRTHQ 219

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT-APL 311
           +RVH   MG P+ GD  Y         SP   +  LHA  +++PHP      +  AP+
Sbjct: 220 IRVHFSDMGHPLTGDRLYGG-------SPAFPRQALHAAKLEVPHPFTEEAVVCYAPV 270


>gi|227357295|ref|ZP_03841652.1| ribosomal large subunit pseudouridine synthase A [Proteus mirabilis
           ATCC 29906]
 gi|227162558|gb|EEI47547.1| ribosomal large subunit pseudouridine synthase A [Proteus mirabilis
           ATCC 29906]
          Length = 217

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 109/235 (46%), Gaps = 22/235 (9%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           + +          +LY+D  I V NKP+G+    G  + +H    + S + +        
Sbjct: 2   MEVYNPPTDPWLHVLYQDEHIIVVNKPSGLLSVPGKALEHHDS--IMSRIKADFPDAESV 59

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA  +AA + L   FR R  +K Y + VWG  +  +  +   L+    
Sbjct: 60  HRLDMATSGVMVVALNKAAERELKRQFREREPKKTYIARVWGKLEKPQGLVDLPLI---- 115

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V++ + +    +++ P TGR+HQLRVH L +G P
Sbjct: 116 --CDWPNRPKQKVCYETGKSAQTFYEVLE-YEENATRVKLSPITGRSHQLRVHMLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           I+GD  Y           +  +L LHA+ + + HP        +P+  H     D
Sbjct: 173 ILGDRFYAHPQ----ARALAPRLQLHAQELFITHPA-----FHSPI--HFECLAD 216


>gi|90408903|ref|ZP_01217040.1| putative ribosomal large subunit pseudouridine synthase A
           [Psychromonas sp. CNPT3]
 gi|90309987|gb|EAS38135.1| putative ribosomal large subunit pseudouridine synthase A
           [Psychromonas sp. CNPT3]
          Length = 219

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 60/223 (26%), Positives = 97/223 (43%), Gaps = 11/223 (4%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           +          +LY+D  I V NKPAG+    G  I +     L+           + HR
Sbjct: 5   VYNPPQTPYLDILYQDDDIVVLNKPAGLLSVPGREIKHRDSLALRILR--VWPNACVVHR 62

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++V+A  ++A  H+   F+ + I K Y++ V G  K     +   +       
Sbjct: 63  LDLATSGLIVLAMRKSAQSHIGRQFQQKVIAKTYFARVEGYIKEDAGLVDLPI----RCD 118

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +       + +    + + +KV+         +E+ P TGRTHQLRVH   +G PI+GD
Sbjct: 119 WENRPRQIVDFEQGKSSQTQWKVVSRENDS-TLVELTPLTGRTHQLRVHMQQIGHPILGD 177

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPL 311
             Y +      ++    +L LHA  + L HP    R+    P+
Sbjct: 178 DFYGSELAKKLST---QRLALHAAKISLIHPTTEERISFDCPV 217


>gi|119469873|ref|ZP_01612711.1| ribosomal large subunit pseudouridine synthase A [Alteromonadales
           bacterium TW-7]
 gi|119446856|gb|EAW28128.1| ribosomal large subunit pseudouridine synthase A [Alteromonadales
           bacterium TW-7]
          Length = 550

 Score =  169 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 111/250 (44%), Gaps = 22/250 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++K   +  S + L   +   +  ++Y+D  + + NKPA      G  I   +
Sbjct: 319 CQPILGHMLKGVNVEPSPL-LNNPAQGKELTVVYQDDDLVIVNKPAEFLSVPGITIDDSV 377

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K+    +   P + HRLD  TSG+L++A  + A + + + F  R I+K Y +LV G
Sbjct: 378 FLRMKTQF-PEATGPLIVHRLDMSTSGLLIIALNKRAHKAIQKQFIERTIEKRYVALVDG 436

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             + +   I   L        D     K   +    A++ ++V++        L++ P T
Sbjct: 437 NIEQESGTIELPLT----PDFDDKPRQKVCYQKGKPALTTWQVLERK-NNTTRLQLYPKT 491

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVH  H   +  PI+GD  Y             ++L+LHA Y+   HP    RL
Sbjct: 492 GRTHQLRVHCAHVLGLNTPIIGDTHYGKK---------ADRLHLHAEYLAFTHPINHERL 542

Query: 306 QITAPLPAHM 315
           +    + A  
Sbjct: 543 EFK--IDADF 550


>gi|219666529|ref|YP_002456964.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
 gi|219536789|gb|ACL18528.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
          Length = 233

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 67/215 (31%), Positives = 107/215 (49%), Gaps = 9/215 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V +KP  I  Q  S     I   LK  +  +  KP      L HRLD+   
Sbjct: 6   IVYEDNHLLVVDKPPNILSQKDSTGDMDILTLLKQDIKIRYNKPGNVYLGLVHRLDRPVG 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  +A  L+E  R R   K Y +L+ G P  +K  + ++L+K      + V  
Sbjct: 66  GVMVFAKTSKSAARLSEQIRNREFTKTYLALIQGQPAKQKNTLIHYLVKDEK--SNKVSA 123

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           VK+  KGA  AI  ++V+   +     +++   TGR HQ+RV   H+G P+ GD+KY   
Sbjct: 124 VKKGAKGAKEAILDYEVVHSQSD-LSLVKVNLRTGRPHQIRVQFAHLGHPLYGDYKYGKI 182

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
            K + TS  +  L L +  +   HP   G++   +
Sbjct: 183 VKTSKTSLTKPHLGLWSYEISCLHPISKGQIHFKS 217


>gi|326204205|ref|ZP_08194065.1| pseudouridine synthase [Clostridium papyrosolvens DSM 2782]
 gi|325985716|gb|EGD46552.1| pseudouridine synthase [Clostridium papyrosolvens DSM 2782]
          Length = 223

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 67/221 (30%), Positives = 108/221 (48%), Gaps = 14/221 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQE 153
             ++YED+ + V  KP  I VQ  +     +   LK ++  K  KP      L HRLD+ 
Sbjct: 3   PNIIYEDNHLLVVEKPVNIPVQADNTKDTDMLTLLKKYLKEKYNKPGEVYLGLVHRLDRP 62

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
             G++V A+T  AA  L+E  R R  +K+Y +++ G+PK +K  + N+L+K S    + V
Sbjct: 63  VGGVMVFAKTSKAASRLSEQVRTRTFKKVYLAVIRGVPKEQKTKLRNFLVKDS--SENMV 120

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           +VVK+  K A  A+  ++V+         ++++ HTGR HQ+RV   H G P+ GD +Y 
Sbjct: 121 YVVKEGTKDAKEAVLEYEVLKSDGL-LSMIKVKLHTGRPHQIRVQLSHSGYPLYGDQRYG 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPA 313
                        ++ L A  + L HP     +      P 
Sbjct: 180 ITVNKP-----GQQIALWASSLTLEHPTKKEEMIFNCETPD 215


>gi|157960566|ref|YP_001500600.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157845566|gb|ABV86065.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 225

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 63/213 (29%), Positives = 104/213 (48%), Gaps = 12/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  I V NKP+G+    G   A+    +  + V ++    ++ HRLD  TSG++VV
Sbjct: 16  VLHQDKDIMVVNKPSGLLSVPGRDPAHADSTY--TRVLAEFPHAKIVHRLDMATSGVIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R+A   L   FR R  QK Y++ V G  K     I   L+             K + 
Sbjct: 74  ALLRSAESELKRQFRDRETQKTYYARVAGHVKQSHGTINLPLICDWPNRPK----QKVDH 129

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K    + +H++VI  + ++   +++ P TGR+HQLRVH + +G PI+GD+ Y        
Sbjct: 130 KIGKPSQTHYEVI-SYGKRSTLVKLTPITGRSHQLRVHMMALGHPILGDNFYADPLAKR- 187

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              +  +L LHA+ + + HP     +  +   P
Sbjct: 188 ---LAPRLLLHAQSLTITHPYTKEPMTFSCDAP 217


>gi|168699207|ref|ZP_02731484.1| pseudouridine synthase, RluA family protein [Gemmata obscuriglobus
           UQM 2246]
          Length = 354

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 77/354 (21%), Positives = 139/354 (39%), Gaps = 41/354 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSG 62
           M  +Q+ VV+  +    L    K+ +  +++   ++++    V+V  +       R++ G
Sbjct: 1   MPPIQF-VVDRRDAGQTLAAVLKSRF-GLSWAQAKRLVEKRHVKVSGQVETDVARRLKLG 58

Query: 63  QVVRIPPVINALNHIIKEQKI-----LDSSVNLTKHSDFL-------------KSILLYE 104
           + V +      +   +  +K       +     T+                     ++Y 
Sbjct: 59  KRVELAAGTVEIKQALPSKKTGAAKKAEPGKKATERPRPPAPRPKPALELGLSPDAIVYV 118

Query: 105 DSKIYVFNKPAGISV------------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           D  + V NKPAG++              G   +   + G L + + +  +     HRLD+
Sbjct: 119 DDAVVVVNKPAGLTTMRHKEEAEEFGAHGQRFLTKTLAGLLPTLLGTPDRAVTAVHRLDR 178

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG++V ARTRAA ++LT  FR    ++ Y +L  G+PK     IA+  +     G   
Sbjct: 179 DTSGLVVFARTRAAGENLTAQFRKHSTERRYLALTRGVPKP--GRIASVFVSDRGDGR-- 234

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                        A++H  V++     F  +E +  TGRTHQ+R+H    G P+ G+  Y
Sbjct: 235 RGTTTDLAADGKRAVTHVAVLEPLG-PFALVECRLETGRTHQVRIHLGEAGAPLCGEGVY 293

Query: 273 CANFKGNFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
                G          +  LHA  +   HP+ G  +    P P    +    L 
Sbjct: 294 DRPIDGQPLPDGSGAQRPMLHATRLGFAHPDTGAAVSWEVPPPEDFRRLLAKLR 347


>gi|304411822|ref|ZP_07393433.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307303410|ref|ZP_07583165.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304349682|gb|EFM14089.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306913770|gb|EFN44192.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 223

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 61/213 (28%), Positives = 101/213 (47%), Gaps = 8/213 (3%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        + Y+D  + + NKP+G+    G   A H      + + +   +  L HRLD
Sbjct: 7   QPPAVPWLDIRYKDRDLIIINKPSGLLSNPGR--AAHTFDCALTRLQTLYPETILVHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V AR + A  HL   F+ R+ +K+Y + V G    ++  I   +   +     
Sbjct: 65  CATSGIMVFARNKKAESHLKTQFQDRQSKKVYIAEVMGHVPQEQGMIDLAIAPDTEHS-P 123

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y   ++  E G   A+++++V++   +    +E+ P TGRTHQLRVH L +G  I+GD  
Sbjct: 124 YQKTLQAGETGGKSALTYYRVLERR-ENSTLVELSPETGRTHQLRVHMLALGHAILGDEF 182

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           Y              +L LHA+ + L HP   +
Sbjct: 183 YG----DAEVIKAAPRLCLHAQSLSLTHPYSAK 211


>gi|302806002|ref|XP_002984751.1| hypothetical protein SELMODRAFT_121195 [Selaginella moellendorffii]
 gi|300147337|gb|EFJ14001.1| hypothetical protein SELMODRAFT_121195 [Selaginella moellendorffii]
          Length = 355

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 80/315 (25%), Positives = 133/315 (42%), Gaps = 58/315 (18%)

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G ++ +P  +  +    +  +  D +    +  + LK  +LY+D  + V NKP G+ VQG
Sbjct: 4   GALICVPDSVTKIEASSQSHEPDDPT---EEEIEQLKDAVLYKDEDLIVLNKPPGLPVQG 60

Query: 122 GSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-- 178
           GS +   +   +   +     + PRL HRLD++ SG++++ RT  +   +      +   
Sbjct: 61  GSKVERSLVSMMSLALQFEYKEPPRLVHRLDKDVSGVMILGRTYESTVKIQSFLCSKDNL 120

Query: 179 --------------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV---VKQNEK 221
                         + + Y +LV G P   K  I+  LLK     G    V        +
Sbjct: 121 MPSVITTQGSVGKGLDRKYIALVIGSPTADKGFISAPLLKMVLEDGKSDRVLIAADPKSE 180

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYCANFKGNF 280
            A  AI+ ++V+        WL+++P TGR HQLRVH    +G PIVGD KY  N    +
Sbjct: 181 NAIPAITEYQVLKRSVLGCTWLQLRPLTGRKHQLRVHCAQGLGLPIVGDMKYGFNTHKKW 240

Query: 281 ----------TSPIQNK-------------LYLHARYMDLPHPEG-----------GRLQ 306
                        I+ +             L+LH+R + +P                R++
Sbjct: 241 MAERNMNTVDPQDIKARNKMAGSVVSKNPLLHLHSRELTIPRLRKKPGAVDFGLDPERMR 300

Query: 307 ITAPLPAHMVKTWDS 321
             APLP HM  +W++
Sbjct: 301 FVAPLPTHMESSWEA 315


>gi|327402055|ref|YP_004342893.1| pseudouridine synthase [Fluviicola taffensis DSM 16823]
 gi|327317563|gb|AEA42055.1| pseudouridine synthase [Fluviicola taffensis DSM 16823]
          Length = 561

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 67/247 (27%), Positives = 111/247 (44%), Gaps = 22/247 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++ E + +D +  L   ++     +++ED  I + NKPA      G  I+  +
Sbjct: 329 CEPILGHMLGETE-MDENPMLLNPAENKDLEIVFEDDYIVIVNKPAEFLSVPGKSISDSV 387

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K         P + HRLD  TSG+LV+A+ +   +HL + F  R +QK Y +L+ G
Sbjct: 388 YTRMKEKY-PHATGPLIVHRLDMSTSGLLVIAKDKIVHKHLQKQFIKRNVQKRYVALLEG 446

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I   +   I   L +          V  ++      A++ ++VI+        +   P T
Sbjct: 447 IISERLGTIDLPL-RVDLDDRPRQLVCYEH---GKRAVTKWEVIEHR-NNQTLIYFYPIT 501

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-- 304
           GRTHQLRVHA H   +  PI+GD  Y              +L+LHA+++   HP      
Sbjct: 502 GRTHQLRVHAAHTLGLNAPILGDDLYGNR---------ATRLHLHAQFLQFTHPITKEAI 552

Query: 305 -LQITAP 310
            +++ A 
Sbjct: 553 KIKVDAE 559


>gi|170725279|ref|YP_001759305.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169810626|gb|ACA85210.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 225

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 65/213 (30%), Positives = 108/213 (50%), Gaps = 12/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NKP+G+    G   A+     + + V ++    ++ HRLD  TSGI+V+
Sbjct: 16  IIYQDKDILVVNKPSGLLSVPGRDPAHRDS--IYARVLAEYPNAQVVHRLDMATSGIIVL 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R A + L   FR R  +K Y++ V G  ++    +   L+             K + 
Sbjct: 74  ALRRNAEKELKRQFRERETKKTYYARVAGHIRSDSGKVELPLICDWPNRPK----QKVDH 129

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K    +++H++VI   A++   +++ P TGR+HQLRVH L +G PI+GD+ Y      + 
Sbjct: 130 KVGKPSLTHYEVISR-AKRSTLVKLTPITGRSHQLRVHMLAIGHPILGDNFYADPLAKSL 188

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            S    +L LHA+ + +  P  G  L  T  +P
Sbjct: 189 AS----RLLLHAQELTIKQPYSGETLTFTCEVP 217


>gi|261879059|ref|ZP_06005486.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           bergensis DSM 17361]
 gi|270334340|gb|EFA45126.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           bergensis DSM 17361]
          Length = 421

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 67/233 (28%), Positives = 106/233 (45%), Gaps = 23/233 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D   N  +  +  +  ++YED  + V +KPAG+    G G    +   ++         
Sbjct: 207 MDVDPNPLEQEETHELKIVYEDDTLCVVDKPAGMLSVPGKGCRESVLDVMRRRC-PDATG 265

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLD  TSG++VVA+T  A + L   F  R ++K Y +++   P+  K  IA  L 
Sbjct: 266 ALVVHRLDMATSGLMVVAKTAEAYRELQRQFATRSVRKRYVAILSRQPREPKGEIALPL- 324

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
                  D       +      A++H+++ID      C + + P TGRTHQLRVH  H  
Sbjct: 325 ---RPDLDDRPRQVVDSVYGKPALTHYEIIDG-----CRVALYPRTGRTHQLRVHCAHRD 376

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            +  PI GD  Y    +         +LYLHA ++   HP  G  ++ T+  P
Sbjct: 377 GLDSPIKGDELYGRRAE---------RLYLHAEWLAFRHPATGEEVEFTSVAP 420


>gi|313675894|ref|YP_004053890.1| ribosomal large subunit pseudouridine synthase d [Marivirga
           tractuosa DSM 4126]
 gi|312942592|gb|ADR21782.1| ribosomal large subunit pseudouridine synthase D [Marivirga
           tractuosa DSM 4126]
          Length = 231

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 70/227 (30%), Positives = 115/227 (50%), Gaps = 16/227 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-----HRLDQET 154
           I++YED+ + V NKP+G+ VQG       I    K ++  K  KP        HR+D+  
Sbjct: 9   IVMYEDNHLLVVNKPSGMLVQGDQTGDTPISEHAKEYIAKKYDKPGKVFCGTPHRIDRPV 68

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG LV+ART  A + +++ F    + K YW++    P   ++ I +WL K S    +  H
Sbjct: 69  SGTLVLARTSKALERVSKLFHDGEVDKTYWAITEKRPPKTEDTITHWLKKDS--NKNLTH 126

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               ++KG   +   ++++     +   +E++PHTGR HQ+RV    +GCPI+GD KY  
Sbjct: 127 AHMSDKKGGLKSTLSYRLVRALGDRN-LIEVKPHTGRPHQIRVQLARIGCPIIGDVKYG- 184

Query: 275 NFKGNFTSPIQNK-LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
                F  P ++  + LHAR +   HP       + +P+P   V ++
Sbjct: 185 -----FPKPTKDGSIALHARAISFVHPVKKEPFNVVSPIPKAFVWSF 226


>gi|315127724|ref|YP_004069727.1| pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
 gi|315016238|gb|ADT69576.1| pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
          Length = 209

 Score =  169 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 62/211 (29%), Positives = 101/211 (47%), Gaps = 12/211 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  + + NKP+ +    G    +     L + V+      ++ HRLD  TSGIL +
Sbjct: 7   ILFQDDDLLIVNKPSELLTVPGKDPKH--ADSLINRVNRVFPSAKIVHRLDMATSGILCL 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +AA +HL+  F+ R   K Y + V+G  + +   +   L+         +     + 
Sbjct: 65  AMNKAAHRHLSMQFQERETAKRYIARVYGQLETETGSVDLPLICDWPNRPKQM----VDH 120

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                +++HFKV++  AQ    +E+ P TGR+HQLRVH L +G PI+GD  Y        
Sbjct: 121 DNGKPSLTHFKVLEREAQ-ATRVELTPITGRSHQLRVHMLSLGHPILGDRLYAHKD---- 175

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
                 +L LHA+ + L HP   + L   A 
Sbjct: 176 ALAAAPRLQLHAQMLQLKHPVTEQVLTFEAE 206


>gi|153004836|ref|YP_001379161.1| pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152028409|gb|ABS26177.1| pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
          Length = 238

 Score =  169 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 111/239 (46%), Gaps = 16/239 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           ++     +L  D+ + V +KPAG  V  G G        L+  +++   +  + HRLD+ 
Sbjct: 5   AEAGGPRVLLADAALLVVDKPAGRLVIPGRGGDELS---LREELEAAHGRLWVVHRLDRG 61

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G+LV ART  A + L  +F     +K Y ++V G P  +  C+   +   +      +
Sbjct: 62  TTGVLVFARTAEAHRALNLAFDRGEPRKRYAAIVRGDPPAEA-CLDAPI---APARRGRM 117

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFC------WLEMQPHTGRTHQLRVHALHMGCPIV 267
              +  +  A  A++  + ++ F  +         +E  P TGRTHQ+RVH +H G P+ 
Sbjct: 118 RPARPGDPRAKAAVTRIRTLETFPPRAWAGGALALVEAAPETGRTHQIRVHLMHAGYPLA 177

Query: 268 GDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            D  Y       G     + ++  LHA  ++L HP  G  L + APLPA M +   +L 
Sbjct: 178 VDPDYGDEGPLHGPDARVLLSRTPLHASRLELRHPSTGATLVLEAPLPADMAEALQALR 236


>gi|119390059|pdb|2I82|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
           Sequence Readout Through Protein-Induced Rna Structure
 gi|119390060|pdb|2I82|B Chain B, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
           Sequence Readout Through Protein-Induced Rna Structure
 gi|119390061|pdb|2I82|C Chain C, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
           Sequence Readout Through Protein-Induced Rna Structure
 gi|119390062|pdb|2I82|D Chain D, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
           Sequence Readout Through Protein-Induced Rna Structure
          Length = 217

 Score =  169 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 71/226 (31%), Positives = 110/226 (48%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 6   PPQEPWLVILYQDDHIXVVNKPSGLLSVPGR-LEEHKDS-VXTRIQRDYPQAESVHRLDX 63

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 64  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDW 117

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 118 PNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHXLALGHPILGDR 177

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y A+ +    +P   +L LHA  + + HP  G      A  PA  
Sbjct: 178 FY-ASPEARAXAP---RLLLHAEXLTITHPAYGNSXTFKA--PADF 217


>gi|281421312|ref|ZP_06252311.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella copri DSM 18205]
 gi|281404847|gb|EFB35527.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella copri DSM 18205]
          Length = 222

 Score =  169 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 105/229 (45%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ I + +K +G  VQG       +   +K ++  K  KP      + HRLD+  S
Sbjct: 3   VVYEDNHIIIVSKRSGEIVQGDKTGDEPLSETVKQYIKEKYHKPGNVFLGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L   FR   + K YW++V  +PK  +  + +W+++       Y + 
Sbjct: 63  GLVVFAKTSKALSRLNNMFRDGEVHKTYWAIVKNMPKEPEATLTHWIVRNEKQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                K +  AI  +KVI      +  LE+   TGR HQ+R     MGCPI GD KY + 
Sbjct: 122 -DHEVKNSKKAILKYKVIG-HTDHYTLLEVNLMTGRHHQIRCQLAKMGCPIKGDLKYGSP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 S     + L +  ++  HP     +   APLP      W ++ 
Sbjct: 180 RSNADGS-----ISLLSHRVEFVHPVSKETIVAEAPLPDD--NLWRAIA 221


>gi|260102907|ref|ZP_05753144.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DSM 20075]
 gi|260083278|gb|EEW67398.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DSM 20075]
          Length = 275

 Score =  169 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 121/305 (39%), Gaps = 41/305 (13%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRS----GQVRVDKKRVKFNNRI 59
           MT +  +VV+  +   +L  +   +    +    Q ++++    G + V+ KR   +  +
Sbjct: 1   MTSLFKLVVQEKD-PKKLGSFLLKN--GFSH---QALIKARHHHGMILVNHKRRYLSFHL 54

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            +G  V         N  +K       S N             +E     V NKPAG+  
Sbjct: 55  SAGDEVIFVSGEEKKNQFLK------PSNNPVDPG--------FETKNYIVLNKPAGVLS 100

Query: 120 QGGSGIAYH-IDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                     +   L  +    + K  KP +  RLD++TSG+++V +   A    ++  +
Sbjct: 101 IPSRYEDNDAVVNRLMGYFLQQNKKDLKPHVITRLDRDTSGLVLVGKNAIAHARFSKIGK 160

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              ++K + ++V G     +       +    IG +   V +        A + ++V+  
Sbjct: 161 DNFVKKYH-AIVHGNFAEDELT----GIIDEPIGKEGDGVKRAVVANGKKAQTRYRVLKQ 215

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             +    +E++  TGRTHQ+RVH  ++G P+ GD  Y  N          ++  L+  Y+
Sbjct: 216 V-EGASLVELRLLTGRTHQIRVHMAYLGHPLFGDPLYGINDN-------FSRQALNCFYL 267

Query: 296 DLPHP 300
             P P
Sbjct: 268 AFPDP 272


>gi|302808237|ref|XP_002985813.1| hypothetical protein SELMODRAFT_123269 [Selaginella moellendorffii]
 gi|300146320|gb|EFJ12990.1| hypothetical protein SELMODRAFT_123269 [Selaginella moellendorffii]
          Length = 355

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 80/315 (25%), Positives = 133/315 (42%), Gaps = 58/315 (18%)

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G ++ +P  +  +    +  +  D +    +  + LK  +LY+D  + V NKP G+ VQG
Sbjct: 4   GALICVPDSVTKIEASSQSHEPDDPT---EEEIEQLKDAVLYKDEDLIVLNKPPGLPVQG 60

Query: 122 GSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-- 178
           GS +   +   +   +     + PRL HRLD++ SG++++ RT  +   +      +   
Sbjct: 61  GSKVERSLVSMMSLALQFEYKEPPRLVHRLDKDVSGVMILGRTYESTVKIQSFLCSKDNL 120

Query: 179 --------------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV---VKQNEK 221
                         + + Y +LV G P   K  I+  LLK     G    V        +
Sbjct: 121 MPSVITIQGSVGKGLDRKYIALVIGSPTADKGFISAPLLKMVLEDGKSDRVLIAADPKSE 180

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYCANFKGNF 280
            A  AI+ ++V+        WL+++P TGR HQLRVH    +G PIVGD KY  N    +
Sbjct: 181 NAIPAITEYQVLKRSVLGCTWLQLRPLTGRKHQLRVHCAQGLGLPIVGDMKYGFNTHKKW 240

Query: 281 ----------TSPIQNK-------------LYLHARYMDLPHPEG-----------GRLQ 306
                        I+ +             L+LH+R + +P                R++
Sbjct: 241 MAERNMNTVDPQDIKARNKMAGSVVSKNPLLHLHSRELTIPRLRKKPGAVDFGLDPERMR 300

Query: 307 ITAPLPAHMVKTWDS 321
             APLP HM  +W++
Sbjct: 301 FVAPLPTHMESSWEA 315


>gi|284039250|ref|YP_003389180.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283818543|gb|ADB40381.1| pseudouridine synthase [Spirosoma linguale DSM 74]
          Length = 248

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 79/248 (31%), Positives = 117/248 (47%), Gaps = 22/248 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQ 152
              ++YED+ + + NK  GI VQG       +   LK ++  K  KP      L HRLD+
Sbjct: 5   PFQVVYEDNHLLIVNKDPGILVQGDRTGDITLLDVLKDYIKEKYNKPGEVFLGLVHRLDR 64

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
             SG++V ART  A + + E FR R++QK YW++V   P    + + NWL+K      + 
Sbjct: 65  PVSGLVVFARTSKALERMNEIFRKRQVQKTYWAVVRRKPPKDSDKLVNWLIKDEQ--KNQ 122

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V V       +  A   ++V+    + +  LE+ P TGR HQ+R    HMGCPI GD KY
Sbjct: 123 VTVYDYEVPKSQKAELSYRVLGKINEHY-LLEVNPITGRPHQIRSQLAHMGCPIRGDIKY 181

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP------EGGRLQITAPLPAHMVKTWDSLGFKY 326
             +      +    K+YLHAR +   HP      E   +   A LP      W+    + 
Sbjct: 182 GYD-----RAVADKKIYLHARRLYFIHPIKQAGAEDRPIICKAGLPND--PFWEEF-LEL 233

Query: 327 DRNLYIKR 334
           D  +Y  +
Sbjct: 234 DTEIYNDK 241


>gi|224100817|ref|XP_002312025.1| predicted protein [Populus trichocarpa]
 gi|222851845|gb|EEE89392.1| predicted protein [Populus trichocarpa]
          Length = 377

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 84/361 (23%), Positives = 136/361 (37%), Gaps = 82/361 (22%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKI---LRSGQVRVDKKRVK-FNNRIQSGQVV 65
           VV  + +  + L  ++ + Y +     LQ     + +GQ+ +D + VK     ++ G  +
Sbjct: 30  VVSTSSDSGLTLIHFYSSKYKNS--APLQGWLQRIHNGQITIDGEVVKEPKAILRDGMEL 87

Query: 66  ---RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
              R+P       ++++                     +LYED  +   NKP G+ V  G
Sbjct: 88  VYHRLPWREPDAPYLLQ---------------------VLYEDDDMVALNKPPGLQVLPG 126

Query: 123 SGIAYHIDGFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHL---- 170
                        W  SKG          P   HRL + TSGIL+ A+T+ A   L    
Sbjct: 127 GLFQQRTVLMQLQWRASKGSSSLAIQGSHPVPVHRLGRGTSGILLCAKTKVAKTSLAAYF 186

Query: 171 --------------TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
                          E  + R+I KIY +LV GI    K  I   +    + G      V
Sbjct: 187 ADGTSLIGDSSNANMEQSKRRKISKIYRALVNGILNQDKIIIKQPIGTMRYPGVAKGLYV 246

Query: 217 KQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--- 272
                    A+S  +V++  +Q     ++++  +GR HQ+R+H   +G P++GD  Y   
Sbjct: 247 A--SPSGKPALSKVEVLERDSQLNQTLVQVEIESGRPHQIRIHLSFIGHPLLGDPLYDVG 304

Query: 273 ------------------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR--LQITAPLP 312
                                 +     P     YLHA  + L HP      ++ITAPLP
Sbjct: 305 GQPMCFDSEHEDESFAEDGGYERPAKPVPGDCGYYLHAHQLVLSHPTKNEQVIKITAPLP 364

Query: 313 A 313
           +
Sbjct: 365 S 365


>gi|315185268|gb|EFU19047.1| pseudouridine synthase [Spirochaeta thermophila DSM 6578]
          Length = 300

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 130/325 (40%), Gaps = 32/325 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   Q      D+   RLDR  +    H+    + + LR+G++ ++ KRV  + R+  G 
Sbjct: 1   MGDYQVFESGPDDHGKRLDRIVRTLLSHLPLSRVFRALRTGEILLEGKRVPPSTRVSRGA 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I         ++ E+K         +        +L E   + + NKP G  V G  
Sbjct: 61  RIHID------RSLLPERKP-------QQKGKASSLPILLETDHLLILNKPPGAVVHGPG 107

Query: 124 GIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +   +  +LK  +  S    P   HRLD+ TSGILV +R+   A+  T++ R  RI+K 
Sbjct: 108 SLTDQVRSYLKDRIPPSLAFTPSPLHRLDRLTSGILVFSRSIHGARWFTQALREGRIEKT 167

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L+ G          + L ++        H           A++  + +   A     
Sbjct: 168 YLALLEGTLAEPARW-EDLLTREGRRSRPSPH--------GRPALTDVRPLLA-APTATL 217

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +    HTGR HQ+RV A   G P++GD  Y +  +      I+  L+        P P  
Sbjct: 218 VLCTIHTGRMHQIRVQAALRGHPLLGDTAYGSTRR------IRPVLHAWRLRPLSPSPLF 271

Query: 303 GRLQITAPLPAHMVKTWDSL--GFK 325
               + APLP         +  G++
Sbjct: 272 PADGVQAPLPDESETILSRILPGWE 296


>gi|114569344|ref|YP_756024.1| ribosomal large subunit pseudouridine synthase A [Maricaulis maris
           MCS10]
 gi|114339806|gb|ABI65086.1| ribosomal large subunit pseudouridine synthase A [Maricaulis maris
           MCS10]
          Length = 223

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 58/221 (26%), Positives = 101/221 (45%), Gaps = 12/221 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   +++ D  I V +KP+G+    G+         L++   ++    R+ HRLD 
Sbjct: 13  PPPAGALPVIHADDHILVVDKPSGLLTVPGNRPE--RADCLEARARAEFPTARIIHRLDM 70

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG++V+A T  A  H+ + F  R   K Y + V G    +   +   ++         
Sbjct: 71  DTSGVIVLALTTHAQAHIGKQFEKRMTSKSYVARVQGEMTGRSGRVDQPIITDWPNRPKQ 130

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +    +       A++ ++V+D  A     + + P TGR+HQLRVH L +G PI+GD+ Y
Sbjct: 131 MICHDR----GRNAVTDWEVMD-IADGVTRVRLCPLTGRSHQLRVHMLFLGHPILGDNLY 185

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                        ++L LHA+ +   HP+GG  +   +P P
Sbjct: 186 APP----AALTASDRLCLHAQQLGFRHPDGGAPVSFESPAP 222


>gi|86132103|ref|ZP_01050699.1| ribosomal large subunit pseudouridine synthase D [Dokdonia
           donghaensis MED134]
 gi|85817437|gb|EAQ38617.1| ribosomal large subunit pseudouridine synthase D [Dokdonia
           donghaensis MED134]
          Length = 229

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 72/227 (31%), Positives = 107/227 (47%), Gaps = 14/227 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LT 147
           HS      ++YED+ I V NK +G  VQG       +   +K ++  K  KP      + 
Sbjct: 2   HSTPENLNVIYEDNHIIVVNKRSGDIVQGDKTGDLPLSEVVKKYIAVKYNKPGAVYLGVV 61

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSGI++ ART  A   L + F  R+ +K YW+LV   P  +   + ++L +   
Sbjct: 62  HRLDRPTSGIVIFARTSKALPRLNKMFSERQTKKTYWALVKNPPPAESGTLTHFLKRNPK 121

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y H  K     +  AI  ++VI    + F  LE+  HTGR HQ+R     +GCPI 
Sbjct: 122 QNKSYAH--KHEVPDSKKAILDYRVIKKL-KTFYLLEIDLHTGRHHQIRAQLTAIGCPIK 178

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           GD KY  +      S     + L +R + L HP +   +   A +P 
Sbjct: 179 GDLKYGFDRSNPDGS-----ISLLSRKLTLTHPVKKEEMTFVAQVPE 220


>gi|320155234|ref|YP_004187613.1| ribosomal large subunit pseudouridine synthase A [Vibrio vulnificus
           MO6-24/O]
 gi|319930546|gb|ADV85410.1| ribosomal large subunit pseudouridine synthase A [Vibrio vulnificus
           MO6-24/O]
          Length = 250

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 59/210 (28%), Positives = 97/210 (46%), Gaps = 14/210 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I   NKP+G+    G    +H    + S +  +  + ++ HRLD  TSG++V 
Sbjct: 16  IIFEDDHILAVNKPSGLLSVPGRLPEHHDS--MWSRLQEQYPEIQVVHRLDMSTSGLMVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ + A   L + F+ R   KIY++ VWG  +     I   L+           + K   
Sbjct: 74  AKNKRAEAALKKQFQYRLTHKIYYARVWGHVEADSGMIDLPLICD----WPNRPMQKVCH 129

Query: 221 KGANYAISHFKV----IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           +    + + F+V    +     +   + + P TGR+HQLRVH   +G PIVGD  Y    
Sbjct: 130 EHGKPSQTEFQVAKREVHANGAQTTIMRLLPVTGRSHQLRVHMQALGHPIVGDEFYAQGD 189

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
              F+     +L LHA  +   HP+   L+
Sbjct: 190 AFTFSE----RLELHAAELSFYHPKSHWLR 215


>gi|87300869|ref|ZP_01083711.1| Pseudouridine synthase [Synechococcus sp. WH 5701]
 gi|87284740|gb|EAQ76692.1| Pseudouridine synthase [Synechococcus sp. WH 5701]
          Length = 328

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 69/321 (21%), Positives = 126/321 (39%), Gaps = 45/321 (14%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +  +    Y H      ++ L+ G++ ++ +R+  +  + +G  ++              
Sbjct: 26  ISVFLAERYRHSAAPLWRQRLQEGEILLNGRRLDGDGPLHAGDRLQWQ------------ 73

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                      + +   +  ++++D  +YV +KP+G+ V    G   H    L     + 
Sbjct: 74  ------RPPWREEAVPARWRVIHDDGDLYVIDKPSGLPVLPAGGFLEHTLLRLLERSCAA 127

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHL--------------------TESFRMRRIQ 180
              PR  HRL + TSG+LV AR   +   L                    + + R    +
Sbjct: 128 QALPRPVHRLGRHTSGLLVCARRPQSRAWLSARLRESTAQLLNQPGSEARSAATRAGACR 187

Query: 181 KIYWSLVWGIP----KNKKECIANWLLKKSHIGGDYVHVVK-QNEKGANYAISHFKVIDC 235
           K+Y +L    P      +   I   + ++ H G   +      ++ GA  A S  ++++ 
Sbjct: 188 KVYRALTVPAPLQLAPGESLAITTPIGRRPHAGLGQIWAADGPDDPGALPAWSEMRLLER 247

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARY 294
             Q    +E+  HTGR HQ+R+H    G P++GD  Y           P      LHA  
Sbjct: 248 RPQGH-LVEVSIHTGRPHQIRIHLASAGVPLLGDPLYRPGGEPRPGALPGDGGYLLHAHR 306

Query: 295 MDLPHPEGGRLQITAPLPAHM 315
           + LP P GG L + AP+P  +
Sbjct: 307 LRLPLPAGGWLDLEAPVPPEL 327


>gi|110004533|emb|CAK98870.1| hypothetical rna pseudouridylate synthase c protein [Spiroplasma
           citri]
          Length = 312

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/288 (23%), Positives = 122/288 (42%), Gaps = 25/288 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRI 59
           M   T V  + V+ ++ N  +  + K  +       + K+ R+ +++V+ K +K  N ++
Sbjct: 1   MEPKTVV-TLTVKANDVNQTIFNFIKKMFQTTPLSVIYKLFRNKKIKVNNKVMKERNYKL 59

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           Q G  + I       N ++ E+    +      + + L   ++YED  I V +KP G  V
Sbjct: 60  QLGDQIIIFDK----NLVVTER----NQAVTYNNVETLPLQVVYEDDNILVVDKPHG--V 109

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHL 170
           +  S     +D  ++ ++  K +              HRLD+ T G+++ A+ +     L
Sbjct: 110 EMYSKFHTSLDAMVQHYLIQKHEYHPEDEQSFVISHVHRLDKLTRGLVLYAKNKITLDLL 169

Query: 171 -TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
             +  +   I+K Y +   GI K     +  +L K        +   K  +  A    +H
Sbjct: 170 LAKINQKESIEKKYLAKCEGIIKETDFTLTGYLYKNE--DKQKMVFTKTVQPHAKVVKTH 227

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           F+V         WLE+   TGR HQ+R    ++  PIV D KY A  +
Sbjct: 228 FRV-QHQLTNATWLEVTLITGRKHQIRASLSYLHHPIVNDIKYGAKQE 274


>gi|284799501|ref|ZP_05984156.2| tRNA pseudouridine synthase [Neisseria subflava NJ9703]
 gi|284798057|gb|EFC53404.1| tRNA pseudouridine synthase [Neisseria subflava NJ9703]
          Length = 238

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 99/232 (42%), Gaps = 20/232 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ DS+    NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L
Sbjct: 2   LDIIHRDSRTVAVNKPAGMLVHRSWLDKHETRFAVQTLRDQIGQHVYPVHRLDRPTSGVL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A    AA+ LT+ F  + I+K YW++V G   +              I         Q
Sbjct: 62  LFALDTEAARLLTQQFENKTIEKTYWAIVRGHLPSDGLIDYALKYMPDKIAE------AQ 115

Query: 219 NEKGANYAISHFKV-----------IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            E     A + ++            +     ++ W E+ PHTGR HQLR H  H+  PIV
Sbjct: 116 TEATLQEAQTTYRCLAQTELPFQSALRYPTSRYSWAELTPHTGRKHQLRRHMKHIFHPIV 175

Query: 268 GDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
           GD  Y    + +  +      +L LHA+ +     E G R+ + AP+     
Sbjct: 176 GDTNYGDLRQNHAVAEHIGTQRLMLHAQSLSFQSIEDGSRMTVQAPIDNDWQ 227


>gi|298207134|ref|YP_003715313.1| hypothetical protein CA2559_02735 [Croceibacter atlanticus
           HTCC2559]
 gi|83849768|gb|EAP87636.1| hypothetical protein CA2559_02735 [Croceibacter atlanticus
           HTCC2559]
          Length = 283

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 81/324 (25%), Positives = 137/324 (42%), Gaps = 50/324 (15%)

Query: 4   MTYVQYVVVENDEENMRLDRW---FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  V+   V+    ++R+  +     N  P  +  +++K ++ G + ++ K+    + I+
Sbjct: 1   MQLVEKHTVKEVTAHIRIQEYGPLVFNTLP--SRSSVKKAIKKGLIFINGKQADSADWIE 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            GQ++ +  +     H                    L   +L+ED  + V NKPAG    
Sbjct: 59  EGQLLEVFQLKPTTKHF------------------KLNLDVLFEDDYVAVINKPAGYPTS 100

Query: 121 GG--SGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G     IA  +   LK    +     P+  HRLD  TSG+LVVA+T+++  +L +   ++
Sbjct: 101 GNFFKTIAKALPYNLKISTKNDALLIPQPIHRLDNPTSGVLVVAKTKSSQINLNKQLELK 160

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            IQK Y ++V   P +                 + +     + K +   +   K      
Sbjct: 161 GIQKTYIAVVHNTPDS-----------------NMLFNDNIDGKESESKLEIIKTFKVKD 203

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +  +E+ P TGRTHQLR+H    G PIVGD  Y  + + N       KL LHA+ +  
Sbjct: 204 DIYSLVELFPKTGRTHQLRIHTSKAGYPIVGDQLYGISSEKN------KKLLLHAKSIQF 257

Query: 298 PHPEGG-RLQITAPLPAHMVKTWD 320
            HP  G  +  T+ LP    K  +
Sbjct: 258 KHPVTGNEVFTTSELPKRFEKLLN 281


>gi|15598442|ref|NP_251936.1| pseudouridine synthase RluA [Pseudomonas aeruginosa PAO1]
 gi|107102775|ref|ZP_01366693.1| hypothetical protein PaerPA_01003843 [Pseudomonas aeruginosa PACS2]
 gi|218890561|ref|YP_002439425.1| pseudouridine synthase RluA [Pseudomonas aeruginosa LESB58]
 gi|254236207|ref|ZP_04929530.1| pseudouridine synthase RluA [Pseudomonas aeruginosa C3719]
 gi|254241933|ref|ZP_04935255.1| pseudouridine synthase RluA [Pseudomonas aeruginosa 2192]
 gi|9949369|gb|AAG06634.1|AE004747_7 pseudouridine synthase RluA [Pseudomonas aeruginosa PAO1]
 gi|126168138|gb|EAZ53649.1| pseudouridine synthase RluA [Pseudomonas aeruginosa C3719]
 gi|126195311|gb|EAZ59374.1| pseudouridine synthase RluA [Pseudomonas aeruginosa 2192]
 gi|218770784|emb|CAW26549.1| pseudouridine synthase RluA [Pseudomonas aeruginosa LESB58]
          Length = 211

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/216 (28%), Positives = 107/216 (49%), Gaps = 11/216 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  ++++D  + V +KP  +    G       D  +    ++   + R+ HRLD ETSG+
Sbjct: 5   QIRIVHQDDALLVVDKPTLLLSVPGRADDN-KDCLVTRLQENGYPEARIVHRLDWETSGL 63

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+AR   + + L+  F  R  +K Y +L WG+P+     I   L         +V    
Sbjct: 64  MVLARDADSHRELSRQFHDRETEKAYTALCWGLPELDSGRIELPLRYDPPTKPRHV---- 119

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +   +A++ ++VI+   +++  +E+ P TGR+HQLRVH L +G P++GD  Y     
Sbjct: 120 VDFEHGRHALTFWRVIERH-ERWSRVELTPITGRSHQLRVHMLSIGHPLLGDRLY----A 174

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                    +L LHA  + L HP  G RL+  +P P
Sbjct: 175 NPEALAAHERLCLHASLLCLTHPQSGERLRFESPAP 210


>gi|330448797|ref|ZP_08312444.1| 23S rRNA and tRNA pseudouridine synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
 gi|328492988|dbj|GAA06941.1| 23S rRNA and tRNA pseudouridine synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
          Length = 232

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 63/210 (30%), Positives = 101/210 (48%), Gaps = 12/210 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ DS I   NKP+GI    G    +H   F  + V ++  + ++ HRLD  TSG++V+A
Sbjct: 17  LFLDSDIIAVNKPSGILSNPGRAPEHHDSIF--ARVLAEHPESQIVHRLDMGTSGLIVLA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
             + + +HL   FR R  QK+Y++ VWG        +   L+           V   N  
Sbjct: 75  LNKNSERHLKAQFRERETQKVYYARVWGHIAQDTGTVDLPLICD-WPNRPRQKVCFDN-- 131

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               +++H++V+    +K   + + P TGR+HQLRVH   +G PI+GD  Y  +     +
Sbjct: 132 -GKPSVTHYEVVSRD-EKTTLVRLLPVTGRSHQLRVHMQALGHPILGDQFYATDEALEAS 189

Query: 282 SPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
                +L LHA  +   HP     + + AP
Sbjct: 190 ----PRLLLHAAELTFTHPGTDEPMHLFAP 215


>gi|315123230|ref|YP_004065236.1| ribosomal large subunit pseudouridine synthase A (pseudouridylate
           synthase, 23S RNA-specific) [Pseudoalteromonas sp.
           SM9913]
 gi|315016990|gb|ADT70327.1| ribosomal large subunit pseudouridine synthase A (pseudouridylate
           synthase, 23S RNA-specific) [Pseudoalteromonas sp.
           SM9913]
          Length = 563

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/243 (27%), Positives = 107/243 (44%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++K   + ++ + LT  +      ++Y+D  + V NKPA      G  I   +
Sbjct: 332 CQPILGHMLKGLNVEENPL-LTNPAKGKDLTIVYQDDDLLVINKPAEFLSVPGINIDDSV 390

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K+   +    P + HRLD  TSG+L++A  + A + L + F  R I+K Y +LV G
Sbjct: 391 YMRIKTQFPA-ASGPLIVHRLDMSTSGLLIIALNKRAHKALQKQFIERTIEKRYVALVAG 449

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   I   L+         +       K    +++ + V++        L++ P T
Sbjct: 450 NITENSGVINLPLVLDFDDKPRQMVCY----KTGKPSLTTWHVLERK-NNTTRLQLYPKT 504

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVH  H   +  PIVGD  Y    +         +L+LHA Y+   HP    RL
Sbjct: 505 GRTHQLRVHCAHQLGLNTPIVGDTHYGEEAE---------RLHLHAEYLAFTHPISHQRL 555

Query: 306 QIT 308
           +  
Sbjct: 556 EFE 558


>gi|312793770|ref|YP_004026693.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312180910|gb|ADQ41080.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 311

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/289 (23%), Positives = 123/289 (42%), Gaps = 24/289 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +V+ +   +++++  K  YP I    + K+LR G++ V     +    ++ G  V    
Sbjct: 5   FIVDKELAGVKVEKAIKKKYPSIPMSVIFKMLRKGEIIVSFLPAQKGQVLRFGDTVSFEI 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H               K  + LK   +YED  I V +KP GI     S   Y +
Sbjct: 65  EDRFLEH---------------KKVEILK---VYEDDNIVVIDKPYGIPSHPDSNNEYSV 106

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             +++    SK + P+L HRLD+ T+G++++A+ R     + +    R I+K Y  +   
Sbjct: 107 VSWIEDNY-SKDELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRAIKKRYLCITKK 165

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               K   + ++L K       Y+    Q+  G +  ++ +K++         ++++  T
Sbjct: 166 AELPKSGVLVHYLKKDPKKSKVYISDFPQD--GYSEVVTAYKIV-RQKDDLQLVDVEIKT 222

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           G+THQ+R    H+G  I+GD KY             +   L A Y+   
Sbjct: 223 GKTHQIRAQLAHVGLCILGDSKYGDWELNKKYK--ADMQALCAYYLKFE 269


>gi|253582659|ref|ZP_04859880.1| pseudouridylate synthase [Fusobacterium varium ATCC 27725]
 gi|251835529|gb|EES64069.1| pseudouridylate synthase [Fusobacterium varium ATCC 27725]
          Length = 289

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 71/318 (22%), Positives = 127/318 (39%), Gaps = 38/318 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++  ++E + +   +  + K    +         LR+ ++ ++ KRVK N++        
Sbjct: 2   MKKFIIEPEYDGYEIGTYLKETKGYSGRG-----LRNLEIYLNGKRVKNNSK-------- 48

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
               +  LN ++ ++K  ++ +        +   + YED  I + +K   I V       
Sbjct: 49  ---KVRKLNRLLIKEKDKETGI----IPMEIPIKVAYEDKNILLIDKEPYIIVHPTQKKV 101

Query: 125 IAYHIDGFLKSWVDS--KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +G +  ++ +  K   PR  +RLD  TSG+++VA+   A   L E      + K 
Sbjct: 102 DKTLANGVVNYFLKTTRKIMVPRFYNRLDMNTSGLIIVAKNSYAQSFLQE---KGIVNKF 158

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V GI +  +  I   + K   +G D        E G   A +  KVI    +    
Sbjct: 159 YKAIVKGIIEKDEFLIDKPIGK---VGDDLRRREISVENGGQEAQTKIKVIKRL-KDLTL 214

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +E +  TGRTHQ+R H    G P++GD  Y    K         +  LH+        E 
Sbjct: 215 IEAELLTGRTHQIRAHMALEGYPLLGDELYGGEDKRA------KRQMLHSYKTQFSDIET 268

Query: 303 GRL-QITAPLPAHMVKTW 319
           G L  +   +P  M    
Sbjct: 269 GELKTVEIDIPDDMKSIL 286


>gi|238782665|ref|ZP_04626695.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           bercovieri ATCC 43970]
 gi|238716325|gb|EEQ08307.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           bercovieri ATCC 43970]
          Length = 217

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 66/216 (30%), Positives = 100/216 (46%), Gaps = 14/216 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G     H D  + + + +        
Sbjct: 1   MEPYNPPRDPWLHILYQDQHIMVVNKPSGLLSVPGRAPE-HKDSVM-TRIQADYPTAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG+++VA T+AA + L   FR R  +K Y + VWG     +  I   L+    
Sbjct: 59  HRLDMATSGVIIVALTKAAERELKRQFREREPKKTYIARVWGHLAQDEGLIDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V+   A     +++ P TGR+HQLRVH L MG P
Sbjct: 115 --CDWPNRPKQKVCYETGKSAQTEYQVLSRDADGSTRVKLSPITGRSHQLRVHMLAMGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           I+GD  Y              +L LHA+ + + HPE
Sbjct: 173 ILGDGFYAHPEAKAMA----PRLQLHAQELCITHPE 204


>gi|332298758|ref|YP_004440680.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332181861|gb|AEE17549.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 254

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 73/238 (30%), Positives = 110/238 (46%), Gaps = 24/238 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDG-FLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  I V NK +G+ V   +   Y  D   L +    +  K    HR+D++TSGI++
Sbjct: 9   VLYGDDSIVVLNKRSGLLV---AADRYDPDAPRLDTAASDEFGKLYAVHRIDKDTSGIVI 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            ART  A + L+  F+ R ++K+Y +LV G P  +   +   L+      GD  H    N
Sbjct: 66  YARTAEAHRVLSLQFQNREVEKVYHALVNGRPAWQSLHVDLKLI----PDGDARHRTVVN 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-- 277
           ++    A++ F ++      + W+E +P TGRTHQ+R H    G  IV D  Y  N K  
Sbjct: 122 KREGKSAVTDFTLLGVCP-PYSWIEARPETGRTHQIRAHLAANGLGIVCDPLYSGNQKPV 180

Query: 278 ------------GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
                        +   P+  +L LHA  + + HPE G R+  TAP    M      L
Sbjct: 181 RLSEIKRSWNGDPDDERPLLARLALHAYRLTVTHPETGERMTFTAPYQRDMDAVRKQL 238


>gi|321309582|ref|YP_004191911.1| pseudouridylate synthase [Mycoplasma haemofelis str. Langford 1]
 gi|319801426|emb|CBY92072.1| pseudouridylate synthase [Mycoplasma haemofelis str. Langford 1]
          Length = 304

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 73/301 (24%), Positives = 128/301 (42%), Gaps = 31/301 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSG 62
           M  ++  ++  D +   L+++ K   P    V + K++R   + ++  K     +R++ G
Sbjct: 1   MQKIRRTIL-ADFDGYCLNKFLKLEQPSWTKVFIYKMIRKKNITINGLKISDIRHRLKEG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-G 121
            VV                   ++     K        +++E   + + +K A + VQ  
Sbjct: 60  DVVEFYGC--------------ETPTKPIKWEGLKPLRVVFESENLIIVDKEAKMPVQED 105

Query: 122 GSGIAYHIDGFLK---SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                 H++  L    ++ + +G KP   HRLD  T+G+L+ A+       L +S +  +
Sbjct: 106 DKHPFNHMNNRLLKHLNYSNREGWKPVFIHRLDLNTTGLLIGAKNYKTFLKLNKSQKSLK 165

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I+K Y +LV G    KK  I+ +LLKK       V + ++  +GA  A +    +  F  
Sbjct: 166 IKKSYKALVQGNVSFKKREISCFLLKKDG----RVSISREQVEGAKEAKTIANFLHFFPS 221

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMD 296
                LE+   TGRTHQ+R H  ++  PI GD KY     K  F  P      L A  ++
Sbjct: 222 INSTLLELTLITGRTHQIRAHMSYIKHPIRGDQKYGVEKDKREFPYP-----ALCAYKIE 276

Query: 297 L 297
            
Sbjct: 277 F 277


>gi|238918767|ref|YP_002932281.1| tRNA pseudouridine synthase C [Edwardsiella ictaluri 93-146]
 gi|238868335|gb|ACR68046.1| tRNA pseudouridine synthase C [Edwardsiella ictaluri 93-146]
          Length = 263

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/257 (24%), Positives = 109/257 (42%), Gaps = 18/257 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG  V             +++  D  G+     HRLD+ TSG+L++
Sbjct: 3   IIYQDDHLVAVNKPAGWLVHRSWLDRKEKVVVMQTVRDMIGRHVYTVHRLDRPTSGVLLL 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
             +   A+ L + F   +I K+Y ++V G  + +         +   I   +    +  +
Sbjct: 63  GLSSEIARALAQQFEQHQIHKVYHAVVRGYLQGEALLDYPLTPELDKIADRF----RSPD 118

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +    A ++++ +               +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 119 RAPQPAQTYYRGLATAEVPLAIGRYPTSRFSLVELRPQTGRKHQLRRHMAHLRHPIIGDT 178

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +      +G         L LHA  + L HP  G  L + A L        D LG++  
Sbjct: 179 AHGDLRQNRGIAVHFDTPGLMLHASELCLTHPVSGEALCLRAGLDLRWQALMDGLGWQT- 237

Query: 328 RNLYIKRLYSQDECKQN 344
               + R+    +C Q+
Sbjct: 238 YLPELDRVEFIPDCLQD 254


>gi|164686622|ref|ZP_02210650.1| hypothetical protein CLOBAR_00215 [Clostridium bartlettii DSM
           16795]
 gi|164604351|gb|EDQ97816.1| hypothetical protein CLOBAR_00215 [Clostridium bartlettii DSM
           16795]
          Length = 221

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/218 (28%), Positives = 102/218 (46%), Gaps = 14/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  KP  I  QG +     +   LK ++  K  KP      L HRLD+   
Sbjct: 4   VIYEDNHLLVVEKPVNILSQGDNTNDDDMVNLLKKYLKEKYNKPGNVFVGLVHRLDRPVG 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  AA  L+E  R +  +K Y +++ G  K K++ ++++L K        V V
Sbjct: 64  GIMVFAKTSKAASRLSEQVRNKTFKKTYKAVLHGEMKKKQDNLSDYLYKDKKTN--MVSV 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V +N K A  A   +K +      F  +E+   TGR HQ+RV       P+ GD +Y  N
Sbjct: 122 VNKNHKDAKDAKLSYKTLASN-NGFSLVEIDLQTGRPHQIRVQFSSRNHPLYGDQRYGKN 180

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
                      ++ L +  +++ HP    +++     P
Sbjct: 181 VNKK-----GQQIALWSYKIEIEHPTKKEKMEFVCEPP 213


>gi|312876831|ref|ZP_07736808.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796346|gb|EFR12698.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
          Length = 311

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/289 (23%), Positives = 123/289 (42%), Gaps = 24/289 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            +V+ +   +++++  K  YP I    + K+LR G++ V     +    ++ G  V    
Sbjct: 5   FIVDKELAGVKVEKAIKKKYPSIPMSVIFKMLRKGEIIVSFLPAQKGQVLRFGDTVSFEI 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H               K  + LK   +YED  I V +KP GI     S   Y +
Sbjct: 65  EDRFLEH---------------KKVEILK---VYEDDNIVVIDKPYGIPSHPDSNNEYSV 106

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             +++    SK + P+L HRLD+ T+G++++A+ R     + +    R I K Y  +   
Sbjct: 107 VSWIEDNY-SKDELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRAIIKKYLCITKK 165

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               +   + ++L K S     Y+    Q+  G +  ++ +K++         ++++  T
Sbjct: 166 ADLPESGVLVHYLKKDSKKSKVYISDFPQD--GYSEVVTAYKIV-RQKDDLQLVDVEIKT 222

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           G+THQ+R    H+G  I+GD KY             +   L A Y+   
Sbjct: 223 GKTHQIRAQLAHVGLCILGDSKYGDWELNKKYK--ADMQALCAYYLKFE 269


>gi|189426227|ref|YP_001953404.1| pseudouridine synthase [Geobacter lovleyi SZ]
 gi|189422486|gb|ACD96884.1| pseudouridine synthase, RluA family [Geobacter lovleyi SZ]
          Length = 295

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 135/328 (41%), Gaps = 46/328 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVV 65
           ++   V  +    RLD         I+    ++I+  G   V++  V+  +R +++   +
Sbjct: 2   IKQFSVAKEMAGQRLDETLA-QLAGISKGEARRIIDRGGCAVNQAMVRVASRGMKAEDQL 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +  +        ++ + L+  +            ++Y+D ++   NKP+GI+ Q     
Sbjct: 61  TVGFM--------EQGRFLELLLP--------PEAIVYQDKELLAINKPSGIASQRTP-- 102

Query: 126 AYHIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            Y + G L+ WV  +       +  R+ HRLD+ TSG+++  + R AA  L+E F+   I
Sbjct: 103 -YQLKGTLEYWVAEEFVRQGIKEPVRVVHRLDRGTSGLMLFPKHRQAAAWLSELFKQGGI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           QK Y +LV G P  ++      + K        +            A++ F+ +   A+ 
Sbjct: 162 QKRYLALVTGKPVEERWSCDGPIGKLGSARWGIMS-------EGRAALTDFR-LLAAAEG 213

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E  P TGRTHQ+RVH    G PIVGD  Y           +  +L LH   +    
Sbjct: 214 LALVEAFPRTGRTHQIRVHLSAAGLPIVGDATYGG--------LVSERLMLHCAGLQFAG 265

Query: 300 PEGGRLQITAPLPAHMVKTWDSLGFKYD 327
             G    + A LP          G  +D
Sbjct: 266 RHGLPCNLEA-LPD--SSFIGRCGLCWD 290


>gi|319901461|ref|YP_004161189.1| pseudouridine synthase [Bacteroides helcogenes P 36-108]
 gi|319416492|gb|ADV43603.1| pseudouridine synthase [Bacteroides helcogenes P 36-108]
          Length = 549

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 106/240 (44%), Gaps = 20/240 (8%)

Query: 70  VINALNHIIKEQKILDSSV--NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
               L H+++  ++ ++ +   L       +   +YED  + V +KPAG+    G     
Sbjct: 315 CEPILKHMLQGLEVDENPLLKELQSAGKEKELETVYEDKWLVVVSKPAGMLTVPGKEETV 374

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   ++     +   P + HRLD  TSG+LV+A+T+   QHL   F+ R ++K Y +L+
Sbjct: 375 SVYSLMRERY-PEADGPLIVHRLDMATSGLLVIAKTKQVHQHLQAQFKNRSVKKRYIALL 433

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                     I   L          +     + +    A+++F+V++        +   P
Sbjct: 434 KDTVTRDWGTIELPLCLNPLDRPRQM----VHPEHGKPALTNFEVLERKG-NHTRIAFYP 488

Query: 248 HTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            TGRTHQLRVH  H   + CPI+GD  Y    +         +LYLHA  ++  HP  G 
Sbjct: 489 RTGRTHQLRVHTAHPLGLHCPIIGDELYGEKAE---------RLYLHAEVLEFIHPITGE 539


>gi|327312478|ref|YP_004327915.1| RNA pseudouridine synthase [Prevotella denticola F0289]
 gi|326944338|gb|AEA20223.1| RNA pseudouridine synthase [Prevotella denticola F0289]
          Length = 225

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 108/229 (47%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I +  K AG  VQG       +   ++ W+  K QKP      + HRLD+  S
Sbjct: 3   VLYEDNHIIIVYKEAGEIVQGDKSGDEPLSETVRRWIKEKYQKPGNVFLGIVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L   FR   + K YW++V   P   +  + +WL++       Y + 
Sbjct: 63  GLVIFAKTSKALARLNNMFRNGEVHKTYWAIVTRPPFEPEATLTDWLVRNERQNKSYAY- 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +  +I H+K+I+  + ++  LE+   TGR HQ+R    +M CPI GD KY A 
Sbjct: 122 -NHQVPTSKKSILHYKIINR-SDRYTLLEINLMTGRHHQIRCQLSNMDCPIKGDLKYGAP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 S     + L +  ++  HP     + I +PLP      W ++G
Sbjct: 180 RSNPDGS-----ISLLSHRVEFVHPVSKENICIESPLPDD--TLWHAIG 221


>gi|325298043|ref|YP_004257960.1| pseudouridine synthase [Bacteroides salanitronis DSM 18170]
 gi|324317596|gb|ADY35487.1| pseudouridine synthase [Bacteroides salanitronis DSM 18170]
          Length = 543

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/222 (30%), Positives = 103/222 (46%), Gaps = 18/222 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           ++ +    + +   +  ++YED  + V NKP G+    G  I   +   L +   +    
Sbjct: 325 VEPNPLAGRETKKKELEIVYEDEWLIVVNKPEGMLSTPGKLITDSVYTRLHTLYPT-ATG 383

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+L+VA+T+     L + F  RRIQK Y + + GI    +  I N  +
Sbjct: 384 PLIVHRLDMATSGLLLVAKTKEIHYALQKMFASRRIQKRYTAWLNGIVTTDEGII-NLPI 442

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
              +    Y  V   + +    AI+ +KV+    +    +   P TGRTHQLRVHA H  
Sbjct: 443 CPDYDNRPYQMV---HSEYGKPAITRYKVLGRK-EGKTRIAFYPLTGRTHQLRVHAAHPD 498

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            + CPI+GD  Y             ++LYLHA  +   HP  
Sbjct: 499 GLNCPIIGDELYGKK---------ADRLYLHAAGLSFIHPVT 531


>gi|254463248|ref|ZP_05076664.1| ribosomal large subunit pseudouridine synthase A [Rhodobacterales
           bacterium HTCC2083]
 gi|206679837|gb|EDZ44324.1| ribosomal large subunit pseudouridine synthase A [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 216

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 63/216 (29%), Positives = 105/216 (48%), Gaps = 11/216 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           ++   +       +L++D +I + NKPAG+    G G    +   L + +     +  L 
Sbjct: 1   MSSAYNPPNDPLDILHDDHEILIVNKPAGLLSVPGKG--EELADCLIARIQKVFPQALLV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG++V A TR A +HL   F  R  QK Y + V G+ + K   +   L+    
Sbjct: 59  HRLDRDTSGVMVFALTRHAQRHLGLQFEKRMTQKTYVARVAGVLEPKTGSVELPLI---- 114

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +      + K   +    A + ++V+  + +    + + P TGR+HQLRVH L +G PI+
Sbjct: 115 VDWPNRPLQKVCHETGKAAHTDYRVM-RYGEGETRVRLTPRTGRSHQLRVHMLALGHPIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           GD  Y +            +L LH+  + L HP+GG
Sbjct: 174 GDPFYASGTD----LSDHPRLMLHSEELRLKHPDGG 205


>gi|119470572|ref|ZP_01613275.1| pseudouridylate synthase [Alteromonadales bacterium TW-7]
 gi|119446273|gb|EAW27550.1| pseudouridylate synthase [Alteromonadales bacterium TW-7]
          Length = 209

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/211 (28%), Positives = 100/211 (47%), Gaps = 12/211 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  + + NKP+ +    G    +     L + V+      R+ HRLD  TSGIL +
Sbjct: 7   ILFQDDDLLIVNKPSELLTVPGKDPKH--ADSLINRVNRVFPTARIVHRLDMATSGILCL 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +AA +HL+  F+ R   K Y + V+G  +     +   L+         +     + 
Sbjct: 65  AMNKAAHRHLSMQFQDRETAKRYIARVFGKLEQNNGSVDLPLICDWPNRPKQM----VDH 120

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    +++HFKV++   +    +E+ P TGR+HQLRVH L +G PI+GD  Y        
Sbjct: 121 ENGKPSLTHFKVLERD-ESATRVELTPITGRSHQLRVHMLSLGHPILGDRLYAHKE---- 175

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
                 +L LHA+ + L HP   + +   A 
Sbjct: 176 ALAAAPRLQLHAQMLQLKHPVTEQVMTFEAE 206


>gi|217972743|ref|YP_002357494.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217497878|gb|ACK46071.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 223

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 61/213 (28%), Positives = 102/213 (47%), Gaps = 8/213 (3%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        + Y+D  + + NKP+G+    G   A H      + + +   +  L HRLD
Sbjct: 7   QPPAVPWLDIRYKDRDLIIINKPSGLLSNPGR--AAHTFDCALTRLQTLYPETILVHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V AR + A  HL   F+ R+ +K+Y + V G    ++  I   +   +     
Sbjct: 65  CATSGIMVFARNKKAESHLKTQFQDRQSKKVYIAEVMGHVPQEQGMIDLAIAPDTEHP-P 123

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y   ++  E G   A+++++V++   +    +E+ P TGRTHQLRVH L +G  I+GD  
Sbjct: 124 YQKTLQAGETGGKSALTYYRVLERR-ENSTLVELSPETGRTHQLRVHMLALGHAILGDEF 182

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           Y            + +L LHA+ + L HP   +
Sbjct: 183 YG----DAEVIKAKPRLCLHAQSLSLTHPYSAK 211


>gi|117619994|ref|YP_855705.1| RNA pseudouridine synthase family protein [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
 gi|117561401|gb|ABK38349.1| RNA pseudouridine synthase family protein [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
          Length = 257

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/256 (26%), Positives = 112/256 (43%), Gaps = 19/256 (7%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHR 149
            +  + L+  LLY+D  +   NKP+G+ V             ++   D  G +     HR
Sbjct: 6   AQEQNALQLTLLYQDDWLVAVNKPSGLLVHRSWLDKAETRFAMQMTRDLIGGRHVYPVHR 65

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ TSG+L+ A   A A+ LTE+F  R++ K Y +LV G    ++  I   L +     
Sbjct: 66  LDRPTSGVLLFALDPAVARTLTEAFAARQVHKEYLALVRG-WAPEQGLIDYPLKE---QL 121

Query: 210 GDYVHVVKQNEKGANYAISHFKVI-----------DCFAQKFCWLEMQPHTGRTHQLRVH 258
                 +   ++ A  A++ F+ +                ++  + + P TGR HQLR H
Sbjct: 122 DKIADAMSDPDRPAQEAVTAFRRLHQVELPHAVSKKHPTSRYSLVRLFPKTGRKHQLRRH 181

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
             H+  PIVGD  +       F       ++L L AR +   HP     ++I APL   +
Sbjct: 182 MDHLFHPIVGDTTHGDGRHNRFFREHYGCDRLLLVARTLSFEHPVLKVPMRIQAPLGQEV 241

Query: 316 VKTWDSLGFKYDRNLY 331
           ++ +  LG+    + Y
Sbjct: 242 LQLFAELGWPASESDY 257


>gi|313899587|ref|ZP_07833096.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
 gi|312955694|gb|EFR37353.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
          Length = 293

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 106/280 (37%), Gaps = 32/280 (11%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           +V ++ + +  N+ +Q    VRI         +  E+  ++          +    +L+E
Sbjct: 42  RVSINNRIIHGNHMLQEQDTVRIF--------LAMEEDTIE--------PWYEDLEILFE 85

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFL---KSWVDSKGQKPRLTHRLDQETSGILVVA 161
           D    + NKPA + V        H    L      ++      R  HRLD ETSG ++  
Sbjct: 86  DELFCIVNKPANLLVHSDGIEHAHTVCNLVKAHYLLEGHNTCVRPLHRLDYETSGAMIFC 145

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +       L    + ++I + Y +   G    K   I   + +  H          +  +
Sbjct: 146 KVPFLQPLLDAMLKNKQIYREYEAFARGYIAQKHCTITRGIARDRHDARK-----MRISE 200

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               A +   V       F W+  + +TGRTHQ+RVH   +  P++ D  Y         
Sbjct: 201 HGKSARTDVFV-KQNFMDFTWIRCRLYTGRTHQIRVHLAAIQHPLLSDPLYG------IR 253

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWD 320
                +L LHA  + +PHP    + ++  PLP  + +  D
Sbjct: 254 DSRCPRLALHACRVSIPHPLSNDMLRVECPLPQDLRQLLD 293


>gi|256829455|ref|YP_003158183.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256578631|gb|ACU89767.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 234

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 102/228 (44%), Gaps = 17/228 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +++ED  + V NKP+G+    G       D  L S V    +  +  HRLD 
Sbjct: 10  PPTEPRLAVIHEDRDMVVVNKPSGLLSVPGR-TPELFDSVL-SRVREIHRGAQAVHRLDL 67

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+LVVA  R A   L + F+ R  +K+Y + V G+       +   L+         
Sbjct: 68  GTSGVLVVATRRKAETILRQQFQDRLTRKLYLARVQGVMSEDSGQVDLPLICD--WPNRP 125

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + +V  +      A++ ++V++   +    + ++PHTGR+HQLRVH   +G PI+GD+ Y
Sbjct: 126 MQMVCHD--TGKPALTDYQVLESDGES-TLVLLRPHTGRSHQLRVHMASLGHPILGDNLY 182

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
                G        +L LHA  + L HP  G      AP      +  
Sbjct: 183 GEQRPGE-------RLLLHASQLGLYHPYSGEWTTFHAPC--DFAEHI 221


>gi|160875996|ref|YP_001555312.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160861518|gb|ABX50052.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315268192|gb|ADT95045.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 223

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 61/213 (28%), Positives = 101/213 (47%), Gaps = 8/213 (3%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        + Y+D  + + NKP+G+    G   A H      + + +   +  L HRLD
Sbjct: 7   QPPAVPWLDIRYKDRDLIIINKPSGLLSNPGR--AAHTFDCALTRLQTLYPETILVHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V AR + A  HL   F+ R+ +K+Y + V G    ++  I   +   +     
Sbjct: 65  CATSGIMVFARNKKAESHLKTQFQDRQSKKVYIAEVMGHVPQEQGMIDLAIAPDTEHP-P 123

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y   ++  E G   A+++++V++   +    +E+ P TGRTHQLRVH L +G  I+GD  
Sbjct: 124 YQKTLQAGETGGKSALTYYRVLERR-ENSTLVELSPETGRTHQLRVHMLALGHAILGDEF 182

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           Y              +L LHA+ + L HP   +
Sbjct: 183 YG----DAEVIKAAPRLCLHAQSLSLTHPYSAK 211


>gi|109897951|ref|YP_661206.1| pseudouridylate synthase [Pseudoalteromonas atlantica T6c]
 gi|109700232|gb|ABG40152.1| Pseudouridylate synthase [Pseudoalteromonas atlantica T6c]
          Length = 223

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/222 (27%), Positives = 106/222 (47%), Gaps = 12/222 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   +LY+D  +   NKP+G+    G          +   +  +     + HRLD 
Sbjct: 11  PPCDEAVTVLYQDEYLLAVNKPSGLLSLSGKNPLN--KDSVHYRIVQEFPTALMAHRLDF 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+L++A  + +   LT+ F+ R ++K Y +++ G  +  +  ++  + K        
Sbjct: 69  GTSGVLLLALDKNSNAQLTKQFQARTVKKRYTAVLLGKIEQTEGRVSVPIAKDPPN---- 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               K        AISH++VI+      C  +E  P TGRTHQLR+H+L MG PI+G   
Sbjct: 125 FPRQKICYDTGKEAISHYRVIEYVDNPLCTRVEFTPETGRTHQLRLHSLAMGHPILGCDL 184

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y      + +  + ++L LHA ++   HP  G+ ++I AP+P
Sbjct: 185 YG----NSHSVQMASRLLLHASHIKFTHPYSGKSMEIEAPIP 222


>gi|225848540|ref|YP_002728703.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225644519|gb|ACN99569.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 271

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 118/303 (38%), Gaps = 49/303 (16%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +      +I+    + I+ S  V V+ KRV   ++ ++ G VV I          +K   
Sbjct: 16  FIAASL-NISKNQAKDIIDSRNVLVNNKRVWIASHTLKEGDVVEILQPQQPATKELK--- 71

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             ++YED  I   NKP  +           ++  L+    SK  
Sbjct: 72  ------------------IIYEDEYIVAVNKPPTLLSDREK---DSVEFILRE--KSKNP 108

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           K +  HRLD+ETSGIL++A+     +   E +  + + K+Y ++                
Sbjct: 109 KIKAIHRLDKETSGILLLAKDYKVFERFKELWEDKIVFKLYLAI---------------- 152

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
              SH   ++ H+          A+SH K++      F + +++  TGR HQ+R H   +
Sbjct: 153 ---SHNEANFNHLTVNLPVDDKPAVSHIKLVK-KGNGFSYFQVRIETGRKHQIRKHLSSI 208

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDS 321
             PIVGD  Y      +      N+  LH+  +   HP +  ++ + A +P       + 
Sbjct: 209 RHPIVGDKIYGVKKLEHNLLKRVNRQMLHSYKLSFFHPYKNKKIDLVAEIPTDFKNVLNY 268

Query: 322 LGF 324
           L  
Sbjct: 269 LNL 271


>gi|126741336|ref|ZP_01757013.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           SK209-2-6]
 gi|126717592|gb|EBA14317.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           SK209-2-6]
          Length = 217

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 59/220 (26%), Positives = 102/220 (46%), Gaps = 13/220 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             +       +L+ D++I V NKP G+    G G   H+   L + V     +  L HRL
Sbjct: 6   DYNPPQEPLEILHHDAEILVVNKPEGLLSVPGRG--EHLADCLIARVQRVFPEALLVHRL 63

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG++V   +  A +HL+  F  R  +K Y + + G  + K   +   L+       
Sbjct: 64  DRDTSGVMVFGLSPHAQRHLSMQFEKRTTKKTYVARLAGRLEPKSGTVDLPLIVD-WPNR 122

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               V  ++      A++ +KV+   A++   + + P TGR+HQLRVH L +G  I+GD 
Sbjct: 123 PRQKVCNES---GKPAVTDWKVVKQSAEE-TRVRLTPKTGRSHQLRVHMLSLGHAILGDP 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
            Y              ++ LH+  + + HP+ G  ++  A
Sbjct: 179 LYAEGAALEHP-----RMMLHSEELRIKHPQSGESMRFRA 213


>gi|302187306|ref|ZP_07263979.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. syringae 642]
          Length = 211

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/214 (29%), Positives = 99/214 (46%), Gaps = 11/214 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++++D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIHQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGYPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR     + L+  F  R  +K Y +L WG P      I   L           HVV  +
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLPLRYDPPT--KPRHVV--D 121

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +   +A++ +KVI+      C +E+ P TGR+HQLRVH L +G P++GD  Y       
Sbjct: 122 HEAGKHALTFWKVIERH-DTHCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAHPQ--- 177

Query: 280 FTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                  +L LHA  +   HP  G RL      P
Sbjct: 178 -ALAAYPRLCLHASMLSFTHPGTGERLTFECAAP 210


>gi|163744079|ref|ZP_02151445.1| ribosomal large subunit pseudouridine synthase A [Phaeobacter
           gallaeciensis 2.10]
 gi|161382626|gb|EDQ07029.1| ribosomal large subunit pseudouridine synthase A [Phaeobacter
           gallaeciensis 2.10]
          Length = 217

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/227 (26%), Positives = 103/227 (45%), Gaps = 15/227 (6%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +V+           +L+ D+++ V NKP G+    G G   H+   L S + +   +  L
Sbjct: 2   TVSSDYTPPTDPLDILHHDAQLLVVNKPHGLLSVPGRG--EHLADCLLSRLQAVFPEALL 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG++V   T  A +HL+  F  R  +K Y + V G  + +   +   L+   
Sbjct: 60  VHRLDRDTSGVMVFGVTPHAQRHLSMQFEKRSAKKAYVARVDGRLEPRSGTVDLPLIVD- 118

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                   V          A++ ++V+  +      + + P TGR+HQLRVH L +G  I
Sbjct: 119 WPNRPRQMVCHDT---GKEAVTDWRVMK-YEDTATRVRLTPKTGRSHQLRVHMLSLGHAI 174

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
           +GD  Y      +       ++ LHA  + + HP+ G     ++ AP
Sbjct: 175 LGDPLYAEGHALDHP-----RMMLHAEELRIKHPDSGESMKFRVKAP 216


>gi|160876810|ref|YP_001556126.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160862332|gb|ABX50866.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315269012|gb|ADT95865.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 225

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 66/217 (30%), Positives = 109/217 (50%), Gaps = 16/217 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D  I V NKP+G+    G   A++    + + V ++    ++ HRLD  TSG++
Sbjct: 14  LDILYQDKDIIVINKPSGLLSVPGRDPAHYDS--VYARVKAEHPHSQIVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  R+A + L   F  R   K Y++ V G  KN    +   L+       D+ +  KQ
Sbjct: 72  VVALIRSAERELKRQFHDRETSKTYFARVAGHVKNDTGSVDYPLI------CDWPNRPKQ 125

Query: 219 NEKG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                    +++H++VI   A++   +++ P TGR+HQLRVH + +G PI+GD  Y    
Sbjct: 126 KVDHLVGKPSLTHYQVISR-AKRSTLVKLTPITGRSHQLRVHMMALGHPILGDGFYADPL 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
             +    +  +L LHA  + + HP  G  +  +A  P
Sbjct: 185 AKS----LAPRLLLHAAELTIKHPYTGVSMTFSAEAP 217


>gi|325925856|ref|ZP_08187225.1| tRNA pseudouridine synthase C [Xanthomonas perforans 91-118]
 gi|325543687|gb|EGD15101.1| tRNA pseudouridine synthase C [Xanthomonas perforans 91-118]
          Length = 296

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 105/237 (44%), Gaps = 24/237 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V +KPAG+ V          D       +  G+   L HRLD+ TSG L++
Sbjct: 68  ILYQDDVLAVVDKPAGLMVHDSKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLLL 127

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R +A  L ++   R ++K Y ++  G P  ++  + + L       G     VK   
Sbjct: 128 AFDRDSASALGKALMAREVEKDYLTVCRGWPAEERFIVDHDL------DGGPGKPVK--- 178

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD 
Sbjct: 179 ---KPAVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGDT 235

Query: 271 KYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
            +       +F     +++ LHA  +  PHP GG R+ ITAPL A   K     G+ 
Sbjct: 236 SHGDGRHNRSFRMLGIHRMLLHAERLGFPHPGGGRRISITAPLDAEFTKACALFGWD 292


>gi|52424286|ref|YP_087423.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52306338|gb|AAU36838.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 219

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 63/212 (29%), Positives = 98/212 (46%), Gaps = 15/212 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y D+ I V NKP+G+    G+   Y+      S V  K       HRLD  TSGIL
Sbjct: 14  LDIVYHDNHILVVNKPSGLLSVPGNQPRYYDSAM--SRVKDKYGFCEPAHRLDMATSGIL 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A ++AA   L   FR R  +K Y +LVWG  +     +   L+       D+ +  +Q
Sbjct: 72  LFAMSKAADSELKRQFRERETKKYYEALVWGHLEQDSGEVNLPLV------CDWENRPRQ 125

Query: 219 NE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               +    A++ ++V+         +++ P TGR+HQLR+H L +G PI+GD  Y    
Sbjct: 126 TICFERGKSAVTKYEVLQRLPNNTTRVKLTPITGRSHQLRLHMLALGHPILGDKFYAHPQ 185

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
                     +L LHA  + + HP  G  +  
Sbjct: 186 AKTMA----PRLCLHAESLTIKHPISGEEMTF 213


>gi|313203182|ref|YP_004041839.1| ribosomal large subunit pseudouridine synthase d [Paludibacter
           propionicigenes WB4]
 gi|312442498|gb|ADQ78854.1| ribosomal large subunit pseudouridine synthase D [Paludibacter
           propionicigenes WB4]
          Length = 227

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 73/225 (32%), Positives = 109/225 (48%), Gaps = 15/225 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I   NK     VQG       +   +K ++  K  KP      +THRLD+  S
Sbjct: 3   VLYEDNHIIAVNKTCSEIVQGDKTGDEPLSDTIKKYLKEKYNKPGEVFCGVTHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E FR + ++K YW++V   PK  +  + ++L++         H 
Sbjct: 63  GVVLFAKTSKALTRLNEMFRTQEVKKTYWAIVKEKPKQPEGRLEHFLVRNEKQNKSVAHE 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  A  A   +K+I   ++ +  LE+   TGR HQ+R     MGCPI GD KY   
Sbjct: 123 KMV--PNAKAAALSYKLI-AHSETYYLLEVHLETGRHHQIRCQLAKMGCPIKGDLKYG-- 177

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
                 S     + LHAR ++  HP   + +QITAP+PA   K W
Sbjct: 178 ---FARSNPNGGISLHARNVEFIHPVSKQLIQITAPVPAD-DKLW 218


>gi|297183963|gb|ADI20083.1| pseudouridylate synthases, 23S RNA-specific [uncultured alpha
           proteobacterium EB080_L06A09]
          Length = 217

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 60/225 (26%), Positives = 104/225 (46%), Gaps = 12/225 (5%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
                   +   +LY D  + V NKP+G+    G  + +     ++  V ++     L H
Sbjct: 3   PFVYSPPKIPLDILYIDEDVLVVNKPSGLLSVPGKELKHRDS--MELRVKAQYPNSFLVH 60

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD +TSGI++ A  +   + L   F  R ++K+Y + V+G  K +   I   L+    +
Sbjct: 61  RLDMDTSGIMIFALNKNTQRLLNMQFEKRMVKKLYEARVFGNMKARNGSINLPLI----V 116

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 + K + +    A++H++V+    +    +E+ P TGRTHQLRVH   +G  I+G
Sbjct: 117 DWPNRPMQKVDIENGKSALTHWRVLK-KEKNESRVELMPETGRTHQLRVHMKSLGHTILG 175

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           D  Y           + +KL LHA+ + + HP+   +    A  P
Sbjct: 176 DRFYG----NAMEISLADKLQLHAKRLIIIHPKSDKQFTFEASTP 216


>gi|315038927|ref|YP_004032495.1| ribosomal protein large subunit [Lactobacillus amylovorus GRL 1112]
 gi|312277060|gb|ADQ59700.1| ribosomal protein large subunit [Lactobacillus amylovorus GRL 1112]
 gi|327184070|gb|AEA32517.1| ribosomal protein large subunit [Lactobacillus amylovorus GRL 1118]
          Length = 285

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 71/314 (22%), Positives = 119/314 (37%), Gaps = 36/314 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M Y   +    + + + ++   +     I     +  LR    V ++ K   FN  ++ G
Sbjct: 1   MVYNFTLFYPKNLDPLPVNEVLRKLL--IPR-KWRHYLRIEQNVTINGKYRYFNELVKPG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I      L+ I         S+  T  +      ++YED  + + NK  G      
Sbjct: 58  DKIDI-----VLDQI--------DSMQQTYPASRRMPDVIYEDDNLLIINKKKGQKTHPN 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  D  L       G  P + HRLD  T G+L+VA+  A    L      +   + 
Sbjct: 105 ---LNETDTALNDCATYLGSSPYIVHRLDMLTGGLLLVAKNPAVVPILNRELTTKTFHRE 161

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V    K  K   I   + +        +       K   +A++H++++  ++    
Sbjct: 162 YLAKVIHADKLKKNGTIDLPIGQDPDDQRKRMV-----NKTGLHAVTHYELLKKYSDNTA 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++   TGRTHQ+RVH   +GCPIVGD  Y  +F G         L L A  + L  P 
Sbjct: 217 LVKLTLETGRTHQIRVHLAAIGCPIVGDPLYNPDFAGEN-------LALDAYEISLIKPF 269

Query: 302 G-GRLQITAPLPAH 314
              +L +   LP  
Sbjct: 270 SFEKLHVK--LPDE 281


>gi|116051259|ref|YP_789909.1| pseudouridine synthase RluA [Pseudomonas aeruginosa UCBPP-PA14]
 gi|313108585|ref|ZP_07794586.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           aeruginosa 39016]
 gi|115586480|gb|ABJ12495.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|310881088|gb|EFQ39682.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           aeruginosa 39016]
          Length = 211

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 61/216 (28%), Positives = 107/216 (49%), Gaps = 11/216 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  ++++D  + V +KP  +    G       D  +    ++   + R+ HRLD ETSG+
Sbjct: 5   QIRIVHQDDALLVVDKPTLLLSVPGRADDN-KDCLVTRLQENGYPEARIVHRLDWETSGL 63

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+AR   + + L+  F  R  +K Y +L WG+P+     I   L         +V    
Sbjct: 64  MVLARDADSHRELSRQFHDRETEKAYTALCWGLPELDSGRIELPLRYDPPTKPRHV---- 119

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +   +A++ ++V++   +++  +E+ P TGR+HQLRVH L +G P++GD  Y     
Sbjct: 120 VDFEHGRHALTFWRVVERH-ERWSRVELTPITGRSHQLRVHMLSIGHPLLGDRLY----A 174

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                    +L LHA  + L HP  G RL+  +P P
Sbjct: 175 NPEALAAHERLCLHASLLCLTHPQSGERLRFESPAP 210


>gi|325184958|emb|CCA19450.1| ribosomal large subunit pseudouridine synthase C pu [Albugo
           laibachii Nc14]
          Length = 344

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 89/329 (27%), Positives = 152/329 (46%), Gaps = 35/329 (10%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK--------KRVKFNNRIQSGQV 64
             ++ N+RLDRW    +   +   +QK +R G +R+          +R   N ++QSG +
Sbjct: 18  SPNDHNIRLDRWLSQEFGDKSNSFIQKHIRKGNIRLSVSQTKHERVRRAPANQKLQSGNL 77

Query: 65  VRI-PPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGG 122
           V I     +  +    E   L+  ++  K   + L   + Y D+  ++ +KP+G++VQGG
Sbjct: 78  VAIRKNTFHEFSQKTNEFLPLEPFISSEKRYFEALYERIRYRDANYFILDKPSGLAVQGG 137

Query: 123 SGIAYHIDGFLKSW-------------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
                 +  +   +              +   + PRL HR+D+ TSG++V+AR R AA  
Sbjct: 138 ERSTKSLADYFHMFHERLSKTDDPEMDYEILPELPRLVHRIDKGTSGLVVIARHRRAAAA 197

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
            +E  R RRI+K Y + V  IP    E      L+    G + + + K  +  +   I+ 
Sbjct: 198 FSELLRERRIEKEYQAFV--IPSRTFEVPETGRLESVIEGKEAITMYKVIDPVSRE-ITL 254

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC-PIVGDHKYCANFKGNFTSPIQNKL 288
            K+   F Q  C  ++ P TGR HQ+R+H   +   PI+GD +Y    + N    + N++
Sbjct: 255 AKLSFEFPQGKCL-KVWPITGRKHQIRIHCATILHAPILGDGRYGCR-ESNALDLLPNRM 312

Query: 289 YLHARYMDLPHP------EGGRLQITAPL 311
           YLHA  +  P+P          ++I  PL
Sbjct: 313 YLHAAKISFPNPFFYSAQTPRTIEIECPL 341


>gi|258544489|ref|ZP_05704723.1| tRNA pseudouridine synthase C [Cardiobacterium hominis ATCC 15826]
 gi|258520224|gb|EEV89083.1| tRNA pseudouridine synthase C [Cardiobacterium hominis ATCC 15826]
          Length = 244

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 107/243 (44%), Gaps = 18/243 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY D+ +   NKPAG+ V       Y  +  L+   +  G K    HRLD+ TSG+L
Sbjct: 4   LPILYRDAHLIAVNKPAGLLVHRSPLERYADETVLQILQEQTGLKGYPAHRLDRPTSGVL 63

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A     A+ L E    +R++K Y ++V G    +   I   L   +++        +Q
Sbjct: 64  LLALDPTTARLLGELIAQQRLEKTYHAIVRG-WLAETGEIDYPL---AYLPDKMADRNRQ 119

Query: 219 NEKGANYAISHFKVI-----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            EK    A++ ++ +                ++   E++P  GR HQLR H  H+  PI+
Sbjct: 120 REKPPQEALTRYRCLARSELPFASDGKHPTSRYSLAELRPLQGRKHQLRRHLKHIFHPII 179

Query: 268 GDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
           GD  +  N +           +L LHA  + LPHP  G  L + AP  AH  +   +L  
Sbjct: 180 GDTTHGDNRQNRVLGERYGALRLMLHASRLQLPHPHTGAPLDLRAPFDAHWAQLAAALTL 239

Query: 325 KYD 327
             +
Sbjct: 240 NIN 242


>gi|149237721|ref|XP_001524737.1| DRAP deaminase [Lodderomyces elongisporus NRRL YB-4239]
 gi|146451334|gb|EDK45590.1| DRAP deaminase [Lodderomyces elongisporus NRRL YB-4239]
          Length = 622

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/258 (22%), Positives = 100/258 (38%), Gaps = 28/258 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        +K + SG V ++ K    +  +++G ++         +   KE
Sbjct: 130 LDVFLSE-FRDRTPEAYKKAIESGMVCINSKPADLSTIVRNGDLISHRGFRREGHVSSKE 188

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            K                  ++Y+D  + V +KP+GI         Y  +   K      
Sbjct: 189 IK------------------IVYQDDDLLVIDKPSGIPAHPSG--RYRYNSVTKILQHEM 228

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ + +T   +  L    + R + K Y + V G    +   +  
Sbjct: 229 GIVLHPCNRLDRLTSGLMFLGKTAKGSTKLMTQIKDRNVSKEYIARVKGKFPKESITVDQ 288

Query: 201 WLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVH 258
            LL     +  + V  VK        A + FK I    +     ++  P TGRTHQ+RVH
Sbjct: 289 PLLTLNPRLTLNVVDFVK-----GKEASTEFKRISYDPKTNTSVIKCHPLTGRTHQIRVH 343

Query: 259 ALHMGCPIVGDHKYCANF 276
             ++G PI  D  Y   +
Sbjct: 344 LQYIGYPIANDPIYSNGY 361


>gi|240948986|ref|ZP_04753340.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           minor NM305]
 gi|240296573|gb|EER47191.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           minor NM305]
          Length = 222

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 63/217 (29%), Positives = 101/217 (46%), Gaps = 14/217 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+      + V  K       HRLD  TSGIL+ A
Sbjct: 17  VYRDNHILVINKPSGLLSVPGNRPEYYDSAM--TRVQQKYGFTEPAHRLDMATSGILLFA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHVVKQN 219
            ++ A + L   FR R  +K Y +L+WG    +     + N+ L           +  + 
Sbjct: 75  LSKVAEKELKRQFREREPKKHYIALLWGKLGERVGDKGVMNFPLICDWENRPRQKICYER 134

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 A++H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y       
Sbjct: 135 ---GKKAVTHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGDKFY----ANP 187

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
               + ++L LHA  + + HP  G  +  +A   A  
Sbjct: 188 LAKSLASRLCLHAESLTITHPITGELMTFSAE--ADF 222


>gi|332306836|ref|YP_004434687.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332174165|gb|AEE23419.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 563

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 120/242 (49%), Gaps = 23/242 (9%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I      LNH+++   + D+ + L   +D  +  ++Y+D ++ + NKPA +    G  I 
Sbjct: 327 IGKCQPILNHMLQGLSVEDNQL-LQNTADNKQIDIVYQDDEMLIINKPAQLLSVPGKHIQ 385

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   +K+          + HRLD  TSG++V+A + A+ + L + F  R+++K Y +L
Sbjct: 386 DSVYTRIKTLFPHATGSL-IVHRLDMSTSGLMVIALSAASHKALQKQFISRQVEKSYVAL 444

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCF-AQKFCWL 243
           + G+ + ++  I   L       GD+    +Q   EK    A + + VI+   +Q+   +
Sbjct: 445 IDGLLEKQQGTITLPL------AGDFYDRPRQCVCEKTGKPAHTTWHVIERRSSQQQTKV 498

Query: 244 EMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            +QP TGRTHQLRVH  H   +  PI+GD  Y             ++L+LHA+ + L HP
Sbjct: 499 LLQPKTGRTHQLRVHCAHERGLNMPIIGDDLYGNR---------DSRLHLHAQSLSLFHP 549

Query: 301 EG 302
             
Sbjct: 550 VS 551


>gi|254294726|ref|YP_003060749.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254043257|gb|ACT60052.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
          Length = 219

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/221 (28%), Positives = 103/221 (46%), Gaps = 12/221 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
            +     +++YED    V +KP+G+    G    +     L++   +   + R  HRLD 
Sbjct: 9   PAKDPSIVVIYEDEAFLVLDKPSGLLSVPGKPPEHS--DCLETRAQAVYPEARTVHRLDM 66

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+ V+AR  A  +HL   F  R   K Y + VWG  ++ +  I   ++         
Sbjct: 67  ATSGVWVMAREHAMMRHLGLQFERRHTSKTYIARVWGDIEDDEGFIDEPIICDWPNRPKQ 126

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +   ++       + + +KVI+        +E+ P TGRTHQLR+H  H+G PI+ D  Y
Sbjct: 127 MICYEK----GKPSQTKWKVIERK-DGITRVELTPITGRTHQLRLHMQHIGHPILADRIY 181

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             +          ++L LHA  + + HP GG  +  T+P+P
Sbjct: 182 AHDEAFEAA----DRLQLHAHSITMHHPIGGEKITFTSPVP 218


>gi|255690880|ref|ZP_05414555.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           finegoldii DSM 17565]
 gi|260623516|gb|EEX46387.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           finegoldii DSM 17565]
          Length = 561

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 71/248 (28%), Positives = 115/248 (46%), Gaps = 27/248 (10%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ +  + H D  +  ++YED  + V NKPAG+    G       
Sbjct: 320 CEPILQHMLQGLEVDENPLLNSIHEDE-ELEIVYEDEWLVVVNKPAGMLSVPGKEEDRDS 378

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                         P + HRLD  TSG+L+VA+T+   QHL   F  R I+K Y +++ G
Sbjct: 379 VYHRLKKKYPDATGPMIVHRLDMATSGLLLVAKTKEVHQHLQAQFASRSIKKRYVAVLDG 438

Query: 190 ---------IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
                    +P  +   I   L     +      V +++      AI+ +++I   ++K 
Sbjct: 439 ATATVEKTALPPGRTGRIELPLCLN-PLDRPRQIVSREH---GKEAITEYRII-SESEKH 493

Query: 241 CWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +   P TGRTHQLRVHA H   + CPI+GD  Y             ++LYLHA Y++ 
Sbjct: 494 IRIAFYPLTGRTHQLRVHAAHPEGLSCPILGDELYGKK---------ADRLYLHAEYIEF 544

Query: 298 PHPEGGRL 305
            HP  G++
Sbjct: 545 RHPISGKI 552


>gi|260779409|ref|ZP_05888300.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260604499|gb|EEX30799.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 245

 Score =  168 bits (425), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 66/227 (29%), Positives = 105/227 (46%), Gaps = 16/227 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ED  I V NKP+G+    G     H D       D      +  HRLD  TSG+++ A
Sbjct: 17  VFEDEGILVVNKPSGLLSVPGRA-EEHYDSMWSRLKD-IYPDIQPVHRLDMSTSGLMLFA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE- 220
           + +     L + F+ R   K+Y++ VWG  + ++  +   L+       D+ +  KQ   
Sbjct: 75  KNKPTESALKKQFQFRLTHKVYYARVWGRVEQQEGEVDLPLI------CDWPNRPKQKVC 128

Query: 221 -KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +    + + F+V     Q    + + P TGR+HQLRVH   +G PIVGD  Y       
Sbjct: 129 FEQGKPSKTLFEVAKREEQ-TTIVRLLPITGRSHQLRVHMQALGHPIVGDEFYSQGEAFE 187

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
           F+S    +L LHA  +   HP+  RL+ +  +P       ++L F Y
Sbjct: 188 FSS----RLELHAAELSFYHPQDERLR-SIFVPCDFYPEAEALIFNY 229


>gi|149921425|ref|ZP_01909878.1| pseudouridine synthase, RluA family protein [Plesiocystis pacifica
           SIR-1]
 gi|149817745|gb|EDM77210.1| pseudouridine synthase, RluA family protein [Plesiocystis pacifica
           SIR-1]
          Length = 311

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 80/322 (24%), Positives = 138/322 (42%), Gaps = 32/322 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           MS+ +  +   +   E+   L          ++      ++++G V V++ RV+     +
Sbjct: 4   MSMASAPKRFRIIPTEQGSTLRNVLMRRVK-LDRKQAAAVIQAGGVYVNRLRVRLPQVLV 62

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
             G+ + +   + AL+                K  D  +   ++      V +KPAG+ V
Sbjct: 63  AHGERITV--YLEALD---------------AKPLDPERVRFVHRGEDFVVLDKPAGVPV 105

Query: 120 --QGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFR 175
                + +    +  +        ++P +   HRLDQ  SG+++      A + L + FR
Sbjct: 106 SAVRETCVGSLSEALIHQLESEGLERPYVGVVHRLDQGASGLVLFTIRDVANKSLHKQFR 165

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---V 232
              I++ Y   V G P  +  C    L+K    G   V V    +  +  A +HF+    
Sbjct: 166 DHEIRRGYRVRVTGEPPAQLRC-DAPLIKLRSGG---VKVGSPGDGRSKPATTHFRHVAR 221

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           +D  A     L+++  TGRTHQ+R HA H+G PIVGD +Y A+ +G   S   ++L LHA
Sbjct: 222 VDGEAGPEHLLDVEIETGRTHQIRAHAAHLGFPIVGDRRYGADGEGEAGSD-HSRLCLHA 280

Query: 293 RYMDLPHPEGG-RLQITAPLPA 313
           R ++  HP  G     T  LP 
Sbjct: 281 RSLEFEHPLTGAPQSFTCELPD 302


>gi|84387506|ref|ZP_00990524.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           splendidus 12B01]
 gi|84377554|gb|EAP94419.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           splendidus 12B01]
          Length = 570

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 65/242 (26%), Positives = 109/242 (45%), Gaps = 20/242 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +  L H++K  ++ D +  L   ++     +L++D  I V +KPAG     G  I    
Sbjct: 339 CVPILGHMMKGLEV-DPNPLLENPAEGKDLDILFQDDHIVVVHKPAGFLSVPGKTIKDSA 397

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++       + P + HRLD  TSGIL+ A TR A + L + F  R ++K Y +++ G
Sbjct: 398 YTRVQEM-HQDVEGPFVIHRLDMATSGILIFALTRRANKSLQKQFITREVEKRYVAMIEG 456

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           + +  +  +   L    +     +   +        A + ++VI+   Q    + + P T
Sbjct: 457 VLEQDEGYVRLPLRGDLYDRPRQIVCFEH----GKPAETKWEVIERN-QDTTKVYLHPKT 511

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVH  H   +  PIVGD  Y             ++L+LHA  + L HP     +
Sbjct: 512 GRTHQLRVHCSHEEGLNMPIVGDGLYGNK---------ADRLHLHAERLALHHPVTKEWM 562

Query: 306 QI 307
           + 
Sbjct: 563 EF 564


>gi|329769221|ref|ZP_08260640.1| hypothetical protein HMPREF0433_00404 [Gemella sanguinis M325]
 gi|328839352|gb|EGF88932.1| hypothetical protein HMPREF0433_00404 [Gemella sanguinis M325]
          Length = 294

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/306 (20%), Positives = 117/306 (38%), Gaps = 43/306 (14%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
            KN+        + K    G ++V+ K       ++   VV I       +  ++  +  
Sbjct: 21  LKNNISRKTLTRI-KFDNDGSIKVNGKEENVRYILKKNDVVEITLPSEEFSEHVRFFE-- 77

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK- 143
                        K  ++YED  + + NKPA +          + D  L   V+   +K 
Sbjct: 78  ------------DKLDIIYEDEYLLIVNKPADLPSIPSR---NNEDSSLLEIVNGYFKKN 122

Query: 144 -----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                P +  RLD+ T+G++++A+ R      ++      I K Y +LV G  ++    I
Sbjct: 123 HYSTIPHIVTRLDKNTTGLVLIAKHRHIHALFSK----EEIDKFYLALVVGKVED--GII 176

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRV 257
              + + S        + +      +YA +        F      ++++  TGRTHQ+RV
Sbjct: 177 EANIKRASD-----SIITRCVADDGDYAKTQVWSEKYNFKNNISLVKLKLFTGRTHQIRV 231

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           H      P++GD  Y  N +      I ++  LH   +   HP   + +   A LP  M 
Sbjct: 232 HMSFSNNPLLGDELYGGNKQ------IIDRQALHCYNLKFKHPITRKNIDAVAQLPEDMN 285

Query: 317 KTWDSL 322
              ++L
Sbjct: 286 NIVENL 291


>gi|225375845|ref|ZP_03753066.1| hypothetical protein ROSEINA2194_01477 [Roseburia inulinivorans DSM
           16841]
 gi|225212280|gb|EEG94634.1| hypothetical protein ROSEINA2194_01477 [Roseburia inulinivorans DSM
           16841]
          Length = 216

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 65/211 (30%), Positives = 108/211 (51%), Gaps = 9/211 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +LYED ++ V  KPAG++ Q        ++  LK++   KG++P +   HRLDQ   G++
Sbjct: 5   ILYEDEEVIVCEKPAGVAAQTRRLGQADMESLLKNYRAGKGEQPYIGVVHRLDQPVRGVM 64

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+T+ AA  L+   + +   K Y+++  G+P+ KK  + ++LL+          VV +
Sbjct: 65  VFAKTKEAAADLSRQVQTKMADKFYYAVTDGVPEQKKGTLEDYLLRDGKTNTSK--VVSK 122

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +GA  A   ++V            ++  TGR HQ+RV   + G PIVGD KY  NFK 
Sbjct: 123 STEGAKSARLDYEVTAQNKTNAVL-RIRLDTGRHHQIRVQLANAGIPIVGDTKY--NFKE 179

Query: 279 NFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
             T    N L L +  +   HP+   +++  
Sbjct: 180 TMTRSG-NGLLLCSYKIGFKHPKTHKKMEFE 209


>gi|320539613|ref|ZP_08039277.1| putative pseudouridine synthase for 23S rRNA [Serratia symbiotica
           str. Tucson]
 gi|320030225|gb|EFW12240.1| putative pseudouridine synthase for 23S rRNA [Serratia symbiotica
           str. Tucson]
          Length = 216

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 65/221 (29%), Positives = 101/221 (45%), Gaps = 11/221 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             H      ++LY+D  I V NKP+G+    G  +  + D  L + + +     +  HRL
Sbjct: 3   PYHPPQEPMLILYQDQHIMVVNKPSGLLSVPGR-LPENKDSLL-TRIQADFPAAQAVHRL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG++VVA  +AA + L   FR R  +K Y + VWG     +  +A  L+       
Sbjct: 61  DMATSGVIVVALNKAAERELKRQFREREPKKYYIARVWGHLVQDEGVVALPLICD-WPNR 119

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               V          A + ++V+   A     +++ P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PRQKVCFDT---GRAAQTEYRVLSRDADGCTRVKLVPITGRSHQLRVHMLALGHPILGDG 176

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
            Y  +        +  +L LHA+ + L HP     +   A 
Sbjct: 177 FYAHSQAQA----LAQRLQLHAQTLHLTHPAFHTPMHFHAE 213


>gi|50312303|ref|XP_456184.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49645320|emb|CAG98892.1| KLLA0F24794p [Kluyveromyces lactis]
          Length = 597

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 105/253 (41%), Gaps = 23/253 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +  + +   +    +K + +G+V ++      ++ +++G ++      +  +   + 
Sbjct: 113 IDIFI-DEFRDRSPEYYRKTIAAGKVYLNDSVADLDSVVRNGDLITHEIHRHEPSVTSRL 171

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            K                   ++ED  + V +KP+GI V       Y  +   K     +
Sbjct: 172 IKT------------------VFEDDDLLVIDKPSGIPVHPTG--RYRFNTVTKILEKER 211

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+    A  + +  + R + K Y + V G        +  
Sbjct: 212 GYTVHPCNRLDRLTSGLMFLAKNPRGADRMADQMKAREVSKEYVARVVGEFPVGLIVVDK 271

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L       G  V   K  ++GA  A + F+ I  F  K   +  +P TGRTHQ+RVH  
Sbjct: 272 PLRTVDPKVGLNVT-CKITDEGAKEARTSFERI-SFDGKTSIVRCKPFTGRTHQIRVHLQ 329

Query: 261 HMGCPIVGDHKYC 273
           H+G PI  D  Y 
Sbjct: 330 HLGHPIANDPIYS 342


>gi|261378502|ref|ZP_05983075.1| tRNA pseudouridine synthase C [Neisseria cinerea ATCC 14685]
 gi|269145046|gb|EEZ71464.1| tRNA pseudouridine synthase C [Neisseria cinerea ATCC 14685]
          Length = 234

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 66/218 (30%), Positives = 101/218 (46%), Gaps = 8/218 (3%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y D +    NKPAGI V      +      +++  D  GQ     HRLD+ TSG+L
Sbjct: 2   LDIIYRDGRTVAVNKPAGILVHRSWLDSRETVFAMQTLRDQIGQHVYPVHRLDRPTSGVL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A    AA+ LT+ F  + I+K YW++V G   +              I   +   V Q
Sbjct: 62  LFALDTEAARLLTQQFEQKNIRKTYWAIVRGHLPSDGIIDYPLKYCPDKIAEAHTESVIQ 121

Query: 219 NEKGANYAISHFKV-----IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           + + A   I+  ++     +     ++ W E+ PHTGR HQLR H  H+  PIVGD  Y 
Sbjct: 122 DAQTACRCIARTELPFQSALRYPTSRYSWAELTPHTGRKHQLRRHMKHIFHPIVGDTNYG 181

Query: 274 ANFKGN--FTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
              + +         +L LHAR +    P+GG+  +TA
Sbjct: 182 DLRQNHAVAAHLGTQRLMLHARSLTFRSPDGGQ-TVTA 218


>gi|319935050|ref|ZP_08009493.1| hypothetical protein HMPREF9488_00324 [Coprobacillus sp. 29_1]
 gi|319810068|gb|EFW06437.1| hypothetical protein HMPREF9488_00324 [Coprobacillus sp. 29_1]
          Length = 301

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 58/291 (19%), Positives = 110/291 (37%), Gaps = 32/291 (10%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           H++   +  + ++    V+K+ V  +  +  G    +            + + +D     
Sbjct: 28  HLSKKTIHLLKQNKDYTVNKRFVSSSTILLKGDHFSVKAFQENDQLYPPQYEDID----- 82

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQK--PRLT 147
                     ++YED  + V NKP  +SV   +      +   + ++    G     R  
Sbjct: 83  ----------IIYEDEFLLVVNKPPFLSVFPDNLSHTDSLANRVSAYYQQCGYNIPVRYI 132

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KKECIANWLLKKS 206
           HRLD ET+G+ +  +       +     ++ IQ+ Y ++V G     K+  I   + +  
Sbjct: 133 HRLDYETTGLTLFCKCSFIQPLMDYQLSIKEIQRKYLAIVKGKLTGYKQHSICQPIGRDR 192

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           H     +            A ++++ I    Q    +E    TGR HQ+RVH   +G P+
Sbjct: 193 HHNQRMIV-----SSSGKRACTYYQCIATN-QDLSVVECTLDTGRKHQIRVHMSAIGHPL 246

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
           +GD  Y         S + N+  LHA  +   HP    ++ +    P  M 
Sbjct: 247 LGDCLYGEK------SHLMNRQALHAFQLIFTHPITKEKMTLICHPPVDMK 291


>gi|119477573|ref|ZP_01617723.1| putative 23S rRNA pseudouridylate 746 synthase [marine gamma
           proteobacterium HTCC2143]
 gi|119449076|gb|EAW30316.1| putative 23S rRNA pseudouridylate 746 synthase [marine gamma
           proteobacterium HTCC2143]
          Length = 223

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 56/208 (26%), Positives = 96/208 (46%), Gaps = 10/208 (4%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  ++Y+D    + NKP G+    G          +   +        L HRLD  TSGI
Sbjct: 17  EITVIYQDDSFLLINKPTGLLSLSGKHPRN--KDSVHYRLVQDFPTATLVHRLDFGTSGI 74

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA ++    +LT  F+ R ++K Y +L++G   +    I   + K      D   + K
Sbjct: 75  MLVALSKEVNGNLTRQFQARSVKKTYKALLYGEMADNSGVIDFPIAKD----KDNFPLQK 130

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              +    A++ ++VI+  A     +E  P +GRTHQLR+H+  +G PI+G   Y ++  
Sbjct: 131 ICYRDGKEAVTRYRVIEKIAGNCTKVEFTPSSGRTHQLRIHSREIGHPILGCDLYGSDEA 190

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRL 305
                    +L LHA  ++  HP  G +
Sbjct: 191 FVMAE----RLMLHATTLEFFHPATGEI 214


>gi|91202037|emb|CAJ75097.1| similar to pseudouridine synthase C [Candidatus Kuenenia
           stuttgartiensis]
          Length = 244

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 104/241 (43%), Gaps = 19/241 (7%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-----YHIDGFLKSWVD 138
           +    + +K        +LYED  I V +KPAG+   G          Y ++ +++    
Sbjct: 1   MPKKKHFSKRYHPRGLAILYEDEDILVIDKPAGLLTMGTDTNKTKTAYYMLNDYVRKGCV 60

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              +   + HRLD++ SG+L+ A+   +  +L   ++    +K Y ++V G    K   I
Sbjct: 61  KSRKHVFIIHRLDRDASGLLLFAKNIRSKLNLQSQWQN--TEKKYLTVVHGRLAKKAGTI 118

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           + +L +        V     + K    + + ++V+    + F  LE++  TGR +Q+RVH
Sbjct: 119 STYLAEN----KAQVVYSTSDTKKGKLSHTVYRVLK-ETKYFSLLEIKLLTGRKNQIRVH 173

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
              +G PIVGD KY              +L LHA  +   HP  G+ +      P +  K
Sbjct: 174 LTELGHPIVGDKKYGKE------KGAYKRLALHAYSISFKHPFSGKPITFETKAPGYFNK 227

Query: 318 T 318
            
Sbjct: 228 L 228


>gi|58336973|ref|YP_193558.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus NCFM]
 gi|227903532|ref|ZP_04021337.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus ATCC 4796]
 gi|58254290|gb|AAV42527.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus NCFM]
 gi|227868419|gb|EEJ75840.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus ATCC 4796]
          Length = 300

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 73/331 (22%), Positives = 130/331 (39%), Gaps = 42/331 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT +  ++V+  +         K  + H    N +     G + V+ KR   +  ++ G 
Sbjct: 1   MTSLFKLIVQERDPKKLGPFLLKKGFSHQALNNAKH--HHGMILVNHKRRYTSFNLKIGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V         N  +K             HS+     +L E     + NKPA +      
Sbjct: 59  EVIFVSGEEKKNQWLK-------------HSNNPVDPVL-ETKNYILVNKPANVLSIPSR 104

Query: 124 G-IAYHIDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                 I   L  +      K  KP +  RLD++TSG+++V +   A    ++  + + I
Sbjct: 105 YEDDDAIVNRLMGYFMEKKEKDLKPHVITRLDRDTSGLVLVGKNSIAHARFSKIGKEKFI 164

Query: 180 QKIYWSLVWGIPKNKK--ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +K + ++V G     K    I   + K          V +        A + ++V+D  +
Sbjct: 165 KKYH-AIVHGNFAEDKLEGLIDQPIGKID------AGVKRGVVLNGKSAQTEYRVLDQVS 217

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +E++  TGRTHQ+RVH +++G P+ GD  Y  +          ++  L+  Y+  
Sbjct: 218 -GASLVELRLLTGRTHQIRVHMMYLGHPLYGDPLYGIDDN-------FSRQALNCFYLSF 269

Query: 298 PHPEGGR---LQITAPLPAHMVKTWDSLGFK 325
           P P   +   ++I  PL   M K W  L +K
Sbjct: 270 PDPFDNKDKIIKIDDPL--DMRKLWQKLKYK 298


>gi|126174998|ref|YP_001051147.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125998203|gb|ABN62278.1| Pseudouridylate synthase [Shewanella baltica OS155]
          Length = 223

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 61/213 (28%), Positives = 102/213 (47%), Gaps = 8/213 (3%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        + Y+D  + + NKP+G+    G   A H      + + +   +  L HRLD
Sbjct: 7   QPPAVPWLDIRYKDRDLIIINKPSGLLSNPGR--AAHTFDCALTRLQTLFPETILVHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V AR + A  HL   F+ R+ +K+Y + V G    ++  I   +   +     
Sbjct: 65  CATSGIMVFARNKKAESHLKTQFQDRQSKKVYIAEVMGHVPQEQGMIDLAIAPDTEHP-P 123

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y   ++  E G   A+++++V++   +    +E+ P TGRTHQLRVH L +G  I+GD  
Sbjct: 124 YQKTLQAGETGGKSALTYYRVLERR-ENSTLVELSPETGRTHQLRVHMLALGHAILGDEF 182

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           Y            + +L LHA+ + L HP   +
Sbjct: 183 YG----DAEVIKAKPRLCLHAQSLCLTHPYSAK 211


>gi|262164736|ref|ZP_06032474.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus VM223]
 gi|262027116|gb|EEY45783.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus VM223]
          Length = 559

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 69/243 (28%), Positives = 111/243 (45%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ D+ + L+  +   +  ++Y+D  I V NKPA      G  +   +
Sbjct: 328 CQPILAHMLQGMELDDNPL-LSNPAADKEISIVYQDEAIVVVNKPAEFLSVPGVHVHDSV 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++   S+ +     HRLD  TSG+LV A TR A +HL + F  R +QK Y +++ G
Sbjct: 387 LTRLQAQF-SEAEGVFALHRLDMSTSGLLVFALTRRANKHLQKQFITRAVQKRYVAMLDG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              +++  I   L            V  Q       A++H++ +    Q    + + PHT
Sbjct: 446 TLADEQGEIELPLCGD-LDDRPRQKVCWQQ---GKPALTHWETV-AVEQGRTRVYLYPHT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVH  H   + CPIVGD  Y              +L+LHA  +   HP   + +
Sbjct: 501 GRTHQLRVHCAHHLGLNCPIVGDDLYGTQ---------DQRLHLHAEKLSFSHPYTKQPM 551

Query: 306 QIT 308
              
Sbjct: 552 TFE 554


>gi|322514814|ref|ZP_08067833.1| pseudouridine synthase A [Actinobacillus ureae ATCC 25976]
 gi|322119196|gb|EFX91337.1| pseudouridine synthase A [Actinobacillus ureae ATCC 25976]
          Length = 226

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 68/228 (29%), Positives = 105/228 (46%), Gaps = 14/228 (6%)

Query: 87  SVNLTKHSDFLKSIL--LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           ++ L ++   L+  L  +Y D+ I V NKP+G+    G+   Y+      + V  K    
Sbjct: 4   NMALIEYHPPLEPFLTEVYRDNHILVINKPSGLLSVPGNRPEYYDSAM--TRVQQKYGFT 61

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA--NWL 202
              HRLD  TSGIL+ A ++AA + L   FR R  +K Y +L+WG    K       N+ 
Sbjct: 62  EPAHRLDMATSGILLFALSKAAEKELKRQFREREPKKHYIALLWGKLGEKVGDTGEMNFP 121

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L           +  +       AI+H++V+         +++ P TGR+HQLRVH L +
Sbjct: 122 LICDWENRPRQKICYER---GKKAITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHLLAL 178

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           G PI+GD  Y           +  +L LHA  + + HP  G  +   A
Sbjct: 179 GHPILGDKFY----ANPLAKSLAPRLCLHAESLTITHPISGEVMTFNA 222


>gi|258624340|ref|ZP_05719289.1| conserved hypothetical protein [Vibrio mimicus VM603]
 gi|258583491|gb|EEW08291.1| conserved hypothetical protein [Vibrio mimicus VM603]
          Length = 559

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 69/243 (28%), Positives = 111/243 (45%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ D+ + L+  +   +  ++Y+D  I V NKPA      G  +   +
Sbjct: 328 CQPILAHMLQGMELDDNPL-LSNPAADKEISIVYQDEAIVVVNKPAEFLSVPGVHVHDSV 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++   S+ +     HRLD  TSG+LV A TR A +HL + F  R +QK Y +++ G
Sbjct: 387 LTRLQAQF-SEAEGVFALHRLDMSTSGLLVFALTRRANKHLQKQFITRAVQKRYVAMLDG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              +++  I   L            V  Q       A++H++ +    Q    + + PHT
Sbjct: 446 TLADEQGEIELPLCGD-LDDRPRQKVCWQQ---GKPALTHWETV-AVEQGRTRVYLYPHT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVH  H   + CPIVGD  Y              +L+LHA  +   HP   + +
Sbjct: 501 GRTHQLRVHCAHHLGLNCPIVGDDLYGTQ---------DQRLHLHAEKLSFSHPYTKQPM 551

Query: 306 QIT 308
              
Sbjct: 552 TFE 554


>gi|149204830|ref|ZP_01881792.1| pseudouridine synthase [Roseovarius sp. TM1035]
 gi|149141700|gb|EDM29755.1| pseudouridine synthase [Roseovarius sp. TM1035]
          Length = 214

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/223 (28%), Positives = 107/223 (47%), Gaps = 13/223 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
                     +L++D +I V NKPAG+    G G   H+   L + V        L HRL
Sbjct: 3   DYDPPTDPLEVLHDDHEIVVVNKPAGLLSVPGKG--EHLADCLMARVRDVFPTALLVHRL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D++TSG+++ A T  A +HL   F  R+ +K Y + VWG  + +   +   L+    +  
Sbjct: 61  DRDTSGVMIFALTPHAQRHLGLQFEKRQTRKTYVARVWGRLEPEVGVVDLPLI----VDW 116

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               + K   +    A++ ++V+   + +   + + P TGR+HQLRVH L +G  I+GD 
Sbjct: 117 PNRPLQKVCHETGRAALTEWRVL-RASDEESRVRLSPKTGRSHQLRVHMLALGHVILGDP 175

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            Y +            +L LH+  + L HP+GG  ++  A +P
Sbjct: 176 LYASGAAREHP-----RLMLHSEELRLRHPDGGAGVKFRAAVP 213


>gi|27364845|ref|NP_760373.1| ribosomal large subunit pseudouridine synthase A [Vibrio vulnificus
           CMCP6]
 gi|34395775|sp|Q8DCG0|RLUA_VIBVU RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|27360990|gb|AAO09900.1| Ribosomal large subunit pseudouridine synthase A [Vibrio vulnificus
           CMCP6]
          Length = 250

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 59/207 (28%), Positives = 96/207 (46%), Gaps = 8/207 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I   NKP+G+    G    +H    + S +  +  + ++ HRLD  TSG++V 
Sbjct: 16  IIFEDDHILAVNKPSGLLSVPGRLPEHHDS--MWSRLQEQYPEIQVVHRLDMSTSGLMVF 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ + A   L + F+ R   K+Y++ VWG  +     I   L+           V  ++ 
Sbjct: 74  AKNKRAEAALKKQFQYRLTHKVYYARVWGHVEADSGMIDLPLICD-WPNRPMQKVCHEHG 132

Query: 221 KGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           K +  A    K  +     +   + + P TGR+HQLRVH   +G PIVGD  Y       
Sbjct: 133 KPSQTAFQVAKREVHANGAQTTIMRLLPVTGRSHQLRVHMQALGHPIVGDEFYAQGDAFT 192

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           F+     +L LHA  +   HP+   L+
Sbjct: 193 FSE----RLELHAAELSFYHPKSHWLR 215


>gi|288803452|ref|ZP_06408884.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           melaninogenica D18]
 gi|288334062|gb|EFC72505.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           melaninogenica D18]
          Length = 571

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 70/253 (27%), Positives = 107/253 (42%), Gaps = 19/253 (7%)

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P +   L  I  + K  D + N T+        +LYED  + V  KP+ +    G G   
Sbjct: 329 PILEWMLEGIDVDDKECDRTNNETETVPSEGLKILYEDDYLAVVVKPSDMLSVPGKGCQP 388

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   L      K     + HRLD  TSG+LVVART    + L   F  R ++K Y +L+
Sbjct: 389 SVYSILSERWKGKS-DAFMVHRLDMATSGLLVVARTSEVHKALQAQFIERTVKKKYVALL 447

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-----FCW 242
                 K+      +     +  D     + +      AI+ +++I              
Sbjct: 448 PLSILEKQLPAEGRIELPLSLDPDDRPRQRVDRTNGKPAITEYRLIGKTTYGKETLKAVK 507

Query: 243 LEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +E+ P TGRTHQLRVH  H   +G PI+GD+ Y    +         +L+LHA +++  H
Sbjct: 508 IELYPLTGRTHQLRVHCAHPDGLGTPIIGDNLYGQRAE---------RLWLHAAHLEFTH 558

Query: 300 PEG-GRLQITAPL 311
           P    R+    PL
Sbjct: 559 PITQERMSFDTPL 571


>gi|237729353|ref|ZP_04559834.1| ribosomal large subunit pseudouridine synthase A [Citrobacter sp.
           30_2]
 gi|226909082|gb|EEH95000.1| ribosomal large subunit pseudouridine synthase A [Citrobacter sp.
           30_2]
          Length = 219

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 106/226 (46%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LDEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   L+       D+
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPAPAEGLVDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    A + ++V++  A     + ++P TGR+HQLRVH L +G PI+GD 
Sbjct: 120 PNRPKQKVCYETGKSAQTEYEVVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDR 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
            Y           +     LHA  + + HPE G  +     +PA  
Sbjct: 180 FYAPPEALALAPRLL----LHAEMLTITHPEYGNSMTFK--VPADF 219


>gi|218676955|ref|YP_002395774.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           splendidus LGP32]
 gi|218325223|emb|CAV27163.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           splendidus LGP32]
          Length = 570

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 65/242 (26%), Positives = 110/242 (45%), Gaps = 20/242 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +  L H++K  ++ D +  L   ++     +L++D  I V +KPAG     G  I    
Sbjct: 339 CVPILGHMMKGLEV-DPNPLLENPAEGKDLDILFQDDHIVVVHKPAGFLSVPGKTIKDSA 397

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++       + P + HRLD  TSGIL+ A TR A + L + F  R ++K Y +++ G
Sbjct: 398 YTRVQEM-HPDVEGPFVIHRLDMATSGILIFALTRRANKSLQKQFITREVEKRYVAMIEG 456

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           + +  +  +   L    +     +   +        A + ++VI+  +Q    + + P T
Sbjct: 457 VLEQDEGYVRLPLRGDLYDRPRQIVCFEH----GKPAETKWEVIER-SQDTTKVYLHPKT 511

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVH  H   +  PIVGD  Y             ++L+LHA  + L HP     +
Sbjct: 512 GRTHQLRVHCSHEEGLNMPIVGDGLYGNK---------ADRLHLHAERLALHHPVTKEWM 562

Query: 306 QI 307
           + 
Sbjct: 563 EF 564


>gi|319425230|gb|ADV53304.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 225

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/215 (29%), Positives = 108/215 (50%), Gaps = 16/215 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G   A++    + + V ++    ++ HRLD  TSG++V+
Sbjct: 16  ILYQDKDIIVINKPSGLLSVPGRDPAHYDS--VYARVKAEHPHCQIVHRLDMATSGVIVL 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R+A + L   F  R   K Y + V G  K+    I   L+       D+ +  KQ  
Sbjct: 74  ALIRSAERELKRQFHDRETSKTYIARVAGHIKHDTGSIDYPLI------CDWPNRPKQKV 127

Query: 221 KG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  +++H++V+   A++   +++ P TGR+HQLRVH + +G PI+GD  Y      
Sbjct: 128 DHFVGKPSLTHYQVMSR-AKRSTLVKLTPITGRSHQLRVHMMAIGHPILGDGFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           +    +  +L LHA  + + HP  G  +  +A  P
Sbjct: 187 S----LAPRLLLHAAELTIKHPYTGVSMTFSAEAP 217


>gi|261251312|ref|ZP_05943886.1| pseudouridylate synthase LSU rRNA-specific [Vibrio orientalis CIP
           102891]
 gi|260938185|gb|EEX94173.1| pseudouridylate synthase LSU rRNA-specific [Vibrio orientalis CIP
           102891]
          Length = 559

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 110/242 (45%), Gaps = 20/242 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   + D+ +     ++  +  +L+ED  + V NKP+G+    G  I    
Sbjct: 328 CQPILGHMMQGMLVDDNPLE-ENWAEDKELEILFEDESMVVVNKPSGLLSVPGKTITDSA 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+       + P + HRLD  TSG+LV A T+ A + L + F  R ++K Y +L+ G
Sbjct: 387 YTRLQQRY-PDVEGPFVIHRLDMATSGLLVFALTKRANKSLQKQFISRSVKKRYVALLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +  +  I N  ++   +      V  ++      A +H++ I     +     + P T
Sbjct: 446 SVEETQGDI-NLPMRGDPVDRPRQLVCYEH---GKPAETHWEAISTIDNRTKLY-LYPKT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH  H   +  P+VGD  Y             ++L+LHA  ++  HP  G RL
Sbjct: 501 GRTHQLRVHCAHHLGLNIPMVGDTLYGEK---------ADRLHLHAERLEFDHPYSGERL 551

Query: 306 QI 307
             
Sbjct: 552 TF 553


>gi|257438416|ref|ZP_05614171.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Faecalibacterium prausnitzii A2-165]
 gi|257198995|gb|EEU97279.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Faecalibacterium prausnitzii A2-165]
          Length = 305

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 63/330 (19%), Positives = 119/330 (36%), Gaps = 53/330 (16%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V  + + + L  + +            K   SG    D   +  N R+Q+GQ +R     
Sbjct: 7   VPLEADGVLLRGFLRRCAVSTELARAVKFHGSGF-FADDAPILANRRVQAGQTIRF---- 61

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHID 130
                       L +  +  +    +   ++YED+   V  KP  ++V    +     + 
Sbjct: 62  -----------ALPADGSGVEPQPEIPVRVVYEDAFAVVLEKPPHLAVHPTLNYPRDTLA 110

Query: 131 GFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               +W  + G+ P  R  +R+D++TSG+++ A+   AA  L E      ++K+Y+++V 
Sbjct: 111 NGYAAWAVAHGESPVFRPVNRIDKDTSGLVLAAKNGYAAPLLAE-----GVEKLYYAIVE 165

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        I   + ++         + +        + + + ++   AQ        P 
Sbjct: 166 GELPLGPGVIDAPIGRRGD-----SIIGRCVTPEGKPSRTEYTIL-RAAQGLSLAACVPV 219

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-------- 300
           TGRTHQ+R H   +G P+ GD  Y  +           +  LH        P        
Sbjct: 220 TGRTHQIRAHFASIGHPLAGDDLYGGHRDR------IARQALHCARQSFRVPAYTEVPGG 273

Query: 301 ---------EGGRLQITAPLPAHMVKTWDS 321
                        + + +PLP  M    D+
Sbjct: 274 IRLETPVGEHARTIAVESPLPEDMRALLDA 303


>gi|300715284|ref|YP_003740087.1| ribosomal large subunit pseudouridine synthase A [Erwinia
           billingiae Eb661]
 gi|299061120|emb|CAX58227.1| Ribosomal large subunit pseudouridine synthase A [Erwinia
           billingiae Eb661]
          Length = 217

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 107/231 (46%), Gaps = 17/231 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G  +  H D  + + V          
Sbjct: 1   MEPYNPPQEPWLHILYQDEHIMVINKPSGLLSVPGR-LEDHKDSVM-TRVQRDFPAAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  QK Y + +WG P+  K  +   L+    
Sbjct: 59  HRLDMATSGVIVVALTKAAERELKRQFREREPQKQYVARIWGHPEKAKGLVDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V+D        ++++P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCFETGKSAQTEYEVLDYADDNSARIQLKPITGRSHQLRVHMLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
           I+GD+ Y  +           +L LHA  + + HP+    +      PA  
Sbjct: 173 ILGDNFYAHDEAKAMA----PRLQLHAEMLTITHPQYHTPMTFRQ--PADF 217


>gi|296388259|ref|ZP_06877734.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           aeruginosa PAb1]
          Length = 211

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 61/216 (28%), Positives = 107/216 (49%), Gaps = 11/216 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  ++++D  + V +KP  +    G       D  +    ++   + R+ HRLD ETSG+
Sbjct: 5   QIRIVHQDDALLVVDKPTLLLSVPGRADDN-KDCLVTRLQENGYPEARIVHRLDWETSGL 63

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+AR   + + L+  F  R  +K Y +L WG+P+     I   L         +V    
Sbjct: 64  MVLARDADSHRELSRQFHDRETEKAYTALCWGLPELDSGRIELPLRYDPPTKPRHV---- 119

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +   +A++ ++V++   +++  +E+ P TGR+HQLRVH L +G P++GD  Y     
Sbjct: 120 VDFEHGRHALTFWRVVERH-ERWSRVELTPITGRSHQLRVHMLSIGHPLLGDRLY----A 174

Query: 278 GNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                    +L LHA  + L HP  G RL+  +P P
Sbjct: 175 NPEALVAHERLCLHASLLCLTHPQSGERLRFESPAP 210


>gi|256847649|ref|ZP_05553094.1| pseudouridine synthase [Lactobacillus coleohominis 101-4-CHN]
 gi|256715338|gb|EEU30314.1| pseudouridine synthase [Lactobacillus coleohominis 101-4-CHN]
          Length = 305

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 65/286 (22%), Positives = 109/286 (38%), Gaps = 29/286 (10%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           QV ++      N  +  G+ V +  V +         +   S +            +L+E
Sbjct: 44  QVLINGDYRNMNEPVAPGEQVTLKFVGDEFRTPTSNYQPTSSPM----------LDILFE 93

Query: 105 DSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           +  + V NKPAG        +    +   +  +++       + HR+DQ TSG ++VA+ 
Sbjct: 94  NRDLLVVNKPAGQKTHPNQPLETGTLMNDVAGYLEGSSAAAYMVHRIDQATSGAVIVAKN 153

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
                 L       +I + Y ++V G    K       +                N   A
Sbjct: 154 PVVVPILDHYIAAGKIHRRYVAVVEGTFAQKGGRFNWPIGFNPTDQRKR----CVNGLKA 209

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
             A++ ++V+   +     +++Q  TGRTHQ+RVH  H G PIVGD  Y           
Sbjct: 210 KPAVTDYQVLQT-SDNLSLVQLQLQTGRTHQIRVHLAHSGHPIVGDPLYNGQPN------ 262

Query: 284 IQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFKYDR 328
             +++ LH     L  P    L +I APLP +          KYD+
Sbjct: 263 --SRMLLHGIAQQLIVPFKKTLREIYAPLPNYFPPAL----VKYDQ 302


>gi|114797970|ref|YP_759136.1| RNA pseudouridine synthase family protein [Hyphomonas neptunium
           ATCC 15444]
 gi|114738144|gb|ABI76269.1| RNA pseudouridine synthase family protein [Hyphomonas neptunium
           ATCC 15444]
          Length = 215

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 57/212 (26%), Positives = 99/212 (46%), Gaps = 12/212 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D  + + +KP+G+    G G+         + V ++       HRLD  TSG+L++A
Sbjct: 14  IYRDDHLILIDKPSGLLSVPGRGVD--KADCAITRVQAEFPDALTVHRLDMATSGLLLMA 71

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R++   + L+  F    ++K Y + VWG+P   +  I   L+           + K + +
Sbjct: 72  RSKEIQRALSGLFERGEVEKSYLADVWGVPAPARGEIDLPLI----TDWPNRPLQKVDHE 127

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               + + ++ ++  +     L++ P TGR+HQLRVH   +G PI+GD  Y A       
Sbjct: 128 IGKPSRTLYETLNPQS-AHTRLKLTPLTGRSHQLRVHLAAIGHPILGDEFYAAGE----A 182

Query: 282 SPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
              + +L LHA  +   HP  G R+    P P
Sbjct: 183 LTARPRLALHAARLAFAHPVTGERMDFELPCP 214


>gi|254883850|ref|ZP_05256560.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           4_3_47FAA]
 gi|254836643|gb|EET16952.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           4_3_47FAA]
          Length = 538

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 112/230 (48%), Gaps = 19/230 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ + L KH   +   ++YED+ + V NKPAG+    G G    +
Sbjct: 325 CGPILGHMLQGLEVEENPL-LKKHYHEMPLEIVYEDNYLVVINKPAGMLSVPGKGEIDSV 383

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K         P + HRLD  TSG+L++A+ +   QHL   F+ R I+K Y +L+ G
Sbjct: 384 YQHIKILYPDTT-GPLIVHRLDMATSGVLLIAKNKEVHQHLQAQFKNRMIKKRYIALLDG 442

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              +K+  I   L +   +      V   + +    AI+ ++V++   +    +   P T
Sbjct: 443 KISSKEGTIILPL-RMDPLDRPRQVV---DHEHGKTAITQYQVLNEQ-EGNTLIAFYPLT 497

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           GRTHQLRVHA H   + CPI GD  Y             ++LYLHA  ++
Sbjct: 498 GRTHQLRVHAAHPEGLHCPIRGDELYGQK---------ADRLYLHAESLE 538


>gi|163755046|ref|ZP_02162167.1| guanosine 5'-monophosphate oxidoreductase [Kordia algicida OT-1]
 gi|161325113|gb|EDP96441.1| guanosine 5'-monophosphate oxidoreductase [Kordia algicida OT-1]
          Length = 231

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 71/220 (32%), Positives = 107/220 (48%), Gaps = 14/220 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I + NK AG  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 13  VLYEDNHIIIVNKRAGDIVQGDKTGDKPLSDVVKEYIAEKYNKPGNVFLGVVHRLDRPTT 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V ART  A   L + F  ++ +K YW++V  +P  +++ + +WL K           
Sbjct: 73  GIIVFARTSKALPRLNKLFAEKKAKKTYWAIVNNMPPKQQDTLIHWLRKNPKNNKS--TA 130

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   G+  AI  + V      ++  LE+  HTGR HQ+R     +GC I GD KY  +
Sbjct: 131 FNKEIPGSKKAILDYTV-QKKLDRYVLLEIALHTGRHHQIRTQLSAIGCKIKGDLKYGFD 189

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
                 S     ++LHAR +   HP     L+I APLP  
Sbjct: 190 RSNKDAS-----IHLHARKLVFTHPVKKELLEIIAPLPND 224


>gi|262377519|ref|ZP_06070741.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter lwoffii
           SH145]
 gi|262307575|gb|EEY88716.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter lwoffii
           SH145]
          Length = 235

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 108/231 (46%), Gaps = 13/231 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + +           ++YED  + V  KPAG+    G    +H   +L+  V  K  +
Sbjct: 15  MPINNDFVYCPPQEPLHIVYEDDDLVVIEKPAGLLSVPGRLPEHHDSAYLR--VLDKYPQ 72

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSGIL+ A+ R A   +++ F+ R + K Y +LV G  + +       + 
Sbjct: 73  AKITHRLDMATSGILMFAKHRDAEVAVSKMFQARTVLKNYVALVQGKLEGEGSVEVPLIT 132

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +    A + ++ ++   Q     + + P TGR+HQLRVH LH+
Sbjct: 133 DWENRPRQMVHF-----ELGKAAKTLYQALEYLPQQDISRVLLTPITGRSHQLRVHMLHI 187

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           G PI GD  Y    + +      N++ LHA Y+    P  G  ++I A +P
Sbjct: 188 GHPITGDKIYHPEPQRS----PLNRMALHASYLAFTQPLSGVPVEIKAAIP 234


>gi|305667192|ref|YP_003863479.1| putative ribosomal large subunit pseudouridine synthase [Maribacter
           sp. HTCC2170]
 gi|88708126|gb|EAR00364.1| putative ribosomal large subunit pseudouridine synthase [Maribacter
           sp. HTCC2170]
          Length = 230

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 67/220 (30%), Positives = 103/220 (46%), Gaps = 14/220 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-----HRLDQETS 155
           +LYED+ +   NK  G  VQG       +   +K ++  K  KP        HRLD+ TS
Sbjct: 13  ILYEDNHLIAINKRPGDIVQGDKTGDNPLSDIVKQYIKEKYNKPGNVYLGVPHRLDRPTS 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A++  A   L + F  +  +K YW++V   P ++ + + +WL + +     Y + 
Sbjct: 73  GIVVFAKSSKALPRLNKLFAEKEAKKTYWAIVKNQPPSQADQLVHWLKRNTRQNKSYAN- 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+    +  AI  +K I      +  LE+   TGR HQ+R     +G PI GD KY  +
Sbjct: 132 -KKEVPDSKKAILEYK-IRKKLNSYFLLEIDLKTGRHHQIRAQLTAIGSPIKGDLKYGFD 189

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
                 S     ++LHAR +   HP     L+I AP P  
Sbjct: 190 RSNKGGS-----IHLHARKLSFIHPVKKEPLEIVAPTPND 224


>gi|26553585|ref|NP_757519.1| pseudouridine synthase [Mycoplasma penetrans HF-2]
 gi|26453591|dbj|BAC43923.1| pseudouridine synthase [Mycoplasma penetrans HF-2]
          Length = 298

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 73/315 (23%), Positives = 132/315 (41%), Gaps = 32/315 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            RLD    + +  ++    +  + +  V V+ K + K N ++                 I
Sbjct: 5   QRLDILVSSKFS-LSRSIAKHKIENNLVTVNGKIISKPNTKV-----------DEESEII 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSW 136
           +KE+KI++ +  LT     ++  ++YED  I + NKP  I V   S  ++  +   +K  
Sbjct: 53  LKEEKIVEETKVLTPWKKDIE--IVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYI 110

Query: 137 VDSKGQK-------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            DSK  K         + HRLD+ T G+++VA++  +    T+ F  ++I+K Y +L+  
Sbjct: 111 FDSKKIKYNGDPLRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHN 170

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             + +   +   + +        V      +  A  A + FK I+ + + F   E++  T
Sbjct: 171 HLQTRTVEVDAPIKRVETSTRREVSR----DIDAKEARTIFKEINKY-KNFTLAEVELFT 225

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
           GRTHQ+RVHA  +   ++ D  Y        T       YL A  +   HP     + I 
Sbjct: 226 GRTHQIRVHAEFIKNHVINDPIYGPKHINKTTKYG---QYLVAYKLKFIHPFTQKEVNIN 282

Query: 309 APLPAHMVKTWDSLG 323
             +P    +     G
Sbjct: 283 LDMPKEFKEYIKKYG 297


>gi|259907390|ref|YP_002647746.1| 23S rRNA/tRNA pseudouridine synthase A [Erwinia pyrifoliae Ep1/96]
 gi|224963012|emb|CAX54495.1| Ribosomal large subunit pseudouridine synthase A [Erwinia
           pyrifoliae Ep1/96]
 gi|283477223|emb|CAY73130.1| ribosomal large subunit pseudouridine synthase A [Erwinia
           pyrifoliae DSM 12163]
          Length = 217

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 66/215 (30%), Positives = 103/215 (47%), Gaps = 14/215 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G  +A + D  + + V          
Sbjct: 1   MEPYNPPPEPWLHVLYQDEHIIVVNKPSGLLSVPGR-LAEYKDSVM-TRVQRDYPAAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  QK Y + VWG P+     +   L+    
Sbjct: 59  HRLDMATSGVMVVALTKAAERELKRQFREREPQKTYVARVWGHPQPATGLVDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ         A + ++V+D  +     ++++P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCFDSGKSAQTEYQVLDYASDNSARVQLKPITGRSHQLRVHMLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           ++GD+ Y  +           +L LHA  + + HP
Sbjct: 173 MLGDNFYAHDEARAMA----PRLQLHAESLSITHP 203


>gi|260771000|ref|ZP_05879929.1| ribosomal large subunit pseudouridine synthase A [Vibrio furnissii
           CIP 102972]
 gi|260614237|gb|EEX39427.1| ribosomal large subunit pseudouridine synthase A [Vibrio furnissii
           CIP 102972]
 gi|315179046|gb|ADT85960.1| ribosomal large subunit pseudouridine synthase A [Vibrio furnissii
           NCTC 11218]
          Length = 259

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 58/207 (28%), Positives = 98/207 (47%), Gaps = 11/207 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++ED  I   NKP+G+    G    +H    + S + ++  + ++ HRLD  TSG+++
Sbjct: 29  DVVFEDDYILAVNKPSGLLSVPGRLAEHHDS--MWSRLQAQYPEIQVVHRLDMSTSGLML 86

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+ +     L + F+ R   KIY++ VWG+    +  I   L+         +      
Sbjct: 87  FAKDKYMEAALKKQFQYRLTHKIYYARVWGVMAQDEGEIDLPLICDWPNRPKQMVC---- 142

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            +    + + F+V+   A     + + P TGR+HQLRVH   +G PIVGD  Y      +
Sbjct: 143 HETGKPSQTLFQVVKREAH-TTVVRLLPITGRSHQLRVHMQALGHPIVGDEFYAPQEAID 201

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           FT    ++L LHA  +   HP    L+
Sbjct: 202 FT----DRLALHAAELSFYHPRSHWLR 224


>gi|261344629|ref|ZP_05972273.1| pseudouridine synthase A [Providencia rustigianii DSM 4541]
 gi|282567545|gb|EFB73080.1| pseudouridine synthase A [Providencia rustigianii DSM 4541]
          Length = 232

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 59/211 (27%), Positives = 94/211 (44%), Gaps = 16/211 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP+G+    G          +   +     +  L HRLD  TSG++VVA
Sbjct: 20  LYQDDHLILINKPSGLLSLSGKNPQN--LDSVHHRMVKIFPECTLVHRLDFGTSGLMVVA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L   F  R + K+Y +L+ G   + +  I   + K   +      ++  +  
Sbjct: 78  RNKAINAALCHQFSQRTVGKMYSALLCGHLDDDEGVIDAPIAKDPAL----FPLMSISAI 133

Query: 222 GANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               A SH++VI+ F +            +++ P TGRTHQLR+H   +G PI+G   Y 
Sbjct: 134 NGKPARSHYRVIERFYRELDDGGQLPLTRVQLTPETGRTHQLRIHCQLLGHPILGCDLYG 193

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                   +    +L LHA  +D  HP  G 
Sbjct: 194 GRLL--LGTEQTPRLMLHACELDFIHPVTGE 222


>gi|325957347|ref|YP_004292759.1| ribosomal protein large subunit [Lactobacillus acidophilus 30SC]
 gi|325333912|gb|ADZ07820.1| ribosomal protein large subunit [Lactobacillus acidophilus 30SC]
          Length = 285

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 71/314 (22%), Positives = 119/314 (37%), Gaps = 36/314 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M Y   +    + + + ++   +     I     +  LR    V ++ K   FN  ++ G
Sbjct: 1   MVYNFTLFYPKNLDPLPVNEVLRKLL--IPR-KWRHYLRIEQNVTINGKYRYFNELVKPG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I      L+ I         S+  T  +      ++YED  + + NK  G      
Sbjct: 58  DKIDI-----VLDQI--------DSMQQTYPASRRMPDVIYEDDNLLIINKKKGQKTHPN 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  D  L       G  P + HRLD  T G+L+VA+  A    L      +   + 
Sbjct: 105 ---LNETDTALNDCATYLGSSPYIVHRLDMLTGGLLLVAKNPAVVPILNRELTTKTFHRE 161

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V    K  K   I   + +        +       K   +A++H++++  ++    
Sbjct: 162 YLAKVIHADKLKKNGTIDLPISQDPDDQRKRMV-----NKTGLHAVTHYELLKKYSDNTA 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++   TGRTHQ+RVH   +GCPIVGD  Y  +F G         L L A  + L  P 
Sbjct: 217 LVKLTLETGRTHQIRVHLAAIGCPIVGDPLYNPDFAGEN-------LALDAYEISLIKPF 269

Query: 302 G-GRLQITAPLPAH 314
              +L +   LP  
Sbjct: 270 SFEKLHVK--LPDE 281


>gi|34499206|ref|NP_903421.1| pseudouridine synthase A [Chromobacterium violaceum ATCC 12472]
 gi|34105057|gb|AAQ61413.1| pseudouridine synthase A [Chromobacterium violaceum ATCC 12472]
          Length = 225

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 102/230 (44%), Gaps = 14/230 (6%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           ++            ++Y D  + V +KP+G+    G G        L S           
Sbjct: 5   NLEHYNPPPDTGLDVIYADDCLLVLDKPSGLLSVPGRGED--KADCLISRAQKVYPDALT 62

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD +TSG++V+ R     + L+ +F  R+++K Y ++V GI ++    I   L+   
Sbjct: 63  VHRLDMDTSGLVVMGRGPEMQRALSIAFMDRKVKKRYIAVVDGIIESNSGTIDLPLI--- 119

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHM--G 263
            I        K +      AI+H++VI     +    +E+ P TGR HQLR+H L++  G
Sbjct: 120 -IDWPNRPRQKVDFDQGKEAITHYRVILRDTGRNISRVELDPQTGRAHQLRMHMLNLESG 178

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
            PI+GD  Y             ++L LHA  + L HP     ++  AP P
Sbjct: 179 HPILGDTIYAPPEALAKA----DRLLLHASRLVLRHPVTFEEMEFEAPAP 224


>gi|328542499|ref|YP_004302608.1| Pseudouridylate synthase for 23S rRNA [polymorphum gilvum
           SL003B-26A1]
 gi|326412246|gb|ADZ69309.1| Pseudouridylate synthase for 23S rRNA [Polymorphum gilvum
           SL003B-26A1]
          Length = 223

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/221 (28%), Positives = 106/221 (47%), Gaps = 12/221 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +L+ D  I V  KP+G+    G G  +     L+S    +  + R+ HRLD 
Sbjct: 13  PPREPRLDVLHADDDILVVVKPSGLLSVPGKGEGH--ADCLESRARERFAQARIVHRLDM 70

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG++V+A   AA +HL   F  RR  K Y + +WG  + +   +   L+         
Sbjct: 71  DTSGVMVLALNAAAHRHLGLQFERRRTAKAYVARLWGELEGEAGEVDLPLVCD----WPN 126

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             + K   +    A++ ++V+    +    + + P TGR+HQLRVH L +G PI+GD+ Y
Sbjct: 127 RPMQKVCVETGRPALTRWQVLARQ-RGVTRVRLMPVTGRSHQLRVHMLSLGHPILGDNLY 185

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLP 312
             +   +      ++L LHA  +++ HP  GR     AP P
Sbjct: 186 AHDDALSAA----DRLQLHAEDLEIHHPADGRRCAFHAPCP 222


>gi|86145699|ref|ZP_01064028.1| putative ribosomal large chain pseudouridine synthase A [Vibrio sp.
           MED222]
 gi|85836398|gb|EAQ54527.1| putative ribosomal large chain pseudouridine synthase A [Vibrio sp.
           MED222]
          Length = 570

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 65/242 (26%), Positives = 110/242 (45%), Gaps = 20/242 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +  L H++K  ++ D +  L   ++     +L++D  I V +KPAG     G  I    
Sbjct: 339 CVPILGHMMKGLEV-DPNPLLENPAEGKDLDILFQDDHIVVVHKPAGFLSVPGKTIKDSA 397

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++       + P + HRLD  TSGIL+ A TR A + L + F  R ++K Y +++ G
Sbjct: 398 YTRVQEM-HPDVEGPFVIHRLDMATSGILIFALTRRANKSLQKQFITREVEKRYVAMIEG 456

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           + +  +  +   L    +     +   +        A + ++VI+  +Q    + + P T
Sbjct: 457 VLEQDEGYVRLPLRGDLYDRPRQIVCFEH----GKPAETKWEVIER-SQDTTKVYLHPKT 511

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVH  H   +  PIVGD  Y             ++L+LHA  + L HP     +
Sbjct: 512 GRTHQLRVHCSHEEGLNMPIVGDGLYGNK---------ADRLHLHAERLALHHPVTKEWM 562

Query: 306 QI 307
           + 
Sbjct: 563 EF 564


>gi|91214528|ref|ZP_01251501.1| ribosomal large subunit pseudouridine synthase D [Psychroflexus
           torquis ATCC 700755]
 gi|91186955|gb|EAS73325.1| ribosomal large subunit pseudouridine synthase D [Psychroflexus
           torquis ATCC 700755]
          Length = 229

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/220 (27%), Positives = 104/220 (47%), Gaps = 14/220 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +++ED+ + V NK  G  VQG       +   +K ++  K  KP      + HRLD+ TS
Sbjct: 10  VIFEDNHLIVINKRPGDIVQGDKTGDLPLSEVVKLYLKEKYNKPGEAYLGVVHRLDRPTS 69

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ++T  A   L ++F  R   K+YW++V   PK +   + ++L + +     Y H+
Sbjct: 70  GVVVFSKTSKALSRLNKAFADRDTHKVYWAVVKNKPKPESARLVHYLKRNTKQNKSYAHI 129

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  + +  A+  ++ I          E+   TGR HQ+R     +GCPI GD KY  +
Sbjct: 130 --KPVEDSKEAVLSYQKIQSLDNYHVL-EITLETGRHHQIRSQLSAIGCPIKGDLKYGFD 186

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
                 S     ++LH++ + + HP     +   A LP  
Sbjct: 187 RSNKNAS-----IHLHSKKLTITHPVRKEDISFEAKLPDD 221


>gi|332970317|gb|EGK09309.1| tRNA pseudouridine synthase C [Kingella kingae ATCC 23330]
          Length = 252

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 99/236 (41%), Gaps = 18/236 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L +     V NKPAG+ V      +      +++  D  GQ     HRLD+ TSG ++ 
Sbjct: 4   ILTQTEHYVVVNKPAGMLVHRSRLDSQETVFLMQTLRDQLGQLVYPVHRLDKPTSGAMLW 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    AA+  T+ F  ++I+K Y ++V G       CI   L            +  Q++
Sbjct: 64  ALNSEAARWFTQQFEQKQIRKHYLAIVRG-WTENVGCIDYPL---KEQLDKIADMHAQSD 119

Query: 221 KGANYAISHFKVIDCF-----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           K A  A + ++ +                ++  L + P TGR HQ+R H  H+  PIVGD
Sbjct: 120 KTAQAACTEYQTLQRSECPFASSARYATSRYSLLHITPKTGRKHQIRRHMKHIFHPIVGD 179

Query: 270 HKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             +    +    +      +L LHA  +    P   + + I AP  +   +T  +L
Sbjct: 180 TTHGDLHQNQAVNQFCSNRRLLLHASSLHFTDPISQQNISIHAPTDSAWQQTQAAL 235


>gi|282931619|ref|ZP_06337112.1| pseudouridine synthase YjbO [Lactobacillus jensenii 208-1]
 gi|281304230|gb|EFA96339.1| pseudouridine synthase YjbO [Lactobacillus jensenii 208-1]
          Length = 290

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 57/319 (17%), Positives = 118/319 (36%), Gaps = 42/319 (13%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +++  RL  +       ++   +     +G  + V+ +R   N  +++G  V        
Sbjct: 3   EKDPKRLGLFLSK--KKLSKQVIVNAKHNGGMLLVNHRRRFTNFMLKNGDEVLFVMGKEK 60

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGF 132
           +N  +K                     ++ E     V NKPA +            +   
Sbjct: 61  VNEFLK--------------PSNKPIEIVLETDNYLVINKPANVLSIPSRYEDGDAVVNR 106

Query: 133 LKSWVDSK------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +  +   K        KP +  RLD++TSG+++V +   A    +E  +   +++ + ++
Sbjct: 107 VMGYFSKKKSSEQAFLKPHIVTRLDRDTSGLVLVGKNAVAHSKFSELKKDVFVKEYH-AI 165

Query: 187 VWGI--PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           V     P+ +   I   + K       YV            +++ ++V+    +    ++
Sbjct: 166 VHSNFNPEEQAGLIDAPIGKIDDSVKRYVI------PNGQKSLTQYEVL-AQKEGASLVK 218

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
           ++  TGRTHQ+RVH  H+G P+ GD  Y  +           +  L+  ++  P P    
Sbjct: 219 LRLFTGRTHQIRVHMAHIGHPLFGDKLYGIDDN-------FARQALNCSHLSFPDPFTNE 271

Query: 304 RLQITAPLPAHMVKTWDSL 322
              +    P  M   W +L
Sbjct: 272 EKIVEVSDPQDMTDLWRNL 290


>gi|227114231|ref|ZP_03827887.1| ribosomal large subunit pseudouridine synthase A [Pectobacterium
           carotovorum subsp. brasiliensis PBR1692]
          Length = 217

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 65/216 (30%), Positives = 100/216 (46%), Gaps = 14/216 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G     H D  + + + +        
Sbjct: 1   MEPYNPPTDPWLHILYQDQHIMVVNKPSGLLSVPGRAPE-HKDSVM-NRIQADYPTAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++ VA T+AA + L   FR R  +K Y + VWG     +  I   L+    
Sbjct: 59  HRLDMATSGVIAVALTKAAERELKRQFREREPKKSYLARVWGHMAQDEGVIDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V+   A     +++ P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCFETGKAAQTEYQVLSRDADGTTRVKLMPITGRSHQLRVHLLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           I+GD  Y           +  +L LHA+ + + HPE
Sbjct: 173 ILGDGFYAHPDAKA----LAPRLLLHAQELAITHPE 204


>gi|28899453|ref|NP_799058.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|260363379|ref|ZP_05776231.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
 gi|260879313|ref|ZP_05891668.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|260895728|ref|ZP_05904224.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|34395765|sp|Q87LD3|RLUA_VIBPA RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|28807689|dbj|BAC60942.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|308087397|gb|EFO37092.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|308093125|gb|EFO42820.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|308111223|gb|EFO48763.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
          Length = 250

 Score =  167 bits (423), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 107/231 (46%), Gaps = 15/231 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++ED  I   NKP+G+    G    +H    + S +  +    ++ HRLD  TSG++V
Sbjct: 15  DIVFEDDHILAVNKPSGLLSVPGRLAEHHDS--MWSRLQEEYPDIQVVHRLDMSTSGLMV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A   L + F+ R   KIY++ VWG  + ++  I   L+           V  ++
Sbjct: 73  LAKNKRAESALKKQFQFRLTHKIYYARVWGHVEQEEGEIDLPLICD-WPNRPLQKVCFED 131

Query: 220 EKGANYAISHFKVIDCFAQ----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K +    + F+V     Q    K   + + P TGR+HQLRVH   +G PIVGD  Y   
Sbjct: 132 GKPSK---TLFQVAKREEQEDGTKTTIVRLLPITGRSHQLRVHMQALGHPIVGDEFYATE 188

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
               F+     +L LHA  +   HP+   L+ +  +P       + + F Y
Sbjct: 189 EAKVFSE----RLELHASELSFYHPKSHWLR-SIFVPCDFYPEAEEMIFDY 234


>gi|88797409|ref|ZP_01112999.1| putative 23S rRNA pseudouridylate 746 synthase [Reinekea sp.
           MED297]
 gi|88780278|gb|EAR11463.1| putative 23S rRNA pseudouridylate 746 synthase [Reinekea sp.
           MED297]
          Length = 223

 Score =  167 bits (423), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 60/222 (27%), Positives = 105/222 (47%), Gaps = 13/222 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   +++ED  + V NKP+G+    G          + + +  +    R+ HRLD 
Sbjct: 12  PPCLDDIEIVHEDDALLVINKPSGLLALSGKDPRNRDS--VHARLVKRCPSIRMIHRLDF 69

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V+A+++  A  L   F+ R + K+Y +++WG   N    I   + +      D 
Sbjct: 70  GTSGLMVLAKSKTMATTLNRQFQQREVTKVYQAILWGQLANASGRINAHIARD-----DE 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                +  +G   A + ++V+    +     +E  P TGRTHQLR+H+ H+G PI+G   
Sbjct: 125 NFPKMRIGEGGKPAQTDYQVLVTDMRANTSTVEFYPRTGRTHQLRIHSAHIGHPILGCDI 184

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y        ++   ++L LHA  + L HPE  + L+  +P P
Sbjct: 185 YGTQ----ASTQAASRLLLHATELTLKHPETDQLLRFQSPRP 222


>gi|332664097|ref|YP_004446885.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
 gi|332332911|gb|AEE50012.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
          Length = 237

 Score =  167 bits (423), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 71/239 (29%), Positives = 114/239 (47%), Gaps = 13/239 (5%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
            +       + +   +LY+++++  FNKPAGI  Q            L+          +
Sbjct: 6   ETPESVNAQERIGDWVLYKNNQLIAFNKPAGIPTQTDKTGD---KSLLQLAEIFTKSAVQ 62

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+  SGI++V++T  A  +L E FR R+IQK Y ++V  +P   K  + +W+ K 
Sbjct: 63  LVHRLDRPASGIVLVSKTAKALANLNEQFRNRQIQKTYLAVVEALPAEPKGRLEHWIWKN 122

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                  V   ++    A  AI  ++++   + ++  LE++  TGR HQ+R     MGC 
Sbjct: 123 GQTNRS-VISTEKGHANAQEAILEYQLLGS-SDRYHLLEVKLLTGRHHQIRAQLAAMGCI 180

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           I GD KY A       S     ++LHA  +   HP     + +TAPLP      WD++G
Sbjct: 181 IKGDVKYGARRSNKDRS-----IHLHAWKLSFQHPVSHETVVLTAPLPVD--AVWDAMG 232


>gi|255732273|ref|XP_002551060.1| DRAP deaminase [Candida tropicalis MYA-3404]
 gi|240131346|gb|EER30906.1| DRAP deaminase [Candida tropicalis MYA-3404]
          Length = 590

 Score =  167 bits (423), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 54/257 (21%), Positives = 105/257 (40%), Gaps = 26/257 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +  + +   +    ++ + +G V+V+ K       +++G ++             +E
Sbjct: 111 VDVFI-DEFRDRSAEAYREAVDTGLVKVNSKVANLETVLKNGDLISHRSYR-------RE 162

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            ++YE+  I V +KP+GI V       Y  +   K      
Sbjct: 163 PPVTSRDIK-----------IVYENDDILVIDKPSGIPVHPTG--RYRYNTVTKIIEQEF 209

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G+     +RLD+ TSG++ + ++   A  +    R R + K Y + V G    ++  I  
Sbjct: 210 GKTVHPCNRLDRLTSGLMFLGKSSKGANEMMSQIRDRNVSKEYIARVKGEFPIERIVIEK 269

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHA 259
            L   +      + +   +E+    A + F+ I          ++  P TGRTHQ+RVH 
Sbjct: 270 PLSTIAP----KLTLNVVDEENGKEAKTEFQRISYDPITDTSVVKCHPLTGRTHQIRVHL 325

Query: 260 LHMGCPIVGDHKYCANF 276
            ++G PI  D  Y + F
Sbjct: 326 QYIGHPIANDPMYSSQF 342


>gi|225077010|ref|ZP_03720209.1| hypothetical protein NEIFLAOT_02062 [Neisseria flavescens
           NRL30031/H210]
 gi|224951567|gb|EEG32776.1| hypothetical protein NEIFLAOT_02062 [Neisseria flavescens
           NRL30031/H210]
          Length = 238

 Score =  167 bits (423), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 100/235 (42%), Gaps = 21/235 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ DS+    NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L
Sbjct: 2   LDIIHRDSRTIAVNKPAGMLVHRSWLDKHETRFAVQTLRDQIGQHVYPVHRLDRPTSGVL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A    AA+ LT+ F  + I+K YW++V G   +              I         Q
Sbjct: 62  LFALDTEAARLLTQQFENKTIEKTYWAIVRGHLPSDGLIDYALKYMPDKIAE------AQ 115

Query: 219 NEKGANYAISHFKV-----------IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            E     A + ++            +     ++ W E+ PHTGR HQLR H  H+  PIV
Sbjct: 116 TEATLQEAQTAYRCLAQTELPFQSALRYPTSRYSWAELTPHTGRKHQLRRHMKHIFHPIV 175

Query: 268 GDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           GD  Y    + +  +      +L LHAR +     E G R+ + AP      + W
Sbjct: 176 GDTNYGDLRQNHAVAEHIGTQRLMLHARSLSFQSIEDGSRMTVQAPTDNDW-RLW 229


>gi|171778899|ref|ZP_02919961.1| hypothetical protein STRINF_00822 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171282545|gb|EDT47969.1| hypothetical protein STRINF_00822 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 286

 Score =  167 bits (423), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 59/293 (20%), Positives = 111/293 (37%), Gaps = 34/293 (11%)

Query: 22  DRWFKNHYPH---INFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           D   K        I    ++  LR    + ++ + + + + +++G  +++    +     
Sbjct: 13  DSTVKELLEEHLLIPR-KIRHFLRTKKHLLINGENINWQSLVKTGDTIQLTFDDD----- 66

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                  D         D      LY+D  + + NKP GI   G       +   + ++V
Sbjct: 67  -------DYPQKTIPFGDSKLVDCLYQDEHLIIVNKPEGIKTHGNEPNEIALLNHVSAYV 119

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              G+   + HRLD ETSG ++ A+       L      + I + YW+L  G  + K + 
Sbjct: 120 ---GKTCYVIHRLDMETSGAVMFAKNPFVLPILNRLLENKDISREYWALAQGKFEPKHQV 176

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             + + +  H           + +    A++    +  F +    ++ +  TGRTHQ+RV
Sbjct: 177 FQDKIGRDRHD----RRKRVVDRRNGQTALTIVDRLKVFPKG-SLVKCRLKTGRTHQIRV 231

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           H    G  I+GD  Y              +L LHA  +   HP    ++ + A
Sbjct: 232 HLSAHGHAIIGDPLYSNTPA--------KRLMLHAHKLSFTHPFTLEKISVEA 276


>gi|320333923|ref|YP_004170634.1| pseudouridine synthase [Deinococcus maricopensis DSM 21211]
 gi|319755212|gb|ADV66969.1| pseudouridine synthase [Deinococcus maricopensis DSM 21211]
          Length = 294

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 104/249 (41%), Gaps = 14/249 (5%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +V+    +  L   +L+     +V NKP               D    +       +   
Sbjct: 48  AVSAPTATPILPPEVLFSAESYHVLNKPPLWLTHQVHARFEVPDALGWARATLGEPELAP 107

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ETSG+L++ R+ +AA+     F  RR++K Y ++V G P  ++  +   L    
Sbjct: 108 AHRLDRETSGVLILTRSSSAARGFHRLFLDRRVEKTYLAIVHGQPAWEEVTLDAPLGFLG 167

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               + + V +        A++HF+V+      +  L   P TGR HQLR H  H+G P+
Sbjct: 168 LSDTNSIRVRQGVVPDGKPAVTHFEVLGRRG-AYALLRCSPRTGRMHQLRAHLAHLGHPM 226

Query: 267 VGDHKYCANF------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
           VGD  Y  +                  +    +  LHA  +  P   G  ++ TAP PA 
Sbjct: 227 VGDKIYGPHPEAFVQFVQTGLTPALLRTLQLPRQALHAHEVAFPF-GGTTVRHTAPFPAD 285

Query: 315 MVKTWDSLG 323
           +   WD+ G
Sbjct: 286 LQAFWDAAG 294


>gi|312898764|ref|ZP_07758153.1| pseudouridine synthase, RluA family [Megasphaera micronuciformis
           F0359]
 gi|310620195|gb|EFQ03766.1| pseudouridine synthase, RluA family [Megasphaera micronuciformis
           F0359]
          Length = 291

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 58/292 (19%), Positives = 110/292 (37%), Gaps = 42/292 (14%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++    +G    +       + +  G  + +         I++ +  ++       
Sbjct: 28  SRRKIKN---NGICLQNGVPASMKDLVHQGDSLEV---------ILQPKDTIE------- 68

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQ--GGSGIAYHIDGFLKSW-VDSKGQKPRLTHR 149
            ++ +   + YED  + V NKP G+ +            +  +  + V          HR
Sbjct: 69  -AEDIPLSVAYEDDYLIVVNKPPGMLMHQTSSERFGTLANAIMYYYKVHGYDHDYHPVHR 127

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW-SLVWGIPKNKKECIANWLLKKSHI 208
           LD+ TSG+ ++A+            + R      + +L  G        +         I
Sbjct: 128 LDRNTSGLCLIAKESYVQHLF---DKNRLFYARTYTALAQGRFPAMLATVHTP------I 178

Query: 209 GGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           G D   ++K+N +     A S F  +      F  + +  HTGRTHQ+RVH+ ++G P++
Sbjct: 179 GRDPDSIIKRNTREDGKEAHSDFTRLAVC-DDFSLIRITLHTGRTHQIRVHSAYLGHPLI 237

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKT 318
           GD  Y  + +        N+  LHA  +   HP  G +  +  PLP  M   
Sbjct: 238 GDDLYGGSRR------FLNRQALHAGSVRFIHPVTGHMTYVNVPLPTDMQTL 283


>gi|325189052|emb|CCA23580.1| ribosomal large subunit pseudouridine synthase A put [Albugo
           laibachii Nc14]
          Length = 350

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 107/228 (46%), Gaps = 12/228 (5%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           + +  S+            + Y D  I V +KP+G+    G G        L+  +    
Sbjct: 127 ERVVPSIESAALRKQCGVEIHYCDDAIAVVSKPSGMLTVDGKGSQLS----LQRQLKKLH 182

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               + HRLD +TSG+LVVA ++ AA  L   FR R I+K+Y + V G P + +  I+ +
Sbjct: 183 GNVWVVHRLDMDTSGLLVVAWSKLAADRLGSQFRDRTIRKVYHARVHGHPNDDEGVISGY 242

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHAL 260
           +   +     +   + + +    ++ + ++V+   +  K   LE+ P TGRTHQLRVH  
Sbjct: 243 M--NAQPDERFRQRMVETQTDGKWSQTGWRVLSRSSNPKSSLLELTPVTGRTHQLRVHLS 300

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           H+G PI+GD  Y           + ++L LHA  ++  HP    R+  
Sbjct: 301 HIGHPILGDEWYAPQH----VYKLADRLLLHATALEFVHPLTRKRVHF 344


>gi|89075565|ref|ZP_01161970.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium sp. SKA34]
 gi|89048705|gb|EAR54277.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium sp. SKA34]
          Length = 233

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 70/210 (33%), Positives = 101/210 (48%), Gaps = 12/210 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ DS I   NKPAGI    G    +H   F  + V  K  K ++ HRLD  TSG++V+A
Sbjct: 20  LFLDSDIIAVNKPAGILSNPGRAPEHHDSIF--ARVLEKYPKSQIVHRLDMGTSGLIVLA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
             + A  HL   FR R  QK+Y++ VWG  K     +   L+           V   +  
Sbjct: 78  LNKKAECHLKAQFRERETQKVYYARVWGHIKQNTGTVDLPLICD-WPNRPRQKVCFDD-- 134

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               +++H++V+    +K   + + P TGR+HQLRVH   +G  I+GD  Y AN      
Sbjct: 135 -GKPSVTHYEVLSRD-EKSTLVRLLPVTGRSHQLRVHMQALGHSILGDKFY-ANEDAMAA 191

Query: 282 SPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           SP   +L LHA  +   HP     + + AP
Sbjct: 192 SP---RLQLHAAELTFTHPGSDEPMHLFAP 218


>gi|50084392|ref|YP_045902.1| putative ribosomal large subunit pseudouridine synthase
           A(RluA-like) [Acinetobacter sp. ADP1]
 gi|49530368|emb|CAG68080.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. ADP1]
          Length = 214

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 70/223 (31%), Positives = 107/223 (47%), Gaps = 15/223 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           S+FL   L++ D+   V +KPAGI    G G A   D  L   V+ +  K  L HRLD++
Sbjct: 2   SNFLTDYLIHRDNDFMVIHKPAGILSVPGKGDA-LFDSLLVRLVEIE-PKTLLIHRLDRD 59

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV    + A   ++  F+ R+  KIY +LV G    +   I   ++  +      +
Sbjct: 60  TSGILVFGLNKMAQSAISRQFQERQTDKIYQALVVGEVYGE-GLIDVPVVYDA--ARPPL 116

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+          A + ++ ++ F    +    + + P TGR+HQLRVH  ++G PIVGD 
Sbjct: 117 HIADPAHH--KPAQTEWQALEQFELNGKMVTRMRLTPITGRSHQLRVHMQYIGHPIVGDT 174

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
            Y +       S    +L LHA  +   HP+ G L     P+P
Sbjct: 175 LYASLADQQLVS----RLCLHAEQLSFYHPKTGELVTFHCPVP 213


>gi|295095907|emb|CBK84997.1| Pseudouridylate synthases, 23S RNA-specific [Enterobacter cloacae
           subsp. cloacae NCTC 9394]
          Length = 228

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 60/227 (26%), Positives = 101/227 (44%), Gaps = 17/227 (7%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I+D+ +    H D     +L++D  + + NKP+G+    G          +   +     
Sbjct: 4   IIDTFIAPPCHDDI---EILWQDEHLLLINKPSGLLSLSGKNPQN--LDSVHHRLVQTFP 58

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD  TSG++V+AR +A    L   F  R + K+Y +L+ G  +  +  +   +
Sbjct: 59  GCTLVHRLDFGTSGLMVIARNKAINAALCHQFSQRAVNKVYTALLCGHVEQDEGTVDAPI 118

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL----EMQPHTGRTHQLRVH 258
            K   +      ++    +    A S ++V++   Q         E+ P TGRTHQLR+H
Sbjct: 119 AKDPAL----FPLMTICARTGKPARSRYRVVERIYQDTTMPLTRVELTPETGRTHQLRIH 174

Query: 259 ALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              +G PI+G   Y    + G   +P   +L LHA  ++  HP  G 
Sbjct: 175 CQQLGHPILGCDLYGGLEWPGAEETP---RLMLHASALNFIHPLSGE 218


>gi|255712643|ref|XP_002552604.1| KLTH0C08756p [Lachancea thermotolerans]
 gi|238933983|emb|CAR22166.1| KLTH0C08756p [Lachancea thermotolerans]
          Length = 610

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 57/267 (21%), Positives = 106/267 (39%), Gaps = 23/267 (8%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +  N +        +K +  G V +++      + +++G ++              E
Sbjct: 125 IDIFV-NEFRDREESYYRKTIARGAVFLNENPANLESIVRNGDLISHKIHR-------HE 176

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  ++V +KP+GI V       Y  +   K      
Sbjct: 177 PPVTSRPIK-----------IVFEDQDLFVIDKPSGIPVHPTG--RYRFNTITKILQKQI 223

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                  +RLD+ TSG++ +A+T   A H+    + R ++K Y + V G    ++  +  
Sbjct: 224 NGSVHPCNRLDRLTSGLMFLAKTPRGADHMANQLKAREVKKEYIARVVGEFPAERISVEK 283

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K          V    E+GA  A + F  +    +    ++ QPHTGRTHQ+RVH  
Sbjct: 284 PL-KCVEPRLALNGVCNSEEEGAKEAKTVFTRVSFDGE-TSLVKCQPHTGRTHQIRVHLQ 341

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNK 287
           ++G PI  D  Y        +     +
Sbjct: 342 YLGHPIANDPLYSNPQIWGPSLGKGQR 368


>gi|213861507|ref|ZP_03385977.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
          Length = 208

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 65/213 (30%), Positives = 110/213 (51%), Gaps = 9/213 (4%)

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +V GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R +
Sbjct: 1   AVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREK 59

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            +QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +A
Sbjct: 60  GMQKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERYA 116

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARY 294
                +   P TGRTHQ+RVH  + G PI  D +Y     + +         +L+LHA  
Sbjct: 117 -FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAA 175

Query: 295 MDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
           +   HP  G  ++I AP+   + +  + L  K 
Sbjct: 176 LKFTHPGTGDVMRIEAPMDKQLKRCLEVLRSKA 208


>gi|262173056|ref|ZP_06040733.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus MB-451]
 gi|261890414|gb|EEY36401.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus MB-451]
          Length = 559

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 70/243 (28%), Positives = 111/243 (45%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ D+ + L+  +   +  ++Y+D  I V NKPA      G  +   +
Sbjct: 328 CQPILAHMLQGMELDDNPL-LSNPAADKEISIVYQDEAIVVVNKPAEFLSVPGVHVHDSV 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++   S+ +     HRLD  TSG+LV A TR A +HL + F  R +QK Y +++ G
Sbjct: 387 LTRLQAQF-SEAEGVFALHRLDMSTSGLLVFALTRRANRHLQKQFITRAVQKRYVAMLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              + +  IA  L            V  Q       A++H++ +    Q    + + PHT
Sbjct: 446 TLADAQGEIALPLCGD-LDDRPRQKVCWQQ---GKPALTHWETV-AVEQGRTRVYLYPHT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVH  H   + CPIVGD  Y              +L+LHA  +   HP   + +
Sbjct: 501 GRTHQLRVHCAHHLGLNCPIVGDDLYGTQ---------DQRLHLHAEKLSFSHPYTKQPM 551

Query: 306 QIT 308
              
Sbjct: 552 TFE 554


>gi|153839608|ref|ZP_01992275.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ3810]
 gi|260900301|ref|ZP_05908696.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
 gi|149746879|gb|EDM57867.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ3810]
 gi|308107572|gb|EFO45112.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
          Length = 250

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 106/231 (45%), Gaps = 15/231 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++ED  I   NKP+G+    G    +H    + S +  +    ++ HRLD  TSG++V
Sbjct: 15  DIVFEDDHILAVNKPSGLLSVPGRLAEHHDS--MWSRLQEEYPDIQVVHRLDMSTSGLMV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A   L + F+ R   KIY++ VWG  + ++  I   L+           V  ++
Sbjct: 73  LAKNKRAESALKKQFQFRLTHKIYYARVWGHVEQEEGEIDLPLICD-WPNRPLQKVCFED 131

Query: 220 EKGANYAISHFKVIDCFAQ----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K +    + F+V          K   + + P TGR+HQLRVH   +G PIVGD  Y   
Sbjct: 132 GKPSK---TLFQVAKREEHEDGTKTTIVRLLPITGRSHQLRVHMQALGHPIVGDEFYATE 188

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
               F+     +L LHA  +   HP+   L+ +  +P       + + F Y
Sbjct: 189 EAKAFSE----RLELHASELSFYHPKSHWLR-SIFVPCDFYPEAEEMIFDY 234


>gi|238758998|ref|ZP_04620169.1| Ribosomal large subunit pseudouridine synthase A [Yersinia aldovae
           ATCC 35236]
 gi|238702809|gb|EEP95355.1| Ribosomal large subunit pseudouridine synthase A [Yersinia aldovae
           ATCC 35236]
          Length = 206

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 67/214 (31%), Positives = 100/214 (46%), Gaps = 15/214 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           I+LY+D  I V NKP+G+    G   A      + + + +        HRLD  TSG++V
Sbjct: 2   IVLYQDKHIIVINKPSGLLSVPGR--APENKDSVMTRIQADYPTAESVHRLDMATSGVIV 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA T+AA + +   FR R  +K Y + VWG     +  I   L+       D+ +  KQ 
Sbjct: 60  VALTKAAEREIKRQFREREPKKCYIARVWGHLAQDEGVIDLPLI------CDWPNRPKQK 113

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              +    A + + V+         +++ P TGR+HQLRVH L MG PI+GD  Y     
Sbjct: 114 VCYETGKSAQTEYLVLSRDEDGSTRVKLSPITGRSHQLRVHMLAMGHPILGDGFYAHPEA 173

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
               S    +L LHA+ + + HPE G  +     
Sbjct: 174 KAMAS----RLQLHAQELCITHPEFGTVMHFKCE 203


>gi|223042061|ref|ZP_03612237.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           minor 202]
 gi|223017136|gb|EEF15572.1| ribosomal large subunit pseudouridine synthase A [Actinobacillus
           minor 202]
          Length = 222

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 63/217 (29%), Positives = 100/217 (46%), Gaps = 14/217 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+      + V  K       HRLD  TSGIL+ A
Sbjct: 17  VYRDNHILVINKPSGLLSVPGNRPEYYDSAM--TRVQQKYGFTEPAHRLDMATSGILLFA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHVVKQN 219
            ++ A + L   FR R  +K Y +L+WG    +     + ++ L           +  + 
Sbjct: 75  LSKVAEKELKRQFREREPKKHYIALLWGKLGEQVGDKGVMDFPLICDWENRPRQKICYER 134

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 AI+H++V+         +++ P TGR+HQLRVH+L +G PI+GD  Y       
Sbjct: 135 ---GKKAITHYEVLAHLPNNTTRVKLTPITGRSHQLRVHSLALGHPILGDKFY----ANP 187

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
               +  +L LHA  + + HP  G  +  +A   A  
Sbjct: 188 LAKSLAPRLCLHAESLTITHPITGELMTFSAE--ADF 222


>gi|308187414|ref|YP_003931545.1| ribosomal large subunit pseudouridine synthase A [Pantoea vagans
           C9-1]
 gi|308057924|gb|ADO10096.1| ribosomal large subunit pseudouridine synthase A [Pantoea vagans
           C9-1]
          Length = 243

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 63/226 (27%), Positives = 93/226 (41%), Gaps = 17/226 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
              F K  LL++D  + V NKP G+    G          +   +  +     L HRLD 
Sbjct: 22  PPCFDKITLLFQDDHLLVINKPGGLLSLSGKNPQN--LDSVHHRLVKRFPGCTLVHRLDF 79

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVAR +A    L + F  R + K Y +L+ G   + +  I   + K   +    
Sbjct: 80  GTSGLMVVARNKAINAALCQQFSQRTVSKTYQALLCGHLADDEGVIDAAIAKDPALFPRM 139

Query: 213 VHVVKQNEKGANYAISHFKVIDC--------FAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           V    Q       A S ++V +                +E+ P TGRTHQLR+H   +G 
Sbjct: 140 VICAAQ----GKPARSRYRVTERSFYRRKEGKELPVTRVELTPETGRTHQLRIHCQQLGH 195

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           PI+G   Y              +L LHA  +   HP  G  L ++A
Sbjct: 196 PILGCDLYGGLVLPGAEQ--AERLMLHASGLTFVHPVSGETLHLSA 239


>gi|114562064|ref|YP_749577.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114333357|gb|ABI70739.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 579

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 109/243 (44%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++K   + D  + +    D     ++Y+D  + + NKPA +    G  I   +
Sbjct: 347 CRPILTHMLKGMLVDDDPLLINPGKDQ-HIDIIYQDDAMVIINKPAELLSVPGKNITDSV 405

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++         P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ G
Sbjct: 406 FSRMQQQF-PNATGPLIVHRLDMSTSGLMVIALTKEANKALQQQFIQRSVTKRYIALIEG 464

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +P   +  I+  L          +   +       +A +H++V     Q+   + + P T
Sbjct: 465 VPSQDEGDISLPLRVDLDDRPKQLVCYEH----GKHAETHWQVYQRQGQR-TLVYLYPKT 519

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
           GRTHQLR+H  H   +  PIVGD  Y             N+L+LHA+Y+ L HP  G  +
Sbjct: 520 GRTHQLRMHCAHHDGLHMPIVGDDLYGV---------ATNRLHLHAQYLSLNHPVSGKEM 570

Query: 306 QIT 308
              
Sbjct: 571 VFE 573


>gi|255534329|ref|YP_003094700.1| Ribosomal large subunit pseudouridine synthase D [Flavobacteriaceae
           bacterium 3519-10]
 gi|255340525|gb|ACU06638.1| Ribosomal large subunit pseudouridine synthase D [Flavobacteriaceae
           bacterium 3519-10]
          Length = 233

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 68/224 (30%), Positives = 110/224 (49%), Gaps = 14/224 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLD 151
           ++S +++ED+ + V NK AG  VQG       +   +K ++  +  K       L HR+D
Sbjct: 9   IESQIVFEDNHLLVINKKAGQLVQGDKTGDASLLDLIKDFIKKRDNKAGNVFLGLVHRID 68

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG+++ A+T  A   LT+  + R I+K YW++V          + ++L K       
Sbjct: 69  RPTSGLVIYAKTSKALTRLTQMVKNREIKKTYWAVVPKEVIPHSARLLHYLQKNEKTNKS 128

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V +  +  + A  ++ ++ VI      F  LE+   TGR HQ+R     +G PI GD K
Sbjct: 129 TVFI--KPTENAKESVLNYTVIKTL-DNFQLLEIDLETGRHHQIRAQLSKIGVPIKGDLK 185

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAH 314
           Y A+      S     ++LHAR ++  HP      +I APLPAH
Sbjct: 186 YGAS-----RSNPDGGIHLHARKLEFIHPVSLKNTEIVAPLPAH 224


>gi|325261335|ref|ZP_08128073.1| ribosomal large subunit pseudouridine synthase family protein
           [Clostridium sp. D5]
 gi|324032789|gb|EGB94066.1| ribosomal large subunit pseudouridine synthase family protein
           [Clostridium sp. D5]
          Length = 226

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 68/215 (31%), Positives = 98/215 (45%), Gaps = 11/215 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLD 151
           +   +LYED  I V  KPAG+  Q        +   LK+ +    +K       + HRLD
Sbjct: 1   MNPEILYEDQDIIVCAKPAGVPTQSSRVGTPDMVSILKNHIYKNSEKKQQPYLAVIHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q   G+LV A+T AAA+ L          K Y +L+ GIP   +  + ++L+K      +
Sbjct: 61  QPVEGLLVFAKTPAAARELNRQLTQYGFGKHYRALLAGIPVCMEGDLEDYLVKDGR--NN 118

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              V   +  GA  A  H+K+I+  +   C   ++   TGR HQ+RV   HMG PI GD 
Sbjct: 119 TAQVCTPDTPGAKKARLHYKIIETCSTPDCSLADITLETGRHHQIRVQMAHMGTPIAGDK 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           KY         S    KL L A  +   HP  G++
Sbjct: 179 KYGKESPALAAS---RKLQLFACRLKFKHPRTGKI 210


>gi|127511717|ref|YP_001092914.1| pseudouridylate synthase [Shewanella loihica PV-4]
 gi|126637012|gb|ABO22655.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           loihica PV-4]
          Length = 225

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 67/213 (31%), Positives = 108/213 (50%), Gaps = 12/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ED  I V NKP+G+    G   AY+   + +   D      ++ HRLD  TSGI+VV
Sbjct: 16  ILHEDKDILVVNKPSGLLSVPGRDPAYYDSVYTRVLRDH--PNAQIVHRLDMATSGIIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R+A + L   FR R   KIY++ V G  K ++  +   L+             K + 
Sbjct: 74  ALRRSAERELKRQFRDRETHKIYYARVAGHLKAEQGSVDYPLICDWPNRPK----QKVDH 129

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    + + F+VI   A++   +++ P TGR+HQLRVH + +G PI+GD+ Y        
Sbjct: 130 QIGKASKTLFEVISR-AKRSTLVKLTPITGRSHQLRVHMMAIGHPILGDNFYADPLAKR- 187

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              +  +L LHA+ + L HP   + +  + P+P
Sbjct: 188 ---LAPRLLLHAQSLSLTHPYSKQPMTFSTPIP 217


>gi|323138304|ref|ZP_08073375.1| pseudouridine synthase [Methylocystis sp. ATCC 49242]
 gi|322396387|gb|EFX98917.1| pseudouridine synthase [Methylocystis sp. ATCC 49242]
          Length = 238

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 111/233 (47%), Gaps = 11/233 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L S LL+ D  + + +KPAG+ V  G      ++           + P L HRLD++TSG
Sbjct: 3   LLSRLLHRDGLMLIIDKPAGVPVHRGPKGGPSLEDAFDELRFGLPRAPALAHRLDKDTSG 62

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R R A   L + F+  RI K YW++V G P+ ++  I   L +     G ++   
Sbjct: 63  CLVLGRHRKALDRLGKLFKSGRISKTYWAVVEGAPEAEEGEIDLALGRLDAARGWWMR-- 120

Query: 217 KQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              +     + + ++V+         ++E  PHTGRTHQ+RVHA  MG PI+GD  Y   
Sbjct: 121 --PDPLGLPSRTSWRVLGRSPDASLAFVEFTPHTGRTHQIRVHAQAMGWPILGDPIYGHG 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            +          L+LHAR + +P  +    ++  AP P HM +     G   D
Sbjct: 179 RREGAP-----PLHLHARAITIPMQDSKEPVRAEAPPPDHMSEALALCGLAPD 226


>gi|210624201|ref|ZP_03294256.1| hypothetical protein CLOHIR_02212 [Clostridium hiranonis DSM 13275]
 gi|210153188|gb|EEA84194.1| hypothetical protein CLOHIR_02212 [Clostridium hiranonis DSM 13275]
          Length = 226

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 60/220 (27%), Positives = 104/220 (47%), Gaps = 15/220 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ + V  KP  I  QG +     +   LK+++  K  KP      L HRLD+   
Sbjct: 8   VLYEDNHLLVVEKPVNILSQGDNTNDKDMVNLLKAYLKEKYNKPGNVYLGLVHRLDRPVG 67

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G +V A+T  AA  L+E  R +  +K Y +++ G  + + + + ++L K        V V
Sbjct: 68  GAMVFAKTSKAASRLSEQVRNKTFKKTYRAVINGKMRKQSDTLKDYLYKNKKTN--MVSV 125

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V ++ K + YA   +  +  F  K   +++   TGR HQ+RV       P+VGD +Y  N
Sbjct: 126 VSESHKDSKYAELSYATL-AFKDKMSLVQIDLKTGRPHQIRVQFASRNNPLVGDQRYGKN 184

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAH 314
            K      +  ++ L +  +++ HP    +++     P  
Sbjct: 185 SK------VGQQIALWSYKIEIVHPVTKEKMEFVCEPPKE 218


>gi|187918668|ref|YP_001884235.1| tRNA pseudouridine synthase A [Borrelia hermsii DAH]
 gi|119861516|gb|AAX17311.1| tRNA pseudouridine synthase A [Borrelia hermsii DAH]
          Length = 320

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 69/324 (21%), Positives = 131/324 (40%), Gaps = 25/324 (7%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V  ++   RLD              + + +R+G + ++  +V F++R+     + +
Sbjct: 13  RVIDVLKNDNGKRLDAVLIKFLK-FPKSKIMRHIRNGDILLNNLKVTFSHRVFKDDQIYL 71

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              +     + K   + D    L      +K  ++YED  + V NK  G  V G      
Sbjct: 72  YKPLLQGLSLSK-MTVKDEDAILR----DVKRRIVYEDEDLLVINKRRGALVHGDKYSLG 126

Query: 128 HIDG--FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +     L   ++S   KP   HRLD+ TSG+++ A+   +A+ L+ +F    + K Y +
Sbjct: 127 ALINSYLLDENLESLSFKPSSVHRLDRNTSGLIIFAKNIDSARILSRAFSSGIVTKKYLA 186

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVV--KQNEKGANYAISHFKVIDCFAQKFCWL 243
           L+ G        I   L  ++ +  D +       N++G   AI+  K I   ++     
Sbjct: 187 LLDGE-------IKKPLTYRNFLYRDRIARKTFVVNDEGRCNAITDVKPI-LVSKSSTLA 238

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E+   TG THQ+R         ++ D KY + FK       +N  +LH+  +        
Sbjct: 239 EVSIRTGFTHQIRAQCAFNKHALINDKKYDSKFK-------KNNYFLHSFLIKFNQSLFL 291

Query: 304 RLQITAPLPAHMVKTWDSLGFKYD 327
           R +      +  +K   ++   YD
Sbjct: 292 RNEFFVEPSSDFLKQISNIFGVYD 315


>gi|310765109|gb|ADP10059.1| 23S rRNA/tRNA pseudouridine synthase A [Erwinia sp. Ejp617]
          Length = 217

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 66/215 (30%), Positives = 103/215 (47%), Gaps = 14/215 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G  +A + D  + + V          
Sbjct: 1   MEPYNPPPEPWLHVLYQDEHIIVVNKPSGLLSVPGR-LAEYKDSVM-TRVQRDYPAAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  QK Y + VWG P+     +   L+    
Sbjct: 59  HRLDMATSGVMVVALTKAAERELKRQFREREPQKTYVARVWGHPQPATGLVDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ         A + ++V+D  +     ++++P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCFDSGKSAQTEYQVLDNASDNSARVQLKPITGRSHQLRVHMLAIGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           ++GD+ Y  +           +L LHA  + + HP
Sbjct: 173 MLGDNFYAHDEARAMA----PRLQLHAESLSITHP 203


>gi|325568271|ref|ZP_08144638.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158040|gb|EGC70193.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus ATCC 12755]
          Length = 284

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 63/262 (24%), Positives = 108/262 (41%), Gaps = 27/262 (10%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
             V V+++   F+  ++ G  + +         II++       + L       K  +L+
Sbjct: 38  KNVAVNQQPAMFHQEVRGGDQITL---------IIEDSDYSYQPIQL---GQADKVDVLF 85

Query: 104 EDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           ED  + V NKPA +       + A  +     +++  K Q+P + HRLD+ETSG+++ A+
Sbjct: 86  EDEHLLVLNKPARVKTHPNQPLEADTLLNDAAAYLAPKQQQPYVVHRLDKETSGVVLFAK 145

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  L      ++I + Y + V G     +  IA  + +  H     +     + + 
Sbjct: 146 NPLVLPILGRMLENKQIFRRYQATVLGKLTQDQ-TIAKKIGRDRHDRRKRII----DSRN 200

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++H   I    QK   +     TGRTHQ+RVH   +G P+VGD  Y          
Sbjct: 201 GQSAVTHV-TIAHAQQKTTNVYCVLETGRTHQIRVHLASIGHPVVGDPLYQNKPA----- 254

Query: 283 PIQNKLYLHARYMDLPHPEGGR 304
               +L LH   + L HP    
Sbjct: 255 ---PRLLLHGYELHLEHPFTKE 273


>gi|309804686|ref|ZP_07698751.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
 gi|308166078|gb|EFO68296.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
          Length = 274

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 62/270 (22%), Positives = 106/270 (39%), Gaps = 35/270 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              +    R G V V+ +R   N  +  G  V         N  +K              
Sbjct: 34  RSLINCRHRGGNVLVNHRRRYNNYLLHDGDEVIFILGKEKPNATLK-------------- 79

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG---QKPRLTHR 149
              L   ++ E +   + NK A +            + G L  +++       KP +  R
Sbjct: 80  FSNLPIAIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITR 139

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSH 207
           LD++TSG+++V +   A      S + R I+K + ++V G   P   +  I   + KK  
Sbjct: 140 LDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYH-AIVHGNFSPSQLQGVIDAPIGKKDD 198

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y+       +G   +++ ++VI   A     +E+Q  TGRTHQ+RVH  ++G P+ 
Sbjct: 199 PIKRYIM------EGGKNSVTKYRVIKQVA-GASLVELQLLTGRTHQIRVHMQYLGHPLF 251

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           GDH Y              +  LH  ++ L
Sbjct: 252 GDHLYGVEDD-------FPRQALHCFFISL 274


>gi|257455986|ref|ZP_05621197.1| ribosomal large subunit pseudouridine synthase A [Enhydrobacter
           aerosaccus SK60]
 gi|257446614|gb|EEV21646.1| ribosomal large subunit pseudouridine synthase A [Enhydrobacter
           aerosaccus SK60]
          Length = 243

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 69/239 (28%), Positives = 110/239 (46%), Gaps = 13/239 (5%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I ++ + +S    +   DF KS+ LY D  I+V +KP G+    G  +       L+S +
Sbjct: 13  IAQRNLEESQQPQSFFDDFAKSVTLYRDDDIWVIDKPHGLLSVDGKELKVS----LQSRL 68

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                  +L HRLD +TSGI++ AR   A  H+++ F  R   K Y +LVWG P  + E 
Sbjct: 69  LKADPNVKLIHRLDMDTSGIIIFARHSEAQTHISKQFIDRIPSKEYQALVWGTPPQQGEI 128

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQ 254
                          V +          A + ++ +       +    + + P TGR+HQ
Sbjct: 129 DVPVRYDPPQKPKHIVDMSWD-----KRAYTKYETLHHELREGKAVSRVALYPVTGRSHQ 183

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           LRVH LH+G  ++GD  Y  +        +  +L LHAR + L HP  G  ++  +P+P
Sbjct: 184 LRVHMLHIGHVMLGDPIYAQDVLNGQAFDLSPRLCLHARKLRLKHPNTGVWMEWESPVP 242


>gi|262278251|ref|ZP_06056036.1| conserved hypothetical protein [Acinetobacter calcoaceticus
           RUH2202]
 gi|262258602|gb|EEY77335.1| conserved hypothetical protein [Acinetobacter calcoaceticus
           RUH2202]
          Length = 212

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 69/223 (30%), Positives = 108/223 (48%), Gaps = 17/223 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V  +  K  L HRLD++
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLVAIE-PKTLLIHRLDRD 58

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     +   F+ R+  KIY +LV G  + +   +   ++         +
Sbjct: 59  TSGILVFGLSKRGQSAIARQFQDRQTSKIYEALVAGHLEGE-GTVDIPVIYDP--SRPPL 115

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+V  +      A++H++V++ F    Q    +++ P TGR+HQLRVH  ++G PIVGD 
Sbjct: 116 HIVDASHN--KPALTHWQVLENFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDT 173

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            Y    +      +  +L LHA+ +   HP     L    P+P
Sbjct: 174 LYATPEQQ-----LVPRLCLHAKQLSFNHPVTAETLTFDCPVP 211


>gi|291547301|emb|CBL20409.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus sp.
           SR1/5]
          Length = 245

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 63/216 (29%), Positives = 103/216 (47%), Gaps = 15/216 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQ 152
           ++  +LYED +I V  K AG+ VQ        ++  LK+++  K         + HRLDQ
Sbjct: 6   IEENILYEDKEILVCRKTAGMPVQAAKIGTMDMESALKNYLAQKTPGKIPYLGVVHRLDQ 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              GILV A+T  AA +L++        K Y ++  G  K+ +  + ++L K        
Sbjct: 66  PVEGILVFAKTSEAAGNLSKQMMAGGAGKYYLAVTEGKAKSSEGTLTDYLKKNGKAN--M 123

Query: 213 VHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             VV  N  GA  AI H+KV+   +   +    L+++  TGR HQ+RV   H G PI+GD
Sbjct: 124 SQVVSANTPGAKKAILHYKVLDQQEINGKSRTLLKIRLETGRHHQIRVQLSHEGLPILGD 183

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            KY  + +   +  +       +  ++  HP  G++
Sbjct: 184 RKYNPSGEKGTSLGL------CSSCLEFKHPRTGKM 213


>gi|71909763|ref|YP_287350.1| ribosomal large subunit pseudouridine synthase A [Dechloromonas
           aromatica RCB]
 gi|71849384|gb|AAZ48880.1| ribosomal large subunit pseudouridine synthase A [Dechloromonas
           aromatica RCB]
          Length = 218

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 61/222 (27%), Positives = 98/222 (44%), Gaps = 13/222 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                 S +++ D  + V +KPA +    G G    +D  L + V ++       HRLD 
Sbjct: 7   PPPAGISPVIFADEWLIVADKPAELLSVPGRGAG--MDDCLVTRVQNEYPDALSVHRLDM 64

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+LV+AR +   + L+  F+ R++ K Y ++V G+   +   I   L+         
Sbjct: 65  STSGLLVLARGKEIHRQLSRLFQDRQVSKRYIAVVDGLLAEEVGEIDLPLICDWPNRPRQ 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +            +++ F+V           LE++P TGR+HQLRVH   +G PI+GD  
Sbjct: 125 MVDFTI----GKPSLTRFRVNGHDTVANTTRLELEPITGRSHQLRVHMASLGHPILGDDL 180

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           Y     G        +L LHA  +   HP  G  +Q  +  P
Sbjct: 181 YGGEAHGKA-----GRLLLHAMDLAFVHPATGSPVQFHSDAP 217


>gi|307565639|ref|ZP_07628117.1| RNA pseudouridine synthase [Prevotella amnii CRIS 21A-A]
 gi|307345671|gb|EFN91030.1| RNA pseudouridine synthase [Prevotella amnii CRIS 21A-A]
          Length = 235

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 112/228 (49%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + +  K AG  VQG       +   +K W+  K  KP      + HRLD+  +
Sbjct: 3   VIYEDNHLIIVYKEAGEIVQGDKTGDQPLSETVKLWIKDKYNKPGNVFLGIVHRLDRPVA 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ ART  A   L + FR   I K YW++V   P   ++ + +WL++ +     Y + 
Sbjct: 63  GLVIFARTSKALSRLNDMFRNGNIHKTYWAIVQQQPLKPEDTLTDWLIRNTQQNKSYAYN 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +      A  ++ H+K I+  ++ +  LE+   TGR HQ+R    +MGCPI GD KY A 
Sbjct: 123 IPL--PTAKKSVLHYKTINT-SKHYTLLEINLMTGRHHQIRCQLANMGCPIKGDLKYGAA 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     L+ H   ++  HP   + ++I +P+P      W ++
Sbjct: 180 RSNPDGSIS---LFSH--KIEFIHPVSKKTIRIVSPIPND--NLWQAI 220


>gi|283780592|ref|YP_003371347.1| pseudouridine synthase [Pirellula staleyi DSM 6068]
 gi|283439045|gb|ADB17487.1| pseudouridine synthase [Pirellula staleyi DSM 6068]
          Length = 245

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 76/235 (32%), Positives = 114/235 (48%), Gaps = 13/235 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIA---YHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           L   +L EDS + V NKPAGI  Q   GI    + I  +L+S   S+     + HRLD+ 
Sbjct: 4   LPFEILLEDSAVLVVNKPAGILTQAPLGIDSLEWQIKRYLQSTEKSEVPYLGVPHRLDRP 63

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
            SG +  A+ + AA+ +++ F  R +QK YW+LV GI    +    + L K    G    
Sbjct: 64  VSGCICFAKNQKAARKISQQFEARLVQKTYWALVSGIVHPTRSTWVDHLKKLD--GEPRT 121

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            VV + +     AI H+++++   +    L +   TGRTHQ+RV     G P++GD  Y 
Sbjct: 122 IVVDERDPEGKNAILHYELLETR-EGRSLLAITLETGRTHQIRVQCGSRGFPLLGDRLYG 180

Query: 274 -ANFKGNFTSPIQNKL-YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            A   G   +  +++L  LHAR +   HP     L  TA +PA     W   G +
Sbjct: 181 SAEPFGPLAADERDQLIALHARTLAFRHPVTKEDLIFTAQVPA----IWSPFGLE 231


>gi|312216765|emb|CBX96715.1| hypothetical protein [Leptosphaeria maculans]
          Length = 791

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 63/282 (22%), Positives = 114/282 (40%), Gaps = 56/282 (19%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           F + +        ++ ++ G+V V+ K V   +  I++G V+         +H +   + 
Sbjct: 107 FADEFRDRPKEYYEQAIKDGRVVVNGKPVPSTSTMIKNGDVI---------SHTLHRHEP 157

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ- 142
             ++  +          +++ED+ + V NKPAG+ V       Y+ +  ++     +G  
Sbjct: 158 PCTAQPIG---------IVHEDNDLIVINKPAGMPVHPAG--RYNFNSIIEIMRADRGYN 206

Query: 143 -KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIAN 200
             P   +RLD+ TSGI+ + + R AA+H++   R R ++K Y + V G  P+ +  C   
Sbjct: 207 WNPLPCNRLDRLTSGIMFIGKHRKAAEHMSAQIRGRTVKKEYITRVVGEFPEGEVVCEKP 266

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----------------------- 237
            L     +G + V            A + FK +  +                        
Sbjct: 267 ILQISPKLGLNRVRA------DGKEAFTVFKRLAYYPPKEEEAPPEKDARGKADSDGQPW 320

Query: 238 ---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              + +  +   P TGRTHQLRVH   +G PI  D  Y    
Sbjct: 321 KRLRGYSIVRCFPVTGRTHQLRVHLQFLGHPISNDPIYANQR 362


>gi|258622273|ref|ZP_05717299.1| conserved hypothetical protein [Vibrio mimicus VM573]
 gi|258585597|gb|EEW10320.1| conserved hypothetical protein [Vibrio mimicus VM573]
          Length = 559

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 69/243 (28%), Positives = 111/243 (45%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ D+ + L+  +   +  ++Y+D  I V NKPA      G  +   +
Sbjct: 328 CQPILAHMLQGMELDDNPL-LSNPAADKEISIVYQDEAIVVVNKPAEFLSVPGVHVHDSV 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++   S+ +     HRLD  TSG+LV A TR A +HL + F  R ++K Y +++ G
Sbjct: 387 LTRLQAQF-SEAEGVFALHRLDMSTSGLLVFALTRRANKHLQKQFITRAVEKRYVAMLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              + +  IA  L            V  Q       A++H++ +    Q    + + PHT
Sbjct: 446 TLADVQGEIALPLCGD-LDDRPRQKVCWQQ---GKPALTHWETV-AVEQGRTRVYLYPHT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVH  H   + CPIVGD  Y              +L+LHA  +   HP   + +
Sbjct: 501 GRTHQLRVHCAHHLGLNCPIVGDDLYGTQ---------DQRLHLHAEKLSFSHPYTKQPM 551

Query: 306 QIT 308
              
Sbjct: 552 TFE 554


>gi|117618171|ref|YP_856003.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117559578|gb|ABK36526.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 243

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 95/228 (41%), Gaps = 16/228 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   +L+ED  + + NKP+G+    G          +   +        L HRLD 
Sbjct: 11  PPCAATIEILFEDEHLLLINKPSGLLSLSGKNPQN--LDSVHHRLVQAYPGCALVHRLDF 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++VAR +A    L   F  R + K Y +L+ G     +  I   + K   +    
Sbjct: 69  GTSGIMLVARNKAINALLCRQFSQRAVSKAYSALLCGHLAKDEGVIDAPIAKDPAL-FPL 127

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ-------KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           + +   N      A S ++VI+  AQ           + + P TGRTHQLR+H+  +G P
Sbjct: 128 MSICAVN---GKPARSRYQVIERLAQQIQGQTVPLTSVRLVPETGRTHQLRIHSQQLGHP 184

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           I+G   Y              +L LHA  +D  HP  G  +QI +  P
Sbjct: 185 ILGCDLYGGLLPPGCER--APRLMLHASELDFVHPVSGEPMQIRSEAP 230


>gi|308070410|ref|YP_003872015.1| RNA pseudouridine synthase (RNA-uridine isomerase) [Paenibacillus
           polymyxa E681]
 gi|305859689|gb|ADM71477.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Paenibacillus polymyxa E681]
          Length = 304

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 66/311 (21%), Positives = 111/311 (35%), Gaps = 48/311 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D+W  N    +     +++    ++ +            +G  +R+             
Sbjct: 33  VDQWLLNRL-ELPEKLWRRLRHEKEIEL------------TGDRLRL------------- 66

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY---HIDGFLKSWV 137
              L   +NL     +    +LYED    V +KPAG++V     +      +D  + S+ 
Sbjct: 67  --ALFPVMNLGITPRWYDLKVLYEDDFCLVVHKPAGVAVHPDGAVQDGPLTLDHAVASYY 124

Query: 138 DSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +  G     R  HRLD +T+G ++ A+   A   L E  R + I + Y +LV G      
Sbjct: 125 EVNGIHAAVRHVHRLDVDTTGPVLYAKNEFALLKLDEQMRAKDIGRRYVALVRGKVPPSL 184

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---VIDCFAQKFCWLEMQPHTGRT 252
             +   + K  H                  A++H +   V          + +   TGRT
Sbjct: 185 RTLDWPIGKDRHHKQRRRI-----SPTGQKAVTHIELGGVWGSGPSAVSLVYLTLETGRT 239

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           HQ+RVH  H G P++GD  Y              +  LH   +   HP  G  + +    
Sbjct: 240 HQIRVHLSHAGYPLLGDVLYGGRATD------FGRQALHGERLTFCHPLSGETITVEDAW 293

Query: 312 PAHMVKTWDSL 322
           P    K    L
Sbjct: 294 PDDFQKLHKQL 304


>gi|163802917|ref|ZP_02196805.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. AND4]
 gi|159173324|gb|EDP58150.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. AND4]
          Length = 250

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 109/233 (46%), Gaps = 19/233 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++ED +I   NKP+G+    G    +H    + S ++ +  + ++ HRLD  TSG++V
Sbjct: 15  DIVFEDEQILAVNKPSGLLSVPGRLAEHHDS--MSSRLEKEYPEIQVVHRLDMSTSGLMV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A   L + F+ R   KIY++ VWG    ++  +   L+           V  ++
Sbjct: 73  LAKNKLAESALKKQFQYRLTHKIYYARVWGHVAQEEGEVDLPLICD-WPNRPLQKVCFED 131

Query: 220 EKGANYAISHFKVIDCFAQ----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K +    + F+V          K   + + P TGR+HQLRVH   +G PIVGD  Y   
Sbjct: 132 GKPSK---TLFQVAKREEHADGLKTTIVRLLPITGRSHQLRVHMQALGHPIVGDEFYATE 188

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ--ITAPLPAHMVKTWDSLGFKY 326
               F++    +L LHA  +   HPE  +L       +P       +++ F Y
Sbjct: 189 EAQAFST----RLELHATELSFYHPESHQLSRLF---VPCDFYPEVEAMIFDY 234


>gi|312148138|gb|ADQ30797.1| RNA pseudouridine synthase family [Borrelia burgdorferi JD1]
          Length = 305

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 72/306 (23%), Positives = 136/306 (44%), Gaps = 21/306 (6%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++   RLD        + +  ++ K +R G +R++  +  F+ R+  G  + +   + A
Sbjct: 3   ANDNGKRLDSILIKIL-NFSKASIIKHIRKGDIRLNGLKSHFSCRVCKGDKIYLYKSL-A 60

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGF 132
            N  +   K   S+++      +++  ++YEDS + V +K  GI V GG   + + ++ +
Sbjct: 61  QNLNLTTDKCFKSNIDF----QYIRKRIIYEDSDLLVLDKQKGILVHGGKNSLDFLVNSY 116

Query: 133 LKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L S  + S   KP   HRLD+ TSGI++ A+    A+ L+ +F    I K Y++++ G  
Sbjct: 117 LLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTARKLSAAFSGGSIIKKYFAILLGEV 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K+      N L +   +   +V      +K    AI+    I    ++   +E+   TG 
Sbjct: 177 KSP-VVYKNHLFRNKRLRKTFV----LEDKNFVNAITKVNPILSC-KRATLVEIVIETGF 230

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           THQ+R        P++ D KYC  FK +         +LHA  +        + +  +  
Sbjct: 231 THQIRSQCSFNNHPLINDKKYCNKFKKSD-------YFLHAFLVKFNGTFFKKNEFCSKP 283

Query: 312 PAHMVK 317
               +K
Sbjct: 284 SLEFLK 289


>gi|24111502|ref|NP_706012.1| hypothetical protein SF0053 [Shigella flexneri 2a str. 301]
 gi|24050255|gb|AAN41719.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
          Length = 228

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 64/209 (30%), Positives = 103/209 (49%), Gaps = 13/209 (6%)

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            P  +  N  + E K+   + N  +       ++LY+D  I V NKP+G+    G  +  
Sbjct: 5   CPAFDRCNASVTEPKMGMENYNPPQEPWL---VILYQDDHIMVVNKPSGLLSVPGR-LEE 60

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           H D  + + +     +    HRLD  TSG++VVA T+AA + L   FR R  +K Y + V
Sbjct: 61  HKDSVM-TRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARV 119

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEM 245
           WG P   +  +   L+       D+ +  KQ    +    A + ++V++  A     + +
Sbjct: 120 WGHPSPAEGLVDLPLI------CDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVL 173

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +P TGR+HQLRVH L +G PI+GD  Y +
Sbjct: 174 KPITGRSHQLRVHMLALGHPILGDRFYAS 202


>gi|332140106|ref|YP_004425844.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity [Alteromonas
           macleodii str. 'Deep ecotype']
 gi|332143096|ref|YP_004428834.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity [Alteromonas
           macleodii str. 'Deep ecotype']
 gi|327550128|gb|AEA96846.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity [Alteromonas
           macleodii str. 'Deep ecotype']
 gi|327553118|gb|AEA99836.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity [Alteromonas
           macleodii str. 'Deep ecotype']
          Length = 238

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 109/228 (47%), Gaps = 15/228 (6%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           +          +LY+D  + V +KP+G+    G  + +     L S V++      + HR
Sbjct: 7   VYNPPMTPYLDILYQDEDMVVAHKPSGLLSVPGKALEHRDS--LISRVNTVYPTATVVHR 64

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSGILV+A  + + +H+++ F +R  QK Y++ V G  +     +   L+      
Sbjct: 65  LDMATSGILVLALNKDSHRHISKQFELRLTQKRYFARVHGHIEEDSGEVDLPLICDWPNR 124

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCF----AQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              +     + +    AI+ F+VI+      A+++  + + P TGR+HQLRVH L +G P
Sbjct: 125 PKQM----VDFERGKKAITRFEVIERATDDAARRYTLVALYPITGRSHQLRVHMLALGHP 180

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           I+GD  Y  +   +       +L LHA  + L HP   + L    P+P
Sbjct: 181 ILGDRLYAHDEALSMA----PRLQLHAESLSLTHPTLEKWLHFKTPIP 224


>gi|241888711|ref|ZP_04776018.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Gemella haemolysans ATCC 10379]
 gi|241864734|gb|EER69109.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Gemella haemolysans ATCC 10379]
          Length = 293

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 59/326 (18%), Positives = 127/326 (38%), Gaps = 44/326 (13%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR---SGQVRVDKKRVKFNNRI 59
           +   V    ++ ++    L  +   +   I+   L + ++    G ++V+ K       +
Sbjct: 1   MTNIVLKYTIKEEQI---LREFLLEN--SISRKTLTR-IKFDSDGSIKVNGKEENVRYLL 54

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +   +V I       +  +   + +D  +N           ++YED+   + NK   +  
Sbjct: 55  KKNDIVEITLPSENFSEFV---RFIDKDIN-----------IIYEDAYFLIVNKEINLPS 100

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                +       + ++   K      P +  RLD+ TSG++++A+ R      +     
Sbjct: 101 IPSRNLEDESLLEIVNYYFKKKNINTIPHIVTRLDKNTSGLVLIAKHRHVHALFSNM--- 157

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             I K Y +LV G  K   E I   + + +        + ++  +G  +A + + + D  
Sbjct: 158 -EIDKFYTALVSGKVK-DNEIIEAPIRRVTS-----SIIEREVGEGGEFAKTEYWLDDYI 210

Query: 237 AQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             K    ++++ +TGRTHQ+RVH  +   P++GD  Y  +          ++  LH   +
Sbjct: 211 VDKDISVVKLKLYTGRTHQIRVHMKYKDYPLLGDELYGGDVSN------ISRQALHCTNL 264

Query: 296 DLPHPEGGR-LQITAPLPAHMVKTWD 320
              HP     + + A LP  ++    
Sbjct: 265 KFIHPITDEVVNVRADLPEDIISIIK 290


>gi|325269819|ref|ZP_08136429.1| ribosomal large subunit pseudouridine synthase [Prevotella
           multiformis DSM 16608]
 gi|324987792|gb|EGC19765.1| ribosomal large subunit pseudouridine synthase [Prevotella
           multiformis DSM 16608]
          Length = 249

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 106/229 (46%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ I +  K  G  VQ        +   ++ W+  K QKP      + HRLD+  S
Sbjct: 28  VLYEDNHIIIVYKEPGEIVQADKSGDEPLSEIVRRWIKEKYQKPGNVFLGVVHRLDRPVS 87

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L   FR   I K YW++V   P + +  + +WL++       Y + 
Sbjct: 88  GLVVFAKTSKALTRLNNMFRNGEIHKTYWAIVTRPPLDPEATLTDWLVRNERQNKSYAYN 147

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +     A  ++ H+K I+  + ++  LE+   TGR HQ+R    ++  PI GD KY A 
Sbjct: 148 HQI--PTAKKSVLHYKTINR-SDRYTLLEINLMTGRHHQIRCQLSNIDSPIKGDLKYGAP 204

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 S     + L +  ++  HP     + + +PLP      W ++G
Sbjct: 205 RSNPDGS-----ISLLSHRVEFVHPVSKENICVESPLPDD--ALWQAIG 246


>gi|295133553|ref|YP_003584229.1| pseudouridylate synthase [Zunongwangia profunda SM-A87]
 gi|294981568|gb|ADF52033.1| pseudouridylate synthase [Zunongwangia profunda SM-A87]
          Length = 235

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 109/231 (47%), Gaps = 16/231 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ I + NK  G  VQG       +   +K+++  K  KP      + HRLD+ TS
Sbjct: 14  VLHEDNHIIIVNKRVGDIVQGDKTGDKPLSEVVKAYLKEKHNKPGNVYLGVVHRLDRPTS 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ ++T  A   L + F+ +  +K YW++V   P   ++ + ++L +       + H 
Sbjct: 74  GIVLFSKTSKALPRLNKLFQQKDAKKTYWAVVKNRPPKDQDILVHYLKRNPKQNKSFAH- 132

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K     +  AI  ++++      +  LE+   TGR HQ+R     +GCPI GD KY  +
Sbjct: 133 -KNEVPDSKKAILEYRILKEL-DNYFLLEVDLKTGRHHQIRSQLSAIGCPIKGDLKYGFD 190

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
              N        ++LHAR ++  HP     + + A +P      W +   +
Sbjct: 191 RSNN-----DAGIHLHARKLEFIHPVKKETIIVFAEVPDE--ALWQACKIQ 234


>gi|313206986|ref|YP_004046163.1| ribosomal large subunit pseudouridine synthase d [Riemerella
           anatipestifer DSM 15868]
 gi|312446302|gb|ADQ82657.1| ribosomal large subunit pseudouridine synthase D [Riemerella
           anatipestifer DSM 15868]
 gi|315024062|gb|EFT37064.1| Ribosomal large subunit pseudouridine synthase D [Riemerella
           anatipestifer RA-YM]
 gi|325335579|gb|ADZ11853.1| Pseudouridylate synthase, 23S RNA-specific [Riemerella
           anatipestifer RA-GD]
          Length = 229

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 70/225 (31%), Positives = 113/225 (50%), Gaps = 14/225 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
            ++  +LYED+ + V NK AG  VQG       +   +K ++ S+  KP      L HR+
Sbjct: 1   MIQEQILYEDNHLLVINKKAGQLVQGDKTGDVSLLELIKDFIKSRDNKPGNVFLGLVHRI 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSG+++ A+T  A   LT+  + R I+K YW++V     +  + + ++L K      
Sbjct: 61  DRPTSGLVIYAKTSKALTRLTQMIKNREIKKTYWAIVPKEMISPSQKLVHYLKKNEK--N 118

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           +   +  +  +GA  AI  + +I      +  LE+   TGR HQ+R     +G PI GD 
Sbjct: 119 NKAIIFTKPTEGAKQAILSYNLILSL-DNYLLLEVDLETGRHHQIRAQLSKIGIPIKGDL 177

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAH 314
           KY A+      S     + LHAR +D  HP    ++ I AP+P+H
Sbjct: 178 KYGAS-----RSNSDGGISLHARRLDFIHPVSKEKITIVAPVPSH 217


>gi|312135354|ref|YP_004002692.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
 gi|311775405|gb|ADQ04892.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
          Length = 311

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 67/289 (23%), Positives = 122/289 (42%), Gaps = 24/289 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV+ +   +++++  K  YP I    + K+LR G++ V     +    ++ G  V    
Sbjct: 5   FVVDKELAGVKVEKAIKKKYPTIPMSVIFKMLRKGEIIVSFLPAQKGQVLKFGDTVSFEI 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H               K  + +K   +YED  I V +KP GI     S   Y +
Sbjct: 65  EDRFLEH---------------KKVEIIK---VYEDDNIVVIDKPYGIPSHPDSNNEYSV 106

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             +++    SK + P+L HRLD+ T+G++++A+ R     + +    R I K Y  +   
Sbjct: 107 VSWIEDNY-SKDELPQLCHRLDRNTAGLMIIAKNRQVLSEMLKYMSRRAIIKKYLCITKK 165

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               +   + ++L K S     Y+    Q+  G +  ++ +K++         L+++  +
Sbjct: 166 ADLPESGVLVHYLKKDSKKSKVYISDFPQD--GYSEVVTAYKIV-RQKDDLQLLDVEIKS 222

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           G+THQ+R    H+G  I+GD KY                 L A Y+   
Sbjct: 223 GKTHQIRAQLAHVGLCILGDSKYGDWELNKKYKTDM--QALCAYYLKFE 269


>gi|326335663|ref|ZP_08201850.1| ribosomal large subunit pseudouridine synthase [Capnocytophaga sp.
           oral taxon 338 str. F0234]
 gi|325692429|gb|EGD34381.1| ribosomal large subunit pseudouridine synthase [Capnocytophaga sp.
           oral taxon 338 str. F0234]
          Length = 235

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 107/229 (46%), Gaps = 15/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +   NK AG  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 10  VLYEDNHLIAINKRAGDIVQGDKTGDIPLSEIVKEYLVKKYNKPGDAYLGVVHRLDRPTT 69

Query: 156 GILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           GI++ A+T  A   L  +F  +  + K YW+LV       +  + ++L++ +     Y +
Sbjct: 70  GIVLFAKTSKALPRLNAAFATKEEVCKRYWALVEKKTIPAEGTLTHFLVRNTSQNKSYAY 129

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                +  +  A+  +KV+      +  +E+   TGR HQ+R     +GCP+ GD KY A
Sbjct: 130 QT--EKPQSQKAVLTYKVLATLTH-YLLVEINLLTGRHHQIRAQFAALGCPLKGDLKYGA 186

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                  S     + LHAR ++L HP     L ITAPLP         +
Sbjct: 187 KRSNPDGS-----ICLHARTLELLHPIKKEPLSITAPLPESFNNLLKKI 230


>gi|224105621|ref|XP_002313876.1| predicted protein [Populus trichocarpa]
 gi|222850284|gb|EEE87831.1| predicted protein [Populus trichocarpa]
          Length = 324

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 99/328 (30%), Positives = 147/328 (44%), Gaps = 74/328 (22%)

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + +P  +  L    ++    +  +N      F++ + LY+D+ I V NKP G+ VQG
Sbjct: 4   GDRIFLPISVKVLPAEKQDCHCNEEEIN------FIRGLELYKDAAIIVVNKPPGMPVQG 57

Query: 122 GSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-- 178
           G GI   +D    S   S   + PRL HRLD++ SGILV+ RT+ +A  L   FR +   
Sbjct: 58  GIGIKRSLDELSASCFSSDYSEPPRLVHRLDRDCSGILVMGRTQTSATVLHAIFREKTLA 117

Query: 179 ------------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGG--DYVHVVKQNEK-GA 223
                       +Q+ YW+LV G P+  K  I+  L K     G  D + VV+ ++   +
Sbjct: 118 ASNDDVGNKRRILQRKYWALVIGSPRRPKGLISAPLGKVVVDNGKSDRITVVENSQNLSS 177

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNFT- 281
            +A++ ++VI+  +  F WLE+ P TGR HQLRVH    +G PIVGD+KY      N+  
Sbjct: 178 QHAVTQYRVIES-SHGFTWLELSPLTGRKHQLRVHCAEVLGTPIVGDYKYAWQAHRNWKQ 236

Query: 282 -------------------------------SPIQNKLYLHARYMDLPHPEG-------- 302
                                          S    +L+LH + M LP            
Sbjct: 237 LQWSNIEDNSNDKSLSEKILPFALDLDSGSISEKHPRLHLHCKQMVLPDVSKALQDVQLS 296

Query: 303 --------GRLQITAPLPAHMVKTWDSL 322
                     L+  APLP +M K+WD L
Sbjct: 297 SDYDFSQLASLKFDAPLPPYMKKSWDIL 324


>gi|120434465|ref|YP_860167.1| RNA pseudouridylate synthase [Gramella forsetii KT0803]
 gi|117576615|emb|CAL65084.1| RNA pseudouridylate synthase [Gramella forsetii KT0803]
          Length = 289

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 131/322 (40%), Gaps = 46/322 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M  ++  +V    E +RL  +  + +  I    +L+K ++   V ++ ++ + ++ I+ G
Sbjct: 1   MKILESHIVPAISEKIRLQEYAVSIFTSIQTRSSLKKAIKKRLVLINGEKAQTSDWIKPG 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q + +         + K                 L   +L+ED  I V +KP G      
Sbjct: 61  QKIDLLKPFAETKKVFK-----------------LNFEVLFEDEHIAVVHKPPGFPT--S 101

Query: 123 SGIAYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 I+  L   + S  +      P   HRLD  TSGIL+ A+T ++   L E+F  +
Sbjct: 102 GNYFKTIENALPHNLSSSSEIDTLPYPLPAHRLDNPTSGILLCAKTNSSLIKLQEAFAQK 161

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +IQK Y+++V G  K K E I + +                ++K +   +   +      
Sbjct: 162 QIQKTYYAIVSGEIKEKIE-IDSPI----------------DQKISKTILIPIEFYQIEN 204

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           + +  +E+ P TGRTHQLR+H      PI+GD+ Y         +     +YL A  +  
Sbjct: 205 KNYTLVELNPLTGRTHQLRIHLSENNTPIIGDNLYGKEETNLLKN---KSIYLFAGKISF 261

Query: 298 PHPEGGR-LQITAPLPAHMVKT 318
            HP   + +     LP      
Sbjct: 262 DHPLSKKLMTFQLQLPKKFRNL 283


>gi|93006645|ref|YP_581082.1| pseudouridylate synthase [Psychrobacter cryohalolentis K5]
 gi|92394323|gb|ABE75598.1| tRNA pseudouridine synthase C [Psychrobacter cryohalolentis K5]
          Length = 256

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 105/241 (43%), Gaps = 18/241 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  ++YED  +   NK AG+ V             ++   D+ G      HRLD+ TSG+
Sbjct: 14  QIEIIYEDEFLVAINKEAGLLVHRSWLDKGETRFAMQLTRDAVGCHVFPVHRLDKPTSGV 73

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A++ A A+ LTE+F   ++ K Y ++V G    +         +   I   + ++  
Sbjct: 74  LLFAKSSAVARSLTEAFTEHKVTKQYLAVVRGYMSEQGTVDYALSFQPDAIADKFANL-- 131

Query: 218 QNEKGANYAISHFKVI-----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             +K A  A++H++ +                ++  + + P TGR HQLR H  H+   I
Sbjct: 132 --DKPAQEAVTHWQSLAQIELPFAVSKKHDTSRYSLMRLTPETGRKHQLRRHMRHLFHHI 189

Query: 267 VGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           VGD  +       F  T     ++ LHA+ + L HP  G  L + A L    ++  +   
Sbjct: 190 VGDTSHGDGRHNRFFRTQYGCARMLLHAQTLALSHPVTGEPLLLKAGLDDQWLRIMEEFA 249

Query: 324 F 324
           +
Sbjct: 250 W 250


>gi|183219523|ref|YP_001837519.1| pseudouridine synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Paris)']
 gi|189909665|ref|YP_001961220.1| pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167774341|gb|ABZ92642.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167777945|gb|ABZ96243.1| Pseudouridine synthase (Uracil hydrolyase) [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 237

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 61/218 (27%), Positives = 105/218 (48%), Gaps = 19/218 (8%)

Query: 101 LLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           ++YED  + V +KPAG+       +        +  ++K   +    +  + HRLD++TS
Sbjct: 16  IIYEDRDLLVVDKPAGLLTIATESEKSKTAYASLMDYVKKGSERSKNRIFIVHRLDRDTS 75

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GILV A+T  A Q L +++   + +K Y ++  G  K K+  I ++L +       +   
Sbjct: 76  GILVFAKTEIAKQTLQDNWD--QTKKNYIAVTHGQWKEKQGTIKSYLTE----SKAHRVY 129

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              + K   Y+ + +KV+   +  +  LE+   TGR +Q+RVH      PIVGD KY + 
Sbjct: 130 SVDDPKEGKYSETKYKVLK-ESNLYSLLEIDLITGRKNQIRVHFAENKHPIVGDTKYGSE 188

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            K         ++ LH+  +DL HP   + L   A +P
Sbjct: 189 TKS------YPRMALHSFSIDLIHPFQKKPLSFNAKIP 220


>gi|313158249|gb|EFR57651.1| pseudouridine synthase, RluA family [Alistipes sp. HGB5]
          Length = 228

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 105/225 (46%), Gaps = 14/225 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
           F    +LYED+ + + NK  G  VQ        ++  +K++V  +  KP      + HR+
Sbjct: 2   FTPEDILYEDNHLLIVNKRCGDLVQPDPSGESALEDQIKAFVKRRDAKPGDVFLGVVHRI 61

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+  SG ++ A+T  A   L E  R  RI+K+YW+L    P  +   + +++L+ +    
Sbjct: 62  DRPVSGAVLFAKTSKALTRLNEMIREGRIRKVYWALTERTPDPESGELRHYILRDARTNR 121

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                    + GA  A   ++ +      +  +E++  TGR HQ+R     +GCPI GD 
Sbjct: 122 SR--ACDGPKPGAKEARLRYETLGA-GTNYTLVEVELLTGRHHQIRAQLSKIGCPIRGDL 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAH 314
           KY A       S     + LH+R ++  HP     + +TAP PA 
Sbjct: 179 KYGAR-----RSLPGGGISLHSRRVEFEHPVRREPVSVTAPAPAD 218


>gi|312149422|gb|ADQ29493.1| RNA pseudouridine synthase family [Borrelia burgdorferi N40]
          Length = 305

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 69/306 (22%), Positives = 131/306 (42%), Gaps = 21/306 (6%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++   RLD        + +   + K +R G +R++  +  F+ R+  G  + +   +  
Sbjct: 3   ANDNGKRLDSILIKIL-NFSKAIIIKHIRKGDIRLNGLKSHFSCRVCKGDKIYLYKSLAQ 61

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGF 132
             ++      +D          +++  ++YEDS + V +K  GI V GG   + + ++ +
Sbjct: 62  NLNL-----TMDECFKSNIDFKYIRKRIIYEDSDLLVLDKQKGILVHGGKNSLDFLVNSY 116

Query: 133 LKSW-VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L S  + S   KP   HRLD+ TSGI++ A+    A+ L+ +F    I K Y++++ G  
Sbjct: 117 LLSQNLRSLSFKPSAVHRLDRNTSGIIIFAKNINTARKLSAAFSGGSIIKKYFAILLGEV 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K+      N L +   +   +V      +K    AI+    I    ++   +E+   TG 
Sbjct: 177 KSP-VVYKNHLFRNKRLRKTFV----LEDKNFVNAITKVNPILSC-KRATLVEIVIETGF 230

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           THQ+R        P++ D KYC  FK +         +LHA  +        + +  +  
Sbjct: 231 THQIRSQCSFNNHPLINDKKYCNKFKKSD-------YFLHAFLVKFNGTFFKKNEFCSKP 283

Query: 312 PAHMVK 317
               +K
Sbjct: 284 SLEFLK 289


>gi|229552586|ref|ZP_04441311.1| pseudouridylate synthase RluD [Lactobacillus rhamnosus LMS2-1]
 gi|229314138|gb|EEN80111.1| pseudouridylate synthase RluD [Lactobacillus rhamnosus LMS2-1]
          Length = 310

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 65/293 (22%), Positives = 117/293 (39%), Gaps = 37/293 (12%)

Query: 25  FKNHYPH--INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
            ++      I      ++  +  ++V+     FN  +++G ++ +               
Sbjct: 47  LRDQLQDWLIPRKRQHQMRVAQTIQVNGHYRHFNEPVKNGDLISLTY------------- 93

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKG 141
             D  V+ T   +       YED  + + +KPAG+       G    +     +++    
Sbjct: 94  --DELVHRTYVPETPHLNTRYEDDDLLIVDKPAGMKTHPNQPGETGTLMNQAAAYLAP-- 149

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKECIAN 200
               +THRLD  TSG+LV+A+   A   +      + + + Y ++V  GIP  +K  I  
Sbjct: 150 FPALITHRLDMATSGLLVIAKNPLAQAIINRQLTTKTMHRDYLAVVPSGIP--EKGTIQA 207

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +          +           +A++H+  I   A     +E+   TGRTHQ+RVH  
Sbjct: 208 PIGHDPDDKRKRMIRA-----DGAFAVTHYHRIAETADTAT-IELNLETGRTHQIRVHLA 261

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
            +G PI+GD  Y A       +    ++ LHA  + L  P     L +T+P P
Sbjct: 262 SIGFPIIGDPLYAA-------TETATRMQLHAFRVRLIRPLTIEPLTVTSPSP 307


>gi|328471410|gb|EGF42305.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 10329]
          Length = 250

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 106/231 (45%), Gaps = 15/231 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++ED  I   NKP+G+    G    +H    + S +  +    ++ HRLD  TSG++V
Sbjct: 15  DIVFEDDHILAVNKPSGLLSVPGRLAEHHDS--MWSRLQEEYPDIQVVHRLDMSTSGLMV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A   L + F+ R   KIY++ VWG  + ++  I   L+           V  ++
Sbjct: 73  LAKNKRAESALKKQFQFRLTHKIYYARVWGHVEQEEGEIDLPLICD-WPNRPLQKVCFED 131

Query: 220 EKGANYAISHFKVIDCFAQ----KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K +    + F+V          K   + + P TGR+HQLRVH   +G PIVGD  Y   
Sbjct: 132 GKPSK---TLFQVAKREEHEDGTKTTIVRLLPITGRSHQLRVHMQALGHPIVGDEFYATE 188

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
               F+     +L LHA  +   HP+   L+ +  +P       + + F Y
Sbjct: 189 EAKVFSE----RLELHASELSFYHPKSHWLR-SIFVPCDFYPEAEEMIFDY 234


>gi|227530166|ref|ZP_03960215.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus vaginalis
           ATCC 49540]
 gi|227349919|gb|EEJ40210.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus vaginalis
           ATCC 49540]
          Length = 291

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 63/271 (23%), Positives = 118/271 (43%), Gaps = 32/271 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
            G+  VD ++V+   +I   Q + I          I + ++ D SV L+         ++
Sbjct: 36  QGKFLVDHRKVRPTTKILPNQPLTI----------IAQPELRDLSVKLS----DAPLNIV 81

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSK--GQKPRLTHRLDQETSGIL 158
           YED    V +KPAG++   G  +      +  +   V+ K   Q+P L  RLD+ T G+L
Sbjct: 82  YEDDNWLVIDKPAGVTSIPGPTVDNGTVLNRAVHYLVEEKSADQRPHLITRLDRYTGGLL 141

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+   A+  +++  +  ++ K Y + V GI   + + I   + ++         V + 
Sbjct: 142 LIAKHHVASSMISQQVQQHQMLKEYTAFVSGIFDKEHDIIDKPIARREGQ------VQRV 195

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             +    A++ + V +     +  L ++ HTGRTHQ+RVH   +  P++GDH Y  +   
Sbjct: 196 IAEDGQRAVTEYWV-EEEGADWTKLRVRLHTGRTHQIRVHLASINHPLIGDHLYGGDTSK 254

Query: 279 NFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
                      L A  +    P    +L  +
Sbjct: 255 ------YQHQALWATKLSFKDPFTLKQLTFS 279


>gi|226327118|ref|ZP_03802636.1| hypothetical protein PROPEN_00983 [Proteus penneri ATCC 35198]
 gi|225204336|gb|EEG86690.1| hypothetical protein PROPEN_00983 [Proteus penneri ATCC 35198]
          Length = 217

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 112/235 (47%), Gaps = 22/235 (9%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           + +          +LY+D  I   NKP+G+    G   A   +  + S + ++       
Sbjct: 2   MEVYNPPTDPWLHVLYQDEHIIAVNKPSGLLSVPGK--APEHNDSIMSRIKAEFPNAECV 59

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA  + A + L   FR R  +K Y + VWG  + ++  +   L+    
Sbjct: 60  HRLDMATSGVIVVALNKEAERELKRQFREREPKKTYIARVWGHVEKEEGLVDLPLI---- 115

Query: 208 IGGDYVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V++ + +    +++ P TGR+HQLRVH L +G P
Sbjct: 116 --CDWPNRPKQKVCHETGKAAQTFYEVLE-YEENATRVKLSPITGRSHQLRVHMLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           I+GD  Y A+ +    +P   +L LHA+ + + HP        +P+  H     D
Sbjct: 173 ILGDRFY-AHPQARAMAP---RLQLHAQELFITHPA-----FRSPI--HFECLAD 216


>gi|224083652|ref|XP_002197702.1| PREDICTED: RNA pseudouridylate synthase domain containing 4
           [Taeniopygia guttata]
          Length = 351

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 81/280 (28%), Positives = 128/280 (45%), Gaps = 40/280 (14%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQ 142
            V+    +  LK   LY++ +I V +KP G+ V GG GI   I   L    K   + K +
Sbjct: 75  QVHPNVLAKILKQKTLYQNEEIVVIDKPYGLPVHGGPGIKNCIADVLPILAKMLENMKTE 134

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD+ET+G++V+AR++ AA+ +   F+ R+++KIYW++V G P   +  +   +
Sbjct: 135 PLHLCHRLDKETTGVMVLARSKEAAEKIRLLFKTRQVEKIYWAIVLGDPDPVEGVVEIPI 194

Query: 203 LKKSHIGG-----------------DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           ++K                      D   +  +  + A  A++ ++ + C A     LE+
Sbjct: 195 VEKEVQSHQSHYKMTLAPNYRLCPEDGKVMKIRGHRHAERAVTRYRRL-CAASACSLLEL 253

Query: 246 QPHTGRTHQLRVHALH-MGCPIVGDHKYC---------------ANFKGNFTSPIQNKLY 289
           QP TG  HQ+RVH  + +GCPI+GDHKY                   K   +      L+
Sbjct: 254 QPITGVKHQIRVHLAYGLGCPILGDHKYSHWSKLAPQKLPEHTLRRLKLEQSKARHLPLH 313

Query: 290 LHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           LHA  + L  P G  L     LP    KT   L     ++
Sbjct: 314 LHAHRLCL--PLGQPLDFVCKLPLFFQKTLRKLELDIPKD 351


>gi|113461656|ref|YP_719725.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           somnus 129PT]
 gi|112823699|gb|ABI25788.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           somnus 129PT]
          Length = 221

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 107/236 (45%), Gaps = 20/236 (8%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            ++D    L  + D     ++Y D  I V NKP+G+    G+   Y+      S V  K 
Sbjct: 2   ALIDYRPPLEPYLD-----IVYRDDHILVVNKPSGLLSVSGNQPQYYDSAM--SRVKEKY 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGIL+ A ++ A + L   FR R  +K Y +L+WG        +   
Sbjct: 55  GFCEPAHRLDMATSGILLFAMSKMADRELKRQFREREPKKHYQALIWGHLAQDTGSVNLP 114

Query: 202 LLKK-SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           L+    +     V  V         A+++FKV+  F      + + P TGR+HQLR+H L
Sbjct: 115 LICDWENRPRQKVCFVH-----GKRAVTNFKVLHRFENNITQVRLTPITGRSHQLRLHML 169

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            +G PI+GD  Y      +    +  +L LHA ++ + HP   + +Q +   PA  
Sbjct: 170 ALGHPILGDKFYAHPQAKS----LAPRLCLHAEFLQITHPLTKKVIQFST--PADF 219


>gi|88859129|ref|ZP_01133770.1| pseudouridylate synthase for 23S rRNA [Pseudoalteromonas tunicata
           D2]
 gi|88819355|gb|EAR29169.1| pseudouridylate synthase for 23S rRNA [Pseudoalteromonas tunicata
           D2]
          Length = 209

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 58/213 (27%), Positives = 103/213 (48%), Gaps = 12/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  + + NKP+G+    G    +     L+          ++ HRLD  TSG++ +
Sbjct: 7   IIYQDEDLLILNKPSGLLTVPGKDPLH--ADCLEKRAQRVFPTAKIVHRLDMATSGLICL 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +AA  H++  F+ R+ QK Y + V+G    +   +   L+         +     N 
Sbjct: 65  ALNKAAHSHVSRQFQDRKTQKRYIARVFGKLTPETGSVDLPLICDWPNRPKQM----VNF 120

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    +++H++V++ + +    + + P TGR+HQLRVH L  G  I+GD  Y        
Sbjct: 121 EYGKPSLTHWQVLN-YEEHATRVALTPITGRSHQLRVHMLSQGHVILGDKLYAHPEAFQM 179

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            S    +L LHA ++ + HP   + L+ TAP P
Sbjct: 180 AS----RLQLHAEWLAITHPVTAQALEFTAPCP 208


>gi|227327724|ref|ZP_03831748.1| ribosomal large subunit pseudouridine synthase A [Pectobacterium
           carotovorum subsp. carotovorum WPP14]
          Length = 217

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 65/215 (30%), Positives = 99/215 (46%), Gaps = 14/215 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G     H D  + S + +        
Sbjct: 1   MEPYNPPTDPWLHILYQDQHIMVVNKPSGLLSVPGRAPE-HKDSVM-SRIQADYPTAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++ VA T+AA + L   FR R  +K Y + VWG     +  I   L+    
Sbjct: 59  HRLDMATSGVIAVALTKAAERELKRQFREREPKKSYLARVWGHMAQDEGVIDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V+   A     +++ P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCFETGKAAQTEYQVLSRDADGTTRVKLMPITGRSHQLRVHLLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           I+GD  Y           +  +L LHA+ + + HP
Sbjct: 173 ILGDGFYAHPDAKA----LAPRLLLHAQELAITHP 203


>gi|284008559|emb|CBA75113.1| ribosomal large subunit pseudouridine synthase A [Arsenophonus
           nasoniae]
          Length = 215

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 71/212 (33%), Positives = 105/212 (49%), Gaps = 16/212 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G  +  H D  + + V +        HRLD  TSGI+VV
Sbjct: 13  VLYQDQHIIVVNKPSGLLSVPGKAVE-HKDSIM-TRVQADFPTAESVHRLDMATSGIMVV 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + A + L   FR R  +KIY + VWG   NKK  I   L+       D+ +  KQ  
Sbjct: 71  ALNKTAEKELKRQFREREPEKIYQARVWGHITNKKGLIDLPLI------CDWPNRPKQKV 124

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A + +KV+  + ++   +++ P TGR+HQLRVH L +G PI+GD  Y      
Sbjct: 125 CFTTGKPAQTKYKVL-AYEEQTTLVKLIPITGRSHQLRVHLLSLGHPIIGDQFYAHQ--- 180

Query: 279 NFTSPIQNKLYLHARYMDLPHPE-GGRLQITA 309
                + ++L LHA  + + HP  G  +  T 
Sbjct: 181 -AALILSSRLQLHAEELYITHPIYGSPIHFTC 211


>gi|145637747|ref|ZP_01793398.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae PittHH]
 gi|145269045|gb|EDK08997.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae PittHH]
          Length = 219

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 63/226 (27%), Positives = 107/226 (47%), Gaps = 15/226 (6%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            +++ +  L  + D     ++Y+D+ + V NKP+G+    G+   Y+    + S V  K 
Sbjct: 2   ALIEYNPPLEPYLD-----IIYQDNHLCVVNKPSGLLSVSGNQPQYYDS--VMSRVKEKF 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSGI+V A ++AA + L   FR R  +K Y ++VWG  +N    +   
Sbjct: 55  GFCEPAHRLDMATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLENDYGEVNLP 114

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           ++       +     + +      A++ F+V+         +++ P TGR+HQLR+H L 
Sbjct: 115 MICD----WENRPRQRLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLA 170

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           +G PI+GD  Y        +     +L LHA  + + HP  G   I
Sbjct: 171 LGHPILGDKFYSHPQAKVMS----PRLCLHAEELTITHPITGETMI 212


>gi|302307964|ref|NP_984770.2| AEL091Cp [Ashbya gossypii ATCC 10895]
 gi|299789245|gb|AAS52594.2| AEL091Cp [Ashbya gossypii ATCC 10895]
          Length = 609

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 62/253 (24%), Positives = 109/253 (43%), Gaps = 23/253 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +  + +   +    +K++ SG V ++ K    ++ +++G ++         +H +  
Sbjct: 130 LDVFV-DEFRDRDRPYYEKVIGSGGVLLNGKSSTLDSVLRNGDLI---------SHELHR 179

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            +   SS  +           +YED  I V +KP+GI         Y  +   K      
Sbjct: 180 HEPPVSSRPIRT---------VYEDDDILVIDKPSGIPAHPTG--RYRFNSITKILEKQL 228

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A  + +  + R ++K Y + V G      E + +
Sbjct: 229 GYTVHPCNRLDRLTSGLMFLAKTPKGADEMGDQMKAREVKKEYVARVVGEFPI-GEIVVD 287

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             LK          V    ++    A + FK I    Q    ++ QP+TGRTHQ+RVH  
Sbjct: 288 MPLKTIEPKLALNMVCDPEDEAGKGAKTQFKRISYDGQ-TSIVKCQPYTGRTHQIRVHLQ 346

Query: 261 HMGCPIVGDHKYC 273
           ++G PI  D  Y 
Sbjct: 347 YLGFPIANDPIYS 359


>gi|188995238|ref|YP_001929490.1| putative ribosomal large subunit pseudouridine synthase D
           [Porphyromonas gingivalis ATCC 33277]
 gi|188594918|dbj|BAG33893.1| putative ribosomal large subunit pseudouridine synthase D
           [Porphyromonas gingivalis ATCC 33277]
          Length = 227

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 109/228 (47%), Gaps = 15/228 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + + NK  G  VQG       +   +K W+  K  KP      + HRLD+  +
Sbjct: 3   VVYEDNHLIIVNKAVGEIVQGDKTGDSPLSETVKQWIKEKYAKPGKVFLGVAHRLDRPVA 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L   FR  ++QK+Y ++V   P    + + +++ +   +   +  V
Sbjct: 63  GLVVFAKTSKALARLNNMFRDGKVQKVYRAIVKQRPPKDGDTLVHYISRNERLNKSFASV 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K     +  A   ++++   +  +  LE++ HTGR HQ+R     MGCPI GD KY   
Sbjct: 123 CKV--PNSKKASLSYRLLAS-SDNYHLLEIELHTGRHHQIRCQLAAMGCPIKGDLKYGFG 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     + L A  +   HP  G  + +TAPLP++  K W  L
Sbjct: 180 -----RSNPDGGISLLAHRIRFTHPVSGVLIDLTAPLPSN-DKLWSLL 221


>gi|152987872|ref|YP_001347260.1| pseudouridine synthase RluA [Pseudomonas aeruginosa PA7]
 gi|150963030|gb|ABR85055.1| pseudouridine synthase RluA [Pseudomonas aeruginosa PA7]
          Length = 211

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 60/216 (27%), Positives = 107/216 (49%), Gaps = 11/216 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  ++++D  + V +KP  +    G       D  +    ++   + R+ HRLD ETSG+
Sbjct: 5   QIRIVHQDDALLVVDKPTLLLSVPGRADDN-KDCLVTRLQENGYPEARIVHRLDWETSGL 63

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+AR   + + L+  F  R  +K Y +L WG+P+     I   L         +V    
Sbjct: 64  MVLARDADSHRELSRQFHDRETEKAYTALCWGLPELDSGRIELPLRYDPPTKPRHV---- 119

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +   +A++ ++V++   +++  +E+ P TGR+HQLRVH L +G P++GD  Y     
Sbjct: 120 VDFEHGRHALTFWRVLERH-ERWSRVELTPITGRSHQLRVHMLSIGHPLLGDRLY----A 174

Query: 278 GNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
                   ++L LHA  + L HP  G RL+  +  P
Sbjct: 175 NPEALAAHDRLCLHASLLCLTHPRSGERLRFESAAP 210


>gi|253689991|ref|YP_003019181.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251756569|gb|ACT14645.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 217

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 65/216 (30%), Positives = 99/216 (45%), Gaps = 14/216 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G     H D  + S + +        
Sbjct: 1   MEPYNPPTDPWLHILYQDQHIMVVNKPSGLLSVPGRAPE-HKDSVM-SRIQADYPTAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++ VA T+AA + L   FR R  +K Y + VWG  +  +  I   L+    
Sbjct: 59  HRLDMATSGVIAVALTKAAERELKRQFREREPKKSYLARVWGHMEQDEGVIDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V+         +++ P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCFETGKAAQTEYQVLSRDDDGTTRVKLMPITGRSHQLRVHLLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           I+GD  Y              +L LHA+ + + HPE
Sbjct: 173 ILGDGFYAHPDAKAMA----PRLLLHAQELAITHPE 204


>gi|328948215|ref|YP_004365552.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
 gi|328448539|gb|AEB14255.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
          Length = 314

 Score =  166 bits (420), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 63/328 (19%), Positives = 136/328 (41%), Gaps = 33/328 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHY--PHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           M ++++   + D++  RLD+  K  +    +   N+ K++R   ++++  +    +RI+S
Sbjct: 1   MEFIEF-EAKEDDDGRRLDKAAKRIFESKGLQPENIFKLIRKTLIKLNNAKSAPEDRIKS 59

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + I   +   N   K +    S+  +      +     +++  +++ NK +GI VQ 
Sbjct: 60  GDKIFIADFLLKENAARKSKTEKKSTQKIH---GDISLQTAFKNEHLWIINKQSGIEVQP 116

Query: 122 GSGIAYHIDGFLKSWVD--SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               ++ +  F+       S   +P   HR+D+ T+G++  +++   A+  +E+ +   I
Sbjct: 117 SKNSSFCLADFVAQNTKNASLSFRPGPLHRIDKFTTGLITFSQSLQGAKWFSENIKNHSI 176

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---F 236
           +K Y ++V       +  I + +                       A +  K I      
Sbjct: 177 KKTYLAVVENFLPENELAIYDTI-------------------EEKTACTKIKKIAQGIFC 217

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            ++    ++Q  TGR HQ+R+H    G P++GD  Y      N         +LHA  ++
Sbjct: 218 GKEISLAKIQIETGRKHQIRIHCASRGFPLLGDKLYGGTKIPN-GEFSSCGFFLHAWKLE 276

Query: 297 LP--HPEGGRLQITAPLPAHMVKTWDSL 322
            P  +P     +I A +     K  ++ 
Sbjct: 277 FPKDNPLLLPSEIQAEISPLFKKFIENF 304


>gi|325103254|ref|YP_004272908.1| pseudouridine synthase [Pedobacter saltans DSM 12145]
 gi|324972102|gb|ADY51086.1| pseudouridine synthase [Pedobacter saltans DSM 12145]
          Length = 238

 Score =  166 bits (420), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 97/239 (40%), Gaps = 22/239 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
            K I+L+ED  I + NKP  +S           +  L        +  ++ HRLD+ETSG
Sbjct: 6   FKDIILFEDEDIIIVNKPPFLSS---LDEREGKEISLLKMAKQYVEDAQVCHRLDKETSG 62

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LVVA+   A +H++  F  RR+ KIY ++V G    +   +   +L            V
Sbjct: 63  LLVVAKNPEAYRHMSILFERRRVNKIYHAIVDGTHVFEDLLVDLPILNVGKGN------V 116

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +      A + F+ ++ F + +  LE +P TGR HQ+R+H       I GD  Y    
Sbjct: 117 VISRGEGKRAETWFRSLEYF-KHYTLLECRPVTGRMHQIRIHLATQRASITGDKMYGGQP 175

Query: 277 K------------GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
                             P+  +  LHAR +    P G  + I A  P         L 
Sbjct: 176 AFLSKIKRGYKLTDEEEQPVMKRFALHARQLSFVKPNGEEITIEAEYPKDFAVLLKLLR 234


>gi|212711202|ref|ZP_03319330.1| hypothetical protein PROVALCAL_02274 [Providencia alcalifaciens DSM
           30120]
 gi|212686370|gb|EEB45898.1| hypothetical protein PROVALCAL_02274 [Providencia alcalifaciens DSM
           30120]
          Length = 216

 Score =  166 bits (420), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 66/214 (30%), Positives = 102/214 (47%), Gaps = 16/214 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D  I V NKP+G+    G    +H    + S +          HRLD  TSG++
Sbjct: 12  LYVLYQDEHIIVVNKPSGLLSVPGKAPEHHDS--IMSRIQRDHPAAESVHRLDMATSGVM 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  +AA + L   FR R  +K Y + VWG  +  +  +   L+       D+ +  KQ
Sbjct: 70  VVALHKAAERELKRQFREREPKKHYVARVWGHLEKPEGLVDLPLI------CDWPNRPKQ 123

Query: 219 NE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               +    A + + V++   Q    +++ P TGR+HQLRVH L +G PI+GD  Y    
Sbjct: 124 KVCFETGKSAQTEYLVLEYEEQ-ATRVKLSPITGRSHQLRVHMLALGHPILGDRFYAHEE 182

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
                  +  +L LHA+ + + HPE G  +  T 
Sbjct: 183 ----ALALAPRLQLHAQELYITHPEYGTPMHFTC 212


>gi|283833280|ref|ZP_06353021.1| pseudouridine synthase A [Citrobacter youngae ATCC 29220]
 gi|291070917|gb|EFE09026.1| pseudouridine synthase A [Citrobacter youngae ATCC 29220]
          Length = 232

 Score =  166 bits (420), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 96/221 (43%), Gaps = 18/221 (8%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
              + +  +LY+D  + + NKPAG+    G          +   +        L HRLD 
Sbjct: 11  PPCYDEIEILYQDEHLVLINKPAGLLSLSGKNPQN--LDSVHHRLVQIYPGCTLVHRLDF 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V+AR +A    L + F  R + K Y +L+ G  +N    I   + K   +    
Sbjct: 69  GTSGLMVIARNKAINAALCQQFSQRVVTKAYSALLCGHLENDAGVIDAAIAKDPAL-FPR 127

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGC 264
           + +   N      A S ++VI+ F  +           +++ P TGRTHQLR+H   +G 
Sbjct: 128 MSICAMN---GKPARSRYQVIERFLHRQEDGALLPLTRVQLTPETGRTHQLRIHCQQLGH 184

Query: 265 PIVGDHKYCANF-KGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           PI+G   Y      G   +P   +L LHA  +   HP   R
Sbjct: 185 PILGCDLYGGRLWPGTERTP---RLMLHASALHFRHPVSER 222


>gi|325122993|gb|ADY82516.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter calcoaceticus PHEA-2]
          Length = 212

 Score =  166 bits (420), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 70/223 (31%), Positives = 108/223 (48%), Gaps = 17/223 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V  +  K  L HRLD++
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLVAIE-PKTLLIHRLDRD 58

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     +   F+ R+  KIY +LV G  + +   +   ++         +
Sbjct: 59  TSGILVFGLSKRGQSAIARQFQDRQTSKIYEALVAGHLEGE-GTVDIPVIYDP--SRPPL 115

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+V  +      A++H++VI+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD 
Sbjct: 116 HIVDASHN--KPALTHWQVIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDT 173

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            Y    +      +  +L LHA+ +   HP     L    P+P
Sbjct: 174 LYATPEQQ-----LVPRLCLHAKQLSFNHPVTAETLTFDCPVP 211


>gi|291540830|emb|CBL13941.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis XB6B4]
          Length = 221

 Score =  166 bits (420), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 64/219 (29%), Positives = 108/219 (49%), Gaps = 9/219 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++  ++YED  I V  KPAG++ Q        ++  LK++  SKG+ P +   HRLDQ  
Sbjct: 5   MQPAIIYEDEDIIVCKKPAGVATQTRRIGQADMESLLKNYRASKGELPYIGVVHRLDQPV 64

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G++V A+ + AA  L+   + +   K Y+++  G+P+ KK  + + LL+          
Sbjct: 65  EGVMVFAKNKEAAADLSRQIKTKLADKYYYAMTDGVPEKKKGTLEDELLQNGKTNAS--E 122

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV++    A +A   ++V++   +      ++  TGR HQ+RV   H G PIVGD KY  
Sbjct: 123 VVERGTPQAKHASLSYEVVEQDGKHAVL-RIKLDTGRHHQIRVQLAHAGMPIVGDKKYNF 181

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                  +P   +L L +  +   HP+  R L+     P
Sbjct: 182 K---ENIAPSGGQLALCSFKIAFRHPKTHRKLEFEIDKP 217


>gi|329296582|ref|ZP_08253918.1| 23S rRNA/tRNA pseudouridine synthase A [Plautia stali symbiont]
          Length = 219

 Score =  166 bits (420), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 64/216 (29%), Positives = 99/216 (45%), Gaps = 10/216 (4%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G  +  H D  + + +     +    
Sbjct: 3   MEPYNPPLDPWLHILYQDEHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDFPQAESV 60

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R   K Y + VWG P  ++  I   L+    
Sbjct: 61  HRLDMATSGVIVVALTKAAERELKRQFREREPAKQYVARVWGHPAAEQGMIDLPLICDWP 120

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                +  V    +    A + ++V+   A     ++++P TGR+HQLRVH L +G PI+
Sbjct: 121 NRPKQMVSV----ELGKPAQTEYQVLAYDADNSARVQLKPITGRSHQLRVHLLALGHPIL 176

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           GD  Y           +  +L LH   + + HP  G
Sbjct: 177 GDRFYAHPE----ALAMAPRLQLHTESLTITHPAFG 208


>gi|241896391|ref|ZP_04783687.1| pseudouridylate synthase, 23S RNA-specific [Weissella
           paramesenteroides ATCC 33313]
 gi|241870371|gb|EER74122.1| pseudouridylate synthase, 23S RNA-specific [Weissella
           paramesenteroides ATCC 33313]
          Length = 297

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 63/273 (23%), Positives = 118/273 (43%), Gaps = 23/273 (8%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           ++ ++ +    +  ++   V+ +          + E  +   S  +   S  L+  +LYE
Sbjct: 41  RIYLNGQYQPTSTILKPYDVLTLNW--------LPEDFMTPDSQYVPDDSQSLQ--VLYE 90

Query: 105 DSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           + ++ V NK  G+     S      +  F ++++  + ++  + HRLD +T+G L++A+ 
Sbjct: 91  NDELMVVNKRKGVKTHPNSPGENGTMMNFAQAYLMKQDKRAYMVHRLDGQTTGALIIAKV 150

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
                 L +    + I++ Y + V G   +    I   +                +   A
Sbjct: 151 PYVVPILNQMLHDKTIKRTYLAWVDGHLTDSTGAITLAIGDHPTNSRLRQI----DGANA 206

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
             AI+H+  I    Q+   + +Q  TGRTHQ+R+H   +G P+VGD  Y      N  S 
Sbjct: 207 KPAITHWTKIKSVYQQ-TLVRLQLETGRTHQIRLHMAAIGHPLVGDDLY------NQQSA 259

Query: 284 IQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHM 315
             + L LH+  + LP P    ++ I APLPA  
Sbjct: 260 YADGLLLHSASVQLPMPFSSEIKSIGAPLPASF 292


>gi|256423396|ref|YP_003124049.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
 gi|256038304|gb|ACU61848.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
          Length = 570

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 66/236 (27%), Positives = 108/236 (45%), Gaps = 20/236 (8%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   +D    L       +  ++Y+D  + V NKP+G+    G  I   +   LK  +  
Sbjct: 349 EGMPVDEDPLLRTPETVGELDIIYQDESVVVVNKPSGLRSVPGVTIQDSVYTRLKHALGD 408

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P + HRLD +TSG+LVVA+T+AA +H+   F  R + K Y +L+  +    +  I 
Sbjct: 409 --IEPLIVHRLDMDTSGLLVVAKTQAAHKHIQRQFLQRTVSKRYTALLSKVIDTSEGEID 466

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L          +            +++ +KV+  + Q    ++  P TGRTHQLR+H+
Sbjct: 467 LPLTADLFNRPRQIVCFT----TGKKSVTRWKVVTRY-QAMTKIDFWPLTGRTHQLRMHS 521

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPL 311
            H   +  PIVGD  Y              ++YLHA +++  HP    R+   AP+
Sbjct: 522 AHPLGLNAPIVGDDLYG---------TAAERMYLHAAHIEFTHPLSRQRISFDAPV 568


>gi|283778696|ref|YP_003369451.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
 gi|283437149|gb|ADB15591.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
          Length = 341

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 69/357 (19%), Positives = 132/357 (36%), Gaps = 60/357 (16%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVR 66
           ++  V + E+   L    +     I++ +++ ++    V+V+         R++ G+VV+
Sbjct: 6   EHFHVTSREQGQTLAAAIRRWLGQISWRDVKSLVLGQHVQVNGNLCLDEARRLKPGEVVK 65

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QG--- 121
           +                      L K +D     + + D+ + V  KPAG++        
Sbjct: 66  VYQH------------------PLAKPADEKDVRIRHVDNHLVVVEKPAGMTTERHPEEK 107

Query: 122 -----GSGIAYHIDGFLKSWVD-------------------------SKGQKPRLTHRLD 151
                   +   +D  L   +                           K  +    HRLD
Sbjct: 108 NWPSRRKQLQPTLDEVLPRLLAKHLGWKIPREAAGSAAAKGRRTQPAPKLPRIFAVHRLD 167

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG++V ART  A+  L + F+   + + Y ++V G P  +K  I  +L++    G  
Sbjct: 168 RDTSGLMVFARTPEASTALIKLFKKHHVTRAYVAVVHGTPVEQK--IETYLVRDRGDGLR 225

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                 +  + A  A++H +++      +  +E +  TGRTHQ+R+H    G  + G+  
Sbjct: 226 GSSPAGKVAEEAQRAVTHVRLMQTIG-PYSVVECRLETGRTHQIRIHLAEAGHMLCGEKV 284

Query: 272 YCANF--KGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
           Y      K         +  LHA  +   HP     L     LP  +      L  +
Sbjct: 285 YTHKLGEKSQRDESGAPRQALHAAELGFVHPITSEPLIWRMQLPQELADWIRGLAME 341


>gi|146278941|ref|YP_001169100.1| pseudouridine synthase [Rhodobacter sphaeroides ATCC 17025]
 gi|145557182|gb|ABP71795.1| ribosomal large subunit pseudouridine synthase A [Rhodobacter
           sphaeroides ATCC 17025]
          Length = 215

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 65/220 (29%), Positives = 103/220 (46%), Gaps = 13/220 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
              +   L++ D++I V +KPAG+    G G        L   +     +  L HRLD++
Sbjct: 7   PPDVPLSLIHHDAQIVVVDKPAGLLSVPGKG--EDKADCLIERLRGVFPEILLVHRLDRD 64

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V A TRAA   L + F  R+ +K+Y + + G  + ++  +   L           
Sbjct: 65  TSGVMVFALTRAAQAALGQQFEKRQTKKVYVARLEGRLEPREGRVDLPLCVD-WPNRPRQ 123

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           HV   N      A + ++V+     +   + + P TGR+HQLRVH    G PI+GD  Y 
Sbjct: 124 HVDHVN---GRPAQTDWRVVKYLPNE-TRVRLMPVTGRSHQLRVHMAETGHPILGDALYA 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           A            +L LHA  + + HP+ G+ L  +AP P
Sbjct: 180 AGAAREHP-----RLMLHAESLRVRHPDTGKSLTYSAPCP 214


>gi|307718151|ref|YP_003873683.1| ribosomal large subunit pseudouridine synthase C [Spirochaeta
           thermophila DSM 6192]
 gi|306531876|gb|ADN01410.1| ribosomal large subunit pseudouridine synthase C [Spirochaeta
           thermophila DSM 6192]
          Length = 300

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 126/325 (38%), Gaps = 32/325 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   Q      D+   RLDR  +    HI    + + LR+G++ ++ KRV  + R+  G 
Sbjct: 1   MEDYQVFESGPDDHGKRLDRIVRTLLSHIPLSRVFRALRTGEILLEGKRVPPSTRVSRGA 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I    + L      QK    ++            +L E   + + NKP G  V G  
Sbjct: 61  RIHI--HRSLLPEREPRQKWEPRALP-----------ILLETDHLLILNKPPGAVVHGPG 107

Query: 124 GIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            +   +  +LK  +  S    P   HRLD+ TSGILV +R+   A+  T + R   I+K 
Sbjct: 108 SLTDQVRSYLKDRIPPSLAFTPSPLHRLDRLTSGILVFSRSIHGARWFTRALREGGIEKT 167

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L+ G          + L ++                    A++  + +   A     
Sbjct: 168 YLALLEGTLAEPARW-EDLLTREGRRSR--------PSPHGRPALTDVRPLLA-APTATL 217

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
                HTGR HQ+RV A   G P++GD  Y +  +      I+  L+        P P  
Sbjct: 218 ALCIIHTGRMHQIRVQAALRGHPLLGDTAYGSTRR------IRPVLHAWRLRPLSPSPLF 271

Query: 303 GRLQITAPLPAHMVKTWDSL--GFK 325
               + APLP         +  G++
Sbjct: 272 PADGLQAPLPDESETILSRILPGWE 296


>gi|260772177|ref|ZP_05881094.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           metschnikovii CIP 69.14]
 gi|260613044|gb|EEX38246.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           metschnikovii CIP 69.14]
          Length = 245

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 61/216 (28%), Positives = 103/216 (47%), Gaps = 12/216 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++YED  I   NKP+G+    G  I  H D      V    +  ++ HRLD  TSG+++
Sbjct: 15  DVVYEDEYILAVNKPSGLLSVPGKHIE-HYDSMWSRLVAEHSE-IQVVHRLDMSTSGLML 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+ +     L + F+ R   K+Y++ VWG  + ++  +   L+           V  ++
Sbjct: 73  FAKNKYMEAALKKQFQYRLTHKVYYARVWGKLEQQQGEVDLPLICD-WPNRPRQKVCFEH 131

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K +    + ++V+    ++   + + P TGR+HQLRVH L +G PIVGD  Y +     
Sbjct: 132 GKASK---TLYQVVK-QEEQTTIVRLFPVTGRSHQLRVHMLAIGHPIVGDEFYASPEALA 187

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           F+    ++L LHA  +   HP    L+ T  +P   
Sbjct: 188 FS----DRLALHAAELSFYHPRSHWLR-TIFVPCDF 218


>gi|218658410|ref|ZP_03514340.1| RNA-pseudouridine synthase protein, ribosomal large subunit C
           [Rhizobium etli IE4771]
          Length = 161

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 84/157 (53%), Positives = 111/157 (70%), Gaps = 2/157 (1%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ VR+PP+   ++  
Sbjct: 7   GMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQTVRVPPL--DVDAK 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +K   I    +  +   + L  ++L+ED K+ V NKP GI+VQGGSG+A HID  L++W 
Sbjct: 65  LKSGPIAGKDLKHSSDFELLSRMVLHEDEKVIVLNKPPGIAVQGGSGVARHIDQMLEAWT 124

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             KG+KPRL HRLD++TSG+LV+ARTR AAQ LT +F
Sbjct: 125 SPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLTAAF 161


>gi|169795158|ref|YP_001712951.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii AYE]
 gi|184158990|ref|YP_001847329.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|213158176|ref|YP_002320227.1| pseudouridine synthase A [Acinetobacter baumannii AB0057]
 gi|215482708|ref|YP_002324906.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB307-0294]
 gi|301348011|ref|ZP_07228752.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB056]
 gi|301512677|ref|ZP_07237914.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB058]
 gi|301597067|ref|ZP_07242075.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB059]
 gi|169148085|emb|CAM85948.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii AYE]
 gi|183210584|gb|ACC57982.1| Pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|213057336|gb|ACJ42238.1| pseudouridine synthase A [Acinetobacter baumannii AB0057]
 gi|213988340|gb|ACJ58639.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB307-0294]
 gi|322508972|gb|ADX04426.1| rluA [Acinetobacter baumannii 1656-2]
 gi|323518957|gb|ADX93338.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           TCDC-AB0715]
          Length = 212

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 70/223 (31%), Positives = 108/223 (48%), Gaps = 17/223 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V  + +   L HRLD++
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLVAIEPRTL-LIHRLDRD 58

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     +   F+ R+  KIY +LV G  + +   +   ++         +
Sbjct: 59  TSGILVFGLSKRGQSAIARQFQDRQTSKIYEALVAGHLEGE-GTVDIPVVYDP--SRPPL 115

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+V  +      A++H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD 
Sbjct: 116 HIVDASHN--KPALTHWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDT 173

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            Y A         +  +L LHA+ +   HP  G  L    P+P
Sbjct: 174 LYAAP-----EQLLVPRLCLHAKQLSFNHPVTGESLTFNCPVP 211


>gi|260063065|ref|YP_003196145.1| ribosomal large subunit pseudouridine synthase D [Robiginitalea
           biformata HTCC2501]
 gi|88784634|gb|EAR15804.1| ribosomal large subunit pseudouridine synthase D [Robiginitalea
           biformata HTCC2501]
          Length = 236

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 68/231 (29%), Positives = 107/231 (46%), Gaps = 16/231 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQE 153
            ++LYED+ +   +K AG  VQG       +   +K ++  K QKP      + HRLD+ 
Sbjct: 11  LMVLYEDNHLIAVSKRAGDIVQGDKTGDTPLPETVKDYIAHKYQKPGKVFLGVVHRLDRP 70

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G++V ART  A   +   F     +K YW+LV   P      + +WL +       Y 
Sbjct: 71  TTGVIVFARTSKALSRMNRLFAEGGTRKTYWALVGTPPPETAGRLVHWLERNQKQNKSYA 130

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               +   G+  AI +++++     ++  LE+   TGR HQ+R     +G PI GD KY 
Sbjct: 131 RA--KEVPGSKQAILNYRLLGSL-DRYHLLEIDLETGRHHQIRAQLAAIGSPIKGDLKYG 187

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
                   S     ++LHAR ++  HP     + I APLP      W++ G
Sbjct: 188 FP-----RSNPDGGIHLHARRLEFIHPVRQDPVSILAPLPDD--PLWEACG 231


>gi|226952509|ref|ZP_03822973.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. ATCC 27244]
 gi|226836736|gb|EEH69119.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. ATCC 27244]
          Length = 228

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 64/223 (28%), Positives = 102/223 (45%), Gaps = 15/223 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L++ D    V +KPAG+    G      +   L + +     K  L HRLD++
Sbjct: 16  SDFLSEYLIHRDEDFMVIHKPAGLLTVPGKTPD--LQDCLINRLLKLEPKTLLIHRLDRD 73

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     ++  F+ R+  KIY +LV G  + +       +   S      V
Sbjct: 74  TSGILVFGLSKFGQSTISRQFQDRQTSKIYQALVAGHLEGQGTVDIPVIYDPSRPPLHIV 133

Query: 214 HVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                       A++ ++ I+      Q    +++ P TGR+HQLRVH  ++G PI+GD 
Sbjct: 134 DATHH-----KPALTEWQAIEHLEIQGQAVTRVKLIPITGRSHQLRVHMQYLGHPILGDT 188

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y    +      +  +L LHA  +   HP+ G +L    P+P
Sbjct: 189 LYATPEQQQ----LYERLCLHATQLSFAHPKTGTQLDFDCPVP 227


>gi|163748427|ref|ZP_02155681.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           benthica KT99]
 gi|161332005|gb|EDQ02682.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           benthica KT99]
          Length = 225

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 65/213 (30%), Positives = 107/213 (50%), Gaps = 12/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NK +G+    G   A      + S V ++    ++ HRLD  TSG+++V
Sbjct: 16  IIYQDKDILVVNKHSGLLSVPGR--APEHQDSVYSRVLAEYPNAQVVHRLDMATSGVILV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R A + L   FR R  +K Y++ V G  K +K  +   L+             K + 
Sbjct: 74  ALRRNAEKELKRQFRERETKKTYYARVAGHIKQQKGSVDLPLICDWPNRPK----QKVDH 129

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    +++HF+VI  +A++   +++ P TGR+HQLRVH + +G PI+GD+ Y        
Sbjct: 130 EIGKPSLTHFEVI-SYAKRSTLVKLTPITGRSHQLRVHMMAIGHPILGDNFYADPLAKRL 188

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            S    +L LHA+ + +  P  GR L     +P
Sbjct: 189 AS----RLLLHAQELTIKQPYSGRVLTFNCEVP 217


>gi|212637049|ref|YP_002313574.1| pseudouridylate synthase [Shewanella piezotolerans WP3]
 gi|212558533|gb|ACJ30987.1| Pseudouridylate synthase [Shewanella piezotolerans WP3]
          Length = 225

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 61/215 (28%), Positives = 105/215 (48%), Gaps = 12/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L++D  I V NKP+G+    G   A++   +  S V ++  + ++ HRLD  TSG++
Sbjct: 14  LDILHQDQDIMVLNKPSGLLSVPGRDPAHNDSTY--SRVLAQYPEAKIVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  R+A   L   FR R   K Y++ V G  K     +   L+             K 
Sbjct: 72  VVALLRSAESELKRQFRDRETAKTYYARVAGHVKADSGTVNLPLICDWPNRPK----QKV 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    + +H+ V+   A++   +++ P TGR+HQLRVH + +G PI+GD+ Y      
Sbjct: 128 DHQIGKASQTHYDVVSR-AKRSTLVKLTPITGRSHQLRVHMMALGHPILGDNFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                + ++L LHA+ + + HP     +  +   P
Sbjct: 187 R----LASRLLLHAQSLTITHPYTKEPMTFSCEAP 217


>gi|170718603|ref|YP_001783805.1| pseudouridine synthase [Haemophilus somnus 2336]
 gi|168826732|gb|ACA32103.1| pseudouridine synthase [Haemophilus somnus 2336]
          Length = 221

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 68/236 (28%), Positives = 106/236 (44%), Gaps = 20/236 (8%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            ++D    L  + D     ++Y D  I V NKP+G+    G+   Y+      S V  K 
Sbjct: 2   ALIDYRPPLEPYLD-----IVYRDDHILVVNKPSGLLSVSGNQPQYYDSAM--SRVKEKY 54

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD  TSG+L+ A ++ A + L   FR R  +K Y +L+WG        +   
Sbjct: 55  GFCEPAHRLDMATSGVLLFAMSKMADRELKRQFREREPKKHYQALIWGHLAQDTGSVNLP 114

Query: 202 LLKK-SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           L+    +     V  V         A+++FKV+  F      + + P TGR+HQLR+H L
Sbjct: 115 LICDWENRPRQKVCFVH-----GKRAVTNFKVLHRFENNITQVRLTPITGRSHQLRLHML 169

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            +G PI+GD  Y      +    +  +L LHA ++ + HP   + +Q     PA  
Sbjct: 170 ALGHPILGDKFYAHPQAKS----LAPRLCLHAEFLQITHPLTKKVIQFRT--PADF 219


>gi|77361542|ref|YP_341117.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity
           [Pseudoalteromonas haloplanktis TAC125]
 gi|76876453|emb|CAI87675.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 233

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 57/218 (26%), Positives = 99/218 (45%), Gaps = 12/218 (5%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   +LY+D  + + NKP+ +    G    +     L   V+      ++ HRLD 
Sbjct: 23  PPTDPYLTILYQDEDLLIVNKPSELLTVPGKDPKH--ADCLIGRVNRVFPTAKIVHRLDM 80

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGIL +A  +AA +H++  F+ R   K Y + ++G  + +   +   L+         
Sbjct: 81  ATSGILCLAMNKAAHRHVSMQFQERETAKRYIARIYGQLEAQTGSVDLPLICDWPNRPKQ 140

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +     + +    +++HFK+++        +E+ P TGR+HQLRVH L +G PI+GD  Y
Sbjct: 141 M----VDHENGKPSLTHFKILEREPH-ATRVELTPITGRSHQLRVHMLSLGHPILGDRLY 195

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITA 309
                         +L LHA+ + L HP   ++    A
Sbjct: 196 AHKE----ALAAAPRLQLHAQMLSLKHPTTEQILTFEA 229


>gi|326933214|ref|XP_003212702.1| PREDICTED: tRNA pseudouridine synthase 3-like [Meleagris gallopavo]
          Length = 710

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 73/277 (26%), Positives = 127/277 (45%), Gaps = 40/277 (14%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L+  ++Y++ ++ V NKP G+ V GG G+   I   L    K  ++ K + 
Sbjct: 431 VHHNVLAKALRQRIVYQNEELVVLNKPYGLPVHGGPGVKNCIADVLPILAKMLMNMKAEP 490

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+AR+R  A  +   F+ R+++KIYW++  G P   +  +   ++
Sbjct: 491 LHLCHRLDKETTGLMVLARSREVADRIRLLFKTRQVEKIYWAISVGSPDPAEGIVEIPMV 550

Query: 204 KKSHIGGDYVHVVK-----------------QNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           ++        + +                  +  + A  A++ ++V+   +     LE+Q
Sbjct: 551 EREVQSHQPHYKMTLAPNYRMSPEDGKVLKIRKNRNAENAVTRYRVLAT-SSACSLLELQ 609

Query: 247 PHTGRTHQLRVHALH-MGCPIVGDHKYC---------------ANFKGNFTSPIQNKLYL 290
           P TG  HQLRVH  + +GCPI+GDHKY                   K   +      L+L
Sbjct: 610 PITGVKHQLRVHLAYGLGCPILGDHKYSHWSKLAPQKLPEITLKRLKLQQSKSRHLPLHL 669

Query: 291 HARYMDLPHPEGG--RLQITAPLPAHMVKTWDSLGFK 325
           HA  + LP   GG  +  +    P+   +T   L   
Sbjct: 670 HAYRLSLPLGTGGSKQTDLVCEPPSFFHRTLRQLELD 706


>gi|307132626|ref|YP_003884642.1| Ribosomal large subunit pseudouridine synthase A [Dickeya dadantii
           3937]
 gi|306530155|gb|ADN00086.1| Ribosomal large subunit pseudouridine synthase A [Dickeya dadantii
           3937]
          Length = 235

 Score =  165 bits (419), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 63/219 (28%), Positives = 99/219 (45%), Gaps = 14/219 (6%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
            +  +            +LY+D  I V NKP+G+    G     H D  + + + +    
Sbjct: 15  PEPFMEPYDPPRDPWLHILYQDQHIMVVNKPSGLLSVPGRA-EEHKDSIM-TRIQADFPA 72

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG  +     +   L+
Sbjct: 73  AESVHRLDMATSGVMVVALTKAAERELKRQFREREPKKSYIARVWGHLEQDDGLVDLPLI 132

Query: 204 KKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
                  D+ +  KQ    +    A + + V+   +     +++ P TGR+HQLRVH L 
Sbjct: 133 ------CDWPNRPKQKVCFEQGKPAQTGYVVLSRDSDGTTRVKLMPITGRSHQLRVHMLA 186

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           +G PI+GD  Y              +L LHA+ + + HP
Sbjct: 187 LGHPILGDGFYAHPQAKAMA----PRLLLHAQELAIVHP 221


>gi|118101844|ref|XP_001231937.1| PREDICTED: hypothetical protein [Gallus gallus]
          Length = 344

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 75/277 (27%), Positives = 125/277 (45%), Gaps = 40/277 (14%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L+   +Y+D ++ V NKP G+ V GG G+   I   L    K  V+ K + 
Sbjct: 65  VHPNVLAKALRQRAVYQDEEVVVLNKPYGLPVHGGPGVKNCIADVLPILAKMLVNMKAEP 124

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+AR + AA  +   F+ R+++KIYW++  G P   +  +   ++
Sbjct: 125 LHLCHRLDKETTGVMVLARNKEAADRIRLLFKTRQVEKIYWAISVGSPDPAEGIVEIPMV 184

Query: 204 KKSHIGGDYVHVVK-----------------QNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           ++          +                  +  + A  A++ ++V+   +     LE+Q
Sbjct: 185 EREVQSHQPHFKMTLAPNYRMSPEDGKVLKIRKNRNAESAVTQYRVLAS-SSACSLLELQ 243

Query: 247 PHTGRTHQLRVHALH-MGCPIVGDHKYC---------------ANFKGNFTSPIQNKLYL 290
           P TG  HQLRVH  + +GCPI+GDHKY                   K   +      L+L
Sbjct: 244 PITGVKHQLRVHLAYGLGCPILGDHKYSHWSKLAPQKLPEITLKRLKLQQSKSRHLPLHL 303

Query: 291 HARYMDLPHPEGG--RLQITAPLPAHMVKTWDSLGFK 325
           HA  + LP    G  R+ +    P+   +T   L   
Sbjct: 304 HAYRLSLPLGTSGSKRIDLVCEPPSFFHRTLRKLELD 340


>gi|167624902|ref|YP_001675196.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167354924|gb|ABZ77537.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 279

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 65/263 (24%), Positives = 115/263 (43%), Gaps = 19/263 (7%)

Query: 80  EQKILDSSVNLTKHSDFLKSIL--LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           E + +  S  L   ++ +   +  L+ED  +   +KPAG+ V             ++   
Sbjct: 4   ETREVADSELLDIEAEEIAPHIEVLFEDDDVVAIHKPAGLLVHRSYLARRERFFAMQLTR 63

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D  G      HRLD+ TSGIL+ A++   A  L   F    + K Y ++V G   ++   
Sbjct: 64  DKVGCHVFPVHRLDRPTSGILLFAKSSEMANALCGQFADHTVDKEYLAIVRGNM-HEAGT 122

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQP 247
           +   L ++    GD         K A  A++ ++ +               ++  +++ P
Sbjct: 123 LDYALKEELDELGDK---DVDPNKAAQDAVTSYQPLLNSEIPFSSGRYATSRYALVQLSP 179

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-R 304
           HTGR HQLR H  H+  PI+GD  +    +  F  +    N+L+L A+ +   HP  G R
Sbjct: 180 HTGRKHQLRRHMAHLRHPILGDTTHGDGKQNKFFRSHFGINRLWLIAKKLSFNHPRTGER 239

Query: 305 LQITAPLPAHMVKTWDSLGFKYD 327
           ++I   L    ++ ++ LG+  D
Sbjct: 240 IEIETELETEWLQLFEGLGWHED 262


>gi|120436437|ref|YP_862123.1| pseudouridylate synthase [Gramella forsetii KT0803]
 gi|117578587|emb|CAL67056.1| pseudouridylate synthase [Gramella forsetii KT0803]
          Length = 232

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 67/227 (29%), Positives = 112/227 (49%), Gaps = 16/227 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ I + NK  G  VQG       +   +KS++  K +KP      + HRLD+ TS
Sbjct: 15  VLHEDNHIIIVNKRPGDIVQGDKTGDKPLSEVVKSYLKEKYKKPGNVYLGVVHRLDRPTS 74

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI++ ++T  A   L + F+ ++ +K YW++V   P+ K   + +++ + S     Y H 
Sbjct: 75  GIVLFSKTSKALPRLNKLFQDKKAKKTYWAIVKNAPQEKSGELVHFMKRNSKQNKSYAH- 133

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K     +  A+  ++++      +  LE+  HTGR HQ+R     +G PI GD KY  N
Sbjct: 134 -KNEVPDSKKAMLDYRLLKKL-DNYYLLEIDLHTGRHHQIRSQLSAIGSPIKGDLKYGFN 191

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
                 S     ++LH+R +   HP     + I AP P+     WD+
Sbjct: 192 RSNKDAS-----IHLHSRELKFTHPVKKEFIHIIAPPPSD--PIWDA 231


>gi|295425346|ref|ZP_06818049.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           amylolyticus DSM 11664]
 gi|295065122|gb|EFG56027.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           amylolyticus DSM 11664]
          Length = 279

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 65/296 (21%), Positives = 110/296 (37%), Gaps = 27/296 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           MTY   ++   D   M +    +           Q +LR   QV V+     FN  +++ 
Sbjct: 1   MTYNFKLIYPEDMPAMSVRDLLRKLL--FPR-KWQHLLRTKKQVTVNGHYRYFNQLVKAN 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V        L+ +  +Q+   +S +L          +++EDS + V NK  G      
Sbjct: 58  DEVCF-----KLDFVDSQQQSYPASGHL--------PQIIFEDSNVLVINKRKGQKTHPN 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               +  +  L       GQ P + HRLD  T G+L+VA+  A    L      +   + 
Sbjct: 105 ---LFETNTALNDCATYLGQSPYIVHRLDMLTGGLLLVAKNPAVVPILNRQLTQKIFHRE 161

Query: 183 YWSLVW-GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V           I+  + K        +            A +H++++    +   
Sbjct: 162 YLAQVNLNAALPDHGTISFPIGKDPDDQRKRMVRS-----DGLKATTHYQILKKENEIA- 215

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            +++Q  TGRTHQ+RVH   +GCPIVGD  Y  ++K      +             
Sbjct: 216 LIKLQLETGRTHQIRVHLAAIGCPIVGDPLYNPDYKEGQDLQLTAYQMSFIEPFSF 271


>gi|293392894|ref|ZP_06637212.1| pseudouridine synthase A [Serratia odorifera DSM 4582]
 gi|291424753|gb|EFE97964.1| pseudouridine synthase A [Serratia odorifera DSM 4582]
          Length = 216

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 61/200 (30%), Positives = 94/200 (47%), Gaps = 10/200 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G   A      L + +          HRLD  TSG++VV
Sbjct: 13  ILYQDEHIIVVNKPSGLLSVPGR--APENKDSLMTRIQVDFPAAESVHRLDMATSGVIVV 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +AA + L   FR R  +K Y + VWG  ++ +  +   L+           V     
Sbjct: 71  ALNKAAERELKRQFREREPKKSYIARVWGHLEHDEGMVDLPLICD-WPNRPLQKVCF--- 126

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    A + ++V+   A     +++ P TGR+HQLRVH L +G PI+GD  Y        
Sbjct: 127 ETGKSAQTEYQVLSRDADGSTRVKLTPITGRSHQLRVHMLALGHPILGDGFYAHPQAKAM 186

Query: 281 TSPIQNKLYLHARYMDLPHP 300
            +    +L LHA+ + + HP
Sbjct: 187 AA----RLQLHAQELRITHP 202


>gi|169632854|ref|YP_001706590.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii SDF]
 gi|239501123|ref|ZP_04660433.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii AB900]
 gi|260556640|ref|ZP_05828858.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 19606]
 gi|169151646|emb|CAP00433.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii]
 gi|193077967|gb|ABO12881.2| putative ribosomal large subunit pseudouridine synthase
           A(RluA-like) [Acinetobacter baumannii ATCC 17978]
 gi|260409899|gb|EEX03199.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 19606]
          Length = 212

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 69/223 (30%), Positives = 107/223 (47%), Gaps = 17/223 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V  + +   L HRLD++
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLVAIEPRTL-LIHRLDRD 58

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     +   F+ R+  KIY +LV G  + +   +   ++         +
Sbjct: 59  TSGILVFGLSKRGQSAIARQFQDRQTSKIYEALVAGHLEGE-GTVDIPVVYDP--SRPPL 115

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+V  +      A++H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD 
Sbjct: 116 HIVDASHN--KPALTHWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDT 173

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            Y           +  +L LHA+ +   HP  G  L    P+P
Sbjct: 174 LY-----ATPEQLLVPRLCLHAKQLSFNHPVTGESLTFNCPVP 211


>gi|228473894|ref|ZP_04058636.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga gingivalis ATCC 33624]
 gi|228274735|gb|EEK13569.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga gingivalis ATCC 33624]
          Length = 235

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 110/232 (47%), Gaps = 15/232 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +   NK AG  VQG       +   +KS++  K  KP      + HRLD+ T+
Sbjct: 10  VLYEDNHLIAINKRAGDIVQGDKTGDIPLSEIVKSYLVEKYHKPGEAYLGVVHRLDRPTT 69

Query: 156 GILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           G++V A+T  A   L  +F  +  + K YW+LV       +  + ++L++ +     Y +
Sbjct: 70  GVVVFAKTSKALPRLNAAFATKEEVSKQYWALVEKKAIPHQGTLTHFLVRNTSQNKSYAY 129

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              + +  +  A+  +KV+      +  +E+   TGR HQ+R     +GCP+ GD KY A
Sbjct: 130 P--EEKPQSQKAVLTYKVLATLTH-YLLVEITLLTGRHHQIRAQFAALGCPLKGDLKYGA 186

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
                  S     + LHAR ++L HP     L I APLP    K    +  +
Sbjct: 187 KRSNPDGS-----ISLHARALELLHPVRKEPLHIVAPLPESFCKLLKDIQLE 233


>gi|152996227|ref|YP_001341062.1| pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150837151|gb|ABR71127.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 242

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 102/237 (43%), Gaps = 12/237 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +L++D  +   NKPAG+ V   +      D  ++   D  G+     HRLD+ TSG
Sbjct: 1   MTLDILFQDEHLVAVNKPAGLLVHRTNLAKDEEDAVVQRLRDQTGKWVFPVHRLDRGTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV+A +   A+ L+  F   + QK Y  LV G   N+   I   L K +   G     +
Sbjct: 61  VLVMAFSPEVARRLSTQFAESKTQKTYHCLVRGYC-NESGVINYPLAKLNEQKGRSRFKI 119

Query: 217 KQNEKGANYAISH-------FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +  E+ A    +          V    + +  WLE+ P  GR HQ+R H  H   P+VGD
Sbjct: 120 EGTEREAETGFTRLIQYQLPVPVSRYDSMRLSWLEVTPKQGRKHQIRRHFKHHLNPLVGD 179

Query: 270 HKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
             Y           + +   +L LHA  ++  HP   + + + A L   ++   + L
Sbjct: 180 SCYGCRHINKVAKELWSEDFRLMLHASSLEFNHPITNQPITLKADLSDKIINILNKL 236


>gi|163739826|ref|ZP_02147233.1| pseudouridine synthase [Phaeobacter gallaeciensis BS107]
 gi|161386860|gb|EDQ11222.1| pseudouridine synthase [Phaeobacter gallaeciensis BS107]
          Length = 207

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 58/218 (26%), Positives = 100/218 (45%), Gaps = 15/218 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
                +L+ D+++ V NKP G+    G G   H+   L S + +   +  L HRLD++TS
Sbjct: 1   MDPLDILHHDAQLLVVNKPHGLLSVPGRG--EHLADCLLSRLQAAFPEALLVHRLDRDTS 58

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V   T  A +HL+  F  R  +K Y + + G  + +   +   L+           V
Sbjct: 59  GVMVFGVTPHAQRHLSMQFEKRSAKKAYVARLDGRLEPRSGTVDLPLIVD-WPNRPRQMV 117

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A++ ++V+  +      + + P TGR+HQLRVH L +G  I+GD  Y   
Sbjct: 118 CHDT---GKEAVTDWRVMK-YEDTATRVRLTPKTGRSHQLRVHMLSLGHAILGDPLYAEG 173

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
              +       ++ LHA  + + HP+ G     ++ AP
Sbjct: 174 RALDHP-----RMMLHAEELRIKHPDSGESMKFRVKAP 206


>gi|58579971|ref|YP_198987.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|58424565|gb|AAW73602.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
          Length = 290

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 103/249 (41%), Gaps = 24/249 (9%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           N           +LY+D  + V +K AG+ V          D       +  G+   L H
Sbjct: 50  NPPVSIAPDPLQILYQDDVLAVVDKTAGLMVHDSKLARGEDDFLADRLREQLGRPIFLVH 109

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG L++A  R  A  L ++     +QK Y ++  G P   +  + + L      
Sbjct: 110 RLDRATSGCLLLAFDRETASALGKALMSGDVQKDYLAVCRGWPAEPRFTVDHDL------ 163

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVH 258
            G     VK        A++HF+ +               ++  L  QP TGR  Q+R H
Sbjct: 164 DGGPGKPVK------KPALTHFQRLATGELQVPSTGFATSRYALLRCQPQTGRFRQIRRH 217

Query: 259 ALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
             H+   ++GD  +       +F     +++ LHA+ +  PHP +G R+++TAPL     
Sbjct: 218 LKHLSHHLIGDTSHGDGRHNRSFRMLGIHRMLLHAKRLAFPHPADGRRIRVTAPLDDEFT 277

Query: 317 KTWDSLGFK 325
           K     G+ 
Sbjct: 278 KACALFGWD 286


>gi|148975781|ref|ZP_01812612.1| putative ribosomal large chain pseudouridine synthase A
           [Vibrionales bacterium SWAT-3]
 gi|145964854|gb|EDK30106.1| putative ribosomal large chain pseudouridine synthase A
           [Vibrionales bacterium SWAT-3]
          Length = 570

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 65/242 (26%), Positives = 109/242 (45%), Gaps = 20/242 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +  L H++K  ++ D    L   ++  +  +L++D  I V +KPAG     G  I    
Sbjct: 339 CVPILGHMMKGLEV-DPKPLLENPAEGKELDILFQDEHIVVVHKPAGFLSVPGKTIKDSA 397

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++       + P + HRLD  TSGIL+ A TR A + L + F  R ++K Y +++ G
Sbjct: 398 YTRVQEM-HPDVEGPFVIHRLDMATSGILIFALTRRANKSLQKQFITREVEKRYVAMIEG 456

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +    +  +   L    +     +   +        A + ++VI+   Q+   + + P T
Sbjct: 457 VLAEDEGYVRLPLRGDLYDRPRQIVCYEH----GKPAETKWEVIERN-QETTKVYLHPKT 511

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVH  H   +  PIVGD  Y             ++L+LHA  + L HP     +
Sbjct: 512 GRTHQLRVHCSHEEGLYMPIVGDGLYGNK---------ADRLHLHAERLALHHPITKEWM 562

Query: 306 QI 307
           + 
Sbjct: 563 EF 564


>gi|259145207|emb|CAY78471.1| Pus9p [Saccharomyces cerevisiae EC1118]
          Length = 462

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 108/255 (42%), Gaps = 23/255 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +        ++ + +G V ++ +    +  I++G ++              E
Sbjct: 129 VDVFISE-FRDRESEYYKRTIENGDVHINDETADLSTVIRNGDLITHQVHR-------HE 180

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  I V +KP+GI V       Y  +   K   ++ 
Sbjct: 181 PPVTSRPIK-----------VIFEDDNIMVIDKPSGIPVHPTG--RYRFNTITKMLQNNL 227

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A ++ +  + R + K Y + V G     +  +  
Sbjct: 228 GFVVNPCNRLDRLTSGLMFLAKTPKGADNIGDQLKAREVTKEYVAKVVGEFPETEVIVEK 287

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K          V + +EKGA +A + F  I     K   ++ +P TGR+HQ+RVH  
Sbjct: 288 PL-KLIEPRLALNAVCQMDEKGAKHAKTVFNRISYDG-KTSIVKCKPLTGRSHQIRVHLQ 345

Query: 261 HMGCPIVGDHKYCAN 275
           ++G PI  D  Y  +
Sbjct: 346 YLGHPIANDPIYSND 360


>gi|251788208|ref|YP_003002929.1| pseudouridine synthase [Dickeya zeae Ech1591]
 gi|247536829|gb|ACT05450.1| pseudouridine synthase [Dickeya zeae Ech1591]
          Length = 217

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 63/215 (29%), Positives = 98/215 (45%), Gaps = 14/215 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G     H D  + + + +        
Sbjct: 1   MEPYNPPRDPWQHILYQDQHIMVVNKPSGLLSVPGRA-EEHKDSIM-TRIQADFPAAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG        +   L+    
Sbjct: 59  HRLDMATSGVMVVALTKAAERELKRQFREREPKKSYIARVWGHLTQDDGLVDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A +++ V+         +++ P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCFEQGKPAQTNYTVLSRDNDGTTRVKLMPITGRSHQLRVHMLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           I+GD  Y           +  +L LHA+ + + HP
Sbjct: 173 ILGDGFYAHPEAKA----LAPRLLLHAQELAITHP 203


>gi|85058407|ref|YP_454109.1| ribosomal large subunit pseudouridine synthase A [Sodalis
           glossinidius str. 'morsitans']
 gi|84778927|dbj|BAE73704.1| ribosomal large subunit pseudouridine synthase A [Sodalis
           glossinidius str. 'morsitans']
          Length = 217

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 103/231 (44%), Gaps = 17/231 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D+ I   NKP+G+    G     H D  + + + +   +    
Sbjct: 1   MEPYHPPQMPWLHILYQDTHIMAVNKPSGLLSVPGRAPE-HRDSVM-TRIQANFPQAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG+LVVA T+AA + L   FR R  +K Y + V+G P   +  I   L+    
Sbjct: 59  HRLDMATSGVLVVALTKAAERELKRQFREREPRKTYIASVYGHPACDEGDIDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  +Q         A++H++V+         + + P TGR+HQLRVH   +G P
Sbjct: 115 --CDWPNRPRQKVCFGTGKAALTHYEVLSRDPDGSARVRLTPMTGRSHQLRVHIQSLGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
           I+GD  Y              +L LHA+ + + HP+ G  +       A  
Sbjct: 173 ILGDGFYATPEAKAMA----PRLLLHAQTLAITHPQYGSPIHFHCE--ADF 217


>gi|6320168|ref|NP_010248.1| Pus9p [Saccharomyces cerevisiae S288c]
 gi|3915436|sp|Q12069|PUS9_YEAST RecName: Full=tRNA pseudouridine synthase 9, mitochondrial;
           AltName: Full=tRNA pseudouridylate synthase 9; AltName:
           Full=tRNA-uridine isomerase 9; Flags: Precursor
 gi|1279680|emb|CAA96453.1| unknown [Saccharomyces cerevisiae]
 gi|1431018|emb|CAA98595.1| unnamed protein product [Saccharomyces cerevisiae]
 gi|285810994|tpg|DAA11818.1| TPA: Pus9p [Saccharomyces cerevisiae S288c]
          Length = 462

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 108/255 (42%), Gaps = 23/255 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +        ++ + +G V ++ +    +  I++G ++              E
Sbjct: 129 VDVFISE-FRDRESEYYKRTIENGDVHINDETADLSTVIRNGDLITHQVHR-------HE 180

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  I V +KP+GI V       Y  +   K   ++ 
Sbjct: 181 PPVTSRPIK-----------VIFEDDNIMVIDKPSGIPVHPTG--RYRFNTITKMLQNNL 227

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A ++ +  + R + K Y + V G     +  +  
Sbjct: 228 GFVVNPCNRLDRLTSGLMFLAKTPKGADNIGDQLKAREVTKEYVAKVVGEFPETEVIVEK 287

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K          V + +EKGA +A + F  I     K   ++ +P TGR+HQ+RVH  
Sbjct: 288 PL-KLIEPRLALNAVCQMDEKGAKHAKTVFNRISYDG-KTSIVKCKPLTGRSHQIRVHLQ 345

Query: 261 HMGCPIVGDHKYCAN 275
           ++G PI  D  Y  +
Sbjct: 346 YLGHPIANDPIYSND 360


>gi|294142362|ref|YP_003558340.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293328831|dbj|BAJ03562.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 225

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 63/213 (29%), Positives = 106/213 (49%), Gaps = 12/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NKP+G+    G    +     + S V ++    ++ HRLD  TSG++VV
Sbjct: 16  IIYQDKDILVINKPSGLLSVPGRAPEHRDS--VYSRVLAEHPNAQIVHRLDMATSGVIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R A + L   FR R  +K Y++ V G  K     +   L+             K + 
Sbjct: 74  ALRRNAEKELKRQFRDRETKKTYYARVAGYIKEHTGSVDLPLICDWPNRPK----QKVDH 129

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +    +++HF+VI   A++   +++ P TGR+HQLRVH + +G PI+GD+ Y        
Sbjct: 130 EVGKSSLTHFEVI-SKAKRSTLVKLTPITGRSHQLRVHMMAIGHPILGDNFYADPLAKR- 187

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
              + ++L LHA  + +  P  G  L  ++ +P
Sbjct: 188 ---LASRLLLHAHKLTIKQPYSGKELTFSSEVP 217


>gi|257413410|ref|ZP_04742958.2| ribosomal large subunit pseudouridine synthase family protein
           [Roseburia intestinalis L1-82]
 gi|257203607|gb|EEV01892.1| ribosomal large subunit pseudouridine synthase family protein
           [Roseburia intestinalis L1-82]
          Length = 221

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 65/219 (29%), Positives = 108/219 (49%), Gaps = 9/219 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++  ++YED  I V  KPAG++ Q        ++  LK++  SKG+ P +   HRLDQ  
Sbjct: 5   MQPAIIYEDEDIIVCKKPAGVATQTRRIGQADMESLLKNYRASKGELPYIGVVHRLDQPV 64

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            GI+V A+ + AA  L+   + +   K Y+++  G+P+ KK  + + LL+          
Sbjct: 65  EGIMVFAKNKEAAADLSRQIKTKLADKYYYAMTDGVPEKKKGTLEDELLQNGKTNTS--E 122

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV++    A +A   ++V++   +      ++  TGR HQ+RV   H G PIVGD KY  
Sbjct: 123 VVERGTPQAKHASLSYEVVEQDGKHAVL-RIKLDTGRHHQIRVQLAHAGMPIVGDKKYNF 181

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                  +P   +L L +  +   HP+  R L+     P
Sbjct: 182 K---ENIAPSGGQLALCSFKIAFRHPKTHRKLEFEIDKP 217


>gi|56750191|ref|YP_170892.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 6301]
 gi|81300183|ref|YP_400391.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 7942]
 gi|56685150|dbj|BAD78372.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 6301]
 gi|81169064|gb|ABB57404.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 7942]
          Length = 543

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 71/212 (33%), Positives = 101/212 (47%), Gaps = 18/212 (8%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
            + L+  +LYED+ +    KPAG+ SV G  G+       L            + HRLDQ
Sbjct: 333 DEPLELPILYEDADLLAIIKPAGLLSVPGTRGLQQASAIQLLRQQFPDLPTYCVVHRLDQ 392

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGIL+VAR R     L E FR R++ K+Y +L+ G P      I   L          
Sbjct: 393 ATSGILLVARNRPTQVALFEQFRRRQVHKVYEALLEGQPDCTAGTIDLPL----RPDWTR 448

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGD 269
                 +      A+++++ ID    + C +E++P TGRTHQLRVH  H   +G PI+GD
Sbjct: 449 RPYQLVDRDRGRPALTYYRCIDQTGDR-CRMELEPITGRTHQLRVHMAHPEGLGQPILGD 507

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             Y  +          ++LYLHAR +   HP 
Sbjct: 508 DLYGQS---------SDRLYLHARSIRFRHPS 530


>gi|307944492|ref|ZP_07659832.1| pseudouridine synthase A [Roseibium sp. TrichSKD4]
 gi|307772241|gb|EFO31462.1| pseudouridine synthase A [Roseibium sp. TrichSKD4]
          Length = 223

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 65/230 (28%), Positives = 102/230 (44%), Gaps = 12/230 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                 + +        +L+ D  I V NKP+G+    G   A      ++     +   
Sbjct: 4   PSPPKFVYRPPMEPYLEVLHVDQDILVVNKPSGLLSVPGK--AAEHADCVEQRAQEQFPD 61

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            R+ HRLD +TSG+ V+A  R A +HL   F  R+  K Y + V G+P  +K  +   L 
Sbjct: 62  ARIVHRLDLDTSGVFVLAMNREAHRHLGLQFERRKTSKTYVARVSGVPVTEKGRVTLPL- 120

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +          V  ++      A + ++V++   +      + P TGR+HQLRVH L +G
Sbjct: 121 RCDWPNRPKQMVCFEH---GKAAHTDWQVMEHDLKTAKL-RLIPITGRSHQLRVHLLAIG 176

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
            PI+GD  Y             ++L LHA+ + L HP  G R+  T P P
Sbjct: 177 HPILGDRFY----AQGDALTASDRLLLHAQTLTLHHPSNGERVTFTVPCP 222


>gi|183597816|ref|ZP_02959309.1| hypothetical protein PROSTU_01145 [Providencia stuartii ATCC 25827]
 gi|188022571|gb|EDU60611.1| hypothetical protein PROSTU_01145 [Providencia stuartii ATCC 25827]
          Length = 217

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 103/225 (45%), Gaps = 16/225 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I   NKP+G+    G    +H    + S +          
Sbjct: 2   MEPYHPPTDPWLYVLYQDEHIITVNKPSGLLSVPGKAPEHHDS--IMSRIQRDHPHAESV 59

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA  +AA + L   FR R  +K Y + VWG  + ++  +   L+    
Sbjct: 60  HRLDMATSGVMVVALNKAAERELKRQFREREPKKHYIARVWGHLEKQEGLVDLPLI---- 115

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V++   Q    +++ P TGR+HQLRVH L +G P
Sbjct: 116 --CDWPNRPKQKVCFETGKAAQTEYQVLEYEEQ-ATRVKLSPITGRSHQLRVHMLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           I+GD  Y           +  +L LHA+ + + HP  G  +  + 
Sbjct: 173 ILGDRFYAHEQ----ARALAPRLQLHAQELYITHPAYGTPMHFSC 213


>gi|56459957|ref|YP_155238.1| pseudouridylate synthase Rlu family protein [Idiomarina loihiensis
           L2TR]
 gi|56178967|gb|AAV81689.1| Predicted pseudouridylate synthase, Rlu family [Idiomarina
           loihiensis L2TR]
          Length = 236

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 99/236 (41%), Gaps = 18/236 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  ++Y D  + V NKP+G+ V      +   +  ++   +  G      HRLD+ TSG+
Sbjct: 3   QLEVVYLDEHLAVINKPSGLLVHRSRIASGAREFAMQMLRNQLGCHVYPVHRLDRPTSGL 62

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+       A+ LTE    R + K Y ++V G    +   I   L ++            
Sbjct: 63  LIFGLNSDVARTLTEQLTAREVSKTYHAVVRGYVP-ENGTIDYALKEEL---DKLADKDA 118

Query: 218 QNEKGANYAISHFKVI-----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             +K    A++H++ +                ++  ++MQP TGR HQLR H  H+  PI
Sbjct: 119 DPDKDKQPAVTHYQCLKQIELPYKVSKKHDTTRYSLVQMQPETGRKHQLRRHMAHIRHPI 178

Query: 267 VGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           VGD  +      NF     N  +L L A  +   HP  G  + +  PLP    + +
Sbjct: 179 VGDTNHGDGRHNNFFREHFNCHRLLLAATGLSFKHPVSGESINLEIPLPDEFHQPF 234


>gi|312127395|ref|YP_003992269.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
 gi|311777414|gb|ADQ06900.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
          Length = 311

 Score =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 69/289 (23%), Positives = 123/289 (42%), Gaps = 24/289 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            VV+ +   +++++  K  YP I    + K+LR G++ V     +    ++ G  V    
Sbjct: 5   FVVDKELAGVKVEKAIKKKYPIIPMSVIFKMLRRGEIIVSFLPAQKGQVLRFGDTVSFEI 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H               K  + LK   +YED  I V +KP GI     S   Y +
Sbjct: 65  EDRFLEH---------------KKVEILK---VYEDDNIVVIDKPYGIPSHPDSNNEYSV 106

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             +++    SK + P+L HRLD+ T+G+++VA+ R     + +    R I K Y  +   
Sbjct: 107 VSWIEDNY-SKNELPQLCHRLDRNTAGLMIVAKNRQVLSEMLKYMSRRAIIKKYLCITKK 165

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               +   + ++L K S     Y+    Q+  G +  ++ +K++         ++++  T
Sbjct: 166 ADLPESGVLVHYLKKDSKKSKVYISDFPQD--GYSEVVTAYKIV-RQKDDLQLVDVEIKT 222

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           G+THQ+R    H+G  I+GD KY             +   L A Y+   
Sbjct: 223 GKTHQIRAQLAHVGLCILGDSKYGDWKLNKKYK--ADMQALCAYYLKFE 269


>gi|227357259|ref|ZP_03841616.1| TruC protein [Proteus mirabilis ATCC 29906]
 gi|227162522|gb|EEI47511.1| TruC protein [Proteus mirabilis ATCC 29906]
          Length = 260

 Score =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 106/238 (44%), Gaps = 9/238 (3%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   ++Y+D  +   NKPAG  V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MMLDIIYQDEYLVAVNKPAGWLVHRSWLDRHETVFVMQTLRDQIGQHVFPVHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A +   A+ L+  F   +++K+Y ++V G  +      +  + +   I   +    
Sbjct: 61  VLLMALSSEVARTLSVCFEQHQMEKVYHAVVRGYVEEPMIIDSPLVEEHDKIADKFASQP 120

Query: 217 KQNEKGANYAISHFKVID------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            + +    + +   KV            +F  LE++P TGR HQLR H  H+  PI+GD 
Sbjct: 121 PKIQHCITHCVPLAKVEKEVAIGRYPTSRFSLLELRPETGRKHQLRRHMSHIRHPIIGDT 180

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +      +G       ++L LHA  ++L HP   + L +TA          +  G++
Sbjct: 181 AHGDLRQNRGVVNHFQSHRLMLHASQLNLIHPITQQPLNLTAKWDLPWQHLINQFGWR 238


>gi|197286139|ref|YP_002152011.1| tRNA pseudouridine synthase C [Proteus mirabilis HI4320]
 gi|194683626|emb|CAR44534.1| tRNA pseudouridine synthase C [Proteus mirabilis HI4320]
          Length = 259

 Score =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 105/236 (44%), Gaps = 9/236 (3%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y+D  +   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L
Sbjct: 2   LDIIYQDEYLVAVNKPAGWLVHRSWLDRHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A +   A+ L+  F   +++K+Y ++V G  +      +  + +   I   +     +
Sbjct: 62  LMALSSEVARTLSVCFEQHQMEKVYHAVVRGYVEEPMIIDSPLVEEHDKIADKFASQPPK 121

Query: 219 NEKGANYAISHFKVID------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +    + +   KV            +F  LE++P TGR HQLR H  H+  PI+GD  +
Sbjct: 122 IQHCITHCVPLAKVEKEVAIGRYPTSRFSLLELRPETGRKHQLRRHMSHIRHPIIGDTAH 181

Query: 273 CA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
                 +G       ++L LHA  ++L HP   + L +TA          +  G++
Sbjct: 182 GDLRQNRGVVNHFQSHRLMLHASQLNLIHPITQQPLNLTAKWDLPWQHLINQFGWR 237


>gi|145300305|ref|YP_001143146.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142853077|gb|ABO91398.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 218

 Score =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 64/215 (29%), Positives = 102/215 (47%), Gaps = 12/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L++D  I V NKP G+    G G     +  +   V  +  K    HRLD  T+G++
Sbjct: 12  LDILFKDKDIMVVNKPTGLLSVPGRGPEN--EDSVLHRVKQQHPKAAAAHRLDMSTTGVI 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+  T  + + L+  FR R  +K Y + VWG P+     +   L              K 
Sbjct: 70  VIPLTPNSHRELSRQFRERETEKHYLAWVWGEPEADSGQVDLPLCVDWPNRPK----QKV 125

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +   +A++ ++ +         +++ P TGR+HQLRVH L +G PI+GD+ Y A+   
Sbjct: 126 DFEEGRHALTLWEKLK-VENGNSLIKLTPITGRSHQLRVHMLELGHPILGDNLY-AHPDA 183

Query: 279 NFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
              +P    LYLHA  + + HP  G R+   AP P
Sbjct: 184 LAAAPH---LYLHAAMLTISHPRSGERMTFEAPAP 215


>gi|254361974|ref|ZP_04978105.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261493691|ref|ZP_05990210.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261494358|ref|ZP_05990852.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|153093521|gb|EDN74501.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261310007|gb|EEY11216.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261310691|gb|EEY11875.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 222

 Score =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 68/228 (29%), Positives = 107/228 (46%), Gaps = 14/228 (6%)

Query: 88  VNLTKHSDFLKSIL--LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           + L +++  L+  L  +Y D+ I V NKP+G+    G+   Y+      + V  K     
Sbjct: 1   MALIEYNPPLEPFLDEVYRDNHILVINKPSGLLSVPGNRPEYYDSAM--TRVQQKYGFTE 58

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLL 203
             HRLD  TSGIL+ A ++AA + L   FR R  +K Y +L+WG    K       N+ L
Sbjct: 59  PAHRLDMATSGILLFALSKAAEKELKRQFREREPKKHYIALLWGKLGEKVGDKGEMNFPL 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                      +  +       AI+H++V+  +      +++ P TGR+HQLRVH+L +G
Sbjct: 119 ICDWENRPRQKICYER---GKKAITHYEVLAHYPNNIARVKLTPITGRSHQLRVHSLALG 175

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            PI+GD  Y           +  +L LHA  + + HP     +  TA 
Sbjct: 176 HPIIGDKFY----ANPLAKSLSPRLCLHAESLTITHPITRELMTFTAE 219


>gi|291549821|emb|CBL26083.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           torques L2-14]
          Length = 222

 Score =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 67/223 (30%), Positives = 100/223 (44%), Gaps = 20/223 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--------DSKGQKPRLTH 148
           L   ++YED  I V +KPAG+  Q        +   LK+ +         S+     + H
Sbjct: 5   LTPEIIYEDKDIIVCHKPAGVPTQSSRIGTKDMVSILKNHLIKNTAKKTASREPYLAVIH 64

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLDQ   G+LV A+T AAA+ L+         K Y +   GI ++ +  + ++L+K    
Sbjct: 65  RLDQPVEGLLVFAKTPAAAKELSRQLTTSGFGKYYRAQALGIFEHNEGTLEDYLVKDGRT 124

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                 V K+N   A YA  H+KVI        + F  LE+   TGR HQ+RV   H G 
Sbjct: 125 NTSR--VCKENVPDAKYARLHYKVIHTGTLPSGEPFSQLEIHLDTGRHHQIRVQFAHAGH 182

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           P++GD KY         +    +L L A  ++  HP  G   +
Sbjct: 183 PLIGDRKYGT------AACTSRQLMLCACRLEFTHPTTGEKMV 219


>gi|271502078|ref|YP_003335104.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270345633|gb|ACZ78398.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 217

 Score =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 101/231 (43%), Gaps = 17/231 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G     H D  + + + +        
Sbjct: 1   MEPYSPPREPWLHILYQDQHIMVVNKPSGLLSVPGRA-EEHKDSIM-TRIQTDFPTAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG     +  +   L+    
Sbjct: 59  HRLDMATSGVMVVALTKAAERELKRQFREREPKKSYVARVWGHLAQDEGLVDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + + V+   +     +++ P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCFEQGKPAQTDYIVLSRDSDGTTRVKLMPITGRSHQLRVHMLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
           I+GD  Y           +  +L LHA+ + + HP     +       A  
Sbjct: 173 ILGDGFYAHPEAKA----LAPRLLLHAQELAITHPIFTTPMHFRCE--ADF 217


>gi|153001327|ref|YP_001367008.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151365945|gb|ABS08945.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 223

 Score =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 61/213 (28%), Positives = 99/213 (46%), Gaps = 8/213 (3%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        + Y+D  + + NKP+G+    G   A H        + +   +  L HRLD
Sbjct: 7   QPPAVPWLDIRYKDRDLIIINKPSGLLSNPGR--AAHTFDCALIRLQTLYPETILVHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V AR + A  HL   F+ R+ +K+Y + V G    ++  I   +   +     
Sbjct: 65  CATSGIMVFARNKKAESHLKTQFQDRQSKKVYIAEVMGHVPQEQGMIDLAIAPDTEHP-P 123

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y   ++  E G   A+++++V++        +E+ P TGRTHQLRVH L +G  I+GD  
Sbjct: 124 YQKTLQAGETGGKSALTYYRVLERRVNS-TLVELSPETGRTHQLRVHMLALGHAILGDEF 182

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           Y              +L LHA+ + L HP   +
Sbjct: 183 YG----DAEVIKAAPRLCLHAQSLSLSHPYSAK 211


>gi|294155753|ref|YP_003560137.1| ribosomal large subunit pseudouridylate synthase C [Mycoplasma
           crocodyli MP145]
 gi|291600008|gb|ADE19504.1| ribosomal large subunit pseudouridylate synthase C [Mycoplasma
           crocodyli MP145]
          Length = 280

 Score =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 62/307 (20%), Positives = 119/307 (38%), Gaps = 39/307 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           ++ ++  +++    L +    +  ++    ++K+ R   ++V+  R  + +  I     +
Sbjct: 1   MKTIIATSNDAGRTLYKLITKYLDNVPLSRIEKLFRKKDIKVNGIRTNQKDYTIAFNDQI 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I  +I+    I KE+  L SS +  K         +YED+ I + +KP GI V      
Sbjct: 61  EIYGLID----IKKEEAPLISSFSFKK---------IYEDNNILIIDKPNGIEVHSSPNC 107

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             +       +      KP    RLD+ETSGI++ A+   A ++L ++         + S
Sbjct: 108 LDNQVLAYLKFKQVDSFKPSHVGRLDKETSGIMLYAKNYQALKYLNDNMENIIKTYTFKS 167

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
                   + + +  +L K        +         +  + +HF  ++   +       
Sbjct: 168 ----DFNEESKDVELYLYKDE--DKKRMAASFTKVPYSKLSKTHFY-LESNKKYATLS-- 218

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-- 303
              +GR HQ+RV  + +G PI GD KY     G        +L LH   +     EG   
Sbjct: 219 ---SGRKHQIRVSLMKLGKPIYGDFKYGGKKAG--------RLMLHCLQIKFQQLEGEFK 267

Query: 304 ---RLQI 307
               L+ 
Sbjct: 268 YLNELEF 274


>gi|167752914|ref|ZP_02425041.1| hypothetical protein ALIPUT_01176 [Alistipes putredinis DSM 17216]
 gi|167659983|gb|EDS04113.1| hypothetical protein ALIPUT_01176 [Alistipes putredinis DSM 17216]
          Length = 537

 Score =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 101/238 (42%), Gaps = 21/238 (8%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           + LD      +        LLYED  I    KPAG+    G   A  I  + +    +  
Sbjct: 317 RGLDVEPEPDRACPQSAPELLYEDRWIAAVFKPAGMLSVPGKSEAPSILDWARERYPA-A 375

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
             P + HRLD +TSG+L++A T+ A Q L   F+ R ++K Y +L+ G     K  I   
Sbjct: 376 TGPLVVHRLDMDTSGVLLLALTKEAHQDLQAQFKHRTVRKRYIALLEGRITPPKGRIELP 435

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L    H           +      AI+ ++V++ F      +   P TGRTHQLRVHA H
Sbjct: 436 LRPDLHDRP----RQAVDPLHGKPAITEYEVLE-FRNGRTRIAFYPLTGRTHQLRVHAAH 490

Query: 262 ---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
              +  PI GD  Y              +L LHA  ++  HP  G R+ I    PA  
Sbjct: 491 PSGLNAPIAGDRLYG---------TAGRRLLLHAERIEFRHPATGDRIAIE--KPADF 537


>gi|300727412|ref|ZP_07060821.1| ribosomal large chain pseudouridine synthase A [Prevotella bryantii
           B14]
 gi|299775292|gb|EFI71891.1| ribosomal large chain pseudouridine synthase A [Prevotella bryantii
           B14]
          Length = 531

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 73/234 (31%), Positives = 106/234 (45%), Gaps = 28/234 (11%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I D+ +NL K  +  +   +Y D  + V  KPAG+    G  I   +   LK     K  
Sbjct: 319 IEDNLLNLQKKQELEE---IYSDHDLIVVYKPAGMLSVPGKNIRESVLSILKERY-PKAT 374

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P + HRLD  TSG+LVV +   A  +L + F    I+K Y +L+  IP      +   L
Sbjct: 375 GPMIVHRLDMATSGLLVVTKNLEAYINLQKQFAEHTIKKRYVALLEHIPDQSIGIVDLPL 434

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH- 261
           L             K ++K    AI+ ++VI         + + P TGRTHQLR+H  H 
Sbjct: 435 LPDIMDRP----RQKVDKKNGKKAITKYQVIAQN-----RVWLYPLTGRTHQLRMHCAHE 485

Query: 262 --MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT--AP 310
             +  PI+GD+ Y             ++LYLHA Y++  HP  G R+     AP
Sbjct: 486 EGLNNPILGDNLYGKP---------ADRLYLHAEYLEFTHPSTGKRIHFEYKAP 530


>gi|151941961|gb|EDN60317.1| tRNA-pseudouridine synthase [Saccharomyces cerevisiae YJM789]
          Length = 462

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 108/255 (42%), Gaps = 23/255 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +        ++ + +G V ++ +    +  I++G ++              E
Sbjct: 129 VDVFISE-FRDRESEYYKRTIENGDVHINDETADLSTVIRNGDLITHQVHR-------HE 180

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  I V +KP+GI V       Y  +   K   ++ 
Sbjct: 181 PPVTSRPIK-----------VIFEDDNIMVIDKPSGIPVHPTG--RYRFNTITKMLQNNL 227

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A ++ +  + R + K Y + V G     +  +  
Sbjct: 228 GFVVNPCNRLDRLTSGLMFLAKTPKGADNIGDQLKAREVTKEYVAKVVGEFPETEVIVEK 287

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K          V + +EKGA +A + F  I     K   ++ +P TGR+HQ+RVH  
Sbjct: 288 PL-KLIEPRLALNAVCQMDEKGAKHAKTVFNRISYDG-KTSIVKCKPLTGRSHQIRVHLQ 345

Query: 261 HMGCPIVGDHKYCAN 275
           ++G PI  D  Y  +
Sbjct: 346 YLGHPIANDPIYSND 360


>gi|51012815|gb|AAT92701.1| YDL036C [Saccharomyces cerevisiae]
          Length = 462

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 108/255 (42%), Gaps = 23/255 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +        ++ + +G V ++ +    +  I++G ++              E
Sbjct: 129 VDVFISE-FRDRESEYYKRTIENGDVHINDETADLSTVIRNGDLITHQVHR-------HE 180

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  I V +KP+GI V       Y  +   K   ++ 
Sbjct: 181 PPVTSRPIK-----------VIFEDDNIMVIDKPSGIPVHPTG--RYRFNTITKMLQNNL 227

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A ++ +  + R + K Y + V G     +  +  
Sbjct: 228 GFVVNPCNRLDRLTSGLMFLAKTPKGADNIGDQLKAREVTKEYVAKVVGEFPETEVIVEK 287

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K          V + +EKGA +A + F  I     K   ++ +P TGR+HQ+RVH  
Sbjct: 288 PL-KLIEPRLALNAVCQMDEKGAKHAKTVFNRISYDG-KTSIVKCKPLTGRSHQIRVHLQ 345

Query: 261 HMGCPIVGDHKYCAN 275
           ++G PI  D  Y  +
Sbjct: 346 YLGHPIANDPIYSND 360


>gi|291535586|emb|CBL08698.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis M50/1]
          Length = 217

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 65/219 (29%), Positives = 108/219 (49%), Gaps = 9/219 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++  ++YED  I V  KPAG++ Q        ++  LK++  SKG+ P +   HRLDQ  
Sbjct: 1   MQPAIIYEDEDIIVCKKPAGVATQTRRIGQADMESLLKNYRASKGELPYIGVVHRLDQPV 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            GI+V A+ + AA  L+   + +   K Y+++  G+P+ KK  + + LL+          
Sbjct: 61  EGIMVFAKNKEAAADLSRQIKTKLADKYYYAMTDGVPEKKKGTLEDELLQNGKTNTS--E 118

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV++    A +A   ++V++   +      ++  TGR HQ+RV   H G PIVGD KY  
Sbjct: 119 VVERGTPQAKHASLSYEVVEQDGKHAVL-RIKLDTGRHHQIRVQLAHAGMPIVGDKKYNF 177

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                  +P   +L L +  +   HP+  R L+     P
Sbjct: 178 K---ENIAPSGGQLALCSFKIAFRHPKTHRKLEFEIDKP 213


>gi|59710878|ref|YP_203654.1| pseudouridine synthase for 23S rRNA and tRNAphe [Vibrio fischeri
           ES114]
 gi|197334224|ref|YP_002155030.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
 gi|59478979|gb|AAW84766.1| pseudouridine synthase for 23S rRNA and tRNAphe [Vibrio fischeri
           ES114]
 gi|197315714|gb|ACH65161.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
          Length = 245

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 62/212 (29%), Positives = 104/212 (49%), Gaps = 15/212 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   ++Y+D  I V NKP+G+    G    ++    + S +  +    ++ HRLD 
Sbjct: 8   PPQDPWIDIVYQDESILVVNKPSGLLSVPGRAPEHYDS--MWSRLKVEFPDIQVVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+++ A  + + +HL + F+ R   KIY++ VWG  +  +  I   L+       D+
Sbjct: 66  STSGLMLFAMNKYSERHLKKQFQYRLTHKIYYARVWGNIEQDEGEIDLPLI------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    + + ++V+    +K   + + P TGR+HQLRVH L +G PIVGD 
Sbjct: 120 ENRPKQKVCFEHGKPSQTRYQVV-RREEKTTIVRLLPITGRSHQLRVHMLSIGHPIVGDE 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            Y      NF+S    +L LHA  +   HP+ 
Sbjct: 179 FYANEEAKNFSS----RLELHAAELSFYHPKS 206


>gi|304397365|ref|ZP_07379243.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304354983|gb|EFM19352.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 232

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 94/229 (41%), Gaps = 17/229 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
              F +   L++D+ + V NKP G+    G          +   +        L HRLD 
Sbjct: 11  PPCFDEITFLFQDAHLLVINKPGGLLSLSGKNPQN--LDSVHHRLVGLFPGCTLVHRLDF 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVAR +A    L + F  R + K Y +L+ G   + +  I   + K   +    
Sbjct: 69  GTSGLMVVARNKAINAALCQQFSQRSVNKTYQALLCGHLSDDEGVIDAAIAKDPALFPRM 128

Query: 213 VHVVKQNEKGANYAISHFKVIDC--------FAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                +       A S ++V +          A     +E+ P TGRTHQLR+H   +G 
Sbjct: 129 TICTIR----GKPARSRYRVTERGYYQGSEGDALPVTRVELTPETGRTHQLRIHCQQLGH 184

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           PI+G   Y              +L LHA  +   HP  G  +Q++A  P
Sbjct: 185 PILGCDLYGGLLMPGAEK--AERLMLHASGLTFIHPVSGEVMQLSAASP 231


>gi|167463935|ref|ZP_02329024.1| pseudouridine synthase [Paenibacillus larvae subsp. larvae
           BRL-230010]
 gi|322384790|ref|ZP_08058452.1| RNA pseudouridine synthase [Paenibacillus larvae subsp. larvae
           B-3650]
 gi|321150361|gb|EFX43862.1| RNA pseudouridine synthase [Paenibacillus larvae subsp. larvae
           B-3650]
          Length = 243

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 64/236 (27%), Positives = 108/236 (45%), Gaps = 19/236 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L+ED+ + V  KP  +  Q  S     +   LK+ +  +  KP      L HRLD+   
Sbjct: 16  VLFEDNHLLVVEKPVNMPTQEDSSRDPDLLSVLKADLKHRYGKPGNVYLGLIHRLDRPVG 75

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  ++++ R R   K Y ++V G P + +  + + L K +        V
Sbjct: 76  GVMVFAKTSKAASRISDAVRTRAFDKTYLAVVHGKPADPQGTLRHHLRKDTRTN--TALV 133

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V+   +GA  AI  ++V+   A+    ++++ HTGR HQ+RV    +GCP+ GD +Y A 
Sbjct: 134 VRPGAEGAKEAILDYRVLG-HAEGLSLVQVKLHTGRPHQIRVQLAAIGCPLYGDQRYGAG 192

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAH-----MVKTWDSLGFK 325
                 +    +L L +  +   HP     L+ TA  P         +    L   
Sbjct: 193 -----RNKPGQQLALWSALLAFSHPTLKEPLRFTAAPPDTYPWYLWKELIAKLKLD 243


>gi|162147092|ref|YP_001601553.1| RNA pseudouridine synthase [Gluconacetobacter diazotrophicus PAl 5]
 gi|209544152|ref|YP_002276381.1| pseudouridine synthase [Gluconacetobacter diazotrophicus PAl 5]
 gi|161785669|emb|CAP55240.1| putative RNA pseudouridine synthase [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209531829|gb|ACI51766.1| pseudouridine synthase [Gluconacetobacter diazotrophicus PAl 5]
          Length = 227

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 107/234 (45%), Gaps = 16/234 (6%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                    +L+ D++  V +KP G+ V  G      ++      +  +   P L HRLD
Sbjct: 5   PDDRPDPFPVLFRDNRFIVIDKPPGLPVHPGPSGGPSVEDSFP-LLSRRADGPWLAHRLD 63

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG L++A  + A      +F   +++K YW++V G P      +A  + + S   G 
Sbjct: 64  RDTSGCLLIALRKQALLAAQAAFAAGQVRKTYWAVVQGRPAADSGTVAMTMARHSDRQGW 123

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +            + + ++V+    ++  WLE+   TGRTHQ R+H   +GCPI+GD  
Sbjct: 124 RMVAA----PDGQASRTDWRVLASDGRE-SWLELHLLTGRTHQARLHCASLGCPILGDPV 178

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           Y               L+L +R++ L  P    +  TAP PAH+  T D  G++
Sbjct: 179 YGGAEGPT--------LHLMSRHLAL--PLSPPVSATAPPPAHIRATLDRHGWQ 222


>gi|254721425|ref|ZP_05183214.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. A1055]
          Length = 168

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 50/178 (28%), Positives = 86/178 (48%), Gaps = 12/178 (6%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HR+D++TSG+L+VA+   A + L      + + + Y ++V G+  + K  I   + +  
Sbjct: 1   MHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKGTIDAPIARD- 59

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                        ++   +A++HF+V++ F + F  +E +  TGRTHQ+RVH  ++G P+
Sbjct: 60  ----KKERQSMTVDENGKHAVTHFQVLERF-KDFTLVECRLETGRTHQIRVHMKYIGYPL 114

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            GD KY      +      N   LHA  +   HP  G  +Q  AP+P       + L 
Sbjct: 115 AGDPKYGPKKTLDM-----NGQALHAGILGFDHPRTGEYIQFEAPIPEVFEDALNILR 167


>gi|261344776|ref|ZP_05972420.1| hypothetical protein PROVRUST_06041 [Providencia rustigianii DSM
           4541]
 gi|282567221|gb|EFB72756.1| pseudouridine synthase A [Providencia rustigianii DSM 4541]
          Length = 216

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 67/212 (31%), Positives = 103/212 (48%), Gaps = 16/212 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+ +    G    +H    + S +          HRLD  TSG++VV
Sbjct: 14  ILYQDEHIIVVNKPSELLSVPGKAPEHHDS--IISRIQRDHPAAESVHRLDMATSGVMVV 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +AA + L   FR R  +K Y + VWG  +NK+  I   L+       D+ +  KQ  
Sbjct: 72  ALNKAAERELKRQFREREPKKHYVARVWGHLENKEGLIDLPLI------CDWPNRPKQKV 125

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             +    A + ++V++   Q    +++ P TGR+HQLRVH L +G PI+GD  Y      
Sbjct: 126 CFETGKSAQTEYQVLEYEEQ-ATRVKLSPITGRSHQLRVHMLALGHPILGDRFYAHEE-- 182

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
                +  +L LHA+ + + HP  G  +  T 
Sbjct: 183 --ALALAPRLQLHAQELYITHPAYGTPMHFTC 212


>gi|117618521|ref|YP_855405.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117559928|gb|ABK36876.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 218

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/215 (29%), Positives = 101/215 (46%), Gaps = 12/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L++D  I V NKP G+    G G     +  +   V  +  K    HRLD  T+G++
Sbjct: 12  LDILFKDKDIMVVNKPTGLLSVPGRGPEN--EDSVLHRVKQQHPKAAAAHRLDMSTTGVI 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+     + + L+  FR R  +K Y + VWG P+     +   L              K 
Sbjct: 70  VIPLNPNSHRELSRQFRERETEKHYLAWVWGEPEAASGQVDLPLCVDWPNRPK----QKV 125

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +   +A++ ++ +         +++ P TGR+HQLRVH L +G PI+GD+ Y A+   
Sbjct: 126 DHEEGRHALTLWEKLK-VENGNSLIKLTPITGRSHQLRVHMLELGHPILGDNLY-AHPDA 183

Query: 279 NFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
              +P    LYLHA  + + HP  G R+   AP P
Sbjct: 184 LAAAPH---LYLHAASLTISHPRSGERMTFEAPAP 215


>gi|146291939|ref|YP_001182363.1| pseudouridylate synthase [Shewanella putrefaciens CN-32]
 gi|145563629|gb|ABP74564.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           putrefaciens CN-32]
          Length = 226

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/215 (29%), Positives = 107/215 (49%), Gaps = 16/215 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G   A++    + + V ++    ++ HRLD  TSG++V+
Sbjct: 17  ILYQDKDIIVINKPSGLLSVPGRDPAHYDS--VYARVKAEHPHCQIVHRLDMATSGVIVL 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R+A + L   F  R   K Y + V G  K+    I   L+       D+ +  KQ  
Sbjct: 75  ALIRSAERELKRQFHDRETSKTYIARVAGHIKHDTGSIDYPLI------CDWPNRPKQKV 128

Query: 221 KG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  +++H++V+   A++   +++ P TGR+HQLRVH + +G PI+GD  Y      
Sbjct: 129 DHFVGKPSLTHYQVMSR-AKRSTLVKLTPITGRSHQLRVHMMAIGHPILGDGFYADPLAK 187

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           +    +  +L LHA  + + HP  G  +  +   P
Sbjct: 188 S----LAPRLLLHAAELTIKHPYTGVSMTFSTEAP 218


>gi|261823062|ref|YP_003261168.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
 gi|261607075|gb|ACX89561.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
          Length = 217

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 64/215 (29%), Positives = 97/215 (45%), Gaps = 14/215 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G     H D  + S + +        
Sbjct: 1   MEPYNPPTDPWLHILYQDQHIMVVNKPSGLLSVPGRAPE-HKDSVM-SRIQADYPAAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++ VA T+AA + L   FR R  +K Y + VWG     +  I   L+    
Sbjct: 59  HRLDMATSGVIAVALTKAAERELKRQFREREPKKCYLARVWGHMAQDEGVIDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V+         +++ P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCFETGKSAQTEYQVLSRDDDGTTRVKLMPITGRSHQLRVHLLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           I+GD  Y              +L LHA+ + + HP
Sbjct: 173 ILGDGFYAHPDAKAMA----PRLLLHAQELAITHP 203


>gi|110834055|ref|YP_692914.1| ribosomal large subunit pseudouridine synthase A [Alcanivorax
           borkumensis SK2]
 gi|110647166|emb|CAL16642.1| ribosomal large subunit pseudouridine synthase A [Alcanivorax
           borkumensis SK2]
          Length = 229

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 59/213 (27%), Positives = 96/213 (45%), Gaps = 12/213 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D  + + NKPA +    G   A          +  +    RL HRLD +TSGI+V  
Sbjct: 26  IYRDEHLLLINKPAYLLSVPGR--APENKDCAIRRLQQRYPDIRLVHRLDLDTSGIMVFG 83

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
            T  A   L+  F++R ++K Y ++V G+ +     I   L+           + K   +
Sbjct: 84  LTAFAQSKLSRLFQLRTVKKRYQAIVHGLVEKNAGSIDLPLIAD----WPKRPLQKVCHE 139

Query: 222 GANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               A++H++V++         L + P TGR+HQLR+H   +G PI+G   Y        
Sbjct: 140 TGKNALTHYRVLERDIPGNRTRLALSPVTGRSHQLRIHCRELGHPIIGCDMYAP----AE 195

Query: 281 TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
              +  +L LHA ++   HP  G   + T+P P
Sbjct: 196 IEALSPRLLLHAEWLAFNHPLTGLWQEFTSPCP 228


>gi|313638581|gb|EFS03722.1| ribosomal large subunit pseudouridine synthase D [Listeria
           seeligeri FSL S4-171]
          Length = 207

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 56/218 (25%), Positives = 101/218 (46%), Gaps = 22/218 (10%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGILVVAR 162
            + NKPAGI+        YH  G + ++V    +         +  RLD+ETSG++++A+
Sbjct: 1   LIINKPAGIASIPSQ---YHPSGSVANFVKGHYETQGLTSAIHIVTRLDRETSGLMLIAK 57

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            R A   L+   +   +++ Y + V G    +   I   + +K+        + +     
Sbjct: 58  NRFAHARLSTFLQQGLLKRSYQAFVSGELAEQVGSIEAPIGRKA-----VSIMERVVTPE 112

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             YA ++++V+  + Q F  + +Q  TGRTHQ+RVH  ++G P++GD  Y  +       
Sbjct: 113 GKYAKTNYQVLARY-QAFDHVAIQLETGRTHQIRVHFSYIGHPLIGDDMYGGDTD----- 166

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
            +  +  LH+ ++ L HP     L    PLP  M +  
Sbjct: 167 -LLKRQALHSCHLHLIHPLTEEYLAFDLPLPYDMEEII 203


>gi|320168809|gb|EFW45708.1| pseudouridine synthase [Capsaspora owczarzaki ATCC 30864]
          Length = 748

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 83/294 (28%), Positives = 127/294 (43%), Gaps = 34/294 (11%)

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           +VV     +N +    +               D ++  +L++D  I V NKPAG+SV   
Sbjct: 327 EVVDADVDVNEVPIGAQSPPRPAPRPITDAERDRIRQCVLHKDQHIIVINKPAGLSVMAD 386

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              A  +   L +        P + HRLD+ T+G L++AR    A+ L+ +F+ +RI K 
Sbjct: 387 GFEALDLSRLLPALQFEAPCLPHIVHRLDKNTTGALLLARNPRVARILSRAFQKQRIGKT 446

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK------------------QNEKGAN 224
           Y ++V G P      I   L   S      V V                    +  + A 
Sbjct: 447 YTAIVAGAPPFDSGIINCPLEVISATTARKVGVTPGTVLCRHDLVYANETSYLRTRRDAL 506

Query: 225 YAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYCANFKGNFTS 282
            AI+HF V+   ++     +E  P +GR HQLRVH+  ++G PI+GD++Y          
Sbjct: 507 SAITHFSVVGRSSRGPAALIEFVPMSGRKHQLRVHSSKYLGHPILGDNRYGNGCPVELHE 566

Query: 283 PIQ----------NKLYLHARYMDLPHPEGGR----LQITAPLPAHMVKTWDSL 322
           P+            KL LHAR + +P  +  R    L + APLPAHM +  D L
Sbjct: 567 PLGIAGWDAKNDVVKLQLHARSIVVPSLDQQRNNKPLVVLAPLPAHMKEVMDKL 620


>gi|256830138|ref|YP_003158866.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256579314|gb|ACU90450.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 243

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 60/226 (26%), Positives = 102/226 (45%), Gaps = 19/226 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIA-----YHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +++YED  I V NKPAG+              Y +  +++        +  + HRLD+E
Sbjct: 16  LVIIYEDRDIIVVNKPAGMLTMATETEKTRTAYYALTDYVRKGNAKSRYRIFIVHRLDRE 75

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGI++ A+T  A + L + +      KIY ++V G        +++ L++     G + 
Sbjct: 76  TSGIVLFAKTEVAKRTLQDQWED--TTKIYAAVVHGQMGKASGMLSSHLVE----SGVHK 129

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               ++      A + + V+      +  L++   TGR HQ+RV     G PI GD KY 
Sbjct: 130 VYATRDAALGKLARTAWTVLKERG-GYSLLDVTLLTGRKHQIRVQMADAGHPIAGDKKYG 188

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
                       ++L LHAR +   HP  GR + + AP+P+   + 
Sbjct: 189 VKGD------TFSRLALHARSITFAHPFSGRSMTLDAPVPSVFAQL 228


>gi|257455430|ref|ZP_05620665.1| tRNA pseudouridine synthase C [Enhydrobacter aerosaccus SK60]
 gi|257447392|gb|EEV22400.1| tRNA pseudouridine synthase C [Enhydrobacter aerosaccus SK60]
          Length = 266

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 66/260 (25%), Positives = 101/260 (38%), Gaps = 36/260 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D      NKPAG+ V       +  +  +++  D   Q     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEHCVAVNKPAGMLVHRSWLDRHETEFVMQTLRDQLAQYVYPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIP---KNKKECIANWLL-KKSHIGGDYVHVV 216
           A +  +A+ L E F  R++QK Y ++V G           I   L      IG       
Sbjct: 64  ALSSESARQLCEQFENRQVQKSYLAIVRGYLTVNAQTSGLIDYPLTQILDKIGDKPSLQA 123

Query: 217 KQNEKGA------------------NYAISHFKVIDCFAQ-----------KFCWLEMQP 247
            Q  K +                    A +H++ +    Q           +F    + P
Sbjct: 124 LQQRKVSSTDMFAEALSSPAELTLLQPAQTHWQCLATTEQPFQARARYPTSRFSLARLTP 183

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-R 304
            TGR HQLR H  H+  PI+GD  Y  + +          ++L LHA  +         R
Sbjct: 184 ITGRKHQLRRHMKHVFHPIIGDTSYGDHHQNRAIRQHIGVHRLMLHAHTLAFNRLTDNRR 243

Query: 305 LQITAPLPAHMVKTWDSLGF 324
           + ITAP+    +      GF
Sbjct: 244 VDITAPVDTDWLTMCAQFGF 263


>gi|168014236|ref|XP_001759658.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162689197|gb|EDQ75570.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 283

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 85/273 (31%), Positives = 128/273 (46%), Gaps = 56/273 (20%)

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVAR 162
           +D++I V NKP+G++VQGGS +   +D  +++ +     + PRL HRLD+ETSG LV+ R
Sbjct: 1   QDAEIIVINKPSGLAVQGGSDVVKSLDSMMEAALSYNYNEGPRLVHRLDKETSGALVLGR 60

Query: 163 TRAAAQHLTESFRMRRIQ------KIYWSLVWGIPKNKKECIANWLLKKSHIGG--DYVH 214
           T  +   L    R +  +      + Y +LV G+P+ K+  I+  L K     G  D + 
Sbjct: 61  THQSTVFLQALLRNKTEKISQAPGRCYLALVIGVPEKKEGRISAPLAKVVSDSGKLDKMR 120

Query: 215 VVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKY 272
           VV  +   A  AI+ +KV+         WLE++P TGR HQ+RVH    +G PIVGD+KY
Sbjct: 121 VVHGSHPNAQEAITDYKVLGSSLFAGCSWLELRPLTGRKHQIRVHCAEVLGMPIVGDYKY 180

Query: 273 C----------ANFKGNFTSPIQNK-----------LYLHARYMDLPH------------ 299
                         +   +S +  +           L+LH R + LP             
Sbjct: 181 GWRALRLWPPTDRTEDTKSSVLGLRESGHVWSSKPYLHLHCRQLILPDVAQAFKSQSRER 240

Query: 300 ------------PEGGRLQITAPLPAHMVKTWD 320
                            L+I APLP HMV +W+
Sbjct: 241 SSAQTGARVSGSQFAEPLEIIAPLPPHMVVSWN 273


>gi|299473311|emb|CBN77710.1| pseudouridylate synthases, 23S RNA-specific [Ectocarpus
           siliculosus]
          Length = 256

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 114/235 (48%), Gaps = 12/235 (5%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +  E+  L+   N       L+  +L+ D +I V NKP+ +    G      +       
Sbjct: 30  VAAEEMWLNGPFNAPVPPGPLE--ILFVDEEIVVCNKPSDLLCVPGRIEKDSLATRAALE 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +        + HRLD  TSG +++ART AA + L   FR R+++K Y ++V G+    + 
Sbjct: 88  LGHYRVDRMIVHRLDMATSGCVIMARTDAALKDLNRQFRERQVRKRYVAIVHGVLWADEG 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +   L +    G   +H+V  N +    +++ ++V+D  A +   +E+ P +GR+HQLR
Sbjct: 148 EVDLPLCRNR--GCPPLHMV--NFEHGKPSLTKWRVLDRAADR-TRVELIPVSGRSHQLR 202

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
           +H   +G PI+GDH Y        +  +  +  LHA  + L HP+ G R   TAP
Sbjct: 203 LHMNAIGHPILGDHFYGTTD----SLALAGRCLLHAHTLCLRHPKTGERTMFTAP 253


>gi|303236245|ref|ZP_07322841.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
 gi|302483559|gb|EFL46558.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
          Length = 532

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 71/244 (29%), Positives = 115/244 (47%), Gaps = 28/244 (11%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           K ++ + N  + S+     ++YED+ + V  KP G+    G      ++  L++  +   
Sbjct: 301 KGMNVAPNPLETSEEQSLKIIYEDNDLAVIVKPCGMLTVAGRSQRQSVEAILRTRWNLSN 360

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK----KEC 197
             P + HRLD  TSG+LVVAR + A + L   F  R ++K Y +L+      K    +  
Sbjct: 361 M-PIIVHRLDMATSGLLVVARNKEAHKDLQAQFNNRSVKKRYTALLSTALLTKDLPTEGT 419

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI------DCFAQKFCWLEMQPHTGR 251
           I+  L +   +      V   + +    A +++K+I      D   ++   +E+QP TGR
Sbjct: 420 ISLPL-RADLLDRPRQIV---DHEQGKPATTYYKIIGKTPFKDSKIKEAVRVELQPLTGR 475

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           THQLRVH  H   +  PI+GD  Y  +          ++LYLHA Y+   HP  G  LQ 
Sbjct: 476 THQLRVHCAHLEGLNTPILGDTLYGTH---------ADRLYLHAEYLSFVHPRTGKELQF 526

Query: 308 TAPL 311
             P+
Sbjct: 527 QYPM 530


>gi|169350972|ref|ZP_02867910.1| hypothetical protein CLOSPI_01749 [Clostridium spiroforme DSM 1552]
 gi|169292034|gb|EDS74167.1| hypothetical protein CLOSPI_01749 [Clostridium spiroforme DSM 1552]
          Length = 310

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 58/313 (18%), Positives = 121/313 (38%), Gaps = 37/313 (11%)

Query: 9   YVVVENDEENMRL-DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
            ++++ND  +  + D +   +Y H++   +  + +     ++ + V  N+ +     ++I
Sbjct: 19  TLIIDNDFHHKTIRDIF---NYLHLSKKTIHLLKQDKNYTLNNQFVNDNHLLNKNDHLKI 75

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIA 126
                             +  ++          + YE+  I + NKP   ++        
Sbjct: 76  KAF---------------NQESIDYVPQEYPLSIAYENDFILIVNKPINTTIYPETKKEL 120

Query: 127 YHIDGFLKSWVDSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +  ++ ++     Q    R  HRLD++T+G+++  +       L      + I++ Y 
Sbjct: 121 NTLCNYVANYYLETNQYLLIRHIHRLDKDTTGLVLFCKCPLLQPILDNMMANKLIKRSYI 180

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWL 243
           ++  GI       I + L     I  D      +       AI+  K+I    Q  +   
Sbjct: 181 AICKGI-------IDHDLTINRDIARDRHVNKMRITNKGLKAITEIKIIKHDKQKNYTVC 233

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +    TGR HQ+RVH   +  P++ D  Y    K      + ++L LHA  ++  HP   
Sbjct: 234 KCDLKTGRKHQIRVHLASINHPLLSDPLYGNKSK------LIDRLALHAYKLEFIHPVTK 287

Query: 304 -RLQITAPLPAHM 315
            ++ + A LP  M
Sbjct: 288 QQIIVKADLPQDM 300


>gi|260549688|ref|ZP_05823905.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           RUH2624]
 gi|260407205|gb|EEX00681.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           RUH2624]
          Length = 212

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 69/223 (30%), Positives = 106/223 (47%), Gaps = 17/223 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V  + +   L HRLD++
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLVAIEPRTL-LIHRLDRD 58

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     +   F+ R+  KIY +LV G    +   +   ++         +
Sbjct: 59  TSGILVFGLSKRGQSAIARQFQDRQTSKIYEALVAGHLDGE-GTVDIPVVYDP--SRPPL 115

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+V  +      A++H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD 
Sbjct: 116 HIVDASHN--KPALTHWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDT 173

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            Y           +  +L LHA+ +   HP  G  L    P+P
Sbjct: 174 LY-----ATPEQLLVPRLCLHAKQLSFNHPVTGESLTFNCPVP 211


>gi|91225595|ref|ZP_01260669.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
 gi|91189715|gb|EAS75989.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
          Length = 250

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 109/232 (46%), Gaps = 15/232 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED  I   NKP+G+    G  +A H D  + S +     + ++ HRLD  TSG++
Sbjct: 14  VDIVFEDDDILAVNKPSGLLSVPGR-LAEHYDS-MWSRLKELHPEIQVVHRLDMSTSGLM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+ + A + L + F+ R   K+Y++ VWG  ++++  I   L+           V   
Sbjct: 72  LLAKNKPAERALKKQFQYRLTHKVYYARVWGHVESQEGNIDLPLICD-WPNRPRQKVCFD 130

Query: 219 NEKGANYAISHFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +      + + F+V+             + + P TGR+HQLRVH + +G  IVGD  Y +
Sbjct: 131 D---GKPSQTLFQVVKREVHPDGTHTTVVRLLPITGRSHQLRVHLMAIGHAIVGDEFYAS 187

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                F+     +L LHA  +   HP   +L  +  +P       +++ F Y
Sbjct: 188 EEAYQFSE----RLELHAAELSFYHPATDQLS-SIFVPCDFYSEAEAMIFNY 234


>gi|254474013|ref|ZP_05087406.1| 23S rRNA (position 746) and tRNAphe (position 32) specific
           pseudoryidylate sytnthase [Pseudovibrio sp. JE062]
 gi|211956902|gb|EEA92109.1| 23S rRNA (position 746) and tRNAphe (position 32) specific
           pseudoryidylate sytnthase [Pseudovibrio sp. JE062]
          Length = 212

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 64/215 (29%), Positives = 107/215 (49%), Gaps = 12/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++++D ++ V NKP+G+    G   A      L++   S        HRLD +TSG+L
Sbjct: 5   LDVVHQDEQLLVLNKPSGLLSVPGR--AEEHKDCLETRAQSIHPTATTIHRLDMDTSGLL 62

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A  + A +H+   F  R  +K Y + VWG  ++ +  +   L          +     
Sbjct: 63  VMAMNKDAHRHVGLQFEKRMTRKTYIARVWGHLRDDEGEVDLPLRCDWPNRPKQM----V 118

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    A++ ++VI+   +    +++ P TGR+HQLRVH L +G PIVGD  Y      
Sbjct: 119 DHELGRSALTKWEVINR-EEHTTLVKLMPVTGRSHQLRVHMLELGHPIVGDRFYAQGEAL 177

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
           +F+     +L+LHA+ ++L HP GG     TA  P
Sbjct: 178 SFSE----RLHLHAQTLELRHPIGGEYNTFTASCP 208


>gi|190405049|gb|EDV08316.1| tRNA pseudouridine synthase [Saccharomyces cerevisiae RM11-1a]
          Length = 462

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 108/255 (42%), Gaps = 23/255 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +        ++ + +G V ++ +    +  I++G ++              E
Sbjct: 129 VDVFISE-FRDRESEYYKRTIENGDVHINDETADLSTVIRNGDLITHQVHR-------HE 180

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  I V +KP+GI V       Y  +   K   ++ 
Sbjct: 181 PPVTSRPIK-----------VIFEDDNIMVIDKPSGIPVHPTG--RYRFNTITKMLQNNL 227

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A ++ +  + R + K Y + V G     +  +  
Sbjct: 228 GFVVNPCNRLDRLTSGLMFLAKTPRGADNIGDQLKAREVTKEYVAKVVGEFPETEVIVEK 287

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K          V + +EKGA +A + F  I     K   ++ +P TGR+HQ+RVH  
Sbjct: 288 PL-KLIEPRLALNAVCQMDEKGAKHAKTVFNRISYDG-KTSIVKCKPLTGRSHQIRVHLQ 345

Query: 261 HMGCPIVGDHKYCAN 275
           ++G PI  D  Y  +
Sbjct: 346 YLGHPIANDPIYSND 360


>gi|81428235|ref|YP_395235.1| pseudouridine synthase, 23S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78609877|emb|CAI54924.1| Pseudouridine synthase, 23S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 296

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/289 (21%), Positives = 116/289 (40%), Gaps = 29/289 (10%)

Query: 36  NLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
            +Q  LR + ++ V+ +   FN  ++ G  + +     ++     E     S        
Sbjct: 31  KMQHFLRINREILVNGQYRAFNRNVEPGDEITLNFSEVSVKVQNYELDATQS-------- 82

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQE 153
                 +L+E   + + NKPAGI            +   +  ++  +G+K  + HR+D+ 
Sbjct: 83  ----FSVLFESDDLLIVNKPAGIKTHPNRPGENGTLMNQVAFYLAQQGKKAYMVHRIDEA 138

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG L++ +T      L      +++ + Y ++V     + K  +A      S IG D  
Sbjct: 139 TSGTLLIGKTPIVIGILNRQLSQKKMARQYIAIV----DDPKHELAEHATINSPIGVDPE 194

Query: 214 HVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +  ++         AI+H++V+           +   TGRTHQ+RVH   +G PI+GD  
Sbjct: 195 NDRQRCVDYINGLSAITHYRVLSRKGATAVLA-VDLETGRTHQIRVHLASIGHPILGDPL 253

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           Y         +    +L LH + +    P       +TAP+P       
Sbjct: 254 YNP-------TDTTPRLLLHGQTLRYTEPYTDQPRTVTAPVPDAFEPYL 295


>gi|50122775|ref|YP_051942.1| ribosomal large subunit pseudouridine synthase A [Pectobacterium
           atrosepticum SCRI1043]
 gi|49613301|emb|CAG76752.1| ribosomal large subunit pseudouridine synthase A [Pectobacterium
           atrosepticum SCRI1043]
          Length = 217

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/215 (29%), Positives = 97/215 (45%), Gaps = 14/215 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G     H D  + + + +        
Sbjct: 1   MEPYNPPTDPWLHVLYQDQHIMVVNKPSGLLSVPGRAPE-HKDSVM-NRIQADYPTAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++ VA T+AA + L   FR R  +K Y + VWG     +  I   L+    
Sbjct: 59  HRLDMATSGVIAVALTKAAERELKRQFREREPKKSYLARVWGHMAQDEGVIDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V+         +++ P TGR+HQLRVH L +G P
Sbjct: 115 --CDWPNRPKQKVCFETGKSAQTEYQVLSRDDDGTTRVKLMPITGRSHQLRVHLLALGHP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           I+GD  Y              +L LHA+ + + HP
Sbjct: 173 ILGDGFYAHPDAKAMA----PRLLLHAQELAITHP 203


>gi|88800575|ref|ZP_01116137.1| hypothetical protein MED297_15425 [Reinekea sp. MED297]
 gi|88776720|gb|EAR07933.1| hypothetical protein MED297_15425 [Reinekea sp. MED297]
          Length = 249

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 60/245 (24%), Positives = 103/245 (42%), Gaps = 22/245 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHID---GFLKSWV--DSKGQKPRLTHRLDQETS 155
           ++YED  + V +KP+G+ +          D   G  K+++   S+G K    HRLD+ TS
Sbjct: 6   IVYEDDVLLVVDKPSGLLMHPSWLDRRETDTLAGRAKAYLAQQSEGAKVHTVHRLDRPTS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V+ +   AA+ L E F+ + + K YW++  G     +      + +   I   +   
Sbjct: 66  GLVVMCKDDHAAKALVEQFQEKTVNKRYWAICRGFAPVAETLDYPLIEEHDRIADKFA-- 123

Query: 216 VKQNEKGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              ++K A  AI+ F+          V      +  W+E  P TGR HQ+R H  H+  P
Sbjct: 124 --DSDKPAQEAITEFRRLGITELAIPVSRYPKMRLSWMECVPVTGRKHQIRRHLKHLRYP 181

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHAR--YMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           I+GD ++              +L++  R   M   HP     +              D L
Sbjct: 182 ILGDTRHGCRHLNRAVEGSFGELFMGLRAVEMSFQHPVTNELMTFNVGADNVWSCWLDRL 241

Query: 323 GFKYD 327
           G+ + 
Sbjct: 242 GWSFP 246


>gi|296452795|ref|ZP_06894482.1| ribosomal large subunit pseudouridine synthase [Clostridium
           difficile NAP08]
 gi|296879953|ref|ZP_06903925.1| ribosomal large subunit pseudouridine synthase [Clostridium
           difficile NAP07]
 gi|296258343|gb|EFH05251.1| ribosomal large subunit pseudouridine synthase [Clostridium
           difficile NAP08]
 gi|296429067|gb|EFH14942.1| ribosomal large subunit pseudouridine synthase [Clostridium
           difficile NAP07]
          Length = 226

 Score =  165 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 62/225 (27%), Positives = 109/225 (48%), Gaps = 14/225 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHR 149
           + +   ++YED+ + V  KP  I  QG +     +   LK ++  K  KP      L HR
Sbjct: 3   EKIMIKVIYEDNHLLVVEKPVNILSQGDNTNDKDMVNLLKDYIKKKYNKPGNVYIGLIHR 62

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+   G++V A+T  AA  L+E  R +  +K Y ++V G  K+  + + ++L K     
Sbjct: 63  LDRPVGGVMVFAKTSKAASRLSEQVRSKTFKKTYLAVVHGKIKSNSDILKDFLYKNKKTN 122

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
              V VVK+N K A  A  ++ V++ F +    +++   TGR+HQ+RV       P+ GD
Sbjct: 123 --MVTVVKKNHKDAKEAELNYNVLN-FKENLSLVQVNLKTGRSHQIRVQFASRKHPLYGD 179

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
            +Y         + I  ++ L +  +++ HP    +++ T   P 
Sbjct: 180 QRYGKEI-----NKIGQQISLWSNKIEIYHPTTKEKMEFTCHPPD 219


>gi|332534330|ref|ZP_08410173.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332036240|gb|EGI72713.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 217

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 59/211 (27%), Positives = 101/211 (47%), Gaps = 12/211 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  + + NKP+ +    G    +     L + V+      R+ HRLD  TSGIL +
Sbjct: 15  ILFQDDDLLIVNKPSELLTVPGKDPKH--ADSLINRVNRVFPTARIVHRLDMATSGILCL 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +AA +HL+  F+ R   K Y + ++G  + +   +   L+         +     + 
Sbjct: 73  AMNKAAHRHLSMQFQERETAKRYIARIYGQLEAETGSVDLPLICDWPNRPKQM----VDH 128

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                +++HFK+++   +    +E+ P TGR+HQLRVH L +G PI+GD  Y        
Sbjct: 129 DRGKPSLTHFKILER-EENVTRVELTPITGRSHQLRVHMLSLGHPILGDRLYAHKE---- 183

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
                 +L LHA+ + L HP+  + L   A 
Sbjct: 184 ALAAAPRLQLHAQMLQLKHPKTEQVLTFEAE 214


>gi|291166431|gb|EFE28477.1| ribosomal large subunit pseudouridine synthase family protein
           [Filifactor alocis ATCC 35896]
          Length = 223

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 66/217 (30%), Positives = 106/217 (48%), Gaps = 15/217 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQ 152
           K  +LYED+ + V  KP  I  Q  +     +   +K ++  K QKP      L HRLD+
Sbjct: 3   KIQVLYEDNHVIVVVKPYRIPSQEDNSNDTDMLTIVKEYIKEKYQKPGNVFVGLVHRLDR 62

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G++V A+T  AA  L+E  R  +I+K Y ++V G  K     + +++ K S    + 
Sbjct: 63  VTGGLMVFAKTSKAASRLSEQIRTNQIEKKYLAVVHGSLKTSSGQLEDFIKKSS--SKNI 120

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V V  +++K A   I ++ VI C    +  + +   TGR+HQ+RV     G  IVGD KY
Sbjct: 121 VSVCSKHDKNAKKCILNYHVISCLPD-YSLINVHLLTGRSHQIRVQFSSRGHSIVGDVKY 179

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQIT 308
            +  K      ++  + L A  +   HP    +++ T
Sbjct: 180 GSAEK------LRGHIALWAYKLSFFHPTKKEKMEFT 210


>gi|58584466|ref|YP_198039.1| pseudouridylate synthase, 23S RNA-specific [Wolbachia endosymbiont
           strain TRS of Brugia malayi]
 gi|58418782|gb|AAW70797.1| Pseudouridylate synthases, 23S RNA-specific [Wolbachia endosymbiont
           strain TRS of Brugia malayi]
          Length = 389

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 79/256 (30%), Positives = 133/256 (51%), Gaps = 14/256 (5%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++ + V+++  N+RLDR+ +  +P++    ++K LR G ++V+  + K ++R+ SGQ
Sbjct: 1   MGNIKTISVKDN--NVRLDRYIRRIFPNLKQSVIEKSLRRGLIKVNDCKAKSSDRVNSGQ 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++ I      L++I  E    D   N  K  + L+S +LYED  I   NKPAG+ VQGG 
Sbjct: 59  IITIKY----LDYI--ENANSDCKHN-EKLVELLRSNILYEDEYILAINKPAGVIVQGGI 111

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            +   I   L      +G+  ++ HRLD++TSG ++ AR    A++L E F+ RR++K Y
Sbjct: 112 KVKISISDLLDQVR--EGETFKIVHRLDRDTSGAIIFARNANVARYLMEEFKGRRVKKTY 169

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L  GIP   +  I   L+KK   G + V + K + +    A + F +I  F      +
Sbjct: 170 LALTSGIPSKNRGVIDYPLVKKYVSGQEKVVIDKNSPQD---ATTRFSIIAKFKLNKPLV 226

Query: 244 EMQPHTGRTHQLRVHA 259
           +         QL  H 
Sbjct: 227 QRPIIQVADTQLYEHC 242



 Score =  100 bits (248), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 43/122 (35%), Positives = 66/122 (54%), Gaps = 8/122 (6%)

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDC------FAQKFCWLEMQPHTGRTHQLRVHAL 260
           H+    +   K + K A+Y     K +D         +   +L++QP TGRTHQLR H  
Sbjct: 266 HLSAPILVSSKTDHKQAHYTTFSIKKLDSSIMCRNDTRSVAYLKLQPITGRTHQLRTHLA 325

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           ++ CPI+GD KY    K  F   I +K++LH+  + L  P   ++ ITAPLP H+ K+ +
Sbjct: 326 YINCPILGDGKYGG--KKAFVDGIASKIHLHSYSLSLKLPNNKKITITAPLPEHIKKSIE 383

Query: 321 SL 322
           +L
Sbjct: 384 AL 385


>gi|197286814|ref|YP_002152686.1| ribosomal large subunit pseudouridine synthase [Proteus mirabilis
           HI4320]
 gi|194684301|emb|CAR45870.1| putative ribosomal large subunit pseudouridine synthase [Proteus
           mirabilis HI4320]
          Length = 232

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 60/220 (27%), Positives = 95/220 (43%), Gaps = 17/220 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + V NKP+G+    G          +   +     +  L HRLD  TSG++V+A
Sbjct: 20  LYQDEHLLVINKPSGLLSLSGKNPQN--IDSVHYRLVPLFPECTLVHRLDFGTSGVMVIA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
             +A  + L + F  R + K Y +L+ G  +N    I   + K       +   +  +  
Sbjct: 78  LNKAINRALCQQFSQRTVTKAYDALLCGHLQNDSGVIEAPIAKDPQ----HFPRMSISTT 133

Query: 222 GANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               A S+++VI+ F Q            + + P TGRTHQLR+H  ++G PI+G   Y 
Sbjct: 134 QGKAARSYYQVIERFYQTLADGTRLPLTRVRLTPETGRTHQLRIHCQYIGHPILGCDLYG 193

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                        +L LHA  +   HP   + + I  P P
Sbjct: 194 GLLLSGTEHT--PRLMLHACELHFIHPVSEQPMDIYLPSP 231


>gi|320157974|ref|YP_004190352.1| pseudouridylate synthase 23S RNA-specific [Vibrio vulnificus
           MO6-24/O]
 gi|319933286|gb|ADV88149.1| pseudouridylate synthase 23S RNA-specific [Vibrio vulnificus
           MO6-24/O]
          Length = 565

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 103/228 (45%), Gaps = 19/228 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D +      ++  +  ++Y+D  + V NKP+G+    G  I       L++      + 
Sbjct: 347 IDPNPLEENWAEDKELEIVYQDEAMVVVNKPSGLLSVPGKTITDSAYTRLQALF-PDVEG 405

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I   + 
Sbjct: 406 PFVIHRLDMATSGLLVFALTRRANKSLQKQFISRGVQKRYVALLEGEVSQSQGEITLPM- 464

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V  ++      A + +++I+    +     + P TGRTHQLRVH  H  
Sbjct: 465 RGDPDDRPRQLVCFEH---GKPAHTDWQLIETRDGRSKLY-LYPRTGRTHQLRVHCAHHL 520

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
            +  P+VGD  Y             N+L+LHA  ++L HP    R+  
Sbjct: 521 GLNMPMVGDGLYGEK---------ANRLHLHAESLELDHPYSKERMHF 559


>gi|197120696|ref|YP_002132647.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196170545|gb|ACG71518.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 312

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 117/315 (37%), Gaps = 32/315 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR   +    +    +++    G+VRV  +R + ++    G +V +            
Sbjct: 14  RLDRALADAL-GLGRAAVKRAFALGEVRVRGRRARASDPAAPGALVELD----------- 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVD 138
               ++      +        +L E  +  V  KPAG++V     G    +   + +   
Sbjct: 62  ----VEVPAGPPEPQPDAPLSVLLERPRYLVVEKPAGVAVHPLAPGEGGTLANAVAARHP 117

Query: 139 SKGQ---KPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              +   +PR      RLD ETSG ++ AR   A + L        + K+Y +L  G   
Sbjct: 118 ECAEASPEPREGGAVQRLDLETSGCVLFARDPEAWEALHAQLGAHTVDKVYLALAVGRLP 177

Query: 193 NKKECIANWLLKKSH----IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
               C      +          +    ++        A +H++    FA     L ++  
Sbjct: 178 AGGVCSVPLAQRGGRVVPAPDLEAEERLQARGLRPRPAETHYEPERRFAD-HTLLRVRIV 236

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           TG  HQ+R H   +G P+ GD  Y     G    P   + +LHA  +    P+G GR+ +
Sbjct: 237 TGVMHQIRAHLALLGHPVAGDALYGGAAAG---LPGLERQFLHAWRLAFDDPDGAGRVAV 293

Query: 308 TAPLPAHMVKTWDSL 322
            +PLP  +      L
Sbjct: 294 ESPLPPELEAVLARL 308


>gi|89891166|ref|ZP_01202673.1| ribosomal large subunit pseudouridine synthase A [Flavobacteria
           bacterium BBFL7]
 gi|89516478|gb|EAS19138.1| ribosomal large subunit pseudouridine synthase A [Flavobacteria
           bacterium BBFL7]
          Length = 561

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 71/247 (28%), Positives = 107/247 (43%), Gaps = 20/247 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ D+ + +    D     ++YED  I + NKP       G  I   +
Sbjct: 330 CEPILGHMLEGIEVEDNPLLINPGIDK-TMEVIYEDDAIIIVNKPEEFLSVPGKTIKDSV 388

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              LK         P L HRLD  TSGILV  +       + E F  R I K Y +L+ G
Sbjct: 389 YSRLKELY-PDATGPILVHRLDMSTSGILVATKNLEYYHFIQEQFINRTISKRYVALLNG 447

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           + +N +  I   L     +  D         +    A + ++V++   +K   +   P T
Sbjct: 448 VLENNEGMIELPL----RVDLDNRPTQLVCYEYGKSARTKYQVLERR-EKETLVHFYPIT 502

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVHA H   +  PIVGD  Y             N+L+LHA ++   HP   + +
Sbjct: 503 GRTHQLRVHAAHASGLNAPIVGDDLYG---------TATNRLHLHAEFIKFIHPITHKTV 553

Query: 306 QITAPLP 312
              AP+P
Sbjct: 554 SFKAPVP 560


>gi|312889804|ref|ZP_07749350.1| ribosomal large subunit pseudouridine synthase D [Mucilaginibacter
           paludis DSM 18603]
 gi|311297730|gb|EFQ74853.1| ribosomal large subunit pseudouridine synthase D [Mucilaginibacter
           paludis DSM 18603]
          Length = 253

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 66/236 (27%), Positives = 108/236 (45%), Gaps = 15/236 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHR 149
           D     +LYED+ +   NK AG  VQ        +D  +K ++  K  KP      + HR
Sbjct: 24  DITDKDVLYEDNHLIAINKRAGDIVQVDDTGDESLDEKVKKYIAKKYNKPNGAFLGVVHR 83

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+  SG+++ A+T  A + +   F+ R I K Y ++V   P  +   + +WL+K     
Sbjct: 84  LDRPVSGVIMFAKTSKALERMNALFKGREIHKTYLAVVRNRPVPESGNLVHWLIKNPQ-- 141

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +          G+  +  ++++I      +  +E+ P TGR HQ+RV    +GCPIVGD
Sbjct: 142 KNVTKPYDHEVPGSLRSELNYRLIGEL-NGYYLIEVDPITGRPHQIRVQLSTLGCPIVGD 200

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH-MVKTWDSLG 323
           +KY           ++  + LHAR +   HP     + I A LP       ++ L 
Sbjct: 201 NKYGYPRGS-----LKKSICLHARRIQFIHPIKKEPVDIYAKLPKDGFWDKFEPLA 251


>gi|241955527|ref|XP_002420484.1| DRAP deaminase, putative; pseudouridine synthase, putative [Candida
           dubliniensis CD36]
 gi|223643826|emb|CAX41563.1| DRAP deaminase, putative [Candida dubliniensis CD36]
          Length = 589

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 103/260 (39%), Gaps = 32/260 (12%)

Query: 21  LDRWF---KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +D +    ++  P        K +  G V+V+ K       +++G ++            
Sbjct: 112 IDVFIDEFRDRTPDAYR----KAVEGGLVKVNSKVANLETILRNGDLISHRSYRREPPVS 167

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +E K                  +++ED  + V +KP+GI V       Y  +   K + 
Sbjct: 168 SREIK------------------IVFEDDDLLVIDKPSGIPVHPTG--RYRYNTITKVFE 207

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              G+     +RLD+ TSG++ + ++   A ++    R R + K Y + V G    ++  
Sbjct: 208 HEMGKIVHPCNRLDRLTSGLMFLGKSSKGANNMMSQIRDRNVTKEYIARVKGEFPLERLI 267

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLR 256
           +   L  KS      + +   + +    A + F+ +          ++  P TGRTHQ+R
Sbjct: 268 VDKPLSTKSP----KLTLNVVDTENGKEAKTEFQRVSYDPMTNTSVVKCHPLTGRTHQIR 323

Query: 257 VHALHMGCPIVGDHKYCANF 276
           VH   +G PI  D  Y + F
Sbjct: 324 VHLQFLGYPIANDPLYSSEF 343


>gi|227354995|ref|ZP_03839406.1| ribosomal large subunit pseudouridine synthase [Proteus mirabilis
           ATCC 29906]
 gi|227164782|gb|EEI49629.1| ribosomal large subunit pseudouridine synthase [Proteus mirabilis
           ATCC 29906]
          Length = 232

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 60/220 (27%), Positives = 95/220 (43%), Gaps = 17/220 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + V NKP+G+    G          +   +     +  L HRLD  TSG++V+A
Sbjct: 20  LYQDEHLLVINKPSGLLSLSGKNPQN--IDSVHYRLVPLFPECTLVHRLDFGTSGVMVIA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
             +A  + L + F  R + K Y +L+ G  +N    I   + K       +   +  +  
Sbjct: 78  LNKAINRALCQQFSQRTVTKAYDALLCGHLQNDSGVIEAPIAKDPQ----HFPRMSISTT 133

Query: 222 GANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               A S+++VI+ F Q            + + P TGRTHQLR+H  ++G PI+G   Y 
Sbjct: 134 QGKAARSYYQVIERFYQTLADGTRLPLTRVRLTPETGRTHQLRIHCQYIGHPILGCDLYG 193

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                        +L LHA  +   HP   + + I  P P
Sbjct: 194 GLLLSGTEHT--PRLMLHACELHFIHPVSEQPMDIYPPSP 231


>gi|85712033|ref|ZP_01043087.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
 gi|85694219|gb|EAQ32163.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
          Length = 239

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 112/240 (46%), Gaps = 18/240 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           S+     ++Y+D  + V +KP+G+ V      +      ++   D  GQ+    HRLD+ 
Sbjct: 2   SEPDLLQVVYKDEYLVVIDKPSGLLVHRSWLASDAKRFAMQMLRDQLGQRVYPVHRLDRP 61

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+L+ A +   A+ L E F  R I+K+Y ++V G   +    I ++ LK+ H      
Sbjct: 62  TSGLLIFALSSEIARALNEQFAERDIKKVYHAVVRGYVDDAG--IIDYALKEEH--DKIA 117

Query: 214 HVVKQNEKGANYAISHFKVI-----------DCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
               Q +K A  A++ ++ +                ++  +++ P TGR HQLR H  H+
Sbjct: 118 DKQAQADKPAQEAVTEYQCVARVELPFKVSKKHDTSRYSLVKLMPLTGRKHQLRRHMSHI 177

Query: 263 GCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
             PI+GD ++       F     +  +L L +  ++  HP+ G+ L +   +P  + + +
Sbjct: 178 RHPIIGDTRHGEGRHNRFFREHFDCHRLLLASTAIEFQHPKTGKLLSVEIEVPEILSRPF 237


>gi|209809356|ref|YP_002264894.1| putative RNA pseudouridylate synthase [Aliivibrio salmonicida
           LFI1238]
 gi|208010918|emb|CAQ81323.1| putative RNA pseudouridylate synthase [Aliivibrio salmonicida
           LFI1238]
          Length = 561

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 68/243 (27%), Positives = 105/243 (43%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ D+S+  T         ++YED  I + NKPA      G  I   +
Sbjct: 330 CFEILEHMLEGIELDDNSLKQTPSYGK-DLEIVYEDEAIVIVNKPAEFLSVPGKFITDSV 388

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K+        P + HRLD  TSG+LV+  T    + + + F  R ++K Y +L+ G
Sbjct: 389 QTRIKARYPQ-ATGPLIVHRLDMSTSGLLVLTLTAETNKQVQKQFIDRTVEKRYTALLEG 447

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   I   L          +     + K    A + F+VI+        + + P T
Sbjct: 448 NIALNDGIIDLPLTGDLEDRPRQM----VDHKQGRKAETTFQVIERN-NNQTKVYLYPKT 502

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RL 305
           GRTHQLRVH  H   +G PIVGD  Y             N+L+LHA Y+   HP  G  +
Sbjct: 503 GRTHQLRVHCAHQAGLGTPIVGDDLYGFK---------SNRLHLHAGYLKFTHPITGNEV 553

Query: 306 QIT 308
           + +
Sbjct: 554 EFS 556


>gi|154252639|ref|YP_001413463.1| pseudouridine synthase [Parvibaculum lavamentivorans DS-1]
 gi|154156589|gb|ABS63806.1| pseudouridine synthase [Parvibaculum lavamentivorans DS-1]
          Length = 226

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/215 (28%), Positives = 103/215 (47%), Gaps = 12/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            ++L++D +I V  K +G+    G  + +     L+S   +     R+ HRLD++TSG++
Sbjct: 22  LVVLHKDDEILVLAKQSGLLCVAGRPVEHS--DCLESRARATFPNARIVHRLDRDTSGVI 79

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A T AA +HL   F  R+I+K Y + VWG    +   +   L          +     
Sbjct: 80  IMAMTPAAHRHLGLQFERRKIRKTYLARVWGQLAQEYGRVDLPLACHWPNRPKQM----V 135

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      A + ++V++   +    + + P TGR+HQLRVH L +G PI+GD  Y      
Sbjct: 136 DVDAGRPAQTDWEVVER-EKNATRVRLSPLTGRSHQLRVHMLSLGHPILGDSFYATGEAF 194

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
                  ++L LHA  +   HP  GR+ +   P P
Sbjct: 195 AAA----DRLQLHAETLTFHHPADGRICRFAVPCP 225


>gi|242240403|ref|YP_002988584.1| tRNA pseudouridine synthase C [Dickeya dadantii Ech703]
 gi|242132460|gb|ACS86762.1| pseudouridine synthase [Dickeya dadantii Ech703]
          Length = 261

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 98/238 (41%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  G+     HRLD+ TSG+L++
Sbjct: 4   ILYQDDYLVAVNKPAGWLVHRSWLDRKEKVVVMQTVRDQIGRHVFTVHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L   F   +++K Y ++V G   ++         +   I   Y        
Sbjct: 64  ALSPEVARMLALQFEQHQMEKTYHAVVRGYVADEGVIDYALTEELDRIADKYA----DPN 119

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A+S ++ +               ++  LE+ P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVSAYRALARAEMPVAIGRYETSRYSLLELHPKTGRKHQLRRHMAHIRHPIIGDT 179

Query: 271 KYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
            +      +G  T    ++L LHA  + L HP     L I A             G++
Sbjct: 180 THGDLRQNRGMATHFSCSRLMLHASRLRLNHPITHVPLDIYARWDQSWQGVMSQFGWQ 237


>gi|115522347|ref|YP_779258.1| pseudouridine synthase [Rhodopseudomonas palustris BisA53]
 gi|115516294|gb|ABJ04278.1| pseudouridine synthase [Rhodopseudomonas palustris BisA53]
          Length = 278

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 75/285 (26%), Positives = 124/285 (43%), Gaps = 50/285 (17%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E  +  ++  LT   D + + +L+ D  + V +KPAG+ V  G     +++    +    
Sbjct: 3   ESDLEPTAKELT--PDEILARVLHRDGLMLVIDKPAGLPVHRGPKGGANLESSFDALCYG 60

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             + P L HRLD++TSG LV+ R R A   L   F+  +I K YW++V G P+  +  I 
Sbjct: 61  LPRPPVLAHRLDRDTSGCLVLGRHRKATATLGLLFKHGKISKTYWAVVEGGPEQDQGTID 120

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-------------------------- 233
             + + +   G +  +    +     +++++ V+                          
Sbjct: 121 LPIGRLNAERGWWQKI----DPEGLPSVTNWTVLGRSFSPPPCGEGSGVGVPNGSLALGP 176

Query: 234 ------------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
                        C + +  WL ++P TGRTHQLRVH   MG PI GD+ Y      N  
Sbjct: 177 PHPSPPHKGEGAGCASGQLTWLALEPLTGRTHQLRVHCAAMGWPIFGDNIYG-----NGP 231

Query: 282 SPIQNKLYLHARYMDLPHPEGGRLQI-TAPLPAHMVKTWDSLGFK 325
              + KL+LHAR + +P        + TAP PAH+ +     G+ 
Sbjct: 232 RFGEPKLHLHAREIVIPISRNKPPVVATAPAPAHLHERLRMCGWD 276


>gi|296282152|ref|ZP_06860150.1| pseudouridine synthase [Citromicrobium bathyomarinum JL354]
          Length = 225

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 64/225 (28%), Positives = 108/225 (48%), Gaps = 16/225 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED +  V +KPAG+S+         +D +L+       + P   HRLD +TSG L++
Sbjct: 8   ILYEDGEALVIDKPAGLSIDRPRKGGPCLDDYLEQLKLGFQRPPSAVHRLDTDTSGCLLL 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR   A +  + +F  +++ K+Y  ++ GIP  ++  +   L K S     +  +     
Sbjct: 68  ARNPKAHKRFSAAFEAQQVTKVYHGILAGIPAQEEGVVELALSKISSAEKGWRMI---PA 124

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGN 279
           K    +++ ++V+    +    +E +P TGRTHQ+RVHA   +G  +VGD  Y       
Sbjct: 125 KKGKPSVTAWRVVATH-EGRALVEFRPATGRTHQIRVHAASGIGIALVGDPVYG------ 177

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
            T     +  LHA  + +       +  T+PLPA       +LGF
Sbjct: 178 -TKQGAPRTMLHASALTVERESKTDIAATSPLPADFQ----ALGF 217


>gi|255657533|ref|ZP_05402942.1| putative pseudouridylate synthase [Clostridium difficile QCD-23m63]
          Length = 221

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 62/219 (28%), Positives = 107/219 (48%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  KP  I  QG +     +   LK ++  K  KP      L HRLD+   
Sbjct: 4   VIYEDNHLLVVEKPVNILSQGDNTNDKDMVNLLKDYIKKKYNKPGNVYIGLIHRLDRPVG 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  L+E  R +  +K Y ++V G  K+  + + ++L K        V V
Sbjct: 64  GVMVFAKTSKAASRLSEQVRSKTFKKTYLAVVHGKIKSNSDILKDFLYKNKKTN--MVTV 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           VK+N K A  A  ++ V++ F +    +++   TGR+HQ+RV       P+ GD +Y   
Sbjct: 122 VKKNHKDAKEAELNYNVLN-FKENLSLVQVNLKTGRSHQIRVQFASRKHPLYGDQRYGKE 180

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
                 + I  ++ L +  +++ HP    +++ T   P 
Sbjct: 181 I-----NKIGQQISLWSNKIEIYHPTTKEKMEFTCHPPD 214


>gi|197336758|ref|YP_002158083.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
 gi|197314010|gb|ACH63459.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
          Length = 568

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 68/249 (27%), Positives = 106/249 (42%), Gaps = 20/249 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++     DS +  T  S   +  ++YED  + V NKPA      G  I+  +
Sbjct: 337 CFEILEHMLEGISTNDSPLEQTP-SYGKELEIVYEDDVLVVVNKPAEFLSVSGKYISDSV 395

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +++        P + HRLD  TSG+LV+  T  + + + + F  R ++K Y +L+ G
Sbjct: 396 HARIQARY-PNATGPLIVHRLDMSTSGLLVLTLTAESNKQVQKQFIERTVEKRYTALLEG 454

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +     I   L          +       K    A +H++VI    ++   + + PHT
Sbjct: 455 NIETDNGTINLPLTGDMEDRPRQMVC----HKSGRKAETHYQVIAQEGKR-TKVHLYPHT 509

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           GRTHQLRVH  H   +  PIVGD  Y             N+L+LHA Y+   HP      
Sbjct: 510 GRTHQLRVHCAHQAGLNTPIVGDDLYGFK---------ANRLHLHAGYLKFKHPITDE-T 559

Query: 307 ITAPLPAHM 315
           +    P   
Sbjct: 560 VEFSCPEDF 568


>gi|86156693|ref|YP_463478.1| pseudouridine synthase RluD [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85773204|gb|ABC80041.1| Pseudouridine synthase, RluD [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 312

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/315 (20%), Positives = 112/315 (35%), Gaps = 32/315 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR   +    +    +++    G+VRV  +R + ++    G +V +            
Sbjct: 14  RLDRALADAL-GLGRAAVKRAFALGEVRVRGRRARASDPAAPGALVELD----------- 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG--GSGIAYHIDGFLKSWV 137
               ++      +        +L E  +  V +KPAG++V            +       
Sbjct: 62  ----VELPAGPPEPEPDAPLAVLLERPRYLVVDKPAGVAVHPLAPGEGGTLANAVAARHP 117

Query: 138 DSKGQKPRL-----THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +  G  P         RLD ETSG ++ AR   A + L        + K+Y +L  G   
Sbjct: 118 ECAGASPEPREGGAVQRLDLETSGCVLFARDPEAWEALHAQLGAHTVDKVYLALAVGRVP 177

Query: 193 NKKECIANWLLKKSH----IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
               C      +          +    ++        A +H++  +        L ++  
Sbjct: 178 AGGVCSVPLAQRGGRVLPAPDAEAEERLRARGLRPRPAETHYEP-ERRFAGHTLLRVRIV 236

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQI 307
           TG  HQ+R H   +G P+ GD  Y              + +LHA  +    P+ GGR+ +
Sbjct: 237 TGVMHQIRAHLALLGHPVAGDALYGG---AAAELAGLERQFLHAWRLAFDDPDGGGRVAV 293

Query: 308 TAPLPAHMVKTWDSL 322
            +PLPA +      L
Sbjct: 294 ESPLPAELEAVLARL 308


>gi|323495785|ref|ZP_08100855.1| pseudouridylate synthase, 23S RNA-specific [Vibrio sinaloensis DSM
           21326]
 gi|323319252|gb|EGA72193.1| pseudouridylate synthase, 23S RNA-specific [Vibrio sinaloensis DSM
           21326]
          Length = 559

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 111/242 (45%), Gaps = 20/242 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++   ++ D+ +     ++  +  +LY D  + V NKP+G+    G  I+   
Sbjct: 328 CQPILGHMLSGMEVDDNPLE-ENWAEDKELQILYSDDAMVVVNKPSGLLSVPGKTISDSA 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++      + P + HRLD  TSG+LV A TR A + L + F  R ++K Y +L+ G
Sbjct: 387 YTRLQALY-PDVEGPFVIHRLDMATSGLLVFALTRRANKSLQKQFISRSVKKRYVALLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               +   I   + +          V    E+    A +H+++I+   ++     M P T
Sbjct: 446 EVSAQSGDIDLPM-RGDPEDRPRQLVC---EQHGKPAKTHWQLIETIDKRSKLY-MYPLT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH  H   +  P+VGD  Y             ++L+LHA  +++ HP    R+
Sbjct: 501 GRTHQLRVHCAHHLGLNMPMVGDVLYGNK---------ADRLHLHAERLEIDHPYSKERM 551

Query: 306 QI 307
             
Sbjct: 552 TF 553


>gi|229918468|ref|YP_002887114.1| pseudouridine synthase, RluA family [Exiguobacterium sp. AT1b]
 gi|229469897|gb|ACQ71669.1| pseudouridine synthase, RluA family [Exiguobacterium sp. AT1b]
          Length = 287

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/300 (21%), Positives = 112/300 (37%), Gaps = 40/300 (13%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +       I+   L  +   G + V+       + ++ G  V +              + 
Sbjct: 19  FLMQDM-GISRKMLTLVKHEGDIEVNGMHRTVRHELEPGDEVSV--------------RF 63

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
              S +L   +      +LYED  +   +KPAGI+         H    L + V    Q+
Sbjct: 64  PPESPSLDMVASERPIRILYEDDTLLAVDKPAGIATIPSR---LHPTDTLANAVLGYYQR 120

Query: 144 P------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                   + +RLD++TSG+++ A+        +E  +   + + Y +LV      +   
Sbjct: 121 IGLSSAIHVINRLDRDTSGVVLFAKYGFIHHRFSELQKANGLMRTYKALVEEEVTPQ--T 178

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +  +   + V   +        AI+H      F      L ++  TGRTHQ+RV
Sbjct: 179 IDAPIGRAENSIMERVVTTE-----GQRAITHILACQPFGSG-SLLTIRLETGRTHQIRV 232

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
           H  H+G  ++GD  Y    +         +  LH+      HP  G  +QI AP+P    
Sbjct: 233 HLRHIGHSLIGDSMYGGTAR-------MPRHALHSASARFIHPMTGDTIQIEAPIPEDFR 285


>gi|262276531|ref|ZP_06054340.1| tRNA pseudouridine synthase C [Grimontia hollisae CIP 101886]
 gi|262220339|gb|EEY71655.1| tRNA pseudouridine synthase C [Grimontia hollisae CIP 101886]
          Length = 243

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 100/240 (41%), Gaps = 17/240 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +LY D  +   NKP+G+ V             +++  D  GQ     HRLD+ TSG+
Sbjct: 4   ELEILYRDEWLVAVNKPSGMLVHRSWLDKGETRFVMQTLRDQIGQHVFPLHRLDRPTSGV 63

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A +   A  +   F  R I K Y ++V G  + +         +   +   Y     
Sbjct: 64  LLFALSSEMAAEMMPKFAGRDIHKTYHAVVRGWIQEEATLDYPLKEELDKVADKYATA-- 121

Query: 218 QNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             E  A  A++ ++ +             + ++  +EM+PHTGR HQLR H  H+  PI+
Sbjct: 122 --EPEAKEAVTEYRPVAHAELPIPLGRYQSCRYTLVEMKPHTGRKHQLRRHMHHLSHPII 179

Query: 268 GDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           GD  +           + N  +L LHA      HP  G  + I A +     +  + LG+
Sbjct: 180 GDVNHGDGRHNRLFREVFNCHQLLLHASRTAFQHPVTGENIVIDANVDDVWRRVLEGLGW 239


>gi|224533917|ref|ZP_03674502.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi CA-11.2a]
 gi|224512920|gb|EEF83286.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi CA-11.2a]
          Length = 251

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/252 (25%), Positives = 117/252 (46%), Gaps = 19/252 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQK 143
               +   ++YEDS + V NKP GI    G         + + YHI   LK   + +  +
Sbjct: 3   RPSNIPIAIIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKS-LKINFNEEKIR 61

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD++TSG+L+ A+  +  + L + F+ +R  K+Y ++V G   +    I +++ 
Sbjct: 62  PGIVHRLDKDTSGVLICAKNISTLRFLAQQFKDKRTNKVYIAIVKGNFNSFFGSIESFID 121

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +  H    +     +       A++ ++++  F + +  L ++P TGRTHQLRVH  ++ 
Sbjct: 122 RDKHNRKKFSVSKDR----GKKALTEYRLLLNFGE-YSLLALKPKTGRTHQLRVHMKYLN 176

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
            PI+GD  Y     G+        L LH+  +++   +    +  +  P   +    +  
Sbjct: 177 FPILGDEVYG-RVDGSLKKIT---LMLHSYKLEIDVGKNSFKKFISEFPKRFIIFLSNFY 232

Query: 324 FKYDRNLYIKRL 335
              + NL I  L
Sbjct: 233 KSDELNLIIDNL 244


>gi|294649803|ref|ZP_06727205.1| ribosomal large subunit pseudouridine synthase A [Acinetobacter
           haemolyticus ATCC 19194]
 gi|292824286|gb|EFF83087.1| ribosomal large subunit pseudouridine synthase A [Acinetobacter
           haemolyticus ATCC 19194]
          Length = 228

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 64/223 (28%), Positives = 102/223 (45%), Gaps = 15/223 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L++ D    V +KPAG+    G      +   L + +     K  L HRLD++
Sbjct: 16  SDFLSEHLIHRDEDFMVIHKPAGLLTVPGKTPD--LQDCLINRLLKLEPKTLLIHRLDRD 73

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     ++  F+ R+  KIY +LV G  + +       +   S      V
Sbjct: 74  TSGILVFGLSKFGQSTISRQFQDRQTSKIYQALVAGHLEGQGTVDIPVIYDPSRPPLHIV 133

Query: 214 HVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                       A++ ++ I+      Q    +++ P TGR+HQLRVH  ++G PI+GD 
Sbjct: 134 DATHH-----KPALTEWQAIEHLEIQGQAVTRVKLIPITGRSHQLRVHMQYLGHPILGDT 188

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            Y    +      +  +L LHA  +   HP+ G +L    P+P
Sbjct: 189 LYATPEQQQ----LYERLCLHATQLSFAHPKTGTQLDFDCPVP 227


>gi|254993270|ref|ZP_05275460.1| ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes FSL J2-064]
          Length = 243

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 119/262 (45%), Gaps = 33/262 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE +E+ + L  + K+   HI+   L   K    G++ V+ K       ++ G  VR+  
Sbjct: 7   VETEEDGLLLRTFLKS--KHISKQLLTAVKFGAEGKIEVNNKEQNVLYHVKVGDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTDLDIIFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           +G + ++V    +         +  RLD+ETSG++++A+ R A   L+   +   +++ Y
Sbjct: 108 NGSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRY 167

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +   G+   +K  I   + +K     +   + +       YA ++++V+  + + F  +
Sbjct: 168 QAFTSGVLVEQKGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLARY-RAFDHV 221

Query: 244 EMQPHTGRTHQLRVHALHMGCP 265
            +Q  TGRTHQ+RVH  ++G P
Sbjct: 222 AIQLETGRTHQIRVHFSYIGHP 243


>gi|156846788|ref|XP_001646280.1| hypothetical protein Kpol_1032p14 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156116955|gb|EDO18422.1| hypothetical protein Kpol_1032p14 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 612

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 99/253 (39%), Gaps = 23/253 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        +K +  G V ++ K     + I++G ++              E
Sbjct: 131 LDVFVTE-FRDREESYYKKTIAGGLVFLNDKPANLESIIRNGDLITHNVHR-------HE 182

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +             ++ED  I V +KP+GI V       +  +   K      
Sbjct: 183 PPVTSRPIKT-----------VFEDDNILVIDKPSGIPVHPTG--RFRFNTITKILEKKL 229

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A  + +  + R + K Y + V G     +  +  
Sbjct: 230 GYSVHPCNRLDKLTSGLMFLAKTPKGADEMADQLKAREVTKEYVARVVGEFPVGEVTVEK 289

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +K          V    ++ A +A + F  +     K   ++ +P TGRTHQ+RVH  
Sbjct: 290 P-VKTVDPRVSLNSVCSLEDENAKHAKTIFNRVSYDG-KTSIVKCKPLTGRTHQIRVHLQ 347

Query: 261 HMGCPIVGDHKYC 273
           ++G PI  D  Y 
Sbjct: 348 YIGFPIANDPIYS 360


>gi|90578254|ref|ZP_01234065.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio angustum S14]
 gi|90441340|gb|EAS66520.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio angustum S14]
          Length = 557

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 60/243 (24%), Positives = 110/243 (45%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++   ++ ++ +     ++  +  ++Y+D  + + NKPA      G  I   +
Sbjct: 326 CEPILAHMLSGIEVDENPLE-QNPAEGKELSIVYQDDAMVIVNKPAEFLSVPGKTITDSV 384

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +++   +    P + HRLD  TSG++V+A T+ A + L + F  R ++K Y +L+ G
Sbjct: 385 YSRMQAMFPNSD-SPLIVHRLDMSTSGLMVIALTKDAHKALQKQFIERTVEKRYVALLEG 443

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             ++    I ++ ++          V  Q       A + ++V++        +   P T
Sbjct: 444 NSESDSGLI-DFPMRVDLDDRPRQIVCYQ---YGKPAQTTWEVLERK-NGRTKVYYYPKT 498

Query: 250 GRTHQLRVHALHM---GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVH+ H+     PIVGD  Y             ++L LHA+Y+   HP    R+
Sbjct: 499 GRTHQLRVHSAHIKGMNMPIVGDDLYGQKG---------DRLCLHAQYLAFNHPTTNERM 549

Query: 306 QIT 308
              
Sbjct: 550 VFE 552


>gi|124003349|ref|ZP_01688199.1| ribosomal large subunit pseudouridine synthase C [Microscilla
           marina ATCC 23134]
 gi|123991447|gb|EAY30878.1| ribosomal large subunit pseudouridine synthase C [Microscilla
           marina ATCC 23134]
          Length = 250

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 72/228 (31%), Positives = 111/228 (48%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-----HRLDQETS 155
           +LYED+ + + NK  G+ VQG       +  ++K ++  K  KP        HR+D+  S
Sbjct: 15  VLYEDNHLIIVNKKGGMLVQGDKTGDKTLGDWVKEYIKEKYDKPGAVFLGIPHRIDRPVS 74

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+++ART  A + + + F+ R+IQK YW++V   P  ++  + +WL K      + V  
Sbjct: 75  GIVILARTSKALERMNQLFKTRKIQKTYWAIVKRKPAEEEGKLVHWLKKDG--AKNVVTA 132

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +   GA  A + +KV+         LE+ P TGR HQ+RV    MGCPI GD KY   
Sbjct: 133 HDEPVDGAQKAETRYKVLGNLND-HWLLEVNPITGRPHQIRVQLASMGCPIRGDIKYGFP 191

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            K          ++LHAR +   HP     L   A +P    + W+  
Sbjct: 192 RKDP-----DKNIHLHARRVYFMHPVKKEPLVCIAGVPE--TQFWEQF 232


>gi|221133960|ref|ZP_03560265.1| pseudouridylate synthase for 23S rRNA (position 746) and
           tRNAphe(position 32), dual specificity [Glaciecola sp.
           HTCC2999]
          Length = 227

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 66/211 (31%), Positives = 100/211 (47%), Gaps = 11/211 (5%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        +L++D  I V  KP G+    G   A +    L+  V       R+ HRLD
Sbjct: 7   QPPTDPFLDILHQDEDIIVLAKPPGLLSVRGR--AANHQDSLQKRVTDVYPNARIVHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V+A  ++A QHL+  F  R+ QK Y++ V G     +  I   L+        
Sbjct: 65  MATSGIIVMAMHKSANQHLSAQFAERKTQKRYFARVLGQMSVSEGEITAPLIVD-WPNRP 123

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              V     +    +++HFKV++   +K   +E+ P TGR+HQLRVH L +G PI+GD  
Sbjct: 124 KQKVCY---ETGKKSLTHFKVVE-VGEKTTLVELHPVTGRSHQLRVHLLSIGHPILGDRL 179

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           Y       +T     +L+LHA  +   HP  
Sbjct: 180 Y----TEAYTREGVTRLWLHAAELGFYHPTT 206


>gi|120600133|ref|YP_964707.1| pseudouridylate synthase [Shewanella sp. W3-18-1]
 gi|120560226|gb|ABM26153.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           W3-18-1]
          Length = 226

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/215 (29%), Positives = 107/215 (49%), Gaps = 16/215 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G   A++    + + V ++    ++ HRLD  TSG++V+
Sbjct: 17  ILYQDKDIIVINKPSGLLSVPGRDPAHYDS--VYARVKAEHPHCQIVHRLDMATSGVIVL 74

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R+A + L   F  R   K Y + V G  K+    I   L+       D+ +  KQ  
Sbjct: 75  ALIRSAERELKRQFHDRETSKTYIARVAGHIKHDTGSIDYPLI------CDWPNRPKQKV 128

Query: 221 KG--ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  +++H++V+   A++   +++ P TGR+HQLRVH + +G PI+GD  Y      
Sbjct: 129 DHFVGKPSLTHYQVMSR-AKRSTLVKLTPITGRSHQLRVHMMAIGHPILGDGFYADPLAK 187

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           +    +  +L LHA  + + HP  G  +  +   P
Sbjct: 188 S----LAPRLLLHAAELTIKHPYTGVSMTFSTEAP 218


>gi|330945855|gb|EGH47236.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 216

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 62/221 (28%), Positives = 104/221 (47%), Gaps = 19/221 (8%)

Query: 122 GSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G      ++  L    D     +  + HRLD++T+G++VVA+T  A   L    + R + 
Sbjct: 4   GHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVS 63

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           +IY  +V G+       I   + +        + V+    +G   A+SH++V++ F +  
Sbjct: 64  RIYECIVIGVV-TAGGKIDAPIGRHGQQ-RQRMAVM----EGGKQAVSHYRVLERF-RSH 116

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHA 292
             + ++  TGRTHQ+RVH  H+  P+VGD  Y   F+    + +          +  LHA
Sbjct: 117 THVRVKLETGRTHQIRVHMAHINYPLVGDPAYGGRFRIPPAASLTMVDSLKTFPRQALHA 176

Query: 293 RYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYI 332
           R+++L HP  G R+   +PLP   V     L  K DR  +I
Sbjct: 177 RFLELDHPTTGKRMSWESPLPDDFVWLLSLL--KQDREAFI 215


>gi|239832937|ref|ZP_04681266.1| pseudouridine synthase [Ochrobactrum intermedium LMG 3301]
 gi|239825204|gb|EEQ96772.1| pseudouridine synthase [Ochrobactrum intermedium LMG 3301]
          Length = 222

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 103/230 (44%), Gaps = 11/230 (4%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +L +   +          +L+ D+   V +KP+G+    G   A      L + V     
Sbjct: 3   VLSAVAPIYHPPLEPYVSILHRDAGFLVLDKPSGLLSVPGRHPALSDS--LATRVQETFP 60

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           + ++ +RLD++TSGI++++  R     +   F  R  QK Y ++VWG  +  +  I   L
Sbjct: 61  QAQMINRLDKDTSGIVLMSLDRKTHAAIAAQFEARTTQKSYIAVVWGNVEEDEGLIDLPL 120

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                 G    H V  + +    A + ++V+D  +++   L + P TGRTHQLRVH   +
Sbjct: 121 AIDP--GNKPRHRV--DHEHGKPAQTRWQVLDR-SERTTRLRLFPLTGRTHQLRVHMKAI 175

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           G  I+GD  Y           +     LHA  +   HP+G  +  TAP P
Sbjct: 176 GHVILGDEFYAEGEALAAADRLL----LHAEELSFRHPDGRAVTFTAPCP 221


>gi|281421451|ref|ZP_06252450.1| ribosomal large subunit pseudouridine synthase A [Prevotella copri
           DSM 18205]
 gi|281404523|gb|EFB35203.1| ribosomal large subunit pseudouridine synthase A [Prevotella copri
           DSM 18205]
          Length = 556

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 101/233 (43%), Gaps = 27/233 (11%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           T+ + + K   LYED ++ V  KP G+    G   A      L      +   P + HRL
Sbjct: 331 TETTIYNKVETLYEDRELAVIYKPEGLLSVPGKDAAQPSVYALMRRKYQEATGPLIVHRL 390

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-----------KECIA 199
           D  TSG++++A+T  A   L + F   R+QK Y ++V G  K             +  I+
Sbjct: 391 DMATSGLMIIAKTEFAYHRLQKEFLNHRVQKKYVAIVCGKDKESCNRILKEAEGGRGYIS 450

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L+         +     N +    AI+ ++V++        L + P TGRTHQLRVH 
Sbjct: 451 LPLIADFLDRPRQM----VNREQGKEAITEYEVLERIDDTHLRLALYPKTGRTHQLRVHC 506

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
            H   +  PI+GD  Y              +L+LHA  +   HP  G ++ +T
Sbjct: 507 AHQEGLNAPIIGDPLYGNEPA--------TRLHLHAEEITFEHPMTGKKMTVT 551


>gi|325268497|ref|ZP_08135127.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           multiformis DSM 16608]
 gi|324989025|gb|EGC20978.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           multiformis DSM 16608]
          Length = 568

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 72/240 (30%), Positives = 103/240 (42%), Gaps = 26/240 (10%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           +  + T+ +      +LYED  + V  KP G+    G G    +   LK      G  P 
Sbjct: 341 APDDKTEAAGAAGLEILYEDDSLAVVAKPPGLLSVPGKGRQPSVYSLLKERWQRSG-APY 399

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK----KECIANW 201
           + HRLD  TSG+LVVART  A + L   F  R +QK Y +L+ G    +    +  I   
Sbjct: 400 MVHRLDMATSGLLVVARTAEAHKALQAQFAARTVQKRYVALLPGSFPEQRFPAEGRIELP 459

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-----AQKFCWLEMQPHTGRTHQLR 256
           L   S    D        EKG   AI+ ++V          ++   + + P TGRTHQLR
Sbjct: 460 L---SPCPDDRPRQRVDLEKG-KPAITEYRVAGRTKYGKEGREAVKIILHPLTGRTHQLR 515

Query: 257 VHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           +H  H   +G PI+GD  Y              +L+LHA ++   HP   +  I    P 
Sbjct: 516 MHCAHPDGLGTPIIGDSLYGQR---------AGRLWLHAEHLAFTHPVTQQRMIFDRPPE 566


>gi|78045806|ref|YP_361981.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
 gi|78034236|emb|CAJ21881.1| Pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
          Length = 238

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 104/237 (43%), Gaps = 24/237 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V +KPAG+ V          D       +  G+   L HRLD+ TSG L++
Sbjct: 10  ILYQDDVLAVVDKPAGLMVHDSKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLLL 69

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R +A  L ++     ++K Y ++  G P  ++  + + L       G     VK   
Sbjct: 70  AFDRDSASALGKALMAGEVEKDYLTVCRGWPAEERFIVDHDL------DGGPGKPVK--- 120

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD 
Sbjct: 121 ---KPAVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGDT 177

Query: 271 KYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
            +       +F     +++ LHA  +  PHP GG R+ ITAPL A   K     G+ 
Sbjct: 178 SHGDGRHNRSFRMLGIHRMLLHAERLGFPHPGGGRRISITAPLDAEFTKACALFGWD 234


>gi|258539958|ref|YP_003174457.1| ribosomal large subunit 23S pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
 gi|257151634|emb|CAR90606.1| Ribosomal large subunit 23S pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
          Length = 278

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 65/293 (22%), Positives = 117/293 (39%), Gaps = 37/293 (12%)

Query: 25  FKNHYPH--INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
            ++      I      ++  +  ++V+     FN  +++G ++ +               
Sbjct: 15  LRDQLQDWLIPRKRQHQMRVAQTIQVNGHYRHFNEPVKNGDLISLTY------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKG 141
             D  V+ T   +       YED  + + +KPAG+       G    +     +++    
Sbjct: 62  --DELVHRTYVPETPHLNTRYEDDDLLIVDKPAGMKTHPNQPGETGTLMNQAAAYLAP-- 117

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIAN 200
               +THRLD  TSG+LV+A+   A   +      + + + Y ++V  GIP  +K  I  
Sbjct: 118 FPALITHRLDMATSGLLVIAKNPLAQAIINRQLTTKTMHRDYLAVVPSGIP--EKGTIQA 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +          +           +A++H+  I   A     +E+   TGRTHQ+RVH  
Sbjct: 176 PIGHDPDDKRKRMIRA-----DGAFAVTHYHRIAETADTAT-IELNLETGRTHQIRVHLA 229

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
            +G PI+GD  Y A       +    ++ LHA  + L  P     L +T+P P
Sbjct: 230 SIGFPIIGDPLYAA-------TETATRMQLHAFRVRLIRPLTIEPLTVTSPSP 275


>gi|119953592|ref|YP_945802.1| tRNA pseudouridine synthase A [Borrelia turicatae 91E135]
 gi|119862363|gb|AAX18131.1| tRNA pseudouridine synthase A [Borrelia turicatae 91E135]
          Length = 331

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 131/322 (40%), Gaps = 25/322 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +++  RLD              + + +R+G V ++  +V F++RI     + +  
Sbjct: 26  IDVLKNDDGKRLDAVLIKFLK-FPKSKIIRHIRNGDVLLNNLKVSFSHRIFKDDKIYLYK 84

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +     + +     + ++        +K  ++YED+ + V NK  GI V G       +
Sbjct: 85  PLLQGLSLNRVTVKDEVAILR-----DIKKRIVYEDADLLVINKRRGILVHGDKYSLDTL 139

Query: 130 DG--FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                L   + S   KP   HRLD+ TSG+++ A+   +A+ L+++F    + K Y +L+
Sbjct: 140 INAYLLDESLGSLSFKPSAVHRLDRNTSGLIIFAKNINSARILSQAFSSGVVIKKYLALL 199

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVV--KQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            G+       I   L  K+ +  D +       N+     A++  K I   ++     E+
Sbjct: 200 DGV-------ITKPLTYKNFLYRDKIARKTFVINDIDKCNAVTDIKPI-LVSKSSTLAEV 251

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              TG THQ+R         ++ D KY + F       ++   +LH+  +        R 
Sbjct: 252 SIKTGFTHQIRAQCAFNKHALINDKKYDSQF-------VKTNYFLHSFLIKFNQSLFLRN 304

Query: 306 QITAPLPAHMVKTWDSLGFKYD 327
           +      +  +K   ++   YD
Sbjct: 305 EFFVEPSSDFLKQISNIFGVYD 326


>gi|291239041|ref|XP_002739435.1| PREDICTED: hypothetical protein [Saccoglossus kowalevskii]
          Length = 467

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 67/263 (25%), Positives = 119/263 (45%), Gaps = 32/263 (12%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL---KSWVDSKGQKPRLTHRL 150
           +  L   ++Y+   +   +KP G+   GG  I  +++  L      +D    K  L HRL
Sbjct: 204 AKILHERIIYDHDDVIAIDKPYGLPSHGGPTITNNVNDTLTILAKLIDKSLPKLYLVHRL 263

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ET+G++++A++   A+ L   FR + + K YW L  G+P+  +  +   + +    G 
Sbjct: 264 DKETTGVMLLAKSEIIAKQLNALFRKKMVIKRYWVLTVGVPEPSEGVVDIPMEEGEVAGK 323

Query: 211 DYV-----------HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + +           +++K +      A+++FKV+         +E+QP TG  HQ+R H 
Sbjct: 324 NRMLLRPDYGLVYKNLIKSSSGKGATALTNFKVLASEG-NCALVELQPETGIKHQIRCHL 382

Query: 260 LH-MGCPIVGDHKYCA-------NFKGNFTSPIQNKL--------YLHARYMDLPHPEGG 303
              +GCPI+GDHKY            G+    +  +         +LHA+ + +P    G
Sbjct: 383 ASGLGCPILGDHKYSHHDKLAPQKLPGDMLQRLNIRQAKVRTVPMHLHAKQLIIPQFRDG 442

Query: 304 R-LQITAPLPAHMVKTWDSLGFK 325
           R L I+  LP    K    L  +
Sbjct: 443 RNLFISTKLPEFFKKNMTRLKIQ 465


>gi|119897756|ref|YP_932969.1| hypothetical protein azo1465 [Azoarcus sp. BH72]
 gi|119670169|emb|CAL94082.1| hypothetical protein azo1465 [Azoarcus sp. BH72]
          Length = 260

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/237 (25%), Positives = 101/237 (42%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   +KP+G+ V   +  A+     ++   D  G+     HRLD+ TSG+LV 
Sbjct: 4   ILYQDEHLVAIHKPSGLLVHRSALDAHEERFAVQLLRDQLGRHVHPVHRLDKGTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R  A  L   F  R ++K Y ++V G P  +   I + L ++        HV +   
Sbjct: 64  ALDRDTAGRLATQFETRAVRKQYVAIVRGHPA-EAGTIDHPLSRRFDPVE---HVAEDKV 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                AI+ F+ +               ++  L ++P TGR HQ+R H  H+  PI+GD 
Sbjct: 120 FAPQPAITRFRRLATAELPWAVDRYPTSRYALLALEPETGRRHQIRRHLKHISHPIIGDS 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
            +                ++ L    ++L HP     LQ+ A          D+LG+
Sbjct: 180 TFGKGKHNRMFQAHFGSERMLLACTDIELRHPQRDAPLQLHAAPAPDFRAVADALGW 236


>gi|59713668|ref|YP_206443.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           ES114]
 gi|59481916|gb|AAW87555.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           ES114]
          Length = 566

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 62/228 (27%), Positives = 99/228 (43%), Gaps = 19/228 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D +  L   ++     ++YED  + V NKPA      G  I   +   ++         
Sbjct: 348 MDENPLLINPAEGKDLEIVYEDEFMVVVNKPADFLSVPGKNIHDSVYARIQQRYPDATGG 407

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLD  TSG+LV+  T  A + L + F  R ++K Y +L+ G+ +  +  I   + 
Sbjct: 408 L-IIHRLDMATSGLLVLGLTPKAHKRLQQQFINRTVEKRYTALLDGVLEQDEGLITLPM- 465

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V  ++      A + ++VI+    K     + P TGRTHQLRVH  H  
Sbjct: 466 RGDLYDRPRQLVCFEH---GKPAETTYQVIERKENKTKVY-LYPKTGRTHQLRVHCAHYL 521

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
            +  PI GD  Y             N+L+LHA Y+ L HP     ++ 
Sbjct: 522 GLNMPITGDGLYGKK---------ANRLHLHAGYLSLIHPITKEPMEF 560


>gi|197303943|ref|ZP_03168975.1| hypothetical protein RUMLAC_02680 [Ruminococcus lactaris ATCC
           29176]
 gi|197296911|gb|EDY31479.1| hypothetical protein RUMLAC_02680 [Ruminococcus lactaris ATCC
           29176]
          Length = 230

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 64/223 (28%), Positives = 105/223 (47%), Gaps = 15/223 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSG 156
             +L+ED +I V +KP+G+  Q        +   LK+ +  + + P L   HRLDQ   G
Sbjct: 7   PRILFEDQEILVCHKPSGVPAQTNRIGTPDLVSILKNHLRKESRSPYLALIHRLDQPVEG 66

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V A+T  +A+ L+         K Y ++  G+P   +  + ++L+K +       H+ 
Sbjct: 67  LMVFAKTPRSAKELSRQLTTSGFGKYYLAVAEGVPSEAEADLTDYLVKDARSNTS--HIC 124

Query: 217 KQNEKGANYAISHFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++   A  A  H+KV+             L++   TGR HQ+RV   HMG P++GD KY
Sbjct: 125 SKDTPQAKIAKLHYKVLAAGTTADGSSCSLLKIHLDTGRHHQIRVQMAHMGHPLIGDRKY 184

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAH 314
                 N T     KL L A  +   HP  G +++ T P+P  
Sbjct: 185 ------NLTGTSSPKLLLCAFRLSFRHPVTGKKMEFTLPVPEE 221


>gi|150024977|ref|YP_001295803.1| 23S rRNA pseudouridine synthase [Flavobacterium psychrophilum
           JIP02/86]
 gi|149771518|emb|CAL42987.1| Probable 23S rRNA pseudouridine synthase [Flavobacterium
           psychrophilum JIP02/86]
          Length = 231

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 70/220 (31%), Positives = 104/220 (47%), Gaps = 14/220 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +L++D+ I V NK  G  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 14  ILHQDNHIIVVNKRVGDIVQGDKTGDKPLSEVVKEYIKDKYDKPGEVFLGVVHRLDRPTT 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V ART  A   L E F  R  QK YW++V   P+  +  + ++L +         H+
Sbjct: 74  GIVVFARTSKALTRLNEMFSNRETQKTYWAVVKNKPEKNEAKLVHYLKRNEKNNTSKAHI 133

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +  E  +  A   +K+I      F   E+  HTGR HQ+R     +G PI GD KY  +
Sbjct: 134 KEVPE--SKLASLDYKIIKELNNYFAL-EINLHTGRHHQIRAQLSAIGTPIKGDLKYGFD 190

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
                 S     ++LHAR +   HP     +QI AP+P  
Sbjct: 191 -----RSNPNGGIHLHARKLVFIHPVTKENIQIIAPVPDD 225


>gi|77360181|ref|YP_339756.1| ribosomal large subunit pseudouridine synthase A (pseudouridylate
           synthase, 23S RNA-specific) [Pseudoalteromonas
           haloplanktis TAC125]
 gi|76875092|emb|CAI86313.1| ribosomal large subunit pseudouridine synthase A (Pseudouridylate
           synthase, 23S RNA-specific) [Pseudoalteromonas
           haloplanktis TAC125]
          Length = 570

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 108/246 (43%), Gaps = 21/246 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++K   + ++ + L   +      ++Y+D  I V NKPA      G  I   +
Sbjct: 339 CQPILGHMLKGLHVEENPL-LINPAIGKDLTIIYQDQDILVINKPAEFLSVPGVNIEDSV 397

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +K+        P + HRLD  TSG+L++A  + A + L + F  R I+K Y +LV G
Sbjct: 398 YLRIKTQF-PHATGPLIVHRLDMSTSGLLIIALNKRAHKALQKQFIERTIEKRYVALVAG 456

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   I   L +          V  Q+      +++ ++V++        L + P T
Sbjct: 457 NVVQNSGTIDLPL-RLDFDDKPRQLVCYQH---GKASLTTWQVLERK-DNITRLHLYPKT 511

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVH  H   +  PIVGD  Y             N+L+LHA Y+   HP    +L
Sbjct: 512 GRTHQLRVHCAHKLGLNMPIVGDDHYGEK---------ANRLHLHAEYLSFCHPINHQQL 562

Query: 306 QIT-AP 310
           +   AP
Sbjct: 563 EFEVAP 568


>gi|171909579|ref|ZP_02925049.1| ribosomal large subunit pseudouridine synthase, Rlu family protein
           [Verrucomicrobium spinosum DSM 4136]
          Length = 253

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/235 (26%), Positives = 111/235 (47%), Gaps = 21/235 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA---YHIDGF--LKSWVDSKGQKPRLTHRLDQETS 155
           +L E     V +KPA + +             DG   L ++  + G +  + +RLD+ETS
Sbjct: 11  ILDETEDWLVVDKPAPLQIHPSKPSDAGLTLWDGIRELLAYELANGGQVSIINRLDRETS 70

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++VA+T  AA+ L ++   R++ K Y ++V G P+ ++  +   +L++  +    + V
Sbjct: 71  GVVLVAKTGPAARRLGKAMMRRQMDKTYLAVVAGWPEWEETTVTAPILRQGDVMDSRIWV 130

Query: 216 VKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++ ++      SHF+V +       +F  +E  PHTGR HQLRVH  H+G  +VGD  Y
Sbjct: 131 KQRVDERGVPCESHFQVRERHETHRGRFSLVECAPHTGRMHQLRVHLAHLGHYVVGDKIY 190

Query: 273 CANF------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
             +                    +  +  LH+  + L     GR +  APLP  +
Sbjct: 191 GPSEDCYLEFIETGWTPRLEAQLLLPRQALHSHRLILDD-GQGRQEWVAPLPEAL 244


>gi|242238059|ref|YP_002986240.1| pseudouridine synthase [Dickeya dadantii Ech703]
 gi|242130116|gb|ACS84418.1| pseudouridine synthase [Dickeya dadantii Ech703]
          Length = 217

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 65/213 (30%), Positives = 96/213 (45%), Gaps = 10/213 (4%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G     H D  + S + +        
Sbjct: 1   MEPYNPPRDPWLHVLYQDQHIIVVNKPSGLLSVPGRA-DEHKDSIM-SRIQADIPTAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG     +  +   L+    
Sbjct: 59  HRLDMATSGVMVVALTKAAERELKRQFREREPKKSYLARVWGHMAQDEGLVDLPLICD-W 117

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  V  +  K A  A   ++V+   A     +++ P TGR+HQLRVH L +G PI+
Sbjct: 118 PNRPRQKVCFEQGKPAQTA---YQVLARDADGTTRVKLMPITGRSHQLRVHMLALGHPIL 174

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           GD  Y              +L LHA+ + + HP
Sbjct: 175 GDGFYAHPDAKAMA----PRLLLHAQELVITHP 203


>gi|91789312|ref|YP_550264.1| ribosomal large subunit pseudouridine synthase A [Polaromonas sp.
           JS666]
 gi|91698537|gb|ABE45366.1| ribosomal large subunit pseudouridine synthase A [Polaromonas sp.
           JS666]
          Length = 223

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 60/219 (27%), Positives = 102/219 (46%), Gaps = 10/219 (4%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ D    V  KP+G+    G G        L + V  +  +  + HRLD  TSG+
Sbjct: 10  PLEIVHTDDLFLVLRKPSGLLAVPGRGED--KQDCLSTRVQQQHPEALVVHRLDMGTSGL 67

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-- 215
           +V+AR+R A + L+++F  R + K Y ++V G+     +    W      I  D+     
Sbjct: 68  VVMARSREAQRALSKAFAERAVHKRYVAVVDGLMAAPADSPDGWGRIDLPIIVDWARRPL 127

Query: 216 VKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              + +    +++ +++      +    L ++P TGR+HQLRVH   +G PIVGD  Y  
Sbjct: 128 RVIDAERGKPSVTRWQIQHHDRQRNTTRLLLEPVTGRSHQLRVHLQAIGHPIVGDALY-- 185

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                  +    +L LHA  +   HP GG+ +Q  +P P
Sbjct: 186 --ATPAVAAGAGRLLLHACRLAFAHPLGGQWMQFESPPP 222


>gi|330831288|ref|YP_004394240.1| ribosomal large subunit pseudouridine synthase A [Aeromonas veronii
           B565]
 gi|328806424|gb|AEB51623.1| Ribosomal large subunit pseudouridine synthase A [Aeromonas veronii
           B565]
          Length = 218

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/215 (29%), Positives = 101/215 (46%), Gaps = 12/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L++D  I V NKP G+    G G     +  +   V  +  K    HRLD  T+G++
Sbjct: 12  LDILFKDKDIMVVNKPTGLLSVPGRGPEN--EDSVLHRVKQQHPKAAAAHRLDMSTTGVI 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+     + + L+  FR R  +K Y + VWG P+     +   L              K 
Sbjct: 70  VIPLNPNSHRELSRQFRERETEKHYLAWVWGEPELDAGEVDLPLCVDWPNRPK----QKV 125

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +   +A++ ++ +         +++ P TGR+HQLRVH L +G PI+GD+ Y A+   
Sbjct: 126 DHEEGRHALTLWQKLK-VENGNSLIKLTPITGRSHQLRVHMLELGHPILGDNLY-AHPDA 183

Query: 279 NFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
              +P    LYLHA  + + HP  G R+   AP P
Sbjct: 184 LAAAPH---LYLHAAMLTISHPRSGERMTFEAPAP 215


>gi|323489453|ref|ZP_08094682.1| putative RNA pseudouridine synthase yhcT [Planococcus donghaensis
           MPA1U2]
 gi|323396947|gb|EGA89764.1| putative RNA pseudouridine synthase yhcT [Planococcus donghaensis
           MPA1U2]
          Length = 281

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/226 (25%), Positives = 94/226 (41%), Gaps = 14/226 (6%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSKG 141
           L  + +  +    ++  +L+ED    V  KP G++            I+  L   + + G
Sbjct: 62  LPPAESPYEPKHDVELPVLFEDDHFIVARKPKGMATHPNEVGQTDTFINAILGHIIRNGG 121

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLDQ TSG+L+VA+   A   L      +++ + Y ++V G   NK   I   
Sbjct: 122 SYGEHVHRLDQGTSGLLMVAKHPVAKNVLDRMLEQKQLVRDYEAVVKGKVHNKSGTIDFA 181

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +  H     +       +    A++H++V+    +    L +   TGRTHQ+R H  H
Sbjct: 182 IGRDRHHPTRRMV-----SQTGQSAVTHYRVLKLM-EGKSLLHLTLETGRTHQIRTHLSH 235

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           +G PIVGD  Y      +         +LHA  M   HP      +
Sbjct: 236 IGHPIVGDTLYDGPPTQDGA------YHLHAFRMSFIHPFTNEKVV 275


>gi|146310754|ref|YP_001175828.1| pseudouridylate synthase [Enterobacter sp. 638]
 gi|145317630|gb|ABP59777.1| Pseudouridylate synthase [Enterobacter sp. 638]
          Length = 232

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/213 (26%), Positives = 92/213 (43%), Gaps = 16/213 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + + NKP+G+    G          +   +        L HRLD  TSG++V+
Sbjct: 19  ILYQDEHLVIINKPSGLLSLSGKNPQN--LDSVHYRLVKTFPGCTLIHRLDFGTSGLMVI 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +     L + F  R + KIY +L+ G  +N +  I   + K   +      ++    
Sbjct: 77  ARNKTINAALCQQFSQRTVTKIYSALLCGHLENNEGAIDAPIAKDPAL----FPLMSICA 132

Query: 221 KGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                A S ++VI+ F +            +E+ P TGRTHQLR+H   +G PI+G   Y
Sbjct: 133 ITGKPARSRYRVIERFYRVGEDGAELPLTRVELTPETGRTHQLRIHCQQLGHPILGCDLY 192

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
               +         +L LHA  +   HP    +
Sbjct: 193 GGLLRPGTEKT--PRLMLHASELHFVHPIRKEI 223


>gi|42524230|ref|NP_969610.1| pseudouridylate synthase, 23S RNA-specific [Bdellovibrio
           bacteriovorus HD100]
 gi|39576438|emb|CAE80603.1| Pseudouridylate synthase, 23S RNA-specific [Bdellovibrio
           bacteriovorus HD100]
          Length = 230

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/238 (26%), Positives = 105/238 (44%), Gaps = 19/238 (7%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----- 143
            + K        +L+ED  + V NK AG+          +    L +    KG       
Sbjct: 3   KIPKKHQPRGFEILHEDLDVIVGNKAAGVLTVAAKWDRDNTVHNLLNLYVRKGNPRSNKC 62

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLDQ T+G+L+ A+T      L + +  +   K Y+++V G    K   I ++L 
Sbjct: 63  VYVVHRLDQATTGVLIFAKTEQVQHFLKDDW--KSTIKTYYAIVHGKMPKKSGTITSYLE 120

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +      +YV    ++      AI+ ++V+    +KF  L++   TG+ +Q+RVH    G
Sbjct: 121 EDE----NYVVHSSKDSDKGKLAITEYEVLK-ETEKFSLLKINLLTGKKNQIRVHLAGEG 175

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWD 320
            PIVGD KY         +    +L LH+  ++  HP    R+ I AP+P +     D
Sbjct: 176 HPIVGDPKYGK------PTTNLKELRLHSASLEFTHPHSKKRITIKAPVPNYFRTLID 227


>gi|258508779|ref|YP_003171530.1| ribosomal large subunit 23S pseudouridine synthase D [Lactobacillus
           rhamnosus GG]
 gi|257148706|emb|CAR87679.1| Ribosomal large subunit 23S pseudouridine synthase D [Lactobacillus
           rhamnosus GG]
 gi|259650085|dbj|BAI42247.1| pseudouridylate synthase [Lactobacillus rhamnosus GG]
          Length = 278

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/293 (21%), Positives = 116/293 (39%), Gaps = 37/293 (12%)

Query: 25  FKNHYPH--INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
            ++      I      ++  +  ++V+      N  +++G ++ +               
Sbjct: 15  LRDQLQDWLIPRKRQHQMRVAQTIQVNGHYRHLNEPVKNGDLISLTY------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKG 141
             D  V+ T   +     + YED  + + +K AG+       G    +     +++    
Sbjct: 62  --DELVHRTYVPETPHLNIRYEDDDLLIVDKTAGMKTHPNQPGETGTLMNQAAAYLAP-- 117

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKECIAN 200
               +THRLD  TSG+LV+A+   A   +      + + + Y ++V  GIP  +K  I  
Sbjct: 118 FPALITHRLDMATSGLLVIAKNPLAQAIINRQLATKTMHRDYLAVVPRGIP--EKGTIQA 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +          +           +A++H+  I   A     +E+   TGRTHQ+RVH  
Sbjct: 176 PIGHDPDDKRKRMIRA-----DGAFAVTHYHRIAETADTAT-IELNLETGRTHQIRVHLA 229

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
            +G PI+GD  Y A       +    ++ LHA  + L  P     L +T+P P
Sbjct: 230 SIGFPIIGDPLYAA-------TETATRMQLHAFRVRLIRPLTIEPLTVTSPSP 275


>gi|254438633|ref|ZP_05052127.1| RNA pseudouridine synthase family [Octadecabacter antarcticus 307]
 gi|198254079|gb|EDY78393.1| RNA pseudouridine synthase family [Octadecabacter antarcticus 307]
          Length = 215

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 64/220 (29%), Positives = 106/220 (48%), Gaps = 13/220 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                  +++ D +I + NKP+G+    G G   H+   L   V     +  L HRLD++
Sbjct: 7   PPDSPLDVIHADHEILIVNKPSGLLSVPGKGP--HLADCLIMRVQVAFPQALLIHRLDRD 64

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V A TR A +H+   F  R  +K Y + VWG+ + K   +   L+       +  
Sbjct: 65  TSGVMVFALTRHAQRHIGLQFEKRMTKKTYVARVWGMIEPKTGTVDLPLIVD----WENR 120

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + K   +    A + ++V+   A +   + + P TGR+HQLRVH L +G  I+GD  Y 
Sbjct: 121 PLQKVCHETGKSAQTDWRVLRGDATE-SRVRLMPKTGRSHQLRVHMLSLGHAILGDPFYA 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                 +     ++L LH+  + L HP+GG  ++  A  P
Sbjct: 180 VGEAREY-----DRLMLHSEELRLRHPDGGEGVKFRAKAP 214


>gi|149184985|ref|ZP_01863302.1| pseudouridylate synthase [Erythrobacter sp. SD-21]
 gi|148831096|gb|EDL49530.1| pseudouridylate synthase [Erythrobacter sp. SD-21]
          Length = 218

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 106/229 (46%), Gaps = 16/229 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ED +  V +KPAG+SV         ++   +       + P   HRLD +TSG 
Sbjct: 3   DIPIIFEDGEALVIDKPAGLSVDRPKRGGPCLEDHFEQLKLGFQRPPAAVHRLDTDTSGC 62

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++AR   A +   ++F  R ++K Y  ++ GIP  ++  IA  L K S  G  +  +  
Sbjct: 63  LLLARNPKALKRFAKAFEDRLVEKRYLGVLAGIPDGEEGTIALSLSKISSAGKGWRMIA- 121

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA-LHMGCPIVGDHKYCANF 276
              K    +++H++ +         LE +P TGRTHQ+R+H    +G P++GD  Y    
Sbjct: 122 --AKKGKPSVTHWRKL-MEHDGKALLEFRPETGRTHQIRIHCEAGLGLPLLGDPVYG--- 175

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
               T     +  LHA  + +P      ++  APLP        +LGF 
Sbjct: 176 ----TGKGAPRTMLHAAGLMVPRESKPAIEAAAPLPRDFA----ALGFS 216


>gi|157961914|ref|YP_001501948.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157846914|gb|ABV87413.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 260

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 67/254 (26%), Positives = 109/254 (42%), Gaps = 32/254 (12%)

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           Q I  ++ N      F +  +L++D  + + NKP+G+    G   A      +   +   
Sbjct: 16  QLIPTAADNFIAPPCFEEITILFQDEHLLLINKPSGLLSLSGKNPAN--LDSVHYRLVKD 73

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                L HRLD  TSGI+V+AR +     L   F  R + K Y +L+ G  KN+   I  
Sbjct: 74  FPDCTLVHRLDLGTSGIMVIARNKTVNALLCRQFSERSVLKAYTALLLGEIKNEDGFIDA 133

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------------------- 239
            + K          ++K  +K    A S ++V+   +                       
Sbjct: 134 PIAKDKPN----FPLMKICDKEGKQARSLYRVLAKESCASLDEKTQLLNNKREHIADSVA 189

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +E  P TGRTHQLR+H+ + G PI+G   Y ++    F+  + ++L LHA  ++  H
Sbjct: 190 VTRVEFIPETGRTHQLRIHSQYFGHPIIGCDLYGSD----FSYRLASRLMLHATRLEFDH 245

Query: 300 PEGG-RLQITAPLP 312
           P  G R+   +P P
Sbjct: 246 PITGERIVANSPCP 259


>gi|282859900|ref|ZP_06268988.1| pseudouridine synthase, RluA family [Prevotella bivia JCVIHMP010]
 gi|282587303|gb|EFB92520.1| pseudouridine synthase, RluA family [Prevotella bivia JCVIHMP010]
          Length = 577

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 110/249 (44%), Gaps = 28/249 (11%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           L    K +++ +  ++  +    ++  +L+ED+ + V +KPAG+    G  +A  +   L
Sbjct: 337 LEEKYKIKELPNEEIHRHRQDVSIEIPILFEDNYLAVIDKPAGLLSVPGKKLATSVYALL 396

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW----G 189
           K     +  KP + HRLD +TSG++VVA+       L + F  R + K Y + +      
Sbjct: 397 KQKWQGRC-KPYMVHRLDMDTSGLMVVAKQAHVYHDLQQQFINRTVNKRYTAFLPLSLLD 455

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI------DCFAQKFCWL 243
                K  I   L              K +++    AI+ ++++      +   Q    +
Sbjct: 456 KNLPPKGKIILPLTADLFDRP----RQKVDKEVGKIAITTYEIVGKTHYGERLKQLAVRV 511

Query: 244 EMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            + PHTGRTHQLRVH  H   +G PI+GD+ Y             N+L+L+A  +   HP
Sbjct: 512 LLYPHTGRTHQLRVHCAHSEGLGTPIIGDNLYGNK---------ANRLHLYADRLRFVHP 562

Query: 301 EG-GRLQIT 308
                +  +
Sbjct: 563 ITHKEMTFS 571


>gi|291514879|emb|CBK64089.1| ribosomal large subunit pseudouridine synthase D [Alistipes shahii
           WAL 8301]
          Length = 228

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/224 (28%), Positives = 102/224 (45%), Gaps = 14/224 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
           F    +LYED+ + + NK  G  VQ        ++  +K+++  +  KP      + HR+
Sbjct: 2   FNPDDILYEDNHLLIVNKRCGDLVQPDPSGESALEDQIKAFIKRRDAKPGEVFLGVVHRI 61

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+  SG +V A+T  A   L E  R  RI K+YW+L    P  +   + +++L+      
Sbjct: 62  DRPVSGAVVFAKTSKALVRLNEMIREGRIHKVYWALTEATPDPESGELRHYILRDGRTNR 121

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                    +  A  A   +  +      +  +E++  TGR HQ+R     +GCPI GD 
Sbjct: 122 SR--ACDAPKGDAKEARLRYATLGA-GTNYTLVEVELLTGRHHQIRAQLSKIGCPIRGDL 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPA 313
           KY A       S     + LH+R ++  HP     L +TAP+PA
Sbjct: 179 KYGAR-----RSLPGGGISLHSRRVEFEHPVRREPLSVTAPVPA 217


>gi|39995777|ref|NP_951728.1| ribosomal large subunit pseudouridine synthase C [Geobacter
           sulfurreducens PCA]
 gi|39982541|gb|AAR34001.1| ribosomal large subunit pseudouridine synthase C [Geobacter
           sulfurreducens PCA]
 gi|298504786|gb|ADI83509.1| RNA pseudouridine synthase, RluA family [Geobacter sulfurreducens
           KN400]
          Length = 296

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/300 (20%), Positives = 117/300 (39%), Gaps = 45/300 (15%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + +N  P      ++K++ +G ++++   V  +  + +G    I         +   +  
Sbjct: 18  FLRNLLPAAPSAYIRKLISAGHLKINGGAVAPDTLLAAGNTATIKESDRTRQLLAAAKPQ 77

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQ 142
           LD               +L+ED    + NKPAG+ V   +     ++    + ++  +G 
Sbjct: 78  LD---------------ILWEDDYCVIVNKPAGLPVHRTAEAGEANLVELAEHFMAGRGT 122

Query: 143 --KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
             K R  +RLD+ TSG  ++A++ ++A  L    +   + K+Y ++  G        I  
Sbjct: 123 AVKLRPVNRLDRGTSGATILAKSSSSAGMLGRYVKEEGLDKLYLAVTDGSLP-DAGTIDT 181

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L                       A + F+ +        +  + P +GR HQ+R H  
Sbjct: 182 PL-------------------DGKDAHTDFRTLARDT-AVSFALVIPISGRMHQIRKHLS 221

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
            +G P+ GD +Y       +   +      HA  + L HP  GR L + APLP   ++  
Sbjct: 222 AIGHPVRGDRRYRGTLLTGYPGHLL-----HAFRVALIHPVTGRKLIVHAPLPPAFIQYL 276


>gi|304438848|ref|ZP_07398773.1| RluA family ribosomal large subunit pseudouridine synthase
           [Peptoniphilus duerdenii ATCC BAA-1640]
 gi|304372689|gb|EFM26270.1| RluA family ribosomal large subunit pseudouridine synthase
           [Peptoniphilus duerdenii ATCC BAA-1640]
          Length = 313

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 119/301 (39%), Gaps = 31/301 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +++ +++++ RLDR+   +  +     + K +R   + V+ K+      ++    V 
Sbjct: 1   MKEIIINSNDKDQRLDRFMGKYLQNAKKSLIMKSIRKKNITVNNKKSAPEYILKENDRVE 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI- 125
           I              + ++    +  H       ++YED  I +  KP G+         
Sbjct: 61  IYFS----------DETIEKFTKIKNHVKRDFPDIIYEDENIALVKKPRGLLTHNDKKDY 110

Query: 126 AYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             +      S++  KG+         +P   +RLD+ TSGIL+  +   A + + ++ + 
Sbjct: 111 EKNALDMFVSYMIHKGEYVPRVEKSFRPSFCNRLDRNTSGILIGCKNAQALREINDAIKR 170

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R I+K Y +LV G    +   I+ +L K      +   V            +  + ++  
Sbjct: 171 REIEKHYMALVDGSIDEEIHDIS-YLEKD----REKNKVSLNERGDGKEIETIIRPMEKL 225

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            + +  +++   TGRTHQ+R         IVGD KY         S   N  +LH   + 
Sbjct: 226 GE-YTLVDINLITGRTHQIRATLKKYNRSIVGDLKYKGR-----RSFGLNSQFLHNYKII 279

Query: 297 L 297
            
Sbjct: 280 F 280


>gi|298384162|ref|ZP_06993723.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           1_1_14]
 gi|298263766|gb|EFI06629.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           1_1_14]
          Length = 549

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 68/243 (27%), Positives = 114/243 (46%), Gaps = 22/243 (9%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++  + ++   H    +  +++ED  + V NKP+G+    G       
Sbjct: 313 CEPILQHMLQGLEVDGNPLSPQAHRKK-ELEIVFEDEWLVVVNKPSGMLSVPGKEEETDS 371

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                     +   P + HRLD  TSG+L+VA+T+   QHL E F  R I+K Y +L+  
Sbjct: 372 VYHRVKAKYPEATGPMIVHRLDMATSGLLLVAKTKEVHQHLQEQFINRSIKKRYVALLDR 431

Query: 190 IPKNKK----ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
              N++      I   L          +     +E+    A++ ++V++ ++ K+  +  
Sbjct: 432 NGLNQQLEETGTINLPLCLNPLDRPRQM----VSEEYGKPAVTEYRVLN-YSDKYIRIAF 486

Query: 246 QPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            P TGRTHQLRVHA H   + CPI+GD  Y             ++LYLHA Y++  HP  
Sbjct: 487 YPLTGRTHQLRVHAAHHQGLNCPILGDELYGKK---------ADRLYLHAEYIEFRHPVY 537

Query: 303 GRL 305
           G +
Sbjct: 538 GDI 540


>gi|90580967|ref|ZP_01236768.1| putative pseudouridine synthase Rlu family protein [Vibrio angustum
           S14]
 gi|90437845|gb|EAS63035.1| putative pseudouridine synthase Rlu family protein [Vibrio angustum
           S14]
          Length = 245

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 58/244 (23%), Positives = 98/244 (40%), Gaps = 17/244 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY D  +   NKPAG+ V      ++     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELEILYRDDYLIAVNKPAGMLVHRSWLDSHETVFVMQTLRDQIGQHVFPLHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+   +   A  +   F  R + K Y ++V G  K          ++   I        
Sbjct: 61  VLLFGLSSEIASQMMPLFAGRDMHKTYHAVVRGWIKEAAVLDYPLKVELDKIADKNAS-- 118

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              EK A  A++ ++ +               ++C +EM+P TGR HQLR H  H+   I
Sbjct: 119 --EEKEAQPAVTAYEPLATVETDIAVGRYSTSRYCLVEMKPETGRKHQLRRHMHHLSHHI 176

Query: 267 VGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD  +             +  +L LHA  +   HP  G  + I A +         +  
Sbjct: 177 IGDVNHGDGRHNRMFREHYDCHRLMLHASRLQFDHPITGEAIDIRAGIDETWRNVMAAFN 236

Query: 324 FKYD 327
           +  +
Sbjct: 237 WSPN 240


>gi|304373355|ref|YP_003856564.1| Ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyorhinis HUB-1]
 gi|304309546|gb|ADM22026.1| Ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyorhinis HUB-1]
          Length = 289

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 60/294 (20%), Positives = 114/294 (38%), Gaps = 23/294 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           ++ + ++    L ++      + +   ++K+ R  +++V+KK       +Q   +++I  
Sbjct: 4   IIAKENDHGRTLLKFVAKILQNYSTSQIEKLFRKKEIKVNKKPQTKKYIVQQDDIIQI-- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
             N     +K Q++ + +             ++YED  I V NK   ++V  G     + 
Sbjct: 62  YTNEKLDKLKTQELENQTKKYIPRKIKFDFDVIYEDENILVLNKHINVAVHDGVWSLDNQ 121

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                         P    RLD+ TSG+++ A+   +   L +         I+ S    
Sbjct: 122 VSKYLKTQKINSFTPSHIGRLDKATSGLIIYAKNYFSLVELNKKQNSFLKYYIFQS---D 178

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I   KK  +   + K   +      +   N++ A  A++HF               Q  T
Sbjct: 179 IEIKKKFEVKIKIEKNEKLKK----MQVTNKETATVALTHFFSSKN------LKIAQILT 228

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           G+ HQ+RV   H+G PI GD KY              +L+LH+  +   + EG 
Sbjct: 229 GKKHQIRVSLEHLGYPIYGDTKYGGKKN--------KRLFLHSYKIICLNLEGK 274


>gi|126701209|ref|YP_001090106.1| putative pseudouridylate synthase [Clostridium difficile 630]
 gi|254977209|ref|ZP_05273681.1| putative pseudouridylate synthase [Clostridium difficile QCD-66c26]
 gi|255094537|ref|ZP_05324015.1| putative pseudouridylate synthase [Clostridium difficile CIP
           107932]
 gi|255102795|ref|ZP_05331772.1| putative pseudouridylate synthase [Clostridium difficile QCD-63q42]
 gi|255308616|ref|ZP_05352787.1| putative pseudouridylate synthase [Clostridium difficile ATCC
           43255]
 gi|255316290|ref|ZP_05357873.1| putative pseudouridylate synthase [Clostridium difficile QCD-76w55]
 gi|255518951|ref|ZP_05386627.1| putative pseudouridylate synthase [Clostridium difficile QCD-97b34]
 gi|255652130|ref|ZP_05399032.1| putative pseudouridylate synthase [Clostridium difficile QCD-37x79]
 gi|260685103|ref|YP_003216388.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260688761|ref|YP_003219895.1| putative pseudouridylate synthase [Clostridium difficile R20291]
 gi|306521862|ref|ZP_07408209.1| putative pseudouridylate synthase [Clostridium difficile QCD-32g58]
 gi|115252646|emb|CAJ70489.1| putative pseudouridine synthase RsuA-like [Clostridium difficile]
 gi|260211266|emb|CBA66814.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260214778|emb|CBE07493.1| putative pseudouridylate synthase [Clostridium difficile R20291]
          Length = 221

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 62/219 (28%), Positives = 107/219 (48%), Gaps = 14/219 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  KP  I  QG +     +   LK ++  K  KP      L HRLD+   
Sbjct: 4   VIYEDNHLLVVEKPVNILSQGDNTNDKDMVNLLKDYIKKKYNKPGNVYIGLIHRLDRPVG 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  L+E  R +  +K Y ++V G  K+  + + ++L K        V V
Sbjct: 64  GVMVFAKTSKAASRLSEQVRSKTFKKTYLAVVHGKIKSNSDILKDFLYKNKKTN--MVTV 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           VK++ K A  A  ++ V+D F +    +++   TGR+HQ+RV       P+ GD +Y   
Sbjct: 122 VKKSHKDAKEAELNYNVLD-FKENLSLVQVNLKTGRSHQIRVQFASRKHPLYGDQRYGKE 180

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
                 + I  ++ L +  +++ HP    +++ T   P 
Sbjct: 181 I-----NKIGQQISLWSNKIEICHPTTKEKMEFTCHPPD 214


>gi|330448662|ref|ZP_08312310.1| RNA pseudouridylate synthase family protein [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
 gi|328492853|dbj|GAA06807.1| RNA pseudouridylate synthase family protein [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
          Length = 557

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 61/243 (25%), Positives = 110/243 (45%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++   ++ ++ +     ++  +  ++Y+D  + + NKPA      G  I   +
Sbjct: 326 CEPILTHMLAGIEVDENPLE-QNPAEGKELSIVYQDDDMVIINKPAEFLSVPGKTIIDSV 384

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +++        P + HRLD  TSG++V+A T+ A + L + F  R ++K Y +L+ G
Sbjct: 385 YSRMQAMFPDSD-SPLIVHRLDMSTSGLIVIALTKDAHKALQKQFIERTVEKRYVALLEG 443

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I +  +  I ++ ++          V  Q       A + ++V++        +   P T
Sbjct: 444 ISEADEGLI-DFPMRVDLDDRPRQIVCYQ---YGKPAQTKWQVLERK-NGRTKVYYYPKT 498

Query: 250 GRTHQLRVHALHM---GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVH+ H+     PIVGD  Y             ++L LHA+Y+   HP    R+
Sbjct: 499 GRTHQLRVHSAHIKGMNMPIVGDDLYGQKG---------DRLCLHAQYLAFNHPTTNERV 549

Query: 306 QIT 308
              
Sbjct: 550 VFE 552


>gi|330723753|gb|AEC46123.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyorhinis MCLD]
          Length = 289

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 61/294 (20%), Positives = 114/294 (38%), Gaps = 23/294 (7%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +V + ++    L ++      + +   ++K+ R  +++V+KK       +Q   +++I  
Sbjct: 4   IVAKENDHGRTLLKFVAKILQNYSTSQIEKLFRKKEIKVNKKPQTKKYIVQQDDIIQI-- 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
             N     +K Q++ + +             ++YED  I V NK   ++V  G     + 
Sbjct: 62  YTNEKLDKLKTQELENQTKKYIPRKIKFDFDVIYEDENILVLNKHINVAVHDGVWSLDNQ 121

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                         P    RLD+ TSG+++ A+   +   L +         I+ S    
Sbjct: 122 VSKYLKTQKINSFTPSHIGRLDKATSGLIIYAKNYFSLVELNKKQNSFLKYYIFQS---D 178

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I   KK  +   + K   +      +   N++ A  A++HF               Q  T
Sbjct: 179 IEIKKKFEVKIKIEKNEKLKK----MQVTNKETATVALTHFFSSKN------LKIAQILT 228

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           G+ HQ+RV   H+G PI GD KY              +L+LH+  +   + EG 
Sbjct: 229 GKKHQIRVSLEHLGYPIYGDTKYGGKKN--------KRLFLHSYKIICLNLEGK 274


>gi|260220462|emb|CBA28023.1| Ribosomal large subunit pseudouridine synthase A [Curvibacter
           putative symbiont of Hydra magnipapillata]
          Length = 224

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 65/224 (29%), Positives = 103/224 (45%), Gaps = 14/224 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  ++Y D  + V NKPAG+    G G        L         +  + HRLD+
Sbjct: 10  PPAQTELPVVYMDDAMLVLNKPAGLLTVPGRG--ESKQDCLSKRAQDVYPEALIVHRLDR 67

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLLKKSHIGG 210
           +TSG++V+AR   A + +  SF  R + K Y ++V G+    +  E I   LL       
Sbjct: 68  DTSGLVVMARGVNAQRAINLSFEKRLVDKRYEAVVIGLLPVSDDWEEIDLPLLVDWPNRP 127

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                   N      A++ ++ I          +E++P TGRTHQLRVH   +G P++GD
Sbjct: 128 KR----TVNHAEGQQALTRWRCISVDEVIGCSRVELEPVTGRTHQLRVHMQALGHPMLGD 183

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             Y           + ++L LHAR + +PHP   + ++ TAP+P
Sbjct: 184 TLY----ATPEALALSDRLQLHARSLSIPHPVSAQVVEFTAPVP 223


>gi|293380440|ref|ZP_06626509.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
 gi|290923019|gb|EFD99952.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
          Length = 285

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 62/299 (20%), Positives = 108/299 (36%), Gaps = 33/299 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M++   +    +     ++   +     I     +  LR    + V+     FN  I  G
Sbjct: 1   MSFHFTLFYPENLAPASVNEVLRQLL--IPR-KWRHFLRIEQNILVNGNYRYFNQNILPG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I      L+H+  +Q+    S  +          ++YED  + + NK  G      
Sbjct: 58  DKIEIN-----LDHVESDQQAYAPSGKM--------PDVIYEDDNLLIINKKKGQKTHPN 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  +  L       GQ P + HRLD  T G+L++A+  A    L      +   + 
Sbjct: 105 ---LNETNTALNDCTTYLGQSPYIVHRLDMLTGGLLLIAKNPAVVPILNRELTSKIFHRD 161

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V       ++  I   +                 +     A++H++V+        
Sbjct: 162 YLAKVINADHLAERGTINAPIGHDPLDQRKRKI-----DPTGLRAVTHYQVLQKNDDNTT 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            +++   TGRTHQ+RVH   +G PIVGD  Y  +F          +L L A  + L  P
Sbjct: 217 IVKLTLETGRTHQIRVHLASLGSPIVGDPLYNPDFASE-------RLALDAYEISLVQP 268


>gi|171059743|ref|YP_001792092.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170777188|gb|ACB35327.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
          Length = 256

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 66/257 (25%), Positives = 108/257 (42%), Gaps = 17/257 (6%)

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V +    +  +  I         ++           +L+ D  + V  KPAG+    G 
Sbjct: 9   IVSVRISRSGCDGTIATAHSRFRPLHRRAVPSEPLIDILHHDDSLLVVRKPAGLLSVPGR 68

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G   H+   + + V +      + HRLD  TSG++V+AR  AA + L  +F  R + K Y
Sbjct: 69  G--EHLQDCVAARVQAIWPDALIVHRLDMATSGLMVMARGPAAQRALGSAFEHRSVTKQY 126

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---- 239
            ++V G        +   L              K +      +++H++      +     
Sbjct: 127 VAVVAGDVAGDAGSVDLPLCAD----WPNRPRQKVDAAMGRPSLTHWRRATPAHEGSTTG 182

Query: 240 ---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 LE++P TGR+HQLRVH L +G PI+GD  Y  +           +L LHA  + 
Sbjct: 183 DIDRTRLELEPVTGRSHQLRVHLLALGHPILGDTLYAPDAVQRMA----PRLLLHASRIA 238

Query: 297 LPHPEGGRLQITAPLPA 313
           LPHP GG + + +  PA
Sbjct: 239 LPHPAGGGICVFSDPPA 255


>gi|148554296|ref|YP_001261878.1| pseudouridine synthase [Sphingomonas wittichii RW1]
 gi|148499486|gb|ABQ67740.1| pseudouridine synthase [Sphingomonas wittichii RW1]
          Length = 250

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 67/256 (26%), Positives = 111/256 (43%), Gaps = 16/256 (6%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                    K ++ L       +    L   +L+ D +  V +KP+G+ V      +  +
Sbjct: 6   WGRIAARRPKGKEALCRRGRPVQGRRVLDEHILFIDGEAMVIDKPSGLPVDPPRDGSISL 65

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +  L+S      + P   HRLD++TSG L++AR   A +    +F   +++K Y +++ G
Sbjct: 66  ENHLQSLSFGFKRWPSAVHRLDRDTSGCLLLARNPKAHKRYALAFEEGKVEKTYLAILDG 125

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           IP  +   +   L K S     +  V    +     A + ++V+         +E +P T
Sbjct: 126 IPAQESGLVDLPLAKISTREAGWRMV---GDPRGKPATTAWRVVATV-DGRALVEFRPTT 181

Query: 250 GRTHQLRVHALH-MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT 308
           GRTHQ+RVHA   +G PI GD  Y    +   T        LHA  + +P      ++  
Sbjct: 182 GRTHQIRVHAATGIGLPIHGDPVYGREGQAGVT-------LLHASALVVPREGKNPIEAK 234

Query: 309 APLPAHMVKTWDSLGF 324
           APLPA       +LGF
Sbjct: 235 APLPARFT----ALGF 246


>gi|134082733|emb|CAK42625.1| unnamed protein product [Aspergillus niger]
          Length = 484

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 59/258 (22%), Positives = 104/258 (40%), Gaps = 37/258 (14%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +        +K L+ G V V+      N  +++GQ++      +      KE
Sbjct: 66  VDIFLSE-FRDRPAEYYRKALQDGLVAVNGTPAGPNTVVKNGQIISHTLHRHEPPVTGKE 124

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +++ED  + V +KPAG+ V       YH +  L+     +
Sbjct: 125 ------------------IGIIHEDDDLIVIDKPAGVPVHSAG--RYHYNSVLEIMRSQR 164

Query: 141 GQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             +  PR  +RLD+ TSG++ + +T  AA+++T   + R +QK Y + V G   +     
Sbjct: 165 HPEWVPRPCNRLDRLTSGVMFLGKTAKAAENMTGKLKARTLQKEYVARVKGKFPDGVIVC 224

Query: 199 ANWLL-KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
              ++     +G + V            A + F+ +         +   P TGRTHQ+RV
Sbjct: 225 DQPIMSVSPKVGLNRVRA------TGKEAKTKFRRL-------AIVHCLPLTGRTHQIRV 271

Query: 258 HALHMGCPIVGDHKYCAN 275
           H   +G PI  D  Y   
Sbjct: 272 HLQFLGHPISNDPIYSNR 289


>gi|6324506|ref|NP_014575.1| Rib2p [Saccharomyces cerevisiae S288c]
 gi|2501674|sp|Q12362|RIB2_YEAST RecName: Full=Bifunctional protein RIB2; Includes: RecName:
           Full=tRNA pseudouridine synthase 8, cytoplasmic;
           AltName: Full=tRNA pseudouridylate synthase 8; AltName:
           Full=tRNA-uridine isomerase 8; Includes: RecName:
           Full=Diaminohydroxyphosphoribosylaminopyrimidine
           deaminase; Short=DRAP deaminase; AltName:
           Full=Riboflavin-specific deaminase
 gi|642221|emb|CAA79742.1| DRAP deaminase [Saccharomyces cerevisiae]
 gi|1419887|emb|CAA99076.1| RIB2 [Saccharomyces cerevisiae]
 gi|285814824|tpg|DAA10717.1| TPA: Rib2p [Saccharomyces cerevisiae S288c]
          Length = 591

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 102/253 (40%), Gaps = 23/253 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +         K +  G+V ++ +    +  I+ G ++              E
Sbjct: 102 VDVFVSE-FRDREPSYYSKTIAEGKVYLNDEPANLDTIIRDGDLITHKVHR-------HE 153

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    ++           +++ED  I V +KP+ I V       Y  +   K      
Sbjct: 154 PPVTSKPID-----------IVFEDEDILVIDKPSSIPVHPTG--RYRFNTITKMLERQL 200

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A  + +  + R + K Y + V G        +  
Sbjct: 201 GYSVHPCNRLDKPTSGLMFLAKTPLGADRMGDQMKAREVTKEYVARVKGEFPIGIVEVDK 260

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             ++  +       V + +++ A +A + F+ +    Q    ++ +P TGRTHQ+RVH  
Sbjct: 261 P-VRSVNPKVALNAVCEMSDENAKHAKTVFQRVSYDGQ-TSIVKCKPLTGRTHQIRVHLQ 318

Query: 261 HMGCPIVGDHKYC 273
           ++G PI  D  Y 
Sbjct: 319 YLGFPIANDPIYS 331


>gi|257457444|ref|ZP_05622614.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
 gi|257445173|gb|EEV20246.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
          Length = 246

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 105/244 (43%), Gaps = 24/244 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFLKSWVDSKGQ---KPRLTHRLDQ 152
              L+Y D  +   NK AG+ V      A    +D  ++  +        K    HR+D+
Sbjct: 5   PFTLIYADDDMVAVNKAAGLLVAADRWDAEAPRLDLLIQKELPQIAPSCNKLYAVHRIDK 64

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSGIL+ A    A + L  +F+ R I+K Y  L+ G    ++  +   L       GD 
Sbjct: 65  DTSGILLYALNAEAHRTLNTAFQNREIKKTYRLLIHGRVSEEQFTVDLPL----RADGDA 120

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +H    +++    A++HF V++ F ++F  LE  P TGRTHQ+R H    G PIV D  Y
Sbjct: 121 LHRTVVDKRRGKEAVTHFTVLETF-RQFSLLEACPVTGRTHQIRAHLAAAGYPIVCDSLY 179

Query: 273 CANFKGNFTS-------------PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
            +      +              P+  +L LHA  ++  HP  G+    TA        T
Sbjct: 180 GSGKPVLLSELKQRWRGDVYTEQPLIGRLALHAYRLEGVHPRSGQPFAFTAEYAKDFKST 239

Query: 319 WDSL 322
              L
Sbjct: 240 VHQL 243


>gi|299769211|ref|YP_003731237.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. DR1]
 gi|298699299|gb|ADI89864.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. DR1]
          Length = 212

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 68/223 (30%), Positives = 108/223 (48%), Gaps = 17/223 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V  +  K  L HRLD++
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLVAIE-PKTLLIHRLDRD 58

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     +   F+ R+  KIY +LV G  + +   +   ++         +
Sbjct: 59  TSGILVFGLSKRGQSAIARQFQDRQTSKIYEALVAGHLEGE-GTVDIPVIYDP--SRPPL 115

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+V  +      A++H++ ++ F    Q    +++ P TGR+HQLRVH  ++G PIVGD 
Sbjct: 116 HIVDASHN--KPALTHWQAVEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDT 173

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            Y  + +      +  +L LHA+ +   HP     L    P+P
Sbjct: 174 LYATSEQQ-----LVPRLCLHAKQLSFNHPVTAETLTFDCPVP 211


>gi|269118930|ref|YP_003307107.1| pseudouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268612808|gb|ACZ07176.1| pseudouridine synthase, RluA family [Sebaldella termitidis ATCC
           33386]
          Length = 283

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 60/317 (18%), Positives = 120/317 (37%), Gaps = 42/317 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +E +    ++  + +    +         LR+ +V +D K+V+   +I+   +++
Sbjct: 1   MKKFKIEKEHHGYKISEYLREIQNYSGRG-----LRNIEVFLDGKKVRTTQKIRKQGLLK 55

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-- 124
           +                ++           +   +++ED  I V NK   +         
Sbjct: 56  V----------------VEKEKGTNIKPIKIPLDIVFEDEDILVVNKQPYLVTHPTKKKV 99

Query: 125 IAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +G +  + +  G++  PR  +RLD +TSG++++A+       L        ++K 
Sbjct: 100 DVTLANGIVYYFQEKYGKEMVPRFYNRLDMDTSGLIIIAKNSFTQAFLQN---FGDVKKY 156

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFC 241
           Y +LV GI K +   I   + +        +           YA +  K I    +    
Sbjct: 157 YMALVHGIIKEEMINIEKPIARVGDDLRRKIL------DEGQYAKTVVKTIKRNEEKNIT 210

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             E +  TGRTHQ+RVH  + G PI+GD  Y              +  LH+  +   HP 
Sbjct: 211 LTECELFTGRTHQIRVHLSNEGYPILGDKLYGDMDDNV------KRQMLHSYKVSFIHPR 264

Query: 302 G-GRLQITAPLPAHMVK 317
              R ++   +   M +
Sbjct: 265 TKERKELEIEMYDDMKE 281


>gi|255505168|ref|ZP_05344870.3| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Bryantella formatexigens DSM 14469]
 gi|255269406|gb|EET62611.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Bryantella formatexigens DSM 14469]
          Length = 272

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 67/230 (29%), Positives = 112/230 (48%), Gaps = 15/230 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP----RLTHRLD 151
            +   ++YED ++ V  KPAG++VQ  S     ++  +++++  K  KP     + HRLD
Sbjct: 52  DIMPDIIYEDKQLLVCRKPAGLAVQNASFGRMDLESMVRNYLMEKSGKPNPYLGVVHRLD 111

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q   G+LV A+T AAA  L+   +  R+ K Y ++V G    K+  + ++L K+    G+
Sbjct: 112 QPVQGLLVFAKTPAAAAALSAQVQDGRMTKEYLAVVCGKLPEKEGELVHFLKKEP--AGN 169

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V +   GA  A   ++V+   A     + ++  TGR HQ+RV  +  G P+ GD K
Sbjct: 170 CSRAVGEKTPGAKRAELSYRVL-AEADGRALVRIKLKTGRHHQIRVQMVACGAPLYGDAK 228

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
           Y    +         +L L A  +   HP GG R++ T   P +    W+
Sbjct: 229 YNPGAQRG------ERLALCADRLSFVHPAGGKRVEFTCR-PDNFPAPWE 271


>gi|261212690|ref|ZP_05926974.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. RC341]
 gi|260837755|gb|EEX64432.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. RC341]
          Length = 396

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 68/225 (30%), Positives = 103/225 (45%), Gaps = 18/225 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ +  L   ++  +  ++Y+D  I V NKP+      G  +   +   L++      + 
Sbjct: 178 LEENPLLNNPAEGQEIDIVYQDDAIVVVNKPSEFLSVPGVHVHDSVLSRLQAQFR-DAEG 236

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD  TSG+LV A TR A +HL + F  R +QK Y +L+ G     +  I   L 
Sbjct: 237 VFALHRLDMSTSGLLVFALTRRANKHLQKQFITRAVQKRYVALLEGTLDADRGEIQLPLC 296

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
                       ++Q       A++H++VI    Q    + + PHTGRTHQLRVH  H  
Sbjct: 297 GDLDDRPRQKVCLQQ----GKPALTHWEVI-RIEQGRTRVYLYPHTGRTHQLRVHCAHQL 351

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            + CPIVGD  Y    +         +L+LHA  +   HP   +L
Sbjct: 352 GLDCPIVGDDLYGQQAQ---------RLHLHAEQLCFTHPYTKQL 387


>gi|212711745|ref|ZP_03319873.1| hypothetical protein PROVALCAL_02820 [Providencia alcalifaciens DSM
           30120]
 gi|212685847|gb|EEB45375.1| hypothetical protein PROVALCAL_02820 [Providencia alcalifaciens DSM
           30120]
          Length = 232

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 99/230 (43%), Gaps = 19/230 (8%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I+D+ +    H D     +LY+D ++ + NKP+G+    G          +   +     
Sbjct: 4   IIDTFIAPPCHEDI---EILYQDEQLIIINKPSGLLSLSGKNPQN--LDSVHYRLVQIYP 58

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +  L HRLD  TSG++V AR +A    L + F  R + K Y +L+ G  +N +  I   +
Sbjct: 59  ECTLVHRLDFGTSGVMVAARNKAINAALCQQFSQRTVTKAYHALLCGHVENNEGVIDAPI 118

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQ 254
            K   +       +   E     A S++ VI+ F              ++  P TGRTHQ
Sbjct: 119 AKDPAL----FPRMSICETHGKSARSYYHVIERFYDEQSDGNQLPLTRVKFIPETGRTHQ 174

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           LR+H+   G PI+G   Y              +L LHA  ++  HP  G+
Sbjct: 175 LRIHSQLFGHPILGCDLYGGLLP--IGIEPAPRLMLHASELNFVHPITGK 222


>gi|62185009|ref|YP_219794.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           abortus S26/3]
 gi|62148076|emb|CAH63831.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           abortus S26/3]
          Length = 274

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 68/296 (22%), Positives = 126/296 (42%), Gaps = 48/296 (16%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINAL 74
           +   RL  + ++  P      +   +R    RV+ +  +F + R+Q G  + +       
Sbjct: 9   QHEERLSSFLRSRLPDYKKHIIMDSVRYHGCRVNGRVERFESYRVQPGDRITLTVQTR-- 66

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                 L+  +L+ED+   ++NKP+  S +  + I         
Sbjct: 67  ----------------------LEPQILWEDAHCCIYNKPSHTSTEDLAKIT-------- 96

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                   +  + HRLD++T+G ++ A+  +AA  L+E F+ R+I K Y +LV+G PK  
Sbjct: 97  --------RLNIVHRLDRDTTGCILFAKHASAANALSELFKKRKIHKQYTALVFGHPKKS 148

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              + ++   KS   G  +       +G    I+ + ++  + Q +  +  +P TGRTHQ
Sbjct: 149 SGTVISYTAPKSRRCGSVIFGNTPKNQG-KLTITQWSILRTYKQ-YTLMRCEPITGRTHQ 206

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           +R+H   +G PIVGD  Y    +         +  LHA  +    P    ++ +TA
Sbjct: 207 IRLHMQTLGHPIVGDVDYGRKEQPKHVF----RPLLHAHALTFTSPFSKEKVAVTA 258


>gi|166710213|ref|ZP_02241420.1| Pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 238

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 104/237 (43%), Gaps = 24/237 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V +KPAG+ V          D       +  G+   L HRLD+ TSG L++
Sbjct: 10  ILYQDDVLAVVDKPAGLMVHDSKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLLL 69

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R +A  L +      ++K Y ++  G P  ++  + + L       G     VK   
Sbjct: 70  AFDRDSASALGKVLMAGEVEKNYLTVCRGWPAEEQFIVDHDL------DGGPGKPVK--- 120

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD 
Sbjct: 121 ---KPAVTHFRRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGDT 177

Query: 271 KYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            +       +F     +++ LHA  +  PHP +G R+++TAPL A   K     G+ 
Sbjct: 178 SHGDGRHNRSFRMLGIHRMLLHAERLAFPHPADGRRIRVTAPLDAEFTKACALFGWD 234


>gi|149916925|ref|ZP_01905426.1| pseudouridine synthase [Plesiocystis pacifica SIR-1]
 gi|149822203|gb|EDM81594.1| pseudouridine synthase [Plesiocystis pacifica SIR-1]
          Length = 255

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 61/250 (24%), Positives = 106/250 (42%), Gaps = 7/250 (2%)

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-DGFLKSWVDS 139
               D+     +        +L+ D ++    KP+G+ V  G      +    L++ +D 
Sbjct: 3   DAEPDAEKPDAEPEVGTALTILHRDDRLLAVAKPSGMLVHRGWAADEAVLVDLLRAQLD- 61

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI--QKIYWSLVWGIPKNKKEC 197
            G      HRLD+ TSG+L +A  + AA  + + F        K Y +LV G+     + 
Sbjct: 62  -GADVFPLHRLDRGTSGVLCLALDKEAAAFVGQQFEAHAPPLTKTYLALVRGLAPEAVDV 120

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                   S  G             A       +      + +  ++  P TGRTHQ+R 
Sbjct: 121 DHGLRPHDSKTGKRRKAADALPRIPAQTRFERIEARQIGERSYSLVKALPRTGRTHQIRR 180

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           H  H+  PI+GD +Y    +  +     +  ++ LHA  + L HP+GG L++ AP+PA +
Sbjct: 181 HLKHLAHPIIGDVRYGKGNQNRYFRAHFDFHRMALHAAALTLEHPDGGALELRAPVPADL 240

Query: 316 VKTWDSLGFK 325
            +   ++GF+
Sbjct: 241 REPLRAMGFE 250


>gi|115375687|ref|ZP_01462942.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|310821153|ref|YP_003953511.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115367335|gb|EAU66315.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|309394225|gb|ADO71684.1| Pseudouridine synthase, RluA family [Stigmatella aurantiaca
           DW4/3-1]
          Length = 298

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 67/297 (22%), Positives = 111/297 (37%), Gaps = 29/297 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +    Y H      ++ L  G+V +D         ++ GQ +         N    E+K 
Sbjct: 25  YLVASYRHSPEPVWRERLARGEVLLDDLPATGEELLKPGQRLVW-------NRPPWEEKE 77

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                 L           +Y D  I   +KP G+    G G        L   V  +  +
Sbjct: 78  TPRDYTL-----------VYADEAILAVDKPGGLPTMPGGGFL---VNTLLHVVRERFPE 123

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRL + TSG+++ ART  AA  L+ ++R   ++K Y +L   +       I   + 
Sbjct: 124 VSPLHRLGRGTSGLVLFARTHDAAAKLSRAWREHEVEKRYRALSSHVASQDAYDITAPIG 183

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +  H G   + +          + S  +V+   A      E+   TGR+ Q+R+H   +G
Sbjct: 184 EAVHPGRGLLSMAL---PSGKASRSLARVLQRRA-ASTLFEVDIQTGRSQQIRIHLAFIG 239

Query: 264 CPIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
            P+ GD  Y                    LHA  +   HP  G RL++ A LP+ ++
Sbjct: 240 HPLEGDPVYTVGGVPRAEQPGLLGDTGYLLHAERLCFVHPLTGERLELHATLPSELL 296


>gi|207341390|gb|EDZ69458.1| YOL066Cp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 589

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 102/253 (40%), Gaps = 23/253 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +         K +  G+V ++ +    +  I+ G ++              E
Sbjct: 102 VDVFVSE-FRDREPSYYSKTIAEGKVYLNDEPANLDTIIRDGDLITHKVHR-------HE 153

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    ++           +++ED  I V +KP+ I V       Y  +   K      
Sbjct: 154 PPVTSKPID-----------IVFEDEDILVIDKPSSIPVHPTG--RYRFNTITKMLERQL 200

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A  + +  + R + K Y + V G        +  
Sbjct: 201 GYSVHPCNRLDKPTSGLMFLAKTPLGADRMGDQMKAREVTKEYVARVKGEFPIGIVEVDK 260

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             ++  +       V + +++ A +A + F+ +    Q    ++ +P TGRTHQ+RVH  
Sbjct: 261 P-VRSVNPKVALNAVCEMSDENAKHAKTVFQRVSYDGQ-TSIVKCKPLTGRTHQIRVHLQ 318

Query: 261 HMGCPIVGDHKYC 273
           ++G PI  D  Y 
Sbjct: 319 YLGFPIANDPIYS 331


>gi|188579049|ref|YP_001915978.1| tRNA pseudouridine synthase C [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188523501|gb|ACD61446.1| tRNA pseudouridine synthase C [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 238

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 102/240 (42%), Gaps = 24/240 (10%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +LY+D  + V +K AG+ V          D       +  G+   L HRLD+ TSG 
Sbjct: 7   PLQILYQDDVLAVVDKTAGLMVHDSKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGC 66

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A  R  A  L ++     +QK Y ++  G P   +  + + L       G     VK
Sbjct: 67  LLLAFDRETASALGKALMSGDVQKDYLAVCRGWPAEPRFTVDHDL------DGGPGKPVK 120

Query: 218 QNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++
Sbjct: 121 ------KPALTHFQRLATGELQVPSTGFATSRYALLRCQPQTGRFRQIRRHLKHLSHHLI 174

Query: 268 GDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           GD  +       NF     +++ LHA+ +  PHP +G R+++TAPL     K     G+ 
Sbjct: 175 GDTSHGDGRHNRNFRMLGIHRMLLHAKRLAFPHPADGRRIRVTAPLDDEFTKACALFGWD 234


>gi|291617372|ref|YP_003520114.1| RluA [Pantoea ananatis LMG 20103]
 gi|291152402|gb|ADD76986.1| RluA [Pantoea ananatis LMG 20103]
          Length = 232

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 101/239 (42%), Gaps = 20/239 (8%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I+D+ +    H +     +LY+D  + + +KP+G+    G          +   + +   
Sbjct: 4   IVDTFIAPPCHEEI---RILYQDDHLVLIDKPSGLLSLSGKNPQN--LDSVHYRLVTIFP 58

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD  TSG++VVAR +     L++ F  R + K Y +L+ G   +++  I   +
Sbjct: 59  GCTLVHRLDFGTSGLIVVARNKTINAALSQQFSARTVAKHYSALLCGHLPDEEGIIDAPI 118

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF--------CWLEMQPHTGRTHQ 254
            K           +    +    A S ++V++ F  K           + + P TGRTHQ
Sbjct: 119 AKDPA----RFPRMSICAEWGKPARSRYRVVERFNLKRDDARVIPLTRVTLIPETGRTHQ 174

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           LR+H   +G PI+G   Y              +L LHA  +   HP  G    I +P P
Sbjct: 175 LRIHCQLLGHPILGCDLYGGLLLPGMEQT--PRLMLHASELQFIHPVTGEPFHIVSPSP 231


>gi|190407280|gb|EDV10547.1| DRAP deaminase [Saccharomyces cerevisiae RM11-1a]
          Length = 591

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 102/253 (40%), Gaps = 23/253 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +         K +  G+V ++ +    +  I+ G ++              E
Sbjct: 102 VDVFVSE-FRDREPSYYSKTIAEGKVYLNDEPANLDTIIRDGDLITHKVHR-------HE 153

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    ++           +++ED  I V +KP+ I V       Y  +   K      
Sbjct: 154 PPVTSKPID-----------IVFEDEDILVIDKPSSIPVHPTG--RYRFNTITKMLERQL 200

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A  + +  + R + K Y + V G        +  
Sbjct: 201 GYSVHPCNRLDKPTSGLMFLAKTPLGADRMGDQMKAREVTKEYVARVKGEFPIGIVEVDK 260

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             ++  +       V + +++ A +A + F+ +    Q    ++ +P TGRTHQ+RVH  
Sbjct: 261 P-VRSVNPKVALNAVCEMSDENAKHAKTVFQRVSYDGQ-TSIVKCKPLTGRTHQIRVHLQ 318

Query: 261 HMGCPIVGDHKYC 273
           ++G PI  D  Y 
Sbjct: 319 YLGFPIANDPIYS 331


>gi|78485000|ref|YP_390925.1| pseudouridine synthase [Thiomicrospira crunogena XCL-2]
 gi|78363286|gb|ABB41251.1| ribosomal large subunit pseudouridine synthase A [Thiomicrospira
           crunogena XCL-2]
          Length = 241

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 59/217 (27%), Positives = 102/217 (47%), Gaps = 12/217 (5%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
            F    +LYED  I V NKPAG+    G  +   ++  L + V        + HRLD +T
Sbjct: 23  PFQLDWVLYEDDDIIVVNKPAGLLSVPGKDLDPEMN--LLAQVQKHVPTALIVHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI+++A+ +A+ +HL+  F+ R  +K Y ++ +G P   +  +   +        +   
Sbjct: 81  SGIMILAKHKASHRHLSIQFQDRLTEKTYQAICFGKPSTSQGHLNLPM----RCDWENRP 136

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +   + K    A +H+K +         + + P TGR+HQLR+H   +G PI+GD+ Y  
Sbjct: 137 LQIIDLKQGKAASTHWK-LTAQYDNAFEVNLTPVTGRSHQLRLHMKMLGHPILGDNLY-- 193

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
                 +     +L LHA  + + HP   + +    P
Sbjct: 194 --ADPQSFAASKRLLLHAASLKVTHPVTKKTMLFEHP 228


>gi|34497801|ref|NP_902016.1| pseudouridylate synthase [Chromobacterium violaceum ATCC 12472]
 gi|34103657|gb|AAQ60018.1| probable pseudouridylate synthases [Chromobacterium violaceum ATCC
           12472]
          Length = 249

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 103/237 (43%), Gaps = 17/237 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  +   +KP+ + V       +     ++   D  G++    HRLD+ TSG L+ 
Sbjct: 4   ILYRDDLLIAIHKPSNLLVHRTELDRHETRFAIQMLRDQIGRRVYPVHRLDKGTSGALLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + A + L+  F  +++ K Y ++V G P +    I + L ++     D   + ++ E
Sbjct: 64  ALDKDAGRELSLQFERQQVYKRYLAVVRGHP-DDAGHIDHPLSRRP---DDLEWIGEKVE 119

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++ ++ +               ++  LE++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 TAPQPAVTDYRTLARVELPIMVERYPTSRYSLLELEPQTGRKHQLRRHLKHIAHPIIGDS 179

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            +                ++ L    M L HP  G+ L +  PL ++       LG+
Sbjct: 180 THGKGRHNRMFADQLGCRRMLLACVEMRLTHPITGQPLLLNCPLESNFSALLARLGW 236


>gi|37675814|ref|NP_936210.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
 gi|37200353|dbj|BAC96180.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
          Length = 565

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 103/228 (45%), Gaps = 19/228 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D +      ++  +  ++Y+D  + V NKP+G+    G  I       L++      + 
Sbjct: 347 MDPNPLEENWAEDKELEIVYQDEAMVVVNKPSGLLSVPGKTITDSAYARLQALF-PDVEG 405

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I   + 
Sbjct: 406 PFVIHRLDMATSGLLVFALTRRANKSLQKQFISRGVQKRYVALLEGEVPQSQGEITLPM- 464

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V  ++      A + +++I+    +     + P TGRTHQLRVH  H  
Sbjct: 465 RGDPDDRPRQLVCFEH---GKPAHTDWQLIEIHDGRSKLY-LYPRTGRTHQLRVHCAHHL 520

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
            +  P+VGD  Y             N+L+LHA  ++L HP    R+  
Sbjct: 521 GLHMPMVGDGLYGEK---------ANRLHLHAESLELDHPYSKERMHF 559


>gi|323331668|gb|EGA73082.1| Rib2p [Saccharomyces cerevisiae AWRI796]
 gi|323335647|gb|EGA76930.1| Rib2p [Saccharomyces cerevisiae Vin13]
 gi|323346638|gb|EGA80923.1| Rib2p [Saccharomyces cerevisiae Lalvin QA23]
 gi|323352328|gb|EGA84863.1| Rib2p [Saccharomyces cerevisiae VL3]
          Length = 591

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 102/253 (40%), Gaps = 23/253 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +         K +  G+V ++ +    +  I+ G ++              E
Sbjct: 102 VDVFVSE-FRDREPSYYSKTIAEGKVYLNDEPANLDTIIRDGDLITHKVHR-------HE 153

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    ++           +++ED  I V +KP+ I V       Y  +   K      
Sbjct: 154 PPVTSKPID-----------IVFEDEDILVIDKPSSIPVHPTG--RYRFNTITKMLERQL 200

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A  + +  + R + K Y + V G        +  
Sbjct: 201 GYSVHPCNRLDKPTSGLMFLAKTPLGADRMGDQMKAREVTKEYVARVKGEFPIGIVEVDK 260

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             ++  +       V + +++ A +A + F+ +    Q    ++ +P TGRTHQ+RVH  
Sbjct: 261 P-VRSVNPKVALNAVCEMSDENAKHAKTVFQRVSYDGQ-TSIVKCKPLTGRTHQIRVHLQ 318

Query: 261 HMGCPIVGDHKYC 273
           ++G PI  D  Y 
Sbjct: 319 YLGFPIANDPIYS 331


>gi|319954878|ref|YP_004166145.1| ribosomal large subunit pseudouridine synthase d [Cellulophaga
           algicola DSM 14237]
 gi|319423538|gb|ADV50647.1| ribosomal large subunit pseudouridine synthase D [Cellulophaga
           algicola DSM 14237]
          Length = 232

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 67/230 (29%), Positives = 106/230 (46%), Gaps = 16/230 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQE 153
            +++YED+ +   NK  G  VQG       +   +K ++  K  KP      + HRLD+ 
Sbjct: 12  LLVIYEDNHLIAINKRPGDIVQGDKTGDAPLSDVVKEYIKIKYNKPGNVYLGVAHRLDRP 71

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGI+V A+T  A   L + F  +  +K YW++V   P  + + + +WL + +     Y 
Sbjct: 72  TSGIVVFAKTSKALPRLNKLFAEKEAKKTYWAVVKNQPPKQNDLLTHWLKRNTKQNKSYA 131

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           +  +  E  +  AI  +  I      +  LE+  HTGR HQ+R     +GC I GD KY 
Sbjct: 132 NTKEVPE--SKKAILSY-TIAKKLDNYFLLEIDLHTGRHHQIRAQLTAIGCVIKGDLKYG 188

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           A+      S     ++LHAR +   HP     + I A  P      W++ 
Sbjct: 189 ADRSNKDGS-----IHLHARKLSFIHPVKKEAITIIAEPPNE--AIWNAC 231


>gi|297588693|ref|ZP_06947336.1| RluA family pseudouridine synthase [Finegoldia magna ATCC 53516]
 gi|297574066|gb|EFH92787.1| RluA family pseudouridine synthase [Finegoldia magna ATCC 53516]
          Length = 273

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 71/308 (23%), Positives = 130/308 (42%), Gaps = 45/308 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           ++ +RLD + K    HI+   L   +    + ++ K  K N++++ G  V I       N
Sbjct: 9   DKKIRLDEFLK--VNHISKN-LFLSIYKDDILINGKHAKRNSKLKPGDKVTIDLKDEENN 65

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           +                    L   +LYED  I+V NKP  +++   +     +  F+  
Sbjct: 66  Y----------------EPINLDIEVLYEDDDIFVLNKPDKLTM--NTDGEESLANFVSY 107

Query: 136 WVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             + +   QK R  +RLDQ+TSG+++VA+ + A  +  ++   ++    Y ++V G PKN
Sbjct: 108 LFEQRNINQKVRFINRLDQDTSGVVMVAKNKIAQAYYQKTSFEKK----YLAIVEGNPKN 163

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +K  I   L++          +  + ++    +++  K I  +   +  + ++  TGRTH
Sbjct: 164 QK--IELNLIRD--------CIKTEIDENGKKSVTILKNIKSYGD-YSLVSLKLLTGRTH 212

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           Q+RV   ++ CPIV D  Y    +G           LHA  +D    +G    I    P 
Sbjct: 213 QIRVSMEYINCPIVADSLYGEKIEGFS-------QMLHANEIDFVDMKGNEHIIATDFPQ 265

Query: 314 HMVKTWDS 321
                   
Sbjct: 266 RFNNFLKK 273


>gi|269968014|ref|ZP_06182052.1| Ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
 gi|269827371|gb|EEZ81667.1| Ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
          Length = 250

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 108/232 (46%), Gaps = 15/232 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED  I   NKP+G+    G  +A H D  + S +     + ++ HRLD  TSG++
Sbjct: 14  VDIVFEDDDILAVNKPSGLLSVPGR-LAEHYDS-MWSRLKELHPEIQVVHRLDMSTSGLM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+ + A + L + F+ R   K+Y++ VWG  + ++  I   L+           V   
Sbjct: 72  LLAKNKPAERALKKQFQYRLTHKVYYARVWGHVEPQEGNIDLPLICD-WPNRPRQKVCFD 130

Query: 219 NEKGANYAISHFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +      + + F+V+             + + P TGR+HQLRVH + +G  I+GD  Y  
Sbjct: 131 D---GKPSQTLFQVVKREVHPDGTHTTVVRLLPITGRSHQLRVHLMAIGHAIIGDEFYAT 187

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                F+     +L LHA  +   HP   +L+ +  +P       +++ F Y
Sbjct: 188 EEAYQFSE----RLELHAAELSFYHPATDQLR-SIFVPCDFYPEAEAMIFNY 234


>gi|293609771|ref|ZP_06692073.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292828223|gb|EFF86586.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 212

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 69/223 (30%), Positives = 107/223 (47%), Gaps = 17/223 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L+Y D    V +KP+ I    G G  +  D  L   V  +  K  L HRLD++
Sbjct: 2   SDFLSEHLIYRDDDFMVIHKPSDILSVPGKGDLH--DSVLTRLVAIE-PKTLLIHRLDRD 58

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++     +   F+ R+  KIY +LV G  + +   +   ++         +
Sbjct: 59  TSGILVFGLSKLGQSAIARQFQDRQTSKIYEALVAGHLEGE-GTVDIPVIYDP--SRPPL 115

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+V  +      A++H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD 
Sbjct: 116 HIVDASHN--KPALTHWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDT 173

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            Y    +      +  +L LHA+ +   HP     L    P+P
Sbjct: 174 LYATPEQQ-----LVPRLCLHAKQLSFNHPVTAETLTFDCPVP 211


>gi|27367689|ref|NP_763216.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           CMCP6]
 gi|27359261|gb|AAO08206.1|AE016812_188 Pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           CMCP6]
          Length = 565

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 103/228 (45%), Gaps = 19/228 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D +      ++  +  ++Y+D  + V NKP+G+    G  I       L++      + 
Sbjct: 347 MDPNPLEENWAEDKELEIVYQDEAMVVVNKPSGLLSVPGKTITDSAYTRLQALF-PDVEG 405

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I   + 
Sbjct: 406 PFVIHRLDMATSGLLVFALTRRANKSLQKQFISRGVQKRYVALLEGEVPQSQGEITLPM- 464

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V  ++      A + +++I+    +     + P TGRTHQLRVH  H  
Sbjct: 465 RGDPDDRPRQLVCFEH---GKPAHTDWQLIETRDGRSKLY-LYPRTGRTHQLRVHCAHHL 520

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
            +  P+VGD  Y             N+L+LHA  ++L HP    R+  
Sbjct: 521 GLHMPMVGDGLYGEK---------ANRLHLHAESLELDHPYSKERMHF 559


>gi|289664969|ref|ZP_06486550.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 272

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 105/237 (44%), Gaps = 24/237 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V +KPAG+            D       +  G+   L HRLD+ TSG L++
Sbjct: 44  ILYQDDVLAVVDKPAGLMAHDSKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLLL 103

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  RA+A  L ++     ++K Y ++  G P  ++  + + L       G     VK   
Sbjct: 104 AFDRASASVLGKALMAGEVEKNYLTVCRGWPAEEQFIVDHDL------DGGPGKPVK--- 154

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD 
Sbjct: 155 ---KPAVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGDT 211

Query: 271 KYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            +       +F     +++ LHA  ++ PHP +G R+ +TAPL A   K     G+ 
Sbjct: 212 SHGDGRHNRSFRMLGIHRMLLHAERLEFPHPADGRRISVTAPLDAEFTKACTLFGWD 268


>gi|302346005|ref|YP_003814358.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
 gi|302149550|gb|ADK95812.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
          Length = 571

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 66/223 (29%), Positives = 97/223 (43%), Gaps = 19/223 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +LYED  + V  KP+G+    G G    I   L      K     + HRLD  TSG+
Sbjct: 359 RLQILYEDDYLAVVVKPSGLLSIPGKGCQASIYSILCERWKGKS-DAFMVHRLDMATSGL 417

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LVVART    + L   F  R ++K Y +L+      K+      +        D     +
Sbjct: 418 LVVARTSEVHKALQAQFIGRTVKKKYVALLPLSILEKQLPAEGRIELPLSPDPDDRPRQR 477

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLE-----MQPHTGRTHQLRVHALH---MGCPIVGD 269
            +      AI+ +++I         LE     + P TGRTHQLRVH  H   +G PI+GD
Sbjct: 478 VDRTNGKPAITEYRLIGKTTYGKEALEAVKIALYPLTGRTHQLRVHCAHPDGLGTPIIGD 537

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPL 311
           + Y    +         +L+LHA +++  HP    R+    PL
Sbjct: 538 NLYGQRAE---------RLWLHATHLEFTHPITQERMSFDTPL 571


>gi|298373557|ref|ZP_06983546.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroidetes oral taxon 274 str. F0058]
 gi|298274609|gb|EFI16161.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroidetes oral taxon 274 str. F0058]
          Length = 223

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 67/228 (29%), Positives = 109/228 (47%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQETS 155
           +LYED+ I   NK +   VQG       +   ++ ++  +  K       + HRLD+  S
Sbjct: 3   ILYEDNHIIAINKSSSDIVQGDKTGDKPLVDTVREYLKERYSKSGNVFCGVVHRLDRPVS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T  A   L E  R   I+K YW++V   P+ ++  + ++L++       Y + 
Sbjct: 63  GVVLFAKTSKALARLNEMLRGHEIKKKYWAIVVKPPQEQEATLKHYLVRNEKQNKSYAYT 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               +K +  A+ H+  I   ++++  LE+  HTGR HQ+R     +G  I GD KY A 
Sbjct: 123 T--EKKDSKLAVLHYVTIG-KSERYTLLEVDLHTGRHHQIRCQLAAVGAVIKGDLKYGAP 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
                 S     + LHAR ++  HP    L  ITAPLP    K W + 
Sbjct: 180 -----RSNPDGGISLHARSVEFVHPVRKELVVITAPLPTD--KLWTAF 220


>gi|87119362|ref|ZP_01075260.1| putative ribosomal large subunit pseudouridine synthase A
           [Marinomonas sp. MED121]
 gi|86165753|gb|EAQ67020.1| putative ribosomal large subunit pseudouridine synthase A
           [Marinomonas sp. MED121]
          Length = 212

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 65/222 (29%), Positives = 98/222 (44%), Gaps = 15/222 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
              L   +LYED    V NKPA      G G        +         +    HRLD  
Sbjct: 2   PTPLSLEILYEDEWFAVINKPANFLSVPGRGPE--KQDSVTHRAQCLFGEAHAVHRLDFA 59

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK-SHIGGDY 212
           TSG+++VA+T  + + L+E FR RR+QK Y +++ G    ++  +   L+    +     
Sbjct: 60  TSGLILVAKTLESHKRLSEHFRERRVQKEYRAILRGKVLAQEGVVNKPLICDWPNRPRQI 119

Query: 213 VHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           VH      +    A +H+K +          + + P TGR+HQLRVH   M  PI+GD  
Sbjct: 120 VHR-----EWGKAATTHWKKLKTPPGSIHSHVALFPITGRSHQLRVHMQSMSHPILGDEF 174

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y        +SP   +L+LHA  ++  HP     L+  A  P
Sbjct: 175 Y-----DALSSPADERLHLHAYRLEFNHPFTTAWLKFIAVCP 211


>gi|260945269|ref|XP_002616932.1| hypothetical protein CLUG_02376 [Clavispora lusitaniae ATCC 42720]
 gi|238848786|gb|EEQ38250.1| hypothetical protein CLUG_02376 [Clavispora lusitaniae ATCC 42720]
          Length = 590

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 53/270 (19%), Positives = 108/270 (40%), Gaps = 32/270 (11%)

Query: 21  LDRW---FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +D +   F++  P        + + +GQV ++K     ++ +++G ++            
Sbjct: 115 IDVFVDEFRDKEPEFYR----RAIAAGQVLLNKTPTTLDSIVRNGDLISHRCHR------ 164

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E  +    +            +++ED+     NKP+GI V       Y  +   K + 
Sbjct: 165 -HEPAVSSRPIE-----------IVFEDADKIAINKPSGIPVHPTG--RYRYNTITKIFQ 210

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              G+     +RLD+ TSG++ + +    A+   +  R R ++K Y + V G     +  
Sbjct: 211 HEFGKTVHPCNRLDRLTSGLMFLGKNARGAEFFVKQIRERTVRKEYIARVKGKFPLGELT 270

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLR 256
           +   L    H       +   + +    A + F  I    +     ++ +P TGRTHQ+R
Sbjct: 271 VDEPL----HTVSPKHALNVVDHEKGKEAKTLFSRISYDPESDTSVVKCRPLTGRTHQIR 326

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           VH  ++G PI  D  Y + +    ++  + 
Sbjct: 327 VHLQYIGHPIANDPIYSSEYVWGDSNLGKG 356


>gi|209963797|ref|YP_002296712.1| RNA pseudouridine synthase, putative [Rhodospirillum centenum SW]
 gi|209957263|gb|ACI97899.1| RNA pseudouridine synthase, putative [Rhodospirillum centenum SW]
          Length = 242

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 65/208 (31%), Positives = 102/208 (49%), Gaps = 11/208 (5%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           +   +  +++ +L+ D+ + + +KP G+ V  G+    H++ +L      + + PRL HR
Sbjct: 1   MPYTAGEIRARVLHRDADVLILDKPHGLPVHYGTKTVEHLEQYLPWIAFEREEPPRLAHR 60

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG LV+AR    A  L   F    + K YW++V G P+     I   LLK    G
Sbjct: 61  LDKDTSGCLVLARDAEVAARLGRLFLHGHVGKTYWAVVLGRPRGDAGRIDLPLLKVHIPG 120

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
              V V    +     A++ ++++    +   WLE+ P TGR HQLR H    G PI+GD
Sbjct: 121 CSKVVV----DPDGKPALTDWRLLATDGR-LSWLELTPRTGRMHQLRAHCACSGFPILGD 175

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDL 297
             Y A        P    L+LHAR +  
Sbjct: 176 PIYGAE------QPPPVPLHLHARTVSF 197


>gi|148377981|ref|YP_001256857.1| ribosomal large subunit pseudouridine synthaseC [Mycoplasma
           agalactiae PG2]
 gi|148292027|emb|CAL59419.1| Ribosomal large subunit pseudouridine synthaseC [Mycoplasma
           agalactiae PG2]
          Length = 284

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 59/292 (20%), Positives = 114/292 (39%), Gaps = 30/292 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           +   + ++ +   +L ++  + +  +    + ++ R   ++V+ KR+   N  +++G  +
Sbjct: 1   MHKFIAQSSDNGRKLIKYIGSLFKKLPEGRIYRLFRQKSIKVNNKRITDSNYVVKTGDEI 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I  + +  + +I +             S  L S ++YED  I + NK AG  V G S  
Sbjct: 61  IIYGIKDEPSFVIYDN------------SWKLDSEIVYEDDNILLINKKAGTIVHGDSNC 108

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             +       +  +   +P    RLD+ TSG+++ A+       L       + + +   
Sbjct: 109 LDNQVFSYFKFRQNSAFRPSHVGRLDKWTSGLIMYAKNYQTLTEL-----NHKTEFLDKI 163

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V     N  + I +  +    +    V            A + F       +K   L  
Sbjct: 164 YVLKSDYNPHDEIVSVYIHHDELQQKMVATKNMQHPNDKIAKTRFF------KKDNKLYA 217

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q  TGR HQ+R    ++G PI GD KY +  KG        ++YLH   +  
Sbjct: 218 QLFTGRKHQIRATLEYLGYPIYGDSKYGSKTKGT------KRVYLHCYKLKF 263


>gi|238791583|ref|ZP_04635221.1| Pseudouridine synthase [Yersinia intermedia ATCC 29909]
 gi|238729199|gb|EEQ20715.1| Pseudouridine synthase [Yersinia intermedia ATCC 29909]
          Length = 232

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 57/220 (25%), Positives = 91/220 (41%), Gaps = 16/220 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                K  +LY+D  + + NKPAG+    G          +   +        L HRLD 
Sbjct: 11  PPCHDKIEILYQDDHLVLINKPAGLLSLSGKNPQN--LDSVHHRLVQIFPGCTLVHRLDF 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V+AR +     L + F  R + K+Y +L+ G   + +  I   + K   +    
Sbjct: 69  GTSGLMVIARNKVINAALCQQFSQRTVTKVYSALLCGHLDDNEGVIDAAIAKDPAL---- 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGC 264
             ++         A SH++V++ F              +++ P TGRTHQLR+H   +G 
Sbjct: 125 FPLMSICSIHGKPARSHYQVVERFYHELEDSTLLPLTRVQLTPETGRTHQLRIHCQQLGH 184

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           PI+G   Y              +L LHA  +   HP G  
Sbjct: 185 PILGCDLYGGRLLPGTER--APRLMLHASELHFNHPIGEE 222


>gi|256843689|ref|ZP_05549177.1| ribosomal protein large subunit [Lactobacillus crispatus 125-2-CHN]
 gi|312984138|ref|ZP_07791485.1| pseudouridylate synthase [Lactobacillus crispatus CTV-05]
 gi|256615109|gb|EEU20310.1| ribosomal protein large subunit [Lactobacillus crispatus 125-2-CHN]
 gi|310894492|gb|EFQ43567.1| pseudouridylate synthase [Lactobacillus crispatus CTV-05]
          Length = 285

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 62/299 (20%), Positives = 108/299 (36%), Gaps = 33/299 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M++   +    +     ++   +     I     +  LR    + V+     FN  I  G
Sbjct: 1   MSFRFTLFYPENLAPASVNEVLRQLL--IPR-KWRHFLRIEQNILVNGNYRYFNQNILPG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I      L+H+  +Q+    S  +          ++YED  + + NK  G      
Sbjct: 58  DKIEIN-----LDHVESDQQAYAPSGKM--------PDVIYEDDNLLIINKKKGQKTHPN 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  +  L       GQ P + HRLD  T G+L++A+  A    L      +   + 
Sbjct: 105 ---LNETNTALNDCTTYLGQSPYIVHRLDMLTGGLLLIAKNPAVVPILNRELTSKIFHRD 161

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V       ++  I   +                 +     A++H++V+        
Sbjct: 162 YLAKVINADHLAERGTINAPIGHDPLDQRKRKI-----DPTGLRAVTHYQVLQKNDDNTA 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            +++   TGRTHQ+RVH   +G PIVGD  Y  +F          +L L A  + L  P
Sbjct: 217 IVKLTLETGRTHQIRVHLASLGSPIVGDPLYNPDFASE-------RLALDAYEISLVQP 268


>gi|254423098|ref|ZP_05036816.1| pseudouridine synthase, RluA family [Synechococcus sp. PCC 7335]
 gi|196190587|gb|EDX85551.1| pseudouridine synthase, RluA family [Synechococcus sp. PCC 7335]
          Length = 328

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 73/334 (21%), Positives = 124/334 (37%), Gaps = 52/334 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V        +  ++   Y H      +  + + Q+ +D  R + N  ++ GQ++      
Sbjct: 12  VPAAAVGQTVLDFYTQRYRHSKRAVWKARIETEQILLDGDRTQENTLLKLGQILSY---- 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                         +     + +  L   +LYED  ++V NKPAG+ V    G   H   
Sbjct: 68  --------------ARSPWEEPAVPLDFDVLYEDEDLWVINKPAGLPVLPSGGFLEHTLL 113

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-------------- 177
           +         Q     HRL + TSG +++A++  A   L+E FR R              
Sbjct: 114 YQLRVRYRDCQSA-PVHRLGRGTSGAMLIAKSHIAKVQLSEQFRKRSANLSSNTTPNTAS 172

Query: 178 --RIQKIYWSLVWGIPKN--KKECIANWLLKK----------SHIGGDYVHVVKQNEKGA 223
              + K Y +L+     +  +   I  + + K           H+   + H        +
Sbjct: 173 TCTLGKTYRALIAPTTPDQLRDRFICTYPIGKLPHTRLGYIYGHLRDAHSHEKTIGPINS 232

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNF 280
             + S   V+   A     +E+   TGR HQ+R+H    G P++GD  Y          +
Sbjct: 233 MVSRSEGSVLRRRAHS-TLVEITIQTGRPHQIRIHLAAAGYPLLGDPLYSAGGVPDPHGY 291

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
             P     +LHA  +   HP  G+ + ITAP PA
Sbjct: 292 ALPGDCGYHLHAHRLQFAHPRTGQSIAITAPPPA 325


>gi|167752282|ref|ZP_02424409.1| hypothetical protein ALIPUT_00526 [Alistipes putredinis DSM 17216]
 gi|167660523|gb|EDS04653.1| hypothetical protein ALIPUT_00526 [Alistipes putredinis DSM 17216]
          Length = 236

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 61/225 (27%), Positives = 103/225 (45%), Gaps = 14/225 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
           F    +LYED+ + + NK  G  VQ        ++  +K ++  +  KP      + HR+
Sbjct: 2   FAPEDILYEDNHLLIVNKRCGDLVQPDPSGGDALERQIKEFIRRRDAKPGEVFLGVVHRI 61

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+  SG ++ A+T  A   L E  R   I+K YW+L    P  ++  + +++L+      
Sbjct: 62  DRPVSGAVIFAKTSKALARLNEMIRRGEIKKTYWALTESRPDPEEGELCHYILRNEKTNR 121

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                  + +  A  A   ++ +   A+ +  +E+   TGR HQ+R     +GCPI GD 
Sbjct: 122 SRALDAPRGD--AKLAKLRYRTLGASAR-YTLVEVDLLTGRHHQIRAQLSKIGCPIKGDL 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAH 314
           KY A       S     + LH+  +D  HP    R+ +TAP+P  
Sbjct: 179 KYGAR-----RSNPDGGISLHSYRVDFIHPVRRERIVVTAPVPKE 218


>gi|94499372|ref|ZP_01305910.1| hypothetical protein RED65_11299 [Oceanobacter sp. RED65]
 gi|94429004|gb|EAT13976.1| hypothetical protein RED65_11299 [Oceanobacter sp. RED65]
          Length = 236

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 111/243 (45%), Gaps = 24/243 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   NKP+G+ V          +  L+   D  G+     HRLD+ TSG
Sbjct: 5   MTPSILYQDDDLIAINKPSGLLVHKSWVAKDAKEFALQIVRDMSGKHVFPVHRLDRPTSG 64

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+   +   AQ +   +   +  K YW++V G    ++  + + L          +   
Sbjct: 65  VLLFGFSGEIAQQVQAQWE--QANKTYWAVVRG-WLKEQTLVDHAL--------KGMADY 113

Query: 217 KQNEKGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            Q+ +    A +HFK ID              +F W+E +P  GRTHQ+R H  H+  PI
Sbjct: 114 GQDVEIVQEAQTHFKPIDYVEIDAEIDRYPKSRFSWVEAKPKQGRTHQIRRHLKHLSHPI 173

Query: 267 VGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           +GD +Y       + +   +  +L LH + +++ HP  G +L ITAPL   M   + +  
Sbjct: 174 IGDARYGKGKYNRYITEHYDCPRLLLHHQQLEMTHPVSGSKLMITAPLEGAMQSLFSTFD 233

Query: 324 FKY 326
           +K+
Sbjct: 234 WKH 236


>gi|151945568|gb|EDN63809.1| DRAP deaminase [Saccharomyces cerevisiae YJM789]
 gi|256273956|gb|EEU08875.1| Rib2p [Saccharomyces cerevisiae JAY291]
 gi|323303146|gb|EGA56948.1| Rib2p [Saccharomyces cerevisiae FostersB]
 gi|323307078|gb|EGA60361.1| Rib2p [Saccharomyces cerevisiae FostersO]
          Length = 591

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 102/253 (40%), Gaps = 23/253 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +         K +  G+V ++ +    +  I+ G ++              E
Sbjct: 102 VDVFVSE-FRDREPSYYSKTIAEGKVYLNDEPANLDTIIRDGDLITHKVHR-------HE 153

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    ++           +++ED  I V +KP+ I V       Y  +   K      
Sbjct: 154 PPVTSKPID-----------IVFEDEDILVIDKPSSIPVHPTG--RYRFNTITKMLERQL 200

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G      +RLD+ TSG++ +A+T   A  + +  + R + K Y + V G        +  
Sbjct: 201 GYSVHPCNRLDKPTSGLMFLAKTPLGADRMGDQMKAREVTKEYVARVKGEFPIGIVEVDK 260

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             ++  +       V + +++ A +A + F+ +    Q    ++ +P TGRTHQ+RVH  
Sbjct: 261 P-VRSVNPKVALNAVCEMSDENAKHAKTVFQRVSYDGQ-TSIVKCKPLTGRTHQIRVHLQ 318

Query: 261 HMGCPIVGDHKYC 273
           ++G PI  D  Y 
Sbjct: 319 YLGFPIANDPIYS 331


>gi|269303280|gb|ACZ33380.1| RNA pseudouridine synthase family protein [Chlamydophila pneumoniae
           LPCoLN]
          Length = 283

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 65/292 (22%), Positives = 124/292 (42%), Gaps = 46/292 (15%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHII 78
           RL  + ++  P+ +   +   +R  + RV+    +F + ++Q G  V +  + +      
Sbjct: 13  RLSSFLRSQLPNHSKQEILASIRQHRCRVNGFIERFESYKVQPGDRVSLSLIPSTKQQ-- 70

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                 +L+ED    ++ KP  ++ +  + +             
Sbjct: 71  --------------------PSILWEDDYSIIYEKPPHLTTEQMAHMT------------ 98

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +    HRLD+ TSG L++ +++ AA  L + F+ R+I K Y +LV+G PK K   +
Sbjct: 99  ----RFFTVHRLDKGTSGCLLMGKSKQAATELMKLFKQRKIHKQYMALVFGHPKKKFGTV 154

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            ++        G  +       +G    I+ + V+D + +++  +  +P TGRTHQ+R+ 
Sbjct: 155 KSYTAPVYRRCGAVIFGAASPSQG-KLTITEWSVLDSY-KRYSLMLCKPITGRTHQIRLQ 212

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
              +G PIVGD  Y    +     P   +  LHA  ++   P     L+I A
Sbjct: 213 MGLLGHPIVGDVDYGPKEQP----PQIFRPLLHAHSLEFISPFTNLPLKICA 260


>gi|331007525|ref|ZP_08330690.1| Ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium IMCC1989]
 gi|330418674|gb|EGG93175.1| Ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium IMCC1989]
          Length = 248

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 101/229 (44%), Gaps = 25/229 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  I V NKP+G+    G          +   +  +     + HRLD  TSG++V+
Sbjct: 25  VVFEDEHILVINKPSGLLSLSGKNPLN--KDSVHYRLVQQYPTATMAHRLDFGTSGVMVL 82

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +    HLT  F+ R + K Y +++ G  ++ +  I   ++K +    +     K   
Sbjct: 83  ALNKTVNGHLTGQFQERTVSKTYTAILRGHIESDEGRIDIPIIKDT----NNFPYQKVCY 138

Query: 221 KGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                A+SH++V++         +   PHTGRTHQLR+H+  +G PI+G   Y  N +  
Sbjct: 139 TTGKSALSHYQVMERLHTPCSTRVLFTPHTGRTHQLRIHSQAIGHPILGCDLYGDNERDT 198

Query: 280 ---------------FTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
                           +  +  +L LHA  +   HP  G     ++T P
Sbjct: 199 DEKHSESVDNNNVTVSSLAMAERLLLHATTLGFEHPVSGERLVFEVTCP 247


>gi|312883220|ref|ZP_07742948.1| pseudouridylate synthase, 23S RNA-specific [Vibrio caribbenthicus
           ATCC BAA-2122]
 gi|309369083|gb|EFP96607.1| pseudouridylate synthase, 23S RNA-specific [Vibrio caribbenthicus
           ATCC BAA-2122]
          Length = 556

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 106/234 (45%), Gaps = 19/234 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   + ++ +  +   D     +++ED  + V NKP+G+    G  I    
Sbjct: 325 CQPILGHMLEGLNVDENPLEESWAKDK-PLDIIFEDDAMVVVNKPSGLLSVPGKTIKDSA 383

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++      + P + HRLD  TSG+LV A T+ A + L + F  RR+QK Y +L+ G
Sbjct: 384 YTRLQARY-PDAEGPFVIHRLDMATSGLLVFALTKRANKSLQKQFISRRVQKRYVALLSG 442

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   I+  + +   +      V  ++      A +H+++I+    K     + P T
Sbjct: 443 EVSQLSGDISLPM-RGDPVDRPRQLVCFEH---GKPAQTHWQLIENMEGKSKLY-LYPKT 497

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           GRTHQLRVH  H   +  PI GD  Y              +L LHA+ ++  HP
Sbjct: 498 GRTHQLRVHCAHHLGLNLPIDGDGLYGQK---------STRLCLHAQRLEFDHP 542


>gi|300775344|ref|ZP_07085206.1| ribosomal large subunit pseudouridine synthase D [Chryseobacterium
           gleum ATCC 35910]
 gi|300506084|gb|EFK37220.1| ribosomal large subunit pseudouridine synthase D [Chryseobacterium
           gleum ATCC 35910]
          Length = 225

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 67/223 (30%), Positives = 108/223 (48%), Gaps = 14/223 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           +K  ++YED+ + V NK  G  VQG       +   +K+++  +  KP      L HR+D
Sbjct: 1   MKEQIIYEDNHLLVVNKKVGQLVQGDKTGDESLLESIKNFIKIRDAKPGNVFLGLVHRID 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG+++ A+T  A   LT+  + R ++K YW++V      + + + ++L K      +
Sbjct: 61  RPTSGLVIYAKTSKALSRLTQMVKNREVKKTYWAVVGKEMIPQSQRLVHYLKKNEK--NN 118

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              V  +  +GA  AI  + VI      +  LE+   TGR HQ+R      G PI GD K
Sbjct: 119 KAIVFPKATEGAKEAILTYHVIKTL-DNYLLLEIDLETGRHHQIRAQLSKTGVPIKGDLK 177

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           Y A       S     + LHAR ++  HP     ++I AP+P 
Sbjct: 178 YGAP-----RSNPDGGINLHARKLEFIHPVTKENIEIIAPVPQ 215


>gi|121591256|ref|ZP_01678555.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           2740-80]
 gi|229527559|ref|ZP_04416951.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           12129(1)]
 gi|262401797|ref|ZP_06078362.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. RC586]
 gi|297581352|ref|ZP_06943275.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC385]
 gi|121546902|gb|EAX57056.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           2740-80]
 gi|229335191|gb|EEO00676.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           12129(1)]
 gi|262351769|gb|EEZ00900.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. RC586]
 gi|297534190|gb|EFH73028.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC385]
 gi|327484993|gb|AEA79400.1| Ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           LMA3894-4]
          Length = 245

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 69/254 (27%), Positives = 111/254 (43%), Gaps = 23/254 (9%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   ++YED  I   NKP+G+    G  +  H D      VD      ++ HRLD 
Sbjct: 8   PPKDPWIDVIYEDEHIIAANKPSGLLSVPGRPVE-HYDSMWARLVD-YCPDVKVVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+++ A+ +     L + F+ R   KIY++ VWG+ +  +  +   L        D+
Sbjct: 66  STSGLILFAKGKHMESALKKQFQYRLTHKIYYARVWGVMEQDEGEVNLPLC------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    +++ ++V+    +K   + + P TGR+HQLRVH   +G PIVGD 
Sbjct: 120 PNRPKQKVCFEEGRDSLTRYQVVKR-EEKTTVVRLIPITGRSHQLRVHMQSLGHPIVGDD 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM-----VKTWDSLGFK 325
            Y       F     ++L LHA  +   HP    L+ T  +P         +      F 
Sbjct: 179 LYAPQEAVEFA----DRLQLHAAELCFYHPRSHWLR-TLFVPCDFYPEAEEQILQH--FD 231

Query: 326 YDRNLYIKRLYSQD 339
            +R L   +  SQD
Sbjct: 232 PERKLPDYKKLSQD 245


>gi|58337856|ref|YP_194441.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus NCFM]
 gi|227904506|ref|ZP_04022311.1| pseudouridylate synthase RluD [Lactobacillus acidophilus ATCC 4796]
 gi|58255173|gb|AAV43410.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus NCFM]
 gi|227867761|gb|EEJ75182.1| pseudouridylate synthase RluD [Lactobacillus acidophilus ATCC 4796]
          Length = 281

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 68/295 (23%), Positives = 112/295 (37%), Gaps = 24/295 (8%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M Y   +    +   + ++   +     I     +  LR    V ++     FN ++  G
Sbjct: 1   MVYNFTLFYPKNLNPLPVNEVLRKLL--IPR-KWRHYLRIERNVTINGTYHHFNEQVFPG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I      L+HI   Q+I  +S NL          ++YED  + V NK  G      
Sbjct: 58  DRINI-----KLDHIDSLQQIYPASGNLPN--------IVYEDDDVLVINKNKGQKTHPN 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  D  L       G  P + HRLD  T G+L+VA+  A    L      +   + 
Sbjct: 105 ---LNETDTALNDCATYLGSSPYIVHRLDMLTGGLLLVAKNPAVVPILNRELTTKMFHRE 161

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y + V    K K + I ++ + +         V     K    A++H++++         
Sbjct: 162 YIAKVNNTDKLKNKGIIDFPIGQDPDDQRKRMVRSDGLK----AVTHYEILKTNPDNTGT 217

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +++   TGRTHQ+RVH    GCPI+GD  Y  NF+      +        +  D 
Sbjct: 218 VKLTLETGRTHQIRVHLAAKGCPIIGDPLYNPNFQEGEELQLTAYQMSFIKPFDF 272


>gi|327299994|ref|XP_003234690.1| DRAP deaminase [Trichophyton rubrum CBS 118892]
 gi|326463584|gb|EGD89037.1| DRAP deaminase [Trichophyton rubrum CBS 118892]
          Length = 517

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 107/283 (37%), Gaps = 46/283 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        +  +  G++ +D K    ++ I +GQV+              E
Sbjct: 64  LDIY-STEFRDRPNGYYKAAIDGGRITIDGKVATADSIINNGQVISHTLHR-------HE 115

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  I V +KPAGI V       Y+    +       
Sbjct: 116 PPVTSRPIK-----------IIHEDEDIIVIDKPAGIPVHPAGRYNYNSIIEIMRSERGL 164

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P   +RLD+ TSGI+ + +   AA+ + +S R R ++K Y + V G   +       
Sbjct: 165 GWIPYPCNRLDRLTSGIMFLGKHPKAAEQMAKSLRSRTLRKEYIARVKGYFPDGVVLCDQ 224

Query: 201 WLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCF----------------------- 236
            +LK S I G + V    ++ +     I+++  ++                         
Sbjct: 225 PMLKVSPILGLNRVRATGKDAQTKFRRIAYYPPVEKEDKNGEATSSQGPDSRASTPPPLP 284

Query: 237 ---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               + +  +   P TGRTHQ+RVH   +G PI  D  Y    
Sbjct: 285 ADVDEGYSIVHCLPLTGRTHQIRVHLQFLGHPITNDPIYSNRR 327


>gi|302663414|ref|XP_003023349.1| hypothetical protein TRV_02451 [Trichophyton verrucosum HKI 0517]
 gi|291187343|gb|EFE42731.1| hypothetical protein TRV_02451 [Trichophyton verrucosum HKI 0517]
          Length = 517

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 107/283 (37%), Gaps = 46/283 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        +  +  G++ +D K    ++ I +GQV+              E
Sbjct: 64  LDIY-STEFRDRPNGYYKAAIDGGRITIDGKVATADSIINNGQVISHTLHR-------HE 115

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  I V +KPAGI V       Y+    +       
Sbjct: 116 PPVTSRPIK-----------IIHEDEDIIVIDKPAGIPVHPAGRYNYNSIIEIMRSERGL 164

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P   +RLD+ TSGI+ + +   AA+ + +S R R ++K Y + V G   +       
Sbjct: 165 GWIPYPCNRLDRLTSGIMFLGKHPKAAEQMAQSLRSRTLRKEYIARVKGYFPDGVVLCDQ 224

Query: 201 WLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCF----------------------- 236
            +LK S I G + V    ++ +     I+++  ++                         
Sbjct: 225 PMLKVSPILGLNRVRATGKDAQTKFRRIAYYPPVEKEDKNGEATGSQGPDSRASTPPPLP 284

Query: 237 ---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               + +  +   P TGRTHQ+RVH   +G PI  D  Y    
Sbjct: 285 ADVDEGYSIVHCLPLTGRTHQIRVHLQFLGHPITNDPIYSNRR 327


>gi|325973159|ref|YP_004250223.1| tRNA pseudouridine synthase [Mycoplasma suis str. Illinois]
 gi|325989602|ref|YP_004249301.1| putative pseudouridine synthase [Mycoplasma suis KI3806]
 gi|323574687|emb|CBZ40343.1| probable pseudouridine synthase [Mycoplasma suis]
 gi|323651761|gb|ADX97843.1| tRNA pseudouridine synthase [Mycoplasma suis str. Illinois]
          Length = 337

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 69/270 (25%), Positives = 133/270 (49%), Gaps = 10/270 (3%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +  + +   E   L ++ K H+P+   + + K LR   + ++ +   F  +++ G  ++I
Sbjct: 6   ELKITDIRWEGYTLWKYIKLHFPYYTKLLIIKELRLKHILLNDESTYFQYKLKFGDTIKI 65

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA- 126
             + +      K              ++ +K  +++E++ + + NK A   VQ  S  + 
Sbjct: 66  FLLPDLSEIGKKRVNRAKLLDREEFKAETIKFQIVFENNDVIIINKKATQIVQPDSSSSN 125

Query: 127 YHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           Y ++  L+S++  K      KP+  HRLD+   G+++ A+   A   L+++ + R+IQK 
Sbjct: 126 YSLEELLQSYLKKKDPDSTYKPKFIHRLDKPVEGLIIGAKNAQAHSVLSQAIKDRKIQKF 185

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G    +++ + NW+L K       V V+ Q   G  Y+IS  + I  F   +  
Sbjct: 186 YKAIVLGCFPYREKQLENWILDKQ----SKVKVLDQENHGTKYSISIVRGIKKFP-NYSI 240

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +E++  TGR +Q+R    H+G PIVGD KY
Sbjct: 241 VEIKLVTGRKNQIRAQLSHLGYPIVGDRKY 270


>gi|90021296|ref|YP_527123.1| ribosomal large subunit pseudouridine synthase A [Saccharophagus
           degradans 2-40]
 gi|89950896|gb|ABD80911.1| ribosomal large subunit pseudouridine synthase A [Saccharophagus
           degradans 2-40]
          Length = 214

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 66/216 (30%), Positives = 106/216 (49%), Gaps = 18/216 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL+ D  I V NKP  +    G     +    L   V ++     + HRLD  TSG+++ 
Sbjct: 12  LLHCDEDIVVVNKPTDLLSVPGLASPQN----LFDRVKAQFPTALVVHRLDMATSGLMIF 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + A  HL + F  R I+K+Y ++V G+ + +   I++ L+       D+ +  KQ  
Sbjct: 68  ALNKPAQSHLGKQFERRTIKKMYVAVVHGLVEQQSGEISSPLI------CDWENRPKQKV 121

Query: 221 K--GANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                  A++ + V+D   A +   + + PHTGR+HQLRVH   +G PI+GD+ Y     
Sbjct: 122 DWLHGKPALTQYSVVDRNTAMQATRVHLFPHTGRSHQLRVHMQQIGHPIIGDYFYAPQDA 181

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            +  S    +L LHA+ ++L HP  G  +    P P
Sbjct: 182 DSCNS----RLLLHAQTLNLSHPTSGANIHFDCPAP 213


>gi|300869701|ref|YP_003784572.1| ribosomal large subunit pseudouridine synthase D [Brachyspira
           pilosicoli 95/1000]
 gi|300687400|gb|ADK30071.1| ribosomal large subunit pseudouridine synthase D [Brachyspira
           pilosicoli 95/1000]
          Length = 222

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 71/223 (31%), Positives = 109/223 (48%), Gaps = 17/223 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED    + NK +GI V         ID   K + + K  +  L HRLD+ TSGIL++
Sbjct: 13  IIYEDEYFLIINKESGIEV-----DDSLIDTIKKDYPNIK--ELFLVHRLDKYTSGILIL 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+      +   +F+ R I K+Y ++V G+PKN K  I   + K +      + V    +
Sbjct: 66  AKDNNTKTYFENAFKNREINKVYHAIVEGVPKNIKGTIDIQIAKDTKNPNKRIAV----K 121

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           KG   AI+H+KV+  F +    LE++P TGRTHQ+RVH  ++G PI+GD  Y  N K   
Sbjct: 122 KGGEIAITHYKVLKKF-KLHSLLELKPITGRTHQIRVHLSYLGNPIIGDKIYSKNAK--- 177

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                    L A+ +   HP   + + I        + +   L
Sbjct: 178 -LYNIKSFALIAKEIHFIHPITKKNIDIEIKYNKEFLNSLKVL 219


>gi|89074786|ref|ZP_01161240.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           sp. SKA34]
 gi|89049361|gb|EAR54923.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           sp. SKA34]
          Length = 557

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 109/243 (44%), Gaps = 20/243 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++   +I ++ +     ++  +  ++Y+D  + + NKPA      G  I   +
Sbjct: 326 CEPILAHMLSGIEIDENPLE-QNPAEGKELSIVYQDDAMVIINKPAEFLSVPGKAITDSV 384

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +++        P + HRLD  TSG++V+A T+ A + L + F  R ++K Y +L+ G
Sbjct: 385 YSRMQTMFPDSD-SPLIVHRLDMSTSGLMVIALTKDAHKALQKQFIERTVEKRYVALLEG 443

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             ++    I ++ ++          V  Q       A + ++V++        +   P T
Sbjct: 444 NSESDSGLI-DFPIRVDLDDRPRQIVCYQ---YGKPAQTTWEVLERK-NGRTKVYYYPKT 498

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVH+ H   M  PIVGD  Y             ++L LHA+Y+   HP    R+
Sbjct: 499 GRTHQLRVHSAHVKGMNMPIVGDDLYGQKG---------DRLCLHAQYLAFNHPTTNERM 549

Query: 306 QIT 308
              
Sbjct: 550 VFE 552


>gi|261200229|ref|XP_002626515.1| DRAP deaminase [Ajellomyces dermatitidis SLH14081]
 gi|239593587|gb|EEQ76168.1| DRAP deaminase [Ajellomyces dermatitidis SLH14081]
 gi|239607533|gb|EEQ84520.1| DRAP deaminase [Ajellomyces dermatitidis ER-3]
 gi|327352524|gb|EGE81381.1| DRAP deaminase [Ajellomyces dermatitidis ATCC 18188]
          Length = 549

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 62/305 (20%), Positives = 105/305 (34%), Gaps = 73/305 (23%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        QK +  G V ++ K V  + +IQ+G V+              E
Sbjct: 66  LDVFGAE-FRDRPREYYQKAIEDGAVCINGKAVSIDTKIQNGDVISHTLHR-------HE 117

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED+ + V +KPAG+ V       Y+    +       
Sbjct: 118 PPVTSQPIG-----------IIHEDNDMIVIDKPAGVPVHPAGRYNYNSVLEIMKAERGN 166

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P   +RLD+ TSG++ + +    A+ + E  R R ++K Y + V G   +       
Sbjct: 167 GWVPYPCNRLDRLTSGVMFIGKHPKGAEQIGEKLRSRTVRKEYVARVKGKFPDGVVLCDQ 226

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----------------------- 237
            +LK S I G     + +       A + F+ I  +                        
Sbjct: 227 PMLKISPILG-----LNRARASGKEARTKFRRIAYYPPHKQAEKTSGSSTGPATPPATLP 281

Query: 238 --------------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                                     + +  +   P TGRTHQLRVH  ++G PI  D  
Sbjct: 282 DQMNISDSPTDTPTGATTPIPMSLDEEGYSIVHCLPLTGRTHQLRVHLQYLGHPITNDPI 341

Query: 272 YCANF 276
           Y    
Sbjct: 342 YSNRR 346


>gi|227530063|ref|ZP_03960112.1| pseudouridylate synthase RluD [Lactobacillus vaginalis ATCC 49540]
 gi|227350031|gb|EEJ40322.1| pseudouridylate synthase RluD [Lactobacillus vaginalis ATCC 49540]
          Length = 300

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 70/296 (23%), Positives = 114/296 (38%), Gaps = 33/296 (11%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
               + H      Q       V V+ K    N  I  G  V +    +   H    Q I 
Sbjct: 31  LPKRFVHYLRSRRQ-------VLVNGKYHSMNTAIHPGDQVVLQFRGDEFRHPGNNQYIP 83

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
            ++  L          +LYE+  + V NKP G                +         + 
Sbjct: 84  TNNPKLD---------VLYENRDLLVVNKPRGQKSHPNETGETG--TLMNDVAGYLHHQA 132

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HR+D +TSG ++VA+       L     + +I + Y +LV G  K   E   +W + 
Sbjct: 133 YMVHRIDLQTSGAVIVAKNPVVVPILDRLISLGKIHREYLALVEGQIKGSGEW--DWPIG 190

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                   +   K N + +  A + ++ +   + K+  ++++  TGRTHQLRVH  + G 
Sbjct: 191 NDPSD---IRKRKVNGEHSQRAQTFYQTVKSNS-KYSLVDLRLGTGRTHQLRVHLEYSGH 246

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           PIVGD  Y  +           K++L+     L  P   R + ITAPLP +  +  
Sbjct: 247 PIVGDPIYNPSSAA--------KMHLNGYKQRLVVPFSNREITITAPLPDYFSQDL 294


>gi|156975908|ref|YP_001446815.1| ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           ATCC BAA-1116]
 gi|156527502|gb|ABU72588.1| hypothetical protein VIBHAR_03674 [Vibrio harveyi ATCC BAA-1116]
          Length = 250

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 106/231 (45%), Gaps = 15/231 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++ED +I   NKP+G+    G  +A H D       +      ++ HRLD  TSG++V
Sbjct: 15  DVVFEDEQILAVNKPSGLLSVPGR-LAEHYDSMWSRLTEQ-YPDIQVVHRLDMCTSGLMV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A   L + F+ R   KIY++ VWG  + ++  I   L+           V  ++
Sbjct: 73  LAKNKRAESALKKQFQYRLTHKIYYARVWGHIEQEEGEIDLPLICD-WPNRPLQKVCFED 131

Query: 220 EKGANYAISHFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K +    + F+V          K   + + P TGR+HQLRVH   +G PIVGD  Y   
Sbjct: 132 GKPSK---TLFQVAKREKHSDGSKTTIVRLLPITGRSHQLRVHMQALGHPIVGDEFYATE 188

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
               F+     +L LHA  +   HP    L+ +  +P       +++ F Y
Sbjct: 189 EAKAFSE----RLELHAAELSFYHPICHSLR-SIFVPCDFYPEAEAMIFDY 234


>gi|301168229|emb|CBW27818.1| putative ribosomal large subunit pseudouridine synthase D
           [Bacteriovorax marinus SJ]
          Length = 333

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 73/337 (21%), Positives = 142/337 (42%), Gaps = 31/337 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK--FNNRIQSGQVVRIPPVINALNH 76
           MRLD++ + +    +   ++K +  G + +  +  K   + +I +  ++ +  V      
Sbjct: 1   MRLDQYLQIYLASWSREQVKKKIAGGDILIKGRPGKHRPSTKIYTRDIITLVTVKTEHED 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                ++L+           LK  +++ED ++ + +KP  +S        ++        
Sbjct: 61  EYWNGELLELE---------LKPSIIFEDDELIIISKPPYMSTHPTGKHLFNCATVYFES 111

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKK 195
           +  K       HRLD+ETSG+L++A+T   AQ +T+ F    ++K Y+ + +      ++
Sbjct: 112 LYKK--TVHSIHRLDRETSGVLMLAKTPKCAQSMTDCFEKDLVRKCYFFIAYNKSWNGEQ 169

Query: 196 ECIANWLLKKSHIGGDYVHV--VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               N  L  S  G   V++    +       A + F+VI      +      P TGR H
Sbjct: 170 SFEDNHRLGASEEGLKRVYINHFPKESSEGKSARTLFRVIHSEGD-YVLGLAFPITGRQH 228

Query: 254 QLRVHALHMGCPIVGDHKYCANF------------KGNFTSPIQNKLYLHARYMDLPHPE 301
           Q+RVHA+  G P+VGD  Y  NF            K +      ++  LHA  +  P+ +
Sbjct: 229 QIRVHAMINGLPLVGDKLYLGNFKMFQRFKDNIATKEDHDLMEISRHALHAIALRAPY-K 287

Query: 302 GGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
           G     ++ +P  + + W +     D N   ++L  +
Sbjct: 288 GEEKVFSSHIPKDLQE-WITTNMTIDLNHLQEQLEEE 323


>gi|223986801|ref|ZP_03636783.1| hypothetical protein HOLDEFILI_04106 [Holdemania filiformis DSM
           12042]
 gi|223961234|gb|EEF65764.1| hypothetical protein HOLDEFILI_04106 [Holdemania filiformis DSM
           12042]
          Length = 225

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 62/223 (27%), Positives = 99/223 (44%), Gaps = 15/223 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           +K  +LYED+ + +  KP  ++VQ        +   LK  +  + QKP      L HRLD
Sbjct: 1   MKFKILYEDNHLLIVVKPVNMAVQADDSRDPDLLTLLKQDLKERYQKPGNVYLGLVHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +   G++V A+T  AA  L++  R R ++K Y +++ G P+     + +WL+K       
Sbjct: 61  RPVGGVMVFAKTSKAASRLSDQVRTRGLKKTYQAVLCGRPQAASATLKDWLIKNEKTN-- 118

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V     N   A  AI  ++ I    +     E+Q  TGR HQ+RV       P+ GD +
Sbjct: 119 TVRTAAPNTPKAKEAILSYQ-IQGEKEGLTLAEIQLETGRPHQIRVQFASRRTPLWGDQR 177

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           Y    +         ++ L A  + L HP     +  T P P 
Sbjct: 178 YNPQARPG------QQIALWAVSLTLRHPVTQETMTFTCPPPD 214


>gi|147673149|ref|YP_001218003.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|153829796|ref|ZP_01982463.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           623-39]
 gi|229513432|ref|ZP_04402896.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           TMA 21]
 gi|254225904|ref|ZP_04919506.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V51]
 gi|254291423|ref|ZP_04962215.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           AM-19226]
 gi|258622801|ref|ZP_05717819.1| Ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM573]
 gi|258625826|ref|ZP_05720705.1| Ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM603]
 gi|262166537|ref|ZP_06034274.1| ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM223]
 gi|262167535|ref|ZP_06035240.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC27]
 gi|262170551|ref|ZP_06038229.1| ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           MB-451]
 gi|125621530|gb|EAZ49862.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V51]
 gi|146315032|gb|ABQ19571.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|148874714|gb|EDL72849.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           623-39]
 gi|150422613|gb|EDN14568.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           AM-19226]
 gi|227014395|gb|ACP10605.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|229349309|gb|EEO14265.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           TMA 21]
 gi|258582064|gb|EEW06934.1| Ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM603]
 gi|258584989|gb|EEW09720.1| Ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM573]
 gi|261891627|gb|EEY37613.1| ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           MB-451]
 gi|262023988|gb|EEY42684.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC27]
 gi|262026253|gb|EEY44921.1| ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM223]
          Length = 245

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 69/247 (27%), Positives = 111/247 (44%), Gaps = 23/247 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++YED  I   NKP+G+    G  +  H D      VD      ++ HRLD  TSG+++
Sbjct: 15  DVIYEDEHIIAANKPSGLLSVPGRPVE-HYDSMWARLVD-YCPDVKVVHRLDMSTSGLIL 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+ +     L + F+ R   KIY++ VWG+ +  +  +   L        D+ +  KQ 
Sbjct: 73  FAKGKHMESALKKQFQYRLTHKIYYARVWGVMEQDEGEVNLPLC------CDWPNRPKQK 126

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              +    +++ ++V+    +K   + + P TGR+HQLRVH   +G PIVGD  Y     
Sbjct: 127 VCFEEGRDSLTRYQVVKR-EEKTTVVRLIPITGRSHQLRVHMQSLGHPIVGDDLYAPQEA 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM-----VKTWDSLGFKYDRNLYI 332
             F     ++L LHA  +   HP    L+ T  +P         +      F  +R L  
Sbjct: 186 VEFA----DRLQLHAAELCFYHPRSHWLR-TLFVPCDFYPEAEEQILQH--FDPERKLPD 238

Query: 333 KRLYSQD 339
            +  SQD
Sbjct: 239 YKKLSQD 245


>gi|329897136|ref|ZP_08271879.1| tRNA pseudouridine synthase C [gamma proteobacterium IMCC3088]
 gi|328921394|gb|EGG28785.1| tRNA pseudouridine synthase C [gamma proteobacterium IMCC3088]
          Length = 239

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 103/237 (43%), Gaps = 24/237 (10%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y D  +   NKP G+ V      A+     L+   D  GQ+    HRLD+ TSG+L
Sbjct: 8   PQVIYSDDNLVAINKPPGMLVHRTKLDAHETVFALQWVRDHVGQRVYPLHRLDKATSGVL 67

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
             A++   A+H ++++    + K Y +LV G P N K  I + L                
Sbjct: 68  AFAKSSKVARHWSDAWHTDAVHKDYLALVRGWP-NSKGTIDHPLRDPDSAPDSPR----- 121

Query: 219 NEKGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                  A + F++ID              +F  L++ P TGR HQLR H  H+  PI+G
Sbjct: 122 -----KEAETTFEIIDKYLININIDRYPMSRFSLLQLSPLTGRRHQLRQHLKHINHPIIG 176

Query: 269 DHKYCANF--KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
           D +Y      +       + +L+LHA  + L      R+ ITAP   H+ +T +   
Sbjct: 177 DVRYGKGTYNRWARDQFGETRLFLHAHQLRLDDGVT-RITITAPPNPHLQQTLEFFR 232


>gi|325111150|ref|YP_004272218.1| hypothetical protein Plabr_4625 [Planctomyces brasiliensis DSM
           5305]
 gi|324971418|gb|ADY62196.1| UPF0176 protein yceA [Planctomyces brasiliensis DSM 5305]
          Length = 621

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 70/313 (22%), Positives = 123/313 (39%), Gaps = 27/313 (8%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T  + + V     +  L  +  +++PH++  +   +  +G +R   +  + +  +  GQ 
Sbjct: 314 TNERPLNVPQKYHDWTLLDFLADYHPHVSREDWASVCEAGLIRYRDRAWQADQLVWEGQR 373

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +           +  E   ++  VN           L+   +++ VF+KPA + V     
Sbjct: 374 L-----------LRLEPNTIEPDVNPNIK-------LITWQNQLVVFDKPAPLPVHPCGR 415

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              +    L      +  K R  HRLD  T+G++V    R  +  +   F     +K Y 
Sbjct: 416 FNKNSMTMLLDLAFPET-KLRPAHRLDANTTGLIVFTSHRDHSLRIQRQFERGEAEKTYL 474

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
             V G P  +K      + + +   G        +E+    A + F+V+         +E
Sbjct: 475 CRVNGQPTEEKFRCDLPISRDTAEAGAR----CIDEENGLSASTEFRVLKRLDDGTALVE 530

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT---SPIQNKLYLHARYMDLPHPE 301
            +P TGRT+Q+RVH  H+G PI+ D  Y    K             + LH+  + L  PE
Sbjct: 531 AKPLTGRTNQIRVHLWHLGFPILNDSVYLPEQKIGEKITHDVSAQPMCLHSWKLRLREPE 590

Query: 302 GGR-LQITAPLPA 313
            G  L    PLPA
Sbjct: 591 TGEGLNFETPLPA 603


>gi|317054867|ref|YP_004103334.1| pseudouridine synthase [Ruminococcus albus 7]
 gi|315447136|gb|ADU20700.1| pseudouridine synthase [Ruminococcus albus 7]
          Length = 276

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 63/301 (20%), Positives = 114/301 (37%), Gaps = 41/301 (13%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           YV+ + V  +E+   +    +      +   L K+  S  + +D  +++       GQ +
Sbjct: 5   YVRTLTVTLEEDGRSVKDILRAR--GFSRRLLTKLKLSDGICLDGAKIRVTAPAYEGQKI 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                 +      + +  L   +LYED  + VF+KPA + V      
Sbjct: 63  TVT----------------EPGQTAPEPNPLLDVPVLYEDGDVIVFDKPADMPVHES--- 103

Query: 126 AYHIDGFLKSWV--DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             H    L ++     KG   R  +RLD++T+G + VA+TR AA  L  S        I 
Sbjct: 104 INHRGDTLANFFACRCKGLTFRTVNRLDRDTAGCVCVAKTRYAANALAGSISKVYCGLIP 163

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            + + G        +   + ++         +++       Y+ + ++VI+         
Sbjct: 164 LTKLSG------GRVCAPIARERE-----SVILRCVRADGKYSATCWQVIERRKDSV-LC 211

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                TGRTHQ+RVH  H+G P++GD  Y  +              L    +    PE G
Sbjct: 212 RFLLETGRTHQIRVHMAHIGLPLIGDEMYGGDTSNR------KGQALMCSEVSFISPESG 265

Query: 304 R 304
           +
Sbjct: 266 K 266


>gi|289669903|ref|ZP_06490978.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 272

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 105/237 (44%), Gaps = 24/237 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V +KPAG+            D       +  G+   L HRLD+ TSG L++
Sbjct: 44  ILYQDDVLAVVDKPAGLMAHDSKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLLL 103

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  RA+A  L ++     ++K Y ++  G P  ++  + + L       G     VK   
Sbjct: 104 AFDRASASVLGKALMAGEVEKNYLTVCRGWPAEEQFIVDHDL------DGGPGKPVK--- 154

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD 
Sbjct: 155 ---KPAVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGDA 211

Query: 271 KYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            +       +F     +++ LHA  ++ PHP +G R+ +TAPL A   K     G+ 
Sbjct: 212 SHGDGRHNRSFRMLGIHRMLLHAERLEFPHPADGRRISVTAPLDAEFTKACTFFGWD 268


>gi|255037507|ref|YP_003088128.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
 gi|254950263|gb|ACT94963.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
          Length = 255

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 98/243 (40%), Gaps = 24/243 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
            K I+++ED    V NKP  ++            G +         + +  HRLD+ETSG
Sbjct: 20  FKDIIIFEDEDFLVVNKPPHLATLDERTADRG--GSVLRLAKEYNPELQAAHRLDKETSG 77

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            L  A+  AA +HL   F  R + K Y ++V GI   +   +   +L            V
Sbjct: 78  ALAFAKNPAAYRHLAMQFEHREVTKRYHAVVNGIHDLEGISVYLPIL-----PLKNGTAV 132

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K +      A + F  +  + + +  +E  P TGR HQ+R+H   +  PIV D +Y    
Sbjct: 133 KIDRADGKEAETIFNTLQVY-RGYTLVECIPITGRMHQIRIHLSCLKAPIVNDPQYGGEP 191

Query: 277 -------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM---VKTWD 320
                        K     P+  ++ LHAR +      G  +++ AP P      VK  +
Sbjct: 192 IFLSNLKRKFNLKKDTEEQPLIQRVALHARSLSFALMNGEDIRVEAPYPKDFEVLVKQLN 251

Query: 321 SLG 323
             G
Sbjct: 252 KFG 254


>gi|161507907|ref|YP_001577871.1| ribosomal protein large subunit [Lactobacillus helveticus DPC 4571]
 gi|160348896|gb|ABX27570.1| ribosomal protein large subunit [Lactobacillus helveticus DPC 4571]
          Length = 285

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 69/317 (21%), Positives = 117/317 (36%), Gaps = 34/317 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M Y   +    + E + ++   +     I     +  LR    + ++     FN  +  G
Sbjct: 1   MVYHFTLFYPKNLEPLPVNDVLRKLL--IPR-KWRHYLRIEQNITINGTYRYFNQNVLPG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I      L+ +   Q+   +S  L          ++YED  + + NK  G      
Sbjct: 58  DKIDI-----ILDQVDSAQQKYPASGKL--------PDIIYEDDNLLIINKKKGQKTHPN 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  +  L       GQ P + HRLD  T G+L+VA+  A    L      +   + 
Sbjct: 105 ---LNETNTTLNDCATYLGQSPYIVHRLDMLTGGLLLVAKNPAVVPILNRELTSKTFHRD 161

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V    K + +  I   +          +           +A++H++V+        
Sbjct: 162 YLAKVDHADKLSDQGTINQPIDHDPEDQRKRMI-----SPAGLHAVTHYQVLKRNDNNTA 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++   TGRTHQ+RVH   +G PI+GD  Y  NF G         L L A  + L  P 
Sbjct: 217 VVKLTLETGRTHQIRVHLASLGTPIIGDPLYNPNFGGED-------LALDAYEISLIKPF 269

Query: 302 GGRLQITAPLPAHMVKT 318
               ++T  LP   +K 
Sbjct: 270 SFE-KLTVKLPEEGIKL 285


>gi|269103546|ref|ZP_06156243.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268163444|gb|EEZ41940.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 241

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 67/247 (27%), Positives = 113/247 (45%), Gaps = 19/247 (7%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E  +    +            +L+ D  I   NKP+G+    G   A++    + S V  
Sbjct: 8   ESAMKPLPLLDYNPPQDPWLDVLHLDRDIIAVNKPSGLLSVPGRDPAHYDS--IYSRVLR 65

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              K ++ HRLD  TSG++V+A  + A +HL   FR R+  K+Y++ VWG  + +   + 
Sbjct: 66  DHPKSQIVHRLDMTTSGLIVLAINKNAERHLKAQFRERQTHKVYYARVWGHLEQQHGSVD 125

Query: 200 NWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             L+       D+ +  KQ    +    +++H++V+  + +    + + P TGR+HQLRV
Sbjct: 126 LPLI------CDWPNRPKQKVCYEEGKPSLTHYEVV-RYEENATLVRLLPVTGRSHQLRV 178

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP---LPA 313
           H + +G PI+GD  Y  +           +L LHA  +   HP     + I AP    P 
Sbjct: 179 HMMAIGHPILGDRFYAHDEAREMA----PRLQLHAAELTFAHPYTEEPMHIFAPCDFYPD 234

Query: 314 HMVKTWD 320
              +T D
Sbjct: 235 APTRTLD 241


>gi|89075424|ref|ZP_01161841.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           sp. SKA34]
 gi|89048840|gb|EAR54410.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           sp. SKA34]
          Length = 245

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 59/244 (24%), Positives = 99/244 (40%), Gaps = 17/244 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +LY D  +   NKPAG+ V      ++     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELEILYRDDYLIAVNKPAGMLVHRSWLDSHETVFVMQTLRDQIGQHVFPLHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+   +   A  +   F  R + K Y ++V G  K          ++   I        
Sbjct: 61  VLLFGLSSEIASQMMPLFAGRDMHKTYHAVVRGWIKEAAVLDYPLKVELDKIADKNAS-- 118

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              EK A  A++ ++ +               ++C +EM+P TGR HQLR H  H+   I
Sbjct: 119 --EEKEAQPAVTAYEPLATVETDIAVGRYSTSRYCLVEMKPETGRKHQLRRHMHHLSHHI 176

Query: 267 VGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD  +             +  +L LHA  +   HP  G  + I A +     K   +  
Sbjct: 177 IGDVNHGDGRHNRMFREHYDCHRLMLHASRLQFDHPITGDSIDICADIDETWHKVMTAFN 236

Query: 324 FKYD 327
           +  +
Sbjct: 237 WSLN 240


>gi|223940477|ref|ZP_03632327.1| pseudouridine synthase [bacterium Ellin514]
 gi|223890839|gb|EEF57350.1| pseudouridine synthase [bacterium Ellin514]
          Length = 536

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 65/217 (29%), Positives = 103/217 (47%), Gaps = 15/217 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +    ++L+ED  + V NKPAG++    S  A           + +     + HRLD+ET
Sbjct: 6   EEAGRLILFEDEHLLVVNKPAGMNTHAPSPYAGEGIYEWLKHREPRWASLAIVHRLDKET 65

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++V  +T  A + LTE F    I+K Y  L   +  ++   + + L++   +G  Y+ 
Sbjct: 66  SGVMVFGKTTVANRSLTEQFTNHSIRKKYLLLTDKVVSSQTSTMVSCLVR---VGEKYLS 122

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             +    G   A +HF+VI   A+    +E +P TGRTHQ+RVHA   G PI+GD  Y  
Sbjct: 123 --RPVHAGGEKAETHFEVI-TKAEGGTLVEAEPITGRTHQIRVHAAEQGFPILGDALYGG 179

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
                      +++ LHA  + L HP     +   A 
Sbjct: 180 TKA--------SRVCLHAAELKLKHPGTNAEMTFRAE 208


>gi|269963388|ref|ZP_06177716.1| Ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           1DA3]
 gi|269831867|gb|EEZ85998.1| Ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           1DA3]
          Length = 250

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 108/231 (46%), Gaps = 15/231 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++ED +I   NKP+G+    G    +H    + S +  +    ++ HRLD  TSG++V
Sbjct: 15  DVVFEDEQILAVNKPSGLLSVPGRLAEHHDS--MWSRLTEQYPDIQVVHRLDMCTSGLMV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A   L + F+ R   KIY++ VWG  K ++  I   L+           V  ++
Sbjct: 73  LAKNKRAESALKKQFQYRLTHKIYYARVWGHLKQEEGEIDLPLICD-WPNRPLQKVCFED 131

Query: 220 EKGANYAISHFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K +    + F+V          K   + + P TGR+HQLRVH   +G PIVGD  Y   
Sbjct: 132 GKPSK---TLFQVAKREEHPDGSKTTIVRLLPITGRSHQLRVHMQALGHPIVGDEFYATE 188

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
               F+     +L LHA  +   HP+   L+ +  +P       +++ F Y
Sbjct: 189 EAKAFSE----RLELHAAELSFYHPKCHWLR-SIFVPCDFYPEAEAMIFDY 234


>gi|226952242|ref|ZP_03822706.1| RluA-like dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification [Acinetobacter sp. ATCC 27244]
 gi|294648812|ref|ZP_06726269.1| conserved hypothetical protein [Acinetobacter haemolyticus ATCC
           19194]
 gi|226837080|gb|EEH69463.1| RluA-like dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification [Acinetobacter sp. ATCC 27244]
 gi|292825304|gb|EFF84050.1| conserved hypothetical protein [Acinetobacter haemolyticus ATCC
           19194]
          Length = 221

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 105/225 (46%), Gaps = 13/225 (5%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           N           +LYED  + V NKPAG+    G    +    +L+  V  K    ++TH
Sbjct: 6   NFIYTPPQQPLEILYEDDDLVVVNKPAGLLSVMGRLPEHQDSAYLR--VLEKYPSAKVTH 63

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G  + +       +    + 
Sbjct: 64  RLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKYYEALVQGKIQAEGSVEVPLITDWENR 123

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               VH      +    A + ++ +   A+     + ++P TGR+HQLRVH +H+G PI+
Sbjct: 124 PRQMVHF-----ELGKPAKTLYQSLHYDAETDQSRVRLEPVTGRSHQLRVHMMHIGHPIM 178

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           GD  Y              ++ LHA Y+   HP   + ++I A +
Sbjct: 179 GDKLYHPEP----AKFHLKRMALHAAYLAFQHPFHQQNIEIHAEV 219


>gi|253988053|ref|YP_003039409.1| ribosomal large subunit pseudouridine synthase A [Photorhabdus
           asymbiotica subsp. asymbiotica ATCC 43949]
 gi|253779503|emb|CAQ82664.1| ribosomal large subunit pseudouridine synthase A [Photorhabdus
           asymbiotica]
          Length = 230

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 104/236 (44%), Gaps = 22/236 (9%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           S+            +LY+D  I V NKP+G+    G     H D  + + +  +      
Sbjct: 14  SMEAYNPPTDPWLHVLYQDQHIIVVNKPSGLLSVPGRA-EEHKDSIM-TRIQQQFPAAES 71

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  TSGI+VVA T+ A + L   FR R  +K Y + VWG  K +   +   L+   
Sbjct: 72  VHRLDMATSGIMVVALTKDAERELKRQFREREPKKTYIARVWGYLKPETGTVDLPLI--- 128

Query: 207 HIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               D+ +  KQ         A + ++V+  +  +   +++ P TGR+HQLRVH L +  
Sbjct: 129 ---CDWPNRPKQKVCFDTGKSAQTEYEVL-VYEDQATRVKLSPITGRSHQLRVHMLALEH 184

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           PI+GD  Y              +L LHA+ + + HP  G        P H   T D
Sbjct: 185 PILGDRFYAHQQARAMA----PRLQLHAQELYITHPAYGT-------PMHFQCTAD 229


>gi|91215096|ref|ZP_01252068.1| hypothetical protein P700755_12402 [Psychroflexus torquis ATCC
           700755]
 gi|91186701|gb|EAS73072.1| hypothetical protein P700755_12402 [Psychroflexus torquis ATCC
           700755]
          Length = 292

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 75/296 (25%), Positives = 133/296 (44%), Gaps = 49/296 (16%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
               L+K ++ G + +D +  + ++ I+ GQV+ +         ++ ++K+         
Sbjct: 37  TKSALKKAIKKGLLFLDGRVAETSDWIEEGQVLELF-----AEELLYKKKVFP------- 84

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLK-SWVDSKGQKPRLTHR 149
               L+  +++ED  + V NKP G    G     I   +   LK S    K   P+  HR
Sbjct: 85  ----LQLKVIFEDDSMAVVNKPEGYPTNGNYFKTIENALTYNLKTSSEKDKLPYPQPVHR 140

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG+L++A+T ++  +L+  F   ++ KIY ++V G  +   + I+  +       
Sbjct: 141 LDNPTSGLLIIAKTLSSKSYLSVLFEHNKVHKIYLAIVEGHFEGLSDIISLDI------- 193

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                           + +++ V   F     +F  L ++P +GRTHQLR+H   +G PI
Sbjct: 194 ------------DGKQSSTNYGVEKMFKINQDEFSLLSLKPSSGRTHQLRIHLSKIGHPI 241

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           VGD  Y +         + NKL LHA  ++L HP+  + L     +P   VK  + 
Sbjct: 242 VGDKTYGS-------LTLSNKLMLHASSLELRHPKTDKSLSFETEVPHKFVKFINR 290


>gi|225556035|gb|EEH04325.1| DRAP deaminase [Ajellomyces capsulatus G186AR]
          Length = 545

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 69/351 (19%), Positives = 118/351 (33%), Gaps = 82/351 (23%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        QK +  G V ++ K V  + +IQ+G V+         +H +  
Sbjct: 66  LDVF-GTEFRDRPKEYYQKAIEDGAVCINGKAVSIDTKIQNGDVI---------SHTLHR 115

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            +   +S  ++         +++ED  + V +KPAG+ V       Y+    +       
Sbjct: 116 HEPPVTSQPIS---------IIHEDDDMIVIDKPAGVPVHPAGRYNYNSILEIMKAERGN 166

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P   +RLD+ TSG++ + +    A+ + E  R R ++K Y + V G   +       
Sbjct: 167 GWVPYPCNRLDRLTSGVMFIGKHPKGAEQIGEKLRSRTVRKEYVARVKGKFPDGVVLCDQ 226

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----------------------- 237
            +LK S I G     + +       A + F+ I  +                        
Sbjct: 227 PMLKISPILG-----LNRARASGKEARTKFRRIAYYPPHKQAGKKQGLSAGPATPPATLP 281

Query: 238 --------------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                                     + +  +   P TGRTHQLRVH  ++G PI  D  
Sbjct: 282 DQMNISDSQTDTPTGAAIPVPMSPDEEGYSIVHCLPLTGRTHQLRVHLQYLGHPITNDPI 341

Query: 272 YCANF-------KGNFTSPIQNKLYLHARYMDLPHPEG--GRLQITAPLPA 313
           Y           K + T     ++      M    P           P P 
Sbjct: 342 YSNRRVFGHSLGKADATGENDEQIIYRLSKMGKTEPVDSLSYQTFQTPPPE 392


>gi|260593437|ref|ZP_05858895.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           veroralis F0319]
 gi|260534713|gb|EEX17330.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           veroralis F0319]
          Length = 565

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 73/258 (28%), Positives = 115/258 (44%), Gaps = 30/258 (11%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  ++  L   + E+KI+ S+    K ++ +K   LYED  + V  KP+G+    G G  
Sbjct: 325 LEWMLKGLQTPLCEEKIVPSN---KKEAERIKLETLYEDDYLAVVVKPSGLLSVPGKGDK 381

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   LK+  + K     + HRLD  TSG+LVVAR+    + L   F  R ++K Y +L
Sbjct: 382 PSVYSLLKTQWNGKS-DVFIVHRLDMATSGLLVVARSLEIYKALQAQFIQRSVKKTYVAL 440

Query: 187 VWGIPKNK----KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--- 239
           +     +K       I   L     I       V         AI+ + VI   +     
Sbjct: 441 LPMSFLDKAYPSSGRIELPL--SPDINDRPRQCVDYLH--GKRAITDYHVIGETSYGKEN 496

Query: 240 --FCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                +E+ P TGRTHQLR+H  H   +  PI+GD+ Y    +         +L+LHA +
Sbjct: 497 LPAVKIELHPLTGRTHQLRIHCAHPDGLDTPIIGDNLYGQRAE---------RLWLHAEH 547

Query: 295 MDLPHPEG-GRLQITAPL 311
           ++  +P    R+   APL
Sbjct: 548 LEFTYPITQERMVFNAPL 565


>gi|227878113|ref|ZP_03996093.1| pseudouridylate synthase RluD [Lactobacillus crispatus JV-V01]
 gi|256850157|ref|ZP_05555587.1| ribosomal protein large subunit [Lactobacillus crispatus MV-1A-US]
 gi|262047720|ref|ZP_06020673.1| ribosomal protein large subunit [Lactobacillus crispatus MV-3A-US]
 gi|295693421|ref|YP_003602031.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|227862283|gb|EEJ69822.1| pseudouridylate synthase RluD [Lactobacillus crispatus JV-V01]
 gi|256713129|gb|EEU28120.1| ribosomal protein large subunit [Lactobacillus crispatus MV-1A-US]
 gi|260572005|gb|EEX28572.1| ribosomal protein large subunit [Lactobacillus crispatus MV-3A-US]
 gi|295031527|emb|CBL51006.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
          Length = 285

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 62/299 (20%), Positives = 108/299 (36%), Gaps = 33/299 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M++   +    +     ++   +     I     +  LR    + V+     FN  I  G
Sbjct: 1   MSFHFTLFYPENLAPASVNEVLRQLL--IPR-KWRHFLRIEQNILVNGNYRYFNQNILPG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I      L+H+  +Q+    S  +          ++YED  + + NK  G      
Sbjct: 58  DKIEIN-----LDHVESDQQAYAPSGKM--------PDVIYEDDNLLIINKKKGQKTHPN 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  +  L       GQ P + HRLD  T G+L++A+  A    L      +   + 
Sbjct: 105 ---LNETNTALNDCTTYLGQSPYIVHRLDMLTGGLLLIAKNPAVVPILNRELTSKIFHRD 161

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V       ++  I   +                 +     A++H++V+        
Sbjct: 162 YLAKVINADHLAERGTINAPIGHDPLDQRKRKI-----DPTGLRAVTHYQVLQKNDDNTA 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            +++   TGRTHQ+RVH   +G PIVGD  Y  +F          +L L A  + L  P
Sbjct: 217 IVKLTLETGRTHQIRVHLASLGSPIVGDPLYNPDFASE-------RLALDAYEISLVQP 268


>gi|197128104|gb|ACH44602.1| putative RIKEN cDNA 2410001E19 [Taeniopygia guttata]
          Length = 283

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 80/280 (28%), Positives = 127/280 (45%), Gaps = 40/280 (14%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQ 142
            V+    +  LK   LY++ +I V +KP G+ V GG GI   I   L    K   + K +
Sbjct: 7   QVHPNVLAKILKQRTLYQNEEIVVIDKPYGLPVHGGPGIKNCIADVLPILAKMLENMKAE 66

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD+ET+G++V+AR++ AA+ +   F+ R+++KIYW++V G P   +  +   +
Sbjct: 67  PLHLCHRLDKETTGVMVLARSKEAAEKIRLLFKTRQVEKIYWAIVLGDPDPVEGVVEIPI 126

Query: 203 LKKSHIGG-----------------DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           ++K                      D   +  +  + A  A++ ++ + C A     LE+
Sbjct: 127 VEKEVQSHQSHYKMTLAPNYRLCPEDGKVMKTRGSRHAERAVTRYRRL-CAASACSLLEL 185

Query: 246 QPHTGRTHQLRVHALH-MGCPIVGDHKYC---------------ANFKGNFTSPIQNKLY 289
           QP TG  HQ+RVH  + +GCPI+GDHKY                   K   +      L+
Sbjct: 186 QPVTGVKHQIRVHLAYGLGCPILGDHKYSHWSKLAPQKLPEHTLRRLKLEQSKARHLPLH 245

Query: 290 LHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
           LHA  + L    G  L     LP    KT   L     ++
Sbjct: 246 LHAHRLCLH--LGQPLDFVCKLPLFFQKTLRKLELDIPKD 283


>gi|149194782|ref|ZP_01871877.1| Pseudouridine synthase, RluD [Caminibacter mediatlanticus TB-2]
 gi|149135205|gb|EDM23686.1| Pseudouridine synthase, RluD [Caminibacter mediatlanticus TB-2]
          Length = 293

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 64/298 (21%), Positives = 115/298 (38%), Gaps = 45/298 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +        N    ++ +  G+V ++ KRV   +   SG  +    V     + +K 
Sbjct: 16  LD-FLVKKL-GFNLREAKRAIDRGRVSINGKRVTQKSFKASG--ILKCIVFEPNGYGLKP 71

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                                ++E     +F+KP+G+++        +    L       
Sbjct: 72  ---------------------IFETDHFAIFDKPSGVAIHPKK--LANTKSLLDDVRLLY 108

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G    L HRLD+ETSG+++ ++ + A   L ++F+ + IQK Y +L+ G   +K+  I  
Sbjct: 109 GNDANLVHRLDKETSGLVIASKNKFAESILKQAFQNKEIQKKYLALIKGHL-DKEITIKK 167

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +        + + V          +I+  K I    +    +E  P TGR HQ+R+H  
Sbjct: 168 PIAVNK---DENIKVKVIISDEGKESITLVKPIKKIGKN-TLVECIPLTGRQHQIRIHLY 223

Query: 261 HMGCPIVGDHKYCANFK-------------GNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            +G PIVGD  Y  + +                     N+L LHA  ++        +
Sbjct: 224 SIGHPIVGDPLYGVDNEFADKYLKKLVDENERIQKTGANRLMLHAYKLEFEFMNNKYI 281


>gi|59713667|ref|YP_206442.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           ES114]
 gi|59481915|gb|AAW87554.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           ES114]
          Length = 576

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 104/249 (41%), Gaps = 20/249 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++ E    D S      S   +  ++YED  + + NKP       G  I+  +
Sbjct: 345 CFEILEHML-EGISTDGSPLEQTPSYGKELEIVYEDDVLVIVNKPVEFLSVSGKYISDSV 403

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +++        P + HRLD  TSG+LV+  T  + + + + F  R ++K Y +L+ G
Sbjct: 404 HARIQARY-PNATGPLIVHRLDMSTSGLLVLTLTAESNKQVQKQFIERTVEKRYTALLEG 462

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +     I   L          +     N K    A +H++VI    ++   + + PHT
Sbjct: 463 NIETDNGTINLPLTGDMEDRPRQM----VNHKSGRKAETHYQVIAQEGKR-TKVHLYPHT 517

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           GRTHQLRVH  H   +  PIVGD  Y             ++L+LHA Y+   HP      
Sbjct: 518 GRTHQLRVHCAHQAGLNTPIVGDDLYGFK---------ADRLHLHAGYLKFKHPTTNE-T 567

Query: 307 ITAPLPAHM 315
           +    P   
Sbjct: 568 VEFSCPEDF 576


>gi|33864307|ref|NP_895867.1| pseudouridine synthase [Prochlorococcus marinus str. MIT 9313]
 gi|33641087|emb|CAE22216.1| Pseudouridine synthase [Prochlorococcus marinus str. MIT 9313]
          Length = 338

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 135/322 (41%), Gaps = 46/322 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PP 69
           +   +    L      HY H +    Q+ L++GQ+R++ + V+ +  + SG  V    PP
Sbjct: 27  IAAVDAGRGLVELLAVHYTHSSRDVWQQRLQAGQIRLNGELVRLDQLLASGDQVCWQRPP 86

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYH 128
            + A      E                    ++++D  + V NKP+G+ V  G G + + 
Sbjct: 87  WLEAAVPASWE--------------------VIFDDGDLLVVNKPSGLPVIPGGGFLDHT 126

Query: 129 IDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRM--------RR 178
           + G L+      G+   PR  HRL + TSG+L+ AR R     L+  FR         ++
Sbjct: 127 LTGLLQRRCQLDGESRLPRPVHRLGRFTSGLLICARQRETRAKLSAMFRRATAGDQGCKK 186

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHI---------GGDYVHVVKQNEKGANYAISH 229
           I +        +  ++   I   +++ +H               H  KQ+E     A+S 
Sbjct: 187 IYRALAHRNLNVHCDEVATIRVPIVQTAHPMVGKVWVAADSSRQHDSKQSESRVLTALST 246

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKL 288
            ++++   Q    LE+   TGR HQ+R+H   +G P++GD  Y  + +  +  +P     
Sbjct: 247 VRLLERR-QDADLLEVAIQTGRPHQIRIHLAAIGSPLIGDPLYGFDGQISSAATPGDGGY 305

Query: 289 YLHARYMDLPHPEGGRLQ-ITA 309
            LHA  + L  P   RL   TA
Sbjct: 306 CLHAHRL-LDVPYRNRLHGFTA 326


>gi|148926270|ref|ZP_01809955.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|145845441|gb|EDK22534.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
          Length = 250

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 100/231 (43%), Gaps = 21/231 (9%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRL 146
                +LYED  + V NKP+ + V G S +    +  L  W+  K           +  L
Sbjct: 2   DFDIDVLYEDEDLLVLNKPSNLVVHGASSV---KNATLVDWLIEKKYTLSNLGGEIRAGL 58

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++TSG +++A+     Q L+E    + + +IY +L+    K  K  +  +L++  
Sbjct: 59  VHRLDKDTSGSILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKFLMRSP 118

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                 + + K+N+   N   +   V+    +    +  +  TGRTHQ+R H   +   I
Sbjct: 119 SNAIKKIAIDKENKFSKNAKSAFINVVKT--ENLTLMAAKLFTGRTHQIRAHLASLNRYI 176

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           +GD  Y    K         ++ LHA ++   HP+    + + APL     
Sbjct: 177 LGDSLYGYKGK------YDCRIMLHAYFLYFIHPKTKEQIFVKAPLMEDFK 221


>gi|153215725|ref|ZP_01950106.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           1587]
 gi|153801105|ref|ZP_01955691.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-3]
 gi|229521570|ref|ZP_04410988.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           TM 11079-80]
 gi|261211068|ref|ZP_05925357.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. RC341]
 gi|262191021|ref|ZP_06049230.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           CT 5369-93]
 gi|124114643|gb|EAY33463.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           1587]
 gi|124123338|gb|EAY42081.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-3]
 gi|229341164|gb|EEO06168.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           TM 11079-80]
 gi|260839569|gb|EEX66180.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. RC341]
 gi|262033084|gb|EEY51613.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           CT 5369-93]
          Length = 245

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 69/247 (27%), Positives = 111/247 (44%), Gaps = 23/247 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++YED  I   NKP+G+    G  +  H D      VD      ++ HRLD  TSG+++
Sbjct: 15  DVIYEDEHIIAANKPSGLLSVPGRPVE-HYDSMWARLVD-YCPDVKVVHRLDMSTSGLIL 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+ +     L + F+ R   KIY++ VWG+ +  +  +   L        D+ +  KQ 
Sbjct: 73  FAKGKHMESALKKQFQYRLTHKIYYARVWGVMEQDEGEVNLPLC------CDWPNRPKQK 126

Query: 220 E--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              +    +++ ++V+    +K   + + P TGR+HQLRVH   +G PIVGD  Y     
Sbjct: 127 VCFEEGRDSLTRYQVVKR-EEKTTVVRLIPITGRSHQLRVHMQSLGHPIVGDDLYAPPEA 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM-----VKTWDSLGFKYDRNLYI 332
             F     ++L LHA  +   HP    L+ T  +P         +      F  +R L  
Sbjct: 186 VEFA----DRLQLHAAELCFYHPRSHWLR-TLFVPCDFYPEAEEQILQH--FDPERKLPD 238

Query: 333 KRLYSQD 339
            +  SQD
Sbjct: 239 YKKLSQD 245


>gi|253569722|ref|ZP_04847131.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           1_1_6]
 gi|251840103|gb|EES68185.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           1_1_6]
          Length = 549

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 68/243 (27%), Positives = 114/243 (46%), Gaps = 22/243 (9%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  K+  + ++   H    +  +++ED  + V NKP+G+    G       
Sbjct: 313 CEPILQHMLQGLKVDGNPLSPHAHRKE-ELEIVFEDEWLVVVNKPSGMLSVPGKEEETDS 371

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                     +   P + HRLD  TSG+L+VA+T+   QHL E F  R I+K Y +L+  
Sbjct: 372 VYHRVKAKYPEATGPMIVHRLDMATSGLLLVAKTKEVHQHLQEQFINRSIKKRYVALLDR 431

Query: 190 IPKNKK----ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
              N++      I   L          +     +E+    A++ +++++  + K+  + +
Sbjct: 432 NGLNQQLEETGTINLPLCLNPLDRPRQM----VSEEYGKPAVTEYRILN-NSDKYIRIAL 486

Query: 246 QPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            P TGRTHQLRVHA H   + CPI+GD  Y             ++LYLHA Y++  HP  
Sbjct: 487 YPLTGRTHQLRVHAAHHQGLNCPILGDELYGKK---------ADRLYLHAEYIEFRHPVY 537

Query: 303 GRL 305
           G +
Sbjct: 538 GDI 540


>gi|317053991|ref|YP_004118016.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316951986|gb|ADU71460.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 232

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 58/211 (27%), Positives = 91/211 (43%), Gaps = 16/211 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKPAG+    G          +   +        L HRLD  TSG++V+A
Sbjct: 20  LYQDEHLVLINKPAGLLSLSGKNPQN--LDSVHHRLVKIFPGCTLVHRLDFGTSGLMVIA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L + F  R + K+Y +L+ G  +N +  I   + K          ++     
Sbjct: 78  RNKAINAALCQQFSQRSVTKVYSALLCGHLENHEGVIDAAIAKDPA----RFPLMSICAT 133

Query: 222 GANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               A S ++V++ F              +++ P TGRTHQLR+H   +G PI+G   Y 
Sbjct: 134 HGKPARSRYQVVERFNHELEEGTLLPLTRVQLIPETGRTHQLRIHCQLLGHPILGCDLYG 193

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                   S    +L LHA  ++  HP  G 
Sbjct: 194 GRLLPG--SEKAPRLMLHASALNFVHPISGE 222


>gi|332994526|gb|AEF04581.1| Pseudouridylate synthase [Alteromonas sp. SN2]
          Length = 259

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 63/254 (24%), Positives = 108/254 (42%), Gaps = 35/254 (13%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           + +   +          +LY+D  I V NKP+G+    G   A      L S V++    
Sbjct: 1   MANPAFVYNPPVQPYLTILYQDDDILVANKPSGLLSVPGK--AEEHKDSLISRVNTVFPT 58

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLD  TSGI+V+A  + + +H+++ F +R+ +K Y++ V+G  K+ +  +   L+
Sbjct: 59  ATVVHRLDMATSGIMVMALNKESHRHISKQFELRKTKKRYFARVFGNVKSNQGEVNLPLI 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------------------------ 239
                    +     + +    A++H++V+D   +                         
Sbjct: 119 CDWPNRPKQM----VDFERGKKALTHYEVVDVIPKASPQPVNSAASASSCASPSTTSELS 174

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              + + P TGR+HQLRVH L +G PI+GD  Y              +L LHA  +   H
Sbjct: 175 ETLVALYPVTGRSHQLRVHMLELGHPILGDRLYAHEEALGMAE----RLQLHAESLSFAH 230

Query: 300 PEGGR-LQITAPLP 312
           P     L    P+P
Sbjct: 231 PASEDWLTFQTPIP 244


>gi|260103209|ref|ZP_05753446.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DSM 20075]
 gi|260083000|gb|EEW67120.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DSM 20075]
 gi|328464673|gb|EGF36019.1| ribosomal protein large subunit [Lactobacillus helveticus MTCC
           5463]
          Length = 285

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 68/313 (21%), Positives = 115/313 (36%), Gaps = 34/313 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M Y   +    + E + ++   +     I     +  LR    + ++     FN  +  G
Sbjct: 1   MVYHFTLFYPKNLEPLPVNDVLRKLL--IPR-KWRHYLRIEQNITINGTYRYFNQNVLPG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I      L+ +   Q+   +S  L          ++YED  + + NK  G      
Sbjct: 58  DKIDI-----ILDQVDSAQQKYPASGKL--------PDIIYEDDNLLIINKKKGQKTHPN 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  +  L       GQ P + HRLD  T G+L+VA+  A    L      +   + 
Sbjct: 105 ---LNETNTTLNDCATYLGQSPYIVHRLDMLTGGLLLVAKNPAVVPILNRELTSKTFHRD 161

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V    K + +  I   +          +           +A++H++V+        
Sbjct: 162 YLAKVDHADKLSDQGTINQPIDHDPEDQRKRMI-----SPAGLHAVTHYQVLKRNDNNTA 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++   TGRTHQ+RVH   +G PI+GD  Y  NF G         L L A  + L  P 
Sbjct: 217 VVKLTLETGRTHQIRVHLASLGTPIIGDPLYNPNFGGED-------LALDAYEISLIKPF 269

Query: 302 GGRLQITAPLPAH 314
               ++T  LP  
Sbjct: 270 SFE-KLTVKLPEE 281


>gi|145492917|ref|XP_001432455.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124399567|emb|CAK65058.1| unnamed protein product [Paramecium tetraurelia]
          Length = 469

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 64/277 (23%), Positives = 110/277 (39%), Gaps = 22/277 (7%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +V    V++    M L    +  +   N    +  +  G++ V+  RV    +++ G  +
Sbjct: 22  HVYKTNVKSRWLGMTLLDAMEKEFRAYNKEYYENAINEGKITVNSVRVSPEYKLEHGMQI 81

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                         E  ILD           L   +++ED    V +KP  + V  G G 
Sbjct: 82  EHATTRV-------EPPILD-----------LPVDIVFEDDSFVVVSKPPSMIVHTGGGY 123

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            Y+    +  +     +   + HRLD+ TSG+L+ ++ R  AQ   ++     +QK Y +
Sbjct: 124 HYNCLSAILHFEHGL-KDLYVLHRLDRLTSGLLIFSKNRLLAQKFHDANSKLNVQKTYLA 182

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFA-QKFCW 242
            V G      +         S     +    +++ +   A  A + F+ +          
Sbjct: 183 RVQGNFSEDIKENNKPQYCVSMKDAIFACCTEEDAQKLDAKSATTKFEKLWYDPISDSSL 242

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           LE +P TGRTHQ+RVH   +G PI+ D  Y   F GN
Sbjct: 243 LECKPITGRTHQIRVHLADLGHPILNDIGYGGKFIGN 279


>gi|325860423|ref|ZP_08173535.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
 gi|325482081|gb|EGC85102.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
          Length = 577

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 64/223 (28%), Positives = 96/223 (43%), Gaps = 27/223 (12%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  + V  KP G+    G      +   LK     + + P + HRLD  TSG+LVVA
Sbjct: 363 LYEDDSLAVVAKPPGLLSVPGRDGLPSVYSILKERWKGRYE-PFMVHRLDMATSGLLVVA 421

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK----KECIANWLLKKSHIGGDYVHVVK 217
           R+  A + L   F    ++K Y +L+     +K    +  I   L   S +  D      
Sbjct: 422 RSPEAHRALQAQFTNHTVRKQYTALLSPSFLDKHLPPEGRIELPL---SPLPDDRPRQCV 478

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLE-----MQPHTGRTHQLRVHALH---MGCPIVGD 269
                   A++ ++V           E     + P TGRTHQLR+H  H   +G PI+GD
Sbjct: 479 DYV-NGKTAVTEYRVAGKTTYGKTGQEAVKVILYPLTGRTHQLRIHCAHPDGLGTPIIGD 537

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
             Y  +           +L+LHA +++  HP  G ++    PL
Sbjct: 538 SLYGQH---------AGRLWLHAGHLEFTHPVTGKKMVFDVPL 571


>gi|84621977|ref|YP_449349.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|84365917|dbj|BAE67075.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 238

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 102/240 (42%), Gaps = 24/240 (10%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +LY+D  + V +K AG+ V          D       +  G+   L HRLD+ TSG 
Sbjct: 7   PLQILYQDDVLAVVDKTAGLMVHDSKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGC 66

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A  R  A  L ++     +QK Y ++  G P   +  + + L       G     VK
Sbjct: 67  LLLAFDRETASALGKALMSGDVQKDYLAVCRGWPAEPRFTVDHDL------DGGPGKPVK 120

Query: 218 QNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++
Sbjct: 121 ------KPALTHFQRLATGELQVPSTGFATSRYALLRCQPQTGRFRQIRRHLKHLSHHLI 174

Query: 268 GDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           GD  +       +F     +++ LHA+ +  PHP +G R+++TAPL     K     G+ 
Sbjct: 175 GDTSHGDGRHNRSFRMLGIHRMLLHAKRLAFPHPADGRRIRVTAPLDDEFTKACALFGWD 234


>gi|261879207|ref|ZP_06005634.1| ribosomal large subunit pseudouridine synthase [Prevotella
           bergensis DSM 17361]
 gi|270334154|gb|EFA44940.1| ribosomal large subunit pseudouridine synthase [Prevotella
           bergensis DSM 17361]
          Length = 230

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 63/221 (28%), Positives = 107/221 (48%), Gaps = 14/221 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQET 154
            ++YED+ + +  K +G  VQG       +   +K ++  K  KP      + HRLD+  
Sbjct: 2   RVVYEDNHLIIVYKESGEIVQGDKTGDLPLSEIVKGYIKEKYHKPGAVFLGVVHRLDRPV 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ ART  A   L + FR   + K YW++    P N    + NWL++ +     Y +
Sbjct: 62  SGLVIFARTSKALARLNDMFRRGDVHKTYWAITKNAPPNPMGTLTNWLVRNTKQNKSYAY 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             +     +  AI ++++I   ++ +  LE+   TGR HQ+R    HMGCP+ GD KY A
Sbjct: 122 DKEM--PDSKKAILNYRLI-AHSENYNLLEIHLLTGRHHQIRCQLSHMGCPVKGDLKYGA 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
                  S     + L +R ++  HP   + + + +PLP  
Sbjct: 179 KRSNPDGS-----ISLLSRRVEFTHPVSKKQIALNSPLPDD 214


>gi|126663902|ref|ZP_01734897.1| putative ribosomal large subunit pseudouridine synthase
           [Flavobacteria bacterium BAL38]
 gi|126624166|gb|EAZ94859.1| putative ribosomal large subunit pseudouridine synthase
           [Flavobacteria bacterium BAL38]
          Length = 231

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 71/228 (31%), Positives = 109/228 (47%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +++ED+ I V NK  G  VQG       +   +K ++  K  KP      + HRLD+ T+
Sbjct: 14  IIHEDNHIIVVNKRVGDIVQGDITGDKPLSDVVKEYIKIKYNKPGDVFLGVVHRLDRPTT 73

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  A   L ESF+ R  QK YW++V   P  +K+ + ++L + S       H+
Sbjct: 74  GIVVFAKTSKALTRLNESFKNRETQKTYWAVVKNTPPKEKDTLTHFLKRNSKNNTSKAHL 133

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +     +  A   +++I      F   E+  HTGR HQ+R     +GCPI GD KY  +
Sbjct: 134 KEI--PDSKKASLSYQIIKKLDNYFAL-EIDLHTGRHHQIRAQLQAIGCPIKGDLKYGFD 190

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     ++LHA+ + L HP     +   A  P      W+SL
Sbjct: 191 -----RSNPDGGIHLHAKKLVLKHPVSKEIITFNATTPND--SIWNSL 231


>gi|327312606|ref|YP_004328043.1| RluA family pseudouridine synthase [Prevotella denticola F0289]
 gi|326945498|gb|AEA21383.1| pseudouridine synthase, RluA family [Prevotella denticola F0289]
          Length = 577

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 63/223 (28%), Positives = 94/223 (42%), Gaps = 27/223 (12%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  + V  KP G+    G      +   LK     + + P + HRLD  TSG+LVVA
Sbjct: 363 LYEDDSLAVVAKPPGLLSVPGRDGLPSVYSILKERWKGRYE-PFMVHRLDMATSGLLVVA 421

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVW----GIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           R+  A + L   F    ++K Y +L+           +  I   L   S +  D      
Sbjct: 422 RSPEAHRALQAQFTNHTVRKQYTALLSLSFLDKHLPPEGRIELPL---SPLPDDRPRQCV 478

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLE-----MQPHTGRTHQLRVHALH---MGCPIVGD 269
                   A++ ++V           E     + P TGRTHQLR+H  H   +G PI+GD
Sbjct: 479 DYV-NGKTAVTEYRVAGKTTYGKTGQEAVKVILYPLTGRTHQLRIHCAHPDGLGTPIIGD 537

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
             Y  +           +L+LHA +++  HP  G ++    PL
Sbjct: 538 SLYGQH---------AGRLWLHAGHLEFTHPVTGKKMVFDVPL 571


>gi|90962277|ref|YP_536193.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|90821471|gb|ABE00110.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
          Length = 295

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 122/305 (40%), Gaps = 35/305 (11%)

Query: 24  WFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           + K     I+   L K +R   G++ ++ K         SG+ +      + +  ++   
Sbjct: 18  FLKKQ--GISRRLLAK-VRYSDGKILINGK---------SGRKIDKIKKNDKITLVVP-- 63

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSW 136
              D     +    F+   +LYED    + +KPA ++           +   + G+    
Sbjct: 64  ---DEEFRRSVPPSFVPIKILYEDDNYLLVDKPAFVASIPSPLHPNDSLVNRVVGY-YQI 119

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +G  P +  RLD++TSGI++ A+ R A   L    +  +I K Y +++ GI  N   
Sbjct: 120 RGYRGIIPHIVTRLDRDTSGIVIFAKHRYAHALLDSQLKEHKISKTYTAILSGILHNNHY 179

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   + + S      +       + A  + +   V +         +++ HTGRTHQ+R
Sbjct: 180 IIDLPIGRDST---SLIKRKVLFSEKAKRSKTEIFVEERIRDN-TLCKIKLHTGRTHQIR 235

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH-PEGGRLQITAPLPAHM 315
           VH  ++G P+V D  Y     G  + P+Q +  LH   +          +++ + +   M
Sbjct: 236 VHCSYLGYPLVSDTLYG----GTISMPLQ-RQALHCSEVVFWDQFSSQYIKVKSNISQDM 290

Query: 316 VKTWD 320
           +    
Sbjct: 291 MNYLK 295


>gi|169775969|ref|XP_001822451.1| DRAP deaminase (Rib2) [Aspergillus oryzae RIB40]
 gi|238502633|ref|XP_002382550.1| DRAP deaminase (Rib2), putative [Aspergillus flavus NRRL3357]
 gi|83771186|dbj|BAE61318.1| unnamed protein product [Aspergillus oryzae]
 gi|220691360|gb|EED47708.1| DRAP deaminase (Rib2), putative [Aspergillus flavus NRRL3357]
          Length = 522

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 56/282 (19%), Positives = 103/282 (36%), Gaps = 51/282 (18%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +        ++ L +G+V V+ K    + ++++G V+      +      +E
Sbjct: 66  VDIFISE-FRDRPPEYYREALEAGRVCVNGKPAGPDTKVKNGDVISHTLHRHEPPVTSQE 124

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +++ED  + V +KPAG+ V       Y+    +       
Sbjct: 125 ------------------IGIIHEDDGLIVIDKPAGVPVHSAGRYHYNSVIEILRSERGG 166

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
           G  PR  +RLD+ TSG++ +A+   AA+ +    + R + K Y + V G  P     C  
Sbjct: 167 GWVPRPCNRLDRLTSGVMFIAKEPKAAEMVARRLKERTVHKEYVTRVKGKFPDGVVVCDQ 226

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---------------------- 237
             +     +G + V            A + F+ +  +                       
Sbjct: 227 PIMQVSPKLGLNRVRA------TGKTAKTKFRRLAYYPPHDPEPVAANKDRAATPPPAYA 280

Query: 238 ---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
              + +  +   P TGRTHQ+RVH   +G PI  D  Y    
Sbjct: 281 NEEEGYSIVHCLPLTGRTHQIRVHLQFLGHPITNDPIYSNRR 322


>gi|149566907|ref|XP_001518233.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4, partial [Ornithorhynchus anatinus]
          Length = 301

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 74/275 (26%), Positives = 127/275 (46%), Gaps = 38/275 (13%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS----KGQK 143
           ++    +  LK  +LY+D ++ V +KP G+ V GG GI   I   L          + + 
Sbjct: 23  IHPNVLAKVLKDGILYQDKELVVIDKPYGLPVHGGPGIQRCITDVLPILAKMLDGFRAEP 82

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+AR+R  A  +   F+MR++ K YW++  G+P + +  +   ++
Sbjct: 83  LHLCHRLDKETTGVMVLARSRDVAHQVQGQFKMRQVAKTYWAVCVGVPVHSEGVVDIPIV 142

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K                    D   V ++  + A+ A++ ++ +         LE++P 
Sbjct: 143 EKEVQSQQQHHKMTLAPNYHLEDGKMVKRRVSRDADSAVTQYRTL-SGTTSCTLLELRPI 201

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYCANFKGN---------FTSPIQNK------LYLHA 292
           TG  HQLRVH    +GCPI+GDHKY    K            +  ++ +      L+LHA
Sbjct: 202 TGVKHQLRVHLAFGLGCPILGDHKYSNWNKLAPQKLPPVILKSLGLEQRKSRYIPLFLHA 261

Query: 293 RYMDLPHP--EGGRLQITAPLPAHMVKTWDSLGFK 325
           + + LP        L +  P  A   +    LG +
Sbjct: 262 QRLTLPALGNRSRDLDLECPPSAFFERCLSRLGLE 296


>gi|302497041|ref|XP_003010521.1| hypothetical protein ARB_03222 [Arthroderma benhamiae CBS 112371]
 gi|291174064|gb|EFE29881.1| hypothetical protein ARB_03222 [Arthroderma benhamiae CBS 112371]
          Length = 482

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 105/269 (39%), Gaps = 46/269 (17%)

Query: 36  NLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
            LQK  +  G++ +D K    ++ I +GQV+              E  +    +      
Sbjct: 42  YLQKAAIDGGRITIDGKVATADSIINNGQVISHTLHR-------HEPPVTSRPIK----- 89

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
                 +++ED  I V +KPAGI V       Y+    +       G  P   +RLD+ T
Sbjct: 90  ------IIHEDEDIIVIDKPAGIPVHPAGRYNYNSIIEIMRSERGLGWIPYPCNRLDRLT 143

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI-GGDYV 213
           SGI+ + +   AA+ + +S R R ++K Y + V G   +        +LK S I G + V
Sbjct: 144 SGIMFLGKHPKAAEQMAQSLRSRTLRKEYIARVKGYFPDGVVLCDQPMLKVSPILGLNRV 203

Query: 214 HVVKQNEKGANYAISHFKVIDCF--------------------------AQKFCWLEMQP 247
               ++ +     I+++  ++                             + +  +   P
Sbjct: 204 RATGKDAQTKFRRIAYYPPVEKEDKNGEATGTQGPDSRASTPPPLPADVDEGYSIVHCLP 263

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            TGRTHQ+RVH   +G PI  D  Y    
Sbjct: 264 LTGRTHQIRVHLQFLGHPITNDPIYSNRR 292


>gi|157373960|ref|YP_001472560.1| pseudouridylate synthase [Shewanella sediminis HAW-EB3]
 gi|157316334|gb|ABV35432.1| pseudouridylate synthase [Shewanella sediminis HAW-EB3]
          Length = 225

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 63/213 (29%), Positives = 104/213 (48%), Gaps = 12/213 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  I V NKP+G+    G   A+    F  + V ++    ++ HRLD  TSG++VV
Sbjct: 16  IIYQDKDILVVNKPSGLLSVPGRDPAHSDSIF--TRVLAEHPNAQIVHRLDMATSGVIVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  ++A + L   FR R  +K Y++ V G  K     +   L+             K + 
Sbjct: 74  ALRKSAERELKRQFRDRETKKTYYARVAGHVKADNGSVDLPLICDWPNRPK----QKVDH 129

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                +++HF+VI   A++   +++ P TGR+HQLRVH + +G PI+GD+ Y        
Sbjct: 130 DIGKASLTHFEVISR-AKRSTLVKLTPITGRSHQLRVHMMAVGHPILGDNFYADPLAKRL 188

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            S    +L LHA+ + +  P  G  +      P
Sbjct: 189 AS----RLLLHAQELTIKQPYSGEEMTFNCDTP 217


>gi|153835569|ref|ZP_01988236.1| ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           HY01]
 gi|148867844|gb|EDL67073.1| ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           HY01]
          Length = 250

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 107/231 (46%), Gaps = 15/231 (6%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++ED +I   NKP+G+    G  +A H D       +      ++ HRLD  TSG++V
Sbjct: 15  DVVFEDEQILAVNKPSGLLSVPGR-LAEHYDSMWSRLTEQ-YPDIQVVHRLDMSTSGLMV 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+ + A   L + F+ R   KIY++ VWG  + ++  I   L+           V  ++
Sbjct: 73  LAKNKRAESALKKQFQYRLTHKIYYARVWGHIEQEEGEIDLPLICD-WPNRPLQKVCFED 131

Query: 220 EKGANYAISHFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K +    + F+V          K   + + P TGR+HQLRVH   +G PIVGD  Y   
Sbjct: 132 GKPSK---TLFQVAKREEHPDGSKTTIVRLLPITGRSHQLRVHMQALGHPIVGDEFYATE 188

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
               F+     +L LHA  +   HP+   L+ +  +P       +++ F Y
Sbjct: 189 EAKVFSE----RLELHAAELSFYHPKCHWLR-SIFVPCDFYPEAEAMIFDY 234


>gi|323466046|gb|ADX69733.1| Ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus H10]
          Length = 285

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 68/313 (21%), Positives = 116/313 (37%), Gaps = 34/313 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M Y   +    + E + ++   +     I     +  LR    + ++     FN  +  G
Sbjct: 1   MVYHFTLFYPKNLEPLPVNDVLRKLL--IPR-KWRHYLRIEQNITINGTYRYFNQNVLPG 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             + I      L+ +   Q+   +S  L          ++YED  + + NK  G      
Sbjct: 58  DKIDI-----ILDQVDSAQQKYPASGKL--------PDIIYEDDNLLIINKKKGQKTHPN 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  +  L       GQ P + HRLD  T G+L+VA+  A    L      +   + 
Sbjct: 105 ---LNETNTTLNDCATYLGQSPYIVHRLDMLTGGLLLVAKNPAVVPILNRELTSKTFHRD 161

Query: 183 YWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V    K + +  I   +          +           +A++H++V+        
Sbjct: 162 YLAKVDHADKLSDQGTINQPIDHDPEDQRKRMI-----SPAGLHAVTHYQVLKRNDNNTA 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++   TGRTHQ+RVH   +G PI+GD  Y  NF G         L L A  + L  P 
Sbjct: 217 VVKLTLETGRTHQIRVHLASLGTPIIGDPLYNPNFGGED-------LALDAYEISLIKPF 269

Query: 302 GGRLQITAPLPAH 314
             + ++T  LP  
Sbjct: 270 SFK-KLTVKLPEE 281


>gi|326480203|gb|EGE04213.1| DRAP deaminase [Trichophyton equinum CBS 127.97]
          Length = 517

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 60/283 (21%), Positives = 107/283 (37%), Gaps = 46/283 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        +  +  G++ +D K    ++ I +GQV+              E
Sbjct: 64  LDIY-STEFRDRPNGYYKAAIDGGRITIDGKVATADSIINNGQVISHTLHR-------HE 115

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  I V +KPAGI V       Y+    +       
Sbjct: 116 PPVTSRPIK-----------IIHEDEDIIVIDKPAGIPVHPAGRYNYNSIIEIMRSERGL 164

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P   +RLD+ TSGI+ + +   +A+ + +S R R ++K Y + V G   +       
Sbjct: 165 GWIPYPCNRLDRLTSGIMFLGKHPKSAEQMAQSLRSRTLRKEYIARVKGYFPDGVVLCDQ 224

Query: 201 WLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCFA---------------------- 237
            +LK S I G + V    ++ +     I+++  ++                         
Sbjct: 225 PMLKVSPILGLNRVRATGKDAQTKFRRIAYYPPVEKENKNGETTGSQGPDSRASTPPPLP 284

Query: 238 ----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               + +  +   P TGRTHQ+RVH   +G PI  D  Y    
Sbjct: 285 ADVDEGYSIVHCLPLTGRTHQIRVHLQFLGHPITNDPIYSNRR 327


>gi|262376261|ref|ZP_06069491.1| dual specificity pseudouridine synthase for 23S rRNA and tRNA-Phe
           modification [Acinetobacter lwoffii SH145]
 gi|262308862|gb|EEY89995.1| dual specificity pseudouridine synthase for 23S rRNA and tRNA-Phe
           modification [Acinetobacter lwoffii SH145]
          Length = 214

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 64/223 (28%), Positives = 106/223 (47%), Gaps = 15/223 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           S+FL   L++ D    V +KPAG+    G      +   L + +     K  L HRLD++
Sbjct: 2   SNFLTEHLIHRDDDFMVIHKPAGLLTVPGK--TEDLQDCLINRLVKLEPKTLLIHRLDRD 59

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGIL    T+   + ++  F+ R+  K Y ++V G  + +   I   ++         +
Sbjct: 60  TSGILAFGLTKWGQKTISRQFQERQTDKTYQAVVAGTLEGE-GTIEVPVVYDP--SRPPL 116

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+          AI+H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PI+GD 
Sbjct: 117 HIADPAHH--KPAITHWQAIEHFNIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIIGDT 174

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
            Y    +   +S    +L LHA  +   HP+  +L +   P P
Sbjct: 175 LYATPEQQQLSS----RLCLHAERLSFYHPQTEQLVEFYCPAP 213


>gi|149912122|ref|ZP_01900709.1| pseudouridine synthase-like protein [Moritella sp. PE36]
 gi|149804799|gb|EDM64840.1| pseudouridine synthase-like protein [Moritella sp. PE36]
          Length = 238

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 61/224 (27%), Positives = 100/224 (44%), Gaps = 20/224 (8%)

Query: 101 LLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGI 157
           +LY D+ + V NKPAG+ SV   +    H    L+  +            HRLD++TSG+
Sbjct: 31  ILYSDNDLVVINKPAGLLSVASANENKQHALAILRKQLSHAKNSVALWPVHRLDRDTSGV 90

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A +R     + E +     +K Y ++V G PK  +  I   L     +  +   ++ 
Sbjct: 91  LMFATSREMRDAVNEGWSG--AEKTYLAVVEGSPKPSQGRIDQPL----RMDPEKYQMIV 144

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                A  A++HFK +    +    LE++  TGR HQ+RVH   +G  ++GD +Y  +  
Sbjct: 145 GPHSEAKNAVTHFKTLRTVKE-LTLLEVKLETGRQHQIRVHMAWLGHSVIGDPRYGTDGP 203

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
                    ++ LHA  + +  P  G RL   AP P   +    
Sbjct: 204 ---------RMGLHALSLSITRPNTGKRLTFEAPAPVEFLDLLR 238


>gi|85710030|ref|ZP_01041095.1| pseudouridylate synthase [Erythrobacter sp. NAP1]
 gi|85688740|gb|EAQ28744.1| pseudouridylate synthase [Erythrobacter sp. NAP1]
          Length = 234

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 60/226 (26%), Positives = 99/226 (43%), Gaps = 10/226 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   ++YED +  V +KPAG+ V         +   ++       + P   HRLD +TSG
Sbjct: 1   MNIPIIYEDGEALVIDKPAGLPVDRPKRGGPALFDHIEQLKLGFQRPPVPVHRLDTDTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            L++AR   A +   ++F  R + K Y +++   P      I   L K S     +  + 
Sbjct: 61  CLLLARNPKALKRFNKAFEDRLVGKTYLAVIDFEPSESSGTIELSLSKISSAEKGWRMIA 120

Query: 217 KQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVH-ALHMGCPIVGDHKY 272
            +       AISH+++I+   +       +  +P TGRTHQLRVH    +G P++GD  Y
Sbjct: 121 ARK---GKPAISHWELIETIGEGDKKRSLIRFRPETGRTHQLRVHALQGLGAPLLGDPVY 177

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                 N  +P   +  LHA  + +       +   AP PA   + 
Sbjct: 178 GPVRGQNKGAP---RTMLHAETISVKREGKNTIFAHAPFPADFERA 220


>gi|253575685|ref|ZP_04853021.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251845023|gb|EES73035.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 310

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 69/324 (21%), Positives = 120/324 (37%), Gaps = 55/324 (16%)

Query: 17  ENM-RLDRWFKNHYPHI--NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +   RLD         +      L+++   G +++            +G  +R+      
Sbjct: 25  DGQDRLDAAMAWLEEGLQAPPKLLRRLRAEGGIKL------------AGDRLRLLAFPAR 72

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----------S 123
            +     +  L                LLYED    V +KPAG+ V             S
Sbjct: 73  ASQYAPVEAEL---------------SLLYEDDFCLVVHKPAGLKVHPDGNEGGASRRDS 117

Query: 124 GIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                +   +  W  S GQ       HRLD+ TSG ++ A+   A   L E+   + I +
Sbjct: 118 APPDTLANRVAGWYASLGQPIAAAHIHRLDEYTSGPVLFAKNEYAHLKLDEAMSRKEIGR 177

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-F 240
            Y + V G+  +  + I   + +  H          +       AI+H ++++ + +   
Sbjct: 178 TYIAFVQGVVSSALKIIDQPIGRDRHHNQRR-----RVSPTGKPAITHVELMEVYPKHEV 232

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + +   TGRTHQ+RVH    G P+VGD  Y  + K            LH   +  PHP
Sbjct: 233 SLVRLTLETGRTHQIRVHLSAAGHPLVGDALYGGSTKW------LPYQALHGERLVFPHP 286

Query: 301 EGGR-LQITAPLPAHMVKTWDSLG 323
             G  +++  P P+ +++  D   
Sbjct: 287 LTGETVELDDPWPSAIIQLRDRFR 310


>gi|253576492|ref|ZP_04853821.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251844129|gb|EES72148.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 256

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 65/224 (29%), Positives = 101/224 (45%), Gaps = 20/224 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +    KP  I  Q  +     +   LK+ +  +  KP      L HRLD+   
Sbjct: 16  ILYEDNHLLGIEKPVNIPTQEDASGDPDLLNLLKADIKERYGKPGNVYLGLVHRLDRPVG 75

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++ A+T  AA  L E  R RR  K Y ++V G P  ++  + + LLK        V V
Sbjct: 76  GAMIFAKTSKAASRLAEMVRSRRFSKTYVAVVHGTPPQRQGHLTDTLLKDERTN--TVSV 133

Query: 216 VKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V     G   A   ++V+   A ++   ++++ HTGR HQ+RV    +GCP+ GD KY A
Sbjct: 134 VPAGTSGGKEARLDYRVLGTSASERLSLVQVELHTGRPHQIRVQMSQIGCPLYGDQKYGA 193

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                  +    ++ L + Y+  PHP           P  +V  
Sbjct: 194 G-----RNKPGQQIALWSLYVGFPHPVTKE-------PIDLVSL 225


>gi|227892311|ref|ZP_04010116.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
 gi|227865860|gb|EEJ73281.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
          Length = 297

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 122/305 (40%), Gaps = 35/305 (11%)

Query: 24  WFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           + K     I+   L K +R   G++ ++ K         SG+ +      + +  ++   
Sbjct: 20  FLKKQ--GISRRLLAK-VRYSDGKILINGK---------SGRKIDKIKKNDKITLVVP-- 65

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSW 136
              D     +    F+   +LYED    + +KPA ++           +   + G+    
Sbjct: 66  ---DEEFRRSVPPSFVPIKILYEDDNYLLVDKPAFVASIPSPLHPNDSLVNRVVGY-YQI 121

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +G  P +  RLD++TSGI++ A+ R A   L    +  +I K Y +++ GI  N   
Sbjct: 122 RGYRGIIPHIVTRLDRDTSGIVIFAKHRYAHALLDSQLKEHKISKTYTAILSGILHNNHY 181

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   + + S      +       + A  + +   V +         +++ HTGRTHQ+R
Sbjct: 182 IIDLPIGRDST---SLIKRKVLFSEKAKRSKTEIFVEERIRDN-TLCKIKLHTGRTHQIR 237

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH-PEGGRLQITAPLPAHM 315
           VH  ++G P+V D  Y     G  + P+Q +  LH   +          +++ + +   M
Sbjct: 238 VHCSYLGYPLVSDTLYG----GTISMPLQ-RQALHCSEVVFWDQFSSQYIKVKSNISQDM 292

Query: 316 VKTWD 320
           +    
Sbjct: 293 MNYLK 297


>gi|169797705|ref|YP_001715498.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter
           baumannii AYE]
 gi|169150632|emb|CAM88541.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter
           baumannii AYE]
          Length = 232

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 110/231 (47%), Gaps = 13/231 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + N           +L+ED  + V +KPAG+    G    +H   +L+  V  K   
Sbjct: 12  MPLNDNFVYAPPQDPLSILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPL 69

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G  K +       + 
Sbjct: 70  AKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLIT 129

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +   +A + F+ +   A      + ++P TGR+HQLRVH +H+
Sbjct: 130 DWENRPRQIVHF-----ELGKHAKTLFQPLVYDATTDQSRVLLEPVTGRSHQLRVHMMHI 184

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G PI+GD  Y    K        N++ LHA Y+   HP  G  + I + +P
Sbjct: 185 GHPIMGDKLYHPEPK----RFHLNRMALHAAYLAFQHPLKGTDVVIESQVP 231


>gi|251796507|ref|YP_003011238.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247544133|gb|ACT01152.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
          Length = 242

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 64/222 (28%), Positives = 106/222 (47%), Gaps = 13/222 (5%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---- 145
           +T  +D ++  +LYED+ I    K  GI  Q        +   +K  +  +  KP     
Sbjct: 1   MTAGNDAIQIPVLYEDNHIIAVVKLPGIPSQEDETGDPDMLTLIKQDLKIRHNKPGNVFL 60

Query: 146 -LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HRLD+   G ++ A+T  AA  L+E+ R R   K Y  +V G P  +++ + +++ K
Sbjct: 61  GLIHRLDRPVGGAMLFAKTSKAASRLSEAVRSRTFGKTYVCVVHGKPAKQQDRLRHYIRK 120

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            +    + V V K+    A  AI  ++V    A  +  + ++ HTGR HQ+R    ++GC
Sbjct: 121 DAK--RNQVTVYKEPAADAKEAILEYRVC-AQAGGYSLIAVKLHTGRPHQIRAQMAYIGC 177

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P+V D KY A    + T      + L +  ++ PHP    LQ
Sbjct: 178 PLVADRKYGAPNTASVTD-----IALWSTSVEAPHPVTKELQ 214


>gi|196232099|ref|ZP_03130954.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
 gi|196223821|gb|EDY18336.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
          Length = 265

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 113/249 (45%), Gaps = 25/249 (10%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGF--LKSWVDSKGQKPR 145
           + +  D  +  ++ E +   V +KP  +       +G     DG   L ++    G +  
Sbjct: 4   IPQPKDPPRFTVIDETADWLVVDKPPFMEAHPSKPNGRPTLWDGLRGLLAYEIVNGGQVS 63

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + +RLD+ETSG+ +VA+ RAAA+ L    + RR++K Y +LVWG P+ +   I   +L++
Sbjct: 64  IINRLDRETSGLTLVAKHRAAARELHLQMQGRRVEKEYLALVWGWPERETFTIDAPILRQ 123

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCF------AQKFCWLEMQPHTGRTHQLRVHA 259
                  +H+ +        A + F+V   F        +F  +   P TGRTHQ+RVH 
Sbjct: 124 GECMPSPIHLKQAVHPDGAAARTRFQVECTFTLETSNGNRFALVRAFPETGRTHQIRVHL 183

Query: 260 LHMGCPIVGDHKYCANFK------------GNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            H G P+VGD  Y  + +               +  +  +  LH+  + L  P+ G L  
Sbjct: 184 AHAGHPVVGDKIYGPDEQCYLEFIRTGWTPELGSRLLLPRHALHSTVLRL--PDAG-LAW 240

Query: 308 TAPLPAHMV 316
             PL   ++
Sbjct: 241 RTPLAPDLM 249


>gi|301089114|ref|XP_002894895.1| ribosomal large subunit pseudouridine synthase A, putative
           [Phytophthora infestans T30-4]
 gi|262105251|gb|EEY63303.1| ribosomal large subunit pseudouridine synthase A, putative
           [Phytophthora infestans T30-4]
          Length = 363

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 71/230 (30%), Positives = 109/230 (47%), Gaps = 20/230 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L   +L+ D  + V NKPA I    G+     +   +   V       R+ HRLDQETSG
Sbjct: 115 LPLKILFRDDAVIVVNKPANILSVDGTDPDALMS--VHRCVARVYPNARMVHRLDQETSG 172

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK-----KSHIGGD 211
           +LVVA T++AAQ L   FR R + K Y + V G   N  E  +    +     + H+   
Sbjct: 173 LLVVALTKSAAQSLNAQFRDRSVDKTYVARVDGWMMNDLEEKSESPRRVQIPMEKHLTKS 232

Query: 212 YVHVVKQNEK----GANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMG 263
            +  V  + +     + ++ + + V+        +K   +E++P TG+THQLR+H  H+G
Sbjct: 233 LIQHVVSDREVDPSSSLWSTTEYSVLSRDESGDDRKSTLVELKPVTGKTHQLRLHMQHLG 292

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
            PI+GD  Y  +   +  S    +L LHA  +   HP    RL   +P P
Sbjct: 293 HPILGDSLYSPDVVYHRAS----RLCLHAAKLSFTHPVTNERLTFESPCP 338


>gi|254504534|ref|ZP_05116685.1| RNA pseudouridine synthase superfamily [Labrenzia alexandrii
           DFL-11]
 gi|222440605|gb|EEE47284.1| RNA pseudouridine synthase superfamily [Labrenzia alexandrii
           DFL-11]
          Length = 200

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 59/205 (28%), Positives = 97/205 (47%), Gaps = 12/205 (5%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D+ + V +KP+G+    G  + +     +++       + R+ HRLD +TSG++V+A   
Sbjct: 2   DADLLVVDKPSGLLSVPGKALEHS--DCIEARAQQTHPEARIVHRLDMDTSGVMVLAMNA 59

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            A +HL   F  R+ +K Y + VWG  +     I   L+         +   +       
Sbjct: 60  QAHRHLGLQFERRKTEKTYVAEVWGQIEKNAGVIDLPLVCDWPNRPKQMVSFEH----GK 115

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
            A++ ++VI    ++   + + P TGR+HQLRVH L +G PIVGD  Y        +   
Sbjct: 116 PALTRWQVIMRN-ERTTRVRLFPFTGRSHQLRVHMLSLGHPIVGDRFYATGDALEAS--- 171

Query: 285 QNKLYLHARYMDLPHPEGG-RLQIT 308
             +L LHA  + L HP GG R+   
Sbjct: 172 -PRLRLHAESLTLHHPTGGKRVTFE 195


>gi|254229275|ref|ZP_04922693.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262393167|ref|YP_003285021.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. Ex25]
 gi|151938199|gb|EDN57039.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262336761|gb|ACY50556.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. Ex25]
          Length = 250

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 15/232 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED  I   NKP+G+    G  +A H D  + S +     + ++ HRLD  TSG++
Sbjct: 14  VDIVFEDDDILAVNKPSGLLSVPGR-LAEHYDS-MWSRLKEVHPEIQVVHRLDMSTSGLM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+ + + + L + F+ R   K+Y++ VWG  + ++  I   L+           V   
Sbjct: 72  LLAKNKPSERALKKQFQYRLTHKVYYARVWGHVEPQEGNIDLPLICD-WPNRPRQKVCFD 130

Query: 219 NEKGANYAISHFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +      + + F+V+             + + P TGR+HQLRVH + +G  IVGD  Y  
Sbjct: 131 D---GKPSQTLFQVVKREVHSDGTHTTVVRLLPITGRSHQLRVHLMAIGHAIVGDEFYAT 187

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                F+     +L LHA  +   HP   +L  +  +P       +++ F Y
Sbjct: 188 EEAYQFSE----RLELHAAELSFYHPATDQLS-SIFVPCDFYPEAEAMIFNY 234


>gi|304382859|ref|ZP_07365342.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
 gi|304336044|gb|EFM02291.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
          Length = 229

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 103/229 (44%), Gaps = 16/229 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQETS 155
           + YED+ I + +K +G  VQG       +   +K+++     K       + HRLD+   
Sbjct: 4   IEYEDNHIIIVSKRSGEIVQGDKTGDKPLSESVKAYLKEAYAKHGNVFLGVVHRLDRPVE 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  A   L E FR   ++K YW++    P   +  + +WL++       Y + 
Sbjct: 64  GLVVFAKTSKALSRLNEMFRTGAVRKTYWAITKNRPTTPEGTLIHWLVRNEKQNKSYAY- 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  +  A   +++I     ++  L ++  TGR HQ+R    H+GCPI GD KY A 
Sbjct: 123 -DHEVPHSKKAELQYRII-AQGDRYTLLAIKLLTGRHHQIRCQLSHIGCPIKGDLKYGAP 180

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLG 323
                 S     + L AR++   HP    L  +TAPLP      W  L 
Sbjct: 181 RSNPDGS-----ISLLARHIAFTHPVSKELVSVTAPLPDD--TLWTVLA 222


>gi|284008525|emb|CBA75052.1| tRNA pseudouridine synthase C [Arsenophonus nasoniae]
          Length = 248

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 61/236 (25%), Positives = 98/236 (41%), Gaps = 17/236 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L++D  +   +KPAG  V       +     +++  D  GQ     HRLD+ TSG+L++A
Sbjct: 2   LFQDQHLIAIHKPAGWLVHRSWLDRHETRFVMQTVRDQIGQYVFPVHRLDKPTSGVLLMA 61

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
            +   A  L + F    ++K Y ++V G              +K  I   Y   + Q   
Sbjct: 62  LSSEVACLLAQQFEYHAVEKKYHAIVRGYVNEAGIIDYPLKEEKDKIADKYASKISQP-- 119

Query: 222 GANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                I+H+  +               +F  L ++P TGR HQLR H  H+  PI+GD  
Sbjct: 120 --QSCITHYSPLAKVECPIEIGRYPTSRFSLLALKPKTGRKHQLRRHMAHVRHPIIGDTT 177

Query: 272 YCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
           +      +G       ++L LHA Y+   HP  G +LQ+ A      +      G+
Sbjct: 178 HGDLRQNRGVAHHFATSRLMLHASYLSFKHPMTGDKLQLIAKWDDAWIHLLSQFGW 233


>gi|15642501|ref|NP_232134.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|153817992|ref|ZP_01970659.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           NCTC 8457]
 gi|153822421|ref|ZP_01975088.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|227082624|ref|YP_002811175.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           M66-2]
 gi|229507437|ref|ZP_04396942.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           BX 330286]
 gi|229509638|ref|ZP_04399119.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|229516763|ref|ZP_04406209.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC9]
 gi|229606943|ref|YP_002877591.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MJ-1236]
 gi|254851050|ref|ZP_05240400.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MO10]
 gi|255744517|ref|ZP_05418469.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholera
           CIRS 101]
 gi|262154659|ref|ZP_06028785.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           INDRE 91/1]
 gi|298500664|ref|ZP_07010468.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MAK 757]
 gi|34395834|sp|Q9KP71|RLUA_VIBCH RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|9657087|gb|AAF95647.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|126511427|gb|EAZ74021.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           NCTC 8457]
 gi|126520064|gb|EAZ77287.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|227010512|gb|ACP06724.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           M66-2]
 gi|229345826|gb|EEO10798.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC9]
 gi|229353112|gb|EEO18051.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|229354942|gb|EEO19863.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           BX 330286]
 gi|229369598|gb|ACQ60021.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MJ-1236]
 gi|254846755|gb|EET25169.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MO10]
 gi|255738042|gb|EET93435.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholera
           CIRS 101]
 gi|262030499|gb|EEY49137.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           INDRE 91/1]
 gi|297540833|gb|EFH76890.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MAK 757]
          Length = 245

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 69/254 (27%), Positives = 111/254 (43%), Gaps = 23/254 (9%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   ++YED  I   NKP+G+    G  +  H D      VD      ++ HRLD 
Sbjct: 8   PPKDPWIDVIYEDEHIIAANKPSGLLSVPGRPVE-HYDSMWARLVD-YCPDVKVVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+++ A+ +     L + F+ R   KIY++ VWG+ +  +  +   L        D+
Sbjct: 66  STSGLILFAKGKHMESALKKQFQYRLTHKIYYARVWGVMEQNEGEVNLPLC------CDW 119

Query: 213 VHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            +  KQ    +    +++ ++V+    +K   + + P TGR+HQLRVH   +G PIVGD 
Sbjct: 120 PNRPKQKVCFEEGRDSLTRYQVVKR-EEKTTVVRLIPITGRSHQLRVHMQSLGHPIVGDD 178

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM-----VKTWDSLGFK 325
            Y       F     ++L LHA  +   HP    L+ T  +P         +      F 
Sbjct: 179 LYAPPEAVEFA----DRLQLHAAELCFYHPRSHWLR-TLFVPCDFYPEAEEQILQH--FD 231

Query: 326 YDRNLYIKRLYSQD 339
            +R L   +  SQD
Sbjct: 232 PERKLPDYKKLSQD 245


>gi|295087068|emb|CBK68591.1| Pseudouridylate synthases, 23S RNA-specific [Bacteroides
           xylanisolvens XB1A]
          Length = 564

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 71/254 (27%), Positives = 116/254 (45%), Gaps = 33/254 (12%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ + L    +  +  +++ED  + + NKPAG+    G   A   
Sbjct: 317 CEPILQHMLQGLEVDENPL-LNPVHEEEELEIVFEDEWLLIVNKPAGMLSVPGK--AEDR 373

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           D           +   P + HRLD  TSG+L+VA+T+   Q L   F  R I+K Y +++
Sbjct: 374 DSVYHRLKKKYPEATGPMIVHRLDMATSGLLLVAKTKKVHQDLQAQFANRSIKKRYVAVL 433

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID------------- 234
            GI  +++       L  + +      V K   +    AI+ +K+I              
Sbjct: 434 DGIVLSERTGRIELPLCLNPLDRPRQIVSK---EYGKEAITEYKIISESEKIIDESERSI 490

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
              +K+  +   P TGRTHQLRVHA H   +GCPI+GD  Y             ++LYLH
Sbjct: 491 NEPRKYTRIVFYPLTGRTHQLRVHAAHPEGLGCPILGDELYGKK---------ADRLYLH 541

Query: 292 ARYMDLPHPEGGRL 305
           A Y++  HP  G +
Sbjct: 542 AEYIEFRHPIYGDI 555


>gi|262379133|ref|ZP_06072289.1| pseudouridylate synthase [Acinetobacter radioresistens SH164]
 gi|262298590|gb|EEY86503.1| pseudouridylate synthase [Acinetobacter radioresistens SH164]
          Length = 221

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 57/218 (26%), Positives = 96/218 (44%), Gaps = 12/218 (5%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
                       ++YED  + + +KPAG+    G    +    +L+  +  K    ++TH
Sbjct: 6   PFIYAPPQQPLSIIYEDDDLIIIDKPAGLLSVPGRLPEHQDSAYLR--LLEKYPHAKITH 63

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSGIL+ A+ R A   +++ F+ R + K Y +L+ G    +       +    + 
Sbjct: 64  RLDMATSGILMFAKHRDAEVAISKMFQARTVTKRYVALIQGQLNEQGSIDVPLITDWENR 123

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               VH      +    A + F+V+    +     + + P TGR+HQLRVH  ++G PI+
Sbjct: 124 PRQIVHF-----ELGKSAKTLFQVLQYHEEHDMTRVLLTPITGRSHQLRVHMQYIGHPIM 178

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           GD  Y     G +      ++ LHA Y+    P    L
Sbjct: 179 GDKLYHPEPGGFY----LKRMALHASYLAFQQPLSKDL 212


>gi|197337902|ref|YP_002158084.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
 gi|197315154|gb|ACH64603.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
          Length = 566

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 62/228 (27%), Positives = 99/228 (43%), Gaps = 19/228 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D +  L   ++     ++YED  + V NKPA      G  I   +   ++         
Sbjct: 348 MDDNPLLINPAEGKDLEIVYEDEFMVVVNKPADFLSVPGKNIHDSVYARIQQRYPDATGG 407

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLD  TSG+LV+  T  A + L + F  R ++K Y +L+ G+ +  +  I   + 
Sbjct: 408 L-IIHRLDMATSGLLVLGLTPKAHKRLQQQFINRTVEKRYTALLDGVLEQDEGLITLPM- 465

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V  ++      A + ++VI+    K     + P TGRTHQLRVH  H  
Sbjct: 466 RGDLYDRPRQLVCFEH---GKPAETTYQVIERKESKTKVY-LYPKTGRTHQLRVHCAHYL 521

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
            +  PI GD  Y             N+L+LHA Y+ L HP     ++ 
Sbjct: 522 GLNMPITGDGLYGKK---------ANRLHLHAGYLSLIHPITKEPMEF 560


>gi|114326764|ref|YP_743921.1| ribosomal large subunit pseudouridine synthase A [Granulibacter
           bethesdensis CGDNIH1]
 gi|114314938|gb|ABI60998.1| ribosomal large subunit pseudouridine synthase A [Granulibacter
           bethesdensis CGDNIH1]
          Length = 224

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 66/220 (30%), Positives = 101/220 (45%), Gaps = 13/220 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D    V NKPAG+    G      ++ +    +  + + P L HRLD +TSG L
Sbjct: 11  PDILYQDQHFVVLNKPAGLPAHAGPAGGPSVEDWFP-LLSRRKEGPWLAHRLDTDTSGCL 69

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-GDYVHVVK 217
           ++A  +         F   +  K YW++V G P   +  I   L ++S  G     H   
Sbjct: 70  IIALRKTPLLEAQAMFAKGQAGKRYWAVVRGAPPAAEGRIDRKLSRRSESGEAGRGHWRM 129

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             +     A + +++++       WLE+ P TGRTHQLRVH   +GCPI+GD  Y     
Sbjct: 130 VEDAQGQSASTSWRIMEHQ-DGLSWLELSPLTGRTHQLRVHCALLGCPILGDPVYGDGRD 188

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
                     L L A  + L  P    +++ AP+PAHM +
Sbjct: 189 A--------PLCLLACEIRL--PLDPVIKVRAPVPAHMRR 218


>gi|225850422|ref|YP_002730656.1| RNA pseudouridine synthase family protein [Persephonella marina
           EX-H1]
 gi|225646434|gb|ACO04620.1| RNA pseudouridine synthase family protein [Persephonella marina
           EX-H1]
          Length = 272

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 64/294 (21%), Positives = 117/294 (39%), Gaps = 48/294 (16%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       +     ++I+ S  V V+ KRV   ++ ++ G +V I  + N+ +   ++  
Sbjct: 15  FISEVL-GLTKNKAKEIIDSKNVFVNSKRVWIASHTLKKGDIVEIADIDNSFSWKPEK-- 71

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             ++YED  I    KP  +  +G  G   +             +
Sbjct: 72  -----------------SVIYEDQFILAVQKPPFLESEGRKGSVEY------QLRKVLDR 108

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           + +  HRLD+ETSG+L+ A+         + +  + + K+Y S+ +G  K KK+ +   +
Sbjct: 109 RLKAIHRLDRETSGVLLFAKNEKIFHRFKDLWHRKEVVKVYLSISYGEAKFKKKVVNMPV 168

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            K                    YA S F      ++ F   E++  TGR HQ+R+H+  +
Sbjct: 169 DK-------------------KYAKSIFFT-KKISKGFTLFEVEIKTGRKHQIRIHSSKI 208

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             PIVGD  Y      +  +    +  LH   +   HP  G+ + I AP+    
Sbjct: 209 RHPIVGDKIYGLKKVEDPLTKNVKRQMLHGYRLRFLHPFTGKVVDIKAPVYHDF 262


>gi|219846960|ref|YP_002461393.1| pseudouridine synthase [Chloroflexus aggregans DSM 9485]
 gi|219541219|gb|ACL22957.1| pseudouridine synthase [Chloroflexus aggregans DSM 9485]
          Length = 307

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 78/334 (23%), Positives = 130/334 (38%), Gaps = 38/334 (11%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS  + +  ++V   E  + L     N +        Q  +R G  +   +RV  +   +
Sbjct: 1   MS--SAIISLIVTEPEAGLSLGAIVANRFGERGR---QAAIRGGLWQH-GRRVSADTPAR 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA----G 116
           +G+ + +                    V   + +    + ++YED  + V NKP     G
Sbjct: 55  AGETLLVRL----------------PPVGGYRDAPLTLNHIIYEDDDLLVINKPPACYTG 98

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            +     G    +   L +  D       L H+LD  TSGILV+++   A   L  +F  
Sbjct: 99  DTPWDTQGSVLAVARRLLTERDGLVPTLHLAHQLDAGTSGILVISKHPRANAPLQAAFNH 158

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH------VVKQNEKGANYAISHF 230
            ++ K Y +L  G P    E I      ++  G   ++       V  N +    A +  
Sbjct: 159 GQVDKRYLALCAGHPPTATELITGH--GRAAAGRWRLYEQAEIGKVLPNGQRVKRAHTQI 216

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           + +         +  +P TGRTHQ+R+H + +GCP++GD +Y           I + L  
Sbjct: 217 E-LRRQYGDVALVWAKPLTGRTHQIRLHLVALGCPLLGDERYGG-PTTVAGMLIPHPLL- 273

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           HA  + LPHP  GR L I  P P+         G
Sbjct: 274 HAAELALPHPRSGRLLNIFCPPPSIFTGVLKCFG 307


>gi|197122401|ref|YP_002134352.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196172250|gb|ACG73223.1| pseudouridine synthase [Anaeromyxobacter sp. K]
          Length = 241

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 106/235 (45%), Gaps = 16/235 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +L+ED+ +   +KPAG  V  G          L++ ++++  +  + HRLD+ TSG+
Sbjct: 8   PVTVLHEDAHLLAVDKPAGRLVIPGRDGGEPS---LRAELEARFGRLWVVHRLDRNTSGV 64

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV+ART AA + L  +F     +K Y +LV G+P  ++          +      +    
Sbjct: 65  LVLARTAAAHRTLNLAFDRGEPRKRYLALVRGVPPAEQRIEVAI----APGRKGRMRPAP 120

Query: 218 QNEKGANYAISHFKVIDCFAQKF------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            ++     +++  + ++ F            +E  P TGRTHQ+RVH    G P+  D  
Sbjct: 121 PDDPRGKASVTVVRRLEAFPGHALGGGPLALVEALPETGRTHQIRVHLAAAGTPLAVDPA 180

Query: 272 YC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           Y   A   G     +  +  LHA  + L HP  GR L + APLP  +  T   L 
Sbjct: 181 YGDAAPLLGPGGEAVLARTPLHAARLALRHPADGRELVLEAPLPPDLAGTLALLR 235


>gi|119898153|ref|YP_933366.1| pseudouridine synthase A [Azoarcus sp. BH72]
 gi|119670566|emb|CAL94479.1| pseudouridine synthase A [Azoarcus sp. BH72]
          Length = 236

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 100/232 (43%), Gaps = 12/232 (5%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
               S  +           L+ D    V +KP+G+    G G        L   V     
Sbjct: 14  PTPMSNPVYLPPPEHPLQYLHIDPHFVVVSKPSGLLSVPGRGAE--KQDCLWRRVVHDFP 71

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HRLD ETSG++V+AR     + L+  F  R ++K Y ++V G+P + +  I   L
Sbjct: 72  DALTVHRLDMETSGLMVLARDAETHRRLSGLFHDRLVEKRYVAMVDGLPTSDRGQIDLPL 131

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALH 261
           L             K + +G   +++ F+V+  +  +    + + P TGR+HQLRVH L 
Sbjct: 132 LAD----WPNRPRQKVDFEGGKPSLTRFEVMARYPDRDVSRIALMPETGRSHQLRVHLLA 187

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           +G PI+GD  Y +            +L LHA ++   HP  G R+    P P
Sbjct: 188 LGHPILGDALYGSPSVQAKAE----RLLLHAEFLAFRHPHSGARVACECPAP 235


>gi|169632120|ref|YP_001705856.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter
           baumannii SDF]
 gi|169150912|emb|CAO99519.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter
           baumannii]
          Length = 229

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 110/231 (47%), Gaps = 13/231 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + N           +L+ED  + V +KPAG+    G    +H   +L+  V  K   
Sbjct: 9   MPLNDNFVYAPPQDPLSILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPL 66

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G  K +       + 
Sbjct: 67  AKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLIT 126

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +   +A + F+ +   A      + ++P TGR+HQLRVH +H+
Sbjct: 127 DWENRPRQIVHF-----ELGKHAKTLFQPLVYDATTDQSRVLLEPVTGRSHQLRVHMMHI 181

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G PI+GD  Y    K        N++ LHA Y+   HP  G  + I + +P
Sbjct: 182 GHPIMGDKLYHPEPK----RFHLNRMALHAAYLAFQHPLKGTDVVIESQVP 228


>gi|153810858|ref|ZP_01963526.1| hypothetical protein RUMOBE_01242 [Ruminococcus obeum ATCC 29174]
 gi|149833254|gb|EDM88336.1| hypothetical protein RUMOBE_01242 [Ruminococcus obeum ATCC 29174]
          Length = 288

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 97/240 (40%), Gaps = 20/240 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTH 148
              ++YED+ I + NKPAG+  Q        +  +L  ++   G           P + +
Sbjct: 41  DLDIIYEDTDILLINKPAGMLSQPDDTKEPSMVEYLIGYLLQNGSLTEENLRTFHPSVCN 100

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG++   ++ A  Q L+  F  R + K Y  +V G    +   I  +L K +++
Sbjct: 101 RLDKNTSGVIAAGKSLAGLQELSTLFHDRTVHKDYLCIVKGKL-TRSRHIRGYLHKDANL 159

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               V V    EK A    + +  I C  +    L+++  TGRTHQ+R H    G P+ G
Sbjct: 160 N--KVSVSPTKEKDAQPIETQYTPI-CNNEHATLLKVRLITGRTHQIRAHLASEGHPLAG 216

Query: 269 DHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-----RLQITAPLPAHMVKTWDS 321
           D KY +     +           LHA  +  P  EG           A LP         
Sbjct: 217 DAKYGSQEFNRYFRDHYGLKHQLLHAYRLTFPELEGKLHNLSEKHFEAVLPVQFQHILKE 276


>gi|332307059|ref|YP_004434910.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332174388|gb|AEE23642.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 233

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 63/235 (26%), Positives = 114/235 (48%), Gaps = 14/235 (5%)

Query: 80  EQKILDSSV--NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            QKI+++ +  +      F    +LY+D  +   NKP+G+    G          +   +
Sbjct: 6   PQKIVETPIVDSFIAPPCFEAVTVLYQDDYLLAVNKPSGLLSLSGKNPLN--KDSVHYRI 63

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +     + HRLD  TSG+L++A  + +   LT+ F+ R ++K Y ++++G  ++++  
Sbjct: 64  VKQFPTALMAHRLDFGTSGVLLLALDKKSNGELTKQFQARSVKKRYSAVLFGKVQDREGR 123

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
           ++  + K            +Q       AISH++VI+         +E  P TGRTHQLR
Sbjct: 124 VSVPIAKDPANFPRQKICFEQ----GKEAISHYRVIEYLENPPRTHVEFTPETGRTHQLR 179

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           +H+L MG PI+G   Y      + +  +  +L LHA +++  HP   + + I AP
Sbjct: 180 IHSLAMGHPILGCDLY----ANDQSEQLAERLLLHASWIEFLHPHSNQPMTIEAP 230


>gi|315223482|ref|ZP_07865338.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga ochracea F0287]
 gi|314946517|gb|EFS98509.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga ochracea F0287]
          Length = 226

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 105/221 (47%), Gaps = 15/221 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQE 153
             +LYED+ +   NK  G  VQG       +   +K ++  K  KP      + HRLD+ 
Sbjct: 10  VDVLYEDNHVIAVNKRVGDIVQGDKTGDTPLSDIVKQYLKQKYNKPGEVFLGVVHRLDRP 69

Query: 154 TSGILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           T+G+++ A+T  A   L   F  ++ +QK YW+LV   P  +++ + +WL++        
Sbjct: 70  TTGVVLFAKTSKALARLNTMFSNKQEVQKTYWALVDAKPPVEEDTLTHWLVRNEKQNKSV 129

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  +  +  +  A+ H+K++  + +++  LE+   TGR HQ+R     +G  I GD KY
Sbjct: 130 AYNKEMQQ--SKKAVLHYKLLKSY-ERYYLLEIDLITGRHHQIRAQLAAIGLHIKGDLKY 186

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            A       S     + LHA  +   HP     ++I A  P
Sbjct: 187 GAK-----RSNPDGGICLHAYSLSFVHPVKKEPIKIIAEAP 222


>gi|158319738|ref|YP_001512245.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158139937|gb|ABW18249.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 230

 Score =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 61/222 (27%), Positives = 109/222 (49%), Gaps = 13/222 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           +   +L+ED+ + V  KP+ I  Q        +   LK  +  +  KP      L HRLD
Sbjct: 3   VAIPILFEDNHLLVVEKPSNILSQEDHTGDLDMLTLLKEDIKERYNKPGNVYLGLVHRLD 62

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +   G++V A+T  +A  L++  R R  +K Y ++V G P  +KE + ++LLK +    +
Sbjct: 63  RPVGGVMVFAKTSKSAARLSDQIRKREFKKTYMAVVHGRPMKEKETLVHYLLKDNK--SN 120

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V VVK++ +GA  AI  +++++   + +  +++  HTGR HQ+RV    +G P+ GD +
Sbjct: 121 IVSVVKKDREGAKEAILDYEIVETV-ESYSLVKINLHTGRPHQIRVQFATIGNPLHGDQR 179

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           Y           +  ++ L +  +   HP      +   LP 
Sbjct: 180 YGKGVNQ-----VGQQIALWSHEIACQHPTSKEDMVFTSLPE 216


>gi|269137963|ref|YP_003294663.1| ribosomal large subunit pseudouridine synthase A [Edwardsiella
           tarda EIB202]
 gi|267983623|gb|ACY83452.1| ribosomal large subunit pseudouridine synthase A [Edwardsiella
           tarda EIB202]
 gi|304558011|gb|ADM40675.1| Ribosomal large subunit pseudouridine synthase A [Edwardsiella
           tarda FL6-60]
          Length = 235

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 70/230 (30%), Positives = 108/230 (46%), Gaps = 17/230 (7%)

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                  +  S+    +H D  +     +LY+D+ I V NKP+G+    G  +  H D  
Sbjct: 4   RTPAGGALPPSATPALEHYDPPREPWLHVLYQDAHIIVVNKPSGLLSVPGR-LPEHQDSI 62

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L + + ++       HRLD  TSG+LVVA T+ A + L   FR R  +K Y + VWG P+
Sbjct: 63  L-TRIQAQFPGAESVHRLDMATSGVLVVALTKDAERELKRQFREREPKKNYVARVWGHPQ 121

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             +  I   L+       D+ +  KQ    +    A + ++V+   A     + + P TG
Sbjct: 122 QDEGVIDLPLI------CDWPNRPKQKVCFEQGKPAQTEYQVLARDADGTARVLLTPITG 175

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           R+HQLRVH L +G PI+GD  Y         S +     LHA+ + + HP
Sbjct: 176 RSHQLRVHLLALGHPILGDGFYAPPQALALASRLL----LHAQELRIVHP 221


>gi|85375216|ref|YP_459278.1| pseudouridylate synthase [Erythrobacter litoralis HTCC2594]
 gi|84788299|gb|ABC64481.1| pseudouridylate synthase [Erythrobacter litoralis HTCC2594]
          Length = 229

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 61/223 (27%), Positives = 106/223 (47%), Gaps = 12/223 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +L+ED +  V +KPAG+ ++        ++  L +      + P   HR+D +TSG
Sbjct: 1   MDIPILFEDGEALVIDKPAGLPIERPRRGGPSLEDHLDALKLGFQRAPVPVHRIDTDTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            L++AR   A +   ++F  RR+ K Y  +V G+P+ ++  IA  L K S     +  + 
Sbjct: 61  CLLLARNPKALKRFAKAFEERRVGKRYLGIVDGVPQPEEGEIALALAKISSAEKGWRMI- 119

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCAN 275
               K    +++ ++++    +    LE +P TGRTHQ+RVH    +G P++GD  Y   
Sbjct: 120 --PAKKGKASLTRWRLLQKLERGA-LLEFEPETGRTHQIRVHVASGLGLPLLGDPVYGDA 176

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
             G        +  LHA  + +       +  TAPLPA  +  
Sbjct: 177 STG-------PRTMLHAAGLTVERDGKPSISATAPLPADFLAL 212


>gi|117926248|ref|YP_866865.1| ribosomal large subunit pseudouridine synthase A [Magnetococcus sp.
           MC-1]
 gi|117610004|gb|ABK45459.1| ribosomal large subunit pseudouridine synthase A [Magnetococcus sp.
           MC-1]
          Length = 224

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 69/223 (30%), Positives = 103/223 (46%), Gaps = 13/223 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D+ + +FNKP  + +  G G    +   L      +G+ P   HRLD  TSG LV+
Sbjct: 13  ILHMDADLLIFNKPNRMPIYRGPGGGETLADHLPQLCFERGKPPAAVHRLDSATSGCLVL 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R +   + L+  F    ++K+YW++V G P   +  I   L      G   V V     
Sbjct: 73  GRHKGMRRSLSNLFAQGGVEKLYWAVVQGRPLMDQGLIELPLQDVGWPGRPRVKVRM--- 129

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            G  +  + F+V+  + Q    L + P TGRTHQLRVH   MGCPIVGD  Y        
Sbjct: 130 -GGKWGRTLFQVMG-YGQNETLLALMPQTGRTHQLRVHCAAMGCPIVGDPLYGGAACDG- 186

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
                  ++LHAR + L      +   TAP P H+ +  + + 
Sbjct: 187 -----PPMHLHARRILLHGAI--QQSFTAPAPPHLQRFLEQMR 222


>gi|108762448|ref|YP_633384.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108466328|gb|ABF91513.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 303

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 71/296 (23%), Positives = 117/296 (39%), Gaps = 29/296 (9%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
             + Y H +    +     G+VR+D      +  ++ GQ +              E+   
Sbjct: 27  MTDKYRHSSEEEWRARFARGEVRLDDVTADGSEPLRPGQWLCWH-------RPPWEEADT 79

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
             S  L           +YED+++ V  KP+G+      G        L S+V ++  + 
Sbjct: 80  PQSFEL-----------VYEDAELVVVVKPSGLPTLPSGGFL---KNTLLSFVQARWPEA 125

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRL + TSG+++  RTR AA  L   +R  R+ K Y +L  G+   +   I   +  
Sbjct: 126 VPMHRLGRATSGLVLFTRTRDAAARLASDWREGRVHKRYRALSQGLAAQESYDIRAPIGL 185

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             H     VH           + S  +V++   +     E+  HTGR+ Q+R+H   +G 
Sbjct: 186 VPHPRLGEVHGASAR---GKPSHSTARVLERRTE-HTLFEVDIHTGRSEQIRIHLAFIGH 241

Query: 265 PIVGDHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           P+VGD  +         N   P      LHA  +   HP  G  +Q+ AP P  + 
Sbjct: 242 PLVGDPLFAVGGLPLAENPGLPGDGGYLLHAESLTFQHPRSGEHVQLQAPAPLELR 297


>gi|237731372|ref|ZP_04561853.1| pseudouridylate synthase [Citrobacter sp. 30_2]
 gi|226906911|gb|EEH92829.1| pseudouridylate synthase [Citrobacter sp. 30_2]
          Length = 232

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/210 (26%), Positives = 91/210 (43%), Gaps = 16/210 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP+G+    G          +   +        L HRLD  TSG++VVA
Sbjct: 20  LYQDEHLVLINKPSGLLSLSGKNPQN--LDSVHHRLVQIYPGCTLVHRLDFGTSGLMVVA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L + F  R + K+Y +L+ G  +N +  I   + K   +      ++     
Sbjct: 78  RNKAINAALCQQFSQRTVTKVYSALLCGHLENDEGVIDAAIAKDPAL----FPLMSICAL 133

Query: 222 GANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               A S ++V++ F  +           +++ P TGRTHQLR+H   +G PI+G   Y 
Sbjct: 134 NGKPARSRYQVVERFYHRQEEGTLLPLTRVQLTPETGRTHQLRIHCQQLGHPILGCDLYG 193

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                       ++L LHA  +   HP   
Sbjct: 194 GRLLPGTEQT--SRLMLHASELHFRHPISE 221


>gi|330830420|ref|YP_004393372.1| Pseudouridine synthase [Aeromonas veronii B565]
 gi|328805556|gb|AEB50755.1| Pseudouridine synthase [Aeromonas veronii B565]
          Length = 231

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 63/219 (28%), Positives = 95/219 (43%), Gaps = 16/219 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ED  + + NKP+G+    G          +   +        L HRLD  TSGI+VVA
Sbjct: 20  LFEDEHLLLINKPSGLLSLSGKNPQN--LDSVHYRLVQDYPGCTLVHRLDFGTSGIMVVA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L + F  R + K Y +L+ G   + +  I   + K   +      ++K    
Sbjct: 78  RNKAINALLCQQFSQRAVSKAYSALLCGHLIDDEGVIDAPIAKDPAL----FPLMKICAA 133

Query: 222 GANYAISHFKVIDCFAQ-------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               A S ++VI+  AQ           + + P TGRTHQLR+H+  +G PI+G   Y  
Sbjct: 134 SGKPARSRYRVIERLAQQIQGQTVPLTRVRLVPETGRTHQLRLHSQLLGYPILGCDLYGG 193

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                       +L LHA  +D  HP  G  +Q+    P
Sbjct: 194 LLPPGCEQ--APRLMLHASKLDFTHPVSGEPMQVRCAAP 230


>gi|310817977|ref|YP_003950335.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309391049|gb|ADO68508.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 557

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 98/231 (42%), Gaps = 23/231 (9%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK---PR 145
                +      +++ED  + V +KP G+    G G        + + + ++      P 
Sbjct: 342 PPEPTASAGALSIVFEDDWLVVIDKPCGLLSVPGKGAE--WVDSVLTRLQARYPHATGPL 399

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD +TSG+LV A        L   F  R + K Y + + G  + ++  I   L   
Sbjct: 400 LVHRLDLDTSGLLVAALDARTHAALQRQFIHREVHKRYVAWIDGRVRGEQGLIDLPLRVD 459

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---M 262
            H     +H    +      A++ ++V++    +   + + P +GRTHQLRVHA H   +
Sbjct: 460 LHDRPRQIH----DPLHGKPAVTEWQVLERQGDR-TRVALFPQSGRTHQLRVHAAHPLGL 514

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           G PIVGD  Y            + +L LHA  +   HP  G R+    P P
Sbjct: 515 GAPIVGDRLYGHE---------EVRLLLHAEALSFRHPGTGLRVSFERPAP 556


>gi|270263927|ref|ZP_06192195.1| hypothetical protein SOD_f01410 [Serratia odorifera 4Rx13]
 gi|270042120|gb|EFA15216.1| hypothetical protein SOD_f01410 [Serratia odorifera 4Rx13]
          Length = 216

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 60/210 (28%), Positives = 94/210 (44%), Gaps = 10/210 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             +       +LY+D  I V NK +G+    G   A      L + + +        HRL
Sbjct: 3   PYNPPQDPMHILYQDEHIIVVNKASGLLSVPGR--APENKDSLMTRIQADFPAAESVHRL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG++VVA  +AA + L   FR R  +K Y + VWG  ++ +  +   L+       
Sbjct: 61  DMATSGVIVVALNKAAERELKRQFREREPKKSYIARVWGHLEHDEGLVDLPLICD----W 116

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               + K   +    A + + V+   A     +++ P TGR+HQLRVH L +G PI+GD 
Sbjct: 117 PNRPLQKVCFETGKAAQTEYLVMSRDADGSTRVKLTPITGRSHQLRVHMLALGHPILGDG 176

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            Y              +L LHA+ + + HP
Sbjct: 177 FYAHPEAKAMA----PRLQLHAQELRITHP 202


>gi|13508287|ref|NP_110237.1| pseudouridine synthase [Mycoplasma pneumoniae M129]
 gi|2501681|sp|P75230|Y548_MYCPN RecName: Full=Uncharacterized RNA pseudouridine synthase MG370
           homolog; AltName: Full=RNA pseudouridylate synthase;
           AltName: Full=RNA-uridine isomerase
 gi|1673965|gb|AAB95942.1| pseudouridine synthase [Mycoplasma pneumoniae M129]
 gi|301633599|gb|ADK87153.1| pseudouridine synthase, RluA family [Mycoplasma pneumoniae FH]
          Length = 326

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 78/303 (25%), Positives = 133/303 (43%), Gaps = 22/303 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  ++ VV    EN+R++++     P+I      K+LR G+V ++  + K   R+ SG 
Sbjct: 1   MSTAKF-VVPKAVENVRIEKFCLKLLPNIKLSQFFKLLRLGKVLLNNTKAKLGQRVSSGD 59

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +     I    H   E       V+LT+  D L+  +++ED ++ V +KPAG+  Q  +
Sbjct: 60  TIVFQFAIEPYLHNHSE------VVDLTQVQDDLQ--VIFEDEQLIVVDKPAGVVCQPDA 111

Query: 124 GIA--YHIDGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                   +  LK    ++  K      PR  HR+D+ T G+++ A+T  A Q L   FR
Sbjct: 112 KHELFNLANSLLKHCGYNQYFKNSLSFIPRFAHRIDRNTCGLVIGAKTNQALQELEAVFR 171

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
              + K Y  LV+G P N K     +  K ++     V V  +    A    + F+    
Sbjct: 172 HNLLMKQYQGLVFG-PFNFKGTQKAYWAKDAYQA--LVTVKAKPFPNAKPITTIFENSKY 228

Query: 236 FAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
             +     L ++  +G+THQ+R     +   +VGD KY      N     ++   LHA  
Sbjct: 229 LTKLDLSLLTIRLVSGKTHQIRACLNLLNTQLVGDRKYQLLQFKNRNRDFKH-QALHATN 287

Query: 295 MDL 297
           +  
Sbjct: 288 LSF 290


>gi|72127019|ref|XP_792641.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4 [Strongylocentrotus purpuratus]
 gi|115753235|ref|XP_001180714.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4 [Strongylocentrotus purpuratus]
          Length = 414

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 136/315 (43%), Gaps = 40/315 (12%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           R K    +++ + +     I      ++ Q      ++    +  L+  ++++   I   
Sbjct: 100 RRKLQAHMKAQKPIEEKEDIPKKRTDLRYQTRDLGRLSGEVVAKILRDRVIFDKGDIIAL 159

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSW---VDSKG----QKPRLTHRLDQETSGILVVARTR 164
           +KP G+ V GG G+ + ID  L      +++KG    ++  L HRLD+ET+G++++AR  
Sbjct: 160 DKPYGLPVHGGPGMKHSIDSLLPQLAWTLNNKGGGNTEELHLIHRLDKETTGVMLLARNE 219

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV----------- 213
             A+ L E FR R+I K Y  +  GIP  K+  +   +++K   G   +           
Sbjct: 220 RTARVLHEMFRKRQIIKRYLVITVGIPSPKEGILDMPMIEKEIDGKHRMVIKPDMADLYP 279

Query: 214 ----HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVG 268
                   +  + +  AI+ +KV+         ++++P TG  HQ+RVH    +GCPI+G
Sbjct: 280 DTIGMRSGRKSRDSKEAITRYKVLSERG-NCALVQLEPETGVKHQIRVHLAQGLGCPILG 338

Query: 269 DHKYCANFKGNFTSPIQN---------------KLYLHARYMDLPHPEGGR-LQITAPLP 312
           DHKY  + +                         ++LHAR + +P     +   I+  +P
Sbjct: 339 DHKYSHHDRLAPQKLTAGILHSLGITQPKARTVPMHLHARQLVIPETFDQQNYFISTKVP 398

Query: 313 AHMVKTWDSLGFKYD 327
                    L  KYD
Sbjct: 399 WFFSDNMKKLKLKYD 413


>gi|255318642|ref|ZP_05359873.1| ribosomal large subunit pseudouridine synthase A [Acinetobacter
           radioresistens SK82]
 gi|255304324|gb|EET83510.1| ribosomal large subunit pseudouridine synthase A [Acinetobacter
           radioresistens SK82]
          Length = 221

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 57/218 (26%), Positives = 96/218 (44%), Gaps = 12/218 (5%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
                       ++YED  + + +KPAG+    G    +    +L+  +  K    ++TH
Sbjct: 6   PFIYAPPQQPLSIIYEDDDLIIIDKPAGLLSVPGRLPEHQDSAYLR--LLEKYPHAKITH 63

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSGIL+ A+ R A   +++ F+ R + K Y +L+ G    +       +    + 
Sbjct: 64  RLDMATSGILMFAKHRDAEVAISKMFQARTVTKRYVALIQGQLNEQGSIDVPLITDWENR 123

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               VH      +    A + F+V+    +     + + P TGR+HQLRVH  ++G PI+
Sbjct: 124 PRQIVHF-----ELGKSAKTLFQVLQYHEEHDMTRVLLTPITGRSHQLRVHMQYIGHPIM 178

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           GD  Y     G +      ++ LHA Y+    P    L
Sbjct: 179 GDKLYHPEPGGFY----LRRMALHASYLAFQQPLSKDL 212


>gi|119944340|ref|YP_942020.1| pseudouridine synthase [Psychromonas ingrahamii 37]
 gi|119862944|gb|ABM02421.1| ribosomal large subunit pseudouridine synthase A [Psychromonas
           ingrahamii 37]
          Length = 222

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 62/217 (28%), Positives = 94/217 (43%), Gaps = 15/217 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D  I V NKP G+    G          L+           + HRLD  TSG+L
Sbjct: 14  LDILYQDDDIVVLNKPYGLLSVPGRAKKNRDSLALRILR--VWPNASVVHRLDMATSGLL 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++   ++A  H+   F+ + I K Y++ V GI K     I         I  D+ +  +Q
Sbjct: 72  ILTMRKSAQSHIGRQFQQKIIDKTYYARVEGIIKEDNGVIDLP------IRCDWENRPRQ 125

Query: 219 --NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             +      + + + V+    +    + ++P TGRTHQLRVH   +G  IVGD  Y   F
Sbjct: 126 IVDFAEGKSSQTEWSVVKR-EKLTTLVCLKPLTGRTHQLRVHLQAIGHAIVGDEFYSTEF 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
               +     +L LHA  + L HP    R+    P P
Sbjct: 185 GKKLSP---QRLALHAASITLTHPSTQQRITFNCPPP 218


>gi|294667753|ref|ZP_06732963.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
 gi|292602379|gb|EFF45820.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
          Length = 244

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 105/240 (43%), Gaps = 24/240 (10%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +LY+D  + V +KPAG+ V          D       +  G    L HRLD+ TSG 
Sbjct: 7   QLQILYQDDVLAVVDKPAGLMVHDSKLARGEDDFLADRLREQLGNPIFLVHRLDRATSGC 66

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A  R +A  L ++     ++K Y ++  G P  ++  + + L       G     VK
Sbjct: 67  LLLAFDRDSASALGKALMAGEVEKQYLTVCRGWPAEERFIVDHDL------DGGPGKPVK 120

Query: 218 QNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++
Sbjct: 121 ------KPAVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMI 174

Query: 268 GDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           GD  +       +F     +++ LHA  ++ PHP +G R+ +TAPL     K     G++
Sbjct: 175 GDTSHGDGRHNRSFRMLGIHRMLLHAERLEFPHPADGRRIGVTAPLDVEFSKACALFGWE 234


>gi|167623481|ref|YP_001673775.1| lysozyme [Shewanella halifaxensis HAW-EB4]
 gi|167353503|gb|ABZ76116.1| Lysozyme [Shewanella halifaxensis HAW-EB4]
          Length = 222

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 65/202 (32%), Positives = 96/202 (47%), Gaps = 13/202 (6%)

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           NKP+G+      GIA +      + +  + +   L HRLD  TSGI+V AR + A   L 
Sbjct: 27  NKPSGLLSNP--GIAEYTHDCALTRLQQRFKDAILVHRLDCATSGIMVFARNKKAESSLK 84

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F+ R+ QK Y + V GI K +   I   +          +            AI+H+K
Sbjct: 85  TQFQNRQTQKTYIAEVDGILKQQSGVIELAIAADKLNPPKQIV-----SASGKTAITHYK 139

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V+       C +E++P TGRTHQLRVH L +G  I+GD  Y  +   N       +L LH
Sbjct: 140 VLAQKP-ASCLVELKPVTGRTHQLRVHMLALGHTILGDDFYGEDQVINAA----KRLQLH 194

Query: 292 ARYMDLPHPEGGR-LQITAPLP 312
           A+ +   HP  G+ +Q ++  P
Sbjct: 195 AQTLSFTHPYSGKAMQFSSAHP 216


>gi|86158289|ref|YP_465074.1| ribosomal large subunit pseudouridine synthase A [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|85774800|gb|ABC81637.1| ribosomal large subunit pseudouridine synthase A [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 241

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 105/238 (44%), Gaps = 16/238 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
                 +L+ED+ +   +KPAG  V  G          L+  ++++  +  + HRLD+ T
Sbjct: 5   PAAPVAVLHEDAALLAVDKPAGRLVIPGREGGEPS---LREELEARFGRLWVVHRLDRNT 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+LV+ART AA + L  +F     +K Y +LV G+P  ++          +      + 
Sbjct: 62  SGVLVLARTAAAHRALNLAFDRGEPRKRYLALVRGVPPAEQRIEVAI----APARKGRMR 117

Query: 215 VVKQNEKGANYAISHFKVIDCF------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               ++     + +  + ++ +            +E  P TGRTHQ+RVH    G P+  
Sbjct: 118 PAAPDDPRGKPSATVVRRLEAYPSHPLGGGPLALVEALPETGRTHQIRVHLAAAGTPLAL 177

Query: 269 DHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           D  Y   A   G    P+  +  LHA  + L HP  GR L + APLPA +      L 
Sbjct: 178 DPAYGDAAPLLGPGGEPVLARTPLHAARLALRHPADGRELVLEAPLPADLAGVLALLR 235


>gi|67900736|ref|XP_680624.1| hypothetical protein AN7355.2 [Aspergillus nidulans FGSC A4]
 gi|40742536|gb|EAA61726.1| hypothetical protein AN7355.2 [Aspergillus nidulans FGSC A4]
          Length = 1054

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 61/298 (20%), Positives = 109/298 (36%), Gaps = 68/298 (22%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +K L SG V V+ K    +  +++G+V+              E  +  + +         
Sbjct: 564 KKALESGNVCVNGKPAGPHTVLKNGEVISHTLHR-------HEPPVTGNEIG-------- 608

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETS 155
              +++E   + V +KPAG+ V   S   YH +  ++      G    PR  +RLD+ TS
Sbjct: 609 ---IIHETDDLLVIDKPAGVPVH--STGRYHYNSVMEILRIQNGGAYVPRPCNRLDRLTS 663

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-KKSHIGGDYVH 214
           G++ V +T   A  +T   + R +QK Y + V G   +    +   ++     +G + V 
Sbjct: 664 GVMFVGKTAQGADRMTVKLKERTVQKEYVARVKGRFPDGVVVVDQPIMSVSPKVGLNRVR 723

Query: 215 VVKQNEKGANYAISHFKVIDCF----------------------------AQKFCWLEMQ 246
                      A + F+ +  +                            ++ +  +   
Sbjct: 724 A------TGKEAKTKFRRLAYYPPPSPTTSTSDEGENARPATPPPSYVNESEGYSIVHCF 777

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANF-----------KGNFTSPIQNKLYLHAR 293
           P TGRTHQ+RVH   +G PI  D  Y                 +    I ++L    R
Sbjct: 778 PLTGRTHQIRVHLQFLGHPISNDPIYSNRRVFGPDLGKNDSSADLDEEIIDRLMAMGR 835


>gi|329851218|ref|ZP_08265975.1| RNA pseudouridylate synthase family protein [Asticcacaulis
           biprosthecum C19]
 gi|328840064|gb|EGF89636.1| RNA pseudouridylate synthase family protein [Asticcacaulis
           biprosthecum C19]
          Length = 200

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 60/212 (28%), Positives = 101/212 (47%), Gaps = 16/212 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++Y D  + V +KPAG+    G G        L + V          HRLD  TSG++V
Sbjct: 1   MIVYADEAMVVADKPAGLLSVPGRGPD--KQDCLVARVRDTYPDALTVHRLDMATSGLIV 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R   A + L+++F  RR +K Y ++V G   ++ E     +    +     V     +
Sbjct: 59  LGRGPNAQRALSQAFENRRTEKRYIAVVHGHTPDEGEVNLPLITDWPNRPRQKV-----D 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 +++ +++I         +E++P TGR+HQLRVH L +G PIVGD  YC +    
Sbjct: 114 HDIGKPSLTRYRIISRD-DTTSRVELEPVTGRSHQLRVHMLAIGHPIVGDEFYCPDIPA- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRL-QITAP 310
                  ++ LHA  + +PHP  G + +  +P
Sbjct: 172 ------PRMLLHAERLAVPHPLTGEMVRFYSP 197


>gi|299469961|emb|CBN79138.1| Ribosomal large subunit pseudouridine synthase D [Ectocarpus
           siliculosus]
          Length = 543

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 74/311 (23%), Positives = 128/311 (41%), Gaps = 59/311 (18%)

Query: 26  KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILD 85
           ++ +P ++     K +R  ++ ++   V+ ++++  G  V +             ++   
Sbjct: 182 RDDFPSVSSAR--KAVRRKELLLNGTEVRNDSKVNPGDTVTMQ------------KRTQP 227

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--- 142
                 K S  L   +L+ED  I V  KPAG++V GG+G      G  +S   +      
Sbjct: 228 GLFPQGKPSCTLP--ILWEDDFIAVIIKPAGVAVHGGTGEDDPGPGGRRSVRQALPYMLT 285

Query: 143 ----------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                     +P   HRLD+ T G+L+ A+TR A   + ++F  R + K Y +LV G  +
Sbjct: 286 PTKSEDRPLHRPLHCHRLDKATGGLLICAKTRPALSAVGDAFEQRLVSKRYVALVAGELE 345

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-----CWLEMQP 247
                I   L                        +++++V     +         +++ P
Sbjct: 346 G-SGAIVTPL-------------------DGKACLTNYRVRGPPVRSLKTSVITTVDLWP 385

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
            TGR HQLR H L +GCPI+GD +Y  +         +  +YL A  +  PHP  G  + 
Sbjct: 386 VTGRLHQLRRHLLSIGCPILGDRRYTPDE----VPFQEGGMYLQAVGLTFPHPITGEEMN 441

Query: 307 ITAPLPAHMVK 317
            + P PA   K
Sbjct: 442 FSIPEPAKFEK 452


>gi|187735932|ref|YP_001878044.1| pseudouridine synthase [Akkermansia muciniphila ATCC BAA-835]
 gi|187425984|gb|ACD05263.1| pseudouridine synthase [Akkermansia muciniphila ATCC BAA-835]
          Length = 258

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 59/254 (23%), Positives = 105/254 (41%), Gaps = 20/254 (7%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI----DGFLKSWVDSKGQ 142
            ++    + F    +  E     V +K A + V   +G            L S+  + G 
Sbjct: 4   PISEAPIACFPHFEVAAESGDWIVVDKGAPLIVHPSNGKKEPCLLEGVEALLSYEIANGA 63

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L +RLD+ETSG+ +VA+ + AA+ L  + + R I K Y ++V   P+  +      +
Sbjct: 64  ALSLVNRLDRETSGLTLVAKHKRAARELGRAMQRRLIHKEYLAIVQEWPEWTETACTAPI 123

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHA 259
           L++  +    + V +          + F+    +         +   P TGR HQ+RVH 
Sbjct: 124 LRQGEVAESRIWVKQAVHPAGKACTTVFRKERTWNTRRGPLALVRCIPETGRMHQIRVHL 183

Query: 260 LHMGCPIVGDHKYCAN-------FKGNFTSPIQNKL-----YLHARYMDLPHPEGGRLQI 307
            H+G PI+GD  Y  +        +  ++  ++ +L      LHA  ++ P  E      
Sbjct: 184 AHLGHPILGDKIYGPSEHCYLEYIQHGWSRELEERLVLPRHALHACRLEFPFDE-ETFTA 242

Query: 308 TAPLPAHMVKTWDS 321
            APLP  M    ++
Sbjct: 243 EAPLPEDMRLLLET 256


>gi|332994209|gb|AEF04264.1| Pseudouridylate synthase [Alteromonas sp. SN2]
          Length = 265

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 100/253 (39%), Gaps = 17/253 (6%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           +             +    +LY+D  I   +KP G+ V       +     +++  D   
Sbjct: 11  ETPSEKAGSNSVQPYPPLNILYQDEHIVAIDKPPGLLVHRSPIDRHETRFAVQTLRDQLN 70

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           +     HRLD+ TSG+L+ +     A  L +    +++QK Y ++V G  K+        
Sbjct: 71  KHVFPAHRLDRPTSGVLLFSFDSKTAALLGQQLMNKQVQKQYHAIVRGYVKHSGLIDYAL 130

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGR 251
             +   I   +    K+ ++    A + ++ +               ++  +++ P TGR
Sbjct: 131 KYRYDKIADKH----KRPQQAPQQATTVYESLANYELPFAVGKYETARYSLVKLLPSTGR 186

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
            HQLR H +H+  PI+GD  +    +  F  T      L L    M   HP  G+ L + 
Sbjct: 187 KHQLRRHMVHIRHPILGDTTHGDGKQNKFLQTHFSFQNLALSCTQMGFYHPITGKWLSVF 246

Query: 309 APLPAHMVKTWDS 321
             + + M +  D+
Sbjct: 247 VRMHSEMQRVLDA 259


>gi|209693957|ref|YP_002261885.1| ribosomal large subunit pseudouridine synthase A [Aliivibrio
           salmonicida LFI1238]
 gi|208007908|emb|CAQ78038.1| ribosomal large subunit pseudouridine synthase A [Aliivibrio
           salmonicida LFI1238]
          Length = 244

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 110/247 (44%), Gaps = 15/247 (6%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           L  +       ++Y+D  I   NKPAG+    G     H D      V ++    +L HR
Sbjct: 4   LEYNPPMEPLDIVYQDEAILAVNKPAGLLSNPGRAPE-HYDSVWSRVV-AEFPDAQLVHR 61

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG+++ A  + A +H+ + F+ R   K+Y++ VWG  +  +  I   L+      
Sbjct: 62  LDMSTSGLMIFALYKEAERHIKKQFQYRLTHKVYYARVWGNVEKVEGQIDLPLICD-WPN 120

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                V  ++      + + ++VI    +K   + + P TGR+HQLRVH +  G  IVGD
Sbjct: 121 RPRQKVCYEH---GKSSQTGYEVIQ-VEEKTTLVRLLPITGRSHQLRVHMMEEGHEIVGD 176

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP---LPAHMVKTWDSLGFK 325
             Y +     F+    ++L LH+  +   HPE  + + + AP    P       D++   
Sbjct: 177 EFYASKEALAFS----DRLQLHSAELSFYHPETDKFISLFAPCAFYPEAQAGVLDAMDIA 232

Query: 326 YDRNLYI 332
             R  Y 
Sbjct: 233 PVRPDYK 239


>gi|333030807|ref|ZP_08458868.1| pseudouridine synthase [Bacteroides coprosuis DSM 18011]
 gi|332741404|gb|EGJ71886.1| pseudouridine synthase [Bacteroides coprosuis DSM 18011]
          Length = 312

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 63/301 (20%), Positives = 119/301 (39%), Gaps = 30/301 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + +   P  +   L+  L    V VDKK V   +  ++ G +V+I    ++   +  +  
Sbjct: 29  FLQAKMPEASRTKLKSFLSRRIVFVDKKIVTHPDYPVERGMLVQIDHNKHSNTELRSKD- 87

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
                             +LYED+ + V  K AG+     G          L  ++    
Sbjct: 88  ----------------INVLYEDAYLIVIEKKAGVLSIAVGKNKGKSAHAILNHYLKKTN 131

Query: 142 QK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            +    L H+L+ + SGI++ A+      +L ++++   I   +  LV G  + +     
Sbjct: 132 HRGQALLVHKLEVDESGIMIFAKDEETKFNLQKNWKELIINHTFVGLVEGDVQEESGLNI 191

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +W+ +++    ++ + ++   +    AI+ F+ I   A     LE  P   R +++RV  
Sbjct: 192 SWIDEETG-KLNFSNNLETAPRDPVKAITRFRTIK-KANGLSMLEFDPREDRNNKIRVQM 249

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             MG PI+GD KY       F SP+  +  LHA  +   HP     ++     P      
Sbjct: 250 AEMGHPILGDKKYG-----EFISPL-KRFALHAFLIRFRHPVTKELMKFEISYPKEFRSL 303

Query: 319 W 319
            
Sbjct: 304 M 304


>gi|256822673|ref|YP_003146636.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
 gi|256796212|gb|ACV26868.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
          Length = 222

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 54/217 (24%), Positives = 103/217 (47%), Gaps = 10/217 (4%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +L+ D      NKPAG+    G           +     K +   + HRLD  TSG+
Sbjct: 13  PVRILHPDKHFLFVNKPAGLLSIPGRHEENKDCVVTRLQNHPKSKTASIVHRLDMATSGV 72

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+T+ A + +++ F +R+  K Y ++V  I +     I   ++             K
Sbjct: 73  MILAQTKFAHREISKQFELRQTDKYYIAVVDAIVEKDSGVIDLPMIADWPNRPK----QK 128

Query: 218 QNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + +    A++ ++V++    ++   L+++P TGR+HQLR+H   +G PI+G H Y    
Sbjct: 129 IDFEEGKKAVTEWEVLERDLEKQTTRLKLKPITGRSHQLRLHCFELGHPILGCHLY---- 184

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             N +     +L LHA  + + HP+  + + + +P P
Sbjct: 185 HKNGSETKAKRLLLHAASLTITHPKSCKNITVESPCP 221


>gi|262372045|ref|ZP_06065324.1| 23S RNA-specific pseudouridylate synthase [Acinetobacter junii
           SH205]
 gi|262312070|gb|EEY93155.1| 23S RNA-specific pseudouridylate synthase [Acinetobacter junii
           SH205]
          Length = 228

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 63/223 (28%), Positives = 102/223 (45%), Gaps = 15/223 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           SDFL   L++ D    V +KPAG+    G      +   L + +     K  L HRLD++
Sbjct: 16  SDFLSEHLIHRDEDFMVIHKPAGLLTVPGKTPD--LQDCLINRLLKLEPKTLLIHRLDRD 73

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   ++    H++  F+ R+  KIY +LV G  + +       +   S      V
Sbjct: 74  TSGILVFGLSKFGQSHISRQFQDRQTSKIYQALVAGHLEGEGIVDIPVIYDPSRPPLHIV 133

Query: 214 HVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                       A++ ++VI+           +++ P TGR+HQLRVH  ++G PI+GD 
Sbjct: 134 DASHH-----KPALTEWQVIEHLEIKGHPVTRVQLVPITGRSHQLRVHMQYLGHPILGDT 188

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
            Y    +      + ++L LHA  +   HP+   +L     +P
Sbjct: 189 LYATPEQQQ----LYDRLCLHATELSFTHPKTAQQLTFNCLVP 227


>gi|254428126|ref|ZP_05041833.1| RNA pseudouridine synthase superfamily [Alcanivorax sp. DG881]
 gi|196194295|gb|EDX89254.1| RNA pseudouridine synthase superfamily [Alcanivorax sp. DG881]
          Length = 204

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 62/212 (29%), Positives = 99/212 (46%), Gaps = 12/212 (5%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y D+ I + NKPA +    G   A          + ++    RL HRLD +TSGI+V A 
Sbjct: 2   YRDAHILLINKPAYLLSVPGR--APENKDCAVRRLQAQYADIRLVHRLDLDTSGIMVFAL 59

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           T  A   L+  F++R +QK Y ++V G+ ++    I   L+           + K   + 
Sbjct: 60  TAQAQSRLSRLFQLRTVQKRYQAVVHGLVEHDSGSIDLPLIAD----WPNRPLQKVCHET 115

Query: 223 ANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
              A++H++V++         L + P TGR+HQLR+H   +G PI+G   Y         
Sbjct: 116 GKNALTHYRVLERDIPGNRTRLLLSPVTGRSHQLRIHCRELGHPIIGCDMYAP----AEI 171

Query: 282 SPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
             +  +L LHA ++   HP  G   + T+P P
Sbjct: 172 EALSPRLLLHAEWLAFNHPVTGLWQEFTSPSP 203


>gi|157376031|ref|YP_001474631.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157318405|gb|ABV37503.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 218

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 62/215 (28%), Positives = 102/215 (47%), Gaps = 13/215 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             + Y+D  I V NKP+G+    G   A   D  +   +  +  +  L HRLD  TSGI+
Sbjct: 14  LDIRYKDRDIIVINKPSGLLSNPGRA-ANTFDCAINRLLQ-RYPEAILVHRLDCATSGIM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A  + A  ++   F+ R  +K Y + V G   +++  I   +        +   + K 
Sbjct: 72  VFALNKKAESNIKTQFQNRMSKKTYIAEVQGHIVDEEGVIELAM----KPDTERPPLQKL 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E+G   + ++FKV++   +    +E++P TGRTHQLR+H L +G PI+GD  Y      
Sbjct: 128 AEEG-KPSKTYFKVLERR-KNSTLVELKPVTGRTHQLRLHMLAIGHPILGDDFYG----D 181

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                   +L LHA  + + HP  G+ +   +  P
Sbjct: 182 EKVIAASKRLCLHAMSLSITHPYSGKAMTFHSAHP 216


>gi|260769549|ref|ZP_05878482.1| pseudouridylate synthase LSU rRNA-specific [Vibrio furnissii CIP
           102972]
 gi|260614887|gb|EEX40073.1| pseudouridylate synthase LSU rRNA-specific [Vibrio furnissii CIP
           102972]
          Length = 558

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 67/228 (29%), Positives = 101/228 (44%), Gaps = 19/228 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           LD +  L   ++  +  ++Y+D  I V NKPA      G  I       L+     + + 
Sbjct: 340 LDDNPLLNNPAEGQEIEIVYQDEAIVVINKPAEFLSVPGVNIKDSALTRLEQQF-PEVEG 398

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+LV A TR A + L + F  R ++K Y +L+ G   + + CI   L 
Sbjct: 399 PFVLHRLDMSTSGLLVFALTRRANKSLQKQFITRGVEKRYVALLSGEIAHGEGCITLPL- 457

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM- 262
           +          V  ++      A ++++ I    Q    + + P TGRTHQLRVH  H  
Sbjct: 458 RPDLDDRPRQMVCFEH---GKAAETYWQTIGT-EQGRTRVYLFPKTGRTHQLRVHCAHAQ 513

Query: 263 --GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
               PI+GD  Y             N+L+LHA  +   HP    R+  
Sbjct: 514 GFNTPILGDDLYGEK---------ANRLHLHAESLSFDHPYTKQRMTF 552


>gi|148259875|ref|YP_001234002.1| pseudouridine synthase [Acidiphilium cryptum JF-5]
 gi|146401556|gb|ABQ30083.1| pseudouridine synthase [Acidiphilium cryptum JF-5]
          Length = 224

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 60/183 (32%), Positives = 90/183 (49%), Gaps = 6/183 (3%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +  ++LY  + + V +KPAG+    G G    ++ +   W       P L HRLD +T+
Sbjct: 1   MIDPVILYHSTHLVVIDKPAGLPSHRGRGGGPSVEDWFPRWRRG-ADGPWLVHRLDADTA 59

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L +AR +     L  +F  RR+ K YW++V G+P      I   L +++  GG  V  
Sbjct: 60  GCLAIARRKTTLVALQRAFAQRRVGKTYWAIVEGVPAAAHGTIELALARRTVPGGWRVA- 118

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               +   + AI+ ++ +    Q    LE++P TGRTHQLRVH    G PIVGD  Y   
Sbjct: 119 ---PDPRGDPAITDWRCLAA-GQGRALLELRPRTGRTHQLRVHCAESGFPIVGDPLYGTE 174

Query: 276 FKG 278
             G
Sbjct: 175 AGG 177


>gi|317122830|ref|YP_004102833.1| pseudouridine synthase [Thermaerobacter marianensis DSM 12885]
 gi|315592810|gb|ADU52106.1| pseudouridine synthase [Thermaerobacter marianensis DSM 12885]
          Length = 414

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 76/416 (18%), Positives = 127/416 (30%), Gaps = 106/416 (25%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  ++YVV   DE   +L R  +     +    + ++LR G++ V+ +R   +  +++G 
Sbjct: 1   MPRLRYVVTPADE-GQKLHRLARRWLRDVPLSAVFRLLRQGRITVNGRRAPRDAVLRAGD 59

Query: 64  VVR----------------------IPPVINALNHIIKEQKILDSSVNL----------- 90
           V+                        P    A  H    +        L           
Sbjct: 60  VIEAELERVEGPGPDPSGLRPGAAGRPGPRPAAPHPPGPRPAAPQPPGLRPAAPHPPAPH 119

Query: 91  --TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG------- 141
                   L  +++YED  + V NKPAG+   G     + +  +++  +  +G       
Sbjct: 120 VPGPRVPELDPVIVYEDDHVLVVNKPAGMLTHGDGHAEWTLLAWVRDQLARRGTLPAGAL 179

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQH--------------------------LTESFR 175
            +P   HRLD+ TSG++   +TR  A                            L     
Sbjct: 180 FQPSPAHRLDRNTSGLVAFGKTRHGAARLAEALRSGQAIKEYLAVVRGRPPEGLLQHRLW 239

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN----------- 224
             R  ++   +            +  +   S  G         +E G             
Sbjct: 240 RDRDHRVSRVIGQDGEAPTAATTSRDIRASSGAGRTLPARPAADEPGPGAAGAPPAATGD 299

Query: 225 ----------------YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                           +A     V+      F    +   TGRTHQ+R      G P+ G
Sbjct: 300 LRRTGAAAPGAAREARHAALRLAVL-AVGHGFSLCRIHLLTGRTHQIRAQLAATGHPLAG 358

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           D KY          P   +  LH   + LP    G + + APLP  +      LG 
Sbjct: 359 DRKYGGP-----KVPGLQRPALHCYRLVLP----GGVDVVAPLPPDLTGLCRRLGL 405


>gi|239994623|ref|ZP_04715147.1| pseudouridylate synthase, 23S RNA-specific [Alteromonas macleodii
           ATCC 27126]
          Length = 279

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 105/253 (41%), Gaps = 9/253 (3%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           EQ I    V      + L   +LY+D  I    KP G+ V       +     +++  D 
Sbjct: 23  EQTIGKVDVGEEDSVNALHLPVLYQDEHIIAIEKPPGLLVHRSPIDRHETVFAVQTLRDQ 82

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            GQ     HRLD+ TSG+LV + +   A  L +    +++ K Y ++V G   +      
Sbjct: 83  IGQHVYPAHRLDRPTSGVLVFSFSSEIAAKLGQQMMDKQVVKTYHAIVRGFVHHTGYIDY 142

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGAN--YAISHFKVID----CFAQKFCWLEMQPHTGRTH 253
               +   I   +    +  +  +    +++ F+V +      + ++  +++ P TGR H
Sbjct: 143 ALKYRYDKIADKHKRPQQPPQPASTMYQSVAKFEVPEPVGKYQSARYSLVKLSPSTGRKH 202

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGGR-LQITAP 310
           QLR H +H+  PI+GD  +    +  F       N L L    M   HP  G+ + I + 
Sbjct: 203 QLRRHMVHIRHPIIGDTTHGDGKQNKFAKQHFNFNNLALSCTQMGFSHPVTGKWVSINSQ 262

Query: 311 LPAHMVKTWDSLG 323
           + + M    + L 
Sbjct: 263 MHSEMRLWLEKLA 275


>gi|89891472|ref|ZP_01202977.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BBFL7]
 gi|89516246|gb|EAS18908.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BBFL7]
          Length = 227

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 67/223 (30%), Positives = 108/223 (48%), Gaps = 14/223 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           + + +L+ED+ +   NK +G  VQG       +   +K ++  K  KP      +THRLD
Sbjct: 3   INNRILFEDNHLIAVNKKSGDLVQGDKTGDVILPEMIKEYIAVKYDKPGAVFLGVTHRLD 62

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG++V ART  A   + + F     +K YW++V G    K++ + + L++ +     
Sbjct: 63  RPTSGVVVFARTSKALPRMNKLFANHETRKTYWAVVEGTTPKKQDRLIHHLVRNTKQNKS 122

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y H        +  AI  + VI     ++  LE+   TGR HQ+R     +GC I GD K
Sbjct: 123 YAH--DHGVPNSKEAILSYTVIQKL-DRYTLLEIALETGRHHQIRAQLSKIGCVIKGDLK 179

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           Y A       S     ++LHAR ++  HP     ++I AP+P 
Sbjct: 180 YGARRSNKDGS-----IHLHARQLEFIHPVKKEPVKIIAPVPD 217


>gi|293611211|ref|ZP_06693509.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292826462|gb|EFF84829.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 221

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 108/231 (46%), Gaps = 13/231 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + N           +L+ED  + V +KPAG+    G    +H   +L+  V  K   
Sbjct: 1   MPLNDNFVYAPPQDPLSILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPL 58

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G    +       + 
Sbjct: 59  AKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKHYIALVQGQVAQEGSVEVPLIT 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +   +A + F+ +          + ++P TGR+HQLRVH +H+
Sbjct: 119 DWENRPRQIVHF-----ELGKHAKTLFQPLIYDEKNNQSRVLLEPVTGRSHQLRVHMMHI 173

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G PI+GD  Y    K        N++ LHA Y+   HP  G  + I + +P
Sbjct: 174 GHPIMGDKLYHPEPK----RFRLNRMALHAAYLAFQHPLNGTDVVIESQVP 220


>gi|190347088|gb|EDK39300.2| hypothetical protein PGUG_03398 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 611

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 95/237 (40%), Gaps = 25/237 (10%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +  +  G V +++K    ++ +++G ++              E  +    +         
Sbjct: 147 KAAISEGSVTLNRKPANIDSIVRNGDLISHRCHR-------HEPAVSSRPIK-------- 191

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ED  +   +KP+GI V       Y  +   K +    G+     +RLD+ TSG+
Sbjct: 192 ---IVHEDDDVIAIDKPSGIPVHPVG--RYRYNTITKIFQHEFGRVVHPCNRLDRLTSGL 246

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           + + +T   A    +  + R ++K Y + V G    ++  +   +   S        +  
Sbjct: 247 MFLGKTPKGADKFVQQIKDRTVRKEYIARVIGKFPCEEITVEVPIKTVSP----KHTLNM 302

Query: 218 QNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + K    A + FK I    A     ++  P TGRTHQ+RVH  H+G  I  D  Y 
Sbjct: 303 VDPKNGKEAKTKFKRISYDPASNTSIVKCYPLTGRTHQIRVHLQHIGHAIANDPIYS 359


>gi|119469549|ref|ZP_01612453.1| putative 23S rRNA pseudouridylate 746 synthase [Alteromonadales
           bacterium TW-7]
 gi|119447084|gb|EAW28354.1| putative 23S rRNA pseudouridylate 746 synthase [Alteromonadales
           bacterium TW-7]
          Length = 235

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 64/220 (29%), Positives = 107/220 (48%), Gaps = 17/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK------GQKPRLTHRLDQET 154
           +LY+D+ I V NKP+G+    G   + + D      V+ +        K +L HRLD  T
Sbjct: 24  ILYQDNDILVINKPSGLLSLSGKN-SENWDSVHYRLVNGQKGLTPAFLKAKLVHRLDLGT 82

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI++V+    +++HL + F++R ++K Y +++ G     +  I   + K + +      
Sbjct: 83  SGIMLVSLNDVSSKHLNKQFQLRSVKKHYVAVLQGCISEDRGQIDAPIAKDTQL----FP 138

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            VK  +     A++ F VI   A     ++   P TGRTHQLR+H+  +G PI+G   Y 
Sbjct: 139 RVKICKLEGKPAVTEFNVIKRLANPVRTYVHFSPLTGRTHQLRIHSHFIGHPILGCDLY- 197

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              K   +  +  +L LHA  +   HP   + + I  P P
Sbjct: 198 ---KSAHSEKLSKRLQLHASDLFFEHPTTNQAIHIHCPSP 234


>gi|291320720|ref|YP_003515985.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           agalactiae]
 gi|290753056|emb|CBH41032.1| Ribosomal large subunit pseudouridine synthaseC [Mycoplasma
           agalactiae]
          Length = 284

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 60/292 (20%), Positives = 115/292 (39%), Gaps = 30/292 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +   + ++ +   +L ++  + +  +    + ++ R   ++V+ KR+   N  +++G  +
Sbjct: 1   MHKFIAQSSDNGRKLIKYISSLFKKLPEGRIYRLFRQKSIKVNNKRIADSNYVVKTGDEI 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I  + +  + +I +             S  L S ++YED  I + NK AG  V G S  
Sbjct: 61  IIYGIKDEPSFVIYDN------------SWKLDSDIVYEDDNILLINKKAGTIVHGDSNC 108

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             +       +  +   +P    RLD+ TSG+++ A+   A   L      R+ + +   
Sbjct: 109 LDNQVFSYLKFKQNSAFRPSHVGRLDKWTSGLIMYAKNYPALAEL-----NRKTEFLDKI 163

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V     N  + I +  +    +    V            A + F       +K   L  
Sbjct: 164 YVLKSDYNPHDEIVSVYVHHDELQQKMVATKNMQHPDDKMAKTRFF------KKDNKLYA 217

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           Q  TGR HQ+R    ++  PI GD KY +  KG        ++YLH   +  
Sbjct: 218 QLFTGRKHQIRATLEYLEYPIYGDSKYGSKAKGT------KRVYLHCYKLKF 263


>gi|116493188|ref|YP_804923.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
 gi|116103338|gb|ABJ68481.1| Pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
          Length = 294

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 73/301 (24%), Positives = 134/301 (44%), Gaps = 34/301 (11%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +  +     ++   LQ+I   G+ +  ++  V+F++++   + + I              
Sbjct: 17  KVLQR--SGMSQRLLQRIQNEGRLIDENENDVEFSDKLMPFEPIWI-------------- 60

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK---SWV 137
           ++ D   +           +++ED    + NKPAG+ +V G S     +   +K     +
Sbjct: 61  ELPDEEQDQNVAISDGPLDIIFEDKNWLLVNKPAGLTAVPGPSDREDTLVNRIKGHWQAI 120

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +SK   P L  RLD+ TSGI +VAR + +   L+E     +I+KIY ++V G+ + +K  
Sbjct: 121 ESKNMMPHLVTRLDRFTSGITLVARHQVSNSLLSEQVAHHKIKKIYLAMVDGVVQAEKGT 180

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               L     +  D +H   +++     A + FKV+  F +    +++   TGRTHQ+RV
Sbjct: 181 FNQSLG----LAADGIHREVRDD--GQQATTSFKVLKRF-ENQTLVQIHLKTGRTHQIRV 233

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
           H  + G P+VGD  Y              +  LHA  +    P    ++  TA LP  + 
Sbjct: 234 HFANAGHPLVGDQLYDGPMDR-----GIKRQALHASSIRFFDPFIDEKVSFTAELPDDLK 288

Query: 317 K 317
           +
Sbjct: 289 Q 289


>gi|124267382|ref|YP_001021386.1| ribosomal large subunit pseudouridine synthase A [Methylibium
           petroleiphilum PM1]
 gi|124260157|gb|ABM95151.1| ribosomal large subunit pseudouridine synthase A [Methylibium
           petroleiphilum PM1]
          Length = 213

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 65/216 (30%), Positives = 97/216 (44%), Gaps = 17/216 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY D  + V +KP G+    G G        L + V       R+ HRLD+ TSG++V A
Sbjct: 9   LYRDEALLVVDKPPGLLAVPGRGPL--KQDCLAARVQRAWPDARVVHRLDEATSGLMVFA 66

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
                 + L+ +F  R ++K Y ++V G  +     I   L      G D+ +  +Q  +
Sbjct: 67  LDVEMQRRLSRAFEQREVEKRYVAVVAGHVEPAAGRIDLPL------GADWPNRPRQQVD 120

Query: 220 EKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                 A +H++V+    +     LE+ P TGRTHQLRVH + +G  I+GD  Y      
Sbjct: 121 HARGKPARTHWQVLSYDTSGDSTRLELTPETGRTHQLRVHLMAIGHAILGDALYAPPS-- 178

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR--LQITAPLP 312
                   +L LHA  +   HP  GR  L   +P P
Sbjct: 179 --MMARSPRLLLHASALAFAHPMPGRPALAFESPPP 212


>gi|331092518|ref|ZP_08341340.1| hypothetical protein HMPREF9477_01983 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330400739|gb|EGG80342.1| hypothetical protein HMPREF9477_01983 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 217

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 62/219 (28%), Positives = 104/219 (47%), Gaps = 11/219 (5%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRL 150
            +K  ++YED  + V +K   I+ Q        +   LK+++  +  K       + HRL
Sbjct: 2   DIKDYIVYEDEHLLVCHKLPKIATQTSRIGEKDMVSLLKNYLHQQSSKKQEPYLAVIHRL 61

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           DQ   G+LV A+T  AA+ L+   + +   K Y ++V   P+ ++  + N+++K      
Sbjct: 62  DQMVEGLLVFAKTPFAAKELSRQLQQKGFGKEYRAVVCKTPQQQEGTLVNYMVKDKRSNT 121

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               V  +NE GA  A+ H+KV +        L +   TGR HQ+RV   ++GC I+GD 
Sbjct: 122 SR--VCGENEMGAKKAVLHYKVTEEQGDGTAVLHICLETGRHHQIRVQLSNIGCGIMGDA 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
           KY A   GN+     +K+ L A  +   HP+    +   
Sbjct: 180 KYNA---GNYEQEKWDKIALCAYRLRFVHPKTKKEMVFE 215


>gi|295661807|ref|XP_002791458.1| RNA pseudouridylate synthase domain-containing protein
           [Paracoccidioides brasiliensis Pb01]
 gi|226280015|gb|EEH35581.1| RNA pseudouridylate synthase domain-containing protein
           [Paracoccidioides brasiliensis Pb01]
          Length = 525

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 68/351 (19%), Positives = 115/351 (32%), Gaps = 82/351 (23%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        +K +  G V ++ K V  + +IQ+G V+              E
Sbjct: 65  LDVF-GTEFRDRPREYYKKAIEDGAVCINGKAVTIDTKIQNGDVISHTLHR-------HE 116

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    + L           ++ED+ + V +KPAG+ V       Y+    +       
Sbjct: 117 PPVTSQPIGL-----------IHEDNDMIVIDKPAGVPVHPAGRYNYNSVLEIMKAERGH 165

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P   +RLD+ TSG++ + +    A+ + E  R R ++K Y + V G   +       
Sbjct: 166 GWVPYPCNRLDRLTSGVMFIGKHPRGAEQIGEKLRSRTVRKEYVARVKGKFPDGVVLCDQ 225

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----------------------- 237
            +LK S I G     + +       A + F+ I  +                        
Sbjct: 226 PMLKISPILG-----LNRARASGKEARTKFRRIAYYPPYEPAEKSSVSSAEPATPPATLP 280

Query: 238 --------------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                                     + +  +   P TGRTHQ+RVH  ++G PI  D  
Sbjct: 281 NEMNISNSSTATPTGVATPVPKSSDEEGYSIVHCLPLTGRTHQIRVHLQYLGYPITNDPI 340

Query: 272 YCANF-------KGNFTSPIQNKLYLHARYMDLPHPEG--GRLQITAPLPA 313
           Y           K + T     ++      M    P          AP P 
Sbjct: 341 YSNRRVFGHSLGKADATGENDEQIIYRLSKMGKTEPADSLSYQTFQAPPPE 391


>gi|225682103|gb|EEH20387.1| DRAP deaminase [Paracoccidioides brasiliensis Pb03]
          Length = 525

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 68/351 (19%), Positives = 115/351 (32%), Gaps = 82/351 (23%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        +K +  G V ++ K V  + +IQ+G V+              E
Sbjct: 65  LDVF-GTEFRDRPREYYKKAIEDGAVCINGKAVTIDTKIQNGDVISHTLHR-------HE 116

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED+ + V +KPAG+ V       Y+    +       
Sbjct: 117 PPVTSQPIG-----------VIHEDNDMIVIDKPAGVPVHPAGRYNYNSVLEIMKAERGH 165

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P   +RLD+ TSG++ V +    A+ + E  R R ++K Y + V G   +       
Sbjct: 166 GWVPYPCNRLDRLTSGVMFVGKHPKGAEQIGEKLRSRTVRKEYVARVKGKFPDGVVLCDQ 225

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----------------------- 237
            +LK S I G     + +       A + F+ I  +                        
Sbjct: 226 PMLKISPILG-----LNRARASGKEARTKFRRIAYYPPYEPAEKGSVSSTEPATPPATLP 280

Query: 238 --------------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                                     + +  +   P TGRTHQ+RVH  ++G PI  D  
Sbjct: 281 DEMNISNSSTATPTGVATPLPKSSDEEGYSIVHCLPLTGRTHQIRVHLQYLGYPITNDPI 340

Query: 272 YCANF-------KGNFTSPIQNKLYLHARYMDLPHPEG--GRLQITAPLPA 313
           Y           K + T     ++      M    P          AP P 
Sbjct: 341 YSNRRVFGHSLGKADATGDNDEQIIYRLSKMGKTEPADSLSYQTFQAPPPE 391


>gi|226289283|gb|EEH44795.1| RNA pseudouridylate synthase domain-containing protein
           [Paracoccidioides brasiliensis Pb18]
          Length = 525

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 68/351 (19%), Positives = 115/351 (32%), Gaps = 82/351 (23%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        +K +  G V ++ K V  + +IQ+G V+              E
Sbjct: 65  LDVF-GTEFRDRPREYYKKAIEDGAVCINGKAVTIDTKIQNGDVISHTLHR-------HE 116

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED+ + V +KPAG+ V       Y+    +       
Sbjct: 117 PPVTSQPIG-----------VIHEDNDMIVIDKPAGVPVHPAGRYNYNSVLEIMKAERGH 165

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P   +RLD+ TSG++ V +    A+ + E  R R ++K Y + V G   +       
Sbjct: 166 GWVPYPCNRLDRLTSGVMFVGKHPKGAEQIGEKLRSRTVRKEYVARVKGKFPDGVVLCDQ 225

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----------------------- 237
            +LK S I G     + +       A + F+ I  +                        
Sbjct: 226 PMLKISPILG-----LNRARASGKEARTKFRRIAYYPPYEPAEKSSVSSTEPATPPATLP 280

Query: 238 --------------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                                     + +  +   P TGRTHQ+RVH  ++G PI  D  
Sbjct: 281 DEMNISNSSTATPTGVATPVPKSSDEEGYSIVHCLPLTGRTHQIRVHLQYLGYPITNDPI 340

Query: 272 YCANF-------KGNFTSPIQNKLYLHARYMDLPHPEG--GRLQITAPLPA 313
           Y           K + T     ++      M    P          AP P 
Sbjct: 341 YSNRRVFGHSLGKADATGDNDEQIIYRLSKMGKTEPADSLSYQTFQAPPPE 391


>gi|331087231|ref|ZP_08336301.1| hypothetical protein HMPREF0987_02604 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330408917|gb|EGG88378.1| hypothetical protein HMPREF0987_02604 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 227

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 60/218 (27%), Positives = 100/218 (45%), Gaps = 15/218 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-----KGQKPRLTHRLD 151
           ++S +LYED  + V  KPAG+ VQ        +   LK++        +     + HRLD
Sbjct: 3   IQSYILYEDRDLIVCRKPAGVPVQTKQIQTKDMVSLLKNYRYQQEGGKEEPYLGVIHRLD 62

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q   GI+V A+T  AA+ L    +     K Y +++  +P+  +  + ++L+K       
Sbjct: 63  QPVEGIVVFAKTPQAAKELNRQLQAGGFGKYYQAVLCKVPEKAQGQLTDYLVKDGRTNLS 122

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              + ++++ GA  A   +K I   A+      +   TGR HQ+RV    MGCPI+GD K
Sbjct: 123 K--ICRKSDAGAKEARLSYK-IQGEAEGKALANIHLDTGRHHQIRVQMSGMGCPILGDVK 179

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           Y    K         ++ L A  +   HP+  + +Q  
Sbjct: 180 YGGEEKAR------GQIALCASSLTFVHPKTKKQMQFE 211


>gi|301511962|ref|ZP_07237199.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) protein [Acinetobacter
           baumannii AB058]
          Length = 221

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 110/231 (47%), Gaps = 13/231 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + N           +L+ED  + V +KPAG+    G    +H   +L+  V  K   
Sbjct: 1   MPLNDNFVYAPPQDPLSILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPL 58

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G  K +       + 
Sbjct: 59  AKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLIT 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +   +A + F+ +   A      + ++P TGR+HQLRVH +H+
Sbjct: 119 DWENRPRQIVHF-----ELGKHAKTLFQPLVYDATTDQSRVLLEPVTGRSHQLRVHMMHI 173

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G PI+GD  Y    K        N++ LHA Y+   HP  G  + I + +P
Sbjct: 174 GHPIMGDKLYHPEPK----RFHLNRMALHAAYLAFQHPLKGTDVVIESKVP 220


>gi|238918644|ref|YP_002932158.1| hypothetical protein NT01EI_0701 [Edwardsiella ictaluri 93-146]
 gi|238868212|gb|ACR67923.1| conserved hypothetical protein [Edwardsiella ictaluri 93-146]
          Length = 235

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 109/246 (44%), Gaps = 20/246 (8%)

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                  +  S+    +H D  +     +LY+D+ I V NKP+G+    G  +  H D  
Sbjct: 4   RTPAGGALPPSATPALEHYDPPREPWLHILYQDAHIIVVNKPSGLLSVPGR-LPEHQDSI 62

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           + + + ++       HRLD  TSG+LVVA T+ A + L   FR R  +K Y + VWG P 
Sbjct: 63  I-TRIQAQFPDAESVHRLDMATSGVLVVALTKDAERELKRQFREREPKKNYVARVWGHPP 121

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             +  I   L+       D+ +  KQ    +    A + ++V+   A     + + P TG
Sbjct: 122 QDQGVIDLPLI------CDWPNRPKQKVCFEQGKPAQTEYQVLAHDADGTARVLLTPITG 175

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           R+HQLRVH L +G PI+GD  Y         S +     LHA+ + + HP     +    
Sbjct: 176 RSHQLRVHLLALGHPILGDGFYAPPQALALASRLL----LHAQELRIVHPAFTTPMHFRC 231

Query: 310 PLPAHM 315
              A  
Sbjct: 232 E--ADF 235


>gi|223935079|ref|ZP_03626997.1| pseudouridine synthase [bacterium Ellin514]
 gi|223895963|gb|EEF62406.1| pseudouridine synthase [bacterium Ellin514]
          Length = 260

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 58/201 (28%), Positives = 95/201 (47%), Gaps = 2/201 (0%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++ED+++ V NKPAG+      G  Y                P L +RLD+ETSGI++
Sbjct: 27  DVVHEDAELLVINKPAGLVCHPTKGDEYSSLISRVRLHLGPESHPHLVNRLDRETSGIVI 86

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+    A+ L   +  R +QK Y ++V G  + ++  I   L K +         V + 
Sbjct: 87  VAKDDTTARGLRRIWEGREVQKEYLAIVHGHVREEQGTIQAALGKDTSSIIAIKDTVVEG 146

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              +    +  K        F  L + PHTGR HQ+R+H  H+  PIVGD  Y  + +  
Sbjct: 147 GAASQTDFTVKKRFSREEGDFTLLRVLPHTGRKHQIRIHLAHIDHPIVGDKMYGGD-EDL 205

Query: 280 FTSPIQNKLYLHA-RYMDLPH 299
           + + +Q++L     + + LPH
Sbjct: 206 YMALVQDRLTEEQWKKLILPH 226


>gi|254457610|ref|ZP_05071038.1| tRNA pseudouridine synthase C [Campylobacterales bacterium GD 1]
 gi|207086402|gb|EDZ63686.1| tRNA pseudouridine synthase C [Campylobacterales bacterium GD 1]
          Length = 250

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 60/217 (27%), Positives = 97/217 (44%), Gaps = 16/217 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +LY+D  +   NKP+G+ V       + I   +K   D  GQ     HRLD+ TSG+
Sbjct: 6   KLEILYQDGYLVCINKPSGLLVHKSMIDRHEIYFAMKMLRDQIGQWVYPIHRLDKPTSGV 65

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A  +  A+ ++E F+    +K Y  +V G        I + L +K     D      
Sbjct: 66  LLFALDKETAKLMSEQFKEHTTKKTYICVVRGY-TEVFGLIDHALKEKLDKIADK---DA 121

Query: 218 QNEKGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           + EK A  A + ++ +D              ++  ++++P TGR HQ+R H  H+   I+
Sbjct: 122 KEEKEAQEAATEYERLDTVELDFAVGRYDKTRYSLVKVKPKTGRKHQIRRHMKHISHHIL 181

Query: 268 GDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEG 302
           GD KY       F     +  +L LHA  ++  HP  
Sbjct: 182 GDTKYGRGEHNVFVREEFDCHRLLLHALSLEFKHPYT 218


>gi|46111497|ref|XP_382806.1| hypothetical protein FG02630.1 [Gibberella zeae PH-1]
          Length = 512

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 63/274 (22%), Positives = 106/274 (38%), Gaps = 58/274 (21%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           Q ++R G + V+ +RV  +  +++G ++              E  + +  V         
Sbjct: 138 QSMIR-GSIFVNGRRVGPDYILRNGDLISHTLHR-------HEPPVTEDPV--------- 180

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETS 155
              +++ED  + V NKPAG+ V       Y+ +  ++     +G    P L +RLD+ TS
Sbjct: 181 --QIIHEDEDMIVINKPAGVPVHPAG--RYNFNSVVEIMKSDRGPAFLPYLCNRLDRLTS 236

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVH 214
           GI+ +A+   AA+ L    + R ++K Y + V G  P  +  C    L     +G + V 
Sbjct: 237 GIMFIAKNPVAAEALGIKIKDRTVRKEYIARVMGEFPDGEVVCDQPILQISPKLGLNRVR 296

Query: 215 VVKQNEKGANYAISHFKVIDCFAQ----------------------------KFCWLEMQ 246
                      A + FK +  + +                             +  +   
Sbjct: 297 A------NGKTARTVFKKLAYYPEDENEDVDERPKTPEQLQDETHRPWVNKKGYSIVRCL 350

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           P TGRTHQLRVH  H+G PI  D  Y        
Sbjct: 351 PVTGRTHQLRVHLQHLGHPIQNDPIYANRRVWGM 384


>gi|260833883|ref|XP_002611941.1| hypothetical protein BRAFLDRAFT_126415 [Branchiostoma floridae]
 gi|229297314|gb|EEN67950.1| hypothetical protein BRAFLDRAFT_126415 [Branchiostoma floridae]
          Length = 335

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 84/301 (27%), Positives = 136/301 (45%), Gaps = 36/301 (11%)

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            +  +        +  K Q    + V+    +  LK  LLY++  I    KP G+ V GG
Sbjct: 33  DIRELDLSREKFLYKWKHQVADLTHVSPYTLASILKKSLLYDEGDIVAIEKPYGVPVHGG 92

Query: 123 SGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            G+   I   L     + K  +  L HRLD+ET+G++++A+T   A+ L   FR+R++ K
Sbjct: 93  PGMGVSIADSLPLLQQALKTDRLYLVHRLDKETTGVMLLAKTDDMARQLHSLFRLRKVIK 152

Query: 182 IYWSLVWGIPKNKKECIANWL--LKKSHIGGDYVHVV---------------KQNEKGAN 224
            YW L  G+P +++  +   +  L+ +  G  +  +V               K+    A 
Sbjct: 153 KYWVLTMGVPSHEEGVVDIPIKELEVTAQGRPHHRMVCVPEYSEETKLIVKKKRKSSDAQ 212

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK---GNF 280
            AI++F+V+D        +E QP TG  HQ+R H  + +GCPI+GDHKY  + K      
Sbjct: 213 IAITNFRVLDSCGSCA-LVECQPETGVKHQIRSHLSYGLGCPILGDHKYSHHSKLAPQRL 271

Query: 281 TSPIQNK------------LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
            + +  +            ++LHAR + LP    GR L  TA LP    +    L  +  
Sbjct: 272 PTGMLERFGIQQPKARYLPMHLHARQIVLPGFRDGRSLYFTARLPDFFNRNVKKLRIRVP 331

Query: 328 R 328
           R
Sbjct: 332 R 332


>gi|326403197|ref|YP_004283278.1| putative pseudouridine synthase [Acidiphilium multivorum AIU301]
 gi|325050058|dbj|BAJ80396.1| putative pseudouridine synthase [Acidiphilium multivorum AIU301]
          Length = 224

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 61/183 (33%), Positives = 91/183 (49%), Gaps = 6/183 (3%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +  ++LY  + + V +KPAG+    G G    ++ +   W       P L HRLD +T+
Sbjct: 1   MIDPVILYHSTHLVVIDKPAGLPSHRGRGGGPSVEDWFPRWRRG-ADGPWLVHRLDADTA 59

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L +AR +     L  +F  RR+ K YW++V G+P      I   L +++  GG  V  
Sbjct: 60  GCLAIARRKTTLVALQRAFAQRRVGKTYWAIVEGVPAAAHGTIELALARRTVPGGWRVA- 118

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
               +   + AI+ ++ +    Q    LE++P TGRTHQLRVH    G PIVGD  Y A 
Sbjct: 119 ---PDPRGDPAITDWRCL-VAGQGRALLELRPRTGRTHQLRVHCAESGFPIVGDPLYGAE 174

Query: 276 FKG 278
             G
Sbjct: 175 AGG 177


>gi|154275958|ref|XP_001538824.1| hypothetical protein HCAG_06429 [Ajellomyces capsulatus NAm1]
 gi|150413897|gb|EDN09262.1| hypothetical protein HCAG_06429 [Ajellomyces capsulatus NAm1]
          Length = 545

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 68/351 (19%), Positives = 113/351 (32%), Gaps = 82/351 (23%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        QK +  G V ++ K V  + +IQ+G V+              E
Sbjct: 66  LDVF-GTEFRDRPKEYYQKAIEDGAVCINGKAVSIDTKIQNGDVISHTLHR-------HE 117

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  + V +KPAG+ V       Y+    +       
Sbjct: 118 PPVTSQPIG-----------IIHEDDDMIVIDKPAGVPVHPAGRYNYNSILEIMKAERGN 166

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P   +RLD+ TSG++ + +    A+ + E  R R ++K Y + V G   +       
Sbjct: 167 GWVPYPCNRLDRLTSGVMFIGKHPKGAEQIGEKLRSRTVRKEYVARVKGKFPDGVVLCDQ 226

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----------------------- 237
            +LK S I G     + +       A + F+ I  +                        
Sbjct: 227 PMLKISPILG-----LNRARASGKEARTKFRRIAYYPPHKQAGKKQGLSAGPATPPATLP 281

Query: 238 --------------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                                     + +  +   P TGRTHQLRVH  ++G PI  D  
Sbjct: 282 DQMNISDSQTDTPIGAAIPVPMSPDEEGYSIVHCLPLTGRTHQLRVHLQYLGHPITNDPI 341

Query: 272 YCANF-------KGNFTSPIQNKLYLHARYMDLPHPEG--GRLQITAPLPA 313
           Y           K + T     ++      M    P           P P 
Sbjct: 342 YSNRRVFGHSLGKADATGENDEQIIYRLSKMGKTEPVDSLSYQTFQTPPPE 392


>gi|149372343|ref|ZP_01891531.1| Ribosomal large subunit pseudouridine synthase D [unidentified
           eubacterium SCB49]
 gi|149354733|gb|EDM43296.1| Ribosomal large subunit pseudouridine synthase D [unidentified
           eubacterium SCB49]
          Length = 300

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 125/324 (38%), Gaps = 53/324 (16%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           ++  V+   E N RL       +  I +    +K ++ G V ++ K+    + +    ++
Sbjct: 10  IEECVLTAVEANTRLSDLTAGTFKTITSRKAFKKAIKQGCVTLNNKQAYTGDYVNENDLI 69

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I                 D S++  K S  +   +L+ED+ + + +KPAG+ V G    
Sbjct: 70  TIY---------------KDKSIS-KKPSIQIPLKVLFEDNHLAIIHKPAGVEVSGNK-- 111

Query: 126 AYHIDGFLKSWVDSKGQK-----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
            Y I+  L S +    QK     P   HRLD  TSG L++ +T    Q L   F  R I 
Sbjct: 112 KYTIENALPSLLKKSNQKDALDRPLPAHRLDYPTSGCLLIGKTSETLQALHRMFEKREIS 171

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--- 237
           K Y ++  G    +   I   +                       +++ FK +       
Sbjct: 172 KKYIAVTLGNQITE-GKIDKPI-------------------DDKASLTTFKTLQTITSKK 211

Query: 238 -QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 + + PHTGR HQLR H + +G PI G+  Y         S     L+LHA  + 
Sbjct: 212 YNALNLVLLTPHTGRRHQLRKHMMQLGNPIFGEKTYGDINDQGKGS----GLFLHAIALS 267

Query: 297 LPHPEGGR-LQITAPLPAHMVKTW 319
             HP   + L I +  P    K +
Sbjct: 268 FKHPIDNKTLIIKSEAPRKFQKLF 291


>gi|88801890|ref|ZP_01117418.1| ribosomal large subunit pseudouridine synthase A [Polaribacter
           irgensii 23-P]
 gi|88782548|gb|EAR13725.1| ribosomal large subunit pseudouridine synthase A [Polaribacter
           irgensii 23-P]
          Length = 556

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 104/235 (44%), Gaps = 19/235 (8%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   +D+++ L   S   +  ++YED+ + V +KP  +    G  I   +   +K     
Sbjct: 334 EDLPMDANLLLENLSKDKELEVIYEDAAMIVVHKPTELLSVPGKEIKDAVYTRMKEKY-P 392

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
               P + HRLD  TSGIL++ +T+ A + L   F  R I+K Y +L+ G        I 
Sbjct: 393 NATGPLIVHRLDMSTSGILLLTKTKEANKILQSQFVNRTIKKRYVALLDGNLSEDSGTIK 452

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L     +  D       +      A + ++V+         +   P TGRTHQLRVHA
Sbjct: 453 LPL----RVDLDDRPKQLVDFSYGKAAETTWEVLGR-ENGKTRVYFYPVTGRTHQLRVHA 507

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
            H   +  PIVGD  Y            +N+L+LHA +++  HP    ++  T P
Sbjct: 508 AHKKGLNTPIVGDDLYGTK---------ENRLHLHAEFIEFLHPTTNKKMSFTVP 553


>gi|315646518|ref|ZP_07899636.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315278161|gb|EFU41481.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 244

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 107/232 (46%), Gaps = 15/232 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-- 145
           ++  + + +    +L+ED+ +    KP  +  Q  +     +   LK  +  +  KP   
Sbjct: 1   MSRRESAVYPVVPILFEDNHVLGVAKPVNVPSQEDATGDPDMLTILKQDIKERFNKPGNV 60

Query: 146 ---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD+   G +V A+T  AA  L+E+ R R  +K Y ++V GIP      + + L
Sbjct: 61  FLGLVHRLDRPVGGAMVFAKTSKAASRLSEAVRSRSFRKQYVAVVHGIPSKPSGRLVDML 120

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            K +      VHV  +   GA  AI  + V+   ++ F  + ++ HTGR HQ+RV   H 
Sbjct: 121 YKDAKTN--TVHVTSEGTDGAKEAILDYTVLQT-SEGFSLVLIELHTGRPHQIRVQLNHA 177

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA-PLP 312
           G P+ GD KY +       +    ++ L +  +  PHP     + I + P P
Sbjct: 178 GHPLFGDQKYGSKV-----NKAGQQIALWSVLVGFPHPVTKEDISIHSMPPP 224


>gi|301166302|emb|CBW25878.1| putative pseudouridine Synthase [Bacteriovorax marinus SJ]
          Length = 313

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 74/301 (24%), Positives = 133/301 (44%), Gaps = 28/301 (9%)

Query: 31  HINFVNLQK----ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
             +    QK    +L+  ++R+       ++ ++S     I   +N    I K Q +   
Sbjct: 29  DFSLSLSQKSFDELLKQNRIRISGAP--PSHELKS-----IKKGVNFSISISKSQ-LKSW 80

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           S+ +    +F +S+L++E++   V NKPA +S    +         + +   S G K   
Sbjct: 81  SLPIENKREFKESMLIHEENLFLVANKPAMLSSTATTNSKQDNLHAILTRYISGGHKEKY 140

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KKECIANWL 202
             + HR+D ETSG+L+  + ++  +  ++ F  R+++K Y +L+     + K + + N+L
Sbjct: 141 LSIHHRIDFETSGLLIFCKKKSQNKFFSDLFEQRKVKKTYLALIKDPDHSFKDQKVENFL 200

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            +        +        G   A ++FK I    +    +E +P TGR HQ+RVH   +
Sbjct: 201 ERDPKNKMKMMSTTH----GGKKATTYFKEI-THQEGMTLVEAKPETGRFHQIRVHLAEL 255

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           G PI+GD  Y         S    +  LHA  +  PHP+    L+  APLP    +    
Sbjct: 256 GFPIIGDSIYSQK------SEQFPRTMLHAYKLSFPHPQSDESLEFIAPLPHDFPQNIIQ 309

Query: 322 L 322
           L
Sbjct: 310 L 310


>gi|182412318|ref|YP_001817384.1| pseudouridine synthase [Opitutus terrae PB90-1]
 gi|177839532|gb|ACB73784.1| pseudouridine synthase [Opitutus terrae PB90-1]
          Length = 268

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 62/255 (24%), Positives = 103/255 (40%), Gaps = 34/255 (13%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHID--GFLKSWVDSKGQKPRLTHRLDQETSG 156
             +L+ED  +  F+KP+G+ +          +  G + +     G      HRLD +TSG
Sbjct: 4   PPILFEDDAMIAFDKPSGLLIAPDRWDKQRENLMGLVHARF---GHGVANVHRLDADTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS---------- 206
           +L+ A+T+ A   L+  F+ + +QK Y SLV  +P  +   +   +   +          
Sbjct: 61  LLLCAKTKPALDFLSGQFQAKTVQKTYLSLVVVLPPEEAMKVVKPIRDDAGGLPDAFQVD 120

Query: 207 ----HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                       +     +G    ++ F+V++ F + F  +   P TGRTHQ+RVH    
Sbjct: 121 LALGQDERQPGRMRVFKGRGGKDCVTDFRVLERFGR-FALVSCHPQTGRTHQIRVHLAAA 179

Query: 263 GCPIVGDHKYCAN-------------FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           G PI+ D  Y                   +   P+ ++L LHA  +   HP     L + 
Sbjct: 180 GAPILNDPFYGNPEIKLLLSDLKRRYKGRDEEKPLIDRLALHASELTFRHPATRELLTLQ 239

Query: 309 APLPAHMVKTWDSLG 323
           APLP         L 
Sbjct: 240 APLPHEFEIALKYLR 254


>gi|124024405|ref|YP_001018712.1| pseudouridine synthase [Prochlorococcus marinus str. MIT 9303]
 gi|123964691|gb|ABM79447.1| Pseudouridine synthase [Prochlorococcus marinus str. MIT 9303]
          Length = 338

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 77/322 (23%), Positives = 132/322 (40%), Gaps = 46/322 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PP 69
           +   +    L      HY H +    Q+ L++GQ+R++ + V+ +  + SG  V    PP
Sbjct: 27  IAAVDAGRGLVELLAVHYTHSSRDVWQQRLQAGQIRLNGELVRLDQLLASGDQVCWQRPP 86

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            + A      E                    ++++D  + V NKP+G+ V  G G   H 
Sbjct: 87  WLEAAVPASWE--------------------VIFDDGDLLVVNKPSGLPVIPGGGFLDHT 126

Query: 130 DGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--------RR 178
              L      +D + + PR  HRL + TSG+L+ AR R     L+  FR         ++
Sbjct: 127 LTGLLQRRCQLDGESRLPRPVHRLGRFTSGLLICARQRETRAKLSAMFRRATAGDQGCKK 186

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHI---------GGDYVHVVKQNEKGANYAISH 229
           I +        +  ++   I   +++ +H               H  KQ+E     A+S 
Sbjct: 187 IYRALAHRNLNVHCDEVATIRVPIVQTAHPMVGKVWVAADSSRQHDSKQSESRVLTALST 246

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKL 288
            ++++   Q    LE+   TGR HQ+R+H   +G P++GD  Y  + +  +  +P     
Sbjct: 247 VRLLERR-QDADLLEVAIQTGRPHQIRIHLAAIGSPLIGDPLYGFDGQISSAATPGDGGY 305

Query: 289 YLHARYMDLPHPEGGRLQ-ITA 309
            LHA  +    P   RL   TA
Sbjct: 306 CLHAHRLVDV-PYRNRLHGFTA 326


>gi|329924939|ref|ZP_08279886.1| RNA pseudouridine synthase [Paenibacillus sp. HGF5]
 gi|328940323|gb|EGG36652.1| RNA pseudouridine synthase [Paenibacillus sp. HGF5]
          Length = 239

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 64/227 (28%), Positives = 102/227 (44%), Gaps = 14/227 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LT 147
            + +    +L+ED+ +    KP  I  Q  +     +   LK  +  +  KP      L 
Sbjct: 6   PASYPAVPILFEDNHVLGVTKPVNIPSQEDATGDPDMLTILKQDIKERYNKPGNVFLGLV 65

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+   G +V A+T  AA  L+E+ R R   K Y ++V G+P      + N L K + 
Sbjct: 66  HRLDRPVGGAMVFAKTSKAASRLSEAVRSRSFLKQYVAVVHGVPAKTSGRLVNMLYKDAK 125

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                VHV  +   GA  AI  + V+   A+    + ++ HTGR HQ+RV   H G P+ 
Sbjct: 126 TN--TVHVTSKGTDGAKEAILDYTVLQA-AEGVSLVRIELHTGRPHQIRVQLSHAGHPLF 182

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           GD KY +       +    ++ L +  +  PHP     + I +  P+
Sbjct: 183 GDQKYGSKV-----NKAGQQIALWSVLVGFPHPVTKEDISIRSMPPS 224


>gi|325265622|ref|ZP_08132312.1| tRNA pseudouridine synthase C [Kingella denitrificans ATCC 33394]
 gi|324982892|gb|EGC18514.1| tRNA pseudouridine synthase C [Kingella denitrificans ATCC 33394]
          Length = 242

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 96/239 (40%), Gaps = 17/239 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L +       NKPA + V             L++  D  G+     HRLD+ TSGI++ 
Sbjct: 4   ILAQTDDYIAVNKPADMLVHRTWLSCGETVFLLQTLRDQLGRHVFPVHRLDRPTSGIMLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R AAQ+ T  F  R ++K Y ++  G   +   CI   L +               +
Sbjct: 64  ALHREAAQYFTGQFGSRLVRKTYLAIARG-WTDDAGCIDYPLKE---QLDKIADQHADGD 119

Query: 221 KGANYAISHFKVIDCF-----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           K A  A + ++ +                ++  L + PHTGR HQ+R H  H+  PIVGD
Sbjct: 120 KPAQAACTEYRTLARSELPIVSTPRYATSRYSLLRLMPHTGRKHQIRRHLKHIFHPIVGD 179

Query: 270 HKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
             +    +           +L LHA  +    P+   + I AP  A   +   +L  +Y
Sbjct: 180 TTHGDLRQNRAIHQFYGNTRLLLHAESLQFTDPQQREIHIAAPTDAAWRQVQAALFPEY 238


>gi|103486532|ref|YP_616093.1| pseudouridine synthase [Sphingopyxis alaskensis RB2256]
 gi|98976609|gb|ABF52760.1| pseudouridine synthase [Sphingopyxis alaskensis RB2256]
          Length = 227

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 105/240 (43%), Gaps = 16/240 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L   +L+ D +  V +KPAG+ V      +  I+  L        + P   HRLD++TS
Sbjct: 2   LLSDRVLFLDGEALVIDKPAGLPVDAPRDGSLSIENHLDLLRFGFKRWPLPVHRLDRDTS 61

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L++AR   A    T +F  R ++K Y +++ G+P +    I   L K S     +  V
Sbjct: 62  GCLLLARNPKAHGRFTRAFENREVEKQYLAIIDGVPADDGGTIDLPLAKTSTAEAGWRMV 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCA 274
           V   +     +ISH++ +   A     L  +P TGRTHQLRVHA+  +G P+ GD  Y  
Sbjct: 122 V---DPAGKPSISHWEKL-AVADGRALLRFRPETGRTHQLRVHAIEGLGFPLAGDPVYG- 176

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
                     + +  LHA  + +       +   AP P        ++GF+        R
Sbjct: 177 ------RGGAKGRTLLHAERLVVSRDVKPPIIAEAPFPEAFA----AMGFQPPEGAAPTR 226


>gi|260818260|ref|XP_002604301.1| hypothetical protein BRAFLDRAFT_88590 [Branchiostoma floridae]
 gi|229289627|gb|EEN60312.1| hypothetical protein BRAFLDRAFT_88590 [Branchiostoma floridae]
          Length = 369

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/258 (22%), Positives = 102/258 (39%), Gaps = 27/258 (10%)

Query: 22  DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           D +  + +      + +K ++ G++ ++ + VK +  ++    ++     +    +    
Sbjct: 38  DIF-SSEFRAHPPEHYEKAIKLGRLLLNGECVKLDTVLKDNDFMQNTVHRHEPPVVA--- 93

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
                              ++ E   + V NKPA + V    G  ++   F+    +   
Sbjct: 94  ---------------DPVQIVEETDDLVVINKPASMPVHPCGGYRHNSVIFVLG-KEHGF 137

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           Q     HRLD+ TSGIL+ A+       L    + R ++K+Y + V G    K EC    
Sbjct: 138 QNLHPIHRLDRLTSGILIFAKNLETKHRLDAQIKGREVKKVYLARVEGEFPEKAECDKPI 197

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
              K  +G      V +       A + F+ +  F  K   +   P TGR HQ+RVH  +
Sbjct: 198 FAVKHKLG------VCRVCPEGKPAKTTFERV-SFDGKSSVVRCFPETGRMHQIRVHLQY 250

Query: 262 MGCPIVGDHKYCANFKGN 279
           +G PIV D  Y +   G 
Sbjct: 251 LGHPIVNDPLYNSTAWGA 268


>gi|262281369|ref|ZP_06059150.1| dual specificity pseudouridine synthase [Acinetobacter
           calcoaceticus RUH2202]
 gi|262257195|gb|EEY75932.1| dual specificity pseudouridine synthase [Acinetobacter
           calcoaceticus RUH2202]
          Length = 232

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 109/231 (47%), Gaps = 13/231 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + N           +L+ED  + V +KPAG+    G    +H   +L+  V  K   
Sbjct: 12  MPLNDNFVYAPPQDPLSILFEDDDLVVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPL 69

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y ++V G    +       + 
Sbjct: 70  AKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKHYIAVVQGRVNQEGSVEVPLIT 129

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +   +A + F+ +   A      + ++P TGR+HQLRVH +H+
Sbjct: 130 DWENRPRQIVHF-----ELGKHAKTLFQPLVYDAHTDQTRVLLEPVTGRSHQLRVHMMHI 184

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G PI+GD  Y    K        N++ LHA Y+   HP  G  + I + +P
Sbjct: 185 GHPIMGDKLYHPEPKQ----FHLNRMALHAAYLAFHHPLNGTDVVIESQVP 231


>gi|116073082|ref|ZP_01470344.1| putative pseudouridylate synthase [Synechococcus sp. RS9916]
 gi|116068387|gb|EAU74139.1| putative pseudouridylate synthase [Synechococcus sp. RS9916]
          Length = 210

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 66/215 (30%), Positives = 104/215 (48%), Gaps = 13/215 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             LL++D  + V +KPAG+  Q G G        L + +  +     L HRLD++TSG+L
Sbjct: 7   PPLLHQDPWLLVVDKPAGLLSQPGLGPELRDS--LITRLQRQEPGLALVHRLDRDTSGVL 64

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ART  + + L+  F  RR+ K+Y + V   P     CI   L +       Y      
Sbjct: 65  LLARTPESLRALSALFAARRVHKLYGADVCAPPPGLGGCIDVPLARLQRHPPRY-----G 119

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +       + +++    A       +QP TGR+HQLR H   +GCPI+GD  Y A+   
Sbjct: 120 ADPDGRACRTRWRLSGRDASSRRIW-LQPLTGRSHQLRAHLASLGCPILGDPIYAADQGR 178

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           + T     +++LHA  + L HP  G RL+  + +P
Sbjct: 179 SAT----GRMHLHATALSLRHPFTGERLRCRSAMP 209


>gi|188989643|ref|YP_001901653.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. B100]
 gi|167731403|emb|CAP49578.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris]
          Length = 258

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 59/249 (23%), Positives = 101/249 (40%), Gaps = 24/249 (9%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           N    +      +LY+D+ + V +KPAG+ V          D          G+   L H
Sbjct: 10  NPPVSTSPDPLQILYQDAVLAVVDKPAGLMVHDSKLARGEDDFLADRLRVQLGRPIFLVH 69

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG L++A  R  A  L ++     ++K Y ++  G P  ++  + + L      
Sbjct: 70  RLDRATSGCLLLAFDRDTASALGKALMAGEVEKDYLAICRGWPAEERFIVDHDLDG---- 125

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVH 258
                      +     A++HF+ +               ++  L  QP TGR  Q+R H
Sbjct: 126 --------GPGKPIKKPAVTHFQRLATGELEIPSTGFATSRYALLRCQPQTGRFRQIRRH 177

Query: 259 ALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMV 316
             H+   ++GD  +       +F     +++ LHA  +  PHP +G R+ + APL     
Sbjct: 178 LKHLSHHMIGDTSHGDGRHNRSFRMLGIHRMLLHAERLGFPHPADGRRISVVAPLDVEFA 237

Query: 317 KTWDSLGFK 325
           K     G+ 
Sbjct: 238 KACALFGWD 246


>gi|290474823|ref|YP_003467703.1| 23S rRNA pseudouridylate 746 synthase [Xenorhabdus bovienii
           SS-2004]
 gi|289174136|emb|CBJ80923.1| 23S rRNA pseudouridylate 746 synthase [Xenorhabdus bovienii
           SS-2004]
          Length = 217

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 66/212 (31%), Positives = 105/212 (49%), Gaps = 16/212 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+ +    G     H D  + + + ++       HRLD  TSG++VV
Sbjct: 15  VLYQDEHIMVVNKPSELLSVPGKA-EDHKDSIM-TRIQAEFPTAESVHRLDMATSGVMVV 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A T+AA + L   FR R  +K+Y + VWG  + +K  +   L+       D+ +  KQ  
Sbjct: 73  ALTKAAERELKRQFREREPKKVYIARVWGKLEREKGLVDLPLI------CDWPNRPKQKV 126

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             +    A + ++V++  AQ    + + P TGR+HQLRVH L +G PI+GD  Y      
Sbjct: 127 CFETGKSAQTEYQVLEYEAQ-ATRVRLAPITGRSHQLRVHMLALGNPILGDRFYAHQQ-- 183

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
                +  +L LHA+ + + HP  G  +    
Sbjct: 184 --ARELAPRLQLHAQELSITHPAYGTPMHFEC 213


>gi|319794856|ref|YP_004156496.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315597319|gb|ADU38385.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 220

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 54/218 (24%), Positives = 97/218 (44%), Gaps = 17/218 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
               ++ED  + V  KPAG+    G G        L +    +     + HRLD  TSG+
Sbjct: 5   PLQPIHEDVHLLVLEKPAGLLCVPGRGDD--KQDCLSARAMHRWPDALIVHRLDMATSGL 62

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHV 215
           +V+AR+    + L+ +F  R++ K Y ++V G    +++   I   L     +       
Sbjct: 63  VVMARSLEMQRALSAAFADRQVHKRYEAIVDGAMPMREDWSIIDAPL-----MADWPRRP 117

Query: 216 VKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +++ +     +++ ++ +    Q       + ++P TGR+HQLRVH L +G PI+GD  Y
Sbjct: 118 LQKTDPAGKPSLTRWRALASSMQGEFSATHVLLEPETGRSHQLRVHLLSIGHPILGDALY 177

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
                         +L LHA  +   HP   + L+  +
Sbjct: 178 G----DAAVQARAPRLMLHASELAFVHPATQQSLRFES 211


>gi|226229096|ref|YP_002763202.1| ribosomal large subunit pseudouridine synthase A [Gemmatimonas
           aurantiaca T-27]
 gi|226092287|dbj|BAH40732.1| ribosomal large subunit pseudouridine synthase A [Gemmatimonas
           aurantiaca T-27]
          Length = 476

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 104/250 (41%), Gaps = 19/250 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH- 128
            +  L H++    +    +  +      +  ++YED  + V NKP+G+    G G     
Sbjct: 238 CLPILTHMLGGLSVDPPPLYGSAALGPNEPAVVYEDDHLLVVNKPSGMLTVPGRGPTMQD 297

Query: 129 --IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +      + D+ GQ   + HRLD +TSG+L+ A+    A  L   F +R I K Y + 
Sbjct: 298 CVMTRLRARYPDATGQ--MVVHRLDLDTSGLLLAAKDPITASALQRLFSLREIDKHYVAW 355

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           + G+  +    I   L     +  D       +      A + ++V+         +   
Sbjct: 356 LDGVVTDDHGHIHLPL----RMDVDDRPRNIHDPVFGKPAHTEWQVMAR-TDGRTRVRFT 410

Query: 247 PHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           PHTGRTHQLRVHA H   +  PIVGD  Y              +L LHA  +   HP  G
Sbjct: 411 PHTGRTHQLRVHAAHPDGLDAPIVGDRLYGRTAPDE-----DERLQLHAERLAFVHPVSG 465

Query: 304 -RLQITAPLP 312
            ++ +  P P
Sbjct: 466 AKVVVEQPAP 475


>gi|294626410|ref|ZP_06705011.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
 gi|292599295|gb|EFF43431.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
          Length = 244

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 106/240 (44%), Gaps = 24/240 (10%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +LY+D  + V +KPAG+ V          D       +  G+   L HRLD+ TSG 
Sbjct: 7   QLQILYQDDVLAVVDKPAGLMVHDSKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGC 66

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A  R +A  L ++     ++K Y ++  G P  ++  + + L       G     VK
Sbjct: 67  LLLAFDRDSASALGKALMAGEVEKQYLTVCRGWPAEERFIVDHDL------DGGPGKPVK 120

Query: 218 QNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++
Sbjct: 121 ------KPAVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMI 174

Query: 268 GDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           GD  +       +F     +++ LHA  ++ PHP +G R+ +TAPL     K     G++
Sbjct: 175 GDTSHGDGRHNRSFRMLGIHRMLLHAERLEFPHPADGRRIGVTAPLDVEFSKACALFGWE 234


>gi|254449188|ref|ZP_05062638.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium HTCC5015]
 gi|198261234|gb|EDY85529.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium HTCC5015]
          Length = 217

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 54/205 (26%), Positives = 94/205 (45%), Gaps = 11/205 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D      +KP+G+    G   A      + S +     +  + HRLD +TSG++
Sbjct: 13  LRILYQDEHCLFIDKPSGLLSVPGRHPANRDS--VASRLQQDFPEAHIVHRLDMDTSGVM 70

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A    + + L+  F+ RR QK Y ++V   P  ++  +   L+           + K 
Sbjct: 71  VIALNVESHRFLSRQFQERRSQKRYEAIVSATPTPEQGSVDLPLICD----WPNRPLQKV 126

Query: 219 NEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           + +    +++H++    +       + + PHTGR+HQLRVH   +GCPI+GD  Y     
Sbjct: 127 DHEIGKPSLTHYETTGPWQDGAGTRVVLTPHTGRSHQLRVHMAAIGCPILGDSFYAPKV- 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEG 302
              T     +L LHA  + +    G
Sbjct: 186 ---TQEAAPRLLLHASELSIDTLTG 207


>gi|86144243|ref|ZP_01062575.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp.
           MED222]
 gi|85837142|gb|EAQ55254.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp.
           MED222]
          Length = 560

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 104/231 (45%), Gaps = 19/231 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ +  +   +      ++YED +I V NKP       G  I   +   +K+        
Sbjct: 342 LEENPLIVNPAVGKSFDIVYEDDEIVVVNKPEEFLSVPGKFIEDSVYTRIKARY-PDATG 400

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+L++A T  + +H+ + F  R ++K Y +L+ G    K   I+  L 
Sbjct: 401 PLIIHRLDMSTSGLLILALTAESNKHIQKQFIDRTVEKRYIALLDGEIDGKSGDISLPL- 459

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
            +  I      +V         A +H++ +     K   + + P TGRTHQLRVH  H  
Sbjct: 460 -RGDITDRPRQLVCHEH--GRNAETHWEAVSTNNGK-TKVHLYPKTGRTHQLRVHCAHPS 515

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            +G PI GD  Y    +         +L+LHA Y+ L HP  G  L+   P
Sbjct: 516 GLGVPIRGDDLYGYKRE---------RLHLHAGYLKLIHPTTGEWLEFEVP 557


>gi|188533189|ref|YP_001906986.1| Pseudouridylate synthase [Erwinia tasmaniensis Et1/99]
 gi|188028231|emb|CAO96089.1| Pseudouridylate synthase [Erwinia tasmaniensis Et1/99]
          Length = 232

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 94/229 (41%), Gaps = 17/229 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +LY+D  + + NKPAG+    G          +   +        L HRLD 
Sbjct: 11  PPCVEEIEILYQDEHLALINKPAGLLSLSGKNPQN--IDSVHHRLVRIFPGCTLVHRLDF 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++++AR +A    L + F  R++ K+Y +L+ G   N    I   + K   +    
Sbjct: 69  GTSGLMLIARNKAINAALCQQFSQRKVAKMYSALLCGHLDNDGGVIDAAIAKDPAL---- 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGC 264
             ++         A S ++V   F              +++ P TGRTHQLR+H   +G 
Sbjct: 125 FPLMSICAIHGKPARSRYQVTARFYHALQDGTRLPLTRVQLTPETGRTHQLRIHCQQLGH 184

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           PI+G   Y              +L LHA  +   HP GG  ++   P P
Sbjct: 185 PILGCDLYGGRLLPGTERT--PRLMLHASELHFVHPIGGEEIKAHHPCP 231


>gi|115376321|ref|ZP_01463560.1| ribosomal large subunit pseudouridine synthase A [Stigmatella
           aurantiaca DW4/3-1]
 gi|115366671|gb|EAU65667.1| ribosomal large subunit pseudouridine synthase A [Stigmatella
           aurantiaca DW4/3-1]
          Length = 495

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 98/231 (42%), Gaps = 23/231 (9%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK---PR 145
                +      +++ED  + V +KP G+    G G        + + + ++      P 
Sbjct: 280 PPEPTASAGALSIVFEDDWLVVIDKPCGLLSVPGKGAE--WVDSVLTRLQARYPHATGPL 337

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD +TSG+LV A        L   F  R + K Y + + G  + ++  I   L   
Sbjct: 338 LVHRLDLDTSGLLVAALDARTHAALQRQFIHREVHKRYVAWIDGRVRGEQGLIDLPLRVD 397

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---M 262
            H     +H    +      A++ ++V++    +   + + P +GRTHQLRVHA H   +
Sbjct: 398 LHDRPRQIH----DPLHGKPAVTEWQVLERQGDR-TRVALFPQSGRTHQLRVHAAHPLGL 452

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           G PIVGD  Y            + +L LHA  +   HP  G R+    P P
Sbjct: 453 GAPIVGDRLYGHE---------EVRLLLHAEALSFRHPGTGLRVSFERPAP 494


>gi|260551283|ref|ZP_05825484.1| dual specificity pseudouridine synthase [Acinetobacter sp. RUH2624]
 gi|260405597|gb|EEW99088.1| dual specificity pseudouridine synthase [Acinetobacter sp. RUH2624]
          Length = 232

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 108/231 (46%), Gaps = 13/231 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + N           +L+ED  + V +KPAG+    G    +H   +L+  V  K   
Sbjct: 12  MPLNDNFVYAPPQDPLSILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPL 69

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G  K +       + 
Sbjct: 70  AKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLIT 129

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +   +A + F+ +          + ++P TGR+HQLRVH +H+
Sbjct: 130 DWENRPRQIVHF-----ELGKHAKTLFQPLVYDETTDQSRVLLEPVTGRSHQLRVHMMHI 184

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G PI+GD  Y    K         ++ LHA Y+   HP  G  + I + +P
Sbjct: 185 GHPIMGDKLYHPEPK----RFHLKRMALHAAYLAFQHPLKGTDVVIESQVP 231


>gi|332535329|ref|ZP_08411128.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332035242|gb|EGI71749.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 245

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 71/252 (28%), Positives = 114/252 (45%), Gaps = 19/252 (7%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I  + N+ +    EQ I+       K   F++  +LY+D  I + NKP+G+    G    
Sbjct: 2   INLMANSTSQTPSEQPIIVDDFVAPKCDGFIE--ILYQDDDILLINKPSGLLSLSGKNPL 59

Query: 127 YHIDGFLKSWVDSK------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              D      V  +        + +L HRLD  TSGI++V     A++HL + F+ R IQ
Sbjct: 60  N-WDSVHYRLVHGQKGLTAAFAEAKLPHRLDLGTSGIMIVGLNAKASKHLNKQFQARTIQ 118

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y +++ G        I   + K   +       VK  +     A+S + V++   Q  
Sbjct: 119 KRYVAMLEGCLAVDVGSITAPIAKDKLL----FPRVKICQTMGKVAVSEYSVLERLKQPC 174

Query: 241 -CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              ++  P TGRTHQLR+H+  +G PI+G   Y    K   +  +  +L LHA  +   H
Sbjct: 175 RTLVQFTPVTGRTHQLRIHSQFIGHPILGCDLY----KSAQSEYMAGRLQLHASDLYFEH 230

Query: 300 PEGG-RLQITAP 310
           P  G ++ I +P
Sbjct: 231 PATGAQIHINSP 242


>gi|184156437|ref|YP_001844776.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|215485059|ref|YP_002327300.1| RNA pseudouridylate synthase family protein [Acinetobacter
           baumannii AB307-0294]
 gi|239503104|ref|ZP_04662414.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) protein [Acinetobacter
           baumannii AB900]
 gi|260557648|ref|ZP_05829862.1| pseudouridylate synthase [Acinetobacter baumannii ATCC 19606]
 gi|332853596|ref|ZP_08434848.1| pseudouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332869273|ref|ZP_08438684.1| pseudouridine synthase A [Acinetobacter baumannii 6013113]
 gi|332875566|ref|ZP_08443379.1| pseudouridine synthase A [Acinetobacter baumannii 6014059]
 gi|183208031|gb|ACC55429.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|193075994|gb|ABO10578.2| dual specificity pseudouridine synthase [Acinetobacter baumannii
           ATCC 17978]
 gi|213988186|gb|ACJ58485.1| RNA pseudouridylate synthase family protein [Acinetobacter
           baumannii AB307-0294]
 gi|260408821|gb|EEX02125.1| pseudouridylate synthase [Acinetobacter baumannii ATCC 19606]
 gi|323516174|gb|ADX90555.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter
           baumannii TCDC-AB0715]
 gi|332728560|gb|EGJ59933.1| pseudouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332732830|gb|EGJ64044.1| pseudouridine synthase A [Acinetobacter baumannii 6013113]
 gi|332736269|gb|EGJ67283.1| pseudouridine synthase A [Acinetobacter baumannii 6014059]
          Length = 221

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 110/231 (47%), Gaps = 13/231 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + N           +L+ED  + V +KPAG+    G    +H   +L+  V  K   
Sbjct: 1   MPLNDNFVYAPPQDPLSILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPL 58

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G  K +       + 
Sbjct: 59  AKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLIT 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +   +A + F+ +   A      + ++P TGR+HQLRVH +H+
Sbjct: 119 DWENRPRQIVHF-----ELGKHAKTLFQPLVYDATTDQSRVLLEPVTGRSHQLRVHMMHI 173

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G PI+GD  Y    K        N++ LHA Y+   HP  G  + I + +P
Sbjct: 174 GHPIMGDKLYHPEPK----RFHLNRMALHAAYLAFQHPLKGTDVVIESQVP 220


>gi|119773744|ref|YP_926484.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119766244|gb|ABL98814.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           amazonensis SB2B]
          Length = 225

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 58/215 (26%), Positives = 101/215 (46%), Gaps = 13/215 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L++D  I V NKP+G+    G    +H   +  S + ++    ++ HRLD  TSG++
Sbjct: 15  LDILHQDKDIIVINKPSGLLSVPGRDPIHHDSAW--SRIKAEHPNSQVVHRLDMATSGVM 72

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A  ++A   L   FR R   K Y++ V G  K         +    +     V     
Sbjct: 73  VYALRKSAEVELKRQFRDRETHKTYFARVAGHVKANCSVDLPLICDWPNRPRQKV----- 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + +    +++H  VI  + ++   +++ P TGR+HQLRVH + +G PI+GD  Y      
Sbjct: 128 DHEIGKPSLTHVDVI-SYGKRSTLVKLTPITGRSHQLRVHMMALGHPILGDGFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +    + ++L LHA  +   HP  G  +  +  +P
Sbjct: 187 S----LADRLLLHAASLSFTHPYSGEAMTFSTEVP 217


>gi|300865112|ref|ZP_07109937.1| Pseudouridine synthase [Oscillatoria sp. PCC 6506]
 gi|300336883|emb|CBN55087.1| Pseudouridine synthase [Oscillatoria sp. PCC 6506]
          Length = 562

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 61/225 (27%), Positives = 105/225 (46%), Gaps = 22/225 (9%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD--SKGQKPRLTHRLDQ 152
           +     ++YED  +   NKP+G+    G       D  L         G      HRLD 
Sbjct: 350 EAENLQIIYEDEWLIAVNKPSGLLSVPGR-YRDRQDSVLSRLRQLLPDGMNIIPVHRLDL 408

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIANWLLKKSHIGGD 211
           ETSGI+++AR+    + L+  F+ + ++K+Y +++ G   N     I+  L        +
Sbjct: 409 ETSGIMLLARSLPIYRELSSQFQHKLVKKVYEAVLSGNVVNDYCGEISLPLWGNP----E 464

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL---HMGCPIVG 268
           +    + + +    +++ F+VI    + +  +E  P TGRTHQ+RVHA     +G PI+G
Sbjct: 465 HRPYQQVDIERGKPSLTRFQVIAREGE-YTRVEFMPLTGRTHQIRVHASDKRGLGIPILG 523

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
           D  Y             ++L+LHAR +   HP+ G+   L++  P
Sbjct: 524 DRLYGCQADA-------SRLHLHARELYFEHPQLGKNINLEVETP 561


>gi|148240644|ref|YP_001226031.1| pseudouridylate synthase [Synechococcus sp. WH 7803]
 gi|147849183|emb|CAK24734.1| Pseudouridylate synthase [Synechococcus sp. WH 7803]
          Length = 314

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 69/301 (22%), Positives = 122/301 (40%), Gaps = 35/301 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPP 69
           +E  E    L     + Y H +    Q  +R+G++ ++   ++ +  + S  VV  R PP
Sbjct: 19  IERSESGQMLTAVMASRYGHSSRDVWQSRIRTGELLLNGTCLQNDVPVGSKDVVQWRRPP 78

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +        E  I D            +  ++Y+D  + V NKP+G+ V  G G   H 
Sbjct: 79  WL--------EPAIPD------------RWSVVYDDGDVLVINKPSGLPVMPGGGFLQHT 118

Query: 130 DGFLK---SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKI 182
              L    S +    Q P+  HRL + TSG+ V AR       L+  FR     R+    
Sbjct: 119 LSALLMETSRLAGSSQAPKPVHRLGRFTSGLQVCARRPQTRARLSRQFRPEGGCRKTYLA 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQ 238
           +   + G+  ++   +   ++++SH    +V     ++         A S  +++   +Q
Sbjct: 179 WAQPMAGLRADQPLVVTTDVVERSHPLLGWVWGPDPSDGEPLRRRLQARSELRLLRRCSQ 238

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDL 297
               +E+   TGR HQ+R+H   +G P++GD  Y    +      P      LHA  +  
Sbjct: 239 GD-LVEVAISTGRPHQIRIHLAQLGSPLLGDPLYLPQQRINTAAVPGDGGYRLHAHTLVF 297

Query: 298 P 298
            
Sbjct: 298 E 298


>gi|320103316|ref|YP_004178907.1| pseudouridine synthase [Isosphaera pallida ATCC 43644]
 gi|319750598|gb|ADV62358.1| pseudouridine synthase [Isosphaera pallida ATCC 43644]
          Length = 285

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 114/237 (48%), Gaps = 15/237 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRL 150
            ++ + LYED+ + V +KPAG+  QG          +  D   + +    G    LTHRL
Sbjct: 1   MIEPLRLYEDNHLLVVSKPAGLLSQGDRTGDPDLTTWARDDLKRRYNKPGGVFVGLTHRL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-----NKKECIANWLLKK 205
           D+  SG++++ART  AA  L + FR   I+K Y +++   P       +   + ++LLK 
Sbjct: 61  DRPVSGLVILARTGKAAARLAQQFRAGTIRKRYVAVLESSPNASFRFEESGILEDYLLKL 120

Query: 206 SHIGGDYV--HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           S      V        E G   AIS + V++ + Q++  + ++P TGR HQLR      G
Sbjct: 121 SDSNRSSVLGESRGHAESGTRQAISSYMVLERW-QRYLLILLEPVTGRFHQLRAQTASRG 179

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTW 319
            PI GD KY A+           ++ LH+  ++  HP    R++++AP P+     W
Sbjct: 180 WPIAGDVKYGASRALRAADGY-GRIALHSWQVEFEHPTRRERMRLSAPKPSDWPAGW 235


>gi|294634980|ref|ZP_06713497.1| pseudouridine synthase A [Edwardsiella tarda ATCC 23685]
 gi|291091579|gb|EFE24140.1| pseudouridine synthase A [Edwardsiella tarda ATCC 23685]
          Length = 235

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 109/246 (44%), Gaps = 20/246 (8%)

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           H      +  S+    +H D  +     +LY+D+ I V NKP+G+    G  +  H D  
Sbjct: 4   HTPAGGSLPPSATPALEHYDPPREPWLHVLYQDAHIMVVNKPSGLLSVPGR-LPAHQDSI 62

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           + + + ++       HRLD  TSG+LVVA T+ A + L   FR R  QK Y + VWG P 
Sbjct: 63  M-TRIQAQFPCAESVHRLDMATSGVLVVALTKEAERELKRQFREREPQKNYVARVWGHPT 121

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             +  I   L+       D+ +  KQ    +    A + ++V+         L + P TG
Sbjct: 122 QDEGLIDLPLI------CDWPNRPKQKVCFEQGKPAQTAYRVLARDDDGTARLLLTPITG 175

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           R+HQLRVH L +G PI+GD  Y           +     LHA+ + + HP  G  +    
Sbjct: 176 RSHQLRVHLLAIGHPILGDGFYAPPQALALAPRLL----LHAQELRIVHPAFGTPMHFRC 231

Query: 310 PLPAHM 315
              A  
Sbjct: 232 E--ADF 235


>gi|21241018|ref|NP_640600.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21106308|gb|AAM35136.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 244

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 105/237 (44%), Gaps = 24/237 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V +KPAG+ V          D       +  G+   L HRLD+ TSG L++
Sbjct: 10  ILYQDDVLAVVDKPAGLMVHDSKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLLL 69

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R +A  L ++     ++K Y ++  G P  ++  + + L       G     VK   
Sbjct: 70  AFDRDSASALGKALMAGEVEKQYLTVCRGWPAEERFIVDHDL------DGGPGKPVK--- 120

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++HF+ +               ++  L  QP TGR  Q+R H  H+   +VGD 
Sbjct: 121 ---KPAVTHFQRLATGELEIPSTGFTTSRYALLRCQPQTGRFRQIRRHMKHLSHHMVGDT 177

Query: 271 KYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            +       +F     +++ LHA  ++ PHP +G R+ +TAPL     K     G++
Sbjct: 178 SHGDGRHNRSFRMLGIHRMLLHAERLEFPHPADGRRIGVTAPLDVEFSKACALFGWE 234


>gi|325124079|gb|ADY83602.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter
           calcoaceticus PHEA-2]
          Length = 221

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 109/231 (47%), Gaps = 13/231 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + N           +L+ED  + V +KPAG+    G    +H   +L+  V  K   
Sbjct: 1   MPLNDNFVYAPPQDTLSILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPL 58

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G    +       + 
Sbjct: 59  AKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKHYIALVQGQVAQEGSVEVPLIT 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +   +A + F+ +    +     + ++P TGR+HQLRVH +H+
Sbjct: 119 DWENRPRQIVHF-----ELGKHAKTLFQPLLYDGKTDQSRVLLEPVTGRSHQLRVHMMHI 173

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G PI+GD  Y    K        N++ LHA Y+   HP  G  + I + +P
Sbjct: 174 GHPIMGDKLYHPEPK----RFHLNRMALHAAYLAFQHPLNGTDVVIESQVP 220


>gi|328469904|gb|EGF40815.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus 10329]
          Length = 559

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 114/245 (46%), Gaps = 20/245 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  + +     ++  +  ++Y+D  + V NKP+G+    G  I    
Sbjct: 328 CQPILGHMMQGLDVEPNPLA-ENWAEDKELEIIYQDDAMVVVNKPSGLLSVPGKTIKDSA 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++      + P + HRLD  TSGILV A T+ A + L + F  R +QK Y +L+ G
Sbjct: 387 YTRLQAMF-PDVEGPFVIHRLDMATSGILVFALTKRANKSLQKQFMARGVQKRYMALLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +    +  I+  + +          V  ++     +A +++++I+        + M P T
Sbjct: 446 VLNAPEGEISLPM-RGDPDDRPRQLVCFEH---GKHAETYWQLIE-VKDGRSKVYMYPKT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH+ H   +  P+VGD  Y             N+L+LHA  ++L HP    R+
Sbjct: 501 GRTHQLRVHSAHHMGLNMPMVGDGLYGEK---------ANRLHLHAEMLELDHPYSKERM 551

Query: 306 QITAP 310
              A 
Sbjct: 552 VFKAE 556


>gi|326522893|dbj|BAJ88492.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 357

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 85/341 (24%), Positives = 149/341 (43%), Gaps = 71/341 (20%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIY 109
           KR+K +  ++ G  + +P  +       + + I  ++++  +   ++LK +++Y+DS I 
Sbjct: 10  KRIKHSEVMEPGMRIHLPVSVAEAEIKKRYETIPTATLHPNRDEIEYLKRLVIYKDSAIL 69

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQ 168
           V NKP  + ++G   +   +D    + +    ++ P+L HRLD+++SG+L++ RTR    
Sbjct: 70  VLNKPPKVPMKGNLPVHNSMDVLAAAALSFGNEEGPKLVHRLDRDSSGLLLMGRTREGFT 129

Query: 169 HLTESFRMRRIQKI---------------YWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
            L   F   ++ K                YW+LV G P   +  I+  L K     G   
Sbjct: 130 RLHWLFTSIKLAKTASQTWNTACESYLQRYWALVIGTPTESEGVISAPLTKVLLDDGKAE 189

Query: 214 HVVKQNE---KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGD 269
            V+  +     GA  A++ ++V+        W+E++P TGR HQLRVH    +G PIVGD
Sbjct: 190 RVILAHPSGIDGAQEAVTEYRVMGPTINGCSWIELRPLTGRKHQLRVHCAEALGTPIVGD 249

Query: 270 HKYC------------ANFKGNFTSPIQNK------------------LYLHARYMDLPH 299
           +KY              +F+     P + +                  L+LH R M +P+
Sbjct: 250 YKYGWFVHQRWKQNPQPDFEPFTGEPYKLRRPEGLEVQKGSVLSKVPLLHLHCREMVVPN 309

Query: 300 ----------------PEGGR----LQITAPLPAHMVKTWD 320
                           P        L+  AP+PAHM  +W+
Sbjct: 310 IAKFLSNTGEWHDNGTPWSKEKPNLLRFIAPMPAHMKISWN 350


>gi|325663710|ref|ZP_08152114.1| hypothetical protein HMPREF0490_02855 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325470203|gb|EGC73436.1| hypothetical protein HMPREF0490_02855 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 227

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 60/218 (27%), Positives = 100/218 (45%), Gaps = 15/218 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLD 151
           ++S +LYED  + V  KPAG+ VQ        +   LK++   +          + HRLD
Sbjct: 3   IQSYILYEDRDLIVCRKPAGVPVQTKQIQTKDMVSLLKNYRYQQEGGKGEPYLGVIHRLD 62

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q   GI+V A+T  AA+ L    +     K Y +++  +P+  +  + ++L+K       
Sbjct: 63  QPVEGIIVFAKTPQAAKELNRQLQAGDFGKYYQAVLCKVPEKAQGQLTDYLVKDGRTNLS 122

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              + ++++ GA  A   +K I   A+      +   TGR HQ+RV    MGCPI+GD K
Sbjct: 123 K--ICRKSDAGAKEARLSYK-IQGEAEGKALANIHLDTGRHHQIRVQMSGMGCPILGDVK 179

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           Y    K         ++ L A  +   HP+  + +Q  
Sbjct: 180 YGGEEKER------GQIALCASSLTFVHPKTKKQMQFE 211


>gi|91226723|ref|ZP_01261412.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
 gi|91189020|gb|EAS75303.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
          Length = 559

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 114/245 (46%), Gaps = 20/245 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  + +     ++  +  ++Y+D  + V NKP+G+    G  I    
Sbjct: 328 CQPILGHMMQGLDVEPNPLA-ENWAEDKELEIIYQDDAMVVVNKPSGLLSVPGKTIKDSA 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++      + P + HRLD  TSGILV A T+ A + L + F  R +QK Y +L+ G
Sbjct: 387 YTRLQAMF-PDVKGPFVIHRLDMATSGILVFALTKRANKSLQKQFMARGVQKRYMALLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +    +  I+  + +          V  ++     +A +++++I+        + M P T
Sbjct: 446 VLNEPEGEISLPM-RGDPDDRPRQLVCFEH---GKHAETYWQLIE-VKDGRSKVYMYPKT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH+ H   +  P+VGD  Y             N+L+LHA  ++L HP    R+
Sbjct: 501 GRTHQLRVHSAHHMGLNMPMVGDGLYGEK---------ANRLHLHAEMLELDHPYSKERM 551

Query: 306 QITAP 310
              A 
Sbjct: 552 VFKAE 556


>gi|212634509|ref|YP_002311034.1| pseudouridylate synthase [Shewanella piezotolerans WP3]
 gi|212555993|gb|ACJ28447.1| Pseudouridylate synthase [Shewanella piezotolerans WP3]
          Length = 217

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 66/208 (31%), Positives = 100/208 (48%), Gaps = 13/208 (6%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y D  I + NKP+G+      GIA +      S +  + +   L HRLD  TSG++V AR
Sbjct: 18  YVDRDIIIINKPSGLLSNP--GIADYTHDCALSRIQQRFKDAILVHRLDCSTSGVMVFAR 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            + A  +L   F+ R+ QK Y + V G  +N +  I   +              +Q    
Sbjct: 76  NKKAESNLKTQFQDRKTQKTYITEVSGHLQNAQGVIELPITADKANPPK-----QQVSAT 130

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              AI+HF+ ++  A     LE++P TGRTHQLRVH L +G PI+GD  Y      +   
Sbjct: 131 GKVAITHFETLEVRANS-TLLELKPVTGRTHQLRVHLLAIGNPILGDDFYAEQHIVDSA- 188

Query: 283 PIQNKLYLHARYMDLPHP-EGGRLQITA 309
               +L LHA+ +   HP  G ++  ++
Sbjct: 189 ---PRLKLHAQSLSFTHPYSGKQMHFSS 213


>gi|50365380|ref|YP_053805.1| 23S rRNA pseudouridine synthase [Mesoplasma florum L1]
 gi|50363936|gb|AAT75921.1| 23S rRNA pseudouridine synthase [Mesoplasma florum L1]
          Length = 323

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 61/315 (19%), Positives = 123/315 (39%), Gaps = 29/315 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           +       +++N  L ++ K +Y       + K LR G ++++ KR+K  +  I++   +
Sbjct: 22  MNTFKANQNDDNQSLFKFLKKNYKTTPLSVIYKWLRKGDIKINGKRIKDKDYLIKANDEI 81

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +             + +L        + D     ++YEDS + +  KP  + V   S +
Sbjct: 82  IVYDN---------NKPVLRDDFKKITNYDI---DVIYEDSNLLIVKKPYNVEVH--SPV 127

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +D  +K+++    Q              HRLD+ TSG+++ A+ +     + E+ + 
Sbjct: 128 KTSMDDIVKNYLFDTNQYNPSEENSYVISHIHRLDKLTSGLIMYAKNKQTHDIMVEAIQD 187

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-C 235
           +   + Y+     +P  +      W+     I        ++       A + F V+   
Sbjct: 188 KEKIEKYYRCRIDVPVTESLIAKGWIKYDPIIQKS--VFSEEFRSDYKEATTIFNVVSLD 245

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--PIQNKLYLHAR 293
              +   LE+Q  TGR HQ+R    + G  I+ D +Y      N        NKL  +  
Sbjct: 246 VTNEQTELEVQILTGRKHQIRATLEYYGASIINDSRYSGTIINNEKMIFLFANKLVFNGF 305

Query: 294 YMDLPHPEGGRLQIT 308
             +L +  G  ++I 
Sbjct: 306 EGNLENLNGKIIEIE 320


>gi|94501077|ref|ZP_01307601.1| 23S rRNA pseudouridylate 746 synthase [Oceanobacter sp. RED65]
 gi|94426824|gb|EAT11808.1| 23S rRNA pseudouridylate 746 synthase [Oceanobacter sp. RED65]
          Length = 201

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 67/214 (31%), Positives = 109/214 (50%), Gaps = 18/214 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  + V +KP+G+  Q GS         LK +         L HRLDQ TSG++++
Sbjct: 3   ILYEDKHLLVIDKPSGLLSQQGSLDDSVPHRLLKDYA-----YVGLVHRLDQATSGVMMM 57

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + A  HL + F+ R+  K+Y + V+G    ++  I   L        D+ +  KQ  
Sbjct: 58  ALNKKAHGHLAKQFQDRKTFKVYQARVFGSLPGERGQIDLPL------RCDWPNRPKQEV 111

Query: 221 K-GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 +++H++ I+  +Q +  + + PHTGR+HQLRVH   MG PI+GD  Y  +   +
Sbjct: 112 HIEGKSSLTHWQCIER-SQHWSRVALIPHTGRSHQLRVHMAAMGYPILGDRFYAHHEAKS 170

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                  +L LHA  + + HP  G R++  + +P
Sbjct: 171 MA----KRLNLHAASLAVNHPISGKRMRFFSSVP 200


>gi|310658221|ref|YP_003935942.1| pseudouridylate synthase [Clostridium sticklandii DSM 519]
 gi|308824999|emb|CBH21037.1| putative pseudouridylate synthase [Clostridium sticklandii]
          Length = 223

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 111/232 (47%), Gaps = 17/232 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           +   ++YED+ I V  KP G+  Q        +  ++K++V  K  KP      L HRLD
Sbjct: 1   MTPEVIYEDNHIIVVVKPFGMPSQEDDSKDLDMLSWVKAYVKEKYNKPGEVFIGLVHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + + G++V ART  AA  L++  R ++I+K Y  +  G  + K   + ++LLK      +
Sbjct: 61  RVSGGLMVFARTSKAASRLSDQIRKKQIEKKYTLVAEGSLEKKSGFMEDFLLKDK--SNN 118

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V   K   K +  A   ++V+D   Q    + +   TGR+HQ+RV      CP+ GD K
Sbjct: 119 KVKAFKNEVKDSKDAKLSYEVMDER-QGLSLVSVDLITGRSHQIRVQFSSRRCPLYGDLK 177

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
           Y +      ++P +  + L + Y+   HP    +L+    LP H  K WD  
Sbjct: 178 YGS------SNPQKKSIALWSYYLSFEHPTKKEKLEFKIELPDH--KPWDIF 221


>gi|50083937|ref|YP_045447.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. ADP1]
 gi|49529913|emb|CAG67625.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) [Acinetobacter sp.
           ADP1]
          Length = 219

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 105/228 (46%), Gaps = 13/228 (5%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           S N           ++YED  + V +KPAG+    G    +    +L+  +  +    R+
Sbjct: 2   STNFVYMPPQDPMCMVYEDDDLIVIDKPAGLLSVMGRLPEHQDSAYLR--IRQQYPLARV 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
           THRLD  TSG+L+ A+ R A   +++ F+ R IQK Y +LV G  + +    A  +    
Sbjct: 60  THRLDMATSGLLMFAKHRRAEIAISKLFQTRCIQKYYIALVDGEVQAQGMVEAPLITDWP 119

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +     +  V+        A + ++ +D  A      ++++P TGR+HQLRVH  H+G P
Sbjct: 120 NRPKQKIDFVE-----GKAAKTCYQPLDYNAAFNQTRIQLEPITGRSHQLRVHMQHIGHP 174

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           I+GD  Y              ++ LHA  +    P   + L I A +P
Sbjct: 175 IMGDKLYHPEP----AKFALKRMALHATSLKFIQPFTQQPLDIVATVP 218


>gi|116630078|ref|YP_815250.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           ATCC 33323]
 gi|116095660|gb|ABJ60812.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           ATCC 33323]
          Length = 285

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 71/303 (23%), Positives = 121/303 (39%), Gaps = 34/303 (11%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNR 58
           M  MT Y  ++    +   + ++   +     I     +  LR   Q+ ++   +  N  
Sbjct: 1   MEKMTTYHYFLTYPANLGPISVNELMRKLL--IPR-KWRHFLRTEKQILINDHYLPLNFL 57

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +++G  + I      L+H+  +Q+   +S  L K        ++YEDS I V +KP G  
Sbjct: 58  VKAGDKIDIY-----LDHVESDQQTYPASGKLPK--------VVYEDSDILVIDKPTGQK 104

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                      D  L       G  P + HRLD  T+G+L+VA+  A    L      + 
Sbjct: 105 THPN---LDEKDTALNDCATYLGYSPFIVHRLDMLTNGLLLVAKNPAVVPILNRQLTNKT 161

Query: 179 IQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           + + Y + V       +   I+  +          +  +         AI+H++VI    
Sbjct: 162 LHREYLAWVSKSNQLKQSGTISLSIGHDPDDQRKRMVRL-----DGQKAITHYEVIKECE 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            K   +++   TGRTHQ+RVH   +G PI+GD  Y  N++         KL L A  +  
Sbjct: 217 NKE-LVKLTLETGRTHQIRVHLAALGAPIIGDPLYNPNYQNG------EKLQLTAYQLTF 269

Query: 298 PHP 300
             P
Sbjct: 270 MGP 272


>gi|261406141|ref|YP_003242382.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261282604|gb|ACX64575.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
          Length = 239

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 64/227 (28%), Positives = 103/227 (45%), Gaps = 14/227 (6%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LT 147
            + +    +L+ED+ +    KP  I  Q  +     +   LK  +  +  KP      L 
Sbjct: 6   PATYPAVPILFEDNHVLGVTKPVNIPSQEDATGDPDMLTILKQDIKERYNKPGNVFLGLV 65

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+   G +V A+T  AA  L+E+ R R  +K Y ++V G+P      + N L K + 
Sbjct: 66  HRLDRPVGGAMVFAKTSKAASRLSEAVRSRSFRKQYVAVVHGVPAKTSGRLVNMLYKDAK 125

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                VHV  +   GA  AI  + V+   A+    + ++ HTGR HQ+RV   H G P+ 
Sbjct: 126 TN--TVHVTSKGTDGAKEAILDYTVLQA-AEGVSLVLIELHTGRPHQIRVQLSHAGHPLF 182

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           GD KY +       +    ++ L +  +  PHP     + I +  P+
Sbjct: 183 GDQKYGSKV-----NKAGQQIALWSVLVGFPHPVTKEDISIRSMPPS 224


>gi|295104735|emb|CBL02279.1| Pseudouridylate synthases, 23S RNA-specific [Faecalibacterium
           prausnitzii SL3/3]
          Length = 303

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 111/322 (34%), Gaps = 51/322 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
            + + +  + +      +     K  R G    D   V  N RI  GQ++          
Sbjct: 14  HDGVLVRSFLRQCAVSTDLARAVK-FRGGGFFADGVPVLANRRIYPGQMLSF-------- 64

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---SGIAYHIDGF 132
                   L    +       +   ++YED+   V  KP  ++V       G        
Sbjct: 65  -------ALPPEGDGVTPQPEIPVKVVYEDAFAVVLEKPPQLAVHPTLNYPGGTLANGYA 117

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             +         R  +R+D++TSG+++ A+   AA  L       R+ K+Y+++  G   
Sbjct: 118 AWAAAHGHSPVFRPVNRIDKDTSGLVLAAKNAYAAPLLA-----GRVTKLYYAIAQGALP 172

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +  I   + ++         + +        + + + +I             P TGRT
Sbjct: 173 LGEGAIDAPIGRRGD-----SIIGRCVTPEGKPSRTEYTIIK-EENGLSLAACVPVTGRT 226

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL------PHPEGGRLQ 306
           HQ+RVH   +G P+ GD  Y  + +         +  LH            P P+G R++
Sbjct: 227 HQIRVHFASIGHPLAGDDLYGGSRER------IARQALHCARQSFAVPVYTPLPDGIRVE 280

Query: 307 ---------ITAPLPAHMVKTW 319
                    + +PLP  M   +
Sbjct: 281 MPLRLRTVTVESPLPPDMEALF 302


>gi|199598043|ref|ZP_03211467.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|199591133|gb|EDY99215.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
          Length = 278

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 63/292 (21%), Positives = 115/292 (39%), Gaps = 35/292 (11%)

Query: 25  FKNHYPH--INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
            ++      I      ++  +  ++V+     FN  +++G ++ +               
Sbjct: 15  LRDQLQDWLIPRKRQHQMRVAQTIQVNGHYRHFNEPVKNGDLISLTY------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
             D  V+ T   +     + YED  + + +KPAG+                ++       
Sbjct: 62  --DELVHRTYVPETPHLNIRYEDDDLLIVDKPAGMKTHPNQPGETGTL-MNQAAAYLAPY 118

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKECIANW 201
              +THRLD  TSG+LV+A+   A   +      + + + Y ++V  GIP  +K  I   
Sbjct: 119 PALITHRLDMATSGLLVIAKNPLAQAIINRQLATKAMHRDYLAMVPRGIP--EKGTIQAP 176

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           +          +            A++H++ I   A     +++   TGRTHQ+RVH   
Sbjct: 177 IGHDPDDKRKRMIRA-----DGAVAVTHYRRIAETATTAT-IQLNLETGRTHQIRVHLAS 230

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           +G PI+GD  Y A       +    ++ LHA  + L  P     L +T+P P
Sbjct: 231 IGFPIIGDPLYAA-------TETATRMQLHAFRVRLIRPLTIEPLTVTSPSP 275


>gi|327393813|dbj|BAK11235.1| ribosomal large subunit pseudouridine synthase A RluA [Pantoea
           ananatis AJ13355]
          Length = 232

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 60/239 (25%), Positives = 100/239 (41%), Gaps = 20/239 (8%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I+D+ +    H +     +LY+D  + + +KP+ +    G          +   + +   
Sbjct: 4   IVDTFIAPPCHEEI---RILYQDDHLVLIDKPSELLSLSGKNPQN--LDSVHYRLVTIFP 58

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD  TSG++VVAR +     L++ F  R + K Y +L+ G   +++  I   +
Sbjct: 59  GCTLVHRLDFGTSGLMVVARNKTINAALSQQFSARTVAKHYSALLCGHLPDEEGIIDAPI 118

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF--------CWLEMQPHTGRTHQ 254
            K           +    +    A S ++V++ F  K           + + P TGRTHQ
Sbjct: 119 AKDPA----RFPRMSICAEWGKPARSRYRVVERFNLKRDDARVIPLTRVTLIPETGRTHQ 174

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           LR+H   +G PI+G   Y              +L LHA  +   HP  G    I +P P
Sbjct: 175 LRIHCQLLGHPILGCDLYGGLLLPGMEQT--PRLMLHASELQFIHPVTGEPFHIVSPSP 231


>gi|189485425|ref|YP_001956366.1| ribosomal large subunit pseudouridine synthase C [uncultured
           Termite group 1 bacterium phylotype Rs-D17]
 gi|170287384|dbj|BAG13905.1| ribosomal large subunit pseudouridine synthase C [uncultured
           Termite group 1 bacterium phylotype Rs-D17]
          Length = 238

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 107/241 (44%), Gaps = 25/241 (10%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  ++Y+D  I V NKP+G+ V  G  I Y     ++   +   QK  + H +D++ SG+
Sbjct: 4   QIEIIYQDENILVVNKPSGMFVIPGRNI-YENKTLVEILRNQLKQKLWVVHIIDRDASGV 62

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV A+     ++++  F   +I+K Y +L+ G+ +  +  I   L+    I G  V +  
Sbjct: 63  LVFAKNPETHRNISVQFENSKIRKKYIALLSGVLEENEGTINKPLI----ISGKNVRI-- 116

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---- 273
             +     +I+ FKV++ F + +  +   P T + HQ+R+H   +G P+  D +Y     
Sbjct: 117 --DITGKESITDFKVLENF-RSYTLVNALPLTVKRHQIRIHFWSLGHPLAIDGEYGTLDP 173

Query: 274 ----------ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                        KG   +P+ ++L LHA  + L  P  G      A L          L
Sbjct: 174 IFLSSFKRGYKIKKGKTENPLISRLTLHAAALTLILPGSGEEKTFEAALAKDFEVAVKQL 233

Query: 323 G 323
            
Sbjct: 234 R 234


>gi|114563871|ref|YP_751385.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114335164|gb|ABI72546.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 217

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 62/219 (28%), Positives = 100/219 (45%), Gaps = 13/219 (5%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        + Y+D  I V NKP+G+    G     H      + +     +  L HRLD
Sbjct: 7   QPPSIPWLDIRYKDRDIIVINKPSGLLSNPGRSPDTHDTAI--TRLQRCYPEAILIHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSGI++ ART+ A  HL   F+ R+ +K+Y + V G    ++  +   L         
Sbjct: 65  CDTSGIMIFARTKKAESHLKIQFQNRQAKKVYIAEVIGHVDEQQGKVNFALGANPDSP-- 122

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                +        A+++F V++  A     +E++PHTGRTHQLRVH L +G  I+GD  
Sbjct: 123 ---PFQMLTDSGKAALTYFSVLEHRAYS-TLMELKPHTGRTHQLRVHMLALGHTILGDEF 178

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           Y      N +     +L LHA+ + + HP     +   +
Sbjct: 179 YGDESTINAS----KRLNLHAQSLTITHPYSQVEMTFFS 213


>gi|254444612|ref|ZP_05058088.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198258920|gb|EDY83228.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 224

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 61/226 (26%), Positives = 94/226 (41%), Gaps = 12/226 (5%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           +        +  +LY D  I + NKP+G+    G   A      +   +        + H
Sbjct: 8   DFIAPPCHEEIEILYRDDAILLINKPSGLLSLSGKNPAN--LDSVHYRLVQSYSGALMIH 65

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSGI+V+A ++ A  +L   F+ R + K Y +L+ G        I   ++K    
Sbjct: 66  RLDLGTSGIMVLALSKTANANLCLQFKNRSVAKTYTALLNGRLAETIGTIDIPIIKD--- 122

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             +     K   K    A S ++V+D         +   P TGRTHQLR+H+   G  I+
Sbjct: 123 -KENFPYQKTCYKTGKPAQSEYQVLDYDAGNDVSRVLFTPLTGRTHQLRIHSQAFGHSIL 181

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           G   Y +           N+L LHA  +   HP  G R++   P P
Sbjct: 182 GCDLYASK----AIEEKANRLMLHATSLSFDHPTSGKRIEAECPCP 223


>gi|260902224|ref|ZP_05910619.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
 gi|308110528|gb|EFO48068.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
          Length = 559

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 113/245 (46%), Gaps = 20/245 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  + +     ++  +  ++Y+D  + V NKP+G+    G  I    
Sbjct: 328 CQPILGHMMQGLDVEPNPLA-ENWAEDKELEIIYQDDAMVVVNKPSGLLSVPGKTIKDSA 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++      + P + HRLD  TSGILV A T+ A + L + F  R +QK Y +L+ G
Sbjct: 387 YTRLQAMF-PDVEGPFVIHRLDMATSGILVFALTKRANKSLQKQFMARGVQKRYMALLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +    +  I+  + +          V  ++     +A + +++I+        + M P T
Sbjct: 446 VLNEPEGEISLPM-RGDPDDRPRQLVCFEH---GKHAETSWQLIE-VKDGRSKVYMYPKT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH+ H   +  P+VGD  Y             N+L+LHA  ++L HP    R+
Sbjct: 501 GRTHQLRVHSAHHMGLNMPMVGDGLYGEK---------ANRLHLHAEMLELDHPYSKERM 551

Query: 306 QITAP 310
              A 
Sbjct: 552 VFKAE 556


>gi|254227499|ref|ZP_04920931.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262396236|ref|YP_003288089.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. Ex25]
 gi|151940111|gb|EDN58937.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262339830|gb|ACY53624.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. Ex25]
          Length = 559

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 66/244 (27%), Positives = 113/244 (46%), Gaps = 20/244 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  + +     ++  +  ++Y+D  + V NKP G+    G  I    
Sbjct: 328 CQPILGHMMQGLDVEPNPLA-ENWAEDKELEIIYQDDAMVVVNKPTGLLSVPGKTIKDSA 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++      + P + HRLD  TSGILV A T+ A + L + F  R +QK Y +L+ G
Sbjct: 387 YTRLQAMF-PDVEGPFVIHRLDMATSGILVFALTKRANKSLQKQFMARGVQKRYMALLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +    +  I+  + +          V  ++     +A +++++I+        + M P T
Sbjct: 446 VLNEPEGEISLPM-RGDPDDRPRQLVCFEH---GKHAETYWQLIE-VKDGRSKVYMYPKT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH+ H   +  P+VGD  Y             N+L+LHA  ++L HP    R+
Sbjct: 501 GRTHQLRVHSAHHMGLNMPMVGDGLYGEK---------ANRLHLHAEMLELDHPYSKERM 551

Query: 306 QITA 309
              A
Sbjct: 552 VFKA 555


>gi|310764748|gb|ADP09698.1| Pseudouridine synthase [Erwinia sp. Ejp617]
          Length = 232

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 57/220 (25%), Positives = 92/220 (41%), Gaps = 16/220 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                K  +LY+D ++ + NKPAG+    G          +   +        L HRLD 
Sbjct: 11  PPCHDKIEILYQDDRLVLINKPAGLLSLSGKNPQN--IDSVHYRLVQIFPGCTLVHRLDF 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V+AR +A    L + F  R + K+Y +L+ G   + +  I   + K   +    
Sbjct: 69  GTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLDDNEGVIDAAIAKDPAL---- 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGC 264
             ++         A S ++V++ F              +++ P TGRTHQLR+H   +G 
Sbjct: 125 FPLMSICSIHGKPARSRYRVVERFYHPLENRTLLPLTRVQLTPETGRTHQLRIHCQQLGH 184

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           PI+G   Y              +L LHA  +   HP  G 
Sbjct: 185 PILGCDLYGGRLLPGTERT--PRLMLHASELHFVHPINGE 222


>gi|300724846|ref|YP_003714171.1| 23S rRNA pseudouridylate 746 synthase [Xenorhabdus nematophila ATCC
           19061]
 gi|297631388|emb|CBJ92085.1| 23S rRNA pseudouridylate 746 synthase [Xenorhabdus nematophila ATCC
           19061]
          Length = 217

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 68/225 (30%), Positives = 106/225 (47%), Gaps = 16/225 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G     H D  + + + ++       
Sbjct: 2   LESYHPPTDPWLYVLYQDEHIMVVNKPSGLLSVPGKA-EEHKDSIM-TRIQAEFPTAESV 59

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSGI+VVA T+AA + L   FR R  +K+Y + VWG    +K  +   L+    
Sbjct: 60  HRLDMATSGIMVVALTKAAERELKRQFREREPKKVYIARVWGKLVPEKGRVDLPLI---- 115

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V++   Q    + + P TGR+HQLRVH L +G P
Sbjct: 116 --CDWPNRPKQKVCFETGKSAQTEYQVLEYEEQ-ATRVRLAPITGRSHQLRVHMLALGNP 172

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           I+GD  Y  +        +  +L LHA+ + + HP  G  L    
Sbjct: 173 IMGDRFYAHSQ----ARELAPRLQLHAQELFITHPAYGTPLHFEC 213


>gi|119896305|ref|YP_931518.1| pseudouridine synthase A [Azoarcus sp. BH72]
 gi|119668718|emb|CAL92631.1| pseudouridine synthase A [Azoarcus sp. BH72]
          Length = 214

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 61/220 (27%), Positives = 99/220 (45%), Gaps = 14/220 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L   LLY D  + V +KPAG+      G        L   V ++     + HRLD  TSG
Sbjct: 4   LTPTLLYTDDSLIVADKPAGLLSVPAGGED--RQDCLAHRVQAQFDDALIVHRLDAATSG 61

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++++AR     + ++  F  R + K Y +LV G        IA  L          +   
Sbjct: 62  LVLLARGMEMLRRMSLGFEQRVVGKRYVALVHGRVAQDDGEIALPLAADPLNRPRQI--- 118

Query: 217 KQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             +      A++ ++V++           LE++P TGR+HQLRVH + +G PIVGD  Y 
Sbjct: 119 -VDAARGRPALTRYRVLERSGAGDAAVSRLELKPMTGRSHQLRVHLMAIGHPIVGDPLYA 177

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                  ++    +++LHA  +   HP+    +Q  +P+P
Sbjct: 178 PPE----SAAAHPRMFLHAAGIAFMHPDRRVPMQFDSPVP 213


>gi|257060968|ref|YP_003138856.1| pseudouridine synthase [Cyanothece sp. PCC 8802]
 gi|256591134|gb|ACV02021.1| pseudouridine synthase [Cyanothece sp. PCC 8802]
          Length = 551

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 66/212 (31%), Positives = 105/212 (49%), Gaps = 18/212 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS--KGQKPRLTHRLDQETS 155
           +  ++YED  I   +KP+G+    G       D  L    +S    Q+ R  HRLDQ+TS
Sbjct: 343 EIKVIYEDQWIIAIDKPSGLLSVPGRYFE-TFDSVLTRLQNSLPDAQELRTVHRLDQDTS 401

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GIL++AR R   +HL++ F  R+++KIY +++ G     +  I   L    +        
Sbjct: 402 GILLLARDRYTHRHLSQQFAQRKVEKIYEAILAGSVMMNEGVIQLPLWGDPNNRP----Y 457

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA---LHMGCPIVGDHKY 272
            K + +    +I+ FKVI    +    ++  P TGRTHQ+RVHA     +G  I+GD+ Y
Sbjct: 458 QKVDWELGKPSITQFKVITTQ-ENLTRIQFIPLTGRTHQIRVHAVDTQGLGSVILGDYLY 516

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             N          ++L+LHAR +   HP+  +
Sbjct: 517 GCNA-------GVSRLHLHARELKFEHPQQQK 541


>gi|299822133|ref|ZP_07054019.1| ribosomal large subunit pseudouridine synthase D [Listeria grayi
           DSM 20601]
 gi|299815662|gb|EFI82900.1| ribosomal large subunit pseudouridine synthase D [Listeria grayi
           DSM 20601]
          Length = 294

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 101/238 (42%), Gaps = 18/238 (7%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKG 141
           +L         S      ++YED  I V NKPA +                +++++++ G
Sbjct: 62  VLPLLEKAVVTSADRPIDIVYEDDFILVANKPANLKTHPNDSSEIDSCQQRVQAYLNATG 121

Query: 142 QK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           Q        HRLD+ TSG+L+ A+   A    +     R I + Y ++   I K      
Sbjct: 122 QSGASASPVHRLDEATSGLLLFAKNAIALAAFSYQLEQRTIHRHYLAITDNIWKGP---- 177

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRV 257
           AN+ ++K      +    ++   G   A++H  ++    AQ    LE +  TGRTHQ+RV
Sbjct: 178 ANFTIRKPISSDRHHPNKRRVSPGGQTAVTHVAILARHQAQNNTLLECRLDTGRTHQIRV 237

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAH 314
           H    G PI+GD  Y  + +         +L LHA+ ++  HP     L+   P P  
Sbjct: 238 HLSDAGFPIIGDSLYGGSNRAA-------RLLLHAKQLETYHPFLDNTLKWEQP-PDD 287


>gi|325104427|ref|YP_004274081.1| pseudouridine synthase [Pedobacter saltans DSM 12145]
 gi|324973275|gb|ADY52259.1| pseudouridine synthase [Pedobacter saltans DSM 12145]
          Length = 559

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 111/248 (44%), Gaps = 24/248 (9%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               LNH++   ++ ++ + L   +D     ++Y+D  + + NKPA      G  +   +
Sbjct: 328 CEPILNHMLLGMEVEENPM-LRNPADGKALDIVYDDDYLCIVNKPAEFLSVPGINVTDSV 386

Query: 130 DGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              +K  + D+ G  P + HRLD  TSGI+++A+++     L   F  R +QK Y +L+ 
Sbjct: 387 LERIKVKYPDATG--PLIVHRLDMSTSGIMLIAKSKDVYIQLQSQFINRTVQKRYIALLD 444

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+ ++ +  I   L          +            A + ++ ++        +   P 
Sbjct: 445 GLVESNEGTIDLPLRVDLEDRPRQLVCYDY----GKPAKTKWRALE-HKNGKTRVHFWPI 499

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           TGRTHQLRVH+ H   + CPIVGD  Y             ++L+LHA ++   HP   + 
Sbjct: 500 TGRTHQLRVHSAHKSGLNCPIVGDDIYGKKG---------DRLHLHAEWLQFYHPILEKT 550

Query: 305 --LQITAP 310
             + + A 
Sbjct: 551 MTITVEAE 558


>gi|218676329|ref|YP_002395148.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio splendidus
           LGP32]
 gi|218324597|emb|CAV26131.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio splendidus
           LGP32]
          Length = 563

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 104/231 (45%), Gaps = 19/231 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ +  +   +      ++YED +I V NKP       G  I   +   +K+        
Sbjct: 345 LEENPLIVNPAVGKSFDIVYEDDEIVVVNKPEEFLSVPGKFIEDSVYTRIKARY-PDATG 403

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+L++A T  + +H+ + F  R ++K Y +L+ G    K   I+  L 
Sbjct: 404 PLIIHRLDMSTSGLLILALTAESNKHIQKQFIDRTVEKRYTALLDGEIDGKSGDISLPL- 462

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
            +  I      +V         A +H++ +     K   + + P TGRTHQLRVH  H  
Sbjct: 463 -RGDITDRPRQLVCHEH--GRNAETHWEAVSTNNGK-TKVHLYPKTGRTHQLRVHCAHPS 518

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            +G PI GD  Y    +         +L+LHA Y+ L HP  G  ++   P
Sbjct: 519 GLGVPIRGDDLYGYKRE---------RLHLHAGYLKLIHPTTGEWIEFEVP 560


>gi|322506303|gb|ADX01757.1| Dual specificity pseudouridine synthase [Acinetobacter baumannii
           1656-2]
          Length = 221

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 109/231 (47%), Gaps = 13/231 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + N           +L+ED  + V +KPAG+    G    +H   +L+  V  K   
Sbjct: 1   MPLNDNFVYAPPQDPLSILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPL 58

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G  K +       + 
Sbjct: 59  AKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGSVEVPLIT 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +   +A + F+ +          + ++P TGR+HQLRVH +H+
Sbjct: 119 DWENRPRQIVHF-----ELGKHAKTLFQPLVYDETTDQSRVLLEPVTGRSHQLRVHMMHI 173

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G PI+GD  Y    K        N++ LHA Y+   HP  G  + I + +P
Sbjct: 174 GHPIMGDKLYHPEPK----RFHLNRMALHAAYLAFQHPLKGTDVVIESQVP 220


>gi|238763442|ref|ZP_04624405.1| Pseudouridine synthase [Yersinia kristensenii ATCC 33638]
 gi|238763523|ref|ZP_04624485.1| Pseudouridine synthase [Yersinia kristensenii ATCC 33638]
 gi|238698305|gb|EEP91060.1| Pseudouridine synthase [Yersinia kristensenii ATCC 33638]
 gi|238698386|gb|EEP91140.1| Pseudouridine synthase [Yersinia kristensenii ATCC 33638]
          Length = 256

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 59/220 (26%), Positives = 89/220 (40%), Gaps = 16/220 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                K   LY+D  + + NKPAG+    G          +   +        L HRLD 
Sbjct: 35  PPCHDKIETLYQDDHLVLINKPAGLLSLSGKNPQN--LDSVHHRLVQIFPGCTLVHRLDF 92

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V+AR +     L + F  R + K+Y +L+ G   N +  I   + K   +    
Sbjct: 93  GTSGLMVIARNKTINAALCQQFSQRTVTKVYSALLCGHLGNNEGVIDAAIAKDPAL---- 148

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGC 264
             ++         A SH++VI+ F  K           +++ P TGRTHQLR+H   +G 
Sbjct: 149 FPLMSICPINGKPARSHYQVIERFYHKLADQKLLPLTRVQLTPETGRTHQLRIHCQQLGH 208

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           PI G   Y              +L LHA  +   HP    
Sbjct: 209 PIWGCDLYGGRLLPGTEQT--PRLMLHASELHFVHPISNE 246


>gi|68482658|ref|XP_714726.1| hypothetical protein CaO19.10687 [Candida albicans SC5314]
 gi|68482929|ref|XP_714595.1| hypothetical protein CaO19.3177 [Candida albicans SC5314]
 gi|46436176|gb|EAK95543.1| hypothetical protein CaO19.3177 [Candida albicans SC5314]
 gi|46436316|gb|EAK95680.1| hypothetical protein CaO19.10687 [Candida albicans SC5314]
          Length = 589

 Score =  160 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 103/260 (39%), Gaps = 32/260 (12%)

Query: 21  LDRWF---KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +D +    ++  P    + +      G V+V+ +       +++G ++            
Sbjct: 112 IDVFIDEFRDRTPDAYRMAV----EEGLVKVNSQVANLETILRNGDLISHRSYR------ 161

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +E  +    +            +++ED  + V +KP GI V       Y  +   K + 
Sbjct: 162 -REPPVSSRDIK-----------IVFEDDDLLVIDKPGGIPVHPTG--RYRYNTVTKIFE 207

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             KG+     +RLD+ TSG++ + ++   A ++    R R + K Y + V G     +  
Sbjct: 208 HEKGKIVHPCNRLDRLTSGLMFLGKSSKGANNMMSQIRDRNVTKEYIARVKGEFPLDRII 267

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLR 256
           +   L  KS      + +   + +    A + F+ +          ++  P TGRTHQ+R
Sbjct: 268 VDKPLSTKSP----KLTLNVVDMENGKEAKTEFQRVSYDPITNTSVVKCHPLTGRTHQIR 323

Query: 257 VHALHMGCPIVGDHKYCANF 276
           VH   +G PI  D  Y + F
Sbjct: 324 VHLQFLGYPIANDPIYSSEF 343


>gi|297180864|gb|ADI17069.1| pseudouridylate synthases, 23S RNA-specific [uncultured alpha
           proteobacterium HF0010_30A23]
          Length = 265

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 113/246 (45%), Gaps = 21/246 (8%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
               ++E + ++  +        L   +L+ED+ +   NKP G+    G  + +     L
Sbjct: 33  PARRLREARNMEPFIYTPPAPGPLP--VLFEDAALIALNKPEGLLSVPGRRVEHQDS--L 88

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            + V +   +  + HRLD  TSG++V+A+TR A + L+  F+ R ++K Y ++V G+P  
Sbjct: 89  YTRVRALHPEAMVVHRLDLATSGVIVMAKTREANRALSWQFQQRTVEKTYEAVVEGVPVE 148

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVI---DCFAQKFCWLEMQPH 248
              C+   L+       D+ +  +Q  +      + + +  +   D   +    + ++P 
Sbjct: 149 ASGCVDLPLI------CDWPNRPRQIVDPVQGKPSQTEWVALGAQDVSGRTGTRVRLRPL 202

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG--RLQ 306
           TGR+HQLRVH   MG  I GD  Y +      +     +L LHA  + L HP+     L+
Sbjct: 203 TGRSHQLRVHMAEMGHAIFGDRFYASEDGAAAS----KRLLLHAHVLTLTHPDDSARTLR 258

Query: 307 ITAPLP 312
             A  P
Sbjct: 259 FEALCP 264


>gi|315182443|gb|ADT89356.1| ribosomal large chain pseudouridine synthase A [Vibrio furnissii
           NCTC 11218]
          Length = 558

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 65/228 (28%), Positives = 99/228 (43%), Gaps = 19/228 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           LD +  L   ++  +  ++Y+D  I V NKPA      G  +       L+     + + 
Sbjct: 340 LDDNPLLNNPAEGQEIEIVYQDEAIVVINKPAEFLSVPGVNVKDSALTRLEQQF-PEVEG 398

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+LV A TR A + L + F  R ++K Y +L+ G   + +  I   L 
Sbjct: 399 PFVLHRLDMSTSGLLVFALTRRANKSLQKQFITRGVEKRYVALLSGEIAHGEGIITLPL- 457

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM- 262
           +          V  ++      A ++++ I    Q    + + P TGRTHQLRVH  H  
Sbjct: 458 RPDLDDRPRQMVCFEH---GKAAETYWQTIGT-EQGRTRVYLSPKTGRTHQLRVHCAHAQ 513

Query: 263 --GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
               PI GD  Y             N+L+LHA  +   HP    R+  
Sbjct: 514 GFNTPIWGDDLYGEK---------ANRLHLHAESLSFDHPYTKQRMTF 552


>gi|296216599|ref|XP_002754668.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 4
           [Callithrix jacchus]
          Length = 397

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 137/326 (42%), Gaps = 39/326 (11%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           R +   ++   + V   PV   +  +++  + L   V+    +  L   +L++D  + V 
Sbjct: 51  RAQKQEQVTKKEPVSTNPVQRRVQELVRYTRQLQR-VHPNVLAKALTRGILHQDKNLVVI 109

Query: 112 NKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G++V+A  +  A
Sbjct: 110 NKPYGLPVHGGPGVQLCISDVLPILAKMLHGRKAEPLHLCHRLDKETTGVMVLAWDKDMA 169

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG---------------GDY 212
             + E FR+R++ K YW++   +P      +   +++K   G                D 
Sbjct: 170 HQVQELFRIRQVVKKYWAITVRVPIPSAGVVDIPIVEKEAQGQQQHHKMTLSPSYRMEDG 229

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHK 271
             V  ++ + A  A++ ++V+         +E+ P TG  HQLRVH    + CP++GDHK
Sbjct: 230 KMVKMRSSRNAQVAVTQYRVLSS-TLSSALMELHPITGVKHQLRVHLSFGLDCPVLGDHK 288

Query: 272 YC------------ANFKGNFTSPIQNK---LYLHARYMDLPH--PEGGRLQITAPLPAH 314
           Y                K       + +   L+LHAR + LP        L +    P  
Sbjct: 289 YSDWNRLAPQKLSVGTLKKLGLEQSKARYIPLHLHARQLILPALGSRKEELNLVCKPPHF 348

Query: 315 MVKTWDSLGFKYDRNLYIKRLYSQDE 340
            V++   LG +       K     ++
Sbjct: 349 FVRSLRRLGLEMPNQDQSKNSEHSED 374


>gi|238795691|ref|ZP_04639205.1| Pseudouridine synthase [Yersinia mollaretii ATCC 43969]
 gi|238720417|gb|EEQ12219.1| Pseudouridine synthase [Yersinia mollaretii ATCC 43969]
          Length = 232

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 100/231 (43%), Gaps = 19/231 (8%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H    K   LY+D  + + NKPAG+    G          +   +    
Sbjct: 3   KIIDTFIAPPCHD---KIETLYQDDHLVLINKPAGLLSLSGKNPQN--LDSVHHRLVQIF 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   + +  I   
Sbjct: 58  PGCTLVHRLDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLDDNEGVIDAA 117

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTH 253
           + K   +      ++         A S ++V++ F              +++ P TGRTH
Sbjct: 118 IAKDPAL----FPLMSICAIHGKPARSGYRVVERFYHELEDGTLLPLTRVQLTPETGRTH 173

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           QLR+H   +G PI+G   Y           +  +L LHA  +   HP GG+
Sbjct: 174 QLRIHCQQLGHPILGCDLYGGRLLPGTERTL--RLMLHASELHFVHPIGGK 222


>gi|300773309|ref|ZP_07083178.1| ribosomal large subunit pseudouridine synthase A [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|300759480|gb|EFK56307.1| ribosomal large subunit pseudouridine synthase A [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 560

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 100/228 (43%), Gaps = 18/228 (7%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +L+ +  L          +LY+D  I V NKPA      G  I   +   +++    +  
Sbjct: 341 LLEDNPLLEAPKAQADLEILYDDEDIAVVNKPAEFLSVPGVHIQDSVYTRMQAAF-PEAT 399

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P + HRLD  TSGIL++A+ + A + + + F    I+K Y +L+ G+ K  K  I   L
Sbjct: 400 GPIIVHRLDMSTSGILLIAKHKDAHKFIQQQFIDHSIEKRYVALLDGVIKEDKGIIDLPL 459

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                     +   +        A++ ++V+         +   P TGRTHQLRVHA H+
Sbjct: 460 RLDLDDRPRQMVCYEY----GKKAVTKYQVLSRI-NGQTKILFFPVTGRTHQLRVHAAHL 514

Query: 263 G---CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
                PIVGD  Y             N+L+LHA ++   HP   +  I
Sbjct: 515 LGLHTPIVGDDLYGTK---------SNRLHLHAAHLSFVHPRTKKTVI 553


>gi|148977056|ref|ZP_01813702.1| ribosomal large subunit pseudouridine synthase A [Vibrionales
           bacterium SWAT-3]
 gi|145963716|gb|EDK28977.1| ribosomal large subunit pseudouridine synthase A [Vibrionales
           bacterium SWAT-3]
          Length = 560

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 107/231 (46%), Gaps = 19/231 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ +  +   +      ++YED +I V NKP       G  I   +   +K+    +   
Sbjct: 342 LEDNPLIVNPAVGKSFDIVYEDEEIVVVNKPEEFLSVPGKFIEDSVYTRIKARY-PEATG 400

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+L++A T  + +H+ + F  R ++K Y +L+ G+   +   I+  L 
Sbjct: 401 PLIIHRLDMSTSGLLILALTAESNKHIQKQFIDRTVEKRYTALLDGVITGESGDISLPL- 459

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
            +  I      +V         A +H++ +   + K   + + P TGRTHQLRVH  H  
Sbjct: 460 -RGDITDRPRQLVCHEH--GRNAETHWQAVSTNSGK-TKVHLYPKTGRTHQLRVHCAHPQ 515

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            +G PI GD  Y    +         +L+LHA Y+ L HP  G  ++   P
Sbjct: 516 GLGVPIRGDDLYGYKRE---------RLHLHAGYLKLIHPTTGEWMEFEVP 557


>gi|296436545|gb|ADH18715.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           G/11222]
          Length = 303

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 70/315 (22%), Positives = 128/315 (40%), Gaps = 58/315 (18%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPV 70
           +   +  +RL  + +   PH+    + + +R    RV+ +  +F + ++Q G  V +  +
Sbjct: 5   IGTADRQIRLSSFLRTSLPHLPKKTILESVRYHGCRVNGRIERFESYKLQPGDRVSLQII 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            ++                           LL+ED  + ++NKPA              +
Sbjct: 65  EHS------------------------SPQLLWEDEHLCIYNKPA----------KQTSE 90

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                          L HRLD++TSG ++ A+   A+  +T+ F+ R I K Y +LV+G 
Sbjct: 91  DLAHQL------NVHLVHRLDRDTSGCILFAKHAKASSLITQLFKNREIDKRYIALVFGQ 144

Query: 191 PKNKKECIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           P+ +   I  +       IG        QN       I+ ++++  +  K+  L  +P T
Sbjct: 145 PRQESGIITTYTAPCYRRIGAVLFGNTDQNS--GKITITKWEILTRYP-KYTLLLCRPVT 201

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
           GRTHQ+R+H   +G PIVGD  Y    +         +  LHA  +    P    +++++
Sbjct: 202 GRTHQIRLHMKTIGHPIVGDVDYGNQEQPKNVV----RTLLHAASLAFTSPFSNEKIEVS 257

Query: 309 A------PLP--AHM 315
           +      P P  A  
Sbjct: 258 SLTPSQDPYPFYADF 272


>gi|227892867|ref|ZP_04010672.1| pseudouridylate synthase RluD [Lactobacillus ultunensis DSM 16047]
 gi|227865369|gb|EEJ72790.1| pseudouridylate synthase RluD [Lactobacillus ultunensis DSM 16047]
          Length = 285

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 65/310 (20%), Positives = 116/310 (37%), Gaps = 34/310 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSG 62
           M Y   +    + + + ++   +     I     +  LR    ++++ +   FN ++   
Sbjct: 1   MVYHFTLFYPKNLDPLPVNEVLRKLL--IPR-KWRHYLRIEQNIKINGQYRYFNMKVFPN 57

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + + I      L+ +  +Q+   +S NL          ++YED  + + NK  G      
Sbjct: 58  EQIDIY-----LDQVESDQQNYPASGNL--------PDVVYEDKNLLIINKKKGQKTHPN 104

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  +  L       G  P + HRLD  T G+L+VA+  A    L      +   + 
Sbjct: 105 ---LNETNTALNDCATYLGSSPYIVHRLDMLTGGLLLVAKNPAVVPILNRELTTKIFHRN 161

Query: 183 YWSLV-WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           Y + V           I   +          +            AI+H+++++       
Sbjct: 162 YLAKVDHAENLKDTGTINVPIGHDPTDQRKRMVR-----NDGQKAITHYQILERNNNGSA 216

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +++   TGRTHQ+RVH  ++G PI+GD  Y  NF G         L L A  + L  P 
Sbjct: 217 IVQLTLETGRTHQIRVHLAYLGAPIIGDPLYNPNFTGEE-------LALDAYEISLIKPF 269

Query: 302 G-GRLQITAP 310
              RL +  P
Sbjct: 270 SFERLNVKLP 279


>gi|225420028|ref|ZP_03762331.1| hypothetical protein CLOSTASPAR_06371 [Clostridium asparagiforme
           DSM 15981]
 gi|225041284|gb|EEG51530.1| hypothetical protein CLOSTASPAR_06371 [Clostridium asparagiforme
           DSM 15981]
          Length = 254

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 105/238 (44%), Gaps = 30/238 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----------RLTHR 149
           +LYEDS + V  KPAG+  Q   G    +   +++ +      P            + HR
Sbjct: 4   VLYEDSDVIVVEKPAGVESQSARGFEPDMVSRIRTHIHKLSPTPSPKSTNHPPYVGVIHR 63

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+   G++V A+ + +A +L+   +  +++KIY ++V G P + +    ++LLK     
Sbjct: 64  LDKPVRGVMVYAKNQKSAANLSAQIQEGKMRKIYAAVVCGKPVDNQGVYVDYLLKNQGNS 123

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE----------MQPHTGRTHQLRVHA 259
           G    +V  +  GA  A   ++V++         E          ++  TGR HQ+RV  
Sbjct: 124 GS--EIVDNSVDGAKRAELVYRVLETVKAGRWMAENPEMELSLLDIELMTGRYHQIRVQM 181

Query: 260 LHMGCPIVGDHKYCANFKGNFT------SPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
              G P+ GD++Y     G         S  +  L L AR +   HP  GR +IT  +
Sbjct: 182 AGHGTPLFGDNRYGNCLGGGKRAGESGFSGPRQPLALCARKLTFYHPSTGR-EITCEI 238


>gi|332305526|ref|YP_004433377.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332172855|gb|AEE22109.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 252

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 95/242 (39%), Gaps = 17/242 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  I   +KPAG+ V       +     ++   D  GQ     HRLD+ TSG
Sbjct: 1   MMLTILYQDEFIVAIHKPAGLLVHRSMIDRHETQFAMQLLRDQIGQHVFPVHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV A +   A+ L E F    + K Y+++V G  K           K   I     +  
Sbjct: 61  VLVFALSADIARILGEQFAANTVSKTYFAIVRGHVKAPGFIDYALKEKLDKIADKRANQ- 119

Query: 217 KQNEKGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              +K    A + F  I             + ++  +++ P TGR HQLR H  H+  PI
Sbjct: 120 ---DKDPQEAQTEFVPIKQFELPFAVSRYPSARYTLVKLHPKTGRKHQLRRHMCHINHPI 176

Query: 267 VGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLG 323
           VGD  +       F       N L L  + M + HP    +L I       M       G
Sbjct: 177 VGDTTHGDGKHNKFMRDQFSFNGLALTCQQMRITHPMSNEKLAIVNEFDPRMSTLMTQWG 236

Query: 324 FK 325
           ++
Sbjct: 237 WE 238


>gi|317035512|ref|XP_001397201.2| DRAP deaminase (Rib2) [Aspergillus niger CBS 513.88]
          Length = 518

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 59/285 (20%), Positives = 106/285 (37%), Gaps = 57/285 (20%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +        +K L+ G V V+      N  +++GQ++      +      KE
Sbjct: 66  VDIFLSE-FRDRPAEYYRKALQDGLVAVNGTPAGPNTVVKNGQIISHTLHRHEPPVTGKE 124

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +++ED  + V +KPAG+ V       YH +  L+     +
Sbjct: 125 ------------------IGIIHEDDDLIVIDKPAGVPVHSAG--RYHYNSVLEIMRSQR 164

Query: 141 GQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             +  PR  +RLD+ TSG++ + +T  AA+++T   + R +QK Y + V G   +     
Sbjct: 165 HPEWVPRPCNRLDRLTSGVMFLGKTAKAAENMTGKLKARTLQKEYVARVKGKFPDGVIVC 224

Query: 199 ANWLL-KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-------------------- 237
              ++     +G + V            A + F+ +                        
Sbjct: 225 DQPIMSVSPKVGLNRVRA------TGKEAKTKFRRLAYIPPQAPEPQSASDAEGRVATPP 278

Query: 238 -------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                  + +  +   P TGRTHQ+RVH   +G PI  D  Y   
Sbjct: 279 PIYTNEDEGYSIVHCLPLTGRTHQIRVHLQFLGHPISNDPIYSNR 323


>gi|238882595|gb|EEQ46233.1| DRAP deaminase [Candida albicans WO-1]
          Length = 589

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 103/260 (39%), Gaps = 32/260 (12%)

Query: 21  LDRWF---KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +D +    ++  P    + +      G V+V+ +       +++G ++            
Sbjct: 112 IDVFIDEFRDRTPDAYRMAV----EEGLVKVNSQVANLETILRNGDLISHRSYR------ 161

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +E  +    +            +++ED  + V +KP GI V       Y  +   K + 
Sbjct: 162 -REPPVSSRDIK-----------IVFEDDDLLVIDKPGGIPVHPTG--RYRYNTVTKIFE 207

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             KG+     +RLD+ TSG++ + ++   A ++    R R + K Y + V G     +  
Sbjct: 208 HEKGKIVHPCNRLDRLTSGLMFLGKSSKGANNMMSQIRDRNVTKEYIARVKGEFPLDRII 267

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLR 256
           +   L  KS      + +   + +    A + F+ +          ++  P TGRTHQ+R
Sbjct: 268 VDKPLSTKSP----KLTLNVVDMENGKEAKTEFQRVSYDPITNTSVVKCHPLTGRTHQIR 323

Query: 257 VHALHMGCPIVGDHKYCANF 276
           VH   +G PI  D  Y + F
Sbjct: 324 VHLQFLGYPIANDPIYSSEF 343


>gi|190572297|ref|YP_001970142.1| putative tRNA pseudouridine synthase C [Stenotrophomonas
           maltophilia K279a]
 gi|190010219|emb|CAQ43827.1| putative tRNA pseudouridine synthase C [Stenotrophomonas
           maltophilia K279a]
          Length = 246

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 63/254 (24%), Positives = 103/254 (40%), Gaps = 23/254 (9%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           +        ++     LL+ D ++ V NKPAG+ V          D       +  G+  
Sbjct: 4   EPDTLAAVETETAPLQLLHLDERLAVVNKPAGLMVHDSKLARGEDDFLADRLREQLGRPI 63

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HRLD+ TSG L++A  R  A  L ++     + K Y ++  G P         W + 
Sbjct: 64  FLVHRLDRATSGCLLLAFDRETASALGKALMGGEVLKDYLTVCRGWPAE-----LAWQVD 118

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQ 254
               GG         +     A++ F+ +          +    ++  L  QP TGR  Q
Sbjct: 119 HDLDGG-------PGKPVKKPAVTDFQRLATGELSVPVGEFTRSRYALLRCQPQTGRFRQ 171

Query: 255 LRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           +R H  H+   ++GD  +        F     +++ LHA  +  PHPEGG + ++APL  
Sbjct: 172 IRRHLKHLSHHMIGDTSHGDGRHNRIFRMQGVHRMLLHAERLRFPHPEGGNVDVSAPLDR 231

Query: 314 HMVKTWDSLGFKYD 327
              K  D  G++ D
Sbjct: 232 EFQKALDLFGWQVD 245


>gi|310642458|ref|YP_003947216.1| ribosomal large subunit pseudouridine synthase d [Paenibacillus
           polymyxa SC2]
 gi|309247408|gb|ADO56975.1| Ribosomal large subunit pseudouridine synthase D [Paenibacillus
           polymyxa SC2]
          Length = 248

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 69/221 (31%), Positives = 106/221 (47%), Gaps = 14/221 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +    KP  +  Q  +     +   LK  +  +  KP      L HRLD+   
Sbjct: 18  VLYEDNHVLAVVKPVNVPTQEDASGDPDLLSLLKEDLKIRHNKPGNVFLGLVHRLDRPVG 77

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++ A+T  AA  L+ES R R   K+Y +++ G+P   +  + ++LLK S      V  
Sbjct: 78  GAMIFAKTSKAASRLSESVRSRHFHKLYTAVLNGVPAALQGRLTHYLLKDSRTN--TVKT 135

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V+    GA  AI  ++VI   A     +E++ HTGR+HQ+RV    +GCP+ GD KY   
Sbjct: 136 VRPGTAGAKEAILEYRVIG-QAAGLSLVEIKLHTGRSHQIRVQMQAIGCPLYGDQKYG-- 192

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             GN + P Q +L L +     PHP     +   +  P   
Sbjct: 193 --GNLSRPGQ-QLALWSLLAGAPHPVSKEAMSFHSLPPVQF 230


>gi|194212968|ref|XP_001502415.2| PREDICTED: similar to RNA pseudouridylate synthase
           domain-containing protein 4 [Equus caballus]
          Length = 377

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 121/275 (44%), Gaps = 38/275 (13%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   ++++D  + V NKP G+ V GG G+   I   L    K     K   
Sbjct: 86  VHPNVLAKALSRGIIHQDKDLLVINKPYGLPVHGGPGVQLCISDVLPILAKILHGHKADP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P      +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWEKEVAHQVQELFRTRQVAKKYWAITVRVPVPSAGVVDIPII 205

Query: 204 KKSHIGGDYVH---------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G  + H               V  +  + A+ A++ ++V+         LE+QP 
Sbjct: 206 EKEVQGRQHHHKMTLSPSYRMDSGKMVRVRMRRNAHVAVTQYQVL-SNTLSSALLELQPA 264

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC---------------ANFKGNFTSPIQNKLYLHA 292
           TG  HQLRVH    + CPI+GDHKY                       +      L+LHA
Sbjct: 265 TGIKHQLRVHLSFGLDCPILGDHKYSDWNRLAPQKLSVGTLKKLGLQQSKARHIPLHLHA 324

Query: 293 RYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGFK 325
           R + LP        L +   LP + V++ + LG +
Sbjct: 325 RQLILPALGSRKEELNLVCRLPRYFVRSLNRLGLE 359


>gi|331005540|ref|ZP_08328915.1| tRNA pseudouridine synthase C [gamma proteobacterium IMCC1989]
 gi|330420660|gb|EGG94951.1| tRNA pseudouridine synthase C [gamma proteobacterium IMCC1989]
          Length = 237

 Score =  160 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 108/228 (47%), Gaps = 17/228 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   ++Y+D  +   +KPAG+ V       +     ++   D  GQ     HRLD+ TSG
Sbjct: 1   MHLPIIYQDEYLVAIHKPAGLLVHKSLIDKHESQYAMQILRDQIGQWVYPLHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+   ++  AQ + E F  R +QK YW++V G   NK+  I + +   +    D   + 
Sbjct: 61  VLLFGLSKEVAQLMGEQFEQRLLQKTYWAIVRGYI-NKEGIIDHPIKPTADFKRDKQRIA 119

Query: 217 KQNEKGANYAISHFKVIDCFAQKFC----------WLEMQPHTGRTHQLRVHALHMGCPI 266
              +K A  AI+ ++ +      +C           +E+ P TGR HQLR H  H+  PI
Sbjct: 120 ---QKEAQEAITGYRRLGTLELPYCVDQFPISRYSLVELSPQTGRKHQLRKHMKHLSHPI 176

Query: 267 VGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPL 311
           +GD KY  +   +F     N  +L L A  + L HP   + L ++AP+
Sbjct: 177 IGDPKYGKSKHNHFFKEHFNCHRLLLAATQLTLNHPITHQSLTLSAPI 224


>gi|227536848|ref|ZP_03966897.1| pseudouridine synthase [Sphingobacterium spiritivorum ATCC 33300]
 gi|227243275|gb|EEI93290.1| pseudouridine synthase [Sphingobacterium spiritivorum ATCC 33300]
          Length = 444

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 103/234 (44%), Gaps = 21/234 (8%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +L+ +  L          +LY+D  I V NKPA      G  I   +   +++    +  
Sbjct: 225 LLEDNPLLEAPKAQADLEILYDDEDIAVVNKPAEFLSVPGIHIQDSVYTRMQAAF-PEAT 283

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P + HRLD  TSGIL++A+ + A + + + F    I+K Y +L+ G+ K  +  I   L
Sbjct: 284 GPIIVHRLDMSTSGILLIAKHKDAHKFIQQQFINHSIEKRYVALLDGVVKEDEGIIDLPL 343

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                     +   +        A++ ++V+         +   P TGRTHQLRVHA H+
Sbjct: 344 RLDLDDRPRQMVCYEY----GKKAVTKYQVLSR-TDGQTKILFFPVTGRTHQLRVHAAHL 398

Query: 263 --GC-PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
                PIVGD  Y             N+L+LHA Y+   HP   +    ++ AP
Sbjct: 399 LGLHIPIVGDDLYGTK---------SNRLHLHAAYLSFVHPRTKKTVVFEVKAP 443


>gi|303314793|ref|XP_003067405.1| ribosomal large subunit pseudouridine synthase D, putative
           [Coccidioides posadasii C735 delta SOWgp]
 gi|240107073|gb|EER25260.1| ribosomal large subunit pseudouridine synthase D, putative
           [Coccidioides posadasii C735 delta SOWgp]
          Length = 531

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 70/358 (19%), Positives = 123/358 (34%), Gaps = 90/358 (25%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        +  + SG V ++ K    ++++++G VV         +H +  
Sbjct: 62  LDIF-TTEFRDRPAEYYRAAIESGHVTINGKPGGVDSKVKNGDVV---------SHTLHR 111

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            +   +S+ +          +++ED ++ V +KPAG+ V       Y+    +       
Sbjct: 112 HEPPVTSLPIG---------VIHEDDEMIVIDKPAGVPVHPAGRYNYNSIIEIMRAERGH 162

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P   +RLD+ TSG++ + +   AA+ ++   R R +QK Y + V G   +       
Sbjct: 163 GFNPLPCNRLDRLTSGVMFIGKDPKAAERISHGLRARTMQKEYIARVKGKFPDGIILCDQ 222

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----------------------- 237
            +LK SH  G     + +       A S F+ +  +                        
Sbjct: 223 PMLKISHQLG-----LNRVRASGKEAKSKFRRLAYYPATAVKKASSSEDDPATPPATLAD 277

Query: 238 -------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC----- 273
                              + +  +   P TGRTHQLRVH   +G PI  D  Y      
Sbjct: 278 DVPLDFGNNGKATISPPEDEGYSIVHCLPLTGRTHQLRVHLQFLGHPITNDPIYSNRRVF 337

Query: 274 ------ANFKGNFTSPIQNKLYLHARY--------MDLPHPEGGRLQITAPLPAHMVK 317
                 A+  G     I  +L    +             +          P P HM K
Sbjct: 338 GRNLGKADNTGEHDQEIMARLSRMGKTETADTVGDFGFKYET-----FQNPPPEHMTK 390


>gi|238795199|ref|ZP_04638786.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           intermedia ATCC 29909]
 gi|238725486|gb|EEQ17053.1| Ribosomal large subunit pseudouridine synthase A [Yersinia
           intermedia ATCC 29909]
          Length = 196

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 63/205 (30%), Positives = 95/205 (46%), Gaps = 15/205 (7%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V NKP+G+    G   A      + + + +        HRLD  TSG+++VA T+AA +
Sbjct: 1   MVVNKPSGLLSVPGR--APENKDSIMTRIQADFPAAESVHRLDMATSGVIIVALTKAAER 58

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYA 226
            L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ    +    A
Sbjct: 59  ELKRQFREREPKKSYIARVWGHLAEDEGLIDLPLI------CDWPNRPKQKVCYETGKSA 112

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
            + ++V+         +++ P TGR+HQLRVH L MG PI+GD  Y         S    
Sbjct: 113 QTEYRVLSRDTDGSTRVKLSPITGRSHQLRVHMLAMGHPILGDGFYAHPEAKAMAS---- 168

Query: 287 KLYLHARYMDLPHPEGGR-LQITAP 310
           +L LHA+ + + HPE G  +  T  
Sbjct: 169 RLQLHAQELCITHPEFGTAMHFTCE 193


>gi|157368974|ref|YP_001476963.1| pseudouridine synthase [Serratia proteamaculans 568]
 gi|157320738|gb|ABV39835.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 216

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 97/221 (43%), Gaps = 11/221 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             +       +LY+D  I V NKP+G+    G   A      L + + +        HRL
Sbjct: 3   PYNPPQGPMHILYQDEHIMVVNKPSGLLSVPGR--APENKDSLMTRILADHPAAESVHRL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG++VVA  +AA + L   FR R  +K Y + V G  ++ +  +   L+       
Sbjct: 61  DMATSGVIVVALNKAAERELKRQFRDREPKKSYIARVSGHLEHDEGLVDLPLICD----W 116

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               + K   +    A + + V+   A     +++ P TGR+HQLRVH L +G PI+GD 
Sbjct: 117 PNRPLQKVCFETGKAAQTEYLVLSRDADGSTRVKLMPITGRSHQLRVHMLALGHPILGDG 176

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
            Y           +  +L LHA+ + + HP     +   A 
Sbjct: 177 FYAPPE----VKAMAPRLQLHAQELRITHPAFQTPMHFRAE 213


>gi|37524616|ref|NP_927960.1| ribosomal large subunit pseudouridine synthase A (pseudouridylate
           synthase) (uracil hydrolyase) [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|36784040|emb|CAE12909.1| ribosomal large subunit pseudouridine synthase A (pseudouridylate
           synthase) (uracil hydrolyase) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 216

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 102/225 (45%), Gaps = 16/225 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +            +LY+D  I V NKP+G+    G   A H D  + + +  +       
Sbjct: 1   MEAYNPPTDPWLHVLYQDQYIIVVNKPSGLLSVPGRA-AEHKDSIM-TRIQQQFPAAESV 58

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSG++VVA T+ A + L   FR R  +K Y + VWG  + +   +   L+    
Sbjct: 59  HRLDMATSGVMVVALTKDAERELKRQFREREPEKTYIARVWGRLEPETGLVDLPLI---- 114

Query: 208 IGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              D+ +  KQ    +    A + ++V+  +  +   +++ P TGR+HQLRVH L +  P
Sbjct: 115 --CDWPNRPKQKVCFETGKSAQTEYEVL-AYEDEATRIKLSPITGRSHQLRVHMLALEHP 171

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           I+GD  Y              +L LHA+ + + HP  G  +    
Sbjct: 172 ILGDQFYAHQQARAMA----PRLQLHAQELYITHPVYGTPMHFQC 212


>gi|114564164|ref|YP_751678.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114335457|gb|ABI72839.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 219

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 61/227 (26%), Positives = 102/227 (44%), Gaps = 12/227 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
                        +LY+D  + + NKP G+    G          +   +        L 
Sbjct: 2   AEFIAPPCDGNIEVLYQDEHLLLINKPTGLLSLSGKNPLN--KDSVHHRLVQDYPSATLV 59

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD  TSGI++VA  +     LT+ F++R + K Y ++++G    +   I   + K S 
Sbjct: 60  HRLDFGTSGIMLVALNKVINGLLTKQFQLRTVSKTYTAVLYGDLVEQHGDIELPIAKDS- 118

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPI 266
              D   ++K  ++    A S ++VI+   Q+    +   P TGRTHQLR+H+L +G PI
Sbjct: 119 ---DNFPLMKICQQTGKPAHSQYQVIERHQQRLSTRVTFTPITGRTHQLRIHSLQIGHPI 175

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           +G   Y    +  ++  + ++L LHA  +   HP    R+    P P
Sbjct: 176 LGCDLY----RNEYSQAMSDRLMLHATSLSFTHPVTEQRIDYVCPSP 218


>gi|78778288|ref|YP_394603.1| pseudouridine synthase, RluD [Sulfurimonas denitrificans DSM 1251]
 gi|78498828|gb|ABB45368.1| Pseudouridine synthase, RluD [Sulfurimonas denitrificans DSM 1251]
          Length = 304

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 66/295 (22%), Positives = 117/295 (39%), Gaps = 43/295 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHI 77
            R   + K     ++   +Q+ +  G+V V+    VK ++ +Q G+V  I          
Sbjct: 14  ERAFSFLKREL-ELSQREIQRYIAIGRVLVNGAPIVKPSDYLQ-GEVEYIY--------- 62

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                    S  L  H         + + +  VF+KP+G+ +   +   +     +    
Sbjct: 63  -----FEPISKGLAPH---------FIEERFVVFDKPSGMLIHPQN--RFTEYSLIDELK 106

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              G    + HR+DQETSG+++ A+ + +   +   F+ R ++K Y ++V G  K +   
Sbjct: 107 AQFGMNANIAHRIDQETSGLVLCAKDKKSEVDIKMMFQERDMKKKYLAMVHGELKEEL-R 165

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLR 256
           I   LL+        V +V + +     +++  + +  F       +E  PHTGR HQ+R
Sbjct: 166 IDAPLLRYDDEKSALVRMVVKVDPTGKESLTFVRPLKYFPITDTTLVECSPHTGRQHQIR 225

Query: 257 VHALHMGCPIVGDHKYCA-------------NFKGNFTSPIQNKLYLHARYMDLP 298
           VH  HM  PIVGD  Y                           +L LHA  ++  
Sbjct: 226 VHMFHMKHPIVGDPVYGQSEESVVRYLDRKIERDERVKLSGAKRLLLHANELEFE 280


>gi|301346056|ref|ZP_07226797.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) protein [Acinetobacter
           baumannii AB056]
 gi|301596091|ref|ZP_07241099.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) protein [Acinetobacter
           baumannii AB059]
          Length = 221

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 109/231 (47%), Gaps = 13/231 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + N           +L+ED  + V +KPAG+    G    +H   +L+  V  K   
Sbjct: 1   MPLNDNFVYAPPQDPLSILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPL 58

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G  K +       + 
Sbjct: 59  AKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKHYIALVQGQVKQEGRVEVPLIT 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +   +A + F+ +          + ++P TGR+HQLRVH +H+
Sbjct: 119 DWENRPRQIVHF-----ELGKHAKTLFQPLVYDETTDQSRVLLEPVTGRSHQLRVHMMHI 173

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           G PI+GD  Y    K        N++ LHA Y+   HP  G  + I + +P
Sbjct: 174 GHPIMGDKLYHPEPK----RFHLNRMALHAAYLAFQHPLKGTDVVIESQVP 220


>gi|238757890|ref|ZP_04619072.1| Pseudouridine synthase [Yersinia aldovae ATCC 35236]
 gi|238703875|gb|EEP96410.1| Pseudouridine synthase [Yersinia aldovae ATCC 35236]
          Length = 232

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 96/231 (41%), Gaps = 19/231 (8%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H        LY+D  + V NKP G+    G          +   +    
Sbjct: 3   KIIDTFIAPPCHDKIEN---LYQDDHLLVINKPTGLLSLSGKNPQN--LDSVHHRLVQIF 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   + +  I   
Sbjct: 58  PSCTLVHRLDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLDDNEGVIDAA 117

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTH 253
           + K   +      ++         A S+++V++ F  K           +++ P TGRTH
Sbjct: 118 IAKDPAL----FPLMSICAIHGKPARSYYRVVERFYHKLEDGTLLPLTRVQLTPETGRTH 173

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           QLR+H   +G PI+G   Y              +L LHA  +   HP    
Sbjct: 174 QLRIHCQQLGHPILGCDLYGGRLLPGTEQT--PRLMLHASELHFVHPISEE 222


>gi|119175237|ref|XP_001239884.1| hypothetical protein CIMG_09505 [Coccidioides immitis RS]
 gi|320037744|gb|EFW19681.1| DRAP deaminase [Coccidioides posadasii str. Silveira]
          Length = 531

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 70/358 (19%), Positives = 123/358 (34%), Gaps = 90/358 (25%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        +  + SG V ++ K    ++++++G VV         +H +  
Sbjct: 62  LDIF-TTEFRDRPAEYYRAAIESGHVTINGKPGGVDSKVKNGDVV---------SHTLHR 111

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            +   +S+ +          +++ED ++ V +KPAG+ V       Y+    +       
Sbjct: 112 HEPPVTSLPIG---------VIHEDDEMIVIDKPAGVPVHPAGRYNYNSIIEIMRAERGH 162

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P   +RLD+ TSG++ + +   AA+ ++   R R +QK Y + V G   +       
Sbjct: 163 GFNPLPCNRLDRLTSGVMFIGKDPKAAERISHGLRARTMQKEYIARVKGKFPDGIILCDQ 222

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----------------------- 237
            +LK SH  G     + +       A S F+ +  +                        
Sbjct: 223 PMLKISHQLG-----LNRVRASGKEAKSKFRRLAYYPATAVKKASSSEDDPATPPATLAD 277

Query: 238 -------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC----- 273
                              + +  +   P TGRTHQLRVH   +G PI  D  Y      
Sbjct: 278 DVPLDFGNNGKATISPPEDEGYSIVHCLPLTGRTHQLRVHLQFLGHPITNDPIYSNRRVF 337

Query: 274 ------ANFKGNFTSPIQNKLYLHARY--------MDLPHPEGGRLQITAPLPAHMVK 317
                 A+  G     I  +L    +             +          P P HM K
Sbjct: 338 GRNLGKADNTGEHDQEIMARLSRMGKTETADTVGDFGFKYET-----FQNPPPEHMTK 390


>gi|29349909|ref|NP_813412.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|29341820|gb|AAO79606.1| ribosomal large subunit pseudouridine synthase A [Bacteroides
           thetaiotaomicron VPI-5482]
          Length = 549

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 113/243 (46%), Gaps = 22/243 (9%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++  + ++   H    +  +++ED  + V NKP+G+    G       
Sbjct: 313 CEPILQHMLQGLEVDGNPLSPQAHRKE-ELEIVFEDEWLVVVNKPSGMLSVPGKEEETDS 371

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                     +   P + HRLD  TSG+L+VA+T+   QHL E F  R I+K Y +L+  
Sbjct: 372 VYHRVKAKYPEATGPMIVHRLDMATSGLLLVAKTKEVHQHLQEQFISRSIKKRYVALLDR 431

Query: 190 IPKNKK----ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
              N++      I   L          +     +E+    A++ +++++ ++ K+  +  
Sbjct: 432 NGLNQQLEETGTINLPLCLNPLDRPRQM----VSEEYGKPAVTEYRILN-YSDKYIRIAF 486

Query: 246 QPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            P TGRTHQLRVHA H   +  PI+GD  Y             ++LYLHA Y++  HP  
Sbjct: 487 YPLTGRTHQLRVHAAHHQGLNYPILGDELYGKK---------ADRLYLHAEYIEFRHPVY 537

Query: 303 GRL 305
           G +
Sbjct: 538 GDI 540


>gi|326472889|gb|EGD96898.1| DRAP deaminase [Trichophyton tonsurans CBS 112818]
          Length = 528

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 61/268 (22%), Positives = 105/268 (39%), Gaps = 46/268 (17%)

Query: 37  LQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           LQK  +  G++ +D K    ++ I +GQV+              E  +    +       
Sbjct: 89  LQKAAIDGGRITIDGKVATADSIINNGQVISHTLHR-------HEPPVTSRPIK------ 135

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
                +++ED  I V +KPAGI V       Y+    +       G  P   +RLD+ TS
Sbjct: 136 -----IIHEDEDIIVIDKPAGIPVHPAGRYNYNSIIEIMRSERGLGWIPYPCNRLDRLTS 190

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI-GGDYVH 214
           GI+ + +   +A+ + +S R R ++K Y + V G   +        +LK S I G + V 
Sbjct: 191 GIMFLGKHPKSAEQMAQSLRSRTLRKEYIARVKGYFPDGVVLCDQPMLKVSPILGLNRVR 250

Query: 215 VVKQNEKGANYAISHFKVIDCFA--------------------------QKFCWLEMQPH 248
              ++ +     I+++  ++                             + +  +   P 
Sbjct: 251 ATGKDAQTKFRRIAYYPPVEKENKNGETTGSQGPDSRASTPPPLPADVDEGYSIVHCLPL 310

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANF 276
           TGRTHQ+RVH   +G PI  D  Y    
Sbjct: 311 TGRTHQIRVHLQFLGHPITNDPIYSNRR 338


>gi|171678031|ref|XP_001903966.1| hypothetical protein [Podospora anserina S mat+]
 gi|170937084|emb|CAP61743.1| unnamed protein product [Podospora anserina S mat+]
          Length = 479

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 64/274 (23%), Positives = 103/274 (37%), Gaps = 59/274 (21%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
            + SGQV V+ K V  +  + +G +V              E  +    V           
Sbjct: 103 AMESGQVAVNGKIVSPDYVMVNGDLVSHTTHR-------HEPPVTQDPV----------- 144

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGI 157
            +++ED  + V NKP+G+ V       YH +  ++     +G    PR  +RLD+ TSGI
Sbjct: 145 QVIHEDDDMIVINKPSGVPVHPAG--RYHYNSVVEIMKAERGPTFAPRPCNRLDRLTSGI 202

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVV 216
           + +A+T  AA+ L+     R ++K Y + V G  P  +  C    L     +G + V   
Sbjct: 203 MFIAKTAKAAESLSAQIFRRSVRKEYLARVVGRFPDGEVVCDQPILQISPKLGLNRVRA- 261

Query: 217 KQNEKGANYAISHFKVIDCFA------------------------------QKFCWLEMQ 246
                    A + FK +  +                               + +  +   
Sbjct: 262 -----NGKSAKTVFKRLAYYPSPIIKPSSSNSPSPDEAETGGPEDQFTRETEGYSIVRCL 316

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           P TGRTHQ+RVH   +G P+  D  Y       F
Sbjct: 317 PVTGRTHQIRVHLQFLGHPVQNDPIYANQKVWGF 350


>gi|166154327|ref|YP_001654445.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 434/Bu]
 gi|166155202|ref|YP_001653457.1| tRNA pseudouridine synthase A [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|301335578|ref|ZP_07223822.1| tRNA pseudouridine synthase A [Chlamydia trachomatis L2tet1]
 gi|165930315|emb|CAP03801.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 434/Bu]
 gi|165931190|emb|CAP06755.1| tRNA pseudouridine synthase A [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
          Length = 274

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 71/320 (22%), Positives = 130/320 (40%), Gaps = 57/320 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVV 65
           +Q  +   D   +RL  + +   PH+    + + +R    RV+ +  +F + ++Q G  V
Sbjct: 1   MQEFIGTADRH-IRLSSFLRTSLPHLPKKTILESVRYHGCRVNGRIERFESYKLQPGDRV 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +  + ++                           LL+ED  + ++NKPA          
Sbjct: 60  SLQIIEHS------------------------SPQLLWEDEHLCIYNKPA---------- 85

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               +               L HRLD++TSG ++ A+   A+  +T+ F+ R I K Y +
Sbjct: 86  KQTSEDLAHQL------NVHLVHRLDRDTSGCILFAKHAKASSLITQLFKNREIDKRYIA 139

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV+G P+ +   I  +        G  V     ++      I+ ++++  +  K+  L  
Sbjct: 140 LVFGQPRQESGIITTYTAPCYRRTG-AVLFGNTDQNSGKITITKWEILTRYP-KYTLLLC 197

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
           +P TGRTHQ+R+H   +G PIVGD  Y    +         +  LHA  +    P    +
Sbjct: 198 RPVTGRTHQIRLHMKTIGHPIVGDVDYGNQEQPKNVV----RTLLHAASLAFISPFSNEK 253

Query: 305 LQITA------PLP--AHMV 316
           ++I++      P P  A   
Sbjct: 254 IEISSLTPSQDPYPFYADFR 273


>gi|304414221|ref|ZP_07395589.1| 23S rRNA and tRNA pseudouridine synthase [Candidatus Regiella
           insecticola LSR1]
 gi|304283435|gb|EFL91831.1| 23S rRNA and tRNA pseudouridine synthase [Candidatus Regiella
           insecticola LSR1]
          Length = 212

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 62/208 (29%), Positives = 101/208 (48%), Gaps = 20/208 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V NKP+G+    G          ++  + +   +    HRLD  TSG++VV
Sbjct: 3   VLYQDQHIMVINKPSGLLSVPGRAPENKDSVMMR--IQAAFPQAESVHRLDMATSGVMVV 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A T+AA + L   FR R  +K+Y + V+G  K  +  I   L+       D+ +  KQ  
Sbjct: 61  ALTKAAERELKRQFREREPKKVYVARVYGHVKKDQGLIDLPLI------CDWPNRPKQKV 114

Query: 221 --KGANYAISHFKVIDC------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +    A + ++V+         +     +++ P TGR+HQLRVH L +G PI+GD  Y
Sbjct: 115 CYETGKSAQTEYQVLSRHDETPGHSNSSTRVKLSPITGRSHQLRVHMLALGHPILGDGFY 174

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP 300
                 +  +    +L LHA+ + + HP
Sbjct: 175 APPGAKSMAT----RLQLHAQELYIRHP 198


>gi|262368495|ref|ZP_06061824.1| pseudouridylate synthase [Acinetobacter johnsonii SH046]
 gi|262316173|gb|EEY97211.1| pseudouridylate synthase [Acinetobacter johnsonii SH046]
          Length = 214

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 64/223 (28%), Positives = 105/223 (47%), Gaps = 15/223 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           S+FL   L++ D    V +KPAGI    G      +   + + +     K  L HRLD++
Sbjct: 2   SNFLTEHLIHRDEDFMVIHKPAGILTVPGK--TEDLQDCMINRLVKLEPKTLLIHRLDRD 59

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGILV   +R   + ++  F+ R   K Y ++V G     +  +   ++         +
Sbjct: 60  TSGILVFGLSRWGQKTISRQFQERLTDKTYQAIVAGHLDG-QGTVDVPVIYDP--SRPPL 116

Query: 214 HVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           H+ + +      A++ +K I+ F    Q    + + P TGR+HQLRVH   +G PIVGD 
Sbjct: 117 HIAEPSHN--KPAVTEWKAIEHFEIQGQPVTRVALTPITGRSHQLRVHMQFLGHPIVGDT 174

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
            Y A  + +    +  +L LHA  +   HP+   R++   P P
Sbjct: 175 LYAAPDQQD----LMPRLCLHAERLSFHHPQTNERIEFICPAP 213


>gi|149907518|ref|ZP_01896265.1| pseudouridylate synthase for 23S rRNA (position 746)
           andtRNAphe(position 32), dual specificity [Moritella sp.
           PE36]
 gi|149809188|gb|EDM69117.1| pseudouridylate synthase for 23S rRNA (position 746)
           andtRNAphe(position 32), dual specificity [Moritella sp.
           PE36]
          Length = 229

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 104/231 (45%), Gaps = 18/231 (7%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           +       +  ++Y+D  I V NKP+G+    G    +     + S V  +     + HR
Sbjct: 5   IYAPPQHPRLDIIYQDDAIIVLNKPSGLLSVPGRLPEHTDS--IASRVQERFPTATIVHR 62

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++++A ++AA  H++  F+ R   K Y++ + GIP  K   I   L +     
Sbjct: 63  LDMCTSGVILMALSKAAQSHISRQFQQRSTAKYYYARLEGIPTAKSGSIDLPL-RCDWPN 121

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE-------MQPHTGRTHQLRVHALHM 262
                +   +      A++H++VI          +       ++P TGR+HQLRVH L +
Sbjct: 122 RPRQMIDFID---GKPALTHWQVIAEQPANNNNNQQASATVLLKPVTGRSHQLRVHMLAL 178

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           G PI+GD  Y +         +Q    LHA  +++ HP    R++     P
Sbjct: 179 GTPILGDELYASAQGVAAAEHLQ----LHAAMLEIDHPLTSERIEFKVKPP 225


>gi|332667785|ref|YP_004450573.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
 gi|332336599|gb|AEE53700.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
          Length = 233

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 113/233 (48%), Gaps = 15/233 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           +   ++YED+ +   NKPAGI VQG +     +  ++K ++  + +KP      + HRLD
Sbjct: 1   MNLQVIYEDNHLIAVNKPAGILVQGDATEDTPLVDYVKDYIKFRYKKPGDVFLGVVHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +  SG ++ ART  A   + E F+ R+++K YW++    P  +   + +++LK       
Sbjct: 61  RPVSGAVIFARTSKALTRMNELFKERKVEKNYWAVTERRPSPEAGHLTHYILKDHEKNIS 120

Query: 212 YV-HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                +    K A  +   +++I     K   L ++P TGR HQ+RV    +GCPIVGD 
Sbjct: 121 KALDQMSNRSKDAKKSDLDYELIGALEGKH-LLLVKPITGRPHQIRVQLSKIGCPIVGDL 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           KY      N  S     +YLH R M   HP    L +I A  P    + W+ +
Sbjct: 180 KYGHTQPNNDGS-----IYLHCRSMIFLHPVTKELVKIVADAPHE--RLWNQM 225


>gi|325914340|ref|ZP_08176687.1| tRNA pseudouridine synthase C [Xanthomonas vesicatoria ATCC 35937]
 gi|325539348|gb|EGD10997.1| tRNA pseudouridine synthase C [Xanthomonas vesicatoria ATCC 35937]
          Length = 245

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 61/237 (25%), Positives = 101/237 (42%), Gaps = 24/237 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V +KPAG+ V          D       +  G+   L HRLD+ TSG L++
Sbjct: 10  ILYQDDVLAVVDKPAGLMVHDSKLARGEDDFLADRLREQLGKPIFLVHRLDRATSGCLLL 69

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R +A  L ++     + K Y ++  G P   +  + + L       G     VK   
Sbjct: 70  AFDRDSASALGKALMAGEVDKNYLTVCRGWPAEDRFIVDHDL------DGGPGKPVK--- 120

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++GD 
Sbjct: 121 ---KPAVTHFQRLATGELEIPSTGFATSRYALLRCQPQTGRFRQIRRHMKHLSHHMIGDT 177

Query: 271 KYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
            +       +F     +++ LHA  ++ PHP +G R+ + APL     K     G+ 
Sbjct: 178 SHGDGRHNRSFRMLGIHRMLLHAERLEFPHPADGRRISVVAPLDVEFAKACALFGWD 234


>gi|170726105|ref|YP_001760131.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169811452|gb|ACA86036.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 219

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 58/212 (27%), Positives = 99/212 (46%), Gaps = 13/212 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             + Y+D  + V NKP+G+    G       D  L   +    +   L HRLD  TSGI+
Sbjct: 14  LDIRYQDRDMIVINKPSGLLSNPGRA-ENTFDCALTRLLQRYPETI-LVHRLDCATSGIM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A  + A  ++   F+ R  +K Y + V G     +  I   +   S         +++
Sbjct: 72  VFALNKKAESNIKTQFQNRLSKKTYIAEVQGHLDKTEGVIELAMKADSERP-----PLQK 126

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             +    + +++KV++   +    +E+ P TGRTHQLR+H L +G PI+GD  Y      
Sbjct: 127 IAEDGKPSKTYYKVLEKR-ENSTLVELNPVTGRTHQLRLHMLAIGHPILGDDFYGEQEVI 185

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           + +    ++L LHA  + + HP  G+ +  T+
Sbjct: 186 DAS----HRLCLHAMTLAITHPYSGKLMSFTS 213


>gi|297464864|ref|XP_002703537.1| PREDICTED: RNA pseudouridylate synthase domain containing 4-like
           [Bos taurus]
 gi|110331955|gb|ABG67083.1| RNA pseudouridylate synthase domain containing 4 [Bos taurus]
          Length = 377

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 79/290 (27%), Positives = 126/290 (43%), Gaps = 43/290 (14%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   ++++D ++ V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKALSRGIVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P  +   +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIV 205

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G                D   V  ++ + A  A++ ++V    +     LE+QP 
Sbjct: 206 EKEAQGQQHHHKMTLSPSYRMDDGKMVRVRSSRNAQLAVTQYRV-LSSSLSAALLELQPI 264

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC---------------ANFKGNFTSPIQNKLYLHA 292
           TG  HQLRVH    + CPI+GDHKY                       +      L+LHA
Sbjct: 265 TGIKHQLRVHMSFGLDCPILGDHKYSDWNRLAPQKLSAGILKKLGLQQSKARHLPLHLHA 324

Query: 293 RYMDLP--HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
             + LP   P+   L +    P + V +   LG K        R +S DE
Sbjct: 325 CQLTLPALQPQKEELTLLCRPPRYFVNSLRRLGLKMP-----SRDHSADE 369


>gi|293395440|ref|ZP_06639724.1| ribosomal large subunit pseudouridine synthase A [Serratia
           odorifera DSM 4582]
 gi|291422124|gb|EFE95369.1| ribosomal large subunit pseudouridine synthase A [Serratia
           odorifera DSM 4582]
          Length = 284

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 56/225 (24%), Positives = 94/225 (41%), Gaps = 17/225 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +LY+D ++ + +KPAG+    G          +   +        L HRLD 
Sbjct: 63  PPCLDRIEILYQDEQLVLIDKPAGLLSLSGKNAQN--IDSVHHRLVQIFPGCTLVHRLDF 120

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++++AR +A    L + F  R + K Y +L+ G  ++ +  I   + K   +    
Sbjct: 121 GTSGLMLIARNKAINAALCQQFSQRTVSKEYHALLCGHLEHNEGVIDAAIAKDPAL---- 176

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGC 264
             ++         A S ++V++                + + P TGRTHQLR+H   +G 
Sbjct: 177 FPLMSICSIHGKPARSRYQVVERGYHAVAEQRPVPVTRVRLTPETGRTHQLRIHCQQLGH 236

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           PI+G   Y              +L LHA  +   HP   R +ITA
Sbjct: 237 PILGCDLYGGRLLPGTEQT--PRLMLHASELQFVHPVSQR-RITA 278


>gi|296815982|ref|XP_002848328.1| DRAP deaminase [Arthroderma otae CBS 113480]
 gi|238841353|gb|EEQ31015.1| DRAP deaminase [Arthroderma otae CBS 113480]
          Length = 519

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 63/293 (21%), Positives = 103/293 (35%), Gaps = 57/293 (19%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L   F   +           +  G++ +D      ++ I +GQVV      +     
Sbjct: 60  GKKLLEIFTTEFRDRPKGYYTDAIEGGRITIDGVIATADSIINNGQVVSHTLHRH----- 114

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                              L+  +++ED+ I V +KPAGI V       Y+    +    
Sbjct: 115 -------------EPPVTSLRIKIIHEDNDIIVIDKPAGIPVHPAGRYNYNSIVEIMRAE 161

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              G  P   +RLD+ TSGI+ + +   AA+ + ++ R R IQK Y + V G   +    
Sbjct: 162 RGHGWNPYPCNRLDRLTSGIMFIGKHPKAAEQMAQALRSRTIQKEYIARVKGYFPDGVVL 221

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-------------------- 237
               +LK S I G     + +       A + F+ I  +                     
Sbjct: 222 CDQPMLKVSPILG-----LNRVRASGKEATTKFRRIAYYPPMKRADNPDETKPVVSQDPE 276

Query: 238 --------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                         + +  +   P TGRTHQ+RVH   +G PI  D  Y    
Sbjct: 277 TRAATPPPSPADVDEGYSIVHCLPLTGRTHQIRVHLQFLGHPITNDPIYSNRR 329


>gi|224373761|ref|YP_002608133.1| ribosomal large subunit pseudouridine synthase C [Nautilia
           profundicola AmH]
 gi|223589203|gb|ACM92939.1| ribosomal large subunit pseudouridine synthase C [Nautilia
           profundicola AmH]
          Length = 294

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 113/290 (38%), Gaps = 45/290 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +        N    ++ +  G+V V+ KR+   ++  +G++  I             
Sbjct: 16  LD-FLVKKL-GFNVREAKRAIDRGRVSVNDKRITKKSQRATGRLKCI------------- 60

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                         +      ++E +   VF+KP+G+++        +    L       
Sbjct: 61  ----------VFEPNGYGLKPIFETTHFAVFDKPSGVAIHPKK--LANTKSLLDDVRSLW 108

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G    L HRLD+ETSG+++ ++ + +   L ++F+ + IQK Y +LV G  +     I  
Sbjct: 109 GNDANLVHRLDKETSGLVMASKNKFSESVLKKAFQDKEIQKKYLALVKGHLEKDL-TIKK 167

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +        + + V          +++  K I    +    +E  P TGR HQ+RVH  
Sbjct: 168 PIAVNK---DENIKVKVMIHPEGKESVTIIKPIKKIGEN-TLVECIPLTGRQHQIRVHLF 223

Query: 261 HMGCPIVGDHKYCA-------------NFKGNFTSPIQNKLYLHARYMDL 297
            +G PIVGD  Y               + K         +L LHA Y++ 
Sbjct: 224 SIGHPIVGDPLYGVDNEFADRYLNKLIDEKERIEKTGAKRLMLHAYYLEF 273


>gi|163788545|ref|ZP_02182990.1| putative ribosomal large chain pseudouridine synthase A
           [Flavobacteriales bacterium ALC-1]
 gi|159875782|gb|EDP69841.1| putative ribosomal large chain pseudouridine synthase A
           [Flavobacteriales bacterium ALC-1]
          Length = 561

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 109/247 (44%), Gaps = 20/247 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  + +  T  +   +  ++YED  + V NKP       G  I   +
Sbjct: 330 CEPILGHMMQGLDVEPNPIE-TAGTFNGELEIIYEDDFLVVLNKPHEFLSVPGKTIKDSV 388

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +++++      P L HRLD  TSG+L+VA+     ++L + F  R ++K Y +L+ G
Sbjct: 389 LTRMQNYL-PDATGPLLLHRLDMSTSGLLLVAKNERTHKNLQKQFIKRIVKKRYVALLNG 447

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             +  +  I   L +          V  ++ K A    + ++VI+    K   +   P T
Sbjct: 448 KLEPSEGTIDLPL-RVDLNNRPRQLVCDEHGKLAK---TKYEVIEIKNNK-TRIHFYPIT 502

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
           GRTHQLRVHA H   +  PI+GD  Y             N+L+LHA  +   HP     +
Sbjct: 503 GRTHQLRVHAAHYKGLNMPIIGDDLYG---------TASNRLHLHAEMLSFEHPVKREWV 553

Query: 306 QITAPLP 312
             +   P
Sbjct: 554 SFSCKAP 560


>gi|330444402|ref|YP_004377388.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           pecorum E58]
 gi|328807512|gb|AEB41685.1| Ribosomal large subunit pseudouridine synthase C [Chlamydophila
           pecorum E58]
          Length = 275

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 73/296 (24%), Positives = 131/296 (44%), Gaps = 47/296 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINAL 74
           E   RL  +     P+ + + + + +R    R++    +F + ++Q G  V I       
Sbjct: 9   ENPERLSSFLCARLPNHSKLTVLRSIRYQHCRINGSIERFESYKVQPGDRVAIS------ 62

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             I+  Q+               +  LL+ED+   +++KP  ++           +   K
Sbjct: 63  --IVHNQQ---------------QPSLLWEDAHSCIYDKPPYLTT----------EEIAK 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           +   +      L HRLD++T+G L+ A+T+ A Q L++ F+ R I K Y +LV+G+PK  
Sbjct: 96  TLGRN------LVHRLDRDTTGCLLFAKTQDAMQKLSDLFKQRNIHKQYITLVFGLPKQC 149

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              +  +   K    G  +       +G    I+ + V+  + + +  L  +P TGRTHQ
Sbjct: 150 SGTLTTFTAPKYKRCGAVLFGTTTPSQG-KLTITKWTVLQRY-KHYSLLLCEPITGRTHQ 207

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +R+H  H+G PIVGD  Y +  +         +  LHA  +    P  G  + +TA
Sbjct: 208 IRLHMKHLGHPIVGDIDYGSKQQPKGVF----RPLLHAHSLKFVSPFSGETIYVTA 259


>gi|297182825|gb|ADI18977.1| pseudouridylate synthases, 23S RNA-specific [uncultured delta
           proteobacterium HF0010_10I05]
          Length = 316

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 64/297 (21%), Positives = 119/297 (40%), Gaps = 38/297 (12%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L  +    + +         ++SG + VD ++ K   ++++ Q V               
Sbjct: 22  LLEFLLRRFRYYGPKEWGDHIKSGHLLVDGQQGKAGQKLRNNQRVVY------------- 68

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +   S+  +  +D+    +L+ED  +   NK   +          +    L   V  +
Sbjct: 69  --LRPDSLEPSVDADY---EVLFEDEWLIGLNKSGDLPTSPS---GRYFKNTLMHLVRER 120

Query: 141 G--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              QK    HRLD+ETSG+++ A+T   AQ +   FR ++I+K Y ++V      ++  +
Sbjct: 121 FGWQKLYTIHRLDRETSGVVLFAKTHQMAQQMAALFRDKQIRKEYRAVVTTPLPKEEILV 180

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +  +             V ++      + + F+ +    +     ++ P TGRTHQ+R+H
Sbjct: 181 SKPIGPDRSSSIRIKQSVCED---GKPSETRFRQLKTIRECAYL-QIHPMTGRTHQIRIH 236

Query: 259 ALHMGCPIVGDHKYCANFKGNFT-----------SPIQNKLYLHARYMDLPHPEGGR 304
           A   G PIVGD  Y    K                 + N+  LHA  +D  HP+  +
Sbjct: 237 AAASGFPIVGDKLYGLAEKDFLRWLEEGEAFLKARNLPNRQLLHAYQIDFIHPQTNQ 293


>gi|225013036|ref|ZP_03703452.1| pseudouridine synthase [Flavobacteria bacterium MS024-2A]
 gi|225002852|gb|EEG40832.1| pseudouridine synthase [Flavobacteria bacterium MS024-2A]
          Length = 227

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 62/213 (29%), Positives = 99/213 (46%), Gaps = 13/213 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           +K  +L+ED+ + + NK A   VQG       +   LK+++  K +KP      + HR+D
Sbjct: 3   IKERILFEDNHLIIVNKEAKELVQGDKTGDPTLADHLKAYIKVKYKKPGEVYLGIVHRID 62

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG++V  +T  A   L   F  R  +K YW++V      +K  + +W+ +       
Sbjct: 63  RPTSGVVVFTKTSKALARLNAQFEKRSPRKTYWAVVDKSFPTQKGNLTHWMTRNQKQNKS 122

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             H+       +  A   +K I  F + +C LE+   TGR HQ+R     +G PI GD K
Sbjct: 123 KAHI--NEVPNSKIAKLSYKRIQEF-EHYCLLEVTLETGRHHQIRAQLSSLGFPIQGDLK 179

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           Y A+      S     + LHAR + + HP    
Sbjct: 180 YGADRSNKDGS-----ISLHARKLQIEHPITNE 207


>gi|254525135|ref|ZP_05137190.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219722726|gb|EED41251.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 247

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 65/254 (25%), Positives = 105/254 (41%), Gaps = 23/254 (9%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           +        ++     LL+ D ++ V NKPAG+ V          D       +  G+  
Sbjct: 4   EPDTLAAVETETAPLQLLHLDERLAVVNKPAGLMVHDSKLARGEDDFLADRLREQLGRPI 63

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HRLD+ TSG L++A  R  A  L ++     + K Y ++  G P      + + L  
Sbjct: 64  FLVHRLDRATSGCLLLAFDRDTASALGKALMGGEVLKDYLTVCRGWPAELSWQVDHDL-- 121

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQ 254
                G     VK        AI+ F+ +          +  + ++  L  QP TGR  Q
Sbjct: 122 ----DGGPGKPVK------KPAITDFQRLATGELSVPIGEFSSSRYALLRCQPQTGRFRQ 171

Query: 255 LRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           +R H  H+   ++GD  +        F     +++ LHA  +  PHP+GG + + APL A
Sbjct: 172 IRRHLKHLSHHMIGDTSHGDGRHNRIFRMQGVHRMLLHAERLRFPHPDGGVVDVRAPLDA 231

Query: 314 HMVKTWDSLGFKYD 327
              K  D  G++ D
Sbjct: 232 GFQKALDLFGWQVD 245


>gi|160943889|ref|ZP_02091119.1| hypothetical protein FAEPRAM212_01390 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444565|gb|EDP21569.1| hypothetical protein FAEPRAM212_01390 [Faecalibacterium prausnitzii
           M21/2]
          Length = 303

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 59/322 (18%), Positives = 110/322 (34%), Gaps = 51/322 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
            + + +  + +      +     K  R G    D   V  N RI  GQ++          
Sbjct: 14  HDGVLVRSFLRQCAVSTDLARAVK-FRGGGFFADGVPVLANRRIFPGQMLSF-------- 64

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---SGIAYHIDGF 132
                   L    +       +   ++YED+   V  KP  ++V       G        
Sbjct: 65  -------ALPPEGDGVTPQPEIPVKVVYEDAFAVVLEKPPQLAVHPTLNYPGGTLANGYA 117

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             +         R  +R+D++TSG+++ A+   AA  L        + K+Y+++  G   
Sbjct: 118 AWAAAHGHSPVFRPVNRIDKDTSGLVLAAKNAYAAPLLA-----GGVTKLYYAIAQGALP 172

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +  I   + ++         + +        + + + +I             P TGRT
Sbjct: 173 LGEGAIDAPIGRRGD-----SIIGRCVTPEGKPSRTEYTIIK-EENGLSLAACVPVTGRT 226

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL------PHPEGGRLQ 306
           HQ+RVH   +G P+ GD  Y  + +         +  LH            P P+G R++
Sbjct: 227 HQIRVHFASIGHPLAGDDLYGGSRER------IARQALHCARQSFAVPVYTPLPDGIRVE 280

Query: 307 ---------ITAPLPAHMVKTW 319
                    + +PLP  M   +
Sbjct: 281 MPLQLRTVTVESPLPPDMEALF 302


>gi|87311869|ref|ZP_01093981.1| putative 23S rRNA pseudouridine synthase [Blastopirellula marina
           DSM 3645]
 gi|87285400|gb|EAQ77322.1| putative 23S rRNA pseudouridine synthase [Blastopirellula marina
           DSM 3645]
          Length = 250

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 67/244 (27%), Positives = 113/244 (46%), Gaps = 17/244 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHR 149
                 +LYE    +   KPAG+  Q    I   ++   K+++  +  K       + HR
Sbjct: 5   PPANVDILYEQGPCFCIAKPAGLLTQAPPHID-SLESRFKAFIRQRDFKTGKVYLGVPHR 63

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+  SG+L  AR   AA+ +++ F  R ++K+YW+ V G P + +    + + K   + 
Sbjct: 64  LDRPVSGVLTFARNVRAARRISQQFETRLVRKLYWAFVAGQPPDDQGVWEDPIRKIPDVA 123

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                +V  ++ GA +A   ++V+    Q     E++  TGR HQ+RV     G PI+GD
Sbjct: 124 --MAEIVSPSDPGARWAKLKYEVLQRTEQGAWL-EIELDTGRYHQIRVQCASRGFPILGD 180

Query: 270 HKYCAN--FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSL-GFK 325
             Y     F           + LHARY+ L HP    +  +TAPLP     +W+++ G+ 
Sbjct: 181 VSYGGEIPFGPQSEDERARHIALHARYLRLKHPMVDEIVAVTAPLPE----SWNAIAGWN 236

Query: 326 YDRN 329
            +  
Sbjct: 237 PEWE 240


>gi|238854112|ref|ZP_04644459.1| pseudouridine synthase, RluA family [Lactobacillus gasseri 202-4]
 gi|311110296|ref|ZP_07711693.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus gasseri MV-22]
 gi|238833188|gb|EEQ25478.1| pseudouridine synthase, RluA family [Lactobacillus gasseri 202-4]
 gi|311065450|gb|EFQ45790.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus gasseri MV-22]
          Length = 282

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 69/300 (23%), Positives = 120/300 (40%), Gaps = 33/300 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQS 61
           + TY  ++    +   + ++   +     I     +  LR   Q+ ++   +  N  +++
Sbjct: 1   MTTYHYFLTYPANLGPISVNELMRKLL--IPR-KWRHFLRTEKQILINDHYLPLNFLVKA 57

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + I      L+H+  +Q+   +S  L K        ++YEDS I V +KP G     
Sbjct: 58  GDKIDIY-----LDHVESDQQTYPASGKLPK--------VVYEDSDILVIDKPTGQKTHP 104

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                   D  L       G  P + HRLD  T+G+L+VA+  A    L      + + +
Sbjct: 105 N---LDEKDTALNDCATYLGYSPFIVHRLDMLTNGLLLVAKNPAVVPILNRQLTNKTLHR 161

Query: 182 IYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
            Y + V       +   I+  +          +  +         AI+H++VI     K 
Sbjct: 162 EYLAWVSKSNQLKQSGTISLSIGHDPDDQRKRMVRL-----DGQKAITHYEVIKECENKE 216

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +++   TGRTHQ+RVH   +G PI+GD  Y  N++         KL L A  +    P
Sbjct: 217 -LVKLTLETGRTHQIRVHLAALGAPIIGDPLYNPNYQNG------EKLQLTAYQLTFMGP 269


>gi|33152775|ref|NP_874128.1| pseudouridylate synthase [Haemophilus ducreyi 35000HP]
 gi|34395751|sp|P59831|RLUA_HAEDU RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|33148999|gb|AAP96517.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           ducreyi 35000HP]
          Length = 222

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 60/206 (29%), Positives = 98/206 (47%), Gaps = 11/206 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +Y D+ I V NKP+G+    G+   Y+    + + V  +       HRLD  TSGI+++A
Sbjct: 17  VYRDNHIVVINKPSGLLSVPGNRPEYYDS--VMTRVQQRYGFAEPAHRLDMATSGIILLA 74

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHVVKQN 219
            ++ A + L   FR R  +K Y +L+WG   ++       N+ L           +  + 
Sbjct: 75  LSKVAEKELKRQFRDREPKKHYIALLWGKLGDRVGQTGEINFPLICDWENRPRQKICYER 134

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 A +H++V++  A     ++  P TGR+HQLRVH+L +G PI+GD  Y       
Sbjct: 135 ---GKKATTHYEVLEHLANNTTRVKFTPITGRSHQLRVHSLALGHPIIGDKFY----ANP 187

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRL 305
               +  +L LHA  + + HP    L
Sbjct: 188 LAKSLAPRLCLHAESLTIAHPISAEL 213


>gi|325847067|ref|ZP_08169893.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481039|gb|EGC84084.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 249

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 104/240 (43%), Gaps = 18/240 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSK------GQKP 144
            ++ +   ++YE+    + +K   + V     I     ++G L  +  +         +P
Sbjct: 18  EAEKMDLKIVYENEDYAIIDKDENVIVHPAGSIVSGTLVNGLLYHFGYNNLSHIGGDDRP 77

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HRLD++T+G++V+A++ ++ + L   F  R+I K Y ++  GI K K   I  ++ +
Sbjct: 78  GIVHRLDKDTTGLMVIAKSNSSYKFLKNLFEKRKIDKEYLAICNGIFKKKSGEIHTFMDR 137

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             +                  AIS ++V+      +  ++++  TGRTHQ+RVH  H+  
Sbjct: 138 DPNNRRKMAVR-----NSGRDAISKYEVL-SENDGYSLVKIKILTGRTHQIRVHMTHINH 191

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           P++GD  Y  N K  F     +   LH   +     +G   +    +     K    LG 
Sbjct: 192 PLLGDPVYG-NVKHKFN---LDHQLLHCHKLGFTDKDGIYREFETDVHEDFKKYQKVLGL 247


>gi|218512946|ref|ZP_03509786.1| RNA-pseudouridine synthase protein, ribosomal large subunit C
           [Rhizobium etli 8C-3]
          Length = 303

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 80/174 (45%), Positives = 115/174 (66%), Gaps = 2/174 (1%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           RVK + R+Q GQ VR+PP+   ++  +K   I    +  +   D L  ++L+ED K+ V 
Sbjct: 2   RVKSDARVQPGQTVRVPPL--DVDAKLKSGPIAGKDLKHSSDFDLLSRMVLHEDEKVIVL 59

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           NKP GI+VQGGSG+A HID  L++W   KG+KPRL HRLD++TSG+LV+ARTR AAQ LT
Sbjct: 60  NKPPGIAVQGGSGVARHIDQMLEAWTSPKGEKPRLVHRLDRDTSGVLVIARTRGAAQKLT 119

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
            +FR R  +K YW+LV G+P+  ++ I+ WL+K++   GD + + K   K A  
Sbjct: 120 AAFRERDTKKTYWALVKGVPRKHEDKISTWLVKEATADGDRMRIAKTRRKTAPT 173


>gi|59857911|gb|AAX08790.1| hypothetical protein FLJ14494 [Bos taurus]
 gi|157279001|gb|AAI34591.1| RNA pseudouridylate synthase domain containing 4 [Bos taurus]
 gi|296471773|gb|DAA13888.1| RNA pseudouridylate synthase domain-containing protein 4 [Bos
           taurus]
          Length = 377

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 79/290 (27%), Positives = 126/290 (43%), Gaps = 43/290 (14%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   ++++D ++ V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKALSRGIVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P  +   +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIV 205

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G                D   V  ++ + A  A++ ++V    +     LE+QP 
Sbjct: 206 EKEAQGQQHHHKMTLSPSYRMDDGKMVRVRSSRNAQLAVTQYRV-LSSSLSAALLELQPI 264

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC---------------ANFKGNFTSPIQNKLYLHA 292
           TG  HQLRVH    + CPI+GDHKY                       +      L+LHA
Sbjct: 265 TGIKHQLRVHMSFGLDCPILGDHKYSDWNRLAPQKLSAGILKKLGLQQSKARHLPLHLHA 324

Query: 293 RYMDLP--HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
             + LP   P+   L +    P + V +   LG K        R +S DE
Sbjct: 325 CQLTLPALQPQKEELTLLCRPPRYFVNSLRRLGLKMP-----SRDHSADE 369


>gi|194363955|ref|YP_002026565.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
 gi|194346759|gb|ACF49882.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
          Length = 253

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 64/254 (25%), Positives = 104/254 (40%), Gaps = 23/254 (9%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           +        +D     LL+ D ++ V NKPAG+ V          D       +  G+  
Sbjct: 12  EPDTLAAVETDTAPLQLLHLDERLAVVNKPAGLMVHDSKLARGEDDFLADRLREQLGRPI 71

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HRLD+ TSG L++A  R  A  L ++     + K Y ++  G P      + + L  
Sbjct: 72  FLVHRLDRATSGCLLLAFDRDTASLLGKALMGGEVLKDYLTVCRGWPAELSWRVDHDL-- 129

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQ 254
                G     VK        A++ F+ +          +  + ++  L  QP TGR  Q
Sbjct: 130 ----DGGPGKPVK------KPAVTDFQRLATGELSVPIGEFTSSRYALLRCQPQTGRFRQ 179

Query: 255 LRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           +R H  H+   ++GD  +        F     +++ LHA  +  PHP+GG + + APL  
Sbjct: 180 IRRHLKHLSHHMIGDTSHGDGRHNRIFRMQGVHRMLLHAERLRFPHPDGGTVDVRAPLDG 239

Query: 314 HMVKTWDSLGFKYD 327
              K  D  G++ D
Sbjct: 240 GFQKALDLFGWQVD 253


>gi|146302439|ref|YP_001197030.1| pseudouridine synthase [Flavobacterium johnsoniae UW101]
 gi|146156857|gb|ABQ07711.1| ribosomal large subunit pseudouridine synthase D [Flavobacterium
           johnsoniae UW101]
          Length = 229

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 71/227 (31%), Positives = 105/227 (46%), Gaps = 14/227 (6%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTH 148
           SD     +L+ED+ I V NK  G  VQG       +   +K ++  K  KP      + H
Sbjct: 5   SDKNNLQILHEDNHIIVVNKRVGDIVQGDKTGDKPLSDIVKEYIKDKYNKPGDVFLGVIH 64

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ T+GI+V ART  A   + E F  R  +K YW++V   P      + ++L +    
Sbjct: 65  RLDRPTTGIVVFARTSKALSRMNELFSNRETKKTYWAVVKNKPVEAAAKLVHYLKRNEKN 124

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                H+  +    +  A   +K+I    Q +  LE+  HTGR HQ+R     +G PI G
Sbjct: 125 NTSKAHL--KEVPDSKLASLDYKIIKEL-QNYTALEINLHTGRHHQIRAQLSAIGSPIKG 181

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           D KY A+      S     ++LHAR +   HP     + I AP+P  
Sbjct: 182 DLKYGAD-----RSNPDGGIHLHARKLVFVHPVSKENITIIAPVPDE 223


>gi|229526265|ref|ZP_04415669.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae bv.
           albensis VL426]
 gi|229336423|gb|EEO01441.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae bv.
           albensis VL426]
          Length = 570

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 102/240 (42%), Gaps = 21/240 (8%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   +
Sbjct: 348 EGMPLEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-T 406

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +     H LD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I 
Sbjct: 407 QAEGVFALHCLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEIQ 466

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L            V  Q       A++H++ +    Q    + + PHTGRTHQLRVH 
Sbjct: 467 LPLCGD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHC 521

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            H   +  PIVGD  Y    K         +L+LHA  +   HP   + +     + A  
Sbjct: 522 AHHLGLNTPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTFQ--VDADF 570


>gi|166365046|ref|YP_001657319.1| ribosomal large subunit pseudouridine synthase D [Microcystis
           aeruginosa NIES-843]
 gi|166087419|dbj|BAG02127.1| ribosomal large subunit pseudouridine synthase D [Microcystis
           aeruginosa NIES-843]
          Length = 501

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 65/218 (29%), Positives = 106/218 (48%), Gaps = 17/218 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L   ++YED  I   NKPAG+    G          + +    +G+     HRLD+ETSG
Sbjct: 298 LSLEIIYEDEGIIAINKPAGLLSVAGRYQD--SQDAVVNRFRRQGKNLIPVHRLDRETSG 355

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           IL++A++    + L++ F+ R ++KIY +++  I + +   I   L         Y  V 
Sbjct: 356 ILLLAKSLDIYRCLSQQFQRREVEKIYEAILSEIIERESGIIDLPLWGN-PQNRPYQTVD 414

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA-LHMGCPIVGDHKYCAN 275
            Q  K +    ++FKV+      +  LE  P+TGRTHQ+RVH+   +G  I+GD  Y   
Sbjct: 415 WQRGKASQ---TYFKVVGKEG-NYSRLEFIPYTGRTHQIRVHSQQGLGIGILGDRLYNGK 470

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                     ++L+LHA+ +   HP+   +L +  P P
Sbjct: 471 Q--------SDRLHLHAKQLSFRHPQTENKLDLIIPTP 500


>gi|170078760|ref|YP_001735398.1| putative pseudouridine synthase [Synechococcus sp. PCC 7002]
 gi|169886429|gb|ACB00143.1| putative pseudouridine synthase [Synechococcus sp. PCC 7002]
          Length = 282

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 66/306 (21%), Positives = 110/306 (35%), Gaps = 39/306 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           ++   Y H       K L + Q+ VD K      R+   Q +                  
Sbjct: 3   FYAEFYRHSTRQEWAKRLENQQIFVDGKPATATQRLAKNQRLEYH--------------- 47

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQ 142
                   +    L   +L++D   ++ +KPAG+ V       +  +  L         +
Sbjct: 48  ---RPPWEEPDVPLNFQILHQDPHFWIIDKPAGLPVLPAGN--FLENTLLAQLKRQFPDE 102

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P   HRL + TSG++++ R+    Q LT   R  +I KIY +++       +  I   +
Sbjct: 103 TPVPIHRLGRGTSGLMILGRSPLGRQSLTRQLREHQITKIYRAVIPAGDYPDQITITTPI 162

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            K  H     +     +      A S  +V++  A K   +E+Q  TGR HQ+R+H   M
Sbjct: 163 GKIFHPSLGTIFAATAD---GLSAHSEMRVLERLA-KVSRVEVQIFTGRPHQIRIHMAAM 218

Query: 263 GCPIVGDHKYCA-------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           G P+VGD  Y             +   P      L+A Y+   HP   +       P   
Sbjct: 219 GFPLVGDRLYLPGGLPAIYEDANHSPLPGDCGYSLNAYYLKFQHPHQDK-------PIDF 271

Query: 316 VKTWDS 321
                +
Sbjct: 272 FSQLQA 277


>gi|240278475|gb|EER41981.1| DRAP deaminase [Ajellomyces capsulatus H143]
          Length = 545

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 62/305 (20%), Positives = 104/305 (34%), Gaps = 73/305 (23%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        QK +  G V ++ K V  + +IQ+G V+              E
Sbjct: 66  LDVF-GTEFRDRPKEYYQKAVEDGAVCINGKAVSIDTKIQNGDVISHTLHR-------HE 117

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  + V +KPAG+ V       Y+    +       
Sbjct: 118 PPVTSQPIG-----------IIHEDDDMIVIDKPAGVPVHPAGRYNYNSILEIMKAERGN 166

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G  P   +RLD+ TSG++ + +    A+ + E  R R ++K Y + V G   +       
Sbjct: 167 GWVPYPCNRLDRLTSGVMFIGKHPKGAEQIGEKLRSRTVRKEYVARVKGKFPDGVVLCDQ 226

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----------------------- 237
            +LK S I G     + +       A + F+ I  +                        
Sbjct: 227 PMLKISPILG-----LNRARASGKEARTKFRRIAYYPPHKQAGKKQGLSAGPATPPATLP 281

Query: 238 --------------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                                     + +  +   P TGRTHQLRVH  ++G PI  D  
Sbjct: 282 DQMNISDSQTDTPTGAAIPVPMSPDEEGYSIVHCLPLTGRTHQLRVHLQYLGHPITNDPI 341

Query: 272 YCANF 276
           Y    
Sbjct: 342 YSNRR 346


>gi|125604035|gb|EAZ43360.1| hypothetical protein OsJ_27960 [Oryza sativa Japonica Group]
          Length = 509

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 83/341 (24%), Positives = 150/341 (43%), Gaps = 71/341 (20%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIY 109
           K++K N+ ++ G  + +P  +       + + I  ++++  K   ++L+ +++++DS I 
Sbjct: 162 KKIKHNDVMEPGMRIHLPVSVAEGEIKKRYETIPTATLHPNKDEIEYLRRLVIHKDSAIL 221

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQ 168
           V NKP  + ++G   +   +D    + +    ++ P+L HRLD+E+SG+L+  RT+ +  
Sbjct: 222 VLNKPPKVPMKGNLPVHNSMDVLAAAALSYGNEEGPKLVHRLDRESSGLLLFGRTKESFT 281

Query: 169 HLTE---------------SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
            L                 +       + YW+LV G PK ++  I+  L K     G   
Sbjct: 282 RLHWLFTSVNLAKTNSQVWNAACEAYMQRYWALVIGTPKEREGIISAPLSKVLLDDGKAE 341

Query: 214 HVVKQNE---KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGD 269
            V+  +     GA  A++ ++V+        W+E++P TGR HQLRVH    +G PIVGD
Sbjct: 342 RVILAHPSGIDGAQEAVTAYRVMGPTIHGCSWIELRPLTGRKHQLRVHCAEALGTPIVGD 401

Query: 270 HKYC------------ANFKGNFTSPIQNK------------------LYLHARYMDLPH 299
           +KY              +F+     P + +                  L+LH R M +P+
Sbjct: 402 YKYGWFVHQRWKQNPQPDFEPFTGEPYKLRRPEGLEIQKGSVLSKVPLLHLHCREMVIPN 461

Query: 300 ----------------PEGGR----LQITAPLPAHMVKTWD 320
                           P        L+  AP+PAHM  +W+
Sbjct: 462 IAKFLSSNGEWHENGAPWSKEKPNLLRFIAPMPAHMKISWN 502


>gi|238855152|ref|ZP_04645474.1| pseudouridine synthase, RluA family [Lactobacillus jensenii 269-3]
 gi|260665529|ref|ZP_05866375.1| ribosomal protein large subunit [Lactobacillus jensenii SJ-7A-US]
 gi|282932565|ref|ZP_06337987.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 208-1]
 gi|238832233|gb|EEQ24548.1| pseudouridine synthase, RluA family [Lactobacillus jensenii 269-3]
 gi|260560650|gb|EEX26628.1| ribosomal protein large subunit [Lactobacillus jensenii SJ-7A-US]
 gi|281303313|gb|EFA95493.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 208-1]
          Length = 287

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 67/289 (23%), Positives = 117/289 (40%), Gaps = 34/289 (11%)

Query: 25  FKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
            +     I     +  LR    + ++ +   FN  +    +  I     +L H+  +Q  
Sbjct: 22  LRKLL--IPR-KWRHFLRIEKNILINGQYRNFNELVYPNDLYSI-----SLTHVENQQHP 73

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  S +L +        ++YED  I V NKP+                 + +++   G  
Sbjct: 74  ILPSGHLPQ--------IIYEDKNILVINKPSKQKTHPNLFETNTAMNDVTTYL---GYT 122

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  T+G+L+ A+  A    L      + +Q+ Y++ V      +K  I++ + 
Sbjct: 123 PYIIHRLDMLTNGLLLFAKNPAVVPILNRQLTTKTMQRNYYATVKLKDIAQKGTISSPIA 182

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHM 262
           +        +            A++H++VI    ++    L++   TGRTHQ+RVH   +
Sbjct: 183 QDPTDQRKRIIA-----DNGLKAVTHYEVIGRDLSKNTMVLKLTLETGRTHQIRVHLASI 237

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
             PI+GD  Y  NF G         L L A  M L  P    +L +T P
Sbjct: 238 NLPIIGDPLYNPNFNGE-------PLALIAYEMTLIKPFTFEKLTVTLP 279


>gi|311279889|ref|YP_003942120.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308749084|gb|ADO48836.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 232

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 58/220 (26%), Positives = 94/220 (42%), Gaps = 16/220 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +L++D+++ + NKPAG+    G          +   +        L HRLD 
Sbjct: 11  PPCHDEIEILWQDAQLVIINKPAGLLSLSGKNPQN--LDSVHYRLVKLFPGCALVHRLDF 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++VVAR +A    L + F  R + K+Y +L+ G  +  +  +   + K   +    
Sbjct: 69  GTSGLIVVARDKAVNAALCQQFSQRAVSKVYTALLCGHLEENEGTVDAPIAKDPAL---- 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKF--------CWLEMQPHTGRTHQLRVHALHMGC 264
              +         A S F+V++ F Q+           + + P TGRTHQLR+H  H+G 
Sbjct: 125 FPRMSICATHGKPARSRFQVVERFTQRLEDGRELPLTRVMLTPQTGRTHQLRIHCQHLGH 184

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           PI+G   Y              +L LHA  +   HP  G 
Sbjct: 185 PILGCDLYGGLLPPGTGR--APRLMLHASELHFTHPASGE 222


>gi|115477338|ref|NP_001062265.1| Os08g0520100 [Oryza sativa Japonica Group]
 gi|122234516|sp|Q0J4D4|PUS3_ORYSJ RecName: Full=RNA pseudourine synthase 3, mitochondrial; AltName:
           Full=RNA pseudouridylate synthase 3; AltName:
           Full=RNA-uridine isomerase 3; Flags: Precursor
 gi|113624234|dbj|BAF24179.1| Os08g0520100 [Oryza sativa Japonica Group]
 gi|125562210|gb|EAZ07658.1| hypothetical protein OsI_29911 [Oryza sativa Indica Group]
          Length = 475

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 83/341 (24%), Positives = 150/341 (43%), Gaps = 71/341 (20%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIY 109
           K++K N+ ++ G  + +P  +       + + I  ++++  K   ++L+ +++++DS I 
Sbjct: 128 KKIKHNDVMEPGMRIHLPVSVAEGEIKKRYETIPTATLHPNKDEIEYLRRLVIHKDSAIL 187

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQ 168
           V NKP  + ++G   +   +D    + +    ++ P+L HRLD+E+SG+L+  RT+ +  
Sbjct: 188 VLNKPPKVPMKGNLPVHNSMDVLAAAALSYGNEEGPKLVHRLDRESSGLLLFGRTKESFT 247

Query: 169 HLTE---------------SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
            L                 +       + YW+LV G PK ++  I+  L K     G   
Sbjct: 248 RLHWLFTSVNLAKTNSQVWNAACEAYMQRYWALVIGTPKEREGIISAPLSKVLLDDGKAE 307

Query: 214 HVVKQNE---KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGD 269
            V+  +     GA  A++ ++V+        W+E++P TGR HQLRVH    +G PIVGD
Sbjct: 308 RVILAHPSGIDGAQEAVTAYRVMGPTIHGCSWIELRPLTGRKHQLRVHCAEALGTPIVGD 367

Query: 270 HKYC------------ANFKGNFTSPIQNK------------------LYLHARYMDLPH 299
           +KY              +F+     P + +                  L+LH R M +P+
Sbjct: 368 YKYGWFVHQRWKQNPQPDFEPFTGEPYKLRRPEGLEIQKGSVLSKVPLLHLHCREMVIPN 427

Query: 300 ----------------PEGGR----LQITAPLPAHMVKTWD 320
                           P        L+  AP+PAHM  +W+
Sbjct: 428 IAKFLSSNGEWHENGAPWSKEKPNLLRFIAPMPAHMKISWN 468


>gi|269101936|ref|ZP_06154633.1| tRNA pseudouridine synthase C [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268161834|gb|EEZ40330.1| tRNA pseudouridine synthase C [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 259

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 59/248 (23%), Positives = 103/248 (41%), Gaps = 17/248 (6%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           T     ++  +LY+D  +   NKP+G+ V      ++     +++  D  GQ     HRL
Sbjct: 8   TPLIPKVELEILYQDEYLVAVNKPSGMLVHRSWLDSHETVFVMQTLRDQIGQHVFPLHRL 67

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ TSG+L+ A +   A  +   F  R + K Y ++V G  K     + ++ LKK     
Sbjct: 68  DRPTSGVLLFALSSEMAAEMMPKFAGRDVHKTYHAVVRGWVKEA--AVLDYPLKKEL--D 123

Query: 211 DYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHAL 260
                    E+ A  A++ +  I               ++  +EM+P TGR HQLR H  
Sbjct: 124 KIADKNASKEQEAQPAVTAYAPIAKVEVPIAVGRYSCSRYSLVEMKPETGRKHQLRRHMH 183

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGRL-QITAPLPAHMVK 317
           H+   I+GD  +             +  +L LHA  +   HP   ++  I A +    ++
Sbjct: 184 HLSHHIIGDVNHGDGRHNRMFRDNYDCHRLMLHASRIQFEHPITKQMLDIRAQVDETWLR 243

Query: 318 TWDSLGFK 325
              +  + 
Sbjct: 244 VMAAFNWD 251


>gi|15604825|ref|NP_219609.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           D/UW-3/CX]
 gi|255348466|ref|ZP_05380473.1| pseudouridine synthetase family protein [Chlamydia trachomatis 70]
 gi|255503008|ref|ZP_05381398.1| pseudouridine synthetase family protein [Chlamydia trachomatis 70s]
 gi|255506680|ref|ZP_05382319.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           D(s)2923]
 gi|3328503|gb|AAC67697.1| predicted pseudouridine synthetase family [Chlamydia trachomatis
           D/UW-3/CX]
 gi|289525149|emb|CBJ14622.1| tRNA pseudouridine synthase A [Chlamydia trachomatis Sweden2]
 gi|296434693|gb|ADH16871.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           E/150]
 gi|296435622|gb|ADH17796.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           G/9768]
 gi|296437482|gb|ADH19643.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           G/11074]
 gi|296438411|gb|ADH20564.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           E/11023]
 gi|297139981|gb|ADH96739.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           G/9301]
 gi|297748235|gb|ADI50781.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D-EC]
 gi|297749115|gb|ADI51793.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D-LC]
          Length = 303

 Score =  159 bits (402), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 127/305 (41%), Gaps = 50/305 (16%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPV 70
           +   +  +RL  + +   PH+    + + +R    RV+ +  +F + ++Q G  V +  +
Sbjct: 5   IGTADRQIRLSSFLRTSLPHLPKKTILESVRYHGCRVNGRIERFESYKLQPGDRVSLQII 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            ++                           LL+ED  + ++NKPA              +
Sbjct: 65  EHS------------------------SPQLLWEDEHLCIYNKPA----------KQTSE 90

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                          L HRLD++TSG ++ A+   A+  +T+ F+ R I K Y +LV+G 
Sbjct: 91  DLAHQL------NVHLVHRLDRDTSGCILFAKHAKASSLITQLFKNREIDKRYIALVFGQ 144

Query: 191 PKNKKECIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           P+ +   I  +       IG        QN       I+ ++++  +  K+  L  +P T
Sbjct: 145 PRQESGIITTYTAPCYRRIGAVLFGNTDQNS--GKITITKWEILTRYP-KYTLLLCRPVT 201

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
           GRTHQ+R+H   +G PIVGD  Y    +         +  LHA  +    P    +++++
Sbjct: 202 GRTHQIRLHMKTIGHPIVGDVDYGNQEQPKNVV----RTLLHAASLAFISPFSNEKIEVS 257

Query: 309 APLPA 313
           +  P+
Sbjct: 258 SLTPS 262


>gi|300214932|gb|ADJ79348.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 295

 Score =  159 bits (402), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 122/305 (40%), Gaps = 35/305 (11%)

Query: 24  WFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +FK     I+   L K +R   G++ ++ K         SG+ +      + +  ++   
Sbjct: 18  FFKKQ--GISRRLLAK-VRYSDGKILINGK---------SGRKIDKIKKNDKITLVVP-- 63

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSW 136
              D          F+   +LYED    + +KPA ++           +   + G+    
Sbjct: 64  ---DEEFRRNVPPSFVPIKILYEDDNYLLVDKPAFVASIPSPLHPNDSLVNRVVGY-YQI 119

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +G  P +  RLD++TSGI++ A+ R A   L    +  +I K Y +++ GI  N   
Sbjct: 120 RGYRGIIPHIVTRLDRDTSGIVIFAKHRYAHALLDSQLKEHKISKTYTAILSGILHNNHY 179

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   + + S      +       + A  + +   V +         +++ HTGRTHQ+R
Sbjct: 180 IIDLPIGRDST---SLIKRKVLFSEKAKRSKTEIFVKERIRDN-TLCKIKLHTGRTHQIR 235

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH-PEGGRLQITAPLPAHM 315
           VH  ++G P+V D  Y     G  + P+Q +  LH   +          +++ + +   M
Sbjct: 236 VHCSYLGYPLVSDTLYG----GAISMPLQ-RQALHCSEVVFWDQFSSQYIKVKSNIFQDM 290

Query: 316 VKTWD 320
           +    
Sbjct: 291 MNYLK 295


>gi|21229703|ref|NP_635620.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66766580|ref|YP_241342.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|21111188|gb|AAM39544.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66571912|gb|AAY47322.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
          Length = 245

 Score =  159 bits (402), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 99/240 (41%), Gaps = 24/240 (10%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +LY+D+ + V +KPAG+ V          D          G+   L HRLD+ TSG 
Sbjct: 7   PLQILYQDAVLAVVDKPAGLMVHDSKLARGEDDFLADRLRVQLGRPIFLVHRLDRATSGC 66

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A  R  A  L ++     ++K Y ++  G P  ++  + + L               
Sbjct: 67  LLLAFDRDTASALGKALMAGEVEKDYLAICRGWPAEERFIVDHDLDG------------G 114

Query: 218 QNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             +     A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++
Sbjct: 115 PGKPIKKPAVTHFQRLATGELEIPSTGFATSRYALLRCQPQTGRFRQIRRHLKHLSHHMI 174

Query: 268 GDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           GD  +       +F     +++ LHA  +  PHP +G R+ + APL     K     G+ 
Sbjct: 175 GDTSHGDGRHNRSFRMLGIHRMLLHAERLGFPHPADGRRISVVAPLDVEFAKACALFGWD 234


>gi|12045231|ref|NP_073042.1| RluA family pseudouridine synthase [Mycoplasma genitalium G37]
 gi|1351560|sp|P47610|Y370_MYCGE RecName: Full=Uncharacterized RNA pseudouridine synthase MG370;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|3844958|gb|AAC71597.1| pseudouridine synthase, RluA family [Mycoplasma genitalium G37]
 gi|166078817|gb|ABY79435.1| pseudouridine synthase, RluA family [synthetic Mycoplasma
           genitalium JCVI-1.0]
          Length = 323

 Score =  159 bits (402), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 80/317 (25%), Positives = 134/317 (42%), Gaps = 29/317 (9%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      +V  + EN R+D++     P I   +  K LR G+V ++K + + N R+++  
Sbjct: 1   MRIANKFLVPKESENQRIDQFCLKILPLIKRSDFFKYLRLGKVLLNKTKPQVNTRLKTKD 60

Query: 64  VV----RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            +     I P +   N  +        S++L K     K  +++ED  I V +KP GI  
Sbjct: 61  EIAFLFDINPYLQTNNDYL--------SLDLVKD----KLKIIFEDENIIVVDKPTGIVC 108

Query: 120 QGGSGIA--YHIDGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           Q     +     +  LK         +     P+  HR+D+ TSGI++ A+T  A + L 
Sbjct: 109 QPDKKHSIINLSNMLLKHCGYRQFDSNKLNFYPQFAHRIDRNTSGIVIGAKTNKALKELN 168

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           + F+   + K Y  LV+G   N       +  K ++ G   V V  +    A    + F+
Sbjct: 169 KVFKNNHLTKRYKGLVFGQF-NHLGLQTAYWKKDNNNG--IVTVKWKPFPEAKKISTFFE 225

Query: 232 VIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
                AQK    + ++  +GRTHQ+R         +VGD KY      N  +  ++   L
Sbjct: 226 NSSYIAQKDMSLITIRLISGRTHQIRACLNLFSNQLVGDKKYSLIQFKNRNNKYKH-QAL 284

Query: 291 HARYMDLPHPEGGRLQI 307
           HA  +  P  E  +  I
Sbjct: 285 HAYELVFPKLETSKFPI 301


>gi|330837755|ref|YP_004412396.1| ribosomal large subunit pseudouridine synthase D [Spirochaeta
           coccoides DSM 17374]
 gi|329749658|gb|AEC03014.1| ribosomal large subunit pseudouridine synthase D [Spirochaeta
           coccoides DSM 17374]
          Length = 233

 Score =  159 bits (402), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 110/234 (47%), Gaps = 17/234 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           + S +LYED+ +   NK  G  VQG       +   ++ ++  K  KP      + HRLD
Sbjct: 9   VASRVLYEDNHLIAVNKLPGELVQGDKTGDVTLADAVRDYLKVKYGKPGNVYLGIPHRLD 68

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG+++  RT  A   + E FR   + K+YW++V  +P+N +  + +++ + +     
Sbjct: 69  RPTSGVVLYCRTEKALGRMNEMFRGSDVSKVYWAVVDALPQNTEGTLVHYIFRDTRTNKS 128

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V+    G+ +A   +++I   ++ +  LE+  HTGR HQ+R     +G  I GD K
Sbjct: 129 VARPVETV--GSKFAKLDYRIIGA-SRNYHLLEIVLHTGRHHQIRAQLAAIGLHIKGDLK 185

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR--LQITAPLPAHMVKTWDSLG 323
           Y A       S     ++LHAR +  PHP      + + A  P      WD   
Sbjct: 186 YGA-----ARSNPDGGIHLHARSISFPHPVKKEDVVTVIARPPHD--AVWDVFA 232


>gi|325920613|ref|ZP_08182526.1| tRNA pseudouridine synthase C [Xanthomonas gardneri ATCC 19865]
 gi|325548904|gb|EGD19845.1| tRNA pseudouridine synthase C [Xanthomonas gardneri ATCC 19865]
          Length = 245

 Score =  159 bits (402), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 102/240 (42%), Gaps = 24/240 (10%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +L++D  + V NKPAG+ V          D       +  G+   L HRLD+ TSG 
Sbjct: 7   PLQILHQDDVLAVVNKPAGLMVHDSKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGC 66

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++A  R +A  L ++     ++K Y ++  G P  ++  + + L       G     VK
Sbjct: 67  LLLAFDRESASTLGKALMAGELEKDYLTVCRGWPAEEQFIVDHDL------DGGPGKPVK 120

Query: 218 QNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   A++HF+ +               ++  L  QP TGR  Q+R H  H+   ++
Sbjct: 121 ------KPAVTHFQRLATGELEIPSTGFATSRYALLRCQPQTGRFRQIRRHMKHLSHHMI 174

Query: 268 GDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           GD  +       +F     +++ LHA  +  PHP +G RL + APL     K     G+ 
Sbjct: 175 GDTSHGDGRHNRSFRMLGIHRMLLHAERLGFPHPADGRRLSVVAPLDVEFAKACALFGWD 234


>gi|33863383|ref|NP_894943.1| putative pseudouridylate synthase [Prochlorococcus marinus str. MIT
           9313]
 gi|33640832|emb|CAE21287.1| putative pseudouridylate synthase [Prochlorococcus marinus str. MIT
           9313]
          Length = 207

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 64/218 (29%), Positives = 99/218 (45%), Gaps = 19/218 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L++DS +    KP G+  Q G G+       L   +     + RL HRLD++TSG+L+
Sbjct: 2   RILFQDSWLIAVEKPPGLLSQPGLGVD--QQDSLIGRMQFIDPELRLVHRLDRDTSGLLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + +  +  F  RR++K+Y ++V G        I+  + +       Y       
Sbjct: 60  LARGAESLRRCSMLFSARRVRKLYLAVVVGRMNRNAGTISFPIARLQKNPPLY-----GK 114

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 + S ++V  C A       + P TGR+HQLR H   +G PI+GD  Y       
Sbjct: 115 NPQGKESRSQWRVRSCHANGSTLW-LWPLTGRSHQLRAHLASVGHPILGDPIYGKEV--- 170

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG---RLQITAP-LPA 313
                  ++YLHA  +   HP  G   RL+  AP LPA
Sbjct: 171 ----FFERMYLHATALSFRHPFTGLRLRLRSRAPFLPA 204


>gi|28899917|ref|NP_799572.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|260363211|ref|ZP_05776080.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
 gi|260880498|ref|ZP_05892853.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|260898549|ref|ZP_05907045.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|28808200|dbj|BAC61405.1| putative ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|308084943|gb|EFO34638.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|308092677|gb|EFO42372.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|308111932|gb|EFO49472.1| ribosomal large chain pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
          Length = 559

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 114/245 (46%), Gaps = 20/245 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  + +     ++  +  ++Y+D  + V NKP+G+    G  I    
Sbjct: 328 CQPILGHMMQGLDVEPNPLA-ENWAEDKELEIIYQDDAMVVVNKPSGLLSVPGKTIKDSA 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +++      + P + HRLD  TSGILV A T+ A + L + F  R +QK Y +L+ G
Sbjct: 387 YTRIQAMF-PDVEGPFVIHRLDMATSGILVFALTKRANKSLQKQFMARGVQKRYMALLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +    +  I+  + +          V  ++     +A +++++ID        + M P T
Sbjct: 446 VLNEPEGEISLPM-RGDPDDRPRQLVCFEH---GKHAETYWQLID-VKDGRSKVYMYPKT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH+ H   +  P+VGD  Y             N+L+LHA  ++L HP    R+
Sbjct: 501 GRTHQLRVHSAHHMGLNMPMVGDGLYGEK---------ANRLHLHAEMLELDHPYSKERM 551

Query: 306 QITAP 310
              A 
Sbjct: 552 VFRAE 556


>gi|284038283|ref|YP_003388213.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283817576|gb|ADB39414.1| pseudouridine synthase [Spirosoma linguale DSM 74]
          Length = 244

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 60/238 (25%), Positives = 100/238 (42%), Gaps = 23/238 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +LY+D+++   NKP G+ V      +   +  ++   D  GQ+    HRLD++T+G+
Sbjct: 10  PLSILYQDTELVAINKPHGLLVHRSMIASDASEFAVQLLRDQLGQRVYPVHRLDRKTAGV 69

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A + +    + + F    +QK Y ++V G     +  I   L K    G   V    
Sbjct: 70  LLFALSESMNAIMQQQFMEGAVQKTYLAIVRGY-TPDELTIDYPLCKDDGNGAVGVL--- 125

Query: 218 QNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   A++H K +               ++  +E+ P TGR HQLR H  H+  PI+
Sbjct: 126 ------QEAVTHLKTLRQTEIPVAFGKHPTSRYSLVELTPTTGRMHQLRRHMAHILHPII 179

Query: 268 GDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           GD  +  N +          N + LHA+ ++  HP       I AP  A   +    L
Sbjct: 180 GDRPHGCNKQNKLFKEHFEMNTMLLHAQRIEFTHPVTQETTTIAAPFQAEFRRMLGVL 237


>gi|269104819|ref|ZP_06157515.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268161459|gb|EEZ39956.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 560

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 114/242 (47%), Gaps = 20/242 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++K  + L+ ++ L   ++  +  ++Y+D  + + NKPA      G  I+  +
Sbjct: 329 CEPILGHMLKGIE-LEENLLLKNPAEGKELEIIYQDEAMVIVNKPAEFLSVPGKTISDSV 387

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +++        P + HRLD  TSG+LV+A T+ A ++L + F  R ++K Y +L+ G
Sbjct: 388 YTRMQAMF-PDADSPLIVHRLDMSTSGLLVIALTKRAHKNLQKQFITRTVEKRYVALLDG 446

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +  + +  I+  +  +  I      +V         A + ++VI         +   P T
Sbjct: 447 LADSDEGIISLPM--RGDINDRPRQLVCFEH--GKPAETKWQVISRK-DGKTKVYYYPKT 501

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVH+ H   M  PI+GD  Y             N+L+LHA Y+ L HP     +
Sbjct: 502 GRTHQLRVHSAHPMGMNMPIIGDDLYGQK---------SNRLHLHAEYLSLEHPITHEPM 552

Query: 306 QI 307
           + 
Sbjct: 553 EF 554


>gi|95767470|gb|ABF57296.1| RNA pseudouridylate synthase domain containing 4 [Bos taurus]
          Length = 373

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 79/290 (27%), Positives = 126/290 (43%), Gaps = 43/290 (14%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   ++++D ++ V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 82  VHPNVLAKALSRGIVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKP 141

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P  +   +   ++
Sbjct: 142 LHLCHRLDKETTGVMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIV 201

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G                D   V  ++ + A  A++ ++V    +     LE+QP 
Sbjct: 202 EKEAQGQQHHHKMTLSPSYRMDDGKMVRVRSSRNAQLAVTQYQV-LSSSLSAALLELQPI 260

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC---------------ANFKGNFTSPIQNKLYLHA 292
           TG  HQLRVH    + CPI+GDHKY                       +      L+LHA
Sbjct: 261 TGIKHQLRVHMSFGLDCPILGDHKYSDWNRLAPQKLSAGILKKLGLQQSKARHLPLHLHA 320

Query: 293 RYMDLP--HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
             + LP   P+   L +    P + V +   LG K        R +S DE
Sbjct: 321 CQLTLPALQPQKEELTLLCRPPRYFVNSLRRLGLKMP-----SRDHSADE 365


>gi|259907745|ref|YP_002648101.1| Pseudouridine synthase [Erwinia pyrifoliae Ep1/96]
 gi|224963367|emb|CAX54853.1| Pseudouridine synthase [Erwinia pyrifoliae Ep1/96]
 gi|283477602|emb|CAY73518.1| ribosomal large subunit pseudouridine synthase A [Erwinia
           pyrifoliae DSM 12163]
          Length = 232

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 56/220 (25%), Positives = 92/220 (41%), Gaps = 16/220 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                K  +LY+D ++ + NKPAG+    G          +   +        L HRLD 
Sbjct: 11  PPCHNKIEILYQDDRLVLINKPAGLLSLSGKNPQN--IDSVHYRLVQIFPGCTLVHRLDF 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V+AR +A    L + F  R + K+Y +L+ G   + +  I   + K   +    
Sbjct: 69  GTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLDDNEGVIDAAIAKDPAL---- 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGC 264
             ++         + S ++V++ F              +++ P TGRTHQLR+H   +G 
Sbjct: 125 FPLMSICSIHGKPSRSRYRVVERFYHPLENRTLLPLTRVQLTPETGRTHQLRIHCQQLGH 184

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           PI+G   Y              +L LHA  +   HP  G 
Sbjct: 185 PILGCDLYGGRLLPGTERT--PRLMLHASELHFVHPINGE 222


>gi|154302617|ref|XP_001551718.1| hypothetical protein BC1G_09885 [Botryotinia fuckeliana B05.10]
 gi|150855374|gb|EDN30566.1| hypothetical protein BC1G_09885 [Botryotinia fuckeliana B05.10]
          Length = 453

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 102/280 (36%), Gaps = 49/280 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHIIK 79
           LD +  + +        +  +  G + V+ K V+  +  I++G V+      +       
Sbjct: 67  LDIF-SSEFRDRPIEYYKDAMERGAIAVNGKPVESISQIIKNGDVISHTLHRH------- 118

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                            L   +++ED  I V NKP+G+ V       Y+    +      
Sbjct: 119 -----------EPPVTALPISIVHEDEDIIVINKPSGVPVHPAGRYNYNSVVEIMRAERG 167

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G  P   +RLD+ TSGI+ + +   AA+ L+     R ++K Y + V G   + +    
Sbjct: 168 HGWNPLPCNRLDRLTSGIMFIGKHAKAAEALSLQISGRTVRKEYIARVKGKFPDGEVVCD 227

Query: 200 NWLL-KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--------------------- 237
             +L     +G + V            A + FK +  +                      
Sbjct: 228 MPILQISPKLGLNRVRA------NGKAARTVFKRLAYYPPEQAHDNPEQTELDKTRPPMA 281

Query: 238 -QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + +  +   P TGRTHQLRVH   +G PI  D  YC   
Sbjct: 282 KEGYSIVRCLPVTGRTHQLRVHLQFLGHPIGNDPIYCNQR 321


>gi|213403308|ref|XP_002172426.1| DRAP deaminase [Schizosaccharomyces japonicus yFS275]
 gi|212000473|gb|EEB06133.1| DRAP deaminase [Schizosaccharomyces japonicus yFS275]
          Length = 401

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 101/237 (42%), Gaps = 30/237 (12%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           + +R+GQV+V+ +    +  IQ+G V+              E  + D  V          
Sbjct: 63  RAIRNGQVKVNNEPGNVDTVIQNGYVISHAAHR-------HEPPVTDEPV---------- 105

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGI 157
             +++ED +  V +KPAGI V       Y+ +  L   +   K       +RLD+ TSG+
Sbjct: 106 -RIVHEDEEYVVIDKPAGIPVHPTG--RYNHNTVLHILMHENKCPLLYPCNRLDRLTSGL 162

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW--LLKKSHIGGDYVHV 215
           +  ++T   A+ +      + +QK Y + V G    +K    +   L     +G + VH 
Sbjct: 163 MFFSKTPKGAERMRVHMISKDLQKEYVARVVGEFPAEKTITCDAKLLTVAPTLGLNRVH- 221

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                     A++ FK +         +  +P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 222 -----PDGKDAVTIFKRLAFDGH-TSLVHCKPLTGRTHQIRVHLQYLGYPIANDPIY 272


>gi|316971885|gb|EFV55608.1| pseudouridylate synthase 6 [Trichinella spiralis]
          Length = 404

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 65/289 (22%), Positives = 116/289 (40%), Gaps = 30/289 (10%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           YV  +      RL    +N   +      ++ + +G+V V+ +    +  +++G ++R  
Sbjct: 59  YVFAKKRWFGRRLVDVLQNELYNPIGNFFEEAILAGRVTVNGQPTSVDYVVENGDLIRHM 118

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                      E  +LDS+V+           ++ +   I V NKP  I V       YH
Sbjct: 119 CHR-------HELPVLDSAVD-----------IVTDTEDILVVNKPCSIPVHPCG--RYH 158

Query: 129 IDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  +       G    +  HRLD+ TSG+++  +     + L +     +I+K Y  LV
Sbjct: 159 FNSLVLYLKHIGGMDNLKTFHRLDRLTSGLVIFLKNEKIEKKLRQQMIENQIKKEYLCLV 218

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G    ++      L   S   G     +         +++ F  +     K   L+  P
Sbjct: 219 DGEFPEEEVVCDKPLDVLSQSMG-----IMYITADGKPSLTKFYKLFSDG-KTSILKCCP 272

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
            TGRTHQ+RVH  ++G PIV D+ Y      +   P + KL  + + +D
Sbjct: 273 ETGRTHQIRVHLQYLGYPIVNDYIYN---NSDAFGPNKGKLCDYGKSLD 318


>gi|260587511|ref|ZP_05853424.1| pseudouridine synthase, RluA family [Blautia hansenii DSM 20583]
 gi|260541776|gb|EEX22345.1| pseudouridine synthase, RluA family [Blautia hansenii DSM 20583]
          Length = 244

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 62/214 (28%), Positives = 100/214 (46%), Gaps = 9/214 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++  +LYED  I V  KPAG  VQ        ++  L++++  KGQ+P +   HRLDQ  
Sbjct: 26  IEDTVLYEDKYILVCQKPAGFPVQSKRLGTLDMECALRNYLAKKGQEPYVAVIHRLDQPV 85

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G+LV A+ + +A  L++  +  + +K Y +   G    K+E + + L K          
Sbjct: 86  QGVLVFAKDKESAAKLSKQMQQGKFEKTYLAYTQGHTDKKQETLIDELEKDGRTNTSK-- 143

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV +    +  A   +KV+    +    LE+   TGR HQ+RV   H G PI GD KY  
Sbjct: 144 VVAKKTANSKRAELSYKVLKETEEG-SLLEVSLKTGRHHQIRVQLAHAGLPIFGDAKYNV 202

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
                  +   +   L A  +   HP +G +++ 
Sbjct: 203 KCTKEDANHGVS---LCAYKLSFLHPAKGKKMEF 233


>gi|307543955|ref|YP_003896434.1| tRNA pseudouridine synthase C [Halomonas elongata DSM 2581]
 gi|307215979|emb|CBV41249.1| tRNA pseudouridine synthase C [Halomonas elongata DSM 2581]
          Length = 256

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 100/241 (41%), Gaps = 21/241 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L+ D  +   +KPAG+ V   +         L++  D  GQ+    HRLD+ TSG++
Sbjct: 5   LPILHHDDHLIAVHKPAGMLVHRSALARGERHFLLQTLRDQIGQRVYPVHRLDRPTSGLM 64

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A     A  L ++F  +R+ K Y ++V G     +               D      +
Sbjct: 65  VFALDPEVAGRLADAFATQRVAKRYLAVVRGQGPEAERLDYAL--------RDEDGRRPK 116

Query: 219 NEKGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            E  A  A +  + +D            + ++  +E +P TGR HQ+R H    G PI+G
Sbjct: 117 AEMPAREARTEVRRLDSVELPVRVDRYPSARYSLMEARPLTGRRHQIRRHLSRRGYPIIG 176

Query: 269 DHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           D K+       F +   +  +L L A  +D  HP  G RL +   L A M   +   G+ 
Sbjct: 177 DAKHGKGVHNRFFAEQLDCPRLLLAAVGLDFEHPVDGRRLTLGCALDAPMTALFQRFGWS 236

Query: 326 Y 326
            
Sbjct: 237 A 237


>gi|95769474|gb|ABF57439.1| RNA pseudouridylate synthase domain containing 4 [Bos taurus]
          Length = 375

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 79/290 (27%), Positives = 126/290 (43%), Gaps = 43/290 (14%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   ++++D ++ V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 84  VHPNVLAKALSRGIVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKP 143

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P  +   +   ++
Sbjct: 144 LHLCHRLDKETTGVMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIV 203

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G                D   V  ++ + A  A++ ++V    +     LE+QP 
Sbjct: 204 EKEAQGQQHHHKMTLSPSYRMDDGKMVRVRSSRNAQLAVTQYQV-LSSSLSAALLELQPI 262

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC---------------ANFKGNFTSPIQNKLYLHA 292
           TG  HQLRVH    + CPI+GDHKY                       +      L+LHA
Sbjct: 263 TGIKHQLRVHMSFGLDCPILGDHKYSDWNRLAPQKLSAGILKKLGLQQSKARHLPLHLHA 322

Query: 293 RYMDLP--HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
             + LP   P+   L +    P + V +   LG K        R +S DE
Sbjct: 323 CQLTLPALQPQKEELTLLCRPPRYFVNSLRRLGLKMP-----SRDHSADE 367


>gi|113955599|ref|YP_731829.1| pseudouridine synthase [Synechococcus sp. CC9311]
 gi|113882950|gb|ABI47908.1| Pseudouridine synthase [Synechococcus sp. CC9311]
          Length = 327

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 68/315 (21%), Positives = 133/315 (42%), Gaps = 32/315 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  E++ RL       + H      Q+ L SG++ ++      +  +++G  +R     
Sbjct: 22  VQPGEQSTRLSAVLALRHRHSCPATWQQRLASGEITLNGLACSDDVEVKAGDWIRW---- 77

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHID 130
                         +     + +   +  ++++D  + V NKP+G+ V  G G + + + 
Sbjct: 78  --------------ARPPWVEAAVPDQLEVIHDDGDVLVVNKPSGLPVMPGGGFLVHTLT 123

Query: 131 GFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKIYW 184
             L+    S G+   P+  HRL + TSG+ V AR       L++ FR     R+      
Sbjct: 124 SLLERSSRSVGEVLVPKPIHRLGRFTSGLQVCARRPETRAALSKQFRPEGDCRKTYLGLT 183

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQKF 240
             +  + + +   I   ++++ H    +V   + +          A S  ++ +   ++ 
Sbjct: 184 HRLESLQQGQTLVIQTDVVERQHPLLGWVWGPEPSTPEPLRRRLSAHSEVQLRER-GERE 242

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMD-LP 298
             LE+Q HTGR HQ+R+H   +G P++GD  Y ++     T+ P     +LHA  ++ L 
Sbjct: 243 DLLEVQIHTGRPHQIRIHLAQLGFPLLGDPLYQSDQGLCATATPGDGGYHLHAWRLEGLC 302

Query: 299 HPEGGRLQITAPLPA 313
            P    L + A  P 
Sbjct: 303 WPTSKWLSLKAQPPK 317


>gi|127512389|ref|YP_001093586.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126637684|gb|ABO23327.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 217

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 57/219 (26%), Positives = 98/219 (44%), Gaps = 13/219 (5%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        + Y+D  I + NKP+G+    G     H      + +  +  +  L HRLD
Sbjct: 7   QPPAIPWLDIRYQDRDIIIINKPSGLLSNPGRAAETHDCAI--NRLLQRFPEAILVHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V A  + A  HL   F+ R  +K Y + V G+       I   +   S     
Sbjct: 65  CATSGIMVFALNKKAESHLKTQFQNRTTEKYYVAEVEGLMAQDSGKIELAMKPDSEQP-- 122

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               +++  +    A ++F+V++  +     ++++P TGRTHQLR+H   +G  I+GD  
Sbjct: 123 ---PLQKIAEDGKPATTYFEVLERRSNS-TLVKLKPITGRTHQLRLHMKALGHTILGDDF 178

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           Y              +L+LHA ++ + HP    RL  ++
Sbjct: 179 YG----DEAIIAAAPRLHLHAEHLSITHPYKQTRLSFSS 213


>gi|315042395|ref|XP_003170574.1| DRAP deaminase [Arthroderma gypseum CBS 118893]
 gi|311345608|gb|EFR04811.1| DRAP deaminase [Arthroderma gypseum CBS 118893]
          Length = 516

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 61/267 (22%), Positives = 106/267 (39%), Gaps = 46/267 (17%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +  + +G++ +D K    ++ I +GQV+         +H +   +   +S  +       
Sbjct: 80  KAAIDNGRITIDGKIATADSIINNGQVI---------SHTLHRHEPPVTSQRI------- 123

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ED  I V +KPAGI V       Y+    +       G  P   +RLD+ TSGI
Sbjct: 124 --KIIHEDDDIIVIDKPAGIPVHPAGRYNYNSIIEILRAERGVGWVPYPCNRLDRLTSGI 181

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI-GGDYVHVV 216
           + + +   AA+ +  S R R +QK Y + V G   +        +LK S I G + V   
Sbjct: 182 MFLGKHPKAAEQMAHSLRSRTLQKEYIARVKGYFPDGVVLCDQPMLKVSPILGLNRVRAT 241

Query: 217 KQNEKGANYAISHFKVIDC---------------------------FAQKFCWLEMQPHT 249
            ++ +     I+++  +                               + +  +   P T
Sbjct: 242 GKDAQTKFRRIAYYPPVKKGDESNGETANSQDPDSRASTPPPSPADVDEGYSIVHCLPLT 301

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANF 276
           GRTHQ+RVH   +G PI  D  Y    
Sbjct: 302 GRTHQIRVHLQFLGHPITNDPIYSNRR 328


>gi|90413524|ref|ZP_01221515.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum 3TCK]
 gi|90325456|gb|EAS41939.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum 3TCK]
          Length = 244

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 59/244 (24%), Positives = 104/244 (42%), Gaps = 18/244 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +L++D  +   NKP+G+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELDILFQDEYLVAVNKPSGMLVHRSWLDRHETVFVMQTLRDQIGQHVFPLHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+   +   A  +   F  R I K Y ++V G  K+    + ++ LKK     D +   
Sbjct: 61  VLLFGLSSEIASQMMPVFSGRDIHKTYHAVVRGWIKDA--AVLDYPLKKEL---DKIADK 115

Query: 217 KQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              E+ A  A++ +  +               ++C +EM+P TGR HQLR H  H+   I
Sbjct: 116 NAAEQEAQDAVTAYSPLATIETNIPVGRYATSRYCLVEMKPETGRKHQLRRHMHHLNHHI 175

Query: 267 VGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           +GD  +             +  +L LHA  +   HP   + L I A +    ++      
Sbjct: 176 IGDVNHGDGRHNRMFRENYDCHRLMLHASRLQFVHPITKQALDIRASIDETWLRVMSKFN 235

Query: 324 FKYD 327
           +  +
Sbjct: 236 WSTE 239


>gi|304404376|ref|ZP_07386037.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
 gi|304346183|gb|EFM12016.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
          Length = 258

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 56/215 (26%), Positives = 95/215 (44%), Gaps = 10/215 (4%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQ 152
           +  +L+ED+ + V  KP G+  Q        +   LK  +  +  KP      L HRLD+
Sbjct: 17  RIPVLFEDNHLLVVVKPPGVPSQEDDSGDPDMLTLLKEDLKERHNKPGNVFLGLVHRLDR 76

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              G +V A+T  AA  L+E+ R R   K Y ++V G P      + +++ K +    + 
Sbjct: 77  PVGGAMVFAKTSKAASRLSETVRSRVFGKTYMAIVHGTPAQPYGTLKHYMRKDNK--RNV 134

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                +    A  A+  + V+D        + ++ HTGR+HQ+R     +GCP+ GD KY
Sbjct: 135 SETFDRPVADAKEAVLDYAVMDRIG-NLSLVAVKLHTGRSHQIRAQMAAIGCPLYGDAKY 193

Query: 273 CANFK--GNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            A      +        + L +  + +PHP    +
Sbjct: 194 GAPAASGNDKRHASHGTVLLWSTSVTIPHPVTKEM 228


>gi|62751988|ref|NP_001015616.1| RNA pseudouridylate synthase domain-containing protein 4 [Bos
           taurus]
 gi|75057865|sp|Q5E9Z1|RUSD4_BOVIN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 4
 gi|59857799|gb|AAX08734.1| hypothetical protein FLJ14494 [Bos taurus]
 gi|59857921|gb|AAX08795.1| hypothetical protein FLJ14494 [Bos taurus]
          Length = 377

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 79/290 (27%), Positives = 126/290 (43%), Gaps = 43/290 (14%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   ++++D ++ V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKALSRGIVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P  +   +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIV 205

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G                D   V  ++ + A  A++ ++V    +     LE+QP 
Sbjct: 206 EKEAQGQQHHHKMTLSPSYRMDDGKMVRVRSSRNAQLAVTQYQV-LSSSLSAALLELQPI 264

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC---------------ANFKGNFTSPIQNKLYLHA 292
           TG  HQLRVH    + CPI+GDHKY                       +      L+LHA
Sbjct: 265 TGIKHQLRVHMSFGLDCPILGDHKYSDWNRLAPQKLSAGILKKLGLQQSKARHLPLHLHA 324

Query: 293 RYMDLP--HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
             + LP   P+   L +    P + V +   LG K        R +S DE
Sbjct: 325 CQLTLPALQPQKEELTLLCRPPRYFVNSLRRLGLKMP-----SRDHSADE 369


>gi|299133083|ref|ZP_07026278.1| pseudouridine synthase [Afipia sp. 1NLS2]
 gi|298593220|gb|EFI53420.1| pseudouridine synthase [Afipia sp. 1NLS2]
          Length = 244

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 123/250 (49%), Gaps = 11/250 (4%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
               ++ +++ +L+ D  + V +KPAGI+V  G     +++    +      + P L HR
Sbjct: 4   PQPTAEEMQARVLHRDGLMLVIDKPAGIAVHKGPKGGPNLEASFDALRYGLPRPPVLAHR 63

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG LV+ R R A   L   F+  +I K YW++V G P   +  I   L +     
Sbjct: 64  LDRDTSGCLVLGRHRKATASLGLLFKHGKIGKTYWAVVEGGPAENQGEIDIPLGRLDETR 123

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           G +     + +     + S + V+        WL ++P TGRTHQLRVH   MG PIVGD
Sbjct: 124 GWWQ----KPDPNGLPSQSRWSVMGR-GDGLTWLALEPITGRTHQLRVHCAAMGFPIVGD 178

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
           + Y      N     +  L+LH+R + +P  +    +++ AP+P H+ +   + G+  + 
Sbjct: 179 NIYG-----NGPRFGEPSLHLHSREIVVPLSKNKPPVRVVAPVPEHLHERLRACGWNGEE 233

Query: 329 NLYIKRLYSQ 338
            L  +++ S 
Sbjct: 234 ALAPEQVVSH 243


>gi|257066371|ref|YP_003152627.1| pseudouridine synthase [Anaerococcus prevotii DSM 20548]
 gi|256798251|gb|ACV28906.1| pseudouridine synthase [Anaerococcus prevotii DSM 20548]
          Length = 277

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 62/297 (20%), Positives = 133/297 (44%), Gaps = 42/297 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M Y++Y V     EN  + ++ K    + +  +++ IL++G + ++ K+ + +  ++   
Sbjct: 1   MKYIKYEV----HENTSVRQFLKA--KNFSKKSIEDILKTGYI-LNGKKQRKSLNLKKSD 53

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            ++I      +++  K+  I                 ++YED    V +K A I+V   S
Sbjct: 54  ELKIIIEDERVDYEPKKGGI----------------NIVYEDDNSLVISKEANITV--NS 95

Query: 124 GIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                +  ++ ++    GQ  K RL +RLD +TSG++++A+ + +  +  +      ++K
Sbjct: 96  KNQISLSNYIANYFIDSGQESKIRLVNRLDMDTSGLMLIAKNKYSHAYYQKQLEENTMKK 155

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V G+         + L +      +     + ++KG   + ++FK I      F 
Sbjct: 156 KYLAVVEGMLD------IDSLYENKFSYNEKKKNYEPSDKG-KISRTYFKSI-RINCDFS 207

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +E +  TGRTHQ+R     +G PI GD  Y ++          ++  LH+  ++  
Sbjct: 208 IIECEILTGRTHQIRASLTDLGHPIWGDKLYGSDKN-------LDRFLLHSYRLEFT 257


>gi|311748604|ref|ZP_07722389.1| ribosomal large subunit pseudouridine synthase family protein
           [Algoriphagus sp. PR1]
 gi|126577128|gb|EAZ81376.1| ribosomal large subunit pseudouridine synthase family protein
           [Algoriphagus sp. PR1]
          Length = 245

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 107/231 (46%), Gaps = 16/231 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQ 152
              ++YED+ + + NK AG+ VQG       +  + K ++  K  KP        HRLD+
Sbjct: 6   PFSVVYEDNHLLIVNKTAGVLVQGDKTGDKTLTDYCKDYIAKKYDKPGAVFLHPVHRLDR 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
             SG++  ART    + + E FR R I K+YW++V   PK K   + +WL+K      + 
Sbjct: 66  PVSGLVAFARTSKGLERMMELFRKRDIHKVYWAVVKRKPKEKSGKLTHWLVKDEQ--RNV 123

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V        G+  A  ++K +         LE++P +GR HQ+RV    MGCPI GD KY
Sbjct: 124 VTAHDHEVPGSQKAELNYKTLGFMND-HWLLEVRPISGRPHQIRVQLSSMGCPIRGDLKY 182

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
                    S        HA ++   HP +  ++ + A LP    + W+  
Sbjct: 183 GFAKPNPDASINL-----HAFHLVFVHPVKKEKMYLRAALPEE--EFWEQF 226


>gi|331084165|ref|ZP_08333271.1| hypothetical protein HMPREF0992_02195 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330402020|gb|EGG81593.1| hypothetical protein HMPREF0992_02195 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 224

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 64/214 (29%), Positives = 103/214 (48%), Gaps = 9/214 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQET 154
           ++  +LYED  I V  KPAG  VQ        ++  L++++  KGQ+P +   HRLDQ  
Sbjct: 6   IEDTVLYEDKYILVCQKPAGFPVQSKRLGTLDMECALRNYLAKKGQEPYVAVIHRLDQPV 65

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G+LV A+ + +A  L++  +  + +K Y +   G    K+E + + L K    G +   
Sbjct: 66  QGVLVFAKDKESAAKLSKQMQQGKFEKTYLAYTQGHTDKKQETLIDELEKDG--GTNTSK 123

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           VV +    +  A   +KV+    +    LE+   TGR HQ+RV   H G PI GD KY A
Sbjct: 124 VVAKKTANSKRAELSYKVLKETEEG-SLLEVSLKTGRHHQIRVQLAHAGLPIFGDAKYNA 182

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
                  +   +   L A  +   HP +G +++ 
Sbjct: 183 KCTKEDANHGVS---LCAYKLSFLHPAKGKKMEF 213


>gi|169824723|ref|YP_001692334.1| putative 23S RNA-specific pseudouridylate synthase [Finegoldia
           magna ATCC 29328]
 gi|167831528|dbj|BAG08444.1| putative 23S RNA-specific pseudouridylate synthase [Finegoldia
           magna ATCC 29328]
          Length = 273

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 69/308 (22%), Positives = 133/308 (43%), Gaps = 45/308 (14%)

Query: 16  EENMRLDRWFKN-HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++ +RLD + K  H  H  F+++ K      + ++ K  K N++++ G +V I       
Sbjct: 9   DKKIRLDEFLKKNHISHNLFISIYK----DDIFINGKHAKRNSKLEKGDIVTINLRDEEN 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFL 133
            +                    +   +LYED  I+V NKP  +++ + G     +   +L
Sbjct: 65  KY----------------EPINMDIEVLYEDDDIFVLNKPDKLTMNKDGEKSLANFVSYL 108

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
               + K QK R  +RLDQ+TSG+++VA+ + A  +  ++   ++    Y ++V G PK+
Sbjct: 109 FEQRNIK-QKVRFINRLDQDTSGVVMVAKNKIAQAYYQKNSFKKK----YLAIVKGNPKD 163

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +K  I   L +          +  + ++    +++  + +  +   +  + ++  TGRTH
Sbjct: 164 QK--IELNLKRDG--------IKTEIDENGKKSVTILENLKNYGD-YSLVSLELLTGRTH 212

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           Q+RV   ++ CPIV D  Y    +            LHA  ++    +G    IT  LP 
Sbjct: 213 QIRVSMEYINCPIVADSLYGEKIENFT-------QMLHANEIEFVDMKGEYHNITTNLPQ 265

Query: 314 HMVKTWDS 321
                   
Sbjct: 266 RFKDYLKE 273


>gi|292489024|ref|YP_003531911.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           CFBP1430]
 gi|292900157|ref|YP_003539526.1| RNA pseudouridylate synthase [Erwinia amylovora ATCC 49946]
 gi|291200005|emb|CBJ47129.1| putative RNA pseudouridylate synthase [Erwinia amylovora ATCC
           49946]
 gi|291554458|emb|CBA21962.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           CFBP1430]
 gi|312173188|emb|CBX81443.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           ATCC BAA-2158]
          Length = 232

 Score =  158 bits (401), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 94/233 (40%), Gaps = 17/233 (7%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           D S          +  +L +D  + + NKPAG+    G          +   +       
Sbjct: 3   DISDTFIAPPCHDEIEVLCQDEHLVLINKPAGLLSLSGKNPQN--LDSVHHRLVQIFPGC 60

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HRLD  TSG++V+ART+A    L + F  R + K+Y +L+ G   + +  I   + K
Sbjct: 61  TLVHRLDFGTSGLMVIARTKAINAALCQQFSQRTVTKVYCALLCGHLNDNEGVIDAAIAK 120

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLR 256
              +      ++         A S ++V+                 +E+ P TGRTHQLR
Sbjct: 121 DPAL----FPLMSICSIHGKPARSRYRVLQRCYHALQDGTLLPLTRVELTPETGRTHQLR 176

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           +H   +G PI+G   Y             ++L LHA  +   HP     +I A
Sbjct: 177 IHCQQLGYPILGCDLYGGRLLPGTERT--SRLMLHASELQFVHPVSEE-RIKA 226


>gi|226939012|ref|YP_002794083.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
 gi|226713936|gb|ACO73074.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 253

 Score =  158 bits (401), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 105/249 (42%), Gaps = 18/249 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y D  +   +KPAG+ V       +     L+   D  GQK   +HRLD+ TSG+L
Sbjct: 6   LPVIYRDDWLVAVHKPAGLLVHRSEIDRHETRFALQIVRDQLGQKVWSSHRLDKPTSGLL 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++  T  A + L+ +F  + + K Y ++V G P +    I + L +      D       
Sbjct: 66  LLGLTPEAGRSLSMAFEAQAVDKQYLAVVRGWP-DAAGTIDHPLARIV----DAYAPGAS 120

Query: 219 NEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            E     A++ F  +               ++  +E+ PHTGR HQLR H  H+  PI+G
Sbjct: 121 REAEPQPAVTGFSTLATTELPWAVDRYPTSRYALVELTPHTGRRHQLRRHLKHVSHPIIG 180

Query: 269 DHKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           D  Y  +        +   ++L L    M   HP  G RL +  PL     +   +LG+ 
Sbjct: 181 DTSYGKSRHNRAFADAFGVSRLLLACTGMSFTHPVTGERLALDCPLADDFARVVSALGWD 240

Query: 326 YDRNLYIKR 334
                 + R
Sbjct: 241 AALPAPLVR 249


>gi|261339742|ref|ZP_05967600.1| pseudouridine synthase A [Enterobacter cancerogenus ATCC 35316]
 gi|288318572|gb|EFC57510.1| pseudouridine synthase A [Enterobacter cancerogenus ATCC 35316]
          Length = 228

 Score =  158 bits (401), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 62/227 (27%), Positives = 98/227 (43%), Gaps = 17/227 (7%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I+D+ +      D     +L++D  + + NKP+G+    G          +   +     
Sbjct: 4   IIDTFIAPPCKQDI---EILWQDDDLILINKPSGLLSLSGKNPQN--LDSVHYRLVQTFP 58

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD  TSGI+V+AR +A    L   F  R + K Y +L+ G  K+ +  I   +
Sbjct: 59  GCTLVHRLDFGTSGIMVIARNKAINAALCHQFSQRAVSKAYTALLCGHVKDDEGIIDAPI 118

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVH 258
            K   +      ++         A S F+V++   +        +E+ P TGRTHQLR+H
Sbjct: 119 AKDPAL----FPLMSICAISGKPARSRFRVVERIDKDEELPLTRVELIPETGRTHQLRIH 174

Query: 259 ALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              +G  I+G   Y      G   +P   +L LHA  +D  HP  G 
Sbjct: 175 CQQLGHSILGCDLYGGLEMPGAEGTP---RLMLHASGLDFVHPVSGE 218


>gi|114321104|ref|YP_742787.1| tRNA pseudouridine synthase C [Alkalilimnicola ehrlichii MLHE-1]
 gi|114227498|gb|ABI57297.1| tRNA pseudouridine synthase C [Alkalilimnicola ehrlichii MLHE-1]
          Length = 246

 Score =  158 bits (401), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 64/252 (25%), Positives = 99/252 (39%), Gaps = 29/252 (11%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
            ++ LT  SD     +++ D  +   +KPAG+ V             L+   D  GQ   
Sbjct: 5   PTIPLTMTSDA-PLDIIHRDHDLVAVDKPAGMPVHRSRRHPGDAV-LLQRLRDQLGQWLW 62

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD  TSG++V A    AA+ L   F+ R ++K Y ++V G P  ++  + + L + 
Sbjct: 63  PVHRLDPPTSGLVVFALHPEAARALAAQFQQREVEKRYLAVVRGWPL-EQGRVEHPLRRP 121

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQL 255
                               A++ F  +               ++  LE++P TGR HQL
Sbjct: 122 GRSER-------------QPAVTDFHRLATTELPIPMPPHPTARYALLELRPITGRQHQL 168

Query: 256 RVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           R H  H+  PI+GD  Y               ++L L A  +   HP  G RL +  PL 
Sbjct: 169 RRHMKHISHPIIGDTTYGKGPHNRLFRERFGASELLLRATRLAFRHPGTGARLHLDCPLN 228

Query: 313 AHMVKTWDSLGF 324
                     G 
Sbjct: 229 EAWRAVLRGSGL 240


>gi|301300163|ref|ZP_07206378.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300852251|gb|EFK79920.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 295

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 122/305 (40%), Gaps = 35/305 (11%)

Query: 24  WFKNHYPHINFVNLQKILR--SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +FK     I+   L K +R   G++ ++ K         SG+ +      + +  ++   
Sbjct: 18  FFKKQ--GISRRLLAK-VRYSDGKILINGK---------SGRKIDKIKKNDKITLVVP-- 63

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKSW 136
              D          F+   +LYED    + +KPA ++           +   + G+    
Sbjct: 64  ---DEEFRREVPPSFVPIKILYEDDNYLLVDKPAFVASIPSPLHPNDSLVNRVVGY-YQI 119

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +G  P +  RLD++TSGI++ A+ R A   L    +  +I K Y +++ GI  N   
Sbjct: 120 RGYRGIIPHIVTRLDRDTSGIVIFAKHRYAHALLDSQLKEHKISKTYTAILSGILHNNHY 179

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   + + S      +       + A  + +   V +         +++ HTGRTHQ+R
Sbjct: 180 IIDLPIGRDST---SLIKRKVLFSEKAKRSKTEIFVKERIRDN-TLCKIKLHTGRTHQIR 235

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH-PEGGRLQITAPLPAHM 315
           VH  ++G P+V D  Y     G  + P+Q +  LH   +          +++ + +   M
Sbjct: 236 VHCSYLGYPLVSDTLYG----GAISMPLQ-RQALHCSEVVFWDQFSSQYIKVKSNIFQDM 290

Query: 316 VKTWD 320
           +    
Sbjct: 291 MNYLK 295


>gi|19113793|ref|NP_592881.1| tRNA pseudouridylate synthase (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|1175381|sp|Q09709|YA32_SCHPO RecName: Full=Uncharacterized protein C18B11.02c
 gi|929888|emb|CAA90587.1| tRNA pseudouridylate synthase (predicted) [Schizosaccharomyces
           pombe]
          Length = 394

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 101/241 (41%), Gaps = 30/241 (12%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           K +R+GQV+V+ +    +  I++G +V              E  + D  V          
Sbjct: 63  KAIRNGQVKVNNQIGNVDTLIENGYIVSHHAHR-------HEPPVSDQPVG--------- 106

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGI 157
             +++ED    V +KPAG+ V       Y+ +  L   +   K       +RLD+ TSG+
Sbjct: 107 --IVHEDESYVVIDKPAGVPVHPTG--RYNHNTVLHILMKENKCSLLYPCNRLDRLTSGL 162

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW--LLKKSHIGGDYVHV 215
           +  +++  AA+ +      + ++K Y + V G   N  E I +   L     +G + +H 
Sbjct: 163 MFFSKSPKAAEEMRVHMISKSLKKEYVARVIGEFPNSGEVICDAPLLTVAPTLGLNRIH- 221

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                     A + FK I         +  +P TGRTHQLRVH  ++G PI  D  Y   
Sbjct: 222 -----PDGKEASTVFKRIAFDGH-TSLVLCKPLTGRTHQLRVHLQYLGYPIANDPIYANK 275

Query: 276 F 276
            
Sbjct: 276 R 276


>gi|313678868|ref|YP_004056608.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma bovis PG45]
 gi|312950295|gb|ADR24890.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma bovis PG45]
          Length = 284

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 68/293 (23%), Positives = 120/293 (40%), Gaps = 32/293 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           +   V   ++   +L ++  + +  +    + K+LR   V+++ KR+   N+ I  G  V
Sbjct: 1   MHKFVAHKNDGGRKLIKYISSLFKDLPESRIYKLLRQKCVKINGKRITDSNHIINEGDEV 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I        + IKEQ    +++ +      L S ++YED  I + NK AG  V G    
Sbjct: 61  VI--------YGIKEQ----ATIYIYDVGLQLDSKIIYEDDNILIINKKAGKVVHGELLC 108

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF-RMRRIQKIYW 184
             +       +  +   KP    RLD+ TSG++V A+   A + L +      +I  +  
Sbjct: 109 LDNQVLSYLKFKQNSSFKPSHVGRLDKWTSGLIVYAKNYKALRELNDKIGFFDKIYTLKS 168

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
               G        ++ ++     +      +V +N  G N  I   K+     + +    
Sbjct: 169 DYNGG-----DNVVSAYIHHDEKMQK---MIVTKNPAGLNNQIVKTKIYVDSNKLYA--- 217

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            Q  TGR HQ+R    ++G PI GD KY    K N       ++YLH+  +  
Sbjct: 218 -QLLTGRKHQIRATMEYLGYPIYGDIKYGWRKKTN------KRIYLHSYKLGF 263


>gi|303235055|ref|ZP_07321679.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
 gi|302493910|gb|EFL53692.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
          Length = 273

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/308 (22%), Positives = 132/308 (42%), Gaps = 45/308 (14%)

Query: 16  EENMRLDRWFKN-HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++  RLD + K  H  H  F+++ K      + ++ K  K N++++ G +V I       
Sbjct: 9   DKKTRLDEFLKKNHISHNLFISIYK----DDIFINGKHAKRNSKLEKGDIVTINLRDEEN 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFL 133
            +                    +   +LYED  I+V NKP  +++ + G     +   +L
Sbjct: 65  KY----------------EPINMDIEVLYEDDDIFVLNKPDKLTMNKDGEKSLANFVSYL 108

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
               + K QK R  +RLDQ+TSG+++VA+ + A  +  ++   ++    Y ++V G PK+
Sbjct: 109 FKQRNIK-QKVRFINRLDQDTSGVVMVAKNKIAQAYYQKNSFKKK----YLAIVKGNPKD 163

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +K  I   L +          +  + ++    +++  + +  +   +  + ++  TGRTH
Sbjct: 164 QK--IELNLKRDG--------IKTEIDENGKKSVTILENLKNYGD-YSLVSLELLTGRTH 212

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           Q+RV   ++ CPIV D  Y    +            LHA  ++    +G    IT  LP 
Sbjct: 213 QIRVSMEYINCPIVADSLYGEKIENFS-------QMLHANEIEFVDMKGEYHNITTNLPQ 265

Query: 314 HMVKTWDS 321
                   
Sbjct: 266 RFKDYLKE 273


>gi|308069397|ref|YP_003871002.1| Pseudouridylate synthase, 23S RNA-specific [Paenibacillus polymyxa
           E681]
 gi|305858676|gb|ADM70464.1| Pseudouridylate synthase, 23S RNA-specific [Paenibacillus polymyxa
           E681]
          Length = 248

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 118/244 (48%), Gaps = 20/244 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +    KP  +  Q  +     +   LK  +  +  KP      L HRLD+   
Sbjct: 18  VLYEDNHVLAVVKPVNVPTQEDASGDPDLLSLLKEDLKIRHNKPGNVFLGLVHRLDRPVG 77

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++ A+T  AA  L+ES R R   K+Y +++ G+P   +  + ++LLK S      V  
Sbjct: 78  GAMIFAKTSKAASRLSESVRSRHFHKLYTAVLNGVPTAPQGRLTHYLLKDSRTN--TVQA 135

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V+    GA  AI  ++VI   A     ++++ HTGR+HQ+RV    +GCP+ GD KY   
Sbjct: 136 VRPGTAGAKEAILEYRVIG-QADGLSLVQIKLHTGRSHQIRVQMQAIGCPLYGDQKYG-- 192

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
             GN + P Q +L L +     PHP     ++  +  P      W+    ++ R+LY   
Sbjct: 193 --GNLSRPGQ-QLALWSLLAGAPHPVSKDDMRFHSLPPVQFP--WN----EWPRSLYENM 243

Query: 335 LYSQ 338
           + S+
Sbjct: 244 ITSE 247


>gi|253579159|ref|ZP_04856429.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251849257|gb|EES77217.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 233

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 65/225 (28%), Positives = 100/225 (44%), Gaps = 21/225 (9%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ----KPRLTHRLD 151
            ++  +LYED  I V +KPAG++VQ     +  ++  LK+++  K         + HRLD
Sbjct: 5   DIRDYILYEDKDILVCHKPAGLAVQNARVGSMDMESLLKNYIAQKVPGKMPYLGIIHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q   G+LV A    AA  L+      +I+K Y ++  G  K K   + +WL K       
Sbjct: 65  QPVEGVLVFALNPKAAADLSRQMTAGKIKKTYLAVTEGTVKVKSAKLVDWLKKDGRTNSS 124

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMG 263
              VV+    GA  AI  ++V++ +  K           + +   TGR HQ+RV   H G
Sbjct: 125 --AVVEGGTSGAKKAILSYEVLETWKNKEDAQDCGERNLIRIDLDTGRHHQIRVQMAHAG 182

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
            P+VGD KY            Q  L L +  +   HP   + L+ 
Sbjct: 183 MPLVGDRKYNPGQNS------QEPLALCSAKLGFQHPVTKKQLEF 221


>gi|212696263|ref|ZP_03304391.1| hypothetical protein ANHYDRO_00799 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676892|gb|EEB36499.1| hypothetical protein ANHYDRO_00799 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 282

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 65/301 (21%), Positives = 117/301 (38%), Gaps = 39/301 (12%)

Query: 25  FKNHYPHINFV-NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
            K      N      K + +  V V+ +++  N  +++G  V+I                
Sbjct: 14  LKELLKSKNISTRAYKKIINNLVYVNDEKISKNIGLKAGDKVKI---------------- 57

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L    NL       K  +LYED  I   +KP  ++V   S     +  +L  +      K
Sbjct: 58  LIEDENLNYEPINKKIKILYEDKDIVAVDKPPNLTV--NSKNQESLSNYLAYYFKENKIK 115

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
              RL +RLD  TSGI++VA+   +  +         + K Y +LV G        I ++
Sbjct: 116 SQIRLINRLDMNTSGIMLVAKNPFSHAYYQNQIENNELDKEYLALVEGNL-----IIDDF 170

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
                 I  D  +   +     N+  ++FK +  +  KF  +  + +TG+THQ+R+   +
Sbjct: 171 CEID--IDYDKENKKMKVVSDKNHVKTYFKTLKNYG-KFSLIYCKIYTGKTHQIRLSLAY 227

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWD 320
           +  PI+GD+ Y + +          +  LHA  +         ++ I +       K  +
Sbjct: 228 LNHPILGDNLYGSKYD-------IERFLLHAYRIKFKSFRDQKKITILSK--PDFDKYLN 278

Query: 321 S 321
           S
Sbjct: 279 S 279


>gi|146416095|ref|XP_001484017.1| hypothetical protein PGUG_03398 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 611

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 94/237 (39%), Gaps = 25/237 (10%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +  +  G V +++K    ++ +++G ++              E  +    +         
Sbjct: 147 KAAISEGLVTLNRKPANIDSIVRNGDLISHRCHR-------HEPAVSSRPIK-------- 191

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ED  +   +KP GI V       Y  +   K +    G+     +RLD+ TSG+
Sbjct: 192 ---IVHEDDDVIAIDKPLGIPVHPVG--RYRYNTITKIFQHEFGRVVHPCNRLDRLTSGL 246

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           + + +T   A    +  + R ++K Y + V G    ++  +   +   S        +  
Sbjct: 247 MFLGKTPKGADKFVQQIKDRTVRKEYIARVIGKFPCEEITVEVPIKTVSP----KHTLNM 302

Query: 218 QNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + K    A + FK I    A     ++  P TGRTHQ+RVH  H+G  I  D  Y 
Sbjct: 303 VDPKNGKEAKTKFKRISYDPASNTSIVKCYPLTGRTHQIRVHLQHIGHAIANDPIYS 359


>gi|184154365|ref|YP_001842706.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|183225709|dbj|BAG26226.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
          Length = 309

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 64/300 (21%), Positives = 121/300 (40%), Gaps = 31/300 (10%)

Query: 22  DRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           D+W   N   H   +          V V+      N  ++    +++    + +      
Sbjct: 29  DQWLLPNRLIHYLRIR-------RTVLVNGNYRSMNEIVEKNDNIQLLFCGDEIRTPTAN 81

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDS 139
             I  S  +L          +LYE+  + V NKP G        G    +   +  ++  
Sbjct: 82  DYIPSSQSHLE---------VLYENRDLLVVNKPRGQKTHPNYHGETGTLMNDVAGYLAH 132

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                 + HR+D +TSG ++VA+       L       +I + Y ++V G      +   
Sbjct: 133 SQNNAYMVHRIDLQTSGAVIVAKNPIVVPILNRLISDGQIHRQYLAVVEGEMAQSGKL-- 190

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +W + ++ +     H+ + N + A  A+++++ +    ++   ++++  TGRTHQLRVH 
Sbjct: 191 DWAIGRNPVN---PHLHQVNGQNAQPALTYYETLASNHER-SLVKLRLATGRTHQLRVHL 246

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
            H G PIVGD  Y  +            L+  ++ + LP      L I+APLP++     
Sbjct: 247 AHSGHPIVGDPLYNPSSTEGML------LHGVSQKLILPF-VMKSLNISAPLPSYFKNYL 299


>gi|118361718|ref|XP_001014087.1| RNA pseudouridylate synthase family protein [Tetrahymena
           thermophila]
 gi|89295854|gb|EAR93842.1| RNA pseudouridylate synthase family protein [Tetrahymena
           thermophila SB210]
          Length = 881

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 80/309 (25%), Positives = 135/309 (43%), Gaps = 36/309 (11%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-----KRVKFNNRIQSGQVVRIPP-VIN 72
           MRLD++ K HY  I + +LQ  LR  ++ V       K    +  ++ G ++RIP   + 
Sbjct: 1   MRLDKYLKEHY-GIPWTSLQICLRKKEIFVKDVQDLSKHKNPDYILKEGDIIRIPFSFVE 59

Query: 73  ALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
               I   QK   + + L +   D  K +++YE+  I + NK  G+S QGG  ++ ++  
Sbjct: 60  KKEQIQNSQKQEQNEIKLDQSQIDKFKQMIIYENKNIIILNKANGVSCQGGQDVSLNLVT 119

Query: 132 FLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWG 189
             + ++ +   QK  + HRLD+ TSG+L+V + +  A+     F  +  I K Y +LV  
Sbjct: 120 MGQQYLINQTNQKYLVAHRLDKVTSGVLMVPKNQQIAKIYGNLFNDKSNINKYYIALVRN 179

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF------------- 236
            PKN K  I   +  +         V    ++ +  A +H++V+  F             
Sbjct: 180 SPKNFKAMINAPI--EYSQSKQRAIVSNIIDENSKSAHTHYQVLAQFKMEDKNLAAKIIN 237

Query: 237 --------AQKFCWLEMQPHTGRTHQLRVHALHMG-CPIVGDHKYCANFKGN--FTSPIQ 285
                      F  L+++   GR HQ+RVH   +   PIVGD +Y         F     
Sbjct: 238 SEHDYIKDWGDFSLLKIRIQEGRKHQIRVHLSEISKTPIVGDARYFDKNHQESLFQYNKD 297

Query: 286 NKLYLHARY 294
             ++LH   
Sbjct: 298 QSIFLHCYQ 306


>gi|109899489|ref|YP_662744.1| pseudouridylate synthase [Pseudoalteromonas atlantica T6c]
 gi|109701770|gb|ABG41690.1| tRNA pseudouridine synthase C [Pseudoalteromonas atlantica T6c]
          Length = 252

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 94/242 (38%), Gaps = 17/242 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LY+D  +   +KPAG+ V       +     ++   D  GQ     HRLD+ TSG
Sbjct: 1   MTLTILYQDECLVAIHKPAGLLVHRSMIDRHETQFAMQMLRDQIGQHVFPVHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV A +   A+ L E F    I K Y+++V G  K           K   I        
Sbjct: 61  VLVFALSADIARLLGEQFAGNTIAKTYFAIVRGHVKEAGLIDYALKEKLDKIADKRAKQ- 119

Query: 217 KQNEKGANYAISHF----------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              +K A  A + +           V    + ++  + + P TGR HQLR H  H+  PI
Sbjct: 120 ---DKDAQEAQTEYVPLQQFELPFAVSRYPSARYTLVRLHPKTGRKHQLRRHMCHINHPI 176

Query: 267 VGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLG 323
           VGD  +       F       N L L  + M + HP    +L I       M       G
Sbjct: 177 VGDTTHGDGKHNKFMRDQFSFNGLALTCQQMCMTHPVSNEKLAIVNDFDQRMSTLMVQWG 236

Query: 324 FK 325
           ++
Sbjct: 237 WE 238


>gi|148545031|ref|YP_001272401.1| pseudouridine synthase [Lactobacillus reuteri DSM 20016]
 gi|227364179|ref|ZP_03848276.1| pseudouridylate synthase RluD [Lactobacillus reuteri MM2-3]
 gi|325683382|ref|ZP_08162898.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
 gi|148532065|gb|ABQ84064.1| pseudouridine synthase [Lactobacillus reuteri DSM 20016]
 gi|227070818|gb|EEI09144.1| pseudouridylate synthase RluD [Lactobacillus reuteri MM2-3]
 gi|324977732|gb|EGC14683.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
          Length = 306

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 64/300 (21%), Positives = 121/300 (40%), Gaps = 31/300 (10%)

Query: 22  DRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           D+W   N   H   +          V V+      N  ++    +++    + +      
Sbjct: 26  DQWLLPNRLIHYLRIR-------RTVLVNGNYRSMNEIVEKNDNIQLLFCGDEIRTPTAN 78

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDS 139
             I  S  +L          +LYE+  + V NKP G        G    +   +  ++  
Sbjct: 79  DYIPSSQSHLE---------VLYENRDLLVVNKPRGQKTHPNYHGETGTLMNDVAGYLAH 129

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                 + HR+D +TSG ++VA+       L       +I + Y ++V G      +   
Sbjct: 130 SQNNAYMVHRIDLQTSGAVIVAKNPIVVPILNRLISDGQIHRQYLAVVEGEMAQSGKL-- 187

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +W + ++ +     H+ + N + A  A+++++ +    ++   ++++  TGRTHQLRVH 
Sbjct: 188 DWAIGRNPVN---PHLHQVNGQNAQPALTYYETLASNHER-SLVKLRLATGRTHQLRVHL 243

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
            H G PIVGD  Y  +            L+  ++ + LP      L I+APLP++     
Sbjct: 244 AHSGHPIVGDPLYNPSSTEGML------LHGVSQKLILPF-VMKSLNISAPLPSYFKNYL 296


>gi|229522777|ref|ZP_04412191.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TM
           11079-80]
 gi|229339994|gb|EEO05002.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TM
           11079-80]
          Length = 570

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 103/240 (42%), Gaps = 21/240 (8%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   +
Sbjct: 348 EGMPLEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-T 406

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I 
Sbjct: 407 QAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEIQ 466

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L            V  Q       A++H++ +    Q    + + PHTGRTHQLRVH 
Sbjct: 467 LPLCGD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHC 521

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            H   +  PIVGD  Y    K         +L+LHA  +   HP   + +     + A  
Sbjct: 522 AHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTFQ--VDADF 570


>gi|153807696|ref|ZP_01960364.1| hypothetical protein BACCAC_01978 [Bacteroides caccae ATCC 43185]
 gi|149129305|gb|EDM20519.1| hypothetical protein BACCAC_01978 [Bacteroides caccae ATCC 43185]
          Length = 590

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 71/269 (26%), Positives = 112/269 (41%), Gaps = 50/269 (18%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ +    H D  +  +++ED  + V NKP+G+    G      +
Sbjct: 330 CEPILQHMLQGLEVDENPLLSNTHKDT-ELEIVFEDEWLVVVNKPSGMLSVPGK--EEDM 386

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           D       +       P + HRLD  TSG+L+VA+T+   QHL   F  R I+K Y +L+
Sbjct: 387 DSVYHRLKEKYPDATGPMIVHRLDMATSGLLLVAKTKEVHQHLQAQFENRSIKKRYIALL 446

Query: 188 WGIPK----------------------------NKKECIANWLLKKSHIGGDYVHVVKQN 219
            G                                K   I   L                +
Sbjct: 447 DGCITETEETTNQTTGNTRKTEKVRATEVISTTGKVGRIELPLCPNPLDRP----CQSVD 502

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANF 276
           E+    AI+ +++I   ++K   +   P TGRTHQLRVHA H   + CPI+GD  Y    
Sbjct: 503 EEHGKEAITEYQII-TNSEKHTRIAFCPLTGRTHQLRVHAAHPKGLNCPILGDELYGKK- 560

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
                    ++LYLHA Y++  HP  G +
Sbjct: 561 --------ADRLYLHAEYIEFRHPIYGDI 581


>gi|329942738|ref|ZP_08291517.1| RNA pseudouridylate synthase family protein [Chlamydophila psittaci
           Cal10]
 gi|332287335|ref|YP_004422236.1| pseudouridylate synthase protein [Chlamydophila psittaci 6BC]
 gi|313847919|emb|CBY16914.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           psittaci RD1]
 gi|325507344|gb|ADZ18982.1| pseudouridylate synthase protein [Chlamydophila psittaci 6BC]
 gi|328814998|gb|EGF84987.1| RNA pseudouridylate synthase family protein [Chlamydophila psittaci
           Cal10]
          Length = 275

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 123/296 (41%), Gaps = 48/296 (16%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINAL 74
               RL  + ++  P      +   +R    RV+ +  +F + R+Q G  V +       
Sbjct: 9   HHEERLSSFLRSRLPDHKKHIILDSIRYHGCRVNGRLERFESYRVQPGDRVTLTVQTR-- 66

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                 L+  +L+ED    ++NKP+       +     I G   
Sbjct: 67  ----------------------LEPQILWEDEHYCIYNKPS----HTSTEDLAKITGL-- 98

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                      + HRLD++T+G ++ A+  +AA  L+E F+ R+I K Y +LV+G PK  
Sbjct: 99  ----------NIVHRLDRDTTGCILFAKHASAAHALSELFKKRKIHKQYTALVFGHPKKS 148

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              + ++   KS   G  +    Q +      I+ + ++  + Q +  +  +P TGRTHQ
Sbjct: 149 SGTLISYTAPKSRRCGAVIFGNTQ-KNHGKLTITQWSILCAYKQ-YTLMRCEPITGRTHQ 206

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           +R+H   +G PIVGD  Y    +         +  LHA  +    P    ++++TA
Sbjct: 207 IRLHMHTLGHPIVGDVDYGRKEQPKHVF----RPLLHAHALTFTSPFSKEKVEVTA 258


>gi|330686161|gb|EGG97779.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU121]
          Length = 284

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 60/301 (19%), Positives = 119/301 (39%), Gaps = 40/301 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +Y + + +     L  + + H    +   +  I  +G + V+++ V    ++  G  + +
Sbjct: 4   RYTITQQE----TLKSFLQRH--DFSKKTISAIKTNGALLVNQRHVTVRYQLNFGDQLEV 57

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIA 126
              I               S NLT +   L   +L+ED  I + +KP G +         
Sbjct: 58  QLPIEV------------PSANLTPYMKPLD--ILFEDDYIIIVSKPNGQNCAPSREHPH 103

Query: 127 YHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             +   +  ++  KG++  P +  RLD+ T+GI++ A+        +++    ++ K+Y 
Sbjct: 104 ESLVEQVLGYLHHKGERTNPHIVTRLDRNTTGIVLFAKYGYIHHLFSKA----KMDKVYT 159

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            L +G        I   + +      D   + +   +   YA + F+ +    +     E
Sbjct: 160 CLAYG-MTEPSGMIEAPIARS-----DESIIERCVSENGKYAKTVFRTLK-QKENVSCCE 212

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +Q  TGRTHQ+RVH  ++G P++GD  Y                 LH   +   HP    
Sbjct: 213 VQLCTGRTHQIRVHFQYIGHPLIGDTLYGGKHGK------IEGQCLHCSKLIFEHPVNKN 266

Query: 305 L 305
           +
Sbjct: 267 M 267


>gi|225572906|ref|ZP_03781661.1| hypothetical protein RUMHYD_01097 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039719|gb|EEG49965.1| hypothetical protein RUMHYD_01097 [Blautia hydrogenotrophica DSM
           10507]
          Length = 221

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 60/218 (27%), Positives = 102/218 (46%), Gaps = 15/218 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----PRLTHRLD 151
            L+ +++YED  + V +KPAG++VQ        ++  LK+ +  +  +      + HRLD
Sbjct: 1   MLREVIVYEDEDLIVCHKPAGMAVQSAGIGRMDLESALKNELAMRNPEKLPYVAVIHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q   G++V A+   AA  L+       ++K Y ++        KE + +WL +      +
Sbjct: 61  QPVEGLVVFAKNPKAASGLSSQSARGEMKKCYLAVAQDAKVPDKERLEDWLRRDGR--KN 118

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y  VV +N  G+  A+  ++++     K   L +Q  TGR HQ+RV   H G P++GD K
Sbjct: 119 YSMVVPKNTSGSKRAVLEYRLLKRQNGKM-LLHIQLLTGRHHQIRVQMAHRGMPLLGDRK 177

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
           Y    +          L L A  +   HP  GG++   
Sbjct: 178 YNPGTQNVH-------LGLCACELSFTHPLSGGKMDFC 208


>gi|169614099|ref|XP_001800466.1| hypothetical protein SNOG_10184 [Phaeosphaeria nodorum SN15]
 gi|160707276|gb|EAT82519.2| hypothetical protein SNOG_10184 [Phaeosphaeria nodorum SN15]
          Length = 474

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 110/283 (38%), Gaps = 52/283 (18%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIK 79
           LD +  + +        +K +  G+V V+ + V      I++G ++         +H + 
Sbjct: 70  LDIF-SSEFRDRPAEYYEKAIVEGRVVVNGQPVPSTKTTIKNGDII---------SHTLH 119

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             +   ++  +          +++ED  + V NKPAG+ V       ++    +      
Sbjct: 120 RHEPPCTATPIG---------IVHEDDNLIVINKPAGMPVHPAGRYNFNSIIEILRADRG 170

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECI 198
            G  P   +RLD+ TSGI+ + + R AA+ ++   R R ++K Y + V G  P+ +  C 
Sbjct: 171 YGWNPLPCNRLDRLTSGIMFIGKHRQAAEDMSAQIRTRTVKKEYITRVAGEFPEGEVVCE 230

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--------------------- 237
              L     +G + V            A++ FK +  +                      
Sbjct: 231 KPILQISPKLGLNRVRA------NGKEALTVFKRLAYYPPKDDGKPGEEQDVEEGPDGQP 284

Query: 238 ----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               + +  +   P TGRTHQLRVH   +G PI  D  Y    
Sbjct: 285 WKKLRGYSIVRCFPVTGRTHQLRVHLQFLGHPISNDPIYANQR 327


>gi|229506727|ref|ZP_04396236.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae BX
           330286]
 gi|229510479|ref|ZP_04399959.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae B33]
 gi|229517390|ref|ZP_04406835.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae RC9]
 gi|229605200|ref|YP_002875904.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           MJ-1236]
 gi|298499967|ref|ZP_07009773.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae MAK
           757]
 gi|229345426|gb|EEO10399.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae RC9]
 gi|229352924|gb|EEO17864.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae B33]
 gi|229357078|gb|EEO21996.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae BX
           330286]
 gi|229371686|gb|ACQ62108.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           MJ-1236]
 gi|297541948|gb|EFH77999.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae MAK
           757]
          Length = 570

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 103/240 (42%), Gaps = 21/240 (8%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   +
Sbjct: 348 EGMPLEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-T 406

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I 
Sbjct: 407 QAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEIQ 466

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L            V  Q       A++H++ +    Q    + + PHTGRTHQLRVH 
Sbjct: 467 LPLCGD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHC 521

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            H   +  PIVGD  Y    K         +L+LHA  +   HP   + +     + A  
Sbjct: 522 AHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTFQ--VDADF 570


>gi|153825763|ref|ZP_01978430.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae
           MZO-2]
 gi|149740602|gb|EDM54713.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae
           MZO-2]
          Length = 570

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 103/240 (42%), Gaps = 21/240 (8%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   +
Sbjct: 348 EGMPLEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-T 406

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I 
Sbjct: 407 QAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEIQ 466

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L            V  Q       A++H++ +    Q    + + PHTGRTHQLRVH 
Sbjct: 467 LPLCGD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHC 521

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            H   +  PIVGD  Y    K         +L+LHA  +   HP   + +     + A  
Sbjct: 522 AHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTFQ--VDADF 570


>gi|153816535|ref|ZP_01969203.1| hypothetical protein RUMTOR_02788 [Ruminococcus torques ATCC 27756]
 gi|317502168|ref|ZP_07960343.1| pseudouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331088735|ref|ZP_08337645.1| hypothetical protein HMPREF1025_01228 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145846127|gb|EDK23045.1| hypothetical protein RUMTOR_02788 [Ruminococcus torques ATCC 27756]
 gi|316896433|gb|EFV18529.1| pseudouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330407258|gb|EGG86761.1| hypothetical protein HMPREF1025_01228 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 262

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 63/256 (24%), Positives = 105/256 (41%), Gaps = 49/256 (19%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---------DSKGQKPRLTHR 149
            +++YED +I V +KPAG   Q        ++  LK+ +          S      + HR
Sbjct: 7   PLIIYEDEQIIVCHKPAGTPTQSSHIGTSDMESLLKNHLFSSRKFHRAKSGEPYLAIIHR 66

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LDQ   GILV A+T AAA+ L      +   K Y +++ GIP+ ++  + N+L+K +   
Sbjct: 67  LDQPVEGILVFAKTPAAAKELNRQLTSQEFGKYYLAVISGIPEPQEGSLENYLVKDTRTN 126

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFA------------------------------QK 239
                V  +   GA  A  H++ I+ +                               + 
Sbjct: 127 SS--AVCTKTTPGAKLARLHYRTIETYGAPGNEKFTDSKSTDTPKHTSRNHRQPPLQNES 184

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-------PIQNKLYLHA 292
              +E+   TGR HQ+RV   + G P++GD KY      +  S           +L+L A
Sbjct: 185 SALIEIHLDTGRHHQIRVQMAYFGHPLIGDRKYGKEITDHMNSVQSSTKRFQAGQLHLCA 244

Query: 293 RYMDLPHPEGG-RLQI 307
             +   HP+ G  ++ 
Sbjct: 245 YKLTFHHPKTGKEMEF 260


>gi|255317207|ref|ZP_05358453.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           6276s]
          Length = 303

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 70/315 (22%), Positives = 128/315 (40%), Gaps = 58/315 (18%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPV 70
           +   +  +RL  + +   PH+    + + +R    RV+ +  +F + ++Q G  V +  +
Sbjct: 5   IGTADRQIRLSSFLRTSLPHLPKKTILESVRYHGCRVNGRIERFESYKLQPGDRVSLQII 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            ++                           LL+ED  + ++NKPA              +
Sbjct: 65  EHS------------------------SPQLLWEDEHLCIYNKPA----------KQTSE 90

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                          L HRLD++TSG ++ A+   A+  +T+ F+ R I K Y +LV+G 
Sbjct: 91  DLAHQL------NVHLVHRLDRDTSGCILFAKHAKASSLITQLFKNRGIDKRYIALVFGQ 144

Query: 191 PKNKKECIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           P+ +   I  +       IG        QN       I+ ++++  +  K+  L  +P T
Sbjct: 145 PRQESGIITTYTAPCYRRIGAVLFGNTDQNS--GKITITKWEILTRYP-KYTLLLCRPVT 201

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT 308
           GRTHQ+R+H   +G PIVGD  Y    +         +  LHA  +    P    +++++
Sbjct: 202 GRTHQIRLHMKTIGHPIVGDVDYGNQEQPKNVV----RTLLHAASLAFISPFSNEKIEVS 257

Query: 309 A------PLP--AHM 315
           +      P P  A  
Sbjct: 258 SLTPSQDPYPFYADF 272


>gi|255310907|ref|ZP_05353477.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           6276]
          Length = 303

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 67/304 (22%), Positives = 128/304 (42%), Gaps = 48/304 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPV 70
           +   +  +RL  + +   PH+    + + +R    RV+ +  +F + ++Q G  V +  +
Sbjct: 5   IGTADRQIRLSSFLRTSLPHLPKKTILESVRYHGCRVNGRIERFESYKLQPGDRVSLQII 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            ++                           LL+ED  + ++NKPA              +
Sbjct: 65  EHS------------------------SPQLLWEDEHLCIYNKPA----------KQTSE 90

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                          L HRLD++TSG ++ A+   A+  +T+ F+ R I K Y +LV+G 
Sbjct: 91  DLAHQL------NVHLVHRLDRDTSGCILFAKHAKASSLITQLFKNRGIDKRYIALVFGQ 144

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P+ +   I  +     H  G  V     ++      I+ ++++  +  K+  L  +P TG
Sbjct: 145 PRQESGIITTYTAPCYHRIG-AVLFGNTDQNSGKITITKWEILTRYP-KYTLLLCRPVTG 202

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           RTHQ+R+H   +G PIVGD  Y    +         +  LHA  +    P    ++++++
Sbjct: 203 RTHQIRLHMKTIGHPIVGDVDYGNQEQPKNVV----RTLLHAASLAFISPFSNEKIEVSS 258

Query: 310 PLPA 313
             P+
Sbjct: 259 LTPS 262


>gi|148656758|ref|YP_001276963.1| pseudouridine synthase [Roseiflexus sp. RS-1]
 gi|148568868|gb|ABQ91013.1| pseudouridine synthase [Roseiflexus sp. RS-1]
          Length = 299

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 72/288 (25%), Positives = 112/288 (38%), Gaps = 36/288 (12%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++  G V VD  R            VR P +    +  I  Q+  D    + +       
Sbjct: 31  LIARGGVWVDGVR------------VRDPGMRLPADATIVVQRPPD---GIYREPVVTPE 75

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHID----GFLKSWVDSKGQKPRLTHRLDQETS 155
           ++LYED  +   NKP    V+     A            +  +       L HRLD++TS
Sbjct: 76  MILYEDDDLIALNKPIDTYVEATPWDAEGHLRAALARFLALRNGTAPPLHLAHRLDRDTS 135

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++++T      L   FR     K Y ++  G+P   +  I     +    G   +  
Sbjct: 136 GVLLISKTPDVNAALQRVFRDGAAHKTYLAICAGLPSFDEIEIETGHGR----GRGGMFR 191

Query: 216 VKQNEKGANY---------AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           V   E                + F+V+         +   P TGRTHQ+R+H   +G P+
Sbjct: 192 VFPPEAIGRTLPQGGTVKSMRTRFRVVRRL-DDAALVRAWPLTGRTHQIRLHLAFLGHPL 250

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPA 313
           +GD KY        T    +  +LHA  ++LPHP+ G  L I AP P 
Sbjct: 251 IGDSKYGGLSIWRGTPAFHH--HLHAERLELPHPQSGAPLVIVAPAPE 296


>gi|113931514|ref|NP_001039205.1| RNA pseudouridylate synthase domain-containing protein 4 [Xenopus
           (Silurana) tropicalis]
 gi|123892314|sp|Q28C59|RUSD4_XENTR RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 4
 gi|89268931|emb|CAJ83700.1| RNA pseudouridylate synthase domain containing 4 [Xenopus
           (Silurana) tropicalis]
          Length = 324

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 72/265 (27%), Positives = 122/265 (46%), Gaps = 38/265 (14%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQ 152
           LKS ++ ED ++ + NKP G+ V GG  +   +   L    K     K +  +L HRLD+
Sbjct: 47  LKSQVVREDPELVLVNKPHGLPVHGGPTVERSVASLLPALAKHHFGWKAEPLKLCHRLDR 106

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +T+G L++ART  AA+ + ++ R R + ++YW+L  G P  ++  +   +++K   G   
Sbjct: 107 DTTGALILARTTEAAERVQQALREREVHRVYWALCLGTPSPREGILDIPIMEKETSGPQK 166

Query: 213 VHVV----------------KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + +                 +  + A+ A++ ++ +   A     +E+ P TG  HQLR
Sbjct: 167 HYKMALSPRFRVSEEGAVERVRVPRSAHEAVTRYRTLGA-ASGASLVELHPITGVKHQLR 225

Query: 257 VHAL-HMGCPIVGDHKYCANFKGNFTSPIQN---------------KLYLHARYMDLPHP 300
           VH    + CPI+GDHKY    +     P  +                L+LHA  + LP  
Sbjct: 226 VHLALGLNCPILGDHKYSHWGRLAPQKPPDSVLRALGLTVPQARTLSLHLHAVQLTLPSS 285

Query: 301 EGG-RLQITAPLPAHMVKTWDSLGF 324
           +G   + +  PLP    KT   L  
Sbjct: 286 DGSTPIVLQCPLPYTFRKTLRKLRI 310


>gi|229514608|ref|ZP_04404069.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TMA 21]
 gi|229348588|gb|EEO13546.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TMA 21]
          Length = 570

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 103/240 (42%), Gaps = 21/240 (8%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   +
Sbjct: 348 EGMPLEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-T 406

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I 
Sbjct: 407 QAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEIQ 466

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L            V  Q       A++H++ +    Q    + + PHTGRTHQLRVH 
Sbjct: 467 LPLCGD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHC 521

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            H   +  PIVGD  Y    K         +L+LHA  +   HP   + +     + A  
Sbjct: 522 AHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTFQ--VDADF 570


>gi|262369254|ref|ZP_06062582.1| pseudouridylate synthase [Acinetobacter johnsonii SH046]
 gi|262315322|gb|EEY96361.1| pseudouridylate synthase [Acinetobacter johnsonii SH046]
          Length = 227

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 57/217 (26%), Positives = 96/217 (44%), Gaps = 12/217 (5%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           N          +++YED  + V  KPAG+    G    +    +L+  V ++    ++TH
Sbjct: 12  NFIYTPPQEDLVIVYEDDDLVVIEKPAGLLSVPGRLPEHQDSAYLR--VLAQYPHAKITH 69

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSGIL+ A+ R A   +++ F+ R + K Y +LV G    +       +    + 
Sbjct: 70  RLDMATSGILMFAKHRDAEVAVSKMFQARTVDKHYIALVQGQLDAEGSVEVPLITDWENR 129

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               VH      +    A + ++ +    +     + + P TGR+HQLRVH  ++G PI 
Sbjct: 130 PRQIVHF-----ELGKPAKTLYQALSYDIETDITRVLLTPITGRSHQLRVHMQYIGHPIT 184

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GD  Y        T     ++ LHA ++    P  G+
Sbjct: 185 GDKLYHPEP----TRSPLKRMALHASFLAFQQPLSGK 217


>gi|227538361|ref|ZP_03968410.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
 gi|227241876|gb|EEI91891.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
          Length = 230

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 114/231 (49%), Gaps = 14/231 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP----RLTHRLDQE 153
              ++YED+ +   NK AG  VQ        +D  +K +++ K +KP     + HRLD+ 
Sbjct: 7   DKDVIYEDNHLIAINKRAGDIVQVDDSGDKSLDMMVKEYLERKYEKPNAFIGVIHRLDRP 66

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
            SG++V A+T      + + F  R ++K Y ++V   P+     + NWL++         
Sbjct: 67  VSGLIVFAKTSKGLDRMNKLFHDRDVEKSYLAVVRNKPEQMSAKLQNWLVRDRK--KMIT 124

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               +  KG++YA   ++VI    + +  L ++P TGRTHQ+RV    MGCPIVGD+KY 
Sbjct: 125 KAYNREIKGSSYAELDYEVIGEL-EGYYLLHVKPKTGRTHQIRVQLSTMGCPIVGDNKYG 183

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH-MVKTWDSL 322
                     ++  + LH+R +   HP     +++ A LP     + ++ L
Sbjct: 184 YPRGS-----LRRSICLHSRSLSFVHPVKDEPMKLVAGLPVDGFWEKFNVL 229


>gi|300774195|ref|ZP_07084062.1| ribosomal large subunit pseudouridine synthase [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|300758874|gb|EFK55703.1| ribosomal large subunit pseudouridine synthase [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 228

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 114/231 (49%), Gaps = 14/231 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP----RLTHRLDQE 153
              ++YED+ +   NK AG  VQ        +D  +K +++ K +KP     + HRLD+ 
Sbjct: 5   DKDVIYEDNHLIAINKRAGDIVQVDDSGDKSLDMMVKEYLERKYEKPNAFIGVIHRLDRP 64

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
            SG++V A+T      + + F  R ++K Y ++V   P+     + NWL++         
Sbjct: 65  VSGLIVFAKTSKGLDRMNKLFHDRDVEKSYLAVVRNKPEQMSAKLQNWLVRDRK--KMIT 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               +  KG++YA   ++VI    + +  L ++P TGRTHQ+R+    MGCPIVGD+KY 
Sbjct: 123 KAYNREIKGSSYAELDYEVIGEL-EGYYLLHVKPKTGRTHQIRIQLSTMGCPIVGDNKYG 181

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH-MVKTWDSL 322
                     ++  + LH+R +   HP     ++I A LP     + ++ L
Sbjct: 182 YPRGS-----LRRSICLHSRSLSFVHPVKDEPMKIVAGLPVDGFWEKFNVL 227


>gi|119478011|ref|ZP_01618111.1| 23S rRNA pseudouridylate 746 synthase [marine gamma proteobacterium
           HTCC2143]
 gi|119448924|gb|EAW30166.1| 23S rRNA pseudouridylate 746 synthase [marine gamma proteobacterium
           HTCC2143]
          Length = 221

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 57/207 (27%), Positives = 93/207 (44%), Gaps = 10/207 (4%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +L+ D  + + NKPAG+    G   A      L + V  +    R+ HRLD +TSGI
Sbjct: 14  DVEILFTDDDLLLVNKPAGLLSVPGRHPAN--KDCLITRVQRQYADARIVHRLDMDTSGI 71

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+A +  + + L++ F  R+I K Y + V+G   +    I   LL             K
Sbjct: 72  MVLALSADSHRALSQLFAERKIIKEYEANVYGTIIDDHRLIDLPLLCD----WPNRPRQK 127

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +      A +  + +      +  + ++P TGR+HQLRVH   +G PI+G   Y     
Sbjct: 128 VDFHHGKNAQTWVERVSQHPDGWTRVLLKPVTGRSHQLRVHLAEIGHPILGCEFYAHQRA 187

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +      ++L LHA  ++  HP  G 
Sbjct: 188 VSMA----DRLQLHATKLEFCHPNSGE 210


>gi|121716811|ref|XP_001275916.1| DRAP deaminase (Rib2), putative [Aspergillus clavatus NRRL 1]
 gi|119404073|gb|EAW14490.1| DRAP deaminase (Rib2), putative [Aspergillus clavatus NRRL 1]
          Length = 538

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 58/281 (20%), Positives = 108/281 (38%), Gaps = 47/281 (16%)

Query: 22  DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           D +    +         + L  G+V V+ K    N  I++G+++      +       E 
Sbjct: 67  DIFVSE-FRDRPAEYYVQALTDGRVTVNGKTAAPNTVIKNGEIISHTLHRHEPPVTGHE- 124

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
                              +++ED+ I V +KPAG+ V       YH +  ++     +G
Sbjct: 125 -----------------IGVIHEDNDILVIDKPAGVPVHAAG--RYHYNSIVEILRSQRG 165

Query: 142 QK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           Q+  PR  +RLD+ TSG++ +A+    A  +T   + R +QK Y + V G   +      
Sbjct: 166 QEFVPRPCNRLDRLTSGVMFIAKHPQGADMITRKLKQRTVQKEYIARVKGRFPDGVVVCD 225

Query: 200 NWLL-KKSHIGGDYVHVVKQNEKGANYAISHF-----------------------KVIDC 235
             ++     +G + V    ++ K     ++++                        ++  
Sbjct: 226 QPIMSVSPKLGLNRVRATGKDAKTKFRRLAYYPAASPAPETDEVTASGERPATPPPLLAN 285

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             + +  +   P TGRTHQ+RVH   +G PI  D  Y    
Sbjct: 286 EDEGYSIVHCLPLTGRTHQIRVHLQFLGHPITNDPIYSNRR 326


>gi|108758087|ref|YP_634154.1| ribosomal large subunit pseudouridine synthase A [Myxococcus
           xanthus DK 1622]
 gi|108461967|gb|ABF87152.1| ribosomal large subunit pseudouridine synthase A [Myxococcus
           xanthus DK 1622]
          Length = 559

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 62/249 (24%), Positives = 98/249 (39%), Gaps = 21/249 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L +++    +                 +++ED  + V  KP G+       ++   
Sbjct: 325 CGPLLPYMLDGLPVSAPRPFTVPVLPSRGLDIVFEDEWLVVVEKPEGLLSVPAKDVSVE- 383

Query: 130 DGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           D  L        +     L HRLD +TSG+LV A+       L   F  R + K Y + V
Sbjct: 384 DSVLARLRARAPEAAGTMLAHRLDLDTSGLLVAAKDARTYAALQRQFAGREVHKRYAAWV 443

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  + ++  I   +          +H    +      A++ + V++  +     + + P
Sbjct: 444 EGNVQGERGTIDFPMRVDLDDRPRQIH----DPVHGKPAVTEWHVLER-SHGRTKVALFP 498

Query: 248 HTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
            TGRTHQLRVHA H   +G PIVGD  Y              +L+LHA  +   HP  G 
Sbjct: 499 LTGRTHQLRVHAAHPLGLGAPIVGDRLYGHPGP---------RLHLHAEALSFQHPVTGQ 549

Query: 304 RLQITAPLP 312
           RL +  P P
Sbjct: 550 RLTLERPAP 558


>gi|297579761|ref|ZP_06941688.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae
           RC385]
 gi|297535407|gb|EFH74241.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae
           RC385]
          Length = 570

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 103/240 (42%), Gaps = 21/240 (8%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   +
Sbjct: 348 EGMPLEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-T 406

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I 
Sbjct: 407 QAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEIQ 466

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L            V  Q       A++H++ +    Q    + + PHTGRTHQLRVH 
Sbjct: 467 LPLCGD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHC 521

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            H   +  PIVGD  Y    K         +L+LHA  +   HP   + +     + A  
Sbjct: 522 AHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTFQ--VDADF 570


>gi|269124164|ref|YP_003306741.1| pseudouridine synthase, RluA family [Streptobacillus moniliformis
           DSM 12112]
 gi|268315490|gb|ACZ01864.1| pseudouridine synthase, RluA family [Streptobacillus moniliformis
           DSM 12112]
          Length = 289

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 63/304 (20%), Positives = 124/304 (40%), Gaps = 38/304 (12%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           ++ +  + +         LRS +V +D K+++   ++         P I  L  I KE+ 
Sbjct: 17  QYLREFHNYSGRS-----LRSIEVFLDNKQIRTTTKL---------PKIGILTVIEKEK- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSWVDSK 140
                         +   ++YED  + + NK   +              +G +  +++  
Sbjct: 62  ------GSNIVPIKMNLDIVYEDDDLLIVNKEPYLLTHPTLKKVDKTLANGIVYHFIEKY 115

Query: 141 GQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +   PR   RLD  TSG++++A+   +   +        + K Y +L   + + ++  +
Sbjct: 116 NKNLVPRFISRLDMNTSGLIMIAKNSFSQSFIQSGKAN--VTKKYLALAENMFEKEEIIV 173

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRV 257
              + K    G +   ++        YA + FK+I  +       +E +  TGRTHQ+RV
Sbjct: 174 EEKIYKD---GDELARIIDDR---GQYAKTKFKLIKNYPHLDISLIECELFTGRTHQIRV 227

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMV 316
           H  H+G PI+GD  Y  +   +  + I  +  LH+  +   HP  G R+ +  P+   M+
Sbjct: 228 HLKHLGHPIIGDSLYNPD---SIFNKIAKRQMLHSYKLSFTHPSSGKRIDVEIPIYHDML 284

Query: 317 KTWD 320
               
Sbjct: 285 DILK 288


>gi|124009089|ref|ZP_01693772.1| ribosomal large subunit pseudouridine synthase C [Microscilla
           marina ATCC 23134]
 gi|123985303|gb|EAY25223.1| ribosomal large subunit pseudouridine synthase C [Microscilla
           marina ATCC 23134]
          Length = 238

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 67/241 (27%), Positives = 111/241 (46%), Gaps = 27/241 (11%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
            K ++++ED    + NKP  +S      S    +I G  K +++S     ++ HRLD+ET
Sbjct: 6   FKDLIVFEDEDYLIINKPPHMSTLDDRASEGKDNIIGMAKDYLES----AQVCHRLDKET 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGIL +A+   A +HL   F  R++ K+Y +++ GI + K   +   +L           
Sbjct: 62  SGILAIAKNPEAYRHLAIQFEKRQVNKVYHAVIGGIQEYKDTLVDRAILPN------RTG 115

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            VK + KG   A ++FK +  + +    +E +P TGR HQ+R+H   +G PIV D +Y  
Sbjct: 116 TVKIDLKG-KPAQTYFKTLKIY-KAHTLIEARPVTGRMHQIRIHLAVLGSPIVQDEQYGG 173

Query: 275 NF-------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
                          K     P+ +++ LHA  +      G    + AP P  M    + 
Sbjct: 174 KPVFLSQIKRHFNLKKYEEERPLISRVALHAHALHFKLLNGETQIVEAPYPKDMRALVNQ 233

Query: 322 L 322
           L
Sbjct: 234 L 234


>gi|259483290|tpe|CBF78558.1| TPA: DRAP deaminase (Rib2), putative (AFU_orthologue; AFUA_2G16360)
           [Aspergillus nidulans FGSC A4]
          Length = 572

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 61/298 (20%), Positives = 109/298 (36%), Gaps = 68/298 (22%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +K L SG V V+ K    +  +++G+V+              E  +  + +         
Sbjct: 82  KKALESGNVCVNGKPAGPHTVLKNGEVISHTLHR-------HEPPVTGNEIG-------- 126

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETS 155
              +++E   + V +KPAG+ V   S   YH +  ++      G    PR  +RLD+ TS
Sbjct: 127 ---IIHETDDLLVIDKPAGVPVH--STGRYHYNSVMEILRIQNGGAYVPRPCNRLDRLTS 181

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-KKSHIGGDYVH 214
           G++ V +T   A  +T   + R +QK Y + V G   +    +   ++     +G + V 
Sbjct: 182 GVMFVGKTAQGADRMTVKLKERTVQKEYVARVKGRFPDGVVVVDQPIMSVSPKVGLNRVR 241

Query: 215 VVKQNEKGANYAISHFKVIDCF----------------------------AQKFCWLEMQ 246
                      A + F+ +  +                            ++ +  +   
Sbjct: 242 A------TGKEAKTKFRRLAYYPPPSPTTSTSDEGENARPATPPPSYVNESEGYSIVHCF 295

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANF-----------KGNFTSPIQNKLYLHAR 293
           P TGRTHQ+RVH   +G PI  D  Y                 +    I ++L    R
Sbjct: 296 PLTGRTHQIRVHLQFLGHPISNDPIYSNRRVFGPDLGKNDSSADLDEEIIDRLMAMGR 353


>gi|307293297|ref|ZP_07573143.1| pseudouridine synthase [Sphingobium chlorophenolicum L-1]
 gi|306881363|gb|EFN12579.1| pseudouridine synthase [Sphingobium chlorophenolicum L-1]
          Length = 225

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 63/224 (28%), Positives = 101/224 (45%), Gaps = 14/224 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L   +L+ D +  + +KPAG+ V      +  ++  L S      + P   HRLD++TS
Sbjct: 3   LLHDRVLFIDGEAIILDKPAGLPVDAPRDGSLALENHLSSLTFGFQRWPLPVHRLDRDTS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L++AR   A +  + +F    + K Y ++V G+P  +   I   L K S     +  +
Sbjct: 63  GCLLLARNPKAHKRFSAAFEAGTVAKRYVAVVDGVPAEESSVIELALKKISTQAQGWRMI 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCA 274
                +    AI+ ++ I         +   P TGRTHQ+R HALH +G  IVGD  Y +
Sbjct: 123 ---PARAGKAAITEWRKI-AEKDGRALVVFTPRTGRTHQIRTHALHGLGFGIVGDPVYGS 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                        + LH+R++ +P  E    + TAPLP      
Sbjct: 179 ---------GDGPMLLHSRFLSIPRGEKAPAEATAPLPETFAAA 213


>gi|242242285|ref|ZP_04796730.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242234241|gb|EES36553.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 284

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 65/284 (22%), Positives = 120/284 (42%), Gaps = 44/284 (15%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQK 82
           + KN     +   L  I  +G + ++   V   + +  G  + +  P      ++I   K
Sbjct: 16  FLKNQ--DYSKRTLSAIKLNGALLLNGSPVTVRHVMNKGDRLEVHFPCETPSENLIPYDK 73

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVD 138
            L+               ++YED+ + + NKP    +Q  +    H  G L     ++  
Sbjct: 74  ELE---------------VIYEDAYLIIVNKPQ---MQNCAPSREHPHGSLVEQVLAYYT 115

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            KG+K  P +  RLD+ TSG++V A+        ++    +     Y +L +G       
Sbjct: 116 KKGEKINPHIVTRLDRNTSGLVVFAKFGHVHHLFSKVKFKKE----YVALAYGH-TQSSG 170

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   + ++S    D +   + N+KG  YAI+ ++ +    +     +++  TGRTHQ+R
Sbjct: 171 VIEAPIARRS----DSIIKREVNDKG-KYAITVYQRL-MQNETASLCKVKLLTGRTHQIR 224

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           VH  ++G P++GD  Y  N       P  +   LH   ++  HP
Sbjct: 225 VHFEYIGHPLIGDDLYGGN------HPCVHGQALHCCSVEFIHP 262


>gi|220917183|ref|YP_002492487.1| pseudouridine synthase [Anaeromyxobacter dehalogenans 2CP-1]
 gi|219955037|gb|ACL65421.1| pseudouridine synthase [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 241

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 106/235 (45%), Gaps = 16/235 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +L+ED+ +   +KPAG  V  G          L+  ++++  +  + HRLD+ TSG+
Sbjct: 8   PVTVLHEDAHLLAVDKPAGRLVIPGRDGGEPS---LREELEARFGRLWVVHRLDRNTSGV 64

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV+ART AA + L  +F     +K Y +LV G+P  ++          +      +    
Sbjct: 65  LVLARTAAAHRTLNLAFDRGEPRKRYLALVRGVPPAEQRIEVAI----APGRKGRMRAAA 120

Query: 218 QNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            ++     + +  + +D F +          +E  P TGRTHQ+RVH    G P+  D  
Sbjct: 121 PDDPRGKASATVVRRLDAFPRHPLGGGPLALVEALPETGRTHQIRVHLAAAGTPLAVDPA 180

Query: 272 YC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
           Y   A   G     +  +  LHA  + L HP  GR L + APLPA +  T   L 
Sbjct: 181 YGDAAPLLGPGGEAVLARTPLHAARLALRHPADGRELVLEAPLPADLAGTLALLR 235


>gi|114561701|ref|YP_749214.1| pseudouridylate synthase [Shewanella frigidimarina NCIMB 400]
 gi|114332994|gb|ABI70376.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           frigidimarina NCIMB 400]
          Length = 225

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 61/214 (28%), Positives = 103/214 (48%), Gaps = 12/214 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y+D  I V NKP+G+    G    YH    + S V ++    ++ HRLD  TSG++
Sbjct: 14  LDIVYQDKDILVANKPSGLLSVPGREAIYHDS--IYSRVLAEHPNAQIVHRLDMATSGVI 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VVA  R+A + L   FR R   K Y++ V G  K+    +   L+             K 
Sbjct: 72  VVALRRSAERELKRQFRDRETAKTYFARVAGHMKSNISKVDLPLICDWPNRPK----QKV 127

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      +++  +V+  +  K   +++ P TGR+HQLRVH + +G PI+GD  Y      
Sbjct: 128 DHTVGKPSVTLVEVV-SYGAKSTLVKLTPITGRSHQLRVHMMALGHPILGDGFYADPLAK 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +    +  +L LHA  + + HP   + +   +P+
Sbjct: 187 S----LSPRLLLHAAALSITHPYSQQVMHFESPV 216


>gi|229527911|ref|ZP_04417302.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           12129(1)]
 gi|229334273|gb|EEN99758.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           12129(1)]
          Length = 570

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 103/240 (42%), Gaps = 21/240 (8%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   +
Sbjct: 348 EGMPLEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-T 406

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I 
Sbjct: 407 QAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEIQ 466

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L            V  Q       A++H++ +    Q    + + PHTGRTHQLRVH 
Sbjct: 467 LPLCGD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHC 521

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            H   +  PIVGD  Y    K         +L+LHA  +   HP   + +     + A  
Sbjct: 522 AHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTFQ--VDADF 570


>gi|159027410|emb|CAO86894.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 501

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 65/214 (30%), Positives = 105/214 (49%), Gaps = 17/214 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  I   NKPAG+    G          + +    +G+     HRLD+ETSGIL++
Sbjct: 302 IIYEDEGIIAINKPAGLLSVAGRYQD--SQDAVVNRFRRQGKNLIPVHRLDRETSGILLL 359

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++    + L++ F+ R ++KIY +++  I + +   I   L         Y  V  Q  
Sbjct: 360 AKSLDIYRCLSQQFQRREVEKIYEAILSEIIERESGIIDLPLWGN-PQNRPYQTVDWQRG 418

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA-LHMGCPIVGDHKYCANFKGN 279
           K +    ++FKV+      +  LE  P+TGRTHQ+RVH+   +G  I+GD  Y       
Sbjct: 419 KASQ---TYFKVVGKEG-NYSRLEFIPYTGRTHQIRVHSQQGLGIGILGDFLYNGKQ--- 471

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                 ++LYLHA+ +   HP+   +L +  P P
Sbjct: 472 -----SDRLYLHAKQLSFRHPQTENKLDLIIPTP 500


>gi|71278963|ref|YP_270317.1| tRNA pseudouridine synthase C [Colwellia psychrerythraea 34H]
 gi|71144703|gb|AAZ25176.1| tRNA pseudouridine synthase C [Colwellia psychrerythraea 34H]
          Length = 304

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 117/299 (39%), Gaps = 61/299 (20%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ +++     +     +LY+D  +   +KPAG+ V         I   L+   D  GQ 
Sbjct: 6   LEVAISEDIEPEKPVLDILYQDEYMVAVDKPAGLFVHRSYMDKDEIYFALQLVRDQVGQY 65

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ----------------------- 180
               HRLD+ TSG+L+ A T+  A  L+E+F  +  Q                       
Sbjct: 66  VYPVHRLDRPTSGVLLFALTKDVATKLSEAFANKSSQAEFKSDTELEGKVHDKTQTGQQG 125

Query: 181 ----------------------KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
                                 K Y++L  G      + I + L +K    GD       
Sbjct: 126 QQSMTEGLTTDKNIDGSDLAMVKTYYALARGHLAVPVDLIDHPLKEKLDKLGDK---NVS 182

Query: 219 NEKGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +K A  A S+++V    +           ++  +E++P TGR HQ+R H  H+  PI+G
Sbjct: 183 RDKPAQSAQSYYQVKQQASLPIKVGKFDSVRYSLIEVRPITGRRHQIRRHLAHLRHPILG 242

Query: 269 DHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGF 324
           D  Y  N +  F        +L L A+ ++  HP    R++I+AP      + + +  +
Sbjct: 243 DINYGDNKQNPFFIEHFGFKRLMLIAKSLEFNHPINNDRIKISAPFDEQWQQVFTTFEW 301


>gi|328914578|gb|AEB55411.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           psittaci 6BC]
          Length = 279

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 123/296 (41%), Gaps = 48/296 (16%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINAL 74
               RL  + ++  P      +   +R    RV+ +  +F + R+Q G  V +       
Sbjct: 13  HHEERLSSFLRSRLPDHKKHIILDSIRYHGCRVNGRLERFESYRVQPGDRVTLTVQTR-- 70

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                 L+  +L+ED    ++NKP+       +     I G   
Sbjct: 71  ----------------------LEPQILWEDEHYCIYNKPS----HTSTEDLAKITGL-- 102

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                      + HRLD++T+G ++ A+  +AA  L+E F+ R+I K Y +LV+G PK  
Sbjct: 103 ----------NIVHRLDRDTTGCILFAKHASAAHALSELFKKRKIHKQYTALVFGHPKKS 152

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              + ++   KS   G  +    Q +      I+ + ++  + Q +  +  +P TGRTHQ
Sbjct: 153 SGTLISYTAPKSRRCGAVIFGNTQ-KNHGKLTITQWSILCAYKQ-YTLMRCEPITGRTHQ 210

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           +R+H   +G PIVGD  Y    +         +  LHA  +    P    ++++TA
Sbjct: 211 IRLHMHTLGHPIVGDVDYGRKEQPKHVF----RPLLHAHALTFTSPFSKEKVEVTA 262


>gi|266622468|ref|ZP_06115403.1| ribosomal large subunit pseudouridine synthase family protein
           [Clostridium hathewayi DSM 13479]
 gi|288865823|gb|EFC98121.1| ribosomal large subunit pseudouridine synthase family protein
           [Clostridium hathewayi DSM 13479]
          Length = 239

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 61/220 (27%), Positives = 96/220 (43%), Gaps = 14/220 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQ 152
           K  +LYED +I V  KPAGI  Q        +   +K  ++S   K       + HRLD+
Sbjct: 4   KMNILYEDDQIIVVEKPAGIESQSSRTFEPDMVSEVKKHINSLSPKKGDPYVGVIHRLDK 63

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              GILV  +T+ AA  L++     + +K Y ++V G P        ++L K      + 
Sbjct: 64  PVGGILVFGKTKEAAGALSKQISEHQTEKRYLAVVCGKPVENFGTYVDYLWKDGK--NNI 121

Query: 213 VHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             +V +    A  A   ++V+   +      C +E+   TGR HQ+RV     G P++GD
Sbjct: 122 SKIVDKGITDAKRAELSYRVLAELEGEGGPLCLMEIDLKTGRHHQIRVQLSGHGTPLLGD 181

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
            KY  +         Q  + L A  +   HP    R++ T
Sbjct: 182 LKYNPDGPKV---TGQRNVALCAWKLSFTHPGNKKRMKFT 218


>gi|270285168|ref|ZP_06194562.1| pseudouridine synthetase family protein [Chlamydia muridarum Nigg]
 gi|301336563|ref|ZP_07224765.1| pseudouridine synthetase family protein [Chlamydia muridarum
           MopnTet14]
          Length = 274

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 70/306 (22%), Positives = 126/306 (41%), Gaps = 55/306 (17%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHII 78
           RL  + +   PH+    + + +R    RV+ +  +F + ++  G  V +  +  +     
Sbjct: 13  RLACFLRTSLPHLPKKTILESIRYHGCRVNGRIERFESYKLHPGDRVCLQIIERS----- 67

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                               + LL+ED  + ++NKPA                 L   + 
Sbjct: 68  -------------------SAQLLWEDEHLCIYNKPA-----------KQTSEALACQL- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                  L HRLD++TSG ++ A+   A   +T+ F+ R+I K Y +LV+G P+ +   I
Sbjct: 97  ----HVHLVHRLDRDTSGCILFAKHEKAITPITQLFKTRQIDKRYIALVFGHPRQQSGII 152

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +     H     V     +EK     I+ ++V+  ++ K+  L  +P TGRTHQ+R+H
Sbjct: 153 TTY-TAPCHRRIGAVLFGNTDEKLGKKTITEWEVLTHYS-KYALLLCRPITGRTHQIRLH 210

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA-------P 310
              +G PIVGD  Y    +         +  LHA  +    P    ++++++       P
Sbjct: 211 MKTIGHPIVGDIDYGNKEQPKHVV----RPLLHANSLCFISPFSKKKIEVSSLTPDTLYP 266

Query: 311 LPAHMV 316
             A   
Sbjct: 267 FDADFK 272


>gi|227811730|ref|YP_002811740.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           M66-2]
 gi|254850369|ref|ZP_05239719.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae
           MO10]
 gi|227010872|gb|ACP07083.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           M66-2]
 gi|227014735|gb|ACP10944.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|254846074|gb|EET24488.1| ribosomal large chain pseudouridine synthase A [Vibrio cholerae
           MO10]
          Length = 559

 Score =  158 bits (399), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 103/240 (42%), Gaps = 21/240 (8%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   +
Sbjct: 337 EGMPLEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-T 395

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I 
Sbjct: 396 QAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEIQ 455

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L            V  Q       A++H++ +    Q    + + PHTGRTHQLRVH 
Sbjct: 456 LPLCGD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHC 510

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            H   +  PIVGD  Y    K         +L+LHA  +   HP   + +     + A  
Sbjct: 511 AHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTFQ--VDADF 559


>gi|91792050|ref|YP_561701.1| pseudouridine synthase [Shewanella denitrificans OS217]
 gi|91714052|gb|ABE53978.1| pseudouridine synthase [Shewanella denitrificans OS217]
          Length = 593

 Score =  158 bits (399), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 70/254 (27%), Positives = 118/254 (46%), Gaps = 26/254 (10%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA-GISVQGGSGIAYH 128
               L+H+++  K+ D +  L   +D  +  ++Y+D  + V +KPA  +SV G +     
Sbjct: 358 CHPILSHMLEGLKV-DPNPLLENPADDKQITVIYQDEHLLVISKPAEFLSVPGKNISDSV 416

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               ++ +  + G  P + HRLD  TSG++V+A  + A + L + F +R + K Y +L+ 
Sbjct: 417 HTRIIRDFPSASG--PIIVHRLDMSTSGLMVIALNKEAHESLQKQFILRTVTKRYIALLD 474

Query: 189 GIPKNK---KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           G+  N+    E I +  L+          V  ++      A + +++ID   Q    + +
Sbjct: 475 GLLPNRTAGDEGIISLPLRGDLDDRPRQLVCHEH---GKSAETRWQIIDIQ-QGRTKVFL 530

Query: 246 QPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            P TGRTHQLRVH  H   +  PIVGD  Y             ++L+LHA  +   HP+ 
Sbjct: 531 YPKTGRTHQLRVHCAHSQGLHLPIVGDDHYGVR---------ASRLHLHAESLSFTHPQS 581

Query: 303 GR-LQITAPLPAHM 315
              L     L A  
Sbjct: 582 REALHFQ--LDADF 593


>gi|327485332|gb|AEA79738.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio cholerae
           LMA3894-4]
          Length = 559

 Score =  158 bits (399), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 103/240 (42%), Gaps = 21/240 (8%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   +
Sbjct: 337 EGMPLEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-T 395

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I 
Sbjct: 396 QAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEIQ 455

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L            V  Q       A++H++ +    Q    + + PHTGRTHQLRVH 
Sbjct: 456 LPLCGD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHC 510

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            H   +  PIVGD  Y    K         +L+LHA  +   HP   + +     + A  
Sbjct: 511 AHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTFQ--VDADF 559


>gi|149277745|ref|ZP_01883885.1| pseudouridylate synthase [Pedobacter sp. BAL39]
 gi|149231433|gb|EDM36812.1| pseudouridylate synthase [Pedobacter sp. BAL39]
          Length = 240

 Score =  158 bits (399), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 60/239 (25%), Positives = 99/239 (41%), Gaps = 22/239 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
            K I+L+E+    V NKP  ++     G +  ++  +           ++ HRLD+ETSG
Sbjct: 6   FKDIILFENDDYIVVNKPPFVASLDERGGSGEVN--ILRLAKQYSPDAQVCHRLDKETSG 63

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            +++A+T  A +++   F  R+I K Y ++V G        I   +L   +        V
Sbjct: 64  AIIIAKTPEAYRNVAIQFEKRKINKTYHAIVDGQFSFNDLFIDLPILNDGNKS------V 117

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             + K    A + F  I  + + +  +E +P TGR HQ+R+H       I GD  Y    
Sbjct: 118 TIDRKEGKRAETIFNSIKNY-RHYTLVECKPITGRMHQIRIHLATQRAAIAGDDMYRGKP 176

Query: 277 -------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                        K +   PI  +  LHAR++     +G  + I AP P         L
Sbjct: 177 VYLSSMKKGYRISKDDEEQPIMKRFALHARHLVFKGTDGQDIVIEAPYPKDFATLLKLL 235


>gi|256852163|ref|ZP_05557549.1| ribosomal protein large subunit [Lactobacillus jensenii 27-2-CHN]
 gi|260661804|ref|ZP_05862715.1| ribosomal protein large subunit [Lactobacillus jensenii 115-3-CHN]
 gi|282933665|ref|ZP_06339024.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 208-1]
 gi|297205672|ref|ZP_06923068.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii JV-V16]
 gi|256615209|gb|EEU20400.1| ribosomal protein large subunit [Lactobacillus jensenii 27-2-CHN]
 gi|260547551|gb|EEX23530.1| ribosomal protein large subunit [Lactobacillus jensenii 115-3-CHN]
 gi|281302198|gb|EFA94441.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 208-1]
 gi|297150250|gb|EFH30547.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii JV-V16]
          Length = 287

 Score =  158 bits (399), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 107/270 (39%), Gaps = 30/270 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
             ++ ++     FN  +       I      L H+  +Q  +  S +L          ++
Sbjct: 38  EKKILINGNYRNFNELVFPNDEYSIM-----LTHVENQQHSITPSGHL--------PTII 84

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  I V NKP+           +  D  +       G  P + HRLD  T+G+L+ A+
Sbjct: 85  YEDKNILVINKPSNQKTHPN---LFETDTAMNDVTTYLGYTPYIIHRLDMLTNGLLLFAK 141

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
             A    L      + +++ Y++ V       +  I   + +  +     +      +  
Sbjct: 142 NPAVVPILNRQLTTKIMKRNYYATVKLKNIPNQGTIDLPIAQDPNDQRKRIV-----DDN 196

Query: 223 ANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
              AI+H++VI   + Q    L++   TGRTHQ+RVH   +  PI+GD  Y  +F G   
Sbjct: 197 GLKAITHYQVIARNSIQNTMTLKLTLETGRTHQIRVHLASINLPIIGDPLYNPDFNGEA- 255

Query: 282 SPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
                 L L A  + L  P     L++T P
Sbjct: 256 ------LALTAYELSLISPFTFDTLKVTLP 279


>gi|188990499|ref|YP_001902509.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. B100]
 gi|167732259|emb|CAP50451.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris]
          Length = 259

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 55/202 (27%), Positives = 91/202 (45%), Gaps = 16/202 (7%)

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +  + HRLD++TSG++VVART  A   L E    R + + Y ++V G         A+ 
Sbjct: 64  PRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSARDVHRQYLAVVVGAL--VSGGTADA 121

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            + +       + V          A++H+++ + F +    LE +  TGRTHQ+RVH  H
Sbjct: 122 PIDRHPRDRLKMAVRD----DGRDAVTHYRLRERF-RAHTALECRLETGRTHQIRVHMAH 176

Query: 262 MGCPIVGDHKYCANFKGNFTSP--------IQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +  PIVGD  Y    K    +            +  LHA  ++  HP  G  ++ +AP+P
Sbjct: 177 LKSPIVGDPLYGGALKLPKGATDTLVAELRGFKRQALHAETLEFLHPVSGEPVRASAPVP 236

Query: 313 AHMVKTWDSLGFKYDRNLYIKR 334
             + +   +L     R   + R
Sbjct: 237 EDLQRLMSALREDSARAAELAR 258



 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 9/46 (19%), Positives = 19/46 (41%)

Query: 3  LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV 48
          L + ++  VV +     R D      +P  +   L + ++SG   +
Sbjct: 9  LDSSLRQAVVPDSAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALL 54


>gi|256831089|ref|YP_003159817.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256580265|gb|ACU91401.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 245

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 57/243 (23%), Positives = 106/243 (43%), Gaps = 9/243 (3%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
             ++ ++  +L+ D  +   +KPAG+ V   +         L+   D  GQ+    HRLD
Sbjct: 2   PDTELVEIPVLHRDEHLIAVHKPAGLLVHRNAHAGREP-FLLQILRDQLGQRLYPVHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG++++A +  AA  L   F  + + K Y ++  G     +  I + L  +S   G 
Sbjct: 61  RPTSGLMIMALSPQAAHALALQFASQEVHKTYLAVTRGFVPP-QGLIDDALKSES---GS 116

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                 +  + A   I H  V      ++  + ++P TGRTHQ+R H  H+  P++GD  
Sbjct: 117 LQEARTEFTRLATAEIPH-PVGPNPTARYSMVRVRPRTGRTHQIRRHFAHIRHPLIGDVL 175

Query: 272 YCANFKGNF--TSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLGFKYDR 328
                +  F       ++L L +  +   HPE    + +T P    ++  +  LG+    
Sbjct: 176 RGDGRQNRFFRDHFGLHRLLLASVELTFRHPEDTSPMTLTCPPARELLDLFGQLGWNAAI 235

Query: 329 NLY 331
           + +
Sbjct: 236 DAF 238


>gi|238783433|ref|ZP_04627456.1| Pseudouridine synthase [Yersinia bercovieri ATCC 43970]
 gi|238715678|gb|EEQ07667.1| Pseudouridine synthase [Yersinia bercovieri ATCC 43970]
          Length = 267

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 56/220 (25%), Positives = 88/220 (40%), Gaps = 16/220 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                K   LY+D  + + NKPAG+    G          +   +        L HRLD 
Sbjct: 46  PPCHDKIETLYQDDHLVLINKPAGLLSLSGKNPQN--IDSVHHRLVQIFPGCTLVHRLDF 103

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V+AR +A    L + F  R + K+Y +L+ G   + +  I   + K   +    
Sbjct: 104 GTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLDDNQGVIDAAIAKDPAL---- 159

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGC 264
             ++         A S ++V++ F              +++ P TGRTHQLR+H   +G 
Sbjct: 160 FPLMSICSIHGKPARSRYRVVERFYHELEDRTLLPLTRVQLTPETGRTHQLRIHCQQLGH 219

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           PI G   Y              +L LHA  +   HP    
Sbjct: 220 PIWGCDLYGGRLLPGTERT--PRLMLHASELHFVHPISEE 257


>gi|270264957|ref|ZP_06193221.1| ribosomal large subunit pseudouridine synthase A [Serratia
           odorifera 4Rx13]
 gi|270041255|gb|EFA14355.1| ribosomal large subunit pseudouridine synthase A [Serratia
           odorifera 4Rx13]
          Length = 232

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 63/236 (26%), Positives = 99/236 (41%), Gaps = 20/236 (8%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H        LY+D  + + NKPAG+    G          +   +    
Sbjct: 3   KIIDTFIAPPCHDKIEN---LYQDESLVLINKPAGLLSLSGKNPQN--LDSVHHRLVQIF 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +     L + F  R + K+Y +L+ G   N +  I   
Sbjct: 58  PGCTLVHRLDFGTSGLMVIARNKTVNAALCQQFSQRTVTKVYSALLCGHLDNDEGVIDAA 117

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTH 253
           + K   +      ++         A S ++V++ F +            +++ P TGRTH
Sbjct: 118 IAKDPAL----FPLMSICATHGKPARSGYRVVERFYRELEGGTLLPVTRVQLTPETGRTH 173

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           QLR+H   +G PI+G   Y              +L LHA  +   HP G   QI A
Sbjct: 174 QLRIHCQLLGHPILGCDLYGGRLLPGTER--IPRLMLHASELHFVHPIGKE-QIKA 226


>gi|126664148|ref|ZP_01735141.1| pseudouridine synthase [Flavobacteria bacterium BAL38]
 gi|126623862|gb|EAZ94557.1| pseudouridine synthase [Flavobacteria bacterium BAL38]
          Length = 559

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 100/232 (43%), Gaps = 19/232 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           ++++      ++     +++ED  + V NKPA      G  I+  +   +K         
Sbjct: 337 MEANPFQENPAEGKNIKIVFEDEILAVINKPAEFLSVPGKNISDSVYQRVKELY-PNATG 395

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG++++A+       L   F  R I+K Y +L+ G+ + K+  I   L 
Sbjct: 396 PLIVHRLDMSTSGLMLIAKDEETYVKLQSQFIKRTIKKRYVALLDGVLEEKEGFIDLPL- 454

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V  ++      A + ++ I+        +   P TGRTHQLRVHA H  
Sbjct: 455 RVDLDDRPRQLVCYEH---GKPAQTKWEKIEVR-NNQTLVYFYPITGRTHQLRVHASHEL 510

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
            +  PIVGD  Y             N+L+LHA  +   HP     + + A +
Sbjct: 511 GLKTPIVGDDLYGKK---------ANRLHLHAESLTFEHPVSKELITLKAEI 553


>gi|238789504|ref|ZP_04633289.1| Pseudouridine synthase [Yersinia frederiksenii ATCC 33641]
 gi|238722454|gb|EEQ14109.1| Pseudouridine synthase [Yersinia frederiksenii ATCC 33641]
          Length = 249

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 55/220 (25%), Positives = 90/220 (40%), Gaps = 16/220 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                K   LY+D  + + NKP G+    G          +   +        L HRLD 
Sbjct: 28  PPCHDKIETLYQDDHLVLINKPTGLLSLSGKNPQN--LDSVHHRLVQIFPGCTLVHRLDF 85

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++V+AR +A    L + F  R + K+Y +++ G   + +  I   + K   +    
Sbjct: 86  GTSGLMVIARNKAINAALCQQFSQRTVTKVYSAVLCGHLDDNEGVIDAAIAKDPAL---- 141

Query: 213 VHVVKQNEKGANYAISHFKVIDCFA--------QKFCWLEMQPHTGRTHQLRVHALHMGC 264
             ++         A S ++V++ F         Q    +++ P TGRTHQLR+H   +G 
Sbjct: 142 FPLMSICAIHGKPARSRYQVVERFYHELEDKTLQPLTRVQLTPETGRTHQLRIHCQQLGH 201

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           PI G   Y         + +  +L LHA  +   HP    
Sbjct: 202 PIWGCDLYGGRLLPG--TELTPRLMLHASELHFVHPISKE 239


>gi|288927126|ref|ZP_06421012.1| ribosomal large subunit pseudouridine synthase A [Prevotella buccae
           D17]
 gi|288336112|gb|EFC74507.1| ribosomal large subunit pseudouridine synthase A [Prevotella buccae
           D17]
          Length = 575

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 67/230 (29%), Positives = 103/230 (44%), Gaps = 31/230 (13%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +LYED+ I V NKPAG+    G      +   L+       + P + HRLD  TSG+
Sbjct: 361 ELPILYEDASIVVVNKPAGMLSVPGKTDTPSVYSLLRECCPQ-AEGPIIVHRLDMATSGL 419

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIANWLLKKSHI 208
           LV A+T  A   L + F  R + K Y +++            PK     +    +    +
Sbjct: 420 LVAAKTSKAYFGLQQQFTDRMVTKRYVAVLEANGPRPSSHPAPKTDSSLLPKGAI-SLPL 478

Query: 209 GGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MG 263
             D++   +Q  + +    A++ ++ +         L + PHTGRTHQLRVH  H   +G
Sbjct: 479 SPDFMDRPRQKVDREHGRPAVTDYQFVSSD-----RLLLYPHTGRTHQLRVHCAHREGLG 533

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
            PI GD+ Y             ++LYLHA Y+   HP  G R++     P
Sbjct: 534 RPIKGDNLYGTK---------ADRLYLHAEYLSFVHPQTGERVEFECSAP 574


>gi|332530661|ref|ZP_08406593.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
 gi|332039889|gb|EGI76283.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
          Length = 229

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 61/216 (28%), Positives = 100/216 (46%), Gaps = 15/216 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ED  + V +KPAG+    G G        L +   ++  +  + HRLDQ TSG++++
Sbjct: 13  VVHEDEALVVLDKPAGLLSAPGRGAE--KQDCLVARALARWPEALIVHRLDQATSGLMLL 70

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR     + L+  F  R + K Y ++V G  +   E      +    +        ++ +
Sbjct: 71  ARGPEMQRALSICFAARDVHKRYEAVVDGCVRGSAEHEDEGEIALPLMADWPRRPRQKVD 130

Query: 221 KGANYAISHFKVIDCFAQKF---------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                +++ +KV+   +              L + P TGR+HQLRVH   +G PI+GD  
Sbjct: 131 AQGKPSLTRWKVLARDSVGHQSASNASQTTRLALFPVTGRSHQLRVHLQAIGHPILGDAL 190

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           Y A+      SP   +L LHA  + LPHP  G L I
Sbjct: 191 Y-ADPATLARSP---RLLLHACELSLPHPRTGALTI 222


>gi|307719808|ref|YP_003875340.1| pseudouridine synthase [Spirochaeta thermophila DSM 6192]
 gi|306533533|gb|ADN03067.1| pseudouridine synthase [Spirochaeta thermophila DSM 6192]
          Length = 256

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 69/243 (28%), Positives = 116/243 (47%), Gaps = 19/243 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKG----QKPRLTHRLDQET 154
            ++YED+ I   NK     VQ  S +     +  L+      G     +  L +RLD+ T
Sbjct: 2   DIIYEDAHIIAVNKTGEELVQQNSVMEGTLQESLLEHLRMRDGAEAPPRLHLVNRLDRPT 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI++ AR R AA   +  FR R + K+YW+++   P    + + +++++   I   +  
Sbjct: 62  SGIVLFARHRKAAGKFSHLFRRRGVYKLYWAVLDAPPPLPSDTVEHYIVENRRINKSFAF 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K  ++G+ YA   ++VI     ++ ++ ++ HTGR HQ+R     +GC I GD KY A
Sbjct: 122 AEK--KEGSEYARLSYQVIGS-GDRYFFVVVRLHTGRHHQIRAQFSALGCHIKGDIKYGA 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
                        ++LHAR +   HP  G R+ ITA  PA     W+       ++ + +
Sbjct: 179 KRTNR-----GGGIHLHARLLAFIHPFTGERVVITADPPAD--SLWEEFAR---QDAHFR 228

Query: 334 RLY 336
           R Y
Sbjct: 229 REY 231


>gi|145612127|ref|XP_362534.2| hypothetical protein MGG_08117 [Magnaporthe oryzae 70-15]
 gi|145019360|gb|EDK03588.1| hypothetical protein MGG_08117 [Magnaporthe oryzae 70-15]
          Length = 487

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 61/276 (22%), Positives = 107/276 (38%), Gaps = 49/276 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +        ++ +  G V V+ K+V  N+ +++G+++      +        
Sbjct: 93  VDVFESE-FRDRPIEYYRECMEKGSVLVNAKKVGPNHILKNGELIAHICHRH-------- 143

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +L+ED ++ V NKP+G+ V       ++    +     S+
Sbjct: 144 ----------EPPCTADPVQVLHEDDEMIVINKPSGMPVHPAGRYNFNSVVEVMRSERSR 193

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
             K    +RLD+ TSGI+ +A+T  AA  + E    R ++K Y + V G  P  +  C  
Sbjct: 194 DFKAYPCNRLDRLTSGIMFIAKTPQAACKMGEQIMGRTVRKEYLARVIGRFPDGEVICNE 253

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---------------------- 237
             L     +G + V           +A + FK +  +                       
Sbjct: 254 PILQISPKLGLNRVRA------NGRHARTVFKRLAYYPPAEGQGNEAKPGEAANGRPWRN 307

Query: 238 -QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            Q +  +   P TGRTHQ+RVH  H+G PI  D  Y
Sbjct: 308 KQGYSIVRCLPVTGRTHQIRVHLQHLGHPIENDPIY 343


>gi|254564943|ref|XP_002489582.1| DRAP deaminase, catalyzes the third step of the riboflavin
           biosynthesis pathway [Pichia pastoris GS115]
 gi|238029378|emb|CAY67301.1| DRAP deaminase, catalyzes the third step of the riboflavin
           biosynthesis pathway [Pichia pastoris GS115]
 gi|328350006|emb|CCA36406.1| DRAP deaminase [Pichia pastoris CBS 7435]
          Length = 547

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 54/259 (20%), Positives = 100/259 (38%), Gaps = 25/259 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
            FK+ +    F      + +G+V+++ +    ++ +++G ++      +     + E +I
Sbjct: 77  VFKSEFRMKPFSYYYNAIANGEVKLNDQVANVDSVLRNGDLISHRIHRHEPPVTLDEIEI 136

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                              YED +I V NKP+GI V       Y  +          G  
Sbjct: 137 A------------------YEDDEITVINKPSGIPVHPTG--RYRHNSITMIMKQEMGTI 176

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               +RLD+ TSGI+ + +T      + +  + R + K+Y +   G      + +   LL
Sbjct: 177 AHTCNRLDRLTSGIMFLGKTAMKTAKMVQQIKERNVGKVYIAKCKGKFPLGLQVVDKPLL 236

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHM 262
                    +     + +    A + F+ I          ++  P TGRTHQ+RVH   +
Sbjct: 237 TIDP----RLTFNLVDLEDGKEAKTLFRRISYDTKDNTSIVKCMPLTGRTHQIRVHLQFI 292

Query: 263 GCPIVGDHKYCANFKGNFT 281
           G PI  D  Y + +    T
Sbjct: 293 GYPIANDPVYSSPYVWGLT 311


>gi|119482145|ref|XP_001261101.1| DRAP deaminase (Rib2), putative [Neosartorya fischeri NRRL 181]
 gi|119409255|gb|EAW19204.1| DRAP deaminase (Rib2), putative [Neosartorya fischeri NRRL 181]
          Length = 525

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 57/266 (21%), Positives = 107/266 (40%), Gaps = 48/266 (18%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           + L  G+V V+ K    +  I++G+++      +       E                  
Sbjct: 83  QALADGKVTVNGKTAAPDTVIKNGEIISHTLHRHEPPVTGHE------------------ 124

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSG 156
             +++ED+ I V +KPAG+ V       YH +  ++     +GQ+  PR  +RLD+ TSG
Sbjct: 125 IGIIHEDNDILVIDKPAGVPVHAAG--RYHYNSIVEILRSQRGQEFVPRPCNRLDRLTSG 182

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-KKSHIGGDYVHV 215
           ++ +A+   AA  +T   + R +QK Y + V G   +        ++     +G + V  
Sbjct: 183 VMFIAKHPKAADAITIKLKQRTVQKEYIARVKGRFPDGVVVCDQPIMSVSPKLGLNRVRA 242

Query: 216 VKQNEKGANYAISHF-------------------------KVIDCFAQKFCWLEMQPHTG 250
             ++ K     ++++                          ++   ++ +  +   P TG
Sbjct: 243 TGKDAKTKFRRLAYYPPASPAPERDESEVTASGDRPATPPPLLANESEGYSIVHCLPLTG 302

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANF 276
           RTHQ+RVH   +G PI  D  Y    
Sbjct: 303 RTHQIRVHLQFLGHPITNDPIYSNRR 328


>gi|302892903|ref|XP_003045333.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256726258|gb|EEU39620.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 525

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 61/268 (22%), Positives = 101/268 (37%), Gaps = 55/268 (20%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G + V+ +RV  +  +++G ++              E  + +  +            +++
Sbjct: 154 GTIFVNGRRVGPDYVLRNGDLISHTLHR-------HEPPVTEDPL-----------QVIH 195

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           ED  + V NKPAG+ V       Y+    +      +G  P L +RLD+ TSGI+ +A+ 
Sbjct: 196 EDEDMIVINKPAGVPVHPAGRYNYNSVIEIMKSERGQGFLPYLCNRLDRLTSGIMFIAKN 255

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
             AA+ L    + R ++K Y + V G  P  +  C    L     +G + V         
Sbjct: 256 PPAAEALGIKIKQRTVRKEYIARVMGKFPDGEVVCDQPILQISPKLGLNRVRA------N 309

Query: 223 ANYAISHFKVIDCFA------------------------------QKFCWLEMQPHTGRT 252
              A + FK +  +                               + +  +   P TGRT
Sbjct: 310 GKTARTVFKRLAYYPPPDGEETEGDGRPKTPEEELDEKHHPWINKRGYSIVRCLPVTGRT 369

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNF 280
           HQLRVH  H+G PI  D  Y       F
Sbjct: 370 HQLRVHLQHLGHPIQNDPIYANRRVWGF 397


>gi|326799397|ref|YP_004317216.1| pseudouridine synthase [Sphingobacterium sp. 21]
 gi|326550161|gb|ADZ78546.1| pseudouridine synthase [Sphingobacterium sp. 21]
          Length = 232

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 67/230 (29%), Positives = 116/230 (50%), Gaps = 14/230 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---RLTHRLDQE 153
           +   +LYED  +   NKP+G  V+  +     ++  L +++  K  K    R  HRLD+ 
Sbjct: 7   IDQHILYEDEHLVAINKPSGYLVEASAKEKRALEEMLSAYLSEKHHKDIQTRAVHRLDRR 66

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
            SG+L+ A+T  A + +   F+ R ++K YW++V   P    + + +WL +       Y 
Sbjct: 67  VSGLLLFAKTTVALEGMIALFKARLVEKTYWAIVANPPLVPSDKLVHWLTRDKEQNISYT 126

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H   + +  +  A   +++++  A  F  +E+ P TGRTHQ+R     +GCPIVGD+KY 
Sbjct: 127 H--NEPQPHSVKAELAYRLLE-KADDFFLIEVYPFTGRTHQIRAQLAAIGCPIVGDYKYG 183

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
              +    +     + LHA+ +  PHP   R + + AP+P    + W+S 
Sbjct: 184 FPREKPRRA-----IALHAKQLRFPHPIDHRSVYLEAPIPD--AQLWNSF 226


>gi|221194862|ref|ZP_03567919.1| ribosomal large subunit pseudouridine synthase D [Atopobium rimae
           ATCC 49626]
 gi|221185766|gb|EEE18156.1| ribosomal large subunit pseudouridine synthase D [Atopobium rimae
           ATCC 49626]
          Length = 248

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 59/245 (24%), Positives = 101/245 (41%), Gaps = 33/245 (13%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGI----------AYHIDGFLKSWVDSKG-----QKP 144
            ++Y+DS I   NKPAGI +                A  +    + ++++ G     Q  
Sbjct: 2   DIIYQDSYILAVNKPAGIIIHSDGTSHAGERADMCAAETLTDLARVYLENNGCVQQAQDV 61

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           +  HRLD++T+GI++ +  +       E  R R + K Y ++V G     ++ I   + +
Sbjct: 62  QALHRLDKDTTGIVLFSLDKETQPLFDELIRSRNVHKTYLAVVKGEFPEGEQDITLPIGR 121

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALH 261
             H     +HV     K    A++H + ++   +       +  +  TGR HQ+RVH   
Sbjct: 122 DRHDAR-RMHV----SKTGKAALTHVRRLEVQRRGQSTRSLMLAELGTGRKHQIRVHFSA 176

Query: 262 MGCPIVGDHKYCANFKGNF---------TSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +G PIVGD  Y    + +           +  Q  L LHA  +   HP  G  L +    
Sbjct: 177 LGFPIVGDGLYGPIARDSMYGRAPSTRTAAFTQASLMLHAYELSFVHPVTGESLVLKTEW 236

Query: 312 PAHMV 316
           P+   
Sbjct: 237 PSRFT 241


>gi|186681130|ref|YP_001864326.1| pseudouridine synthase [Nostoc punctiforme PCC 73102]
 gi|186463582|gb|ACC79383.1| pseudouridine synthase [Nostoc punctiforme PCC 73102]
          Length = 575

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 72/243 (29%), Positives = 113/243 (46%), Gaps = 18/243 (7%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P    A   +     + +   +L +  + +   ++YED  +   NKP G+    G    
Sbjct: 336 VPFPAFAQRLVGVRLSVSEREASLREEREEVTLPIIYEDEWLIAVNKPPGLLSVPGR-YR 394

Query: 127 YHIDGFLKSWVD--SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              D  L         G      HRLDQETSGIL++AR R   + L++ F+ R++ K+Y 
Sbjct: 395 DRQDSVLSRLRHLLPDGMALASVHRLDQETSGILLLARDRQTHKQLSQQFQQRQVHKVYE 454

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +++ G+   +K  I   L         Y  V  QN      +++ F+VI    Q +  +E
Sbjct: 455 AILSGVAIAEKGVIDLPLWGD-PENRPYQKVDWQN---GKPSLTQFQVISR-EQDYTRIE 509

Query: 245 MQPHTGRTHQLRVHAL---HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             P TGRTHQLRVHA     +G  I+GD  Y  +        + ++LYLHAR +D  HP+
Sbjct: 510 FTPLTGRTHQLRVHAADVRGLGITILGDRLYGCDA-------VTSRLYLHARELDFEHPQ 562

Query: 302 GGR 304
             +
Sbjct: 563 LKK 565


>gi|302340475|ref|YP_003805681.1| pseudouridine synthase [Spirochaeta smaragdinae DSM 11293]
 gi|301637660|gb|ADK83087.1| pseudouridine synthase [Spirochaeta smaragdinae DSM 11293]
          Length = 229

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 66/222 (29%), Positives = 108/222 (48%), Gaps = 15/222 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQE 153
             +LYED+ + V NK  G  VQG       +   +K ++  K  KP      + HRLD+ 
Sbjct: 2   PEVLYEDNHLIVVNKRCGDIVQGDKSGDPTLADEVKEYLREKYNKPGNVFLGIPHRLDRP 61

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++ ART  A + L+ SFR + ++KIYW++V  +P  +   + ++L +      +  
Sbjct: 62  TSGVVLYARTEKALRRLSLSFREQHVEKIYWAVVDKMPPAESGTLVHYLRRDRK--KNKS 119

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                    +  A   ++++     ++  LE++  TGR HQ+R     +GC I GD KY 
Sbjct: 120 FASDTPTADSQEAKMRYRLVGA-TNRYYLLEIELLTGRHHQIRAQLAAVGCRIRGDLKYG 178

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG--RLQITAPLPA 313
                         ++LHAR + L HP G   R+ ITA  P+
Sbjct: 179 YPRSNR-----DGGIHLHARKVSLDHPVGERNRITITADPPS 215


>gi|70608135|ref|NP_001020455.1| RNA pseudouridylate synthase domain-containing protein 4 [Rattus
           norvegicus]
 gi|81918145|sp|Q4QQT0|RUSD4_RAT RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 4
 gi|67678357|gb|AAH98023.1| RNA pseudouridylate synthase domain containing 4 [Rattus
           norvegicus]
 gi|149027812|gb|EDL83272.1| RNA pseudouridylate synthase domain containing 4 [Rattus
           norvegicus]
          Length = 377

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 120/275 (43%), Gaps = 38/275 (13%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   +L++D  + V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKELSRRILHQDKDLVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGHKAEP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R+++K YW++   +P      +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWEKDMAHQVQELFRTRQVEKKYWAITVRVPLPSAGVVDIPIM 205

Query: 204 KKSHIGGDYVH---------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G    H               V  +  + A+ A++ ++V+         +E+QP 
Sbjct: 206 EKEVAGQQQHHKMTLRPSYRMDNGKMVKVRASRDAHVAVTQYQVLSSTPSSA-LVELQPV 264

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC------------ANFKGNFTSPIQNK---LYLHA 292
           TG  HQLRVH    + CPI+GDHKY                K       + +   L+LHA
Sbjct: 265 TGIKHQLRVHLAFGLDCPILGDHKYSDWNRLAPQKLSAGTLKKLGLQQSKARYIPLHLHA 324

Query: 293 RYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGFK 325
           R + LP        L +   LP    ++   LG  
Sbjct: 325 RQLILPALGSRTEELLLACKLPHFFARSLRRLGLD 359


>gi|255318375|ref|ZP_05359608.1| ribosomal large subunit pseudouridine synthase A [Acinetobacter
           radioresistens SK82]
 gi|262378605|ref|ZP_06071762.1| conserved hypothetical protein [Acinetobacter radioresistens SH164]
 gi|255304367|gb|EET83551.1| ribosomal large subunit pseudouridine synthase A [Acinetobacter
           radioresistens SK82]
 gi|262299890|gb|EEY87802.1| conserved hypothetical protein [Acinetobacter radioresistens SH164]
          Length = 214

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 67/222 (30%), Positives = 105/222 (47%), Gaps = 15/222 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +FL   L++ D    V +KP+GI    G G A   D  L   V  +  K  L HRLD++T
Sbjct: 3   NFLAEHLIHRDEDFMVIHKPSGILSVPGKGEALS-DSVLTRLVAIE-PKTLLIHRLDRDT 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGILV   +R     +   F+ R+  K Y +LV G  + +   +   ++        ++ 
Sbjct: 61  SGILVFGLSRRGQNSIARQFQERQTTKTYQALVAGHLQGE-GTVDVPVVYDPAHPPLHIA 119

Query: 215 VVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               N      A++H++ I+ F    Q+   +++ P TGR+HQLRVH  ++G  IVGD  
Sbjct: 120 DAHHN----KPALTHWQAIEQFEINGQQVTRVKLVPVTGRSHQLRVHMQYLGHAIVGDTL 175

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y    +      +  +L LHA  +   HP+ G  L    P+P
Sbjct: 176 YADLEQQQ----LMPRLCLHAEQLGFAHPQTGEALNFYCPVP 213


>gi|242280738|ref|YP_002992867.1| pseudouridine synthase [Desulfovibrio salexigens DSM 2638]
 gi|242123632|gb|ACS81328.1| pseudouridine synthase [Desulfovibrio salexigens DSM 2638]
          Length = 214

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 74/224 (33%), Positives = 107/224 (47%), Gaps = 18/224 (8%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK-SWVDSKGQKPRLTHRLDQ 152
           SD     ++Y D KI V NKP+G+    G G         +   +  + +K    HRLD 
Sbjct: 2   SDEKLLDIVYADRKIVVVNKPSGLLSVPGRGPENQDCVVTRVQKMFPECRKFPAVHRLDM 61

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+LV+  T  A + L E F+ R+++K Y +L+ GI K     I     +       Y
Sbjct: 62  DTSGLLVLGLTARAVRELMEQFQKRQVKKRYEALLEGIVKEDSGVIEMA-FRLDPYNRPY 120

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGD 269
                 + K     I+H++ +         +E  P TGRTHQLRVH+ H   +GCPIVGD
Sbjct: 121 QVYDPIHGKLG---ITHWRKLG-VENGMTRVEFTPLTGRTHQLRVHSAHPQGLGCPIVGD 176

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQIT-APL 311
             Y +      T P Q KL  HA Y+   HP+   +++   APL
Sbjct: 177 RLYGSG-----TEPGQLKL--HAGYLCFEHPKTKEKMEFEIAPL 213


>gi|254444369|ref|ZP_05057845.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198258677|gb|EDY82985.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 249

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 61/243 (25%), Positives = 99/243 (40%), Gaps = 8/243 (3%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
            LT+ +      +LY D ++   +KP+G+ V             ++   D  GQ     H
Sbjct: 4   PLTEPTPQPPLEILYRDERLVAIHKPSGLLVHRSPIDRRETRFAIQLLRDQIGQHVYPAH 63

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           R+D+ TSGIL+     AA   L+  F+ R IQK Y ++  G    +   I + L K    
Sbjct: 64  RIDRPTSGILLFGLDEAAGTALSLLFQNREIQKNYLAVTRGHLP-ESGLIDSPLHKYEDA 122

Query: 209 GGDYVHVVKQNEKGA--NYAISH--FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            G       Q  + A    A +   +        ++  +E+ PHTGR HQ+R H  H+  
Sbjct: 123 DGHIKSSETQEAETAYRRLATTELPYPTERYDTTRYSLVELTPHTGRRHQIRRHLAHIRH 182

Query: 265 PIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDS 321
           PI+GD ++  N       +    ++L L A ++   HP     L+I  P           
Sbjct: 183 PIIGDVRHGCNKANKLARSHFAIHRLLLAATHVVFVHPFTNAPLKIHCPPETSFQTALQC 242

Query: 322 LGF 324
           +  
Sbjct: 243 IDL 245


>gi|194364569|ref|YP_002027179.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
 gi|194347373|gb|ACF50496.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
          Length = 204

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 55/212 (25%), Positives = 95/212 (44%), Gaps = 16/212 (7%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y D  + V  KPAG+    G          + + + ++       HRLDQ TSG+L+ AR
Sbjct: 6   YIDDALLVAEKPAGLLSVPGRSAENQ--DCVVARLQARYPDALTVHRLDQVTSGLLLHAR 63

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            +     L+  F  R++ K Y ++V G+ +     +   L+         +     + + 
Sbjct: 64  GKDMQAALSMQFEQRQVGKRYEAIVEGLLEGDAGEVDLPLIVDWPNRPKQM----VDHER 119

Query: 223 ANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
              A++ ++V+    + +   + ++P TGR+HQLR+H   +G PIVGD  Y A       
Sbjct: 120 GKPALTRWRVMARDVEAQRTRVALEPITGRSHQLRLHMASLGHPIVGDVLYGAAPA---- 175

Query: 282 SPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                +++LHAR +   HP  G  L   +  P
Sbjct: 176 ----QRVHLHARSLQFTHPVTGEALAFESATP 203


>gi|327282066|ref|XP_003225765.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like [Anolis carolinensis]
          Length = 361

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 77/284 (27%), Positives = 128/284 (45%), Gaps = 45/284 (15%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  LK  +L+++S+I V NKP G+ V GG  +   I   L    K     K + 
Sbjct: 79  VHPNVMAKALKKGVLFQNSEIVVINKPYGLPVHGGPKVKTCITDVLPTLAKMLYGMKAEP 138

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+AR +  A  + E F+ R+++K YW++  G PK  +  +   ++
Sbjct: 139 LHLCHRLDKETTGVMVLARDQDIAHKVQELFKTRQVEKKYWAVCVGHPKPTEGLVDIPIV 198

Query: 204 KK-------------------SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +K                   SH  G    V  +  + A+ A++ ++V+   +      E
Sbjct: 199 EKEVESHQSHFKMALAPNYYMSHEDGKTFKV--RQHRDAHSAVTRYRVLSSCSSCSFL-E 255

Query: 245 MQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNFTSPIQN---------------KL 288
           + P TG  HQLRVH    +GCPI+GDHKY    K       Q+                L
Sbjct: 256 LHPITGVKHQLRVHMAFGLGCPILGDHKYSHWNKLAPQKLPQSALKRLGLEQVKARYLPL 315

Query: 289 YLHARYMDLPHPEG---GRLQITAPLPAHMVKTWDSLGFKYDRN 329
           +LHA  + LP   G    ++ +    P    ++   L  ++  +
Sbjct: 316 HLHAYTLILPEINGSGEKKIHLVCKPPLFFSRSLKRLKLEFPES 359


>gi|92115011|ref|YP_574939.1| tRNA pseudouridine synthase C [Chromohalobacter salexigens DSM
           3043]
 gi|91798101|gb|ABE60240.1| tRNA pseudouridine synthase C [Chromohalobacter salexigens DSM
           3043]
          Length = 261

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 67/260 (25%), Positives = 112/260 (43%), Gaps = 17/260 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L+  +LY+D ++    KP+G+ V             L++  +  G+     HRLD+ TSG
Sbjct: 3   LELPVLYQDERMVAVQKPSGMLVHRSPIARDARVFALQTLRNQLGRHVYPVHRLDRPTSG 62

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A     AQ L E F   R+ K Y ++V G+   +   + ++ L++           
Sbjct: 63  LLLFALDPEMAQALGEEFTAHRVHKRYLAVVRGVGPEQD--LLDYGLREEDGSRPK---A 117

Query: 217 KQNEKGANYAISHFKVID-------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +  E  A  A+     ++           ++  +E +P TGR HQ+R H    G PI+GD
Sbjct: 118 EMPELEAWTAVRRLDSVELPVRIDRYPQVRYSLMEARPWTGRRHQIRRHLARRGYPIIGD 177

Query: 270 HKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            K+       F     +  +L L A  M + HPE  R LQ+ APL   M   +   G++ 
Sbjct: 178 AKHGKGAHNRFFRERLDSPRLLLAAVGMTVWHPEQARTLQLDAPLADDMQALFARFGWQ- 236

Query: 327 DRNLYIKRLYSQDECKQNIL 346
             +    R+    E    +L
Sbjct: 237 -GHAPAARVAWHAERPAALL 255


>gi|160897919|ref|YP_001563501.1| pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160363503|gb|ABX35116.1| pseudouridine synthase [Delftia acidovorans SPH-1]
          Length = 319

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 66/272 (24%), Positives = 101/272 (37%), Gaps = 31/272 (11%)

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
              +A  H +  Q     S       D     +L+ D  +    KPAG  V      A+ 
Sbjct: 21  WADSAYTHALMFQPSSIPSPAQPPEPDDAPLHILWRDEHLVAVYKPAGWLVHRTGLDAHE 80

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               L++  D  G      HRLD+ T G+LV+A    AAQ L ++F  + ++K Y +LV 
Sbjct: 81  TRFVLQTLRDQLGCHVYPAHRLDKGTCGVLVMALHAQAAQRLGQAFAGQEVRKQYLALVR 140

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-----------FA 237
           G   +  E         +             +  A  A +  + +              A
Sbjct: 141 GWLPDAVEVDHALRPDDAP-----------EDAPAQPAQTSLRCLARLEWPEAFDPRHAA 189

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYM 295
            +   +E  P TGR HQ+R H  H+  PI+GD  +       + +      +L+LHA  +
Sbjct: 190 TRISLVEALPATGRRHQIRRHLKHVAHPIIGDATHGKGPLNRWWAERLGLQRLWLHAHAL 249

Query: 296 DLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
           +L HP  G        P      W  LG   D
Sbjct: 250 ELAHPMTGE-------PLRFEADWRQLGHVAD 274


>gi|71002582|ref|XP_755972.1| DRAP deaminase (Rib2) [Aspergillus fumigatus Af293]
 gi|66853610|gb|EAL93934.1| DRAP deaminase (Rib2), putative [Aspergillus fumigatus Af293]
 gi|159130027|gb|EDP55141.1| DRAP deaminase (Rib2), putative [Aspergillus fumigatus A1163]
          Length = 526

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 58/266 (21%), Positives = 107/266 (40%), Gaps = 48/266 (18%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           + L  G+V V+ K    +  I++G+V+      +       E                  
Sbjct: 83  QALADGKVTVNGKTAAPDTVIKNGEVISHTLHRHEPPVTGHE------------------ 124

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSG 156
             +++ED+ I V +KPAG+ V       YH +  ++     +GQ+  PR  +RLD+ TSG
Sbjct: 125 IGIIHEDNDILVIDKPAGVPVHAAG--RYHYNSIVEILRSQRGQEFVPRPCNRLDRLTSG 182

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-KKSHIGGDYVHV 215
           ++ +A+   AA  +T   + R +QK Y + V G   +        ++     +G + V  
Sbjct: 183 VMFIAKHPKAADAITIKLKQRTVQKEYIARVKGRFPDGVVVCDQPIMSVSPKLGLNRVRA 242

Query: 216 VKQNEKGANYAISHF-------------------------KVIDCFAQKFCWLEMQPHTG 250
             ++ K     ++++                          ++   ++ +  +   P TG
Sbjct: 243 TGKDAKTKFRRLAYYPPASPAPERDEDEVTASGDRPATPPPLLANESEGYSIVHCLPLTG 302

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANF 276
           RTHQ+RVH   +G PI  D  Y    
Sbjct: 303 RTHQIRVHLQFLGHPITNDPIYSNRR 328


>gi|306820227|ref|ZP_07453869.1| ribosomal large subunit pseudouridine synthase [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304551724|gb|EFM39673.1| ribosomal large subunit pseudouridine synthase [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 228

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 65/217 (29%), Positives = 102/217 (47%), Gaps = 16/217 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQ 152
           K  +LYED+ + V  K +GI  Q        +   +KS++  K  K       L HRLD 
Sbjct: 6   KLNVLYEDNHVIVVEKKSGILSQADKSGDVDMLTLVKSYIKEKYDKKGEVFLGLVHRLDT 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI+V ART  AA  L++  R  ++ K Y ++   + + KK    ++L K S     Y
Sbjct: 66  LTSGIMVFARTSKAASRLSDDIRQGKMNKKYLAVFEEVIEKKKGSFEDYLAKDSIKNISY 125

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              V +++K   Y+   ++V++        +++   TGR+HQ+RV     G  IVGD KY
Sbjct: 126 ---VTKDKKNGKYSKLEYEVLE-IKDGMSLVKINLITGRSHQIRVQFASRGYHIVGDAKY 181

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
            A  K       ++K+ LHA  +   HP     +   
Sbjct: 182 KAKSKD------KDKIALHACELGFYHPTKKELMTFE 212


>gi|153001908|ref|YP_001367589.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151366526|gb|ABS09526.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 245

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 100/233 (42%), Gaps = 19/233 (8%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +LY+DS I + +KP+G+    G          +   +        L HRLD 
Sbjct: 18  PPCLGQIRVLYQDSDILLIDKPSGLLSLSGKNPLN--LDSVHYRLVQDFPTATLLHRLDF 75

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++VA  ++    LT+ F+ R ++K Y +L+ G        I   + K      D+
Sbjct: 76  GTSGIMLVALNKSVNGLLTKQFQARTVEKRYTALLHGHIAADSGVINLPIAKD----CDH 131

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             + K        AIS ++V++   + F   +E  P +GRTHQLR+H+   G  I+G   
Sbjct: 132 FPLQKICHSTGKPAISEYRVLERLTEPFATRVEFTPVSGRTHQLRIHSQQFGHSILGCDL 191

Query: 272 YCA---NFKGNFTSPIQN--------KLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y     +   N  +P  +        +L LHA  +   HP  G R+      P
Sbjct: 192 YGGVGESVADNAAAPDPDITKMTNNSRLMLHATRLAFDHPITGERIDWICECP 244


>gi|315607191|ref|ZP_07882195.1| ribosomal large subunit pseudouridine synthase A [Prevotella buccae
           ATCC 33574]
 gi|315251245|gb|EFU31230.1| ribosomal large subunit pseudouridine synthase A [Prevotella buccae
           ATCC 33574]
          Length = 575

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 69/245 (28%), Positives = 106/245 (43%), Gaps = 31/245 (12%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +  SS +        +  +LYED+ I V NKPAG+    G      +   L+       +
Sbjct: 346 LPASSAHQLPLKTAPELPILYEDASIVVVNKPAGMLSVPGKTDTPSVYSLLRECCPQ-AE 404

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKN 193
            P + HRLD  TSG+LV A+T  A   L + F  R + K Y +++            PK 
Sbjct: 405 GPIIVHRLDMATSGLLVAAKTSKAYFGLQQQFTDRMVTKRYVAVLEANGPRPSFHPAPKT 464

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQ--NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
               +    +    +  D +   +Q  + +    A++ ++ +         L + PHTGR
Sbjct: 465 DSSLLPKGAI-SLPLSPDLMDRPRQKVDREHGRPAVTDYQFVSSD-----RLLLYPHTGR 518

Query: 252 THQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQI 307
           THQLRVH  H   +G PI GD+ Y             ++LYLHA Y+   HP  G R++ 
Sbjct: 519 THQLRVHCAHREGLGRPIKGDNLYGTK---------ADRLYLHAEYLSFVHPQTGERVEF 569

Query: 308 TAPLP 312
               P
Sbjct: 570 ECSAP 574


>gi|46447425|ref|YP_008790.1| putative 23S rRNA pseudouridine synthase [Candidatus Protochlamydia
           amoebophila UWE25]
 gi|46401066|emb|CAF24515.1| putative 23S rRNA pseudouridine synthase [Candidatus Protochlamydia
           amoebophila UWE25]
          Length = 219

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 62/218 (28%), Positives = 106/218 (48%), Gaps = 16/218 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQETS 155
           ++YED+ ++V NKPAG+  Q        ++   K+++    QKP        HRLD+  S
Sbjct: 7   IVYEDNHLFVLNKPAGLLTQPSGTAHDSLESQAKAYLKIVYQKPGNVFLEAVHRLDKPVS 66

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V  +T  A   L  S R ++ +KIY++ V  +P ++++ + N+L+           V
Sbjct: 67  GIVVFGKTSKALTRLNASVRAKQTKKIYYAWVDSVPVDEQKTLENFLIHNDFQA----QV 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V      A  A   ++VI+  +     LE++  TGR HQ+R    H+GCPI GD +Y + 
Sbjct: 123 VSSKHPQAKLAKLTYRVIERKSVGA-LLEIKLETGRYHQIRAQLAHLGCPIRGDIRYGSQ 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +     +     + LH   +++ HP     +     LP
Sbjct: 182 YPFTPHA-----IALHHESLEISHPIHQETMLFQTALP 214


>gi|71066542|ref|YP_265269.1| ribosomal large subunit pseudouridine synthase A [Psychrobacter
           arcticus 273-4]
 gi|71039527|gb|AAZ19835.1| ribosomal large subunit pseudouridine synthase A [Psychrobacter
           arcticus 273-4]
          Length = 237

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 115/233 (49%), Gaps = 14/233 (6%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
            +++        F K I +YED  I+V +KPAG+    G  +       L + ++     
Sbjct: 14  EENTRPPEFFQVFAKQITVYEDDDIWVVDKPAGLLSVDGKTLKVS----LLARLERANPA 69

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            +L HRLD +TSG+L+ A+  AA  ++++ F  R  QK Y + V+G  ++        + 
Sbjct: 70  VKLIHRLDMDTSGLLIFAKNAAAQTNISKQFIDRLPQKSYQARVFGQWESAGATGKISVP 129

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +        H+V  +   + +A++ ++V+   +C  Q    + ++P TGR+HQLRVH +
Sbjct: 130 VRYEPTTKPRHIVDHD--WSKHALTLYEVLAHEECNGQTVTRVLLKPVTGRSHQLRVHMV 187

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
           H+G  ++GD  Y      +    I  +L LHA+ + L HP  G  +   +P P
Sbjct: 188 HVGHVMIGDPIYAEGQALD----IAPRLNLHAQQLRLKHPTLGAWMDWESPTP 236


>gi|289615384|emb|CBI57785.1| unnamed protein product [Sordaria macrospora]
          Length = 476

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 57/274 (20%), Positives = 99/274 (36%), Gaps = 57/274 (20%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G V V+ K V  +  +++G ++      +      +                     +++
Sbjct: 107 GLVVVNGKAVGPDYVLKNGDLISHTTHRHEPPTTAE------------------PIGVIH 148

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVA 161
           ED  + V NKP+G+ V       Y+ +  ++     +G    PR  +RLD+ TSGI+ +A
Sbjct: 149 EDDDLIVINKPSGVPVHPAG--RYNYNSVVEIIKSQRGPDFLPRPCNRLDRLTSGIMFLA 206

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           + + AA+ L      R ++K Y + V G  P  +  C    L     +  + V       
Sbjct: 207 KNQRAAERLVAQISQRSVRKEYIARVVGRFPDGEVVCDQPILQISPKLTLNRVRA----- 261

Query: 221 KGANYAISHFKVIDCF----------------------------AQKFCWLEMQPHTGRT 252
                A + FK +  +                             + +  +   P TGRT
Sbjct: 262 -NGKSARTVFKRLAYYPPPDAAGKDQTEQPATPDAEQTAQRRGEGEGYSIVRCLPVTGRT 320

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           HQ+RVH   +G PI  D  Y       F     +
Sbjct: 321 HQIRVHLQFLGHPIQNDPIYANQKVWGFDLGRDD 354


>gi|160895409|ref|ZP_02076178.1| hypothetical protein CLOL250_02966 [Clostridium sp. L2-50]
 gi|156862911|gb|EDO56342.1| hypothetical protein CLOL250_02966 [Clostridium sp. L2-50]
          Length = 233

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 58/219 (26%), Positives = 96/219 (43%), Gaps = 12/219 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLD 151
           +K  +LYED+ I V  KP G+  Q     + ++   LK  +  K  +         HRLD
Sbjct: 1   MKIEVLYEDNDILVAVKPYGLPSQPDKKNSENMVSMLKLRIFEKEHRTEEPYLAPIHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +   GI++ A+ + AA  L++      + K Y +++ G   N    I N+L+  +     
Sbjct: 61  RPVGGIMLFAKNKEAAAKLSKQSEDGEMVKYYQAILTGELPNDAGTITNYLIHDNQTN-- 118

Query: 212 YVHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              +V ++  GA  A   ++V+   +       ++ +   TGRTHQ+RV        I G
Sbjct: 119 VTRIVDKDTPGAKLAELDYEVLDVMETDDGILSYVLINLITGRTHQIRVQMAGKKAGIWG 178

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           D KY   F+    S  Q  L  HA  ++  HP  G   +
Sbjct: 179 DTKYNPKFRKTKKSYKQIGL--HASRLEFEHPVTGEHMV 215


>gi|220934229|ref|YP_002513128.1| tRNA pseudouridine synthase C [Thioalkalivibrio sp. HL-EbGR7]
 gi|219995539|gb|ACL72141.1| tRNA pseudouridine synthase C [Thioalkalivibrio sp. HL-EbGR7]
          Length = 235

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 97/242 (40%), Gaps = 28/242 (11%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
                +L++D  +   NKP  + V     I+      L+   D  GQ+    HRLD+ TS
Sbjct: 4   PAPFTILHQDDDLVAINKPEQMLVHRSP-ISRDEVFVLQRLRDQLGQRVYTVHRLDRPTS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+     AAA  +   F    + K Y ++V G    +   I + L             
Sbjct: 63  GVLLFGLHPAAATAMARQFEAGEVHKRYLAVVRGY-TEESGEIDHPLE------------ 109

Query: 216 VKQNEKGANYAISHFKVIDCFA----------QKFCWLEMQPHTGRTHQLRVHALHMGCP 265
             ++ +G   A++ ++ +               ++  LE+ P +GR HQ+R H  H+  P
Sbjct: 110 -SEDGRGLQQAVTRYRRLATVELDIPVGRYPVARYSLLEVWPRSGRRHQIRRHFKHIFHP 168

Query: 266 IVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           + GD  Y                +L LHA ++ L HP  G  L + APLP         L
Sbjct: 169 LAGDTTYGEGRHNRLFREHFGVERLLLHASHLSLRHPSTGEALNLHAPLPEAFSVLLQRL 228

Query: 323 GF 324
           G+
Sbjct: 229 GW 230


>gi|238749474|ref|ZP_04610979.1| Pseudouridine synthase [Yersinia rohdei ATCC 43380]
 gi|238712129|gb|EEQ04342.1| Pseudouridine synthase [Yersinia rohdei ATCC 43380]
          Length = 232

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 95/231 (41%), Gaps = 19/231 (8%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H    K   LY+D  + + NKPAG+    G          +   +    
Sbjct: 3   KIIDTFIAPPCHD---KIETLYQDDHLVLINKPAGLLSLSGKNPQN--LDSVHHRLVQIF 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   N +  I   
Sbjct: 58  PGCTLAHRLDFGTSGLMVIARNKAVNAALCQQFSQRTVTKVYSALLCGHLDNNEGVIDAA 117

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTH 253
           + K   +      V+         A S ++V++ F              +++ P TGRTH
Sbjct: 118 IAKDPAL----FPVMSICALHGKPARSGYRVVERFYHPLEDGTLLPLTRVQLTPETGRTH 173

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           QLR+H   +G PI G   Y              +L LHA  +   HP    
Sbjct: 174 QLRIHCQLLGHPIWGCDLYGGRLLPGTERT--PRLMLHASELHFIHPISQE 222


>gi|255532415|ref|YP_003092787.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
 gi|255345399|gb|ACU04725.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
          Length = 240

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 99/241 (41%), Gaps = 22/241 (9%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
              K ++L+E+    V NKP  ++     G +  ++  +           ++ HRLD+ET
Sbjct: 4   PNFKDLILFENDDYVVVNKPPFVASLDERGGSGEVN--ILRLAKQYTADAQVCHRLDKET 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG +++A+T  A +++   F  R++ K Y ++V G    K+  I   +L   +       
Sbjct: 62  SGAIIIAKTPEAYRNVAMQFEKRKVNKTYHAVVDGQFTFKELFIDLPILNDGNKS----- 116

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            V  + K    A + F  +  + + +  +E +P TGR HQ+R+H       I GD  Y  
Sbjct: 117 -VTIDRKEGKRAETIFNTLKHY-RHYTLVECKPITGRMHQIRIHLATQRAAIAGDDMYRG 174

Query: 275 NF-------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
                          K     PI  +  LHAR++      G  + I AP P         
Sbjct: 175 KPVYLSSLKKGYRLAKDEEEQPIMKRFALHARHLVFKGLNGQDIVIEAPYPKDFATLIKL 234

Query: 322 L 322
           L
Sbjct: 235 L 235


>gi|15805985|ref|NP_294685.1| ribosomal large subunit pseudouridine synthase A [Deinococcus
           radiodurans R1]
 gi|6458684|gb|AAF10535.1|AE001948_4 ribosomal large subunit pseudouridine synthase, Rlu family
           [Deinococcus radiodurans R1]
          Length = 257

 Score =  157 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 95/242 (39%), Gaps = 14/242 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
               K  ++ E    YV +KPA              D       ++        HRLD+E
Sbjct: 17  PPTEKPRIIVEHPDFYVVHKPALWLTHPVRARVDVPDLLTFMQAETGETDLAPPHRLDRE 76

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG  ++ R   AA+     F+   + K Y ++V G P+  +  +   L      G + +
Sbjct: 77  TSGAQLLTRDSDAARTFFTLFKTHLVGKTYLAIVHGEPEWDRRTLDAPLGDLGLGGANKI 136

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + +        A++ F+V+   A     +E  P +GR HQ+R H  H+G P+VGD  Y 
Sbjct: 137 QIRQAVVPDGKPAVTDFRVVGRRA-GHALIECYPRSGRLHQIRAHLAHLGLPMVGDKIYG 195

Query: 274 ANFK------------GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
            + +                     +  LHA  +  P   G ++ +  PL   +V  W+ 
Sbjct: 196 RDPQVFLDFMEQGQTPELTARLGLPRQALHAARIAFPW-AGAQMAVEVPLAPDLVAYWEG 254

Query: 322 LG 323
           LG
Sbjct: 255 LG 256


>gi|294011514|ref|YP_003544974.1| pseudouridylate synthase [Sphingobium japonicum UT26S]
 gi|292674844|dbj|BAI96362.1| pseudouridylate synthase [Sphingobium japonicum UT26S]
          Length = 225

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 64/224 (28%), Positives = 99/224 (44%), Gaps = 14/224 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L   +L+ D +  + +KPAG+ V      +  ++  L S      + P   HRLD++TS
Sbjct: 3   LLHDRVLFIDGEAIILDKPAGLPVDAPRDGSLSLENHLSSLTFGFQRWPLPVHRLDRDTS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L++AR   A +    +F    + K Y ++V G+P      I   L K S     +  +
Sbjct: 63  GCLLLARNPKAHKRFAAAFEAGTVAKRYVAVVDGVPAEDSGAIDLSLKKVSTPAQGWRMI 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCA 274
                K    A + ++ I         +   P TGRTHQ+R HALH +G  I GD  Y +
Sbjct: 123 ---PAKAGKAAFTEWRKI-AEKDGRALIVFTPRTGRTHQIRTHALHGLGFGIAGDPVYGS 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                     Q  + LH+R++ +P  E    + TAPLPA     
Sbjct: 179 ---------GQGPMLLHSRFLSIPRGEKPPAEATAPLPATFAAA 213


>gi|262191904|ref|ZP_06050072.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae CT
           5369-93]
 gi|262032204|gb|EEY50774.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae CT
           5369-93]
          Length = 474

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 103/240 (42%), Gaps = 21/240 (8%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E   L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   +
Sbjct: 252 EGMPLEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-T 310

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +     HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I 
Sbjct: 311 QAEGVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEIQ 370

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L            V  Q       A++H++ +    Q    + + PHTGRTHQLRVH 
Sbjct: 371 LPLCGD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHC 425

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            H   +  PIVGD  Y    K         +L+LHA  +   HP   + +     + A  
Sbjct: 426 AHHLGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTFQ--VDADF 474


>gi|218887114|ref|YP_002436435.1| pseudouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|218758068|gb|ACL08967.1| pseudouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
          Length = 393

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 85/402 (21%), Positives = 136/402 (33%), Gaps = 107/402 (26%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + +VV   E   +L ++ +          +Q+ +R+GQVR++  R K  +R+  G VVR+
Sbjct: 3   EPLVVTAAEAGQKLVQYLQRRC-GAPQSAIQRWVRTGQVRINGGRCKPFDRVAEGDVVRV 61

Query: 68  PPVINA-----------------------------------LNHIIKEQKILDSSV---- 88
           PP   A                                        +    LD       
Sbjct: 62  PPFALAGGEGDPVVGGGAPDAGQGATRAASANAGGGKERGSAPRPARGPYPLDPEPGEGA 121

Query: 89  ---------NLTKHSDFLKSILLYEDSKIYVFNKPAGISV---------QGGSGIAYHID 130
                              +   ++ S + V  +  G+ V         Q G+G    + 
Sbjct: 122 ACGTAAAGSTAAPGPRACGTRPEFQASPLSVAGRAEGLLVLLKPAGLAVQPGTGHDDCVT 181

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWG 189
             L +        P   HRLD++TSG+L+VA + A  + L+++F  R  + K Y + V G
Sbjct: 182 ARLAAQYAGADFLPTPAHRLDRDTSGLLLVATSYARLRALSDAFAAREGLVKEYLAWVAG 241

Query: 190 IPKNKK-ECIANWLLKKSHIGGDYVHVVKQNEKGANYA---------------------- 226
              ++    + + L K+   G   V  V         A                      
Sbjct: 242 RWPHEGARTLHDRLEKQGAPGRQKVRRVGGEGSVPRAASGNEAVRVESGTDAAHAAAGAD 301

Query: 227 --------ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                   ++  +           L ++ HTGRTHQ+RV     G PI+GD KY     G
Sbjct: 302 AGRHAACTVTPLR----RGDGASLLLVRLHTGRTHQIRVQLAERGHPIMGDRKYGGPACG 357

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                    + LHA  + L  P+G R   TA LP      W 
Sbjct: 358 -------QGMLLHAVRLTL--PDGER--FTA-LP-DWTGRWQ 386


>gi|153212875|ref|ZP_01948492.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           1587]
 gi|124116253|gb|EAY35073.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           1587]
          Length = 221

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 100/229 (43%), Gaps = 19/229 (8%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
            L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   ++ +
Sbjct: 2   PLEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-TQAE 60

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I   L
Sbjct: 61  GVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEIQLPL 120

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH- 261
                       V  Q       A++H++ +    Q    + + PHTGRTHQLRVH  H 
Sbjct: 121 CGD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHCAHH 175

Query: 262 --MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
             +  PIVGD  Y    K         +L+LHA  +   HP   + +  
Sbjct: 176 LGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTF 215


>gi|224009936|ref|XP_002293926.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220970598|gb|EED88935.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 337

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 102/246 (41%), Gaps = 31/246 (12%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETS 155
              ++YED  I V NKP+G+    G      ++  +      +  +    + HRL  +TS
Sbjct: 91  DLDVVYEDEHIVVINKPSGVLTVPGKDDNPSLNKVVFERFGCESNRMDKMVVHRLGMDTS 150

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYV 213
           G++V ART +A + L   FR R++ + Y +LV G        I   L++   + IG D  
Sbjct: 151 GLVVFARTNSALRELNSLFRTRKVTRKYEALVCGHLAKDSGDIDLSLMRDYEALIGLDSG 210

Query: 214 HVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
            V K+  +    +++ F+VI   +   +K   + +   +GRTHQL VH   +G PIVGD 
Sbjct: 211 EVGKKLLESPKESMTKFEVISKEEMNGKKVTRIALTSISGRTHQLNVHCAAIGHPIVGDT 270

Query: 271 KYCANFKGNFTSPIQ-----------------------NKLYLHARYMDLPHPEGGR-LQ 306
            Y    +      ++                         + +HA+ +   HP     L 
Sbjct: 271 VYGFGGEAAPNGGLEESDLPEDRASEALQKDIAEAVAGKPMCVHAKSISFDHPVTKEALS 330

Query: 307 ITAPLP 312
                P
Sbjct: 331 FDCAAP 336


>gi|294657495|ref|XP_459803.2| DEHA2E11374p [Debaryomyces hansenii CBS767]
 gi|199432736|emb|CAG88042.2| DEHA2E11374p [Debaryomyces hansenii]
          Length = 582

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 55/254 (21%), Positives = 103/254 (40%), Gaps = 26/254 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD + K  +   +    +K + +GQV ++KK    ++ +++G ++              E
Sbjct: 108 LDIFVKE-FRDRDADFYKKTIAAGQVTLNKKPADLDSIVRNGDLISHRCHR-------HE 159

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  I   +KP+GI+V       Y  +   K +    
Sbjct: 160 PSVSSRGIK-----------IVHEDENIIAIDKPSGIAVHPTG--RYRYNTITKIFQHEF 206

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G+     +RLD+ TSG++ + +    A    +  R R ++K Y + V G        +  
Sbjct: 207 GKVVHPCNRLDRLTSGLMFLGKNAKGADAFVQQIRDRTVKKEYIARVVGKFDIGDVEVDK 266

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHA 259
            L   S   G    + + +      A + F+ I    +     ++  P TGRTHQ+RVH 
Sbjct: 267 PLKTVSPKHG----LNRVDFDEGKEAKTVFRRISYDPESDTSIVKCFPFTGRTHQIRVHL 322

Query: 260 LHMGCPIVGDHKYC 273
            ++G  I  D  Y 
Sbjct: 323 QYIGHAIANDPMYS 336


>gi|118587136|ref|ZP_01544565.1| pseudouridine synthase [Oenococcus oeni ATCC BAA-1163]
 gi|118432415|gb|EAV39152.1| pseudouridine synthase [Oenococcus oeni ATCC BAA-1163]
          Length = 302

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 58/281 (20%), Positives = 113/281 (40%), Gaps = 34/281 (12%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKI 108
           + + +  +  +  G  +         +   K Q  L ++          +  +L E    
Sbjct: 45  NGRNIPTSELVSPGDKLS---FSLETSDFSKGQNYLPNN--------DRRLRILSEKEDY 93

Query: 109 YVFNKPAGISVQG-----GSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVAR 162
            + +KPAG+ +          +  +++  LK  +         + HR+D++TSG++++A+
Sbjct: 94  LLVDKPAGMKMHPHSPNETDTLLNYVEAQLKGHLSRSCPAHAFMVHRIDRDTSGVVIIAK 153

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
              A   L +    +RI++ Y + V G  +NKK  I   +          +      ++ 
Sbjct: 154 NPLAVGILDQLLAKKRIKRTYLAWVSGNLENKKGSIDQAIAVDPINPYKRIV-----DQA 208

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++H+  I    Q    + +   TGRTHQ+RVH   +G PIVGDH Y  +       
Sbjct: 209 GQKAVTHWTKIHTVYQN-TLVRVSLETGRTHQIRVHFAAIGHPIVGDHLYNGSPY----- 262

Query: 283 PIQNKLYLHARYMDLPHPEGGR---LQITAPLPAHMVKTWD 320
              ++L LH+  +++P           IT  +P    +   
Sbjct: 263 ---SRLLLHSATIEIPELFSESRQGHTITTAIPKDFPRQLK 300


>gi|315268828|gb|ADT95681.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 268

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 100/233 (42%), Gaps = 19/233 (8%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +LY+DS I + +KP+G+    G          +   +        L HRLD 
Sbjct: 41  PPCLGQIRVLYQDSDILLIDKPSGLLSLSGKNPLN--LDSVHYRLVQDFPTATLLHRLDF 98

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++VA  ++    LT+ F+ R ++K Y +L+ G        I   + K      D+
Sbjct: 99  GTSGIMLVALNKSVNGLLTKQFQARTVEKRYTALLHGHIAADSGVINLPIAKDV----DH 154

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             + K        AIS ++V++   + F   +E  P +GRTHQLR+H+   G  I+G   
Sbjct: 155 FPLQKICHSTGKPAISEYRVLERLTEPFATRVEFTPVSGRTHQLRIHSQQFGHSILGCDL 214

Query: 272 YCA---NFKGNFTSPIQN--------KLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y     +   N  +P  +        +L LHA  +   HP  G R+      P
Sbjct: 215 YGGVGESVADNADAPEPDITKMTSNSRLMLHATRLAFDHPITGERIDWLCECP 267


>gi|296420214|ref|XP_002839670.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295635864|emb|CAZ83861.1| unnamed protein product [Tuber melanosporum]
          Length = 456

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 59/209 (28%), Positives = 97/209 (46%), Gaps = 12/209 (5%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSIL-LYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           I +++  ++   +L  +++  +     K I  +YED ++ V NKPAG+ V       Y+ 
Sbjct: 158 IASVDSKLENGDMLVHTLHRHEPPVTAKPIETVYEDDRLIVINKPAGVPVHPAG--RYNF 215

Query: 130 DGFLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  ++    D  G  P   +RLD+ TSG++ +A+T  AA       + R I+K Y + V 
Sbjct: 216 NTVIEIMKHDYNGHAPLPCNRLDRLTSGLMFMAKTPEAANDFMGQLQTRTIKKQYLARVK 275

Query: 189 GI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQ 246
           G  P  +  C    L     +G + V            A + FK +    +  +  +E  
Sbjct: 276 GKFPAGEVTCSQPILSVSPKLGLNRVRA------SGKTAKTLFKRLKYNTEKNYSIVECH 329

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           P TGRTHQ+RVH   +G PI+ D  YC  
Sbjct: 330 PFTGRTHQIRVHLQFLGHPIINDPIYCNR 358


>gi|313143115|ref|ZP_07805308.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
 gi|313128146|gb|EFR45763.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
          Length = 327

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 61/305 (20%), Positives = 127/305 (41%), Gaps = 25/305 (8%)

Query: 32  INFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIP-PVINALNHIIKEQKILDSSVN 89
           ++   +Q+++++  + ++    VK    ++    + I  P  ++L+   +       S +
Sbjct: 1   MSKNQIQQLIQANNITLNALPCVKNGTLLKLNDEIHITFPKPDSLDSNTQN-----ISPS 55

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---- 145
           L    + L   +LYED  I + NKP  + +     +    D  L  W+            
Sbjct: 56  LQNLYENLSIDILYEDDDILIINKPPHLVIHDAPSV---KDLTLTQWLKLHAHTLHTLSG 112

Query: 146 -----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC--- 197
                + HRLD++TSG+L +A++  A + L    + R++ + Y +++    K   +    
Sbjct: 113 RERYGIIHRLDKQTSGVLCIAKSLLAYEILPNQLKSRQMGRYYLAIIDTPLKQNLQVQCF 172

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLR 256
           +      +  +   ++   +   KG   + S F  +          + ++ HTGRTHQ+R
Sbjct: 173 MGRCPTNRLKMSKIHIDENENPPKGVRDSKSSFVKLATSNDGLLELIAIKLHTGRTHQIR 232

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            H   +   I+GD  Y        +   + ++ LHA  + L HP+ G+     AP+   M
Sbjct: 233 THLESLSRHILGDSLYGYKPSAK-SFFYEGRILLHAYILYLAHPKNGQNHTFKAPILLDM 291

Query: 316 VKTWD 320
           ++   
Sbjct: 292 LEFIQ 296


>gi|269964797|ref|ZP_06179034.1| Ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
 gi|269830457|gb|EEZ84679.1| Ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
          Length = 225

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 109/231 (47%), Gaps = 19/231 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           ++ +      ++  +  ++Y+D  + V NKP+G+    G  I       L++      + 
Sbjct: 7   VEPNPLAENWAEDKELEIIYQDDAMVVVNKPSGLLSVPGKTIKDSAYTRLQAMF-PDVEG 65

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSGILV A T+ A + L + F  R +QK Y +L+ G+    +  I+  + 
Sbjct: 66  PFVIHRLDMATSGILVFALTKRANKSLQKQFMARGVQKRYMALLEGVLNEPEGEISLPM- 124

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V  ++     +A +++++I+        + M P TGRTHQLRVH+ H  
Sbjct: 125 RGDPDDRPRQLVCFEH---GKHAETYWQLIE-VKDGRSKVYMYPKTGRTHQLRVHSAHHM 180

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
            +  P+VGD  Y             N+L+LHA  ++L HP    R+   A 
Sbjct: 181 GLNMPMVGDGLYGEK---------SNRLHLHAEMLELDHPYSKERMVFQAE 222


>gi|76788821|ref|YP_327907.1| tRNA pseudouridine synthase A [Chlamydia trachomatis A/HAR-13]
 gi|237802537|ref|YP_002887731.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/Jali20/OT]
 gi|237804454|ref|YP_002888608.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/TZ1A828/OT]
 gi|76167351|gb|AAX50359.1| tRNA pseudouridine synthase A [Chlamydia trachomatis A/HAR-13]
 gi|231272754|emb|CAX09659.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231273771|emb|CAX10553.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/Jali20/OT]
          Length = 274

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 69/320 (21%), Positives = 129/320 (40%), Gaps = 57/320 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVV 65
           +Q  +   D   +RL  + +   PH+    + + +R    RV+ +  +F + ++Q G  V
Sbjct: 1   MQEFIGTADRH-IRLSSFLRTSLPHLPKKTILESVRYHGCRVNGRIERFESYKLQPGDRV 59

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +  + ++                           LL+ED  + ++NKPA          
Sbjct: 60  SLQIIEHS------------------------SPQLLWEDEHLCIYNKPA---------- 85

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
               +               L HRLD++TSG ++ A+   A+  +T+ F+   I K Y +
Sbjct: 86  KQTSEDLAHQL------NVHLVHRLDRDTSGCILFAKHAKASSLITQLFKNPEIDKRYIA 139

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV+G P+ +   I  +        G  V     ++      I+ ++++  +  K+  L  
Sbjct: 140 LVFGQPRQESGIITTYTAPCYRRTG-AVLFGNTDQNSGKITITKWEILTRYP-KYTLLLC 197

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GR 304
           +P TGRTHQ+R+H   +G PIVGD  Y    +         +  LHA  +    P    +
Sbjct: 198 RPVTGRTHQIRLHMKTIGHPIVGDVDYGNQEQPKNVV----RTLLHAASLAFISPFSNEK 253

Query: 305 LQITA------PLP--AHMV 316
           +++++      P P  A   
Sbjct: 254 IEVSSLTPSQDPYPFYADFR 273


>gi|32474288|ref|NP_867282.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica SH 1]
 gi|32444826|emb|CAD74828.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica SH 1]
          Length = 256

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 59/250 (23%), Positives = 108/250 (43%), Gaps = 17/250 (6%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----IAYHIDGFL 133
           + +  I   +  +    +  +  ++YED+ + V NKP  ++  G +G     +   D   
Sbjct: 8   LADSPIGGETFFIRDSRNMSEVDVIYEDNHLLVVNKPTKLATMGAAGQPTLHSLGCDYIR 67

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR---IQKIYWSLVWGI 190
           ++          +  RLD  TSG++V+ART  AA  LT  F        +K Y ++V G 
Sbjct: 68  RTCNKPNKVYLGIVSRLDSMTSGVIVMARTSKAASRLTPQFANHSGDGAKKTYLAVVSGR 127

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            + ++  + + + K        + V   +   A  A   ++V+ C  ++   L ++P TG
Sbjct: 128 VEQQQGTLVDDVYKDD--AAHRMRVAHHSRSDAKEARLEYEVLGCD-RELTLLMVKPLTG 184

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITA 309
           R HQ+R+    +G PI+GD KY +             + LH+  + + HP    R+   A
Sbjct: 185 RKHQIRLQWAEVGFPILGDTKYGSERSWP------TGIALHSWRLSIMHPTKKERMTFEA 238

Query: 310 PLPAHMVKTW 319
           P+P       
Sbjct: 239 PIPDAWASRL 248


>gi|218247695|ref|YP_002373066.1| pseudouridine synthase [Cyanothece sp. PCC 8801]
 gi|218168173|gb|ACK66910.1| pseudouridine synthase [Cyanothece sp. PCC 8801]
          Length = 551

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 65/212 (30%), Positives = 104/212 (49%), Gaps = 18/212 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS--KGQKPRLTHRLDQETS 155
           +  ++YED  I   +KP+ +    G       D  L    +S    Q+ R  HRLDQ+TS
Sbjct: 343 EIKVIYEDQWIIAIDKPSSLLSVPGRYFE-TFDSVLTRLQNSLPDAQELRTVHRLDQDTS 401

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GIL++AR R   +HL++ F  R+++KIY +++ G     +  I   L    +        
Sbjct: 402 GILLLARDRYTHRHLSQQFAQRKVEKIYEAILAGSVMMNEGVIQLPLWGDPNNRP----Y 457

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA---LHMGCPIVGDHKY 272
            K + +    +I+ FKVI    +    ++  P TGRTHQ+RVHA     +G  I+GD+ Y
Sbjct: 458 QKVDWELGKPSITQFKVITTQ-ENLTRIQFIPLTGRTHQIRVHAVDTQGLGSVILGDYLY 516

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             N          ++L+LHAR +   HP+  +
Sbjct: 517 GCNA-------GVSRLHLHARELKFEHPQQQK 541


>gi|91794398|ref|YP_564049.1| pseudouridylate synthase [Shewanella denitrificans OS217]
 gi|91716400|gb|ABE56326.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           denitrificans OS217]
          Length = 225

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 61/218 (27%), Positives = 100/218 (45%), Gaps = 16/218 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  + V NKP+G+    G   A+     + S V ++     + HRLD  TSG++VV
Sbjct: 16  ILHQDKDVLVVNKPSGLLSVPGRDPAHSDS--IYSRVLAQFPNAHIVHRLDMATSGVMVV 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R+A + L   F  R  +K+Y++ V G        +   L+             K + 
Sbjct: 74  ALRRSAERELKRQFHDRETKKVYYARVAGHLSPVHTRVDLPLICDWPNRPK----QKVDH 129

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K    + +  K+I  + ++   +++ P TGR+HQLRVH + +G PI+GD  Y        
Sbjct: 130 KLGKPSSTLVKII-SYGKRSTLVKLSPITGRSHQLRVHMMALGHPILGDGFY----ADAL 184

Query: 281 TSPIQNKLYLHARYMDLPHPEGG-RLQITAP----LPA 313
              +  +L LHA  +   HP     L  +A     LP 
Sbjct: 185 AKRLAPRLLLHAAELTFCHPYSQDTLHFSADASFMLPE 222


>gi|238755849|ref|ZP_04617179.1| Pseudouridine synthase [Yersinia ruckeri ATCC 29473]
 gi|238705934|gb|EEP98321.1| Pseudouridine synthase [Yersinia ruckeri ATCC 29473]
          Length = 232

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 93/231 (40%), Gaps = 19/231 (8%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H        LY+D  + + NKPAG+    G          +   +    
Sbjct: 3   KIIDTFIAPPCHDKIEN---LYQDDHLVLINKPAGLLSLSGKNPQN--LDSVHYRLVQIF 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   + +  I   
Sbjct: 58  PGCTLVHRLDFGTSGLMVIARNKAINAALCQQFSQRSVTKVYSALLCGHLDDNEGVIDAA 117

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTH 253
           + K   +       +         A S ++V++ F              +++ P TGRTH
Sbjct: 118 IAKDPAL----FPRMSICATHGKPARSGYRVVERFYHELEDGTLLPLTRVQLTPETGRTH 173

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           QLR+H   +G PI G   Y              +L LHA  +   HP    
Sbjct: 174 QLRIHCQQLGHPIWGCDLYGGRLLPGTERT--PRLMLHASELHFVHPISEE 222


>gi|94497492|ref|ZP_01304062.1| pseudouridylate synthase [Sphingomonas sp. SKA58]
 gi|94423123|gb|EAT08154.1| pseudouridylate synthase [Sphingomonas sp. SKA58]
          Length = 225

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 61/225 (27%), Positives = 102/225 (45%), Gaps = 14/225 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
             L   +L+ D +  + +KPAG+ V      +  ++  L S      + P   HRLD++T
Sbjct: 2   PLLTDHVLFLDGEALILDKPAGLPVDAPRDGSMSLENHLASLTFGFQRWPLAVHRLDRDT 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L++AR   A +    +F    + K Y +++ G+P   +  IA  L K S     +  
Sbjct: 62  SGCLLLARNPKAHKRFAAAFEAGTVTKRYIAVLDGVPAETEGTIALSLKKVSTPTQGWRM 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC 273
           +     K    A++H++ +         +   P TGRTHQ+RVHA H +G  I+GD  Y 
Sbjct: 122 IA---AKAGKAAVTHWRKL-AERDGRALVAFTPETGRTHQIRVHAQHGLGFGIMGDPVYG 177

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                      +  + LH+R++ +P  +    + TAPLP      
Sbjct: 178 N---------GEGPMLLHSRFLSVPRGDKPAAEATAPLPQTFAAA 213


>gi|254785816|ref|YP_003073245.1| pseudouridine synthase for 23S rRNA and tRNAphe [Teredinibacter
           turnerae T7901]
 gi|237686915|gb|ACR14179.1| pseudouridine synthase for 23S rRNA and tRNAphe [Teredinibacter
           turnerae T7901]
          Length = 208

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 57/209 (27%), Positives = 96/209 (45%), Gaps = 19/209 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
              ++Y+D  I   NKPAG+    G +      D  +    +S     R+ HRLD  TSG
Sbjct: 3   DLAIIYQDDHIIAINKPAGLLTVPGLATPDNAFDQLVHQHPNS-----RVVHRLDMATSG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++  ++  +       F  R++ K Y + V GI    +  I   L+       D+ +  
Sbjct: 58  LVIFPQSHESLVRFGRLFEQRKMTKTYTATVAGIVAEDRGEITLPLI------CDWPNRP 111

Query: 217 KQNE--KGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           KQ    +   +A + +KV++     +   +E+ P TGR+HQLRVH   +G PI+GD  Y 
Sbjct: 112 KQKVDLEQGKHAHTQYKVLERRLDLQTTRIELTPITGRSHQLRVHMQQLGHPILGDAFYA 171

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            +     +    ++L LHA  ++  HP  
Sbjct: 172 PDAIQQAS----DRLLLHATTLEFVHPFT 196


>gi|114775713|ref|ZP_01451281.1| RNA pseudouridine synthase family protein [Mariprofundus
           ferrooxydans PV-1]
 gi|114553824|gb|EAU56205.1| RNA pseudouridine synthase family protein [Mariprofundus
           ferrooxydans PV-1]
          Length = 291

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 60/294 (20%), Positives = 120/294 (40%), Gaps = 39/294 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V       RLD+     +  ++    ++ +  G V ++ KR +    ++     +R+   
Sbjct: 14  VTTALAGQRLDQGLAEVF-TLSRRRSRRAIDEGGVYLNGKRCRTAGRKLSCHDNIRV--- 69

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG----ISVQGGSGIA 126
                 +++ ++++           F  + L+++   +Y+ +K +G     ++    G  
Sbjct: 70  -----VMLEGERLIP----------FTPAQLVWQQPPLYLIHKKSGQYAQEALHRSRGTL 114

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                       ++  + R  HRLD++TSG+++ + + A  QHL   +    ++K Y ++
Sbjct: 115 PDELARHLELTPAQASELRPVHRLDRDTSGLMLFSASAAMLQHLQAHWHD-AVEKRYLAV 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V   P    + I   + +     G Y               S   V++        +E+ 
Sbjct: 174 VSPAPDWDDQRIRLAIDRNRDAHGRY-----HLSPDGRACDSEAHVVERR-DNRALVELV 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           PHTGR+HQLRVH   +GCPI+GD +Y              +L LHA  + +  P
Sbjct: 228 PHTGRSHQLRVHLSALGCPILGDSRYGGKPH--------PRLMLHAVSLCIRPP 273


>gi|295698280|ref|YP_003602935.1| ribosomal large subunit pseudouridine synthase D [Candidatus Riesia
           pediculicola USDA]
 gi|291157095|gb|ADD79540.1| ribosomal large subunit pseudouridine synthase D [Candidatus Riesia
           pediculicola USDA]
          Length = 282

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 66/280 (23%), Positives = 119/280 (42%), Gaps = 21/280 (7%)

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
              ++   Q+    P I  L       K +D    +      +   +L+ED  I V +KP
Sbjct: 3   PKKKVYVDQIPINKPSIRILGEKSILIKDIDLEKKIQCIPKNIPLKILHEDDSIIVIDKP 62

Query: 115 AGISVQGGSGIAYH--IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
             + V  G+    +  +   +  +   K   +  + HRLD++TSG+++VA+  +    + 
Sbjct: 63  YNLCVHPGTHHEKNTLMHALMYHFPILKNIPRAGIVHRLDKDTSGLMIVAKKSSIQNQMM 122

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           + F+ R++ K Y ++V+G   N    I   + +       Y  +          A +H+ 
Sbjct: 123 KLFKSRKVYKEYEAIVYGNI-NSDGTIDKPIKRHP-----YERIKNFVCDFGRKAKTHYY 176

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA----NFKGNFTSPIQN- 286
           V + FA  F  + +   +GR HQ RVH  ++G PIVGD+ Y        K N+ S +   
Sbjct: 177 VKEKFA-NFTRIILSLESGRHHQARVHMKYIGHPIVGDYLYQDRQIIRKKKNYISNLIKI 235

Query: 287 -----KLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWD 320
                +  LHAR + + HP+   ++   +  P  M    D
Sbjct: 236 DQVISRQALHARKIKILHPQFKKKVTWKSNTPEDMRNLID 275


>gi|190572979|ref|YP_001970824.1| putative ribosomal large subunit pseudouridine synthase A
           [Stenotrophomonas maltophilia K279a]
 gi|190010901|emb|CAQ44510.1| putative ribosomal large subunit pseudouridine synthase A
           [Stenotrophomonas maltophilia K279a]
          Length = 245

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 55/212 (25%), Positives = 95/212 (44%), Gaps = 16/212 (7%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y D  + V  KPAG+    G          + + + +        HRLDQ TSG+L+ AR
Sbjct: 47  YIDDALLVAEKPAGLLSVPGRSAENQ--DCVVARLQALYPDALTVHRLDQVTSGLLLHAR 104

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            +     L+  F  R++ K Y ++V G+ +     +   L+         +     + + 
Sbjct: 105 GKDMQAALSMQFEQRQVGKRYEAVVQGLLEGDSGEVDLPLIVDWPNRPKQM----VDHER 160

Query: 223 ANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
              A++ ++V+    + +   + ++P TGR+HQLR+H   +G PIVGD  Y A       
Sbjct: 161 GKPALTRWRVLARDVEARRTRVALEPITGRSHQLRLHMASIGHPIVGDVLYDAAPA---- 216

Query: 282 SPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
               ++++LHAR +   HP  G  L   +  P
Sbjct: 217 ----HRVHLHARSLRFTHPLTGEVLAFESAAP 244


>gi|297583854|ref|YP_003699634.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297142311|gb|ADH99068.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 305

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 54/314 (17%), Positives = 110/314 (35%), Gaps = 30/314 (9%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVV 65
           ++  + +     + L    +N+   I+   L ++  + G + V+ K    ++++ +G  +
Sbjct: 13  IKTYIADPAWHGLMLREVLRNNL-MISRKLLAEVKFQGGALFVNGKNANVSDQVFTGDHI 71

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +      ++  IK                     + YED    V +KPAG+        
Sbjct: 72  EVWFPREDISSSIK--------------MSCKPLSIRYEDEWCIVIDKPAGLLTIPNETY 117

Query: 126 AYHIDGFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                             P       RLD++TSG++++A+ R +     +      I K 
Sbjct: 118 ENDSVAGRVIGYFKSCDHPATFHPVTRLDRQTSGLMLIAKDRHSHSLFMKQQCAGLIDKE 177

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++           +   + +      + +            A +    ++  A     
Sbjct: 178 YVAVTPPGFPWIAATVDAPIARHPDSIIERMV-----HHEGQKAKTRLVKVNENASG-SL 231

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-E 301
           +  +  TGRTHQ+RVH    G  I+GD  Y    +   ++    +  LHA  +    P  
Sbjct: 232 IRCKLETGRTHQIRVHLAFTGWSILGDGLY----REEKSADEHKRTLLHACSLRWDEPFT 287

Query: 302 GGRLQITAPLPAHM 315
           G R++I   +P   
Sbjct: 288 GERIEIHESVPEDF 301


>gi|15600875|ref|NP_232505.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O1 biovar eltor str. N16961]
 gi|121586851|ref|ZP_01676632.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           2740-80]
 gi|121727007|ref|ZP_01680203.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V52]
 gi|147672092|ref|YP_001214876.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|153801249|ref|ZP_01955835.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-3]
 gi|153817723|ref|ZP_01970390.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           NCTC 8457]
 gi|153821627|ref|ZP_01974294.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|254225870|ref|ZP_04919473.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V51]
 gi|254284827|ref|ZP_04959794.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           AM-19226]
 gi|9657491|gb|AAF96018.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|121548894|gb|EAX58935.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           2740-80]
 gi|121630641|gb|EAX63030.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V52]
 gi|124123267|gb|EAY42010.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-3]
 gi|125621597|gb|EAZ49928.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V51]
 gi|126511765|gb|EAZ74359.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           NCTC 8457]
 gi|126520824|gb|EAZ78047.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|146314475|gb|ABQ19015.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|150425612|gb|EDN17388.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           AM-19226]
          Length = 221

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 102/237 (43%), Gaps = 21/237 (8%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
            L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   ++ +
Sbjct: 2   PLEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-TQAE 60

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HRLD  TSG+LV A TR A + L + F  R +QK Y +L+ G     +  I   L
Sbjct: 61  GVFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAVQKRYVALIEGKLSETQGEIQLPL 120

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH- 261
                       V  Q       A++H++ +    Q    + + PHTGRTHQLRVH  H 
Sbjct: 121 CGD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHCAHH 175

Query: 262 --MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             +  PIVGD  Y    K         +L+LHA  +   HP   + +     + A  
Sbjct: 176 LGLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTFQ--VDADF 221


>gi|299772005|ref|YP_003734031.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) protein [Acinetobacter
           sp. DR1]
 gi|298702093|gb|ADI92658.1| putative dual specificity pseudouridine synthase for 23S rRNA and
           tRNAphe modification (RluA-like) protein [Acinetobacter
           sp. DR1]
          Length = 221

 Score =  156 bits (395), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 104/221 (47%), Gaps = 12/221 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + N           +L+ED  + V +KPAG+    G    +H   +L+  V  K   
Sbjct: 1   MPLNDNFVYAPPQDPLSILFEDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPL 58

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G    +       + 
Sbjct: 59  AKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKHYIALVQGQVTEEGSVEVPLIT 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +   +A + F+ +    +     + ++P TGR+HQLRVH +H+
Sbjct: 119 DWENRPRQIVHF-----ELGKHAKTLFQPLVYDEKVDQTRVLLEPVTGRSHQLRVHMMHI 173

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           G PI+GD  Y    K        +++ LHA ++   HP  G
Sbjct: 174 GHPIMGDKLYHPEPK----RFHLSRMALHAAHLAFQHPLKG 210


>gi|228475873|ref|ZP_04060583.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Staphylococcus hominis SK119]
 gi|314936097|ref|ZP_07843444.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus hominis subsp. hominis C80]
 gi|228270028|gb|EEK11498.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Staphylococcus hominis SK119]
 gi|313654716|gb|EFS18461.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus hominis subsp. hominis C80]
          Length = 274

 Score =  156 bits (395), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 59/276 (21%), Positives = 109/276 (39%), Gaps = 34/276 (12%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +   +L ++  S  + ++++  K  +++ +  VV IP      N++              
Sbjct: 23  LPKKDLHQLNMSKDITINQQSSKLTDKVVTNDVVYIPTPKEKSNYL-------------- 68

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHRL 150
               +  + + YED+ + +  KP G+            +  +   + +         HRL
Sbjct: 69  --PSYRYAQIAYEDNDLAIVVKPKGVKTHP--NDLKESNTLMNHVIYTMDSDYVEPIHRL 124

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS-HIG 209
           DQET G+L+VA+     + L       +I +IY + V  +   K + I   + K   H  
Sbjct: 125 DQETVGLLIVAKNPLMKKILDRMLEENQITRIYRANVKALLPLKPQTIDMPIGKDKFHPN 184

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
              +            AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD
Sbjct: 185 KRRI------SNTGQRAITHILTSKMIKEGICQLEIKLDTGRTHQIRVHLAEIGHPVIGD 238

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
             Y              +L L++  ++  HP    L
Sbjct: 239 PLYG--------DATLRQLELNSYKIEFTHPLTQEL 266


>gi|212635320|ref|YP_002311845.1| 23S RNA-specific pseudouridylate synthase [Shewanella piezotolerans
           WP3]
 gi|212556804|gb|ACJ29258.1| Pseudouridylate synthase, 23S RNA-specific [Shewanella
           piezotolerans WP3]
          Length = 256

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 97/229 (42%), Gaps = 24/229 (10%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           +      + +  +LY+D  + + NKP+G+    G   A      +   +        L H
Sbjct: 27  DFIAPPCYEEITILYQDEVMLLINKPSGLLSLSGKNPAN--LDSVHYRLVKLFPGCSLVH 84

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSGI+V+A  +     L   F  R + K Y +++ G  K  K  I   + K    
Sbjct: 85  RLDFGTSGIMVIALNKDINALLCRQFSERSVLKRYTAILLGELKEDKGVICAAIAKDKPN 144

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------------FCWLEMQPHTGRTHQ 254
                 ++K  E     A S ++V+                       +E+ P TGRTHQ
Sbjct: 145 ----FPLMKLCELEGKAARSLYQVLSKEYLGSANSAAERALDEVSVTRVELTPETGRTHQ 200

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           LR+H+ ++G PI+G   Y +     ++  + ++L LHA  ++  HP  G
Sbjct: 201 LRIHSQYIGHPIIGCDLYGS----AYSRQLASRLMLHATRLEFDHPVTG 245


>gi|153832681|ref|ZP_01985348.1| pseudouridylate synthase, 23S RNA-specific [Vibrio harveyi HY01]
 gi|148871026|gb|EDL69910.1| pseudouridylate synthase, 23S RNA-specific [Vibrio harveyi HY01]
          Length = 559

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 63/245 (25%), Positives = 112/245 (45%), Gaps = 20/245 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  + +     ++  +  +L++D  + + NKP+G+    G  I    
Sbjct: 328 CQPILGHMLQGLDVEPNPLA-ENWAEDKELEILFQDEAMVIVNKPSGLLSVPGKTIKDSA 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++      + P + HRLD  TSGILV A T+ A + L + F  R +QK Y +L+ G
Sbjct: 387 YTRLQAMF-PDVEGPFVIHRLDMATSGILVFALTKRANKSLQKQFITRGVQKRYMALLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +    +  I+  + +          V  ++      A +++++I+        + M P T
Sbjct: 446 VLTEPEGEISLPM-RGDPDDRPRQLVCFEH---GKPAETYWQLIE-VKDGRSKVYMYPKT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH+ H   +   +VGD  Y             ++L+LHA  ++L HP    R+
Sbjct: 501 GRTHQLRVHSAHHMGLNMAMVGDGLYGEK---------ADRLHLHAEMLELDHPYSKERM 551

Query: 306 QITAP 310
              A 
Sbjct: 552 CFQAE 556


>gi|332208640|ref|XP_003253415.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 4
           [Nomascus leucogenys]
          Length = 377

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 79/306 (25%), Positives = 128/306 (41%), Gaps = 41/306 (13%)

Query: 60  QSGQVVRIPPVINALNHIIKEQKILD---SSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           +     ++P   NA+   ++E          V+    +  L   +L++D  + V NKP G
Sbjct: 55  REQDTKKVPVSTNAVQRRVQEIVRFTRQLQQVHPNVLAKALTRGILHQDKNLVVINKPYG 114

Query: 117 ISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           + V GG G+   I   L    K     K +   L HRLD+ET+G++V+A  +  A  + E
Sbjct: 115 LPVHGGPGVQLCITDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWDKDMAHQVQE 174

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG---------------GDYVHVVK 217
            FR R++ K YW++   +P      +   +++K   G                D   V  
Sbjct: 175 LFRTRQVVKKYWAITVRVPMPSAGVVDIPIVEKEVQGQQQHHKMTLSPSYRVDDGKMVKV 234

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC--- 273
           +  + A  A++ ++V+         +E+QP TG  HQLRVH    + CPI+GDHKY    
Sbjct: 235 RRSRNAQVAVTQYQVLSS-TLSSALVELQPITGIKHQLRVHLSFGLDCPILGDHKYSDWN 293

Query: 274 ---------ANFKGNFTSPIQNK---LYLHARYMDLPH--PEGGRLQITAPLPAHMVKTW 319
                       K       + +   L+LHAR + LP        L +   LP   V + 
Sbjct: 294 RLAPQKLSVGTLKKLGLEQSKARYIPLHLHARQLILPALGSRKEELNLVCKLPRFFVHSL 353

Query: 320 DSLGFK 325
             L  +
Sbjct: 354 HRLRLE 359


>gi|27467615|ref|NP_764252.1| hypothetical protein SE0697 [Staphylococcus epidermidis ATCC 12228]
 gi|251810369|ref|ZP_04824842.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|282875499|ref|ZP_06284370.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|293367012|ref|ZP_06613686.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|27315159|gb|AAO04294.1|AE016746_84 conserved hypothetical protein [Staphylococcus epidermidis ATCC
           12228]
 gi|251806106|gb|EES58763.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|281295526|gb|EFA88049.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|291318867|gb|EFE59239.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|329733393|gb|EGG69726.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU028]
 gi|329738101|gb|EGG74319.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU045]
          Length = 284

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 64/284 (22%), Positives = 119/284 (41%), Gaps = 44/284 (15%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQK 82
           + KN     +   L  I  +G + ++   V   + +  G  + +  P      ++I   K
Sbjct: 16  FLKNQ--DYSKRTLSAIKLNGALLLNGSPVTVRHVMNKGDRLEVHFPCETPSENLIPYDK 73

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVD 138
            L+               ++YED+ + + NKP    +Q  +    H  G L     ++  
Sbjct: 74  ELE---------------VIYEDAYLIIVNKPQ---MQNCAPSREHPHGSLVEQVLAYYT 115

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            KG+K  P +  RLD+ TSG++V A+        ++    +     Y +L +G       
Sbjct: 116 KKGEKINPHIVTRLDRNTSGLVVFAKFGHVHHLFSKVKFKKE----YVALAYGH-TQSSG 170

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   + ++S    D +   + N+KG  YA + ++ +    +     +++  TGRTHQ+R
Sbjct: 171 VIEAPIARRS----DSIIKREVNDKG-KYAKTVYQRL-MQNETASLCKVKLLTGRTHQIR 224

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           VH  ++G P++GD  Y  N       P  +   LH   ++  HP
Sbjct: 225 VHFEYIGHPLIGDDLYGGN------HPCVHGQALHCCSVEFIHP 262


>gi|301782173|ref|XP_002926501.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 1 [Ailuropoda melanoleuca]
 gi|281338700|gb|EFB14284.1| hypothetical protein PANDA_016152 [Ailuropoda melanoleuca]
          Length = 377

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 79/310 (25%), Positives = 132/310 (42%), Gaps = 39/310 (12%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           R +   +    Q V   PV   +  +++  + L   V+    +  L   ++++D  + V 
Sbjct: 51  RAQKQEQKTKNQPVPTSPVQRRVQELVRFTQQLQR-VHPNVLAKALSRGIVHQDMDLVVI 109

Query: 112 NKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G++V+A  +  A
Sbjct: 110 NKPYGLPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEKEVA 169

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG---------------GDY 212
             + E FR R++ K YW++   +P      +   +++K   G                D 
Sbjct: 170 HQVQELFRTRQVAKKYWAVTVRVPVPPAGVVDIPVIEKEVQGQQQHYKMTLSPSYRMEDG 229

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHK 271
             V  + ++ A+ A++ ++V+         +E+QP TG  HQLRVH    + CPI+GDHK
Sbjct: 230 KMVRTRRDRNAHTAVTQYQVLSS-TLSSALVELQPITGVKHQLRVHLSFGLDCPILGDHK 288

Query: 272 YC------------ANFKGNFTSPIQNK---LYLHARYMDLPH--PEGGRLQITAPLPAH 314
           Y                K       + +   L+LHAR + LP        L +    P +
Sbjct: 289 YSDWNKLAPQKLSLGTLKKLGLQQAKARHIPLHLHARQLILPALGSRKEELNLVCKPPRY 348

Query: 315 MVKTWDSLGF 324
            V +   L  
Sbjct: 349 FVCSLRRLDL 358


>gi|114641168|ref|XP_508851.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein 4
           [Pan troglodytes]
          Length = 377

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 76/275 (27%), Positives = 119/275 (43%), Gaps = 38/275 (13%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   +L++D  + V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKALTRGILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P      +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWDKDMAHQVQELFRTRQVVKKYWAITVHVPMPSAGVVDIPIV 205

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G                D   V  +  + A  A++ ++V+         +E+QP 
Sbjct: 206 EKEAQGQQQHHKMTLSPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSS-TLSSALVELQPI 264

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC------------ANFKGNFTSPIQNK---LYLHA 292
           TG  HQLRVH    + CPI+GDHKY                K       + +   L+LHA
Sbjct: 265 TGIKHQLRVHLSFGLDCPILGDHKYSDWNRLAPQKLSVGTLKKLGLEQSKARYIPLHLHA 324

Query: 293 RYMDLPHPEGG--RLQITAPLPAHMVKTWDSLGFK 325
           R + LP    G   L +   LP   V +   L  +
Sbjct: 325 RQLILPALGSGKEELNLVCKLPRFFVHSLHRLRLE 359


>gi|221316663|ref|NP_116184.2| RNA pseudouridylate synthase domain-containing protein 4 isoform a
           [Homo sapiens]
 gi|74731354|sp|Q96CM3|RUSD4_HUMAN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 4
 gi|15559540|gb|AAH14131.1| RNA pseudouridylate synthase domain containing 4 [Homo sapiens]
          Length = 377

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 76/275 (27%), Positives = 119/275 (43%), Gaps = 38/275 (13%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   +L++D  + V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKALTRGILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P      +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWDKDMAHQVQELFRTRQVVKKYWAITVHVPMPSAGVVDIPIV 205

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G                D   V  +  + A  A++ ++V+         +E+QP 
Sbjct: 206 EKEAQGQQQHHKMTLSPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSS-TLSSALVELQPI 264

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC------------ANFKGNFTSPIQNK---LYLHA 292
           TG  HQLRVH    + CPI+GDHKY                K       + +   L+LHA
Sbjct: 265 TGIKHQLRVHLSFGLDCPILGDHKYSDWNRLAPQKLSVGTLKKLGLEQSKARYIPLHLHA 324

Query: 293 RYMDLPHPEGG--RLQITAPLPAHMVKTWDSLGFK 325
           R + LP    G   L +   LP   V +   L  +
Sbjct: 325 RQLILPALGSGKEELNLVCKLPRFFVHSLHRLRLE 359


>gi|153839865|ref|ZP_01992532.1| pseudouridylate synthase, 23S RNA-specific [Vibrio parahaemolyticus
           AQ3810]
 gi|149746612|gb|EDM57600.1| pseudouridylate synthase, 23S RNA-specific [Vibrio parahaemolyticus
           AQ3810]
          Length = 441

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 114/245 (46%), Gaps = 20/245 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  + +     ++  +  ++Y+D  + V NKP+G+    G  I    
Sbjct: 210 CQPILGHMMQGLDVEPNPLA-ENWAEDKELEIIYQDDAMVVVNKPSGLLSVPGKTIKDSA 268

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +++      + P + HRLD  TSGILV A T+ A + L + F  R +QK Y +L+ G
Sbjct: 269 YTRIQAMF-PDVEGPFVIHRLDMATSGILVFALTKRANKSLQKQFMARGVQKRYMALLEG 327

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +    +  I+  + +          V  ++     +A +++++ID        + M P T
Sbjct: 328 VLNEPEGEISLPM-RGDPDDRPRQLVCFEH---GKHAETYWQLID-VKDGRSKVYMYPKT 382

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH+ H   +  P+VGD  Y             N+L+LHA  ++L HP    R+
Sbjct: 383 GRTHQLRVHSAHHMGLNMPMVGDGLYGEK---------ANRLHLHAEMLELDHPYSKERM 433

Query: 306 QITAP 310
              A 
Sbjct: 434 VFRAE 438


>gi|289449819|ref|YP_003475504.1| RluA family pseudouridine synthase [Clostridiales genomosp. BVAB3
           str. UPII9-5]
 gi|289184366|gb|ADC90791.1| pseudouridine synthase, RluA family [Clostridiales genomosp. BVAB3
           str. UPII9-5]
          Length = 354

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 74/368 (20%), Positives = 132/368 (35%), Gaps = 79/368 (21%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V+  +    + +       H + + ++++   G++ +D K        QSGQ + +  +
Sbjct: 6   TVKMADSGRPVYQILMERL-HFSRLLIKRVKLHGRMEIDGKPELMKTPAQSGQKIVVFYM 64

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
             A           + +  +    D     +L++D    + NKPA +         +H +
Sbjct: 65  DPAG----------EVNRPIEAQPDI---PILFQDEWFIICNKPANLVTHP--TYLHHAN 109

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                            +RLD++TSG++++A+   A   LT     +R    Y +LV G 
Sbjct: 110 NLTARLCSDL---LHPVNRLDRDTSGLVILAKNGYAHHALTTVSIAKR----YLALVHGT 162

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHT 249
                  I+  + +          ++++       AIS F  +  + A +   LE  P T
Sbjct: 163 HVPDAGEISLPIARSPG-----SIILREINASGQTAISRFICLKRWPAAQVSLLEYTPVT 217

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN------------------------FKGNFTSPIQ 285
           GRTHQLR+H+L    PIVG+  Y  N                        ++G F  P +
Sbjct: 218 GRTHQLRLHSLMSSWPIVGETLYGCNRFYPGWPRLRPLFARADAKLKDEAYEGEFLVPRE 277

Query: 286 N-------------------------KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
                                     +  LHA  ++  HP  G ++ +   LP  M  T 
Sbjct: 278 KIGDLAELCPAYFDRDLCLRWDESMPRQALHAYKLEFVHPLTGEKIAVETALPDDMSHTV 337

Query: 320 DSLGFKYD 327
           D L    D
Sbjct: 338 DLLNKFTD 345


>gi|325972566|ref|YP_004248757.1| pseudouridine synthase [Spirochaeta sp. Buddy]
 gi|324027804|gb|ADY14563.1| pseudouridine synthase [Spirochaeta sp. Buddy]
          Length = 417

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 62/226 (27%), Positives = 99/226 (43%), Gaps = 21/226 (9%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQET 154
            L   ++Y+D  I V NKP+G+    G               +         THRLD +T
Sbjct: 203 MLGLDIVYQDEHIVVVNKPSGLLSVPGRTQDKIDSVETRIRLLYPHAPLQCATHRLDMDT 262

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+LVVA  + A   +   FR ++++K Y +L+ G+ K K   I              ++
Sbjct: 263 SGLLVVALNKQAHSRMHIQFREQQVKKSYIALLQGVVKQKSGSITLPFRVDITNRPHQIY 322

Query: 215 VVKQNEKGANYAISHFKVID----CFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIV 267
               +E    +  +H+  +        +    +  +P TGRTHQLR+H+ H   +G PIV
Sbjct: 323 ----DEVHGKWGTTHYTRLGVERTAEGELVTRMLFEPQTGRTHQLRLHSSHPKGLGIPIV 378

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           GD  Y         S +  +LYLHA+ +   HP  G+ +     +P
Sbjct: 379 GDRLYG--------SGMTERLYLHAQRISFSHPISGQMMDFCTEIP 416


>gi|145349937|ref|XP_001419383.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144579614|gb|ABO97676.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 243

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 59/247 (23%), Positives = 101/247 (40%), Gaps = 16/247 (6%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRL 146
           + +    D     +++E+ +  V NKP  +         +  +  L   +    G  P +
Sbjct: 1   LAIELVRDETPLDVVFENDEFLVVNKPPNLRFHPNH--RFEGNSLLSRALHHMDGATPYI 58

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC--IANWLLK 204
            HRLD +TSG+ V  + +    ++   F+ +  +K Y ++  G+         I +  + 
Sbjct: 59  VHRLDMDTSGVAVFVKKQHLVANVAGQFQEKTAKKTYLAVSVGVVPPDCGDSFIVDAPIG 118

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALH 261
              I  +   V    E     A +  ++I      A     + + P TGRTHQ+RVH  H
Sbjct: 119 DHGIVQEARTVDFSGE--GKDARTTCEIIARATPPAAVAALVRVTPLTGRTHQIRVHLAH 176

Query: 262 MGCPIVGDHKYCANFKGNF-----TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            G PIV D  Y  + +         +    +  LHA  ++L HPE G  L   A +P+ M
Sbjct: 177 AGLPIVSDALYGPHLRWKPYDDWGGALSIRRQALHAFNLELKHPETGESLTFQAKMPSDM 236

Query: 316 VKTWDSL 322
               D+L
Sbjct: 237 RSVCDAL 243


>gi|313676263|ref|YP_004054259.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
 gi|312942961|gb|ADR22151.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
          Length = 548

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 109/239 (45%), Gaps = 19/239 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++K   + D  + L   ++      LYED +I V  KPAG+       I   +
Sbjct: 315 CKPILGHMLKGLNLEDDPL-LQYTAEDKVIEKLYEDEQIVVIVKPAGLLSIPSKEIKDSV 373

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++     K   P L HRLD+ TSGI+++++   + + L + F  + IQK Y +++ G
Sbjct: 374 LTRMQKTY-PKATGPLLAHRLDKMTSGIMLISKDLDSHKFLQKQFMDKTIQKRYCAVLEG 432

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  +   L        D   + K + +    A++ +++I     K   +   P T
Sbjct: 433 TLDKSEGEVNLPLAVDE----DNRPMQKVDFESGRKALTKWRLI-SNNDKKSMVTFIPVT 487

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           GRTHQLRVHA H   +  PI+GD  Y    +         +L LHA Y+   HP+ GR+
Sbjct: 488 GRTHQLRVHAAHPKGLDAPIIGDTLYGNKAE---------RLMLHAEYIQFKHPQNGRI 537


>gi|304410331|ref|ZP_07391950.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307301958|ref|ZP_07581716.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304351740|gb|EFM16139.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306913996|gb|EFN44417.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 245

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 100/233 (42%), Gaps = 19/233 (8%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +LY+DS I + +KP+G+    G          +   +        L HRLD 
Sbjct: 18  PPCLGQIRVLYQDSDILLIDKPSGLLSLSGKNPLN--LDSVHYRLVQDFPTATLLHRLDF 75

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++VA  ++    LT+ F+ R ++K Y +L+ G        I   + K S    D+
Sbjct: 76  GTSGIMLVALNKSVNGLLTKQFQARTVEKRYTALLHGHIAADSGMINLPIAKDS----DH 131

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             + K        AIS ++V++     F   +E  P +GRTHQLR+H+   G  I+G   
Sbjct: 132 FPLQKICHSTGKPAISEYRVLERLTAPFATRVEFTPVSGRTHQLRIHSQQFGHSILGCDL 191

Query: 272 YCA---NFKGNFTSPIQN--------KLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y     +   N  +P  +        +L LHA  +   HP  G R+      P
Sbjct: 192 YGGVGESVADNAAAPDPDITKMASNSRLMLHATRLAFDHPITGERIDWICECP 244


>gi|217968528|ref|YP_002353762.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|217505855|gb|ACK52866.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 217

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 57/215 (26%), Positives = 93/215 (43%), Gaps = 14/215 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ D  + V +KPAG+      G        L + + ++    R+ HRLD  TSG+++ A
Sbjct: 12  LHVDECLLVVDKPAGLLSVPAGGEG--RQDCLAARIQARWADARIVHRLDAATSGLVLFA 69

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R     + ++ +F  R + K Y ++V G        I   L + +    D       +  
Sbjct: 70  RGAEMLRRMSLAFEQRIVGKQYVAVVHGHLAQDDGEIDLPLAEDA----DNRPRQIVDAL 125

Query: 222 GANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
               A++ ++V+D           LE++P TGR HQLRVH L +G PI GD  Y      
Sbjct: 126 RGRRALTRYRVLDRQGAGADACSRLELKPVTGRAHQLRVHLLCLGHPIFGDPLYAPPESA 185

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                   +++LHA  +   HP     +   +P P
Sbjct: 186 ARF----GRMHLHAARIAFMHPHTRVPMVFDSPAP 216


>gi|146329295|ref|YP_001209214.1| ribosomal large subunit pseudouridine synthase, RluA [Dichelobacter
           nodosus VCS1703A]
 gi|146232765|gb|ABQ13743.1| ribosomal large subunit pseudouridine synthase, RluA [Dichelobacter
           nodosus VCS1703A]
          Length = 203

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 57/214 (26%), Positives = 105/214 (49%), Gaps = 16/214 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   +KPAG+    G G        ++  +  +       HRLD  TSGI+++
Sbjct: 3   VVYQDEDMIAVDKPAGLLSVPGRGAEKRDS--VEWRIKQEYCGAAAVHRLDMSTSGIMLI 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ + A ++   +F  RR++K Y ++  G+    +  +   L+      GD+V+  KQ  
Sbjct: 61  AKHKDAERYYKTAFEQRRVKKGYVAICHGLIAEDEGEMNAPLI------GDWVNRPKQKV 114

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             +    A++ F V+    +    + + PHTGR+HQLRVH    G PIVGD+ Y      
Sbjct: 115 CYETGKAALTRFCVLSRQ-RDQTRVALFPHTGRSHQLRVHLADKGHPIVGDNLYG----- 168

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           +    +  +L LHA ++     +G  ++++  +P
Sbjct: 169 DAADCLLPRLLLHAEWLLFTRRDGAPIKLSTKIP 202


>gi|262041866|ref|ZP_06015050.1| ribosomal large subunit pseudouridine synthase A [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|259040771|gb|EEW41858.1| ribosomal large subunit pseudouridine synthase A [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
          Length = 232

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 56/223 (25%), Positives = 89/223 (39%), Gaps = 16/223 (7%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   +  LLY+D  + + NKPAG+    G          +   +  +     L HR
Sbjct: 8   FVAPPCREQITLLYQDEHLVLINKPAGLLSLSGK--DPRNLDSVHHRLVQRFPGCTLVHR 65

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++V+AR +     L + F  R + K+Y +L+ G     +  +   + K     
Sbjct: 66  LDFGTSGLMVIARNKGINALLCQQFSQRTVDKVYTALLCGHLAEDEGIVEAAIAKDPA-- 123

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKF--------CWLEMQPHTGRTHQLRVHALH 261
                 +    +    A S ++VID   Q            + + P TGRTHQLR+H   
Sbjct: 124 --RFPRMALCARHGKPARSRYRVIDRLYQAREGERALALTRVTLTPETGRTHQLRIHCQL 181

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +G PI+G   Y         +   ++L LHA  +   HP    
Sbjct: 182 LGYPILGCDLYGGRELPG--TECASRLMLHASELRFVHPVSHE 222


>gi|89898424|ref|YP_515534.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           felis Fe/C-56]
 gi|89331796|dbj|BAE81389.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           felis Fe/C-56]
          Length = 274

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 65/293 (22%), Positives = 120/293 (40%), Gaps = 48/293 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
            RL  + ++  P      +   +R    RV+ +  +F + ++Q G  + +   I +    
Sbjct: 12  ERLSSFLRSKLPDYTKQIIFDSIRYHGCRVNGRLERFESYKVQPGDCIALTLQIRS---- 67

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                               +  +L+ED    +++KP        +       G      
Sbjct: 68  --------------------EPKILWEDQHCCIYDKP----THTTTEDLAKTTGL----- 98

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                   + HRLD++T+G ++ A+   +A  L+E F+ R+I K Y +LV+G PK     
Sbjct: 99  -------HIVHRLDRDTTGCILFAKNTNSAHALSELFKKRKIHKQYTALVFGHPKKSSGT 151

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + ++   KS   G  V     ++      I+H+ V+  + + +  +  QP TGRTHQ+R+
Sbjct: 152 LISYTAPKSRRCG-AVIFGNTDKHSGKLTITHWSVLHSY-KHYTLMLCQPFTGRTHQIRL 209

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           H   +G PIVGD  Y    +         +  LHA  +    P    ++ + A
Sbjct: 210 HMHMLGNPIVGDLDYGRKEQPKNIF----RPLLHAHSLTFTSPLSQEKVDVVA 258


>gi|255037524|ref|YP_003088145.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
 gi|254950280|gb|ACT94980.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
          Length = 243

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 72/223 (32%), Positives = 102/223 (45%), Gaps = 14/223 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQ 152
              ++YED+ + + NK  GI VQ        +   +K ++     KP        HRLD+
Sbjct: 5   PFRVVYEDNHLIIVNKEPGILVQADVTGDACLLDLVKDYIKEAYNKPGAVFLGTVHRLDR 64

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
             SG++V ART  A + + E FR R +QK YW++V   P  KK  + +WL K      + 
Sbjct: 65  PVSGLVVFARTSKALERMNEIFRKRDVQKTYWAVVKNKPAEKKGKLVHWLTKNE--ARNV 122

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                +   G+  A   ++ +     KF  LE+ P TGR HQ+RV    M CPI GD KY
Sbjct: 123 TTAHDEEVPGSQRAELSYRWVGEI-NKFHLLEVMPVTGRPHQIRVQLASMNCPIRGDVKY 181

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
               KGN    I     LHAR +   HP     +   A +P  
Sbjct: 182 GY-PKGNPDGSIN----LHARRLYFEHPVKKEPIICRAGVPND 219


>gi|258566750|ref|XP_002584119.1| hypothetical protein UREG_04808 [Uncinocarpus reesii 1704]
 gi|237905565|gb|EEP79966.1| hypothetical protein UREG_04808 [Uncinocarpus reesii 1704]
          Length = 537

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 69/346 (19%), Positives = 118/346 (34%), Gaps = 80/346 (23%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           +        ++ + SG V ++ K    + R+ +G +V         +H +   +   +S+
Sbjct: 75  FRDRPAEYYKEAIESGHVAINGKPGNLDTRVMNGDMV---------SHTLHRHEPPVTSL 125

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
            +          +++ED K+ V +KPAG+ V       Y+    +          PR  +
Sbjct: 126 PIG---------VIHEDDKMIVIDKPAGVPVHPAGRYNYNSIIEIMRAERGHSFNPRPCN 176

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG++ + +   AA+ + E  R R +QK Y + V G   +        +LK S  
Sbjct: 177 RLDRLTSGVMFIGKDPKAAEKIAEGLRARTMQKEYIARVKGKFPDGIILCDQPMLKISPQ 236

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFA------------------------------- 237
            G     + +       A + F+ +  +                                
Sbjct: 237 LG-----LNRVRSSGKEAKTKFRRLAYYPPTAVTKKSSSEDEPATPPATLPDDAPMDFPN 291

Query: 238 -----------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----------AN 275
                      + +  +   P TGRTHQLRVH   +G PI  D  Y            A+
Sbjct: 292 NNNKATTTPDDEGYSIVHCLPLTGRTHQLRVHLQFLGHPITNDPIYSNRRVFGRDLGKAD 351

Query: 276 FKGNFTSPIQNKLYLHARYMDLP----HPEGGRLQITAPLPAHMVK 317
             G     I  +L    +         H          P P HM K
Sbjct: 352 NTGEHDQEIIARLSKMGKTETAQTIGDHRSKNYETFQTPPPEHMTK 397


>gi|170726728|ref|YP_001760754.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169812075|gb|ACA86659.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 238

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 99/229 (43%), Gaps = 27/229 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +L+ED  I V NKP+G+    G          +   +        L HRLD  TSGI
Sbjct: 16  EIQILFEDEHILVINKPSGLLSLSGKHPLN--IDSVHHRLAKIYPGCTLIHRLDFGTSGI 73

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+AR +     L + F  RR+ K Y +L+ G  +N    +   + K +    +   +++
Sbjct: 74  MVLARNKVINALLCKQFSERRVSKRYTALLQGTVENDSGIVDIGIAKDT----ENFPLMR 129

Query: 218 QNEKGANYAISHFKVIDCFAQKF----------------CWLEMQPHTGRTHQLRVHALH 261
              +    A S ++V+  F Q                    +E +P TGRTHQLR+H+ H
Sbjct: 130 LCNRTGKPAKSQYEVLSRFTQTAQDSFYVDDHRAGERAVSLVEFEPITGRTHQLRLHSKH 189

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           +G PI+G   Y  +     TS    +L LHA  +   HP     + I  
Sbjct: 190 LGHPILGCDLYATDEAFFMTS----RLMLHASLLTFEHPVSTKTMTIKC 234


>gi|302380202|ref|ZP_07268674.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
 gi|302311985|gb|EFK93994.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
          Length = 273

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 68/308 (22%), Positives = 132/308 (42%), Gaps = 45/308 (14%)

Query: 16  EENMRLDRWFKN-HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++ +RLD + K  H  H  F+++ K      + ++ K  K N++++ G +V I       
Sbjct: 9   DKKIRLDEFLKKNHISHNLFISIYK----DDIFINGKHAKRNSKLEKGDIVTINLRDEEN 64

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFL 133
            +                    +   +LYED  I+V NKP  +++ + G     +   +L
Sbjct: 65  KY----------------EPINMDIEVLYEDDDIFVLNKPDKLTMNKDGEKSLANFVSYL 108

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
               + K QK R  +RLDQ+TSG+++VA+ + A  +  ++   ++    Y ++V G PK+
Sbjct: 109 FKQRNIK-QKVRFINRLDQDTSGVVMVAKNKIAQAYYQKNSFKKK----YLAIVKGNPKD 163

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +K  I   L +          +  + ++    +++  + +  +   +  + ++  TGRTH
Sbjct: 164 QK--IELNLKRDG--------IKTEIDENGKKSVTILENLKNYGD-YSLVSLELLTGRTH 212

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           Q+RV   ++ CPIV D  Y    +            LHA  ++    +G    I   LP 
Sbjct: 213 QIRVSMEYINCPIVADSLYGEKIENFS-------QMLHANEIEFVDMKGEFHNIATNLPE 265

Query: 314 HMVKTWDS 321
                   
Sbjct: 266 RFKDYLKE 273


>gi|14042050|dbj|BAB55086.1| unnamed protein product [Homo sapiens]
          Length = 377

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 76/275 (27%), Positives = 119/275 (43%), Gaps = 38/275 (13%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   +L++D  + V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKALTRGILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P      +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWDKDMAHQVQELFRTRQVVKKYWAITVHVPMPSAGVVDIPIV 205

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G                D   V  +  + A  A++ ++V+         +E+QP 
Sbjct: 206 EKEAQGQQQHHKMTLSPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSS-TLSSALVELQPI 264

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC------------ANFKGNFTSPIQNK---LYLHA 292
           TG  HQLRVH    + CPI+GDHKY                K       + +   L+LHA
Sbjct: 265 TGIKHQLRVHLSFGLDCPILGDHKYSDWNRLAPQKLSVGTLKKLGLEQSKARYIPLHLHA 324

Query: 293 RYMDLPHPEGG--RLQITAPLPAHMVKTWDSLGFK 325
           R + LP    G   L +   LP   V +   L  +
Sbjct: 325 RQLILPALGSGKEELNLVCKLPRFFVHSLHRLRLE 359


>gi|158520422|ref|YP_001528292.1| pseudouridine synthase [Desulfococcus oleovorans Hxd3]
 gi|158509248|gb|ABW66215.1| pseudouridine synthase [Desulfococcus oleovorans Hxd3]
          Length = 258

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 105/230 (45%), Gaps = 18/230 (7%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR---- 145
            T      +  +LYED+ +    KPAG+ VQG S     +    + W+  +  KP     
Sbjct: 4   PTPDFFIPQWPVLYEDNHLLALYKPAGLLVQGDSTGDPTLLELGRCWLKIRYNKPGKVFL 63

Query: 146 -LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HRLD+  +G+++  RT  AA  ++  FR     K Y ++V G+    +  +AN + +
Sbjct: 64  GMVHRLDRPVAGVVLFCRTSKAAGRISAQFRDGVTAKQYVAVVEGVIPENEGRLANHIFR 123

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +        H++      +  A   F VID        +++   TGR HQ+RV   H+G 
Sbjct: 124 RGPTS----HIIDVPTPKSREARLAFHVIDR-TDSRTLVKIDLETGRHHQIRVQFAHLGF 178

Query: 265 PIVGDHKYCANFKGNFTSPIQNKL-YLHARYMDLPHPE-GGRLQITAPLP 312
           P+VGD +Y A       +P+  +   L AR + + HP  G  L  T+  P
Sbjct: 179 PVVGDLRYGA------PAPLPGRQIALLARRLTVTHPTLGHALTFTSSFP 222


>gi|108759188|ref|YP_631900.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108463068|gb|ABF88253.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 234

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 112/234 (47%), Gaps = 16/234 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +L+E   + V +KP G+ V  G      +   L++      QK  + HRLD++TSG 
Sbjct: 3   DVRILFEGGGVLVVDKPPGMLVIPGREGGPSLRELLETQRR---QKIFVVHRLDRDTSGA 59

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV A   A  + L+ +F   +++K Y +LV G  +  +   A  +  +       + V +
Sbjct: 60  LVFALDAAVHRALSGAFETGKVRKRYVALVEGRVEAPQMVDAPLVAGR----KGRMRVAR 115

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---- 273
             +  A  + +  + ++ F ++   +E +P TGRTHQ+RVH L +G P++ DH+Y     
Sbjct: 116 PGDTDAKASRTRVRPVETF-ERASLVEAEPLTGRTHQIRVHLLSLGHPLLVDHQYGREAP 174

Query: 274 ---ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSLG 323
               +  G   S + ++  LHA  ++ P   G   + + AP+P  M +  + L 
Sbjct: 175 LTEKDLGGEGDSVVLSRTPLHAARVEWPALAGVEARAVEAPVPEDMARARELLR 228


>gi|120555026|ref|YP_959377.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120324875|gb|ABM19190.1| tRNA pseudouridine synthase C [Marinobacter aquaeolei VT8]
          Length = 245

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 54/239 (22%), Positives = 98/239 (41%), Gaps = 20/239 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSG 156
               +Y D  +   +KPAG+ V       +  +  L+     + G+     HRLD+ TSG
Sbjct: 4   PLTEIYRDDWLLAVHKPAGLLVHRSPIDKHETEFALQYARAMNGGEHVYPVHRLDRPTSG 63

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ AR    A+ L  +     + K Y ++V G    ++  I + L ++          +
Sbjct: 64  VLLFARDPETARALGLAMMAGAVSKTYLAMVRG-WAPEQGVIDHPLREEPEDRR-----L 117

Query: 217 KQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           K  E+    A++ ++ +               ++  +E++P TGR HQLR H  H+  PI
Sbjct: 118 KGQEQPVREALTRYRRLATTELPVAIERYPTSRYSLVELKPETGRKHQLRRHMKHINHPI 177

Query: 267 VGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +GD  +       +      Q +L L A  + L HP     L + A   +  ++     
Sbjct: 178 IGDANHGRGRHNRYFAERFGQGRLMLAATELRLRHPVTDEPLCLKAHPESSFLQVLAIF 236


>gi|116490290|ref|YP_809834.1| pseudouridylate synthase, 23S RNA-specific [Oenococcus oeni PSU-1]
 gi|290889676|ref|ZP_06552765.1| hypothetical protein AWRIB429_0155 [Oenococcus oeni AWRIB429]
 gi|116091015|gb|ABJ56169.1| Pseudouridylate synthase, 23S RNA-specific [Oenococcus oeni PSU-1]
 gi|290480673|gb|EFD89308.1| hypothetical protein AWRIB429_0155 [Oenococcus oeni AWRIB429]
          Length = 302

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 58/281 (20%), Positives = 112/281 (39%), Gaps = 34/281 (12%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKI 108
           + + +  +  +  G  +         +   K Q  L ++          +  +L E    
Sbjct: 45  NGRNIPTSELVSPGDKLS---FSLETSDFSKGQNYLPNN--------DRRLRILSEKEDY 93

Query: 109 YVFNKPAGISVQG-----GSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVAR 162
            + +KPAG+ +          +  +++  LK  +         + HR+D++TSG++++A+
Sbjct: 94  LLVDKPAGMKMHPHSPNETDTLLNYVEAQLKGHLSRSCPAHAFMVHRIDRDTSGVVIIAK 153

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
              A   L +    +RI++ Y + V G  +NKK  I   +          +      ++ 
Sbjct: 154 NPLAVGILDQLLAKKRIKRTYLAWVSGNLENKKGSIDQAIAVDPINPYKRIV-----DQA 208

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++H+  I    Q    + +   TGRTHQ+RVH   +G PIVGDH Y          
Sbjct: 209 GQKAVTHWTKIHTVYQN-TLVRVSLETGRTHQIRVHFAAIGHPIVGDHLYNG-------- 259

Query: 283 PIQNKLYLHARYMDLPHPEGG---RLQITAPLPAHMVKTWD 320
              ++L LH+  +++P           IT  +P    +   
Sbjct: 260 LAYSRLLLHSATIEIPELFSESRQSHTITTAIPKDFPRQLK 300


>gi|209809357|ref|YP_002264895.1| putative RNA pseudouridylate synthase [Aliivibrio salmonicida
           LFI1238]
 gi|208010919|emb|CAQ81324.1| putative RNA pseudouridylate synthase [Aliivibrio salmonicida
           LFI1238]
          Length = 561

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 58/228 (25%), Positives = 101/228 (44%), Gaps = 19/228 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D +  L   ++     ++YED  + + NKPA      G  I   +   ++    +    
Sbjct: 343 MDENPLLINPAEGKDIDIIYEDEFMLIINKPADFLSVPGKNINDSVYTRVQQRYPNATGG 402

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLD   SG++V+  T  A + L + F  R ++K Y +L+ G+  +++  I   L 
Sbjct: 403 L-IVHRLDMAASGLMVLGLTSKAHKRLQKQFINRTVEKRYTALLDGLLPHREGQITLPLR 461

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
              +     +   +        A + + VI+   +K   + + P TGRTHQLRVH  H  
Sbjct: 462 GDLYDRPRQLVCFEY----GKQAETTYNVIEYK-EKQTLVHLYPKTGRTHQLRVHCAHHL 516

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
            +  PI+GD  Y             ++LYLHA Y+ + HP     ++ 
Sbjct: 517 GLNMPIIGDGLYGQK---------ADRLYLHAGYLSVTHPITKEPMEF 555


>gi|34763384|ref|ZP_00144336.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
 gi|27886957|gb|EAA24077.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
          Length = 214

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 56/221 (25%), Positives = 95/221 (42%), Gaps = 20/221 (9%)

Query: 117 ISVQGGSG-IAYHIDGFLKSWVDSK-----GQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           + V    G  +  +   L  + ++        +P + HRLD++TSG+++VA+   A   L
Sbjct: 1   MVVHPAYGNYSGTLVNALLYYTNNLSSINGNIRPGIIHRLDKDTSGLILVAKNNYAHAKL 60

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
              F  + I K Y  +V G    +     I N + + S      + VVK+N      AIS
Sbjct: 61  ASMFTDKTIHKTYLCIVKGNFSEENLNGRIENLIGRDSK-DRKKMAVVKEN---GKTAIS 116

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
           ++KVI+     +  +E+   TGRTHQ+RVH   +   I+GD  Y    K         + 
Sbjct: 117 NYKVIEQV-DGYSLVEIAIETGRTHQIRVHMKSINHVILGDSTYGNEDKNV------KRQ 169

Query: 289 YLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
            LHA  ++  +P +         L    ++    L F  ++
Sbjct: 170 MLHAYKLEFLNPLDNKEYIFKGRLFDDFIEVAKRLKFNIEK 210


>gi|119588079|gb|EAW67675.1| RNA pseudouridylate synthase domain containing 4, isoform CRA_a
           [Homo sapiens]
 gi|119588080|gb|EAW67676.1| RNA pseudouridylate synthase domain containing 4, isoform CRA_a
           [Homo sapiens]
          Length = 377

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 76/275 (27%), Positives = 119/275 (43%), Gaps = 38/275 (13%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   +L++D  + V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKALTRGILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P      +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWDKDMAHQVQELFRTRQVVKKYWAITVHVPMPSAGVVDIPIV 205

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G                D   V  +  + A  A++ ++V+         +E+QP 
Sbjct: 206 EKEAQGQQQHHKMTLSPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSS-TLSSALVELQPI 264

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC------------ANFKGNFTSPIQNK---LYLHA 292
           TG  HQLRVH    + CPI+GDHKY                K       + +   L+LHA
Sbjct: 265 TGIKHQLRVHLSFGLDCPILGDHKYSDWNRLAPQKLSVGTLKKLGLEQSKARYIPLHLHA 324

Query: 293 RYMDLPHPEGG--RLQITAPLPAHMVKTWDSLGFK 325
           R + LP    G   L +   LP   V +   L  +
Sbjct: 325 RQLILPALGSGKEELNLVCKLPRFFVHSLHRLRLE 359


>gi|261856729|ref|YP_003264012.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261837198|gb|ACX96965.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
          Length = 222

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 60/216 (27%), Positives = 101/216 (46%), Gaps = 14/216 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              LL E +   +  KP  +  Q G     H    L + V+ +  + R+ HRLD +TSG+
Sbjct: 19  PWRLLAETADFLIIAKPTRMLTQPGK--EAHKTDSLITRVNQEFPEARIVHRLDWDTSGV 76

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+AR   A + L+ +F+ RR +K Y + V   P   +  I   +        ++    +
Sbjct: 77  MVLARHARAHRALSIAFQDRRTKKCYIAHVDRAPAPPQGLIDRPIGSD----REHRPRYR 132

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +E+    + + + V++  A       ++P TGR+HQLRVH L +G PI GD  Y  + +
Sbjct: 133 IDEEQGRPSQTRYVVLNETADFARLA-LEPITGRSHQLRVHLLSIGHPIQGDTLYHPHAQ 191

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            +       +L LHA  +  P P  G     + P+P
Sbjct: 192 NHA------RLMLHAESLSFPDPASGITQTFSDPVP 221


>gi|330684742|gb|EGG96437.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU121]
          Length = 276

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 61/288 (21%), Positives = 113/288 (39%), Gaps = 37/288 (12%)

Query: 22  DRW-FKNHYPHI--NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           D++  +  +  +     +L  +  S  + ++K+  + ++++ SG  V IP      N++ 
Sbjct: 10  DQYTLREIFQDLKLPKKDLHLLNMSKDITINKQTSRLSDKVNSGDEVFIPTPEEKSNYL- 68

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                            +  + + YE+    +  KP G+            +  +   + 
Sbjct: 69  ---------------PSYRYAQVYYENDDFAIVLKPKGVKTHP--NDLKESNTLMNHLIY 111

Query: 139 S-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +         HRLDQET G+L+VA+     + L        I +IY + V  +   K + 
Sbjct: 112 TIDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEENDITRIYKAHVKALLPIKPQT 171

Query: 198 IANWLLKKS-HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           I   + K   H     +            AI+H    +   +  C LE++  TGRTHQ+R
Sbjct: 172 IDMPIGKDKFHPNKKRI------SNTGQRAITHILSSNMIKENVCELEIKLDTGRTHQIR 225

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           VH   +G P++GD  Y  +           +L LH+  ++L HP    
Sbjct: 226 VHLAEIGHPVIGDPLYGDS--------TLRQLELHSYKIELEHPLTKE 265


>gi|114776527|ref|ZP_01451572.1| pseudouridylate synthase, 23S RNA-specific [Mariprofundus
           ferrooxydans PV-1]
 gi|114553357|gb|EAU55755.1| pseudouridylate synthase, 23S RNA-specific [Mariprofundus
           ferrooxydans PV-1]
          Length = 579

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 63/217 (29%), Positives = 92/217 (42%), Gaps = 19/217 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED ++ V NKPAG+    G  I   +   L         +  L HRLD +TSG+L+V
Sbjct: 376 IVYEDDQLLVVNKPAGLMSTPGREIEESLFSRLAQRYPQI-PELTLVHRLDMDTSGLLLV 434

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWS-LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           A+     + L + F  R ++K Y + LV  +P    +      L+          V  Q+
Sbjct: 435 AKDLRTHKRLQKQFIERSVEKCYEAVLVKRLPAQPDQGRIELPLRVDLDDRPRQMVCYQH 494

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANF 276
                 A + +++I     +       P TGRTHQLRVHA H   +   IVGD  Y    
Sbjct: 495 ---GKPATTRWQIIARENNRTRIW-FYPETGRTHQLRVHASHRDGLNAAIVGDGLYG--- 547

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
                     +L LHAR +   HP     +    P P
Sbjct: 548 ------LPAERLMLHARRLCFTHPVSREPMVFELPAP 578


>gi|332140394|ref|YP_004426132.1| pseudouridylate synthase, 23S RNA-specific [Alteromonas macleodii
           str. 'Deep ecotype']
 gi|327550416|gb|AEA97134.1| pseudouridylate synthase, 23S RNA-specific [Alteromonas macleodii
           str. 'Deep ecotype']
          Length = 265

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 55/252 (21%), Positives = 100/252 (39%), Gaps = 17/252 (6%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           +  +        L   +LY+D  I   +KP G+ V       +     +++  D  GQ  
Sbjct: 14  EDVLKKQVEHQPLHLPVLYQDEHIIAIDKPPGLLVHRSPIDKHETVFAVQTLRDQIGQHV 73

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRLD+ TSG+LV + +   A  L +    +++ K Y ++V G   +          +
Sbjct: 74  FPAHRLDRPTSGVLVFSFSADTAAKLGKQMMDKQVVKQYHAIVRGFVHHTGYIDYALKYR 133

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQ 254
              I   +    K+ ++    A + ++ +             + ++  + + P TGR HQ
Sbjct: 134 YDKIADKH----KRPQQPPQPASTMYESLAKFDVPEPVGRYQSARYSLVRLSPSTGRKHQ 189

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPL 311
           LR H +H+  PI+GD  +    +  F     N   L L    M   HP   + + I   +
Sbjct: 190 LRRHMVHIRHPIIGDTTHGDGKQNKFAKSHFNFTHLALSCTQMGFSHPVTQKWITINGEM 249

Query: 312 PAHMVKTWDSLG 323
            + M +  D L 
Sbjct: 250 HSEMRQFTDRLA 261


>gi|225571170|ref|ZP_03780168.1| hypothetical protein CLOHYLEM_07258 [Clostridium hylemonae DSM
           15053]
 gi|225160001|gb|EEG72620.1| hypothetical protein CLOHYLEM_07258 [Clostridium hylemonae DSM
           15053]
          Length = 242

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 101/236 (42%), Gaps = 34/236 (14%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKGQKPRLTHRLDQ 152
           +  +LYED  I V  KP G +VQ  +  A  +   LK+ +      +      + HRLDQ
Sbjct: 5   RLDILYEDKDIIVCVKPHGTAVQTKNTSAPDMVSMLKTHIFSQEPQNGEPYLAVIHRLDQ 64

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              GILV A++  AA+ L    + +   K Y +LV GIP  +++ + N++LK        
Sbjct: 65  PVEGILVFAKSPFAAKELNRQLQNKGFGKYYRALVDGIPPREEDTLENYMLKDGRTNTSR 124

Query: 213 VHVVKQNEKGANYAISHFKVID------------------------CFAQKFCWLEMQPH 248
             +   +  GA  A  H+K+I                           A     L++Q  
Sbjct: 125 --ICTPDTPGAKQARLHYKIIQEGHGYFKKGHGETKRGRGKSQFPPSPAGPQTELDIQLD 182

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           TGR HQ+RV   H+GCPI GD KY     G        ++ L A  +   HP  GR
Sbjct: 183 TGRHHQIRVQMAHLGCPIAGDTKYNP---GAPNDGEWQQIQLCAYKLSFRHPRTGR 235


>gi|294054835|ref|YP_003548493.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
 gi|293614168|gb|ADE54323.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
          Length = 260

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 106/246 (43%), Gaps = 20/246 (8%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           D L++ +L +D ++ V NKP  +      +G    + G ++    +  +K  L  RLD+E
Sbjct: 15  DALQAWILRDDEELLVINKPGWLVCHPSKNGPLSSLVGAVREL--TGAEKLHLVARLDRE 72

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V A+  AAA+    + + R + K Y +++ G  +     + +  + +   G  +V
Sbjct: 73  TSGLVVFAKRPAAARKYQMAIQNRIVAKTYLAILEGTLEES--ILVDQSIARRKQGLVHV 130

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                  +GA  AI+ +  I      +    ++P TGR HQ+RVHA  +   +VGD  Y 
Sbjct: 131 KNEVSYVRGAQSAITRYVPI-AHGGGYTLARVEPETGRKHQIRVHAEWLEHRVVGDKIYG 189

Query: 274 ANF------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW-D 320
            +                  +    +  LH        PE   + +TAPL   M     D
Sbjct: 190 PDESLYLDFIENGWTPKLEAALPMKRQALHCYEYCFQFPE-QPVTLTAPLLEDMQSFCRD 248

Query: 321 SLGFKY 326
            +G + 
Sbjct: 249 EMGLEA 254


>gi|239637869|ref|ZP_04678830.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Staphylococcus warneri L37603]
 gi|239596432|gb|EEQ78968.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Staphylococcus warneri L37603]
          Length = 276

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 61/288 (21%), Positives = 113/288 (39%), Gaps = 37/288 (12%)

Query: 22  DRW-FKNHYPHI--NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           D++  +  +  +     +L  +  S  + ++K+  + ++++ SG  V IP      N++ 
Sbjct: 10  DQYTLREIFQDLKLPKKDLHLLNMSKDITINKETSRLSDKVNSGDEVFIPTPEEKSNYL- 68

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                            +  + + YE+    +  KP G+            +  +   + 
Sbjct: 69  ---------------PSYRYAQVYYENDDFAIVLKPKGVKTHP--NDLKESNTLMNHLIY 111

Query: 139 S-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +         HRLDQET G+L+VA+     + L        I +IY + V  +   K + 
Sbjct: 112 TIDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEENDITRIYKAHVKALLPIKPQT 171

Query: 198 IANWLLKKS-HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           I   + K   H     +            AI+H    +   +  C LE++  TGRTHQ+R
Sbjct: 172 IDKPIGKDKFHPNKKRI------SNTGQRAITHILSSNMVKENVCELEIKLDTGRTHQIR 225

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           VH   +G P++GD  Y  +           +L LH+  ++L HP    
Sbjct: 226 VHLAEIGHPVIGDPLYGDS--------TLRQLELHSYKIELEHPLTKE 265


>gi|163749714|ref|ZP_02156960.1| Pseudouridylate synthase, 23S RNA-specific [Shewanella benthica
           KT99]
 gi|161330527|gb|EDQ01485.1| Pseudouridylate synthase, 23S RNA-specific [Shewanella benthica
           KT99]
          Length = 227

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 58/215 (26%), Positives = 95/215 (44%), Gaps = 13/215 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             + Y D  I V NKP+G+    G       D  L   +    +   L HRLD  TSGI+
Sbjct: 24  LDIRYRDRDILVINKPSGLLSNPGRA-ENTYDCALTRLLQRYPETI-LVHRLDCATSGIM 81

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A  + A  ++   F+ R  +K Y + V G+    +  I   +             +++
Sbjct: 82  VFALNKKAESNIKTQFQNRMSKKTYIAEVRGLLSQDQGVIELAMKAN-----KTRPPLQE 136

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  + +++KV++   +    +E++P TGRTHQLR+H L +G PI+GD  Y      
Sbjct: 137 IAADGKASKTYYKVLERR-ENRTLVELKPVTGRTHQLRLHMLAIGHPILGDDFYGDKEVI 195

Query: 279 NFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
             +S    +L LHA  + + HP     +   +  P
Sbjct: 196 AASS----RLRLHAMSLSIRHPFSAKEITFKSSHP 226


>gi|194467273|ref|ZP_03073260.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
 gi|194454309|gb|EDX43206.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
          Length = 306

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 64/300 (21%), Positives = 120/300 (40%), Gaps = 31/300 (10%)

Query: 22  DRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           D+W   N   H   +          V V+      N  ++    +++    + +      
Sbjct: 26  DQWLLPNRLIHYLRIR-------RTVLVNGNYRSMNEIVEKNDNIQLLFCGDEIRTPAAN 78

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDS 139
             I  S  +L          +LYE+  + V NKP G        G    +   +  ++ +
Sbjct: 79  DYIPSSQPHLE---------VLYENRDLLVVNKPRGQKTHPNYHGETGTLMNDVAGYLVN 129

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                 + HR+D +TSG ++VA+       L       +I + Y ++V G      +   
Sbjct: 130 SENNAYMVHRIDLQTSGAVIVAKNPIVVPILNRLISDGQIHRQYLAVVEGKMAQSGKF-- 187

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +W + ++ +     H+ + N + A  A++++  +    ++   ++++  TGRTHQLRVH 
Sbjct: 188 DWAIGRNPVN---PHLHQVNGQNAQPALTYYDTLASN-RERSLVKLRLVTGRTHQLRVHL 243

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
            + G PIVGD  Y               L+  A+ + LP      L I+APLP++     
Sbjct: 244 AYSGHPIVGDPLYNPLSTEGML------LHGVAQKLILPF-VMKSLNISAPLPSYFENYL 296


>gi|162454823|ref|YP_001617190.1| hypothetical protein sce6541 [Sorangium cellulosum 'So ce 56']
 gi|161165405|emb|CAN96710.1| hypothetical protein sce6541 [Sorangium cellulosum 'So ce 56']
          Length = 666

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 63/259 (24%), Positives = 106/259 (40%), Gaps = 40/259 (15%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQ---KPRLTHR 149
            D     +L ED  + V +KPAG+S     +     +   L++++  +G       +  R
Sbjct: 12  PDIHPEWILAEDGDLIVVDKPAGLSTHAPEAERIDDMVTRLRAFLRGRGDAEAYLGIHQR 71

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLL----- 203
           LD++TSG+L+  R R A   +   F  R +QK Y + V G   +  +  + + L+     
Sbjct: 72  LDRDTSGVLLFTRRREANAAVARQFEGRTVQKTYVAAVSGFGDRPPRGTLRHRLVPAPGG 131

Query: 204 -----------KKSHIGGDYVHVVKQNEKGANY---------AISHFKVIDCFAQKFCWL 243
                      ++            + ++ A           AI+ +++++    +   L
Sbjct: 132 AMRALAESGGAREDRAAKREDRAAGREDRAAKREDRAASGVLAITRYRLLERRGDRA-LL 190

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E++P TGRTHQLRV    +G PI GD  Y          P   +L LHA  + L HP  G
Sbjct: 191 ELRPETGRTHQLRVQLAAIGLPIAGDPLYGG--------PEAPRLLLHAAELRLDHPATG 242

Query: 304 -RLQITAPLPAHMVKTWDS 321
                 + LPA       +
Sbjct: 243 AAATFRSRLPAVFEAWLAA 261


>gi|145299818|ref|YP_001142659.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142852590|gb|ABO90911.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 232

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 60/220 (27%), Positives = 90/220 (40%), Gaps = 16/220 (7%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   +L+ED  + + NKP+G+    G          +   +        L HRLD 
Sbjct: 11  PPCEAAIEILFEDEHLLLINKPSGLLSLSGKNPQN--LDSVHYRLVQDYPGCTLVHRLDF 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI+VVAR +A    L + F  R + K Y +L+     + +  I   + K   +    
Sbjct: 69  GTSGIMVVARNKAINALLCQQFSQRAVSKAYSALLCDHLTDDEGMIDAPIAKDPAL---- 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLE--------MQPHTGRTHQLRVHALHMGC 264
             ++K        A S ++V D   ++    E        + P TGRTHQLR+H   +G 
Sbjct: 125 FPLMKICAASGKPARSRYEVEDRLCRESEHGETQLLTRVRLVPETGRTHQLRIHCQLVGH 184

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           PI+G   Y              +L LHA  +DL HP  G 
Sbjct: 185 PILGCDLYGGLLLPGCEQ--APRLMLHASELDLVHPVSGE 222


>gi|261884230|ref|ZP_06008269.1| ribosomal pseudouridine synthase [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 238

 Score =  155 bits (393), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 101/237 (42%), Gaps = 27/237 (11%)

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---------KPRLTHRLDQETSGILVVAR 162
           NKP+ ++V     +    +  L  W+   G          +  + HRLD+ TSG++VVA+
Sbjct: 4   NKPSNLTVHPAPSV---KEATLVEWLKQNGYMLSTLNGDIRAGIVHRLDKGTSGVIVVAK 60

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
             A+   L      + + ++Y +L+       K  I   + +         + V  N + 
Sbjct: 61  NNASHSALAAQLSDKSMGRVYLALI-DFNLKDKLIIDRPIGRNPX--NRLKNSVAANGRA 117

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
           A  A ++             +  +  TGRTHQ+RVH   +   I+GD+ Y    K     
Sbjct: 118 AKSAFTNI----ICEDDLNLIAAKLFTGRTHQIRVHLASINRHILGDNLYGFKSKNCK-- 171

Query: 283 PIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
               ++ LHA  ++L HP  G ++Q  APLP      +D L  K D+ +  +++  +
Sbjct: 172 --IKRVMLHAYILNLTHPKSGEKMQFIAPLPTDF---YDILSKKIDKEILNEKIDPE 223


>gi|327404859|ref|YP_004345697.1| ribosomal large subunit pseudouridine synthase D [Fluviicola
           taffensis DSM 16823]
 gi|327320367|gb|AEA44859.1| ribosomal large subunit pseudouridine synthase D [Fluviicola
           taffensis DSM 16823]
          Length = 235

 Score =  155 bits (393), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 68/228 (29%), Positives = 107/228 (46%), Gaps = 16/228 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQE 153
             +LYED+ + V NK AG +VQG     + +   ++ ++  K  KP      L HRLD+ 
Sbjct: 7   EDVLYEDNHLLVVNKHAGENVQGDISGDFPLVEKVREFIRHKFDKPGNVFCGLIHRLDRP 66

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
            SG +  ART  A   + + F  +  +KIYW++V   PK K   + + L +       Y 
Sbjct: 67  VSGAIAFARTSKALTRMNKLFAEKHPRKIYWAVVEKAPKEKSGSLTHHLERNEKQNKTYA 126

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              ++  K    A   ++ +   +  +  LE++  TGR HQ+R     +GC I GD KY 
Sbjct: 127 F--QEERKNTKEARLKYRQLLS-SDNYTLLEVELETGRHHQIRAQLSAIGCIIKGDLKYG 183

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           A       S     +YLH+R ++  HP     ++I AP+P    K W 
Sbjct: 184 AKRSNPDGS-----IYLHSRELEFEHPTSKEVVKIIAPVPQD--KLWQ 224


>gi|325473944|gb|EGC77132.1| RNA pseudouridylate synthase [Treponema denticola F0402]
          Length = 264

 Score =  155 bits (393), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 60/290 (20%), Positives = 106/290 (36%), Gaps = 37/290 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS    + Y  +  D+   RLDR  +     +    +   +R G++RV+ K+       Q
Sbjct: 1   MSKENKIFY--IGEDDSGRRLDRVIRKFLGKMPLSGVYSAIRRGKIRVNGKKENGAYLTQ 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G  + +   +  L     E +          +    K  +L +   +   NK +G  V 
Sbjct: 59  KGDEISMDLSLFGLTAPASEDQT---------NYSISKPDVLLKTDDLLFINKRSGELVH 109

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G   +   +  +  S   S   K    HRLD++TSGIL  +++   AQ  + + +  +I 
Sbjct: 110 GEKSLCEAVLKYFPSKEKSLSFKVGALHRLDKDTSGILAFSQSLKGAQGFSRALQEGKIG 169

Query: 181 KIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFA 237
           K Y  +  G P     K  I                            +   +++D    
Sbjct: 170 KFYIGITEGRPSLSEFKSIID-----------------------GKECLCLIRILDFSKE 206

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +    +     TGR HQ+R+     G P++ D KY +  K  F+  +  K
Sbjct: 207 ENLSLVLFNLITGRKHQIRIQCSQFGTPLLNDKKYGSKQKKAFSEDLSKK 256


>gi|290508924|ref|ZP_06548295.1| ribosomal large subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
 gi|289778318|gb|EFD86315.1| ribosomal large subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
          Length = 263

 Score =  155 bits (393), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 57/223 (25%), Positives = 88/223 (39%), Gaps = 16/223 (7%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   +  LLY+D  + + NKPAG+    G          +   +  +     L HR
Sbjct: 39  FVAPPCREQITLLYQDEHLLLINKPAGLLSLSGK--DPRNLDSVHHRLVQRFPGCTLVHR 96

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++VVAR +     L + F  R + K+Y +L+ G     +  +   + K     
Sbjct: 97  LDFGTSGLMVVARNKDVNALLCQQFSQRTVAKVYTALLCGHLAEDEGIVEAAIAKDPA-- 154

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALH 261
                 +    +    A S ++VID   Q            + + P TGRTHQLR+H   
Sbjct: 155 --RFPRMSLCARHGKPARSRYRVIDRLYQSRDGERALALTRVALTPETGRTHQLRIHCQL 212

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +G PI+G   Y         +    +L LHA  +   HP    
Sbjct: 213 LGYPILGCDLYGGRELPG--TEQAPRLMLHASELRFVHPVSHE 253


>gi|330991266|ref|ZP_08315217.1| Putative RNA pseudouridine synthase [Gluconacetobacter sp. SXCC-1]
 gi|329761285|gb|EGG77778.1| Putative RNA pseudouridine synthase [Gluconacetobacter sp. SXCC-1]
          Length = 242

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 102/237 (43%), Gaps = 18/237 (7%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
             +  L   +LY DS+  V +KP G+ V         ++ +    +      P L HRLD
Sbjct: 2   PPARSLPCAVLYHDSRFIVLDKPPGLPVHPARAGGPSVEDWFP-LISRHRNGPWLAHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q+T+G LVVA  + A     E F   R +K YW++V G+P      +   L +   +   
Sbjct: 61  QDTAGCLVVALRKQALVAAQECFAAGRARKTYWAIVQGMPAGPSGTVDAPLAR---VEQG 117

Query: 212 YVHVVKQNEKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               ++   +G   A + ++ +    D       WLE+   TGRTHQ R H   +GCPI+
Sbjct: 118 RQWRMQVTARGGQPARTRWRTLATGQDGAGNPISWLELVLETGRTHQARAHCAALGCPIL 177

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           GD          + +     L+L +R + L  P    +   A  PAHM +     G+
Sbjct: 178 GDA--------RYGARAAGALHLMSRSIHL--PLDVPVHAMAMPPAHMDRLMAQAGW 224


>gi|332665601|ref|YP_004448389.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
 gi|332334415|gb|AEE51516.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
          Length = 224

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 70/226 (30%), Positives = 114/226 (50%), Gaps = 12/226 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETS 155
            +  L E       NKP G SV+   G    I+  + +++  +   P   + HRLD+ TS
Sbjct: 6   PNWWLAETGAWIAVNKPFGFSVEKTLGADDTIEDQVLAYLSRQTTMPFVGIVHRLDRVTS 65

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GIL++A+ ++A + L E F  R ++K+YW++V GIP+  +  ++ WL K          V
Sbjct: 66  GILLLAKKKSALRKLNEQFSQRSVKKMYWAMVEGIPQVPEATLSQWLYKDQKE--KKAVV 123

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +  +  +    H++V+    Q    LE++  TG+ HQ+RV    +G PI+GD KY A 
Sbjct: 124 FDEPAENRDACQLHYRVVQ-HNQTKALLEIELFTGKFHQIRVQMAALGSPIIGDEKYGA- 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
              +  S     + LHAR ++   P+ G  + + A LPAH    WD
Sbjct: 182 ---SHFSYADKGIALHARSLEFVDPQSGAPVVLVANLPAH--PVWD 222


>gi|311693912|gb|ADP96785.1| tRNA pseudouridine synthase C [marine bacterium HP15]
          Length = 247

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 94/231 (40%), Gaps = 10/231 (4%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSG 156
              +LY D  +   +KPAG+ V       +  +  L+      G Q     HRLD+ TSG
Sbjct: 4   PLTVLYRDEHLLAVHKPAGLLVHRSPIDKHETEFALQYARALNGGQHVYPVHRLDRPTSG 63

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-----D 211
           +LV AR    A+ L  +     + K Y ++V G P    E I + L ++           
Sbjct: 64  VLVFARDSDTARTLGMALMAGEVTKTYLAMVRGWPPEHGE-IDHPLREEPEDRRLKGEEQ 122

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            V       +         ++    + ++  +E+ P TGR HQLR H  H+  PI+GD  
Sbjct: 123 PVRDALTYYRTLTTTEIPVEIEKYPSSRYAVVELNPKTGRKHQLRRHMKHINHPIIGDAN 182

Query: 272 YCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           +       +      Q +L L A  M   HP  G+ L I+A   A  ++  
Sbjct: 183 HGRGRHNRYFAERFGQGRLMLAATRMAFQHPVSGKPLTISAAPEASFLEVL 233


>gi|329729823|gb|EGG66216.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU144]
          Length = 284

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 64/284 (22%), Positives = 119/284 (41%), Gaps = 44/284 (15%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP-PVINALNHIIKEQK 82
           + KN     +   L  I  +G + ++   V   + +  G  + +  P      ++I   K
Sbjct: 16  FLKNQ--DYSKRTLSAIKLNGALLLNGSPVTVRHVMNKGDRLEVHFPCETPSENLIPYDK 73

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVD 138
            L+               ++YED+ + + NKP    +Q  +    H  G L     ++  
Sbjct: 74  ELE---------------VIYEDAYLIIVNKPQ---MQNCAPSREHPHGSLVEQVLAYYT 115

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            KG+K  P +  RLD+ TSG++V A+        ++    +     Y +L +G       
Sbjct: 116 KKGEKINPHIVTRLDRNTSGLVVFAKFGHVHHLFSKVKFKKE----YVALAYGH-TQSSG 170

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   + ++S    D +   + N+KG  YA + ++ +    +     +++  TGRTHQ+R
Sbjct: 171 VIEEPIARRS----DSIIKREVNDKG-KYAKTVYQRL-MQNETASLCKVKLLTGRTHQIR 224

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           VH  ++G P++GD  Y  N       P  +   LH   ++  HP
Sbjct: 225 VHFEYIGHPLIGDDLYGGN------HPCVHGQALHCCSVEFIHP 262


>gi|73663086|ref|YP_301867.1| RNA pseudouridylate synthase [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72495601|dbj|BAE18922.1| putative RNA pseudouridylate synthase [Staphylococcus saprophyticus
           subsp. saprophyticus ATCC 15305]
          Length = 284

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 56/287 (19%), Positives = 112/287 (39%), Gaps = 36/287 (12%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L  + + H  H +   +  I  +G + V+ + V    ++  G ++ +       +  +K 
Sbjct: 13  LRSFLQRH--HFSKRTISAIKHNGALVVNGQTVTVRKQLAIGDILEVYLGKEIPSTNLKP 70

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDS 139
            +                  +L+ED  + V +KP   +       + Y I   +  +++ 
Sbjct: 71  YQQ--------------PLNILFEDDYLIVVSKPPYQNCAPSRDHLHYSIVEQVLGYLNE 116

Query: 140 K--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           K  G  P +  RLD+ TSGI+++A+       ++     ++    Y  + +G    K+  
Sbjct: 117 KQPGINPHIVTRLDRNTSGIVILAKHGFIHHLMSNLNIDKK----YLCICYGK-TEKEGV 171

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +          + ++ +     A + FK ++   + F   E+   TGRTHQ+RV
Sbjct: 172 IDAPIARHPE-----SIIQRRVDAAGKTAQTRFKRVEYK-EGFSMCEVTLLTGRTHQIRV 225

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           H  H+G  IVGD  Y    +        +   L    +   HP   +
Sbjct: 226 HFQHIGHSIVGDALYGGKHES------YHHQLLRCTQVAFIHPIKNQ 266


>gi|124022639|ref|YP_001016946.1| pseudouridylate synthase [Prochlorococcus marinus str. MIT 9303]
 gi|123962925|gb|ABM77681.1| putative pseudouridylate synthase [Prochlorococcus marinus str. MIT
           9303]
          Length = 207

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 59/214 (27%), Positives = 97/214 (45%), Gaps = 18/214 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L++DS +    KP G+  Q G G+       L   +     + RL HRLD++TSG+L+
Sbjct: 2   RVLFQDSWLIAVEKPPGLLSQPGLGVD--QQDSLIGRLQFFDSELRLVHRLDRDTSGLLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   + +  +  F  RR++K+Y ++V G        I+  + +       Y    +  
Sbjct: 60  LARGAESLRRCSMLFSARRVRKLYLAVVVGRMNRNAGTISFPMARLQKNPPLYGKHSQ-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 + S ++V  C A       + P TGR+HQLR H   +G PI+GD  Y       
Sbjct: 118 ---GKESRSQWRVRSCHANGSTLW-LWPLTGRSHQLRAHLASVGHPILGDPIYGKKV--- 170

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG---RLQITAP 310
                  +++LH+  +   HP  G   RL+  AP
Sbjct: 171 ----FFERMHLHSTALSFRHPFTGLRLRLRSRAP 200


>gi|42523281|ref|NP_968661.1| ribosomal large subunit pseudouridine synthase C [Bdellovibrio
           bacteriovorus HD100]
 gi|39575486|emb|CAE79654.1| ribosomal large subunit pseudouridine synthase C [Bdellovibrio
           bacteriovorus HD100]
          Length = 231

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 104/229 (45%), Gaps = 11/229 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSK---GQKPRLTHRLDQETSG 156
           +L+ED       KPAG+  Q             LK+ + ++        L HRLD++TSG
Sbjct: 4   ILFEDEFFLAAAKPAGMPSQATVDKSRQDFFTALKNQLRNERGDAFYLALHHRLDRDTSG 63

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++ A+T+ A + L + F+  +IQK Y  L     K       +  L +          +
Sbjct: 64  VMIFAKTKEANEPLADLFKTHKIQKTYLCLTKRTQKAADAWEVDNHLVEMKDTKLKKTKM 123

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            + + G + A + F+ ++ F +    +E QP TGR HQ+RVH    G  I GD  Y    
Sbjct: 124 VRTQSGGDRAYTKFRKLEVFPEAL-LIEAQPLTGRMHQIRVHLADRGMGIYGDDIY---- 178

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
                +P+  +L LHA  ++  HP     ++I   +PA M +   +L F
Sbjct: 179 -QAPKNPVAPRLMLHAHALEFTHPFTKEFVRIECAVPADMAQFMKTLTF 226


>gi|294140341|ref|YP_003556319.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293326810|dbj|BAJ01541.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 218

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 59/212 (27%), Positives = 97/212 (45%), Gaps = 13/212 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             + Y+D  I V NKP+G+    G   A   D  L   +  +  +  L HRLD  TSGI+
Sbjct: 14  LDIRYQDRDILVINKPSGLLSNPGRA-ANTYDCALTRLLQ-RYPEIILVHRLDCATSGIM 71

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A  + A  ++   F+ R  +K Y + V G     +  I   +             +++
Sbjct: 72  VFALNKKAESNIKTQFQNRMSKKTYIAEVLGQLNQDQGVIDLAMKAD-----KIRPPLQE 126

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             +    + +++KV++   +    +E++P TGRTHQLR+H L +G PI+GD  Y      
Sbjct: 127 IAEDGKVSKTYYKVLERR-ETSTLVELKPVTGRTHQLRLHMLALGHPILGDEFYG----D 181

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
                  N+L LHA  + + HP  G  +   +
Sbjct: 182 ADVIAASNRLKLHAMSLTIAHPFSGKEMTFKS 213


>gi|153828997|ref|ZP_01981664.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           623-39]
 gi|148875528|gb|EDL73663.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           623-39]
          Length = 221

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 102/236 (43%), Gaps = 21/236 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ +  L+  +      ++Y+D  I V NKPA      G  +   +   LK+   ++ + 
Sbjct: 3   LEDNPLLSNPAQGQDITIVYQDDAIVVVNKPAEFLSVPGVHVHDSVLTRLKAQF-TQAEG 61

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD  TSG+LV A TR A + L + F  R IQK Y +L+ G     +  I   L 
Sbjct: 62  VFALHRLDMSTSGLLVFALTRRANKQLQKQFISRAIQKRYVALIEGKLSETQGEIQLPLC 121

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
                      V  Q       A++H++ +    Q    + + PHTGRTHQLRVH  H  
Sbjct: 122 GD-LDDRPRQKVCWQQ---GKPALTHWETVQ-VEQNRTRVYLYPHTGRTHQLRVHCAHHL 176

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            +  PIVGD  Y    K         +L+LHA  +   HP   + +     + A  
Sbjct: 177 GLNAPIVGDDLYGLQDK---------RLFLHAEQLSFAHPYTKQPMTFQ--VDADF 221


>gi|308048388|ref|YP_003911954.1| ribosomal large subunit pseudouridine synthase A [Ferrimonas
           balearica DSM 9799]
 gi|307630578|gb|ADN74880.1| ribosomal large subunit pseudouridine synthase A [Ferrimonas
           balearica DSM 9799]
          Length = 219

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 62/224 (27%), Positives = 97/224 (43%), Gaps = 16/224 (7%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        +LYED  I V +KP+G+    G   A+     + S V  +       HRLD
Sbjct: 7   QPPMEPYLTVLYEDKDIVVVDKPSGLLSVPGRDPAHRDS--VYSRVAERYGTVYDVHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG++V+A  + A + L   FR R   K Y + VWG     +  I   L+       D
Sbjct: 65  MATSGVMVLALRKNAERELKRQFRDRETSKTYLARVWGHLAQPEGEIDLPLI------CD 118

Query: 212 YVHVVKQN--EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           + +  KQ         +++ ++V+         LE+ P TGR+HQLRVH L +G PI+GD
Sbjct: 119 WPNRPKQKVCHDTGKPSLTRYRVLSTD-DHSSLLELTPITGRSHQLRVHLLALGHPILGD 177

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             Y           +    +     +++  P  G+ L+  A  P
Sbjct: 178 GFYAEGEALAAADRLLLHAHT----LEIKQPYSGQPLRFEAAAP 217


>gi|315185514|gb|EFU19284.1| pseudouridine synthase [Spirochaeta thermophila DSM 6578]
          Length = 256

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 67/246 (27%), Positives = 115/246 (46%), Gaps = 19/246 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQET 154
            ++YED+ I   NK     VQ    +   +  FL   +  +       +  L +RLD+ T
Sbjct: 2   DIIYEDAHIIAVNKSGEELVQQNDVMKGTLQEFLLEHLRRRDGAGAPPRLHLVNRLDRPT 61

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI++ AR R AA   ++ FR R + K+YW+++   P    + + +++++   +   +  
Sbjct: 62  SGIVLFARHRKAAGKFSDLFRRRGVYKLYWAVLDAPPPLPSDTVEHFIVESRRVNKSFAF 121

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K+    + YA   ++VI      + ++ ++ HTGR HQ+R     +GC I GD KY A
Sbjct: 122 PEKRER--SEYARLSYQVIGS-GDCYFFVVVRLHTGRHHQIRAQFSALGCHIKGDIKYGA 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
                        ++LHAR +   HP  G R+ ITA  PA     W+       ++ + +
Sbjct: 179 KRTNR-----GGGIHLHARLLAFVHPFTGERVVITADPPAD--SLWEEFAR---QDAHFR 228

Query: 334 RLYSQD 339
           R Y  D
Sbjct: 229 RTYRYD 234


>gi|93007115|ref|YP_581552.1| pseudouridine synthase [Psychrobacter cryohalolentis K5]
 gi|92394793|gb|ABE76068.1| ribosomal large subunit pseudouridine synthase A [Psychrobacter
           cryohalolentis K5]
          Length = 237

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 64/221 (28%), Positives = 111/221 (50%), Gaps = 14/221 (6%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           F K + +YED  I+V +KPAG+    G  +       L + ++      +L HRLD +TS
Sbjct: 26  FAKKVTVYEDEDIWVVDKPAGLLSVDGKSLKVS----LLARLERANPAVKLIHRLDMDTS 81

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+ A+  AA  ++++ F  R  QK Y + V+G   +        +  +        H+
Sbjct: 82  GLLIFAKNAAAQTNISKQFIDRLPQKNYQARVFGQWDSVGATGKISVPVRYEPATKPRHI 141

Query: 216 VKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V  N   + +A++ ++++   +C  Q    + ++P TGR+HQLRVH +H+G  ++GD  Y
Sbjct: 142 VDPN--WSKHALTLYEILAHEECDGQIVTRVLLKPVTGRSHQLRVHMVHIGHVMIGDPIY 199

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
                 +    I  +L LHA+ + L HP  G  +   +P P
Sbjct: 200 AEGIALD----IAPRLNLHAQQLRLKHPTLGAWMDWESPTP 236


>gi|300718134|ref|YP_003742937.1| tRNA pseudouridine synthase C [Erwinia billingiae Eb661]
 gi|299063970|emb|CAX61090.1| tRNA pseudouridine synthase C [Erwinia billingiae Eb661]
          Length = 259

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 106/238 (44%), Gaps = 17/238 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDQWLVAVNKPAGWLVHRSWLDRHETVFVMQTLRDQIGQHVFTVHRLDRPTSGVLLL 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A+ L++ F    +QK Y ++V G  + ++        +   I   + +     +
Sbjct: 64  ALSSEVARLLSQQFEQHAMQKTYHAVVRGWLEGEETLDYALTEELDKIADKFTN----PD 119

Query: 221 KGANYAISHFK----------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K    A++H+K          V    + +F  +E++P TGR HQLR H  H+  PI+GD 
Sbjct: 120 KAPQPAVTHWKSLAKAELPVAVSRYDSSRFSLVELKPETGRKHQLRRHLRHLRHPIIGDS 179

Query: 271 KYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +      +         +L LHA  + L HP  G  L + A L +       +  ++
Sbjct: 180 AHGDLKQNRSAAQHFGMKRLMLHASELSLLHPVTGEPLVLRAGLDSVWQGCMTAFCWQ 237


>gi|330002097|ref|ZP_08304182.1| pseudouridine synthase, RluA family [Klebsiella sp. MS 92-3]
 gi|328537466|gb|EGF63703.1| pseudouridine synthase, RluA family [Klebsiella sp. MS 92-3]
          Length = 232

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 56/223 (25%), Positives = 90/223 (40%), Gaps = 16/223 (7%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   +  LLY+D  + + NKPAG+    G          +   +  +     L HR
Sbjct: 8   FVAPPCREQITLLYQDEHLVLINKPAGLLSLSGK--DPRNLDSVHHRLVQRFPGCPLVHR 65

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++V+AR +     L + F  R ++K+Y +L+ G     +  +   + K     
Sbjct: 66  LDFGTSGLMVIARNKGINALLCQQFSQRTVEKVYTALLCGHLAEDEGIVEAAIAKDPA-- 123

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKF--------CWLEMQPHTGRTHQLRVHALH 261
                 +    +    A S ++VID   Q            + + P TGRTHQLR+H   
Sbjct: 124 --RFPRMALCARHGKPARSRYRVIDRLYQAREGERALALTRVTLTPETGRTHQLRIHCQL 181

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +G PI+G   Y         +   ++L LHA  +   HP    
Sbjct: 182 LGYPILGCDLYGGRELPG--TECASRLMLHASELRFVHPVSHE 222


>gi|300774785|ref|ZP_07084648.1| tRNA pseudouridine synthase C [Chryseobacterium gleum ATCC 35910]
 gi|300506600|gb|EFK37735.1| tRNA pseudouridine synthase C [Chryseobacterium gleum ATCC 35910]
          Length = 231

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 101/230 (43%), Gaps = 8/230 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY D  +   NKP+G+ V             ++      GQK    HRLD++TSG+L+ 
Sbjct: 4   ILYRDEHLIAINKPSGLLVHKSFYAGEADTYAIQELKKQIGQKVYPVHRLDRKTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
              +   + ++E F  R ++K Y +++ G    ++E I   L+ ++ +  + V   ++  
Sbjct: 64  TLDKDTLRIMSEQFSSREVEKKYLAILRG-WTKEEETIDYDLINENEVRQNAVTNYRR-- 120

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                +      +     ++  +E  P TGR HQLR H  H+  PI+G  K+  N +   
Sbjct: 121 --LQTSEIDLPFLKHQTSRYSLVEAIPETGRFHQLRKHFKHILHPILGCRKHGCNKQNKL 178

Query: 281 T--SPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
              +   NK+ LHA  +   HP    R+ + A +     +  D L F   
Sbjct: 179 WLQTFEINKMTLHAHQLIFNHPVSNERITVNATIDEEFKRVGDILKFDLS 228


>gi|237738430|ref|ZP_04568911.1| LOW QUALITY PROTEIN: conserved hypothetical protein [Fusobacterium
           mortiferum ATCC 9817]
 gi|229420310|gb|EEO35357.1| LOW QUALITY PROTEIN: conserved hypothetical protein [Fusobacterium
           mortiferum ATCC 9817]
          Length = 181

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 52/192 (27%), Positives = 92/192 (47%), Gaps = 14/192 (7%)

Query: 132 FLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           + K+++  K  K    + HRLD++TSG+++ A++  A   L  ++     ++ Y +LV G
Sbjct: 1   YFKNYLKEKNPKDKIFVVHRLDRDTSGVMIFAKSEKAQDILQTTWNDSVKERTYVALVEG 60

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             K   + I ++L +        +     NE+    A+SH+KV+    + +  LE+   T
Sbjct: 61  NVKKDSDTIISYLAEN----KAMITYSTANEEEGKKAVSHYKVLKRN-KNYSLLEVNIET 115

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GR +Q+RVH   +G  +VGD KY +      T     +L LHA  +   HP     L  T
Sbjct: 116 GRKNQIRVHMQDLGHSVVGDKKYGS------TKNPIKRLGLHAHTIVFKHPITKEVLSFT 169

Query: 309 APLPAHMVKTWD 320
           + +P   +  + 
Sbjct: 170 SKIPEAFLSLFK 181


>gi|73954899|ref|XP_546413.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4 [Canis familiaris]
          Length = 404

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 74/275 (26%), Positives = 119/275 (43%), Gaps = 38/275 (13%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   +L++D  + V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 87  VHPNVLAKALSRGVLHQDKDLVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGHKAEP 146

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P      +   + 
Sbjct: 147 LHLCHRLDKETTGVMVLAWEKEVAHQVQEFFRTRQVAKKYWAITVRVPVPSAGVVDIPIT 206

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K+  G                +   V  ++ + A+ A++ + V+         +E+QP 
Sbjct: 207 EKAVQGQQQHYKMTLSPDYRMDNGKMVRVRSNRNAHIAVTQYHVLSS-TLSSALVELQPI 265

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC------------ANFKGNFTSPIQNK---LYLHA 292
           TG  HQLRVH    + CPI+GDHKY                K       + +   L+LHA
Sbjct: 266 TGIKHQLRVHLSFGLNCPILGDHKYSDWNKLAPQKLSLGTLKKLGLQQTKARHLPLHLHA 325

Query: 293 RYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGFK 325
           R + LP        L +   LP   V +   L  +
Sbjct: 326 RQLILPALGSRKEELSLVCKLPRFFVLSLRRLDLQ 360


>gi|224476909|ref|YP_002634515.1| hypothetical protein Sca_1425 [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222421516|emb|CAL28330.1| conserved hypothetical protein [Staphylococcus carnosus subsp.
           carnosus TM300]
          Length = 275

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 60/283 (21%), Positives = 115/283 (40%), Gaps = 34/283 (12%)

Query: 25  FKNHYPH--INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
            +  +    +    L ++  S +++++    K  +++ +G    IP      N++     
Sbjct: 14  LREIFQDVKLPKKELHQLNMSKEIKINNDEAKLTDKVHTGDTAFIPTPDEKSNYL----- 68

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKG 141
                        +  + + YED+ I +  KP G+         +  +   +   +DS+ 
Sbjct: 69  -----------PSYRYAEIFYEDNDIAIIKKPKGVKTHPNDLKESNTLMNHVIYTLDSEY 117

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +P   HRLDQET G+L+VA+     + L       +I +IY + V      K + I   
Sbjct: 118 AEP--IHRLDQETVGLLIVAKNPLMKKLLDRMLEDNQISRIYKARVKSQLPLKPQTIDKP 175

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + K       +    ++      +AI+H        +  C L+++  TGRTHQ+RVH   
Sbjct: 176 IGKD-----KFHSNRRRVSPTGQHAITHILDSRMIKENECELDIKLDTGRTHQIRVHLAA 230

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +G P++GD  Y  +           +L LH+  ++  HP    
Sbjct: 231 IGHPVLGDPLYGDSK--------LRQLQLHSHQIEFTHPLTKE 265


>gi|92116023|ref|YP_575752.1| pseudouridine synthase [Nitrobacter hamburgensis X14]
 gi|91798917|gb|ABE61292.1| pseudouridine synthase [Nitrobacter hamburgensis X14]
          Length = 292

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 69/287 (24%), Positives = 117/287 (40%), Gaps = 59/287 (20%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           ++ +++ +L+ D  + V +KPAGI V  G     +++   ++      + P L HRLD++
Sbjct: 8   AEQIQARVLHRDGLMLVIDKPAGIPVHRGPKGGANLEASFEALRFGLPRPPVLAHRLDRD 67

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG LV+ R R A   L   F+  +I K YW++V G P   +  I   L + +H  G + 
Sbjct: 68  TSGCLVLGRHRKATASLGLLFKHGKISKTYWAVVEGGPTEDEGTIDIPLGRLNHERGWWQ 127

Query: 214 HVVKQNEKGANYAISHFKVIDC-------------------------------------- 235
               + +     +++ +KV+                                        
Sbjct: 128 ----KPDPNGLPSVTRWKVLGRGIFTAASDRFSPSPCGVETSEARPEGAGARGNSDGIAP 183

Query: 236 ---------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-------NFKGN 279
                       +  WL ++P TGRTHQLRVH   M  PI GD+ Y           +  
Sbjct: 184 DHPPPRAREEGIQLTWLALEPVTGRTHQLRVHCAAMRWPIAGDNIYGTQASLRRLRNEQY 243

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
                +  L+LHAR + +P  +    + +TA  P H+     + G+ 
Sbjct: 244 IPQFGEPSLHLHAREIAIPLSKNKPPIVVTASAPVHLHARLKACGWN 290


>gi|42572641|ref|NP_974416.1| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|229891781|sp|Q5M721|PUS5_ARATH RecName: Full=RNA pseudourine synthase 5; AltName: Full=RNA
           pseudouridylate synthase 5; AltName: Full=RNA-uridine
           isomerase 5
 gi|332645400|gb|AEE78921.1| RNA pseudourine synthase 5 [Arabidopsis thaliana]
          Length = 369

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 128/333 (38%), Gaps = 74/333 (22%)

Query: 37  LQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +Q+ +++GQ+++D + VK  N  ++SG                   K++ S +   +   
Sbjct: 53  IQR-IQNGQIQIDGEVVKDPNTLLRSG------------------SKLVYSRLPWKEPDT 93

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRL 146
                +LYED  +   NKP+G+ V  G             W   K            P  
Sbjct: 94  PYSLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVP 153

Query: 147 THRLDQETSGILVVARTRAAAQHL-----------------TESFRMRRIQKIYWSLVWG 189
            HRL + TSGIL+ A+T+ A   L                  E    R++ KIY +L  G
Sbjct: 154 VHRLGRGTSGILLCAKTKLAKTKLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADG 213

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPH 248
           I +  +  I   +    + G      V   E     A S   V++   +K C  ++++  
Sbjct: 214 IVEEDEVVIKQPIGVVRYPGVAQGLYVASPE--GKPAFSKVFVLERDREKNCSLVKVEIQ 271

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY-----------------------CANFKGNFTSPIQ 285
           +GR HQ+R+H  +MG P+VGD  Y                           + N   P  
Sbjct: 272 SGRPHQIRIHLAYMGHPLVGDPLYVAGGQPKCFDPDLVDDAAAFAEDGGYRRPNQAVPGD 331

Query: 286 NKLYLHARYMDLPHP--EGGRLQITAPLPAHMV 316
              +LHA  ++LP+       ++I APLP  + 
Sbjct: 332 CGYHLHAHQVELPNLLNTHKVVKIVAPLPPILQ 364


>gi|332975616|gb|EGK12505.1| pseudouridylate synthase for 23S rRNA and tRNAphe(position 32)
           [Psychrobacter sp. 1501(2011)]
          Length = 237

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 62/222 (27%), Positives = 107/222 (48%), Gaps = 14/222 (6%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           DF+  + +YED  I + +KPAG+    G  +       L S ++    + +L HRLD +T
Sbjct: 25  DFMTQVTVYEDDDILLVDKPAGLLSIDGKDLKVS----LLSRLERANPEVKLIHRLDMDT 80

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++  + +AA  H+++ F  R  QK Y ++V G      +     +  +        H
Sbjct: 81  SGLMIFGKNKAAQTHISKQFIERIPQKEYQAIVNGTLATPGKKGEINIPVRYEPSIKPKH 140

Query: 215 VVKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           V   N K   +A++H++V+       +    + + P TGR+HQLRVH +H+G  I+GD  
Sbjct: 141 VADPNWK--KHALTHYEVLHHELRQGKPVTRVALHPVTGRSHQLRVHMVHLGHVIIGDPI 198

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y           + ++L LHA  + L HP     +   + +P
Sbjct: 199 Y----AEGEALTLSSRLNLHAHKLRLKHPTMNTWMAWESVVP 236


>gi|256545084|ref|ZP_05472450.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Anaerococcus vaginalis ATCC 51170]
 gi|256399125|gb|EEU12736.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Anaerococcus vaginalis ATCC 51170]
          Length = 286

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 64/307 (20%), Positives = 126/307 (41%), Gaps = 43/307 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MTY+++      +  + L ++  +   +I+     K +    + V+ K+++ N ++ S  
Sbjct: 1   MTYIEF----KADRKISLKKFLLDR--NIS-NRAYKKIIKNSILVNDKKIEKNIKLNSDD 53

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            ++I          I E +I      L       +  +LYED  I   +K A ++V   S
Sbjct: 54  NIKI----------IIEDEI------LNYEPINKELEILYEDQDIIAIDKDANLTV--NS 95

Query: 124 GIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                +  ++  +      K   R  +RLD  TSGI+++AR   A  +  +        K
Sbjct: 96  KGQESLANYISYYFWKNNIKSQVRFINRLDMNTSGIILIARNPYAQAYYQKLIENNDFDK 155

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y +LV G  +  K  +   L          + +  +         ++FK I  +  KF 
Sbjct: 156 EYLALVEGNLEIDKTIV---LKINYDENKKKMKIADE----GYEIKTYFKNIKLY-DKFS 207

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HP 300
            +  +  TG+THQ+R+   ++  PI+GD  Y + +K        ++  LH+  +      
Sbjct: 208 LIYCKIFTGKTHQIRISLSNLNHPIIGDKLYGSKYK-------LDRFLLHSYKVSFIRFR 260

Query: 301 EGGRLQI 307
           +G ++ I
Sbjct: 261 DGEKITI 267


>gi|225028057|ref|ZP_03717249.1| hypothetical protein EUBHAL_02326 [Eubacterium hallii DSM 3353]
 gi|224954657|gb|EEG35866.1| hypothetical protein EUBHAL_02326 [Eubacterium hallii DSM 3353]
          Length = 237

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 61/220 (27%), Positives = 98/220 (44%), Gaps = 13/220 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKGQKPRLTHRLDQ 152
           +  +++ED  + V  KPAG+ VQ        +   LK  +       +     + HRLD+
Sbjct: 6   RVPIVFEDDAVIVCEKPAGMPVQSDHTRDMDVLTILKHHIFEEQNSEEEPYLAVVHRLDR 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              G++V+A+T+ AA +L+E  +    +K Y ++V G  +       ++LLK        
Sbjct: 66  PVGGLMVLAKTKEAAANLSEQIQNFEFEKNYQAVVCGNLREDFGTFEDYLLKNGKTN--K 123

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             VVK    GA  A   +++IDC   K     W+ +  HTGR HQ+RV     G  + GD
Sbjct: 124 TEVVKAGTPGARKAELDYELIDCIETKEGVLTWILVILHTGRHHQIRVQFASRGLGLYGD 183

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
            KY   F+       +  LY  +  +   HP  G R+   
Sbjct: 184 TKYNPKFQKTKKKYTEIGLY--STRISFNHPVTGERMTFK 221


>gi|317968138|ref|ZP_07969528.1| pseudouridine synthase [Synechococcus sp. CB0205]
          Length = 318

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 68/311 (21%), Positives = 131/311 (42%), Gaps = 41/311 (13%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNHIIKEQ 81
           ++   Y H +    ++ L +G++  + ++++ +  + +G  +    PP   A   ++   
Sbjct: 30  YYAERYGHSDPSVWRERLAAGEIWCNGQQLRADAALAAGDQLIWHRPPWEEAAVPVLS-- 87

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
                           +  ++++D  + V NKP+G+ V    G   H    L + + +  
Sbjct: 88  ----------------QRAVVFDDGDLLVLNKPSGLPVLPAGGFLEH---TLLTQLQTWA 128

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--------RRIQKIYWSLVWGIPKN 193
            + R  HRL + TSG+LV AR R     L+   R         R   K+Y +L   +  +
Sbjct: 129 PEARPVHRLGRFTSGLLVCARQRETRGQLSAQLRESTAASAASRGCLKVYRALTEPLAAD 188

Query: 194 ----KKECIANWLLKKSH-IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
               +   I   + ++ H + G         +  A  + S   +++   ++ C +EM+  
Sbjct: 189 WRCGESRAITVPIGRRPHALLGQLWCAALPGDSSALESRSALTLLERRPER-CLVEMEIA 247

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY-CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           TGR HQ+R+H   +G P++GD  Y           P      LHA  + L  P G  L +
Sbjct: 248 TGRPHQIRIHTAALGSPLLGDPLYLPGGVARPEVLPGAGGYQLHAHRLRLE-PRG--LAL 304

Query: 308 TAPLPAHMVKT 318
            APLP+ +++ 
Sbjct: 305 EAPLPSGLLEC 315


>gi|148654105|ref|YP_001281198.1| pseudouridine synthase [Psychrobacter sp. PRwf-1]
 gi|148573189|gb|ABQ95248.1| ribosomal large subunit pseudouridine synthase A [Psychrobacter sp.
           PRwf-1]
          Length = 237

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 62/236 (26%), Positives = 114/236 (48%), Gaps = 18/236 (7%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           + +++ +     DF+  + +YED  + + +KPAG+    G  +       L S ++    
Sbjct: 13  LEEAARDTQFFKDFMTQVTVYEDEDLLLVDKPAGLLSIDGKDLKVS----LLSRLERANP 68

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIAN 200
           + +L HRLD +TSG+++ A+ + A  H+++ F  R  QK Y ++V G      KK  I  
Sbjct: 69  EVKLIHRLDMDTSGLMIFAKNKQAQTHISKQFIERIPQKEYQAIVQGTLAIPGKKGEINI 128

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRV 257
            +  +  I   +V     + +   +A++H++V+       +    + + P TGR+HQLRV
Sbjct: 129 PVRYEPSIKPKHVA----DPEWKKHALTHYEVLHHELRKGRPVTRVALHPVTGRSHQLRV 184

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           H +H+G  I+GD  Y           +  +L LHA  + L HP     +   + +P
Sbjct: 185 HMVHLGHVIIGDPIY----AEGEALSLAPRLNLHAHKLRLKHPTMNTWMAWESAVP 236


>gi|325846771|ref|ZP_08169686.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481529|gb|EGC84570.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 264

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 109/283 (38%), Gaps = 36/283 (12%)

Query: 25  FKNHYPHINFV-NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
            K             K + +  V V+ +++  N  +++G  V+I                
Sbjct: 14  LKELLKSKKISNRAYKKIINNLVYVNDEKINKNIGLKAGDKVKI---------------- 57

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L    NL       K  +LYED  I   +KP  ++V   S     +  +L  +      K
Sbjct: 58  LIEDENLNYEPINKKIKILYEDKDIVAVDKPPNLTV--NSKNQESLSNYLAYYFKENKIK 115

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
              RL +RLD  TSGI++VA+   +  +         + K Y +LV G        I ++
Sbjct: 116 SQIRLINRLDMNTSGIMLVAKNPFSHAYYQNQIENNELDKEYLALVEGNL-----IIDDF 170

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
                 I  D  +   +     N+  ++FK +  +  KF  +  + +TG+THQ+R+   +
Sbjct: 171 CEID--IDYDKENKKMKVVSDKNHVKTYFKTLKNYG-KFSLIYCKIYTGKTHQIRLSLAY 227

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +  PI+GD  Y + +          +  LHA  +        +
Sbjct: 228 LNHPILGDDLYGSKYD-------IERFLLHAYRIKFKSFRDQK 263


>gi|226724701|sp|Q0DST9|PUS5_ORYSJ RecName: Full=RNA pseudourine synthase 5; AltName: Full=RNA
           pseudouridylate synthase 5; AltName: Full=RNA-uridine
           isomerase 5
          Length = 397

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 122/332 (36%), Gaps = 81/332 (24%)

Query: 39  KILRSGQVRVDKKRVK-FNNRIQSGQVV---RIPPVINALNHIIKEQKILDSSVNLTKHS 94
           K +R GQ+ VD +     +  ++ G  +   R+P       H++                
Sbjct: 71  KRIRDGQITVDGEVATDPDMILREGSKLVYHRLPWQEPFAPHLL---------------- 114

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ------------ 142
                 +LYED  +   NKP+G+ V                  D K              
Sbjct: 115 -----DVLYEDDDMIALNKPSGLQVLPKGLFQQRTVLAQLQLKDWKMPSSFCSKRKDAQS 169

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHL-----------------TESFRMRRIQKIYWS 185
            P   HRL + TSG+L+ A+T+ A   L                 T+  + R+I K Y +
Sbjct: 170 HPVPVHRLGRGTSGLLLCAKTKLAKAQLAAYFAEGATNAGKSRDETDICKARKISKFYRA 229

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLE 244
           LV GI +N +  I   +    + G         +      A+S  +V++         ++
Sbjct: 230 LVTGILENDEVMITQPIGLVRYPGVAEGLYAACSS--GKPAMSKVRVLERLKIHNHTLIQ 287

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS---------------------- 282
           ++ H+GR HQ+R+H  ++G P+V D  Y    +  F                        
Sbjct: 288 VEIHSGRPHQIRIHLAYIGHPLVDDPLYGIGGQPKFDEPEPTSTADSFAYDGGYERPLQP 347

Query: 283 -PIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
            P     +LHA ++ L HP    + +ITAPLP
Sbjct: 348 VPGDCGYHLHAHWLVLCHPTTNEMIKITAPLP 379


>gi|49484092|ref|YP_041316.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257425962|ref|ZP_05602386.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257428627|ref|ZP_05605025.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257431264|ref|ZP_05607641.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257433944|ref|ZP_05610302.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257436860|ref|ZP_05612904.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M876]
 gi|282904425|ref|ZP_06312313.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus C160]
 gi|282906248|ref|ZP_06314103.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282909167|ref|ZP_06316985.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282911473|ref|ZP_06319275.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282914645|ref|ZP_06322431.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M899]
 gi|282919611|ref|ZP_06327346.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           C427]
 gi|282924991|ref|ZP_06332657.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|283958603|ref|ZP_06376054.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Staphylococcus aureus subsp. aureus A017934/97]
 gi|293503717|ref|ZP_06667564.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           58-424]
 gi|293510738|ref|ZP_06669443.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M809]
 gi|293537280|ref|ZP_06671960.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M1015]
 gi|295428428|ref|ZP_06821057.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297590605|ref|ZP_06949243.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus MN8]
 gi|49242221|emb|CAG40928.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257271656|gb|EEV03802.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257275468|gb|EEV06955.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257278212|gb|EEV08860.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257282037|gb|EEV12174.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257284211|gb|EEV14334.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M876]
 gi|282313357|gb|EFB43753.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|282317421|gb|EFB47795.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           C427]
 gi|282321826|gb|EFB52151.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M899]
 gi|282325168|gb|EFB55478.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282327431|gb|EFB57726.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282331540|gb|EFB61054.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282596043|gb|EFC01007.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus C160]
 gi|283471121|emb|CAQ50332.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus ST398]
 gi|283790752|gb|EFC29569.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Staphylococcus aureus subsp. aureus A017934/97]
 gi|290920125|gb|EFD97193.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M1015]
 gi|291095383|gb|EFE25648.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           58-424]
 gi|291466629|gb|EFF09150.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M809]
 gi|295127828|gb|EFG57465.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297575491|gb|EFH94207.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus MN8]
 gi|312437685|gb|ADQ76756.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|315195761|gb|EFU26148.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS00]
          Length = 273

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 59/264 (22%), Positives = 107/264 (40%), Gaps = 32/264 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  + +  KP G+         +  +   +   VDS   +P   HRLDQET G+L+VA
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHVIYTVDSDYVEP--IHRLDQETVGLLIVA 135

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +     + L        I +IY + V  +   K + I   + K       +    ++   
Sbjct: 136 KNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTIDMPIGKD-----KFHSNKRRVSP 190

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y  +      
Sbjct: 191 TGQRAITHILTSKMIKETVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLYGDS------ 244

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL 305
                +L L +  ++  HP    +
Sbjct: 245 --TLRQLELESYKIEFVHPLTKEV 266


>gi|160876630|ref|YP_001555946.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160862152|gb|ABX50686.1| pseudouridine synthase [Shewanella baltica OS195]
          Length = 245

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 100/233 (42%), Gaps = 19/233 (8%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +LY+DS I + +KP+G+    G          +   +        L HRLD 
Sbjct: 18  PPCLGQIRVLYQDSDILLIDKPSGLLSLSGKNPLN--LDSVHYRLVQDFPTATLLHRLDF 75

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++VA  ++    LT+ F+ R ++K Y +L+ G        I   + K      D+
Sbjct: 76  GTSGIMLVALNKSVNGLLTKQFQARTVEKRYTALLHGHIAADSGVINLPIAKDV----DH 131

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             + K        AIS ++V++   + F   +E  P +GRTHQLR+H+   G  I+G   
Sbjct: 132 FPLQKICHSTGKPAISEYRVLERLTEPFATRVEFTPVSGRTHQLRIHSQQFGHSILGCDL 191

Query: 272 YCA---NFKGNFTSPIQN--------KLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y     +   N  +P  +        +L LHA  +   HP  G R+      P
Sbjct: 192 YGGVGESVADNADAPEPDITKMTSNSRLMLHATRLAFDHPITGERIDWLCECP 244


>gi|293363350|ref|ZP_06610172.1| pseudouridine synthase, RluA family [Mycoplasma alligatoris A21JP2]
 gi|292553019|gb|EFF41770.1| pseudouridine synthase, RluA family [Mycoplasma alligatoris A21JP2]
          Length = 280

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 56/298 (18%), Positives = 115/298 (38%), Gaps = 34/298 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           ++ +   +++    L +    +  ++    ++K+ R   ++++ +R  + +  I    V+
Sbjct: 1   MKKITATSNDAGRTLYKLVIKYLNNVPLSRVEKLFRKKDIKINGQRTNQKDYIIAFNDVI 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I  +I+      KE+  L +S +  K         +YED+ + + +KP GI V      
Sbjct: 61  EIYGLIDTK----KEEAPLLTSFSFKK---------IYEDANVLIIDKPNGIEVHSAPNC 107

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             +       +      KP    RLD+ETSGI++ A+   A ++L +     +    + S
Sbjct: 108 LDNQVLAYLKYKQVDSFKPSHIGRLDKETSGIMLYAKNYQALKYLNDYMENIKKTYTFKS 167

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
                  ++ + +  +L K        +         +  + +H    +   +       
Sbjct: 168 ----DFNDESKEVELFLYKDEE--KKRMAASFTKVPYSKLSKTHLYT-ESNKKYATLF-- 218

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +GR HQ+RV  + +G PI GD KY              +L LH   +     EG 
Sbjct: 219 ---SGRKHQIRVTLMKLGKPIYGDFKYGGKKAA--------RLMLHCLQIKFVGLEGE 265


>gi|291528756|emb|CBK94342.1| Pseudouridylate synthases, 23S RNA-specific [Eubacterium rectale
           M104/1]
          Length = 244

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 106/242 (43%), Gaps = 29/242 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETS 155
           K  ++YED+ I V  KPAGI+ Q        ++ F++++  +K + P   + HRLDQ   
Sbjct: 3   KPDIIYEDNDIIVCYKPAGIATQTRHIGQQDMESFIRNYRAAKNEPPYVGIVHRLDQPVE 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSL-----VWGIPKNKKECIANWLLKKSHIGG 210
           G++V A+ + AA  L+   +    +K Y +      V G  K +    + W     +I  
Sbjct: 63  GVMVFAKNQKAAASLSRQIKEHTTEKYYRAASRGQGVSGADKEEDNHDSAWHTLTDYISF 122

Query: 211 DYV----HVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVH 258
           D       +  + ++ A  A+  ++VI     +            +++  TGR HQ+R+ 
Sbjct: 123 DKRTNTSKITSEKDRLAKKAVLQYRVISVTPDRDSSQNECIRTEFDIKLLTGRHHQIRLQ 182

Query: 259 ALHMGCPIVGDHKYC---------ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
             H+G P++GD KY           +  G     ++ +L L +  +   HP  G R+   
Sbjct: 183 LAHIGYPLIGDTKYGKPASNNSGTGSKSGRTGGGVREQLALCSYKLVFDHPATGERMTFE 242

Query: 309 AP 310
            P
Sbjct: 243 LP 244


>gi|302333515|gb|ADL23708.1| RluA, Pseudouridylate synthases, 23S RNA-specific [Staphylococcus
           aureus subsp. aureus JKD6159]
          Length = 273

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 59/264 (22%), Positives = 107/264 (40%), Gaps = 32/264 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  + +  KP G+         +  +   +   VDS   +P   HRLDQET G+L+VA
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHVIYTVDSDYVEP--IHRLDQETVGLLIVA 135

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +     + L        I +IY + V  +   K + I   + K       +    ++   
Sbjct: 136 KNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTIDMPIGKD-----KFHSNKRRVSP 190

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y  +      
Sbjct: 191 TGQRAITHILTSKMIKETVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLYGDS------ 244

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL 305
                +L L +  ++  HP    +
Sbjct: 245 --TLRQLELESYKIEFVHPLTKEV 266


>gi|255952943|ref|XP_002567224.1| Pc21g01540 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211588935|emb|CAP95051.1| Pc21g01540 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 526

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 57/269 (21%), Positives = 99/269 (36%), Gaps = 56/269 (20%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +K L  G V+V+    +    +++GQV+      +                        L
Sbjct: 79  RKALEDGLVQVNGVTARPETTLKNGQVISHTLHRH------------------EPPVTSL 120

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETS 155
              ++YED  + V +KPAG+ V       Y+ +  ++     +G +  PR  +RLD+ TS
Sbjct: 121 PVGIIYEDDDLMVIDKPAGVPVHAAG--RYNFNTVIQILRSERGSEWLPRPCNRLDRLTS 178

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVH 214
           GI+ + +    A  +  + + R +QK Y + V G  P     C    +     +G + V 
Sbjct: 179 GIMFIGKHAKGADKMAAALKARSVQKEYVARVKGKFPDGVVVCDQPIMQVSPKLGLNRVR 238

Query: 215 VVKQNEKGANYAISHFKVIDCFA---------------------------QKFCWLEMQP 247
                      A + F+ +  +                            + +  +   P
Sbjct: 239 A------TGKEATTKFRRLAYYPPESAKETESSSDDERPATPPASFANETEGYSIVHCLP 292

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            TGRTHQ+RVH   +G PI  D  Y    
Sbjct: 293 LTGRTHQIRVHLQFLGHPISNDPIYSNRR 321


>gi|300175850|emb|CBK21846.2| Pseudouridylate synthase [Blastocystis hominis]
          Length = 273

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 57/266 (21%), Positives = 109/266 (40%), Gaps = 29/266 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +   +    ++ +R+G++RV+ +RV  ++ +++G  +      +        
Sbjct: 25  IDVF-SKEFGAYSPEYYEEAIRNGRIRVNGERVTRDHILKNGDRITHTVHRH-------- 75

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                          +   ++L E   I   NKPA + V       Y+    +    ++K
Sbjct: 76  ----------EPPVPYSPVVILGETDDIIAVNKPAALPVHPCGAYRYNSLETILR-KENK 124

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
             +    HRLD+ TSG++++A+ +  A  L+E        K+Y +   G    K E    
Sbjct: 125 LSEFYFIHRLDRVTSGVMLLAKRKDIASKLSEQLVKGGFHKVYLAEAEGNCFEKPEIPGV 184

Query: 201 WLLKKSHIGGDYVHVV--------KQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251
           +  +++ I  D    V        K +EK    A ++   +    Q     +E  P TGR
Sbjct: 185 FYTQQNGIAVDRNIAVVSQKEGIFKVDEKEGKPAYTYLFPLYYSKQSNTTLMECVPITGR 244

Query: 252 THQLRVHALHMGCPIVGDHKYCANFK 277
           THQ+R+H  ++G PI  D  Y  +  
Sbjct: 245 THQIRLHLKYIGHPIDDDVNYNESIH 270


>gi|189218287|ref|YP_001938929.1| pseudouridylate synthase, 23S RNA-specific [Methylacidiphilum
           infernorum V4]
 gi|189185145|gb|ACD82330.1| Pseudouridylate synthase, 23S RNA-specific [Methylacidiphilum
           infernorum V4]
          Length = 268

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 59/243 (24%), Positives = 100/243 (41%), Gaps = 18/243 (7%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTH 148
           ++    +L   ++ E     + +KP  +            I  +L++     G   +L H
Sbjct: 2   ISPEPPYLP-RIVEECQDYLIVDKPPFLLSHPTRKKKGPSILEWLQNL--HPGISFKLIH 58

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ETSG+LVVA+  AAA +       R IQK Y ++ WG  K     I   L      
Sbjct: 59  RLDRETSGLLVVAKNSAAAAYFGRQMEKRLIQKGYLAISWGELKADYLKIEAPLGYLGGA 118

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            G+ + + +        +++    +      +  L ++P TG+ HQ+RVH   +  P+VG
Sbjct: 119 KGNEIVIRQGIVPHGTQSVTEIYPLG-HGGGYSLLWVRPLTGKLHQIRVHLSTIRHPVVG 177

Query: 269 DHKYCANF------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y  N             +      +  +  LHA Y+     +G + Q  +PLP  + 
Sbjct: 178 DKLYGPNPSFFLEFAKRGWTEEMEKVLLLPRHALHAAYLSF-FWKGDKKQFYSPLPEDLK 236

Query: 317 KTW 319
           K  
Sbjct: 237 KFL 239


>gi|206579623|ref|YP_002237870.1| pseudouridine synthase, RluA family [Klebsiella pneumoniae 342]
 gi|206568681|gb|ACI10457.1| pseudouridine synthase, RluA family [Klebsiella pneumoniae 342]
          Length = 232

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 56/223 (25%), Positives = 88/223 (39%), Gaps = 16/223 (7%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   +  LLY+D  + + NKPAG+    G          +   +  +     L HR
Sbjct: 8   FVAPPCREQITLLYQDEHLLLINKPAGLLSLSGK--DPRNLDSVHHRLVQRFPGCTLVHR 65

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++V+AR +     L + F  R + K+Y +L+ G     +  +   + K     
Sbjct: 66  LDFGTSGLMVIARNKGINALLCQQFSQRTVAKVYTALLCGHLAEDEGIVEAAIAKDPA-- 123

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALH 261
                 +    +    A S ++VID   Q            + + P TGRTHQLR+H   
Sbjct: 124 --RFPRMSLCARHGKPARSRYRVIDRLYQSRDGERALALTRVALTPETGRTHQLRIHCQL 181

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +G PI+G   Y         +    +L LHA  +   HP    
Sbjct: 182 LGYPILGCDLYGGRELPG--TEQAPRLMLHASELRFVHPVSHE 222


>gi|294461273|gb|ADE76199.1| unknown [Picea sitchensis]
          Length = 386

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 79/368 (21%), Positives = 121/368 (32%), Gaps = 82/368 (22%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +   +          + + +GQ+ VD K V      +   V+RI P +       +E
Sbjct: 30  IDFYSSRYESSAPRKGWLQRIHNGQITVDGKTVN-----EPDTVLRIGPKLVYHRLSWRE 84

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                            K  +L+ED  +   NKP+G+ V  G             W  S+
Sbjct: 85  PIAP------------CKLYVLFEDDHLLAVNKPSGLQVLPGGLFQQRTVLTQLKWKASQ 132

Query: 141 GQK----------------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM-------- 176
             K                P   HRL + TSGIL+ A++  A   L   F          
Sbjct: 133 SSKYRSVAGKAVADFQESQPVPVHRLGRGTSGILLCAKSEIAKSQLAADFADGTSFISRN 192

Query: 177 -----------RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
                      RRI K Y +L  GI +  K  I   + K  + G      V         
Sbjct: 193 SSSDIDAGEIKRRIYKTYRALADGIIEQNKIAIKQPIGKMRYPGVRSGLYVA--SPTGKQ 250

Query: 226 AISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY------------ 272
           A S   V+     +    +E++ ++GR HQ+R+H   +G P++GD  Y            
Sbjct: 251 AESRITVLSRDKNRNCTLVEVEIYSGRPHQIRIHLSFIGHPLLGDPLYVAGGRPSITVSD 310

Query: 273 --------------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
                             K     P     YLHA  +   HP     ++I AP P  +  
Sbjct: 311 SYSESREGDNFAEDGGYQKPLNPVPGDCGYYLHAYRLAFHHPVSDEVVEIVAPPPPMLSA 370

Query: 318 TWDSLGFK 325
             +  G  
Sbjct: 371 CNEDAGLD 378


>gi|313677455|ref|YP_004055451.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
 gi|312944153|gb|ADR23343.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
          Length = 237

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 65/240 (27%), Positives = 104/240 (43%), Gaps = 24/240 (10%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           LK +++ E       NKP  +S          I   +K + D      ++ HRLD+ETSG
Sbjct: 6   LKPLIIEESEDYIFINKPPFVSTLADRNDTVTILSLVKKYNDDY----QICHRLDKETSG 61

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+VA+   A ++ +  F  R+++KIY ++V G+ + K E +   L   +   G     V
Sbjct: 62  VLLVAKNPEAYRNASMQFEHRQVEKIYTAIVDGLHQFKDEEVNLPL--HTTASG----YV 115

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K + +    A + F  I+ F +K   +  +P TGR HQ+RVH   +   I GD  Y    
Sbjct: 116 KISHRQGKNAKTIFNTIETF-KKHTLVACRPETGRMHQIRVHLASLNASITGDETYGGQP 174

Query: 277 -------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
                        K     PI  +  LHA  + L   +G  + + AP P  +      L 
Sbjct: 175 LYLSSFKRNFVRGKEKEEHPIIKRFALHAVSISLTDLKGKVVSVEAPYPKDIEVALKQLR 234


>gi|156055472|ref|XP_001593660.1| hypothetical protein SS1G_05088 [Sclerotinia sclerotiorum 1980]
 gi|154702872|gb|EDO02611.1| hypothetical protein SS1G_05088 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 399

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 58/267 (21%), Positives = 98/267 (36%), Gaps = 51/267 (19%)

Query: 37  LQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           ++  +  G + V+ K V+  +  I++G V+      +                       
Sbjct: 25  VKDAMERGAIAVNGKPVESTSQIIKNGDVISHTLHRH------------------EPPVT 66

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L   +++ED  I V NKP+G+ V       Y+    +       G  P   +RLD+ TS
Sbjct: 67  ALPISIVHEDEDIIVINKPSGVPVHPAGRYNYNSVVEIMRAERGHGWNPLPCNRLDRLTS 126

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-KKSHIGGDYVH 214
           GI+ + +   AA+ L+     R ++K Y + V G   + +      +L     +G + V 
Sbjct: 127 GIMFIGKHAKAAEALSLQISGRTVRKEYIARVKGKFPDGEVVCDMPILQISPKLGLNRVR 186

Query: 215 VVKQNEKGANYAISHFKVIDCFA-------------------------QKFCWLEMQPHT 249
                      A + FK +  +                          + +  +   P T
Sbjct: 187 A------SGKAARTVFKRLAYYPPENLEQVEDSSEPMEPDKSKPSMNKEGYSIVRCLPVT 240

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANF 276
           GRTHQLRVH   +G PI  D  YC   
Sbjct: 241 GRTHQLRVHLQFLGHPIGNDPIYCNQR 267


>gi|75909345|ref|YP_323641.1| pseudouridine synthase [Anabaena variabilis ATCC 29413]
 gi|75703070|gb|ABA22746.1| Pseudouridine synthase [Anabaena variabilis ATCC 29413]
          Length = 549

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 69/225 (30%), Positives = 106/225 (47%), Gaps = 18/225 (8%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           S +    + D  +  ++YED  +   NKPAG+    G       D  L        Q+  
Sbjct: 329 SGLKPDSNFDKEQINVIYEDEWLIAVNKPAGLLSVPGRYFD-TQDSVLSRLRRLLTQETM 387

Query: 146 L--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           L   HRLDQ+TSGIL++AR R   + L++ F+ R++ K+Y +++ G+   +   I   L 
Sbjct: 388 LAAVHRLDQDTSGILLLARDRQTYRQLSQQFQQRQVHKVYEAILAGVVSTETGIIDLPLW 447

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL--- 260
                   Y  V  Q       ++++F+ I      +  +E  P TGRTHQLRVHA    
Sbjct: 448 GD-PENRPYQQVDWQR---GKPSVTNFRAIAREGD-YTRVEFVPLTGRTHQLRVHASDVQ 502

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            +G  I+GD  Y    K        N+L+LHAR +   HP  G++
Sbjct: 503 GLGVVILGDRFYGCTAKA-------NRLHLHARELCFLHPHSGKI 540


>gi|152970825|ref|YP_001335934.1| putative ribosomal large subunit pseudouridine synthase A
           [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
 gi|150955674|gb|ABR77704.1| putative ribosomal large subunit pseudouridine synthase A
           [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
          Length = 263

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 56/223 (25%), Positives = 88/223 (39%), Gaps = 16/223 (7%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   +  LLY+D  + + NKPAG+    G          +   +  +     L HR
Sbjct: 39  FVAPPCREQITLLYQDEHLVLINKPAGLLSLSGK--DPRNLDSVHHRLVQRYPGCTLVHR 96

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++V+AR +     L + F  R + K+Y +L+ G     +  +   + K     
Sbjct: 97  LDFGTSGLMVIARNKGINALLCQQFSQRTVDKVYTALLCGHLAEDEGIVEAAIAKDPA-- 154

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKF--------CWLEMQPHTGRTHQLRVHALH 261
                 +    +    A S ++VID   Q            + + P TGRTHQLR+H   
Sbjct: 155 --RFPRMALCARHGKPARSRYRVIDRLYQAREGERALALTRVTLTPETGRTHQLRIHCQL 212

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +G PI+G   Y         +    +L LHA  +   HP    
Sbjct: 213 LGYPILGCDLYGGRELPG--TEQAPRLMLHASELRFVHPVSHE 253


>gi|270289187|ref|ZP_06195489.1| pseudouridine synthetase family protein [Chlamydia muridarum Weiss]
          Length = 253

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 68/286 (23%), Positives = 119/286 (41%), Gaps = 47/286 (16%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHII 78
           RL  + +   PH+    + + +R    RV+ +  +F + ++  G  V +  +  +     
Sbjct: 13  RLACFLRTSLPHLPKKTILESIRYHGCRVNGRIERFESYKLHPGDRVCLQIIERS----- 67

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                               + LL+ED  + ++NKPA                 L   + 
Sbjct: 68  -------------------SAQLLWEDEHLCIYNKPA-----------KQTSEALACQL- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                  L HRLD++TSG ++ A+   A   +T+ F+ R+I K Y +LV+G P+ +   I
Sbjct: 97  ----HVHLVHRLDRDTSGCILFAKHEKAITPITQLFKTRQIDKRYIALVFGHPRQQSGII 152

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +     H     V     +EK     I+ ++V+  ++ K+  L  +P TGRTHQ+R+H
Sbjct: 153 TTY-TAPCHRRIGAVLFGNTDEKLGKKTITEWEVLTHYS-KYALLLCRPITGRTHQIRLH 210

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              +G PIVGD  Y    +         +  LHA  +    P   +
Sbjct: 211 MKTIGHPIVGDIDYGNKEQPKHVV----RPLLHANSLCFISPFSKK 252


>gi|258423127|ref|ZP_05686021.1| pseudouridine synthase [Staphylococcus aureus A9635]
 gi|257846691|gb|EEV70711.1| pseudouridine synthase [Staphylococcus aureus A9635]
 gi|323438855|gb|EGA96592.1| RNA pseudouridylate synthase [Staphylococcus aureus O11]
 gi|323441699|gb|EGA99344.1| RNA pseudouridylate synthase [Staphylococcus aureus O46]
          Length = 273

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 58/264 (21%), Positives = 107/264 (40%), Gaps = 32/264 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  + +  KP G+         +  +   +   +DS   +P   HRLDQET G+L+VA
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHVIYTIDSDYVEP--IHRLDQETVGLLIVA 135

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +     + L        I +IY + V  +   K + I   + K       +    ++   
Sbjct: 136 KNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTIDMPIGKD-----KFHSNKRRVSP 190

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y  +      
Sbjct: 191 TGQRAITHILTSKMIKETVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLYGDS------ 244

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL 305
                +L L +  ++  HP    +
Sbjct: 245 --TLRQLELESYKIEFVHPLTKEV 266


>gi|323339779|ref|ZP_08080049.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           ruminis ATCC 25644]
 gi|323092858|gb|EFZ35460.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           ruminis ATCC 25644]
          Length = 301

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 63/301 (20%), Positives = 126/301 (41%), Gaps = 34/301 (11%)

Query: 24  WFKNHYPHINFVNLQKIL-RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + +     I+   L KI    G + VD    +  + I    VV +          ++++ 
Sbjct: 18  FLRQQ--GISRGLLAKIRHEGGAIDVDGTSGRKLDMIFPNAVVTLTMPPEK----VRKEP 71

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS---WVDS 139
           ++ S V L          +LYED    + +KPA ++        +  D  +     + + 
Sbjct: 72  VIPSYVPL---------KILYEDRDFLIVDKPAHLATIPSPDKKHRYDSLVNRVVGYYEL 122

Query: 140 KGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +G K  + H   RLD++T+GI+++A+ R A   + +      I+K Y +L+ G    +  
Sbjct: 123 RGIKDTVVHVITRLDRDTTGIVLIAKHRYAHALIDKQVHDHSIKKEYLALLSGKVDRRHF 182

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +   + ++         + +   +    + S +  ++   +      ++ H+GRTHQ+R
Sbjct: 183 FVNLPIGREPG-----SMIKRTITEDGKPSSSEYF-LEKKLRDASLYRVRLHSGRTHQIR 236

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           VH+  +G P+V D  Y     G  + P+Q +  LH  ++   HP   + L+I    P   
Sbjct: 237 VHSKAIGHPLVADTLY----DGKNSLPLQ-RQGLHCFHLVFYHPFLEKQLEIYCNPPRDF 291

Query: 316 V 316
            
Sbjct: 292 E 292


>gi|156230593|gb|AAI52263.1| Zgc:92006 protein [Danio rerio]
          Length = 358

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 72/275 (26%), Positives = 126/275 (45%), Gaps = 40/275 (14%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----SKG 141
           SV+ +  +  L    LYED  I   NKP  + +   +GI   I   L            G
Sbjct: 77  SVHPSVFAKALYRSSLYEDQNIIAINKPYDVPLHNINGIRNSIAECLPLLAKISDNMRPG 136

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +  L H+L++ET+G+L++A+T  AA+H+    +  +++  Y ++  G+P   +  I   
Sbjct: 137 SQLHLCHKLEKETTGVLILAKTEEAAEHVQTLIQSHKVEMKYLAITVGVPVPSEGVIDIP 196

Query: 202 LLKKSHIGGDYVHVV------KQNEKG-----------ANYAISHFKVIDCFAQKFCWLE 244
           +++++ +G      +      K NE G           A+ A++ ++V+D  +     +E
Sbjct: 197 VIERAVVGPQPHFKMALSPLFKVNEDGDGVTRVRAHRQAHAAVTRYRVLDNTS-GCSLVE 255

Query: 245 MQPHTGRTHQLRVHAL-HMGCPIVGDHKYCANFK---GNFTSPIQNK------------L 288
           +QP TG  +QLRVH    + CPI+GDHKY    K            +            L
Sbjct: 256 LQPLTGVKNQLRVHMALALTCPILGDHKYSHWSKLAPQKLPEGTLRRLGLVQSKTRYLPL 315

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +LH+R + LP  +G R + ++ PLP + +     L
Sbjct: 316 HLHSRRIVLPGFKGHRDITVSCPLPKYFINALKRL 350


>gi|149199657|ref|ZP_01876690.1| ribosomal large subunit pseudouridine synthase D [Lentisphaera
           araneosa HTCC2155]
 gi|149137310|gb|EDM25730.1| ribosomal large subunit pseudouridine synthase D [Lentisphaera
           araneosa HTCC2155]
          Length = 221

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 64/220 (29%), Positives = 105/220 (47%), Gaps = 14/220 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQ 152
           ++ +L+ED+ I + NK AG  VQ        +   +++++  K +K       +THRLD+
Sbjct: 3   EADVLHEDNHIIIVNKRAGQVVQIDESGDTPLCEIVQAFLKKKHKKEGNVFLGVTHRLDR 62

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
             SG+++ A+T  A   L + F+ + IQK YW+     P    + + ++L+K        
Sbjct: 63  PVSGVIIFAKTSKALTRLNKMFQEKEIQKTYWAFCLANPAKASDLLTHYLVKDRRKNKTK 122

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            H  K  E    ++   +K I    ++   LE+ P TGR HQ+RV    +GC I GD KY
Sbjct: 123 AHNKKVTE--GKFSQLEYKEIKRSGRQ-SLLEVNPLTGRPHQIRVQLASIGCIIKGDLKY 179

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPL 311
            A       S     + LH+R +   HP     + + APL
Sbjct: 180 GAPKANEDKS-----ICLHSRRVRFIHPVSKEEIDLEAPL 214


>gi|15639223|ref|NP_218671.1| hypothetical protein TP0231 [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189025464|ref|YP_001933236.1| hypothetical protein TPASS_0231 [Treponema pallidum subsp. pallidum
           SS14]
 gi|3322502|gb|AAC65220.1| conserved hypothetical protein [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189018039|gb|ACD70657.1| hypothetical protein TPASS_0231 [Treponema pallidum subsp. pallidum
           SS14]
 gi|291059635|gb|ADD72370.1| RNA pseudouridine synthase superfamily [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 216

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 111/230 (48%), Gaps = 16/230 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   ++++D+ +   +KPAG++VQ G+ +   +   L+  +   G +    HRLD++T+G
Sbjct: 1   MALPIIFQDAAVVAVDKPAGLAVQPGARVRVCVVDVLQKQL---GVRLFPLHRLDKDTAG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A+   AA          R+ K Y +L +G P  +   I   +  ++        VV
Sbjct: 58  VLLFAKHARAAALYQGILGSMRVIKRYRALCFGRPPRECGDIRVPI--RTGTAARRRQVV 115

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--A 274
           +        A + ++V+        +LE+  H+GRTHQ+R+H   +GCPI+GD KY   A
Sbjct: 116 R-------AAHTAYRVL-RATDTHTYLELTLHSGRTHQIRIHLAALGCPIIGDDKYGDFA 167

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
             K    +    +L L A  + LP      L + A +P H ++  D++  
Sbjct: 168 RNKACARAWGVKRLQLFAHSLVLPC-ACKPLVLRARMPVHFLRALDAVAL 216


>gi|297172314|gb|ADI23291.1| pseudouridylate synthases, 23S RNA-specific [uncultured
           actinobacterium HF0770_13M05]
          Length = 244

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 77/264 (29%), Positives = 128/264 (48%), Gaps = 25/264 (9%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +Q G  +RIPPV     +      I ++++N       ++  ++YED ++ V NKP G++
Sbjct: 1   MQRGDRLRIPPVRIDSRNASH---IGEATIN------QIRRAIIYEDEELLVLNKPVGVA 51

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           V GGSGI + I   L+        +  L HRLD++TSG +++A+TR     L  +FR  R
Sbjct: 52  VHGGSGIRHGIIEILRQTRSDVAFE--LVHRLDRDTSGCMLIAKTRRMLLELHAAFREAR 109

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y ++V G        + + L + +   G+    +  +    + A + F+V    A+
Sbjct: 110 VKKRYDAVVAGDWPQGLRTVRHSLRRHTLQSGERRVRIDLH---GDKARTDFEVQQRGAR 166

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
                 + PHTGRTHQ+RVHA   G  +VGD+KY          P   ++ LH+  + LP
Sbjct: 167 VTRLW-VYPHTGRTHQIRVHAAAEGHAVVGDNKY------QLNGPDVPRMMLHSSSLKLP 219

Query: 299 HPEGGRLQITAPLPAHMVKTWDSL 322
                  +  A      ++TW  L
Sbjct: 220 DGR----RFDADPDETFLETWSHL 239


>gi|109109212|ref|XP_001112402.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 1 [Macaca mulatta]
          Length = 377

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 79/298 (26%), Positives = 130/298 (43%), Gaps = 39/298 (13%)

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V   PV   +  I++  + L   V+    +  L   +L++++ + V NKP G+ V GG G
Sbjct: 64  VSTNPVQRRVQEIVRFTRQLQR-VHPNVLAKALTRGILHQNNNLVVINKPYGLPVHGGPG 122

Query: 125 IAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           +   I   L    K     K +   L HRLD+ET+G++V+A  +  A  + E FR R++ 
Sbjct: 123 VQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWDKDMAHQVQELFRTRQVV 182

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH---------------VVKQNEKGANY 225
           K YW++   +P      +   +++K   G    H               V  ++ + A  
Sbjct: 183 KKYWAITVRVPMPSAGVVDIPIVEKEAQGQQQHHKMTLSPSYRMDNGKMVKVRHSRNAQV 242

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC----------- 273
           A++ ++V+         +E+QP TG  HQLRVH    + CPI+GDHKY            
Sbjct: 243 AVTRYQVLSS-TLSSALVELQPITGIKHQLRVHLSFGLDCPILGDHKYSDWNRLAPQKLS 301

Query: 274 -ANFKGNFTSPIQNK---LYLHARYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGFK 325
               K       + +   L+LHA+ + LP        L +   LP   V +   LG +
Sbjct: 302 VGTLKKLGLEQSKARYIPLHLHAQQLILPALGSRKEDLNLVCKLPRFFVCSLRRLGLE 359


>gi|77919951|ref|YP_357766.1| 23S RNA-specific pseudouridylate synthase [Pelobacter carbinolicus
           DSM 2380]
 gi|77546034|gb|ABA89596.1| 23S RNA-specific pseudouridylate synthase [Pelobacter carbinolicus
           DSM 2380]
          Length = 296

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 118/322 (36%), Gaps = 41/322 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + +   +    +        P      L+++LRSG++R +   +  N  ++  + +++P 
Sbjct: 4   ITLTEQDAGQTVLETLHARIPAAPRSYLRQLLRSGKIRCNGSILTENICLRGHESLQLPD 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYH 128
                             +         +  +L E  +     KPAG++V    G    +
Sbjct: 64  SKR---------------LREVCTDRVPELTILLETDEFLAVFKPAGLAVHSSVGHTEDN 108

Query: 129 IDGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           +   LK+W+       +    HRLD  TSG ++  + R A   L    +   + K Y +L
Sbjct: 109 LTDRLKAWIKQCKAPYRIAPVHRLDIGTSGPVIFGKGRKATAELGRLLQNGHMSKTYLAL 168

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G P                  G  V  V+   K    A + F+V+   A         
Sbjct: 169 VNGHPPE---------------TGMMVTSVRVQGKPKQAA-TRFRVLGRHASAALLELEL 212

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRL 305
              GR HQ+R      G P+ GDH+Y          P +++L+LH   +  P   +    
Sbjct: 213 LS-GRKHQIRQQCADAGWPLYGDHRYGGP-----ELPGRDRLFLHCWQLAWPIQGDQPSH 266

Query: 306 QITAPLPAHMVKTWDSLGFKYD 327
           +IT+PLP  +     S+  +  
Sbjct: 267 RITSPLPEELSVILTSMDIESP 288


>gi|15924840|ref|NP_372374.1| hypothetical protein SAV1850 [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|15927424|ref|NP_374957.1| hypothetical protein SA1668 [Staphylococcus aureus subsp. aureus
           N315]
 gi|21283520|ref|NP_646608.1| hypothetical protein MW1791 [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49486667|ref|YP_043888.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|57650639|ref|YP_186732.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus COL]
 gi|87160591|ref|YP_494483.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus USA300_FPR3757]
 gi|88195673|ref|YP_500479.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus NCTC 8325]
 gi|148268322|ref|YP_001247265.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH9]
 gi|150394384|ref|YP_001317059.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1]
 gi|151221954|ref|YP_001332776.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|156980166|ref|YP_001442425.1| hypothetical protein SAHV_1835 [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|161510067|ref|YP_001575726.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|253315181|ref|ZP_04838394.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus str. CF-Marseille]
 gi|253735270|ref|ZP_04869435.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|255006638|ref|ZP_05145239.2| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Mu50-omega]
 gi|257793791|ref|ZP_05642770.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9781]
 gi|258413728|ref|ZP_05682001.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9763]
 gi|258420765|ref|ZP_05683704.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9719]
 gi|258438426|ref|ZP_05689710.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9299]
 gi|258443871|ref|ZP_05692210.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8115]
 gi|258447326|ref|ZP_05695473.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A6300]
 gi|258448191|ref|ZP_05696318.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus A6224]
 gi|258452660|ref|ZP_05700659.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus A5948]
 gi|258453376|ref|ZP_05701359.1| pseudouridine synthase [Staphylococcus aureus A5937]
 gi|262050142|ref|ZP_06022996.1| hypothetical protein SAD30_1106 [Staphylococcus aureus D30]
 gi|262052669|ref|ZP_06024861.1| hypothetical protein SA930_0805 [Staphylococcus aureus 930918-3]
 gi|269203487|ref|YP_003282756.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282895148|ref|ZP_06303367.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8117]
 gi|282924181|ref|ZP_06331856.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|282928588|ref|ZP_06336187.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|284024896|ref|ZP_06379294.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 132]
 gi|294850278|ref|ZP_06791013.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9754]
 gi|295406157|ref|ZP_06815965.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|296276018|ref|ZP_06858525.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus MR1]
 gi|297207434|ref|ZP_06923871.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297244920|ref|ZP_06928797.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8796]
 gi|300911518|ref|ZP_07128963.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|13701643|dbj|BAB42936.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           N315]
 gi|14247622|dbj|BAB58012.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|21204961|dbj|BAB95656.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49245110|emb|CAG43576.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|57284825|gb|AAW36919.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus COL]
 gi|87126565|gb|ABD21079.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus USA300_FPR3757]
 gi|87203231|gb|ABD31041.1| ribosomal large subunit pseudouridine synthase, RluD subfamily,
           putative [Staphylococcus aureus subsp. aureus NCTC 8325]
 gi|147741391|gb|ABQ49689.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH9]
 gi|149946836|gb|ABR52772.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1]
 gi|150374754|dbj|BAF68014.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|156722301|dbj|BAF78718.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|160368876|gb|ABX29847.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|253726677|gb|EES95406.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|257787763|gb|EEV26103.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9781]
 gi|257839515|gb|EEV63986.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9763]
 gi|257843369|gb|EEV67779.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9719]
 gi|257848470|gb|EEV72461.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9299]
 gi|257851277|gb|EEV75220.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8115]
 gi|257853913|gb|EEV76869.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A6300]
 gi|257858430|gb|EEV81306.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus A6224]
 gi|257859635|gb|EEV82484.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus A5948]
 gi|257864468|gb|EEV87213.1| pseudouridine synthase [Staphylococcus aureus A5937]
 gi|259159418|gb|EEW44470.1| hypothetical protein SA930_0805 [Staphylococcus aureus 930918-3]
 gi|259161767|gb|EEW46355.1| hypothetical protein SAD30_1106 [Staphylococcus aureus D30]
 gi|262075777|gb|ACY11750.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282589797|gb|EFB94882.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|282592976|gb|EFB97978.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|282762492|gb|EFC02633.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8117]
 gi|285817530|gb|ADC38017.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus 04-02981]
 gi|294822894|gb|EFG39328.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9754]
 gi|294969154|gb|EFG45175.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|296887897|gb|EFH26793.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297178000|gb|EFH37248.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8796]
 gi|300887150|gb|EFK82350.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|312830222|emb|CBX35064.1| RNA pseudouridylate synthase family protein [Staphylococcus aureus
           subsp. aureus ECT-R 2]
 gi|315130506|gb|EFT86492.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS03]
 gi|315196801|gb|EFU27145.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320141300|gb|EFW33145.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320143572|gb|EFW35352.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|329727339|gb|EGG63795.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21172]
 gi|329729507|gb|EGG65909.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21189]
 gi|329732958|gb|EGG69302.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 273

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 58/264 (21%), Positives = 107/264 (40%), Gaps = 32/264 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  + +  KP G+         +  +   +   +DS   +P   HRLDQET G+L+VA
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHVIYTIDSDYVEP--IHRLDQETVGLLIVA 135

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +     + L        I +IY + V  +   K + I   + K       +    ++   
Sbjct: 136 KNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTIDMPIGKD-----KFHSNKRRVSP 190

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y  +      
Sbjct: 191 TGQRAITHILTSKMIKEAVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLYGDS------ 244

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL 305
                +L L +  ++  HP    +
Sbjct: 245 --TLRQLELESYKIEFVHPLTKEV 266


>gi|217974457|ref|YP_002359208.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499592|gb|ACK47785.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 574

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 105/236 (44%), Gaps = 25/236 (10%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E  ++D +  LT  ++     +LY+D  + + NKPA      G  I   +   ++     
Sbjct: 345 EGLVVDENPLLTNPAEGKTLAILYQDDAMAIVNKPAEFLSVPGKEIEDSVYSRIRQAF-P 403

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-----KNK 194
               P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ GIP     K  
Sbjct: 404 HATGPLIVHRLDMSTSGLMVIALTKDAHKQLQKQFIQRTVTKRYVALLAGIPAVMANKQA 463

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--IDCFAQKFCWLEMQPHTGRT 252
              I+  L +          V     +    A +H+++  +D  A+      + P TGRT
Sbjct: 464 TGHISLPL-RGDLDDRPRQLVC---HEFGKAAETHWELSQLDEMARTARVY-LYPKTGRT 518

Query: 253 HQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           HQLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP    L
Sbjct: 519 HQLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHPVTREL 565


>gi|33866818|ref|NP_898377.1| pseudouridine synthase [Synechococcus sp. WH 8102]
 gi|33639419|emb|CAE08803.1| probable pseudouridine synthase [Synechococcus sp. WH 8102]
          Length = 315

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 66/298 (22%), Positives = 129/298 (43%), Gaps = 34/298 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V        L  W    Y H      ++ + SG++  + +R+  + R+  G+ V      
Sbjct: 16  VPVGAAGTWLSCWLAERYQHSAGEVWRQRIHSGELDCNGQRLTADRRLAGGEAV------ 69

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                + +    L+ ++     +       +++D  + V NKP+G+ V  G G   H   
Sbjct: 70  -----LWRRPPWLEEAIPDQWET-------IHDDGDLLVINKPSGLPVMPGGGFLLH--- 114

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKIYWSLV 187
            L + ++  G +P   HRL + TSG+ V AR       L++ FR     R++ + +   V
Sbjct: 115 TLTALLEPTGARP--VHRLGRFTSGLQVCARDPMTRAALSKQFRPEGSCRKVYQAWAQRV 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVH----VVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            G+ + +   + N ++++ H    +V     + ++  +    A S  ++++  A+     
Sbjct: 173 PGLEQGQTLTVTNDVVERQHPLLGWVWGPEPLKQEPIRKRLTARSELELLERTAEGDRL- 231

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMD-LPH 299
           ++   TGR HQ+R+H   +G P++GD  Y  N +     +P      LHA  +  LPH
Sbjct: 232 QVTITTGRPHQIRIHLAQLGSPLLGDPLYLLNREISATATPGDGGYRLHAWQLSGLPH 289


>gi|238895332|ref|YP_002920067.1| putative ribosomal large subunit pseudouridine synthase A
           [Klebsiella pneumoniae NTUH-K2044]
 gi|238547649|dbj|BAH64000.1| putative ribosomal large subunit pseudouridine synthase A
           [Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044]
          Length = 232

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 56/223 (25%), Positives = 88/223 (39%), Gaps = 16/223 (7%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   +  LLY+D  + + NKPAG+    G          +   +  +     L HR
Sbjct: 8   FVAPPCREQITLLYQDEHLLLINKPAGLLSLSGK--DPRNLDSVHHRLVQRFPGCTLVHR 65

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++V+AR +     L + F  R + K+Y +L+ G     +  +   + K     
Sbjct: 66  LDFGTSGLMVIARNKGINALLCQQFSQRTVDKVYTALLCGHLAEDEGIVEAAIAKDPA-- 123

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKF--------CWLEMQPHTGRTHQLRVHALH 261
                 +    +    A S ++VID   Q            + + P TGRTHQLR+H   
Sbjct: 124 --RFPRMALCARHGKPARSRYRVIDRLYQAREGERALALTRVTLTPETGRTHQLRIHCQL 181

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +G PI+G   Y         +    +L LHA  +   HP    
Sbjct: 182 LGYPILGCDLYGGRELPG--TEQAPRLMLHASELRFVHPVSHE 222


>gi|217972240|ref|YP_002356991.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217497375|gb|ACK45568.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 244

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 100/233 (42%), Gaps = 19/233 (8%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +LY+DS I + +KP+G+    G          +   +        L HRLD 
Sbjct: 17  PPCLGQIRVLYQDSDILLIDKPSGLLSLSGKNPLN--LDSVHYRLVQDFPTATLLHRLDF 74

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++VA  ++    LT+ F+ R I+K Y +L+ G        I   + K      D+
Sbjct: 75  GTSGIMLVALNKSVNGLLTKQFQARTIEKRYTALLHGHIAADSGVINLPIAKDV----DH 130

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             + K        AIS ++V++   + F   +E  P +GRTHQLR+H+   G  I+G   
Sbjct: 131 FPLQKICHSTGKPAISEYRVLERLTEPFATRVEFTPVSGRTHQLRIHSQQFGHSILGCDL 190

Query: 272 YCA---NFKGNFTSPIQN--------KLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y     +   N  +P  +        +L LHA  +   HP  G R+      P
Sbjct: 191 YGGVGESVADNAAAPDPDITKMTSNSRLMLHATRLAFDHPLTGERIDWLCECP 243


>gi|223043536|ref|ZP_03613581.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus capitis SK14]
 gi|222443024|gb|EEE49124.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus capitis SK14]
          Length = 276

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 60/285 (21%), Positives = 112/285 (39%), Gaps = 36/285 (12%)

Query: 25  FKNHYPHI--NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
            +  + ++     +L ++  S  + ++ +  K  + +++G  V IP      N++     
Sbjct: 14  LREIFQNLNLPKKDLHQLNMSKDITINNQSAKLTDVVRTGDSVFIPTPEEKSNYL----- 68

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KG 141
                        +  + + YED    +  KP G+            +  +   + +   
Sbjct: 69  -----------PSYRYAQVYYEDDDFAIVMKPKGVKTHP--NDLKESNTLMNHVIYTVDS 115

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           +     HRLDQET G+L+VA+     + L        I +IY + V  +   K + I   
Sbjct: 116 EYVEPIHRLDQETVGLLIVAKNPIMKKILDRMLEENEITRIYKANVKALLPIKPQTIDMP 175

Query: 202 LLKKS-HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           + K   H     +            AI+H    +   +  C L+++  TGRTHQ+RVH  
Sbjct: 176 IGKDKFHPNKRRI------SNTGQRAITHILNSEMIKEGICQLDIKLDTGRTHQIRVHLA 229

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            +G P++GD  Y  +           KL L++  ++L HP    L
Sbjct: 230 EIGHPVIGDPLYGDS--------TLRKLELNSHKIELIHPLTREL 266


>gi|82548298|gb|ABB82988.1| putative RNA pseudouridylate synthase [uncultured organism
           HF10_3D09]
          Length = 294

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 66/294 (22%), Positives = 132/294 (44%), Gaps = 29/294 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIK 79
           LD   K   P  +   L+K+L + ++ V++K + +  + + +G+ V I P          
Sbjct: 12  LD-VLKIMQPQASTNVLRKMLTNRRITVEEKIIHRAKHPVLAGETVEIRP---------- 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWV 137
            +  L         ++     +++ED  I V  KPAG+       +      +  ++   
Sbjct: 61  -KPKLSIEETRQTSAETHSLDIIFEDDAILVVEKPAGLLSVATDRLEVDTLHNRCVEYCR 119

Query: 138 DSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           + K +    + HRLD+ TSG++V A+T    + L E F  R + + Y +LV G+ +  + 
Sbjct: 120 ELKKKAWCFIVHRLDKATSGLMVFAKTEDVKRDLQEQFAERLVHRHYVALVEGVAEPGQA 179

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                L++  ++    V V  +  K + +AI+ + +++    +   L +   TGR HQ+R
Sbjct: 180 I--QHLVEDRNL---RVFVSDKKTKTSKHAITTWDILE-KGDESTLLSVVIETGRRHQIR 233

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           V     G P++GD  + A      T+ +  ++ LHA  ++  HP     ++  +
Sbjct: 234 VAMAENGTPVMGDTMHGA------TTNLHGRICLHAVALEFLHPLTDDPIRFES 281


>gi|221142167|ref|ZP_03566660.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus str.
           JKD6009]
 gi|304380548|ref|ZP_07363223.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|269941321|emb|CBI49718.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TW20]
 gi|302751659|gb|ADL65836.1| RluA, Pseudouridylate synthase, 23S RNA-specific [Staphylococcus
           aureus subsp. aureus str. JKD6008]
 gi|304340877|gb|EFM06802.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|329314526|gb|AEB88939.1| RluA, Pseudouridylate synthase, 23S RNA-specific [Staphylococcus
           aureus subsp. aureus T0131]
          Length = 273

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 58/264 (21%), Positives = 106/264 (40%), Gaps = 32/264 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  + +  KP G+         +  +   +   +DS   +P   HRLDQET G+L+VA
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHVIYTIDSDYVEP--IHRLDQETVGLLIVA 135

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +     + L        I +IY + V  +   K + I   + K       +    +    
Sbjct: 136 KNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTIDMPIGKD-----KFHSNKRCVSP 190

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y  +      
Sbjct: 191 TGQRAITHILTSKMIKEAVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLYGDS------ 244

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL 305
                +L L +  ++  HP    +
Sbjct: 245 --TLRQLELESYKIEFVHPLTKEV 266


>gi|156978129|ref|YP_001449035.1| ribosomal large chain pseudouridine synthase A [Vibrio harveyi ATCC
           BAA-1116]
 gi|156529723|gb|ABU74808.1| hypothetical protein VIBHAR_06934 [Vibrio harveyi ATCC BAA-1116]
          Length = 523

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 63/245 (25%), Positives = 112/245 (45%), Gaps = 20/245 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  + +     ++  +  +L++D  + + NKP+G+    G  I    
Sbjct: 292 CQPILGHMLQGLDVEPNPLA-ENWAEDKELEILFQDEAMVIVNKPSGLLSVPGKTIKDSA 350

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++      + P + HRLD  TSGIL+ A T+ A + L + F  R +QK Y +L+ G
Sbjct: 351 YTRLQTMF-PDVEGPFVIHRLDMATSGILIFALTKRANKSLQKQFITRGVQKRYMALLEG 409

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +    +  I+  + +          V  ++      A +++++I+        + M P T
Sbjct: 410 VLTEPEGEISLPM-RGDPDDRPRQLVCFEH---GKPAETYWQLIE-VKDGRSKVYMYPKT 464

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH+ H   +   +VGD  Y             N+L+LHA  ++L HP    R+
Sbjct: 465 GRTHQLRVHSAHHMGLNMAMVGDGLYGEK---------ANRLHLHAEMLELDHPYSKERM 515

Query: 306 QITAP 310
              A 
Sbjct: 516 CFQAE 520


>gi|115477922|ref|NP_001062556.1| Os09g0103500 [Oryza sativa Japonica Group]
 gi|75117672|sp|Q69K07|PUS4_ORYSJ RecName: Full=RNA pseudourine synthase 4, mitochondrial; AltName:
           Full=RNA pseudouridylate synthase 4; AltName:
           Full=RNA-uridine isomerase 4; Flags: Precursor
 gi|50725212|dbj|BAD34146.1| ribosomal large subunit pseudouridine synthase C-like [Oryza sativa
           Japonica Group]
 gi|51091882|dbj|BAD36694.1| ribosomal large subunit pseudouridine synthase C-like [Oryza sativa
           Japonica Group]
 gi|113630789|dbj|BAF24470.1| Os09g0103500 [Oryza sativa Japonica Group]
          Length = 448

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 70/265 (26%), Positives = 122/265 (46%), Gaps = 40/265 (15%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVD-----------------KKRVKFNNRIQSGQVV 65
           +W +   P +    +QK+ R  +V+ +                  +RV   +++  G ++
Sbjct: 88  KWVRRCCPDLPTSLVQKLFRLRKVKKNVVTAEISSADASAEQHRLRRVSAKDQLMPGDIL 147

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKIYVFNKPAGISVQGGS 123
            +P         +KE  + + +      ++  FL+ + +Y+D  I V NKP G+ VQGG 
Sbjct: 148 FLPVN-------LKESSVAEKTKKFDNRNEINFLRGLEIYKDEAIIVVNKPPGMPVQGGV 200

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR----- 178
           GI   ID     + ++  + PRL HRLD++ SGILV+ R + +   L   FR +      
Sbjct: 201 GIKNSIDVLASMFEENSSEAPRLVHRLDRDCSGILVLGRNQLSTSMLHAIFREKTADALA 260

Query: 179 ------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA---NYAISH 229
                 +Q+ Y +LV G P++ K  ++  L K     G    +  +    A     A++ 
Sbjct: 261 DGTQHVLQRKYVALVIGTPRHPKGLLSAPLAKILLQDGKSERLTIRASSNAASVQDALTE 320

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQ 254
           ++VI+   Q + WLE+ P TGR HQ
Sbjct: 321 YRVIESCPQGYTWLELFPRTGRKHQ 345


>gi|332161266|ref|YP_004297843.1| putative ribosomal large subunit pseudouridine synthase [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|318605161|emb|CBY26659.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325665496|gb|ADZ42140.1| putative ribosomal large subunit pseudouridine synthase [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|330860585|emb|CBX70883.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica W22703]
          Length = 232

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 54/211 (25%), Positives = 86/211 (40%), Gaps = 16/211 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+    G          +   +        L HRLD  TSG++V+A
Sbjct: 20  LYQDDHLVLINKPTGLLSLSGKNPQN--LDSVHHRLVQIFPGCTLVHRLDFGTSGLMVIA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L + F  R + K+Y +L+ G   + +  I   + K   +      ++     
Sbjct: 78  RNKAINAALCQQFSQRTVTKVYSALLCGHLDDNEGVIDAAIAKDPAL----FPLMSICAT 133

Query: 222 GANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               A S ++V++ F              +++ P TGRTHQLR+H   +G PI G   Y 
Sbjct: 134 HGKPARSGYRVVERFYHELEDGRLLPLTRVQLTPETGRTHQLRIHCQQLGHPIWGCDLYG 193

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                        +L LHA  +   HP    
Sbjct: 194 GRLLPGTEQT--PRLMLHASELHFVHPISEE 222


>gi|283770934|ref|ZP_06343826.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
 gi|283461081|gb|EFC08171.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
          Length = 273

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 59/264 (22%), Positives = 107/264 (40%), Gaps = 32/264 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  + +  KP G+         +  +   +   VDS   +P   HRLDQET G+L+VA
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHVIYTVDSDYVEP--IHRLDQETVGLLIVA 135

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +     + L        I +IY + V  +   K + I   + K       +    ++   
Sbjct: 136 KNPLMKKILDRMLEDNDITRIYKANVNALLPLKPQTIDMPIGKD-----KFHSNKRRVSP 190

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y  +      
Sbjct: 191 TGQRAITHILTSKMIKETVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLYGDS------ 244

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL 305
                +L L +  ++  HP    +
Sbjct: 245 --TLRQLELESYKIEFVHPLTKEV 266


>gi|227545266|ref|ZP_03975315.1| pseudouridylate synthase RluD [Lactobacillus reuteri CF48-3A]
 gi|300908664|ref|ZP_07126127.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
 gi|154705590|gb|ABS84221.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           reuteri]
 gi|227184756|gb|EEI64827.1| pseudouridylate synthase RluD [Lactobacillus reuteri CF48-3A]
 gi|300894071|gb|EFK87429.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
          Length = 306

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 65/300 (21%), Positives = 117/300 (39%), Gaps = 31/300 (10%)

Query: 22  DRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           D+W   N   H   +          V V+ +    N  +     +++    + +      
Sbjct: 26  DQWLLPNRLIHYLRIR-------RTVLVNGEYRSMNELVGRNDNIQLLFCGDEIRTPAAN 78

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDS 139
             I     +L          +LYE+  + V NKP G        G    +   +  ++  
Sbjct: 79  DYIPSLQSHLE---------VLYENRDLLVVNKPRGQKTHPNYHGETGTLMNDVAGYLAH 129

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                 + HR+D +TSG ++VA+       L       +I + Y +LV G      +   
Sbjct: 130 SQNNAYMVHRIDLQTSGAVIVAKNPIVVPILNRLISDGQIHRQYLALVEGKMAQSGKF-- 187

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +W + ++ +     H+ + N + A  A+++++ +    ++   + +   TGRTHQLRVH 
Sbjct: 188 DWAIGRNPVN---PHLHQVNGQNAQPALTYYETLASNHER-SLVRLHLVTGRTHQLRVHL 243

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
            H G PIVGD  Y               L+  A+ + LP      L I+APLP++     
Sbjct: 244 AHSGHPIVGDPLYNPLSTEGML------LHGVAQKLILPF-VMKSLNISAPLPSYFENYL 296


>gi|262374552|ref|ZP_06067826.1| dual specificity pseudouridine synthase [Acinetobacter junii SH205]
 gi|262310548|gb|EEY91638.1| dual specificity pseudouridine synthase [Acinetobacter junii SH205]
          Length = 221

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 13/231 (5%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  + +           ++YED  + V NKPAG+    G    +H   +L+  V      
Sbjct: 1   MPLNDHFIYRPPQEPLEIMYEDEDLVVVNKPAGLLSVMGRLPEHHDSVYLR--VLDLHPT 58

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K Y +LV G  + +       + 
Sbjct: 59  AKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKKYYEALVQGAIQAEGSVDVPLIT 118

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
              +     VH      +    A + F+++D   +     + ++P TGR+HQLRVH +H+
Sbjct: 119 DWENRPRQIVHF-----ELGKQAKTLFQLMDYDVETDQSRVRLEPVTGRSHQLRVHMMHI 173

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
           G PI+GD  Y              ++ LHA ++   HP    L +I + +P
Sbjct: 174 GHPIMGDKLYHPEP----AKFHLKRMALHAAFLSFQHPLQQHLVEIKSVIP 220


>gi|212530788|ref|XP_002145551.1| DRAP deaminase (Rib2), putative [Penicillium marneffei ATCC 18224]
 gi|210074949|gb|EEA29036.1| DRAP deaminase (Rib2), putative [Penicillium marneffei ATCC 18224]
          Length = 511

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 62/268 (23%), Positives = 98/268 (36%), Gaps = 55/268 (20%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +K +  G+V V  K       + +G +V              E  +    +         
Sbjct: 70  KKAIEDGRVLVGGKVANLETIVPNGAIVSHSTHR-------HEPPVSSRPIG-------- 114

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSG 156
              +++ED  + V +KPAGI V G     YH +  L+    D  G KP   +RLD+ TSG
Sbjct: 115 ---IIHEDDDMIVIDKPAGIPVHGAG--RYHFNTILEIMKADRPGFKPLPCNRLDRLTSG 169

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHV 215
           ++ +A+   AA+      + R +QK Y + V G  P     C    +     +G + V  
Sbjct: 170 VMFIAKNPKAAEKFALQLKSRTLQKEYVARVSGRFPDGVVLCDQPIMSVSPKLGLNRVRA 229

Query: 216 VKQNEKGANYAISHFKVIDCFA---------------------------QKFCWLEMQPH 248
                     A + F+ I  +                            + +  +   P 
Sbjct: 230 ------TGKEARTKFRRIAYYPAPPKTDAESATTSGDRPATPPATATEDEGYSIVHCLPL 283

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANF 276
           TGRTHQ+RVH   +G PI  D  Y    
Sbjct: 284 TGRTHQIRVHLQFLGYPISNDPIYSNRR 311


>gi|119513806|ref|ZP_01632778.1| ribosomal large chain pseudouridine synthase A [Nodularia spumigena
           CCY9414]
 gi|119461540|gb|EAW42605.1| ribosomal large chain pseudouridine synthase A [Nodularia spumigena
           CCY9414]
          Length = 331

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 69/220 (31%), Positives = 106/220 (48%), Gaps = 19/220 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSG 156
             ++YED  +   NKP G+    G       D  L  W         +   HRLDQETSG
Sbjct: 124 LPIIYEDEWLIAVNKPPGLLAVPGR-YRDTQDSVLSRWRYWFPDDAEIMAVHRLDQETSG 182

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           IL++AR R   + L++ F+ R++ K+Y ++++G   +++  I   L   S     Y  V 
Sbjct: 183 ILLLARVRQIHRQLSQQFQQRQVHKVYEAILFGAVTDEQGVIELPLWG-SPENRPYQQV- 240

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL---HMGCPIVGDHKYC 273
             N +    +++ F+VI      +  +E  P TGRTHQLRVHA     +G  I+GD  Y 
Sbjct: 241 --NWQYGKISVTQFRVIGREG-NYTRVEFIPVTGRTHQLRVHAADQLGLGMTILGDRLYG 297

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
            N          ++L+LHAR +   HP+ G  + + A  P
Sbjct: 298 CNAAA-------SRLHLHARQLSFKHPQLGETIDLVAKTP 330


>gi|91793876|ref|YP_563527.1| pseudouridylate synthase [Shewanella denitrificans OS217]
 gi|91715878|gb|ABE55804.1| Pseudouridylate synthase [Shewanella denitrificans OS217]
          Length = 230

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 58/216 (26%), Positives = 102/216 (47%), Gaps = 13/216 (6%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        + Y D  I V NKP+G+    G     +      + +     +  L HRLD
Sbjct: 20  QPPSIPWLDIRYLDRDIIVINKPSGLLSNPGRAPETYDTAI--TRLQRLYPETILIHRLD 77

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSGI++ AR + A  +L   F+ R+ +K+Y + V G  +++   +   L         
Sbjct: 78  CDTSGIMIFARNKKAESNLKTQFQNRQAKKVYIAEVSGCFEHQDGKVNFPLGPDPMTP-- 135

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                +Q  +    A++++++++  A     +E++PHTGRTHQLRVH   +G  I+GD  
Sbjct: 136 ---PFQQVIESGKPALTYYRLLEHRAS-TSLVELKPHTGRTHQLRVHMKALGHTIIGDEF 191

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           Y             ++L LHA+ + L HP   +++I
Sbjct: 192 YG----DETVIAASHRLNLHAQSLTLLHPF-KQIEI 222


>gi|195118760|ref|XP_002003904.1| GI18161 [Drosophila mojavensis]
 gi|193914479|gb|EDW13346.1| GI18161 [Drosophila mojavensis]
          Length = 545

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 65/269 (24%), Positives = 114/269 (42%), Gaps = 34/269 (12%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ + +G + V+ ++V  + R++                    
Sbjct: 165 LDVF-SREFRAQPPEEYKRSIEAGNLTVNYEKVPVDYRLKHND----------------- 206

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             +L ++V+  +     + I +++ D  I V NKPA I V       ++   F+ +  + 
Sbjct: 207 --LLANTVHRHEVPVTAQPISIVHIDDDILVVNKPASIPVHPCGRYRHNTVIFILA-KEY 263

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECI 198
             +  R  HRLD+ TSG+L+  R    A+ + +  R R++QK Y   V G  P    EC 
Sbjct: 264 NLKNLRTIHRLDRLTSGLLLFGRNSEKARQMEQQIRNRQVQKEYVCCVEGHFPDGIIECN 323

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +    IG      V +  K      + FK I   A  +  ++ +P TGR HQ+RVH
Sbjct: 324 EPIEVVSYKIG------VCKVSKKGKDCQTTFKRI-AQAGDYSIVQCKPLTGRMHQIRVH 376

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
             ++G PIV D  Y     G    P++ +
Sbjct: 377 LQYLGYPIVNDPLYNHEVFG----PLKGR 401


>gi|85075514|ref|XP_955780.1| hypothetical protein NCU03846 [Neurospora crassa OR74A]
 gi|28916789|gb|EAA26544.1| hypothetical protein NCU03846 [Neurospora crassa OR74A]
          Length = 473

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 58/281 (20%), Positives = 102/281 (36%), Gaps = 53/281 (18%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           +        +  + +G V V+ K V   + +++G ++              E  +    +
Sbjct: 92  FRDRPAEYYRNAVETGLVVVNGKAVGPEHVLKNGDLISHTTHR-------HEPPVTAEPI 144

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
                       +++ED+ + V NKP+G+ V       Y+    +       G  PR  +
Sbjct: 145 -----------RVIHEDNDLIVINKPSGVPVHPAGRYNYNSVVEIIKSERGPGFLPRPCN 193

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSH 207
           RLD+ TSGI+ +A+++ AA+ L      R ++K Y + V G  P  +  C    L     
Sbjct: 194 RLDRLTSGIMFLAKSQHAAERLVAQISQRSVRKEYIARVVGRFPDGEVVCDQPILQISPK 253

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCF----------------------------AQK 239
           +  + V            A + FK +  +                             + 
Sbjct: 254 LTLNRVRA------NGKAARTVFKRLAYYPPVDPPTKGQTEQPAMPDAEQAAQRRGEGEG 307

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +  +   P TGRTHQ+RVH   +G PI  D  Y       F
Sbjct: 308 YSIVRCLPVTGRTHQIRVHLQFLGHPIQNDPIYANQKVWGF 348


>gi|314934014|ref|ZP_07841379.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus caprae C87]
 gi|313654164|gb|EFS17921.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus caprae C87]
          Length = 276

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 60/285 (21%), Positives = 112/285 (39%), Gaps = 36/285 (12%)

Query: 25  FKNHYPHI--NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
            +  + ++     +L ++  S  + ++ +  K  + +++G  V IP      N++     
Sbjct: 14  LREIFQNLKLPKKDLHQLNMSKDITINNQSAKLTDVVRTGDSVFIPTPEEKSNYL----- 68

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KG 141
                        +  + + YED    +  KP G+            +  +   + +   
Sbjct: 69  -----------PSYRYAQVFYEDDDFAIVMKPKGVKTHP--NDLKESNTLMNHVIYTVDS 115

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           +     HRLDQET G+L+VA+     + L        I +IY + V  +   K + I   
Sbjct: 116 EYVEPIHRLDQETVGLLIVAKNPIMKKILDRMLEENEITRIYKANVKALLPIKPQTIDMP 175

Query: 202 LLKKS-HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           + K   H     +            AI+H    +   +  C L+++  TGRTHQ+RVH  
Sbjct: 176 IGKDKFHPNKRRI------SNTGQRAITHILNSEMIKEGICQLDIKLDTGRTHQIRVHLA 229

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            +G P++GD  Y  +           KL L++  ++L HP    L
Sbjct: 230 EIGHPVIGDPLYGDS--------TLRKLELNSHKIELIHPLTREL 266


>gi|322832332|ref|YP_004212359.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321167533|gb|ADW73232.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 232

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 56/216 (25%), Positives = 91/216 (42%), Gaps = 17/216 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+    G          +   +        L HRLD  TSG++V+A
Sbjct: 20  LYQDEHLVLINKPTGLLSLSGKNPQN--LDSVHHRLVKIFPGCTLVHRLDFGTSGLMVIA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L   F  R + K+Y +L+ G  ++ +      + K   +      ++     
Sbjct: 78  RNKAINAALCHQFSQRTVTKVYSALLCGHLQHNEGVTDAPIAKDPAL----FPLMSICAV 133

Query: 222 GANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               A S ++V++ F +            + + P TGRTHQLR+H  ++G PI+G   Y 
Sbjct: 134 HGKPARSGYRVVERFYREQENGELLPLTRVLLTPQTGRTHQLRIHCQYLGHPILGCDLYG 193

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
                        +L LHA  +   HP  G  +I A
Sbjct: 194 GRLLPGTEQT--PRLMLHASELHFVHPVSGE-RIEA 226


>gi|88859724|ref|ZP_01134364.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           tunicata D2]
 gi|88818741|gb|EAR28556.1| ribosomal large subunit pseudouridine synthase A [Pseudoalteromonas
           tunicata D2]
          Length = 557

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 70/250 (28%), Positives = 115/250 (46%), Gaps = 20/250 (8%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      L+H+++  ++ D+ + L   ++ L+  ++Y+D  + V NKPA      G  I 
Sbjct: 323 LSKCQPILSHMLQGLEVDDNPL-LVNPAEGLELSIIYQDDVMLVINKPAEFLSVPGKSIT 381

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   +K+        P + HRLD  TSG++V+A  + + Q L + F +R + K Y +L
Sbjct: 382 DSVYTRIKAQF-PNASGPLIVHRLDMSTSGLMVIALNKRSHQALQKQFILRTVTKRYAAL 440

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           + G    +   I+  L +          V  ++      A ++F+VI   A     + + 
Sbjct: 441 LDGELSVQSGDISLPL-RVDLADRPRQMVCYEH---GKAAHTYFEVISHQA-GRTKVHLY 495

Query: 247 PHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           P TGRTHQLRVH  H   +  PIVGD  Y            + +L+LHA  + L HP  G
Sbjct: 496 PKTGRTHQLRVHCAHTLGLNTPIVGDDLYGKK---------EQRLHLHAELLALAHPITG 546

Query: 304 R-LQITAPLP 312
             L   A  P
Sbjct: 547 EVLTFIAQAP 556


>gi|242280174|ref|YP_002992303.1| pseudouridine synthase [Desulfovibrio salexigens DSM 2638]
 gi|242123068|gb|ACS80764.1| pseudouridine synthase [Desulfovibrio salexigens DSM 2638]
          Length = 302

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 59/297 (19%), Positives = 119/297 (40%), Gaps = 34/297 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +  +  ++  + ++ +RLD++     P       ++++ +G V V+ +  +   ++  G 
Sbjct: 27  LNEIDRIIAGDSDDGLRLDKFLLKLLPDSGLRERRRLIENGLVMVNGRSCRSGLKMFPGA 86

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            V +                L++           +  ++ +        KP G+     +
Sbjct: 87  EVVL----------------LEAEDRSCAVEILSQVKVVKQGEGFGTVYKPEGL---HSA 127

Query: 124 GIAYHIDGFLKSWVDS--KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            IA   +  ++  +     G++P L +RLD  TSG+L++A          E      + K
Sbjct: 128 AIAGSAESSVEECLSGIFPGKEPILANRLDFLTSGMLLIAFGVERENEFRECEDSGTVDK 187

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           +Y + V GIP+        +++K S    D       +++      S  +V++ +     
Sbjct: 188 VYHAKVHGIPEG------PFVVKNSLDTADRKRTKVLDDQAPEERWSSAEVVERYDDGTS 241

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            LE++   G  HQ+R H  H G PIVGD  Y             +++YLH R + LP
Sbjct: 242 LLEVRIAKGARHQIRAHLAHAGFPIVGDPIYGREDSA-------DRMYLHHRKIVLP 291


>gi|54310089|ref|YP_131109.1| tRNA pseudouridine synthase C [Photobacterium profundum SS9]
 gi|46914528|emb|CAG21307.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum SS9]
          Length = 245

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 101/241 (41%), Gaps = 11/241 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  +L++D  +   NKP+G+ V       +     +++  D  GQ     HRLD+ TSG
Sbjct: 1   MELDILFQDEYLVAVNKPSGMLVHRSWLDRHETVFVMQTLRDQIGQHVFPLHRLDRPTSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+   +   A  +   F  R I K Y ++V G  K+    +   L K+     D     
Sbjct: 61  VLLFGLSSEIASQMMPVFSGREIHKTYHAVVRGWIKDAA-VLDYPLKKELDKIADKNAAE 119

Query: 217 KQNEKGANYAISHFKVIDCF-------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +Q  + A  A S    ++           ++C +EM+P TGR HQLR H  H+   I+GD
Sbjct: 120 EQEAQEAVTAYSPLATVETNIPVGRYATSRYCLVEMKPETGRKHQLRRHMHHLNHHIIGD 179

Query: 270 HKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
             +             +  +L LHA  +   HP   + L I A +    ++      +  
Sbjct: 180 VNHGDGRHNRMFRENYDCHRLMLHASCLQFVHPVTKQALDIRASIDETWLRVMSEFNWST 239

Query: 327 D 327
           +
Sbjct: 240 E 240


>gi|120597834|ref|YP_962408.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|120557927|gb|ABM23854.1| pseudouridine synthase [Shewanella sp. W3-18-1]
          Length = 236

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 61/225 (27%), Positives = 97/225 (43%), Gaps = 11/225 (4%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +LY+DS I + +KP+G+    G          +   +        L HRLD 
Sbjct: 17  PPCLGQIRVLYQDSDILLIDKPSGLLSLSGKNPLN--LDSVHYRLVQDFPTATLLHRLDF 74

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++VA  +     LT+ F+ R ++K Y +L+ G   +    I   + K      D 
Sbjct: 75  GTSGIMLVALNKTVNGLLTKQFQARTVEKRYTALLHGHLTDDSGVINLPIAKDV----DN 130

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             + K        AIS ++V++   + F   +E  P +GRTHQLR+H+  +G  I+G   
Sbjct: 131 FPLQKICHSTGKLAISEYRVLERLPEPFATRVEFTPVSGRTHQLRIHSQQLGHSILGCDL 190

Query: 272 Y---CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y         N  +    +L LHA  +   HP  G R+      P
Sbjct: 191 YAGVGEKITDNDYALHHTRLMLHATRLAFDHPITGERIDWICKCP 235


>gi|253732507|ref|ZP_04866672.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|253723788|gb|EES92517.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
          Length = 273

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 57/264 (21%), Positives = 107/264 (40%), Gaps = 32/264 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  + +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDIFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  + +  KP G+         +  +   +   +DS   +P   HRLDQET G+L+VA
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHVIYTIDSDYVEP--IHRLDQETVGLLIVA 135

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +     + L        I +IY + V  +   K + I   + K       +    ++   
Sbjct: 136 KNPLMKKILDRMLEDNDITRIYKAHVKALLPLKPQTIDMPIGKD-----KFHSNKRRVSP 190

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y  +      
Sbjct: 191 TGQRAITHILTSKMIKEAVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLYGDS------ 244

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL 305
                +L L +  ++  HP    +
Sbjct: 245 --TLRQLELESYKIEFVHPLTKEV 266


>gi|224500659|ref|ZP_03669008.1| hypothetical protein LmonF1_13701 [Listeria monocytogenes Finland
           1988]
          Length = 191

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 47/203 (23%), Positives = 95/203 (46%), Gaps = 15/203 (7%)

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                +A  + G  ++          +  RLD+ETSG++++A+ R A   L+   +   +
Sbjct: 1   HPNGSVANFVKGHYEA--QGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLL 58

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           ++ Y + + G+   +K  I   + +K     +   + +       YA ++++V+  + + 
Sbjct: 59  KRRYQAFISGVLVEQKGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLARY-RA 112

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           F  + +Q  TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L H
Sbjct: 113 FDHVAIQLETGRTHQIRVHFSYIGHPLIGDDMYGGD------TNLLKRQALHSCHLHLVH 166

Query: 300 PEGGR-LQITAPLPAHMVKTWDS 321
           P     +    PLPA M +    
Sbjct: 167 PLTEEYMAFDLPLPADMEEIIQK 189


>gi|326431501|gb|EGD77071.1| hypothetical protein PTSG_07411 [Salpingoeca sp. ATCC 50818]
          Length = 418

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 63/281 (22%), Positives = 106/281 (37%), Gaps = 31/281 (11%)

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIA 126
           P        ++   ++ D+ +  +     +   ++YED  I   NKP G+ VQ  G+   
Sbjct: 131 PAQDGPRAVLVDNSRLQDNVIVTSTDPSSIDLDIIYEDEAIVCVNKPPGLPVQPQGADQL 190

Query: 127 YHIDGFLKSWVDSKGQK----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +++   L              PRL HRLD  TSG+LVVA  R  A  +    + R++ K 
Sbjct: 191 HNVLAALHHRYRQNDGALDVVPRLVHRLDVNTSGVLVVALDRKIAGRMGALLQSRQVIKQ 250

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK-VIDCFAQKFC 241
           Y +LV G  +  +  I   + +                     + + ++ V         
Sbjct: 251 YSALVHGELRG-QGVITAPIARAPKDPEGSRIQKFTVSPHGKPSETEYEGVHASAHWNAS 309

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY----------------------CANFKGN 279
            +  +P TGRTHQ+RVH+ H+G P++ D +Y                      C+     
Sbjct: 310 LVTFRPRTGRTHQIRVHSHHLGHPLLFDDRYHLHDHQQQAQQQQHEQQQQQSACSQLDNE 369

Query: 280 FTSPIQ-NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           F S ++  +  LH   M   HP     + + A  P      
Sbjct: 370 FASHVRMRRCALHCDSMTFTHPATAETVTVRADWPRDFAHA 410


>gi|298695119|gb|ADI98341.1| probable RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus ED133]
          Length = 273

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 59/264 (22%), Positives = 107/264 (40%), Gaps = 32/264 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  N++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMNKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  + +  KP G+         +  +   +   +DS   +P   HRLDQET G+L+VA
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHVIYTIDSDYVEP--IHRLDQETVGLLIVA 135

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +     + L        I +IY + V  +   K + I   + K       +    ++   
Sbjct: 136 KNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTIDMPIGKD-----KFHSNKRRVSP 190

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y  +      
Sbjct: 191 TGQRAITHILTSKMIKETVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLYGDS------ 244

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL 305
                +L L +  ++  HP    +
Sbjct: 245 --TLRQLELESYKIEFVHPLTKEV 266


>gi|123440998|ref|YP_001004987.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|122087959|emb|CAL10747.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. enterocolitica 8081]
          Length = 196

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 61/205 (29%), Positives = 94/205 (45%), Gaps = 15/205 (7%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V NK +G+    G   A      + + + +        HRLD  TSG++VVA T+AA +
Sbjct: 1   MVVNKASGLLSVPGR--APENKDSVMTRIQADFPSAESVHRLDMATSGVIVVALTKAAER 58

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYA 226
            L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ    +    +
Sbjct: 59  ELKRQFREREPKKSYVARVWGHLAQDEGLIDLPLI------CDWPNRPKQKVCYETGKSS 112

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
            + ++V+   A     +++ P TGR+HQLRVH L +G PI+GD  Y         S    
Sbjct: 113 QTQYQVLSRDADGSTRVKLSPITGRSHQLRVHMLAIGHPILGDGFYAHPEAKAMAS---- 168

Query: 287 KLYLHARYMDLPHPEGGR-LQITAP 310
           +L LHA+ + + HPE G  +     
Sbjct: 169 RLQLHAQELCITHPEFGTVMHFKCE 193


>gi|115372594|ref|ZP_01459901.1| pseudouridylate synthase, 23S RNA-specific [Stigmatella aurantiaca
           DW4/3-1]
 gi|115370315|gb|EAU69243.1| pseudouridylate synthase, 23S RNA-specific [Stigmatella aurantiaca
           DW4/3-1]
          Length = 555

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 56/248 (22%), Positives = 95/248 (38%), Gaps = 18/248 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L ++++  ++          S+     L+YED  +   +KP G+    G       
Sbjct: 320 CGGVLPYMLEGLRVDPPLPPGKTPSEGDALRLVYEDPWLLAVDKPCGLLSVPGRHSPQRD 379

Query: 130 DGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               +      +  +P + H L+ +TSG+L+  +       L   F  +   K Y + + 
Sbjct: 380 SVLTRLRRRAPEAPEPLIVHPLESDTSGLLLATKDAETHAALQRQFARKEADKHYIAWLE 439

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        I   L  ++H       +V         A++ ++V+         +   P 
Sbjct: 440 GPVLGDHGVIELPL--RAHPEERPRQIVDPVH--GKRAVTEWRVLRRRG-PQTQVSFLPR 494

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           TG  HQLRVHA H   +G PI GD  Y ++           +L LHA  + + HP  G R
Sbjct: 495 TGHPHQLRVHAAHPLGLGAPIAGDRLYGSS--------GGTRLMLHAESLTVLHPRTGER 546

Query: 305 LQITAPLP 312
           L +  P P
Sbjct: 547 LHLECPAP 554


>gi|302417027|ref|XP_003006345.1| DRAP deaminase [Verticillium albo-atrum VaMs.102]
 gi|261355761|gb|EEY18189.1| DRAP deaminase [Verticillium albo-atrum VaMs.102]
          Length = 549

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 64/297 (21%), Positives = 109/297 (36%), Gaps = 67/297 (22%)

Query: 21  LDRW---FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +D +   F++  P        K +  G++  + K V  +  I++G +V            
Sbjct: 155 IDVFSCEFRDRTPEYYR----KCMDDGKIAANGKVVGADYVIRNGDLVSHTSHR------ 204

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E  +    +            +++ED+   + NKPAG+ V       Y+ +  ++   
Sbjct: 205 -HEPPVTAEPI-----------AVIHEDNDYLIVNKPAGVPVHPAG--RYNFNSVVEILK 250

Query: 138 DSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G    PR  HRLD+ TSGIL   +T  AA  L+   + R ++K Y + V G   + +
Sbjct: 251 SERGAHFMPRPCHRLDRLTSGILCFGKTAQAATDLSRQIQARMVRKEYVARVIGHFPDGE 310

Query: 196 ECIANWLL-KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----------------- 237
                 LL     +G + V           +A + FK +  +                  
Sbjct: 311 VVCDQPLLQISPRLGLNRVRA------NGKFARTVFKRLAYYPPPLSDVDGGPEQRPKTP 364

Query: 238 --------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                         + +  +   P TGRTHQ+RVH   +G PI  D  Y       F
Sbjct: 365 EEAADEEQRPWTAKKGYSIVRCLPLTGRTHQIRVHLQFLGYPIQNDPIYANQRVWGF 421


>gi|70726113|ref|YP_253027.1| hypothetical protein SH1112 [Staphylococcus haemolyticus JCSC1435]
 gi|68446837|dbj|BAE04421.1| unnamed protein product [Staphylococcus haemolyticus JCSC1435]
          Length = 274

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 110/280 (39%), Gaps = 42/280 (15%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +   +L ++  S  + ++    K  +++  G  + IP  +   N++              
Sbjct: 23  LPKKDLHQLNMSKDITINNHPAKLTDKVVIGDDIYIPTPVEKSNYL-------------- 68

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQG-----GSGIAYHIDGFLKSWVDSKGQKPRL 146
               +  + + YED  + +  KP G+          + +  H+   L+S           
Sbjct: 69  --PSYRYAQISYEDDDLAIVMKPKGVKTHPNDLKESNTLMNHVIYTLES------DYVEP 120

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLDQET G+L+VA+     + L        I +IY + V  +   K + I + + K  
Sbjct: 121 IHRLDQETVGLLIVAKNPLMKKILDRMLEENEITRIYKANVKSLLPIKPQTIDSPIGKDK 180

Query: 207 -HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            H     +            AI+H        +  C L+++  TGRTHQ+RVH   +G P
Sbjct: 181 FHPNKRRI------SNTGQRAITHILSSKMIKEGVCQLDIKLDTGRTHQIRVHLAEIGHP 234

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           ++GD  Y  +           +L L++  ++  HP    L
Sbjct: 235 VIGDPLYGDS--------TLRQLELNSHKIEFKHPLTQEL 266


>gi|325104653|ref|YP_004274307.1| tRNA pseudouridine synthase C [Pedobacter saltans DSM 12145]
 gi|324973501|gb|ADY52485.1| tRNA pseudouridine synthase C [Pedobacter saltans DSM 12145]
          Length = 228

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 96/238 (40%), Gaps = 28/238 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y D  I   NKP G+ V          +  L+   D  GQ     HRLD++T G+L+ 
Sbjct: 4   IIYRDEHIVAVNKPHGLLVHQSPIARDAEEFALQILRDQIGQTVWPCHRLDRKTGGLLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +    +L   F+   +QK Y ++V G    ++  I   + K      D         
Sbjct: 64  ALDKETEINLQTQFQNGLVQKKYLAIVRGH-TMERMTIDYPIAKDDGKLQD--------- 113

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A++HF+ +               ++  +E  P TGR HQLR H  H+  PI+GD 
Sbjct: 114 -----AVTHFRTLSLTEIDLPFGKHATSRYALIEAIPETGRMHQLRRHFAHILHPIIGDR 168

Query: 271 KYCANFKGNF--TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
            +  N +          + + LHA  +   HP    ++ + A   +   +T   L F+
Sbjct: 169 PHGCNKQNKLFKEKWQMDTMMLHASELSFEHPFTKKKIHLQAIPQSEFSRTLQLLKFE 226


>gi|269959540|ref|ZP_06173922.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
 gi|269835727|gb|EEZ89804.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
          Length = 559

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 63/245 (25%), Positives = 111/245 (45%), Gaps = 20/245 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  + +     ++  +  +L++D  + + NKP+G+    G  I    
Sbjct: 328 CQPILGHMLQGLDVEPNPLA-ENWAEDKELEILFQDEAMVIVNKPSGLLSVPGKTIKDSA 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++      + P + HRLD  TSGILV A T+ A + L + F  R +QK Y + + G
Sbjct: 387 YTRLQTMF-PDVEGPFVIHRLDMATSGILVFALTKRANKSLQKQFITRGVQKRYMAQLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +    +  I+  + +          V  ++      A +++++I+        + M P T
Sbjct: 446 VLTKPEGEISLPM-RGDPDDRPRQLVCFEH---GKPAETYWQLIE-VKDGRSKVYMYPKT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH+ H   +   +VGD  Y             N+L+LHA  ++L HP    R+
Sbjct: 501 GRTHQLRVHSAHHMGLNMAMVGDGLYGEK---------ANRLHLHAEMLELDHPYSKERM 551

Query: 306 QITAP 310
              A 
Sbjct: 552 CFQAE 556


>gi|304320980|ref|YP_003854623.1| ribosomal large subunit pseudouridine synthase A [Parvularcula
           bermudensis HTCC2503]
 gi|303299882|gb|ADM09481.1| ribosomal large subunit pseudouridine synthase A [Parvularcula
           bermudensis HTCC2503]
          Length = 217

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 69/213 (32%), Positives = 104/213 (48%), Gaps = 14/213 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  + V +KPAG+    G+         L++ V  +     + HRLD  TSG++V 
Sbjct: 17  VLYEDHALIVLDKPAGLLSVPGNISRDS----LETRVVDRFPDAYVAHRLDMATSGVIVF 72

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR + A   L + F  R  +K Y + VWG     +  I   L +          V  +  
Sbjct: 73  ARGKQALADLGQQFEHRLTEKRYIADVWGCVSEDEGTIDLPL-RTDWPNRPLQMVCHER- 130

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A++H++VI    ++    E++P TGR+HQLR+H   +G PI+GD  Y        
Sbjct: 131 --GRPALTHWRVITRSPKQTRL-ELRPVTGRSHQLRIHCRELGHPILGDEWY----AEGE 183

Query: 281 TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
                N+L+LHA ++ L HP   GR+  TAPLP
Sbjct: 184 ARAAANRLHLHALHLSLTHPTNKGRVTYTAPLP 216


>gi|51011075|ref|NP_001003495.1| RNA pseudouridylate synthase domain-containing protein 4 [Danio
           rerio]
 gi|82182079|sp|Q6DBR0|RUSD4_DANRE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 4
 gi|50418114|gb|AAH78405.1| Zgc:92006 [Danio rerio]
          Length = 358

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 72/275 (26%), Positives = 126/275 (45%), Gaps = 40/275 (14%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----SKG 141
           SV+ +  +  L    LYED  I   NKP  + +   +GI   I   L            G
Sbjct: 77  SVHPSVFAKALYRSSLYEDQNIIAINKPYDVPLHNINGIRNSIAECLPLLAKITDNMRPG 136

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +  L H+L++ET+G+L++A+T  AA+H+    +  +++  Y ++  G+P   +  I   
Sbjct: 137 SQLHLCHKLEKETTGVLILAKTEEAAEHVQTLIQSHKVEMKYLAITVGVPVPSEGVIDIP 196

Query: 202 LLKKSHIGGDYVHVV------KQNEKG-----------ANYAISHFKVIDCFAQKFCWLE 244
           +++++ +G      +      K NE G           A+ A++ ++V+D  +     +E
Sbjct: 197 VIERAVVGPQPHFKMALSPLFKVNEDGDGVTRVRAHRQAHAAVTRYQVLDNTS-GCSLVE 255

Query: 245 MQPHTGRTHQLRVHAL-HMGCPIVGDHKYCANFK---GNFTSPIQNK------------L 288
           +QP TG  +QLRVH    + CPI+GDHKY    K            +            L
Sbjct: 256 LQPLTGVKNQLRVHMALALTCPILGDHKYSHWSKLAPQKLPEGTLRRLGLVQSKTRYLPL 315

Query: 289 YLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +LH+R + LP  +G R + ++ PLP + +     L
Sbjct: 316 HLHSRRIVLPGFKGHRDITVSCPLPKYFINALKRL 350


>gi|310823851|ref|YP_003956209.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309396923|gb|ADO74382.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 575

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 56/248 (22%), Positives = 95/248 (38%), Gaps = 18/248 (7%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L ++++  ++          S+     L+YED  +   +KP G+    G       
Sbjct: 340 CGGVLPYMLEGLRVDPPLPPGKTPSEGDALRLVYEDPWLLAVDKPCGLLSVPGRHSPQRD 399

Query: 130 DGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               +      +  +P + H L+ +TSG+L+  +       L   F  +   K Y + + 
Sbjct: 400 SVLTRLRRRAPEAPEPLIVHPLESDTSGLLLATKDAETHAALQRQFARKEADKHYIAWLE 459

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        I   L  ++H       +V         A++ ++V+         +   P 
Sbjct: 460 GPVLGDHGVIELPL--RAHPEERPRQIVDPVH--GKRAVTEWRVLRRRG-PQTQVSFLPR 514

Query: 249 TGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-R 304
           TG  HQLRVHA H   +G PI GD  Y ++           +L LHA  + + HP  G R
Sbjct: 515 TGHPHQLRVHAAHPLGLGAPIAGDRLYGSS--------GGTRLMLHAESLTVLHPRTGER 566

Query: 305 LQITAPLP 312
           L +  P P
Sbjct: 567 LHLECPAP 574


>gi|329113807|ref|ZP_08242578.1| Putative RNA pseudouridine synthase [Acetobacter pomorum DM001]
 gi|326696817|gb|EGE48487.1| Putative RNA pseudouridine synthase [Acetobacter pomorum DM001]
          Length = 206

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 67/220 (30%), Positives = 99/220 (45%), Gaps = 16/220 (7%)

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
            NKPAG+ V  G      ++ +    +  +   P L HRLD +TSG L +A  +     L
Sbjct: 1   MNKPAGLPVHAGPAGGPSVEDWFP-LLSRRKDGPWLAHRLDTDTSGCLAIALRKQPLLAL 59

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            ++F  +  QKIYW++V   P+     I   L K+S   G  +           +A + +
Sbjct: 60  QQAFATKTAQKIYWAVVQTGPQANTGRIDLPLEKQSSKKGWQMVA----SPSGTHAATKW 115

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           KV+   ++  CWLE+   TGRTHQ RVH   MG PI+GD  Y         +P    L+L
Sbjct: 116 KVLGR-SKGVCWLELTLETGRTHQARVHCAAMGWPIIGDPLYG--------TPHSEGLHL 166

Query: 291 HARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
            AR + L  P    +   AP    M     + G+K +   
Sbjct: 167 LARSLTL--PLSPPITAVAPPRPGMAPALQACGWKPNEEA 204


>gi|288929792|ref|ZP_06423635.1| ribosomal large subunit pseudouridine synthase A [Prevotella sp.
           oral taxon 317 str. F0108]
 gi|288328893|gb|EFC67481.1| ribosomal large subunit pseudouridine synthase A [Prevotella sp.
           oral taxon 317 str. F0108]
          Length = 542

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 56/217 (25%), Positives = 101/217 (46%), Gaps = 18/217 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ +    K  D     ++YED  + V +KP G+    G      +   ++         
Sbjct: 319 LEVACVPQKPVDRAALRVVYEDEGLVVVSKPHGMLSVPGKDGGTSVAQMMRQRYPDTD-S 377

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWL 202
           P + HRLDQ+TSG++++A+T+   + L  +F    ++K Y +++ G +P  K+    +  
Sbjct: 378 PLIVHRLDQDTSGLMIIAKTKEMHRTLQLAFENHEVKKRYVAVLDGLLPPEKQRGEISLP 437

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH- 261
           L  +++      V   N      A++ ++VI    +    + + P TGRTHQLRVH  H 
Sbjct: 438 LNSNYLDRPRQMVDWLN---GKSAVTRYEVIG-HEEGRTIVALYPLTGRTHQLRVHCAHP 493

Query: 262 --MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
             +  PI+GD  Y             +++YLHA  ++
Sbjct: 494 DGLNLPILGDPLYGRK---------ADRMYLHAEVIE 521


>gi|42408521|dbj|BAD09700.1| putative ribosomal large subunit pseudouridine synthase C protein
           [Oryza sativa Japonica Group]
 gi|42409169|dbj|BAD10435.1| putative ribosomal large subunit pseudouridine synthase C protein
           [Oryza sativa Japonica Group]
          Length = 340

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 80/333 (24%), Positives = 144/333 (43%), Gaps = 71/333 (21%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGI 117
           ++ G  + +P  +       + + I  ++++  K   ++L+ +++++DS I V NKP  +
Sbjct: 1   MEPGMRIHLPVSVAEGEIKKRYETIPTATLHPNKDEIEYLRRLVIHKDSAILVLNKPPKV 60

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTE---- 172
            ++G   +   +D    + +    ++ P+L HRLD+E+SG+L+  RT+ +   L      
Sbjct: 61  PMKGNLPVHNSMDVLAAAALSYGNEEGPKLVHRLDRESSGLLLFGRTKESFTRLHWLFTS 120

Query: 173 -----------SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE- 220
                      +       + YW+LV G PK ++  I+  L K     G    V+  +  
Sbjct: 121 VNLAKTNSQVWNAACEAYMQRYWALVIGTPKEREGIISAPLSKVLLDDGKAERVILAHPS 180

Query: 221 --KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYC---- 273
              GA  A++ ++V+        W+E++P TGR HQLRVH    +G PIVGD+KY     
Sbjct: 181 GIDGAQEAVTAYRVMGPTIHGCSWIELRPLTGRKHQLRVHCAEALGTPIVGDYKYGWFVH 240

Query: 274 --------ANFKGNFTSPIQNK------------------LYLHARYMDLPH-------- 299
                    +F+     P + +                  L+LH R M +P+        
Sbjct: 241 QRWKQNPQPDFEPFTGEPYKLRRPEGLEIQKGSVLSKVPLLHLHCREMVIPNIAKFLSSN 300

Query: 300 --------PEGGR----LQITAPLPAHMVKTWD 320
                   P        L+  AP+PAHM  +W+
Sbjct: 301 GEWHENGAPWSKEKPNLLRFIAPMPAHMKISWN 333


>gi|258545740|ref|ZP_05705974.1| pseudouridine synthase A [Cardiobacterium hominis ATCC 15826]
 gi|258518985|gb|EEV87844.1| pseudouridine synthase A [Cardiobacterium hominis ATCC 15826]
          Length = 205

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 61/206 (29%), Positives = 97/206 (47%), Gaps = 12/206 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   + YED  IYV NKPAG+    G G   +    ++S            HRLD  TSG
Sbjct: 1   MNLDIHYEDPDIYVINKPAGLLSVPGRGDDKYDS--VQSRCQISAPAAMAAHRLDMATSG 58

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A+ +AA +H  + F  RR++K Y ++V G   + +  I   L+       +     
Sbjct: 59  LLLIAKHKAAERHYKQEFAARRVEKRYIAVVHGSLADDRGDIEYPLI----TDWERRPRQ 114

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K   +    A + ++V+         + + PHTGR+HQLRVH   +G PI+GD  Y    
Sbjct: 115 KICYEHGKTAHTSYEVLARDG-ATTRVALTPHTGRSHQLRVHLAAIGHPILGDEFY---- 169

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEG 302
             +   P   +L LHA  + + +  G
Sbjct: 170 -ADENPPAAPRLLLHAETLAVTNLHG 194


>gi|160892611|ref|ZP_02073401.1| hypothetical protein CLOL250_00141 [Clostridium sp. L2-50]
 gi|156865652|gb|EDO59083.1| hypothetical protein CLOL250_00141 [Clostridium sp. L2-50]
          Length = 328

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 65/326 (19%), Positives = 135/326 (41%), Gaps = 22/326 (6%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++ +++  +E   R++++   +        + K++R   ++++ K+++ N  I  G  ++
Sbjct: 1   MKEIIISQNEAGQRVNKFLLKYLNKAPSSFVYKMMRKKNIKLNNKKIEGNEYIYIGDTIQ 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I       +  I   +   S  + T     +   ++Y D  I + +KPAG+  Q  S   
Sbjct: 61  IYM----SDETIANFREDVSGTDCTSSKKKIPVEIIYSDENILIADKPAGVLSQKASKDD 116

Query: 127 YHIDGFLKSWVDSKG---------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           Y  +  L  ++   G          +P + +RLD+ TSG+++   +   +Q L+   R  
Sbjct: 117 YSFNEALIDYLLDSGHITTEELRTYRPSVCNRLDRNTSGLILCGVSLTGSQELSRIIREH 176

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y++LV G    K +    +L K +      +      +  +    S F  +    
Sbjct: 177 LLHKYYYTLVRGRLTQKLDSTC-YLQKDNAKNKVRISDRPWEQGKSEEIHSIFYPVK-KN 234

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--NKLYLHARYM 295
             +  ++++  TG++HQ+R    H+G P+VGD KY       + S         LH   +
Sbjct: 235 DDYTLVKVELITGKSHQIRAQLKHLGYPVVGDTKYGIPEVNRYFSDSYHVKHQLLHCGNI 294

Query: 296 DLPHPEG-----GRLQITAPLPAHMV 316
                +G     G  + +A LP    
Sbjct: 295 IFKETDGPLSYLGGKEYSAFLPEPFR 320


>gi|332297218|ref|YP_004439140.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332180321|gb|AEE16009.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 244

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 62/244 (25%), Positives = 99/244 (40%), Gaps = 18/244 (7%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQ- 142
            S+       DF +  +LYED+ + V  KPAG+      G  A      L   +  +G+ 
Sbjct: 5   PSAPAEPSVPDFRRLSILYEDASVAVVYKPAGLLSVSYPGSTAKTALDVLCDLMRKRGRV 64

Query: 143 ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW----GIPKNK 194
               +P + HRLD++TSG++V A T  A   L + +     ++ Y +L       I    
Sbjct: 65  SARVRPAVVHRLDRDTSGVMVFALTAQAKALLMDDWNRLVTERRYRALAENPSGKIALGD 124

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I + L   +           + E  A  A++ + V+     ++   E++  TGR +Q
Sbjct: 125 RGVIDSPLSYNAQHRAYVAKGAGRRENEAVSAVTRYSVV-RRGSRYTLFELELETGRKNQ 183

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           +R H    G  I GD  Y         S    +L LHAR +    P  G  L+   P P 
Sbjct: 184 IRAHLASEGFVIAGDGSY------RAKSDPFGRLCLHARTLAFTQPLTGESLRFEIPEPP 237

Query: 314 HMVK 317
              K
Sbjct: 238 EWEK 241


>gi|116073981|ref|ZP_01471243.1| probable pseudouridine synthase [Synechococcus sp. RS9916]
 gi|116069286|gb|EAU75038.1| probable pseudouridine synthase [Synechococcus sp. RS9916]
          Length = 333

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 127/323 (39%), Gaps = 37/323 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +   E    L       Y H +    ++ L SG++R D   ++ +  ++ G+ +      
Sbjct: 27  ITASEAGQWLTAVMAARYNHSSAEQWKQRLESGELRRDGHLLQVDVMVERGERISW---- 82

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                       L+++V     +       +++D  + V NKP+G+ V  G G   H   
Sbjct: 83  -------HRPPWLEAAVPDQWQT-------IHDDGDLLVINKPSGLPVMPGGGFLLHTLT 128

Query: 132 FL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKIYW 184
            L   +S    +   P+  HRL + TSG+ V AR       L+  FR     R++ + + 
Sbjct: 129 ALLEQRSRERGESLAPKPVHRLGRFTSGLQVCARRPETRAALSAHFRPQGGCRKLYQAWS 188

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE---------KGANYAISHFKVIDC 235
             V G+       +   ++++ H    +V   +  +         +    A S   ++  
Sbjct: 189 QRVEGLDLEASVEVCTDVVERPHPLLGWVWGPEPPDDARGDATPVRRRRNAHSELTLLQR 248

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARY 294
             Q     ++   TGR HQ+R+H   +G P++GD  Y          +P     +LHA  
Sbjct: 249 GEQGDRL-QVAITTGRPHQIRIHLAQLGSPLLGDPLYLRGRRLAPSATPGDGGYWLHAWR 307

Query: 295 MD-LPHPEGGRLQITAPLPAHMV 316
           ++ LP      L + APLPA  +
Sbjct: 308 LEKLPSRGSDGLALEAPLPAAFL 330


>gi|163801533|ref|ZP_02195432.1| putative ribosomal large chain pseudouridine synthase A [Vibrio sp.
           AND4]
 gi|159175022|gb|EDP59822.1| putative ribosomal large chain pseudouridine synthase A [Vibrio sp.
           AND4]
          Length = 559

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 66/244 (27%), Positives = 111/244 (45%), Gaps = 20/244 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   +  + +     ++  +  +L++D  + V NKP+G+    G  I    
Sbjct: 328 CQPILGHMLQGLDVEPNPLA-ENWAEDKELEVLFQDEAMVVVNKPSGLLSVPGKTIKDSA 386

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++      + P + HRLD  TSGILV A T+ A + L + F  R +QK Y +L+ G
Sbjct: 387 YSRLQAMF-PNVEGPFVIHRLDMATSGILVFALTKRANKSLQKQFITRGVQKRYMALLEG 445

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I+  + +          V  ++      A + +++ID        + M P T
Sbjct: 446 TLSEPEGEISLPM-RGDPEDRPRQLVCFEH---GKPADTFWQLID-VKDGRSRVYMYPKT 500

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLRVH+ H   +   +VGD  Y             N+L+LHA  ++L HP    R+
Sbjct: 501 GRTHQLRVHSAHHMGLNMAMVGDGLYGEK---------ANRLHLHAEMLELDHPYSKERM 551

Query: 306 QITA 309
           +  A
Sbjct: 552 RFQA 555


>gi|149280788|ref|ZP_01886893.1| tRNA pseudouridine synthase C [Pedobacter sp. BAL39]
 gi|149228467|gb|EDM33881.1| tRNA pseudouridine synthase C [Pedobacter sp. BAL39]
          Length = 235

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 96/228 (42%), Gaps = 8/228 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  +   NKP G+ V   S      +  L+   D   +     HRLD++T GIL+ 
Sbjct: 4   ILYEDEHLIAINKPHGLLVHRSSIANDAKEFALQLLRDQVNKHVSPVHRLDRKTGGILLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + A   + + F+   + K Y +++ G   ++ +       +   I   +   V  + 
Sbjct: 64  AFDKEAEIAMHQQFQNGEVTKKYMAILRGHAPDQMDINYPLAKENGTIQEAFTSFVTLD- 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A            ++  +E  P TGR HQLR H  H+  PI+GD K+  N +  F
Sbjct: 123 ----RAELAVPFGKHETSRYSLVEASPTTGRMHQLRRHFAHIFYPIIGDRKHGCNKQNRF 178

Query: 281 --TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
                    + LHA  ++  HP   R + I+APL     +    + ++
Sbjct: 179 FKEQWGMTTMLLHASALEFTHPVTKRKIFISAPLNDEFERMMTLMNWE 226


>gi|160874211|ref|YP_001553527.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160859733|gb|ABX48267.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315266445|gb|ADT93298.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 574

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 107/239 (44%), Gaps = 26/239 (10%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E  ++D +  LT  ++     +LY+D  + + NKPA      G  I   +   ++     
Sbjct: 345 EGLVVDENPLLTNPAEGKTLAILYQDDAMAIVNKPAEFLSVPGKEIEDSVYSRMRQTFPH 404

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-----KNK 194
               P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ G+P     K  
Sbjct: 405 TT-GPLIVHRLDMSTSGLMVIALTKEAHKQLQKQFIQRTVTKRYVALLAGMPAVMANKQA 463

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--IDCFAQKFCWLEMQPHTGRT 252
              I+  L +          V     +    A +H+++  +D  A+      + P TGRT
Sbjct: 464 TGHISLPL-RGDLDDRPRQLVC---HEFGKAAETHWELSQLDEMARTARVY-LYPKTGRT 518

Query: 253 HQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           HQLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP    R++ 
Sbjct: 519 HQLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHPVTRERMRF 568


>gi|326796257|ref|YP_004314077.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326547021|gb|ADZ92241.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
          Length = 211

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 59/213 (27%), Positives = 93/213 (43%), Gaps = 13/213 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LYED  + V NKP       G G     D  L       G+     HRLD  TSG++
Sbjct: 7   LDILYEDEWLLVLNKPENCLSVPGRGPEKL-DSILHRAEQYCGE-AYAVHRLDHATSGLI 64

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VA++    + + ++FR + + K Y ++V G P  +   +   L +          +  +
Sbjct: 65  LVAKSLECQKRMYKAFREKEVDKEYLAIVRGTPIGQCGSVRKPL-RCDWPNRPRQMICTE 123

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K    AI+ +K I         + + P TGR+HQLRVH   +G  IVGD  Y      
Sbjct: 124 WGKD---AITQWKPIKQVGNN-TLVSLSPITGRSHQLRVHMQSLGHSIVGDEFY-----D 174

Query: 279 NFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           +  +    +L LHA  ++  HP     ++  AP
Sbjct: 175 DLYTNQDERLLLHAYRIEFAHPFTSAWVKFIAP 207


>gi|195051252|ref|XP_001993060.1| GH13297 [Drosophila grimshawi]
 gi|193900119|gb|EDV98985.1| GH13297 [Drosophila grimshawi]
          Length = 562

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 59/269 (21%), Positives = 104/269 (38%), Gaps = 33/269 (12%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +   F   +        ++ + +G + V+ ++V  + R++   ++      + +      
Sbjct: 173 ILNVFSREFRAHPAEEYKRSIEAGSLTVNHEKVPIDYRLKHNDLLANTVHRHEVPVTAH- 231

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +++ D  I V NKPA I V       Y  +  +       
Sbjct: 232 -----------------PITIVHMDDDILVVNKPASIPVHPCG--RYRHNTMIFILAKEF 272

Query: 141 GQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECI 198
             +  R  HRLD+ TSG+L+  RT   A+ + +  R R++QK Y   V G  P    EC 
Sbjct: 273 NMRNLRTIHRLDRLTSGLLLFGRTAEKAREMEQQIRNRQVQKEYVCCVEGCFPDGNIECN 332

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +    IG      V +         + FK +      +  ++ +P TGR HQ+RVH
Sbjct: 333 EPIEVVSYKIG------VCKVSPKGKDCKTTFKRLGQVGD-YSIVQCKPLTGRMHQIRVH 385

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
             ++G PIV D  Y     G    P++ +
Sbjct: 386 LQYLGYPIVNDPLYNHEVFG----PLKGR 410


>gi|242374099|ref|ZP_04819673.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
 gi|242348224|gb|EES39826.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
          Length = 275

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 56/285 (19%), Positives = 115/285 (40%), Gaps = 36/285 (12%)

Query: 25  FKNHYPHI--NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
            +  +  +     +L ++  S ++++++++ K  +++ +G  V +P      N++     
Sbjct: 14  LREIFQQLKLPKKDLHQLNMSKEIKINEQQAKLTDKVVTGDEVIVPTPKEKSNYL----- 68

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KG 141
                        +  + + YED+ + +  KP G+            +  +   + +   
Sbjct: 69  -----------PSYRYAQIYYEDNDLAIVMKPKGVKTHP--NDLKESNTLMNHIIYTIDS 115

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLDQET G+L+VA+     + L       +I ++Y + V  +   K + I   
Sbjct: 116 DYVEPIHRLDQETVGLLIVAKNPIMKKILDRMLEDNQITRVYKANVKALLPIKPQTIDMP 175

Query: 202 LLKKS-HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           + K   H     +            AI+H        +  C L+++  TGRTHQ+RVH  
Sbjct: 176 IGKDKFHPNKRRI------SNTGQRAITHILSSQMIKEGVCQLDIKLDTGRTHQIRVHLA 229

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            +G P++GD  Y  +           +L L++  ++  HP    L
Sbjct: 230 EIGHPVIGDPLYGDS--------TLRQLELNSHQIEFIHPLTHEL 266


>gi|213155501|ref|YP_002317546.1| dual specificity pseudouridine synthase [Acinetobacter baumannii
           AB0057]
 gi|213054661|gb|ACJ39563.1| dual specificity pseudouridine synthase [Acinetobacter baumannii
           AB0057]
          Length = 229

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 64/211 (30%), Positives = 103/211 (48%), Gaps = 13/211 (6%)

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           ED  + V +KPAG+    G    +H   +L+  V  K    ++THRLD  TSG+L+ A+ 
Sbjct: 29  EDDDLIVVDKPAGLLSVMGRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMFAKH 86

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
           R A   +++ F+ R ++K Y +LV G  K +       +    +     VH      +  
Sbjct: 87  RDAEVAVSKMFQARTVKKHYIALVQGQVKQEGRVEVPLITDWENRPRQIVHF-----ELG 141

Query: 224 NYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
            +A + F+ +          + ++P TGR+HQLRVH +H+G PI+GD  Y    K     
Sbjct: 142 KHAKTLFQPLVYDETTDQSRVLLEPVTGRSHQLRVHMMHIGHPIMGDKLYHPEPK----R 197

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              N++ LHA Y+   HP  G  + I + +P
Sbjct: 198 FHLNRMALHAAYLAFQHPLKGTDVVIESQVP 228


>gi|86135056|ref|ZP_01053638.1| ribosomal large subunit pseudouridine synthase A [Polaribacter sp.
           MED152]
 gi|85821919|gb|EAQ43066.1| ribosomal large subunit pseudouridine synthase A [Polaribacter sp.
           MED152]
          Length = 558

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 64/236 (27%), Positives = 98/236 (41%), Gaps = 21/236 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +DS+  LT  S      +++ED  + V NKPA      G  I   +   +K+        
Sbjct: 340 MDSNSLLTNLSSEKNLEIIFEDDDLIVVNKPAEFLSVPGKTIKDSMYTRIKNQY-PNATG 398

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSGILV+ +T+ A + +   F  R ++K Y +L+ G+   +   I   L 
Sbjct: 399 PLIVHRLDMSTSGILVLTKTKEANKIVQSQFINRTVKKRYVALLDGMLTKESGKIKLPL- 457

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V   + K A    +              +   P TGRTHQLRVH+ H  
Sbjct: 458 RVDLDDRPKQLVDFIHGKNAETKWTKI----SIENGKTRVYFYPITGRTHQLRVHSAHKN 513

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
            +  PI+GD  Y             N+L+LHA  +   HP    ++     + A  
Sbjct: 514 GLDTPIIGDDLYGNK---------SNRLHLHAEQISFIHPTTKEKMTFK--VDADF 558


>gi|77360149|ref|YP_339724.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875060|emb|CAI86281.1| putative 23S rRNA pseudouridylate 746 synthase [Pseudoalteromonas
           haloplanktis TAC125]
          Length = 237

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 62/223 (27%), Positives = 99/223 (44%), Gaps = 16/223 (7%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK------GQ 142
           N           ++Y D  I + NKP+G+    G       D      V+ +        
Sbjct: 14  NFVAPQCDQSVQIVYHDEDILLINKPSGLLSLSGKNPLN-WDSVHYRLVNGQTGITAAYP 72

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           + +L HRLD  TSGI++V    AA++HL + F+ R I+K Y +++ G   + +  I+  +
Sbjct: 73  EAKLPHRLDLGTSGIMIVGLNAAASKHLNKQFQARTIKKRYVAMLHGWLIDDEGQISASI 132

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALH 261
            K   +       VK  E     A+S +KV+    Q     ++  P TGRTHQLR+H+  
Sbjct: 133 AKDKLL----FPRVKICETTGKTAVSEYKVLQRLTQPQRTLVQFTPITGRTHQLRIHSQF 188

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +G PI+G   Y        +  +  +L LHA  +   HP    
Sbjct: 189 IGHPILGCDLY----NNAQSEHMAARLQLHASDLYFQHPVSNE 227


>gi|329894521|ref|ZP_08270335.1| Ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium IMCC3088]
 gi|328923046|gb|EGG30371.1| Ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium IMCC3088]
          Length = 217

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 60/214 (28%), Positives = 92/214 (42%), Gaps = 12/214 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +LY+D  +    KP  +    G          L S +       R+ HRLD +TSG 
Sbjct: 12  PIGILYQDEHLLFVAKPHFLLSVPGKHPLN--KDCLISRLQQTYPDARIVHRLDLDTSGT 69

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+A  +     L+  FR+R++ K Y ++V G  K     I   +        +     K
Sbjct: 70  MVIALGKERHAELSRQFRLRQVAKSYIAVVAGEIKENAGTIDLPI----RADWENRPRQK 125

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              +    +I+HF VI         L + P TGR+HQLR+H L +G PI+G   Y     
Sbjct: 126 VCFERGKPSITHFTVIAR-GNNSTRLRLHPVTGRSHQLRLHLLSIGHPILGCDLY----A 180

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
              +    ++L LHA  + L HP  G+ L I + 
Sbjct: 181 DPESLSRSDRLLLHAERLALKHPVTGQWLSIESE 214


>gi|221316667|ref|NP_001138299.1| RNA pseudouridylate synthase domain-containing protein 4 isoform b
           [Homo sapiens]
          Length = 346

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 74/260 (28%), Positives = 114/260 (43%), Gaps = 39/260 (15%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   +L++D  + V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKALTRGILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P      +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWDKDMAHQVQELFRTRQVVKKYWAITVHVPMPSAGVVDIPIV 205

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-M 262
                           EK A  A++ ++V+         +E+QP TG  HQLRVH    +
Sbjct: 206 ----------------EKEAQVAVTQYQVLSS-TLSSALVELQPITGIKHQLRVHLSFGL 248

Query: 263 GCPIVGDHKYC------------ANFKGNFTSPIQNK---LYLHARYMDLPHPEGG--RL 305
            CPI+GDHKY                K       + +   L+LHAR + LP    G   L
Sbjct: 249 DCPILGDHKYSDWNRLAPQKLSVGTLKKLGLEQSKARYIPLHLHARQLILPALGSGKEEL 308

Query: 306 QITAPLPAHMVKTWDSLGFK 325
            +   LP   V +   L  +
Sbjct: 309 NLVCKLPRFFVHSLHRLRLE 328


>gi|166033157|ref|ZP_02235986.1| hypothetical protein DORFOR_02879 [Dorea formicigenerans ATCC
           27755]
 gi|166027514|gb|EDR46271.1| hypothetical protein DORFOR_02879 [Dorea formicigenerans ATCC
           27755]
          Length = 249

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 110/236 (46%), Gaps = 20/236 (8%)

Query: 89  NLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKGQ 142
            +TK  D + +I +LYED++I V  KPAG++ Q     +  +   LK+ +      S   
Sbjct: 13  EITKEYDMINNINILYEDTQILVCVKPAGVATQSKRIGSPDMVSLLKNHISMTSGKSGEP 72

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              + HRLDQ  SGILV A+T AAA+ L          K Y++LV G P+     + N+L
Sbjct: 73  YLAVIHRLDQPVSGILVFAKTPAAAKDLNRQLTTSGFGKHYYALVAGTPEPTSADLENFL 132

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---------FAQKFCWLEMQPHTGRTH 253
           +K +        + ++    A  A  H+ ++D                 L+++  TGR H
Sbjct: 133 VKDARTNTSR--ICQKGTADAKLAKLHYDLVDTTFFADIASSIPVATSQLKIKLDTGRHH 190

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           Q+RV    MGCPI+GD KY  +      +  +  L L A  ++  HP   + +  +
Sbjct: 191 QIRVQLSGMGCPIIGDTKYNPDSPK--LTARRTPLCLCAYQLEFRHPVTKKAMTFS 244


>gi|78213448|ref|YP_382227.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           CC9605]
 gi|78197907|gb|ABB35672.1| putative pseudouridylate synthase [Synechococcus sp. CC9605]
          Length = 195

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 62/202 (30%), Positives = 100/202 (49%), Gaps = 17/202 (8%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
              +KPAG+  Q   G+       + + +  + Q+ RL HRLD++TSG+L++AR+  A +
Sbjct: 1   MAVDKPAGLLSQP--GLGPEQSDSVITRLQQQDQRLRLVHRLDRDTSGVLLLARSADALR 58

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            L+  F  RRI K+Y ++V G       CIA+ L + S     Y      +      A +
Sbjct: 59  RLSALFAERRINKLYQAVVEGELHG-CGCIASPLARLSRQPPRY-----GSHPKGRLAQT 112

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
            ++V    A+      ++P TGR+HQLR H   +G PIVGD  Y    +         +L
Sbjct: 113 IWRVRTVGARSTRLW-LRPLTGRSHQLRAHLAELGHPIVGDPIYGDAGR-------SCRL 164

Query: 289 YLHARYMDLPHPEG-GRLQITA 309
           +LHA+ +   HP    R+++ A
Sbjct: 165 HLHAQSLSFCHPFTQQRVRLIA 186


>gi|160899764|ref|YP_001565346.1| pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160365348|gb|ABX36961.1| pseudouridine synthase [Delftia acidovorans SPH-1]
          Length = 245

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 63/218 (28%), Positives = 107/218 (49%), Gaps = 15/218 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED+++ V +KP+G+    G G        L      +     + HRLDQ TSG++V+A
Sbjct: 35  LYEDAELLVLDKPSGLLCVPGRGPD--KQDCLSGRALQRWPDALVVHRLDQATSGLVVMA 92

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ--N 219
           R+ A+ + L+E+F  RR+ K+Y ++V G P  ++     W      I  D+     +  +
Sbjct: 93  RSLASQRLLSEAFAQRRVHKLYVAVVAGRPAAQQA--DAWQSIDLPIAADWERRPLRIID 150

Query: 220 EKGANYAISHFKVI----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                 + + ++ +    +        +++QP TGRTHQLRVH   +G  I+GD  Y   
Sbjct: 151 ALQGKPSQTLWRAMPAATEGHDTPTTRVQLQPVTGRTHQLRVHMAALGHAILGDALY--- 207

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                   +  +L LHA  ++L HP  G+ L+  + +P
Sbjct: 208 -ADAAVQALSPRLLLHAHQLELAHPLSGQTLRFESAVP 244


>gi|330846924|ref|XP_003295235.1| hypothetical protein DICPUDRAFT_160487 [Dictyostelium purpureum]
 gi|325074072|gb|EGC28238.1| hypothetical protein DICPUDRAFT_160487 [Dictyostelium purpureum]
          Length = 533

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 59/269 (21%), Positives = 113/269 (42%), Gaps = 24/269 (8%)

Query: 21  LDRWFKNHYPHINF-VNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           LD +    +   +  V L+K ++ G ++V+ K V  + +I+   ++              
Sbjct: 194 LDMF-TTEFSTNSRDVYLRK-IKRGLIKVNDKMVSPDFKIKLNDII-------------- 237

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
               L S           K  ++  D ++ V +KP+ I V       ++   F+ +    
Sbjct: 238 ----LHSVHRHEPPVTGDKIKIVAMDDQVVVIDKPSSIPVHPCGRFRHNCVLFILAAEHG 293

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             +     HRLD+ TSG+L++ART  AA+      +   + K Y++ V G      +   
Sbjct: 294 INE-LYGVHRLDRLTSGLLMLARTPDAAKKRASQIQSGDVSKQYFAKVVGKFPIGTDLPD 352

Query: 200 NWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRV 257
             ++    I    + + +    +G   +++HFK+     +     +   P TGRTHQ+RV
Sbjct: 353 GTVIVNQPIVIQNMRLGINHVGEGGKPSVTHFKLYSYDEKSNQSIVLCSPKTGRTHQIRV 412

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           H   +G PI  D  Y  +F+ +F +   +
Sbjct: 413 HLKWLGYPITNDPLYNNDFRDSFKALTSD 441


>gi|226941069|ref|YP_002796143.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
 gi|226715996|gb|ACO75134.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 222

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 62/214 (28%), Positives = 102/214 (47%), Gaps = 13/214 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L++D+ + V +KPAG+    G G        L + V +      + HRLD  TSG++V A
Sbjct: 18  LHQDAALLVVDKPAGLLTVPGRGPD--KQDCLLTRVRADFPDAEIVHRLDMATSGLVVFA 75

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R     + L  +F  R++ K Y ++V G P + +  I   L+             K + +
Sbjct: 76  RGLLHQKCLMRAFAERKVDKRYVAVVAGRPPSNRGDINLPLI----TDWPNRPRQKIDAE 131

Query: 222 GANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               +++ + V+           L+++P TGRTHQLRVH   +G PI+GD  Y      +
Sbjct: 132 AGKPSLTRYLVLASLTDPLPCSRLQLEPVTGRTHQLRVHLDAIGHPILGDPLYGTPSSQS 191

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                  +L LHA ++ LPHP+ G+  + + P P
Sbjct: 192 AA----PRLLLHAEHLALPHPDNGKPCRWSCPAP 221


>gi|126173232|ref|YP_001049381.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125996437|gb|ABN60512.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 574

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 106/238 (44%), Gaps = 24/238 (10%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E  ++D +  LT  ++     +LY+D  + + NKPA      G  I   +   ++     
Sbjct: 345 EGLVVDDNPLLTNPAEGKTLSILYQDDAMAIVNKPAEFLSVPGKEIEDSVYSRMRQTF-P 403

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK----NKK 195
               P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ G+P      + 
Sbjct: 404 HATGPLIVHRLDMSTSGLMVIALTKDAHKQLQKQFIQRTVTKRYVALLAGMPAVMANTQA 463

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--IDCFAQKFCWLEMQPHTGRTH 253
               +  L+          V     +    A +H+++  +D  A+      + P TGRTH
Sbjct: 464 TGNISLPLRGDLDDRPRQLVC---HEFGKTAETHWELSQLDEMARTARVY-LYPKTGRTH 519

Query: 254 QLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           QLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP    R++ 
Sbjct: 520 QLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHPVTRERMRF 568


>gi|256820360|ref|YP_003141639.1| pseudouridine synthase [Capnocytophaga ochracea DSM 7271]
 gi|256581943|gb|ACU93078.1| pseudouridine synthase [Capnocytophaga ochracea DSM 7271]
          Length = 215

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 59/218 (27%), Positives = 101/218 (46%), Gaps = 17/218 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSG 156
           LYED+ +   NK  G  VQG       +   +K ++  K  KP      + HRLD+ T+G
Sbjct: 2   LYEDNHVIAVNKRVGDIVQGDKTGDTPLSDIVKQYLKQKYNKPGEVFLGVVHRLDRPTTG 61

Query: 157 ILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           +++ A+T  A   L   F  ++ +QK YW+LV   P  +++ + +WL++         + 
Sbjct: 62  VVLFAKTSKALARLNTMFANKQEVQKTYWALVDAKPPVEEDTLTHWLVRNEKQNKSVAYN 121

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +   + +  A+ H+K++  + +++  LE+   TGR HQ+R     +   I GD KY A 
Sbjct: 122 KEM--QHSKKAVLHYKLLKSY-ERYYLLEIDLITGRHHQIRAQLAAIELHIKGDLKYGAK 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
                 S     + LHA  +   HP       +   AP
Sbjct: 179 -----RSNPDGGICLHAYSLSFVHPVKKEPTKIIAEAP 211


>gi|159108280|ref|XP_001704412.1| Ribosomal large subunit pseudouridine synthase D [Giardia lamblia
           ATCC 50803]
 gi|157432474|gb|EDO76738.1| Ribosomal large subunit pseudouridine synthase D [Giardia lamblia
           ATCC 50803]
          Length = 250

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 103/231 (44%), Gaps = 25/231 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E+    V NKP  + + G      +       ++ ++G+ PR  ++LD  TSG++V+
Sbjct: 4   VVFENDDYTVINKPPNLHIDGD-----YPQTVRSWYLATRGRAPRFVNQLDYPTSGLMVI 58

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +R AA      F+ R + K Y +LV G      + I+  +        D         
Sbjct: 59  ASSRKAAGFAGREFQARAVAKTYVALVVGDVA--SQTISAPIADD---AADPRQFCMCIS 113

Query: 221 KGANYAISHFKVIDCFAQK------------FCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           +   ++ +H + I    +             +  + ++P TGR HQLR+H  H+G PIVG
Sbjct: 114 ETGKHSETHVERIAAIPEDLRELSPSLPQGLYTLVVLRPVTGRRHQLRLHLAHIGHPIVG 173

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL--PAHMVK 317
           D  Y            + +L LHA  + +P+  G  L + APL  P+ ++ 
Sbjct: 174 DQLYGGGLTDTNQCGEEERLCLHALMLSIPNLSGLPL-LEAPLEFPSDLLA 223


>gi|261251066|ref|ZP_05943640.1| ribosomal large subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
 gi|260937939|gb|EEX93927.1| ribosomal large subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
          Length = 248

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 97/230 (42%), Gaps = 19/230 (8%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK----- 143
           +           +LY+D  I + NKP+G+    G     + D      V+ +        
Sbjct: 14  HFVAPECHASVEILYQDDDILLINKPSGLLSLSGKN-QLNWDSVHYRLVNGQDANQSAKA 72

Query: 144 ------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                  +L HRLD  TSG++VV    AA++ L + F+ R +QK Y +++ G        
Sbjct: 73  TPAFVDAKLPHRLDLGTSGVMVVGLNSAASKSLNQQFQARTVQKRYLAMLAGWVDGDHGQ 132

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLR 256
           I+  + K           VK        AIS ++VI      +   ++  P TGRTHQLR
Sbjct: 133 ISAPIAKD----KTLFPRVKICHDTGKSAISDYQVISRLDNPRRTLVQYTPITGRTHQLR 188

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGR 304
           +H+L  G PI+G   Y     G+    I    +L LHA  +   HP  G 
Sbjct: 189 IHSLEFGHPILGCDLYNDPQLGSHHETIDIPQRLMLHASDIYFTHPTTGE 238


>gi|254445479|ref|ZP_05058955.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198259787|gb|EDY84095.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 262

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 115/250 (46%), Gaps = 22/250 (8%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
            + L++ +L  D  + + NKPA +      +G    + G  + ++ S  ++  L  RLD+
Sbjct: 12  PEELETWILQNDDHVLLINKPALLVCHPSKNGPWSSLAGACREYLQS--ERSHLVSRLDR 69

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           ETSGI++ A+ R  ++HL  +   R++ K Y +++ G  K ++  +   L   +      
Sbjct: 70  ETSGIVLFAKHRLKSRHLQMALEQRKVSKTYLAILEGELK-EETLVDAPLGPDTQSIVHS 128

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            + V+++ +    A + +  +    + +   ++ P TGR HQ+R HALH+G  IVGD  Y
Sbjct: 129 KNTVRRDGR-KQEAQTKYTPLHSNGR-YTLAKVDPITGRKHQIRAHALHIGHHIVGDKLY 186

Query: 273 CANFKGNFTSPIQ-------------NKLYLHARYMDLPHPEGGRLQITAPLPAHMVK-T 318
             + +G F   I+             N+  LHA  M     E G     APL   +V   
Sbjct: 187 GPD-EGLFLDFIEDGWTEQMAKILPINRHALHAYRMVF-DLETGPETYIAPLTPDLVDFC 244

Query: 319 WDSLGFKYDR 328
             +L    DR
Sbjct: 245 LKNLDLDEDR 254


>gi|288934799|ref|YP_003438858.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|288889508|gb|ADC57826.1| pseudouridine synthase [Klebsiella variicola At-22]
          Length = 232

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 56/223 (25%), Positives = 88/223 (39%), Gaps = 16/223 (7%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   +  LLY+D  + + NKPAG+    G          +   +  +     L HR
Sbjct: 8   FVAPPCREQITLLYQDEHLLLINKPAGLLSLSGK--DPRNLDSVHHRLVQRFPGCTLVHR 65

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG++V+AR +     L + F  R + K+Y +L+ G     +  +   + K     
Sbjct: 66  LDFGTSGLMVIARNKGINALLCQQFSQRTVAKVYTALLCGHLAEDEGIVEAAIAKVPA-- 123

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALH 261
                 +    +    A S ++VID   Q            + + P TGRTHQLR+H   
Sbjct: 124 --RFPRMSLCARHGKPARSRYRVIDRLYQSRDGERALALTRVALTPETGRTHQLRIHCQL 181

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +G PI+G   Y         +    +L LHA  +   HP    
Sbjct: 182 LGYPILGCDLYGGRELPG--TEQAPRLMLHASELRFVHPVSHE 222


>gi|222151816|ref|YP_002560976.1| ribosomal large subunit pseudouridine synthase homolog [Macrococcus
           caseolyticus JCSC5402]
 gi|222120945|dbj|BAH18280.1| ribosomal large subunit pseudouridine synthase homolog [Macrococcus
           caseolyticus JCSC5402]
          Length = 273

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 59/270 (21%), Positives = 103/270 (38%), Gaps = 33/270 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++     F + + +G  + +P      N+                 S +    + 
Sbjct: 34  SKAITINDAAATFRDTLSTGDELYLPVAQEKSNY----------------KSSYRMCEVK 77

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + +  KP G+     + ++        +      +     HRLDQET G+L+VA+
Sbjct: 78  YEDEYLAILVKPKGVKTHP-NDMSESNTLLNHAIYTLDSEYVEPIHRLDQETVGLLLVAK 136

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS-HIGGDYVHVVKQNEK 221
                + L      R I++ Y + V      K + I   + K   H     V       +
Sbjct: 137 NPFIKKILDRMLEERLIKRTYRAKVKSHLPLKHQTIDMPIGKDKFHPNKRRV------SQ 190

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
             + A++H             +E+Q  TGRTHQ+RVH   +G P++GD  Y  +      
Sbjct: 191 TGDRAVTHIVSSKANRDGTADVELQLETGRTHQIRVHLAEIGHPVIGDPLYSDSH----- 245

Query: 282 SPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                +L L +  ++  HP  G   +TA L
Sbjct: 246 ---LRQLALESYKLEFIHPFTGE-TVTATL 271


>gi|238922884|ref|YP_002936397.1| putative 23S rRNA pseudouridine synthase [Eubacterium rectale ATCC
           33656]
 gi|238874556|gb|ACR74263.1| probable 23S rRNA pseudouridine synthase [Eubacterium rectale ATCC
           33656]
          Length = 244

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 106/242 (43%), Gaps = 29/242 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETS 155
           K  ++YED+ I +  KPAGI+ Q        ++ F++++  +K + P   + HRLDQ   
Sbjct: 3   KPDIIYEDNDIIICYKPAGIATQTRRIGQQDMESFIRNYRAAKNEPPYVGIVHRLDQPVE 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSL-----VWGIPKNKKECIANWLLKKSHIGG 210
           G++V A+ + AA  L+   +    +K Y +      V G  K +    + W     +I  
Sbjct: 63  GVMVFAKNQKAAASLSRQIKEHTTEKYYRAASRGQGVSGADKEEDNHDSAWHTLTDYISF 122

Query: 211 DYV----HVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVH 258
           D       +  + ++ A  A+  ++VI     +            +++  TGR HQ+R+ 
Sbjct: 123 DKRTNTSKITSEKDRLAKKAVLQYRVISVTPDRDSSQNECIRTEFDIKLLTGRHHQIRLQ 182

Query: 259 ALHMGCPIVGDHKYC---------ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
             H+G P++GD KY           +  G     ++ +L L +  +   HP  G R+   
Sbjct: 183 LAHIGYPLIGDTKYGKPASNNSGTGSKSGRTCGGVREQLALCSYKIVFDHPATGERMTFE 242

Query: 309 AP 310
            P
Sbjct: 243 LP 244


>gi|152989807|ref|YP_001355529.1| ribosomal large subunit pseudouridine synthase D [Nitratiruptor sp.
           SB155-2]
 gi|151421668|dbj|BAF69172.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Nitratiruptor sp. SB155-2]
          Length = 299

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 57/313 (18%), Positives = 125/313 (39%), Gaps = 45/313 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M +++ ++     + ++L       + +I+    QK++ + ++  + K +   + +  G+
Sbjct: 1   MPFIRKII--KTNKPIKLFLLLMRSF-NISQSQAQKMIDTKKIYQNGKLLTDKSAVVEGE 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +                       +     +  LK   ++E     +++KP+GI V   +
Sbjct: 58  I---------------------EVIVFEPITKGLKP--IFETKDFVLYDKPSGIMVHPRN 94

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                    +       G +  + HR+D+ETSG+++ +  + A + L + F  ++IQK Y
Sbjct: 95  --RNTHYTLIDEIRYRYGPQANIVHRIDKETSGLVLASTNKEAEKALKQMFEHKQIQKRY 152

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV G  + +        L + +     + +  + +    YA +    +  F   F  +
Sbjct: 153 LALVRGNIEKQLVIEEPIALNRDY---SKIKLKVKIDPSGKYAKTIINPLKQFGS-FTLV 208

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-------------NFKGNFTSPIQNKLYL 290
           E  P TGR HQ+R+H  H+  PI+GD  Y               + +         +L L
Sbjct: 209 EAIPITGRQHQIRIHLFHVKHPILGDPIYGPSTNESIRYLDGLMDEEERLVVTGATRLML 268

Query: 291 HARYMDLPHPEGG 303
           HA  ++  + +  
Sbjct: 269 HAYAVEFTYNDTK 281


>gi|86140463|ref|ZP_01059022.1| pseudouridylate synthase [Leeuwenhoekiella blandensis MED217]
 gi|85832405|gb|EAQ50854.1| pseudouridylate synthase [Leeuwenhoekiella blandensis MED217]
          Length = 297

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 71/283 (25%), Positives = 114/283 (40%), Gaps = 47/283 (16%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G + +D +       I+ G+ + +       N                     L   +LY
Sbjct: 25  GYLSIDGRPASTATWIKGGEQLSLRIPQQPNNQ----------------KKLRLVLDVLY 68

Query: 104 EDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ED  + V +KPAGI V G S   +A  +   L +        P+  HRLD  T+G ++V 
Sbjct: 69  EDEFLAVVHKPAGILVSGNSFKTVARALPQNLNASSAPDACTPQPAHRLDYATTGAVLVG 128

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +TR + + L + F  + I K Y+++  G+       I   +                   
Sbjct: 129 KTRESIRQLNQLFEDKAITKTYYAVTLGVMPA-SGTINTPV------------------- 168

Query: 222 GANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
               A+S + ++   A    ++   + +QP TGR HQLR H   +G PI+GD  YC    
Sbjct: 169 DGKAAVSVYTLVASVASPRFEQLNLVRLQPQTGRRHQLRKHLAGIGHPILGDRDYCPKE- 227

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
                     +YLHA  +   HP+    + ITAPLP   +K +
Sbjct: 228 ---LLLQGKGMYLHAFSLRFNHPQKLQPVAITAPLPQKFLKLF 267


>gi|126175503|ref|YP_001051652.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125998708|gb|ABN62783.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 244

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 98/233 (42%), Gaps = 19/233 (8%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +LY+DS I + +KP+G+    G          +   +        L HRLD 
Sbjct: 17  PPCLGQIRVLYQDSDILLIDKPSGLLSLSGKNPLN--LDSVHYRLVQDFPTATLLHRLDF 74

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++VA  ++    LT+ F+ R ++K Y +L+ G        I   + K      D+
Sbjct: 75  GTSGIMLVALNKSVNGLLTKQFQARTVEKRYTALLHGHIAADSGVINLPIAKDV----DH 130

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             + K        AIS ++V++   + F   +E  P +GRTHQLR+H+   G  I+G   
Sbjct: 131 FPLQKICHSTGKPAISEYRVLERLTEPFATRVEFTPVSGRTHQLRIHSQQFGHSILGCDL 190

Query: 272 YCA-----NFKGNFTSPIQ------NKLYLHARYMDLPHP-EGGRLQITAPLP 312
           Y           +   P        ++L LHA  +   HP  G R+      P
Sbjct: 191 YGGVGECKADNADAPDPHITEVVSNSRLMLHATRLAFDHPITGERIDWLCECP 243


>gi|195384880|ref|XP_002051140.1| GJ14588 [Drosophila virilis]
 gi|194147597|gb|EDW63295.1| GJ14588 [Drosophila virilis]
          Length = 552

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 62/268 (23%), Positives = 117/268 (43%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ + +G + V+ ++V  + +++   +         L + +  
Sbjct: 167 LDVF-SREFRAHPAEEYKRSIEAGTLTVNYEKVPIDYKLKHNDL---------LANTVHR 216

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +T         +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 217 HEVPVTSQPIT---------IVHMDEDILVVNKPASIPVHPCGRYRHNTVIFILA-KEFN 266

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
            +  R  HR+D+ TSG+L+  R    A+ + +  R R++QK Y   V G  P    EC  
Sbjct: 267 LKNLRTIHRIDRLTSGLLLFGRNSEKARQMEQQIRNRQVQKEYICCVEGQFPDGIIECNE 326

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  ++    A  +  ++ +P TGR HQ+RVH 
Sbjct: 327 PIEVVSYKIG-----VCKVSPKGKDCKTTFKRI--AQAGDYSIVQCKPLTGRMHQIRVHL 379

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PIV D  Y     G    P++ +
Sbjct: 380 QYLGYPIVNDPLYNHEVFG----PLKGR 403


>gi|229496355|ref|ZP_04390075.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas endodontalis ATCC 35406]
 gi|229316933|gb|EEN82846.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas endodontalis ATCC 35406]
          Length = 234

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 104/232 (44%), Gaps = 16/232 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           L   ++YED+ + V +K  G  V         ++  +  ++  K  KP      + HRLD
Sbjct: 7   LLMKVVYEDNHLLVVSKLPGEIVHADKTGDPSLEDMVALYLKKKYNKPGNVFVGVVHRLD 66

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +   G+++ A+T  A   + + F    + K Y ++V   PK  +    +WL + +     
Sbjct: 67  RPVGGLVLFAKTSKALARMNKLFAEGGVHKTYRAVVQNSPKGTQGECIDWLWRNAKQNKT 126

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y  +VK+N   A  A   ++ I   A++F  LE++  TGR HQ+R     MGCPI GD K
Sbjct: 127 Y--IVKENHPDAKRAHLRWRRIAT-AERFQMLEIELLTGRHHQIRAQLAGMGCPIKGDLK 183

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
           Y A       S     + L +  M   HP    ++++ A  P    K W  L
Sbjct: 184 YGAPRSNPDGS-----ISLLSYSMVFEHPVSHQKIELHATPPHD--KLWQLL 228


>gi|312129383|ref|YP_003996723.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
 gi|311905929|gb|ADQ16370.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
          Length = 550

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 69/243 (28%), Positives = 109/243 (44%), Gaps = 23/243 (9%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++  + +  T   D     ++YED  + V NKP+G+    G  I   +
Sbjct: 322 CEPILGHMLEGIELDPNPLLDTVEKDI---EIIYEDDYLAVVNKPSGLLSVPGIQIYDSV 378

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L++  D +   P + HRLDQ+TSGILV+AR +   +HL   F  R + K Y +L+ G
Sbjct: 379 YSRLQARWDHEA--PLVVHRLDQDTSGILVMARNKNVHKHLQSQFIRRTVIKHYIALLEG 436

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                K  I   L +          V  ++      A + ++ I      +  ++  P T
Sbjct: 437 HLVEDKGEIHLPL-RVDLDDRPRQMVCYEH---GKKAHTIWEKIGIEG-PYTRVKFFPVT 491

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
           GRTHQLR+HA H   +  PI GD  Y              +L LHA Y++  HP +  R+
Sbjct: 492 GRTHQLRMHAAHHEGLNAPIKGDDMYGK---------AAERLCLHAAYLEFLHPVKKERM 542

Query: 306 QIT 308
              
Sbjct: 543 SFE 545


>gi|319427367|gb|ADV55441.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 236

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 62/225 (27%), Positives = 96/225 (42%), Gaps = 11/225 (4%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +LY+DS I + +KP+G+    G       D      V        L HRLD 
Sbjct: 17  PPCLGQIRVLYQDSDILLIDKPSGLLSLSGKNPLN-FDSVHYRLVQ-DFPTATLLHRLDF 74

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++VA  +     LT+ F+ R ++K Y +L+ G   +    I   + K      D 
Sbjct: 75  GTSGIMLVALNKTVNGLLTKQFQARTVEKRYTALLHGHLTDDSGVINLPIAKDV----DN 130

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             + K        AIS ++V++   + F   +E  P +GRTHQLR+H+  +G  I+G   
Sbjct: 131 FPLQKICHSTGKLAISEYRVLERLTEPFATRVEFTPVSGRTHQLRIHSQQLGHSILGCDL 190

Query: 272 YCA---NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y         N  +    +L LHA  +   HP  G  +      P
Sbjct: 191 YGGVGEKITDNDYALHHIRLMLHATRLGFDHPITGEHIDWICKCP 235


>gi|146294028|ref|YP_001184452.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|145565718|gb|ABP76653.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
          Length = 236

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 60/225 (26%), Positives = 96/225 (42%), Gaps = 11/225 (4%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                +  +LY+DS I + +KP+G+    G          +   +        L HRLD 
Sbjct: 17  PPCLGQIRVLYQDSDILLIDKPSGLLSLSGKNPLN--LDSVHYRLVQDFPTATLLHRLDF 74

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI++VA  +     LT+ F+ R ++K Y +L+ G   +    I   + K      D 
Sbjct: 75  GTSGIMLVALNKTVNGLLTKQFQARTVEKRYTALLHGHLTDDSGVINLPIAKDV----DN 130

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
             + K        AIS ++V++   + F   +E  P +GRTHQLR+H+  +G  I+G   
Sbjct: 131 FPLQKICHSTGKLAISEYRVLERLPEPFATRVEFTPVSGRTHQLRIHSQQLGHSILGCDL 190

Query: 272 YCA---NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Y         N  +    +L LHA  +   HP  G  +      P
Sbjct: 191 YGGVGEKITDNDYALHHIRLMLHATRLAFDHPITGEHIDWICKCP 235


>gi|254521992|ref|ZP_05134047.1| ribosomal large subunit pseudouridine synthase A [Stenotrophomonas
           sp. SKA14]
 gi|219719583|gb|EED38108.1| ribosomal large subunit pseudouridine synthase A [Stenotrophomonas
           sp. SKA14]
          Length = 204

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 56/212 (26%), Positives = 94/212 (44%), Gaps = 16/212 (7%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y D  + V  KPAG+    G          + + + +        HRLDQ TSG+L+ AR
Sbjct: 6   YIDDALLVAEKPAGLLSVPGRSAENQ--DCVVARLQALYPDALTVHRLDQVTSGLLLHAR 63

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            +     L+  F  R++ K Y ++V G+ +     +   L+         +     + + 
Sbjct: 64  GKDMQAALSMQFEQRQVGKRYEAIVEGLLEGDAGEVDLPLIVDWPNRPKQMI----DHER 119

Query: 223 ANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
              A++ ++V+   A  +   +E++P TGR+HQLR+H   +G PIVGD  Y A       
Sbjct: 120 GKPALTRWRVLARDAGAQRTRMELEPITGRSHQLRLHMASLGHPIVGDVLYDAAPA---- 175

Query: 282 SPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                +++LHA  +   HP  G  L   +  P
Sbjct: 176 ----QRVHLHASALAFTHPLTGAALAFESAAP 203


>gi|152981434|ref|YP_001352926.1| pseudouridylate synthases, 23S RNA-specific [Janthinobacterium sp.
           Marseille]
 gi|151281511|gb|ABR89921.1| Pseudouridylate synthases, 23S RNA-specific [Janthinobacterium sp.
           Marseille]
          Length = 223

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 56/207 (27%), Positives = 92/207 (44%), Gaps = 11/207 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  ++Y+D  I + NKP+G+    G          +   +  +  +  + HRLD  TSG+
Sbjct: 16  EIEIIYQDEAILLINKPSGLLTLSGKNPLN--LDSVHHRLVQQFPQALMIHRLDLGTSGL 73

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LVVA  +A A ++   F++R + K Y +++ G        I   + K           + 
Sbjct: 74  LVVALNKAVAANINRQFQLRTVAKTYQAVLAGQVAEDHGKITLPIAKDPLNFPKLKICLA 133

Query: 218 QNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                   A SH++V+D         +   PHTGRTHQLR+H+  +G PI+G   Y    
Sbjct: 134 ----SGKAASSHYEVLDRQVDADTTRVLFTPHTGRTHQLRIHSAGIGHPILGCDLYGT-- 187

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGG 303
               +     +L LHA  ++  HP  G
Sbjct: 188 --AESEQGAERLLLHATTLEFDHPLSG 212


>gi|221133320|ref|ZP_03559625.1| pseudouridylate synthase [Glaciecola sp. HTCC2999]
          Length = 245

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 96/239 (40%), Gaps = 18/239 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  ++Y+D  I   NKP+G+ V       +     ++   +   Q     HRLD+ TSG+
Sbjct: 7   QLPIIYQDEHIIAINKPSGLLVHRSMIDRHETRFAMQMVRNMIDQHVYTVHRLDKPTSGV 66

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV A +   A+ +TE F  + I K Y +L  G     +        K   I         
Sbjct: 67  LVFALSSDVARLMTEQFTEKTIHKTYHALTRG-WTKSQFVDYALKEKLDKIADK----DA 121

Query: 218 QNEKGANYAISHFKVIDCFAQ----------KFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           Q +K    A +H   +  F            +  W+E+ P TGR HQLR H  H+  PI+
Sbjct: 122 QQDKAPQEAQTHIACLQRFTYPKAVGRYPQARLSWVELNPQTGRKHQLRRHLAHVRHPIM 181

Query: 268 GDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           GD  +    +  F     N   L LH   M   HP     L ++APL   +     +L 
Sbjct: 182 GDTTHGDGKQNKFMRDTFNFHHLALHNSSMKFCHPVTQHPLALSAPLWPELEHVLATLA 240


>gi|327539595|gb|EGF26204.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica WH47]
          Length = 231

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 102/230 (44%), Gaps = 17/230 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSG----IAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +  ++YED+ + V NKP  ++  G +G     +   D   ++          +  RLD  
Sbjct: 3   EVDVIYEDNHLLVVNKPTKLATMGAAGQPTLHSLGCDYIRRTCNKPNKVYLGIVSRLDSM 62

Query: 154 TSGILVVARTRAAAQHLTESFRMRR---IQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           TSG++V+ART  AA  LT  F        +K Y ++V G  + ++  + + + K      
Sbjct: 63  TSGVIVMARTSKAASRLTPQFANHSGDGAKKTYLAVVPGRVEQQQGTLVDDVYKDD--AA 120

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             + V   +   A  A   ++V   + ++   L+++P TGR HQ+R+     G PI+GD 
Sbjct: 121 YRMRVAHHSRSDAKEARLEYEV-SGYDRELTLLKVKPLTGRKHQIRLQWAEAGFPILGDT 179

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTW 319
           KY +             + LH+  + + HP    R+   AP+P   V   
Sbjct: 180 KYGSERSWP------TGIALHSWRLSIMHPTKKERMTFEAPVPDAWVSRL 223


>gi|227499607|ref|ZP_03929714.1| possible pseudouridylate synthase [Anaerococcus tetradius ATCC
           35098]
 gi|227218366|gb|EEI83620.1| possible pseudouridylate synthase [Anaerococcus tetradius ATCC
           35098]
          Length = 280

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 63/296 (21%), Positives = 121/296 (40%), Gaps = 42/296 (14%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M Y++Y +      N+ + ++ +      +  ++ +IL S    ++ K    +  ++ G 
Sbjct: 1   MKYIKYKI----NNNITVRKFLEA--KDYSKRSIDEILNSAY-LLNGKLKNKSFDLKKGD 53

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                           E KI+    +L       K  +L+ED+   V +K + ++V   S
Sbjct: 54  ----------------EFKIIIEDEDLDYEPIEGKLKVLFEDANSLVVSKTSNLTV--NS 95

Query: 124 GIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
               ++  +L  +        K RL +RLD  TSG+++VA+ + A  +         I+K
Sbjct: 96  KNQVNLSNYLAYYFKENDIRNKIRLVNRLDMNTSGLMLVAKNKYAHAYYQRQVENNLIKK 155

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++V              LL ++ I  D  +           A ++FK ID     + 
Sbjct: 156 KYLAVVDPN-------TDLDLLYEARISYDEENKKYIASNNGKLARTYFKTID-KNDSYS 207

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            +E +  TG+THQ+RV    +G PI GD  Y ++          ++  LH+  ++ 
Sbjct: 208 LIECEIFTGKTHQIRVSLQSLGHPIYGDKLYGSDKD-------LDRFLLHSYKLEF 256


>gi|153854758|ref|ZP_01995992.1| hypothetical protein DORLON_01990 [Dorea longicatena DSM 13814]
 gi|149752665|gb|EDM62596.1| hypothetical protein DORLON_01990 [Dorea longicatena DSM 13814]
          Length = 296

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 72/290 (24%), Positives = 110/290 (37%), Gaps = 50/290 (17%)

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            ++ I    N          ++  S  LTK        +LYED  I V  KP GI+ Q  
Sbjct: 5   DIISISASANVCLQFFPLHDLISISFVLTKEKYMATLNILYEDPHILVCVKPHGIATQSK 64

Query: 123 SGIAYHIDGFLKSWVDSKG---------------------QKPRLTHRLDQETSGILVVA 161
           S     +   +K+ +                             + HRLDQ  +GILV A
Sbjct: 65  SIRYPDMVSLIKNHLAKASGTSGKSGAPKSIGSRTPGSAEPYLAVIHRLDQPVAGILVFA 124

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +T AAA+ L +  + +   K Y +LV   P  ++  + ++++K +      +   K+N  
Sbjct: 125 KTPAAAKDLNKQLQNQGFGKYYRALVTNAPSEEEGTLEDYMVKDARTNTSRICSAKEN-- 182

Query: 222 GANYAISHFKVIDCFAQKF-----------------------CWLEMQPHTGRTHQLRVH 258
           GA  A  H+  +    + F                         LE+   TGR HQ+RV 
Sbjct: 183 GAKIARLHYDTVPDHGRLFSTVSGSSSSVDVSLSSQSQECHETELEIHLDTGRHHQIRVQ 242

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
              +GCPIVGD KY     GN       +L   A  +D  HP   + +  
Sbjct: 243 LASIGCPIVGDTKYNPELTGNKGWQTI-RLC--AYKLDFKHPVTHKAMHF 289


>gi|330946151|ref|XP_003306701.1| hypothetical protein PTT_19907 [Pyrenophora teres f. teres 0-1]
 gi|311315680|gb|EFQ85200.1| hypothetical protein PTT_19907 [Pyrenophora teres f. teres 0-1]
          Length = 475

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 59/283 (20%), Positives = 104/283 (36%), Gaps = 52/283 (18%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIK 79
           LD +  + +        ++ +  G+V ++ K V      +++G V+      +      +
Sbjct: 70  LDIF-SSEFRDRPAEYYEQAIIDGRVVLNGKPVPSTKTIVKNGDVISHTLHRHEPPCTAQ 128

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                                +++ED  + V NKPAG+ V       ++    +      
Sbjct: 129 ------------------PIGIVHEDDNMIVINKPAGMPVHPAGRYNFNSIIEIMRADRG 170

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECI 198
            G  P   +RLD+ TSGI+ + + + AA+ L+   R R ++K Y + V G  P+ +  C 
Sbjct: 171 YGWNPLPCNRLDRLTSGIMFIGKHKQAAEELSAQIRGRTVKKEYITRVVGEFPEGEILCE 230

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--------------------- 237
              L     +G + V            A + FK +  +                      
Sbjct: 231 KPILQISPKLGLNRVRA------NGKEAKTVFKRMAYYPPTDHGKRPNGEDSETDPQGQP 284

Query: 238 ----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               + +  +   P TGRTHQLRVH   +G PI  D  Y    
Sbjct: 285 WKKLRGYSIVRCFPVTGRTHQLRVHLQFLGHPISNDPIYANQR 327


>gi|322705188|gb|EFY96776.1| DRAP deaminase [Metarhizium anisopliae ARSEF 23]
          Length = 513

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 103/283 (36%), Gaps = 70/283 (24%)

Query: 42  RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
             G + V+  RV  +  +++G ++              E  +    V            +
Sbjct: 118 EKGDIFVNGTRVGPDYILRNGDLISHTLHR-------HEPPVTSDPVG-----------I 159

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILV 159
           ++ED  + V NKP+G+ V       Y  +  L+     +GQ+  P   +RLD+ TSGI+ 
Sbjct: 160 IHEDDDMIVINKPSGVPVHPAG--RYKFNSVLEIMKAERGQEFMPYPCNRLDRLTSGIMF 217

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VA++  AA+ L    + R ++K Y + V G  P+ +  C    L     +G + V     
Sbjct: 218 VAKSVKAAEALGNQIKSRTVRKEYMARVVGEFPEGEIVCDQPILSISPKLGLNRVRA--- 274

Query: 219 NEKGANYAISHFKVIDCFA----------------------------------------- 237
                  A + FK +  +                                          
Sbjct: 275 ---EGKAARTVFKRLAYYPPRGDAEANGQQGGVPEPTDKELSRLPAEEGDESNGKPWINK 331

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           + +  +   P TGRTHQ+RVH  ++G PI  D  Y       F
Sbjct: 332 RGYSIVRCLPVTGRTHQIRVHLQYLGHPIQNDPIYANQRVWGF 374


>gi|319785749|ref|YP_004145224.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317464261|gb|ADV25993.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
          Length = 273

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 97/239 (40%), Gaps = 25/239 (10%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L+ D  + V +KPAG+ V      A   D          G++  L HRLD+ TSG L
Sbjct: 39  LPVLHADQWLAVVDKPAGLMVHDSVLAADETDFAADRLRAQFGRQVFLVHRLDRATSGCL 98

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A  R  A  L ++   +++ K Y ++  G P+ +   I + L                
Sbjct: 99  LLAFDRDTASALGKAVMAQQLDKRYLAVCRGWPE-EGFTIDHPLDG------------GP 145

Query: 219 NEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            +     A++ F+ + C             ++  LE  P TGR  Q+R H  H    ++G
Sbjct: 146 GKPQKKPAVTRFRRLACGELDEPSAGFPTSRYALLECAPVTGRFRQIRRHLKHASHHLIG 205

Query: 269 DHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFK 325
           D  +        F     +++ LHA  +  PHP +G  + + AP     +K     G+ 
Sbjct: 206 DTSHGDGRHNRAFRMRGVHRMLLHAWQLGFPHPKDGQEMTVVAPPSGEFLKAMALFGWS 264


>gi|224476102|ref|YP_002633708.1| putative pseudouridylate synthase [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222420709|emb|CAL27523.1| putative pseudouridylate synthase [Staphylococcus carnosus subsp.
           carnosus TM300]
          Length = 294

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 59/291 (20%), Positives = 115/291 (39%), Gaps = 40/291 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L  + + +    +   +  I R G + V++  V     ++ G V+ +             
Sbjct: 13  LKNFLQQN--QYSKKMISAIKRDGALIVNEVPVTVRKTLEIGDVLVV------------- 57

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGFLKS 135
            K+ D   +     D+    +L+ED      +K    +           +   + G+LK 
Sbjct: 58  -KLPDEQASENLVPDYQPIDVLFEDQYFIAVSKGKKQNCAPSREHPHGSLIEQVIGYLKD 116

Query: 136 WVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                  +  P +  RLD++TSGI++ A+      HL        ++K+Y  +  G  +N
Sbjct: 117 QAADGNYQSIPHIVTRLDRDTSGIVLFAK----HGHLHHRMSSTEMKKVYHCICNGKLEN 172

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + +A  +     I      + ++ ++   YA + ++ I+  ++++   E++ HTGRTH
Sbjct: 173 TSKIVAPIMRAGDSI------IERKVDQAGKYAATSYQPINA-SEQYTLCEVRLHTGRTH 225

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           Q+RVH  ++  PIVGD  Y                 L   Y+   HP    
Sbjct: 226 QIRVHFQYINHPIVGDGLYGG------LHTFVTGQALACCYLSFKHPITHE 270


>gi|123442854|ref|YP_001006830.1| putative ribosomal large subunit pseudouridine synthase [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|122089815|emb|CAL12670.1| putative ribosomal large subunit pseudouridine synthase [Yersinia
           enterocolitica subsp. enterocolitica 8081]
          Length = 232

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 54/211 (25%), Positives = 85/211 (40%), Gaps = 16/211 (7%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+    G          +   +        L HRLD  TSG++V+A
Sbjct: 20  LYQDDHLVLINKPTGLLSLSGKNPQN--LDSVHHRLVQIFPGCTLVHRLDFGTSGLMVIA 77

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R +A    L + F  R + K+Y +L+ G   + +  I   + K   +    +        
Sbjct: 78  RNKAINAALCQQFSQRTVTKVYSALLCGHLDDNEGVIDAAIAKDPALFPLMLICATH--- 134

Query: 222 GANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               A S ++V++ F              +++ P TGRTHQLR+H   +G PI G   Y 
Sbjct: 135 -GKPARSGYRVVERFYHELEDGRSLPLTRVQLIPETGRTHQLRIHCQQLGHPIWGCDLYG 193

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                        +L LHA  +   HP    
Sbjct: 194 GRLLPGTEQT--PRLMLHASELHFVHPISEE 222


>gi|149916984|ref|ZP_01905485.1| ribosomal large subunit pseudouridine synthase A [Plesiocystis
           pacifica SIR-1]
 gi|149822262|gb|EDM81653.1| ribosomal large subunit pseudouridine synthase A [Plesiocystis
           pacifica SIR-1]
          Length = 509

 Score =  152 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 69/268 (25%), Positives = 107/268 (39%), Gaps = 52/268 (19%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKG 141
               V L +  D     ++YED  + V +KP G+    G G      ++  LK+  +   
Sbjct: 254 PAPDVGLGQVPDDAP-RVVYEDDDLLVVDKPPGMLSVPGRGPRRRDSVEYRLKARANPDA 312

Query: 142 QK-----------------------------PRLTHRLDQETSGILVVARTRAAAQHLTE 172
            +                             PRL HRLD  TSG+L+ A+ R A   L  
Sbjct: 313 IEAAVAAQSKSKPPAGSEARTAAGPRLDQLWPRLVHRLDLATSGLLIAAKHREAYVALQR 372

Query: 173 SFRMRRIQKIYWSLVWGIPKN---KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
            F  R+I K Y +LV G   +   +   I   L +      D     K + +    A + 
Sbjct: 373 QFSSRQIGKRYVALVRGPLPDALGEGGEIELPLARD----LDDRPRQKVDRREGKVARTR 428

Query: 230 FKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQ 285
           ++++    +     + + PHTGRTHQLR+HA H   +  P+VGD  Y             
Sbjct: 429 WQLLAHEPEHAASRVALYPHTGRTHQLRLHAAHPEGLDAPLVGDLLYGYGEGA------- 481

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLP 312
            +L LHA  +   HP  G  +++ +P P
Sbjct: 482 -RLMLHAERLTFLHPTRGEPMELRSPCP 508


>gi|297269584|ref|XP_002799894.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 2 [Macaca mulatta]
          Length = 346

 Score =  152 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 77/283 (27%), Positives = 124/283 (43%), Gaps = 40/283 (14%)

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           V   PV   +  I++  + L   V+    +  L   +L++++ + V NKP G+ V GG G
Sbjct: 64  VSTNPVQRRVQEIVRFTRQLQR-VHPNVLAKALTRGILHQNNNLVVINKPYGLPVHGGPG 122

Query: 125 IAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           +   I   L    K     K +   L HRLD+ET+G++V+A  +  A  + E FR R++ 
Sbjct: 123 VQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWDKDMAHQVQELFRTRQVV 182

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K YW++   +P      +   ++                EK A  A++ ++V+       
Sbjct: 183 KKYWAITVRVPMPSAGVVDIPIV----------------EKEAQVAVTRYQVLSS-TLSS 225

Query: 241 CWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC------------ANFKGNFTSPIQNK 287
             +E+QP TG  HQLRVH    + CPI+GDHKY                K       + +
Sbjct: 226 ALVELQPITGIKHQLRVHLSFGLDCPILGDHKYSDWNRLAPQKLSVGTLKKLGLEQSKAR 285

Query: 288 ---LYLHARYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGFK 325
              L+LHA+ + LP        L +   LP   V +   LG +
Sbjct: 286 YIPLHLHAQQLILPALGSRKEDLNLVCKLPRFFVCSLRRLGLE 328


>gi|239636478|ref|ZP_04677480.1| pseudouridylate synthase, 23S RNA-specific [Staphylococcus warneri
           L37603]
 gi|239597833|gb|EEQ80328.1| pseudouridylate synthase, 23S RNA-specific [Staphylococcus warneri
           L37603]
          Length = 284

 Score =  152 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 52/287 (18%), Positives = 107/287 (37%), Gaps = 40/287 (13%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + + H    +   +  I  +G + V+++      ++  G  + +   +   +  +     
Sbjct: 16  FLQRH--DFSKKTISAIKTNGALLVNQRPFTVRYQLNLGDQLVVQLPLEIPSANL----- 68

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKP-----AGISVQGGSGIAYHIDGFLKSWVD 138
                            +L+ED  I + +KP     A         +   + G+L     
Sbjct: 69  ---------LPYLKPLDILFEDDYIIIVSKPNRQNCAPSCEHPHESLVEQVLGYLLH--K 117

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +   P +  RLD+ T+GI++ A+        +++    ++ K+Y  L  GI       I
Sbjct: 118 GEHTNPHIVTRLDRNTTGIVLFAKYGYIHHLFSKT----KMDKVYTCLAHGI-TEPSGVI 172

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + +      +   + +Q  +   YA + ++ I    +     E+Q  TGRTHQ+RVH
Sbjct: 173 EAPIARN-----EASIIERQVSENGKYAKTLYRTIK-QKENVSCCEVQLCTGRTHQIRVH 226

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
             ++G P++GD  Y                 LH   +   HP   ++
Sbjct: 227 FQYIGHPLIGDTLYGGKHGK------IEGQCLHCSKLCFEHPVNKKM 267


>gi|325283148|ref|YP_004255689.1| pseudouridine synthase [Deinococcus proteolyticus MRP]
 gi|324314957|gb|ADY26072.1| pseudouridine synthase [Deinococcus proteolyticus MRP]
          Length = 253

 Score =  152 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 104/239 (43%), Gaps = 16/239 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETS 155
           +  LL E    Y  +KPA        S  +  +   +  W    G+      HRLD+ETS
Sbjct: 12  RPRLLLEHPDFYALHKPALWLTHPVRSHGSSRVPDVVSFWQSETGESSLGPPHRLDRETS 71

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+++R   +A+     F  R + K Y ++V G+P      +   L +    GG+ V +
Sbjct: 72  GLLLLSRDSESARRFFVLFGQRLVAKTYRAIVRGVPAWTDYELDAPLGELGLGGGNRVIM 131

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +        A++ F+V++  A     +E +P TGR HQ+R H  H+G P+VGD  Y   
Sbjct: 132 RQGVVPDGRPAVTAFRVLERRA-GHTLIEARPRTGRLHQIRAHLYHLGLPLVGDKIYGPE 190

Query: 276 FKGNF------------TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                                  +  LHA  +  P  +G ++++  PLPA M   WD L
Sbjct: 191 RDAFLEFRETGQTPELTRRLGMARQALHAASLHFPW-DGAQVRLHDPLPADMQAFWDGL 248


>gi|73662254|ref|YP_301035.1| pseudouridylate synthase [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72494769|dbj|BAE18090.1| putative pseudouridylate synthase [Staphylococcus saprophyticus
           subsp. saprophyticus ATCC 15305]
          Length = 275

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 63/293 (21%), Positives = 112/293 (38%), Gaps = 35/293 (11%)

Query: 25  FKNHYP--HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
            +  +   H+   +L  +  S  + +++       ++ +G  V IP      N++     
Sbjct: 14  LREIFQQLHLPKKDLHTLNMSKAITINESPGTLTTKVNTGDNVYIPTPDEVSNYL----- 68

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KG 141
                        +  + + YED  I +  KP G+            +  +   + + K 
Sbjct: 69  -----------PSYRFAQIYYEDDDIAIVMKPKGVKTHP--NDLKESNTLMNHVIYTIKS 115

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLDQET G+L+VA+     + L       +I +IY + V  +   K + I   
Sbjct: 116 DYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEENKIDRIYKANVHSLLPIKPQTIDMP 175

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + K       +    ++       AI+H        +  C LE++  TGRTHQ+RVH   
Sbjct: 176 IGKD-----KFHSNKRRVSSTGQSAITHILNSKMIKEDVCELEIKLDTGRTHQIRVHLAE 230

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
           +G P++GD  Y  +           KL L++  ++  HP      IT  L   
Sbjct: 231 IGHPVIGDPLYGNS--------TLRKLELNSHKIEFIHPLTQE-SITVSLDDE 274


>gi|323697656|ref|ZP_08109568.1| pseudouridine synthase [Desulfovibrio sp. ND132]
 gi|323457588|gb|EGB13453.1| pseudouridine synthase [Desulfovibrio desulfuricans ND132]
          Length = 275

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 103/280 (36%), Gaps = 29/280 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           ++   + +RLDR  +   P       +++   G++ VD +  K   R+++GQ+V +    
Sbjct: 9   IDASGDGLRLDRALEAVMPGSGLRLRRRLCDEGRILVDGRARKPGYRVRTGQLVEVK--- 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG---GSGIAYH 128
                             +T   +    I+ +ED      NKP G  V            
Sbjct: 66  --------------EGREMTTPGELGVRIVKWED-GFAAVNKPGG--VHSAIISGRDEPC 108

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           ++  L +     G +P L +RLD+ TSG+L+VA T  A     E      I+K Y + V 
Sbjct: 109 VEAVLPALFP--GMEPVLLNRLDRLTSGLLLVALTPEARDAYLEYEDQGAIKKFYLARVR 166

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G    + + I +   +          V+ + ++ A        +    A     +     
Sbjct: 167 G----RLDGIVSVRNRLDTDDRKTTRVLAEPDEDARRWTGVTALSHDNAADTSLVRCLIT 222

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
            G  HQ+R H   +G PIVGD  Y              +L
Sbjct: 223 KGARHQIRAHLASIGHPIVGDPLYGGGESPRGLMLQHQRL 262


>gi|189200266|ref|XP_001936470.1| DRAP deaminase [Pyrenophora tritici-repentis Pt-1C-BFP]
 gi|187983569|gb|EDU49057.1| DRAP deaminase [Pyrenophora tritici-repentis Pt-1C-BFP]
          Length = 475

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 59/283 (20%), Positives = 104/283 (36%), Gaps = 52/283 (18%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIK 79
           LD +  + +        ++ +  G+V ++ K V      +++G V+      +      +
Sbjct: 70  LDIF-SSEFRDRPAEYYEQAIIDGRVVLNGKPVPSTKTIVKNGDVISHTLHRHEPPCTAQ 128

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                                +++ED  + V NKPAG+ V       ++    +      
Sbjct: 129 ------------------PIGIVHEDDNMIVINKPAGMPVHPAGRYNFNSIIEIMRADRG 170

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECI 198
            G  P   +RLD+ TSGI+ + + + AA+ L+   R R ++K Y + V G  P+ +  C 
Sbjct: 171 YGWNPLPCNRLDRLTSGIMFIGKHKQAAEELSAQIRGRTVKKEYITRVVGEFPEGEILCE 230

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--------------------- 237
              L     +G + V            A + FK +  +                      
Sbjct: 231 KPILQISPKLGLNRVRA------NGKEAKTVFKRMAYYPPKDDGRRPNGEDSETDPQGQP 284

Query: 238 ----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
               + +  +   P TGRTHQLRVH   +G PI  D  Y    
Sbjct: 285 WKKLRGYSIVRCFPVTGRTHQLRVHLQFLGHPISNDPIYANQR 327


>gi|284041381|ref|YP_003391311.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283820674|gb|ADB42512.1| pseudouridine synthase [Spirosoma linguale DSM 74]
          Length = 240

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 98/239 (41%), Gaps = 20/239 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
            + ++++E+    + NKP  ++              L+    +     +L HRLD+ETSG
Sbjct: 5   FEDLIVFENEDYILINKPPHVASLDERTTDRGGQSILR-LAKAYHADAQLGHRLDKETSG 63

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           IL +A+   A +HL   F  R + K Y ++  G+  +  E I+ +L       G     V
Sbjct: 64  ILAIAKNPEAYRHLAMQFEHREVTKRYHAVTNGV--HNFEGISVYLPISPIKDG---TAV 118

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           + + +    A + F  +  + +    +E  P TGR HQ+RVH + +  PIV D  Y    
Sbjct: 119 RIDREKGKVAETIFNTLQAY-RTTTLVECMPVTGRMHQIRVHLMCLKAPIVNDPTYGGKP 177

Query: 277 -------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                        +G    P+ +++ LHA  +     +G      AP P         L
Sbjct: 178 VFLSDVKRKFNLKEGTEELPLIHRVALHAHSLTFALLDGEEQTFVAPYPKDFNVLVKQL 236


>gi|94985003|ref|YP_604367.1| pseudouridine synthase [Deinococcus geothermalis DSM 11300]
 gi|94555284|gb|ABF45198.1| pseudouridine synthase [Deinococcus geothermalis DSM 11300]
          Length = 251

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 95/242 (39%), Gaps = 14/242 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
               K  +L E    YV +KPA              D       ++        HRLD+E
Sbjct: 9   PPTEKPRVLVEHPDFYVVHKPALWLTHPVRARVDVPDVLSYMRAETGEPDLAPPHRLDRE 68

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG  +++R   AA+     F+   + K Y ++V G P  ++  +   L      G + V
Sbjct: 69  TSGTQLLSRDPDAARRFFTLFKTHLVGKTYLAVVHGSPDWERYTLDAPLGDLGLGGANRV 128

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + +        A++ F+V++     F  +E  P +GR HQ+R H  H+G P+VGD  Y 
Sbjct: 129 IIRQAVVPDGRPAVTDFRVVEQRG-GFTLIEAYPRSGRLHQIRAHLSHLGLPLVGDKIYG 187

Query: 274 ANFKG------------NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
            + +                  +  +  LHA  +  P   G +    APL   +   W+ 
Sbjct: 188 PDPQAFLDFMHHGQTLELTERLLLPRQALHAARIAFPW-AGAQFAAEAPLAPDLRMFWED 246

Query: 322 LG 323
           L 
Sbjct: 247 LA 248


>gi|156742179|ref|YP_001432308.1| pseudouridine synthase [Roseiflexus castenholzii DSM 13941]
 gi|156233507|gb|ABU58290.1| pseudouridine synthase [Roseiflexus castenholzii DSM 13941]
          Length = 309

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 73/317 (23%), Positives = 126/317 (39%), Gaps = 38/317 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V +   +  + L           +      ++  G V V+ +RV+  +       VR+P 
Sbjct: 3   VTIPITDPGVSLRDALTAALG--SEGEAAWLIARGGVWVNGRRVRDPD-------VRLPV 53

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-H 128
               +     +    D  V          +++LYED+ +   +KP    V+     A  H
Sbjct: 54  DATVVVQRPPDGIYRDPVVT--------SAMILYEDADLIALDKPIDTYVEATPWDAEGH 105

Query: 129 IDGFLKSWV---DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           +   L  ++   D       L HRLD++TSG+L++++       L  +FR   ++K Y +
Sbjct: 106 LRAALAHFLEVRDGSAPPLHLAHRLDRDTSGVLLLSKAPDVNAALQRAFREGAVRKTYLA 165

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA---------NYAISHFKVIDCF 236
           L  G+P   +  I     +    G   V  V  +E+               +  +V+   
Sbjct: 166 LCAGLPAFDEIEIETGHGR----GRGGVFRVFPHEEIGRALPQGGTVKAMRTRLRVVRRM 221

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                     P TGRTHQ+R+H   +G P++GD KY       +   +    +LHA  ++
Sbjct: 222 -DDAALACATPLTGRTHQIRLHLAFLGHPLIGDVKYGG--PSTWRGVVVQHHHLHAWRLE 278

Query: 297 LPHPEGGR-LQITAPLP 312
           LPHP  G  L I +P P
Sbjct: 279 LPHPRSGTALIIESPAP 295


>gi|239816627|ref|YP_002945537.1| pseudouridine synthase [Variovorax paradoxus S110]
 gi|239803204|gb|ACS20271.1| pseudouridine synthase [Variovorax paradoxus S110]
          Length = 225

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 102/232 (43%), Gaps = 20/232 (8%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
                L++ED+ + V NKPAG+    G G        L +    +     + HRLD  TS
Sbjct: 1   MPDIDLIHEDAHLLVLNKPAGLLCVPGRG--EDKQDCLSARAMRRWPDALIVHRLDMATS 58

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYV 213
           G++++AR  A  + L ++F  RR+ K Y ++V G    + E   I   L     +     
Sbjct: 59  GLVLMARGAAMQRALGDAFAERRVHKRYEAIVDGAMPVQDEWSVIDAPL-----MADWPN 113

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQ------KFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             +++ +     +++ ++ +   +       +   L ++P TGR+HQLRVH L +G  I+
Sbjct: 114 RPLQKVDPAGKPSLTRWRALSSSSSAPDGNTQASHLLLEPLTGRSHQLRVHLLSIGHSIL 173

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
           GD  Y +            +L LHA  +   HP   + L + +P      + 
Sbjct: 174 GDALYGSADVQARA----PRLLLHASELGFVHPVTQQSLCLQSPSGFDFSRL 221


>gi|260910942|ref|ZP_05917583.1| ribosomal large subunit pseudouridine synthase A [Prevotella sp.
           oral taxon 472 str. F0295]
 gi|260634933|gb|EEX52982.1| ribosomal large subunit pseudouridine synthase A [Prevotella sp.
           oral taxon 472 str. F0295]
          Length = 537

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 56/217 (25%), Positives = 102/217 (47%), Gaps = 18/217 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           LD +    K  D     ++YED  + V +KP G+    G G    +   ++         
Sbjct: 319 LDVACVPQKAVDRDALRVVYEDDALVVVSKPHGMLSVPGKGGGTSVAQLMRERY-PDADS 377

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWL 202
           P + HRLDQ+TSG++++A+T+   + L  +F    ++K Y +++ G +P  +++   +  
Sbjct: 378 PLIVHRLDQDTSGLMLIAKTKEMHRTLQLAFENHEVKKRYVAVLDGLLPPERQQGEISLP 437

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH- 261
           L  +++      V          A++ ++VI    +    + + P TGRTHQLRVH  H 
Sbjct: 438 LNSNYLDRPRQMVDWLQ---GKPAVTRYEVIG-QEEGRTIVALYPLTGRTHQLRVHCAHP 493

Query: 262 --MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
             +  PI+GD  Y             +++YLHA  ++
Sbjct: 494 DGLNLPILGDPLYGRK---------AHRMYLHAEAIE 521


>gi|110639592|ref|YP_679802.1| ribosomal large subunit pseudouridine synthase D [Cytophaga
           hutchinsonii ATCC 33406]
 gi|110282273|gb|ABG60459.1| ribosomal large subunit pseudouridine synthase D [Cytophaga
           hutchinsonii ATCC 33406]
          Length = 242

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 58/228 (25%), Positives = 107/228 (46%), Gaps = 16/228 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +++ED+ +   NK  G+ VQG       +   +K ++  K  KP      + HR+D+  S
Sbjct: 22  VVFEDNHLIAVNKKNGVLVQGDDTGDKPLSELVKEYLKKKYNKPGNVFAGVIHRIDRPVS 81

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++++A+T  A + + + F  ++IQK Y  +    P      + +WL K +    +    
Sbjct: 82  GLVLLAKTSKALERMNKQFADKKIQKAYLMVSGSKPNPASAKLVHWLTKDAK--RNIAKA 139

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                K + Y    + ++   + ++  +E++P TGR+HQ+R     +GC I GD KY A 
Sbjct: 140 HTSEVKESKYCELSYSLL-TSSDRYFLIEVKPVTGRSHQIRCQMASIGCVIKGDLKYGAP 198

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S     + LH+  +   HP  G  +Q+ A  P    + W++L
Sbjct: 199 -----RSNPDGGICLHSHKLSFQHPVTGDNMQLKADPPKG--EPWNAL 239


>gi|288800367|ref|ZP_06405825.1| ribosomal large subunit pseudouridine synthase A [Prevotella sp.
           oral taxon 299 str. F0039]
 gi|288332580|gb|EFC71060.1| ribosomal large subunit pseudouridine synthase A [Prevotella sp.
           oral taxon 299 str. F0039]
          Length = 540

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 65/224 (29%), Positives = 109/224 (48%), Gaps = 21/224 (9%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K    L    L+ED  I V  KP G+    G      ++  +++   +    P + HRLD
Sbjct: 328 KPDAELTLATLFEDESIRVVVKPCGMPSVEGHHSLVSVEQLMRNEYPT-ADSPLIVHRLD 386

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSHIG 209
            +TSGI+++A+T+ A + L E F + +++K Y +++ G+ K++    CI   LL      
Sbjct: 387 MDTSGIMIIAKTKQAHKCLQEQFALHQVKKRYIAVLEGVFKHQPTCGCIELPLL----PN 442

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPI 266
            +   +   ++     A ++++VI    Q+   + + P TGRTHQLRVH  H   +  PI
Sbjct: 443 VNERPLQMVDDVYGKEATTYYRVIGVENQR-TRVALYPQTGRTHQLRVHCSHGEGLALPI 501

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITA 309
           VGD  Y             ++L+LHA  + L HP  G R+   +
Sbjct: 502 VGDCLYGKP---------DSRLHLHAAAIALKHPVNGKRMVFKS 536


>gi|285019825|ref|YP_003377536.1| pseudouridine synthase (rna-uridine isomerase) protein [Xanthomonas
           albilineans GPE PC73]
 gi|283475043|emb|CBA17542.1| probable pseudouridine synthase (rna-uridine isomerase) protein
           [Xanthomonas albilineans]
          Length = 276

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 94/237 (39%), Gaps = 23/237 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I V +KPAG+            D          G+   L HRLD+ TSG L++
Sbjct: 10  ILYQDPLIAVVDKPAGLMAHDSKLARGEDDFLADRLRVQLGRPIFLIHRLDRATSGCLLL 69

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R  A  L ++     + K Y ++  G P   +  + + L                 +
Sbjct: 70  AFDRDTASLLGKALMGGEVDKDYLAICRGWPAEIRFEVDHPLDG------------GPGK 117

Query: 221 KGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                A + F+ + C             ++  L   P TGR  Q+R H  H+   ++GD 
Sbjct: 118 PLKKPAQTRFQRLACGELTVPSGEFPTSRYALLRCCPVTGRFRQIRRHLKHLSHHLIGDT 177

Query: 271 KYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
            +        F     +++ LHA  +   HP G R+++ APL A  V+ +   G+  
Sbjct: 178 SHGDGRHNRIFRMQGIHRMLLHAERLAFAHPHGHRVEVRAPLDAQFVRAFGLFGWSA 234


>gi|310792938|gb|EFQ28399.1| RluA family pseudouridine synthase [Glomerella graminicola M1.001]
          Length = 476

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 62/289 (21%), Positives = 108/289 (37%), Gaps = 54/289 (18%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L   F++ +        +  + +G + V+ K V  ++ +++G +V         NH 
Sbjct: 80  GRKLIEIFEDEFRDRTLEYYRHAMETGAIVVNGKAVGPDHVVKNGDLV---------NHT 130

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I   +   +   +          +++ED ++ V +KP+G+ V       Y+    +    
Sbjct: 131 IHRHEPPVTGEPI---------RIIHEDDEMIVVDKPSGVPVHPAGRYKYNSLIEIMKAE 181

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
             +   P   HRLD+ TSGIL + +T  AA  LT   R   ++K Y + V G  P  +  
Sbjct: 182 RGEHFLPYPCHRLDRLTSGILFIGKTPQAAVKLTAQIRAHTVRKEYLARVAGKFPDGEVV 241

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA------------------- 237
           C    L     +G + V            A + FK +  +                    
Sbjct: 242 CDQPILQISPRLGLNRVRA------NGKSARTVFKRLAYYPPDKQDALPMEQPKTPEQLA 295

Query: 238 ----------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                     + +  +   P TGRTHQ+RVH   +G PI  D  Y    
Sbjct: 296 EEKRRPWIKKEGYSIVRCLPLTGRTHQIRVHLQFLGHPIQNDPLYANQR 344


>gi|167623992|ref|YP_001674286.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167354014|gb|ABZ76627.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 246

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 61/251 (24%), Positives = 99/251 (39%), Gaps = 32/251 (12%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
              + +        +  +L++D  + + NKP+G+    G   A      +   +      
Sbjct: 5   PPPADDFIAPPCLEEIEILFQDEHLLLINKPSGLLSLSGKNPAN--LDSVHYRLVKDFPG 62

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD  TSGI+V+AR +     L + F  R + K Y SL+ G   +    I   + 
Sbjct: 63  CTLVHRLDLGTSGIMVIARNKQINALLCKQFSERTVLKTYTSLLLGELSHDDGFIDAPIA 122

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK---------------------FCW 242
           K          ++K  +K    A S + V+   +                          
Sbjct: 123 KDKPN----FPLMKICDKEGKTARSLYHVLGLESYSSLDDDAPLLSTNEQAVDRSVSVTR 178

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-E 301
           +E  P TGRTHQLR+H+ + G PI+G   Y +         +  +L LHA  ++  HP  
Sbjct: 179 VEFIPQTGRTHQLRIHSQYFGHPIIGCDLYGSETSYR----LAPRLMLHATRLEFDHPIT 234

Query: 302 GGRLQITAPLP 312
           G R+   +P P
Sbjct: 235 GERIFANSPSP 245


>gi|157372174|ref|YP_001480163.1| pseudouridine synthase [Serratia proteamaculans 568]
 gi|157323938|gb|ABV43035.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 232

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 97/231 (41%), Gaps = 19/231 (8%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H    +  +LY+D  + + NKP G+    G          +   +  + 
Sbjct: 3   KIIDTFIAPPCHE---QIEILYQDESLVLINKPTGLLSLSGKNPQN--LDSVHHRLVQQF 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   + +  I   
Sbjct: 58  PGCTLIHRLDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLADNEGVIDAA 117

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTH 253
           + K   +      ++         A S ++VI+ F              +++ P TGRTH
Sbjct: 118 IAKDPAL----FPLMSICAIHGKPARSGYQVIERFYHELEDGTSLPLTRVQLTPETGRTH 173

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           QLR+H   +G PI+G   Y              +L LHA  +   HP    
Sbjct: 174 QLRIHCQQLGHPILGCDLYGGLLLPGTERT--PRLMLHASELHFVHPISQE 222


>gi|58037279|ref|NP_082316.1| RNA pseudouridylate synthase domain-containing protein 4 [Mus
           musculus]
 gi|81904256|sp|Q9CWX4|RUSD4_MOUSE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 4
 gi|12845681|dbj|BAB26852.1| unnamed protein product [Mus musculus]
 gi|38511726|gb|AAH61256.1| RNA pseudouridylate synthase domain containing 4 [Mus musculus]
 gi|74140035|dbj|BAE33761.1| unnamed protein product [Mus musculus]
 gi|148693444|gb|EDL25391.1| RNA pseudouridylate synthase domain containing 4 [Mus musculus]
          Length = 377

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 77/275 (28%), Positives = 121/275 (44%), Gaps = 38/275 (13%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   +L++D+ + V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKELSRRILHQDNDLVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGHKAEP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R+++K YW++   +P      +   + 
Sbjct: 146 LHLCHRLDKETTGVMVLAWEKDMAHQVQELFRTRQVEKKYWAITVRVPLPSAGVVDIPIK 205

Query: 204 KKSHIGGDYVH---------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G    H               V  +  + A+ A++ ++V    A     +E+QP 
Sbjct: 206 EKEVQGPQQHHKMTLSPSYRLDNGKMVKVRASRDAHVAVTQYQV-LSSASSSALVELQPV 264

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC------------ANFKGNFTSPIQNK---LYLHA 292
           TG  HQLRVH    + CPI+GDHKY                K       + +   L+LHA
Sbjct: 265 TGIKHQLRVHLSFGLDCPILGDHKYSDWTRLAPQKLSAGTLKKLGLQQSKARYIPLHLHA 324

Query: 293 RYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGFK 325
           R + LP        L +T  LP    ++   LG  
Sbjct: 325 RQLILPALGSRTEELLLTCKLPHFFARSLLRLGLD 359


>gi|318040646|ref|ZP_07972602.1| pseudouridine synthase [Synechococcus sp. CB0101]
          Length = 349

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 124/318 (38%), Gaps = 51/318 (16%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI--PPVINALNHIIKEQ 81
           ++   Y H +     + L +G+V  + + +  +  + +G  +    PP +     ++ E 
Sbjct: 36  FYAGRYTHSDRALWSERLAAGEVWRNGQPLLADAPLSAGDRLVWHRPPWLEPAVPVLNE- 94

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
                            + ++++D  + V NKP+G+ V    G   H    L + +    
Sbjct: 95  -----------------ASVVFDDGDLLVLNKPSGLPVLPAGGFLEH---TLLAQLQGWA 134

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR---------------------IQ 180
            + R  HRL + TSG+LV AR   +   L+   R                          
Sbjct: 135 PEARPVHRLGRFTSGLLVCARRAESRAWLSAQLRESTAAAQPHGDQEYFGAEEHPHSGCL 194

Query: 181 KIYWSLVWGIPKN----KKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDC 235
           KIY +L   +P +    +   +   + ++ H   G+       + + A  + S F +++ 
Sbjct: 195 KIYRALTQPLPADWQVGESRDVTTAIGRRPHPLLGEIWCAADVSPRAALPSRSCFTLLER 254

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT-SPIQNKLYLHARY 294
             +  C +E+   TGR HQ+R+HA  +G P+ GD  Y A  + +    P      LHA  
Sbjct: 255 RPES-CLVEVAIATGRPHQIRIHAAAIGAPLEGDPLYRAGGRADPQVLPGDGGYLLHACR 313

Query: 295 MDLPHPEGGRLQITAPLP 312
             L  P    L + AP P
Sbjct: 314 FVLRPPARAPLHLEAPPP 331


>gi|120610952|ref|YP_970630.1| tRNA pseudouridine synthase C [Acidovorax citrulli AAC00-1]
 gi|120589416|gb|ABM32856.1| tRNA pseudouridine synthase C [Acidovorax citrulli AAC00-1]
          Length = 277

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 98/238 (41%), Gaps = 18/238 (7%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           + L          +L +D  +    KPAG  V      A      +++  D  G++    
Sbjct: 1   MPLPNAPRHPPLAILRQDDDLVAVYKPAGWLVHRTGLDAGETRFVMQALRDQLGRRVYPV 60

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ T G+LV+     AA+ L+++F   R+ K Y +LV G   ++ +         + 
Sbjct: 61  HRLDKGTCGVLVMGLHAEAARALSQAFEQHRVDKRYLALVRGHAPDRVQVDHALRPDDAP 120

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-----CWLEMQPHTGRTHQLRVHALHM 262
                     Q  + A   ++  ++ +    +F       +E  P TGR HQ+R H  H+
Sbjct: 121 PD-----AAVQPARTALRCLARLELPEASDARFATTRASLVEALPETGRRHQIRRHLKHI 175

Query: 263 GCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGRLQITA------PLP 312
             PI+GD  +       + +      +L+LHA  + LPHP  G   +        PLP
Sbjct: 176 AHPILGDATHGKGPLNRWWAQRLGLQRLWLHAWRLALPHPATGETVVVDSGLRGGPLP 233


>gi|332298456|ref|YP_004440378.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332181559|gb|AEE17247.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 478

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 62/252 (24%), Positives = 99/252 (39%), Gaps = 45/252 (17%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQKPRLTHRLD 151
              L   ++Y D    V NKPAG+    G G          L+        +P   HRLD
Sbjct: 238 PVMLGIEIVYRDEHCIVLNKPAGLLSVPGRGEDKQDCAVHRLRRLYPDCIAQPS-VHRLD 296

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN------------------ 193
            +TSG+LV+A T  A + L+  F    + K Y +L+ G P+                   
Sbjct: 297 MDTSGLLVLALTADAHRCLSRQFMEGTVHKEYEALLRGKPRGAAAQSVCADRDGLCGFRA 356

Query: 194 -KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI--DCFAQKF------CWLE 244
            +   I         +  +       +       ++ +++I  +   ++         + 
Sbjct: 357 AESGRIELPF----RLDVENRPRQVFDPVYGKTGVTEWRLIGFERCGKETSSDGVLTRVR 412

Query: 245 MQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP- 300
             P TGRTHQLR+H++H   +G PI GD  Y    +G        +L LHA  +   HP 
Sbjct: 413 FTPLTGRTHQLRLHSMHPNGLGAPIRGDRLYGTRLEGE-------RLALHAALLSFTHPV 465

Query: 301 EGGRLQITAPLP 312
            G R+  T+ +P
Sbjct: 466 SGERMTFTSAVP 477


>gi|17231572|ref|NP_488120.1| ribosomal large chain pseudouridine synthase A [Nostoc sp. PCC
           7120]
 gi|17133215|dbj|BAB75779.1| ribosomal large chain pseudouridine synthase A [Nostoc sp. PCC
           7120]
          Length = 549

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 108/233 (46%), Gaps = 21/233 (9%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           S +  T++ +  +  ++YED  +   NKP+G+    G  I    D  L        ++  
Sbjct: 329 SGLKPTRNLEKEQINVIYEDEWLIAVNKPSGLLSVPGRYID-TQDSVLSRLRHMLPEEEM 387

Query: 146 L--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           L   HRLDQ+TSGIL++AR     +  ++ F+ R++ K+Y +++ G+       I   L 
Sbjct: 388 LAAVHRLDQDTSGILLLARDSQTYRQFSQQFQQRQVYKVYEAILAGVINTDTGIIDLPLW 447

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL--- 260
                   Y  V  Q       ++++F+ I      +  +E  P TGRTHQLRVHA    
Sbjct: 448 GD-PENRPYQQVDWQR---GKPSVTNFREIAREGD-YTRVEFVPLTGRTHQLRVHASDVQ 502

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
            +G  I+GD  Y    K        N+L+LHAR +   HP  G+   L I  P
Sbjct: 503 GLGVVILGDRFYGCTAKA-------NRLHLHARELSFLHPRSGKTIHLHIKTP 548


>gi|325285555|ref|YP_004261345.1| pseudouridine synthase [Cellulophaga lytica DSM 7489]
 gi|324321009|gb|ADY28474.1| pseudouridine synthase [Cellulophaga lytica DSM 7489]
          Length = 287

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 74/313 (23%), Positives = 129/313 (41%), Gaps = 48/313 (15%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHIN-FVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M  ++  +    +E +R   +    +  I+    L+K ++ G + +D+K+      I   
Sbjct: 1   MITIETHIAVTQKEPIRFQDYGTGIFTGISTKSALKKAIKKGLIYIDEKKASTGTFIYGS 60

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + +                       N TK    LK  ++++D+ + + NKP GI V G 
Sbjct: 61  EKITFN----------------KPEENNTKKRLNLKLEVVFQDNYLAIINKPPGILVSGN 104

Query: 123 --SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               I   ++  +         KPR  HRLD  T+G+L++ +T A+   L + F  ++IQ
Sbjct: 105 TFKTIDNALEQNITKSSLPDATKPRPVHRLDFPTTGLLIIGKTSASILALNKLFENKKIQ 164

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--- 237
           K Y ++  G            ++KK  I  +  +           A + + V+       
Sbjct: 165 KTYLAVTIGE-----------MIKKGTINTNVDN---------KEAFTTYNVLKTVTSNK 204

Query: 238 -QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 ++++P TGR HQLRVH   +  PI+GD KY    K          LYLHA  +D
Sbjct: 205 FNYLNLVKLEPKTGRKHQLRVHLSSINNPILGDAKYGIPGKIIKG----KGLYLHAYSLD 260

Query: 297 LPHPEG-GRLQIT 308
             HP    ++ +T
Sbjct: 261 FTHPFTNKKISVT 273


>gi|241574172|ref|XP_002403064.1| ribosomal pseudouridine synthase, putative [Ixodes scapularis]
 gi|215502139|gb|EEC11633.1| ribosomal pseudouridine synthase, putative [Ixodes scapularis]
          Length = 443

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 75/318 (23%), Positives = 131/318 (41%), Gaps = 42/318 (13%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL-------TKHSDFLKSIL 101
           D K      +  +   +R     +++    K  +IL S +         T+  D L+ ++
Sbjct: 125 DGKPPDSEEQQTAYDYLRRESPPSSVKLDSKGFRILKSEIRPDLSRLLHTEAVDLLRKLV 184

Query: 102 LYEDSKIYVFNKPAGISVQ-GGSGIAYHID------GFLKSWVDSKGQKPRLTHRLDQET 154
           LY D+ I V NKP G+       G++              +    +  K    HRLD++ 
Sbjct: 185 LYNDNDILVLNKPYGMLCHGPAPGVSDACVLTKLLPDLSSALYPRQDAKLYTVHRLDRDV 244

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV- 213
           +G+L++ART+  A  L   F+  ++ K Y ++  G+P + +  I   L +    G   + 
Sbjct: 245 TGVLLLARTQRMADMLNSLFQKHQVSKTYLAITAGVPDHLEGVIDMPLAEGEVEGAKRMV 304

Query: 214 ---------HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA-LHMG 263
                      +    + +  A++ ++V+    +     E++P TG  HQLR H  L + 
Sbjct: 305 LNPKLDPEFQRLVPKFRKSFAAVTTYRVLASCGRAGYL-ELRPTTGVKHQLRAHLGLGLR 363

Query: 264 CPIVGDHKYCA-------NFKGNFTSPIQNK--------LYLHARYMDLPHPEGGR-LQI 307
           CPI+GDHKY            G+    +  +        L+LHAR + +P    GR L +
Sbjct: 364 CPILGDHKYSHLRRLAPQKLPGDMLDRLGIRQSKVRDAPLHLHARAVVVPEILDGRNLTV 423

Query: 308 TAPLPAHMVKTWDSLGFK 325
            A +P H  K    L   
Sbjct: 424 AAEVPYHFAKNLRRLKLN 441


>gi|118362444|ref|XP_001014449.1| pseudouridine synthase, RluD subfamily protein [Tetrahymena
           thermophila]
 gi|89296216|gb|EAR94204.1| pseudouridine synthase, RluD subfamily protein [Tetrahymena
           thermophila SB210]
          Length = 446

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 65/262 (24%), Positives = 109/262 (41%), Gaps = 25/262 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
             +  +        Q  +  G++ V+K++   + R +   +                 ++
Sbjct: 44  VLEKEFHAYTKEYYQNAIEKGKILVNKQKQNIDYRFKHNDLFEHFTS-----------RV 92

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
               +NL          +++ED K+ V +KP  ISV    G  ++    L  +      +
Sbjct: 93  EPPIINLLPK-------VIFEDDKLLVLSKPPYISVHASGGFHFNSLVGLLKFEMGYNIE 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLD+ TSG+L++A+ R   +   ES     I+K Y + V G   ++       + 
Sbjct: 146 LYVLHRLDKLTSGVLIMAKDRDLTKKFHESETE-LIKKTYLARVHGNFNHQYLEYEKPIY 204

Query: 204 KKSHIGGDYVHVVKQNE-----KGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRV 257
                 G Y  +   +E     KGA  + + FK I    +     LE QP TGRTHQ+RV
Sbjct: 205 CIYKKVGTYAVLDTTDEEEIKSKGAKQSKTIFKKIWYDEKSDSSLLECQPITGRTHQIRV 264

Query: 258 HALHMGCPIVGDHKYCANFKGN 279
           H   +G PI+ D +Y   F GN
Sbjct: 265 HLSSLGFPIINDTQYGGQFLGN 286


>gi|163755956|ref|ZP_02163073.1| hypothetical protein KAOT1_11066 [Kordia algicida OT-1]
 gi|161324127|gb|EDP95459.1| hypothetical protein KAOT1_11066 [Kordia algicida OT-1]
          Length = 300

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 67/297 (22%), Positives = 111/297 (37%), Gaps = 57/297 (19%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           ++ ++ K       I    V+ I      +  I K                 L   +++E
Sbjct: 43  RILINNKIATTATFISENDVIEIYAEETIVKKIFK-----------------LVISVIFE 85

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG----QKPRLTHRLDQETSGILVV 160
           D +I + NKPAG     G+      +    +   S        P+  HRLD  TSGIL++
Sbjct: 86  DDEIAIINKPAGFPT-NGNYFKTIENALPHNLKPSNSIDALPFPKPVHRLDNPTSGILII 144

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+T++A   L + F  + I K Y ++V G    + E  +                     
Sbjct: 145 AKTKSAQISLYQQFEQQEISKTYQAIVIGKTDKEGEITSAV------------------- 185

Query: 221 KGANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                A+++++ +   +         +++ P TGRTHQLR+H   +  PIVGD  Y    
Sbjct: 186 -AEKEALTNYETLQTVSSLQNGHLSLVKLFPKTGRTHQLRIHLASINHPIVGDQLYG--- 241

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDS-----LGFKYD 327
                   +  L+L A  + L HP+   +L  T   P              L F+ D
Sbjct: 242 --KAEENYKKGLFLCATSIQLIHPKTKEKLVFTIHPPNKYKSLLAREEKRFLKFRID 296


>gi|116749359|ref|YP_846046.1| pseudouridine synthase [Syntrophobacter fumaroxidans MPOB]
 gi|116698423|gb|ABK17611.1| pseudouridine synthase [Syntrophobacter fumaroxidans MPOB]
          Length = 304

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 72/326 (22%), Positives = 128/326 (39%), Gaps = 43/326 (13%)

Query: 1   MSLM----TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN 56
           M+ M            +   +   L R    +   I+    + ++  G V +D +  +  
Sbjct: 1   MTPMDFRIPDTDRWTADPALKGTGLARLIARYLL-ISEDRAEDLIDFGSVYIDGRVERNP 59

Query: 57  NR-IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
            R ++ G+ + +    +                    H +   + +LY D+ +  ++K A
Sbjct: 60  ARTLRGGEEIVVNWPRHGTQR----------------HYEIDPARILYRDAHLLAYDKEA 103

Query: 116 GISVQGGSGIAYHID-----GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           G+  Q     AY+        FL     +      L HRLD+ETSG++V A  RA  + L
Sbjct: 104 GVPSQQTPADAYNNLYAALIRFLAGEARASAPYVALHHRLDRETSGVMVFALDRAVNRRL 163

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            ESF+ +R+ K Y + V G+P      +  W   +     D  +      +G   A +  
Sbjct: 164 GESFQEKRVVKDYLAWVDGVP-----VLDRWTAVEDICRKDGRYRTCPQGRG-KAARTLL 217

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           +V+     +   +  +P TGRTHQ+R+H    G P++GD  Y                  
Sbjct: 218 RVLLRAGDRA-LIAARPVTGRTHQIRLHLAACGHPVIGDRLYGGTSGERLHLHAL----- 271

Query: 291 HARYMDLPHPEGG-RLQITAPLPAHM 315
               + LPHP+    L ++AP+P + 
Sbjct: 272 ---RLRLPHPKHDSELVLSAPVPEYW 294


>gi|121604183|ref|YP_981512.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120593152|gb|ABM36591.1| ribosomal large subunit pseudouridine synthase A [Polaromonas
           naphthalenivorans CJ2]
          Length = 233

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 61/214 (28%), Positives = 95/214 (44%), Gaps = 11/214 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++ D  + V NKPAG+    G G        L   V S      + HRLD  TSG++++
Sbjct: 24  IIHADDSLLVLNKPAGLLAVPGRG--EDKQDCLSRRVQSLYPDALIVHRLDMATSGLMLM 81

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ-- 218
            R  A  + L + F  R + K Y ++V G      E    W L    I  D+     +  
Sbjct: 82  GRGIAMQRALGQLFERREVYKRYLAVVDGRLAPAPEP-GGWGLIDLPIAVDWPRRPLRII 140

Query: 219 NEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +      + + ++ +   A      +E++P TGR+HQLRVH   +G PI+GD  Y     
Sbjct: 141 DAASGKPSQTRWRSVAFDAAANSTRVELEPLTGRSHQLRVHLQALGHPILGDALYAPEAV 200

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
               +    +L LHA  + L HP  G  L + +P
Sbjct: 201 QARAA----RLLLHACALRLLHPASGALLSVESP 230


>gi|300770686|ref|ZP_07080565.1| tRNA pseudouridine synthase C [Sphingobacterium spiritivorum ATCC
           33861]
 gi|300763162|gb|EFK59979.1| tRNA pseudouridine synthase C [Sphingobacterium spiritivorum ATCC
           33861]
          Length = 230

 Score =  152 bits (384), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 103/242 (42%), Gaps = 28/242 (11%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY+D +I   NKP G+ V          +  L+   D   Q+    HRLD++T GIL
Sbjct: 2   LDILYQDQEIVAINKPHGLLVHRSPIARDASEFALQLLRDQLQQRVYPAHRLDRKTGGIL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + + T+   + L + F+ R++ K Y ++V G  ++  +   N+ LKK +           
Sbjct: 62  LFSLTKEMDKSLQQLFQDRKMNKSYLAVVRGYTEDDGQI--NYPLKKDN----------- 108

Query: 219 NEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                  A++H+K +               ++  +E  P TGR HQLR H  H+  PI+G
Sbjct: 109 --GEEQEALTHYKTLSRSEIDLPTGNFTTSRYSLVEANPETGRMHQLRKHFAHIFHPILG 166

Query: 269 DHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGFK 325
           D  +  N +          + + LHA  +   HP  G +  I APL     +    L  +
Sbjct: 167 DRPHGCNKQNKLWKERFEMDTMMLHASQLSFEHPTTGNIVHIKAPLQPEFERVLSILKLE 226

Query: 326 YD 327
             
Sbjct: 227 SP 228


>gi|255071781|ref|XP_002499565.1| predicted protein [Micromonas sp. RCC299]
 gi|226514827|gb|ACO60823.1| predicted protein [Micromonas sp. RCC299]
          Length = 318

 Score =  152 bits (384), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 63/265 (23%), Positives = 109/265 (41%), Gaps = 35/265 (13%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--- 143
           S       +      L+ED  + V +KPAG+               +++ +D+ G +   
Sbjct: 59  SPERVDADEGENVRTLWEDEHLAVVSKPAGMLTHPNEASGGATRTLVEALLDAFGDEGLS 118

Query: 144 -------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                    + HRLD+ TSG ++VA+T  A      ++  R++ K Y +LV G+P  ++ 
Sbjct: 119 AINGADARGIVHRLDKPTSGAMLVAKTDLAHAMCVAAWYQRKVTKTYLALVEGVPGRRRG 178

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPH 248
                   +    GD +            A S ++V++ F ++           +E+ P 
Sbjct: 179 R-------RRGDDGDAMEGTCVAPADGRPARSDWRVVETFGEEDGDDAEQLCSLVEVTPR 231

Query: 249 TGRTHQLRVHA-LHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPH 299
           TGR HQ+R H  + +  P+VGD  Y    + N  +           + L+LH+  + L H
Sbjct: 232 TGRRHQIRQHMGMALDAPLVGDPLYRRGKRPNTPATAAPFLVGKPGSVLFLHSAALALRH 291

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLG 323
           P  G  L  + PLPA       +L 
Sbjct: 292 PVTGEALSFSDPLPAAFEGLVSALR 316


>gi|210616986|ref|ZP_03291321.1| hypothetical protein CLONEX_03543 [Clostridium nexile DSM 1787]
 gi|210149509|gb|EEA80518.1| hypothetical protein CLONEX_03543 [Clostridium nexile DSM 1787]
          Length = 227

 Score =  152 bits (384), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 58/219 (26%), Positives = 100/219 (45%), Gaps = 15/219 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKGQKPRLTHRLD 151
           +   +L+ED+ + V  KPAG+  Q     +  +   LK+++     + K     + HRLD
Sbjct: 1   MNLKILFEDTHVIVCYKPAGVPTQTSKIGSQDMVSILKNYLYKNQKEKKEPYVAVIHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q   GILV  +T  AA+ L+   +     K Y ++V G  + K   + ++++K   +   
Sbjct: 61  QPVEGILVFGKTPFAAKELSAQMQGAGFGKYYQAVVCGKFEEKSGKLEHYMVKDGRVNLS 120

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              V   + K A  A+  ++V +   +       + ++  TGR HQ+RV     GCPI G
Sbjct: 121 K--VCDPSIKDAKRAVLFYEVEEEGLEDGEERSLVNIKLETGRHHQIRVQMAAAGCPIWG 178

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           D KY         S  + K+ L A +++  HP+     I
Sbjct: 179 DAKYNEK-----QSNGRRKIALCASHLEFLHPKTKEKMI 212


>gi|328774056|gb|EGF84093.1| hypothetical protein BATDEDRAFT_8379 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 379

 Score =  152 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 109/263 (41%), Gaps = 27/263 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            M +   F   +        ++ +  G+++++ K V  +  I++  +V            
Sbjct: 25  GMTVFEVFSKEFHDRPAEVYRQAILKGRIKINGKAVPLDYVIRNSDLVENTVHR------ 78

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E  I D+ +            ++++   + V NKP+ I V       Y+    L  + 
Sbjct: 79  -HEPVITDTPIE-----------IVHQSDSVLVVNKPSSIPVHPTGRYRYNTVIHLLEY- 125

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           ++K     L +R+D+ TSG++++AR +  A ++ +  R RRI K Y + V G  P +  E
Sbjct: 126 ENKMNDLFLVNRIDRLTSGLVLIARDKNKAAYMMQEMRERRIHKTYLARVKGEFPADAIE 185

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C       +  +G + V              + FK +         ++ +P TGRTHQ+R
Sbjct: 186 CHEPIETVEFKVGVNIV------SPTGKPCSTLFKRLSYNGL-TSVVQCEPLTGRTHQIR 238

Query: 257 VHALHMGCPIVGDHKYCANFKGN 279
           VH   +G PI  D  Y  +  G 
Sbjct: 239 VHLQFLGHPIANDPIYGCSEWGK 261


>gi|326795397|ref|YP_004313217.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326546161|gb|ADZ91381.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
          Length = 250

 Score =  152 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 59/244 (24%), Positives = 108/244 (44%), Gaps = 21/244 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKP+G+ V         ++  ++   D  GQ+    HRLD+ TSG+L++
Sbjct: 4   ILYQDDFLVAVNKPSGLLVHRTELARGEMEAAVQLLRDQIGQRVYPVHRLDRGTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
                +A  L E F  R ++K Y +LV G   +    I   L K   +  +      + E
Sbjct: 64  TLDSESASQLGEQFMNREVKKEYSTLVRGHI-HDSGSIDYPLAK---LNEEKGRSRFKIE 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                 +SH+++I+            + +   ++++P  GR HQ+R H  H+  P++GD 
Sbjct: 120 GTEQECVSHYELIEKYTVPIPVSKYPSTRLSHIKVRPEQGRKHQIRRHFKHVFHPLIGDT 179

Query: 271 KYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR-LQITAP---LPAHMVKTWDSLG 323
           +Y      +      N   +L LH+  + + HP+ G  L IT+    +    +   +   
Sbjct: 180 RYGCRHCNHVFRETYNPDLRLMLHSASLTVTHPKSGDNLTITSDNRGVFDDFLAFIEPYA 239

Query: 324 FKYD 327
            K+ 
Sbjct: 240 LKHS 243


>gi|88705946|ref|ZP_01103654.1| ribosomal large subunit pseudouridine synthase A [Congregibacter
           litoralis KT71]
 gi|88699660|gb|EAQ96771.1| ribosomal large subunit pseudouridine synthase A [Congregibacter
           litoralis KT71]
          Length = 233

 Score =  152 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 100/243 (41%), Gaps = 15/243 (6%)

Query: 74  LNHIIKEQKILDSSVNLTK---HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +N     ++    S  L             ++Y D  + +  KP  +    G        
Sbjct: 1   MNTPPAPEETSGDSQELPPYIVPHSPEPVRVIYVDESLLLIRKPDLLLSVPGRHPLNR-- 58

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             + + +        + HRLD +TSGI++VAR +     L+  F+ R + K Y + V G 
Sbjct: 59  DCMITRLQEHYPDALVVHRLDLDTSGIMMVARGKTTQGALSRLFQERAVDKRYRAWVAGS 118

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             + +  I   + +      +   + K   +    ++++FKV+D        LE+QP TG
Sbjct: 119 VSDDEGKIELPIARD----WENRPLQKICAETGKKSLTYFKVLDRQNGN-SLLELQPATG 173

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TA 309
           RTHQLR+H   MG PI+G   Y              +L LHA  +  PHP  GR  +   
Sbjct: 174 RTHQLRIHCREMGHPILGCDMYAPP----AVLGAAPRLMLHATRIAFPHPVSGRKLVGHC 229

Query: 310 PLP 312
           P P
Sbjct: 230 PAP 232


>gi|167768426|ref|ZP_02440479.1| hypothetical protein CLOSS21_02985 [Clostridium sp. SS2/1]
 gi|317499212|ref|ZP_07957487.1| RNA pseudouridylate synthase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167709950|gb|EDS20529.1| hypothetical protein CLOSS21_02985 [Clostridium sp. SS2/1]
 gi|316893526|gb|EFV15733.1| RNA pseudouridylate synthase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 236

 Score =  152 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 63/221 (28%), Positives = 98/221 (44%), Gaps = 13/221 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----SKGQKPRLTHRLDQ 152
           K  ++Y+D +I V  KP GI V         +   LK+ +          +  L HRLD+
Sbjct: 6   KINIIYKDDQIVVCEKPKGIPVSSDKTGDMDLLHQLKNQLFFEENTDGEPQLYLVHRLDR 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              G++V ART+ AA  LTE  +    +K Y +++ G   + +    ++LLK        
Sbjct: 66  PVGGVMVFARTKKAAASLTEQIKDHTFEKDYQAVLTGWLPDDEGTFRDYLLKDPKNNVSK 125

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             +VK+   GA  AI  ++VID       K+ +  +   TGR HQ+RV     G  I GD
Sbjct: 126 --IVKEGTPGAKEAILDYEVIDMMEDSKMKYTYCLIHLETGRHHQIRVQTSSRGFGIWGD 183

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
            KY   ++       +  L+  A  +   HP  G R+   A
Sbjct: 184 TKYNPIYQKTKKKYKEIGLF--AARIAFEHPTTGERMVFKA 222


>gi|75764813|ref|ZP_00744194.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|74487697|gb|EAO51532.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
          Length = 192

 Score =  152 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 40/185 (21%), Positives = 79/185 (42%), Gaps = 21/185 (11%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N R+D++        +   +Q+ ++   V V+ K VK N +++    + +          
Sbjct: 15  NERIDKFVAGINNEWSRSQVQQWIKDDVVTVNGKAVKVNYKVKEEDEITVT--------- 65

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKS 135
                 +     L    + +   + YED+ + V NKP G+ V    G      ++G +  
Sbjct: 66  ------IPDPEALDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHH 119

Query: 136 WVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             D  G     +P + HR+D++TSG+L+VA+   A + L      + + + Y ++V G+ 
Sbjct: 120 CTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLLNQLVAKTVTRRYKAIVHGVI 179

Query: 192 KNKKE 196
              K 
Sbjct: 180 PLIKG 184


>gi|308806025|ref|XP_003080324.1| RNA pseudouridylate synthases (ISS) [Ostreococcus tauri]
 gi|116058784|emb|CAL54491.1| RNA pseudouridylate synthases (ISS) [Ostreococcus tauri]
          Length = 434

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 66/255 (25%), Positives = 104/255 (40%), Gaps = 44/255 (17%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSK------GQK 143
           +H D +   +LY+D  I    KPAG+      G A    +D  L  + D+         K
Sbjct: 195 EHPDLVNLRVLYDDGSIAAVFKPAGVLTHPAEGGAATSLMDAALARFGDTGLSDLNGSDK 254

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             +  RLD+ TSG++++AR  AA   L   F  RR+ K Y  LV G P +++  +   + 
Sbjct: 255 RGIVSRLDKPTSGVILLARHNAAHAKLVTDFYQRRVSKTYIVLVDGAPTDERGTVTAPID 314

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC---WLEMQPHTGRTHQLRVHAL 260
            +                    A S +KV++ F    C    + ++P +GR HQ+R H  
Sbjct: 315 DR-------------------PATSEYKVLERFNSASCSYALVRVKPKSGRKHQIRRHMA 355

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNK-------------LYLHARYMDLPHPEGGRLQI 307
            +GCP+VGD  Y         +                   +LHA  ++    +G  + +
Sbjct: 356 MIGCPLVGDTVYRKGRAKTLNAKPPACVAEVLSHGKPGTIFFLHACEVEFE-TDGKIITV 414

Query: 308 TAPLPAHMVKTWDSL 322
            APL A      D L
Sbjct: 415 EAPLAAEFETLVDRL 429


>gi|225443375|ref|XP_002267010.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 479

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 74/288 (25%), Positives = 128/288 (44%), Gaps = 38/288 (13%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-----VDK------------KRVKFNNRIQSGQVVR 66
           W K ++  I    +Q     G V      +D             +++K N  +++G  + 
Sbjct: 86  WIKYYFDEIPGSVVQSHFNKGLVHMERSNLDDSSLEKEGQIKPLRKIKPNEVMEAGTRIY 145

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +P  +       +   I   +++      ++L+ ++ Y+D  I V NKP  + ++G   +
Sbjct: 146 VPVSVAEARISKRFDTIPSGTLHPNADEIEYLQRLVTYKDPAILVLNKPPKVPLKGNLPV 205

Query: 126 AYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRM-------- 176
              +D    + +    ++ P+L HRLD+E+SG+L++ RT+ +  HL   F          
Sbjct: 206 HNSMDALAAAALTFDYEEGPKLVHRLDRESSGLLLMGRTKESVAHLHWLFSDINKAKSLS 265

Query: 177 -------RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG---ANYA 226
                      + YW+LV G PK K+  I   L K     G    V+  N+ G   +  A
Sbjct: 266 KAWDDACEATCQRYWALVIGSPKQKEGVIHAPLSKVLLDDGKTERVILANQSGLEASQEA 325

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYC 273
           I+ ++V+        W+E+ P T R HQLRVH    +G PIVGD+KY 
Sbjct: 326 ITEYRVLGPMINGCSWIELCPRTSRKHQLRVHCAEALGTPIVGDYKYG 373


>gi|116071041|ref|ZP_01468310.1| putative pseudouridylate synthase [Synechococcus sp. BL107]
 gi|116066446|gb|EAU72203.1| putative pseudouridylate synthase [Synechococcus sp. BL107]
          Length = 219

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 60/208 (28%), Positives = 93/208 (44%), Gaps = 9/208 (4%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +LY D  +   +KP+G+  Q G G         +     +    RL HRLD++TSG+L
Sbjct: 6   VRVLYRDRWLLAVDKPSGLLSQPGLGPDQADSLISRVQAHDQAPDWRLVHRLDRDTSGVL 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A    A +  +  F  R + K+Y + V G+   +  CI N L +       Y      
Sbjct: 66  VLAAGLEALRRTSALFSNRCVNKLYLAHVHGVLAGR-GCIHNRLARLQRQPPRY-----G 119

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      A + ++V    A+      ++P TGR+HQLR H   +  PI+GD  Y     G
Sbjct: 120 SHPEGREASTLWRVRSSAAEVTQLW-LRPITGRSHQLRSHLAEIAHPIIGDPIYGDPIDG 178

Query: 279 N--FTSPIQNKLYLHARYMDLPHPEGGR 304
           +    SP   +L LHA  +   HP  G+
Sbjct: 179 DQAAESPFSQRLRLHAIALSFCHPFTGQ 206


>gi|34556846|ref|NP_906661.1| putative ribosomal pseudouridine synthase [Wolinella succinogenes
           DSM 1740]
 gi|34482561|emb|CAE09561.1| PUTATIVE RIBOSOMAL PSEUDOURIDINE SYNTHASE [Wolinella succinogenes]
          Length = 308

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 71/290 (24%), Positives = 123/290 (42%), Gaps = 43/290 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +    +  I+    QK +  G+VR+  +                 P ++    +  E ++
Sbjct: 19  FLMREFS-ISQKEAQKWIDKGRVRIQGE-----------------PFLDKSARVSGELEV 60

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                 L    D      L+      +F+KPA + V       ++    +       GQ+
Sbjct: 61  ------LFFRPDSRGLEPLFIAPFFALFDKPADLLVHPKGTFEHY--SLMDEVRLRFGQE 112

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HR+D+ETSGI+++ R++     L  +F  R ++K YW+LV G  K + E I ++ L
Sbjct: 113 ADLAHRIDKETSGIVLITRSKKEGAILKINFFNREVKKCYWALVRG--KMEGERILDFPL 170

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHM 262
           K      D    ++ +EKG   +++  K +D  A      +E  P TGRTHQ+R+H  H 
Sbjct: 171 KAQSKRLDLGVRMRVDEKG-KSSLTQIKALDYEALSDTTLVEASPLTGRTHQIRLHLAHA 229

Query: 263 GCPIVGDHKYCA-------------NFKGNFTSPIQNKLYLHARYMDLPH 299
           G PI+GD  Y               + +        ++L LHA+ +  P+
Sbjct: 230 GYPILGDPLYGTSDELSRAYLEQAMDQEERRRCFGASRLMLHAQGLGFPY 279


>gi|319762874|ref|YP_004126811.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|330824953|ref|YP_004388256.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
 gi|317117435|gb|ADU99923.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|329310325|gb|AEB84740.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
          Length = 225

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/216 (26%), Positives = 95/216 (43%), Gaps = 9/216 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
              +       ++ D  + V +KPAG+    G G        L +   +      + HRL
Sbjct: 5   PPRAAHAGVDHVHADDTLLVLDKPAGLLCVPGRGPD--KQDSLSTRAQALWPDALIVHRL 62

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           DQ TSG++++AR  A  + L+ +F  R + K Y ++V G+ +  +     W      I  
Sbjct: 63  DQPTSGLVLMARGGAMQRALSHAFAQRLVHKRYQAVVAGLLRPARGSAGEWSEIALPIAA 122

Query: 211 DYVHV--VKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           D+        +      +++ ++V+    A     +E++P TGRTHQLRVH   +G PI+
Sbjct: 123 DWERRPLRVVDAGRGQASLTRWRVLAHDEAGGTTRVELEPVTGRTHQLRVHLAALGHPIL 182

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           GD  Y        T     +L LHA  +   HP  G
Sbjct: 183 GDALY----ADAATQARAPRLLLHACALGFGHPLHG 214


>gi|82751504|ref|YP_417245.1| RNA pseudouridylate synthase [Staphylococcus aureus RF122]
 gi|82657035|emb|CAI81472.1| probable RNA pseudouridylate synthase [Staphylococcus aureus RF122]
          Length = 273

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/264 (21%), Positives = 106/264 (40%), Gaps = 32/264 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +   V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTDDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  + +  KP G+         +  +   +   VDS   +P   HRLDQET G+L+VA
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHVIYTVDSDYVEP--IHRLDQETVGLLIVA 135

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +     + L        I +IY + V  +   K + I   + K       +    ++   
Sbjct: 136 KNPLMKKILDRMLEDNDITRIYKANVKALLPLKPQTIDMPIGKD-----KFHSNKRRVSP 190

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               AI+H        +  C LE++  TGRTHQ+RVH   +G P++GD  Y  +      
Sbjct: 191 TGQRAITHILTSKMIKETVCQLEIKLDTGRTHQIRVHLAEIGHPVIGDPLYGDS------ 244

Query: 282 SPIQNKLYLHARYMDLPHPEGGRL 305
                +L L +  ++  HP    +
Sbjct: 245 --TLRQLELESYKIEFVHPLTKEV 266


>gi|332160263|ref|YP_004296840.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|318607167|emb|CBY28665.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325664493|gb|ADZ41137.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|330863027|emb|CBX73159.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica W22703]
          Length = 196

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 61/205 (29%), Positives = 94/205 (45%), Gaps = 15/205 (7%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V NK +G+    G   A      + + + +        HRLD  TSG++VVA T+AA +
Sbjct: 1   MVVNKASGLLSVPGR--APENKDSVMTRIQADFPSAESVHRLDMATSGVIVVALTKAAER 58

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYA 226
            L   FR R  +K Y + VWG     +  I   L+       D+ +  KQ    +    +
Sbjct: 59  ELKRQFREREPKKSYVARVWGHLAQDEALIDLPLI------CDWPNRPKQKVCYETGKSS 112

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
            + ++V+   A     +++ P TGR+HQLRVH L +G PI+GD  Y         S    
Sbjct: 113 QTQYQVLSRDADGSTRVKLSPITGRSHQLRVHMLAIGHPILGDGFYAHPEAKAMAS---- 168

Query: 287 KLYLHARYMDLPHPEGGR-LQITAP 310
           +L LHA+ + + HPE G  +     
Sbjct: 169 RLQLHAQELCITHPEFGTVMHFKCE 193


>gi|330861063|emb|CBX71332.1| ribosomal large subunit pseudouridine synthase C [Yersinia
           enterocolitica W22703]
          Length = 200

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 61/188 (32%), Positives = 97/188 (51%), Gaps = 6/188 (3%)

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             +  + +   L HRLD++TSG+L+VA+ R+A + L E  R++ +QK Y +LV G  ++ 
Sbjct: 6   RALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRLKGMQKDYLALVRGQWQSH 65

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + +   LLK     G+ +  V         + + FK+ + F +    ++  P TGRTHQ
Sbjct: 66  CKAVQAPLLKNIMQSGERMVKVSSE---GKPSETRFKIEERF-EHATLVKASPITGRTHQ 121

Query: 255 LRVHALHMGCPIVGDHKYCAN-FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +RVHALH G PI  D +Y    F         ++L+LHA  +   HP  G  ++I APL 
Sbjct: 122 IRVHALHAGHPIAFDDRYGDREFDSQLQGTGLHRLFLHAAALRFEHPNTGETMRIEAPLD 181

Query: 313 AHMVKTWD 320
             +   W 
Sbjct: 182 NQLRIAWR 189


>gi|289550433|ref|YP_003471337.1| Putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus lugdunensis HKU09-01]
 gi|289179965|gb|ADC87210.1| Putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus lugdunensis HKU09-01]
          Length = 278

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 65/299 (21%), Positives = 117/299 (39%), Gaps = 44/299 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  D  N+ L   F+     +   +L ++  S ++ ++    + +N++ +   V IP   
Sbjct: 5   IPEDYNNLTLREIFQTL--KVPKKDLHQLNMSKEITINNAPARLSNQVHTMDCVEIPTDE 62

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-----GSGIA 126
              N++                  +  + + YED  + +  KP G+          + + 
Sbjct: 63  EKSNYL----------------PSYRYAQIYYEDDDLAIVMKPKGVKTHPNDLKESNTLM 106

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            HI   L S      +     HRLDQET G+L++A+     + L       +I +IY + 
Sbjct: 107 NHIIYTLDS------EYAEPIHRLDQETVGLLIIAKNPLMKKILDRMLEDNKITRIYKAN 160

Query: 187 VWGIPKNKKECIANWLLKKS-HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           V  +   K + I   + K   H     +            AI+H        +  C L++
Sbjct: 161 VNALLPIKPQTIDMPIGKDKFHPNKRRI------SNTGQRAITHILASTMLKEGVCQLDI 214

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +  TGRTHQ+RVH   +G P++GD  Y  +           KL L +  +D  HP   +
Sbjct: 215 KLDTGRTHQIRVHLAEIGHPVIGDPLYGDSK--------LRKLELKSYQIDFVHPLTQQ 265


>gi|196004434|ref|XP_002112084.1| hypothetical protein TRIADDRAFT_1807 [Trichoplax adhaerens]
 gi|190585983|gb|EDV26051.1| hypothetical protein TRIADDRAFT_1807 [Trichoplax adhaerens]
          Length = 418

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 96/239 (40%), Gaps = 25/239 (10%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
            +++G++ V+ K    N  ++   V+R             E  +  + + + K       
Sbjct: 59  AIQNGKITVNNKIPSANTIVRDNDVIRNTVHR-------HEPPVTANPIQIIKM------ 105

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
                D  I V NKPA I V       ++   F+ +  D   Q     HRLD+ TSGIL+
Sbjct: 106 -----DDDIVVINKPASIPVHPCGRYRHNSVVFMLAR-DYGLQNLHTIHRLDRLTSGILI 159

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            ART   AQ L +  R R+I+K Y   V G    +       +   SH  G     V + 
Sbjct: 160 FARTLQKAQELEKQVRDRQIEKQYVCRVDGEFPTETIDCKEPIDVVSHKLG-----VCRV 214

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                   + F+ +     K   ++  P TGR HQ+RVH   +G PIV D  Y     G
Sbjct: 215 SPKGKSCQTIFQRLSYNG-KTSLVKCIPLTGRMHQIRVHLQWLGYPIVNDPIYNHEAWG 272


>gi|328786842|ref|XP_624656.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Apis mellifera]
          Length = 535

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 59/255 (23%), Positives = 114/255 (44%), Gaps = 25/255 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             ++   F   +        ++ +R+G + V+ ++V  + R++   +         L ++
Sbjct: 136 GEKILEVFAREFRAHPAEEYERCIRAGTLTVNYQKVDVDYRLRHNDL---------LANV 186

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +   ++  +S  +T         +++ D  + V NKPA I V       ++   F+ +  
Sbjct: 187 VHRHEVPVTSEPIT---------VIHMDEDVVVVNKPASIPVHPCGRYRHNTVVFILA-K 236

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +   +  R  HRLD+ TSGIL+  RT   A+ +    R R++ K Y   V G    ++  
Sbjct: 237 EYNLKNLRTIHRLDRLTSGILLFGRTPKKARQMEHQIRNRQVHKQYVCRVEGEFPEEEVV 296

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            +  +   S+     + V K +EKG    ++ FK +    +    +  +P TGR HQ+RV
Sbjct: 297 CSEPIEVVSY----KIGVCKISEKG-KDCVTRFKRLSYNGKS-SVVLCKPQTGRMHQIRV 350

Query: 258 HALHMGCPIVGDHKY 272
           H  ++G P+V D  Y
Sbjct: 351 HLQYLGYPVVNDPLY 365


>gi|319951753|ref|YP_004163020.1| pseudouridine synthase [Cellulophaga algicola DSM 14237]
 gi|319420413|gb|ADV47522.1| pseudouridine synthase [Cellulophaga algicola DSM 14237]
          Length = 269

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 64/295 (21%), Positives = 111/295 (37%), Gaps = 47/295 (15%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    L+K ++   + ++         IQ G+ + +          I E+     ++   
Sbjct: 8   LTKSALKKAIKKRYITINGIAATTATFIQGGERISLY---------IPEETTASKTL--- 55

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTHR 149
                    +L+ED  + + +KP GI V G S   IA  +   L         KP+  HR
Sbjct: 56  ----IFPLKVLFEDDYLAIIHKPGGILVSGNSFKTIANALTQNLSPSTLPDATKPQPVHR 111

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  T+GIL+  +T ++ + L + F  +++ K Y+++  G    + E             
Sbjct: 112 LDYATTGILLAGKTSSSIRALNKMFEDKKVAKTYYAVTIGTMDVEGEISTTI-------- 163

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFC----WLEMQPHTGRTHQLRVHALHMGCP 265
                           + S + VI     K       +++ P TGR HQLR H   +G P
Sbjct: 164 ------------DDKPSYSMYTVITSAPSKRFGTLNLVQLDPKTGRRHQLRKHLSSIGNP 211

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
           I+GD +Y               +YLHA  +   HP     + +    P    K +
Sbjct: 212 ILGDKEYGT----ASLILNGKGMYLHAYSLQFVHPFTKKEIILRDDFPERFKKLF 262


>gi|167759623|ref|ZP_02431750.1| hypothetical protein CLOSCI_01981 [Clostridium scindens ATCC 35704]
 gi|167662749|gb|EDS06879.1| hypothetical protein CLOSCI_01981 [Clostridium scindens ATCC 35704]
          Length = 229

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 64/227 (28%), Positives = 97/227 (42%), Gaps = 21/227 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLDQ 152
           +  +LYEDS I V  KP G+  Q        ++  +K+ +     +       + HRLDQ
Sbjct: 5   RIEILYEDSHILVCIKPHGVPTQSRRAGTPDMESLIKNHICQSAPEKGEPYLAVIHRLDQ 64

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              GILV A+T  AA+ L    +     K Y +L  G P  K+  + ++L+K        
Sbjct: 65  PVKGILVFAKTPFAAKELNRQLQSHGFGKYYRALADGHPSQKEGTLEDYLIKDGRTNTSR 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFA----------QKFCWLEMQPHTGRTHQLRVHALHM 262
           V V      GA  A  H+ V++                  L+++  TGR HQ+RV   HM
Sbjct: 125 VCV--SGTAGAKLARLHYTVVEQGPFLFDQSKDDDAPRTELDIRLDTGRHHQIRVQLSHM 182

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQIT 308
           GCPI GD KY  N   +        + L A  ++  HP+  + +   
Sbjct: 183 GCPIAGDTKYNPNVHKD---EGWQNICLCAYRLEFLHPKTHKNMTFH 226


>gi|152999592|ref|YP_001365273.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151364210|gb|ABS07210.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 574

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 67/248 (27%), Positives = 110/248 (44%), Gaps = 25/248 (10%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++   + D+ + LT  ++     +LY+D  + + NKPA      G  I   +
Sbjct: 336 CQPILGHMLEGLAVDDNPL-LTNPAEGKTLAILYQDDSMAIVNKPAEFLSVPGKEIEDSV 394

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++         P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ G
Sbjct: 395 YSRMRQ-TFPHATGPLIVHRLDMSTSGLMVIALTKEAHKQLQKQFIQRTVTKRYVALLAG 453

Query: 190 IPK----NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--IDCFAQKFCWL 243
           +P      +     +  L+          V     +    A +H+++  +D  A+     
Sbjct: 454 MPAVMANKQATGNISLPLRGDLDDRPRQLVC---HEFGKAAETHWELSQLDEMARTARVY 510

Query: 244 EMQPHTGRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            + P TGRTHQLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP
Sbjct: 511 -LYPKTGRTHQLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHP 560

Query: 301 EG-GRLQI 307
               R++ 
Sbjct: 561 VTRERMRF 568


>gi|84387868|ref|ZP_00990882.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           12B01]
 gi|84377214|gb|EAP94083.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           12B01]
          Length = 517

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 104/231 (45%), Gaps = 19/231 (8%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ +  +   +      ++YED +I V NKP       G  I   +   +K+        
Sbjct: 299 LEDNPLIVNPAVGKSFDIVYEDDEIVVVNKPEEFLSVPGKFIEDSVYTRIKARY-PNATG 357

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+L++A T  + +H+ + F  R ++K Y +L+ G    +   I+  L 
Sbjct: 358 PLIIHRLDMSTSGLLILALTAESNKHIQKQFIDRTVEKRYTALLDGEITGESGDISLPL- 416

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
            +  I      +V         A ++++ I   +     + + P TGRTHQLRVH  H  
Sbjct: 417 -RGDITDRPRQLVCHEH--GRNAETYWEAIGT-SNGKTKVHLYPKTGRTHQLRVHCAHPL 472

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            +G PI GD  Y    +         +L+LHA Y+ L +P  G  ++   P
Sbjct: 473 GLGVPIRGDDLYGYKRE---------RLHLHAGYLKLINPTTGEWMEFEVP 514


>gi|312885611|ref|ZP_07745247.1| tRNA pseudouridine synthase C [Mucilaginibacter paludis DSM 18603]
 gi|311301923|gb|EFQ78956.1| tRNA pseudouridine synthase C [Mucilaginibacter paludis DSM 18603]
          Length = 234

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 60/224 (26%), Positives = 96/224 (42%), Gaps = 8/224 (3%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y D  +   NKP G+ V   S      +  L+   D   +     HRLD++T G+L
Sbjct: 4   LDIIYHDDYLVAINKPHGLLVHRSSIAHDVTEFALQILRDQLNRHVFPAHRLDRKTGGVL 63

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A  +   + +   F    ++K Y +LV G   +++E I   L K++    D     K 
Sbjct: 64  LFALDKETEKLMQTQFMENAVKKKYLALVRGHTPDEQE-IDYPLRKENGTLQDAFTRYKT 122

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             +    A     + +    ++  +E QP TGR HQLR H  H+  PI+GD  +  N + 
Sbjct: 123 LAR----AELKVPLGNHPTSRYSLIEAQPETGRMHQLRKHFSHIFHPIIGDRTHGCNKQN 178

Query: 279 NF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
                      + LHA  +   HP  G  LQI APL    ++  
Sbjct: 179 KLFKERWGMETMLLHATQLSFTHPVTGEQLQIQAPLHEEFLRVM 222


>gi|42561291|ref|NP_975742.1| RNA pseudouridylate synthase [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
 gi|42492789|emb|CAE77384.1| RNA pseudouridylate synthase [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
 gi|301320799|gb|ADK69442.1| pseudouridine synthase, RluA family [Mycoplasma mycoides subsp.
           mycoides SC str. Gladysdale]
          Length = 302

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 63/307 (20%), Positives = 136/307 (44%), Gaps = 38/307 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +   VV  +++N  L ++ K  +       + K +R+  ++++ KR+   N  ++   ++
Sbjct: 1   MTKFVVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRISDKNYLLKVNDII 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +    ++   II++Q    S+VNL          ++YED+ I + NKP  + +     +
Sbjct: 61  EVY---DSNKPIIRDQFNYISNVNLD---------IIYEDNNILIVNKPNNLEMHSTYNL 108

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +D  +KS++  K +              HRLD+ TSG+++ A+ + ++  LT +F++
Sbjct: 109 --CLDDMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSTILTNAFKL 166

Query: 177 R-RIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + +I K Y++L        +   +  ++   S+I     H     +    Y  + FK+I+
Sbjct: 167 KDQINKYYYALTSCDWNLDEFLQVNGYINYDSNI--KRAHFSLDQKNNYKYCQTEFKLIN 224

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                   + ++  TG+ HQ+R        PI+ D +Y      +        +YL A  
Sbjct: 225 KN-----LILVKLITGKKHQIRSVLSFYNHPILNDFRYNGKKINDLKM-----IYLSAFK 274

Query: 295 MDLPHPE 301
           ++  + E
Sbjct: 275 IEFKNLE 281


>gi|291523779|emb|CBK89366.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale DSM 17629]
          Length = 241

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 55/241 (22%), Positives = 106/241 (43%), Gaps = 30/241 (12%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETS 155
           K  ++YED+ I V  KPAGI+ Q        ++ F++++  +K + P   + HRLDQ   
Sbjct: 3   KPDIIYEDNDIIVCYKPAGIATQTRRIGQQDMESFIRNYRAAKNEPPYVGIVHRLDQPVE 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSL-----VWGIPKNKKE---CIANWLLKKSH 207
           G++V A+ + AA  L+   +    +K Y +      V G    ++E    + +++     
Sbjct: 63  GVMVFAKNQKAAASLSRQIKEHTTEKYYRAASRGQGVSGTAVEEEEAWHTLTDYISFDKR 122

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHA 259
                  +  + ++ A  A+  ++VI     +            +++  TGR HQ+R+  
Sbjct: 123 TNTSK--ITSEKDRLAKKAVLQYRVISVTPDRDGFKNECIRTEFDIKLLTGRHHQIRLQL 180

Query: 260 LHMGCPIVGDHKYC---------ANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
            ++G P++GD KY           +  G     ++ +L L +  +   HP  G R+    
Sbjct: 181 ANIGYPLIGDTKYGKPASNNSGTGSKSGRTGGGVREQLALCSYKLVFDHPATGERMTFEL 240

Query: 310 P 310
           P
Sbjct: 241 P 241


>gi|123452968|ref|XP_001314542.1| ribosomal large subunit pseudouridine synthases [Trichomonas
           vaginalis G3]
 gi|121897072|gb|EAY02204.1| ribosomal large subunit pseudouridine synthases, putative
           [Trichomonas vaginalis G3]
          Length = 353

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 67/333 (20%), Positives = 124/333 (37%), Gaps = 54/333 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +  N +   +    ++ +R+G++ V+ +++  + RI     ++         HI   
Sbjct: 54  IDVF-TNEFRVASREEYEEKIRNGKIIVNGRKIPVDYRIGPLDSIK---------HICTR 103

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            +    +  L K         L E      + KPA ++V    G  Y+      S V   
Sbjct: 104 IEAPVFNKPLLK---------LGETDNYVAYLKPASVTVNTVGGYFYN------SMVKRL 148

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                + HRLD+ TSGI+V A+ +AAA +  +     ++ K Y + V G     +     
Sbjct: 149 PPHLHVVHRLDRVTSGIIVFAKNKAAATNFNQYLVGEKVSKTYIARVIGRFPKGE----- 203

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            ++    +G D+             + + FK++    ++   +E  P TGRTHQ+R H  
Sbjct: 204 -IICDQPLGTDFNLHRTVVTPTGKPSKTIFKLLKTNGKE-SIVEAHPITGRTHQIRCHLQ 261

Query: 261 HMGCPIVGDHKYCANF-------KGNFTSPIQNKLYLHAR-------------YMDLPHP 300
           ++G PI  D  Y           K       +  L+                 Y+   H 
Sbjct: 262 YLGYPITNDEMYGGKREVYTKEMKDALKKAEKLGLWPCDYCQDKTNPRVEFQVYLHSCHY 321

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
           +       AP+P    +  D  G K   + + +
Sbjct: 322 QTPEFDFHAPMPD--WEDLDKFGLKESESSFCR 352


>gi|116201645|ref|XP_001226634.1| hypothetical protein CHGG_08707 [Chaetomium globosum CBS 148.51]
 gi|88177225|gb|EAQ84693.1| hypothetical protein CHGG_08707 [Chaetomium globosum CBS 148.51]
          Length = 475

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 61/295 (20%), Positives = 105/295 (35%), Gaps = 64/295 (21%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L   F++ +        ++ + SG V V+ K V  ++ +++G ++            
Sbjct: 71  GRQLIEVFQSEFRDRPLEYYREAMESGLVAVNGKTVGPHHILKNGHLISHTTHR------ 124

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E  +    +            +++ED  + V NKP+G+ V       Y+    +    
Sbjct: 125 -HEPPVTSDPIG-----------IIHEDDDMIVINKPSGVPVHPAGRYNYNSIVEIMKAE 172

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKE 196
                 PR  +RLD+ TSGI+ +A+   AA+ L      R ++K Y + V G  P  +  
Sbjct: 173 RGLDFTPRPCNRLDRLTSGIMFIAKHTKAAEQLGVQIFQRSVRKEYVARVIGKFPDGEVV 232

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA------------------- 237
           C    L     +G + V            A + FK +  +                    
Sbjct: 233 CDQPILQISPKLGLNRVRA------NGKAARTVFKRLAYYPPASGLAVSPNDGGTTGPAE 286

Query: 238 --------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                               + +  +   P TGRTHQLRVH   +G PI  D  Y
Sbjct: 287 EPVSGRSESAPRPTGGRKADEGYSIVRCLPVTGRTHQLRVHLQFLGHPIQNDPIY 341


>gi|332290332|ref|YP_004421184.1| tRNA pseudouridine synthase C [Gallibacterium anatis UMN179]
 gi|330433228|gb|AEC18287.1| tRNA pseudouridine synthase C [Gallibacterium anatis UMN179]
          Length = 232

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 60/203 (29%), Positives = 93/203 (45%), Gaps = 19/203 (9%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQET 154
            +   ++ +     V NKP G+SV        +  G      +  G ++  L HRLD+ T
Sbjct: 8   LMPFQIVAQTENFVVINKPCGVSVHK----DDNEQGLTTQLAEQLGVEQVWLVHRLDKST 63

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+ A  R AA  L+  F   ++QKIY +L  G PK K+  I   +++          
Sbjct: 64  SGLLLCALNRQAAAELSAQFAAHQVQKIYLALATGKPKKKQGLIKGDMIR------SRRA 117

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           + K +   +N AI+ F  I C +       ++P TG+THQLRV    +G PI+GD  Y  
Sbjct: 118 MWKLSPSCSNPAITRFYSISCES-GLRLFVLKPQTGKTHQLRVAMKSLGSPILGDPLYGD 176

Query: 275 NFKGNFTSPIQNKLYLHARYMDL 297
                      ++ YLHA  +  
Sbjct: 177 KSPA-------DRCYLHAALLAF 192


>gi|116748594|ref|YP_845281.1| pseudouridine synthase [Syntrophobacter fumaroxidans MPOB]
 gi|116697658|gb|ABK16846.1| ribosomal large subunit pseudouridine synthase D [Syntrophobacter
           fumaroxidans MPOB]
          Length = 255

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 62/220 (28%), Positives = 103/220 (46%), Gaps = 17/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ +    KPAG+ VQG       +    K W+     KP      + HRLD+  +
Sbjct: 13  IIYEDNHLLGLYKPAGLLVQGDRTGEASLLDLGKKWLKECCGKPGKVFLAMVHRLDRPVA 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++  RT  AA  ++  FR  RI+K Y ++  G        + N L +          +
Sbjct: 73  GVVLFCRTSKAAARISAQFRSGRIRKHYLAVAEGDVTPSAGRLVNQLERHDERS---SVI 129

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V +    +  A   ++V+D    +   LE++  TGR HQ+R+   H+G PI+GD +Y A 
Sbjct: 130 VAEATPRSREARLSYRVLDVAGSR-SLLEIELETGRHHQIRLQLAHLGFPILGDLRYGA- 187

Query: 276 FKGNFTSPIQNKL-YLHARYMDLPHPEGGR-LQITAPLPA 313
                ++P+  +   L A  ++L HP     L +  PLP 
Sbjct: 188 -----SAPLPGRQVALFATQLELEHPTRKESLLLRCPLPQ 222


>gi|295108996|emb|CBL22949.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           obeum A2-162]
          Length = 233

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 59/222 (26%), Positives = 103/222 (46%), Gaps = 19/222 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQ 152
           +++++LYED +I V +K AGI+VQ        ++  LK+++ SK         + HRLDQ
Sbjct: 5   IENMILYEDKEIIVCHKAAGIAVQSARIGIPDMESTLKNYLASKNPGTMPYLGIVHRLDQ 64

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              G+LV A+ + AA  LT       + K Y ++    P+N +  + ++L K        
Sbjct: 65  PVEGVLVFAKNKRAAAGLTGQITSGSVTKEYLAVTDQKPENVQGHLEDYLKKDGKTNTSA 124

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFC------WLEMQPHTGRTHQLRVHALHMGCPI 266
           V   K +   A  A+  ++V++  + +         + +Q  TGR HQ+RV   H G P+
Sbjct: 125 VVTSKTDR--AKKAVLDYEVLNEVSDERTSTGKRILVRIQLGTGRHHQIRVQMAHAGMPL 182

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           +GD KY           +       + ++   HP  G +L+ 
Sbjct: 183 LGDRKYNPEDSSGLPLGL------CSCHLVFRHPVTGKKLEF 218


>gi|257458049|ref|ZP_05623208.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
 gi|257444762|gb|EEV19846.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
          Length = 240

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 92/233 (39%), Gaps = 17/233 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKG-----QKPRLTHRLD 151
           K  +LYED  + V NKP+G+      G +       L+  + SKG      +P   HRLD
Sbjct: 11  KLDILYEDPSLIVINKPSGLLSVPYQGSSVRTAADILERIMRSKGAYSKHHRPFAVHRLD 70

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN---KKECIANWLLKKSHI 208
           ++TSG+++ A           S+     ++IY ++     +        I   L   ++ 
Sbjct: 71  RDTSGVMLFALNERTKDEFMRSWHTLVTERIYRAVAENPAEGGLADSGIIDAPLAYNAYN 130

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                   K        A + +K+I+     +   E+   TG+ +Q+R H    G PI G
Sbjct: 131 RAFVPTAEKHAHFDTVAARTRYKIIER-GAAYTLFELSLDTGKKNQIRAHLAANGYPIAG 189

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
           D        G+  +    +L LHAR +   HP   + ++   P P   +    
Sbjct: 190 DPI------GHARTDPFGRLALHARSLAFTHPVTRKVMRFEVPEPEAWLAYIR 236


>gi|291560401|emb|CBL39201.1| ribosomal large subunit pseudouridine synthase D
           [butyrate-producing bacterium SSC/2]
          Length = 236

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 63/221 (28%), Positives = 98/221 (44%), Gaps = 13/221 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----SKGQKPRLTHRLDQ 152
           K  ++Y+D +I V  KP GI V         +   LK+ +          +  L HRLD+
Sbjct: 6   KINIIYKDDQIVVCEKPKGIPVSSDKTGDMDLLHQLKNQLFFEENTDGEPQLYLVHRLDR 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              G++V ART+ AA  LTE  +    +K Y +++ G   + +    ++LLK        
Sbjct: 66  PVGGVMVFARTKKAAASLTEQIKDHTFEKDYQAVLTGWLSDDEGTFRDYLLKDPKNNVSK 125

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             +VK+   GA  AI  ++VID       K+ +  +   TGR HQ+RV     G  I GD
Sbjct: 126 --IVKEGTPGAKEAILDYEVIDMMEDSKMKYTYCLIHLETGRHHQIRVQTSSRGFGIWGD 183

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
            KY   ++       +  L+  A  +   HP  G R+   A
Sbjct: 184 TKYNPIYQKTKKKYKEIGLF--AARIAFEHPTTGERMVFKA 222


>gi|289805198|ref|ZP_06535827.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 191

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 61/205 (29%), Positives = 97/205 (47%), Gaps = 17/205 (8%)

Query: 114 PAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           P+G+    G  +  H D  + + +     +    HRLD  TSG++VVA T+AA + L   
Sbjct: 1   PSGLLSVPGR-LEAHKDSIM-TRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQ 58

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFK 231
           FR R  +K Y + VWG P   +  +   L+       D+ +  KQ    +    A + + 
Sbjct: 59  FREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQKVCYETGKPAQTEYN 112

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           V++  A     + ++P TGR+HQLRVH L +G PI+GD  Y +         +  +L LH
Sbjct: 113 VVEFAADNTARVVLKPITGRSHQLRVHMLALGHPILGDQFYASPE----ALSLAPRLQLH 168

Query: 292 ARYMDLPHPE-GGRLQITAPLPAHM 315
           A  + + HP  G  +     +PA  
Sbjct: 169 AEMLTITHPAYGNSMTFK--VPADF 191


>gi|255026385|ref|ZP_05298371.1| hypothetical protein LmonocytFSL_08685 [Listeria monocytogenes FSL
           J2-003]
          Length = 180

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 45/178 (25%), Positives = 89/178 (50%), Gaps = 13/178 (7%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            +  RLD+ETSG++++A+ R A   L+   +   +++ Y + + G+   +K  I   + +
Sbjct: 13  HIVTRLDRETSGLMLIAKNRFAHARLSTFLQKGLLKRRYQAFISGVLVEQKGSIEAPIGR 72

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           K     +   + +       YA ++++V+  + + F  + +Q  TGRTHQ+RVH  ++G 
Sbjct: 73  K-----EVSIMERFVTPEGKYAKTNYEVLARY-RAFDHVAIQLETGRTHQIRVHFSYIGH 126

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           P++GD  Y  +      + +  +  LH+ ++ L HP     +    PLPA M +    
Sbjct: 127 PLIGDDMYGGD------TNLLKRQALHSCHLHLVHPLTEEYMAFDLPLPADMEEIIQK 178


>gi|42563328|ref|NP_178012.2| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|75110951|sp|Q5XET6|PUS3_ARATH RecName: Full=RNA pseudourine synthase 3, mitochondrial; AltName:
           Full=RNA pseudouridylate synthase 3; AltName:
           Full=RNA-uridine isomerase 3; Flags: Precursor
 gi|53850479|gb|AAU95416.1| At1g78910 [Arabidopsis thaliana]
 gi|56790228|gb|AAW30031.1| At1g78910 [Arabidopsis thaliana]
 gi|332198052|gb|AEE36173.1| RNA pseudourine synthase 3 [Arabidopsis thaliana]
          Length = 478

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 89/342 (26%), Positives = 142/342 (41%), Gaps = 72/342 (21%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIY 109
           +++K N  +Q G  + +P  I  +    +   I   ++        +L+ ++ ++DS I 
Sbjct: 130 RKIKHNEVMQIGDKIWLPVSIAEMRISKRYDTIPSGTLYPNADEIAYLQRLVRFKDSAII 189

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           V NKP  + V+G   I   +D    + +     + PRL HRLD+ETSG+LV+ RT+ +  
Sbjct: 190 VLNKPPKLPVKGNVPIHNSMDALAAAALSFGNDEGPRLVHRLDRETSGLLVMGRTKESID 249

Query: 169 HLTESFRMRR---------------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           +L   F   +               + + YW+LV G PK K+  I+  L K     G   
Sbjct: 250 YLHSVFSDYKGRNSSCKAWNKACEAMYQQYWALVIGSPKEKEGLISAPLSKVLLDDGKTD 309

Query: 214 HVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGD 269
            VV     G   +  AI+ +KV+        W+E++P T R HQLRVH    +G PIVGD
Sbjct: 310 RVVLAQGSGFEASQDAITEYKVLGPKINGCSWVELRPITSRKHQLRVHCAEALGTPIVGD 369

Query: 270 HKYC------------ANFKGNFTSPIQNK------------------LYLHARYMDLPH 299
           +KY              + +     P + +                  L+LH R M LP+
Sbjct: 370 YKYGWFVHKRWKQMPQVDIEPTTGKPYKLRRPEGLDVQKGSVLSKVPLLHLHCREMVLPN 429

Query: 300 ----------PEGGRLQ-----------ITAPLPAHMVKTWD 320
                      E   L              A +P+HM  +W+
Sbjct: 430 IAKFLHVMNQQETEPLHTGIIDKPDLLRFVASMPSHMKISWN 471


>gi|57866557|ref|YP_188179.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           epidermidis RP62A]
 gi|57637215|gb|AAW54003.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus epidermidis RP62A]
          Length = 284

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 65/283 (22%), Positives = 115/283 (40%), Gaps = 42/283 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + KN     +   L  I  +G + ++   V     +  G  + +                
Sbjct: 16  FLKNQ--DYSKRTLSAIKLNGALLLNGSPVTVRQVMDKGDRLEVHFPSET---------- 63

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDS 139
              S NL  +   L+  ++YED+ + + NKP    +Q  +    H  G L     ++   
Sbjct: 64  --PSENLIPYDKELE--VIYEDAYLIIVNKPQ---MQNCAPSREHPHGSLVEQVLAYYTK 116

Query: 140 KGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           KG+K  P +  RLD+ TSG++V A+        ++    +     Y +L +G        
Sbjct: 117 KGEKINPHIVTRLDRNTSGLVVFAKFGHVHNLFSKVKFKKE----YVALAYGQ-TQSSGV 171

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + + S    D +   + NEKG  YA + ++ +    +     ++   TGRTHQ+RV
Sbjct: 172 IEVPIARLS----DSIIKREVNEKG-KYAKTVYQKL-MQNETASLCKINLLTGRTHQIRV 225

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           H  ++G P++GD  Y  N       P  +   LH   ++  HP
Sbjct: 226 HFEYIGHPLIGDDLYGGN------HPCVHGQALHCCSVEFIHP 262


>gi|210631097|ref|ZP_03296753.1| hypothetical protein COLSTE_00638 [Collinsella stercoris DSM 13279]
 gi|210160185|gb|EEA91156.1| hypothetical protein COLSTE_00638 [Collinsella stercoris DSM 13279]
          Length = 227

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 91/230 (39%), Gaps = 24/230 (10%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKGQKPRLTHRLDQE 153
             +LY D  +   +KPAGI V G    A  +   +++ +      S     +   RLD++
Sbjct: 7   LRVLYRDPWLMAVDKPAGIIVHGDGTGAPTLTDAVRAHLVASGEASASAAAQALQRLDRD 66

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+GI++ +  + A          R IQK Y ++V G     K  +   L +  H      
Sbjct: 67  TTGIVLFSLDKEAQPAFDRMIAERSIQKRYLAIVHGRFPAAK-TMCQPLGRDRHDSRR-- 123

Query: 214 HVVKQNEKGANYAISHFKVI-----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +  +    A +  K I     D  A +   L +  HTGR HQ+RVH  H   P++G
Sbjct: 124 ---MRVSRTGKPAHTDAKRIAYAKADARAPERSLLAIDLHTGRKHQIRVHLAHAKFPLLG 180

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
           D  Y               L LHA  +   HP  G    I AP PA   +
Sbjct: 181 DSLYGGPS-------CSGGLMLHASELSFTHPITGAPTHIQAPYPARFQR 223


>gi|296127170|ref|YP_003634422.1| pseudouridine synthase [Brachyspira murdochii DSM 12563]
 gi|296018986|gb|ADG72223.1| pseudouridine synthase [Brachyspira murdochii DSM 12563]
          Length = 216

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 60/225 (26%), Positives = 100/225 (44%), Gaps = 19/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGIL 158
           ++YED      NK AGI V          D  +K   +         L HR+D+ TSGI+
Sbjct: 3   IIYEDDYFIAVNKEAGIEV---------DDNLIKKIKEKHNHINNLYLVHRIDKFTSGIV 53

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR     ++  ESF+ + I K+Y ++  G  KN    I   +          + +  +
Sbjct: 54  ILARDENTKKYFEESFKNKTISKVYHAISEGYLKNNSGVINISIGIDKKNPNKRIPLSVK 113

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             +G   A++++KV+    +    LE++P TGRTHQ+RVH  ++G PI+GD  Y      
Sbjct: 114 --EGGESAVTYYKVLKKLNE-HTLLELKPVTGRTHQIRVHLSYIGHPIIGDKIYSK---- 166

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           N          L A+ ++  HP   + ++I        +     L
Sbjct: 167 NAGIYKMKGFALIAKEINFVHPITKKNIEIKIKYNKEFLIRLKLL 211


>gi|312130454|ref|YP_003997794.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
 gi|311907000|gb|ADQ17441.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
          Length = 250

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 63/250 (25%), Positives = 102/250 (40%), Gaps = 21/250 (8%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           S       +  +K ++++E+    V NKP  +        A      LK   ++ G   +
Sbjct: 4   SKFKKAPKNLDIKDLVIFENEHYVVINKPPFVPSL-DERTADKSLSILKLAREAYG-DIQ 61

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ETSG LV+A+   A ++L   F  R +QK Y ++V G        +   +   
Sbjct: 62  LCHRLDKETSGALVLAKNPEAYRNLAMQFEHREVQKEYHAVVNGAHDFDSIGVFLPIAIL 121

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                     V+ + +    A + F  +  F Q+   +   P TGR HQ+RVH   +  P
Sbjct: 122 -----KDGTAVRIDRQKGKLAETIFFTLQKF-QRHTLVRCVPITGRMHQIRVHLQCLNAP 175

Query: 266 IVGDHKYCANF-------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           IV D  Y  ++               +   P+  ++ LHA  +     +G  L ITAP P
Sbjct: 176 IVCDPTYGGDYIFLSQIKRKFNLKAESEELPLIKRVALHAHKIHFRDVDGTVLSITAPYP 235

Query: 313 AHMVKTWDSL 322
                  + L
Sbjct: 236 NDFEVLVNQL 245


>gi|332874770|ref|ZP_08442640.1| pseudouridine synthase A [Acinetobacter baumannii 6014059]
 gi|332737031|gb|EGJ67988.1| pseudouridine synthase A [Acinetobacter baumannii 6014059]
          Length = 196

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 63/208 (30%), Positives = 100/208 (48%), Gaps = 17/208 (8%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V +KP+ I    G G  +  D  L   V  + +   L HRLD++TSGILV   ++    
Sbjct: 1   MVIHKPSDILSVPGKGDLH--DSVLTRLVAIEPRTL-LIHRLDRDTSGILVFGLSKRGQS 57

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            +   F+ R+  KIY +LV G  + +   +   ++         +H+V  +      A++
Sbjct: 58  AIARQFQDRQTSKIYEALVAGHLEGE-GTVDIPVVYDP--SRPPLHIVDASHN--KPALT 112

Query: 229 HFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD  Y A         + 
Sbjct: 113 HWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDTLYAAP-----EQLLV 167

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLP 312
            +L LHA+ +   HP  G  L    P+P
Sbjct: 168 PRLCLHAKQLSFNHPVTGESLTFNCPVP 195


>gi|255033891|ref|YP_003084512.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
 gi|254946647|gb|ACT91347.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
          Length = 228

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 97/241 (40%), Gaps = 28/241 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +LY    +   NKP G+ V      +      ++   D   QK    HRLD++TSG+
Sbjct: 3   PLEILYRSDDLVAINKPNGLLVHRSPIASDADVFAVQLLRDQLSQKVYPAHRLDRKTSGV 62

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A        +   F    I K Y ++V G     +  I   L +   +  D      
Sbjct: 63  LLFALNENVNSEMQGKFMEGEITKTYHAIVRGH-TADRGEIDYPLKRDDGVTQD------ 115

Query: 218 QNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   A++HF+ +               ++  +++ P TGR HQLR H  H+  PI+
Sbjct: 116 --------AVTHFETLARAEVPFALGKHATSRYSLVQLNPLTGRMHQLRKHMAHIMHPII 167

Query: 268 GDHKYCANFKGNFTSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
           GD  +  N +  F        ++ LHA  ++  HP  G+ + I AP  +  V+    LG 
Sbjct: 168 GDRPHGCNKQNRFFKEELGMIQMMLHAVSVEFVHPVSGQHVTIVAPYLSEFVRMRSVLGL 227

Query: 325 K 325
           +
Sbjct: 228 E 228


>gi|119505063|ref|ZP_01627139.1| pseudouridylate synthase for 23S rRNA and tRNA-Phe, dual
           specificity [marine gamma proteobacterium HTCC2080]
 gi|119459045|gb|EAW40144.1| pseudouridylate synthase for 23S rRNA and tRNA-Phe, dual
           specificity [marine gamma proteobacterium HTCC2080]
          Length = 238

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 107/242 (44%), Gaps = 13/242 (5%)

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + +  ++    L  HS      +LY D  + + +KP  +    G          L + ++
Sbjct: 4   EPETGMELPPYLVPHSRE-SIRILYADDSLLIIDKPHLLLSVPGRHPLNRDS--LITRLE 60

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                    HRLD +TSGILVV R +A    + + F+ R + K Y +LV+G  K+ +  I
Sbjct: 61  RLFPGVAAAHRLDLDTSGILVVPRNKATLVAINKQFQDRTVLKTYRALVYGEVKDDQGQI 120

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L++  H         K   +    +++H++V+D        LE++P TGR+HQLR+H
Sbjct: 121 DLPLIRDWHNRP----RQKICTETGKPSVTHYRVLDRQPS-ATLLELKPITGRSHQLRIH 175

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVK 317
            + +G PI+G   Y           +     LHA  +   HP   G L+  +P P  +  
Sbjct: 176 LMALGHPILGCDLYAHQKALAAAPRLL----LHACQLTFKHPLTQGNLRAYSPPPFDITG 231

Query: 318 TW 319
            +
Sbjct: 232 LF 233


>gi|321311023|ref|YP_004193352.1| ribosomal large subunit pseudouridine synthase D (fragment)
           [Mycoplasma haemofelis str. Langford 1]
 gi|319802867|emb|CBY93513.1| ribosomal large subunit pseudouridine synthase D (fragment)
           [Mycoplasma haemofelis str. Langford 1]
          Length = 219

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 96/230 (41%), Gaps = 18/230 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E+    + NK +GI+V     I       +      +     L HR+D+ TSG +++
Sbjct: 6   IIFENKNFLIVNKASGIAVH--KNIYDREFNLINEVNKDQKANYSLVHRIDKYTSGAVLI 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ +     L   F    ++K Y +L       KK  I   L +  +   D +    +N 
Sbjct: 64  AKNKETLLLLQNLFLNNEVEKHYLALTSKELPAKKLKITLSLGRSKN---DKLRFTNRNA 120

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGN 279
           K    A +  +VID +     +L++   TGRTHQ+R H   + CP++ D  Y    F   
Sbjct: 121 KNYKPACTEVEVIDRY-----FLKILLKTGRTHQIRAHLFSINCPVLNDPIYGNRCFNPE 175

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDR 328
           F        YLHA  ++   P     + +TAPLP         L  +Y  
Sbjct: 176 FG------QYLHAYKLEFTCPITNEFISVTAPLPQEFKDKLSELNIEYTE 219


>gi|221067278|ref|ZP_03543383.1| pseudouridine synthase [Comamonas testosteroni KF-1]
 gi|220712301|gb|EED67669.1| pseudouridine synthase [Comamonas testosteroni KF-1]
          Length = 220

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 58/211 (27%), Positives = 96/211 (45%), Gaps = 13/211 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +YED  + V +KP+G+    G G        L++          + HRLDQ TSG++++A
Sbjct: 7   VYEDEHLLVLDKPSGLLCVPGRGPDKQDCLSLRAL--QHFGDALVVHRLDQATSGLVIMA 64

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN--WLLKKSHIGGDYVHV--VK 217
           R     + L ++F  R++ K Y ++V G  +   E      W L    I  D+       
Sbjct: 65  RNPVVQRQLGQAFAERQVDKRYIAVVAGDLQAGPETADAQGWQLIDLPIAADWERRPLRV 124

Query: 218 QNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            N +    + + ++ ++   Q+      + + P TGRTHQLR+H    G  I+GD  Y  
Sbjct: 125 INHENGKSSQTLWQALEQTGQQEMTCTRVLLSPLTGRTHQLRLHMAASGHAILGDALYAD 184

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
               + +     +L LHA  ++L HP  G L
Sbjct: 185 ETVASAS----PRLLLHATALELVHPVTGTL 211


>gi|319401727|gb|EFV89935.1| pseudouridine synthase, RluA family protein [Staphylococcus
           epidermidis FRI909]
          Length = 284

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 64/283 (22%), Positives = 116/283 (40%), Gaps = 42/283 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + KN     +   L  I  +G + ++   V   + +  G  + +                
Sbjct: 16  FLKNQ--DYSKRTLSAIKLNGALLLNGSPVTVRHVMDKGDRLEVHFPSET---------- 63

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDS 139
              S NL  +   L+  ++YED+ + + NKP    +Q  +    H  G L     ++   
Sbjct: 64  --PSENLIPYDKELE--VIYEDAYLIIVNKPQ---MQNCAPSREHPHGSLVEQVLAYYTK 116

Query: 140 KGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           KG+K  P +  RLD+ TSG++V A+        ++    +     Y +L +G        
Sbjct: 117 KGEKINPHIVTRLDRNTSGLVVFAKFGHVHHLFSKVKFKKE----YVALAYGQ-TQSSGV 171

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + + S    D +   + NEKG   A + ++ +    +     +++  TGRTHQ+RV
Sbjct: 172 IEAPIARLS----DSIIKREVNEKG-KCAKTVYQKL-MQNETASLCKIKLLTGRTHQIRV 225

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           H  ++G P++GD  Y  N       P  +   LH   ++  HP
Sbjct: 226 HFEYIGHPLIGDDLYGGN------HPCVHGQALHCCSVEFIHP 262


>gi|254515173|ref|ZP_05127234.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium NOR5-3]
 gi|219677416|gb|EED33781.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium NOR5-3]
          Length = 228

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 62/236 (26%), Positives = 105/236 (44%), Gaps = 13/236 (5%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I + + L+    L  HS      ++Y D ++ +  KP  +    G     H    + + +
Sbjct: 4   IADTQDLEPPPYLVPHSKE-PVRVIYADDELLLIRKPDLLLSVPGRHPLNH--DCMITRL 60

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                   + HRLD +TSGI++VAR +A+   L+  F+ R ++K Y + V G    ++  
Sbjct: 61  QESYPDALVVHRLDLDTSGIMMVARGKASQAALSRLFQERAVEKRYRAWVAGNVAAEEGK 120

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   + +      +   + K   +    ++++FKV+    +    LE+ P TGRTHQLR+
Sbjct: 121 LEYPIARD----WENRPLQKICAETGKKSLTYFKVLMRK-EGNSLLELNPATGRTHQLRI 175

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAPLP 312
           H   MG PI+G   Y              +L LHA  +   HP  GR  +   P P
Sbjct: 176 HCREMGHPILGCDMYAPP----AILGAAPRLMLHATRIAFRHPGTGRKIVGHCPAP 227


>gi|256383973|gb|ACU78543.1| 23S rRNA pseudouridine synthase [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|256384805|gb|ACU79374.1| 23S rRNA pseudouridine synthase [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|296455605|gb|ADH21840.1| 23S rRNA pseudouridine synthase [synthetic Mycoplasma mycoides
           JCVI-syn1.0]
          Length = 302

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 65/307 (21%), Positives = 137/307 (44%), Gaps = 38/307 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +   VV  +++N  L ++ K  +       + K +R+  ++++ KR+   N  ++   V+
Sbjct: 1   MTKFVVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRISDKNYLLKINDVI 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +    ++   II++Q    S+VNL          ++YED+ I + NKP  + +     +
Sbjct: 61  EVY---DSNKPIIRDQFNYISNVNLD---------IVYEDNNILIVNKPNNLEMHSTYNL 108

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +D  +KS++  K +              HRLD+ TSG+++ A+ + ++  LT +F+ 
Sbjct: 109 --CLDDMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSTILTNAFKS 166

Query: 177 R-RIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + +I K Y++L        +   +  ++   S+I      + K+N     Y  + FK+I+
Sbjct: 167 KDQINKYYYALTSSDWSLDEFLQVNGYINYDSNIKKADFSLDKKN--NYKYCQTEFKLIN 224

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                   + ++  TG+ HQ+R        PI+ D +Y      +        +YL A  
Sbjct: 225 KN-----LILVKLITGKKHQIRSVLSFYNHPILNDFRYNGKKINDLKM-----IYLSAFK 274

Query: 295 MDLPHPE 301
           ++  + E
Sbjct: 275 IEFKNLE 281


>gi|326317665|ref|YP_004235337.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
 gi|323374501|gb|ADX46770.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
          Length = 281

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 55/225 (24%), Positives = 96/225 (42%), Gaps = 12/225 (5%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           + L          +L++D  +    KPAG  V      A      +++  D  G++    
Sbjct: 1   MPLPTAPRHPPLSILWQDDDLVAVYKPAGWLVHRTGLDAGETRFVMQALRDQMGRRVYPV 60

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ T G+LV+     AA+ L+++F   R+ K Y +LV G   ++ +         + 
Sbjct: 61  HRLDKGTCGVLVMGLHADAARALSQAFEHHRVDKRYLALVRGHAPDRVQVDHALRPDDAP 120

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-----CWLEMQPHTGRTHQLRVHALHM 262
                     Q  + A   ++  ++ +    +F       +E  P TGR HQ+R H  H+
Sbjct: 121 PD-----AAVQPARTALRCLARLELPEASDTRFATTRASLVEALPETGRRHQIRRHLKHI 175

Query: 263 GCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGRL 305
             PI+GD  +       + +      +L+LHA  + LPHP  G +
Sbjct: 176 AHPILGDATHGKGPLNRWWAQRLGLQRLWLHAWRLALPHPATGDM 220


>gi|297839759|ref|XP_002887761.1| hypothetical protein ARALYDRAFT_477057 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297333602|gb|EFH64020.1| hypothetical protein ARALYDRAFT_477057 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 477

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 86/342 (25%), Positives = 143/342 (41%), Gaps = 72/342 (21%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIY 109
           +++K N  ++ G  + +P  I  +    +   I   ++        +L+ ++ ++DS I 
Sbjct: 129 RKIKHNEVMEIGDKIWLPVSIAEMRISKRYDTIPSGTLYPNADEIAYLQRLVRFKDSAII 188

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           V NKP  + V+G   I   +D    + +   K + PRL HRLD+ETSG+LV+ R++ +  
Sbjct: 189 VLNKPPKLPVKGNVPIHNSMDALAAAALSFGKDEGPRLVHRLDRETSGLLVMGRSKESIH 248

Query: 169 HLTESFRMRR---------------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           +L   F   +               + + YW+LV G PK K+  I+  L K     G   
Sbjct: 249 YLHSVFSDYKGRNSSCKAWNKACEAMYQQYWALVIGSPKEKEGLISAPLSKVLLDDGKTD 308

Query: 214 HVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGD 269
            VV     G   +  AI+ ++V+        WLE++P T R HQLRVH    +G  IVGD
Sbjct: 309 RVVLAQGSGFEASQEAITEYRVLGPMINGCSWLELRPITSRKHQLRVHCAEALGTSIVGD 368

Query: 270 HKYC------------ANFKGNFTSPIQNK------------------LYLHARYMDLPH 299
           +KY              + +     P + +                  L+LH R M LP+
Sbjct: 369 YKYGWFVHKRWKQMPQVDIEPTTGKPYKLRRPEGLDVQKGSVLSKVPLLHLHCREMVLPN 428

Query: 300 ---------------PEGGRL------QITAPLPAHMVKTWD 320
                             G +      +  A +P+HM  +W+
Sbjct: 429 IAKFLHVLNQQETEPLRTGIIDKPDLLRFVASMPSHMKISWN 470


>gi|170079422|ref|YP_001736060.1| ribosomal large chain pseudouridine synthase A [Synechococcus sp.
           PCC 7002]
 gi|169887091|gb|ACB00805.1| ribosomal large chain pseudouridine synthase A [Synechococcus sp.
           PCC 7002]
          Length = 538

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 63/212 (29%), Positives = 93/212 (43%), Gaps = 22/212 (10%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
             +   ++YED  +   +KPAG+    G     +   F  S +    Q   L HRLDQ+T
Sbjct: 335 PEIPLEIIYEDHSLIAIHKPAGLPSIPGRSSQTYDSAF--SRLRRDYQDIFLVHRLDQDT 392

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGIL+ A+     Q L   FR R+I K Y +L+    +  +  I   L       GD   
Sbjct: 393 SGILLFAKNAETQQDLQTQFRRRKIHKEYEALLEEKIQRPEGMITLPLWADP---GDRPR 449

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHK 271
             K + +    + ++F  +D        L+++P TGRTHQLRVH  H   +  PI+GD  
Sbjct: 450 -QKVDAQRGKPSETYFVKLDSH-----RLKLKPITGRTHQLRVHCAHPNGLNNPILGDRL 503

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           Y              +L+L A  +   HPE  
Sbjct: 504 YGNR--------AAPRLHLQATALTFMHPETK 527


>gi|160879192|ref|YP_001558160.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
 gi|160427858|gb|ABX41421.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
          Length = 237

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 57/210 (27%), Positives = 92/210 (43%), Gaps = 14/210 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGIL 158
           +L+ED  I V  KP G+  Q G G    +   L+ +  +  +     L HRLD+   G++
Sbjct: 4   ILFEDKHIIVCIKPIGVLSQPGQGEGMDMITLLQEYRKNNKESDYIGLVHRLDRNVGGVM 63

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+T  A + L+ + R R   K Y +++ G P      + + + K S    +   VV +
Sbjct: 64  VFAKTELATKKLSVAIRERNFTKEYMAVIHGRPSESSGILKDLMFKDS--SKNKSFVVNR 121

Query: 219 NEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             KG   A   ++ I+       +F ++ ++ HTGRTHQ+RV       P+VGD KY   
Sbjct: 122 MRKGVKEASLEYRTIETIEVAKGEFSFIRVKLHTGRTHQIRVQFASRKLPLVGDGKYGGK 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
                         L +  +   HP    L
Sbjct: 182 DNQCDA-------ALWSYRLAFVHPLTKAL 204


>gi|295094341|emb|CBK83432.1| ribosomal large subunit pseudouridine synthase D [Coprococcus sp.
           ART55/1]
          Length = 233

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 56/219 (25%), Positives = 98/219 (44%), Gaps = 12/219 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLD 151
           +K  +L+ED+ I V  KP G+  Q     +  +   LK  +  K  +         HRLD
Sbjct: 1   MKLNILHEDNDIIVAVKPCGVPTQPDKTNSESMVSMLKLRIYEKENRKEEPYLVPIHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +   G++V A+T  AA +L++      + K Y +++ G   N +  + ++LL  +    +
Sbjct: 61  RPVGGVMVFAKTPEAAANLSKQSEDGSMMKYYQAILTGELPNDQGVLKDYLLHDTK--DN 118

Query: 212 YVHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              VV ++  GA Y+   ++V+   D       ++ ++  TGR HQ+R       C I G
Sbjct: 119 VTKVVDKDTPGAKYSELEYEVLDVMDTDEGTLTYVLVELITGRHHQIRAQFAKRKCGIWG 178

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           D KY   F+       +  L  HA  ++  HP  G   +
Sbjct: 179 DTKYNPKFQKTKKKYKEIGL--HASRLEFDHPTTGEHMV 215


>gi|328768352|gb|EGF78399.1| hypothetical protein BATDEDRAFT_90882 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 490

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 82/349 (23%), Positives = 149/349 (42%), Gaps = 41/349 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK------RVKFNNRIQS 61
           +  VV      + L ++       +N + +++ + +  V V         R+     + +
Sbjct: 109 KQFVVNEACHLLTLAKFLGK-MTLMNTLKIREKINANLVWVTGSAHAEHVRISPKGILHT 167

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G VV +           ++    D+   L       K  +LY+D  IYV +K  G++ QG
Sbjct: 168 GDVVHVAYATKPHGDKTEQNDTEDAIKKL-------KMRILYKDQHIYVIDKEHGLASQG 220

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF-RMRRIQ 180
           GS I  H+D  +      K +  RL HRLD+ TSG +++ART+ +A  ++  F +  RI 
Sbjct: 221 GSKIDMHLDKLISHLETDKSKTLRLVHRLDKNTSGAMIIARTKESAARVSAMFRQEGRIS 280

Query: 181 KIYWSLVWGIPKNKK--------ECIANWLLKKSHIGGDYVHVVKQ----------NEKG 222
           + Y +L+     +          + ++  +        + + +V+           N   
Sbjct: 281 RKYLALLTPTLLDHSNFKDGGQHKIVSGIVSNGREAPHERMDLVEWHDGIPKQMSTNGDP 340

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYC----ANFK 277
              A++   ++         + ++P TGR HQLR+H    +G  IVGD+KY      NFK
Sbjct: 341 VKKAVTKVTLLQSNPL-TSLVCLEPTTGRKHQLRLHCADALGSFIVGDYKYGQGCLKNFK 399

Query: 278 GNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPAHMVKTWDSLGF 324
            + +   +  L+LH   + +     +G  L ++APLP +  KT  S G 
Sbjct: 400 AHVSDWKKVPLHLHLYQLSIKDWFRDGLDLTVSAPLPIYFQKTLTSTGL 448


>gi|225573997|ref|ZP_03782642.1| hypothetical protein RUMHYD_02093 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038727|gb|EEG48973.1| hypothetical protein RUMHYD_02093 [Blautia hydrogenotrophica DSM
           10507]
          Length = 310

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 66/336 (19%), Positives = 131/336 (38%), Gaps = 43/336 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSG 62
           M  + Y  V + ++   ++R  K     +N   + ++  +   + VD  + +  + ++ G
Sbjct: 1   MGKMWYYYVRDSKQEDSIERILKREL-GLNRKQISRLKFQENGLSVDGCQRRSTDWLRRG 59

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           + + +  +      + + ++               +  +LYED  + V  K +G      
Sbjct: 60  ETLAVSLMDRQGGTLEELKE---------------EPRVLYEDESLVVVEKRSGQVCHPS 104

Query: 123 SGIAYHIDGFLKSWV-----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               ++ D      V       +    R+  RLD++TSGI+V A+ + AAQ L+      
Sbjct: 105 G--MHYRDSLANQLVWHFQNRQENTSVRIIGRLDKDTSGIVVAAKHKIAAQKLSWQRDRG 162

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
              K Y +LV G   +    +   + +            +        A + + VI    
Sbjct: 163 IFGKEYLALVHGEFSDFDGFLREPIARVQGHPLKMKVCAQ-----GKPAKTQYHVI-AQN 216

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----------K 287
           + +  +  + +TGRTHQ+RVH   +G P+V D  Y    + +F   ++N          K
Sbjct: 217 RGYALVSCRLYTGRTHQIRVHMQSIGHPLVNDVIYGLGEQDDFAKTLENEQKIAGDRHKK 276

Query: 288 LYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           L LHA  + + HP  G  L + +      +   + L
Sbjct: 277 LGLHAAKVWMRHPLSGEELILESAC--DFLAWIEVL 310


>gi|27468449|ref|NP_765086.1| hypothetical protein SE1531 [Staphylococcus epidermidis ATCC 12228]
 gi|57867268|ref|YP_188955.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           epidermidis RP62A]
 gi|251811192|ref|ZP_04825665.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|282875767|ref|ZP_06284634.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|293366172|ref|ZP_06612858.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|27315996|gb|AAO05130.1|AE016749_76 conserved hypothetical protein [Staphylococcus epidermidis ATCC
           12228]
 gi|57637926|gb|AAW54714.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus epidermidis RP62A]
 gi|251805320|gb|EES57977.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|281294792|gb|EFA87319.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|291319694|gb|EFE60054.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|329734308|gb|EGG70623.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU045]
          Length = 274

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 58/279 (20%), Positives = 111/279 (39%), Gaps = 32/279 (11%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
            Y  +   +L ++  S ++ ++K+     N +++G  V IP      N++          
Sbjct: 19  QYLKLPKKDLHQLNMSKEILINKEYGTLLNNVKTGDHVEIPTPNEVSNYL---------- 68

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRL 146
                   +  + + YED  + +  KP G+            +  +   + +   +    
Sbjct: 69  ------PSYRYAQIYYEDDDLAIVMKPKGVKTHP--NDLKESNTLMNHVIYTVDSEYVEP 120

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLDQET G+L+VA+     + L        I +IY + V  +   K + I   + K  
Sbjct: 121 IHRLDQETVGLLIVAKNPLMKKILDRMLEYNEITRIYKANVKALLPIKPQTIDMPIGKD- 179

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                +    ++       AI+H        +  C L+++  TGRTHQ+RVH   +G P+
Sbjct: 180 ----KFHSNKRRISNTGQRAITHIINSKMIKEGVCQLDIKLDTGRTHQIRVHLAEIGHPV 235

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +GD  Y  +           +L L++  ++  HP    +
Sbjct: 236 IGDPLYGTS--------TLRQLELNSHQIEFTHPLTQEI 266


>gi|311264325|ref|XP_003130109.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 1 [Sus scrofa]
          Length = 376

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 75/282 (26%), Positives = 119/282 (42%), Gaps = 41/282 (14%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   ++++D  + V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 85  VHPNVLAKALSRGIVHQDKDLLVINKPYGLPVHGGPGVQLCISDVLPILAKILHGHKAEP 144

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P      +   ++
Sbjct: 145 LHLCHRLDKETTGVMVLAWEKEVAHQVQELFRTRQVAKKYWAITVRVPVPSAGVVDIPII 204

Query: 204 KKSHIGGDYVH---------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G    H               V  +  + A+ A++ ++V+            QP 
Sbjct: 205 EKEVQGQQQHHKMTLCPSYRMDNGKMVRVRTSRNAHLAVTQYQVLSSTLSSALLEL-QPV 263

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC---------------ANFKGNFTSPIQNKLYLHA 292
           TG  HQLRVH    + CPI+GDHKY                       +      L+LHA
Sbjct: 264 TGIKHQLRVHLSFGLDCPILGDHKYSDWNRLAPQKLSVGVLKKLGLPQSKARHIPLHLHA 323

Query: 293 RYMDLP--HPEGGRLQITAPLPAHMVKTWDSLGFK---YDRN 329
           R + LP        L +    P + V +   LG K   +D+N
Sbjct: 324 RQLILPALQSRKEELNLVCKPPRYFVHSLRRLGLKMPSHDQN 365


>gi|18855035|gb|AAL79727.1|AC091774_18 putative ribosomal large subunit pseudouridine synthase [Oryza
           sativa Japonica Group]
          Length = 275

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 53/226 (23%), Positives = 92/226 (40%), Gaps = 23/226 (10%)

Query: 12  VENDEENMRLDRWFKNHYPH--INFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           V   E   R+D W         ++   +Q  +R+G V V+ + V K ++ ++ G +V   
Sbjct: 65  VPAGEGRSRIDAWISARLGGGGVSRARIQASIRAGLVVVNGRPVSKVSHMVKGGDIVSCT 124

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
            +                   L    + +   ++YED  + V NKPA + V    G A  
Sbjct: 125 VL---------------ELQPLRAEPEDIPLDIVYEDDHLLVVNKPAHMVVHPAPGNANG 169

Query: 128 -HIDGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             ++  L     S      +P + HRLD+ TSG+LVVA+   +   L E F++  I+++Y
Sbjct: 170 TLVNAILHHCKISTFTSLVRPGIVHRLDKGTSGLLVVAKDEHSHAQLAEQFKLHTIRRVY 229

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
            SL  G P      I   + +  +     +       + A +A S 
Sbjct: 230 ISLTCGAPNPNSGRIEVPIARDPNNRIRMIATPGSGHRYARHAASR 275


>gi|224007791|ref|XP_002292855.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220971717|gb|EED90051.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 280

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 115/253 (45%), Gaps = 8/253 (3%)

Query: 27  NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
             +        +  + +G++ V  + V    +IQ G  +      +     +    I D+
Sbjct: 29  EEFGSYPKSYYEAAIDAGRILVSGRPVDREYKIQGGDELNHLVHRHEPAVGLS-DIIYDN 87

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---K 143
                 +++     ++YED+ + + +KP+ I++       Y+    + S+ + +     +
Sbjct: 88  GTITADYTEHPPVQIVYEDNSLLIVDKPSTIAIHTSGAYNYNSLFEILSYWNPQAYGLGR 147

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGI-PKNKKECIANW 201
               HRLD+ TSG++++A+T   A+ + +    R   +K+Y + V G  P N  E +A+ 
Sbjct: 148 LFTVHRLDRLTSGLVLIAKTPELARSMGKCIMERDGCEKLYLTRVKGKFPLNVMEKVASD 207

Query: 202 LLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHA 259
               +    ++ H+ ++ + KG   A + F ++   A      +  +P TGRTHQ+R+H 
Sbjct: 208 GGIDAQNDNEHPHLTEEADRKGIKPAQTSFTLLTYDAVSDTSVVLAKPVTGRTHQIRLHL 267

Query: 260 LHMGCPIVGDHKY 272
             +G PI  DH Y
Sbjct: 268 QQLGHPIANDHCY 280


>gi|126642499|ref|YP_001085483.1| putative ribosomal large subunit pseudouridine synthase
           A(RluA-like) [Acinetobacter baumannii ATCC 17978]
          Length = 196

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 62/208 (29%), Positives = 99/208 (47%), Gaps = 17/208 (8%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V +KP+ I    G G  +  D  L   V  + +   L HRLD++TSGILV   ++    
Sbjct: 1   MVIHKPSDILSVPGKGDLH--DSVLTRLVAIEPRTL-LIHRLDRDTSGILVFGLSKRGQS 57

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            +   F+ R+  KIY +LV G  + +   +   ++         +H+V  +      A++
Sbjct: 58  AIARQFQDRQTSKIYEALVAGHLEGE-GTVDIPVVYDP--SRPPLHIVDASHN--KPALT 112

Query: 229 HFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD  Y           + 
Sbjct: 113 HWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDTLY-----ATPEQLLV 167

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLP 312
            +L LHA+ +   HP  G  L    P+P
Sbjct: 168 PRLCLHAKQLSFNHPVTGESLTFNCPVP 195


>gi|224543721|ref|ZP_03684260.1| hypothetical protein CATMIT_02934 [Catenibacterium mitsuokai DSM
           15897]
 gi|224523374|gb|EEF92479.1| hypothetical protein CATMIT_02934 [Catenibacterium mitsuokai DSM
           15897]
          Length = 289

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 128/318 (40%), Gaps = 38/318 (11%)

Query: 1   MSLMTYVQY--VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR 58
           M +    Q+  + ++ + EN  L   + +   H++   +  + ++   +++      N  
Sbjct: 1   MRIKKQGQHLLITIDEEYENRPLSDLWADL--HLSRKTIHLLKQNKDYKINH-VFNMNPI 57

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           + +  V+ +    +                  T   DF    ++YED  I V NKP GI+
Sbjct: 58  LHTNDVLDVLAYEHDDE---------------TYAPDFQDIDIVYEDDLILVVNKPIGIA 102

Query: 119 VQGG-SGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           V          +   + ++  ++G     R  HRLD +TSG++V  +      +L  +  
Sbjct: 103 VYPDDPHKTDSLSNRVSAYYMTQGYDIPVRYIHRLDNDTSGLVVFCKCHLIQAYLDHALS 162

Query: 176 MRRIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           ++ IQ+ Y + V G  K  KE  I   L K  H         K        A+++++ ++
Sbjct: 163 IKEIQREYLAYVEGHIKEGKEYKIEQNLGKDRHSPSKMRVHSK-----GISAVTYYQCLE 217

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              +    +  +  TGR HQ+RVH   +G PI+GD  Y              +L LHA Y
Sbjct: 218 -NKEDHALVRCRLETGRKHQIRVHMASIGHPILGDSLYNEGSD-------YPRLALHAAY 269

Query: 295 MDLPHPEGG-RLQITAPL 311
           +    P     + + +P+
Sbjct: 270 IKFEEPITHLEIDLYSPM 287


>gi|242817540|ref|XP_002486976.1| DRAP deaminase (Rib2), putative [Talaromyces stipitatus ATCC 10500]
 gi|218713441|gb|EED12865.1| DRAP deaminase (Rib2), putative [Talaromyces stipitatus ATCC 10500]
          Length = 514

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 63/323 (19%), Positives = 115/323 (35%), Gaps = 56/323 (17%)

Query: 22  DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           D +  + +        ++ +  G+V +  K    +  + +G +V              E 
Sbjct: 55  DIF-TSEFRDRTAEYYKQAIEEGRVLISGKVANLDTIVPNGAIVSHSTHR-------HEP 106

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSK 140
            +    +            +++ED  + V +KPAGI V G     YH +  ++    D  
Sbjct: 107 PVSSQPIG-----------IIHEDDDMIVIDKPAGIPVHGAG--RYHYNSIIEIMKADRP 153

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
           G K    +RLD+ TSG++ +++   AA+  +   + R +QK Y + V G  P     C  
Sbjct: 154 GSKILPCNRLDRLTSGVMFISKNARAAEEFSAQLKERSVQKEYVARVSGRFPDGVVLCDQ 213

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI---------------------DCFAQ 238
             +     +G + V    +  +     I+++ V                          +
Sbjct: 214 PIMAVSPKLGLNRVRAAGKEARTKFRRIAYYPVSPKKSVDATTASGDRPATPPATTTEEE 273

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-----------KGNFTSPIQNK 287
            +  +   P TGRTHQ+RVH   +G PI  D  Y                      I ++
Sbjct: 274 GYSIVHCLPLTGRTHQIRVHLQFLGYPISNDPIYSNRRVFGPSLGKHDDSAENDKEIIDR 333

Query: 288 LYLHARYMDLPHPEGGRLQITAP 310
           L    +  +L      R  +T P
Sbjct: 334 LSNMGKT-ELADTTTYRTHLTCP 355


>gi|226327444|ref|ZP_03802962.1| hypothetical protein PROPEN_01315 [Proteus penneri ATCC 35198]
 gi|225203970|gb|EEG86324.1| hypothetical protein PROPEN_01315 [Proteus penneri ATCC 35198]
          Length = 238

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 96/232 (41%), Gaps = 21/232 (9%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I+D+ +    H +     +LY+D  + + NKP G+    G          +   +     
Sbjct: 4   IIDTFIAPPCHDEI---EILYQDEHLVIINKPTGLLSLSGKNPQN--IDSVHYRLVKLFP 58

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD  TSG+++VAR +A    L + F  R I KIY +L+ G  K  +  I   +
Sbjct: 59  GCTLVHRLDFGTSGLMIVARNKAINALLCQQFSQRNITKIYNALLCGHLKKNEGVIDAPI 118

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQ 254
            K   +    + +   N      A S + VI+ F              ++  P TGRTHQ
Sbjct: 119 AKDPAL-FPRMSICPIN---GKPARSGYHVIERFYHTLEDGTLLPLTRVQFTPETGRTHQ 174

Query: 255 LRVHALHMGCPIVGDHKYCANFKG----NFTSPIQNKLYLHARYMDLPHPEG 302
           LR+H+  +G  I+G   Y     G       +    +L LHA  +   HP  
Sbjct: 175 LRIHSQFIGHSILGCDLYGGCDGGLIEKREGTERTPRLMLHASELHFVHPIS 226


>gi|307722069|ref|YP_003893209.1| pseudouridine synthase [Sulfurimonas autotrophica DSM 16294]
 gi|306980162|gb|ADN10197.1| pseudouridine synthase [Sulfurimonas autotrophica DSM 16294]
          Length = 302

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 63/289 (21%), Positives = 115/289 (39%), Gaps = 42/289 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +             Q+++  G++ V  K                      +     E + 
Sbjct: 19  YLIQEL-GYTQKEAQRLIAKGRLFVSGKP---------------------MTKTAGEIEG 56

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
               +     +  L+    YE+ +  +F+KP+G+ +   +   Y     +       G+ 
Sbjct: 57  EFEFIYFEPITKGLEPT--YEEEEFVIFDKPSGVLIHPQN--RYTPYSLIDELKYQYGRD 112

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             +THR+DQETSG+++ A+ + + + +   F  R ++K Y + V G  + K+  +   LL
Sbjct: 113 ANITHRIDQETSGLVLCAKNKQSERDIKMMFEQRDMKKKYLAFVHGHFE-KELTVEAPLL 171

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
           +          VVK +EKG   + + FK +  F++     +E  P+TGR HQ+RVH  H+
Sbjct: 172 RAEDESAIVRMVVKVDEKG-KASKTDFKPLQYFSEVDMTLVECSPYTGRQHQIRVHLFHV 230

Query: 263 GCPIVGDHKYCANFKG-------------NFTSPIQNKLYLHARYMDLP 298
             PIVGD  Y  + +                      +L LHA  +   
Sbjct: 231 KHPIVGDPIYGQSEENIIKFLERELSEEERIKYSGAKRLLLHASELGFE 279


>gi|225165838|ref|ZP_03727617.1| pseudouridine synthase [Opitutaceae bacterium TAV2]
 gi|224799926|gb|EEG18376.1| pseudouridine synthase [Opitutaceae bacterium TAV2]
          Length = 244

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 102/237 (43%), Gaps = 21/237 (8%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQ 152
           ++ +++ +++ED ++ V NKP  +                 +  ++KG +K  L  RLD+
Sbjct: 4   AEEIEAWVVHEDERLLVVNKPGDVVCHPSKAGP--WSSLAGAVREAKGLEKAHLIFRLDR 61

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           ETSG++V A+    A  L  + + RR++K Y +++ G  + +   +   L          
Sbjct: 62  ETSGVVVFAKDERMASRLQRAMQERRVRKEYLAVLEGELR-EAVTVDQPLGDDL---ASP 117

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V V          A+SHF  +   A  F  + ++  TGR HQ+R HA  +G P+VGD  Y
Sbjct: 118 VFVKTCVRADGKAAVSHFYPV-ACAGGFSLVRVRLETGRKHQIRAHASWLGTPVVGDKIY 176

Query: 273 CANFK------------GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
             + +                     +  LH   +DL +  G  L + APL   +  
Sbjct: 177 GPDARIYLDFIDTGYTPELAAKLHLPRQALHCAEIDL-NEAGVPLVLRAPLAGDLAA 232


>gi|283780483|ref|YP_003371238.1| pseudouridine synthase [Pirellula staleyi DSM 6068]
 gi|283438936|gb|ADB17378.1| pseudouridine synthase [Pirellula staleyi DSM 6068]
          Length = 230

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 114/240 (47%), Gaps = 20/240 (8%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTH 148
                  +L+ED+ + V NK   ++ QG +     +   ++ ++  K +KP      +  
Sbjct: 2   PRTPSLDILHEDNHLLVINKRPLLATQGVAEGTPSLVTEVQQYLKVKYKKPGNVYVGVVS 61

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD  TSG++V+ART  AA  L E FR + ++K YW+ V   P+     + +W++K    
Sbjct: 62  RLDAHTSGVVVLARTSKAASRLAEQFREQGVEKTYWAAVEAAPEPASGELVSWVVKDDK- 120

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIV 267
               + +  +   G   A+  ++ ++   +    + ++  TGR HQ+R+     +  P++
Sbjct: 121 -NRRMTIADRKLAGCQKAVLTYETLE-QNKSAALVSVKLETGRKHQIRLQLADELSLPVI 178

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKY 326
           GD KY +  +          + LHAR +   HP GG RL   APLPA    TW  L FK 
Sbjct: 179 GDRKYGSRIE------FPEGIALHARELAFDHPVGGKRLSFVAPLPA----TWKGLKFKA 228


>gi|218132751|ref|ZP_03461555.1| hypothetical protein BACPEC_00612 [Bacteroides pectinophilus ATCC
           43243]
 gi|217992477|gb|EEC58480.1| hypothetical protein BACPEC_00612 [Bacteroides pectinophilus ATCC
           43243]
          Length = 217

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 57/212 (26%), Positives = 95/212 (44%), Gaps = 8/212 (3%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQET 154
           +K  ++YED  + +  KPAG+  QG       +   L ++   KG+     + +RLD+  
Sbjct: 1   MKPDIIYEDDGMIICRKPAGVLAQGSRSFDADMVSMLMTYRRKKGEDTYIGVINRLDRPV 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G++V A++   A  L    +     K Y ++VWG     +  + ++L+K +  G +  H
Sbjct: 61  EGLMVFAKSSRDAARLNRLMQQDTFNKTYIAVVWGCIDAVEGTLTDYLVKDA--GNNTSH 118

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V  + E GA  A  +++VI         + +Q  TGR HQ+RV     G  +VGD KY +
Sbjct: 119 VASEGEPGAKRAELNYRVIGSL-DGMSVVRIQLVTGRHHQIRVQFASRGHALVGDAKYGS 177

Query: 275 NFKGNFTSPIQNK---LYLHARYMDLPHPEGG 303
           N        + N    L   A  +   H E  
Sbjct: 178 NSNIAGRLVLANGQIALCACAVDVAGRHYETE 209


>gi|315657924|ref|ZP_07910798.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           lugdunensis M23590]
 gi|315496960|gb|EFU85281.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           lugdunensis M23590]
          Length = 278

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 64/299 (21%), Positives = 117/299 (39%), Gaps = 44/299 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  D  N+ L   F+     +   +L ++  S ++ ++    + +N++ +   V IP   
Sbjct: 5   IPEDYNNLTLREIFQTL--KVPKKDLHQLNMSKEITINNAPARLSNQVHTMDCVEIPTDE 62

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-----GSGIA 126
              N++                  +  + + YED  + +  KP G+          + + 
Sbjct: 63  EKSNYL----------------PSYRYAQIYYEDDDLAIVMKPKGVKTHPNDLKESNTLM 106

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            HI   L S      +     HRLDQET G+L++A+     + L       +I +IY + 
Sbjct: 107 NHIIYTLDS------EYAEPIHRLDQETVGLLIIAKNPLMKKILDRMLEDNKITRIYKAN 160

Query: 187 VWGIPKNKKECIANWLLKKS-HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +  +   K + I   + K   H     +            AI+H        +  C L++
Sbjct: 161 INALLPIKPQTIDMPIGKDKFHPNKRRI------SNTGQRAITHILASTMLKEGVCQLDI 214

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +  TGRTHQ+RVH   +G P++GD  Y  +           KL L +  +D  HP   +
Sbjct: 215 KLDTGRTHQIRVHLAEIGHPVIGDPLYGDSK--------LRKLELKSYQIDFVHPLTQQ 265


>gi|326559332|gb|EGE09759.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis 7169]
 gi|326569969|gb|EGE20016.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis BC1]
          Length = 242

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 70/240 (29%), Positives = 119/240 (49%), Gaps = 23/240 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ S +     +F KSI +YED  I+V +KPAG+    G  +       L+S +      
Sbjct: 14  LELSHDDLFFHEFAKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPN 69

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANW 201
            RL HRLD +TSG+++ A++  A  H+++ F  R  QK Y ++V+G     +KK  +   
Sbjct: 70  IRLIHRLDMDTSGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVP 129

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--------FAQKFCWLEMQPHTGRTH 253
           +  +      ++  +  N      A++H++V+           A     + ++P TGR+H
Sbjct: 130 VRYEPTTKPRHIVDMDWN----KRALTHYEVMHHELRCDDNGRAYPVTRVALKPITGRSH 185

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           QLRVH +H+G  ++GD  Y  +        + N+L LHA  + L HP  G  +   +P+P
Sbjct: 186 QLRVHMVHLGHVMIGDPIYAEDV----ALKLSNRLNLHAHKLRLKHPTHGIWMDWFSPVP 241


>gi|317052476|ref|YP_004113592.1| pseudouridine synthase [Desulfurispirillum indicum S5]
 gi|316947560|gb|ADU67036.1| pseudouridine synthase [Desulfurispirillum indicum S5]
          Length = 267

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 105/246 (42%), Gaps = 19/246 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQ 152
           +  +L++D+   V  KPA + VQ  S     +   ++ ++ ++ QKP      +  RLD+
Sbjct: 34  ELQVLHQDNHTIVVFKPARVPVQSDSSGDISLLEVVRQYIAAEYQKPGNVFVGMVQRLDR 93

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
             SG++V ART   A  L+E  R  RI K Y +LV G P   +  + + L  +       
Sbjct: 94  PVSGLVVFARTSKGAARLSEQLRQHRIYKHYLALVHGAPSESEGTLRHLLEYREGTA--- 150

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +         A+ H++V+         L ++  TGR HQ+R     +GCPI+GD +Y
Sbjct: 151 ---IAGRHGQGKTAVLHYRVLQHLPD-ASLLHIRLETGRKHQIRFQLSRIGCPILGDLRY 206

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV-KTWDSLGFKYDRNLY 331
            A       S     + L A  +   HP   R  I   LPA ++ +    L         
Sbjct: 207 GARAPLPDQS-----IALCAWALSYEHPTS-RQPIMVRLPAGLLPQAIQPLAEILPDPFT 260

Query: 332 IKRLYS 337
            + L+ 
Sbjct: 261 KETLHE 266


>gi|325279229|ref|YP_004251771.1| pseudouridine synthase [Odoribacter splanchnicus DSM 20712]
 gi|324311038|gb|ADY31591.1| pseudouridine synthase [Odoribacter splanchnicus DSM 20712]
          Length = 230

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 65/220 (29%), Positives = 103/220 (46%), Gaps = 16/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT-----HRLDQETS 155
           +LYED+ I   NK     VQ        +   +K+++  K  KP        HR+D+  S
Sbjct: 4   VLYEDNHIIAVNKKISDIVQADKTGDTPLSEEVKAYIKKKYNKPGEVYLGVPHRVDRPVS 63

Query: 156 GILVVARTRAAAQHLTESFRMRR--IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           G+++ ART  A   L + F+     I KIYW++V  +P      + ++L++      +  
Sbjct: 64  GVVIFARTSKALTRLNKMFQEHEKEISKIYWAIVGNLPAEDHAVLTHYLMRDPE--KNKS 121

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           H   Q + GA  A   +K++   +Q++  LE++ +TGR HQ+R     +GCPI GD KY 
Sbjct: 122 HAYNQPKAGAKEATLEYKLLGS-SQRYYLLEVKLYTGRHHQIRCQLAKIGCPIKGDLKYG 180

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
                         + LHAR +   HP    +  ITA  P
Sbjct: 181 FPRSNE-----GGGISLHARSITFKHPVSREMITITAKPP 215


>gi|195434112|ref|XP_002065047.1| GK15252 [Drosophila willistoni]
 gi|194161132|gb|EDW76033.1| GK15252 [Drosophila willistoni]
          Length = 532

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 61/268 (22%), Positives = 112/268 (41%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        Q+ + +G++ V+ + V  +  ++   +         L +++  
Sbjct: 157 LDVF-SREFRAHPAEVYQRSIEAGKLTVNHEIVPADYSLKHNDL---------LANVVHR 206

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  ++  +          +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 207 HEVPVTAQPI---------RIIHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 256

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R    A+ L +  R R++QK Y  LV G  P    EC  
Sbjct: 257 LKDLRTIHRLDRLTSGLLLFGRNANKARELEQQIRQRQVQKEYVCLVEGKFPDGIIECNE 316

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +  +    IG      V +         + F+ +         +  +P TGR HQ+RVH 
Sbjct: 317 SIEVVSYKIG------VCRVSPKGKDCKTTFQRLSNVGDS-SLVLCKPLTGRMHQIRVHL 369

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PIV D  Y     G    P++ +
Sbjct: 370 QYLGYPIVNDPLYNHEVFG----PLKGR 393


>gi|156402477|ref|XP_001639617.1| predicted protein [Nematostella vectensis]
 gi|156226746|gb|EDO47554.1| predicted protein [Nematostella vectensis]
          Length = 330

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 75/307 (24%), Positives = 137/307 (44%), Gaps = 53/307 (17%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK--SWVDSKGQKPR 145
           +     + +L   +++ ++ +   NKP G+ V GG G+   +   L+  + + +   KP 
Sbjct: 12  LKTVIDAQYLADNVIFSNNDLIAINKPYGLPVHGGPGVVLSVAELLEEFAAIKNYQNKPE 71

Query: 146 LTHRLDQ----------ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           L HRLD+          + SG+L++ R + AAQ + E F+ R ++K Y ++  G+P+ ++
Sbjct: 72  LAHRLDKYGTDYTIMLIDCSGVLLLTRNKTAAQKIAEMFQSRMVKKRYLAVSVGVPRYEE 131

Query: 196 ECIANWLLKKSHIGGDYVHVVKQN----------EKGANYAISHFKVIDCFAQKFCWLEM 245
             I+   +    +G     +++Q+          E G   AI+ FK++D        LE+
Sbjct: 132 GTIS-IPVGYGRVGPWERIIIRQDLVGKTHKEITEAGFKQAITKFKILDENQSTCSLLEI 190

Query: 246 QPHTGRTHQLRVHAL-HMGCPIVGDHKYCANFKGNFTSPI-------------------- 284
           +P TG   Q+RVH    + CPI+GDHK+ ++       P+                    
Sbjct: 191 EPITGHKQQIRVHLADALRCPILGDHKFSSDKPQPQVIPLRLLQLLQISGVKGVDGKKGR 250

Query: 285 -------QNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLY 336
                  Q  L+LH+  + LP    G  L I+APLP + + T   L     R   + +  
Sbjct: 251 IRPWQRGQIPLHLHSHQLVLPKYHTGSDLVISAPLPKYYLDTLSRLNLHPKRKK-MNQSR 309

Query: 337 SQDECKQ 343
            ++E  +
Sbjct: 310 EEEEYYR 316


>gi|322697720|gb|EFY89497.1| DRAP deaminase [Metarhizium acridum CQMa 102]
          Length = 512

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 60/283 (21%), Positives = 103/283 (36%), Gaps = 70/283 (24%)

Query: 42  RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL 101
            +G + V+  RV  +  +++G ++              E  +    V            +
Sbjct: 118 ETGDIFVNGTRVGPDYILRNGDLISHTLHR-------HEPPVTSDPVG-----------I 159

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILV 159
           ++ED  + V NKP+G+ V       Y  +  L+     +G +  P   +RLD+ TSGI+ 
Sbjct: 160 IHEDEDMIVINKPSGVPVHPAG--RYKFNSVLEIMKAERGPEFMPYPCNRLDRLTSGIMF 217

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           VA++  AA+ L    + R ++K Y + V G  P+ +  C    L     +G + V     
Sbjct: 218 VAKSVKAAEALGNQIKSRTVRKEYMARVVGEFPEGEIVCDQPILSISPKLGLNRVRA--- 274

Query: 219 NEKGANYAISHFKVIDCFA----------------------------------------- 237
                  A + FK +  +                                          
Sbjct: 275 ---EGKAARTVFKRLAYYPPRAHAEANGQQGGVPEPTDKELSRLPAEEGDESNGKPWINK 331

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           + +  +   P TGRTHQ+RVH  ++G PI  D  Y       F
Sbjct: 332 RGYSIVRCLPVTGRTHQIRVHLQYLGHPIQNDPIYANQRVWGF 374


>gi|152996905|ref|YP_001341740.1| pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150837829|gb|ABR71805.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 212

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 59/219 (26%), Positives = 98/219 (44%), Gaps = 13/219 (5%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +  +  +LYED    V NKPA      G G     D  L       G+     HRLD+ T
Sbjct: 5   ELSRLEILYEDEWFAVINKPANCLSVPGRGPDKL-DSILYRAECLFGE-AFAIHRLDEAT 62

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++VA+T    + +   FR R +QK Y +L+ G    +K  +   L        +   
Sbjct: 63  SGLILVAKTHECQKRMYAHFREREVQKEYRALLRGHLLGEKGEVRKPLRCDWP---NRPR 119

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +   ++ +  +I++++ +  +      + + P TGR+HQLRVH   +G  I+GD  Y  
Sbjct: 120 QIICTDEWSKDSITYWEKM-AYENNTTRVRLVPFTGRSHQLRVHMQSLGHSIIGDEFYDP 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            F+ +       +L LHA  ++  HP     +   A  P
Sbjct: 179 EFQND------PRLLLHAYRLEFRHPFTKAWIAFVAACP 211


>gi|302384824|ref|YP_003820646.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
 gi|302195452|gb|ADL03023.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
          Length = 242

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 106/234 (45%), Gaps = 14/234 (5%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHR 149
           + ++  +LYED +I V  KP G+  Q        +   +K  ++    K       + HR
Sbjct: 8   EAMELNILYEDEEILVAEKPVGMESQSARSFEPDMVSEVKKHINRLSPKQGEPYVGVIHR 67

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+   G++V A+T+ AA+ L+    M +++KIY+++V G P        ++L K     
Sbjct: 68  LDKPVGGVMVYAKTKDAAESLSRQVSMHQMEKIYYAVVCGKPVENFGAYVDYLWKDGKNN 127

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                +V +  KGA  A   ++++D  +   +     ++   TGR HQ+RV     G P+
Sbjct: 128 CSK--IVDKGIKGAKLAELSYQIVDERSIGNEVCSLAKIILKTGRHHQIRVQMAGHGTPL 185

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
            GD KY   F+  + S     + L A  +   HP    R+  +      + +T+
Sbjct: 186 WGDQKYNPLFQKGYRS---GNVALFAYSLTFTHPVTKKRMTFSVKPKGDIFETF 236


>gi|294141898|ref|YP_003557876.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293328367|dbj|BAJ03098.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 567

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 65/228 (28%), Positives = 100/228 (43%), Gaps = 18/228 (7%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E    D +  L   ++     ++Y+D  I V NKPA      G  I   +   +K     
Sbjct: 345 EGLATDENPLLINPAEGKLLDIIYQDRDILVINKPAEFLSVPGRNIDDSVYSRIKQLY-P 403

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +   P + HRLD  TSG++V+A  +AA + L + F  R ++K Y +L+ G     +  I+
Sbjct: 404 EATGPLIVHRLDMSTSGLMVIALNKAANKSLQKQFITRTVKKRYVALLTGELSQDEGIIS 463

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L +          V  ++      A + ++VI         + + P TGRTHQLRVH+
Sbjct: 464 LPL-RGDFDDRPRQLVCFEH---GKPAETKWQVISRR-DGLTKVHLYPKTGRTHQLRVHS 518

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            H   +  PIVGD  Y              +L+LHA  + L HP  G 
Sbjct: 519 AHPKGLNMPIVGDDLYGKK---------SQRLHLHAELLALNHPTTGE 557


>gi|194761918|ref|XP_001963138.1| GF15796 [Drosophila ananassae]
 gi|190616835|gb|EDV32359.1| GF15796 [Drosophila ananassae]
          Length = 524

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 117/268 (43%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ L +G++ V+ ++V  + +I+   +         L +++  
Sbjct: 160 LDVF-SREFRAAPPEVYERSLEAGKLTVNNEKVPKDYKIKHNDL---------LANVVHR 209

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +T         ++Y D  I V NKPA I V       ++   F+ +  +  
Sbjct: 210 HEVPVTSQPIT---------IVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEHN 259

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
            +  R  HRLD+ TSG+L+  RT   A+ L +  R R++QK Y   V G  P    EC  
Sbjct: 260 LKNLRTIHRLDRLTSGLLLFGRTSDKARELEQQIRNRQVQKEYVCRVEGRFPDGIIECCE 319

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  ++ +        +  +P TGR HQ+RVH 
Sbjct: 320 PIDVVSYKIG-----VCKVSPKGKDCKTTFQRIGEV--GDCSIVHCKPLTGRMHQIRVHL 372

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI  D  Y     G    P++ +
Sbjct: 373 QYLGYPISNDPLYNHEVFG----PLKGR 396


>gi|226355886|ref|YP_002785626.1| ribosomal large subunit pseudouridine synthase Rlu family
           [Deinococcus deserti VCD115]
 gi|226317876|gb|ACO45872.1| putative Ribosomal large subunit pseudouridine synthase, Rlu family
           [Deinococcus deserti VCD115]
          Length = 252

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 58/244 (23%), Positives = 97/244 (39%), Gaps = 14/244 (5%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
               K  ++ E    YV +KPA              D       ++        HRLD+E
Sbjct: 8   PPPGKPRVIVEHPDFYVVHKPALWLTHPVRARIDVPDVLTYMQTETGEPDLAPPHRLDRE 67

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG  +++R   AA+     F+   + K Y ++V G P  ++  +   L      G + V
Sbjct: 68  TSGAQILSRDSDAARRFFTLFKTHLVGKTYLAIVHGNPTWERYTLDAPLGDLGLGGANRV 127

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + +        A++ F+V+D  A     +E  P +GR HQ+R H  H+G P+VGD  Y 
Sbjct: 128 TIRQAVVPDGRAAVTDFQVVDRRA-GHSLIEAYPRSGRLHQIRAHLHHLGLPMVGDKIYG 186

Query: 274 ANFKGNF------------TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
            + +                     +  LHA  +     +G ++ +  PL   +   WDS
Sbjct: 187 RDPQAFLDFMETGQTPALTERLGLPRQALHAARIAFSW-DGAQMSVEVPLARDLQAYWDS 245

Query: 322 LGFK 325
           L  +
Sbjct: 246 LAGE 249


>gi|326570051|gb|EGE20097.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis BC7]
          Length = 242

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 70/240 (29%), Positives = 119/240 (49%), Gaps = 23/240 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ S +     +F KSI +YED  I+V +KPAG+    G  +       L+S +      
Sbjct: 14  LELSHDDLFFHEFAKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPN 69

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANW 201
            RL HRLD +TSG+++ A++  A  H+++ F  R  QK Y ++V+G     +KK  +   
Sbjct: 70  IRLIHRLDMDTSGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVP 129

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--------FAQKFCWLEMQPHTGRTH 253
           +  +      ++  +  N      A++H++V+           A     + ++P TGR+H
Sbjct: 130 VRYEPTTKPRHIVDMDWN----KRALTHYEVMHHELRCDDNGRAYPVTRVALKPITGRSH 185

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           QLRVH +H+G  ++GD  Y  +        + N+L LHA  + L HP  G  +   +P+P
Sbjct: 186 QLRVHMVHLGHVMIGDPIYAEDV----ALKLSNRLNLHAHKLRLKHPTHGIWMDWVSPVP 241


>gi|146292104|ref|YP_001182528.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|145563794|gb|ABP74729.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
          Length = 574

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 105/246 (42%), Gaps = 26/246 (10%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E  ++D +  LT  ++     +LY+D  + + NKPA      G  I   +   ++     
Sbjct: 345 EGLVVDDNPLLTNPAEGKTLSILYQDEAMAIVNKPAEFLSVPGKEIEDSVYSRMQQ-TFP 403

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-----KNK 194
               P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ GIP     K  
Sbjct: 404 NATGPLIVHRLDMSTSGLMVIALTKDAHKQLQKQFIQRTVTKRYVALLAGIPTAMADKQA 463

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTH 253
              I+  L +          V     +    A +H+++           + + P TGRTH
Sbjct: 464 AGQISLPL-RGDLDDRPRQLVC---HEFGKAAQTHWELSHIDEMARTARVYLFPKTGRTH 519

Query: 254 QLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           QLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP    +++   
Sbjct: 520 QLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHPVTREQMRFQ- 569

Query: 310 PLPAHM 315
            +    
Sbjct: 570 -IDPDF 574


>gi|15828588|ref|NP_325948.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [Mycoplasma pulmonis UAB
           CTIP]
 gi|14089530|emb|CAC13290.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE C (PSEUDOURIDYLATE
           SYNTHASE) (URACIL HYDROLYASE) [Mycoplasma pulmonis]
          Length = 282

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 56/312 (17%), Positives = 113/312 (36%), Gaps = 39/312 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVV 65
           +   +  N++    + +   ++  ++    +QK+ R   ++V+ KR +  N  +    ++
Sbjct: 1   MFEFIATNNDHGRIIFKVLLSYLNNVPVSRIQKLFREKDIKVNGKRNIDKNFIVSKDDLI 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +I  + N                 L       K  +++ED  I V NK AG+S+      
Sbjct: 61  QIYGLTNVKQ-------------KLVFKKIEQKFNVIFEDQNILVINKQAGVSMHSDENS 107

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                    ++       P    RLD+ TSG++V A+  +  + L  +  +R+      +
Sbjct: 108 LDKQVLSYLNFKQVDSFVPSSIGRLDKVTSGVVVYAKNYSILKTLKSNEHLRKTYVFMSN 167

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +         + I +    K +       + K+N + +    +    +            
Sbjct: 168 IT----LEPNQKIEHVFYHKYNPIKKKAELFKENVEESKITKTLLYKVKNNNY------A 217

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +  TGR HQ+R     +G PI GD KY              ++YLH+  +   H   G  
Sbjct: 218 ELITGRKHQIRATLSKLGFPIFGDVKYGGKKD--------KRVYLHSYKIKF-HSLKGEF 268

Query: 306 ------QITAPL 311
                 +  AP+
Sbjct: 269 EYLNNQEFIAPI 280


>gi|45402|emb|CAA78140.1| putative protein of unknown function [Pseudomonas aeruginosa PAO1]
          Length = 185

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 50/205 (24%), Positives = 89/205 (43%), Gaps = 26/205 (12%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS M   +   V  +    RLD+     +P  +   L   ++ G++ VD   V+  + + 
Sbjct: 1   MSDMIQ-RAAEVPFELGGQRLDQIAAQLFPEHSRSRLAGWIKDGRLTVDGAVVRPRDIVH 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           SG  + +     A    + +   L+               ++YED  I V +KPAG+ V 
Sbjct: 60  SGAQLVLEAEQEAQGEWLAQDIELE---------------IVYEDEHILVIDKPAGLVVH 104

Query: 121 GGSGIAYHIDGFLKSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             +G   H DG L + +       +   +  + HRLD++T+G++VVA+T  A   L    
Sbjct: 105 PAAG---HQDGTLLNALLYHVPDIANVPRAGIVHRLDKDTTGLMVVAKTLEAHTKLVAQL 161

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIA 199
           + R + +IY ++V G+       I 
Sbjct: 162 QARSVSRIYEAIVIGVI-TSGGTID 185


>gi|121613293|ref|YP_999742.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|218561715|ref|YP_002343494.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|112359421|emb|CAL34203.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|121504235|gb|EAQ72031.2| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
          Length = 300

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 60/307 (19%), Positives = 118/307 (38%), Gaps = 47/307 (15%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           Y+ ++      +  +    +   I+    QK++   ++  D   V+  N+I +G +V + 
Sbjct: 3   YIKIKLSNNGKKAFQVLMENLK-ISINEAQKLIDKKRLFCDGILVEEKNKILNG-LVEL- 59

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAY 127
                                +   ++     +++E+    +  K +GI     G    Y
Sbjct: 60  ---------------------IVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKY 98

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   +       G++  + HRLD+ETSG++++A+ + A   L   F  + +QK Y +L 
Sbjct: 99  SLSDEIWHL---WGKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALA 155

Query: 188 WGIPKNKKECIANW-LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEM 245
            G  +          L K        + + K+       AI+ F++++ F +     L  
Sbjct: 156 HGKIEENFIVDKAINLTKNYDDVKTRMQICKE----GKQAITEFEILEYFPKINATLLLC 211

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-------------ANFKGNFTSPIQNKLYLHA 292
           +P TGR HQ+RVH  +    I+GD  Y               N K         +L LH+
Sbjct: 212 KPLTGRQHQIRVHLHYKNHTILGDPLYGLSKQQIESILDEKLNPKERLKLTGALRLCLHS 271

Query: 293 RYMDLPH 299
             +   +
Sbjct: 272 YRLKFQY 278


>gi|326567226|gb|EGE17346.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis 12P80B1]
          Length = 242

 Score =  150 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 70/240 (29%), Positives = 119/240 (49%), Gaps = 23/240 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ S +     +F KSI +YED  I+V +KPAG+    G  +       L+S +      
Sbjct: 14  LELSHDDLFFHEFAKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLCINPN 69

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANW 201
            RL HRLD +TSG+++ A++  A  H+++ F  R  QK Y ++V+G     +KK  +   
Sbjct: 70  IRLIHRLDMDTSGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVP 129

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--------FAQKFCWLEMQPHTGRTH 253
           +  +      ++  +  N      A++H++V+           A     + ++P TGR+H
Sbjct: 130 VRYEPTTKPRHIVDMDWN----KRALTHYEVMHHELRCDDNGRAYPVTRVALKPITGRSH 185

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           QLRVH +H+G  ++GD  Y  +        + N+L LHA  + L HP  G  +   +P+P
Sbjct: 186 QLRVHMVHLGHVMIGDPIYAEDV----ALKLSNRLNLHAHKLRLKHPTHGIWMDWVSPVP 241


>gi|157375387|ref|YP_001473987.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157317761|gb|ABV36859.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 238

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 102/232 (43%), Gaps = 27/232 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +LY+D  + + NKP+G+    G          +   +        + HRLD  TSGI
Sbjct: 16  EIEILYQDEALILINKPSGLLSLSGKHPDN--KDSVHFRLVQDFPSCTMIHRLDFGTSGI 73

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++VA  +     L + F  R + K Y +L+ G  K  +  I   + K +    +   ++K
Sbjct: 74  MLVAMNKQVNAQLCKQFSERTVSKRYTALLHGHLKMDEGLIDFAIAKDT----ENFPLMK 129

Query: 218 QNEKGANYAISHFKVIDCFAQKF----------------CWLEMQPHTGRTHQLRVHALH 261
             ++    A+S FKV++ F Q                    +E +P +GRTHQLR+H+  
Sbjct: 130 VCQQTGKPAVSKFKVLERFVQTHNNAFFQEHKKAGDRAVTRVEFEPVSGRTHQLRLHSQQ 189

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
           +  PI+G   Y  +          ++L LHA  +   HP  G R+ I +P P
Sbjct: 190 IKHPILGCDLYATDE----AFFTSSRLLLHASELSFDHPITGERMNIISPSP 237


>gi|328773939|gb|EGF83976.1| hypothetical protein BATDEDRAFT_85504 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 264

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 101/228 (44%), Gaps = 15/228 (6%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           ++++   +  +LY D K+ V NKP  + + G       I+  LK+   +  ++  L H++
Sbjct: 36  SRYNRLFEVSILYNDGKLLVINKPWNVRIDGPVDETTTIEFLLKATFPT-YRRLFLLHQI 94

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+ +   T+  A  +   F  R+IQK Y ++V G    ++  I   L  +     
Sbjct: 95  DYATSGVHMWGLTKHTATIMGRMFLRRQIQKTYLAIVCGTVDQQEFQIQLPLAPRPENDR 154

Query: 211 DYVHVVK--QNEKGANYAISHFKVIDCFAQ-----KFCWLEMQPHTGRTHQLRVHALHMG 263
             +HV    ++      A +  +V+              LE+QPHTGR HQLRVH   +G
Sbjct: 155 -LMHVPTLGEDVPDTKAAQTFVRVLRRGTLAETQIPVTLLELQPHTGRRHQLRVHLSSIG 213

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
            PIV D  Y A        PI +++ LH+       P  G      AP
Sbjct: 214 HPIVNDRVYGA-----LNVPIYHRMMLHSWRTQFVWPGSGVPFNFEAP 256


>gi|225619928|ref|YP_002721185.1| RsuA/RluD family pseudouridine synthase [Brachyspira hyodysenteriae
           WA1]
 gi|225214747|gb|ACN83481.1| Pseudouridine synthase, RsuA/RluD family [Brachyspira
           hyodysenteriae WA1]
          Length = 217

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 56/204 (27%), Positives = 96/204 (47%), Gaps = 14/204 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED+     +K AGI V        ++   +K           L HR+D+ TSGI+++
Sbjct: 3   IIYEDNYFIAIDKEAGIEV------DDNLINIIKKEYSHIDN-LYLVHRIDKFTSGIVIL 55

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR     ++  ++F+ + I K+Y ++V G  K +   I   +          + +    +
Sbjct: 56  ARDEETKKYFEDAFKNKTINKVYHAIVNGKVKKENGTIDISIGIDKKNPNRRIPLS--IK 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +G   AI+H+KV+    +    LE++P TGRTHQ+RVH  ++G PI+GD  Y      N 
Sbjct: 114 EGGESAITHYKVLKRLNE-HTLLELKPLTGRTHQIRVHLSYIGHPIIGDKIYSK----NA 168

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR 304
                    L A+ +   HP   +
Sbjct: 169 DIYKMKGFALIAKEIHFVHPFTKK 192


>gi|332187172|ref|ZP_08388912.1| RNA pseudouridylate synthase family protein [Sphingomonas sp. S17]
 gi|332012872|gb|EGI54937.1| RNA pseudouridylate synthase family protein [Sphingomonas sp. S17]
          Length = 214

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 57/219 (26%), Positives = 101/219 (46%), Gaps = 15/219 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L+ D +  V +KPAG+ V      +  ++  L+S      + P+  HRLD++TSG L
Sbjct: 4   DRVLFIDGEALVIDKPAGLPVDPPRDGSLSLENHLESLRFGFKRWPQAVHRLDRDTSGCL 63

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +++R   A     ++F   +++K Y +++ G+ + +   I   L K S     +  V   
Sbjct: 64  LLSRNPKAHARFQQAFEAGQVEKRYLAVLDGVVEGE-GMIDLALAKVSTREAGWRMVA-- 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFK 277
            +     A + ++ +         +E +P TGRTHQ+RVHA   +G  +VGD  Y A   
Sbjct: 121 -DPAGKAARTGWRAL-RHEGGRTLVEFRPETGRTHQIRVHAATGLGAAVVGDPVYGAGEA 178

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           G         + LHA  + +P  +    +   AP+P   
Sbjct: 179 GG--------MLLHAASLTVPRGDAKDPITAEAPVPERF 209


>gi|319425400|gb|ADV53474.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 574

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 105/246 (42%), Gaps = 26/246 (10%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E  ++D +  LT  ++     +LY+D  + + NKPA      G  I   +   ++     
Sbjct: 345 EGLVVDDNPLLTNPAEGKTLSILYQDEAMAIVNKPAEFLSVPGKEIEDSVYSRMQQ-TFP 403

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-----KNK 194
               P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ GIP     K  
Sbjct: 404 NATGPLIVHRLDMSTSGLMVIALTKDAHKQLQKQFIQRTVTKRYVALLAGIPTAMADKQA 463

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTH 253
              I+  L +          V     +    A +H+++           + + P TGRTH
Sbjct: 464 AGQISLPL-RGDLDDRPRQLVC---HEFGKAAQTHWELSHIDEMARTARVYLFPKTGRTH 519

Query: 254 QLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           QLRVH  H   +  PIVGD  Y             N+L+LHA  + L HP    +++   
Sbjct: 520 QLRVHCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHPVTREQMRFQ- 569

Query: 310 PLPAHM 315
            +    
Sbjct: 570 -IDPDF 574


>gi|326564292|gb|EGE14522.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis 103P14B1]
 gi|326573848|gb|EGE23801.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis O35E]
 gi|326574731|gb|EGE24667.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis 101P30B1]
          Length = 242

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 70/240 (29%), Positives = 119/240 (49%), Gaps = 23/240 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ S +     +F KSI +YED  I+V +KPAG+    G  +       L+S +      
Sbjct: 14  LELSHDDLFFHEFTKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPN 69

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANW 201
            RL HRLD +TSG+++ A++  A  H+++ F  R  QK Y ++V+G     +KK  +   
Sbjct: 70  IRLIHRLDMDTSGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVP 129

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--------FAQKFCWLEMQPHTGRTH 253
           +  +      ++  +  N      A++H++V+           A     + ++P TGR+H
Sbjct: 130 VRYEPTTKPRHIVDMDWN----KRALTHYEVMHHELRCDDNGRAYPVTRVSLKPITGRSH 185

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           QLRVH +H+G  ++GD  Y  +        + N+L LHA  + L HP  G  +   +P+P
Sbjct: 186 QLRVHMVHLGHVMIGDPIYAEDV----ALKLSNRLNLHAHKLRLKHPTHGIWMDWVSPVP 241


>gi|329724870|gb|EGG61373.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU144]
          Length = 274

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 58/279 (20%), Positives = 111/279 (39%), Gaps = 32/279 (11%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
            Y  +   +L ++  S ++ ++K+     N +++G  V IP      N++          
Sbjct: 19  QYLKLPKKDLHQLNMSKEILINKEYGTLLNNVKTGDHVEIPTPNEVSNYL---------- 68

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRL 146
                   +  + + YED  + +  KP G+            +  +   + +   +    
Sbjct: 69  ------PSYRYAQIYYEDDDLAIVMKPKGVKTHP--NDLKESNTLMNHVIYTVDSEYVEP 120

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLDQET G+L+VA+     + L        I +IY + V  +   K + I   + K  
Sbjct: 121 IHRLDQETVGLLIVAKNPLMKKILDRMLEYNEITRIYKANVKALLPIKPQTIDMPIGKD- 179

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                +    ++       AI+H        +  C L+++  TGRTHQ+RVH   +G P+
Sbjct: 180 ----KFHSNKRRISNTGQRAITHIIDSKMIKEGVCQLDIKLDTGRTHQIRVHLAEIGHPV 235

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +GD  Y  +           +L L++  ++  HP    +
Sbjct: 236 IGDPLYGTS--------TLRQLELNSHQIEFTHPLTQEI 266


>gi|153810096|ref|ZP_01962764.1| hypothetical protein RUMOBE_00477 [Ruminococcus obeum ATCC 29174]
 gi|149834274|gb|EDM89354.1| hypothetical protein RUMOBE_00477 [Ruminococcus obeum ATCC 29174]
          Length = 236

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 56/222 (25%), Positives = 100/222 (45%), Gaps = 19/222 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG----QKPRLTHRLDQ 152
           ++ ++++ED  I V +K AGI+VQ     A  ++  LK+++  K         + HRLDQ
Sbjct: 8   IEDMIIFEDKDILVCHKAAGIAVQNARIGAADMESSLKNYLALKNTETVPYLGVVHRLDQ 67

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              G+LV A+ + AA  LT       I K Y ++   + +  +  + ++L+K        
Sbjct: 68  PVEGVLVFAKNKKAAAGLTRQITTGNIVKEYLAVTDRMSEKHQGRLEDYLIKNGRTNTS- 126

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFC------WLEMQPHTGRTHQLRVHALHMGCPI 266
             VV     GA  A+  ++VI   + +         +++   TGR HQ+RV   H G P+
Sbjct: 127 -EVVTSKTSGAKKAVLDYEVIHQISDERTESGKRILIKIHLETGRHHQIRVQMAHAGMPL 185

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           +GD KY           +       + ++   HP  G +++ 
Sbjct: 186 LGDRKYNPGEISQLPLGL------CSCHLIFRHPITGKKMEF 221


>gi|291383615|ref|XP_002708351.1| PREDICTED: RNA pseudouridylate synthase domain containing 4
           [Oryctolagus cuniculus]
          Length = 367

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 74/275 (26%), Positives = 119/275 (43%), Gaps = 38/275 (13%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   +L++D  + V +KP G+ V GG G+   I   L    K     K + 
Sbjct: 85  VHPNVLAKALSRGILHQDKDLVVISKPYGLPVHGGPGVRLCISDVLPILAKMLRGHKAEP 144

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+   +  A  + E FR R++ K YW++   +P      +   ++
Sbjct: 145 LHLCHRLDKETTGVMVLTWEKEVAHQVQELFRTRQVVKKYWAITVHVPVPSAGVVDIPII 204

Query: 204 KKSHIGGDYVH---------------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G    H               V  ++ + A+ A++ ++V+            QP 
Sbjct: 205 EKEVQGQRQHHKMTLSPSYRMDNGKMVKVRSSRSAHLAVTQYQVLSSTLSSALLEL-QPI 263

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKY------------CANFKGNFTSPIQNK---LYLHA 292
           TG  HQLRVH    + CPI+GDHKY                K       + +   L+LHA
Sbjct: 264 TGIKHQLRVHLSFGLECPILGDHKYSDWNRLAPQKLPGGTLKKLGLEQSKARHIPLHLHA 323

Query: 293 RYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGFK 325
           R + LP        L +T  LP   V++   LG +
Sbjct: 324 RQLILPALGSRKEELNLTCKLPHFFVRSLSRLGLE 358


>gi|326568269|gb|EGE18351.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis BC8]
          Length = 242

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 70/240 (29%), Positives = 119/240 (49%), Gaps = 23/240 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ S +     +F KSI +YED  I+V +KPAG+    G  +       L+S +      
Sbjct: 14  LELSHDDLFFHEFAKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPN 69

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANW 201
            RL HRLD +TSG+++ A++  A  H+++ F  R  QK Y ++V+G     +KK  +   
Sbjct: 70  IRLIHRLDMDTSGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVP 129

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--------FAQKFCWLEMQPHTGRTH 253
           +  +      ++  +  N      A++H++V+           A     + ++P TGR+H
Sbjct: 130 VRYEPTTKPRHIVDMDWN----KQALTHYEVMHHELRCDDNGRAYPVTRVALKPITGRSH 185

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           QLRVH +H+G  ++GD  Y  +        + N+L LHA  + L HP  G  +   +P+P
Sbjct: 186 QLRVHMVHLGHVMIGDPIYAEDV----ALKLSNRLNLHAHKLRLKHPTHGIWMDWVSPVP 241


>gi|315126893|ref|YP_004068896.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
 gi|315015407|gb|ADT68745.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
          Length = 237

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 61/220 (27%), Positives = 101/220 (45%), Gaps = 17/220 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQET 154
           ++Y+D  + V NKP+G+    G       D      V+ +  K       +L HRLD  T
Sbjct: 26  IIYQDEALLVINKPSGLLSLSGKNPLN-WDSVHYRLVNGQQGKTAAFAEAKLPHRLDFGT 84

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI++VA    +A++L + F+   I K Y +++ G   +    I   + K       +  
Sbjct: 85  SGIMLVALNSESAKNLNQQFQSHTISKRYVAMLQGKVCDNHGQINYPIAKDKL----HFP 140

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            VK        A++H+ V+  F Q     ++  P TGRTHQLR+H+  +G PI+G   Y 
Sbjct: 141 RVKLCNTTGKAALTHYTVLKRFIQPIKTLVQFTPVTGRTHQLRIHSHAIGHPILGCDLY- 199

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
              K   +  + ++L LHA  +   HP   + + +    P
Sbjct: 200 ---KSEQSEQMASRLQLHASDIYFHHPSTQKPMHLHCASP 236


>gi|299148873|ref|ZP_07041935.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_23]
 gi|298513634|gb|EFI37521.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_23]
          Length = 612

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 70/295 (23%), Positives = 117/295 (39%), Gaps = 71/295 (24%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ + L    +  +  +++ED  + V NKPAG+    G   A   
Sbjct: 317 CEPILQHMLQGLEVDENPL-LNPVHEEEELEIVFEDEWLLVVNKPAGMLSVPGK--AEDR 373

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           D           +   P + HRLD  TSG+L+VA+T+   + L   F  R I+K Y +++
Sbjct: 374 DSVYHRLKKKYPEATGPMIVHRLDMATSGLLLVAKTKEVHRDLQAQFANRSIKKRYVAVL 433

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYV----------------------------HVVKQN 219
            G+    ++ I     K   I  + V                                 +
Sbjct: 434 DGVIIKTEKEIKPIAEKAILIAKETVLTKKTAKAERTGNTGRIELPLCLNPLDRPRQMVS 493

Query: 220 EKGANYAISHFKVID--------------------------CFAQKFCWLEMQPHTGRTH 253
            +    AI+ +++I                             ++K+  +   P TGRTH
Sbjct: 494 SEHGKEAITEYQIISESERITSESENTFNESNRIDESERNINESRKYTRIVFYPLTGRTH 553

Query: 254 QLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QLRVHA H   +GCPI+GD  Y             ++LYLHA Y++  HP  G +
Sbjct: 554 QLRVHAAHPEGLGCPILGDELYGKK---------ADRLYLHAEYIEFRHPIYGDI 599


>gi|254457748|ref|ZP_05071176.1| pseudouridine synthase D [Campylobacterales bacterium GD 1]
 gi|207086540|gb|EDZ63824.1| pseudouridine synthase D [Campylobacterales bacterium GD 1]
          Length = 308

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 60/289 (20%), Positives = 117/289 (40%), Gaps = 42/289 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +             Q+++  G++ ++ +                      +     E + 
Sbjct: 19  YLIKEL-DYTQKEAQRLIAKGRLFINGEP---------------------MTRTAGEIEG 56

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
               +     +  L++  +Y   +  VF+KP+G+ +   +         +       G+ 
Sbjct: 57  EFEFIYFEPITKGLEATAVY--DEFVVFDKPSGVLIHPQN--RKTPYSLIDELKYQYGRD 112

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HR+DQETSG+++ A+ + + + +   F  R ++K Y +LV G  K +  CI   LL
Sbjct: 113 ANIAHRIDQETSGLVLCAKNKESERDIKMMFEQRDMKKKYLALVHGELK-ESICIEEPLL 171

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
           ++         VVK +E+G   + +  + +  FA+     +E  P+TGR HQ+RVH  H+
Sbjct: 172 RREDESAIVRMVVKVHEEG-KASKTDIRPLKYFAETDMTLVECSPYTGRQHQIRVHLFHV 230

Query: 263 GCPIVGDHKYCA-------------NFKGNFTSPIQNKLYLHARYMDLP 298
             PIVGD  Y               + +        ++L LHA  ++  
Sbjct: 231 KHPIVGDPIYGQSEEDIVKFLDKELDAEKRIELSGASRLLLHANELEFE 279


>gi|326562457|gb|EGE12775.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis 46P47B1]
          Length = 242

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 70/240 (29%), Positives = 119/240 (49%), Gaps = 23/240 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ S +     +F KSI +YED  I+V +KPAG+    G  +       L+S +      
Sbjct: 14  LELSHDDLFFHEFTKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPN 69

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANW 201
            RL HRLD +TSG+++ A++  A  H+++ F  R  QK Y ++V+G     +KK  +   
Sbjct: 70  IRLIHRLDMDTSGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVP 129

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--------FAQKFCWLEMQPHTGRTH 253
           +  +      ++  +  N      A++H++V+           A     + ++P TGR+H
Sbjct: 130 VRYEPTTKPRHIVDMDWN----KRALTHYEVMHHELRCDDNGRAYPVTRVALKPITGRSH 185

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           QLRVH +H+G  ++GD  Y  +        + N+L LHA  + L HP  G  +   +P+P
Sbjct: 186 QLRVHMVHLGHVMIGDPIYAEDV----ALKLSNRLNLHAHKLRLKHPTHGIWMDWVSPVP 241


>gi|260437803|ref|ZP_05791619.1| ribosomal large subunit pseudouridine synthase family protein
           [Butyrivibrio crossotus DSM 2876]
 gi|292809827|gb|EFF69032.1| ribosomal large subunit pseudouridine synthase family protein
           [Butyrivibrio crossotus DSM 2876]
          Length = 222

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 58/227 (25%), Positives = 108/227 (47%), Gaps = 13/227 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETS 155
           K I++YED  I V NKP G+  Q        +  ++ +    + +     + +RLD+   
Sbjct: 3   KDIIVYEDDNIIVCNKPVGMPSQSDRTFEQDLVSYVLTHRTEQNEPAYAAIINRLDKPVG 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+ + AA  L+       I+K Y++LV G P +K E   ++LLK      +   V
Sbjct: 63  GLVLFAKNKKAAAGLSAVSGEHGIEKNYYALVKGSPCDKGE-FTDYLLKDGK--NNISTV 119

Query: 216 VKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             ++ KG+  A+  ++ +       +K+  + ++  TGR HQ+RV   H G P+ GD KY
Sbjct: 120 TDKDTKGSKKAVLLYEKLGEKTIDGEKYSLMRVRLLTGRHHQIRVQFSHHGYPLYGDIKY 179

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
            ++F+            L A ++   +P G  R+ + A   + + + 
Sbjct: 180 NSDFRNRRDVSP----ALFAYHLSFKNPVGADRITVEAEPESEIFRL 222


>gi|222110929|ref|YP_002553193.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221730373|gb|ACM33193.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 222

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 62/216 (28%), Positives = 98/216 (45%), Gaps = 10/216 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ D  + V  KP+G+    G G        L +   +      + HRLDQ TSG++++A
Sbjct: 12  VHVDDTLLVLEKPSGLLCVPGRGPD--KQDALSTRAQALWPDALIVHRLDQPTSGLVLMA 69

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHV--VKQ 218
           R  A  + L+ SF  R + K Y ++V G  P         W      I  D+        
Sbjct: 70  RGAAMQRALSHSFAQRLVHKRYRAVVAGRMPPPDPAHADGWGEIALPIAADWERRPLRVV 129

Query: 219 NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +      +++ ++V+   A +    +E++P TGRTHQLRVH   +G PI+GD  Y A+  
Sbjct: 130 DATHGQPSLTRWRVLAHDAARDTTSVELEPVTGRTHQLRVHLAALGHPILGDQLY-ADAP 188

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
               +P   +L LHA  ++  HP  G     A  P 
Sbjct: 189 VQARAP---RLLLHACVLEFAHPLQGGWCAFASAPP 221


>gi|315658673|ref|ZP_07911543.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           lugdunensis M23590]
 gi|315496304|gb|EFU84629.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           lugdunensis M23590]
          Length = 284

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 63/297 (21%), Positives = 114/297 (38%), Gaps = 53/297 (17%)

Query: 30  PHINFVNLQK---------ILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           P +    LQ+          ++ +G + V+ + V    ++Q G  + I            
Sbjct: 10  PDVLKSFLQQQGFSKKTTSAIKQNGALLVNHEPVTVRYQLQPGDKLTI------------ 57

Query: 80  EQKILDSSVNLTKHSDFL-KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              IL + +       F     ++YED  + +  KP   S+Q  +    H    L   V 
Sbjct: 58  ---ILPTEIPSANLQAFHHPLDIVYEDDYLLIVCKP---SIQNCAPSREHPHESLIEQVI 111

Query: 139 SKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   +      P +  RLD+ T+G++++A+       L+      +I K Y +L  G   
Sbjct: 112 AYCHENDNDFTPHIVTRLDRNTTGLVLLAKHGHIHHLLSHI----KINKRYIALCHGA-T 166

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +  I   + +      +   + +Q      YA S ++ ++   Q     E+  HTGRT
Sbjct: 167 QPEGIIEAPIAR-----ANDSIITRQVSSTGKYAKSTYRTLNSK-QNVSLCEVTLHTGRT 220

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQIT 308
           HQ+RVH  ++G P++GD  Y  N        +Q         +   HP     + IT
Sbjct: 221 HQIRVHFQYIGHPLIGDALYGGNHDMIHNHCLQ------CTALQFKHPILHKTISIT 271


>gi|121594293|ref|YP_986189.1| ribosomal large subunit pseudouridine synthase A [Acidovorax sp.
           JS42]
 gi|120606373|gb|ABM42113.1| ribosomal large subunit pseudouridine synthase A [Acidovorax sp.
           JS42]
          Length = 222

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 60/216 (27%), Positives = 95/216 (43%), Gaps = 10/216 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ D  + V +KP+G+    G G        L +   +      + HRLDQ TSG++++A
Sbjct: 12  VHVDDTLLVLDKPSGLLCVPGRGPD--KQDALSTRAQALWPDALIVHRLDQPTSGLVLMA 69

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHV--VKQ 218
           R  A  + L+ SF  R + K Y ++V G  P         W      I  D+        
Sbjct: 70  RGAAMQRALSHSFAQRLVHKRYRAVVAGRMPPPDPAHADGWGEIALPIAADWERRPLRVV 129

Query: 219 NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +      +++ ++V+   A +    +E++P TGRTHQLRVH   +G PI+GD  Y     
Sbjct: 130 DATHGQPSLTRWRVLAHDAARDTTSVELEPVTGRTHQLRVHLAALGHPILGDQLY----A 185

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
                    +L LHA  ++  HP  G     A  P 
Sbjct: 186 DASVQARAPRLLLHACVLEFAHPLQGGWCAFASAPP 221


>gi|332527619|ref|ZP_08403666.1| putative ribosomal large subunit pseudouridine synthase A
           [Rubrivivax benzoatilyticus JA2]
 gi|332112022|gb|EGJ11999.1| putative ribosomal large subunit pseudouridine synthase A
           [Rubrivivax benzoatilyticus JA2]
          Length = 210

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 57/210 (27%), Positives = 89/210 (42%), Gaps = 11/210 (5%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L    LY D    V  KPAG+    G G        L +   +        HRLD  TS
Sbjct: 1   MLPPDCLYADEHCLVLAKPAGLLAVPGRGPD--KQDCLVARAQACWPDALTVHRLDMATS 58

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V  R  AA + L+ +F  RR+ K Y ++V G+       +   L+           V
Sbjct: 59  GLMVYGRGAAAQRTLSIAFAERRVDKRYVAVVAGLIAEDTGEVDAPLICD-WPNRPRQKV 117

Query: 216 VKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             ++      +++ ++V+    A     +E++P TGR+HQLR+H   +G P++GD  Y  
Sbjct: 118 CHEH---GKPSLTRWRVLARDRAAGRTRVELEPVTGRSHQLRLHLATIGHPMLGDDLYAP 174

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                    +     LHA  +  PHP  G 
Sbjct: 175 PELAAAAPRLL----LHAERLAFPHPVTGE 200


>gi|317504866|ref|ZP_07962822.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           salivae DSM 15606]
 gi|315664050|gb|EFV03761.1| ribosomal large subunit pseudouridine synthase A [Prevotella
           salivae DSM 15606]
          Length = 522

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 97/233 (41%), Gaps = 22/233 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           ++   N  +         +YED+ I V  KPAG+    G      +   +      +   
Sbjct: 307 IEVETNPLEQETHQTLEWIYEDNDIAVVCKPAGMLSVPGKNQRESVRSLVLHR-HPEATG 365

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+LVVA    +  +L + F+   ++K Y +L+    K  K       L
Sbjct: 366 PLIVHRLDMATSGLLVVALNVESYVNLQQQFKQHHVEKQYVALLSVPHKGAKHGQICLPL 425

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V K +      A++ ++ +D      C +++ P TGRTHQLR+H  H  
Sbjct: 426 RPDLTDRPRQIVDKVH---GKEAVTDYQFMDD-----CRVKLYPRTGRTHQLRMHCAHAE 477

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
            +  PI GD  Y              +L+LHA  +   HP+ G RL      P
Sbjct: 478 GLNNPIRGDELYG---------TGAQRLFLHAEELAFDHPKTGKRLHFECQAP 521


>gi|313672668|ref|YP_004050779.1| pseudouridine synthase [Calditerrivibrio nitroreducens DSM 19672]
 gi|312939424|gb|ADR18616.1| pseudouridine synthase [Calditerrivibrio nitroreducens DSM 19672]
          Length = 211

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 55/225 (24%), Positives = 96/225 (42%), Gaps = 17/225 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   ++Y+D  I V NK  G+ V          +  LK  +     +  + HRLD  TSG
Sbjct: 1   MNFEIVYDDDDILVVNKGHGLLVVPDRYDKDLPN--LKDLLTEIYGRIFVVHRLDYGTSG 58

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I+V A+   + + L+  F    + K Y+++  G+      C+        H         
Sbjct: 59  IMVFAKNERSHRSLSIQFERSEVDKRYYAICKGVFPADLTCMLPISKVNYH------GRY 112

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K N K    A++ F V+D F+ K   +++ P TGR+HQ+RVH   +G P+  D  Y    
Sbjct: 113 KINFKSGRKALTSFSVLDRFSDK-TLIDVVPLTGRSHQIRVHLKALGYPLYYDFLYNEKR 171

Query: 277 KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWD 320
           +         +L L A Y+   HP +   ++  + +   + +   
Sbjct: 172 ED-------KRLTLQAYYLRFRHPVKSTTMEFQSDISEFLREILK 209


>gi|331703735|ref|YP_004400422.1| RNA pseudouridylate synthase [Mycoplasma mycoides subsp. capri LC
           str. 95010]
 gi|328802290|emb|CBW54444.1| RNA pseudouridylate synthase [Mycoplasma mycoides subsp. capri LC
           str. 95010]
          Length = 302

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 65/307 (21%), Positives = 137/307 (44%), Gaps = 38/307 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +   VV  +++N  L ++ K  +       + K +R+  ++++ KR+   N  ++   V+
Sbjct: 1   MTKFVVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRISDKNYLLEINDVI 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +    ++   II++Q    S+VNL          ++YED+ I + NKP  + +     +
Sbjct: 61  EVY---DSNKPIIRDQFNYISNVNLD---------IVYEDNNILIVNKPNNLEMHSTYNL 108

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +D  +KS++  K +              HRLD+ TSG+++ A+ + ++  LT +F+ 
Sbjct: 109 --CLDDMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSTILTNAFKS 166

Query: 177 R-RIQKIYWSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + +I K Y++L        +   +  ++   S+I      + K+N     Y  + FK+I+
Sbjct: 167 KDQINKYYYALTSSDWNLDEFLQVNGYINYDSNIKKADFSLDKKN--NYKYCQTEFKLIN 224

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                   + ++  TG+ HQ+R        PI+ D +Y      +        +YL A  
Sbjct: 225 KN-----LILVKLITGKKHQIRSVLSFYNHPILNDFRYNGKKINDLKM-----IYLSAFK 274

Query: 295 MDLPHPE 301
           ++  + E
Sbjct: 275 IEFKNLE 281


>gi|57169014|ref|ZP_00368142.1| RNA pseudouridylate synthase family [Campylobacter coli RM2228]
 gi|57019559|gb|EAL56249.1| RNA pseudouridylate synthase family [Campylobacter coli RM2228]
          Length = 336

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 61/276 (22%), Positives = 103/276 (37%), Gaps = 46/276 (16%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           QK++   ++  D   V+  N+I  G V                         +   ++  
Sbjct: 69  QKLIDKKRLFCDGILVEEKNKILKGDV-----------------------ELIVYENNPK 105

Query: 98  KSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
              +++E+    V  K +GI     G    Y +   +       G+K  + HRLD+ETSG
Sbjct: 106 GVEIVFENEDFAVLEKESGILSHPNGRHCKYSLSDEIWHL---WGKKACVAHRLDKETSG 162

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN-WLLKKSHIGGDYVHV 215
           +++VA+ + A   L   F  ++IQK Y +L  G  K          L K        + +
Sbjct: 163 LILVAKHKKAQIELKTMFEKKQIQKEYLALASGEIKVNFIVDQAMDLTKDYDDVKTRMQI 222

Query: 216 VKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                +    AI+ F+V+  + +     L  +P TGR HQ+RVH  +    I+GD  Y  
Sbjct: 223 C----ENGKKAITEFEVLSFYPKLNATLLLCKPLTGRQHQIRVHLFYKNHKILGDPLYGL 278

Query: 275 NFKG-------------NFTSPIQNKLYLHARYMDL 297
             K                      +L LH+  +  
Sbjct: 279 EKKDIEKILDDKMDIEERIKLSGAKRLCLHSYRLKF 314


>gi|296113951|ref|YP_003627889.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis RH4]
 gi|295921645|gb|ADG61996.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis RH4]
          Length = 242

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 118/240 (49%), Gaps = 23/240 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ S +     +F KSI +YED  I+V +KPAG+    G  +       L+S +      
Sbjct: 14  LELSHDDLFFHEFAKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPN 69

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANW 201
            RL HRLD +TSG+++ A++  A  H+++ F  R  QK Y ++V+G     +KK  +   
Sbjct: 70  IRLIHRLDMDTSGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVP 129

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--------FAQKFCWLEMQPHTGRTH 253
           +  +      ++  +  N      A++H++V+                 + ++P TGR+H
Sbjct: 130 VRYEPTTKPRHIVDMDWN----KQALTHYEVMHHELRCDDNGRTYPVTRVALKPITGRSH 185

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           QLRVH +H+G  ++GD  Y  +        + N+L LHA  + L HP  G  +   +P+P
Sbjct: 186 QLRVHMVHLGHVMIGDPIYAEDV----ALKLSNRLNLHAHKLRLKHPTHGIWMDWVSPVP 241


>gi|291518263|emb|CBK73484.1| ribosomal large subunit pseudouridine synthase D [Butyrivibrio
           fibrisolvens 16/4]
          Length = 218

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 58/206 (28%), Positives = 103/206 (50%), Gaps = 12/206 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +LYED  I V  KPAG++ Q  +     ++  L +++ SKG+ P   + HRLDQ   G++
Sbjct: 3   VLYEDDSIVVVYKPAGLATQTRNIGEKDMESELSNYLKSKGESPEIHVVHRLDQPVEGVM 62

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+T+ AA +LT        +K Y++++      ++  + ++L+K +        VVK+
Sbjct: 63  VFAKTKEAANNLTRQIADHSFKKHYYAIITRESFPEEGDLVDYLVKDNRTNLSK--VVKE 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           ++  A  A   +  +D +  +   L+++  TGR HQ+R+       PI+GD KY     G
Sbjct: 121 SDPRAKKASLKYHTVDEWDDRK-LLDIELFTGRHHQIRIQLASRTAPILGDVKYGGVSTG 179

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR 304
           +        L L +  +   HP  G+
Sbjct: 180 HN-------LALCSYSIGFTHPTSGK 198


>gi|227539212|ref|ZP_03969261.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
 gi|227240894|gb|EEI90909.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
          Length = 230

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 100/242 (41%), Gaps = 28/242 (11%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L++D +I   NKP G+ V          +  L+   D   Q+    HRLD++T GIL
Sbjct: 2   LDILHQDQEIVAINKPHGLLVHRSPIARDASEFALQLLRDQLQQRVYPAHRLDRKTGGIL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + + T+   + L + F+ R++ K Y ++V G     +  I   L K++            
Sbjct: 62  LFSLTKEMDKSLQQLFQDRKMNKSYLAVVRGY-TEDEGRIDYPLKKEN------------ 108

Query: 219 NEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                  A++H+K +               ++  +E  P TGR HQLR H  H+  PI+G
Sbjct: 109 --GEEQEALTHYKTLSRSEIDLPTGNFTTSRYSLVEANPETGRMHQLRKHFAHIFHPILG 166

Query: 269 DHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSLGFK 325
           D  +  N +          + + LHA  +   HP  G +  I APL     +    L  +
Sbjct: 167 DRPHGCNKQNKLWKERFEMDTMMLHASQLSFEHPTTGNIILIKAPLQPEFERVLSILKLE 226

Query: 326 YD 327
             
Sbjct: 227 SP 228


>gi|330945483|gb|EGH47033.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. pisi str. 1704B]
          Length = 176

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 62/176 (35%), Positives = 95/176 (53%), Gaps = 4/176 (2%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD++TSG+L++A+ R+  +HL E+ R   + K Y +LV G      + +   L+K + 
Sbjct: 1   HRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMALVRGNWATALKQVRAPLMKSNL 60

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             G+ +  V +       A++ FKV+  F      +E +P TGRTHQ+RVH LH G  I 
Sbjct: 61  RSGERMVEVNEE---GKEALTIFKVLRRFGDFATMVEAKPVTGRTHQIRVHTLHAGHAIA 117

Query: 268 GDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           GD KY   NF          +L+LHA  + +P P+G +L + AP+     KT + L
Sbjct: 118 GDTKYGDENFSREIRDLGGKRLFLHAYMLTVPMPDGSKLNVQAPVDDMWAKTVERL 173


>gi|283956200|ref|ZP_06373685.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 1336]
 gi|283792354|gb|EFC31138.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 1336]
          Length = 300

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 60/307 (19%), Positives = 118/307 (38%), Gaps = 47/307 (15%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           Y+ ++      +  +    +   I+    QK++   ++  D   V+  N+I +G +V + 
Sbjct: 3   YIKIKLSNNGKKAFQVLMENLK-ISINEAQKLIDKKRLFCDGILVEEKNKILNG-LVEL- 59

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAY 127
                                +   ++     +++E+    +  K +GI     G    Y
Sbjct: 60  ---------------------IVYKNNPKGVEIVFENEDFAILEKESGILSHPNGRHCKY 98

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   +       G++  + HRLD+ETSG++++A+ + A   L   F  + +QK Y +L 
Sbjct: 99  SLSDEIWHL---WGKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALA 155

Query: 188 WGIPKNKKECIANW-LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEM 245
            G  +          L K        + + K+       AI+ F++++ F +     L  
Sbjct: 156 HGKIEENFIVDKAINLTKNYDDVKTRMQICKE----GKQAITEFEILEYFPKINATLLLC 211

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-------------ANFKGNFTSPIQNKLYLHA 292
           +P TGR HQ+RVH  +    I+GD  Y               N K         +L LH+
Sbjct: 212 KPLTGRQHQIRVHLHYKNHTILGDPLYGLSKEQIESILDEKLNPKERLKLTGALRLCLHS 271

Query: 293 RYMDLPH 299
             +   +
Sbjct: 272 YRLKFQY 278


>gi|308807064|ref|XP_003080843.1| Pseudouridine synthase, RluD (ISS) [Ostreococcus tauri]
 gi|116059304|emb|CAL55011.1| Pseudouridine synthase, RluD (ISS) [Ostreococcus tauri]
          Length = 472

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 70/361 (19%), Positives = 125/361 (34%), Gaps = 90/361 (24%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL----DSSVNLTKHSDFLKSILLYEDS 106
           KR+ F  R   G   R+ P   A    +   ++      +S+ +    D     +++ED 
Sbjct: 111 KRMCFRARDGMGDGERMTPEACAAALGVPTGRVKTTLRRASLAVELARDDAPLDVVHEDD 170

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
           +  V NKP  +         +  +  L ++   +KG+ P + HRLD +TSG+ V  + ++
Sbjct: 171 EFLVVNKPPNLRFHPNH--RFEGNSLLSRALHHTKGETPYIVHRLDMDTSGVAVFVKKQS 228

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
               +   F  +  +K Y ++  G+  P      + +  +    +  +  +V    E   
Sbjct: 229 LVSDVARQFHEKTARKTYLAISVGVTPPGCGDGFVVDAPIGDHGVVKEARNVDFSGE--G 286

Query: 224 NYAISHFKVIDC--------------------------------FAQKFCWLEMQPHTGR 251
             A +  +VI                                   +     + ++P TGR
Sbjct: 287 KEARTVCEVISRKETALFDISDETVAATTTPKGVSATSETNDSSPSATAALVLVKPMTGR 346

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------------------------- 286
           THQ+RVH  H G PIV D  Y  + +    S  +N                         
Sbjct: 347 THQIRVHLAHAGLPIVSDALYGPHIRWGAQSADENEKLTWSASQLAACSSENPTQMHQMT 406

Query: 287 ---------------------KLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSLGF 324
                                +  LHA  ++L HP  G++    A +P  M +  D+LG 
Sbjct: 407 PPDECDSPHPSGVWGGSLSIGRQALHAYKLELVHPVTGQMLAWQAEMPEDMRRVCDALGL 466

Query: 325 K 325
            
Sbjct: 467 D 467


>gi|10045559|emb|CAC07917.1| putative protein [Arabidopsis thaliana]
          Length = 376

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 79/338 (23%), Positives = 130/338 (38%), Gaps = 77/338 (22%)

Query: 37  LQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +Q+ +++GQ+++D + VK  N  ++SG                   K++ S +   +   
Sbjct: 53  IQR-IQNGQIQIDGEVVKDPNTLLRSG------------------SKLVYSRLPWKEPDT 93

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRL 146
                +LYED  +   NKP+G+ V  G             W   K            P  
Sbjct: 94  PYSLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVP 153

Query: 147 THRLDQETSGILVVARTRAAAQHL-----------------TESFRMRRIQKIYWSLVWG 189
            HRL + TSGIL+ A+T+ A   L                  E    R++ KIY +L  G
Sbjct: 154 VHRLGRGTSGILLCAKTKLAKTKLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADG 213

Query: 190 IPKNKK-ECIANWLLKKSHIGGDYVHVVKQN----EKGANYAISHFKVIDCFAQKFC-WL 243
           I +  +      +++ K  IG      V Q           A S   V++   +K C  +
Sbjct: 214 IVEEDEARPFLLFVVIKQPIGVVRYPGVAQGLYVASPEGKPAFSKVFVLERDREKNCSLV 273

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY-----------------------CANFKGNF 280
           +++  +GR HQ+R+H  +MG P+VGD  Y                           + N 
Sbjct: 274 KVEIQSGRPHQIRIHLAYMGHPLVGDPLYVAGGQPKCFDPDLVDDAAAFAEDGGYRRPNQ 333

Query: 281 TSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPAHMV 316
             P     +LHA  ++LP+       ++I APLP  + 
Sbjct: 334 AVPGDCGYHLHAHQVELPNLLNTHKVVKIVAPLPPILQ 371


>gi|163755084|ref|ZP_02162205.1| ribosomal large subunit pseudouridine synthase D [Kordia algicida
           OT-1]
 gi|161325151|gb|EDP96479.1| ribosomal large subunit pseudouridine synthase D [Kordia algicida
           OT-1]
          Length = 224

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 59/220 (26%), Positives = 102/220 (46%), Gaps = 11/220 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETS 155
           K  +++E+    V NK +G+  +     A  ++  +   +    +KP   + HRLD+ TS
Sbjct: 3   KLEIIHENKDYIVVNKASGLISEKSPYEAVTVEDQVFQHILKSKRKPYVGIIHRLDRVTS 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A+ ++      + F  R++QK Y ++V   P   K  + N+L+K +        +
Sbjct: 63  GVLILAKKKSILVAFNKLFSSRKVQKTYLAIVKNKPTKSKGNLVNFLIKNNKE--KKAEI 120

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V    K A   +  ++VI      +  L ++P TGR HQ+R    ++G PIVGD KY ++
Sbjct: 121 VTTKSKEAQSCMLSYEVIGKNNIGY-LLAVKPKTGRFHQIRAQLANIGLPIVGDSKYGSD 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAH 314
                 S     + LHA  +     E        A LP H
Sbjct: 180 VSYKSLS-----ICLHAWKLTFEDVETKEQKTFEASLPNH 214


>gi|195384878|ref|XP_002051139.1| GJ13872 [Drosophila virilis]
 gi|194147596|gb|EDW63294.1| GJ13872 [Drosophila virilis]
          Length = 807

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 119/268 (44%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   +         L +I+  
Sbjct: 382 LDIF-SKEFRAHPAEEYERCIQTGTLTVNFEKVPIDYRLKHNDL---------LANIVHR 431

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +   +T         +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 432 HEVPVTCQPIT---------IVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 481

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V GI P    EC  
Sbjct: 482 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGIFPDGVVECKE 541

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K ++KG +   +  K+      K   +  +P TGR HQ+RVH 
Sbjct: 542 PIEVVSYKIG-----VCKVSQKGKDCTTTFQKL--SQNGKTSVVLCKPLTGRMHQIRVHL 594

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI+ D  Y     G    P++ +
Sbjct: 595 QYLGFPILNDPLYNHEVFG----PLKGR 618


>gi|86133978|ref|ZP_01052560.1| RNA pseudouridylate synthase [Polaribacter sp. MED152]
 gi|85820841|gb|EAQ41988.1| RNA pseudouridylate synthase [Polaribacter sp. MED152]
          Length = 288

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 76/294 (25%), Positives = 116/294 (39%), Gaps = 47/294 (15%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
               ++K ++   + +D +       I  G+ + +                L+S+     
Sbjct: 31  TKSGIKKAIKKQLILIDNELASTAKFISGGEKIML----------------LESNKQQEF 74

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               L   +L ED  + V  KPAGI V G     IA  +   LK        KP+  HRL
Sbjct: 75  SRLKLDLQVLLEDDFLAVIYKPAGILVSGNKFVTIANALSQNLKKSNQVDAVKPQPVHRL 134

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D  TSG+L+V +T +A Q L+E F+ + I+K Y+++  G  K     I   +        
Sbjct: 135 DYATSGLLLVGKTSSAIQKLSELFQKKEIKKTYYAVTIGKMKP-LGIIDKPI-------- 185

Query: 211 DYVHVVKQNEKGANYAISHFKV----IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                          A + +KV    I         +E+ P TGR HQLR H L +  PI
Sbjct: 186 -----------DDKEAYTQYKVISNEISKRFNFLNLVELSPKTGRKHQLRKHLLSLKNPI 234

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
           +GD +Y    K          LYLHA  ++  HP    ++ I   LP      +
Sbjct: 235 LGDKEYFIEGK----ILKGKGLYLHAAKLEFTHPFTAEKITIRKELPNKFKSIF 284


>gi|312886597|ref|ZP_07746205.1| pseudouridine synthase [Mucilaginibacter paludis DSM 18603]
 gi|311301000|gb|EFQ78061.1| pseudouridine synthase [Mucilaginibacter paludis DSM 18603]
          Length = 239

 Score =  149 bits (377), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 100/240 (41%), Gaps = 25/240 (10%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            + ++L+E+  I V NKP  IS      G   ++    K++        ++ HRLD+ETS
Sbjct: 6   FQDLILFENPDIIVVNKPPFISSLDEREGGEINMLRLAKNYWA----DAQICHRLDKETS 61

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L++A+   A + ++  F  RR++KIY +++ G    +   I   +L            
Sbjct: 62  GALIIAKNPEAYRFVSIQFEKRRVRKIYHAIIEGTHVFEDLQIDLPILNAGKGN------ 115

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V  + +    A +HF+ +  F + +  ++ +P TGR HQ+R+H       I GD  Y   
Sbjct: 116 VTISRQEGKRAETHFQSLKYF-KHYTLVQCRPVTGRMHQIRIHLATQRASIAGDEMYKGK 174

Query: 276 F-------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                         K     PI  +  LHA  +     E   + I AP P         L
Sbjct: 175 PVFLSAIKRGYRLGKEQEELPIMKRFALHAYEVTFKTDEDNEITIHAPYPKDFDTLLKLL 234


>gi|45201401|ref|NP_986971.1| AGR305Wp [Ashbya gossypii ATCC 10895]
 gi|44986335|gb|AAS54795.1| AGR305Wp [Ashbya gossypii ATCC 10895]
          Length = 381

 Score =  149 bits (377), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 109/261 (41%), Gaps = 17/261 (6%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRV--DKKRVKFNNRIQSGQVVRIPPVINALN 75
              L +     + H +   +Q  + +G  ++  D   +  N      ++++   V  +  
Sbjct: 29  GRTLAQVLMEEF-HFSSEQVQAKILAGHCQLLRDGVVLNANT-----ELIKNKDVFQSKQ 82

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           H   E  +L   +      +     +++ED+ + V +KP GI +   +   ++ +   + 
Sbjct: 83  HN-HEPPVLQWPLLHNVAHNTAGLKVVFEDNDLLVIDKPCGIPIHPTAY--FYKNTLTEV 139

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             D++G      +RLD+ TSG+L+ A+T+  A  L    R + + K Y + V G     K
Sbjct: 140 LEDARGYPLFPCYRLDKITSGLLIFAKTQQTASRLQSQIRDQNMNKWYLARVDGNFDFNK 199

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
           +  ++ +        +    +K        A++ F  +    +     +  +P TGRTHQ
Sbjct: 200 KTASSPIY-----TFEPKKSLKGAFAPVRDALTEFYHVAYNEELNQSLVLCKPLTGRTHQ 254

Query: 255 LRVHALHMGCPIVGDHKYCAN 275
           +R+H   +G PIV D  Y   
Sbjct: 255 IRIHLARLGHPIVNDPFYNVK 275


>gi|257458419|ref|ZP_05623561.1| ribosomal large subunit pseudouridine synthase C [Treponema
           vincentii ATCC 35580]
 gi|257444223|gb|EEV19324.1| ribosomal large subunit pseudouridine synthase C [Treponema
           vincentii ATCC 35580]
          Length = 240

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 70/225 (31%), Positives = 108/225 (48%), Gaps = 13/225 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YED  + + NKP GI VQGG+ I+  +   L   +   G +    HRLD+ETSG+LV 
Sbjct: 15  IVYEDEALCIVNKPYGIPVQGGAHISVCLTEILSKQL---GSEIFPVHRLDKETSGLLVT 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA+     F  + ++K Y +L +G  +          +KK    G     V +N 
Sbjct: 72  AKSADAARSCRALFESQAVEKEYLALCFGGFEPSA---HKKPVKKLLPEGIIDTPVVENG 128

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKG 278
                A S +K++      +    ++ HTGR HQ+R+H   +G PI+GD K+   A  K 
Sbjct: 129 SP-KPASSAYKLLAS-TDAYSLFSVRLHTGRMHQIRIHLAGIGYPIIGDDKHGNFALNKQ 186

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSL 322
            + +    KL L A  +    P GG+    T P P H+    D L
Sbjct: 187 LWKTARIKKLQLCAYRLMF--PIGGKKCLFTVPAPEHIQAAIDVL 229


>gi|329737470|gb|EGG73724.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU028]
          Length = 274

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 57/279 (20%), Positives = 110/279 (39%), Gaps = 32/279 (11%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
            Y  +   +L ++  S ++ ++K+     N +++G  V IP       ++          
Sbjct: 19  QYLKLPKKDLHQLNMSKEILINKEYGTLLNNVKTGDHVEIPTPNEVSYYL---------- 68

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRL 146
                   +  + + YED  + +  KP G+            +  +   + +   +    
Sbjct: 69  ------PSYRYAQIYYEDDDLAIVMKPKGVKTHP--NDLKESNTLMNHVIYTVDSEYVEP 120

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLDQET G+L+VA+     + L        I +IY + V  +   K + I   + K  
Sbjct: 121 IHRLDQETVGLLIVAKNPLMKKILDRMLEYNEITRIYKANVKALLPIKPQTIDMPIGKD- 179

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                +    ++       AI+H        +  C L+++  TGRTHQ+RVH   +G P+
Sbjct: 180 ----KFHSNKRRISNTGQRAITHIINSKMIKEGVCQLDIKLDTGRTHQIRVHLAEIGHPV 235

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +GD  Y  +           +L L++  ++  HP    +
Sbjct: 236 IGDPLYGTS--------TLRQLELNSHQIEFTHPLTQEI 266


>gi|318043192|ref|NP_001187897.1| RNA pseudouridylate synthase domain-containing protein 4 [Ictalurus
           punctatus]
 gi|308324268|gb|ADO29269.1| RNA pseudouridylate synthase domain-containing protein 4 [Ictalurus
           punctatus]
          Length = 386

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 71/281 (25%), Positives = 116/281 (41%), Gaps = 40/281 (14%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----SKG 141
           SV+    +  L   +LY+D  +   NKP G+ V    GI   I   L            G
Sbjct: 105 SVHPNVFAKALSKSILYQDQNLIAINKPYGVPVYSTGGIGNSIAESLPVLAKIIDCTKGG 164

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            K  + + L+++T+G+L +ART   A+ +    R  + +K Y  +  G+P   +  I   
Sbjct: 165 SKLHVCYNLEKDTTGVLFLARTEETAERIHNLIRSHQAEKRYMVITVGVPVPSEGVIDIP 224

Query: 202 LLKKSHIGGDYVHVV------KQNEKG-----------ANYAISHFKVIDCFAQKFCWLE 244
           +++K  +G  +   +      +  E+G           A  A++H+KV+D  +     +E
Sbjct: 225 IIEKEVMGDQHHFKMGLSPLYRPTEEGDGLVRVRANRQAQSAVTHYKVLDS-SSGCSLVE 283

Query: 245 MQPHTGRTHQLRVHAL-HMGCPIVGDHKY---CANFKGNFTSPIQNK------------L 288
           +QP TG  HQLRVH    + CPI+GDHKY              +  +            L
Sbjct: 284 LQPVTGVKHQLRVHMALALACPILGDHKYTHWNKLAPQKLPEGVLRRLGLEQSKTRHLPL 343

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDR 328
           +LH R + LP   G   L ++  LP         L  +   
Sbjct: 344 HLHVRQITLPGVRGHDDLTVSCLLPKFFTAALKKLQIELPE 384


>gi|301168046|emb|CBW27632.1| putative tRNA pseudouridylate synthase [Bacteriovorax marinus SJ]
          Length = 254

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 109/236 (46%), Gaps = 20/236 (8%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +      +LY+D ++ +  KP+G+ V          D  ++   D  GQ+    HRLD+ 
Sbjct: 9   TPPEPIEILYQDEQVVIVTKPSGLLVHPYWKETNERDNLMRRVRDQIGQRVYPIHRLDRP 68

Query: 154 TSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            SG+L+        + + E +  + ++ K Y +LV+G  +N+               G +
Sbjct: 69  VSGVLLFGLNGEIVKRIQEHWHDKTKVHKEYLALVFGEIENE---------------GVF 113

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +  ++K    A++ ++ +   +++   +++   TGRTHQ+R H       ++GD K+
Sbjct: 114 DFQLTNDKKIKQDALTKYRPLQS-SERATLMQITIETGRTHQIRRHFSRSRHHLIGDTKH 172

Query: 273 CANFKGNF--TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                  +  +    N+++LH+  + L + +  ++ I +PLP+ + +  D++   Y
Sbjct: 173 GKGNINRYYRSEHDFNRIFLHSYRLKL-NLDFLKVDIESPLPSELTELLDTIKIDY 227


>gi|293369136|ref|ZP_06615730.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|292635719|gb|EFF54217.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
          Length = 612

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 71/295 (24%), Positives = 116/295 (39%), Gaps = 71/295 (24%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ + L    +  +  +++ED  + V NKPAG+    G   A   
Sbjct: 317 CEPILQHMLQGLEVDENPL-LNPVHEEEELEIVFEDEWLLVVNKPAGMLSVPGK--AEDR 373

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           D           +   P + HRLD  TSG+L+VA+T+   Q L   F  R I+K Y +++
Sbjct: 374 DSVYHRLKKKYPEATGPMIVHRLDMATSGLLLVAKTKEVHQDLQAQFANRSIKKRYVAVL 433

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYV----------------------------HVVKQN 219
            G     ++ I     K   I  + V                                 +
Sbjct: 434 DGAIIKTEKEIKPIAEKAILIAKETVLTKKTAKAERTGNTGRIELPLCLNPLDRPRQMVS 493

Query: 220 EKGANYAISHFKVID--------------------------CFAQKFCWLEMQPHTGRTH 253
            +    AI+ +++I                             ++K+  +   P TGRTH
Sbjct: 494 SEHGKEAITEYQIISESERITSESENTFNESNRIDESERNINESRKYTRIVFYPLTGRTH 553

Query: 254 QLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QLRVHA H   +GCPI+GD  Y             ++LYLHA Y++  HP  G +
Sbjct: 554 QLRVHAAHPEGLGCPILGDELYGKK---------ADRLYLHAEYIEFRHPIYGDI 599


>gi|326800504|ref|YP_004318323.1| pseudouridine synthase [Sphingobacterium sp. 21]
 gi|326551268|gb|ADZ79653.1| pseudouridine synthase [Sphingobacterium sp. 21]
          Length = 245

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 59/250 (23%), Positives = 98/250 (39%), Gaps = 24/250 (9%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
               L         ++++ED  + V NKP  I+              L+    S     +
Sbjct: 2   EEKALNFKFPKFNQLIIFEDDNLIVVNKPPFIASLDER--EGREINILR-MAKSYHADAQ 58

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HR+D+ETSG+L++A+     + ++  F  RR++KIY +++ G    +   +   +L  
Sbjct: 59  VCHRIDKETSGLLLIAKNPDTYRSVSIEFEKRRVKKIYHAIIGGTHIFEDLKVDLPILNL 118

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            +        V  ++     A + FK +  F + +  +E +P TGR HQ+R+H       
Sbjct: 119 GNKN------VTIDKANGKLAETWFKSLAYF-KHYTLVECRPITGRMHQIRIHLATQHAS 171

Query: 266 IVGDHKYCANF-------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           IVGD  Y                 KG    PI  +  LHAR +      G      AP P
Sbjct: 172 IVGDSLYKGKPVYLSQIKRGYTLSKGQEELPIMKRFALHARALSF-SINGKDYSFEAPYP 230

Query: 313 AHMVKTWDSL 322
                    L
Sbjct: 231 KDFATLLKQL 240


>gi|195146688|ref|XP_002014316.1| GL19135 [Drosophila persimilis]
 gi|194106269|gb|EDW28312.1| GL19135 [Drosophila persimilis]
          Length = 478

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 65/260 (25%), Positives = 108/260 (41%), Gaps = 30/260 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ + +G++ V+ ++V  + R++                    
Sbjct: 94  LDVF-AREFRAHPAEEYKRSIETGKLTVNYEKVPVDYRLKHND----------------- 135

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             +L + V+  +    L+SI +++ D  I V NKPA I V       ++   F+ +   +
Sbjct: 136 --LLANIVHRHEVPVSLQSITIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILAKSHN 193

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECI 198
                R  HRLD+ TSG+L+  RT   A+ L +  R R++QK Y   V G  P    EC 
Sbjct: 194 LKN-LRTIHRLDRLTSGLLIFGRTSKKARELEQQIRNRQVQKEYICRVEGRFPDGIIECN 252

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +    IG      V +         + F+ I         +  +P TGR HQ+RVH
Sbjct: 253 EPIQVVSYKIG------VCRVSPNGKDCRTTFRRISEVGD-CSIVLCKPLTGRMHQIRVH 305

Query: 259 ALHMGCPIVGDHKYCANFKG 278
             ++G PIV D  Y     G
Sbjct: 306 LQYLGYPIVNDPLYNHEVFG 325


>gi|304410411|ref|ZP_07392029.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307304503|ref|ZP_07584253.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304350895|gb|EFM15295.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306911905|gb|EFN42329.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 574

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 103/238 (43%), Gaps = 24/238 (10%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E  ++D +  LT  ++     +LY+D  + + +KPA      G  I   +   +      
Sbjct: 345 EGLVVDENPLLTNPAEGKTLTILYQDDAMAIVSKPAEFLSVPGKEIEDSVYSRM-CQTFP 403

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK----NKK 195
               P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ GIP      + 
Sbjct: 404 HATGPLIVHRLDMSTSGLMVIALTKDAHKQLQKQFIQRTVTKRYVALLAGIPAVMANTQT 463

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV--IDCFAQKFCWLEMQPHTGRTH 253
               +  L+          V     +    A +H+ +  ID  A+      + P TGRTH
Sbjct: 464 TGNISLPLRGDLDDRPRQLVC---HEFGKTAETHWDLSHIDEMARTARVY-LYPKTGRTH 519

Query: 254 QLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           QLRVH  H   +  PI+GD  Y             N+L+LHA  + L HP    R+  
Sbjct: 520 QLRVHCAHSEGLNTPIIGDDLYGTR---------ANRLHLHADLLMLQHPVTRERMHF 568


>gi|88808956|ref|ZP_01124465.1| putative pseudouridylate synthase [Synechococcus sp. WH 7805]
 gi|88786898|gb|EAR18056.1| putative pseudouridylate synthase [Synechococcus sp. WH 7805]
          Length = 215

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 58/228 (25%), Positives = 93/228 (40%), Gaps = 18/228 (7%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           L          L+ +  ++ V +KPAG+  Q   G+  H    L S +       RL HR
Sbjct: 2   LAADRQVAGLPLVLDHPRLMVVDKPAGLLCQP--GLGSHQQDSLISRLQLACPALRLVHR 59

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++TSG++++A+     + L   F  RR++K+Y + V G  KN    I   L +     
Sbjct: 60  LDRDTSGLVLLAKDPDMLRLLGMFFASRRVRKLYVADVQGQMKNVSGLIGLPLARLKRQP 119

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             Y         G    ++ ++ +             P TGR+HQLR H   +  PI+GD
Sbjct: 120 PTY-----GVHPGGKACVTLWRRLKLMESSTRLWLC-PRTGRSHQLRAHLAALHHPIIGD 173

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPE--GGRLQITAPLPAHM 315
             Y                   A  +  P P+   G++++ AP PA  
Sbjct: 174 PIYNPGCAVGLRL--------RAMALRFPDPDDPSGQVRVRAPWPAWF 213


>gi|320536263|ref|ZP_08036307.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
 gi|320146881|gb|EFW38453.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
          Length = 312

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 72/308 (23%), Positives = 129/308 (41%), Gaps = 35/308 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V++N++ + RLDR  +   P +    + K LRSG++RV+ ++   + + +   V+ I  
Sbjct: 6   FVLDNNDSDRRLDRVVRLFLPKMPLSVIYKALRSGKIRVNGQKKHPDYKTKENDVLSIEE 65

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           ++   +  ++E K  ++ +        ++S+ +Y+   + V NKP  I+V G   +A  I
Sbjct: 66  LL--FSSFLQEHKTRNNPIR------QIESLYIYKGKDLLVLNKPVDIAVHGRGSLAESI 117

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               K   DS   KP   HRLD+ T GI+  +++   AQ  +   +     K Y  ++ G
Sbjct: 118 ASSYKK--DSLSFKPGPLHRLDKGTEGIICFSQSLKGAQLFSACLKEGTCAKFYLGIIEG 175

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             K +   I                   QN      AI    +     Q          T
Sbjct: 176 ALKKETVHIE------------------QNTSEEITAI--IPIAQNTEQTLSLAVFHLIT 215

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           G+ HQ+R H   +G  + GD +Y  +   +  + I ++ YL A  +    P+   L I +
Sbjct: 216 GKKHQIRRHCHAIGYQLFGDLRYGGS--KSIQNIIAHRYYLLAWRL--YMPKNSAL-IDS 270

Query: 310 PLPAHMVK 317
            LP     
Sbjct: 271 DLPDFFEA 278


>gi|289551172|ref|YP_003472076.1| Putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus lugdunensis HKU09-01]
 gi|289180704|gb|ADC87949.1| Putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus lugdunensis HKU09-01]
          Length = 284

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 63/296 (21%), Positives = 116/296 (39%), Gaps = 51/296 (17%)

Query: 30  PHINFVNLQK---------ILR-SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           P +    LQ+          ++ +G + V+ + V    ++Q G  + I          I 
Sbjct: 10  PDVLKSFLQQQGFSKKTTSAIKQNGALLVNHEPVTVRYQLQPGDKLTI----------IL 59

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             +I  +++    H       ++YED  + +  KP   S+Q  +    H    L   V +
Sbjct: 60  PTEIPSANLQAFHH----PLDIVYEDDYLLIVCKP---SLQNCAPSREHPHESLIEQVLA 112

Query: 140 KGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              +      P +  RLD+ T+G++++A+       L+      +I K Y +L  G    
Sbjct: 113 YCHENDNDFTPHIVTRLDRNTTGLVLLAKHGHIHHLLSHI----KINKRYIALCHGA-TQ 167

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            +  I   + +      +   + +Q      YA S ++ ++   Q     E+  HTGRTH
Sbjct: 168 PEGIIEAPIAR-----ANDSIITRQVSSTGKYAKSTYRTLNSK-QNVSLCEVTLHTGRTH 221

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQIT 308
           Q+RVH  ++G P++GD  Y  N        +Q         +   HP     + IT
Sbjct: 222 QIRVHFQYIGHPLIGDALYGGNHDMIHNHCLQ------CTALQFKHPILHKTISIT 271


>gi|134095434|ref|YP_001100509.1| 23S rRNA pseudouridylate 746 synthase [Herminiimonas
           arsenicoxydans]
 gi|133739337|emb|CAL62387.1| Ribosomal large subunit pseudouridine synthase A (rRNA-uridine
           isomerase A) (rRNA pseudouridylate synthase A)
           [Herminiimonas arsenicoxydans]
          Length = 223

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 55/216 (25%), Positives = 90/216 (41%), Gaps = 11/216 (5%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   +  +LY+D  + + NKP+G+    G          +   +  +     + HR
Sbjct: 8   FVAPPCVDEIEILYQDEALLLINKPSGLLSLSGKNPLN--LDSVHYRLVQQFPTALMLHR 65

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG+LVVA  +  A  +   F++R + K Y +++ G   +    I   + K     
Sbjct: 66  LDFGTSGLLVVALNKTVAADIYRQFQLRTVVKTYQAVLAGRMDSDAGDIELPIAKDPVNF 125

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 +         A SHF+V+D  +      +   P TGRTHQLR+H+  +G PI+G
Sbjct: 126 PKLKICLT----TGKTASSHFQVLDRQSGPDTTRVVFTPLTGRTHQLRIHSAGVGHPILG 181

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              Y             ++L LHA  ++  HP  G 
Sbjct: 182 CDLYGTPESQQMA----DRLLLHATTVEFDHPISGE 213


>gi|323456553|gb|EGB12420.1| hypothetical protein AURANDRAFT_19938 [Aureococcus anophagefferens]
          Length = 283

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 71/295 (24%), Positives = 121/295 (41%), Gaps = 45/295 (15%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           ++ +  +  + ++ G  + +   +N  +++    +   +  +L          + YED  
Sbjct: 2   LNGRTARCGDAVKQGDRLELRARVNVTSYVQARFRSAKAPFDLE---------VAYEDDY 52

Query: 108 IYVFNKPAGISV------QGGSGIAYHIDGFLK------SWVDSKGQKPRLTHRLDQETS 155
           + V  KPAG+         GG         F           D   ++P+  HRLD+ TS
Sbjct: 53  LAVVVKPAGVPTYSPGGDHGGRANLRSCLPFALKPPASCRAGDEVLRRPQPVHRLDKATS 112

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+++ A+T+ AA     +F  R ++K Y +++ G P  ++  +                 
Sbjct: 113 GLVLCAKTKLAAVGAARAFATRAVKKRYSAVLLGEPAARRGVVTAP-------------- 158

Query: 216 VKQNEKG---ANYAISHFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIV 267
           V  N KG      A + + V        A K C ++  P TGRTHQLR H    +G PIV
Sbjct: 159 VPVNVKGLSVLKSARTVYAVEAVVDSLKASKLCLVKCAPRTGRTHQLRRHFAEALGRPIV 218

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321
           GD  Y         +  ++ L+  AR ++L HP  G RLQ+   LP       + 
Sbjct: 219 GDVLYDGGGP-EALNFRRSGLFFCARSLELDHPVTGARLQVRTGLPGKFSSLLER 272


>gi|301782175|ref|XP_002926502.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 2 [Ailuropoda melanoleuca]
          Length = 345

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 75/295 (25%), Positives = 124/295 (42%), Gaps = 41/295 (13%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           R +   +    Q V   PV   +  +++  + L   V+    +  L   ++++D  + V 
Sbjct: 51  RAQKQEQKTKNQPVPTSPVQRRVQELVRFTQQLQR-VHPNVLAKALSRGIVHQDMDLVVI 109

Query: 112 NKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           NKP G+ V GG G+   I   L    K     K +   L HRLD+ET+G++V+A  +  A
Sbjct: 110 NKPYGLPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEKEVA 169

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             + E FR R++ K YW++   +P      +   +++K                    A+
Sbjct: 170 HQVQELFRTRQVAKKYWAVTVRVPVPPAGVVDIPVIEKEVQ-----------------AV 212

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC------------A 274
           + ++V+         +E+QP TG  HQLRVH    + CPI+GDHKY              
Sbjct: 213 TQYQVLSS-TLSSALVELQPITGVKHQLRVHLSFGLDCPILGDHKYSDWNKLAPQKLSLG 271

Query: 275 NFKGNFTSPIQNK---LYLHARYMDLPH--PEGGRLQITAPLPAHMVKTWDSLGF 324
             K       + +   L+LHAR + LP        L +    P + V +   L  
Sbjct: 272 TLKKLGLQQAKARHIPLHLHARQLILPALGSRKEELNLVCKPPRYFVCSLRRLDL 326


>gi|163814966|ref|ZP_02206353.1| hypothetical protein COPEUT_01116 [Coprococcus eutactus ATCC 27759]
 gi|158449649|gb|EDP26644.1| hypothetical protein COPEUT_01116 [Coprococcus eutactus ATCC 27759]
          Length = 238

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 57/219 (26%), Positives = 101/219 (46%), Gaps = 12/219 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSKGQKPRLT--HRLD 151
           +K  +L+EDS I V  KP G+  Q     +  +   LK  +   +++ ++P L   HRLD
Sbjct: 6   MKLNILHEDSDIIVAVKPCGVPTQPDKTNSESMVSMLKLRIYERENRKEEPYLVPIHRLD 65

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +   G++V A+T  AA  L++      + K Y +++ G   N +  + ++LL  +    +
Sbjct: 66  RPVGGVMVFAKTPEAAAALSKQSEDGTMLKYYQAILTGELPNDQGVLKDYLLHDTK--DN 123

Query: 212 YVHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               V ++  GA Y+   ++V+   D       ++ ++  TGR HQ+R       C I G
Sbjct: 124 VTKTVDKDTPGAKYSELEYEVLDVMDTDEGVLSYVLVELITGRHHQIRAQFAKRKCGIWG 183

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           D KY   F+       +  L  HA  ++  HP  G   +
Sbjct: 184 DTKYNPKFQKTKKKYKEIGL--HASRLEFDHPTTGEHMV 220


>gi|305432550|ref|ZP_07401711.1| RNA pseudouridine synthase [Campylobacter coli JV20]
 gi|304444261|gb|EFM36913.1| RNA pseudouridine synthase [Campylobacter coli JV20]
          Length = 334

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 60/276 (21%), Positives = 103/276 (37%), Gaps = 46/276 (16%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           QK++   ++  D   V+  N+I  G V                         +   ++  
Sbjct: 67  QKLIDKKRLFCDGILVEEKNKILKGDV-----------------------ELIVYENNPK 103

Query: 98  KSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
              +++E+    +  K +GI     G    Y +   +       G+K  + HRLD+ETSG
Sbjct: 104 GVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL---WGKKACVAHRLDKETSG 160

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN-WLLKKSHIGGDYVHV 215
           +++VA+ + A   L   F  ++IQK Y +L  G  K          L K        + +
Sbjct: 161 LILVAKHKEAQIELKTMFEKKQIQKEYLALASGEIKVNFIVDQAMDLTKDYDDVKTRMQI 220

Query: 216 VKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                +    AI+ F+V+  + +     L  +P TGR HQ+RVH  +    I+GD  Y  
Sbjct: 221 C----ENGKKAITEFEVLSFYPKLNATLLLCKPLTGRQHQIRVHLFYKNHKILGDPLYGL 276

Query: 275 NFKG-------------NFTSPIQNKLYLHARYMDL 297
             K                      +L LH+  +  
Sbjct: 277 EKKDIEKILDDKMDIEERIKLSGAKRLCLHSYRLKF 312


>gi|120599960|ref|YP_964534.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|120560053|gb|ABM25980.1| pseudouridine synthase [Shewanella sp. W3-18-1]
          Length = 574

 Score =  148 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 104/242 (42%), Gaps = 18/242 (7%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E  ++D +  L   ++     +LY+D  + + NKPA      G  I   +   ++     
Sbjct: 345 EGLVVDDNPLLMNPAEGKTLSILYQDEAMAIVNKPAEFLSVPGKEIEDSVYSRMQQ-TFP 403

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
               P + HRLD  TSG++V+A T+ A + L + F  R + K Y +L+ GIP    + +A
Sbjct: 404 NATGPLIVHRLDMSTSGLMVIALTKDAHKQLQKQFIQRTVTKRYVALLAGIPTAMADKLA 463

Query: 200 NWLLKKSHIGG-DYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRV 257
              +     G  D         +    A +H+++           + + P TGRTHQLRV
Sbjct: 464 AGQISLPLRGDLDDRPRQLVCHEFGKAAQTHWELSHIDEMARTARVYLFPKTGRTHQLRV 523

Query: 258 HALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
           H  H   +  PIVGD  Y             N+L+LHA  + L HP    +++    +  
Sbjct: 524 HCAHSEGLNTPIVGDDLYGTR---------ANRLHLHADLLMLQHPVTREQMRFQ--IDP 572

Query: 314 HM 315
             
Sbjct: 573 DF 574


>gi|195051256|ref|XP_001993061.1| GH13618 [Drosophila grimshawi]
 gi|193900120|gb|EDV98986.1| GH13618 [Drosophila grimshawi]
          Length = 753

 Score =  148 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 119/268 (44%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   +         L +I+  
Sbjct: 337 LDIF-SKEFRAHPAEEYERCIQTGTLTVNFEKVPIDYRLKHNDL---------LANIVHR 386

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +   +T         +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 387 HEVPVTCQPIT---------IVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 436

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    EC  
Sbjct: 437 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGVVECKE 496

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K ++KG     + FK +     K   +  +P TGR HQ+RVH 
Sbjct: 497 PIEVVSYKIG-----VCKVSQKG-KDCTTTFKKLSQNG-KTSVVLCKPLTGRMHQIRVHL 549

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI+ D  Y     G    P++ +
Sbjct: 550 QYLGYPILNDPLYNHEVFG----PLKGR 573


>gi|294140903|ref|YP_003556881.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293327372|dbj|BAJ02103.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 238

 Score =  148 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 99/242 (40%), Gaps = 27/242 (11%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
             +          +  +L+ D  I V +KP+G+    G          +   +       
Sbjct: 3   PQADPFIVPKCLDEINILFRDEHILVIDKPSGLLSLSGKHPLN--IDSVHYRLVQDYPTC 60

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HRLD  TSG++++A  +     L + F  RR+ K Y +L+ G  K     +   + K
Sbjct: 61  TLIHRLDFGTSGVMLLAMNKQINALLCKQFSERRVSKRYTALLHGDLKPDSGLVDCAVAK 120

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----------------AQKFCWLEMQPH 248
                 D   ++K  +     A S FKV+  F                 ++   +E +P 
Sbjct: 121 D----IDNFPLMKLCQDTGKPAQSKFKVLSRFIQTQDDNFFVDDIRAGERQVTRVEFEPV 176

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQLR+H+ H+G PI+G   Y  +        + ++L LHA  +   HP  G  + I
Sbjct: 177 TGRTHQLRLHSQHLGHPILGCDLYATDE----AYFMSSRLMLHASQLCFEHPVSGVPMVI 232

Query: 308 TA 309
            +
Sbjct: 233 ES 234


>gi|88809883|ref|ZP_01125389.1| probable pseudouridine synthase [Synechococcus sp. WH 7805]
 gi|88786267|gb|EAR17428.1| probable pseudouridine synthase [Synechococcus sp. WH 7805]
          Length = 298

 Score =  148 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 66/292 (22%), Positives = 120/292 (41%), Gaps = 37/292 (12%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVINALNHII 78
           L     + Y H         +RSG++ ++ + ++ +  + S  VV  R PP +       
Sbjct: 2   LSAVMASRYGHSPRDVWDSRIRSGELLLNGQSLQNDVPVGSRDVVQWRRPPWL------- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL---KS 135
            E  I D            +  ++Y+D  + V NKP+G+ V  G G   H    L    S
Sbjct: 55  -EPAIPD------------QWSVVYDDGDVLVINKPSGLPVMPGGGFLQHTLSALLMEAS 101

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKIYWSLVWGIP 191
                 Q P+  HRL + TSG+ V AR       L+  FR     R+    + + V G+ 
Sbjct: 102 RSAGASQVPKPVHRLGRFTSGLQVCARRPQTRAELSRQFRPEGGCRKTYLAWANPVKGLR 161

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN----YAISHFKVIDCFAQKFCWLEMQP 247
            ++   +   ++++ H    +V      +        +A S  +++    Q    +E+  
Sbjct: 162 ADQPLVVTTDVVERVHPLLGWVWGPDPFDGEPLRRRLHARSELRLLKRCDQGD-LVEVAI 220

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMD 296
            TGR HQ+R+H   +G P++GD  Y    + N  +   +   +L+ H   ++
Sbjct: 221 STGRPHQIRIHLAQLGSPLLGDPLYLPQQRINAAAVPGDGGYRLHAHTLALE 272


>gi|291522040|emb|CBK80333.1| Pseudouridylate synthases, 23S RNA-specific [Coprococcus catus
           GD/7]
          Length = 234

 Score =  148 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 60/222 (27%), Positives = 99/222 (44%), Gaps = 14/222 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQ 152
           +  +LYED  I V  KPAG++ Q    +   +  +LK+++  +          + HRLD+
Sbjct: 3   EVKILYEDKDIIVVVKPAGMASQEERSVDVDMVSWLKTYLVRQKKVKGMPYIGVIHRLDK 62

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              G++V A+T+ AA  L+E  R  ++ K Y +++ G    K+  + + LL         
Sbjct: 63  PVGGVMVYAKTQQAAAKLSEQVRNNKMTKEYLAVLTGNLPKKEGRLEDMLLSNGKTNR-- 120

Query: 213 VHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             VV     GA  A+  +KV        Q++  + +   TGR HQ+RV   H G  + GD
Sbjct: 121 TEVVDAKTSGAKKAVLEYKVKRTKFEEGQQYSLVNVHLITGRRHQIRVQMAHAGAGLWGD 180

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            +Y   F           L L A +++  HP   + L    P
Sbjct: 181 TRYNPVFTDKKGWFD---LALFAWHLEFDHPVTKKHLAFKVP 219


>gi|332008660|gb|AED96043.1| RNA pseudourine synthase 7 [Arabidopsis thaliana]
          Length = 410

 Score =  148 bits (375), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 60/293 (20%), Positives = 106/293 (36%), Gaps = 26/293 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V        +   F + +           ++SG+++VD + V  +  ++S Q +      
Sbjct: 67  VNKRWTGKTIVDLFADEFKGRPRDYYVGAVKSGRIKVDGEIVPVSYIVKSSQKITHFLHR 126

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHID 130
           +    +I +                   ++L+++  +    KPA + V   G      I 
Sbjct: 127 HEPPVMIDD------------------VVILHQEPDVVTVCKPASVPVHPCGQYRKNTIV 168

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G L +  D         HRLD+  SG+L++ART A A    +      ++K Y + V G+
Sbjct: 169 GILDAEHDLG--TLFPIHRLDRLVSGLLIIARTAAKADFFRQQIEGGMVKKRYIAKVIGV 226

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKG----ANYAISHFKVIDCFAQKFCWLEMQ 246
               +  +   +      G         +          A + F  ID        +  +
Sbjct: 227 FPEDEMIVDANINYNGSEGRSTAEDANSSGDDKKVKGKPACTKFTRIDTNG-THSLVSCE 285

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           P TGRTHQ+RVH  + G PI  D  Y      N  + I  ++    R +  P 
Sbjct: 286 PVTGRTHQIRVHLQYTGHPIANDPLYLNQHIDNLETYIAKRIDAGERKIVSPD 338


>gi|15241389|ref|NP_199927.1| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|75264240|sp|Q9LU60|PUS7_ARATH RecName: Full=RNA pseudourine synthase 7; AltName: Full=RNA
           pseudouridylate synthase 7; AltName: Full=RNA-uridine
           isomerase 7
 gi|8843850|dbj|BAA97376.1| unnamed protein product [Arabidopsis thaliana]
 gi|332008659|gb|AED96042.1| RNA pseudourine synthase 7 [Arabidopsis thaliana]
          Length = 395

 Score =  148 bits (375), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 60/293 (20%), Positives = 106/293 (36%), Gaps = 26/293 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V        +   F + +           ++SG+++VD + V  +  ++S Q +      
Sbjct: 67  VNKRWTGKTIVDLFADEFKGRPRDYYVGAVKSGRIKVDGEIVPVSYIVKSSQKITHFLHR 126

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHID 130
           +    +I +                   ++L+++  +    KPA + V   G      I 
Sbjct: 127 HEPPVMIDD------------------VVILHQEPDVVTVCKPASVPVHPCGQYRKNTIV 168

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G L +  D         HRLD+  SG+L++ART A A    +      ++K Y + V G+
Sbjct: 169 GILDAEHDLG--TLFPIHRLDRLVSGLLIIARTAAKADFFRQQIEGGMVKKRYIAKVIGV 226

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKG----ANYAISHFKVIDCFAQKFCWLEMQ 246
               +  +   +      G         +          A + F  ID        +  +
Sbjct: 227 FPEDEMIVDANINYNGSEGRSTAEDANSSGDDKKVKGKPACTKFTRIDTNG-THSLVSCE 285

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           P TGRTHQ+RVH  + G PI  D  Y      N  + I  ++    R +  P 
Sbjct: 286 PVTGRTHQIRVHLQYTGHPIANDPLYLNQHIDNLETYIAKRIDAGERKIVSPD 338


>gi|195146686|ref|XP_002014315.1| GL19017 [Drosophila persimilis]
 gi|194106268|gb|EDW28311.1| GL19017 [Drosophila persimilis]
          Length = 644

 Score =  148 bits (375), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 66/326 (20%), Positives = 132/326 (40%), Gaps = 41/326 (12%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   ++      + +    + 
Sbjct: 320 LDIF-SREFRAHPSEEYERCIQAGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQ- 377

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +++ +  + V NKPA I V       ++   F+ +  +  
Sbjct: 378 -----------------PIKIVHMNEDLVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 419

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V GI P    EC  
Sbjct: 420 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGIFPDEIVECKE 479

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K +++G +   +  K+      K   +  +P TGR HQ+RVH 
Sbjct: 480 PIEVVSYKIG-----VCKVSQRGKDCTTTFQKI--SQNGKTSVVLCKPLTGRMHQIRVHL 532

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
            ++G PI+ D  Y     G    P++ + +               + I      H  + W
Sbjct: 533 QYLGYPILNDPLYNHEVFG----PLKGR-FGDIGGKSDDELIRDLINI------HNAENW 581

Query: 320 DSLGFKYDRNLYIKRLYSQDECKQNI 345
             LG  YD ++ I +    +   +++
Sbjct: 582 --LGIDYDSDISIFKSSKDETDGESL 605


>gi|169846844|ref|XP_001830136.1| tRNA-pseudouridine synthase [Coprinopsis cinerea okayama7#130]
 gi|116508906|gb|EAU91801.1| tRNA-pseudouridine synthase [Coprinopsis cinerea okayama7#130]
          Length = 583

 Score =  148 bits (375), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 69/328 (21%), Positives = 120/328 (36%), Gaps = 51/328 (15%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           + MT ++++          L       +   +    +  L SG   V+ +       ++ 
Sbjct: 74  TTMTKMRWI-------GRELLEVVSTEFRDRSMEYYRYALESGVTTVNGQVASPTTILKD 126

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS--KIYVFNKPAGISV 119
           G  +              E  + D+ V            +L+ D   +  V +KP  I V
Sbjct: 127 GDRIENVVHR-------HEPPVTDTPV-----------RILHRDDEREFIVVDKPGSIPV 168

Query: 120 QGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                  Y+ +  ++  V   G +K    +RLD+ TSG++++  +   A+ LTE F    
Sbjct: 169 HASG--RYYKNTLIEILVHDFGIKKCYPANRLDRLTSGLMIMPLSPERARTLTEEFTAGT 226

Query: 179 IQKIYWSLVWGI-PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           ++K Y + V G  P+    C    L     +G + VH           A + F +I    
Sbjct: 227 VKKEYVARVKGKFPEGSVVCEQPLLTVDRQMGLNIVH------PDGKPAKTVFTLIRYDE 280

Query: 238 Q-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                 ++ +PHTGR+HQLRVH  ++G PI  D  Y                    +   
Sbjct: 281 NTNSSVVKCEPHTGRSHQLRVHLQYLGHPIANDPIYSEERIWGK---------KCGKGGI 331

Query: 297 LPHPEGGRLQITAP-LPAHMVKTWDSLG 323
              P   R   +AP  P H+    + +G
Sbjct: 332 DTTPSNER---SAPAPPPHLQALTECVG 356


>gi|294645548|ref|ZP_06723244.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|294808025|ref|ZP_06766800.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|292639122|gb|EFF57444.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|294444778|gb|EFG13470.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
          Length = 615

 Score =  148 bits (375), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 74/295 (25%), Positives = 118/295 (40%), Gaps = 71/295 (24%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ + L    +  +  +++ED  + V NKPAG+    G   A   
Sbjct: 317 CEPILQHMLQGLEVDENPL-LNPVHEDEELEIVFEDEWLLVVNKPAGMLSVPGK--AEDR 373

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           D           +   P + HRLD  TSG+L+VA+T+   Q L   F  R I+K Y +++
Sbjct: 374 DSVYHRLKKKYPEATGPMIVHRLDMATSGLLLVAKTKEVHQDLQAQFANRSIKKRYVAVL 433

Query: 188 WG-IPKNKKEC----IANWLLKKSHIGGDY-----------------------VHVVKQN 219
            G I K +KE         LL K  +                                 +
Sbjct: 434 DGAIIKTEKETKPIAEKAILLAKETVSTKKTAKAERTGNTGRIELPLCLNPLDRPRQMVS 493

Query: 220 EKGANYAISHFKVID--------------------------CFAQKFCWLEMQPHTGRTH 253
            +    AI+ +++I                             ++K+  +   P TGRTH
Sbjct: 494 REHGKEAITEYQIISESERITSESENTFNESNRIDESERSINESRKYTRIIFYPLTGRTH 553

Query: 254 QLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QLRVHA H   +GCPI+GD  Y             ++LYLHA Y++  HP  G +
Sbjct: 554 QLRVHAAHPEGLGCPILGDELYGKK---------ADRLYLHAEYIEFRHPIYGDI 599


>gi|156401575|ref|XP_001639366.1| predicted protein [Nematostella vectensis]
 gi|156226494|gb|EDO47303.1| predicted protein [Nematostella vectensis]
          Length = 418

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 57/261 (21%), Positives = 103/261 (39%), Gaps = 26/261 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD + +  +   +    +K + SG++ V+ ++V     ++   V+R             E
Sbjct: 29  LDIF-REEFRSESISYYEKAIESGKITVNGEKVLPTTVLRGNDVLRNRVHR-------HE 80

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             + D  +            ++     I V NKP+ I V       ++   FL    +  
Sbjct: 81  PPVTDQPLE-----------IICNTDDIVVLNKPSSIPVHPCGRYRHNTVVFLLG-KEHN 128

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            +     HR+D+ TSGIL+ A+T   A+ L    R R+++K Y   V G   ++      
Sbjct: 129 LRNLYTIHRIDRLTSGILMFAKTLTRARMLEAQVRDRQVEKEYLCRVQGEFPSEPVDCEQ 188

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            ++  SH  G     + +         + F  +    +    ++  P+TGR HQ+RVH  
Sbjct: 189 PIIVVSHKVG-----ICRVSPDGKSCRTVFTKLHSNGKS-SVVKCIPYTGRMHQIRVHLQ 242

Query: 261 HMGCPIVGDHKYCANFKGNFT 281
            +G PI+ D  Y     G   
Sbjct: 243 WLGYPIIDDPIYNHPAWGTKR 263


>gi|314933208|ref|ZP_07840573.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus caprae C87]
 gi|313653358|gb|EFS17115.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus caprae C87]
          Length = 284

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 61/303 (20%), Positives = 114/303 (37%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + + H    +   +  I  +G + V+   V     +  G    +               I
Sbjct: 16  FLQRH--DYSKKTISAIKHNGALLVNGHPVTVRKEMAVGDQFEVHM------------PI 61

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKG 141
            + S NL  +   L   +++ED  I + NKP   +        +   ++  L   ++   
Sbjct: 62  EEPSSNLLPYPKPLD--IVFEDEFILIVNKPQSQNCAPSREHPHESLVEQVLAYLMNKDV 119

Query: 142 Q-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           Q  P +  RLD+ TSG+++ A+        ++    +     Y  L +G     +  +  
Sbjct: 120 QTNPHIVTRLDRNTSGLVLFAKFGHIHHLFSKVKFEKE----YICLAYGR-TQPEGVVEA 174

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + + S    D +   K ++KG  YA + +  I          +++ HTGRTHQ+RVH  
Sbjct: 175 PIARDS----DSIITRKVSDKG-KYAKTSYYTI-VQNNTLSLCKVKLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
            MG PIVGD  Y           +     L    +   HP    ++ I       +++ +
Sbjct: 229 FMGHPIVGDDLYGGVHH------LVKGQSLQCCSLKFVHPINHNKISINIDY-KQLIQLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NVL 284


>gi|254481870|ref|ZP_05095113.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2148]
 gi|214037999|gb|EEB78663.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2148]
          Length = 220

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 47/207 (22%), Positives = 97/207 (46%), Gaps = 11/207 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +LYED+ + +  KP  +    G          L + +        + HRLD +TSGI
Sbjct: 15  EIRILYEDADLLLVRKPDLLLSIPGRHPLN--KDCLITRLQQDYPTASIVHRLDLDTSGI 72

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++   +    H++  F+ R ++K Y ++V+G+ +     +   +        +   +  
Sbjct: 73  MIIPLNKPTHAHISRQFQERLVEKCYHAVVFGLVEQDSGEVELPI----RCDWENRPLQM 128

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            + +   +A++ ++V+D  + +   L ++P TGR+HQLR+H   +G PI+G   Y     
Sbjct: 129 IDHEQGKHALTRYEVLDRLSDRTRLL-LKPVTGRSHQLRIHMRELGHPILGCDMYAHQQ- 186

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGR 304
                 + +++ LHA ++   HP  G 
Sbjct: 187 ---ALEMADRMLLHASFIGFEHPTSGE 210


>gi|86150522|ref|ZP_01068746.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|86152341|ref|ZP_01070551.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|315123634|ref|YP_004065638.1| RNA pseudouridylate synthase family [Campylobacter jejuni subsp.
           jejuni ICDCCJ07001]
 gi|85838974|gb|EAQ56239.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|85840638|gb|EAQ57890.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|315017356|gb|ADT65449.1| RNA pseudouridylate synthase family [Campylobacter jejuni subsp.
           jejuni ICDCCJ07001]
          Length = 298

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 61/276 (22%), Positives = 103/276 (37%), Gaps = 46/276 (16%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           QK++   ++  D   V+  N+I  G V                         +   ++  
Sbjct: 31  QKLIDKKRLFCDGILVEEKNKILKGDV-----------------------ELIVYENNPK 67

Query: 98  KSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
              +++E+    V  K +GI     G    Y +   +       G+K  + HRLD+ETSG
Sbjct: 68  GVEIVFENEDFAVLEKESGILSHPNGRHCKYSLSDEIWHL---WGKKACVAHRLDKETSG 124

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN-WLLKKSHIGGDYVHV 215
           +++VA+ + A   L   F  ++IQK Y +L  G  K          L K        + +
Sbjct: 125 LILVAKHKKAQIELKTMFEKKQIQKEYLALASGEIKVNFIVDQAMDLTKDYDDVKTRMQI 184

Query: 216 VKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                +    AI+ F+V+  + +     L  +P TGR HQ+RVH  +    I+GD  Y  
Sbjct: 185 C----ENGKKAITEFEVLSFYPKLNATLLLCKPLTGRQHQIRVHLFYKNHKILGDPLYGL 240

Query: 275 NFKG-------------NFTSPIQNKLYLHARYMDL 297
             K                      +L LH+  +  
Sbjct: 241 EKKDIEKILDDKMDIEERIKLSGAKRLCLHSYRLKF 276


>gi|16974566|gb|AAL31256.1| AT5g51140/MWD22_8 [Arabidopsis thaliana]
 gi|23507777|gb|AAN38692.1| At5g51140/MWD22_8 [Arabidopsis thaliana]
          Length = 367

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 60/293 (20%), Positives = 106/293 (36%), Gaps = 26/293 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V        +   F + +           ++SG+++VD + V  +  ++S Q +      
Sbjct: 39  VNKRWTGKTIVDLFADEFKGRPRDYYVGAVKSGRIKVDGEIVPVSYIVKSSQKITHFLHR 98

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHID 130
           +    +I +                   ++L+++  +    KPA + V   G      I 
Sbjct: 99  HEPPVMIDD------------------VVILHQEPDVVTVCKPASVPVHPCGQYRKNTIV 140

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G L +  D         HRLD+  SG+L++ART A A    +      ++K Y + V G+
Sbjct: 141 GILDAEHDLG--TLFPIHRLDRLVSGLLIIARTAAKADFFRQQIEGGMVKKRYIAKVIGV 198

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKG----ANYAISHFKVIDCFAQKFCWLEMQ 246
               +  +   +      G         +          A + F  ID        +  +
Sbjct: 199 FPEDEMIVDANINYNGSEGRSTAEDANSSGDDKKVKGKPACTKFTRIDTNG-THSLVSCE 257

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           P TGRTHQ+RVH  + G PI  D  Y      N  + I  ++    R +  P 
Sbjct: 258 PVTGRTHQIRVHLQYTGHPIANDPLYLNQHIDNLETYIAKRIDAGERKIVSPD 310


>gi|320354847|ref|YP_004196186.1| pseudouridine synthase [Desulfobulbus propionicus DSM 2032]
 gi|320123349|gb|ADW18895.1| pseudouridine synthase [Desulfobulbus propionicus DSM 2032]
          Length = 219

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 70/224 (31%), Positives = 109/224 (48%), Gaps = 19/224 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           +LY D ++ V +KP G+    G G      +   L+  V    ++P   HRLD +T+G++
Sbjct: 8   VLYLDKELAVVDKPGGLLAVPGRGPDKQDCVVSRLRQMVPWCIEQPA-VHRLDMDTAGVM 66

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+  T AA +HL+  F  RR++K Y +L+ G+   +K  I              V+   +
Sbjct: 67  VLGLTGAAHRHLSRQFAERRVEKQYLALLEGVVSGEKGEICLAFRLDPDNRPHQVYDAVR 126

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYCAN 275
            + G    +SH++ I+   Q+   +E  P TGRTHQLR+HA H   +GCPIVGD  Y A 
Sbjct: 127 GKMG----VSHWRRIEIRGQR-TLVEFIPQTGRTHQLRLHASHPLGLGCPIVGDRLYGAG 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             G+        L LHA  +   HP   R ++  +  P    + 
Sbjct: 182 RDGDS-------LKLHATRLHFLHPATYRPMEFVSRAPFDWRQA 218


>gi|113953912|ref|YP_730201.1| pseudouridine synthase RluA [Synechococcus sp. CC9311]
 gi|113881263|gb|ABI46221.1| pseudouridine synthase RluA PA3246 [Synechococcus sp. CC9311]
          Length = 220

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 56/206 (27%), Positives = 98/206 (47%), Gaps = 13/206 (6%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
             V  KP+G+  Q   G+       L + + +   + RL HRLD++TSG+L++AR   + 
Sbjct: 25  FLVVEKPSGLLSQP--GLGDSQSDSLITRLQAVRPELRLVHRLDRDTSGLLLLARDPESL 82

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           + L   F  R++ K Y + V G PK++   +   L + S     Y        +     +
Sbjct: 83  KVLGGLFAERKVHKFYAADVHGHPKSRSGAVRLPLARLSAHPPRY-----GPRRDGRSCL 137

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           + ++     + +     + P TGR+HQLR H   +G PI+GD  Y ++  G+       +
Sbjct: 138 TLWRCAQMGSDRSRLW-LAPRTGRSHQLRAHLAAIGLPIIGDPIYASSGLGSPGE----R 192

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLP 312
           L+LHA  +    P  G R+++ + LP
Sbjct: 193 LHLHALGLSFSDPFSGQRIRVRSSLP 218


>gi|237721623|ref|ZP_04552104.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_2_4]
 gi|229449419|gb|EEO55210.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           2_2_4]
          Length = 613

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 71/295 (24%), Positives = 116/295 (39%), Gaps = 71/295 (24%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ + L    +  +  +++ED  + V NKPAG+    G   A   
Sbjct: 317 CEPILQHMLQGLEVDENPL-LNPVHEEEELEIVFEDEWLLVVNKPAGMLSVPGK--AEDR 373

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           D           +   P + HRLD  TSG+L+VA+T+   Q L   F  R I+K Y +++
Sbjct: 374 DSVYHRLKKKYPEATGPMIVHRLDMATSGLLLVAKTKEVHQDLQAQFANRSIKKRYVAVL 433

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVK----------------------------QN 219
            G     ++       K   I  + V   K                             +
Sbjct: 434 DGAIIKTEKETKPITEKAILIAKETVSTKKTAKAERTGNTGRIELPLCLNPLDRPRQMVS 493

Query: 220 EKGANYAISHFKVID--------------------------CFAQKFCWLEMQPHTGRTH 253
            +    AI+ +++I                             ++K+  +   P TGRTH
Sbjct: 494 SEHGKEAITEYQIISESERITSESENTFNESNRIDESEKSINESRKYTRIIFYPLTGRTH 553

Query: 254 QLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QLRVHA H   +GCPI+GD  Y             ++LYLHA Y++  HP  G +
Sbjct: 554 QLRVHAAHPEGLGCPILGDELYGKK---------ADRLYLHAEYIEFRHPIYGDI 599


>gi|297621954|ref|YP_003710091.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
 gi|297377255|gb|ADI39085.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
          Length = 214

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 68/213 (31%), Positives = 102/213 (47%), Gaps = 16/213 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-----PRLTHRLD 151
           +   +LYED+ + V  KP G+  Q        ++   K W+     K         HRLD
Sbjct: 1   MTLKILYEDNHLLVLEKPGGVLTQPSGTNQISLEEMGKQWIKKSYGKQGNVFLEAVHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           Q   GI+V A+TR A   L  + R +R++K Y + V   P+  +  + ++L+ K H    
Sbjct: 61  QAACGIVVFAKTRKALSRLMLAIREKRVKKWYRTQVECAPQQNEGRLIHYLMHKKH---- 116

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              VV  +E GA YA   +KVI     K+  LE+Q  TGR HQ+R     +GCPI+GD K
Sbjct: 117 RAEVVSGDELGAKYASLTYKVIK--PGKYPILEIQLETGRYHQIRCQLSAIGCPIIGDKK 174

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           Y ++   +        + L    M++PHP  G 
Sbjct: 175 YGSSIPYHGP-----GIALCHVRMEIPHPVTGE 202


>gi|281354950|ref|ZP_06241444.1| pseudouridine synthase [Victivallis vadensis ATCC BAA-548]
 gi|281317830|gb|EFB01850.1| pseudouridine synthase [Victivallis vadensis ATCC BAA-548]
          Length = 321

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 64/322 (19%), Positives = 122/322 (37%), Gaps = 40/322 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+       L  +    + +      +  + +G++ ++ +      R++    +   P  
Sbjct: 19  VDWSGAGFTLAEYLAGRFTYRAIDEWRDRIAAGEIMLNGELSDPERRLELHDRIEYFP-- 76

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                            ++ +    L   + YED  + V +KP  + V        H   
Sbjct: 77  ----------------ADIAEPEADLDYRIAYEDDALLVVDKPGNLCVHPSGPFFKH--- 117

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L   + SK  K  L +RLD+ETSG+LV A+   AA  L +      ++K Y +LV+G  
Sbjct: 118 TLWHLLSSKYGKIHLVNRLDRETSGLLVAAKNPKAAAKLGKPGWP--MRKEYLALVFGNF 175

Query: 192 KNKKECIANWLLKKSHIGGDYVHVV--KQNEKGANYAISHFKVI--DCFAQKFCWLEMQP 247
            ++ E     +   + +       V  ++  +GA    S   V+      +++  +   P
Sbjct: 176 ADRIEAYGFLVPDLASVVRKKRRFVAGERPPEGAVRPESARTVLLPARSGERYSLVRALP 235

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANF------------KGNFTSPIQNKLYLHARYM 295
            TGR HQ+R     +G P++GD  Y  +               +    I  +  LH+  +
Sbjct: 236 ETGRLHQIRATLFSLGFPLLGDKLYGPDDGIFLKIRSNAITAADRERLILLRQALHSAKL 295

Query: 296 DLPHPEGGR-LQITAPLPAHMV 316
              HP+ G  + + +PLP    
Sbjct: 296 AFRHPDTGETVAVESPLPPDFR 317


>gi|159897698|ref|YP_001543945.1| pseudouridine synthase [Herpetosiphon aurantiacus ATCC 23779]
 gi|159890737|gb|ABX03817.1| pseudouridine synthase [Herpetosiphon aurantiacus ATCC 23779]
          Length = 312

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 72/306 (23%), Positives = 123/306 (40%), Gaps = 34/306 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +        ++    Q ++  G + ++  RV                  + L     E
Sbjct: 3   LWQLLMARL-DLSPTLAQTLMVRGAIWINSVRVT-----------------DPLAEAPPE 44

Query: 81  QKILD--SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSW- 136
            +++       L  +     + +L+ED  I V NKPA           + H++G L+ + 
Sbjct: 45  GELVVHTPPAGLYANPVVTPADILFEDEWILVLNKPAAWYSVATPWDTFGHLEGALQRFF 104

Query: 137 --VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
              D +     L HRLD  TSG L+V++  +        F   R+QK Y +L  G+P   
Sbjct: 105 LERDGEAVPFHLVHRLDHGTSGALIVSKNPSLNSRFQRMFNEGRVQKTYLALCSGLPDWT 164

Query: 195 KECIANWLLKKS------HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           K  +     +        +       +    ++    A + F V          L  + H
Sbjct: 165 KLEVVTGHSRGEFGLWSVYPAAMIDQLYGPKDRRVRRAHTSFTV-QAVGNAAALLAARLH 223

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QI 307
           TGRTHQ+R+HA H+G P+VGD +Y    +  F +       LHA ++  PHP  G + ++
Sbjct: 224 TGRTHQIRLHAKHIGHPLVGDQRYGGVTQ--FGNLSIPDQLLHAAWLQFPHPRYGSMLEL 281

Query: 308 TAPLPA 313
            AP+P+
Sbjct: 282 IAPVPS 287


>gi|156537257|ref|XP_001605561.1| PREDICTED: similar to ribosomal pseudouridine synthase [Nasonia
           vitripennis]
          Length = 552

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 117/270 (43%), Gaps = 27/270 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             ++   F   +        ++ +R+G + V+ ++V  + R++   +         L ++
Sbjct: 138 GEKILEVFAREFRAHPAEEYERCIRAGTLTVNYQKVDVDYRLRHNDL---------LANV 188

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +   ++  +S  +T         +++ D  + V NKPA I V       ++   F+ +  
Sbjct: 189 VHRHEVPVTSEPIT---------VIHMDEDVVVVNKPASIPVHPCGRYRHNTVVFILA-K 238

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSGIL+  RT   A+ +    R R++QK Y   V G  P+ +  
Sbjct: 239 EYNLKNLRTIHRLDRLTSGILLFGRTPKKARQMEHQIRNRQVQKQYVCRVEGEFPEEEIV 298

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG     V K ++KG    I+ FK +    +    +  +P TGR HQ+R
Sbjct: 299 CSEAIEVVSYKIG-----VCKVSDKG-KDCITKFKRLSYNGKS-SVVLCKPQTGRMHQIR 351

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           VH  ++G P+V D  Y     G       N
Sbjct: 352 VHLQYLGYPVVNDPLYNHVVFGPHKGKGGN 381


>gi|326572905|gb|EGE22890.1| ribosomal large subunit pseudouridine synthase A [Moraxella
           catarrhalis CO72]
          Length = 242

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 71/240 (29%), Positives = 119/240 (49%), Gaps = 23/240 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+ S +     +F KSI +YED  I+V +KPAG+    G  +       L+S +      
Sbjct: 14  LELSHDDLFFHEFAKSITIYEDEDIWVLDKPAGLLSVDGRMLKVS----LQSRLLRINPN 69

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANW 201
            RL HRLD +TSG+++ A++  A  H+++ F  R  QK Y ++V+G     +KK  +   
Sbjct: 70  IRLIHRLDMDTSGLIIFAKSSEAQTHISKQFIDRIPQKEYQAVVFGTLMIDDKKGVVDVP 129

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--------FAQKFCWLEMQPHTGRTH 253
           +  +      ++  +  N      A++H++V+           A     + ++P TGR+H
Sbjct: 130 VRYEPTTKPRHIVDMDWN----KRALTHYEVMHHELRCDDNSRAYPVTRVALKPITGRSH 185

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           QLRVH LH+G  ++GD  Y  +        + N+L LHA  + L HP  G  +   +P+P
Sbjct: 186 QLRVHMLHLGHVMIGDPIYAEDV----ALKLSNRLNLHAHKLRLKHPMHGIWMDWVSPVP 241


>gi|319401115|gb|EFV89334.1| RNA pseudouridylate synthase family protein [Staphylococcus
           epidermidis FRI909]
          Length = 274

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 57/279 (20%), Positives = 111/279 (39%), Gaps = 32/279 (11%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
            Y  +   +L ++  S ++ ++++     N +++G  V IP      N++          
Sbjct: 19  QYLKLPKKDLHQLNMSKEILINEEYGTLLNNVKTGDYVEIPTPNEVSNYL---------- 68

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRL 146
                   +  + + YED  + +  KP G+            +  +   + +   +    
Sbjct: 69  ------PSYRYAQIYYEDDDLAIVMKPKGVKTHP--NDLKESNTLMNHVIYTVDSEYVEP 120

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLDQET G+L+VA+     + L        I +IY + V  +   K + I   + K  
Sbjct: 121 IHRLDQETVGLLIVAKNPLMKKILDRMLEYNEITRIYKANVKALLPIKPQTIDMPIGKD- 179

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                +    ++       AI+H        +  C L+++  TGRTHQ+RVH   +G P+
Sbjct: 180 ----KFHSNKRRISNTGQRAITHIIDSKMIKEGVCQLDIKLDTGRTHQIRVHLAEIGHPV 235

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +GD  Y  +           +L L++  ++  HP    +
Sbjct: 236 IGDPLYGTS--------TLRQLELNSHQIEFTHPLTQEI 266


>gi|328948965|ref|YP_004366302.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
 gi|328449289|gb|AEB15005.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
          Length = 440

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 100/231 (43%), Gaps = 22/231 (9%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKSWVDSKGQKPRLTHRLD 151
            + L   +LY D+ + V NK +G+    G G      I   LK       ++P   HRLD
Sbjct: 215 PEILGLKILYRDNDLIVVNKQSGLLSVPGRGPEKQDCIVNRLKKLFPECIEQPS-VHRLD 273

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            ETSG++++A T+ A ++L   F    +QK Y +L+ GI   K    +  +     +  +
Sbjct: 274 METSGLMILAFTKDAHRNLCRQFEEGLVQKKYVALLDGILAKKGIPQSGTMELYFRLDIE 333

Query: 212 YVHVVKQNEKGANYAISHFKVIDC--------FAQKFCWLEMQPHTGRTHQLRVHAL--- 260
                  +      AI+ +K++D           +    +   PHTGRTHQLR+ +    
Sbjct: 334 NRPHQIWDSVYGKKAITEWKILDVEKYLSPLENKKNVTRVLFIPHTGRTHQLRLASADSH 393

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
             G PI+GD  Y     G        +L LH+ Y+   HP  G+ ++    
Sbjct: 394 GFGVPIIGDTLYGHCEPGE-------RLMLHSCYIKFTHPSTGKVMEFNCE 437


>gi|223042701|ref|ZP_03612749.1| pseudouridylate synthase, 23S RNA-specific [Staphylococcus capitis
           SK14]
 gi|222443555|gb|EEE49652.1| pseudouridylate synthase, 23S RNA-specific [Staphylococcus capitis
           SK14]
          Length = 284

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 57/303 (18%), Positives = 114/303 (37%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + + +    +   +  I  +G + V+ + V     +  G    +   I            
Sbjct: 16  FLQRN--DYSKKTISAIKHNGALSVNGRSVTVRKEMAIGDYFEVHMPIET---------- 63

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQ 142
              S NL  +   L   ++YED  I + NKP   +           +   + +++ +K +
Sbjct: 64  --PSSNLLPYPKPLD--IVYEDEFILIVNKPQLQNCAPSREHPHESLVEQVLAYLMNKDE 119

Query: 143 K--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           +  P +  RLD+ TSG+++ A+        ++    +     Y  L +G     +  I  
Sbjct: 120 QTNPHIVTRLDRNTSGLVLFAKFGHIHHLFSKVKFEKE----YICLAYGR-TQSEGVIEA 174

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +      +   + ++      YA + +  I          +++ HTGRTHQ+RVH  
Sbjct: 175 PIARD-----NESIITRKVSDKGKYAKTSYYTI-AQNNNLSLCKVKLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
            MG PIVGD  Y          P+     L    +   HP +  ++ I       +++ +
Sbjct: 229 FMGHPIVGDDLYGG------IHPLVKGQSLQCCSLKFVHPIKHNKITINVDY-KQLIQLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NVL 284


>gi|254282028|ref|ZP_04956996.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium NOR51-B]
 gi|219678231|gb|EED34580.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium NOR51-B]
          Length = 228

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 102/237 (43%), Gaps = 13/237 (5%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +I +    DS   L  H+      LLY+D+ + +  KP  +    G          L + 
Sbjct: 1   MITDPATPDSPPYLVPHTRE-PIRLLYQDNDLLIVEKPTLLLSVPGRHPLNRDS--LMTR 57

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +  +       HRLD +TSG++VV   R+A   L   F+ RR++K Y ++VWG+  +   
Sbjct: 58  LMPRFPDVAAVHRLDLDTSGLMVVPTRRSALSALGRLFQERRVEKEYLAVVWGVLAHDSG 117

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   ++   H       + K        AI+ + V+     +   L + P TGR+HQLR
Sbjct: 118 TIDLPIIADWH----RRPLQKICHDTGKSAITRYTVLKRGTDR-TLLRLNPVTGRSHQLR 172

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLP 312
           +H   +G PI+G   Y           +     LHA  +  PHP  G RL   +P P
Sbjct: 173 IHCREIGHPILGCDLYAHADALAAAPRLL----LHATRLAFPHPTLGHRLAAVSPAP 225


>gi|228469450|ref|ZP_04054458.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           uenonis 60-3]
 gi|228309025|gb|EEK17668.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           uenonis 60-3]
          Length = 232

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 47/199 (23%), Positives = 92/199 (46%), Gaps = 21/199 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           V V+  +  +R+DR+  +  PH +   +Q   ++G + VD + VK N +++  + + +  
Sbjct: 48  VRVDPGQTPLRIDRFLVDRMPHTSRHRIQLAAKAGLIWVDGEPVKSNYKVKPLETITMM- 106

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG----- 124
                        +     + +   + +   ++YED ++ V NKPAG+ V  G G     
Sbjct: 107 -------------LAHPKQDWSITPEDIPLDIVYEDDQLLVVNKPAGMVVHPGHGNYSGT 153

Query: 125 IAYHIDGFLKS--WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           + + +  +L++    D       L HR+D++TSG+L+VA+   A   L   F ++   + 
Sbjct: 154 LVHALAYYLRNDPLYDPNDASVGLVHRIDKDTSGLLLVAKRTEAKIRLARQFFLKTTGRR 213

Query: 183 YWSLVWGIPKNKKECIANW 201
           Y +LVWG     +  I   
Sbjct: 214 YQALVWGKLDQPQGTIRAI 232


>gi|242243072|ref|ZP_04797517.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242233530|gb|EES35842.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 274

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 57/279 (20%), Positives = 110/279 (39%), Gaps = 32/279 (11%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
            Y  +   +L ++  S ++ ++++     N +++G  V IP      N++          
Sbjct: 19  QYLKLPKKDLHQLNMSKEILINEEYGTLLNNVKTGDYVEIPTPNEVSNYL---------- 68

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRL 146
                   +  + + YED  + +  KP G+            +  +   + +   +    
Sbjct: 69  ------PSYRYAQIYYEDDDLAIVMKPKGVKTHP--NDLKESNTLMNHVIYTVDSEYVEP 120

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLDQET G+L+VA+     + L        I +IY + V  +   K + I   + K  
Sbjct: 121 IHRLDQETVGLLIVAKNPLMKKILDRMLEYNEITRIYKANVKALLPIKPQTIDMPIGKD- 179

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                +    ++       AI+H        +  C L ++  TGRTHQ+RVH   +G P+
Sbjct: 180 ----KFHSNKRRISNTGQRAITHIIDSKMIKEGVCQLNIKLDTGRTHQIRVHLAEIGHPV 235

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +GD  Y  +           +L L++  ++  HP    +
Sbjct: 236 IGDPLYGTS--------TLRQLELNSHQIEFTHPLTQEI 266


>gi|194862300|ref|XP_001969970.1| GG10383 [Drosophila erecta]
 gi|190661837|gb|EDV59029.1| GG10383 [Drosophila erecta]
          Length = 721

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 62/268 (23%), Positives = 117/268 (43%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   +         L +I+  
Sbjct: 300 LDIF-SREFRAHPAEEYERCIQTGTLTVNFEKVPIDYRLKHNDL---------LANIVHR 349

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +          +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 350 HEVPVTSQPI---------KIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 399

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    EC  
Sbjct: 400 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGIVECKE 459

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  K+          +  +P TGR HQ+RVH 
Sbjct: 460 PIEVVSYKIG-----VCKVSSKGKDCTTTFQKL--SQNGTTSVVLCKPLTGRMHQIRVHL 512

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI+ D  Y     G    P++ +
Sbjct: 513 QYLGYPILNDPLYNHEVFG----PLKGR 536


>gi|183220733|ref|YP_001838729.1| putative ribosomal large subunit pseudouridine synthase [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
 gi|189910834|ref|YP_001962389.1| pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167775510|gb|ABZ93811.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167779155|gb|ABZ97453.1| Putative ribosomal large subunit pseudouridine synthase [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 320

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 54/265 (20%), Positives = 111/265 (41%), Gaps = 22/265 (8%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V+        +  +    +P+ +      ++  G++ V       +  +  G+V+   P+
Sbjct: 7   VIRPPFVGKTVIEYLTGKFPYHSLEEWTFLVEEGRITVSGNLASMHKPLLDGEVIEYNPI 66

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                  IKE ++                 +L E        KP  + +        +  
Sbjct: 67  PGR----IKEPEV------------DTNYSILKETEDFLFVEKPGNLPMHPA---GRYRT 107

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L S++++K  K    HRLD+ETSGI++ A++  + + L + F  R + K Y+++V G 
Sbjct: 108 KTLLSFLETKYPKIIPVHRLDRETSGIVIFAKSEESRKWLQKKFETRVVYKEYFAIVLGK 167

Query: 191 PKNKKECIANWLLKKSH-IGGDYVHVVKQNEKGANYAISHF-KVIDCFAQKFCWLEMQPH 248
              K++ +  ++ +  H +    +         +    +HF  ++    +K   + ++P 
Sbjct: 168 F-TKEQKLDGFIGRDIHSVIRKKMIFSPVEFPDSKSCATHFVPILYNEDKKISLVLVKPI 226

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC 273
           TGR HQ+R   L++G PI+GD  Y 
Sbjct: 227 TGRIHQIRASLLYLGFPIIGDKMYG 251


>gi|257784215|ref|YP_003179432.1| pseudouridine synthase [Atopobium parvulum DSM 20469]
 gi|257472722|gb|ACV50841.1| pseudouridine synthase [Atopobium parvulum DSM 20469]
          Length = 246

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 52/229 (22%), Positives = 86/229 (37%), Gaps = 20/229 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPRLTH---RLDQET 154
           LY+D  +   NKPAG+ V         +       L +   S            RLD+ET
Sbjct: 13  LYQDDYLLAVNKPAGMIVHSDGTNEPSLTDLVCEKLCALESSNKIDLSQVQALNRLDKET 72

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           +GI++ +  +       +    + + K Y ++V G     K  I   + K  H       
Sbjct: 73  TGIVLFSLKKETQPQFDQLIASKELSKEYLAVVKGDFGLNKLLIDKAIGKDRHDAQK--- 129

Query: 215 VVKQNEKGANYAISHFKVID----CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
              +       + +  ++I        Q    L +   TGR HQ+RVH   +G P+VGD 
Sbjct: 130 --MRISDTGKPSQTEVRLIKVASSAQGQIQSLLLVNLLTGRKHQIRVHLSSLGFPLVGDV 187

Query: 271 KYCANFKGNFTSPIQNK---LYLHARYMDLPHPEGG-RLQITAPLPAHM 315
            Y         +  +++   L LHA  +   HP  G ++ I   +P   
Sbjct: 188 LYGGMSSLQRKTKKKHRPQPLMLHAYRIGFIHPVTGAKIVIKTDIPERF 236


>gi|109391494|gb|ABG33874.1| Yen4 [Yersinia sp. MH-1]
          Length = 232

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 98/232 (42%), Gaps = 19/232 (8%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H        LY+D  + + NKP+G+    G          +   +    
Sbjct: 3   KIIDTFIAPPCHDKIEN---LYQDDHLVLINKPSGLLSLSGKNPQN--LDSVHHRLVQIF 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +A    L + F  R + K+Y +L+ G   N +  I   
Sbjct: 58  PGCTLVHRLDFGTSGLMVIARNKAINAALCQQFSRRTVTKVYSALLCGHLDNDEGVIDAA 117

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTH 253
           + K + +      ++         A SH++V++ F +            + + P TGRTH
Sbjct: 118 IAKDAAL----FPLMSICSIRGKPARSHYRVVERFYRELEDGRLLPLTRVRLIPETGRTH 173

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QLR+H   +G PI+G   Y              +L LHA  +   HP    L
Sbjct: 174 QLRIHCQQLGHPILGCDLYGGLRLPGTEQTA--RLMLHASELHFVHPISQEL 223


>gi|308321724|gb|ADO28005.1| RNA pseudouridylate synthase domain-containing protein 4 [Ictalurus
           furcatus]
          Length = 386

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 70/281 (24%), Positives = 114/281 (40%), Gaps = 40/281 (14%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----SKG 141
           SV+    +  L   +LY+D  +   NKP G+ V    GI   I   L            G
Sbjct: 105 SVHPNVFAKALSKSILYQDQNLIAINKPYGVPVYSTGGIGNSIAESLPVLAKIIDCTKGG 164

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            K  + + L+++T+G+L +A T   A+ +    R  + +K Y  +  G+P   +  I   
Sbjct: 165 SKLHVCYNLEKDTTGVLFLAWTEETAERIHNLIRSHQAEKRYMVITVGVPVPSEGVIDIP 224

Query: 202 LLKKSHIGGDYVHVV------KQNEKG-----------ANYAISHFKVIDCFAQKFCWLE 244
           +++K  +G  +   +      +  E+G           A  A++ +KV+D  +     +E
Sbjct: 225 IIEKEVMGDQHHFKMGLSPLYRPTEEGDGLVRVRANRQAQSAVTRYKVLDS-SSGCSLVE 283

Query: 245 MQPHTGRTHQLRVHAL-HMGCPIVGDHKYCANFK---GNFTSPIQNK------------L 288
            QP TG  HQLRVH    + CPI+GDHKY    K         +  +            L
Sbjct: 284 FQPVTGVKHQLRVHMALALACPILGDHKYSHWNKLAPQKLPEGVLRRLGLEQSKTRHFPL 343

Query: 289 YLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDR 328
           +LH R + LP   G   L ++  LP         L  +   
Sbjct: 344 HLHVRQITLPGVRGHDDLTVSCLLPKFFTAALKKLQIELPE 384


>gi|72058953|ref|XP_781802.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
 gi|115955042|ref|XP_001182766.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
          Length = 613

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 58/270 (21%), Positives = 102/270 (37%), Gaps = 30/270 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD + K  +   +    +  +  G +RV+K +   +  +++                   
Sbjct: 59  LDVF-KKEFRLESAEYYETAIHEGLIRVNKGKASPDLILKNND----------------- 100

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              + S V+  +     + I ++ +     V NKP+ I V       Y  +  +      
Sbjct: 101 --FMQSKVHRHEPPVSGEPIQIIADTQDYLVINKPSSIPVHPCG--KYRHNTIVFILGKD 156

Query: 140 KGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            G K     HRLD+ TSG+L+ ART   +  L    R R+++K Y     G   +     
Sbjct: 157 YGFKGLHTIHRLDRLTSGLLLFARTLQVSHRLDAYVRERKLEKTYVCKAHGEFPSTPVVC 216

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +   SH  G     V + ++      + F+ +    +    ++  PHTGR HQ+RVH
Sbjct: 217 EEPIFIVSHKIG-----VCRVKEDGKPCKTRFERLSYDGE-TSIIKCHPHTGRMHQIRVH 270

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
             ++G PI+ D  Y     G       N  
Sbjct: 271 LQYLGFPIINDPLYNNTVWGQHRGRGGNNQ 300


>gi|158298572|ref|XP_553504.3| AGAP009693-PA [Anopheles gambiae str. PEST]
 gi|157013948|gb|EAL39149.3| AGAP009693-PA [Anopheles gambiae str. PEST]
          Length = 494

 Score =  148 bits (373), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 58/266 (21%), Positives = 110/266 (41%), Gaps = 26/266 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   +         L +I+  
Sbjct: 83  LDVF-AREFRAHPAEEYERCIKAGTLTVNYEKVPTDYRLKHNDL---------LANIVHR 132

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +T         +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 133 HEVPVTSQPIT---------IVHMDDDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEYN 182

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            +  R  HRLD+ TSG+L+  R+   A+ +    R R++QK Y   V G   +    I  
Sbjct: 183 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEHQIRNRQVQKEYICRVEGEFPD--GIIE- 239

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K+      Y   V +         + F+ +         +  +P TGR HQ+RVH  
Sbjct: 240 --CKEPIEVVSYKIGVCKVSPKGKECTTTFQKLGFNGNS-SVVLCKPLTGRMHQIRVHLQ 296

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++G P+V D  Y  +  G       +
Sbjct: 297 YLGYPVVNDPLYNHDVFGPAKGRGGD 322


>gi|120611810|ref|YP_971488.1| ribosomal large subunit pseudouridine synthase A [Acidovorax
           citrulli AAC00-1]
 gi|120590274|gb|ABM33714.1| ribosomal large subunit pseudouridine synthase A [Acidovorax
           citrulli AAC00-1]
          Length = 239

 Score =  148 bits (373), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 95/241 (39%), Gaps = 22/241 (9%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
            +  L           L+ D  + V  KP+G+    G G        L +          
Sbjct: 6   PAQALADADAGAPPGCLHADDDLLVLAKPSGLLCVPGRGPD--KQDCLSARATLHWPGAC 63

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLDQ TSGI+V+AR   A + L ++F  R++ K Y ++V           A W    
Sbjct: 64  IVHRLDQATSGIVVMARHAQAQRALGDAFAARQVHKRYVAVVHAPRPAGDG--AAWREID 121

Query: 206 SHIGGDYVH-----VVKQNEKGANYAISHFKVIDCFAQKFCWLE--------MQPHTGRT 252
             I  D+       VV     G   +++ ++          W          ++P TGRT
Sbjct: 122 MPIAADWERRPLRVVVPHGAPGGKASLTRWRPAVPGDGAGTWPAADGTLRVLLEPVTGRT 181

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
           HQLRVH   +G PI+GD  Y           +  +L LHA+++   HP  G  L    P 
Sbjct: 182 HQLRVHMAAVGQPILGDTLY----ALPAVQALAPRLLLHAQHIAFAHPRTGTPLAFELPA 237

Query: 312 P 312
           P
Sbjct: 238 P 238


>gi|163750410|ref|ZP_02157650.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           benthica KT99]
 gi|161329900|gb|EDQ00886.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           benthica KT99]
          Length = 599

 Score =  148 bits (373), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 64/226 (28%), Positives = 101/226 (44%), Gaps = 18/226 (7%)

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E    D +  LT  ++     ++Y+DS + V NKPA      G  I   +   +K     
Sbjct: 377 EGLATDENPLLTNPAEGKLLEIIYQDSDMLVVNKPAEFLSVPGRNIDDSVYSRIKQLY-P 435

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +   P + HRLD  TSG++V+A  + A + L + F  R ++K Y +L+ G     +  I+
Sbjct: 436 EATGPLIVHRLDMSTSGLMVIALNKEANKSLQKQFITRTVKKRYVALLTGDLSQDEGIIS 495

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L +          V  ++      A + ++VI         + + P TGRTHQLRVH+
Sbjct: 496 LPL-RGDFDDRPRQLVCFEH---GKPAETKWQVISRR-DGRTKVHLYPKTGRTHQLRVHS 550

Query: 260 LH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            H   +  PIVGD  Y              +L+LHA  ++L HP  
Sbjct: 551 AHPQGLNMPIVGDDLYGKK---------SQRLHLHAELLELNHPRT 587


>gi|21536736|gb|AAM61068.1| unknown [Arabidopsis thaliana]
          Length = 395

 Score =  148 bits (373), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 60/293 (20%), Positives = 106/293 (36%), Gaps = 26/293 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V        +   F + +           ++SG+++VD + V  +  ++S Q +      
Sbjct: 67  VNKRWTGKTIVDLFADEFKGRPRDYYVGAVKSGRIKVDGEIVPVSYIVKSSQKITHFLHR 126

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHID 130
           +    +I +                   ++L+++  +    KPA + V   G      I 
Sbjct: 127 HEPPVMIDD------------------VVILHQEPDVVTVCKPASVPVHPCGQYRKNTIV 168

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G L +  D         HRLD+  SG+L++ART A A    +      ++K Y + V G+
Sbjct: 169 GILDAEHDLG--TLFSIHRLDRLVSGLLIIARTAAKADFFRQQIEGGMVKKRYIAKVIGV 226

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKG----ANYAISHFKVIDCFAQKFCWLEMQ 246
               +  +   +      G         +          A + F  ID        +  +
Sbjct: 227 FPEDEMIVDANINYNGSEGRSTAEDANSSGDDKKVKGKPACTKFTRIDTNG-THSLVSCE 285

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           P TGRTHQ+RVH  + G PI  D  Y      N  + I  ++    R +  P 
Sbjct: 286 PVTGRTHQIRVHLQYTGHPIANDPLYLNQHIDNLETYIAKRIDAGERKIVSPD 338


>gi|313113631|ref|ZP_07799215.1| RNA pseudouridine synthase [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310624047|gb|EFQ07418.1| RNA pseudouridine synthase [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 229

 Score =  148 bits (373), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 64/235 (27%), Positives = 100/235 (42%), Gaps = 39/235 (16%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED+ + V +KPAG+S + G   A      L+           + HRLD   SG++V 
Sbjct: 3   ILYEDAALVVLDKPAGLSSEEGVPAA------LRQLWGQPDAFVGVVHRLDTGVSGLMVF 56

Query: 161 ARTRAAAQHLTESFRMRRIQKI------------------YWSLVWGIPKNK---KECIA 199
           ART  AA  L+      +                      Y +++ G P      +  + 
Sbjct: 57  ARTPGAAAALSRQITQSQNAYAVQDGRAEGEPEVPQFIKQYRAVIAGGPDEALPAESTLR 116

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +WL K S  G   V  V +  +G   A+  ++++    +     E+  HTGRTHQ+RV  
Sbjct: 117 DWLFKDSRRGR--VFPVSRPRRGVREAVLEYRIVKTAGE-MSLAEITLHTGRTHQIRVQF 173

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                P+ GD KY +  KG+        + L +  +   HPE G+ +  T PLP 
Sbjct: 174 ASRKHPLTGDGKYGSRVKGS--------IALQSCGLQFLHPETGKPMAFTLPLPD 220


>gi|195118758|ref|XP_002003903.1| GI20532 [Drosophila mojavensis]
 gi|193914478|gb|EDW13345.1| GI20532 [Drosophila mojavensis]
          Length = 798

 Score =  148 bits (373), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 64/268 (23%), Positives = 119/268 (44%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   +         L +I+  
Sbjct: 377 LDIF-SKEFRAHPAEEYERCIQTGTLTVNFEKVPIDYRLKHNDL---------LANIVHR 426

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +   +T         +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 427 HEVPVTCQPIT---------IVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 476

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V GI P    EC  
Sbjct: 477 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGIFPDGVVECKE 536

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K ++KG +   +  K+      K   +  +P TGR HQ+RVH 
Sbjct: 537 PIEVVSYKIG-----VCKVSQKGKDCTTTFQKL--SQNGKTSVVLCKPLTGRMHQIRVHL 589

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI+ D  Y     G    P++ +
Sbjct: 590 QYLGFPILNDPLYNHEVFG----PLKGR 613


>gi|313683665|ref|YP_004061403.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
 gi|313156525|gb|ADR35203.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
          Length = 305

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 61/293 (20%), Positives = 116/293 (39%), Gaps = 45/293 (15%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHIIKEQ 81
           R+       I     Q+++  G++  +   +  N   I+ G    I      L  +    
Sbjct: 18  RFLMQEL-GITQSEAQRLIAKGRLSQNGIVMSNNAGYIEEGDFDFICFEPVTLGLVPT-- 74

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSK 140
                                + + +  V++KP+G+ V        Y ++  +K      
Sbjct: 75  ---------------------FVEEEFAVYDKPSGLLVHPQNRHTPYSLNDEIKHRF--- 110

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G +  +THR+DQETSG+++ AR + + + L   F  R+I K Y ++V G  K   +    
Sbjct: 111 GHEANITHRIDQETSGLVLAARNKLSERTLKMMFEERQITKKYIAMVKGHLKEPLDIQEP 170

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHA 259
            L ++       V ++ +       + +  K ++ F       +E  P+TGR HQ+RVH 
Sbjct: 171 LLRRED--ASSIVRMIVRVHPEGKPSRTFIKPLEYFPDTDTTLVEASPYTGRQHQIRVHL 228

Query: 260 LHMGCPIVGDHKYCAN-------------FKGNFTSPIQNKLYLHARYMDLPH 299
            H+  PI+GD  Y  +              +    +   ++L LHA  ++  +
Sbjct: 229 FHVEHPIIGDPIYGQDEENAVRFLDREMSVEERLNNTGASRLLLHAHSLEFIY 281


>gi|255571790|ref|XP_002526838.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223533842|gb|EEF35573.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 468

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 72/286 (25%), Positives = 124/286 (43%), Gaps = 36/286 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRV---DK------------KRVKFNNRIQSGQVVRIP 68
           W K ++  I    +Q     G   +   +             +++K N+ +++G  V + 
Sbjct: 79  WVKYYFDEILDSAIQSHFNKGLAHIECPNGSGSIEYGGQMSLRKIKHNDIMEAGARVHVA 138

Query: 69  PVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
             +       +   I   ++        +L+ ++ Y+DS I V NKP  + V+G   +  
Sbjct: 139 VSVAETRISKRFDTIPSGTLYPNADEIQYLQRLVKYKDSAIIVLNKPPRLPVKGNLPLHN 198

Query: 128 HIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRM---------- 176
            +D    + +     + P+L  RLD+E+SG+L++ RT+ +  HL   F            
Sbjct: 199 SMDALAAAALSYDYDEGPKLVQRLDRESSGLLLMGRTKESIDHLQWLFSDVNKSNSRCKA 258

Query: 177 -----RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG---ANYAIS 228
                +   + YW+LV G PK K+  I   L K     G    VV     G   +  A++
Sbjct: 259 WNDACKATYQRYWALVIGSPKEKEGLIRAPLSKVLLNDGKTERVVLAQHSGLEASQEALT 318

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYC 273
            ++V+        W+E++P T R HQLRVH    +G PIVGD+KY 
Sbjct: 319 EYRVLGPRINGCSWIELRPLTSRKHQLRVHCAEALGTPIVGDYKYG 364


>gi|242373163|ref|ZP_04818737.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
 gi|242349114|gb|EES40715.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
          Length = 284

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 58/280 (20%), Positives = 110/280 (39%), Gaps = 36/280 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + + H    +   +  I R+G + V+K+ V     +  G  + +               I
Sbjct: 16  FLQRH--DYSKKTISAIKRNGALIVNKQPVTVRKEMSFGDHLEVHM------------PI 61

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQ 142
              S NL  +   L+  +++ED  + + NKP   +           +   + +++ +KG+
Sbjct: 62  EQPSSNLIPYQKALE--IIFEDDFLVIVNKPQYQNCAPSREHPHESLVEQVLAYLINKGE 119

Query: 143 K--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           K  P +  RLD+ T GI+V A+        ++    +     Y  L +G     K  I  
Sbjct: 120 KSNPHIVTRLDRNTMGIVVFAKYGHVHHLFSKVKFEKE----YVCLAYGR-TKSKGVIEA 174

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +      +   + ++  K   YA + +  +          +++ HTGRTHQ+RVH  
Sbjct: 175 PIARD-----NKSIITRKISKDGKYAKTSYYTL-VQKDNASLCKVKLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           H+  PIVGD  Y  + +      +Q         +   HP
Sbjct: 229 HIEHPIVGDDLYGGHHRQIKGQSLQ------CCAVKFLHP 262


>gi|315639323|ref|ZP_07894485.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
 gi|315480649|gb|EFU71291.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
          Length = 308

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 72/315 (22%), Positives = 122/315 (38%), Gaps = 50/315 (15%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +       I     QK++   ++  +   VK  N I  G VV +    NA   +      
Sbjct: 21  FLMQSLK-IPINEAQKLIDKKRLFCNGNLVKKKNEILQG-VVELIVYENAPKGV------ 72

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYH-IDGFLKSWVDSKG 141
                            ++YE+ +  V  KP+G+     G   AY   D   + W    G
Sbjct: 73  ----------------KIVYENEEFAVLEKPSGVLSHPNGRHCAYSLCDEIWELW----G 112

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +  + HRLD+ETSG+++VA+T+ +       F  R IQK Y +L  G+ K + E     
Sbjct: 113 MEACVVHRLDKETSGLILVAKTKNSQVEFKTMFEKREIQKEYLALTQGLIKEEFEVD--- 169

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHAL 260
           L  +     D V    Q  +    A+S FK +  +       +  +P TGR HQLR+H  
Sbjct: 170 LPMRLTQNYDDVKTRMQICEDGKRALSFFKRVRFYPDLNASLVLCKPFTGRQHQLRLHLF 229

Query: 261 HMGCPIVGDHKYCANFKG-------------NFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           H G  I+G+  Y    +                      +L LH++ +   + +  +  I
Sbjct: 230 HSGHQILGEPLYGLKKEQIEQILDGKLSQDERIKLTGAKRLMLHSQRLYFTY-KAKKFDI 288

Query: 308 TAPLPAHMVKTWDSL 322
           ++    +  + +  L
Sbjct: 289 SSK--ENFWEDFKGL 301


>gi|297690649|ref|XP_002822725.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 1 [Pongo abelii]
          Length = 377

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 116/275 (42%), Gaps = 38/275 (13%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   +L++D  + V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKALTRGILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P      +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWDKDMAHQVQELFRTRQVVKKYWAITVRVPMPSAGVVDIPIV 205

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G                D   V  +  + A  A++ ++V+            QP 
Sbjct: 206 EKEAQGQQQHHKMTLSPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSSTLSSALLEL-QPI 264

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYC------------ANFKGNFTSPIQNK---LYLHA 292
           TG  HQLRVH    + CPI+GDHKY                K       + +   L+LHA
Sbjct: 265 TGIKHQLRVHLSFGLDCPILGDHKYSDWNRLAPQKLSVGTLKKLGLEQSKARYIPLHLHA 324

Query: 293 RYMDLPHPEGG--RLQITAPLPAHMVKTWDSLGFK 325
           R + LP    G   L +   LP   V +   L  +
Sbjct: 325 RQLILPALGSGKEELNLVCKLPRFFVHSLHRLHLE 359


>gi|218675156|ref|ZP_03524825.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli GR56]
          Length = 199

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 45/211 (21%), Positives = 92/211 (43%), Gaps = 28/211 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHY-PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64
           ++ V+  ++    RLD W         +   ++ +++ GQV +  + V     +++ G  
Sbjct: 3   IRKVLTADETAEGRLDAWLTAQVGEDFSRSRIKALIKDGQVSMRGEPVTDPQRKVRVGDS 62

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
             I                L    + T   + +   +LYED  + V +KPAG+ V   SG
Sbjct: 63  FEIT---------------LPEPEDPTPRGEDIPLDILYEDDDLIVISKPAGLVVHPASG 107

Query: 125 --IAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
                 ++  +     +       ++P + HRLD++T+G++VVA+   A +HL+  F   
Sbjct: 108 NWTGTLVNALIHHCGATLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADH 167

Query: 178 R----IQKIYWSLVWGIPKNKKECIANWLLK 204
                +++ Y ++VWG P++    +   L +
Sbjct: 168 GRTMPLERAYQAIVWGRPRSLTGTVDAPLGR 198


>gi|194761916|ref|XP_001963137.1| GF14093 [Drosophila ananassae]
 gi|190616834|gb|EDV32358.1| GF14093 [Drosophila ananassae]
          Length = 755

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 59/268 (22%), Positives = 112/268 (41%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   ++      + +    + 
Sbjct: 336 LDIF-SREFRAHPAEEYERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQ- 393

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 394 -----------------PIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 435

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    EC  
Sbjct: 436 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGVVECKE 495

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  K+          +  +P TGR HQ+RVH 
Sbjct: 496 PIEVVSYKIG-----VCKVSPKGKDCTTTFQKL--SQNGTTSVVLCKPLTGRMHQIRVHL 548

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI+ D  Y     G    P++ +
Sbjct: 549 QYLGYPILNDPLYNHEVFG----PLKGR 572


>gi|297795919|ref|XP_002865844.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297311679|gb|EFH42103.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 392

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 57/282 (20%), Positives = 103/282 (36%), Gaps = 26/282 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V        +   F + +           ++SG+++VD + V  +  ++S Q +      
Sbjct: 64  VNKRWTGKTIVDLFADEFKGRPREYYIGAVKSGRIKVDGEIVPVSYIVKSSQKITHFLHR 123

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHID 130
           +    +I +                   ++L+++  +    KPA + V   G      + 
Sbjct: 124 HEPPVMIDD------------------VVILHQEPDVVTVCKPASVPVHPCGQYRKNTVV 165

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G L +  D         HRLD+  SG+L++ART A A    +      ++K Y + V G+
Sbjct: 166 GILDAEHDLG--TLFPIHRLDRLVSGLLIIARTAAKADFFRQQIEGGMVKKRYIAKVIGV 223

Query: 191 PKNKKECIANWLLKKSHIGG----DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
               +  +   +      G     D        +     A +    ID        +  +
Sbjct: 224 FPEDEMIVDANINYNGSEGRSTAEDPDSSGDDKKVKGKPACTKLTRIDTNG-THSLVSCE 282

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
           P TGRTHQ+RVH  + G PI  D  Y      N  + I  ++
Sbjct: 283 PVTGRTHQIRVHLQYTGHPIANDPLYLNQHIDNLETYIAKRI 324


>gi|254432671|ref|ZP_05046374.1| ribosomal large subunit pseudouridine synthase A [Cyanobium sp. PCC
           7001]
 gi|197627124|gb|EDY39683.1| ribosomal large subunit pseudouridine synthase A [Cyanobium sp. PCC
           7001]
          Length = 206

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 62/209 (29%), Positives = 97/209 (46%), Gaps = 15/209 (7%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           + D+ +   +KP+G+  Q G G A        S +  +    RL HRLD++TSG+L++A 
Sbjct: 2   HADAWLLAVHKPSGLLSQPGLGPALRDSAL--SRLQQRWPTARLAHRLDRDTSGLLLLAL 59

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
             A+ +HL+  F+   ++K Y + V G    ++ CI   L + S     Y  V      G
Sbjct: 60  DAASHRHLSLQFQRGLVRKAYVAEVHGQLARRRGCIDAPLARVSTRPPRYGVV-----PG 114

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              +++ ++ +         L + P TGR+HQLR H   +G PI+GD  Y          
Sbjct: 115 GKPSLTLWRRL-ALGPASTRLLLLPRTGRSHQLRAHLAAIGHPILGDPLYGP--ADAAAD 171

Query: 283 PIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           P   +L LHA  +   HP  G     APL
Sbjct: 172 PGSGRLRLHALGLRFHHPHSG-----APL 195


>gi|326438031|gb|EGD83601.1| hypothetical protein PTSG_04209 [Salpingoeca sp. ATCC 50818]
          Length = 293

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 71/286 (24%), Positives = 117/286 (40%), Gaps = 46/286 (16%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFLKSWVDSKG------ 141
           L + +  L   +L+ED  +   NK   + VQGG+          +L   +  KG      
Sbjct: 6   LRQLARRLWRAVLFEDRHVLCINKWPQLVVQGGTNEPSIARALPYLAQELPPKGSSGRKL 65

Query: 142 ------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                   P + HRLD++T+G+ V+A+   AA+ L   F   ++ K Y ++  G P  +K
Sbjct: 66  VGPNHDFAPSIVHRLDKDTTGVTVIAKHAGAARILNNLFAEHQVDKRYLAMTLGAPYPEK 125

Query: 196 ECIANWLL--KKSHIGGDYVHVVKQNEKGANY----AISHFKVIDCFAQKFCWLEMQPHT 249
             +   +   K +         +  +E+ A      A ++++VID        ++++PHT
Sbjct: 126 GRLDFPIGTNKDTGATACITPTMSADERSALTNVVDAATNYRVIDNIDHHIALVDLKPHT 185

Query: 250 GRTHQLRVHAL-HMGCPIVGDHKYCANF------------KGNFTSPIQNKLYLHARYMD 296
           GR HQLRVH    + CPIVGD+KY                K          L+LHA  + 
Sbjct: 186 GRKHQLRVHCAQALHCPIVGDNKYGPGVTPWLSLAMRTPSKTKRKELWSPPLFLHAARIT 245

Query: 297 LPHPEGG-------------RLQITAPLPAHMVKTWDSLGFKYDRN 329
           +P                  RL ++ PLP    +    L  +  R+
Sbjct: 246 IPRYADHFAEIDDNSKTLKPRLDVSCPLPPWFDEVAQRLKLRLPRS 291


>gi|37519752|ref|NP_923129.1| pseudouridine synthase [Gloeobacter violaceus PCC 7421]
 gi|35210743|dbj|BAC88124.1| gll0183 [Gloeobacter violaceus PCC 7421]
          Length = 314

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 72/310 (23%), Positives = 122/310 (39%), Gaps = 27/310 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  +   + +  ++   Y H      Q  + +GQV +D +       ++S QV+      
Sbjct: 27  IGPESAGLTVLEYYLLRYRHSGDHEWQARIETGQVLLDHRSTSSTELLRSAQVLTYC--- 83

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                               + S  L  +++Y D ++ V  KP G+ V  G G   H   
Sbjct: 84  ---------------RPPWQEPSVPLDIVIIYADEQVLVVAKPGGLPVLPGGGFLEHTLL 128

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           +      +  + P   HRL + TSG++++ART ++   L+E  R +RI K+Y +L  G  
Sbjct: 129 WQVRRRFAGEEPPVPIHRLGRGTSGLVLLARTHSSRAALSEQMRRQRIGKLYRALASGTG 188

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
              +  I   + K  H     +     +      A S   V+         L +   TGR
Sbjct: 189 MRDRFTIRQPIGKVPHPLLGTLWAAAAD---GLPARSDCVVLRRQCTD-SLLAVAISTGR 244

Query: 252 THQLRVHALHMGCPIVGDHKYC----ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            HQ+R+H    G P+VGD  +     A    + + P     +LHA  +   HP  G RL 
Sbjct: 245 PHQIRIHLAAAGYPLVGDPLFGPGGVARLDNDASVPGDGGYFLHAHRLSFLHPTSGRRLV 304

Query: 307 ITAPLPAHMV 316
           +  P P  + 
Sbjct: 305 LECPPPPELT 314


>gi|254431229|ref|ZP_05044932.1| ribosomal large subunit pseudouridine synthase D [Cyanobium sp. PCC
           7001]
 gi|197625682|gb|EDY38241.1| ribosomal large subunit pseudouridine synthase D [Cyanobium sp. PCC
           7001]
          Length = 350

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 70/324 (21%), Positives = 121/324 (37%), Gaps = 61/324 (18%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           R++   YPH       + + +G++  + ++++ +  +Q G  +           +     
Sbjct: 26  RFYAGRYPHSPASVWLERIAAGEIVRNGQQLRADGELQPGDQL-----------VWHRPP 74

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW------ 136
            L+ +V             L++D  + V  KPAG+ V    G   H    L         
Sbjct: 75  WLEPAVPDLPGP-------LFDDGDLLVLAKPAGLPVLPAGGYLEHTVLRLLERQVRAGR 127

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ---------------- 180
           +D +   PR  HRL + TSG+LV AR RA+   L+   R    +                
Sbjct: 128 LDGRFGLPRPVHRLGRFTSGLLVCARRRASRAWLSALLRDGTAEASRAVPLELQEMVGEA 187

Query: 181 -----KIYWSLVWGIPKNKKE--------CIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
                K+Y +L   +P +            I   + ++ H       V     + A  A+
Sbjct: 188 PAACRKLYRALAGPLPVSGPGALELGETLRITTPIGRRPHQ--RLGEVWSAGGRNALPAL 245

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPI 284
           +   +++      C +E    TGR HQ+R+H   +G P++GD  Y        G      
Sbjct: 246 TTITLLERRGHG-CLVEAAIGTGRPHQIRIHLAAVGAPLLGDPLYRPGGGVNPGALPGDP 304

Query: 285 QNKLYLHARYMDLPHPEGGRLQIT 308
             +L  HA  + LP P G RL + 
Sbjct: 305 GYRL--HAHRLTLPWPPGQRLALE 326


>gi|311264327|ref|XP_003130110.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 2 [Sus scrofa]
          Length = 345

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 73/267 (27%), Positives = 112/267 (41%), Gaps = 42/267 (15%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   ++++D  + V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 85  VHPNVLAKALSRGIVHQDKDLLVINKPYGLPVHGGPGVQLCISDVLPILAKILHGHKAEP 144

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P      +   ++
Sbjct: 145 LHLCHRLDKETTGVMVLAWEKEVAHQVQELFRTRQVAKKYWAITVRVPVPSAGVVDIPII 204

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-M 262
                           EK    A++ ++V+            QP TG  HQLRVH    +
Sbjct: 205 ----------------EKEVQVAVTQYQVLSSTLSSALLEL-QPVTGIKHQLRVHLSFGL 247

Query: 263 GCPIVGDHKYCA-----------NFKGNFTSPIQN----KLYLHARYMDLP--HPEGGRL 305
            CPI+GDHKY                     P        L+LHAR + LP        L
Sbjct: 248 DCPILGDHKYSDWNRLAPQKLSVGVLKKLGLPQSKARHIPLHLHARQLILPALQSRKEEL 307

Query: 306 QITAPLPAHMVKTWDSLGFK---YDRN 329
            +    P + V +   LG K   +D+N
Sbjct: 308 NLVCKPPRYFVHSLRRLGLKMPSHDQN 334


>gi|163748995|ref|ZP_02156246.1| putative 23S rRNA pseudouridylate 746 synthase [Shewanella benthica
           KT99]
 gi|161331371|gb|EDQ02259.1| putative 23S rRNA pseudouridylate 746 synthase [Shewanella benthica
           KT99]
          Length = 238

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 58/218 (26%), Positives = 93/218 (42%), Gaps = 26/218 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  I V +KP+G+    G          +   +        L HRLD  TSGI+++
Sbjct: 19  ILFRDEHILVIDKPSGLLSLSGKHPLN--IDSVHYRLVQDYPTCTLIHRLDFGTSGIMLL 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +     L + F  RR+ K Y +L+ G  +     +   + K      D   ++K  +
Sbjct: 77  AMNKQINALLCKQFSERRVSKRYTALLHGNLEPDSGLVDCGIAKDV----DNFPLMKLCQ 132

Query: 221 KGANYAISHFKVIDCF----------------AQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                A S F+VI  F                 ++   +E +P TGRTHQLR+H+ H+G 
Sbjct: 133 DTGKPAQSQFRVISRFIQTDNDNFFLDDTRAGHRQVTRVEFEPVTGRTHQLRLHSQHLGH 192

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           PI+G   Y  +        + ++L LHA  +   HP  
Sbjct: 193 PILGCDLYATDE----AYFMSSRLMLHASRLCFEHPVS 226


>gi|269467869|gb|EEZ79612.1| pseudouridylate synthase, 23S RNA-specific [uncultured SUP05
           cluster bacterium]
          Length = 296

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 71/281 (25%), Positives = 109/281 (38%), Gaps = 42/281 (14%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
            ++    QK+L   +V  D+     N +I  G  V++                       
Sbjct: 25  GLSLSISQKLLSKNRVFNDQGNTLKNGQILKGDYVQV--------------------AVF 64

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             H+  LK   L+E     VF+KP+GI V        +    L       G++  L HR+
Sbjct: 65  EGHTRGLKP--LFEVEDFAVFDKPSGIMVHPTRKDTPYC--LLDEIRYHFGEEASLAHRI 120

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ETSG+++VA+ + A+  L   F  R   K Y +LV G  KN    I   + K S I G
Sbjct: 121 DAETSGLVLVAKNKQASTVLKNLFENRECNKEYLALVKGQLKNN-ITIDKPISKSSGIIG 179

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             +    Q+      + +H + +    Q     ++  P TGR HQ+RVH   +G  IVGD
Sbjct: 180 IKMTCENQD---GKASTTHIQPLKFNEQDNTTLVKAIPVTGRQHQIRVHLDSIGHTIVGD 236

Query: 270 HKYCANFK-------------GNFTSPIQNKLYLHARYMDL 297
             Y  + +                      +L LHA  +  
Sbjct: 237 PIYGVDDQIADQCLKKTLTDEQRIELTGAKRLMLHANNLSF 277


>gi|328868208|gb|EGG16588.1| pseudouridine synthase family protein [Dictyostelium fasciculatum]
          Length = 558

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 99/248 (39%), Gaps = 30/248 (12%)

Query: 27  NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
           +  P    +  QK + +G +RV+ ++   +  +    ++              E  +  +
Sbjct: 197 SQLPE--RIYRQK-IENGWIRVNGQQTTVDYCVGRKDMIEHRVHR-------HEPPVTSA 246

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPR 145
            +            ++  D +    +KP+ I V       +  +  +       G     
Sbjct: 247 PIK-----------IVANDDEYVAVDKPSSIPVHPCG--RFRHNSLIYVLAKEYGLNNLF 293

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD+ TSG+L++A++  +AQ ++ +     + K Y +LV G   N +  +   L  +
Sbjct: 294 GVHRLDRLTSGLLILAKSTESAQKMSGAIMKGEVSKRYVALVKGKFSNDEVVVDQPLKVQ 353

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM-QPHTGRTHQLRVHALHMGC 264
           +H  G  +            + + F ++   A+    +    P TGRTHQ+R+H   +G 
Sbjct: 354 NHRLGLNMVA-----PDGKPSTTVFNIVSYDAETDTSVVCATPKTGRTHQIRLHLQWLGH 408

Query: 265 PIVGDHKY 272
           PI+ D  Y
Sbjct: 409 PILNDPLY 416


>gi|148926838|ref|ZP_01810517.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|145844563|gb|EDK21670.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
          Length = 244

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 60/272 (22%), Positives = 106/272 (38%), Gaps = 34/272 (12%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           Y+ ++      +  +    +   I+    QK++   ++  D   V+  N+I  G V    
Sbjct: 3   YIKIKLSNNGKKAFQVLMENLK-ISINEAQKLIDKKRLFCDGILVEEKNKILKGDV---- 57

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAY 127
                                +   ++     +++E+    V  K +GI     G    Y
Sbjct: 58  -------------------ELIVYENNPKGVEIVFENEDFAVLEKESGILSHPNGRHCKY 98

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   +       G+K  + HRLD+ETSG+++VA+ + A   L   F  ++IQK Y +L 
Sbjct: 99  SLSDEIWHL---WGKKACVAHRLDKETSGLILVAKHKKAQIELKTMFEKKQIQKEYLALA 155

Query: 188 WGIPKNKKECIAN-WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEM 245
            G  K          L K        + +     +    AI+ F+V+  + +     L  
Sbjct: 156 SGEIKVNFIVDQAMDLTKDYDDVKTRMQIC----ENGKKAITEFEVLSFYPKLNATLLLC 211

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +P TGR HQ+RVH  +    I+GD  Y    K
Sbjct: 212 KPLTGRQHQIRVHLFYKNHKILGDPLYGLEKK 243


>gi|330881340|gb|EGH15489.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           glycinea str. race 4]
          Length = 190

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 46/196 (23%), Positives = 84/196 (42%), Gaps = 19/196 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ +    
Sbjct: 11  VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLELIAEQ 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-- 129
            A    + +   LD               ++YED +I V NKPAG+ V   +G A     
Sbjct: 71  EAQGEWVAQDIELD---------------IIYEDDQILVINKPAGLVVHPAAGHADGTLL 115

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +  L    D     +  + HRLD++T+G++VVA+T  A   L    + R + +IY  +V 
Sbjct: 116 NALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVI 175

Query: 189 GIPKNKKECIANWLLK 204
           G+       I   + +
Sbjct: 176 GVV-TAGGKIDAPIGR 190


>gi|302336155|ref|YP_003801362.1| pseudouridine synthase [Olsenella uli DSM 7084]
 gi|301319995|gb|ADK68482.1| pseudouridine synthase [Olsenella uli DSM 7084]
          Length = 355

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 62/325 (19%), Positives = 112/325 (34%), Gaps = 58/325 (17%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +     ++L  G++ +D   +   +R+  G VV                 +  +  ++  
Sbjct: 40  SRQMSARVLARGRLSLDGAGLAPASRLAPGDVV----------------GLAFAHTHVPG 83

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--------- 143
            +   + ++++ D      +KPAGI V    G+   +   ++  +D +G+          
Sbjct: 84  PASEAEPVVVWRDRFALAVDKPAGILVHADGGVGETLTARVQGLLDREGRPDHEGRPDGQ 143

Query: 144 ------------------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                             P+   RLD ETSG+++ +               R  +K Y +
Sbjct: 144 GPPGRMPDGGRDSVARLVPQALQRLDVETSGLVLFSLAEETQPAFDALMAGRVTEKRYLA 203

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           +V G   +    I   + +  H          +   G   + +  + +         L +
Sbjct: 204 VVRGPWPSGTMLIDRPIGRDRHDARR-----MRVSAGGKSSRTWARPLATRGD-HTLLLV 257

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCA--------NFKGNFTSPIQNKLYLHARYMDL 297
           +  TGR HQ+RVH    G PIVGD  Y A          +G   S     L LHA    L
Sbjct: 258 RIGTGRRHQIRVHLASTGHPIVGDRLYGALPAGCGGRAGRGGHGSRATGGLMLHAIEERL 317

Query: 298 PHPEGG-RLQITAPLPAHMVKTWDS 321
            HP  G  L +    P      + +
Sbjct: 318 VHPVTGEELVLRTAWPKRFDAFFSA 342


>gi|315652683|ref|ZP_07905658.1| RluA family pseudouridine synthase [Eubacterium saburreum DSM 3986]
 gi|315485061|gb|EFU75468.1| RluA family pseudouridine synthase [Eubacterium saburreum DSM 3986]
          Length = 215

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 59/216 (27%), Positives = 103/216 (47%), Gaps = 10/216 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LYED+ I V  KP G+  Q  SG    +   +K  +  K     + HRLD+   G
Sbjct: 1   MALKILYEDNDIIVVIKPRGVFSQSSSGFEEDMVSLIKKHL-GKDSYIGVVHRLDKPVYG 59

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I+V  + + A   L    R + I+KIY +LV G+P   +  + +++ K ++I      VV
Sbjct: 60  IMVYGKNKKATGILCNELRKKNIRKIYEALVEGVPSENRGKLRDFIKKDNNISR----VV 115

Query: 217 KQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           +++ + A  A+  +++I+      +    L++   TGR HQ+R+     G PI+GDHKY 
Sbjct: 116 EKDTEDAKEAVLEYEIIETKYSADRYITRLKINLLTGRHHQIRLQCAAHGFPILGDHKYN 175

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
                      +    L A  ++  HP+ G  ++  
Sbjct: 176 ERVIKEKLDYNKVP-ALAAVALEFKHPKTGKEMKFK 210


>gi|163848084|ref|YP_001636128.1| pseudouridine synthase [Chloroflexus aurantiacus J-10-fl]
 gi|222525978|ref|YP_002570449.1| pseudouridine synthase [Chloroflexus sp. Y-400-fl]
 gi|163669373|gb|ABY35739.1| pseudouridine synthase [Chloroflexus aurantiacus J-10-fl]
 gi|222449857|gb|ACM54123.1| pseudouridine synthase [Chloroflexus sp. Y-400-fl]
          Length = 306

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 74/331 (22%), Positives = 126/331 (38%), Gaps = 37/331 (11%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V ++ V +++    L     +       V  Q+    G + + K+R   +    +G+
Sbjct: 1   MKAVSFL-VTSEDHGRPLGDIAADRLGEAGRVAAQR----GGLWLGKRRAAASTLAIAGE 55

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA----GISV 119
            + +                     +    +      ++YED+ + V NKP     G + 
Sbjct: 56  TLSVRF----------------PPTHGYCDAPLTLENIIYEDNDVLVVNKPPACYVGDTP 99

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               G    +   L +  D       L H+LD  TSGILV+++T  A   L  +F     
Sbjct: 100 WDTQGSVLAVVQRLLTVRDGVPPVLHLAHQLDFGTSGILVLSKTPRANAPLQTAFARGLA 159

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH------VVKQNEKGANYAISHFKVI 233
            K Y ++  G P    + +      ++  G   ++       V  + +    A + F  +
Sbjct: 160 MKQYLAVCSGHPPVTADLVTGH--GRAAGGRWRLYDQADIGRVLPDGQRVRLAHTRF-TL 216

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                    +E  P TGRTHQ+R+H   +GCPI+GD +Y               L  HA 
Sbjct: 217 RRQFANAALVEAMPLTGRTHQIRLHLAALGCPILGDERYGGVVDVAGLHLTHPLL--HAA 274

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            + LPHP  GR L +  P P+ ++   D L 
Sbjct: 275 ELQLPHPIHGRSLHLFCPPPSLILTVIDRLR 305


>gi|302795552|ref|XP_002979539.1| hypothetical protein SELMODRAFT_36043 [Selaginella moellendorffii]
 gi|300152787|gb|EFJ19428.1| hypothetical protein SELMODRAFT_36043 [Selaginella moellendorffii]
          Length = 229

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 51/233 (21%), Positives = 88/233 (37%), Gaps = 29/233 (12%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
            +  +  + R+D W     PH +   +Q  +R G   V+ K + K +  +  G  V    
Sbjct: 12  TIPEETVSTRIDVWLSGQLPHTSRARVQDSIRKGLALVNGKTITKPSFPVIGGDEVVCTL 71

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AY 127
              A      E+  LD               +++ED  + V NK A + V    G     
Sbjct: 72  CGAAPLEATPEKIQLD---------------IVHEDDHVIVVNKAADMVVHPAPGHYGGT 116

Query: 128 HIDGFLKSWV----------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
            ++  L                   +P + HRLD+ TSG++VVA+   +   L+E F+ R
Sbjct: 117 LVNAILHHCGLPATPSRFRGPRPVIRPGIVHRLDKGTSGLIVVAKDEQSQLSLSEQFKSR 176

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISH 229
           ++++ Y SL  G P      I   +L+               + + A +A S 
Sbjct: 177 KVRRTYLSLTCGTPSTTSGRIEAEILRDPRDRKRMTTSDTVPSARNARFAASR 229


>gi|302765707|ref|XP_002966274.1| hypothetical protein SELMODRAFT_168290 [Selaginella moellendorffii]
 gi|300165694|gb|EFJ32301.1| hypothetical protein SELMODRAFT_168290 [Selaginella moellendorffii]
          Length = 359

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 67/343 (19%), Positives = 118/343 (34%), Gaps = 74/343 (21%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   +    +     + +  GQ+ ++ + V   + +     +R    +       +E   
Sbjct: 36  YASRYQSSASREGWLRRILKGQIEINGEVVTSPDAL-----IRNNASLVYHRFPWEE--- 87

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---DSK 140
                     S      +LYED  +   NKP+G+ V  G             W      +
Sbjct: 88  ---------PSAPFMLEILYEDEHLLAINKPSGLQVLPGGLFQQRTVLSQLQWRVTDQVE 138

Query: 141 GQKPRLTHRLDQETSGI----------------------LVVARTRAAAQHLTESFRMRR 178
              P   HRL + TSG+                      L+ A++  A       +R   
Sbjct: 139 RNHPTPVHRLGRGTSGVYVCGTSLTKTFVYFKYLHFSGVLLCAKSDQAR------YRFEM 192

Query: 179 IQKIYWSLVWGIPKNKKECI-ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           + K+Y +LV GI ++ K  I  +  + ++H  G    +     KG   + S    +    
Sbjct: 193 LSKVYRALVCGIVQDDKVIISIDQAIGRAHYPGVRGGLYMAVAKG-KPSHSKVTTLKRNT 251

Query: 238 Q-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY----------------------CA 274
           +     +E++  +GR HQ+R+H   +G P+VGD  Y                        
Sbjct: 252 EENSTVVEVEIFSGRAHQIRIHLASIGHPLVGDPLYVRGGQPSMQVVSTLERASVAEDGG 311

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMV 316
             +     P     +LHA  +   HP    RL+I APLP  + 
Sbjct: 312 YERPENPLPGDCGYHLHAHRLTFHHPVTNQRLEIVAPLPPELE 354


>gi|297735761|emb|CBI18448.3| unnamed protein product [Vitis vinifera]
          Length = 481

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 74/290 (25%), Positives = 128/290 (44%), Gaps = 40/290 (13%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-----VDK------------KRVKFNNRIQSGQVVR 66
           W K ++  I    +Q     G V      +D             +++K N  +++G  + 
Sbjct: 86  WIKYYFDEIPGSVVQSHFNKGLVHMERSNLDDSSLEKEGQIKPLRKIKPNEVMEAGTRIY 145

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILL--YEDSKIYVFNKPAGISVQGGS 123
           +P  +       +   I   +++      ++L+ + L  ++D  I V NKP  + ++G  
Sbjct: 146 VPVSVAEARISKRFDTIPSGTLHPNADEIEYLQRLWLLKFQDPAILVLNKPPKVPLKGNL 205

Query: 124 GIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRM------ 176
            +   +D    + +    ++ P+L HRLD+E+SG+L++ RT+ +  HL   F        
Sbjct: 206 PVHNSMDALAAAALTFDYEEGPKLVHRLDRESSGLLLMGRTKESVAHLHWLFSDINKAKS 265

Query: 177 ---------RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG---AN 224
                        + YW+LV G PK K+  I   L K     G    V+  N+ G   + 
Sbjct: 266 LSKAWDDACEATCQRYWALVIGSPKQKEGVIHAPLSKVLLDDGKTERVILANQSGLEASQ 325

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYC 273
            AI+ ++V+        W+E+ P T R HQLRVH    +G PIVGD+KY 
Sbjct: 326 EAITEYRVLGPMINGCSWIELCPRTSRKHQLRVHCAEALGTPIVGDYKYG 375


>gi|298483420|ref|ZP_07001597.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D22]
 gi|298270368|gb|EFI11952.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D22]
          Length = 612

 Score =  147 bits (371), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 72/295 (24%), Positives = 117/295 (39%), Gaps = 71/295 (24%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++S+ L    +  +  +++ED  + V NKPAG+    G   A   
Sbjct: 317 CEPILQHMLQGLEVDENSL-LNPVHEEEELEIVFEDEWLLVVNKPAGMLSVPGK--AEDR 373

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           D           +   P + HRLD  TSG+L+VA+T+   Q L   F  R I+K Y +++
Sbjct: 374 DSVYHRLKKKYPEATGPMIVHRLDMATSGLLLVAKTKEVHQDLQAQFANRSIKKRYVAVL 433

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVK----------------------------QN 219
            G     ++       K   I  + V   K                             +
Sbjct: 434 DGAIIKTEKETKPIAEKAILIAKNTVSTKKTAKAERTGSTGRIELPLCLNPLDRPRQMVS 493

Query: 220 EKGANYAISHFKVID--------------------------CFAQKFCWLEMQPHTGRTH 253
            +    AI+ +++I                             ++K+  +   P TGRTH
Sbjct: 494 SEHGKEAITEYQIISESERITSESENTFNESNRIDESERSINESRKYTRIIFYPLTGRTH 553

Query: 254 QLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QLRVHA H   +GCPI+GD  Y             ++LYLHA Y++  HP  G +
Sbjct: 554 QLRVHAAHPEGLGCPILGDELYGKK---------ADRLYLHAEYIEFRHPIYGDI 599


>gi|331005741|ref|ZP_08329102.1| pseudouridine synthase A [gamma proteobacterium IMCC1989]
 gi|330420458|gb|EGG94763.1| pseudouridine synthase A [gamma proteobacterium IMCC1989]
          Length = 219

 Score =  147 bits (371), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 64/222 (28%), Positives = 99/222 (44%), Gaps = 19/222 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHI--------DGFLKSWVDSKGQKPRLTHRLDQ 152
           +LYED  + + +KPAG+    G G                +++  +   +  R+ HRLD 
Sbjct: 6   VLYEDPHLLIVDKPAGLLTVPGRGPDKQDCLIHRIVGHDSIQNNTEQHWETARIIHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI+V+A        + + F  R+I K Y ++V G  +     I   L+       D 
Sbjct: 66  ATSGIIVIALDHPVQAAMGKLFAERQINKSYTAVVEGKVRP-TATIELPLICD----WDN 120

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               K + +   YA +   ++    Q     + + P TGR+HQLRVH L +G  I+GD  
Sbjct: 121 RPKQKVDHEHGKYAKTELALMSYCEQNHTSRVALTPFTGRSHQLRVHMLAIGHHILGDFF 180

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           Y      N +S    +L LHA  +D  HP    +L I +P P
Sbjct: 181 YAPEDIKNKSS----RLLLHASAIDFIHPMTQEKLSIQSPAP 218


>gi|145642181|ref|ZP_01797749.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae R3021]
 gi|145273105|gb|EDK12983.1| DL-methionine transporter ATP-binding subunit [Haemophilus
           influenzae 22.4-21]
          Length = 186

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 52/179 (29%), Positives = 86/179 (48%), Gaps = 6/179 (3%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K        ++Y+D+ + V NKP+G+    G+   Y+      S V  K       HRLD
Sbjct: 7   KPPLEPYLDIIYQDNHLCVVNKPSGLLSVPGNQPQYYDSAM--SRVKEKFGFCEPAHRLD 64

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSGI+V A ++AA + L   FR R  +K Y ++VWG  +     +   ++       +
Sbjct: 65  MATSGIIVFALSKAADRELKRQFREREPKKHYQAIVWGHLEKDYGEVNLPMICD----WE 120

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                + +      A++ F+V+         +++ P TGR+HQLR+H L +G PI+GD 
Sbjct: 121 NRPRQRLDFVLGKRAVTKFEVLARLPNNSTRVKLTPVTGRSHQLRLHMLALGHPILGDK 179


>gi|300812671|ref|ZP_07093082.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
 gi|300496357|gb|EFK31468.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
          Length = 282

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 62/258 (24%), Positives = 95/258 (36%), Gaps = 30/258 (11%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           QV V+ +   FN  I+  + V +                   S+     +      ++YE
Sbjct: 40  QVLVNGQYRSFNQLIKGNEKVDLYLDQV-------------ESLQGDYPASGKMPKVVYE 86

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  + V +KP G       G          S++   G  P + HRLD  T G+L+VA+  
Sbjct: 87  DENVLVIDKPKGQKTHPNQGENGTALNDCASYL---GYSPYIVHRLDMLTGGLLLVAKNP 143

Query: 165 AAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
           A    L      + +++ Y + V        +  I   + +                   
Sbjct: 144 AVVPILNRQLTSKTLRRDYLATVDLNKEIPDQGTIDLPIGQDPADQRKRQVRA-----DG 198

Query: 224 NYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             A+SHF+V++   +K    L +   TGRTHQ+RVH    G PIVGD  Y  NF G    
Sbjct: 199 LRAVSHFQVLEKDEEKKQAKLLVTLETGRTHQIRVHLSASGWPIVGDPLYNPNFAGED-- 256

Query: 283 PIQNKLYLHARYMDLPHP 300
                L L    +    P
Sbjct: 257 -----LALTGWQLTFVKP 269


>gi|289422501|ref|ZP_06424344.1| ribosomal large subunit pseudouridine synthase family protein
           [Peptostreptococcus anaerobius 653-L]
 gi|289157073|gb|EFD05695.1| ribosomal large subunit pseudouridine synthase family protein
           [Peptostreptococcus anaerobius 653-L]
          Length = 234

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 57/225 (25%), Positives = 99/225 (44%), Gaps = 20/225 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  K   I  Q  +     +    K +V  K  KP      L HRLD+   
Sbjct: 13  VIYEDNHLLVVEKIPNILSQSDNTKDVDMLSMCKEYVKIKYNKPGAVFMGLVHRLDRPVG 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V ART  AA  L++  R R ++K Y +++ G P    + + ++L K +    + V  
Sbjct: 73  GVMVFARTSKAASRLSDQVRTRTMKKSYQAIINGNPPKAGDFV-DYLYKDT--NKNMVRC 129

Query: 216 VKQNEKGANYAISHFKVIDC-----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           V ++  G   A   ++++D        + +  +E+  HTGR HQ+RV        + GD 
Sbjct: 130 VDKSFNGGKEARLSYRLLDSSISPEDKKDYSLVEIDLHTGRPHQIRVQFASRKYALYGDQ 189

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           +Y    K         ++ L A  ++L HP     +   +  P  
Sbjct: 190 RYSKVAKKG------QQIALWATRLELVHPTTKETMVFRSRPPKE 228


>gi|317154375|ref|YP_004122423.1| pseudouridine synthase [Desulfovibrio aespoeensis Aspo-2]
 gi|316944626|gb|ADU63677.1| pseudouridine synthase [Desulfovibrio aespoeensis Aspo-2]
          Length = 215

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 63/221 (28%), Positives = 99/221 (44%), Gaps = 20/221 (9%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQKPRLTHRLDQETSG 156
            ++++ D    V +KP G+    G G          LK+ +     +P   HRLDQ+TSG
Sbjct: 8   LVIVHRDPLFVVVDKPGGLLSVPGRGPENQDCVVNRLKALLPECLDQPS-VHRLDQDTSG 66

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV+A T  A + L+  F  R + K Y +L+ G+       I         +  D     
Sbjct: 67  LLVLALTAQAHRALSVQFMERLVGKRYVALIDGVLGPDSGIIELAF----RLDPDNRPYH 122

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKYC 273
             + +     ++ ++ +    Q    +E  P TGRTHQLR+H+ H   +G PIVGD  Y 
Sbjct: 123 VYDPEQGKPGVTRWRKLG-VEQGRTRVEFMPLTGRTHQLRLHSAHEKGLGHPIVGDRLYG 181

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                  T+P Q +L  HA  +   HP   + L+  + LP 
Sbjct: 182 TG-----TAPGQLRL--HASALRFRHPATRQNLEFFS-LPP 214


>gi|167004717|ref|ZP_02270475.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
          Length = 281

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 111/284 (39%), Gaps = 46/284 (16%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+    QK++   ++  D   V+  N+I +G +V +                      + 
Sbjct: 6   ISINEAQKLIDKKRLFCDGILVEEKNKILNG-LVEL----------------------IV 42

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             ++     +++E+    +  K +GI     G    Y +   +       G++  + HRL
Sbjct: 43  YENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL---WGKEACVAHRL 99

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-LLKKSHIG 209
           D+ETSG++++A+ + A   L   F  + +QK Y +L  G  +          L K     
Sbjct: 100 DKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALAHGKIEENFIVDKAINLTKNYDDV 159

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              + + K+       AI+ F++++ F +     L  +P TGR HQ+RVH  +    I+G
Sbjct: 160 KTRMQICKE----GKQAITEFEILEYFPKINATLLLCKPLTGRQHQIRVHLHYKNHTILG 215

Query: 269 DHKYC-------------ANFKGNFTSPIQNKLYLHARYMDLPH 299
           D  Y               N K         +L LH+  +   +
Sbjct: 216 DPLYGLSKQQIESILDEKLNPKERLKLTGALRLCLHSYRLKFQY 259


>gi|325685780|gb|EGD27854.1| pseudouridine synthase [Lactobacillus delbrueckii subsp. lactis DSM
           20072]
          Length = 282

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 62/258 (24%), Positives = 95/258 (36%), Gaps = 30/258 (11%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           QV V+ +   FN  I+  + V +                   S+     +      ++YE
Sbjct: 40  QVLVNGQYRSFNQLIKGNEKVDLYLDQV-------------ESLQGDYPASGKMPKVVYE 86

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  + V +KP G       G          S++   G  P + HRLD  T G+L+VA+  
Sbjct: 87  DENVLVIDKPKGQKTHPNQGENGTALNDCASYL---GYSPYIVHRLDMLTGGLLLVAKNP 143

Query: 165 AAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
           A    L      + +++ Y + V        +  I   + +                   
Sbjct: 144 AVVPILNRQLTSKTLRRDYLATVDLNKEIPDQGTIDLPIGQDPADQRKRQVRA-----DG 198

Query: 224 NYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             A+SHF+V++   +K    L +   TGRTHQ+RVH    G PIVGD  Y  NF G    
Sbjct: 199 LRAVSHFQVLEKDEEKKQAKLLVTLETGRTHQIRVHLSASGWPIVGDPLYNPNFAGED-- 256

Query: 283 PIQNKLYLHARYMDLPHP 300
                L L    +    P
Sbjct: 257 -----LALTGWQLTFVKP 269


>gi|319789701|ref|YP_004151334.1| pseudouridine synthase [Thermovibrio ammonificans HB-1]
 gi|317114203|gb|ADU96693.1| pseudouridine synthase [Thermovibrio ammonificans HB-1]
          Length = 274

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 57/292 (19%), Positives = 114/292 (39%), Gaps = 50/292 (17%)

Query: 33  NFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    ++++  G V V+ ++ +    R++ G+VVR P         + E      +V L 
Sbjct: 29  SKKRAKRLIDEGLVSVNGQKELLARRRLKGGEVVRFP---------LTEAPFKPPNVKL- 78

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                     L+ +  ++VF KP  I+   G                      ++ HRLD
Sbjct: 79  ----------LFRERGVWVFEKPPFITTNEGEKSLEETV------RKLFNPNLKVVHRLD 122

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T+G ++   +    +   + F+ R ++K Y  LV G  ++++  +   +         
Sbjct: 123 KQTTGPVIAVESEKLFEAFKKQFKRREVKKEYLCLVKGKLRSRQ-TVRRPI--------- 172

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                         A+S    ++ F ++     ++  TGR HQ+R H   +G P+VG+  
Sbjct: 173 ----------DGKSAVSLVTPLEHF-KRATLCRVEIETGRKHQIRRHLASVGYPVVGEFL 221

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
           Y              ++ LH R +   HP  G R+ + + LP  + +    L
Sbjct: 222 Y-YRGSWPEELLFCPRIALHFRKLSFTHPATGKRITVESELPKDLKEFIGEL 272


>gi|296114348|ref|ZP_06833002.1| pseudouridine synthase [Gluconacetobacter hansenii ATCC 23769]
 gi|295979109|gb|EFG85833.1| pseudouridine synthase [Gluconacetobacter hansenii ATCC 23769]
          Length = 293

 Score =  147 bits (370), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 97/236 (41%), Gaps = 17/236 (7%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P   A+  +        +     ++   L   +L       V +KP G+    G    
Sbjct: 1   MKPRRPAIPRVTSPAPRAVTRAVSDRNDGELPFPVLLRTRHFIVIDKPPGLPAHAGRAGG 60

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             ++    + +      P L HRLD++TSG L+VA  + A     E F   R  K+YW++
Sbjct: 61  PSVEDAF-ALMSRHRNGPWLAHRLDRDTSGCLLVALRKQALIAAQECFASGRTTKVYWAI 119

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC----FAQKFCW 242
             G P      +   LL+++  G   + +          A + ++ +            W
Sbjct: 120 THGHPTAGHGVVDAPLLRRAERGQWRMEIT----PDGQDARTAWRCLARGHMPDGSPASW 175

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           LE++  TGRTHQ RVH   +GCP++GD +Y      +        L+L +R + LP
Sbjct: 176 LELRLETGRTHQARVHCAALGCPVMGDGQYGRADGKS--------LHLMSRELYLP 223


>gi|116072039|ref|ZP_01469307.1| probable pseudouridine synthase [Synechococcus sp. BL107]
 gi|116065662|gb|EAU71420.1| probable pseudouridine synthase [Synechococcus sp. BL107]
          Length = 315

 Score =  147 bits (370), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 75/308 (24%), Positives = 134/308 (43%), Gaps = 35/308 (11%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E   L +W  N Y H +       + +G++  + + ++ + ++ SG  +R          
Sbjct: 32  EGEWLSQWMANRYQHSDVTVWLGRIAAGELHRNGEPLRGDTQLASGDEIRW--------- 82

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
             +    L+ ++     +       +++D  + V NKP+G+ V  G G   H    L + 
Sbjct: 83  --QRPPWLEEAIPDQWDT-------IHDDGDLLVINKPSGLPVMPGGGFLEH---TLTAL 130

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKIYWSLVWGIPK 192
           + S G KP   HRL + TSG+ V ART A    L++ FR     ++I + +   V G+  
Sbjct: 131 LASTGAKP--VHRLGRFTSGLQVCARTAATRAALSKQFRPDSRCQKIYQAWAHRVEGLEP 188

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGAN----YAISHFKVIDCFAQKFCWLEMQPH 248
            K   ++  ++++ H    ++   +  +K        A S  +++D  A      E+   
Sbjct: 189 GKSLVVSTDVVERQHPLLGWLWGPEPRDKEPTRKRLTAHSTVRLLDRCAAGDRL-EVTIR 247

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           TGR HQ+R+H   +G P++GD  Y  N K  +  +P      LHA  +D      G L +
Sbjct: 248 TGRPHQIRIHLAQLGSPLLGDPLYLLNRKISDHATPGDGGYGLHAWRLD--GLTAGGLSL 305

Query: 308 TAPLPAHM 315
            A LP   
Sbjct: 306 QAALPKSF 313


>gi|104774376|ref|YP_619356.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|116514473|ref|YP_813379.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|103423457|emb|CAI98343.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|116093788|gb|ABJ58941.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|325126179|gb|ADY85509.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           delbrueckii subsp. bulgaricus 2038]
          Length = 282

 Score =  147 bits (370), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 62/258 (24%), Positives = 96/258 (37%), Gaps = 30/258 (11%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           QV V+ +   FN  I+  + V +                   S+     +      ++YE
Sbjct: 40  QVLVNGQYRSFNQLIKGNEKVDLYLDQV-------------ESLQGDYPASGKMPKVVYE 86

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  + V +KP G       G          S++   G  P + HRLD  T G+L+VA+  
Sbjct: 87  DENVLVIDKPKGQKTHPNQGENGTALNDCASYL---GYSPYIVHRLDMLTGGLLLVAKNP 143

Query: 165 AAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
           A    L +    + +++ Y + V        +  I   + +                   
Sbjct: 144 AVVPILNQQLTSKTLRRDYLATVNLNKEIPDQGTIDLPIGQDPADQRKRQVRA-----DG 198

Query: 224 NYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             A+SHF+V++    +K   L +   TGRTHQ+RVH    G PIVGD  Y  NF G    
Sbjct: 199 LRAVSHFQVLEKDEVKKKAKLLVTLETGRTHQIRVHLSASGWPIVGDPLYNPNFAGED-- 256

Query: 283 PIQNKLYLHARYMDLPHP 300
                L L    +    P
Sbjct: 257 -----LALTGWQLTFVKP 269


>gi|118580263|ref|YP_901513.1| pseudouridine synthase [Pelobacter propionicus DSM 2379]
 gi|118502973|gb|ABK99455.1| pseudouridine synthase [Pelobacter propionicus DSM 2379]
          Length = 238

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 61/224 (27%), Positives = 99/224 (44%), Gaps = 19/224 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQK----PRLTHRLDQETS 155
           +LYED  I +  KP G+   G G      +   L  +V     +      + HRLD+ETS
Sbjct: 13  VLYEDRDIIIIEKPCGLLTIGTGRDKTRTVHSILNDYVRKGDPRSRNRVYIVHRLDRETS 72

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GIL++A++ A   +L E ++     K Y ++V G    K   I+++L + S +       
Sbjct: 73  GILILAKSEANKIYLQEHWQE--TDKHYVAVVHGTLALKSGTISSYLAENSAM----RVY 126

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              ++     + + + V+    +    L +   TGR HQ+RVH    G  +VGD KY  +
Sbjct: 127 STTDQAQGKLSHTEY-VVMKENRGLSLLAIHLLTGRKHQIRVHLSEGGNAVVGDSKYGTD 185

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
                       L LHAR +   HP  G R+ I   +P +  + 
Sbjct: 186 RYARAN------LALHARSLTFTHPVSGRRMAIETGIPDYFTRL 223


>gi|298252221|ref|ZP_06976024.1| pseudouridine synthase [Ktedonobacter racemifer DSM 44963]
 gi|297546813|gb|EFH80681.1| pseudouridine synthase [Ktedonobacter racemifer DSM 44963]
          Length = 348

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 114/315 (36%), Gaps = 86/315 (27%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG---SGIAYHIDGFLKSWVDSK 140
           L +S+ +  + + +   +LY+D  + + NKPAG+ +      +      D  L+     +
Sbjct: 33  LAASIPILPNMEEMGITILYQDHYLLIVNKPAGMVIHPTYKHTDGGTMWDALLRHLEAQE 92

Query: 141 GQ----------------------------------------KPRLTHRLDQETSGILVV 160
            +                                        +P L HRLD++TSG++ +
Sbjct: 93  PEQWSPPALADDPAWARAPLEIQDMLRERRRAQILQEEGLLPRPCLVHRLDKDTSGVVAL 152

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG------------------------------- 189
           ART  +  HL   F    I K Y ++V                                 
Sbjct: 153 ARTERSRTHLVHQFHDHTIVKSYLAVVEPGSPDWTQPRAPLSVAFPHNGRVLTHFPTSFI 212

Query: 190 --IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
             +  + +  I   L +        V +     +G   A +  +V+   A     LE++P
Sbjct: 213 QELVPDTEFLIDGPLWRDPDDRRRCVVI-----EGGQEARTWVRVLAHEA-GRSLLEVRP 266

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
            TGRTHQ+R H   +G  I GD  Y    +   +  +  + +LHAR + L H    R + 
Sbjct: 267 VTGRTHQIRAHLAALGQAIAGDPVY---RELQPSDLVLGRQFLHARSLTLRHYVDNRVMT 323

Query: 307 ITAPLPAHMVKTWDS 321
            TAPL A ++   + 
Sbjct: 324 FTAPLTADLLAWLER 338


>gi|294897749|ref|XP_002776058.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Perkinsus marinus ATCC 50983]
 gi|239882591|gb|EER07874.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Perkinsus marinus ATCC 50983]
          Length = 604

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 72/253 (28%), Positives = 117/253 (46%), Gaps = 31/253 (12%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETS 155
           L+  +L+ D+     NKP G+SV  G  + Y +   L+++   S  + P L HRLD  T+
Sbjct: 268 LEDAVLHRDADFIAINKPWGLSVTDGPKVKYSLQRHLRAFTSPSSSEVPILIHRLDTATA 327

Query: 156 GILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGI----PKNKKECIANWLLKKSHIGG 210
           G+ ++AR ++AA    +    R    +IYW LVWG     P+     I   L+ + H   
Sbjct: 328 GVQLLARHKSAATMARDRIGARSFWNRIYWVLVWGRVQLGPRQFSGTINIPLIHRGH--- 384

Query: 211 DYVHVVKQNEKGAN-YAISHFKVID--CFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPI 266
              HV   +   A   AI+ ++++    FA     L+++P+TGR  QL+ H    +  PI
Sbjct: 385 ---HVKPASFHTAELSAITRWEILKFSPFAGGITLLKLEPYTGRRDQLQAHCAFGLRTPI 441

Query: 267 VGDHKYCAN---------------FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
           VGD  Y                   K  F   +  K  + +R + +    G ++ I AP+
Sbjct: 442 VGDDVYSKEAIRWNDAYPEKHMLQRKEMFGEELICKRMVCSRQISMHSFGGDQIDIIAPV 501

Query: 312 PAHMVKTWDSLGF 324
           P HM + +D LG+
Sbjct: 502 PPHMQQMFDKLGW 514


>gi|237715778|ref|ZP_04546259.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D1]
 gi|262408787|ref|ZP_06085333.1| conserved hypothetical protein [Bacteroides sp. 2_1_22]
 gi|229444487|gb|EEO50278.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D1]
 gi|262353652|gb|EEZ02746.1| conserved hypothetical protein [Bacteroides sp. 2_1_22]
          Length = 615

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 74/295 (25%), Positives = 118/295 (40%), Gaps = 71/295 (24%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H+++  ++ ++ + L    +  +  +++ED  + V NKPAG+    G   A   
Sbjct: 317 CEPILQHMLQGLEVDENPL-LNPVHEEEELEIVFEDEWLLVVNKPAGMLSVPGK--AEDR 373

Query: 130 DGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           D           +   P + HRLD  TSG+L+VA+T+   Q L   F  R I+K Y +++
Sbjct: 374 DSVYHRLKKKYPEATGPMIVHRLDMATSGLLLVAKTKEVHQDLQAQFANRSIKKRYVAVL 433

Query: 188 WG-IPKNKKEC----IANWLLKKSHIGGDY-----------------------VHVVKQN 219
            G I K +KE         LL K  +                                 +
Sbjct: 434 DGAIIKTEKETKPIAEKAILLAKETVSTKKTAKAERTGNTGRIELPLCLNPLDRPRQMVS 493

Query: 220 EKGANYAISHFKVID--------------------------CFAQKFCWLEMQPHTGRTH 253
            +    AI+ +++I                             ++K+  +   P TGRTH
Sbjct: 494 REHGKEAITEYQIISESERITSESENTFNESNRIDESERSINESRKYTRIIFYPLTGRTH 553

Query: 254 QLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           QLRVHA H   +GCPI+GD  Y             ++LYLHA Y++  HP  G +
Sbjct: 554 QLRVHAAHPEGLGCPILGDELYGKK---------ADRLYLHAEYIEFRHPIYGDI 599


>gi|157414343|ref|YP_001481599.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|157385307|gb|ABV51622.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
          Length = 281

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 111/284 (39%), Gaps = 46/284 (16%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+    QK++   ++  D   V+  N+I +G +V +                      + 
Sbjct: 6   ISINEAQKLIDKKRLFCDGILVEEKNKILNG-LVEL----------------------IV 42

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             ++     +++E+    +  K +GI     G    Y +   +       G++  + HRL
Sbjct: 43  YENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL---WGKEACVAHRL 99

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-LLKKSHIG 209
           D+ETSG++++A+ + A   L   F  + +QK Y +L  G  +          L K     
Sbjct: 100 DKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALAHGKIEENFIVDKAINLTKNYDDI 159

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              + + K+       AI+ F++++ F +     L  +P TGR HQ+RVH  +    I+G
Sbjct: 160 KTRMQICKE----GKQAITEFEILEYFPKINATLLLCKPLTGRQHQIRVHLHYKNHTILG 215

Query: 269 DHKYC-------------ANFKGNFTSPIQNKLYLHARYMDLPH 299
           D  Y               N K         +L LH+  +   +
Sbjct: 216 DPLYGLSKQQIESILDEKLNPKERLKLTGALRLCLHSYRLKFQY 259


>gi|195471882|ref|XP_002088231.1| GE18464 [Drosophila yakuba]
 gi|194174332|gb|EDW87943.1| GE18464 [Drosophila yakuba]
          Length = 939

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 64/261 (24%), Positives = 112/261 (42%), Gaps = 28/261 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD + +  +        ++ L +G++ V+ ++V  + +I+   +         L +++  
Sbjct: 559 LDVFVRE-FRAAPPEEYERSLEAGKLTVNYEKVPKDYKIKHNDL---------LANVVHR 608

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +          ++Y D  I V NKPA I V       ++   F+ +  +  
Sbjct: 609 HEVPVTSQPI---------KIVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEHN 658

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
            +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    EC  
Sbjct: 659 LKNLRTIHRLDRLTSGLLLFGRTAERARELELQIRTRQVQKEYVCRVEGRFPDGTVECNE 718

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  ++ +  +        +P TGR HQ+RVH 
Sbjct: 719 KIDVVSYKIG-----VCKVSPKGKDCKTTFKRIGEVGSDSIVL--CKPLTGRMHQIRVHL 771

Query: 260 LHMGCPIVGDHKYCANFKGNF 280
            ++G PI  D  Y     G  
Sbjct: 772 QYLGYPISNDPLYNHEVFGPL 792


>gi|78185673|ref|YP_378107.1| pseudouridine synthase [Synechococcus sp. CC9902]
 gi|78169967|gb|ABB27064.1| probable pseudouridine synthase [Synechococcus sp. CC9902]
          Length = 315

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 71/313 (22%), Positives = 134/313 (42%), Gaps = 35/313 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V++  E   L +W  N + H       + + +G++  + + +  + ++ SG  +      
Sbjct: 27  VQSHGEGAWLSQWMANRHQHSAAAVWLERIAAGEMHRNGEPLAGDMQLTSGDDICW---- 82

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +    L+ ++     +       +++D  + V NKP+G+ V  G G   H   
Sbjct: 83  -------QRPPWLEEAIPDQWDT-------IHDDGDLLVINKPSGLPVMPGGGFLEH--- 125

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKIYWSLV 187
            L + + S G KP   HRL + TSG+ V ART A    L++ FR     ++I + +   V
Sbjct: 126 TLTALLASTGAKP--VHRLGRFTSGLQVCARTAATRAALSKQFRPESRCQKIYQAWARRV 183

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN----YAISHFKVIDCFAQKFCWL 243
            G+   +   ++  ++++ H    ++   +  ++        A S  +++D  A      
Sbjct: 184 EGLEPGQSLVVSTDVVERQHPLLGWIWGPEPLDQEPTRKRLTAHSTVRLLDRCAAGDRL- 242

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEG 302
           E+   TGR HQ+R+H   +G P++GD  Y  N K     +P      LH+  ++      
Sbjct: 243 EVTIRTGRPHQIRIHLAQLGSPLLGDPLYLLNRKISETATPGDGGYGLHSWRLN--ALTA 300

Query: 303 GRLQITAPLPAHM 315
             L  TAPLP   
Sbjct: 301 AGLSFTAPLPKEF 313


>gi|315500070|ref|YP_004088873.1| pseudouridine synthase [Asticcacaulis excentricus CB 48]
 gi|315418082|gb|ADU14722.1| pseudouridine synthase [Asticcacaulis excentricus CB 48]
          Length = 205

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 58/209 (27%), Positives = 100/209 (47%), Gaps = 12/209 (5%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY D  + VF+KPAG+    G          L   V +      + HRLD  TSG++++A
Sbjct: 4   LYADDSVLVFDKPAGLLSVPGRLPEN--KDSLALRVQALWPDALIVHRLDMATSGLILMA 61

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R   A + L+ +F  R++ K Y ++V G    ++  +   L+             K + +
Sbjct: 62  RGAEAHRSLSIAFAERQVAKRYVAVVAGEVAAEQGEVDLPLICD----WPNRPRQKVDHE 117

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               +++ + V+   A     + ++P TGR+HQLR+H + +G PI+GD  Y  +      
Sbjct: 118 VGKPSLTRYAVLAREA-GRTRVALEPVTGRSHQLRLHMMALGHPILGDEFYAPDE----V 172

Query: 282 SPIQNKLYLHARYMDLPHPEGG-RLQITA 309
             +  +L LHA Y+  PHP    R+++ A
Sbjct: 173 RALSPRLLLHAEYLAFPHPADERRIEVAA 201


>gi|110639414|ref|YP_679623.1| pseudouridylate synthase [Cytophaga hutchinsonii ATCC 33406]
 gi|110282095|gb|ABG60281.1| pseudouridylate synthase [Cytophaga hutchinsonii ATCC 33406]
          Length = 240

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 99/242 (40%), Gaps = 26/242 (10%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
            +K ++++E+   +  NKP  IS     +G A  I    K +        +L HR+D+ET
Sbjct: 5   DIKDLIIFENDDYFFINKPPFISSLDERTGGAPSIIRMAKEY----WPDAQLCHRIDKET 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L VA+  AA +HL+ +F  R + K Y ++V G        +   +L           
Sbjct: 61  SGVLAVAKNPAAYRHLSMAFESRNVTKEYHAVVNGTHDLDGVDVYLPILVLPT------G 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            VK ++     A + F  I  + +K   +   P TGR HQ+R+H   +G  IVGD  Y  
Sbjct: 115 TVKIDKSKGKLAETIFFTIQAY-KKATLVRCLPITGRMHQIRIHLATLGASIVGDETYGG 173

Query: 275 NF--------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                           K +   P+  +  LHA  +         L I AP P        
Sbjct: 174 KPLFLSEIKRKKFNLKKDSEERPLIQRFALHANSLIFTDMNEQILDIKAPYPKDFDVLVK 233

Query: 321 SL 322
            L
Sbjct: 234 KL 235


>gi|115379301|ref|ZP_01466412.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|310821464|ref|YP_003953822.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115363683|gb|EAU62807.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|309394536|gb|ADO71995.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 232

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 99/234 (42%), Gaps = 16/234 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +L+E + + V  KP G  V  G G         +       +K  + HRLD++TSG 
Sbjct: 3   ELRVLHEGAGLLVVAKPPGTLVIPGRGEGDT--SLREQLEAQLRRKVFVVHRLDRDTSGA 60

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV A      + L+ +F   R+ K Y +LV G  +  +      +               
Sbjct: 61  LVFALDAERHRALSMAFEEGRVHKRYLALVEGRVEAPRLVEEALV-----PARKGRMRPA 115

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---- 273
           +  +    + +  + ++ FAQ    +E +P TGRTHQ+RVH   +G P++ DH+Y     
Sbjct: 116 RPGEEGKPSRTRIRPVETFAQ-ASLVEAEPLTGRTHQIRVHLRSLGHPLLVDHQYGRAEP 174

Query: 274 ---ANFKGNFTSPIQNKLYLHARYMDLPH-PEGGRLQITAPLPAHMVKTWDSLG 323
                  G   + + ++  LHA  ++ P  P      + APLP  M    + L 
Sbjct: 175 LVRRELGGEGEAVVLSRTPLHAARIEWPPLPGVEAGAVEAPLPGDMALALELLR 228


>gi|157116527|ref|XP_001658535.1| ribosomal pseudouridine synthase [Aedes aegypti]
 gi|108883445|gb|EAT47670.1| ribosomal pseudouridine synthase [Aedes aegypti]
          Length = 516

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 58/266 (21%), Positives = 109/266 (40%), Gaps = 26/266 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   +         L +I+  
Sbjct: 83  LDVF-AREFRAHPAEEYERCIKAGTLTVNYEKVPTDYRLKHNDL---------LANIVHR 132

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +T         +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 133 HEVPVTSQPIT---------IVHMDDDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEYN 182

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            +  R  HRLD+ TSG+L+  R+   A+ +    R R++QK Y   V G   +    I  
Sbjct: 183 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEHQIRNRQVQKEYICRVEGEFPD--GIIE- 239

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K+      Y   V +         + F+ +         +  +P TGR HQ+RVH  
Sbjct: 240 --CKEPIEVVSYKIGVCKVSPKGKECTTTFQKLGYNG-TSSVVLCKPLTGRMHQIRVHLQ 296

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQN 286
           ++G P+V D  Y     G       +
Sbjct: 297 YLGYPVVNDPLYNHEVFGPAKGRGGD 322


>gi|61554746|gb|AAX46608.1| hypothetical protein FLJ14494 [Bos taurus]
          Length = 304

 Score =  146 bits (369), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 62/207 (29%), Positives = 101/207 (48%), Gaps = 21/207 (10%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   ++++D ++ V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKALSRGIVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P  +   +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIV 205

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G                D   V  ++ + A  A++ ++V    +     LE+QP 
Sbjct: 206 EKEAQGQQHHHKMTLSPSYRMDDGKMVRVRSSRNAQLAVTQYRV-LSSSLSAALLELQPI 264

Query: 249 TGRTHQLRVHALH-MGCPIVGDHKYCA 274
           TG  HQLRVH    + CPI+GDHKY  
Sbjct: 265 TGIKHQLRVHMSFGLDCPILGDHKYSD 291


>gi|163755644|ref|ZP_02162763.1| pseudouridylate synthase, 23S RNA-specific [Kordia algicida OT-1]
 gi|161324557|gb|EDP95887.1| pseudouridylate synthase, 23S RNA-specific [Kordia algicida OT-1]
          Length = 229

 Score =  146 bits (369), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 56/243 (23%), Positives = 98/243 (40%), Gaps = 29/243 (11%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG-FLKSWVDSKGQKPR-LTHRLDQETSGI 157
           ++LYED  +    KP  I V          D   L   +  K +K     HRLD++TSGI
Sbjct: 1   MILYEDDFVIAVAKPNNILVHHSQMARNQSDEQTLLELLFEKFEKNYYPMHRLDRKTSGI 60

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+ +       + F    IQK+Y+ +V G    +   I +              V  
Sbjct: 61  VLCAKEKRFVSKFQDLFVADAIQKVYYGVVRGF-SPENGVIDSP-------------VKG 106

Query: 218 QNEKGANYAISHFKVIDCF----------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           ++      A++H+K +               ++  +++ P TGR HQLR+H   +  P++
Sbjct: 107 RDANVYKSALTHYKTLATKELPIAVQPFETSRYSLVKLLPKTGRMHQLRIHLNKINHPLI 166

Query: 268 GDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLGF 324
           GD KY   F      +    + L+LHA  +   HP     + +    P H  +  +   +
Sbjct: 167 GDPKYGDRFHNRMFQSEFEISNLFLHAHSLTFVHPFLEKEIVVQCSFPRHWCQILEKFAW 226

Query: 325 KYD 327
           +  
Sbjct: 227 EIS 229


>gi|321475493|gb|EFX86456.1| hypothetical protein DAPPUDRAFT_313092 [Daphnia pulex]
          Length = 670

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 104/253 (41%), Gaps = 28/253 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ ++SG + V+ ++V  + R++   ++     I   + +  E
Sbjct: 190 LDVF-AREFRAHPVEEYERCIKSGSLTVNYEKVDIDYRLKHNDLL---ANIVHRHEVPVE 245

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            KI++               ++Y+D  + V +KP  + V       ++   F+ +  +  
Sbjct: 246 SKIIE---------------IVYQDDDMIVIDKPCSVPVHPCGRYRHNTVAFILA-KEHN 289

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
            +  R  HRLD+ TSG+L+  R +  A+ +    R R + K Y   V G  P     C  
Sbjct: 290 LRNLRTIHRLDRLTSGLLMFGRNQEKARQMEVQIRTRLVSKEYVCRVGGEFPSGHIMCTE 349

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG      V +         + F+ +     K   +  +P TGR HQ+RVH 
Sbjct: 350 PIEVVSYKIG------VCRVSPKGKDCQTEFERLSYNG-KTSVVLCKPRTGRMHQIRVHL 402

Query: 260 LHMGCPIVGDHKY 272
            ++G PI  D  Y
Sbjct: 403 QYLGYPIANDPLY 415


>gi|297819936|ref|XP_002877851.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297323689|gb|EFH54110.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 387

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 77/339 (22%), Positives = 127/339 (37%), Gaps = 80/339 (23%)

Query: 37  LQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +Q+ +++GQ+++D + VK  N  ++SG                   K++   +   +   
Sbjct: 56  IQR-IQNGQIQIDGEVVKDPNTLLRSG------------------SKLVYHRLPWKEPDT 96

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRL 146
                +LYED  +   NKP+G+ V  G             W   K            P  
Sbjct: 97  PYSLQVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLTQLQWCFRKNDSYTGSRESPHPVP 156

Query: 147 THRLDQETSGILVVARTRAAAQHL-----------------TESFRMRRIQKIYWSLVWG 189
            HRL + TSGIL+ A+T+ A   L                  E  + R++ KIY +L  G
Sbjct: 157 VHRLGRGTSGILLCAKTKLAKTKLAAYFAEGTSLVGSGNLEQECGKGRKLSKIYRALADG 216

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPH 248
           I +  +  I   L    + G      V   E     A S   V++   QK C  ++++  
Sbjct: 217 IVEEDEVVIKQPLGVVRYPGVAKGLYVASPE--GKPAFSKVAVLERDKQKNCTLVKVEIQ 274

Query: 249 TGRTHQLRVHALHMGCPIVG------DHKY-----------------------CANFKGN 279
           +GR HQ+R+H  +MG P++       D  Y                           + N
Sbjct: 275 SGRPHQIRIHLAYMGHPLLASYNCMRDPLYVAGGQPKCFDPDLVDDDAAFAEDGGYRRPN 334

Query: 280 FTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPAHMV 316
              P     +LHA  ++LP+       ++I APLP  + 
Sbjct: 335 QAVPGDCGYHLHAHQVELPNLLNTHKVVKIVAPLPPILQ 373


>gi|328725051|ref|XP_001944933.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Acyrthosiphon pisum]
          Length = 522

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 108/252 (42%), Gaps = 24/252 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ ++SG + V+ ++V    +++   +         L +++  
Sbjct: 126 LDVF-AREFRAHPAEEYERCIKSGSLTVNYQKVDTQYKLKHNDL---------LANVVHR 175

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  ++  +T         +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 176 HEVPVTNDPIT---------IVHMDDDIVVVNKPASIPVHPCGRYRHNTVVFVLA-KEHN 225

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            +  R  HRLD+ TSG+L+  RT   A+ +    R R++ K Y   V G    +     +
Sbjct: 226 LRNLRTIHRLDRLTSGLLMFGRTPRYARIMEAQIRNRQVNKQYVCRVEGRFPEQTIECNH 285

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            +   S+     + V K + KG N + +   V          +   PH+GR HQ+RVH  
Sbjct: 286 PIEVVSY----KIGVCKVSNKGKNCSTTFQLVGYNEKTNISVVLCFPHSGRMHQIRVHLQ 341

Query: 261 HMGCPIVGDHKY 272
           ++G P+  D  Y
Sbjct: 342 YLGFPVKNDPLY 353


>gi|328949329|ref|YP_004366666.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
 gi|328449653|gb|AEB15369.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
          Length = 305

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 97/230 (42%), Gaps = 18/230 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKG-----QKPRLTHRLD 151
           +  +LYED  I V NK +G+      G  +      L+  +  KG     ++P + HRLD
Sbjct: 26  RIEILYEDKDIVVINKASGLLSVPYPGSKSRTAIELLEKIMRKKGTFSESRRPFVVHRLD 85

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--HIG 209
           ++TSG+++ A      + +  S++     ++Y ++     +N  E   + L+ +      
Sbjct: 86  RDTSGVMMFALNERVQKKIMSSWKTMVTDRLYRAVAENPRRNHPELTDSGLIDEPLAKNA 145

Query: 210 GDYVHVVKQNEKGANY--AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               +V K+    A    A ++F+V+    +     E+   TG+ +Q+R H      P+ 
Sbjct: 146 CHQGYVPKKLGDNAETCEARTNFRVVLR-GRTHTLFELSLDTGKKNQIRAHLASRHYPLA 204

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           GD  Y         +   ++L LHAR +   HP  G  +    P P    
Sbjct: 205 GDENY------RARTDPFHRLALHARTLAFIHPVTGEKMSFEIPEPEEWE 248


>gi|332235181|ref|XP_003266785.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 2
           [Nomascus leucogenys]
          Length = 545

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 60/255 (23%), Positives = 112/255 (43%), Gaps = 26/255 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L   F   +        +  +R+G++ +++K V                    LN ++K+
Sbjct: 162 LLHVFSTEFRAQPLAYYEAAVRAGRLHLNEKPV------------------QDLNVVLKD 203

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+    + 
Sbjct: 204 NDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-KEH 262

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++    
Sbjct: 263 QLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVTCK 322

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             +L  S     Y   V + +       + F+ +    Q    +  +P TGRTHQ+RVH 
Sbjct: 323 EPILVVS-----YKVGVCRVDPRGKPCETVFQRLSYNGQS-SVVRCRPLTGRTHQIRVHL 376

Query: 260 LHMGCPIVGDHKYCA 274
             +G PI+ D  Y +
Sbjct: 377 QFLGHPILNDPIYNS 391


>gi|313674292|ref|YP_004052288.1| tRNA pseudouridine synthase c [Marivirga tractuosa DSM 4126]
 gi|312940990|gb|ADR20180.1| tRNA pseudouridine synthase C [Marivirga tractuosa DSM 4126]
          Length = 233

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 101/242 (41%), Gaps = 28/242 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              ++Y+D  +   NKP G+ V             L+   D  GQ+    HR+D++TSG+
Sbjct: 5   PLEIIYQDDYLVAINKPHGLLVHRTKIATETDVFALQLLRDQLGQRVYPVHRIDRKTSGV 64

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A         T  FR ++I+K Y ++V G   + +  I   L K+S           
Sbjct: 65  LLFALDEENNSKTTALFRDQQIEKTYLAIVRGF-TDSEGTIDYALRKESGQ--------- 114

Query: 218 QNEKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   +++H+K +               ++  +E++P TGR HQ+R H  H+  PI+
Sbjct: 115 -----LQESVTHYKTLAKTEIPVPLGKFETSRYSLVEVRPETGRMHQIRKHLAHIHHPII 169

Query: 268 GDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
            D  +  N +          + + LHA+ +   HP     + I A + +   +T   L F
Sbjct: 170 ADRPHGCNKQNKLFKEKWAMDSMLLHAKEVIFKHPVSHDVVHIKANISSEFERTLSFLNF 229

Query: 325 KY 326
            +
Sbjct: 230 DF 231


>gi|220915408|ref|YP_002490712.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219953262|gb|ACL63646.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 312

 Score =  146 bits (368), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 63/315 (20%), Positives = 113/315 (35%), Gaps = 32/315 (10%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR   +    +    +++    G+VRV  +R + ++    G +V +            
Sbjct: 14  RLDRALADAL-GLGRAAVKRAFALGEVRVRGRRARASDPAAPGALVELD----------- 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVD 138
               ++      +        +L E  +  V  KPAG++V     G    +   + +   
Sbjct: 62  ----VELPAGPPEPEPDAPLSVLLERPRYLVVEKPAGVAVHPLAPGEGGTLANAVAARHP 117

Query: 139 SKGQ---KPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              +   +PR      RLD ETSG ++ AR   A + L        + K+Y +L  G   
Sbjct: 118 ECAEASPEPREGGAVQRLDLETSGCVLFARDPEAWEALHAQLGAHTVDKVYLALAVGRLP 177

Query: 193 NKKECIANWLLKKSH----IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
               C      +          +    ++        A +H++    FA     L ++  
Sbjct: 178 AGGVCSVPLAQRGGRVVPAPDVEAEERLQARGLRPRPAETHYEPERRFAD-HTLLRVRIV 236

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
           TG  HQ+R H   +G P+                P   + +LHA  +    P+G GR+ +
Sbjct: 237 TGVMHQIRAHLALLGHPV---AGDALYGGAAAALPGLERQFLHAWRLAFDDPDGAGRVAV 293

Query: 308 TAPLPAHMVKTWDSL 322
            +PLP  +      L
Sbjct: 294 ESPLPPELEAVLARL 308


>gi|331002782|ref|ZP_08326296.1| hypothetical protein HMPREF0491_01158 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330413271|gb|EGG92639.1| hypothetical protein HMPREF0491_01158 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 216

 Score =  146 bits (368), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 61/211 (28%), Positives = 100/211 (47%), Gaps = 8/211 (3%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   +LYED  I V  KP GIS Q  SG    +   LK  +  K     + HRLD+   G
Sbjct: 1   MDIKILYEDEDIIVAVKPRGISSQSSSGFEDDMVSLLKKHL-GKDAYIGVIHRLDKPVYG 59

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           I++  +T+ A + L+   R + I+K Y +LV G+P+NK+  + ++L K  +   +   VV
Sbjct: 60  IILYGKTKVATEILSNELRKKNIEKTYEALVEGLPENKEGELRDYLKKYDN---NISKVV 116

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWL---EMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +N  GA  ++  + V + + +   ++    +   TGR HQ+R+     G P+ GD KY 
Sbjct: 117 DKNTPGAKESVLKYSVEESYQRDDTFITRLRINLLTGRNHQIRLQCAAHGFPLFGDFKYN 176

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
              +          L L A  +   HP+   
Sbjct: 177 KRLQKQ-RLEYDKVLALAAVELRFKHPKTKE 206


>gi|315931284|gb|EFV10253.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 281

 Score =  146 bits (368), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 112/284 (39%), Gaps = 46/284 (16%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+    QK++   ++  D   V+  N+I +G +V +                      + 
Sbjct: 6   ISINEAQKLIDKKRLFCDGILVEEKNKILNG-LVEL----------------------IV 42

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             ++     +++E+    +  K +GI     G    Y +   +       G++  + HRL
Sbjct: 43  YENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL---WGKEACVAHRL 99

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-LLKKSHIG 209
           D+ETSG++++A+ + A   L   F  + +QK Y +L  G  +          L K     
Sbjct: 100 DKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALAHGKIEENFIVDKAINLTKNYDDI 159

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              + + K+       AI+ F++++ F +     L  +P TGR HQ+RVH  +    I+G
Sbjct: 160 KTRMQICKE----GKQAITEFEILEYFPKINATLLLCKPLTGRQHQIRVHLHYKNHTILG 215

Query: 269 DHKYC-------------ANFKGNFTSPIQNKLYLHARYMDLPH 299
           D  Y               N K         +L LH+ ++   +
Sbjct: 216 DPLYGLSKQQIESILDEKLNPKERLKLTGALRLCLHSYHLKFQY 259


>gi|291403226|ref|XP_002717836.1| PREDICTED: RNA pseudouridylate synthase domain containing 2
           [Oryctolagus cuniculus]
          Length = 561

 Score =  146 bits (368), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 59/255 (23%), Positives = 111/255 (43%), Gaps = 26/255 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L   F   +        Q  LR+G++ ++++ V                    L+ ++K+
Sbjct: 179 LLHVFSTEFRAQPLAYYQAALRAGRLHLNEEPV------------------QDLSIVLKD 220

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+    + 
Sbjct: 221 NDFLRNTVHRHEPPVTAEPIRLLAENDDVVVVDKPSSIPVHPCGRFRHNTVIFILG-KEH 279

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++    
Sbjct: 280 QLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPVEEVTCK 339

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             +L  S     Y   V + +       + F+ +         +  +P TGRTHQ+RVH 
Sbjct: 340 EPILVVS-----YKVGVCRVDPRGKPCETVFQRLSYNGHS-SVVRCRPLTGRTHQIRVHL 393

Query: 260 LHMGCPIVGDHKYCA 274
             +G PI+ D  Y +
Sbjct: 394 QFLGHPILNDPIYNS 408


>gi|329767055|ref|ZP_08258583.1| hypothetical protein HMPREF0428_00280 [Gemella haemolysans M341]
 gi|328837780|gb|EGF87405.1| hypothetical protein HMPREF0428_00280 [Gemella haemolysans M341]
          Length = 283

 Score =  146 bits (368), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 59/272 (21%), Positives = 116/272 (42%), Gaps = 31/272 (11%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           ++++    + N+ ++ G ++ +   +    +        +S+V++TK          +ED
Sbjct: 41  IKINSNEAELNSPLKVGDILEVNIDLATSKY------KENSTVSITKE---------FED 85

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
             + V +KP GI            D  L +++ S        HRLD +T G++++A+T  
Sbjct: 86  EYLLVVSKPFGIKTHP--NDIELEDDTLVNYLISNYNYLEPIHRLDIDTCGLVILAKTPL 143

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
               L +    R+I++ Y +L+    K +   I + + + S    + + V     K    
Sbjct: 144 IKAKLDQMLEQRQIKRYYSALIKNNIKPQ--TINSNIGRDSKE-KNKMAVT----KNGKN 196

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           AI++    +   Q    + +   TGRTHQ+RVH    G  I+GD  Y  +          
Sbjct: 197 AITNILSCEKIDQNRFLVTVSLETGRTHQIRVHLASNGVAIIGDKLYSKDGYK------Y 250

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
           +K+YL A  ++  HP  G  + + + L    +
Sbjct: 251 DKMYLGALKVEFSHPVTGHSIAVKSSLEKKFL 282


>gi|42563248|ref|NP_177732.2| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|332197668|gb|AEE35789.1| RNA pseudourine synthase 2 [Arabidopsis thaliana]
          Length = 313

 Score =  146 bits (368), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 97/249 (38%), Gaps = 51/249 (20%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
           +V+  +  +RLD W  +    ++   +Q  +R G V V+ + V K ++ ++SG  V    
Sbjct: 74  IVDAAKGKIRLDSWISSRINGVSRARVQSSIRLGLVTVNGRVVDKVSHNVKSGDEVNCT- 132

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAY 127
                         +     L   ++ +   ++YED  + V NKPA + V    G     
Sbjct: 133 --------------ISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGT 178

Query: 128 HIDGFLKSWV--------------------------------DSKGQKPRLTHRLDQETS 155
            ++G L                                     +   +P + HRLD+ T+
Sbjct: 179 LVNGILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRPGIVHRLDKGTT 238

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+LVVA+   +  HL E F++  I+++Y SL  G+P   +  I   + + S      +  
Sbjct: 239 GLLVVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPSPPQGRIEIPIGRDSS-NRIRMAA 297

Query: 216 VKQNEKGAN 224
           +    +G  
Sbjct: 298 IPGGVRGGR 306


>gi|57236934|ref|YP_178049.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
 gi|57165738|gb|AAW34517.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
          Length = 300

 Score =  146 bits (368), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 60/307 (19%), Positives = 117/307 (38%), Gaps = 47/307 (15%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           Y+ ++      +  +    +   I+    QK++   ++  D   V+  N I +G +V + 
Sbjct: 3   YIKIKLSNNGKKAFQVLMENLK-ISINEAQKLIDKKRLFCDGILVEEKNEILNG-LVEL- 59

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAY 127
                                +   ++     +++E+    +  K +GI     G    Y
Sbjct: 60  ---------------------IVYENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKY 98

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   +       G++  + HRLD+ETSG+++VA+ + A   L   F  + +QK Y +L 
Sbjct: 99  SLSDEIWHL---WGKEACVAHRLDKETSGLILVAKNKKAQIDLKALFEKKLVQKEYLALA 155

Query: 188 WGIPKNKKECIANW-LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEM 245
            G  +          L K        + + K+       AI+ F++++ F +     L  
Sbjct: 156 NGKIEENFIIDKAINLAKNYDDVKTRMQICKE----GKQAITEFEILEYFPKINATLLLC 211

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------------FKGNFTSPIQNKLYLHA 292
           +P TGR HQ+RVH  +    I+GD  Y  +              K         +L LH+
Sbjct: 212 KPLTGRQHQIRVHLHYKNHTILGDPLYGLSKEQIESILDEKLTPKERLKLTGALRLCLHS 271

Query: 293 RYMDLPH 299
             +   +
Sbjct: 272 YRLKFQY 278


>gi|14043412|gb|AAH07697.1| RPUSD2 protein [Homo sapiens]
          Length = 554

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 60/255 (23%), Positives = 113/255 (44%), Gaps = 26/255 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L   F   +        +  +R+G++++++K V                    LN ++K+
Sbjct: 171 LLHVFSTEFRAQPLAYYEAAVRAGRLQLNEKPV------------------QDLNIVLKD 212

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+    + 
Sbjct: 213 NDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-KEH 271

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++    
Sbjct: 272 QLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVTCK 331

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             +L  S     Y   V + +       + F+ +    Q    +  +P TGRTHQ+RVH 
Sbjct: 332 EPILVVS-----YKVGVCRVDPRGKPCETVFQRLSYNGQS-SVVRCRPLTGRTHQIRVHL 385

Query: 260 LHMGCPIVGDHKYCA 274
             +G PI+ D  Y +
Sbjct: 386 QFLGHPILNDPIYNS 400


>gi|195339845|ref|XP_002036527.1| GM11650 [Drosophila sechellia]
 gi|194130407|gb|EDW52450.1| GM11650 [Drosophila sechellia]
          Length = 739

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 59/268 (22%), Positives = 112/268 (41%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   ++      + +    + 
Sbjct: 317 LDIF-SREFRAHPAEEYERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQ- 374

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 375 -----------------PIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 416

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    EC  
Sbjct: 417 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGIVECKE 476

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  K+          +  +P TGR HQ+RVH 
Sbjct: 477 PIEVVSYKIG-----VCKVSPKGKDCTTTFQKL--SQNGTTSVVLCKPLTGRMHQIRVHL 529

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI+ D  Y     G    P++ +
Sbjct: 530 QYLGYPILNDPLYNHEVFG----PLKGR 553


>gi|302669413|ref|YP_003829373.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
 gi|302393886|gb|ADL32791.1| RNA pseudouridylate synthase [Butyrivibrio proteoclasticus B316]
          Length = 257

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 59/250 (23%), Positives = 108/250 (43%), Gaps = 31/250 (12%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV---------DSKGQKPRLTHRLDQ 152
           +YED+ I V +KP+G++ +G       +    ++++         D K       HRLDQ
Sbjct: 7   IYEDNDILVCHKPSGVATEGARTYNMDVVSAARNYIGRQNREKTSDRKPPYVATVHRLDQ 66

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH----- 207
              G+L++A+T+ AA  L    + R  +K Y++L  G   +KK  + N+L++K       
Sbjct: 67  PVEGVLILAKTKKAATKLAAQIKDRTTEKYYYALCKGNFADKKGRLENYLVRKEDGLAAV 126

Query: 208 -------------IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                        I       ++     A  AI  ++VI    ++   + ++  TGR HQ
Sbjct: 127 VTEEESKKINDNVITRSNGETIRIIGGEAKKAILEYEVI-AENEETTLVRVKLLTGRFHQ 185

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHPEGG-RLQITA-PL 311
           +RV   ++  PI+GD KY        T  I  + + L +    + HP  G +++    P 
Sbjct: 186 IRVQMANVDHPIIGDQKYGTEESRTLTDKIGARDVCLVSYKYIIKHPSTGKKMEFEIKPD 245

Query: 312 PAHMVKTWDS 321
              + +  + 
Sbjct: 246 NPQIREMLEK 255


>gi|261378685|ref|ZP_05983258.1| pseudouridine synthase Rlu family protein [Neisseria cinerea ATCC
           14685]
 gi|269145031|gb|EEZ71449.1| pseudouridine synthase Rlu family protein [Neisseria cinerea ATCC
           14685]
          Length = 223

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 93/221 (42%), Gaps = 23/221 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV    G                 +K  L HRLD++T GIL+ 
Sbjct: 4   ILFRHQDFVAINKPQGISVHRSDGEVSLTATLAAQL---GVEKVWLLHRLDKQTGGILLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I   + K          + K   
Sbjct: 61  ALNPQSAAVLAAQFAERKMKKTYLALSDRKPSKKQGWIKGGMEKS------RRGMWKLTR 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F  I   ++K     ++PHTG+THQLRV    +G PI+GD  Y        
Sbjct: 115 NMENIAVTRFFSI-RISEKMRLFILEPHTGKTHQLRVAMKSLGSPILGDRLYGGTESET- 172

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
                  ++L+A  +   + +   ++ITAPL       W +
Sbjct: 173 -------MFLYAWKIQFTY-QQQEIEITAPL----KNAWQA 201


>gi|205355761|ref|ZP_03222531.1| hypothetical protein Cj8421_0022c [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|205346538|gb|EDZ33171.1| hypothetical protein Cj8421_0022c [Campylobacter jejuni subsp.
           jejuni CG8421]
          Length = 300

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 60/307 (19%), Positives = 118/307 (38%), Gaps = 47/307 (15%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           Y+ ++      +  +    +   I+    QK++   ++  D   V+  N I +G +V + 
Sbjct: 3   YIKIKLSNNGKKAFQVLMENLK-ISINEAQKLIDKKRLFCDGILVEEKNEILNG-LVEL- 59

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAY 127
                                +   ++     +++E+  + +  K +GI     G    Y
Sbjct: 60  ---------------------IVYENNPKGVEIVFENEDLAILEKESGILSHPNGRHCKY 98

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +   +       G++  + HRLD+ETSG+++VA+ + A   L   F  + +QK Y +L 
Sbjct: 99  SLSDEIWHL---WGKEACVAHRLDKETSGLILVAKNKKAQIDLKALFEKKLVQKEYLALA 155

Query: 188 WGIPKNKKECIANW-LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEM 245
            G  +          L K        + + K+       AI+ F++++ F +     L  
Sbjct: 156 NGKIEENFIIDKAINLAKNYDDVKTRMQICKE----GKQAITEFEILEYFPKINATLLLC 211

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-------------FKGNFTSPIQNKLYLHA 292
           +P TGR HQ+RVH  +    I+GD  Y  +              K         +L LH+
Sbjct: 212 KPLTGRQHQIRVHLHYKNHTILGDPLYGLSKEQIESILDEKLTPKERLKLTGALRLCLHS 271

Query: 293 RYMDLPH 299
             +   +
Sbjct: 272 YRLKFQY 278


>gi|194377234|dbj|BAG63178.1| unnamed protein product [Homo sapiens]
          Length = 524

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 60/255 (23%), Positives = 113/255 (44%), Gaps = 26/255 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L   F   +        +  +R+G++++++K V                    LN ++K+
Sbjct: 141 LLHVFSTEFRAQPLAYYEAAVRAGRLQLNEKPV------------------QDLNIVLKD 182

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+    + 
Sbjct: 183 NDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-KEH 241

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++    
Sbjct: 242 QLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVTCK 301

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             +L  S     Y   V + +       + F+ +    Q    +  +P TGRTHQ+RVH 
Sbjct: 302 EPILVVS-----YKVGVCRVDPRGKPCETVFQRLSYNGQS-SVVRCRPLTGRTHQIRVHL 355

Query: 260 LHMGCPIVGDHKYCA 274
             +G PI+ D  Y +
Sbjct: 356 QFLGHPILNDPIYNS 370


>gi|195339847|ref|XP_002036528.1| GM18469 [Drosophila sechellia]
 gi|194130408|gb|EDW52451.1| GM18469 [Drosophila sechellia]
          Length = 537

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 116/268 (43%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD + +  +        ++ L +G++ V+ ++V  + RI+   +         L +++  
Sbjct: 157 LDVFVRE-FRAAPPEEYERSLEAGKLTVNSEKVPKDYRIKHNDL---------LANVVHR 206

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +          ++Y D  I V NKPA I V       ++   F+ +  +  
Sbjct: 207 HEVPVTSQPI---------KIVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEHN 256

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
            +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    EC  
Sbjct: 257 LKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIRTRQVQKEYVCRVEGRFPDGIVECNE 316

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  ++ +  +        +P TGR HQ+RVH 
Sbjct: 317 KIDVVSYKIG-----VCKVSPKGKDCKTTFKRIGEVGSDSIVL--CKPLTGRMHQIRVHL 369

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI  D  Y     G    P++ +
Sbjct: 370 QYLGYPISNDPLYNHEVFG----PLKGR 393


>gi|332518993|ref|ZP_08395460.1| pseudouridine synthase, RluA family [Lacinutrix algicola 5H-3-7-4]
 gi|332044841|gb|EGI81034.1| pseudouridine synthase, RluA family [Lacinutrix algicola 5H-3-7-4]
          Length = 288

 Score =  145 bits (367), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 67/282 (23%), Positives = 114/282 (40%), Gaps = 47/282 (16%)

Query: 47  RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
            V+         I+  +++++   +                    K    LK  ++YED 
Sbjct: 45  TVNNIPATSATFIKGEEIIKLNIPVKKT----------------FKTKLKLKLDVIYEDE 88

Query: 107 KIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
            + +  KPAGI V G S   I   +   LK         P+  HRLD  TSG+L+V +T 
Sbjct: 89  YLAIIKKPAGILVSGNSFKTITNALPQNLKPSQLKDATLPQPVHRLDYPTSGLLLVGKTN 148

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            + + L + F  + I+K Y+++  G  +  +  I   +                      
Sbjct: 149 TSIRFLNKLFETKTIEKTYYAITIGNMQT-QGIIKTPIEN-------------------K 188

Query: 225 YAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            +I+H+ V +       +K   +++QP TGR HQLR+H   +  PI+GD +Y        
Sbjct: 189 ISITHYLVENSVDSKRFEKLNLVKLQPKTGRKHQLRIHLSSLKNPILGDREYGIPS---- 244

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
                  LYLHA  +   HP   + ++I   LP    K +++
Sbjct: 245 LILKGKGLYLHAYKLKFTHPFSKKIIEIEDELPKKFKKIFET 286


>gi|283953645|ref|ZP_06371176.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
 gi|283794686|gb|EFC33424.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
          Length = 300

 Score =  145 bits (367), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 62/293 (21%), Positives = 113/293 (38%), Gaps = 47/293 (16%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +   ++   I+    QK++   ++  D   ++  N+I +G V               E  
Sbjct: 17  QVLMDNLK-ISINEAQKLIDKKRLFCDGILIEEKNKILNGLV---------------ELI 60

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
           I +++    K        +++E+    V  K +GI     G    Y +   +       G
Sbjct: 61  IYENNPKGVK--------IVFENEDFAVLEKESGILSHPNGRHCKYSLSDEIWHL---WG 109

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN- 200
           ++  + HRLD+ETSG+++VA+ + A  +L   F  + +QK Y +L  G            
Sbjct: 110 KEACVAHRLDKETSGLILVAKNKKAQINLKSLFEKKLVQKEYLALASGEITENFIVDKAM 169

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHA 259
            L K        + +  Q       AI+ F++++ F       L  +P TGR HQ+RVH 
Sbjct: 170 DLAKNYDDVKTRMQICAQ----GKQAITEFEILEYFPTLNATLLLCKPLTGRQHQIRVHL 225

Query: 260 LHMGCPIVGDHKYC-------------ANFKGNFTSPIQNKLYLHARYMDLPH 299
            +    I+GD  Y               + K         +L LH+  +   +
Sbjct: 226 HYKNHTILGDPLYGLAKEQIESILDEKLSPKQRLKLTGALRLCLHSYRLKFQY 278


>gi|332843544|ref|XP_510311.3| PREDICTED: RNA pseudouridylate synthase domain-containing protein 2
           isoform 2 [Pan troglodytes]
          Length = 545

 Score =  145 bits (367), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 60/255 (23%), Positives = 113/255 (44%), Gaps = 26/255 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L   F   +        +  +R+G++++++K V                    LN ++K+
Sbjct: 162 LLHVFSTEFRAQPLAYYEAAVRAGRLQLNEKPV------------------QDLNIVLKD 203

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+    + 
Sbjct: 204 NDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-KEH 262

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++    
Sbjct: 263 QLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVTCK 322

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             +L  S     Y   V + +       + F+ +    Q    +  +P TGRTHQ+RVH 
Sbjct: 323 EPILVVS-----YKVGVCRVDPRGKPCETVFQRLSYNGQS-SVVRCRPLTGRTHQIRVHL 376

Query: 260 LHMGCPIVGDHKYCA 274
             +G PI+ D  Y +
Sbjct: 377 QFLGHPILNDPIYNS 391


>gi|27734094|ref|NP_775626.1| RNA pseudouridylate synthase domain-containing protein 2 [Mus
           musculus]
 gi|158564131|sp|Q149F1|RUSD2_MOUSE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 2
 gi|26336789|dbj|BAC32077.1| unnamed protein product [Mus musculus]
 gi|126540740|emb|CAM45958.1| RNA pseudouridylate synthase domain containing 2 [Mus musculus]
          Length = 553

 Score =  145 bits (367), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 116/262 (44%), Gaps = 26/262 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
              L   F   +        +  +R+G++ ++++ V                    L+ +
Sbjct: 172 GRSLLHVFSTEFRSQPLSYYEAAVRAGRLHLNEEPV------------------QDLSIV 213

Query: 78  IKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +K+   L ++V+  +     + I LL E++ + V +KP+ I V       ++   F+   
Sbjct: 214 LKDNDFLRNTVHRHEPPVTAEPIHLLAENNDVVVIDKPSSIPVHPCGRFRHNTVIFILG- 272

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            + + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G   +K+ 
Sbjct: 273 KEHQLKELHPLHRLDRLTSGVLMFAKTAAVSEKIHEQVRDRQLEKEYVCRVAGEFPDKEV 332

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +L  S     Y   V + +       + F+ +    +    ++ +P TGRTHQ+R
Sbjct: 333 ICKEPILVVS-----YKVGVCRVDPRGKPCETVFQRLSYNGRS-SVVQCRPLTGRTHQIR 386

Query: 257 VHALHMGCPIVGDHKYCANFKG 278
           VH   +G PI+ D  Y +   G
Sbjct: 387 VHLQFLGHPILNDPIYNSTAWG 408


>gi|24583445|ref|NP_723592.1| RluA-1, isoform A [Drosophila melanogaster]
 gi|24583447|ref|NP_723593.1| RluA-1, isoform B [Drosophila melanogaster]
 gi|24583449|ref|NP_723594.1| RluA-1, isoform C [Drosophila melanogaster]
 gi|22946167|gb|AAF52959.2| RluA-1, isoform A [Drosophila melanogaster]
 gi|22946168|gb|AAF52960.2| RluA-1, isoform B [Drosophila melanogaster]
 gi|22946169|gb|AAN10755.1| RluA-1, isoform C [Drosophila melanogaster]
 gi|206725570|gb|ACI16540.1| FI04540p [Drosophila melanogaster]
          Length = 739

 Score =  145 bits (367), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 59/268 (22%), Positives = 112/268 (41%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   ++      + +    + 
Sbjct: 318 LDIF-SREFRAHPAEEYERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQ- 375

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 376 -----------------PIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 417

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    EC  
Sbjct: 418 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGIVECKE 477

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  K+          +  +P TGR HQ+RVH 
Sbjct: 478 PIEVVSYKIG-----VCKVSAKGKDCTTTFQKL--SQNGTTSVVLCKPLTGRMHQIRVHL 530

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI+ D  Y     G    P++ +
Sbjct: 531 QYLGYPILNDPLYNHEVFG----PLKGR 554


>gi|313124222|ref|YP_004034481.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ND02]
 gi|312280785|gb|ADQ61504.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ND02]
          Length = 282

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 62/258 (24%), Positives = 94/258 (36%), Gaps = 30/258 (11%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           QV V+ +   FN  I+  + V +                   S+     +      ++YE
Sbjct: 40  QVLVNGQYRSFNQLIKGNEKVDLYLDQV-------------ESLQGDYPASGKMPKVVYE 86

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  + V +KP G       G          S++   G  P + HRLD  T G+L+VA+  
Sbjct: 87  DENVLVIDKPKGQKTHPNQGENGTALNDCASYL---GYSPYIVHRLDMLTGGLLLVAKNP 143

Query: 165 AAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
           A    L      + +++ Y + V        +  I   + +                   
Sbjct: 144 AVVPILNRQLTSKTLRRDYLATVDLNKEIPDQGTIDLPIGQDPADQRKRQVRA-----DG 198

Query: 224 NYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             A+SHF+V+    +K    L +   TGRTHQ+RVH    G PIVGD  Y  NF G    
Sbjct: 199 LRAVSHFQVLKKDEEKKQAKLLVTLETGRTHQIRVHLSASGWPIVGDPLYNPNFAGED-- 256

Query: 283 PIQNKLYLHARYMDLPHP 300
                L L    +    P
Sbjct: 257 -----LALTGWQLTFVKP 269


>gi|192361541|ref|YP_001981578.1| ribosomal large subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
 gi|190687706|gb|ACE85384.1| ribosomal large subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
          Length = 221

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 54/222 (24%), Positives = 93/222 (41%), Gaps = 16/222 (7%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
            +D  + L    + ++  LL ED    + +KP  +    G           +   D  G 
Sbjct: 4   PIDQLIVLPPCQEDIE--LLREDEDFLLIHKPTRLLSVPGRHPQNRDSVIARLLPDYPG- 60

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              + HRLD +TSG++V+   + A  H+++ F+ R + K Y ++V G+   ++  I   +
Sbjct: 61  -ATIVHRLDFDTSGVMVIPLNKPALSHISKQFQARSVSKHYTAVVAGLVGQEQGVIDLPI 119

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALH 261
                         K        +++ F+V+    A     L + P TGR+HQLR+H   
Sbjct: 120 ASGEGP------TYKICRTSGKPSVTEFRVLARDQAANTSRLVLHPITGRSHQLRLHLQA 173

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +G PI+G   Y   +          +L LHA  +   HP  G
Sbjct: 174 IGHPILGCEFYGGTYASAAP-----RLLLHATDLGFRHPSTG 210


>gi|281423381|ref|ZP_06254294.1| RNA pseudouridine synthase family protein [Prevotella oris F0302]
 gi|281402717|gb|EFB33548.1| RNA pseudouridine synthase family protein [Prevotella oris F0302]
          Length = 522

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 93/230 (40%), Gaps = 22/230 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D   N  + +D      +YED  I V  KPAG+    G  +  ++   ++     +   
Sbjct: 307 IDIEENPLERADQQALEWIYEDKDIVVVCKPAGMLSVPGKSLRENVRSLVRQR-HPEATG 365

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG+LVVA    +   L   F    +QK Y +L+       +    +  L
Sbjct: 366 PMIVHRLDMATSGLLVVALNLKSYIDLQRQFEEHSVQKRYVALLSRPHHGARSGQISLPL 425

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V   +      A+++++           + + P TGRTHQLR+H  H  
Sbjct: 426 RPDLYDRPRQIV---DAVHGRKAVTNYQ-----QTGENRMNLYPLTGRTHQLRMHCAHAD 477

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
            +  PI GD  Y    +         +LYLHA  +   HP  G R+    
Sbjct: 478 GLNNPIKGDELYGTRDE---------RLYLHAEELSFVHPGTGKRMHFEC 518


>gi|195434114|ref|XP_002065048.1| GK15253 [Drosophila willistoni]
 gi|194161133|gb|EDW76034.1| GK15253 [Drosophila willistoni]
          Length = 761

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 61/268 (22%), Positives = 115/268 (42%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   +         L +I+  
Sbjct: 336 LDIF-SREFRAHPAEEYERCIQTGTLTVNFEKVPIDYRLKHNDL---------LANIVHR 385

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +   +T         +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 386 HEVPVTCQPIT---------IVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 435

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V GI P    EC  
Sbjct: 436 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGIFPDGIVECKE 495

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG      V +         + F+ +     K   +  +P TGR HQ+RVH 
Sbjct: 496 PIEVVSYKIG------VCKVSPRGKDCTTTFQKLSQNG-KTSVVLCKPLTGRMHQIRVHL 548

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI+ D  Y     G    P++ +
Sbjct: 549 QYLGYPILNDPLYNHEVFG----PLKGR 572


>gi|194376328|dbj|BAG62923.1| unnamed protein product [Homo sapiens]
          Length = 538

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 60/255 (23%), Positives = 113/255 (44%), Gaps = 26/255 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L   F   +        +  +R+G++++++K V                    LN ++K+
Sbjct: 155 LLHVFSTEFRAQPLAYYEAAVRAGRLQLNEKPV------------------QDLNIVLKD 196

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+    + 
Sbjct: 197 NDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-KEH 255

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++    
Sbjct: 256 QLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVTCK 315

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             +L  S     Y   V + +       + F+ +    Q    +  +P TGRTHQ+RVH 
Sbjct: 316 EPILVVS-----YKVGVCRVDPRGKPCETVFQRLSYNGQS-SVVRCRPLTGRTHQIRVHL 369

Query: 260 LHMGCPIVGDHKYCA 274
             +G PI+ D  Y +
Sbjct: 370 QFLGHPILNDPIYNS 384


>gi|109730743|gb|AAI17829.1| RNA pseudouridylate synthase domain containing 2 [Mus musculus]
 gi|109734876|gb|AAI17828.1| RNA pseudouridylate synthase domain containing 2 [Mus musculus]
          Length = 553

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 116/262 (44%), Gaps = 26/262 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
              L   F   +        +  +R+G++ ++++ V                    L+ +
Sbjct: 172 GRSLLHVFSTEFRSQPLSYYEAAVRAGRLHLNEEPV------------------QDLSIV 213

Query: 78  IKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +K+   L ++V+  +     + I LL E++ + V +KP+ I V       ++   F+   
Sbjct: 214 LKDNDFLRNTVHRHEPPVTAEPIRLLAENNDVVVIDKPSSIPVHPCGRFRHNTVIFILG- 272

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            + + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G   +K+ 
Sbjct: 273 KEHQLKELHPLHRLDRLTSGVLMFAKTAAVSEKIHEQVRDRQLEKEYVCRVAGEFPDKEV 332

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +L  S     Y   V + +       + F+ +    +    ++ +P TGRTHQ+R
Sbjct: 333 ICKEPILVVS-----YKVGVCRVDPRGKPCETMFQRLSYNGRS-SVVQCRPLTGRTHQIR 386

Query: 257 VHALHMGCPIVGDHKYCANFKG 278
           VH   +G PI+ D  Y +   G
Sbjct: 387 VHLQFLGHPILNDPIYNSTAWG 408


>gi|58266206|ref|XP_570259.1| hypothetical protein [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|134111034|ref|XP_775981.1| hypothetical protein CNBD3880 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50258647|gb|EAL21334.1| hypothetical protein CNBD3880 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|57226492|gb|AAW42952.1| conserved hypothetical protein [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 520

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 52/265 (19%), Positives = 101/265 (38%), Gaps = 22/265 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             V+      +L       +   +    +  L SG  RV+    + +  +++G  +    
Sbjct: 32  TFVKQRWIGRQLLEVITTEFRDRSMEYYRHALESGVTRVNGVVAQPDLILRNGDRIDNTV 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
             +                     +D +  + +  + +  V +KP  + V        H 
Sbjct: 92  HRH----------------EPPVTNDPILVLHIDREREFIVISKPGSLPVHAAGRYFKH- 134

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+      G K    +RLD+ TSG++++A +  AA  L   F   +++K Y + V G
Sbjct: 135 -TVLEMMESDYGLKCYSVNRLDRLTSGLMILALSGKAASKLAREFVEGKVKKEYVARVKG 193

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPH 248
               ++  +   ++    +      V+   E  +  A++ F  I     +    +  +P 
Sbjct: 194 KFPKEEITVDKPMM---TVDRQMGLVIITPEGKSQDAVTIFNRIAYDPVRDQSVVRCRPQ 250

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC 273
           TGRTHQ+RVH  ++G PI  D  Y 
Sbjct: 251 TGRTHQIRVHLQYLGHPIANDPLYG 275


>gi|209529662|ref|NP_001129317.1| RNA pseudouridylate synthase domain-containing protein 2 [Rattus
           norvegicus]
 gi|149022995|gb|EDL79889.1| RNA pseudouridylate synthase domain containing 2 (predicted)
           [Rattus norvegicus]
          Length = 553

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 115/262 (43%), Gaps = 26/262 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
              L   F   +        +  +R+G++ ++++ V                    LN +
Sbjct: 172 GRSLLHVFSTEFRSQPLAYYEAAVRAGRLHLNEEPV------------------QDLNIV 213

Query: 78  IKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+   
Sbjct: 214 LKDNDFLRNTVHRHEPPVTAEPIRLLAENDDVVVIDKPSSIPVHPCGRFRHNTVIFILG- 272

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            + + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G   +K+ 
Sbjct: 273 KEHQLKELHPLHRLDRLTSGVLMFAKTAAVSEKIHEQVRDRQLEKEYVCRVAGEFPDKEV 332

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +L  S     Y   V + +       + F+ +    +    ++ +P TGRTHQ+R
Sbjct: 333 ICKEPILVVS-----YKVGVCRVDPQGKPCETVFQRLSYNGRS-SVVQCRPLTGRTHQIR 386

Query: 257 VHALHMGCPIVGDHKYCANFKG 278
           VH   +G PI+ D  Y +   G
Sbjct: 387 VHLQFLGHPILNDPIYNSTAWG 408


>gi|57505358|ref|ZP_00371287.1| ribosomal large subunit pseudouridine synthase C [Campylobacter
           upsaliensis RM3195]
 gi|57016494|gb|EAL53279.1| ribosomal large subunit pseudouridine synthase C [Campylobacter
           upsaliensis RM3195]
          Length = 308

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 122/319 (38%), Gaps = 50/319 (15%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +       I     QK++   ++  +   VK  N I  G VV +    NA   +      
Sbjct: 21  FLMQSLK-IPINEAQKLIDKKRLFCNGNLVKKKNEILQG-VVELIVYENAPKGV------ 72

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYH-IDGFLKSWVDSKG 141
                            ++YE+ +  V  KP+G+     G   AY   D   + W    G
Sbjct: 73  ----------------KIVYENEEFAVLEKPSGVLSHPNGRHCAYSLCDEIWELW----G 112

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +  + HRLD+ETSG+++ A+T+ +       F  R IQK Y +L  G+ K + E     
Sbjct: 113 MEACVVHRLDKETSGLILAAKTKNSQVEFKTMFEKREIQKEYLALTQGLIKEEFEVD--- 169

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHAL 260
           L  +     D V    Q  +    A+S FK +  +       +  +P TGR HQLR+H  
Sbjct: 170 LPMRLTQNYDDVKTRMQICEDGKRALSFFKRVRFYPDLNVSLVLCKPFTGRQHQLRLHLF 229

Query: 261 HMGCPIVGDHKYCANFKG-------------NFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           H G  I+G+  Y    +                      +L LH++ +   + +  +  I
Sbjct: 230 HSGHQILGEPLYGLKKEQIEQILDGKLSQDERIKLTGAKRLMLHSQRLYFTY-KAKKFDI 288

Query: 308 TAPLPAHMVKTWDSLGFKY 326
           ++    +  + +  L   +
Sbjct: 289 SSK--ENFWEDFKGLKCDF 305


>gi|307746984|gb|ADN90254.1| Pseudouridine synthase [Campylobacter jejuni subsp. jejuni M1]
          Length = 281

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 58/284 (20%), Positives = 111/284 (39%), Gaps = 46/284 (16%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+    QK++   ++  D   V+  N+I +G +V +                      + 
Sbjct: 6   ISINEAQKLIDKKRLFCDGILVEEKNKILNG-LVEL----------------------IV 42

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             ++     +++E+    +  K +GI     G    Y +   +       G++  + HR+
Sbjct: 43  YENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL---WGKEACVAHRI 99

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-LLKKSHIG 209
           D+ETSG++++A+ + A   L   F  + +QK Y +L  G  +          L K     
Sbjct: 100 DKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALAHGKIEENFIVDKAINLTKNYDDV 159

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              + + K+       AI+ F++++ F +     L  +P TGR HQ+RVH  +    I+G
Sbjct: 160 KTRMQICKE----GKQAITEFEILEYFPKINATLLLCKPLTGRQHQIRVHLHYKNHTILG 215

Query: 269 DHKYC-------------ANFKGNFTSPIQNKLYLHARYMDLPH 299
           D  Y               N K         +L LH+  +   +
Sbjct: 216 DPLYGLSKQQIESILDEKLNPKERLKLTGALRLCLHSYRLKFQY 259


>gi|145355423|ref|XP_001421961.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582200|gb|ABP00255.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 264

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 64/264 (24%), Positives = 105/264 (39%), Gaps = 34/264 (12%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY------------------HIDGFL 133
           +  D     +L+ED ++   NK AG +    S +A                   H     
Sbjct: 6   ETEDVEALEILHEDEEMTCVNKRAGTASTPESRVADSSAASLVVARWRRRLVDAHDGALA 65

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            + V      P + HRLD ETSG LVV +   AA     +F  R ++K Y +L      +
Sbjct: 66  SNVVLGASLVPYVAHRLDLETSGALVVCKNAKAAARAQGAFERREVEKTYLALCRCDEFD 125

Query: 194 ------KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                     I   L K+          V+ +      A + + ++    ++   +  +P
Sbjct: 126 VSGGGASSGTIDLALAKRDDGAR---FFVETSSADGKPASTEWTIVARN-RRHALVRCRP 181

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
            TGRTHQ+RVH   +G PIVGD  Y         + + ++  LHA  +  P  +  G  +
Sbjct: 182 KTGRTHQIRVHLAAIGLPIVGDAAYGC-----LDADVVDRHALHAWTLRFPAKDFAGVPR 236

Query: 307 ITAPLPAHMVKTWDSLGFKYDRNL 330
           I AP+P    +  + +G  +D + 
Sbjct: 237 IVAPVPDDFRRACERVGVDFDFDA 260


>gi|23308689|ref|NP_689473.1| RNA pseudouridylate synthase domain-containing protein 2 [Homo
           sapiens]
 gi|158563848|sp|Q8IZ73|RUSD2_HUMAN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 2
 gi|16550833|dbj|BAB71059.1| unnamed protein product [Homo sapiens]
 gi|119612834|gb|EAW92428.1| RNA pseudouridylate synthase domain containing 2 [Homo sapiens]
 gi|127796558|gb|AAH16967.2| RNA pseudouridylate synthase domain containing 2 [Homo sapiens]
          Length = 545

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 60/255 (23%), Positives = 113/255 (44%), Gaps = 26/255 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L   F   +        +  +R+G++++++K V                    LN ++K+
Sbjct: 162 LLHVFSTEFRAQPLAYYEAAVRAGRLQLNEKPV------------------QDLNIVLKD 203

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+    + 
Sbjct: 204 NDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-KEH 262

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++    
Sbjct: 263 QLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVTCK 322

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             +L  S     Y   V + +       + F+ +    Q    +  +P TGRTHQ+RVH 
Sbjct: 323 EPILVVS-----YKVGVCRVDPRGKPCETVFQRLSYNGQS-SVVRCRPLTGRTHQIRVHL 376

Query: 260 LHMGCPIVGDHKYCA 274
             +G PI+ D  Y +
Sbjct: 377 QFLGHPILNDPIYNS 391


>gi|254673709|emb|CBA09336.1| pseudouridylate synthase, 23S RNA-specific [Neisseria meningitidis
           alpha275]
          Length = 217

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 91/221 (41%), Gaps = 23/221 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV    G                 +K  L HRLD++T GIL+ 
Sbjct: 4   ILFRHQDFVAINKPQGISVHRSDGEVSLTATLAAQL---GVEKVWLLHRLDKQTGGILLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I   + K          + K   
Sbjct: 61  ALNPQSAAVLAAQFAERKMKKTYLALSDRKPSKKQGWIKGGMEKS------RRGMWKLTR 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F  I    +K     ++PHTG+THQLRV    +G PI+GD  Y        
Sbjct: 115 NMENIAVTRFFSI-RIGEKMRLFILEPHTGKTHQLRVAMKSLGSPILGDRLYGGTESETT 173

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
                   +L+A  +   + +   ++ITAPL       W +
Sbjct: 174 --------FLYAWKIQFTY-QQQEIEITAPL----KNAWQA 201


>gi|148695986|gb|EDL27933.1| RNA pseudouridylate synthase domain containing 2 [Mus musculus]
          Length = 553

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 116/262 (44%), Gaps = 26/262 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
              L   F   +        +  +R+G++ ++++ V                    L+ +
Sbjct: 172 GRSLLHVFSTEFRSQPLSYYEAAVRAGRLHLNEEPV------------------QDLSIV 213

Query: 78  IKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +K+   L ++V+  +     + I LL E++ + V +KP+ I V       ++   F+   
Sbjct: 214 LKDNDFLRNTVHRHEPPVTAEPIHLLAENNDVVVIDKPSSIPVHPCGRFRHNTVIFILG- 272

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            + + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G   +K+ 
Sbjct: 273 KEHQLKELHPLHRLDRLTSGVLMFAKTAAVSEKIHEQVRDRQLEKEYVCRVAGEFPDKEV 332

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +L  S     Y   V + +       + F+ +    +    ++ +P TGRTHQ+R
Sbjct: 333 ICKEPILVVS-----YKVGVCRVDPRGKPCETMFQRLSYNGRS-SVVQCRPLTGRTHQIR 386

Query: 257 VHALHMGCPIVGDHKYCANFKG 278
           VH   +G PI+ D  Y +   G
Sbjct: 387 VHLQFLGHPILNDPIYNSTAWG 408


>gi|195471884|ref|XP_002088232.1| GE13593 [Drosophila yakuba]
 gi|194174333|gb|EDW87944.1| GE13593 [Drosophila yakuba]
          Length = 738

 Score =  145 bits (366), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 58/259 (22%), Positives = 108/259 (41%), Gaps = 28/259 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   ++      + +    + 
Sbjct: 317 LDIF-SREFRAHPAEEYERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQ- 374

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 375 -----------------PIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 416

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    EC  
Sbjct: 417 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGIVECKE 476

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  K+          +  +P TGR HQ+RVH 
Sbjct: 477 PIEVVSYKIG-----VCKVSSKGKDCTTTFQKL--SQNGSTSVVLCKPLTGRMHQIRVHL 529

Query: 260 LHMGCPIVGDHKYCANFKG 278
            ++G PI+ D  Y     G
Sbjct: 530 QYLGYPILNDPLYNHEVFG 548


>gi|153952071|ref|YP_001397292.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
 gi|152939517|gb|ABS44258.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
          Length = 300

 Score =  145 bits (366), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 60/293 (20%), Positives = 111/293 (37%), Gaps = 47/293 (16%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +    +   I+    QK++   ++  D   V+  N+I  G +V +               
Sbjct: 17  QVLVENLK-ISINEAQKLIDKKRLFCDGILVEEKNKILKG-LVEL--------------- 59

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
                  +   ++     +++E+    +  K +GI     G    Y +   +       G
Sbjct: 60  -------IVYENNPKGVEIVFENENFAILEKESGILSHPNGRHCKYSLSDEIWHL---WG 109

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           +   + HRLD+ETSG+++VA+ + A   L   F  + +QK Y +L  G  +         
Sbjct: 110 KGACVAHRLDKETSGLILVAKNKKAQIDLKSLFEKKLVQKEYLALAHGKIEKNFIVDKAI 169

Query: 202 -LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHA 259
            L K        + + K+       AI+ FK+++ F +     L  +P TGR HQ+RVH 
Sbjct: 170 NLAKNYDDVKTRMQICKE----GKQAITEFKILEYFPKINATLLLCKPLTGRQHQIRVHL 225

Query: 260 LHMGCPIVGDHKYC-------------ANFKGNFTSPIQNKLYLHARYMDLPH 299
            +    I+GD  Y               + K         +L LH+  +   +
Sbjct: 226 HYKNHTILGDPLYGLSKEQIESILDEKLSPKERLKLTGALRLCLHSYRLKFQY 278


>gi|222624713|gb|EEE58845.1| hypothetical protein OsJ_10432 [Oryza sativa Japonica Group]
          Length = 458

 Score =  145 bits (366), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 69/324 (21%), Positives = 115/324 (35%), Gaps = 80/324 (24%)

Query: 39  KILRSGQVRVDKKRVK-FNNRIQSGQVV---RIPPVINALNHIIKEQKILDSSVNLTKHS 94
           K +R GQ+ VD +     +  ++ G  +   R+P       H++                
Sbjct: 71  KRIRDGQITVDGEVATDPDMILREGSKLVYHRLPWQEPFAPHLL---------------- 114

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ------------ 142
                 +LYED  +   NKP+G+ V                  D K              
Sbjct: 115 -----DVLYEDDDMIALNKPSGLQVLPKGLFQQRTVLAQLQLKDWKMPSSFCSKRKDAQS 169

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHL-----------------TESFRMRRIQKIYWS 185
            P   HRL + TSG+L+ A+T+ A   L                 T+  + R+I K Y +
Sbjct: 170 HPVPVHRLGRGTSGLLLCAKTKLAKAQLAAYFAEGATNAGKSRDETDICKARKISKFYRA 229

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLE 244
           LV GI +N +  I   +    + G         +      A+S  +V++         ++
Sbjct: 230 LVTGILENDEVMITQPIGLVRYPGVAEGLYAACSS--GKPAMSKVRVLERLKIHNHTLIQ 287

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS---------------------- 282
           ++ H+GR HQ+R+H  ++G P+V D  Y    +  F                        
Sbjct: 288 VEIHSGRPHQIRIHLAYIGHPLVDDPLYGIGGQPKFDEPEPTSTADSFAYDGGYERPLQP 347

Query: 283 -PIQNKLYLHARYMDLPHPEGGRL 305
            P     +LHA ++ L HP    L
Sbjct: 348 VPGDCGYHLHAHWLVLCHPTTNEL 371


>gi|238018444|ref|ZP_04598870.1| hypothetical protein VEIDISOL_00271 [Veillonella dispar ATCC 17748]
 gi|237864915|gb|EEP66205.1| hypothetical protein VEIDISOL_00271 [Veillonella dispar ATCC 17748]
          Length = 334

 Score =  145 bits (366), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 58/320 (18%), Positives = 122/320 (38%), Gaps = 67/320 (20%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
            +  +L K+     + ++  +    + I  G  + I      +++   E           
Sbjct: 40  YSRKSLVKLFEEKLIHINGHKATPKDVISEGDEIWIAMAKEKIDYEPIE----------- 88

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHR 149
                +   +LYED  + + +KPAG++V   S     +   +  +    G  +K R  +R
Sbjct: 89  -----MDLHILYEDDDLLIVDKPAGVTV--NSKDQVSLANGVAYYFKENGIKRKVRFLNR 141

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--- 206
           LD++T+G +V+A++  A     +       +K Y + V GI +  ++ +   + + +   
Sbjct: 142 LDRDTTGCIVIAKSGLAQSLYQQQMDDNTFEKWYMATVEGIVEADEDSLVLPMDRSTDGI 201

Query: 207 ---------HIGGDYVHVVKQNEKGANYAISHF--------------------------- 230
                        D+  + + + +  + ++                              
Sbjct: 202 HYEVNPKGKETRTDFSFLCRHSSQPVDNSVHKLVKSVDIAQENVDIELQNVDKHGVNVDK 261

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
            V +     +  + ++ +TG+THQ+RV   H+G P+VGD  Y A   G    P Q +   
Sbjct: 262 SVHNSSKCGYTEVLVRLYTGKTHQIRVAFSHIGHPLVGDTLYGAQPTGQ---PFQLR--- 315

Query: 291 HARYMDLPHPEGG-RLQITA 309
            A+ +   H   G R+ +TA
Sbjct: 316 -AQKVVFTHMRTGERITVTA 334


>gi|282849749|ref|ZP_06259133.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
 gi|282580686|gb|EFB86085.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
          Length = 372

 Score =  145 bits (366), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 63/326 (19%), Positives = 120/326 (36%), Gaps = 79/326 (24%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
               +L K+     + ++  +    + I  G  + I      ++H   E           
Sbjct: 78  YPRKSLVKLFEEKLIHINGHKATPKDTISEGDEIWIAMAKEKIDHDPIE----------- 126

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHR 149
                +   +LYED+ + + +KP G++V   S     +   +  +    G  +K R  +R
Sbjct: 127 -----MDLRILYEDTDLLIVDKPCGLTV--NSKDQVSLANGVAHYFKEHGIKRKVRFLNR 179

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD++T+G +V+A++  A     +       +K Y + V GI +  ++ +   + ++S  G
Sbjct: 180 LDRDTTGCIVIAKSGLAQSLYQQQMDDNTFEKWYMATVEGIVEADEDSLVFPM-ERSADG 238

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFA-------------------------------- 237
             Y   VK          + F V+   +                                
Sbjct: 239 IHYEVNVK-----GKETRTDFSVLCRHSSQAVDNSVNKSKNSVDIAPKNVDINLGDVDKS 293

Query: 238 -------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
                          +  + ++ +TG+THQ+RV   H+G P+VGD  Y A   G    P 
Sbjct: 294 SQNVDKTVYKSNKCGYSKVLVRLYTGKTHQIRVAFSHIGHPLVGDILYGAQPTGQ---PF 350

Query: 285 QNKLYLHARYMDLPHPEGG-RLQITA 309
           Q +    A+ +   H   G R+ +TA
Sbjct: 351 QLR----AQKVVFTHMRTGERITVTA 372


>gi|326316917|ref|YP_004234589.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
 gi|323373753|gb|ADX46022.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
          Length = 241

 Score =  145 bits (366), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 62/225 (27%), Positives = 94/225 (41%), Gaps = 22/225 (9%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ D  + V  KP+G+    G G        L +          + HRLDQ TSGI+V+A
Sbjct: 24  LHADDDLLVLAKPSGLLCVPGRGPD--KQDCLSARAALHWPGACIVHRLDQATSGIVVMA 81

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH-----VV 216
           R   A + L ++F  R++ K Y ++V           A W      I  D+       VV
Sbjct: 82  RHAQAQRALGDAFAARQVHKRYVAVVHAPHPAGDG--AAWREIDLPIAADWERRPLRVVV 139

Query: 217 KQNEKGANYAISHFK--------VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                G   +++ ++        V     +    + ++P TGRTHQLRVH   +  PI+G
Sbjct: 140 PHGAPGGKASLTRWRPAAPGDGAVTWRATEGTLRVLLEPVTGRTHQLRVHMAAVDQPILG 199

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           D  Y           +  +L LHA+++   HP  G  L    P P
Sbjct: 200 DTLYAPP----AIQALAPRLLLHAQHIAFAHPRTGTPLAFDLPAP 240


>gi|189439004|ref|YP_001954085.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium longum
           DJO10A]
 gi|189427439|gb|ACD97587.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium longum
           DJO10A]
          Length = 258

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 42/160 (26%), Positives = 73/160 (45%), Gaps = 6/160 (3%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +  +  RLD  TSG+++V ++  A   +   F    ++K Y +LV G  K  K  I   +
Sbjct: 65  REGIVSRLDVGTSGLMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQGGLKENKATIEAPI 124

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            +                     A++H+ V++ F  +   + +   TGRTHQ+RVH   +
Sbjct: 125 GR-----AKVSDFRFCVTPAGKPAVTHWDVLERFGHEATLVSVNLETGRTHQIRVHFSSI 179

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           G P+ GD  Y AN   +    + ++ +LHA  ++  HP  
Sbjct: 180 GHPLCGDPMYGANPVLSEALGL-DRQWLHAMKLEFRHPRT 218


>gi|154482915|ref|ZP_02025363.1| hypothetical protein EUBVEN_00612 [Eubacterium ventriosum ATCC
           27560]
 gi|149736199|gb|EDM52085.1| hypothetical protein EUBVEN_00612 [Eubacterium ventriosum ATCC
           27560]
          Length = 204

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 43/207 (20%), Positives = 94/207 (45%), Gaps = 18/207 (8%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +Q + +  ++   R D++   ++       + K+LR   + ++ K+     ++  G  ++
Sbjct: 1   MQEIKITENQAGQRFDKFLFKYFKEATSGFIYKMLRKKNIVLNGKKSDGKEKLNVGDSIK 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I    + +     E K+             +   ++YED  I + NKP+G+  Q      
Sbjct: 61  IFMADDTILKFRGETKV--------DIVKPIDLDIVYEDDNILIINKPSGMLSQKAEASD 112

Query: 127 YHIDGFLKSWV---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
             ++ ++ S++           K  KP + +RLD+ TSG+++  ++    Q +++ F+ R
Sbjct: 113 VSVNEYIISYLVSTNKLSEEQLKTFKPGVCNRLDRNTSGLIIAGKSLKGLQTMSKMFKER 172

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLK 204
            + K Y++LV G  +NK   I  +L K
Sbjct: 173 TMDKYYFALVNGKIENKIN-IKGYLKK 198


>gi|325295044|ref|YP_004281558.1| pseudouridine synthase [Desulfurobacterium thermolithotrophum DSM
           11699]
 gi|325065492|gb|ADY73499.1| pseudouridine synthase [Desulfurobacterium thermolithotrophum DSM
           11699]
          Length = 280

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 58/295 (19%), Positives = 113/295 (38%), Gaps = 49/295 (16%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    +K++  G   V+  + +F  + ++   +V                          
Sbjct: 25  SKKRAKKVIDEGLCAVNGIKERFYRKNLKPNTIVEFSIPKLLFTKT-------------- 70

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                 K  +LYED    V NKP  I+              ++S +  + +   + HRLD
Sbjct: 71  ------KIEILYEDEYFLVVNKPPFINSNKNFPD-------VESLLRKRFKSIYVAHRLD 117

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG L++A+++   +     F+ + ++K Y +LV G  K     I   +         
Sbjct: 118 KQTSGALIIAKSKEVFELFKLKFKKKEVKKKYLALVAGNLKKNSGKIKFSI--------- 168

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                         AIS ++V++   +     E++  TGR HQ+R H + +  PI+G+  
Sbjct: 169 ----------DGKEAISRYQVVERVGKTDFL-EVEILTGRKHQIRKHFVSVNHPIIGEFV 217

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFK 325
           Y              ++ LHA+ +   HP     +++ APL     + +  L  +
Sbjct: 218 YWKRTFPQKIHLFSPRIMLHAKLLKFKHPIKEHHVEVKAPLFEDFKEYFKILKGE 272


>gi|237807990|ref|YP_002892430.1| pseudouridine synthase Rlu family protein [Tolumonas auensis DSM
           9187]
 gi|237500251|gb|ACQ92844.1| pseudouridine synthase Rlu family protein, TIGR01621 [Tolumonas
           auensis DSM 9187]
          Length = 211

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 54/210 (25%), Positives = 98/210 (46%), Gaps = 19/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++     V NK  GI +   +G+     G +       GQ     HRLD+ TSG++++
Sbjct: 10  VVFDQPDFLVVNKMTGIDMHDDAGVP----GLVSRVSAFLGQNVYPVHRLDKVTSGLVLL 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ + A + L+++F  R ++K Y ++    PK K+  I   + K  +     +H      
Sbjct: 66  AKNKEATRLLSQAFADRLVKKTYLAISDRAPKKKQGWIKGDMAKGRNGSWKLLHSSD--- 122

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F+ +     +     + PHTG+THQ+RV    +G PI+GD +Y  +     
Sbjct: 123 ---NPAVTRFQSVSLTLPRHRLYIVSPHTGKTHQIRVALKSIGAPILGDERYGGS----- 174

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                ++ YLHA  +   +  G    + AP
Sbjct: 175 ---AADRTYLHAWQLHFTY-AGAEYTVEAP 200


>gi|88597629|ref|ZP_01100862.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|88189933|gb|EAQ93909.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
          Length = 281

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 58/284 (20%), Positives = 110/284 (38%), Gaps = 46/284 (16%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+    QK++   ++  D   V+  N+I +G +V +                      + 
Sbjct: 6   ISINEAQKLIDKKRLFCDGILVEEKNKILNG-LVEL----------------------IV 42

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             ++     +++E+    +  K +GI     G    Y +   +       G++  + HRL
Sbjct: 43  YENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL---WGKEACVAHRL 99

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-LLKKSHIG 209
           D+ETSG++++ + + A   L   F  + +QK Y +L  G  +          L K     
Sbjct: 100 DKETSGLILITKNKKAQIDLKSLFEKKLVQKEYLALAHGKIEENFIVDKAINLTKNYDDV 159

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              + + K+       AI+ F++++ F +     L  +P TGR HQ+RVH  +    I+G
Sbjct: 160 KTRMQICKE----GKQAITEFEILEYFPKINATLLLCKPLTGRQHQIRVHLHYKNHTILG 215

Query: 269 DHKYC-------------ANFKGNFTSPIQNKLYLHARYMDLPH 299
           D  Y               N K         +L LH+  +   +
Sbjct: 216 DPLYGLSKQQIESILDEKLNPKERLKLTGALRLCLHSYRLKFQY 259


>gi|322383212|ref|ZP_08057023.1| RNA pseudouridine synthase [Paenibacillus larvae subsp. larvae
           B-3650]
 gi|321152481|gb|EFX45267.1| RNA pseudouridine synthase [Paenibacillus larvae subsp. larvae
           B-3650]
          Length = 193

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 48/198 (24%), Positives = 86/198 (43%), Gaps = 13/198 (6%)

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            +    +    +  + R  HRLD ET+G ++ A+   +   L E  R++ +++ Y +L  
Sbjct: 5   QNSAHPAGRKGQRCRVRHIHRLDAETTGAVLYAKNEWSHLLLDEGMRLKTVRREYAALAE 64

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G  +     I   + +  H        +K       +A++ + V     ++   L +   
Sbjct: 65  GCIEPTVGVIDLPIGRDRHHKSKRRVTLK-----GQHAVTRYAV-AAQLEQAALLHLSLE 118

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  H+G P++GD  Y  N      + + ++  LH   +   HP  G  L+I
Sbjct: 119 TGRTHQIRVHLSHIGHPLLGDSLYGGN------TALISRQALHGERISFSHPITGEDLRI 172

Query: 308 TAPLPAHMVKTWDSLGFK 325
            AP P      +  L  +
Sbjct: 173 EAPWPGDFTALYAKLKAE 190


>gi|28316862|gb|AAO39454.1| RH45372p [Drosophila melanogaster]
          Length = 739

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 59/268 (22%), Positives = 112/268 (41%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   ++      + +    + 
Sbjct: 318 LDIF-SREFRAHPTEEYERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQ- 375

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 376 -----------------PIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 417

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    EC  
Sbjct: 418 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGIVECKE 477

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  K+          +  +P TGR HQ+RVH 
Sbjct: 478 PIEVVSYKIG-----VCKVSAKGKDCTTTFQKL--SQNGTTSVVLCKPLTGRMHQIRVHL 530

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI+ D  Y     G    P++ +
Sbjct: 531 QYLGYPILNDPLYNHEVFG----PLKGR 554


>gi|66813276|ref|XP_640817.1| pseudouridine synthase family protein [Dictyostelium discoideum
           AX4]
 gi|60468845|gb|EAL66845.1| pseudouridine synthase family protein [Dictyostelium discoideum
           AX4]
          Length = 578

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 56/287 (19%), Positives = 104/287 (36%), Gaps = 43/287 (14%)

Query: 21  LDRWFKNHYPHINF-VNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           LD +    +   +  V L+K ++ G ++V+ + V  + +I+    +              
Sbjct: 181 LDMF-SQEFSTNSRDVYLKK-IKRGLIKVNDQLVSPSYKIKLNDTIIHTVHR-------H 231

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E  +   S+ +              D  + V +KP+ I V       +  +  +      
Sbjct: 232 EPPVTGESIKIVSL-----------DENVVVVDKPSSIPVHPCG--RFRHNSLMYILASE 278

Query: 140 KG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC- 197
            G  +    HRLD+ TSG+L++ART  +A       +   + K Y + V G         
Sbjct: 279 HGINQLYGVHRLDRLTSGLLLLARTPDSANKKANQIQSGLVSKQYLAKVIGKFPGSDTIN 338

Query: 198 -----------------IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQK 239
                               +++ +  +       +     G   +I+H K+     +  
Sbjct: 339 SSSSSFNEQIKLCKHLEDGTFIIDQPIVIQSMRLGINHVGVGGKPSITHIKLFSYDQSTN 398

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
              +   P TGRTHQ+RVH   +G PI  D  Y   FK +F +   +
Sbjct: 399 TSIVLCTPKTGRTHQIRVHLKWLGFPIANDPLYNNEFKESFKALTSD 445


>gi|261364898|ref|ZP_05977781.1| pseudouridine synthase Rlu family protein [Neisseria mucosa ATCC
           25996]
 gi|288566947|gb|EFC88507.1| pseudouridine synthase Rlu family protein [Neisseria mucosa ATCC
           25996]
          Length = 207

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 54/215 (25%), Positives = 85/215 (39%), Gaps = 19/215 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP G+SV    G                 ++  L HRLD+ TSG+L+ 
Sbjct: 4   ILFRHPDFVAINKPCGVSVHQEEGEVSLTQTLAAQL---GLEQIWLLHRLDKLTSGVLLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L + F  + ++K Y +L    P  K+  I   + K        +       
Sbjct: 61  ALNPQSASALAQQFAAKTMRKTYLALSTDKPSKKQGWIKGDMEKSRRGAWKLMR------ 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F              + PHTG+THQLRV    +G PI+GD  Y        
Sbjct: 115 STENPAVTEFNC-QSLEPGLRLFVLHPHTGKTHQLRVAMKSLGSPILGDTLYGGK----- 168

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
                ++++LHA  +   + +    +I APL    
Sbjct: 169 ---AASRMFLHAWKIKFDY-QDQTFEIVAPLSEEW 199


>gi|218132201|ref|ZP_03461005.1| hypothetical protein BACPEC_00058 [Bacteroides pectinophilus ATCC
           43243]
 gi|217992894|gb|EEC58894.1| hypothetical protein BACPEC_00058 [Bacteroides pectinophilus ATCC
           43243]
          Length = 297

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 107/243 (44%), Gaps = 20/243 (8%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKP 144
            D +K  ++YED  I + +KP+G+  Q  S     +  ++  ++   G          +P
Sbjct: 42  PDKIKLKVMYEDEDIVIIDKPSGMLSQKASAGDKSLVEYVTEYLLDTGSLTQKDLITFRP 101

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + +RLD+ TSG++V  +T    Q ++E+FR R + K Y  +V G   N++  ++ +L++
Sbjct: 102 GICNRLDRNTSGLVVAGKTIKGLQEMSEAFRDRTLHKYYICVVAGRI-NERSRVSGYLVR 160

Query: 205 KSHIGG-----DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
                      DY   +   E      I    +       F  L+++  TGRTHQ+R H 
Sbjct: 161 DEKTNKSTIYADYKEAMDNAEADMINNIETEYIPAVSNDNFTLLKVKLITGRTHQIRAHL 220

Query: 260 LHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
             +G PI GD KY +       S         LHA  +D  +P+ G L +   +P    +
Sbjct: 221 ASLGHPIAGDVKYGSRQINKRMSDQYHIKSQMLHAYELD--YPQRG-LCVRTDIPKEFDR 277

Query: 318 TWD 320
              
Sbjct: 278 VLK 280


>gi|87311611|ref|ZP_01093729.1| ribosomal large subunit pseudouridine synthase D [Blastopirellula
           marina DSM 3645]
 gi|87285733|gb|EAQ77649.1| ribosomal large subunit pseudouridine synthase D [Blastopirellula
           marina DSM 3645]
          Length = 242

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 104/232 (44%), Gaps = 17/232 (7%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--- 145
           N      +   ++LYED+ +   +KPA ++  G          + K ++     KP    
Sbjct: 15  NDDHPMKYATPLVLYEDNHLLAISKPALLATMGAQEGEPSAAQWAKDYLKRTYNKPGNVY 74

Query: 146 --LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             +  R+D   +G+L+ ART  AA  L+E FR R   K Y +L+   PK +   + +W+ 
Sbjct: 75  VGIVSRIDAHVTGVLLFARTSKAASRLSEQFRDRSTVKEYAALIPAGPKIRNGELVDWIR 134

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHM 262
           K+  +    + +  +    A+ A    ++++   +  C  L ++  TGR HQ+R+     
Sbjct: 135 KEDRL--HRMVIAAEGTADADRA--EMEILEQQRRPNCQMLHLRLITGRKHQIRLQLASR 190

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
           G PI+GD KY +      T      + LHA  +   HP    +  I APLP 
Sbjct: 191 GAPILGDKKYGS------TDRYSPGIALHAHRLVFTHPTLKTMVTIEAPLPE 236


>gi|297690651|ref|XP_002822726.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like isoform 2 [Pongo abelii]
          Length = 346

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 73/260 (28%), Positives = 111/260 (42%), Gaps = 39/260 (15%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   +L++D  + V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKALTRGILHQDKNLVVINKPYGLPVHGGPGVQLCITDVLPILAKMLHGHKAEP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P      +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWDKDMAHQVQELFRTRQVVKKYWAITVRVPMPSAGVVDIPIV 205

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-M 262
                           EK A  A++ ++V+            QP TG  HQLRVH    +
Sbjct: 206 ----------------EKEAQVAVTQYQVLSSTLSSALLEL-QPITGIKHQLRVHLSFGL 248

Query: 263 GCPIVGDHKYC------------ANFKGNFTSPIQNK---LYLHARYMDLPHPEGG--RL 305
            CPI+GDHKY                K       + +   L+LHAR + LP    G   L
Sbjct: 249 DCPILGDHKYSDWNRLAPQKLSVGTLKKLGLEQSKARYIPLHLHARQLILPALGSGKEEL 308

Query: 306 QITAPLPAHMVKTWDSLGFK 325
            +   LP   V +   L  +
Sbjct: 309 NLVCKLPRFFVHSLHRLHLE 328


>gi|224009938|ref|XP_002293927.1| psedouridylate synthase [Thalassiosira pseudonana CCMP1335]
 gi|220970599|gb|EED88936.1| psedouridylate synthase [Thalassiosira pseudonana CCMP1335]
          Length = 329

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 56/256 (21%), Positives = 99/256 (38%), Gaps = 48/256 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFLKSWVDSKGQKPR-LTHRLDQETSGI 157
           +++ED  I V +KP+G+    G   +           +    G+  + + HRL  +TSG+
Sbjct: 71  VVFEDEHIVVVSKPSGVLTVPGKDESNPSLNKAVFDRYGSESGRMDKMVVHRLGMDTSGL 130

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V ART AA + +   FR R++ + Y +LV G     +  I   L++       ++ V  
Sbjct: 131 VVFARTNAALRAMNALFRTRKVTRKYEALVCGHVSQDEGSIDLPLMRDYECP-PFMRVST 189

Query: 218 QNEKGA-----------------NYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRV 257
            + + A                   +++ ++V+   D        L +   +GRTHQL V
Sbjct: 190 DDHQRALIELDADEVGKKLLESPKDSLTKYEVVSREDMGGHDVSRLILTSISGRTHQLNV 249

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQ-----------------------NKLYLHARY 294
           H   +G PIVGD  Y  N +      +                          + +HA+ 
Sbjct: 250 HCAAIGHPIVGDTVYGYNGEAASNGGLDAVDLPADKASDDLQKAIAEACAGKPMCVHAKS 309

Query: 295 MDLPHPEGGR-LQITA 309
           +   HP     L   +
Sbjct: 310 ISFRHPVTKEDLSFES 325


>gi|167748371|ref|ZP_02420498.1| hypothetical protein ANACAC_03115 [Anaerostipes caccae DSM 14662]
 gi|167652363|gb|EDR96492.1| hypothetical protein ANACAC_03115 [Anaerostipes caccae DSM 14662]
          Length = 238

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 58/222 (26%), Positives = 92/222 (41%), Gaps = 13/222 (5%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----SKGQKPRLTHRLDQ 152
           +  +LY+D  I V  KPAG+           +   LK+ +       +  +  + HRLD+
Sbjct: 6   EVKVLYKDQDIAVCEKPAGMPTADDKSGDMDVFHSLKNQLFFEENLDREPELYVVHRLDR 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
              G++V ART+ AA  L+   R    +K Y ++V G    +     ++LLK      + 
Sbjct: 66  PVGGVMVFARTKEAAAELSRQIREHIFEKDYQAIVNGWLPEEDGVFTDYLLKDDK--KNT 123

Query: 213 VHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
              V +  KGA  A   ++V+   +    K  +  +   TGR HQ+RV     G  + GD
Sbjct: 124 SCTVPEETKGAKKAELSYEVLDMVETGEGKLTYCLIHLMTGRHHQIRVQFAVRGFGLYGD 183

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
            KY   F+       +  LY  A  +   HP  G      A 
Sbjct: 184 TKYNKKFQKTKKQYEEIGLY--ATRISFRHPVTGEACTFKAE 223


>gi|148243361|ref|YP_001228518.1| pseudouridylate synthases, 23S RNA-specific [Synechococcus sp.
           RCC307]
 gi|147851671|emb|CAK29165.1| Pseudouridylate synthases, 23S RNA-specific [Synechococcus sp.
           RCC307]
          Length = 323

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 61/313 (19%), Positives = 125/313 (39%), Gaps = 33/313 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+  E            + H +     + L++G+ +++   V+    +Q           
Sbjct: 19  VQLAEAGQAALELLVQRWQHSDRATWAQRLQAGECQLNGAPVQAEQVLQ----------- 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  ++ ++L       + +   +   + +D  + V NKP+G+ V  G G   H   
Sbjct: 68  -------RDDELLWQRPPWLEPAIPDQWETIVDDGDLLVINKPSGLPVMPGGGFLQH--- 117

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKIYWSLV 187
            L + ++  G KP   HRL + TSG+ V AR       L+   +     R++ + +   V
Sbjct: 118 TLTALLEPTGAKP--VHRLGRFTSGLQVCARRPETRAQLSRQMQPQGGCRKLYQAWAQRV 175

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE----KGANYAISHFKVIDCFAQKFCWL 243
             +   +   I   ++++ H    ++   + ++    +    A S  ++++  A      
Sbjct: 176 PALDVGQCLAITTAVVERQHPLLGWIWGPRADDLELLRRQLSAHSEIRLLERAAIGDRL- 234

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEG 302
           ++  HTGR HQ+R+H   +G P++GD  Y A  +     +P      LHA+ +      G
Sbjct: 235 DVVIHTGRPHQIRIHLAQIGSPLLGDPLYLAEQRIAEHATPGDGGYRLHAQQLGGLEHNG 294

Query: 303 GRLQITAPLPAHM 315
             L++ A  P   
Sbjct: 295 QTLKLMASPPQDF 307


>gi|219119374|ref|XP_002180449.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217407922|gb|EEC47857.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 216

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 97/234 (41%), Gaps = 43/234 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK----------------SWVDSKGQKP 144
           ++Y D  + + +KP G++VQGG          L                 S +DS   KP
Sbjct: 1   VIYSDLYLAIIDKPQGMAVQGGENQTLGRSDLLLPLALKPGTKVPWPTQNSILDSALTKP 60

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R+ HRLD  T GILV+A+TR A   L + F  R  +K Y +L++G    ++  I   L  
Sbjct: 61  RVCHRLDAGTGGILVLAKTRVAEVKLKQCFADRACRKRYRALLYGKLPKQEGTIEASL-- 118

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----QKFCWLEMQPHTGRTHQLRVHAL 260
                                A +H+ V+             ++++P TGR HQLR H  
Sbjct: 119 -----------------SGKPAETHYSVLRYVRSLDFGWLTLIDLRPVTGRKHQLRRHMQ 161

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGRL-QITAP 310
            MG  I GD +Y    +       ++   +L L A  + LPHP  G     T P
Sbjct: 162 GMGHAIYGDQRYGPKLEPRPNEGSEDPHSRLCLWAMEIALPHPSTGEYKTFTLP 215


>gi|19921090|ref|NP_609411.1| RluA-2, isoform A [Drosophila melanogaster]
 gi|16198203|gb|AAL13915.1| LD40728p [Drosophila melanogaster]
 gi|22946170|gb|AAF52961.2| RluA-2, isoform A [Drosophila melanogaster]
 gi|220946196|gb|ACL85641.1| RluA-2-PA [synthetic construct]
 gi|220955960|gb|ACL90523.1| RluA-2-PA [synthetic construct]
          Length = 547

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 115/268 (42%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD + +  +        ++ L +G++ V+ ++V  + +I+   +         L +++  
Sbjct: 157 LDVFVRE-FRAAPPEEYERSLEAGKLTVNSEKVPKDYKIKHNDL---------LANVVHR 206

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +          ++Y D  I V NKPA I V       ++   F+ +  +  
Sbjct: 207 HEVPVTSQPI---------KIVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEHN 256

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
            +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    EC  
Sbjct: 257 LKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIRTRQVQKEYVCRVEGRFPDGIVECNE 316

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  ++ +  +        +P TGR HQ+RVH 
Sbjct: 317 KIDVVSYKIG-----VCKVSPKGKDCKTTFKRIGEVGSDSIVL--CKPLTGRMHQIRVHL 369

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
             +G PI  D  Y     G    P++ +
Sbjct: 370 QFLGYPISNDPLYNHEVFG----PLKGR 393


>gi|219115441|ref|XP_002178516.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217410251|gb|EEC50181.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 240

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 104/237 (43%), Gaps = 25/237 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQETSGILV 159
           +LY D  I V NKP+GI    G      I   +   ++        + HR+D +TSG+LV
Sbjct: 3   ILYCDEHICVVNKPSGILSVPGPRRNPSIANLVYEILNPPIDIDQMVVHRIDMDTSGVLV 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A T  A + L + FR RR++K Y +L+ G  +   +   +  L++      ++    + 
Sbjct: 63  FALTELALRQLHDDFRSRRVKKTYEALLAGHFRKATQVEIDVALERDPYHPPFMRRYWEP 122

Query: 220 EKGANYAISH---FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           ++ A Y+      ++           + M PHTGRTHQLRVHA  +G PI+GD  Y    
Sbjct: 123 QRSATYSRQFSQIYQPSAQAHLPVSRVHMSPHTGRTHQLRVHAAALGYPIIGDDIYGFEG 182

Query: 277 KGN-------FTSPIQNKL-------------YLHARYMDLPHPEGG-RLQITAPLP 312
           +G+           I N++              LHA+ + + HP  G  +      P
Sbjct: 183 EGDCGVNSTILDQLIPNRMSLHQQLQELQLPLCLHAKQLCIFHPFSGAPMIFECEAP 239


>gi|160936866|ref|ZP_02084231.1| hypothetical protein CLOBOL_01755 [Clostridium bolteae ATCC
           BAA-613]
 gi|158440247|gb|EDP17993.1| hypothetical protein CLOBOL_01755 [Clostridium bolteae ATCC
           BAA-613]
          Length = 274

 Score =  145 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 63/279 (22%), Positives = 123/279 (44%), Gaps = 45/279 (16%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD--------------SKGQKP 144
             +LYED  I V  KPAG+  Q   G A  +   ++ ++               ++    
Sbjct: 2   VPILYEDKDIIVVQKPAGLESQVSRGFAPDMVSEIRRYLHNPQDIHNHPQGVSTAQPPYV 61

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HRLD+   GI+V A  + +A  L+ + +  +I+K Y ++V G P +K+    ++L  
Sbjct: 62  GVIHRLDKPVEGIMVYALNQKSAASLSAALQAGKIKKSYLAVVCGKPVDKQGTYVDYL-- 119

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVH 258
           +     +   +V ++++ +  A+ +++V++              ++++  TGR HQ+RV 
Sbjct: 120 RHCKENNTSKIVDKSDENSKKAVLNYRVLEVINNPKNQEQILSLIDIELLTGRHHQIRVQ 179

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNK-------------LYLHARYMDLPHPEGGR- 304
                 P+ GD +Y        T+   ++             L L AR +  PHP  G+ 
Sbjct: 180 FAGHATPLYGDERYGGGLSTKSTTMTVDRGRKKSSFGDAHRPLALCARRLAFPHPSTGKI 239

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQ 343
           ++ +      MV +  +  +  DR    ++L SQ EC +
Sbjct: 240 MEFS------MVPSSGAFAWFPDR---ARKLISQSECDK 269


>gi|320544924|ref|NP_001188782.1| RluA-2, isoform B [Drosophila melanogaster]
 gi|318068416|gb|ADV37032.1| RluA-2, isoform B [Drosophila melanogaster]
          Length = 583

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 115/268 (42%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD + +  +        ++ L +G++ V+ ++V  + +I+   +         L +++  
Sbjct: 193 LDVFVRE-FRAAPPEEYERSLEAGKLTVNSEKVPKDYKIKHNDL---------LANVVHR 242

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +          ++Y D  I V NKPA I V       ++   F+ +  +  
Sbjct: 243 HEVPVTSQPI---------KIVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEHN 292

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
            +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    EC  
Sbjct: 293 LKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIRTRQVQKEYVCRVEGRFPDGIVECNE 352

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  ++ +  +        +P TGR HQ+RVH 
Sbjct: 353 KIDVVSYKIG-----VCKVSPKGKDCKTTFKRIGEVGSDSIVL--CKPLTGRMHQIRVHL 405

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
             +G PI  D  Y     G    P++ +
Sbjct: 406 QFLGYPISNDPLYNHEVFG----PLKGR 429


>gi|328351783|emb|CCA38182.1| hypothetical protein PP7435_Chr2-0494 [Pichia pastoris CBS 7435]
          Length = 327

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 50/201 (24%), Positives = 89/201 (44%), Gaps = 9/201 (4%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFL 133
           + +IK    + ++ +  +    +   ++Y+D  I V NKP G+ V   G      +   +
Sbjct: 49  STLIKSGDCVVNTEHKHEPEVGIGEEIVYQDDNILVVNKPCGVPVHPTGKYYYNTMTEIM 108

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+ +      P   HRLD+ TSGIL++ +T  AA       +   IQK Y + V G    
Sbjct: 109 KNELGVSSLYP--CHRLDRLTSGILIIGKTPRAAAKYQTQLKQNSIQKTYIARVDGEFPM 166

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRT 252
                ++ ++   +I           E     A+++F+ +    +     ++  P TGRT
Sbjct: 167 GNIVCSDKIV---NIDCKRGKENGITEP--KEALTNFQRLAYSTSLNQSIVKCSPKTGRT 221

Query: 253 HQLRVHALHMGCPIVGDHKYC 273
           HQ+R+H  ++G PI  D  Y 
Sbjct: 222 HQIRIHLRNLGHPIANDPLYG 242


>gi|313683666|ref|YP_004061404.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
 gi|313156526|gb|ADR35204.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
          Length = 305

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 73/318 (22%), Positives = 128/318 (40%), Gaps = 48/318 (15%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +  N    ++    Q+++  G++  +   +        G    I                
Sbjct: 19  FLMNEL-GLSRSEGQRLIARGRLSQNGSVMDDQFGFIEGDCEFICF-------------- 63

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQ 142
                      D      ++  +   +++KP+G+SV        Y ++  +K      G 
Sbjct: 64  ---------EPDTRGFKPMFVANDFVIYDKPSGLSVHPHSRQSPYTLNDEIKH---QFGD 111

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +   THR+DQETSG+++V+R + +   L   F  R I K Y ++V G  ++  + I   L
Sbjct: 112 EANATHRIDQETSGLVLVSRHKKSESVLKRLFSERAITKRYLAMVKGCVEHPID-IQEPL 170

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALH 261
            +K H       VVK + KG   A +    +  F +     +E  P TGRTHQ+RVH  H
Sbjct: 171 YRKDHPNLLISMVVKVDPKG-KPAHTVINPLRYFPEHDMTLVEASPLTGRTHQIRVHLFH 229

Query: 262 MGCPIVGDHKYCA------NFKGNFTSPIQN-------KLYLHARYMDLPHPEGGRLQIT 308
           +  PI+GD  Y         F     SPI+        +L LHA  ++  + E    ++ 
Sbjct: 230 VKHPIIGDPVYGPTEENVIRFIKKELSPIERMEIGGSTRLLLHAHSLEFEY-ENEVYKVE 288

Query: 309 APLPAHMVK-TWDSLGFK 325
           +      VK  ++++G  
Sbjct: 289 SE--KDFVKECFEAMGIS 304


>gi|254569206|ref|XP_002491713.1| Mitochondrial tRNA pseudouridine synthase involved in
           pseudouridylation of mitochondrial tRNAs [Pichia
           pastoris GS115]
 gi|238031510|emb|CAY69433.1| Mitochondrial tRNA pseudouridine synthase involved in
           pseudouridylation of mitochondrial tRNAs [Pichia
           pastoris GS115]
          Length = 358

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 50/201 (24%), Positives = 89/201 (44%), Gaps = 9/201 (4%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFL 133
           + +IK    + ++ +  +    +   ++Y+D  I V NKP G+ V   G      +   +
Sbjct: 80  STLIKSGDCVVNTEHKHEPEVGIGEEIVYQDDNILVVNKPCGVPVHPTGKYYYNTMTEIM 139

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+ +      P   HRLD+ TSGIL++ +T  AA       +   IQK Y + V G    
Sbjct: 140 KNELGVSSLYP--CHRLDRLTSGILIIGKTPRAAAKYQTQLKQNSIQKTYIARVDGEFPM 197

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRT 252
                ++ ++   +I           E     A+++F+ +    +     ++  P TGRT
Sbjct: 198 GNIVCSDKIV---NIDCKRGKENGITEP--KEALTNFQRLAYSTSLNQSIVKCSPKTGRT 252

Query: 253 HQLRVHALHMGCPIVGDHKYC 273
           HQ+R+H  ++G PI  D  Y 
Sbjct: 253 HQIRIHLRNLGHPIANDPLYG 273


>gi|320544926|ref|NP_001188783.1| RluA-2, isoform C [Drosophila melanogaster]
 gi|318068417|gb|ADV37033.1| RluA-2, isoform C [Drosophila melanogaster]
          Length = 543

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 115/268 (42%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD + +  +        ++ L +G++ V+ ++V  + +I+   +         L +++  
Sbjct: 157 LDVFVRE-FRAAPPEEYERSLEAGKLTVNSEKVPKDYKIKHNDL---------LANVVHR 206

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +          ++Y D  I V NKPA I V       ++   F+ +  +  
Sbjct: 207 HEVPVTSQPI---------KIVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEHN 256

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
            +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    EC  
Sbjct: 257 LKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIRTRQVQKEYVCRVEGRFPDGIVECNE 316

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  ++ +  +        +P TGR HQ+RVH 
Sbjct: 317 KIDVVSYKIG-----VCKVSPKGKDCKTTFKRIGEVGSDSIVL--CKPLTGRMHQIRVHL 369

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
             +G PI  D  Y     G    P++ +
Sbjct: 370 QFLGYPISNDPLYNHEVFG----PLKGR 393


>gi|192358936|ref|YP_001982457.1| ribosomal large subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
 gi|190685101|gb|ACE82779.1| ribosomal large subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
          Length = 212

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 62/201 (30%), Positives = 90/201 (44%), Gaps = 12/201 (5%)

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           NKP+G+    G G        L     +     R+ HRLDQ TSGI++        + LT
Sbjct: 19  NKPSGLLTVPGKGPENQH--CLYKQALAFNPNARIVHRLDQATSGIVMFPLNYPCLKQLT 76

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F  R I K Y ++V G+    +  +   L+           V  ++      A + +K
Sbjct: 77  HQFEARAIHKRYLAVVHGLVGQDEGEVTLPLICD-WPNRPRQKVCFEH---GKSAHTRYK 132

Query: 232 VIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           VI      +   LE++P +GRTHQLRVH L +G PI+GD  Y  +           +L L
Sbjct: 133 VIHRDQGLQQTRLELEPVSGRTHQLRVHMLSLGHPILGDRLYAPDE----IIAQAPRLLL 188

Query: 291 HARYMDLPHPEGGR-LQITAP 310
           HA+ + L HP   + L I AP
Sbjct: 189 HAQELWLNHPISAQPLHIKAP 209


>gi|283769208|ref|ZP_06342112.1| RNA pseudouridine synthase [Bulleidia extructa W1219]
 gi|283104184|gb|EFC05563.1| RNA pseudouridine synthase [Bulleidia extructa W1219]
          Length = 225

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 54/213 (25%), Positives = 93/213 (43%), Gaps = 18/213 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           ++YED+ + V  KP  +  Q  +     +   LK  +  + QKP      L HRLD+   
Sbjct: 7   IIYEDNHLLVVEKPVNVLSQADNSQEDDMVSRLKKLIKIRDQKPGQVFIGLVHRLDRPVG 66

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T   A  L++S R    +KIY ++V  +   ++  + ++L K S        V
Sbjct: 67  GLMVFAKTSKGASRLSDSIRCHTFKKIYLAIVDSVSLPQEGTLEDYLYKDSQKNR----V 122

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              + K    A  H++V+    +    + +   TGR HQ+RV       P+V D +Y  +
Sbjct: 123 FVVDAKKGKLARLHYQVL-AKKRGKSLVRIVLETGRPHQIRVQFASRNWPLVNDQRYHPH 181

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQI 307
                  P +  + L A  +  PHP     +  
Sbjct: 182 -------PNRGSICLFAYQLSFPHPTKREEISF 207


>gi|241764053|ref|ZP_04762092.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241366658|gb|EER61130.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 198

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 58/202 (28%), Positives = 90/202 (44%), Gaps = 14/202 (6%)

Query: 113 KPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           KPAG+    G G        L +          + HRLDQ TSG++++AR   A + L+ 
Sbjct: 4   KPAGLLCVPGRGPD--KQDCLSARAQQHWPGALIVHRLDQATSGLVLMARHIEAQRRLSH 61

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV--VKQNEKGANYAISHF 230
           +F  R++ K Y ++V G+          W      I  D+        +      +++ +
Sbjct: 62  AFADRQVHKRYQAVVQGLLSVDG----AWNEIDLPIAADWERRPLRVIDHALGKPSLTRW 117

Query: 231 KVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           + +   A+ +   +E++P TGRTHQLRVH   MG PI+GD  Y        T  +  +L 
Sbjct: 118 RALAQDAEAQTTRIELEPVTGRTHQLRVHLAAMGHPILGDALY----ADAATQAMAPRLL 173

Query: 290 LHARYMDLPHPEGGR-LQITAP 310
           LHA  +   HP  G      AP
Sbjct: 174 LHASALRFTHPVHGVACAFEAP 195


>gi|298694246|gb|ADI97468.1| probable RNA pseudoridylate synthase [Staphylococcus aureus subsp.
           aureus ED133]
          Length = 284

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 70/303 (23%), Positives = 124/303 (40%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPQE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++  L+  +LYED+ I +  KP   +        +            V  +
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCIPSREHPHESLIEQVLYHCQVHGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKGNLKKIYTCLVYG--KTHSSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|295090745|emb|CBK76852.1| ribosomal large subunit pseudouridine synthase D [Clostridium cf.
           saccharolyticum K10]
          Length = 266

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 64/251 (25%), Positives = 105/251 (41%), Gaps = 43/251 (17%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--------------------- 137
             ++YEDS+I V  KPAG+  Q        +   +++++                     
Sbjct: 2   VKIIYEDSEILVAEKPAGLESQASRKFEPDMVSEIRNYLVRSQKKREREQRRELSTKPST 61

Query: 138 ----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                +      + HRLD+  SG++V A+TR+AA  L+   +  R+ KIY ++V G P +
Sbjct: 62  SLSTPAAAPYVGVIHRLDKPVSGVMVYAKTRSAAAFLSRELQAHRVTKIYHAVVCGKPVD 121

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRT 252
                 + L         Y  +V +++K    A   ++V+    +     LE+Q  TGR 
Sbjct: 122 NVGNFVDNLYMNREEN--YSVLVDKSKKEGKRAELSYRVLSRAEEKNLTLLEIQLKTGRH 179

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGN-------------FTSPI-QNKLYLHARYMDLP 298
           HQ+RV     G PI GD +Y   F G              F +P  +  L L A  +  P
Sbjct: 180 HQIRVQLAGHGLPIWGDARYNPQFGGTLPVEEREEKGSESFRTPASRGPLALAAVSLSFP 239

Query: 299 HPEGG-RLQIT 308
           HP  G ++  +
Sbjct: 240 HPSSGKKMTFS 250


>gi|294794416|ref|ZP_06759552.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           3_1_44]
 gi|294454746|gb|EFG23119.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           3_1_44]
          Length = 300

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 58/320 (18%), Positives = 121/320 (37%), Gaps = 67/320 (20%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
               +L K+     + ++  +    + I  G  + I      ++H   E           
Sbjct: 6   YPRKSLVKLFEEKLIHINGHKATPKDAIYEGDEIWIAMAKEKIDHDPIE----------- 54

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHR 149
                +   +LYED+ + + +KP+G++V   S     +   +  +    G  +K R  +R
Sbjct: 55  -----MDLRILYEDTDLLIVDKPSGVTV--NSKDQVSLANGVAHYFKEHGIKRKVRFLNR 107

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK---- 205
           LD++T+G +V+A++  A     +       +K Y + V GI +  ++ +   + +     
Sbjct: 108 LDRDTTGCIVIAKSGLAQSIYQQQMDDNTFEKWYMATVEGIVEADEDSLVFPMERSVDGI 167

Query: 206 --------SHIGGDYVHVVKQNEKGANYAISHFK-------------------------- 231
                        D+  + + + +  + +++  K                          
Sbjct: 168 HYEVNPKGKETRTDFSVLCRHSSETVDNSVNKSKNSVDIAPKNVDINLGDVDKSNQNVDK 227

Query: 232 -VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
            V       +  + ++ +TG+THQ+RV   H+G P+VGD  Y A        P +    L
Sbjct: 228 TVYKSNKCGYSEVLVRLYTGKTHQIRVAFSHIGHPLVGDTLYGAQ-------PTEQPFQL 280

Query: 291 HARYMDLPHPEGG-RLQITA 309
            A+ +   H   G R+ +TA
Sbjct: 281 RAQKVVFTHMRTGERITVTA 300


>gi|194862296|ref|XP_001969969.1| GG23644 [Drosophila erecta]
 gi|190661836|gb|EDV59028.1| GG23644 [Drosophila erecta]
          Length = 537

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 116/268 (43%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD + +  +        ++ L +G++ V+ ++V  + +I+   +         L +++  
Sbjct: 157 LDVFVRE-FRAAPPEEYERSLEAGKLTVNYEKVPKDYKIKHNDL---------LANVVHR 206

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +          ++Y D  I V NKPA I V       ++   F+ +  +  
Sbjct: 207 HEVPVTSQPI---------KIVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEHN 256

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
            +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    EC  
Sbjct: 257 LKNLRTIHRLDRLTSGLLLFGRTAERARELELQIRTRQVQKEYVCRVEGRFPDGIVECNE 316

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  ++ +  +        +P TGR HQ+RVH 
Sbjct: 317 KIDVVSYKIG-----VCKVSPKGKDCKTTFKRIGEVGSDSIVL--CKPLTGRMHQIRVHL 369

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI  D  Y     G    P++ +
Sbjct: 370 QYLGYPISNDPLYNHEVFG----PLKGR 393


>gi|308813053|ref|XP_003083833.1| pseudouridine synthase family protein (ISS) [Ostreococcus tauri]
 gi|116055715|emb|CAL57800.1| pseudouridine synthase family protein (ISS) [Ostreococcus tauri]
          Length = 476

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 90/432 (20%), Positives = 148/432 (34%), Gaps = 137/432 (31%)

Query: 23  RWFKNHYPHINF------------VNLQKILRSGQVRV----------DKK--------R 52
           +W + H  H+                + K+ R  +VRV          D +        R
Sbjct: 47  QWLRKHLRHVPSDGERDFKGPHAGAAVFKLFRDRRVRVGTSAEDGRVPDGRLESARGLRR 106

Query: 53  VKFNNRIQSGQVVRIPPVIN-------ALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
                 +  G+ + +P   +         +    E  + D    L    + L++ + Y D
Sbjct: 107 ASRARTLTPGEFLCVPDGASGYWASWSDADQGGGENIMSDRDWAL---GEGLRARVRYRD 163

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
             + V +KP+G++   G+G    +     +      + P + HRLD++TSG+LV+ART  
Sbjct: 164 EHVVVVDKPSGLATVPGAGNEVSVYDLRHTL-----EAPYVVHRLDRDTSGVLVLARTSF 218

Query: 166 AAQHLTESFRMR------------------------RIQKIYWSLVWGIPK--NKKECIA 199
           AA  L   F+ +                         IQ+ YW++    P     +  I 
Sbjct: 219 AANKLNAMFQRKSKTDFAAVLRAEMELGKAPRYDDSEIQRTYWAICANPPPRGTLEGWID 278

Query: 200 NWLLKKSHIGG----------------------------DYVHVVKQNEKGANYAISHFK 231
             L       G                            ++  V K+    +  A + FK
Sbjct: 279 APLADTDEGDGRGDNVRLVGGWRVYDVQNGDVIVGAGEQEFARVNKEENVSSRAATTRFK 338

Query: 232 VIDCFA-QKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYCANFKG----------- 278
           V+          LE+ P TGR HQLRVH    +  PIVGD+KY    K            
Sbjct: 339 VLASAGDDGPTLLELVPITGRKHQLRVHLSKALSSPIVGDYKYGFTDKQKPWRARFAEIE 398

Query: 279 -----NFTSPIQNK-------------------LYLHARYMDLPHPEGGR-LQITAPLPA 313
                  +S   ++                   L+LHA  +   HPEG R +++ A  P+
Sbjct: 399 RLERERASSAAADRDDVWRALRRDSLRGASKLPLHLHAHSIKFSHPEGDRSVRVVAEPPS 458

Query: 314 HMVKTWDSLGFK 325
             V+  D+ G  
Sbjct: 459 SFVQALDAFGLS 470


>gi|297619316|ref|YP_003707421.1| pseudouridine synthase [Methanococcus voltae A3]
 gi|297378293|gb|ADI36448.1| pseudouridine synthase [Methanococcus voltae A3]
          Length = 372

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 59/336 (17%), Positives = 121/336 (36%), Gaps = 55/336 (16%)

Query: 28  HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
               ++  ++ K  ++  + V+ K +   ++I+  + + I          + +    D +
Sbjct: 42  QIIGLSRKSINKFDKNKYILVNNKYISLKSKIKDNETITIY---------LGKNIETDEN 92

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--AYHIDGFLKSWVDSKGQ--- 142
           +      D     ++YED  I V NKP  + V     I      +  +     +K +   
Sbjct: 93  LINNTELDNTPMDIMYEDMDILVVNKPKNMVVHPTKTIKSGTLANAIMDYQNHNKSESER 152

Query: 143 -KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK------- 194
            K R  +R+D +T+GI+++A+   A Q +   F+   ++K Y +++ G            
Sbjct: 153 FKIRFINRIDMDTTGIVLIAKNSFAHQKIANQFQGC-MKKEYLAVISGNMDVDNLDTNLN 211

Query: 195 ------------KECIANWLLKKSHI----GGDYVHVVKQNEKGANYAISHFKVIDC--- 235
                        E     L  +  I       +  ++   +       ++F++I     
Sbjct: 212 NSLDTELNNNLNDEKYNLPLNLRLKIYKENNSKFSVIIFDRDTDELIEHTNFEIIKNTKD 271

Query: 236 -----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
                       +  F  ++    TG+THQ+R H  ++G  IVGD  Y  N + N     
Sbjct: 272 TKDNKDNKDTEISNNFTLIKASLITGKTHQIRRHLAYLGFSIVGDELYTNNNELNDNFKN 331

Query: 285 QNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
            + L LH+      HP     +++    P       
Sbjct: 332 YS-LMLHSYKTTFIHPRTNELIELIEEPPKDFKILL 366


>gi|21282618|ref|NP_645706.1| hypothetical protein MW0889 [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49485783|ref|YP_043004.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|297208359|ref|ZP_06924789.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|300912435|ref|ZP_07129878.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|21204056|dbj|BAB94754.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49244226|emb|CAG42652.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|296887098|gb|EFH26001.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|300886681|gb|EFK81883.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH70]
          Length = 284

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 123/303 (40%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPRE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++  L+  +LYED+ I +  KP   +        +             + +
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQENGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+        ++      ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAKYGYIHHLFSKVN----LKKIYTCLVYG--KTHTSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|78213934|ref|YP_382713.1| pseudouridine synthase [Synechococcus sp. CC9605]
 gi|78198393|gb|ABB36158.1| probable pseudouridine synthase [Synechococcus sp. CC9605]
          Length = 315

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 62/309 (20%), Positives = 129/309 (41%), Gaps = 34/309 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V        +  W  + Y H +    Q+ + +G++  +   +  +  +Q G+ +      
Sbjct: 16  VPRAAAGNLVSDWLADRYRHSDAAVWQQRIAAGELDWNGALLCSDRALQGGEALCW---- 71

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +    L+ ++     +       +++D  + V NKP+G+ V  G G   H   
Sbjct: 72  -------RRPPWLEEAIPDQWDT-------IHDDGDLLVINKPSGLPVMPGGGFLRH--- 114

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKIYWSLV 187
            L + ++  G +P   HRL + TSG+ V A T       ++ FR     R++ + +   V
Sbjct: 115 TLMALLEPTGARP--VHRLGRFTSGLQVCACTPQTRALWSKQFRPDGGCRKVYQAWSQRV 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQ----NEKGANYAISHFKVIDCFAQKFCWL 243
            G+   +   +++ ++++ H    ++   +       +    A S F++++  A+     
Sbjct: 173 PGLELGQCLTVSSDVVERLHPLLGWIWGPEPLNDAPIRKRLSAHSEFELLERTAEGDRL- 231

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMD-LPHPE 301
           ++   TGR HQ+R+H   +G P++GD  Y  + +     +P      LHA  +  LPH  
Sbjct: 232 QVTITTGRPHQIRIHLAQLGSPLLGDPLYLPDREISASATPGDGGYRLHAWRLSGLPHLG 291

Query: 302 GGRLQITAP 310
               Q+  P
Sbjct: 292 DKTFQVNPP 300


>gi|47230110|emb|CAG10524.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 516

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 62/266 (23%), Positives = 117/266 (43%), Gaps = 28/266 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
              L   FK+ +   +    QK  + G++R++++ V                  + L+ +
Sbjct: 114 GKTLLEVFKSEFRAESIDYYQKAAKEGRIRLNEQAV------------------DDLSLV 155

Query: 78  IKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           ++    + ++V+  +     K + +L +D ++ V +KPA I V       +  +  +   
Sbjct: 156 LRNNDHMKNTVHRHEPPVVGKPLEVLVDDGEVLVVDKPASIPVHPCG--RFRHNTVIFIL 213

Query: 137 VDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               G  +    HRLD+ TSG+L+ ART   ++ L +  R R+++K Y   V G    ++
Sbjct: 214 GKELGISELHTVHRLDRLTSGVLLFARTLETSKKLDQLVRDRKLEKEYVCRVEGEFPEEE 273

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 +L  S      V + + + KG     + F+ +  F  K   +   P TGRTHQ+
Sbjct: 274 VICEQPILVVSF----KVGLCRVDPKG-KECRTVFQRL-SFNGKTSVVRCLPVTGRTHQI 327

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFT 281
           RVH  ++G PI+ D  Y ++  G   
Sbjct: 328 RVHLQYLGFPILNDPIYGSSAWGPHR 353


>gi|307243209|ref|ZP_07525382.1| RNA pseudouridine synthase [Peptostreptococcus stomatis DSM 17678]
 gi|306493470|gb|EFM65450.1| RNA pseudouridine synthase [Peptostreptococcus stomatis DSM 17678]
          Length = 226

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 60/227 (26%), Positives = 104/227 (45%), Gaps = 20/227 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           +   ++YED+ + V  KP  +  Q  +     +    K +V  K +KP      L HRLD
Sbjct: 1   MDLKVIYEDNHLLVVEKPVNVLSQADNTQDIDMVSMCKVYVKEKYKKPGNVYIGLVHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +   G++V A+T  AA  L++  R R ++K Y ++V G  +   +C+ ++L K +     
Sbjct: 61  RPVGGVMVFAKTSKAASRLSDQVRTRTMKKTYRTVVVGKCQKAGDCV-DYLYKNTKTN-- 117

Query: 212 YVHVVKQNEKGANYAISHFKVI-----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            V +V ++ K    A   +K +     D     +  LE+  HTGR HQ+RV       P+
Sbjct: 118 MVKIVDKSNKDGKMASLSYKKLGETYSDKDKLDYSLLEVDLHTGRPHQIRVQFSSRNHPL 177

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            GD +Y         S +  ++ L +  ++L HP     +   A +P
Sbjct: 178 YGDQRYSK------FSKVGQQIALWSARIELVHPTTKEVMAFEAKMP 218


>gi|195578239|ref|XP_002078973.1| GD23709 [Drosophila simulans]
 gi|194190982|gb|EDX04558.1| GD23709 [Drosophila simulans]
          Length = 541

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 116/268 (43%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD + +  +        ++ L +G++ V+ ++V  + RI+   +         L +++  
Sbjct: 157 LDVFVRE-FRAAPPEEYERSLEAGKLTVNSEKVPKDYRIKHNDL---------LANVVHR 206

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++  +S  +          +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 207 HEVPVTSQPI---------KIVFMDKDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEHN 256

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
            +  R  HRLD+ TSG+L+  RT   A+ L    R R++QK Y   V G  P    EC  
Sbjct: 257 LKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIRTRQVQKEYVCRVEGRFPDGIVECNE 316

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  ++ +  +        +P TGR HQ+RVH 
Sbjct: 317 KIDVVSYKIG-----VCKVSPKGKDCKTTFKRIGEVGSDSIVL--CKPLTGRMHQIRVHL 369

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI  D  Y     G    P++ +
Sbjct: 370 QYLGYPISNDPLYNHEVFG----PLKGR 393


>gi|328870665|gb|EGG19038.1| hypothetical protein DFA_02281 [Dictyostelium fasciculatum]
          Length = 579

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 62/259 (23%), Positives = 107/259 (41%), Gaps = 29/259 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           +D + K + PH     L +I +  G++ V+      +  I+SG             HI+ 
Sbjct: 157 IDMFMKEYRPH-PRE-LYEIKIAMGKILVNDLPTTADYVIKSGDT---------FKHIVH 205

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             +I             L+  L+ E     V +KP  I V       ++   FL +    
Sbjct: 206 RHEI---------DVLALEPTLIAETLDYLVVDKPPSIPVHPAGPYRHNSLTFLLAR-QF 255

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECI 198
                   HRLD+ TSG++V+A+   A+  L + F+   I KIY + V G  P  ++  +
Sbjct: 256 GYTNLLACHRLDRLTSGVVVLAKNSTASGRLGKVFKKGDIDKIYLAKVKGMFPYLEETMV 315

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRV 257
           A  ++  + I G     +   +     + + FK+     +     +  +P TGR HQ+R+
Sbjct: 316 AKPIMVLNEITG-----LGVEDARGKPSTTFFKLAHYNKESDTSIIWCRPITGRGHQIRI 370

Query: 258 HALHMGCPIVGDHKYCANF 276
           H   +G PI  D  Y  +F
Sbjct: 371 HLKSIGFPITNDPLYNDDF 389


>gi|319891978|ref|YP_004148853.1| hypothetical protein SPSINT_0688 [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317161674|gb|ADV05217.1| hypothetical protein SPSINT_0688 [Staphylococcus pseudintermedius
           HKU10-03]
 gi|323464932|gb|ADX77085.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           pseudintermedius ED99]
          Length = 284

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 53/300 (17%), Positives = 110/300 (36%), Gaps = 39/300 (13%)

Query: 27  NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
             +       +++    G + V+         +Q G ++ +       +  ++       
Sbjct: 20  QQFSKKTLSAIKQ---DGALLVNGTARTVRYSLQVGDILEVHLPTELPSSYLE------- 69

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQK-- 143
                         +LYED+ + +  KP+  +           +     + +  +G++  
Sbjct: 70  -------PYDAPLNILYEDTWLLIVAKPSHQNTAPSREHPHESLVEQALAHMQKRGERGI 122

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P +  RLD+ T GI+++A++R     + +    +     Y+  +       K  I   + 
Sbjct: 123 PHIVTRLDRNTMGIVIIAKSRHMHHLMNQCDIEK-----YYECICERVLTAKGEIDQPIA 177

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           + S    + +       +    A + +  +  F + + W  ++  TGRTHQ+RVH   +G
Sbjct: 178 RASDSIINRIV-----SEQGKRARTIYWPLKNF-KTYTWCRVKLETGRTHQIRVHFQWLG 231

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
            P+VGD  Y            Q +L   A  +   HP    RL I +  P H  +   +L
Sbjct: 232 APLVGDTLYG-----QAHHTYQTQLLKCA-EVRFVHPLTQERLTIKSEQP-HFEQLLTTL 284


>gi|283470219|emb|CAQ49430.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus ST398]
          Length = 284

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 123/303 (40%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   +    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARN--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPRE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++  L+  +LYED+ I +  KP   +        +            V  +
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQVHGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+        ++      ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVN----LKKIYTCLVYG--KTHTSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHGKIHGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|254671778|emb|CBA09633.1| pseudouridylate synthase, 23S RNA-specific [Neisseria meningitidis
           alpha153]
          Length = 231

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 61/223 (27%), Positives = 92/223 (41%), Gaps = 23/223 (10%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L+        NKP GISV    G                 +K  L HRLD++T GIL
Sbjct: 16  VEILFRHQDFVAINKPQGISVHRSDGEVSLTATLAAQL---GVEKVWLLHRLDKQTGGIL 72

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A    +A  L   F  R+++K Y +L    P  K+  I   + K          + K 
Sbjct: 73  LFALNSQSAAVLAAQFAERKMKKTYLALSDRKPSKKQGWIKGGMEKS------RRGMWKL 126

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                N A++ F  I   ++K     ++PHTG+THQLRV    +G PI+GD  Y      
Sbjct: 127 TRNMENIAVTQFFSI-RISEKMRLFILEPHTGKTHQLRVAMKSLGSPILGDRLYGGTESE 185

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
                     +L+A  +   + +   ++ITAPL       W +
Sbjct: 186 TT--------FLYAWKIQFTY-QQQEIEITAPL----KNAWQA 215


>gi|225076909|ref|ZP_03720108.1| hypothetical protein NEIFLAOT_01960 [Neisseria flavescens
           NRL30031/H210]
 gi|224951795|gb|EEG33004.1| hypothetical protein NEIFLAOT_01960 [Neisseria flavescens
           NRL30031/H210]
          Length = 216

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 55/198 (27%), Positives = 86/198 (43%), Gaps = 17/198 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++E     V NKP G+SV   S     +   L   +    ++  L HRLD+ TSG+L+
Sbjct: 3   DIVFEHEDFVVINKPCGVSVHSESEGDVCLTASLAQQL--GVERVWLVHRLDKATSGLLL 60

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R +A  L+  F  + ++K Y +L    P  K+  +      K  +        K  
Sbjct: 61  FALNRDSAAALSAQFAEKTMRKTYLALGTHKPAKKQGWV------KGGMARSRRGTWKLT 114

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N+A++ F              +QP TG+THQLRV    +G PI+GD  Y  +  G+
Sbjct: 115 RDEDNFAVTRFSS-QSLQPGLRLFVLQPFTGKTHQLRVAMKSIGSPILGDTLYGGDEAGH 173

Query: 280 FTSPIQNKLYLHARYMDL 297
                   L+LHA  +  
Sbjct: 174 --------LFLHAWRLVF 183


>gi|223939788|ref|ZP_03631659.1| pseudouridine synthase [bacterium Ellin514]
 gi|223891564|gb|EEF58054.1| pseudouridine synthase [bacterium Ellin514]
          Length = 269

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 59/258 (22%), Positives = 107/258 (41%), Gaps = 29/258 (11%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID--GFLKSWVDSKGQKPRL-- 146
            +  +F +  +LYED  +   +KP+ +            +    L + ++      +   
Sbjct: 11  PETREFWEISVLYEDEHLLAVDKPSKLLTSPDRYDPKRPNLMKLLHAGIERGTPWAKSRG 70

Query: 147 ------THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                  HRLD ETSG++++A+ +     +   F   +  K Y +LV   P+ K   +  
Sbjct: 71  LTYLMNAHRLDFETSGVILLAKDKPMLVAVANLFGSEKPVKTYSALVQRSPEEKSFEVDA 130

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L       G    +++ +EK    + + F++++ FA  +  L+ +P +GR HQ+RVH  
Sbjct: 131 KLAPHPVKLG----LIRVDEKNGKRSRTQFELVEKFA-GYSLLKCRPLSGRQHQIRVHLQ 185

Query: 261 HMGCPIVGDHKYCANF-------------KGNFTSPIQNKLYLHARYMDLPHP-EGGRLQ 306
           + G PIVGD  Y                       P+ +++ LHA  + L HP     ++
Sbjct: 186 YAGLPIVGDSLYGGQPLMLSSLKRDYRLKPNKTERPLLDRVSLHAEELSLVHPLTNAEIK 245

Query: 307 ITAPLPAHMVKTWDSLGF 324
           I AP P  +      L  
Sbjct: 246 IVAPWPKDLKVAVKYLRL 263


>gi|255532252|ref|YP_003092624.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
 gi|255345236|gb|ACU04562.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
          Length = 225

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 53/227 (23%), Positives = 94/227 (41%), Gaps = 8/227 (3%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKP G+ V   S      +  L+   D   +     HRLD++T G+L+ 
Sbjct: 4   IVYQDDHLIAINKPHGLLVHRSSIANDAKEFALQLLRDQVNRHVSPVHRLDRKTGGLLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +     + + F    +QK Y +++ G   ++         +   I   +   V    
Sbjct: 64  AFEKDVETAMQQKFMNGEVQKKYLAVLRGYAPDQMAIDYPLAKENGTIQEAFTAFV---- 119

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A            ++  +E  P TGR HQLR H  H+  PI+GD K+  N +  F
Sbjct: 120 -TLKRAELDIAFGKHPTSRYSLVEASPTTGRMHQLRKHFAHIFYPIIGDRKHGCNKQNKF 178

Query: 281 TSPIQN--KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGF 324
                +   + LHA  +   HP  G+ +Q+ A +    ++  D + +
Sbjct: 179 FKETWDMTTMLLHASELTFLHPVTGKQVQLKASVQTEFLRVMDLMKW 225


>gi|296086047|emb|CBI31488.3| unnamed protein product [Vitis vinifera]
          Length = 347

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 71/344 (20%), Positives = 116/344 (33%), Gaps = 70/344 (20%)

Query: 11  VVENDEENMRL-DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           VV   +  + L D +   H          + +  GQ+ VD   V      +++G      
Sbjct: 21  VVSASDSELTLIDYYSSKHKNSAPLQGWLQRINKGQITVDGTVVTEPKTILRAG------ 74

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                        K++   +   +        +LYED  +   NKP+G+ V  G      
Sbjct: 75  ------------SKLVYHRLPWQEPDAPYLLEILYEDDDVIALNKPSGLQVLPGGLFQQR 122

Query: 129 IDGFLKSWVDSKGQKP--------RLTHRLDQETSGILVVARTRAAAQHL---------- 170
                  W  +K               HRL + TSGIL+ A+T+ A   L          
Sbjct: 123 TVLTQLQWRANKQNSLPACQESHSVPVHRLGRGTSGILLCAKTKLAKTRLAAYFADGTSV 182

Query: 171 --------TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                    +S  MR+I KIY +LV GI    +  I   +    + G      V      
Sbjct: 183 VGGNRDADMKSRTMRKISKIYRALVNGILDKDEIVIEQPIGMVQYPGVAKGLYVA--SPS 240

Query: 223 ANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--------- 272
              A+S   +++   Q     ++++  +GR HQ+R+H   +G P++GD  Y         
Sbjct: 241 GKPALSKVSILERDVQGDHMIVQVEIQSGRPHQIRIHLSFIGHPLLGDPLYVPGGQPKCC 300

Query: 273 ------------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                           +     P     +LHA  + L HP    
Sbjct: 301 DAEFTNESYALDGGYQRPVKPVPGDCGYHLHAHQLVLSHPTTNE 344


>gi|157165235|ref|YP_001466990.1| RNA pseudouridine synthase family protein [Campylobacter concisus
           13826]
 gi|112800923|gb|EAT98267.1| hypothetical RNA pseudouridine synthase aq_1758 (RNA-uridine
           isomerase) (RNA pseudouridylate synthase) [Campylobacter
           concisus 13826]
          Length = 252

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 75/310 (24%), Positives = 120/310 (38%), Gaps = 65/310 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       +I+    ++++ SG V               GQ V I   + + N       
Sbjct: 8   KILAKQ-KNISNNEAKELIDSGLVY------------AKGQKVMIARALMSENTKF---- 50

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                       +  K  +++ED  +   NKPA I+ +  S I                 
Sbjct: 51  ---------SIEEMPKPSVIFEDENLIAINKPAAITSEKISQI----------------Y 85

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           K  L HRLD++TSG+L++ +    A      F+  +++KIY + V GI   +       L
Sbjct: 86  KFPLLHRLDKDTSGVLLLVKNDEFASLAINEFKKMKVEKIYVAAVRGIMSEEVVVNEPIL 145

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             K+  G        +  K    AIS    +    +K   +++   TGRTHQ+RVH   +
Sbjct: 146 TIKNKNG-----AFSKISKDGKEAISEISPLMVVGKK-TLVKVVIKTGRTHQIRVHLASL 199

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
             PIVGD KY  N          N+++LHA  + L        +  AP+P       +SL
Sbjct: 200 NLPIVGDEKYGKNRA--------NRMFLHAYSIALLD-----YKFKAPIPREF----NSL 242

Query: 323 GFKYDRNLYI 332
           GF+      I
Sbjct: 243 GFELSNKFEI 252


>gi|323440839|gb|EGA98547.1| RNA pseudoridylate synthase [Staphylococcus aureus O11]
 gi|323443872|gb|EGB01484.1| RNA pseudoridylate synthase [Staphylococcus aureus O46]
          Length = 284

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 123/303 (40%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPRE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++  L+  +LYED+ I +  KP   +        +               +
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+      H+   F    ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAK----YGHIHHLFSKGNLKKIYTCLVYG--KTHTSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|51246609|ref|YP_066493.1| ribosomal large subunit pseudouridine synthase D [Desulfotalea
           psychrophila LSv54]
 gi|50877646|emb|CAG37486.1| related to ribosomal large subunit pseudouridine synthase D
           [Desulfotalea psychrophila LSv54]
          Length = 238

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 52/239 (21%), Positives = 96/239 (40%), Gaps = 19/239 (7%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI-----DGFLKSWVDSKGQKP 144
             K        ++YED+ I + +K AG++         +        ++K  V     + 
Sbjct: 10  PPKKYQPRGLPIVYEDNDIILVDKVAGLATTSRDKDNENTAYFRLTNYVKKGVAKSSNRV 69

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L H +D+E SG+L+ A+T  A +HL +++        Y + V G+P   +  +   L +
Sbjct: 70  FLIHHVDKEASGLLIFAKTEKARRHLLDNWSD--FNVSYVAAVHGVPVQTEGVLRANLAE 127

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                   ++V    EK    A + + ++   A  +  L ++P T   HQ+RV     G 
Sbjct: 128 NM---IHKMYVTVAGEKT-RPAETEYSLLQHSA-NYSLLSLRPKTEVKHQVRVQLADKGH 182

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
            I+ D  Y              +L LHA ++ + HP     +   + +P H      +L
Sbjct: 183 SIIADKIYGVKSDE------MKRLALHAAHLTITHPHTKKEMSFESRVPGHFYALTAAL 235


>gi|33865271|ref|NP_896830.1| putative pseudouridylate synthase [Synechococcus sp. WH 8102]
 gi|33632440|emb|CAE07252.1| putative pseudouridylate synthase [Synechococcus sp. WH 8102]
          Length = 213

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 58/216 (26%), Positives = 93/216 (43%), Gaps = 18/216 (8%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           S      + + D  + V  KP+G+  Q G G   H+   L + +        L HRLD++
Sbjct: 5   SSPDDLTIAHWDPWLLVVLKPSGLLSQPGRGS--HLQDSLITRLQHWSGDHHLVHRLDRD 62

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++VAR   + +  +  F  RR+ K+Y + V G  + +   I + L +       Y 
Sbjct: 63  TSGLVLVARGLESLRRCSAIFAARRVNKLYEAEVVGQLQGR-GRIDSRLARLDRDPPRY- 120

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                +      + + ++V            ++P TGR+HQLR H   MG PIVGD  Y 
Sbjct: 121 ----GDHPKGRPSTTLWRVRARQPNSTQLW-LRPLTGRSHQLRAHLAGMGHPIVGDPIYG 175

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQIT 308
                            HAR +   HP  G RL+++
Sbjct: 176 EASTTPMRL--------HARALGFEHPFTGLRLRVS 203


>gi|291562536|emb|CBL41352.1| Pseudouridylate synthases, 23S RNA-specific [butyrate-producing
           bacterium SS3/4]
          Length = 266

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 64/252 (25%), Positives = 103/252 (40%), Gaps = 46/252 (18%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-------DSKGQKPRLTHRLDQE 153
           +LYED +I V  KPAG+  Q     A  +   +K  +         K     + HRLD+ 
Sbjct: 4   VLYEDDEILVVIKPAGVESQAAKRFAPDMVSEVKKHLVINKSCTPGKEPYVGVIHRLDKP 63

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
            SG++V A+T+ AA  L+E  +  +++KIY ++V G P N  +   ++++K     G+Y 
Sbjct: 64  VSGVMVYAKTKRAAAALSEQIQSHKMKKIYTAVVHGRPVNMVDNYVDYMVK--TPDGNYS 121

Query: 214 HVVKQNEKGANYAISHFKVIDC--------FAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            VV +   GA  A   ++V+            ++   + +   TGR HQ+RV   H G P
Sbjct: 122 QVVDKGITGAKKAELSYEVLKTIDGEAAGMPGKELSLVRVALKTGRHHQIRVQMAHHGTP 181

Query: 266 IVGDHKYCA------------------NFKGNFTSPIQNK----------LYLHARYMDL 297
           + GD KY                       GN   P              + L A  ++ 
Sbjct: 182 LYGDMKYGVPVGTAKLDMKENADQGTMKAAGNRNMPGIRTAGNMGSGRESIALCASSLNF 241

Query: 298 PHPEG-GRLQIT 308
            HP     +   
Sbjct: 242 FHPVTKKEMTFE 253


>gi|319892885|ref|YP_004149760.1| ribosomal large subunit pseudouridine synthase D, YhcT
           [Staphylococcus pseudintermedius HKU10-03]
 gi|317162581|gb|ADV06124.1| ribosomal large subunit pseudouridine synthase D, YhcT
           [Staphylococcus pseudintermedius HKU10-03]
          Length = 276

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 57/280 (20%), Positives = 101/280 (36%), Gaps = 42/280 (15%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
            +    L  +  S  + V+ +       + +G  + IP                D     
Sbjct: 22  QLPKKELHTLNMSKSITVNDEAANLQTIVHTGDEIYIP----------------DEDAKS 65

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-----GSGIAYHIDGFLKSWVDSKGQKPR 145
                +  + + YED  + +  KP G+          + +  H+   L            
Sbjct: 66  QYLPSYRYAQIAYEDDFLAIVYKPKGVKTHPNDLKESNTLMNHVIYTLNH------PYVE 119

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLDQET G+L+VA+     + L        I +IY + V  +   K + I   + K 
Sbjct: 120 PIHRLDQETVGLLIVAKHPIIKKILDRMLENNDIHRIYKAQVKSLLPIKPQTIDLPIGKD 179

Query: 206 S-HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             H     V            A++H    +   +  C + ++  TGRTHQ+RVH   +G 
Sbjct: 180 KFHPNKRRV------SPTGQRAVTHILSSEMIEEGVCEVMLKLDTGRTHQIRVHLAEIGY 233

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           P++GD  Y  +           +L L +  +++ HP   +
Sbjct: 234 PVLGDPLYSDSK--------LRQLQLESYQIEMTHPITQQ 265


>gi|195578233|ref|XP_002078970.1| GD22253 [Drosophila simulans]
 gi|194190979|gb|EDX04555.1| GD22253 [Drosophila simulans]
          Length = 555

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 59/268 (22%), Positives = 112/268 (41%), Gaps = 32/268 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   ++      + +    + 
Sbjct: 133 LDIF-SREFRAHPAEEYERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQ- 190

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +++ D  I V NKPA I V       ++   F+ +  +  
Sbjct: 191 -----------------PIKIVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 232

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V G+ P    EC  
Sbjct: 233 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGVFPDGIVECKE 292

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K + KG +   +  K+          +  +P TGR HQ+RVH 
Sbjct: 293 PIEVVSYKIG-----VCKVSPKGKDCTTTFQKL--SQNGTTSVVLCKPLTGRMHQIRVHL 345

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++G PI+ D  Y     G    P++ +
Sbjct: 346 QYLGYPILNDPLYNHEVFG----PLKGR 369


>gi|121635675|ref|YP_975920.1| putative psedouridine synthase [Neisseria meningitidis FAM18]
 gi|254804170|ref|YP_003082391.1| pseudouridylate synthase, 23S RNA-specific [Neisseria meningitidis
           alpha14]
 gi|120867381|emb|CAM11153.1| putative psedouridine synthase [Neisseria meningitidis FAM18]
 gi|254667712|emb|CBA03587.1| pseudouridylate synthase, 23S RNA-specific [Neisseria meningitidis
           alpha14]
 gi|308390117|gb|ADO32437.1| pseudouridylate synthase [Neisseria meningitidis alpha710]
          Length = 236

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 64/212 (30%), Positives = 98/212 (46%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 23  ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 78

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R +A  L+  F  + I+K Y +L    P  K+  I   + K          + K  
Sbjct: 79  FALNRESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGMEK------SRRGMWKLT 132

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 133 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTESET 191

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 192 --------MFLYAWKIQFAY-QNRQIEIVAPL 214


>gi|326499976|dbj|BAJ90823.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326504092|dbj|BAK02832.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 389

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 125/326 (38%), Gaps = 73/326 (22%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +R+GQ+ VD + V   + I                 + +  K++   ++  +        
Sbjct: 67  IRNGQITVDGQVVTDPDII-----------------LSEGSKLVYHRLSWKEPFAPYLLQ 109

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ------------KPRLTH 148
           +LYED  +   NKP+G+ V                W + K               P   H
Sbjct: 110 VLYEDDDMLALNKPSGLQVLPKGLFQQRTVLAQLQWKEWKMPPSSCSKKKNVQLHPVPVH 169

Query: 149 RLDQETSGILVVARTRAAAQHL-----------------TESFRMRRIQKIYWSLVWGIP 191
           RL + TSG+L+ A+T+ A   L                 TE  +  +I K Y +LV GI 
Sbjct: 170 RLGRGTSGLLLCAKTKLAKVQLASYFAEGAANAEKKRDGTEVGKEWKISKFYRALVTGIL 229

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTG 250
           ++ ++ I   +    + G      V  +      A+S   V++  A Q    ++++ H+G
Sbjct: 230 EHDEDVITQPIGLVHYPGVAEGLYVACSS--GKPAMSKVCVLERLAHQNQTLVQVEIHSG 287

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-----------------------PIQNK 287
           R HQ+R+H  ++G P+V D  Y    +  F                         P    
Sbjct: 288 RPHQIRIHLAYIGHPLVDDPLYGIGGQPKFHDLEPTSTDISFAYDGGYERPLQPVPGDCG 347

Query: 288 LYLHARYMDLPHPEGGRL-QITAPLP 312
            +LHA ++ L HP   ++ +ITA LP
Sbjct: 348 YHLHAHWLVLCHPTTNKMLKITAHLP 373


>gi|241766964|ref|ZP_04764762.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241362555|gb|EER58438.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 224

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 59/224 (26%), Positives = 96/224 (42%), Gaps = 23/224 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ D  +    KPAG  V      A      +++  +  GQ     HRLD+ T G+LV+
Sbjct: 6   ILWRDEHLVAVYKPAGWLVHRTGLDAGETRFVMQALRNQLGQHVFPVHRLDKGTCGVLVM 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI---------ANWLLKKSHIG-G 210
           A    AA+ L+++F  +   K Y +LV G    + E           A+  ++ +H    
Sbjct: 66  ALHSDAARALSQAFEQQATTKRYLALVRGWAPARAEVDHALKPDDAPAHAPVQDAHTRFR 125

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               +V      A +A +              +E  P TGR HQ+R H  H+  PI+GD 
Sbjct: 126 RLAQLVLPEPSDARFATTR----------ASLVEAVPTTGRRHQIRRHLKHLAHPIIGDA 175

Query: 271 KYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-RLQITAPL 311
            +       + +      +L+LHA  + +PHP  G RL + + L
Sbjct: 176 THGKGPLNRWWAERLGHQRLWLHAWQLTVPHPVTGARLTLDSGL 219


>gi|328721920|ref|XP_001945972.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Acyrthosiphon pisum]
          Length = 565

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 55/240 (22%), Positives = 96/240 (40%), Gaps = 28/240 (11%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           +  G + ++ +RV  +  ++   +         L +++   ++  +S  +          
Sbjct: 172 IEKGSLTINNERVSPDYVLKHNDL---------LANVVHRHEVPVASSTID--------- 213

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILV 159
           +++ D  I V NKP+ I V       Y  +  +       G +  +  HRLD+ TSG+L+
Sbjct: 214 VIHLDDDIVVVNKPSSIPVHPCG--RYRHNTMVFVLAKEYGLRDLKTIHRLDRLTSGVLM 271

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             RT+  A+ L    R R + K Y   V G      EC     +    IG      V + 
Sbjct: 272 FGRTQNRARTLEAQIRDRVVNKQYVCRVEGKFPESVECEQPIEVISYKIG------VCKV 325

Query: 220 EKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                   + F++I    Q     +  +P +GR HQ+RVH  ++G PI  D  Y     G
Sbjct: 326 SPNGKQCSTSFQLIGYNEQANTSVVLCKPRSGRMHQIRVHLQYLGHPIQNDPLYNDTVFG 385


>gi|320168624|gb|EFW45523.1| RNA pseudouridylate synthase domain-containing protein 2
           [Capsaspora owczarzaki ATCC 30864]
          Length = 515

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 97/241 (40%), Gaps = 27/241 (11%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           + +R G+V V+ K V  +  IQ   V+              E  +  + +          
Sbjct: 145 QAIRDGRVTVNGKVVAPSYIIQDSDVLVHTAHR-------HEPPVTAAPI---------- 187

Query: 99  SILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
             ++ E   + V +KPA I V   G    + +   +KS  +         HRLD+ TSG+
Sbjct: 188 -RVIAETDDLVVIDKPASIPVHVAGRFNVHTVISIMKS--EMGYSNLLGCHRLDRLTSGV 244

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           LV+A+ RAAA  +T     R ++K Y   V G+   ++      LL            + 
Sbjct: 245 LVMAKNRAAAAAVTRLITEREVEKFYICRVTGVFPQEQVTCTEPLL-----SFCPKFGLN 299

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             +     A + F V +        ++  P TGR HQ+RVH  ++G PI  D  Y +   
Sbjct: 300 GVDPSGKPAETVF-VREQTNGVISIVKCFPKTGRAHQIRVHLQYLGYPIENDPIYNSPAF 358

Query: 278 G 278
           G
Sbjct: 359 G 359


>gi|313665599|ref|YP_004047470.1| pseudouridine synthase, RluA family [Mycoplasma leachii PG50]
 gi|312949399|gb|ADR23995.1| pseudouridine synthase, RluA family [Mycoplasma leachii PG50]
          Length = 302

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 62/303 (20%), Positives = 136/303 (44%), Gaps = 38/303 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +   +V  +++N  L ++ K  +       + K +R+  ++++ KR+   N  ++   ++
Sbjct: 1   MTKFIVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRINDKNYLLKVNDII 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +    ++   II++Q    S+VNL          ++YED+ I + NK   + +     +
Sbjct: 61  EVY---DSNKPIIRDQFNYISNVNLD---------IVYEDNNILIVNKSNNLEMHSTYNL 108

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +D  +KS++  K +              HRLD+ TSG+++ A+ + ++  LT +F+ 
Sbjct: 109 --CLDDMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSTILTNAFKS 166

Query: 177 R-RIQKIYWSLV-WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             +I K Y++L  +    N    +  ++   S+       +V++N     Y  + FK+I+
Sbjct: 167 NDQINKYYYALTSYDWNLNDFLQVNGYISYDSNTQKADFSLVEKN--NYKYCQTEFKLIN 224

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                   + ++  TG+ HQ+R        PI+ D +Y    + +     Q  +YL A  
Sbjct: 225 KN-----LILVKLITGKKHQIRSVLSFYNNPILNDFRYNGKKEND-----QKMIYLAAFK 274

Query: 295 MDL 297
           ++ 
Sbjct: 275 IEF 277


>gi|302332618|gb|ADL22811.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus JKD6159]
          Length = 284

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 121/303 (39%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPQE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++   K  +LYED+ I +  KP   +        +               +
Sbjct: 63  -IPSVNLIPYAR--KVEVLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+        ++      ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAKYGHIHHLFSK----GNLKKIYTCLVYG--KTHTSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|323464082|gb|ADX76235.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus pseudintermedius ED99]
          Length = 276

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 57/280 (20%), Positives = 101/280 (36%), Gaps = 42/280 (15%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
            +    L  +  S  + V+ +       + +G  + IP                D     
Sbjct: 22  QLPKKELHTLNMSKSITVNDEAANLQTIVHTGDEIYIP----------------DEDAKS 65

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-----GSGIAYHIDGFLKSWVDSKGQKPR 145
                +  + + YED  + +  KP G+          + +  H+   L            
Sbjct: 66  QYLPSYRYAQIAYEDDFLAIVYKPKGVKTHPNDLKESNTLMNHVIYTLNH------PYVE 119

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLDQET G+L+VA+     + L        I +IY + V  +   K + I   + K 
Sbjct: 120 PIHRLDQETVGLLIVAKHPIIKKILDRMLENNDIHRIYKAQVKSLLPIKPQTIDLPIGKD 179

Query: 206 S-HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             H     V            A++H    +   +  C + ++  TGRTHQ+RVH   +G 
Sbjct: 180 KFHPNKRRV------SPTGQRAVTHILSSEMIEEGVCEVMLKLDTGRTHQIRVHLAEIGY 233

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           P++GD  Y  +           +L L +  +++ HP   +
Sbjct: 234 PVLGDPLYSDSK--------LRQLQLESYQIEMTHPITQQ 265


>gi|283798477|ref|ZP_06347630.1| ribosomal large subunit pseudouridine synthase family protein
           [Clostridium sp. M62/1]
 gi|291073736|gb|EFE11100.1| ribosomal large subunit pseudouridine synthase family protein
           [Clostridium sp. M62/1]
          Length = 266

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 63/251 (25%), Positives = 104/251 (41%), Gaps = 43/251 (17%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--------------------- 137
             ++YEDS+I V  KPAG+  Q        +   +++++                     
Sbjct: 2   VKIIYEDSEILVAEKPAGLESQASRKFEPDMVSEIRNYLVRSQKKREREQRRELSTKPST 61

Query: 138 ----DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                +      + HRLD+  SG++V A+TR+AA  L+   +  R+ KIY ++V G P +
Sbjct: 62  SLSTPAAAPYVGVIHRLDKPVSGVMVYAKTRSAAAFLSRELQAHRVTKIYHAVVCGKPVD 121

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRT 252
                 + L         Y  +V +++K    A   ++V+    +     LE+Q  TGR 
Sbjct: 122 NVGNFVDNLYMNREEN--YSVLVDKSKKEGKRAELSYRVLSRAEEKNLTLLEIQLKTGRH 179

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGN-------------FTSPI-QNKLYLHARYMDLP 298
           HQ+RV     G PI GD +Y   F G              F +P  +  L L A  +   
Sbjct: 180 HQIRVQLAGHGLPIWGDARYNPQFGGTLPVEEREEKGSESFRTPASRGPLALAAVSLSFT 239

Query: 299 HPEGG-RLQIT 308
           HP  G ++  +
Sbjct: 240 HPSSGKKMTFS 250


>gi|225449104|ref|XP_002276664.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 348

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 71/345 (20%), Positives = 116/345 (33%), Gaps = 71/345 (20%)

Query: 11  VVENDEENMRL-DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP 68
           VV   +  + L D +   H          + +  GQ+ VD   V      +++G      
Sbjct: 21  VVSASDSELTLIDYYSSKHKNSAPLQGWLQRINKGQITVDGTVVTEPKTILRAG------ 74

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                        K++   +   +        +LYED  +   NKP+G+ V  G      
Sbjct: 75  ------------SKLVYHRLPWQEPDAPYLLEILYEDDDVIALNKPSGLQVLPGGLFQQR 122

Query: 129 IDGFLKSWVDSKGQKP--------RLTHRLDQETSGILVVARTRAAAQHL---------- 170
                  W  +K               HRL + TSGIL+ A+T+ A   L          
Sbjct: 123 TVLTQLQWRANKQNSLPACQESHSVPVHRLGRGTSGILLCAKTKLAKTRLAAYFADGTSV 182

Query: 171 ---------TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
                     +S  MR+I KIY +LV GI    +  I   +    + G      V     
Sbjct: 183 VGGNRLDADMKSRTMRKISKIYRALVNGILDKDEIVIEQPIGMVQYPGVAKGLYVA--SP 240

Query: 222 GANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-------- 272
               A+S   +++   Q     ++++  +GR HQ+R+H   +G P++GD  Y        
Sbjct: 241 SGKPALSKVSILERDVQGDHMIVQVEIQSGRPHQIRIHLSFIGHPLLGDPLYVPGGQPKC 300

Query: 273 -------------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                            +     P     +LHA  + L HP    
Sbjct: 301 CDAEFTNESYALDGGYQRPVKPVPGDCGYHLHAHQLVLSHPTTNE 345


>gi|182414459|ref|YP_001819525.1| pseudouridine synthase [Opitutus terrae PB90-1]
 gi|177841673|gb|ACB75925.1| pseudouridine synthase [Opitutus terrae PB90-1]
          Length = 279

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 57/277 (20%), Positives = 99/277 (35%), Gaps = 21/277 (7%)

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           P             + +         ++ L++ +++ED ++ V  KP  +          
Sbjct: 10  PLPEIMSRRACAWPRRMQQGPARLITAEELRTWIVHEDERLLVVAKPGDVVCHPSKAGP- 68

Query: 128 HIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                + +  +  G     L  RLD+ETSGI+V+A+    A  L  + + R+I K Y ++
Sbjct: 69  -WSSLVGAVREFTGLATVHLVFRLDRETSGIVVLAKDPKTASRLQVAMQERKIGKAYVAI 127

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEM 245
           + G  +     +   L          V V          +++HF  I   A   F  + +
Sbjct: 128 LTGAMREP-VTVDQPLGDDV---ASPVFVKSAVRADGQRSVTHFSPITVAADDAFSLVRV 183

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK------------GNFTSPIQNKLYLHAR 293
              TGR HQ+R HA  +G  +VGD  Y  + +                  +  +  LH  
Sbjct: 184 VTETGRKHQIRAHAQWLGHSLVGDKIYGPDARCYLDFIDTGWTPALADKLLLPRQALHCA 243

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
            +DL    G      AP+   M +     G      L
Sbjct: 244 EIDLTR-TGLAHVFRAPMAEDMRRFCAERGIVAPAEL 279


>gi|213860017|ref|ZP_03385721.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
          Length = 238

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 51/207 (24%), Positives = 92/207 (44%), Gaps = 17/207 (8%)

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +++  D  GQ     HRLD+ TSG+L++  +  A + L + F    I+K Y ++V G  
Sbjct: 13  VMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAGRRLAQQFEQHHIRKRYHAIVRGWL 72

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI----------DCFAQKFC 241
            +        + ++  I   +       +K    A++ ++ +               ++ 
Sbjct: 73  IDDAVLDYPLVEERDKIADKFAR----EDKAPQPAVTQYRGLATVEMAVPTGRYPTTRYG 128

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPH 299
            +E++P TGR HQLR H  H+  PI+GD K+      +         +L LHA  ++L H
Sbjct: 129 LVELEPKTGRKHQLRRHLAHLRHPIIGDSKHGDLRQNRSAAEHFACRRLMLHASRLELTH 188

Query: 300 PEGGR-LQITAPLPAHMVKTWDSLGFK 325
           P  G+ L I A L    ++     G++
Sbjct: 189 PFTGQPLIIQAGLDETWMQVLTQFGWR 215


>gi|148267440|ref|YP_001246383.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150393493|ref|YP_001316168.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp.
           aureus JH1]
 gi|257795259|ref|ZP_05644238.1| pseudouridine synthase [Staphylococcus aureus A9781]
 gi|258406908|ref|ZP_05680061.1| pseudouridine synthase [Staphylococcus aureus A9763]
 gi|258421876|ref|ZP_05684797.1| pseudouridine synthase [Staphylococcus aureus A9719]
 gi|258446966|ref|ZP_05695119.1| pseudouridine synthase [Staphylococcus aureus A6300]
 gi|258449944|ref|ZP_05698042.1| pseudouridine synthase [Staphylococcus aureus A6224]
 gi|258455040|ref|ZP_05703003.1| pseudouridine synthase [Staphylococcus aureus A5937]
 gi|282927229|ref|ZP_06334851.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|295405811|ref|ZP_06815620.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|297245402|ref|ZP_06929273.1| RluA family pseudouridine synthase [Staphylococcus aureus A8796]
 gi|147740509|gb|ABQ48807.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus JH9]
 gi|149945945|gb|ABR51881.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus JH1]
 gi|257789231|gb|EEV27571.1| pseudouridine synthase [Staphylococcus aureus A9781]
 gi|257841447|gb|EEV65888.1| pseudouridine synthase [Staphylococcus aureus A9763]
 gi|257842209|gb|EEV66637.1| pseudouridine synthase [Staphylococcus aureus A9719]
 gi|257854298|gb|EEV77248.1| pseudouridine synthase [Staphylococcus aureus A6300]
 gi|257856864|gb|EEV79767.1| pseudouridine synthase [Staphylococcus aureus A6224]
 gi|257862920|gb|EEV85685.1| pseudouridine synthase [Staphylococcus aureus A5937]
 gi|282590918|gb|EFB95993.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|285816686|gb|ADC37173.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus 04-02981]
 gi|294969246|gb|EFG45266.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|297177705|gb|EFH36955.1| RluA family pseudouridine synthase [Staphylococcus aureus A8796]
 gi|315130414|gb|EFT86401.1| pseudouridine synthase, RluA family protein [Staphylococcus aureus
           subsp. aureus CGS03]
          Length = 284

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 125/303 (41%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPRE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQ 142
              SVNL  ++  L+  +LYED+ I +  KP   +       +   +   +       G+
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCTPSREHLHESLIEQVLYHCQEHGE 119

Query: 143 K--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+        ++      ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVN----LKKIYTCLVYG--KTHTSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|258423513|ref|ZP_05686403.1| conserved hypothetical protein [Staphylococcus aureus A9635]
 gi|257846214|gb|EEV70238.1| conserved hypothetical protein [Staphylococcus aureus A9635]
          Length = 284

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 122/303 (40%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPRE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++  L+  +LYED+ I +  KP   +        +               +
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+        ++      ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVN----LKKIYTCLVYG--KTHTSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|159482266|ref|XP_001699192.1| pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158273039|gb|EDO98832.1| pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 303

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 65/300 (21%), Positives = 115/300 (38%), Gaps = 30/300 (10%)

Query: 12  VENDEENMRLDRWFKNHYP-HINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPP 69
           ++       L  ++ + +P   N    +  +R+GQV V+  + V+    ++ G VV    
Sbjct: 25  IKGRHAGQTLIEFYTSVHPASANLSQWEVRIRNGQVAVNDVEAVEPTRVLRVGDVVSY-- 82

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                             +   +        ++YED+ +   +KP+G+ V   +   +H 
Sbjct: 83  ----------------RRLPWVEPPSPCHVDVVYEDADMVALSKPSGLQVLPAA--MFHQ 124

Query: 130 DGFLKSWVDSKGQK-PRLTHRLDQETSGI-LVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
              L      +    P   HRL + TSG          ++   + S     ++K Y +LV
Sbjct: 125 RTVLSLLRRRQYLDVPAPVHRLGRGTSGCGAAALAALISSAPASGSGCQLPLRKFYRALV 184

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G  K  +  +   +    H G D              A S ++   C   +   +E++ 
Sbjct: 185 QGRVKADQGRVDVPIGPIPHPGVDRGLFAA--TPDGKPAASVWR-AGCMEAECTLMEVEI 241

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPEGGR 304
            TGR HQ+R+H   MG P+VGD  Y A  +      +       YLH+  + LPHP  G+
Sbjct: 242 LTGRPHQIRIHMAAMGHPLVGDPLYGAGGRPKVRYRLYGSDCGYYLHSLELHLPHPITGQ 301


>gi|325127296|gb|EGC50231.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis N1568]
 gi|325131261|gb|EGC53972.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M6190]
 gi|325135413|gb|EGC58033.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M0579]
 gi|325201344|gb|ADY96798.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M01-240149]
 gi|325208870|gb|ADZ04322.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis NZ-05/33]
          Length = 217

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 64/212 (30%), Positives = 98/212 (46%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 4   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R +A  L+  F  + I+K Y +L    P  K+  I   + K          + K  
Sbjct: 60  FALNRESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGMEK------SRRGMWKLT 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 114 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTESET 172

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 173 --------MFLYAWKIQFAY-QNRQIEIVAPL 195


>gi|161869184|ref|YP_001598350.1| putative psedouridine synthase [Neisseria meningitidis 053442]
 gi|161594737|gb|ABX72397.1| putative psedouridine synthase [Neisseria meningitidis 053442]
          Length = 236

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 63/212 (29%), Positives = 98/212 (46%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 23  ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 78

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + +A  L+  F  + I+K Y +L    P  K+  I   + K          + K  
Sbjct: 79  FALNKESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGMEK------SRRGMWKLT 132

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 133 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTESET 191

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 192 --------MFLYAWRIQFAY-QNRQIEIVAPL 214


>gi|15923998|ref|NP_371532.1| hypothetical protein SAV1008 [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|15926596|ref|NP_374129.1| hypothetical protein SA0866 [Staphylococcus aureus subsp. aureus
           N315]
 gi|156979333|ref|YP_001441592.1| hypothetical protein SAHV_1002 [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253316169|ref|ZP_04839382.1| hypothetical protein SauraC_08502 [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
 gi|253731614|ref|ZP_04865779.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|255005796|ref|ZP_05144397.2| hypothetical protein SauraM_04985 [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|258435274|ref|ZP_05689013.1| conserved hypothetical protein [Staphylococcus aureus A9299]
 gi|258441486|ref|ZP_05690846.1| conserved hypothetical protein [Staphylococcus aureus A8115]
 gi|269202622|ref|YP_003281891.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282894033|ref|ZP_06302264.1| hypothetical protein SGAG_01384 [Staphylococcus aureus A8117]
 gi|296275572|ref|ZP_06858079.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus MR1]
 gi|13700811|dbj|BAB42107.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           N315]
 gi|14246778|dbj|BAB57170.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|156721468|dbj|BAF77885.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253724613|gb|EES93342.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|257848935|gb|EEV72918.1| conserved hypothetical protein [Staphylococcus aureus A9299]
 gi|257852276|gb|EEV76202.1| conserved hypothetical protein [Staphylococcus aureus A8115]
 gi|262074912|gb|ACY10885.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282763519|gb|EFC03648.1| hypothetical protein SGAG_01384 [Staphylococcus aureus A8117]
 gi|329728975|gb|EGG65387.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 284

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 122/303 (40%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPRE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++  L+  +LYED+ I +  KP   +        +               +
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+        ++      ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVN----LKKIYTCLVYG--KTHTSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|329770323|ref|ZP_08261706.1| hypothetical protein HMPREF0433_01470 [Gemella sanguinis M325]
 gi|328836681|gb|EGF86337.1| hypothetical protein HMPREF0433_01470 [Gemella sanguinis M325]
          Length = 254

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 62/272 (22%), Positives = 110/272 (40%), Gaps = 33/272 (12%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           + V+    K N  +    V+ +   ++  N++  +      S+++TK          YED
Sbjct: 10  ILVNNDIAKLNTSLAKNDVLELNIELSKSNYLTNK------SISITKE---------YED 54

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
             + + +KP GI            D  L +++ S  Q     HRLD +T G+++ ++T  
Sbjct: 55  PYLLIVSKPFGIKTHPNDISIE--DDTLVNYLISDYQYLEPIHRLDIDTCGLVIFSKTPL 112

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-AN 224
               L +  + R I++ Y +L     K K          K++IG D     K        
Sbjct: 113 IKSKLDQMLKNREIKRYYTALTKNNIKPK--------TIKTNIGRDIREKNKMAVTNKGK 164

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
            A ++    +   Q    + +   TGRTHQ+RVH   +G  I+GD  Y  +         
Sbjct: 165 QATTNILSCEKIDQNKFVVTISLETGRTHQIRVHLSSIGNAIIGDKLYSNDGYK------ 218

Query: 285 QNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
            +K+YL A  +   HP    +++I + L    
Sbjct: 219 YDKMYLGALKVVFNHPVTNDKIEINSSLRTEF 250


>gi|162454763|ref|YP_001617130.1| hypothetical protein sce6481 [Sorangium cellulosum 'So ce 56']
 gi|161165345|emb|CAN96650.1| hypothetical protein predicted by Glimmer/Critica [Sorangium
           cellulosum 'So ce 56']
          Length = 368

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 63/322 (19%), Positives = 110/322 (34%), Gaps = 27/322 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIP 68
           + +   +   RLD+      P +     +++   G+VRV    +     R   G V    
Sbjct: 57  ITITELDAGTRLDKLLVQLLPGLGRAGAKRLFSEGRVRVLGVGKSGAGRRASKGDV---- 112

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV---QGGSGI 125
               A   +++       +             ++ E   + V NKPAG+       G   
Sbjct: 113 ---AAAGEVLEVDVEPTEASGAATPDPSAPLDVVLERDDLVVVNKPAGVPTAPLHPGER- 168

Query: 126 AYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
               +  +  + +  G     ++P L HRLD +TSG+++ ART AA   L    +  R+ 
Sbjct: 169 GTVANALVARYPEMAGIGFSPREPGLCHRLDTDTSGLVLAARTAAAFAALGAGLKEGRLD 228

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDY---VHVVKQNEKGANYAISHFKVIDCFA 237
           K Y  +       +   I   L             +H           A + +K +    
Sbjct: 229 KRYLLICQIGDLPEMGSIEVPLAPHPKDKKRVYPCIHPRDVARYAPRPAATMYKRVRQVG 288

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +E +      HQ+R H   +G P+ GD  Y             ++  LHA Y+  
Sbjct: 289 LWE-LVEARAPRALRHQIRAHFASVGHPLAGDVLYGGP-----AVEGLSRHALHAHYIGW 342

Query: 298 PHPEGGR-LQITAPLPAHMVKT 318
              +      +T+ LPA M   
Sbjct: 343 GGSDAVPAFVVTSSLPADMAAL 364


>gi|49483170|ref|YP_040394.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257425058|ref|ZP_05601484.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257427722|ref|ZP_05604120.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257430357|ref|ZP_05606739.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257433061|ref|ZP_05609419.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257435958|ref|ZP_05612005.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M876]
 gi|282903554|ref|ZP_06311442.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus C160]
 gi|282905328|ref|ZP_06313183.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282908301|ref|ZP_06316132.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WW2703/97]
 gi|282910585|ref|ZP_06318388.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WBG10049]
 gi|282913781|ref|ZP_06321568.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Staphylococcus aureus subsp. aureus M899]
 gi|282918706|ref|ZP_06326441.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C427]
 gi|282923814|ref|ZP_06331490.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|283957751|ref|ZP_06375202.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Staphylococcus aureus subsp. aureus A017934/97]
 gi|293500819|ref|ZP_06666670.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|293509774|ref|ZP_06668483.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus M809]
 gi|293526360|ref|ZP_06671045.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M1015]
 gi|295427495|ref|ZP_06820127.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297591555|ref|ZP_06950193.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus MN8]
 gi|49241299|emb|CAG39980.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|257272034|gb|EEV04166.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257274563|gb|EEV06050.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257278485|gb|EEV09104.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257281154|gb|EEV11291.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257284240|gb|EEV14360.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M876]
 gi|282313786|gb|EFB44178.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|282316516|gb|EFB46890.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C427]
 gi|282321849|gb|EFB52173.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Staphylococcus aureus subsp. aureus M899]
 gi|282325190|gb|EFB55499.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WBG10049]
 gi|282327966|gb|EFB58248.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus WW2703/97]
 gi|282330620|gb|EFB60134.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282595172|gb|EFC00136.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus C160]
 gi|283789900|gb|EFC28717.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Staphylococcus aureus subsp. aureus A017934/97]
 gi|290920432|gb|EFD97495.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M1015]
 gi|291095824|gb|EFE26085.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|291467224|gb|EFF09741.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus M809]
 gi|295127853|gb|EFG57487.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297576441|gb|EFH95157.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus MN8]
 gi|312438620|gb|ADQ77691.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|315193667|gb|EFU24062.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus CGS00]
          Length = 284

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 66/303 (21%), Positives = 122/303 (40%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPRE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++  L+  +LYED+ + +  KP   +        +               +
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFVIIVTKPNNQNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+        ++      ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVN----LKKIYTCLVYG--KTHTFGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|332857041|ref|ZP_08436347.1| pseudouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332869978|ref|ZP_08438954.1| pseudouridine synthase A [Acinetobacter baumannii 6013113]
 gi|332726856|gb|EGJ58370.1| pseudouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332732478|gb|EGJ63729.1| pseudouridine synthase A [Acinetobacter baumannii 6013113]
          Length = 190

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 60/200 (30%), Positives = 97/200 (48%), Gaps = 16/200 (8%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V +KP+ I    G G  +  D  L   V  + +   L HRLD++TSGILV   ++    
Sbjct: 1   MVIHKPSDILSVPGKGDLH--DSVLTRLVAIEPRTL-LIHRLDRDTSGILVFGLSKRGQS 57

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            +   F+ R+  KIY +LV G  + +   +   ++         +H+V  +      A++
Sbjct: 58  AIARQFQDRQTSKIYEALVAGHLEGE-GTVDIPVVYDP--SRPPLHIVDASHN--KPALT 112

Query: 229 HFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           H++ I+ F    Q    +++ P TGR+HQLRVH  ++G PIVGD  Y A         + 
Sbjct: 113 HWQAIEHFQIQGQPVTRVKLTPITGRSHQLRVHMQYLGHPIVGDTLYAAP-----EQLLV 167

Query: 286 NKLYLHARYMDLPHPEGGRL 305
            +L LHA+ +   HP  G +
Sbjct: 168 PRLCLHAKQLSFNHPVTGGI 187


>gi|282916259|ref|ZP_06324021.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus D139]
 gi|283770074|ref|ZP_06342966.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
 gi|282319699|gb|EFB50047.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus D139]
 gi|283460221|gb|EFC07311.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
          Length = 284

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 122/303 (40%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPQE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++  L+  +LYED+ I +  KP   +        +               +
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+        ++      ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVN----LKKIYTCLVYG--KTHTSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|74000106|ref|XP_544620.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 2 [Canis familiaris]
          Length = 518

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 113/255 (44%), Gaps = 26/255 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L   F   +        +  +R+G++ ++++ V                    L+ ++K+
Sbjct: 135 LLHVFSTEFRAQPLSYYEAAVRAGRLHLNEEPV------------------QDLSIMLKD 176

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              L + V+  +     + + LL E+  + V +KP+ I V       ++   F+    + 
Sbjct: 177 NDFLRNRVHRHEPPVTAEPVRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-KEH 235

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++    
Sbjct: 236 QLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVTCK 295

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             +L  S+     V V + + +G     + F+ +         +  +P TGRTHQ+RVH 
Sbjct: 296 EPILVVSY----KVGVCRVDTRG-KPCETVFQRLSYNGHS-SVVRCRPLTGRTHQIRVHL 349

Query: 260 LHMGCPIVGDHKYCA 274
             +G PI+ D  Y +
Sbjct: 350 QFLGHPILNDPIYNS 364


>gi|238013094|gb|ACR37582.1| unknown [Zea mays]
          Length = 272

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 79/267 (29%), Positives = 115/267 (43%), Gaps = 61/267 (22%)

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           + VQGG GI   ID     + +   + PRL HRLD++ SG+LV+ RT+ +A  +   FR 
Sbjct: 1   MPVQGGVGIKNSIDILAPMFENGSSEVPRLVHRLDRDCSGVLVLGRTQFSASLMHAIFRE 60

Query: 177 RR-----------IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKG 222
           +            +Q+ Y +LV G P++ K  ++  L K     G    +      N   
Sbjct: 61  KTADALGDGTQQVLQRKYVALVIGRPRHPKGLLSAPLAKVVLQDGRSERLTVCAGSNTAS 120

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNF- 280
              A++ ++VI+ F Q + WLE+ P TGR HQLRVH    +G PIVGD+KY      N+ 
Sbjct: 121 VQDALTEYRVIESFPQGYTWLELFPRTGRKHQLRVHCAEVLGTPIVGDYKYGRQAHQNWM 180

Query: 281 ----------------------------TSPIQNKLYLHARYMDLP-------------- 298
                                        +  Q +L+LH + M LP              
Sbjct: 181 PLPMPQTIDKEMLKKRKLPFGLTLGGGSVAEQQPQLHLHCKQMILPDISAAMQQLRSSDA 240

Query: 299 -HPEG--GRLQITAPLPAHMVKTWDSL 322
            H      +L   APLP HM  +W  L
Sbjct: 241 DHDFSDLEKLSFVAPLPLHMQLSWKIL 267


>gi|83319852|ref|YP_424674.1| ribosomal large subunit pseudouridine synthase A [Mycoplasma
           capricolum subsp. capricolum ATCC 27343]
 gi|90110089|sp|P45614|Y714_MYCCT RecName: Full=Uncharacterized RNA pseudouridine synthase MCAP_0714;
           AltName: Full=ORF2; AltName: Full=RNA pseudouridylate
           synthase; AltName: Full=RNA-uridine isomerase
 gi|83283738|gb|ABC01670.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Mycoplasma capricolum subsp. capricolum ATCC 27343]
          Length = 302

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 66/303 (21%), Positives = 138/303 (45%), Gaps = 38/303 (12%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +   +V  +++N  L ++ K  +       + K +R+  ++++ KRV   N  ++   VV
Sbjct: 1   MTKFIVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRVNDKNYLLKINDVV 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +    ++   II++Q    S+VNL          ++YED+ I + NKP  + +   S  
Sbjct: 61  EVY---DSNKPIIRDQFNYISNVNLD---------IVYEDNNILIVNKPNNLEMH--SIY 106

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +D  +KS++  K +              HRLD+ TSG+++ A+ + ++  LT +F+ 
Sbjct: 107 NLCLDDMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSIILTNAFKT 166

Query: 177 R-RIQKIYWSLV-WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           + +I K Y++L  +    N    +  ++   S+       +V++N     Y  + FK+++
Sbjct: 167 KDQINKYYYALTSYDWNLNDFLQVNGYINYNSNTQKADFSLVEKN--NYKYCQTEFKLVN 224

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                   + ++  TG+ HQ+R        PI+ D +Y    + +     Q  +YL A  
Sbjct: 225 KN-----LILVKLITGKKHQIRSVLSFYNNPILNDFRYNGKKEND-----QKMIYLAAFK 274

Query: 295 MDL 297
           ++ 
Sbjct: 275 IEF 277


>gi|42523026|ref|NP_968406.1| pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
 gi|39575232|emb|CAE79400.1| Pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
          Length = 290

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 102/269 (37%), Gaps = 25/269 (9%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG---FL 133
           I+    I+  S       +     LLY+D      NKP+G  V     + + +      L
Sbjct: 29  ILTRPPIITISRVARPPGERTLVELLYKDEYFIAVNKPSGFHVHPHENVQHRVSRDKICL 88

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                   Q     HRLD  TSG+L+ A +  +A  L   F  R   K Y ++V G  K 
Sbjct: 89  YHARRMMKQHVYPVHRLDAGTSGVLLFALSSESASKLCRLFTERATHKTYQAVVRGFVKE 148

Query: 194 KKEC------IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           + E        +   L  +H     +  V+          +          ++ W+E+ P
Sbjct: 149 EGEVQLPLELDSTGDLVDAHTSFKRLATVEFPVAVGKKFPT---------ARYSWVEVTP 199

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHP-EGGR 304
           HTGR HQ+R H   +  P++GD  +  +    F         L L A  ++  HP  G +
Sbjct: 200 HTGRYHQIRRHFNRISHPLLGDAVHGDSHHNRFFRNHLEIEGLCLKALRLEFTHPWSGEK 259

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
           + I AP P      W  +   +D  L ++
Sbjct: 260 VSIEAP-PCD---KWKKIQLLFDPALPLE 284


>gi|329120090|ref|ZP_08248760.1| RNA pseudouridine synthase [Neisseria bacilliformis ATCC BAA-1200]
 gi|327463621|gb|EGF09939.1| RNA pseudouridine synthase [Neisseria bacilliformis ATCC BAA-1200]
          Length = 377

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 52/292 (17%), Positives = 102/292 (34%), Gaps = 28/292 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +    +P++        L +G +     + +  +     G  +                 
Sbjct: 104 YLCRRFPYVPRETWLSRLAAGGIFDASGRPLAPDAPFVPGGRLFYYR------------- 150

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVD 138
               +V   +     +  +LY D  +   +KP  + V  G                   D
Sbjct: 151 ---EAVAFDEPEIPFREEILYADKHLLAVDKPHFLPVVPGGRFLRETLLTRLRLHPELQD 207

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +        HR+D++T+G+++  R R + +     F+ RR++K Y ++       ++  +
Sbjct: 208 ADPDGLAPLHRIDKDTAGVVLFCRRRESRRAYQMLFQARRVEKSYEAVAA-----ERAGM 262

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L  +S I       + +   GA  A +  +  +          ++P +G+ HQLRVH
Sbjct: 263 TFPLHIRSRIERGEPFFLMRETGGAANAHTVVEAAEPLGGGLARYRLRPVSGKKHQLRVH 322

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
              +G PI+ D  Y A             L L AR +    P  G R+   +
Sbjct: 323 MAALGLPILNDPLYPAPLPDAAPD-YAKPLKLLARSVAFVDPFTGKRMCFES 373


>gi|325204968|gb|ADZ00422.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M01-240355]
          Length = 217

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 63/212 (29%), Positives = 98/212 (46%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 4   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + +A  L+  F  + I+K Y +L    P  K+  I   + K          + K  
Sbjct: 60  FALNKESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGMEK------SRRGMWKLT 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 114 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTESET 172

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 173 --------MFLYAWKIQFAY-QNRQIEIVAPL 195


>gi|304388631|ref|ZP_07370694.1| pseudouridine synthase Rlu family protein [Neisseria meningitidis
           ATCC 13091]
 gi|304337403|gb|EFM03574.1| pseudouridine synthase Rlu family protein [Neisseria meningitidis
           ATCC 13091]
 gi|325137288|gb|EGC59876.1| RNA pseudouridylate synthase family protein [Neisseria meningitidis
           ES14902]
          Length = 219

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 64/212 (30%), Positives = 98/212 (46%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 6   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 61

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R +A  L+  F  + I+K Y +L    P  K+  I   + K          + K  
Sbjct: 62  FALNRESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGMEK------SRRGMWKLT 115

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 116 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTESET 174

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 175 --------MFLYAWKIQFAY-QNRQIEIVAPL 197


>gi|326803085|ref|YP_004320903.1| RNA pseudouridine synthase [Aerococcus urinae ACS-120-V-Col10a]
 gi|326650339|gb|AEA00522.1| RNA pseudouridine synthase [Aerococcus urinae ACS-120-V-Col10a]
          Length = 234

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 106/224 (47%), Gaps = 16/224 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLD 151
           +   ++YED+ + +  KP  + VQ  +     +   LK+++  +  KP      L HRLD
Sbjct: 1   MPIPIIYEDNHLLIVEKPINMPVQEDASGDLDLLSALKAFIKERDHKPGNVYLALLHRLD 60

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIG 209
           +   G++   +T  AA  L++ FR  R+++ Y ++V    +    +E   ++L K     
Sbjct: 61  RPVGGVMAFGKTSKAASRLSDDFRRHRVKRDYLAVVQDQKLTLKNQETWTDYLYKNRK-- 118

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            + V VV + +K    A+  ++++    Q    + ++ HTGR+HQ+RV       P+ GD
Sbjct: 119 KNKVSVVNKADKRGKKAVLDYQLLKQRKQ-VALVRVRLHTGRSHQIRVQFQSRQHPLWGD 177

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
            KY   +     S    ++ L A+++ L HP     +  T+  P
Sbjct: 178 QKYGQKY-----SHKGQQIALWAQHLSLIHPTKKETMTFTSTPP 216


>gi|258405801|ref|YP_003198543.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
 gi|257798028|gb|ACV68965.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
          Length = 285

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 56/305 (18%), Positives = 109/305 (35%), Gaps = 27/305 (8%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M     ++ + V  +   +R+D+  +   P       Q+   SG+VR + +  +   R++
Sbjct: 1   MGNSEQIERIAVPEEWHGVRIDQGLRLLAPESGLRQRQQWCASGRVRQNGRTERKGGRLE 60

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +G  + + P                     +K        ++   + +    KP  +  +
Sbjct: 61  AGATLELLPEPLP-----------------SKPQPASGVRVVSVVNALAAVFKPGNVHCE 103

Query: 121 G-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    ++  L +      Q+PRL +RLD  TSG+++VA ++ A           R+
Sbjct: 104 AQSHNPEPSVESVLPNLFPR--QRPRLLNRLDYPTSGLVLVALSQGAFDQYQIWQDEGRV 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQ 238
           +K YW+ + G     +      LLK          V    E   +    +H + +   A 
Sbjct: 162 RKTYWAEIHGEWTGPE------LLKWRIETAKRKRVAVVFEPDPDPLRWTHVRALYRIAP 215

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E+    GR H +R H    G PI GD  Y  +           ++++     + P
Sbjct: 216 GRTRVEVVIAKGRRHHIRAHLAAAGTPIQGDSLYGEDSPSAPLYLHHLRVHMPGFTAETP 275

Query: 299 HPEGG 303
            P   
Sbjct: 276 PPWSE 280


>gi|194206789|ref|XP_001501154.2| PREDICTED: similar to RPUSD2 protein [Equus caballus]
          Length = 559

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 114/255 (44%), Gaps = 26/255 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L   F   +        +  +R+G++ ++++ V                    L+ ++K+
Sbjct: 176 LLHVFSTEFRAQPLAYYEAAVRAGRLHLNEEPV------------------QDLSIVLKD 217

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              L ++V+  +     + + LL E+  + V +KP+ I V       ++   F+    + 
Sbjct: 218 NDFLRNTVHRHEPPVTAEPVRLLAENEDMVVVDKPSSIPVHPCGRFRHNTVIFILG-KEH 276

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++    
Sbjct: 277 QLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVTCK 336

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             +L  S+     V V + + +G     + F+ +         +  +P TGRTHQ+RVH 
Sbjct: 337 EPILVVSY----KVGVCRVDTRG-KPCETVFQRLSYNGHS-SVVRCRPLTGRTHQIRVHL 390

Query: 260 LHMGCPIVGDHKYCA 274
             +G PI+ D  Y +
Sbjct: 391 QFLGHPILNDPIYNS 405


>gi|298713781|emb|CBJ27153.1| ribosomal large subunit pseudouridine synthase A [Ectocarpus
           siliculosus]
          Length = 332

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 57/185 (30%), Positives = 91/185 (49%), Gaps = 12/185 (6%)

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L + V S+  + R  HRLDQ+TSG++V+A T  AA+ +   FR R   K Y +++ G 
Sbjct: 156 DCLLTRVQSRWPEARHVHRLDQDTSGLVVMALTVEAAREMCRQFRERVPSKTYTAVLEGR 215

Query: 191 PKN--KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
                K   +   L   +      +      E+  N A ++++ I     +  W++  P 
Sbjct: 216 MAKTPKSGEVTAKLRPDTDNRPKQMFC----EEKGNEAHTNWERIKRKEDR-TWVDFTPV 270

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+R+HA+H+G P++GD  Y        +     +L LHAR +  PHP  G  ++ 
Sbjct: 271 TGRTHQIRMHAVHLGHPVMGDSLYGTPEGTAKSE----RLLLHARRISFPHPRTGETVEF 326

Query: 308 TAPLP 312
             P P
Sbjct: 327 ECPPP 331


>gi|282852228|ref|ZP_06261580.1| S4 domain protein [Lactobacillus gasseri 224-1]
 gi|282556647|gb|EFB62257.1| S4 domain protein [Lactobacillus gasseri 224-1]
          Length = 163

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 43/180 (23%), Positives = 85/180 (47%), Gaps = 23/180 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT   ++V+E  EE  RLD+        ++   +++++    + V+ K  K + ++Q+G 
Sbjct: 1   MTENYHLVIE--EEKGRLDKVIAEKLKDLSRTKIKELVNDKNILVNHKAEKVSYKVQAGD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I                +  +  L+  +  L   ++YED+ + V NKP G+ V   +
Sbjct: 59  SIDIT---------------VPPAKPLSLEAQNLNLDIVYEDADVIVVNKPQGMVVHPSA 103

Query: 124 GIAYHI--DGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           G   H   +G L    +     +G +P + HR+D++TSG+L+VA+   A + L +    +
Sbjct: 104 GHPDHTLVNGLLYHTHELADSPEGFRPGIVHRIDKDTSGLLMVAKNDKARESLEKQLAEK 163


>gi|57650200|ref|YP_185880.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus COL]
 gi|87161458|ref|YP_493609.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88194701|ref|YP_499497.1| hypothetical protein SAOUHSC_00944 [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|151221090|ref|YP_001331912.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|161509205|ref|YP_001574864.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|258452042|ref|ZP_05700058.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A5948]
 gi|262049353|ref|ZP_06022227.1| hypothetical protein SAD30_1651 [Staphylococcus aureus D30]
 gi|262052363|ref|ZP_06024565.1| hypothetical protein SA930_0105 [Staphylococcus aureus 930918-3]
 gi|282923686|ref|ZP_06331365.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|284023934|ref|ZP_06378332.1| RluA family pseudouridine synthase [Staphylococcus aureus subsp.
           aureus 132]
 gi|294847992|ref|ZP_06788739.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9754]
 gi|304381438|ref|ZP_07364089.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|57284386|gb|AAW36480.1| ribosomal large subunit pseudouridine synthases, RluD subfamily
           [Staphylococcus aureus subsp. aureus COL]
 gi|87127432|gb|ABD21946.1| pseudouridine synthases, RluA subfamily [Staphylococcus aureus
           subsp. aureus USA300_FPR3757]
 gi|87202259|gb|ABD30069.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           NCTC 8325]
 gi|150373890|dbj|BAF67150.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|160368014|gb|ABX28985.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|257860257|gb|EEV83089.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A5948]
 gi|259159735|gb|EEW44777.1| hypothetical protein SA930_0105 [Staphylococcus aureus 930918-3]
 gi|259162585|gb|EEW47153.1| hypothetical protein SAD30_1651 [Staphylococcus aureus D30]
 gi|269940506|emb|CBI48884.1| putative RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus TW20]
 gi|282593072|gb|EFB98072.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|294824792|gb|EFG41214.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9754]
 gi|302750832|gb|ADL65009.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus str. JKD6008]
 gi|304340011|gb|EFM05954.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|315197538|gb|EFU27874.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320141176|gb|EFW33023.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320143233|gb|EFW35023.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|329731131|gb|EGG67502.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21189]
          Length = 284

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 123/303 (40%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++ +  ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMTNDILEI--------HLPRE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++  L+  +LYED+ I +  KP   +        +               +
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+        ++      ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVN----LKKIYTCLVYG--KTHTSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKD----RIITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|253732634|ref|ZP_04866799.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|253729412|gb|EES98141.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
          Length = 284

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 122/303 (40%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPRE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++  L+  +LYED+ I +  KP   +        +               +
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+        ++      ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVN----LKKIYTCLVYG--KTHTSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPIKKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|86153961|ref|ZP_01072163.1| ribosomal large subunit pseudouridylate synthase D [Campylobacter
           jejuni subsp. jejuni HB93-13]
 gi|85842499|gb|EAQ59712.1| ribosomal large subunit pseudouridylate synthase D [Campylobacter
           jejuni subsp. jejuni HB93-13]
 gi|284925325|gb|ADC27677.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni IA3902]
 gi|315057463|gb|ADT71792.1| Putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni S3]
          Length = 281

 Score =  142 bits (359), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 110/284 (38%), Gaps = 46/284 (16%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+    QK++   ++  D   V+  N I +G +V +                      + 
Sbjct: 6   ISINEAQKLIDKKRLFCDGILVEEKNEILNG-LVEL----------------------IV 42

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             ++     +++E+    +  K +GI     G    Y +   +       G++  + HRL
Sbjct: 43  YENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL---WGKEACVAHRL 99

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-LLKKSHIG 209
           D+ETSG+++VA+ + A   L   F  + +QK Y +L  G  +          L K     
Sbjct: 100 DKETSGLILVAKNKKAQIDLKALFEKKLVQKEYLALANGKIEENFIIDKAINLAKNYDDV 159

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              + + K+       AI+ F++++ F +     L  +P TGR HQ+RVH  +    I+G
Sbjct: 160 KTRMQICKE----GKQAITEFEILEYFPKINATLLLCKPLTGRQHQIRVHLHYKNHTILG 215

Query: 269 DHKYCAN-------------FKGNFTSPIQNKLYLHARYMDLPH 299
           D  Y  +              K         +L LH+  +   +
Sbjct: 216 DPLYGLSKEQIESILDEKLTPKERLKLTGALRLCLHSYRLKFQY 259


>gi|325129374|gb|EGC52208.1| RNA pseudouridylate synthase family protein [Neisseria meningitidis
           OX99.30304]
          Length = 208

 Score =  142 bits (359), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 64/212 (30%), Positives = 98/212 (46%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 4   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R +A  L+  F  + I+K Y +L    P  K+  I   + K          + K  
Sbjct: 60  FALNRESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGMEK------SRRGMWKLT 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 114 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTESET 172

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 173 --------MFLYAWKIQFAY-QNRQIEIVAPL 195


>gi|257460774|ref|ZP_05625875.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           gracilis RM3268]
 gi|257442105|gb|EEV17247.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           gracilis RM3268]
          Length = 495

 Score =  142 bits (359), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 51/225 (22%), Positives = 96/225 (42%), Gaps = 32/225 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHI 77
            RLD +  +    I+   +  +++S  VRV+     K   ++ +G++VRI    +A    
Sbjct: 10  ERLDVFLSSQL-GISRNQISNLIKSAAVRVNGAVQTKPGYKLSAGELVRIDYPASAPQQT 68

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+   D               +LYED  + V NKPAG++V   + +    +  L  W+
Sbjct: 69  SAERLNFD-------------VEILYEDDDLLVVNKPAGLTVHPAASV---KEPTLVDWL 112

Query: 138 DSKGQ---------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            S+G          +  + HRLD+ TSG L+VA+  AA   L+     + + +IY +L+ 
Sbjct: 113 KSRGYLLSTLGGELRAGIVHRLDKLTSGALLVAKNNAAHAALSAQLSDKSMGRIYLALI- 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            +P  +   I   + +           +    + A  A   ++++
Sbjct: 172 DLPLKEPCVIERPISRNP--ANRLKMGIVPGGRSAKSAF--YEIL 212



 Score = 80.8 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 5/88 (5%)

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           +K+     + F  +  +  TGRTHQ+RVH   +   I+GDH Y    +    S    ++ 
Sbjct: 377 YKLPPINLKSFNLVAAKLFTGRTHQIRVHLSSINRHILGDHLYGFKSENAKIS----RIL 432

Query: 290 LHARYMDLPHPEGG-RLQITAPLPAHMV 316
           LHA  +   HP  G  ++I A LP+  +
Sbjct: 433 LHAYLLYFIHPRSGKEVKICAGLPSEFL 460


>gi|163785435|ref|ZP_02180045.1| hypothetical protein HG1285_12602 [Hydrogenivirga sp. 128-5-R1-1]
 gi|159879297|gb|EDP73191.1| hypothetical protein HG1285_12602 [Hydrogenivirga sp. 128-5-R1-1]
          Length = 179

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 42/192 (21%), Positives = 88/192 (45%), Gaps = 22/192 (11%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQS 61
           + + V    V++  +N RLD++  + YP  +    QK+++ G V   +K + K + +++ 
Sbjct: 1   MSSEVLTFKVDSQYKNKRLDQFLASVYPEFSRSYYQKLIKQGNVLEGEKELKKPSLKLKE 60

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           GQ + +               I+     +    + +   + YED  + V  KP  + V  
Sbjct: 61  GQEITL---------------IIPPPEEIEVKPENIPLDIYYEDEDLAVVYKPPHMVVHP 105

Query: 122 --GSGIAYHIDGFLKSWVD----SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
             G      ++  L  + +       ++  + HRLD+ET+G+L++A++  A + L   F+
Sbjct: 106 SVGHTSGTLVNALLYHFKNVSTYGGRERAGIVHRLDKETAGLLIIAKSEFAHKELQRQFQ 165

Query: 176 MRRIQKIYWSLV 187
            R + K Y ++V
Sbjct: 166 ERTVDKRYKAIV 177


>gi|321257772|ref|XP_003193704.1| hypothetical protein CGB_D5020C [Cryptococcus gattii WM276]
 gi|317460174|gb|ADV21917.1| Conserved hypothetical protein [Cryptococcus gattii WM276]
          Length = 497

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 52/265 (19%), Positives = 101/265 (38%), Gaps = 22/265 (8%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             V+      +L       +   +    +  L SG  RV+    + +  +++G  +    
Sbjct: 32  TFVKQRWIGRQLLEVITTEFRDRSMEYYRHALESGVTRVNGVVARPDLILRNGDRIDNTV 91

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
             +                     +D +  + +  + +  V +KP  + V        H 
Sbjct: 92  HRH----------------EPPVTNDPILILHIDREREFIVISKPGSLPVHAAGRYFKH- 134

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+      G K    +RLD+ TSG++++A +  AA  L   F   +++K Y + V G
Sbjct: 135 -TVLEMMESDYGLKCYSVNRLDRLTSGLMILALSGKAASKLAREFVEGKVKKEYVARVKG 193

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPH 248
               ++  +   ++    +      V+   E  +  A++ F  I     +    +  +P 
Sbjct: 194 KFPEEEVTVDKPMM---TVDRQMGLVIITPEGKSQDAVTIFNRIAYDPVRDQSVVRCRPQ 250

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYC 273
           TGRTHQ+RVH  ++G PI  D  Y 
Sbjct: 251 TGRTHQIRVHLQYLGYPIANDPLYG 275


>gi|299532146|ref|ZP_07045540.1| pseudouridine synthase [Comamonas testosteroni S44]
 gi|298719808|gb|EFI60771.1| pseudouridine synthase [Comamonas testosteroni S44]
          Length = 214

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 61/208 (29%), Positives = 99/208 (47%), Gaps = 13/208 (6%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + V +KP+G+    G G        L++          + HRLDQ TSG++V+AR
Sbjct: 2   YEDEHLLVLDKPSGLLCVPGRGPDKQDCLSLRALRH--FGDALVVHRLDQATSGLVVMAR 59

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN--WLLKKSHIGGDYVHV--VKQ 218
             A  + L+++F  R++ K Y ++V G  +   E   +  W L    I  D+        
Sbjct: 60  NPAVQRQLSQAFAERKVDKRYIAVVAGELQAHSEAADDRGWQLIDLPIAADWERRPLRVI 119

Query: 219 NEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           N +    + + ++VI+   Q       + + P TGRTHQLR+H   +G P++GD  Y + 
Sbjct: 120 NHETGKSSQTLWQVIEHTDQPGIPRTRVLLSPLTGRTHQLRLHMAAIGHPMLGDALYAS- 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 +    +L LHA  ++L HP  G
Sbjct: 179 ---EAVACASPRLLLHAAALELVHPVTG 203


>gi|317153563|ref|YP_004121611.1| pseudouridine synthase [Desulfovibrio aespoeensis Aspo-2]
 gi|316943814|gb|ADU62865.1| pseudouridine synthase [Desulfovibrio aespoeensis Aspo-2]
          Length = 289

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 58/298 (19%), Positives = 103/298 (34%), Gaps = 22/298 (7%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +  +V      +RLDR      P       +++  +GQV VD +      +++SGQ
Sbjct: 1   MPQRETCIVAPGLAGVRLDRAMTGLIPGSGLRLRRRLCEAGQVTVDGRARGPGYKVRSGQ 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           V+ +          +  Q I +               ++          KP G  V   +
Sbjct: 61  VLALLAPPTDRMADLMPQDIPE-------------LRVVERTDLFAAVYKPGG--VHSAA 105

Query: 124 GIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                      +         P L +RLD  TSG+L+VA     A+    S     ++K 
Sbjct: 106 IAGKDGLSVEAALPALFPDAAPVLLNRLDFPTSGLLLVALGPDGAETYRASEEAGGVRKF 165

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++V G    + + + +   +           + + +  A    S   +     +    
Sbjct: 166 YLAVVHG----RLDGMISVRNRLDTDDRPRTRALAEEDADARRWTSVNALAHDHDRDTTL 221

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK--LYLHARYMDLP 298
           +      G  HQ+R H   +  PIVGD  Y           I +   L+LH + ++LP
Sbjct: 222 VRCLIMKGARHQIRAHLASLDHPIVGDTLYGVPDAATGGEEIGSGPLLHLHHQRIELP 279


>gi|289805997|ref|ZP_06536626.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 201

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 49/205 (23%), Positives = 86/205 (41%), Gaps = 16/205 (7%)

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
             +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++  +  
Sbjct: 1   PWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSE 60

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           A + L + F    I+K Y ++V G   +        + ++  I   +       +K    
Sbjct: 61  AGRRLAQQFEQHHIRKRYHAIVRGWLIDDAVLDYPLVEERDKIADKFAR----EDKAPQP 116

Query: 226 AISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
           A++ ++ +               ++  +E++P TGR HQLR H  H+  PI+GD K+   
Sbjct: 117 AVTQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDSKHGDL 176

Query: 275 -NFKGNFTSPIQNKLYLHARYMDLP 298
              +         +L LHA  ++L 
Sbjct: 177 RQNRSAAEHFACRRLMLHASRLELT 201


>gi|315928439|gb|EFV07751.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni DFVF1099]
          Length = 281

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 110/284 (38%), Gaps = 46/284 (16%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+    QK++   ++  D   V+  N I +G +V +                      + 
Sbjct: 6   ISINEAQKLIDKKRLFCDGILVEEKNEILNG-LVEL----------------------IV 42

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             ++     +++E+    +  K +GI     G    Y +   +       G++  + HRL
Sbjct: 43  YENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL---WGKEACVAHRL 99

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-LLKKSHIG 209
           D+ETSG+++VA+ + A   L   F  + +QK Y +L  G  +          L K     
Sbjct: 100 DKETSGLILVAKNKKAQIDLKTLFEKKLVQKEYLALANGKIEENFIIDKAINLAKNYDDV 159

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              + + K+       AI+ F++++ F +     L  +P TGR HQ+RVH  +    I+G
Sbjct: 160 KTRMQICKE----GKQAITEFEILEYFPKINATLLLCKPLTGRQHQIRVHLHYKNHTILG 215

Query: 269 DHKYCAN-------------FKGNFTSPIQNKLYLHARYMDLPH 299
           D  Y  +              K         +L LH+  +   +
Sbjct: 216 DPLYGLSKEQIESILDEKLTPKERLKLTGALRLCLHSYRLKFQY 259


>gi|51970580|dbj|BAD43982.1| unnamed protein product [Arabidopsis thaliana]
          Length = 326

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 82/296 (27%), Positives = 126/296 (42%), Gaps = 71/296 (23%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQET 154
           +L+ ++ ++DS I V NKP  + V+G   I   +D    + +     + PRL HRLD+ET
Sbjct: 24  YLQRLVRFKDSAIIVLNKPPKLPVKGNVPIHNSMDALAAAALSFGNDEGPRLVHRLDRET 83

Query: 155 SGILVVARTRAAAQHLTESFRMRR---------------IQKIYWSLVWGIPKNKKECIA 199
           SG+LV+ RT+ +  +L   F   +               + + YW+LV G PK K+  I+
Sbjct: 84  SGLLVMGRTKESIDYLHSVFSDYKGRNSSCKAWNKACEAMYQQYWALVIGSPKEKEGLIS 143

Query: 200 NWLLKKSHIGGDYVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             L K     G    VV     G   +  AI+ +KV+        W+E++P T R HQLR
Sbjct: 144 APLSKVLLDDGKTDRVVLAQGSGFEASQDAITEYKVLGPKINGCSWVELRPITSRKHQLR 203

Query: 257 VHAL-HMGCPIVGDHKYC------------ANFKGNFTSPIQNK---------------- 287
           VH    +G PIVGD+KY              + +     P + +                
Sbjct: 204 VHCAEALGTPIVGDYKYGWFVHKRWKQMPQVDIEPTTGKPYKLRRPEGLDVQKGSVLSKV 263

Query: 288 --LYLHARYMDLPH----------PEGGR-----------LQITAPLPAHMVKTWD 320
             L+LH R M LP+           E              L+  A +P+HM  +W+
Sbjct: 264 PLLHLHCREMVLPNIAKFLHVMNQQETEPLHTGIIDKPDLLRFVASMPSHMKISWN 319


>gi|89901537|ref|YP_524008.1| pseudouridine synthase [Rhodoferax ferrireducens T118]
 gi|89346274|gb|ABD70477.1| ribosomal large subunit pseudouridine synthase A [Rhodoferax
           ferrireducens T118]
          Length = 215

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 58/216 (26%), Positives = 106/216 (49%), Gaps = 13/216 (6%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  ++Y D  + V +KP G+    G G        L +          + HRLD  TSG+
Sbjct: 5   ELKVIYADKSLLVLDKPTGLLSVPGRG--EDKQDCLSARAQRLYPDALVVHRLDMATSGL 62

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+AR  AA + L+ +F  R ++K Y ++V G        + +W +    I  D+    +
Sbjct: 63  MVMARGAAAQRALSLAFASRSVRKRYVAIVDGQLAPS---LQDWGVIDLPIIVDWPERPR 119

Query: 218 Q--NEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +  + +    ++++++V+    + +   +E++P TGR+HQLRVH L +G  IVGD  Y +
Sbjct: 120 RIIDHQRGKPSVTYWRVLAHNTSDETTRVELEPVTGRSHQLRVHLLALGHAIVGDALYGS 179

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
                      ++L LHA  ++L HP  G+ +   +
Sbjct: 180 PRVQAMA----DRLLLHACLLELRHPVSGQSMCFDS 211


>gi|323450233|gb|EGB06115.1| hypothetical protein AURANDRAFT_29586 [Aureococcus anophagefferens]
          Length = 244

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 71/252 (28%), Positives = 101/252 (40%), Gaps = 37/252 (14%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI---------DGFLKSWVD 138
              +  +      +L+ED  I V +KP  +    G                D    +   
Sbjct: 2   AEPSAATSTPAIRILHEDDHIVVVDKPTNLLSVPGRHPDAPPPTKKRRRVADALSLARAA 61

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--------------RIQKIYW 184
                 R+ HRLD ETSG+LV A+T AAA  L  SFR                +++K+Y 
Sbjct: 62  VGLPDLRVVHRLDFETSGVLVFAKTSAAAAALCASFRADAAEASGAAATAAAPKMRKVYV 121

Query: 185 SLVWGIPKNKKE---CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           + V G      E    +A     ++  G            GA  A + ++     A    
Sbjct: 122 AAVRGELAGSGEWAWPLAPDDAARAADGKPRYAACDAGAPGAKAATTLWE-----AAGAS 176

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            L ++P TGR+HQLRVH L  G PIVGD  Y      +     + +L LHA  +DL HP 
Sbjct: 177 RLRLRPQTGRSHQLRVHCLAAGHPIVGDPLYGPPPADH-----EPRLCLHAAELDLTHPG 231

Query: 302 GG-RLQITAPLP 312
            G R+   +P P
Sbjct: 232 TGDRVTFASPAP 243


>gi|261414458|ref|YP_003248141.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261370914|gb|ACX73659.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302326709|gb|ADL25910.1| putative pseudouridine synthase, RluD family [Fibrobacter
           succinogenes subsp. succinogenes S85]
          Length = 321

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 62/320 (19%), Positives = 111/320 (34%), Gaps = 45/320 (14%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD    + + + +  +    L  G V ++            G  V       +   +  +
Sbjct: 24  LDS-LCDRFTYHSREDWIDRLTRGLVTINGATANVETVAHRGDKVVYHVENYSEPEVPTD 82

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDS 139
            +                   ++ED +  +  KPAG+ V     I Y+     ++   DS
Sbjct: 83  FET------------------VFEDDEFILVAKPAGVPVHHTGRIFYNTFAAIIRREFDS 124

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +   P   HRLD++T G+++ AR    A    ++     ++K Y ++V G     +    
Sbjct: 125 ETATP--MHRLDRDTGGLILFARYGETAARFQKNLDRILLRKFYLAVVRGKFPEGEVECH 182

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-----FAQKFCWLEMQPHTGRTHQ 254
             L +      D + +   + +G     + FK++        A +   +E +  TGR HQ
Sbjct: 183 MPLREDPE---DPIRLRMHHREGGKECFTRFKLVRHLDCPEIAPELSLVEAELITGRKHQ 239

Query: 255 LRVHALHMGCPIVGDHKY-------------CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +R H   MG PIVGD  Y                   +      +   L A  ++L  P 
Sbjct: 240 IRAHLAEMGYPIVGDRLYYRDGEFYQKLAQGGELTDEDIKVLGAHNQMLFAYKVELQLPY 299

Query: 302 GGR-LQITA-PLPAHMVKTW 319
                   +   PA M K  
Sbjct: 300 WKEPRTFESHAYPADMAKLL 319


>gi|160944255|ref|ZP_02091484.1| hypothetical protein FAEPRAM212_01764 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444437|gb|EDP21441.1| hypothetical protein FAEPRAM212_01764 [Faecalibacterium prausnitzii
           M21/2]
          Length = 231

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 64/236 (27%), Positives = 106/236 (44%), Gaps = 39/236 (16%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++LYED+ + V +KPAG+S + G   A      L++  ++      + HRLD   SG++V
Sbjct: 1   MILYEDAALVVLDKPAGLSSEEGVPAA------LRAHWNAPDAFVGVVHRLDTGVSGLMV 54

Query: 160 VARTRAAAQHLTESFRMRRIQKI------------------YWSLVWGIPKNK---KECI 198
            ART AAA  L+      +                      Y +++ G P  +      +
Sbjct: 55  YARTPAAAAALSRQVTQSQDAYAVQDGRAEGKAAAPQFVKQYRAIIAGAPDAQLPAAGVL 114

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            ++L K S  G   V  V +  KG   A+  ++++    +     E+  HTGRTHQ+RV 
Sbjct: 115 RDYLFKDSRKGR--VFPVSRPRKGVREAVLEYRILATAGEN-SLAEITLHTGRTHQIRVQ 171

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                 P+ GD KY +  KG+        + L +  +   HP+ G+ +  + PLPA
Sbjct: 172 FASRRHPLYGDGKYGSRQKGS--------IALQSCGLRFVHPDTGKPMAFSLPLPA 219


>gi|264678303|ref|YP_003278210.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
 gi|262208816|gb|ACY32914.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
          Length = 214

 Score =  142 bits (358), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 61/208 (29%), Positives = 99/208 (47%), Gaps = 13/208 (6%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + V +KP+G+    G G        L++          + HRLDQ TSG++V+AR
Sbjct: 2   YEDEHLLVLDKPSGLLCVPGRGPDKQDCLSLRALRH--FGDALVVHRLDQATSGLVVMAR 59

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN--WLLKKSHIGGDYVHV--VKQ 218
             A  + L+++F  R++ K Y ++V G  +   E   +  W L    I  D+        
Sbjct: 60  NPAVQRQLSQAFAERKVDKRYIAVVAGELQAHSEAADDRGWQLIDLPIAADWERRPLRVI 119

Query: 219 NEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           N +    + + ++VI+   Q       + + P TGRTHQLR+H   +G P++GD  Y + 
Sbjct: 120 NHETGKSSQTLWQVIEHTVQPGILRTRVLLSPLTGRTHQLRLHMAAIGHPMLGDALYAS- 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                 +    +L LHA  ++L HP  G
Sbjct: 179 ---EAVACASPRLLLHAAALELVHPVTG 203


>gi|294792637|ref|ZP_06757784.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           6_1_27]
 gi|294456536|gb|EFG24899.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           6_1_27]
          Length = 300

 Score =  142 bits (358), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 122/322 (37%), Gaps = 73/322 (22%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
               +L K+     + ++  +    + I     + I      ++H   E           
Sbjct: 6   YPRKSLVKLFEEKLIHINGHKATPKDAISVDDEIWIAMAKEKIDHDPIE----------- 54

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHR 149
                +   +LYED  +++ +KP+G++V   S     +   +  +    G  +K R  +R
Sbjct: 55  -----MDLSVLYEDEDLFIVDKPSGVTV--NSKDQLSLANGVAHYFKEHGIKRKVRFLNR 107

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--- 206
           LD++T+G +V+A++  A     +       +K Y + V GI +  ++ +   + + +   
Sbjct: 108 LDRDTTGCIVIAKSGLAQSLYQQQMDDNTFEKWYMATVEGIVEADEDTLVFPMERSADGI 167

Query: 207 -------------------------------------HIGGDYVHV--VKQNEKGANYAI 227
                                                HIG   V +  V  ++   N   
Sbjct: 168 HYEVNAKGKETRTDFSVLCRHSSQPVDNSVNKSENSVHIGLKNVDIELVDVDKNNPNVDK 227

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           + +K   C    +  + ++ +TG+THQ+RV   H+G P+VGD  Y A   G    P Q +
Sbjct: 228 TVYKFNKC---GYTEVLVRLYTGKTHQIRVAFSHLGHPLVGDTLYGAQPTGQ---PFQLR 281

Query: 288 LYLHARYMDLPHPEGG-RLQIT 308
               A+ +   H   G R+ +T
Sbjct: 282 ----AQKVVFTHMRTGERITVT 299


>gi|281211774|gb|EFA85936.1| pseudouridine synthase family protein [Polysphondylium pallidum
           PN500]
          Length = 530

 Score =  142 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 107/260 (41%), Gaps = 27/260 (10%)

Query: 25  FKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           F N +  +    + ++ ++ G ++V+ K V  N ++ +   +              E  +
Sbjct: 175 FTNEFSQLPES-IYRLKIKLGWIKVNGKIVSPNYKLTNKDEIEHRVHR-------HEPPV 226

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
             + +++    D +  +           +KP+ I +       ++   ++ +  +    +
Sbjct: 227 SGAPIHVVAVDDDVVVV-----------DKPSSIPIHPCGRFRHNTLIYILAA-ELGYNR 274

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD+ TSG+L++AR+ AAA   +E+     + K Y + V G   +    +   L 
Sbjct: 275 LYGVHRLDRLTSGLLILARSPAAATKKSEAIMSGNVTKRYVAQVRGRFPDGDITVDQPLK 334

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
            ++H  G     + Q       A++    +   A+     +   P TGRTHQ+R+H   +
Sbjct: 335 VQNHRLG-----LNQVSPDGKPALTVITRLSYDAETDTSVVSCLPKTGRTHQIRLHLQWI 389

Query: 263 GCPIVGDHKYCANFKGNFTS 282
           G PI  D  Y  +FK N   
Sbjct: 390 GHPITNDPLYNEHFKLNAGK 409


>gi|261393344|emb|CAX50980.1| putative RNA pseudouridine synthase (RNA-uridine isomerase; RNA
           pseudouridylate synthase) [Neisseria meningitidis 8013]
          Length = 220

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 64/212 (30%), Positives = 98/212 (46%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 6   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 61

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R +A  L+  F  + I+K Y +L    P  K+  I   + K          + K  
Sbjct: 62  FALNRESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGMEK------SRRGMWKLT 115

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 116 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTESET 174

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 175 --------MFLYAWKIQFAY-QNRQIEIVAPL 197


>gi|193216441|ref|YP_001999683.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           arthritidis 158L3-1]
 gi|193001764|gb|ACF06979.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           arthritidis 158L3-1]
          Length = 277

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 51/278 (18%), Positives = 107/278 (38%), Gaps = 37/278 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHIIK 79
           L ++      ++    ++K  R   ++V+  R      ++Q G VV +  + +A    ++
Sbjct: 15  LFKYLFKMLNNVPKSRIEKAFRQKDIKVNGVRTNDKQYKMQLGDVVEVYGISDATKAFVQ 74

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            +               +   +++ED  + + +K   I++               ++  +
Sbjct: 75  NE-------------SKINFKVIFEDKNLLIVDKAINIAMHSEENSLDDQILKYLNYRLT 121

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +P    R+D++TSG++V A+       L E  + ++     +  V    ++K +   
Sbjct: 122 SSFRPASIGRIDKKTSGLVVYAKN---YAALVEFEKQQKYFDKVYQFVSDFNEDKLDITV 178

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           N    K  IG + + V   + K    A + F V             Q  TG+THQ+R   
Sbjct: 179 NL---KKDIGNEKMIV---DPKFGVKARTIFWV------DGKHKFAQILTGKTHQIRATL 226

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            ++  PI+GD KY              +L+LH+  +  
Sbjct: 227 SYLKYPILGDSKYGGKRA--------KRLFLHSYSITF 256


>gi|168061155|ref|XP_001782556.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162665963|gb|EDQ52631.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 365

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 67/313 (21%), Positives = 113/313 (36%), Gaps = 64/313 (20%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKI--LDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
            RIQ+GQ +R+   +      +    +  +   +   +     +  +LYED  +   NKP
Sbjct: 54  QRIQNGQQIRVDGNVITDPGFLLRDGVTLVYQRLPWREPEVPYRLGVLYEDDHLVAINKP 113

Query: 115 AGISVQGGS------------GIAYHIDGFLKSWV-------DSKGQKPRLTHRLDQETS 155
           +G+ V  G                   +  L++ +       +++  KP   HRL + TS
Sbjct: 114 SGLQVLPGGLFQQRTVLKQLEWDNEEKEKHLQACLASVSSSDETRLWKPAPVHRLGRGTS 173

Query: 156 GILVVARTRAAAQHLTE-------------SFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           GIL+ A++ AA   L               +   R+I K Y +L  GI     E  A+  
Sbjct: 174 GILLCAKSPAAKSKLAADLAAGTSVSIDRSALIDRKITKTYRALASGIIMED-EVFADIP 232

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALH 261
           + K    G    +    E G   + S   V+     +    +E+Q +TGR HQ+R+H   
Sbjct: 233 IGKVKYSGVAGGLNMATEIGGKPSQSKVTVLWRDIVENQTLVEVQIYTGRPHQIRIHLAA 292

Query: 262 MGCPIVGDHKY----------------------------CANFKGNFTSPIQNKLYLHAR 293
           +G P+VGD  Y                                +     P      LHA 
Sbjct: 293 LGHPLVGDPLYVAGGRPREDLNTVNAENCEDKSMDPADDGGYQRPKSVLPGDCGYLLHAW 352

Query: 294 YMDLPHPEGGRLQ 306
            +   HP   +++
Sbjct: 353 RLSFFHPVTSQVE 365


>gi|86133476|ref|ZP_01052058.1| tRNA pseudouridine synthase C [Polaribacter sp. MED152]
 gi|85820339|gb|EAQ41486.1| tRNA pseudouridine synthase C [Polaribacter sp. MED152]
          Length = 234

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 105/235 (44%), Gaps = 11/235 (4%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID--GFLKSWVDSKGQKPRLTHRLDQET 154
           +   ++YED+ +    KP  + V          D    L+   +  G K    HRLD++T
Sbjct: 1   MSLEIIYEDAYLLCVTKPNNVLVHHAYHSRNMADEKSLLQLVSEETGLKVYPIHRLDRKT 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG +++A+ +       + F   +IQKIY+ +V G   + K   +    + +++  + + 
Sbjct: 61  SGAILLAKEKEYVAKFQDLFTKNQIQKIYYGVVRGFSPSTKRIDSPVKGRDANVHKEALT 120

Query: 215 VVKQNEKGANYAIS-HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +K   K     I+    V    + ++  +E+ P TGR HQLRVH+  +  P++GD KY 
Sbjct: 121 ELKTLAK-----ITLDIAVKPYDSSRYSLIELFPKTGRMHQLRVHSNKISHPLIGDAKYG 175

Query: 274 ANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
                     +     L+LHA  ++  HP     L + +  P   ++ ++   +K
Sbjct: 176 DKNHDMMFEQNFGFKNLFLHAGKLEFIHPYTQETLILKSTFPTDWIQLFEKFNWK 230


>gi|260579312|ref|ZP_05847194.1| ribosomal large subunit pseudouridine synthase C [Corynebacterium
           jeikeium ATCC 43734]
 gi|258602441|gb|EEW15736.1| ribosomal large subunit pseudouridine synthase C [Corynebacterium
           jeikeium ATCC 43734]
          Length = 269

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 105/237 (44%), Gaps = 11/237 (4%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           +  Q ++V + + + RLD++ ++    +    L +++R+ Q+ V+  + K + R  +G  
Sbjct: 4   SEPQTLIVSDSQADRRLDKYIRSQVKGVPATVLFRLMRTKQITVNGAKCKPDQRTVAGDK 63

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VR+P    AL    ++           + +  L   +++ED  + V NKPA I+V  GSG
Sbjct: 64  VRLP----ALEVAAEKPTPTGDRKAAEQLARRLSRHIVFEDGALLVVNKPANIAVHVGSG 119

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--RIQKI 182
           +   +   L+  +  K ++  L HRLD+ETSG+L+VA+     +HL    R     IQ+ 
Sbjct: 120 VKAGVIEALR-VLRPKEKELELAHRLDKETSGLLIVAKNSKMLRHLQGLLRTGGEDIQRY 178

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           Y ++V G  K          +     G         + +    A +   V   +   
Sbjct: 179 YLAVVAGGMKRGGGQPRRIDVPLRKTG----AATVVDRRAGQRAETKVWVKKPWGDC 231


>gi|240949536|ref|ZP_04753876.1| RNA pseudouridine synthase [Actinobacillus minor NM305]
 gi|240296109|gb|EER46770.1| RNA pseudouridine synthase [Actinobacillus minor NM305]
          Length = 212

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 63/203 (31%), Positives = 91/203 (44%), Gaps = 20/203 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           + ++     V NKP G+SV           G  +      G  +  L HRLD+ TSG+L+
Sbjct: 7   VCFQHPDFIVINKPEGVSVHKD----NEASGLTERIAQQLGVPQIWLVHRLDKATSGLLI 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A T+ AA      F+  +IQK YW+L    PK K+  I   + K  +      H  +  
Sbjct: 63  LALTKEAAVEFYHLFKQHKIQKTYWALSTTKPKKKQGKIIGDMKKSRNSAWKLCHTKE-- 120

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A +  W  + PHTGRTHQLRV    +G PI+GD  Y       
Sbjct: 121 ----NPAITQF-TSQSVAPQLRWFTLNPHTGRTHQLRVAMRSLGSPILGDSLYGGEKA-- 173

Query: 280 FTSPIQNKLYLHARYMDLPHPEG 302
                 ++LYLHA  ++  +   
Sbjct: 174 ------DRLYLHAYQLEFEYQNT 190


>gi|294628458|ref|ZP_06707018.1| RNA pseudouridylate synthase [Streptomyces sp. e14]
 gi|292831791|gb|EFF90140.1| RNA pseudouridylate synthase [Streptomyces sp. e14]
          Length = 324

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 57/281 (20%), Positives = 103/281 (36%), Gaps = 27/281 (9%)

Query: 25  FKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
                       ++++  +G+ V  D + V  +   + G  V     + A   +      
Sbjct: 45  LVERLSGAAPGVVEEMFAAGRIVAADGRAVPPDAPYEPGMFVWFHRELPAETPVP----- 99

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQ 142
                           ++++ D  I V +KP  ++    GS +       L+  +D    
Sbjct: 100 -------------FPLVVVHRDEHIVVVDKPHFLATTPRGSHVTETALARLRRELDL--P 144

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HRLD+ T+G+++              FR RR++K Y ++    P      +A   
Sbjct: 145 TLGAAHRLDRLTAGLVLFTVRPEERGAYQTLFRDRRVRKEYEAVAPYDPD-----LALPR 199

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             +S I  +   +  +   G   A++  +++           + P TG+THQLRVH   +
Sbjct: 200 TVRSRIVKERGVLTAEEVPGEPNAVTDVELVGRRPGGPARYRLTPRTGQTHQLRVHMNAL 259

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           G PI+GD  Y A             L L AR ++   P  G
Sbjct: 260 GVPILGDPLYPAVTPDGPPGDFSRPLQLLARALEFTDPVTG 300


>gi|152993942|ref|YP_001359663.1| ribosomal large subunit pseudouridine synthase D [Sulfurovum sp.
           NBC37-1]
 gi|151425803|dbj|BAF73306.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Sulfurovum sp. NBC37-1]
          Length = 309

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 68/326 (20%), Positives = 115/326 (35%), Gaps = 51/326 (15%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +    + +      Q++L  G++ +D + +        G+V  +     +          
Sbjct: 19  FIMRQF-NFTQGQAQRVLAKGRLLIDGESIFNTGASVEGEVEVVYFKAASQGRCP----- 72

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                             L+ +    +F KP+G+ V             L       G  
Sbjct: 73  ------------------LFSNRDFMIFEKPSGVLVHP--NTMSTPYSMLDEIRHISGDN 112

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
              THR+D ETSG+L+ ++ + A  HL  SF  + I+K Y + V G              
Sbjct: 113 ANATHRIDMETSGLLLASKHKKAETHLKNSFEAKTIKKSYLAWVDGRLNEPFSV-----S 167

Query: 204 KKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHAL 260
           +K  I  DY  V  +         + + F  +    +     +   P TGRTHQ+RVH  
Sbjct: 168 EKIKINNDYSRVKHKVFISDAGKASHTDFIPLRYNERLDATLVACYPQTGRTHQIRVHLF 227

Query: 261 HMGCPIVGDHKYCANF-------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           H+  PI+GD  Y   F             +  F      +L LHA  +   +  G R  I
Sbjct: 228 HVKHPILGDPIYGTTFDTANRYLEDEISEEERFLETGARRLMLHAHTLSFTY--GNRFHI 285

Query: 308 TAPLPAHMVKTWDSLGFKYDRNLYIK 333
            +   +   + +D +  K +R    K
Sbjct: 286 KSK--SDFGQMYDLICPKDERTFNKK 309


>gi|325201066|gb|ADY96521.1| pantetheine-phosphate adenylyltransferase [Neisseria meningitidis
           H44/76]
          Length = 399

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 63/212 (29%), Positives = 98/212 (46%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 185 ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 240

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + +A  L+  F  + I+K Y +L    P  K+  I   + K          + K  
Sbjct: 241 FALNKESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGMEKS------RCGMWKLT 294

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 295 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTESET 353

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 354 --------MFLYAWKIQFDY-QNRQIEIVAPL 376


>gi|222823069|ref|YP_002574642.1| ribosomal pseudouridine synthase [Campylobacter lari RM2100]
 gi|222538290|gb|ACM63391.1| putative ribosomal pseudouridine synthase [Campylobacter lari
           RM2100]
          Length = 300

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 68/315 (21%), Positives = 124/315 (39%), Gaps = 56/315 (17%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M Y++  +  N ++  RL     +    I+    QK++   ++  +              
Sbjct: 1   MAYIKKKLANNGKKAFRL---LMDELK-ISMHEAQKLIDKKRLFCNG------------- 43

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK-SILLYEDSKIYVFNKPAGISVQG- 121
                      N + ++ K LD  V L  + +  K   +++E+    +  KP+G+     
Sbjct: 44  -----------NLVEEKNKFLDGLVELIVYENNPKGLEIVFENEDFAIVEKPSGVLTHPN 92

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G    Y +   +       GQ   + HRLD+ETSG+L++A+ + A   L   F  R +QK
Sbjct: 93  GRNCTYSLCDEIWHL---WGQNACVAHRLDKETSGLLLIAKHKNAQIELKTMFEKRLVQK 149

Query: 182 IYWSLVWGIPKNKKECIAN---WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            Y +LV G  K K+E I +    L K        +H+     +    A++ F  ++ F  
Sbjct: 150 SYLALVKG--KTKEEFIVDKSMDLAKDYDAVKTRMHIC----ENGKEALTQFYTLEYFEN 203

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-------------NFTSPI 284
                +  +P TGR HQ+R+H  H+   I+G+  Y                         
Sbjct: 204 LDVSLILAKPLTGRQHQIRLHLFHVKHKILGEPLYGLEKTQIEQILDGKMSDIKRAHITG 263

Query: 285 QNKLYLHARYMDLPH 299
             +L LH+  ++  +
Sbjct: 264 AKRLLLHSFSLEFIY 278


>gi|148239908|ref|YP_001225295.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           WH 7803]
 gi|147848447|emb|CAK23998.1| Ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           WH 7803]
          Length = 197

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 56/208 (26%), Positives = 89/208 (42%), Gaps = 17/208 (8%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + V +KPAG+  Q G G+  H    L S +       RL HRLD++TSG++++A+     
Sbjct: 1   MLVVDKPAGLLCQPGLGV--HQRDSLISRLQHACPDLRLVHRLDRDTSGLVLLAKDADTQ 58

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           + L   F  RR+ K+Y + V G        I   L + +     Y              +
Sbjct: 59  RVLGALFAARRVGKLYLADVQGSMGAVSGRIDLPLARLNRQPPTY-----GVHPDGKACL 113

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           + ++ +     +       P TGR+HQLR H   +  PI+GD  Y               
Sbjct: 114 TLWRRLQRMETRTRLWLC-PRTGRSHQLRAHLAALHHPIIGDPIYNPGCAA-------GG 165

Query: 288 LYLHARYMDLPHPE--GGRLQITAPLPA 313
           L L A  +  P P+  G ++++ AP PA
Sbjct: 166 LRLRAIALRFPDPDQPGSQVRVRAPWPA 193


>gi|316983895|gb|EFV62874.1| RNA pseudouridylate synthase family protein [Neisseria meningitidis
           H44/76]
 gi|325133346|gb|EGC56011.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M13399]
 gi|325139340|gb|EGC61880.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis CU385]
 gi|325143576|gb|EGC65896.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M01-240013]
 gi|325199109|gb|ADY94565.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis G2136]
 gi|325206923|gb|ADZ02376.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis M04-240196]
          Length = 218

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 63/212 (29%), Positives = 98/212 (46%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 4   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + +A  L+  F  + I+K Y +L    P  K+  I   + K          + K  
Sbjct: 60  FALNKESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGMEKS------RCGMWKLT 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 114 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTESET 172

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 173 --------MFLYAWKIQFDY-QNRQIEIVAPL 195


>gi|88857157|ref|ZP_01131800.1| putative 23S rRNA pseudouridylate 746 synthase [Pseudoalteromonas
           tunicata D2]
 gi|88820354|gb|EAR30166.1| putative 23S rRNA pseudouridylate 746 synthase [Pseudoalteromonas
           tunicata D2]
          Length = 221

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 59/214 (27%), Positives = 88/214 (41%), Gaps = 14/214 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  I + NKP+G+    G   A      +   +        L HRLD  TSGI++V
Sbjct: 19  ILYQDEAILLINKPSGLLSLSGKNPAN--LDSVHYRLCQDFPAATLLHRLDFGTSGIMLV 76

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +     L   F+ R I+K Y +++ G        I   + K          V  Q  
Sbjct: 77  ALNKTINAVLMSQFQQRTIKKSYTAILAGQLTPLNGSINLPIAKAEFP---RHAVCLQR- 132

Query: 221 KGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               +A S ++V     +     +   P TGRTHQLR+H+  +G PI+G   Y       
Sbjct: 133 --GKHAQSDYQVHAYCKSTDSTKVTYLPVTGRTHQLRIHSQAIGHPILGCDLYGT----V 186

Query: 280 FTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
            +     +L LHA  +   HP    R +   P P
Sbjct: 187 HSLSQAPRLMLHATSLTFTHPITLQRFEGVCPSP 220


>gi|241889793|ref|ZP_04777091.1| ribosomal large subunit pseudouridine synthase D [Gemella
           haemolysans ATCC 10379]
 gi|241863415|gb|EER67799.1| ribosomal large subunit pseudouridine synthase D [Gemella
           haemolysans ATCC 10379]
          Length = 251

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 58/271 (21%), Positives = 110/271 (40%), Gaps = 31/271 (11%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           ++++ K     + + +   + +               +L +S  L+  +  +K    YED
Sbjct: 10  IKINGKEADLTSSLSTNDSLELNI-------------VLATSKYLSNTAARIKKE--YED 54

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
             I V +KP GI            +  L +++ +        HRLD +T G++++A+T  
Sbjct: 55  DYILVVSKPFGIKTHP--NDIETENDTLVNYLIADYSYLEPIHRLDIDTCGLVILAKTPL 112

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
               L +    R I++ Y +L+    K +   I   + + S    + + V +        
Sbjct: 113 IKAKLDQMLEQRAIKRYYTALIKNNIKPQ--TINTNIGRDSKE-KNKMAVTR----NGKN 165

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           AI++        Q    + +   TGRTHQ+RVH   +G  I+GD  Y  +          
Sbjct: 166 AITNILECSKLDQNRFSVLISLETGRTHQIRVHLASIGVSIIGDKLYSKDGYK------Y 219

Query: 286 NKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315
           +K+YL A  ++  HP  G  L+I + +    
Sbjct: 220 DKMYLGALKVNFQHPVTGNTLEIKSSIEKDF 250


>gi|223935694|ref|ZP_03627610.1| pseudouridine synthase [bacterium Ellin514]
 gi|223895702|gb|EEF62147.1| pseudouridine synthase [bacterium Ellin514]
          Length = 283

 Score =  141 bits (356), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 71/231 (30%), Positives = 101/231 (43%), Gaps = 24/231 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS---------WVDSKGQK-PRLTHRL 150
           +LYED  +   +KPAG  +   S      +  L           W  S+  K  R  HRL
Sbjct: 18  ILYEDRSVLAVDKPAGWMLAPDSWDKTGRNLQLALQSSLNAGDFWAHSRNIKFLRYVHRL 77

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D ET+G+L++ ++  A +   E F  R ++K Y ++V GIPK  +      L+    + G
Sbjct: 78  DAETTGVLLLCKSLGALRAYGELFETRSVEKFYLAVVQGIPKQSEWTCKLPLIADPVVKG 137

Query: 211 DYVHVV------KQNEKGA----NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               V       K + +G       A +HF+VI     K   +E QP TGRTHQ+RVH  
Sbjct: 138 KMQVVTPGKPLPKSDPRGPQAELKDAETHFRVIQTLQDKA-LVEAQPMTGRTHQIRVHLA 196

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
             G PIVGD  Y         S     + L A  +    P   R ++I AP
Sbjct: 197 ASGHPIVGDPLYGNAPAA--ASKGAQIIALRAIKLIYWDPFQKRQIRIAAP 245


>gi|149198149|ref|ZP_01875196.1| tRNA pseudouridine synthase [Lentisphaera araneosa HTCC2155]
 gi|149138751|gb|EDM27157.1| tRNA pseudouridine synthase [Lentisphaera araneosa HTCC2155]
          Length = 246

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 100/241 (41%), Gaps = 8/241 (3%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED  + V  K A ISV                     GQ     HRLD+  SG L+ A
Sbjct: 10  LYEDEYLVVAKKLAKISVHRSEMCRDRRTLLTMVRNKLGGQYVYAVHRLDRPVSGPLLFA 69

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           ++    + L + F  + ++K Y +LV G  + K +     L K +    D +   +    
Sbjct: 70  KSPEMCRELQKQFNEKTVEKKYIALVRGWLEGKGKVDKQLLKKSNGTIQDCLTRYR---- 125

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF- 280
           G   A     +      ++  +E++P TGR HQLR H   +  PI+GD     + +  F 
Sbjct: 126 GLATAEIDEPLGKFPTVRYGLVELEPVTGRYHQLRRHMRDLAYPIIGDSTDGDSHQNRFF 185

Query: 281 -TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQ 338
                  +L LH  Y+   HP     ++I       +++ ++ LG  Y++   ++R Y  
Sbjct: 186 REKFELRRLMLHCFYLSFKHPVSQELIKIYLEPDRDLLRIYEQLGM-YEQFKQLEREYED 244

Query: 339 D 339
           +
Sbjct: 245 E 245


>gi|170725275|ref|YP_001759301.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169810622|gb|ACA85206.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 566

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 103/233 (44%), Gaps = 21/233 (9%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           LD +  L   +      ++Y+D ++ + NKPA      G  I   +   +K+        
Sbjct: 348 LDKNPLLNNPAVGKAIDIIYQDEEMAIINKPAEFLSVPGKSIQDSVYLRMKTQF-PDATG 406

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + HRLD  TSG++V+A T+ A + L   F  R ++K Y +L+ G  +  +  I+  + 
Sbjct: 407 PLIVHRLDMSTSGLMVIALTKEANKSLQAQFIARTVKKRYTALLTGELREDEGSISLPM- 465

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-- 261
           +          V   +      A + ++VI+        + + P TGRTHQLRVH+ H  
Sbjct: 466 RGDFDDRPRQLVCFDH---GKPAETKWQVIERK-DGKTKVHLYPKTGRTHQLRVHSAHAQ 521

Query: 262 -MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR---LQITAP 310
            +  PIVGD  Y             ++L+LHA  ++L HP         I A 
Sbjct: 522 GLNMPIVGDDLYGTK---------ADRLHLHAELLELNHPSTKEFMSFCIEAE 565


>gi|168018525|ref|XP_001761796.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162686851|gb|EDQ73237.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 346

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 57/268 (21%), Positives = 106/268 (39%), Gaps = 28/268 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+   E   +   F   +        ++ ++ G++RV+ K V  +  ++  Q +      
Sbjct: 16  VKKRWEGKTVVDLFAQEFRQRPREYYEEAVKRGRIRVEGKVVAPSYVVRDSQTMSHFVHR 75

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHID 130
                   E  +L             + I+L E   I V +KPA + V   G      + 
Sbjct: 76  -------HEPPVLAG-----------RVIVLEEGPDIIVVSKPATVPVHPCGQYRKNSVI 117

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L++  + K       HRLD+  SG+L++AR    A    +      +QK Y + V G+
Sbjct: 118 SILEA--EHKTGPLFPVHRLDRLVSGLLILARNSRTADFFRQEIEAGVVQKQYVAKVKGV 175

Query: 191 PKNKKECIANWLLKKSHIGGDYV------HVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
              ++  +   ++     G   V       V  +++  +  + + F+ +         ++
Sbjct: 176 FPAEEVELNAAVIYDPREGRSSVEVQNNLEVTPESDAKSKESCTKFRRLSTDGVD-SIVQ 234

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             P TGRTHQ+RVH  ++G PI  D  Y
Sbjct: 235 CMPLTGRTHQIRVHLQYLGFPIANDDLY 262


>gi|308189690|ref|YP_003922621.1| Pseudouridylate synthase [Mycoplasma fermentans JER]
 gi|307624432|gb|ADN68737.1| predicted Pseudouridylate synthase [Mycoplasma fermentans JER]
          Length = 280

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 60/292 (20%), Positives = 107/292 (36%), Gaps = 34/292 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65
           +   +   +++  +L  + K    +    ++ KILR+  ++++  R+      I    ++
Sbjct: 1   MLEFIATKNDDGRKLISYLKRILINTPTSHIYKILRNKDIKINGVRINDPQYIINEKDII 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +I        + I+     +     +   DF    ++YED  I + +KP  +SV   +  
Sbjct: 61  QI--------YGIEANDYQNKKFENSAKKDF---KIIYEDDNILIVSKPINLSVHSENNC 109

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                     +      KP    RLD+ TSG+++ A+       L E        +  + 
Sbjct: 110 LDKQVLSYLKYNQKDSFKPSHVGRLDKATSGLMIYAKN---YATLVELNYKTSFFEKIYK 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L     + KK    N      H    Y  VV  N K    A + F        K   +  
Sbjct: 167 LKSDFKEAKKLVEINI----QHDEKLYKMVVTNNTKDP-LAKTLFYT------KNNKIFA 215

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
              TG+ HQ+R+   H+  PI GD KY             ++LYLH   +  
Sbjct: 216 SILTGKKHQIRLSMAHLKTPIYGDIKYGGKKA--------DRLYLHCYSITF 259


>gi|319762713|ref|YP_004126650.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|317117274|gb|ADU99762.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
          Length = 282

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 93/237 (39%), Gaps = 18/237 (7%)

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   + +   L          LL++D  +    KPAG  V      A      +++  D
Sbjct: 15  PEHHPVHAGARLLTPDATPPLHLLWQDEHMVALYKPAGWLVHRTGLDAGETRFVVQALRD 74

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             G+     HRLD+ T G+LV+    AAA+ L  SF    + K Y +LV G         
Sbjct: 75  QIGRHVYPVHRLDKGTCGVLVMGLHPAAARALAGSFARHAVHKRYLALVRGW-------- 126

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTG 250
           A  L    H             + A+  ++    ++            +   +  +P TG
Sbjct: 127 APPLADVDHPLRPDDAPQDAPAQPAHTLLTRLARLELPESSDPRFATTRASLVLAEPTTG 186

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGRL 305
           R HQ+R H  H   PI+GD  +       + +      +L+LHA  + LPHP+ GR+
Sbjct: 187 RRHQIRRHLKHAAHPILGDATHGKGPLNRWWAERLGLQRLWLHAWRLRLPHPQDGRM 243


>gi|317495180|ref|ZP_07953550.1| RNA pseudouridylate synthase [Gemella moribillum M424]
 gi|316914602|gb|EFV36078.1| RNA pseudouridylate synthase [Gemella moribillum M424]
          Length = 282

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 52/265 (19%), Positives = 104/265 (39%), Gaps = 31/265 (11%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           + ++ +     +++     + I   +   N+      I ++S+++ K          YED
Sbjct: 41  IIINGQSADLQSKLNKDDNLEINIELGTSNY------IANNSLSIIKE---------YED 85

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
             + + +KP GI            +  L +++ +        HRLD +T G+++ A+T  
Sbjct: 86  DYLLIASKPFGIKTHPNDITDE--NNTLVNYLITDYPYLEPIHRLDTDTCGLVIFAKTPF 143

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
               L +    R I++ Y +LV        + I   + + +          K        
Sbjct: 144 VKSKLDQMLEHRVIKRFYTALVKNNI--HVQTINTNIGRDNREKNKMAVTNK-----GKN 196

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           AI++    +   Q      +   TGRTHQ+R+H  + G PI+GD  Y  +          
Sbjct: 197 AITNILSCEKIEQNKFATTISLETGRTHQIRIHLAYKGNPIIGDKLYSNDGHK------Y 250

Query: 286 NKLYLHARYMDLPHPEG-GRLQITA 309
            K+YL A  +   HP    ++++ +
Sbjct: 251 EKMYLGALKVIFNHPVTNKKIEVNS 275


>gi|218192587|gb|EEC75014.1| hypothetical protein OsI_11092 [Oryza sativa Indica Group]
          Length = 461

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 66/321 (20%), Positives = 112/321 (34%), Gaps = 74/321 (23%)

Query: 39  KILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           K +R GQ+ V  +     +  ++ G                   K++   +   +     
Sbjct: 74  KRIRDGQITVCGEVATDPDIILREG------------------SKLVYHRLPWQEPCAPH 115

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ------------KPR 145
              +LYED  +   NKP+G+ V                  D K               P 
Sbjct: 116 LLDVLYEDDDMIALNKPSGLQVLPKGLFQQRTVLAQLQLKDWKMPSSFCSKRKDAQSHPV 175

Query: 146 LTHRLDQETSGILVVARTRAAAQHL-----------------TESFRMRRIQKIYWSLVW 188
             HRL + TSG+L+ A+T+ A   L                 T+  + R+I K Y +LV 
Sbjct: 176 PVHRLGRGTSGLLLCAKTKLAKAQLAAYFAEGATNAGKSRDETDICKARKISKFYRALVT 235

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQP 247
           GI +N +  I   +    + G         +      A+S  +V++         ++++ 
Sbjct: 236 GILENDEVMITQPIGLVRYPGVAEGLYAACSS--GKPAMSKVRVLERLKIHNHTLIQVEI 293

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-----------------------PI 284
           H+GR HQ+R+H  ++G P+V D  Y    +  F                         P 
Sbjct: 294 HSGRPHQIRIHLAYIGHPLVDDPLYGIGGQPKFDEPEPTSTADSFAYDGGYERPLQPVPG 353

Query: 285 QNKLYLHARYMDLPHPEGGRL 305
               +LHA ++ L HP    L
Sbjct: 354 DCGYHLHAHWLVLCHPTTNEL 374


>gi|15677843|ref|NP_275010.1| hypothetical protein NMB2018 [Neisseria meningitidis MC58]
 gi|7227280|gb|AAF42341.1| conserved hypothetical protein [Neisseria meningitidis MC58]
 gi|319409672|emb|CBY89973.1| K06177 ribosomal large subunit pseudouridine synthase A [Neisseria
           meningitidis WUE 2594]
 gi|325141436|gb|EGC63913.1| ribosomal large subunit pseudouridine synthase C [Neisseria
           meningitidis 961-5945]
          Length = 220

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 63/212 (29%), Positives = 98/212 (46%), Gaps = 21/212 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           +L+        NKP GISV   SG      G  ++     G ++  L HRLD++TSGIL+
Sbjct: 6   ILFRHQDFVAINKPGGISVHQDSGET----GLARTLAIQLGVERVWLLHRLDKQTSGILL 61

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  + +A  L+  F  + I+K Y +L    P  K+  I   + K          + K  
Sbjct: 62  FALNKESASALSGQFAGKSIKKTYLALSDRKPSKKQGWIKGGMEKS------RCGMWKLT 115

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y       
Sbjct: 116 RNTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTESET 174

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                   ++L+A  +   + +  +++I APL
Sbjct: 175 --------MFLYAWKIQFDY-QNRQIEIVAPL 197


>gi|139438597|ref|ZP_01772113.1| Hypothetical protein COLAER_01111 [Collinsella aerofaciens ATCC
           25986]
 gi|133776136|gb|EBA39956.1| Hypothetical protein COLAER_01111 [Collinsella aerofaciens ATCC
           25986]
          Length = 205

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 44/215 (20%), Positives = 80/215 (37%), Gaps = 24/215 (11%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVART 163
              +KPAG+ V G       +  +    + + G        +  +RLD+ T+G+++ +  
Sbjct: 1   MAIDKPAGMIVHGDGTGERTLTDYASDLLLAMGDGFAATDMQPLNRLDRNTTGVVLFSLD 60

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
           +       +       +K Y +L  G     ++ I   + +  H          +     
Sbjct: 61  KQTQPAFDQMVNDHAFEKHYLALAEGKIDWNEKLIDKPIARDRHDSRK-----MRVGASG 115

Query: 224 NYAISHFKVIDCFAQKF-----CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             + +  KV+     +       +++++  TGR HQ+RVH      P+VGD  Y      
Sbjct: 116 KPSQTRVKVLKRLKSRRGLPTRSYIDVELLTGRKHQIRVHLASEHHPLVGDDLYGTARP- 174

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
                    L LHA  +   HP  G  + I AP P
Sbjct: 175 -------CGLMLHAHSVSFTHPVTGEHIHIEAPCP 202


>gi|314936786|ref|ZP_07844133.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus hominis subsp. hominis C80]
 gi|313655405|gb|EFS19150.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus hominis subsp. hominis C80]
          Length = 288

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 49/291 (16%), Positives = 108/291 (37%), Gaps = 40/291 (13%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + + H  + +   +  I R G + ++++ V     ++    + +              K+
Sbjct: 16  FLQRH--NYSKKTISAIKRDGALIINRQPVTVRYMLKKDDHLIV--------------KL 59

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQ 142
            +   +           +LYED+ + + +KP  ++           +   +  +++    
Sbjct: 60  PEEVPSTYLRPSNKHIEILYEDTYLIIVSKPVHLNCAPSREHPHDSLIERVMYYLNHSTN 119

Query: 143 K-----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           K     P +  RLD+ T+GI++  +       ++     +R    Y  + +G    ++  
Sbjct: 120 KVQYIVPHIVTRLDRNTTGIVIFTKHGHIHHLMSTFEIDKR----YICVCYGK-TKEQSM 174

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +          + +       YA + +K +          E++ HTGRTHQ+RV
Sbjct: 175 IEAPIGRN-----KDSIITRCITPSGKYAKTEYKTLSSH-HSASLCEVKLHTGRTHQIRV 228

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQI 307
           H  H+G P++GD  Y      +   P      L    +   HP     ++I
Sbjct: 229 HFKHIGHPLIGDDLY------DGFHPRIQTQSLQCYKVKFIHPIYNKEIEI 273


>gi|332298344|ref|YP_004440266.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332181447|gb|AEE17135.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 238

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 68/245 (27%), Positives = 105/245 (42%), Gaps = 38/245 (15%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++E+ +I + NK  G++VQGG+GI + +D  L   V   G K    HRLD++T+G+L
Sbjct: 12  LPVVFENGEIIIVNKKCGLAVQGGAGIRFSLDRLLSEQV---GYKVYPVHRLDKDTAGLL 68

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A+T AAA   T       ++K Y +L  GIP  KK      +               +
Sbjct: 69  VLAKTAAAAAVWTNLIASGEVRKEYAALCAGIPPGKKGTFTAPI---------------E 113

Query: 219 NEKGANYAISHFKVIDCFAQKF--------------CWLEMQPHTGRTHQLRVHALHMGC 264
            +     A++ + V       F                L +   TGR HQ+R+H    GC
Sbjct: 114 TKGERKSAVTDYVVCRTAETVFPDAPGLDGVQTVPVSLLRLTLGTGRMHQIRIHLAQAGC 173

Query: 265 PIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           PIV D KY          +     KL L A  + +P   G +      LP H+    ++ 
Sbjct: 174 PIVADDKYGDFRLNKLFRSGRGIRKLQLAAVKLTIP-LAGNKNVFEIDLPEHLR---NAC 229

Query: 323 GFKYD 327
           G  +D
Sbjct: 230 GLLFD 234


>gi|257464999|ref|ZP_05629370.1| RNA pseudouridine synthase [Actinobacillus minor 202]
 gi|257450659|gb|EEV24702.1| RNA pseudouridine synthase [Actinobacillus minor 202]
          Length = 212

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 62/203 (30%), Positives = 90/203 (44%), Gaps = 20/203 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           + ++     V +KP GISV           G  +      G  +  L HRLD+ TSG+L+
Sbjct: 7   VCFQHPDFIVIDKPEGISVHKD----NEATGLTERIAQQLGVPQVWLVHRLDKATSGLLI 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A T+ AA      F+  +IQK YW+L    PK K+  I   + K  +      H  +  
Sbjct: 63  LALTKEAAVEFYHLFKQHKIQKTYWALSTAKPKKKQGKIVGDMKKSRNSAWKLCHTKE-- 120

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 AI+ F      A +  W  + PHTGRTHQLRV    +G PI+GD  Y       
Sbjct: 121 ----TPAITQF-TSQSVAPQLRWFTLNPHTGRTHQLRVAMKSLGSPILGDSLYGGEKA-- 173

Query: 280 FTSPIQNKLYLHARYMDLPHPEG 302
                 ++LYLHA  ++  +   
Sbjct: 174 ------DRLYLHAYQLEFEYQNT 190


>gi|291059569|gb|ADD72304.1| putative S4 domain protein [Treponema pallidum subsp. pallidum str.
           Chicago]
          Length = 404

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 62/315 (19%), Positives = 119/315 (37%), Gaps = 33/315 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+      ++   R+DR  +   P    V +   LR   +R++ + V+   R+Q G V+ 
Sbjct: 77  VECFRCTKNDAGRRVDRVLRILLPACPRVGVYAALRRTAIRLNGRPVQPAKRVQVGDVLS 136

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P  +            +  +  L      +   ++++   +  F+KPAG+ V G   + 
Sbjct: 137 LPESLCRARAASSRLSKMPGTPKLR-----VLPSVVFKTQDLLFFHKPAGLCVHGPRSLD 191

Query: 127 YHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             + G  ++ V  +   +P   HRLD+ T G++  +R+   AQ  + + +   ++K Y  
Sbjct: 192 AWVRGQGRAHVPPALSFRPGPLHRLDRGTEGLIAFSRSLRGAQWFSAALQQHTLRKFYL- 250

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK-VIDCFAQKFCWLE 244
                               +        +V+  E      ++H + V+           
Sbjct: 251 --------------AITAAPARTAAAARTLVRPGE------VTHVQTVLHSCDSALVLRV 290

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           + P TG+ HQ+R +    G P+VGD  Y         +    + +L A  +  P      
Sbjct: 291 IVPVTGKKHQIRRYCAAQGFPLVGDRTYGG--ASQHGNARYTRFFLLAWCVRFPSSRLQA 348

Query: 305 L---QITAPLPAHMV 316
           L     T P PA M 
Sbjct: 349 LPAQVWTTPSPAFMR 363


>gi|162451128|ref|YP_001613495.1| pseudouridylate synthase/tRNA pseudouridine synthase C [Sorangium
           cellulosum 'So ce 56']
 gi|161161710|emb|CAN93015.1| Pseudouridylate synthase/tRNA pseudouridine synthase C [Sorangium
           cellulosum 'So ce 56']
          Length = 241

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 72/226 (31%), Positives = 111/226 (49%), Gaps = 20/226 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL+ D ++  F KP+G+ V  G G A     F+     + G+K    HRLD+ TSG+L+V
Sbjct: 10  LLHLDDRVAAFAKPSGLLVHRGWGDA--PVVFVDLAERALGRKVYPVHRLDRATSGVLLV 67

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A   AAA  L   F     +K Y +LV G+P     C+ + + ++   GG  V       
Sbjct: 68  ALDPAAAALLCAQFEQGLARKRYLALVRGVPPEH-GCVDHPIPRRE--GGPRV------- 117

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A++ F+ +    +++  +E +P TGR HQ+R H  H+  PI+GD  Y        
Sbjct: 118 ----PAVTDFERLHAL-ERYAVVEARPRTGRLHQVRRHLKHISHPIIGDVNYGKGEHNRL 172

Query: 281 TSP--IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
                  ++L LHA  + + HPE G  L++ APLP  +   +D LG
Sbjct: 173 FRERYALHRLALHAAELAVAHPETGAPLRVAAPLPDDLRGPFDQLG 218


>gi|281338228|gb|EFB13812.1| hypothetical protein PANDA_001071 [Ailuropoda melanoleuca]
          Length = 545

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 112/255 (43%), Gaps = 26/255 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L   F   +        +  +R G++ ++++ V                    L+ ++K+
Sbjct: 162 LLHVFSTEFRAQPLAYYEAAVREGRLHLNEEPV------------------QDLSIVLKD 203

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              L + V+  +     + + LL E+  + V +KP+ I V       ++   F+    + 
Sbjct: 204 NDFLRNRVHRHEPPVTAEPVRLLAENEDMVVVDKPSSIPVHPCGRFRHNTVIFILG-KEH 262

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++    
Sbjct: 263 QLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVICK 322

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             +L  S+     V V + + +G     + F+ +         +  +P TGRTHQ+RVH 
Sbjct: 323 EPILVVSY----KVGVCRVDARG-KPCETVFQRLSYNGHS-SVVRCRPLTGRTHQIRVHL 376

Query: 260 LHMGCPIVGDHKYCA 274
             +G PI+ D  Y +
Sbjct: 377 QFLGHPILNDPIYNS 391


>gi|213616279|ref|ZP_03372105.1| 23S rRNA/tRNA pseudouridine synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 165

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 56/177 (31%), Positives = 86/177 (48%), Gaps = 15/177 (8%)

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +    HRLD  TSG++VVA T+AA + L   FR R  +K Y + VWG P   +  +   
Sbjct: 1   PQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLP 60

Query: 202 LLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           L+       D+ +  KQ    +    A + + V++  A     + ++P TGR+HQLRVH 
Sbjct: 61  LI------CDWPNRPKQKVCYETGKPAQTEYNVVEFAADNTARVVLKPITGRSHQLRVHM 114

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHM 315
           L +G PI+GD  Y +         +  +L LHA  + + HP  G  +     +PA  
Sbjct: 115 LALGHPILGDQFYASPE----ALSLAPRLQLHAEMLTITHPAYGNSMTFK--VPADF 165


>gi|255540129|ref|XP_002511129.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223550244|gb|EEF51731.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 385

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 54/288 (18%), Positives = 111/288 (38%), Gaps = 27/288 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
               +   F   +    +      ++ G+++VD + V  +  ++S Q +         +H
Sbjct: 54  AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDGETVPVSYIVKSSQKI---------SH 104

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKS 135
            +   +   ++ ++          +LY+D  +    KPA + V   G      + G L++
Sbjct: 105 FLHRHEPPVTAWDIP---------VLYKDPDVVTVYKPATVPVHPCGQYRKNTVVGILQA 155

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +         HRLD+  SG+L++AR    A    +      +QK Y + V G+    +
Sbjct: 156 --EHNLAPLFPVHRLDRLVSGLLILARNALKADLFRQEIEAGMVQKQYVAKVVGVFPEDE 213

Query: 196 ECI---ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           + +    N+  ++     +  +    +      A + F  I         +  +P TGRT
Sbjct: 214 QVVGVNINYNAREGRSTAEVGNSCVDSPPKGKTACTKFTRISTNG-THSIVLCKPITGRT 272

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--NKLYLHARYMDLP 298
           HQ+RVH  + G PI  D  Y +    + ++     ++    + Y   P
Sbjct: 273 HQIRVHLQYTGHPIANDFLYLSEHAASRSAEGMSADRAACSSSYCVTP 320


>gi|261379361|ref|ZP_05983934.1| pseudouridine synthase Rlu family protein [Neisseria subflava
           NJ9703]
 gi|284797801|gb|EFC53148.1| pseudouridine synthase Rlu family protein [Neisseria subflava
           NJ9703]
          Length = 216

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 58/212 (27%), Positives = 90/212 (42%), Gaps = 19/212 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++E     V NKP G+SV   S     +   L   +    ++  L HRLD+ TSG+L+
Sbjct: 3   DIVFEHKDFVVINKPCGVSVHSESEGDVCLTASLAQQL--GVERVWLVHRLDKATSGLLL 60

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  R +A  L+  F  + ++K Y +L    P  K+  +      K  +        K  
Sbjct: 61  FALNRDSAAALSAQFAEKTMRKTYLALGTHKPAKKQGWV------KGGMARSRRGTWKLT 114

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N+A++ F              +QP TG+THQLRV    +G PI+GD  Y  +   +
Sbjct: 115 RDEDNFAVTRFSS-QSLKPGLRLFVLQPFTGKTHQLRVAMKSIGSPILGDTLYGGDEAEH 173

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQIT-AP 310
                   L+LHA  +   +  G    I  AP
Sbjct: 174 --------LFLHAWRLVFDY-RGEHFDIRIAP 196


>gi|88802941|ref|ZP_01118468.1| pseudouridine synthase Rlu family protein [Polaribacter irgensii
           23-P]
 gi|88781799|gb|EAR12977.1| pseudouridine synthase Rlu family protein [Polaribacter irgensii
           23-P]
          Length = 234

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 103/244 (42%), Gaps = 29/244 (11%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID--GFLKSWVDSKGQKPRLTHRLDQET 154
           +   +++ED+ +    KP  I V          D    L+  ++ KG K    HRLD++T
Sbjct: 1   MHLEIIFEDAYVMCVCKPNNIVVHHAYHSRSVADERSLLQWILEVKGLKVYPIHRLDRKT 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI+++A+           F    I K Y+ +V G    +K       +  S + G    
Sbjct: 61  SGIILLAKETTYVSEFQALFTENTIDKTYYGVVRGFSPEEK-------IIDSPVKGRDAS 113

Query: 215 VVKQNEKGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           V ++       A++H K +             + ++  +E++P +GRTHQLR+H L +  
Sbjct: 114 VYRE-------ALTHLKTLAQRTLDIPVKPYDSSRYSLVELKPKSGRTHQLRLHTLKISH 166

Query: 265 PIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           P++GD KY               N L+LHA  ++  HP     L + A  PA     +  
Sbjct: 167 PLIGDSKYGDKNHDLMYAEKFGWNNLFLHAGKLEFQHPFSKENLVLKANFPADWTSLFQE 226

Query: 322 LGFK 325
             ++
Sbjct: 227 FSWE 230


>gi|145355458|ref|XP_001421978.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582217|gb|ABP00272.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 321

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 75/318 (23%), Positives = 122/318 (38%), Gaps = 91/318 (28%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           + +++ +L+ D  + V +KP G++   G+G+   +   L+  +DS+     + HRLD++T
Sbjct: 9   EAIRARVLHADEHVTVVDKPPGLATTRGNGVDVSVYD-LRHALDSEY----VVHRLDRDT 63

Query: 155 SGILVVARTRAAAQHLTESFRMRR------------------------IQKIYWSLVWGI 190
           SG+LV+ART  AA  L   F  +                         + K YW+L    
Sbjct: 64  SGVLVLARTAFAANRLNAMFAKKSRMDFTEIMRADMERGDAPSLSNDPVVKTYWALTSNP 123

Query: 191 PK--NKKECIANWLLK---------KSHIGGDYVHVVKQ------------------NEK 221
           P    +   I   L +            +GG  V+  K                      
Sbjct: 124 PPRGARSGWIEAPLTEVGDGDGYSTARLVGGWRVYDAKGGGVVVGTGESMRDKSNDAGSP 183

Query: 222 GANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYC------ 273
            +  A++HFKV+          LE+ P TGR HQLRVH    +  PI+GD+KY       
Sbjct: 184 ASKAAMTHFKVLASAGEDGPTLLELTPITGRKHQLRVHLAKALSSPIIGDYKYGFNDRRA 243

Query: 274 ---------------ANFKGNFTSPIQN---------KLYLHARYMDLPHPEGG-RLQIT 308
                          +  + +F   ++           L+LHAR +   HPE G   ++ 
Sbjct: 244 PWKSRFTDIESADVESEKESDFWRKLRRASLRGVSKIPLHLHARALQFVHPESGVSTRVV 303

Query: 309 APLPAHMVKTWDSLGFKY 326
           A  P H      +   K+
Sbjct: 304 AEPPPHFAAALRAFDLKF 321


>gi|319954748|ref|YP_004166015.1| pseudouridine synthase [Cellulophaga algicola DSM 14237]
 gi|319423408|gb|ADV50517.1| pseudouridine synthase [Cellulophaga algicola DSM 14237]
          Length = 222

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 63/223 (28%), Positives = 105/223 (47%), Gaps = 13/223 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           ++ E++   V NK AG   +        I+  L   +  K +KP +   HRLD+ TSG+L
Sbjct: 6   VVEENNDYIVVNKTAGYISEKNPYEDNTIEDQLFKHLLQKKRKPYIGVIHRLDRVTSGVL 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A+ ++      E F  R++QK Y ++V   P N K  + N+L+K +        +++ 
Sbjct: 66  IFAKKKSVLVAFNELFSSRQVQKTYLAIVKNKPANTKGDLVNFLVKNNK--DKRADIIQT 123

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K +      ++VI      +  LE+QP TGR HQ+R    H+G PI+GD KY ++ + 
Sbjct: 124 KSKESLDCSLSYEVIAKNNFGY-LLEVQPKTGRFHQIRAQLAHIGLPIIGDEKYGSDQEY 182

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWD 320
              S     + LH+  +              APLP +  K W+
Sbjct: 183 YPLS-----VCLHSWKLTYQVSGSNESKTFVAPLPKN--KFWE 218


>gi|126335409|ref|XP_001373489.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 1 [Monodelphis domestica]
          Length = 307

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 101/232 (43%), Gaps = 19/232 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSK-----GQKPRLTHRLDQET 154
           +LY+ S   V NK   + +          +   LK               R  H+LD  T
Sbjct: 11  ILYQSSDFIVVNKHWDLRIDSKMWYETLTLQSQLKHHFPELADPDTYYGFRFCHQLDFST 70

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L VA  +AAA    + F+ R++ K Y +LV G  +  +  I + + K +  G  ++ 
Sbjct: 71  SGALCVALNKAAAGRAYKCFKERQVTKAYLALVRGHVQESRMTINHAIGKNTTEGLTHMM 130

Query: 215 VVKQNE--KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            ++  E  + A   ++   V++           + +QP TGRTHQLRVH    G PIVGD
Sbjct: 131 CIEGTEGCENAKPCLTELTVLERGLYDGDPVSKVLLQPLTGRTHQLRVHCSSSGHPIVGD 190

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
             Y              ++ LHA Y+ +P   G  ++++ P P   V T D+
Sbjct: 191 FTYSFKKDIRPF-----RMMLHAFYLRIP-TCGELIEVSTPDP--FVPTLDA 234


>gi|115387957|ref|XP_001211484.1| DRAP deaminase [Aspergillus terreus NIH2624]
 gi|114195568|gb|EAU37268.1| DRAP deaminase [Aspergillus terreus NIH2624]
          Length = 507

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 52/233 (22%), Positives = 95/233 (40%), Gaps = 30/233 (12%)

Query: 72  NALNHIIKEQKILDSSVNLTKHSDF-LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            A + I+K  + L  +++  +     L   +++ED  + V +KPAG+ V       YH +
Sbjct: 78  PAPHRILKNGEKLQHTLHRHEPPVTGLPIGIIHEDDDLLVIDKPAGVPVHAAG--RYHYN 135

Query: 131 GFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             ++   +  G +  PR  +RLD+ TSG++ + +T   A+ +    + R +QK Y + V 
Sbjct: 136 SIIEILRNENGVEWMPRPCNRLDRLTSGVMFIGKTAKGAEKMCAKLQQRTVQKEYIARVK 195

Query: 189 GIPKNKKECIANWLL-KKSHIGGDYVHVVKQNEK------------------------GA 223
           G   +        ++     +G + V    ++ K                        G 
Sbjct: 196 GRFPDGVVICDQPIMQVSPKLGLNRVRATGKDAKTKFRRIAYYPPAAPAAGEEDSQGEGE 255

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
             A +    +    + +  +   P TGRTHQ+RVH   +G PI  D  Y    
Sbjct: 256 ERAATPPPALANEDEGYSIVHCLPLTGRTHQIRVHLQFLGHPITNDPIYSNRR 308


>gi|42522844|ref|NP_968224.1| pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
 gi|39574040|emb|CAE79217.1| Pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
          Length = 228

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 99/235 (42%), Gaps = 12/235 (5%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           +++ S  ++  ++ +     V NKP+G+SV         +    K       Q     HR
Sbjct: 1   MSRPSAPIQIPIVEKSKHWLVINKPSGVSVHNDPPDVRTL--LKKQLTPGTYQDIHPVHR 58

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ETSG+L+V      A +L+  F+  +++K Y++L+ G          +W    + I 
Sbjct: 59  LDKETSGLLLVGLDAETAANLSGQFQEHKVEKTYYALLRGELP----VSTDWQEWNTPIS 114

Query: 210 GDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                        K    A + +KV++   + F  +E++  TGR HQ+R H   +   IV
Sbjct: 115 DKAEGRKNPQGLLKDRVEARTLYKVLEAN-KYFSLVEVRLITGRQHQIRKHTALIRHAIV 173

Query: 268 GDHKYCANFKGNFTSPI--QNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           GD +Y         + I    +++LHA  M      G +    APLP    +   
Sbjct: 174 GDTRYGDPKYNERMANIYQTKRMFLHAARMT-VMINGYKHSFEAPLPPEFKEAMK 227


>gi|115529387|ref|NP_001070221.1| RNA pseudouridylate synthase domain-containing protein 1 [Danio
           rerio]
 gi|123908280|sp|Q08C69|RUSD1_DANRE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 1
 gi|115313685|gb|AAI24363.1| Zgc:153465 [Danio rerio]
          Length = 293

 Score =  140 bits (354), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 100/241 (41%), Gaps = 19/241 (7%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSK-----GQKPR 145
           + +      +LY+ +   V NK   I +          +   LK               R
Sbjct: 2   EPASLENLSVLYQSTNYIVVNKHWDIRIDSKMWYEKQTVQSQLKHHFPELADPGTYYGFR 61

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             H+LD  TSG L VA  +AAA      F+ RR+ K Y +LV G    +   +   + K 
Sbjct: 62  FCHQLDFSTSGALCVALNKAAAGQAYRCFKDRRVTKAYLALVRGTVTEENLSLDFAIGKN 121

Query: 206 SHIGGDYVHVVKQNE--KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHAL 260
           +  G  ++   +  E  +      +   V++       +   + +QP TGRTHQLRVH  
Sbjct: 122 TTEGKTHMMCTEGTEGCENPKPCQTEVTVLEYGTYDGDQVTKVLLQPLTGRTHQLRVHCS 181

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
            +G PIVGD+ Y      +       ++ LHA ++ +P      + +TAP P   V + D
Sbjct: 182 AIGHPIVGDYTYSLRTDNSPY-----RMMLHAYFLHIP-LHNEPIHVTAPDP--FVPSLD 233

Query: 321 S 321
           +
Sbjct: 234 A 234


>gi|320528188|ref|ZP_08029353.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
 gi|320131536|gb|EFW24101.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
          Length = 296

 Score =  140 bits (354), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 56/259 (21%), Positives = 104/259 (40%), Gaps = 31/259 (11%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKI 108
           D   VK    I   + + I     A++ I  E +                  ++YED+ I
Sbjct: 49  DGNTVKHGKEIIDHKTITITLPEEAVDWIPAETEC----------------KVVYEDAFI 92

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAA 166
           Y+ +K AG+ + G  G    ++ +   +  + G  Q  R  HRLD++T G+++ ++    
Sbjct: 93  YIVHKDAGMIIHGDPGDTTCLNAYAARYQINHGIKQPVRPIHRLDKDTVGLVIYSKIPFF 152

Query: 167 AQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
                     ++I + Y ++  G I  + +  I   L +  H  G     + +       
Sbjct: 153 QPWFDAQLSSKKIHRHYLAITNGNIDPSFRMTINKPLGRDRHNSG-----MYRVSSTGVE 207

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           AI++ + +  + Q +  L     TGRTHQ+RVH   +  PIV D  Y    K      + 
Sbjct: 208 AITYVEALGNY-QSYSLLGCTLETGRTHQIRVHLASIDHPIVNDILYGVKTKDFPAMGL- 265

Query: 286 NKLYLHARYMDLPHPEGGR 304
                 A +++  +P   +
Sbjct: 266 -----WANWIEFKNPITNK 279


>gi|219122503|ref|XP_002181583.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406859|gb|EEC46797.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 271

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 59/258 (22%), Positives = 104/258 (40%), Gaps = 23/258 (8%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        +  ++ G++RV  ++V     I+S  V+      +        
Sbjct: 31  LDVYVSE-FGSYPESYYRTAIQQGRIRVGNEKVDVAYTIRSNDVLTHTVHRH-------- 81

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               ++       V +KP  + V      AYH++  L    ++ 
Sbjct: 82  -----EPAVAVSQPQAPFVKVVANSETWLVVDKPGTMPVHPSG--AYHLNSLLPILENTY 134

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWG-IPKNKKECI 198
           G K    HRLD+ TSG++++ +T  AA+ L ++ + R    K+Y + V G  P N    +
Sbjct: 135 G-KLYPIHRLDRLTSGLVILGKTPEAARQLGKAIKERDSCTKLYIARVRGRFPFNCASHV 193

Query: 199 ANWLLKKSHIGG---DYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
            N    KS+        V      +K    A + F ++   A+     +  +P TGRTHQ
Sbjct: 194 PNLSSHKSYPPRYGEWSVLQDMDGKKDMKAAETSFALLKFDAKSDSSVVLCRPATGRTHQ 253

Query: 255 LRVHALHMGCPIVGDHKY 272
           +R+H  ++G PI  D  Y
Sbjct: 254 IRLHLQYLGHPIANDPNY 271


>gi|121997063|ref|YP_001001850.1| pseudouridine synthase [Halorhodospira halophila SL1]
 gi|121588468|gb|ABM61048.1| tRNA pseudouridine synthase C [Halorhodospira halophila SL1]
          Length = 249

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 93/238 (39%), Gaps = 6/238 (2%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHR 149
           T   D     +LY D ++    KPAG+ V   + I    D  L+   D  G       HR
Sbjct: 3   TADQDDRSLAILYRDERLIAVYKPAGLLVHRSN-IDRDRDVVLQRLRDQLGGHWVYPVHR 61

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+LV      AA  L  +FR +RI K Y ++V G        I   L       
Sbjct: 62  LDRATAGVLVFGLDPDAASVLAAAFREQRIGKRYQAVVRG-WVEAPGRIDRPLGAGRRGE 120

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           G        +     +      V      +F  L + P TGR HQLR H   +  PI+GD
Sbjct: 121 GGAPQPAVTDYVPLAWTELPIPVSRYDTARFTRLALHPQTGRQHQLRRHMKAISHPILGD 180

Query: 270 HKYCANFKGNF--TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGF 324
             +       F        +L L A  + +PHP +GG +++     A +   +   G 
Sbjct: 181 TTHGDGANNRFFREHFGARRLLLVATELVVPHPADGGAVRLATEPDAELQAIFRRAGL 238


>gi|319778799|ref|YP_004129712.1| ribosomal large subunit pseudouridine synthase A-like protein
           [Taylorella equigenitalis MCE9]
 gi|317108823|gb|ADU91569.1| ribosomal large subunit pseudouridine synthase A-like protein
           [Taylorella equigenitalis MCE9]
          Length = 289

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 65/287 (22%), Positives = 112/287 (39%), Gaps = 24/287 (8%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +PHI    LQK L+ G   V+ + +  +        +  P V ++     +E
Sbjct: 2   ID-FLIFRFPHIPPTILQKRLKKGD-FVNSEGISAD--------IDSPYVPDSWLWYFRE 51

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                      + ++  +  +LYED  I   +KP  ++   G G   H    +K      
Sbjct: 52  VD--------EEPTNPFELTILYEDDLIVAIDKPHLLASVPG-GYHLHESALIKLRRLLN 102

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                  HRLD+ET+G+LV  +           F+ R I K Y  +         +    
Sbjct: 103 NININPIHRLDRETAGVLVFCKQSKYRNAYQVMFQDRVINKSYECIA----PKPIDLSIF 158

Query: 201 WLLKKSHIGG-DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            L++KS+I   +    + +N +    + +  + +           + P TG+ HQLRVH 
Sbjct: 159 PLVRKSYICRSNNFFTMIENTELIPNSETRIEFVHTVKGGNALYRLFPSTGKKHQLRVHM 218

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
             +G PIV D+ Y         +   N L L AR ++   P  G  +
Sbjct: 219 SGLGLPIVHDNFYPVLLAQRDKNDFSNPLQLLARSIEFKDPISGEHR 265


>gi|257437725|ref|ZP_05613480.1| pseudouridine synthase, RluD [Faecalibacterium prausnitzii A2-165]
 gi|257200032|gb|EEU98316.1| pseudouridine synthase, RluD [Faecalibacterium prausnitzii A2-165]
          Length = 253

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 98/229 (42%), Gaps = 41/229 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED+ + V +KPAG++ + G   A      L+           + HRLD   SG++V 
Sbjct: 3   ILYEDTALVVLDKPAGLTSEEGVPAA------LRQRWGRPDAYVGVIHRLDTGVSGLMVY 56

Query: 161 ARTRAAAQHLTESFRMRR---------------------IQKIYWSLVWGIPKN---KKE 196
           ART  AA  LT+     +                       K Y +++ G P      + 
Sbjct: 57  ARTPGAAAALTKQVTESQQAYAILDGRVEAGPGAPAQPCFLKTYRAVIAGGPDEQLPPEG 116

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQL 255
            + ++L K S  G   V  VK+  KG   A+  +++++          E+  HTGRTHQ+
Sbjct: 117 ILRDYLFKDSRKGR--VFPVKRPRKGVREAVLEYRIVETAPDGSLSLAEITLHTGRTHQI 174

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           RV       P+ GD KY + FKG+        + L +  +   HPE G 
Sbjct: 175 RVQFASRKHPLYGDGKYGSRFKGD--------IALQSAGLQFVHPETGE 215


>gi|299530540|ref|ZP_07043960.1| pseudouridine synthase [Comamonas testosteroni S44]
 gi|298721516|gb|EFI62453.1| pseudouridine synthase [Comamonas testosteroni S44]
          Length = 255

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 62/262 (23%), Positives = 103/262 (39%), Gaps = 33/262 (12%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
               L   S      +L++D  + V  KPAG  V      A+     +++  D  G    
Sbjct: 2   PDTALPDGSANPPLHILWQDEHMVVVYKPAGWLVHRTGLDAHETRFVMQTLRDQLGHHVW 61

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD+ T G+L++A  + AAQ L  SF     +K Y +LV G      E + + L   
Sbjct: 62  PVHRLDKGTCGVLLMALHKQAAQALAASFAAHETRKEYRALVRGWLPETLE-VDHPLKPD 120

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-----------KFCWLEMQPHTGRTHQ 254
                         +     A +H + +   +            +   +E  P TGR HQ
Sbjct: 121 D----------APEDAPVQDAHTHLRCLARLSWPESYDGRHPETRISLVEALPTTGRRHQ 170

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +R H  H+  PI+GD  +       + +    Q +L+LHAR +++ HP  G+ ++  A  
Sbjct: 171 IRRHLKHVAHPIIGDATHGKGPLNRWWAERLGQQRLWLHARALEIAHPVSGQLMRFEADW 230

Query: 312 PA--------HMVKTWDSLGFK 325
            +           K     G++
Sbjct: 231 SSLTQLQEARDWQKLLALPGWQ 252


>gi|47459310|ref|YP_016172.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma mobile
           163K]
 gi|47458640|gb|AAT27961.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma mobile
           163K]
          Length = 314

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 56/311 (18%), Positives = 111/311 (35%), Gaps = 31/311 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIP 68
            +V+ ++    + ++       I    L+K+ R+  ++++ KR+      +Q    + + 
Sbjct: 23  FIVQENDTKRTIYKYLLRMLNTIPKSKLEKLFRNKDIKINGKRISSKTYVLQFNDEIEVF 82

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            + +  +    E          T  +   K  +++E+  I + NKP  + +         
Sbjct: 83  GIFDEDSI---ENFTRSKQKKQTTKTFDKKLEIIFENLDILIINKPNNLIMHSSKNSLDE 139

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                 ++V      P    RLD+ETSG++V A+       L +          +     
Sbjct: 140 QVLNYLNYVKIDSFVPTHIGRLDKETSGLVVYAKNYKTLIELLDKQSDFEKIYTFIPFCN 199

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
              K+    +        +I  D ++   Q       +I+       +         Q  
Sbjct: 200 LSEKDVLVTV--------NISEDEINKKMQISNEGKKSITRIF----YDGNSQRYYAQIL 247

Query: 249 TGRTHQLR-VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ- 306
           TGR HQ+R V A  + CPI+G+ KY    K         +L+LH+  +   H     L+ 
Sbjct: 248 TGRKHQIRLVLADFLKCPILGERKYANLTKD-------KRLFLHSYKLTF-HNLNEPLEY 299

Query: 307 -----ITAPLP 312
                  A +P
Sbjct: 300 LNEKVFKAKIP 310


>gi|86142154|ref|ZP_01060664.1| ribosomal large subunit pseudouridine synthase D [Leeuwenhoekiella
           blandensis MED217]
 gi|85830906|gb|EAQ49363.1| ribosomal large subunit pseudouridine synthase D [Leeuwenhoekiella
           blandensis MED217]
          Length = 203

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 59/210 (28%), Positives = 97/210 (46%), Gaps = 15/210 (7%)

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTES 173
           +QG       +   +KS++  K  KP      + HRLD+ TSGI++ ART  A   L + 
Sbjct: 1   MQGDKTGDKPLSEVVKSYIAEKYNKPGAVYLGVVHRLDRPTSGIVIFARTSKALPRLNKL 60

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F  +  +K YW+LV   P    + + ++L +       Y H+ + ++  +   I  ++V+
Sbjct: 61  FAAKEAKKTYWALVKESPPKTSDRLVHYLKRNPKQNKSYSHINEVSD--SKKGILEYRVL 118

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                 +  LE+  HTGR HQ+R     +GCPI GD KY  +      S     ++LH+R
Sbjct: 119 KEL-NNYTLLEVDLHTGRHHQIRSQLSAIGCPIKGDLKYGFDRSNPDGS-----IHLHSR 172

Query: 294 YMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
            + L HP     +   A  P+     W + 
Sbjct: 173 KLTLVHPVQKKEMTFIAEPPSE-DALWQAC 201


>gi|126278380|ref|XP_001381115.1| PREDICTED: similar to RPUSD2 protein [Monodelphis domestica]
          Length = 503

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 69/339 (20%), Positives = 132/339 (38%), Gaps = 40/339 (11%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
              L   +   +   +    +   ++G++R++++ V+                   L  I
Sbjct: 120 GRSLLHVYSTEFRAHSVAYYEAAAQAGRLRLNEQPVR------------------DLGVI 161

Query: 78  IKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +K+   L ++V+  +     + I LL E+  + V +KP+ + V       ++   F+   
Sbjct: 162 LKDNDFLRNTVHRHEPPVTAEPIHLLAENDDVVVVDKPSSMPVHPCGRFRHNTVIFVLG- 220

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            + + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G   +++ 
Sbjct: 221 KEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPSEEV 280

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +L  S     Y   + + +       + F+ +         +  +P TGRTHQ+R
Sbjct: 281 TCKEPILVVS-----YKVGLCRVDPRGKPCETVFQRLSYNGHS-SVVRCRPLTGRTHQIR 334

Query: 257 VHALHMGCPIVGDHKY------CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ---- 306
           VH   +G PI+ D  Y       A  +G       ++L    R +   H     L     
Sbjct: 335 VHLQFLGHPIINDPIYNTAAWGPARGRGGHIPKTDDELL---RDLVEEHRAKQSLDILDL 391

Query: 307 ITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNI 345
               LP  +    D L  K D           +E  Q  
Sbjct: 392 FEGDLPPDLKPPSDPL-LKQDLKEPKATTRDLEEPNQAA 429


>gi|85713493|ref|ZP_01044483.1| pseudouridine synthase [Nitrobacter sp. Nb-311A]
 gi|85699397|gb|EAQ37264.1| pseudouridine synthase [Nitrobacter sp. Nb-311A]
          Length = 298

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 68/267 (25%), Positives = 105/267 (39%), Gaps = 64/267 (23%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
              + +++ +L+ D  + V +KPAGI+V  G     +++    +      + P L HRLD
Sbjct: 6   PTPEEIQARVLHRDGLMLVIDKPAGIAVHRGPKGGANLEASFDALRFGLPRPPVLAHRLD 65

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++TSG LV+ R R A   L   F+  +I K YW++V G P + +  I   L + +   G 
Sbjct: 66  RDTSGCLVLGRHRKATASLGLLFKHGKISKTYWAVVEGGPTDDEGTIDIPLGRMNEERGW 125

Query: 212 YVHVVKQNEKGANYAISHFK-----VIDCFAQKF-------------------------- 240
           +     + +     +I+ +K     V+      F                          
Sbjct: 126 WQ----KPDPNGLPSITTWKVLGRGVLTAAGDHFSPSRCGEGPGVGANGFDIPTNHPPPQ 181

Query: 241 ----------------------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                                  WL ++P TGRTHQLRVH   MG PIVGD  Y      
Sbjct: 182 PSPTREEGAEIPPSDIDRTTLLTWLALEPMTGRTHQLRVHCAAMGWPIVGDSIYGTQASL 241

Query: 279 NFTSPIQ-------NKLYLHARYMDLP 298
                 Q         L+LHAR + +P
Sbjct: 242 RRLRNEQYIPRLDDPGLHLHAREIAVP 268


>gi|301612808|ref|XP_002935894.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 1
           [Xenopus (Silurana) tropicalis]
          Length = 299

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 64/226 (28%), Positives = 94/226 (41%), Gaps = 17/226 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSK-----GQKPRLTHRLD 151
           K  +LY+ +   V NK   I +          +   LK               R  H+LD
Sbjct: 8   KLSILYQSADFLVVNKHWDIRIDSKMWYEKLTVQSQLKHRFPELADPGTYYGFRFCHQLD 67

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG L VA  + AA    + F+ R + K Y +LV G    K   I+  + K +  G  
Sbjct: 68  FSTSGALCVALNKEAAGRAYQCFKDRTVTKAYLALVRGTVSEKYMRISLAIGKNTQEGLT 127

Query: 212 YVHVVK--QNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           ++  V+     K A    +   V+            + +QP TGRTHQLRVH   +G PI
Sbjct: 128 HMMCVEGAPGCKNAKPCQTDLVVLQHGSYKGDPVTKVLLQPLTGRTHQLRVHCSALGFPI 187

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           VGD  Y              ++ LHA Y+ +P  +   +++TAP P
Sbjct: 188 VGDFTYSFKKDSEPY-----RMMLHAYYLRIP-TDHELIEVTAPDP 227


>gi|264679457|ref|YP_003279364.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
 gi|262209970|gb|ACY34068.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
          Length = 255

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 62/262 (23%), Positives = 102/262 (38%), Gaps = 33/262 (12%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
               L   S      +L++D  + V  KPAG  V      A+     +++  D  G    
Sbjct: 2   PDTALPDGSANPPLHILWQDEHMVVVYKPAGWLVHRTGLDAHETRFVMQTLRDQLGHHVW 61

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD+ T G+L++A  + AAQ L  SF     +K Y +LV G      E + + L   
Sbjct: 62  PVHRLDKGTCGVLLMALHKQAAQALAASFAAHETRKEYRALVRGWLPETLE-VDHPLKPD 120

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-----------KFCWLEMQPHTGRTHQ 254
                         +     A +H + +   +            +   +E  P TGR HQ
Sbjct: 121 D----------APEDAPVQDAHTHLRCLARLSWPESYDGRHPETRISLVEALPTTGRRHQ 170

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           +R H  H+  PI+GD  +       + +    Q +L+LHAR +++ HP  G+ +   A  
Sbjct: 171 IRRHLKHVAHPIIGDATHGKGPLNRWWAERLGQQRLWLHARALEIAHPVSGQLMHFEADW 230

Query: 312 PA--------HMVKTWDSLGFK 325
            +           K     G++
Sbjct: 231 SSLTQLQEARDWQKLLALPGWQ 252


>gi|219126856|ref|XP_002183664.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217404901|gb|EEC44846.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 235

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 62/236 (26%), Positives = 91/236 (38%), Gaps = 34/236 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGIL 158
           ++Y DS I V NKP  +    G      +   +        Q     + HRLD  TSGI+
Sbjct: 3   IVYHDSDIVVVNKPPDVLTVPGIHSRSCVLDLVHDRFGEAVQDKAHMIVHRLDMATSGIV 62

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +  RT    + +   FR R + K Y +L+ G     K  I   L +  H    ++ +   
Sbjct: 63  LFGRTLNITKRMQAIFRDRLVLKTYQALLMGHFPIDKGTIDLPLQRD-HEYPPFMRISTP 121

Query: 219 NE---------------------KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQ 254
                                  K    + + F+V+         F  +E+ P TGRTHQ
Sbjct: 122 TSEADAVQAVKDLQQHGWKKLIRKKPKPSQTSFRVLARSFRNGLPFTRMELVPVTGRTHQ 181

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           LRVH   +G PIVGD  Y      +   P +  + LHA  +   HP  G  +   A
Sbjct: 182 LRVHCAALGYPIVGDPTY------DEYVPNEKAMCLHAALLQCEHPTTGMPIVFEA 231


>gi|269798687|ref|YP_003312587.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269095316|gb|ACZ25307.1| pseudouridine synthase [Veillonella parvula DSM 2008]
          Length = 372

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 55/320 (17%), Positives = 120/320 (37%), Gaps = 67/320 (20%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
               +L K+     + ++  +    + I     + I      ++H   E           
Sbjct: 78  YPRKSLVKLFEEKLIHINGHKATPKDAISVDDEIWIAMAKEKIDHDPIE----------- 126

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRLTHR 149
                +   +LYED  +++ +KP+G++V   S     +   +  +    G  +K R  +R
Sbjct: 127 -----MDLSVLYEDEDLFIVDKPSGVTV--NSKDRLSLANGVAHYFKEHGIKRKVRFLNR 179

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS--- 206
           LD++T+G +V+A++  A     +       +K Y + V GI +  ++ +   + + +   
Sbjct: 180 LDRDTTGCIVIAKSGLAQSLYQQQMDDNTFEKWYMATVEGIVEADEDTLVFPMERSADGI 239

Query: 207 ---------HIGGDYVHVVKQNEKGANYAISHFK-------------------------- 231
                        D+  + + + +  + +++  +                          
Sbjct: 240 HYEVNAKGKETRTDFSVLCRHSSQPVDNSVNKSENSVDIGLKNVDIELVDVDKNNLNVDK 299

Query: 232 -VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
            V       +  + ++ +TG+THQ+RV   H+G P+VGD  Y A   G    P Q +   
Sbjct: 300 TVYKSNKCGYTEVLVRLYTGKTHQIRVAFSHIGHPLVGDTLYGAQPTGQ---PFQLR--- 353

Query: 291 HARYMDLPHPEGGR-LQITA 309
            A+ +   H   G  + + A
Sbjct: 354 -AQKVVFTHIRTGEHITVMA 372


>gi|91791480|ref|YP_561131.1| pseudouridine synthase RluA-like protein [Shewanella denitrificans
           OS217]
 gi|91713482|gb|ABE53408.1| Pseudouridine synthase RluA-like protein [Shewanella denitrificans
           OS217]
          Length = 226

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 57/197 (28%), Positives = 90/197 (45%), Gaps = 17/197 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ ++S   V +K AG+      G A    G +       G K    HRLD  TSG+L++
Sbjct: 4   IISDESDFIVIDKYAGVHFHSQDGSA----GVVAQLEADLGIKLFAVHRLDTPTSGLLIL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+   AA+  TE F   ++QK Y ++  G PK K+  +   + K          + K   
Sbjct: 60  AKNPLAARRFTEMFTEHKVQKYYLAIAQGKPKKKQGWVIGDMAKA------RRSMFKLLR 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F       +      ++PH+G+THQLRV    +G PI+GD  Y  N   + 
Sbjct: 114 STENPAVTQFFS-HSIVEGLRLYLLKPHSGKTHQLRVALASIGVPILGDKLYGVNSAEH- 171

Query: 281 TSPIQNKLYLHARYMDL 297
                ++ YLHA  +D 
Sbjct: 172 -----DRCYLHAYCLDF 183


>gi|255067175|ref|ZP_05319030.1| pseudouridine synthase Rlu family protein [Neisseria sicca ATCC
           29256]
 gi|255048543|gb|EET44007.1| pseudouridine synthase Rlu family protein [Neisseria sicca ATCC
           29256]
          Length = 207

 Score =  140 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 56/223 (25%), Positives = 91/223 (40%), Gaps = 20/223 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP G+SV    G                 ++  L HRLD+ TSG+L+ 
Sbjct: 4   ILFRHPDFVAVNKPCGVSVHQEEGEVSLTQTLAAQL---GLEQVWLLHRLDKLTSGVLLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + +A  L + F  + ++K Y +L    P  K+  I   + K           ++   
Sbjct: 61  ALNQQSASELAQQFAAKTMRKTYLALATDKPSKKQGWIKGDMEKSRRGAWKLTRGME--- 117

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F              + PHTG+THQLRV    +G PI+GD  Y        
Sbjct: 118 ---NPAVTEFGS-HSLEPGLRLFVLHPHTGKTHQLRVAMKSLGSPILGDTLYGGKPA--- 170

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM-VKTWDSL 322
                ++++LHA  +   + +G   +I A L     ++  D L
Sbjct: 171 -----SRMFLHAWKIKFDY-QGQTFEIVASLSEEWPLRNIDFL 207


>gi|242309404|ref|ZP_04808559.1| ribosomal large subunit pseudouridine synthase [Helicobacter
           pullorum MIT 98-5489]
 gi|239523975|gb|EEQ63841.1| ribosomal large subunit pseudouridine synthase [Helicobacter
           pullorum MIT 98-5489]
          Length = 313

 Score =  140 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 66/274 (24%), Positives = 113/274 (41%), Gaps = 36/274 (13%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
            K  + I  G   RI      L +  K + +      L           L+E+  + +F+
Sbjct: 29  AKAQSFINKG---RIFYGNKTLGNNEKNKILEKEVEILLFVPQSKGLKPLFENEDLAIFD 85

Query: 113 KPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           KPA + +      A+H    +    ++ GQ+  L HR+D+ETSG+++V + + + Q L E
Sbjct: 86  KPAKMLIHPKGRFAHH--SLIDEVREACGQESTLIHRIDKETSGLVLVGKHKRSIQELGE 143

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD-------YVHVVKQNEKGANY 225
            F  ++I+K Y +LV G  +    C++  L      GGD       +  ++K        
Sbjct: 144 LFAKKKIKKEYLALVRGEMRGGDFCLSLPLA-MQKKGGDLSVRSIYWGQILKAQSLNFKA 202

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN---------- 275
           A S F+++         L++ P TGRTHQ+R+H   +G PI+GD  Y             
Sbjct: 203 AKSEFEILGYINGN-TLLKVYPITGRTHQIRIHLFALGFPILGDPLYGCEDWQSREYLDS 261

Query: 276 ------------FKGNFTSPIQNKLYLHARYMDL 297
                        +         +L LHA  ++ 
Sbjct: 262 EFISKNDSLGLCEEKRIEYFGAERLMLHAYSLEF 295


>gi|312829403|emb|CBX34245.1| RNA pseudouridylate synthase family protein [Staphylococcus aureus
           subsp. aureus ECT-R 2]
          Length = 284

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 124/303 (40%), Gaps = 38/303 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPRE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQ 142
              SVNL  ++  L+  +LYED+ I +  KP   +       +   +   +       G+
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCTPSREHLHESLIEQVLYHCQEHGE 119

Query: 143 K--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD  T+GI++ A+        ++      ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDHNTTGIVIFAKYGHIHHLFSKVN----LKKIYTCLVYG--KTHTSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
           H+G PIVGD  Y           +Q         +   HP     + IT      ++K +
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLF 281

Query: 320 DSL 322
           + L
Sbjct: 282 NQL 284


>gi|218767409|ref|YP_002341921.1| putative psedouridine synthase [Neisseria meningitidis Z2491]
 gi|121051417|emb|CAM07710.1| putative psedouridine synthase [Neisseria meningitidis Z2491]
          Length = 220

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 62/211 (29%), Positives = 95/211 (45%), Gaps = 19/211 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV   SG            +    ++  L HRLD++TSGIL+ 
Sbjct: 6   ILFRHQDFVAINKPGGISVHQDSGETRLARTL---AIQLGVERVWLLHRLDKQTSGILLF 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  R +A  L+  F  + I+K Y +L    P  K+  I   + K          + K   
Sbjct: 63  ALNRESASALSGQFVGKSIKKTYLALSDRKPSKKQGWIKGGMEKS------RCGMWKLTR 116

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F  I   A+K     ++PHTG+THQLRV    +G PI+GD  Y        
Sbjct: 117 NTENIAVTRFHSI-SIAEKLRLFILEPHTGKTHQLRVAMKSLGSPILGDSLYGGTESET- 174

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                  ++L+A  +   + +  +++I APL
Sbjct: 175 -------MFLYAWKIQFDY-QNRQIEIVAPL 197


>gi|189237270|ref|XP_973027.2| PREDICTED: similar to ribosomal pseudouridine synthase [Tribolium
           castaneum]
          Length = 487

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 108/262 (41%), Gaps = 27/262 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             R+   F   +        ++ +++G + V+  +V  + +++   +         L ++
Sbjct: 65  GERILDVFAREFRAHPAEEYERCIQAGTLTVNYDKVPIDYKLKHNDL---------LANV 115

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +   ++  +S  +T         +++ D  I V NKPA I V       ++   F+ +  
Sbjct: 116 VHRHEVPVTSQPIT---------IVHMDEDIVVVNKPASIPVHPCGRYRHNTVVFILA-K 165

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
           +   +  R  HRLD+ TSG+L+  R+   A+ +    R R +QK Y   V G  P    E
Sbjct: 166 EYNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEHQIRNRLVQKEYVCRVEGEFPDEIIE 225

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C     +    IG      V +         + F+ +     K   +  +P TGR HQ+R
Sbjct: 226 CKEPIEVVSYKIG------VCKVSPKGKDCNTIFQKLGFNG-KTSIVLCKPKTGRMHQIR 278

Query: 257 VHALHMGCPIVGDHKYCANFKG 278
           VH  ++G P+V D  Y     G
Sbjct: 279 VHLQYLGYPVVNDPLYNHEVFG 300


>gi|311251719|ref|XP_003124746.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Sus scrofa]
          Length = 312

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 64/236 (27%), Positives = 101/236 (42%), Gaps = 23/236 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---------RLTHRLD 151
           ++Y      V NK   + +      A+     L+  +  +  +          R  H+LD
Sbjct: 11  VVYRSHDFLVVNKHWDVRI---DSKAWRETLTLQKQLRHRFPELADPDTCYGFRFCHQLD 67

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG L VA  +AAA      F+ RR+ K Y +LV G  +  +  I+  + K S  G  
Sbjct: 68  FSTSGALCVALNKAAAGSAYRCFKDRRVTKAYLALVRGHIQESRVTISYAIGKNSTEGRT 127

Query: 212 YVHVVK--QNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           +   ++  Q  +    +++   V++           + +QP TGRTHQLRVH   +G PI
Sbjct: 128 HTMCIEGTQGCENPKPSLTELVVLEHGLYGGDPVSKVLLQPLTGRTHQLRVHCSALGHPI 187

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           VGD  Y     G    P   ++ LHA Y+ +P     R++   P P   V   D+ 
Sbjct: 188 VGDLTYG-QASGREDQPF--RMMLHAFYLRVP-TCTERVEACTPDP--FVPALDAC 237


>gi|294954338|ref|XP_002788118.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239903333|gb|EER19914.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 393

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 61/289 (21%), Positives = 111/289 (38%), Gaps = 58/289 (20%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
            ++ G++ +D  +V+ ++ +Q  +++                 I ++ VN        + 
Sbjct: 79  AIKEGKITIDFNKVEPDHVLQGNELL-----------------IHETIVNENPVPFDGEL 121

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-----KPRLTHRLDQET 154
            ++ E   +   +KP+G+ V  G G   H    L + +  +            HRLD+ T
Sbjct: 122 KIVGETDDVVAVDKPSGMPVHSGGG---HRVNCLSAILKEQDPSRFSLAIHTLHRLDRLT 178

Query: 155 SGILVVARTRAAAQHLTESFRMR--RIQKIYWSLVWGIPKNKKECIAN------------ 200
           SGI+++ +    A+  +E+F+     IQK Y + V G  +     +              
Sbjct: 179 SGIVILGKNPDVARAFSEAFKKHDQEIQKCYLARVKGKFEGSNVVVEGFMRCVDFRVGKF 238

Query: 201 WLLKKSH----------------IGGDYVHVVKQNEKGANYAISHF-KVIDCFAQKFCWL 243
            L+K +                   GD    V++      ++ + F KV          +
Sbjct: 239 ILVKSNKGTASEDANQGDAPTSTPSGDDKSAVEEEHIEDKWSQTSFDKVWYDEQNDETII 298

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           +  P TGRTHQ+RVH   +G PI  D  Y   +K +   P    L  HA
Sbjct: 299 KCYPKTGRTHQIRVHLESIGHPIANDSCYGGEYKAD--HPFAFPLAPHA 345


>gi|301754896|ref|XP_002913309.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Ailuropoda melanoleuca]
          Length = 511

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 112/255 (43%), Gaps = 26/255 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L   F   +        +  +R G++ ++++ V                    L+ ++K+
Sbjct: 128 LLHVFSTEFRAQPLAYYEAAVREGRLHLNEEPV------------------QDLSIVLKD 169

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              L + V+  +     + + LL E+  + V +KP+ I V       ++   F+    + 
Sbjct: 170 NDFLRNRVHRHEPPVTAEPVRLLAENEDMVVVDKPSSIPVHPCGRFRHNTVIFILG-KEH 228

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++    
Sbjct: 229 QLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVICK 288

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             +L  S+     V V + + +G     + F+ +         +  +P TGRTHQ+RVH 
Sbjct: 289 EPILVVSY----KVGVCRVDARG-KPCETVFQRLSYNGHS-SVVRCRPLTGRTHQIRVHL 342

Query: 260 LHMGCPIVGDHKYCA 274
             +G PI+ D  Y +
Sbjct: 343 QFLGHPILNDPIYNS 357


>gi|298736716|ref|YP_003729246.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori B8]
 gi|298355910|emb|CBI66782.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori B8]
          Length = 298

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 71/300 (23%), Positives = 121/300 (40%), Gaps = 29/300 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVSLI------------HFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +     L++E     VF+KP  +      G  YH +  L       G+     HRLD E
Sbjct: 64  PNEKTQALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D  
Sbjct: 122 TSGLVLAGKTLQSAKDLKALFMQKKVKKTYLALAHGLV-DKNIVIDKPILTPQNIQKDLR 180

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              K +      + +  + +          L++ P TGRTHQ+R+H   +G  IVG+  Y
Sbjct: 181 IRSKIS-PLGKPSTTLVEPLSYNPFLDISLLKITPITGRTHQIRLHLSSVGHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
               +         +      L LHA  ++    +    +IT+P+P   +     L   Y
Sbjct: 240 GVIDENAREYLQLKRENNAPLLMLHASSLEFEF-KKAFYEITSPMPKRFMPFLKDLALFY 298


>gi|332876875|ref|ZP_08444629.1| RNA pseudouridine synthase [Capnocytophaga sp. oral taxon 329 str.
           F0087]
 gi|332685158|gb|EGJ58001.1| RNA pseudouridine synthase [Capnocytophaga sp. oral taxon 329 str.
           F0087]
          Length = 202

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 57/201 (28%), Positives = 92/201 (45%), Gaps = 15/201 (7%)

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHL 170
           G  VQG       +   LK+++  K  KP      + HRLD+ T+G+++ A+T  A   L
Sbjct: 2   GDIVQGDKTGDIPLSEHLKAYLKKKYNKPGEAYLGVVHRLDRPTTGVVLFAKTSKALSRL 61

Query: 171 TESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
              F  + ++QK YW+LV  +P   +  + +WL++         H   +  + +  A+ H
Sbjct: 62  NAMFADKAQVQKTYWALVDAMPPATEGTLTHWLVRNEKQNKSVAH--NKEVQHSKKAVLH 119

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           +K++  F   +  LE+   TGR HQ+R     +G  I GD KY A       S     + 
Sbjct: 120 YKLLKSF-DHYHLLEIDLITGRHHQIRAQLAAIGLHIKGDLKYGAK-----RSNPDGGIC 173

Query: 290 LHARYMDLPHPEGGR-LQITA 309
           LHA  +   HP     + I A
Sbjct: 174 LHAYKLTFEHPVKKEVISIEA 194


>gi|145636754|ref|ZP_01792420.1| hypothetical protein CGSHiHH_06555 [Haemophilus influenzae PittHH]
 gi|145270052|gb|EDK09989.1| hypothetical protein CGSHiHH_06555 [Haemophilus influenzae PittHH]
          Length = 224

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 60/201 (29%), Positives = 92/201 (45%), Gaps = 16/201 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  ++Y+ S   + NKP GISV          +   K        K  L HRLD+ TSG
Sbjct: 1   MEIEVVYQHSDFIIINKPEGISVHKDQEEQGLTELVAKQL---NVPKVWLVHRLDKVTSG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A    +A   +  F   +I K Y +L    PK K+  I   + KK+  G   +   
Sbjct: 58  LLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGDM-KKARDGAWKLCQT 116

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K+N      AI+ F  + C         ++P TG+THQLRV    +G PI+GD  Y  N 
Sbjct: 117 KEN-----PAITRFASVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDGLYGKNT 170

Query: 277 KGNFTSPIQNKLYLHARYMDL 297
           +        ++ YLHA  ++ 
Sbjct: 171 EK------IDRTYLHATQLEF 185


>gi|190573986|ref|YP_001971831.1| hypothetical protein Smlt2019 [Stenotrophomonas maltophilia K279a]
 gi|190011908|emb|CAQ45529.1| conserved hypothetical protein [Stenotrophomonas maltophilia K279a]
          Length = 295

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 70/305 (22%), Positives = 112/305 (36%), Gaps = 28/305 (9%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  MT   ++ +        LD      +P I     Q     G+V+  + R      + 
Sbjct: 1   MDAMTLPSHLQLPPGHWPSLLD-GLCARFPRIGRAQWQDRFARGRVQDAQGRA-----LA 54

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
                ++   I     +  E +I                 +L+ D+ + V +KP  + V 
Sbjct: 55  PDMPWQVGLEIQYFREVADEPEIP------------FAETILHLDAHLLVADKPHFLPVT 102

Query: 121 GGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              G  Y  +  L   V   G  +    HRLD+ T+G+++ +   A        FR RRI
Sbjct: 103 PAGG--YVRETLLSRLVARTGNTELAPLHRLDRLTAGLVLFSTQAATRDAYQRLFRERRI 160

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
           +K Y +L   +P      +A  LL+ S +             G   A S  + I+     
Sbjct: 161 EKTYEALAPALP-----GLAFPLLRDSRLVPGEPFFRMAEVPGEPNARSLIEPIEAEG-P 214

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
                ++P TGR HQLRVH   +G PI GD  Y    +       ++ L L A+ +    
Sbjct: 215 VWRYRLKPETGRKHQLRVHMAMLGAPIEGDDLY-PQLRPRRDDTFESPLQLLAQGLAFDD 273

Query: 300 PEGGR 304
           P  G 
Sbjct: 274 PLTGE 278


>gi|109947518|ref|YP_664746.1| putative ribosomal pseudouridine synthase [Helicobacter acinonychis
           str. Sheeba]
 gi|109714739|emb|CAJ99747.1| putative ribosomal pseudouridine synthase [Helicobacter acinonychis
           str. Sheeba]
          Length = 293

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 68/287 (23%), Positives = 120/287 (41%), Gaps = 29/287 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q+VR   +I  +  +I                +  +  
Sbjct: 28  LKEAQRHLDKQRLKQNQ-----QIVRKSQIIQGIVSLI------------YFKPNEKQGK 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     +F+KP  +      G  YH +  L       G+     HRLD ETSG+++V
Sbjct: 71  LVFETKDFGIFDKPTQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLV 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  + + L   F  ++++K Y +LV G+  ++   I   +L   +I  D     K   
Sbjct: 129 GKTPQSTKDLKALFMQKKVKKTYLALVHGLM-DQNTTIDKPILTPENIQKDLRIRSKI-S 186

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                + +  + +   +      L++ P TGRTHQ+R+H   M   IVG+  Y    +  
Sbjct: 187 PLGKPSTTLVEPLAYNSFLDVSLLKITPLTGRTHQIRLHLSSMNHRIVGEGLYGVADENA 246

Query: 280 FTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                  +      L LHA  ++    +G   +IT+P+P   +    
Sbjct: 247 REYLQLKRENNAPLLMLHALSLEFEF-KGAHYKITSPMPKRFMPFLK 292


>gi|303228653|ref|ZP_07315478.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302516633|gb|EFL58550.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 335

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 55/354 (15%), Positives = 115/354 (32%), Gaps = 86/354 (24%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +  +Q+   +       LD              + K+     + V+  +   +  +    
Sbjct: 20  IESIQHATTDAITLGQLLD-------TKYPRKAMVKLFDEKLIHVNGHKATPHTEVAVDD 72

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I      ++H                    +   +LYED  + + +KPAG++V   S
Sbjct: 73  EIWIAMAKEKIDH----------------EPIAMDLHILYEDDDLLIVDKPAGVTV--NS 114

Query: 124 GIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                +   +  +    G  +K R  +RLD++T+G +V+A++  A     +       +K
Sbjct: 115 KDQVSLANGIAHYFMEHGIKRKVRFLNRLDRDTTGCIVIAKSGLAQSLYQQQMDDNTFEK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-- 239
            Y ++V G+ ++  + +         +      +  +         + F V+  +     
Sbjct: 175 WYMAIVEGLVESDSDSLVLP------MDRSIDGIHYEVNSKGKETRTDFTVLHRYPDGAV 228

Query: 240 -------------------------------------------FCWLEMQPHTGRTHQLR 256
                                                         + ++ +TG+THQ+R
Sbjct: 229 DNSVHNLQNIVDISHENVDSTVNTVDKQGGIVDNSVHNLENQPCTAVAVRLYTGKTHQIR 288

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           V   H+G P++GD  Y A   G           L A  +   H   G R+ + A
Sbjct: 289 VAFSHIGHPLLGDTLYGAKSTGE-------PFALRAMKVVFTHMRSGDRITVQA 335


>gi|148825678|ref|YP_001290431.1| hypothetical protein CGSHiEE_03090 [Haemophilus influenzae PittEE]
 gi|229846961|ref|ZP_04467067.1| hypothetical protein CGSHi7P49H1_05916 [Haemophilus influenzae
           7P49H1]
 gi|148715838|gb|ABQ98048.1| hypothetical protein CGSHiEE_03090 [Haemophilus influenzae PittEE]
 gi|229810045|gb|EEP45765.1| hypothetical protein CGSHi7P49H1_05916 [Haemophilus influenzae
           7P49H1]
 gi|309972824|gb|ADO96025.1| Probable pseudouridylate synthase [Haemophilus influenzae R2846]
          Length = 224

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 60/201 (29%), Positives = 92/201 (45%), Gaps = 16/201 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  ++Y+ S   + NKP GISV          +   K        K  L HRLD+ TSG
Sbjct: 1   MEIEVVYQHSDFIIINKPEGISVHKDQEEQGLTELVAKQL---NVPKVWLVHRLDKVTSG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A    +A   +  F   +I K Y +L    PK K+  I   + KK+  G   +   
Sbjct: 58  LLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGDM-KKAREGAWKLCQT 116

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K+N      AI+ F  + C         ++P TG+THQLRV    +G PI+GD  Y  N 
Sbjct: 117 KEN-----PAITRFASVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDGLYGKNT 170

Query: 277 KGNFTSPIQNKLYLHARYMDL 297
           +        ++ YLHA  ++ 
Sbjct: 171 EK------IDRTYLHATQLEF 185


>gi|301622434|ref|XP_002940545.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Xenopus (Silurana) tropicalis]
          Length = 497

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 56/221 (25%), Positives = 103/221 (46%), Gaps = 10/221 (4%)

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS-ILLYEDSKIYVFNKPAGIS 118
           Q+G++      +  LN ++K    L ++V+  +     +   +L E+ ++ V +KP+ + 
Sbjct: 130 QAGRLRLNEETVRDLNVVLKNNDFLRNTVHRHEPPVTAEPLRILAENDEMVVIDKPSSLP 189

Query: 119 VQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           V   G      +   L    + KG      HRLD+ TSG+L+ A+T   ++ + E  R R
Sbjct: 190 VHPCGRFRHNTVIFILGKEYNLKG--LHTIHRLDRMTSGVLMFAKTLEVSKKIDEQVRQR 247

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +++K Y   V G    ++      +   S+     + V + + KG     + F+ +    
Sbjct: 248 QLEKEYVCRVCGEFPKEEVTCEEPIFVVSY----KIGVCRVDPKG-KPCKTVFQRLSYNG 302

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +    ++  P+TGRTHQ+RVH  ++G PIV D  Y     G
Sbjct: 303 KS-SVVKCFPYTGRTHQIRVHLQYLGHPIVNDPIYNTEAWG 342


>gi|297479512|ref|XP_002690866.1| PREDICTED: RNA pseudouridylate synthase domain containing 2 [Bos
           taurus]
 gi|296483299|gb|DAA25414.1| RNA pseudouridylate synthase domain containing 2 [Bos taurus]
          Length = 518

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 57/251 (22%), Positives = 110/251 (43%), Gaps = 26/251 (10%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           +        +  +R+G++ ++++ V                    L+ ++K+   L ++V
Sbjct: 143 FRAQPLAYYEAAVRAGRLHLNEEPV------------------QDLSIVLKDNDFLRNTV 184

Query: 89  NLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +  +     + I LL E+  + V +KP+ I V       ++   F+    + + ++    
Sbjct: 185 HRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-KEHQLKELHPL 243

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++      +L  S 
Sbjct: 244 HRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVVGEFPTEEVTCKEPILVVS- 302

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y   V + +       S F+ +         +  +P TGRTHQ+RVH   +G PI+
Sbjct: 303 ----YKVGVCRVDPQGKPCESVFQRLSYNGHS-SVVRCRPLTGRTHQIRVHLQFLGHPIL 357

Query: 268 GDHKYCANFKG 278
            D  Y +   G
Sbjct: 358 NDPIYNSAAWG 368


>gi|15639147|ref|NP_218593.1| hypothetical protein TP0154 [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189025387|ref|YP_001933159.1| hypothetical protein TPASS_0154 [Treponema pallidum subsp. pallidum
           SS14]
 gi|3322421|gb|AAC65144.1| conserved hypothetical protein [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189017962|gb|ACD70580.1| hypothetical protein TPASS_0154 [Treponema pallidum subsp. pallidum
           SS14]
          Length = 345

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 61/315 (19%), Positives = 119/315 (37%), Gaps = 33/315 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V+      ++   R+DR  +   P    V +   +R   +R++ + V+   R+Q G V+ 
Sbjct: 18  VECFRCTKNDAGRRVDRVLRILLPACPRVGVYARVRRTAIRLNGRPVQPAKRVQVGDVLS 77

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P  +            +  +  L      +   ++++   +  F+KPAG+ V G   + 
Sbjct: 78  LPESLCRARAASSRLSKMPGTPKLR-----VLPSVVFKTQDLLFFHKPAGLCVHGPRSLD 132

Query: 127 YHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             + G  ++ V  +   +P   HRLD+ T G++  +R+   AQ  + + +   ++K Y  
Sbjct: 133 AWVRGQGRAHVPPALSFRPGPLHRLDRGTEGLIAFSRSLRGAQWFSAALQQHTLRKFYL- 191

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK-VIDCFAQKFCWLE 244
                               +        +V+  E      ++H + V+           
Sbjct: 192 --------------AITAAPARTAAAARTLVRPGE------VTHVQTVLHSCDSALVLRV 231

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           + P TG+ HQ+R +    G P+VGD  Y         +    + +L A  +  P      
Sbjct: 232 IVPVTGKKHQIRRYCAAQGFPLVGDRTYGG--ASQHGNARYTRFFLLAWCVRFPSSRLQA 289

Query: 305 L---QITAPLPAHMV 316
           L     T P PA M 
Sbjct: 290 LPAQVWTTPSPAFMR 304


>gi|324519170|gb|ADY47302.1| RNA pseudouridylate synthase domain-containing protein 4 [Ascaris
           suum]
          Length = 331

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 57/260 (21%), Positives = 111/260 (42%), Gaps = 23/260 (8%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW---VDSKGQK 143
            +N  +  + +   ++YED  +  F+KP  ++  G       +D  L++    +  + Q+
Sbjct: 70  KMNDAELVELMCKRIIYEDDDLLAFDKPYQMAYSGSKAGQAQMDRILQNLKASIAPEVQR 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L   LD++ +G+++ A+     + + E ++   +++ Y ++V G+P+  +  I   L+
Sbjct: 130 LCLVKSLDKDLTGVILFAKNELVQKSIMEKYKDGAVEQRYRTIVRGVPEENEAIINIPLV 189

Query: 204 KKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA-LH 261
           KKS+     +  +  N K    +  + ++VI    +     +       +HQ+R H  L 
Sbjct: 190 KKSYKQNFIMRPLMPNSKVRPFHVTTEYRVIKDNGECSSL-QCIIRNDISHQVRSHLGLG 248

Query: 262 MGCPIVGDHKYCAN---FKGNFTSPIQNKL------------YLHARYMDLPHPEGG--R 304
           +GCPI+GD KY            S    +L            YLH   + +P    G   
Sbjct: 249 LGCPIIGDFKYSGYKEFRPPKLPSGTMQRLQLTGNQYRRLPMYLHLSEVSIPVASSGSRT 308

Query: 305 LQITAPLPAHMVKTWDSLGF 324
           + I +PLPA    T   L  
Sbjct: 309 INIRSPLPAFFAYTLRKLRL 328


>gi|319763272|ref|YP_004127209.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|317117833|gb|ADV00322.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
          Length = 316

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 64/298 (21%), Positives = 113/298 (37%), Gaps = 32/298 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRI 67
           VV+ +  + + LD +     P ++  +  + L +G+V VD   +    ++    G  VR 
Sbjct: 21  VVLPSQGQGLLLD-FLARRLPAVSREDWLRRLHAGEV-VDEWGRAATAHSPFTPG--VRY 76

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                    +  E +I              +  +LY+D  I V +KP  + V        
Sbjct: 77  YYYRE----LAHEAEIP------------FQETVLYQDEHILVADKPHFLPVVPAGRYLQ 120

Query: 128 HIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           H    L       G +     HR+D++T+G+++ +  RA        FR R+++K+Y ++
Sbjct: 121 H--TLLVRLKRRLGLRELSPVHRIDRDTAGLVLFSVQRATRGRYQALFRDRQVRKVYEAV 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                      +       S +             G   A++   V +  A  +    ++
Sbjct: 179 APWRAD-----LRFPRTHASRLQESGHFFRMHEVPGEPNAVTTMDVAE-QAGGWARYRLE 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           P TG+ HQLRVH   +G P+ GD  Y             N L L AR +    P  G+
Sbjct: 233 PVTGKRHQLRVHMAALGLPLCGDGFY-PEVNDPPEGDYSNPLQLLARTLSFTDPVTGQ 289


>gi|260914045|ref|ZP_05920518.1| ribosomal large subunit pseudouridine synthase C [Pasteurella
           dagmatis ATCC 43325]
 gi|260631678|gb|EEX49856.1| ribosomal large subunit pseudouridine synthase C [Pasteurella
           dagmatis ATCC 43325]
          Length = 220

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 63/199 (31%), Positives = 93/199 (46%), Gaps = 16/199 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+ S   V +KP  ISV   +          +        +  L HRLD+ TSG+L++
Sbjct: 6   IVYQHSDFIVIDKPTNISVHKDAEKIGLTSLVAQQL---NVPQVWLVHRLDKVTSGLLIL 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + AA  L+  F   RIQK Y +L    PK K+  I   + +K+  G   +   KQN 
Sbjct: 63  ALNQNAASELSRLFAEHRIQKTYLALSTQKPKKKQGLIIGDM-EKARRGAWKLCTTKQN- 120

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                AI+ F  ++C         ++P TG+THQLRV    +G PI+GD  Y  NF    
Sbjct: 121 ----PAITRFYSVNCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDALYGGNFDKV- 174

Query: 281 TSPIQNKLYLHARYMDLPH 299
                N+ YLHA  +   +
Sbjct: 175 -----NRTYLHAYRLQFEY 188


>gi|28076995|ref|NP_082285.1| RNA pseudouridylate synthase domain-containing protein 1 [Mus
           musculus]
 gi|81901914|sp|Q8VCZ8|RUSD1_MOUSE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 1; AltName: Full=Ribosomal large subunit
           pseudouridine synthase C-like protein
 gi|17390411|gb|AAH18186.1| RNA pseudouridylate synthase domain containing 1 [Mus musculus]
 gi|26340054|dbj|BAC33690.1| unnamed protein product [Mus musculus]
 gi|148690493|gb|EDL22440.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_b
           [Mus musculus]
          Length = 306

 Score =  139 bits (351), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 59/245 (24%), Positives = 103/245 (42%), Gaps = 23/245 (9%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------- 144
           +        ++Y+ S   V NK   + +   +   +     L+  +     +        
Sbjct: 2   EPGSMENLSIVYQSSDFLVVNKHWDLRIDSKT---WRETLTLQKQLRHHFPELADPDTCY 58

Query: 145 --RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             R  H+LD  TSG L VA  +AAA    + F+ RR+ K Y +LV G  +  +  I   +
Sbjct: 59  GFRFCHQLDFSTSGALCVALNKAAAGSAYKCFKERRVTKAYLALVRGHVQESQVTINYAI 118

Query: 203 LKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRV 257
            + S  G  +   ++     +    +++   V++           + ++P TGRTHQLRV
Sbjct: 119 GRNSTEGRTHTMCIEGTHGCENPKPSLTELLVLEHGLYAGDPVSKVLLKPLTGRTHQLRV 178

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
           H   +G PIVGD  Y    +     P   ++ LHA Y+ +P  +  R++   P P   + 
Sbjct: 179 HCSALGHPIVGDLTYG-QAEDQEDQPF--RMMLHAFYLRIP-TQAERVEACTPDP--FLP 232

Query: 318 TWDSL 322
             D+ 
Sbjct: 233 ALDAC 237


>gi|227540229|ref|ZP_03970278.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
 gi|227239953|gb|EEI89968.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
          Length = 247

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 90/238 (37%), Gaps = 25/238 (10%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            ++++ED  I V NKP  I+              +           ++ HRLD+ETSGIL
Sbjct: 16  DLIIHEDENIIVINKPPFIASLDEREGGEVN---ILRLAKKYYADAQICHRLDKETSGIL 72

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+     + ++  F  RR+ K Y +++ G    +   I   +L + +        V  
Sbjct: 73  LIAKNPETYRLISIEFEKRRVDKTYHAIIEGTHIFQDLKIDLPILNQGNKN------VTI 126

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-- 276
           +      A + F  I  F + F  +E +P TGR HQ+R+H       IVGD  Y      
Sbjct: 127 DRYNGKPAETIFNSIQYF-KHFTLVECKPITGRMHQIRIHLATQHAAIVGDSMYRGKPVY 185

Query: 277 ------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                       K     PI  +  LH++ +          +  A  P         L
Sbjct: 186 LSQIKKRGFTLSKDEEEQPIMKRFALHSKKVRFKV-ADKSYEFEAEYPKDFAILLKQL 242


>gi|224070740|ref|XP_002186856.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 1, partial [Taeniopygia guttata]
          Length = 257

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 63/224 (28%), Positives = 94/224 (41%), Gaps = 19/224 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSK-----GQKPRLTHRLDQET 154
           +LY+ S   V NK   + +          +   LK               R  H+LD  T
Sbjct: 11  ILYQSSDFIVVNKHWDLRIDSKMWYETLTLQSQLKHRFPELADPDTYYGFRFCHQLDFST 70

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L VA  +AAA    + F+ R + K Y +LV G     +  I   + K +  G  ++ 
Sbjct: 71  SGALCVALNKAAAGSAYKCFKERLVTKAYLALVRGHVSQSRMTIRYAIGKNTTEGMTHMM 130

Query: 215 VVKQNE--KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            ++  E  +      S   V++           + +QP TGRTHQLRVH   +G PIVGD
Sbjct: 131 CIEGTEGCENPKPCQSELVVLEHGSYSGDPVTKVLLQPLTGRTHQLRVHCSAIGHPIVGD 190

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
             Y      N       ++ LHA Y+ +  P G   +++ AP P
Sbjct: 191 FTYSQRQDSNPY-----RMMLHAYYLRI--PTGSELIEVCAPDP 227


>gi|51246961|ref|YP_066845.1| ribosomal large subunit pseudouridine synthase A [Desulfotalea
           psychrophila LSv54]
 gi|50877998|emb|CAG37838.1| probable ribosomal large subunit pseudouridine synthase A
           [Desulfotalea psychrophila LSv54]
          Length = 211

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 57/217 (26%), Positives = 95/217 (43%), Gaps = 19/217 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHI--DGFLKSWVDSKGQKPRLTHRLDQETS 155
           +  ++Y D  + V  KP G+    G G          L++ +     +P   HRLD  TS
Sbjct: 3   ELKIIYRDDHLVVVIKPGGLLSVPGRGPENSDCVSSRLQAKIPEMITQPA-VHRLDMYTS 61

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A ++   + L+  F+ +++ K Y +L+ G  +     I         +  D   +
Sbjct: 62  GLMVYAVSKEIHRALSIQFQEQQVDKKYTALLEGCLQEVSGEIRLPF----RVDLDNRPI 117

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGDHKY 272
              + +     I+ ++ +D        +E  P TGRTHQLRVHA H   +G PI+GD  Y
Sbjct: 118 QILDYQHGKMGITLWRKMD-EKNGITRVEFTPMTGRTHQLRVHAAHAKGLGIPIIGDSFY 176

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
            +   G+        + LHA  +   HP  G +L   
Sbjct: 177 GSGRDGDE-------MMLHAHQLSFTHPIIGEKLYFK 206


>gi|296214181|ref|XP_002753587.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Callithrix jacchus]
          Length = 484

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 53/201 (26%), Positives = 95/201 (47%), Gaps = 8/201 (3%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+    
Sbjct: 141 KDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-K 199

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G   N++  
Sbjct: 200 EHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPNEEVT 259

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               +L  S     Y   V + +       + F+ +         ++ +P TGRTHQ+RV
Sbjct: 260 CKEPILVVS-----YKVGVCRVDPQGKPCETVFQRLSYNGHS-SVVQCRPLTGRTHQIRV 313

Query: 258 HALHMGCPIVGDHKYCANFKG 278
           H   +G PI+ D  Y +   G
Sbjct: 314 HLQFLGHPILNDPIYNSAAWG 334


>gi|330824854|ref|YP_004388157.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
 gi|329310226|gb|AEB84641.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
          Length = 256

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 57/223 (25%), Positives = 89/223 (39%), Gaps = 18/223 (8%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   LL++D  +    KPAG  V      A      +++  D  G+     HRLD+
Sbjct: 3   PDATPPLHLLWQDEHMVALYKPAGWLVHRTGLDAGETRFVVQALRDQIGRHVYPVHRLDK 62

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+LV+    AAA+ L  SF    + K Y +LV G         A  L    H     
Sbjct: 63  GTCGVLVMGLHPAAARALAGSFARHAVHKRYLALVRGW--------APPLADVDHPLRPD 114

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ--------KFCWLEMQPHTGRTHQLRVHALHMGC 264
                   + A+  ++    ++            +   +  +P TGR HQ+R H  H   
Sbjct: 115 DAPQDAPAQPAHTLLTRLARLELPESSDPRFATTRASLVLAEPTTGRRHQIRRHLKHAAH 174

Query: 265 PIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGRL 305
           PI+GD  +       + +      +L+LHA  + LPHP+ GR+
Sbjct: 175 PILGDATHGKGPLNRWWAERLGLQRLWLHAWRLRLPHPQDGRM 217


>gi|145629099|ref|ZP_01784898.1| hypothetical protein CGSHi22121_09865 [Haemophilus influenzae
           22.1-21]
 gi|145633401|ref|ZP_01789131.1| hypothetical protein CGSHi3655_04195 [Haemophilus influenzae 3655]
 gi|145635226|ref|ZP_01790930.1| exonuclease III [Haemophilus influenzae PittAA]
 gi|145639669|ref|ZP_01795272.1| hypothetical protein CGSHiII_09136 [Haemophilus influenzae PittII]
 gi|229845388|ref|ZP_04465519.1| pseudouridine synthase-like protein [Haemophilus influenzae 6P18H1]
 gi|144978602|gb|EDJ88325.1| hypothetical protein CGSHi22121_09865 [Haemophilus influenzae
           22.1-21]
 gi|144985964|gb|EDJ92566.1| hypothetical protein CGSHi3655_04195 [Haemophilus influenzae 3655]
 gi|145267505|gb|EDK07505.1| exonuclease III [Haemophilus influenzae PittAA]
 gi|145271226|gb|EDK11140.1| hypothetical protein CGSHiII_09136 [Haemophilus influenzae PittII]
 gi|229811696|gb|EEP47394.1| pseudouridine synthase-like protein [Haemophilus influenzae 6P18H1]
 gi|301168643|emb|CBW28233.1| conserved hypothetical pseudouridine synthase [Haemophilus
           influenzae 10810]
 gi|309750639|gb|ADO80623.1| Probable pseudouridylate synthase [Haemophilus influenzae R2866]
          Length = 224

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 59/201 (29%), Positives = 92/201 (45%), Gaps = 16/201 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  ++Y+ S   + NK  GISV          +   K        K  L HRLD+ TSG
Sbjct: 1   MEIEVVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQL---NVPKVWLVHRLDKVTSG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A    +A   +  F   +I K Y +L    PK K+  I   + KK+  G   +   
Sbjct: 58  LLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGDM-KKAREGAWKLCQT 116

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K+N      AI+ F+ + C         ++P TG+THQLRV    +G PI+GD  Y  N 
Sbjct: 117 KEN-----PAITRFESVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDGLYGKNT 170

Query: 277 KGNFTSPIQNKLYLHARYMDL 297
           +        ++ YLHA  ++ 
Sbjct: 171 EK------IDRTYLHATQLEF 185


>gi|303256625|ref|ZP_07342639.1| tRNA pseudouridine synthase C [Burkholderiales bacterium 1_1_47]
 gi|302860116|gb|EFL83193.1| tRNA pseudouridine synthase C [Burkholderiales bacterium 1_1_47]
          Length = 257

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 55/234 (23%), Positives = 88/234 (37%), Gaps = 15/234 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V +KP  +            +  L+   D  G++    +RLD+ TSGIL+ 
Sbjct: 6   ILYQDEDLVVVSKPEKMLTHRTEIANGDTEFALQLLRDQIGRRVSPVYRLDRGTSGILMF 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
              R     L++        K Y+++V G      E               Y+ V K   
Sbjct: 66  GLNREIVSALSQQTHE-TFHKRYYAVVRGWAPEDIEVRHAL----KPPVDPYLRVQKTEA 120

Query: 221 KGA-----NYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           + A       A S   V        +   + ++  TGR HQLR H  H+  PI+GD  Y 
Sbjct: 121 QDALSYLHRLAESEVPVSSGKFDTTRLSLVLLELATGRRHQLRRHLKHLAHPIIGDATYG 180

Query: 274 ANFKGNFTSP--IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF 324
                   +     ++L LH   +   HP    RL I       M++  + L +
Sbjct: 181 KGPLNRALAEYFGGDRLLLHCGRISFIHPRTQKRLTIEDQPSGLMLQIIERLRW 234


>gi|89900681|ref|YP_523152.1| pseudouridine synthase [Rhodoferax ferrireducens T118]
 gi|89345418|gb|ABD69621.1| pseudouridine synthase [Rhodoferax ferrireducens T118]
          Length = 302

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 58/285 (20%), Positives = 112/285 (39%), Gaps = 28/285 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +  I      + +  G V VD          + G  V++ P      H    
Sbjct: 31  LD-FLTERFSAIPRDVWHQRMAQGDV-VD----------EHG--VQLAPHSAYQGH---- 72

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +++        +       ++L++D ++ V +KP  + V    G  Y  +  L       
Sbjct: 73  RRVYYYRAVPDEPRIPFDEVILFQDEQLIVVDKPHFLPVMPSGG--YLAETVLVRLKQKL 130

Query: 141 GQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           G       HR+D++T+G+++ +            F  R ++K Y ++        +E +A
Sbjct: 131 GIDTLVPVHRIDRDTAGLVMFSVQPETRAAYHALFSQRSVKKTYEAI-----APWREGLA 185

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + ++S I      +++    G    ++  +V+          ++QP TG+ HQLRVH 
Sbjct: 186 LPMTRQSRIVEAGHFMLQHEVSGPPNTVTRIEVLQVQG-GLARYQLQPVTGKRHQLRVHM 244

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             +G PI+GD  Y            ++ L L AR ++   P  G+
Sbjct: 245 AALGLPILGDGLY-PTLTPEGQVDYEHPLQLLARRIEFVDPVSGQ 288


>gi|194670657|ref|XP_583460.4| PREDICTED: RNA pseudouridylate synthase domain containing 2 isoform
           1 [Bos taurus]
          Length = 505

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 57/251 (22%), Positives = 110/251 (43%), Gaps = 26/251 (10%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
           +        +  +R+G++ ++++ V                    L+ ++K+   L ++V
Sbjct: 130 FRAQPLAYYEAAVRAGRLHLNEEPV------------------QDLSIVLKDNDFLRNTV 171

Query: 89  NLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
           +  +     + I LL E+  + V +KP+ I V       ++   F+    + + ++    
Sbjct: 172 HRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-KEHQLKELHPL 230

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++      +L  S 
Sbjct: 231 HRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVVGEFPTEEVTCKEPILVVS- 289

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               Y   V + +       S F+ +         +  +P TGRTHQ+RVH   +G PI+
Sbjct: 290 ----YKVGVCRVDPQGKPCESVFQRLSYNGHS-SVVRCRPLTGRTHQIRVHLQFLGHPIL 344

Query: 268 GDHKYCANFKG 278
            D  Y +   G
Sbjct: 345 NDPIYNSAAWG 355


>gi|323453198|gb|EGB09070.1| hypothetical protein AURANDRAFT_53496 [Aureococcus anophagefferens]
          Length = 430

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 48/252 (19%), Positives = 93/252 (36%), Gaps = 35/252 (13%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
           F   +         + L  G++ V+ +    +  +++G V+      +            
Sbjct: 111 FAAEFKMNPASYYAEALADGRILVNGELCGDDLVLKNGDVLVHRAHRH------------ 158

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
                           ++  D+++   +KP  + +      +YH +  L S +       
Sbjct: 159 ------EPPVRGGPIAVVGLDARVLAVDKPGTVPMHPCG--SYHYNA-LSSLLAEDFTPR 209

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRLD+ TSG++++AR+  AA  L +     R +K Y + V G               
Sbjct: 210 SFVHRLDRLTSGLVLLARSAEAATELCDCIGAGRARKTYVARVAGRFPE----------- 258

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           ++          + +E  +    + F+++   A     +E  P TGRTHQ+R+H   +G 
Sbjct: 259 RAPAATRGPDAARPDEDASR---TRFRLLHRHADGTSTVECHPRTGRTHQIRLHLQWLGH 315

Query: 265 PIVGDHKYCANF 276
           PI  D  Y    
Sbjct: 316 PIANDPNYGGTL 327


>gi|325955599|ref|YP_004239259.1| pseudouridine synthase [Weeksella virosa DSM 16922]
 gi|323438217|gb|ADX68681.1| pseudouridine synthase [Weeksella virosa DSM 16922]
          Length = 552

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 65/242 (26%), Positives = 107/242 (44%), Gaps = 20/242 (8%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               L H++    + D+ + +  + D  +   LYED  I V NKP       G  +   +
Sbjct: 321 CQPILGHMLSATLVDDNPLLIDTNKDK-EIEFLYEDDAIIVINKPENFLSVPGIQVKDSV 379

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L+         P + HRLD +TSG++V+A+++ A + L + F  ++++K Y +L+ G
Sbjct: 380 QTRLQQQYPHIS-SPMIVHRLDMQTSGLMVIAKSKIAHEKLQKQFLKKKVKKRYVALLGG 438

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   I N  L+          V  Q  K A    + ++V +  +     +   P T
Sbjct: 439 EVNKYSGEI-NLPLRVDLEDRPRQLVCYQYGKNAK---TLYQV-ESISNGITRIFFYPIT 493

Query: 250 GRTHQLRVHALH---MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRL 305
           GRTHQLRVHA H   +  PI+GD  Y             ++L+LHA  ++  HP    +L
Sbjct: 494 GRTHQLRVHAAHSLGLDSPILGDDLYGQK---------ASRLFLHAECLEFFHPISNKKL 544

Query: 306 QI 307
             
Sbjct: 545 TF 546


>gi|300771948|ref|ZP_07081819.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33861]
 gi|300761334|gb|EFK58159.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33861]
          Length = 247

 Score =  139 bits (350), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 90/238 (37%), Gaps = 25/238 (10%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            ++++ED  I V NKP  I+              +           ++ HRLD+ETSGIL
Sbjct: 16  DLIIHEDENIIVINKPPFIASLDEREGGEIN---ILRLAKKYYADAQICHRLDKETSGIL 72

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+     + ++  F  RR+ K Y +++ G    +   I   +L + +        V  
Sbjct: 73  LIAKNPETYRLISIEFEKRRVDKTYHAIIEGTHIFQDLKIDLPILNQGNKN------VTI 126

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-- 276
           +      A + F  I  F + F  +E +P TGR HQ+R+H       IVGD  Y      
Sbjct: 127 DRYNGKPAETIFNSIQYF-KHFTLVECKPITGRMHQIRIHLATQHAAIVGDSMYRGKPVY 185

Query: 277 ------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                       K     PI  +  LH++ +          +  A  P         L
Sbjct: 186 LSQIKKRGFTLSKDEEEQPIMKRFALHSKKVRFKV-ADKSYEFEAEYPKDFAILLKQL 242


>gi|330825467|ref|YP_004388770.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
 gi|329310839|gb|AEB85254.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
          Length = 316

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 64/298 (21%), Positives = 113/298 (37%), Gaps = 32/298 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRI 67
           VV+ +  + + LD +     P ++  +  + L +G+V VD   +    ++    G  VR 
Sbjct: 21  VVLPSQGQGLLLD-FLARRLPAVSREDWLRRLHAGEV-VDEWGRAATAHSPFTPG--VRY 76

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                    +  E +I              +  +LY+D  I V +KP  + V        
Sbjct: 77  YYYRE----LAHEAEIP------------FQETVLYQDEHILVADKPHFLPVVPAGRYLQ 120

Query: 128 HIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           H    L       G +     HR+D++T+G+++ +  RA        FR R+++K+Y ++
Sbjct: 121 H--TLLVRLKRRLGLRELSPVHRIDRDTAGLVLFSVQRATRGRYQALFRDRQVRKVYEAV 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                      +       S +             G   A++   V +  A  +    ++
Sbjct: 179 APWRAD-----LRFPRTHASRLQESGHFFRMHEVPGEPNAVTAMDVAE-QAGGWARYRLE 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           P TG+ HQLRVH   +G P+ GD  Y             N L L AR +    P  G+
Sbjct: 233 PVTGKRHQLRVHMAALGLPLCGDGFY-PEVNDPPEGDYSNPLQLLARTLSFTDPVTGQ 289


>gi|308812997|ref|XP_003083805.1| Pseudouridine synthase, RluD (ISS) [Ostreococcus tauri]
 gi|116055687|emb|CAL57772.1| Pseudouridine synthase, RluD (ISS) [Ostreococcus tauri]
          Length = 383

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 72/249 (28%), Positives = 104/249 (41%), Gaps = 27/249 (10%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSW-----VDSKGQKPRLTHRL 150
              + YED+ + V NK AG         G        +  W     V      P + HRL
Sbjct: 141 DDDIAYEDATMTVVNKRAGTPSTPRRRVGDDSAASACVARWRTVDGVQGASLVPYVAHRL 200

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW--GIPKNKKE---CIANWLLKK 205
           D +TSG LV+ RT A A+ +   F  RR++K YW+L    G   +       I   L+K+
Sbjct: 201 DLDTSGALVICRTSARAKEVQGWFENRRVEKTYWALCEARGDASDDSGEWHTIEFPLVKR 260

Query: 206 SHIGGDY-------VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +    +        V   +   + A  A + F+++   +     +E +P TGRTHQ+R H
Sbjct: 261 ARDDAEPGTFFVEAVLTPEDAPEDAKPATTLFRIV-SKSAAHVLVEARPKTGRTHQIRTH 319

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
               G PIVGD  Y A       S I ++  LHAR +  P  E   + I A  P      
Sbjct: 320 LAAAGLPIVGDTIYGA------PSDIIDRHALHARTLTFPSDEY-PVPIVAHPPDDFKDA 372

Query: 319 WDSLGFKYD 327
             S+G   D
Sbjct: 373 CASVGIVVD 381


>gi|91974996|ref|YP_567655.1| pseudouridine synthase [Rhodopseudomonas palustris BisB5]
 gi|91681452|gb|ABE37754.1| pseudouridine synthase [Rhodopseudomonas palustris BisB5]
          Length = 298

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 69/258 (26%), Positives = 104/258 (40%), Gaps = 58/258 (22%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            + +++ +L+ D  + V +KPAG+ V  G     +++   +       + P L HRLD++
Sbjct: 16  PEDIQARVLHRDGLMLVIDKPAGLPVHRGPKGGPNLETSFEFLRFGLPRPPVLAHRLDRD 75

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG LV+ R R A   L   F+  +I K YW++V G P+     I   + + +   G + 
Sbjct: 76  TSGCLVLGRHRKATATLGLLFKHSKISKTYWAIVEGGPEQDHGTIDLPIGRLNAERGWWQ 135

Query: 214 HV---------------VKQNEKGANYAISHFKV-------------------------- 232
            V                      A  AIS   V                          
Sbjct: 136 KVDPEGLPSLTKWTVLGRSHPVAPAPAAISSEPVASDSSPPCGEGSGVGVDNGSFASGAP 195

Query: 233 ------------IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                            ++  WL ++P TGRTHQLRVH   MG PIVGD+ Y      N 
Sbjct: 196 HPTPPPQAGEGAGGARGKRLTWLALEPITGRTHQLRVHCAAMGWPIVGDNIYG-----NG 250

Query: 281 TSPIQNKLYLHARYMDLP 298
               + KL+LHAR + +P
Sbjct: 251 PRFGEPKLHLHAREIVIP 268


>gi|195621906|gb|ACG32783.1| RNA binding protein [Zea mays]
          Length = 379

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 67/319 (21%), Positives = 111/319 (34%), Gaps = 72/319 (22%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           K +R+GQ+ VD + V                  +    ++   K++       +      
Sbjct: 61  KRIRNGQITVDGEVVT-----------------DPDMTLVDGSKLVYHRFPWQEPFAPYL 103

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK------------GQKPRL 146
             +LYED  +   NKP+G+ V                  D K               P  
Sbjct: 104 LEVLYEDDDMVALNKPSGLQVLPKGLFQQRTVLAQLQLKDWKMASSCRFKRKDVQSHPVP 163

Query: 147 THRLDQETSGILVVARTRAAAQHL-----------------TESFRMRRIQKIYWSLVWG 189
            HRL + TSG+L+ A+T+ A   L                 +E    R+I K Y +LV G
Sbjct: 164 VHRLGRGTSGLLLCAKTKVAKVRLASYFAEGAINAAKKRDKSEFSEERKISKFYRALVTG 223

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPH 248
           I  + +  +   +    + G         +      A+S   V++  A Q    ++++ H
Sbjct: 224 ILDDDEVVVTQPIGLVHYPGVAEGLYAACSS--GKPAMSKVCVLERLAHQNHTLVQVEIH 281

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-----------------------PIQ 285
           +GR HQ+R+H  ++G P+V D  Y      NF                         P  
Sbjct: 282 SGRPHQIRIHLAYIGHPLVDDPLYGIGGHPNFVEPESTGTDSSFASDGGYERPLQPVPGD 341

Query: 286 NKLYLHARYMDLPHPEGGR 304
              +LHA  + L HP   +
Sbjct: 342 CGYHLHAHCLVLCHPTTNK 360


>gi|327287587|ref|XP_003228510.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Anolis carolinensis]
          Length = 300

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 98/233 (42%), Gaps = 21/233 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSK-----GQKPRLTHRLDQET 154
           +LY+ +   V NK   + +          +   LK               R  H+LD  T
Sbjct: 11  ILYQSADFIVVNKHWDVRIDSKMWYEKLTLQSQLKHRFPELADPDTYYGFRFCHQLDFST 70

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L VA  +AAA    + F+ R + K Y +LV G  +  K  I   + K +  G  ++ 
Sbjct: 71  SGALCVALNKAAAGSAYKCFKERMVTKAYLALVRGHVQEAKLTIEYAIGKNTTEGMTHMM 130

Query: 215 VVKQNE--KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            ++  E  +      S   V++           + +QP TGRTHQLRVH   +G PIVGD
Sbjct: 131 CIEGTEGCENPKPCQSELTVLEHGLYSGDPVSKVLLQPLTGRTHQLRVHCSAVGHPIVGD 190

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTWDS 321
             Y     G        ++ LHA Y+ +  P    L +++AP P   V   DS
Sbjct: 191 FTYSLKTDGGPF-----RMMLHAYYLRI--PTAKELVEVSAPDP--FVPALDS 234


>gi|207346913|gb|EDZ73262.1| YDL036Cp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 265

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 48/167 (28%), Positives = 79/167 (47%), Gaps = 4/167 (2%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V +KP+GI V       Y  +   K   ++ G      +RLD+ TSG++ +A+T   A 
Sbjct: 1   MVIDKPSGIPVHPTG--RYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFLAKTPKGAD 58

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           ++ +  + R + K Y + V G     +  +   L K          V + +EKGA +A +
Sbjct: 59  NIGDQLKAREVTKEYVAKVVGEFPETEVIVEKPL-KLIEPRLALNAVCQMDEKGAKHAKT 117

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            F  I     K   ++ +P TGR+HQ+RVH  ++G PI  D  Y  +
Sbjct: 118 VFNRISYDG-KTSIVKCKPLTGRSHQIRVHLQYLGHPIANDPIYSND 163


>gi|118474442|ref|YP_892925.1| RNA pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40]
 gi|118413668|gb|ABK82088.1| RNA pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40]
          Length = 319

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 63/304 (20%), Positives = 116/304 (38%), Gaps = 64/304 (21%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
             +    QK+   G++ V+      N+ +                           +  +
Sbjct: 24  GYSMKEAQKLCDKGRLLVNDAVCGKNDPVFG------------------------EAYFI 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
               +      ++E  +  VF+KP+G+     G    Y +   + S     G+K  + HR
Sbjct: 60  DYECEPKGLKPIFECDEFGVFDKPSGVLSHPNGRNCEYSLCDEIWSL---WGKKACVAHR 116

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN---KKECIANW----- 201
           LD+ETSG++VVA+   +A +L +SF  R + K Y + V G        K  I ++     
Sbjct: 117 LDRETSGVIVVAKNANSALNLKKSFENRAVAKTYLAFVRGKFDGNGLDKFHINDFEDFKD 176

Query: 202 ------------LLKKSHIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQ 246
                       + K   I  DY  + +  +       A++  K+++ + +     +E  
Sbjct: 177 KLEFFDNIQGFVIDKNMDITKDYDDIKIRMEICPEGKRAVTVVKLVEYYPKFDISLVECY 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANF-------------KGNFTSPIQNKLYLHAR 293
           P TGR HQ+R+H  HM   I+GD  Y  +              +    +   ++L LHA+
Sbjct: 237 PLTGRQHQIRLHLFHMKHRILGDPIYGLDKFNVEQILDGVMSERDRVKNTGASRLMLHAK 296

Query: 294 YMDL 297
            +  
Sbjct: 297 SVKF 300


>gi|302840927|ref|XP_002952009.1| pseudouridine synthase [Volvox carteri f. nagariensis]
 gi|300262595|gb|EFJ46800.1| pseudouridine synthase [Volvox carteri f. nagariensis]
          Length = 367

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 60/257 (23%), Positives = 95/257 (36%), Gaps = 44/257 (17%)

Query: 41  LRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +  GQV ++   V + ++ ++ G VV                          +       
Sbjct: 55  IVGGQVAINGSTVLEPDHVLRVGDVVSYTRR------------------PWREPPSPSYV 96

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL--KSWVDSKGQKPRL----THRLDQE 153
            +LYED  +    KPAG+ V   + +       L    + +  G +  +     HRL + 
Sbjct: 97  DVLYEDDDVVALCKPAGLQVLPAAMLHQRTVLTLLQHHYGNPPGTRACVAVAPVHRLGRG 156

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQ----------------KIYWSLVWGIPKNKKEC 197
           TSG+L+ ART  A Q LTE    +                    IY SLV GI    +  
Sbjct: 157 TSGLLLCARTTHARQRLTELMSGKTAAAAAAAAAATAGTEARGLIYRSLVQGIVAEDEGR 216

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLR 256
           +   +    + G D          G   A S ++V++           ++  TGR HQ+R
Sbjct: 217 VDVPIGPVQYPGVDGGLFAA--TPGGKPAASIWRVLERRPGGGRSRQAVEILTGRPHQIR 274

Query: 257 VHALHMGCPIVGDHKYC 273
           +H   MG P+VGD  Y 
Sbjct: 275 IHMAAMGHPLVGDPLYG 291


>gi|171059970|ref|YP_001792319.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170777415|gb|ACB35554.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
          Length = 258

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 53/221 (23%), Positives = 89/221 (40%), Gaps = 25/221 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSG 156
           +  +L+ D  +   +KPA   V      A      +++  D  G Q     HRLD+ T G
Sbjct: 3   ELPVLWRDEHLIAIHKPARWLVHRTGLDAGETRFIVQTLRDQLGGQHVYPAHRLDKGTCG 62

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A    AA+ L  SF    ++K Y +LV G    + E + + L              
Sbjct: 63  VLLLALHPEAARGLAMSFARHEVKKRYLALVRGWMPAEVE-VDHPLRPDDTP-------- 113

Query: 217 KQNEKGANYAISHFKVIDCFAQ-----------KFCWLEMQPHTGRTHQLRVHALHMGCP 265
              +  A  A +  + +                +   +E +P TGR HQ+R H  H+  P
Sbjct: 114 --PDSPAQSAHTRLRRLAALDWPEAADPGFTTTRASLVEARPTTGRRHQIRRHLKHIAHP 171

Query: 266 IVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR 304
           I+GD  +       + +      +L+LHA  + + HP  G 
Sbjct: 172 ILGDATHGKGPLNRWWAERLGLQRLWLHAWRLQIAHPITGE 212


>gi|221065999|ref|ZP_03542104.1| pseudouridine synthase [Comamonas testosteroni KF-1]
 gi|220711022|gb|EED66390.1| pseudouridine synthase [Comamonas testosteroni KF-1]
          Length = 250

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 100/247 (40%), Gaps = 33/247 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++D  +    KPAG  V      A+     +++  D  G+     HRLD+ T G+L++
Sbjct: 12  ILWQDEHLVAVYKPAGWLVHRTGLDAHETRFVMQTLRDQLGRHVWPVHRLDKGTCGVLLM 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + AAQ L   F     +K Y +LV G      E + + L                 +
Sbjct: 72  ALNKEAAQALAARFAAHETRKEYRALVRGWLPEVVE-VDHPLKPDD----------APED 120

Query: 221 KGANYAISHFKVIDCFAQKFCW-----------LEMQPHTGRTHQLRVHALHMGCPIVGD 269
                A +  + +   +    W           +E  P TGR HQ+R H  H+  PI+GD
Sbjct: 121 APVQEAHTRLRCLARLSWPESWDGRHPETRISLVEALPTTGRRHQIRRHLKHVAHPIIGD 180

Query: 270 HKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGR-LQITAP---LP-----AHMVKT 318
             +       + +    Q +L+LHAR +++ HP  G+ L+  A    LP         K 
Sbjct: 181 ATHGKGPLNRWWAERLGQQRLWLHARALEIAHPVSGQLLRFEADWSALPQVQEAQDWQKL 240

Query: 319 WDSLGFK 325
               G++
Sbjct: 241 LALPGWQ 247


>gi|260582044|ref|ZP_05849839.1| pseudouridylate synthase [Haemophilus influenzae NT127]
 gi|260094934|gb|EEW78827.1| pseudouridylate synthase [Haemophilus influenzae NT127]
          Length = 224

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 59/201 (29%), Positives = 92/201 (45%), Gaps = 16/201 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  ++Y+ S   + NK  GISV          +   K        K  L HRLD+ TSG
Sbjct: 1   MEIEVVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQL---NVPKVWLVHRLDKVTSG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A    +A   +  F   +I K Y +L    PK K+  I   + KK+  G   +   
Sbjct: 58  LLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGDM-KKAREGAWKLCQT 116

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K+N      AI+ F+ + C         ++P TG+THQLRV    +G PI+GD  Y  N 
Sbjct: 117 KEN-----PAITRFESVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDGLYGKNT 170

Query: 277 KGNFTSPIQNKLYLHARYMDL 297
           +        ++ YLHA  ++ 
Sbjct: 171 EK------IDRTYLHATQLEF 185


>gi|90581195|ref|ZP_01236993.1| putative pseudouridine synthase Rlu family protein [Vibrio angustum
           S14]
 gi|90437566|gb|EAS62759.1| putative pseudouridine synthase Rlu family protein [Vibrio angustum
           S14]
          Length = 231

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 94/221 (42%), Gaps = 23/221 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           L+Y+     V NK  GISV             L +  +  G +K  L HRLD+ TSG+L+
Sbjct: 4   LVYQHPDFLVINKHPGISVHKDDNDQP----LLAAVAEQTGDEKLYLIHRLDKMTSGLLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R + AA  L+ +F  R ++K Y ++    PK K+  +   + +            K  
Sbjct: 60  LGRNKEAASILSSNFAERVVEKFYVAIGTKKPKKKQGVVIGDMTR------SRRSSWKLE 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F       +       +PHTG+THQ+RV    +G  I GD  Y       
Sbjct: 114 STKENPAITQFFS-TAAGEGRRLFLCKPHTGKTHQIRVALRSVGSGITGDDIYG------ 166

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
             +   ++ YLHA  +  P+ +G   +   P P    K W 
Sbjct: 167 --TEASDRGYLHAYALSFPY-KGETQRFICP-PTD-GKLWQ 202


>gi|148827198|ref|YP_001291951.1| exonuclease III [Haemophilus influenzae PittGG]
 gi|148718440|gb|ABQ99567.1| exonuclease III [Haemophilus influenzae PittGG]
          Length = 224

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 62/217 (28%), Positives = 99/217 (45%), Gaps = 18/217 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  ++Y+ S   + NK  GISV          +   K        K  L HRLD+ TSG
Sbjct: 1   MEIEVVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQL---NVPKVWLVHRLDKVTSG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A    +A   +  F   +I K Y +L    PK K+  I   + KK+  G   +   
Sbjct: 58  LLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGDM-KKAREGAWKLCQT 116

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K+N      AI+ F+ + C         ++P TG+THQLRV    +G PI+GD  Y  N 
Sbjct: 117 KEN-----PAITRFESVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDGLYGKNT 170

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           +        ++ YLHA  ++  +     + +T  LP+
Sbjct: 171 EK------IDRTYLHATQLEFDYLNDC-ISVTC-LPS 199


>gi|16272017|ref|NP_438215.1| pseudouridine synthase-like protein [Haemophilus influenzae Rd
           KW20]
 gi|260580654|ref|ZP_05848481.1| conserved hypothetical protein [Haemophilus influenzae RdAW]
 gi|1175071|sp|P43930|Y042_HAEIN RecName: Full=Uncharacterized RNA pseudouridine synthase HI_0042;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|1572988|gb|AAC21720.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|260092716|gb|EEW76652.1| conserved hypothetical protein [Haemophilus influenzae RdAW]
          Length = 224

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 59/201 (29%), Positives = 91/201 (45%), Gaps = 16/201 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  ++Y+ S   + NK  GISV          +   K        K  L HRLD+ TSG
Sbjct: 1   MEIEVVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQL---NVPKVWLVHRLDKVTSG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A    +A   +  F   +I K Y +L    PK K+  I   + KK+  G   +   
Sbjct: 58  LLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGDM-KKAREGAWKLCQT 116

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K N      AI+ F+ + C         ++P TG+THQLRV    +G PI+GD  Y  N 
Sbjct: 117 KDN-----PAITRFESVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDGLYGKNT 170

Query: 277 KGNFTSPIQNKLYLHARYMDL 297
           +        ++ YLHA  ++ 
Sbjct: 171 EK------IDRTYLHATQLEF 185


>gi|315635420|ref|ZP_07890686.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
 gi|315480178|gb|EFU70845.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
          Length = 300

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 70/262 (26%), Positives = 113/262 (43%), Gaps = 27/262 (10%)

Query: 50  KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIY 109
            +R+    RI           INA + I  E   +      TK    LK +L +ED    
Sbjct: 31  GQRLTSKGRIFD----ENMNQINAGDEIPTEHIFIAVFEGQTK---GLKPLLEFED--FA 81

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           +F+KP  + V   S         L       G+   L HR+D ETSG+++V + + +   
Sbjct: 82  IFDKPTNLMVHPIS--KNTSYSLLDEIRYHFGENANLIHRIDAETSGLVIVGKNKKSEIE 139

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           L + F+ ++  K Y ++V G  K + + I   L ++    G  + V  Q E+G   +I+ 
Sbjct: 140 LKDMFQEKKYHKSYLAIVQGEIKEELK-IDKALDREGKAIGVRMKVCTQ-EEGGKESITI 197

Query: 230 FK-VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------------- 275
            K +I    +    +E  P TGR HQ+RVH   MG  I+GD  Y  +             
Sbjct: 198 IKPIIYDKEKNLTLVEALPLTGRQHQIRVHLHSMGHTILGDPIYGVDDENAENYLNKTLS 257

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
            +  F     ++L+LHA Y++ 
Sbjct: 258 KEDRFKVTKSHRLWLHANYLEF 279


>gi|82750620|ref|YP_416361.1| RNA pseudoridylate synthase [Staphylococcus aureus RF122]
 gi|82656151|emb|CAI80562.1| probable RNA pseudoridylate synthase [Staphylococcus aureus RF122]
          Length = 284

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 62/283 (21%), Positives = 112/283 (39%), Gaps = 36/283 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++    ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMPNDILEI--------HLPQE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++  L+  +LYED+ I +  K    +        +               +
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKLNNQNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
              P +  RLD+ T+GI++ A+        ++      ++KIY  LV+G  K     I  
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVN----LKKIYTCLVYG--KTHTSGIIE 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +++S        + ++      YA + ++VI+    K+   ++  HTGRTHQ+RVH  
Sbjct: 174 ANIRRSKDS----IITREVASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQ 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           H+G PIVGD  Y           +Q         +   HP   
Sbjct: 229 HIGHPIVGDSLYDGFHDKIHGQVLQ------CTQIYFVHPINK 265


>gi|256079649|ref|XP_002576098.1| ribosomal pseudouridine synthase [Schistosoma mansoni]
 gi|238661358|emb|CAZ32333.1| ribosomal pseudouridine synthase, putative [Schistosoma mansoni]
          Length = 455

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 59/286 (20%), Positives = 101/286 (35%), Gaps = 43/286 (15%)

Query: 23  RWFKNHYPHI--------NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           RW       +        +   + +   SG++ V+  +V  +  I               
Sbjct: 83  RWINRKLRDVMQSEFNNNSDEAIAQKCESGEILVNNAKVDPDYIINDSD----------- 131

Query: 75  NHIIKEQKILDSSVNLTKHSDF-LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                   +L   V+  +     L    +++   I V NKP  I +       Y ++   
Sbjct: 132 --------LLSQKVHRHECPVLNLPIEFVHDSDDILVVNKPPSIPIHPCG--QYTLNSIT 181

Query: 134 KSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                  G +P R THRLD+ TSG+L++A+    +  L      + + K Y   V G   
Sbjct: 182 HILAKDYGLRPLRFTHRLDRMTSGLLLIAKNYDTSVRLQSQISSKEVAKYYICHVEGCFP 241

Query: 193 NK------KECIANWLLKKSHIGGDYVHVVKQNE-----KGANYAISHFKVIDCFA-QKF 240
            +         I N ++  S   G     +  +       G  +A +HF  +        
Sbjct: 242 TEPIDQCTGFEINNGVVVCSQPVGPISRRMGVHGVLPESAGGKFARTHFLRLSYNPVTDT 301

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
             +  +  TGRTHQ+R+H  ++G PIV D  Y +   G       N
Sbjct: 302 SLVICRLFTGRTHQIRIHVQYLGYPIVDDPLYNSADWGELKGKGAN 347


>gi|299142544|ref|ZP_07035675.1| ribosomal large subunit pseudouridine synthase A [Prevotella oris
           C735]
 gi|298575979|gb|EFI47854.1| ribosomal large subunit pseudouridine synthase A [Prevotella oris
           C735]
          Length = 522

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 90/230 (39%), Gaps = 24/230 (10%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +D   N  + +       +YED  I V  KP G+    G     ++   ++     +   
Sbjct: 307 IDIEENPLERASQQALEWIYEDKDIVVVCKPVGMLSVPGKIQRENVRSLVRQR-HPEATG 365

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW-GIPKNKKECIANWL 202
           P + HRLD  TSG+LVVA    +   L   F    +QK Y +L+       +   I   L
Sbjct: 366 PMIVHRLDMATSGLLVVALNLKSYIDLQCQFEEHSVQKRYVALLSRPHHGARSGQICLPL 425

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH- 261
               H     +     +      A+++++           + + P TGRTHQLR+H  H 
Sbjct: 426 RPDLHDRPRQI----VDAVHGRKAVTNYQ-----QTGENRMNLYPLTGRTHQLRMHCAHA 476

Query: 262 --MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
             +  PI GD  Y    +         +LYLHA  +   HP  G R+   
Sbjct: 477 DGLNNPIKGDELYGTRAE---------RLYLHAEELSFVHPGTGERMHFE 517


>gi|325479463|gb|EGC82559.1| pseudouridine synthase, RluA family [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 279

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 55/301 (18%), Positives = 115/301 (38%), Gaps = 38/301 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M Y++Y +     E   + ++  +     +  +++ IL  G   ++ +  K +  +++G 
Sbjct: 1   MRYIKYEL----SEKTTVRKFLLS--KGYSKRSVEAILSEGF-LLNNQLSKKSKNLKAGD 53

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +               I D +++       LK  ++YED    V +K   I+V    
Sbjct: 54  KLFV--------------IIRDENIDYEPVRGNLK--IIYEDRDTLVISKDPNITVNSKG 97

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
            I+   +       ++   K R  +RLD +TSG+++VA+ + A     +      + K Y
Sbjct: 98  QISLANNIAYYFKSNNINSKVRFVNRLDMDTSGLILVAKNKYAHAFYQKQIENNEMIKKY 157

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++V              +L +     D         +    A + FK +     +   +
Sbjct: 158 IAIVDPNANLD-------MLYEEKFAYDEKSKSYVVSEDGKTAKTIFKPLKLLKDR-TIV 209

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           E Q  TG+THQ+R     +  PI GD  Y ++          ++  LH+  +   + +  
Sbjct: 210 ECQILTGKTHQIRASLSSLDYPIFGDKLYGSDKN-------LDRFLLHSYKLSFRNFKDE 262

Query: 304 R 304
            
Sbjct: 263 E 263


>gi|170578286|ref|XP_001894351.1| Hypothetical 50.0 kDa protein K07E8.7 in chromosome IV, putative
           [Brugia malayi]
 gi|158599118|gb|EDP36813.1| Hypothetical 50.0 kDa protein K07E8.7 in chromosome IV, putative
           [Brugia malayi]
          Length = 430

 Score =  138 bits (349), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 60/265 (22%), Positives = 98/265 (36%), Gaps = 28/265 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPVINALNH 76
             RL   F   +  +N        + G++ V+  +    N  +Q    +           
Sbjct: 60  GRRLVDIFAEEFVSLNRHYPAAACKLGRIWVNCNQMTNVNYIVQQNDSIEHIGHR----- 114

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKS 135
              E  ILD  +            ++  D+ + V +KP  + V   G    + + G L+ 
Sbjct: 115 --HEHPILDHYIK-----------VIDNDNDMLVVDKPPSMPVHPCGRYSVHTVLGMLRE 161

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI-YWSLVWGIPKNK 194
               +G   R+ HRLD+ TSG+L+ AR       L +  R+  I    Y   V G+    
Sbjct: 162 QRGLRG--LRVVHRLDRTTSGVLLFARNAETDTKLKKMLRVGEIWHKEYICKVEGVFPGD 219

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           KE + +  +    +      +          A S F  +    Q    +     TGRTHQ
Sbjct: 220 KEIVCDRPIGPLVVSMGIQCIRD----DGKSARSRFWRLWTDGQ-TSIVRCMLETGRTHQ 274

Query: 255 LRVHALHMGCPIVGDHKYCANFKGN 279
           +RVH  ++G PIV D+ Y     G 
Sbjct: 275 IRVHLQYLGYPIVDDYIYNTTAWGE 299


>gi|326317327|ref|YP_004234999.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
 gi|323374163|gb|ADX46432.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
          Length = 328

 Score =  138 bits (349), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 62/298 (20%), Positives = 112/298 (37%), Gaps = 33/298 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV   +    L  +     P ++     + +  G+V                 +      
Sbjct: 43  VVTPSQGGGLLIDFLAERLPVVDRTEWLQRMERGEV-----------------MDEHACP 85

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHI 129
           +      +   +I       ++     +  +LY+D  + V +KP  + V   G  + + +
Sbjct: 86  VTHGRPFVPGLRIYYYRELASEAVIPFEETVLYQDEHLVVADKPHFLPVVPTGRYLQHTL 145

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              LK  +   G  P   HR+D++T+G+++ +  RA        FR R + K Y ++   
Sbjct: 146 LVRLKRRLGLDGLSP--VHRIDRDTAGLVLFSVQRATRGRYQALFRDRAVDKTYEAVAPW 203

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   +A    + S I             G   +++  +V+D     +    + P T
Sbjct: 204 RVD-----VAFPRERSSRIEESPQFFRMHEVPGEANSLTRMEVLDVDG-AWARYRLSPVT 257

Query: 250 GRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GR HQLRVH   +G P+ GD  Y       +G+F+ P+Q    L AR +    P  GR
Sbjct: 258 GRRHQLRVHMAALGLPLRGDAFYPEVNDPPEGDFSRPLQ----LLARAIAFTDPVTGR 311


>gi|328948465|ref|YP_004365802.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
 gi|328448789|gb|AEB14505.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
          Length = 223

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 72/230 (31%), Positives = 108/230 (46%), Gaps = 24/230 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E+ +I + NK  G+SVQGG+GIA+ +D  L   +   G K  L HRLD+ETSGILVV
Sbjct: 6   IIFENEEILLVNKEGGVSVQGGAGIAHPLDAELSIQL---GYKIFLVHRLDKETSGILVV 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+   AA   T      +++K Y ++ +GIP    +   + +L+ +              
Sbjct: 63  AKNAQAAAKWTNLISGGKVKKEYVAVCFGIPVVDGKKCYSGVLEGTVEAHGRT------- 115

Query: 221 KGANYAISHFKVIDCFAQK---------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                A + FKV   +  K           +L++   TGR HQ+R+      CPI GD K
Sbjct: 116 ---QAAKTFFKVESVWNVKIPESEKELELSFLKLTLGTGRMHQIRIQLAKASCPIAGDDK 172

Query: 272 YCANFKGNFTSPI-QNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           +    K      I   KL L +  + LP  +G       PLP H+  T D
Sbjct: 173 HGDFKKNKLARKIGIKKLQLASVKLSLPV-DGKTQTFEIPLPEHIKTTLD 221


>gi|315586335|gb|ADU40716.1| pseudouridine synthase D [Helicobacter pylori 35A]
          Length = 293

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 69/294 (23%), Positives = 122/294 (41%), Gaps = 29/294 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQCHLDKQRLKQNQ-----QAVRKSQMIQGVVSLI------------HFR 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +     L++E     VF+KP  +      G  YH +  L       G+     HRLD E
Sbjct: 64  PNEKTQALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  +A+ L   F  ++++K Y +LV G+  ++   I   +L   +I  D +
Sbjct: 122 TSGLVLAGKTLQSAKDLKALFMQKKVKKTYLALVHGLV-DRSIVIDKPILTPQNIQKD-L 179

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  +       + +  + +          L++ P TGRTHQ+R+H   +G  IVG+  Y
Sbjct: 180 RIKSKISPLGKPSTTLVEPLSYNPFLDISLLKITPITGRTHQIRLHLSSVGHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +         +      L LHA  ++    +G   +IT+P+P   +    
Sbjct: 240 GVIDENAREYLQLKRENNAPLLMLHASSLEFEF-KGAIHEITSPMPKRFMPFLK 292


>gi|325141924|gb|EGC64364.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis 961-5945]
          Length = 173

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 42/159 (26%), Positives = 68/159 (42%), Gaps = 21/159 (13%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V  +    RLD       P  +   L   ++ G V V+ K  +  +++  G+ +R+  
Sbjct: 30  LTVPLELAGGRLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKPSQPKDKMIGGEQIRVT- 88

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI---- 125
                        +  S  NL    + +   ++YED  + V NKPAG+ V   +G     
Sbjct: 89  -------------VRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWEGD 135

Query: 126 -AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
            A    G L     S      + HRLD+ETSG++VVA+T
Sbjct: 136 AAQRPVGALSRIEPSTA--CSIVHRLDKETSGLMVVAKT 172


>gi|50311419|ref|XP_455734.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49644870|emb|CAG98442.1| KLLA0F14553p [Kluyveromyces lactis]
          Length = 377

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 64/313 (20%), Positives = 117/313 (37%), Gaps = 37/313 (11%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           K+LR G             +   G  +     I        E  + +    +      + 
Sbjct: 64  KLLREG-------------KQLEGDPIIKNKDILLTYQHNHEPPVKNWGEPICDEKHIMG 110

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++++D ++ V NKP GI V   +   ++ +   +   DS G      +RLD+ TSG+L
Sbjct: 111 IPIVHQDEQLLVINKPNGIPVHPTAY--FYKNTLTELLKDSLGYPVHPCYRLDKITSGLL 168

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+    A  +    R R ++K Y + V G             + KS I    + +  +
Sbjct: 169 ILAKNPIDANRVQSKIRDRDMKKYYLARVKGKFPETA-------VDKSPIYTCDLKIKSE 221

Query: 219 NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                  A + F++++  A      +  +P TGRTHQ+R+H    G PI  D  Y  +  
Sbjct: 222 PLSPLKDAHTEFELMEYDAVTDQSIVLCKPFTGRTHQIRIHLARQGHPITNDPFYNLD-- 279

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQ-----ITAPLPAHMVKTWDSLGFKYDRNLYI 332
            N T P++++        D       R++         L       WD L    +R    
Sbjct: 280 -NSTYPLRSR--FIIETPDWTQLTNERIEKLRKRFEVELDD----VWDQLNENQERCPEC 332

Query: 333 KRLYSQDECKQNI 345
                +D   +++
Sbjct: 333 DEEMPKDPTPESL 345


>gi|322418714|ref|YP_004197937.1| pseudouridine synthase [Geobacter sp. M18]
 gi|320125101|gb|ADW12661.1| pseudouridine synthase [Geobacter sp. M18]
          Length = 293

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 62/289 (21%), Positives = 109/289 (37%), Gaps = 29/289 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +    +P I     ++ +  G+V   D   V       + + V            ++E++
Sbjct: 25  FLVQRFPKIPESVWERRVAEGKVLAEDGSPVSATTPYAAQRRVFYF-------REVEEER 77

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
           ++             +  +LY+  ++ V  KP  + V  G    Y     L       G 
Sbjct: 78  VIP-----------FQEEILYQTDELLVACKPHFLPVTPGG--VYLDQSLLHRLRKRTGI 124

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HR+D+ET+GI++ +          E FR   I+K Y +L  GI     E    W
Sbjct: 125 HHLVPLHRIDRETAGIVLFSVNPQTRGRYGELFRDGSIEKSYRALSAGIAAAGGE---EW 181

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            ++   + G+        + G   A S  ++I+          + P TG+THQLRVH   
Sbjct: 182 QVENRLVHGEP-WFTMTTQPGPPNARSQIRLIEERG-GVSHFSLTPLTGKTHQLRVHMSG 239

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +G PI+ D  Y    K       +  L L A+ +    P  G+ ++  +
Sbjct: 240 LGMPIMHDRLY-PQLKPRHPDDFEKPLQLLAQRLRFKDPVSGKWMEFQS 287


>gi|323309473|gb|EGA62684.1| Pus9p [Saccharomyces cerevisiae FostersO]
          Length = 265

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 48/167 (28%), Positives = 79/167 (47%), Gaps = 4/167 (2%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V +KP+GI V       Y  +   K   ++ G      +RLD+ TSG++ +A+T   A 
Sbjct: 1   MVIDKPSGIPVHPTG--RYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFLAKTPRGAD 58

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           ++ +  + R + K Y + V G     +  +   L K          V + +EKGA +A +
Sbjct: 59  NIGDQLKAREVTKEYVAKVVGEFPETEVIVEKPL-KLIEPRLALNAVCQMDEKGAKHAKT 117

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            F  I     K   ++ +P TGR+HQ+RVH  ++G PI  D  Y  +
Sbjct: 118 VFNRISYDG-KTSIVKCKPLTGRSHQIRVHLQYLGHPIANDPIYSND 163


>gi|78184312|ref|YP_376747.1| putative pseudouridylate synthase [Synechococcus sp. CC9902]
 gi|78168606|gb|ABB25703.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           CC9902]
          Length = 214

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 58/215 (26%), Positives = 95/215 (44%), Gaps = 11/215 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +L++D  +   +KP+G+  Q G G         +     +G   RL HRLD++TSG+L
Sbjct: 6   VRILHQDRWLLAVDKPSGLLSQPGLGPEQADSLISRVQAHDEGPDWRLVHRLDRDTSGVL 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A    A +  +  F  R + K+Y + V G+   +   I N L +       Y      
Sbjct: 66  LLAAGLEALRRTSALFSSRSVNKLYLAHVCGVMAGR-GSINNRLARLQRQPPRY-----G 119

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +      A + ++V    A       ++P TGR+HQLR H   +  PI+GD  Y      
Sbjct: 120 SHPEGREACTLWRVRSSAAGVTQLW-LRPITGRSHQLRSHLAEIAHPILGDPIYGDQSVD 178

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
                   +L+LHA  +   HP  G RL++ +  P
Sbjct: 179 RLR---LQRLHLHAIALSFSHPFTGQRLRLVSADP 210


>gi|323334235|gb|EGA75617.1| Pus9p [Saccharomyces cerevisiae AWRI796]
          Length = 276

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 48/167 (28%), Positives = 79/167 (47%), Gaps = 4/167 (2%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V +KP+GI V       Y  +   K   ++ G      +RLD+ TSG++ +A+T   A 
Sbjct: 1   MVIDKPSGIPVHPTG--RYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFLAKTPRGAD 58

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           ++ +  + R + K Y + V G     +  +   L K          V + +EKGA +A +
Sbjct: 59  NIGDQLKAREVTKEYVAKVVGEFPETEVIVEKPL-KLIEPRLALNAVCQMDEKGAKHAKT 117

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            F  I     K   ++ +P TGR+HQ+RVH  ++G PI  D  Y  +
Sbjct: 118 VFNRISYDG-KTSIVKCKPLTGRSHQIRVHLQYLGHPIANDPIYSND 163


>gi|170117367|ref|XP_001889871.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164635211|gb|EDQ99522.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 478

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 62/281 (22%), Positives = 110/281 (39%), Gaps = 33/281 (11%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           + MT ++++          L       +   +    +  L SG   V+ +  K + +++ 
Sbjct: 26  TTMTKMRWI-------GRELLEVVSTEFRDRSMEYYRYALESGVTTVNGQIAKPDTKLRD 78

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK--IYVFNKPAGISV 119
           G  +              E  +  + V            +LY D +    V +KP  I V
Sbjct: 79  GDRIENIVHR-------HEPPVTSTPVK-----------VLYHDVEREFLVVDKPGSIPV 120

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                  Y+ +  ++  V+  G K     +RLD+ TSG++++  +   A+ LT+ F    
Sbjct: 121 HASG--RYYRNTLIEILVNDFGYKKCYPANRLDRLTSGLMIIPLSPDRARVLTDEFTTGT 178

Query: 179 IQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVV-KQNEKGANYAISHFKVIDCF 236
           ++K Y + V G  P  +  C    L     +G + VH   K        A + F +I   
Sbjct: 179 VRKEYVARVRGRFPAQEIVCEEPLLTVDRQMGLNIVHPEGKVLFIHLQPAKTVFNLIRYD 238

Query: 237 AQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                  +  +P TGR+HQLRVH  ++G PI  D  Y  + 
Sbjct: 239 ENTNSSVVRCEPLTGRSHQLRVHLQYLGFPIANDPIYSESR 279


>gi|68248593|ref|YP_247705.1| putative pseudouridine synthase [Haemophilus influenzae 86-028NP]
 gi|68056792|gb|AAX87045.1| conserved hypothetical pseudouridine synthase [Haemophilus
           influenzae 86-028NP]
          Length = 224

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 60/201 (29%), Positives = 91/201 (45%), Gaps = 16/201 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  ++Y+ S   + NK  GISV          +   K        K  L HRLD+ TSG
Sbjct: 1   MEIEVVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQL---NVPKVWLVHRLDKVTSG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A    +A   +  F   +I K Y +L    PK K+  I   + KKS  G   +   
Sbjct: 58  LLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGDM-KKSREGAWKLCQT 116

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K+N      AI+ F  + C         ++P TG+THQLRV    +G PI+GD  Y  N 
Sbjct: 117 KEN-----PAITRFASVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDGLYGKNT 170

Query: 277 KGNFTSPIQNKLYLHARYMDL 297
           +        ++ YLHA  ++ 
Sbjct: 171 EK------IDRTYLHATQLEF 185


>gi|184199951|ref|YP_001854158.1| putative pseudouridine synthase [Kocuria rhizophila DC2201]
 gi|183580181|dbj|BAG28652.1| putative pseudouridine synthase [Kocuria rhizophila DC2201]
          Length = 326

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 52/218 (23%), Positives = 91/218 (41%), Gaps = 8/218 (3%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             + +  +   +L+ED  I   +KP G+      G        + +       +    HR
Sbjct: 93  PDEDAPPVTLDVLHEDEWIMAVDKPHGLCSTP-KGENVRRSVVVAARCQFDNDEISALHR 151

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T G+L++ +           F+ R ++K YW++     +  ++ +      +S I 
Sbjct: 152 LDRSTGGVLLLCKRAEDRSAFHRLFQERTVRKTYWAVAGVNERVGEQTVR----VESRIR 207

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPI 266
                V    E G   A++  + ++ F      +   E+ P TGRTHQ+RVH   +G P+
Sbjct: 208 KIQGVVQAFEEPGEVNAVTDVRRVETFTDADGTWGLYEIAPLTGRTHQIRVHMTSLGLPL 267

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            GD  Y    +       +N L L AR ++  HP  GR
Sbjct: 268 RGDKLYPQPRQDFDVEDPENPLQLIARSIEFVHPVTGR 305


>gi|325955275|ref|YP_004238935.1| pseudouridine synthase [Weeksella virosa DSM 16922]
 gi|323437893|gb|ADX68357.1| pseudouridine synthase [Weeksella virosa DSM 16922]
          Length = 232

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 55/244 (22%), Positives = 98/244 (40%), Gaps = 29/244 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILV 159
           +LY+DS++   +KP G+ V             ++   +   GQ     HRLD++T+G+L+
Sbjct: 4   ILYQDSRLVAIHKPPGLLVHRSYYARDVKQFAVQELRNFLGGQHVYPIHRLDRKTAGVLL 63

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A  +     + E F  R + K YW++V G    ++  I   L        D        
Sbjct: 64  FALDKEMLSLMNEIFNSRAVTKEYWAIVRGY-TEQEGVIDYPLTNDDGQRQD-------- 114

Query: 220 EKGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 A ++++ +               ++  ++  P TGR HQLR H  H+  PI+G 
Sbjct: 115 ------AKTYYQTLQHAEINLPFGKHATSRYSLVKALPETGRMHQLRKHLRHIAHPILGS 168

Query: 270 HKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKY 326
             +  N +      +    ++ L AR +   HPE    + I A   A  ++  + L    
Sbjct: 169 RPHGCNKQNKLWLENFQLEQMMLLARSLRFTHPESQEEVCIKANPTAEFLRVCEILKINM 228

Query: 327 DRNL 330
            + L
Sbjct: 229 TKFL 232


>gi|70726951|ref|YP_253865.1| ibosomal large subunit pseudouridine synthase RluD subfamily
           protein [Staphylococcus haemolyticus JCSC1435]
 gi|68447675|dbj|BAE05259.1| hypothetical protein, ribosomal large subunit pseudouridine
           synthase, RluD subfamily [Staphylococcus haemolyticus
           JCSC1435]
          Length = 287

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 55/302 (18%), Positives = 113/302 (37%), Gaps = 44/302 (14%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           + N  L  + + H    +   +  I  +G + ++   V     + +G  + I        
Sbjct: 8   QHNEMLKSFLQRH--QYSKKTISAIKHNGALIINNSHVTVRKMMMAGDKLTIM------- 58

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                  + D + +           +LYED  + + +KP  ++        +  D  ++ 
Sbjct: 59  -------LPDETPSSYLIPSRNPIEILYEDDYLIIVSKPNYLNSTPSR--EHPHDSLIER 109

Query: 136 WVDSKG--------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +              P +  RLD+ T GI++ A+       +T S   +R    Y  + 
Sbjct: 110 VLYYLNVGQLIDTSIVPHIVTRLDRNTKGIVIFAKHGHIHHLMTTSAIDKR----YMCVC 165

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
           +G  +     I   + + S        + ++ +    YA + ++ +    +     E++ 
Sbjct: 166 YGQMQL-SGVIEEPIARDSQ-----SIITRKVDASGKYAKTSYETVMTKPE-ASLCEIKL 218

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQ 306
           HTGRTHQ+RVH  ++G P+VGD  Y  +    +T  +Q         +   HP     ++
Sbjct: 219 HTGRTHQIRVHFNYVGHPLVGDDLYEGSHPEIYTQSLQ------CYKVTFIHPIYNREIE 272

Query: 307 IT 308
           I 
Sbjct: 273 IE 274


>gi|319639018|ref|ZP_07993776.1| pseudouridine synthase Rlu family protein [Neisseria mucosa C102]
 gi|317399922|gb|EFV80585.1| pseudouridine synthase Rlu family protein [Neisseria mucosa C102]
          Length = 219

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 58/212 (27%), Positives = 91/212 (42%), Gaps = 19/212 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++E     V NKP G+SV   S     +   L   +    ++  L HRLD+ TSG+L+
Sbjct: 3   DIVFEHKDFVVINKPCGVSVHSESEGEVCLTASLAQKL--GVERVWLVHRLDKATSGLLL 60

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A  R +A  L+  F  + ++K Y +L    P  K+  +      K  +        K  
Sbjct: 61  LALNRDSAAALSTQFAEKTMRKTYLALGTHKPAKKQGWV------KGGMARSRRGTWKLT 114

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N+A++ F              +QP TG+THQLRV    +G PI+GD  Y  +   +
Sbjct: 115 RDEDNFAVTRFSS-QSLKPGLRLFVLQPFTGKTHQLRVAMKSIGSPILGDTLYGGDEAEH 173

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQIT-AP 310
                   L+LHA  +   +  G    I  AP
Sbjct: 174 --------LFLHAWRLVFDY-RGEHFDIRVAP 196


>gi|332673190|gb|AEE70007.1| pseudouridine synthase D [Helicobacter pylori 83]
          Length = 293

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 70/294 (23%), Positives = 123/294 (41%), Gaps = 29/294 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGIVSLI------------HFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +     L++E     VF+KP  +      G  YH +  L       G+     HRLD E
Sbjct: 64  PNEKTQALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++V +T  +A+ L   F  ++++K Y +LV G+  ++   I   +L   +I  D +
Sbjct: 122 TSGLVLVGKTLQSAKDLKTLFMQKKVKKTYLALVHGLV-DRSIVIDKPILTPQNIQKD-L 179

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  +       + +  + +          L++ P TGRTHQ+R+H   +G  IVG+  Y
Sbjct: 180 RIKSKISPLGKPSTTLVEPLSYNPFLDISLLKITPITGRTHQIRLHLSSVGHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +         +      L LHA  ++    +G   +IT+P+P   +    
Sbjct: 240 GVIDENAREYLQLKRENNAPLLMLHATSLEFEF-KGAIYKITSPMPKRFMPFLK 292


>gi|317012185|gb|ADU82793.1| pseudo uridine synthase D [Helicobacter pylori Lithuania75]
          Length = 298

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 72/300 (24%), Positives = 121/300 (40%), Gaps = 29/300 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVRLI------------YFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +     L++E     VF+KPA +      G  YH +  L       G+     HRLD E
Sbjct: 64  PNEKAQALVFETKDFGVFDKPAQVYTHP-KGYFYH-ESLLDCIQSHLGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  + + L   F  ++++K Y +L  G+ + K   I   +L   +I  D  
Sbjct: 122 TSGLVLSGKTLQSVKDLKALFMQKKVKKTYLALAHGLVE-KSMKIDKPILTPQNIQKDLR 180

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              K +      + +  + +          L++ P TGRTHQ+R+H   MG  IVG+  Y
Sbjct: 181 IRSKIS-PLGKPSTTLVEPLSYNPFLDISLLKITPLTGRTHQIRLHLSSMGHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
               +         +      L LHA  ++    +    +IT+P+P   +     L   Y
Sbjct: 240 GVADEEAREYLQLKRENHAPLLMLHASSLEFEF-KKAFYEITSPMPERFMPFLKDLPLFY 298


>gi|326508344|dbj|BAJ99439.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 394

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 101/260 (38%), Gaps = 25/260 (9%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
               +   F + +           ++ G+++VD++ V+ +  ++S Q +           
Sbjct: 49  AGKTIVDLFTDEFKGRPREYYVHAVKCGRLQVDEQMVQADYIVKSSQKISHFLHR----- 103

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
              E  +L  ++           ++L  +  +    KPA + V       Y  +  +   
Sbjct: 104 --HEPPVLGGNI-----------VILQNEVDVVTVCKPASVPVHPCG--QYRKNTVVGIM 148

Query: 137 VDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               G  P    HRLD+  SG+L+ A++   A+   +      +QK Y + V G+    +
Sbjct: 149 EAEHGLTPLFPVHRLDRLVSGLLIFAKSAERAERFRQQIEANLLQKEYVAKVVGVFPEGE 208

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           + +   +   +  G   V V     K       A + F+ I C       +  +P TGRT
Sbjct: 209 QTVDANVNFNAREGRSTVEVSNGPGKAIPSGKQACTKFQRI-CTDGNHSIVLCKPVTGRT 267

Query: 253 HQLRVHALHMGCPIVGDHKY 272
           HQ+RVH  H+G PI  D  Y
Sbjct: 268 HQIRVHLKHLGYPIANDELY 287


>gi|319896464|ref|YP_004134657.1| pseudouridine synthase [Haemophilus influenzae F3031]
 gi|317431966|emb|CBY80314.1| conserved hypothetical pseudouridine synthase [Haemophilus
           influenzae F3031]
          Length = 224

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 59/201 (29%), Positives = 92/201 (45%), Gaps = 16/201 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  ++Y+ S   + NK  GISV          +   K        K  L HRLD+ TSG
Sbjct: 1   MEIEVVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQL---NVPKVWLVHRLDKVTSG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A    +A   +  F   +I K Y +L    PK K+  I   + KK+  G   +   
Sbjct: 58  LLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGDM-KKAREGAWKLCQT 116

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K+N      AI+ F+ + C         ++P TG+THQLRV    +G PI+GD  Y  N 
Sbjct: 117 KEN-----PAITRFESVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDGLYGKNT 170

Query: 277 KGNFTSPIQNKLYLHARYMDL 297
           +        ++ YLHA  ++ 
Sbjct: 171 EK------IDRTYLHATQLEF 185


>gi|3834304|gb|AAC83020.1| Contains similarity to gi|1786244 hypothetical 24.9 kD protein in
           surA-hepA intergenic region yab0 from Escherichia coli
           genome gb|AE000116, and to hypothetical YABO family
           PF|00849 [Arabidopsis thaliana]
          Length = 491

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 89/355 (25%), Positives = 142/355 (40%), Gaps = 85/355 (23%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIY 109
           +++K N  +Q G  + +P  I  +    +   I   ++        +L+ ++ ++DS I 
Sbjct: 130 RKIKHNEVMQIGDKIWLPVSIAEMRISKRYDTIPSGTLYPNADEIAYLQRLVRFKDSAII 189

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLT-------HRLDQETSGILVVA 161
           V NKP  + V+G   I   +D    + +     + PRL        HRLD+ETSG+LV+ 
Sbjct: 190 VLNKPPKLPVKGNVPIHNSMDALAAAALSFGNDEGPRLVKLTFLGVHRLDRETSGLLVMG 249

Query: 162 RTRAAAQHLTESFRMRR---------------IQKIYWSLVWGIPKNKKECIANWLLKKS 206
           RT+ +  +L   F   +               + + YW+LV G PK K+  I+  L K  
Sbjct: 250 RTKESIDYLHSVFSDYKGRNSSCKAWNKACEAMYQQYWALVIGSPKEKEGLISAPLSKVL 309

Query: 207 HIGGDYVHVVKQNEKG---ANYAISHFKVIDCFAQKFCWLEMQPHTGRTH------QLRV 257
              G    VV     G   +  AI+ +KV+        W+E++P T R H      QLRV
Sbjct: 310 LDDGKTDRVVLAQGSGFEASQDAITEYKVLGPKINGCSWVELRPITSRKHQPPSKKQLRV 369

Query: 258 HAL-HMGCPIVGDHKYC------------ANFKGNFTSPIQNK----------------- 287
           H    +G PIVGD+KY              + +     P + +                 
Sbjct: 370 HCAEALGTPIVGDYKYGWFVHKRWKQMPQVDIEPTTGKPYKLRRPEGLDVQKGSVLSKVP 429

Query: 288 -LYLHARYMDLPH----------PEGGRLQ-----------ITAPLPAHMVKTWD 320
            L+LH R M LP+           E   L              A +P+HM  +W+
Sbjct: 430 LLHLHCREMVLPNIAKFLHVMNQQETEPLHTGIIDKPDLLRFVASMPSHMKISWN 484


>gi|297296167|ref|XP_001096617.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Macaca mulatta]
          Length = 484

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 53/197 (26%), Positives = 96/197 (48%), Gaps = 8/197 (4%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+    
Sbjct: 141 KDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-K 199

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++  
Sbjct: 200 EHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVT 259

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               +L  S+     V V + + +G     + F+ +    Q    +  +P TGRTHQ+RV
Sbjct: 260 CKEPILVVSY----KVGVCRVDTRG-KPCETVFQRLSYNGQS-SVVRCRPLTGRTHQIRV 313

Query: 258 HALHMGCPIVGDHKYCA 274
           H   +G PI+ D  Y +
Sbjct: 314 HLQFLGHPILNDPIYNS 330


>gi|223992757|ref|XP_002286062.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220977377|gb|EED95703.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 246

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 93/239 (38%), Gaps = 25/239 (10%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           LT     L   +LY D  I V +KPA +    G    +  +            +  + HR
Sbjct: 12  LTNVPPHLTIRVLYSDDDIVVIDKPANLRSVPG----HASNSPDADDGSKSKYQLHVVHR 67

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNK-----KECIANWLL 203
           LD +TSGI+VVAR   AA  L  ++R R  +QK Y +     P        +  I   L 
Sbjct: 68  LDCQTSGIMVVARNSTAASKLCHAWRERDIVQKTYLAYCQRWPPYHDEQLSEGTIDLPLA 127

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                   +   V+  E G     S   V +        LE++P TGRTHQLR+H   +G
Sbjct: 128 ASRTERIKWE--VRALEDGGKPLKSELTV-ERDNDNGVVLELKPITGRTHQLRIHCATIG 184

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYL-----------HARYMDLPHPEGG-RLQITAP 310
             IVGD  Y  +    F    Q+               HA  +  PHP  G  +   +P
Sbjct: 185 SGIVGDSLYGDSPVEWFGDKPQHGQQTISQSDTQTLRLHAHKLVFPHPSTGSEVTFVSP 243


>gi|257453802|ref|ZP_05619080.1| YabO/YceC/SfhB family protein [Enhydrobacter aerosaccus SK60]
 gi|257448729|gb|EEV23694.1| YabO/YceC/SfhB family protein [Enhydrobacter aerosaccus SK60]
          Length = 285

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 57/294 (19%), Positives = 120/294 (40%), Gaps = 31/294 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPVINALNH 76
             RL  +   H+ HI+  + Q+   SG + ++  + +K ++   +GQ +           
Sbjct: 2   GGRLIDYLAAHFSHISLASWQRRFDSGLISLERGEPLKQDSPYLAGQTILYY-------R 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKS 135
            ++ + I+             +  +L+ D  + V +KP  + V   G  ++  +   L++
Sbjct: 55  QVENEPIIP-----------FEPNILHLDGHLLVVDKPHFLPVTPSGRYVSQTLLAKLRN 103

Query: 136 WVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             D +          HRLD++T+G+++++   ++       F  R I K Y ++      
Sbjct: 104 HPDLQQLAVNDISPLHRLDKDTAGVMLLSVNPSSRACYHALFADRHIHKTYHAIA----P 159

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            + +    + +      G+   + K   +G   A +  ++I+     F    + P TG+ 
Sbjct: 160 TRSDLCYPFHIHSRLERGEPFFLTK-TTQGEPNAHTTIELIENNG-AFSLYRLTPVTGKK 217

Query: 253 HQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           HQLRVH   +G P++ D+ Y      K   +S     L L A+ +    P   +
Sbjct: 218 HQLRVHMASLGMPLLHDNFYPTVKTVKPQCSSDFTKPLQLLAKSIAFIDPITQQ 271


>gi|255077107|ref|XP_002502205.1| pseudouridine synthase [Micromonas sp. RCC299]
 gi|226517470|gb|ACO63463.1| pseudouridine synthase [Micromonas sp. RCC299]
          Length = 363

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 70/282 (24%), Positives = 117/282 (41%), Gaps = 34/282 (12%)

Query: 64  VVRIPPVINALNHIIKEQKILDSSVN--LTKHSDFLKSI--LLYEDSKIYVFNKPAG--I 117
           V  + P IN L  +    ++   SV+  + +    L+    L++ED+   V NKP    +
Sbjct: 91  VNEVQPRINYLRFLDDNDRLDGESVSSCIARQPQSLERDFHLVHEDADYAVVNKPWCVRL 150

Query: 118 SVQGGS------GIAYHIDGFLKSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQ 168
               G          Y  D  ++ W++ +       R  H+LD  TSG+LV A  + AA 
Sbjct: 151 DTPRGWPGKVRFTPKYPGDLSVEDWLERRYPDWDTVRFCHQLDNATSGVLVAASNKRAAG 210

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
              + FR RR +K Y ++V+G P+  +  +   + +       +   V  + +      +
Sbjct: 211 AAAKLFRERRARKTYLAIVFGHPEQDEWTVDVPMGRDPDDPKGFRERV--DPEHGKACET 268

Query: 229 HFKVIDC---------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            F+V+                  +E+ P TGR HQ+R+H    G PIVGD+ Y  +    
Sbjct: 269 RFRVLKRGRLNLRGKFEGVPVSKVEVTPVTGRRHQIRLHLQFSGHPIVGDNAYSQDTDSF 328

Query: 280 FTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWD 320
                  + +LHA  + LP  E  G +Q  AP P       +
Sbjct: 329 -------RTFLHAHKLTLPFDEPRGTMQFVAPEPESFAAAME 363


>gi|145630664|ref|ZP_01786443.1| hypothetical protein CGSHi22421_01939 [Haemophilus influenzae
           R3021]
 gi|144983790|gb|EDJ91240.1| hypothetical protein CGSHi22421_01939 [Haemophilus influenzae
           R3021]
          Length = 224

 Score =  138 bits (347), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 59/201 (29%), Positives = 91/201 (45%), Gaps = 16/201 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  ++Y+ S   + NK  GISV          +   K        K  L HRLD+ TSG
Sbjct: 1   MEIEVVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQL---NVPKVWLVHRLDKVTSG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A    +A   +  F   +I K Y +L    PK K+  I   + KK+  G   +   
Sbjct: 58  LLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGDM-KKAREGAWKLCQT 116

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K+N      AI+ F  + C         ++P TG+THQLRV    +G PI+GD  Y  N 
Sbjct: 117 KEN-----PAITRFASVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDGLYGKNT 170

Query: 277 KGNFTSPIQNKLYLHARYMDL 297
           +        ++ YLHA  ++ 
Sbjct: 171 EK------IDRTYLHATQLEF 185


>gi|154175159|ref|YP_001407354.1| putative prophage LambdaCh01, recombination protein Bet
           [Campylobacter curvus 525.92]
 gi|112802454|gb|EAT99798.1| putative prophage LambdaCh01, recombination protein Bet
           [Campylobacter curvus 525.92]
          Length = 305

 Score =  138 bits (347), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 64/291 (21%), Positives = 117/291 (40%), Gaps = 53/291 (18%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           Q+++  G++  D   V   N + SG++  I   +N                         
Sbjct: 31  QRLIDKGRLLCDGAVVSEKNAVLSGEICLIDYEMNPRGLSP------------------- 71

Query: 98  KSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
               ++E  +  VF+KP+G+     G    Y ++  +       G++  +THRLD+ETSG
Sbjct: 72  ----IFECDEFAVFDKPSGVLSHPNGRRCEYSLNDEIWHLY---GREAAVTHRLDRETSG 124

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG----DY 212
           ++VV++  AA + L   F  R ++K Y +L  G        I    +  + +      D 
Sbjct: 125 LIVVSKNLAAQKELKAMFESRAVKKRYVALAGGE-------ICEPFIVDAKMDLASDYDD 177

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           V +  Q  +    A++ F+ ++ FA      +   P TGR HQ+R+H  H+   I+G+  
Sbjct: 178 VKMRMQICENGKAAVTEFEPMEYFADIDATLVRAVPLTGRQHQIRLHLFHVKHAIIGEPL 237

Query: 272 YCANFK-------------GNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           Y    +                     ++L LHA  ++     G +  I +
Sbjct: 238 YGLAKERIIKILDGKMSEMERINLTGASRLLLHADEIEFKF-RGRKFHIKS 287


>gi|313229293|emb|CBY23879.1| unnamed protein product [Oikopleura dioica]
          Length = 390

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 53/216 (24%), Positives = 98/216 (45%), Gaps = 4/216 (1%)

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLK-SILLYEDSKIYVFNKPAGISVQGGSG 124
            I       N IIK+  ++ +  +  +    +    ++ +  + YV NKP+ + +   + 
Sbjct: 126 EIINASELKNRIIKDGDMISTKDHRHEPPVRIPLPEVIADTDEFYVVNKPSSLPIHPVA- 184

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             Y  +  +            + HRLD+ TSG+++ A+T+  A+ +++    R ++K Y 
Sbjct: 185 -QYRHNSLIFLIAREYKVNYHVIHRLDRLTSGLVIFAKTKEVAKRVSKEISDRVVRKQYL 243

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWL 243
             V G   +K  C  +     +  G   V     +EK    A++ F++++ F +     +
Sbjct: 244 LRVVGKFPDKAVCDKSLFEISAKKGIYRVAKADDDEKKVKTALTEFELVEYFKEADQSLV 303

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              P TGRTHQ+RVH  ++GCPIV D  Y     G 
Sbjct: 304 RAIPKTGRTHQIRVHTQYLGCPIVNDPVYNDPLFGK 339


>gi|323495007|ref|ZP_08100098.1| pseudouridine synthase Rlu family protein [Vibrio brasiliensis LMG
           20546]
 gi|323310802|gb|EGA63975.1| pseudouridine synthase Rlu family protein [Vibrio brasiliensis LMG
           20546]
          Length = 231

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 100/238 (42%), Gaps = 23/238 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      V NK   +SV    G    ++   K    +   K  L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFIVINKHPNVSVHKDDGDTMLLEEVAK---QTGDNKLYLIHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R+ +AA  L+  F  R ++K Y ++    PK K+  I+  + +        V+     
Sbjct: 60  LGRSSSAASELSRQFAERSVEKFYLAIGCNKPKKKQGLISGDMQRSRRSAWKLVN----- 114

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  +     +      +PHTG+THQ+RV    +G  I GD  Y A+    
Sbjct: 115 -SNTNPAVTQFFSLAAMPGER-LFLCKPHTGKTHQIRVALKSLGSAIAGDPIYNASHHA- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
                 ++ YLHA  +     +     +  P      +    LG K++  +  + + S
Sbjct: 172 ------DRGYLHAFALRFEFQQQAYQFVCDP------RNSAVLGEKWNEQMTSQGIES 217


>gi|327404189|ref|YP_004345027.1| pseudouridine synthase [Fluviicola taffensis DSM 16823]
 gi|327319697|gb|AEA44189.1| pseudouridine synthase [Fluviicola taffensis DSM 16823]
          Length = 227

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 55/235 (23%), Positives = 98/235 (41%), Gaps = 29/235 (12%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGI 157
             L+YED    V +KP+ + V          +  L   +  +G  +    HRLD++TSG+
Sbjct: 6   VKLIYEDEYCLVVSKPSNLIVHHSYYARNIEETSLTDLIREQGCLEACPVHRLDRKTSGL 65

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++ A+         + F    I+K Y +L+ G  + +   I +               VK
Sbjct: 66  ILFAKKAEWVADFQKLFENGEIEKKYLALLRGHLEAE-GSIDSP--------------VK 110

Query: 218 QNEKGANYAISHFKVIDCFA----------QKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +      A++ +  ++ F           Q++  +E+ P TGR HQLR+HA  +  PI+
Sbjct: 111 NDRGNYKDALTKYTCLEHFERAYVIPPYEKQRYSLVELTPITGRMHQLRIHANKIAHPII 170

Query: 268 GDHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGRLQI-TAPLPAHMVKTW 319
            D KY      ++   +   ++L+LHA+ +    P  G L     P P    +  
Sbjct: 171 NDPKYGNRHHNHYFQEVLGIHELFLHAQSLKFKQPFTGELVWLQEPFPDFWNRFL 225


>gi|121594845|ref|YP_986741.1| tRNA pseudouridine synthase C [Acidovorax sp. JS42]
 gi|120606925|gb|ABM42665.1| tRNA pseudouridine synthase C [Acidovorax sp. JS42]
          Length = 268

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 57/214 (26%), Positives = 91/214 (42%), Gaps = 2/214 (0%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                  LL++D+ +    KPAG  V      A      +++  D  GQ     HRLD+ 
Sbjct: 3   PAHPPLRLLWQDAHMVAVFKPAGWLVHRTGLDAGETRFVMQALRDQIGQHVYPVHRLDKG 62

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T G+LV+A   AAA+ L ++F    ++K Y +LV G    + E         +       
Sbjct: 63  TCGVLVMALHPAAARALADAFARHAVRKQYLALVRGWAPAQAEVDHPLRPDDAPPDAPTQ 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               +  + A   +           +   +  +P TGR HQ+R H  H+  PI+GD  + 
Sbjct: 123 PAHTRLTRLARLELPECSDPRFATTRASLVRAEPTTGRRHQIRRHLKHLAHPILGDATHG 182

Query: 274 ANFKGNFTSP--IQNKLYLHARYMDLPHPEGGRL 305
                 + +     ++L+LHA  + LPHP  GRL
Sbjct: 183 KGPLNRWWAQRLGLHRLWLHAWQLSLPHPADGRL 216


>gi|289449613|ref|YP_003475167.1| RNA pseudouridine synthase [Clostridiales genomosp. BVAB3 str.
           UPII9-5]
 gi|289184160|gb|ADC90585.1| RNA pseudouridine synthase [Clostridiales genomosp. BVAB3 str.
           UPII9-5]
          Length = 233

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 61/226 (26%), Positives = 98/226 (43%), Gaps = 18/226 (7%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRL 150
            ++  ++Y D+ +    KPAG   Q     A  I  + K++V  K  KP      L HRL
Sbjct: 3   LIEPKVIYCDNHLLAVYKPAGYLSQADGTAAPDILAWSKAYVKKKYDKPGDVYLGLVHRL 62

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN--KKECIANWLLKKSHI 208
           D+  +G+LV+ART  AA  L E  R    QKIY ++     +     E   +++ K   +
Sbjct: 63  DRPVAGVLVLARTSKAAGRLAEQIRSHSWQKIYLAICHDEQRTLAAGERWEDYIFKDKRL 122

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 +V +    A YA  +++ I         + ++  TGR+HQ+RV   H G P+  
Sbjct: 123 NS--AAIVDRGHPEAKYAALNYECIQHSGD-LALVRIKLETGRSHQIRVQFKHHGHPLYA 179

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPA 313
           D +Y  + +    + +       A  + L HP     L  TA  P 
Sbjct: 180 DRRYGVSGEHGDIALL-------AFQLRLLHPTTKEELIFTAEYPK 218


>gi|110640132|ref|YP_680342.1| ribosomal pseudouridine synthase C large subunit [Cytophaga
           hutchinsonii ATCC 33406]
 gi|110282813|gb|ABG60999.1| ribosomal pseudouridine synthase C, large subunit [Cytophaga
           hutchinsonii ATCC 33406]
          Length = 223

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 54/219 (24%), Positives = 101/219 (46%), Gaps = 14/219 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----SKGQKPRLTHRLD 151
           +   +LYED+ I V NKP  + V+       ++   ++ +V      +K    +  HRLD
Sbjct: 7   VPDHILYEDNYILVVNKPCSLMVEPDRNGHPNLLQQVQKYVKKSLHPNKEVYVQHIHRLD 66

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +  SGI++ A+ ++  + L+E F  R ++K Y +L   +  N K  + +W  K S    +
Sbjct: 67  RPVSGIVLFAKKKSMLKELSEQFAQRTVKKYYQALTRKVTTNGKGALNHWHFKDSK---N 123

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              ++ + E+    A+S       +   +   ++Q +TG+ HQ+R      G PI+GD  
Sbjct: 124 KKAILYKEEQQETSAVSLGYSTSDYNADYTLWDIQLNTGKYHQIRAQLSFEGYPILGDEC 183

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           Y      +      N + LHA  ++  HP     +++ A
Sbjct: 184 Y-----KSTDVYAPNAIALHACKLEFVHPVSKESMRLEA 217


>gi|86147049|ref|ZP_01065366.1| pseudouridine synthase Rlu family protein [Vibrio sp. MED222]
 gi|85835114|gb|EAQ53255.1| pseudouridine synthase Rlu family protein [Vibrio sp. MED222]
          Length = 232

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 100/231 (43%), Gaps = 23/231 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L   S   + NK  G+SV    G    +    K+       K  L HRLD+ TSG+L+
Sbjct: 3   DILLNHSDFLLINKHPGVSVHKDDGDTMLLQEVAKAI---NEPKLYLVHRLDKMTSGVLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+   AA  L++ F  R ++K Y ++    PK K+  I+  + +        +   +  
Sbjct: 60  LAKNAPAASELSQLFAKREVEKYYLAIGSKKPKKKQGLISGDMERSRRSSWKLLTTKE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F +          L  +P+TGRTHQ+RV    +G  IVGD  Y  + +  
Sbjct: 118 ----NPAITQF-LSATAEPGERLLLCKPYTGRTHQIRVAMKSIGSAIVGDPIYNPSNEA- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
                 ++ YLHA  +   +       +  P      +  DSLG K+ + +
Sbjct: 172 ------DRGYLHAFAIRFTYQSQAYECVCDP------RNLDSLGEKWHQEI 210


>gi|194041320|ref|XP_001928432.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 3
           isoform 1 [Sus scrofa]
          Length = 352

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 63/285 (22%), Positives = 112/285 (39%), Gaps = 44/285 (15%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQ 142
             +++  +  D L+  ++ +   +   NKP G+ V G  G    +     L   +    +
Sbjct: 68  PENLSREELVDVLREAVVDQKGPLVTLNKPQGLPVTGKPGELTLVSVLPELSQCLGLGER 127

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKECI 198
           + ++     +ETSG+++++     A  L +    S R R+    Y ++  GIP   +  I
Sbjct: 128 ELQVVRASGKETSGLVLLSSCPQTASRLQKFFTHSQRARKPTATYCAVTDGIPAASEGKI 187

Query: 199 ANWLLKKSHIGGDYVHVVKQNE-----KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
              L  +   G   V  VK        KG  + +SHF+V+         +++QP T    
Sbjct: 188 QAALKMEHTDGASLVVPVKSPSRKDFLKGVKWTLSHFRVLAS-GSGCALVQLQPLTAFPS 246

Query: 254 QLRVHALHMGCPIVGDHKY----CANFKGNFTSPIQN----KLYLHARYMDLPH------ 299
           QL+VH +   CP++GDHKY           F  P +N    +  L    +   H      
Sbjct: 247 QLQVHMVLQLCPVLGDHKYSACVGTVLGQRFLLPAENTKPQRQVLDEALLSRLHLTPAQA 306

Query: 300 ------------------PEGGRLQITAPLPAHMVKTWDSLGFKY 326
                             P    +++ APLP++  +T   LG +Y
Sbjct: 307 AQLPLHIHLHRLHLPGTRPRDAPIELLAPLPSYFSRTLQCLGLQY 351


>gi|323700314|ref|ZP_08112226.1| pseudouridine synthase [Desulfovibrio sp. ND132]
 gi|323460246|gb|EGB16111.1| pseudouridine synthase [Desulfovibrio desulfuricans ND132]
          Length = 214

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 62/224 (27%), Positives = 99/224 (44%), Gaps = 17/224 (7%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL-THRLDQ 152
           +      ++YED+ + V +KP+G+    G G A       +      G   +   HRLDQ
Sbjct: 2   TPADDLRIVYEDAVVVVVDKPSGLLSVPGKGEANQDCVVARVKARHPGCIDQPSVHRLDQ 61

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG+LV+A +  A + L+  F  R + K Y +L+ G+ + +   I      K  +  D 
Sbjct: 62  DTSGLLVLALSAEAHRDLSGQFMDRLVGKRYVALIDGVVEGQGGIIEL----KFRLDPDN 117

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH---MGCPIVGD 269
                 +       ++ ++ +         +E  PHTGRTHQLR+H+ H   +G PIVGD
Sbjct: 118 RPYQVYDPVNGKRGVTRWRKL-SVEDGRTRVEFMPHTGRTHQLRLHSAHEKGLGLPIVGD 176

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
             Y        T     +L LHA  +   HP     L+  +  P
Sbjct: 177 RLYG-------TGTGPGQLKLHASLLRFRHPVTRAPLEFVSAPP 213


>gi|149910466|ref|ZP_01899106.1| pseudouridine synthase Rlu family protein [Moritella sp. PE36]
 gi|149806426|gb|EDM66398.1| pseudouridine synthase Rlu family protein [Moritella sp. PE36]
          Length = 226

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 104/246 (42%), Gaps = 36/246 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L++++   V NK AGI      G+    DG         G+     HRLD+ TSG+L++
Sbjct: 4   ILFQNNDFLVINKAAGIGFHDEDGV----DGICSIVRKDIGRLVFPVHRLDKVTSGLLLL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA  L + F +  IQK Y  ++   PK K+  +      K  +      + +  +
Sbjct: 60  AKSSEAAAKLAKLFELHEIQKYYLGIIDSKPKKKQGLV------KGDMERSRRSMWRLTK 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              + A++ F            + ++PHTG+THQLRV    +G PI GD  Y +     +
Sbjct: 114 TLTSPAVTQFFT-QSIGDGKRLVVLKPHTGKTHQLRVALNSLGSPICGDPLYQSADAWKY 172

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
                ++ YLHA  +                      T D   F +  + +   L++   
Sbjct: 173 -----DRAYLHAYCLQF--------------------TLDGEDFSFVADEFSGELFATPA 207

Query: 341 CKQNIL 346
           CK+ ++
Sbjct: 208 CKEALV 213


>gi|154345323|ref|XP_001568603.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134065940|emb|CAM43722.1| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 754

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 60/240 (25%), Positives = 93/240 (38%), Gaps = 36/240 (15%)

Query: 101 LLYEDSKIYVFNKPAGISV--QG--------------GSGIAYHIDGFLKSWVDSKGQKP 144
           +LYED  + V +KPAG++    G                 +A    G L   V  +GQ  
Sbjct: 514 VLYEDDDVLVIDKPAGLATSRHGLSCTQLGTQTTDLISVLLATDRAGALARGVFRQGQ-- 571

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRLD ETSG L++A++  AA  L            +  +   +       +    L+
Sbjct: 572 --VHRLDVETSGCLLIAKSNVAADSLRHQIGTSAAFSHHTKIYHALC-----VVLEPSLR 624

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMG 263
              + GD +       K      + ++VI  F   +  W+E +   G+ HQ+R H    G
Sbjct: 625 NVRLHGDIIDAADPKIK------TRYRVIRFFPKHRIVWVECRIQQGKKHQIRRHLASRG 678

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
            PI+ D  +           I ++  LHA  +   HP  G  +  TAPLP       + L
Sbjct: 679 FPILADMDHGG---AVCCQSIMSRTALHAHSLSFIHPITGDPIIATAPLPEDFRCCLELL 735


>gi|331217838|ref|XP_003321597.1| hypothetical protein PGTG_03134 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
 gi|309300587|gb|EFP77178.1| hypothetical protein PGTG_03134 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
          Length = 572

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 95/236 (40%), Gaps = 32/236 (13%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G ++++ K +K +  I++G  +      +                            +L+
Sbjct: 150 GVIKINGKNIKKDVIIRNGDRITNTLHRH------------------EPPVAGDPVRILH 191

Query: 104 EDS--KIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQETSGILVV 160
            D    + V  KP  + V       Y+ +  L     D        ++RLD+ TSG++V 
Sbjct: 192 RDDEKGLLVVEKPGSMPVHPTG--RYNYNTLLSILRFDYDLPLVHTSNRLDRLTSGVMVC 249

Query: 161 ARTRAAAQHLTESFR-MRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           A T  A++ L++ F     ++K Y +   G  P ++  C    L     IG + VH    
Sbjct: 250 ALTVEASRGLSKFFSTEGAVKKEYIARCRGNFPDDEVTCEEPLLTIDRQIGLNVVH---- 305

Query: 219 NEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                 +A + FK +    +     L  +P TGR+HQLRVH   +G PI+ D  YC
Sbjct: 306 --PEGKHAKTIFKKLSYDPESDSSVLHCRPITGRSHQLRVHLQFLGFPILNDTIYC 359


>gi|213963503|ref|ZP_03391756.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga sputigena Capno]
 gi|213953783|gb|EEB65112.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga sputigena Capno]
          Length = 201

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 52/195 (26%), Positives = 89/195 (45%), Gaps = 14/195 (7%)

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHL 170
           G  VQG       +   +K+++  K  KP      + HRLD+ T+G+++ A+T  A   L
Sbjct: 2   GDIVQGDKTGDIPLSEIVKAYLKKKYNKPGEVFLGVVHRLDRPTTGVVLFAKTSKALARL 61

Query: 171 TESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
              F  +  +QK YW+LV  +P  ++  + +WL++             +  + +  A+ H
Sbjct: 62  NAMFANKEEVQKTYWALVDAMPPAEEGTLIHWLVRNEKQNKS--VAYNKEVQHSKKAVLH 119

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           +K++  +  ++  LE+   TGR HQ+R     +G  I GD KY A       S     + 
Sbjct: 120 YKLLKTY-DRYYLLEIDLITGRHHQIRAQLAAIGLHIKGDLKYGAK-----RSNPDGGIC 173

Query: 290 LHARYMDLPHPEGGR 304
           LHA  +   HP    
Sbjct: 174 LHAHSLRFLHPVKKE 188


>gi|305665502|ref|YP_003861789.1| hypothetical protein FB2170_04365 [Maribacter sp. HTCC2170]
 gi|88710258|gb|EAR02490.1| hypothetical protein FB2170_04365 [Maribacter sp. HTCC2170]
          Length = 308

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 64/277 (23%), Positives = 108/277 (38%), Gaps = 39/277 (14%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           + V+         I  G+ +++       +                K +      +LYED
Sbjct: 67  ITVNNVIGTTATFIHGGETIKLSFPKKTSS----------------KKTLLFPLKMLYED 110

Query: 106 SKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
             +   +KP+GI V G S   I + +   L+         P+  HRLD  T+GIL++ +T
Sbjct: 111 EHLAAIHKPSGILVSGNSFKTITHALSQNLEPSNLPDSTLPQPVHRLDYATTGILLIGKT 170

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
            +  + L   F  + I+K Y+++  G  + + E       K +                +
Sbjct: 171 SSVIRALNGMFERKEIKKTYYAITMGKMEIRGEVTLKIDNKNAQ---------------S 215

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
            Y +      + F Q    +++ P TGR HQLR+H   +G PI+GD  Y           
Sbjct: 216 KYVVEETVPSERFGQ-LNLVKLTPITGRRHQLRIHMSGIGNPILGDSDYGTKD----LIL 270

Query: 284 IQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
               LYLHA  ++  HP    +L I +  P    K +
Sbjct: 271 KGKGLYLHAYSIEFNHPYTNEKLLIKSEFPKRFKKIF 307


>gi|329728300|gb|EGG64739.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21172]
          Length = 258

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 66/284 (23%), Positives = 120/284 (42%), Gaps = 36/284 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           +G + V+ + V    ++    ++ I        H+ +E      SVNL  ++  L+  +L
Sbjct: 7   NGALIVNDEPVTVRKQLMPNDILEI--------HLPRE----IPSVNLIPYARKLE--VL 52

Query: 103 YEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILV 159
           YED+ I +  KP   +       +   +   +       G+   P +  RLD+ T+GI++
Sbjct: 53  YEDAFIIIVTKPNNQNCTPSREHLHESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVI 112

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+        ++      ++KIY  LV+G  K     I    +++S        + ++ 
Sbjct: 113 FAKYGHIHHLFSKVN----LKKIYTCLVYG--KTHTSGIIEANIRRSKDS----IITREV 162

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                YA + ++VI+    K+   ++  HTGRTHQ+RVH  H+G PIVGD  Y       
Sbjct: 163 ASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQHIGHPIVGDSLYDGFHDKI 221

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
               +Q         +   HP     + IT      ++K ++ L
Sbjct: 222 HGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLFNQL 258


>gi|283850858|ref|ZP_06368144.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
 gi|283573781|gb|EFC21755.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
          Length = 313

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 55/292 (18%), Positives = 108/292 (36%), Gaps = 34/292 (11%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +   V  +    RLDR  +  +P       ++++ +G V VD +      R+++G+++  
Sbjct: 13  REAAVPPEAAGWRLDRATELLWPETGLRGRRRLIAAGAVLVDGQLRGPAYRVRTGEIL-- 70

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIA 126
                    I    +   ++ ++          +L +       +KPAG+       G  
Sbjct: 71  ------AGQIPARPEGAFTAADVP---------VLVQTGDFAAVSKPAGLHSAAIAHGGG 115

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +D  L +    +     L  RLD+ TSGI+ VA T  A     +     ++ K Y ++
Sbjct: 116 QSLDDLLPALFPDRA--AILLSRLDRLTSGIVAVALTPGAGTRYRDLEDAGQVAKDYLAV 173

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G+  +    + ++ L  +      V    + +       +  + +D        +  +
Sbjct: 174 VHGVIADPF--VVDFRLDTADRAKTRVRFKSEPDP---LRHTQVEPLDRL-DGLTLVRCR 227

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              G  HQ+R H    G P+VGD  Y              +L+LH   +  P
Sbjct: 228 IAKGARHQIRAHLAGAGHPLVGDPVYGRGEGE--------RLHLHCAALACP 271


>gi|319941266|ref|ZP_08015597.1| hypothetical protein HMPREF9464_00816 [Sutterella wadsworthensis
           3_1_45B]
 gi|319805187|gb|EFW02010.1| hypothetical protein HMPREF9464_00816 [Sutterella wadsworthensis
           3_1_45B]
          Length = 457

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 54/217 (24%), Positives = 87/217 (40%), Gaps = 15/217 (6%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +  +  L+  +L E        KP+G+    G+G   +            G      HRL
Sbjct: 239 SPVTQSLRPRILLEHRDFIAVFKPSGLLSVPGTGGLPNALTIASEM---TGTSLTAVHRL 295

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D +TSGIL+  +T    + L  +FR  R++K Y +++ G    +   I   +        
Sbjct: 296 DMDTSGILLYGKTPEGIRSLMAAFREGRVEKRYRAILEGTLTAECGLIDFPITTHPLDRL 355

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH----MGCPI 266
             +  +     G   A + ++ +         ++  P TGRTHQLR+HA H    +  PI
Sbjct: 356 RQIAAL-----GGRPARTQWRRL-SEKNGRTLVDFLPLTGRTHQLRLHAAHPTLGLNAPI 409

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            GD  Y     G      +  L LHA  +  P P+ G
Sbjct: 410 AGDPYYS--RPGLLVDRPETPLLLHAAEIIFPDPQNG 444


>gi|332843546|ref|XP_003314668.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 2
           isoform 1 [Pan troglodytes]
          Length = 484

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 52/197 (26%), Positives = 93/197 (47%), Gaps = 8/197 (4%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+    
Sbjct: 141 KDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-K 199

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++  
Sbjct: 200 EHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVT 259

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               +L  S     Y   V + +       + F+ +    Q    +  +P TGRTHQ+RV
Sbjct: 260 CKEPILVVS-----YKVGVCRVDPRGKPCETVFQRLSYNGQS-SVVRCRPLTGRTHQIRV 313

Query: 258 HALHMGCPIVGDHKYCA 274
           H   +G PI+ D  Y +
Sbjct: 314 HLQFLGHPILNDPIYNS 330


>gi|148979501|ref|ZP_01815558.1| pseudouridine synthase Rlu family protein [Vibrionales bacterium
           SWAT-3]
 gi|145961779|gb|EDK27074.1| pseudouridine synthase Rlu family protein [Vibrionales bacterium
           SWAT-3]
          Length = 232

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 101/230 (43%), Gaps = 23/230 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L   S   + NK  GISV    G    +    K+       K  L HRLD+ TSGIL+
Sbjct: 3   DILLNHSDFLLINKHPGISVHKDDGDTMLLQEVAKAI---NEPKLYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A++ +AA  L++ F  R ++K Y ++    PK K+  I+  + +        +   +  
Sbjct: 60  LAKSASAASELSQLFAKREVEKFYLAIGSKKPKKKQGLISGDMERSRRSSWKLLTTKE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F +          L  +P TGRTHQ+RV    +G  IVGD  Y  + +  
Sbjct: 118 ----NPAITQF-LSASAEPGERLLLCKPFTGRTHQIRVAMKSIGSAIVGDPIYNPSSEA- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
                 ++ YLHA  +   +       +  P      ++ DSLG K+ + 
Sbjct: 172 ------DRGYLHAFAIRFTYQSQAYQFVCDP------RSLDSLGEKWHQE 209


>gi|157786596|ref|NP_001099244.1| RNA pseudouridylate synthase domain-containing protein 1 [Rattus
           norvegicus]
 gi|149052128|gb|EDM03945.1| RNA pseudouridylate synthase domain containing 1 (predicted),
           isoform CRA_a [Rattus norvegicus]
 gi|171847409|gb|AAI61966.1| Rpusd1 protein [Rattus norvegicus]
          Length = 306

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/245 (22%), Positives = 100/245 (40%), Gaps = 23/245 (9%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------- 144
           +        ++Y+ +   V NK   + +   +   +     L+  +     +        
Sbjct: 2   EPGSMENLSIVYQSNDFLVVNKHWDLRIDSKT---WRETLTLQKQLRHHFPELADPDTCY 58

Query: 145 --RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             R  H+LD  TSG L VA  +AAA    + F+ RR+ K Y +LV G  +  +  I   +
Sbjct: 59  GFRFCHQLDFSTSGALCVALNKAAAGSAYKCFKERRVTKAYLALVRGHVQESQVTINYAI 118

Query: 203 LKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRV 257
            + S  G  +   ++     +    +++   V++           + ++P TGRTHQLRV
Sbjct: 119 GRNSTEGRTHTMCIEGTHGCENPKPSLTELLVLEHGLYSGDPVSKVLLKPLTGRTHQLRV 178

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
           H   +G PIVGD  Y    + +       ++ LHA Y+ +  P      + A  P   + 
Sbjct: 179 HCSALGHPIVGDLTYG---QADDQEDQPFRMMLHAFYLRI--PTRAE-CVEACTPDPFLP 232

Query: 318 TWDSL 322
             D+ 
Sbjct: 233 ALDAC 237


>gi|261886282|ref|ZP_06010321.1| RNA pseudouridine synthase [Campylobacter fetus subsp. venerealis
           str. Azul-94]
          Length = 319

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 64/304 (21%), Positives = 117/304 (38%), Gaps = 64/304 (21%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
             +    QK+   G++ V+      N+ +                           +  +
Sbjct: 24  GYSMKEAQKLCDKGRLLVNDAVCGKNDPVFG------------------------EAYFI 59

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
               +      ++E  +  VF+KP+G+     G    Y +   + S     G+K  + HR
Sbjct: 60  DYECEPKGLKPIFECDEFGVFDKPSGVLSHPNGRNCEYSLCDEIWSL---WGKKACVAHR 116

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN---KKECIANW----- 201
           LD+ETSG++VVA+   +A +L +SF  R + K Y + V G        K  I ++     
Sbjct: 117 LDRETSGVIVVAKNANSALNLKKSFENRAVAKTYLAFVRGKFDGNGLDKFHINDFEDFKD 176

Query: 202 ------------LLKKSHIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQ 246
                       + K   I  DY  + +  +       A++  K+++ + +     +E  
Sbjct: 177 KLEFFDNIQGFVIDKNMDITKDYDDIKIRMEICPEGKRAVTVVKLVEYYPKFDISLVECY 236

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANF-------------KGNFTSPIQNKLYLHAR 293
           P TGR HQ+R+H  HM   I+GD  Y  +              +    +   ++L LHA+
Sbjct: 237 PLTGRQHQIRLHLFHMKHRILGDPIYGLDKFNVEQILDGVMSERDRVKNTGASRLMLHAK 296

Query: 294 YMDL 297
            + L
Sbjct: 297 SVKL 300


>gi|157736289|ref|YP_001488972.1| ribosomal large subunit pseudouridine synthase [Arcobacter butzleri
           RM4018]
 gi|157698143|gb|ABV66303.1| ribosomal large subunit pseudouridine synthase [Arcobacter butzleri
           RM4018]
          Length = 300

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 70/262 (26%), Positives = 112/262 (42%), Gaps = 27/262 (10%)

Query: 50  KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIY 109
            +R+    RI           INA + I  E   +      TK    LK +L +ED    
Sbjct: 31  GQRLTSKGRIFD----ENMNQINAGDEIPTEHIFIAVFEGQTK---GLKPLLEFED--FA 81

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           +F+KP  + V   S         L       G+   L HR+D ETSG+++V + + +   
Sbjct: 82  IFDKPTNLMVHPIS--KNTSYSLLDEIRYHFGENANLIHRIDAETSGLVIVGKNKKSEIE 139

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           L + F+ ++  K Y ++V G  K + + I   L ++    G  + V  Q E+G   +I+ 
Sbjct: 140 LKDMFQEKKYHKSYLAIVQGEIKEELK-INKALDREGKAIGVRMKVCTQ-EEGGKESITI 197

Query: 230 FK-VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN------------- 275
            K +I    +    +E  P TGR HQ+RVH   MG  I+GD  Y  +             
Sbjct: 198 IKPIIYDKEKNLTLVEALPLTGRQHQIRVHLHSMGHTILGDPIYGVDDENAENYLNKTLS 257

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
            +  F      +L+LHA Y++ 
Sbjct: 258 EEDRFKVTKSYRLWLHANYLEF 279


>gi|89095232|ref|ZP_01168154.1| RluA protein [Oceanospirillum sp. MED92]
 gi|89080486|gb|EAR59736.1| RluA protein [Oceanospirillum sp. MED92]
          Length = 238

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 61/243 (25%), Positives = 99/243 (40%), Gaps = 26/243 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L + +   + NK  GISV    G        +      +  +  L HRLD+ TSG++V 
Sbjct: 13  ILTQTADFIIINKSPGISVHKDQGDEGL---TMLLQRQLELDEIFLIHRLDKVTSGVMVF 69

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ R  A  L+  F+ R ++K Y ++    PK K+  +   + K        +       
Sbjct: 70  AKNRETAADLSMQFQNREVEKFYLAVSANKPKRKQGLVCGDMEKSRRGSWKLLRSKI--- 126

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F V       F    ++P TG+THQ+RV     G PI+GD+ Y        
Sbjct: 127 ---NPAMTQF-VSVAMKPGFRLFLLKPSTGKTHQIRVALKSEGAPILGDNMYGGEEA--- 179

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
                ++ YLHA  +        R    A LP   V       F +  +  ++  +SQ E
Sbjct: 180 -----DRTYLHAYQLAFT-LNEERYIFRA-LPTDGVH------FDHQFSTLVESSFSQPE 226

Query: 341 CKQ 343
            + 
Sbjct: 227 MEN 229


>gi|303231322|ref|ZP_07318057.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514002|gb|EFL56009.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 335

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 54/352 (15%), Positives = 114/352 (32%), Gaps = 86/352 (24%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +  +Q+   +       LD              + K+     + V+  +   +  +    
Sbjct: 20  IESIQHATTDAITLGQLLD-------TKYPRKAMVKLFDEKLIHVNGHKATPHTEVAVDD 72

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I      ++H                    +   +LYED  + + +KPAG++V   S
Sbjct: 73  EIWIAMAKEKIDH----------------EPIAMDLHILYEDDDLLIVDKPAGVTV--NS 114

Query: 124 GIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                +   +  +    G  +K R  +RLD++T+G +V+A++  A     +       +K
Sbjct: 115 KDKVSLANGIAHYFMEHGIKRKVRFLNRLDRDTTGCIVIAKSGLAQSLYQQQMDDNTFEK 174

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-- 239
            Y ++V G+ ++  + +         +      +  +         + F V+  +     
Sbjct: 175 WYMAIVEGLVESDSDSLVLP------MDRSIDGIHYEVNSKGKETRTDFTVLHRYPDGAV 228

Query: 240 -------------------------------------------FCWLEMQPHTGRTHQLR 256
                                                         + ++ +TG+THQ+R
Sbjct: 229 DNSVHNLQNIVDISHENVDSTVNTVDKQGGIVDNSVHNLENQPCTAVAVRLYTGKTHQIR 288

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           V   H+G P++GD  Y A   G           L A  +   H   G R+ +
Sbjct: 289 VAFSHIGHPLLGDTLYGAKSTGE-------PFALRAMKVVFTHMRSGDRITV 333


>gi|115495425|ref|NP_001069342.1| RNA pseudouridylate synthase domain-containing protein 1 [Bos
           taurus]
 gi|122144661|sp|Q17QT4|RUSD1_BOVIN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 1
 gi|109658212|gb|AAI18197.1| RNA pseudouridylate synthase domain containing 1 [Bos taurus]
 gi|296473482|gb|DAA15597.1| RNA pseudouridylate synthase domain-containing protein 1 [Bos
           taurus]
          Length = 308

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 61/236 (25%), Positives = 98/236 (41%), Gaps = 23/236 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---------RLTHRLD 151
           ++Y      V NK   + +      A+     L+  +  +  +          R  H+LD
Sbjct: 11  VVYRSHDFLVVNKHWDVRI---DSKAWRETLTLQKQLRHRFPELADPDTYYGFRFCHQLD 67

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG L VA  +AAA      F+ RR+ K Y +LV G  +  +  I+  + K S  G  
Sbjct: 68  FSTSGALCVALNKAAAGSAYRCFKDRRVTKAYLALVRGHVQESRMTISYAIGKNSTEGRT 127

Query: 212 YVHVVK--QNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           +   ++  Q  +    +++   V++           + +QP TGRTHQLRVH   +G PI
Sbjct: 128 HTMCIEGTQGCENPKPSLTELVVLEHGLYAGDPVSKVLLQPLTGRTHQLRVHCSALGHPI 187

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           VGD  Y              ++ LHA Y+ +  P      + A  P   V + D+ 
Sbjct: 188 VGDLTYGHALGQEDQPF---RMMLHAFYLRI--PTSAE-CVEACTPDPFVPSLDAC 237


>gi|319774994|ref|YP_004137482.1| pseudouridine synthase [Haemophilus influenzae F3047]
 gi|329123104|ref|ZP_08251674.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           aegyptius ATCC 11116]
 gi|317449585|emb|CBY85790.1| conserved hypothetical pseudouridine synthase [Haemophilus
           influenzae F3047]
 gi|327471659|gb|EGF17101.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           aegyptius ATCC 11116]
          Length = 224

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 59/201 (29%), Positives = 92/201 (45%), Gaps = 16/201 (7%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  ++Y+ S   + NK  GISV          +   K        K  L HRLD+ TSG
Sbjct: 1   MEIEVVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQL---NVPKVWLVHRLDKVTSG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A    +A   +  F   +I K Y +L    PK K+  I   + KK+  G   +   
Sbjct: 58  LLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGDM-KKAREGAWKLCQT 116

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K+N      AI+ F+ + C         ++P TG+THQLRV    +G PI+GD  Y  N 
Sbjct: 117 KEN-----PAITRFESVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDGLYAKNT 170

Query: 277 KGNFTSPIQNKLYLHARYMDL 297
           +        ++ YLHA  ++ 
Sbjct: 171 EK------IDRTYLHATQLEF 185


>gi|251792493|ref|YP_003007219.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           aphrophilus NJ8700]
 gi|247533886|gb|ACS97132.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           aphrophilus NJ8700]
          Length = 238

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 67/213 (31%), Positives = 97/213 (45%), Gaps = 24/213 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGIL 158
           ++++     V NKP GISV        H D  L   V  +    +  L HRLD+ TSG+L
Sbjct: 5   IVFQHPDFIVINKPNGISVH-----KDHADVGLTRLVAQQLGVPQVWLVHRLDKVTSGLL 59

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A    AA  L+  F   +IQKIY +L    PK K+  I+  + K            K 
Sbjct: 60  ILALNEKAAVTLSRKFAEHQIQKIYLALSTQKPKKKQGRISGDMQKA------RRGAWKL 113

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +   N AI+ F V    A       + P TG+THQ+RV    +G PI+GD  Y      
Sbjct: 114 CQSKENPAITDF-VSHSLAPNLRLFILYPKTGKTHQIRVAMKSLGSPILGDELYGGE--- 169

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQI-TAP 310
                + ++ YLHA  +   +  G  +QI T+P
Sbjct: 170 -----VADRTYLHAYQLSFDY-FGEAVQISTSP 196


>gi|194375494|dbj|BAG56692.1| unnamed protein product [Homo sapiens]
          Length = 484

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 52/197 (26%), Positives = 93/197 (47%), Gaps = 8/197 (4%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+    
Sbjct: 141 KDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-K 199

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++  
Sbjct: 200 EHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVT 259

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               +L  S     Y   V + +       + F+ +    Q    +  +P TGRTHQ+RV
Sbjct: 260 CKEPILVVS-----YKVGVCRVDPRGKPCETVFQRLSYNGQS-SVVRCRPLTGRTHQIRV 313

Query: 258 HALHMGCPIVGDHKYCA 274
           H   +G PI+ D  Y +
Sbjct: 314 HLQFLGHPILNDPIYNS 330


>gi|268592403|ref|ZP_06126624.1| ribosomal large subunit pseudouridine synthase A [Providencia
           rettgeri DSM 1131]
 gi|291312190|gb|EFE52643.1| ribosomal large subunit pseudouridine synthase A [Providencia
           rettgeri DSM 1131]
          Length = 210

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 51/179 (28%), Positives = 75/179 (41%), Gaps = 14/179 (7%)

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              +        L HRLD  TSG++VVAR +A    L++ F  R + KIY +L+ G   N
Sbjct: 28  HHRLVKIFPDCTLVHRLDFGTSGLMVVARNKAINAALSQQFSQRSVIKIYQALLCGHLAN 87

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF--------CWLEM 245
            +  I   + K           +   E     A SH++VI+                +++
Sbjct: 88  DEGVIDAAIAKDPAQ----FPRMSLCEVNGKPARSHYQVIERLYHPVENGISLPVTRVQL 143

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TGRTHQLR+H   +G PI+G   Y              +L LHA  +   HP   +
Sbjct: 144 TPETGRTHQLRIHCQKLGYPILGCDLYGGRLLQGTEQT--PRLLLHASELHFVHPASQK 200


>gi|228474393|ref|ZP_04059128.1| pseudouridine synthase YjbO [Staphylococcus hominis SK119]
 gi|228271752|gb|EEK13099.1| pseudouridine synthase YjbO [Staphylococcus hominis SK119]
          Length = 288

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 48/291 (16%), Positives = 108/291 (37%), Gaps = 40/291 (13%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + + H  + +   +  I   G + ++++ V     ++    + +              K+
Sbjct: 16  FLQRH--NYSKKTISAIKCDGALIINRQPVTVRYILKKDDHLIV--------------KL 59

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQ 142
            +   +           +LYED+ + + +KP  ++        +  +   +  +++    
Sbjct: 60  PEEVPSTYLRPSNKHIEILYEDTYLIIVSKPVHLNCAPSREHPHDSLIERVMYYLNHSTN 119

Query: 143 K-----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           K     P +  RLD+ T+GI++  +       ++     +R    Y  + +G    ++  
Sbjct: 120 KVQYVVPHIVTRLDRNTTGIVIFTKHGHIHHLMSTFEIDKR----YICVCYGK-TKEQSM 174

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +          + +       YA + +K +          E++ HTGRTHQ+RV
Sbjct: 175 IEAPIGRN-----KDSIITRCITPSGKYAKTEYKTLSSH-HSASLCEVKLHTGRTHQIRV 228

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQI 307
           H  H+G P++GD  Y      +   P      L    +   HP     ++I
Sbjct: 229 HFKHIGHPLIGDDLY------DGFHPRIQTQSLQCYKVKFIHPIYNKEIEI 273


>gi|84391790|ref|ZP_00991692.1| pseudouridine synthase Rlu family protein [Vibrio splendidus 12B01]
 gi|84376503|gb|EAP93382.1| pseudouridine synthase Rlu family protein [Vibrio splendidus 12B01]
          Length = 232

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 99/231 (42%), Gaps = 23/231 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L   S   + NK  G+SV    G    +    K+       K  L HRLD+ TSGIL+
Sbjct: 3   DILLNHSDFLLINKHPGVSVHKDDGDTMLLQEVAKAI---NEPKLYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+  +AA  L++ F  R ++K Y ++    PK K+  I+        +        K  
Sbjct: 60  LAKNASAASELSQLFAKREVEKYYLAIGSKKPKKKQGLISG------DMERSRRSSWKLL 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F +             +P+TGRTHQ+RV    +G  IVGD  Y  + +  
Sbjct: 114 TSKENPAITQF-LSATAEPGERLFLCKPYTGRTHQIRVAMKSIGSAIVGDPIYNPSSEA- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
                 ++ YLHA  +   +       +  P      ++ +SLG K+ + +
Sbjct: 172 ------DRGYLHAFAIRFTYQSQAYEYVCDP------RSLNSLGEKWHQEI 210


>gi|297696328|ref|XP_002825346.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Pongo abelii]
          Length = 484

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 52/197 (26%), Positives = 93/197 (47%), Gaps = 8/197 (4%)

Query: 79  KEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           K+   L ++V+  +     + I LL E+  + V +KP+ I V       ++   F+    
Sbjct: 141 KDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKPSSIPVHPCGRFRHNTVIFILG-K 199

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + + ++    HRLD+ TSG+L+ A+T A ++ + E  R R+++K Y   V G    ++  
Sbjct: 200 EHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQLEKEYVCRVEGEFPTEEVT 259

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               +L  S     Y   V + +       + F+ +    Q    +  +P TGRTHQ+RV
Sbjct: 260 CKEPILVVS-----YKVGVCRVDPRGKPCETVFQRLSYNGQS-SVVRCRPLTGRTHQIRV 313

Query: 258 HALHMGCPIVGDHKYCA 274
           H   +G PI+ D  Y +
Sbjct: 314 HLQFLGHPILNDPIYNS 330


>gi|224419163|ref|ZP_03657169.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
 gi|253828096|ref|ZP_04870981.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
 gi|253511502|gb|EES90161.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
          Length = 319

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 65/309 (21%), Positives = 119/309 (38%), Gaps = 60/309 (19%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +    + ++N    Q  +  G+V            +   +++        L   ++    
Sbjct: 19  FLMRQF-NLNMAQAQSYINKGRV------------VYESKILGNNEKNKVLEREVEVWIF 65

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
             +S+ L           +YE+    +FNKPA + +       +H    +    +  G +
Sbjct: 66  KPNSIGLKP---------IYENEDFALFNKPAQMLIHPKGRFFHH--SLMDEVREYFGTE 114

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-- 201
             L HR+D+ETSG+++V + + +   L E F   RI+K Y +L+ G      + + ++  
Sbjct: 115 ASLIHRIDKETSGLVLVGKHKRSIVELGELFANNRIKKKYLALIKGKMCKTSKIVGDFCL 174

Query: 202 --LLKKSHIGGDYVHVV-------KQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              L     GGD            +++ K  G   A S F+++  F      L++ P TG
Sbjct: 175 LMPLSLQEKGGDLSVRSVFLGQNLRKDSKLLGFRDAKSEFEILGEFGGN-TLLKVYPITG 233

Query: 251 RTHQLRVHALHMGCPIVGDHKYCAN----------------------FKGNFTSPIQNKL 288
           RTHQ+RVH   +G PI+GD  Y                          +        ++L
Sbjct: 234 RTHQIRVHLFSLGFPILGDPLYGCEDWQSREYLDSEFIEENRDFGLCAEKRKEYFGADRL 293

Query: 289 YLHARYMDL 297
            LHA  ++ 
Sbjct: 294 MLHAYSLEF 302


>gi|168702909|ref|ZP_02735186.1| ribosomal large subunit pseudouridine synthase D [Gemmata
           obscuriglobus UQM 2246]
          Length = 204

 Score =  137 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 65/208 (31%), Positives = 93/208 (44%), Gaps = 20/208 (9%)

Query: 126 AYHIDGFLKSWVDSKGQKPR-----LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +D  +K+++  K  KP      + HRLD+  SG LV ART  AA  L+E FR   ++
Sbjct: 1   DETVDRLVKAYLKEKYDKPGNVFLGVVHRLDKPVSGSLVFARTSKAAARLSEQFREGGVE 60

Query: 181 KIYWSLVWGIPKN-----KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           K+YW+++               + +WL K        V  V     GA +A   F+V   
Sbjct: 61  KVYWAVIEAQAPGPWVTADNGSLEDWLQKDDDNAR--VETVAPETPGAQFARLLFQVRGR 118

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                 WLE++PHTGR HQLRV     G  I GDHKY +        P  N + LHAR +
Sbjct: 119 H-NGLIWLELRPHTGRKHQLRVQLASRGASIYGDHKYGSKL------PFGNGIALHARSL 171

Query: 296 DLPHPEGG-RLQITAPLPAHMVKTWDSL 322
              HP     + + + +P      +  L
Sbjct: 172 TFLHPTSKNPVTVKSEVPKIWRGRFAHL 199


>gi|31794480|ref|NP_856973.1| hypothetical protein Mb3328c [Mycobacterium bovis AF2122/97]
 gi|31620076|emb|CAD95420.1| CONSERVED HYPOTHETICAL PROTEIN [Mycobacterium bovis AF2122/97]
          Length = 305

 Score =  137 bits (344), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 96/252 (38%), Gaps = 12/252 (4%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVF 111
           V    ++ +G+VV     +     ++    ++    +L  +        +L++D+ I V 
Sbjct: 38  VAARAKVLAGEVVDNDGAVVDSGTVLPPGSVVHLYRDLPDEVPVPFDVPVLHQDADIVVV 97

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   +    +    HRLD+ T+G+L+    R       
Sbjct: 98  DKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTTRREVRGSYQ 156

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    ++K Y +     P      +A   L +S I     H+    E G   A +  +
Sbjct: 157 TMFARGLVRKTYLARAPVAP-----GLALPRLVRSRIVKRRGHLQAVCEPGVPNAETLVE 211

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
            I           + P TGRTHQLRVH   +G PI+GD  Y  N            L L 
Sbjct: 212 RIARDG----LYRLTPTTGRTHQLRVHMAALGIPIMGDPLY-PNVISVAAHDFSTPLQLL 266

Query: 292 ARYMDLPHPEGG 303
           A+ ++   P  G
Sbjct: 267 AQRIEFDDPLTG 278


>gi|332645402|gb|AEE78923.1| RNA pseudourine synthase 5 [Arabidopsis thaliana]
          Length = 416

 Score =  137 bits (344), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 75/341 (21%), Positives = 120/341 (35%), Gaps = 90/341 (26%)

Query: 46  VRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           +++D + VK  N  ++SG                   K++ S +   +        +LYE
Sbjct: 91  IQIDGEVVKDPNTLLRSG------------------SKLVYSRLPWKEPDTPYSLEVLYE 132

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRLTHRLDQETS 155
           D  +   NKP+G+ V  G             W   K            P   HRL + TS
Sbjct: 133 DDDLIALNKPSGLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVPVHRLGRGTS 192

Query: 156 GILVVARTRAAAQHL-----------------TESFRMRRIQKIYWSLVWGIPKNKKECI 198
           GIL+ A+T+ A   L                  E    R++ KIY +L  GI +  +  I
Sbjct: 193 GILLCAKTKLAKTKLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADGIVEEDEVVI 252

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRV 257
              +    + G      V   E     A S   V++   +K C  ++++  +GR HQ+R+
Sbjct: 253 KQPIGVVRYPGVAQGLYVASPE--GKPAFSKVFVLERDREKNCSLVKVEIQSGRPHQIRI 310

Query: 258 HALHMGCPIV-----------------GDHKY-----------------------CANFK 277
           H  +MG P+V                 GD  Y                           +
Sbjct: 311 HLAYMGHPLVEMTMFTGSECLRADQSAGDPLYVAGGQPKCFDPDLVDDAAAFAEDGGYRR 370

Query: 278 GNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPAHMV 316
            N   P     +LHA  ++LP+       ++I APLP  + 
Sbjct: 371 PNQAVPGDCGYHLHAHQVELPNLLNTHKVVKIVAPLPPILQ 411


>gi|222110555|ref|YP_002552819.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221729999|gb|ACM32819.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 268

 Score =  137 bits (344), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 57/214 (26%), Positives = 91/214 (42%), Gaps = 2/214 (0%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                  LL++D+ +    KPAG  V      A      +++  D  GQ     HRLD+ 
Sbjct: 3   PAHPPLRLLWQDAHMVAVFKPAGWLVHRTGLDAGETRFVMQALRDQIGQHVYPVHRLDKG 62

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T G+LV+A   AAA+ L ++F    ++K Y +LV G    + E         +       
Sbjct: 63  TCGVLVMALHPAAARALADAFARHAVRKQYLALVRGWAPAQAEVDHPLRPDDAPPDAPTQ 122

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
               +  + A   +           +   +  +P TGR HQ+R H  H+  PI+GD  + 
Sbjct: 123 PAHTRLTRLARLELPESSDPRFATTRASLVRAEPTTGRRHQIRRHLKHLAHPILGDATHG 182

Query: 274 ANFKGNFTSP--IQNKLYLHARYMDLPHPEGGRL 305
                 + +     ++L+LHA  + LPHP  GRL
Sbjct: 183 KGPLNRWWAQRLGLHRLWLHAWQLSLPHPADGRL 216


>gi|329313677|gb|AEB88090.1| Pseudouridine synthase [Staphylococcus aureus subsp. aureus T0131]
          Length = 258

 Score =  137 bits (344), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 65/284 (22%), Positives = 118/284 (41%), Gaps = 36/284 (12%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           +G + V+ + V    ++ +  ++ I        H+ +E      SVNL  ++  L+  +L
Sbjct: 7   NGALIVNDEPVTVRKQLMTNDILEI--------HLPRE----IPSVNLIPYARKLE--VL 52

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           YED+ I +  KP   +        +               +   P +  RLD+ T+GI++
Sbjct: 53  YEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVI 112

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+        ++      ++KIY  LV+G  K     I    +++S        + ++ 
Sbjct: 113 FAKYGHIHHLFSKVN----LKKIYTCLVYG--KTHTSGIIEANIRRSKD----RIITREV 162

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                YA + ++VI+    K+   ++  HTGRTHQ+RVH  H+G PIVGD  Y       
Sbjct: 163 ASDGKYAKTSYEVIN-QNDKYSLCKVHLHTGRTHQIRVHFQHIGHPIVGDSLYDGFHDKI 221

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
               +Q         +   HP     + IT      ++K ++ L
Sbjct: 222 HGQVLQ------CTQIYFVHPINKNNIYITIDY-KQLLKLFNQL 258


>gi|94501093|ref|ZP_01307617.1| Pseudouridylate synthases, 23S RNA-specific [Oceanobacter sp.
           RED65]
 gi|94426840|gb|EAT11824.1| Pseudouridylate synthases, 23S RNA-specific [Oceanobacter sp.
           RED65]
          Length = 223

 Score =  137 bits (344), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 58/221 (26%), Positives = 95/221 (42%), Gaps = 29/221 (13%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   ++YE     + NKP G+     +G      GF +   D  G      HRLD+ TSG
Sbjct: 1   MSIDIVYEHQDWILVNKPEGVDFHSQNG----EVGFHRQLCDQLGFNVFPVHRLDKATSG 56

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L+ A+++ A + L E F  R+++K Y ++V    K K+  +   ++K  +         
Sbjct: 57  LLLFAKSQDACRGLVELFSQRKVEKYYLAIVSNKLKKKQGKVFGDMVKSRNGS------Y 110

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K  ++  N A + F +       +    ++P TG+THQLRV    +G  IVGD +Y    
Sbjct: 111 KLTQERRNPAFTQF-LSQALKPGYRLALLKPKTGKTHQLRVAMKSLGSAIVGDQRYGGES 169

Query: 277 KGNFTSPIQNKLYLHARYMDLPH----------PEGGRLQI 307
                    N+LYLHA  +              P  G +  
Sbjct: 170 A--------NRLYLHAYALKFDWQGRDYCFQYLPHSGEMFF 202


>gi|56755719|gb|AAW26038.1| SJCHGC01065 protein [Schistosoma japonicum]
          Length = 438

 Score =  137 bits (344), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 57/276 (20%), Positives = 106/276 (38%), Gaps = 33/276 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
             ++ + H++   + +   SG + V+  RV  +  +    ++       +      E  +
Sbjct: 75  VLQSEFSHMSNDVIAQKCNSGDILVNGARVDPDYVLNDNDLL-------SQQVHRHEFPV 127

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+  +             +++   + V NKP  I +       Y ++          G +
Sbjct: 128 LNLPIEF-----------IHDSHDMLVINKPPSIPIHPCG--RYTLNSITHILAKDYGLR 174

Query: 144 P-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK------KE 196
           P R THRLD+ TSG+L++A+    +  L      + + K Y   V G    +        
Sbjct: 175 PLRFTHRLDRMTSGLLLIAKDYDTSVRLQSQIASKEVTKHYICHVDGCFPTEPIDHCTGF 234

Query: 197 CIANWLLKKSHIGGDY-----VHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTG 250
            I N ++  S   G       +H V     G   A +HF  ++  +      +  +  TG
Sbjct: 235 EINNGVVVCSQPVGPISPKMGIHAVLPESAGGKPARTHFLRLNYNSVTNTSLVICRLFTG 294

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           RTHQ+R+H  ++G PIV D  Y +   G       +
Sbjct: 295 RTHQIRIHTQYLGYPIVEDPIYNSTDWGELKGKYAD 330


>gi|219363655|ref|NP_001136977.1| hypothetical protein LOC100217137 [Zea mays]
 gi|194697832|gb|ACF83000.1| unknown [Zea mays]
          Length = 386

 Score =  137 bits (344), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 55/264 (20%), Positives = 101/264 (38%), Gaps = 24/264 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+N      +   F + +   +       ++ G+++VD + V  +  ++S Q +      
Sbjct: 44  VKNRWAGKTIVDLFTDEFKGRSRDYYVHAVKCGRLQVDGQMVHTDYIVKSSQKISHFLHR 103

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                   E  +L   +++ K+              +    KPA + V       Y  + 
Sbjct: 104 -------HEPPVLAGDISILKNE-----------VDVVTICKPASVPVHPCG--QYRKNT 143

Query: 132 FLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            +       G  P    HRLD+  SG+L+ A+    A+   +      +QK Y + V G+
Sbjct: 144 VVGILQAEHGLTPLFPVHRLDRLVSGLLIFAKNADRAECFRQQIEAGLLQKEYVAKVVGV 203

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVV--KQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
             + ++ +   +   +  G   V +      E     A++ F+ I C       +  +P 
Sbjct: 204 FPDGEQTVDANVNFNAREGRSTVEISGGAGEEPNGKQALTRFQRI-CTDGTHSIVLCKPV 262

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY 272
           TGRTHQ+RVH    G PI  D  Y
Sbjct: 263 TGRTHQIRVHLKQAGYPIANDELY 286


>gi|54309675|ref|YP_130695.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum SS9]
 gi|46914113|emb|CAG20893.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum SS9]
          Length = 246

 Score =  137 bits (344), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 60/221 (27%), Positives = 95/221 (42%), Gaps = 21/221 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+++     V NK  G+SV    G    +    K    +  +K  L HRLD+ TSG+L++
Sbjct: 22  LVHQHPDFLVINKHPGVSVHKDDGDQPLLAEVAK---QTGDEKLYLIHRLDKMTSGLLLL 78

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R R AA  L+ +F  R ++K Y ++    PK K+  +         +        K + 
Sbjct: 79  GRNRQAAAELSGNFAKRDVEKFYLAIGTKKPKKKQGVVIG------DMSRSRRSSWKLDS 132

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F        + C+L  +PHTG+THQ+RV    +G  I GD  Y        
Sbjct: 133 TKDNPAITQFFSTAAGNGRRCFL-CKPHTGKTHQIRVALKSVGSGITGDEIYGNEEA--- 188

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
                ++ YLHA  +  P+    +  I  P      + W +
Sbjct: 189 -----DRGYLHAYALSFPYKGENQQFICVP---DNGELWQA 221


>gi|241765468|ref|ZP_04763435.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241364778|gb|EER59767.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 303

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 66/300 (22%), Positives = 111/300 (37%), Gaps = 38/300 (12%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRI 67
           VV+ +  +   LD +     P +      + + +G V VD   + V    R + G  +  
Sbjct: 21  VVLPSQGQGSMLD-FLAQRLPAVPRGEWLQRMEAGDV-VDERGEPVLPQRRFEPGIRLYY 78

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              + A  HI  E+                   +LY+D  + V +KP  + V        
Sbjct: 79  YRHLQAEPHIPFEE------------------TVLYQDEHLLVADKPHFMPVTPTGRYLQ 120

Query: 128 HIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           H    L       G  +    HR+D++T+G+++ +  R         FR R+I K Y ++
Sbjct: 121 H--TLLVRLKRRLGLPELSPLHRIDRDTAGLVLFSVQRRTRGTYQALFRDRQISKHYDAV 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                      +       S +             GA  + +H +V    A  +    + 
Sbjct: 179 APWHAD-----VPFPREHISRMEESPQFFRMHEVAGAPNSHTHMEV-QAVAGGWALYRLS 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           P TG+ HQLRVH   +G P+  D  Y       +G+F+ P+Q    L AR +    P  G
Sbjct: 233 PITGKRHQLRVHMAALGLPLRNDPFYPLVNDPPEGDFSRPLQ----LLARSLAFVDPLTG 288


>gi|332285853|ref|YP_004417764.1| pseudouridine synthase [Pusillimonas sp. T7-7]
 gi|330429806|gb|AEC21140.1| pseudouridine synthase [Pusillimonas sp. T7-7]
          Length = 306

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 60/285 (21%), Positives = 110/285 (38%), Gaps = 28/285 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +    +PH+             V +D        R+  G +V    V   L+   +    
Sbjct: 39  YLLERFPHVPR----------DVLLD--------RLARGDIVDEAGVAQTLDSPYQPLGW 80

Query: 84  LDSSVNLTKHSDFL-KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
           L     + + +       +L+ D  + V +KP  ++   G    Y  +  L     S G 
Sbjct: 81  LWYYREVPQETRVPYDLPVLFRDDHLVVADKPHFLASIPGG--RYLKETALVRLRQSLGL 138

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +    HRLD++T+G+L+      +       F+ R ++K Y ++        +  +A  
Sbjct: 139 PELSPIHRLDRDTAGVLLFCADPESRGVYQALFQTRNVRKEYEAI-----APLRSDLAFP 193

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L+ +S +     H   +   G   + +  ++++    K+    ++PHTGR HQLRVH   
Sbjct: 194 LVHRSSMAARPGHFTMREVPGEPNSETQIELMEAMG-KWGRYRLRPHTGRKHQLRVHMSA 252

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           +G PI  D  Y               L L AR ++   P  G+L+
Sbjct: 253 LGMPIRHDDFYPELKAYARDDDFSRPLQLLARSIEFVDPVSGQLR 297


>gi|90412159|ref|ZP_01220165.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum 3TCK]
 gi|90326883|gb|EAS43268.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum 3TCK]
          Length = 228

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 96/221 (43%), Gaps = 21/221 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+++     V NK  G+SV    G    +    K    +  +K  L HRLD+ TSG+L++
Sbjct: 4   LVHQHPDFLVINKHPGVSVHKDDGDQPLLAEVAK---QTGDEKLYLIHRLDKMTSGLLLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R R AA  L+ +F  R ++K Y ++    PK K+  +         +        K + 
Sbjct: 61  GRNRQAAAELSGNFAKRDVKKFYLAIGTKKPKKKQGVVIG------DMSRSRRSSWKLDS 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F        + C+L  +PHTG+THQ+RV    +G  I GD  Y        
Sbjct: 115 TKDNPAITQFFSTAAGNGRRCFL-CKPHTGKTHQIRVALRSVGSGITGDEIYGNEEA--- 170

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
                ++ YLHA  +  P+    +  I AP      + W +
Sbjct: 171 -----DRGYLHAYALSFPYKGENQQFICAP---DKGELWQA 203


>gi|167521497|ref|XP_001745087.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163776701|gb|EDQ90320.1| predicted protein [Monosiga brevicollis MX1]
          Length = 401

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 87/240 (36%), Gaps = 27/240 (11%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLK 98
            +  G + V+ +RV                    L+ II    I+ + V+  +       
Sbjct: 71  AITEGLITVNSERV-------------------PLDFIIDNNHIILNKVHRHEPPVTNDP 111

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++ E   +   +KPA I V       ++    +      +  +    HRLD+ TSG+L
Sbjct: 112 LSIVGETPDLLAIDKPASIPVHPCGRYRHNTVQAILGHEHDRW-RVYPCHRLDRLTSGLL 170

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +  +  A A+   +     +++K Y   V G  +         L        D    +  
Sbjct: 171 IFCKNPAMAKQFEQWITQHQVEKQYICRVQGRVEQSVLFCDAPLKI-----CDQRLGLCC 225

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  +++ F+VI             P TGR HQ+RVH  ++G PIV D  Y +   G
Sbjct: 226 VHPEGKASLTRFRVIRRDKDTTVL-HCFPKTGRMHQIRVHVQYLGHPIVNDPVYNSELWG 284


>gi|312084667|ref|XP_003144368.1| hypothetical protein LOAG_08790 [Loa loa]
 gi|307760466|gb|EFO19700.1| hypothetical protein LOAG_08790 [Loa loa]
          Length = 379

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 61/272 (22%), Positives = 100/272 (36%), Gaps = 35/272 (12%)

Query: 18  NMR------LDR-WFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPP 69
             R       DR +F   +  ++        + G++ V+  +    N  +Q    +    
Sbjct: 2   GQRTMGWASFDRIFFAEEFVSLSPHYPAAACKLGRIWVNCNQMTNVNYIVQHNDSIEHIG 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYH 128
                     E  ILD  +            ++  D+ I V +KPA + V   G    + 
Sbjct: 62  HR-------HEHPILDHYI-----------RVIDNDNNIIVVDKPASMPVHPCGRYCVHT 103

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI-YWSLV 187
           + G L+     +    R+ HRLD+ TSG+L+ AR       L +  R+  +    Y   V
Sbjct: 104 VLGMLREQRGLR--DLRVVHRLDRTTSGVLLFARNSETDTKLKKMLRVGEVWHKEYLCKV 161

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+    KE I +  +    +      +          A S F  +    Q    +    
Sbjct: 162 EGVFPADKEIICDRPIGPLVLSMGIQCIRD----DGKCARSRFWRLWTDGQ-TSIVRCML 216

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            TGRTHQ+RVH  ++G PIV D+ Y     G 
Sbjct: 217 ETGRTHQIRVHLQYLGYPIVDDYIYNTAAWGQ 248


>gi|308184144|ref|YP_003928277.1| hypothetical protein HPSJM_01820 [Helicobacter pylori SJM180]
 gi|308060064|gb|ADO01960.1| hypothetical protein HPSJM_01820 [Helicobacter pylori SJM180]
          Length = 293

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 68/294 (23%), Positives = 121/294 (41%), Gaps = 29/294 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----QAVRKSQIIQGVVRLI------------YFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +  +  L++E +    F+KPA I         +H +  L       G+     HRLD E
Sbjct: 64  PNEKQERLVFETNDFGAFDKPAQIYTHPKGY--FHHESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  +A+ L   F  ++++K Y +L  G+ +   + I   +L   +I  D +
Sbjct: 122 TSGLVLAGKTLQSAKDLKALFMQKKVKKTYLALTHGLIEKNMK-IDKPILTPQNIQKD-L 179

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  Q       +I+  + +          L++ P TGRTHQ+R+H   +   IVG+  Y
Sbjct: 180 RIRSQISPLGKPSITLVEPLSYNPFLDISLLKITPLTGRTHQIRLHLSSINHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +         +      L LHA  ++    +G   QI +P+P   +    
Sbjct: 240 GVADENAREYLQLKRENNAPTLMLHAASLEFEF-KGAIYQIASPMPERFMPFLK 292


>gi|303327488|ref|ZP_07357929.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio sp.
           3_1_syn3]
 gi|302862428|gb|EFL85361.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio sp.
           3_1_syn3]
          Length = 241

 Score =  136 bits (343), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 108/250 (43%), Gaps = 31/250 (12%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           ++   KPAG+    G+G +  +   L         KP   HRLD++TSGIL+VA T +A 
Sbjct: 8   VWALFKPAGLPTHPGTGHSDSLATRLADHYAQAAFKPTPAHRLDKDTSGILLVAATFSAL 67

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-DYVHVV--KQNEKGAN 224
           + L E+ R R + K Y   V G     +  +    L+K    G + +  V     E+ A 
Sbjct: 68  RELQEAIRQRSLIKEYVVWVRGRWPWPEARLLRHQLRKGLERGFEKMRAVLTAAGEERAL 127

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
            A+   + +    +    L ++  TGRTHQ+RV    +G P++GD KY    +     P 
Sbjct: 128 EALCLARPL-RICENESLLLIRLFTGRTHQIRVQLASLGHPVLGDVKYGPPEQRVGGGP- 185

Query: 285 QNKLYLHARYMDLPHPEGGRLQITAP----------LPAHMVKTWDSLGFKYDRNLYIKR 334
              +YLHA  + LP   GGR+    P          LP  M+          D   +  R
Sbjct: 186 ---MYLHALRVILP---GGRIFACLPDWDAEHAVGVLPEVMM----------DGTAFPAR 229

Query: 335 LYSQDECKQN 344
           +  ++ C  +
Sbjct: 230 VGEEETCPAS 239


>gi|309791057|ref|ZP_07685593.1| pseudouridine synthase [Oscillochloris trichoides DG6]
 gi|308226912|gb|EFO80604.1| pseudouridine synthase [Oscillochloris trichoides DG6]
          Length = 301

 Score =  136 bits (343), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 68/289 (23%), Positives = 123/289 (42%), Gaps = 34/289 (11%)

Query: 44  GQVRVDKKRVK-FNNRIQSGQVV--RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           G   ++ +RV       Q GQ++  R+PP     + +++                   S 
Sbjct: 32  GGAWLNGQRVTDPATPCQPGQMLALRLPPAGGYTDVVLQ------------------ASD 73

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSK---GQKPRLTHRLDQETSG 156
           +LYED+ +   NK  G  V      A  H+   L+ ++ ++        L H+LD++TSG
Sbjct: 74  ILYEDAWLIATNKRLGWYVNATPWDAQGHVLAALQRYLHARDGAAPPLHLAHQLDRDTSG 133

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL-----LKKSHIGGD 211
           +L+++R  A    LT +F    + K Y  +V G+P    E  +        L +++   +
Sbjct: 134 VLLISREPAINAALTAAFAGGHVAKTYTCIVAGVPDASGEVRSGHGRSAKGLWRTYPLEE 193

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               +         A + + +     +    ++  PHTGRTHQ+R+H   +G P++GD +
Sbjct: 194 VGRELPSGGGRVKLAHTSY-LRQRILEDAAQVQCTPHTGRTHQIRLHMALLGHPLLGDSR 252

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           Y       +         LHA ++ L HP     L I++PLP  + +  
Sbjct: 253 YGG--PSVYAGISLPGHLLHAAHLALKHPHTQEVLAISSPLPDLLQRLL 299


>gi|269114816|ref|YP_003302579.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hominis]
 gi|268322441|emb|CAX37176.1| Ribosomal large subunit pseudouridine synthaseC [Mycoplasma hominis
           ATCC 23114]
          Length = 278

 Score =  136 bits (343), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 46/287 (16%), Positives = 107/287 (37%), Gaps = 36/287 (12%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72
            D+E   L ++      ++    ++++ R   ++V+  RV     +++ G ++ I  +I 
Sbjct: 8   KDDEGRILFKYLVKVCDNVPISRIERLFREKDIKVNNIRVSDKQYKVKEGDLISIYGLIE 67

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
              HI              K +  +   ++YED  + + +K   I++             
Sbjct: 68  TSKHID------------NKANTNINFKVIYEDKNLLIIDKAPNIAMHSEENCLDDQVLK 115

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             ++      +P    R+D++TSG++V A+                 ++  +  ++    
Sbjct: 116 YLNFKKVSSFRPASIGRIDKKTSGLVVYAKNYKTLVEF-------ENKQNKFDKIYQFVS 168

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           +  E + +  ++      +   +V  N      A + F       ++      +  TG+ 
Sbjct: 169 DFDEDVLDITVRLKKDIKNEKMIVDNN--FGVKAQTIFY------KEGNRKFAKIITGKK 220

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           HQ+R    ++  PI+GD KY   F          ++YLH+  +    
Sbjct: 221 HQIRATLAYLKTPILGDIKYGGKFA--------KRMYLHSYSIKFHD 259


>gi|307174606|gb|EFN65027.1| RNA pseudouridylate synthase domain-containing protein 2
           [Camponotus floridanus]
          Length = 376

 Score =  136 bits (343), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 52/189 (27%), Positives = 85/189 (44%), Gaps = 7/189 (3%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ D  + V NKPA I V       ++   F+ +  +   +  R  HRLD+ TSGI
Sbjct: 39  PITVIHMDEDVVVVNKPASIPVHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDRLTSGI 97

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+  RT   A+ +    R R++ K Y   V G    ++   +  +   S+     + V K
Sbjct: 98  LLFGRTPKKARQMEHQIRNRQVHKQYVCRVEGEFPEEEVICSEPIEVVSY----KIGVCK 153

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +EKG    ++ FK +    +    +  +P TGR HQ+RVH  ++G P+V D  Y     
Sbjct: 154 VSEKG-KDCVTRFKRLSYNGKS-SVVLCKPQTGRMHQIRVHLQYLGYPVVNDPLYNHVVF 211

Query: 278 GNFTSPIQN 286
           G       N
Sbjct: 212 GPHKGKGGN 220


>gi|154149073|ref|YP_001406285.1| pseudouridine synthase [Campylobacter hominis ATCC BAA-381]
 gi|153805082|gb|ABS52089.1| pseudouridine synthase [Campylobacter hominis ATCC BAA-381]
          Length = 248

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 120/308 (38%), Gaps = 65/308 (21%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       +I+    + ++ +G V               GQ++++     + N     QK
Sbjct: 6   KLLAKQ-ENISNNEAKDLIDAGLVS------------AKGQILKVARAEMSENTKFSVQK 52

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +              K  +++E+  I V NKP     +                   K  
Sbjct: 53  VA-------------KPAIVFENDDILVVNKPPFFVSE----------------KLEKIF 83

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           K +L +RLD+ETSGI+++ +     +   + F+  R++K Y ++V GI   + E     L
Sbjct: 84  KFKLLNRLDKETSGIVLLYKNEEFKERAIKEFKNMRVKKTYIAIVQGIVSEEMEFDEPIL 143

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             K   G        +       AI+    +   + K   ++++  TGRTHQ+RVH  + 
Sbjct: 144 TIKGKTG-----AFSRISPHGKSAITRIFPL-MISGKKSLVKIEIDTGRTHQIRVHLSNA 197

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G  I+GD KY  N           +++LHA  ++L       L+  A +P       +  
Sbjct: 198 GFGIIGDEKYAKNS--------SKRMFLHAYELELLD-----LKFRAKIPNDF----NVF 240

Query: 323 GFKYDRNL 330
           GF+  + +
Sbjct: 241 GFEIGKEI 248


>gi|46200775|ref|ZP_00056471.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 166

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 52/172 (30%), Positives = 87/172 (50%), Gaps = 12/172 (6%)

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++ R   + + L   F   R++K+YWS+  G P+     +   LLK S  G  +   V 
Sbjct: 1   MILGRHAKSIKRLGRMFEHHRVEKLYWSVCHGSPEGDSGTVDAPLLKVSGRGQGWRIKV- 59

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
             +     +I+ + V+        W+E +P TGRTHQ+R+HA H+GCP++GD  Y  + +
Sbjct: 60  --DPAGQSSITDWSVLGR-GGGLSWIEWRPRTGRTHQIRIHAQHLGCPLLGDAYYGPDPE 116

Query: 278 GNFTSPIQNKLYLHARYMDLP--HPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
                    +L+L AR +  P   P    +++TAP P HMV+     G++ D
Sbjct: 117 ------TMTRLHLLAREVSFPALSPSKDPVRVTAPPPGHMVEALRVCGWRED 162


>gi|331698896|ref|YP_004335135.1| pseudouridine synthase [Pseudonocardia dioxanivorans CB1190]
 gi|326953585|gb|AEA27282.1| pseudouridine synthase [Pseudonocardia dioxanivorans CB1190]
          Length = 252

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 59/240 (24%), Positives = 97/240 (40%), Gaps = 24/240 (10%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           S+   +I+L+ED    V +KP G+SV G        D  L +     G+  R  +R+D+ 
Sbjct: 5   SELRSAIVLWEDESCLVVDKPPGLSVMG-----ERHDTDLVTIAADAGEDLRWVNRIDKV 59

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL---------- 203
           TSG +++A+++ A   LT  F+ R + K Y ++        +  I   L+          
Sbjct: 60  TSGAVLLAKSKEAHGALTRQFQQRTVAKSYLAICRPGGFPTRATIDLPLMTAGSGRIRVA 119

Query: 204 -KKSHIGGD--YVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHA 259
             + HI  D    HV  ++E    +  S  +            +   P TGR HQ+RVH 
Sbjct: 120 ADREHIRLDDSRWHVRPEDEHARKHFPSRTECSAIHDDGDTVVVRADPVTGRKHQIRVHL 179

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
             +G  IVGD  +        T P + + YLH+  +    P    + + A          
Sbjct: 180 AWVGHAIVGDPLFLRK-----TDPPEARTYLHSFRVGFRAPSDEEVTVEARPADDFWAPL 234


>gi|241760243|ref|ZP_04758339.1| pseudouridine synthase Rlu family protein [Neisseria flavescens
           SK114]
 gi|241319354|gb|EER55819.1| pseudouridine synthase Rlu family protein [Neisseria flavescens
           SK114]
          Length = 216

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 58/213 (27%), Positives = 89/213 (41%), Gaps = 21/213 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGIL 158
            +++E     V NKP G+SV               S     G ++  L HRLD+ TSG+L
Sbjct: 3   DIVFEHKDFVVINKPCGVSVHS---ELEEDVCLTASLTQQLGVERVWLVHRLDKATSGLL 59

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A  R +A  L+  F  + ++K Y +L    P  K+  +      K  +   +    K 
Sbjct: 60  LFALNRDSAAALSAQFAEKTVRKTYLALGTHKPAKKQGWV------KGGMARSWRGTWKL 113

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                N+A++ F              +QP TG+THQLRV    +G PI+GD  Y  +   
Sbjct: 114 TRDEDNFAVTRFSS-QSLQPGLRLFVLQPFTGKTHQLRVAIKSIGSPILGDTLYGGDEAE 172

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQIT-AP 310
           +        L+LHA  +   +  G    I  AP
Sbjct: 173 H--------LFLHAWRLVFDY-RGEHFDIRVAP 196


>gi|330882959|gb|EGH17108.1| pseudouridine synthase [Pseudomonas syringae pv. glycinea str. race
           4]
          Length = 328

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 60/294 (20%), Positives = 106/294 (36%), Gaps = 30/294 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +  G+V   + K +  +   + G  +RI       N        
Sbjct: 62  LCAKFTAISREQWLDRIARGRVLDENGKAIAPDLAYREG--LRIHYFREVPN-------- 111

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +   G  
Sbjct: 112 --------ETPIPVFETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 161

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  R+I K Y ++   +P      +    
Sbjct: 162 DLVPLHRIDRHTAGLVLFSANRQTRSAYQALFPTRQIDKFYEAIAPALP-----GLEFPR 216

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++   Q + +  + P TG+ HQLRVH   +
Sbjct: 217 LHESRLVEGEPFFRMQEGAGASNTRTQIEVLERQDQLWRYG-LYPVTGKKHQLRVHMAAL 275

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           G  I  D  Y  +   N     QN L L A+ +    P  G+  Q  + L    
Sbjct: 276 GAGICNDPFY-PDVVKNPVDDYQNPLKLLAKGLRFIDPLSGKQRQFESLLELDW 328


>gi|226724697|sp|Q0E0Y3|PUS7_ORYSJ RecName: Full=RNA pseudourine synthase 7; AltName: Full=RNA
           pseudouridylate synthase 7; AltName: Full=RNA-uridine
           isomerase 7
 gi|222622934|gb|EEE57066.1| hypothetical protein OsJ_06883 [Oryza sativa Japonica Group]
          Length = 393

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 57/267 (21%), Positives = 102/267 (38%), Gaps = 24/267 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+N      +   F + +           ++ G+++VD + V  +  +QS Q +      
Sbjct: 42  VKNRWAGKTIVDLFTDEFKGRPREYYVHAVKCGRLQVDDQMVHADYVVQSSQKISHFLHR 101

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                   E  +L   +            +L  ++ +    KPA + V       Y  + 
Sbjct: 102 -------HEPPVLGGDI-----------TILQNEADVVTVCKPASVPVHPCG--QYRKNT 141

Query: 132 FLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            +       G  P    HRLD+  SG+L+ A+    A+   +      +QK Y + V G+
Sbjct: 142 VVGILQAEHGLVPLFPVHRLDRLVSGLLIFAKNADKAESFRQQIEASLLQKEYVAKVVGV 201

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPH 248
             + ++ +   +   +  G     V   + K      A + F+ I C       +  +P 
Sbjct: 202 FPDGEQTVNANVHFNAREGRSTAEVCDGDGKAPIGKQACTKFQRI-CTDGIHSIVLCKPV 260

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCAN 275
           TGRTHQ+RVH  H+G PI  D  Y + 
Sbjct: 261 TGRTHQIRVHLKHIGYPIANDEVYLSE 287


>gi|218190831|gb|EEC73258.1| hypothetical protein OsI_07380 [Oryza sativa Indica Group]
          Length = 393

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 57/267 (21%), Positives = 102/267 (38%), Gaps = 24/267 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+N      +   F + +           ++ G+++VD + V  +  +QS Q +      
Sbjct: 42  VKNRWAGKTIVDLFTDEFKGRPREYYVHAVKCGRLQVDDQMVHADYVVQSSQKISHFLHR 101

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                   E  +L   +            +L  ++ +    KPA + V       Y  + 
Sbjct: 102 -------HEPPVLGGDI-----------TILQNEADVVTVCKPASVPVHPCG--QYRKNT 141

Query: 132 FLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            +       G  P    HRLD+  SG+L+ A+    A+   +      +QK Y + V G+
Sbjct: 142 VVGILQAEHGLVPLFPVHRLDRLVSGLLIFAKNADKAESFRQQIEASLLQKEYVAKVVGV 201

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAISHFKVIDCFAQKFCWLEMQPH 248
             + ++ +   +   +  G     V   + K      A + F+ I C       +  +P 
Sbjct: 202 FPDGEQTVNANVHFNAREGRSTAEVCDGDGKAPIGKQACTKFQRI-CTDGIHSIVLCKPV 260

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCAN 275
           TGRTHQ+RVH  H+G PI  D  Y + 
Sbjct: 261 TGRTHQIRVHLKHIGYPIANDEVYLSE 287


>gi|290961710|ref|YP_003492892.1| RNA pseudouridine synthase [Streptomyces scabiei 87.22]
 gi|260651236|emb|CBG74358.1| putative RNA pseudouridine synthase [Streptomyces scabiei 87.22]
          Length = 305

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 47/214 (21%), Positives = 80/214 (37%), Gaps = 6/214 (2%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +        ++Y D  I V +KP  ++     G         +   +         HR
Sbjct: 65  PHEVPVPFPLDIVYRDDHIVVVDKPHFLATTP-RGSHITETALARLRRELAVPTLSAAHR 123

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+++              FR R + K Y ++    P      +      +S I 
Sbjct: 124 LDRLTAGLVLFTVRPGERGAYQSLFRDRLVTKEYEAVAPYDPS-----VVLPCTVRSRIV 178

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +   +  +  +G   A+S  +++D  A       + P TG+THQLR H   +G PI+GD
Sbjct: 179 KERGVMAAREVEGEPNAVSGVELLDRRAGGPARYRLLPRTGQTHQLRAHMASLGLPILGD 238

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             Y            +  L L AR ++   P  G
Sbjct: 239 PLYPLVRDPVPPGDFRRPLQLLARALEFTDPVTG 272


>gi|222110970|ref|YP_002553234.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221730414|gb|ACM33234.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 304

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 69/298 (23%), Positives = 112/298 (37%), Gaps = 32/298 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRI 67
           VV+ +  + + +D +     P ++  +  + LR+ +V VD         +    G  VR 
Sbjct: 21  VVLPSAGQGLLVD-FLAQRLPAVSREDWLRRLRASEV-VDEFGAAATERSAFTPG--VRY 76

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                           L     L  H       +LY+D+ I V +KP  + V       Y
Sbjct: 77  YYYRE-----------LPPEPELPFHE-----TVLYQDAHILVADKPHFLPVVPAG--RY 118

Query: 128 HIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                L       G  +    HR+D++T+G+++ +  RA        FR RR+ K+Y ++
Sbjct: 119 LQQTLLVRLKRRLGLSELSPVHRIDRDTAGLVLFSVQRATRGTYQALFRDRRVHKVYEAV 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                     CI    L++S               G   A +H  V++  A  +    ++
Sbjct: 179 APWRADLPLPCIHESRLEESG-----HFFRMHEVPGTPNARTHIDVLE-VASPWARYRLE 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           P TG+ HQLRVH   +G P+ GD  Y             N L L AR +    P  G 
Sbjct: 233 PITGKRHQLRVHMAALGLPLRGDAFY-PEVNDPPEGDYSNPLQLLARTLAFTDPLSGE 289


>gi|317179260|dbj|BAJ57048.1| hypothetical protein HPF30_0951 [Helicobacter pylori F30]
          Length = 293

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 68/287 (23%), Positives = 118/287 (41%), Gaps = 29/287 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q VR   +I  +  +I                +     
Sbjct: 28  LKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGIVSLI------------HFKPNEKTQA 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  +A+ L   F  ++++K Y +L  G+  ++   I   +L   +I  D     K + 
Sbjct: 129 GKTLQSAKDLKALFMQKKVKKTYLALAHGLV-DRSIVIDKPILTPQNIQKDLRIRSKIS- 186

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                + +  + +          L++ P TGRTHQ+R+H   +G  IVG+  Y    +  
Sbjct: 187 PLGKPSTTLVEPLSYNPFLDISLLKITPITGRTHQIRLHLSSVGHRIVGEGLYGVIDENA 246

Query: 280 FTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                  +      L LHA  ++    +G   +IT+P+P   +    
Sbjct: 247 REYLQLKRKNNAPLLMLHASSLEFEF-KGAIYEITSPMPKRFMPFLK 292


>gi|291279974|ref|YP_003496809.1| ribosomal large subunit pseudouridine synthase A [Deferribacter
           desulfuricans SSM1]
 gi|290754676|dbj|BAI81053.1| ribosomal large subunit pseudouridine synthase A [Deferribacter
           desulfuricans SSM1]
          Length = 219

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 56/225 (24%), Positives = 95/225 (42%), Gaps = 17/225 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D+ I V NK   I V             +K+ +  +  +  + HRLD  T G++V 
Sbjct: 9   IVYQDNDIIVLNKSHSILVIPDRYNKNIPS--IKNILQREFNEIYVVHRLDFGTGGLIVF 66

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ R + + L+  F   +I K Y  +  G+ K     +   + K+++ G       K N 
Sbjct: 67  AKNRYSHKSLSTQFSKNQIVKKYLCITDGVIKYPFTSL-LPISKRNYHGK-----YKINF 120

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           K    +I+ F  I+ +  K+  +E  P TGR+HQ+RVH      P+  D  Y        
Sbjct: 121 KSGRKSITTFIPIN-YNNKYSLIEAIPKTGRSHQIRVHLKAYKAPLYQDFLYNKKIDD-- 177

Query: 281 TSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSLGF 324
                 +L L A Y+   HP    +++    L   M +     G 
Sbjct: 178 -----KRLTLFAYYLSFTHPTKNKKVEFKIKLSDFMNEKLKETGL 217


>gi|303280505|ref|XP_003059545.1| pseudouridine synthase [Micromonas pusilla CCMP1545]
 gi|226459381|gb|EEH56677.1| pseudouridine synthase [Micromonas pusilla CCMP1545]
          Length = 423

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 67/267 (25%), Positives = 104/267 (38%), Gaps = 34/267 (12%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG--ISVQGGSGIA-----------YH 128
           + +  ++    HS   +  L++E     V NKP    +    G   A           Y 
Sbjct: 161 ESVADAIARQPHSLERRFHLVHECEDYAVVNKPWCVRLDTPRGWKDAAGNPLNRFTPKYP 220

Query: 129 IDGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            D  ++ W++ +       R  H+LD  TSG+LV A  + AA    + FR R  +K Y +
Sbjct: 221 GDLSVEDWLEERYPGWDTVRFVHQLDNATSGVLVAASNKRAAGRAAKLFRERAARKAYIA 280

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK----GANYAISHFKVIDC------ 235
           LV+G P+  +      L +       +   V  + +        + + FKV+        
Sbjct: 281 LVFGHPREDEWTCDAKLGRDPSDPKGFKERVVVDGEEEGVEGKASETRFKVLQRGTFALR 340

Query: 236 ---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                     + + P TGR HQ+RVH  H G PIVGD  Y  + K  F +     L+ HA
Sbjct: 341 GKHEGADVSKVLVTPITGRRHQIRVHLAHGGYPIVGDAAYSED-KDTFRTF----LHAHA 395

Query: 293 RYMDLPHPEGGRLQITAPLPAHMVKTW 319
             +     +GG    TAP P       
Sbjct: 396 LTLPFDAKDGGTKTFTAPEPPSFAAAI 422


>gi|17158025|ref|NP_478072.1| RNA pseudouridylate synthase domain-containing protein 1 [Homo
           sapiens]
 gi|74753357|sp|Q9UJJ7|RUSD1_HUMAN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 1; AltName: Full=Ribosomal large subunit
           pseudouridine synthase C-like protein
 gi|14336724|gb|AAK61255.1|AE006465_1 ribosomal large subunit pseudouridine synthase C like [Homo
           sapiens]
 gi|5748546|emb|CAB53055.1| RNA pseudouridylate synthase domain containing 1 [Homo sapiens]
 gi|15079997|gb|AAH11783.1| RNA pseudouridylate synthase domain containing 1 [Homo sapiens]
 gi|119606118|gb|EAW85712.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_a
           [Homo sapiens]
 gi|119606119|gb|EAW85713.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_a
           [Homo sapiens]
 gi|119606121|gb|EAW85715.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_a
           [Homo sapiens]
 gi|123988657|gb|ABM83844.1| RNA pseudouridylate synthase domain containing 1 [synthetic
           construct]
 gi|123999171|gb|ABM87166.1| RNA pseudouridylate synthase domain containing 1 [synthetic
           construct]
          Length = 312

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 101/233 (43%), Gaps = 17/233 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------RLTHRLDQET 154
           ++Y      V NK   + +   +            +   +   P      R  H+LD  T
Sbjct: 11  IVYRSRDFLVVNKHWDVRIDSKAWRETLTLQKQLRYRFPELADPDTCYGFRFCHQLDFST 70

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L VA  +AAA      F+ RR+ K Y +L+ G  +  +  I++ + + S  G  +  
Sbjct: 71  SGALCVALNKAAAGSAYRCFKERRVTKAYLALLRGHIQESRVTISHAIGRNSTEGRAHTM 130

Query: 215 VVK--QNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            ++  Q  +    +++   V++           + ++P TGRTHQLRVH   +G P+VGD
Sbjct: 131 CIEGSQGCENPKPSLTDLVVLEHGLYAGDPVSKVLLKPLTGRTHQLRVHCSALGHPVVGD 190

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
             Y     G    P   ++ LHA Y+ +P  +   +++  P P   + + D+ 
Sbjct: 191 LTYG-EVSGREDRPF--RMMLHAFYLRIP-TDTECVEVCTPDP--FLPSLDAC 237


>gi|320324274|gb|EFW80353.1| pseudouridine synthase [Pseudomonas syringae pv. glycinea str.
           B076]
 gi|320328603|gb|EFW84605.1| pseudouridine synthase [Pseudomonas syringae pv. glycinea str. race
           4]
          Length = 324

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 60/294 (20%), Positives = 106/294 (36%), Gaps = 30/294 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +  G+V   + K +  +   + G  +RI       N        
Sbjct: 58  LCAKFTAISREQWLDRIARGRVLDENGKAIAPDLAYREG--LRIHYFREVPN-------- 107

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +   G  
Sbjct: 108 --------ETPIPVFETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 157

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  R+I K Y ++   +P      +    
Sbjct: 158 DLVPLHRIDRHTAGLVLFSANRQTRSAYQALFPTRQIDKFYEAIAPALP-----GLEFPR 212

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++   Q + +  + P TG+ HQLRVH   +
Sbjct: 213 LHESRLVEGEPFFRMQEGAGASNTRTQIEVLERQDQLWRYG-LYPVTGKKHQLRVHMAAL 271

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           G  I  D  Y  +   N     QN L L A+ +    P  G+  Q  + L    
Sbjct: 272 GAGICNDPFY-PDVVKNPVDDYQNPLKLLAKGLRFIDPLSGKQRQFESLLELDW 324


>gi|315634204|ref|ZP_07889493.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           segnis ATCC 33393]
 gi|315477454|gb|EFU68197.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           segnis ATCC 33393]
          Length = 226

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 60/197 (30%), Positives = 85/197 (43%), Gaps = 18/197 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++  S   V NKP GISV              +        K  L HRLD+ TSG+L++
Sbjct: 5   IVFRHSDFIVINKPNGISVHKDDADVGLTQLVAQQL---GVPKVWLVHRLDKVTSGLLIL 61

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    AA  L++ F   +IQK Y +L    PK K+  I+  + K            K  +
Sbjct: 62  ALNERAAVTLSQKFAQHQIQKTYIALATHKPKKKQGRISGDMQKA------RRGTWKLCQ 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F V    A       +QP TG+THQLRV    +G PI+GD  Y  +     
Sbjct: 116 SKENPAVTDF-VSHSLAPNLRLFILQPKTGKTHQLRVAMKSLGSPILGDELYGGDKAE-- 172

Query: 281 TSPIQNKLYLHARYMDL 297
                 + YLHA  +  
Sbjct: 173 ------RTYLHAYQLSF 183


>gi|296274039|ref|YP_003656670.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
 gi|296098213|gb|ADG94163.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
          Length = 249

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 58/293 (19%), Positives = 107/293 (36%), Gaps = 56/293 (19%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       +I+    + ++  G V+V  K+V     I  G +      I      IK   
Sbjct: 8   KVLAKQ-ENISNSKAKDLIDKGLVKVGDKKV----LIARGDISENTKFIVKEVAPIK--- 59

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             ++++D  I   +KPA ++                  V  K  
Sbjct: 60  ------------------VIFQDDDILAVDKPAFLT---------------ADEVSRKFP 86

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L +RLD+ETSG+++ A+           F+   + K Y ++V G   ++       L
Sbjct: 87  NYLLLNRLDKETSGVMLFAKNEEFQTKAIREFKNNNVYKEYVAVVEGKVIDEIVVDKPIL 146

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             K++ G     V  +  K A    + + ++         +++   TGRTHQ+RVH  ++
Sbjct: 147 TIKNNKGVARSKVDMKKGKSAKT--TVYPML--VEGNKSKIKVVIDTGRTHQIRVHLNYI 202

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
             PI+GD+ Y         S   N++ LH++   +           A +P   
Sbjct: 203 DYPIIGDNVYGK------PSTHVNRVLLHSKITKIFD-----YTFEAKVPREF 244


>gi|91217548|ref|ZP_01254506.1| ribosomal large subunit pseudouridine synthase D [Psychroflexus
           torquis ATCC 700755]
 gi|91184228|gb|EAS70613.1| ribosomal large subunit pseudouridine synthase D [Psychroflexus
           torquis ATCC 700755]
          Length = 222

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 65/223 (29%), Positives = 105/223 (47%), Gaps = 16/223 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +L E++   V NK AG+  +        ++  +   +  K +KP +   HRLD+ TSG+L
Sbjct: 6   VLQENNDYIVVNKMAGLISEKSPYENLTVENQVLHHLLKKKRKPYIGVIHRLDRVTSGVL 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+ ++      E F  R++QK Y ++V   P   K+ + N+L+K +        +V  
Sbjct: 66  VFAKKKSILVGFNELFSGRKVQKTYLAIVQKKPLKSKKTLTNFLVKNNLE--KRADIVSL 123

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K +   I  ++VID     +  LE++P TGR HQ+R    HM  PI+GD KY ++ + 
Sbjct: 124 KSKESLKCILSYQVIDENNFGY-LLEIKPKTGRFHQIRAQLAHMELPIIGDEKYGSDQEY 182

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQI---TAPLPA-HMVK 317
              S     + LHA  +       G   I    AP+P     K
Sbjct: 183 LPLS-----ICLHAWKLSYQ--VTGSTDIKTYEAPVPKNDFWK 218


>gi|71737653|ref|YP_274327.1| RNA pseudouridine synthase family protein [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71558206|gb|AAZ37417.1| RNA pseudouridine synthase family protein [Pseudomonas syringae pv.
           phaseolicola 1448A]
          Length = 296

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 60/294 (20%), Positives = 106/294 (36%), Gaps = 30/294 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +  G+V   + K +  +   + G  +RI       N        
Sbjct: 30  LCAKFTAISREQWLDRIARGRVLDENGKAIAPDLAYREG--LRIHYFREVPN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +   G  
Sbjct: 80  --------ETPIPVFETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  R+I K Y ++   +P      +    
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANRQTRSAYQALFPTRQIDKFYEAIAPALP-----GLEFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++   Q + +  + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGAGASNTRTQIEVLERQDQLWRYG-LYPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           G  I  D  Y  +   N     QN L L A+ +    P  G+  Q  + L    
Sbjct: 244 GAGICNDPFY-PDVVKNPVDDYQNPLKLLAKGLRFIDPLSGKQRQFESLLELDW 296


>gi|330999262|ref|ZP_08322979.1| RNA pseudouridine synthase [Parasutterella excrementihominis YIT
           11859]
 gi|329575120|gb|EGG56671.1| RNA pseudouridine synthase [Parasutterella excrementihominis YIT
           11859]
          Length = 257

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 92/253 (36%), Gaps = 21/253 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  + V +KP  +            +  L+   D  G++    +RLD+ TSGIL+ 
Sbjct: 6   ILYQDEDLVVVSKPEKMLTHRTEIANGDTEFALQLLRDQIGRRVSPVYRLDRGTSGILMF 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
              R     L++        K Y+++V G      E               Y+ V K   
Sbjct: 66  GLNREIVSALSQQTHE-TFHKRYYAVVRGWAPEDIEVRHAL----KPPVDPYLRVQKTEA 120

Query: 221 KGA-----NYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           + A       A S   V        +   + ++  TGR HQLR H  H+  PI+GD  Y 
Sbjct: 121 QDALSYLHRVAESEVPVSSGKFDTTRLSLVLLELATGRRHQLRRHLKHLAHPIIGDATYG 180

Query: 274 ANFKGNFTSP--IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGF------ 324
                   +     ++L LH   +   HP    RL I       M +  + L +      
Sbjct: 181 KGPLNRVLAEYFGGDRLLLHCGRISFIHPRTQKRLTIDDQPSGLMRQVIERLEWGNYLHA 240

Query: 325 KYDRNLYIKRLYS 337
            Y R+ ++     
Sbjct: 241 SYSRDWHLFDYSD 253


>gi|224013560|ref|XP_002296444.1| hypothetical protein THAPSDRAFT_263801 [Thalassiosira pseudonana
           CCMP1335]
 gi|220968796|gb|EED87140.1| hypothetical protein THAPSDRAFT_263801 [Thalassiosira pseudonana
           CCMP1335]
          Length = 341

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 66/286 (23%), Positives = 123/286 (43%), Gaps = 27/286 (9%)

Query: 27  NHYPHINFVNLQKILRSGQVR-----VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
             YP  +     K +R   +      V++       + Q G+V+      + +    +  
Sbjct: 6   ETYPTQSRAR--KSIRQRAICISRYDVNEPNANAAFK-QLGKVITRVYPGDTIGFQRRAG 62

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
               +   +       +  ++YED  + + NKP+G+ +    G          +  +   
Sbjct: 63  SDYYALQGVPYRLPPFEVPVVYEDDHMAIVNKPSGVVLYRAEGGRGGGARDEDTPQNVPL 122

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           ++P+  HRLD+ TSG++VVA+T+ AA HL++ F  R+ +K Y ++V GIP  ++  +   
Sbjct: 123 KRPQPVHRLDRPTSGLVVVAKTKLAAVHLSQQFEFRKAEKTYVAIVNGIP--RQSGVRAE 180

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC------FAQKFCWLEMQPHTGRTHQL 255
            ++ + I  D              A++ ++V+               +EM+P TGR HQL
Sbjct: 181 PMQWNTIDYDL---------EEKTAVTRWRVLRKVKSLHGNDGTLTLVEMKPKTGRYHQL 231

Query: 256 RVHALHM-GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           R H   +   P+VGD  Y    +G      +  L+L +  + L HP
Sbjct: 232 RRHCAWVCNSPLVGDTTYDGGSEGALRLR-KRGLFLCSSEIALEHP 276


>gi|242212896|ref|XP_002472279.1| predicted protein [Postia placenta Mad-698-R]
 gi|220728646|gb|EED82536.1| predicted protein [Postia placenta Mad-698-R]
          Length = 448

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 56/254 (22%), Positives = 99/254 (38%), Gaps = 27/254 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
                +   +    +  L SG   ++ K  K +  +Q+G  +              E  +
Sbjct: 29  VVSTEFRDRSMEYYRYALESGVTTINGKIAKPDTIVQNGDRIENVVHR-------HEPPV 81

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQ 142
             + V +  H           + +  + +KP  I V   G      +   LK+  D   +
Sbjct: 82  TATPVRIIHH---------DREREFIIIDKPGSIPVHASGRFFRNSLVEILKN--DFGFK 130

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANW 201
           K    +RLD+ TSG++++  + + A  LT+ F    I+K Y +   G  P+ +  C    
Sbjct: 131 KVYTINRLDRLTSGLMIIPLSSSMANTLTQEFAAGTIRKEYIARCRGQFPEEELACEVPL 190

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHAL 260
           L     +G + VH           A + FK +   A      +  +P TGR+HQ+RVH  
Sbjct: 191 LTIDRQMGLNVVH------PEGKPAKTIFKRMHYDANTDTSVVHCEPLTGRSHQIRVHLQ 244

Query: 261 HMGCPIVGDHKYCA 274
           ++G P+  D  Y  
Sbjct: 245 YLGHPVANDPIYSE 258


>gi|226308249|ref|YP_002768209.1| pseudouridine synthase [Rhodococcus erythropolis PR4]
 gi|226187366|dbj|BAH35470.1| putative pseudouridine synthase [Rhodococcus erythropolis PR4]
          Length = 323

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 59/255 (23%), Positives = 108/255 (42%), Gaps = 9/255 (3%)

Query: 53  VKFNNRIQSGQVV-RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           V+   ++ +G+VV      I   +     + +        +     +  +LY D  I V 
Sbjct: 57  VRLREKVAAGEVVDEKGVAITETSGFAPRRFVYLYRDAPVEARVPFEIDILYRDENILVV 116

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   D    +    HRLD+ T+G+L+    +AA +   
Sbjct: 117 DKPHFLASTP-RGRYIAESALVRLRRDLDLPELSPAHRLDRVTAGLLLFTVHQAARRGYQ 175

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F  RR+ K Y ++     +     ++  ++ +S I  +   +     +G   + S  +
Sbjct: 176 TMFAERRVTKEYEAIARYDAQ-----VSTPVVVRSRIVKERGVLKAAEIEGEPNSESRIE 230

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           +I+     F    + PHTG+THQLR+H   +G PI GD+ Y  +F         N L L 
Sbjct: 231 LIETR-DGFARYRLIPHTGKTHQLRLHMTSLGLPIHGDNFY-PDFYDVAAEDYSNPLRLL 288

Query: 292 ARYMDLPHPEGGRLQ 306
           ++ ++   P  GRLQ
Sbjct: 289 SKVLEFEDPTTGRLQ 303


>gi|325578565|ref|ZP_08148665.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325159801|gb|EGC71931.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 225

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 57/203 (28%), Positives = 87/203 (42%), Gaps = 18/203 (8%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETS 155
           +K  ++Y+     +  KP G+SV           G      +  G  +  L HRLD+ TS
Sbjct: 1   MKLDIVYQTDDFIIIYKPCGLSVHKDQ----SEIGLTTLLAEQLGVPQVWLVHRLDKVTS 56

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A    +A      F    IQK Y +L    PK K+  I   + K  +        
Sbjct: 57  GLLILALNAESAAEFFRLFSEHHIQKTYLALSNQKPKKKQGLIVGDMQKVRN------GA 110

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K  +   N AI+ F+ + C         ++P TG+THQLRV    +G PI+GD  Y  N
Sbjct: 111 WKLCQSKENPAITRFESVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDLLYGKN 169

Query: 276 FKGNFTSPIQNKLYLHARYMDLP 298
            +        ++ YLHA  +   
Sbjct: 170 TEN------IDRTYLHAARLQFE 186


>gi|303289713|ref|XP_003064144.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226454460|gb|EEH51766.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 360

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 62/263 (23%), Positives = 102/263 (38%), Gaps = 25/263 (9%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGI----------------SVQGGSGIAYHIDGF 132
           ++    D     +LYED  +   +KP G+                +V    G+     G 
Sbjct: 27  DVPLRPDPAPLTVLYEDEHVLAVDKPPGVMTYPAHRLRGGSVVNRAVHHLRGVTRDGSGG 86

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              +      +P   HRLD ETSG+L++A+ + +A  L  +F  R  +K Y ++   +  
Sbjct: 87  GAGFGFGAATEPIAVHRLDLETSGVLMLAKDKPSASALQGAFERREARKTYLAVCAILED 146

Query: 193 --NKKECIANWLLKKSHIGGDYVH----VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             N  +   +    + H G          V         A  H             +  +
Sbjct: 147 AANASDESDDDFDFERHPGHRRRERRRRAVHTRGDAGREAREHRFTGKRIV-GTALVLAR 205

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-QNKLYLHARYMDLPHPEGG-R 304
           P TGRTHQ+R+H  H G PIVGD  Y  +      S   + ++ LHA  + + HP     
Sbjct: 206 PLTGRTHQVRLHLAHAGLPIVGDALYGYDDALRPASGGFEGRMALHAWNLAVKHPRTKNT 265

Query: 305 LQITAPLPAHMVKTWDSLGFKYD 327
           +++   +PA M      LG + +
Sbjct: 266 MRLAVDMPADMQALSVGLGLRVE 288


>gi|229488989|ref|ZP_04382855.1| pseudouridylate synthase [Rhodococcus erythropolis SK121]
 gi|229324493|gb|EEN90248.1| pseudouridylate synthase [Rhodococcus erythropolis SK121]
          Length = 307

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 59/255 (23%), Positives = 109/255 (42%), Gaps = 9/255 (3%)

Query: 53  VKFNNRIQSGQVV-RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           V+   ++ +G+VV      I   +     + +        +     +  +LY D  I V 
Sbjct: 41  VRLREKVAAGEVVDEKGVGITETSAFAPRRFVYLYRDAPVEARVPFEIDILYRDENILVV 100

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   D +  +    HRLD+ T+G+L+    +AA +   
Sbjct: 101 DKPHFLASTP-RGRYIAESALVRLRRDLELPELSPAHRLDRVTAGLLLFTVHQAARRDYQ 159

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F  RR+ K Y ++           ++  ++ +S I  +   +     +G   + S  +
Sbjct: 160 TMFAERRVAKEYEAIAR-----HDAQVSTPVVVRSRIVKERGVLKAAEIEGEPNSESRIE 214

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           +I+     F    + PHTG+THQLR+H   +G PI GD+ Y  +F         N L L 
Sbjct: 215 LIETR-DGFARYRLTPHTGKTHQLRLHMTSLGLPIHGDNFY-PDFYDVAAEDYSNPLRLL 272

Query: 292 ARYMDLPHPEGGRLQ 306
           ++ ++   P+ GRLQ
Sbjct: 273 SKVLEFEDPKTGRLQ 287


>gi|317010619|gb|ADU84366.1| putative ribosomal pseudouridine synthase [Helicobacter pylori
           SouthAfrica7]
          Length = 293

 Score =  135 bits (341), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 68/287 (23%), Positives = 121/287 (42%), Gaps = 29/287 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q+VR   +I  +  +I                +  +  
Sbjct: 28  LKESQRHLDKQRLKQNQ-----QIVRKSQIIQGVVSLI------------YFKPNEKQGK 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  +A+ L   F  +++QK Y +LV G+  ++   I   +L   +I  D + +  Q  
Sbjct: 129 GKTLQSAKDLKALFMQKKVQKTYLALVHGLV-DESIIIDKPILTPENIQKD-LRIRSQIS 186

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                + +  + +   +      L++ P TGRTHQ+R+H   +   IVG+  Y    +  
Sbjct: 187 PLGKPSTTLVEPLSYNSFLDVSLLKITPLTGRTHQIRLHLSSVNHRIVGEGLYGVIDENA 246

Query: 280 FTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                  +      L LHA  ++    +G   +I +P+P   +    
Sbjct: 247 REYLQLKRENNAPLLMLHATSLEFEF-KGAHYKIASPMPQRFMPFLK 292


>gi|317008986|gb|ADU79566.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori India7]
          Length = 293

 Score =  135 bits (341), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 70/294 (23%), Positives = 121/294 (41%), Gaps = 29/294 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKHNQ-----QAVRKSQMIQGVVRLI------------HFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +  +  L++E     VF+KP  +      G  YH +  L       G+     HRLD E
Sbjct: 64  PNEKQGKLVFETKDFGVFDKPTQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D  
Sbjct: 122 TSGLVLAGKTLQSAKDLKALFMQKKVKKTYLALTHGLV-DKSIIIDKPILTPQNIQKDLR 180

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              K +      + +  + +          L++ P TGRTHQ+R+H   +G  IVG+  Y
Sbjct: 181 IRSKIS-PLGKPSTTLVEPLSYNPFLDISLLKITPLTGRTHQIRLHLSSVGHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +         +      L LHA  ++    +G   +IT+P+P   +    
Sbjct: 240 GVADEEAREYLQLKRENHAPLLMLHAFGLEFEF-KGAIYEITSPMPKRFMPFLK 292


>gi|208434290|ref|YP_002265956.1| pseudo uridine synthase D [Helicobacter pylori G27]
 gi|208432219|gb|ACI27090.1| pseudo uridine synthase D [Helicobacter pylori G27]
          Length = 297

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 71/289 (24%), Positives = 120/289 (41%), Gaps = 29/289 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q VR   +I  +  +I                +     
Sbjct: 28  LKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVRLI------------HFKPNEKAQA 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KPA +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPAQVYTHP-KGYFYH-ESLLDCIQSHLGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  + + L   F  ++++K Y +L  G+ + K   I   +L   +I  D + +  Q  
Sbjct: 129 GKTLQSVKDLKALFMQKKVKKTYLALAHGLVE-KSMKIDKPILTLQNIQKD-LRIRSQIS 186

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                +I+  + +          L++ P TGRTHQ+R+H   +G  IVG+  Y    +  
Sbjct: 187 PLGKPSITLVESLSYDPFLDISLLKITPLTGRTHQIRLHLSSVGHRIVGEGLYGVADEEA 246

Query: 280 FTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                  +      L LHA  ++    +G   QI +P+P   +     L
Sbjct: 247 RGYLQLKRENHAPLLMLHAASLEFEF-KGAIYQIASPMPERFMPFLKDL 294


>gi|308061695|gb|ADO03583.1| hypothetical protein HPCU_02050 [Helicobacter pylori Cuz20]
          Length = 293

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 70/287 (24%), Positives = 118/287 (41%), Gaps = 29/287 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q VR   +I  +  +I                +     
Sbjct: 28  LKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVSLI------------HFKPNEKTQA 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D     K + 
Sbjct: 129 GKTLQSAKDLKTLFMQKKVKKTYLALAHGLV-DKNIVIDKPILTPQNIQKDLRIRSKIS- 186

Query: 221 KGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                + +  + +   A      L++ P TGRTHQ+R+H   +G  IVG+  Y    +  
Sbjct: 187 PLGKPSTTLVEPLSYNAFFDISLLKITPLTGRTHQIRLHLSSVGHRIVGEGLYGVIDENA 246

Query: 280 FTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                  +      L LHA  +     +G   +IT+P+P   +    
Sbjct: 247 REYLQLKRENNAPLLMLHASSLAFEF-KGAIHEITSPMPKRFMPFLK 292


>gi|218709959|ref|YP_002417580.1| RNA pseudouridine synthase [Vibrio splendidus LGP32]
 gi|218322978|emb|CAV19155.1| RNA pseudouridine synthase [Vibrio splendidus LGP32]
          Length = 270

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 100/231 (43%), Gaps = 23/231 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L   S   + NK  G+SV    G    +    K+       K  L HRLD+ TSGIL+
Sbjct: 41  DILLNHSDFLLINKHPGVSVHKDDGDTMLLQEVAKAI---NEPKLYLVHRLDKMTSGILL 97

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+   AA  L++ F  R ++K Y ++    PK K+  I+  + +        +   +  
Sbjct: 98  LAKDAPAASELSQLFAKREVEKYYLAIGSKKPKKKQGLISGDMERSRRSSWKLLTTKE-- 155

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F +          L  +P+TGRTHQ+RV    +G  IVGD  Y  + +  
Sbjct: 156 ----NPAITQF-LSATAEPGERLLLCKPYTGRTHQIRVAMKSIGSAIVGDPIYNPSNEA- 209

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
                 ++ YLHA  +   +       +  P      +  DSLG K+ + +
Sbjct: 210 ------DRGYLHAFAIRFTYQSQAYEYVCDP------RNLDSLGEKWHQEI 248


>gi|32266234|ref|NP_860266.1| hypothetical protein HH0735 [Helicobacter hepaticus ATCC 51449]
 gi|32262284|gb|AAP77332.1| conserved hypothetical protein [Helicobacter hepaticus ATCC 51449]
          Length = 303

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 109/280 (38%), Gaps = 34/280 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H         QK+L       DKKR++ +NR+                  I + +I
Sbjct: 19  FLMRH-RGYTQAQAQKVL-------DKKRLRQHNRV------------------IAKNEI 52

Query: 84  LDSSVNLTK-HSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
           +   V L++  +  ++   L+ +    V++KP  +     G    Y ++  LK      G
Sbjct: 53  ICGQVELSEFEACDIELEPLFFNEDFCVYDKPHNLLTHPKGRFYHYSLNDALKLRF---G 109

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD++TSG+++ A    +   L E    R+I K Y+++V G     +EC+ + 
Sbjct: 110 NYANAIHRLDKQTSGLVLCAINPQSEPELKELISTRQILKTYYAIVEGKLT--QECLIDE 167

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHAL 260
            +      G  + +          + +    +   +      + + P TGRTHQ+R+H  
Sbjct: 168 PIALQKYKGTDLSIKSIISPYGKPSRTKLYPLAYHSPTDSTLIRVLPLTGRTHQIRLHCA 227

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           H+G  I+GD  Y    + +        L  H        P
Sbjct: 228 HIGHRILGDPLYGTKEEYSRFYLESPALPPHQYESYFGAP 267


>gi|261493419|ref|ZP_05989944.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261310913|gb|EEY12091.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 217

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 61/214 (28%), Positives = 96/214 (44%), Gaps = 20/214 (9%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             + Y+     + NKP G+SV          +   +       ++  L HRLD+ TSG+L
Sbjct: 5   LPICYQHRDFIIINKPEGLSVHKDEAEIGLTELVARQL---NVKQVWLVHRLDKITSGLL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A  + AA      F   +I K YW+L    PK K+  I   + K S  G   +   K+
Sbjct: 62  ILALNKEAAARFYHLFEQHKIYKTYWALSDKKPKKKQGRIVGDMQK-SRNGAWKLCYSKE 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           N      A++ F +            +QP TG+THQLRV    +G PI+GD  Y  +   
Sbjct: 121 N-----PAVTQF-ISHSVEDSLRHFILQPKTGKTHQLRVAMKSLGSPILGDKLYSGSQA- 173

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                  +++YLHA  +D  + E  ++ + A LP
Sbjct: 174 -------DRVYLHAYQLDFEY-ENEKISVQA-LP 198


>gi|224134072|ref|XP_002321729.1| predicted protein [Populus trichocarpa]
 gi|222868725|gb|EEF05856.1| predicted protein [Populus trichocarpa]
          Length = 388

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 56/279 (20%), Positives = 102/279 (36%), Gaps = 25/279 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+N      +   F   +    +      ++ G+++VD + V  +  ++S Q +      
Sbjct: 52  VKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDGEMVPVSYIVKSSQKISHFVHR 111

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
           +    +  +                    +L ++  +    KPA + V       Y  + 
Sbjct: 112 HEPPVMAWD------------------VPILDKEDDVVTVWKPATVPVHPCG--QYRKNT 151

Query: 132 FLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            +       G  P    HRLD+  SG+L++AR    A    +     ++QK Y + V G+
Sbjct: 152 VVGVLQAEHGLAPLFPVHRLDRLVSGLLILARNATRADLFRQEIEAGKVQKQYVAKVIGV 211

Query: 191 PKNKKECIANWLLKKSHIGGDYVHV---VKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
               ++ +   +   +  G   V V      +      A + F  I         +  +P
Sbjct: 212 FPEDEQIVDVNVNYNAREGRSTVEVGNSCDGSPIKGKTACTKFTRIGTNG-IHSIVLCKP 270

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
            TGRTHQ+RVH  + G PI  D  Y +    N +S   N
Sbjct: 271 ITGRTHQIRVHLQYTGHPIANDILYLSENVTNRSSEGVN 309


>gi|302692494|ref|XP_003035926.1| hypothetical protein SCHCODRAFT_30820 [Schizophyllum commune H4-8]
 gi|300109622|gb|EFJ01024.1| hypothetical protein SCHCODRAFT_30820 [Schizophyllum commune H4-8]
          Length = 262

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 96/253 (37%), Gaps = 26/253 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD   +   P          LRSG + ++ +    +  +++G  ++     +        
Sbjct: 30  LDVAAERFKPPRPREFYAYALRSGLLTLNGRLTDPDTTVRAGDQLQTVAHRHEPPVTGAG 89

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            + +  S                    + V  KP G+ V       Y+    +    +  
Sbjct: 90  VRAISQS------------------EDLLVVEKPGGVPVHPVGRYRYNCLTHM--MREQG 129

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIA 199
               R   RLD+ TSG+++      AA  L  + R  R++K Y + V G  P+    C  
Sbjct: 130 LPAVRPVSRLDRLTSGVMLFPLNARAAGRLGVALRDGRVRKEYLARVRGRFPREPVLCKE 189

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             LL    +G   VH     E+G   A +  +V          +  +P+TGRTHQ+RVH 
Sbjct: 190 KLLLVHRQLGLSIVH-----EEGKPSATAFVRVSYDAKTDTSLVLCRPYTGRTHQIRVHL 244

Query: 260 LHMGCPIVGDHKY 272
           LH+G PI  D  Y
Sbjct: 245 LHLGHPIPNDPYY 257


>gi|332704296|ref|ZP_08424384.1| pseudouridine synthase [Desulfovibrio africanus str. Walvis Bay]
 gi|332554445|gb|EGJ51489.1| pseudouridine synthase [Desulfovibrio africanus str. Walvis Bay]
          Length = 278

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/287 (20%), Positives = 99/287 (34%), Gaps = 30/287 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V   E   RLDR  +   P ++    ++++  G+  VD +      ++  GQ + +    
Sbjct: 11  VSAAEAWQRLDRLLERIVPELSLRGRRRLIDLGKALVDGQPKPAGFKVGPGQTITVRMDD 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              +                  +      ++  D +     KPAG+  +  +G    +D 
Sbjct: 71  TPAS-----------------DASASGPYVVQADERFAAVYKPAGMHSESLAGGGQGLDA 113

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L   +       RL +RLD  TSGI++ A    A Q   +     +++K Y  LV G  
Sbjct: 114 LLPELLGRT--DARLVNRLDLPTSGIVLAALGADAEQEFRKLENAGQVRKEYAVLVHG-- 169

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             + E      L         V  +  +            V          L      G 
Sbjct: 170 --RVEVPTVLRLALDTSDRKKVRALGGDSPDPLRWTEIEPVAYDAILDRTRLRAVILMGA 227

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            HQ+R H      PIVGD  Y  + +G        +LYLH   +++P
Sbjct: 228 RHQIRAHLAMHDHPIVGDTLYGPDAEGE-------RLYLHHGRLEMP 267


>gi|154174351|ref|YP_001408557.1| ribosomal large subunit pseudouridine synthase C [Campylobacter
           curvus 525.92]
 gi|112803057|gb|EAU00401.1| ribosomal large subunit pseudouridine synthase C [Campylobacter
           curvus 525.92]
          Length = 252

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 73/310 (23%), Positives = 120/310 (38%), Gaps = 65/310 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       +I+    + ++ SG V               GQ V I   +  +N     Q+
Sbjct: 8   KILAMQL-NISNNEAKDLIDSGLVF------------AKGQKVAIARALMNVNTKFSVQE 54

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
               S             +++ED  +   NKPA I+ +                  S+  
Sbjct: 55  TSKPS-------------VIFEDENLLAINKPAFITSE----------------KISQMY 85

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           K  L HRLD+ETSG+L++ +    A+   E F+  R++KIY + V GI   +       L
Sbjct: 86  KFPLLHRLDKETSGVLLLVKNEEFAKRAIEEFKHMRVEKIYIAAVRGILSEETRVSEPIL 145

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             KS         + +  K    A+S    +    +K   +++   TGRTHQ+R+H   +
Sbjct: 146 TIKSKGA-----AISKISKDGKEAVSDVTPLMVVGKK-TLVKVAIKTGRTHQIRLHLASI 199

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
             PI+GD KY  N           ++YLHA ++ L        +  A +P       + L
Sbjct: 200 NAPIIGDEKYGKNRA--------KRMYLHAYFIALL-----GYKFKADVPKDF----NEL 242

Query: 323 GFKYDRNLYI 332
           GF+      I
Sbjct: 243 GFEISNKFDI 252


>gi|72549946|ref|XP_843613.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|323364132|emb|CBZ13139.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 741

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 95/251 (37%), Gaps = 28/251 (11%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QG------GSGIAYHIDGFLKS--- 135
           +  +    +     +LYED  + V +KPAG++    G      G+     I   L +   
Sbjct: 500 TAAMAAEVNLPVIPVLYEDDDVLVVDKPAGLATSRHGLSCTQLGTPTTDLISVLLATDRA 559

Query: 136 -WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             +     +    HRLD ETSG L++A++  AA  L            +  +   +    
Sbjct: 560 GALARGVFRQGQVHRLDAETSGCLLIAKSDVAADSLRHQLGTSAAFSHHSKIYHALC--- 616

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTH 253
              +    L+   +  D +       +      + ++VI  F   +  W+E +   G+ H
Sbjct: 617 --VVLEPSLRNVRLHDDIIDAADPKIR------TRYRVIRFFPKHRVAWVECRIQQGKKH 668

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
           Q+R H    G PI+ D ++           + +++ LHA  +   HP     +   APLP
Sbjct: 669 QIRRHLASRGFPILADLEHGG---AVCCQSMISRVALHAHSLSFIHPVTADPITAAAPLP 725

Query: 313 AHMVKTWDSLG 323
           A   +    L 
Sbjct: 726 ADFRRCLSLLR 736


>gi|330958926|gb|EGH59186.1| pseudouridine synthase [Pseudomonas syringae pv. maculicola str.
           ES4326]
          Length = 296

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 56/282 (19%), Positives = 99/282 (35%), Gaps = 29/282 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +P I+       +  G+V   D   +  +   + G  ++I       N        
Sbjct: 30  LCAKFPAISREQWLDRIARGRVLDADGNTIAPDLAYREG--LKIHYFREVPN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQ 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +      
Sbjct: 80  --------ETPIPVVETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLDNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  RRI K Y ++   +P      +    
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANRQTRSAYQALFPTRRIDKFYEAIAPALP-----GLEFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           + +S +         Q   GA+   +  +V++     + +  + P TG+ HQLRVH   +
Sbjct: 185 VHESRLVEGEPFFRMQEGPGASNTQTRIEVLERQEHLWRYG-LYPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G  I  D  Y    K       QN L L A+ +    P  G 
Sbjct: 244 GAAICNDPFYPDALKNPLDD-YQNPLKLLAKGLRFVDPLSGE 284


>gi|296219230|ref|XP_002755784.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Callithrix jacchus]
          Length = 312

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 103/236 (43%), Gaps = 23/236 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---------RLTHRLD 151
           ++Y      V NK   + +   +   +     L+  +  +  +          R  H+LD
Sbjct: 11  IVYRSHDFLVVNKHWDLRIDSKT---WRETLTLQKQLRHRFPELADPGTCYGFRFCHQLD 67

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG L VA  +AAA     SF+ RR+ K Y +L+ G  +  +  I++ + + S  G  
Sbjct: 68  FSTSGALCVALNKAAAGSAYRSFKERRVTKAYLALLRGHIQESRVTISHAIGRNSTEGRA 127

Query: 212 YVHVVK--QNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           +   ++  Q  +    +++   V++           + ++P TGRTHQLRVH   +G P+
Sbjct: 128 HTMCIEGTQGCENPKPSLTELVVLEHGLYAGDPVSKVLLKPLTGRTHQLRVHCSALGHPV 187

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           VGD  Y     G    P   ++ LHA Y+ +  P  G   + A  P   + + D+ 
Sbjct: 188 VGDLTYG-EPSGREDRPF--RMMLHALYLRI--PTDGE-CVEACTPDPFLPSLDAC 237


>gi|330445575|ref|ZP_08309227.1| RNA pseudouridylate synthase family protein [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
 gi|328489766|dbj|GAA03724.1| RNA pseudouridylate synthase family protein [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
          Length = 228

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 58/221 (26%), Positives = 92/221 (41%), Gaps = 23/221 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           L+Y+     V NK  GISV             L +  +  G +K  L HRLD+ TSG+L+
Sbjct: 4   LVYQHPDFLVINKHPGISVHKDDNDQP----LLAAVAEQTGDEKLYLIHRLDKMTSGLLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R + AA  L+ +F  R ++K Y ++    PK K+  +         +        K  
Sbjct: 60  LGRNKEAASILSSNFAERVVEKFYVAIGTKKPKKKQGVVIG------DMSRSRRSSWKLE 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F       +       +PHTG+THQ+RV    +G  I GD  Y       
Sbjct: 114 STKENPAVTQFFS-AAAGEGRRVFLCKPHTGKTHQIRVALRSVGSGITGDDIYG------ 166

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
             +   ++ YLHA  +  P+ +G   +   P      + W 
Sbjct: 167 --TEAADRGYLHAYALSFPY-KGETQRFICPPTEG--ELWQ 202


>gi|313142669|ref|ZP_07804862.1| conserved hypothetical protein [Helicobacter canadensis MIT
           98-5491]
 gi|313131700|gb|EFR49317.1| conserved hypothetical protein [Helicobacter canadensis MIT
           98-5491]
          Length = 299

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 61/255 (23%), Positives = 108/255 (42%), Gaps = 39/255 (15%)

Query: 79  KEQKILDSSVNL-TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           ++ K+L+  V +     + +    +YE+    +FNKPA + +       +H    +    
Sbjct: 31  EKNKVLEREVEVWIFKPNSIGLKPIYENEDFALFNKPAQMLIHPKGRFFHH--SLMDEVR 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +  G +  L HR+D+ETSG+++V + + +   L E F   RI+K Y +L+ G      + 
Sbjct: 89  EYFGTEASLIHRIDKETSGLVLVGKHKRSIVELGELFANNRIKKKYLALIKGKMCKTSKI 148

Query: 198 IANW----LLKKSHIGGDYVHVV-------KQNEK--GANYAISHFKVIDCFAQKFCWLE 244
           + ++     L     GGD            +++ K  G   A S F+++  F      L+
Sbjct: 149 VGDFCLLMPLSLQEKGGDLSVRSVFLGQNLRKDSKLLGFRDAKSEFEILGEFGGN-TLLK 207

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----------------------FKGNFTS 282
           + P TGRTHQ+RVH   +G PI+GD  Y                          +     
Sbjct: 208 VYPITGRTHQIRVHLFSLGFPILGDPLYGCEDWQSREYLDSEFIEENRDFGLCAEKRKEY 267

Query: 283 PIQNKLYLHARYMDL 297
              ++L LHA  ++ 
Sbjct: 268 FGADRLMLHAYSLEF 282


>gi|257486202|ref|ZP_05640243.1| RNA pseudouridine synthase family protein [Pseudomonas syringae pv.
           tabaci ATCC 11528]
 gi|330989270|gb|EGH87373.1| pseudouridine synthase [Pseudomonas syringae pv. lachrymans str.
           M301315]
 gi|331010530|gb|EGH90586.1| pseudouridine synthase [Pseudomonas syringae pv. tabaci ATCC 11528]
          Length = 324

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 60/294 (20%), Positives = 106/294 (36%), Gaps = 30/294 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +  G+V   + K +  +   + G  +RI       N        
Sbjct: 58  LCAKFTAISRKQWLDRIARGRVLDENGKAIAPDLAYREG--LRIHYFREVPN-------- 107

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +   G  
Sbjct: 108 --------ETPIPVLETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 157

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  R+I K Y ++   +P      +    
Sbjct: 158 DLVPLHRIDRHTAGLVLFSANRQTRSAYQALFPTRQIDKFYEAIAPALP-----GLEFPR 212

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++   Q + +  + P TG+ HQLRVH   +
Sbjct: 213 LHESRLVEGEPFFRMQEGAGASNTRTQIEVLERQDQLWRYG-LYPVTGKKHQLRVHMAAL 271

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           G  I  D  Y  +   N     QN L L A+ +    P  G+  Q  + L    
Sbjct: 272 GAGICNDPFY-PDVVKNPVDDYQNPLKLLAKGLRFIDPLNGKQRQFESLLELDW 324


>gi|325265762|ref|ZP_08132449.1| RNA pseudouridine synthase [Kingella denitrificans ATCC 33394]
 gi|324982745|gb|EGC18370.1| RNA pseudouridine synthase [Kingella denitrificans ATCC 33394]
          Length = 309

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 56/293 (19%), Positives = 112/293 (38%), Gaps = 30/293 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRIPPVINALN 75
              L  +    +P +     +  L SG V V+   + +  +   Q G+ +      +  +
Sbjct: 31  GQPLLHFLCARFPFVGEAAWKARLNSGMV-VNQHGRPINEHASFQPGETIFYYRETSRES 89

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLK 134
                    +  +   +H       +L+ D  + V +KP  + V   G  +   +   L+
Sbjct: 90  ---------EPRIPFDEH-------ILHIDQHLIVVDKPHFLPVIPSGRFLRETLLTRLR 133

Query: 135 SWVDSKGQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
              D +          HRLD++T+G+++++   A+     + F  + +QK Y +L     
Sbjct: 134 LRADLQHLNVADITPVHRLDKDTAGVMLLSHNPASRAAYQQMFAEKTVQKTYHALAPTRL 193

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 +   L  +S +       + Q   G   A +  ++++         E++P TG+
Sbjct: 194 D-----LPYPLTVQSRLVRGESFFLTQEVDGTPNAQTEIRLLEMHGD-VSLYELKPLTGK 247

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            HQLRVH + +G P++ D  Y  +     T      L L A+ +    P  G 
Sbjct: 248 KHQLRVHMMKLGMPLLNDALY-PDVLPAGTEDYAKPLKLLAKSIGFIDPISGE 299


>gi|289623665|ref|ZP_06456619.1| pseudouridine synthase [Pseudomonas syringae pv. aesculi str.
           NCPPB3681]
          Length = 296

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 61/294 (20%), Positives = 107/294 (36%), Gaps = 30/294 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +  G+V   + K +  +   + G  +RI       N        
Sbjct: 30  LCAKFTAISREQWLDRIARGRVLDENGKAIAPDLAYREG--LRIHYFREVPN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +   G  
Sbjct: 80  --------ETPIPVLETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  +         F  R+I K Y ++   +P      +    
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANQQTRSAYQALFPTRQIDKFYEAIAPALP-----GLEFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++   Q + +  + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGAGASNTRTQIEVLERQDQLWRYG-LYPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           G  I  D  Y A  K N     QN L L A+ +    P  G+  Q  + L    
Sbjct: 244 GAGICNDPFYPAVVK-NPVDDYQNPLKLLAKGLRFIDPLSGKQRQFESLLELDW 296


>gi|262276093|ref|ZP_06053902.1| putative pseudouridine synthase Rlu family protein [Grimontia
           hollisae CIP 101886]
 gi|262219901|gb|EEY71217.1| putative pseudouridine synthase Rlu family protein [Grimontia
           hollisae CIP 101886]
          Length = 223

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 53/199 (26%), Positives = 86/199 (43%), Gaps = 18/199 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++++    V +K  GISV         +    K    +  +K  L HRLD+ TSG+L++
Sbjct: 4   LIFQNDDFLVIDKHPGISVHKDDNDQPLLSEVAK---KTGNEKLYLIHRLDKMTSGLLLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +   AA  L+  F  + +QK Y +L    P  K+  I   + K          + K   
Sbjct: 61  GKHPQAASDLSLMFAEKTVQKFYLALSAKKPGKKQGTIVGDMAK------SRRSMWKLLP 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             +N AI+ F       +       +P+TG+THQ+RV    +G PI+GD  Y        
Sbjct: 115 TKSNPAITQFFS-TAGGEGKRLFLCKPYTGKTHQIRVALKSVGSPILGDSTY-------- 165

Query: 281 TSPIQNKLYLHARYMDLPH 299
                ++ YLHA  +   +
Sbjct: 166 RGADADRGYLHAFALQFTY 184


>gi|163801147|ref|ZP_02195047.1| pseudouridine synthase Rlu family protein [Vibrio sp. AND4]
 gi|159175496|gb|EDP60293.1| pseudouridine synthase Rlu family protein [Vibrio sp. AND4]
          Length = 230

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 101/231 (43%), Gaps = 23/231 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      V NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL+
Sbjct: 3   DILHTQPDFLVINKHPNVSVHKDDGDTMLLQEVAK---QSGDEQLYLIHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R   AA  L+++F  R ++K Y ++    PK K+  +   + +        V+     
Sbjct: 60  LGRNAKAASALSQAFADREVEKFYLAIGSKKPKKKQGLVIGDMERSRRSSWKLVNSKT-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F  +   + +      +PHTG+THQ+RV    +G  IVGDH Y A     
Sbjct: 118 ----NPAITQFFSLAAESGER-LFLCKPHTGKTHQIRVALKSVGSGIVGDHIYNAGNDA- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
                 ++ YLHA  +  P+ +G   +       H      +LG K+ + +
Sbjct: 172 ------DRGYLHAFSLCFPY-QGETHRFVCDPRTH-----KALGIKWHKEI 210


>gi|326492367|dbj|BAK01967.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 346

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/297 (19%), Positives = 117/297 (39%), Gaps = 45/297 (15%)

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
            PV      + K+ ++  +     +   +  + +++ED  + V +KPAG+  +  + ++ 
Sbjct: 54  CPVSPPYPAVSKDVELRRAMTASARSGAYSSAAVVFEDEWLAVVDKPAGVYCE--ALLSA 111

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                  S   S      L +RLD++TSG++V+ +    A  L ++F   +++K Y +L 
Sbjct: 112 LPCSTASSGDPSSKPNLHLANRLDRDTSGLMVITKCNKVAAKLVKAFTEHKVKKTYLALC 171

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG--ANYAI----SHFKVIDCFAQK-- 239
            G     ++        +S  G   V+ +    +      ++    + F+V+    +   
Sbjct: 172 IGYLPAWEKVKVCSGHGRSKHGAWRVYAMSDVGRTLPGGSSVRDMSTKFEVLGTDGKGQY 231

Query: 240 --------------------------------FCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                                             ++   P +GRTHQ+R+H  ++G PI 
Sbjct: 232 REPSNVDIDDIESITVQEKAADQTSNVDVKSHMVFVRAYPQSGRTHQIRLHCQYLGIPIR 291

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           GD KY    + N      +   LHA  +   HP  G  +   APLP+   +   ++G
Sbjct: 292 GDVKYGGVIEWNGVD--CDGHALHAESLSFVHPVTGLPVTFQAPLPSWANEIISTMG 346


>gi|118473504|ref|YP_886109.1| RNA pseudouridine synthase family protein [Mycobacterium smegmatis
           str. MC2 155]
 gi|118174791|gb|ABK75687.1| RNA pseudouridine synthase family protein [Mycobacterium smegmatis
           str. MC2 155]
          Length = 291

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 56/247 (22%), Positives = 92/247 (37%), Gaps = 13/247 (5%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAG 116
           ++++G+V      +   + ++     +    +L    D      +LY D  I V +KP  
Sbjct: 45  KVRAGEVFSRDGTVLDESTVLPPGSHVYLYRDLPDEVDVPFDIPVLYRDDDIVVVDKPHF 104

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           ++     G        ++   +    +    HRLD+ T+G+L+    R         F  
Sbjct: 105 LATMP-RGGHVTQTALVRLRRELDLPELAPAHRLDRLTAGVLLFTVRRELRGAYQTMFAR 163

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
             +QK Y +   G+PK     IA     +S I      +    E G   A ++ + +   
Sbjct: 164 GDVQKTYLAHAEGVPK-----IALPATLRSRIVKHRGRLQAFEEPGEPNAETYVEAV--- 215

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
                   + P TGRTHQLRVH   +G PI GD  Y               L L A+ + 
Sbjct: 216 --GDGLYRLTPRTGRTHQLRVHMASIGLPITGDPFY-PTVIDVAPGDFSRPLQLLAKRLM 272

Query: 297 LPHPEGG 303
              P  G
Sbjct: 273 FDDPVSG 279


>gi|254360710|ref|ZP_04976858.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261496892|ref|ZP_05993260.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|153091280|gb|EDN73254.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261307416|gb|EEY08751.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
          Length = 217

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/214 (27%), Positives = 93/214 (43%), Gaps = 20/214 (9%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             + Y+     + NKP G+SV          +   +       ++  L HRLD+ TSG+L
Sbjct: 5   LPICYQHRDFIIINKPEGLSVHKDEAEIGLTELVARQL---NVKQVWLVHRLDKITSGLL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A  + AA      F   +I K YW+L    PK K+  I   + K  +         K 
Sbjct: 62  ILALNKEAAARFYHLFEQHKIYKTYWALSDKKPKKKQGRIVGDMQKSRN------GAWKL 115

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                N A++ F +            +QP TG+THQLRV    +G PI+GD  Y  +   
Sbjct: 116 CHSKENPAVTQF-ISHSVEDSLRHFILQPKTGKTHQLRVAMKSLGSPILGDKLYSGSQA- 173

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                  +++YLHA  +D  + E  ++ + A LP
Sbjct: 174 -------DRVYLHAYQLDFEY-ENEKISVQA-LP 198


>gi|71009880|ref|XP_758324.1| hypothetical protein UM02177.1 [Ustilago maydis 521]
 gi|46098066|gb|EAK83299.1| hypothetical protein UM02177.1 [Ustilago maydis 521]
          Length = 1096

 Score =  135 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 86/238 (36%), Gaps = 25/238 (10%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
            +  G   V+ K+   +  +  G  +              E  + D  + +    D    
Sbjct: 16  AIHKGICTVNAKKADLHQILGDGDKICNSVHR-------HEPPVTDEPIKIIHRDD---- 64

Query: 100 ILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
                D  I V  KP  I V   G  + + + G L+S  +        T+RLD+ TSGI+
Sbjct: 65  -----DEGILVIVKPGSIPVHAAGRYLRHTLVGLLQS--EHGVDMVYTTNRLDRLTSGIM 117

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V +  +  A  L   F   ++ K Y   V G     +      +L      G     V  
Sbjct: 118 VCSTKKETASRLGAQFAAGQVNKAYVCRVRGKFPQGEVVCKQPILTIDRQSG-----VNI 172

Query: 219 NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                 +  + F  +   A      +  +P TGRTHQ+RVH  ++G PI  D  Y  +
Sbjct: 173 VHPKGKHCETIFVRLSYDASDDSSVVFCRPITGRTHQIRVHVQYLGHPICNDPIYGHD 230


>gi|322791282|gb|EFZ15806.1| hypothetical protein SINV_13849 [Solenopsis invicta]
          Length = 360

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 53/189 (28%), Positives = 85/189 (44%), Gaps = 7/189 (3%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ D  + V NKPA I V       ++   F+ +  +   +  R  HRLD+ TSGI
Sbjct: 10  PITVIHMDEDVVVVNKPASIPVHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDRLTSGI 68

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+  RT   A+ +    R R++ K Y   V G    ++   +  +   S+     + V K
Sbjct: 69  LLFGRTPKKARQMEHQIRNRQVHKQYVCRVEGEFPEEEVICSEPIEVVSY----KIGVCK 124

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +EKG    I+ FK +    +    +  +P TGR HQ+RVH  ++G P+V D  Y     
Sbjct: 125 VSEKG-KDCITRFKRLSYNGKS-SVVLCKPQTGRMHQIRVHLQYLGYPVVNDPLYNHVVF 182

Query: 278 GNFTSPIQN 286
           G       N
Sbjct: 183 GPHKGKGGN 191


>gi|237801044|ref|ZP_04589505.1| pseudouridine synthase [Pseudomonas syringae pv. oryzae str. 1_6]
 gi|331023901|gb|EGI03958.1| pseudouridine synthase [Pseudomonas syringae pv. oryzae str. 1_6]
          Length = 296

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 58/284 (20%), Positives = 104/284 (36%), Gaps = 29/284 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +  G+V   D K +K +   + G  ++I       N        
Sbjct: 30  LCAKFTAISREQWLDRMARGRVLDADGKTIKADLAYREG--LKIHYFREVPN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +   G  
Sbjct: 80  --------ETPIPVLETILYADDHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  RRI K Y ++   +P      +    
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANRQTRAAYQTLFPTRRIDKFYEAIAPALPD-----LEFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +H +V++   Q + +  + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGPGASNTQTHIEVLERQEQLWRYG-LHPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           G  I  D  Y  +   +     +  L L A+ +    P  G  +
Sbjct: 244 GAAICNDPFY-PDVIKDPQDDYRQPLKLLAKRLRFVDPLNGEQR 286


>gi|296271632|ref|YP_003654263.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
 gi|296095807|gb|ADG91757.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
          Length = 300

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 105/270 (38%), Gaps = 36/270 (13%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY------------- 103
            +IQ   V  +    +     I + ++ D + N  K+ D + S L+Y             
Sbjct: 14  EKIQVHLVKNLKIKTSTAQKSISKGRVFDEAFNTLKYGDIIDSDLIYMAQFEGHTRGLKP 73

Query: 104 --EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
             + +   +F KP+GI V   S    +    L       G    L HR+D ETSG+++ A
Sbjct: 74  LFQTNYFAIFEKPSGIVVHPISKNTEYC--LLDEVRYHFGPDANLVHRIDAETSGLIMCA 131

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           + R     L   F  ++ QK Y ++V G  K +   I   + K+    G  +        
Sbjct: 132 KDRDIESKLKLMFEEKKYQKSYLAIVRGHIK-ESVIIDTSIQKEGKNIGVRMAA----GA 186

Query: 222 GANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------ 274
               + +    I    +K    +E  P TGR HQ+RVH   +G PI GD  Y        
Sbjct: 187 EGKKSKTIINPIKYNEKKDLTLIEAIPVTGRQHQIRVHLYSIGHPIFGDPIYGVDDDFAD 246

Query: 275 -------NFKGNFTSPIQNKLYLHARYMDL 297
                  + K        ++L+LHA Y++ 
Sbjct: 247 AYLDRLLDDKRREEVSGSHRLWLHANYLEF 276


>gi|54022650|ref|YP_116892.1| putative RNA pseudouridylate synthase [Nocardia farcinica IFM
           10152]
 gi|54014158|dbj|BAD55528.1| putative RNA pseudouridylate synthase [Nocardia farcinica IFM
           10152]
          Length = 260

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 100/247 (40%), Gaps = 33/247 (13%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  LL ED  +   NKPAGISV G        D  +       G++    HR+D+ TSG+
Sbjct: 10  ERCLLAEDDAVLALNKPAGISVTG-----ERHDTDIVELAAGAGERLFPVHRIDKVTSGL 64

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL----LKKSHIGGDYV 213
           +++A+  AA   LT  F  R  +K Y ++V G     +  I   L      +  I     
Sbjct: 65  VLLAKDLAAHGTLTRQFTKRTAEKAYLAVVAGGGLPDRGVIELPLSVGRKNRVRIAAPRE 124

Query: 214 HVVKQNEK-----------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            +  ++ +               + + F  +   A +     ++P TGR HQ+RVH   +
Sbjct: 125 SIRAEDGRWFVDDADLLAVKNYPSRTEFVTLARTADRTVLA-LRPVTGRRHQIRVHLAWI 183

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPAHMVKTWD 320
           G  IVGD  +         S    + +LH+  + L  P      L +TAP  A     W 
Sbjct: 184 GHAIVGDPLF-------DKSAAHPRAHLHSWRLVLDAPWRTPPELDLTAPPDAGF---WA 233

Query: 321 SLGFKYD 327
            LG   D
Sbjct: 234 PLGAGAD 240


>gi|298369779|ref|ZP_06981096.1| pseudouridine synthase Rlu family protein [Neisseria sp. oral taxon
           014 str. F0314]
 gi|298282336|gb|EFI23824.1| pseudouridine synthase Rlu family protein [Neisseria sp. oral taxon
           014 str. F0314]
          Length = 215

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 59/211 (27%), Positives = 91/211 (43%), Gaps = 18/211 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+ +      +KPAGI+V    G          +       +  LTHRLD+ TSG+L++
Sbjct: 4   ILFRNQDFAAVDKPAGIAVHQEEGADNL---LAMAAAQLNVPRLWLTHRLDKPTSGVLLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    AA  L + F  + ++K Y +L    P  K+  +   + K                
Sbjct: 61  ALNAQAASELAQQFAAKTMRKTYLALSDRRPAKKQGLVKGGMEKSRRGAWKLTR-----G 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            GAN A++ F      A       +QP TG+THQLRV   ++  PI+GD  Y        
Sbjct: 116 DGANLAVTRFHS-QSIAPNLRLFVLQPQTGKTHQLRVAMKNLSSPILGDTLYGGTPAE-- 172

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                 +L+LHA  ++  +  GG   + APL
Sbjct: 173 ------RLFLHAWRLEFEY-RGGAFSVCAPL 196


>gi|255711220|ref|XP_002551893.1| KLTH0B02376p [Lachancea thermotolerans]
 gi|238933271|emb|CAR21455.1| KLTH0B02376p [Lachancea thermotolerans]
          Length = 397

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 56/271 (20%), Positives = 100/271 (36%), Gaps = 21/271 (7%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSG------QVRVDKKRVKFNNRIQSGQVVRIPPVI 71
              LDR   +        N ++    G      Q+  D   +     ++    +R   VI
Sbjct: 28  GRWLDRTLLDVLSDEFRANTKEEYEKGILQKKFQIIRDGAELSVEEVLKG--QIRNKDVI 85

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              +H  +      +    +         +++E   + V +KP+GI +        +   
Sbjct: 86  RTTSHKHEPPVRQWAKEENSGLGWVAGMKVVHECEDLLVIDKPSGIPIHP---TGQYYQN 142

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L   + S G+    +HRLD+ TSG+L++ +    A  +    R R + KIY + V G  
Sbjct: 143 TLVEVLKSHGKTVFPSHRLDKITSGVLILTKNPHMANKIQHQIRQRTMSKIYLARVDGAF 202

Query: 192 K--NKKECIANWLLKKSHIGGDYVHVVKQNEK-------GANYAISHFKVIDCFAQ-KFC 241
              +    +  +         D      + +K           A + F  +  + +    
Sbjct: 203 PMADTLGSLTPFESPDKTQTVDSAIYTVELKKQFPAAFSPPREAKTKFYPLKYYPKSDET 262

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  QP TGRTHQ+R+H   +G PIV D  Y
Sbjct: 263 LVACQPITGRTHQIRIHLARLGHPIVNDPFY 293


>gi|145348517|ref|XP_001418694.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144578924|gb|ABO96987.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 334

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/260 (23%), Positives = 102/260 (39%), Gaps = 45/260 (17%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ------ 142
              K+ D    ++L +   I    KPAG+      G    +     +     GQ      
Sbjct: 89  KRAKNDDEWSMVVLRDSDGIAAVVKPAGVLTHPVEGGGSELTLMDAALSRFDGQLSDLNG 148

Query: 143 --KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
             K  +  RLD+ TSG++++A+  A+   L   F  R + K Y +L+ G         + 
Sbjct: 149 LDKRGIVSRLDKPTSGVVLLAKNNASHAELLTQFYQRCVVKQYCALLDGTLPA-SGSEST 207

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRV 257
            L                       A S ++V++ F   +  +  + ++P +GR HQ+R 
Sbjct: 208 PL-------------------DGRSATSEYEVMETFIGPSWSYSLVRVEPKSGRKHQIRR 248

Query: 258 HALHMGCPIVGDHKY-CANFKGNFTSPIQNKL------------YLHARYMDLP-HPEGG 303
           H   +G P+VGD  Y  A  K    +P +  L            +LHA  ++    P G 
Sbjct: 249 HMALLGAPLVGDPLYRTARTKQINPNPPECVLKALSVGKPGTIFWLHASAVEYSGMPNGE 308

Query: 304 RLQITAPLPAHMVKTWDSLG 323
           R+ ++APLP+       SL 
Sbjct: 309 RIVVSAPLPSAFETLLASLR 328


>gi|323495632|ref|ZP_08100703.1| pseudouridylate synthase, 23S RNA-specific [Vibrio sinaloensis DSM
           21326]
 gi|323319267|gb|EGA72207.1| pseudouridylate synthase, 23S RNA-specific [Vibrio sinaloensis DSM
           21326]
          Length = 231

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 53/198 (26%), Positives = 91/198 (45%), Gaps = 17/198 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y      + NK   +SV    G    +    K    S  ++  L HRLD+ TSG+L+
Sbjct: 3   DIVYTHPDFILINKHPDVSVHKDDGDTMLLAEVAKR---SGDEQLYLIHRLDKMTSGLLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R  A+A  L++ F  R ++K Y ++    PK K+  ++  + +        ++  +  
Sbjct: 60  LGRNAASASELSQLFSAREVEKYYLAIGSKKPKKKQGLVSGDMERSRRSSWKLINSQR-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F+ +     +      +PHTG+THQ+RV    +G PI+GD  Y A     
Sbjct: 118 ----NPAITQFQSLAGEPGQR-LFLCKPHTGKTHQIRVALKSIGSPILGDPIYNA----- 167

Query: 280 FTSPIQNKLYLHARYMDL 297
             S   ++ YLHA  +  
Sbjct: 168 --SSAADRGYLHAFAIRF 183


>gi|146306485|ref|YP_001186950.1| pseudouridine synthase [Pseudomonas mendocina ymp]
 gi|145574686|gb|ABP84218.1| pseudouridine synthase [Pseudomonas mendocina ymp]
          Length = 293

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/291 (20%), Positives = 117/291 (40%), Gaps = 30/291 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
             +H+P I+     + +  G+V   +   +   +  Q G  VR    +     I  E + 
Sbjct: 25  LCDHFPAIDRSTWLQRMERGRVLDAEGAPIGPQHPYQVGLKVRYFREVPNETPIPFEAR- 83

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                            +L++D  + V +KP  + V       Y     L   +   G  
Sbjct: 84  -----------------VLWQDEHLLVADKPHFLPVMPAG--EYVEQTLLARLIKRTGNP 124

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +   ++       FR R ++K Y ++   +P+ +   +    
Sbjct: 125 DLVPIHRIDRLTAGLVLFSVAPSSRGQYQALFRQRAVEKRYEAIAPALPQLQFPHVH--- 181

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            +   + G+    +++    AN + +  +V++   + + +  + P TGR HQLRVH   +
Sbjct: 182 -RSRMVEGEPFFRMQEVAGEAN-SETRIEVLERRGELWRYG-LSPVTGRKHQLRVHLAGL 238

Query: 263 GCPIVGDHKYCANFKG-NFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPL 311
           G PIVGD  Y    +  N        L L AR +    P  G+L +  + L
Sbjct: 239 GAPIVGDDFYPELHESRNQPDDYAKPLKLLARGLRFVDPLSGQLREFESQL 289


>gi|313246104|emb|CBY35058.1| unnamed protein product [Oikopleura dioica]
          Length = 446

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 55/216 (25%), Positives = 98/216 (45%), Gaps = 8/216 (3%)

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLK-SILLYEDSKIYVFNKPAGISVQGGSG 124
            I       N IIK+  ++ +  +  +    +    ++ +  + YV NKP+ + +   + 
Sbjct: 132 EIIHASELKNRIIKDGDMISTKDHRHEPPVRIPLPEVIADTDEFYVVNKPSSLPIHPVA- 190

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             Y  +  +            + HRLD+ TSG+++ A+T+  A+ +++    R +QK Y 
Sbjct: 191 -QYRHNSLIFLISREYKVNYHVIHRLDRLTSGLVIFAKTKEVAKRVSKEISDRVVQKQYL 249

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWL 243
             V G   +K  C  +   K    G   V     +EK    A++ F++++ F +     +
Sbjct: 250 LRVVGKFPDKAVCDKSGTKK----GIYRVAKADDDEKKVKTALTEFELVEYFKEADQSLV 305

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              P TGRTHQ+RVH  ++GCPIV D  Y     G 
Sbjct: 306 RAIPKTGRTHQIRVHTQYLGCPIVNDPVYNDPLFGK 341


>gi|59711627|ref|YP_204403.1| 23S rRNA and tRNA pseudouridine synthase (RluA-like) [Vibrio
           fischeri ES114]
 gi|59479728|gb|AAW85515.1| 23S rRNA and tRNA pseudouridine synthase (RluA-like) [Vibrio
           fischeri ES114]
          Length = 228

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 58/212 (27%), Positives = 92/212 (43%), Gaps = 20/212 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGIL 158
            +LY++S   V NK   +SV    G        L       G K   L HRLD+ TSG+L
Sbjct: 3   DILYQNSDFLVINKHPNVSVHKDDGET----SLLIELAKETGDKQLYLIHRLDKMTSGLL 58

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ R +AAA  L++ F  R ++K Y ++    PK K+  +   + +        V+  + 
Sbjct: 59  LIGRNQAAASELSQLFANRLVEKYYLAIGDKKPKKKQGLVIGDMERSRRASWKLVNSKE- 117

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                N A++ F               +PHTG+THQ+RV    +G  I+GD  Y ++   
Sbjct: 118 -----NPAVTQFFS-TAANDGNRLFLCKPHTGKTHQIRVALKSVGSGILGDPIYSSSNA- 170

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                  ++ YLHA  +   + E     I  P
Sbjct: 171 -------DRGYLHAYALRFTYQEQAFEFIETP 195


>gi|119475020|ref|ZP_01615373.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2143]
 gi|119451223|gb|EAW32456.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2143]
          Length = 297

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 60/292 (20%), Positives = 111/292 (38%), Gaps = 26/292 (8%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           LD +    +P I     Q+ +  G+V   D   ++   R Q+ Q V     +     I  
Sbjct: 23  LD-YLVKKFPRIEPSVWQQRMLDGKVHWHDGSFIRPETRFQAQQRVYYYREVEQETPIP- 80

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                                +L++D  + V +KP  +++  G           +  + +
Sbjct: 81  -----------------FTETILFQDEHLLVAHKPHFLALTPGGVFVNECLQN-RLRLRT 122

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                +  HRLD+ T+G+++ +          + F  R+I+K Y ++       +K    
Sbjct: 123 GIDSLQALHRLDRVTAGLVLFSTNPTTRHLYHQLFSHRQIEKTYHAIAQ-TDSRQKLTTK 181

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            W +K           ++     AN + S  + +     K    E++P TG+THQLRVH 
Sbjct: 182 EWQVKNRLEPSAQRFRMQVVAGEAN-SHSFIRSLRQNGDKA-LFELKPITGKTHQLRVHM 239

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAP 310
             +G PI+ D KY    +       +  L L A+ +    P   ++Q   +P
Sbjct: 240 QTIGWPILND-KYYPRLEQQSADDFEKPLQLLAKQLRFIDPVSQKMQFFESP 290


>gi|242212124|ref|XP_002471897.1| predicted protein [Postia placenta Mad-698-R]
 gi|220728995|gb|EED82877.1| predicted protein [Postia placenta Mad-698-R]
          Length = 435

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 65/313 (20%), Positives = 113/313 (36%), Gaps = 45/313 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
                +   +    +  L SG   ++    K +  +Q+G  +              E  +
Sbjct: 29  VVSTEFRDRSMEYYRYALESGVTTINGTIAKPDTIVQNGDRIENVVHR-------HEPPV 81

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQ 142
             + V +  +           + +  + +KP  I V   G      +   LK+  D   +
Sbjct: 82  TSTPVRIIHY---------DREREFIIIDKPGSIPVHASGRFFRNSLVEILKN--DFGFK 130

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANW 201
           K    +RLD+ TSG++++  + + A  LT+ F    I+K Y +   G  PK +  C    
Sbjct: 131 KVYTINRLDRLTSGLMIIPLSSSMANTLTQEFAAGTIRKEYIARCRGQFPKEELACEVPL 190

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHAL 260
           L     +G + VH           A + FK +   A      +  +P TGR+HQ+RVH  
Sbjct: 191 LTIDRQMGLNVVH------PEGKPAKTIFKRMHYDANTDTSVVHCKPLTGRSHQIRVHLQ 244

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           ++G P+  D  Y              +L      +    P   R    AP P       +
Sbjct: 245 YLGHPVANDPIYSETKIWG------ERLGDGGIDLT---PSEER---AAPAPP------E 286

Query: 321 SLGFKYDRNLYIK 333
            LGF   +N   +
Sbjct: 287 QLGFDPSQNPESE 299


>gi|183602524|ref|ZP_02963889.1| pseudouridine synthase [Bifidobacterium animalis subsp. lactis
           HN019]
 gi|241190598|ref|YP_002967992.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|241196004|ref|YP_002969559.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|183218165|gb|EDT88811.1| pseudouridine synthase [Bifidobacterium animalis subsp. lactis
           HN019]
 gi|240248990|gb|ACS45930.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|240250558|gb|ACS47497.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|295793585|gb|ADG33120.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium animalis
           subsp. lactis V9]
          Length = 242

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 93/237 (39%), Gaps = 19/237 (8%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + +        ++YE+ +I V +KP  ++     G+ Y     ++     +       HR
Sbjct: 2   IEEPHIPFDLTVVYENERIIVVDKPHFLATTP-RGMWYRETALMRLRERYREPNIIPAHR 60

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN------- 200
           LD+ T+GI+V  R  AA       F+  R +K Y   + +  +   +   + +       
Sbjct: 61  LDRPTAGIVVFVRDPAARGAYQMLFQEHRTRKCYECLAPIRPLATPRTGTVVHGSPPRIW 120

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAIS-------HFKVIDCFAQKFCWLEMQPHTGRTH 253
            L+++S I      +  Q   G   A +       H ++            + P TG+TH
Sbjct: 121 PLVRRSRIRKTRGVLCAQEIPGQVNAETAIELEALHARMSARMGMSIGVYRLLPRTGKTH 180

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           QLRVH   +G PIVGD  Y    +          L L AR +    P  G  L+ ++
Sbjct: 181 QLRVHMNSLGLPIVGDDFY-PRIEERAYDDFSQPLQLVARSLAFTDPFTGDPLEFSS 236


>gi|289647117|ref|ZP_06478460.1| pseudouridine synthase [Pseudomonas syringae pv. aesculi str. 2250]
          Length = 324

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/294 (20%), Positives = 107/294 (36%), Gaps = 30/294 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +  G+V   + K +  +   + G  +RI       N        
Sbjct: 58  LCAKFTAISREQWLDRIARGRVLDENGKAIAPDLAYRQG--LRIHYFREVPN-------- 107

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +   G  
Sbjct: 108 --------ETPIPVLETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 157

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  +         F  R+I K Y ++   +P      +    
Sbjct: 158 DLVPLHRIDRHTAGLVLFSANQQTRSAYQALFPTRQIDKFYEAIAPALP-----GLEFPR 212

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++   Q + +  + P TG+ HQLRVH   +
Sbjct: 213 LHESRLVEGEPFFRMQEGAGASNTRTQIEVLERQDQLWRYG-LYPVTGKKHQLRVHMAAL 271

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           G  I  D  Y A  K N     QN L L A+ +    P  G+  Q  + L    
Sbjct: 272 GAGICNDPFYPAVVK-NPVDDYQNPLKLLAKGLRFIDPLSGKQRQFESLLELDW 324


>gi|119945260|ref|YP_942940.1| pseudouridine synthase [Psychromonas ingrahamii 37]
 gi|119863864|gb|ABM03341.1| pseudouridine synthase [Psychromonas ingrahamii 37]
          Length = 303

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 112/284 (39%), Gaps = 28/284 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +    +P+I+    ++ +  G+V   D   V   +  Q  Q +     + +   I     
Sbjct: 25  YLIIKFPYIDARIWRQRITDGKVHYHDGSLVTARSPFQPQQRIYYYREVESEPSIP---- 80

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
                          K  +L++D  I V +KP  ++V  G          L++ +     
Sbjct: 81  --------------FKETILFQDEHILVAHKPHFLAVTPGGKYVNEC---LQNRLRRSTG 123

Query: 142 -QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            +  +  HRLD+ T+G+++ +          + F+ R+I K Y ++   I   +      
Sbjct: 124 IEALQTLHRLDRVTAGLVMFSVNPDTRHRYHQLFKTRQIHKSYQAIAS-ISDAENLTGQE 182

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           W +K   + G+    ++  E  AN + S  + +   + +    E+ P TG+THQLRVH  
Sbjct: 183 WEIKNRIVQGEPRFRMRVTEGEAN-SHSVIRCL-RQSAQTALFELTPVTGKTHQLRVHMQ 240

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +G PI+ D KY    +          L L A+ +    P   +
Sbjct: 241 ALGLPILND-KYYPQLEPLSADNYAAPLQLLAKELQFIDPVTEK 283


>gi|289178336|gb|ADC85582.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           animalis subsp. lactis BB-12]
          Length = 249

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 93/237 (39%), Gaps = 19/237 (8%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + +        ++YE+ +I V +KP  ++     G+ Y     ++     +       HR
Sbjct: 9   IEEPHIPFDLTVVYENERIIVVDKPHFLATTP-RGMWYRETALMRLRERYREPNIIPAHR 67

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN------- 200
           LD+ T+GI+V  R  AA       F+  R +K Y   + +  +   +   + +       
Sbjct: 68  LDRPTAGIVVFVRDPAARGAYQMLFQEHRTRKCYECLAPIRPLATPRTGTVVHGSPPRIW 127

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAIS-------HFKVIDCFAQKFCWLEMQPHTGRTH 253
            L+++S I      +  Q   G   A +       H ++            + P TG+TH
Sbjct: 128 PLVRRSRIRKTRGVLCAQEIPGQVNAETAIELEALHARMSARMGMSIGVYRLLPRTGKTH 187

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           QLRVH   +G PIVGD  Y    +          L L AR +    P  G  L+ ++
Sbjct: 188 QLRVHMNSLGLPIVGDDFY-PRIEERAYDDFSQPLQLVARSLAFTDPFTGDPLEFSS 243


>gi|255073601|ref|XP_002500475.1| predicted protein [Micromonas sp. RCC299]
 gi|226515738|gb|ACO61733.1| predicted protein [Micromonas sp. RCC299]
          Length = 327

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 75/292 (25%), Positives = 113/292 (38%), Gaps = 76/292 (26%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGIS---VQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
              +    S +L+ D+ + V +KPAG+    V G  G+    D FL          P   
Sbjct: 17  APRAASAVSWVLHRDADVLVVDKPAGVPMRSVHGVKGV----DAFLADLRFDLAHPPMTV 72

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRR---------------------IQKIYWSL 186
           HRLD++T+G L++ARTR A + L   F+ R                      ++++YW+L
Sbjct: 73  HRLDRDTTGCLILARTREAQRTLAGYFQDRARVARRGSGRSTKTTSPESLGDVRRVYWAL 132

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC----- 241
           V            +  L  +H G     V  +   GA  A + ++VI   +   C     
Sbjct: 133 VSATSTLASRGTIDAALVTTHAG-----VTLKPGAGAKPAATDYEVISRASPDSCAPTAA 187

Query: 242 -----WLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYCANFKGNFTSPIQN--------- 286
                 L + P TGR HQLRVH    +   IVGD+KY             +         
Sbjct: 188 GRVPAVLALVPRTGRKHQLRVHCAGALDAAIVGDYKYGYRDVSRTGGVADDWRRVLRDID 247

Query: 287 ----------------------KLYLHARYMDLPHP-EGGRLQITAPLPAHM 315
                                  L+LHAR ++  HP  G R+++ AP P+HM
Sbjct: 248 ERSTRRLNDAGTADGEVRGAGVPLHLHARCVEFTHPSSGERVRVVAPAPSHM 299


>gi|6321608|ref|NP_011685.1| Pus6p [Saccharomyces cerevisiae S288c]
 gi|1723726|sp|P53294|PUS6_YEAST RecName: Full=Pseudouridylate synthase 6; AltName:
           Full=Pseudouridine synthase 6; AltName: Full=Uracil
           hydrolyase; AltName: Full=tRNA pseudouridine 31
           synthase; Short=PSI31 synthase
 gi|1323298|emb|CAA97195.1| unnamed protein product [Saccharomyces cerevisiae]
 gi|285812363|tpg|DAA08263.1| TPA: Pus6p [Saccharomyces cerevisiae S288c]
          Length = 404

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 112/280 (40%), Gaps = 29/280 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRV--DKKRVKFNNRIQSGQVVRIPPVINALN 75
              L     + +           +R G  R+  D   +  ++ + +  +++   V+    
Sbjct: 35  GKLLIDVLVSEFKLRPRAYYLDQIRKGTYRLIRDGVPLVPDHLMTT--IIKNHDVLETTT 92

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSIL-----LYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           H  K +  +    +    ++ L   +     ++ED  I V +KP+GI V           
Sbjct: 93  H--KHEPPVKQWCSQEVEAEDLPGRIAGFNIVFEDESILVIDKPSGIPVHPTGQF---YQ 147

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             +   +   G      +RLD+ TSG+L++A+   +A  + +S R R + KIY + V G 
Sbjct: 148 NTITELLKLHGVDALPCYRLDKITSGLLILAKNSQSAGEIQKSIRSRDMIKIYLARVKGR 207

Query: 191 PKNKKECIANW-------------LLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + +  + N               ++ + I   D           +  AI+ F  I  F
Sbjct: 208 FPHSELILDNENAAETTFEDTSKVTVEMTPIYSIDPKRQFPVGLSTSKDAITKFYPIRYF 267

Query: 237 AQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +      +  +P TGRTHQ+R+H   +G PIV D  YC++
Sbjct: 268 SHADETVVACKPITGRTHQIRIHLARLGHPIVNDSVYCSH 307


>gi|163749894|ref|ZP_02157139.1| hypothetical protein KT99_02081 [Shewanella benthica KT99]
 gi|161330408|gb|EDQ01387.1| hypothetical protein KT99_02081 [Shewanella benthica KT99]
          Length = 224

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 95/237 (40%), Gaps = 33/237 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ ++    V  K A +      G A    G +         K    HRLD  TSG+L+ 
Sbjct: 4   IVADEDDFLVITKSANVHFHSQDGSA----GVMARLEQDLTIKLYSVHRLDSLTSGLLLF 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA   TE F   ++QK Y +L  G PK K+  +   + K          + K   
Sbjct: 60  AKSSRAAAEFTELFTQHKVQKYYVALAKGKPKKKQGWVVGDMAK------SRRSMYKLLR 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F      A+      ++P +G+THQLRV    +G PI+GD  Y        
Sbjct: 114 TTKNPALTQFFS-QSVAEGLRLYLLKPLSGKTHQLRVALASIGVPILGDKLYGGAE---- 168

Query: 281 TSPIQNKLYLHARYMDL----------PHPEGGRLQITAPLPAHMVKTW---DSLGF 324
                ++ YLHA  +             +P  G  + TA      ++ W   + LG+
Sbjct: 169 ----SDRGYLHAFSLSFSFRAKDYRYLNYPSQGE-EFTAADTIKQLQIWSEPEKLGW 220


>gi|323342979|ref|ZP_08083210.1| ribosomal large subunit pseudouridine synthase [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322463043|gb|EFY08238.1| ribosomal large subunit pseudouridine synthase [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 218

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 55/222 (24%), Positives = 92/222 (41%), Gaps = 17/222 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           + YED+ + V  K      QG       +   +K ++  K  KP      L HRLD+   
Sbjct: 3   IFYEDNHVIVVEKKPNQPSQGDESNDLDLLTEVKEYIKVKYDKPGNVYVGLVHRLDRPVG 62

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           GI+V A+T  AA  L++  R R + K Y ++  G  +       + ++K       Y  V
Sbjct: 63  GIMVFAKTSKAAGRLSDQVRTRTLDKTYTAVCTGYVEP--TTFRDTMVKNRKTNTSY--V 118

Query: 216 VKQNEKGANYAISH-FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V +N     YA  H  +           ++++  TGR+HQ+RV     G  + GD +Y  
Sbjct: 119 VDKNHPDGKYAELHIIEAYYHPTDNLSTVKIKLVTGRSHQIRVQFASRGNALWGDARYNK 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHM 315
           + +         ++ L A  +   HP    R+  T+  P+  
Sbjct: 179 HSQPG------QQIALWATELSFDHPITKERMTFTSHTPSKF 214


>gi|10952457|gb|AAG24942.1|AF128845_1 RluD [Sinorhizobium meliloti]
          Length = 163

 Score =  133 bits (336), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 44/161 (27%), Positives = 74/161 (45%), Gaps = 18/161 (11%)

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           +++ Y ++VWG P+  K  I   L +          V +++   A  AI+H++V++ + +
Sbjct: 1   LERAYRAVVWGRPRQLKGKIDAPLGRAG--DRTKRAVKREDSDDAREAITHYEVVERYHE 58

Query: 239 K------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ------- 285
           K         +E    TGRTHQ+RVH  H+G P++GD  Y A F+       +       
Sbjct: 59  KPDGTSLASTVECHLETGRTHQIRVHMAHIGHPLIGDPDYGAAFRTKANLLPEPARAAVN 118

Query: 286 --NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
              +  LHA  +   HP  G  +    P+PA M +   +L 
Sbjct: 119 RFPRQALHAFMLQFEHPATGETMHFETPVPADMQELIAALR 159


>gi|308810719|ref|XP_003082668.1| COG0564: Pseudouridylate synthases, 23S RNA-specific (ISS)
           [Ostreococcus tauri]
 gi|116061137|emb|CAL56525.1| COG0564: Pseudouridylate synthases, 23S RNA-specific (ISS)
           [Ostreococcus tauri]
          Length = 390

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 69/304 (22%), Positives = 127/304 (41%), Gaps = 42/304 (13%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHI--NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           + VVV++  +   + R      P       + ++  R   +  + + V   +R+ SG V+
Sbjct: 28  ETVVVDDARDGDTVSRTLAVMLPKTFPTATSAKRACRRKTIARNGEIVGSGDRVASGDVL 87

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GGSG 124
            +      L   +   +     + L K     K ++LYED+   +  KP   +    GSG
Sbjct: 88  EV------LTRNVP-GRGARGELGLEKERGARKMVVLYEDAHAAIAVKPDDCATIGPGSG 140

Query: 125 IAYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
             +  +  L    +          KP+  HRLD+ T GILV A+TR     L+ +F  R 
Sbjct: 141 GGWSAERMLAISCEVSAADFGVLTKPKPCHRLDEPTGGILVCAKTREGLTTLSSAFASRE 200

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFA 237
           ++K Y +++ G  +     +   +                       A + + V +   +
Sbjct: 201 VKKRYRAILRGRLEKTSGVVDAPV-------------------SGRDASTEYAVVLTRES 241

Query: 238 QKF---CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
           +++     ++  P TGRTHQLR H++ +G PI+GD +Y   F  +   P  + L+L A  
Sbjct: 242 ERYGTLTLVDFFPRTGRTHQLRRHSVALGAPILGDVRYG-RFGKDEAHP--DGLFLWAVG 298

Query: 295 MDLP 298
           + +P
Sbjct: 299 VVIP 302


>gi|298486671|ref|ZP_07004728.1| RNA pseudouridylate synthase [Pseudomonas savastanoi pv. savastanoi
           NCPPB 3335]
 gi|298158754|gb|EFH99817.1| RNA pseudouridylate synthase [Pseudomonas savastanoi pv. savastanoi
           NCPPB 3335]
          Length = 296

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 61/294 (20%), Positives = 107/294 (36%), Gaps = 30/294 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +  G+V   + K +  +   + G  +RI       N        
Sbjct: 30  LCAKFTVISREQWLDRIARGRVLDENGKAIAPDLAYREG--LRIHYFREVPN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +   G  
Sbjct: 80  --------ETPIPVLETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  +         F  R+I K Y ++   +P      +    
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANQQTRSAYQALFPTRQIDKFYEAIAPALP-----GLEFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++   Q + +  + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGAGASNTRTQIEVLERQDQLWRYG-LYPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           G  I  D  Y A  K N     QN L L A+ +    P  G+  Q  + L    
Sbjct: 244 GAGICNDPFYPAVVK-NPVDDYQNPLKLLAKGLRFIDPLSGKQRQFESLLELDW 296


>gi|237753351|ref|ZP_04583831.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           winghamensis ATCC BAA-430]
 gi|229375618|gb|EEO25709.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           winghamensis ATCC BAA-430]
          Length = 312

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 63/322 (19%), Positives = 115/322 (35%), Gaps = 69/322 (21%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
           +++  + Q+ +  G+VR   K ++   ++ +   V++                      L
Sbjct: 5   NLSMSDAQRYINKGKVRYQGKVLQEKAKVLN-DCVQV----------------------L 41

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
               D +    L+E+    +FNKP+ + +       +H    +     S G K  L HR+
Sbjct: 42  IFQPDSIGLKPLFENEDFAIFNKPSKMLIHPKGRFEHH--SLIDEVRASLGLKASLAHRI 99

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-----KKECIANWLLKK 205
           D+ETSG+++V + + +   L   F    I+K Y +L            K  C++  +  +
Sbjct: 100 DRETSGLVLVGKHKKSISELGLMFLNNSIKKEYLALTRAKVGIQNVNFKDFCLSLPIAIQ 159

Query: 206 SHIG---------GDYVHVVKQNEKGANYAISHFKVIDCFAQ-----KFCWLEMQPHTGR 251
              G          +     K        A S F+++          KF   ++ P TGR
Sbjct: 160 EKGGDLCVRSVSLKNAQMCQKFRNLKFKEAKSEFEILGILENTYKNVKFLLFKVLPKTGR 219

Query: 252 THQLRVHALHMGCPIVGDHKYCANF------------------------KGNFTSPIQNK 287
           THQ+RVH   +G PI+GD  Y                            +         +
Sbjct: 220 THQIRVHLDALGYPILGDPLYGVKDVHSREYLDGEFIMQKLESKNALSNEKRLEYFGATR 279

Query: 288 LYLHARYMDLPHPEGGRLQITA 309
           L LHA  +   + +G      +
Sbjct: 280 LMLHAYGLKFVY-KGKEFAFRS 300


>gi|193077696|gb|ABO12544.2| putative pseudouridylate synthase [Acinetobacter baumannii ATCC
           17978]
          Length = 302

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 54/296 (18%), Positives = 111/296 (37%), Gaps = 29/296 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             + ++   ++PHI     Q+  + G + V + +++  N+   +   +     +    H+
Sbjct: 29  QTIYQFLCENFPHIKATEWQQRFQDGLIYVANGEKLTLNSPYIANTHIFYYRFLANEVHV 88

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E +                  +L+E+  + V +KP  +++       Y  +  L    
Sbjct: 89  PFEHQ------------------ILFENDDLLVVDKPHFLTISPTG--QYVQETLLVRLK 128

Query: 138 DSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              G +     HRLD+ET+G+++  +   +     + F  R++ KIY ++     + K  
Sbjct: 129 KQTGNEFLTPIHRLDRETAGVVLFCKRPQSRGIYQQLFADRQVNKIYHAIAAYKAELKF- 187

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 LK     G   + ++          +  ++I+       +  + P TG+ HQLR
Sbjct: 188 ---PQNLKLYLDKGTPFYTMQVIAHTKTNTETKIELIEHNHSWAKYC-LTPTTGKQHQLR 243

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
           VH  H+G PI  D  Y    +          L L A+ +    P     +   + L
Sbjct: 244 VHLNHLGIPIKNDPFY-PIVQHKADDDFSQPLQLLAKQISFIDPLTKQEMVFNSQL 298


>gi|254779038|ref|YP_003057143.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
 gi|254000949|emb|CAX28893.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
          Length = 298

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 69/293 (23%), Positives = 118/293 (40%), Gaps = 29/293 (9%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q VR   +I  +  +I                +     
Sbjct: 28  LKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVRLI------------HFKPNEKTQA 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KPA +      G  YH +  L        +     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPAQVYTHP-KGYFYH-ESLLDCIQSHFSKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  + + L   F  ++++K Y +L  G+ + K   I   +L   +I  D     K + 
Sbjct: 129 GKTLQSVKDLKALFMQKKVKKTYLALAHGLVE-KSMKIDKPILTPQNIQKDLRIRSKIS- 186

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                +I+  + +          L++ P TGRTHQ+R+H   +   IVG+  Y    +  
Sbjct: 187 PLGKPSITLVEPLSYNPFLDISLLKIIPLTGRTHQIRLHLSSINHRIVGEGLYGVADENA 246

Query: 280 FTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                  +      L LHA  ++    +G   +I +P+P   +     L   Y
Sbjct: 247 REYLQLKRKNNAPLLMLHAASLEFEF-KGAIYKIASPMPERFMPFLKDLPLFY 298


>gi|256824745|ref|YP_003148705.1| 23S RNA-specific pseudouridylate synthase [Kytococcus sedentarius
           DSM 20547]
 gi|256688138|gb|ACV05940.1| 23S RNA-specific pseudouridylate synthase [Kytococcus sedentarius
           DSM 20547]
          Length = 316

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 66/284 (23%), Positives = 109/284 (38%), Gaps = 34/284 (11%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           + +G+V VD         +       +P         +      +  V            
Sbjct: 35  VEAGEVVVDDGVPGSRGLVVDATTEYLPTGPRRRVAWLYRPYPTEPEVP-------GGLP 87

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L  D    V +KP  ++         H+   + + V     +    HRLD+ TSG+L+ 
Sbjct: 88  VLQADEHCVVVDKPPFLATIPR---GVHVQQTVVARVREDFPEAVPVHRLDRLTSGVLLC 144

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE---------------CIANWLLK- 204
           ART  A + L + F  R++ K Y +LV   P+                    +   + + 
Sbjct: 145 ARTPEARRPLQQLFEKRQVAKTYEALVSLPPEEAAGAFSVSPGVEGLGLAERVERAIGEQ 204

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMG 263
           + H+             G   A++  +V++   A     L + PHTGRTHQLRV   H+G
Sbjct: 205 EHHLVKKRGSQQVVVVPGPPNALTRIEVVEVDEATGRARLRLFPHTGRTHQLRVQLAHLG 264

Query: 264 CPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            PIVGD  Y        G+F++P+Q    L A  ++   P  G+
Sbjct: 265 LPIVGDPLYPVQTEQVTGDFSTPLQ----LLATRLEWTDPWTGK 304


>gi|52425225|ref|YP_088362.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52307277|gb|AAU37777.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 217

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 59/213 (27%), Positives = 100/213 (46%), Gaps = 18/213 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++++     + +KP G+SV         + G L   +     +  L HRLD+ TSG+L++
Sbjct: 6   IIHKHRDFIIIDKPNGVSVHRDEA-EIGLTGLLAKQL--SVAQVWLVHRLDKVTSGLLIL 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A   +  F    I K Y +L    PK K+  I   + +K+  G   +   KQN 
Sbjct: 63  ALNERSAAEFSLLFARHEISKTYLALSKQKPKKKQGLIIGDM-EKARRGAWKLCQTKQN- 120

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A++ F+ + C         ++P TG+THQLRV    +G PI+GD  Y  N + N 
Sbjct: 121 ----PAVTRFESVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDELYGGNSEKN- 174

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
                ++ YLHA  ++  + +G   ++ + LP 
Sbjct: 175 -----DRTYLHAFRLEFTY-QGEPFRVQS-LPQ 200


>gi|198425133|ref|XP_002130987.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4 [Ciona intestinalis]
          Length = 494

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 61/254 (24%), Positives = 109/254 (42%), Gaps = 34/254 (13%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----SKGQKPR 145
            + +  L+  ++Y D+K+ +FNKP G+ +  G G    +   L          +      
Sbjct: 154 VRLTKLLRKNVIYADNKLVIFNKPYGLPMHDGDGTKQTVKNVLPFLSKMVYGINTDIPLH 213

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L HRLD+ T+GI + +     A ++   FR RR+ + Y ++V G P+  K  +   + + 
Sbjct: 214 LCHRLDKNTTGITICSTDAEMADYVMGLFRQRRVLRKYLAVVVGEPEPMKGVVDMPMSES 273

Query: 206 -----SHIGGDYVHVVKQNEK--------------GANYAISHFKVIDCFAQKFCWLEMQ 246
                         ++K + +              G + AI+H++ ID        +E+Q
Sbjct: 274 IVSATKSTKRHSRMIIKPDVRYDDATGKEYPLRNAGGHTAITHYRTIDTTGD-LSLVELQ 332

Query: 247 PHTGRTHQLRVHAL-HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           P T   HQLRVH    + CPI+GDHKY   +       +  ++    R  ++PH +   +
Sbjct: 333 PQTTVKHQLRVHMADGLSCPILGDHKYS-RYGSLAPQVLPPRVL---RMFNIPHSKSRYM 388

Query: 306 QITAPLPAHMVKTW 319
               PL  H+ +  
Sbjct: 389 ----PLHLHLQQVL 398


>gi|197117718|ref|YP_002138145.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
 gi|197087078|gb|ACH38349.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
          Length = 293

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 63/291 (21%), Positives = 119/291 (40%), Gaps = 28/291 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +P ++    ++ +  G+V               G+     P+ +A ++  ++
Sbjct: 23  LD-FLVGRFPKVSRSCWERRIAQGKVL--------------GE--DGTPITSASSYAPQK 65

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +      +   K   F +  +L+++ ++ V  KP  + V  G    Y     L    +S 
Sbjct: 66  RIFYFREIENEKVIPFAEE-ILFQNDELLVACKPHFLPVTPGG--EYLSQSLLHRLREST 122

Query: 141 GQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           G       HR+D+ET+GI++ +          E FR   I+K Y ++     +  +   A
Sbjct: 123 GIHDLVPLHRIDRETAGIVLFSANPKTRGRYGELFREGSIEKSYEAISAAPVEPGQ---A 179

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            WL++   + G+      + E+G   A S  ++++         ++ P TG+THQLRVH 
Sbjct: 180 EWLVENRLVHGEP-WFTMRTEQGPPNARSLIRLVEQR-DGAARFQLTPVTGKTHQLRVHM 237

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
             +G  I+ D  Y    +          L L AR +    P  GR L+  +
Sbjct: 238 SGLGLQILHDRLY-PQLQPQQPDDFDRPLQLLARRVRFRDPLSGRLLEFES 287


>gi|269963462|ref|ZP_06177789.1| pseudouridine synthase Rlu family protein [Vibrio harveyi 1DA3]
 gi|269831862|gb|EEZ85994.1| pseudouridine synthase Rlu family protein [Vibrio harveyi 1DA3]
          Length = 230

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 60/227 (26%), Positives = 99/227 (43%), Gaps = 23/227 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL+
Sbjct: 3   DILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAK---QSGDEQLYLIHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R   AA  L+++F  R ++K Y ++    PK K+  +   + +        V+     
Sbjct: 60  LGRNAKAASALSQAFADREVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLVNSKT-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F  +     +      +PHTG+THQ+RV    +G  IVGD  Y A  +  
Sbjct: 118 ----NPAITQFFSLAAEPGER-LFLCKPHTGKTHQIRVALKSVGSGIVGDPIYNAGNEA- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                 ++ YLHA  +  P+ +     I  P      + + +LG K+
Sbjct: 172 ------DRGYLHAFSLCFPYQDETHCFICDP------REYKALGSKW 206


>gi|151943445|gb|EDN61756.1| pseudouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|190406816|gb|EDV10083.1| conserved hypothetical protein [Saccharomyces cerevisiae RM11-1a]
 gi|323333566|gb|EGA74960.1| Pus6p [Saccharomyces cerevisiae AWRI796]
          Length = 404

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 112/280 (40%), Gaps = 29/280 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRV--DKKRVKFNNRIQSGQVVRIPPVINALN 75
              L     + +           +R G  R+  D   +  ++ + +  +++   V+    
Sbjct: 35  GKLLIDVLVSEFKLRPRAYYLDQIRKGTYRLIRDGVPLVPDHLMTT--IIKNHDVLETTT 92

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSIL-----LYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           H  K +  +    +    ++ L   +     ++ED  I V +KP+GI V           
Sbjct: 93  H--KHEPPVKQWCSQEVEAEDLPGRIAGFNIVFEDESILVIDKPSGIPVHPTGQF---YQ 147

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             +   +   G      +RLD+ TSG+L++A+   +A  + +S R R + KIY + V G 
Sbjct: 148 NTITELLKLHGVDALPCYRLDKITSGLLILAKNSQSAGEIQKSIRSRDMIKIYLARVKGR 207

Query: 191 PKNKKECIANW-------------LLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + +  + N               ++ + I   D           +  AI+ F  I  F
Sbjct: 208 FPHSELILDNENAAETTFEDTSKVTVEMTPIYSIDPKRQFPVGLSASKDAITKFYPIRYF 267

Query: 237 AQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +      +  +P TGRTHQ+R+H   +G PIV D  YC++
Sbjct: 268 SHADETVVACKPITGRTHQIRIHLARLGHPIVNDSVYCSH 307


>gi|330888288|gb|EGH20949.1| pseudouridine synthase [Pseudomonas syringae pv. mori str. 301020]
          Length = 324

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 59/294 (20%), Positives = 105/294 (35%), Gaps = 30/294 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +  G+V   + K +  +   + G  +RI       N        
Sbjct: 58  LCAKFTAISREQWLDRIACGRVLDENGKAIAPDLAYREG--LRIHYFREVPN-------- 107

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  +   +KP  + V       Y     L+  +   G  
Sbjct: 108 --------ETPIPVLETILYADEHLVGADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 157

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  R+I K Y ++   +P      +    
Sbjct: 158 DLVPLHRIDRHTAGLVLFSANRQTRSAYQALFPTRQIDKFYEAIAPALP-----GLEFPR 212

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++   Q + +  + P TG+ HQLRVH   +
Sbjct: 213 LHESRLVEGEPFFRMQEGAGASNTRTQIEVLERQDQLWRYG-LYPVTGKKHQLRVHMAAL 271

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           G  I  D  Y  +   N     QN L L A+ +    P  G+  Q  + L    
Sbjct: 272 GAGICNDPFY-PDVVKNPVDDYQNPLKLLAKGLRFIDPLSGKQRQFESLLELDW 324


>gi|242083792|ref|XP_002442321.1| hypothetical protein SORBIDRAFT_08g018120 [Sorghum bicolor]
 gi|241943014|gb|EES16159.1| hypothetical protein SORBIDRAFT_08g018120 [Sorghum bicolor]
          Length = 315

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 56/267 (20%), Positives = 102/267 (38%), Gaps = 50/267 (18%)

Query: 100 ILLYEDSKIYVFNKPAG------ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +++ED  + V +KPAG      ++    S ++      L     +K     L +RLD++
Sbjct: 48  DVVFEDEWLAVVDKPAGVYCDAFLTSLPSSVVSGKYFLRLAEDPATK-PNLHLANRLDRD 106

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V+ +    A  L ++F   +++K Y +L  G P   ++        +S  G   V
Sbjct: 107 TSGLMVITKCNKVAGKLVKAFTDHKVKKTYLALCIGCPPTWEKIKICSGHGRSKHGAWRV 166

Query: 214 HVVKQNEKG------ANYAISHFKVIDCFAQK---------------------------- 239
           + +    +            + F+V+    +                             
Sbjct: 167 YAMSDVGRSLPGGSVVRDMSTQFEVLGVNGKCQFREPYNFDTDDIESITVQEKAADQTCS 226

Query: 240 ------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                    +   P +GRTHQ+R+H  ++G PI GD KY    + N      +   LHA 
Sbjct: 227 GDVNNSAILVRAYPQSGRTHQIRLHCQYLGFPIRGDVKYGGVIEWNGVE--CDGHALHAE 284

Query: 294 YMDLPHPEGG-RLQITAPLPAHMVKTW 319
            +   HP  G  +   +PLP+   +  
Sbjct: 285 SLSFVHPITGLPITFRSPLPSWAKECI 311


>gi|183234131|ref|XP_648993.2| hypothetical protein [Entamoeba histolytica HM-1:IMSS]
 gi|169801245|gb|EAL43600.2| hypothetical protein, conserved [Entamoeba histolytica HM-1:IMSS]
          Length = 402

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 92/244 (37%), Gaps = 26/244 (10%)

Query: 35  VNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
             ++K +  G ++++ K ++ +  I     +      +                      
Sbjct: 101 TTIKK-IEKGLIKINNKIIEPSTIIHHHDEIEHQVHRH------------------EPPV 141

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
              K  ++ E +     +KP+ I V       Y  +  +           R  HRLD+ T
Sbjct: 142 YCDKLTIVKETNDFIAIDKPSSIPVHPCG--RYRHNTVIFILAHEGYTNLRPVHRLDRMT 199

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGIL++A+T  AA+       +++ +  Y   V G  + +K  + + + +K         
Sbjct: 200 SGILLLAKTIQAAREFQSYMTIKKKE--YLCRVRG--RLEKTTVTSKIGRKRIDDKKIHV 255

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH-TGRTHQLRVHALHMGCPIVGDHKYC 273
            V + E+      S F  +    +    + +    +GRTHQ+RVH   +  PIV D  Y 
Sbjct: 256 SVNEIEEDGKECHSEFNPLFYDEKTNTTVAVALLGSGRTHQIRVHLQSIHHPIVNDPIYA 315

Query: 274 ANFK 277
           A F 
Sbjct: 316 AQFD 319


>gi|319955825|ref|YP_004167088.1| pseudouridine synthase [Nitratifractor salsuginis DSM 16511]
 gi|319418229|gb|ADV45339.1| pseudouridine synthase [Nitratifractor salsuginis DSM 16511]
          Length = 324

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 63/321 (19%), Positives = 114/321 (35%), Gaps = 47/321 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           W    +  I     Q+I+  G++    + +   +   SG+V  +     +  +       
Sbjct: 19  WLMRTF-GITQGEAQRIIDRGRLLCRGETLPDKSARISGEVEVVYFEPQSRGNAP----- 72

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                             +      Y+F+KP+G+ V             L       GQ 
Sbjct: 73  ------------------IVTTPDFYLFDKPSGVLVHPKK--MTTPYSMLDEVRFHGGQH 112

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HR+D+ETSG+L+ +R + + + L  +F  + IQK Y +   G  +      A  +L
Sbjct: 113 ANAVHRIDKETSGLLLASRHKESERFLKGAFERKAIQKSYRAWATGRIEEPFSVDAPIIL 172

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
              +    +   +    +    A + F  I    +     LE  PHTGRTHQ+R+H  H+
Sbjct: 173 NNDYGPTKHKVFI---HREGKRAYTTFLPIQYDERLDATLLECIPHTGRTHQIRIHLFHV 229

Query: 263 GCPIVGDHKYCANF-------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
             PI+GD  Y  ++             +        ++L LHA  +D  +    +     
Sbjct: 230 KHPILGDPIYGPSYEIAEAYLEERLSSEQRLKYTGASRLMLHAYSLDFHY----KQHWKL 285

Query: 310 PLPAHMVKTWDSLGFKYDRNL 330
             P    +    +    +R  
Sbjct: 286 YSPDDFSQAKTEIALPREREF 306


>gi|301156426|emb|CBW15897.1| unnamed protein product [Haemophilus parainfluenzae T3T1]
          Length = 229

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 56/203 (27%), Positives = 87/203 (42%), Gaps = 16/203 (7%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            +K  ++Y+     +  KP GISV              +        +  L HRLD+ TS
Sbjct: 4   LMKLDIIYQTDDFIIIYKPCGISVHKDQSKIGLTTLLARQL---NVPQVWLVHRLDKVTS 60

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++A    +A      F    IQK Y +L    PK K+  +   + K +  G   +  
Sbjct: 61  GLLILALNAESAAEFFRLFSEHHIQKTYLALSNQKPKKKQGLLVGDMQK-ARNGAWKLCQ 119

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            K+N      AI+ F+ + C         ++P TG+THQLRV    +G PI+GD  Y  N
Sbjct: 120 SKEN-----PAITRFESVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDALYGKN 173

Query: 276 FKGNFTSPIQNKLYLHARYMDLP 298
            +        ++ YLHA  +   
Sbjct: 174 TEK------IDRTYLHAARLQFE 190


>gi|293392235|ref|ZP_06636569.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952769|gb|EFE02888.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 225

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 60/198 (30%), Positives = 88/198 (44%), Gaps = 20/198 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           ++++     V NKP GISV           G  +      G  +  L HRLD+ TSG+L+
Sbjct: 5   IVFQHPDFIVINKPTGISVHKDDAD----IGLTRLVAQQLGVPQVWLVHRLDKVTSGLLM 60

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A     A  L++ F   +IQK Y +L    PK K+  I+  + K            K  
Sbjct: 61  LALNEQTAVTLSQKFAHHQIQKTYLALTTHKPKKKQGRISGDMQKA------RRGAWKLT 114

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +   N A++ F V    A       +QP TG+THQLRV    +G PI+GD  YC +    
Sbjct: 115 QSKENPAVTDF-VSRSLAPNLRLFILQPKTGKTHQLRVAMKSLGSPILGDALYCGDSA-- 171

Query: 280 FTSPIQNKLYLHARYMDL 297
                 ++ YLHA  +  
Sbjct: 172 ------DRTYLHAYQLSF 183


>gi|15644975|ref|NP_207145.1| hypothetical protein HP0347 [Helicobacter pylori 26695]
 gi|3915350|sp|O25114|Y347_HELPY RecName: Full=Uncharacterized RNA pseudouridine synthase HP_0347;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2313436|gb|AAD07404.1| conserved hypothetical protein [Helicobacter pylori 26695]
          Length = 298

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 71/300 (23%), Positives = 123/300 (41%), Gaps = 29/300 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----QAVRKSQIIQGVVRLI------------HFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +     L++E     VF+KP  +      G  YH +  L       G+     HRLD E
Sbjct: 64  PNEKTQALVFETKDFGVFDKPHQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  + + L   F  ++++K Y +L  G+ + K   I   +L   +I  D +
Sbjct: 122 TSGLVLAGKTLQSVKDLKALFMQKKVKKTYLALAHGLVE-KSMKIDKPILTPQNIQKD-L 179

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           H+  +       +I+  + +          L++ P TGRTHQ+R+H   +   IVG+  Y
Sbjct: 180 HIRSKISPLGKQSITLVEPLSYNPFLDISLLKITPLTGRTHQIRLHLSSVDHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
               +         +      L LHA  ++    +G   +I +P+P   +     L F Y
Sbjct: 240 GVADENAREYLQLKRENNAPLLMLHAASLEFEF-KGAIYKIASPMPERFMPFLKDLSFFY 298


>gi|269468780|gb|EEZ80384.1| pseudouridylate synthase, 23S RNA-specific [uncultured SUP05
           cluster bacterium]
          Length = 277

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 71/285 (24%), Positives = 119/285 (41%), Gaps = 44/285 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D    +  P ++   L+  +  G V +  KR K  NR++    V+ P  I     +   
Sbjct: 22  ID-AISSQLP-LSKQVLKSAMDKGCVWL--KRGKKINRLR---RVKKPLNIGDKVFVYFN 74

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +KIL S  +        +  LL + +   V+ KPAG+  QG     +     L   V+ K
Sbjct: 75  EKILSSVAS--------QPQLLLDKNDYSVWFKPAGVFSQGSKWGDHC---ALTRLVEKK 123

Query: 141 GQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             +P  L HRLD+ TSG++++A T+  A+ L++ F  R I K Y ++V G    +K  + 
Sbjct: 124 LDRPTFLVHRLDRATSGLMLIAHTKNMARDLSKMFADRNIDKTYLAIVEGKFTKEKITLE 183

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             +                       A+SH  +++   +    L+++  TGR HQ+R H 
Sbjct: 184 KPI-------------------DGKNAVSHVTLLES-EKFKSLLKVKIETGRKHQIRKHL 223

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                PI+GD  Y    K +        L L A  +    P   +
Sbjct: 224 SEFSHPIIGDRLYGNAAKNHPED-----LQLQAIQLIFNCPIDKQ 263


>gi|113968627|ref|YP_732420.1| pseudouridine synthase Rlu family protein [Shewanella sp. MR-4]
 gi|113883311|gb|ABI37363.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           sp. MR-4]
          Length = 228

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 60/205 (29%), Positives = 93/205 (45%), Gaps = 21/205 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++ +++   V +K   +      G A    G +       G K    HRLD  TSG+L+
Sbjct: 3   RIIADEADFLVISKSPNVHFHSQDGTA----GVVAQLEQDLGIKLFAVHRLDTPTSGLLL 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+  AAA+ LTE FR  R+QK Y +L  G PK K+  +   + K          + K  
Sbjct: 59  LAKHPAAARQLTELFRAHRVQKYYLALAKGKPKKKQGWVIGDMAK------SRRSMFKLL 112

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F              ++PH+G+THQLRV    +G PI+GD  Y ++    
Sbjct: 113 RTKENPAITQFFS-TSVGDGLRLYLLKPHSGKTHQLRVALASLGVPILGDALYGSD---- 167

Query: 280 FTSPIQNKLYLHARYMDL--PHPEG 302
               + ++ YLHA  +     H +G
Sbjct: 168 ----MADRCYLHAYCLHFRYQHEDG 188


>gi|256272036|gb|EEU07049.1| Pus6p [Saccharomyces cerevisiae JAY291]
          Length = 404

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 112/280 (40%), Gaps = 29/280 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRV--DKKRVKFNNRIQSGQVVRIPPVINALN 75
              L     + +           +R G  R+  D   +  ++ + +  +++   V+    
Sbjct: 35  GKLLIDVLVSEFKLRPRAYYLDQIRKGTYRLIRDGVPLVPDHLMTT--IIKNHDVLETTT 92

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSIL-----LYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           H  K +  +    +    ++ L   +     ++ED  I V +KP+GI V           
Sbjct: 93  H--KHEPPVKQWCSQEVEAEDLPGRIAGFNIVFEDESILVIDKPSGIPVHPTGQF---YQ 147

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             +   +   G      +RLD+ TSG+L++A+   +A  + +S R R + KIY + V G 
Sbjct: 148 NTITELLKLHGVDALPCYRLDKITSGLLILAKNSQSAGEIQKSIRSRDMIKIYLARVKGR 207

Query: 191 PKNKKECIANW-------------LLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + +  + N               ++ + I   D           +  AI+ F  I  F
Sbjct: 208 FPHSELILDNENAAETTFEDTSKVTVELTPIYSIDPKRQFPVGLSASKDAITKFYPIRYF 267

Query: 237 AQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +      +  +P TGRTHQ+R+H   +G PIV D  YC++
Sbjct: 268 SHADETVVACKPITGRTHQIRIHLARLGHPIVNDSVYCSH 307


>gi|294954492|ref|XP_002788195.1| RNA pseudouridylate synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239903410|gb|EER19991.1| RNA pseudouridylate synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 309

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 58/261 (22%), Positives = 102/261 (39%), Gaps = 43/261 (16%)

Query: 70  VINALNHIIKEQKIL--DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
               L+H+++  ++L  ++ VN        +  ++ E   +   +KP+G+ V  G G   
Sbjct: 6   YKVELDHVLQGNELLIHETIVNENPVPFDGELKIVGETDDVVAVDKPSGMPVHSGGG--- 62

Query: 128 HIDGFLKSWVDSKGQ-----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR--RIQ 180
           H    L + +  +            HRLD+ TSGI+++ +    A+  +E+F+     IQ
Sbjct: 63  HRVNCLSAILKEQDPSRFSLAIHTLHRLDRLTSGIVILGKNPDVARAFSEAFKKHDQEIQ 122

Query: 181 KIYWSLVWGIPKNKKECIANWLL----------------------------KKSHIGGDY 212
           K Y + V G  +     +  ++                               S   GD 
Sbjct: 123 KCYLARVKGKFEGSNVVVEGFMRCVDFRVGKFILVNSNKGTASEDANQGDAPTSTPSGDD 182

Query: 213 VHVVKQNEKGANYAISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              V+++     ++ + F KV          ++  P TGRTHQ+RVH   +G PI  D  
Sbjct: 183 KSAVEEDHIEDKWSQTSFDKVWYDEQNDETIIKCYPKTGRTHQIRVHLESIGHPIANDSC 242

Query: 272 YCANFKGNFTSPIQNKLYLHA 292
           Y   +K +   P    L  HA
Sbjct: 243 YGGEYKAD--HPFAFPLAPHA 261


>gi|32471769|ref|NP_864762.1| ribosomal large subunit pseudouridine synthase A [Rhodopirellula
           baltica SH 1]
 gi|32397140|emb|CAD72447.1| ribosomal large subunit pseudouridine synthase A [Rhodopirellula
           baltica SH 1]
          Length = 232

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 97/229 (42%), Gaps = 15/229 (6%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--T 147
           L    D     +L++     V NKP G+      G         + +  +      L   
Sbjct: 11  LIGDQDPAMIEILWQCHACVVVNKPVGLPTTSPKGTDSLESCLREQFAQAGNPVSYLTAV 70

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN--KKECIANWLLKK 205
           HRLD+  SG++++A  + AA+ L+E FR+R +QK Y ++V G      K+E   + + K 
Sbjct: 71  HRLDRPVSGLVLIALRKKAARLLSEQFRLRHVQKKYIAMVQGNALEACKQEPWHDTIAKL 130

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGC 264
           +      V +V  +      A +    ++  ++     +E++P TGR HQLR+ + H G 
Sbjct: 131 TDEAR--VEIVGLDSTDGRQAETKVSFLEYDSESDTSRIELRPVTGRMHQLRIQSAHRGH 188

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           PIVGD  Y      +    +       A  +    P  GR  +   LP 
Sbjct: 189 PIVGDPLYGTAEDESALRLV-------AAKLSFRDPTNGR-AVEVELPE 229


>gi|207345036|gb|EDZ71984.1| YGR169Cp-like protein [Saccharomyces cerevisiae AWRI1631]
 gi|323354851|gb|EGA86684.1| Pus6p [Saccharomyces cerevisiae VL3]
          Length = 404

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 112/280 (40%), Gaps = 29/280 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRV--DKKRVKFNNRIQSGQVVRIPPVINALN 75
              L     + +           +R G  R+  D   +  ++ + +  +++   V+    
Sbjct: 35  GKLLIDVLVSEFKLRPRAYYLDQIRKGTYRLIRDGVPLVPDHLMTT--IIKNHDVLETTT 92

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSIL-----LYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           H  K +  +    +    ++ L   +     ++ED  I V +KP+GI V           
Sbjct: 93  H--KHEPPVKQWCSQEVEAEDLPGRIAGFNIVFEDESILVIDKPSGIPVHPTGQF---YQ 147

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             +   +   G      +RLD+ TSG+L++A+   +A  + +S R R + KIY + V G 
Sbjct: 148 NTITELLKFHGVDALPCYRLDKITSGLLILAKNSQSAGEIQKSIRSRDMIKIYLARVKGR 207

Query: 191 PKNKKECIANW-------------LLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + +  + N               ++ + I   D           +  AI+ F  I  F
Sbjct: 208 FPHSELILDNENAAETTFEDTSKVTVEMTPIYSIDPKRQFPVGLSASKDAITKFYPIRYF 267

Query: 237 AQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +      +  +P TGRTHQ+R+H   +G PIV D  YC++
Sbjct: 268 SHADETVVACKPITGRTHQIRIHLARLGHPIVNDSVYCSH 307


>gi|311693193|gb|ADP96066.1| protein containing pseudouridine synthase domain [marine bacterium
           HP15]
          Length = 273

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 64/313 (20%), Positives = 115/313 (36%), Gaps = 47/313 (15%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
             + +   +    +D       P ++   ++  +  G          + ++   G+ +R+
Sbjct: 3   TTIDITVKQPGKAID-ALSEAAPGLSRQKIKDAMTKGA-------CWWTHK---GKRLRL 51

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                 L   I+ Q   D  V   K     K ILL    +  V+ KP G+  QG     +
Sbjct: 52  RRATKELKPGIRLQFYYDEKVLERKPE---KPILLENAGRYTVWFKPHGLLAQGSQWGDH 108

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                L+       Q   L HRLD + +G++++A    AA  L++ F  R + K Y + V
Sbjct: 109 C--SLLRLAEIQLEQPCHLIHRLDADAAGLMLIAHDSKAAGALSQCFSGRTMTKHYKARV 166

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQ 246
            G+   +++ +   +                       A+S    ++     +   +E+ 
Sbjct: 167 AGLIDAREQLVDAPV-------------------EGKAAVSRVSTLELDETGETSLVEVS 207

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-L 305
             TGR HQ+R H   +G PI+GD  Y          P    L L A +++   P   R +
Sbjct: 208 IETGRKHQIRRHLAGLGHPIIGDRLYG--------RPAGAPLQLLAFFLEFDCPLNKRKM 259

Query: 306 QITAPLPAHMVKT 318
                LPA +   
Sbjct: 260 TFE--LPAELSDL 270


>gi|319776874|ref|YP_004136525.1| ribosomal large subunit pseudouridine synthase c [Mycoplasma
           fermentans M64]
 gi|318037949|gb|ADV34148.1| Ribosomal large subunit pseudouridine synthase C [Mycoplasma
           fermentans M64]
          Length = 280

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 55/292 (18%), Positives = 107/292 (36%), Gaps = 34/292 (11%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +   +   +++  +L  + K    +    ++ KILR+  ++++  R+      I    ++
Sbjct: 1   MLEFIATKNDDGRKLISYLKRILINTPTSHIYKILRNKDIKINGVRINDPQYIINEKDII 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
           +I        + I+     +     +   DF    ++YED  I + +KP  ++V   +  
Sbjct: 61  QI--------YGIEANDYQNKKFENSAKKDF---KIIYEDDNILIVSKPINLAVHSENNC 109

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                     +      KP    RLD+ TSG+++ A+  A    L   ++    +KIY  
Sbjct: 110 LDKQVLSYLKYNQKDSFKPSHVGRLDKVTSGLMIYAKNYATLVELN--YKTGFFEKIY-- 165

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
                 K+    +   +            +V  N      A + F        K   +  
Sbjct: 166 ----KLKSDFNEVKKLVEINIQHDEKLHKMVVTNNAKDPLAKTLFYT------KNNEIFA 215

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
              TG+ HQ+R+   H+  PI GD KY             ++LYLH   +  
Sbjct: 216 SILTGKKHQIRLSMSHLKTPIYGDIKYDGKKA--------DRLYLHCYSITF 259


>gi|320527944|ref|ZP_08029110.1| RNA pseudouridine synthase [Solobacterium moorei F0204]
 gi|320131570|gb|EFW24134.1| RNA pseudouridine synthase [Solobacterium moorei F0204]
          Length = 223

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 104/234 (44%), Gaps = 21/234 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----LTHRLDQETS 155
           +LYED+ +    KP  I V         +    K ++  K QKP      L HRLD+   
Sbjct: 4   VLYEDNHVLCVEKPINIPVMEDDSHDMDLLTMCKEYLKEKYQKPGNVYCGLVHRLDRPVG 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++V A+T  AA  L+E+ R  +++K Y +++ GIP  K + + ++L K +        V
Sbjct: 64  GVMVFAKTSKAASRLSEAVRTHQLKKEYIAILDGIPIKKADTLEDYLSKDTRTN----TV 119

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              + K        ++VI   +++   + +   TGR+HQ+RV       P++ D +Y  +
Sbjct: 120 SVTDAKHGKKCHLSYEVIGQKSKQ-SLVHIVLGTGRSHQIRVQFASRKLPLIHDQRYNPH 178

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDR 328
                    +  + L+A  +  PHP     + + A  P+     W      YD+
Sbjct: 179 -------TTKGPIGLYAFRLTFPHPTLKTPIVVQA-TPS--QSIWKEFEVNYDK 222


>gi|218283677|ref|ZP_03489638.1| hypothetical protein EUBIFOR_02232 [Eubacterium biforme DSM 3989]
 gi|218215666|gb|EEC89204.1| hypothetical protein EUBIFOR_02232 [Eubacterium biforme DSM 3989]
          Length = 253

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 43/228 (18%), Positives = 92/228 (40%), Gaps = 9/228 (3%)

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +++ I  +        ++    +LYE++ + V  KP  + V         +   +  ++ 
Sbjct: 29  EKKTIYFNYPEKDVEINYEPVDILYENTFLIVAFKPPFLLVHDDGNNQDTLQARVNGYLQ 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               K   +  HR+D ETSG+++  +      +  ++     I+K Y +LV G    K +
Sbjct: 89  LNQNKYPAQAIHRIDYETSGLVLFCKHPFFQAYCDKNMEEHHIKKEYIALVQGHTNYKNK 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I + + +  H     +            ++S F  +  + +    +++   TGR HQ+R
Sbjct: 149 KIISNIARDRHNAKKMII-----HPNGKESVSIFNTLKNY-KDCSLIQVTILTGRKHQIR 202

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           V    +  PI+ D  Y      N    +Q+  ++    +D+  P+  R
Sbjct: 203 VQCASLNHPILNDSLYGGKKIDNTGLLLQS-HHIQFNDVDITCPQEKR 249


>gi|83814990|ref|YP_445861.1| ribosomal large subunit pseudouridine synthase A [Salinibacter
           ruber DSM 13855]
 gi|294507771|ref|YP_003571829.1| Ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber M8]
 gi|83756384|gb|ABC44497.1| ribosomal large subunit pseudouridine synthase A [Salinibacter
           ruber DSM 13855]
 gi|294344099|emb|CBH24877.1| Ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber M8]
          Length = 232

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 56/223 (25%), Positives = 95/223 (42%), Gaps = 15/223 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK---GQKPRLTHRLDQETSGI 157
           +L+ D  + V +KP G+  Q        +    K  +  +        L HRLD+  SG+
Sbjct: 3   ILHRDEHLLVVSKPPGLLAQPDQTGDPDVVSRGKEMLSDETEGAPFLGLVHRLDRPASGV 62

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           + +AR+  AA+ L+  FR R ++K Y   V G  +       +++ K          +V 
Sbjct: 63  MALARSPEAARELSRQFRERLVEKRYVVAVEGTLQG-IGAWTDYIAKPDRQPR----LVD 117

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            +      A   ++V++  +     L++   TGR+HQ+R+ A   G P+VGD +Y A+  
Sbjct: 118 PDHPEGKRAALDWQVLES-SSAHTLLQVTLQTGRSHQIRLQAASRGHPVVGDDRYGAS-- 174

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTW 319
               S     + LH   +   HP   R +   AP P H     
Sbjct: 175 ---DSLPDRAVALHHVLLRADHPARPRRETFVAPPPTHWSGVL 214


>gi|332307383|ref|YP_004435234.1| pseudouridine synthase Rlu family protein, TIGR01621 [Glaciecola
           agarilytica 4H-3-7+YE-5]
 gi|332174712|gb|AEE23966.1| pseudouridine synthase Rlu family protein, TIGR01621 [Glaciecola
           agarilytica 4H-3-7+YE-5]
          Length = 236

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 64/219 (29%), Positives = 100/219 (45%), Gaps = 21/219 (9%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLD 151
           +S F    ++++     + +KP G+SVQ          G L          K  L HRLD
Sbjct: 3   NSAFPPISVVFDHPDFIIIDKPPGVSVQ----NEASSSGILPMVCTQHAFDKLWLVHRLD 58

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           + TSG+L++A+   AA  L + F  R I+K Y +L    PK K+  +   + K     G 
Sbjct: 59  KVTSGLLILAKHAQAASQLGKLFEAREIEKYYLALGSAKPKKKQGTVTGAMKKIR--DGK 116

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           +      N+ G+  A+S F      +       ++P TG+THQLRV    +G PI+GD  
Sbjct: 117 WAF----NQNGSAVAVSQFFS-KSVSAGIRLYLLKPLTGKTHQLRVMLKSLGSPILGDEL 171

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           Y A          Q++ YLHA  +   + +G  +Q+  P
Sbjct: 172 YKAQ--------AQDRTYLHAYCLRFTY-QGQLVQLVCP 201


>gi|117918741|ref|YP_867933.1| pseudouridine synthase Rlu family protein [Shewanella sp. ANA-3]
 gi|117611073|gb|ABK46527.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           sp. ANA-3]
          Length = 229

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 59/205 (28%), Positives = 92/205 (44%), Gaps = 21/205 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++ +++   V +K   +      G A    G +       G K    HRLD  TSG+L+
Sbjct: 3   RIIADEADFLVISKSPNVHFHSQDGTA----GVVAQLEQDLGIKLFAVHRLDTPTSGLLL 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+  AAA+ LTE F   R+QK Y +L  G PK K+  +   + K          + K  
Sbjct: 59  LAKHPAAARQLTELFSAHRVQKYYLALAKGKPKKKQGWVIGDMAK------SRRSMFKLL 112

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F       +      ++P +G+THQLRV    +G PI+GD  Y ++    
Sbjct: 113 RTKENPAITQFFS-TSVGEGLRLYLLKPLSGKTHQLRVALASLGVPILGDALYGSD---- 167

Query: 280 FTSPIQNKLYLHARYMDL--PHPEG 302
               + ++ YLHA  +     H EG
Sbjct: 168 ----VADRCYLHAYCLHFRYQHEEG 188


>gi|291456224|ref|ZP_06595614.1| RNA pseudouridine synthase [Bifidobacterium breve DSM 20213]
 gi|291381501|gb|EFE89019.1| RNA pseudouridine synthase [Bifidobacterium breve DSM 20213]
          Length = 244

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 96/242 (39%), Gaps = 31/242 (12%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +LYED +I V +KP  ++     G+ Y     ++             HRLD+ T+G+LV
Sbjct: 2   DVLYEDERIIVVDKPHFLATMP-RGMWYRETALIRLRERLGEPDITPAHRLDRMTAGVLV 60

Query: 160 VARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN-------WLLKKSHIGG 210
             R  A        F+ ++  K+Y   +    I + +   I          LL++SHI  
Sbjct: 61  FVRDPACRGAYQMLFQNKQATKVYECLASCAPIRRPRFGTITQAEPPRPFPLLRRSHITK 120

Query: 211 DYVHVVKQNEKGANYAISHFK----VIDCFAQKF---------------CWLEMQPHTGR 251
           +   +    E GA  A +  +    ++     ++               C   + P TG+
Sbjct: 121 ERGTLAAFEEPGAVNAETLIERGELILTSAGGRWREAPEGGPCLENPPICRYTLHPRTGK 180

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
           THQLRVH   +G PIVGD  Y    +          L L AR +    P  G R +  + 
Sbjct: 181 THQLRVHMNSLGLPIVGDDFY-PRIQTRLYDDFSQPLQLVARVLRFTDPVTGKRQEFVSR 239

Query: 311 LP 312
           +P
Sbjct: 240 IP 241


>gi|238809659|dbj|BAH69449.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 296

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 55/293 (18%), Positives = 107/293 (36%), Gaps = 34/293 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQV 64
            +   +   +++  +L  + K    +    ++ KILR+  ++++  R+      I    +
Sbjct: 16  KMLEFIATKNDDGRKLISYLKRILINTPTSHIYKILRNKDIKINGVRINDPQYIINEKDI 75

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           ++I        + I+     +     +   DF    ++YED  I + +KP  ++V   + 
Sbjct: 76  IQI--------YGIEANDYQNKKFENSAKKDF---KIIYEDDNILIVSKPINLAVHSENN 124

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                      +      KP    RLD+ TSG+++ A+  A    L   ++    +KIY 
Sbjct: 125 CLDKQVLSYLKYNQKDSFKPSHVGRLDKVTSGLMIYAKNYATLVELN--YKTGFFEKIY- 181

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
                  K+    +   +            +V  N      A + F        K   + 
Sbjct: 182 -----KLKSDFNEVKKLVEINIQHDEKLHKMVVTNNAKDPLAKTLFYT------KNNEIF 230

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
               TG+ HQ+R+   H+  PI GD KY             ++LYLH   +  
Sbjct: 231 ASILTGKKHQIRLSMSHLKTPIYGDIKYDGKKA--------DRLYLHCYSITF 275


>gi|317013785|gb|ADU81221.1| hypothetical protein HPGAM_01875 [Helicobacter pylori Gambia94/24]
          Length = 293

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 69/287 (24%), Positives = 119/287 (41%), Gaps = 29/287 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q VR   +I  +  +I                +  +  
Sbjct: 28  LKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVSLI------------YFKPNEKQER 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KPA +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFEAKDFGVFDKPAQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  + + L   F  ++++K Y +L  G+  +K   I   +L   +I  D + +  Q  
Sbjct: 129 GKTLQSVKDLKALFMQKKVKKTYLALAHGLV-DKSIIINKPILTPQNIQKD-LRIRSQIS 186

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                +I+  + +          L++ P TGRTHQ+R+H   +   IVG+  Y    +  
Sbjct: 187 PLGKPSITLVEPLSYNPFLDISLLKITPLTGRTHQIRLHLSSINHRIVGEGLYGVADENA 246

Query: 280 FTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                  +      L LHA  ++    +G   QI +P+P   +    
Sbjct: 247 REYLQLKRENNAPTLMLHAASLEFEF-KGAIYQIASPMPKRFMPFLK 292


>gi|297734463|emb|CBI15710.3| unnamed protein product [Vitis vinifera]
          Length = 374

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 58/267 (21%), Positives = 102/267 (38%), Gaps = 23/267 (8%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+N      +   F   +    +      ++SG+++VD + V  +  ++S Q +      
Sbjct: 37  VKNRWAGKTIVDLFTEEFKGRPYDYYVNAVQSGRIQVDGEMVPVSYIVRSSQKISHFVHR 96

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                   E  +L            L   +L ++  +    KPA + V       Y  + 
Sbjct: 97  -------HEPPVL-----------ALDVSVLQKEPDVLTICKPASVPVHPCG--QYRKNT 136

Query: 132 FLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            +       G  P    HRLD+  SG+L++AR+ + A    +      +QK Y + V G+
Sbjct: 137 VVGILQAEHGLAPLFPIHRLDRLVSGLLILARSASKADSFRQQIEAGMVQKQYIAKVTGV 196

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEK-GANYAISHFKVIDCFAQKFCWLEMQPHT 249
             + ++ +   +   +  G   V     N       A + F  I         +  +P T
Sbjct: 197 FPDDEQVVNVNVNYNAREGRSTVGNCCGNTPLKGKSACTKFTRISTNG-THSIVLCEPIT 255

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANF 276
           GRTHQ+RVH  + G PI  D  Y + F
Sbjct: 256 GRTHQIRVHLQYTGHPIANDMLYLSEF 282


>gi|240171345|ref|ZP_04750004.1| pseudouridine synthase [Mycobacterium kansasii ATCC 12478]
          Length = 272

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 58/271 (21%), Positives = 102/271 (37%), Gaps = 28/271 (10%)

Query: 47  RVDKKRV----------KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSD 95
           R++   V              ++ +G+VV     +   + ++     +    +L  +   
Sbjct: 2   RLNGGPVLAELDARFGTAAGRKVLAGEVVDSRGAVIDRDTVLPPGSFVHLYRDLPDEVPV 61

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
             +  +LY+D  I V +KP  ++     G        ++   +    +    HRLD+ T+
Sbjct: 62  PFEMPVLYQDDDIVVADKPHFLATMP-RGRHVAQTALVRLRCELGLPELSPAHRLDRLTA 120

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L+    R         F    + K Y +     P      +    + +S I      +
Sbjct: 121 GVLLFTTRRELRGRYQTLFACGAVHKTYLARAAVNPA-----VVLPRVVRSRIVKRRGQL 175

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA- 274
               E G   A +  ++I           + P TGRTHQLRVH   +G PI GD  Y   
Sbjct: 176 QAVCEPGEPNAETLVELISPQG----LYRLTPRTGRTHQLRVHMASLGLPITGDPLYPKV 231

Query: 275 --NFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                G+F+SP+Q    L A+ ++   P  G
Sbjct: 232 LQEVDGDFSSPLQ----LLAKRIEFDDPLTG 258


>gi|197336314|ref|YP_002155824.1| pseudouridine synthase Rlu family protein [Vibrio fischeri MJ11]
 gi|197317804|gb|ACH67251.1| pseudouridine synthase Rlu family protein [Vibrio fischeri MJ11]
          Length = 227

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 56/215 (26%), Positives = 93/215 (43%), Gaps = 22/215 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGIL 158
            +LY++S   V NK   +SV    G        L       G K   L HRLD+ TSG+L
Sbjct: 3   DILYQNSNFLVINKHPNVSVHKDDGET----SLLIELAKETGDKQLYLIHRLDKMTSGLL 58

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ R +AAA  L++ F  R ++K Y ++    PK K+  +   + +        ++  + 
Sbjct: 59  LIGRNQAAASELSQLFANRLVEKYYLAIGDKKPKKKQGLVIGDMERSRRASWKLINSKE- 117

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                N A++ F               +PHTG+THQ+RV    +G  I+GD  Y ++   
Sbjct: 118 -----NPAVTQFFSTAAQGGNR-LFLCKPHTGKTHQIRVALKSVGSGILGDPIYSSSNA- 170

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
                  ++ YLHA  +   + +    +    LP 
Sbjct: 171 -------DRGYLHAYALRFTY-QTQNFEFV-ELPK 196


>gi|239908035|ref|YP_002954776.1| putative pseudouridine synthase [Desulfovibrio magneticus RS-1]
 gi|239797901|dbj|BAH76890.1| putative pseudouridine synthase [Desulfovibrio magneticus RS-1]
          Length = 290

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 53/290 (18%), Positives = 103/290 (35%), Gaps = 38/290 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +    +  RLD+  +   P +     ++++ SG + V+ + +    R+++GQ V + P  
Sbjct: 11  IPPQADGWRLDKALELMLPEVGLRGRRRLIESGGLTVNGRLLPAGYRVRAGQTVAMVPQD 70

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS---GIAYH 128
                  +E++   + V +   +               + NKP+G+     +   G    
Sbjct: 71  -------RERRFGPADVPVVLTA-----------GDYVLLNKPSGL--HSAALAQGGGES 110

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           ++  L       G+   L  RLD  T+G+L  A +  AA    +      + K Y ++  
Sbjct: 111 VEALLPDIFP--GRPSFLLSRLDSLTTGLLPAAFSPEAAATYRDMEESGEVDKTYLAVGH 168

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G P          L            V+ +    +   ++  + ++              
Sbjct: 169 GEPDVTYFRCDGEL---DAADRKKTRVLDRATIDSLR-MTEVEALETRG-GVTLFRCTIK 223

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            G  HQ+R H    G P+VGD  Y              +L+LH   +D P
Sbjct: 224 KGARHQIRTHLAWAGHPLVGDPLYGQGEGE--------RLFLHCAGIDCP 265


>gi|162450819|ref|YP_001613186.1| RNA methyltransferase [Sorangium cellulosum 'So ce 56']
 gi|161161401|emb|CAN92706.1| RNA methyltransferase [Sorangium cellulosum 'So ce 56']
          Length = 765

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 93/241 (38%), Gaps = 26/241 (10%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-- 143
            ++   + +      ++Y+D  + V  K     V   +    ++   L       G    
Sbjct: 461 ETIAALRRTPPPAPKVIYDDDGVLVVEKGPHEPV---ATQPEYLGSLLARCARIPGSTTT 517

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P + H LD  TSG++++AR+  AA    E+   +  + IY +   G+   K     +   
Sbjct: 518 PIIVHPLDPGTSGLVMLARSEEAAARWGEALA-KTGRLIYLAAAKGVTPGKGAITRDL-- 574

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                         +       A + ++ +   A     L + P  GRTHQ+R H   +G
Sbjct: 575 --------------REGTRTYTARTRYRRL-AVASGHSILRVIPDGGRTHQIRRHLAAIG 619

Query: 264 CPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
            PI+GD +Y       +       ++ ++H   +++ HP  G ++ I + LP  +    +
Sbjct: 620 HPILGDERYGHVPTNRYFEEKHGLDRSFVHLVRIEIEHPRTGVKMIIESTLPGDLRSALE 679

Query: 321 S 321
            
Sbjct: 680 R 680


>gi|66045373|ref|YP_235214.1| pseudouridine synthase [Pseudomonas syringae pv. syringae B728a]
 gi|63256080|gb|AAY37176.1| Pseudouridine synthase [Pseudomonas syringae pv. syringae B728a]
          Length = 313

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 61/294 (20%), Positives = 105/294 (35%), Gaps = 30/294 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +P I+          G+V   + K +  +   + G  +R+       N        
Sbjct: 47  LCAKFPAISREQWLDRFARGRVLDENGKAITPDLAYREG--LRVHYFREVAN-------- 96

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQ 142
                   +    +   +LY D  + V +KP  + V   G  +   +   L   +D+   
Sbjct: 97  --------ETPIPVVETILYADEHLVVADKPHFLPVTPAGEYVEQTLLRRLIHRLDNPDM 148

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P   HR+D+ T+G+++ +  R         F  RRI K Y ++   +P      +A   
Sbjct: 149 VP--LHRIDRHTAGLVLFSANRQTRSAYQALFPTRRIDKFYQAIAPALP-----GLAFPR 201

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++    K     + P TG+ HQLRVH   +
Sbjct: 202 LHESRLVEGEPFFRMQEGIGASNTRTQIEVLERQ-DKLWRYGLYPVTGKKHQLRVHMAAL 260

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           G  I  D  Y  +   +     QN L L A  +    P  G      + L    
Sbjct: 261 GAAICNDPFY-PDVVKDPVDDYQNPLKLLASSLRFVDPLSGEQRHFESLLTLDW 313


>gi|322378491|ref|ZP_08052942.1| Pseudouridine synthase [Helicobacter suis HS1]
 gi|322380818|ref|ZP_08054919.1| 23S rRNA-specific pseudouridylate synthase [Helicobacter suis HS5]
 gi|321146755|gb|EFX41554.1| 23S rRNA-specific pseudouridylate synthase [Helicobacter suis HS5]
 gi|321149093|gb|EFX43542.1| Pseudouridine synthase [Helicobacter suis HS1]
          Length = 250

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 72/300 (24%), Positives = 131/300 (43%), Gaps = 56/300 (18%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +    +  +I+    +K +  G V +  KR+                       + +++ 
Sbjct: 6   KILAKNL-NISHKQAKKYIDMGLVSLQGKRLT----------------------LARQKF 42

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
            LD+  ++    + LK+ +LY+D ++ V NK            A HID +    ++ + +
Sbjct: 43  PLDTHFHI---KECLKTDVLYQDQELLVLNK------------ATHIDSY---TLERQHK 84

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             +L HRLD+ TSG+L++A+     + L  +F+ R + K Y +L+ GI K  K       
Sbjct: 85  PYKLLHRLDKSTSGLLLLAQATFYTKAL-LAFKKREVYKEYLALIEGILKRPKTLTQPLS 143

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           ++ +H+  +   V    +     AI+H   I    ++   L++   TG THQ+R H  H+
Sbjct: 144 VRTNHMHFNKGFVKTFVDLKGKPAITHLYPI-YHTKQQTLLKVVIETGITHQIRAHLSHI 202

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G PIVGD  Y  +   +F        +LHA  + L          +AP+P H  +  + L
Sbjct: 203 GHPIVGDLIYGGSPNPHF--------FLHAYKLALL-----EHHFSAPIPPHFKEFHELL 249


>gi|167375438|ref|XP_001733644.1| ribosomal pseudouridine synthase [Entamoeba dispar SAW760]
 gi|165905188|gb|EDR30257.1| ribosomal pseudouridine synthase, putative [Entamoeba dispar
           SAW760]
          Length = 402

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 50/245 (20%), Positives = 91/245 (37%), Gaps = 28/245 (11%)

Query: 35  VNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
             ++K +  G ++++ K +  +  I     +      +                      
Sbjct: 101 TTIKK-IEKGLIKINNKLIDPSTIIHHHDEIEHQVHRH------------------EPPV 141

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
              K  ++ E +     +KP+ + V       Y  +  +           R  HRLD+ T
Sbjct: 142 YCDKLTIVKETNDFIAIDKPSSVPVHPCG--RYRHNTVIFILSHEGYPNLRPVHRLDRMT 199

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGIL++A+T  AA+       +++ +  Y   V G  +     +    + +  I    +H
Sbjct: 200 SGILLLAKTIQAAREFQNHMVIKKKE--YICRVRGKLEK---TVVTSKIGRKRIDDKKIH 254

Query: 215 V-VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH-TGRTHQLRVHALHMGCPIVGDHKY 272
           V V + E+      S F  +    +    + +    +GRTHQLRVH   +  PIV D  Y
Sbjct: 255 VSVNKIEEDGKECCSEFNPLFYDEKTNTTVAVALLGSGRTHQLRVHLQSIHHPIVNDPIY 314

Query: 273 CANFK 277
            A F 
Sbjct: 315 AAQFD 319


>gi|222617295|gb|EEE53427.1| hypothetical protein OsJ_36505 [Oryza sativa Japonica Group]
          Length = 423

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 103/262 (39%), Gaps = 61/262 (23%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--------DSKGQKPRLTHRLDQ 152
           +++ED  + V +KPAG+          + D  L +          ++      L +RLD+
Sbjct: 164 VVFEDEWLAVVDKPAGV----------YCDALLSALPCSAATLGDEATKPNLHLANRLDR 213

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG++V+ +    A  L ++F   +++K Y +L  G P   ++        +S  G   
Sbjct: 214 DTSGLMVITKCNKVAGKLVKAFTEHKVKKTYLALCIGYPPAWEKIKICSGHGRSKHGAWR 273

Query: 213 VHVVKQ-----------------------NEKGANYAISHFKVIDCFA------------ 237
           V+ +                         N KG     S+F+V +  +            
Sbjct: 274 VYAMSDVGRSLPGGSVVRDMSTRFEVLGINGKGQFREPSNFEVDETESITVQEKAADLTS 333

Query: 238 -----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                     +   P +GRTHQ+R+H  ++G PI GD KY    + N      +   LHA
Sbjct: 334 DGDEKNSIILVRAYPQSGRTHQIRLHCQYLGFPIRGDVKYSGVIEWNGVD--YDGHALHA 391

Query: 293 RYMDLPHPEGG-RLQITAPLPA 313
             +   HP  G  +   +PLP+
Sbjct: 392 ESLSFVHPVTGLPVTFRSPLPS 413


>gi|115489062|ref|NP_001067018.1| Os12g0560500 [Oryza sativa Japonica Group]
 gi|122203511|sp|Q2QNM3|PUS1_ORYSJ RecName: Full=RNA pseudourine synthase 1; AltName: Full=RNA
           pseudouridylate synthase 1; AltName: Full=RNA-uridine
           isomerase 1
 gi|77556134|gb|ABA98930.1| RNA pseudouridylate synthase, putative, expressed [Oryza sativa
           Japonica Group]
 gi|113649525|dbj|BAF30037.1| Os12g0560500 [Oryza sativa Japonica Group]
 gi|125537021|gb|EAY83509.1| hypothetical protein OsI_38723 [Oryza sativa Indica Group]
 gi|215692563|dbj|BAG87983.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 345

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 103/262 (39%), Gaps = 61/262 (23%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--------DSKGQKPRLTHRLDQ 152
           +++ED  + V +KPAG+          + D  L +          ++      L +RLD+
Sbjct: 86  VVFEDEWLAVVDKPAGV----------YCDALLSALPCSAATLGDEATKPNLHLANRLDR 135

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG++V+ +    A  L ++F   +++K Y +L  G P   ++        +S  G   
Sbjct: 136 DTSGLMVITKCNKVAGKLVKAFTEHKVKKTYLALCIGYPPAWEKIKICSGHGRSKHGAWR 195

Query: 213 VHVVKQ-----------------------NEKGANYAISHFKVIDCFA------------ 237
           V+ +                         N KG     S+F+V +  +            
Sbjct: 196 VYAMSDVGRSLPGGSVVRDMSTRFEVLGINGKGQFREPSNFEVDETESITVQEKAADLTS 255

Query: 238 -----QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                     +   P +GRTHQ+R+H  ++G PI GD KY    + N      +   LHA
Sbjct: 256 DGDEKNSIILVRAYPQSGRTHQIRLHCQYLGFPIRGDVKYSGVIEWNGVD--YDGHALHA 313

Query: 293 RYMDLPHPEGG-RLQITAPLPA 313
             +   HP  G  +   +PLP+
Sbjct: 314 ESLSFVHPVTGLPVTFRSPLPS 335


>gi|15602498|ref|NP_245570.1| hypothetical protein PM0633 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|12720907|gb|AAK02717.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 220

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 64/197 (32%), Positives = 91/197 (46%), Gaps = 16/197 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+Y+     V +KP GISV      A  +   +   +D    +  L HRLD+ TSG+L++
Sbjct: 6   LIYQHPDFVVIDKPCGISVHKDE-EAVGLTTLVAQQLD--VPQVWLVHRLDKITSGLLLL 62

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  + AA+ L+  F   RIQK Y +L    PK K+  I   + K            K   
Sbjct: 63  ALNQRAARALSLLFAEHRIQKTYLALSQHKPKKKQGLIVGDMQKA------RRGAWKLCP 116

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  I+C         ++P TG+THQLRV    +G PI+GD  Y  N     
Sbjct: 117 TKTNPAITRFHSINCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDALYAGN----- 170

Query: 281 TSPIQNKLYLHARYMDL 297
            S   ++ YLHA  +  
Sbjct: 171 -SAKIDRTYLHAYRLQF 186


>gi|301167669|emb|CBW27252.1| putative pseudouridine synthase [Bacteriovorax marinus SJ]
          Length = 276

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 72/318 (22%), Positives = 135/318 (42%), Gaps = 49/318 (15%)

Query: 4   MTYVQYVVV---ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M  V+  +       +E++ L  +  +    ++   ++K   +G + + KK V   NRI+
Sbjct: 1   MEEVKKFIFKGKPKGKESITLLDFL-DEVTSLSKSQIKKHAANGGIWIKKKGVGPLNRIR 59

Query: 61  SGQVVRIPPVINALNHII--KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
                R+   + + +HI    +  + +  ++L +         +Y+     V+ KPAG+ 
Sbjct: 60  -----RVKTNLTSEDHIECHYDPNLPEVDMSLVQE--------IYKTKGWGVWYKPAGVL 106

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            Q   G  +     +   V+       L  RLD+ETSG++++A T   A+  T + + R 
Sbjct: 107 SQ---GTKFGDQASILRHVEKNVPNAYLIQRLDRETSGLMIIAYTDKVARIFTNAMKNRL 163

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I+K Y + V G  + ++  IA  L                       A + ++V + F Q
Sbjct: 164 IRKFYQAEVLGTLRQEQGEIAFDL-------------------DGKSAKTLYQVHEEFEQ 204

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               LE++  TGR HQ+R H   +  P++GD KY  + K +      + L L A  ++L 
Sbjct: 205 S-TLLEIEIITGRFHQIRKHFEKIKHPVIGDPKYGRHNKND------DGLKLVAHKLELK 257

Query: 299 HPEGGRLQITAPLPAHMV 316
            P   +  +   LP  + 
Sbjct: 258 DPITKKDHLFT-LPEELR 274


>gi|316975348|gb|EFV58793.1| ribosomal large subunit pseudouridine synthase C [Trichinella
           spiralis]
          Length = 372

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 71/288 (24%), Positives = 115/288 (39%), Gaps = 49/288 (17%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSKGQKP 144
           +   + +      +LY  + + V NKP G+ V  G+G+      I   LK  + +K +  
Sbjct: 85  LPKDEVAQLCAESVLYNKNDLIVLNKPYGLPVTNGAGMFVSLKIILPILKELISAKSEIL 144

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC------- 197
           R  HRLD+ T+G+L++A ++     L + F+   I+K Y  +   +P             
Sbjct: 145 RPVHRLDRCTTGVLMLASSKFRFLELKDMFKREEIKKTYICITKLVPNPSSGIVNNEHTH 204

Query: 198 -------IANWLLKKSHIGGDYVHVVKQNEKG----------ANYAISHFKVIDCFAQKF 240
                  I   L ++   G      +  N KG          A    + +  +    +K 
Sbjct: 205 THIVIRVIEAALGERRISGRFKTSPLSINLKGKEKCLNSGADAKIVKTEYSTL-SVGEKC 263

Query: 241 CWLEMQPHT----GRTHQLRVHA-LHMGCPIVGDHKYC---ANFKGNFTSPIQNK----- 287
             ++   +T    G  HQ+R H  L  G PIVGDHKY     N      S + +K     
Sbjct: 264 ALIKCTTYTVFCLGMKHQIRCHMGLCFGHPIVGDHKYSDFVGNRPQRLPSEMLHKLGIRS 323

Query: 288 -------LYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
                  LYLHA  +++P  P+   L + APLP   + T   L  +Y 
Sbjct: 324 SKSRHLPLYLHASEIEIPEFPKQKNLSVKAPLPNFFLYTLKRLRLRYS 371


>gi|291440659|ref|ZP_06580049.1| ribosomal pseudouridine synthase [Streptomyces ghanaensis ATCC
           14672]
 gi|291343554|gb|EFE70510.1| ribosomal pseudouridine synthase [Streptomyces ghanaensis ATCC
           14672]
          Length = 319

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 50/222 (22%), Positives = 89/222 (40%), Gaps = 9/222 (4%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTH 148
             +        +++ D  I V +KP  ++    GS +A      L+  +     +    H
Sbjct: 88  PAEVPVPFPLEVVHRDEHIVVVDKPHFLATTPRGSHVAQTALARLRRELGI--PELGAAH 145

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ T+G+++              FR RR+ K Y ++    P      +      +S I
Sbjct: 146 RLDRLTAGLVLFTVRPGERGAYQTLFRDRRVHKEYEAVAPYDP-----GLDLPRTVRSRI 200

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +   +  +  +G   A++  ++ +  A       + P TG+THQLRVH   +G PI+G
Sbjct: 201 VKERGELAAREVEGEPNALTLVELTEHRADGPGRYRLVPGTGQTHQLRVHMSALGVPILG 260

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           D  Y            +  L L AR ++   P  G   + T+
Sbjct: 261 DPLYPEVTAPVPAGDFRRPLQLLARVLEFTDPVTGVEHRFTS 302


>gi|312884566|ref|ZP_07744270.1| pseudouridine synthase Rlu family protein [Vibrio caribbenthicus
           ATCC BAA-2122]
 gi|309367878|gb|EFP95426.1| pseudouridine synthase Rlu family protein [Vibrio caribbenthicus
           ATCC BAA-2122]
          Length = 230

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 59/212 (27%), Positives = 93/212 (43%), Gaps = 22/212 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGI 157
            L++      V NK   +SV    G     D  L   + SK   ++  L HRLD+ TSG+
Sbjct: 3   DLVFLHDDFIVINKHPNVSVHKDDG-----DTMLLQEISSKTGDEQLYLVHRLDKMTSGL 57

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++AR   AA+ L+E F +R+++K Y ++  G PK K+  I   +++        V  + 
Sbjct: 58  MLIARHVDAARKLSEQFALRQVEKFYLAIGSGKPKKKQGLICGDMVRSRRSSWKLVKSLD 117

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                 N A + F  I            +P+TG+THQ+RV    +G  I+GD  Y     
Sbjct: 118 ------NPATTQFFSISA-GPGLRLYLCKPYTGKTHQIRVALKSIGGAILGDPIY----- 165

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
                   ++ YLHA  +     EG   Q   
Sbjct: 166 --ADPKASDRGYLHAFALCFRF-EGEHYQFVC 194


>gi|308232412|ref|ZP_07415966.2| hypothetical protein TMAG_02753 [Mycobacterium tuberculosis
           SUMu001]
 gi|308380643|ref|ZP_07490629.2| hypothetical protein TMKG_02560 [Mycobacterium tuberculosis
           SUMu011]
 gi|308406115|ref|ZP_07495174.2| hypothetical protein TMLG_02074 [Mycobacterium tuberculosis
           SUMu012]
 gi|308214050|gb|EFO73449.1| hypothetical protein TMAG_02753 [Mycobacterium tuberculosis
           SUMu001]
 gi|308360844|gb|EFP49695.1| hypothetical protein TMKG_02560 [Mycobacterium tuberculosis
           SUMu011]
 gi|308364529|gb|EFP53380.1| hypothetical protein TMLG_02074 [Mycobacterium tuberculosis
           SUMu012]
          Length = 297

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 96/252 (38%), Gaps = 12/252 (4%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVF 111
           V    ++ +G+VV     +     ++    ++    +L  +        +L++D+ I V 
Sbjct: 30  VAARAKVLAGEVVDDDGAVVDSGTVLPPGSVVHLYRDLPDEVPVPFDVPVLHQDADIVVV 89

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   +    +    HRLD+ T+G+L+    R       
Sbjct: 90  DKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTTRREVRGSYQ 148

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    ++K Y +     P      +A   L +S I     H+    E G   A +  +
Sbjct: 149 TMFARGLVRKTYLARAPVAP-----GLALPRLVRSRIVKRRGHLQAVCEPGVPNAETLVE 203

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
            I           + P TGRTHQLRVH   +G PI+GD  Y  N            L L 
Sbjct: 204 RIARDG----LYRLTPTTGRTHQLRVHMAALGIPIMGDPLY-PNVISVAAHDFSTPLQLL 258

Query: 292 ARYMDLPHPEGG 303
           A+ ++   P  G
Sbjct: 259 AQRIEFDDPLTG 270


>gi|114564709|ref|YP_752223.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114336002|gb|ABI73384.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 326

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 56/287 (19%), Positives = 107/287 (37%), Gaps = 30/287 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +  +H+  I+    Q+ +  G+V             Q+G+++       A   +   +++
Sbjct: 49  FLIDHFKQIDPSVWQQRINDGKVH-----------WQNGELITAESAYQATAKVYYYREV 97

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L  +             +LY+D+   +  KP  + V  G           +  + ++   
Sbjct: 98  LAET------KVPFAEQVLYQDNDTIIVYKPHFLPVTPGGNYVNECL-VHRLRIATQIDT 150

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-------KNKKE 196
               HRLD++T+G++++           + F   +I K Y ++    P        N   
Sbjct: 151 VAPAHRLDKDTAGVMLMTLNPQTRHAYHQLFLDDKITKDYQAIAKLTPTLLSEFADNTCM 210

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
              +W +K   +  +    ++  E  AN   SH ++ +      F   E+ P TG+THQL
Sbjct: 211 LPIHWTVKNRIVAANPSFTMQVVEGEAN---SHSEISLVAVKNGFGLFELSPITGKTHQL 267

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           RVH   +G PI+ D  Y               L L A+ +    P  
Sbjct: 268 RVHMQSLGMPILHDRFYPVLLPKG-PDNFDKPLQLLAKRLRFTDPIS 313


>gi|152991248|ref|YP_001356970.1| ribosomal large subunit pseudouridine synthase D [Nitratiruptor sp.
           SB155-2]
 gi|151423109|dbj|BAF70613.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Nitratiruptor sp. SB155-2]
          Length = 242

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 66/293 (22%), Positives = 110/293 (37%), Gaps = 60/293 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        I+    ++++  G V V  K+V                        +  + 
Sbjct: 7   KVLAQQL-GISNKKAKELIDRGLVYVGDKKV------------------------VIARG 41

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           ++D+     +     K  +L+ED KI   NKPA I+               +   +  G 
Sbjct: 42  LIDTDTKF-RIKRIEKPEILFEDEKILAINKPAHITS--------------EEIKEDSGY 86

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +  L HRLD+ETSG+L++ +  A  +   E FR  R+ K Y + V GI     E     L
Sbjct: 87  E--LLHRLDKETSGVLLLVKNEAFRKKAIEEFRKSRVYKEYVAWVEGIVAEPYEIDYPIL 144

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
                I  D     + +      A ++ + ++   +K   ++    TGRTHQ+RVH    
Sbjct: 145 T----IKKDGKAKSRLSASKGKPAKTYVEPLEIHGKK-SKVKAVIETGRTHQIRVHLART 199

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
             PI+GD  Y              ++ LHA+ + L        +  AP P   
Sbjct: 200 DHPILGDTLYGGKPW--------KRMMLHAKRIKLFD-----YEFEAPEPKDF 239


>gi|239996474|ref|ZP_04716998.1| tRNA pseudouridine synthase A [Alteromonas macleodii ATCC 27126]
          Length = 250

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 67/226 (29%), Positives = 104/226 (46%), Gaps = 29/226 (12%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGG------------SGIAYHIDGFLKSWVDSKG-QKP 144
              +L+E++ + + NKP GI++               +G    IDG +          + 
Sbjct: 3   PIPVLFENTDLIIVNKPIGIAMHDATSEADVREDIAENGEPEKIDGIVTRLKKQLAVTEL 62

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HRLD  TSG L +A+  A A  + E F  RR+ K Y +L    PK K+  I   +  
Sbjct: 63  HLCHRLDTGTSGCLCLAKNAAVAGEIGELFSSRRVSKYYLALSDHKPKKKQGMIMGDM-- 120

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           K+  GG  + +    +   N AI+ F           ++ ++PH+G+THQ+RV    +G 
Sbjct: 121 KNRRGGQRILL----KTTENPAITQFFSSAAKPGTRGFI-VKPHSGKTHQIRVALKSIGA 175

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           PI+GD  Y             ++LYLHA ++ LP    G L +TAP
Sbjct: 176 PILGDTLYGGE--------TSDRLYLHAWHLRLP-LSSGELSVTAP 212


>gi|153834197|ref|ZP_01986864.1| pseudouridine synthase Rlu family protein [Vibrio harveyi HY01]
 gi|148869470|gb|EDL68471.1| pseudouridine synthase Rlu family protein [Vibrio harveyi HY01]
          Length = 230

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 55/200 (27%), Positives = 89/200 (44%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL+
Sbjct: 3   DILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAKH---SGDEQLYLIHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R   AA  L+++F  R ++K Y ++    PK K+  +   + +        V+     
Sbjct: 60  LGRNAKAASALSQAFAEREVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLVNSKT-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F  +     +      +PHTG+THQ+RV    +G  IVGD  Y A  +  
Sbjct: 118 ----NPAITQFFSLAAEPGER-LFLCKPHTGKTHQIRVALKSVGSGIVGDPIYNAGNEA- 171

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +  P+
Sbjct: 172 ------DRGYLHAFSLCFPY 185


>gi|289675117|ref|ZP_06496007.1| pseudouridine synthase [Pseudomonas syringae pv. syringae FF5]
          Length = 265

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 58/291 (19%), Positives = 103/291 (35%), Gaps = 30/291 (10%)

Query: 28  HYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
            +P ++          G+V   + K +  +   + G  +R+       N           
Sbjct: 2   KFPAVSREQWLDRFARGRVLDENGKAIAPDLAYREG--LRVHYFREVAN----------- 48

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPR 145
                +    +   +LY D  + V +KP  + V       Y     L+  +   G     
Sbjct: 49  -----ETPIPVVETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNPDLV 101

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HR+D+ T+G+++ +  R         F  RRI K Y ++   +P+     +    L +
Sbjct: 102 PLHRIDRHTAGLVLFSANRQTRSAYQTLFPTRRIDKFYQAIAPALPE-----LTFPRLHE 156

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           S +         Q   GA+   +  +V++    K     + P TG+ HQLRVH   +G  
Sbjct: 157 SRLVEGEPFFRMQEGVGASNTRTQIEVLERQ-DKLWRYGLYPVTGKKHQLRVHMAALGAA 215

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           I  D  Y  +   +     +N L L A  +    P  G      + LP   
Sbjct: 216 ICNDPFY-PDVVKDPVDDYRNPLKLLASSLRFVDPLNGEQRHFESLLPLDW 265


>gi|167524080|ref|XP_001746376.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163775138|gb|EDQ88763.1| predicted protein [Monosiga brevicollis MX1]
          Length = 289

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 111/268 (41%), Gaps = 36/268 (13%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQETS 155
           L   ++YED+ +   NK  G++VQ  +G    +   +  +  +K G  PRL HRLDQ T+
Sbjct: 9   LLRAVIYEDNHLVALNKWRGLAVQDAAGSPSTVLSNVDVFQQNKDGFVPRLAHRLDQNTT 68

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-------KKSHI 208
           G+LV+A+T  A   L   F++  + K Y +++ G        +              S +
Sbjct: 69  GVLVLAKTAEAVLRLNRLFQLGAVAKTYEAVLAGQVTKPTGTLKGIPELITEEEDANSEL 128

Query: 209 GGDYVHVVKQNEKGANYAISHFKVID----------CFAQKFCWLEMQPHTGRTHQLRVH 258
             +            + A SH+ V+                   +E++P TG  HQLR+ 
Sbjct: 129 TSNQPLFKTSASWSHSTAQSHYTVLASAQVNDGRPSRTKPWLTRVELRPTTGYKHQLRIQ 188

Query: 259 AL-HMGCPIVGDHKYCANFKG---------------NFTSPIQNKLYLHARYMDLP--HP 300
               +  P++GD +Y    +                    P    ++LHA+ + +P  + 
Sbjct: 189 CADGLRAPVLGDKRYGGGQEQVSPIILQHLQRHGLRTAAHPYGLVMHLHAKQLVIPGYNW 248

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           +G  L + A LP HM  T D+ G   D+
Sbjct: 249 DGSDLVLRATLPDHMQLTIDACGLHPDQ 276


>gi|332971512|gb|EGK10462.1| RNA pseudouridine synthase [Kingella kingae ATCC 23330]
          Length = 305

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 117/290 (40%), Gaps = 31/290 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +D +   H+P ++    Q  L SG V V+   + +  N    +G ++     I+  +   
Sbjct: 31  ID-FLCAHFPFVSKPAWQARLNSGMV-VNQQGEPINENEPFVAGNIIYYYREISRDD--- 85

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWV 137
                        +        +L  D  + V +KP  + V   G  +   +   L+   
Sbjct: 86  -------------EPRIPFDEKILLLDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLHP 132

Query: 138 DSKGQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           + +          HRLD++T+G+++++          + F+ + IQK Y +L       +
Sbjct: 133 NLQHLNVADITPIHRLDKDTAGVMLLSHNPQTRAAYQQLFQQKVIQKTYHALA----PTR 188

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            +      ++   + GD   + KQ + G   + +  ++++    K    E++P TG+ HQ
Sbjct: 189 LDLAYPLTVQSRLVRGDSFFLTKQID-GEPNSQTEIRLLEQRG-KHSLYELRPITGKKHQ 246

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           LRVH +H+G P++ D  Y    +   T      L L A+ +    P  G 
Sbjct: 247 LRVHMMHLGMPLLNDALY-PVAQEAGTEDYAKPLKLLAKKIVFIDPISGE 295


>gi|47229673|emb|CAG06869.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 388

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 64/271 (23%), Positives = 115/271 (42%), Gaps = 40/271 (14%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQK- 143
           SV+    +  L   LLY+D  + V NKP G++++  +G+         L   +     K 
Sbjct: 104 SVHPNVLAKHLHRSLLYQDDHVVVINKPYGVALREDTGVTSICSVLPVLSKMMSGNKIKS 163

Query: 144 ---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                    L++E SG L++A+    A+++    R  ++Q  YW +  G+P   +  I  
Sbjct: 164 DFQLLPCLGLEKEASGALLLAKRAEVAENIVNFQRNNQVQITYWVITVGVPVPSEGVIDI 223

Query: 201 WLLKKSHIGGDYVHVV-----------------KQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++++   G    + +                  +  + A+ A++ +KV+D  +     +
Sbjct: 224 PIIEREVTGPQPHYKMALSPLFKMNDAGDGLTRVRAHRQAHSAVTRYKVLDS-SCGCSLV 282

Query: 244 EMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNFTSPIQN---------------K 287
           E+QP TG  HQ+RVH    + CPI+GDHKY    K       +                 
Sbjct: 283 ELQPSTGVKHQMRVHMAFGLTCPILGDHKYSHWNKLAPQKLPERVLKKLGLEQSKSRHLP 342

Query: 288 LYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
           L+LHAR + LP  +   + +  P P +  +T
Sbjct: 343 LHLHARRLTLPGAQRAGVSVRCPAPKYFTQT 373


>gi|281209708|gb|EFA83876.1| putative fatty acid synthase [Polysphondylium pallidum PN500]
          Length = 3329

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 55/241 (22%), Positives = 96/241 (39%), Gaps = 23/241 (9%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                K  ++Y+  K  V NKP  I + G     + +  +++S       + R  +R+D 
Sbjct: 9   PPTNPKFEIIYKSDKYVVVNKPYDICIDGDDR-EFTVKKYIESCYQEVKGEVRFVNRIDY 67

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI---------PKNKKECIANWLL 203
            TSGI++ A T++ A    + F+ R  +K Y +LVWG          P   +  +   + 
Sbjct: 68  ATSGIVLTATTKSDANVAGQLFQNRATKKHYLALVWGHLHPLYDTNEPDTTEITVDKPIA 127

Query: 204 KKSHIGGDYVHV--VKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVH 258
                   +     V   +     + +H +V+       +    + + PHTGR HQLRVH
Sbjct: 128 DDKTDVNAFKMCIGVAGTDNPGRPSTTHVRVLQHGYYNGRPVSKVHLIPHTGRRHQLRVH 187

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP-AHMVK 317
              +G  IVGD  Y       F      ++ LH+  + +P  +   L      P   ++ 
Sbjct: 188 LDTLGHVIVGDETYGPKDAQCF------RMMLHSWKLTIPF-KNETLNFETEDPFKDLLS 240

Query: 318 T 318
            
Sbjct: 241 L 241


>gi|120611342|ref|YP_971020.1| pseudouridine synthase [Acidovorax citrulli AAC00-1]
 gi|120589806|gb|ABM33246.1| pseudouridine synthase [Acidovorax citrulli AAC00-1]
          Length = 307

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 60/298 (20%), Positives = 113/298 (37%), Gaps = 33/298 (11%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           VV   +    L  +     P +      + +  G+V    +       ++      +P +
Sbjct: 21  VVTPSQGGGLLIDFLAGRLPVVEREEWLQRMERGEVM--DEHASPVTPVRP----FVPGL 74

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHI 129
                  +  + ++             +  +LY+D  + V +KP  + V   G  + + +
Sbjct: 75  RIYYYRELASEAVIP-----------FEEAVLYQDEHLVVADKPHFLPVVPTGRYLQHTL 123

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              LK  +     +    HR+D++T+G+++ +  RA        FR R + K Y ++   
Sbjct: 124 LVRLKRRLGLD--ELSPVHRIDRDTAGLVLFSVQRATRGRYQALFRDRAVDKTYEAVAPW 181

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   +A    + S I             G   +++  +V+D     +    + P T
Sbjct: 182 RVD-----VAFPRERASRIEESPQFFRMHEVPGEANSLTRMEVLDVDG-AWARYRLSPVT 235

Query: 250 GRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GR HQLRVH   +G P+ GD  Y       +G+F+ P+Q    L AR +    P  GR
Sbjct: 236 GRRHQLRVHMAALGLPLRGDAFYPEVNDPPEGDFSRPLQ----LLARAIAFTDPVTGR 289


>gi|332844903|ref|XP_510721.3| PREDICTED: RNA pseudouridylate synthase domain-containing protein 1
           [Pan troglodytes]
          Length = 312

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 56/233 (24%), Positives = 100/233 (42%), Gaps = 17/233 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------RLTHRLDQET 154
           ++Y      V NK   + +   +            +   +   P      R  H+LD  T
Sbjct: 11  IVYRSRDFLVVNKHWDVRIDSKAWRETLTLQKQLRYRFPELADPDTCYGFRFCHQLDFST 70

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L VA  +AAA      F+ RR+ K Y +L+ G  +  +  I++ + + S  G  +  
Sbjct: 71  SGALCVALNKAAAGSAYRCFKDRRVTKAYLALLRGHIQESRVTISHAIGRNSTEGRAHTM 130

Query: 215 VVK--QNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            ++  Q  +    +++   V++           + ++P TGRTHQLRVH   +G  +VGD
Sbjct: 131 CIEGSQGCENPKPSLTELVVLEHGLYAGDPVSKVLLKPLTGRTHQLRVHCSALGHSVVGD 190

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
             Y     G    P   ++ LHA Y+ +P  +   +++  P P   + + D+ 
Sbjct: 191 LTYG-EVSGREDRPF--RMMLHAFYLRIP-TDTECVEVCTPDP--FLPSLDAC 237


>gi|239932294|ref|ZP_04689247.1| ribosomal pseudouridine synthase [Streptomyces ghanaensis ATCC
           14672]
          Length = 299

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 50/222 (22%), Positives = 89/222 (40%), Gaps = 9/222 (4%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTH 148
             +        +++ D  I V +KP  ++    GS +A      L+  +     +    H
Sbjct: 68  PAEVPVPFPLEVVHRDEHIVVVDKPHFLATTPRGSHVAQTALARLRRELGI--PELGAAH 125

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ T+G+++              FR RR+ K Y ++    P      +      +S I
Sbjct: 126 RLDRLTAGLVLFTVRPGERGAYQTLFRDRRVHKEYEAVAPYDP-----GLDLPRTVRSRI 180

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +   +  +  +G   A++  ++ +  A       + P TG+THQLRVH   +G PI+G
Sbjct: 181 VKERGELAAREVEGEPNALTLVELTEHRADGPGRYRLVPGTGQTHQLRVHMSALGVPILG 240

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           D  Y            +  L L AR ++   P  G   + T+
Sbjct: 241 DPLYPEVTAPVPAGDFRRPLQLLARVLEFTDPVTGVEHRFTS 282


>gi|306837150|ref|ZP_07470087.1| RNA pseudouridine synthase [Corynebacterium accolens ATCC 49726]
 gi|304566998|gb|EFM42626.1| RNA pseudouridine synthase [Corynebacterium accolens ATCC 49726]
          Length = 313

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 52/274 (18%), Positives = 103/274 (37%), Gaps = 15/274 (5%)

Query: 56  NNRIQSGQVVRIPPVINALNHII-KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
            +R  +G+VV           ++ K+  +    +   +        ++YED  I V +KP
Sbjct: 45  RDRFTAGEVVLRDQTPLKPGTVLGKDVDVFFYRIPAPETPVPYDIPIIYEDDNILVADKP 104

Query: 115 AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             ++    +         ++    +   +    HRLD+ TSG+L+  + +         F
Sbjct: 105 PFMATMPRARHIVE-TATVRLRRSTGNNELVPAHRLDRLTSGLLLFTKHKDVRGAYQSLF 163

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS------ 228
             +++ K Y ++       +      W  + +   G+    + + E  A   +       
Sbjct: 164 AEKKVHKTYRAVAE---FRRLPTPLQWSSRLTKTPGEIQGRIAEGEPNAFTTLESVDPID 220

Query: 229 --HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
              ++ +           ++P TG+THQLR+H    G PI+GD  Y   F       +  
Sbjct: 221 KAPYEKVHGPLPDLGLYTLKPQTGKTHQLRLHMWQAGIPILGDPVYPTIFPEEAED-MSV 279

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
            ++L A  ++   P  G+    T+ LP  M K  
Sbjct: 280 PMHLTATDLEFTDPLSGKPRHFTSGLPLAMHKLL 313


>gi|302561569|ref|ZP_07313911.1| pseudouridylate synthase [Streptomyces griseoflavus Tu4000]
 gi|302479187|gb|EFL42280.1| pseudouridylate synthase [Streptomyces griseoflavus Tu4000]
          Length = 299

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 47/215 (21%), Positives = 86/215 (40%), Gaps = 8/215 (3%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTH 148
             +        +++ D  I V +KP  ++    GS +       L+  +D    +    H
Sbjct: 68  PAEVPVPFPLEVVHRDEHIVVADKPHFLATTPRGSHVTQTALARLRRELDI--PELGAAH 125

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ T+G+++              FR R ++K Y ++    P+     +      +S I
Sbjct: 126 RLDRLTAGLVLFTVRPGERGAYQTLFRDRLVRKEYEAVAPYDPE-----LVLPRTVRSRI 180

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +   +  +   G   A++  ++ +  +       + P TG+THQLRVH   +G PI+G
Sbjct: 181 VKERGVLTAREVAGEPNALTRVEIAERRSDGPARYRLVPGTGQTHQLRVHMNGLGVPILG 240

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           D  Y            +  L L AR ++   P  G
Sbjct: 241 DPLYPEVTGPGPAGDFRRPLQLLARTLEFTDPVTG 275


>gi|330502423|ref|YP_004379292.1| pseudouridine synthase [Pseudomonas mendocina NK-01]
 gi|328916709|gb|AEB57540.1| pseudouridine synthase [Pseudomonas mendocina NK-01]
          Length = 293

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 61/286 (21%), Positives = 115/286 (40%), Gaps = 31/286 (10%)

Query: 25  FKNHYPHINFVN-LQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
             +H+P I+    LQ++ R G+V       +   +  + G  VR    +           
Sbjct: 25  LCDHFPAIDRTTWLQRMAR-GRVLDAAGAPIDATHPYRVGLKVRYFREVP---------- 73

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
                    +        +L++D  + V +KP  + V       Y     L   +   G 
Sbjct: 74  --------NETPIPFDEQVLWQDEHLLVADKPHFLPVMPAG--EYVEQTLLARLIKRTGN 123

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HR+D+ T+G+++ +   A+       FR R ++K Y ++   +P+ +      +
Sbjct: 124 PDLVPIHRIDRLTAGLVLFSVNPASRGQYQALFRQRAVEKCYEAIAPALPQLQF----PY 179

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L +   + G+    +++    AN + +  +V++   + + +  + P TGR HQLRVH   
Sbjct: 180 LHRSRMVEGEPFFRMQEVAGEAN-SETRIEVLERRGELWRYG-LSPVTGRKHQLRVHLAG 237

Query: 262 MGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           +G PIVGD  Y       N        L L AR +    P  G+++
Sbjct: 238 LGAPIVGDDFYPQLRESRNQPDDYSKPLKLLARGLLFADPVSGQVR 283


>gi|148690492|gb|EDL22439.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_a
           [Mus musculus]
          Length = 236

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 54/221 (24%), Positives = 92/221 (41%), Gaps = 20/221 (9%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------- 144
           +        ++Y+ S   V NK   + +   +   +     L+  +     +        
Sbjct: 2   EPGSMENLSIVYQSSDFLVVNKHWDLRIDSKT---WRETLTLQKQLRHHFPELADPDTCY 58

Query: 145 --RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             R  H+LD  TSG L VA  +AAA    + F+ RR+ K Y +LV G  +  +  I   +
Sbjct: 59  GFRFCHQLDFSTSGALCVALNKAAAGSAYKCFKERRVTKAYLALVRGHVQESQVTINYAI 118

Query: 203 LKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRV 257
            + S  G  +   ++     +    +++   V++           + ++P TGRTHQLRV
Sbjct: 119 GRNSTEGRTHTMCIEGTHGCENPKPSLTELLVLEHGLYAGDPVSKVLLKPLTGRTHQLRV 178

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           H   +G PIVGD  Y              ++ LHA Y+ +P
Sbjct: 179 HCSALGHPIVGDLTYGQAEDQEDQPF---RMMLHAFYLRIP 216


>gi|308370221|ref|ZP_07420688.2| hypothetical protein TMBG_01995 [Mycobacterium tuberculosis
           SUMu002]
 gi|308371305|ref|ZP_07424495.2| hypothetical protein TMCG_01723 [Mycobacterium tuberculosis
           SUMu003]
 gi|308372495|ref|ZP_07428863.2| hypothetical protein TMDG_02135 [Mycobacterium tuberculosis
           SUMu004]
 gi|308373700|ref|ZP_07433364.2| hypothetical protein TMEG_03697 [Mycobacterium tuberculosis
           SUMu005]
 gi|308374836|ref|ZP_07437561.2| hypothetical protein TMFG_00509 [Mycobacterium tuberculosis
           SUMu006]
 gi|308376065|ref|ZP_07445963.2| hypothetical protein TMGG_02848 [Mycobacterium tuberculosis
           SUMu007]
 gi|308377296|ref|ZP_07441776.2| hypothetical protein TMHG_02521 [Mycobacterium tuberculosis
           SUMu008]
 gi|308378264|ref|ZP_07482058.2| hypothetical protein TMIG_02817 [Mycobacterium tuberculosis
           SUMu009]
 gi|308379478|ref|ZP_07486410.2| hypothetical protein TMJG_03484 [Mycobacterium tuberculosis
           SUMu010]
 gi|308325101|gb|EFP13952.1| hypothetical protein TMBG_01995 [Mycobacterium tuberculosis
           SUMu002]
 gi|308329322|gb|EFP18173.1| hypothetical protein TMCG_01723 [Mycobacterium tuberculosis
           SUMu003]
 gi|308333153|gb|EFP22004.1| hypothetical protein TMDG_02135 [Mycobacterium tuberculosis
           SUMu004]
 gi|308336840|gb|EFP25691.1| hypothetical protein TMEG_03697 [Mycobacterium tuberculosis
           SUMu005]
 gi|308340673|gb|EFP29524.1| hypothetical protein TMFG_00509 [Mycobacterium tuberculosis
           SUMu006]
 gi|308344407|gb|EFP33258.1| hypothetical protein TMGG_02848 [Mycobacterium tuberculosis
           SUMu007]
 gi|308348411|gb|EFP37262.1| hypothetical protein TMHG_02521 [Mycobacterium tuberculosis
           SUMu008]
 gi|308353248|gb|EFP42099.1| hypothetical protein TMIG_02817 [Mycobacterium tuberculosis
           SUMu009]
 gi|308356988|gb|EFP45839.1| hypothetical protein TMJG_03484 [Mycobacterium tuberculosis
           SUMu010]
          Length = 294

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 96/252 (38%), Gaps = 12/252 (4%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVF 111
           V    ++ +G+VV     +     ++    ++    +L  +        +L++D+ I V 
Sbjct: 27  VAARAKVLAGEVVDDDGAVVDSGTVLPPGSVVHLYRDLPDEVPVPFDVPVLHQDADIVVV 86

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   +    +    HRLD+ T+G+L+    R       
Sbjct: 87  DKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTTRREVRGSYQ 145

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    ++K Y +     P      +A   L +S I     H+    E G   A +  +
Sbjct: 146 TMFARGLVRKTYLARAPVAP-----GLALPRLVRSRIVKRRGHLQAVCEPGVPNAETLVE 200

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
            I           + P TGRTHQLRVH   +G PI+GD  Y  N            L L 
Sbjct: 201 RIARDG----LYRLTPTTGRTHQLRVHMAALGIPIMGDPLY-PNVISVAAHDFSTPLQLL 255

Query: 292 ARYMDLPHPEGG 303
           A+ ++   P  G
Sbjct: 256 AQRIEFDDPLTG 267


>gi|32034411|ref|ZP_00134593.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
 gi|126207717|ref|YP_001052942.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae L20]
 gi|190149500|ref|YP_001968025.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           7 str. AP76]
 gi|303251649|ref|ZP_07337822.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           6 str. Femo]
 gi|303252800|ref|ZP_07338960.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           2 str. 4226]
 gi|307245042|ref|ZP_07527136.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|307247214|ref|ZP_07529264.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|307249442|ref|ZP_07531431.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
 gi|307251759|ref|ZP_07533662.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|307256257|ref|ZP_07538041.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 10
           str. D13039]
 gi|307258451|ref|ZP_07540189.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 11
           str. 56153]
 gi|307262819|ref|ZP_07544444.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 13
           str. N273]
 gi|126096509|gb|ABN73337.1| predicted RNA pseudouridine synthase [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
 gi|189914631|gb|ACE60883.1| predicted RNA pseudouridine synthase [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|302648361|gb|EFL78557.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           2 str. 4226]
 gi|302649491|gb|EFL79674.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           6 str. Femo]
 gi|306854030|gb|EFM86241.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|306856272|gb|EFM88425.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|306858516|gb|EFM90583.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
 gi|306860760|gb|EFM92770.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|306865221|gb|EFM97120.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 10
           str. D13039]
 gi|306867456|gb|EFM99306.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 11
           str. 56153]
 gi|306871834|gb|EFN03553.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 13
           str. N273]
          Length = 216

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 61/226 (26%), Positives = 99/226 (43%), Gaps = 21/226 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  + ++     V +KP G+SV          +   +     + ++  L HRLD+ TSG+
Sbjct: 4   KLTICFQHHDFVVIDKPVGVSVHKDEEAIGLTENLAEQL---QAEQVWLVHRLDKVTSGL 60

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A  + AA H    F   +I+K YW+L    PK K+  I+  + K  +      H  +
Sbjct: 61  LIFALNKQAAVHFYHLFEQHKIEKTYWALSDQKPKKKQGKISGDMQKSRNGAWKLFHSKQ 120

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                 N A++ F V            +QP TG+THQLRV    +G PI+GD +Y     
Sbjct: 121 ------NPAVTQF-VSHSLEPNLRHFILQPKTGKTHQLRVAMKSLGSPILGDQRYAGT-- 171

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
                   +++YLHA  +   + +G    I +   +   + W  LG
Sbjct: 172 ------AADRVYLHAYQLKFDY-QGESFCIQSQPTSG--RFWAKLG 208


>gi|154148734|ref|YP_001407253.1| RNA pseudouridine synthase [Campylobacter hominis ATCC BAA-381]
 gi|153804743|gb|ABS51750.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           (RNA pseudouridylate synthase) [Campylobacter hominis
           ATCC BAA-381]
          Length = 304

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 67/308 (21%), Positives = 116/308 (37%), Gaps = 42/308 (13%)

Query: 41  LRSGQVRVDKKRV-----------KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
           ++    R D KR            K + R+   + +   PV     + I   +I      
Sbjct: 4   IKKFLCRADGKRAFEILINCGFCMKDSQRLIDKKRIFCGPVSVDTKNEILNGEI----FM 59

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTH 148
           +           ++E+    VF+KP+GI     G    Y +   + +     G+   + H
Sbjct: 60  IDYECMSRGIYPIFENDDFAVFDKPSGILSHPNGRHCEYSLCDEIWTLF---GKNANVAH 116

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ETSG+L+ ++   +A  L   F  + +QKIY++LV G     +  I N  + K++ 
Sbjct: 117 RLDRETSGLLIASKNPKSADELKNMFEKKTVQKIYFALVSGRV--NENFICNKPIGKAY- 173

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQ----KFCWLEMQPHTGRTHQLRVHALHMGC 264
             D + +  +       AI+ F  +  +          ++  P TGR HQ+R+H  HM  
Sbjct: 174 SDDEIGIKMRIRDDGKPAITEFYPLKFYENIGESGATIIKAIPKTGRQHQIRLHLFHMKH 233

Query: 265 PIVGDHKYCANFK-------------GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
            I GD  Y                           +L LHA  +     +G    I + +
Sbjct: 234 KIFGDPLYGLETYTAEAIMDKKLSIFDRVKFSGATRLCLHAAEISFEF-KGENFHIKSKI 292

Query: 312 PAHMVKTW 319
                K +
Sbjct: 293 --DFEKEF 298


>gi|322495754|emb|CBZ31060.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 741

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 91/237 (38%), Gaps = 28/237 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV--QG------GSGIAYHIDGFLKS----WVDSKGQKPRLTH 148
           +LYED  + V +KPAG++    G      G+     I   L       +     +    H
Sbjct: 514 VLYEDDDVLVVDKPAGLATSRHGLSCTQLGTPTTDLISVLLARDRAGALARGVFRQGQVH 573

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD ETSG L++A++  AA  L            +  +   +       +    L+   +
Sbjct: 574 RLDAETSGCLLIAKSDVAADSLRHQLGTSAAFSHHSKIYHALC-----VVLEPSLRNVRL 628

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             D +       +      + ++VI  F   +  W+E +   G+ HQ+R H    G PI+
Sbjct: 629 HDDIIDAADPKIR------TRYRVIRFFPKHRVAWVECRIQQGKKHQIRRHLASRGFPIL 682

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            D ++           + +++ LHA  +   HP     +   APLPA   +    L 
Sbjct: 683 ADLEHGG---AVCCQSMISRVALHAHSLSFIHPVTADPIIAAAPLPADFRRCLSLLR 736


>gi|213027660|ref|ZP_03342107.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 176

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 47/128 (36%), Positives = 73/128 (57%), Gaps = 8/128 (6%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +SG  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  ESGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAY 127
            GGSG+++
Sbjct: 114 HGGSGLSF 121


>gi|330951836|gb|EGH52096.1| pseudouridine synthase [Pseudomonas syringae Cit 7]
          Length = 296

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 60/302 (19%), Positives = 104/302 (34%), Gaps = 37/302 (12%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +P I+          G+V   + K +  +   + G  +R+       N        
Sbjct: 30  LCAKFPAISREQWLDRFARGRVLDENGKAIAPDLAYREG--LRVHYFREVAN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQ 142
                   +        +LY D  + V +KP  + V       Y     L+  +      
Sbjct: 80  --------ETPIPGVETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLDNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  RRI K Y ++   +P    E I   L
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANRQTRSAYQALFPTRRIDKFYQAIAPALP----ELIFPRL 185

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            +   + G+    + Q   GA+   +  +V++    K     + P TG+ HQLRVH   +
Sbjct: 186 HESRLVEGEPFFRM-QEGVGASNTRTQIEVLERQ-DKLWRYGLYPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G  I  D  Y  +   +     ++ L L A  +    P  G        P H       L
Sbjct: 244 GAAICNDPFY-PDVVKDPVDDYRHPLKLLASSLRFIDPINGE-------PRHFESLLQ-L 294

Query: 323 GF 324
            +
Sbjct: 295 DW 296


>gi|298526776|ref|ZP_07014185.1| pseudouridine synthase [Mycobacterium tuberculosis 94_M4241A]
 gi|298496570|gb|EFI31864.1| pseudouridine synthase [Mycobacterium tuberculosis 94_M4241A]
          Length = 297

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 96/252 (38%), Gaps = 12/252 (4%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVF 111
           V    ++ +G+VV     +     ++    ++    +L  +        +L++D+ I V 
Sbjct: 30  VAARAKVLAGEVVDDDGAVVDSGTVLPPGSVVHLYRDLPDEVPVPFDVPVLHQDADIVVV 89

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   +    +    HRLD+ T+G+L+    R       
Sbjct: 90  DKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTTRREVRGSYQ 148

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    ++K Y +     P      +A   L +S I     H+    E G   A +  +
Sbjct: 149 TMFARGLVRKTYLARAPVAP-----GLALPRLVRSRIVKRRGHLQAVCEPGVPNAETLVE 203

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
            I           + P TGRTHQLRVH   +G PI+GD  Y  N            L L 
Sbjct: 204 RIARDG----LYRLTPTTGRTHQLRVHMAALGIPIMGDPLY-PNVISVAAHDFSTPLQLL 258

Query: 292 ARYMDLPHPEGG 303
           A+ ++   P  G
Sbjct: 259 AQRIEFDDPLTG 270


>gi|120402627|ref|YP_952456.1| pseudouridine synthase [Mycobacterium vanbaalenii PYR-1]
 gi|119955445|gb|ABM12450.1| pseudouridine synthase [Mycobacterium vanbaalenii PYR-1]
          Length = 285

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 58/278 (20%), Positives = 105/278 (37%), Gaps = 23/278 (8%)

Query: 41  LRSGQVRVD-----KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHS 94
           LR G V V+      +      ++ +G+V      +   + +++   ++    +L  + +
Sbjct: 20  LRGGAVLVELADRFGEAAAA--KVLNGEVFTADGAVVTASTVLQPNSVVYLYRDLPDEVA 77

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
                 +L+ D  + V +KP  ++     G        ++   +    +    HRLD+ T
Sbjct: 78  VPFDVPVLHRDDNLVVVDKPHFLATMP-RGSHVAQTALVRMRRELDLPQLSPAHRLDRLT 136

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN-WLLKKSHIGGDYV 213
           +G+LV    R         F    + K Y +      ++      +  +  +S I     
Sbjct: 137 AGVLVFTTRREVRGAYQTMFARGGVSKTYLA------QSSAGTDRDFPITVRSRIIKRRG 190

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +    E G   A +  + +D          + P TGRTHQLRVH   +G PI GD  Y 
Sbjct: 191 TLQAVEEPGEPNAETLVERVDDRT-----YRLMPRTGRTHQLRVHMNSLGLPIAGDPLY- 244

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAP 310
            N            L L A+ ++   P  G RL+ T+ 
Sbjct: 245 PNVIDVAVGDFSTPLKLLAQCLEFTDPLAGVRLRFTSE 282


>gi|328861018|gb|EGG10122.1| hypothetical protein MELLADRAFT_94488 [Melampsora larici-populina
           98AG31]
          Length = 341

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 68/293 (23%), Positives = 124/293 (42%), Gaps = 27/293 (9%)

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
             ++R+   Q+ R       L H +K ++ L++ +     + F    +LY+D K+ V NK
Sbjct: 47  TASSRLPRSQIKRAKIAEEKLVHHLKAKEELENRL----RASFRPPEILYDDEKVLVINK 102

Query: 114 PAGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           PAG ++Q   G  A+     +     +   K  L  RLD+ TSG L++AR+ + A+ +  
Sbjct: 103 PAGCALQAEEGSEAFIRWNLIHDHFTNIYGKLYLVQRLDKSTSGPLILARSSSVARTIGT 162

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKE----CIANWLLKKSHIGGDYVHVVKQN--EKGANYA 226
            F+   I+K Y +LV  +P  +           +L +     D + + + N        A
Sbjct: 163 QFKQSTIKKRYLALVQFLPTKRGPIQEATTQGKVLCRMRNRSDKMVIAEANRTGPDCKRA 222

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLR-VHALHMGCPIVGDHKYCANFKGN------ 279
            + +K++   +     + + P TGR HQLR V +  +  PIVGD KY   +  +      
Sbjct: 223 ETDWKLVTATS-THAIVSLLPTTGRKHQLRLVCSRFLSAPIVGDFKYDFRYLSDKSQKCI 281

Query: 280 ---FTSPIQNKLYLHARYMDLPHPEGGR-----LQITAPLPAHMVKTWDSLGF 324
                    +++ LH+  ++             +++ AP P       D L  
Sbjct: 282 EDFLKRESDSRIMLHSSQIEFKLYRKEEPKQITIKVRAPFPEDFRILCDQLDL 334


>gi|218892001|ref|YP_002440868.1| putative pseudouridylate synthase [Pseudomonas aeruginosa LESB58]
 gi|218772227|emb|CAW28006.1| putative pseudouridylate synthase [Pseudomonas aeruginosa LESB58]
          Length = 300

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 99/263 (37%), Gaps = 12/263 (4%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAG 116
           R+Q G+V+             +E   +     L   +    ++ +LY D  + V +KP  
Sbjct: 45  RMQRGRVLDAEGRALGPQAAYREGLRVHYFRELPVEAPIPFEARILYRDEHLLVADKPHF 104

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           + V    G  Y     L     S G +     HR+D+ T+G+++ +    +       FR
Sbjct: 105 LPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTAGLVLFSTNPGSRGRYQALFR 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            RRI K Y ++   +P+     +   LL+++ +         +  +G   + +  +V++ 
Sbjct: 163 ERRIDKCYEAIAPALPQ-----LDFPLLRRTRLVPGEPFFRMREGEGEPNSETRIEVVER 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-TSPIQNKLYLHARY 294
               +    + P TG+ HQLRVH   +G  I  D  Y                L L AR 
Sbjct: 218 NG-GWWRYRLYPVTGKKHQLRVHLAALGAGIQNDGFYPELLDAEGSPDDYLRPLKLLARG 276

Query: 295 MDLPHP-EGGRLQITAPLPAHMV 316
           +    P  G R    + L     
Sbjct: 277 LRFDDPLSGERRTFESGLRLDWQ 299


>gi|301769635|ref|XP_002920217.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Ailuropoda melanoleuca]
 gi|281341567|gb|EFB17151.1| hypothetical protein PANDA_008946 [Ailuropoda melanoleuca]
          Length = 302

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 57/245 (23%), Positives = 97/245 (39%), Gaps = 23/245 (9%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------- 144
           +        ++Y+     V NK   + +       +     L+  +     +        
Sbjct: 2   EPGRIENLSVVYQSPDFLVVNKHWDLRI---DSKMWRETPTLQKQLRHHFPELADPDTYY 58

Query: 145 --RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             R  H+LD  TSG L VA  +AAA    + F+ RR+ K Y +LV G  +  +  I   +
Sbjct: 59  GFRFCHQLDFSTSGALCVALNKAAAGSAYKCFKERRVTKAYLALVRGHVQENRMTINYAI 118

Query: 203 LKKSHIGGDYVHVVKQN--EKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRV 257
            + S  G  +   ++     +    +++   V++           + +QP TGRTHQLRV
Sbjct: 119 GRNSTEGRAHTMCIEGTLGCENPKPSLTELVVLEHGLYAGDPVSKVLLQPLTGRTHQLRV 178

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
           H   +  P+VGD  Y              ++ LHA Y+ +P     R++   P P   V 
Sbjct: 179 HCSALSHPVVGDLTYGQAPDQEDQPF---RMMLHAFYLRIP-THTERVEACTPDP--FVP 232

Query: 318 TWDSL 322
             D+ 
Sbjct: 233 ALDAC 237


>gi|302187564|ref|ZP_07264237.1| pseudouridine synthase [Pseudomonas syringae pv. syringae 642]
          Length = 296

 Score =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 57/294 (19%), Positives = 101/294 (34%), Gaps = 30/294 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +P I+          G+V   + K +  +   + G  +R+       N        
Sbjct: 30  LCAKFPAISREQWLDRFARGRVLDENGKAIAPDLAYREG--LRVHYFREVAN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +   G  
Sbjct: 80  --------ETPIPVVETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  RRI K Y ++   +P      +    
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANRQTRSAYQALFPTRRIDKFYQAIAPALP-----GLTFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++    K     + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGAGASNTRTQIEVLERQ-DKLWRYGLYPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           G  I  D  Y  +   +     ++ L L A  +    P  G      + L    
Sbjct: 244 GAAICNDPFY-PDVVKDPVDDYRHPLKLLASSLRFVDPLNGEQRHFESLLTLDW 296


>gi|259146673|emb|CAY79930.1| Pus6p [Saccharomyces cerevisiae EC1118]
          Length = 404

 Score =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 100/253 (39%), Gaps = 23/253 (9%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
            +++R G   V    +     I++  V+      +       EQ                
Sbjct: 63  YRLIRDGVPLVPDHLMT--TIIKNHDVLETTTHKH---EPPVEQWCSQEVEAEDLPGRIA 117

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              +++ED  I V +KP+GI V             +   +   G      +RLD+ TSG+
Sbjct: 118 GFNIVFEDESILVIDKPSGIPVHPTGQF---YQNTITELLKLHGVDALPCYRLDKITSGL 174

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-------------LLK 204
           L++A+   +A  + +S R R + KIY + V G   + +  + N               ++
Sbjct: 175 LILAKNSQSAGEIQKSIRSRDMIKIYLARVKGRFPHSELILDNENAAETTFEDTSKVTVE 234

Query: 205 KSHI-GGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
            + I   D           +  AI+ F  I  F+      +  +P TGRTHQ+R+H   +
Sbjct: 235 MTPIYSIDPKRQFPVGLSASKDAITKFYPIRYFSHADETVVACKPITGRTHQIRIHLARL 294

Query: 263 GCPIVGDHKYCAN 275
           G PIV D  YC++
Sbjct: 295 GHPIVNDSVYCSH 307


>gi|332024709|gb|EGI64898.1| RNA pseudouridylate synthase domain-containing protein 2
           [Acromyrmex echinatior]
          Length = 335

 Score =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 52/182 (28%), Positives = 82/182 (45%), Gaps = 7/182 (3%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  + V NKPA I V       ++   F+ +  +   +  R  HRLD+ TSGIL+  RT 
Sbjct: 2   DEDVVVVNKPASIPVHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDRLTSGILLFGRTP 60

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
             A+ +    R R++ K Y   V G    ++   +  +   S+     + V K +EKG  
Sbjct: 61  KKARQMEHQIRNRQVHKQYVCRVEGEFPEEEVICSEPIEVVSY----KIGVCKVSEKG-K 115

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
             ++ FK +    +    +  +P TGR HQ+RVH  ++G P+V D  Y     G      
Sbjct: 116 DCVTRFKRLSYNGKS-SVVLCKPQTGRMHQIRVHLQYLGYPVVNDPLYNHVVFGPHKGKG 174

Query: 285 QN 286
            N
Sbjct: 175 GN 176


>gi|308182516|ref|YP_003926643.1| hypothetical protein HPPC_01740 [Helicobacter pylori PeCan4]
 gi|308064701|gb|ADO06593.1| hypothetical protein HPPC_01740 [Helicobacter pylori PeCan4]
          Length = 293

 Score =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 70/294 (23%), Positives = 119/294 (40%), Gaps = 29/294 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVSLI------------HFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +     L++E     VF+KP  +      G  YH +  L       G+     HRLD E
Sbjct: 64  PNEKTQALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D  
Sbjct: 122 TSGLVLAGKTLQSAKDLKALFMQKKVKKTYLALAHGLV-DKNIVIDKPILTPQNIQKDLR 180

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              K +      + +  K +          L++ P TGRTHQ+R+H   +G  IVG+  Y
Sbjct: 181 IRSKIS-PLGKPSTTLVKPLSYNPFLDISLLKITPLTGRTHQIRLHLSSVGHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +         +      L LHA  ++    +G   +IT+ +P   +    
Sbjct: 240 GVIDENAREYLQLKRENNAPLLMLHASSLEFEF-KGAIHEITSQMPQRFMPFLK 292


>gi|226952693|ref|ZP_03823157.1| 23S RNA-specific pseudouridylate synthase [Acinetobacter sp. ATCC
           27244]
 gi|226836561|gb|EEH68944.1| 23S RNA-specific pseudouridylate synthase [Acinetobacter sp. ATCC
           27244]
          Length = 302

 Score =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 60/292 (20%), Positives = 118/292 (40%), Gaps = 31/292 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +   H+ HI     Q+    G +   D K++K ++   +   +     +    H+  E +
Sbjct: 34  YLCQHFEHIKIEEWQQRFDDGLIYSADGKKLKSDSPYTANTHIFYYRFLAHEIHVPFEHQ 93

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             +L+ED  + V +KP  +++       Y  +  L       G 
Sbjct: 94  ------------------ILFEDEHLLVVDKPHFLTMSPTG--QYVQETLLVRLKKQTGY 133

Query: 143 K-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIAN 200
           K     HRLD+ET+G+++  +  +A     + F  R++QKIY ++    P+    + +  
Sbjct: 134 KELTPIHRLDRETAGVVLFCKKASARGIYQQLFAERKVQKIYHAIAVYRPELHFPQTVKL 193

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K    G  +  +    EK +N   +  ++++   +      ++P TG+ HQLRVH  
Sbjct: 194 HLEK----GLPFYTMQVNLEKPSNT-ETFIELLE-HNKSHAKYLLKPQTGKQHQLRVHLN 247

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
           ++G PI+ D  Y  +     +    + L L A+ +    P     +   + L
Sbjct: 248 YLGIPILNDEFY-PDIAHKSSDDFSSPLQLLAKEIFFNDPVSKQEMHFNSKL 298


>gi|319948901|ref|ZP_08023012.1| ribosomal pseudouridine synthase [Dietzia cinnamea P4]
 gi|319437439|gb|EFV92448.1| ribosomal pseudouridine synthase [Dietzia cinnamea P4]
          Length = 332

 Score =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 108/303 (35%), Gaps = 39/303 (12%)

Query: 25  FKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
            +  +P      L   L +GQV   D   V    R   G  V +              + 
Sbjct: 38  LRRRFPD-GLAELDAALEAGQVVTADGAAVTPATRRHRGMDVWMY-------------RT 83

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
            D  + +    +     +L+ D ++ V +KP  ++    +G        ++   D     
Sbjct: 84  PDPEIPVPHQIE-----VLHRDDRLVVVDKPHFLATTPRAGHV-TETALVRLRRDLGLDD 137

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD+ T+G+LV     A      + F  RR+ K Y ++      +    +     
Sbjct: 138 LAPAHRLDRLTAGVLVFTADPAYRGAYQDLFAARRVTKTYLAVAPA--PDGVATVRERSS 195

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +     G         E  A+  I+          +     ++P TGRTHQLRVH   +G
Sbjct: 196 RILKTRGVLQATEVDGEPDAHTRITLLDTRGAGPDRLGLYRLEPTTGRTHQLRVHMNALG 255

Query: 264 CPIVGDHKYCANF---KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV--KT 318
            PI+GD  Y        G+FT P+Q    L A  +    P  G+       P H    +T
Sbjct: 256 TPILGDDLYPDVLDMTPGDFTRPLQ----LLASEIAFTDPFTGQ-------PRHFASRRT 304

Query: 319 WDS 321
            D+
Sbjct: 305 LDA 307


>gi|226324130|ref|ZP_03799648.1| hypothetical protein COPCOM_01908 [Coprococcus comes ATCC 27758]
 gi|225207679|gb|EEG90033.1| hypothetical protein COPCOM_01908 [Coprococcus comes ATCC 27758]
          Length = 172

 Score =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 52/184 (28%), Positives = 84/184 (45%), Gaps = 14/184 (7%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLDQ  SGILV ART AAA++L +  +  + +K Y ++V G        + ++L+K 
Sbjct: 1   MIHRLDQPVSGILVFARTPAAAKNLNQQLQNDQFEKYYQAVVCGSLP-DSGTLTDYLVKD 59

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGC 264
                    +  +N  GA  A+  +++++         +++   TGR HQ+RV     G 
Sbjct: 60  GRTNTSR--ICSKNTPGAKKAVLSYEILETSEVTGLSVVQIHLGTGRHHQIRVQMAGAGA 117

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
           P+ GD+KY   F           + L A  +   HP  G R++   P        W+ L 
Sbjct: 118 PLWGDNKYNPEFVNKRGYF---PIALRAFRLSFCHPTTGKRMEFEVPC------NWEQLE 168

Query: 324 FKYD 327
            K D
Sbjct: 169 TKAD 172


>gi|330977680|gb|EGH77583.1| pseudouridine synthase [Pseudomonas syringae pv. aptata str. DSM
           50252]
          Length = 296

 Score =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 59/302 (19%), Positives = 104/302 (34%), Gaps = 37/302 (12%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +P I+          G+V   + K +  +   + G  +R+       N        
Sbjct: 30  LCAKFPAISREQWLDRFARGRVLDENGKAIAPDLAYREG--LRVHYFREVAN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +   G  
Sbjct: 80  --------ETPIPVVETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  RRI K Y ++   +P+     +    
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANRQTRSAYQTLFPTRRIDKFYQAIAPALPE-----LTFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++    K     + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGFGASNTRTQIEVLERQ-DKLWRYGLYPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G  I  D  Y  +   +     +N L L A  +    P  G  +       H       L
Sbjct: 244 GAAICNDPFY-PDVVKHPVDDYRNPLKLLASSLRFVDPLNGEQR-------HFESLLQ-L 294

Query: 323 GF 324
            +
Sbjct: 295 DW 296


>gi|15610436|ref|NP_217817.1| hypothetical protein Rv3300c [Mycobacterium tuberculosis H37Rv]
 gi|121639189|ref|YP_979413.1| hypothetical protein BCG_3329c [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|121639223|ref|YP_979447.1| hypothetical protein BCG_3365c [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148663163|ref|YP_001284686.1| hypothetical protein MRA_3341 [Mycobacterium tuberculosis H37Ra]
 gi|148824502|ref|YP_001289256.1| hypothetical protein TBFG_13329 [Mycobacterium tuberculosis F11]
 gi|167968932|ref|ZP_02551209.1| hypothetical protein MtubH3_13227 [Mycobacterium tuberculosis
           H37Ra]
 gi|215405313|ref|ZP_03417494.1| hypothetical protein Mtub0_16781 [Mycobacterium tuberculosis
           02_1987]
 gi|215428786|ref|ZP_03426705.1| hypothetical protein MtubT9_21303 [Mycobacterium tuberculosis T92]
 gi|218755082|ref|ZP_03533878.1| hypothetical protein MtubG1_17389 [Mycobacterium tuberculosis GM
           1503]
 gi|219559362|ref|ZP_03538438.1| hypothetical protein MtubT1_19482 [Mycobacterium tuberculosis T17]
 gi|224991682|ref|YP_002646371.1| hypothetical protein JTY_3325 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|224991701|ref|YP_002646390.1| hypothetical protein JTY_3345 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|224991720|ref|YP_002646409.1| hypothetical protein JTY_3365 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253800343|ref|YP_003033344.1| hypothetical protein TBMG_03348 [Mycobacterium tuberculosis KZN
           1435]
 gi|254233908|ref|ZP_04927233.1| conserved hypothetical protein [Mycobacterium tuberculosis C]
 gi|254365921|ref|ZP_04981966.1| conserved hypothetical protein [Mycobacterium tuberculosis str.
           Haarlem]
 gi|254552402|ref|ZP_05142849.1| hypothetical protein Mtube_18458 [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260188348|ref|ZP_05765822.1| hypothetical protein MtubCP_20308 [Mycobacterium tuberculosis
           CPHL_A]
 gi|260202462|ref|ZP_05769953.1| hypothetical protein MtubT4_20818 [Mycobacterium tuberculosis T46]
 gi|260206652|ref|ZP_05774143.1| hypothetical protein MtubK8_20352 [Mycobacterium tuberculosis K85]
 gi|289444882|ref|ZP_06434626.1| conserved hypothetical protein [Mycobacterium tuberculosis T46]
 gi|289448989|ref|ZP_06438733.1| conserved hypothetical protein [Mycobacterium tuberculosis CPHL_A]
 gi|289555578|ref|ZP_06444788.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN 605]
 gi|289571527|ref|ZP_06451754.1| conserved hypothetical protein [Mycobacterium tuberculosis T17]
 gi|289576020|ref|ZP_06456247.1| conserved hypothetical protein [Mycobacterium tuberculosis K85]
 gi|289747118|ref|ZP_06506496.1| conserved hypothetical protein [Mycobacterium tuberculosis 02_1987]
 gi|289751996|ref|ZP_06511374.1| conserved hypothetical protein [Mycobacterium tuberculosis T92]
 gi|289763488|ref|ZP_06522866.1| conserved hypothetical protein [Mycobacterium tuberculosis GM 1503]
 gi|294993759|ref|ZP_06799450.1| hypothetical protein Mtub2_04411 [Mycobacterium tuberculosis 210]
 gi|297635954|ref|ZP_06953734.1| hypothetical protein MtubK4_17602 [Mycobacterium tuberculosis KZN
           4207]
 gi|297732951|ref|ZP_06962069.1| hypothetical protein MtubKR_17757 [Mycobacterium tuberculosis KZN
           R506]
 gi|313660283|ref|ZP_07817163.1| hypothetical protein MtubKV_17757 [Mycobacterium tuberculosis KZN
           V2475]
 gi|2181957|emb|CAB09445.1| CONSERVED HYPOTHETICAL PROTEIN [Mycobacterium tuberculosis H37Rv]
 gi|121494837|emb|CAL73318.1| Conserved hypothetical protein [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|121494871|emb|CAL73354.1| Conserved hypothetical protein [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|124599437|gb|EAY58541.1| conserved hypothetical protein [Mycobacterium tuberculosis C]
 gi|134151434|gb|EBA43479.1| conserved hypothetical protein [Mycobacterium tuberculosis str.
           Haarlem]
 gi|148507315|gb|ABQ75124.1| conserved hypothetical protein [Mycobacterium tuberculosis H37Ra]
 gi|148723029|gb|ABR07654.1| conserved hypothetical protein [Mycobacterium tuberculosis F11]
 gi|224774797|dbj|BAH27603.1| hypothetical protein JTY_3325 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|224774816|dbj|BAH27622.1| hypothetical protein JTY_3345 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|224774835|dbj|BAH27641.1| hypothetical protein JTY_3365 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253321846|gb|ACT26449.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN
           1435]
 gi|289417801|gb|EFD15041.1| conserved hypothetical protein [Mycobacterium tuberculosis T46]
 gi|289421947|gb|EFD19148.1| conserved hypothetical protein [Mycobacterium tuberculosis CPHL_A]
 gi|289440210|gb|EFD22703.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN 605]
 gi|289540451|gb|EFD45029.1| conserved hypothetical protein [Mycobacterium tuberculosis K85]
 gi|289545281|gb|EFD48929.1| conserved hypothetical protein [Mycobacterium tuberculosis T17]
 gi|289687646|gb|EFD55134.1| conserved hypothetical protein [Mycobacterium tuberculosis 02_1987]
 gi|289692583|gb|EFD60012.1| conserved hypothetical protein [Mycobacterium tuberculosis T92]
 gi|289710994|gb|EFD75010.1| conserved hypothetical protein [Mycobacterium tuberculosis GM 1503]
 gi|326902472|gb|EGE49405.1| hypothetical protein TBPG_00317 [Mycobacterium tuberculosis W-148]
 gi|328460077|gb|AEB05500.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN
           4207]
          Length = 305

 Score =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 96/252 (38%), Gaps = 12/252 (4%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVF 111
           V    ++ +G+VV     +     ++    ++    +L  +        +L++D+ I V 
Sbjct: 38  VAARAKVLAGEVVDDDGAVVDSGTVLPPGSVVHLYRDLPDEVPVPFDVPVLHQDADIVVV 97

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   +    +    HRLD+ T+G+L+    R       
Sbjct: 98  DKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTTRREVRGSYQ 156

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    ++K Y +     P      +A   L +S I     H+    E G   A +  +
Sbjct: 157 TMFARGLVRKTYLARAPVAP-----GLALPRLVRSRIVKRRGHLQAVCEPGVPNAETLVE 211

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
            I           + P TGRTHQLRVH   +G PI+GD  Y  N            L L 
Sbjct: 212 RIARDG----LYRLTPTTGRTHQLRVHMAALGIPIMGDPLY-PNVISVAAHDFSTPLQLL 266

Query: 292 ARYMDLPHPEGG 303
           A+ ++   P  G
Sbjct: 267 AQRIEFDDPLTG 278


>gi|330898112|gb|EGH29531.1| pseudouridine synthase [Pseudomonas syringae pv. japonica str.
           M301072PT]
          Length = 296

 Score =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 59/302 (19%), Positives = 104/302 (34%), Gaps = 37/302 (12%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +P I+          G+V   + K +  +   + G  +R+       N        
Sbjct: 30  LCAKFPAISREQWLDRFARGRVLDENGKAIAPDLAYREG--LRVHYFREIAN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +   G  
Sbjct: 80  --------ETPIPVVETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  RRI K Y ++   +P+     +    
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANRQTRSAYQTLFPTRRIDKFYQAIAPALPE-----LTFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++    K     + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGVGASNTRTQIEVLERQ-DKLWRYGLYPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G  I  D  Y  +   +     +N L L A  +    P  G  +       H       L
Sbjct: 244 GAAICNDPFY-PDVVKDPVDDYRNPLKLLASSLRFIDPLNGEQR-------HFESLLQ-L 294

Query: 323 GF 324
            +
Sbjct: 295 DW 296


>gi|330829216|ref|YP_004392168.1| Pseudouridine synthase [Aeromonas veronii B565]
 gi|328804352|gb|AEB49551.1| Pseudouridine synthase [Aeromonas veronii B565]
          Length = 219

 Score =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 58/212 (27%), Positives = 94/212 (44%), Gaps = 17/212 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-GQKPRLTHRLDQETSGIL 158
            +L+E     V +K  GI +         ++  L + V +  G      HRLD+ TSG++
Sbjct: 3   RILFEHPAFLVIDKQPGIGMHDEKDDGEAVNPGLVNRVKADTGLTLYPVHRLDKMTSGLV 62

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ART  A + L+ +F  R + K Y +L    PK K+  +   + K    GG ++ V   
Sbjct: 63  LLARTTEANRELSMAFAAREVSKQYLALSDRKPKKKQGWVKGDMQKGR--GGSWMLVRTL 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +    N AIS F  +    +      ++P TG+THQ+RV    +G PI+GD +Y      
Sbjct: 121 D----NPAISWFDSV-SVREGLRLYRIKPQTGKTHQIRVALKSIGAPILGDKRYGGTP-- 173

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                  ++ YLHA  +      G       P
Sbjct: 174 ------SDRGYLHAWRLSFT-LSGEPFDFVCP 198


>gi|258405414|ref|YP_003198156.1| pseudouridine synthase Rlu family protein [Desulfohalobium
           retbaense DSM 5692]
 gi|257797641|gb|ACV68578.1| pseudouridine synthase Rlu family protein, TIGR01621
           [Desulfohalobium retbaense DSM 5692]
          Length = 237

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 57/219 (26%), Positives = 98/219 (44%), Gaps = 19/219 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           + ED +    +K  G+     +G      G +++   +   +    HRLD+ TSG+L++A
Sbjct: 5   IAEDERFLCIHKDPGVDCHTDNG----SSGVIRAVQSAYRIRLFPLHRLDKVTSGLLLLA 60

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           + R  A+ + E F   RI K Y +L    P+ K+  +   + ++S  G   +   ++N  
Sbjct: 61  KDRETARSMGELFSAHRIDKFYLALSAKRPRKKQGTVIGDM-RRSRRGTWRLERSREN-- 117

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               A++ F V   ++       ++P +G+THQLRV    +G PI+GD  Y         
Sbjct: 118 ---PAVTQF-VSRAWSGGKRAFLLRPQSGKTHQLRVALKSLGAPILGDPLYGPRNHS--- 170

Query: 282 SPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
              Q++ YLHA  +     +G R     P P H     D
Sbjct: 171 ---QDRCYLHAMAVSFE-LDGERYSFWTP-PRHGEHFLD 204


>gi|261837781|gb|ACX97547.1| pseudouridine synthase D [Helicobacter pylori 51]
          Length = 293

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 66/287 (22%), Positives = 117/287 (40%), Gaps = 29/287 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q VR   +I  +  +I                +     
Sbjct: 28  LKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGIVSLI------------HFKPNEKTQA 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D + +  +  
Sbjct: 129 GKTLQSAKDLKALFMQKKVKKTYLALAHGLV-DKNIVIDKPILTPQNIQKD-LSIKSKIS 186

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                + +  + +           ++ P TGRTHQ+R+H   +   IVG+  Y    +  
Sbjct: 187 PLGKPSTTLVEPLSYNPFLDISLFKITPLTGRTHQIRLHLSSVDHRIVGEGLYGVIDENA 246

Query: 280 FTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                  +      L LHA  ++    +G   +IT+P+P   +    
Sbjct: 247 REYLQLKRENNAPLLMLHATSLEFEF-KGAIYKITSPMPKRFMPFLK 292


>gi|254240477|ref|ZP_04933799.1| hypothetical protein PA2G_01128 [Pseudomonas aeruginosa 2192]
 gi|126193855|gb|EAZ57918.1| hypothetical protein PA2G_01128 [Pseudomonas aeruginosa 2192]
          Length = 300

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 100/263 (38%), Gaps = 12/263 (4%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAG 116
           R+Q G+V+             +E   +     L   +    ++ +LY D  + V +KP  
Sbjct: 45  RMQRGRVLDAEGRALGPQAAYREGLRVHYFRELPVEAPIPFEARILYRDEHLLVADKPHF 104

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           + V    G  Y     L     S G +     HR+D+ T+G+++ +    +       FR
Sbjct: 105 LPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTAGLVLFSTNPGSRGRYQALFR 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            RRI K Y ++   +P+     +   LL+++ +         +  +G   + +  +V++ 
Sbjct: 163 ERRIDKCYEAIAPALPQ-----LDFPLLRRTRLVPGEPFFRMREGEGEPNSETRIEVVER 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-TSPIQNKLYLHARY 294
             + +    + P TG+ HQLRVH   +G  I  D  Y                L L AR 
Sbjct: 218 NGR-WWRYRLYPVTGKKHQLRVHLAALGAGIQNDGFYPELLDAEGSPDDYLRPLKLLARG 276

Query: 295 MDLPHP-EGGRLQITAPLPAHMV 316
           +    P  G R    + L     
Sbjct: 277 LRFDDPLSGERRTFESGLRLDWQ 299


>gi|165975689|ref|YP_001651282.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           3 str. JL03]
 gi|165875790|gb|ABY68838.1| RNA pseudouridine synthase [Actinobacillus pleuropneumoniae serovar
           3 str. JL03]
          Length = 216

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 61/226 (26%), Positives = 99/226 (43%), Gaps = 21/226 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  + ++     V +KP G+SV          +   +     + ++  L HRLD+ TSG+
Sbjct: 4   KLTICFQHHDFVVIDKPVGVSVHKDEEAIGLTENLAEQL---QAEQVWLVHRLDKVTSGL 60

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A  + AA H    F   +I+K YW+L    PK K+  I+  + K  +      H  +
Sbjct: 61  LIFALNKQAAVHFYHLFEQHKIEKTYWALSDQKPKKKQGKISGDMQKSRNGAWKLSHSKQ 120

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                 N A++ F V            +QP TG+THQLRV    +G PI+GD +Y     
Sbjct: 121 ------NPAVTQF-VSHSLEPNLRHFILQPKTGKTHQLRVAMKSLGSPILGDQRYAGT-- 171

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
                   +++YLHA  +   + +G    I +   +   + W  LG
Sbjct: 172 ------AADRVYLHAYQLKFDY-QGESFCIQSQPTSG--RFWAKLG 208


>gi|270719457|ref|ZP_06223312.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           influenzae HK1212]
 gi|270315435|gb|EFA27693.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           influenzae HK1212]
          Length = 162

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 36/172 (20%), Positives = 75/172 (43%), Gaps = 19/172 (11%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           V+ ++   RLD+     +P  +   L+  + +  V+++ +       ++  G+ + I   
Sbjct: 6   VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEI--- 62

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI- 129
                       I++        ++ +   ++YED  I V NKP  + V  G+G      
Sbjct: 63  ------------IVEVEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTV 110

Query: 130 -DGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            +  L  +    +  +  + HRLD++T+G++VVA+T  A   L    + R+I
Sbjct: 111 LNALLYHYPPIVEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKI 162


>gi|319956455|ref|YP_004167718.1| pseudouridine synthase [Nitratifractor salsuginis DSM 16511]
 gi|319418859|gb|ADV45969.1| pseudouridine synthase [Nitratifractor salsuginis DSM 16511]
          Length = 243

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 68/295 (23%), Positives = 124/295 (42%), Gaps = 59/295 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        I+    ++++  G V V  ++V+                      I + + 
Sbjct: 6   KLLAAQ-EGISNKKAKELIDRGLVYVGDQKVR----------------------IARAEM 42

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
             ++   + + +D     ++Y+D ++   NKPA I                   ++   +
Sbjct: 43  PEETKFRIEEPAD---VKIIYQDEQVVAVNKPAFIDS---------------YEIEEAIE 84

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             +L HRLD++TSG+L++AR  A A+   E+FR R++ K Y + V G+     E I   +
Sbjct: 85  GAQLLHRLDRDTSGVLLLARDEAFAKKAIEAFRQRKVHKEYVAWVEGVVVEPFE-IDLPI 143

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
               H         K ++K    A++     +   +K   + ++  TGRTHQ+RVH  H+
Sbjct: 144 ----HTIKKGKAFSKIDKKLGKPALTKVWPDEVQGKK-SKVRIEIETGRTHQIRVHLAHV 198

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
           G PIVGD +Y +  +         +  LHA+ + L     GR    AP P  + +
Sbjct: 199 GHPIVGDEQYGSPTRA-------KRPLLHAKKITLL----GR-SYEAPEPKDIQR 241


>gi|15611389|ref|NP_223040.1| hypothetical protein jhp0321 [Helicobacter pylori J99]
 gi|11136019|sp|Q9ZMA1|Y347_HELPJ RecName: Full=Uncharacterized RNA pseudouridine synthase jhp_0321;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|4154858|gb|AAD05911.1| putative [Helicobacter pylori J99]
          Length = 293

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 70/294 (23%), Positives = 121/294 (41%), Gaps = 29/294 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----QTVRKSQIIQGVVRLI------------YFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +  +  L++E     VF+KPA I      G  YH +  L       G+     HRLD E
Sbjct: 64  PNEKQEKLVFEAKDFGVFDKPAQIYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  + + L   F  ++++K Y +L  G+  +K   I   +L   +I  D +
Sbjct: 122 TSGLVLAGKTLQSTKDLKALFMQKKVKKTYLALAHGLV-DKSIIINKPILTPQNIQKD-L 179

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  Q       +I+  + +          L++ P TGRTHQ+R+H   +   IVG+  Y
Sbjct: 180 RIRSQISPLGKPSITLVEPLSYNPFLDISLLKITPLTGRTHQIRLHLSSVDHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +         +      L LHA  ++    +G   +I +P+P   +    
Sbjct: 240 GVADENAREYLQLKRENNAPTLMLHAASLEFEF-KGAHYKIASPMPERFMPFLK 292


>gi|149750888|ref|XP_001496449.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 1 [Equus caballus]
          Length = 316

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 94/233 (40%), Gaps = 21/233 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--------RLTHRLDQ 152
           ++Y      V NK     V+  S          K       +          R  H+LD 
Sbjct: 11  IVYRSRDFLVVNKH--WDVRIDSKTWRETLTLQKQLRHRFPELADPDTYYGFRFCHQLDF 68

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG L VA  +AAA      F+ RR+ K Y +LV G  +  +  ++  + + S  G  +
Sbjct: 69  STSGALCVALNKAAAGSAYRCFKERRVTKAYLALVRGHIQESQMTVSYAIGRNSTEGRAH 128

Query: 213 VHVVK--QNEKGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              ++  Q  +    +++   V++           + +QP TGRTHQLRVH   +G P+V
Sbjct: 129 TMCIEGTQGCENPKPSLTELVVLELGLYAGDPVSKVLLQPLTGRTHQLRVHCSALGHPVV 188

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           GD  Y     G        ++ LHA Y+ +P      +++    P   V   D
Sbjct: 189 GDLTYGQASGGEDQPF---RMMLHAFYLRIP-THTECVEVCTSDP--FVPALD 235


>gi|213965321|ref|ZP_03393517.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           amycolatum SK46]
 gi|213951937|gb|EEB63323.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           amycolatum SK46]
          Length = 342

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 56/265 (21%), Positives = 99/265 (37%), Gaps = 18/265 (6%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILD-SSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           R   G VVR   V  + + ++K    +        +H+      ++++D  + V +KP+ 
Sbjct: 56  RFADGLVVRANSVPYSPDDMVKPGAEMWFYRTPAPEHTIAGPMPIVFQDDNLVVVDKPSF 115

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           ++     G        ++   +    +    HRLD+ TSG+L+    R         F  
Sbjct: 116 LATMP-RGRHITETAVVRLRRELGNPELVPAHRLDRLTSGLLIFTARREVRGAYQGLFAS 174

Query: 177 RRIQKIYWSLVWGIP------KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
             + K Y +L    P      +   E       ++  I G       + E  A+  I H 
Sbjct: 175 GEVTKRYHALTSPTPIAGGASEALPETPLELRTRQHKIAGQMQAYTLEGEPNAHTIIEHI 234

Query: 231 KVIDCFAQ---------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
            ++D  +          +    +++P TGRTHQLR+H   +G PI+GD  Y         
Sbjct: 235 SLVDVPSDADGLAADSGRVALWQLKPITGRTHQLRLHLSELGFPILGDQYYPEILPLEAE 294

Query: 282 SPIQNKLYLHARYMDLPHPEGGRLQ 306
           +     L+L    M    P  G  +
Sbjct: 295 NT-SEPLHLVCVEMSFADPVTGEQR 318


>gi|42523804|ref|NP_969184.1| putative RNA pseudouridylate synthase [Bdellovibrio bacteriovorus
           HD100]
 gi|39576011|emb|CAE80177.1| putative RNA pseudouridylate synthase [Bdellovibrio bacteriovorus
           HD100]
          Length = 283

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 54/300 (18%), Positives = 111/300 (37%), Gaps = 31/300 (10%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           V++++    +     D    N    ++   ++ +L  G +  + +R   ++ +  G  +R
Sbjct: 11  VRHILSP--QAGGLCDVLLGNL--ELDREQIEFLLHLGAIYHNHQRTTEDSSVSVGDYIR 66

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +                       T +    +S +++E+    V NK +G+ V     + 
Sbjct: 67  VHTKPRR----------------FTANDGQWRSRIVFENEHFVVTNKISGLPVHAS--VD 108

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
              +        +  Q   +THRLD  T G++V A++        +    R + KIY + 
Sbjct: 109 NLHENLQSYLQQTLHQNVYVTHRLDVPTRGLIVYAKSPEFQTEFNKLLIAREMNKIYRAR 168

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G        + +++             ++   +     I  F  ++    +   + ++
Sbjct: 169 VQGH-SLSTGLLQHYMEPSPRAPKVVSKELQPKWQECLLEILEFSKLE---NEMSEVRIK 224

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
            HTGRTHQ+R      G PIVGD  Y A    +     + ++ L A  +   +P  G   
Sbjct: 225 LHTGRTHQIRAQLSAEGHPIVGDVAYGAVKVWD-----EERIELEACELAFTNPLTGEHH 279


>gi|15842891|ref|NP_337928.1| hypothetical protein MT3399 [Mycobacterium tuberculosis CDC1551]
 gi|13883223|gb|AAK47742.1| RNA pseudouridylate synthase family protein [Mycobacterium
           tuberculosis CDC1551]
 gi|323718169|gb|EGB27351.1| hypothetical protein TMMG_02448 [Mycobacterium tuberculosis
           CDC1551A]
          Length = 305

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 96/252 (38%), Gaps = 12/252 (4%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVF 111
           V    ++ +G+VV     +     ++    ++    +L  +        +L++D+ I V 
Sbjct: 38  VAARAKVLAGEVVDDDGAVVDSGTVLPPGSVVHLYRDLPDEVPVPFDVPVLHQDADIVVV 97

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   +    +    HRLD+ T+G+L+    R       
Sbjct: 98  DKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTTRREVRGSYQ 156

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    ++K Y +     P      +A   L +S I     H+    E G   A +  +
Sbjct: 157 TMFARGLVRKTYLARAPVAP-----GLALPRLVRSRIVKRRGHLQAVCEPGVPNAETLVE 211

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
            I           + P TGRTHQLRVH   +G PI+GD  Y  N            L L 
Sbjct: 212 RIARDG----LYRLTPTTGRTHQLRVHMAALGIPIMGDPLY-PNVISVAAHYFSTPLQLL 266

Query: 292 ARYMDLPHPEGG 303
           A+ ++   P  G
Sbjct: 267 AQRIEFDDPLTG 278


>gi|215413178|ref|ZP_03421879.1| hypothetical protein Mtub9_17501 [Mycobacterium tuberculosis
           94_M4241A]
          Length = 305

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 96/252 (38%), Gaps = 12/252 (4%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVF 111
           V    ++ +G+VV     +     ++    ++    +L  +        +L++D+ I V 
Sbjct: 38  VAARAKVLAGEVVDDDGAVVDSGTVLPPGSVVHLYRDLPDEVPVPFDVPVLHQDADIVVV 97

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   +    +    HRLD+ T+G+L+    R       
Sbjct: 98  DKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTTRREVRGSYQ 156

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    ++K Y +     P      +A   L +S I     H+    E G   A +  +
Sbjct: 157 TMFARGLVRKTYLARAPVAP-----GLALPRLVRSRIVKRRGHLQAVCEPGVPNAETLVE 211

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
            I           + P TGRTHQLRVH   +G PI+GD  Y  N            L L 
Sbjct: 212 RIARDG----LYRLTPTTGRTHQLRVHMAALGIPIMGDPLY-PNVISVAAHDFSTPLQLL 266

Query: 292 ARYMDLPHPEGG 303
           A+ ++   P  G
Sbjct: 267 AQRIEFDDPLTG 278


>gi|210134539|ref|YP_002300978.1| pseudouridine synthase D [Helicobacter pylori P12]
 gi|210132507|gb|ACJ07498.1| pseudouridine synthase D [Helicobacter pylori P12]
          Length = 297

 Score =  132 bits (332), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 70/296 (23%), Positives = 121/296 (40%), Gaps = 29/296 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVRLI------------YFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +  +  L++E     VF+KP  I      G  YH +  L       G+     HRLD E
Sbjct: 64  PNEKQEKLVFETKDFGVFDKPTQIYTHP-KGYFYH-ESLLDCIQSHLGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  + + L   F  ++++K Y +L  G+ + K   I   +L   +I  D +
Sbjct: 122 TSGLVLAGKTLQSVKDLKALFMQKKVKKTYLALAHGLVE-KSMKIDKPILTPQNIQKD-L 179

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  Q       +I+  + +          L++ P TGRTHQ+R+H   +   IVG+  Y
Sbjct: 180 RIRSQISPLGKPSITLVEPLSYNPFLDISLLKITPLTGRTHQIRLHLSSINHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
               +         +      L LHA  ++    +G   +IT+ +P   +     L
Sbjct: 240 GVADENAREYLQLKRENNAPLLMLHAASLEFEF-KGANYKITSQIPKRFMPFLKDL 294


>gi|307260687|ref|ZP_07542377.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 12
           str. 1096]
 gi|306869608|gb|EFN01395.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 12
           str. 1096]
          Length = 216

 Score =  132 bits (332), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 61/226 (26%), Positives = 99/226 (43%), Gaps = 21/226 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  + ++     V +KP G+SV          +   +     + ++  L HRLD+ TSG+
Sbjct: 4   KLTICFQHHDFVVIDKPVGVSVHKDEEAIGLTENLAEQL---QAEQVWLVHRLDKVTSGL 60

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A  + AA H    F   +I+K YW+L    PK K+  I+  + K  +      H  +
Sbjct: 61  LIFALNKQAAVHFYHLFEQHKIEKTYWALSDQKPKKKQGKISGDMQKSRNGAWKLFHSKQ 120

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                 N A++ F V            +QP TG+THQLRV    +G PI+GD +Y     
Sbjct: 121 ------NPAVTQF-VSHSLEPNLRHFILQPKTGKTHQLRVAMKSLGSPILGDQRYAG--- 170

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
                   +++YLHA  +   + +G    I +   +   + W  LG
Sbjct: 171 -----MAADRVYLHAYQLKFDY-QGESFCIQSQPTSG--RFWAKLG 208


>gi|327541913|gb|EGF28421.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification (RluA-like) protein [Rhodopirellula baltica
           WH47]
          Length = 214

 Score =  132 bits (332), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 59/218 (27%), Positives = 99/218 (45%), Gaps = 15/218 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGIL 158
           +L++     V NKP G+      G         + +  +      L   HRLD+  SG++
Sbjct: 4   ILWQCHACVVVNKPVGLPTTSPKGTDSLESCLREQFAQAGNPVSYLTAVHRLDRPVSGLV 63

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN--KKECIANWLLKKSHIGGDYVHVV 216
           ++A  + AA+ L+E FR+R +QK Y ++V G      K+E   + + K +      V +V
Sbjct: 64  LIALRKKAARLLSEQFRLRHVQKKYIAMVQGNALEACKQEPWHDTIAKLTDEAR--VEIV 121

Query: 217 KQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             +      A +    ++  ++     +E++P TGR HQLR+ + H G PIVGD  Y   
Sbjct: 122 GPDSTDGRQAETKVSFLEYDSESDTSRIELRPVTGRMHQLRIQSAHRGHPIVGDPLYG-- 179

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
                T+  ++ L L A  +    P  GR  +   LP 
Sbjct: 180 -----TAEDESTLRLVAAKLSFRDPTNGR-AVEVELPE 211


>gi|156844376|ref|XP_001645251.1| hypothetical protein Kpol_1060p49 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156115910|gb|EDO17393.1| hypothetical protein Kpol_1060p49 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 405

 Score =  132 bits (332), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 92/224 (41%), Gaps = 30/224 (13%)

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
           PPV      I +E  I++  +            ++YED ++ V NKP+GI V        
Sbjct: 93  PPVKQWCTSIEEENSIVEGKIG--------GIDIVYEDDELLVVNKPSGIPVHP---TGQ 141

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
           +    L   +   G+     +RLD+ TSG+L++A+ +  A  L E  R+  + K+Y + V
Sbjct: 142 YYLNTLTEILKKHGKLVSPCYRLDKTTSGLLIMAKNQIIASKLQEKIRVHDMTKLYLARV 201

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE------------------KGANYAISH 229
            G      E   + +L +  I    +    ++                     +  A + 
Sbjct: 202 EGQFPKILEVPTDLILTQEMILERIMTPALKSSVDSDIFTLELKKQFPAGLSPSREAKTD 261

Query: 230 FKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           F  +          +  +P TGRTHQ+R+H   +G PIV DH Y
Sbjct: 262 FYPVKYIPDLDQSIVLCKPLTGRTHQIRIHLARLGFPIVNDHFY 305


>gi|255324086|ref|ZP_05365210.1| RNA pseudouridine synthase family protein [Corynebacterium
           tuberculostearicum SK141]
 gi|255298787|gb|EET78080.1| RNA pseudouridine synthase family protein [Corynebacterium
           tuberculostearicum SK141]
          Length = 316

 Score =  132 bits (332), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 59/306 (19%), Positives = 117/306 (38%), Gaps = 33/306 (10%)

Query: 26  KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILD 85
           ++ +P  +   LQ    SG+V                 V+R    +   + +  ++ +  
Sbjct: 33  RHRHPDDDASALQARFDSGEV-----------------VLRNQTKLRPDSILGNDEDVFF 75

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKP 144
             +   +        +L+ED  I V +KP  ++       I       L+    +   + 
Sbjct: 76  YRIPAPETPVPYDVPILFEDEHILVADKPPFMATMPRARHIVQTATVQLRRM--TGNDEL 133

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRLD+ TSGIL+  + R         F  +++QK Y ++       +      W   
Sbjct: 134 APAHRLDRLTSGILLFTKHRDVRGAYQTLFAEKKVQKTYQAIAEYR---RFPTPLQWASH 190

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM--------QPHTGRTHQLR 256
            +   G+    +      A   ++  ++ID    +    E+        +P TG+THQLR
Sbjct: 191 LTKTPGEIQGRIGDGIPNAFTTLTAVELIDNAPYEKIHGELPQLGKYTLKPTTGKTHQLR 250

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           +H    G PI+GD  Y   +  +    ++  ++L A +++   P  G+  +  + LP + 
Sbjct: 251 LHMWQAGIPILGDPVYPEIYPEDAED-MRIPMHLTATHIEFTDPLSGKYQEFESALPLYT 309

Query: 316 VKTWDS 321
            +  D 
Sbjct: 310 HRLIDQ 315


>gi|225456408|ref|XP_002280549.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 376

 Score =  132 bits (332), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 58/269 (21%), Positives = 102/269 (37%), Gaps = 25/269 (9%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+N      +   F   +    +      ++SG+++VD + V  +  ++S Q +      
Sbjct: 37  VKNRWAGKTIVDLFTEEFKGRPYDYYVNAVQSGRIQVDGEMVPVSYIVRSSQKISHFVHR 96

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                   E  +L            L   +L ++  +    KPA + V       Y  + 
Sbjct: 97  -------HEPPVL-----------ALDVSVLQKEPDVLTICKPASVPVHPCG--QYRKNT 136

Query: 132 FLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            +       G  P    HRLD+  SG+L++AR+ + A    +      +QK Y + V G+
Sbjct: 137 VVGILQAEHGLAPLFPIHRLDRLVSGLLILARSASKADSFRQQIEAGMVQKQYIAKVTGV 196

Query: 191 PKNKKECIANWLLKKSHIGGDYVHV---VKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
             + ++ +   +   +  G   V V             A + F  I         +  +P
Sbjct: 197 FPDDEQVVNVNVNYNAREGRSTVEVGNCCGNTPLKGKSACTKFTRISTNG-THSIVLCEP 255

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            TGRTHQ+RVH  + G PI  D  Y + F
Sbjct: 256 ITGRTHQIRVHLQYTGHPIANDMLYLSEF 284


>gi|192360612|ref|YP_001982437.1| pseudouridine synthase Rlu family protein [Cellvibrio japonicus
           Ueda107]
 gi|190686777|gb|ACE84455.1| pseudouridine synthase Rlu family protein [Cellvibrio japonicus
           Ueda107]
          Length = 347

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 91/246 (36%), Gaps = 38/246 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILV 159
           L+ E     +  K  G+S     G      G  +      G  +    HRLD+ TSG+LV
Sbjct: 115 LVDEQEDFLLVYKKPGVSFHSEQGEP----GLFEIIRQRGGYAQLYPVHRLDKVTSGLLV 170

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+T  A   L   F  R  QK Y ++  G P  K+  I   +                 
Sbjct: 171 FAKTAEANHQLCAQFEQRLTQKYYLAISAGKPIKKQGLIKGDMY------PARRGAWMLG 224

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F              ++PHTG+THQLRV    +G PIVGD  Y     G 
Sbjct: 225 RTLENPAITQFFS-QGLGNGQRLYVLKPHTGKTHQLRVALKSIGAPIVGDSLYGDRHAG- 282

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQD 339
                 +++YLHA  +                      T + + ++Y        ++++D
Sbjct: 283 -----IDRVYLHAFSLAF--------------------TLNGVAYRYSELPREGNIFNED 317

Query: 340 ECKQNI 345
             KQ +
Sbjct: 318 SVKQAM 323


>gi|437185|gb|AAA64631.1| C-terminal sequence of ORF C product shows homology to several
           bacterial ORFs (accession numbers M87501, M59757,
           D10483, M62747, M96791, X57620, Z12154) and human EST
           cDNA (Z13254) [Leishmania donovani]
          Length = 741

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 92/237 (38%), Gaps = 28/237 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV--QG------GSGIAYHIDGFLKS----WVDSKGQKPRLTH 148
           +LYED  + V +KPAG++    G      G+     I   L +     +     +    H
Sbjct: 514 VLYEDDDVLVVDKPAGLATSRHGLSCTQLGTPTTDLISVLLATDRVGALARGIFRQGQVH 573

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD ETSG L++A++  AA  L            +  +   +       +    L+   +
Sbjct: 574 RLDAETSGCLLIAKSDVAADSLRHQLGTSAAFSHHSKIYHALC-----VVLEPSLRNVRL 628

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             D +       +      + ++VI  F   +  W+E +   G+ HQ+R H    G PI+
Sbjct: 629 HDDIIDAADPKIR------TRYRVIRFFPKHRVAWVECRIQQGKKHQIRRHLASRGLPIL 682

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            D ++           + +++ LHA  +   HP     +   APLPA   +    L 
Sbjct: 683 ADLEHGG---AVCCQSMISRVALHAHSLSFIHPVTADPITAAAPLPADFRRCLSLLR 736


>gi|107101470|ref|ZP_01365388.1| hypothetical protein PaerPA_01002511 [Pseudomonas aeruginosa PACS2]
          Length = 295

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 100/263 (38%), Gaps = 12/263 (4%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAG 116
           R+Q G+V+             +E   +     L   +    ++ +LY D  + V +KP  
Sbjct: 40  RMQRGRVLDAEGRALGPQAAYREGLRVHYFRELPVEAPIPFEARILYRDEHLLVADKPHF 99

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           + V    G  Y     L     S G +     HR+D+ T+G+++ +    +       FR
Sbjct: 100 LPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTAGLVLFSTNPGSRGRYQALFR 157

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            RRI K Y ++   +P+     +   LL+++ +         +  +G   + +  +V++ 
Sbjct: 158 ERRIDKCYEAIAPALPQ-----LDFPLLRRTRLVPGEPFFRMREGEGEPNSETRIEVVER 212

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-TSPIQNKLYLHARY 294
             + +    + P TG+ HQLRVH   +G  I  D  Y                L L AR 
Sbjct: 213 NGR-WWRYRLYPVTGKKHQLRVHLAALGAGIQNDGFYPELLDAEGSPDDYLRPLKLLARG 271

Query: 295 MDLPHP-EGGRLQITAPLPAHMV 316
           +    P  G R    + L     
Sbjct: 272 LRFDDPLSGERRTFESGLRLDWQ 294


>gi|303278324|ref|XP_003058455.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226459615|gb|EEH56910.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 417

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 73/287 (25%), Positives = 118/287 (41%), Gaps = 47/287 (16%)

Query: 27  NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
             YP +      K +R G++RVD    K       G          ++   +     LD 
Sbjct: 111 ERYPTLTAAR--KAVRRGELRVDGVPRK-------GDYRVAAGAAVSVVARVSSGDALDV 161

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---- 142
                  SD  +  + YED+ + V  KP G+   G    A++ +  L  ++    +    
Sbjct: 162 ---RDLPSDLPRLEIAYEDNHMAVIVKPEGMPSVGDG--AWNAERALPYYLRETRRVEGA 216

Query: 143 --KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI---PKNKKEC 197
             +PR  HRLD  TSG+LV A+TR A   L+ +F  R  +K Y +++ G     ++  E 
Sbjct: 217 LSRPRPVHRLDAATSGLLVCAKTRLAMTSLSVAFARREPKKRYRAVLAGAAGGWESGSEG 276

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID----CFAQKFCWLEMQPHTGRTH 253
           +A+  L+                      ++ ++V          +   ++  P TGRTH
Sbjct: 277 VADAPLE------------------GKPCVTRWRVDRVAPCSRHGRVTLMDFAPETGRTH 318

Query: 254 QLRVHAL-HMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLP 298
           QLR HA   + CPIVGD +Y       F     ++ L+L A  + LP
Sbjct: 319 QLRRHAAESLRCPIVGDFRYTKKSDDAFGGLDDRDGLFLAAVEISLP 365


>gi|116049993|ref|YP_791196.1| putative pseudouridylate synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|296389546|ref|ZP_06879021.1| putative pseudouridylate synthase [Pseudomonas aeruginosa PAb1]
 gi|115585214|gb|ABJ11229.1| putative pseudouridylate synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
          Length = 300

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 101/263 (38%), Gaps = 12/263 (4%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAG 116
           R+Q G+V+             +E   +     L   +    ++ +LY D  + V +KP  
Sbjct: 45  RMQRGRVLDAEGRALGPQAAYREGLRVHYFRELPAEAPIPFEARILYRDEHLLVADKPHF 104

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           + V    G  Y     L     S G +     HR+D+ T+G+++ +    +       FR
Sbjct: 105 LPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTAGLVLFSTNPGSRGRYQALFR 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            RRI K Y ++   +P+     +   LL+++ +         +  +G   + +  +V + 
Sbjct: 163 ERRIDKYYEAIAPALPR-----LDFPLLRRTRLVPGEPFFRMREGEGEPNSETRIEVAER 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARY 294
             + +    + P TG+ HQLRVH   +G  I  D  Y        +     + L L AR 
Sbjct: 218 NGR-WWRYRLYPVTGKKHQLRVHLAALGAGIQNDGFYPELLDAEDSPDDYRRPLKLLARG 276

Query: 295 MDLPHP-EGGRLQITAPLPAHMV 316
           +    P  G R    + L     
Sbjct: 277 LRFDDPLSGERRTFESGLRLDWQ 299


>gi|326383527|ref|ZP_08205213.1| pseudouridine synthase [Gordonia neofelifaecis NRRL B-59395]
 gi|326197611|gb|EGD54799.1| pseudouridine synthase [Gordonia neofelifaecis NRRL B-59395]
          Length = 291

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 59/261 (22%), Positives = 99/261 (37%), Gaps = 14/261 (5%)

Query: 57  NRIQSGQVVRIPPVINALNH-IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
            R  +G++V        L+  +++   +        +        +L+ D  + V +KP 
Sbjct: 34  ERAAAGEIVDADGRPVDLDAPVLRPVPVFLYRDPPEEFPVPFDMPILHLDDDLAVVDKPH 93

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            ++     G        ++   +    +    HRLD+ T+G+L+  R R       E F 
Sbjct: 94  FLATMP-RGAHVAETALVRLRRELGSDEVAPAHRLDRLTAGVLLFTRRREVRAAYQELFA 152

Query: 176 MRRIQKIYWSLVWGIPKN-KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            RR+ K Y +L        ++  I N ++K     GD    V   E     A+S  ++  
Sbjct: 153 QRRVHKEYRALARADDALVERVRIENRIVK---TAGDLRARVVPGEVN---AVSDIELAV 206

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP----IQNKLYL 290
              +      + P TGRTHQLR+H   +G PI+GD  Y         +P        L L
Sbjct: 207 RHGEGLAEYRLLPSTGRTHQLRMHMAGLGTPIIGDPLYPEVDHDLAAAPDRGDFSRPLAL 266

Query: 291 HARYMDLPHPEGGR-LQITAP 310
            A  +    P  GR     +P
Sbjct: 267 VAHRLSFTDPLSGRERTFESP 287


>gi|319796006|ref|YP_004157646.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315598469|gb|ADU39535.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 305

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 107/290 (36%), Gaps = 29/290 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ-K 82
           +    +P I        L                RI +G V+    +   L    +   +
Sbjct: 34  FLIERFPAITR---DAWLE---------------RIAAGDVIDEHRIPVTLERRYESPLR 75

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +        +     +  +L++D ++ V +KP  + V       Y  +  L         
Sbjct: 76  VYYYRTLDGEVHIPFEEQVLFQDDELVVADKPPFLPVTPTG--KYLQESLLVRLKRKLNI 133

Query: 143 K-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HR+D+ TSG+++ +  R       + F  RRI K Y ++V      ++      
Sbjct: 134 DDLVPLHRIDRSTSGLVLFSVRRETRGAYQQMFPERRIAKHYEAVV----PWQEGVSTVP 189

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            + +S +  D   +  + E G   + +  +V +    +   L + P TGR HQLRVH L 
Sbjct: 190 DIYRSRLVDDEHFMRMREEPGEPNSETRIEVQEIRGGRA-LLRLSPVTGRKHQLRVHCLA 248

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAP 310
           +G PI  D  Y      N T      L L A+ +    P  G L + T+P
Sbjct: 249 LGMPIENDPIYPVLLPEN-TDDFDKPLQLLAKSVAFQDPVTGDLRRFTSP 297


>gi|227543293|ref|ZP_03973342.1| ribosomal pseudouridine synthase [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227180906|gb|EEI61878.1| ribosomal pseudouridine synthase [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 294

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 65/257 (25%), Positives = 100/257 (38%), Gaps = 14/257 (5%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ-KILDSSVNLTKHSDFLKSILLYEDSK 107
           D  R   + R  +G+V      + A   I+     I    +   +         +YEDS+
Sbjct: 45  DDARA-LDKRFAAGEVRDRRGQVIAPEQILAAGVDIFFYRMPAPEPHVPFSIETVYEDSR 103

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + V NKP  ++     G        ++    +  ++    HRLD+ TSG+L+  ++R   
Sbjct: 104 VLVVNKPPFLATVP-KGAHITETAVVRLRRATGNEELSPAHRLDRHTSGLLLFTKSREFR 162

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
               E F  R +QK Y ++  G        +  W  + S + GD        E     A 
Sbjct: 163 GAYQEMFARRAVQKTYHAVSAGPSAVAPGTV--WRSRISKVPGDLQAHTVDGEAN---AE 217

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +H  VI    +        PHTG+THQLR+H    G PIV D  Y A  + +        
Sbjct: 218 TH--VISVSGRVHVLA---PHTGKTHQLRLHMCEAGVPIVNDPLYPA-IRDDLMDDFTRP 271

Query: 288 LYLHARYMDLPHPEGGR 304
           L L A  +    P  GR
Sbjct: 272 LGLTAYSLRFEDPVDGR 288


>gi|261839194|gb|ACX98959.1| RNA pseudouridine synthase family protein [Helicobacter pylori 52]
          Length = 298

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 69/293 (23%), Positives = 119/293 (40%), Gaps = 29/293 (9%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q VR   +I  +  +I                +     
Sbjct: 28  LKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVRLI------------HFKPNEKTQA 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KPA +      G  YH +  L        +     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPAQVYTHP-KGYFYH-ESLLDCIQSHFSKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  + + L   F  ++++K Y +LV G+ + K   I   +L   +I  D +H+  +  
Sbjct: 129 GKTLQSVKDLKALFMQKKVKKTYLALVHGLIE-KSMKIDKPILTPQNIQKD-LHIRSKIS 186

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                + +  + +          L++ P TGRTHQ+R+H   +   IVG+  Y    +  
Sbjct: 187 PLGKPSTTLVEPLSYNPFLDISLLKITPLTGRTHQIRLHLSSVDHRIVGEGLYGVADEEA 246

Query: 280 FTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
                  +      L LHA  +     +G   +IT+ +P   +     L   Y
Sbjct: 247 RGYLQLKRENHAPLLMLHAFRLGFEF-KGANYKITSQIPKRFMPFLKDLSLFY 298


>gi|297198479|ref|ZP_06915876.1| ribosomal pseudouridine synthase [Streptomyces sviceus ATCC 29083]
 gi|197717376|gb|EDY61410.1| ribosomal pseudouridine synthase [Streptomyces sviceus ATCC 29083]
          Length = 317

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 58/261 (22%), Positives = 105/261 (40%), Gaps = 23/261 (8%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-------FLKSILLYEDSKIYVF 111
           +++GQ+V      +A  H +         +++  H +            ++Y D  + V 
Sbjct: 56  LETGQIV------DAAGHPVPRDMAYAPGMSVWFHRELPDEERVPFPIDVIYRDEHLVVA 109

Query: 112 NKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           +KP  ++    GS +A      L+  +D         HRLD+ T+G+++           
Sbjct: 110 DKPHFLATTPRGSHVAETALARLRRQLDI--PALGAAHRLDRLTAGLVMFTVRPEERGAY 167

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              FR RR+ K Y ++    P      +      +S I  +   +  Q   G   A+S  
Sbjct: 168 QSLFRDRRVAKEYEAVARYDP-----TLPLPHTVRSRIVKERGVLAAQEVDGEPNAVSRV 222

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           ++++   ++     + P TG+THQLRVH   +G PI+GD  Y            +  L L
Sbjct: 223 ELLEHRGERA-RYRLTPGTGQTHQLRVHMSALGVPILGDPLYPVVTAPVAPGDFRRPLQL 281

Query: 291 HARYMDLPHPEGG-RLQITAP 310
            AR ++   P  G   +  +P
Sbjct: 282 LARVLEFTDPVTGHEHRFVSP 302


>gi|291277548|ref|YP_003517320.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
 gi|290964742|emb|CBG40597.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
          Length = 245

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/288 (21%), Positives = 106/288 (36%), Gaps = 61/288 (21%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
             I+    ++++  G V V  K+V                            +    S  
Sbjct: 13  KKISHNKAKELIDKGLVSVAGKKVGI-------------------------ARAEYPSHT 47

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           L   +   K  +L++D  +    KPA +        +Y +      WV        L HR
Sbjct: 48  LFDVAPPPKPEILFQDENLLALIKPAFL-------ESYDLAEMFDGWV--------LLHR 92

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ R      +   ++F+ + + K Y +LV G     +   A  L  K   
Sbjct: 93  LDKETSGVILLVRGESDFHKRAKKAFKDQEVYKEYIALVSGFLSEPQTITAPILTTKKGF 152

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +H      +    A+++   +    +K   ++    TGRTHQ+RVH  H+G  I+G
Sbjct: 153 AKSRIH------QDGLSAVTYIDPLKIIGKK-TLIKAVIQTGRTHQIRVHLKHIGHSIIG 205

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              ++ LHA  + +        +  APLP    
Sbjct: 206 DRLYGGMSA--------RRVMLHASKIKIFD-----YEFHAPLPKEFQ 240


>gi|114049225|ref|YP_739775.1| pseudouridine synthase Rlu family protein [Shewanella sp. MR-7]
 gi|113890667|gb|ABI44718.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           sp. MR-7]
          Length = 228

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 56/205 (27%), Positives = 90/205 (43%), Gaps = 21/205 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++ +++   V +K   +      G A    G +       G K    HRLD  TSG+L+
Sbjct: 3   RIIADEADFLVISKSPNVHFHSQDGTA----GVVAQLEQDLGIKLFAVHRLDTPTSGLLL 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+  AAA+ LTE F   ++QK Y +L  G PK K+  +   + K        +      
Sbjct: 59  LAKHPAAARQLTELFSAHQVQKYYLALAKGKPKKKQGWVIGDMAKSRRSMFKLLRTKD-- 116

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A + F              ++PH+G+THQLRV    +G PI+GD  Y ++    
Sbjct: 117 ----NPATTQFFS-TSVGDGLRLYLLKPHSGKTHQLRVALASLGVPILGDALYGSD---- 167

Query: 280 FTSPIQNKLYLHARYMDL--PHPEG 302
               + ++ YLHA  +     H +G
Sbjct: 168 ----MADRCYLHAYCLHFRYQHEDG 188


>gi|127511033|ref|YP_001092230.1| pseudouridine synthase Rlu family protein [Shewanella loihica PV-4]
 gi|126636328|gb|ABO21971.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           loihica PV-4]
          Length = 224

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 54/198 (27%), Positives = 84/198 (42%), Gaps = 19/198 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +++   V +K  G+      G A    G +         K    HRLD  TSG+L+ 
Sbjct: 4   IIADETDFLVIDKAPGVHFHSQDGSA----GVMAQLESDLDIKLYSVHRLDTMTSGLLLF 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA   T+ F   ++QK Y +L  G PK K+  I   + K          + K   
Sbjct: 60  AKSSEAAAAFTQRFSEHKVQKYYLALAKGKPKKKQGSIVGDMAK------SRRSMYKLLR 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F      A+      ++P +G+THQLRV    +G PI+GD  Y        
Sbjct: 114 SKENPAITQFFS-QSVAEGLRLYLLKPLSGKTHQLRVALASLGVPILGDQLYGGEDA--- 169

Query: 281 TSPIQNKLYLHARYMDLP 298
                ++ YLHA  +   
Sbjct: 170 -----DRGYLHAYALGFE 182


>gi|227501848|ref|ZP_03931897.1| ribosomal pseudouridine synthase [Corynebacterium accolens ATCC
           49725]
 gi|227077342|gb|EEI15305.1| ribosomal pseudouridine synthase [Corynebacterium accolens ATCC
           49725]
          Length = 327

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 54/274 (19%), Positives = 100/274 (36%), Gaps = 15/274 (5%)

Query: 56  NNRIQSGQVVRIPPVINALNHII-KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
             R  +G+VV           ++ K+  +    +   +        ++YED  I V +KP
Sbjct: 59  RERFAAGEVVLRDQTPLKPGTVLGKDVDVFFYRIPAPEIPVPYDIPIIYEDDNILVADKP 118

Query: 115 AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             ++    +         ++    +   +    HRLD+ TSG+L+  + +         F
Sbjct: 119 PFMATMPRARHIVE-TATVRLRRSTGNNELVPAHRLDRLTSGLLLFTKHKDVRGAYQSLF 177

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             +++ K Y ++       +      W    +   G+    +   E  A   +   + ID
Sbjct: 178 AEKKVHKTYQAVAE---FRRLPTPLQWSSHLTKTPGEIQGRIADGEPNAFTTLESVQPID 234

Query: 235 CFAQKFC--------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
               +             ++P TG+THQLR+H    G PI+GD  Y   F          
Sbjct: 235 KAPYEKVHGPLPDLGLYTLKPQTGKTHQLRLHMWQAGIPILGDPVYPTIFPEEAEDMAI- 293

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
            ++L A  ++   P  G+    T+ LP  M K  
Sbjct: 294 PMHLTATDLEFTDPLSGKPRHFTSGLPLAMHKLL 327


>gi|15597239|ref|NP_250733.1| hypothetical protein PA2043 [Pseudomonas aeruginosa PAO1]
 gi|9948049|gb|AAG05431.1|AE004630_8 hypothetical protein PA2043 [Pseudomonas aeruginosa PAO1]
          Length = 300

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 100/263 (38%), Gaps = 12/263 (4%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAG 116
           R+Q G+V+             +E   +     L   +    ++ +LY D  + V +KP  
Sbjct: 45  RMQRGRVLDAEGRALGPQAAYREGLRVHYFRELPVEAPIPFEARILYRDEHLLVADKPHF 104

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           + V    G  Y     L     S G +     HR+D+ T+G+++ +    +       FR
Sbjct: 105 LPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTAGLVLFSTNPGSRGRYQALFR 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            RRI K Y ++   +P+     +   LL+++ +         +  +G   + +  +V++ 
Sbjct: 163 ERRIDKCYEAIAPALPQ-----LDFPLLRRTRLVPGEPFFRMREGEGEPNSETRIEVVER 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-TSPIQNKLYLHARY 294
             + +    + P TG+ HQLRVH   +G  I  D  Y                L L AR 
Sbjct: 218 NGR-WWRYRLYPVTGKKHQLRVHLAALGAGIQNDGFYPELLDAEGSPDDYLRPLKLLARG 276

Query: 295 MDLPHP-EGGRLQITAPLPAHMV 316
           +    P  G R    + L     
Sbjct: 277 LCFDDPLSGERRMFESGLRLDWQ 299


>gi|298715052|emb|CBJ27759.1| RNA pseudouridylate synthase domain-containing protein [Ectocarpus
           siliculosus]
          Length = 527

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 54/220 (24%), Positives = 85/220 (38%), Gaps = 18/220 (8%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           S +L          +L+++    V +KP G+        +   D  ++   D  G++  L
Sbjct: 121 SSSLESPQQSPPLEVLHQNEHFAVVSKPPGMHCHRPEFGSRDPDFVMQKARDQLGRRVFL 180

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+ TSG L+V  +  AA+ L ++       K Y ++V G           W     
Sbjct: 181 PHRLDRATSGCLLVGFSSQAAKVLHQTLAQPDSSKTYVAIVRGSGGAFVG--KGWFTVDR 238

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ---KFCWLEMQPHTGRTHQLRVHALHMG 263
            I        K  +K    A + F  +        + C +  QP TGR HQ+R H   + 
Sbjct: 239 PI--------KDEKKILREASTRFLFVRGGNDPDPRCCLVLAQPSTGRFHQIRRHLNGLS 290

Query: 264 CPIVGDHKYCA-----NFKGNFTSPIQNKLYLHARYMDLP 298
            PIVGD  +           +  S    +L LH   + LP
Sbjct: 291 HPIVGDSVHGDCRFNREVADHRNSAPAGRLMLHCLRLSLP 330


>gi|223039515|ref|ZP_03609803.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter rectus RM3267]
 gi|222879311|gb|EEF14404.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter rectus RM3267]
          Length = 252

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 72/310 (23%), Positives = 121/310 (39%), Gaps = 65/310 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        I+    ++++ +G V               GQ + +   + +       QK
Sbjct: 8   KLLAIQ-EGISNNEAKELIDAGLVS------------AKGQRIAVARTVMSAATKFNVQK 54

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +   S             +++ED  +   +KPA ++ +  S I                 
Sbjct: 55  LPRPS-------------VIFEDENLIAVDKPAFLTSEKVSEI----------------Y 85

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           K  L HRLD+ETSG+L++ +     +   E F+  R++K Y + V GI   +       +
Sbjct: 86  KFPLLHRLDKETSGVLLLVKNEEFQKKAIEEFKNCRVKKEYVAAVKGIVSEEFSVNEPII 145

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             K+  G      +  N K A   ++   V    A K   ++++  TGRTHQ+RVH  H 
Sbjct: 146 TLKNRGGA--FSKISPNGKDALSIVTPVMV----AGKKSLVKVEIKTGRTHQIRVHLNHA 199

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G  IVGD KY  N           ++YLHA  ++L        +  + L        + L
Sbjct: 200 GYGIVGDEKYAKNKAA--------RMYLHAYKIELL-----GYKFRSNLSEDF----NRL 242

Query: 323 GFKYDRNLYI 332
           GF+  RN  I
Sbjct: 243 GFEISRNFEI 252


>gi|22331748|ref|NP_190794.2| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|56744228|gb|AAW28554.1| At3g52260 [Arabidopsis thaliana]
 gi|332645401|gb|AEE78922.1| RNA pseudourine synthase 5 [Arabidopsis thaliana]
          Length = 294

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 62/258 (24%), Positives = 104/258 (40%), Gaps = 49/258 (18%)

Query: 37  LQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +Q+ +++GQ+++D + VK  N  ++SG                   K++ S +   +   
Sbjct: 53  IQR-IQNGQIQIDGEVVKDPNTLLRSG------------------SKLVYSRLPWKEPDT 93

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRL 146
                +LYED  +   NKP+G+ V  G             W   K            P  
Sbjct: 94  PYSLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVP 153

Query: 147 THRLDQETSGILVVARTRAAAQHL-----------------TESFRMRRIQKIYWSLVWG 189
            HRL + TSGIL+ A+T+ A   L                  E    R++ KIY +L  G
Sbjct: 154 VHRLGRGTSGILLCAKTKLAKTKLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADG 213

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPH 248
           I +  +  I   +    + G      V   E     A S   V++   +K C  ++++  
Sbjct: 214 IVEEDEVVIKQPIGVVRYPGVAQGLYVASPE--GKPAFSKVFVLERDREKNCSLVKVEIQ 271

Query: 249 TGRTHQLRVHALHMGCPI 266
           +GR HQ+R+H  +MG P+
Sbjct: 272 SGRPHQIRIHLAYMGHPL 289


>gi|328875474|gb|EGG23838.1| Modifier of rudimentary family protein [Dictyostelium fasciculatum]
          Length = 602

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 50/218 (22%), Positives = 88/218 (40%), Gaps = 19/218 (8%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                   ++Y+       NKP       G    + +  F+++         R  +R+D 
Sbjct: 344 PPQNPHFDIIYQSDCFISINKP-FDVCIDGDDREHTVLKFIENRFPELKGLVRFANRIDY 402

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLK- 204
            TSGI++ A T+ A       F  R  +K Y ++VWG          N +  I + + + 
Sbjct: 403 ATSGIVLTALTKEATNSAMNLFSSRETKKEYLAIVWGHAHPVYDGNNNTEMTIDSPIAEM 462

Query: 205 -KSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHAL 260
                    V  V  +      +++ ++V++      +    +++ PHTGR HQLRVH  
Sbjct: 463 QDDPTNFKMVIGVAGSTNAGRASLTKYRVLEHGTLNGKAVSKIQLFPHTGRRHQLRVHMA 522

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            +G  IVGD  Y          P+  ++ LH+  + LP
Sbjct: 523 SIGHVIVGDETYGDK------DPLTPRMMLHSWKLMLP 554


>gi|153864749|ref|ZP_01997543.1| pseudouridylate synthase [Beggiatoa sp. SS]
 gi|152145755|gb|EDN72456.1| pseudouridylate synthase [Beggiatoa sp. SS]
          Length = 162

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/161 (32%), Positives = 78/161 (48%), Gaps = 5/161 (3%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  + + NKP G++V GGSGI   +   L++          L HRLD++TSG L++A+
Sbjct: 2   YEDPLLLIINKPTGMAVHGGSGINGGVIEGLRALY-PNAPYLELVHRLDRDTSGCLMIAK 60

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
             +  + L    R   I K Y +LV G    +   +   L K     G+ +  V  +   
Sbjct: 61  KYSMLRRLHALLREGAIHKQYLALVQGRWDKQTTKVEAPLRKNILQSGERIVRVNSD--- 117

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
              A+S F  I+        L + P TGRTHQ+RVHA + G
Sbjct: 118 GKSAVSQF-SIEQRLTTTTLLRVHPLTGRTHQIRVHAAYKG 157


>gi|268678698|ref|YP_003303129.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
 gi|268616729|gb|ACZ11094.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
          Length = 302

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 66/290 (22%), Positives = 122/290 (42%), Gaps = 45/290 (15%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           R+  + +  I+    QKI+   +V V+ +++   + + SG++  +               
Sbjct: 18  RFLMDTF-GISMKEAQKIIDKRRVFVEDEQLMRKSTLISGKIGVV--------------- 61

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
                       D      ++E     VF+KP+G+ +        Y ++  +KS     G
Sbjct: 62  --------VFEGDSKGLRPIFETEDFAVFDKPSGVMIHPRKRSDGYTLNDEIKSLY---G 110

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           +     HR+D+ TSG+++V + + +   L E F  R++QK Y +LV G  K  +E + + 
Sbjct: 111 KDANAAHRIDKSTSGLVLVGKHKQSEIALKEIFATRKVQKSYIALVKGHLK--EELLIDE 168

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHAL 260
            LK+          V  +E+G   + +    +  F  K    ++  P+TGR HQ+RVH  
Sbjct: 169 KLKRDVETSQIRLKVHVDERG-KPSQTKVIPLHYFEDKDATLVQAFPYTGRQHQIRVHLF 227

Query: 261 HMGCPIVGDHKYCANFKG-------------NFTSPIQNKLYLHARYMDL 297
           H+  PIVGD  Y    +               +   + ++L LHA  +  
Sbjct: 228 HVKHPIVGDMIYGVEEEDAERYLDGSMSAEEQYEKTLSSRLLLHAYSLSF 277


>gi|188527152|ref|YP_001909839.1| hypothetical protein HPSH_01795 [Helicobacter pylori Shi470]
 gi|188143392|gb|ACD47809.1| hypothetical protein HPSH_01795 [Helicobacter pylori Shi470]
          Length = 293

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 70/288 (24%), Positives = 122/288 (42%), Gaps = 31/288 (10%)

Query: 41  LRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           L+  Q  +DK+R+K N + ++  Q+++    + +L H    +KI                
Sbjct: 28  LKEAQRHLDKQRLKHNQQAVRKSQMIQ---GVVSLIHFKPNEKI---------------Q 69

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L++E     VF+KP  I      G  YH +  L       G+     HRLD ETSG+++
Sbjct: 70  ALVFETKDFGVFDKPPQIYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVL 127

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
             +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D     K +
Sbjct: 128 AGKTLQSAKDLKTLFMQKKVKKTYLALAHGLV-DKNIVIDKPILTPQNIQKDLRIRSKIS 186

Query: 220 EKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                 + +  + +   A      L++ P TGRTHQ+R+H   +G  IVG+  Y    + 
Sbjct: 187 -PLGKPSTTLVEPLSYNAFLDISLLKITPLTGRTHQIRLHLSSVGHRIVGEGLYGVIDEN 245

Query: 279 NFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                   +      L LHA  +     +G   +IT+ +P   +    
Sbjct: 246 AREYLQLKRENNAPLLMLHASSLAFEF-KGAIHEITSQMPQRFMPFLK 292


>gi|321474676|gb|EFX85641.1| hypothetical protein DAPPUDRAFT_32502 [Daphnia pulex]
          Length = 250

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 72/251 (28%), Positives = 107/251 (42%), Gaps = 35/251 (13%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS--KGQKPRLTHRLDQETSGILVVARTRA 165
           I   +KP G+      G A  +   L   +    + +K    HRLD++T+GIL++A  + 
Sbjct: 1   IVAIDKPHGLVTTDADGNAKVVLTNLLPGLSQALRVEKLYTVHRLDRDTTGILLLASNQT 60

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV------------ 213
            A  L + F    IQK Y  +  GIP  ++  I   + +KS      +            
Sbjct: 61  VANKLNKLFLDHEIQKKYMVITKGIPSPREGTIDIPMCEKSIGDRQRMALRPVLSHSPDS 120

Query: 214 -HVVKQNEKGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDH 270
               K N KG ++ AI+HF V         ++E++P TG  HQLRVH    + CP++GDH
Sbjct: 121 LKSAKYNAKGKSFKAITHFWV-KTTNAGTAFVELEPETGVRHQLRVHLSEGLDCPVLGDH 179

Query: 271 KYCANFKGNFTSPIQN---------------KLYLHARYMDLPHP--EGGRLQITAPLPA 313
           KY    K       Q+                ++LHA +M +P    EG  L I +PLP 
Sbjct: 180 KYSHAEKFAPQKLSQDILNLLAIKQSKARNIPMHLHAAFMAIPGFGQEGQPLCINSPLPR 239

Query: 314 HMVKTWDSLGF 324
               T   L  
Sbjct: 240 FFRYTMKKLKL 250


>gi|217033363|ref|ZP_03438794.1| hypothetical protein HP9810_9g116 [Helicobacter pylori 98-10]
 gi|216944304|gb|EEC23729.1| hypothetical protein HP9810_9g116 [Helicobacter pylori 98-10]
          Length = 293

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 67/294 (22%), Positives = 119/294 (40%), Gaps = 29/294 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVSLI------------HFR 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +     L++E     VF+KP  +      G  YH +  L        +     HRLD E
Sbjct: 64  PNEKTQALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSYFSKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  + + L   F  ++++K Y +L  G+  +K   I   +L   +I  D +
Sbjct: 122 TSGLVLAGKTLQSTKDLKMLFMQKKVKKTYLALAHGLV-DKNIVIDKPILTPQNIQKD-L 179

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  +       + +  + +          L++ P TGRTHQ+R+H   +G  IVG+  Y
Sbjct: 180 RIKSKISPLGKPSTTLVEPLSYNPFLDISLLKITPITGRTHQIRLHLSSVGHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +         +      L LHA  ++    +G   +IT+P+P   +    
Sbjct: 240 GVIDENAREYLQLKRENNAPLLMLHASSLEFEF-KGAIHEITSPMPKRFMPFLK 292


>gi|260549352|ref|ZP_05823571.1| pseudouridylate synthase [Acinetobacter sp. RUH2624]
 gi|260407461|gb|EEX00935.1| pseudouridylate synthase [Acinetobacter sp. RUH2624]
          Length = 302

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 54/296 (18%), Positives = 111/296 (37%), Gaps = 29/296 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             + ++   ++PHI     Q+  + G +  V+ +++  ++   +   +     +    H+
Sbjct: 29  QTIYQFLCKNFPHIKATEWQQRFQDGLIYAVNGEKLTLDSPYIANTHIFYYRFLANEVHV 88

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E +                  +L+E+  + V +KP  +++       Y  +  L    
Sbjct: 89  PFEHQ------------------ILFENDDLLVVDKPHFLTISPTG--QYVQETLLVRLK 128

Query: 138 DSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              G +     HRLD+ET+G+++  +   +     + F  R + KIY ++     + K  
Sbjct: 129 KQTGNEFLTPIHRLDRETAGVVLFCKRPQSRGIYQQLFADREVHKIYHAIAAYKAELKFP 188

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I    LK     G   + ++          +  ++I+       +  + P TG+ HQLR
Sbjct: 189 QI----LKLYLDKGTPFYTMQVIAHTKTNTETKIELIEHNHSWAKYC-LTPTTGKQHQLR 243

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPL 311
           VH  H+G PI  D  Y    +          L L A+ +    P     +   + L
Sbjct: 244 VHLNHLGIPIKNDPFY-PIVQHKADDDFSQPLQLLAKQISFIDPLIKQEMVFNSQL 298


>gi|307195434|gb|EFN77320.1| RNA pseudouridylate synthase domain-containing protein 2
           [Harpegnathos saltator]
          Length = 357

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 51/182 (28%), Positives = 82/182 (45%), Gaps = 7/182 (3%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  + V NKPA I V       ++   F+ +  +   +  R  HRLD+ TSGIL+  RT 
Sbjct: 2   DEDVVVVNKPASIPVHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDRLTSGILLFGRTP 60

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
             A+ +    R R++ K Y   V G    ++   +  +   S+     + V K ++KG  
Sbjct: 61  KKARQMEHQIRNRQVHKQYVCRVEGEFPEEEVICSEPIEVVSY----KIGVCKVSDKG-K 115

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
             ++ FK +    +    +  +P TGR HQ+RVH  ++G P+V D  Y     G      
Sbjct: 116 DCVTRFKRLSYNGKS-SVVLCKPQTGRMHQIRVHLQYLGYPVVNDPLYNHVVFGPHKGKG 174

Query: 285 QN 286
            N
Sbjct: 175 GN 176


>gi|67478945|ref|XP_654854.1| RNA pseudouridylate synthase [Entamoeba histolytica HM-1:IMSS]
 gi|56471941|gb|EAL49468.1| RNA pseudouridylate synthase, putative [Entamoeba histolytica
           HM-1:IMSS]
          Length = 389

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 52/209 (24%), Positives = 87/209 (41%), Gaps = 11/209 (5%)

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           ++        N I+ +  IL + ++  +        ++YED+ + V NKP+GI     SG
Sbjct: 105 IKRNNNEINENCIVIQGDILLNQIHRHELPVPYLLPIIYEDNDVIVVNKPSGIPTH--SG 162

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
             Y  +  ++     +  K    HRLD+ TSG+L++A++   A  +   F      K Y 
Sbjct: 163 GRYTENTVIRILEKERNIKLFGVHRLDRLTSGVLLIAKSSEIANEIQRHFIN--AYKKYI 220

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWL 243
             V G        +   +++ S I    V V  +       + + F+ I    +     L
Sbjct: 221 CRVIGYM--DSCIVNKPIIETSCITKQRVTVGCE----GKASTTIFEQIQYDEKTDTTLL 274

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              P TGR HQ+RVH  +   PI  D  Y
Sbjct: 275 WAIPKTGRMHQIRVHLSYENHPIANDSMY 303


>gi|213970524|ref|ZP_03398651.1| Pseudouridine synthase [Pseudomonas syringae pv. tomato T1]
 gi|301384145|ref|ZP_07232563.1| pseudouridine synthase [Pseudomonas syringae pv. tomato Max13]
 gi|302064014|ref|ZP_07255555.1| pseudouridine synthase [Pseudomonas syringae pv. tomato K40]
 gi|302132672|ref|ZP_07258662.1| pseudouridine synthase [Pseudomonas syringae pv. tomato NCPPB 1108]
 gi|213924695|gb|EEB58263.1| Pseudouridine synthase [Pseudomonas syringae pv. tomato T1]
          Length = 296

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 54/282 (19%), Positives = 97/282 (34%), Gaps = 29/282 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +   +V   D K +K +   + G  ++I       N        
Sbjct: 30  LCAKFTAISREQWLDRIARDRVLDADGKTIKPDMAYREG--LKIHYFREVPN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQ 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +      
Sbjct: 80  --------ETPIPVVETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLDNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  RRI K Y ++   +P      +    
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANRQTRSAYQTLFPTRRIDKCYEAIAPALP-----GLEFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   G +   +  +V++          + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGPGVSNTQTRIEVLERHG-PLWRYRLHPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G  I  D  Y    K +     ++ L L A+ +    P  G 
Sbjct: 244 GAAICNDPFYPDALK-DPVDDYRHPLKLLAKSLHFTDPLSGE 284


>gi|49084528|gb|AAT51207.1| PA2043 [synthetic construct]
          Length = 301

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 100/263 (38%), Gaps = 12/263 (4%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAG 116
           R+Q G+V+             +E   +     L   +    ++ +LY D  + V +KP  
Sbjct: 45  RMQRGRVLDAEGRALGPQAAYREGLRVHYFRELPVEAPIPFEARILYRDEHLLVADKPHF 104

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           + V    G  Y     L     S G +     HR+D+ T+G+++ +    +       FR
Sbjct: 105 LPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTAGLVLFSTNPGSRGRYQALFR 162

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            RRI K Y ++   +P+     +   LL+++ +         +  +G   + +  +V++ 
Sbjct: 163 KRRIDKCYEAIAPALPQ-----LDFPLLRRTRLVPGEPFFRMREGEGEPNSETRIEVVER 217

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-TSPIQNKLYLHARY 294
             + +    + P TG+ HQLRVH   +G  I  D  Y                L L AR 
Sbjct: 218 NGR-WWRYRLYPVTGKKHQLRVHLAALGAGIQNDGFYPELLDAEGSPDDYLRPLKLLARG 276

Query: 295 MDLPHP-EGGRLQITAPLPAHMV 316
           +    P  G R    + L     
Sbjct: 277 LCFDDPLSGERRMFESGLRLDWQ 299


>gi|73959752|ref|XP_547206.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 1 [Canis familiaris]
          Length = 302

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 97/237 (40%), Gaps = 25/237 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---------RLTHRLD 151
           ++Y+     V NK   + +       +     L+  +     +          R  H+LD
Sbjct: 11  VVYQSRDFLVVNKHWDLRI---DSRMWRETPTLQKQLRHHFPELADPDTYYGFRFCHQLD 67

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG L VA  +AAA    + F+ RR+ K Y +LV G  +  +  I   + + S  G  
Sbjct: 68  FSTSGALCVALNKAAAGSAYKCFKERRVTKAYLALVRGHVQESRMTINYAIGRNSTEGRA 127

Query: 212 YVHVVKQNE--KGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           +   ++  E  +    +++   V++           + +QP TGRTHQLRVH   +  P+
Sbjct: 128 HTMCIEGTEGCENPKPSLTELVVLEHGLYAGDPVSKVLLQPLTGRTHQLRVHCSALSHPV 187

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQITAPLPAHMVKTWDSL 322
           VGD  Y              ++ LHA Y+ +P H E     + A  P   V   D+ 
Sbjct: 188 VGDLTYGQASDQEDQPF---RMMLHAFYLRIPTHSE----CVEACTPDPFVPALDAC 237


>gi|239624699|ref|ZP_04667730.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239521085|gb|EEQ60951.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 250

 Score =  131 bits (330), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 50/231 (21%), Positives = 101/231 (43%), Gaps = 27/231 (11%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD--------------SKGQKP 144
             +LYED  I V +KPAG+  Q   G A  +   ++ ++               S+    
Sbjct: 2   VPILYEDKDIIVVHKPAGLESQSSRGFAPDMVSEIRRYLHNPQDIHRPAAGISGSQPPYV 61

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HRLD+   G++V A+ + +A  L+ + +  +++K Y +++ G   +K+    ++L +
Sbjct: 62  GVIHRLDKPVEGVMVYAKNQKSAAALSAALQDGKMEKFYMAVICGQLVDKQGVYVDYLRQ 121

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA------QKFCWLEMQPHTGRTHQLRVH 258
                     +V ++ K A  A   ++ ++         +    ++++  TGR HQ+RV 
Sbjct: 122 DRKNNTS--EIVDKSVKDAKKAALKYREMEVIHSPEDKEKMLSLIDIELLTGRHHQIRVQ 179

Query: 259 ALHMGCPIVGDHKYCANFK-----GNFTSPIQNKLYLHARYMDLPHPEGGR 304
               G P+ GD +Y  +           + ++  L L A ++   HP  G 
Sbjct: 180 FAGHGTPLYGDGRYGGDISTIVDIKKEPAAVRRPLALCACHLAFLHPVTGE 230


>gi|239978554|ref|ZP_04701078.1| ribosomal pseudouridine synthase [Streptomyces albus J1074]
          Length = 280

 Score =  131 bits (330), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 53/246 (21%), Positives = 97/246 (39%), Gaps = 11/246 (4%)

Query: 60  QSGQVVRIPPVINALNHI-IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
             G+VV       A +   +   ++        +       ++L+ D  + V +KP  ++
Sbjct: 16  AGGEVVTGDGRPVAADAPYVPGGQVWFHRRRAAEVPAPYPPVVLFRDEHLVVVDKPHFLA 75

Query: 119 VQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               G  +       L++ ++    +    HRLD+ T+G++++    A        F  R
Sbjct: 76  TTPRGRHVTQTALALLRTRLEL--PELSPAHRLDRLTAGLVLLTVRPAERAAYQRLFSDR 133

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y ++    P      +A     +S I  +   +  Q   G   A +  +++    
Sbjct: 134 LVRKEYEAVAGYDP-----GLALPRTVRSRIVKERGVIAAQEVPGEPNAETRVELLAHRG 188

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                  + PHTGRTHQLRVH   +G PI+GD  Y  +         +  L L AR ++ 
Sbjct: 189 -TLGRYRLLPHTGRTHQLRVHLNSLGVPILGDPVY-PHLTDPAPDDFRRPLQLLARTVEF 246

Query: 298 PHPEGG 303
             P  G
Sbjct: 247 TDPVTG 252


>gi|296112286|ref|YP_003626224.1| pseudouridine synthase [Moraxella catarrhalis RH4]
 gi|295919980|gb|ADG60331.1| pseudouridine synthase [Moraxella catarrhalis RH4]
 gi|326561795|gb|EGE12130.1| putative pseudouridylate synthase [Moraxella catarrhalis 7169]
 gi|326562263|gb|EGE12589.1| putative pseudouridylate synthase [Moraxella catarrhalis 103P14B1]
 gi|326563232|gb|EGE13499.1| putative pseudouridylate synthase [Moraxella catarrhalis 46P47B1]
 gi|326564758|gb|EGE14971.1| putative pseudouridylate synthase [Moraxella catarrhalis 12P80B1]
 gi|326568979|gb|EGE19048.1| putative pseudouridylate synthase [Moraxella catarrhalis BC1]
 gi|326571956|gb|EGE21961.1| putative pseudouridylate synthase [Moraxella catarrhalis BC8]
 gi|326575466|gb|EGE25391.1| putative pseudouridylate synthase [Moraxella catarrhalis 101P30B1]
 gi|326576445|gb|EGE26353.1| putative pseudouridylate synthase [Moraxella catarrhalis CO72]
 gi|326577916|gb|EGE27780.1| putative pseudouridylate synthase [Moraxella catarrhalis O35E]
          Length = 298

 Score =  131 bits (330), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 62/306 (20%), Positives = 112/306 (36%), Gaps = 28/306 (9%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +  + +  +    + HI     QK    G V+ +D + +  N+  Q G  +     +   
Sbjct: 18  DAPLTIFEYVCKKFHHIGTAVWQKRFNDGLVKDIDGRVLDLNSPYQHGMTITYYRHLCDE 77

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +  E                    ++YED  + V +KP  ++V    G  Y     L 
Sbjct: 78  VVVPFEH------------------HIIYEDQTLLVVDKPHFLTVSPAGG--YVQQTLLT 117

Query: 135 SWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
               + G       HRLD++T+G+++  +T  + +     F  R+I KIY ++      +
Sbjct: 118 RLKQTTGNPHLSPAHRLDKQTAGLMIFTKTCESRRAYQSLFNDRQINKIYHAIAPMTQAH 177

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +     +  L +      Y   V   E   +  I    V +    K+   E++P TG+ H
Sbjct: 178 QFPLQVSLPLVRGEPF--YTMAVGIGEPNTHTDIDILAVSE--DGKWAKYELKPTTGKLH 233

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           QLRVH  ++G PI  D  Y               L L A+++    P   + +   +   
Sbjct: 234 QLRVHLNYLGIPIAHDSFY-PKVMHRAKDDFDKPLQLLAKHLSFTDPITNKPMAFESGFE 292

Query: 313 AHMVKT 318
               K 
Sbjct: 293 LDFSKV 298


>gi|227505675|ref|ZP_03935724.1| ribosomal pseudouridine synthase [Corynebacterium striatum ATCC
           6940]
 gi|227197643|gb|EEI77691.1| ribosomal pseudouridine synthase [Corynebacterium striatum ATCC
           6940]
          Length = 329

 Score =  131 bits (330), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 60/274 (21%), Positives = 106/274 (38%), Gaps = 15/274 (5%)

Query: 49  DKKRVKFNNRIQSGQVV-RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           D        R  +G+VV R   V+     + K+Q +    +   +        +L+ED  
Sbjct: 52  DDNAAALQARFDAGEVVLRDQTVLKPETLLTKDQDVFFYRIPAPEEPVPYDIPILFEDKH 111

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + V +KP  ++    +         ++    +        HRLD+ TSGILV  +T+   
Sbjct: 112 LLVVDKPPFMATMPRAKHIV-QSATVQMRRITGIDDLSPAHRLDRLTSGILVFTKTKEIR 170

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
                 F  RR+ K Y ++    P +     A W  +     G+    +   E  A   +
Sbjct: 171 GAYQTLFAERRVHKTYEAIA---PLSDVPVGAMWESRIEKTPGEIQGRLVAGEPNAFTEV 227

Query: 228 --------SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                     ++ I           ++P TG+THQLR+H    G PI+GD  Y   F  +
Sbjct: 228 AGVNPVDNEPYEAIHGPQPPLAKYTLKPKTGKTHQLRLHMWEAGVPILGDPVYPVTFPAD 287

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
               ++  ++L A  ++   P  G+  +  + LP
Sbjct: 288 AED-MRVPMHLTATRIEFIDPLTGKPREFVSNLP 320


>gi|108562767|ref|YP_627083.1| hypothetical protein HPAG1_0342 [Helicobacter pylori HPAG1]
 gi|107836540|gb|ABF84409.1| pseudouridine synthase D [Helicobacter pylori HPAG1]
          Length = 293

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 69/287 (24%), Positives = 121/287 (42%), Gaps = 29/287 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q VR   +I  +  +I                +    +
Sbjct: 28  LKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVSLI------------HFKPNEKTQV 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPHQVYTHP-KGYFYH-ESLLDCIQSHLGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  + + L   F  ++++K Y +L  G+ + K   I   +L   +I  D + +  Q  
Sbjct: 129 GKTLQSVKDLKALFMQKKVKKTYLALAHGLVE-KSMKIDKPILTPQNIQKD-LRIRSQIS 186

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                +I+  + ++         L++ P TGRTHQ+R+H  +MG  IVG+  Y    +  
Sbjct: 187 PLGKPSITLVEPLNYNPFLDISLLKITPLTGRTHQIRLHLSNMGHRIVGEGLYGVADEEA 246

Query: 280 FTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                  +      L LHA  ++    +G   +IT+ +P   +    
Sbjct: 247 RGYLQLKRENHAPLLMLHAASLEFEF-KGANYKITSQIPKRFMPFLK 292


>gi|114561280|ref|YP_748793.1| pseudouridine synthase Rlu family protein [Shewanella frigidimarina
           NCIMB 400]
 gi|114332573|gb|ABI69955.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           frigidimarina NCIMB 400]
          Length = 225

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 55/201 (27%), Positives = 85/201 (42%), Gaps = 19/201 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L +     V +K   +      G A    G +       G K    HRLD  TSG+L+V
Sbjct: 4   VLSDQPDFIVISKSVNVHFHSQDGSA----GVIAQAEADLGCKLYPVHRLDTPTSGLLIV 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA   T+ F   ++QK Y ++  G PK K+  I   + K          + K   
Sbjct: 60  AKSPQAANVFTKMFTEHKVQKYYLAIACGKPKKKQGWIIGDMAK------SRRSMYKLLR 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F      A       ++P +G+THQLRV    +G PI+GD  Y        
Sbjct: 114 TTENPAVTQFFS-QSIASGMRMYLLKPLSGKTHQLRVALASIGVPILGDKLYG------- 165

Query: 281 TSPIQNKLYLHARYMDLPHPE 301
              + ++ YLHA  +   + E
Sbjct: 166 -DELSDRCYLHAYSVHFTYLE 185


>gi|260792462|ref|XP_002591234.1| hypothetical protein BRAFLDRAFT_106462 [Branchiostoma floridae]
 gi|229276437|gb|EEN47245.1| hypothetical protein BRAFLDRAFT_106462 [Branchiostoma floridae]
          Length = 244

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 58/244 (23%), Positives = 97/244 (39%), Gaps = 27/244 (11%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------- 144
           +   F    +LY      V NKP  + +   +         L+  +  +           
Sbjct: 5   ERPPFSTVEVLYRSGNFLVVNKPYDVVL---NWDDPSRTDTLQHLLQERFPDLVDQSLKH 61

Query: 145 --RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             R  HRLD  TSG + +A  + AA H  ++F  +++ K Y +LV G        I   +
Sbjct: 62  CFRFVHRLDYSTSGPICIALNKKAAGHAGKAFSQKQVIKQYLALVRGHISEDHLSINKAI 121

Query: 203 LKKSHIGGDYVHVVKQNEKGANY---AISHFKVID---CFAQKFCWLEMQPHTGRTHQLR 256
            ++       V +  +   G  +   A++   V++      Q    + + P TGR HQLR
Sbjct: 122 GEQGTPDA-PVPMCVEGTPGCQHLRDAVTQLTVVEKGLYEGQPATKVNLCPMTGRRHQLR 180

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           VH   +G PIVGD+ Y              ++ LHA+ + +P  +G  + I    P    
Sbjct: 181 VHCQSIGHPIVGDYTYSCRQDTTPY-----RMMLHAQRLVIP-LKGEVIDIETDDP--FT 232

Query: 317 KTWD 320
            T+D
Sbjct: 233 TTFD 236


>gi|330973980|gb|EGH74046.1| pseudouridine synthase [Pseudomonas syringae pv. aceris str.
           M302273PT]
          Length = 296

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/294 (20%), Positives = 105/294 (35%), Gaps = 30/294 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +P I+          G+V   + K +  +   + G  +R+       N        
Sbjct: 30  LCAKFPAISREQWLDRFARGRVLDENGKAIAPDLAYREG--LRVHYFREVAN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQ 142
                   +    +   +LY D  + V +KP  + V   G  +   +   L   +D+   
Sbjct: 80  --------ETPIPVVETILYADEHLVVADKPHFLPVTPAGEYVEQTLLRRLIHRLDNPDM 131

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P   HR+D+ T+G+++ +  R         F  RRI K Y ++   +P      +A   
Sbjct: 132 VP--LHRIDRHTAGLVLFSANRQTRSAYQGLFPTRRIDKFYQAIAPALP-----GLAFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++    K     + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGIGASNTRTQIEVLERQ-DKLWRYGLYPMTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           G  I  D  Y  +   +     QN L L A  +    P  G      + L    
Sbjct: 244 GAAICNDPFY-PDVVKDPVDDYQNPLKLLASSLRFVDPLSGEQRHFESLLTLDW 296


>gi|224371098|ref|YP_002605262.1| RluC [Desulfobacterium autotrophicum HRM2]
 gi|223693815|gb|ACN17098.1| RluC [Desulfobacterium autotrophicum HRM2]
          Length = 295

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 57/246 (23%), Positives = 100/246 (40%), Gaps = 18/246 (7%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI---------DGFLKSWVDS 139
            +T         ++   +      KP+G+SV    G              +  + +    
Sbjct: 51  KITPMETTNSVEIVRTGNGWLCAEKPSGMSVHNHPGSDLLCVLERQIRADEDLMVALGAQ 110

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +    HRLDQETSG+++VA      ++L+  F+   +QK Y +LV G      +   
Sbjct: 111 EGFQIHPVHRLDQETSGLILVATDPDRLRYLSNLFQQGAVQKHYIALVHGNFDPPCDPFQ 170

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            W    S   G          KG    + + ++++D     +  LE++  TGR HQ+R H
Sbjct: 171 VWDTPLSKQAGGR---TDPRGKGKRVRSETRYRIMDQSPH-YTLLEIELVTGRKHQIRRH 226

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGGRLQITAP-LPAHM 315
           A   G P+ GD +Y +     F       ++L LH+  ++    +   + IT+  +P  M
Sbjct: 227 AKLAGHPVTGDTRYGSKRSVEFLRENHAYDRLGLHSFKIEFI-LDTVPVIITSRQIPRQM 285

Query: 316 VKTWDS 321
               D 
Sbjct: 286 TALLDQ 291


>gi|28897960|ref|NP_797565.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|153837500|ref|ZP_01990167.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|260364253|ref|ZP_05776956.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           K5030]
 gi|260877117|ref|ZP_05889472.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           AN-5034]
 gi|260895778|ref|ZP_05904274.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           Peru-466]
 gi|260902666|ref|ZP_05911061.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           AQ4037]
 gi|28806174|dbj|BAC59449.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|149749194|gb|EDM59991.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|308088331|gb|EFO38026.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           Peru-466]
 gi|308093765|gb|EFO43460.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           AN-5034]
 gi|308108274|gb|EFO45814.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           AQ4037]
 gi|308111894|gb|EFO49434.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           K5030]
          Length = 230

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 55/200 (27%), Positives = 90/200 (45%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL+
Sbjct: 3   DILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAK---QSGDEQLYLIHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R   AA  L+++F  R+++K Y ++    PK K+  +   + +        V     N
Sbjct: 60  LGRNAKAASALSQAFADRQVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV-----N 114

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K  N A++ F  +     +      +PHTG+THQ+RV    +G  IVGD  Y A  +  
Sbjct: 115 SKN-NPAVTQFFSLAAEPGER-LFLCKPHTGKTHQIRVALKSVGSGIVGDPIYNAGNEA- 171

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +   +
Sbjct: 172 ------DRGYLHAFSLCFQY 185


>gi|330876755|gb|EGH10904.1| pseudouridine synthase [Pseudomonas syringae pv. morsprunorum str.
           M302280PT]
          Length = 296

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 56/302 (18%), Positives = 101/302 (33%), Gaps = 37/302 (12%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +   +V   D K +  +   + G  ++I       N        
Sbjct: 30  LCAKFTAISREQWLDRIARNRVLDADGKTITPDMAYREG--LKIHYFREVPN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQ 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +      
Sbjct: 80  --------ETPIPVVETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLDNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  RRI K Y ++   +P+     +    
Sbjct: 130 NLVPLHRIDRHTAGLVLFSANRQTRSAYQTLFPTRRIDKCYEAIAPALPE-----LEFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   G +   +  +V++     + +  + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGPGVSNTQTRIEVLERHGPLWRYG-LHPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G  I  D  Y    K       Q+ L L A+ +    P  G        P         L
Sbjct: 244 GAAICNDPFYPDALKDPLDD-YQHPLKLLAKSLRFIDPLSGE-------PRQFESLL-KL 294

Query: 323 GF 324
            +
Sbjct: 295 DW 296


>gi|255079804|ref|XP_002503482.1| predicted protein [Micromonas sp. RCC299]
 gi|226518749|gb|ACO64740.1| predicted protein [Micromonas sp. RCC299]
          Length = 545

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 66/344 (19%), Positives = 106/344 (30%), Gaps = 102/344 (29%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-----GSGIAYHIDGFLKSWV--- 137
           +S  +   +D     +++ED  + V NKP G+         G+ +     G ++      
Sbjct: 200 ASRAVPLVADPTPLDVIHEDDDVLVVNKPPGLRFHPVHRFEGNSLLSRAIGHVRRSGRDD 259

Query: 138 ---------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKIYW 184
                    D     P + HRLD +TSG+ V+ +           FR     RR  K Y 
Sbjct: 260 DRLDGDAAGDGHAHVPHVVHRLDMDTSGVCVLVKRPELVDGFARQFRGDAGERRAVKEYL 319

Query: 185 SL-VWGIPKNKKECIANWLLKKSHIGGD-------------------------------- 211
           ++ V   P     C+     K     G+                                
Sbjct: 320 AIGVGAAPPGVTGCVVKADWKPPEASGNEQTTAAEFIGVEFTVDAHVGPHASIPEARAVH 379

Query: 212 -----YVHVVKQNEKGA-----NYAISHFKVIDC--------------FAQKFCWLEMQP 247
                   + K+N  G        A +  +++                 +       ++ 
Sbjct: 380 RPPPTPERIPKRNGSGGDPDAPKPARTDVRIVSSSRVPIDVNDDGDVMQSLTAVLARVRL 439

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--------------------- 286
           HTGRTHQ+RVH  H   PI+ D  Y  + + +  SP  +                     
Sbjct: 440 HTGRTHQIRVHMAHADLPILSDPLYGPHIRWDGASPCADASTSAILPPGVDADVWGGPRW 499

Query: 287 --KLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYD 327
             +  LHA  + L HPE    +   A  P  M     +LG   D
Sbjct: 500 LGRQALHAARLTLRHPETNEEMTFEARAPEDMRGACVALGLDPD 543


>gi|146102317|ref|XP_001469333.1| hypothetical protein [Leishmania infantum]
 gi|134073702|emb|CAM72439.1| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 741

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 92/237 (38%), Gaps = 28/237 (11%)

Query: 101 LLYEDSKIYVFNKPAGISV--QG------GSGIAYHIDGFLKS----WVDSKGQKPRLTH 148
           +LYED  + V +KPAG++    G      G+     I   L +     +     +    H
Sbjct: 514 VLYEDDDVLVVDKPAGLATSRHGLSCTQLGTPTTDLISVLLATDRVGALARGIFRQGQVH 573

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD ETSG L++A++  AA  L            +  +   +       +    L+   +
Sbjct: 574 RLDAETSGCLLIAKSDVAADSLRHQLGTSAAFSHHSKIYHALC-----VVLEPSLRNVRL 628

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             D +       +      + ++VI  F   +  W+E +   G+ HQLR H    G PI+
Sbjct: 629 HDDIIDAADPKIR------TRYRVIRFFPKHRVAWVECRIQQGKKHQLRRHLASRGLPIL 682

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
            D ++           + +++ LHA  +   HP     +   APLPA   +    L 
Sbjct: 683 ADLEHGG---AVCCQSMISRVALHAHSLSFIHPVTADPITAAAPLPADFRRCLSLLR 736


>gi|212637673|ref|YP_002314198.1| pseudouridine synthase RluA-like protein [Shewanella piezotolerans
           WP3]
 gi|212559157|gb|ACJ31611.1| Pseudouridine synthase RluA-like protein [Shewanella piezotolerans
           WP3]
          Length = 237

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 55/208 (26%), Positives = 86/208 (41%), Gaps = 19/208 (9%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           LT     L   ++ +++   V  K A I      G A    G +       G K    HR
Sbjct: 6   LTPVCGILMYQIIADEADFIVICKSANIHFHSQDGSA----GVVAQAELDLGIKLYSVHR 61

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSG+L++A++ A A   T  F   ++QK Y +L  G PK K+  +   + K     
Sbjct: 62  LDTMTSGLLILAKSSAVAAEFTRQFSEHKVQKYYLALAKGKPKKKQGWVIGDMAKSRRSM 121

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
              +  +       N A + F              ++P +G+THQLRV    +G PI+GD
Sbjct: 122 HKLLRSMD------NPAKTQFFS-HSVGDGLRLYLLKPLSGKTHQLRVALASIGVPILGD 174

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDL 297
             Y  +          ++ YLHA  ++ 
Sbjct: 175 ELYGGD--------ASDRGYLHAYSLNF 194


>gi|323304895|gb|EGA58653.1| Pus6p [Saccharomyces cerevisiae FostersB]
 gi|323308935|gb|EGA62166.1| Pus6p [Saccharomyces cerevisiae FostersO]
          Length = 404

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 59/280 (21%), Positives = 112/280 (40%), Gaps = 29/280 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRV--DKKRVKFNNRIQSGQVVRIPPVINALN 75
              L     + +           +R G  R+  D   +  ++ + +  +++   V+    
Sbjct: 35  GKLLIDVLVSEFKLRPRAYYLDQIRKGTYRLIRDGVPLVPDHLMTT--IIKNHDVLETTT 92

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSIL-----LYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           H  K +  +    +    ++ L   +     ++E+  I V +KP+GI V           
Sbjct: 93  H--KHEPPVKQWCSQEVEAEDLPGRIAGFNIVFENESILVIDKPSGIPVHPTGQF---YQ 147

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             +   +   G      +RLD+ TSG+L++A+   +A  + +S R R + KIY + V G 
Sbjct: 148 NTITELLKLHGVDALPCYRLDKITSGLLILAKNSQSAGEIQKSIRSRDMIKIYLARVKGR 207

Query: 191 PKNKKECIANW-------------LLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCF 236
             + +  + N               ++ + I   D           +  AI+ F  I  F
Sbjct: 208 FPHSELILDNESAAETTFEDTSKVTVEMTPIYSIDPKRQFPVGLSASKDAITKFYPIRYF 267

Query: 237 AQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +      +  +P TGRTHQ+R+H   +G PIV D  YC++
Sbjct: 268 SHADETVVACKPITGRTHQIRIHLARLGHPIVNDSVYCSH 307


>gi|323348440|gb|EGA82685.1| Pus6p [Saccharomyces cerevisiae Lalvin QA23]
          Length = 404

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 57/256 (22%), Positives = 105/256 (41%), Gaps = 29/256 (11%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
            +++R G   V       ++ + +  +++   V+    H  +       S  +       
Sbjct: 63  YRLIRDGVPLV------PDHLMTT--IIKNHDVLETTTHKHEPPVXQWCSQEVEAEDLPG 114

Query: 98  KSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
           +     +++ED  I V +KP+GI V             +   +   G      +RLD+ T
Sbjct: 115 RIAGFNIVFEDESILVIDKPSGIPVHPTGQF---YQNTITELLKLHGVDALPCYRLDKIT 171

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW------------- 201
           SG+L++A+   +A  + +S R R + KIY + V G   + +  + N              
Sbjct: 172 SGLLILAKNSQSAGEIQKSIRSRDMIKIYLARVKGRFPHSELILDNENAAETTFEDTSKV 231

Query: 202 LLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHA 259
            ++ + I   D           +  AI+ F  I  F+      +  +P TGRTHQ+R+H 
Sbjct: 232 TVEMTPIYSIDPKRQFPVGLSASKDAITKFYPIRYFSHADETVVACKPITGRTHQIRIHL 291

Query: 260 LHMGCPIVGDHKYCAN 275
             +G PIV D  YC++
Sbjct: 292 ARLGHPIVNDSVYCSH 307


>gi|169633282|ref|YP_001707018.1| putative pseudouridylate synthase [Acinetobacter baumannii SDF]
 gi|169152074|emb|CAP00961.1| putative pseudouridylate synthase [Acinetobacter baumannii]
          Length = 302

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 54/296 (18%), Positives = 110/296 (37%), Gaps = 29/296 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             + ++   ++PHI     Q+  + G +   + +++  N+   +   +     +    H+
Sbjct: 29  QTIYQFLCENFPHIKATEWQQRFQDGLIYAANGEKLTLNSSYIANTHIFYYRFLANEVHV 88

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E +                  +L+E+  + V +KP  +++       Y  +  L    
Sbjct: 89  PFEHQ------------------ILFENDDLLVVDKPHFLTISPTG--QYVQETLLVRLK 128

Query: 138 DSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              G K     HRLD+ET+G+++  +   +     + F  R++ KIY ++     + K  
Sbjct: 129 KQTGNKFLTPIHRLDRETAGVVLFCKRPQSRGIYQQLFADRQVNKIYHAIAAYKAELKF- 187

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 LK     G   + ++          +  ++I+       +  + P TG+ HQLR
Sbjct: 188 ---PQNLKLYLDKGTPFYTMQVITHTKTNTETKIELIEHNHSWAKYC-LTPTTGKQHQLR 243

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
           VH  H+G PI  D  Y    +          L L A+ +    P     +   + L
Sbjct: 244 VHLNHLGIPIKNDPFY-PIVQHKADDDFSQPLQLLAKQISFIDPLTKQEMVFNSQL 298


>gi|328473082|gb|EGF43930.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           10329]
          Length = 230

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 55/200 (27%), Positives = 90/200 (45%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL+
Sbjct: 3   DILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAK---QSGDEQLYLIHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R   AA  L+++F  R+++K Y ++    PK K+  +   + +        V     N
Sbjct: 60  LGRNAKAASALSQAFADRQVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV-----N 114

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K  N A++ F  +     +      +PHTG+THQ+RV    +G  IVGD  Y A  +  
Sbjct: 115 SKN-NPAVTQFFSLAAEPGER-LFLCKPHTGKTHQIRVALKSVGSGIVGDPIYNAGNEA- 171

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +   +
Sbjct: 172 ------DRGYLHAFSLCFQY 185


>gi|71893374|ref|YP_278820.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyopneumoniae J]
 gi|71851501|gb|AAZ44109.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyopneumoniae J]
          Length = 281

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 56/288 (19%), Positives = 104/288 (36%), Gaps = 32/288 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V   ++   +L +  K      N+  +QK  R+ +++V+    + N  I+   ++ I  
Sbjct: 4   FVATKNQSGQKLIQLIKKILLKSNYNEIQKYFRTKKIKVNNTFQEKNYIIKEKDIILIFS 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                    K  +              L   ++Y+D  I + +KP  + V GG       
Sbjct: 64  QEKLKTFSKKVPEF------------KLNLKIIYQDENILLVDKPQNLQVHGGRFNLDLA 111

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                   +++  KP    RLD++TSGI++      +   L +  +       + S +  
Sbjct: 112 VWNYLKIPENQVFKPSHIGRLDKKTSGIILYGLNYQSVVELNQKQKFFEKIYTFKSDI-- 169

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N K  I   +  + +     + V  ++      + + +        K        HT
Sbjct: 170 ---NLKNTIKTDVFIRKNNFQQKMEVTLKSPNSFFASTTFY-------SKNQKKFAILHT 219

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           G+ HQ+RV   H+G PI GD KY               LYLH+  +  
Sbjct: 220 GKKHQIRVSLSHLGFPIFGDEKYGGTRDKI--------LYLHSFSLKF 259


>gi|126172548|ref|YP_001048697.1| pseudouridine synthase Rlu family protein [Shewanella baltica
           OS155]
 gi|125995753|gb|ABN59828.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS155]
          Length = 230

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 55/198 (27%), Positives = 89/198 (44%), Gaps = 19/198 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++ +++   V +K A +      G A    G +       G K    HRLD  TSG+L+
Sbjct: 3   RIIADEADFIVISKSAKVHFHSQDGTA----GVVAQAEQDLGIKLFAVHRLDTPTSGLLI 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A++  AA+  TE F   ++QK Y +L  G PK K+  +   + K          + K  
Sbjct: 59  LAKSAVAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIGDMAK------SRRSMFKLL 112

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F  +   ++      ++PH+G+THQLRV    +G PI+GD  Y       
Sbjct: 113 RTKENPAITQFFSL-SVSEGLRLYLLKPHSGKTHQLRVALASLGVPILGDDLYGG----- 166

Query: 280 FTSPIQNKLYLHARYMDL 297
                 ++ YLHA  +  
Sbjct: 167 ---MAADRCYLHAYCLHF 181


>gi|156974969|ref|YP_001445876.1| hypothetical protein VIBHAR_02690 [Vibrio harveyi ATCC BAA-1116]
 gi|156526563|gb|ABU71649.1| hypothetical protein VIBHAR_02690 [Vibrio harveyi ATCC BAA-1116]
          Length = 230

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 54/200 (27%), Positives = 89/200 (44%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSG+L+
Sbjct: 3   DILHTHPDFLIINKHPNVSVHKDDGDTMLLHEVAK---QSGDEQLYLIHRLDKMTSGVLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R   AA  L+++F  R ++K Y ++    PK K+  +   + +        V+     
Sbjct: 60  LGRNAKAASALSQAFADREVEKFYLTIGSKKPKKKQGLVVGDMERSRRSSWKLVNSKT-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F  +     +      +PHTG+THQ+RV    +G  IVGD  Y A  +  
Sbjct: 118 ----NPAITQFFSLAAEPGER-LFLCKPHTGKTHQIRVALKSVGSGIVGDPIYNAGNEA- 171

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +  P+
Sbjct: 172 ------DRGYLHAFSLCFPY 185


>gi|323337472|gb|EGA78720.1| Pus6p [Saccharomyces cerevisiae Vin13]
          Length = 404

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 58/258 (22%), Positives = 108/258 (41%), Gaps = 33/258 (12%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
            +++R G   V       ++ + +  +++   V+    H  K +  +    +    ++ L
Sbjct: 63  YRLIRDGVPLV------PDHLMTT--IIKNHDVLETTTH--KHEPPVKQWCSQEVEAEDL 112

Query: 98  KSIL-----LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
              +     ++ED  I V +KP+GI V             +   +   G      +RLD+
Sbjct: 113 PGRIAGFNIVFEDESILVIDKPSGIPVHPTGQF---YQNTITELLKLHGVDALPCYRLDK 169

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW----------- 201
            TSG+L++A+   +A  + +S R R + KIY + V G   + +  + N            
Sbjct: 170 ITSGLLILAKNSQSAGEIQKSIRSRDMIKIYLARVKGRFPHSELILDNENAAETTFEDTS 229

Query: 202 --LLKKSHI-GGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRV 257
              ++ + I   D           +  AI+ F  I  F+      +  +P TGRTHQ+R+
Sbjct: 230 KVTVEMTPIYSIDPKRQFPVGLSASKDAITKFYPIRYFSHADETVVACKPITGRTHQIRI 289

Query: 258 HALHMGCPIVGDHKYCAN 275
           H   +G PIV D  YC++
Sbjct: 290 HLARLGHPIVNDSVYCSH 307


>gi|221123607|ref|XP_002156005.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4 [Hydra magnipapillata]
          Length = 329

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 112/246 (45%), Gaps = 15/246 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ---KPRLTHRLDQETSGIL 158
           LY    +   +KP GI V GG  I   I  FL +     G       L HRLD+ TSG+L
Sbjct: 32  LYMKDGLLAIHKPYGIPVHGGPKIKLSIADFLPALEQKHGLLAGSLELAHRLDKNTSGVL 91

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++   +  A++L +    R+I+K Y +++ G        + N  L ++   G +   + +
Sbjct: 92  LLTYKKEMAKYLADLHENRQIEKSYLAILLGNVSRVTGVL-NGELHETLRNGQFKQTINE 150

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG-CPIVGDHKYCANFK 277
                +   +++ ++D           +  TG  HQ+RVHA  +  CPI+GDH+Y AN K
Sbjct: 151 ISINKSSVETNYTILDSNQDTCMLCLFKTFTGNKHQIRVHAYELLKCPILGDHRYHAN-K 209

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP-----LPAHMV-KTWDSLGFKYDRNLY 331
           G  T PI  +L    R   + + E G  +I  P     LP H++ K+    G    ++L 
Sbjct: 210 GPQTLPI--RLIQMLRMRGVKNEETGSSKIR-PWQRGLLPMHLLTKSIRIPGLDGSKDLT 266

Query: 332 IKRLYS 337
           I+    
Sbjct: 267 IETSIP 272


>gi|219683568|ref|YP_002469951.1| pseudouridine synthase [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|219621218|gb|ACL29375.1| pseudouridine synthase [Bifidobacterium animalis subsp. lactis
           AD011]
          Length = 230

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 54/225 (24%), Positives = 90/225 (40%), Gaps = 19/225 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +YE+ +I V +KP  ++     G+ Y     ++     +       HRLD+ T+GI+V  
Sbjct: 2   VYENERIIVVDKPHFLATTP-RGMWYRETALMRLRERYREPNIIPAHRLDRPTAGIVVFV 60

Query: 162 RTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN-------WLLKKSHIGGDY 212
           R  AA       F+  R +K Y   + +  +   +   + +        L+++S I    
Sbjct: 61  RDPAARGAYQMLFQEHRTRKCYECLAPIRPLATPRTGTVVHGSPPRIWPLVRRSRIRKTR 120

Query: 213 VHVVKQNEKGANYAIS-------HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
             +  Q   G   A +       H ++            + P TG+THQLRVH   +G P
Sbjct: 121 GVLCAQEIPGQVNAETAIELEALHARMSARMGMSIGVYRLLPRTGKTHQLRVHMNSLGLP 180

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITA 309
           IVGD  Y    +          L L AR +    P  G  L+ ++
Sbjct: 181 IVGDDFY-PRIEERAYDDFSQPLQLVARSLAFTDPFTGDPLEFSS 224


>gi|320156659|ref|YP_004189038.1| pseudouridylate synthase 23S RNA-specific [Vibrio vulnificus
           MO6-24/O]
 gi|319931971|gb|ADV86835.1| pseudouridylate synthase 23S RNA-specific [Vibrio vulnificus
           MO6-24/O]
          Length = 262

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 60/250 (24%), Positives = 105/250 (42%), Gaps = 25/250 (10%)

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +  +D+S+ L          +L+      + NK   +SV    G    +    K    S 
Sbjct: 17  KPAIDASLGLNAFYAMFD--ILFTHPDFLIINKYPHVSVHKDDGDTMLLQEVAKV---SG 71

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            ++  L HRLD+ TSGIL++ R   AA  L++ F  R ++K Y ++    PK K+  +  
Sbjct: 72  DEQLYLIHRLDKMTSGILLLGRNSTAASALSQRFAQREVEKFYLAIGAKKPKKKQGTVIG 131

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            + +        V+  +      N AI+ F  +     +  +L  +P+TG+THQ+RV   
Sbjct: 132 DMERSRRASWKLVNSKQ------NPAITQFFSLAGEPGERAFL-CKPYTGKTHQIRVALK 184

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
            +G  IVGD  Y             ++ YLHA  +   + +G +            +   
Sbjct: 185 SVGSSIVGDPIYNGGSDS-------DRGYLHAFCLGFQY-QGEQYHFVCDP-----RNQA 231

Query: 321 SLGFKYDRNL 330
           +LG K++   
Sbjct: 232 ALGEKWNSEA 241


>gi|330870692|gb|EGH05401.1| pseudouridine synthase [Pseudomonas syringae pv. aesculi str.
           0893_23]
          Length = 264

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/291 (20%), Positives = 107/291 (36%), Gaps = 30/291 (10%)

Query: 28  HYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
            +  I+       +  G+V   + K +  +   + G  +RI       N           
Sbjct: 1   KFTAISREQWLDRIARGRVLDENGKAIAPDLAYREG--LRIHYFREVPN----------- 47

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPR 145
                +    +   +LY D  + V +KP  + V       Y     L+  +   G     
Sbjct: 48  -----ETPIPVLETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNPDLV 100

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HR+D+ T+G+++ +  +         F  R+I K Y ++   +P      +    L +
Sbjct: 101 PLHRIDRHTAGLVLFSANQQTRSAYQALFPTRQIDKFYEAIAPALP-----GLEFPRLHE 155

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           S +         Q   GA+   +  +V++   Q + +  + P TG+ HQLRVH   +G  
Sbjct: 156 SRLVEGEPFFRMQEGAGASNTRTQIEVLERQDQLWRYG-LYPVTGKKHQLRVHMAALGAG 214

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           I  D  Y A  K N     QN L L A+ +    P  G+  Q  + L    
Sbjct: 215 ICNDPFYPAVVK-NPVDDYQNPLKLLAKGLRFIDPLSGKQRQFESLLELDW 264


>gi|254229878|ref|ZP_04923282.1| pseudouridine synthase Rlu family protein [Vibrio sp. Ex25]
 gi|151937582|gb|EDN56436.1| pseudouridine synthase Rlu family protein [Vibrio sp. Ex25]
          Length = 243

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 98/233 (42%), Gaps = 23/233 (9%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           + F    +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ 
Sbjct: 10  ASFFMFDILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAK---QSGDEQLYLIHRLDKM 66

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSGIL + R   AA  L+++F  R+++K Y ++    PK K+  +   + +        V
Sbjct: 67  TSGILFLGRNAKAASALSQAFADRQVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV 126

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                N K  N A++ F  +     +      +PHTG+THQ+RV    +G  IVGD  Y 
Sbjct: 127 -----NSKN-NPAVTQFFSLAAEPGER-LFLCKPHTGKTHQIRVALKSVGSGIVGDPIYN 179

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
           A  +        ++ YLHA  +   +    + +       H       LG K+
Sbjct: 180 AGNEA-------DRGYLHAFSLCFQY-RDEQYRFVCDPREH-----KMLGKKW 219


>gi|160873422|ref|YP_001552738.1| pseudouridine synthase Rlu family protein [Shewanella baltica
           OS195]
 gi|160858944|gb|ABX47478.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS195]
 gi|315265651|gb|ADT92504.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS678]
          Length = 230

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 55/198 (27%), Positives = 89/198 (44%), Gaps = 19/198 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++ +++   V +K A +      G A    G +       G K    HRLD  TSG+L+
Sbjct: 3   RIIADEADFLVISKSAKVHFHSQDGTA----GVVAQAEQDLGIKLFAVHRLDTPTSGLLI 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A++  AA+  TE F   ++QK Y +L  G PK K+  +   + K          + K  
Sbjct: 59  LAKSAGAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIGDMAK------SRRSMFKLL 112

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F  +   ++      ++PH+G+THQLRV    +G PI+GD  Y       
Sbjct: 113 RTKENPAITQFFSL-SVSEGLRLYLLKPHSGKTHQLRVALASLGVPILGDDLYGG----- 166

Query: 280 FTSPIQNKLYLHARYMDL 297
                 ++ YLHA  +  
Sbjct: 167 ---MAADRCYLHAYCLHF 181


>gi|238916039|ref|YP_002929556.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           eligens ATCC 27750]
 gi|238871399|gb|ACR71109.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           eligens ATCC 27750]
          Length = 225

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 48/212 (22%), Positives = 93/212 (43%), Gaps = 11/212 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
           +++E   I + NKPAG   QG  G    +   + ++  S+G+     + +RLD+  SG++
Sbjct: 4   IIHETKDIIIVNKPAGQLSQGAKGFDLDLVSEVMTYNASQGKPAYAAIINRLDRPVSGLV 63

Query: 159 VVARTRAAAQHLTE-SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           ++A+ ++AA   +    +     K Y +L+ G     K    ++L K        +    
Sbjct: 64  LIAKNKSAAAKYSTLMQKEGGFNKQYEALICGKLSESKGTFVDYLKKDGRTNTSAIVPAD 123

Query: 218 Q--NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-- 272
              N+K A  +   ++VI     +    + +   TGR HQ+RV       P+VGD+KY  
Sbjct: 124 AAANDKEAKLSKLEYEVISYDEVKDITHVRIHLITGRHHQIRVQFASRRHPLVGDYKYAT 183

Query: 273 ---CANFKGNFTSPIQNKLYLHARYMDLPHPE 301
                +      +  +N++ L A  + + +  
Sbjct: 184 ADCGMDNAVKAVAFKRNQIALCAVSLTIENET 215


>gi|326569279|gb|EGE19340.1| putative pseudouridylate synthase [Moraxella catarrhalis BC7]
          Length = 298

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 62/306 (20%), Positives = 112/306 (36%), Gaps = 28/306 (9%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +  + +  +    + HI     QK    G V+ +D + +  N+  Q G  +     +   
Sbjct: 18  DAPLTIFEYVCKKFHHIGTAVWQKRFNDGLVKDIDGRILDLNSPYQHGMTITYYRHLCDE 77

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +  E                    ++YED  + V +KP  ++V    G  Y     L 
Sbjct: 78  VVVPFEH------------------HIIYEDQTLLVVDKPHFLTVSPAGG--YVQQTLLT 117

Query: 135 SWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
               + G       HRLD++T+G+++  +T  + +     F  R+I KIY ++      +
Sbjct: 118 RLKQTTGNPHLSPAHRLDKQTAGLMIFTKTCESRRAYQSLFNDRQINKIYHAIAPMTQAH 177

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +     +  L +      Y   V   E   +  I    V +    K+   E++P TG+ H
Sbjct: 178 QFPLQVSLPLVRGEPF--YTMAVGIGEPNTHTDIDILAVSE--DGKWAKYELKPTTGKLH 233

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           QLRVH  ++G PI  D  Y               L L A+++    P   + +   +   
Sbjct: 234 QLRVHLNYLGIPIAHDSFY-PKVMHRAKDDFDKPLQLLAKHLSFTDPITNKPMAFESGFE 292

Query: 313 AHMVKT 318
               K 
Sbjct: 293 LDFSKV 298


>gi|170097151|ref|XP_001879795.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164645198|gb|EDR09446.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 321

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 104/242 (42%), Gaps = 24/242 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-----GSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQE 153
           LLY D  + V  KP G+  Q       +G   H +  ++        +  P   HRLD+ 
Sbjct: 30  LLYVDPAVAVVTKPHGLVCQLIHRQLPAGRVNHFNVMMQDLKAHLSLETFPYPVHRLDKS 89

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G  ++A T ++A+ L++ F+ R +QK Y +LV G    +K     +   ++ +     
Sbjct: 90  TTGAFLLALTESSARQLSQQFQKRTVQKTYLALVRG---GEKSFPEKFGEIRTTLNKVDG 146

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGC-PIVGDHK 271
           +             + +K++          LE+   TG  HQLRVH       PI+GD +
Sbjct: 147 YPEVDLSSQGQPCATDWKLLASSPIAPISLLELNLLTGYKHQLRVHLAKCLHAPILGDAQ 206

Query: 272 YCANFKGNFTSPI----QNKLYLHARYMDL-------PHPEGGRLQITAPLPAHMVKTWD 320
           Y      +  + +    +++++LHA  +         PH +  RL + APLP   +K   
Sbjct: 207 YSKKPLSSAITDVVKIPEDRIFLHASEISFLKYKSSGPHKQF-RLAVRAPLPREFLKLCK 265

Query: 321 SL 322
            L
Sbjct: 266 DL 267


>gi|326780284|ref|ZP_08239549.1| pseudouridine synthase [Streptomyces cf. griseus XylebKG-1]
 gi|326660617|gb|EGE45463.1| pseudouridine synthase [Streptomyces cf. griseus XylebKG-1]
          Length = 312

 Score =  130 bits (328), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 62/271 (22%), Positives = 103/271 (38%), Gaps = 28/271 (10%)

Query: 36  NLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS 94
            +  +L +G+ V VD   V+ +    +G+ +                          +  
Sbjct: 52  RVAGMLDAGRIVGVDGTAVRGSEPYAAGRYLWFHRDFA------------------PEEP 93

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                 ++Y D +I V +KP  ++    G  I       L+  ++    +P   HRLD+ 
Sbjct: 94  VPFPVRVVYRDERIVVADKPHFLATMPRGRHITETAVARLRRELELPALQP--AHRLDRL 151

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G+++              FR RR++K Y +L    P      +A     +S I  +  
Sbjct: 152 TAGLVLFVVRPEDRGAYQTLFRDRRVRKEYEALAPYDPD-----VALPRTVRSRIVKERG 206

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +  + E G   + S  ++++          + P TGRTHQLRVH   +G PIV D  Y 
Sbjct: 207 VLAAREEPGEANSESRVELVERRG-GVGRYRLLPATGRTHQLRVHMNALGLPIVHDPLYP 265

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                         L L AR +D   P GG 
Sbjct: 266 VVVPEAAVENWDRPLQLLARVLDFTDPVGGE 296


>gi|302533507|ref|ZP_07285849.1| ribosomal pseudouridine synthase [Streptomyces sp. C]
 gi|302442402|gb|EFL14218.1| ribosomal pseudouridine synthase [Streptomyces sp. C]
          Length = 322

 Score =  130 bits (328), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 61/295 (20%), Positives = 103/295 (34%), Gaps = 28/295 (9%)

Query: 13  ENDEENM--RLDRWFKNHYPHINFVN-LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
             D E     L  +    Y        + ++L  G+V  +  RV     ++         
Sbjct: 26  PPDHEGRWPTLGAYLTERYAGTRGSESMARLLSGGRVLGEGGRV-----LRHEDPYEPGG 80

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYH 128
            +     +  E  +                 +++ D  + V +KP  ++    G+ +   
Sbjct: 81  WLWFHRDMPPEPAVP------------FPIGVVHRDRHLLVVDKPHFLATTPRGTHVTET 128

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               L+  +D     P   HRLD+ T+G+++ +            F+ RR+ K Y +L  
Sbjct: 129 ALARLRRELDLPALSP--AHRLDRMTAGLVMFSIRPEDRGAYQLLFQQRRVHKEYEALAA 186

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
             P      +    L +SHI      +      GA         +           + PH
Sbjct: 187 HAPS-----LELPRLVRSHIEKTRGVMAAVEVPGAEPNAESLVELTGVRDGLGRYRLTPH 241

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           TGRTHQLRVH   +G PI+GD  Y    +    +  +  L L AR +    P  G
Sbjct: 242 TGRTHQLRVHMNSLGLPILGDPVYPVVAEAADPADYRRPLQLLARTLAFTDPVTG 296


>gi|239817699|ref|YP_002946609.1| pseudouridine synthase [Variovorax paradoxus S110]
 gi|239804276|gb|ACS21343.1| pseudouridine synthase [Variovorax paradoxus S110]
          Length = 303

 Score =  130 bits (328), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 66/298 (22%), Positives = 107/298 (35%), Gaps = 35/298 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +    +P I        + +  V VD     V    R Q+   V     ++A   I    
Sbjct: 32  FLIERFPAITREAWLARMEARDV-VDEHGVPVTAQRRYQAPLRVYYYRTLDAEVRIP--- 87

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSK 140
                              +L++D ++ V +KP  + V       Y  +  L       K
Sbjct: 88  ---------------FDEQVLFQDDELVVADKPPFLPVTPTG--KYLQESLLVRLKRKLK 130

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                  HR+D+ T+G+++ +            F  RRI K Y ++V   P       + 
Sbjct: 131 LDDLVPLHRIDRSTAGLVLFSVRPETRGAYQAMFPERRIDKHYEAVVPWQP----GVSSV 186

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               +S +  D   +  + E G   + +    +   A     LE+ P TGR HQLRVH +
Sbjct: 187 PGTYRSRLVDDDHFMRVKEEAGEPNSETRIA-LRKTAGGHALLELSPVTGRKHQLRVHCM 245

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAP----LPA 313
            +G PIV D  Y      + +      L L A+ +    P  G L+  T+P    LP 
Sbjct: 246 ALGMPIVNDPFYPTLLPPD-SDDFDKPLQLLAKSVAFQDPVSGELRSFTSPRSLALPP 302


>gi|315453361|ref|YP_004073631.1| putative ribosomal pseudouridine synthase [Helicobacter felis ATCC
           49179]
 gi|315132413|emb|CBY83041.1| putative ribosomal pseudouridine synthase [Helicobacter felis ATCC
           49179]
          Length = 247

 Score =  130 bits (328), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 67/297 (22%), Positives = 115/297 (38%), Gaps = 57/297 (19%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        I+    QK++  G+V +  +++    ++                       
Sbjct: 6   KLLSAQM-GISHKQAQKLIDLGRVCLGGRKLTLARQLC---------------------- 42

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                +         K+ +LY+++     NKPAG++                  ++ +  
Sbjct: 43  ----PLQSKFEVQNSKAQILYQETDWLFLNKPAGVNS---------------YALEKQHP 83

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             +L HRLD  T+G+L +A+  A AQ L E+F+ R + K Y +LV G+ K  +       
Sbjct: 84  PYKLLHRLDLPTTGVLALAQNHAHAQGL-EAFKKRAVYKEYIALVQGVIKKPQTLRMPLR 142

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           ++KSHI      V    +     A +    +  +  K   L++   TG THQ+R H   +
Sbjct: 143 VQKSHIEDAKGFVKTLLDPAGRPACTKITPLKQYKNK-TLLKVVITTGITHQIRAHLSAL 201

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
           GCPIVGD  Y       F        +LHA  + +         I APLP +  +  
Sbjct: 202 GCPIVGDVLYGGRSHQYF--------FLHAHRLKILD-----HYIQAPLPFYFEEEL 245


>gi|184158634|ref|YP_001846973.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|332874330|ref|ZP_08442242.1| pseudouridine synthase, RluA family [Acinetobacter baumannii
           6014059]
 gi|183210228|gb|ACC57626.1| Pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|322507602|gb|ADX03056.1| Pseudouridine synthase [Acinetobacter baumannii 1656-2]
 gi|323518552|gb|ADX92933.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332737458|gb|EGJ68373.1| pseudouridine synthase, RluA family [Acinetobacter baumannii
           6014059]
          Length = 302

 Score =  130 bits (328), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 53/296 (17%), Positives = 110/296 (37%), Gaps = 29/296 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             + ++   ++PHI     Q+  + G +   + +++  N+   +   +     +    H+
Sbjct: 29  QTIYQFLCENFPHIKATEWQQRFQDGLIYAANGEKLTLNSPYIANTHIFYYRFLANEVHV 88

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E +                  +L+E+  + V +KP  +++       Y  +  L    
Sbjct: 89  PFEHQ------------------ILFENDDLLVVDKPHFLTISPTG--QYVQETLLVRLK 128

Query: 138 DSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              G +     HRLD+ET+G+++  +   +     + F  R++ KIY ++     + K  
Sbjct: 129 KQTGNEFLTPIHRLDRETAGVVLFCKRPQSRGIYQQLFADRQVNKIYHAIAAYKAELKF- 187

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 LK     G   + ++          +  ++I+       +  + P TG+ HQLR
Sbjct: 188 ---PQNLKLYLDKGTPFYTMQVIAHTKTNTETKIELIEHNHSWAKYC-LTPTTGKQHQLR 243

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
           VH  H+G PI  D  Y    +          L L A+ +    P     +   + L
Sbjct: 244 VHLNHLGIPIKNDPFY-PIVQHKADDDFSQPLQLLAKQISFIDPLTKQEMVFNSQL 298


>gi|84998092|ref|XP_953767.1| (RNA) pseudouridylate synthase [Theileria annulata]
 gi|65304764|emb|CAI73089.1| (RNA) pseudouridylate synthase, putative [Theileria annulata]
          Length = 441

 Score =  130 bits (328), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 59/296 (19%), Positives = 117/296 (39%), Gaps = 34/296 (11%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V    V+       L +  K+ +       +   +    +++          +Q+G+ 
Sbjct: 51  SNVYKTFVKERWMGKPLRKVLKDEFSAFTPDYIDFAINKNNIKI---------ILQNGEE 101

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGS 123
           +         + +   ++IL  ++     +   K  ++YED +  V +KP  I V Q G+
Sbjct: 102 LDNSSENVLDHILKPNERILHEAIVHEPVALNSKVPVVYEDDQYIVVSKPTSIPVYQTGT 161

Query: 124 GIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +   +K  + S +  K    HR+D+  SG++  A++   A +L+++ R   ++K+
Sbjct: 162 YNYNSLMEIMKREIPSCRDLKLFTVHRIDRLVSGLVAFAKSSQDASNLSQAIRDNEVKKV 221

Query: 183 YWSLVWGIP-----------KNKKECIAN----------WLLKKSHIGGDYVHVVKQNEK 221
           Y + V G             K       N          ++   S   G Y  V + +E 
Sbjct: 222 YIARVKGDFSYLINTSNSDNKESDGDADNSLENVFESIGYMRVISKKEGKYEFVGENDED 281

Query: 222 GA-NYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +   +++ FK+I          +   P TGRTHQ+R H  ++G PI  D  Y  +
Sbjct: 282 ESYKRSVTRFKLIKYNKDLHESLVLCSPITGRTHQIRAHLKYLGYPISNDPWYNND 337


>gi|329939071|ref|ZP_08288445.1| ribosomal pseudouridine synthase [Streptomyces griseoaurantiacus
           M045]
 gi|329301956|gb|EGG45849.1| ribosomal pseudouridine synthase [Streptomyces griseoaurantiacus
           M045]
          Length = 312

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 57/263 (21%), Positives = 101/263 (38%), Gaps = 23/263 (8%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVN-------------LTKHSDFLKSILLYE 104
           R+ +G  V +  +++A   +  + + L                    +        ++Y 
Sbjct: 42  RLAAGDGV-VDAMLDAGAFVGADGRPLAPDAPYVPGMYVWFHRELPAEERVPFAIEVVYR 100

Query: 105 DSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           D+ + V +KP  ++    GS +A      L+  +D         HRLD+ T+G+++    
Sbjct: 101 DAHVLVADKPHFLATTPRGSHVAETALARLRRELDLPALTA--AHRLDRLTAGLVLFTLR 158

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
                     FR RR+ K Y +L    P      +A     +S +  +   +  +   G 
Sbjct: 159 PEERGAYQTLFRDRRVHKEYEALAPYDPA-----LALPRTVRSRLVKERGELRAREVPGE 213

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
             A+S  ++++          + P TG+THQLRVH   +G PI+GD  Y           
Sbjct: 214 PNAVSRVELVEHDG-TVGRYRLLPRTGQTHQLRVHMCALGLPILGDPLYPVVEPAAAPGD 272

Query: 284 IQNKLYLHARYMDLPHPEGGRLQ 306
               L L AR ++   P  GR  
Sbjct: 273 FTRPLRLLARALEFTDPVTGRHH 295


>gi|170729099|ref|YP_001763125.1| pseudouridine synthase Rlu family protein [Shewanella woodyi ATCC
           51908]
 gi|169814446|gb|ACA89030.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           woodyi ATCC 51908]
          Length = 224

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 55/210 (26%), Positives = 83/210 (39%), Gaps = 19/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +++   V  K   +      G A    G +       G K    HRLD  TSG+L+ 
Sbjct: 4   IVADETDFIVIAKSHNVHFHSQDGSA----GVMAKLEQDLGVKLFSVHRLDTLTSGLLLF 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA   T  F   R+QK Y +L  G PK K+  I   + K        +  +    
Sbjct: 60  AKSSQAAAEFTRLFTEHRVQKYYLALAKGKPKKKQGSIIGDMAKSRRSMYKLMRTMD--- 116

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A + F      A+      ++P +G+THQLRV    +G PI+GD  Y        
Sbjct: 117 ---NPAKTQFFS-QSVAEGLRLYLLKPLSGKTHQLRVALASIGVPILGDTLYGGEE---- 168

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                ++ YLHA  +           I  P
Sbjct: 169 ----SDRGYLHAFSLHFIFSGKEYQYINYP 194


>gi|227489029|ref|ZP_03919345.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glucuronolyticum ATCC 51867]
 gi|227090974|gb|EEI26286.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glucuronolyticum ATCC 51867]
          Length = 294

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 99/250 (39%), Gaps = 13/250 (5%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQ-KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
           + R  +G+V      + A + ++     I    +   +         +YEDS++ V NKP
Sbjct: 51  DKRFAAGEVRDRRGQVIAPDQVLAAGVDIFFYRMPAPEPHVPFSIETVYEDSRVLVVNKP 110

Query: 115 AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             ++     G        ++    +  ++    HRLD+ TSG+L+  ++R       E F
Sbjct: 111 PFLATVP-KGAHITETAVVRLRRATGNEELSPAHRLDRHTSGLLLFTKSREFRGAYQEMF 169

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             R +QK Y ++  G        +  W  + S + GD        E     A +H  VI 
Sbjct: 170 ARRAVQKTYHAVSAGPSAVVPGTV--WRSRISKVPGDLQAHTVDGEVN---AETH--VIS 222

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
              +        PHTG+THQLR+H    G PIV D  Y A  + +        L L A  
Sbjct: 223 VSGRVHVLA---PHTGKTHQLRLHMCEAGVPIVNDPLYPA-IRDDLMDDFTRPLGLTAYS 278

Query: 295 MDLPHPEGGR 304
           +    P  GR
Sbjct: 279 LRFEDPVDGR 288


>gi|213609301|ref|ZP_03369127.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 139

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 58/146 (39%), Positives = 93/146 (63%), Gaps = 8/146 (5%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
            + +ILR G+VRV+KKR+K   +++SG  VRIPPV       + E++    S +L K + 
Sbjct: 1   MIYRILRKGEVRVNKKRIKPEYKLESGDEVRIPPVR------VAEREEEAVSPHLQKVA- 53

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            L  ++LYED  I V NKP+G +V GGSG+++ +   L++ +  + +   L HRLD++TS
Sbjct: 54  ALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTS 112

Query: 156 GILVVARTRAAAQHLTESFRMRRIQK 181
           G+L+VA+ R+A + L E  R + +QK
Sbjct: 113 GVLLVAKKRSALRSLHEQLREKGMQK 138


>gi|291450450|ref|ZP_06589840.1| ribosomal pseudouridine synthase [Streptomyces albus J1074]
 gi|291353399|gb|EFE80301.1| ribosomal pseudouridine synthase [Streptomyces albus J1074]
          Length = 318

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 53/246 (21%), Positives = 97/246 (39%), Gaps = 11/246 (4%)

Query: 60  QSGQVVRIPPVINALNHI-IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
             G+VV       A +   +   ++        +       ++L+ D  + V +KP  ++
Sbjct: 54  AGGEVVTGDGRPVAADAPYVPGGQVWFHRRRAAEVPAPYPPVVLFRDEHLVVVDKPHFLA 113

Query: 119 VQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               G  +       L++ ++    +    HRLD+ T+G++++    A        F  R
Sbjct: 114 TTPRGRHVTQTALALLRTRLEL--PELSPAHRLDRLTAGLVLLTVRPAERAAYQRLFSDR 171

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y ++    P      +A     +S I  +   +  Q   G   A +  +++    
Sbjct: 172 LVRKEYEAVAGYDP-----GLALPRTVRSRIVKERGVIAAQEVPGEPNAETRVELLAHRG 226

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                  + PHTGRTHQLRVH   +G PI+GD  Y  +         +  L L AR ++ 
Sbjct: 227 -TLGRYRLLPHTGRTHQLRVHLNSLGVPILGDPVY-PHLTDPAPDDFRRPLQLLARTVEF 284

Query: 298 PHPEGG 303
             P  G
Sbjct: 285 TDPVTG 290


>gi|325918250|ref|ZP_08180393.1| 23S RNA-specific pseudouridylate synthase [Xanthomonas vesicatoria
           ATCC 35937]
 gi|325535530|gb|EGD07383.1| 23S RNA-specific pseudouridylate synthase [Xanthomonas vesicatoria
           ATCC 35937]
          Length = 306

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 60/296 (20%), Positives = 116/296 (39%), Gaps = 33/296 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
                +P ++    Q     G+V   +   +  +   + G  V            +  ++
Sbjct: 37  ALCACFPGVDAATWQDRFARGRVLDAEGSALNASAPYRLGAEV------------LYFRE 84

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
           ++D  V            +++ D+ + V  KP  + V   G+ +   +   L    D+  
Sbjct: 85  VVDEPV------IPFAETVVHADAHLVVACKPHFLPVVPAGAYVRETLLTRLVHRFDNPA 138

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
             P   HR+D+ T+G+++ +   A        FR RRI+K Y ++   +P+        +
Sbjct: 139 LVP--LHRIDRNTAGLVLFSANPATRGIYQALFRERRIRKHYLAVAPPLPR----LTFPY 192

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + +     G+    +++   G   + +   V+   A  + +  ++P TGR HQLRVH   
Sbjct: 193 VYRSRLEPGEPFFRMREGV-GEPNSETVIDVVARGADTWTY-RLEPVTGRKHQLRVHMAA 250

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITA---PLPA 313
           +G PI+ D  Y          P +  L L A  +    P  G  +  TA   P+P+
Sbjct: 251 LGAPILHDRFYPELEDQRPDDP-ERPLQLFAHTLAFDDPITGEPRYFTATVGPMPS 305


>gi|255323619|ref|ZP_05364749.1| RNA pseudouridine synthase family protein [Campylobacter showae
           RM3277]
 gi|255299333|gb|EET78620.1| RNA pseudouridine synthase family protein [Campylobacter showae
           RM3277]
          Length = 307

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 64/276 (23%), Positives = 110/276 (39%), Gaps = 44/276 (15%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +Q+++  G++  D   V   N + SG++  I    N                        
Sbjct: 30  VQRLIDKGRLTCDGAVVSEKNALLSGEICLIDYETNPRGLQP------------------ 71

Query: 97  LKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
                ++E  K  VF+KP+G+     G    Y ++  + S     G++  + HRLD ETS
Sbjct: 72  -----IFECDKFAVFDKPSGVLSHPNGRHCEYSLNDEIWSLY---GREASVAHRLDCETS 123

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++VV + + A  +L + F  R++ K Y +LV+G         AN  L   +        
Sbjct: 124 GLIVVGKDKNAVVNLKKLFENRQVYKSYVALVYGKISENLHIEANMDLANDYDDVKMRMR 183

Query: 216 VKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC- 273
           + ++ KG   A++    I+ FA      +   P TGR HQ+R+H  H+   I+G+  Y  
Sbjct: 184 ICEDGKG---AVTEILPIEYFADIDATLVRAVPLTGRQHQIRLHLFHVEHKILGEPLYGL 240

Query: 274 ------------ANFKGNFTSPIQNKLYLHARYMDL 297
                        N           +L LH+  +  
Sbjct: 241 SRLQIEKILDKEMNEAERILITGAPRLLLHSDEICF 276


>gi|255084742|ref|XP_002504802.1| predicted protein [Micromonas sp. RCC299]
 gi|226520071|gb|ACO66060.1| predicted protein [Micromonas sp. RCC299]
          Length = 345

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 64/264 (24%), Positives = 105/264 (39%), Gaps = 34/264 (12%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK--SWVDSKGQ------- 142
             S     ++++ED  + V +KPAG+S      +     G L     + +KG+       
Sbjct: 56  PASSPRAPVVIHEDDDVLVIDKPAGMSFHNDDLVTNLP-GVLSTVRALQAKGELRGSDYA 114

Query: 143 -KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +    HRLD+ TSGIL++A+    A  L   F  RR+ K Y +L    P  K   +   
Sbjct: 115 GELHSVHRLDKITSGILLLAKNERVASWLARQFARRRVHKYYVALSARKPSKKMGTVRGD 174

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA------QKFCWLEMQPHTGRTHQL 255
           +   +        + + +      A++ F             +    L M+P TG+THQL
Sbjct: 175 M---AQARRGTYKLTRCSSNSTPAAVTKFVSRGVRGASPGGDRPLRVLLMRPLTGKTHQL 231

Query: 256 RVHALHMGCPIVGDHKYCA-----NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
           RV A  +G P++GD  Y       N   N  +  +++ YLHA  + +  P G  +++   
Sbjct: 232 RVCAKSLGAPVLGDAAYGGADTNKNANKNDGAGGEDRGYLHAAALRVAMPGGNVMEVVCK 291

Query: 311 LPA---------HMVKTWDSLGFK 325
                            W S GF 
Sbjct: 292 PTEGREWTHASAGFHDAWTSFGFD 315


>gi|317182255|dbj|BAJ60039.1| hypothetical protein HPF57_0965 [Helicobacter pylori F57]
          Length = 242

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 67/288 (23%), Positives = 111/288 (38%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V V  K++                 + A   + K  +     V 
Sbjct: 12  ENISHKKAKALIDLGLVSVGGKKL-----------------MVARKELPKNTRFSVQKVE 54

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 55  --------KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLALTQGIIEEEQEINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A LP    
Sbjct: 205 DTLYNNEPSSA------KRLMLHAHKISLL-----GYEFEAILPKEFE 241


>gi|316931819|ref|YP_004106801.1| pseudouridine synthase [Rhodopseudomonas palustris DX-1]
 gi|315599533|gb|ADU42068.1| pseudouridine synthase [Rhodopseudomonas palustris DX-1]
          Length = 300

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 62/262 (23%), Positives = 101/262 (38%), Gaps = 65/262 (24%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +D +++ +LY D  + V +KP G+ V  G     +++    +      + P L HRLD++
Sbjct: 16  ADEIQARVLYRDGLMLVIDKPPGLPVHRGPKGGPNLEASFDALRYGLPRPPVLAHRLDRD 75

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG LV+ R R A   L   F+  RI K YW++V G P   +  I   + K   +  +  
Sbjct: 76  TSGCLVLGRHRKATATLGLLFKHSRISKTYWAIVEGGPAEDEGSIDLPIGK---LNAERG 132

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFC-------WLEMQPHTGRTH------------- 253
              K +++    +++ ++V+   +   C            P  GR H             
Sbjct: 133 WWQKIDQESGLPSLTKWRVMGRSSPPVCGDGSGVGAHSGTPSLGRPHPGPLPQAGEGALS 192

Query: 254 -------------------------------------QLRVHALHMGCPIVGDHKYCANF 276
                                                QLRVH   MG PI GD+ Y    
Sbjct: 193 AGAKGDDLSRKPGAKSGAPPPAQLTWLALEPITGRTHQLRVHCAAMGWPIFGDNIYG--- 249

Query: 277 KGNFTSPIQNKLYLHARYMDLP 298
             N     + +L+LHAR + +P
Sbjct: 250 --NGPRFGEPRLHLHAREIVIP 269


>gi|312600987|gb|ADQ90242.1| Ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyopneumoniae 168]
          Length = 281

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 55/288 (19%), Positives = 104/288 (36%), Gaps = 32/288 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V   ++   +L +  K      ++  +QK  R+ +++V+    + N  I+   ++ I  
Sbjct: 4   FVATKNQSGQKLIQLIKKILLKSDYNEIQKYFRTKKIKVNNTYQEKNYIIKEKDIILIFS 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                    K  +              L   ++Y+D  I + +KP  + V GG       
Sbjct: 64  QEKLKTFSKKVPEF------------KLNLKIIYQDENILLVDKPQNLQVHGGKFNLDLA 111

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                   +++  KP    RLD++TSGI++      +   L +  +       + S +  
Sbjct: 112 VWNYLKIPENQVFKPSHIGRLDKKTSGIILYGLNYQSVVELNQKQKFFEKIYTFKSDI-- 169

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N K  I   +  + +     + V  ++      + + +        K        HT
Sbjct: 170 ---NLKNTIKTDVFIRKNNFQQKMEVTLKSPNSFFASTTFY-------SKNQKKFAILHT 219

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           G+ HQ+RV   H+G PI GD KY               LYLH+  +  
Sbjct: 220 GKKHQIRVSLSHLGFPIFGDEKYGGTRDKI--------LYLHSFSLKF 259


>gi|237747439|ref|ZP_04577919.1| pseudouridine synthase [Oxalobacter formigenes HOxBLS]
 gi|229378790|gb|EEO28881.1| pseudouridine synthase [Oxalobacter formigenes HOxBLS]
          Length = 318

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 56/292 (19%), Positives = 106/292 (36%), Gaps = 35/292 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +    +P        + +  G+V +D   K V   N  +  Q +     +          
Sbjct: 37  FLSERFPVFTKEEWSERMAEGEV-LDSTGKPVLPCNSYRGNQKLYYYRYLP--------- 86

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
                     +  +  +  +LY+D  + V +KP  + V       Y  +  L       G
Sbjct: 87  ---------NEWKNPFQETVLYQDEWLVVADKPHFLPVTPSG--KYVRETLLVRLKQKLG 135

Query: 142 QK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                  HR+D+ET+G+++ +            FR   + K Y ++        ++ ++ 
Sbjct: 136 IDSLTPVHRIDRETAGLVLFSTKPEGRNLYQRLFRENLVSKHYEAI-----APYRDDLSF 190

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L  KS +      +  Q   G   A +  +++    + +    ++P TGR HQLRV   
Sbjct: 191 PLRYKSRLVQGDSFMRMQTVSGKPNAETEIRLLQQLGE-WGHYRLKPVTGRKHQLRVQMC 249

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLH-----ARYMDLPHPEGGRLQI 307
            +G PI+ D  Y  +F    T  +Q + Y H     A+ +    P  G  + 
Sbjct: 250 SLGIPILNDRIYPDHFPEAVTQEMQTEEYRHPLQLVAKSISFIDPVTGETRF 301


>gi|19173607|ref|NP_597410.1| similarity to HYPOTHETICAL PROTEIN OF THE FAMILY OF PSEUDOURIDINE
           SYNTHASES YD36_YEAST [Encephalitozoon cuniculi GB-M1]
 gi|19170813|emb|CAD26587.1| similarity to HYPOTHETICAL PROTEIN OF THE FAMILY OF PSEUDOURIDINE
           SYNTHASES YD36_YEAST [Encephalitozoon cuniculi GB-M1]
          Length = 318

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 60/266 (22%), Positives = 98/266 (36%), Gaps = 41/266 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D    + +           L  G + V+ + VK    +  G V+R    I+   H    
Sbjct: 26  ID-VLVSEFRTRTRDYFLSALECGVITVNGEAVKPTRILGMGDVIRHTVHIHDPAHP--- 81

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                            +  ++ E+    V NKP GI      G   +     K+     
Sbjct: 82  -----------------EIGVIKEEGDYIVVNKPPGIPCHPTGGYREYCVT--KALFGD- 121

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            +K    +RLD   SG+L++A       H      +R  +KIY + V+G+  +K +    
Sbjct: 122 -EKVACINRLDMPVSGVLILA----VRNHSKCLEAIRDAKKIYVAKVYGMFPDKVDV--- 173

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
                  IG         N  G    ++ F+ ++     +  +E +P TGRTHQ+R+H  
Sbjct: 174 ----DKRIGCTEGRYRHVNA-GGKACLTLFRRLEYR-DGYSLVECRPVTGRTHQIRIHLQ 227

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQN 286
            +G PI  D  Y     G    P QN
Sbjct: 228 SIGFPIANDIMYG---DGEAPPPPQN 250


>gi|260554620|ref|ZP_05826841.1| pseudouridylate synthase [Acinetobacter baumannii ATCC 19606]
 gi|260411162|gb|EEX04459.1| pseudouridylate synthase [Acinetobacter baumannii ATCC 19606]
          Length = 302

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 53/296 (17%), Positives = 110/296 (37%), Gaps = 29/296 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             + ++   ++PHI     Q+  + G +   + +++  N+   +   +     +    H+
Sbjct: 29  QTIYQFLCENFPHIKATEWQQRFQDGLIYAANGEKLTLNSSYIANTHIFYYRFLANEVHV 88

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E +                  +L+E+  + V +KP  +++       Y  +  L    
Sbjct: 89  PFEHQ------------------ILFENDDLLVVDKPHFLTISPTG--QYVQETLLVRLK 128

Query: 138 DSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              G +     HRLD+ET+G+++  +   +     + F  R++ KIY ++     + K  
Sbjct: 129 KQTGNEFLTPIHRLDRETAGVVLFCKRPQSRGIYQQLFADRQVNKIYHAIAAYKAELKF- 187

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 LK     G   + ++          +  ++I+       +  + P TG+ HQLR
Sbjct: 188 ---PQNLKLYLDKGTPFYTMQVITHTKTNTETKIELIEHNHSWAKYC-LTPTTGKQHQLR 243

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
           VH  H+G PI  D  Y    +          L L A+ +    P     +   + L
Sbjct: 244 VHLNHLGIPIKNDPFY-PIVQHKADDDFSQPLQLLAKQISFIDPLTKQEMVFNSQL 298


>gi|297379564|gb|ADI34451.1| Hypothetical protein HPV225_0363 [Helicobacter pylori v225d]
          Length = 293

 Score =  130 bits (327), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 68/294 (23%), Positives = 118/294 (40%), Gaps = 29/294 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKHNQ-----QAVRKSQMIQGVVSLI------------HFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +    +L++E     VF+KP  +      G  YH +  L       G+     HRLD E
Sbjct: 64  PNEKTQVLVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D  
Sbjct: 122 TSGLVLAGKTLQSAKDLKALFMQKKVKKTYLALAHGLV-DKNIVIDKPILTPQNIQKDLR 180

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              K        + +  + +          L++ P TGRTHQ+R+H   +   IVG+  Y
Sbjct: 181 IRSKI-SPLGKPSTTLVEPLSYNPFLDISLLKITPLTGRTHQIRLHLSSVNHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +         +      L LHA  ++    +G   +IT+ +P   +    
Sbjct: 240 GVIDENAREYLQLKRENNAPLLMLHASSLEFEF-KGAIHEITSQMPKRFMPFLK 292


>gi|54019984|ref|YP_115530.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyopneumoniae 232]
 gi|53987157|gb|AAV27358.1| ribosomal large subunit pseudouridine synthase [Mycoplasma
           hyopneumoniae 232]
          Length = 281

 Score =  130 bits (327), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 55/288 (19%), Positives = 103/288 (35%), Gaps = 32/288 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V   ++   +L +  K       +  +QK  R+ +++V+    + N  I+   ++ I  
Sbjct: 4   FVATKNQSGQKLIQLIKKILLKSKYNEIQKYFRTKKIKVNNTFQEKNYIIKEKDIILIFS 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                    K  +              L   ++Y+D  I + +KP  + V GG       
Sbjct: 64  QEKLKTFSKKVPEF------------KLNLKIIYQDENILLVDKPQNLQVHGGKFNLDLA 111

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                   +++  KP    RLD++TSGI++      +   L +  +       + S +  
Sbjct: 112 VWNYLKIPENQVFKPSHIGRLDKKTSGIILYGLNYQSVVELNQKQKFFEKIYTFKSDI-- 169

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              N K  I   +  + +     + V  ++      + + +        K        HT
Sbjct: 170 ---NLKNTIKTDVFIRKNNFQQKMEVTLKSPNSFFASTTFY-------SKNQKKFAILHT 219

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           G+ HQ+RV   H+G PI GD KY               LYLH+  +  
Sbjct: 220 GKKHQIRVSLSHLGFPIFGDEKYGGTRDKI--------LYLHSFSLKF 259


>gi|223944597|gb|ACN26382.1| unknown [Zea mays]
          Length = 307

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 55/262 (20%), Positives = 99/262 (37%), Gaps = 60/262 (22%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-------DSKGQKPRLTHRLDQ 152
            +++ED  + V +KPAG+          + D  L S+         +      L +RLD+
Sbjct: 48  DVVFEDEWLAVVDKPAGV----------YCDALLTSFPCSAVSENPATKPNLHLANRLDR 97

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG++V+ +    A  L ++F   +++K Y +L  G P   ++        +S  G   
Sbjct: 98  DTSGLMVITKCNKVAGKLVKAFTDHKVKKTYLALCIGFPPAWEKIKICSGHGRSKHGAWR 157

Query: 213 VHVVKQNEKG------ANYAISHFKVIDCFAQK--------------------------- 239
           V+ +    +            + F+V+    +                            
Sbjct: 158 VYAMSDVGRSLPGGSVVRDMSTRFEVLGVNGKGQFREPYSLDTDDIEPITVQEKATDQTC 217

Query: 240 -------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                     +   P +GRTHQ+R+H  ++G PI GD KY    + +          LHA
Sbjct: 218 GGDANSSVILVRAYPQSGRTHQIRLHCQYLGLPIRGDVKYGGVIEWDGVE--CEGHALHA 275

Query: 293 RYMDLPHPEGG-RLQITAPLPA 313
             +   HP  G  + + +PLP 
Sbjct: 276 ESLSFVHPITGLPITLRSPLPP 297


>gi|194365401|ref|YP_002028011.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
 gi|194348205|gb|ACF51328.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
          Length = 292

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 63/286 (22%), Positives = 106/286 (37%), Gaps = 27/286 (9%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
               +P I+    Q     G+V+  + R      + +    ++   I     ++ E  I 
Sbjct: 21  LCARFPRIDREQWQDRFTRGRVQDAQGRA-----LAADMPWQVGLEIQYFREVVDEPVIP 75

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-K 143
                           +++ D+ + V +KP  + V    G  Y  +  L   V S G   
Sbjct: 76  ------------FAETIVHLDAHLLVADKPHFLPVTPAGG--YVRETLLARLVASTGNTD 121

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD+ T+G+++ +   A+       FR RRI K Y +L   +P      +   L 
Sbjct: 122 LVPLHRLDRLTAGLVLFSTQAASRDAYQRLFRERRIDKTYEALAPALPA-----VTFPLH 176

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           + S +             G   A S  ++I+          + P TGR HQLRVH   +G
Sbjct: 177 RHSRLAPAEPFFRMAEVPGEPNARSRIELIEGEG-PIWRYRLLPETGRKHQLRVHMAMLG 235

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
            PI GD  Y    +       +  L L A+ +    P  G  ++ +
Sbjct: 236 APIEGDDLY-PQLRQRPAGTAEVPLQLLAQGLAFDDPLSGERRVFS 280


>gi|317181687|dbj|BAJ59471.1| hypothetical protein HPF57_0397 [Helicobacter pylori F57]
          Length = 293

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 118/287 (41%), Gaps = 29/287 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q VR   +I  +  +I                +     
Sbjct: 28  LKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVSLI------------FFKPNEKTQA 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  +A+ L   F  ++++K Y  L  G+  +K   I   +L   +I  D + +  +  
Sbjct: 129 GKTLQSAKDLKALFMQKKVKKTYLVLAHGLV-DKNIVIDKPILTPQNIQKD-LRIKSKIS 186

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                + +  + ++         L++ P TGRTHQ+R+H   +   IVG+  Y    +  
Sbjct: 187 PLGKPSTTLVEPLNYNPFLDISLLKITPITGRTHQIRLHLSSVNHRIVGEGLYGVIDENA 246

Query: 280 FTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                  +      L LHA  ++    +G   +IT+P+P   +    
Sbjct: 247 REYLQLKRENNAPLLMLHATSLEFEF-KGAIYKITSPMPKRFMPFLK 292


>gi|330720018|gb|EGG98456.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC2047]
          Length = 179

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 47/186 (25%), Positives = 76/186 (40%), Gaps = 18/186 (9%)

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +VVA+T  A   L +  + R + + Y ++V G+                 IG   VH  K
Sbjct: 1   MVVAKTLLAHADLVDQLQTREMGREYEAVVQGVMTGGGRV-------DEPIGRHPVHRKK 53

Query: 218 QNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                    A +++ V + F +    + ++  TGRTHQ+RVH  H+  P++GD  Y    
Sbjct: 54  MGVVPSGKEAATNYSVAERF-RCHTHVRLKLETGRTHQIRVHMTHINYPLIGDQFYGGRP 112

Query: 277 KGNFTSPIQ--------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
           +    +  +         +  LHAR + L HP  G  ++    LP  M +    L    D
Sbjct: 113 RLPPAATEELIAFLQSFKRQALHARRLQLVHPLTGEDMEWEVELPEDMQQLLALLREDSD 172

Query: 328 RNLYIK 333
               IK
Sbjct: 173 LFADIK 178


>gi|72080357|ref|YP_287415.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyopneumoniae 7448]
 gi|71913481|gb|AAZ53392.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           hyopneumoniae 7448]
          Length = 281

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 55/288 (19%), Positives = 103/288 (35%), Gaps = 32/288 (11%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V   ++   +L +  K       +  +QK  R+ +++V+    + N  I+   ++ I  
Sbjct: 4   FVATKNQSGQKLIQLIKKILLKSKYNEIQKYFRTKKIKVNNTYQEKNYIIKEKDIILIFS 63

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                    K  +              L   ++Y+D  I + +KP  + V GG       
Sbjct: 64  QERLRTFSKKVPEF------------KLNLKIIYQDENILLVDKPQNLQVHGGKFNLDLA 111

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                   +++  KP    RLD++TSGI++      +   L +  +       + S +  
Sbjct: 112 VWNYLKIPENQVFKPSHIGRLDKKTSGIILYGLNYQSVVELNQKQKFFEKIYTFKSDI-- 169

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              + K  I   +  K +     + V  ++      + + +        K        HT
Sbjct: 170 ---DLKNTIKTDVFIKKNNFQQKMEVTLKSPNSFFASTTFY-------SKNQKKFAILHT 219

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           G+ HQ+RV   H+G PI GD KY               LYLH+  +  
Sbjct: 220 GKKHQIRVSLSHLGFPIFGDEKYGGTRDKI--------LYLHSFSLKF 259


>gi|269102975|ref|ZP_06155672.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268162873|gb|EEZ41369.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 238

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 54/221 (24%), Positives = 92/221 (41%), Gaps = 21/221 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     + +K  G+SV         +         +  +K  L HRLD+ TSG+L++
Sbjct: 15  LVHEHPDFILIHKHPGVSVHKDDNDQPLLAAVAA---QTGDEKLYLIHRLDKMTSGLLLL 71

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            R + AA  L+ +F  R ++K Y ++    PK K+  +   + +            K   
Sbjct: 72  GRNKEAAAELSGNFANRVVEKFYVAIGSKKPKKKQGIVIGDMTR------SRRSSWKLES 125

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F               +PHTG+THQ+RV    +G  I GD  Y        
Sbjct: 126 SKHNPAITQFFS-TAAGNGRRLFLCKPHTGKTHQIRVALKSVGSGITGDDIYG------- 177

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
            +   ++ YLHA  +  P+ +G + +    +P    + W  
Sbjct: 178 -NEAADRGYLHAYALSFPY-QGEQYRFLC-VPT-FGQLWQE 214


>gi|299740960|ref|XP_001834124.2| hypothetical protein CC1G_08755 [Coprinopsis cinerea okayama7#130]
 gi|298404490|gb|EAU87719.2| hypothetical protein CC1G_08755 [Coprinopsis cinerea okayama7#130]
          Length = 298

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 102/247 (41%), Gaps = 22/247 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQ-----GGSGIAYHIDGFLKS--WVDSKGQKPRLTHRLDQE 153
           +LY D ++ V NKPAG+  Q             +D  LK         +  R  HRLD  
Sbjct: 21  VLYLDRQVLVMNKPAGLVSQLGRQLPEMKTRDTLDKVLKQIERRLELKEALRPLHRLDTA 80

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G L  A T+ +A+ L++ F   +++K Y +LV G  +              +  G   
Sbjct: 81  TTGCLAFATTQTSARSLSKQFAQGQVEKSYLALVSGGKETFPGTSGRIDTPIKYQDG--- 137

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHK 271
                   G   +++ + ++          + +   TG  HQLR+H    +G PI+GD +
Sbjct: 138 -YFDGLGTGGKLSLTEWSLLASSPVLPISLVRLNLLTGNKHQLRIHMAKKLGAPILGDDR 196

Query: 272 YCANFKGNF---TSPIQNKLYLHARYMDLPHPEGG------RLQITAPLPAHMVKTWDSL 322
           Y ++   +       I+  LYLHA  +              RL ITAPLPAH V+   + 
Sbjct: 197 YSSSKVASKLLSEGRIKPNLYLHASDIAFVRYRQRGPQKRFRLGITAPLPAHFVEACKAF 256

Query: 323 GFKYDRN 329
             +  + 
Sbjct: 257 RIELPKE 263


>gi|300780235|ref|ZP_07090091.1| probable ribosomal pseudouridine synthase [Corynebacterium
           genitalium ATCC 33030]
 gi|300534345|gb|EFK55404.1| probable ribosomal pseudouridine synthase [Corynebacterium
           genitalium ATCC 33030]
          Length = 339

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 54/258 (20%), Positives = 96/258 (37%), Gaps = 7/258 (2%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQ-KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           R  +G+VV I         +++    +        +     +  ++YED  I V NKP  
Sbjct: 66  RFTAGEVVLIDGTPLTPGDLVRPGTDVFFYRRPAPEPRVPFEVTVVYEDDAIMVVNKPPF 125

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           ++              ++    +  ++    HRLD+ TSG+L+  +  +      + F  
Sbjct: 126 LATMP-RASHITESATVRLRRSTGNEELTPAHRLDRMTSGLLLFTKKASVRGAYQQLFAS 184

Query: 177 RRIQKIYWSLVWGIPKNKKECIAN--WLLKKSHI-GGDYVHVVKQNEKGANYAISHFKVI 233
           R + K+Y ++   I  +     +    L+ + HI   +              ++++   I
Sbjct: 185 RAVAKLYEAVADDIGPSLPARPSANSPLVWEHHIVKREGELASSITVDAIPNSLTYVTDI 244

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                      +QP TGRTHQLRV     G PI GD  Y      +      N + L A 
Sbjct: 245 TPLQGGAARYLLQPVTGRTHQLRVQMHAAGAPIHGDPVYPELLPASAEDFT-NPMLLTAV 303

Query: 294 YMDLPHPEGG-RLQITAP 310
            +    P  G +   +AP
Sbjct: 304 GLAFTDPLTGVKRTFSAP 321


>gi|269967021|ref|ZP_06181090.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           40B]
 gi|269828375|gb|EEZ82640.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           40B]
          Length = 230

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 55/211 (26%), Positives = 91/211 (43%), Gaps = 17/211 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +    K    S  +   L HRLD+ TSGIL+
Sbjct: 3   DILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAK---QSGDEHLYLIHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R   A   L+++F  R+++K Y ++    PK K+  +   + +        V     N
Sbjct: 60  LGRNAKAGSALSQAFADRQVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV-----N 114

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K  N A++ F  +     +      +PHTG+THQ+RV    +G  IVGD  Y A  +  
Sbjct: 115 SKN-NPAVTQFFSLAAEPGER-LFLCKPHTGKTHQIRVALKSVGSGIVGDPIYNAGNEA- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                 ++ YLHA  +   + +     +  P
Sbjct: 172 ------DRGYLHAFSLCFQYRDEQYCFVCDP 196


>gi|209694692|ref|YP_002262620.1| RNA psedouridine synthase [Aliivibrio salmonicida LFI1238]
 gi|208008643|emb|CAQ78827.1| RNA psedouridine synthase [Aliivibrio salmonicida LFI1238]
          Length = 228

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 57/212 (26%), Positives = 92/212 (43%), Gaps = 20/212 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGIL 158
            +LY++S   V NK   +SV    G        L       G K   L HRLD+ TSG+L
Sbjct: 3   DILYQNSDFLVINKHPNVSVHKDDGDT----SLLIELAKVTGDKQLYLIHRLDKMTSGLL 58

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ R ++AA  L++ F  R ++K Y ++    PK K+  +   + +        ++  + 
Sbjct: 59  LIGRHQSAASELSQLFAKRLVEKYYLAIGDKKPKKKQGLVIGDMERSRRASWKLINSKE- 117

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                N AI+ F               +PHTG+THQ+RV    +G  I+GD  Y ++   
Sbjct: 118 -----NPAITQFFSTAAHNGNR-LFLCKPHTGKTHQIRVALKSVGSGILGDSIYSSSKA- 170

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                  ++ YLHA  +   + E     I  P
Sbjct: 171 -------DRGYLHAYALRFTYQEQAFEFIETP 195


>gi|313111139|ref|ZP_07796964.1| putative pseudouridylate synthase [Pseudomonas aeruginosa 39016]
 gi|310883466|gb|EFQ42060.1| putative pseudouridylate synthase [Pseudomonas aeruginosa 39016]
          Length = 275

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 101/263 (38%), Gaps = 12/263 (4%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAG 116
           R+Q G+V+             +E   +     L   +    ++ +LY D  + V +KP  
Sbjct: 20  RMQRGRVLDAEGRALGPQAAYREGLRVHYFRELPAEAPIPFEARILYRDEHLLVADKPHF 79

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           + V    G  Y     L     S G +     HR+D+ T+G+++ +    +       FR
Sbjct: 80  LPVMPAGG--YVEQTLLARLARSTGNRDLVPLHRIDRHTAGLVLFSTNPGSRGRYQALFR 137

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            RRI K Y ++   +P+     +   LL+++ +         +  +G   + +  +V + 
Sbjct: 138 ERRIDKYYEAIAPALPR-----LDFPLLRRTRLVPGEPFFRMREGEGEPNSETRIEVAER 192

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-LYLHARY 294
             + +    + P TG+ HQLRVH   +G  I  D  Y        +     + L L AR 
Sbjct: 193 NGR-WWRYRLYPVTGKKHQLRVHLAALGAGIQNDGFYPELLDAEDSPDDYRRPLKLLARG 251

Query: 295 MDLPHP-EGGRLQITAPLPAHMV 316
           +    P  G R    + L     
Sbjct: 252 LRFDDPLSGERRMFESGLRLDWQ 274


>gi|149052129|gb|EDM03946.1| RNA pseudouridylate synthase domain containing 1 (predicted),
           isoform CRA_b [Rattus norvegicus]
          Length = 234

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 52/220 (23%), Positives = 91/220 (41%), Gaps = 20/220 (9%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------- 144
           +        ++Y+ +   V NK   + +   +   +     L+  +     +        
Sbjct: 2   EPGSMENLSIVYQSNDFLVVNKHWDLRIDSKT---WRETLTLQKQLRHHFPELADPDTCY 58

Query: 145 --RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             R  H+LD  TSG L VA  +AAA    + F+ RR+ K Y +LV G  +  +  I   +
Sbjct: 59  GFRFCHQLDFSTSGALCVALNKAAAGSAYKCFKERRVTKAYLALVRGHVQESQVTINYAI 118

Query: 203 LKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRV 257
            + S  G  +   ++     +    +++   V++           + ++P TGRTHQLRV
Sbjct: 119 GRNSTEGRTHTMCIEGTHGCENPKPSLTELLVLEHGLYSGDPVSKVLLKPLTGRTHQLRV 178

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           H   +G PIVGD  Y              ++ LHA Y+ +
Sbjct: 179 HCSALGHPIVGDLTYGQADDQEDQPF---RMMLHAFYLRI 215


>gi|319637809|ref|ZP_07992575.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317400964|gb|EFV81619.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 307

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 47/245 (19%), Positives = 96/245 (39%), Gaps = 11/245 (4%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGI 125
           +P   N L    K       +   ++        +L+ D  + V +KP  + V   G  +
Sbjct: 63  VPFDENTLFEPGKTMFYYRETSRESEPRIPFDEKILHIDEHLLVVDKPHFLPVIPSGRFL 122

Query: 126 AYHIDGFLK---SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +   L+          +     HRLD++T+G+++++   A  +     F+ + +QK 
Sbjct: 123 RETLLTRLRLRPELQHLNVEDITPIHRLDKDTAGVMLLSLNPATRRDYQTMFQEKTVQKT 182

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++        +  +   L   S +       + +  +G   A +  ++I+     F  
Sbjct: 183 YEAV-----APTRTDLDYPLHISSRMERGEKFFLTRETEGKPNAHTTIELIENRG-AFSL 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
             + PHTG+ HQLRVH + +  P++ D  Y               L L A+ ++   P  
Sbjct: 237 YRLTPHTGKKHQLRVHMMSLNMPLMNDALYPTPLAAG-DEDYDKPLKLLAKRIEFTDPVS 295

Query: 303 GRLQI 307
           G +++
Sbjct: 296 GEIRV 300


>gi|152998841|ref|YP_001364522.1| pseudouridine synthase Rlu family protein [Shewanella baltica
           OS185]
 gi|151363459|gb|ABS06459.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS185]
          Length = 230

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 55/198 (27%), Positives = 90/198 (45%), Gaps = 19/198 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++ +++   V +K A +      G A    G +       G K    HRLD  TSG+L+
Sbjct: 3   RIIADEADFLVISKSAKVHFHSQDGTA----GVVAQAEQDLGIKLFAVHRLDTPTSGLLI 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A++  AA+  TE F   ++QK Y +L  G PK K+  +   + K          + K  
Sbjct: 59  LAKSAVAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIGDMAK------SRRSMFKLL 112

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F  +   ++      ++PH+G+THQLRV    +G PI+GD  Y       
Sbjct: 113 RTKENPAITQFFSL-SVSEGLRLYLLKPHSGKTHQLRVALASLGVPILGDDLYGG----- 166

Query: 280 FTSPIQNKLYLHARYMDL 297
               + ++ YLHA  +  
Sbjct: 167 ---AVADRCYLHAYCLHF 181


>gi|254506177|ref|ZP_05118321.1| pseudouridine synthase Rlu family protein, TIGR01621 [Vibrio
           parahaemolyticus 16]
 gi|219550995|gb|EED27976.1| pseudouridine synthase Rlu family protein, TIGR01621 [Vibrio
           parahaemolyticus 16]
          Length = 231

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 60/211 (28%), Positives = 88/211 (41%), Gaps = 17/211 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +LY      V  K   +SV    G    +         +   K  L HRLD+ TSG+L+
Sbjct: 3   DILYTHPDFIVVVKHPNVSVHKDEGETMLLQEVAA---KTGDPKLYLVHRLDKMTSGLLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR+  AA  L   F  R I+K Y ++    PK K+  I   + +        ++     
Sbjct: 60  LARSSKAASALATLFSDREIEKYYLAIGSSKPKKKQGAIIGDMERSRRSTWKLINRRD-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F       Q    L  +PHTG+THQ+RV    +G  IVGD  Y A+ K  
Sbjct: 118 ----NPAITQFFS-TASGQGERLLLCKPHTGKTHQIRVALKSIGSAIVGDAIYNASCKA- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                 ++ YLHA  +   +       I+ P
Sbjct: 172 ------DRGYLHAFALRFNYLNEEYKFISDP 196


>gi|229589269|ref|YP_002871388.1| putative ribosomal subunit pseudouridine synthase [Pseudomonas
           fluorescens SBW25]
 gi|229361135|emb|CAY47998.1| putative ribosomal subunit pseudouridine synthase [Pseudomonas
           fluorescens SBW25]
          Length = 296

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 54/282 (19%), Positives = 105/282 (37%), Gaps = 29/282 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
              H+P I   +    +  G+V  ++   +  +   + G  +            +  +K+
Sbjct: 30  LCEHFPAIAREHWLDRIARGRVLDINGSPISLDLAYKEGLCIYYF-------REVPNEKV 82

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-SKGQ 142
           +            ++  +LY D  + V +KP  + V       Y     L+  +      
Sbjct: 83  IP-----------VQETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIRCLDNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +   A+     + F  R+I K Y ++   +P      +    
Sbjct: 130 ALVPLHRIDRHTAGLVLFSANPASRSAYQQLFPTRQIDKFYEAIAPALPN-----LTFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           + KS +         Q   GA+   +  +V +  A  + +  + P TG+ HQLRVH   +
Sbjct: 185 VHKSRLVEGEPFFRMQEGPGASNTETAVEVREKKADLWRYG-LFPVTGKKHQLRVHMTAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G  I  D  Y  +   +      N L L A+ +    P  G 
Sbjct: 244 GASICNDPFY-PDVIKDAVDDYANPLKLLAQGVLFIDPVTGE 284


>gi|225076837|ref|ZP_03720036.1| hypothetical protein NEIFLAOT_01888 [Neisseria flavescens
           NRL30031/H210]
 gi|224951823|gb|EEG33032.1| hypothetical protein NEIFLAOT_01888 [Neisseria flavescens
           NRL30031/H210]
          Length = 307

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 107/260 (41%), Gaps = 14/260 (5%)

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF---LKSILLYEDSKIYVF 111
           +  R+ SG VV    +    N + +  K +      ++ S+     K  +L+ D  + V 
Sbjct: 48  WRRRLNSGFVVGADGMPFDENTLFEPGKTMFYYRETSRESEPRIPFKEKILHIDEHLIVV 107

Query: 112 NKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---LTHRLDQETSGILVVARTRAAA 167
           +KP  + V   G  +   +   L+   + +          HRLD++T+G+++++   A  
Sbjct: 108 DKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITPIHRLDKDTAGVMLLSLNPATR 167

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           +     F+ + +QK Y ++        +  +   L   S +       + +  +G   A 
Sbjct: 168 RDYQTMFQEKTVQKTYEAV-----APTRTDLNYPLDISSRMERGEKFFLTRETEGEPNAH 222

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +  ++I+     F    + PHTG+ HQLRVH + +  P++ D  Y               
Sbjct: 223 TTIELIENRG-AFSLYRLTPHTGKKHQLRVHMMSLNMPLMNDALYPTPLAAG-DEDYDKP 280

Query: 288 LYLHARYMDLPHPEGGRLQI 307
           L L A+ ++   P  G +++
Sbjct: 281 LKLLAKRIEFTDPVSGEIRV 300


>gi|241758655|ref|ZP_04756769.1| YabO/YceC/SfhB family protein [Neisseria flavescens SK114]
 gi|241321166|gb|EER57362.1| YabO/YceC/SfhB family protein [Neisseria flavescens SK114]
          Length = 307

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 48/245 (19%), Positives = 98/245 (40%), Gaps = 11/245 (4%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGI 125
           +P   N L    K       +   ++     +  +L+ D  + V +KP  + V   G  +
Sbjct: 63  VPFDENTLFEPGKTMFYYRETSRESEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFL 122

Query: 126 AYHIDGFLK---SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +   L+          +     HRLD++T+G+++++   A  +     F+ + +QK 
Sbjct: 123 RETLLTRLRLRSELQHLNVEDITPIHRLDKDTAGVMLLSLNPATRRDYQTMFQEKTVQKT 182

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y ++        +  +   L   S +       + +  +G   A +  ++I+     F  
Sbjct: 183 YEAV-----APTRTDLDYPLDLSSRMERGEKFFLTRETEGEPNAHTTIELIENRG-AFSL 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
             + PHTG+ HQLRVH + +  P++ D  Y  N            L L A+ ++   P  
Sbjct: 237 YRLTPHTGKKHQLRVHMMSLNMPLMNDALY-PNPLAAGDEDYDRPLKLLAKRIEFTDPVS 295

Query: 303 GRLQI 307
           G +++
Sbjct: 296 GEIRV 300


>gi|294650008|ref|ZP_06727396.1| RNA pseudouridine synthase [Acinetobacter haemolyticus ATCC 19194]
 gi|292824101|gb|EFF82916.1| RNA pseudouridine synthase [Acinetobacter haemolyticus ATCC 19194]
          Length = 302

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 59/292 (20%), Positives = 116/292 (39%), Gaps = 31/292 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +   H+ HI     Q+    G +   D K++K ++   +   +     +    H+     
Sbjct: 34  YLCQHFEHIKIEEWQQRFDDGLIYSADGKKLKSDSPYTANTHIFYYRFLAHEVHVP---- 89

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                          +  +L+E+  + V +KP  +++       Y  +  L       G 
Sbjct: 90  --------------FQHEILFENEDLLVVDKPHFLTMSPTG--QYVQETLLVRLKKQTGY 133

Query: 143 K-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIAN 200
           K     HRLD+ET+G+++  +  +A     + F  R++QKIY ++    P+    + +  
Sbjct: 134 KELTPIHRLDRETAGVVLFCKKASARGIYQQLFAERKVQKIYHAIAAYCPELHFPQTVKL 193

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K    G  +  +    EK +N   +  ++++   +      ++P TG+ HQLRVH  
Sbjct: 194 HLEK----GLPFYTMQVNLEKPSNT-ETLIELLE-HNKSHAKYLLKPQTGKQHQLRVHLN 247

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
           ++G PI+ D  Y        +    N L L A+ +    P     +   + L
Sbjct: 248 YLGIPILNDEFY-PVIAHKSSDDFSNPLQLLAKEIFFNDPVSKQEMHFNSKL 298


>gi|169795560|ref|YP_001713353.1| putative pseudouridylate synthase [Acinetobacter baumannii AYE]
 gi|213158499|ref|YP_002319797.1| RNA pseudouridine synthase family protein [Acinetobacter baumannii
           AB0057]
 gi|215483047|ref|YP_002325252.1| RNA pseudouridylate synthase family protein [Acinetobacter
           baumannii AB307-0294]
 gi|239501495|ref|ZP_04660805.1| RNA pseudouridylate synthase family protein [Acinetobacter
           baumannii AB900]
 gi|301347863|ref|ZP_07228604.1| putative pseudouridylate synthase [Acinetobacter baumannii AB056]
 gi|301510578|ref|ZP_07235815.1| putative pseudouridylate synthase [Acinetobacter baumannii AB058]
 gi|301596370|ref|ZP_07241378.1| putative pseudouridylate synthase [Acinetobacter baumannii AB059]
 gi|332850622|ref|ZP_08432869.1| pseudouridine synthase, RluA family [Acinetobacter baumannii
           6013150]
 gi|332867097|ref|ZP_08437394.1| pseudouridine synthase, RluA family [Acinetobacter baumannii
           6013113]
 gi|169148487|emb|CAM86353.1| putative pseudouridylate synthase [Acinetobacter baumannii AYE]
 gi|213057659|gb|ACJ42561.1| RNA pseudouridine synthase family protein [Acinetobacter baumannii
           AB0057]
 gi|213989079|gb|ACJ59378.1| RNA pseudouridylate synthase family protein [Acinetobacter
           baumannii AB307-0294]
 gi|332730459|gb|EGJ61775.1| pseudouridine synthase, RluA family [Acinetobacter baumannii
           6013150]
 gi|332734290|gb|EGJ65419.1| pseudouridine synthase, RluA family [Acinetobacter baumannii
           6013113]
          Length = 302

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 53/296 (17%), Positives = 110/296 (37%), Gaps = 29/296 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             + ++   ++PHI     Q+  + G +   + +++  N+   +   +     +    H+
Sbjct: 29  QTIYQFLCENFPHIKATEWQQRFQDGLIYAANGEKLTLNSSYIANTHIFYYRFLANEVHV 88

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E +                  +L+E+  + V +KP  +++       Y  +  L    
Sbjct: 89  PFEHQ------------------ILFENDDLLVVDKPHFLTISPTG--QYVQETLLVRLK 128

Query: 138 DSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              G +     HRLD+ET+G+++  +   +     + F  R++ KIY ++     + K  
Sbjct: 129 KQTGNEFLTPIHRLDRETAGVVLFCKRPQSRGIYQQLFADRQVNKIYHAIAPYKAELKF- 187

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 LK     G   + ++          +  ++I+       +  + P TG+ HQLR
Sbjct: 188 ---PQSLKLYLDKGTPFYTMQVIAHTKTNTETKIELIEHNHSWAKYC-LTPTTGKQHQLR 243

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
           VH  H+G PI  D  Y    +          L L A+ +    P     +   + L
Sbjct: 244 VHLNHLGIPIKNDPFY-PIVQHKADDDFSQPLQLLAKQISFIDPLTKQEMVFNSQL 298


>gi|149197335|ref|ZP_01874386.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Lentisphaera araneosa HTCC2155]
 gi|149139353|gb|EDM27755.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Lentisphaera araneosa HTCC2155]
          Length = 218

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 101/231 (43%), Gaps = 20/231 (8%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-DSKGQKPRLTHRLDQET 154
            L+  ++YE   + V NKP  +     +G     D  L+ W+   +G      H+LD +T
Sbjct: 4   DLEKRIIYEKDGLLVLNKPYDL---PSTGRKLDDDDCLQYWLIQRQGAMVWAVHQLDADT 60

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI +    +   ++  E     +  K Y ++V G+P  K+        +   IG     
Sbjct: 61  SGINLFVTEKKLVKYYKELLEQAQADKQYLAIVHGVPSWKQ------CEEHGRIGKVDAR 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            +  + +G   A SHF+VI    + F  ++++  TGRTHQ+R+H  H+G P+VG+  YC 
Sbjct: 115 SLGIHAEG-KTAHSHFEVIGSV-KDFSLIKVKIFTGRTHQIRIHLSHLGHPLVGEEWYC- 171

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
               +       +  LH   + LP         ++PL   + +   + G  
Sbjct: 172 ----DPPCTAHQRQALHCYKVHLPQTAH---TFSSPLAEDLKQLAQNHGLS 215


>gi|260222881|emb|CBA32891.1| hypothetical protein Csp_B16300 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 308

 Score =  130 bits (326), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 55/285 (19%), Positives = 111/285 (38%), Gaps = 29/285 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +F   +P +     Q    S  +   D +  +  +   +G+  R+    +  +  I    
Sbjct: 33  FFCQRFPSVPASTWQARFASEDIIDADNQAARPTDAATAGR--RLYYFRDVPDEPI---- 86

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
                          +  ++++D  + V +KP  + V   G  +   +   L+  ++   
Sbjct: 87  ------------IPFQEEVIWQDEHLLVVDKPHFLPVVPSGKHVRETLLARLQLRLNL-- 132

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HR+D++T+G+++     A        FR RR+ K Y  +    P      +   
Sbjct: 133 PDLSPVHRIDKDTAGLVMFTTQPAGRNAYQALFRERRVSKTYECIAPWKP-----GLVWP 187

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           + ++S IG     + +    G   AI+  ++++     +    ++P TG+ HQLRVH   
Sbjct: 188 VHRESRIGDAEHFMQQAEVPGEVNAITDIELLEVAGD-WARYALRPLTGQRHQLRVHMHA 246

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           +G PI+ D  Y        T+  +  L L AR ++   P  G  +
Sbjct: 247 LGLPILFDGIY-PVLTPEGTNDYRRPLQLLARTLEFVDPLSGEQR 290


>gi|297571862|ref|YP_003697636.1| pseudouridine synthase [Arcanobacterium haemolyticum DSM 20595]
 gi|296932209|gb|ADH93017.1| pseudouridine synthase [Arcanobacterium haemolyticum DSM 20595]
          Length = 309

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 57/280 (20%), Positives = 103/280 (36%), Gaps = 28/280 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           W    +  +       +L +G V  D  R                  I+     +   ++
Sbjct: 42  WIVTRFGDLGLA----LLDAGDVFADGGR-----------------EISRAEPYVPGMRV 80

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +    ++  ++ ++ +  V +KP G++     G        + +      + 
Sbjct: 81  WIFRPVPDEPESPIELNVIADEERFIVVDKPHGMATIP-RGSHVAQTVTVAARRQFNDED 139

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD ET+G++++ R     +     F  R + K Y ++   IP         W  
Sbjct: 140 LVCAHRLDAETAGLVLLTREPQWRKPYQTLFERRGVGKKYCAVTRDIP-----GFDTWET 194

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            +  +   Y  +      G   +++H +++   A      E+ PHTG+THQLRV   H+G
Sbjct: 195 VELRLERGYRPLATDVVDGEPNSVTHMRIVAR-ADGLAQWELIPHTGKTHQLRVTLEHVG 253

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            PI+GD  Y   F     +     L LHAR +    P  G
Sbjct: 254 APILGDPLYPRLFTKEEEAARAYPLQLHARELSFVDPIDG 293


>gi|91225984|ref|ZP_01260911.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           12G01]
 gi|91189425|gb|EAS75702.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           12G01]
          Length = 230

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 55/200 (27%), Positives = 90/200 (45%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL+
Sbjct: 3   DILHTHPDFLIINKHPYVSVHKDDGDTMLLQEVAK---QSGDEQLYLIHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R   AA  L+++F  R+++K Y ++    PK K+  +   + +        V     N
Sbjct: 60  LGRNAKAASALSQAFADRQVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV-----N 114

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K  N A++ F  +     +      +PHTG+THQ+RV    +G  IVGD  Y A  +  
Sbjct: 115 SKN-NPAVTQFFSLAAEPGER-LFLCKPHTGKTHQIRVALKSVGSGIVGDPIYNAGNEA- 171

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +   +
Sbjct: 172 ------DRGYLHAFSLCFQY 185


>gi|330967328|gb|EGH67588.1| pseudouridine synthase [Pseudomonas syringae pv. actinidiae str.
           M302091]
          Length = 296

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 56/302 (18%), Positives = 101/302 (33%), Gaps = 37/302 (12%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +   +V   D K +  +   + G  ++I       N        
Sbjct: 30  LCAKFTAISREQWLDRIARDRVLDADGKTITPHMAYREG--LKIHYFREVPN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQ 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +      
Sbjct: 80  --------ETPIPVVETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLDNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  RRI K Y ++   +P+     +    
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANRQTRSAYQTLFPTRRIDKCYEAIAPALPE-----LEFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   G +   +  +V++     + +  + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGPGVSNTQTRIEVLERHGPLWRYG-LHPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G  I  D  Y    K       Q+ L L A+ +    P  G        P         L
Sbjct: 244 GAAICNDPFYPDALKDPLDD-YQHPLKLLAKSLRFTDPLSGE-------PRQFESLL-KL 294

Query: 323 GF 324
            +
Sbjct: 295 DW 296


>gi|257461315|ref|ZP_05626412.1| pseudouridine synthase [Campylobacter gracilis RM3268]
 gi|257441343|gb|EEV16489.1| pseudouridine synthase [Campylobacter gracilis RM3268]
          Length = 249

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 60/308 (19%), Positives = 122/308 (39%), Gaps = 65/308 (21%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +       +I+    + ++ +G V     ++                       + +E  
Sbjct: 7   KLLAAQ-ENISHNEAKALIDAGLVSARGAKI----------------------ALAREML 43

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
             ++  ++ K +   K  ++YED  +   NKP  +S +                   K  
Sbjct: 44  GENTKFSVMKPA---KPAIIYEDENVLAVNKPPFMSSEN----------------LEKIY 84

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           K  L +RLD+ETSG++++ +     +     F+  R++K Y ++V GI   + +     L
Sbjct: 85  KFGLLNRLDKETSGVVLLYKNEEFREAAIAEFKNLRVKKSYIAIVKGIVSEEMKFGEPIL 144

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             K+  G        +       A S    +    +K   ++++  TGRTHQ+RVH  + 
Sbjct: 145 TIKTRSG-----AFSKISPNGKSAFSEVYPLMVSGKK-SLVKVRIETGRTHQIRVHLANA 198

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G  ++GD KY  +           +++LH+   ++       L+  APL     K+++  
Sbjct: 199 GFGVIGDEKYAKSRA--------KRMFLHSYETEIL-----GLKFKAPLD----KSFNEF 241

Query: 323 GFKYDRNL 330
           GF+  ++L
Sbjct: 242 GFEIPKDL 249


>gi|332140698|ref|YP_004426436.1| tRNA pseudouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327550720|gb|AEA97438.1| tRNA pseudouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 279

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 100/247 (40%), Gaps = 50/247 (20%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGG---------------------------------SG 124
              +L+ED+ + V NKP G+++                                      
Sbjct: 3   PIPILFEDANLLVVNKPVGVAMHDALDSKSGDPKDNALAIEHEDTDKNAAQKESSACKGE 62

Query: 125 IAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                DG +          +  L HRLD  TSG L +A+    A  + E F  RRI K Y
Sbjct: 63  DTLRTDGIVTQLKKQLSLSELHLCHRLDTGTSGCLCLAKNAKTAAEIGELFSSRRIGKFY 122

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +L    PK K+  I   +  K+  GG  + +  Q     N AI+ F           ++
Sbjct: 123 LALSEHKPKKKQGAIIGDM--KNRRGGQRILLKSQE----NPAITQFFSHAAKPGTRGFI 176

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            ++PH+G+THQ+RV    +G PI+GD  Y             ++LYLHA ++ LP    G
Sbjct: 177 -VKPHSGKTHQIRVALKSIGAPILGDSLYGGAP--------SDRLYLHAWHLRLP-LSAG 226

Query: 304 RLQITAP 310
            L ITAP
Sbjct: 227 ELTITAP 233


>gi|317177158|dbj|BAJ54947.1| hypothetical protein HPF16_0350 [Helicobacter pylori F16]
          Length = 293

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 67/294 (22%), Positives = 119/294 (40%), Gaps = 29/294 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVSLI------------HFR 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +     L++E     VF+KP  +      G  YH +  L       G+     HRLD E
Sbjct: 64  PNEKTQALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  +A+ L   F  ++++K Y  L  G+  ++   I   +L   +I  D +
Sbjct: 122 TSGLVLAGKTLQSAKDLKALFMQKKVKKTYLVLAHGLV-DRSIVIDKPILTPQNIQKD-L 179

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  +       + +  + +          L++ P TGRTHQ+R+H   +   IVG+  Y
Sbjct: 180 RIKSKISPLGKPSTTLVEPLSYNPFLDISLLKITPITGRTHQIRLHLSSVNHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +         +      L LHA  ++    +G   +IT+P+P   +    
Sbjct: 240 GVIDENAREYLQLKRENNAPLLMLHAASLEFEF-KGAIYKITSPMPKRFMPFLK 292


>gi|294143008|ref|YP_003558986.1| ribosomal pseudouridine synthase Rlu family protein [Shewanella
           violacea DSS12]
 gi|293329477|dbj|BAJ04208.1| ribosomal pseudouridine synthase Rlu family protein [Shewanella
           violacea DSS12]
          Length = 224

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 95/237 (40%), Gaps = 33/237 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ ++    V  K   +      G A    G + S       K    HRLD  TSG+L+ 
Sbjct: 4   IIADEDDFLVIAKSPNVHFHSQDGSA----GVMASLEQDLAIKLYSVHRLDSLTSGLLLF 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA   TE F   +IQK Y +L  G PK K+  +   + K          + K   
Sbjct: 60  AKSSRAAAEFTELFTQHKIQKYYVALATGKPKKKQGWVVGDMAK------SRRSMYKLLR 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F      A+      ++P +G+THQLRV    +G PI+GDH Y        
Sbjct: 114 TTENPALTQFFS-QSVAEGLRLYLLKPLSGKTHQLRVALASLGVPILGDHLYGGAE---- 168

Query: 281 TSPIQNKLYLHARYMDL----------PHPEGGRLQITAPLPAHMVKTW---DSLGF 324
                ++ YLHA  +             +P  G  Q TA      ++ W   + L +
Sbjct: 169 ----SDRGYLHAFSLSFSFRGKDYRYLSYPSQGE-QFTAVDTKKQLQIWSEPEKLAW 220


>gi|50290395|ref|XP_447629.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49526939|emb|CAG60566.1| unnamed protein product [Candida glabrata]
          Length = 411

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 57/266 (21%), Positives = 97/266 (36%), Gaps = 42/266 (15%)

Query: 38  QKILRSGQ----VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
            K++R GQ    + V    +K N++++S     +      +      +  +         
Sbjct: 60  YKLIRDGQYLDNLSVLDTPIKNNDKLES----TVHKHEPPVLQWCSNEANIPGK------ 109

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                  ++YED  + V NKP GI +        +    L   +   G      +RLD+ 
Sbjct: 110 -KIAGIDIVYEDENLLVINKPCGIPIHP---TGLYYGNTLTEILKVNGVHALPAYRLDKV 165

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC--------------IA 199
           TSG+L++++    A  + +  R   +QK Y + V G   +  E               I 
Sbjct: 166 TSGLLILSKDTGTASMVQKKIRSHEMQKWYLARVEGAFPHVNEVPHIETLEIQRLDLPIE 225

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANY---------AISHFKVIDCFAQ-KFCWLEMQPHT 249
             +++ + I       V   E    Y         A + F  I  F       +  +P T
Sbjct: 226 EQIIQDNSILTIEDSDVYTVEPKKQYPSGLSVPRSAKTIFYPIKYFPHKNESIVACRPIT 285

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCAN 275
           GRTHQ+R+H   +  PIV D  Y   
Sbjct: 286 GRTHQIRIHLARLNHPIVNDTIYSQK 311


>gi|217971508|ref|YP_002356259.1| Rlu family pseudouridine synthase [Shewanella baltica OS223]
 gi|217496643|gb|ACK44836.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS223]
          Length = 230

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 55/198 (27%), Positives = 88/198 (44%), Gaps = 19/198 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++  ++   V +K A +      G A    G +       G K    HRLD  TSG+L+
Sbjct: 3   RIIANEADFIVISKSAKVHFHSQDGTA----GVVAQAEQDLGIKLFAVHRLDSPTSGLLI 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A++  AA+  TE F   ++QK Y +L  G PK K+  +   + K          + K  
Sbjct: 59  LAKSAVAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIGDMAK------SRRSMFKLL 112

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F  +   ++      ++PH+G+THQLRV    +G PI+GD  Y       
Sbjct: 113 RTKENPAITQFFSL-SVSEGLRLYLLKPHSGKTHQLRVALASLGVPILGDDLYGG----- 166

Query: 280 FTSPIQNKLYLHARYMDL 297
                 ++ YLHA  +  
Sbjct: 167 ---MAADRCYLHAYCLHF 181


>gi|198461946|ref|XP_001352285.2| GA19422 [Drosophila pseudoobscura pseudoobscura]
 gi|198142379|gb|EAL42449.2| GA19422 [Drosophila pseudoobscura pseudoobscura]
          Length = 321

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 54/175 (30%), Positives = 75/175 (42%), Gaps = 9/175 (5%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  I V NKPA I V       ++   F+ +   +     R  HRLD+ TSG+L+  RT 
Sbjct: 2   DEDIVVVNKPASIPVHPCGRYRHNTVVFILAKSHNLKN-LRTIHRLDRLTSGLLIFGRTS 60

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
             A+ L +  R R++QK Y   V G  P    EC     +    IG      V +     
Sbjct: 61  KKARELEQQIRNRQVQKEYVCRVEGRFPDGIIECNEPIQVVSYKIG------VCRVSPNG 114

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
               + F+ I         +  +P TGR HQ+RVH  ++G PIV D  Y     G
Sbjct: 115 KDCRTTFRRISEVGD-CSIVLCKPLTGRMHQIRVHLQYLGYPIVNDPLYNHEVFG 168


>gi|148262340|ref|YP_001229046.1| pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146395840|gb|ABQ24473.1| pseudouridine synthase [Geobacter uraniireducens Rf4]
          Length = 293

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 60/285 (21%), Positives = 111/285 (38%), Gaps = 26/285 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +  +    +P I+    +K +  G+V +D+K           Q + +      L  +   
Sbjct: 22  ILAFLSGRFPAISREIWEKRISEGKV-LDEKA----------QRITLDTEYAPLRRVFYF 70

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +++       T+        +L+ D +I V  KP  + V  G          L     S 
Sbjct: 71  REV------CTEPFIPFAEKILFLDDEILVACKPHFLPVTPGGRYVDEC--LLNRLRGST 122

Query: 141 GQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           G       HR+D+ET+G+++ +  + +     + F    I+K Y +L    P  +    A
Sbjct: 123 GIADLAPLHRIDRETAGLVLFSVNKKSRGLYGKLFLNGLIEKTYQALSACQPLQET---A 179

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +W ++     G+    +K    G   A S   +++       +  +QP TG+THQLR+H 
Sbjct: 180 SWDIRNRIERGEPWFRMK-TAPGGVNARSAINLVEVKGGMARFT-LQPRTGKTHQLRIHM 237

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             +G  I+ D +Y    +          L L A+ +    P  GR
Sbjct: 238 SGLGFGILND-RYYPELQAESEDNFDTPLQLVAQMLRFKDPLSGR 281


>gi|332529225|ref|ZP_08405189.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
 gi|332041448|gb|EGI77810.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
          Length = 319

 Score =  129 bits (325), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 52/284 (18%), Positives = 105/284 (36%), Gaps = 23/284 (8%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +     P ++    ++ +  G+V                +  R  P    +       ++
Sbjct: 35  FLAERLPAVSAAQWRQRMTDGRVL--------------DEQGRSLPPGTPVTAFAPGARV 80

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   + +    + ++++D+ + V +KP  + V       Y  +  L     + G +
Sbjct: 81  YYYRELDAEPALPFDAQIVFQDAHLIVADKPHFMPVTPTG--RYVRNSLLVRLKSATGLE 138

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ET+G+++ +            FR + + K+Y ++     +     +    
Sbjct: 139 TLSPVHRIDRETAGLVLFSVRPQDRGAYQALFRTQAVDKVYEAIAPLRAQGSDRPL--PA 196

Query: 203 LKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L +S I  D     +Q E      + +  ++++          ++P +G+THQLRVH   
Sbjct: 197 LHRSRIEVDPEQFFRQRETEGEPNSETALELVESRP-PHALYRLRPRSGKTHQLRVHMNA 255

Query: 262 MGCPIVGDHKYCANFKG--NFTSPIQNKLYLHARYMDLPHPEGG 303
           +G PIVGD  Y     G           L L AR +    P  G
Sbjct: 256 LGRPIVGDLFYPQVVHGPEAGQDDWTQPLRLLARGLSFLDPVTG 299


>gi|88860180|ref|ZP_01134819.1| hypothetical protein PTD2_19250 [Pseudoalteromonas tunicata D2]
 gi|88818174|gb|EAR27990.1| hypothetical protein PTD2_19250 [Pseudoalteromonas tunicata D2]
          Length = 219

 Score =  129 bits (325), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 63/219 (28%), Positives = 97/219 (44%), Gaps = 30/219 (13%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y  +  Y+FNKPAG+S       +    GF+        +K    HRLD+ TSG+L++
Sbjct: 4   IVYRHTDFYIFNKPAGMSFH-----SETQAGFVVLAEQLCQEKLYSVHRLDKLTSGLLIL 58

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR+  AA   TE F  + I K+Y +L    PK K+  I   ++K        +  ++   
Sbjct: 59  ARSSEAAARFTEMFSQKLINKVYLALSDQKPKKKQGWIKGDMVKARRGAYKLMTSLE--- 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  I   +       ++P +G+THQLRV    +  PI+GD  Y        
Sbjct: 116 ---NPAITRFYSI-SVSPGLRGYLLKPFSGKTHQLRVALKSISAPILGDELYGGTKA--- 168

Query: 281 TSPIQNKLYLHARYMDL----PH------PEGGRLQITA 309
                ++ YLHA  +       H      P  G   +TA
Sbjct: 169 -----DRTYLHAMALWFDWHGTHIKVFLAPTFGEQYLTA 202


>gi|223946633|gb|ACN27400.1| unknown [Zea mays]
          Length = 315

 Score =  129 bits (325), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 100/261 (38%), Gaps = 50/261 (19%)

Query: 100 ILLYEDSKIYVFNKPAG------ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +++ED  + V +KPAG      ++    S ++      L     +K     L +RLD++
Sbjct: 48  DVVFEDEWLAVVDKPAGVYCDALLTSFPCSAVSGKHFLRLAENPATK-PNLHLANRLDRD 106

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG++V+ +    A  L ++F   +++K Y +L  G P   ++        +S  G   V
Sbjct: 107 TSGLMVITKCNKVAGKLVKAFTDHKVKKTYLALCIGFPPAWEKIKICSGHGRSKHGAWRV 166

Query: 214 HVVKQNEKG------ANYAISHFKVIDCFAQK---------------------------- 239
           + +    +            + F+V+    +                             
Sbjct: 167 YAMSDVGRSLPGGSVVRDMSTRFEVLGVNGKGQFREPYSLDTDDIEPITVQEKATDQTCG 226

Query: 240 ------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                    +   P +GRTHQ+R+H  ++G PI GD KY    + +          LHA 
Sbjct: 227 GDANSSVILVRAYPQSGRTHQIRLHCQYLGLPIRGDVKYGGVIEWDGVE--CEGHALHAE 284

Query: 294 YMDLPHPEGG-RLQITAPLPA 313
            +   HP  G  + + +PLP 
Sbjct: 285 SLSFVHPITGLPITLRSPLPP 305


>gi|261379850|ref|ZP_05984423.1| RNA pseudouridine synthase [Neisseria subflava NJ9703]
 gi|284797545|gb|EFC52892.1| RNA pseudouridine synthase [Neisseria subflava NJ9703]
          Length = 307

 Score =  129 bits (325), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 57/295 (19%), Positives = 112/295 (37%), Gaps = 28/295 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNH 76
            + L  +   H+P I   N ++ L SG V   D                 +P   N L  
Sbjct: 29  GLPLLHFLCAHFPFIGEENWRRRLNSGFVVGADG----------------VPFDENTLFE 72

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKS 135
             K       +   ++     +  +L+ D  + V +KP  + V   G  +   +   L+ 
Sbjct: 73  PGKTMFYYRETSRESEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRL 132

Query: 136 WVDSKGQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             + +          HRLD++T+G+++++   A        F+ + +QK Y ++      
Sbjct: 133 RPELQYLNVEDITPIHRLDKDTAGVMLLSLNPATRCDYQTMFQEKTVQKTYEAV-----A 187

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +  +   L   S +       + +  +G   A +  ++I+     F    + PHTG+ 
Sbjct: 188 PTRTDLDYPLHISSRMERGEKFFLTRETEGEPNAHTTIELIENRG-AFSLYRLTPHTGKK 246

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           HQLRVH + +  P++ D  Y               L L A+ ++   P  G +++
Sbjct: 247 HQLRVHMMSLNMPLMNDALYPTPLAAG-DEDYDKPLKLLAKRIEFTDPVSGEIRV 300


>gi|312959799|ref|ZP_07774315.1| pseudouridine synthase [Pseudomonas fluorescens WH6]
 gi|311285965|gb|EFQ64530.1| pseudouridine synthase [Pseudomonas fluorescens WH6]
          Length = 296

 Score =  129 bits (325), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 55/281 (19%), Positives = 103/281 (36%), Gaps = 27/281 (9%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
              H+P I        +  G+V  ++   +  +   + G  + I       N        
Sbjct: 30  LCEHFPAIGREQWLDRIARGRVLDINGGPILQDLAYKEG--LCIYYFREVPN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   + +  ++  +LY D  + V +KP  + V    G         +         
Sbjct: 80  --------EKAIPVQETILYADEHLVVADKPHFLPVTPA-GEYVEQTLLRRLIRRLDNPS 130

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HR+D+ T+G+++ +   A+     + F  R+I K Y ++   +P      +   L+
Sbjct: 131 LVPLHRIDRHTAGLVLFSANPASRAAYQQLFPTRQIDKFYEAIAPALP-----GLTFPLV 185

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            KS +         Q  +GA+   +  +V +     + +  + P TG+ HQLRVH   +G
Sbjct: 186 HKSRLVDSEPFFRMQEGEGASNTETGVQVREKNGDLWRYG-LFPVTGKKHQLRVHMTALG 244

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             I  D  Y  N   +      N L L A+ +    P  G+
Sbjct: 245 ASICNDPFY-PNVIKDAVDDYANPLKLLAQGVRFIDPVTGQ 284


>gi|149189891|ref|ZP_01868170.1| pseudouridine synthase Rlu family protein [Vibrio shilonii AK1]
 gi|148836206|gb|EDL53164.1| pseudouridine synthase Rlu family protein [Vibrio shilonii AK1]
          Length = 228

 Score =  129 bits (325), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 55/199 (27%), Positives = 83/199 (41%), Gaps = 17/199 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            + YE+    V NK  G+SV    G    +       +        L HRLD+ TSG+L+
Sbjct: 3   DIHYENEDFVVINKYPGVSVHKDDGDTMLVSDV---AIAIGASSLHLVHRLDKMTSGLLI 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+    A   +  F  R I K Y ++    PK K+  I   + +        V     N
Sbjct: 60  LAKRAEVAAQFSRLFEQRDIDKYYLAIGSKKPKKKQGTIIGDMERSRRSSWKLV-----N 114

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K  N A++ F        +  +L  +P +G+THQ+RV    +G PI GD  Y       
Sbjct: 115 SKN-NPAVTQFFSAAAENGERVFL-CKPLSGKTHQIRVALKSIGSPIKGDAIYN------ 166

Query: 280 FTSPIQNKLYLHARYMDLP 298
            TS   ++ YLHA  +   
Sbjct: 167 -TSDSSDRGYLHAYALRFE 184


>gi|157963919|ref|YP_001503953.1| pseudouridine synthase Rlu family protein [Shewanella pealeana ATCC
           700345]
 gi|157848919|gb|ABV89418.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           pealeana ATCC 700345]
          Length = 229

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 59/212 (27%), Positives = 91/212 (42%), Gaps = 21/212 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++ ++    V NK A +      G A    G +       G K    HRLD  TSG+++
Sbjct: 3   RVIADERDFIVINKSAEVHFHSQDGNA----GVVAQAEADLGIKLYAVHRLDTMTSGLII 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A++ +AA   T  F    +QK Y +L  G PK K+  +   + K          + K  
Sbjct: 59  LAKSSSAAAEFTRMFSAHLVQKYYLALAKGKPKKKQGWVIGDMAK------SRRSMHKLL 112

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A+      ++PH+G+THQLRV    +G PI+GD  Y       
Sbjct: 113 RTTENPAITQFFS-HSIAEGERLYLLKPHSGKTHQLRVALASIGVPILGDTLYGG----- 166

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQIT-AP 310
                 ++ YLHA  +   +  G   + T AP
Sbjct: 167 ---LSADRGYLHAYSLHFDYL-GQEYEFTVAP 194


>gi|90406918|ref|ZP_01215109.1| tRNA pseudouridine synthase A [Psychromonas sp. CNPT3]
 gi|90311960|gb|EAS40054.1| tRNA pseudouridine synthase A [Psychromonas sp. CNPT3]
          Length = 231

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 54/198 (27%), Positives = 87/198 (43%), Gaps = 17/198 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+YE+ +  V NK   I+     G      G + +   +   K    HRLD+ TSG+L++
Sbjct: 10  LVYENEEFIVINKKENINFHSEDGEF----GVVVAAEKALNIKLYSVHRLDKMTSGLLLL 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++   A HL+  F+  ++QK Y ++    PK K+  I   + K          + K  +
Sbjct: 66  AKSSHIAAHLSALFKAHQVQKYYIAITDKKPKKKQGLIQGGMQK------SRRSMWKLTK 119

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F              ++P TG+THQ+RV    +G  I GD  Y    K   
Sbjct: 120 TKENLAITQFFSF-TLGAGKRLFIIKPKTGKTHQIRVALKSIGSAICGDPLYGEKTKQ-- 176

Query: 281 TSPIQNKLYLHARYMDLP 298
                ++ YLHA  ++  
Sbjct: 177 ----YDRGYLHAYQLEFT 190


>gi|17978940|gb|AAL47436.1| AT3g52260/T25B15_30 [Arabidopsis thaliana]
          Length = 294

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 62/258 (24%), Positives = 104/258 (40%), Gaps = 49/258 (18%)

Query: 37  LQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
           +Q+ +++GQ+++D + VK  N  ++SG                   K++ S +   +   
Sbjct: 53  IQR-IQNGQIQIDGEVVKDPNTLLRSG------------------SKLVYSRLPWKEPDT 93

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG---------QKPRL 146
                +LYED  +   NKP+G+ V  G             W   K            P  
Sbjct: 94  PYSLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVP 153

Query: 147 THRLDQETSGILVVARTRAAAQHL-----------------TESFRMRRIQKIYWSLVWG 189
            HRL + TSGIL+ A+T+ A   L                  E    R++ KIY +L  G
Sbjct: 154 VHRLGRGTSGILLCAKTKLAKTKLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADG 213

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPH 248
           I +  +  I   +    + G      V   E     A S   V++   +K C  ++++  
Sbjct: 214 IVEEDEVVIKQPIGVVRYPGVAQGLYVASPEW--KPAFSKVFVLERDREKNCSLVKVEIQ 271

Query: 249 TGRTHQLRVHALHMGCPI 266
           +GR HQ+R+H  +MG P+
Sbjct: 272 SGRPHQIRIHLAYMGHPL 289


>gi|325989585|ref|YP_004249284.1| pseudouridine synthase, RluA family [Mycoplasma suis KI3806]
 gi|323574670|emb|CBZ40326.1| similar to pseudouridine synthase, RluA family [Mycoplasma suis]
          Length = 231

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 49/227 (21%), Positives = 88/227 (38%), Gaps = 15/227 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           + E     + +K +GI V          D  +    +  G+   L +RLD+ TSG+L++A
Sbjct: 6   ILETKHYLIVDKDSGILVHKDKYTR-GKDTLIDILKEEYGENIYLVNRLDKNTSGLLLIA 64

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           + + +   L   F  ++I K Y +++     + K  I   L +     G  +     N K
Sbjct: 65  KGKLSLLTLKALFEEQKIDKKYLAILSSPLPHPKIKITFSLGRDK---GKKLRFTATNSK 121

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               A+++ + I+        + +   TGRTHQLR H   + CP++ D  Y    + +  
Sbjct: 122 KYKTALTYAETINSQ-----LVLLSLKTGRTHQLRAHLFTLSCPVLNDSVYGVPLENDSF 176

Query: 282 SPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
                  YLH+  +    P E   + +    P         L     
Sbjct: 177 -----GQYLHSYSLSFIDPWEKKPVNVWTLPPLEFTNKLIELNIDTS 218


>gi|326424090|ref|NP_761675.2| Pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           CMCP6]
 gi|319999468|gb|AAO11202.2| Pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           CMCP6]
          Length = 231

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 55/210 (26%), Positives = 92/210 (43%), Gaps = 18/210 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLIINKYPHVSVHKDDGDTMLLQEVAKV---SGDEQLYLIHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R   AA  L++ F  R ++K Y ++    PK K+  +   + +        V+  +  
Sbjct: 60  LGRNSTAASALSQRFAQREVEKFYLAIGAKKPKKKQGTVIGDMERSRRASWKLVNSKQ-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F  +     +  +L  +P+TG+THQ+RV    +G  IVGD  Y A     
Sbjct: 118 ----NPAITQFFSLAGEPGERAFL-CKPYTGKTHQIRVALKSVGSSIVGDPIYNAGSDS- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
                 ++ YLHA  +   + +G +     
Sbjct: 172 ------DRGYLHAFCLGFQY-QGEQYHFVC 194


>gi|258543640|ref|YP_003189073.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256634718|dbj|BAI00694.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256637774|dbj|BAI03743.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-03]
 gi|256640828|dbj|BAI06790.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-07]
 gi|256643883|dbj|BAI09838.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-22]
 gi|256646938|dbj|BAI12886.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-26]
 gi|256649991|dbj|BAI15932.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-32]
 gi|256652981|dbj|BAI18915.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-01-42C]
 gi|256656035|dbj|BAI21962.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase A
           [Acetobacter pasteurianus IFO 3283-12]
          Length = 168

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 54/179 (30%), Positives = 78/179 (43%), Gaps = 15/179 (8%)

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D +TSG L +A  +     L ++F  +  QK YW++V   P+     I   L K+S   G
Sbjct: 2   DTDTSGCLAIALRKQPLLALQQAFATKTAQKTYWAVVQTGPQEDTGRIDLPLEKQSSKRG 61

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +            A + +KV+    +  CWLE+   TGRTHQ RVH   M  PI+GD 
Sbjct: 62  WRMVA----SPSGAAAATRWKVLGRN-KDLCWLELTLETGRTHQARVHCAAMNWPILGDP 116

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
            Y         +P    L+L AR + L  P    +   AP    M  T  + G+  D+ 
Sbjct: 117 LYG--------TPHPQGLHLLARSLTL--PFSPPITAIAPPRTGMKATLQACGWTPDKE 165


>gi|325973143|ref|YP_004250207.1| tRNA pseudouridine synthase [Mycoplasma suis str. Illinois]
 gi|323651745|gb|ADX97827.1| tRNA pseudouridine synthase [Mycoplasma suis str. Illinois]
          Length = 231

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 49/227 (21%), Positives = 88/227 (38%), Gaps = 15/227 (6%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           + E     + +K +GI V          D  +    +  G+   L +RLD+ TSG+L++A
Sbjct: 6   ILETKHYLIVDKDSGILVHKDKYTR-GKDTLIDILKEEYGEDIYLVNRLDKNTSGLLLIA 64

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           + + +   L   F  ++I K Y +++     + K  I   L +     G  +     N K
Sbjct: 65  KGKLSLLTLKALFEEQKIDKKYLAILSSPLPHPKIKITFSLGRDK---GKKLRFTATNSK 121

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
               A+++ + I+        + +   TGRTHQLR H   + CP++ D  Y    + +  
Sbjct: 122 KYKTALTYAETINSQ-----LVLLSLKTGRTHQLRAHLFTLSCPVLNDSVYGVPLENDSF 176

Query: 282 SPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSLGFKYD 327
                  YLH+  +    P E   + +    P         L     
Sbjct: 177 -----GQYLHSYSLSFVDPWEKKPVNVWTLPPLEFTNKLIELNIDTS 218


>gi|198414279|ref|XP_002128102.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 2 [Ciona intestinalis]
          Length = 456

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 54/263 (20%), Positives = 103/263 (39%), Gaps = 22/263 (8%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNH 76
              L   +   +      + ++ +  G V+V+ K V   + +++   ++           
Sbjct: 119 GKTLREVYTTEFSLYPIEHYERAVLEGGVKVNLKPVVSLDVKLRDNDMISARLHR----- 173

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
              E  +LD+ V            ++ ++SK  V NKP+ I +        +   ++ + 
Sbjct: 174 --HEAPVLDTKVE-----------IIEDNSKYVVVNKPSSIPIHPCGRFRNNSLVYILA- 219

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            D   Q     HR+D+ TSGI++  +T+  A  + +    R+++K Y   V G      +
Sbjct: 220 KDLGYQGLLGCHRIDRLTSGIVIFGKTKNIAHKVAKEISERKVEKQYVCKVVGEFP-STD 278

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + N  +   +    Y    K        A + F  +         +  +P TGRTHQ+R
Sbjct: 279 IVCNEPVSLFNRKLGYAVAWKVEGVVGKEASTWFTRMSYDGTN-SVVLCKPKTGRTHQIR 337

Query: 257 VHALHMGCPIVGDHKYCANFKGN 279
           VH  ++G PI+ D  Y     G 
Sbjct: 338 VHLQYLGFPIINDPIYNHPAWGE 360


>gi|331016169|gb|EGH96225.1| pseudouridine synthase [Pseudomonas syringae pv. lachrymans str.
           M302278PT]
          Length = 296

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 53/282 (18%), Positives = 98/282 (34%), Gaps = 29/282 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +   +V   D K +  +   + G  ++I       N        
Sbjct: 30  LCAKFTAISREQWLDRIARDRVLDADGKTITPDMAYREG--LKIHYFREVPN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQ 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +      
Sbjct: 80  --------ETPIPVVETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLDNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  RRI K Y ++   +P      +    
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANRQTRSAYQTLFPTRRIDKCYEAIAPALP-----GLEFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   G +   +  +V++     + +  + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGPGVSNTQTRIEVLERHGSLWRYG-LHPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G  I  D  Y    K +     ++ L L A+ +    P  G 
Sbjct: 244 GAAICNDPFYPDALK-DPVDDYRHPLKLLAKSLRFTDPLSGE 284


>gi|319787217|ref|YP_004146692.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317465729|gb|ADV27461.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
          Length = 282

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 60/281 (21%), Positives = 106/281 (37%), Gaps = 27/281 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
                +P I     +     G+V             QSG  + +         I   +++
Sbjct: 21  ALCARFPRIPESQWRDRFARGRVL-----------DQSGAPLPLDAPYRLGAEIQYFREV 69

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ- 142
                            +L+ D  + V  KP  + V      A+  +  L   V   G  
Sbjct: 70  EQEP------PMPGGEYVLHHDDHLLVAYKPHFLPV--APTGAWVRETLLTRLVALTGNT 121

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HRLD++T+G+++ +   A        FR RRI+K+Y ++   +P          L
Sbjct: 122 DLVPLHRLDRDTAGLVMFSTQPATRGAYQALFRERRIRKLYRAVAPPLP----GLSFPHL 177

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            +     G+    +++ E G   + +   V++     + + +++P TGR HQLRVH   +
Sbjct: 178 HRSRLEAGEPFFRMREVE-GEPNSETVIDVLERNGPTWTY-QLEPVTGRKHQLRVHMAAL 235

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           G PI+GD +Y    +   T  +   L L A  +    P  G
Sbjct: 236 GAPIIGD-RYYPKLQPQDTDDLAAPLQLTAYALGFDDPLSG 275


>gi|262394573|ref|YP_003286427.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. Ex25]
 gi|262338167|gb|ACY51962.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. Ex25]
          Length = 230

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 56/215 (26%), Positives = 92/215 (42%), Gaps = 18/215 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL 
Sbjct: 3   DILHTHPDFLIINKHPNVSVHKDDGDTMLLQEVAK---QSGDEQLYLIHRLDKMTSGILF 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R   AA  L+++F  R+++K Y ++    PK K+  +   + +        V     N
Sbjct: 60  LGRNAKAASALSQAFADRQVEKFYLAIGSKKPKKKQGLVVGDMERSRRSSWKLV-----N 114

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            K  N A++ F  +     +      +PHTG+THQ+RV    +G  IVGD  Y A  +  
Sbjct: 115 SKN-NPAVTQFFSLAAEPGER-LFLCKPHTGKTHQIRVALKSVGSGIVGDPIYNAGNEA- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
                 ++ YLHA  +   +    + +       H
Sbjct: 172 ------DRGYLHAFSLCFQY-RDEQYRFVCDPREH 199


>gi|317180758|dbj|BAJ58544.1| hypothetical protein HPF32_0962 [Helicobacter pylori F32]
          Length = 293

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 67/294 (22%), Positives = 117/294 (39%), Gaps = 29/294 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVSLI------------HFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +     L++E     VF+KP  +      G  YH +  L        +     HRLD E
Sbjct: 64  PNEKTQALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFDKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  + + L   F  ++++K Y +L  G+  +K   I   +L   +I  D  
Sbjct: 122 TSGLVLAGKTLQSVKDLKALFMQKKVKKTYLALAHGLV-DKNIVIDKPILTPQNIQKDLR 180

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              K +      + +  + +          L++ P TGRTHQ+R+H   +   IVG+  Y
Sbjct: 181 IRSKIS-PLGKPSTTLVEPLSYNPFLDISLLKIAPLTGRTHQIRLHLSSVNHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +         +      L LHA  ++    +G   +IT+P+P   +    
Sbjct: 240 GVIDENAREYLQLKRENNAPLLMLHATSLEFEF-KGAIYKITSPIPKRFMPFLK 292


>gi|152991961|ref|YP_001357682.1| ribosomal large subunit pseudouridine synthase D [Sulfurovum sp.
           NBC37-1]
 gi|151423822|dbj|BAF71325.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Sulfurovum sp. NBC37-1]
          Length = 245

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 62/295 (21%), Positives = 113/295 (38%), Gaps = 59/295 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        I+    ++++  G V VD ++V+                      I + + 
Sbjct: 8   KVLAQQ-QGISNKKAKELIDRGLVFVDDRKVR----------------------IARAEI 44

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
             +++  +    D     +LYED  I   NKPA +                   +    +
Sbjct: 45  NTETTFRIEYPEDI---EILYEDEDIIAVNKPAQVDS---------------YEIQDAIE 86

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD++TSG+L++ R R   +   + F+ RR++K Y + V G+     E      
Sbjct: 87  GAELLHRLDRDTSGVLLLGRNREFIERAIKEFKNRRVEKHYVAWVDGVIYETVEIDEPIF 146

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             K       +  V+        A +     +   +K   +++   TGRTHQ+RVH  H+
Sbjct: 147 TVKKGKAFSMIDPVR-----GKKAHTVVHPEEVQGKK-SKVKIDITTGRTHQIRVHLAHI 200

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
           G PIVGD +Y +  +         ++ LH+  M +        +  A  P  + +
Sbjct: 201 GHPIVGDEQYGSRTQA-------KRILLHSAKMKILD-----YEFNAKEPKDIAR 243


>gi|254580497|ref|XP_002496234.1| ZYRO0C13684p [Zygosaccharomyces rouxii]
 gi|238939125|emb|CAR27301.1| ZYRO0C13684p [Zygosaccharomyces rouxii]
          Length = 398

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 58/276 (21%), Positives = 102/276 (36%), Gaps = 26/276 (9%)

Query: 19  MR--LDRWFKNHYPHINFVNLQKILRSGQVRV--DKKRVKFNNRIQSGQVVRIPPVINAL 74
            R  LD    N +   +  +    ++ G + +  + K +  +  + S   +R    +  L
Sbjct: 31  QRTLLD-VMVNEFRSYSENHYLTEIKKGNLAIIREGKTLDPSEVLSS--PIRNNDTVQTL 87

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKS--ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
            H   E  +L  S N         +   +++E+  + V NKP+GI +             
Sbjct: 88  RH-KHEPPVLQWSENEEDIPGIKVAGFDIVHENDNLLVLNKPSGIPIHPTGQF---YQNT 143

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   +   G+     +RLD+ TSG+L++A+    A  +    R   + K Y + V G   
Sbjct: 144 ITEILKRHGKTALPCYRLDKLTSGLLIMAKNTETAGGIQLKIRDHDMSKYYLARVKGKFP 203

Query: 193 --------NKKECIANWLLKKSHIGGDYVHVVKQNEKGA----NYAISHFKVIDCFAQK- 239
                          + LL        Y    K+           A + F  +  F    
Sbjct: 204 HSSSEDFYEPPIPFQDPLLVTQEESPVYTVEPKKQFPSGLSPVKDARTSFYPLKYFPHCD 263

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              +  +P TGRTHQ+R+H   +G PIV D  Y  +
Sbjct: 264 QSLVVCKPLTGRTHQIRIHLARLGHPIVNDPFYNID 299


>gi|119945062|ref|YP_942742.1| pseudouridine synthase Rlu family protein [Psychromonas ingrahamii
           37]
 gi|119863666|gb|ABM03143.1| pseudouridine synthase Rlu family protein, TIGR01621 [Psychromonas
           ingrahamii 37]
          Length = 242

 Score =  129 bits (324), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 55/197 (27%), Positives = 90/197 (45%), Gaps = 14/197 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++E+++  V NK AGI+     G      G + +   +   K    HRLD+ TSG+L++
Sbjct: 18  VVHENNEFIVINKQAGINFHSEDGEF----GVVVAAEKAFSCKLYSVHRLDKMTSGLLLL 73

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  +A  L+  F   +IQK Y ++    PK K+  I   + K          + K  +
Sbjct: 74  AKSSPSAAQLSALFFEHQIQKYYLAISDKKPKKKQGLIKGGMEK------SRRSMWKLTK 127

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +  N AI+ F              ++P TG+THQ+RV    +G  I GD  Y        
Sbjct: 128 QTNNLAITQFFS-YSLENGKRLFVIKPRTGKTHQIRVALNSIGSAICGDPLYAEKSPQ-- 184

Query: 281 TSPIQNKLYLHARYMDL 297
            S   ++ YLHA  +D 
Sbjct: 185 -SAAFDRAYLHAYQIDF 200


>gi|291221038|ref|XP_002730528.1| PREDICTED: hypothetical protein [Saccoglossus kowalevskii]
          Length = 375

 Score =  129 bits (324), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 125/320 (39%), Gaps = 51/320 (15%)

Query: 59  IQSGQVV--RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
           +++   V  R+       N + +   I    +N  +   +LKS ++Y++  +   NKPAG
Sbjct: 50  LKNDDSVALRVVSRKRGRNILERPGVIRPEEMNREQLVQYLKSQIVYDEDGVLALNKPAG 109

Query: 117 ISVQGGS---GIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAA-- 167
           + V         A H    L+   D K Q      +     +++ SG+ ++A+T   A  
Sbjct: 110 LGVHSQREDLDTADHQWSLLEVLPDLKHQIGEKHLQFVKAPEKDCSGVTLLAKTPEIAAD 169

Query: 168 --QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK---- 221
             + L E+   +   +++W++  G+P      I   +  +       V  VK + K    
Sbjct: 170 IDRSLKEARLRQVFTRVFWAVTVGVPSPLSGLIKVPVTNEVVDDEHQVSPVKDSSKRSYK 229

Query: 222 --GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                  ++ ++VI   + +   +E+ P      QLRVH     C I+GDH Y +  +  
Sbjct: 230 MRNTRKLLTKYRVI-SESNQCALVELMPLKAYKDQLRVHMTTKLCRILGDHVYSSRIQTI 288

Query: 280 FTSP------------------IQNK------------LYLHARYMDLPHPEGGR-LQIT 308
              P                  ++++            L+LH   M LP  +    L I+
Sbjct: 289 LGIPVLIDARNAMPGTQVLSEEVRHRMNLTSAVIDSIPLHLHCVAMTLPSWKKKEDLIIS 348

Query: 309 APLPAHMVKTWDSLGFKYDR 328
           APLP +  KT   L  ++ +
Sbjct: 349 APLPKYFWKTLKLLDIEHPQ 368


>gi|170660221|ref|YP_001740051.1| RNA pseudouridine synthase family protein [Pseudomonas syringae pv.
           tomato str. DC3000]
 gi|170652971|gb|ACB22027.1| RNA pseudouridine synthase family protein [Pseudomonas syringae pv.
           tomato str. DC3000]
          Length = 296

 Score =  129 bits (324), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 53/282 (18%), Positives = 98/282 (34%), Gaps = 29/282 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +  I+       +   +V   D K +  +   + G  ++I       N        
Sbjct: 30  LCAKFTAISREQWLDRIARDRVLDADGKTITPDMAYREG--LKIHYFREVPN-------- 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQ 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +      
Sbjct: 80  --------ETPIPVVETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLDNP 129

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  RRI K Y ++   +P      +    
Sbjct: 130 DLVPLHRIDRHTAGLVLFSANRQTRSAYQTLFPTRRIDKCYEAIAPALP-----GLEFPR 184

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   G +   +  +V++     + +  + P TG+ HQLRVH   +
Sbjct: 185 LHESRLVEGEPFFRMQEGPGVSNTQTRIEVLERHGPLWRYG-LHPVTGKKHQLRVHMAAL 243

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G  I  D  Y    K +     ++ L L A+ +    P  G 
Sbjct: 244 GAAICNDPFYPDALK-DPVDDYRHPLKLLAKSLRFTDPLSGE 284


>gi|254820676|ref|ZP_05225677.1| RNA pseudouridine synthase family protein [Mycobacterium
           intracellulare ATCC 13950]
          Length = 271

 Score =  129 bits (324), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 57/250 (22%), Positives = 91/250 (36%), Gaps = 12/250 (4%)

Query: 55  FNNRIQSGQVV-RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
              ++ +G+VV     VI+A   +     +        +     +  +LY D  I V +K
Sbjct: 14  ARAKVLAGEVVGADGAVIDAKTVLPAGASVYLYRELPDEVPVPFEIPVLYRDDDIVVVDK 73

Query: 114 PAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           P  ++     G        ++   +    +    HRLD+ T+G+L+    R         
Sbjct: 74  PHFVATMP-RGRHVAQSALVRLRRELDLPELSPAHRLDRLTAGVLMFTARREVRGAFQTL 132

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F    + K Y +     P      +    + KS I      +    E GA  A +  +++
Sbjct: 133 FSRGLVDKTYLARAAVDPA-----LRLPRVVKSRIVKRRGQLQAVCEPGAANAETLVELV 187

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                      + P TGRTHQLRVH   +G PI GD  Y  N            L L AR
Sbjct: 188 SPDG----LYRLTPRTGRTHQLRVHMASLGIPIEGDPLY-PNVIDVAPDDFSTPLRLLAR 242

Query: 294 YMDLPHPEGG 303
            ++   P  G
Sbjct: 243 RIEFTDPRSG 252


>gi|83645042|ref|YP_433477.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83633085|gb|ABC29052.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 297

 Score =  128 bits (323), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 55/306 (17%), Positives = 109/306 (35%), Gaps = 54/306 (17%)

Query: 24  WFKNHYPHINFVNLQKILRSGQV--RVDKKRVK----FNNRIQSGQVVRIPPVINALNHI 77
           W       ++   ++  +  G V  +   K  K      + +  G V+ +      L   
Sbjct: 36  WLAAQ-TGLSKQKVKDAMLKGAVWWKRGGKPQKRLRRAKSPLAVGDVLELNYDPQILALN 94

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                               +  L+ +     ++ KPAG+  QG     +     +    
Sbjct: 95  SP------------------QPTLVADHDAYSIWCKPAGLLTQGSEWGDHCSLLRMAELH 136

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++  L HRLD+E  G++++A  +AAA       +   + K Y + V G    ++  
Sbjct: 137 FQSKRQVFLLHRLDREAMGLVIIAHNKAAAGRFGALLQDNALDKFYLARVKGRLAQEQGE 196

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLR 256
           I   +                       A+S+++V     A     + ++  TGR HQ+R
Sbjct: 197 IDFPV-------------------DGKSALSYYQVQHYDDATDSSLVRVKLITGRKHQIR 237

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
            H   +G P++GD +Y +  K       ++ L L A  +    P   R +++   +P  +
Sbjct: 238 RHFADLGYPLLGDPRYGSGNK------HEDGLMLAATELAFTCPMRRRAMRVV--MPEAL 289

Query: 316 VKTWDS 321
           +  W  
Sbjct: 290 LPAWSR 295


>gi|189439795|ref|YP_001954876.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium longum
           DJO10A]
 gi|189428230|gb|ACD98378.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium longum
           DJO10A]
          Length = 254

 Score =  128 bits (323), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 60/252 (23%), Positives = 95/252 (37%), Gaps = 31/252 (12%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + +     +  +LYED +I V +KP  ++     G+ Y     ++             HR
Sbjct: 2   IDEPHIPFEMDVLYEDERIIVVDKPHFLATMP-RGMWYRQTALIRLRERLGEPDITPAHR 60

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN------- 200
           LD+ T+G+LV  R  A        F+ R+  K+Y   +    I + +   I         
Sbjct: 61  LDRMTAGVLVFVRDPACRGAYQMLFQNRQAVKVYECLAPCRPISRPRFGTIMKVEPPCPF 120

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-------------------AQKFC 241
            LL++SHI  ++  +    E G   A +  +  D                         C
Sbjct: 121 PLLRRSHITKEHGTMAAFEEPGLANAETLIERGDLCFPPADGRWREAPEGGPHLGNHPIC 180

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
              + P TG+THQLRVH   +G PIVGD  Y    +          L L AR +    P 
Sbjct: 181 RYTLHPRTGKTHQLRVHMNSLGLPIVGDDFY-PRIQTRPYDDFSQPLQLVARMLRFTDPI 239

Query: 302 GGRL-QITAPLP 312
            G   +  + +P
Sbjct: 240 TGEKREFVSRVP 251


>gi|317482547|ref|ZP_07941562.1| RNA pseudouridylate synthase [Bifidobacterium sp. 12_1_47BFAA]
 gi|316915969|gb|EFV37376.1| RNA pseudouridylate synthase [Bifidobacterium sp. 12_1_47BFAA]
          Length = 254

 Score =  128 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 60/252 (23%), Positives = 95/252 (37%), Gaps = 31/252 (12%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + +     +  +LYED +I V +KP  ++     G+ Y     ++             HR
Sbjct: 2   IDEPHIPFEMDVLYEDERIIVVDKPHFLATMP-RGMWYRQTALIRLRERLGEPDITPAHR 60

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN------- 200
           LD+ T+G+LV  R  A        F+ R+  K+Y   +    I + +   I         
Sbjct: 61  LDRMTAGVLVFVRDPACRGAYQMLFQNRQTVKVYECLAPCRPISRPRFGTIMQVEPPRPF 120

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-------------------AQKFC 241
            LL++SHI  ++  +    E G   A +  +  D                         C
Sbjct: 121 PLLRRSHITKEHGTMAAFEEPGLANAETLIERGDLCFPPADGRWREAPEGGPHPGNHPIC 180

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
              + P TG+THQLRVH   +G PIVGD  Y    +          L L AR +    P 
Sbjct: 181 RYTLHPRTGKTHQLRVHMNSLGLPIVGDDFY-PRIQTRPYDDFSQPLQLVARMLRFTDPI 239

Query: 302 GGRL-QITAPLP 312
            G   +  + +P
Sbjct: 240 TGEKREFVSRVP 251


>gi|291276435|ref|YP_003516207.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
 gi|290963629|emb|CBG39461.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
          Length = 284

 Score =  128 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 54/239 (22%), Positives = 101/239 (42%), Gaps = 8/239 (3%)

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           ++    +      +I++ +++   V L +         ++      VF KP  +      
Sbjct: 34  IIDKRRLRYPDGRVIQKSEVICGRVLLDEFVPNGALRAIFVHEDFAVFAKPHNLLTHPKG 93

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              +       S     G +    HRLD ETSG+++++R + A   L   F    ++KIY
Sbjct: 94  --RFLHASLCDSIKMQFGMQANPVHRLDFETSGVVLISRNKRAEIALKTLFERGEVRKIY 151

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            +LV GI ++++   +  LL K       + +  Q       +I+  + ++    +   L
Sbjct: 152 RALVEGIIEHERCIESRILLPKKEDKSKDLGIKCQIHASGKDSITIIRPLEVRGNQ-TLL 210

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYC-----ANFKGNFTSPIQNKLYLHARYMDL 297
           E++P TGRTHQ+R+H   +G  IV +  Y      A         ++  L LHAR ++ 
Sbjct: 211 EIEPLTGRTHQIRLHLASIGHKIVNEPLYGVEEELARAYLQDKLGVKKHLCLHARSLEF 269


>gi|109897688|ref|YP_660943.1| pseudouridine synthase Rlu family protein [Pseudoalteromonas
           atlantica T6c]
 gi|109699969|gb|ABG39889.1| pseudouridine synthase Rlu family protein, TIGR01621
           [Pseudoalteromonas atlantica T6c]
          Length = 238

 Score =  128 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 66/215 (30%), Positives = 98/215 (45%), Gaps = 22/215 (10%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS-WVDSKGQKPRLTHRLDQETSGIL 158
            ++ +    +V +KP GISVQ          G L          K  L HRLD+ TSG+L
Sbjct: 10  RVVLDHPDFFVIDKPHGISVQ----NELDAQGILPVVCAQQAVDKLWLVHRLDKVTSGLL 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A+   AA  L + F  R I+K Y +L    PK K+  I+  + K      D      Q
Sbjct: 66  ILAKHAQAASTLGKLFETRAIEKYYLALGGSKPKKKQGTISGAMKKI----RDGKWAFSQ 121

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +  G   A + F      +       ++P TG+THQLRV    +GCPI+GD  Y      
Sbjct: 122 DGAG--IATTQFFS-KSASAGIRLFLLKPLTGKTHQLRVMLKSLGCPILGDALYKGTE-- 176

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
                 Q++ YLHA  +   + +G  +Q+T  LP+
Sbjct: 177 ------QDRTYLHAYCLRFEY-QGQLIQLTC-LPS 203


>gi|37679587|ref|NP_934196.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
 gi|37198331|dbj|BAC94167.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
          Length = 231

 Score =  128 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 54/210 (25%), Positives = 92/210 (43%), Gaps = 18/210 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +    K    S  ++  L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLIINKYPHVSVHKDDGDTMLLQEVAKV---SGDEQLYLIHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R   AA  L++ F  R ++K Y ++    PK K+  +   + +        V+  +  
Sbjct: 60  LGRNSTAASALSQRFAQREVEKFYLAIGAKKPKKKQGTVIGDMERSRRASWKLVNSKQ-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F  +     +  +L  +P+TG+THQ+RV    +G  I+GD  Y A     
Sbjct: 118 ----NPAITQFFSLAGEPGERAFL-CKPYTGKTHQIRVALKSVGSSIIGDPIYNAGSDS- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
                 ++ YLHA  +   + +G +     
Sbjct: 172 ------DRGYLHAFCLGFQY-QGEQYHFVC 194


>gi|303281963|ref|XP_003060273.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226457744|gb|EEH55042.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 443

 Score =  128 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 82/382 (21%), Positives = 127/382 (33%), Gaps = 144/382 (37%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQK--------PRLT 147
           L S++LY D  + V NKP+G+ V G G+G A      L + + S              + 
Sbjct: 62  LTSMVLYRDDDVLVLNKPSGLPVVGTGTGNANAAAPSLSAMLASLTFHADAPWKPPLTIV 121

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRR----------------------------I 179
           HRLD++ SG +V+AR   AA+ L  +F  +                             I
Sbjct: 122 HRLDKDASGCVVLARRAVAARTLARAFAAKSASGGEGAREEEEEGLLGGGRAESDALYNI 181

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGD---------------------------- 211
           ++ YW+LV G P   +  I   L       G+                            
Sbjct: 182 ERTYWALVAGRPSRDEGVIRAPLRIPGKRNGNTKRRDGGVVFFADDATDERRARLPRPPD 241

Query: 212 ------------YVHVVKQNEKGANYAISHFKVIDCFAQKF----------------CWL 243
                        V    +++     A++ ++VI    +                    L
Sbjct: 242 VAPGGGGGASEGRVEATTEDDPRGVRAVTSYRVIGEVPRDADGDDGDDDEKVTHPRPTLL 301

Query: 244 EMQPHTGRTHQLRVHALH-MGCPIVGDHKYCAN-----FKGNFTSP-------------- 283
           E+   TGR HQ+RVH    +G P+VGD+KY         +G   +P              
Sbjct: 302 ELTLSTGRKHQIRVHLASALGTPVVGDYKYGYRDTPRTRRGREIAPPAWMEALRDVEAAA 361

Query: 284 -----------------------------IQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                                            L+LHAR +  P P GG  +++ APLP 
Sbjct: 362 RRGSGTIRDPASAAAWRARRSLALADDDGGGVPLHLHARSLRFPKPSGGDVVRVVAPLPP 421

Query: 314 HMVKTWDSLGFKYD-RNLYIKR 334
           H+    + LG K    N + +R
Sbjct: 422 HLASALERLGVKVSVENGFRRR 443


>gi|50545681|ref|XP_500379.1| YALI0B01276p [Yarrowia lipolytica]
 gi|49646245|emb|CAG82596.1| YALI0B01276p [Yarrowia lipolytica]
          Length = 337

 Score =  128 bits (323), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/264 (21%), Positives = 115/264 (43%), Gaps = 24/264 (9%)

Query: 21  LDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           LD      +       +L++ + +G +++    ++  +++            +   H+ K
Sbjct: 33  LD-VLSTEFSSVYPSDHLRQTIDAGNIKL----IR-RDKLSEPAT-EYTDWESLSTHVFK 85

Query: 80  EQKILDSSVNLTKHS----DFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLK 134
              IL+S V+  + +    D     +++E+  + V +KP GI V   G  +   +   LK
Sbjct: 86  NGSILESRVHRHEPAVPTRDEKPIRIVFENDALVVVDKPGGIPVHPTGKYLFNSVKEILK 145

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
              ++  ++    HRLD+ T+G+LV A+T  +  H+T+    R  +K Y + V G     
Sbjct: 146 H--ETGLEELYPAHRLDKNTTGVLVFAKTSESVNHVTQQIMSRSAKKEYLARVKGRFPPG 203

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +    + +++ +         +K+N +  +   +  +V     +    +   P TGR HQ
Sbjct: 204 RVETHHPVVENT---------IKRNVQPKDAHTAFERVAYDEHRDLSIVRCLPSTGRNHQ 254

Query: 255 LRVHALHMGCPIVGDHKYCANFKG 278
           +R H LH+G PI  D +Y     G
Sbjct: 255 IRQHLLHLGYPIENDREYNPELAG 278


>gi|17534965|ref|NP_493778.1| hypothetical protein K07E8.7 [Caenorhabditis elegans]
 gi|3915497|sp|O16686|YK27_CAEEL RecName: Full=Uncharacterized protein K07E8.7
 gi|2315726|gb|AAB66153.1| Hypothetical protein K07E8.7 [Caenorhabditis elegans]
          Length = 432

 Score =  128 bits (323), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 53/257 (20%), Positives = 103/257 (40%), Gaps = 28/257 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
            F   +   N    +   + G++ V+ ++    +  +++G   R+    +   H I++  
Sbjct: 90  VFSGEFLSTNRNYAKIACKMGRIYVNGEQMTDVDYVMRNGD--RVEHWAHRHEHPIRD-- 145

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                         L   ++ E   ++V  KP  + V      A H    L     ++G+
Sbjct: 146 --------------LPIRVISETDDLFVVEKPPSLPVHTCGQYAIH--TVLGQLRVNEGR 189

Query: 143 K-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
              R+ HRLD+ TSG+L+ A+          + +     K Y   V G+  ++++     
Sbjct: 190 TGLRVLHRLDRATSGVLLFAKNYETDLEFKTTLKQGEWSKEYICKVDGVFPDEEQVCEQP 249

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           +     +    +  V+ + K A    S F+ +         +++   TGRTHQ+RVH+  
Sbjct: 250 IG--PLVISMGIQCVRPDGKDAK---SRFRKLWSDG-TQSVVQVHIETGRTHQIRVHSQF 303

Query: 262 MGCPIVGDHKYCANFKG 278
           +G PI GD  Y +   G
Sbjct: 304 LGHPIAGDQIYNSAVWG 320


>gi|313904372|ref|ZP_07837749.1| pseudouridine synthase [Eubacterium cellulosolvens 6]
 gi|313470708|gb|EFR66033.1| pseudouridine synthase [Eubacterium cellulosolvens 6]
          Length = 237

 Score =  128 bits (323), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/220 (25%), Positives = 94/220 (42%), Gaps = 17/220 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ----KPRLTHRLDQETS 155
            +L E        KP+G++V+  +     ++  +  ++  K         + +RLDQ   
Sbjct: 2   RVLQETDSYIAVYKPSGLAVESRALGRRTLENEIMKYLALKSPGRKTYVAIINRLDQPVE 61

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLV---------WGIPKNKKECIA--NWLLK 204
           GI++ A+T+  A  L+E  +  RI+K Y ++V             K ++E +A  ++LLK
Sbjct: 62  GIVLAAKTQKGAARLSEQLQAHRIKKHYLAVVRVTEDTASQIRTVKEQREEVALTDYLLK 121

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                     VV +   G+  A   ++V +        LE+   TGR HQ+RV   H G 
Sbjct: 122 DGKTN--TTEVVAEGTTGSRRAELRYRVREILDDGRALLEIDLLTGRHHQIRVQLSHAGL 179

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           PI GD KY             N L L A  +    P+ G+
Sbjct: 180 PIAGDRKYGGEITETAGIGAGNSLALCASELAFSDPDSGK 219


>gi|323486215|ref|ZP_08091543.1| ribosomal large subunit pseudouridine synthase [Clostridium
           symbiosum WAL-14163]
 gi|323400433|gb|EGA92803.1| ribosomal large subunit pseudouridine synthase [Clostridium
           symbiosum WAL-14163]
          Length = 272

 Score =  128 bits (323), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 56/257 (21%), Positives = 102/257 (39%), Gaps = 52/257 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG------------------Q 142
           ++YED  I V  KPAG+  Q   G    +   +K+ +                       
Sbjct: 4   IIYEDHDILVAEKPAGLESQASRGFEPDMVSEIKNHLKRAELSRLSTKPSTKSSTRPVEP 63

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              + HRLD+   GI+V A+ + AA  L++  +  R++KIY ++V G   +      ++L
Sbjct: 64  YVGVIHRLDKPVGGIMVYAKNQKAAASLSKQVQDGRMKKIYNAVVCGKLVDIVGNYVDYL 123

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHA 259
           LK      ++  VV ++   +  A   ++ +D      ++   +E++  +GR HQ+RV  
Sbjct: 124 LKDGR--NNFSFVVDKDTPDSRRAELVYRALDVKTEEEREISLVEIELLSGRHHQIRVQF 181

Query: 260 LHMGCPIVGDHKYCANFKGNFTSP----------------------------IQNKLYLH 291
              G P+ GD KY   + G   +                              + +L L 
Sbjct: 182 AAHGNPLWGDGKYNPEWGGTLPAGERTHADRHTGAKQGSGHAAKVQSSRGRRGERELALA 241

Query: 292 ARYMDLPHPEGGR-LQI 307
           A  +   HP  G+ ++ 
Sbjct: 242 AVKLSFVHPSTGKNMEF 258


>gi|88797158|ref|ZP_01112748.1| probable pseudouridine synthase [Reinekea sp. MED297]
 gi|88780027|gb|EAR11212.1| probable pseudouridine synthase [Reinekea sp. MED297]
          Length = 214

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 59/221 (26%), Positives = 99/221 (44%), Gaps = 22/221 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +L      +V  KP G +VQ  +         +  W++ +G      HRLD+ TSG+
Sbjct: 5   EPTILTATDAYFVIVKPTGWTVQRDA-----QAPSVLEWLNDQGHTAFPVHRLDKPTSGL 59

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+VART  A + L+  F   R++K Y ++    P+ K+  +      +  +        K
Sbjct: 60  LLVARTTEANRALSLGFAEGRVEKTYLAISDRRPRKKQGWV------RGDMAPSRRSQWK 113

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              +  N AI+ F+ +     +  ++ + P TG+THQLRV    +G P++GD  Y     
Sbjct: 114 LLREQNNPAITRFRSVSLDDGERGFV-LYPKTGKTHQLRVALKSLGSPMLGDTLYGGTPA 172

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITA-PLPAHMVK 317
                   ++LYLHA  +     EG RL   A P+     +
Sbjct: 173 --------DRLYLHAWRLAFDF-EGERLSYQADPIDDKFTR 204


>gi|325962091|ref|YP_004239997.1| 23S RNA-specific pseudouridylate synthase [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323468178|gb|ADX71863.1| 23S RNA-specific pseudouridylate synthase [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 327

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 49/266 (18%), Positives = 99/266 (37%), Gaps = 20/266 (7%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPA 115
           +R  +G++V    +    +  +++   +    +L   +     I +L++D  + V +KP 
Sbjct: 45  DRFDAGEIVGEGGIPLDRSTPLQDHTFIWYYRSLPPETRIPVEISILHQDHHLLVVDKPH 104

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +    G G        ++     +       HRLD+ T+G+L+ +            F 
Sbjct: 105 FLPTTPG-GTYIQESALVRLRNQLELPDLIPMHRLDRMTAGVLLFSTNPQTRGKYQVLFE 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R++QK Y  +    P      +   ++ ++ +     +++ +   G   A +  + ++ 
Sbjct: 164 KRQVQKEYECVSAAEPAPGHAAVDFPVVVRNRMTKSRSYLLAEVVDGEPNAETRIERLET 223

Query: 236 FAQKFCW-----------------LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           F                         ++PHTG+THQLRVH   +G  I+ D  Y      
Sbjct: 224 FDAGTSLGAAGAAAAPGDPARLARYRLEPHTGKTHQLRVHMASLGLGIINDAFY-PELLD 282

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGR 304
                    L L AR +    P  G+
Sbjct: 283 KAPDDYGKPLQLLARGIRFVDPITGK 308


>gi|73985013|ref|XP_541778.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 3 [Canis familiaris]
          Length = 404

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 63/273 (23%), Positives = 106/273 (38%), Gaps = 44/273 (16%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQKPRLTHRLDQ 152
           D L++ ++ +   +   NKP G+ V G  G          L   +  + ++  +     +
Sbjct: 130 DALRAAVVDQKGPLVTLNKPPGLPVTGKPGELTLFSVLPELSQSLGLRDRELHVVQASGK 189

Query: 153 ETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           ETSG+++++     A HL +    S R RR    YW++  GIP   +  I   L  +   
Sbjct: 190 ETSGLVLLSSCPQTASHLQKFFIYSRRARRPTATYWAITDGIPATSEGNIQAALKLEHID 249

Query: 209 GGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           G D V  VK   +     G    +SHF V+         +++QP T    QL+VH +   
Sbjct: 250 GVDLVIPVKSPSRKDFQEGVKRTLSHFHVV-AMGSGCALVQLQPLTVFPSQLQVHMVLQL 308

Query: 264 CPIVGDHKYCAN----FKGNFTSPIQN----KLYLHA---RYMDLPH------------- 299
           CP++GDH Y A         F  P ++    +        R + L               
Sbjct: 309 CPVLGDHTYSARVGTVLGQRFLLPAESTKPQRQVPDEALLRRLRLTPSQAAQLPLHLHLH 368

Query: 300 --------PEGGRLQITAPLPAHMVKTWDSLGF 324
                   P    +++ APLP +  ++   LG 
Sbjct: 369 CLHLPGMRPREAPMKLLAPLPPYFSRSLQCLGL 401


>gi|319424672|gb|ADV52746.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           putrefaciens 200]
          Length = 229

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 55/197 (27%), Positives = 88/197 (44%), Gaps = 19/197 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +++   V +K   +      G A    G +       G K    HRLD  TSG+L++
Sbjct: 4   IIADEADFLVISKFPKVHFHSQDGTA----GVVAQIEQDLGIKLFAVHRLDTPTSGLLIL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++ AAA+  TE F   ++QK Y +L  G PK K+  +   + K          + K   
Sbjct: 60  AKSTAAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIGDMAK------SRRSMFKLLR 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  +           ++PH+G+THQLRV    +G PI+GD  Y        
Sbjct: 114 TKENPAITQFFSV-SVGDGLRLYLLKPHSGKTHQLRVALASLGVPILGDELYGG------ 166

Query: 281 TSPIQNKLYLHARYMDL 297
              + ++ YLHA  +  
Sbjct: 167 --AVADRCYLHAYCLHF 181


>gi|239940134|ref|ZP_04692071.1| putative ribosomal pseudouridine synthase [Streptomyces roseosporus
           NRRL 15998]
 gi|239986622|ref|ZP_04707286.1| putative ribosomal pseudouridine synthase [Streptomyces roseosporus
           NRRL 11379]
          Length = 292

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 54/215 (25%), Positives = 87/215 (40%), Gaps = 9/215 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            +        ++Y D +I V +KP  ++    G  I       L+  +D      +  HR
Sbjct: 70  AEEPVPFPVGVVYRDERIVVADKPHFLATMPRGRHITETAVARLRRELDL--PVLQPAHR 127

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+++              FR RR++K Y ++    P      +A     +S I 
Sbjct: 128 LDRLTAGLVLFVVRSQDRGAYQTLFRDRRVRKEYEAVAPYDP-----GVALPRTVRSRIV 182

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +   +  + E G   + SH ++++          + P TGRTHQLRVH   +G PIV D
Sbjct: 183 KERGVLAAREEPGEANSESHVELVERRG-ALGRYRLVPATGRTHQLRVHMNALGLPIVHD 241

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             Y               L L AR ++   P GG 
Sbjct: 242 PLYPVVAAEASADDFSRPLQLLARVLEFTDPVGGE 276


>gi|217033961|ref|ZP_03439384.1| hypothetical protein HP9810_883g31 [Helicobacter pylori 98-10]
 gi|216943594|gb|EEC23042.1| hypothetical protein HP9810_883g31 [Helicobacter pylori 98-10]
          Length = 242

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 63/288 (21%), Positives = 113/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V +  K++                       ++  +++  ++  
Sbjct: 12  ENISHKKAKALIDLGLVSIGGKKL-----------------------MVARKELPKNTHF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ R          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVVLLVRENSEFHLKAKKAFKNRAVKKEYLALAQGIIEEEQEINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKISLL-----EYEFEAIPPKEFE 241


>gi|322514744|ref|ZP_08067770.1| ribosomal large subunit pseudouridine synthase C [Actinobacillus
           ureae ATCC 25976]
 gi|322119339|gb|EFX91455.1| ribosomal large subunit pseudouridine synthase C [Actinobacillus
           ureae ATCC 25976]
          Length = 216

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 59/213 (27%), Positives = 95/213 (44%), Gaps = 19/213 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  + ++     V +KP G+SV          +   +     + ++  L HRLD+ TSG+
Sbjct: 4   KLTICFQHHDFVVIDKPVGVSVHKDEEAVGLTEKLAEQL---QVEQVWLVHRLDKVTSGL 60

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+    + AA +    F   +I+K YW+L    PK K+  I + + K S  G   +   K
Sbjct: 61  LIFTLNKQAAVNFYHLFEPHKIEKTYWALSNQKPKKKQGKIISDMQK-SRNGAWKLCHSK 119

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           QN      A++ F              +QP TG+THQLRV    +G PI+GD  Y  +  
Sbjct: 120 QN-----PAVTQFNS-HSVEPNLRHFILQPKTGKTHQLRVAMKSLGSPILGDQLYTGSEA 173

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                   +++YLHA  +   + +G    I +P
Sbjct: 174 --------DRVYLHAYQLKFEY-QGESFCIQSP 197


>gi|182415562|ref|YP_001820628.1| pseudouridine synthase [Opitutus terrae PB90-1]
 gi|177842776|gb|ACB77028.1| pseudouridine synthase [Opitutus terrae PB90-1]
          Length = 255

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 59/239 (24%), Positives = 99/239 (41%), Gaps = 19/239 (7%)

Query: 99  SILLYEDSK-IYVFNKPAGISVQGGSG-------IAYHIDGFLKSWV-----DSKGQKPR 145
             +L  D   +   +KPAG+      G       +  H D   + +V      +  Q+  
Sbjct: 18  VEILERDPNGLLALSKPAGVLSHPNEGKDQPRSLLTCHFDAVAECYVWTPEGAATSQRWW 77

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L +RLD  TSG++++A     A+ +   F+ +++ K+Y +LV+G P    E   + ++  
Sbjct: 78  LLNRLDSATSGVILLAANEELAREIRAQFKRKQVTKVYQALVFGKPPRPVELWRD-VVAV 136

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +  GG            A   +S  +           L+++P TGR+HQLRV       P
Sbjct: 137 TKQGGQIRTTAGAGRVPAECRMSVVRSRGVGEGALALLQLEPRTGRSHQLRVQCAKRHVP 196

Query: 266 IVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGGRLQI---TAPLPAHMVKTW 319
           IVGD  Y              + +L+LH+      +   GR  +    APLPA   + W
Sbjct: 197 IVGDQTYGDFRHNREFAKRTGEKRLFLHSLATRFEYAWKGRTHVFAAQAPLPAEFGQVW 255


>gi|156538671|ref|XP_001607742.1| PREDICTED: similar to conserved hypothetical protein [Nasonia
           vitripennis]
          Length = 272

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 47/206 (22%), Positives = 88/206 (42%), Gaps = 16/206 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-----GQKPRLTHRLDQETS 155
           +L++     + NKP  + +   +     +   ++    +        +    HRLD  TS
Sbjct: 22  ILHQSDNFLIVNKPYDMVINSNNPSVKSVQLIIREMFPNLVNPNLYHEFYFVHRLDYATS 81

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK-SHIGGDYVH 214
           G++ +A  + +AQ  + +F  R ++K Y +LV G        I   +      + G+   
Sbjct: 82  GVMCLALNKQSAQAASSAFEERTVRKYYLALVHGHIDKYSMVIDIPIGHDVRELNGNRKM 141

Query: 215 VVKQNE--KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
             K ++  + A  + +   V++      +    + + P TGR HQLRVH  H+G  IVGD
Sbjct: 142 CTKDDDFCEKARKSCTALLVLEKGYIDDRPVTKVLLYPKTGRRHQLRVHCAHIGHIIVGD 201

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYM 295
           + Y        T    ++ +LHA  +
Sbjct: 202 YTYSGK-----TDTKPHRTFLHAFRL 222


>gi|311740341|ref|ZP_07714170.1| RNA pseudouridine synthase [Corynebacterium pseudogenitalium ATCC
           33035]
 gi|311304525|gb|EFQ80599.1| RNA pseudouridine synthase [Corynebacterium pseudogenitalium ATCC
           33035]
          Length = 336

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 59/306 (19%), Positives = 116/306 (37%), Gaps = 33/306 (10%)

Query: 26  KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILD 85
           ++ +P  +   LQ    SG+V                 V+R    +   + + +++ +  
Sbjct: 53  RHRHPDDDASALQARFDSGEV-----------------VLRNQTKLRPDSILSQDEDVFF 95

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKP 144
             +   +        +L+ED  I V +KP  ++       I       L+    +   + 
Sbjct: 96  YRMPAPETPVPYDVPILFEDEHILVADKPPFMATMPRARHIVQTATVQLRRM--TGNDEL 153

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRLD+ TSGIL+  + R         F  +++ K Y ++       +      W   
Sbjct: 154 APAHRLDRLTSGILLFTKHRDVRGAYQTLFAEKKVHKTYQAIAEYR---RFPTPLQWASH 210

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM--------QPHTGRTHQLR 256
            +   G+    +      A   ++   +ID    +    E+        +P TG+THQLR
Sbjct: 211 LTKTPGEIQGRIGDGSPNAFTTLAAVDLIDNAPYEKIHGELPQLGKYTLKPTTGKTHQLR 270

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
           +H    G PI+GD  Y   F  +    ++  ++L A +++   P  G+  +  + LP + 
Sbjct: 271 LHMWQAGIPILGDPVYPEIFPEDAED-MRIPMHLTATHIEFTDPLSGKYREFESALPLYT 329

Query: 316 VKTWDS 321
            +  D 
Sbjct: 330 HRLIDQ 335


>gi|312133201|ref|YP_004000540.1| rlua2 [Bifidobacterium longum subsp. longum BBMN68]
 gi|322690629|ref|YP_004220199.1| ribosomal pseudouridine synthase [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|311772402|gb|ADQ01890.1| RluA2 [Bifidobacterium longum subsp. longum BBMN68]
 gi|320455485|dbj|BAJ66107.1| putative ribosomal pseudouridine synthase [Bifidobacterium longum
           subsp. longum JCM 1217]
          Length = 254

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 60/252 (23%), Positives = 95/252 (37%), Gaps = 31/252 (12%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + +     +  +LYED +I V +KP  ++     G+ Y     ++             HR
Sbjct: 2   IDEPHIPFEMDVLYEDERIIVVDKPHFLATMP-RGMWYRQTALIRLRERLGEPDITPAHR 60

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN------- 200
           LD+ T+G+LV  R  A        F+ R+  K+Y   +    I + +   I         
Sbjct: 61  LDRMTAGVLVFVRDPACRGAYQMLFQNRQAVKVYECLAPCRPISRPRFGTIMQVEPPRPF 120

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-------------------AQKFC 241
            LL++SHI  ++  +    E G   A +  +  D                         C
Sbjct: 121 PLLRRSHITKEHGTMAAFEEPGLANAETLIERGDLCFPPADGRWREAPEGGPHPGNHPIC 180

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
              + P TG+THQLRVH   +G PIVGD  Y    +          L L AR +    P 
Sbjct: 181 RYTLHPRTGKTHQLRVHMNSLGLPIVGDDFY-PRIQTRPYDDFSQPLQLVARMLRFTDPI 239

Query: 302 GGRL-QITAPLP 312
            G   +  + +P
Sbjct: 240 TGEKREFVSRVP 251


>gi|302755728|ref|XP_002961288.1| hypothetical protein SELMODRAFT_75008 [Selaginella moellendorffii]
 gi|300172227|gb|EFJ38827.1| hypothetical protein SELMODRAFT_75008 [Selaginella moellendorffii]
          Length = 318

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 70/298 (23%), Positives = 115/298 (38%), Gaps = 44/298 (14%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IP         I+ ++ L +  ++          ++++D  I V NKP G+       + 
Sbjct: 27  IPVTPLTGAKEIEYERALVAEASMKSGPAITIDDVVFQDEWILVINKPCGVYS---EHVL 83

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L            L +RLD++TSGI+V+AR + AA  LT  F+ R ++K Y +L
Sbjct: 84  VSVPSLLGDSYSPHRGFFHLANRLDRDTSGIIVIARDKVAAGKLTNIFKSRELRKSYVAL 143

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG------ANYAISHFKVI------- 233
             G     K  +      KS  G   V+     E+            +  +VI       
Sbjct: 144 CVGKAPEWKRAVVESGHGKSRRGCWRVYSKHDVERSLPDGSVVKDMATKIEVIPSSLDEV 203

Query: 234 ---------------------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                                +       ++   P TGRTHQ+R+H   +G P+VGD KY
Sbjct: 204 KDGEEDDREQRIVVEAKMVDPEPGTGDEVFIRAVPLTGRTHQIRLHCQFLGLPLVGDVKY 263

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRN 329
                 N      +  +LH+  +   HP  G  +++ AP P+   K    L F+  +N
Sbjct: 264 GGPLHWNGEKCQSH--FLHSESIAFQHPMTGEVVEVIAPHPSWAAK----LKFQASKN 315


>gi|182439619|ref|YP_001827338.1| putative ribosomal pseudouridine synthase [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|178468135|dbj|BAG22655.1| putative ribosomal pseudouridine synthase [Streptomyces griseus
           subsp. griseus NBRC 13350]
          Length = 312

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 54/215 (25%), Positives = 88/215 (40%), Gaps = 9/215 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            +        ++Y D +I V +KP  ++    G  I       L+  ++    +P   HR
Sbjct: 90  PEEPVPFPVGVVYRDERIVVADKPHFLATMPRGRHITETAAARLRRELELPALQP--AHR 147

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+++              FR RR++K Y +L    P      +A     +S I 
Sbjct: 148 LDRLTAGLVLFVVRPEDRGAYQTLFRDRRVRKEYEALAPYDPD-----VALPRTVRSRIV 202

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +   +  + E G   + S  ++++          + P TGRTHQLRVH   +G PIV D
Sbjct: 203 KERGVLAAREEPGEANSESRVELVERRG-GVGRYRLLPATGRTHQLRVHMNALGLPIVHD 261

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             Y    +          L L AR ++   P GG 
Sbjct: 262 PLYPVVAEEGAPDDFSRPLQLLARVLEFADPVGGE 296


>gi|126640196|ref|YP_001083180.1| dual specificity pseudouridine synthase [Acinetobacter baumannii
           ATCC 17978]
          Length = 184

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 58/193 (30%), Positives = 94/193 (48%), Gaps = 13/193 (6%)

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G    +H   +L+  V  K    ++THRLD  TSG+L+ A+ R A   +++ F+ R ++K
Sbjct: 2   GRLPEHHDSAYLR--VLEKFPLAKVTHRLDMATSGLLMFAKHRDAEVAVSKMFQARTVKK 59

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KF 240
            Y +LV G  K +       +    +     VH      +   +A + F+ +   A    
Sbjct: 60  HYIALVQGQVKQEGSVEVPLITDWENRPRQIVHF-----ELGKHAKTLFQPLVYDATTDQ 114

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             + ++P TGR+HQLRVH +H+G PI+GD  Y    K        N++ LHA Y+   HP
Sbjct: 115 SRVLLEPVTGRSHQLRVHMMHIGHPIMGDKLYHPEPK----RFHLNRMALHAAYLAFQHP 170

Query: 301 EGGR-LQITAPLP 312
             G  + I + +P
Sbjct: 171 LKGTDVVIESQVP 183


>gi|255321341|ref|ZP_05362501.1| pseudouridine synthase [Campylobacter showae RM3277]
 gi|255301494|gb|EET80751.1| pseudouridine synthase [Campylobacter showae RM3277]
          Length = 252

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 68/310 (21%), Positives = 121/310 (39%), Gaps = 65/310 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        I+    ++++ +G V    +R+                            +
Sbjct: 8   KLLAIQ-EGISNNEAKELIDAGLVSAKGQRI-------------------------AVAR 41

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
            + S+          +  +++ED  +   +KPA ++ +  S I                 
Sbjct: 42  AMMSAATKFNVQKLPRPSVIFEDENLIAVDKPAFLTSEKVSEI----------------Y 85

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           K  L HRLD+ETSG+L++ +     +   E F+  R++K Y + V  I   ++  I   +
Sbjct: 86  KFPLLHRLDKETSGVLLLVKNEEFQKKAIEEFKNCRVKKEYVAAVKSIVS-EEFSINEPI 144

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           +   + GG +  +          A SH   +   A K   ++++  TGRTHQ+RVH  H 
Sbjct: 145 ITLKNRGGAFSKI----SPNGKEAFSHVIPV-MVAGKKSLVKVEIKTGRTHQIRVHLNHA 199

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G  IVGD KY  N           ++YLHA  ++L        +  + L +      + L
Sbjct: 200 GYGIVGDEKYAKNKAA--------RMYLHAYKIELL-----GYKFRSNLSSDF----NRL 242

Query: 323 GFKYDRNLYI 332
           GF+  RN  I
Sbjct: 243 GFEISRNFEI 252


>gi|149923247|ref|ZP_01911658.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
 gi|149815904|gb|EDM75423.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
          Length = 401

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/334 (17%), Positives = 104/334 (31%), Gaps = 81/334 (24%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            V  ++   R D       P ++    + + R+G +RVD  +   + R + GQV+R+   
Sbjct: 18  TVTAEDAGERADVILGRRVPALSRRQARSLARAGHLRVDGLKRPPSTRAREGQVLRL--- 74

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                       + D   +    +      +L E       +KPAG+       +     
Sbjct: 75  -----------ALDDEPSSPELAARLDALEVLAETPDFVYVHKPAGVHTVA---LTPQQP 120

Query: 131 GFLKSWVDSKGQKP----------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           G L + V  +  +              HRLD+ TSG++  AR+        ++F   +++
Sbjct: 121 GVLATAVAERWPECAGASEDPREGGAVHRLDRPTSGVVAFARSPEIWARARKAFSAEQVR 180

Query: 181 KIYWSL--------------------------------VWGIPKNKKE------------ 196
           K Y ++                                V   P+ +              
Sbjct: 181 KRYLAVCLDLGARERGAAMTWPPALPEGGLRGWVLPAEVEAHPRAELGSLAGIDTATATH 240

Query: 197 ---CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-----CFAQKFCWLEMQPH 248
               +   L + +       H   + +     A S    +          +   L ++  
Sbjct: 241 PSFRVRAPLGRVAREAEIPSHTAVRLD--GQRASSVVHPLAQASATSTGAQPWLLALELE 298

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
           TGR HQ R H   +G PIVGD  Y         +
Sbjct: 299 TGRRHQARCHLAWIGLPIVGDSLYGPRAGATPPT 332


>gi|223998226|ref|XP_002288786.1| hypothetical protein THAPSDRAFT_261746 [Thalassiosira pseudonana
           CCMP1335]
 gi|220975894|gb|EED94222.1| hypothetical protein THAPSDRAFT_261746 [Thalassiosira pseudonana
           CCMP1335]
          Length = 383

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 58/267 (21%), Positives = 105/267 (39%), Gaps = 39/267 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQK 82
              + +   +   +Q+++ +  ++V+   V K +  +Q    V        + H  +   
Sbjct: 27  VLSSEFHEFSLKWMQQLIDARLIKVNGVPVSKSDGLLQKEDTVE------RVVHWHEPPI 80

Query: 83  ILDSSVNLTKHSDFLKSI----LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           I+  +++LTKHS    +     +LY        NKPA + V       Y+ +  L     
Sbjct: 81  IVPETISLTKHSLPDTANCGNGILY------CINKPASVPVYPSGP--YYSNSLLMMVEA 132

Query: 139 SKGQKPR---LTHRLDQETSGILVVARTRAAAQHLT-------ESFRMRRIQKIYWSLVW 188
            +G  P+     HR+D+ TSG+L+       ++ +        E      I+K+Y + V 
Sbjct: 133 QEGLPPKSLVPCHRIDRATSGVLLCTIDSKVSRAVQGRMASRNEVGTQHPIKKLYLARVQ 192

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQP 247
           G   +    +           G    + +   +    AIS F+++   A      +   P
Sbjct: 193 GKFPDPSSSV---------PVGAASMMHRSVSRDGKQAISRFRLLSYDAATDQSLVSCCP 243

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCA 274
            TGR HQLRVH   +G PI  D +Y  
Sbjct: 244 ITGRGHQLRVHLQFIGLPIHNDVEYGG 270


>gi|325995626|gb|ADZ51031.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 2018]
 gi|325997222|gb|ADZ49430.1| putative RNA pseudouridylate synthase [Helicobacter pylori 2017]
          Length = 293

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 64/294 (21%), Positives = 114/294 (38%), Gaps = 29/294 (9%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N                    + K Q I      +   
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----------------QAVRKSQIIQGVVSLIYFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +  +  L++E      F+KPA I         +  +  L       G+     HRLD E
Sbjct: 64  PNEKQERLVFEAKDFGAFDKPAQIYTHPKGYFDH--ESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+++  +T  + + L   F  ++++K Y  L  G+  +K   I   +L   +I  D +
Sbjct: 122 TSGLVLAGKTLQSTKDLKALFMQKKVKKTYLVLTHGLV-DKSIIIDKPILTPENIQKD-L 179

Query: 214 HVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +  Q       +I+  + +          L++ P TGRTHQ+R+H   +   IVG+  Y
Sbjct: 180 RIRSQISPLGKPSITLVEPLSYNPFLDISLLKITPLTGRTHQIRLHLSSVNHRIVGEGLY 239

Query: 273 CANFKGNFTSPIQNK------LYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
               +         +      L LHA  ++    +G   +I +P+P   +    
Sbjct: 240 GVADENAREYLQLKRENNAPTLMLHAASLEFEF-KGAHYKIASPMPKRFMPFLK 292


>gi|183981253|ref|YP_001849544.1| pseudouridine synthase [Mycobacterium marinum M]
 gi|183174579|gb|ACC39689.1| pseudouridine synthase [Mycobacterium marinum M]
          Length = 288

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 56/262 (21%), Positives = 99/262 (37%), Gaps = 14/262 (5%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH-SDFLKSILLYEDSKIYVF 111
                ++ +G+VV     I     + +    +    +L +      +  +L++D  I V 
Sbjct: 34  AAARAKVLAGEVVDAAGAIVDTATVAEPGSYVYLYRDLPEEVPVPFEMPVLHQDEDIVVA 93

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   +    +    HRLD+ T+G+L+    R       
Sbjct: 94  DKPHFLATMP-RGRHVAQTALVRLRCELGLPELSPAHRLDRLTAGVLLFTTRRELRGRYQ 152

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    ++K Y +            +A   + +S I     H+    E G   A +  +
Sbjct: 153 TLFARGAVRKTYLARAA-----VDADLAFPRVIRSRIVKRRGHLQAVCEPGEPNAETLVE 207

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLY 289
           +I           + P TGRTHQLRVH   +G PI GD  Y      +    S   + L 
Sbjct: 208 LISPEG----LYRLTPRTGRTHQLRVHMASLGLPIFGDPLYPNVIPESPHDLSDFSSPLS 263

Query: 290 LHARYMDLPHPEGG-RLQITAP 310
           L A+ ++   P  G R +  +P
Sbjct: 264 LLAQRIEFEDPLSGSRREFVSP 285


>gi|213417523|ref|ZP_03350665.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 122

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 47/128 (36%), Positives = 73/128 (57%), Gaps = 8/128 (6%)

Query: 1   MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K   ++
Sbjct: 1   MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           +SG  VRIPPV       + E++    S +L K +  L  ++LYED  I V NKP+G +V
Sbjct: 61  ESGDEVRIPPVR------VAEREEEAVSPHLQKVA-ALADVILYEDDHILVLNKPSGTAV 113

Query: 120 QGGSGIAY 127
            GGSG+++
Sbjct: 114 HGGSGLSF 121


>gi|152983735|ref|YP_001348604.1| RNA pseudouridine synthase family protein [Pseudomonas aeruginosa
           PA7]
 gi|150958893|gb|ABR80918.1| RNA pseudouridine synthase family protein [Pseudomonas aeruginosa
           PA7]
          Length = 275

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 56/297 (18%), Positives = 108/297 (36%), Gaps = 30/297 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +P I+       +R G+V   + + +      + G  +R+                
Sbjct: 5   LCARFPAIDRDTWLARMRRGRVLDAEGRALDARTPYREG--LRVHYFREVP--------- 53

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +     ++ +L++D  + V +KP  + V    G  Y     L     S G +
Sbjct: 54  -------VETPIPFEARILHQDEHLLVADKPHFLPVMPAGG--YVEQTLLARLARSTGNR 104

Query: 144 -PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +    +       FR RRI K Y ++   +P+     +   L
Sbjct: 105 ELVPLHRIDRHTAGLVLFSTNPGSRGRYQALFRERRIDKYYEAIAPALPR-----LDFPL 159

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L+K+ +         +   G   + +  +V +   + +    + P TG+ HQLRVH   +
Sbjct: 160 LRKTRLVPGEPFFRMREGDGEPNSETRIEVAERNGR-WWRYRLYPVTGKKHQLRVHLAAL 218

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNK-LYLHARYMDLPHPEGGRLQ-ITAPLPAHMVK 317
           G  I  D  Y        +     + L L AR +    P  G  +   + L     +
Sbjct: 219 GAAIQNDGFYPGLLDAEDSPDDYRRPLKLLARGLRFDDPLSGEARVFESELRLEWQE 275


>gi|77460185|ref|YP_349692.1| pseudouridine synthase [Pseudomonas fluorescens Pf0-1]
 gi|77384188|gb|ABA75701.1| putative ribosomal subunit pseudouridine synthase [Pseudomonas
           fluorescens Pf0-1]
          Length = 297

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 55/292 (18%), Positives = 103/292 (35%), Gaps = 26/292 (8%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
              H+  I        +  G+V +D +          GQ + +         I   +++ 
Sbjct: 31  LCEHFSAIGRDQWLDRIARGRV-LDGQ----------GQPIALDLPYKEGLRIHYFREVP 79

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           D        S      +LY D  + V +KP  + V    G         +          
Sbjct: 80  DEKPIPVVES------ILYADDHLVVADKPHFLPVTPA-GEYVEQTLLRRLIRRLDNPHL 132

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HR+D+ T+G+++ +            F  R+I+K Y ++   +P      +   L+ 
Sbjct: 133 VPLHRIDRHTAGLVIFSANPQTRSAYQSLFPTRQIEKRYEAIAAALP-----GLDFPLVH 187

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           KS +         Q   G +   +  +V +   + + +  + P TG+ HQLRVH   +G 
Sbjct: 188 KSRMVDGEPFFRMQEGPGVSNTETAVEVREKNGELWRYG-LYPVTGKKHQLRVHMTALGA 246

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHM 315
            I  D  Y    K +      N L L A+ +    P  G++ +  + +    
Sbjct: 247 SICNDPFYPEVLK-DVEDDYANPLKLLAQGLRFIDPVTGQVREFESRITLDW 297


>gi|120597084|ref|YP_961658.1| pseudouridine synthase Rlu family protein [Shewanella sp. W3-18-1]
 gi|120557177|gb|ABM23104.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           sp. W3-18-1]
          Length = 229

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 55/197 (27%), Positives = 88/197 (44%), Gaps = 19/197 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +++   V +K   +      G A    G +       G K    HRLD  TSG+L++
Sbjct: 4   IIADEADFLVISKFPKVHFHSQDGTA----GVVAQVEQDLGIKLFAVHRLDTPTSGLLIL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++ AAA+  TE F   ++QK Y +L  G PK K+  +   + K          + K   
Sbjct: 60  AKSTAAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIGDMAK------SRRSMFKLLR 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  +           ++PH+G+THQLRV    +G PI+GD  Y        
Sbjct: 114 TKENPAITQFFSV-SVGDGLRLYLLKPHSGKTHQLRVALASLGVPILGDELYGG------ 166

Query: 281 TSPIQNKLYLHARYMDL 297
              + ++ YLHA  +  
Sbjct: 167 --AVADRCYLHAYCLHF 181


>gi|330808393|ref|YP_004352855.1| ribosomal subunit pseudouridine synthase [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327376501|gb|AEA67851.1| putative ribosomal subunit pseudouridine synthase [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 296

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 53/280 (18%), Positives = 100/280 (35%), Gaps = 25/280 (8%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
              H+  I+       +  G+V +D            G+ +++         I   +++ 
Sbjct: 30  LCEHFSAISREQWLDRIARGRV-LDG----------EGKAIQVDLPYREGLRIHYFREVP 78

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           D        S      +LY D  + V +KP  + V    G         +          
Sbjct: 79  DEKPIPVVES------ILYADEHLVVADKPHFLPVTPA-GEYVEQTLLRRLIRRLDNPHL 131

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HR+D+ T+G+++ +            F  R+I+K Y ++   +P          + K
Sbjct: 132 VPLHRIDRHTAGLVLFSANPNTRSAYQSLFPTRQIEKRYQAIARALP----GLTFPRVHK 187

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              I G+    + Q   G     +  +V++   + + +  + P TG+ HQLRVH   +G 
Sbjct: 188 SRMIDGEPFFRM-QEGPGEPNTETAIEVLERNGELWRYG-LYPVTGKKHQLRVHMNALGA 245

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            I  D  Y  +   +      N L L A+ +    P  G+
Sbjct: 246 GICNDPFY-PDVLRDVEDDYSNPLKLLAQGLRFVDPVTGQ 284


>gi|302550275|ref|ZP_07302617.1| ribosomal pseudouridine synthase [Streptomyces viridochromogenes
           DSM 40736]
 gi|302467893|gb|EFL30986.1| ribosomal pseudouridine synthase [Streptomyces viridochromogenes
           DSM 40736]
          Length = 317

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 51/219 (23%), Positives = 87/219 (39%), Gaps = 11/219 (5%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTH 148
             +        +++ D  I V +KP  ++    GS +A      L+  +          H
Sbjct: 75  PDEVPVPFPLEVVHRDEHIVVADKPHFLATTPRGSHVAETALARLRRELGIPALTA--AH 132

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ T+G+++              FR RR++K Y ++    P      +A     +S I
Sbjct: 133 RLDRLTAGLVLFTVRLEDRGAYQTLFRDRRVRKEYEAVAPHDP-----GLALPRTVRSRI 187

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMGCP 265
             +   +  +   G   A+S  ++++  A          + P TG+THQLRVH   +G P
Sbjct: 188 VKERGVLTAREVAGEPNAVSRIELVEHRAAGSGGLARYRLVPGTGQTHQLRVHMTALGVP 247

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           I+GD  Y            +  L L AR ++   P  G 
Sbjct: 248 ILGDPLYPEVTAPVPAGDFRRPLQLLARTLEFTDPVTGE 286


>gi|89074028|ref|ZP_01160529.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           sp. SKA34]
 gi|89050166|gb|EAR55677.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           sp. SKA34]
          Length = 231

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 60/224 (26%), Positives = 90/224 (40%), Gaps = 29/224 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           L+Y+     V NK  GISV             L +  +  G +K  L HRLD+ TSG+L+
Sbjct: 4   LVYQHPDFLVINKHPGISVHKDDNDQP----LLAAVAEQTGDEKLYLIHRLDKMTSGLLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG---GDYVHVV 216
           + R + AA  L+ +F  R ++K Y ++                 +   IG          
Sbjct: 60  LGRNKEAASILSSNFAERVVEKFYVAI---------GTKKPKKKQVVVIGDMTRSRRSSW 110

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
           K      N AI+ F       +       +PHTG+THQ+RV    +G  I GD  Y    
Sbjct: 111 KLESTKENPAITQFFS-TAAGEGRRLFLCKPHTGKTHQIRVALRSVGSGITGDDIYG--- 166

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                +   ++ YLHA  +  P+ +G   +   P P    K W 
Sbjct: 167 -----TEASDRGYLHAYALSFPY-KGKTQRFICP-PTD-GKLWQ 202


>gi|291443564|ref|ZP_06582954.1| ribosomal pseudouridine synthase [Streptomyces roseosporus NRRL
           15998]
 gi|291346511|gb|EFE73415.1| ribosomal pseudouridine synthase [Streptomyces roseosporus NRRL
           15998]
          Length = 312

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 54/215 (25%), Positives = 87/215 (40%), Gaps = 9/215 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            +        ++Y D +I V +KP  ++    G  I       L+  +D      +  HR
Sbjct: 90  AEEPVPFPVGVVYRDERIVVADKPHFLATMPRGRHITETAVARLRRELDL--PVLQPAHR 147

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+++              FR RR++K Y ++    P      +A     +S I 
Sbjct: 148 LDRLTAGLVLFVVRSQDRGAYQTLFRDRRVRKEYEAVAPYDP-----GVALPRTVRSRIV 202

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +   +  + E G   + SH ++++          + P TGRTHQLRVH   +G PIV D
Sbjct: 203 KERGVLAAREEPGEANSESHVELVERRG-ALGRYRLVPATGRTHQLRVHMNALGLPIVHD 261

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             Y               L L AR ++   P GG 
Sbjct: 262 PLYPVVAAEASADDFSRPLQLLARVLEFTDPVGGE 296


>gi|229520732|ref|ZP_04410155.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TM
           11079-80]
 gi|229342287|gb|EEO07282.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TM
           11079-80]
          Length = 235

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 56/200 (28%), Positives = 86/200 (43%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +        D +     L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEVATQTGDGQ---LYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   AA  L++ F  R+++K Y ++    PK K+  I   + +        V+  +  
Sbjct: 60  LARNATAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A        +PHTG+THQ+RV    +G  IVGD  Y    K  
Sbjct: 118 ----NPAITQFFS-ATAAPGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYNTADKS- 171

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +   +
Sbjct: 172 ------DRGYLHAFALRFTY 185


>gi|114778309|ref|ZP_01453168.1| hypothetical protein SPV1_13252 [Mariprofundus ferrooxydans PV-1]
 gi|114551411|gb|EAU53967.1| hypothetical protein SPV1_13252 [Mariprofundus ferrooxydans PV-1]
          Length = 298

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 118/293 (40%), Gaps = 27/293 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +F+  +P I     Q  L +G++             + G ++           +   
Sbjct: 27  LD-FFEQRFPFIERAIWQHRLEAGKIT-----------DELGNIITTDTSFRPHARLRYF 74

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +++        +H    +  +L+++  I V +KP  + V  G          L     S 
Sbjct: 75  REVA------YEHPIPFREQILFQNDSILVADKPHFLPVTPGGSYVNEC--LLHRLKRST 126

Query: 141 G-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           G +     HRLD+ET+G+++    +   Q   + FR   I K Y ++     ++++    
Sbjct: 127 GLEHLVPAHRLDRETAGLVLFTVDKKQRQPWFDLFRHGAISKSYEAIAATPAESQQ---R 183

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            WL+ +S I      +  +N  G   A S  ++I+         E+QP TG+THQLR+H 
Sbjct: 184 EWLV-ESRIERGEPWIRFRNTVGEINARSRIRIIESKGS-LSRFELQPITGKTHQLRLHM 241

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPL 311
             +G  IVGD  Y             N L L A+ +    P  G++ Q  + L
Sbjct: 242 GLIGAHIVGDRFYPDYQSPTDPPSYDNPLQLLAKRLAFTDPVSGQMHQFESHL 294


>gi|227495588|ref|ZP_03925904.1| ribosomal pseudouridine synthase [Actinomyces coleocanis DSM 15436]
 gi|226830820|gb|EEH63203.1| ribosomal pseudouridine synthase [Actinomyces coleocanis DSM 15436]
          Length = 358

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 55/265 (20%), Positives = 97/265 (36%), Gaps = 22/265 (8%)

Query: 62  GQVVRIPPVINALNHIIK--EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           G+VV         +      E  I        + ++ +   +++  +   V NKP  I+ 
Sbjct: 90  GEVVDWWGNPQTWDTPATALENPIYIYRPATDEIAEHIHIPIVHRGNGWLVINKPKDIAS 149

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               G        +              HRLD+ TSG+L+            + F+ R++
Sbjct: 150 TP-RGSYIVRTATIALRRQEGNADLTPAHRLDRATSGLLLFTERPELRGMYQDLFQNRQV 208

Query: 180 QKIYWSLVWGIPKN-------KKECIAN-----WLLKKSHIGGDYVHVVKQNEKGANYAI 227
            K Y +    I  N        K  +       W+  +S I         Q+  G   A+
Sbjct: 209 TKTYRATAKAIDFNYIKSSALVKITVDPEEQPGWVKIESRIEKRPGDPGAQHAFGKINAV 268

Query: 228 SHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP- 283
           ++ + +       Q+F   E+QP TG+THQ+R+H   +G P+VGD  Y       F    
Sbjct: 269 TYLRPVKTVTIEGQQFVEYEVQPQTGKTHQIRLHFASLGAPLVGDPLYGGFNAAPFGLEK 328

Query: 284 ---IQNKLYLHARYMDLPHPEGGRL 305
                 +L+L A  ++   P+   +
Sbjct: 329 VPAGYQELHLEACRLEFKDPQTQEM 353


>gi|157377520|ref|YP_001476120.1| pseudouridine synthase Rlu family protein [Shewanella sediminis
           HAW-EB3]
 gi|157319894|gb|ABV38992.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           sediminis HAW-EB3]
          Length = 224

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 50/198 (25%), Positives = 85/198 (42%), Gaps = 19/198 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +++   V +K   +      G A    G +       G K    HRLD  TSG+L+ 
Sbjct: 4   IIADEADFLVISKSHDVHFHSQDGTA----GVMAQVEQDLGVKLFSVHRLDTLTSGLLLF 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++  AA   T+ F   ++QK Y ++  G PK K+  +   + K        +  ++   
Sbjct: 60  AKSSRAAAEFTQLFTEHKVQKYYVAIAKGKPKKKQGWVVGDMAKSRRSMYKLMRTME--- 116

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F      A+      ++P +G+THQLRV    +G PI+GD  Y        
Sbjct: 117 ---NPAMTQFFS-QSVAEGVRLYLLKPLSGKTHQLRVALASIGVPILGDRLYGGGEA--- 169

Query: 281 TSPIQNKLYLHARYMDLP 298
                ++ YLHA  +   
Sbjct: 170 -----DRGYLHAFSLSFI 182


>gi|170724937|ref|YP_001758963.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169810284|gb|ACA84868.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 306

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 55/289 (19%), Positives = 109/289 (37%), Gaps = 28/289 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +    +  I+    Q  +  G+V             Q G ++ +         +   +++
Sbjct: 28  FLVERFAQIDASVWQSRVVEGKVH-----------WQDGSLIELDTPYRPRARVYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  +             ++Y+D +I V  KP  +++     +        +  + +  + 
Sbjct: 77  VSET------KVPFDEEVIYQDERIIVAFKPHFLALHPSGNVINECL-VNRLRIKTGLET 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKE 196
               HRLD+ T+G++++       Q   + F+  +I+K Y +L    P+        +  
Sbjct: 130 IVPAHRLDRATAGLVLLCLHPEHRQRYHDLFKFGQIRKEYQALAKLTPELLLKHQRGELS 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              NW +K   + G+    ++    G     S  ++I+   +      + P TGRTHQLR
Sbjct: 190 LPLNWTVKNRMVKGEPTFTMRV-APGEPNTHSEIQLIEINGE-LGVFNLSPITGRTHQLR 247

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           VH   +G PI+ D  Y    +          L L AR +    P  G+L
Sbjct: 248 VHMQSLGMPILNDRCY-PELQPKAPDDYSKPLKLLARRLTFTDPVSGQL 295


>gi|308063206|gb|ADO05093.1| hypothetical protein HPSAT_01720 [Helicobacter pylori Sat464]
          Length = 293

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 70/290 (24%), Positives = 118/290 (40%), Gaps = 35/290 (12%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L+  Q  +DK+R+K N      Q VR   +I  +  +I                +     
Sbjct: 28  LKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVSLI------------HFKPNEKTQA 70

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L++E     VF+KP  +      G  YH +  L       G+     HRLD ETSG+++ 
Sbjct: 71  LVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYETSGLVLA 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +T  +A+ L   F  ++++K Y +L  G+  +K   I   +L   +I  D     K + 
Sbjct: 129 GKTLQSAKDLKVLFMQKKVKKTYLALAHGLV-DKNIVIDKPILTPQNIQKDLRIRSKIS- 186

Query: 221 KGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA----- 274
                + +  + +          L++ P TGRTHQ+R+H   +G  IVG+  Y       
Sbjct: 187 PLGKPSTTLVEPLSYNPFLDISLLKITPLTGRTHQIRLHLSSVGHRIVGEGLYGVIDENA 246

Query: 275 ----NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
                 K    +P+   L LHA  ++     G   +IT+ +P   +    
Sbjct: 247 REYLQLKHENNAPL---LMLHASSLEFEF-RGAIHEITSQMPQRFMPFLK 292


>gi|240123126|ref|ZP_04736082.1| Pseudouridine synthase [Neisseria gonorrhoeae PID332]
 gi|260440900|ref|ZP_05794716.1| Pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|268681754|ref|ZP_06148616.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID332]
 gi|291044222|ref|ZP_06569931.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|268622038|gb|EEZ54438.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID332]
 gi|291011116|gb|EFE03112.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
          Length = 307

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 94/223 (42%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPR---L 146
           ++     +  +L+ D  + V +KP  + V  GG  +   +   L+   + +         
Sbjct: 87  SEPRIPFEEKILFVDEHLIVVDKPHFLPVIPGGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L        K  +   L   S
Sbjct: 147 IHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEAL-----APTKTDLPYPLDVVS 201

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +         Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 202 RLVRGEKFFTTQEAEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|299769556|ref|YP_003731582.1| putative pseudouridylate synthase [Acinetobacter sp. DR1]
 gi|298699644|gb|ADI90209.1| putative pseudouridylate synthase [Acinetobacter sp. DR1]
          Length = 302

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 55/291 (18%), Positives = 114/291 (39%), Gaps = 31/291 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +   H+ HI     Q+  + G +   + +++  ++  QS   +     +   +H+  E +
Sbjct: 34  YLCQHFQHIKTQEWQQRFQDGLIYGANGQKLTLDSLYQSNTHIFYYRFLAYESHVPFEHR 93

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             +L+E+  + V +KP  +++       Y  +  L       G 
Sbjct: 94  ------------------ILFENDDLLVVDKPHFLTISPTG--QYVQETLLVRLKKQTGN 133

Query: 143 K-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIAN 200
           +     HRLD+ET+G+++  +   +     + F  R++ KIY ++  +    N  + +  
Sbjct: 134 EFLTPIHRLDRETAGVVLFCKRVESRGIYQQLFAERQVNKIYHAIAPYKKDLNFPQTLHL 193

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K     G   + ++  E       ++ ++I+   Q +    + P TG+ HQLRVH  
Sbjct: 194 HLDK-----GHPFYTMRVIENAKTNTETYIELIE-HNQIWAKYRLTPTTGKQHQLRVHLS 247

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           H+G PI  D  Y    +          L L A+++    P     +   + 
Sbjct: 248 HLGIPIKNDPFY-PVVQHKAEDDFSEPLQLLAKHISFIDPLTKEGMSFNSE 297


>gi|240976679|ref|XP_002402471.1| ribosomal pseudouridine synthase, putative [Ixodes scapularis]
 gi|215491192|gb|EEC00833.1| ribosomal pseudouridine synthase, putative [Ixodes scapularis]
          Length = 263

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 100/252 (39%), Gaps = 23/252 (9%)

Query: 101 LLYEDSKIYVFNKPAGIS--VQGGSGIAYHIDGFLKSWVDSK-----GQKPRLTHRLDQE 153
           +L+      V +KPA +    Q        ++  LK               R  HRLD  
Sbjct: 14  VLHLSPHFVVVDKPADVVINTQRPDEHPVTVETLLKRLHPELVDTGVHHSFRFCHRLDFS 73

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG+L +A  + +A+    +F  R  +K Y +++ G  ++    + + + +       + 
Sbjct: 74  TSGVLCLALHKQSARSAQRAFHQRLAKKYYVAILEGHVRDDHVLVDSPIGEDKRPQHSHK 133

Query: 214 HVVKQNEKGANY--AISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                 +   +   A +   V+       +    + ++P TGR HQLRVH   +G  IVG
Sbjct: 134 MCTADKDYCVSPRGAQTRLLVLWRGLLKGRPATKVLLRPVTGRRHQLRVHCASLGHTIVG 193

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           D  Y  +           +++LHA  + LP  E   L +  P P      +D+ G  Y +
Sbjct: 194 DFTYGEDASSR-------RMFLHACRLVLP-TEVETLDVETPDP--FAADFDA-GSDYGQ 242

Query: 329 NLYIKRLYSQDE 340
            +    L+ + E
Sbjct: 243 TVPTASLFEELE 254


>gi|21220121|ref|NP_625900.1| ribosomal pseudouridine synthase [Streptomyces coelicolor A3(2)]
 gi|289772662|ref|ZP_06532040.1| ribosomal pseudouridine synthase [Streptomyces lividans TK24]
 gi|6119667|emb|CAB59478.1| putative ribosomal pseudouridine synthase [Streptomyces coelicolor
           A3(2)]
 gi|289702861|gb|EFD70290.1| ribosomal pseudouridine synthase [Streptomyces lividans TK24]
          Length = 324

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 54/284 (19%), Positives = 96/284 (33%), Gaps = 28/284 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRV--DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +            +  +  +G V V  D + V  +   + G  V     + A        
Sbjct: 37  YLTERLSAAGAGVVDGMFDAG-VFVGADGRPVAGDAPYEPGMFVWFHRELPA-------- 87

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
                     +        ++Y D+ I V +KP  ++     G         +   +   
Sbjct: 88  ----------EVPVPFPLEIVYRDAHIVVADKPHFLATTP-RGGHVTQTALARLRRELDI 136

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD+ T+G+++              F  RR+ K+Y ++           +A  
Sbjct: 137 PALGAAHRLDRLTAGLVLFTVRPGERGAYQGLFADRRVHKVYEAV-----APYDAALALP 191

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              +S I  +   +  +   G   A++  +++            + P TG+THQLRVH  
Sbjct: 192 RTVRSRILKERGVLAAREVAGEPNAVTRVELLAHRPEHGLGRYRLVPGTGQTHQLRVHLN 251

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +G PI+GD  Y            +  L L AR +    P  GR
Sbjct: 252 ALGVPILGDPLYPEVAAPVPAGDFRRPLQLLARELGFTDPVTGR 295


>gi|15641672|ref|NP_231304.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O1
           biovar El Tor str. N16961]
 gi|153213916|ref|ZP_01949118.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 1587]
 gi|153817151|ref|ZP_01969818.1| pseudouridine synthase Rlu family protein [Vibrio cholerae NCTC
           8457]
 gi|153821833|ref|ZP_01974500.1| pseudouridine synthase Rlu family protein [Vibrio cholerae B33]
 gi|227081819|ref|YP_002810370.1| pseudouridine synthase Rlu family protein [Vibrio cholerae M66-2]
 gi|229508222|ref|ZP_04397727.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae BX
           330286]
 gi|229511539|ref|ZP_04401018.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae B33]
 gi|229518678|ref|ZP_04408121.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae RC9]
 gi|229607796|ref|YP_002878444.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           MJ-1236]
 gi|254848788|ref|ZP_05238138.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MO10]
 gi|255744905|ref|ZP_05418855.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholera CIRS
           101]
 gi|262161810|ref|ZP_06030828.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae INDRE
           91/1]
 gi|298498251|ref|ZP_07008058.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MAK 757]
 gi|9656182|gb|AAF94818.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O1
           biovar El Tor str. N16961]
 gi|124115654|gb|EAY34474.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 1587]
 gi|126512300|gb|EAZ74894.1| pseudouridine synthase Rlu family protein [Vibrio cholerae NCTC
           8457]
 gi|126520631|gb|EAZ77854.1| pseudouridine synthase Rlu family protein [Vibrio cholerae B33]
 gi|227009707|gb|ACP05919.1| pseudouridine synthase Rlu family protein [Vibrio cholerae M66-2]
 gi|229343367|gb|EEO08342.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae RC9]
 gi|229351504|gb|EEO16445.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae B33]
 gi|229355727|gb|EEO20648.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae BX
           330286]
 gi|229370451|gb|ACQ60874.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           MJ-1236]
 gi|254844493|gb|EET22907.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MO10]
 gi|255737376|gb|EET92771.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholera CIRS
           101]
 gi|262028542|gb|EEY47197.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae INDRE
           91/1]
 gi|297542584|gb|EFH78634.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MAK 757]
          Length = 235

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 56/200 (28%), Positives = 87/200 (43%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +        D +     L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEVATQTGDGQ---LYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   AA  L++ F  R+++K Y ++    PK K+  I   + +        V+  +  
Sbjct: 60  LARNATAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A        +PHTG+THQ+RV    +G  IVGD  Y       
Sbjct: 118 ----NPAITQFFS-AAAATGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYN------ 166

Query: 280 FTSPIQNKLYLHARYMDLPH 299
            T+   ++ YLHA  +   +
Sbjct: 167 -TADESDRGYLHAFALRFTY 185


>gi|256788767|ref|ZP_05527198.1| ribosomal pseudouridine synthase [Streptomyces lividans TK24]
          Length = 304

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 54/284 (19%), Positives = 96/284 (33%), Gaps = 28/284 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRV--DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +            +  +  +G V V  D + V  +   + G  V     + A        
Sbjct: 17  YLTERLSAAGAGVVDGMFDAG-VFVGADGRPVAGDAPYEPGMFVWFHRELPA-------- 67

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
                     +        ++Y D+ I V +KP  ++     G         +   +   
Sbjct: 68  ----------EVPVPFPLEIVYRDAHIVVADKPHFLATTP-RGGHVTQTALARLRRELDI 116

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD+ T+G+++              F  RR+ K+Y ++           +A  
Sbjct: 117 PALGAAHRLDRLTAGLVLFTVRPGERGAYQGLFADRRVHKVYEAV-----APYDAALALP 171

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              +S I  +   +  +   G   A++  +++            + P TG+THQLRVH  
Sbjct: 172 RTVRSRILKERGVLAAREVAGEPNAVTRVELLAHRPEHGLGRYRLVPGTGQTHQLRVHLN 231

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +G PI+GD  Y            +  L L AR +    P  GR
Sbjct: 232 ALGVPILGDPLYPEVAAPVPAGDFRRPLQLLARELGFTDPVTGR 275


>gi|208434858|ref|YP_002266524.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori G27]
 gi|208432787|gb|ACI27658.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori G27]
          Length = 242

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 65/288 (22%), Positives = 111/288 (38%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V +  K++                 + A   + K  +     V 
Sbjct: 12  ENISHKKAKALIDLGLVSIGGKKL-----------------MVARKELPKNTRFSVQKVE 54

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 55  --------KPSVIFEDENILALFKPPFI-------ESYDLASFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y ++V GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVVLLVKENSEFHLKAKKAFKDRAVKKEYLAIVQGIVEEEREINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEIGSA------KRLMLHAHKISLL-----GYEFEAIPPKEFE 241


>gi|326675673|ref|XP_693475.4| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Danio rerio]
          Length = 599

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 57/225 (25%), Positives = 103/225 (45%), Gaps = 10/225 (4%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKP 114
           N  ++ G++      ++ LN ++K   +L ++V+  +         LL +D ++ V +KP
Sbjct: 215 NAAVKEGRIKLNETPVDDLNVVLKNNDLLRNTVHRHEPPVCGQPLKLLVDDGEVVVVDKP 274

Query: 115 AGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTES 173
           + + V       Y  +  +      KG       HRLD+ TSG+L+ ART   ++ L   
Sbjct: 275 SSLPVHPCG--RYRHNTVIFILGKEKGLVGLHTVHRLDRLTSGVLLFARTLEVSKKLDVM 332

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R R+++K Y   V G     +      +L  S      V + + + KG   + + F+ +
Sbjct: 333 VRERQLEKEYVCRVEGEFPEAEVVCEEPILVVSF----RVGLCRVDPKG-KESRTIFQRL 387

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
               +    +  +P TGRTHQ+RVH   +G PI+ D  Y ++  G
Sbjct: 388 SFNGRS-SVVRCRPLTGRTHQIRVHLQFLGFPILNDPIYGSSAWG 431


>gi|323693993|ref|ZP_08108177.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Clostridium symbiosum WAL-14673]
 gi|323501929|gb|EGB17807.1| ribosomal large subunit pseudouridine synthase D/dephospho-CoA
           kinase [Clostridium symbiosum WAL-14673]
          Length = 272

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 100/253 (39%), Gaps = 51/253 (20%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG------------------Q 142
           ++YED  I V  KPAG+  Q   G    +   +K+ +                       
Sbjct: 4   IIYEDHDILVAEKPAGLESQASRGFEPDMVSEIKNHLKRAELSRLSTKPSTKSSTRPVEP 63

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              + HRLD+   GI+V A+ + AA  L++  +  R++KIY ++V G   +      ++L
Sbjct: 64  YVGVIHRLDKPVGGIMVYAKNQKAAASLSKQVQDGRMKKIYNAVVCGKLVDIVGNYVDYL 123

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHA 259
           LK      ++  VV ++   +  A   ++ +D      ++   +E++  +GR HQ+RV  
Sbjct: 124 LKDGR--NNFSFVVDKDTPDSRRAELVYRALDVKTEEEREISLVEIELLSGRHHQIRVQF 181

Query: 260 LHMGCPIVGDHKYCANFKGNFTSP----------------------------IQNKLYLH 291
              G P+ GD KY   + G   +                              + +L L 
Sbjct: 182 AAHGNPLWGDGKYNPEWGGTLPAGERTHADRHTGAKQGSGHAAKVQSSRGRRGERELALA 241

Query: 292 ARYMDLPHPEGGR 304
           A  +   HP  G+
Sbjct: 242 AVKLSFVHPSTGK 254


>gi|240127829|ref|ZP_04740490.1| Pseudouridine synthase [Neisseria gonorrhoeae SK-93-1035]
 gi|268686227|ref|ZP_06153089.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-93-1035]
 gi|268626511|gb|EEZ58911.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-93-1035]
          Length = 307

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 94/223 (42%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPR---L 146
           ++     +  +L+ D  + V +KP  + V  GG  +   +   L+   + +         
Sbjct: 87  SEPRIPFEEKILFVDEHLIVVDKPHFLPVIPGGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L        K  +   L   S
Sbjct: 147 IHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEAL-----APTKTDLPYPLDVVS 201

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +         Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 202 RLVRGEKFFTTQEAEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|59800875|ref|YP_207587.1| hypothetical protein NGO0433 [Neisseria gonorrhoeae FA 1090]
 gi|194098179|ref|YP_002001227.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|240016189|ref|ZP_04722729.1| Pseudouridine synthase [Neisseria gonorrhoeae FA6140]
 gi|240115283|ref|ZP_04729345.1| Pseudouridine synthase [Neisseria gonorrhoeae PID18]
 gi|240117570|ref|ZP_04731632.1| Pseudouridine synthase [Neisseria gonorrhoeae PID1]
 gi|268600964|ref|ZP_06135131.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID18]
 gi|268603274|ref|ZP_06137441.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID1]
 gi|59717770|gb|AAW89175.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
 gi|193933469|gb|ACF29293.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|268585095|gb|EEZ49771.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID18]
 gi|268587405|gb|EEZ52081.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID1]
          Length = 307

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 48/223 (21%), Positives = 94/223 (42%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPR---L 146
           ++     +  +L+ D  + V +KP  + V  GG  +   +   L+   + +         
Sbjct: 87  SEPRIPFEEKILFVDEHLIVVDKPHFLPVIPGGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L        K  +   L   S
Sbjct: 147 IHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEAL-----APTKTDLPYPLDVVS 201

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +         Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 202 RLVRGEKFFTTQEAEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylate synthase [Herbaspirillum
           seropedicae SmR1]
 gi|300074785|gb|ADJ64184.1| 23S RNA-specific pseudouridylate synthase protease protein
           [Herbaspirillum seropedicae SmR1]
          Length = 299

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 57/284 (20%), Positives = 108/284 (38%), Gaps = 30/284 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +    +  +     ++ L  G+VR +   + ++ +   +SG  +     +      I  +
Sbjct: 31  FLAERFTAVPEPVWRERLLRGEVR-NQHGEALQPDTPYRSGDCIFYYRELPQGEARIPVE 89

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           +                  +L+ D  + V +KP  + V          +  L     + G
Sbjct: 90  E-----------------KILHLDDHLLVADKPHFLPVIPTGRFV--QETLLVRLKKATG 130

Query: 142 -QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            Q     HRLD+ET+G++V +   A+       F+ R + K+Y ++        +  +  
Sbjct: 131 LQDLVPIHRLDRETAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAI-----APLRSDLEL 185

Query: 201 WLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + +S +        K +E +GA  + +H  +I+          ++P TGR HQLRVH 
Sbjct: 186 PRVHRSRVEEIPEQFFKMHEAEGAPNSETHISLIEARG-ALGLYRLEPVTGRRHQLRVHM 244

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +G PI+ D  Y           +   L L AR +    P  G
Sbjct: 245 AALGIPILNDLFYPEAVPVGVADDLDKPLKLLARSLFFIDPLDG 288


>gi|258650803|ref|YP_003199959.1| pseudouridine synthase [Nakamurella multipartita DSM 44233]
 gi|258554028|gb|ACV76970.1| pseudouridine synthase [Nakamurella multipartita DSM 44233]
          Length = 299

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 57/282 (20%), Positives = 107/282 (37%), Gaps = 30/282 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDK--KRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           +    +   +   +++ + +G+V VD   + V  +  + S Q V +         +  E 
Sbjct: 30  YLLERFA-ADATRVREKVDAGEV-VDGEGRVVDPSTPLTSSQWVFLYRDPAPEPRVPFEI 87

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           +                  +L+ DS + V +KP  ++     G+       ++   +   
Sbjct: 88  E------------------ILHRDSDLLVVDKPHFLATMP-RGLHIVESALVRLRRELDL 128

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +    HRLD+ T+G+LV +   A        F  R++ K Y ++        +  +   
Sbjct: 129 PELSPIHRLDRVTAGVLVFSLRPANRGAYQTLFAQRKVTKYYEAV-----AGHRADLTLP 183

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
              +S I         Q   G   A +  + +    ++     + PHTG+ HQLR+H   
Sbjct: 184 TTVESRIVKFRGTPTAQQVPGEPNARTVVERLAARGERA-LYGLHPHTGKVHQLRLHMTS 242

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           +G PIVGD+ Y             + L L AR ++ P P  G
Sbjct: 243 LGVPIVGDNFY-PTLLDTPRDDYSDPLQLLARSIEFPDPFTG 283


>gi|304411759|ref|ZP_07393371.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS183]
 gi|307306189|ref|ZP_07585934.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica BA175]
 gi|304349947|gb|EFM14353.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica OS183]
 gi|306911062|gb|EFN41489.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           baltica BA175]
          Length = 230

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 54/198 (27%), Positives = 88/198 (44%), Gaps = 19/198 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++ +++   V +K   +      G A    G +       G K    HRLD  TSG+L+
Sbjct: 3   RIIADEADFIVISKSVKVHFHSQDGTA----GVVAQAEQDLGIKLFAVHRLDTPTSGLLI 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A++  AA+  TE F   ++QK Y +L  G PK K+  +   + K          + K  
Sbjct: 59  LAKSAVAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIGDMAK------SRRSMFKLL 112

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F  +   ++      ++PH+G+THQLRV    +G PI+GD  Y       
Sbjct: 113 RTKENPAITQFFSL-SVSEGLRLYLLKPHSGKTHQLRVALASLGVPILGDDLYGG----- 166

Query: 280 FTSPIQNKLYLHARYMDL 297
                 ++ YLHA  +  
Sbjct: 167 ---MAADRCYLHAYCLHF 181


>gi|229496692|ref|ZP_04390406.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas endodontalis ATCC 35406]
 gi|229316589|gb|EEN82508.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas endodontalis ATCC 35406]
          Length = 330

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 60/327 (18%), Positives = 119/327 (36%), Gaps = 36/327 (11%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKI 83
                P  +    ++ LR   ++V+ + V   N  +  G  V +                
Sbjct: 31  LSQLLPESSRTTHKQYLRDRCIKVNGQVVSEHNAPVAVGDEVVVY--------------- 75

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-- 141
              SV      D  +  +L++D    +  K  GI          H    + +     G  
Sbjct: 76  ---SVGFAPVLDNTEVKVLWQDDWFILVQKEPGIPTIASKPGDRHTVYRIVADHYKSGDA 132

Query: 142 -QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            +K  L +RLD++T G+++ AR R   Q + +++    + + + +LV G+   +K   A 
Sbjct: 133 REKIFLLNRLDRDTRGLILFARDREVQQEILDNWEKYILSQTFSALVEGVVPEEKGEFAP 192

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
               K  +G           + +        +++   Q    L +    GR + +R    
Sbjct: 193 PPKPKKTVGDKDTKKKVVVSRRSRAT----YLVEERGQWRTLLRISLL-GRYNGIRSQLN 247

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTW 319
               P+VG+ K     KG  +      + L  + + L HP    +L+  +P+P+   K  
Sbjct: 248 EKKYPLVGESK--GVIKGAPS------IALSQQELVLLHPITKEKLRFESPIPSFFYKLL 299

Query: 320 DSLGFKYDRNLYIKRLYSQDECKQNIL 346
                  +R +  KR  S+++   + L
Sbjct: 300 RRRLTTSERKIIEKRTESENDLSFDSL 326


>gi|162456191|ref|YP_001618558.1| hypothetical protein sce7908 [Sorangium cellulosum 'So ce 56']
 gi|161166773|emb|CAN98078.1| rluD4 [Sorangium cellulosum 'So ce 56']
          Length = 326

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 56/302 (18%), Positives = 103/302 (34%), Gaps = 30/302 (9%)

Query: 27  NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
                 +   L      G+  ++ +R +  + +  G  + + P                 
Sbjct: 21  ERAGGASRG-LAGAAAEGRAFLNGRRARPGDAVALGDELAVWPARRDA------------ 67

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
                         +L    ++ V +KPA +  +        +   +   +  +   P  
Sbjct: 68  -------PGAPPVEVLARWGELLVASKPAALPTEPERRGTRSLVTEVAELLGLRDL-PHA 119

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             RLD   SG ++ A      +H+       RI ++Y  +  G  +         +    
Sbjct: 120 ASRLDVGVSGAVLCATGARGRRHVVAMREAGRIARVYVGVAGGRVEG-SGTWDAPIGAAR 178

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLRVHALHMG 263
             GG  +  V      A  A +H++ +            L + P TGRTHQLRVHA H G
Sbjct: 179 ARGGRSLPAV--GGADAKDASTHYRAVASAGGGAAPATLLRLDPVTGRTHQLRVHAAHAG 236

Query: 264 CPIVGDHKYCANFK---GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
            P++GD  +                +++ LHA  + +P   G      AP+P  + + W 
Sbjct: 237 APLLGDRDHGGARSVTTARGRVIPLSRVALHALRVTVPDERGELCAAIAPVPDELRELWV 296

Query: 321 SL 322
           +L
Sbjct: 297 AL 298


>gi|46190854|ref|ZP_00121013.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Bifidobacterium longum DJO10A]
          Length = 244

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 92/242 (38%), Gaps = 31/242 (12%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +LYED +I V +KP  ++     G+ Y     ++             HRLD+ T+G+LV
Sbjct: 2   DVLYEDERIIVVDKPHFLATMP-RGMWYRQTALIRLRERLGEPDITPAHRLDRMTAGVLV 60

Query: 160 VARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN-------WLLKKSHIGG 210
             R  A        F+ R+  K+Y   +    I + +   I          LL++SHI  
Sbjct: 61  FVRDPACRGAYQMLFQNRQAVKVYECLAPCRPISRPRFGTIMKVEPPCPFPLLRRSHITK 120

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCF-------------------AQKFCWLEMQPHTGR 251
           ++  +    E G   A +  +  D                         C   + P TG+
Sbjct: 121 EHGTMAAFEEPGLANAETLIERGDLCFPPADGRWREAPEGGPHLGNHPICRYTLHPRTGK 180

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAP 310
           THQLRVH   +G PIVGD  Y    +          L L AR +    P  G   +  + 
Sbjct: 181 THQLRVHMNSLGLPIVGDDFY-PRIQTRPYDDFSQPLQLVARMLRFTDPITGEKREFVSR 239

Query: 311 LP 312
           +P
Sbjct: 240 VP 241


>gi|215432263|ref|ZP_03430182.1| hypothetical protein MtubE_16739 [Mycobacterium tuberculosis
           EAS054]
 gi|289755423|ref|ZP_06514801.1| conserved hypothetical protein [Mycobacterium tuberculosis EAS054]
 gi|289696010|gb|EFD63439.1| conserved hypothetical protein [Mycobacterium tuberculosis EAS054]
          Length = 304

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 55/252 (21%), Positives = 95/252 (37%), Gaps = 13/252 (5%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVF 111
           V    ++ +G+VV     +     ++    ++    +L  +        +L++D+   V 
Sbjct: 38  VAARAKVLAGEVVDDDGAVVDSGTVLPPGSVVHLYRDLPDEVPVPFDVPVLHQDAD-IVV 96

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   +    +    HRLD+ T+G+L+    R       
Sbjct: 97  DKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTTRREVRGSYQ 155

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    ++K Y +     P      +A   L +S I     H+    E G   A +  +
Sbjct: 156 TMFARGLVRKTYLARAPVAP-----GLALPRLVRSRIVKRRGHLQAVCEPGVPNAETLVE 210

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
            I           + P TGRTHQLRVH   +G PI+GD  Y  N            L L 
Sbjct: 211 RIARDG----LYRLTPTTGRTHQLRVHMAALGIPIMGDPLY-PNVISVAAHDFSTPLQLL 265

Query: 292 ARYMDLPHPEGG 303
           A+ ++   P  G
Sbjct: 266 AQRIEFDDPLTG 277


>gi|326929074|ref|XP_003210696.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Meleagris gallopavo]
          Length = 310

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 58/219 (26%), Positives = 87/219 (39%), Gaps = 19/219 (8%)

Query: 106 SKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSK-----GQKPRLTHRLDQETSGILV 159
               V NK   I +          +   LK               R  H+LD  TSG L 
Sbjct: 23  PDFIVVNKHWDIRIDSKMWYETLTLQSQLKHRFPELADPDTYYGFRFCHQLDFSTSGALC 82

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA  +AAA    + F+ R + K Y +LV G     +  I   + K +  G  ++  ++  
Sbjct: 83  VALNKAAAGSAYKCFKDRLVTKAYLALVRGHVDQSRMTIRYAIGKNTAEGMTHMMCIEGT 142

Query: 220 E--KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           E  +      S   V++           + +QP TGRTHQLRVH   +G PIVGD  Y  
Sbjct: 143 EGCENPKPCQSELIVLEHGSYSGDPVTKVLLQPLTGRTHQLRVHCSAIGHPIVGDFTYSH 202

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
               +       ++ LHA Y+ +  P     +++  P P
Sbjct: 203 KKDSSPY-----RMMLHAYYLRI--PTSKELIEVCTPDP 234


>gi|309356679|emb|CAP36772.2| hypothetical protein CBG_19546 [Caenorhabditis briggsae AF16]
          Length = 438

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 50/241 (20%), Positives = 96/241 (39%), Gaps = 28/241 (11%)

Query: 40  ILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
             + G++ V+ ++    +  +++G   R+   ++   H +++                L 
Sbjct: 112 ACKMGRIYVNGEQMTDVDYVMKNGD--RVEHWVHRHEHPVRD----------------LP 153

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGI 157
             ++ E   + V  KP  + V      A H   G L+   +  G   R+ HRLD+ TSG+
Sbjct: 154 IRIISETDDLLVIEKPPSLPVHTCGQYAIHTVLGQLRENEEKTG--LRVLHRLDRATSGV 211

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A+          + +     K Y   V G+  ++++     +             ++
Sbjct: 212 LLFAKNYETDLEFKTTLKQGEWSKEYVCKVDGVFPDEEQVCEQPIG-----PLVISMGIQ 266

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                   A S F+ +         +++   TGRTHQ+RVH+  +G PIVGD  Y +   
Sbjct: 267 CVRPDGKEAKSTFRKLWSDG-THSVVQVHIETGRTHQIRVHSQFLGYPIVGDQLYNSTVW 325

Query: 278 G 278
           G
Sbjct: 326 G 326


>gi|303389291|ref|XP_003072878.1| pseudouridylate synthase [Encephalitozoon intestinalis ATCC 50506]
 gi|303302021|gb|ADM11518.1| pseudouridylate synthase [Encephalitozoon intestinalis ATCC 50506]
          Length = 317

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 58/264 (21%), Positives = 100/264 (37%), Gaps = 41/264 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D    + +           L  G V V+++ V+    ++ G V+R    I+   H    
Sbjct: 26  ID-VLASEFRTRTKDYFLSALECGAVTVNEEIVEPGRILRIGDVIRHTVHIHEPAHP--- 81

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                            +  ++ E+    V NKP G+      G  Y      ++    K
Sbjct: 82  -----------------EIDIIREEQDYVVVNKPPGMPCHPTGG--YREYSVTRALFGDK 122

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
             K    +RLD   SG+L+VA    + + L      R+I   Y + V G+  +  +    
Sbjct: 123 --KVACINRLDMPVSGVLIVAVKNHS-KCLEAIREARKI---YLAKVQGLFPDSIDVDK- 175

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K S   G + +V  +        ++ F+ +  +      +E +P TGRTHQ+R+H  
Sbjct: 176 ---KISCAEGKHRYVSDE----GKACLTLFRRL-AYKDGHSLVECRPITGRTHQIRIHLQ 227

Query: 261 HMGCPIVGDHKYCANFKGNFTSPI 284
            +G PIV D  Y     G    P+
Sbjct: 228 SIGFPIVNDIMYG---DGELPQPL 248


>gi|291517265|emb|CBK70881.1| Pseudouridylate synthases, 23S RNA-specific [Bifidobacterium longum
           subsp. longum F8]
          Length = 244

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 92/242 (38%), Gaps = 31/242 (12%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +LYED +I V +KP  ++     G+ Y     ++             HRLD+ T+G+LV
Sbjct: 2   DVLYEDERIIVVDKPHFLATMP-RGMWYRQTALIRLRERLGEPDITPAHRLDRMTAGVLV 60

Query: 160 VARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN-------WLLKKSHIGG 210
             R  A        F+ R+  K+Y   +    I + +   I          LL++SHI  
Sbjct: 61  FVRDPACRGAYQMLFQNRQTVKVYECLAPCRPISRPRFGTIMQVEPPRPFPLLRRSHITK 120

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCF-------------------AQKFCWLEMQPHTGR 251
           ++  +    E G   A +  +  D                         C   + P TG+
Sbjct: 121 EHGTMAAFEEPGLANAETLIERGDLCFPPADGRWREAPEGGPHPGNHPICRYTLHPRTGK 180

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAP 310
           THQLRVH   +G PIVGD  Y    +          L L AR +    P  G   +  + 
Sbjct: 181 THQLRVHMNSLGLPIVGDDFY-PRIQTRPYDDFSQPLQLVARMLRFTDPITGEKREFVSR 239

Query: 311 LP 312
           +P
Sbjct: 240 VP 241


>gi|289662056|ref|ZP_06483637.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 349

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 56/289 (19%), Positives = 112/289 (38%), Gaps = 30/289 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
                +P I     ++    G VR  +   +  +   + G  +R           + ++ 
Sbjct: 82  ALCACFPTITTERWRERFARGLVRDANDHALALSAPYRVGAEIRYF-------REVADEP 134

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
           ++                +++ D+ + V  KP  + V   G+ +   +   L   +D+  
Sbjct: 135 VIPY-----------VETVVHADADLVVACKPHFLPVAPAGAYVRETLLTRLVRRLDNPA 183

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
             P   HR+D++T+G+++ +   A        FR RRI+K Y ++   +PK     +   
Sbjct: 184 LVP--LHRIDRDTAGLVLFSANPATRGVYQALFRERRIRKQYLAVAPPLPK-----LTFP 236

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            + +S +         +  +G   + +   V+      + +L ++P TGR HQLRVH   
Sbjct: 237 YVHRSRLEPGEPFFRMREGEGEPNSETVIDVVARAEDTWTYL-LEPVTGRKHQLRVHMAA 295

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITA 309
           +G PI+ D  Y  + +       +  L L A  +    P     +  TA
Sbjct: 296 LGAPILHDRFY-PDLEAQRPDDPERPLQLFAHTLAFDDPITDEPRSFTA 343


>gi|256090913|ref|XP_002581414.1| ribosomal pseudouridine synthase [Schistosoma mansoni]
 gi|238667306|emb|CAZ37653.1| ribosomal pseudouridine synthase, putative [Schistosoma mansoni]
          Length = 165

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 37/179 (20%), Positives = 75/179 (41%), Gaps = 22/179 (12%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RLD+   +  P ++       ++  +V V+    K    +Q G  +          
Sbjct: 3   ESGHRLDKALADLTP-LSRSQANDQIKQKRVLVNGSPKKAKYIVQVGDCISYH------- 54

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFL 133
                   +    +L   +  +   ++Y+D  + + NKP G+ V   +G      ++  L
Sbjct: 55  --------IPEESSLDYQAQDIPLDIVYQDDVLAIINKPQGMVVHPSAGHSTGTLVNALL 106

Query: 134 KSWVDSKGQ----KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               D        +P + HR+D++TSG+L+VA+T  A Q L +  + ++  + Y ++V 
Sbjct: 107 YHVKDLSSINGVIRPGIVHRIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVH 165


>gi|294867086|ref|XP_002764957.1| tRNA pseudouridine synthase C, putative [Perkinsus marinus ATCC
           50983]
 gi|239864810|gb|EEQ97674.1| tRNA pseudouridine synthase C, putative [Perkinsus marinus ATCC
           50983]
          Length = 417

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 47/198 (23%), Positives = 92/198 (46%), Gaps = 9/198 (4%)

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           ++  L   +   G    + HRLD++TSG +++AR   + + +   F+  ++ K Y  LV 
Sbjct: 37  MNEELNPALSGGGGFGPMCHRLDKQTSGPVLIARKLESWKFIRRQFQKEQVTKRYVCLVD 96

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           GI  N    I + +  +      +      +   ++ A S ++V++ + +    + ++  
Sbjct: 97  GICANDSGMIDSPIRVRRTE--KHTSAEIGSGPASSSAHSEYRVLERYEEGCTLMSVRIT 154

Query: 249 TGRTHQLRVHAL-HMGCPIVGDHKYCANFKGNF---TSPIQNKLYLHARYMDL-PHPEGG 303
           TG THQ+RVH    +G PIVGD KY  + +G+     + +  +++LH   + + P    G
Sbjct: 155 TGVTHQIRVHMAQGLGHPIVGDKKYTPSGRGSELPCATRMPGRVFLHCYELGVKPDKTSG 214

Query: 304 R--LQITAPLPAHMVKTW 319
           +    I   LP  +    
Sbjct: 215 QKLTTIKCSLPTELRNLL 232


>gi|89093809|ref|ZP_01166755.1| hypothetical protein MED92_04904 [Oceanospirillum sp. MED92]
 gi|89081939|gb|EAR61165.1| hypothetical protein MED92_04904 [Oceanospirillum sp. MED92]
          Length = 313

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 50/258 (19%), Positives = 99/258 (38%), Gaps = 25/258 (9%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           ++ K     ++   + + L +G VR++ + +  +     G  + +    +    +     
Sbjct: 20  QFLKQRLVSVHAEQVDRWLAAGMVRLNGQPIIEDCVCGKGDRLELDIPDHQEAQV----- 74

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             L++E  ++   NKP  + V   +   Y     L     +   
Sbjct: 75  -------------DDNWQLVWESDELMAINKPPLLPVSRTTRNLYMTLISLVRR-QTPYP 120

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             +L HRLD ETSG++++A+ R A +           +K+Y + V G P      +   L
Sbjct: 121 DAQLLHRLDTETSGLILLAKNREADRKWKPQLAKLIRRKVYQAWVHGSPNWDHLLMECEL 180

Query: 203 LKKSHIGGDYVHVVKQNEKGAN-----YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            +K+         V + +  +       + + F V+     K   ++ +  TGR HQ+R 
Sbjct: 181 SEKAGSDIRSQVYVVEPQSDSQYLKPRPSKTEFLVLQRAGSK-SLIQCELFTGRKHQIRA 239

Query: 258 HALHMGCPIVGDHKYCAN 275
              H+G PI+GD  Y  +
Sbjct: 240 QLAHLGHPIIGDKIYSHD 257


>gi|53690306|ref|ZP_00121875.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Bifidobacterium longum DJO10A]
          Length = 180

 Score =  127 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 36/146 (24%), Positives = 65/146 (44%), Gaps = 6/146 (4%)

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +++V ++  A   +   F    ++K Y +LV G  K  K  I   + +            
Sbjct: 1   MMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQGGLKENKATIEAPIGR-----AKVSDFR 55

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
                    A++H+ V++ F  +   + +   TGRTHQ+RVH   +G P+ GD  Y AN 
Sbjct: 56  FCVTPAGKPAVTHWDVLERFGHEATLVSVNLETGRTHQIRVHFSSIGHPLCGDPMYGANP 115

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEG 302
             +    + ++ +LHA  ++  HP  
Sbjct: 116 VLSEALGL-DRQWLHAMKLEFRHPRT 140


>gi|308184739|ref|YP_003928872.1| hypothetical protein HPSJM_04875 [Helicobacter pylori SJM180]
 gi|308060659|gb|ADO02555.1| hypothetical protein HPSJM_04875 [Helicobacter pylori SJM180]
          Length = 242

 Score =  127 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 63/288 (21%), Positives = 114/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V V  K++                       ++  +++ +++  
Sbjct: 12  ENISHKKAKALIDLGLVSVGGKKL-----------------------MVARKELPENTRF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLALAQGIIEEEREINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIIAPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKIALL-----GYEFEAIPPKEFE 241


>gi|262372214|ref|ZP_06065493.1| pseudouridylate synthase [Acinetobacter junii SH205]
 gi|262312239|gb|EEY93324.1| pseudouridylate synthase [Acinetobacter junii SH205]
          Length = 303

 Score =  127 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 59/295 (20%), Positives = 114/295 (38%), Gaps = 28/295 (9%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIP 68
           V + ND   + +  +    +PHI  +  Q+    G +   D  ++   +R      +   
Sbjct: 21  VFLPNDVSELTIFEYLCVQFPHIQAIEWQQRFEDGLIYASDGMKLSIQDRYTPNTFIFYY 80

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
             +    H+  E +                  +L+ED  + V +KP  +++       Y 
Sbjct: 81  RFLAHEIHVPFEHQ------------------ILFEDEHLLVVDKPHFLTMSPTG--QYV 120

Query: 129 IDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L       G  +    HRLD+ET+G+++  +   +     + F  R++QK Y ++ 
Sbjct: 121 QETLLVRLKKQTGYAELTPIHRLDRETAGVVLFCKKAESRGIYQQLFAERKVQKTYHAIA 180

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
              P+ K        ++K H    +  +    +K AN   +  ++++   Q     ++ P
Sbjct: 181 AYRPEIKFPMSLELHMEKGHP---FYTMRVNYDKTANT-ETFIELLEHNFQ-HAKYQLSP 235

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            TG+ HQLRVH  H+  PI+ D  Y             + L L A+ +    P  
Sbjct: 236 KTGKQHQLRVHLNHLNIPILNDPFYPTVLH-KADDDFNHPLQLLAKEISFIDPIS 289


>gi|242079953|ref|XP_002444745.1| hypothetical protein SORBIDRAFT_07g027030 [Sorghum bicolor]
 gi|241941095|gb|EES14240.1| hypothetical protein SORBIDRAFT_07g027030 [Sorghum bicolor]
          Length = 439

 Score =  127 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 130/325 (40%), Gaps = 78/325 (24%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHS-DFLKSILLYEDSKIY 109
           K++K N+ ++ G  + +P  +       + + I  ++++  K   ++L+ ++++ DS I 
Sbjct: 131 KKIKHNDAMEPGMRIHLPVSVAEGEIKKRYETIPTATLHPNKDEIEYLRRLVIHRDSAIL 190

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           V NKP  + ++G   +   +D  L +   S G K                          
Sbjct: 191 VLNKPPKVPMKGHLPVHNSMD-VLAAAALSYGNKEGP----------------------K 227

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE---KGANYA 226
           LT +       + YW+LV G PK ++  I   + K     G    V+  +     GA  A
Sbjct: 228 LTWNKACEAYVQKYWALVIGTPKEREGVICAPISKVLLDDGKAERVILAHPSGIDGAQEA 287

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYC------------ 273
           I+ ++V+        W+E++P TGR HQLRVH    +G PIVGD+KY             
Sbjct: 288 ITEYRVMGPTINGCSWIELRPLTGRKHQLRVHCAEALGTPIVGDYKYGWFVHQTWKQNPQ 347

Query: 274 ANFKGNFTSPIQNK------------------LYLHARYMDLP------------HPEGG 303
            +F+     P + +                  L+LH R M +P            H  G 
Sbjct: 348 PDFEPFTGEPYKLRRPEGLEIQKGSVLSKVPLLHLHCREMVIPNIAKFLSSTGEWHENGA 407

Query: 304 R--------LQITAPLPAHMVKTWD 320
                    L+  AP+P HM  +W+
Sbjct: 408 PWAKEKPNLLRFVAPMPPHMKISWN 432


>gi|269861115|ref|XP_002650272.1| diaminohydroxyphosphoribosylaminopyrimidine deaminase
           [Enterocytozoon bieneusi H348]
 gi|220066286|gb|EED43774.1| diaminohydroxyphosphoribosylaminopyrimidine deaminase
           [Enterocytozoon bieneusi H348]
          Length = 331

 Score =  127 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 59/285 (20%), Positives = 108/285 (37%), Gaps = 33/285 (11%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           YV     +    N ++    K ++ + +    +  L  G + V+ K V    R+Q     
Sbjct: 5   YVYKTFTKGKWHNKKIIDILKENFNNKSETYFEDALAIGAITVNDKIVSTEYRMQFND-- 62

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                     HI+ + +     +             +Y D +I V NKP GI        
Sbjct: 63  -------YFKHIVHQHEPKQPHIPT-----------IYIDDEITVVNKPFGIPCHPVG-- 102

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART--RAAAQHLTESFRMRRIQKIY 183
           AYH     K+   +K       +RLD   SG+L++     +   ++L  S ++   + I 
Sbjct: 103 AYHYYTVTKTIFKNK--PVGCVNRLDIPVSGVLIINTCNQKRIHEYLLNSKKIYIAKVIG 160

Query: 184 WSLVWGIPKNKKECIANW------LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             +      +K             ++    +  D     ++      +A +HF+++    
Sbjct: 161 QFIFSDEQLHKLGIEKRISNGKSIIIVNKSLLLDPKTKKQKISDDGKFAETHFELVSYQN 220

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
           Q +  ++  P TGRTHQ+RVH  ++G PI+ D  Y +     F S
Sbjct: 221 Q-YSMIKCYPITGRTHQIRVHLAYIGFPILYDTLYGSYPAYKFNS 264


>gi|302526188|ref|ZP_07278530.1| ribosomal pseudouridine synthase [Streptomyces sp. AA4]
 gi|302435083|gb|EFL06899.1| ribosomal pseudouridine synthase [Streptomyces sp. AA4]
          Length = 309

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 51/218 (23%), Positives = 87/218 (39%), Gaps = 10/218 (4%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTH 148
             +        +L+ D  + V +KP  ++    G  +       L+  +D     P   H
Sbjct: 82  PDEVPVPFDVTVLHRDDHLLVVDKPHFLATIPRGRHVLETALVRLRRSLDLPALSP--AH 139

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ T+G+++   T +A       FR R + K Y ++    P      +    + +S I
Sbjct: 140 RLDRVTAGLVMFVITPSARGAYQTMFRDRLVHKEYEAIAPYDP-----TLELPRVVRSRI 194

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +   +  Q   G   A S  ++++          + P TGRTHQLRVH   +G PI+G
Sbjct: 195 VKERGVLAAQEVPGPPNAESTVELLEHR-DGLGRYRLTPATGRTHQLRVHMCSLGIPILG 253

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           D  Y         +     L L A+ ++   P  G  +
Sbjct: 254 DDFY-PELHEKPLNDFTKPLQLLAKVLEFDDPLTGEHR 290


>gi|300744294|ref|ZP_07073313.1| RNA pseudouridine synthase [Rothia dentocariosa M567]
 gi|300380019|gb|EFJ76583.1| RNA pseudouridine synthase [Rothia dentocariosa M567]
          Length = 365

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 89/235 (37%), Gaps = 33/235 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  +   +KP  + V    G         K  V          HRLD+ T+GIL+ 
Sbjct: 110 VLYEDEHLLAVDKPHYLPVTP-RGAYVAQTALTKLRVRENNPLLTPVHRLDRPTAGILLF 168

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-------IANWLLKKSHIGGDYV 213
           A+TR A       F+ R++ K Y ++     ++ +E        + + + K  +I     
Sbjct: 169 AKTREARGPFQTMFQNRQVTKTYLAIAPAPSEDLRESMLGEGVQVRSRIDKDRNILQVRQ 228

Query: 214 HVVKQNEKGANY--AISHFKVID----------------------CFAQKFCWLEMQPHT 249
           +  ++ E+      A +  ++ +                         ++    E+ PHT
Sbjct: 229 YSARECERAGLTMNAETLVRIREIYQAPQSVPLKSGAQNPYLPYPAPGEEVALYELTPHT 288

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G+ HQLR H   +G PI GD  Y         +     L L A  +D  HP   +
Sbjct: 289 GKMHQLRAHLNLLGTPIFGDVLY-PQVLPTAPNDASVPLQLLAHRLDCVHPFTNK 342


>gi|261252619|ref|ZP_05945192.1| pseudouridylate synthase LSU rRNA-specific [Vibrio orientalis CIP
           102891]
 gi|260936010|gb|EEX91999.1| pseudouridylate synthase LSU rRNA-specific [Vibrio orientalis CIP
           102891]
          Length = 231

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 52/200 (26%), Positives = 89/200 (44%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+  +   V +K   +SV    G    +    K   D+   K  L HRLD+ TSGIL+
Sbjct: 3   DILHTHTDFIVISKHPNVSVHKDDGDTMLLQEVAKQTGDT---KLYLIHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + R+  AA  L++ F  R ++K Y ++    PK K+  ++  + +        +      
Sbjct: 60  LGRSSTAASELSQMFAQRSVEKYYLAIGSKKPKKKQGLVSGDMERSRRASWKLLTSQT-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  +     +      +PH+G+THQ+RV    +G  IVGD  Y A  +  
Sbjct: 118 ----NPAVTQFFSLAAEPGER-LFLCKPHSGKTHQIRVALKSVGSGIVGDPIYNAGSES- 171

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +   +
Sbjct: 172 ------DRGYLHAFALRFTY 185


>gi|145352339|ref|XP_001420507.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580741|gb|ABO98800.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 178

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 54/180 (30%), Positives = 82/180 (45%), Gaps = 10/180 (5%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +LYE+  + + NKP G+S    S         L++  D++ ++ R  HRLD+ TSG LV
Sbjct: 1   RVLYENDAVVIVNKPPGVSFH--SEFEPGALARLRASRDAREERLRAVHRLDKGTSGTLV 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+T  AA+ L++ F  R I K Y  +    PK K   +         +        K  
Sbjct: 59  FAKTADAAKKLSDGFATRAIVKYYVGISGKKPKKKMGTVTG------DMARARRKAYKLT 112

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  +   A+       +P TG+THQLRV A  +G P++GD  Y       
Sbjct: 113 NTKDNPAVTKF--VSFGAKGRRMFIFRPLTGKTHQLRVCAKSLGAPLLGDDVYSGAVAER 170


>gi|145299458|ref|YP_001142299.1| pseudouridine synthase RluA-like protein [Aeromonas salmonicida
           subsp. salmonicida A449]
 gi|142852230|gb|ABO90551.1| pseudouridine synthase RluA-like protein [Aeromonas salmonicida
           subsp. salmonicida A449]
          Length = 219

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 56/215 (26%), Positives = 95/215 (44%), Gaps = 17/215 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            +L +     + NK  G+ +   +G +  ++ G +       GQ     HRLD+ TSG++
Sbjct: 3   RILAQHKDFMLINKGPGLGMHDEAGESGLVNPGLVSRVKADTGQVLYPVHRLDKMTSGLV 62

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ART AA + L+ +F  R++ K Y +L    PK K+  +   + K    GG ++     
Sbjct: 63  LLARTTAANRALSMAFADRQVSKQYLALSDRKPKKKQGWVKGDMQKGR--GGSWMLARSL 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +    N AIS F  +    +      ++P TG+THQ+RV    +G PI+GD +Y      
Sbjct: 121 D----NPAISWFDSVPVR-EGLRLYRIKPQTGKTHQIRVALKSIGAPILGDERYGGT--- 172

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
                  ++ YLHA  +              P   
Sbjct: 173 -----AADRGYLHAWRLSFT-LADEAFDFICPPDE 201


>gi|327484276|gb|AEA78683.1| Pseudouridylate synthase, 23S RNA-specific [Vibrio cholerae
           LMA3894-4]
          Length = 235

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 56/200 (28%), Positives = 87/200 (43%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +        D +     L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEVATQTGDGQ---LYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   AA  L++ F  R+++K Y ++    PK K+  I   + +        V+  +  
Sbjct: 60  LARNVTAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A        +PHTG+THQ+RV    +G  IVGD  Y       
Sbjct: 118 ----NPAITQFFS-AAAATGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYN------ 166

Query: 280 FTSPIQNKLYLHARYMDLPH 299
            T+   ++ YLHA  +   +
Sbjct: 167 -TADESDRGYLHAFALRFTY 185


>gi|315179926|gb|ADT86840.1| pseudouridine synthase Rlu family protein [Vibrio furnissii NCTC
           11218]
          Length = 231

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 54/198 (27%), Positives = 87/198 (43%), Gaps = 17/198 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L       + NK   +SV    G    +    K   D++     L HRLD+ TSGIL+
Sbjct: 3   DILLTHPDFLLINKHPNVSVHKDDGDTMLLQEVAKQSGDAQ---LYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   AA  L++ F  R+++K Y +L    PK K+  I+  + +        +      
Sbjct: 60  LARNAKAASELSKGFAERQVEKFYLALGSKKPKKKQGLISGDMERSRRASWKLLTSQT-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F  +     +      +P+TG+THQ+RV    +G  IVGD  Y A  +  
Sbjct: 118 ----NPAVTQFFSLAAEPGER-LFLCKPYTGKTHQIRVALKSVGSGIVGDPIYNAGNQA- 171

Query: 280 FTSPIQNKLYLHARYMDL 297
                 ++ YLHA  +  
Sbjct: 172 ------DRGYLHAFALRF 183


>gi|294786685|ref|ZP_06751939.1| RNA pseudouridine synthase [Parascardovia denticolens F0305]
 gi|315226296|ref|ZP_07868084.1| 23S RNA-specific pseudouridylate synthase [Parascardovia
           denticolens DSM 10105]
 gi|294485518|gb|EFG33152.1| RNA pseudouridine synthase [Parascardovia denticolens F0305]
 gi|315120428|gb|EFT83560.1| 23S RNA-specific pseudouridylate synthase [Parascardovia
           denticolens DSM 10105]
          Length = 263

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 59/258 (22%), Positives = 93/258 (36%), Gaps = 36/258 (13%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +        +LYEDS+I V +KP  +      G+ Y     ++       +     HRLD
Sbjct: 4   EPDIPFNLPVLYEDSRIIVVDKPHFLPTTP-RGMWYRSTALIRLREKYGDEAITPAHRLD 62

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK------------------- 192
           + T+GI+V  R     +     F+ R+ +K Y  L    P                    
Sbjct: 63  RMTAGIVVFVRDPRYRRDYQLLFQNRQARKKYVCLAPAKPVVRPALGTLFPLIDDQSGLR 122

Query: 193 ---NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------L 243
                   +   L++ SHI      +    E     A++  ++     +           
Sbjct: 123 LSCPDDRRLFFPLIRSSHITKTRGVLQACEEADKPNAVTIIRLSADQPRGQTLEKGLRSY 182

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++ P TG+T+QLRVH   +G PIVGD  Y             + L L A+ +D   P  G
Sbjct: 183 DLFPRTGKTYQLRVHMNSLGLPIVGDPLYPEILPEAAYDDFSDPLRLVAQELDFADPVSG 242

Query: 304 -------RLQITAPLPAH 314
                  R  +T P PA 
Sbjct: 243 QDFHFRSRWTVTDPGPAE 260


>gi|224824495|ref|ZP_03697602.1| pseudouridine synthase Rlu family protein, TIGR01621 [Lutiella
           nitroferrum 2002]
 gi|224602988|gb|EEG09164.1| pseudouridine synthase Rlu family protein, TIGR01621 [Lutiella
           nitroferrum 2002]
          Length = 229

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 62/215 (28%), Positives = 91/215 (42%), Gaps = 20/215 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            L+  D + YV  K  G+S       A  ++       D         HRLD+ TSG+L+
Sbjct: 3   DLIATDPRFYVIAKHPGVSFHRQGDEAGLMEALRAQLADD---ALWPVHRLDRLTSGLLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VAR+   A  L E+F  R I+K Y +L    P+ K+  +   ++K            +  
Sbjct: 60  VARSAEVASRLAEAFAAREIEKYYLALSDRKPQKKQGLVRGDMVK------GRGGAWRLL 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              AN AI+ F      A       ++PH+G+THQLRV    +  PI+GD  Y       
Sbjct: 114 PSSANPAITQFFSF-SLAPGLRLFILRPHSGKTHQLRVALKSLSAPILGDELYGGTP--- 169

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
                 ++ YLHA  +   H +G R     P P H
Sbjct: 170 -----SDRGYLHAYSLAF-HLDGERFHFICP-PRH 197


>gi|255079396|ref|XP_002503278.1| predicted protein [Micromonas sp. RCC299]
 gi|226518544|gb|ACO64536.1| predicted protein [Micromonas sp. RCC299]
          Length = 279

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 64/225 (28%), Positives = 104/225 (46%), Gaps = 18/225 (8%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV------DSKGQKPRL 146
             D  +  + +ED+   V  KP G++  G +   +  +  L  ++      +    +PR 
Sbjct: 24  PEDLPRLEVAHEDAHFAVVVKPEGVNTVGDARGGWTAERMLPYFLAPTIGVEGALVRPRP 83

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  TSG+LVVA+TR AA  L+E+F  RR+ K Y +++ G P   +  + +    ++
Sbjct: 84  VHRLDALTSGLLVVAKTRLAATSLSEAFASRRVTKRYRAVLCGTPAEPEVLVDDDDDDEN 143

Query: 207 HIGG--DYVHVVKQNEKGANYAISHFKVID------CFAQKFCWLEMQPHTGRTHQLRVH 258
              G       V          +SH++V+           +   ++M P TGRTHQLR H
Sbjct: 144 DRAGAAALKLGVIDAPMEGKQCVSHWRVVRDAPDASMRHGRLTLVDMWPKTGRTHQLRRH 203

Query: 259 AL-HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           A   +GCPI+GD +Y      +      + L+L A  + LP    
Sbjct: 204 AAGALGCPILGDARYNPK---HSPEDDVDGLFLRAVEVTLPPSAT 245


>gi|146291506|ref|YP_001181930.1| pseudouridine synthase Rlu family protein [Shewanella putrefaciens
           CN-32]
 gi|145563196|gb|ABP74131.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           putrefaciens CN-32]
          Length = 229

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 54/197 (27%), Positives = 87/197 (44%), Gaps = 19/197 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ +++   V +K   +      G      G +       G K    HRLD  TSG+L++
Sbjct: 4   IIADEADFLVISKFPKVHFHSQDGT----VGVVAQVEQDLGIKLFAVHRLDTPTSGLLIL 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A++ AAA+  TE F   ++QK Y +L  G PK K+  +   + K          + K   
Sbjct: 60  AKSTAAAKQFTELFTAHKVQKYYLALAKGKPKKKQGWVIGDMAK------SRRSMFKLLR 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  +           ++PH+G+THQLRV    +G PI+GD  Y        
Sbjct: 114 TKENPAITQFFSV-SVGDGLRLYLLKPHSGKTHQLRVALASLGVPILGDELYGG------ 166

Query: 281 TSPIQNKLYLHARYMDL 297
              + ++ YLHA  +  
Sbjct: 167 --AVADRCYLHAYCLHF 181


>gi|153800993|ref|ZP_01955579.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-3]
 gi|124123463|gb|EAY42206.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-3]
          Length = 235

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 54/200 (27%), Positives = 87/200 (43%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +         +   +  L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEV---ATQTGDAQLYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   +A  L++ F  R+++K Y ++    PK K+  I   + +        V+  +  
Sbjct: 60  LARNATSASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A        +PHTG+THQ+RV    +G  IVGD  Y       
Sbjct: 118 ----NPAITQFFS-ATAAPGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYN------ 166

Query: 280 FTSPIQNKLYLHARYMDLPH 299
            T+   ++ YLHA  +   +
Sbjct: 167 -TADESDRGYLHAFALRFTY 185


>gi|21245032|ref|NP_644614.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21110760|gb|AAM39150.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 298

 Score =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 59/289 (20%), Positives = 115/289 (39%), Gaps = 30/289 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
                +P I     +     G VR  + + +  +   + G  +R           + ++ 
Sbjct: 29  ALCACFPAIAAERWRNRFERGLVRDANDQALALSAPYRVGADIRYF-------REVADEP 81

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
           ++                +++ D+++ V  KP  + V   G+ +   +   L   +D+  
Sbjct: 82  VIPY-----------VETVVHADAQLVVACKPHFLPVAPAGAYVRETLLTRLVRRLDNPA 130

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
             P   HR+D+ET+G+++ +   A        FR RRI+K Y ++   +P+ +   +   
Sbjct: 131 LVP--LHRIDRETAGLVLFSANPATRGIYQALFRERRIRKHYLAVAAPLPELRFPYVH-- 186

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
             +     G+    +++   G   + +  +V+   A  + +  ++P TGR HQLRVH   
Sbjct: 187 --RSRLEPGEPFFRMREGV-GEPNSETVIEVVARNADTWTY-RLEPVTGRKHQLRVHMAA 242

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +G PI+ D  Y A        P    L L A  +    P  G   + TA
Sbjct: 243 LGAPILHDRFYPALEAQRPDDPG-RPLQLFAHTLAFDDPITGEPRRFTA 290


>gi|121727329|ref|ZP_01680476.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V52]
 gi|147675726|ref|YP_001217217.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O395]
 gi|262169679|ref|ZP_06037370.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC27]
 gi|121630335|gb|EAX62732.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V52]
 gi|146317609|gb|ABQ22148.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O395]
 gi|227013574|gb|ACP09784.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O395]
 gi|262021913|gb|EEY40623.1| ribosomal large subunit pseudouridine synthase D [Vibrio cholerae
           RC27]
          Length = 235

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 54/200 (27%), Positives = 86/200 (43%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +         +   +  L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEV---ATQTGDAQLYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   +A  L++ F  R+++K Y ++    PK K+  I   + +        V+  +  
Sbjct: 60  LARNATSASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A        +PHTG+THQ+RV    +G  IVGD  Y    K  
Sbjct: 118 ----NPAITQFFS-ATAAPGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYNTADKS- 171

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +   +
Sbjct: 172 ------DRGYLHAFALRFTY 185


>gi|317177743|dbj|BAJ55532.1| hypothetical protein HPF16_0935 [Helicobacter pylori F16]
          Length = 242

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 63/288 (21%), Positives = 112/288 (38%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V V  K++                       ++  +++  ++  
Sbjct: 12  ENISHKKAKALIDLGLVSVGGKKL-----------------------MVARKELPKNTHF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLALAQGIIEEEQEINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L+    TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKAGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPSSA------KRLMLHAHKISLL-----GYEFEAIPPKEFE 241


>gi|262183262|ref|ZP_06042683.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
          Length = 302

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 61/297 (20%), Positives = 116/297 (39%), Gaps = 33/297 (11%)

Query: 26  KNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
           ++ +P  N   LQ    + +V R D   ++ ++ + +  VV           +   +  +
Sbjct: 20  RHRHPEDNEAALQARFDTNEVVRQDGSPLRPDSTLATNAVVYFY-------RMPAPETPV 72

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
              +            +L+ED  + V +KP  ++    +         ++    +   + 
Sbjct: 73  PYDIP-----------ILFEDEHLLVVDKPPFMATMPRAR-HITETATVRLRRKTGNNEL 120

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRLD+ TSGILV  + R+        F  RR+ K Y ++   +       +  W  +
Sbjct: 121 SPAHRLDRLTSGILVFTKDRSVRGAYQTLFAERRVTKTYEAI-APLADVSPGTV--WRSR 177

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQKFCWLEM-----QPHTGRTHQLR 256
                G+    + + E  A   ++  + ID     +      E+     +P TG+THQLR
Sbjct: 178 MEKTPGELQGRIVEGEVNAITEVAAVEPIDKAPYESIHGSLPELAKYTLKPQTGKTHQLR 237

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +H L  G PI+GD  Y   F       ++  ++L A ++    P   R  +  + LP
Sbjct: 238 LHMLQAGVPIIGDPIYPVIFPAEAED-MRIPMHLTATHISFVDPLTARPREFFSQLP 293


>gi|254523953|ref|ZP_05136008.1| pseudouridine synthase [Stenotrophomonas sp. SKA14]
 gi|219721544|gb|EED40069.1| pseudouridine synthase [Stenotrophomonas sp. SKA14]
          Length = 295

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 60/282 (21%), Positives = 104/282 (36%), Gaps = 29/282 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +P I+    Q     G+V+    + +  +   Q G  ++    +     I      
Sbjct: 24  LCARFPRIDRAQWQDRFARGRVQDAQGRALAPDLPWQVGLEIQYFREVADEPLIP----- 78

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                            +++ D+ + V +KP  + V       +  +  L   +   G  
Sbjct: 79  -------------FAETIVHLDAHLLVADKPHFLPVTPAG--RHVRETLLARLIARTGNP 123

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +    HRLD+ T+G+++ +   A        FR RRI+KIY +L   +P       A  L
Sbjct: 124 ELVPLHRLDRLTAGLVLFSTQPATRDAYQRLFRERRIEKIYEALAPAMPGA-----AFPL 178

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            + S +             G   A S  ++I+          ++P TGR HQLRVH   +
Sbjct: 179 QRHSRLVPGEPFFRMAEVPGEPNARSRIELIEAEG-PIWRFRLRPETGRKHQLRVHMAAL 237

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G PI GD  Y  + +      ++  L L A+ +    P  G 
Sbjct: 238 GAPIEGDDLY-PHLRSRPEGAVELPLQLLAQGLAFDDPLSGE 278


>gi|15611957|ref|NP_223608.1| hypothetical protein jhp0890 [Helicobacter pylori J99]
 gi|11136009|sp|Q9ZKP5|Y956_HELPJ RecName: Full=Uncharacterized RNA pseudouridine synthase jhp_0890;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|4155455|gb|AAD06458.1| putative [Helicobacter pylori J99]
          Length = 242

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 66/288 (22%), Positives = 110/288 (38%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++ SG V +             GQ + +       N     QK+   S  
Sbjct: 12  ENISHKKAKALIDSGLVSI------------GGQKLMVARKELPQNTRFSVQKVEKPS-- 57

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                      +++ED  I    KP  I        +Y +  F K W         L HR
Sbjct: 58  -----------VIFEDENILALFKPPFI-------ESYDLVSFFKGWA--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y ++V GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLAIVQGIIEEEREINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPSSA------KRLMLHAHKIALL-----GYEFEAIAPKEFE 241


>gi|157163990|ref|YP_001467817.1| disulfide isomerase [Campylobacter concisus 13826]
 gi|112801796|gb|EAT99140.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           (RNA pseudouridylate synthase) [Campylobacter concisus
           13826]
          Length = 307

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 71/345 (20%), Positives = 126/345 (36%), Gaps = 57/345 (16%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           M YV   ++  D +     + ++    +  N    Q+ +  G++      V   N I  G
Sbjct: 1   MPYVNKFIITADHQ-----KAYEILLKNGFNMSQTQRFIDKGRLICGGSVVSEKNAILCG 55

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
           +V  I                                  ++E     VF+KP+G+     
Sbjct: 56  EVFLIDYEAKPKGLKP-----------------------IFECESFAVFDKPSGVLSHPN 92

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G    Y ++  + +     G+   + HRLD ETSG++VV + R +   L + F  R + K
Sbjct: 93  GRHCEYSLNDEIYTLF---GRDASVAHRLDCETSGVIVVGKDRNSTIKLKKIFENREVFK 149

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KF 240
            Y ++V G  + ++  I   +        D V +  Q  +    A++    I  F     
Sbjct: 150 SYVAMVQGKIE-REFTIDAKM--DLANNYDDVKMRMQICENGKSAVTKILPIKYFDDIDT 206

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +   P TGR HQ+R+H  H+   I+G+  Y        + P   K+      +D    
Sbjct: 207 TLVRAIPLTGRQHQIRLHLFHVKHKILGEPLYG------LSRPQIEKI------LDKEMS 254

Query: 301 EGGRLQITAPLPAHMVKTW---DSLGFKYDRNLYIKRLYSQDECK 342
           E  R+ +T        +     D + FK+D   Y  +     E +
Sbjct: 255 ERERINLT-----DAKRLLLHSDEISFKFDEIFYKIKSKFDAESE 294


>gi|300859437|ref|YP_003784420.1| hypothetical protein cpfrc_02020 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|300686891|gb|ADK29813.1| hypothetical protein cpfrc_02020 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|302207115|gb|ADL11457.1| Ribosomal pseudouridine synthase [Corynebacterium
           pseudotuberculosis C231]
          Length = 327

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 54/258 (20%), Positives = 87/258 (33%), Gaps = 24/258 (9%)

Query: 62  GQVVRIPP---VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           G  V I P   + +  + +   + I        +         +YED  + V NKP  ++
Sbjct: 68  GDQVIIGPKFRIASPESTLKANEDIWFYRTPAPEIPVPYSCETIYEDDNLLVVNKPPFLA 127

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                G        ++    +        HRLD+ TSGILV  + R         F  R+
Sbjct: 128 TMP-RGKHITQTATVQMRRATGNGDLSPAHRLDRLTSGILVFTKNRKVRGAYQSLFAERK 186

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS---------- 228
           + K Y ++         E +    L + H+      +      G   A +          
Sbjct: 187 VTKTYHAI-----APFSEDLTGNTLWRDHMIKTPGDMQGHIVPGPPNAETLLVDVTELDA 241

Query: 229 ----HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
                 + +           +QPHTGRTHQLR+H    G PI+GD  Y            
Sbjct: 242 QETAQLQKLHHVTTPLARYTLQPHTGRTHQLRLHMWAAGVPILGDPAYPVILAEEVED-F 300

Query: 285 QNKLYLHARYMDLPHPEG 302
           +  ++L A  +    P  
Sbjct: 301 RVPMHLTAYQLTFLDPFS 318


>gi|149200226|ref|ZP_01877248.1| Pseudouridine synthase [Lentisphaera araneosa HTCC2155]
 gi|149136668|gb|EDM25099.1| Pseudouridine synthase [Lentisphaera araneosa HTCC2155]
          Length = 290

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 58/291 (19%), Positives = 107/291 (36%), Gaps = 40/291 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVR------VDKKRVKFNNRIQSGQVVRIPPVINAL 74
           LD +F   +P I+     K    G++       ++    K       G    I       
Sbjct: 21  LD-FFCETFPQISRDTWAKRFTEGKITTTQEETLN---AKAPY---CGDQHLIYYREVEN 73

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +I  Q+                  +LYED  + + +KP  + +       Y  +  + 
Sbjct: 74  EKVIPFQE-----------------QILYEDENLLLVDKPHFLPIHPAGP--YVKETLVY 114

Query: 135 SWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              +          HR+D+ T+G++  ++  +  +     F  R ++K Y ++  G P  
Sbjct: 115 RLRESQNNPDISPLHRIDRLTAGLVFFSKKVSIRKDYQLLFENRLVEKTYHAISAG-PAP 173

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            +     W LK     G+   +    E  AN + S+  VI+         E++P +G+ H
Sbjct: 174 DQGY---WHLKNRIEAGEPWFLSAIKEGKAN-SESYINVIEAK-DNLVKFELKPISGKKH 228

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           QLRVH   +G PI+ D  Y  +F        +  + L A+ +    P   +
Sbjct: 229 QLRVHLASIGYPILHDPLY-PSFVEKPPDNYEKPMQLLAQSIAFTDPFSKK 278


>gi|167386039|ref|XP_001737591.1| ribosomal pseudouridine synthase [Entamoeba dispar SAW760]
 gi|165899521|gb|EDR26097.1| ribosomal pseudouridine synthase, putative [Entamoeba dispar
           SAW760]
          Length = 389

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 50/200 (25%), Positives = 83/200 (41%), Gaps = 11/200 (5%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
            N I ++  IL + ++  +        +++ED+ + V NKP+GI     SG  Y  +  +
Sbjct: 114 ENCIFEQGDILLNQIHRHELPVPCLLPIIHEDNDVIVVNKPSGIPTH--SGGRYTENTVI 171

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 +  K    HRLD+ TSG+L++A++   A  +   F      K Y   V G    
Sbjct: 172 NILEKERNIKLFGVHRLDRLTSGVLIIAKSSEIANEIQRHFIS--AHKKYICRVIGYM-- 227

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRT 252
               +   +++ + I    V V          + + F+ I    +     L   P TGR 
Sbjct: 228 GSCIVNKPIIETTCITKQRVTV----GSEGKISTTIFEQIQYDQKTDTTLLWAIPKTGRM 283

Query: 253 HQLRVHALHMGCPIVGDHKY 272
           HQ+RVH  +   PI  D  Y
Sbjct: 284 HQIRVHLSYENHPIANDSMY 303


>gi|167523214|ref|XP_001745944.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163775745|gb|EDQ89368.1| predicted protein [Monosiga brevicollis MX1]
          Length = 512

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 101/230 (43%), Gaps = 28/230 (12%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-------QKPRLTHRLDQETSGI 157
           D  ++V NK AG+  Q G      +  +LK              +   L HRLD+ T+G+
Sbjct: 118 DPFVWVVNKWAGLVTQ-GEKDGQSLAAYLKYMRMRHDDDMRLLTRPLSLVHRLDRNTTGV 176

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
             +AR       L +     + QKIY++   G+P  +K  I  +L    H  G  +    
Sbjct: 177 SFIARNPVVHALLQDVLATHQAQKIYYATTLGVPFPRKGEIKGYLT--PHKNGVKLDATP 234

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYC--- 273
           QN K + ++ + ++V+D   ++   + ++P TGR HQLR H    +  PI+GD +Y    
Sbjct: 235 QN-KNSVFSHTRYQVVDALDREAALVRLEPVTGRRHQLRAHLAQGLRTPILGDTQYGVGC 293

Query: 274 ANFKGNFTSPIQNK-----------LYLHARYMDLPHPEGGRLQITA-PL 311
           +N       P + +           + LHA  + +P     RLQ  A PL
Sbjct: 294 SNALRPLLFPTKGRPSTKVVVEGLPMMLHAFELVIPDYAT-RLQAVAEPL 342


>gi|283458768|ref|YP_003363408.1| pseudouridylate synthase [Rothia mucilaginosa DY-18]
 gi|283134823|dbj|BAI65588.1| pseudouridylate synthase [Rothia mucilaginosa DY-18]
          Length = 377

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 67/309 (21%), Positives = 113/309 (36%), Gaps = 47/309 (15%)

Query: 22  DRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKE 80
           D      YP+   + +     +G+VR+D   V   ++    G+ +            + +
Sbjct: 76  DYLIARFYPNDPQI-IHARFNTGEVRLDDGTVLTSDSPYMPGERIWYF-------RELAD 127

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +  L S +            +LYED  +   +KP  +      G         K  V  +
Sbjct: 128 EPELPSDMP-----------VLYEDEHVLAIDKPHFLPTTP-RGAYIAQTALTKLRVREQ 175

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY---WSLVWGIPKNKKEC 197
                  HRLD+ T+G+L+ A+T  A +     F+ RR+ K Y     +       ++  
Sbjct: 176 NPLLIPIHRLDRPTAGVLLFAKTVEARRPFQMMFQHRRVSKTYRAVAPVPADPAAAERAL 235

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYA--------ISHFKVIDCFA------------ 237
            A  L  +SHI      +  Q       A        ++  K++  F             
Sbjct: 236 SAEGLQVRSHIQKIRDQLQVQQLSEEQCAAQGVEPNTLTTAKILQTFTPSAQAVEGWRAE 295

Query: 238 --QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
             +++   ++ PHTG+THQLR H   +G PI+GD  Y          P +  L L A  +
Sbjct: 296 PNREWALYDLAPHTGKTHQLRAHLNMLGSPILGDVLYPQVLPDAPDRP-EYPLQLLAYSL 354

Query: 296 DLPHPEGGR 304
              HP  G 
Sbjct: 355 HFEHPITGE 363


>gi|32266140|ref|NP_860172.1| ribosomal pseudouridine synthase [Helicobacter hepaticus ATCC
           51449]
 gi|32262190|gb|AAP77238.1| ribosomal pseudouridine synthase [Helicobacter hepaticus ATCC
           51449]
          Length = 245

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 66/295 (22%), Positives = 112/295 (37%), Gaps = 61/295 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +     + +I+    + ++  G V    K+V          + R+   I+    I+K +K
Sbjct: 8   KVLARTH-NISHNQAKSLIDKGLVFAAGKKVN---------IARLEIPIHTAFEILKPKK 57

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             +L+ D  I    KP  I        +Y +    + W      
Sbjct: 58  ----------------PKVLFTDEHILALEKPPFI-------ESYDLSNMFEGW------ 88

Query: 143 KPRLTHRLDQETSGILVVARTRAA-AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
              L HRLD+ETSG++++ +  +A      E+F+ + + K Y  LV GI  +  E     
Sbjct: 89  --HLLHRLDRETSGVILLIKEGSAFHIKAKEAFKNQEVYKEYVCLVHGILADSIEINKAI 146

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
              K       +      +K    A++    +    +K   L+    TGRTHQ+RVH   
Sbjct: 147 STTKRGFAKSRI------DKKGLNALTLLTPLSIMGKK-TLLKALIKTGRTHQIRVHCQS 199

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           +  PI+GD  Y  N +         +L LHA  + L        + T+PLP  + 
Sbjct: 200 INHPILGDRIYGKNDEA-------KRLMLHAHKIALL-----GYEFTSPLPKELR 242


>gi|88799662|ref|ZP_01115237.1| putative RNA pseudouridylate synthase [Reinekea sp. MED297]
 gi|88777556|gb|EAR08756.1| putative RNA pseudouridylate synthase [Reinekea sp. MED297]
          Length = 309

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 65/283 (22%), Positives = 113/283 (39%), Gaps = 29/283 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +F   +PH+N   L   + +G+V  D    V  +  +  GQ  R                
Sbjct: 36  FFVARFPHLNPQALAAKIAAGRVYYDDGSPVPVDAPLIPGQ--RFWYFRE---------- 83

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
                 N  +      + +LYED +I V +KP  +S    G  + + +   L++   +  
Sbjct: 84  ------NPNEPDIPFDADILYEDEQILVVDKPHFLSTTPVGQFMKHTVTTRLRNRTGNMA 137

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
             P   HRLD+ T+G+L++ + RA  +     F  R ++K Y +L    P+  ++   N 
Sbjct: 138 ITP--AHRLDRATAGVLLLTKQRAVREAYQSLFLRREVEKTYHALCHPNPELPEQFEINL 195

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            LK+     D + V   +      + +  K +   +      E++P +GR HQLR    H
Sbjct: 196 HLKE---NTDNMFVRVLDAPP--NSHTSAKRLARHSTGD-LYELRPSSGRKHQLRCQMAH 249

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +G  IV D  Y    +          L L A+ +    P  G+
Sbjct: 250 LGAGIVNDIWY-PVAQDPSPDDFSRPLQLLAKKLAFIDPFSGQ 291


>gi|153825491|ref|ZP_01978158.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-2]
 gi|149740903|gb|EDM54988.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-2]
          Length = 235

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 54/200 (27%), Positives = 86/200 (43%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +         +   +  L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEV---ATQTGDDQLYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR   +A  L++ F  R+++K Y ++    PK K+  I   + +        V+  +  
Sbjct: 60  LARNATSASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A        +PHTG+THQ+RV    +G  IVGD  Y    K  
Sbjct: 118 ----NPAITQFFS-ATAAPGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYNTADKS- 171

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +   +
Sbjct: 172 ------DRGYLHAFALRFTY 185


>gi|294659113|ref|XP_461454.2| DEHA2F25652p [Debaryomyces hansenii CBS767]
 gi|202953627|emb|CAG89871.2| DEHA2F25652p [Debaryomyces hansenii]
          Length = 433

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 54/249 (21%), Positives = 105/249 (42%), Gaps = 13/249 (5%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           +IQS  ++     I+  + + +  +++  S   T   D     +++E+ ++ V +KPAGI
Sbjct: 85  KIQSQDLIYNSKHIHEPS-VAQGLELVKKSSKCTSQ-DLTDLSIIFENDEMLVIDKPAGI 142

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE--SFR 175
                    Y+    L    D   +     HRLD+ TSGIL++  T+  ++  +   +  
Sbjct: 143 PTHPKGNYRYNSITELVKH-DLNLENVWPCHRLDKVTSGILILGTTKQGSKIYSTIINNE 201

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             RI K Y + V G     +  +   +   +  GG  +    +N      + + F+ ++ 
Sbjct: 202 RDRISKQYVARVMGEFPKDEFVMNCPIFLVNTSGGYIMPSNSRNVP--KNSTTIFRRLNY 259

Query: 236 FAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-----LY 289
             +     +  +P TGR HQ+R+H  + G PIV D++Y        +   + +       
Sbjct: 260 NKELNQSIVLCKPITGRMHQIRIHLRNTGHPIVNDYEYNPQGDATRSHIQRLRNQIELQM 319

Query: 290 LHARYMDLP 298
               Y+D P
Sbjct: 320 YENIYLDFP 328


>gi|317012766|gb|ADU83374.1| hypothetical protein HPLT_04870 [Helicobacter pylori Lithuania75]
          Length = 242

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 65/288 (22%), Positives = 111/288 (38%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +++    + ++  G V +  K++                 + A   + K  +     V 
Sbjct: 12  ENVSHKKAKALIDLGLVSIGGKKL-----------------MVARKELPKNTRFSVQKVE 54

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 55  --------KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +LV GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVEKEYLALVQGIIEEEREINAPILTFKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAYKIALL-----GYEFEAIPPKEFE 241


>gi|307637648|gb|ADN80098.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 908]
 gi|325996243|gb|ADZ51648.1| pseudouridine synthase D [Helicobacter pylori 2018]
 gi|325997837|gb|ADZ50045.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 2017]
          Length = 242

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 65/288 (22%), Positives = 111/288 (38%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++ SG V +  +++                 + A   + K  +     V 
Sbjct: 12  ENISHKKAKALIDSGLVSIGGQKL-----------------MVARKELPKNTRFSVQKVE 54

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   K  +++ED  I    KP  I        +Y +  F K W         L HR
Sbjct: 55  --------KPSVIFEDENILALFKPPFI-------ESYDLVSFFKDWA--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y ++V GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLAIVQGIIEEEREINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    AI+    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAITIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKIALL-----GYEFEAIAPKEFE 241


>gi|302331676|gb|ADL21870.1| Ribosomal pseudouridine synthase [Corynebacterium
           pseudotuberculosis 1002]
          Length = 325

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 54/258 (20%), Positives = 87/258 (33%), Gaps = 24/258 (9%)

Query: 62  GQVVRIPP---VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           G  V I P   + +  + +   + I        +         +YED  + V NKP  ++
Sbjct: 66  GDQVIIGPKFRIASPESTLKANEDIWFYRTPAPEIPVPYSCETIYEDDNLLVVNKPPFLA 125

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                G        ++    +        HRLD+ TSGILV  + R         F  R+
Sbjct: 126 TMP-RGKHITQTATVQMRRATGNGDLSPAHRLDRLTSGILVFTKNRKVRGAYQSLFAERK 184

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS---------- 228
           + K Y ++         E +    L + H+      +      G   A +          
Sbjct: 185 VTKTYHAI-----APFSEDLTGNTLWRDHMIKTPGDMQGHIVPGPPNAETLLVDVTELDA 239

Query: 229 ----HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
                 + +           +QPHTGRTHQLR+H    G PI+GD  Y            
Sbjct: 240 QETAQLQKLHHVTTPLARYTLQPHTGRTHQLRLHMWAAGVPILGDPAYPVILAEEVED-F 298

Query: 285 QNKLYLHARYMDLPHPEG 302
           +  ++L A  +    P  
Sbjct: 299 RVPMHLTAYQLTFLDPFS 316


>gi|237747521|ref|ZP_04578001.1| RNA pseudouridylate synthase [Oxalobacter formigenes OXCC13]
 gi|229378883|gb|EEO28974.1| RNA pseudouridylate synthase [Oxalobacter formigenes OXCC13]
          Length = 319

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 56/291 (19%), Positives = 105/291 (36%), Gaps = 34/291 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV-RIPPVINALNHIIKEQK 82
           +    +P +     QK                  R+ +G V+      +++       QK
Sbjct: 37  FLSERFPVLTKEEWQK------------------RVIAGDVLNENGTPLSSGAPYTPYQK 78

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +        +  +  +  +LY+D  + V +KP  + V       Y  +  L       G 
Sbjct: 79  LYYYRYLPNERPNPFQETVLYQDDWLVVADKPHFLPVTPSG--KYVSETLLVRLRKKLGI 136

Query: 143 K-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HR+D+ET+G+++ +            FR   + K Y ++        ++ IA  
Sbjct: 137 DTLTPIHRIDRETAGLVLFSVKPEGRNLYQRLFRENFVSKHYEAI-----APYRDDIAFP 191

Query: 202 LLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
           +  +S I  GD    ++    G   A +    I   +  F    ++P TGR HQLR+   
Sbjct: 192 MRYRSRIEEGDSFMRMRVIPDGTPNAETEI-SIQQKSNAFAHYHLKPVTGRKHQLRIQMC 250

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQN-----KLYLHARYMDLPHPEGGRLQ 306
            +G P++ D  Y  +     T  +Q       L L A+ +    P   ++ 
Sbjct: 251 SLGIPLLNDRIYPVHLPEAVTDEMQAEEFRYPLQLVAKSVSFKDPVSEKIH 301


>gi|198477421|ref|XP_002136622.1| GA24957 [Drosophila pseudoobscura pseudoobscura]
 gi|198142914|gb|EDY71626.1| GA24957 [Drosophila pseudoobscura pseudoobscura]
          Length = 540

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 52/244 (21%), Positives = 104/244 (42%), Gaps = 28/244 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        ++ +++G + V+ ++V  + R++   ++      + +    + 
Sbjct: 320 LDIF-SREFRAHPSEEYERRIQAGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQ- 377

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                               +++ +  + V NKPA I V       ++   F+ +  +  
Sbjct: 378 -----------------PIKIVHMNEDLVVVNKPASIPVHPCGRYRHNTVVFILA-KEFN 419

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIA 199
            +  R  HRLD+ TSG+L+  R+   A+ + +  R R+++K Y   V GI P    EC  
Sbjct: 420 LKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRNRQVEKEYICRVEGIFPDEIVECKE 479

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              +    IG     V K +++G +   +  K+      K   +  +P TGR HQ+RVH 
Sbjct: 480 PIEVVSYKIG-----VCKVSQRGKDCTTTFQKI--SQNGKTSVVLCKPLTGRMHQIRVHL 532

Query: 260 LHMG 263
            ++G
Sbjct: 533 QYLG 536


>gi|254779554|ref|YP_003057660.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
 gi|254001466|emb|CAX29466.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
          Length = 242

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 62/288 (21%), Positives = 114/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V +  K++                       ++  +++  ++  
Sbjct: 12  ENISHKKAKALIDLGLVSIGGKKL-----------------------MVARKELPKNTHF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPGVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y ++V GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLAIVQGIVEEEREINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKIALL-----GYEFEAIPPKEFE 241


>gi|38234813|ref|NP_940580.1| hypothetical protein DIP2277 [Corynebacterium diphtheriae NCTC
           13129]
 gi|38201077|emb|CAE50801.1| Conserved hypothetical protein [Corynebacterium diphtheriae]
          Length = 349

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 54/260 (20%), Positives = 97/260 (37%), Gaps = 17/260 (6%)

Query: 58  RIQSGQVVRIPPVINALNHII--KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           R ++ QV+  P    A    +      +    +   + +      ++YED  + V +KP 
Sbjct: 84  RFEADQVIIGPRFRIASPDSVLRTNDDVWFYRIPAPEPTIPYSCTVVYEDDTLLVADKPP 143

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            ++     G        ++    +   +    HRLD+ TSG+L+  + +         F 
Sbjct: 144 FLATMP-RGKHITNSATVQLRRSTGIDELSPAHRLDRLTSGLLLFTKRKRVRGAYQTLFS 202

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R ++K Y +     P      I  W    +   G+    +      A   +S  + ID 
Sbjct: 203 ERNVRKTYVATAQYNPSITPGTI--WRSHMTKTAGEIQGHIIDAPPNAETLVSAIERIDA 260

Query: 236 FAQKF-----------CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
             Q+                ++PHTG+THQLR+H L  G PI+GD  Y      +     
Sbjct: 261 PTQQHLHALHGTDVDLAHYTLKPHTGKTHQLRLHMLAAGVPILGDTIYPTILAEDAED-Y 319

Query: 285 QNKLYLHARYMDLPHPEGGR 304
              ++L +  ++   P  GR
Sbjct: 320 SRPMHLTSTELEFIDPLTGR 339


>gi|78485672|ref|YP_391597.1| pseudouridine synthase RluA-like [Thiomicrospira crunogena XCL-2]
 gi|78363958|gb|ABB41923.1| Pseudouridine synthase, Rlu family protein [Thiomicrospira
           crunogena XCL-2]
          Length = 238

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 55/214 (25%), Positives = 99/214 (46%), Gaps = 14/214 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK--GQKPRLTHRLDQET 154
           L   ++++ ++  V +KPAG++              L  +V  +   ++    HRLD+ T
Sbjct: 6   LPITVVFQSTEFIVVDKPAGMNFHSEPDSDGQKQPGLVVFVQQQLGVEELYPVHRLDKMT 65

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+++ A ++A+A+   + F  R+IQK Y ++    PK K+  +   ++           
Sbjct: 66  SGLVIFALSKASAKAFQQLFESRQIQKFYLAISTHKPKKKQGWVKGDMMPARRGS----- 120

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
             K ++   N AI+ F +         W  + PHTG+THQLRV    +G PI GD +Y  
Sbjct: 121 -WKLSKTLENPAITQF-ISQNTRPGERWFLLNPHTGKTHQLRVALKSLGAPIAGDARYAL 178

Query: 275 NFKGNFTSPIQNKLYLHARYMDLP-HPEGGRLQI 307
           + +       +++ YLHA  +    H E     +
Sbjct: 179 SAEAEH----EDRGYLHAFALRFTLHDESYEFCV 208


>gi|83644882|ref|YP_433317.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83632925|gb|ABC28892.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 231

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 58/213 (27%), Positives = 92/213 (43%), Gaps = 17/213 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              ++ +   + V +K  GIS     G      G      D+ G +    HRLD+ TSG+
Sbjct: 5   PFQIVSDYDDLLVVDKAPGISFHDEEGQP----GLCSCVADTLGIRVYPVHRLDKVTSGL 60

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++ +T A A+ LTE F +R+++K Y +L    P+ K+  I   + K            K
Sbjct: 61  LLLPKTPALARELTEQFSLRQVEKYYLALSAHKPQKKQGKIIGDMEKA------RAGAWK 114

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                 N A++ F           ++ ++P TG+THQ+RV    +  PI GD  Y     
Sbjct: 115 LTAGRENPAVTQFFSHSLQPGVRAFM-VRPLTGKTHQIRVALKSVSAPIAGDSLYGGRAN 173

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
             F     ++ YLHA  +   +  G R  I  P
Sbjct: 174 KEF-----DRTYLHAYGVRFNY-RGNRTAILCP 200


>gi|306823384|ref|ZP_07456759.1| possible pseudouridylate synthase [Bifidobacterium dentium ATCC
           27679]
 gi|309802642|ref|ZP_07696746.1| RNA pseudouridine synthase [Bifidobacterium dentium JCVIHMP022]
 gi|304553091|gb|EFM41003.1| possible pseudouridylate synthase [Bifidobacterium dentium ATCC
           27679]
 gi|308220706|gb|EFO77014.1| RNA pseudouridine synthase [Bifidobacterium dentium JCVIHMP022]
          Length = 264

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 86/228 (37%), Gaps = 15/228 (6%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + +     +  +LYED  I V +KP  ++     G+ Y     ++             HR
Sbjct: 26  IAEPHIPFEYEVLYEDDGIIVIDKPHFLATTP-RGMWYRETALIRLRERYGEPDIVPAHR 84

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN------- 200
           LD+ T+G++V  R           F+  R  K Y   + +  + + +   +         
Sbjct: 85  LDRLTAGVVVFVRKPELRGAYQMLFQEHRTVKTYECLAPLAPVVRPRYGTVTRIDRNQPF 144

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----AQKFCWLEMQPHTGRTHQLR 256
            L+++SHI  D   +       A  A S  +  D              + P TG+THQLR
Sbjct: 145 PLVRRSHIAKDRGRLQAYEIPAAVNAESLIERGDNPHIIDGNVVINYVLHPKTGKTHQLR 204

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           VH   +G PI+GD  Y  +            L L AR ++   P  G 
Sbjct: 205 VHMNSLGLPILGDDFY-PDVIQRPYDDFSRPLELVARRLEFDDPVTGE 251


>gi|296453676|ref|YP_003660819.1| pseudouridine synthase [Bifidobacterium longum subsp. longum
           JDM301]
 gi|322688643|ref|YP_004208377.1| ribosomal pseudouridine synthase [Bifidobacterium longum subsp.
           infantis 157F]
 gi|296183107|gb|ADG99988.1| pseudouridine synthase [Bifidobacterium longum subsp. longum
           JDM301]
 gi|320459979|dbj|BAJ70599.1| putative ribosomal pseudouridine synthase [Bifidobacterium longum
           subsp. infantis 157F]
          Length = 254

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 61/252 (24%), Positives = 94/252 (37%), Gaps = 31/252 (12%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + +     +  +LYED +I V +KP  ++     G+ Y     ++             HR
Sbjct: 2   IDEPHIPFEMDVLYEDERIIVVDKPHFLATMP-RGMWYRQTALIRLRERLGEPDITPAHR 60

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN------- 200
           LD+ T+G+LV  R  A        F+ R+  KIY   +    I   +   I         
Sbjct: 61  LDRMTAGVLVFVRDSACRGAYQMLFQNRQAVKIYECLAPCRPISGPRFGTIMQVEPPRPF 120

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-------------------AQKFC 241
            LL++SHI  ++  +    E G   A +  +  D                         C
Sbjct: 121 PLLRRSHITKEHGTMAAFEEPGLANAETLIERGDLCFPPAGGRWREAPEGGPHPGNHPIC 180

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
              + P TG+THQLRVH   +G PIVGD  Y    +          L L AR +    P 
Sbjct: 181 RYTLHPRTGKTHQLRVHMNSLGLPIVGDDFY-PRIQTRPYDDFSQPLQLVARVLRFTDPI 239

Query: 302 GGRL-QITAPLP 312
            G   +  + +P
Sbjct: 240 TGEKREFVSRVP 251


>gi|253701551|ref|YP_003022740.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251776401|gb|ACT18982.1| pseudouridine synthase [Geobacter sp. M21]
          Length = 293

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 61/291 (20%), Positives = 114/291 (39%), Gaps = 28/291 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +P +     ++ +  G+V                      P+ +A ++  ++
Sbjct: 23  LD-FLVGRFPKVGRNCWERRIARGKVL---------------DE-EGNPITSASSYAPQK 65

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +      +   K   F +  +L+++ ++ V  KP  + V  G G  Y     L    +S 
Sbjct: 66  RIFYYREIENEKVIPFAEE-ILFQNDELLVACKPHFLPVTPGGG--YLSQSLLHRLREST 122

Query: 141 GQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           G       HR+D+ET+GI++ +            FR   I+K Y ++     +  +   A
Sbjct: 123 GIHDLVPLHRIDRETAGIVLFSVNPKTRGLYGGVFRDGSIEKSYEAISAARIEPGQ---A 179

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            WL++   + G+    V+    G   A S  ++++         ++ P TG+THQLRVH 
Sbjct: 180 EWLVENRLVQGEPWFRVR-TGDGPPNARSLIRLVEQR-DGAARFQLTPVTGKTHQLRVHM 237

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
             +G  I+ D  Y               L L AR +    P  G+ L+  +
Sbjct: 238 SGLGLQILHDRLY-PQLMPRQPDDFDRPLQLLARRVRFRDPLSGKLLEFES 287


>gi|227546352|ref|ZP_03976401.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium longum
           subsp. infantis ATCC 55813]
 gi|227213333|gb|EEI81205.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium longum
           subsp. infantis ATCC 55813]
          Length = 254

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 61/252 (24%), Positives = 94/252 (37%), Gaps = 31/252 (12%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + +     +  +LYED +I V +KP  ++     G+ Y     ++             HR
Sbjct: 2   IDEPHIPFEMDVLYEDERIIVVDKPHFLATMP-RGMWYRQIALIRLRERLGEPDITPAHR 60

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN------- 200
           LD+ T+G+LV  R  A        F+ R+  KIY   +    I   +   I         
Sbjct: 61  LDRMTAGVLVFVRDSACRGAYQMLFQNRQAVKIYECLASCRPISGPRFGTIMQVEPPRPF 120

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-------------------AQKFC 241
            LL++SHI  ++  +    E G   A +  +  D                         C
Sbjct: 121 PLLRRSHITKEHGTMAAFEEPGLANAETLIERGDLCFPPAGGRWREAPEGGPHPGNHPIC 180

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
              + P TG+THQLRVH   +G PIVGD  Y    +          L L AR +    P 
Sbjct: 181 RYTLHPRTGKTHQLRVHMNSLGLPIVGDDFY-PRIQTRPYDDFSQPLQLVARVLRFTDPI 239

Query: 302 GGRL-QITAPLP 312
            G   +  + +P
Sbjct: 240 TGEKREFVSRVP 251


>gi|261838329|gb|ACX98095.1| pseudouridine synthase C [Helicobacter pylori 51]
          Length = 242

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 65/288 (22%), Positives = 115/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V V  K++                       ++  +++  ++  
Sbjct: 12  ENISHKKAKALIDLGLVSVGGKKL-----------------------MVARKELPKNTHF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPSVIFEDENILALFKPPFI-------ESYDLLSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLALAQGIIEEEREINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y      N  S    +L LHA  + L        +  A  P    
Sbjct: 205 DTLY------NNESSSAKRLMLHAHKIALL-----GYEFEAIPPKEFE 241


>gi|295396160|ref|ZP_06806342.1| RNA pseudouridine synthase [Brevibacterium mcbrellneri ATCC 49030]
 gi|294970948|gb|EFG46841.1| RNA pseudouridine synthase [Brevibacterium mcbrellneri ATCC 49030]
          Length = 315

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 56/265 (21%), Positives = 95/265 (35%), Gaps = 26/265 (9%)

Query: 44  GQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
           G V  + + V     +  G            + I+  ++ +                +++
Sbjct: 61  GLVDENGQPVTLETPVTPG-------GFYFFHRIVPPEERVP-----------FDVTVVH 102

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           ED  + V +KP  ++               +  VD         HRLD+ T+G+L+++R 
Sbjct: 103 EDEHLLVVDKPHFLASTPNGRFVRECVVT-RLRVDRNEPDLVAIHRLDRVTAGLLILSRN 161

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
                     F+ R++ K Y +L   +     +  A     +S I  D      +   G 
Sbjct: 162 PDTRGAYQRLFQDRKVDKTYEAL--AVLPPDFDPAAFPRECESRIEKDKGTRGVKEVDGP 219

Query: 224 NYAISHFK----VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
             A S  +    V            + PHTG+THQLRVH L  G PI+GD  Y  +   +
Sbjct: 220 INARSRIEFSHVVGTYEGDPVGRFVLTPHTGKTHQLRVHMLGAGVPILGDPVYPHDLDQD 279

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR 304
                 + L L A  ++   P  G 
Sbjct: 280 PYD-FSHPLRLCAVGLEFRDPLSGE 303


>gi|320459050|dbj|BAJ69671.1| putative ribosomal pseudouridine synthase [Bifidobacterium longum
           subsp. infantis ATCC 15697]
          Length = 254

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 57/243 (23%), Positives = 93/243 (38%), Gaps = 30/243 (12%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + +     +  +LYED +I V +KP  ++     G+ Y     ++             HR
Sbjct: 2   IDEPHIPFEMDVLYEDERIIVVDKPHFLATMP-RGMWYRQTALIRLRERLGEPDITPAHR 60

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN------- 200
           LD+ T+G+LV  R  A        F+ R+  K+Y   +    I + +   +         
Sbjct: 61  LDRMTAGVLVFVRDPACRGAYQMLFQNRQAVKVYECLAPCRPIVRPRYGTVTRIDPPRPF 120

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-------------------KFC 241
            LL++SHI  +   +      G   A +  +  +  +                      C
Sbjct: 121 PLLRRSHIVKERGVLAAFEMPGLVNAETLIERGEPVSLFPGVKPCMPMAGGPRPSAVPVC 180

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
              ++PHTG+THQLRVH   +G PIVGD  Y    +          L L AR +    P 
Sbjct: 181 RYTLRPHTGKTHQLRVHMNALGLPIVGDDFY-PCIQARRYDDFSQPLQLVARVLRFTDPV 239

Query: 302 GGR 304
            G+
Sbjct: 240 TGQ 242


>gi|167391242|ref|XP_001739694.1| ribosomal pseudouridine synthase [Entamoeba dispar SAW760]
 gi|165896535|gb|EDR23920.1| ribosomal pseudouridine synthase, putative [Entamoeba dispar
           SAW760]
          Length = 378

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 77/347 (22%), Positives = 130/347 (37%), Gaps = 78/347 (22%)

Query: 29  YPHINFVNLQKILRSGQVR--VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
           + HI+   +Q+ +   Q+   ++K  +K    + S               +I+E  IL S
Sbjct: 47  FKHISKEEIQRQINE-QITYLINKNGIKKETSLHS---------------VIEEHDILIS 90

Query: 87  SVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-KP 144
             +L +    +K I ++    +  V NKP+GI V       Y+ +  L   ++       
Sbjct: 91  KCHLHEPPVPIKEIKIIENTPEFLVINKPSGIPVHPTG--RYNQNCILNILLNEHHFSHL 148

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--------IQKIYWSLVWGIPKNKKE 196
           +  +RLD+ TSG+L+ A+T+  A       + +         +QKIY + V G   +  E
Sbjct: 149 KPVYRLDKNTSGVLLFAKTKKFASSFQSFLKEKSSVFSSPSSLQKIYLARVVGYFPDFIE 208

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQL 255
              N  L     G +  + + ++   A  +   FK +          +E  PHTGRTHQL
Sbjct: 209 V--NLPLHLIRFGTESQNSICEDGVEAKSS---FKRLFFDKDSNTSVIECIPHTGRTHQL 263

Query: 256 RVHALHMGCPIVGDH-------------------------KYCANFKGN-------FTSP 283
           R+H   +  PI  D                          KY   F  +          P
Sbjct: 264 RLHLKAINHPIANDSAYLLNQIHNYRQQDGDFIRENKWREKYGWVFDKDCNDCNFPKGDP 323

Query: 284 IQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
           I+++++LHA                A +P      W  L F   R+L
Sbjct: 324 IEDQIWLHAWKYSFNS-----HNWIAEIPE-----WAELNFDARRSL 360


>gi|220911522|ref|YP_002486831.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
 gi|219858400|gb|ACL38742.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
          Length = 326

 Score =  126 bits (316), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 51/266 (19%), Positives = 100/266 (37%), Gaps = 21/266 (7%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPA 115
           +R  +G++V    V  + +  +++   +     L   +   +   +L++D  + V +KP 
Sbjct: 45  DRFDAGEIVGEGGVPLSRHTRLEDHTFIWYYRTLPPETRIPVDLSILHQDEHLLVVDKPH 104

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +    G G        ++             HRLD+ T+G+L+ +            F 
Sbjct: 105 FLPTTPG-GTYIQESALVRLRNQLDLPDLIPMHRLDRMTAGVLLFSTNPQTRGKYQVLFE 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R++QK Y  +    P      +   ++ ++ +     +++ +  +G   A +  + ++ 
Sbjct: 164 KRQVQKEYECVSAADPAPGHPAVEFPVVVRNRMTKSRSYLLAEVVEGEPNAETRIERLET 223

Query: 236 FAQKFC------------------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           F                          ++PHTG+THQLRVH   +G  IV D  Y  +  
Sbjct: 224 FDGGASPDTNGSTAAVPGSPTRLARYRLEPHTGKTHQLRVHMASLGLGIVNDAFY-PDLL 282

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
                     L L AR + L  P  G
Sbjct: 283 DKAPDDYAKPLQLLARGIRLVDPISG 308


>gi|308809005|ref|XP_003081812.1| RNA pseudouridylate synthases (ISS) [Ostreococcus tauri]
 gi|116060279|emb|CAL55615.1| RNA pseudouridylate synthases (ISS) [Ostreococcus tauri]
          Length = 441

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 52/294 (17%), Positives = 98/294 (33%), Gaps = 41/294 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV--DKKRVKFNN-----------R 58
           V+      RL   F   +P       ++  RSG++R+  + +    ++            
Sbjct: 81  VKARWAGERLCEMFAREFPMRPIEYYREAYRSGRLRLEENGRAAASSDGQNRETHEDGPI 140

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +  GQ VR     +    I ++ ++L  +                    +    KPA + 
Sbjct: 141 LVGGQRVRHFIHRHEPPTIAEDVRVLSVT------------------DDVVAVCKPATMP 182

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           V        +    L +       +    HRLD+  SG+L++AR+  AA  + +    R 
Sbjct: 183 VHPTGQYRRNTVLALLASTRRDLGRLFPIHRLDKNVSGLLLLARSSKAANAMRQKMEARE 242

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE----------KGANYAIS 228
           ++K Y + V G                     + V + ++            K    A +
Sbjct: 243 MRKEYVARVKGSFNASDPTPVTIDEALGFDAKNRVALWREKPGTRDLDERALKSFKAAST 302

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
            F  +         ++ +P TGR+HQ+R H    G  I  D  Y      +  +
Sbjct: 303 KFVWLQDLPDGTSLVQCEPFTGRSHQIRAHLAIAGYAIANDVAYGGELLESARA 356


>gi|119963365|ref|YP_946570.1| RNA pseudouridine synthase [Arthrobacter aurescens TC1]
 gi|119950224|gb|ABM09135.1| putative RNA pseudouridine synthase [Arthrobacter aurescens TC1]
          Length = 309

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 54/252 (21%), Positives = 95/252 (37%), Gaps = 6/252 (2%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPA 115
           +R  +G++V    V    +  +++   +     L   +     I +L++D  I V +KP 
Sbjct: 45  DRFDAGEIVGEGGVPLDRSTKLEDHTFIWYYRTLPPETRLPVEINILHQDEHILVVDKPH 104

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +    G G        ++             HRLD+ T+G+L+++            F 
Sbjct: 105 FLPTTPG-GTYIQESALVRLRNLLNLPDLIPMHRLDRMTAGLLLLSTNPETRGKYQVLFE 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV---VKQNEKGANYAISHFKV 232
            R++QK Y  +    P      +    + ++ +     ++   V   E  A   I   K 
Sbjct: 164 KRQVQKEYECVSAATPAAGFPAVEFPAVVRNRMTKSRSYLLAEVIDGEPNAETRIEQTKT 223

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
            D    +     ++PHTG+THQLRVH   +G  IV D  Y  +            L L A
Sbjct: 224 FDAGTHQRALYRLEPHTGKTHQLRVHMASLGLGIVNDAFY-PDLLDKAPDDYTKPLQLLA 282

Query: 293 RYMDLPHPEGGR 304
           R +    P   +
Sbjct: 283 RGITFVDPISKQ 294


>gi|301114795|ref|XP_002999167.1| RNA pseudouridylate synthase, putative [Phytophthora infestans
           T30-4]
 gi|262111261|gb|EEY69313.1| RNA pseudouridylate synthase, putative [Phytophthora infestans
           T30-4]
          Length = 556

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 90/247 (36%), Gaps = 33/247 (13%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
            + SG++ V+ K V  +  I++G ++      +      +E                   
Sbjct: 238 AIASGRITVNNKIVLGDTVIKNGDLIIHTAHRHEPPVSGEE------------------V 279

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++YED  + V +KP  +         ++    +         +  + HRLD+ TS    
Sbjct: 280 RVVYEDDDLIVVSKPPSMPTHPCGAYRHNSLHTILQATRPDLPQLNIVHRLDRLTSADRQ 339

Query: 160 VARTRAAAQH------LTESFRMRRIQKIYW---SLVWGIPKNKKECIANWLLKKSHIGG 210
            ++T  A         L+   + + + +      + +   P+     I+  L   S   G
Sbjct: 340 ASKTYLARVRGRFPDVLSSEVQDKLVTQAKEICPASIITFPEEGAVLISCPLRCLSARDG 399

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                V +  +    + +  +++    +    ++ +P TGRTHQ+R+H   +G PI  D 
Sbjct: 400 -----VWECHEEGKPSETLVRLV-RTDKCTSLVKCKPVTGRTHQIRLHLQLIGFPIANDP 453

Query: 271 KYCANFK 277
            Y     
Sbjct: 454 CYGGELH 460


>gi|223038326|ref|ZP_03608620.1| RNA pseudouridine synthase family [Campylobacter rectus RM3267]
 gi|222880183|gb|EEF15270.1| RNA pseudouridine synthase family [Campylobacter rectus RM3267]
          Length = 303

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 63/291 (21%), Positives = 111/291 (38%), Gaps = 45/291 (15%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           Q+++  G++  D   V   N + SG++  I    N                         
Sbjct: 31  QRLIDKGRLTCDGAVVGEKNALLSGEICLIEYETNPRGLRP------------------- 71

Query: 98  KSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
               ++E  K  VF+KP G+     G    Y ++  + S     G++  + HRLD ETSG
Sbjct: 72  ----IFECEKFAVFDKPNGVLSHPNGRHCEYSLNDEIWSLY---GREASVAHRLDCETSG 124

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++VV + +    +L + F  R++ K Y +L  G         AN  L   +        +
Sbjct: 125 LIVVGKDKNTVVNLKKLFENRQVYKSYVALAQGKISENLRIEANMDLANDYDDVKMRMRI 184

Query: 217 KQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC-- 273
            ++      A++    I+ FA      ++  P TGR HQ+R+H  H+   I+G+  Y   
Sbjct: 185 CED---GKSAVTEISPIEYFADIDATLVQAVPLTGRQHQIRLHLFHVEHKILGEPLYGLM 241

Query: 274 -----------ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
                       +      +    +L LHA  +     +G   +I +   A
Sbjct: 242 RSQIEKILDKEMSEAERILTTGAPRLLLHADEIRFKF-DGIEYEIRSEFDA 291


>gi|227834247|ref|YP_002835954.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
 gi|227455263|gb|ACP34016.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
          Length = 353

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 61/297 (20%), Positives = 116/297 (39%), Gaps = 33/297 (11%)

Query: 26  KNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
           ++ +P  N   LQ    + +V R D   ++ ++ + +  VV           +   +  +
Sbjct: 71  RHRHPEDNEAALQARFDTNEVVRQDGSPLRPDSTLATNAVVYFY-------RMPAPETPV 123

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
              +            +L+ED  + V +KP  ++    +         ++    +   + 
Sbjct: 124 PYDIP-----------ILFEDEHLLVVDKPPFMATMPRAR-HITETATVRLRRKTGNNEL 171

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRLD+ TSGILV  + R+        F  RR+ K Y ++   +       +  W  +
Sbjct: 172 SPAHRLDRLTSGILVFTKDRSVRGAYQTLFAERRVTKTYEAI-APLADVSPGTV--WRSR 228

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVID---CFAQKFCWLEM-----QPHTGRTHQLR 256
                G+    + + E  A   ++  + ID     +      E+     +P TG+THQLR
Sbjct: 229 MEKTPGELQGRIVEGEVNAITEVAAVEPIDKAPYESIHGSLPELAKYTLKPQTGKTHQLR 288

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           +H L  G PI+GD  Y   F       ++  ++L A ++    P   R  +  + LP
Sbjct: 289 LHMLQAGVPIIGDPIYPVIFPAEAED-MRIPMHLTATHISFVDPLTARPREFFSQLP 344


>gi|239998629|ref|ZP_04718553.1| Pseudouridine synthase [Neisseria gonorrhoeae 35/02]
 gi|268594485|ref|ZP_06128652.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae 35/02]
 gi|268547874|gb|EEZ43292.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae 35/02]
 gi|317163901|gb|ADV07442.1| hypothetical protein NGTW08_0470 [Neisseria gonorrhoeae
           TCDC-NG08107]
          Length = 307

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 46/223 (20%), Positives = 87/223 (39%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKGQKPRL 146
            +     +  +L+ D  + V +KP  + V  G                       +    
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPGGRFLRETLLTRLRLHPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L        K  +   L   S
Sbjct: 147 IHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEAL-----APTKTDLPYPLDVVS 201

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +         Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 202 RLVRGEKFFTTQEAEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|30696108|ref|NP_176031.2| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|75140931|sp|Q7XA65|PUS1_ARATH RecName: Full=RNA pseudourine synthase 1; AltName: Full=RNA
           pseudouridylate synthase 1; AltName: Full=RNA-uridine
           isomerase 1
 gi|33589806|gb|AAQ22669.1| At1g56345 [Arabidopsis thaliana]
 gi|110736414|dbj|BAF00174.1| hypothetical protein [Arabidopsis thaliana]
 gi|332195260|gb|AEE33381.1| RNA pseudourine synthase 1 [Arabidopsis thaliana]
          Length = 322

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 62/255 (24%), Positives = 106/255 (41%), Gaps = 52/255 (20%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---SKGQKPRLTHRLDQET 154
           +  +LYED  +   NKP G+          + +  L+S          +  L +RLD++T
Sbjct: 74  RDDILYEDEYLMAVNKPKGV----------YCEAVLRSAPQIVLDSSSEYHLANRLDRDT 123

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++ ++   A  L ++F   +I+K Y +L  G   N +    +    +S  G   V+
Sbjct: 124 SGVMIITKSHKVAAKLVKAFTEHKIRKSYIALCIGSSPNWRRVTVSSGHGRSKHGAWRVY 183

Query: 215 ------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ---------------------- 246
                  V           + F+V+   + K    E++                      
Sbjct: 184 AALDVGRVLPGGSFVRDMETTFEVVSVNSVKNESCELEDVNHVIVAEGERELSCGGDDDD 243

Query: 247 --------PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
                   P +GRTHQ+R+H  ++G PI GD KY   ++ N  +   ++L  HA  + L 
Sbjct: 244 VVVVVRAFPRSGRTHQIRLHCQYLGIPIRGDVKYHGVYEWNGRTFEGHEL--HAECLSLD 301

Query: 299 HPEGGR-LQITAPLP 312
           HP  G  + I APLP
Sbjct: 302 HPVTGDSIVIRAPLP 316


>gi|240080333|ref|ZP_04724876.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae FA19]
 gi|268596481|ref|ZP_06130648.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae FA19]
 gi|268550269|gb|EEZ45288.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae FA19]
          Length = 307

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 44/223 (19%), Positives = 87/223 (39%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKGQKPRL 146
            +     +  +L+ D  + V +KP  + V  G                       +    
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPGGRFLRETLLTRLRLHPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L        +  +   +   S
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEAL-----APTRTDLPYPIDVVS 201

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +         Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 202 RLARGEKFFTTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDAFYPVPSEAG-SEDYRKPLKLLAKKIAFTDPLSGRERVFC 302


>gi|254385032|ref|ZP_05000366.1| ribosomal pseudouridine synthase [Streptomyces sp. Mg1]
 gi|194343911|gb|EDX24877.1| ribosomal pseudouridine synthase [Streptomyces sp. Mg1]
          Length = 324

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 59/266 (22%), Positives = 98/266 (36%), Gaps = 28/266 (10%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +LR+G+V     RV     ++          +     +  E  +                
Sbjct: 55  LLRAGRVLGMGGRV-----LRPEDPYEPGSYLWFHRDMPPEPAVP------------FPI 97

Query: 100 ILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            ++Y D  + V +KP  ++    GS +       L+  +D     P   HRLD+ T+G++
Sbjct: 98  GVVYRDEHLLVADKPHFLATTPRGSHVTQTALARLRDELDLPALSP--AHRLDRLTAGLV 155

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + +            F+ RR+ K Y +L    P      +A     +S I      +   
Sbjct: 156 MFSIRPEDRGAYQLLFQNRRVGKQYEALAPLDPA-----LALPRTLRSRIEKTRGVIAAA 210

Query: 219 NEKGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              G    A +  ++ +          + PHTGRTHQLRVH   +G PI+GD  Y     
Sbjct: 211 EIPGGEPNAETLVELAESKGD-TGRYRLTPHTGRTHQLRVHMNSLGLPILGDPVY-PKVT 268

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG 303
                  +  L L AR ++   P  G
Sbjct: 269 DPDPLDYRRPLQLLARVLEFTDPVTG 294


>gi|224369746|ref|YP_002603910.1| RluD2 [Desulfobacterium autotrophicum HRM2]
 gi|223692463|gb|ACN15746.1| RluD2 [Desulfobacterium autotrophicum HRM2]
          Length = 298

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 61/310 (19%), Positives = 121/310 (39%), Gaps = 37/310 (11%)

Query: 9   YVVVE-NDEEN--MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            V V   + E   + LD +    +P I     Q+ +R    R++  RV   ++       
Sbjct: 9   TVTVPRENPEGFVLLLD-FLDARFPWIGR---QEWVR----RINASRVIQEDK------- 53

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                 N  + +I   K+L      T+     K  +L+ +  +    KP  + V      
Sbjct: 54  ---TPFNISSPLIPGSKVLYYREVETEPLIPFKEEILFHNDHLIAACKPHFLPVVPSGP- 109

Query: 126 AYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
             H++  L + +  +   P +   HRLD+ET+G+++ +            F  ++++K Y
Sbjct: 110 --HVNETLLNRLKIRFSNPDIVPIHRLDRETAGVVLFSVEPETRGAFQHLFMEKKVKKTY 167

Query: 184 WSLV--WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            ++    G   +    I N + +      + +   + N      A +  +++     +  
Sbjct: 168 EAVTRRPGTLPHLPSVIVNRIERGEPWFRNTIVPGRPN------AETRLELVGADRDRA- 220

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
           +  + P TG+ HQLR+H   +G PI  D  Y  +         ++ L L +R +    P 
Sbjct: 221 FFRLYPQTGKKHQLRLHLASLGFPIENDRCY-PDLLPKQGDDWEHPLMLLSREVRFMDPI 279

Query: 302 GGRLQ-ITAP 310
            GR +  T+P
Sbjct: 280 AGRERVFTSP 289


>gi|118618124|ref|YP_906456.1| pseudouridine synthase [Mycobacterium ulcerans Agy99]
 gi|118570234|gb|ABL04985.1| pseudouridine synthase [Mycobacterium ulcerans Agy99]
          Length = 288

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 56/262 (21%), Positives = 98/262 (37%), Gaps = 14/262 (5%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH-SDFLKSILLYEDSKIYVF 111
                ++ +G+VV     I     +      +    +L +      +  +L++D  I V 
Sbjct: 34  AAARAKVLAGEVVDAAGAIVGTATVAGPGSHVYLYRDLPEEVPVPFEMPVLHQDEDIVVA 93

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   +    +    HRLD+ T+G+L+    R       
Sbjct: 94  DKPHFLATMP-RGRHVAQTALVRLRCELGLPELSPAHRLDRLTAGVLLFTTRRELRGRYQ 152

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    ++K Y +            +A   + +S I     H+    E G   A +  +
Sbjct: 153 TLFARGAVRKTYLARAA-----VDADLAFPRVIRSRIVKRRGHLQAVCEPGEPNAETLVE 207

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLY 289
           +I           + P TGRTHQLRVH   +G PI GD  Y      +    S   + L 
Sbjct: 208 LISPEG----LYRLTPRTGRTHQLRVHMASLGLPIFGDPLYPNVIPESPHDLSDFSSPLS 263

Query: 290 LHARYMDLPHPEGG-RLQITAP 310
           L A+ ++   P  G R +  +P
Sbjct: 264 LLAQRIEFEDPLSGSRREFVSP 285


>gi|171741038|ref|ZP_02916845.1| hypothetical protein BIFDEN_00104 [Bifidobacterium dentium ATCC
           27678]
 gi|283455575|ref|YP_003360139.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           dentium Bd1]
 gi|171276652|gb|EDT44313.1| hypothetical protein BIFDEN_00104 [Bifidobacterium dentium ATCC
           27678]
 gi|283102209|gb|ADB09315.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           dentium Bd1]
          Length = 264

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 86/228 (37%), Gaps = 15/228 (6%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + +     +  +LYED  I V +KP  ++     G+ Y     ++             HR
Sbjct: 26  IAEPHIPFEYEVLYEDDGIIVIDKPHFLATTP-RGMWYRETALIRLRERYGEPDIVPAHR 84

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN------- 200
           LD+ T+G++V  R           F+  R  K Y   + +  + + +   +         
Sbjct: 85  LDRLTAGVVVFVRKPELRGAYQMLFQEHRTVKTYECLAPLAPVVRPRYGTVTRIDRNQPF 144

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----AQKFCWLEMQPHTGRTHQLR 256
            L+++SHI  D   +       A  A S  +  D              + P TG+THQLR
Sbjct: 145 PLVRRSHIAKDRGRLQAYEIPAAVNAESLIERGDNPRIIDGNVVINYVLHPKTGKTHQLR 204

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           VH   +G PI+GD  Y  +            L L AR ++   P  G 
Sbjct: 205 VHMNSLGLPILGDVFY-PDVIQRPYDDFSRPLELVARRLEFDDPVTGE 251


>gi|313681623|ref|YP_004059361.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
 gi|313154483|gb|ADR33161.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
          Length = 245

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 55/293 (18%), Positives = 108/293 (36%), Gaps = 60/293 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        I+    + ++  G V V   +V                       +I   +
Sbjct: 8   KLLAEQ-EGISNSEAKSLIDRGLVYVGNSKV-----------------------MIARGE 43

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I   +V + +  + ++   ++E+  + V +KPA ++                  ++ + +
Sbjct: 44  ISPKTVFIVQKVEKVRP--IFENDDLIVVDKPAFVNS---------------DEIERQFK 86

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             +L HRLD+ETSG+L++ +         + F+   + K Y + V G+       +   L
Sbjct: 87  GSQLLHRLDRETSGVLMLVKNEEFRLKAIQEFKKDNVYKEYVAWVEGLVSEP-FVVDQPL 145

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           + +      Y  V K+       AI+    ++   +K   +++  H GRTHQ+R H    
Sbjct: 146 ITEKKGNKAYTKVAKK----GKPAITEVTPLEVSGKK-TKVQLIIHHGRTHQIRAHMKFA 200

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
             PI+GD  Y              ++ LHA+ + L           AP P   
Sbjct: 201 QHPIIGDESYGGRQ--------SKRVMLHAKKVTLL-----GQTFEAPEPKVF 240


>gi|294788439|ref|ZP_06753682.1| RNA pseudouridine synthase [Simonsiella muelleri ATCC 29453]
 gi|294483870|gb|EFG31554.1| RNA pseudouridine synthase [Simonsiella muelleri ATCC 29453]
          Length = 306

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 61/296 (20%), Positives = 123/296 (41%), Gaps = 30/296 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRIPPVINALN 75
              L  +   ++P ++    +K L SG V V+   + +  N   Q+G+ +     I+  +
Sbjct: 28  GKSLLHFLCIYFPFVHEQAWKKRLNSGMV-VNQQGEPINENTPFQAGERIFYYREISRED 86

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLK 134
                           +        +L  D+ + V +KP  + V   G  +   +   L+
Sbjct: 87  ----------------EPRISFDERILSVDNDLIVVDKPHFLPVIPSGRFLRETLLTRLR 130

Query: 135 SWVDSKGQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
              D +          HRLD++T+G+++++          + F+ + I+KIY +L     
Sbjct: 131 LRSDLQHLNVADITPIHRLDKDTAGVILLSHNPKTRAIYQQLFQEKNIRKIYHALAPTRL 190

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 +A  LL +S +       + +   G   + +  ++++    K    E++P TG+
Sbjct: 191 D-----LAYPLLVRSRLVRGDEFFLTKTVDGEPNSETEIRLLENRG-KISLYELKPITGK 244

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            HQLRVH + +G P++ D  Y    +   T   +  L L A+ ++L  P  G L++
Sbjct: 245 KHQLRVHMMSLGMPLLNDMLY-PIVQPVGTEDFEKPLKLLAKRIELIDPVSGSLKV 299


>gi|70731574|ref|YP_261315.1| RNA pseudouridine synthase family protein [Pseudomonas fluorescens
           Pf-5]
 gi|68345873|gb|AAY93479.1| RNA pseudouridine synthase family protein [Pseudomonas fluorescens
           Pf-5]
          Length = 296

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 55/280 (19%), Positives = 103/280 (36%), Gaps = 25/280 (8%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
             +H+  I+       +  G+V +D +          GQ + +         I   +++ 
Sbjct: 30  LCDHFKAISREQWLDRIARGRV-LDGQ----------GQPISLELAYREGLRIHYFREVP 78

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           D  V   + +      +LY D  + V +KP  + V    G         +          
Sbjct: 79  DEKVIPVEET------ILYADEHLVVADKPHFLPVTPA-GEYVEQTLLRRLIRRLGNPHL 131

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HR+D+ T+G+++ +    +       F  R+I+K Y ++   +P+     +   LL 
Sbjct: 132 VPLHRIDRHTAGLVLFSANPDSRSAYQALFPTRKIEKRYEAIAAALPQ-----LNFPLLH 186

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           KS +         Q  +G +   +  +V +   +      + P TG+ HQLRVH   +G 
Sbjct: 187 KSRLVDGEPFFRMQEAQGPSNTETAIEVREKHGE-LWRYALYPVTGKKHQLRVHMNALGA 245

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            I  D  Y    K +        L L A+ +    P  G+
Sbjct: 246 AICNDPFYPEVLK-DIEDDYARPLKLLAQGLRFIDPLSGQ 284


>gi|262370362|ref|ZP_06063688.1| RNA pseudouridine synthase [Acinetobacter johnsonii SH046]
 gi|262314704|gb|EEY95745.1| RNA pseudouridine synthase [Acinetobacter johnsonii SH046]
          Length = 304

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 55/283 (19%), Positives = 108/283 (38%), Gaps = 27/283 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +  + +PHI     Q+    G V                  V    V++  +  ++ Q +
Sbjct: 37  YLSDQFPHIEATEWQQRFHDGLVY---------------DAV--GNVLHTDSAYLENQHV 79

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +     +  +L+E+    V +KP  +++       Y     L       G +
Sbjct: 80  FYYRFLAHEIEVPSQHEILFENDHFLVVDKPHFLTISPTG--QYVQQTLLVRLKKQTGIE 137

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HRLD+ET+G+++ ++   +     + F  R++QK Y ++    P N++  +    
Sbjct: 138 HLTPIHRLDRETAGLVMFSKCIHSRGMYQQMFAERQVQKTYHAIA---PFNRE--LKFPR 192

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           + K H+         Q    A  + +   +++   + +   E++P TG+ HQLRVH   +
Sbjct: 193 IVKLHMQKGEPFYTMQVLDEAPNSETEILLLE-HDETWAKYELKPETGKQHQLRVHLNFL 251

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           G PI  D  Y               L L A+++    P   +L
Sbjct: 252 GLPIKNDPFY-PKVVHKADYDFSQPLQLLAKHLSFKDPVTQQL 293


>gi|145350783|ref|XP_001419777.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580009|gb|ABO98070.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 218

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 53/188 (28%), Positives = 85/188 (45%), Gaps = 19/188 (10%)

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +   G+  R  H+LD  TSG+++ A TR AA +  + FR R  +K Y ++V+G PK  + 
Sbjct: 31  LKYPGKHHRFCHQLDTATSGVVLTAHTREAAGNAAKLFRDRLAKKKYLAVVFGWPKEDEW 90

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---------FAQKFCWLEMQP 247
            +   L K       +   V  +E+    + + FKV+              +   LE +P
Sbjct: 91  TVNAKLGKDPTDVKGFRERV--DEENGKASETSFKVLQRGYCTLDGANRGVEVSRLECRP 148

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TGR HQ+R+H +H G PI+GD  Y  +           +++LHA  + +P  E   L  
Sbjct: 149 VTGRRHQIRLHLMHSGHPILGDMAYSDDTDSY-------RMFLHALELVMPFEE-ETLTF 200

Query: 308 TAPLPAHM 315
               P   
Sbjct: 201 ATEPPESF 208


>gi|239622355|ref|ZP_04665386.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis CCUG
           52486]
 gi|239514352|gb|EEQ54219.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis CCUG
           52486]
          Length = 261

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 61/252 (24%), Positives = 94/252 (37%), Gaps = 31/252 (12%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + +     +  +LYED +I V +KP  ++     G+ Y     ++             HR
Sbjct: 9   IDEPHIPFEMDVLYEDERIIVVDKPHFLATMP-RGMWYRQTALIRLRERLGEPDITPAHR 67

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN------- 200
           LD+ T+G+LV  R  A        F+ R+  KIY   +    I   +   I         
Sbjct: 68  LDRMTAGVLVFVRDSACRGAYQMLFQNRQAVKIYECLAPCRPISGPRFGTIMQVEPPRPF 127

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-------------------AQKFC 241
            LL++SHI  ++  +    E G   A +  +  D                         C
Sbjct: 128 PLLRRSHITKEHGTMAAFEEPGLANAETLIERGDLCFPPAGGRWREAPEGGPHPGNHPIC 187

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
              + P TG+THQLRVH   +G PIVGD  Y    +          L L AR +    P 
Sbjct: 188 RYTLHPRTGKTHQLRVHMNSLGLPIVGDDFY-PRIQTRPYDDFSQPLQLVARVLRFTDPI 246

Query: 302 GGRL-QITAPLP 312
            G   +  + +P
Sbjct: 247 TGEKREFVSRVP 258


>gi|145225398|ref|YP_001136076.1| pseudouridine synthase [Mycobacterium gilvum PYR-GCK]
 gi|145217884|gb|ABP47288.1| pseudouridine synthase [Mycobacterium gilvum PYR-GCK]
          Length = 286

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 99/264 (37%), Gaps = 33/264 (12%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           VD +    +  +  G  V  P     L   + ++  +   +            +L+ D  
Sbjct: 40  VDGEVFCADGTVADGSTVLPPGAYVYLYRDLPDEVPVPFDIP-----------VLHRDDD 88

Query: 108 IYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           I V +KP  ++    GS +A      L+  +D    +    HRLD+ T+G+L+    R  
Sbjct: 89  IVVVDKPHFLATMPRGSHVAQTALVRLRRELDL--PELSPAHRLDRLTAGVLLFTVRREV 146

Query: 167 AQHLTESFRMRRIQKIYWS-LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
                  F      K Y +       +     I N L+K          +    E G   
Sbjct: 147 RGAYQTLFVRGEAAKTYVAHSSHATDREFPMTIRNRLVKH------RGSLQAVEEPGEPN 200

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTS 282
           A +  + +D          + P TGRTHQLRVH   +G PI GD  Y        G+F S
Sbjct: 201 AETVVEYLDEG-----MYRLTPRTGRTHQLRVHMAGLGIPITGDPLYPDVVDVPPGDFGS 255

Query: 283 PIQNKLYLHARYMDLPHPEGGRLQ 306
           P+  +L   A+ ++   P  G L+
Sbjct: 256 PL--RLL--AQALEFTDPISGELR 275


>gi|326795028|ref|YP_004312848.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326545792|gb|ADZ91012.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
          Length = 228

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 56/198 (28%), Positives = 90/198 (45%), Gaps = 21/198 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+ +  +V  KPA  S    SGI +    F +       +     HRLD+ TSG+L+V
Sbjct: 4   VLYQSADFWVVVKPANESFHSESGIGF----FQRLCCAFPNESFFPVHRLDKLTSGLLLV 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A  +  A  LT+ F   +++K Y ++    P+ K+  +      K  +        K + 
Sbjct: 60  ACNKVMAAKLTKLFMETKVEKRYLAISNKKPRKKQGTV------KGKMAPSRKGQWKLSG 113

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +G   AI+ F    CF +      ++P TGRTHQ+RV    +G PI+GD +Y        
Sbjct: 114 EG-KMAITQFH--SCFVEGKRLFYLRPLTGRTHQIRVALKSVGSPILGDERYGGGR---- 166

Query: 281 TSPIQNKLYLHARYMDLP 298
                ++ YLHA  +   
Sbjct: 167 ----SDRGYLHAYKLAFE 180


>gi|188993800|ref|YP_001905810.1| Putative pseudouridylate synthase [Xanthomonas campestris pv.
           campestris str. B100]
 gi|167735560|emb|CAP53778.1| Putative pseudouridylate synthase [Xanthomonas campestris pv.
           campestris]
          Length = 319

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 51/221 (23%), Positives = 87/221 (39%), Gaps = 11/221 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHR 149
            + +      +++ D +I V  KP  + V      AY  +  L   V           HR
Sbjct: 100 DEPTISAVETVVHADGQIVVACKPHFLPVVPAG--AYVRETLLARLVRRFDNPSLVPLHR 157

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D++T+G+++ +   A        FR RRI K Y ++   +P      +    + +S + 
Sbjct: 158 IDRDTAGLVLFSANPATRGIYQALFRERRIHKHYLAVAPPLPA-----LTFPYVHRSRLE 212

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                   +   G   + +   V+   A  + +  ++P TGR HQLRVH   +G PI+ D
Sbjct: 213 PGEPFFRMREGVGEPNSETVIDVVARGADMWTY-RLEPVTGRKHQLRVHMAALGVPILHD 271

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
             Y          P +  L L A  +    P  G   + TA
Sbjct: 272 RFYPELEDQRPDDP-ERPLQLFAHMLAFDDPITGEPRRFTA 311


>gi|15645572|ref|NP_207748.1| hypothetical protein HP0956 [Helicobacter pylori 26695]
 gi|3915400|sp|O25610|Y956_HELPY RecName: Full=Uncharacterized RNA pseudouridine synthase HP_0956;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2314093|gb|AAD07999.1| conserved hypothetical protein [Helicobacter pylori 26695]
          Length = 242

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 62/288 (21%), Positives = 114/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++ SG V +  K++                       ++  +++  ++  
Sbjct: 12  ENISHKKAKALIDSGLVSIGGKKL-----------------------MVARKELPKNTHF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K W         L HR
Sbjct: 49  SVQKVE--KPSVIFEDENILALFKPPFI-------ESYDLASFFKGWA--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVVLLVKENSEFHLKAKKAFKDRAVKKEYLALTQGIIEEEREINAPILTFKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y           +  +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPS------LAKRLMLHAHKIALL-----GYEFEAIAPKEFE 241


>gi|308063784|gb|ADO05671.1| hypothetical protein HPSAT_04685 [Helicobacter pylori Sat464]
          Length = 242

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 63/288 (21%), Positives = 113/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V V  K++                       ++  +++  ++  
Sbjct: 12  ENISHKKAKALIDLGLVSVGGKKL-----------------------MVARKELPKNTHF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRALKKEYLALAQGIIEEEQEINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIIAPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKISLL-----GYEFEAIPPKEFE 241


>gi|150865938|ref|XP_001385357.2| DRAP deaminase and pseudouridylate synthase [Scheffersomyces
           stipitis CBS 6054]
 gi|149387194|gb|ABN67328.2| DRAP deaminase and pseudouridylate synthase [Scheffersomyces
           stipitis CBS 6054]
          Length = 425

 Score =  125 bits (315), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 49/217 (22%), Positives = 98/217 (45%), Gaps = 11/217 (5%)

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  +     +   +  + E  + +  + L + +   +  +++E+  + V +KP+GI    
Sbjct: 81  GDRILDKFDVICNSKHMHEPSVPECPLQLHEDT---RLKIVFENEDMLVVDKPSGIPTHP 137

Query: 122 -GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-- 178
            G+     +   LK  ++ K   P   HRLD+ TSGIL+  +++ A    +  F+  +  
Sbjct: 138 TGNYYYNTMTEILKHDLNMKNVWPF--HRLDKVTSGILIFGKSKTACDTYSSIFQNEKDN 195

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           I K Y + + G     +  +   +   +  GG Y+  +  +    N + + FK +    +
Sbjct: 196 ISKQYLARIEGEFPTTEVMVNCPIFSVNSTGG-YIKPLNADMLPIN-STTVFKRLRYSKE 253

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                +  +P TGR HQ+R+H  ++G PIV D+ Y  
Sbjct: 254 LNQSIVICRPLTGRMHQIRIHLRNIGHPIVNDYLYNP 290


>gi|25029349|ref|NP_739403.1| hypothetical protein CE2793 [Corynebacterium efficiens YS-314]
 gi|23494637|dbj|BAC19603.1| conserved hypothetical protein [Corynebacterium efficiens YS-314]
          Length = 340

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 60/272 (22%), Positives = 103/272 (37%), Gaps = 20/272 (7%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE-QKILDSSVNLTKHSDFLKSILLYEDS 106
           +D  RV    R  +G+VV +     A   I++  + I    +   +     + ++++ED 
Sbjct: 61  LDNARV-LQERFDAGEVVNLWGRPYAPADIVQPGEDIWFYRMPAAERPIPYEILIIHEDE 119

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
            + V +KP  ++     G        +K  V +  Q+    HRLD+ TSG+LV+ +    
Sbjct: 120 DLLVVDKPPYLATMP-RGRHITETALVKMRVLTGHQELTPAHRLDRLTSGVLVMVKRPEL 178

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV---VKQNEKGA 223
                  F  R   K Y ++    P+         L+ +SHI      V   V   E   
Sbjct: 179 RGMYQTLFARREATKTYEAIGDYRPELVPG--DEPLIWESHIEKVRGQVQAYVTDEEPNT 236

Query: 224 NYAI-----------SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +           +  + +     +     + P TG+THQLR+H    G PI+GD  Y
Sbjct: 237 RTRVVSVTPVTDDEQAQLEALHGHLPRQGRYVLAPETGKTHQLRIHMRDAGVPILGDPLY 296

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                          ++L AR +    P+ G 
Sbjct: 297 -PVLHAVDDEDYTTPMHLIARTLTFIDPQSGE 327


>gi|34496612|ref|NP_900827.1| pseudouridine synthase [Chromobacterium violaceum ATCC 12472]
 gi|34102467|gb|AAQ58832.1| probable pseudouridine synthase [Chromobacterium violaceum ATCC
           12472]
          Length = 224

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 58/210 (27%), Positives = 95/210 (45%), Gaps = 19/210 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+++D + Y+ +K  G S     G A  +   L++ +D +   P   HRLD+ TSG+++V
Sbjct: 4   LIHQDPRFYLVDKHPGASFHR-EGDAPGLMDALRAGLDDEALWP--VHRLDRITSGLILV 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR+  AA+ L ++   R ++K Y +L    P  K+  +A  + K            +  E
Sbjct: 61  ARSAEAARALGDALAGREVEKYYLALSDRKPLKKQGRVAGDMAK------GRGGAWRLTE 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N A++ F              ++P TG+THQLRV     G PI+GD  Y  +     
Sbjct: 115 GRENPAVTQFFSYALEP-GLRLFLLRPRTGKTHQLRVAMKSQGAPILGDALYGGSEA--- 170

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                ++ YLHA  +     +G R     P
Sbjct: 171 -----DRGYLHAYALRFE-LDGERFAFVCP 194


>gi|166714232|ref|ZP_02245439.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 295

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 105/261 (40%), Gaps = 12/261 (4%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL-KSILLYEDSKIYV 110
             ++ +R   G V        AL    +    +     +           +++ D+ + V
Sbjct: 39  PERWRDRFARGLVCDANDHALALAAPYRVGAEIRYFREVADEPVIPYVETVVHADANLVV 98

Query: 111 FNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
             KP  + V   G+ +   +   L   +D+    P   HR+D+ET+G+++ +   A    
Sbjct: 99  ACKPHFLPVTPAGAYVRETLLTRLVRRLDNPALVP--LHRIDRETAGLVLFSVNPATRGI 156

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
               FR RRI+K Y ++   +P+     ++   + +S +         +   G   + + 
Sbjct: 157 YQALFRERRIRKQYLAVAPPLPE-----LSFPYVHRSRLEPGEPFFRMREGVGEPNSETV 211

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
             V+   A  + +  ++P TGR HQLRVH   +G PI+ D  Y  + +       +  L 
Sbjct: 212 IDVVAPGADTWTY-RLEPVTGRKHQLRVHMAALGAPILHDRFY-PDLQAQRPDDPERHLQ 269

Query: 290 LHARYMDLPHPEGGRL-QITA 309
           L A  +    P  G L + TA
Sbjct: 270 LFAHTLAFDDPITGELREFTA 290


>gi|224001856|ref|XP_002290600.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220974022|gb|EED92352.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 596

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 73/356 (20%), Positives = 114/356 (32%), Gaps = 111/356 (31%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +P  +      +++ K  D +   TK +       +Y D  I V NKP+G+    G    
Sbjct: 242 VPESVLQYERSLRKVKAADRASK-TKVTIHDHLQTIYFDKDIVVTNKPSGLLCVPGVNHY 300

Query: 127 YHIDGFLKSWVDSKGQKP---------------------------RLTHRLDQETSGILV 159
             +   +                                       + HRLD +TSGI+V
Sbjct: 301 RSLLDLVYEVYGGGANPNDKGISTTQQTTDESATTTLEEPLQKDSMIAHRLDMDTSGIVV 360

Query: 160 VARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNK------------------------ 194
            ARTR A   L +SFR R   +K Y +L+ G                             
Sbjct: 361 FARTRLAMSKLHKSFRERTGTRKRYEALLVGWLDTATWASSANNSSNNNYLGCNAGDTTA 420

Query: 195 ----KECIANWLLKKSHIGGDYVHVVKQNE---------------------KGANYAISH 229
                    N  L++ H    ++ V                          K    + + 
Sbjct: 421 DTDLGGGEINLPLQRDHKHPPFMRVSTPESEVEAAMAVRDLNHAGWKKLVAKRPKPSTTQ 480

Query: 230 FKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC----ANFKGNFTS 282
           F+++            +E+ P TGRTHQLRVH   +G PI+GD  Y     A+  G F  
Sbjct: 481 FRILAHEVWMDHPITRVELTPITGRTHQLRVHCAAIGHPILGDPAYGWCGEAHPNGGFCE 540

Query: 283 PIQNK------------------------LYLHARYMDLPHPEGGR-LQITAPLPA 313
            +  +                        + LHAR +   HP   + ++  A LP+
Sbjct: 541 EVMRQMSPTCAGMELQRDVEESVQASGRTMCLHARRLGFHHPATDKYVEFEA-LPS 595


>gi|108563365|ref|YP_627681.1| hypothetical protein HPAG1_0940 [Helicobacter pylori HPAG1]
 gi|107837138|gb|ABF85007.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori HPAG1]
          Length = 242

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 66/288 (22%), Positives = 111/288 (38%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V V  K++                 + A   + K  +     V 
Sbjct: 12  ENISHKKAKALIDLGLVSVGGKKL-----------------MVARKELPKNTRFSVQKVE 54

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 55  --------KPGVIFEDENILALFKPPFI-------ESYDLLSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKNRAVKKEYLALAQGIIEEEREINAPILTFKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y  +           +L LHA  + L        +  A  P    
Sbjct: 205 DTIYGDSQHSA------KRLMLHAHKIALL-----GYEFEAIPPKEFE 241


>gi|207091718|ref|ZP_03239505.1| hypothetical protein HpylHP_00901 [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 242

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 63/288 (21%), Positives = 111/288 (38%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +++    + ++  G V +  K++                 + A   + K  +     V 
Sbjct: 12  ENVSHKKAKALIDLGLVSIGGKKL-----------------MVARKELPKNTRFSVQKVE 54

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   K  +++ED  +    KP  I        +Y +  F K WV        L HR
Sbjct: 55  --------KPSVIFEDENVLALFKPPFI-------ESYDLLSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L+ GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLALIQGIIEEEREINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKIALL-----GYEFEAIPPKEFE 241


>gi|145354358|ref|XP_001421454.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144581691|gb|ABO99747.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 318

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 108/311 (34%), Gaps = 57/311 (18%)

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-- 121
            +R  P  +A   I  E+            +  +  + +Y D  +YV NKPA   V    
Sbjct: 9   TLRPGPPSDAARAIEGERAESCERAARADAAAGVPLLAVYVDDDVYVLNKPAQTYVHDIE 68

Query: 122 ----------GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
                                 +    +  +  R+ HRLD++TSG LVVAR R A + L+
Sbjct: 69  RLVERGMVKCDDATTVDNRATTRDVPFNASESARVVHRLDRDTSGCLVVARNRDAIRSLS 128

Query: 172 ESFRMRRIQKIYWSLVWGI-----PKNKKECIANW---------LLKKSHIGGDYVHVVK 217
             F    +QK Y +L          ++ +     W         L   + IG       K
Sbjct: 129 AQFADGTVQKTYVALCAATADYDGVEDHRRVFTGWGRAKYGLFRLYDAADIGRALPGNKK 188

Query: 218 QNEKGANYAISHFKVI-----------------DCFAQKFCWLEMQPHTGRTHQLRVHAL 260
              K A   I   +VI                 D    +       P TGRTHQ+R+H  
Sbjct: 189 VKVKHAETTIIVERVITDGVALRFCEPPTADDADRRRHRVALARCSPLTGRTHQIRLHCA 248

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQ-----NKLYL---HARYMDLPHPEGG-RLQITAPL 311
            +G P+VGD +Y          PI       ++     HA  +   HP+   R+ + AP 
Sbjct: 249 SLGLPLVGDVRYGGPIAATRDGPIDAPFSARRVAGALLHAERVAFRHPKSNLRVDVHAPR 308

Query: 312 PAHMVKTWDSL 322
           P      W  L
Sbjct: 309 PP-----WARL 314


>gi|188527777|ref|YP_001910464.1| hypothetical protein HPSH_05040 [Helicobacter pylori Shi470]
 gi|188144017|gb|ACD48434.1| hypothetical protein HPSH_05040 [Helicobacter pylori Shi470]
 gi|308062271|gb|ADO04159.1| hypothetical protein HPCU_05030 [Helicobacter pylori Cuz20]
          Length = 242

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 63/288 (21%), Positives = 113/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V V  K++                       ++  +++  ++  
Sbjct: 12  ENISHKKAKALIDLGLVSVGGKKL-----------------------MVARKELPKNTHF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRALKKEYLALAQGIIEEEQEINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKIALL-----GYEFEAIPPKEFE 241


>gi|298368460|ref|ZP_06979778.1| RNA pseudouridine synthase [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298282463|gb|EFI23950.1| RNA pseudouridine synthase [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 306

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 57/292 (19%), Positives = 110/292 (37%), Gaps = 31/292 (10%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNH 76
            + L  +   H+P +   N ++ L SG V   D   +  N   ++G+V+           
Sbjct: 29  GLPLLHFLCTHFPFVGEDNWRRRLNSGSVVGADGVPLNENTPFKAGEVMYYYR------- 81

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                     +   ++        +L+ D  + V +KP  + V   SG   H     +  
Sbjct: 82  ---------ETSRDSEPRIPFDEKILHVDEHLIVVDKPHFLPVTP-SGRFLHETLLTRLR 131

Query: 137 VDSKGQKPRL-----THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           +  + Q   +      HRLD++T+G+++++   A  +H    F+ + ++K Y +L     
Sbjct: 132 LRPELQHLNVGDITPVHRLDKDTAGVMLLSHNPAVRRHYQAMFQDKAVRKTYEAL----- 186

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
              +  +       S +       + Q   G   A +  ++ +          + P TG+
Sbjct: 187 APTRTDLRYPHRISSRLVRSERFFLTQETDGEPNAHTVIELFENRGD-TSLYRLYPQTGK 245

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            HQLRVH   +G PI+ D  Y      +        L L A+ ++   P  G
Sbjct: 246 KHQLRVHMTSLGIPILNDMYYP--VPSDAEEDYGKPLKLLAKSIEFQDPVSG 295


>gi|134099890|ref|YP_001105551.1| ribosomal pseudouridine synthase [Saccharopolyspora erythraea NRRL
           2338]
 gi|291006074|ref|ZP_06564047.1| ribosomal pseudouridine synthase [Saccharopolyspora erythraea NRRL
           2338]
 gi|133912513|emb|CAM02626.1| ribosomal pseudouridine synthase [Saccharopolyspora erythraea NRRL
           2338]
          Length = 312

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 47/240 (19%), Positives = 88/240 (36%), Gaps = 8/240 (3%)

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           VV +   + A    +    +        +     +  +++ D  + V +KP  ++     
Sbjct: 55  VVDLHGPVAADAPFVPGSFVWFHRDLPDEVPVPFEIGVVHRDDDLLVVDKPHFLATTP-R 113

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           G        ++   +         HRLD+ T+G+++        +   E F+ R + K Y
Sbjct: 114 GRHVAQTALVRLRRELSIPDLSPAHRLDRTTAGLVMFVIRPELRKSYQEMFQNRLVHKEY 173

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            ++    P      +      +S I  +   +  Q   G   A +  ++++         
Sbjct: 174 EAVAPFDP-----GLELPRTVRSRIVKERGVLAAQEVPGPPNAETLVELLEHR-DGLGRY 227

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
            + P TGRTHQLRVH   +G PI+GD  Y               L L A+ ++   P  G
Sbjct: 228 RLLPKTGRTHQLRVHLNSIGIPILGDDTY-PVVNDPAPDDFGRPLQLLAKALEFTDPVSG 286


>gi|302803025|ref|XP_002983266.1| hypothetical protein SELMODRAFT_118202 [Selaginella moellendorffii]
 gi|300148951|gb|EFJ15608.1| hypothetical protein SELMODRAFT_118202 [Selaginella moellendorffii]
          Length = 312

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 65/282 (23%), Positives = 110/282 (39%), Gaps = 40/282 (14%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IP         I+ ++ L +  ++          ++++D  I V NKP G+       + 
Sbjct: 27  IPVTPLTGAKEIEYERALVAEASMKSGPAITIDDVVFQDEWILVINKPCGVYS---EHVL 83

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L            L +RLD++TSGI+V+AR + AA  LT  F+ R ++K Y +L
Sbjct: 84  VSVPSLLGDSYSPHRGFFHLANRLDRDTSGIIVIARDKVAAGKLTNIFKSRELRKSYVAL 143

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG------ANYAISHFKVI------- 233
             G   + K  +      KS  G   V+     E+            +  +V+       
Sbjct: 144 CVGKAPHWKRAVIESGHGKSRRGCWRVYSKHDVERSLPDGSVVKDMSTKIEVMPSSLDEA 203

Query: 234 ---------------------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                                +       ++   P TGRTHQ+R+H   +G P+VGD KY
Sbjct: 204 KDSEEDDGEQRIVVEAKMVDPEPGTGDEVFIRAVPLTGRTHQIRLHCQFLGLPLVGDVKY 263

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
                 N      +  +LH+  +   HP  G  +++ AP P+
Sbjct: 264 GGPLHWNGEKCQSH--FLHSESIAFQHPMTGEVVEVIAPHPS 303


>gi|296168884|ref|ZP_06850555.1| RNA pseudouridine synthase [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295896450|gb|EFG76101.1| RNA pseudouridine synthase [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 279

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 51/253 (20%), Positives = 87/253 (34%), Gaps = 12/253 (4%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH-SDFLKSILLYEDSKIYVF 111
               +++ +G+VV            +     +     L +         +L+ D+ I V 
Sbjct: 27  ASARSKVLAGEVVDADGSPVDEATALPAGASVYLYRELPEEVPVPFDIPVLHRDADIVVV 86

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   +    +    HRLD+ T+G+L+    R       
Sbjct: 87  DKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTARREVRGAYQ 145

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F    ++K Y +     P      +    + +S I      +    E G   A +  +
Sbjct: 146 TLFSRGLVRKTYLARAAVDPA-----LVLPRVVRSRIIKRRGVLQAGCEPGTPNAETLVE 200

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           +            + P TGRTHQLRVH   +G PI GD  Y  +            L L 
Sbjct: 201 LASPDG----LYRLTPRTGRTHQLRVHMAALGVPIDGDPLY-PDIVDVPPDDFSTPLGLL 255

Query: 292 ARYMDLPHPEGGR 304
           AR +    P  G 
Sbjct: 256 ARRIAFDDPLTGE 268


>gi|254493346|ref|ZP_05106517.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae 1291]
 gi|226512386|gb|EEH61731.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae 1291]
          Length = 307

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 87/223 (39%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKGQKPRL 146
            +     +  +L+ D  + V +KP  + V  G                       +    
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPGGRFLRETLLTRLRLHPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L        +  +   L   S
Sbjct: 147 IHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEAL-----APTRTDLPYPLDVVS 201

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +         Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 202 RLARGEKFFTTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDAFYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|157960378|ref|YP_001500412.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157845378|gb|ABV85877.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 312

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 55/287 (19%), Positives = 104/287 (36%), Gaps = 26/287 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +  + +P I     QK +      VD K    +  + + Q   IP         ++++ +
Sbjct: 28  FLVSQFPAIAEAVWQKRI------VDGKVHWRDGTLITAQTAFIPRERVYYYREVEQESL 81

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +             K   L +  +  +  KP  ++V              +  + +  Q+
Sbjct: 82  IP-----------FKEKCLLQTDEFLLVFKPHFLAVNPSGNFVNECL-VNRLRLKTGNQQ 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL------VWGIPKNKKEC 197
               HRLD+ T+G++++++         E F+  +IQK Y ++      +  + +     
Sbjct: 130 IVAAHRLDRATAGVMLLSQKSETRHDYHELFKSGQIQKTYQAVAPLNNQIKQMLEQGSLT 189

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +      K+ I             G   + S  ++I+ F   +   E+ P TGRTHQLRV
Sbjct: 190 LPMHWTVKNRISKTTPSFRMCISDGEANSHSEIRLIETFG-GYGLFELVPVTGRTHQLRV 248

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           H + +G  I+ D  Y               L L AR +    P    
Sbjct: 249 HMMSLGMSILNDRLY-PELLDKAADDFAKPLKLMARRLSFTDPITDE 294


>gi|294056443|ref|YP_003550101.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
 gi|293615776|gb|ADE55931.1| pseudouridine synthase [Coraliomargarita akajimensis DSM 45221]
          Length = 284

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 98/237 (41%), Gaps = 26/237 (10%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW----------VDSKGQKPRLTHRLDQ 152
           + +  +    KPAG+ V                +          VD   ++  L +R+D 
Sbjct: 21  HNEDGLVALEKPAGLMVHPNKPEERKFSMLYAHYHYEKECFHWEVDGVSKRVWLINRIDS 80

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+++VA   A A+ + + F   R+ K+Y ++V  +P N     ++ L K+ +  G  
Sbjct: 81  PTSGVVLVALDEALAKEIKQQFATHRVNKVYHAIVKRVPSNHTGTWSDMLTKEVYRAGRK 140

Query: 213 VHVVKQNEKGAN--YAISHFKVIDCFAQKF--CWLEMQPHTGRTHQLRVHALHMGCPIVG 268
           +        G     A + ++++      F    L++ P TGRTHQLR+       PIVG
Sbjct: 141 I-------PGGQRIPAKATYQLVKSPTGGFPVSLLKLMPVTGRTHQLRIQCQRHRHPIVG 193

Query: 269 DHKYCANF--KGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITA--PLPAHMVKTWD 320
           D  Y +    +         ++ LH+    L +   G+L + +A  PLP    +   
Sbjct: 194 DRSYGSFSFNREVIAETGVKRMLLHSSETSLKYAFKGKLREFSASSPLPEAFNEVLR 250


>gi|229826154|ref|ZP_04452223.1| hypothetical protein GCWU000182_01526 [Abiotrophia defectiva ATCC
           49176]
 gi|229789024|gb|EEP25138.1| hypothetical protein GCWU000182_01526 [Abiotrophia defectiva ATCC
           49176]
          Length = 236

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 64/221 (28%), Positives = 98/221 (44%), Gaps = 18/221 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV--------DSKGQKPRL--T 147
              +LYED  I V  KP GI  QG       +   LK  +         S G++P +   
Sbjct: 4   DIPILYEDEDIIVCVKPVGILSQGDKDGNKDLVRELKKHLVISARKNKQSIGKEPYIAVV 63

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+   GI+V A+T  AA  L++     ++ K Y ++V   P+     I     +  +
Sbjct: 64  HRLDRNVRGIMVYAKTGRAAAGLSKQIAENKLTKRYMAVVSFTPERCTPEINVEKKRIDY 123

Query: 208 IGGDYVH----VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           I  D V     + ++  KGA  A  ++KVI     K   +++   TGR HQ+R+    + 
Sbjct: 124 IAADKVKNISTIAEKESKGAERAELNYKVIKTAGNKA-LVQVDLITGRHHQIRLQLSQIF 182

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             IVGD KY  ++K   T   ++   L A  +   HP  G 
Sbjct: 183 NGIVGDTKYNDDYK--LTDGWKDP-ALEAVELSFVHPVSGE 220


>gi|308051432|ref|YP_003914998.1| pseudouridine synthase Rlu family protein, TIGR01621 [Ferrimonas
           balearica DSM 9799]
 gi|307633622|gb|ADN77924.1| pseudouridine synthase Rlu family protein, TIGR01621 [Ferrimonas
           balearica DSM 9799]
          Length = 235

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 57/211 (27%), Positives = 86/211 (40%), Gaps = 19/211 (9%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
            +        L   ++++     V  KPAG+      G A    G +        +    
Sbjct: 4   PLPSEFTMPSLTPSVIHQHPDFVVVVKPAGVHFHSQDGNA----GLVAQLEAQLNESLYP 59

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  TSG+LV+AR  AAA  LT  F   +++K Y +L    PK K+  +   + K  
Sbjct: 60  VHRLDTPTSGLLVLARHPAAAATLTALFTAHQVEKRYLALSGHKPKKKQGTVKGGMAKA- 118

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                     K      N+AI+ F V            ++P +GRTHQ+RV    +G PI
Sbjct: 119 -----RRGAWKLTPGQENWAITQF-VSHNLRPGIRAFLLRPRSGRTHQIRVALKSLGAPI 172

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +GD  Y  +          ++ YLHA  +  
Sbjct: 173 LGDALYGGSDA--------DRTYLHAWSLGF 195


>gi|259505649|ref|ZP_05748551.1| ribosomal pseudouridine synthase [Corynebacterium efficiens YS-314]
 gi|259166731|gb|EEW51285.1| ribosomal pseudouridine synthase [Corynebacterium efficiens YS-314]
          Length = 308

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 60/272 (22%), Positives = 102/272 (37%), Gaps = 20/272 (7%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHII-KEQKILDSSVNLTKHSDFLKSILLYEDS 106
           +D  RV    R  +G+VV +     A   I+   + I    +   +     + ++++ED 
Sbjct: 29  LDNARV-LQERFDAGEVVNLWGRPYAPADIVQPGEDIWFYRMPAAERPIPYEILIIHEDE 87

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
            + V +KP  ++     G        +K  V +  Q+    HRLD+ TSG+LV+ +    
Sbjct: 88  DLLVVDKPPYLATMP-RGRHITETALVKMRVLTGHQELTPAHRLDRLTSGVLVMVKRPEL 146

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV---VKQNEKGA 223
                  F  R   K Y ++    P+         L+ +SHI      V   V   E   
Sbjct: 147 RGMYQTLFARREATKTYEAIGDYRPELVPG--DEPLIWESHIEKVRGQVQAYVTDEEPNT 204

Query: 224 NYAI-----------SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +           +  + +     +     + P TG+THQLR+H    G PI+GD  Y
Sbjct: 205 RTRVVSVTPVTDDEQAQLEALHGHLPRQGRYVLAPETGKTHQLRIHMRDAGVPILGDPLY 264

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                          ++L AR +    P+ G 
Sbjct: 265 -PVLHAVDDEDYTTPMHLIARTLTFIDPQSGE 295


>gi|240013751|ref|ZP_04720664.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae DGI18]
 gi|240120819|ref|ZP_04733781.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID24-1]
          Length = 307

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 87/223 (39%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKGQKPRL 146
            +     +  +L+ D  + V +KP  + V  G                       +    
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPGGRFLRETLLTRLRLHPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L        +  +   L   S
Sbjct: 147 IHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEAL-----APTRTDLPYPLDVVS 201

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +         Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 202 RLARGEKFFTTQEAEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDAFYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|217032747|ref|ZP_03438231.1| hypothetical protein HPB128_158g26 [Helicobacter pylori B128]
 gi|298736086|ref|YP_003728611.1| pseudouridylate synthase [Helicobacter pylori B8]
 gi|216945563|gb|EEC24218.1| hypothetical protein HPB128_158g26 [Helicobacter pylori B128]
 gi|298355275|emb|CBI66147.1| pseudouridylate synthase [Helicobacter pylori B8]
          Length = 242

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 62/288 (21%), Positives = 113/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V +  K++                       ++  +++  ++  
Sbjct: 12  ENISHKKAKALIDLGLVSIGGKKL-----------------------MVARKELPKNTHF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPGVIFEDENILALFKPPFI-------ESYDLLSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKNRAVKKEYLALTQGIIEEEREINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKIALL-----GYEFEAIPPKEFE 241


>gi|317180199|dbj|BAJ57985.1| hypothetical protein HPF32_0403 [Helicobacter pylori F32]
          Length = 242

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 62/288 (21%), Positives = 113/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V +  K++                       ++  +++  ++  
Sbjct: 12  ENISHKKAKALIDLGLVSIGGKKL-----------------------MVARKELPKNTHF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLALAQGIIEEEQEINAPILTFKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKISLL-----GYEFEAIPPKEFE 241


>gi|109947567|ref|YP_664795.1| putative ribosomal pseudouridine synthase [Helicobacter acinonychis
           str. Sheeba]
 gi|109714788|emb|CAJ99796.1| putative ribosomal pseudouridine synthase [Helicobacter acinonychis
           str. Sheeba]
          Length = 242

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 66/288 (22%), Positives = 111/288 (38%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V +  K++    +        +P  ++     I+          
Sbjct: 12  ENISHKKAKALIDLGLVSIGGKKLSVARK-------ELPQNMHFNVQKIE---------- 54

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   K  +++ED  I    KP  I        +Y +  F K W         L HR
Sbjct: 55  --------KPSVIFEDENILALFKPPFI-------ESYDLVSFFKDWT--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +LV GI   +KE  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKERAVKKEYLALVQGIVGEEKEINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    AI+    +    +K   L+++  TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAITIITPLKIINKK-TLLKVEIKTGRTHQIRVHLKHINHPIMG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPSSA------KRLMLHAHKIALL-----GYEFEAIAPKEFE 241


>gi|237752561|ref|ZP_04583041.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           winghamensis ATCC BAA-430]
 gi|229376050|gb|EEO26141.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           winghamensis ATCC BAA-430]
          Length = 290

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 64/274 (23%), Positives = 113/274 (41%), Gaps = 54/274 (19%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                 +I+    + ++  G V V  K++                 + A   +    +  
Sbjct: 51  LLALQENISNNEAKALIDRGLVNVKGKKI-----------------LIARGLLAPNTRFN 93

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
              +   K         ++ +  I    KPA ++           +  +KS+        
Sbjct: 94  IQQIQTIKE--------IFCNENILALEKPAFLTS----------EEIVKSYPQWT---- 131

Query: 145 RLTHRLDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            L HRLD+ETSGIL++ +   +      E+F+  ++ K Y ++V GI   + E  A  ++
Sbjct: 132 -LLHRLDKETSGILLLVKENSSFHLKAKEAFKQLQVLKQYTAIVEGILDEECEITAPLII 190

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           KK       V + K NE     AI+H   ++ F +K    +++  TG+THQ+R H  H+ 
Sbjct: 191 KKGKSA--KVSISKTNE--GQKAITHITPLEIFGKKTKL-DIEIKTGKTHQIRAHLAHIK 245

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            PI+GD  Y A           N++ LHAR++ L
Sbjct: 246 HPIIGDTLYGAKPA--------NRILLHARHIAL 271


>gi|317178694|dbj|BAJ56482.1| hypothetical protein HPF30_0385 [Helicobacter pylori F30]
          Length = 245

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 63/288 (21%), Positives = 114/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V +  K++                       ++  +++  ++  
Sbjct: 15  ENISHKKAKALIDLGLVSIGGKKL-----------------------MVARKELPKNTHF 51

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 52  SVQKVE--KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 94

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ R          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 95  LDKETSGVILLVRENSEFHLKAKKAFKDRAVKKEYLALAQGIIEEEQEINAPILTIKTTK 154

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 155 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 207

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y  +           +L LHA  + L        +  A  P    
Sbjct: 208 DTLYNNDPGSA------KRLMLHAHKIALL-----GYEFEAIPPKEFE 244


>gi|315586901|gb|ADU41282.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori 35A]
          Length = 242

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 62/288 (21%), Positives = 112/288 (38%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V V  K++                       ++  +++  ++  
Sbjct: 12  ENISHKKAKALIDLGLVSVGGKKL-----------------------MVARKELPKNTHF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLALAQGIIEEEQEINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L+    TGRTHQ+R+H  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKAGIKTGRTHQIRIHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKIALL-----GYEFEAIPPKEFE 241


>gi|159466816|ref|XP_001691594.1| pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158278940|gb|EDP04702.1| pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 694

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 63/330 (19%), Positives = 113/330 (34%), Gaps = 58/330 (17%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK---------------FN 56
           V+  ++   L +     +P ++     + + +G++RV+ K                   +
Sbjct: 117 VKQRQDGRPLMQLMAEEFPMLSEDYYTQAVATGRLRVEGKVPGGGRGSGGGGGGGGWAAS 176

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG 116
             +++G  +R             E  +L   V +   SD                NKPA 
Sbjct: 177 KPLRAGMCIRHFIHR-------HEPPVLQGDVEILGVSD-----------DFVAVNKPAC 218

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           + V        +    +             T+RLD+  SG+L++AR+ A A  +      
Sbjct: 219 MPVHTVGQYRKNTVMGVVQATHPGLWPLYPTYRLDKPVSGVLLLARSSAVAGRMRVLLEE 278

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-------------- 222
           R   K Y + V G+  +        ++  + +G +                         
Sbjct: 279 RGCAKAYVARVQGVFPDTSSLSGGVMVVDTPLGWEAKTNHATPVPASGLAADGATALPPA 338

Query: 223 ----ANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
               A  A +HF+ +          +E  P TGRTHQ+RVH  H+G PI  D +Y  ++ 
Sbjct: 339 LVASAKPAETHFRRLSVSPDGLTSVVEAVPKTGRTHQIRVHLQHVGHPIANDTQYGGSY- 397

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
                  +  +   AR    PH  G R + 
Sbjct: 398 -GLPLFFRRGMGGPAR----PHVNGQRRRF 422


>gi|308183108|ref|YP_003927235.1| hypothetical protein HPPC_04830 [Helicobacter pylori PeCan4]
 gi|308065293|gb|ADO07185.1| hypothetical protein HPPC_04830 [Helicobacter pylori PeCan4]
          Length = 242

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 64/288 (22%), Positives = 114/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V V  K++                       +I  +++  ++  
Sbjct: 12  ENISHKKAKALIDLGLVSVGGKKL-----------------------MIARKELPKNTRF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLALTQGIIEEEREINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y  +           +L LHA  + L        +  A  P    
Sbjct: 205 DTIYGDSQHSA------KRLMLHAHKIALL-----GYEFEAIAPKEFE 241


>gi|87120482|ref|ZP_01076376.1| Pseudouridine synthase RluA-like [Marinomonas sp. MED121]
 gi|86164125|gb|EAQ65396.1| Pseudouridine synthase RluA-like [Marinomonas sp. MED121]
          Length = 226

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 54/203 (26%), Positives = 91/203 (44%), Gaps = 20/203 (9%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-LTHRLDQETS 155
           +   +LY ++  +V NKPAG+S    S       GF++    +  ++     HRLD+ TS
Sbjct: 3   ILPSVLYREADYWVVNKPAGMSFHAES----EEVGFMQWMHQAFPEQVFYPVHRLDRITS 58

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++++A  + AAQ   + F   ++ K Y ++    PK K+  I      K  +       
Sbjct: 59  GLIILAINKRAAQLFGKMFEQHQMAKFYLAISQKKPKKKQGSI------KGGMQQGRRGS 112

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              N+   N+A + F              ++P TG+THQLRV    +G PI+GD +Y   
Sbjct: 113 WLLNQSNENFAHTQFFSTGIKP-GLRLFLLKPKTGKTHQLRVALKSLGSPILGDVRYGGA 171

Query: 276 FKGNFTSPIQNKLYLHARYMDLP 298
                     ++ YLHA ++   
Sbjct: 172 EA--------DRGYLHAFWLSFI 186


>gi|311112905|ref|YP_003984127.1| RNA pseudouridine synthase [Rothia dentocariosa ATCC 17931]
 gi|310944399|gb|ADP40693.1| RNA pseudouridine synthase [Rothia dentocariosa ATCC 17931]
          Length = 365

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 89/235 (37%), Gaps = 33/235 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  +   +KP  + V    G         K  V          HRLD+ T+GIL+ 
Sbjct: 110 VLYEDEHLLAVDKPHYLPVTP-RGAYIAQTALTKLRVRKNNPLLTPVHRLDRPTAGILLF 168

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-------IANWLLKKSHIGGDYV 213
           A+TR A       F+ R++ K Y ++     ++ +E        + + + K  +I     
Sbjct: 169 AKTRDARGPFQTMFQNRQVTKTYLAIAPAPSEDLRESMLGEGVQVRSHIDKDRNILQVRQ 228

Query: 214 HVVKQNEKGANY--AISHFKVID----------------------CFAQKFCWLEMQPHT 249
           +  ++ E+      A +  ++ +                         ++    E+ PHT
Sbjct: 229 YSARECERAGLSVNAETLVRIREIYQAPQSVPLKSGAQNPYLPYPAPGEELALYELTPHT 288

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G+ HQLR H   +G PI GD  Y         +     L L A  +D  HP   +
Sbjct: 289 GKMHQLRAHLNLLGTPIFGDVLY-PQVLPTAPNDASVPLQLLAHRLDCVHPFTNK 342


>gi|71279393|ref|YP_270735.1| pseudouridine synthase Rlu family protein [Colwellia
           psychrerythraea 34H]
 gi|71145133|gb|AAZ25606.1| pseudouridine synthase Rlu family protein, TIGR01621 [Colwellia
           psychrerythraea 34H]
          Length = 230

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 57/213 (26%), Positives = 94/213 (44%), Gaps = 18/213 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILV 159
           + E     V +K AG++      I   +   +K  + S+    +    HRLD+ TSG++V
Sbjct: 5   IAEHHDFIVVDKEAGVNFHDEGDIGSGLFSLVKKQLQSQNNNTELYPVHRLDKMTSGLVV 64

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A+T A AQ   + F    I+K Y ++    P  K+  I   + K        +  ++  
Sbjct: 65  FAKTLACAQIFGQLFNDHDIEKYYLAIGDKKPIKKQGLIKGDMAKSRRGMFKLLRSME-- 122

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F        K     ++PH+G+THQLRV    +G PIVGD  Y       
Sbjct: 123 ----NPAVTQFFSF-SIPNKQRLYLLKPHSGKTHQLRVALASIGAPIVGDPLY------- 170

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           +T+   ++ YLHA  +   +  G   +  + LP
Sbjct: 171 YTTSQADRGYLHAFVLRFNYL-GESFEFIS-LP 201


>gi|325919058|ref|ZP_08181118.1| 23S RNA-specific pseudouridylate synthase [Xanthomonas gardneri
           ATCC 19865]
 gi|325550442|gb|EGD21236.1| 23S RNA-specific pseudouridylate synthase [Xanthomonas gardneri
           ATCC 19865]
          Length = 292

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 58/262 (22%), Positives = 104/262 (39%), Gaps = 16/262 (6%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIK---EQKILDSSVNLTKHSDFLKSILLYEDSKIY 109
           V + +R   G+V  + P  +AL+         +IL     + +       ++++ D+ + 
Sbjct: 34  VTWQDRFARGRV--LDPEGSALDASAPYRLGAEILYFREVVDEPVIPFAEMVVHADAHLV 91

Query: 110 VFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           V  KP  + V      AY     L   V           HR+D++T+G+++ +   A   
Sbjct: 92  VACKPHFLPVVPAG--AYVHQTLLTRLVRRFDNPALVPLHRIDRDTAGLVLFSANAATRG 149

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
                FR RRI+K Y ++   +P         ++       G+    +++   G   + +
Sbjct: 150 IYQALFRERRIRKHYLAIAPPLP----GLTFPYVHHSRLEPGEPFFRMREGV-GEPNSET 204

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
              V+   A  + +  ++P TGR HQLRVH   +G PI+ D  Y          P +  L
Sbjct: 205 VIDVVARGADTWTY-RLEPVTGRKHQLRVHMATLGAPILHDRFYPELEDQRPDDP-ERPL 262

Query: 289 YLHARYMDLPHPEGGR-LQITA 309
            L A  +    P      + TA
Sbjct: 263 QLFAHTLAFDDPITDEPRRFTA 284


>gi|167622075|ref|YP_001672369.1| pseudouridine synthase Rlu family protein [Shewanella halifaxensis
           HAW-EB4]
 gi|167352097|gb|ABZ74710.1| pseudouridine synthase Rlu family protein, TIGR01621 [Shewanella
           halifaxensis HAW-EB4]
          Length = 229

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 56/215 (26%), Positives = 88/215 (40%), Gaps = 19/215 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++ ++    V NK   +      G A    G +       G K    HRLD  TSG+++
Sbjct: 3   RVIADEHDFIVINKSTEVHFHSQDGSA----GVVAQAEADLGIKLYAVHRLDTLTSGLII 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A++ AAA   T  F    +QK Y +L  G PK K+  +   + K        +      
Sbjct: 59  LAKSSAAAAEFTRMFSAHLVQKYYLALAKGKPKKKQGWVIGDMAKSRRSMHKLLRSTD-- 116

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A+      ++PH+G+THQLRV    +G PI+GD  Y       
Sbjct: 117 ----NPAITQFFS-HSIAEGERLYLLKPHSGKTHQLRVALASIGVPILGDTLYGGEEA-- 169

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
                 ++ YLHA  +   + +       AP+   
Sbjct: 170 ------DRGYLHAYSLHFDYQDKQYEYTVAPVTGD 198


>gi|119476986|ref|ZP_01617267.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2143]
 gi|119449793|gb|EAW31030.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2143]
          Length = 280

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 54/280 (19%), Positives = 101/280 (36%), Gaps = 50/280 (17%)

Query: 31  HINFVNLQKILRSGQVRVDKKRV-----KFNNRIQSGQVVRIPPVINALNHIIKEQKILD 85
            ++   +++ ++ G V +   R      +   R++ G  + +    + L   +       
Sbjct: 23  GLSKTKIKQAMQKGAVWISGGRKAERLRRSKKRLKPGDQLHLYYNEDILTKNVP------ 76

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
                          L+ + +   ++ KP G+  QG     +     +      K  +  
Sbjct: 77  ------------MPTLISDHNDYSIWYKPYGVLCQGSKWGDHCTIDRMIEIYTQK--RSY 122

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--NKKECIANWLL 203
           L HRLD+ T+G++++A ++  A  L++ FR R I K Y ++V G      KK+ I + L 
Sbjct: 123 LVHRLDRATTGLMIIAHSKDMAAKLSKLFRDRAIDKRYLAIVDGDFPYCEKKQTITSTL- 181

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHM 262
                                 AISH + +    +     +++   TGR HQ+R      
Sbjct: 182 ------------------DGKKAISHMRRLRYSQRHHQSLIDVNIETGRKHQIRRQLSDQ 223

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           G PIVGD  Y         +       L    +    P  
Sbjct: 224 GYPIVGDRLYNPAGDDKQHTADLK---LCCYSLGFKCPIT 260


>gi|240112543|ref|ZP_04727033.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae MS11]
 gi|240125374|ref|ZP_04738260.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-92-679]
 gi|268598611|ref|ZP_06132778.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae MS11]
 gi|268683976|ref|ZP_06150838.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-92-679]
 gi|268582742|gb|EEZ47418.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae MS11]
 gi|268624260|gb|EEZ56660.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-92-679]
          Length = 307

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 87/223 (39%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKGQKPRL 146
            +     +  +L+ D  + V +KP  + V  G                       +    
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPGGRFLRETLLTRLRLHPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L        +  +   L   S
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEAL-----APTRTDLPYPLDVVS 201

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +         Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 202 RLARGEKFFTTQEAEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDAFYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|54022716|ref|YP_116958.1| putative RNA pseudouridylate synthase [Nocardia farcinica IFM
           10152]
 gi|54014224|dbj|BAD55594.1| putative RNA pseudouridylate synthase [Nocardia farcinica IFM
           10152]
          Length = 309

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 47/253 (18%), Positives = 94/253 (37%), Gaps = 8/253 (3%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
             + +  +++G +V +   I      +    +        +        +++ D  + V 
Sbjct: 44  PERIDELLRAGAIVDLDGPIAPDAPYVPGGAVWFHRDLPDEVEVPFDLTVVHRDETVLVV 103

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++             HRLD+ T+G+++     A      
Sbjct: 104 DKPHFLATIP-RGQHIRQTALVRLREQLGLPDLVPAHRLDRVTAGLILFVVDPARRGAYQ 162

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F  R ++K Y ++    P+     +A   + +S I  +   +  +  +G   A +  +
Sbjct: 163 TMFHRRTVRKQYEAIAPFDPE-----LALPRVVRSRIVKEKHVLAAREVEGEPNAETLVE 217

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           +++          + PHTGRTHQLR+H   +G PI+GD  Y               L L 
Sbjct: 218 LLEHR-DGLGRYRLTPHTGRTHQLRLHMNSLGVPILGDDFY-PVLTDKPVHEFTRPLQLL 275

Query: 292 ARYMDLPHPEGGR 304
           A  ++   P  G 
Sbjct: 276 AAVLEFTDPVTGE 288


>gi|256828761|ref|YP_003157489.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256577937|gb|ACU89073.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 281

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 58/282 (20%), Positives = 97/282 (34%), Gaps = 50/282 (17%)

Query: 28  HYPHINFVNLQKILRSGQV------RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
               +    ++  +  G V      R   +  + +  ++ G+ + I      L  +  + 
Sbjct: 26  RLTGLPKARIKDCMAKGGVWWSRPGRSTSRLRRASAEVKPGERLEINYDPALLALVPAQP 85

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           +++  +                      V+NKPA +  QG     +     L        
Sbjct: 86  ELIAKA------------------KHYSVWNKPAAVLSQGTRFADHCTLPRLAQAKLGSR 127

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +    HRLD+E  GI+++A    AA  L E FR   + K Y ++V GIP          
Sbjct: 128 NELHPVHRLDREARGIMLLAHDGKAAAKLGELFRQGAVVKEYAAIVRGIP---------- 177

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHAL 260
                    D+  +          A S F V+    A     L  +  TGR HQ+R H  
Sbjct: 178 ---------DWTDIEVNEPLDGKEARSRFHVVQSDPASDMTLLLARIDTGRKHQIRRHLN 228

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            +G P++GD +Y    +          L L AR +    P  
Sbjct: 229 GLGHPVMGDPRYGRGTRQVQE------LQLVARSLAFTCPFT 264


>gi|317014367|gb|ADU81803.1| hypothetical protein HPGAM_04945 [Helicobacter pylori Gambia94/24]
          Length = 242

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 64/288 (22%), Positives = 109/288 (37%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V +  K++    +        +P         ++          
Sbjct: 12  ENISHKKAKALIDLGLVSIGGKKLSIARK-------ELPQNTRFSVQKVE---------- 54

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   K  +++ED  I    KP  I        +Y +  F K W         L HR
Sbjct: 55  --------KPSVIFEDENILALFKPPFI-------ESYDLVSFFKDWA--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +LV GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVRKEYLALVQGIVEEEREINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    AI+    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAITIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPSSA------KRLMLHAHKIALL-----GYEFEAIAPKEFE 241


>gi|168024645|ref|XP_001764846.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162683882|gb|EDQ70288.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 327

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 66/311 (21%), Positives = 123/311 (39%), Gaps = 60/311 (19%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           ++    V + PV + L++ ++ Q+ L +   +       +  +L+ED  + + NKP G+ 
Sbjct: 14  LKLDYPVPLSPVPSQLSNEVELQRALVAEAAMKSRPAIGRESVLFEDEWLIIVNKPRGL- 72

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTH---RLDQETSGILVVARTRAAAQHLTESFR 175
                  + H+   + S   S G+ P   H   RLD++TSGI+++ + + AA +LT S+ 
Sbjct: 73  ------YSGHVFETMPSLCSSSGETPLHLHMANRLDRDTSGIMIITKCKVAAANLTRSYM 126

Query: 176 MRRIQKIYWSLVWG-IPKNKKECIANWLLKKS------HIGGDYVHVVKQNEKGANYAIS 228
            R++ K Y +      P  +K  I +   +        +   D    +    +     I+
Sbjct: 127 NRKVHKTYIAQCAQSQPTWRKSRIESGHGRSRYGAWHVYAKHDIGRRLPVKTETVREMIT 186

Query: 229 HFKVIDCF----------------------------------------AQKFCWLEMQPH 248
             +++                                            ++   +   P 
Sbjct: 187 RLEIVSGPDSLRWDNELSVEHDCLEVIVGSEDEVRLVSNEVTKRCSDVDEEVTLVRAFPE 246

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+R+H  ++G P+ GD KY             + L  HA  + L HP   + LQ+
Sbjct: 247 TGRTHQIRLHCQYLGLPLCGDVKYGGPLFWQSVHYDSHTL--HAESLALRHPMTNQLLQV 304

Query: 308 TAPLPAHMVKT 318
            AP P+  V+ 
Sbjct: 305 VAPYPSWAVQL 315


>gi|332673797|gb|AEE70614.1| RNA pseudouridine synthase [Helicobacter pylori 83]
          Length = 242

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 64/288 (22%), Positives = 113/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V V  K++                       ++  +++  ++  
Sbjct: 12  ENISHKKAKALIDLGLVSVGGKKL-----------------------MVARKELPKNTHF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPGVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ R          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVRENSEFHLKAKKAFKDRAVKKEYLALAQGIIEEEQEINAPILTFKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTMITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKIALL-----GYEFEAIPPKEFE 241


>gi|294142528|ref|YP_003558506.1| ribosomal pseudouridine synthase family protein [Shewanella
           violacea DSS12]
 gi|293328997|dbj|BAJ03728.1| ribosomal pseudouridine synthase family protein [Shewanella
           violacea DSS12]
          Length = 316

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 54/287 (18%), Positives = 105/287 (36%), Gaps = 28/287 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +    +  +     ++ +  G+V             Q G ++ +         +   +++
Sbjct: 36  FLVERFQQVGGEIWRQRIIDGKVH-----------WQDGSLIELDTAFKPRARVYYYREV 84

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
              +          +  +LY D +I +  KP  +++              +  + +  + 
Sbjct: 85  KSET------KVPFEEQILYRDEQIILAFKPHFLALHPSGNFVNECL-VNRLRIKTGIET 137

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKE 196
               HRLD+ T+GI+++     A     + F+  +I K Y +L    P+        +  
Sbjct: 138 IVPAHRLDRATAGIVLMILNPEARTQYHDLFKNHQITKEYQALAKLTPELLASHQAGELA 197

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              +W +K   + G+   ++K  E   N   S   +ID         ++ P TGRTHQLR
Sbjct: 198 LPIHWTVKNRMVKGEPSFIMKVVEGEPNT-HSEISLIDIKGDNG-LFKLSPITGRTHQLR 255

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           VH   +G PI+ D  Y    +          L L A+ +    P  G
Sbjct: 256 VHMHSLGMPIINDRCY-PQLQPKSDDDYARPLKLVAKRLKFNDPVTG 301


>gi|293399421|ref|ZP_06643574.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae F62]
 gi|291609990|gb|EFF39112.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae F62]
          Length = 307

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 44/223 (19%), Positives = 88/223 (39%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGG----SGIAYHIDGFLKSWVDSKGQKPRL 146
            +     +  +L+ D  + V +KP  + V  G                       +    
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPGGRFLRETLLTRLRLHPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|213692876|ref|YP_002323462.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis ATCC
           15697]
 gi|213524337|gb|ACJ53084.1| pseudouridine synthase [Bifidobacterium longum subsp. infantis ATCC
           15697]
          Length = 244

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 90/233 (38%), Gaps = 30/233 (12%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +LYED +I V +KP  ++     G+ Y     ++             HRLD+ T+G+LV
Sbjct: 2   DVLYEDERIIVVDKPHFLATMP-RGMWYRQTALIRLRERLGEPDITPAHRLDRMTAGVLV 60

Query: 160 VARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN-------WLLKKSHIGG 210
             R  A        F+ R+  K+Y   +    I + +   +          LL++SHI  
Sbjct: 61  FVRDPACRGAYQMLFQNRQAVKVYECLAPCRPIVRPRYGTVTRIDPPRPFPLLRRSHIVK 120

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQ-------------------KFCWLEMQPHTGR 251
           +   +      G   A +  +  +  +                      C   ++PHTG+
Sbjct: 121 ERGVLAAFEMPGLVNAETLIERGEPVSLFPGVKPCMPMAGGPRPSAVPVCRYTLRPHTGK 180

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           THQLRVH   +G PIVGD  Y    +          L L AR +    P  G+
Sbjct: 181 THQLRVHMNALGLPIVGDDFY-PCIQARRYDDFSQPLQLVARVLRFTDPVTGQ 232


>gi|21233606|ref|NP_639523.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66770572|ref|YP_245334.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|21115472|gb|AAM43405.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66575904|gb|AAY51314.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
          Length = 298

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 51/221 (23%), Positives = 87/221 (39%), Gaps = 11/221 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHR 149
            + +      +++ D +I V  KP  + V      AY  +  L   V           HR
Sbjct: 79  DEPTISAVETVVHADGQIVVACKPHFLPVVPAG--AYVRETLLARLVRRFDNPSLVPLHR 136

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D++T+G+++ +   A        FR RRI K Y ++   +P      +    + +S + 
Sbjct: 137 IDRDTAGLVLFSANPATRGIYQALFRERRIHKHYLAVAPPLPA-----LTFPYVHRSRLE 191

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                   +   G   + +   V+   A  + +  ++P TGR HQLRVH   +G PI+ D
Sbjct: 192 PGEPFFRMREGVGEPNSETVIDVVARGADMWTY-RLEPVTGRKHQLRVHMAALGVPILHD 250

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
             Y          P +  L L A  +    P  G   + TA
Sbjct: 251 RFYPELEDQRPDDP-ERPLQLFAHMLAFDDPITGEPRRFTA 290


>gi|254804732|ref|YP_003082953.1| pseudouridylate synthase [Neisseria meningitidis alpha14]
 gi|254668274|emb|CBA05164.1| pseudouridylate synthase [Neisseria meningitidis alpha14]
          Length = 307

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 46/223 (20%), Positives = 94/223 (42%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQKPR---L 146
            +     +  +L+ D  + V +KP  + V  GG  +   +   L+   + +         
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPGGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|194099471|ref|YP_002002592.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|239999712|ref|ZP_04719636.1| Pseudouridine synthase [Neisseria gonorrhoeae 35/02]
 gi|240081459|ref|ZP_04726002.1| Pseudouridine synthase [Neisseria gonorrhoeae FA19]
 gi|240113658|ref|ZP_04728148.1| Pseudouridine synthase [Neisseria gonorrhoeae MS11]
 gi|240116400|ref|ZP_04730462.1| Pseudouridine synthase [Neisseria gonorrhoeae PID18]
 gi|240118690|ref|ZP_04732752.1| Pseudouridine synthase [Neisseria gonorrhoeae PID1]
 gi|240124238|ref|ZP_04737194.1| Pseudouridine synthase [Neisseria gonorrhoeae PID332]
 gi|240126427|ref|ZP_04739313.1| Pseudouridine synthase [Neisseria gonorrhoeae SK-92-679]
 gi|254494411|ref|ZP_05107582.1| conserved hypothetical protein [Neisseria gonorrhoeae 1291]
 gi|260441622|ref|ZP_05795438.1| Pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|268595524|ref|ZP_06129691.1| conserved hypothetical protein [Neisseria gonorrhoeae 35/02]
 gi|268597560|ref|ZP_06131727.1| conserved hypothetical protein [Neisseria gonorrhoeae FA19]
 gi|268599721|ref|ZP_06133888.1| conserved hypothetical protein [Neisseria gonorrhoeae MS11]
 gi|268602065|ref|ZP_06136232.1| conserved hypothetical protein [Neisseria gonorrhoeae PID18]
 gi|268604405|ref|ZP_06138572.1| conserved hypothetical protein [Neisseria gonorrhoeae PID1]
 gi|268682866|ref|ZP_06149728.1| conserved hypothetical protein [Neisseria gonorrhoeae PID332]
 gi|268685013|ref|ZP_06151875.1| conserved hypothetical protein [Neisseria gonorrhoeae SK-92-679]
 gi|291044997|ref|ZP_06570705.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|193934761|gb|ACF30585.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|226513451|gb|EEH62796.1| conserved hypothetical protein [Neisseria gonorrhoeae 1291]
 gi|268548913|gb|EEZ44331.1| conserved hypothetical protein [Neisseria gonorrhoeae 35/02]
 gi|268551348|gb|EEZ46367.1| conserved hypothetical protein [Neisseria gonorrhoeae FA19]
 gi|268583852|gb|EEZ48528.1| conserved hypothetical protein [Neisseria gonorrhoeae MS11]
 gi|268586196|gb|EEZ50872.1| conserved hypothetical protein [Neisseria gonorrhoeae PID18]
 gi|268588536|gb|EEZ53212.1| conserved hypothetical protein [Neisseria gonorrhoeae PID1]
 gi|268623150|gb|EEZ55550.1| conserved hypothetical protein [Neisseria gonorrhoeae PID332]
 gi|268625297|gb|EEZ57697.1| conserved hypothetical protein [Neisseria gonorrhoeae SK-92-679]
 gi|291011000|gb|EFE02997.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|317164980|gb|ADV08521.1| Pseudouridine synthase [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 177

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 51/174 (29%), Positives = 73/174 (41%), Gaps = 10/174 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV    G                 +K  L HRLD++  GIL+ 
Sbjct: 4   ILFRYQDFVAINKPQGISVHRSGGEVSLTATLAAQL---GVEKVWLLHRLDKQAGGILLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I   + K          + K   
Sbjct: 61  ALNPQSAAVLAAQFAERKMKKTYLALSDRKPSKKQGWIKGGMEK------SRRGMWKLTR 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
              N A++ F  I   ++K     ++PHTG+THQLRV    +G  I GD  Y  
Sbjct: 115 NMENIAVTRFFSI-RISEKMRLFILEPHTGKTHQLRVVMKSLGSSIFGDSLYGG 167


>gi|307253996|ref|ZP_07535844.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
 gi|306863022|gb|EFM94968.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
          Length = 201

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 59/213 (27%), Positives = 94/213 (44%), Gaps = 21/213 (9%)

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
            +KP G+SV          +   +     + ++  L HRLD+ TSG+L+ A  + AA H 
Sbjct: 2   IDKPVGVSVHKDEEAIGLTENLAEQL---QAEQVWLVHRLDKVTSGLLIFALNKQAAVHF 58

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              F   +I+K YW+L    PK K+  I+  + K  +      H  +      N A++ F
Sbjct: 59  YHLFEQHKIEKTYWALSDQKPKKKQGKISGDMQKSRNGAWKLFHSKQ------NPAVTQF 112

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
            V            +QP TG+THQLRV    +G PI+GD +Y             +++YL
Sbjct: 113 -VSHSLEPNLRHFILQPKTGKTHQLRVAMKSLGSPILGDQRYAGT--------AADRVYL 163

Query: 291 HARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
           HA  +   + +G    I +   +   + W  LG
Sbjct: 164 HAYQLKFDY-QGESFCIQSQPTSG--RFWAKLG 193


>gi|325927184|ref|ZP_08188446.1| 23S RNA-specific pseudouridylate synthase [Xanthomonas perforans
           91-118]
 gi|325542445|gb|EGD13925.1| 23S RNA-specific pseudouridylate synthase [Xanthomonas perforans
           91-118]
          Length = 300

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/297 (20%), Positives = 117/297 (39%), Gaps = 36/297 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
                +P I     +     G VR  + + +  +   + G  +R           + ++ 
Sbjct: 29  ALCACFPAIAAERWRDRFARGLVRDANDQALALSAPYRVGADIRYF-------REVADEP 81

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
           ++                +++ D+++ V  KP  + V   G+ +   +   L   +D+  
Sbjct: 82  VIPY-----------VETVVHADAQLVVACKPHFLPVAPAGAYVRETLLTRLVRRLDNPA 130

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
             P   HR+D+ET+G+++ +   A        FR RRI+K Y ++   +P+ +   +   
Sbjct: 131 LVP--LHRIDRETAGLVLFSANPATRGIYQALFRQRRIRKHYLAVAPPLPQLRFPHVHRS 188

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           LL    + G+    + +    AN + +  +V+   A  + +  ++P TGR HQLRVH   
Sbjct: 189 LL----VPGEPFFRMHEGVGEAN-SETVIEVVARNADTWTY-RLEPVTGRKHQLRVHMAA 242

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
           +G PI+ D  Y          P +  L L A  +    P  G        P H   T
Sbjct: 243 LGAPILHDRFYPELEAQRPDDP-ERPLQLFAHTLAFDDPLTGE-------PRHFTAT 291


>gi|327334511|gb|EGE76222.1| RNA pseudouridylate synthase family protein [Propionibacterium
           acnes HL097PA1]
          Length = 281

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 51/218 (23%), Positives = 82/218 (37%), Gaps = 6/218 (2%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            T+        +LY D +I V +KP  +S     G        ++        +  + HR
Sbjct: 53  PTETPVPAGIGILYSDERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHR 111

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRI---QKIYWSLVWGIPKNKKECIANWLLKKS 206
           LD+ T+G+L++ R R   +   E F  R +    ++   +V    +       N    +S
Sbjct: 112 LDRVTAGVLLLTRERKWRRPYQEMFERREVVKKYRLVAPVVHDPAREGIGATKNGWQVRS 171

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            I  +   +  +   G   A++   +I          E  P TGRTHQ+R+H   +G PI
Sbjct: 172 RIIKERGILQAREVPGVPNAVTDIVLIGKCG-GLGLYEASPRTGRTHQIRLHMQRLGAPI 230

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           V D  Y             + L L A  M    P  G 
Sbjct: 231 VNDPFY-PTVLDTPVDDFTHPLQLQAWRMGFTDPVSGE 267


>gi|157738183|ref|YP_001490867.1| ribosomal large subunit pseudouridine synthase [Arcobacter butzleri
           RM4018]
 gi|315636326|ref|ZP_07891576.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
 gi|157700037|gb|ABV68197.1| ribosomal large subunit pseudouridine synthase [Arcobacter butzleri
           RM4018]
 gi|315479415|gb|EFU70098.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
          Length = 251

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 64/297 (21%), Positives = 110/297 (37%), Gaps = 58/297 (19%)

Query: 22  DRW--FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           D+          I+    ++++  G V+V  K+V     I  G++             IK
Sbjct: 6   DKAYKLLALQEKISNSKAKELIDKGVVKVGDKKV----LIARGEI------RTDTKFTIK 55

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E                 K  +++ED  I V +KPA ++                  V  
Sbjct: 56  E---------------INKVKVIFEDKDILVVDKPAFLT---------------ADEVCK 85

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           K +   L +RLD+ETSG+++ A+     +   + F+  R+ K Y ++V G   ++ E   
Sbjct: 86  KFENAILLNRLDKETSGVMMFAKNEEFQKKAIKEFQANRVYKEYVAIVEGKVVDEIEIDK 145

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L  K       +   K + K    A S    +     K   +++   +GRTHQ+RVH 
Sbjct: 146 PILTTKDR----GMAKSKIDVKRGKPAKSTVYPLLVEGNK-SKIKVVIESGRTHQIRVHL 200

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
             +G PI+GD  Y             N++ LH++   +           A  P    
Sbjct: 201 NSVGLPIIGDAIYGRVSSNV------NRVLLHSKITKIFD-----YTFEAHEPKEFK 246


>gi|270284361|ref|ZP_05965988.2| RNA pseudouridine synthase [Bifidobacterium gallicum DSM 20093]
 gi|270276723|gb|EFA22577.1| RNA pseudouridine synthase [Bifidobacterium gallicum DSM 20093]
          Length = 232

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 52/219 (23%), Positives = 87/219 (39%), Gaps = 19/219 (8%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LYED +I V +KP  ++     G+ Y     +++     G++  L HRLD+ T+G+LV+ 
Sbjct: 2   LYEDERIIVVDKPHFLASMP-RGMWYRQTVLMRAR-QQFGEQVTLAHRLDRLTAGVLVLV 59

Query: 162 RTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN-------WLLKKSHIGGDY 212
           R           F  RR  KIY   + +    +     +          L ++S I    
Sbjct: 60  RDPQFRGAYQTLFEQRRTTKIYECLAPLKPARRPPTGTVRALEPPRSFPLERRSRIVKMR 119

Query: 213 VHVVKQNEKGANYAISHFKVID-------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
             +  + ++G   A++  +  +          +      + P TG+THQLRVH   +G P
Sbjct: 120 GVLQAREQRGQVNAVTLIEREELAPGITVADGRAVARYRLHPCTGKTHQLRVHMNSLGLP 179

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++ D  Y               L L AR +    P  G 
Sbjct: 180 MLNDPWY-PRVLDVPYDDFSRPLALVARELQFVDPVSGE 217


>gi|169630733|ref|YP_001704382.1| pseudouridine synthase [Mycobacterium abscessus ATCC 19977]
 gi|169242700|emb|CAM63728.1| Pseudouridine synthase [Mycobacterium abscessus]
          Length = 277

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 58/250 (23%), Positives = 97/250 (38%), Gaps = 11/250 (4%)

Query: 57  NRIQSGQVV-RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           +++  G+VV      + A   +     +        + S      +L+ D  + V +KP 
Sbjct: 25  DQVDRGEVVDSAGMRVTAGTRLPAGAVVYTYREPAEEISVPFAIDVLHWDENVLVVDKPH 84

Query: 116 GISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            ++    G  +       L+  +D    +    HRLD+ T+G+L+    R A       F
Sbjct: 85  FLATMPRGRHVTETALVRLRKMLDL--PELAPAHRLDRLTAGVLLFTVRRDARAAYHSLF 142

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             R++ KIY +L    P      ++  L  +S I      +    E G   A +  +++D
Sbjct: 143 AQRQVVKIYEALAPVKP-----GLSLPLTVRSRIVKRRSILQAVEEPGPANAETRVELVD 197

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                     + P TG+THQLRVH   MG PI+ D  Y  +            L L AR 
Sbjct: 198 RH-HAVGRYRLTPSTGQTHQLRVHMNSMGVPILNDPLY-PDVVEVPPDDFTRPLQLLART 255

Query: 295 MDLPHPEGGR 304
           +    P  G+
Sbjct: 256 LAFRDPLNGK 265


>gi|330945840|gb|EGH47230.1| pseudouridine synthase [Pseudomonas syringae pv. pisi str. 1704B]
          Length = 264

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 52/266 (19%), Positives = 97/266 (36%), Gaps = 31/266 (11%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +P I+          G+V   + K +  +   + G  +R+       N        
Sbjct: 19  LCAKFPAISREQWLDRFSRGRVLDENGKAIAPDLAYREG--LRVHYFREVAN-------- 68

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +    +   +LY D  + V +KP  + V       Y     L+  +   G  
Sbjct: 69  --------ETPIPVVETILYADEHLVVADKPHFLPVTPAG--EYVEQTLLRRLIHRLGNP 118

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R         F  RRI K Y ++   +P+     +    
Sbjct: 119 DLVPLHRIDRHTAGLVLFSANRQTRSAYQTLFPTRRIDKFYQAIAPALPE-----LTFPR 173

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L +S +         Q   GA+   +  +V++    K     + P TG+ HQLRVH   +
Sbjct: 174 LHESRLVEGEPFFRMQEGVGASNTRTQIEVLERQ-DKLWRYGLYPVTGKKHQLRVHMAAL 232

Query: 263 GCPIVGDHKYC---ANFKGNFTSPIQ 285
           G  I  D  Y     +   ++ +P++
Sbjct: 233 GAAICNDPFYPDVAKDPVDDYRNPLK 258


>gi|297380156|gb|ADI35043.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori v225d]
          Length = 242

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 63/288 (21%), Positives = 114/288 (39%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V V +K++                       ++  +++  ++  
Sbjct: 12  ENISHKKAKALIDLGLVSVGEKKL-----------------------MVARKELPKNTHF 48

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +  +  K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 49  SVQKVE--KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLALAQGIIEEEQEINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L+ +  TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIIAPLKIINKK-TLLKARIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKIALL-----GYEFEAIPPKEFE 241


>gi|326919876|ref|XP_003206203.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Meleagris gallopavo]
          Length = 479

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 54/210 (25%), Positives = 100/210 (47%), Gaps = 8/210 (3%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            +  L+ ++K    L ++V+  +     + I +L E+ ++ V +KP+ + V       ++
Sbjct: 120 PVQDLDVVLKNNDFLRNTVHRHEPPVTAQPIQILVENDEVVVVDKPSSLPVHPCGRFRHN 179

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              F+    +   ++    HRLD+ TSG+L+ A+T   ++ + E  R R+++K Y   V 
Sbjct: 180 TVIFILG-KEHNLKELHTIHRLDRMTSGVLMFAKTVEVSKRIDEQVRERQLEKEYVCRVV 238

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G     +      +L  S+     V V + + KG     + F+ +    +    ++  PH
Sbjct: 239 GEFPEHEVVCEEPILVVSY----KVGVCRVDPKG-KCCKTIFQRLSYNGKS-SVVKCLPH 292

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           TGRTHQ+RVH  ++G PIV D  Y     G
Sbjct: 293 TGRTHQIRVHLQYLGYPIVNDPIYNMEAWG 322


>gi|317009613|gb|ADU80193.1| hypothetical protein HPIN_04885 [Helicobacter pylori India7]
          Length = 242

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 64/288 (22%), Positives = 110/288 (38%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V +  K++    +        +P         I+          
Sbjct: 12  ENISHKKAKALIDLGLVSIGGKKLMVARK-------ELPQNTRFSVQKIE---------- 54

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   K  +++ED  I    KP  I        +Y +  F K WV        L HR
Sbjct: 55  --------KPGVIFEDENILALFKPPFI-------ESYDLVSFFKGWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVVLLVKENSEFHLKAKKAFKDRAVKKEYLALAQGIIEEEREINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y  +           +L LHA  + L        +  A  P    
Sbjct: 205 DTIYGDSQHSA------KRLMLHAHKIALL-----GYEFEAIPPKEFE 241


>gi|269955480|ref|YP_003325269.1| pseudouridine synthase [Xylanimonas cellulosilytica DSM 15894]
 gi|269304161|gb|ACZ29711.1| pseudouridine synthase [Xylanimonas cellulosilytica DSM 15894]
          Length = 309

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 58/264 (21%), Positives = 108/264 (40%), Gaps = 13/264 (4%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL----DSSVNLTKHSDFLKSILLYEDSK 107
            V+   ++ +G+VV    V   ++   + +  L    D   +  +     +  +L+ D  
Sbjct: 44  VVRLREKVAAGEVVTGRGVRVDVDTPYEPRGFLYLYRDPPSDEPRALSLAEIEVLHRDEN 103

Query: 108 IYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           + V +KP  ++    G  +   +   L+  +D    +    HRLD+ T+G+LV+    + 
Sbjct: 104 LLVVDKPHLVATMPRGRWVTQTVLVHLRRTLDL--PELAPAHRLDRPTAGVLVLTVRASV 161

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
                + F+ RR++K+Y ++         + +      +S I         Q E G   A
Sbjct: 162 RGAYQDLFQERRVRKVYEAVA----PLPGDGVELPTTVRSRIVKHRGVAPAQEEPGEPNA 217

Query: 227 ISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
            S   +I     +      ++PHTG+THQLR+H   +G PI+ D  +      +   P  
Sbjct: 218 ESRIDLIGRDEGRGLGLYRLEPHTGKTHQLRLHLASLGMPILHDPFWPVLRPDSDGDPA- 276

Query: 286 NKLYLHARYMDLPHPEGGRLQITA 309
             L L AR +    P  G  +  A
Sbjct: 277 TPLQLLARSLTFADPFTGEQRTFA 300


>gi|309379425|emb|CBX21992.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 307

 Score =  124 bits (311), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 48/241 (19%), Positives = 97/241 (40%), Gaps = 11/241 (4%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGI 125
           +P   N L    K       + +  +     +  +L+ D  + V +KP  + V   G  +
Sbjct: 63  VPFDENTLFEPGKTMFYYRETSSEDEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFL 122

Query: 126 AYHIDGFLKSWVDSKGQKPR---LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              +   L+   + +          HRLD++T+G+++++   A        F+ + + K 
Sbjct: 123 RETLLTRLRLRPELQHLNVEDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKT 182

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y +L       + +      +    + G+      Q  +G   A +  ++I+   + F  
Sbjct: 183 YEALA----PTRTDLPYPLDVVSRLVRGEKFF-TTQEAEGVPNAHTTVELIENRGE-FSL 236

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
             + PHTG+ HQLRVH + +G P++ D  Y    +   +   +  L L A+ +    P  
Sbjct: 237 YRLTPHTGKKHQLRVHMMGLGMPLLNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLS 295

Query: 303 G 303
           G
Sbjct: 296 G 296


>gi|308495566|ref|XP_003109971.1| hypothetical protein CRE_06376 [Caenorhabditis remanei]
 gi|308244808|gb|EFO88760.1| hypothetical protein CRE_06376 [Caenorhabditis remanei]
          Length = 426

 Score =  124 bits (311), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 44/184 (23%), Positives = 74/184 (40%), Gaps = 9/184 (4%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQET 154
            L   ++ +   + V  KP  + V      A H    L     ++G    R+ HRLD+ T
Sbjct: 122 DLPIRIISDTDDLLVIEKPPSLPVHTCGQYAIH--TVLGQLRVNEGITGLRVLHRLDRAT 179

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L+ A+          + +     K Y   V G+  ++++     +            
Sbjct: 180 SGVLLFAKNYETDLEFKTTLKQGEWSKEYICKVDGVFPDEEQLCDQPIG-----PLVISM 234

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            ++        A S FK +         +++   TGRTHQ+RVH+  +G PIVGD  Y +
Sbjct: 235 GIQCVRPDGKEAKSRFKKLWSDG-THSVVQVHIETGRTHQIRVHSQFLGHPIVGDQLYNS 293

Query: 275 NFKG 278
              G
Sbjct: 294 TVWG 297


>gi|325144100|gb|EGC66407.1| RNA pseudouridine synthase [Neisseria meningitidis M01-240013]
          Length = 307

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 94/223 (42%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
           ++     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  SEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPIDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|256822239|ref|YP_003146202.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
 gi|256795778|gb|ACV26434.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
          Length = 305

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 58/303 (19%), Positives = 108/303 (35%), Gaps = 40/303 (13%)

Query: 24  WFKNHYPHINFVNLQKILRSGQV----RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           +  + +PH++       +  G+V    RV K  V  +   Q+G+V+     +     I  
Sbjct: 24  FLVDTFPHVSESEWMSRMAEGKVYWENRV-KVPVDADY--QAGRVLYYHREVEQEPTIP- 79

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                               +++  +    +  KP  + V  G           +  +D 
Sbjct: 80  -----------------FAEMIIEHNEHFLIAYKPHFLPVMPGGVFVNEC--LQQRLIDK 120

Query: 140 KG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI----PKNK 194
            G    +  HRLD++T+G+++ +          + F  + I+K Y ++           K
Sbjct: 121 TGNPNLQAVHRLDRDTAGLVMFSTNPHTRSDYHQLFAQQNIKKHYQAIAKTQAGESLSGK 180

Query: 195 KECIANWLLKKSHI-----GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
              I N+L +                   ++K A YA S     +    +     + P T
Sbjct: 181 SWHIKNYLARSEPQFIFQNLDTSPDDTSPHDKDAQYAESLIHC-EDDNLQLGLFTLSPIT 239

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-IT 308
           GRTHQLR+H + +G PI+ D  Y  + +          L L A  +    P     +  T
Sbjct: 240 GRTHQLRLHMMSLGFPILNDRFY-PSLQPKQADNFSQPLQLLAHKLSFIDPVSKEPRAFT 298

Query: 309 APL 311
           +P+
Sbjct: 299 SPV 301


>gi|313682891|ref|YP_004060629.1| pseudouridine synthase rlu family protein, tigr01621 [Sulfuricurvum
           kujiense DSM 16994]
 gi|313155751|gb|ADR34429.1| pseudouridine synthase Rlu family protein, TIGR01621 [Sulfuricurvum
           kujiense DSM 16994]
          Length = 224

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 60/216 (27%), Positives = 95/216 (43%), Gaps = 17/216 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  L++E+    V  KP G++       +    GF+    +  G      HRLD+ TSG+
Sbjct: 3   KMRLIFENDTFVVAIKPEGVNFH-----SEGEAGFVVQVSEQLGCPLFPVHRLDKMTSGL 57

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+    A    + F  R I+K Y ++    PK K   I   +   S   GDY  +V 
Sbjct: 58  VILAKNSETAARFGKMFENREIEKYYLAISMRKPKKKMGWIKGDMA--SARRGDYKLLVT 115

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
            N    N AI+ F        +  +L ++PHTG+THQ+RV    +G PI GD +Y    +
Sbjct: 116 MN----NPAITRFISCALRTHERGFL-IKPHTGKTHQIRVALKSLGSPIAGDERYAQADE 170

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
                  +++ YLHA  +     E       +P   
Sbjct: 171 ARK----EDRGYLHAYALRFRLGE-EEFCFVSPPDE 201


>gi|254673322|emb|CBA08488.1| pseudouridylate synthase [Neisseria meningitidis alpha275]
 gi|325202346|gb|ADY97800.1| RNA pseudouridine synthase [Neisseria meningitidis M01-240149]
 gi|325207901|gb|ADZ03353.1| RNA pseudouridine synthase [Neisseria meningitidis NZ-05/33]
          Length = 307

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 93/223 (41%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
            +     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|308807815|ref|XP_003081218.1| COG0564: Pseudouridylate synthases, 23S RNA-specific (ISS)
           [Ostreococcus tauri]
 gi|116059680|emb|CAL55387.1| COG0564: Pseudouridylate synthases, 23S RNA-specific (ISS)
           [Ostreococcus tauri]
          Length = 377

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 53/185 (28%), Positives = 86/185 (46%), Gaps = 18/185 (9%)

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
               R  H+LD  TSG+++ A T++AA    + FR R+ +K Y ++V+G P+  +     
Sbjct: 187 NMHHRFCHQLDTATSGVILTAHTKSAAAAAAKLFRDRKAKKTYLAVVYGWPERDEWTTTA 246

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---------FAQKFCWLEMQPHTGR 251
            L K  +    +   V  +E+G   + + FKV+              K   L+ +P TGR
Sbjct: 247 KLGKDPNCPKGFRERV--DEEGGKASETRFKVLRRGYCTLDGAHRGIKVTLLQCKPVTGR 304

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
            HQ+RVH  H G PI+GD  Y +    +F      +++LHA  + +P P+   L      
Sbjct: 305 RHQIRVHLQHSGFPILGDIAYYSGVSDSF------RMFLHALELVMPFPD-ETLTFKTDP 357

Query: 312 PAHMV 316
           P    
Sbjct: 358 PLAFE 362


>gi|15676763|ref|NP_273908.1| YabO/YceC/SfhB family protein [Neisseria meningitidis MC58]
 gi|7226104|gb|AAF41278.1| YabO/YceC/SfhB family protein [Neisseria meningitidis MC58]
          Length = 307

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 94/223 (42%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
           ++     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  SEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|302791938|ref|XP_002977735.1| hypothetical protein SELMODRAFT_107717 [Selaginella moellendorffii]
 gi|300154438|gb|EFJ21073.1| hypothetical protein SELMODRAFT_107717 [Selaginella moellendorffii]
          Length = 191

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 44/184 (23%), Positives = 72/184 (39%), Gaps = 23/184 (12%)

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV-VKQNEK 221
              +   L+E F+ R++++ Y SL  G P      I   +L+               + +
Sbjct: 2   DEQSQLSLSEQFKSRKVRRTYLSLTCGTPSTTSGRIEAEILRDPRDRKRMTTSDTVPSAR 61

Query: 222 GANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            A +A S +KV+D  A      ++ +  TGRTHQ+RVHA +MG P++GD  Y        
Sbjct: 62  NARFAASRYKVLDVLANGGVALVQWKLETGRTHQIRVHARYMGFPLLGDDVYGGTVGKAN 121

Query: 281 TSPIQ--------------------NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTW 319
           ++                        +  LHA  +   HP   + +  T P P    + W
Sbjct: 122 STLFSALSATKTNSRKKIHEFTSDIRRPCLHAYSLGFEHPATEKYVHFTCPPPEDFEEAW 181

Query: 320 DSLG 323
             L 
Sbjct: 182 TRLR 185


>gi|218767979|ref|YP_002342491.1| hypothetical protein NMA1085 [Neisseria meningitidis Z2491]
 gi|121051987|emb|CAM08296.1| hypothetical protein NMA1085 [Neisseria meningitidis Z2491]
 gi|308389039|gb|ADO31359.1| YabO/YceC/SfhB family protein [Neisseria meningitidis alpha710]
 gi|316985760|gb|EFV64704.1| RNA pseudouridylate synthase family protein [Neisseria meningitidis
           H44/76]
 gi|319410229|emb|CBY90568.1| putative RNA pseudouridine synthase (RNA-uridine isomerase; RNA
           pseudouridylate synthase) [Neisseria meningitidis WUE
           2594]
 gi|325130001|gb|EGC52795.1| RNA pseudouridine synthase [Neisseria meningitidis OX99.30304]
 gi|325139980|gb|EGC62509.1| RNA pseudouridine synthase [Neisseria meningitidis CU385]
 gi|325200448|gb|ADY95903.1| RNA pseudouridine synthase [Neisseria meningitidis H44/76]
 gi|325203940|gb|ADY99393.1| RNA pseudouridine synthase [Neisseria meningitidis M01-240355]
          Length = 307

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 94/223 (42%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
           ++     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  SEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|307721677|ref|YP_003892817.1| pseudouridine synthase [Sulfurimonas autotrophica DSM 16294]
 gi|306979770|gb|ADN09805.1| pseudouridine synthase [Sulfurimonas autotrophica DSM 16294]
          Length = 244

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 63/294 (21%), Positives = 110/294 (37%), Gaps = 60/294 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        I+  N + ++  G V V  K+V                       +I   +
Sbjct: 8   KLLAQQ-EGISNSNAKSMIDRGLVYVGNKKV-----------------------MIARGE 43

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I + +V   +  + +K   ++E+  I V +KPA ++                  ++ + +
Sbjct: 44  IDERTVFRIQKVEKVKP--IFENDDIIVVDKPAHVNS---------------DEIERQFK 86

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD+ETSG+L++ +     Q   + FR  ++ K Y + V GI     E      
Sbjct: 87  PAVLLHRLDRETSGVLMLVKNEDFRQRAIKEFRDDKVYKEYIAWVEGIMTEPIEVDKAIT 146

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            +K +                  A + F   D  + K   ++   H GRTHQ+RVHA ++
Sbjct: 147 TQKKNN-----KAYSNVSPKGKPARTEFFP-DIVSAKKTKVKCIIHNGRTHQIRVHARYI 200

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
             PIVGD +Y              ++ LHA  + L       ++  A  P    
Sbjct: 201 DHPIVGDEQYGGRRA--------KRVMLHAHKVRLL-----GMEFVAKEPKSFT 241


>gi|332994014|gb|AEF04069.1| tRNA pseudouridine synthase A [Alteromonas sp. SN2]
          Length = 278

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 58/252 (23%), Positives = 104/252 (41%), Gaps = 54/252 (21%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQG------------------------------------ 121
           +  +L +D  + + NKP+GI++                                      
Sbjct: 3   EIPILVDDEDVLIVNKPSGIAMHDCANTVNIANTQSTGTAENISAGEGADACGLNNIGSK 62

Query: 122 -GSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             S I  H  G +    +  G  +  L HRLD  TSG L +A+    A  + ++F  R++
Sbjct: 63  IDSKIDTHAFGIVTLLREQTGYSQLHLCHRLDTGTSGCLCLAKNAQTAALIGDAFASRQV 122

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            K Y ++    PK K+  I   +  K+  GG ++ +  ++    N A++ F         
Sbjct: 123 SKYYLAISADKPKKKQGSIVGDM--KNRRGGQFMLLKSKD----NPAVTQFFS-QSAKPG 175

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           +    ++P TG+THQ+RV    +G  I+GD  Y             ++L+LHA ++ +P 
Sbjct: 176 YRGFIVKPLTGKTHQIRVALKSVGAAILGDTLYSGAP--------SDRLHLHAGWLRIPL 227

Query: 300 PEGGRLQITAPL 311
           P    + + AP+
Sbjct: 228 P-SRTISVKAPI 238


>gi|296123058|ref|YP_003630836.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
 gi|296015398|gb|ADG68637.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
          Length = 396

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 70/371 (18%), Positives = 123/371 (33%), Gaps = 75/371 (20%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-------KRVKFNNRIQ----- 60
           ++      +    +   P  ++  ++K++   +V V++       +R+   +RI+     
Sbjct: 17  DSSLAGQTIVATLRKLLPDQSWSAVRKVIEQRRVLVNRYACFDETRRLTERDRIEVLAHP 76

Query: 61  ------SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYV---- 110
                    +  I      +  +  E  + +   +    +  L+   L  D  + +    
Sbjct: 77  AAALPDENSIELIYVDEQIVVALKPEGMVTERRYDDLPDAPELRWRALTLDEAVTIRLMG 136

Query: 111 ------------------FNKPAGI-SVQGGSGIAYHID------GFLKSWVDSKGQKPR 145
                                PAG   V     +              KS + +    P 
Sbjct: 137 GREATIAGRANPTSPGRPPLLPAGQRPVHRRDQMRRDSQRRDATGSSAKSRLHTPKAPPC 196

Query: 146 LT---HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HRLD++TSG++V++R   A   L   F+   + + Y +LVWG  + ++       
Sbjct: 197 HVRAAHRLDRQTSGLVVLSRVPEAGAKLYAQFQAHDVLREYEALVWGWIEPQRLESELIR 256

Query: 203 LKKSHIGGDYVHVVKQNE-----------KGANYAIS--------HFKVIDCFAQKFCWL 243
            +     G    V                     A +        HFK          W+
Sbjct: 257 DRGDGRRGSRQPVTMLEAGAEDSPAANPLPAGKMAATNLVASRQGHFKSGTGELAPVSWI 316

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
             Q  TGRTHQ+R+H    G PIVGD  Y        +     +LYLHA  +   HP  G
Sbjct: 317 RCQLETGRTHQVRIHLSEKGNPIVGDDVYG-----THSLDGVPRLYLHAARLGFIHPMTG 371

Query: 303 GRLQITAPLPA 313
            RL+ +   P 
Sbjct: 372 KRLEFSLSWPE 382


>gi|261400179|ref|ZP_05986304.1| RNA pseudouridine synthase [Neisseria lactamica ATCC 23970]
 gi|269210178|gb|EEZ76633.1| RNA pseudouridine synthase [Neisseria lactamica ATCC 23970]
          Length = 307

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 55/291 (18%), Positives = 112/291 (38%), Gaps = 28/291 (9%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNH 76
            + L  +   H+P +   N ++ L SG V   D      N   + G+ +      ++ + 
Sbjct: 29  GLPLLHFLCAHFPFVGEENWRRRLNSGFVVGADGVPFDENTLFEPGKTMFYYRETSSED- 87

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLK- 134
                          +     +  +L+ D  + V +KP  + V   G  +   +   L+ 
Sbjct: 88  ---------------EPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRL 132

Query: 135 --SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                    +     HRLD++T+G+++++   A        F+ + + K Y +L      
Sbjct: 133 RPELQHLNVEDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----P 188

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            + +      +    + G+      Q  +G   A +  ++I+   + F    + PHTG+ 
Sbjct: 189 TRTDLPYPLDVVSRLVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKK 246

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           HQLRVH + +G P++ D  Y    +   +   +  L L A+ +    P  G
Sbjct: 247 HQLRVHMMGLGMPLLNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSG 296


>gi|325142086|gb|EGC64512.1| RNA pseudouridine synthase [Neisseria meningitidis 961-5945]
          Length = 307

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 94/223 (42%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
           ++     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  SEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPIDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|87121539|ref|ZP_01077427.1| RNA pseudouridine synthase family protein [Marinomonas sp. MED121]
 gi|86163071|gb|EAQ64348.1| RNA pseudouridine synthase family protein [Marinomonas sp. MED121]
          Length = 313

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 61/288 (21%), Positives = 113/288 (39%), Gaps = 26/288 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           LD +    +P I+ V  Q+ +  G+V   D   +   ++        +P         ++
Sbjct: 27  LD-YLIIKFPFIDAVVWQQRMADGKVHWHDGSLITAQSK-------FLPQQRVYYYREVE 78

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            + ++               I+L++D  I V  KP  + V  G           +    +
Sbjct: 79  NEPVIP-----------FNEIILFQDQDILVAYKPHFLPVTPGGIYVNECLQT-RLRRST 126

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             +  +  HRLD+ T+G+++ +     +Q   E F  R+I K Y ++   + +N+     
Sbjct: 127 GIESLQALHRLDRVTAGLVIFSVNPETSQCYHELFETRQIDKTYQAIAK-VAENENLIDQ 185

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---CWLEMQPHTGRTHQLR 256
            W +K     G     ++  E   N   ++   I    Q+       E++P TG+THQLR
Sbjct: 186 EWQVKNRIAKGKPSFRMQILEASDNSIQANSLSIIRCTQQVDELALFELKPVTGKTHQLR 245

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +H   +G PI+ D KY            Q  L L A+ ++   P   +
Sbjct: 246 LHMQSLGLPILND-KYYPELAPQTADNYQAPLQLLAKELEFIDPISKQ 292


>gi|325198068|gb|ADY93524.1| RNA pseudouridine synthase [Neisseria meningitidis G2136]
          Length = 307

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 94/223 (42%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
           ++     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  SEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPIDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|161869801|ref|YP_001598969.1| YabO/YceC/SfhB family protein [Neisseria meningitidis 053442]
 gi|161595354|gb|ABX73014.1| YabO/YceC/SfhB family protein [Neisseria meningitidis 053442]
          Length = 307

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 93/223 (41%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
            +     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|12323024|gb|AAG51501.1|AC058785_4 unknown protein [Arabidopsis thaliana]
          Length = 293

 Score =  123 bits (309), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 62/255 (24%), Positives = 106/255 (41%), Gaps = 52/255 (20%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---SKGQKPRLTHRLDQET 154
           +  +LYED  +   NKP G+          + +  L+S          +  L +RLD++T
Sbjct: 45  RDDILYEDEYLMAVNKPKGV----------YCEAVLRSAPQIVLDSSSEYHLANRLDRDT 94

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++ ++   A  L ++F   +I+K Y +L  G   N +    +    +S  G   V+
Sbjct: 95  SGVMIITKSHKVAAKLVKAFTEHKIRKSYIALCIGSSPNWRRVTVSSGHGRSKHGAWRVY 154

Query: 215 ------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ---------------------- 246
                  V           + F+V+   + K    E++                      
Sbjct: 155 AALDVGRVLPGGSFVRDMETTFEVVSVNSVKNESCELEDVNHVIVAEGERELSCGGDDDD 214

Query: 247 --------PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
                   P +GRTHQ+R+H  ++G PI GD KY   ++ N  +   ++L  HA  + L 
Sbjct: 215 VVVVVRAFPRSGRTHQIRLHCQYLGIPIRGDVKYHGVYEWNGRTFEGHEL--HAECLSLD 272

Query: 299 HPEGGR-LQITAPLP 312
           HP  G  + I APLP
Sbjct: 273 HPVTGDSIVIRAPLP 287


>gi|261392780|emb|CAX50356.1| putative RNA pseudouridine synthase (RNA-uridine isomerase; RNA
           pseudouridylate synthase) [Neisseria meningitidis 8013]
          Length = 307

 Score =  123 bits (309), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 91/223 (40%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLK---SWVDSKGQKPRL 146
            +     +  +L+ D  + V +KP  + V   G  +   +   L+          +    
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y        +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALY-PVLSEAGSEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|317011193|gb|ADU84940.1| hypothetical protein HPSA_04800 [Helicobacter pylori SouthAfrica7]
          Length = 242

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 64/288 (22%), Positives = 109/288 (37%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +I+    + ++  G V +  K++    +        +P         I+          
Sbjct: 12  ENISHKKAKALIDLGLVSIGGKKLMVARK-------ELPQNTRFNVQKIE---------- 54

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   K  +++ED  I    KP  I        +Y +  F K W         L HR
Sbjct: 55  --------KPSVIFEDENILALLKPPFI-------ESYDLVSFFKGWT--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y +L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLALAQGIVEEEQEINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    AI+    +    +K   L+++  TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAITIIAPLKIINKK-TLLKVEIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNDEPGSA------KRLMLHAHKIALL-----GYEFEAIAPKEFE 241


>gi|254670442|emb|CBA06065.1| pseudouridylate synthase [Neisseria meningitidis alpha153]
 gi|325135925|gb|EGC58535.1| RNA pseudouridine synthase [Neisseria meningitidis M0579]
          Length = 307

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 93/223 (41%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
            +     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|121609561|ref|YP_997368.1| pseudouridine synthase [Verminephrobacter eiseniae EF01-2]
 gi|121554201|gb|ABM58350.1| pseudouridine synthase [Verminephrobacter eiseniae EF01-2]
          Length = 314

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 59/300 (19%), Positives = 103/300 (34%), Gaps = 30/300 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV+    +   LD +     P +     ++                  R+ +G VV    
Sbjct: 30  VVLPTRGQGSMLD-FLAQRLPMVAREQWRQ------------------RMHAGDVVDERG 70

Query: 70  VINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
              A     +    L    +L+          LL++D  + V +KP  + V        H
Sbjct: 71  RCVAPEQPFEGGLRLYYYRSLSAEPVLPFAPTLLHQDPHLVVADKPHFMPVTPSGRYLQH 130

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               L       G  +    HR+D++T+G+++++  +         FR RRI K Y ++ 
Sbjct: 131 --TLLVRLKRQLGLPQLSPVHRIDRDTAGLVLLSVQQCTRGAYQALFRERRITKHYEAIA 188

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                     +       S I         Q   G   + +H +++   A  +    + P
Sbjct: 189 PWRAD-----VVFPRDHTSRIEPGPQFFRMQEVPGPPNSHTHMQLL-AVAGDWAHYRLSP 242

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
            TG+ HQLRVH   +G P+  D  Y               L L AR ++   P  G  ++
Sbjct: 243 STGKRHQLRVHMAALGLPLRNDPFY-PVVDDPPPGDYSRPLQLLARALEFVDPLSGERRV 301


>gi|78049978|ref|YP_366153.1| putative pseudouridylate synthase [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|78038408|emb|CAJ26153.1| putative pseudouridylate synthase [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
          Length = 296

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 59/283 (20%), Positives = 114/283 (40%), Gaps = 29/283 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
                +P I     +     G VR  + + +  +   + G  +R           + ++ 
Sbjct: 29  ALCACFPAIAAERWRDRFARGLVRDANDQALALSAPYRVGADIRYF-------REVADEP 81

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
           ++                +++ D+++ V  KP  + V   G+ +   +   L   +D+  
Sbjct: 82  VIPY-----------VETVVHADAQLVVACKPHFLPVAPAGAYVRETLLTRLVRRLDNPA 130

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
             P   HR+D+ET+G+++ +   A        FR RRI+K Y ++   +P+ +   +   
Sbjct: 131 LVP--LHRIDRETAGLVLFSANPATRGIYQALFRQRRIRKHYLAVAPPLPQLRFPHVHRS 188

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           LL+     G+    + +    AN + +  +V+   A  + +  ++P TGR HQLRVH   
Sbjct: 189 LLEP----GEPFFRMHEGVGEAN-SETVIEVVARNADTWTY-RLEPVTGRKHQLRVHMAA 242

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +G PI+ D  Y          P +  L L A  +    P  G 
Sbjct: 243 LGAPILHDRFYPELEAQRPDDP-ERPLQLFAHTLAFDDPLTGE 284


>gi|330942730|gb|EGH45266.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. pisi str. 1704B]
          Length = 130

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 40/123 (32%), Positives = 69/123 (56%), Gaps = 8/123 (6%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
             VQ V V  +    R+D +   +   +    + +ILR G+VRV+K R+K   ++Q+G +
Sbjct: 9   PGVQLVEVAPELAGQRIDNFLITYLKGVPKTLIYRILRKGEVRVNKGRIKPEYKLQAGDI 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           VRIPP       + +  + +  +  L +    L++ ++YED  + V NKPAGI+V GGSG
Sbjct: 69  VRIPP-----VRVPERDEPVPVAQALLQR---LEAAIVYEDKALIVLNKPAGIAVHGGSG 120

Query: 125 IAY 127
           +++
Sbjct: 121 LSF 123


>gi|325133994|gb|EGC56649.1| RNA pseudouridine synthase [Neisseria meningitidis M13399]
          Length = 307

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 94/223 (42%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
           ++     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  SEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|152995953|ref|YP_001340788.1| pseudouridine synthase Rlu family protein [Marinomonas sp. MWYL1]
 gi|150836877|gb|ABR70853.1| pseudouridine synthase Rlu family protein, TIGR01621 [Marinomonas
           sp. MWYL1]
          Length = 223

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 53/197 (26%), Positives = 85/197 (43%), Gaps = 19/197 (9%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+     ++  KPAG+S    S     +     S+ D   Q     HRLD+ TSG+L+V
Sbjct: 4   ILFRSVDYWIVEKPAGMSFHAESEGLGVMQTLAISYPD---QNFYPVHRLDKMTSGLLIV 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A   AAA    + F    ++K Y +L    PK K+  I+        +        K  +
Sbjct: 61  ACHAAAAAEFGKMFERHEMEKRYLALSAKKPKKKQGTISGG------MAPSRRGQWKLTQ 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N+A++ F        +     ++P TG+THQ+RV    +G PI+GD +Y        
Sbjct: 115 DNENFAVTQFFSSAFHGLRVFI--VRPLTGKTHQIRVALKSLGSPILGDLRYSGE----- 167

Query: 281 TSPIQNKLYLHARYMDL 297
                ++ YLHA  +  
Sbjct: 168 ---GADRGYLHAYSLQF 181


>gi|167622548|ref|YP_001672842.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167352570|gb|ABZ75183.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 312

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 55/296 (18%), Positives = 113/296 (38%), Gaps = 31/296 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +  + +P I     Q  +  G+V   D   +  ++R        IP         ++++ 
Sbjct: 28  FLVSKFPAIAESVWQTRILDGKVHWRDGTPITLDSR-------FIPRERIYYYREVEQET 80

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           I+             +  +L + S+  +  KP  ++V              +  + +  Q
Sbjct: 81  IIP-----------FEEQILLQTSEFMLAFKPHFLAVNPSGNFVNECL-VNRLRIKTGNQ 128

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN-- 200
           +    HRLD+ T+G+++++    +     E F+  +I+K Y ++     + K   +    
Sbjct: 129 EIVAAHRLDRATAGVMLLSLNSGSRHDYHELFKSGQIRKTYQAIAPLNSEIKTMIVQGTL 188

Query: 201 -----WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                W +K          ++   +  AN + S  ++I+     +   E+ P TGRTHQL
Sbjct: 189 TLPMKWTVKNRLQKTVPSFLMCIGDGEAN-SHSEIRLIEVH-NGYGLFELAPVTGRTHQL 246

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
           RVH + +G P++ D  Y               L L A+ +    P    R+ ++  
Sbjct: 247 RVHMMSLGMPLLNDRLY-PELLDKAADDFAAPLKLMAQRLCFTDPMTQERIDVSCE 301


>gi|210135145|ref|YP_002301584.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori P12]
 gi|210133113|gb|ACJ08104.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori P12]
          Length = 242

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 62/288 (21%), Positives = 109/288 (37%), Gaps = 59/288 (20%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +++    + ++  G V +  K++                 + A   + K  +     + 
Sbjct: 12  ENVSHKKAKALIDLGLVSIGGKKL-----------------MVARKELPKNTRFSVQKIE 54

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                   K  +++ED  +    KP  I        +Y +  F K WV        L HR
Sbjct: 55  --------KPSVIFEDENVLALFKPPFI-------ESYDLVSFFKDWV--------LLHR 91

Query: 150 LDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           LD+ETSG++++ +          ++F+ R ++K Y  L  GI + ++E  A  L  K+  
Sbjct: 92  LDKETSGVVLLVKENSEFHLKAKKAFKNRAVKKEYLVLAQGIIEEEREINAPILTIKTTK 151

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+G
Sbjct: 152 AFSKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIG 204

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           D  Y              +L LHA  + L        +  A  P    
Sbjct: 205 DTLYNNEPGSA------KRLMLHAHKIALL-----GYEFEAIPPKEFE 241


>gi|29833249|ref|NP_827883.1| ribosomal pseudouridine synthase [Streptomyces avermitilis MA-4680]
 gi|29610371|dbj|BAC74418.1| putative ribosomal pseudouridine synthase [Streptomyces avermitilis
           MA-4680]
          Length = 321

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 50/215 (23%), Positives = 86/215 (40%), Gaps = 9/215 (4%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTH 148
             +        ++Y D  I V +KP  ++    GS +A  +   L+   D    +    H
Sbjct: 93  PDEERVPFALDVVYRDEHIVVADKPHFLATTPRGSHVAETVLARLRR--DLGIPELGAAH 150

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ T+G+++              FR + + K Y ++    P+     +A     +S I
Sbjct: 151 RLDRLTAGLVLFTVRPGERGAYQSLFRDKLVHKEYEAVATYDPE-----VALPRTVRSRI 205

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +   +  +   G   A+S  ++ +          + P TG+THQLRVH   +G PI+G
Sbjct: 206 LKERGLLAAREVAGEPNAVSRIELTEHR-DGRGRYRLLPRTGQTHQLRVHMNALGLPILG 264

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           D  Y            +  L L AR ++   P  G
Sbjct: 265 DPLYPVVTDPGPAGDFRRPLQLLARVLEFTDPVTG 299


>gi|331226410|ref|XP_003325875.1| hypothetical protein PGTG_07077 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
 gi|309304865|gb|EFP81456.1| hypothetical protein PGTG_07077 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
          Length = 380

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 123/280 (43%), Gaps = 27/280 (9%)

Query: 73  ALNHIIKEQKILDSSVNLTKHSD--FLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHI 129
            L+   +E++ L+    LT + +  F    +L+E+ K+ V +KPAG ++Q   G  AY  
Sbjct: 100 PLSEEEQEKQRLEREEELTANLEKSFKPPKILFENEKVVVIDKPAGCALQAELGSEAYIR 159

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +  +++ +  K  + HRLD+ T+G L++A++  A++ L+  F+   ++K Y++ +  
Sbjct: 160 WKLIMDYLEKRRGKLFIVHRLDKSTTGPLILAKSSTASRTLSTQFKNSTVKKTYYAAIQ- 218

Query: 190 IPKNKKECIANW-----LLKKSHIGGDYVHVVKQNEKGA--NYAISHFKVIDCFAQKFCW 242
              ++   I +      +  +     D + + + N  G       ++++++   +     
Sbjct: 219 FLGDRIGPIQDAKSSGQIECRMRDSKDRMVIAESNRTGTDCKQTKTNWELVTATS-NHAI 277

Query: 243 LEMQPHTGRTHQLRVHALHMGC-PIVGDHKYCANF---------KGNFTSPIQNKLYLHA 292
           + + P TGR HQLR+H       PIVGD KY   +                   +L LH 
Sbjct: 278 VRLTPQTGRKHQLRLHCSRFLAGPIVGDFKYDFRYLSYQSQKAIHNFLNREAPGRLLLHC 337

Query: 293 RYMDL-----PHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
             ++        P    +++++PL        D L    +
Sbjct: 338 SEIEFKLYKKEQPREYTVRVSSPLHDDFRIVCDQLDLSTN 377


>gi|301779327|ref|XP_002925088.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           3-like [Ailuropoda melanoleuca]
 gi|281354153|gb|EFB29737.1| hypothetical protein PANDA_014511 [Ailuropoda melanoleuca]
          Length = 352

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 62/283 (21%), Positives = 109/283 (38%), Gaps = 44/283 (15%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQK 143
            +++     D L++ ++ +   +   NKP G+ V G  G          L   +  + ++
Sbjct: 69  ENLSREGLVDVLRAAVVDQKGPLVTLNKPPGLPVTGKPGELTLCSVLPELSQSLGLRDRE 128

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKECIA 199
            ++     +ETSG+++++     A  L +    S R +R    Y ++  GIP   +  I 
Sbjct: 129 LQIVQASGKETSGLVLLSSCPQTASRLQKFFIHSRRAQRPIATYCAVTDGIPATSEGNIQ 188

Query: 200 NWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             L  +   G D V  VK   +     G     SHF V+         +++QP T    Q
Sbjct: 189 AALKLEHIDGVDLVIPVKSPSRKDFQEGVKKTFSHFHVV-AMGSGCALVQLQPLTVFPSQ 247

Query: 255 LRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQN----KLYLH---ARYMDL------ 297
           L+VH +   CP++GDH Y A         F  P ++    +  L     R + L      
Sbjct: 248 LQVHMVLQLCPVLGDHTYSARVGTVLGQRFLLPAESTKPQRQVLDGALIRRLRLSPAQSA 307

Query: 298 ---------------PHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                            P    +++ APLP +  +T   LG +
Sbjct: 308 QLPLHLHLHCLHLPGLRPREAPMKLLAPLPPYFSRTLQCLGLR 350


>gi|325181219|emb|CCA15633.1| RNA pseudouridylate synthase putative [Albugo laibachii Nc14]
          Length = 440

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 70/286 (24%), Positives = 108/286 (37%), Gaps = 63/286 (22%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
            +RSG+V V+   V    RIQ+G  +          H     +   SS ++         
Sbjct: 99  AVRSGRVTVNHSIVSQTYRIQNGDFI---------VHRTHRHEPPVSSDHIP-------- 141

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGI 157
            ++YED ++ V +KP  I        AY  +      +     +    + HRLD+ TSGI
Sbjct: 142 -IVYEDDELLVVSKPCSIPTHPCG--AYRHNSLHSILLHQIPVESFLHVVHRLDRLTSGI 198

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK------------------------- 192
           ++ A+T AAA+ L+     R++ K Y + V G                            
Sbjct: 199 VIFAKTAAAAKKLSTEMTKRQVHKTYLAGVKGFIPSQWDEESKKQQNEIKERAKQICEAS 258

Query: 193 -----NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK-----VIDCFAQKFCW 242
                 K+  +   L   SH  G     V +  K    + + F+     V        C 
Sbjct: 259 EISFSKKQIRVKCPLKCLSHKNG-----VWECHKDGKESETIFERDQLTVPVENRDVSCV 313

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNK 287
           L   P TGRTHQ+R+H   +G PI  D  Y      G+ T+P+  K
Sbjct: 314 LRCFPVTGRTHQIRLHLQLIGLPIANDPCYGGELHFGSKTTPLDTK 359


>gi|117620216|ref|YP_857174.1| pseudouridine synthase Rlu family protein [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
 gi|117561623|gb|ABK38571.1| pseudouridine synthase Rlu family protein [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
          Length = 219

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 56/215 (26%), Positives = 90/215 (41%), Gaps = 17/215 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            +L +     V NK  G+ +   +  A     G +       G      HRLD+ TSG++
Sbjct: 3   RILAQHKDFMVINKGPGLGMHDETDEAGLLHPGLVSRVKADTGLLLYPVHRLDKMTSGLV 62

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ART  A + L+ +F  R + K Y +L    PK K+  +   + K    GG ++     
Sbjct: 63  LLARTTEANRALSMAFAAREVSKQYLALSDRKPKKKQGWVKGDMQKGR--GGSWMLTRTL 120

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +    N AIS F  +    +      ++P TG+THQ+RV    +G PI+GD +Y      
Sbjct: 121 D----NPAISWFDSV-SVREGLRLYRIKPRTGKTHQIRVALKSVGAPILGDARYGGT--- 172

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
                  ++ YLHA  +      G       P   
Sbjct: 173 -----AADRGYLHAWRLAFT-LAGEAFDFVCPPDE 201


>gi|226360008|ref|YP_002777786.1| pseudouridine synthase [Rhodococcus opacus B4]
 gi|226238493|dbj|BAH48841.1| putative pseudouridine synthase [Rhodococcus opacus B4]
          Length = 297

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 61/284 (21%), Positives = 112/284 (39%), Gaps = 28/284 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +  + YP     +   ++ +G V VD          + G+VV      +        + +
Sbjct: 31  FLVDTYPD-ERAHWLSLIDAGDV-VD----------EHGRVV------DRGTRYAPTRFV 72

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQ 142
                   +     +  +L+ D  + V +KP  ++    G+ I       L+  +D    
Sbjct: 73  YFYRDPAPEIPVPFEIDVLHRDDHLVVIDKPHFLATIPRGAHITETAVVRLRRALDLPDL 132

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P   HRLD+ T+G+LV        +   E F  +++ K Y ++    P      +    
Sbjct: 133 TP--AHRLDRMTAGVLVFLIRPEDRRAYQELFVSQQVTKEYEAVAGHDPA-----LEFPR 185

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             +S I  ++  +    E G   + +   +I+          + P TGRTHQLR+H   +
Sbjct: 186 TIRSRIVKEHGIMTATEEPGEPNSETVVDLIESR-DGRARYRLLPKTGRTHQLRLHMSSL 244

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           G PI GD+ Y  +F+ +        L L AR ++   P  GR++
Sbjct: 245 GLPIEGDN-YYPDFRRSEPGDFSTPLRLLARAIEFTDPRSGRVR 287


>gi|95930635|ref|ZP_01313369.1| pseudouridine synthase [Desulfuromonas acetoxidans DSM 684]
 gi|95133287|gb|EAT14952.1| pseudouridine synthase [Desulfuromonas acetoxidans DSM 684]
          Length = 294

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 56/288 (19%), Positives = 112/288 (38%), Gaps = 26/288 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   ++PH+ +    + +  G+V    ++    +  +  QV+            ++EQ +
Sbjct: 25  FLAGYFPHVTYEEWARRVDDGKVLDADQQPLGRDGYRPQQVIYYY-------REVEEQPL 77

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +                +LY+D  + V  KP  + V  G G     +   +  + +   +
Sbjct: 78  IP-----------FAETILYQDDALLVACKPHFLPVHPG-GRYVTENLVYRLRLATGNDQ 125

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HR+D+ T+G+++ A+           F    I+K Y ++     + ++    +W +
Sbjct: 126 LAPVHRIDRFTAGLVLFAQRSEDRARYNALFSQGNIKKRYDAVAHCPEEPQQ---RHWQV 182

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                 GD     +      N A S  +++D   Q +    +QP TG+THQLR+H   +G
Sbjct: 183 ANRIEQGDPWFRWQVVAGDVN-ARSSIELLDLR-QGYGLFSLQPITGKTHQLRLHMSGLG 240

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
             +V D +Y  N            L L A+ +    P  G+     +P
Sbjct: 241 FGLVND-RYYPNLLPEQPDDFSTPLQLLAKEVIFTDPVTGKHHHFESP 287


>gi|317472094|ref|ZP_07931426.1| RNA pseudouridylate synthase [Anaerostipes sp. 3_2_56FAA]
 gi|316900498|gb|EFV22480.1| RNA pseudouridylate synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 180

 Score =  123 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 50/184 (27%), Positives = 79/184 (42%), Gaps = 13/184 (7%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+   G++V ART+ AA  L+   R    +K Y ++V G    +     ++LLK 
Sbjct: 1   MIHRLDRPVGGVMVFARTKEAAAELSRQIREHIFEKDYQAIVNGWLPEEDGVFTDYLLKD 60

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           +    +    V +  KGA  A   ++V+   +    K  +  +   TGR HQ+RV     
Sbjct: 61  NK--KNTSCTVPEETKGAKKAELSYEVLDMVETGEGKLTYCLIHLMTGRHHQIRVQFAAR 118

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH----MVK 317
           G  + GD KY   F+       +  LY  A  +   HP  G      A  P      M++
Sbjct: 119 GFGLYGDTKYNKKFQKTKKQYEEIGLY--ATRISFRHPVTGEACTFKAE-PKGKAFFMLE 175

Query: 318 TWDS 321
             D+
Sbjct: 176 ELDA 179


>gi|225450607|ref|XP_002278016.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 313

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 114/293 (38%), Gaps = 45/293 (15%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I P + A++  I EQ    S+ + +      +S +L+ED  +   NKP G+       I 
Sbjct: 23  ISPPLPAISKHI-EQSRAMSASSRSSLFSLCRSDILFEDQWLMAVNKPQGVYC---ETIL 78

Query: 127 YHIDGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             +   L  S      +   L +RLD++TSG++V+ ++   A  L ++F  R++ K Y +
Sbjct: 79  LSVSRMLDDSDGHDSCRSLHLANRLDRDTSGVMVITKSHQVAAKLMKAFSDRKVTKTYLA 138

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA------ISHFKVIDCFAQK 239
           L  G     ++        +S  G   V+      +    A      ++ F+V+    Q 
Sbjct: 139 LCIGAAPTWEKITIKSGHGRSKFGAWRVYAASDVGRALPNAPAIKDMVTSFEVLSVNGQG 198

Query: 240 FC-------------------------------WLEMQPHTGRTHQLRVHALHMGCPIVG 268
                                             +   P +GRTHQ+R+H  ++G  I G
Sbjct: 199 NVKELPESRKADETVLVVEERSVIDSNARQDEILVRAFPRSGRTHQIRLHCQYLGISIRG 258

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWD 320
           D KY    +      I +   LHA  +   HP  G  +   APLP+  V+   
Sbjct: 259 DVKYEGVHEWK--GKIYDGHELHAESLSFEHPVTGVDVAFRAPLPSWAVQALQ 309


>gi|325115868|emb|CBZ51423.1| putative RNA pseudouridine synthase domain containing protein
            [Neospora caninum Liverpool]
          Length = 6415

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 56/248 (22%), Positives = 99/248 (39%), Gaps = 59/248 (23%)

Query: 132  FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             L++    +  +  L HR D ETSG L++A+TR A + + E FR R + K Y  L  G  
Sbjct: 4679 RLETVRRWEEMECGLCHRTDLETSGSLLIAKTRRARESIFEQFRKRLVHKEYLLLCHGRL 4738

Query: 192  KNKKECIANWLLKK---SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--------- 239
                  I + +  +   S     +   V   ++G + A++ ++V+  F  +         
Sbjct: 4739 DKLHARIDHPIATRDFDSSRSKSHFSEVVGPDEGGDEALTEYQVVRVFGLRQPVHRKIQA 4798

Query: 240  --------------------------------------------FCWLEMQPHTGRTHQL 255
                                                        F +  ++ HTGRTHQ+
Sbjct: 4799 AMSVAARIAASPSSSSSSDRARGTGASAPAAGAKTAGSGKGSPEFSFCRVRIHTGRTHQI 4858

Query: 256  RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP---EGGRLQITAPLP 312
            RVH  H+G P+VGD KYC  +K         +++LH+  ++  +P   E   +++  PL 
Sbjct: 4859 RVHFRHIGHPLVGDTKYCDLYKCTVDRSWCARMFLHSAVLEFDNPDKTETQHVRVVCPLA 4918

Query: 313  AHMVKTWD 320
              ++   +
Sbjct: 4919 TELLAALE 4926


>gi|111017875|ref|YP_700847.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
 gi|110817405|gb|ABG92689.1| possible pseudouridylate synthase [Rhodococcus jostii RHA1]
          Length = 297

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 62/284 (21%), Positives = 112/284 (39%), Gaps = 28/284 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +    YP     +   ++  G+V VD          + G+VV      +        + +
Sbjct: 31  FLVETYPD-ERAHWLSLIDGGEV-VD----------EHGRVV------DRGTRYAPTRFV 72

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQ 142
                   +     +  +L+ D  + V +KP  ++    G+ I       L+  +D    
Sbjct: 73  YFYRDPAPEIPVPFEIDILHRDDHLVVIDKPHFLATIPRGAHITETAVVRLRRALDLPDL 132

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
            P   HRLD+ T+G+LV    R   +   E F  +++ K Y ++    P      +A   
Sbjct: 133 TP--AHRLDRMTAGVLVFLIRREDRRPYQELFVSQQVTKEYEAVAGHDPA-----LAFPR 185

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             +S I  ++  +    E G   + +   ++D          + P TGRTHQLR+H   +
Sbjct: 186 TIRSRIVKEHGIMTATEEPGEPNSETVVDLLDTR-DGRARYRLLPKTGRTHQLRLHMSSL 244

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           G PI GD+ Y  +F+ +        L L AR ++   P  G ++
Sbjct: 245 GLPIEGDN-YYPDFRRSEPGDFSTPLRLLARAIEFTDPRSGEVR 287


>gi|331697825|ref|YP_004334064.1| pseudouridine synthase [Pseudonocardia dioxanivorans CB1190]
 gi|326952514|gb|AEA26211.1| pseudouridine synthase [Pseudonocardia dioxanivorans CB1190]
          Length = 309

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 87/238 (36%), Gaps = 8/238 (3%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +   +   +  + E  +        +        +++ D  + V +KP  +S     G  
Sbjct: 59  VDGPLRPDSPFVPETFVWLHRDLPDETPVPFPIHVVHRDEHLLVVDKPHFLSTIP-RGRH 117

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                 ++   D    +    HRLD+ T+G+L+    R         FR RR+ K Y ++
Sbjct: 118 VVETALVRLRRDLDLPELSPAHRLDRVTAGLLMFVVRREDRGAYQTMFRDRRVAKTYEAI 177

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
               P      +       S I  +   +V +   G   A ++ ++++          + 
Sbjct: 178 APHDPA-----LLLPRTVTSRIVKERGIIVAREVDGPPNAETYVELVEHR-DGLGRYRLT 231

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           P TGRTHQLR+H   +  PI+GDH Y               L L AR +    P  G 
Sbjct: 232 PATGRTHQLRLHMAALNVPILGDHFY-PELHDKPLDDYTRPLQLLARTLAFTDPLTGE 288


>gi|269796147|ref|YP_003315602.1| 23S RNA-specific pseudouridylate synthase [Sanguibacter keddieii
           DSM 10542]
 gi|269098332|gb|ACZ22768.1| 23S RNA-specific pseudouridylate synthase [Sanguibacter keddieii
           DSM 10542]
          Length = 303

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 98/258 (37%), Gaps = 14/258 (5%)

Query: 54  KFNNRIQSGQVV-RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
           +   ++ +G+VV  I   +      +    +        +     +  +L+ D  + V +
Sbjct: 35  RMREKVAAGEVVDEIGRSLGPDAPYVGGTLVYLYRDAAPEPRVPFEIDVLHHDDDLLVID 94

Query: 113 KPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           KP  ++     G        ++   D    +    HRLD+ T+G+LV+   R       +
Sbjct: 95  KPHFLASTP-RGAYVVESAVVRLRRDLGLPEISPAHRLDRITAGVLVLTTRREVRGAYQQ 153

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F  R I K Y ++    P+     +      +S I  ++  +V Q   G   A S   +
Sbjct: 154 LFASRTIHKTYEAVARVDPR-----LDLPRTVRSRIVKEHGTLVAQEVPGEPNAESRVSL 208

Query: 233 IDCFAQKFCWLE------MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
            +         E      ++PHTG+THQLR+H   +G PI+ D+ Y   F          
Sbjct: 209 AEVAPGAGDGGEALGRYVLEPHTGKTHQLRLHMASLGLPILNDNFY-PRFYDVAPDDYSA 267

Query: 287 KLYLHARYMDLPHPEGGR 304
            L L AR +    P  G 
Sbjct: 268 PLQLLARSISFTDPLSGE 285


>gi|118091027|ref|XP_426389.2| PREDICTED: similar to RPUSD2 protein [Gallus gallus]
          Length = 480

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 53/210 (25%), Positives = 99/210 (47%), Gaps = 8/210 (3%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            +  L+ ++K    L ++V+  +     + I +L E+ ++ V +KP+ + V       ++
Sbjct: 120 PVQDLDVVLKNNDFLRNTVHRHEPPVTAQPIQILVENDEVVVVDKPSSLPVHPCGRFRHN 179

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              F+    +   ++    HRLD+ TSG+L+ A+T   ++ + E  R R+++K Y   V 
Sbjct: 180 TVIFILG-KEHNLKELHTIHRLDRMTSGVLMFAKTVEVSKRIDEQVRERQLEKEYVCRVV 238

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G     +      +L  S+     V V + + KG     + F+ +    +    ++  P 
Sbjct: 239 GEFPEHEVVCEEPILVVSY----KVGVCRVDPKG-KCCKTIFQRLSYNGKS-SVVKCLPR 292

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           TGRTHQ+RVH  ++G PIV D  Y     G
Sbjct: 293 TGRTHQIRVHLQYLGYPIVNDPIYNMEAWG 322


>gi|261839742|gb|ACX99507.1| pseudouridine synthase, RluA family protein [Helicobacter pylori
           52]
          Length = 237

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 60/267 (22%), Positives = 109/267 (40%), Gaps = 54/267 (20%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+    + ++  G V V  K++                       ++  +++  ++    
Sbjct: 14  ISHKKAKALIDLGLVSVGGKKL-----------------------MVARKELPKNTHFSV 50

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +  +  K  +++ED  I    KP  I        +Y +  F K W         L HRLD
Sbjct: 51  QKVE--KPSVIFEDENILALFKPPFI-------ESYDLVSFFKGWA--------LLHRLD 93

Query: 152 QETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           +ETSG++++ +          ++F+ R ++K Y +L+ GI + ++E  A  L  K+    
Sbjct: 94  KETSGVILLVKENSEFHLKAKKAFKDRAVKKEYLALIQGIIEEEQEINAPILTIKTTKAF 153

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +       K    A++    +    +K   L++   TGRTHQ+RVH  H+  PI+GD 
Sbjct: 154 SKI------SKKGQEAVTIITPLKIINKK-TLLKVGIKTGRTHQIRVHLKHINHPIIGDT 206

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDL 297
            Y              +L LHA  + L
Sbjct: 207 LYNNEPGSA------KRLMLHAHKISL 227


>gi|42527698|ref|NP_972796.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
 gi|41818526|gb|AAS12715.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
          Length = 236

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 105/242 (43%), Gaps = 38/242 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +L+ED+   V  K  G               F K++ + K  +    +RLD+  SG+
Sbjct: 4   EVRILFEDNFFAVVLKNCG---------DNSQVFFKKAFSEKKYAEA--VNRLDKPVSGL 52

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK----------------KECIANW 201
           +++A + A    L   F+ ++I+K YW++   I + K                KE   N+
Sbjct: 53  VLIAFSPAMHTKLNNLFKEKKIKKEYWAICKKIEELKSAADSKISDTTPVLYKKEFCENY 112

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L   + I   +V   +Q  K A    S +  +      + +L + P TGRTHQ+R+   H
Sbjct: 113 LEFNTKIQKAFVTESRQRGKKA----SLYWQLAGIGDNYNFLRIFPETGRTHQIRIQLSH 168

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWD 320
           +G PI GD KY         +     + LHA+ +   HPE   R++I+A LP      W 
Sbjct: 169 LGMPIKGDIKYGF-----ARTEKSGGIRLHAQSLKFEHPESKKRIEISA-LPPSPDTLWS 222

Query: 321 SL 322
           + 
Sbjct: 223 AC 224


>gi|270007545|gb|EFA03993.1| hypothetical protein TcasGA2_TC014142 [Tribolium castaneum]
          Length = 552

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 56/307 (18%), Positives = 110/307 (35%), Gaps = 54/307 (17%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ---------VVRIP 68
             R+   F   +        ++ +++G + V+  +V  + +++             V + 
Sbjct: 65  GERILDVFAREFRAHPAEEYERCIQAGTLTVNYDKVPIDYKLKHNDLLANVVHRHEVPVT 124

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILL-------------------------- 102
                + H+ ++  +++   ++   S  +   +L                          
Sbjct: 125 SQPITIVHMDEDIVVVNKPASIPIKSFHVHGPILDRTNIERDAGVPHESLMLLVHYRHET 184

Query: 103 ----------YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                     + D  + V +KP  + V       ++   F+ +  +   +  R  HRLD+
Sbjct: 185 PVLANPIKLIHVDEDLVVLDKPCSLPVHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDR 243

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGD 211
            TSG+L+  R+   A+ +    R R +QK Y   V G  P    EC     +    IG  
Sbjct: 244 LTSGLLLFGRSPKKARQMEHQIRNRLVQKEYVCRVEGEFPDEIIECKEPIEVVSYKIG-- 301

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V +         + F+ +     K   +  +P TGR HQ+RVH  ++G P+V D  
Sbjct: 302 ----VCKVSPKGKDCNTIFQKLGFNG-KTSIVLCKPKTGRMHQIRVHLQYLGYPVVNDPL 356

Query: 272 YCANFKG 278
           Y     G
Sbjct: 357 YNHEVFG 363


>gi|171060976|ref|YP_001793325.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170778421|gb|ACB36560.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
          Length = 310

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 54/289 (18%), Positives = 99/289 (34%), Gaps = 35/289 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +     P +     ++ + +G V  VD + +  +    +   +     + A   I  E +
Sbjct: 34  FLAERLPVLTADQWRERMAAGDVLAVDGRPLPPDAPHVAHTRLWYWRALPAEPRIPFEAE 93

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             +L++D+ +   +KP  + +       Y  +  L       G 
Sbjct: 94  ------------------VLFQDAHLVAVDKPHFLPMTPKG--RYVQETLLVRLKRQLGI 133

Query: 143 K-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD+ET+G+++     A         R R ++K+Y ++           +A  
Sbjct: 134 DTLVPMHRLDRETAGVVLFTVQPATRHAYQSLLRDRSVEKVYEAVAPWRAD-----LALP 188

Query: 202 LLKKSHIGGD----YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           L + S +               E  A  +I   + +   A+      ++P TG+ HQLR 
Sbjct: 189 LTRCSRLQERADAFMQMAEVAGEPNAQTSIELIRRVAA-AEPLALYRLRPRTGQKHQLRA 247

Query: 258 HALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           H   +G PI GD  Y     +            L L AR +    P  G
Sbjct: 248 HMAALGLPIRGDRIYPVLQPDLAEGAQPDYSRPLQLLARSIAFTDPVSG 296


>gi|154486935|ref|ZP_02028342.1| hypothetical protein BIFADO_00768 [Bifidobacterium adolescentis
           L2-32]
 gi|154084798|gb|EDN83843.1| hypothetical protein BIFADO_00768 [Bifidobacterium adolescentis
           L2-32]
          Length = 241

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 50/227 (22%), Positives = 83/227 (36%), Gaps = 15/227 (6%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +     +  +LYED +I V +KP  ++     G+ Y     ++             HRL
Sbjct: 3   EEPHIPFEYEVLYEDERIIVIDKPHFLATTP-RGMWYRETALIRLRERCGEPDIVPAHRL 61

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN-------W 201
           D+ T+G++V  R  A        F+     K Y   + +    + +   +          
Sbjct: 62  DRPTAGVVVFVRDPAVRGAYQMLFQNHMAVKTYECMAPLAPPQRPRYGTVEQVDRHRPFP 121

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFK----VIDCFAQKFCWLEMQPHTGRTHQLRV 257
            +++S I  D   +          A +  +    V     + F    + P TG+THQLRV
Sbjct: 122 TVRRSRINKDRGRLQAYESADMPNAETLIERGDDVWHIDGKPFVNYTLHPRTGKTHQLRV 181

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           H   +G PI+GD  Y  +            L L AR +    P  G 
Sbjct: 182 HMNSLGLPILGDDFY-PDIVQRAYDDFSQPLELVARELRFDDPLNGE 227


>gi|119472936|ref|ZP_01614809.1| hypothetical protein ATW7_13378 [Alteromonadales bacterium TW-7]
 gi|119444654|gb|EAW25963.1| hypothetical protein ATW7_13378 [Alteromonadales bacterium TW-7]
          Length = 222

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 61/208 (29%), Positives = 92/208 (44%), Gaps = 21/208 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++ E +  YV  KPA +S     G      GF+        +K    HRLD+ TSG++++
Sbjct: 7   VVCEHADFYVVEKPAELSFHSEDGP-----GFVVLAERQFNEKLYAVHRLDKVTSGLIIL 61

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR ++AA   TE F    I K Y ++    PK K+  +      K  +        K   
Sbjct: 62  ARNKSAAATFTELFAQHSIDKFYLAITDSKPKKKQGWV------KGDMAKSRRGTYKLLA 115

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  I   A    ++ ++P +G+THQLRV    +G PI+GD  Y        
Sbjct: 116 SNLNPAITRFYSISFKAGFRAFI-LKPFSGKTHQLRVALKSIGSPILGDIAYSGT----- 169

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQIT 308
                ++ YLHA  +     +G  LQ T
Sbjct: 170 ---ASDRTYLHAYALSFTW-QGENLQFT 193


>gi|119025492|ref|YP_909337.1| pseudouridine synthase [Bifidobacterium adolescentis ATCC 15703]
 gi|118765076|dbj|BAF39255.1| pseudouridine synthase [Bifidobacterium adolescentis ATCC 15703]
          Length = 228

 Score =  123 bits (308), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 52/215 (24%), Positives = 81/215 (37%), Gaps = 15/215 (6%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YED  I V +KP  ++     G+ Y     ++             HRLD+ T+G++V  R
Sbjct: 2   YEDENIIVIDKPHFLATTP-RGMWYRETALVRLCERYDEPNITPAHRLDRLTAGVVVFVR 60

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE-----CIAN----WLLKKSHIGGDYV 213
             +A       F+ R+  K Y  L    P  +        I       L+++SHI  D  
Sbjct: 61  NPSARGAYQMLFQNRKTVKTYECLAPLAPTQRPRYGTAVRIDRHLPFPLVRRSHINKDRG 120

Query: 214 HVVKQNEKGANYAISHFK----VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +          A +  +    +     + +    + P TG+THQLRVH   +G  I+GD
Sbjct: 121 RLQAYESADVPNAETLIERGSGIRFVAGRPYVNYTLHPKTGKTHQLRVHMNSLGLAILGD 180

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             Y  +            L L AR +    P  G 
Sbjct: 181 DFY-PDIVQRAYDDFSQPLELVARELRFDDPLNGE 214


>gi|308809467|ref|XP_003082043.1| probable pseudouridine synthase (ISS) [Ostreococcus tauri]
 gi|116060510|emb|CAL55846.1| probable pseudouridine synthase (ISS) [Ostreococcus tauri]
          Length = 300

 Score =  123 bits (308), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 66/300 (22%), Positives = 113/300 (37%), Gaps = 37/300 (12%)

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
              R      AL    ++    D++   +    F + ++L+E   + + NKP G+S    
Sbjct: 19  DRSRRWRRCGALRASTRDDDGRDATARESDAEAFEEMVVLHESEAVVIVNKPRGMSFH-- 76

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
              +    G L       G++  +   HRLD+ TSGILV A+   A   L+++F  R I 
Sbjct: 77  ---SEFAPGALARLRTQMGERTAVMSVHRLDKPTSGILVFAKNARARDALSKAFEEREIV 133

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--- 237
           K Y  +    P+ K   +      +  +               + A + F          
Sbjct: 134 KYYVGMSNRKPRKKMGTV------RGDMTRSRRKAWMLTSTTESPAETKFVSFGARGMGE 187

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +       +P TG+THQLRV A  +G P++GD  Y             ++ YLHA  + +
Sbjct: 188 RALRMFVFRPMTGKTHQLRVAAKSLGSPLLGDDTYGGERD-------VDRTYLHACAIRI 240

Query: 298 PHPEGGR--LQITAPL-------PAHMVKTW-----DSLGFKYDRNLYIKRLYSQDECKQ 343
           P    G     I +P+       PA   + +     +  G  +D    ++     D  +Q
Sbjct: 241 PKSVLGETIQIICSPIGTGDEWDPAAFDRYFPESLANDFGAWFDDQPLLRSTVDGDANEQ 300


>gi|224419009|ref|ZP_03657015.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
 gi|253827954|ref|ZP_04870839.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
 gi|313142521|ref|ZP_07804714.1| conserved hypothetical protein [Helicobacter canadensis MIT
           98-5491]
 gi|253511360|gb|EES90019.1| putative ribosomal pseudouridine synthase [Helicobacter canadensis
           MIT 98-5491]
 gi|313131552|gb|EFR49169.1| conserved hypothetical protein [Helicobacter canadensis MIT
           98-5491]
          Length = 265

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 60/276 (21%), Positives = 107/276 (38%), Gaps = 56/276 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        I+    + ++  G V +  K++K                           +
Sbjct: 29  KLLSAQ-EGISHNEAKNLIDRGLVTIQGKKLKI-------------------------AR 62

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
            L S     K        ++++D  I   +KPA ++           +  +K +      
Sbjct: 63  ALLSPNTHFKIQQLPPIKIIFQDENILALSKPAFLTS----------EEIVKLY-----P 107

Query: 143 KPRLTHRLDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           +  L HRLD+ETSG+L++ +          E F+  +I K Y ++V GI   ++E     
Sbjct: 108 QWALLHRLDKETSGVLLLIKENSPFHLKAKEEFKKEQIFKQYVAIVEGIIDEEQEITEPL 167

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           +++K H        V   +K    A +    I+  ++K    E+   TGRTHQ+R H  H
Sbjct: 168 IIQKGHFAK-----VIVAKKNGIKAYTKITPIEIESKKTKL-EILIKTGRTHQIRAHLAH 221

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +  PI+GD  Y             N++ LHA+ + L
Sbjct: 222 IKHPIIGDTFYGGKPA--------NRILLHAQKIAL 249


>gi|237808063|ref|YP_002892503.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
 gi|237500324|gb|ACQ92917.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
          Length = 316

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 48/214 (22%), Positives = 87/214 (40%), Gaps = 10/214 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-KPRLTHR 149
            +    ++  +LY D  + + +KP  + V       Y     L   V      + +  HR
Sbjct: 99  NEKPIPVQESILYMDEHLLIADKPHFLPVTPAG--DYVSQTLLARLVARLNNFELQPLHR 156

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D+ T+G+++ +  + +       FR R+I+K Y ++   +P+     IA   ++ + I 
Sbjct: 157 IDRHTAGLVMFSVQKKSRAAYQALFRDRKIEKRYEAIAPALPQ-----IAFPHIRATRIE 211

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 + Q   G   + +   VI+  A       + P TG+ HQLR+H   +G PI  D
Sbjct: 212 RGEPFFLSQETAGTANSQTIIDVIERRAD-LWKYALNPVTGKKHQLRLHMSALGAPIYND 270

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             Y  +   +     Q  L L A  +    P  G
Sbjct: 271 AFY-PSVNDDVADDYQKPLQLLASELTFVDPVSG 303


>gi|219116402|ref|XP_002178996.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409763|gb|EEC49694.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 424

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 60/284 (21%), Positives = 104/284 (36%), Gaps = 33/284 (11%)

Query: 29  YPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR-IPPVINALNHIIKEQKILDSS 87
           +P  +     K  R G V + +  +K + +     +   +  V   +   +     +   
Sbjct: 131 FPSFSRAR--KACRKGNVLIHRGALKMDEKTPESTIFDPLMCVRGRVGDRLYPGDTVGKQ 188

Query: 88  VN--------LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           V         L       +  ++ ED    + NKPAGI V       + I     +    
Sbjct: 189 VRIGSGYFPVLNYKKPPFELPVIIEDDHWALVNKPAGIVVYNQRNGGHGIMTVRAALPFV 248

Query: 140 KGQ----------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                        +P   HRLD+ TSGIL +A+T+ A   L+  F  R ++K Y++++ G
Sbjct: 249 LAPPKVGTISVLRRPASVHRLDKPTSGILCIAKTKPAMLCLSRQFHDRIVKKTYFAVING 308

Query: 190 IPKNKKEC-----IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV------IDCFAQ 238
           IP    E       A  L             +  +      A++ ++V      +     
Sbjct: 309 IPTYSNESKISSKTAYELGVDVDPNDLDDWQLIDSPLDEKKAVTVWRVVRSIKSLHANDG 368

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMG-CPIVGDHKYCANFKGNFT 281
               +E++P TGR HQLR H   +   P+VGD +Y    +    
Sbjct: 369 YLTLVELKPKTGRYHQLRRHMAWVCQRPLVGDDEYDGGTESAMR 412


>gi|322817842|gb|EFZ25435.1| hypothetical protein TCSYLVIO_8401 [Trypanosoma cruzi]
          Length = 733

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 60/277 (21%), Positives = 109/277 (39%), Gaps = 37/277 (13%)

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + +   I  ++  ++      SS + +  S      +++ED+ I V NKP  ++    + 
Sbjct: 474 IHVTVKIPRVHECVEAAMQAASSSSTSSFSFASCLPVIFEDNDILVLNKPPHLASSRHAL 533

Query: 125 IAYHIDG---------FLKSWVDSKGQK----PRLTHRLDQETSGILVVARTRAAAQHLT 171
               ++           L S  + +  +        HRLD ETSG LV+A+T  AA  L 
Sbjct: 534 SCTQMNDKRATDVVSLILASTKNGETMRGVFRQGQVHRLDAETSGCLVMAKTDCAADSLR 593

Query: 172 ESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
                     +  K+Y +L           +    L++  + G     +           
Sbjct: 594 HQMGTSAAYSQCNKVYLALCA---------VMEPDLRRIPLRGVLRDPMDPKIS------ 638

Query: 228 SHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           + ++VI  F + +   LE +   G+ HQ+R H    G PI+ D ++        T+P+ +
Sbjct: 639 TKYRVIRFFRKARVALLECRIQQGKKHQIRRHLAAAGLPILQDVEHGG---AACTTPLID 695

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           ++ LHA  + L HP     +   APL     +T   L
Sbjct: 696 RVALHAAALTLVHPRTAEVVTFVAPLAMDFAETIRQL 732


>gi|12321745|gb|AAG50905.1|AC069159_6 RNA pseudouridylate synthase, putative [Arabidopsis thaliana]
          Length = 254

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 62/252 (24%), Positives = 106/252 (42%), Gaps = 54/252 (21%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           +  +LYED  +   NKP G+          + +  L+S       +  L +RLD++TSG+
Sbjct: 14  RDDILYEDEYLMAVNKPKGV----------YCEAVLRS-----APQIVLANRLDRDTSGV 58

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH--- 214
           +++ ++   A  L ++F   +I+K Y +L  G   N +    +    +S  G   V+   
Sbjct: 59  MIITKSHKVAAKLVKAFTEHKIRKSYIALCIGSSPNWRRVTVSSGHGRSKHGAWRVYAAL 118

Query: 215 ---VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ------------------------- 246
               V           + F+V+   + K    E++                         
Sbjct: 119 DVGRVLPGGSFVRDMETTFEVVSVNSVKNESCELEDVNHVIVAEGERELSCGGDDDDVVV 178

Query: 247 -----PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
                P +GRTHQ+R+H  ++G PI GD KY   ++ N  +   ++L  HA  + L HP 
Sbjct: 179 VVRAFPRSGRTHQIRLHCQYLGIPIRGDVKYHGVYEWNGRTFEGHEL--HAECLSLDHPV 236

Query: 302 GGR-LQITAPLP 312
            G  + I APLP
Sbjct: 237 TGDSIVIRAPLP 248


>gi|71649760|ref|XP_813593.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70878491|gb|EAN91742.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 733

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 58/277 (20%), Positives = 106/277 (38%), Gaps = 37/277 (13%)

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS------ 118
           + +   +  ++  ++       S   +  S      +++ED+ I V NKP  ++      
Sbjct: 474 IHVTVKLPRVHECVEAAMQAARSSPTSSFSFASCLPVIFEDNDILVLNKPPHLASSRHAL 533

Query: 119 --VQGGSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQETSGILVVARTRAAAQHLT 171
              Q     A  +   + +   +        +    HRLD ETSG LV+A+T  AA  L 
Sbjct: 534 SCTQMNDKTATDVVSLILASTKNGETTRGVFRQGQVHRLDAETSGCLVMAKTDCAADSLR 593

Query: 172 ESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
                     +  K+Y +L   +  + +      +L+       Y               
Sbjct: 594 HQMGTSAAYSQCNKVYLALCAVMEPDLRRIPLRGVLRDPMDPKIY--------------- 638

Query: 228 SHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           + ++VI  F + +   LE +   G+ HQ+R H    G PI+ D ++        T+P+ +
Sbjct: 639 TKYRVIRFFRKARVALLECRIQQGKKHQIRRHLAAAGLPILQDVEHGG---AACTTPLID 695

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           ++ LHA  + L HP     +   APL     +T   L
Sbjct: 696 RVALHAAALTLVHPRTAEVVTFVAPLAMDFAETIRQL 732


>gi|296475055|gb|DAA17170.1| RNA pseudouridylate synthase domain-containing protein 3 [Bos
           taurus]
          Length = 344

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 61/286 (21%), Positives = 107/286 (37%), Gaps = 46/286 (16%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQ 142
             + +  +  D L++ ++     +   NKP G+ V G  G    +     L   +    Q
Sbjct: 60  PGTFSREELVDVLRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLLSVLPELSRSLGLGEQ 119

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKECI 198
           + ++     +E SG+++++     A  L +    S R R+    Y ++  GIP   +  I
Sbjct: 120 EVQVVRASGKEASGLVLLSSCSQTASRLQKFFTHSRRARKPTATYCAVTDGIPVTSEGKI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNE------KGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              L K  HI G  + V  Q+       +G    +SHF+V+         +++QP T   
Sbjct: 180 QAAL-KLEHIDGVNLVVPVQSPSRKDIMEGVKRTLSHFRVVAT-GSGCALVQLQPLTVFP 237

Query: 253 HQLRVHALHMGCPIVGDHKYCANF------------------KGNFTSPIQNKLYLHARY 294
            QL+ H     CP++GDH Y A                    +      +  +L L A  
Sbjct: 238 SQLQAHMALQLCPVLGDHTYSARVGTVLGQRFLLPVESTKPQRQVLDEALLGRLCLTASQ 297

Query: 295 MDLPH--------------PEGGRLQITAPLPAHMVKTWDSLGFKY 326
                              P    +++ APLP++  +T   LG  Y
Sbjct: 298 AARLPLHLHLHCLRLPGARPRDPPIELLAPLPSYFSRTLQCLGLHY 343


>gi|268680270|ref|YP_003304701.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
 gi|268618301|gb|ACZ12666.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
          Length = 242

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 57/226 (25%), Positives = 92/226 (40%), Gaps = 35/226 (15%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K        +L+ED  I   +KPA I+ +  + I                +K  L HRLD
Sbjct: 49  KIEKIAPIKVLFEDEYIMAVDKPAFITSEEVAEI----------------KKLPLLHRLD 92

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG+L++ +     Q    +F+ R + K Y ++V G      E  A  L  K      
Sbjct: 93  RETSGVLLLTKDDEFRQKAVNAFKKREVHKEYIAIVEGKVVEATEVNAPILTIKKGN--- 149

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                 +       AIS+ + +    ++   +++   TGRTHQ+RVH   +G  I+GD +
Sbjct: 150 --TAYSKISPDGKEAISYIEPLMIEGKR-SKIKVTIETGRTHQIRVHLKSIGASILGDTE 206

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317
           Y              +L LHA  + L     G +   +  P   +K
Sbjct: 207 YGGRPH--------KRLMLHASKIILL----GYI-FQSKEPEDFIK 239


>gi|256379338|ref|YP_003102998.1| pseudouridine synthase [Actinosynnema mirum DSM 43827]
 gi|255923641|gb|ACU39152.1| pseudouridine synthase [Actinosynnema mirum DSM 43827]
          Length = 302

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 50/254 (19%), Positives = 95/254 (37%), Gaps = 9/254 (3%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +  G+V  +   +      +    +        +     +  +++ D  I V +KP  ++
Sbjct: 51  LAEGRVHDLTGPVAPNAPFVPGGAVWFHRDLPVEVPVPFEISVVHRDDAILVVDKPHFLA 110

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                G        ++   D         HRLD+ T+G+++     A        F  R 
Sbjct: 111 TIP-RGKHVVETALVRLRRDLDLPALSPAHRLDRVTAGLVMFVVDPALRGRYQTMFADRL 169

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y ++        ++ +    + +S I  +   +  Q   G   A +  ++ +    
Sbjct: 170 VRKEYEAI-----APVRDDLELPRVVRSRIVKEKGVITAQEVPGPVNAETRVELAERRGD 224

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
                 + P TGRTHQLRVH   +G PIVGD  Y    +        + L L A+ ++  
Sbjct: 225 -LGRYRLLPTTGRTHQLRVHLSGLGVPIVGDDFY-PVLREKPLDDFTDPLQLLAKVLEFT 282

Query: 299 HPEGGRL-QITAPL 311
            P  G   + T+ L
Sbjct: 283 DPVTGEHRRFTSSL 296


>gi|225350851|ref|ZP_03741874.1| hypothetical protein BIFPSEUDO_02425 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225158307|gb|EEG71549.1| hypothetical protein BIFPSEUDO_02425 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 250

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 86/237 (36%), Gaps = 16/237 (6%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           L +     +  +LYE+  I V +KP  ++     G+ Y     ++             HR
Sbjct: 14  LEEPHIPFECEVLYENDAIIVVDKPHFLATTP-RGMWYRETALIRLREQYGEPDIVPAHR 72

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIAN------- 200
           LD+ T+GI+V  R           F+ R+  K Y  L    P+       I         
Sbjct: 73  LDRLTAGIIVFVRKPELRGAYQMLFQNRKTIKTYECLAPLAPEQHPQYGTIVRIDRHQPF 132

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFK----VIDCFAQKFCWLEMQPHTGRTHQLR 256
             ++ SHI  D   +          A +  +    V     + +    + P TG+THQLR
Sbjct: 133 PAIRASHICKDRGRLQAYEIPETINAQTLIERGSTVRCLDGKAYVNYVLHPKTGKTHQLR 192

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           VH   +G PI+GD  Y  N            L L AR +    P  G      + +P
Sbjct: 193 VHMNSLGLPILGDDFY-PNIVQRSYDDFSQPLELVARELRFDDPVTGEPRTFVSKVP 248


>gi|303325510|ref|ZP_07355953.1| RNA pseudouridine synthase family protein [Desulfovibrio sp.
           3_1_syn3]
 gi|302863426|gb|EFL86357.1| RNA pseudouridine synthase family protein [Desulfovibrio sp.
           3_1_syn3]
          Length = 352

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 60/330 (18%), Positives = 108/330 (32%), Gaps = 66/330 (20%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + + V+      RLD+      P +     ++++  G V V+ +      R++ G V+ +
Sbjct: 4   RELRVDAALAGQRLDQALAALTPELGLRGRRRLIARGAVLVNGRVGDAGCRLRPGDVLAL 63

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                         +  +     T  S  +   LL          KPAG+     +    
Sbjct: 64  --------------RGTEDGTGATPCSADMP-RLLSRQGDYCFLYKPAGL--HSAALAGD 106

Query: 128 HIDGFLKSWV------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           +    L++ +      +S+G+ PRL  RLD  TSGI+  A    AAQ    + R  R +K
Sbjct: 107 NGLS-LEALLPVLLSEESEGRAPRLMQRLDYGTSGIVCAALGAKAAQAFRVAERAGRCEK 165

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA---- 237
            Y +L+ G             ++ +    D        +       + F  +  +     
Sbjct: 166 RYLALLRGTLAGPST------VRLALDTADRRQSRVLADTDDRLRWTEFLPLHVWGGAAA 219

Query: 238 -----------------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                                                +   G  HQ+R HA  +G P+ G
Sbjct: 220 TGPLAGLVRDTAHGESTSSASGAGEGEDPGGLTLAACRIRCGARHQIRAHAAALGHPLWG 279

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           D  Y    + + + P     +LH   + LP
Sbjct: 280 DGLYG---RSDQSGPAGTGFFLHHGALLLP 306


>gi|254721426|ref|ZP_05183215.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. A1055]
          Length = 139

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 28/140 (20%), Positives = 56/140 (40%), Gaps = 17/140 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1   MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREND 60

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +                +     L    + +   + YED+ + V NKP G+ V    
Sbjct: 61  EITVT---------------IPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAP 105

Query: 124 GIA--YHIDGFLKSWVDSKG 141
           G      ++G +    D  G
Sbjct: 106 GHTSGTLVNGLMHHCTDLSG 125


>gi|311742421|ref|ZP_07716230.1| RNA pseudouridine synthase [Aeromicrobium marinum DSM 15272]
 gi|311314049|gb|EFQ83957.1| RNA pseudouridine synthase [Aeromicrobium marinum DSM 15272]
          Length = 283

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 57/222 (25%), Positives = 90/222 (40%), Gaps = 12/222 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHR 149
            +     +  +L+ D ++ V +KPA +S        +     +    D  G  +    HR
Sbjct: 52  AEPVVPGELTVLHRDERLVVVDKPAFLSTIPRG--RHVAQSVVVRLRDELGLPELSPVHR 109

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ TSG+LV+   R         F+ RR+ K Y +L    P      +   L  ++H+ 
Sbjct: 110 LDRVTSGVLVLTTERRWRGAYQGMFQHRRVHKAYRALAPLRPD-----LELPLTVRNHLR 164

Query: 210 GDYVHVVKQNEKGANY-AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
            D        +  A   A +  + +D          + P TGRTHQLR H   +G PIVG
Sbjct: 165 KDRGAWQVTVDPDAQPNAETLVE-LDAVVGGLGVYRLTPRTGRTHQLRAHLCGLGIPIVG 223

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           D  Y A  + +        L L A  +    P +GG  + T+
Sbjct: 224 DPLYPAVLEVDVDD-FSTPLQLLAHEVSFTDPVDGGERRFTS 264


>gi|304387818|ref|ZP_07369992.1| RNA pseudouridine synthase [Neisseria meningitidis ATCC 13091]
 gi|304338083|gb|EFM04219.1| RNA pseudouridine synthase [Neisseria meningitidis ATCC 13091]
          Length = 307

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 94/223 (42%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
           ++     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  SEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----LTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEVEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y    +   +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|324509347|gb|ADY43935.1| Unknown [Ascaris suum]
          Length = 386

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 54/222 (24%), Positives = 95/222 (42%), Gaps = 10/222 (4%)

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED-SKIYVFNKPAGIS 118
           + G++      +   +++ K    +    +  +H    K I   E+   + V NKP  + 
Sbjct: 57  KLGRLFVNERQMTDTDYVFKNNDAIVHVAHRHEHPILAKPIEFIENNDDLLVVNKPPSMP 116

Query: 119 VQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           V   G    + + G L +  +  G   R+ HRLD+ TSG+L+ A+   +     E+ +  
Sbjct: 117 VHACGQYRLHTVMGLLHTEHNITG--LRVLHRLDRTTSGVLIFAKNYESDLEFKEALKSG 174

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCF 236
            + K Y   V G+     E +    + +  IG   + +  Q  +     A + FK +   
Sbjct: 175 ELHKEYVCKVEGVFPGNGEEV----ICEEPIGSLVLTMGIQCVRNDGKPARTRFKRLWSD 230

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K   ++    TGRTHQ+RVH  ++G PIV D  Y  +  G
Sbjct: 231 G-KISVVKCFLDTGRTHQIRVHLQYLGFPIVDDELYNTDVWG 271


>gi|260905406|ref|ZP_05913728.1| ribosomal pseudouridine synthase [Brevibacterium linens BL2]
          Length = 332

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 55/304 (18%), Positives = 113/304 (37%), Gaps = 48/304 (15%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR--VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           W +  +P  +    + +L SG +R  V  + +++++ +  G            +  +  +
Sbjct: 40  WLEAEFPEADDEARRSLLTSGDMRDEV-GEPIRWDDAVVPG-------GFYFFHRPVPAE 91

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           + +   ++           +++ED  + V +KP  ++               ++ +D   
Sbjct: 92  ERIPFEIS-----------VVFEDDDLLVVDKPHFLASTPNGRFVRECVVT-RARLDFDQ 139

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD+ T+G+L++++           F+ R + K Y +L    P +    +   
Sbjct: 140 PDLVAIHRLDRVTAGLLILSKRPETRGRYQRLFQDRLVTKTYRALAAMPPAD----LELP 195

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL------------------ 243
           L+K+S +            +G   A S   ++                            
Sbjct: 196 LVKESRLVKPRGGRQVLEVEGEPNAFSKISLLGERTPPSPRWSDATEPPPRRSVGECPSI 255

Query: 244 ---EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
              +++P TG+THQLRVH   +G PI+GD  Y  +   +      + L L A  +    P
Sbjct: 256 GEYQLEPLTGKTHQLRVHMNSLGLPILGDPVYPVDRAPDPYD-FSSPLQLLAASIGFDDP 314

Query: 301 EGGR 304
             GR
Sbjct: 315 LTGR 318


>gi|71894118|ref|YP_278226.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           synoviae 53]
 gi|71850906|gb|AAZ43515.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma
           synoviae 53]
          Length = 281

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 52/305 (17%), Positives = 120/305 (39%), Gaps = 42/305 (13%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
             ++EN  L +    ++P++    ++K+ R  +++V+ KR+      +    +V +  + 
Sbjct: 7   SKNDENRSLFKLICKYFPNLTIATIEKLFRKKEIKVNSKRITDKKFVVSENDLVEVYGIS 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHID 130
            +  ++ + +K+                 ++YED+ I + +K   + + G  + +   + 
Sbjct: 67  ESNLNLPQIKKV------------SFDFQIIYEDANILIIDKKENLVIHGEDNSLDNQVL 114

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-RRIQKIYWSLVWG 189
            +LK        KP    RLD+ETSG++V A+     + L E     +++ +     +  
Sbjct: 115 SYLKH-KQIDSFKPSHVGRLDKETSGLIVYAKNYLTLKQLNEKSFNFKKVYQFKSDFLSS 173

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            P      +  +  K  +   +   + K  ++ +  A S F   +           Q  T
Sbjct: 174 SPLE----LKLYFYKDEN---NKTKISKTQKENSKLAHSIFYCENNKKF------AQIIT 220

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-----GR 304
           GR HQ+R+   ++  PI             +      +L LH+ Y+   + E       +
Sbjct: 221 GRKHQIRLSLAYLNKPI--------YGDKKYKGKKSTRLMLHSYYLKFLNLEDNLKYLNK 272

Query: 305 LQITA 309
           ++  +
Sbjct: 273 MEFYS 277


>gi|296314658|ref|ZP_06864599.1| RNA pseudouridine synthase [Neisseria polysaccharea ATCC 43768]
 gi|296838567|gb|EFH22505.1| RNA pseudouridine synthase [Neisseria polysaccharea ATCC 43768]
          Length = 307

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 44/217 (20%), Positives = 90/217 (41%), Gaps = 11/217 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLK---SWVDSKGQKPRL 146
            +     +  +L+ D  + V +KP  + V   G  +   +   L+          +    
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G++++++  A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSQNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + D  Y    +   +   +  L L A+ +    P  G
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSG 296


>gi|262375387|ref|ZP_06068620.1| pseudouridylate synthase [Acinetobacter lwoffii SH145]
 gi|262309641|gb|EEY90771.1| pseudouridylate synthase [Acinetobacter lwoffii SH145]
          Length = 302

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 91/223 (40%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHR 149
            +     +  +L+E+    V +KP  +++       Y  +  L       G +     HR
Sbjct: 85  HEVHVPFQHQILFENEHFMVVDKPHFLTMSPTG--QYVQETLLVRLKKQTGNEHLTPIHR 142

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ET+G++++++   +     + F  R++QK Y ++    P      +   L+ +  + 
Sbjct: 143 LDRETAGVVLISKCVESRGIYQQMFATRQVQKTYHAIAAYHPD-----LKFPLITRLRME 197

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                       G   + +   ++    + +   E++PHTG+ HQLRVH  H+G PI  D
Sbjct: 198 KGQPFYTMHVLDGTPNSETVIDLLKHNTE-WAKYELKPHTGKQHQLRVHLNHLGIPIQHD 256

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
             Y               L L A+++    P   + +  ++ L
Sbjct: 257 PFY-PQVAHKAEDDFSAPLSLLAKHIQFVDPITQKSMNFSSHL 298


>gi|290981670|ref|XP_002673553.1| predicted protein [Naegleria gruberi]
 gi|284087137|gb|EFC40809.1| predicted protein [Naegleria gruberi]
          Length = 483

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 64/293 (21%), Positives = 117/293 (39%), Gaps = 41/293 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD + +  +P+ +   L K    G+ ++                      +N L     +
Sbjct: 61  LDVY-RAEFPYFSEQYLMKAFELGRFKI------------------NNENLNNLEEKWDK 101

Query: 81  QKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            K +   V+  +   F ++I +LY++S + V +KPA   +       Y  +       ++
Sbjct: 102 SKTIAHRVHFHEKPIFDRNIPILYDESDLLVVDKPASFPIHPCG--RYRKNSLTYILEEN 159

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--IQKIYWSLVWGIPKNK--- 194
                 + HRLD  TSG+LV+A+ +  +  + E  + R   I K Y ++V G  K +   
Sbjct: 160 GYGTLHVVHRLDHSTSGVLVLAKNKKVSGEIVEMIKTREKAIGKYYLAVVKGKWKGEYEV 219

Query: 195 KECIANWLLKKSHIGGDYVHVVK---------QNEKGANYAISHFK-VIDCFAQKFCWLE 244
              + +  L  S +  +     K          +E G   AI+ F  ++    +    + 
Sbjct: 220 SGLVKD--LNNSFVKCEKKVYCKNHKNGTWSADDELGTFEAITLFSGIVYNKEKDISLIM 277

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            +P TGRTHQ+R+H   +G PI+ D  Y   F       +Q K    +  +D 
Sbjct: 278 CKPITGRTHQIRIHLESIGNPIINDFFYNEQFIKEL--EVQKKTLEESWRVDF 328


>gi|121634642|ref|YP_974887.1| hypothetical protein NMC0808 [Neisseria meningitidis FAM18]
 gi|120866348|emb|CAM10091.1| hypothetical protein NMC0808 [Neisseria meningitidis FAM18]
          Length = 307

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 91/223 (40%), Gaps = 11/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLK---SWVDSKGQKPRL 146
            +     +  +L+ D  + V +KP  + V   G  +   +   L+          +    
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----LTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEVEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           + D  Y        +   +  L L A+ +    P  GR ++  
Sbjct: 261 LNDALY-PVLSEAGSEDYRKPLKLLAKKIAFADPLSGRERVFC 302


>gi|255327672|ref|ZP_05368738.1| pseudouridylate synthase [Rothia mucilaginosa ATCC 25296]
 gi|255295346|gb|EET74697.1| pseudouridylate synthase [Rothia mucilaginosa ATCC 25296]
          Length = 383

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 63/293 (21%), Positives = 106/293 (36%), Gaps = 44/293 (15%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           +     +G+VR+D         I +G    +P         + ++  L S +        
Sbjct: 96  IHARFNTGEVRLDDGT------ILTGDSPYMPGERIWYFRELADEPQLPSDMP------- 142

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
               +LYED  +   +KP  +      G         K  V  +       HRLD+ T+G
Sbjct: 143 ----VLYEDEHVLAIDKPHFLPTTP-RGAYIAQTALTKLRVREQNPLLIPIHRLDRPTAG 197

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIY---WSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           +L+ A+T  A +     F+ R++ K Y     +       ++   A  L  +SHI     
Sbjct: 198 VLLFAKTVEARRPFQMMFQHRQVSKTYRAVAPVPADAAAAEQALSAEGLQVRSHIQKIRD 257

Query: 214 HVVKQNEKGANYA--------ISHFKVIDCFA--------------QKFCWLEMQPHTGR 251
            +  Q       A        ++  K++  F               +++   ++ PHTG+
Sbjct: 258 QLQVQQLSEQECAAQGVEPNTLTTAKILRTFTPSAQAVAGWRAEPNREWALYDLAPHTGK 317

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           THQLR H   +  PI+GD  Y          P +  L L A  +   HP  G 
Sbjct: 318 THQLRAHLNMLSSPILGDVLYPQVLPDAPDRP-EYPLQLLAYSLHFEHPITGE 369


>gi|61553985|gb|AAX46489.1| hypothetical protein FLJ14494 [Bos taurus]
          Length = 304

 Score =  122 bits (306), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 53/189 (28%), Positives = 91/189 (48%), Gaps = 20/189 (10%)

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQK 143
           V+    +  L   ++++D ++ V NKP G+ V GG G+   I   L    K     K + 
Sbjct: 86  VHPNVLAKALSRGIVHQDKELVVINKPYGLPVHGGPGVKLCISDVLPVLAKILHGPKAKP 145

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L HRLD+ET+G++V+A  +  A  + E FR R++ K YW++   +P  +   +   ++
Sbjct: 146 LHLCHRLDKETTGVMVLAWEKEVAHQVQELFRTRQVTKKYWAITVRVPVPEAGVVDIPIV 205

Query: 204 KKSHIG---------------GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +K   G                D   V  ++ + A  A++ ++V+   +     LE+QP 
Sbjct: 206 EKEAQGQQHHHKMTLSPSYRMDDGKMVRVRSSRNAQLAVTQYRVL-SSSLSAALLELQPI 264

Query: 249 TGRTHQLRV 257
           TG  HQLRV
Sbjct: 265 TGIKHQLRV 273


>gi|212637300|ref|YP_002313825.1| pseudouridine synthase [Shewanella piezotolerans WP3]
 gi|212558784|gb|ACJ31238.1| Pseudouridine synthase [Shewanella piezotolerans WP3]
          Length = 319

 Score =  122 bits (306), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 55/292 (18%), Positives = 111/292 (38%), Gaps = 36/292 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +  +H+  I        + +G+V             + G++V +         +   +++
Sbjct: 42  FLVSHFKAIAETTWIDRIENGKVH-----------WRDGELVTLESEFIPRARVYYYREV 90

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
              S+         +  +L ++ +I +  KP  ++V             L + +  K   
Sbjct: 91  QQESL------IPFEEKVLLQNEQIIIAFKPHFLAVNPSGNFVNEC---LVNRLRIKTAN 141

Query: 144 PRLT--HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-------WGIPKNK 194
            ++   HRLD+ T+G+++++ +        + F+   I K Y ++          I  + 
Sbjct: 142 EQIVASHRLDRATAGVMLLSLSVDTRHDYHQLFKTGNITKTYQAIARLSDELMAKIAADA 201

Query: 195 KECIANWLLKKSHIGGDYVHVVK--QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                +W +K   +  D   ++K    E  ++  I+  +V       F   E+ P TGRT
Sbjct: 202 LVLPISWTVKNRLVKADPSFMMKISVGESNSHSEITLLQV----KGGFGLFELTPVTGRT 257

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           HQLR+H + +G PI+ D  Y             N L L A+ +    P  G 
Sbjct: 258 HQLRLHMMSLGMPILNDRLY-PELLDKAADDFDNPLKLMAKRLAFTDPITGE 308


>gi|325132280|gb|EGC54973.1| RNA pseudouridine synthase [Neisseria meningitidis M6190]
 gi|325137749|gb|EGC60324.1| RNA pseudouridine synthase [Neisseria meningitidis ES14902]
          Length = 307

 Score =  122 bits (306), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 44/217 (20%), Positives = 91/217 (41%), Gaps = 11/217 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
           ++     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  SEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + + +    +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLLYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+     F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGVPNAHTTVELIENRG-GFSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + D  Y    +   +   +  L L A+ +    P  G
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSG 296


>gi|218513991|ref|ZP_03510831.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli 8C-3]
          Length = 136

 Score =  122 bits (306), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 37/135 (27%), Positives = 64/135 (47%), Gaps = 16/135 (11%)

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------FCWLEMQPHTGRTHQLRVH 258
           ++        V + + + A+ AI+H++VI+ F +          +E +  TGRTHQ+RVH
Sbjct: 1   RATGDRTRRAVKRPDSQDADEAITHYEVIERFHETPDATALASLVECRLETGRTHQIRVH 60

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQ---------NKLYLHARYMDLPHPEGGR-LQIT 308
             H+G P++GD  Y A F+       +         ++  LHA  +   HP  G  +   
Sbjct: 61  MAHIGHPLLGDTVYGAGFRTKANLLPEDIRKVVNRFDRQALHAFMLQFEHPRSGELMHFE 120

Query: 309 APLPAHMVKTWDSLG 323
            PLP  M++  ++L 
Sbjct: 121 VPLPDDMMELVEALR 135


>gi|325674660|ref|ZP_08154347.1| RNA pseudouridine synthase [Rhodococcus equi ATCC 33707]
 gi|325554246|gb|EGD23921.1| RNA pseudouridine synthase [Rhodococcus equi ATCC 33707]
          Length = 297

 Score =  122 bits (306), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 104/258 (40%), Gaps = 10/258 (3%)

Query: 54  KFNNRIQSGQVV-RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
           +   ++ +G+VV      I+A+        +        +     +  +L+ D  + V +
Sbjct: 42  RLQEKVDAGEVVDEHGTPIDAVTAYRPRAFLYLYRDPPAEKRVPFEVDVLHRDQDLLVVD 101

Query: 113 KPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           KP  ++     G        ++   +    +    HRLD+ T+G+L+    R A +    
Sbjct: 102 KPHFLASTP-RGAYVVESALVRLRRELDLPELTPAHRLDRITAGVLLFTVRREARRAYQS 160

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F  RR  K+Y +L    P      +   +  +S I  +   +  +   G   A S  ++
Sbjct: 161 LFDERRATKVYEALARHDPS-----LHLPVTVRSRIIKERGVLQAREVDGEPNAESRIEL 215

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           +D          + P TG+THQLR+H   +G PI+GD+ Y   F    +    + L L A
Sbjct: 216 LDVR-DGVGHYRLLPRTGKTHQLRLHMCSLGVPIIGDNFY-PRFYDVASDDYSDPLRLLA 273

Query: 293 RYMDLPHPEGG-RLQITA 309
           R ++   P  G R +  +
Sbjct: 274 RSLEFDDPYTGVRRRFES 291


>gi|315445746|ref|YP_004078625.1| 23S RNA-specific pseudouridylate synthase [Mycobacterium sp. Spyr1]
 gi|315264049|gb|ADU00791.1| 23S RNA-specific pseudouridylate synthase [Mycobacterium sp. Spyr1]
          Length = 286

 Score =  122 bits (306), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 51/253 (20%), Positives = 94/253 (37%), Gaps = 19/253 (7%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVFNKPAG 116
           ++  G+V      +   + ++     +    +L  +        +L+ D  I V +KP  
Sbjct: 38  KVVDGEVFCADGTVADDSTVLPPGAHVYLYRDLPDEVPVPFDMPVLHRDDDIVVVDKPHF 97

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           ++     G        ++   +    +    HRLD+ T+G+L+    R         F  
Sbjct: 98  LATMP-RGSHVVQTALVRLRRELDLPELSPAHRLDRLTAGVLLFTARREVRGAYQTLFVR 156

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
               K Y +        +       L  ++ +      +    E G   A +   V++  
Sbjct: 157 GEAAKTYVAHSSHAIDREF-----PLTVRNRLVKHRGSLQAVEEPGEPNAET---VVEYL 208

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHAR 293
            +      + P TGRTHQLRVH   +G PI GD  Y        G+F +P+  +L   A+
Sbjct: 209 GEG--MYRLTPRTGRTHQLRVHMAGLGIPITGDPLYPDVVDVPPGDFGAPL--RLL--AQ 262

Query: 294 YMDLPHPEGGRLQ 306
            ++   P  G L+
Sbjct: 263 ALEFTDPISGELR 275


>gi|312138349|ref|YP_004005685.1| tRNA-pseudouridine synthase i [Rhodococcus equi 103S]
 gi|311887688|emb|CBH47000.1| putative tRNA-pseudouridine synthase I [Rhodococcus equi 103S]
          Length = 297

 Score =  122 bits (306), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 104/258 (40%), Gaps = 10/258 (3%)

Query: 54  KFNNRIQSGQVV-RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
           +   ++ +G+VV      I+A+        +        +     +  +L+ D  + V +
Sbjct: 42  RLQEKVDAGEVVDEHGTPIDAVTAYRPRAFLYLYRDPPAEKRVPFEVDVLHRDQDLLVVD 101

Query: 113 KPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           KP  ++     G        ++   +    +    HRLD+ T+G+L+    R A +    
Sbjct: 102 KPHFLASTP-RGAYVVESALVRLRRELDLPELTPAHRLDRITAGVLLFTVRREARRAYQS 160

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F  RR  K+Y +L    P      +   +  +S I  +   +  +   G   A S  ++
Sbjct: 161 LFDERRATKVYEALARHDPS-----LHLPVTVRSRIIKERGVLQAREVDGEPNAESRIEL 215

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           +D          + P TG+THQLR+H   +G PI+GD+ Y   F    +    + L L A
Sbjct: 216 LDVR-DGVGHYRLLPRTGKTHQLRLHMCSLGVPIIGDNFY-PRFYDVASDDYSDPLRLLA 273

Query: 293 RYMDLPHPEGG-RLQITA 309
           R ++   P  G R +  +
Sbjct: 274 RSLEFDDPYTGIRRRFES 291


>gi|255729940|ref|XP_002549895.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
 gi|240132964|gb|EER32521.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
          Length = 392

 Score =  122 bits (306), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 57/301 (18%), Positives = 123/301 (40%), Gaps = 21/301 (6%)

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSIL--LYEDSKIYVFNKPAGI 117
           +  +   +      ++  +  + ++  S +  +        +  +YED ++ V +KP+G+
Sbjct: 65  KPNEKACLKGFDLLISRPLHAKDLVCHSKHRHEPPIPYLGRIKSVYEDDELLVVDKPSGV 124

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
                    Y+ +   +   D  G +     HRLD+ TSG+L+  +T++A    +   + 
Sbjct: 125 PTHPTGN--YYFNSVSEMVKDQFGLEAIWTCHRLDKVTSGVLIFGKTKSAGSKFSRLIKD 182

Query: 177 RR--IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            +   +K Y + V G   N K      +   +  G     V   +E+    + + F+ + 
Sbjct: 183 HKDQTEKTYLARVVGEFPNGKLQYNCPIFAVNLNG---YLVPGNSEELPLDSTTIFQKVS 239

Query: 235 CFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN-----FKGNFTSPIQNKL 288
             A      ++  P TG+ HQ+R+H  ++G PIV D  Y  +      + +    +  KL
Sbjct: 240 YNASLNQSLVKCIPITGKFHQIRIHLRNLGFPIVNDSFYRGDNELTNRRCSIEEELYKKL 299

Query: 289 YLHARYMDLPHPEGGRLQ--ITAP-LPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNI 345
           +   +Y +       R +  I    L   +    D L   + ++L  ++L   +EC +++
Sbjct: 300 FQ--KYPEFKTFGTTRREGFINIDLLDEKLQYGLDELKRDHLQSLNEQKLSYCEECHRSL 357

Query: 346 L 346
            
Sbjct: 358 F 358


>gi|238021958|ref|ZP_04602384.1| hypothetical protein GCWU000324_01863 [Kingella oralis ATCC 51147]
 gi|237866572|gb|EEP67614.1| hypothetical protein GCWU000324_01863 [Kingella oralis ATCC 51147]
          Length = 305

 Score =  122 bits (306), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 58/286 (20%), Positives = 110/286 (38%), Gaps = 30/286 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           + +  +P I     +  L SG V V+   + +  N   Q+G+ +     I+       E 
Sbjct: 33  YLRARFPFIAENIWRARLNSGMV-VNQRGEPLHENVLYQAGEKIFYYREISRD----AEP 87

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSK 140
           +I                 +L+ D+ + V +KP  + V   G  +   +   L+   D +
Sbjct: 88  RIP------------FDEKILWLDNDLIVVDKPHFLPVTPSGRFLHETLLTRLRLHPDLQ 135

Query: 141 GQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                     HRLD++T+G+++ +   A        F    IQK Y +L           
Sbjct: 136 YLNTADITPLHRLDKDTAGVMLFSHNPATRAAYHTLFPSHAIQKTYHALAPTRLD----- 190

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +A  L+ ++ +       + +   G   A +  ++++   +     E+QP TG+ HQLRV
Sbjct: 191 LAYPLIVRTRLVPSEPFFLMREAAGEANAETRVRLLEPRGE-ASLYELQPVTGKKHQLRV 249

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             + +G P++ D  Y    +          L L A+ +    P  G
Sbjct: 250 QMMGLGMPLLNDALY-PVVQPENGDDYSKPLKLLAKRLAFIDPLTG 294


>gi|77360598|ref|YP_340173.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875509|emb|CAI86730.1| conserved protein of unknown function ; putative 23S rRNA
           pseudouridylate synthase. In E.coli Pseudouridine
           synthases are responsible for synthesis of pseudouridine
           from uracil in 23S rRNA [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 226

 Score =  122 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 62/223 (27%), Positives = 96/223 (43%), Gaps = 25/223 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++  S  Y+  KPAG++       +    GF+        +K    HRLD+ TSG+L++
Sbjct: 11  VVHSHSDFYILAKPAGLNFH-----SEDAAGFVVLAEQQLNEKLFAVHRLDKVTSGLLIL 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR + AA   T+ F    I K Y ++    PK K+  I      K  +        K   
Sbjct: 66  ARNKLAAAKFTQMFTEHTINKFYLAISDAKPKKKQGWI------KGDMAKSRRGTFKLLT 119

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             AN AIS F  +        ++ ++P++G+THQLRV    +G PI+GD  Y        
Sbjct: 120 TTANPAISRFYSVSYKPGFRGYI-LKPYSGKTHQLRVALKSIGAPILGDTSYAGAHSA-- 176

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLP---AHMVKTWD 320
                 + YLHA  +D    E  ++Q T  LP       +   
Sbjct: 177 ------RTYLHAFALDFLWNE-QQIQFTL-LPDNGDEFTQLIK 211


>gi|115923337|ref|XP_792877.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 3 [Strongylocentrotus purpuratus]
 gi|115953851|ref|XP_001183657.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 3 [Strongylocentrotus purpuratus]
          Length = 373

 Score =  122 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 68/286 (23%), Positives = 111/286 (38%), Gaps = 52/286 (18%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQG-----GSGIAYHIDGFLKSWVD-SKGQKPRLTHR 149
           +LK  ++Y+   I   NKP G+ V G            +   +    D +      +   
Sbjct: 81  YLKKNIVYQQDGIVAINKPPGLGVSGKVNEDDESSPLTLSSMMSQVADFTDCPSAEIAQG 140

Query: 150 LDQETSGILVVARTRAAAQHLT----ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           L++E SG+L++A  R AA+ L     E+   R+  K Y S+V GIP+ K      +L   
Sbjct: 141 LEKEASGLLLLAENRMAAKKLQSKIKEARNRRQFIKTYRSIVCGIPETKIGVSKMYLG-S 199

Query: 206 SHIGGDYVHVVKQNEKGAN-------YAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLRV 257
             IGG  + V + N  G          A + ++VI +       ++E+QP   + HQL+V
Sbjct: 200 DVIGGINMTVGRHNPSGRQIRDGDVWSAETKYRVISENKELGCAFIELQPLRVKRHQLQV 259

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQ--NKLYLHARYMDLPHP--------------- 300
             ++  CPI+GDH Y    +     PI       L    + +  P               
Sbjct: 260 QMVNDLCPILGDHTYSHQVQTILGKPILMDPHQALGVHNIQVLSPGIRKALAMTRPQVSL 319

Query: 301 ----------------EGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
                               + ITAPLP+H  +    LG +   ++
Sbjct: 320 LPLFLHLHHVVLPEWAGHQDVTITAPLPSHFTRALKELGLRSSEDV 365


>gi|91788766|ref|YP_549718.1| pseudouridine synthase [Polaromonas sp. JS666]
 gi|91697991|gb|ABE44820.1| pseudouridine synthase [Polaromonas sp. JS666]
          Length = 303

 Score =  122 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 48/215 (22%), Positives = 87/215 (40%), Gaps = 10/215 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHR 149
            +     +  +L++D  + V +KP  + V       Y  +  L    +  G       HR
Sbjct: 85  DEPRVPFEETVLHQDEHLVVADKPHFLPVTPSGH--YLQETLLVRLKNRLGIDSLVPIHR 142

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D+ET+G+++ +   A        FR   + K Y +L        +E +   L +KS I 
Sbjct: 143 IDRETAGLVLFSVNPAERDAYQALFRQHAVSKHYEAL-----APWREDLRFPLTRKSRIV 197

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            D     ++   G   + +H +++    ++     + P TG+ HQLRVH   +G PI  D
Sbjct: 198 QDEPFFRQREVPGEPNSETHLELLQISGEQA-RYALSPVTGKKHQLRVHMNALGLPITND 256

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             Y    +       +  L L A+ +    P  G+
Sbjct: 257 RMYPP-VQPTPDDDYRYPLQLLAKSIAFTDPLTGQ 290


>gi|313139743|ref|ZP_07801936.1| pseudouridine synthase [Bifidobacterium bifidum NCIMB 41171]
 gi|313132253|gb|EFR49870.1| pseudouridine synthase [Bifidobacterium bifidum NCIMB 41171]
          Length = 246

 Score =  122 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 56/243 (23%), Positives = 87/243 (35%), Gaps = 23/243 (9%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +        ++YED+ I V +KP  ++     G+ Y     ++             HRL
Sbjct: 3   EEPHIPFDIDVVYEDAGIIVIDKPHFLATTP-RGMWYRQTALIRLREMFDEPDITPAHRL 61

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIAN-------W 201
           D+ T+GI+V  R  A        F+ R++ K Y  L    P  +     +          
Sbjct: 62  DRLTAGIVVFVRDPALRGAYQMMFQGRKVSKTYECLAPCRPTTRPRYGTVERLDPPAVFP 121

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKV-----------IDCFAQKFCWLEMQPHTG 250
           L ++SHI      +    E  A  A +   +           +          E+ P TG
Sbjct: 122 LRRRSHITKLRGVLQAFEEPQAVNAETVIDLAAGGYPSMGGRLCHGRNGLRAYELHPLTG 181

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +THQLRVH   +G PI GD  Y               L L AR +    P  G   +  +
Sbjct: 182 KTHQLRVHMNSIGLPIHGDDFY-PRIVERAYDDFSTPLELVARSLRFTDPVSGEPREFIS 240

Query: 310 PLP 312
            +P
Sbjct: 241 RIP 243


>gi|314929196|gb|EFS93027.1| RNA pseudouridine synthase [Propionibacterium acnes HL044PA1]
          Length = 281

 Score =  122 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 65/271 (23%), Positives = 102/271 (37%), Gaps = 14/271 (5%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           ++K+LR G  RVD         +  G+ V         +     Q  +    +L   +  
Sbjct: 6   VEKLLRVGGPRVD-------EMLDEGRFVDDAGRAFRQDSPFTPQTFVFFHRDLPTETPV 58

Query: 97  LKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
              I +LY D +I V +KP  +S     G        ++        +  + HRLD+ T+
Sbjct: 59  PAGIGILYSDERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTMAHRLDRVTA 117

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE---CIANWLLKKSHIGGDY 212
           G+L++ R R   +   E F  R + K Y  +   +     E      N    +S I  + 
Sbjct: 118 GVLLLTRERQWRRPYQELFERREVVKKYRLVAPAVHDPAGEGAVVTNNGWQVRSRIVKER 177

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +  +   G   A++   V+          E  P TGRTHQ+R+H   +G PIV D  Y
Sbjct: 178 GILQAREVPGEPNAVTDI-VLVSEHGGLGLYEASPRTGRTHQIRLHMQRLGAPIVNDPFY 236

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                G       + L L A  M    P  G
Sbjct: 237 -PIVLGTQIDDFTHPLQLQAWQMGFTDPVSG 266


>gi|317486123|ref|ZP_07944968.1| RNA pseudouridylate synthase [Bilophila wadsworthia 3_1_6]
 gi|316922608|gb|EFV43849.1| RNA pseudouridylate synthase [Bilophila wadsworthia 3_1_6]
          Length = 339

 Score =  122 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 60/326 (18%), Positives = 110/326 (33%), Gaps = 59/326 (18%)

Query: 12  VENDEENMRLDRWFKNHYPHIN------------------FVNLQKILRSGQVRVDKKRV 53
           V  + +  RLD+         +                      +++     V V+ K  
Sbjct: 17  VPEEAQGWRLDKALGLLLASPSPEQEAARPGLFALADLGLRAR-RRLCDRSLVLVNGKPG 75

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
               ++++GQ + I P          E   +                L+Y+D  I    K
Sbjct: 76  IPGLKLRAGQEIIILPD--------PEGAAIPEDAP----------SLVYKDGGIAALYK 117

Query: 114 PAGISVQGGSG-IAYHIDGFLKSWV--DSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           PAG+     +G ++  ++  L   +  + +G   RL +RLD  TSG+++ + T    +  
Sbjct: 118 PAGMHTAALAGSLSPSLETLLGDLLPSEEEGYASRLLNRLDAPTSGLVLASCTDGGERRW 177

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
             + R+    K+Y +L+ G P      +A  L   +      V      +   +  ++  
Sbjct: 178 YRAERIGNTDKLYLALIEGQPLYD-FTVARRLDTDTR-NKTRVRHTDDPDPVRHTDVTLL 235

Query: 231 KVI-----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
             +           D        +  +   G  HQ+R H    G P+ GD  Y A     
Sbjct: 236 APLTAGDVPGLVESDDPDAPLMLVGCRIRKGARHQIRAHLAAAGHPLAGDSLYGAEL--- 292

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRL 305
              P  +   LH   + LP  +  RL
Sbjct: 293 ---PCPSGFLLHHGRVSLPDFQAFRL 315


>gi|326440515|ref|ZP_08215249.1| putative ribosomal pseudouridine synthase [Streptomyces
           clavuligerus ATCC 27064]
          Length = 273

 Score =  122 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 49/252 (19%), Positives = 98/252 (38%), Gaps = 10/252 (3%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
            +       G++V +  V+ A       + +        +     +  +++ D+++ V +
Sbjct: 16  ARVGELFAEGRIVSVDGVVAADEPYAAGRYLWFHRDFAPEPRVPFEIRIVHRDARLLVVD 75

Query: 113 KPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           KP  ++    GS I       L+  +     +P   HRLD+ T+G+++            
Sbjct: 76  KPHFLATTPRGSHITETAVARLRHGLGLPLLQP--AHRLDRLTAGLVLFVVRPEDRGAYQ 133

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             FR R ++K Y ++    P      +      +S I  +   +  +   G   + +  +
Sbjct: 134 TLFRDRGVRKEYEAVAAYDPA-----VELPRTVRSRIVKERGVLAAREVPGEPNSETRIE 188

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           +++          + P TG+THQLRVH   +G PI+ D  Y    + +        L L 
Sbjct: 189 LLEHRG-GLGRYRLLPATGQTHQLRVHMSGLGLPILHDPVY-PVVRADGPEDFGRPLSLL 246

Query: 292 ARYMDLPHPEGG 303
           AR ++   P  G
Sbjct: 247 ARTLEFTDPFTG 258


>gi|261328846|emb|CBH11824.1| RNA pseudouridylate synthase, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 462

 Score =  122 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 74/432 (17%), Positives = 139/432 (32%), Gaps = 117/432 (27%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHIIK 79
           +D +    +P++     ++  R G + V    +K   +   +G   R   V+     + +
Sbjct: 19  ID-FLCCRFPYLTRSAWEQHARDGHISV----IKAARDSCGAGDN-RHGVVVPMDYELQQ 72

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWV- 137
             +I  +     +       ++L+ D  + V  K   + V +GG   A  + G L+    
Sbjct: 73  NDEICFNPPRHLEPDINEHVVVLHSDEALLVCVKNGNLPVAEGGRYSANTLVGVLQRLAG 132

Query: 138 ---------------------DSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESF 174
                                ++ G K      HRLD+ETSG++V+A++  AA+ L+  F
Sbjct: 133 SFTWETANGTAEICLSKATNKETCGLKVNYYPVHRLDKETSGLVVLAKSADAARILSGQF 192

Query: 175 ---------------------------------RMRRIQKIYWSLVWGIPKNKKECI--- 198
                                              + + K Y +++ G      E I   
Sbjct: 193 ERQSQVLNAQLTKYTGGESLTVVTSSQFDELITMDKSVSKSYIAVLDGSVPEGNEFIVCN 252

Query: 199 -----------------ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKF 240
                             +  LKK  +   +  V K  +     A S  +++      + 
Sbjct: 253 RVGLLWEELKDSMKDAEKHTKLKKLKMACYHASVEKNQQLYGRPACSRIRILSSSDTLRV 312

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------------- 285
               +   TGRTHQ+R+H   +G P++GD  Y  +  G                      
Sbjct: 313 SVARVDILTGRTHQIRLHCAQIGFPVLGDKLYETSTPGAVGGLHAVADDIYLYRARETVS 372

Query: 286 ----------NKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
                      +  LHA  +   HP    RL+  A      +        + D    ++ 
Sbjct: 373 MSWGVEGMSVKRHLLHAAILTFTHPTTRERLEFFAAPHEWFLS-----DVECDEATKLEE 427

Query: 335 LYSQDECKQNIL 346
             S  E  +++L
Sbjct: 428 NKSGTEILRDLL 439


>gi|297195328|ref|ZP_06912726.1| ribosomal pseudouridine synthase [Streptomyces pristinaespiralis
           ATCC 25486]
 gi|197719590|gb|EDY63498.1| ribosomal pseudouridine synthase [Streptomyces pristinaespiralis
           ATCC 25486]
          Length = 314

 Score =  122 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 96/252 (38%), Gaps = 10/252 (3%)

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
           + +  ++ G+ V     + A       + +        +     +  +++ D  I + +K
Sbjct: 53  RVDAMVREGRFVDAEGPVTADESYTAGRDLWFHRDFPAEERVPFEIGVVHRDEHIVIADK 112

Query: 114 PAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           P  ++    GS +       ++  +D    +P   HRLD+ T+G+++             
Sbjct: 113 PHFLATMPRGSHVRETALARMRRGLDLPSLQP--AHRLDRLTAGLVLFVVRPGDRGAYQT 170

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            FR R ++K Y ++    P      +A     +S I  +   +    E G   + S  ++
Sbjct: 171 MFRDRLVRKEYEAVAPYDPA-----VALPRTVRSRIVKERGVLTAVEEPGEPNSESRIEL 225

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++          + P TGRTHQLRVH   +G PI+ D  Y               L L A
Sbjct: 226 LEVR-DGLGRYRLLPATGRTHQLRVHMNALGLPILHDPLYPVVLPDG-PDDYARPLQLLA 283

Query: 293 RYMDLPHPEGGR 304
           R ++   P  G 
Sbjct: 284 RALEFTDPVTGE 295


>gi|116669183|ref|YP_830116.1| pseudouridine synthase [Arthrobacter sp. FB24]
 gi|116609292|gb|ABK02016.1| pseudouridine synthase [Arthrobacter sp. FB24]
          Length = 314

 Score =  122 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 97/257 (37%), Gaps = 11/257 (4%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPA 115
           +R  +G++V    V       +++   +     L   +   ++  +L++D  I V +KP 
Sbjct: 45  DRFDAGEIVGEGGVPLDRLTRLEDHTFIWYYRTLPPETRLPVELSILHQDDHILVVDKPH 104

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +    G G        ++             HRLD+ T+GIL+++            F 
Sbjct: 105 FLPTTPG-GTYIQESALVRLRNQLDLPDLIPMHRLDRMTAGILLLSTNPETRGKYQVLFE 163

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R++QK Y  +    P      +   ++ ++ +     +++ +   G   A +  ++   
Sbjct: 164 KRQVQKEYECVSAAEPAAGYPAVGFPVVVRNRMTKSRSYLLAEVVDGEPNAETRIELTKT 223

Query: 236 FAQKFC--------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           F                ++PH+G+THQLRVH   +G  IV D  Y               
Sbjct: 224 FDAGTHASEPARRGLYRLEPHSGKTHQLRVHMASLGLGIVNDAFY-PELLDKAPDDYTRP 282

Query: 288 LYLHARYMDLPHPEGGR 304
           L L AR +    P  G+
Sbjct: 283 LQLLARGIRFIDPITGQ 299


>gi|104782764|ref|YP_609262.1| pseudouridylate synthase [Pseudomonas entomophila L48]
 gi|95111751|emb|CAK16475.1| putative pseudouridylate synthase [Pseudomonas entomophila L48]
          Length = 294

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 57/294 (19%), Positives = 108/294 (36%), Gaps = 31/294 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
             +H+  I           G+V   + R            V +P       H  +E    
Sbjct: 29  LCDHFKGIPREQWLDRFARGRVLDSEGRA---------ITVELPYRQGLRLHYFREVA-- 77

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
                  +    ++  +L+ D  + V +KP  + V   +G         +          
Sbjct: 78  ------NEKPIPVQEEILHVDEHLVVADKPHFLPVTP-TGEYVEQTLLRRLIRRLDNPHL 130

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HR+D+ T+G+++ +            F  RRI K Y ++   +P++        L+ 
Sbjct: 131 VPLHRIDRHTAGLVLFSANPQTRGAYQCLFPERRIDKHYQAIAAAMPQHMF-----PLVH 185

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +S +            +GA+ + +H  V++   + + +  + P TG+THQLRVH   +G 
Sbjct: 186 RSRLVHGEPFFRMHEVEGADNSETHACVLEKQGELWRYG-LSPVTGKTHQLRVHMASLGA 244

Query: 265 PIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHM 315
            I  D  Y   AN + ++T P++    L A  +    P  G  +   + L    
Sbjct: 245 AICNDPFYPQLANEQDDYTRPLK----LLAHSLRFKDPLSGEQRYFESRLALDW 294


>gi|255066777|ref|ZP_05318632.1| RNA pseudouridine synthase [Neisseria sicca ATCC 29256]
 gi|255048852|gb|EET44316.1| RNA pseudouridine synthase [Neisseria sicca ATCC 29256]
          Length = 309

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 50/262 (19%), Positives = 113/262 (43%), Gaps = 16/262 (6%)

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKIL---DSSVNLTKHSDFLKSILLYEDSKIYVF 111
           +  R+ SG VV         + + +  K +     + + ++     +  +L+ D  + V 
Sbjct: 48  WRRRLNSGFVVDADGAPFDEHTLFEPGKTMFYYRETSSDSEPVIPFEEKILHIDDHLIVV 107

Query: 112 NKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRL-----THRLDQETSGILVVARTRA 165
           +KP  + V   G  +   +   L+  +  + Q   +      HRLD++T+G+++++   A
Sbjct: 108 DKPHFLPVIPSGRFLRETLLTRLRLRLRPELQHLNVADITPVHRLDKDTAGVMLLSHNPA 167

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
             +     F+ + ++K Y ++       + + +    +    + G+     ++ E G   
Sbjct: 168 TRRDYQTMFQEKSVRKTYHAVA----PTRTDLVYPLDVVSRMVRGERFFTTQETE-GEPN 222

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           A +  ++++   + F    + PHTG+ HQLRVH + +G P++ D  Y            +
Sbjct: 223 AHTTVELLENRGE-FSLYRLTPHTGKKHQLRVHMMRLGMPLLNDALY-PTPLAVGDEDYE 280

Query: 286 NKLYLHARYMDLPHPEGGRLQI 307
             L L A+ ++   P  G+ +I
Sbjct: 281 KPLKLLAKRIEFTDPIRGQERI 302


>gi|313894448|ref|ZP_07828013.1| RNA pseudouridine synthase [Veillonella sp. oral taxon 158 str.
           F0412]
 gi|313441272|gb|EFR59699.1| RNA pseudouridine synthase [Veillonella sp. oral taxon 158 str.
           F0412]
          Length = 261

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 50/269 (18%), Positives = 99/269 (36%), Gaps = 63/269 (23%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--QKPRL 146
            +      +   +LYED  + + +KPAG++V   S     +   +  +    G  +K R 
Sbjct: 8   KIDHELIEMNLHILYEDDDLLIVDKPAGVTV--NSKDQVSLVNGVAYYFKENGIKRKVRF 65

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            +RLD++T+G + +A++  A     +       +K Y + V GI +  ++ +   + + +
Sbjct: 66  LNRLDRDTTGCIAIAKSGLAQSLYQQQMDDNTFEKWYMATVEGIVEADEDSLVLSMERSA 125

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCF------------------------------ 236
                   +  +         + + V+                                 
Sbjct: 126 D------GIHYEVNPKGKETRTDYSVLCRHQSQPVDNSVNKSKNSVDIASKNVDIELSDV 179

Query: 237 ---------------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
                             +  + ++ +TG+THQ+RV   H+G P+VGD  Y A   G   
Sbjct: 180 DKSGQNVDKSVYNSQECGYTEVLVRLYTGKTHQIRVAFSHIGHPLVGDTLYGAQPTGQ-- 237

Query: 282 SPIQNKLYLHARYMDLPHPEGG-RLQITA 309
            P Q +    A+ +   H   G R+ +TA
Sbjct: 238 -PFQLR----AQKVVFTHMRTGERITVTA 261


>gi|289666985|ref|ZP_06488060.1| putative pseudouridylate synthase [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 296

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 58/283 (20%), Positives = 114/283 (40%), Gaps = 29/283 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
                +P I     +     G VR  + + +  +   + G  +R           + ++ 
Sbjct: 29  ALCACFPAIAAERWRDRFARGLVRDANDQALALSAPYRVGADIRYF-------REVADEP 81

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
           ++                ++Y D+++ V  KP  + V   G+ +   +   L   +D+  
Sbjct: 82  VIPY-----------VETVVYADAQLVVACKPHFLPVAPAGAYVRETLLTRLVRRLDNPA 130

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
             P   HR+D+ET+G+++ +   A        FR RRI+K Y ++   +P+ +   +   
Sbjct: 131 LVP--LHRIDRETAGLVLFSANPATRGIYQALFRQRRIRKHYLAVAPPLPQLRFPHVHRS 188

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           LL+     G+    +++   G   + +  +V+   A  + +  ++P TGR HQLRVH   
Sbjct: 189 LLEP----GEPFFRMREGV-GEPNSETVIEVVARNADTWTY-RLEPVTGRKHQLRVHMAA 242

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +G PI+ +  Y          P +  L L A  +    P  G 
Sbjct: 243 LGAPILHERFYPELEAQRPDDP-ERPLQLFAHTLAFDDPLTGE 284


>gi|50085467|ref|YP_046977.1| putative pseudouridylate synthase [Acinetobacter sp. ADP1]
 gi|49531443|emb|CAG69155.1| putative pseudouridylate synthase [Acinetobacter sp. ADP1]
          Length = 304

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 54/282 (19%), Positives = 103/282 (36%), Gaps = 30/282 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +   H+PHI+    Q+    G V       +  N+  Q+   +     +    H+  E  
Sbjct: 36  FLCRHFPHISASEWQQRFNDGLVFDAQGHLLDLNSPYQANTHIFYYRFLAHEIHVPFEH- 94

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             +L+E+  + V +KP  +++       Y  +  L       G 
Sbjct: 95  -----------------SILFENHDLLVVDKPHFLTISPTG--KYVQETLLVRLKQQTGN 135

Query: 143 K-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIAN 200
           +     HRLD+ET+G+++  +   +       F  R + KIY ++    P     + +  
Sbjct: 136 EDLTPIHRLDRETAGVVLFCKRPESRGIYQTLFAKREVHKIYHAIAAYNPLITFPQTLRL 195

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K     G+  + ++ N  G   + +  + +    Q++    + P TG+ HQLR+H  
Sbjct: 196 CLEK-----GNPFYTMQVNPNGQVNSETRIECL-AHNQQWAKYRLSPSTGKQHQLRLHLS 249

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            +  PI  D  Y    +          L L A+ +    P  
Sbjct: 250 FLNIPIKNDPFY-PVVEHKADDDFSAPLQLLAKELSFFDPIT 290


>gi|240014440|ref|ZP_04721353.1| Pseudouridine synthase [Neisseria gonorrhoeae DGI18]
 gi|240016885|ref|ZP_04723425.1| Pseudouridine synthase [Neisseria gonorrhoeae FA6140]
 gi|240120962|ref|ZP_04733924.1| Pseudouridine synthase [Neisseria gonorrhoeae PID24-1]
          Length = 177

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 51/172 (29%), Positives = 73/172 (42%), Gaps = 10/172 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV    G                 +K  L HRLD++  GIL+ 
Sbjct: 4   ILFRHQDFVAINKPQGISVHRSGGEVSLTATLAAQL---GVEKVWLLHRLDKQAGGILLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I   + K          + K   
Sbjct: 61  ALNPQSAAVLAAQFAERKMKKSYLALSDRKPSKKQGWIKGGMEK------SRRGMWKLTR 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              N A++ F  I   ++K     ++PHTG+THQLRV    +G  I GD  Y
Sbjct: 115 NMENIAVTRFFSI-RISEKMRLFILEPHTGKTHQLRVVMKSLGSSIFGDSLY 165


>gi|84370153|ref|NP_001033650.1| RNA pseudouridylate synthase domain-containing protein 3 [Bos
           taurus]
 gi|122137054|sp|Q2TBK7|RUSD3_BOVIN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 3
 gi|83638710|gb|AAI10001.1| RNA pseudouridylate synthase domain containing 3 [Bos taurus]
          Length = 344

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 61/286 (21%), Positives = 107/286 (37%), Gaps = 46/286 (16%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQ 142
             + +  +  D L++ ++     +   NKP G+ V G  G    +     L   +    Q
Sbjct: 60  PGTFSREELVDVLRAAVVDSKGPLVTLNKPQGLPVTGKPGELTLLSVLPELSRSLGLGEQ 119

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKECI 198
           + ++     +E SG+++++     A  L +    S R R+    Y ++  GIP   +  I
Sbjct: 120 EVQVVRASGKEASGLVLLSSCSQTASRLQKFFTHSRRARKPTATYCAVTDGIPVTSEGKI 179

Query: 199 ANWLLKKSHIGGDYVHVVKQNE------KGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              L K  HI G  + V  Q+       +G    +SHF+V+         +++QP T   
Sbjct: 180 QAAL-KLEHIDGVNLVVPVQSPSRKDIMEGVKRTLSHFRVVAT-GSGCALVQLQPLTVFP 237

Query: 253 HQLRVHALHMGCPIVGDHKYCANF------------------KGNFTSPIQNKLYLHARY 294
            QL+ H     CP++GDH Y A                    +      +  +L L A  
Sbjct: 238 SQLQAHMALQLCPVLGDHTYSARVGTVLGQRFLLPVESTKPQRQVLDEALLGRLCLTASQ 297

Query: 295 MDLPH--------------PEGGRLQITAPLPAHMVKTWDSLGFKY 326
                              P    +++ APLP++  +T   LG  Y
Sbjct: 298 AARLPLHLHLHCLRLPGARPRDPPIELLAPLPSYFSRTLQCLGLHY 343


>gi|149195656|ref|ZP_01872713.1| tRNA pseudouridine synthase A [Lentisphaera araneosa HTCC2155]
 gi|149141118|gb|EDM29514.1| tRNA pseudouridine synthase A [Lentisphaera araneosa HTCC2155]
          Length = 231

 Score =  121 bits (304), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 59/217 (27%), Positives = 89/217 (41%), Gaps = 19/217 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++ E     + NK  G +    SG     +  L   +     +    HRLD+ TSG+L
Sbjct: 5   PEVIEEFEDFILVNKKPGENFHSESG-----EEGLFHQLKEHYGELYPVHRLDKVTSGLL 59

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR   + Q L + F  ++I+K Y ++    PK K+  +   + K    G       K 
Sbjct: 60  LMARNLQSCQELNQLFEAQKIEKFYLAISDRKPKKKQGWVIGDMEKSRRGG------WKL 113

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            E   N A++ F       Q      ++P TG+THQLRV    +G PI GD  Y      
Sbjct: 114 CESRKNPAVTQFFS-YSIGQGKRVYLLRPRTGKTHQLRVAMKAIGAPICGDPNYYP---- 168

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
                 + + YLHA  +     E    Q T  L  HM
Sbjct: 169 GLIKGHEERCYLHAYVIRFTLKE-REYQFT--LKPHM 202


>gi|121605828|ref|YP_983157.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120594797|gb|ABM38236.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
          Length = 302

 Score =  121 bits (304), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/287 (19%), Positives = 102/287 (35%), Gaps = 37/287 (12%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV-----VRIPPVINALNHII 78
           +    +P I     Q  L               +R+ +G V     V + P      H+ 
Sbjct: 34  FLVERFPAITR---QTWL---------------DRMAAGLVADEFGVAVTPERPYRGHM- 74

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              ++        +     ++ +L++D  + V +KP  + V       Y  +  L    +
Sbjct: 75  ---RLYYYRALPVEPRIPFEAAVLFQDEHLVVADKPHFLPVTPSGH--YLQETLLVRLKN 129

Query: 139 SKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             G       HR+D+ET+G+++              FR   + K Y ++    P      
Sbjct: 130 QLGLDSLIPIHRIDRETAGLVLFCVQPGERDAYQALFRRHEVVKHYEAVARWRPD----- 184

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   L +K+ I  D     ++   G   + +   +++   Q+     + P TG+ HQLRV
Sbjct: 185 LRFPLQRKTRIVEDEPFFRQREVPGEPNSETLIDLLEIRGQRA-LYALSPVTGKKHQLRV 243

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           H   +G PI  D  Y    +          L L AR +    P  G+
Sbjct: 244 HMNALGMPICNDRMYPP-VEPTPEDDYALPLQLLARSIAFADPLTGQ 289


>gi|254776711|ref|ZP_05218227.1| RNA pseudouridine synthase family protein [Mycobacterium avium
           subsp. avium ATCC 25291]
          Length = 287

 Score =  121 bits (304), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 44/214 (20%), Positives = 76/214 (35%), Gaps = 11/214 (5%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +        +L+ D  I V +KP  ++     G        ++   +    +    HR
Sbjct: 69  PDEVVVPFDLPVLHRDDDIVVVDKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHR 127

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+L+    R         F    + K Y +     P      +    +    I 
Sbjct: 128 LDRLTAGVLLFTAQREVRGAYQTLFSRGLVDKTYLARAAVDPA-----LVFPRVLAGRIV 182

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                +    E G   A++  +++           ++P TGRTHQLR+    +G PI+GD
Sbjct: 183 KHRGRMQAVCEPGPPNALTEVELLSPDG----LYRLRPRTGRTHQLRLQMASLGIPIIGD 238

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             Y  N            L L A+ ++   P  G
Sbjct: 239 PLY-PNIIDVPADDFSTPLQLLAQRIEFDDPRTG 271


>gi|240128906|ref|ZP_04741567.1| Pseudouridine synthase [Neisseria gonorrhoeae SK-93-1035]
 gi|268687291|ref|ZP_06154153.1| conserved hypothetical protein [Neisseria gonorrhoeae SK-93-1035]
 gi|268627575|gb|EEZ59975.1| conserved hypothetical protein [Neisseria gonorrhoeae SK-93-1035]
          Length = 177

 Score =  121 bits (304), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 51/172 (29%), Positives = 73/172 (42%), Gaps = 10/172 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV    G                 +K  L HRLD++  GIL+ 
Sbjct: 4   ILFRYQDFVAINKPQGISVHRSGGEVSLTATLAAQL---GVEKVWLLHRLDKQAGGILLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I   + K          + K   
Sbjct: 61  ALNPQSAAVLAAQFAERKMKKTYLALSDRKPSKKQGWIKGGMEK------SRRGMWKLTR 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              N A++ F  I   ++K     ++PHTG+THQLRV    +G  I GD  Y
Sbjct: 115 NMENIAVTRFFSI-RISEKMRLFILEPHTGKTHQLRVVMKSLGSSIFGDSLY 165


>gi|72386765|ref|XP_843807.1| hypothetical protein [Trypanosoma brucei TREU927]
 gi|62359821|gb|AAX80250.1| hypothetical protein, conserved [Trypanosoma brucei]
 gi|70800339|gb|AAZ10248.1| hypothetical protein, conserved [Trypanosoma brucei brucei strain
           927/4 GUTat10.1]
          Length = 828

 Score =  121 bits (304), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 62/280 (22%), Positives = 104/280 (37%), Gaps = 47/280 (16%)

Query: 64  VVRIPPVIN--ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-- 119
           VVR+PP          ++    L S + +          ++YED  + V NKP  ++   
Sbjct: 572 VVRLPPEHECVRAAETMRAGDPLKSPLPIFP--------VVYEDDDLLVINKPPHVATSR 623

Query: 120 ------QGGSGIAYHIDGFLKSWVDSKGQKPRL-----THRLDQETSGILVVARTRAAAQ 168
                 Q     A  I     +         R+      HRLD ETSG L++A++  AA 
Sbjct: 624 HALSCSQLCDDKATDIVSLQLTCKKRGDVMRRVFRQGQVHRLDTETSGCLIMAKSDVAAS 683

Query: 169 HLTESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            L           +  KIY +L   +  N      N +L+                    
Sbjct: 684 SLRHQMGTSAAYSQSSKIYLALCAVVESNLTNIPLNGVLRDPADAK-------------- 729

Query: 225 YAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
              + ++++  + + +   +E +   G+ HQ+R H   +G PI+ D ++         SP
Sbjct: 730 -ITTKYRIVHFYKRFRVALVEARIQQGKKHQIRRHLAAVGLPILQDVEHGG---AACCSP 785

Query: 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           +  ++ LHA  + + HP     L   APLP  M      L
Sbjct: 786 LLQRVALHASSVTVVHPRTAEVLTCVAPLPEDMRSAIFRL 825


>gi|118464649|ref|YP_883417.1| RNA pseudouridine synthase family protein [Mycobacterium avium 104]
 gi|118165936|gb|ABK66833.1| RNA pseudouridine synthase family protein [Mycobacterium avium 104]
          Length = 287

 Score =  121 bits (304), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 44/214 (20%), Positives = 76/214 (35%), Gaps = 11/214 (5%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +        +L+ D  I V +KP  ++     G        ++   +    +    HR
Sbjct: 69  PDEVVVPFDLPVLHRDDDIVVVDKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHR 127

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+L+    R         F    + K Y +     P      +    +    I 
Sbjct: 128 LDRLTAGVLLFTARREVRGAYQTLFSRGLVDKTYLARAAVDPA-----LVFPRVLAGRIV 182

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                +    E G   A++  +++           ++P TGRTHQLR+    +G PI+GD
Sbjct: 183 KHRGRMQAVCEPGPPNALTEVELLSPDG----LYRLRPRTGRTHQLRLQMASLGIPIIGD 238

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             Y  N            L L A+ ++   P  G
Sbjct: 239 PLY-PNMIDVPADDFSTPLQLLAQRIEFDDPRTG 271


>gi|219113125|ref|XP_002186146.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|209582996|gb|ACI65616.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 175

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 43/177 (24%), Positives = 80/177 (45%), Gaps = 9/177 (5%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP--RLTHRLDQETSGIL 158
           +++ED  I V +KP+G+           +   +              + HRL  +TSG++
Sbjct: 3   IVHEDEHIIVVDKPSGVLTVPSDKNVPSLAQAVFDHCQPTEVTLDQMVVHRLGMDTSGLI 62

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+A+T    + +   FR R+I + Y +LV G        I+  L++      ++   +++
Sbjct: 63  VLAKTMDTVRQMNALFRTRKITRQYEALVVGHLPQHGGLISLPLMRDY----EHPPYMRK 118

Query: 219 NEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +    +++ ++V+   D        + +   +GRTHQL VH    G PIVGD  Y
Sbjct: 119 LLEMPKESLTKYEVVNREDMDGTPVSRVALTSISGRTHQLNVHLAAFGHPIVGDSVY 175


>gi|296089768|emb|CBI39587.3| unnamed protein product [Vitis vinifera]
          Length = 274

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 101/262 (38%), Gaps = 44/262 (16%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK-SWVDSKGQKPRLTHRLDQETSG 156
           +S +L+ED  +   NKP G+       I   +   L  S      +   L +RLD++TSG
Sbjct: 14  RSDILFEDQWLMAVNKPQGVYC---ETILLSVSRMLDDSDGHDSCRSLHLANRLDRDTSG 70

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++V+ ++   A  L ++F  R++ K Y +L  G     ++        +S  G   V+  
Sbjct: 71  VMVITKSHQVAAKLMKAFSDRKVTKTYLALCIGAAPTWEKITIKSGHGRSKFGAWRVYAA 130

Query: 217 KQNEKGANYA------ISHFKVIDCFAQKFC----------------------------- 241
               +    A      ++ F+V+    Q                                
Sbjct: 131 SDVGRALPNAPAIKDMVTSFEVLSVNGQGNVKELPESRKADETVLVVEERSVIDSNARQD 190

Query: 242 --WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              +   P +GRTHQ+R+H  ++G  I GD KY    +      I +   LHA  +   H
Sbjct: 191 EILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVHEWK--GKIYDGHELHAESLSFEH 248

Query: 300 PEGG-RLQITAPLPAHMVKTWD 320
           P  G  +   APLP+  V+   
Sbjct: 249 PVTGVDVAFRAPLPSWAVQALQ 270


>gi|190346820|gb|EDK38997.2| hypothetical protein PGUG_03095 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 390

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 45/185 (24%), Positives = 83/185 (44%), Gaps = 7/185 (3%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSG 156
              ++Y+D  + V NKP+GI         Y+     +K+ +  +   P   HRLD+ TSG
Sbjct: 101 PISIIYQDPSLIVVNKPSGIPTHPSGNFRYNSVTEIVKAQLHLESIFP--CHRLDKATSG 158

Query: 157 ILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           IL++A T AA  ++ +  + R+ ++K Y + V G     +    + +   +   G Y+  
Sbjct: 159 ILMLATTSAACSNIQKQLQERKDVKKEYIARVKGKFPPSQLVHQDPVFLLNSTAG-YIMP 217

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +     ++   +  K           +  +PH+G+ HQ+R+H  ++G PIV D  Y   
Sbjct: 218 GRYVSIDSSTTFTRLKY--NSELDESIVSCEPHSGKMHQIRIHLRNLGFPIVNDKLYNPG 275

Query: 276 FKGNF 280
                
Sbjct: 276 ESDKL 280


>gi|212696244|ref|ZP_03304372.1| hypothetical protein ANHYDRO_00780 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676873|gb|EEB36480.1| hypothetical protein ANHYDRO_00780 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 195

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 43/205 (20%), Positives = 93/205 (45%), Gaps = 22/205 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  V+   +  ++ N R DR+ + +  +     +QK +R    +++ KR K ++ ++   
Sbjct: 1   MIEVK---INENDSNQRFDRFLRKYLKNAPLSIIQKNIRKKNFKINDKRAKKDDLVKKDD 57

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           +V++       +  +++     S+ NL          ++YED  I + +K +G+     S
Sbjct: 58  IVKMYIKDEDYHKWVRKDDFKASNFNLD---------IIYEDENIIIIDKKSGVLSHAAS 108

Query: 124 GIAYHID--GFLKSWVDSKGQ--------KPRLTHRLDQETSGILVVARTRAAAQHLTES 173
              Y  +    + S++    +        +P + +RLD+ T+G+++ A+   + + L E+
Sbjct: 109 SSDYGKNLVDQMTSYLYKTNKVNSRDLTFRPSIVNRLDRNTAGLIIGAKNAKSLRALNEA 168

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECI 198
            R  +I K Y +LV G  K     I
Sbjct: 169 IRQGKIYKYYLTLVEGEIKKTLLLI 193


>gi|41409520|ref|NP_962356.1| hypothetical protein MAP3422c [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41398351|gb|AAS05972.1| hypothetical protein MAP_3422c [Mycobacterium avium subsp.
           paratuberculosis K-10]
          Length = 290

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 44/214 (20%), Positives = 76/214 (35%), Gaps = 11/214 (5%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +        +L+ D  I V +KP  ++     G        ++   +    +    HR
Sbjct: 72  PDEVVVPFDLPVLHRDDDIVVVDKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHR 130

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+L+    R         F    + K Y +     P      +    +    I 
Sbjct: 131 LDRLTAGVLLFTARREVRGAYQTLFSRGLVDKTYLARAAVDPA-----LVFPRVLAGRIV 185

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                +    E G   A++  +++           ++P TGRTHQLR+    +G PI+GD
Sbjct: 186 KHRGRMQAVCEPGPPNALTEVELLSPDG----LYRLRPRTGRTHQLRLQMASLGIPIIGD 241

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             Y  N            L L A+ ++   P  G
Sbjct: 242 PLY-PNIIDVPADDFSTPLQLLAQRIEFDDPRTG 274


>gi|71033777|ref|XP_766530.1| hypothetical protein [Theileria parva strain Muguga]
 gi|68353487|gb|EAN34247.1| hypothetical protein, conserved [Theileria parva]
          Length = 436

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 50/290 (17%), Positives = 112/290 (38%), Gaps = 31/290 (10%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           + V    V+       L +  K+ +       +   +    ++V          +Q+G+ 
Sbjct: 51  SNVYKTFVKERWLGKPLQKVLKDEFAAFTPDYINFAINKNNIKV---------ILQNGEE 101

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           +         + +   ++I+  ++     +      +++E+ +  V +KP  I V     
Sbjct: 102 LDNTSENVLDHILKPNERIIHEAIVHEPVALNSNIPVVWENEEYIVVSKPTSIPVYQTGT 161

Query: 125 IAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             Y+  ++   +     +G K    HR+D+  SG++  A++  +A  L+++ R   ++K+
Sbjct: 162 YKYNSLMEIMRRELPSCRGIKLFTIHRIDKLVSGLVAFAKSANSASELSQAIRDNEVKKV 221

Query: 183 YWSLVWGIPKN-------KKECIANWLLKKSHIGGDYVHVVKQNE------------KGA 223
           Y + V G   +            ++  L+       Y+ V+ + E            +  
Sbjct: 222 YIARVNGDFSHLLNNSHRDSGDKSDDSLENVFESVGYMRVISKKEGRYEFVGENAEDESY 281

Query: 224 NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +++ FK I          +   P TGRTHQ+R +  ++G PI  D  Y
Sbjct: 282 KPSVTRFKFIKYNKDLDESLVLCSPITGRTHQIRANLRYLGHPISNDPWY 331


>gi|328905742|gb|EGG25518.1| RNA pseudouridine synthase [Propionibacterium sp. P08]
          Length = 322

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 62/265 (23%), Positives = 98/265 (36%), Gaps = 9/265 (3%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-L 101
              +RV   RV  +  +  G+ V         +     Q  +    +L   +     I +
Sbjct: 48  EKLLRVGGPRV--DEMLDEGRFVDDAGRAFRQDSPFTPQTFVFFHRDLPTETPVPAGIGI 105

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY D +I V +KP  +S     G        ++        +  + HRLD+ T+G+L++ 
Sbjct: 106 LYSDERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTMAHRLDRVTAGVLLLT 164

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE---CIANWLLKKSHIGGDYVHVVKQ 218
           R R   +   E F  R + K Y  +   +     E      N    +S I  +   +  +
Sbjct: 165 RERQWRRPYQELFERREVVKKYRLVAPAVHDPAGEGAVVTNNGWQVRSRIVKERGILQAR 224

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              G   A++   V+          E  P TGRTHQ+R+H   +G PIV D  Y     G
Sbjct: 225 EVPGEPNAVTDI-VLVSEHGGLGLYEASPRTGRTHQIRLHMQRLGAPIVNDPFY-PIVLG 282

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGG 303
                  + L L A  M    P  G
Sbjct: 283 TQIDDFTHPLQLQAWQMGFTDPVSG 307


>gi|328857444|gb|EGG06560.1| hypothetical protein MELLADRAFT_116466 [Melampsora larici-populina
           98AG31]
          Length = 486

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 55/280 (19%), Positives = 107/280 (38%), Gaps = 56/280 (20%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +  + +   +     + + SG ++++ K +  +  I++G ++      +    I   
Sbjct: 52  IDVF-SSDFRDRSPEYYAQAVASGVIKINGKTITQDLIIRNGDLITNTLHRHEPPVI--- 107

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDS--KIYVFNKPAGISVQGGSGIAYHIDGFLKSW-V 137
                               +L+ D    + V  KP  + +       Y+ +  L     
Sbjct: 108 ---------------GDPVRILHRDDVKGLLVVEKPGSMPIHPTG--RYNYNTLLSILKF 150

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF-RMRRIQKIYWSLVWGIPKNKKE 196
           D        ++RLD+ TSG+++ A T  A++ L+  F +   ++K Y +   G   +++ 
Sbjct: 151 DYDLPLVHTSNRLDRLTSGVMICALTIEASRGLSAYFGQEGAVKKEYIARCRGNFPDEEI 210

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM-QPHTGRTHQL 255
                LL      G  ++VV    K                       + +P TGR+HQ+
Sbjct: 211 VCEEPLLTIDRQVG--LNVVHPEGK--------------------LPLLGRPITGRSHQI 248

Query: 256 RVHALHMGCPIVGDHKYCANFK--------GNFTSPIQNK 287
           RVH   +G PI+ D  YC+N          G F+SP   +
Sbjct: 249 RVHLQFLGHPILNDVIYCSNVAWGPEGGKGGIFSSPTDQR 288


>gi|261326897|emb|CBH09870.1| hypothetical protein, conserved [Trypanosoma brucei gambiense
           DAL972]
          Length = 828

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 58/277 (20%), Positives = 103/277 (37%), Gaps = 39/277 (14%)

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV----- 119
           VR+   +   +  ++  + + +   L          ++YED  + V NKP  ++      
Sbjct: 569 VRVAVRLPPEHECVRAAETMRAGDPLKSPLPIFP--VVYEDDDLLVINKPPHVATSRHAL 626

Query: 120 ---QGGSGIAYHIDGFLKSWVDSKGQKPRL-----THRLDQETSGILVVARTRAAAQHLT 171
              Q     A  I     +         R+      HRLD ETSG L++A++  AA  L 
Sbjct: 627 SCSQLCDDKATDIVSLQLTCKKRGDVMRRVFRQGQVHRLDTETSGCLIMAKSDVAASSLR 686

Query: 172 ESF----RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
                     +  KIY +L   +  N      N +L+                       
Sbjct: 687 HQMGTSAAYSQSSKIYLALCAVVESNLTNIPLNGVLRDPADAK---------------IT 731

Query: 228 SHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           + ++++  + + +   +E +   G+ HQ+R H   +G PI+ D ++         SP+  
Sbjct: 732 TKYRIVHFYKRFRVALVEARIQQGKKHQIRRHLAAVGLPILQDVEHGG---AACCSPLLQ 788

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
           ++ LHA  + + HP     L   APLP  M      L
Sbjct: 789 RVALHASSVTVVHPRTAEVLTCVAPLPEDMRSAIFRL 825


>gi|170727493|ref|YP_001761519.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169812840|gb|ACA87424.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 283

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 54/302 (17%), Positives = 117/302 (38%), Gaps = 50/302 (16%)

Query: 25  FKNHYPHINFVNLQKILRSGQV----RVDKKRVKFNNR-IQSGQVVRIPPVINALNHIIK 79
             N    ++   +++ +  G V    + +  R++   + ++ G  + +      L H I 
Sbjct: 25  LANK-SGLSKQQIKQAMTKGAVWHTRKHNTSRLRRGKKSLKVGDELHLYYNQEVLEHQID 83

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + +                  L+ +  +  ++ KP G+  QG     +           +
Sbjct: 84  DAE------------------LIADMGQYSLWYKPYGMLCQGSKWGDHTTINRYSETHLT 125

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             +   + HRLD+  +G++++  +++    L + F +R + K Y  +V G          
Sbjct: 126 PDRPAFIVHRLDRAATGLVLIGHSKSITAALAKLFELRELDKYYQVIVEG---------- 175

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVH 258
                + + G + V  V  +      A SH K+++  A Q    ++++  +GR HQ+R+H
Sbjct: 176 -----RFNSGREEVVTVDSDVDN-KSACSHAKLLEYDAKQNRSLVQVKIDSGRKHQIRIH 229

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVK 317
              +G P+VGD  +      +        L L + Y+  P P  G + +    LP  +  
Sbjct: 230 MASLGHPVVGDRLHGIASGSDIN------LQLTSCYLKFPCPVTGEINEFE--LPERLRP 281

Query: 318 TW 319
             
Sbjct: 282 KL 283


>gi|163838844|ref|YP_001623249.1| ribosomal pseudouridine synthase [Renibacterium salmoninarum ATCC
           33209]
 gi|162952320|gb|ABY21835.1| ribosomal pseudouridine synthase [Renibacterium salmoninarum ATCC
           33209]
          Length = 304

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/251 (22%), Positives = 99/251 (39%), Gaps = 11/251 (4%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPA 115
           +R + G+V  +  V+      + E   L     L   +   ++  +L++D  + V +KP 
Sbjct: 46  DRFERGEVQGLGGVVITPQTPLAEHTFLWYYRELPVENRLPVELDVLHQDDHLVVIDKPH 105

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            +    G G+       ++  V          HRLD+ T+GIL+ A            F 
Sbjct: 106 FLPTTPG-GMYVAESALVRLRVLLDLPDLVPIHRLDRMTAGILLFAVNPQTRGKYQLLFE 164

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ---NEKGANYAISHFKV 232
            R+++K Y ++        +E +   L  +S +     +++ Q    E  A   +S  + 
Sbjct: 165 CRQVRKHYEAVAS-----VREDLQLPLTIRSRLYKSRSYLLTQELAGEPNAETRVSLERS 219

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                       ++PH+G+THQLRVH   +G  I+ D  Y            Q  L L A
Sbjct: 220 WPSADGPRGLYRLEPHSGKTHQLRVHMAALGMGILNDPFY-PVLSEQAPDDYQKPLQLLA 278

Query: 293 RYMDLPHPEGG 303
           R ++   P  G
Sbjct: 279 RSLEFTDPISG 289


>gi|320011705|gb|ADW06555.1| pseudouridine synthase [Streptomyces flavogriseus ATCC 33331]
          Length = 312

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 47/215 (21%), Positives = 84/215 (39%), Gaps = 9/215 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            +        +++ D  + + +KP  ++    G  I   +   L+  +   G +P   HR
Sbjct: 90  PERPVPFPVGVVHRDDHLVIADKPHFLATTPRGRHITETLVARLRDTLGLPGLQP--AHR 147

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+++              FR R ++K Y ++    P      +      +S I 
Sbjct: 148 LDRLTAGLVLCVVRAGDRGAYQTLFRDRLVRKEYEAVAPYDP-----GLVRPRTVRSRIV 202

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +   +  + E G   + S  ++++          + P TGRTHQLRVH   +G P+V D
Sbjct: 203 KERGVIAAREEPGPANSESRIELLEHRG-ALGRYRLLPATGRTHQLRVHMNALGLPLVND 261

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             Y               L L AR ++   P  G 
Sbjct: 262 PVYPVVEPDPEREDFGRPLQLLARVLEFTDPVTGE 296


>gi|212716478|ref|ZP_03324606.1| hypothetical protein BIFCAT_01402 [Bifidobacterium catenulatum DSM
           16992]
 gi|212660599|gb|EEB21174.1| hypothetical protein BIFCAT_01402 [Bifidobacterium catenulatum DSM
           16992]
          Length = 250

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 87/237 (36%), Gaps = 16/237 (6%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           L +     +  +LYE+  I V +KP  ++     G+ Y     ++             HR
Sbjct: 14  LEEPHIPFECEVLYENDAIIVVDKPHFLATTP-RGMWYRETALIRLREQYGEPDIVPAHR 72

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIAN------- 200
           LD+ T+GI+V  R           F+ R+  K Y  L    P+       I         
Sbjct: 73  LDRLTAGIVVFVRKPELRGAYQMLFQNRKTIKTYECLAPLAPEQHPQYGTIVRIDRHQPF 132

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFK----VIDCFAQKFCWLEMQPHTGRTHQLR 256
             ++ SHI  D   +          A +  +    V     + +    + P TG+THQLR
Sbjct: 133 PAIRASHICKDRGRLQAYEIPEIVNAQTLIERGNTVRCIDGKAYVNYVLHPKTGKTHQLR 192

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           VH   +G PI+GD  Y  N   +        L L AR +    P  G      + +P
Sbjct: 193 VHMNSLGLPILGDDFY-PNIVQHSYDDFSQPLELVARELHFDDPVTGEPRTFVSKVP 248


>gi|314959443|gb|EFT03545.1| RNA pseudouridine synthase [Propionibacterium acnes HL002PA1]
          Length = 281

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 60/261 (22%), Positives = 99/261 (37%), Gaps = 9/261 (3%)

Query: 47  RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYED 105
           R+  +RV  +  +  G+ V         +     Q  +    +L   +     I +LY D
Sbjct: 11  RIGGQRV--DEMLDEGRFVDESGRTFRRDSPFTPQTFVFFHRDLPTETPVPAGIGILYSD 68

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
            +I V +KP  +S     G        ++        +  + HRLD+ T+G+L++ R R 
Sbjct: 69  ERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHRLDRVTAGVLLLTRERK 127

Query: 166 AAQHLTESFRMRRIQKIY--WSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKG 222
             +   E F  R + K Y   + V   P  +      +    +S I  +   +  +   G
Sbjct: 128 WRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTATKSGWQVRSRIIKERGILQAREVPG 187

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
              A++   +I      +   E  P TGRTHQ+R+H   +G PIV D  Y          
Sbjct: 188 VPNAVTDIALIGEHG-GWGLYEASPRTGRTHQIRLHMQRLGAPIVNDPFY-PVVLDTPVD 245

Query: 283 PIQNKLYLHARYMDLPHPEGG 303
              + L L A  M    P  G
Sbjct: 246 DFTHPLQLQAWRMGFTDPVTG 266


>gi|325127991|gb|EGC50890.1| RNA pseudouridine synthase [Neisseria meningitidis N1568]
          Length = 307

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 43/217 (19%), Positives = 89/217 (41%), Gaps = 11/217 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
            +     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLKETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++            F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPDTRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + D  Y    +   +   +  L L A+ +    P  G
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSG 296


>gi|313886695|ref|ZP_07820405.1| RNA pseudouridine synthase [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|312923857|gb|EFR34656.1| RNA pseudouridine synthase [Porphyromonas asaccharolytica
           PR426713P-I]
          Length = 337

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 54/288 (18%), Positives = 108/288 (37%), Gaps = 35/288 (12%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV--INALNHIIKEQKILDS 86
           P ++   +++ LR+  V +       F+  + +G  + I  +    A+ H + E+     
Sbjct: 38  PDLSRTTVKQYLRNRCVLLAGVTTTQFDAPVTAGDTIEIYNIGTAEAVQHPLIEE----- 92

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWVD-SKGQK 143
                          LY D +  V +K  GI     GG+  +                +K
Sbjct: 93  ---------------LYRDEQFIVLHKRPGIPTISVGGASKSSLFQVVTHHLKKVDPNEK 137

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L +RLD++T GI++VAR R   Q L   +R   +   + +++ G        +     
Sbjct: 138 IFLLNRLDRDTEGIIIVARDRQLQQDLLAEWRSFVLSNSFEAVILGALDTSSGELTTLPT 197

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISH--FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           K    G +     + + + +  A     ++V+         +++   T R + +R     
Sbjct: 198 KDKKRGPNKRRTARSSTRDSKPATFRASYEVL-TTGPYITRVKLSLLT-RNNSIRSTLAS 255

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
           +G P++GDH        +    +   L L A  + + HP    ++Q T
Sbjct: 256 IGHPLLGDH----RASESIAPELSKYLALRATELTIFHPIRRQKMQFT 299


>gi|240047291|ref|YP_002960679.1| Ribosomal large subunit pseudouridine synthase [Mycoplasma
           conjunctivae HRC/581]
 gi|239984863|emb|CAT04854.1| Ribosomal large subunit pseudouridine synthase [Mycoplasma
           conjunctivae]
          Length = 284

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 66/293 (22%), Positives = 124/293 (42%), Gaps = 32/293 (10%)

Query: 11  VVENDEENMR-LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            V  ++ N R + +      P+ ++  ++K+ R  +V+++ K+ K N  +    ++ I  
Sbjct: 5   TVPENQ-NQRSILKLVSKLLPNYSYNQIEKLFRLQKVKINNKKAKKNQIVYKNDLIIIY- 62

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                    KE KI+   +NL      +K  +LYEDS I V  KP   ++        + 
Sbjct: 63  --------TKEAKIVKPDINLAYIK--VKFDILYEDSNILVVIKPRQTAMHSHKFSLDNQ 112

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                +   +   KP    RLD++T+GI++ A+    A  + +       + ++ S    
Sbjct: 113 VHKYLNIKMADIFKPAHIGRLDKDTTGIVIYAKNYQTALEMNKKQHFFVKRYVFKS---D 169

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           I   +K  +  W+ K   +    + V ++  + +  AI+   +I            Q  T
Sbjct: 170 IDLKEKVDVKLWIKKNDDL--KKMEVSQEKTQNSQLAITSLFLIGNNKI------AQLQT 221

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           G+ HQ+R+   H+G PI GD KY         S     ++LH  ++ L + EG
Sbjct: 222 GKKHQIRLTLSHLGYPIYGDQKYS--------SFKLMPMFLHCFFLQLNNLEG 266


>gi|313668670|ref|YP_004048954.1| pseudouridine synthase (rna-uridine isomerase) (rna pseudouridylat
           synthase) [Neisseria lactamica ST-640]
 gi|313006132|emb|CBN87593.1| pseudouridine synthase (rna-uridine isomerase) (rna pseudouridylat
           synthase) [Neisseria lactamica 020-06]
          Length = 307

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 44/217 (20%), Positives = 90/217 (41%), Gaps = 11/217 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
            +     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  DEPRIPFEEKILHIDGHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----PTRTDLPYPIDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEAEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + D  Y    +   +   +  L L A+ +    P  G
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSG 296


>gi|331007320|ref|ZP_08330519.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC1989]
 gi|330418882|gb|EGG93349.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC1989]
          Length = 308

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 50/221 (22%), Positives = 85/221 (38%), Gaps = 33/221 (14%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             LL++  +  ++ KP G+   G     +              +   L HRLD+ TSGI+
Sbjct: 89  PTLLHDHGQYSIWYKPHGMLSHGSKWGDHCSITRWVEQYHQPQRPSFLVHRLDRATSGIM 148

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++A  +  A +L   F  R+  K Y ++V G   + K  + + +                
Sbjct: 149 LIAHNKKVAANLCAQFENRQTDKRYHAVVEGELPSGKHTLTDPI---------------- 192

Query: 219 NEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                  A S    I   A+     +++   TGR HQ+R H    G PI+GD  Y     
Sbjct: 193 ---DNKAAHSEIHTIAYDAENKSSLVDITIKTGRKHQIRRHLSQFGYPILGDKLY----- 244

Query: 278 GNFTSPIQNKL--YLHARYMDLPHPEGGRLQ-----ITAPL 311
            +  SP   +L  +  +   D  H +  +L+      T P+
Sbjct: 245 -DTVSPFTVRLNDHNESSKSDQTHIKTLQLRAYQLAFTCPI 284


>gi|229493462|ref|ZP_04387247.1| RNA pseudouridine synthase family protein [Rhodococcus erythropolis
           SK121]
 gi|229319423|gb|EEN85259.1| RNA pseudouridine synthase family protein [Rhodococcus erythropolis
           SK121]
          Length = 304

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 62/260 (23%), Positives = 105/260 (40%), Gaps = 12/260 (4%)

Query: 50  KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL-DSSVNLTKHSDFLKSILLYEDSKI 108
            +R  + + + +G VV             +  + +        +     +  +LY D  I
Sbjct: 38  GERDLWADLVSAGDVVDEHGRKITSRTPYQPTRFVYFYREPAPEIPVPHEIEILYRDDSI 97

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V +KP  ++     G        ++   D         HRLD+ T+G++V   T    +
Sbjct: 98  LVIDKPHFLATIP-RGAHIVESAVVRLRRDLDLPDLAPVHRLDRMTAGVIVFTVTPDLRR 156

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
              E F  +RI K Y ++    P+          + K H  G+        E  +  +I 
Sbjct: 157 PYQELFAEQRIVKEYEAIAGFAPELTFPRTVRSRINKVH--GEMTATEIAGEPNSETSIE 214

Query: 229 HFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD---HKYCANFKGNFTSPI 284
             +VI D   +      + P TGRTHQLR+H   +G PIVGD    +Y     G+F++P+
Sbjct: 215 LIEVITDSAGRTLGRYRLLPRTGRTHQLRLHLNSLGVPIVGDNYYPEYLPAVPGDFSTPL 274

Query: 285 QNKLYLHARYMDLPHPEGGR 304
             +L   AR ++ P P  G+
Sbjct: 275 --RLL--ARALEYPDPITGQ 290


>gi|224282585|ref|ZP_03645907.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium bifidum
           NCIMB 41171]
          Length = 253

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/243 (23%), Positives = 87/243 (35%), Gaps = 23/243 (9%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +        ++YED+ I V +KP  ++     G+ Y     ++             HRL
Sbjct: 10  EEPHIPFDIDVVYEDAGIIVIDKPHFLATTP-RGMWYRQTALIRLREMFDEPDITPAHRL 68

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIAN-------W 201
           D+ T+GI+V  R  A        F+ R++ K Y  L    P  +     +          
Sbjct: 69  DRLTAGIVVFVRDPALRGAYQMMFQGRKVSKTYECLAPCRPTTRPRYGTVERLDPPAVFP 128

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKV-----------IDCFAQKFCWLEMQPHTG 250
           L ++SHI      +    E  A  A +   +           +          E+ P TG
Sbjct: 129 LRRRSHITKLRGVLQAFEEPQAVNAETVIDLAAGGYPSMGGRLCHGRNGLRAYELHPLTG 188

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +THQLRVH   +G PI GD  Y               L L AR +    P  G   +  +
Sbjct: 189 KTHQLRVHMNSIGLPIHGDDFY-PRIVERAYDDFSTPLELVARSLRFTDPVSGEPREFIS 247

Query: 310 PLP 312
            +P
Sbjct: 248 RIP 250


>gi|194221090|ref|XP_001491378.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 3 [Equus caballus]
          Length = 352

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/223 (25%), Positives = 99/223 (44%), Gaps = 16/223 (7%)

Query: 68  PPVINALNHIIKEQK----ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           P   +  +  ++EQ     +   +++  +  D L++ ++ +   +   NKP G+ V G  
Sbjct: 47  PRGPSKRSGPLEEQPFRGLLRPENLSREELVDVLRAAVVDQKGPLVTLNKPQGLPVTGKP 106

Query: 124 GIAYHIDGF--LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMR 177
           G    +     L   +   GQ+ +L H   +ETSG+++++     A  L +    S R +
Sbjct: 107 GELTLLSVLPELSQGLGLGGQELQLVHASGKETSGLVLLSTCPQTASRLQKFFIHSRRSQ 166

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKV 232
           R    Y ++  GIP   +  I   L  +   G D V  VK   +     G    +SHF+V
Sbjct: 167 RPTATYCAVTDGIPATSEGKIQAALKLEHTDGVDLVVPVKSPSRKDILEGVKRTLSHFRV 226

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +         +++QP T    QL+VH +   CP++GDH Y A 
Sbjct: 227 VAT-GSGCALVQLQPLTAFPSQLQVHMVLELCPVLGDHTYSAR 268


>gi|254443316|ref|ZP_05056792.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198257624|gb|EDY81932.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 194

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 58/203 (28%), Positives = 89/203 (43%), Gaps = 15/203 (7%)

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             G         ++  +  G++    HRLD+ TSG++V+ + R   + L   F  R ++K
Sbjct: 3   SEGGGDREVDLEQAVSELMGRQCWCCHRLDRLTSGVVVLRKGRRFVKELAGQFESRGVRK 62

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKF 240
            YW LV G+   + + + + +   + IG      V   E G   A S F+V+     ++ 
Sbjct: 63  EYWLLVDGLWDRRIQKMESQI---ASIGRGKYANV---ESGGKAAASTFRVLGLDEERRV 116

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            W+     TGRTHQLR+HAL  GCP+VGD  Y  +              LHAR + + HP
Sbjct: 117 SWMSGLLKTGRTHQLRLHALKAGCPVVGDPLYGKSRDDGLFG-------LHARSLRMRHP 169

Query: 301 -EGGRLQITAPLPAHMVKTWDSL 322
             G  L   A  P       +  
Sbjct: 170 ASGEELSFEAEPPDEWRGLLERF 192


>gi|262279505|ref|ZP_06057290.1| RNA pseudouridine synthase [Acinetobacter calcoaceticus RUH2202]
 gi|262259856|gb|EEY78589.1| RNA pseudouridine synthase [Acinetobacter calcoaceticus RUH2202]
          Length = 302

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/290 (18%), Positives = 113/290 (38%), Gaps = 31/290 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +   H+ HI     Q+  + G +   + +++  ++  QS   +     +    H+  E +
Sbjct: 34  YLCQHFQHIKVQEWQQRFQDGLIYGANGQKLTLDSPYQSNTHIFYYRFLAYEPHVPFEHR 93

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             +L+E+  + V +KP  +++       Y  +  L       G 
Sbjct: 94  ------------------ILFENDDLLVVDKPHFLTISPTG--QYVQETLLVRLKKQTGN 133

Query: 143 K-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-KECIAN 200
           +     HRLD+ET+G+++  +   +     + F  R++ KIY ++     + K  + +  
Sbjct: 134 EFLTPIHRLDRETAGVVLFCKRVESRGIYQQLFAERQVNKIYHAVAPYKKELKLPQTLCL 193

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L K     G   + ++          ++ ++I+   Q +    + P TG+ HQLRVH  
Sbjct: 194 HLNK-----GTPFYTMQVVANAKANTQTYIELIE-HNQIWAKYRLTPTTGKQHQLRVHLN 247

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITA 309
           ++  PI  D  Y    +    +     L L A+++    P   G +   +
Sbjct: 248 YLDIPIKNDPFY-PTVQHKADNDFSEPLQLLAKHISFVDPLTKGEMFFNS 296


>gi|226307709|ref|YP_002767669.1| pseudouridine synthase [Rhodococcus erythropolis PR4]
 gi|226186826|dbj|BAH34930.1| putative pseudouridine synthase [Rhodococcus erythropolis PR4]
          Length = 360

 Score =  120 bits (302), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 54/289 (18%), Positives = 108/289 (37%), Gaps = 28/289 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +    + H++  NL +    G+ V +D + +  +  + + + V     + A + +     
Sbjct: 36  YVVAKFDHLDAENLYRRFDDGEFVGIDGQSICRSTELSAHRFVWYYRELPAEDPVP---- 91

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             +L+ D  + V +KP  +     SG        ++  V     
Sbjct: 92  --------------FHEEILHLDDDLVVIDKPHFLPTTP-SGRYLRESALVRLRVRLDNP 136

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW--GIPKNKKECIAN 200
                HRLD+ T+G+++ +   A        F  R++ K+Y ++             +  
Sbjct: 137 DLTPIHRLDRGTAGVVMFSARPATRGAYQSLFEKRQVTKVYEAVSARPSRWDQDAPALDV 196

Query: 201 WLLKKSHIGGDY--VHVVKQNEKGANYAIS---HFKVIDCFAQKFCWLEMQPHTGRTHQL 255
            L+ ++HI      + VV  + +  N   +       +    +      ++P +GR HQL
Sbjct: 197 PLVYRNHIEARRGELRVVVDDSREPNSETTIEARGTGVSASGRAVLHTVLRPQSGRMHQL 256

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           RVH   +G  I+GD +Y  +   +        L L AR ++   P  GR
Sbjct: 257 RVHLAALGAGILGDRRY-PDLLPDAPDDHSLPLQLLARELEFTDPLSGR 304


>gi|254392417|ref|ZP_05007599.1| ribosomal pseudouridine synthase [Streptomyces clavuligerus ATCC
           27064]
 gi|294811738|ref|ZP_06770381.1| Pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|197706086|gb|EDY51898.1| ribosomal pseudouridine synthase [Streptomyces clavuligerus ATCC
           27064]
 gi|294324337|gb|EFG05980.1| Pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
          Length = 309

 Score =  120 bits (302), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 49/252 (19%), Positives = 98/252 (38%), Gaps = 10/252 (3%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
            +       G++V +  V+ A       + +        +     +  +++ D+++ V +
Sbjct: 52  ARVGELFAEGRIVSVDGVVAADEPYAAGRYLWFHRDFAPEPRVPFEIRIVHRDARLLVVD 111

Query: 113 KPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           KP  ++    GS I       L+  +     +P   HRLD+ T+G+++            
Sbjct: 112 KPHFLATTPRGSHITETAVARLRHGLGLPLLQP--AHRLDRLTAGLVLFVVRPEDRGAYQ 169

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             FR R ++K Y ++    P      +      +S I  +   +  +   G   + +  +
Sbjct: 170 TLFRDRGVRKEYEAVAAYDPA-----VELPRTVRSRIVKERGVLAAREVPGEPNSETRIE 224

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           +++          + P TG+THQLRVH   +G PI+ D  Y    + +        L L 
Sbjct: 225 LLEHRG-GLGRYRLLPATGQTHQLRVHMSGLGLPILHDPVY-PVVRADGPEDFGRPLSLL 282

Query: 292 ARYMDLPHPEGG 303
           AR ++   P  G
Sbjct: 283 ARTLEFTDPFTG 294


>gi|146418802|ref|XP_001485366.1| hypothetical protein PGUG_03095 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 390

 Score =  120 bits (302), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 45/185 (24%), Positives = 83/185 (44%), Gaps = 7/185 (3%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSG 156
              ++Y+D  + V NKP+GI         Y+     +K+ +  +   P   HRLD+ TSG
Sbjct: 101 PISIIYQDPSLIVVNKPSGIPTHPSGNFRYNSVTEIVKAQLHLESIFP--CHRLDKATSG 158

Query: 157 ILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           IL++A T AA  ++ +  + R+ ++K Y + V G     +    + +   +   G Y+  
Sbjct: 159 ILMLATTSAACSNIQKQLQERKDVKKEYIARVKGKFPPSQLVHQDPVFLLNSTAG-YIMP 217

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            +     ++   +  K           +  +PH+G+ HQ+R+H  ++G PIV D  Y   
Sbjct: 218 GRYVSIDSSTTFTRLKY--NLELDESIVSCEPHSGKMHQIRIHLRNLGFPIVNDKLYNPG 275

Query: 276 FKGNF 280
                
Sbjct: 276 ESDKL 280


>gi|160899685|ref|YP_001565267.1| pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160365269|gb|ABX36882.1| pseudouridine synthase [Delftia acidovorans SPH-1]
          Length = 305

 Score =  120 bits (302), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 58/298 (19%), Positives = 108/298 (36%), Gaps = 32/298 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD--KKRVKFNNRIQSGQVVRI 67
           VV+ +    + +D +     P +   +  + L   +V VD   +          G  +R 
Sbjct: 21  VVLPSQGGGLLID-FLAERLPAVAREDWLRRLALREV-VDEHGRAADAGTAFAPG--LRY 76

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIA 126
                                   +     ++ +L+ D+ + V +KP  + V   G  + 
Sbjct: 77  YYYRELQ----------------AEPPIPFEAEVLHRDAHLLVADKPHFLPVVPAGKYLQ 120

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   LK   D    +    HR+D++T+G++V +  RA        FR R I K Y ++
Sbjct: 121 QTLLVRLKREFDL--PELSPIHRIDRDTAGLVVFSVQRATRGIYQALFRDRAIHKTYEAV 178

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                   +E +      +S +             G     +H +V++   + +    ++
Sbjct: 179 -----APWREDVVFPRTHESRMEESGHFFRMHEVAGTPNTRTHMQVLEQHGR-WARYRLE 232

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           P +G+ HQLRVH   +G P+ GD  Y               L L AR +    P  G+
Sbjct: 233 PESGKRHQLRVHMAALGLPLWGDGFY-PEVHDMPEGDYSRPLQLLARSLAFTDPLDGQ 289


>gi|325206298|gb|ADZ01751.1| RNA pseudouridine synthase [Neisseria meningitidis M04-240196]
          Length = 307

 Score =  120 bits (302), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 44/217 (20%), Positives = 90/217 (41%), Gaps = 11/217 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPR---L 146
            +     +  +L+ D  + V +KP  + V   G  +   +   L+   + +         
Sbjct: 87  DEPRIPFEEKILHIDEHLIVVDKPHFLPVIPSGRFLRETLLTRLRLRPELQHLNVEDITP 146

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD++T+G+++++   A        F+ + + K Y +L       + +      +   
Sbjct: 147 LHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALA----LTRTDLPYPLDVVSR 202

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P+
Sbjct: 203 LVRGEKFF-TTQEVEGVPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMPL 260

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           + D  Y    +   +   +  L L A+ +    P  G
Sbjct: 261 LNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSG 296


>gi|227832810|ref|YP_002834517.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
 gi|262182701|ref|ZP_06042122.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
 gi|227453826|gb|ACP32579.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
          Length = 268

 Score =  120 bits (302), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 91/247 (36%), Gaps = 18/247 (7%)

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL-KSILLYEDSKIYVFNKPAGIS 118
           ++G     P        ++    +     ++      L    +++ED  + V +KP  + 
Sbjct: 32  EAGDSAFSPGTRLEPGTVLPGPTLAWYHPSVPSEEPILFDYRVVFEDGDLIVADKPHFLP 91

Query: 119 VQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
               G  +   +   L+  ++     P   HRLD+ TSG+++ +R         + F+ R
Sbjct: 92  TTSNGRIVRETLQTRLRVDLNEDSIVP--LHRLDRLTSGLVLCSRNPRTRAAYQQLFQKR 149

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y + V   P +    +    L    + G+    V   +      ++  +     A
Sbjct: 150 VVVKHYRAQVAA-PFSFDGTVR---LGMRRVRGERQVRV---DSTGTPTVTRVRASGTTA 202

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             +      P TG THQ+RV   H+G PIVGD  Y  +   +        L  H   +  
Sbjct: 203 DVW------PLTGHTHQIRVVLNHLGHPIVGDDTYPVDRGLDLYDFSTPLLLSHV-ALSF 255

Query: 298 PHPEGGR 304
             P  GR
Sbjct: 256 SDPVTGR 262


>gi|156089749|ref|XP_001612281.1| RNA pseudouridylate synthase family protein [Babesia bovis]
 gi|154799535|gb|EDO08713.1| RNA pseudouridylate synthase family protein [Babesia bovis]
          Length = 465

 Score =  120 bits (302), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 60/279 (21%), Positives = 107/279 (38%), Gaps = 32/279 (11%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RL    +  +       ++     G ++V  +          G  +   P    L HI +
Sbjct: 83  RLYDVLRAEFAAFTDEYIKHACVHGLIKVYDR---------EGNDLYPDPGDYVLEHICR 133

Query: 80  EQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWV 137
             + +     + +      S+ +L+ED      +KP+ + +   G+     +   LK+ V
Sbjct: 134 PNEKIWHLALVHEQMALDSSVRILHEDDDYIAVSKPSSLPLYHTGTYYYNTLVEVLKNEV 193

Query: 138 -DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN--- 193
                +     HRLD+ TSG++++A++  AA    E  R  R +K+Y + V G   N   
Sbjct: 194 FKDSARTLYPVHRLDKLTSGVIILAKSSKAASEFCEGIRNSRFRKVYIARVKGDFTNVFG 253

Query: 194 KKECI----------------ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
             ECI                  ++   SH    +   +   +K    A + F+++   +
Sbjct: 254 DHECISINDGIGVGNGSVACCHGFMRCVSHKLSMHEFTLDDTKKDVKVAETRFRMLSYNS 313

Query: 238 Q-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                 L   P TGRTHQ+R H  ++G PI  D  Y   
Sbjct: 314 SLDESLLLCYPVTGRTHQIRAHLKYLGYPISNDKCYNDG 352


>gi|332534997|ref|ZP_08410813.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332035564|gb|EGI72057.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 226

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 57/208 (27%), Positives = 94/208 (45%), Gaps = 21/208 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y  +  Y+  KPAG++     G      GF+        QK    HRLD+ TSG++++
Sbjct: 11  VVYTHNDFYILEKPAGLNFHSEEGP-----GFVVLAEQQLSQKLYAVHRLDKVTSGLIIL 65

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR +AAA   T  F    I K Y ++    PK K+  I   + K        +       
Sbjct: 66  ARNKAAAATFTVMFTEHAIAKFYLAISDAKPKKKQGWIKGDMAKSRRGSFKLL------T 119

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
              N AI+ F  +        ++ ++P++G+THQLRV    +G  I+GD  Y  +     
Sbjct: 120 STLNPAITRFYSLSYKPGFRGYI-LKPYSGKTHQLRVALKSVGAAILGDAMYSGS----- 173

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQIT 308
              + N+ YLHA  +     +  ++Q+T
Sbjct: 174 ---LSNRTYLHAYALSFLW-QSEQIQLT 197


>gi|152981592|ref|YP_001355201.1| RNA pseudouridylate synthase family protein [Janthinobacterium sp.
           Marseille]
 gi|151281669|gb|ABR90079.1| RNA pseudouridylate synthase family protein [Janthinobacterium sp.
           Marseille]
          Length = 316

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 57/289 (19%), Positives = 103/289 (35%), Gaps = 29/289 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +  +   H+P I      + L                R+Q G V+     +   + I + 
Sbjct: 44  ILAFLTEHFPAIPHA---EWLA---------------RMQRGDVIDAAGRLLTPDSIYQP 85

Query: 81  Q-KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVD 138
             KI        +       ++LY+D  +   +KP  + V   G  +   +   LK  +D
Sbjct: 86  HSKIYYYRSLPDEPRIPFDEVVLYQDDYLVAVDKPHFLPVTPAGRYLQETLLVRLKRSLD 145

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                P   HR+D+ET+G+++              FR R + K Y ++        +  +
Sbjct: 146 IDTLAP--MHRIDRETAGLVLFTIQPQTRNLYQTLFRERSVSKEYEAI-----APLRADL 198

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                 +S +      +      G   + +   +++     F    +QP +G+ HQLR H
Sbjct: 199 ELPTTYRSRLLESEAFMKMCEVAGEANSETAISLLETRG-NFGRYLLQPVSGQKHQLRAH 257

Query: 259 ALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGGRLQ 306
              +G PIV D  Y   +     T      L L A+ +    P  G+L 
Sbjct: 258 MAALGIPIVNDRIYPHLYPDEGATQDYSQPLQLLAKSISFTDPLSGKLH 306


>gi|309803449|ref|ZP_07697543.1| RNA pseudouridine synthase [Lactobacillus iners LactinV 11V1-d]
 gi|308164458|gb|EFO66711.1| RNA pseudouridine synthase [Lactobacillus iners LactinV 11V1-d]
          Length = 225

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 95/237 (40%), Gaps = 27/237 (11%)

Query: 3   LMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILR-SGQVRVDKKRVKFNNRIQ 60
           +M  Y+ Y+ +  +E N  +D+  +N    I     +  LR    + V+ K +  N ++ 
Sbjct: 9   IMNQYIYYLTISQNENNQNVDQIMRNLL--IPR-KWRHFLRIEKNILVNDKYLPLNFKVH 65

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
           +  ++ I      LNH+   Q+   +S N+          ++YE++ + V NKPAG    
Sbjct: 66  TNDLITI-----KLNHVESLQQQYPASGNMPN--------IIYENADVLVINKPAGQKTH 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                 Y  D  L       G  P + HRLD  T+G+L+VA+  A    L +    + + 
Sbjct: 113 PN---LYETDTALNDCASYLGYSPYIVHRLDMLTNGLLLVAKNPAVVPILNKQLIDKTLS 169

Query: 181 KIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + Y++ +      +    I   +          +            AI+H++V+   
Sbjct: 170 RSYFAWIEATNDISDNGTINLPIGDDPLDMRKRMVRA-----DGLKAITHYQVVKKQ 221


>gi|297853522|ref|XP_002894642.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297340484|gb|EFH70901.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 321

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 58/249 (23%), Positives = 103/249 (41%), Gaps = 46/249 (18%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD---SKGQKPRLTHRLDQET 154
           +  +LYED  +   NKP G+          + +  L+S          +  L +RLD++T
Sbjct: 74  RDHVLYEDEYLMAVNKPKGV----------YCEAVLRSAPQIVLDSSSEFHLANRLDRDT 123

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG++++ ++   A  L ++F   +I+K Y +L  G   N ++   +    +S  G   V+
Sbjct: 124 SGVMIITKSHKVAAKLVKAFTEHKIRKSYIALCIGSSPNWRKITVSSGHGRSKHGAWRVY 183

Query: 215 ------VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ---------------------- 246
                  V           + F+V+     +    E++                      
Sbjct: 184 AALDVGRVLPGGSFVRDMETTFEVVSVNGVETESCEVENVIVVEREQELSCAGDDVVVVR 243

Query: 247 --PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
             P +GRTHQ+R+H  ++G  I GD KY   ++    +   ++L  HA  + L HP    
Sbjct: 244 AFPRSGRTHQIRLHCQYLGISIRGDVKYHGMYEWRGRTFEGHEL--HAECLSLDHPVTDD 301

Query: 304 RLQITAPLP 312
            + I APLP
Sbjct: 302 PIVIRAPLP 310


>gi|254491987|ref|ZP_05105165.1| RNA pseudouridine synthase family [Methylophaga thiooxidans DMS010]
 gi|224462802|gb|EEF79073.1| RNA pseudouridine synthase family [Methylophaga thiooxydans DMS010]
          Length = 279

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 62/279 (22%), Positives = 111/279 (39%), Gaps = 45/279 (16%)

Query: 32  INFVNLQKILRSGQVRVD-KKRV----KFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
           ++   L+K++  G V V   K+     +   ++  GQ + I    + L+    E +    
Sbjct: 31  LSKQQLKKVMLKGAVWVTTGKKTQRLRRAKRQLDIGQTLHIYYDEHVLDCEPAEPE---- 86

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
                         L+ +  +  ++NKP G+  QG     +           +  +   +
Sbjct: 87  --------------LIADMGQYSIWNKPYGMLSQGSKWGDHCTITRWAEQHLTPQRNAFV 132

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+  +G+++VA  + AA  L+  F+ R+I+K Y   V G    ++  + N +    
Sbjct: 133 VHRLDRAANGLIIVAHEKKAAALLSGLFQSRQIEKRYQIWVEGEFS-EQATVDNPVKVDL 191

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCP 265
            + G              +A+S F  +   A K    L+++  TGR HQ+R HA  +G P
Sbjct: 192 DLDG-------------RHAVSFFTRLKFDASKQQSLLDVRIETGRKHQIRQHAASLGHP 238

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           +VGD  Y    +          L L A +M    P    
Sbjct: 239 VVGDRLYGNILQQEN-------LQLKAYFMAFRCPYTAE 270


>gi|50843747|ref|YP_056974.1| putative RNA pseudouridylate synthase [Propionibacterium acnes
           KPA171202]
 gi|50841349|gb|AAT84016.1| putative RNA pseudouridylate synthase [Propionibacterium acnes
           KPA171202]
          Length = 295

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/217 (24%), Positives = 84/217 (38%), Gaps = 6/217 (2%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            T+        +LY D +I V +KP  +S     G        ++        +  + HR
Sbjct: 67  PTETPVPAGIGILYSDERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHR 125

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKEC-IANWLLKKS 206
           LD+ T+G+L++ R R   +   E F  R + K Y   + V   P  +      +    +S
Sbjct: 126 LDRVTAGVLLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTATKSGWQVRS 185

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            I  +   +  +   G   A++   +I      +   E  P TGRTHQ+R+H   +G PI
Sbjct: 186 RIIKERGILQAREVPGVPNAVTDIALIGEHG-GWGLYEASPRTGRTHQIRLHMQRLGAPI 244

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           V D  Y             + L L A  M    P  G
Sbjct: 245 VNDPFY-PVVLDTPVDDFTHPLQLQAWRMGFTDPVTG 280


>gi|189911582|ref|YP_001963137.1| pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167776258|gb|ABZ94559.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
          Length = 222

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 50/217 (23%), Positives = 87/217 (40%), Gaps = 19/217 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           + YE     +  KP GI V      +       L + +     + R  +RLD  TSGI++
Sbjct: 9   IFYECDDFLLAEKPEGIPVHETKDPSRMDFTRLLSNHLQI--PELRTVNRLDLGTSGIVL 66

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + + +     L      +  +K Y  L  GIP  ++  +  +L      G   V++V+  
Sbjct: 67  LGKNKNKNVELDLLL--KEAEKTYIFLCDGIPSWREHRMECFL----KEGNKQVNLVRS- 119

Query: 220 EKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             G   AI+ F ++     +   +   +  TGR HQ+RV    +G PI+GD  Y    K 
Sbjct: 120 --GGKKAITEFSILHSDPNESISFGFAKILTGRRHQIRVMLSSLGFPILGDTVYGKKEK- 176

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
                 + ++YLH+         G +  +   +P   
Sbjct: 177 -----TETRMYLHSFRFYFTDFLGQKQMVQTDVPRDW 208


>gi|126667503|ref|ZP_01738474.1| Pseudouridylate synthases, 23S RNA-specific [Marinobacter sp.
           ELB17]
 gi|126628095|gb|EAZ98721.1| Pseudouridylate synthases, 23S RNA-specific [Marinobacter sp.
           ELB17]
          Length = 304

 Score =  120 bits (301), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 62/307 (20%), Positives = 114/307 (37%), Gaps = 48/307 (15%)

Query: 30  PHINFVNLQKILRSGQV--RVDKKRV---KFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
             +    ++  +  G     +  K V   K    +++G  +++      L     E ++L
Sbjct: 23  SGLPKQRIKDAMAKGACWWTLKGKIVRLRKAKRDVKAGTRMQLYYDEAVLARKAPEVELL 82

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           +                  + S+  V+ KP G+  QG     +     L+       +  
Sbjct: 83  E------------------DKSRYSVWFKPHGLLAQGSQWGDHC--SLLRVAEVQLNRPC 122

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HRLD + +G++++A    AA  L++ F  R I K Y + V G+   +++ I   +  
Sbjct: 123 FLIHRLDADAAGLMLIAHDSKAAAALSQLFAGRAIIKQYLADVTGVLDVEEQTIDGDIDG 182

Query: 205 K---SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF---------CWLEMQPHTGRT 252
           K   SH+   Y +    N    N   ++   I+  +              + ++  TGR 
Sbjct: 183 KAAISHVSTLYSNAGSINTSAVNSNSTNASSINASSINTKAEDTDASTSRVNVRIETGRK 242

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
           HQ+R H   +G PIV D  Y         S     L L A Y+    P    ++ +   L
Sbjct: 243 HQIRRHLASIGHPIVADRLYG--------SAAGVPLQLLAYYLQFNCPMTKSKMTLE--L 292

Query: 312 PAHMVKT 318
           P  + + 
Sbjct: 293 PERLKQL 299


>gi|193222440|emb|CAL63390.2| Putative pseudouridylate synthase 23S RNA-specific [Herminiimonas
           arsenicoxydans]
          Length = 300

 Score =  120 bits (301), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 51/289 (17%), Positives = 100/289 (34%), Gaps = 30/289 (10%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +   H+P I                         R+Q G V+     I  +    + 
Sbjct: 29  ID-FLVEHFPAIPRSEWM------------------TRMQRGDVLDAQGRIIHVASAYQP 69

Query: 81  QKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
              +    +L + +      ++LY+D  +   +KP  + V       Y  +  L     S
Sbjct: 70  HSKIFYFRSLPEEARIPFDEVVLYQDDYLVAVDKPHFLPVTPAG--RYLQETLLVRLKRS 127

Query: 140 KGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                    HR+D++T+G+++              FR R + K Y ++           +
Sbjct: 128 LNIDTLAPMHRIDRDTAGLVLFTIQPHTRNLYQTLFRERSVSKQYEAIAPYRAD-----L 182

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A   + +S +      +  +  +G   A +   +++          ++P +G+ HQLR H
Sbjct: 183 ALPTVYRSRLLESAAFMKMEEVEGVPNAETAIDLMEVQG-ALARYRLEPVSGQKHQLRAH 241

Query: 259 ALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHPEGGRLQ 306
              +G PIV D  Y   +            L L A+ +    P   +L+
Sbjct: 242 MAALGMPIVNDRIYPELYPDEGAEQDYSQPLKLLAKTISFTDPISRQLR 290


>gi|78486049|ref|YP_391974.1| pseudouridine synthase [Thiomicrospira crunogena XCL-2]
 gi|78364335|gb|ABB42300.1| Pseudouridine synthase Rlu family protein [Thiomicrospira crunogena
           XCL-2]
          Length = 300

 Score =  120 bits (301), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 65/324 (20%), Positives = 113/324 (34%), Gaps = 69/324 (21%)

Query: 16  EENMRLDRWFKNHYP---HINFVNLQKILRSGQVRV-------DKKRVKFNNR-----IQ 60
           +    L      H P   H +   L++  + G V +       D++  K   R     ++
Sbjct: 18  QSEKTLLEALSEHLPNEVHFSNQQLKRFCQQGAVWISEPGNQPDQQTKKVRARRAKKQLK 77

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED-SKIYVFNKPAGISV 119
            G  V      + LN  I +                    +L ED     V+ KP G+  
Sbjct: 78  KGSEVSFYFNESVLNATIPDP-------------------VLIEDADDFSVWYKPKGVLS 118

Query: 120 QGGSGIAYHIDGFL--KSWVDSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESF 174
           QG     +          ++  +  +     + HRLD+ T G++++A  + +AQ L   F
Sbjct: 119 QGSKWGDHTTLNRWIETHYLFKEPPEKRPCWIVHRLDKATDGLILIAHNKKSAQMLARRF 178

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
              +I K Y + V G     +                    V   +     A+S    + 
Sbjct: 179 EAHQIGKSYQAWVKGKFGETE-------------------RVFDQDVNGKTALSKAHQLV 219

Query: 235 CFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             +   C  +++   TGR HQ+R+H    G PI+GD  Y    +G+        L L A 
Sbjct: 220 YNSDNDCSLVQVTIATGRKHQIRIHLSKAGFPIIGDRLYGDAQEGDPD------LQLTAV 273

Query: 294 YMDLPHPEGG-RLQITAPLPAHMV 316
            +    P+G    +    LP ++ 
Sbjct: 274 EITFLSPQGTIEQRFQ--LPDNLR 295


>gi|300785329|ref|YP_003765620.1| RNA pseudouridylate synthase [Amycolatopsis mediterranei U32]
 gi|299794843|gb|ADJ45218.1| putative RNA pseudouridylate synthase [Amycolatopsis mediterranei
           U32]
          Length = 311

 Score =  120 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 47/214 (21%), Positives = 84/214 (39%), Gaps = 8/214 (3%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +        +++ D  + V +KP  ++     G        ++   +    +    HR
Sbjct: 81  PDEVPVPFAIDVVHRDEHLLVVDKPHFLATIP-RGQHILETALVRLRRELDLPQLSPAHR 139

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+++   T  +       FR RR+ K Y ++    P      +      +S I 
Sbjct: 140 LDRVTAGLVMFVITPESRGKYQTLFRDRRVHKEYEAIAPHDPA-----LTLPRTVRSRIV 194

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +   +  Q   G   A ++  +++  A       + P TGRTHQLR+H   +G PI+GD
Sbjct: 195 KERGVLAAQEVPGEPNAETYVDLLEHRA-GLGRYRLVPATGRTHQLRLHLSGLGVPILGD 253

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             Y    +          L L A+ +D   P  G
Sbjct: 254 DFY-PQLREKPLGDFTKPLQLLAKVLDFDDPLTG 286


>gi|256828202|ref|YP_003156930.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256577378|gb|ACU88514.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 281

 Score =  120 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 60/288 (20%), Positives = 99/288 (34%), Gaps = 44/288 (15%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
                 +RLDR              + ++ +G+V VD +       I+ GQ +R+     
Sbjct: 8   PEGLPPIRLDRVLALQL-GFGVRRCRALIEAGRVLVDDRPCAKGALIRPGQHIRV----- 61

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                         S+      D     L+  +       KP G+    G          
Sbjct: 62  --------------SLPEDAAPDCHDVRLVDRNESFAALAKPDGLHTVAGQ-----EAAC 102

Query: 133 LKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L+S +   G +   L +RLD  TSG+++ A  +  A          ++ K Y +L  G  
Sbjct: 103 LESCLPGLGLEGWELLNRLDCLTSGLVLAAAEKRDAAAYKVWQDAGQVSKWYLALARGEV 162

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                     L  +  I  D   VV+   ++      +  + +         L ++   G
Sbjct: 163 AT--------LECRGRILDDKRSVVRVTADEDEPLRWTRVRAL-RQIDGNTLLLVKIFKG 213

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           R HQ+R H  H G P++GD  Y     G         LYLH   +D+P
Sbjct: 214 RRHQIRAHLAHAGHPLIGDPVYGVCEPGG--------LYLHHWRLDMP 253


>gi|82617847|gb|ABB84841.1| RNA pseudouridylate synthase [uncultured delta proteobacterium
           DeepAnt-32C6]
          Length = 197

 Score =  120 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 47/209 (22%), Positives = 82/209 (39%), Gaps = 21/209 (10%)

Query: 117 ISVQGGSGIAYHIDGFLK-SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           ++V     +       +  +            HR+D+ TSG+L+ +        +     
Sbjct: 1   MAVHAAGPVDPEAPDLMTWARTHFDAPGLAPAHRIDKATSGLLLCSPDPRVRARVGHWLA 60

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
             ++ K Y +LV+G   ++   I   L+ +                    A + F+ +  
Sbjct: 61  QGQVHKEYRALVFGH-THRSGRIDRPLMDRRRGRR-------------LDACTRFRRLAT 106

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
            +Q   +L + P TGR HQ+R H   +G  IVGD +Y    +         +L+LH R +
Sbjct: 107 ASQ-LSYLAVYPETGRKHQIRRHLRGLGHAIVGDTRYGPTHQRPLP-GCPGRLWLHLRQL 164

Query: 296 DLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
           +LP      L   APLP  +V   + LG 
Sbjct: 165 ELP----EGLTFEAPLPPALVAHLERLGI 189


>gi|188994274|ref|YP_001928526.1| probable RNA pseudouridylate synthase [Porphyromonas gingivalis
           ATCC 33277]
 gi|188593954|dbj|BAG32929.1| probable RNA pseudouridylate synthase [Porphyromonas gingivalis
           ATCC 33277]
          Length = 324

 Score =  120 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 48/301 (15%), Positives = 113/301 (37%), Gaps = 31/301 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        +  ++++IL   QV ++     + +  +++G  V +               
Sbjct: 30  FLVRMLKDNSRTSVKQILTRRQVSINGVPTTRHDAELKAGDRVIVH-------------- 75

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDSKG 141
                  L +        ++++D    +  K AG+S V  G          +   +    
Sbjct: 76  ----RTQLPEELRHPLVRIIWQDDYFVLIEKKAGVSTVASGVNKDRTALRIVSDHLKQYD 131

Query: 142 QKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            + ++   +RLD++++G+++ A+ +     + + +    +++ +   + G   + +  + 
Sbjct: 132 PEVKIFMLNRLDKDSAGMVLFAKNKEVQGFVVDKWSKVVLEQRFVMAIEGEMPDAEGTLD 191

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
               + S I G    +V +     +   + +KVI         +E+   +GR +QLR   
Sbjct: 192 PPRYQTS-IKGKQSRIVAETPSVHSVGTARYKVI-RRGAVCSLVEVTLLSGRNNQLRRQM 249

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
             +G PI GD +  ++F+        + L L        HPE G   +   PLP    + 
Sbjct: 250 GQLGIPIAGDWRQGSSFR------HLDCLALQGTRFVFRHPETGDTQEYKLPLPKLFRRL 303

Query: 319 W 319
            
Sbjct: 304 I 304


>gi|157377205|ref|YP_001475805.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157319579|gb|ABV38677.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 312

 Score =  120 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 59/293 (20%), Positives = 113/293 (38%), Gaps = 33/293 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +    +P I     +  +  G+V             Q G ++ +         +   +++
Sbjct: 28  FLIERFPQIEPQVWRARILDGKVH-----------WQDGALIELDTPFRPRARVYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-- 141
              +V            +LY D +I +  KP  +++     +   I+  L + +  K   
Sbjct: 77  EAEAV------IPFDEEVLYRDGQIIIAFKPHFLALHPSGNV---INECLVNRLRIKNGI 127

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NK 194
           +     HRLD+ T+G++++       Q   E F+   I+K Y +L    P+        +
Sbjct: 128 ETIVPAHRLDRATAGLVLLCLYPEHRQQYHELFKHGEIRKEYQALAKLTPELLEQHRTGE 187

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                +W +K   + G+    +K  E  AN   S   +I+   +   + ++ P TGRTHQ
Sbjct: 188 LTLPVHWTVKNRMVKGEPSFTMKVVEGEANT-HSEITLIEMRGEIGVF-KLSPITGRTHQ 245

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           LRVH   +G  I+ D  Y    +       +  L L A+ +    P  G ++ 
Sbjct: 246 LRVHMQSLGMSILNDRCY-PVLQPKSADDYERPLKLLAKRLKFKDPVTG-IEF 296


>gi|72390299|ref|XP_845444.1| RNA pseudouridylate synthase [Trypanosoma brucei TREU927]
 gi|62359520|gb|AAX79956.1| RNA pseudouridylate synthase, putative [Trypanosoma brucei]
 gi|70801979|gb|AAZ11885.1| RNA pseudouridylate synthase, putative [Trypanosoma brucei brucei
           strain 927/4 GUTat10.1]
          Length = 462

 Score =  120 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 74/432 (17%), Positives = 139/432 (32%), Gaps = 117/432 (27%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHIIK 79
           +D +    +P++     ++  R G + V    +K   +   +G   R   V+     + +
Sbjct: 19  ID-FLCCRFPYLTRSAWEQHARDGHLSV----IKAARDSCGAGDN-RHGVVVPMDYELQQ 72

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWV- 137
             +I  +     +       ++L+ D  + V  K   + V +GG   A  + G L+    
Sbjct: 73  NDEICFNPPRHLEPDINEHVVVLHSDEALLVCVKNGNLPVAEGGRYSANTLVGVLQRLAG 132

Query: 138 ---------------------DSKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESF 174
                                ++ G K      HRLD+ETSG++V+A++  AA+ L+  F
Sbjct: 133 NFTWETANGTAEMCLSKATNKETCGLKVNYYPVHRLDKETSGLVVLAKSADAARILSGQF 192

Query: 175 ---------------------------------RMRRIQKIYWSLVWGIPKNKKECI--- 198
                                              + + K Y +++ G      E I   
Sbjct: 193 ERQSQVLNAQLTKYTGGESLTVVTSSQFDELITMDKSVSKSYIAVLDGSVPEGNEFIVCN 252

Query: 199 -----------------ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKF 240
                             +  LKK  +   +  V K  +     A S  +++      + 
Sbjct: 253 RVGLLWEELKDSMKDAEKHTKLKKLKMACYHASVGKNQQLYGRPACSRIRILSSSDTLRV 312

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------------- 285
               +   TGRTHQ+R+H   +G P++GD  Y  +  G                      
Sbjct: 313 SVARVDILTGRTHQIRLHCAQIGFPVLGDKLYETSTPGRVGGLHAVADDIYLYRARETVS 372

Query: 286 ----------NKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKR 334
                      +  LHA  +   HP    RL+  A      +        + D    ++ 
Sbjct: 373 MSWGVEGMSVKRHLLHAAILTFTHPTTRERLEFFAAPHEWFLS-----DVECDEATKLEE 427

Query: 335 LYSQDECKQNIL 346
             S  E  +++L
Sbjct: 428 NKSGTEILRDLL 439


>gi|313765077|gb|EFS36441.1| RNA pseudouridine synthase [Propionibacterium acnes HL013PA1]
 gi|313792621|gb|EFS40707.1| RNA pseudouridine synthase [Propionibacterium acnes HL110PA1]
 gi|313803157|gb|EFS44353.1| RNA pseudouridine synthase [Propionibacterium acnes HL110PA2]
 gi|313806800|gb|EFS45298.1| RNA pseudouridine synthase [Propionibacterium acnes HL087PA2]
 gi|313817590|gb|EFS55304.1| RNA pseudouridine synthase [Propionibacterium acnes HL046PA2]
 gi|313821584|gb|EFS59298.1| RNA pseudouridine synthase [Propionibacterium acnes HL036PA1]
 gi|313824472|gb|EFS62186.1| RNA pseudouridine synthase [Propionibacterium acnes HL036PA2]
 gi|313826817|gb|EFS64531.1| RNA pseudouridine synthase [Propionibacterium acnes HL063PA1]
 gi|313829136|gb|EFS66850.1| RNA pseudouridine synthase [Propionibacterium acnes HL063PA2]
 gi|313839569|gb|EFS77283.1| RNA pseudouridine synthase [Propionibacterium acnes HL086PA1]
 gi|314916163|gb|EFS79994.1| RNA pseudouridine synthase [Propionibacterium acnes HL005PA4]
 gi|314917426|gb|EFS81257.1| RNA pseudouridine synthase [Propionibacterium acnes HL050PA1]
 gi|314921765|gb|EFS85596.1| RNA pseudouridine synthase [Propionibacterium acnes HL050PA3]
 gi|314926247|gb|EFS90078.1| RNA pseudouridine synthase [Propionibacterium acnes HL036PA3]
 gi|314930967|gb|EFS94798.1| RNA pseudouridine synthase [Propionibacterium acnes HL067PA1]
 gi|314955362|gb|EFS99767.1| RNA pseudouridine synthase [Propionibacterium acnes HL027PA1]
 gi|314961609|gb|EFT05710.1| RNA pseudouridine synthase [Propionibacterium acnes HL002PA2]
 gi|314963927|gb|EFT08027.1| RNA pseudouridine synthase [Propionibacterium acnes HL082PA1]
 gi|314969134|gb|EFT13232.1| RNA pseudouridine synthase [Propionibacterium acnes HL037PA1]
 gi|314979975|gb|EFT24069.1| RNA pseudouridine synthase [Propionibacterium acnes HL072PA2]
 gi|314987166|gb|EFT31258.1| RNA pseudouridine synthase [Propionibacterium acnes HL005PA2]
 gi|314990633|gb|EFT34724.1| RNA pseudouridine synthase [Propionibacterium acnes HL005PA3]
 gi|315079107|gb|EFT51114.1| RNA pseudouridine synthase [Propionibacterium acnes HL053PA2]
 gi|315081549|gb|EFT53525.1| RNA pseudouridine synthase [Propionibacterium acnes HL078PA1]
 gi|315083025|gb|EFT55001.1| RNA pseudouridine synthase [Propionibacterium acnes HL027PA2]
 gi|315086559|gb|EFT58535.1| RNA pseudouridine synthase [Propionibacterium acnes HL002PA3]
 gi|315087963|gb|EFT59939.1| RNA pseudouridine synthase [Propionibacterium acnes HL072PA1]
 gi|315102262|gb|EFT74238.1| RNA pseudouridine synthase [Propionibacterium acnes HL046PA1]
 gi|315107443|gb|EFT79419.1| RNA pseudouridine synthase [Propionibacterium acnes HL030PA1]
 gi|315109736|gb|EFT81712.1| RNA pseudouridine synthase [Propionibacterium acnes HL030PA2]
 gi|327334072|gb|EGE75787.1| RNA pseudouridylate synthase family protein [Propionibacterium
           acnes HL096PA3]
 gi|327444523|gb|EGE91177.1| RNA pseudouridine synthase [Propionibacterium acnes HL013PA2]
 gi|327454203|gb|EGF00858.1| RNA pseudouridine synthase [Propionibacterium acnes HL087PA3]
 gi|327456261|gb|EGF02916.1| RNA pseudouridine synthase [Propionibacterium acnes HL083PA2]
 gi|327457465|gb|EGF04120.1| RNA pseudouridine synthase [Propionibacterium acnes HL092PA1]
 gi|328755960|gb|EGF69576.1| RNA pseudouridine synthase [Propionibacterium acnes HL087PA1]
 gi|328758029|gb|EGF71645.1| RNA pseudouridine synthase [Propionibacterium acnes HL020PA1]
 gi|328758923|gb|EGF72539.1| RNA pseudouridine synthase [Propionibacterium acnes HL025PA2]
          Length = 281

 Score =  120 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 53/217 (24%), Positives = 84/217 (38%), Gaps = 6/217 (2%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            T+        +LY D +I V +KP  +S     G        ++        +  + HR
Sbjct: 53  PTETPVPAGIGILYSDERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHR 111

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKEC-IANWLLKKS 206
           LD+ T+G+L++ R R   +   E F  R + K Y   + V   P  +      +    +S
Sbjct: 112 LDRVTAGVLLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTATKSGWQVRS 171

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            I  +   +  +   G   A++   +I      +   E  P TGRTHQ+R+H   +G PI
Sbjct: 172 RIIKERGILQAREVPGVPNAVTDIALIGEHG-GWGLYEASPRTGRTHQIRLHMQRLGAPI 230

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           V D  Y             + L L A  M    P  G
Sbjct: 231 VNDPFY-PVVLDTPVDDFTHPLQLQAWRMGFTDPVTG 266


>gi|332300035|ref|YP_004441956.1| pseudouridine synthase [Porphyromonas asaccharolytica DSM 20707]
 gi|332177098|gb|AEE12788.1| pseudouridine synthase [Porphyromonas asaccharolytica DSM 20707]
          Length = 337

 Score =  120 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 54/288 (18%), Positives = 108/288 (37%), Gaps = 35/288 (12%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV--INALNHIIKEQKILDS 86
           P ++   +++ LR+  V +       F+  + +G  + I  +    A+ H + E+     
Sbjct: 38  PDLSRTTVKQYLRNRCVLLAGVTTTQFDAPVIAGDTIEIYNIGTAEAVQHPLIEE----- 92

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWVD-SKGQK 143
                          LY D +  V +K  GI     GG+  +                +K
Sbjct: 93  ---------------LYRDEQFIVLHKRPGIPTISVGGASKSSLFQVVTHHLKKVDPNEK 137

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             L +RLD++T GI++VAR R   Q L   +R   +   + +++ G        +     
Sbjct: 138 IFLLNRLDRDTEGIIIVARDRQLQQDLLAEWRSFVLSNSFEAVILGALDTSSGELTTRPT 197

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISH--FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           K    G +     + + + +  A     ++V+         +++   T R + +R     
Sbjct: 198 KDKKRGPNKRRTARSSTRDSKPATFRASYEVL-TTGPYITRVKLSLLT-RNNSIRSTLAS 255

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQIT 308
           +G P++GDH        +    +   L L A  + + HP    ++Q T
Sbjct: 256 IGHPLLGDH----RASESIAPELSKYLALRATELTIFHPIRRQKMQFT 299


>gi|134096436|ref|YP_001101511.1| putative pseudouridylate synthase [Herminiimonas arsenicoxydans]
          Length = 281

 Score =  120 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 54/306 (17%), Positives = 105/306 (34%), Gaps = 38/306 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   Q++ V        +D +   H+P I                         R+Q G 
Sbjct: 1   MPPGQWLTV--------ID-FLVEHFPAIPRSEWM------------------TRMQRGD 33

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAGISVQGG 122
           V+     I  +    +    +    +L + +      ++LY+D  +   +KP  + V   
Sbjct: 34  VLDAQGRIIHVASAYQPHSKIFYFRSLPEEARIPFDEVVLYQDDYLVAVDKPHFLPVTPA 93

Query: 123 SGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
               Y  +  L     S         HR+D++T+G+++              FR R + K
Sbjct: 94  G--RYLQETLLVRLKRSLNIDTLAPMHRIDRDTAGLVLFTIQPHTRNLYQTLFRERSVSK 151

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y ++           +A   + +S +      +  +  +G   A +   +++       
Sbjct: 152 QYEAIAPYRAD-----LALPTVYRSRLLESAAFMKMEEVEGVPNAETAIDLMEVQG-ALA 205

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDLPHP 300
              ++P +G+ HQLR H   +G PIV D  Y   +            L L A+ +    P
Sbjct: 206 RYRLEPVSGQKHQLRAHMAALGMPIVNDRIYPELYPDEGAEQDYSQPLKLLAKTISFTDP 265

Query: 301 EGGRLQ 306
              +L+
Sbjct: 266 ISRQLR 271


>gi|183221495|ref|YP_001839491.1| putative RNA pseudouridine synthase [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
 gi|167779917|gb|ABZ98215.1| Putative RNA pseudouridine synthase (RNA-uridine isomerase; RNA
           pseudouridylate synthase) [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
          Length = 231

 Score =  120 bits (300), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 50/217 (23%), Positives = 87/217 (40%), Gaps = 19/217 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           + YE     +  KP GI V      +       L + +     + R  +RLD  TSGI++
Sbjct: 18  IFYECDDFLLAEKPEGIPVHETKDPSRMDFTRLLSNHLQI--PELRTVNRLDLGTSGIVL 75

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           + + +     L      +  +K Y  L  GIP  ++  +  +L      G   V++V+  
Sbjct: 76  LGKNKNKNVELDLLL--KEAEKTYIFLCDGIPSWREHRMECFL----KEGNKQVNLVRS- 128

Query: 220 EKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             G   AI+ F ++     +   +   +  TGR HQ+RV    +G PI+GD  Y    K 
Sbjct: 129 --GGKKAITEFSILHSDPNESISFGFAKILTGRRHQIRVMLSSLGFPILGDTVYGKKEK- 185

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
                 + ++YLH+         G +  +   +P   
Sbjct: 186 -----TETRMYLHSFRFYFTDFLGQKQMVQTDVPRDW 217


>gi|194696406|gb|ACF82287.1| unknown [Zea mays]
          Length = 242

 Score =  120 bits (300), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 54/216 (25%), Positives = 88/216 (40%), Gaps = 44/216 (20%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHL-----------------TESFRMRRIQKIYWS 185
            P   HRL + TSG+L+ A+T+ A   L                 +E    R+I K Y +
Sbjct: 15  HPVPVHRLGRGTSGLLLCAKTKVAKVRLASYFAEGAINAAKKRDKSEFSEERKISKFYRA 74

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLE 244
           LV GI  + +  +   +    + G         +      A+S   V++  A Q    ++
Sbjct: 75  LVTGILDDDEVVVTQPIGLVHYPGVAEGLYAACSS--GKPAMSKVCVLERLAHQNHTLVQ 132

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS---------------------- 282
           ++ H+GR HQ+R+H  ++G P+V D  Y      NF                        
Sbjct: 133 VEIHSGRPHQIRIHLAYIGHPLVDDPLYGIGGHPNFVEPESTGTDSSFASDGGYERPLQP 192

Query: 283 -PIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMV 316
            P     +LHA ++ L HP   ++ +ITAPLP  + 
Sbjct: 193 VPGDCGYHLHAHWLVLCHPTTNKMVKITAPLPQILQ 228


>gi|224122944|ref|XP_002318955.1| predicted protein [Populus trichocarpa]
 gi|222857331|gb|EEE94878.1| predicted protein [Populus trichocarpa]
          Length = 261

 Score =  120 bits (300), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 59/252 (23%), Positives = 99/252 (39%), Gaps = 54/252 (21%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           KS +LY+D  +   NKP G+          + +  L S       +  L +RLD++TSG+
Sbjct: 14  KSDVLYQDQWLIAVNKPQGV----------YCETVLDSV-----PQLHLANRLDRDTSGV 58

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+ +    A  L ++F   +++K Y +L  G     ++        +S  G   V+   
Sbjct: 59  MVITKLHKVASKLVKAFTDHKVRKTYIALCIGSAPKWEKITIKSGHGRSKFGAFRVYAAS 118

Query: 218 QNEK------GANYAISHFKVIDCFAQKFC------------------------------ 241
              +            + F+V+    Q                                 
Sbjct: 119 DVGRSLPGGSTVKDMETSFEVLSINGQGSFREPSEFNSDKNILVVEEKAVIDTDAKKDEI 178

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +   P +GRTHQ+R+H  ++G PI GD KY    +    +   ++L  HA  + L HP 
Sbjct: 179 LVRAFPRSGRTHQIRLHCQYLGIPIRGDVKYEGVCEWKGRTYDGHEL--HAESLSLEHPV 236

Query: 302 GGR-LQITAPLP 312
            G+ L   APLP
Sbjct: 237 TGQPLMFRAPLP 248


>gi|119776668|ref|YP_929408.1| pseudouridine synthase RluA-like protein [Shewanella amazonensis
           SB2B]
 gi|119769168|gb|ABM01739.1| pseudouridine synthase RluA-like protein [Shewanella amazonensis
           SB2B]
          Length = 224

 Score =  120 bits (300), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 55/198 (27%), Positives = 88/198 (44%), Gaps = 19/198 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++ +++   V +K  G+      G A    G +       G      HRLD  TSG+++
Sbjct: 3   RIIADETDFLVIDKAPGVHFHSQDGSA----GVVAQVESDLGIDLYPVHRLDTLTSGLII 58

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A++ AAA   TE F    +QK Y +L  G PK K+  IA  + K        +  ++  
Sbjct: 59  LAKSSAAAADFTELFSRHGVQKYYLALAKGKPKKKQGKIAGDMAKSRRSQYKLLRTME-- 116

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F      A+      ++P TG+THQLRV    +G PI+GD  Y       
Sbjct: 117 ----NPAVTQFFS-ASVAEGLRAYLLKPLTGKTHQLRVALASLGTPILGDTLYGGES--- 168

Query: 280 FTSPIQNKLYLHARYMDL 297
                 ++ YLHA  ++ 
Sbjct: 169 -----SDRGYLHAWQLEF 181


>gi|224438079|ref|ZP_03659018.1| hypothetical protein HcinC1_08895 [Helicobacter cinaedi CCUG 18818]
 gi|313144523|ref|ZP_07806716.1| conserved hypothetical protein [Helicobacter cinaedi CCUG 18818]
 gi|313129554|gb|EFR47171.1| conserved hypothetical protein [Helicobacter cinaedi CCUG 18818]
          Length = 310

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 97/251 (38%), Gaps = 29/251 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           W           N QK L   ++  D + +    +I    ++                + 
Sbjct: 19  WLMRE-RGYTQANAQKALDKHRLTQDNRPISKAEKIYGNVMLS---------------EF 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQ 142
           + SS+      +      L+ +    +++KP  +     G    Y ++  LKS     G 
Sbjct: 63  VPSSIPHLADIEP-----LFYNDDFAIYDKPHNLLTHPKGRFFHYSLNDILKSRF---GI 114

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +    HRLD++T G+++ +    + + L    + R I K Y ++V G  K   E + N  
Sbjct: 115 QANALHRLDKQTGGLVLCSINPKSKKALESLMQSRSIAKSYCAIVEGRVKA--EILINEP 172

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           +      GD       +EKG   + +  + +  +      +     TGRTHQ+R+H  ++
Sbjct: 173 IMTQKHKGDLAIKSIVSEKG-KESRTLIRPLAYYKDS-TLIHALALTGRTHQIRLHCSYI 230

Query: 263 GCPIVGDHKYC 273
           G  I+GD  Y 
Sbjct: 231 GHRILGDPLYG 241


>gi|219121405|ref|XP_002185927.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|209582776|gb|ACI65397.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 193

 Score =  119 bits (299), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 51/178 (28%), Positives = 80/178 (44%), Gaps = 20/178 (11%)

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSLVW-GIPKNKKECIA 199
           Q   + HRLD ETSG+L+ ART  AA  L+ ++R R  +QK Y + V+          I 
Sbjct: 13  QSLFIVHRLDCETSGVLLFARTSEAASRLSRAWREREHVQKTYVAKVYSWRLPETSGRID 72

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------------LEMQP 247
             L         ++       K    + + + V+    +  C             L + P
Sbjct: 73  LALAPHPTERIKWIA-----SKEGKPSTTLWTVMPDERKATCQNPDSDGCARPVKLRLIP 127

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            TGRTHQLR+H    G  I+GD  Y   F        +++L+LH++ + +PHP  G++
Sbjct: 128 VTGRTHQLRIHCCAHGDGILGDTLYG-KFATQSLPGKRSRLFLHSQALSVPHPTTGKM 184


>gi|310287045|ref|YP_003938303.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium bifidum
           S17]
 gi|309250981|gb|ADO52729.1| 23S RNA-specific pseudouridylate synthase [Bifidobacterium bifidum
           S17]
          Length = 253

 Score =  119 bits (299), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 56/243 (23%), Positives = 87/243 (35%), Gaps = 23/243 (9%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +        ++YED+ I V +KP  ++     G+ Y     ++             HRL
Sbjct: 10  EEPHIPFDIDVVYEDAGIIVIDKPHFLATTP-RGMWYRQTALIRLREMFDEPDITPAHRL 68

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIAN-------W 201
           D+ T+GI+V  R  A        F+ R++ K Y  L    P  +     +          
Sbjct: 69  DRLTAGIVVFVRDPALRGAYQMMFQGRKVSKTYECLAPCRPTTRPRYGTVERLDPPAVFP 128

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKV-----------IDCFAQKFCWLEMQPHTG 250
           L ++SHI      +    E  A  A +   +           +          E+ P TG
Sbjct: 129 LRRRSHITKLRGVLQAFEEPQAVNAETVIDLAAEGYPSMGGRLCHGRNGLRAYELHPLTG 188

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +THQLRVH   +G PI GD  Y               L L AR +    P  G   +  +
Sbjct: 189 KTHQLRVHMNSIGLPIHGDDFY-PRIVERAYDDFSTPLELVARSLRFADPVSGEPREFIS 247

Query: 310 PLP 312
            +P
Sbjct: 248 RIP 250


>gi|289424437|ref|ZP_06426220.1| RNA pseudouridine synthase [Propionibacterium acnes SK187]
 gi|289427345|ref|ZP_06429058.1| RNA pseudouridine synthase [Propionibacterium acnes J165]
 gi|289155134|gb|EFD03816.1| RNA pseudouridine synthase [Propionibacterium acnes SK187]
 gi|289159275|gb|EFD07466.1| RNA pseudouridine synthase [Propionibacterium acnes J165]
 gi|332676702|gb|AEE73518.1| putative RNA pseudouridylate synthase [Propionibacterium acnes 266]
          Length = 322

 Score =  119 bits (299), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 53/217 (24%), Positives = 84/217 (38%), Gaps = 6/217 (2%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            T+        +LY D +I V +KP  +S     G        ++        +  + HR
Sbjct: 94  PTETPVPAGIGILYSDERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHR 152

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKEC-IANWLLKKS 206
           LD+ T+G+L++ R R   +   E F  R + K Y   + V   P  +      +    +S
Sbjct: 153 LDRVTAGVLLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTATKSGWQVRS 212

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            I  +   +  +   G   A++   +I      +   E  P TGRTHQ+R+H   +G PI
Sbjct: 213 RIIKERGILQAREVPGVPNAVTDIALIGEHG-GWGLYEASPRTGRTHQIRLHMQRLGAPI 271

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           V D  Y             + L L A  M    P  G
Sbjct: 272 VNDPFY-PVVLDTPVDDFTHPLQLQAWRMGFTDPVTG 307


>gi|330861062|emb|CBX71331.1| hypothetical protein YEW_JI40630 [Yersinia enterocolitica W22703]
          Length = 122

 Score =  119 bits (299), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 36/121 (29%), Positives = 63/121 (52%), Gaps = 7/121 (5%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           VQ + +  DE   R+D +  N    +    + +I+R G+VRV+K R+K   ++  G    
Sbjct: 8   VQLITISADEAGQRIDNFLLNKLKGVPKSMIYRIVRKGEVRVNKGRIKPEYKLADGD--- 64

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
              V+      + E++ +  S  L K +  L   +L+ED  + V NKP+G +V GGSG++
Sbjct: 65  ---VVRVPPVRVAEREEIQVSAKLDKVA-ALADCILFEDDYLLVLNKPSGTAVHGGSGLS 120

Query: 127 Y 127
           +
Sbjct: 121 F 121


>gi|114561967|ref|YP_749480.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114333260|gb|ABI70642.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 281

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 59/296 (19%), Positives = 112/296 (37%), Gaps = 50/296 (16%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRV-----KFNNRIQSGQVVRIPPVINALNHIIK 79
                  ++   L+  ++ G +     +      +    +Q G  +          H+  
Sbjct: 22  LLAQVSSLSKQVLKDAMQKGAIWHSHGKQTNRIRRAKKPLQPGDKL----------HLYY 71

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            Q ILD  V   +        LL+++++  ++ KP G+  QG     +            
Sbjct: 72  NQYILDEQVTPAE--------LLFDEAEYSIWYKPYGMRCQGSKWSDHTTINRYAELNMQ 123

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             +   + HRLD+  +G+LV+  ++ A   + + F  R ++K Y  +V G   +    I 
Sbjct: 124 PQRNAFIIHRLDRAATGLLVLGHSKKATAAIAKLFETRELEKYYQVIVEGEFPSNPVTIN 183

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVH 258
             +                       A+SH  ++   ++     ++++  TGR HQ+R+H
Sbjct: 184 TPV-------------------DNKPALSHATLLTYNSELNQSKVQVKIDTGRKHQIRIH 224

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
              +G P+VGD  +     G+  SP    L L + Y     P    L+ T  LP H
Sbjct: 225 MASLGHPVVGDRLHG---NGDEHSPD---LALTSCYFRFVCPLSNTLK-TFELPEH 273


>gi|290983884|ref|XP_002674658.1| predicted protein [Naegleria gruberi]
 gi|284088249|gb|EFC41914.1| predicted protein [Naegleria gruberi]
          Length = 314

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 54/309 (17%), Positives = 114/309 (36%), Gaps = 57/309 (18%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHY---PHINFVNLQKILR--SGQ------VRVD 49
           MS    +  + V  D    RLD +  + +     ++  +L K ++  +G+      +  D
Sbjct: 1   MSSFEQIASLTVSVDYHKERLDVFLFDCFFKERQVSKSSLGKTIQYSNGENSKYRFLYND 60

Query: 50  KKRVKFNNRIQSGQVVRIPPVINA----------------LNHIIKEQKILDSSVNLTKH 93
           ++  K   +++ G VV +                       ++  +E     S+ +    
Sbjct: 61  EETNKPALKLRHGDVVIVKERKEKTTTASSESSSSEQLSVASNTTEENAASSSTTSDAIM 120

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGG-------------SGIAYHIDGFLKSWVD-S 139
            + +   +L+ED  + V +KP  ++V                + + +H +G L +     
Sbjct: 121 PENIPLNILFEDDFLIVLDKPKFMTVHPSLKPKPRNTTGTLVNALLFHTNGKLSTCGSCE 180

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR---------RIQKIYWSLVWGI 190
           +  +P + HRLD++TSGI+VVA+       L + F  +         +I + Y +LV   
Sbjct: 181 EHYRPGIVHRLDRDTSGIMVVAKDDETHLALKKLFENKNVGDENNEDKITRYYQALVENE 240

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-------QKFCWL 243
               +  I  ++ +   +           E GA  +I+ +K    F        +    +
Sbjct: 241 LNQSEGRIEIYIKRHHSMPSKREVTNNALETGAKLSITEYKEQKTFPVNNLTGCKVLTLV 300

Query: 244 EMQPHTGRT 252
             +  TG  
Sbjct: 301 RCKLLTGSK 309


>gi|256831879|ref|YP_003160606.1| pseudouridine synthase [Jonesia denitrificans DSM 20603]
 gi|256685410|gb|ACV08303.1| pseudouridine synthase [Jonesia denitrificans DSM 20603]
          Length = 362

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 53/256 (20%), Positives = 100/256 (39%), Gaps = 17/256 (6%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAG 116
           ++++G+VV        L    +   ++    +     +      +L+ED  +YV +KP  
Sbjct: 89  KLRAGEVVDEIGRPLTLESPYRPGGLIHLYRDPDPEPEVPFACDVLFEDDDLYVIDKPHF 148

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           ++     G        ++   D+   +    HRLD+ T+G+LV  + R       E F  
Sbjct: 149 LASTP-KGRYVTETALVRLRKDTGNPELSPAHRLDRLTAGVLVFTKRRELRGAYQELFAQ 207

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R++ K+Y ++    P      +      +S I  ++  +      G     +   + D  
Sbjct: 208 RQVTKVYQAVAPTNPA-----VDLPATVRSRIVKEHGIMRAHTMPGEPNTETLVTLTDTA 262

Query: 237 A---------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
                     Q      + PHTG+THQLR+H   +G  IV D+ Y  +F    +   ++ 
Sbjct: 263 TLPAGHDVAVQDVGLYTLYPHTGKTHQLRIHMASLGLGIVYDN-YYPDFYHVESDDYRHP 321

Query: 288 LYLHARYMDLPHPEGG 303
           L L +  +    P  G
Sbjct: 322 LQLLSSQLAFTDPLSG 337


>gi|226324971|ref|ZP_03800489.1| hypothetical protein COPCOM_02763 [Coprococcus comes ATCC 27758]
 gi|225206319|gb|EEG88673.1| hypothetical protein COPCOM_02763 [Coprococcus comes ATCC 27758]
          Length = 121

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 33/125 (26%), Positives = 58/125 (46%), Gaps = 9/125 (7%)

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           N  + +  I    + +   NEK    A++H++V++ F   + ++  +  TGRTHQ+RVH 
Sbjct: 2   NAPIGRHPIDRKKMSI---NEKNGRNAVTHYRVLERFGD-YTYIACELETGRTHQIRVHM 57

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKT 318
             +  P++GD  Y                 LHA+ + + HP  G+ ++  APLP +    
Sbjct: 58  ASIHHPLLGDCVYGP----AKCPWTLQGQTLHAKILGIIHPRTGKYMEFDAPLPEYFENL 113

Query: 319 WDSLG 323
              L 
Sbjct: 114 LKKLR 118


>gi|219126101|ref|XP_002183303.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217405059|gb|EEC45003.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 383

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 63/243 (25%), Positives = 101/243 (41%), Gaps = 26/243 (10%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-----QKPRLT 147
             D +   +L++D +I V +KP+G++    +         L     + G      +    
Sbjct: 90  PHDDVDVPVLFQDDQILVVHKPSGVAHHNDADTGRLGILNLIRHQQTTGRFAYPHRLYGV 149

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+ TSGILV+A+T  AAQ LT+++R  R+ K Y  L        K+     +  +  
Sbjct: 150 HRLDRVTSGILVLAKTPGAAQILTQAWREDRVTKYYVGLSGNKATTSKQ---GHVRGRMI 206

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVID-----------CFAQKFCWLEMQPHTGRTHQLR 256
            G     ++ +   G+N A + F                       L  +P TGRTHQLR
Sbjct: 207 RGRRRSWLLTRETHGSNVAHTRFFTAGLGHLAPPSSTLTNVSPKTLLLFRPTTGRTHQLR 266

Query: 257 VHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLHARYM--DLPHPEGGRLQITAPLP 312
           V A  +G P+ GD  Y    +   N ++P +  L+    ++  D  HP      +  P P
Sbjct: 267 VAAKSVGLPLWGDPVYRDGRHRTENASTPSRTLLHAAGWHVPADDTHP---EWTLWCPPP 323

Query: 313 AHM 315
              
Sbjct: 324 PEF 326


>gi|67462777|ref|XP_648050.1| RNA pseudouridylate synthase [Entamoeba histolytica HM-1:IMSS]
 gi|56463954|gb|EAL42664.1| RNA pseudouridylate synthase, putative [Entamoeba histolytica
           HM-1:IMSS]
          Length = 373

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 66/270 (24%), Positives = 114/270 (42%), Gaps = 36/270 (13%)

Query: 26  KNHYPHINFVNLQKILRSGQVR--VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           ++ + +I+   +Q  ++  ++   ++K  +K    I               N +I+E  I
Sbjct: 44  RSEFKYISKEEIQNQIKE-EITYLINKNGIKKETTI---------------NSVIEEHDI 87

Query: 84  LDSSVNLTKHSDFLKSILLYED-SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           L S  +L +    +K I + E+ ++  V NKP+GI V       Y+ +  +   ++    
Sbjct: 88  LISKCHLHEPPVPIKEIQIIENTNEYLVINKPSGIPVHPTG--RYNQNCIINILLNEYHF 145

Query: 143 -KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--------IQKIYWSLVWGIPKN 193
              +  +RLD+ TSGIL+ A+T+  A       + +         +QKIY + V G   +
Sbjct: 146 SHLKPVYRLDKNTSGILLFAKTKIFASSFQSILKEKSSVISSTSSLQKIYLARVVGYFPD 205

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRT 252
             E   N  L     G +    + ++      A S FK +          +E  PHTGRT
Sbjct: 206 TIEV--NLPLHLVRFGTESQSCICED---GIEARSSFKRLFFDKDSNTSVIECVPHTGRT 260

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
           HQLR+H   +  PI  D  Y  N   N+  
Sbjct: 261 HQLRLHLKAIHHPIANDSAYLLNQIHNYRQ 290


>gi|229817223|ref|ZP_04447505.1| hypothetical protein BIFANG_02483 [Bifidobacterium angulatum DSM
           20098]
 gi|229785012|gb|EEP21126.1| hypothetical protein BIFANG_02483 [Bifidobacterium angulatum DSM
           20098]
          Length = 264

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 58/246 (23%), Positives = 90/246 (36%), Gaps = 26/246 (10%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +        +LYED +I V +KP  ++     G+ Y     ++             HRL
Sbjct: 12  EEPHIPFDCTVLYEDERIIVVDKPHFLATTP-RGMWYRETALIRLRQTYGEPDIIPAHRL 70

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKECIAN-------W 201
           D+ T+GI+V  R RA+       F+     K Y   + +  I +     I          
Sbjct: 71  DRLTAGIVVFVRDRASRGAYQLLFQNHLAVKTYECLAPLRPIGRPCFGTIRKLEPPRPFP 130

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC--------------WLEMQP 247
           L ++S I      +    E G   A +  + +                         + P
Sbjct: 131 LERRSRIVKQRGILQAYEEPGTPNAETLIERVGLGHMDRTGYPLSGMDGRHMVARYVLHP 190

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-Q 306
            TG+THQLRVH   +G PIVGD  Y      +      N L L AR ++   P  G   +
Sbjct: 191 RTGKTHQLRVHMNSLGLPIVGDDFY-PRIIEHAYDDFSNPLELVARELEFDDPLTGEHRR 249

Query: 307 ITAPLP 312
            T+ +P
Sbjct: 250 FTSRIP 255


>gi|297670733|ref|XP_002813514.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           3-like isoform 1 [Pongo abelii]
          Length = 350

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 109/284 (38%), Gaps = 43/284 (15%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSK 140
           +L  +++  +  D L++ ++     +   NKP G+ V G  G          L   +   
Sbjct: 65  LLPKNLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLG 124

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKE 196
            Q+ ++     +E+SG+++++     A  L +    + R +R    Y ++  GIP   + 
Sbjct: 125 KQELQVVRASGKESSGLVLLSSCPQTASRLQKFFTHARRAQRPTATYCAVTDGIPAASEG 184

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            I   L  +   G +    VK   +     G    +SHF+V+         +++QP T  
Sbjct: 185 KIQAALKLEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFRVVAT-GSGCALVQLQPLTVF 243

Query: 252 THQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQN---KLYLHARYMDLPHPE--- 301
           + QL+VH +   CP++GDH Y A         F  P +N   +  L    +   H     
Sbjct: 244 SSQLQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAENKPQRQVLDEALLRCLHLTPSQ 303

Query: 302 ---------------------GGRLQITAPLPAHMVKTWDSLGF 324
                                   +++ APLP +  +T   LG 
Sbjct: 304 AAQLPLHLHLHRLLLPGTRASDTPIELLAPLPPYFSRTLQCLGL 347


>gi|282864375|ref|ZP_06273431.1| pseudouridine synthase [Streptomyces sp. ACTE]
 gi|282560862|gb|EFB66408.1| pseudouridine synthase [Streptomyces sp. ACTE]
          Length = 314

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 50/225 (22%), Positives = 90/225 (40%), Gaps = 12/225 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            +        +++ D  + V +KP  ++    G  I       L++ +     + +  HR
Sbjct: 90  PEAPVPFPVGVVHRDEHVVVADKPHFLATTPRGRHITETAVARLRAHLGI--AELQPAHR 147

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+++              FR R ++K Y ++    P+     +A     +  I 
Sbjct: 148 LDRLTAGLVLFVVRPEERGAYQTLFRDRLVRKEYEAVAPYDPE-----VALPRTVRGRIV 202

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +   +  + E G   + S  ++++  A       + P TGRTHQLRVH   +G P+V D
Sbjct: 203 KERGVMAARVEPGEANSESRIELLEHRA-GLGRYRLLPATGRTHQLRVHMNALGLPLVHD 261

Query: 270 HKYCANFKGNFTSPIQ--NKLYLHARYMDLPHPEGGR-LQITAPL 311
             Y A               L L AR ++   P  GR  +  + L
Sbjct: 262 PVYPAVLPEPEPGGEDYTRPLQLLARVLEFTDPVTGRPHRFESGL 306


>gi|226306673|ref|YP_002766633.1| pseudouridine synthase [Rhodococcus erythropolis PR4]
 gi|226185790|dbj|BAH33894.1| putative pseudouridine synthase [Rhodococcus erythropolis PR4]
          Length = 304

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 61/260 (23%), Positives = 104/260 (40%), Gaps = 12/260 (4%)

Query: 50  KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL-DSSVNLTKHSDFLKSILLYEDSKI 108
            +R  + + + +G VV             +  + +        +     +  +LY D  I
Sbjct: 38  GERDLWADLVNAGDVVDEHGRKITSRTPYQPTRFVYFYREPAPEIPVPHEIKILYRDDSI 97

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            V +KP  ++     G        ++   D         HRLD+ T+G++V   T    +
Sbjct: 98  LVIDKPHFLATIP-RGAHIVESAVVRLRRDLDLPDLAPVHRLDRMTAGVIVFTVTPDLRR 156

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
              E F  +RI K Y ++    P+          + K H  G+        E  +  +I 
Sbjct: 157 PYQELFAEQRIVKEYEAIAGFDPELTFPRTVRSRINKVH--GEMTATEIDGEPNSETSIE 214

Query: 229 HFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD---HKYCANFKGNFTSPI 284
             + I D   +      + P TGRTHQLR+H   +G PIVGD    +Y     G+F++P+
Sbjct: 215 LIETITDSAGRTLGRYRLLPRTGRTHQLRLHLNSLGVPIVGDNYYPEYLPAVPGDFSTPL 274

Query: 285 QNKLYLHARYMDLPHPEGGR 304
             +L   AR ++ P P  G+
Sbjct: 275 --RLL--ARALEYPDPITGQ 290


>gi|256823775|ref|YP_003147738.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
 gi|256797314|gb|ACV27970.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
          Length = 282

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 55/278 (19%), Positives = 105/278 (37%), Gaps = 48/278 (17%)

Query: 31  HINFVNLQKILRSGQVRVD-KKRVKF----NNRIQSGQVVRIPPVINALNHIIKEQKILD 85
            ++   ++  +  G V +   K+ +     N R++ G+ + +      L+  + + +   
Sbjct: 37  GLSKQRVKDAMTKGAVWLSHGKQARPLRRKNARLRLGEELHLYYNEQVLSETVAKPE--- 93

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
                          L+ ++    V+NKP G+  QG     +     L        ++  
Sbjct: 94  ---------------LIADEGDYSVWNKPNGVWSQGSKWGDHCSISRLVEEHFDYNRQTY 138

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+   G+L++A  + AA  L+  F  R ++K Y + V G   +    I   +   
Sbjct: 139 VVHRLDKAARGLLILAHNKEAAAALSAMFAKRTVEKHYLAWVNGQFPHDSITIDKPI--- 195

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                        + K A   ++  +      +    L +Q  TGR HQ+R+H   +G P
Sbjct: 196 -------------DNKPAKSIVTLKEY--DADKDRSLLSVQILTGRKHQIRIHLSSLGFP 240

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           I+GD  +    +          L L A  +D   P  G
Sbjct: 241 IIGDRLHGEPTQSQD-------LQLMAYKLDFQCPITG 271


>gi|328881321|emb|CCA54560.1| Ribosomal large subunit pseudouridine synthase A [Streptomyces
           venezuelae ATCC 10712]
          Length = 308

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 48/215 (22%), Positives = 85/215 (39%), Gaps = 10/215 (4%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTH 148
             +        +++ D +I V +KP  ++    G  +       L+  +     +P   H
Sbjct: 88  PAETPVPFPIGVVHRDERIVVADKPHFLATMPRGRHVTETALARLRRELGLPYLQP--AH 145

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ T+G+++              FR RR++K Y ++    P      +   +  +S I
Sbjct: 146 RLDRLTAGLVLCVVRPEDRGAYQTLFRDRRVRKEYEAVAPYDPA-----VGLPVTVRSRI 200

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
             +   +  +   G   A S  +++           + P TGRTHQLRVH   +G PI+ 
Sbjct: 201 EKERGVMAARELPGEPNAESRIELVGRAG-GLGRYRLVPETGRTHQLRVHMNGLGLPILH 259

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           D  Y    + +        L L AR ++   P  G
Sbjct: 260 DPIY-PVVRADGPEDFGRPLQLLARTLEFTDPFTG 293


>gi|260949943|ref|XP_002619268.1| hypothetical protein CLUG_00427 [Clavispora lusitaniae ATCC 42720]
 gi|238846840|gb|EEQ36304.1| hypothetical protein CLUG_00427 [Clavispora lusitaniae ATCC 42720]
          Length = 432

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 53/193 (27%), Positives = 92/193 (47%), Gaps = 8/193 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LYED  I V NKPAG+         +  +   +      G      HRLD+ TSG+LV+
Sbjct: 146 VLYEDENILVVNKPAGVPTHPNG--IFRRNSLTEIVRFELGVSVYPCHRLDKGTSGVLVL 203

Query: 161 ARTRAAAQHLTESFRMRR--IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           A+T+   + L E  + ++  ++K Y + V G          + +   +  G  Y+++   
Sbjct: 204 AKTK-TGKMLQEVLQNKKSHVEKWYVARVRGKFPFASCSYTSPVFSINTAGTGYLNIPNA 262

Query: 219 NEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NF 276
               A  + +HFK++    +     +  +P +G+ HQ+RVH  +MG PI  D  Y A N 
Sbjct: 263 ERVPATSS-THFKMVSYSPELDESIVFCRPISGKMHQIRVHLRNMGYPISNDPLYNAENG 321

Query: 277 KGNFTSPIQNKLY 289
            G+  + ++ +LY
Sbjct: 322 LGHAKNQLEKELY 334


>gi|227874155|ref|ZP_03992360.1| pseudouridylate synthase [Oribacterium sinus F0268]
 gi|227840002|gb|EEJ50427.1| pseudouridylate synthase [Oribacterium sinus F0268]
          Length = 206

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 49/209 (23%), Positives = 84/209 (40%), Gaps = 32/209 (15%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ E     VF K AG+  +  +                  +     HRLD+  SG+L+
Sbjct: 1   MIIEETKDYLVFYKEAGLDSEKDAP-----------------KDCLPIHRLDKVASGLLL 43

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLV----WGIPKNKKECIANWLLKKSHIGGDYVHV 215
             + + AA  L+     ++I+K Y  +V     G    ++ C  ++L K S         
Sbjct: 44  YGKNKEAAAALSRQLTEKKIKKRYHIVVPKGEEGKALPEEGCFQDYLYKDSK--KQKCFP 101

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           VK   KG   AI  +K+++   + +  L+++  TGR HQ+R      G P+ GD KY + 
Sbjct: 102 VKSLRKGVKEAILRYKILEENGE-WMLLDVELETGRFHQIRAQFASRGFPLYGDGKYGSR 160

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            KG            H   +     + G 
Sbjct: 161 QKGTVGL--------HCYQLSFLDVKTGE 181


>gi|313811717|gb|EFS49431.1| RNA pseudouridine synthase [Propionibacterium acnes HL083PA1]
 gi|313832484|gb|EFS70198.1| RNA pseudouridine synthase [Propionibacterium acnes HL007PA1]
 gi|313832710|gb|EFS70424.1| RNA pseudouridine synthase [Propionibacterium acnes HL056PA1]
 gi|314975148|gb|EFT19243.1| RNA pseudouridine synthase [Propionibacterium acnes HL053PA1]
 gi|314977558|gb|EFT21653.1| RNA pseudouridine synthase [Propionibacterium acnes HL045PA1]
 gi|314985095|gb|EFT29187.1| RNA pseudouridine synthase [Propionibacterium acnes HL005PA1]
 gi|315096956|gb|EFT68932.1| RNA pseudouridine synthase [Propionibacterium acnes HL038PA1]
 gi|327332450|gb|EGE74185.1| RNA pseudouridylate synthase family protein [Propionibacterium
           acnes HL096PA2]
 gi|327446775|gb|EGE93429.1| RNA pseudouridine synthase [Propionibacterium acnes HL043PA2]
 gi|327448784|gb|EGE95438.1| RNA pseudouridine synthase [Propionibacterium acnes HL043PA1]
 gi|328759846|gb|EGF73436.1| RNA pseudouridylate synthase family protein [Propionibacterium
           acnes HL099PA1]
          Length = 281

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 50/217 (23%), Positives = 82/217 (37%), Gaps = 6/217 (2%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            T+        +LY D +I V +KP  +S     G        ++        +  + HR
Sbjct: 53  PTETPVPAGIGILYSDERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHR 111

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRI---QKIYWSLVWGIPKNKKECIANWLLKKS 206
           LD+ T+G+L++ R R   +   E F  R +    ++   +V            +    +S
Sbjct: 112 LDRVTAGVLLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDSAGEGVTATKSGWQVRS 171

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            I  +   +  +   G   A++   +I      +   E  P TGRTHQ+R+H   +G PI
Sbjct: 172 RIIKERGILQAREVPGVPNAVTDIALIGEHG-GWGLYEASPRTGRTHQIRLHMQRLGAPI 230

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           V D  Y             + L L A  M    P  G
Sbjct: 231 VNDPFY-PVVLDTPVDDFTHPLQLQAWRMGFTDPVTG 266


>gi|168037108|ref|XP_001771047.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162677735|gb|EDQ64202.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 324

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 58/303 (19%), Positives = 107/303 (35%), Gaps = 58/303 (19%)

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
           + + P    L+  ++ Q+ L +   +       +  +L+ED  + + NKP G+       
Sbjct: 20  IPLSPFAGELSKEVELQRALVAEAAMKAGPAIGQESVLFEDDWLMIVNKPRGLYC----- 74

Query: 125 IAYHIDGFLKSWVDSK--GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              H+   + S   S        + +RLD++TSGI+V+ + + AA  LT +F  R +QK 
Sbjct: 75  --EHVLATIPSLCRSSETQLHLHMANRLDRDTSGIMVITKCKEAAAKLTRAFTNREVQKT 132

Query: 183 YWS-LVWGIPKNKKECIANWLLKKSH-----IGGDYVHVVKQNEKGANYAISHFKVID-- 234
           Y +      P  +K  I +   +  +          +             ++  ++I   
Sbjct: 133 YLAQCARAKPTWRKTRIESGHGRSRYGAWRVYAKHDIGRRLPGGSTVRDMVTRVEIIAGT 192

Query: 235 --------------------------------------CFAQKFCWLEMQPHTGRTHQLR 256
                                                    Q+   +   P TGRTHQ+R
Sbjct: 193 NSLKQDPQPSPEHDFVEVVVGREDEVRLGKDEVEDGSLRETQELTVVRAFPETGRTHQIR 252

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
           +H  ++G  + GD KY         S   +   LHA  +   HP     + +  P P+  
Sbjct: 253 LHCQYLGLSLCGDVKYGGPLVWQGLSYDSH--ALHAESLAFRHPITKEPISVVTPCPSWA 310

Query: 316 VKT 318
            + 
Sbjct: 311 AQL 313


>gi|254785984|ref|YP_003073413.1| pseudouridine synthase, Rlu family [Teredinibacter turnerae T7901]
 gi|237683526|gb|ACR10790.1| pseudouridine synthase, Rlu family [Teredinibacter turnerae T7901]
          Length = 231

 Score =  119 bits (298), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 91/231 (39%), Gaps = 28/231 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++ E     + +K  G  V G +      +   L+   D   +     HRLD+ TSG+LV
Sbjct: 5   IVDEQPGFLLIHKYPGAVVHGTADSGEITLTQSLRH--DFSCKSLFPCHRLDRTTSGLLV 62

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           VA+  AA ++ +  F  R I K Y +L    P  K+  +   ++K     G ++     N
Sbjct: 63  VAKGEAANKYFSTLFEKRAIDKCYLALSAKKPAKKQGAVRGDMVKAR--NGSWMLTRSLN 120

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
                 A + F       +      ++P TG+THQLRV    +G PI+GD +Y       
Sbjct: 121 A----PAHTQFFS-KGGVEGKRLFVLRPITGKTHQLRVAMKSLGAPILGDERYGGGDA-- 173

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH--------MVKTWDSL 322
                 ++ YLHA  +     +G       P P H             D L
Sbjct: 174 ------DRCYLHAFALQFSV-DGNEYSYVCP-PEHGDLFCSQNFKSALDDL 216


>gi|314965704|gb|EFT09803.1| RNA pseudouridine synthase [Propionibacterium acnes HL082PA2]
          Length = 281

 Score =  119 bits (298), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 102/264 (38%), Gaps = 15/264 (5%)

Query: 47  RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYED 105
           +V  +RV  +  +  G+ V         +     Q  +    +L   +     I +LY D
Sbjct: 11  KVGGQRV--DEMLDEGRFVDESGRTFRRDSPFTPQTFVFFHRDLPTETPVPAGIGILYSD 68

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
            +I V +KP  +S     G        ++        +  + HRLD+ T+G+L++ R R 
Sbjct: 69  ERILVVDKPPFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHRLDRVTAGVLLLTRERK 127

Query: 166 AAQHLTESFRMRRIQKIY--WSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKG 222
             +   E F  R + K Y   + V   P  +      +    +S I  +   +  +   G
Sbjct: 128 WRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTATKSGWQVRSRIIKERGILQAREVPG 187

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GN 279
               ++   +I      +   E  P TGRTHQ+R+H   +G PIV D  Y         +
Sbjct: 188 VPNTVTDIALIGEHG-GWGLYEASPRTGRTHQIRLHMQRLGAPIVNDPFYPVVLDIPVDD 246

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG 303
           FT P+Q    L A  M    P  G
Sbjct: 247 FTHPLQ----LQAWRMGFTDPVSG 266


>gi|320536011|ref|ZP_08036072.1| RNA pseudouridine synthase [Treponema phagedenis F0421]
 gi|320147136|gb|EFW38691.1| RNA pseudouridine synthase [Treponema phagedenis F0421]
          Length = 233

 Score =  119 bits (298), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 98/238 (41%), Gaps = 28/238 (11%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           ++ +     ++Y+D+ + V  K  G          ++   FL+             +RLD
Sbjct: 9   QNQESENQRIIYKDASLAVIIKKNG-----EDAQKFYQKYFLQHAYAQA------VNRLD 57

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +  SG++++A        L+ +F   +I K Y+++     K KK      +L        
Sbjct: 58  KPVSGLMLIACNSKIHTALSHAFSDGKIVKTYFAICE---KPKKPTTDIPILVPQTCNDT 114

Query: 212 YVHVVKQ------NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
            +   K+      ++KGA  A   +  +    + + +L++ P +GRTHQ+R    H+G P
Sbjct: 115 LIFSSKKQKAFISDKKGAKEACLSW-TLCARGENYDFLQVIPISGRTHQIRAQLAHIGRP 173

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTWDSL 322
           I GD KY A            +L  HA  ++  HP     L I+   P +M   W + 
Sbjct: 174 IKGDLKYGAKRSEKTGGI---RL--HAYSLEFLHPVLHKPLHIST-YPENMDALWAAC 225


>gi|227547691|ref|ZP_03977740.1| ribosomal pseudouridine synthase [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227080217|gb|EEI18180.1| ribosomal pseudouridine synthase [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 323

 Score =  119 bits (298), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 95/261 (36%), Gaps = 23/261 (8%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQ-KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
            R +SG+VV           +++    +        +         +YED  I V +KP 
Sbjct: 58  QRFESGEVVLRDGTALRPEQLVEPGTDVFFYRRPAPEKPVPYDIETVYEDDTILVVDKPP 117

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            ++    +         ++    +  +     HRLD+ TSG+L++ + +       E F 
Sbjct: 118 FLATMPRAA-HITESATVRLRRATGNEDLTPAHRLDRMTSGLLLLTKQKQHRSAYQELFA 176

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHF---- 230
             ++ K Y ++   I       I +    + HI   +  +     +G    A++H     
Sbjct: 177 AHQVHKRYEAIAEDI------GIESPTWWRHHIDKQHGEIASTVIEGREPNALTHVLEAL 230

Query: 231 -------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-NFKGNFTS 282
                  + +           ++P TGRTHQLRV     G PI+GD  Y   N  G    
Sbjct: 231 RIDAPTMQSLHSVTFPLARYLLEPVTGRTHQLRVQMNEAGAPILGDPVYPTVNPFGEEDF 290

Query: 283 PIQNKLYLHARYMDLPHPEGG 303
            +  +L   + Y+    P  G
Sbjct: 291 AVPMRL--KSVYLGFRDPLTG 309


>gi|300933570|ref|ZP_07148826.1| putative pseudouridylate synthase [Corynebacterium resistens DSM
           45100]
          Length = 224

 Score =  118 bits (297), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 47/220 (21%), Positives = 84/220 (38%), Gaps = 11/220 (5%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   ++ E   + V NKP G+               +   V  +       HRLD+ T G
Sbjct: 1   MDIPVIAETPDVLVVNKPHGLPSTPNGRFMRACAQTMLR-VRREESDLVAIHRLDRLTGG 59

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV++R      +L   F+ R ++K+Y + V             + ++ + I  D    V
Sbjct: 60  VLVLSRRPETRSYLQTQFQNRTVRKVYEA-VSAYRLPHLSQWTRFEVEMTKIPHDPQ--V 116

Query: 217 KQNEKGANYAISHFKVI------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           K  +       +  +++                E++P TG THQ+R    H+G P++GD 
Sbjct: 117 KVGQGNGKTTETWVRLLGPVASDQRKEAASWRYEVRPKTGHTHQIRALMNHLGAPLIGDD 176

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
            Y   ++      +   + L A  + L  P G      AP
Sbjct: 177 TY-PEYQPRPAEKLDPTMGLQAVELTLCLPGGEEAIFRAP 215


>gi|311063917|ref|YP_003970642.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           bifidum PRL2010]
 gi|310866236|gb|ADP35605.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           bifidum PRL2010]
          Length = 253

 Score =  118 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 56/243 (23%), Positives = 86/243 (35%), Gaps = 23/243 (9%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +        ++YED+ I V +KP  ++     G+ Y     ++             HRL
Sbjct: 10  EEPHIPFDIDVVYEDAGIIVIDKPHFLATTP-RGMWYRQTALIRLREMFDEPDITPAHRL 68

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIAN-------W 201
           D+ T+GI+V  R  A        F+ R+I K Y  L    P  +     +          
Sbjct: 69  DRLTAGIVVFVRDPALRGAYQMMFQGRKISKTYECLAPCRPTTRPRYGTVERLDPPVVFP 128

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKV-----------IDCFAQKFCWLEMQPHTG 250
           L ++SHI      +    E     A +   +           +          E+ P TG
Sbjct: 129 LRRRSHITKLRGVLQAFEEPQTVNAETVIDLAAGEYPSMGGRLCHGKNGLRAYELHPLTG 188

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
           +THQLRVH   +G PI GD  Y               L L AR +    P  G   +  +
Sbjct: 189 KTHQLRVHMNSIGLPIHGDDFY-PRIVERAYDDFSTPLELVARSLRFTDPVSGEPREFIS 247

Query: 310 PLP 312
            +P
Sbjct: 248 RIP 250


>gi|255542880|ref|XP_002512503.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223548464|gb|EEF49955.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 321

 Score =  118 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 55/262 (20%), Positives = 101/262 (38%), Gaps = 51/262 (19%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS---------WVDSKGQKPRLTH 148
           +S +LYED  +   NKP G+       +   +   L +           +    +  L +
Sbjct: 56  RSDVLYEDQWLIAVNKPQGVYC---ETVLESVPRVLAASAELTDPSEGAEGNPHEFHLAN 112

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD++TSG++V+ ++   A  L ++F   +I+K Y +L  G+    ++        +S  
Sbjct: 113 RLDRDTSGVMVITKSHKVASKLVKAFTDHKIKKTYIALCIGLAPKWEKITIKSGHGRSKF 172

Query: 209 GGDYVHVVK------QNEKGANYAISHFKVIDCFAQKFC--------------------- 241
           G   V+                   + F+++    Q                        
Sbjct: 173 GVWRVYAASDVGQTLPGGSTVKDMETSFELLSVNGQGSFKELSEFEKDENILVVEEKAAK 232

Query: 242 ---------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
                     +   P +GRTHQ+R+H  ++G  I GD KY   ++    +   ++L  HA
Sbjct: 233 NADVKKVEILVRAFPQSGRTHQIRLHCQYLGISIRGDVKYEGVYEWEGRTYDGHEL--HA 290

Query: 293 RYMDLPHPEGG-RLQITAPLPA 313
             +   HP  G  + + APLP+
Sbjct: 291 ETLSFEHPVTGVPVMLRAPLPS 312


>gi|260577609|ref|ZP_05845547.1| pseudouridylate synthase [Corynebacterium jeikeium ATCC 43734]
 gi|258604262|gb|EEW17501.1| pseudouridylate synthase [Corynebacterium jeikeium ATCC 43734]
          Length = 297

 Score =  118 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 57/268 (21%), Positives = 96/268 (35%), Gaps = 29/268 (10%)

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL---KSILLYEDSKIYVFNKPAG 116
            +G        + A   ++  +       +  +  + L      +LY  S   V +KP G
Sbjct: 17  AAGDSPYESGTLLAPGLVLAGRTPTWVYPDFPEEPEELLAADIPVLYSGSDAVVVDKPHG 76

Query: 117 ISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +     G  +       ++  +     +    HRLD++T G+LV+AR       L   F+
Sbjct: 77  LPSTPNGRLLRATAQSLMRVRLQE--PELVAAHRLDRDTRGLLVLARNPVTRGFLQTQFQ 134

Query: 176 MRRIQKIYWSLVWGIPKNKKEC--IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R + K Y +L   IP+   +   +   +LK      D   V   + + +   ++  + +
Sbjct: 135 RREVSKTYQALAADIPEIGSQWQDVQLPMLKI----KDDPQVKVVDGERSRLTVTRIRKL 190

Query: 234 D-------------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                                  E+QP TG THQLRV   H+G PI GD  Y     G  
Sbjct: 191 ASSAGAEARPVEATRAGTPTAVYELQPLTGYTHQLRVLMNHLGAPIYGDDTYPEYRPGAG 250

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQIT 308
                 +L   A  + L      R +I 
Sbjct: 251 AL----RLRAVAIELALVASLKNRQRIE 274


>gi|313771117|gb|EFS37083.1| RNA pseudouridine synthase [Propionibacterium acnes HL074PA1]
          Length = 281

 Score =  118 bits (297), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 50/217 (23%), Positives = 82/217 (37%), Gaps = 6/217 (2%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            T+        +LY D +I V +KP  +S     G        ++        +  + HR
Sbjct: 53  PTETPVPAGIGILYSDERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHR 111

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRI---QKIYWSLVWGIPKNKKECIANWLLKKS 206
           LD+ T+G+L++ R R   +   E F  R +    ++   +V            +    +S
Sbjct: 112 LDRVTAGVLLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDSAGEGVTATKSGWQVRS 171

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            I  +   +  +   G   A++   +I      +   E  P TGRTHQ+R+H   +G PI
Sbjct: 172 RIIKERGILQAREVPGVPNAVTDIALIGEHG-GWGLYEASPRTGRTHQIRLHMQRLGAPI 230

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           V D  Y             + L L A  M    P  G
Sbjct: 231 VNDPFY-PVVLDTPVDDFTHPLQLQAWRMGFTDPVTG 266


>gi|295131837|ref|YP_003582500.1| RNA pseudouridine synthase [Propionibacterium acnes SK137]
 gi|291375421|gb|ADD99275.1| RNA pseudouridine synthase [Propionibacterium acnes SK137]
          Length = 322

 Score =  118 bits (297), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 50/217 (23%), Positives = 82/217 (37%), Gaps = 6/217 (2%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            T+        +LY D +I V +KP  +S     G        ++        +  + HR
Sbjct: 94  PTETPVPAGIGILYSDERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHR 152

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRI---QKIYWSLVWGIPKNKKECIANWLLKKS 206
           LD+ T+G+L++ R R   +   E F  R +    ++   +V            +    +S
Sbjct: 153 LDRVTAGVLLLTRERKWRRPYQEIFERREVVKKYRLVAPVVHDSAGEGVTATKSGWQVRS 212

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            I  +   +  +   G   A++   +I      +   E  P TGRTHQ+R+H   +G PI
Sbjct: 213 RIIKERGILQAREVPGVPNAVTDIALIGEHG-GWGLYEASPRTGRTHQIRLHMQRLGAPI 271

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           V D  Y             + L L A  M    P  G
Sbjct: 272 VNDPFY-PVVLDTPVDDFTHPLQLQAWRMGFTDPVTG 307


>gi|145589394|ref|YP_001155991.1| pseudouridine synthase [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
 gi|145047800|gb|ABP34427.1| pseudouridine synthase [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
          Length = 299

 Score =  118 bits (297), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 55/289 (19%), Positives = 109/289 (37%), Gaps = 27/289 (9%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           L  +F + +PHI+          G ++ +D +       + S    R    +     + +
Sbjct: 24  LLEFFTSQFPHIDPSEWTARFDEGLIKTLDDQP------LLSSDAYRPNTHLIYFRRLAR 77

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                       +     +  +LY+D  I V +KP  + V       Y     L      
Sbjct: 78  ------------EPEIPFEEEILYQDEHILVADKPHFLPVTPSG--LYLHQTLLNRLKKK 123

Query: 140 KG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            G Q     HR+D++T+G+++ +       +    FR R + K+Y ++    P +K+   
Sbjct: 124 TGIQTLSPIHRIDRDTAGLVIFSINPYERANYQNLFRDRTVTKVYEAIA---PYSKELAN 180

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L  +S +      +  Q  +G   A ++ ++++  ++ +    + P +G+ HQLR H
Sbjct: 181 KLPLTYRSRLEESEHFLQMQEVEGEANADTYIELLEA-SEPWARYCLGPGSGKKHQLRCH 239

Query: 259 ALHMGCPIVGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
              +G PI  D  Y        +       L L A+ +    P  G  +
Sbjct: 240 LNALGAPIKHDQIYPVLTPYQEYDLDFSKPLQLLAKEIAFKDPISGEFR 288


>gi|302682125|ref|XP_003030744.1| hypothetical protein SCHCODRAFT_16635 [Schizophyllum commune H4-8]
 gi|300104435|gb|EFI95841.1| hypothetical protein SCHCODRAFT_16635 [Schizophyllum commune H4-8]
          Length = 506

 Score =  118 bits (297), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 93/255 (36%), Gaps = 34/255 (13%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
                +   +    +  L SG   ++ K  + +  I++G  +              E  +
Sbjct: 45  VVSTEFRDRSMEFYRYALESGVTTINGKVARPDTIIRNGDRIENVVHR-------HEPPV 97

Query: 84  LDSSVNLTKHSDFLKSILLYEDS-KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG- 141
             + V           +LL++      V NKP  I V       Y+ +  +   +   G 
Sbjct: 98  TSTPV----------RVLLHDTERGFIVVNKPGSIPVHAAG--RYNRNSLIHILMHEMGF 145

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIAN 200
           +K    +RLD+ TSG++++      A+ LT+ F    ++K Y + V G  P  +  C   
Sbjct: 146 KKVYTVNRLDRLTSGLMIIPLNADLARSLTKEFIEGSVRKEYVARVKGKFPDGEVICEEP 205

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            L     +G + VH           A + F  I         +        +HQLRVH  
Sbjct: 206 LLTVDRQMGLNIVH------PEGRPAKTVFNKIRYDPHTNSSVI------HSHQLRVHLQ 253

Query: 261 HMGCPIVGDHKYCAN 275
           ++G PI  D  Y + 
Sbjct: 254 YLGYPIANDPVYSSE 268


>gi|282852992|ref|ZP_06262329.1| RNA pseudouridine synthase [Propionibacterium acnes J139]
 gi|282582445|gb|EFB87825.1| RNA pseudouridine synthase [Propionibacterium acnes J139]
 gi|314982992|gb|EFT27084.1| RNA pseudouridine synthase [Propionibacterium acnes HL110PA3]
 gi|315091497|gb|EFT63473.1| RNA pseudouridine synthase [Propionibacterium acnes HL110PA4]
 gi|315094599|gb|EFT66575.1| RNA pseudouridine synthase [Propionibacterium acnes HL060PA1]
 gi|315105253|gb|EFT77229.1| RNA pseudouridine synthase [Propionibacterium acnes HL050PA2]
 gi|327328883|gb|EGE70643.1| RNA pseudouridylate synthase family protein [Propionibacterium
           acnes HL103PA1]
          Length = 281

 Score =  118 bits (297), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 102/264 (38%), Gaps = 15/264 (5%)

Query: 47  RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYED 105
           +V  +RV  +  +  G+ V         +     Q  +    +L   +     I +LY D
Sbjct: 11  KVGGQRV--DEMLDEGRFVDESGRTFRRDSPFTPQTFVFFHRDLPTETPVPAGIGILYSD 68

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
            +I V +KP  +S     G        ++        +  + HRLD+ T+G+L++ R R 
Sbjct: 69  ERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHRLDRVTAGVLLLTRERK 127

Query: 166 AAQHLTESFRMRRIQKIY--WSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKG 222
             +   E F  R + K Y   + V   P  +      +    +S I  +   +  +   G
Sbjct: 128 WRRPYQEIFERREVVKKYRLVAPVVHDPAGEGVTATKSGWQVRSRIIKERGILQAREVPG 187

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GN 279
               ++   +I      +   E  P TGRTHQ+R+H   +G PIV D  Y         +
Sbjct: 188 VPNTVTDIALIGEHG-GWGLYEASPRTGRTHQIRLHMQRLGAPIVNDPFYPVVLDIPVDD 246

Query: 280 FTSPIQNKLYLHARYMDLPHPEGG 303
           FT P+Q    L A  M    P  G
Sbjct: 247 FTHPLQ----LQAWRMGFTDPVSG 266


>gi|226944123|ref|YP_002799196.1| RNA pseudouridine synthase family protein [Azotobacter vinelandii
           DJ]
 gi|226719050|gb|ACO78221.1| RNA pseudouridine synthase family protein [Azotobacter vinelandii
           DJ]
          Length = 301

 Score =  118 bits (297), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 53/267 (19%), Positives = 106/267 (39%), Gaps = 13/267 (4%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQ-KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
            R++ G+V+     +    +  +E  ++        +        +L+ D  + V +KP 
Sbjct: 42  ERMRRGRVLDGEGNVLGPEYPYREALRVHYFREVAAETPIPFAEAVLHADDHLVVADKPH 101

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            + V       Y     L   V   G       HR+D+ T+G+++ +   A+       F
Sbjct: 102 FLPV--APVGEYVEQTLLARLVRRLGNPDLVPLHRIDRLTAGLVLFSCNPASRGRYQALF 159

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
           R RRI+K+Y ++   +P      ++  LL++S +       + +  +G   + +  +  +
Sbjct: 160 RERRIRKVYAAIAPALP-----GLSFPLLRRSRLVKGEPFFLMREAEGEPNSETRVEPGE 214

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHA 292
              + + ++ + P TG+THQLRVH   +G  I  D  Y              +  L L A
Sbjct: 215 RRGELWRYV-LHPVTGKTHQLRVHMATLGAGICNDPLYPRLLERSRREIDDYRRPLQLLA 273

Query: 293 RYMDLPHPEGGR-LQITAPLPAHMVKT 318
           + ++   P  GR  +  + L       
Sbjct: 274 QTLNFVDPLSGRERRFDSRLALDFDAC 300


>gi|309813100|ref|ZP_07706824.1| RNA pseudouridine synthase [Dermacoccus sp. Ellin185]
 gi|308432904|gb|EFP56812.1| RNA pseudouridine synthase [Dermacoccus sp. Ellin185]
          Length = 286

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 51/214 (23%), Positives = 83/214 (38%), Gaps = 8/214 (3%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +     +  +L+ED +I V +KP  ++     G        +K+            HRL
Sbjct: 57  EEPEVPFELTVLHEDERIVVVDKPHFLASIP-RGRHVTQSVVVKARAMLDEPTLVPVHRL 115

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ T+G+L++ R           F  R++ K Y ++    P      +      +SHI  
Sbjct: 116 DRLTAGVLLLTREPRWRAAYQGIFEARQVSKTYEAVAAYDPS-----LELPRRVESHIRK 170

Query: 211 DYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            +         GA   AI+  ++         +  + P TGRTHQLR+H   +G PIVGD
Sbjct: 171 QHGLAQAFEVPGAPVNAITDIELGQVRGDVATY-RLTPATGRTHQLRLHLNGLGIPIVGD 229

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             Y      +        L L A+ +    P  G
Sbjct: 230 PLYPHVRLDDDIDDFTRPLQLLAKTLAFVDPVDG 263


>gi|288921576|ref|ZP_06415849.1| pseudouridine synthase [Frankia sp. EUN1f]
 gi|288347046|gb|EFC81350.1| pseudouridine synthase [Frankia sp. EUN1f]
          Length = 279

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 51/261 (19%), Positives = 86/261 (32%), Gaps = 56/261 (21%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ED  +   +KP G++V G        D  L S     G++    HR+D+ TSG+++ A
Sbjct: 13  IFEDEAVLALDKPVGVAVMG-----ERHDTDLVSMAREAGEELFPAHRIDKVTSGVVLFA 67

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL----LKKSHIGGDYVHVVK 217
           +       LT  F  R + K Y +L           I   L      +  I  +   +V 
Sbjct: 68  KQLRHHGDLTRQFNRRTVDKTYLALTRTHGIPATATIDLPLSVGRKNRVRIAANRADIVT 127

Query: 218 QNEKGAN------------------------------------YAISHFKVIDCFAQKFC 241
                                                       +++H   +     +  
Sbjct: 128 VTADAGPADTTGASTAAAAPDPEAAPWLWTVPTAKTFPHVRTYPSVTHLARL-WEGTEHT 186

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +   P +GR HQ+RVH   +G PI GD          F      + +LHA  +      
Sbjct: 187 LVAAHPVSGRRHQIRVHLAWVGHPIEGDPL--------FERAPTTRTFLHAWRLAFDAGW 238

Query: 302 GG--RLQITAPLPAHMVKTWD 320
            G  R+ + A       ++ D
Sbjct: 239 DGGRRMVVEAVPGPDFWRSLD 259


>gi|291299500|ref|YP_003510778.1| pseudouridine synthase [Stackebrandtia nassauensis DSM 44728]
 gi|290568720|gb|ADD41685.1| pseudouridine synthase [Stackebrandtia nassauensis DSM 44728]
          Length = 254

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 50/236 (21%), Positives = 80/236 (33%), Gaps = 32/236 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L ++ ++   NKP GISV G        D  +       G K    HR+D+ TSG+++ A
Sbjct: 15  LVDNDQVLALNKPTGISVMG-----ERHDTDVARLAAEAGDKLHPVHRIDKATSGLVLFA 69

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           R       LT  F  R + K Y ++V          I   L              +    
Sbjct: 70  RDLKCHGVLTRQFNKRTVDKTYLAVVNSAEVPAAARIDLPLSVGRKNRVRVAAPREAITN 129

Query: 222 GAN----------------YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                               +++ +  +         L ++P +GR HQ+RVH    G  
Sbjct: 130 TGTDWTVPETDVFTHVKTYPSVTEYDTLWT-GDGLSLLAVRPISGRRHQIRVHLAWTGFA 188

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP--EGGRLQITAPLPAHMVKTW 319
           I GD  Y  N           ++ LH+  + +  P   G R  + A       +  
Sbjct: 189 ITGDSLYDKNPA--------TRMLLHSWRLAVEAPWLGGERTTLEAAPGPDFWEPL 236


>gi|78356022|ref|YP_387471.1| pseudouridylate synthase 23S RNA-specific-like protein
           [Desulfovibrio desulfuricans subsp. desulfuricans str.
           G20]
 gi|78218427|gb|ABB37776.1| Pseudouridylate synthases 23S RNA-specific-like protein
           [Desulfovibrio desulfuricans subsp. desulfuricans str.
           G20]
          Length = 305

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 98/263 (37%), Gaps = 41/263 (15%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRI-PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           + V+        R Q+G V+ I  P  N   HI+                   ++ +L  
Sbjct: 46  ITVNGVPRAAGYRTQTGDVIDIVCPCRNKTQHILP----------------AAQAEVLCR 89

Query: 105 DSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
            +      KP G+      +  A  ++  L S    +   P L +RLD+ TSG+++ A  
Sbjct: 90  TADYAAIFKPEGLHSARIAASPAPSVEDQLDSLFAGETP-PVLVNRLDRPTSGMVLAAFG 148

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
             AA+   +  +  +++K+Y ++V G  K         +  ++ +      V       A
Sbjct: 149 SHAAEAFRKFEQAGQVEKLYLAVVLGHMK-------APVACRNELNMQNRQVTTVLPHEA 201

Query: 224 NYAISHFKVI--------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
              + H  V+            QK   +    H G  HQ+R H  H G PI GD  Y +N
Sbjct: 202 QDPLRHTTVLPLRALPAESMDGQKTTLVLAAIHRGARHQIRAHLAHAGHPIAGDCVYGSN 261

Query: 276 FKGNFTSPIQNKLYLHARYMDLP 298
                       LYLH   +D+P
Sbjct: 262 QADGT-------LYLHHFKIDMP 277


>gi|78776648|ref|YP_392963.1| pseudouridine synthase [Sulfurimonas denitrificans DSM 1251]
 gi|78497188|gb|ABB43728.1| Pseudouridine synthase [Sulfurimonas denitrificans DSM 1251]
          Length = 244

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 59/294 (20%), Positives = 107/294 (36%), Gaps = 60/294 (20%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +        I+    + ++  G V    K+V     I  G +                  
Sbjct: 8   KLLAAQ-EGISNSEAKSMIDRGLVYAANKKV----MIARGDI------------------ 44

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
               +  L K     K   ++E+  + V +KPA ++                  ++ + +
Sbjct: 45  ---DTKTLFKVEKVEKIRPIFENDDLVVVDKPAHVNS---------------DEIERQFK 86

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L HRLD+ETSG+L++ +     +   + F+  R+ K Y + + GI     + I   +
Sbjct: 87  PAVLLHRLDKETSGVLMLVKNEEFREKAIQEFKKDRVYKEYIAWIEGILSEPVD-IDRPI 145

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L          +V  +       A +     D  +     ++   H GRTHQ+RVH  ++
Sbjct: 146 LTTKKNNRASSNVSSK----GKPARTEVFP-DLVSANKTKVKCIIHHGRTHQIRVHLRYI 200

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
             PIVGD +Y              ++ LHA  + L       ++ TAP P   +
Sbjct: 201 EHPIVGDEQYGGRRA--------KRVMLHAHKVRLL-----GMEFTAPEPKTFL 241


>gi|117922144|ref|YP_871336.1| pseudouridine synthase [Shewanella sp. ANA-3]
 gi|117614476|gb|ABK49930.1| pseudouridine synthase [Shewanella sp. ANA-3]
          Length = 305

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 54/289 (18%), Positives = 104/289 (35%), Gaps = 30/289 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   HY HI     ++ +  G+V             Q G ++ +             +++
Sbjct: 28  FLIEHYAHIGEAVWRQRILDGKVH-----------WQDGSLIGLDTAYRPTARAYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +     +S +L++D  + +  KP  + V              +  + +    
Sbjct: 77  P------VETQVPFESPILFQDDNLILAYKPHFLPVTPSGDYVNECL-VHRLRLSTGIDT 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKE 196
               HRLD+ET+G++++           + F    I+K Y ++    P+        +  
Sbjct: 130 IAPAHRLDRETAGVILMTTRPETRHIYHQLFIDDAIRKDYQAIAKLTPEIMAQYASGELT 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
              +W +K      +    +K  E  AN   +H ++ +     +    E+ P TG+THQL
Sbjct: 190 LPLHWTVKNRMQRSEPSFTMKIVEGEAN---THSEISLVAIHGELGLFELSPITGKTHQL 246

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           RVH   +G P++ D  Y               L L A+ +    P  GR
Sbjct: 247 RVHMQSLGMPLLNDRFY-PTLYPKGPDDFSKPLQLLAQRLRFIDPISGR 294


>gi|167465286|ref|ZP_02330375.1| ribosomal large subunit pseudouridylate synthase D [Paenibacillus
           larvae subsp. larvae BRL-230010]
          Length = 144

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 37/153 (24%), Positives = 66/153 (43%), Gaps = 13/153 (8%)

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
            R++ +++ Y +L  G  +     I   + +  H        +K       +A++ + V 
Sbjct: 1   MRLKTVRREYAALAEGCIEPTVGVIDLPIGRDRHHKSKRRVTLK-----GQHAVTRYAV- 54

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
               ++   L +   TGRTHQ+RVH  H+G P++GD  Y  N      + + ++  LH  
Sbjct: 55  AAQLEQAALLHLSLETGRTHQIRVHLSHIGHPLLGDSLYGGN------TALISRQALHGE 108

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
            +   HP  G  L+I AP P      +  L  +
Sbjct: 109 RISFSHPITGEDLRIEAPWPGDFTALYAKLKAE 141


>gi|325119935|emb|CBZ55488.1| putative RNA pseudouridylate synthase domain-containing protein
            [Neospora caninum Liverpool]
          Length = 2761

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 58/283 (20%), Positives = 96/283 (33%), Gaps = 44/283 (15%)

Query: 80   EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            E++ + + +     S   +  +L+E   + V +KP G                L S V S
Sbjct: 1878 EEEEVITLLPKELASPKKEPDVLWEGDGLTVIDKPPGWHCSDVRYDPQTESRQLCSIVSS 1937

Query: 140  KGQKP---------------------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +P                      L HRLD +TSG +++A+T  A Q + +    R 
Sbjct: 1938 SRPEPLGLYCSLRFNYPTGKLKECNFGLGHRLDVDTSGPIIIAQTLEAWQWIRDQMHKRN 1997

Query: 179  IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            I K Y  L  G        I + ++       D   +          +++  K +     
Sbjct: 1998 ISKEYICLCHGTLAEGFHVIDSPII----TSTDGRRLQSYIHHAGQPSLTVVKPLAHLEH 2053

Query: 239  K------------FCWLEMQPHTGRTHQLRVHALHMG------CPIVGDHKYCANFKGNF 280
            K            F    ++ HTGRTHQ+RVH   +         +V D KY  N +   
Sbjct: 2054 KELRYPASSVPLQFTLNWVKIHTGRTHQIRVHLQSLLDSHGRPHCLVSDDKYG-NGQQVE 2112

Query: 281  TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
                  +L+LH   +             +PL A ++     L 
Sbjct: 2113 DFQWCRRLFLHQHRLSFRDLNDTPQCFVSPLRADLLSALRHLR 2155


>gi|327479400|gb|AEA82710.1| pseudouridylate synthase, 23S RNA-specific [Pseudomonas stutzeri
           DSM 4166]
          Length = 274

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 55/292 (18%), Positives = 101/292 (34%), Gaps = 31/292 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +P I+       +  G+V   D + +      + G  V     +     +  E++ 
Sbjct: 5   LCERFPAIDRATWLDRMARGRVLDADMQPIDAARPYRVGMRVHYFREVPNETPVPFEER- 63

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ- 142
                            +L+ D  + V +KP  +SV       Y  +  L       G  
Sbjct: 64  -----------------ILHVDEHLVVADKPHFLSVMPAG--EYVNETLLARLSKRLGNA 104

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R +       FR RRI K Y ++   +P      +   L
Sbjct: 105 DLVPIHRIDRLTAGLVLFSANRESRDAYQALFRERRIAKRYEAICPALP-----GLEFPL 159

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            ++  +       + +   G   + +  +V++          + P TGR HQLR+H   +
Sbjct: 160 RRQLCMVPGEPFFLMREGDGEPNSETLIEVLERR-DHLWRYALTPITGRKHQLRLHMATL 218

Query: 263 GCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           G  I  D  Y      +          L L AR +    P  G   +  + L
Sbjct: 219 GAGICNDPFYPQLLPREERDQDDYSRPLKLLARGLRFRDPLSGEPREFESSL 270


>gi|294944527|ref|XP_002784300.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239897334|gb|EER16096.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 296

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 58/274 (21%), Positives = 109/274 (39%), Gaps = 51/274 (18%)

Query: 36  NLQKILRSGQVRVDK-------KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV 88
            ++K  R G +R+ K       +R K  + +++G+ +                K  +  V
Sbjct: 57  YIEKACREGYLRIRKAGKNAVPQRAKPESLLKNGESLVHTW------------KAEEPQV 104

Query: 89  NLTKHSDFLKSILLYEDS--KIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPR 145
           + T     +  + + EDS   I   +KPAG+    GG  +   +   L    +    +P 
Sbjct: 105 DFTCGETGI--VFIREDSARGIVAVHKPAGLPTHSGGKYMRTSLVHILARAFNLSTIRP- 161

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             +RLD+ETSG++++A   +  + L    + R +     +L               +   
Sbjct: 162 -INRLDRETSGVVLLAADASVHERL----KDRSLLSKVPALC-----------RTPIAVD 205

Query: 206 SHIGGDY-VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            H+     +  V ++   +    + F+ +         +  +P TG+THQ+RVH  H+G 
Sbjct: 206 RHVPNQPLMSRVVEDSTNSTLCTTLFRNL-----GNGVVACRPVTGKTHQIRVHLSHLGF 260

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           PI GD  Y     G  T   + +L+ H   +  P
Sbjct: 261 PIQGDTLYG----GRSTPEGRLRLHAHCYQVKDP 290


>gi|68536479|ref|YP_251184.1| putative pseudouridylate synthase [Corynebacterium jeikeium K411]
 gi|68264078|emb|CAI37566.1| putative pseudouridylate synthase [Corynebacterium jeikeium K411]
          Length = 291

 Score =  118 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 59/274 (21%), Positives = 96/274 (35%), Gaps = 31/274 (11%)

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL---KSILLYEDSKIYVFNKPAG 116
            +G     P  + A   ++  +       +  +    L      +LY  S   V +KP G
Sbjct: 17  AAGDSPYEPGTLLAPGLVLSGRTPTWVYPDFPEEPAELLEADIPVLYSGSDAVVVDKPHG 76

Query: 117 ISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           +     G  +       ++  +     +    HRLD++T G+LV+AR       L   F+
Sbjct: 77  LPSTPNGRLLRATAQSLMRVRLQE--PELVAAHRLDRDTRGLLVLARNPVTRGFLQTQFQ 134

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            R + K Y +L   IP+   +     L        D   V   + + +   ++  + +  
Sbjct: 135 RREVSKTYQALAADIPEIGSQWQEAQL--PMLKIKDDPQVKVVDGERSRLTVTRIRKLAS 192

Query: 236 FAQ-------------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
            A                   E+QP TG THQLRV   H+G PI GD  Y     G    
Sbjct: 193 RAGMGVTPSEDTHAGTPTAVYELQPLTGYTHQLRVLMNHLGAPIYGDDTYPEYRPGAGAL 252

Query: 283 PIQNKLYLHARYMDLPHPEGGRLQI------TAP 310
               +L   A  + L      R ++       AP
Sbjct: 253 ----RLRAVAIELALVASTKNRQRVVIARCLEAP 282


>gi|332298538|ref|YP_004440460.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332181641|gb|AEE17329.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 296

 Score =  118 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 58/245 (23%), Positives = 94/245 (38%), Gaps = 37/245 (15%)

Query: 99  SILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGF--------------------LKSWV 137
           + +LY D+ + V  K AG   +   +  A+  D                      +++ +
Sbjct: 4   ARVLYADTDLAVVVKYAGEVCELPSAAAAHSADRPAAESPAAAEAPCLADVVRPEIEAAL 63

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVW----GIPK 192
            S        HRLD   SG+ V+A  R  A  L+  F  R  ++K Y ++      G   
Sbjct: 64  GSPVPFCGCVHRLDLPVSGLCVLALNRDCAALLSAQFANRDSVEKTYLAVTELKKNGDDS 123

Query: 193 NKKECIANWLLKKSHIGGDYV----HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
                 +   L   H+  D       +V +  + A  A   ++ I    +++ ++ ++  
Sbjct: 124 VHSGTPSPETLLSCHMIFDPKARKARIVAETTRKAKKAELAYR-IAGTGERYSFVTVRLL 182

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+R      G P+ GD KY A            +L  HA  +   HP  G R   
Sbjct: 183 TGRTHQIRCQLAAEGMPVKGDVKYGARRSDPLGGI---RL--HAYRLRFTHPVTGKRCDF 237

Query: 308 TAPLP 312
           TAP P
Sbjct: 238 TAPPP 242


>gi|225389449|ref|ZP_03759173.1| hypothetical protein CLOSTASPAR_03197 [Clostridium asparagiforme
           DSM 15981]
 gi|225044484|gb|EEG54730.1| hypothetical protein CLOSTASPAR_03197 [Clostridium asparagiforme
           DSM 15981]
          Length = 165

 Score =  118 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 30/129 (23%), Positives = 58/129 (44%), Gaps = 12/129 (9%)

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF-KVIDCFAQKFCWLEMQPHTGR 251
                +   + +        V   + + +    A +H+ +++    +    + +   TGR
Sbjct: 1   PDSGTVTAPIGRVPGS----VIQRRVDPEQGEPACTHYSRLLYNQKKDLSLISLSLETGR 56

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           THQ+RVH   +G P+ GD  YC +++      + N+  LH+  ++  HP  G+ ++ TAP
Sbjct: 57  THQIRVHMASIGHPLPGDFLYCPDYR------LINRQPLHSWRLEFCHPVTGKPIEFTAP 110

Query: 311 LPAHMVKTW 319
           LP  M    
Sbjct: 111 LPQDMAALL 119


>gi|21619426|gb|AAH32135.1| RNA pseudouridylate synthase domain containing 3 [Homo sapiens]
 gi|312151418|gb|ADQ32221.1| RNA pseudouridylate synthase domain containing 3 [synthetic
           construct]
          Length = 343

 Score =  118 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 59/286 (20%), Positives = 111/286 (38%), Gaps = 44/286 (15%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSK 140
           +L  +++  +  D L++ ++     +   NKP G+ V G  G          L   +  +
Sbjct: 57  LLPKNLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLR 116

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKE 196
            Q+ ++     +E+SG+++++     A  L +    + R +R    Y ++  GIP   + 
Sbjct: 117 EQELQVVRASGKESSGLVLLSSCPQTASRLQKYFTHARRAQRPTATYCAVTDGIPAASEG 176

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            I   L  +   G +    VK   +     G    +SHF+V+         +++QP T  
Sbjct: 177 KIQAALKLEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFRVVAT-GSGCALVQLQPLTVF 235

Query: 252 THQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQN----KLYLHARYMDLPHPE-- 301
           + QL+VH +   CP++GDH Y A         F  P +N    +  L    +   H    
Sbjct: 236 SSQLQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAENNKPQRQVLDEALLRRLHLTPS 295

Query: 302 ----------------------GGRLQITAPLPAHMVKTWDSLGFK 325
                                    +++ APLP +  +T   LG +
Sbjct: 296 QAAQLPLHLHLHRLLLPGTRARDTPVELLAPLPPYFSRTLQCLGLR 341


>gi|146281243|ref|YP_001171396.1| pseudouridylate synthase, 23S RNA-specific [Pseudomonas stutzeri
           A1501]
 gi|145569448|gb|ABP78554.1| pseudouridylate synthase, 23S RNA-specific [Pseudomonas stutzeri
           A1501]
          Length = 294

 Score =  118 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 55/292 (18%), Positives = 101/292 (34%), Gaps = 31/292 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
               +P I+       +  G+V   D + +      + G  V     +     +  E++ 
Sbjct: 25  LCERFPAIDRATWLDRMARGRVLDADMQPIDAARPYRVGMRVHYFREVPNETPVPFEER- 83

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ- 142
                            +L+ D  + V +KP  +SV       Y  +  L       G  
Sbjct: 84  -----------------ILHVDEHLVVADKPHFLSVMPAG--EYVNETLLARLSKRLGNA 124

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +  R +       FR RRI K Y ++   +P      +   L
Sbjct: 125 DLVPIHRIDRLTAGLVLFSANRESRDAYQALFRERRIAKRYEAICPALP-----GLEFPL 179

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            ++  +       + +   G   + +  +V++          + P TGR HQLR+H   +
Sbjct: 180 RRQLCMVPGEPFFLMREGDGEPNSETLIEVLERR-DHLWRYALTPITGRKHQLRLHMATL 238

Query: 263 GCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           G  I  D  Y      +          L L AR +    P  G   +  + L
Sbjct: 239 GAGICNDPFYPQLLPRQERDQDDYSRPLKLLARGLRFRDPLSGEPREFESRL 290


>gi|119773646|ref|YP_926386.1| pseudouridine synthase [Shewanella amazonensis SB2B]
 gi|119766146|gb|ABL98716.1| pseudouridine synthase [Shewanella amazonensis SB2B]
          Length = 309

 Score =  118 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 54/302 (17%), Positives = 109/302 (36%), Gaps = 27/302 (8%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           YVV+  D  N  +  +  +H+  I     ++ +  G+V             Q G ++ + 
Sbjct: 15  YVVLPRDNPNTTVFGFLCSHFARIGEEVWRRRILDGKVH-----------WQDGMLITLQ 63

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                   +   ++++  +          +  +L  +  + +  KP  + V         
Sbjct: 64  TPYRPTARVYYYREVVAET------KIPFREKILCRNEHMMLVFKPHFLPVTPSGNYVNE 117

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                +  + +        HRLD+ET+G+++++          + F    I+K Y ++  
Sbjct: 118 CL-VHRLRLATGIDTISPAHRLDRETAGVILMSLNPETRHQYHQLFLNGGIRKDYEAIAR 176

Query: 189 GIPK------NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
             P+      + +     W +K      D   +++     AN + S   ++         
Sbjct: 177 LTPELMALHGDGQSLPQRWTVKNRMQPADPSFLMQVVPGEAN-SHSEIALL-MVKDGRGL 234

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            E+ P TGRTHQLRVH   +G P+  D  Y  + +          L L A+ +    P  
Sbjct: 235 FELSPITGRTHQLRVHMQSLGMPLENDRFY-PSLQPQSADDFNAPLKLVAKRLRFTDPVT 293

Query: 303 GR 304
           G 
Sbjct: 294 GE 295


>gi|296141678|ref|YP_003648921.1| pseudouridine synthase [Tsukamurella paurometabola DSM 20162]
 gi|296029812|gb|ADG80582.1| pseudouridine synthase [Tsukamurella paurometabola DSM 20162]
          Length = 305

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 49/217 (22%), Positives = 85/217 (39%), Gaps = 14/217 (6%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +        +++ D +I V +KP  ++     G        ++   +         HR
Sbjct: 87  PHEVPVPFPMPIIHADDRIVVVDKPHFLATMP-RGARVVQSALVRLRRELGEPSLSPAHR 145

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+L+  R  A      + F     +K Y +L        +  +      +S I 
Sbjct: 146 LDRLTAGVLLFTRDPAVRGPYQQLFAQGLARKEYAAL-----APLRRDLELPATVESRIE 200

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                +      G   A SH + ++          ++P TG+THQLR+H   +G PI+GD
Sbjct: 201 KTPGIMRAYEVNGPVNARSHVE-LEAELGTIARYRLRPETGKTHQLRLHMSRLGVPILGD 259

Query: 270 HKYCANFK---GNFTSPIQNKLYLHARYMDLPHPEGG 303
             Y    +   G+FT P+  +L   AR +    P  G
Sbjct: 260 PLYPEPREVIDGDFTDPL--RLL--ARRLAFVDPIDG 292


>gi|226364380|ref|YP_002782162.1| pseudouridine synthase [Rhodococcus opacus B4]
 gi|226242869|dbj|BAH53217.1| putative pseudouridine synthase [Rhodococcus opacus B4]
          Length = 302

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 95/251 (37%), Gaps = 9/251 (3%)

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILD-SSVNLTKHSDFLKSILLYEDSKIYVFN 112
           +   ++ + +VV         +     ++ +        +     +  +L+ D  + V +
Sbjct: 45  RLREKVATAEVVDERGQPITESTPFAPRRFVYLYRDPPVEKRVPFEIEILHRDENLLVVD 104

Query: 113 KPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           KP  ++     G        ++   D    +    HRLD+ T+G+L+    R   +    
Sbjct: 105 KPHFLASTP-RGAYVAESALVRLRRDLDLPELTPAHRLDRLTAGVLIFTVRREVRRDYQS 163

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F  RR+ K Y ++    P      +      +S I  +   +      G   + S  ++
Sbjct: 164 LFDQRRVTKEYEAVARYDPD-----LLLPATVRSRIVKERGVLKAYEVDGPANSESRIEL 218

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++          + PHTG+THQLRVH   +G PI GD+ Y  +F           L L A
Sbjct: 219 LEVHG-AAARYRLLPHTGKTHQLRVHMSSLGIPIHGDNFY-PDFYDVAADDYSTPLRLLA 276

Query: 293 RYMDLPHPEGG 303
           R ++   P  G
Sbjct: 277 RSVEFADPCSG 287


>gi|41388987|gb|AAH65741.1| RNA pseudouridylate synthase domain containing 3 [Homo sapiens]
          Length = 343

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 59/286 (20%), Positives = 111/286 (38%), Gaps = 44/286 (15%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSK 140
           +L  +++  +  D L++ ++     +   NKP G+ V G  G          L   +  +
Sbjct: 57  LLPKNLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLR 116

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKE 196
            Q+ ++     +E+SG+++++     A  L +    + R +R    Y ++  GIP   + 
Sbjct: 117 EQELQVVRASGKESSGLVLLSSCPQTASRLQKYFTHARRAQRPTATYCAVTDGIPAASEG 176

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            I   L  +   G +    VK   +     G    +SHF+V+         +++QP T  
Sbjct: 177 KIQAALKLEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFRVVAT-GSGCALVQLQPLTVF 235

Query: 252 THQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQN----KLYLHARYMDLPHPE-- 301
           + QL+VH +   CP++GDH Y A         F  P +N    +  L    +   H    
Sbjct: 236 SSQLQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAENNKPQRQVLDEALLRRLHLTPS 295

Query: 302 ----------------------GGRLQITAPLPAHMVKTWDSLGFK 325
                                    +++ APLP +  +T   LG +
Sbjct: 296 QAAQLPLHLHLHRLLLPGTRARDTPVELLAPLPPYFSRTLQCLGLR 341


>gi|216548145|ref|NP_775930.2| RNA pseudouridylate synthase domain-containing protein 3 isoform 1
           [Homo sapiens]
 gi|294862493|sp|Q6P087|RUSD3_HUMAN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 3
 gi|119584411|gb|EAW64007.1| RNA pseudouridylate synthase domain containing 3, isoform CRA_b
           [Homo sapiens]
          Length = 351

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 59/286 (20%), Positives = 111/286 (38%), Gaps = 44/286 (15%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSK 140
           +L  +++  +  D L++ ++     +   NKP G+ V G  G          L   +  +
Sbjct: 65  LLPKNLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLR 124

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKE 196
            Q+ ++     +E+SG+++++     A  L +    + R +R    Y ++  GIP   + 
Sbjct: 125 EQELQVVRASGKESSGLVLLSSCPQTASRLQKYFTHARRAQRPTATYCAVTDGIPAASEG 184

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            I   L  +   G +    VK   +     G    +SHF+V+         +++QP T  
Sbjct: 185 KIQAALKLEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFRVVAT-GSGCALVQLQPLTVF 243

Query: 252 THQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQN----KLYLHARYMDLPHPE-- 301
           + QL+VH +   CP++GDH Y A         F  P +N    +  L    +   H    
Sbjct: 244 SSQLQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAENNKPQRQVLDEALLRRLHLTPS 303

Query: 302 ----------------------GGRLQITAPLPAHMVKTWDSLGFK 325
                                    +++ APLP +  +T   LG +
Sbjct: 304 QAAQLPLHLHLHRLLLPGTRARDTPVELLAPLPPYFSRTLQCLGLR 349


>gi|145351767|ref|XP_001420235.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580469|gb|ABO98528.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 357

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 82/229 (35%), Gaps = 11/229 (4%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPA 115
             +++  + R+    +    ++     +   ++  +       + +L  +  +    KPA
Sbjct: 38  YYVKAHAMGRLCAREHEDGPMLAGGNRVRHFIHRHEPPVMADEVRVLTVNDDVVSVWKPA 97

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            + V        +    L +       +    HRLD+  SG+L++AR+  AA  +     
Sbjct: 98  TVPVHPTGQYRRNTVLALLAASRRDLGRLFPIHRLDKNVSGLLLLARSSEAANEMRVKME 157

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE----------KGANY 225
            R ++K Y + V G   +      + +          V + +  +          K    
Sbjct: 158 AREMRKEYVARVRGAFNDGDATPVSNVESLGFDSKGRVAIWRGKKGVTDLDERTLKSFKD 217

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           A + F  I         +  +P TGR+HQ+R H   +G PI  D  Y  
Sbjct: 218 ASTKFTCIKTLVDGTSLVRCEPFTGRSHQIRAHLAMLGYPIANDVAYGG 266


>gi|114045928|ref|YP_736478.1| pseudouridine synthase [Shewanella sp. MR-7]
 gi|113887370|gb|ABI41421.1| pseudouridine synthase [Shewanella sp. MR-7]
          Length = 308

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 53/288 (18%), Positives = 105/288 (36%), Gaps = 30/288 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +  +H+ HI     ++ +  G+V             Q G ++ +             +++
Sbjct: 28  FLISHFSHIGEAVWRQRILDGKVH-----------WQDGSLIGLDTAYRPTARAYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +     +S +L++D  + +  KP  + V              +  + +    
Sbjct: 77  P------VEAQVPFESPILFQDDNLILAYKPHFLPVTPSGEYVNECL-VHRLRLSTGIDT 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKE 196
               HRLD+ET+G++++           + F    I+K Y ++    P+        +  
Sbjct: 130 IAPAHRLDRETAGVILMTTRPETRHIYHQLFVDDAIRKDYQAIAKLTPEIMAQYACGELT 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
              +W +K      +    +K  E  AN   +H ++ +     +F   E+ P TG+THQL
Sbjct: 190 LPLHWTVKNRMQRSEPSFTMKIVEGEAN---THSEISLVAVKGEFGLFELSPITGKTHQL 246

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G P++ D  Y               L L A+ +    P  G
Sbjct: 247 RVHMQSLGMPLLNDRFY-PTLYPKGPDDFTKPLQLLAQRLRFVDPITG 293


>gi|111021862|ref|YP_704834.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
 gi|110821392|gb|ABG96676.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
          Length = 338

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 99/252 (39%), Gaps = 11/252 (4%)

Query: 54  KFNNRIQSGQVV--RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF 111
           +   ++ + +VV  R  P+  A     ++   L     + K   F    +L+ D  + V 
Sbjct: 81  RLREKVAAAEVVDERGQPITEATPFAPRKFVYLYRDPPVEKRVPF-DIEILHRDEDLLVV 139

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   D    +    HRLD+ T+G+L+    R   +   
Sbjct: 140 DKPHFLASTP-RGAYVAESALVRLRRDFDLPELTPAHRLDRLTAGVLIFTVRREVRRDYQ 198

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
             F  RR+ K Y ++    P      +      +S I  +   +      G   + S  +
Sbjct: 199 SLFDQRRVVKEYEAVARYDPD-----LRLPATVRSRIVKERGVLKAYEMDGPANSESRIE 253

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
           +++          + PHTG+THQLR+H   +G PI GD+ Y  +F           L L 
Sbjct: 254 LLEIHGD-AARYRLLPHTGKTHQLRLHMSSLGIPIHGDNFY-PDFYDVAADDYSTPLRLL 311

Query: 292 ARYMDLPHPEGG 303
           AR ++   P  G
Sbjct: 312 ARSVEFVDPYSG 323


>gi|62391784|ref|YP_227186.1| ribosomal pseudouridine synthase [Corynebacterium glutamicum ATCC
           13032]
 gi|41327126|emb|CAF20969.1| Putative ribosomal pseudouridine synthase [Corynebacterium
           glutamicum ATCC 13032]
          Length = 338

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 48/239 (20%), Positives = 88/239 (36%), Gaps = 13/239 (5%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +  +  I    +   +     K  +++ED  I V +KP  ++     G        +K  
Sbjct: 89  VQPDDDIWFYRMPAAERPIPYKIHVIHEDDDILVIDKPPYLATMP-RGRHITETALVKMR 147

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL---VWGIPKN 193
           V +        HRLD+ TSG+LV+ +           F  R   K Y ++   V G+  +
Sbjct: 148 VLTGNNDLTPAHRLDRLTSGVLVMVKKPELRGAYQTLFARREASKTYEAIAEFVPGLLDD 207

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK-----VIDCFAQKFCWLE---M 245
                 + + K+  I   +V     N +    +++  +     +++             +
Sbjct: 208 GPAIWESRIEKERGIVQAFVVEGPVNARTELVSVTPVEDAEQSILEEMHGPLPRQARYVL 267

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TG+THQLR+H      PI+GD  Y               ++L AR +    P+   
Sbjct: 268 APSTGKTHQLRIHMRDFAAPILGDPLY-PVLHAVDDEDYTTPMHLIARTLTFVDPQTNE 325


>gi|257457321|ref|ZP_05622492.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
 gi|257445243|gb|EEV20315.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
          Length = 231

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 85/230 (36%), Gaps = 43/230 (18%)

Query: 111 FNKPAGISVQGGSGIAY--HIDGFL---------------KSWVDSKGQKPRLTHRLDQE 153
            NKPAGI V G S I         L               +  + S   KP   HRLD++
Sbjct: 1   MNKPAGIPVHGSSSIDTLLSAASVLTPSAEPPAAVPDTDGRVHLHSLSFKPGPLHRLDKD 60

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G+L  +RT A AQ  ++  R + + K Y  +V G    +                   
Sbjct: 61  TTGVLCFSRTLAGAQWFSQCLREKTVGKYYLGVVRGAMPAQP------------------ 102

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +  Q+E GA      + V  C       +  +  TG+ HQ+R H   +G P+ GD KY 
Sbjct: 103 -ITAQDENGATMTQC-YSVEYCKDIDASLMLFRLITGKKHQIRKHTESVGHPLAGDRKY- 159

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL--QITAPLPAHMVKTWDS 321
               G    P      LHA  +  P      +   I APL   M    + 
Sbjct: 160 ---HGGNPLPGCKHYLLHAWRLYFPALRPADIPASIEAPLFPEMETFLNR 206


>gi|163751188|ref|ZP_02158417.1| YabO/YceC/SfhB family protein [Shewanella benthica KT99]
 gi|161329017|gb|EDQ00090.1| YabO/YceC/SfhB family protein [Shewanella benthica KT99]
          Length = 308

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 53/287 (18%), Positives = 102/287 (35%), Gaps = 28/287 (9%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +    +  I     ++ +  G+V             Q G ++ +         +   +++
Sbjct: 28  FLVERFEQIGSDIWRERIIDGKVH-----------WQDGSLIELDTEFKPRARVYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
              +          +  +LY D +I +  KP  +++              +  + +  + 
Sbjct: 77  KSET------KVPFEEKILYRDEQIILAFKPHFLALHPSGNFVNECL-VNRLRIKTGIET 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKE 196
               HRLD+ T+GI+++           + F+  +I K Y +L    P+        +  
Sbjct: 130 LVPAHRLDRATAGIVLMILNPETRTQYHDLFKNHQITKEYQALAKLTPELLASHQVGELA 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
               W +K   + G+    +K  E  +N   S   +ID         ++ P TGRTHQLR
Sbjct: 190 LPLQWTVKNRMVKGEPSFTMKVVEGESNT-HSEISLID-IKDDVGLFKLSPITGRTHQLR 247

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           VH   +G  I+ D  Y    +          L L A+ +    P  G
Sbjct: 248 VHMQSLGMSIINDRCY-PQLQPKADDDYARPLKLVAKRLKFNDPVTG 293


>gi|303248684|ref|ZP_07334938.1| pseudouridine synthase [Desulfovibrio fructosovorans JJ]
 gi|302489940|gb|EFL49866.1| pseudouridine synthase [Desulfovibrio fructosovorans JJ]
          Length = 303

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 56/290 (19%), Positives = 104/290 (35%), Gaps = 38/290 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +  D    RLDR      P       ++++ +G++ VD +      R+++G+ +      
Sbjct: 13  IPGDMAGERLDRAAILVLPDTGLRGRRRLIEAGRLLVDGRARPAAYRVRAGEKL------ 66

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS---GIAYH 128
            A      E +   S +            +L+ D+      KPAG+     +   G    
Sbjct: 67  AARIAARPEGEFRASDIP-----------ILFADAAYAAVAKPAGL--HSAAIACGGGQS 113

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           ++  L       G+   L  RLD+ TSGI+ +A   A+ +         ++ K Y ++V 
Sbjct: 114 LEDLLPELFP--GRAAGLLSRLDRLTSGIVPLAFDAASGERYRRLENAGQVAKTYLAVVH 171

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G   +    + ++ L  +      V     ++      +S              +  +  
Sbjct: 172 GGIPSPF--VVDFRLDMADRAKTRVLRTADSDPLRQTRVSP----RAAKGGLTLVACRIA 225

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            G  HQ+R H    G P+VGD  Y              +LYLH   ++ P
Sbjct: 226 KGARHQIRAHLAASGHPLVGDPVYGRGEGA--------RLYLHCARLESP 267


>gi|19554131|ref|NP_602133.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glutamicum ATCC 13032]
 gi|21325718|dbj|BAC00339.1| Pseudouridylate synthases, 23S RNA-specific [Corynebacterium
           glutamicum ATCC 13032]
          Length = 322

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 48/239 (20%), Positives = 88/239 (36%), Gaps = 13/239 (5%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +  +  I    +   +     K  +++ED  I V +KP  ++     G        +K  
Sbjct: 73  VQPDDDIWFYRMPAAERPIPYKIHVIHEDDDILVIDKPPYLATMP-RGRHITETALVKMR 131

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL---VWGIPKN 193
           V +        HRLD+ TSG+LV+ +           F  R   K Y ++   V G+  +
Sbjct: 132 VLTGNNDLTPAHRLDRLTSGVLVMVKKPELRGAYQTLFARREASKTYEAIAEFVPGLLDD 191

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK-----VIDCFAQKFCWLE---M 245
                 + + K+  I   +V     N +    +++  +     +++             +
Sbjct: 192 GPAIWESRIEKERGIVQAFVVEGPVNARTELVSVTPVEDAEQSILEEMHGPLPRQARYVL 251

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TG+THQLR+H      PI+GD  Y               ++L AR +    P+   
Sbjct: 252 APSTGKTHQLRIHMRDFAAPILGDPLY-PVLHAVDDEDYTTPMHLIARTLTFVDPQTNE 309


>gi|319649950|ref|ZP_08004100.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317398388|gb|EFV79076.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 212

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 40/201 (19%), Positives = 82/201 (40%), Gaps = 26/201 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +   +    +  + K +   I+   L  I    G ++V+ + V     ++ G ++++   
Sbjct: 10  ITAPQAGSLIRGFLKEN--DISKTALTDIKFAGGFIKVNNQEVNVRYELKEGDILQVGFP 67

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
               +  +K               + L   +LYED+ + + NKPAG+S         H  
Sbjct: 68  EEVPSKGMK--------------GEDLPLDILYEDAYLLIVNKPAGVSTIPSR---EHPS 110

Query: 131 GFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
           G L + +    Q+        +  RLD++TSG++++A+ R      ++  R R+IQ+ Y 
Sbjct: 111 GSLANRLIGYYQRIGLKSAAHIVTRLDRDTSGLVLIAKHRHVHHLFSQQQRFRKIQRTYE 170

Query: 185 SLVWGIPKNKKECIANWLLKK 205
           +   G        I   + +K
Sbjct: 171 AFAEGTISRDAGTIEQPIARK 191


>gi|219110967|ref|XP_002177235.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217411770|gb|EEC51698.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 168

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 45/171 (26%), Positives = 79/171 (46%), Gaps = 5/171 (2%)

Query: 105 DSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           D+ +YV NKP+ + V   G  ++  +   +++ V  +    +  HR D+ TSG+ +  ++
Sbjct: 1   DAAVYVCNKPSSVPVHPAGPFLSNSLTIMVEAQVGLQCGSLKPVHRTDRVTSGLTLCCKS 60

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
            A A+          + K+Y + V G   +    +       +    + V +V   +   
Sbjct: 61  SAVARIFHRCLSEGTVDKLYVARVHGKFPSTNSEMHLDAAVHTLDPANGVRIV---DSAG 117

Query: 224 NYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             + S FK++D   A+    +  QP TGR HQLRVH   +G PIV D +Y 
Sbjct: 118 KPSKSVFKLVDFNQAENVSVIACQPITGRNHQLRVHLQMLGYPIVNDTQYG 168


>gi|305680267|ref|ZP_07403075.1| RNA pseudouridine synthase [Corynebacterium matruchotii ATCC 14266]
 gi|305659798|gb|EFM49297.1| RNA pseudouridine synthase [Corynebacterium matruchotii ATCC 14266]
          Length = 339

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 50/248 (20%), Positives = 92/248 (37%), Gaps = 19/248 (7%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           + A   +   Q++    +   +     +   ++ED ++ V +KP  ++     G      
Sbjct: 85  LAAETPLRANQEVWFYRIPAPEVPVPYRCETIFEDERLLVVDKPPFLATMP-RGKHITQS 143

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             ++    +   +    HRLD+ TSG+LV  +TR       + F  R  +K Y ++    
Sbjct: 144 ATVQLRKLTGNGELSPAHRLDRLTSGVLVFTKTREVRGAYQQLFARREAEKTYEAIARYD 203

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE------ 244
           P N K      ++ +  +  +   +      G   AI+    ++    +           
Sbjct: 204 PVNPKA--QPGMVWRDRMTKNPGELQGYFVPGEPNAITTVIAVEPVPTERMRALRATHGS 261

Query: 245 ---------MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                    +QP TGRTHQLR+H    G PI+GD  Y               ++L A+ +
Sbjct: 262 ELPQQARYVLQPATGRTHQLRLHMWKAGVPILGDPAY-PTVLPEAEEDFAVPMHLRAKML 320

Query: 296 DLPHPEGG 303
               P  G
Sbjct: 321 RFTDPLSG 328


>gi|167032660|ref|YP_001667891.1| pseudouridine synthase [Pseudomonas putida GB-1]
 gi|166859148|gb|ABY97555.1| pseudouridine synthase [Pseudomonas putida GB-1]
          Length = 294

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 56/285 (19%), Positives = 106/285 (37%), Gaps = 30/285 (10%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVINALNHIIKEQK 82
             +H+  I+          G+V ++            GQ V   +P       H  +E  
Sbjct: 29  LCDHFKAIDRAQWLDRFARGRV-LN----------AEGQAVSAELPYKRGMRLHYFREVP 77

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                    +    ++ ++L+ D  + V +KP  + V   +G         +        
Sbjct: 78  --------NERPIPVQEVVLHVDEHLVVADKPHFLPVTP-TGEYVEQTLLRRLIRRLGNP 128

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
                HR+D+ T+G+++ +    +       F  RRI K Y ++   +P++    +    
Sbjct: 129 HLVPLHRIDRHTAGLVLFSANPQSRSAYQRLFPERRIDKRYQAIAAALPQHAFPLVH--- 185

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            K   + G+    + + E  AN + +  +V++   + + +  + P TG+THQLRVH   +
Sbjct: 186 -KSRLVHGEPFFRMHEVEGEAN-SETLAQVLEKNGELWRYG-LSPVTGKTHQLRVHMAAL 242

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
           G  I  D  Y      N     Q  L L A  +    P  G  + 
Sbjct: 243 GAGISNDPFYP--QLRNEEDDYQRPLKLLAHSLRFEDPLSGEERF 285


>gi|75764363|ref|ZP_00743883.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|74488148|gb|EAO51844.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
          Length = 103

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 34/105 (32%), Positives = 54/105 (51%), Gaps = 7/105 (6%)

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           ++    A++HF+V++ F + F  +E +  TGRTHQ+RVH  ++G P+ GD KY      +
Sbjct: 4   DENGKNAVTHFQVLERF-KDFTLVECRLETGRTHQIRVHMKYIGYPLAGDPKYGPKKTLD 62

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
                 N   LHA  +   HP  G  +Q  AP+P    +  + L 
Sbjct: 63  M-----NGQALHAGILGFDHPRTGEYIQFEAPIPEVFEEALNILR 102


>gi|311269242|ref|XP_003132405.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 3
           isoform 2 [Sus scrofa]
          Length = 337

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 55/247 (22%), Positives = 94/247 (38%), Gaps = 42/247 (17%)

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRM 176
            G      +   L   +    ++ ++     +ETSG+++++     A  L +    S R 
Sbjct: 91  PGELTLVSVLPELSQCLGLGERELQVVRASGKETSGLVLLSSCPQTASRLQKFFTHSQRA 150

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE-----KGANYAISHFK 231
           R+    Y ++  GIP   +  I   L  +   G   V  VK        KG  + +SHF+
Sbjct: 151 RKPTATYCAVTDGIPAASEGKIQAALKMEHTDGASLVVPVKSPSRKDFLKGVKWTLSHFR 210

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY----CANFKGNFTSPIQN- 286
           V+         +++QP T    QL+VH +   CP++GDHKY           F  P +N 
Sbjct: 211 VLAS-GSGCALVQLQPLTAFPSQLQVHMVLQLCPVLGDHKYSACVGTVLGQRFLLPAENT 269

Query: 287 ---KLYLHARYMDLPH------------------------PEGGRLQITAPLPAHMVKTW 319
              +  L    +   H                        P    +++ APLP++  +T 
Sbjct: 270 KPQRQVLDEALLSRLHLTPAQAAQLPLHIHLHRLHLPGTRPRDAPIELLAPLPSYFSRTL 329

Query: 320 DSLGFKY 326
             LG +Y
Sbjct: 330 QCLGLQY 336


>gi|256831008|ref|YP_003159736.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256580184|gb|ACU91320.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 232

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 48/197 (24%), Positives = 82/197 (41%), Gaps = 16/197 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L+  +    V +K  G+      G        ++  + +   +    HRLD+ TSG+L++
Sbjct: 9   LIAREPGFVVVHKDPGLDFHDCDGRMGLC-SLVRDRLQA---RVFPVHRLDKATSGLLLL 64

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR+R  A  L   FR R +QK Y +L    P  K+  +   +++           ++   
Sbjct: 65  ARSREWAAALAGLFRERAVQKYYIALSDLTPGKKQGLVQGDMVRSRRGSWKLARSME--- 121

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A + F +            ++P +GRTHQLRV    +G PI+GD  Y        
Sbjct: 122 ---RPARTRF-LSWSVRPGMRLFVLKPMSGRTHQLRVAMKSLGAPILGDSLYHPIVPD-- 175

Query: 281 TSPIQNKLYLHARYMDL 297
                +++YLHA  +  
Sbjct: 176 ---WPDRMYLHAHTLRF 189


>gi|170720815|ref|YP_001748503.1| pseudouridine synthase [Pseudomonas putida W619]
 gi|169758818|gb|ACA72134.1| pseudouridine synthase [Pseudomonas putida W619]
          Length = 294

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 45/215 (20%), Positives = 82/215 (38%), Gaps = 9/215 (4%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +    ++  +L+ D  + V +KP  + V   +G         +             HR
Sbjct: 77  PNERPIPVEEAILHVDEHLVVADKPHFLPVTP-TGEYVEQTLLRRLIRRLDNPHLVPLHR 135

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D+ T+G+++ +            F  RRI K Y ++   +P+         L+ KS + 
Sbjct: 136 IDRHTAGLVLFSANPQTRSAYQRLFPERRIDKRYHAIAPALPQRDF-----PLVHKSRLV 190

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                      +G + + +  +V++   + + +  + P TG+THQLRVH   +G  I  D
Sbjct: 191 HGEPFFRMHEVQGDDNSETLAEVLEKQGELWRYG-LSPVTGKTHQLRVHMAALGAAICND 249

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             Y    K       Q  L L A  +    P  G 
Sbjct: 250 PFYPELLK--VEDDYQRPLKLLAHSLRFADPLTGE 282


>gi|255660399|ref|ZP_05405808.1| RluA family pseudouridine synthase [Mycoplasma genitalium G37]
          Length = 210

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 52/198 (26%), Positives = 89/198 (44%), Gaps = 24/198 (12%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M      +V  + EN R+D++     P I   +  K LR G+V ++K + + N R+++  
Sbjct: 1   MRIANKFLVPKESENQRIDQFCLKILPLIKRSDFFKYLRLGKVLLNKTKPQVNTRLKTKD 60

Query: 64  VV----RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            +     I P +   N  +        S++L K     K  +++ED  I V +KP GI  
Sbjct: 61  EIAFLFDINPYLQTNNDYL--------SLDLVKD----KLKIIFEDENIIVVDKPTGIVC 108

Query: 120 QGGSGIA--YHIDGFLKSW------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           Q     +     +  LK         +     P+  HR+D+ TSGI++ A+T  A + L 
Sbjct: 109 QPDKKHSIINLSNMLLKHCGYRQFDSNKLNFYPQFAHRIDRNTSGIVIGAKTNKALKELN 168

Query: 172 ESFRMRRIQKIYWSLVWG 189
           + F+   + K Y  LV+G
Sbjct: 169 KVFKNNHLTKRYKGLVFG 186


>gi|262200450|ref|YP_003271658.1| pseudouridine synthase [Gordonia bronchialis DSM 43247]
 gi|262083797|gb|ACY19765.1| pseudouridine synthase [Gordonia bronchialis DSM 43247]
          Length = 317

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 56/251 (22%), Positives = 87/251 (34%), Gaps = 15/251 (5%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVFNKPAG 116
           R Q+G++V       +L+   +    +    +L  +     +  +LY D  I V +KP  
Sbjct: 51  RAQAGEIVDAAGDPVSLDAPARLNTAIYLYRDLPDEVPIPFELPILYADENIVVVDKPHF 110

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           ++     G        ++             HRLD+ T+G+L+    R       + F  
Sbjct: 111 LATMP-RGRHVTETALVRLRRQLGSDDVAPAHRLDRLTAGVLLFTLRREVRAAYQDLFAT 169

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           R   K Y +L      +          +     GD    V     G   AIS   ++   
Sbjct: 170 RAATKEYRALAP--VDDALTTTVTIRNRIEKTAGDLRARVVD---GPVNAISDITLLSDA 224

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP----IQNKLYLHA 292
                   + PHTGRTHQLR+H   +  PIV D  Y          P        L L A
Sbjct: 225 G----LYRLVPHTGRTHQLRLHMASLRVPIVDDPLYPDVRPELAQRPDVGDFSAPLRLVA 280

Query: 293 RYMDLPHPEGG 303
             ++   P  G
Sbjct: 281 HALEFTDPFTG 291


>gi|330721752|gb|EGG99744.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC2047]
          Length = 287

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 112/305 (36%), Gaps = 54/305 (17%)

Query: 30  PHINFVNLQKILRSGQVRVDKKRV------KFNNR-------IQSGQVVRIPPVINALNH 76
             ++   +++ ++ G +   + R       K   R       +++G  + +      L+ 
Sbjct: 22  SGLSKTQIKQAMQKGALWCKRGRSGREKGSKQAQRTRRVPKNLKTGDSLHLYYDAKVLSE 81

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +  E +++                   ++    V+ KP G+  QG      H   +    
Sbjct: 82  LPPEPQMIA------------------DEGAYSVWYKPYGMRSQGSKW-GDHCALYRWVE 122

Query: 137 VDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           V+ K +KP  L HRLD+  +G+++VA ++ AA  LT+ F  R + K Y  +V G    + 
Sbjct: 123 VNHKPEKPAFLVHRLDRAATGLILVAHSKKAAVALTKLFEERNVDKRYQVIVVGQFSEQS 182

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQ 254
              A                    E     A SH + +   A+K    LE+   TGR HQ
Sbjct: 183 GVWA-------------KKQTFTAEVDGKAATSHARCLAYDAEKDRSLLEVTIETGRKHQ 229

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
           +R H    G P+VGD  Y               L L A  +    P     ++   LP  
Sbjct: 230 IRYHLAAAGFPVVGDRLYGNAKTDEQD------LQLTASLLSFVCPISHEERLY-ELPRE 282

Query: 315 MVKTW 319
           ++   
Sbjct: 283 LLPVL 287


>gi|255319550|ref|ZP_05360764.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter
           radioresistens SK82]
 gi|262378429|ref|ZP_06071586.1| RNA pseudouridylate synthase [Acinetobacter radioresistens SH164]
 gi|255303490|gb|EET82693.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter
           radioresistens SK82]
 gi|262299714|gb|EEY87626.1| RNA pseudouridylate synthase [Acinetobacter radioresistens SH164]
          Length = 303

 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 59/280 (21%), Positives = 108/280 (38%), Gaps = 33/280 (11%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
               +PHIN     +    G V               GQ +R+  +     HI   + + 
Sbjct: 37  LTQQFPHINANEWMQRFEDGLVY-----------TTHGQKLRVDSIYEGNQHIYYYRFLP 85

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QK 143
             +    +H       +L+E  +  V +KP  +++       Y  +  L       G + 
Sbjct: 86  KETPVPFEHH------ILHETDEFLVVDKPHFLTMSPTG--QYVQETLLVRLKKQTGIET 137

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD+ET+G+++ ++         + F  R+++K Y ++    P      +   + 
Sbjct: 138 LTPIHRLDRETAGVVLFSKRPETRGLYQKLFAERKVEKTYHAVAPFKPD-----LNFPIN 192

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            K  +         Q  +G     +   ++D  A  +   +++P TG+ HQLRVH  H+G
Sbjct: 193 LKLRLDKGEPFYTMQIVEGEPNTETLIDLLDVRAH-WAKYQLKPRTGKQHQLRVHLNHLG 251

Query: 264 CPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHP 300
            PI  D  Y         +FT+P+Q    L A+ +    P
Sbjct: 252 IPIQNDSFYPIVQHKSDNDFTAPLQ----LLAKEITFIDP 287


>gi|145296955|ref|YP_001139776.1| hypothetical protein cgR_2855 [Corynebacterium glutamicum R]
 gi|140846875|dbj|BAF55874.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 322

 Score =  117 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 49/239 (20%), Positives = 87/239 (36%), Gaps = 13/239 (5%)

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +  +  I    +   +     K  +++ED  I V +KP  ++     G        +K  
Sbjct: 73  VQPDDDIWFYRMPAAERPIPYKIHVIHEDDDILVIDKPPYLATMP-RGRHITETALVKMR 131

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL---VWGIPKN 193
           V +        HRLD+ TSG+LV+ +           F  R   K Y ++   V G+  N
Sbjct: 132 VLTGNNDLTPAHRLDRLTSGVLVMVKKPELRGAYQTLFARREASKTYEAIAEFVPGLLDN 191

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF-----KVIDCFAQKFCWLE---M 245
                 + + K+  I   +V     N +    +++        +++             +
Sbjct: 192 GPAIWESRIEKERGIVQAFVVEGPVNARTELVSVTPVDDAEQSILEEMHGPLPRQARYVL 251

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P TG+THQLR+H      PI+GD  Y               ++L AR +    P+   
Sbjct: 252 APSTGKTHQLRIHMRDFAAPILGDPLY-PVLHAVDDEDYTTPMHLIARTLTFVDPQTNE 309


>gi|34558398|ref|NP_908213.1| putative ribosomal pseudouridine synthase [Wolinella succinogenes
           DSM 1740]
 gi|34484117|emb|CAE11113.1| PUTATIVE RIBOSOMAL PSEUDOURIDINE SYNTHASE [Wolinella succinogenes]
          Length = 244

 Score =  117 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 51/223 (22%), Positives = 92/223 (41%), Gaps = 34/223 (15%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +  K  +L +D  +   +KP  I+           +  LK   + K +   L HRLD+E
Sbjct: 51  QEAPKPKILMQDENLLAIDKPPFIAS----------EELLK---EHKEKGWTLLHRLDKE 97

Query: 154 TSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           TSG++++ +      +     F+ +++ K Y ++V G+   ++E     L  K H     
Sbjct: 98  TSGVILLVQEGSEFQKSAKAEFKAQKVYKEYVAIVEGMIPEEREITKPILTTKGHFAKSK 157

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +       K    A +  + +    ++    ++   TGRTHQ+RVH   +  PI+GD  Y
Sbjct: 158 I------SKEGESAYTKIEPLAYEGKQTQL-KVIIKTGRTHQIRVHLASINHPIIGDTLY 210

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
                         ++ LHAR + L        +I + LP   
Sbjct: 211 GGKNA--------KRILLHARKIALL-----GYEIESTLPREF 240


>gi|146291626|ref|YP_001182050.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|145563316|gb|ABP74251.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
          Length = 305

 Score =  117 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 53/288 (18%), Positives = 104/288 (36%), Gaps = 30/288 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H+  I     ++ +  G+V             Q G ++ +  +   +  +   +++
Sbjct: 28  FLSTHFARIGEEVWRERILDGKVH-----------WQDGSLIALDTLYRPMARVYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +     +  +L++D  + +  KP  + V              +  + +  + 
Sbjct: 77  P------VETKVPFEEQILFQDDNLILACKPHFLPVTPSGNYVNECL-VHRLRLRTGIET 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-------KNKKE 196
               HRLD+ET+G++++           + F    I K Y ++    P       K    
Sbjct: 130 IAPAHRLDRETAGVILMTIQPETRHLYHQLFVDNAICKDYQAIAKLTPGIIEQYQKGHLT 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
              +W +K     GD    ++  E  AN   SH ++ +           + P TG+THQL
Sbjct: 190 LPLHWTVKNRMQPGDPSFTMQVVEGEAN---SHSEISLVAIKDDLGLFHLSPITGKTHQL 246

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH L +G P++ D  Y    +          L L A+ +    P  G
Sbjct: 247 RVHMLSLGMPLLNDRFY-PKLQPKSPDNFATPLKLMAQRLRFVDPVSG 293


>gi|223997012|ref|XP_002288179.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220975287|gb|EED93615.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 175

 Score =  117 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 51/188 (27%), Positives = 76/188 (40%), Gaps = 36/188 (19%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRR---IQKIYWSLVWGIP----------- 191
           + HRLD++TSG+ ++AR   A + L + F+ +    + K Y +LV G             
Sbjct: 2   VVHRLDRDTSGVFLLARNDEALKTLHDDFKDKTRGRVTKRYVALVCGHWNSDNASCVADR 61

Query: 192 -KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
               +  I   L++   I       V          ++               E+QP TG
Sbjct: 62  MTTDEGEIDLPLVRD--IENPPFMRVATTGNEIKLPVTRV-------------ELQPITG 106

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI-----QNKLYLHARYMDLPHPEGG-R 304
           RTHQLRVH   MG PIVGD  Y    +G+    I     +  L LHA+ + + HP     
Sbjct: 107 RTHQLRVHCAAMGYPIVGDSIYGYGGEGSPREGIEMDEDECLLCLHAQRLTIFHPLTKAP 166

Query: 305 LQITAPLP 312
           +      P
Sbjct: 167 MMFECSPP 174


>gi|297285307|ref|XP_001096202.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein 3
           isoform 3 [Macaca mulatta]
          Length = 351

 Score =  117 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 60/286 (20%), Positives = 112/286 (39%), Gaps = 44/286 (15%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSK 140
           +L  +++  +  D L++ ++     +   NKP G+ V G SG    +     L   +   
Sbjct: 65  LLPKNLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKSGELTLLSVLPELSQSLGLG 124

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKE 196
            Q+ ++     +E+SG+++++     A  L +    S R +R    Y ++  GIP   + 
Sbjct: 125 EQELQVVRASGKESSGLVLLSSCPQTASRLQKFFTHSQRAQRPTATYCAVTNGIPTASEG 184

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            I   L  +   G +    VK   +     G    +SHF+V+         +++QP T  
Sbjct: 185 KIQAALKLEHIDGVNLTVPVKAPSRKDILQGVKKTLSHFRVVAT-GSGCALVQLQPLTVF 243

Query: 252 THQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQN----KLYLHARYMDLPHPE-- 301
           + QL+VH +   CP++GDH Y A         F  P ++    +  L    +   H    
Sbjct: 244 SSQLQVHMVLQLCPVLGDHTYSARVGTVLGQRFLLPAESTKPQRQVLDEALLRRLHLTPS 303

Query: 302 ----------------------GGRLQITAPLPAHMVKTWDSLGFK 325
                                    +++ APLP +  +T   LG +
Sbjct: 304 QAAQLPLHLHLHRLLLPGTRARDTPIELLAPLPPYFSRTLQCLGLR 349


>gi|189233766|ref|XP_001814310.1| PREDICTED: similar to AGAP004401-PA [Tribolium castaneum]
          Length = 274

 Score =  117 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 44/206 (21%), Positives = 91/206 (44%), Gaps = 14/206 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----DSKGQKPRLTHRLDQETS 155
           +++  +   + +K   + +   +     +  F+K  +     +    +    HRLD  TS
Sbjct: 34  IVHRSANFIIIDKAYDLKINSNNRNEETVQTFMKKNLPYLASNQLHHEYYFMHRLDYSTS 93

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++ V   + A Q  +++ + R+ +K Y +LV G   +    +   + + + I  D   +
Sbjct: 94  GLMCVPVHKKACQVASQAIQQRKCKKYYIALVRGYLSSNLLDLNFPIGRDNSIT-DIEKM 152

Query: 216 VKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              ++  +  A +   V++           + ++P TGR HQ+RVH  H+G  IVGD+ Y
Sbjct: 153 CVTHDSNSRSARTLIVVLENGLFENYPSSKVLIRPITGRRHQIRVHCAHIGHTIVGDYTY 212

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLP 298
                 N       ++YLH+  + +P
Sbjct: 213 S-----NKKDTTPERMYLHSLRLVIP 233


>gi|127513475|ref|YP_001094672.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126638770|gb|ABO24413.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 287

 Score =  117 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 53/299 (17%), Positives = 111/299 (37%), Gaps = 40/299 (13%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                  ++   +++ +  G V +   R K+  R++     + P  +    H+    K+L
Sbjct: 26  LLAEASQLSKQEIKQAMAKGAVWL--TRGKYTQRLR---RAKKPLKLGDQLHLYYNPKVL 80

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
              V          + L+ +  +  ++ KP  +  QG     +           +  +  
Sbjct: 81  AQQVE--------DAQLILDKGEYSIWYKPYAMLCQGSKWSDHTTINRFVETHLTPQRPA 132

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            + HRLD+  +G++++  ++     L   F  R + K Y  +V G        I      
Sbjct: 133 FIIHRLDRAATGLVIIGHSKTITAALAAQFEHRELDKQYRVIVKGEFPKATRTIT----- 187

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMG 263
                          E     A SH  +++  ++     ++++  TGR HQ+R+H   +G
Sbjct: 188 --------------TEVDGKPACSHASLVEYDSELDMSLVQVKIETGRKHQIRIHMASIG 233

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
            P+VGD ++     G+        L L A ++D   P   +  +   LP  +  +  +L
Sbjct: 234 FPVVGDRQHGGAETGDVN------LQLTACFLDFTCPLNQQ-PLHVALPEALQPSLAAL 285


>gi|312139708|ref|YP_004007044.1| tRNA-pseudouridine synthase i [Rhodococcus equi 103S]
 gi|311889047|emb|CBH48360.1| tRNA-pseudouridine synthase I [Rhodococcus equi 103S]
          Length = 288

 Score =  117 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 49/216 (22%), Positives = 84/216 (38%), Gaps = 8/216 (3%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
              +        +L+    + V +KP  +S     G        ++   D         H
Sbjct: 69  PAPEVPVPFDIDVLHHVGGLVVVDKPHFLSTIP-RGAHIRETVVVRLRRDLGLPDLVPVH 127

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ T+G+L+        +   E F  RR++K+Y ++        +  I      +S I
Sbjct: 128 RLDRMTAGVLLCTADPRLRRPYQEMFERRRVRKVYEAI-----APYRGDIEFPRTVRSRI 182

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              +  +    E G   + +  ++++          + P TGRTHQLR+H   +G PIVG
Sbjct: 183 VKVHGELTAYEEAGEPNSETLIELVERRGD-LARYRLHPRTGRTHQLRLHLNAIGAPIVG 241

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           D+ Y   F+          L L AR ++   P  G 
Sbjct: 242 DNFY-PQFRRRDRDDFTVPLRLLARSLEFDDPVTGE 276


>gi|221487933|gb|EEE26165.1| RNA pseudouridylate synthase domain-containing protein, putative
            [Toxoplasma gondii GT1]
          Length = 2780

 Score =  117 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 56/283 (19%), Positives = 94/283 (33%), Gaps = 44/283 (15%)

Query: 80   EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            E++   + +     S   +  +L+E   + V +KP G                L   V S
Sbjct: 1890 EEEEAITLLPKELVSPKKEPDVLWEGDGLTVIDKPPGWHCSDVRYDPQTESRQLCCIVSS 1949

Query: 140  KGQKP---------------------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +P                      L HRLD +TSG +++A+T  A Q + +    R 
Sbjct: 1950 SRPEPLGLYCSLRFNYPTGKLKECNFGLGHRLDVDTSGPIIIAQTLEAWQWIRDQMHKRN 2009

Query: 179  IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            I K Y  L  G        I + ++       D   +          +++  K +     
Sbjct: 2010 ISKEYICLCHGTLAEGFHVIDSPII----TSTDGRRLQSYIHHAGQPSLTVVKPLAHLEH 2065

Query: 239  K------------FCWLEMQPHTGRTHQLRVHALHMG------CPIVGDHKYCANFKGNF 280
            +            F    ++ HTGRTHQ+RVH   +         +V D KY  N +   
Sbjct: 2066 RELRYPGSTTPLQFTLNWVKIHTGRTHQIRVHLQSLLDSRGRPHCLVSDDKYG-NGQQVE 2124

Query: 281  TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
                  +L+LH   +             +PL A ++     L 
Sbjct: 2125 DFQWCRRLFLHQHRLSFRDLNDTPQCFVSPLRADLLSALRHLR 2167


>gi|237831069|ref|XP_002364832.1| RNA pseudouridylate synthase domain-containing protein [Toxoplasma
            gondii ME49]
 gi|211962496|gb|EEA97691.1| RNA pseudouridylate synthase domain-containing protein [Toxoplasma
            gondii ME49]
 gi|221507715|gb|EEE33319.1| RNA pseudouridylate synthase domain-containing protein, putative
            [Toxoplasma gondii VEG]
          Length = 2780

 Score =  117 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 56/283 (19%), Positives = 94/283 (33%), Gaps = 44/283 (15%)

Query: 80   EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
            E++   + +     S   +  +L+E   + V +KP G                L   V S
Sbjct: 1890 EEEEAITLLPKELVSPKKEPDVLWEGDGLTVIDKPPGWHCSDVRYDPQTESRQLCCIVSS 1949

Query: 140  KGQKP---------------------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
               +P                      L HRLD +TSG +++A+T  A Q + +    R 
Sbjct: 1950 SRPEPLGLYCSLRFNYPTGKLKECNFGLGHRLDVDTSGPIIIAQTLEAWQWIRDQMHKRN 2009

Query: 179  IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            I K Y  L  G        I + ++       D   +          +++  K +     
Sbjct: 2010 ISKEYICLCHGTLAEGFHVIDSPII----TSTDGRRLQSYIHHAGQPSLTVVKPLAHLEH 2065

Query: 239  K------------FCWLEMQPHTGRTHQLRVHALHMG------CPIVGDHKYCANFKGNF 280
            +            F    ++ HTGRTHQ+RVH   +         +V D KY  N +   
Sbjct: 2066 RELRYPGSTTPLQFTLNWVKIHTGRTHQIRVHLQSLLDSRGRPHCLVSDDKYG-NGQQVE 2124

Query: 281  TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
                  +L+LH   +             +PL A ++     L 
Sbjct: 2125 DFQWCRRLFLHQHRLSFRDLNDTPQCFVSPLRADLLSALRHLR 2167


>gi|76799617|ref|ZP_00781735.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
 gi|76585032|gb|EAO61672.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
          Length = 157

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 37/153 (24%), Positives = 66/153 (43%), Gaps = 13/153 (8%)

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           + A+       + +    + I + YW+LV G    K + + + + +  H     +     
Sbjct: 1   LFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKHQVLRDKIGRNRHDRRKRII---- 56

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           + K   +A++   V+    Q    ++ +  TGRTHQ+RVH  H G P++GD  Y  +   
Sbjct: 57  DSKNGQHAMTIIDVLKYI-QNSSLIKCRLETGRTHQIRVHLSHHGHPLIGDPLYNPSSNN 115

Query: 279 NFTSPIQNKLYLHARYMDLPHPEG-GRLQITAP 310
                   +L LHA  + L HP     + + AP
Sbjct: 116 E-------RLMLHAHRLTLSHPLTCETISVEAP 141


>gi|87121619|ref|ZP_01077507.1| RNA pseudouridine synthase family protein [Marinomonas sp. MED121]
 gi|86163151|gb|EAQ64428.1| RNA pseudouridine synthase family protein [Marinomonas sp. MED121]
          Length = 289

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 56/280 (20%), Positives = 110/280 (39%), Gaps = 44/280 (15%)

Query: 31  HINFVNLQKILRSGQVRVD-KKRV----KFNNRIQSGQVVRIPPVINALNHIIKEQKILD 85
            ++   ++  +  G + +   K+V    +    ++ G+ +        L+ I+ E K++ 
Sbjct: 26  DLSAAEIKNAIAKGALWIGRGKKVQRLRRVKKALKVGEELHFYYNPKVLDQIVPEAKLVA 85

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
             V+ +                  V+ KP G+  QG     +           +  +   
Sbjct: 86  DLVSYS------------------VWYKPYGMLSQGSKWSDHTTISRWAQTHLTPERPVF 127

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD+  +G++++A T+AAA+ L+  F    ++K Y  +V G                
Sbjct: 128 IVHRLDRAATGLIIIAHTKAAARALSGMFEQHALEKHYQIIVHG---------------- 171

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +H   D   V+ Q E     A S F  ++   +     ++++  +GR HQ+R+HA  +G 
Sbjct: 172 NHSEHDQPEVITQ-EIDGKSAQSTFNCLEHAPSSNLSLIDVKIDSGRKHQIRLHAAGIGL 230

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           P+V D  +    +          L L A  +D   P  G 
Sbjct: 231 PVVADRLHGDKSQQYADDLN---LQLCAVTLDFTCPLTGE 267


>gi|254458808|ref|ZP_05072232.1| pseudouridine synthase [Campylobacterales bacterium GD 1]
 gi|207084574|gb|EDZ61862.1| pseudouridine synthase [Campylobacterales bacterium GD 1]
          Length = 244

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 52/224 (23%), Positives = 91/224 (40%), Gaps = 34/224 (15%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K     K   ++E+ +I V +KPA ++                  ++ + +   L HRLD
Sbjct: 51  KVQKIEKIKPIFENDEIIVVDKPAFVNS---------------DEIERQLKPAVLLHRLD 95

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG+L++ +     Q   + F+   + K Y + V GI     E +   +L +      
Sbjct: 96  RETSGVLMLVKDEEFRQKAIKEFKKDNVYKEYIAWVEGIISEPVE-VDKPILTQKKNNKA 154

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y +V  +       A + F   D  +     ++   H GRTHQ+R H  ++  PI+GD +
Sbjct: 155 YSNVSGK----GKPARTEFFP-DLVSANKTKIKCIIHHGRTHQIRTHLRYIDHPIIGDEQ 209

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           Y              ++ LHA  + L       ++  AP P   
Sbjct: 210 YGGRRA--------KRVMLHAYKVRLFD-----MEFVAPEPKVF 240


>gi|120600440|ref|YP_965014.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|120560533|gb|ABM26460.1| pseudouridine synthase [Shewanella sp. W3-18-1]
          Length = 305

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 53/288 (18%), Positives = 104/288 (36%), Gaps = 30/288 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H+  I     ++ +  G+V             Q G ++ +  +   +  +   +++
Sbjct: 28  FLSTHFARIGEEVWRERILDGKVH-----------WQDGSLIALDTLYRPMARVYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +     +  +L++D  + +  KP  + V              +  + +  + 
Sbjct: 77  P------VETKVPFEEQILFQDDNLILAYKPHFLPVTPSGNYVNECL-VHRLRLRTGIET 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-------KNKKE 196
               HRLD+ET+G++++           + F    I K Y ++    P       K    
Sbjct: 130 IAPAHRLDRETAGVILMTIQPETRHLYHQLFVDNAICKDYQAIAKLTPGIIEQYQKGHLT 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
              +W +K     GD    ++  E  AN   SH ++ +           + P TG+THQL
Sbjct: 190 LPLHWTVKNRMQPGDPSFTMQVVEGEAN---SHSEISLVAIKDDLGLFHLSPITGKTHQL 246

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH L +G P++ D  Y    +          L L A+ +    P  G
Sbjct: 247 RVHMLSLGMPLLNDRFY-PKLQPKGPDNFATPLKLMAQRLRFVDPVSG 293


>gi|225022032|ref|ZP_03711224.1| hypothetical protein CORMATOL_02064 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945153|gb|EEG26362.1| hypothetical protein CORMATOL_02064 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 300

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 91/248 (36%), Gaps = 19/248 (7%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           + A   +   Q++    +   +     +   ++ED ++ V +KP  ++     G      
Sbjct: 46  LAAETPLRANQEVWFYRIPAPEVPVPYRCETIFEDERLLVVDKPPFLATMP-RGKHITQS 104

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             ++    +   +    HRLD+ TSG+LV  +TR       + F  R  +K Y ++    
Sbjct: 105 ATVQLRKLTGNGELSPAHRLDRLTSGVLVFTKTREVRGAYQQLFARREAEKTYEAIARYD 164

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE------ 244
           P N        ++ +  +  +   +      G   AI+    ++    +           
Sbjct: 165 PTNPMA--QPGMVWRDRMAKNPGELQGYFIPGEPNAITTVIAVEPVPPERMRALRATHES 222

Query: 245 ---------MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
                    +QP TGRTHQLR+H    G PI+GD  Y               ++L A+ +
Sbjct: 223 ELPQQARYVLQPATGRTHQLRLHMWKAGVPILGDPAYPVVLP-EAEEDFAVPMHLRAKTL 281

Query: 296 DLPHPEGG 303
               P  G
Sbjct: 282 RFTDPLSG 289


>gi|325676532|ref|ZP_08156210.1| RNA pseudouridine synthase [Rhodococcus equi ATCC 33707]
 gi|325552710|gb|EGD22394.1| RNA pseudouridine synthase [Rhodococcus equi ATCC 33707]
          Length = 332

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 46/224 (20%), Positives = 80/224 (35%), Gaps = 12/224 (5%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            T+     +  +++ D  + V +KP  +    G G        ++             HR
Sbjct: 85  PTEEPIPFREEIVHVDDDLVVIDKPHFLPTTPG-GRYLRESALVRLRTRLDNPDLTPIHR 143

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK------KECIANWLL 203
           LD+ T+G+++ +   A        F  RR+ K+Y ++    P  K             L 
Sbjct: 144 LDRATAGLVMFSARPATRGAYQSLFEKRRVTKVYEAVSALPPAWKPDVPALGGHPVPVLY 203

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKV----IDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +           V  +      + +  +V    +    +      ++PHTGR HQLRVH 
Sbjct: 204 RNHIEARRGELRVAVDPSRPPNSETLIEVHGTGVSASGRTVLHTILRPHTGRMHQLRVHL 263

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
             +G  I+GD  Y  +            L L AR ++   P  G
Sbjct: 264 AALGAGILGDSWY-PDLLPEEPDDHSLPLQLLARELEFTDPLSG 306


>gi|256062319|ref|XP_002570309.1| ribosomal pseudouridine synthase [Schistosoma mansoni]
 gi|227294250|emb|CAY19151.1| ribosomal pseudouridine synthase, putative [Schistosoma mansoni]
          Length = 875

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 71/395 (17%), Positives = 130/395 (32%), Gaps = 118/395 (29%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK------ILDSSVNLTKHSDFLKS 99
           VR+ ++R K N  + +G  + IP   +    I ++          +        ++   +
Sbjct: 474 VRIIRQRTKLN--LYTGTTLDIPSNKSTSTSIPEKLDSQGYRIPDEDPYKFDLLTEEEAA 531

Query: 100 ILLYED-----SKIYVFNKPAGISVQGGSGIAYHIDGFL---KSWVDSKGQK-------- 143
           ++LY+        +   NKP GI+ Q G+   ++I   L   +S +  +           
Sbjct: 532 MVLYKSIIEIRENVIALNKPRGIASQPGADCKHNIVDLLPRIESLIRKRNHHGKGEEKYI 591

Query: 144 --PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
                 HRLD+++SGI+++AR + +A  L E+F  R I+K Y  +  GIP++    I   
Sbjct: 592 GELSTVHRLDKDSSGIILIARNKDSALKLQEAFSRRWIKKDYLCITVGIPRSDYGYIQLP 651

Query: 202 LLKKSHIGGDYVHVVKQNEK-----------------------------------GANYA 226
           L++++  G   +   + N +                                     N  
Sbjct: 652 LVERNFNGIRKMCTPQLNRRLQELTCKQTQLDIDNEANEYDVTDAFTVLYDKMRTNNNQP 711

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC-PIVGDHKYCA-------NFKG 278
            + + +ID        +     TG  HQ+R H       PI+GDHKY             
Sbjct: 712 TTWYNLIDKQ-NNAALMLCSTLTGIKHQIRAHLAFGLHTPILGDHKYSHAEYLAPQRLPK 770

Query: 279 NFTSPIQNKL---------------------------------------YLHARYMDLPH 299
           +    +  +                                        +   R  +  H
Sbjct: 771 SLLEVLNIRQSKVRYIGLHLHALSLHLHIPPSSSSSSSSLSSSTNNEGFFDFIRSFEYSH 830

Query: 300 PEG---------GRLQITAPLPAHMVKTWDSLGFK 325
                         L+ +APLP H  +    +G K
Sbjct: 831 SNNTMAKNKFIRNPLKFSAPLPNHFQRNLKRIGLK 865


>gi|167624728|ref|YP_001675022.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167354750|gb|ABZ77363.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 281

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 53/320 (16%), Positives = 117/320 (36%), Gaps = 55/320 (17%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRW-FKNHYPHINFVNLQKILRSGQVRVDKKRV-----K 54
           MS +    ++ V++ E    +D          ++   +++ ++ G V     R      +
Sbjct: 1   MSPLKIETHIKVQSTE----IDAASLLAEETGLSKQVIKQAMQKGAVWHSHGRQTNRLRR 56

Query: 55  FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
               ++ G  + +      L+  + E +                  LL++  +  ++ KP
Sbjct: 57  AKKALKVGDELHLYYNQAVLDETVTEAE------------------LLFDQEQYSIWYKP 98

Query: 115 AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
            G+  QG     +           +  +   L HRLD   +G++V+   +     + + F
Sbjct: 99  FGMRCQGSKWSDHTTINRYIETHLNPARNAYLIHRLDLAATGLIVLGHNKKVTAAIAKLF 158

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
             R + K Y  +V G   + K  I   +                       A+SH + ++
Sbjct: 159 ETRALDKFYQVIVEGKFPDGKVTIDTDV-------------------DNKSALSHAERLE 199

Query: 235 CFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
             ++     ++++  +GR HQ+R+H   +G P+VGD ++    +          L L + 
Sbjct: 200 YNSELNQSKVQVKIESGRKHQIRIHMASLGHPVVGDRQHGNGSEQTPN------LQLTSC 253

Query: 294 YMDLPHPEGGRLQITAPLPA 313
           ++    P  G  ++   LP 
Sbjct: 254 HLSFVCPVTGEDKVF-ELPQ 272


>gi|311893844|dbj|BAJ26252.1| putative pseudouridine synthase [Kitasatospora setae KM-6054]
          Length = 318

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 48/199 (24%), Positives = 74/199 (37%), Gaps = 5/199 (2%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           L+ D +I V +KP  ++     G         +   D    +    HRLD+ T+G+++  
Sbjct: 99  LHRDERIVVADKPHFLATTP-RGSHATETALARLRRDLDLPRLSPAHRLDRLTAGVVLFV 157

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
              A        F  R   K Y ++    P          ++  S I  D   +      
Sbjct: 158 ADPALRGAYQGLFERREAVKEYEAVARHEPDAAARL---PVVVCSRIVKDRGRLDAYEVP 214

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           G   A S  ++ +          + P TGRTHQLRVH   +G PI+GD  Y         
Sbjct: 215 GEPNAESLVELAEERG-GLGRYRLAPRTGRTHQLRVHMNGLGLPILGDPLYPEVLGEGDP 273

Query: 282 SPIQNKLYLHARYMDLPHP 300
              +  L L AR ++   P
Sbjct: 274 EDYRRPLQLLARSLEFTDP 292


>gi|302836415|ref|XP_002949768.1| pseudouridine synthase [Volvox carteri f. nagariensis]
 gi|300265127|gb|EFJ49320.1| pseudouridine synthase [Volvox carteri f. nagariensis]
          Length = 712

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 57/309 (18%), Positives = 104/309 (33%), Gaps = 66/309 (21%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV------------------ 53
           V+  ++   L +     +P ++    ++ + SG++R++                      
Sbjct: 157 VKKRQDGKPLMQLMAEEFPMLSPEYYREAVASGRLRMEPSSCCPGRGGAEGGKGKGRGGG 216

Query: 54  ---KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYV 110
                   +++G  +R     +    +  E +IL  +                       
Sbjct: 217 GIWTPERPLRAGMCIRHFIHRHEPPVLAGEVQILGIT------------------DDFVA 258

Query: 111 FNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
            NKPA + V   G      + G +++           T+RLD+  SG+L++AR+ A A  
Sbjct: 259 VNKPACLPVHTVGQYRKNTVMGVMQAMYPRLWP-LYPTYRLDKPVSGVLLLARSSAVAAR 317

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-------- 221
           +      R   K Y + V G+  +        L+    +G +                  
Sbjct: 318 MRVLLEERGCSKAYVARVQGVFPDTDAA-GGPLVVDVPLGWEAKTNHATPVPREAVEAAA 376

Query: 222 ---------------GANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVHALHMGCP 265
                           A  A +HF+ +          +E  P TGRTHQ+RVH  H+G P
Sbjct: 377 AGGPLPPGLNPELAASAKPAETHFRRLSVAPDGLTSVVEAVPKTGRTHQIRVHLQHLGHP 436

Query: 266 IVGDHKYCA 274
           I  D +Y  
Sbjct: 437 IANDTQYGG 445


>gi|319424856|gb|ADV52930.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 305

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 53/288 (18%), Positives = 104/288 (36%), Gaps = 30/288 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H+  I     ++ +  G+V             Q G ++ +  +   +  +   +++
Sbjct: 28  FLSTHFARIGEEVWRERILDGKVH-----------WQDGSLIALDTLYRPMARVYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +     +  +L++D  + +  KP  + V              +  + +  + 
Sbjct: 77  P------VETKVPFEEQILFQDDNLILAYKPHFLPVTPSGNYVNECL-VHRLRLRTGIET 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-------KNKKE 196
               HRLD+ET+G++++           + F    I K Y ++    P       K    
Sbjct: 130 IAPAHRLDRETAGVILMTIQPETRHLYHQLFVDNAICKDYQAIAKLTPGIIEQYQKGHLT 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
              +W +K     GD    ++  E  AN   SH ++ +           + P TG+THQL
Sbjct: 190 LPLHWTVKNRMQPGDPSFTMQVVEGEAN---SHSEISLVAIKDDLGLFHLSPITGKTHQL 246

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH L +G P++ D  Y    +          L L A+ +    P  G
Sbjct: 247 RVHMLSLGMPLLNDRFY-PKLQPKGPDDFATPLKLMAQRLRFVDPVSG 293


>gi|149036915|gb|EDL91533.1| RNA pseudouridylate synthase domain containing 3 (predicted),
           isoform CRA_b [Rattus norvegicus]
          Length = 346

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 58/305 (19%), Positives = 110/305 (36%), Gaps = 48/305 (15%)

Query: 68  PPVINALNHIIKEQKIL----DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
           P   +    ++++Q         ++ L + +  L++ ++ +   +   NKP G+ V G  
Sbjct: 41  PHRSSKRKDLVEDQPFPGLLRAENLGLEELAQVLRAAVVDQKGPLVTLNKPQGLPVTGRP 100

Query: 124 GIAYHIDGF--LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMR 177
           G    +     L   +  + Q+ ++     +E SG+++++       HL +    S R +
Sbjct: 101 GELTLLSVLPWLSQALGLEHQELQVVRAPGKEASGLVLLSSCPQTTSHLQKFFTHSRRAQ 160

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV-----KQNEKGANYAISHFKV 232
           R    Y ++  G+P+  +  +   L  +   G D    V     K  ++G    +SHF V
Sbjct: 161 RPTATYCAITDGVPEPSEGTVHIALRLERMDGIDLAVPVTSPSRKDIQEGVKRTLSHFHV 220

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPI 284
                     +++QP T    QL+VH     CPI+GDH Y           F     +  
Sbjct: 221 -TATGCGCALVQLQPLTVFPSQLQVHMALQLCPILGDHTYAARVGSVLGQRFLWPAETTK 279

Query: 285 QNKLYLHARYMDLPH------------------------PEGGRLQITAPLPAHMVKTWD 320
             +  L    +   H                        P     ++ APLP +  +T  
Sbjct: 280 PQRQVLDEALLRYLHLSPSQVAQMPLHLHLHRLLLPGTRPRDPPSELLAPLPPYFSRTLQ 339

Query: 321 SLGFK 325
            L   
Sbjct: 340 CLRLS 344


>gi|42522902|ref|NP_968282.1| pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
 gi|39574098|emb|CAE79275.1| Pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
          Length = 239

 Score =  116 bits (290), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 54/219 (24%), Positives = 86/219 (39%), Gaps = 9/219 (4%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG---FLKSWVDSKGQKPRLTHRLDQET 154
              ++Y+D   +  +KP+G  V       Y +      L        +     HRLD  T
Sbjct: 6   PLKIIYQDENFFAIDKPSGFFVHPPELSPYPVPKERICLWHLRKMFRKDVFPVHRLDAPT 65

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SGI++ A +R  A+ L   F  RR+ K Y ++V G        I   L      G   V 
Sbjct: 66  SGIVLFAMSRQDARELNFLFAERRMHKTYHAVVRGFVPA-SGSIDLPLEVDE--GQSIVE 122

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                   A   + +         ++  ++  P TGR HQ+R H   +  P++GD ++  
Sbjct: 123 AQTVFRSLAQVELPYAVGKKYPTSRYSLVQAHPVTGRWHQIRRHFDRIAHPLLGDIEHGD 182

Query: 275 NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAP 310
           +    F     N   L L A  +++  P  G R+ I AP
Sbjct: 183 SHHNRFFRDTLNIKGLCLKATKIEMESPWNGQRVVIEAP 221


>gi|237751452|ref|ZP_04581932.1| conserved hypothetical protein [Helicobacter bilis ATCC 43879]
 gi|229372818|gb|EEO23209.1| conserved hypothetical protein [Helicobacter bilis ATCC 43879]
          Length = 279

 Score =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 55/273 (20%), Positives = 103/273 (37%), Gaps = 53/273 (19%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                 +I+    + ++ SG+V +  KR+     +                         
Sbjct: 41  LLALQRNISTNKAKDLIDSGRVSIKGKRLLIARTL------------------------- 75

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
              +N          ++++ED  I   +K  GI               LK++   K    
Sbjct: 76  -LPLNTKFEVLTTPCVVIFEDDDILALDKSVGI----------ESYSLLKTYPHYK---- 120

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L +RLD++TSG++++A+     Q   ++F+ + ++K+Y++L+ G    +         +
Sbjct: 121 -LINRLDKDTSGVILLAKNEKMRQKAIQAFKQKEVEKMYFALIEGKVYEEINIEKKISTQ 179

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           K      YV      +    YA S    +  F      + +Q  TGRTHQ+R+H   +  
Sbjct: 180 KDSKAKSYV------DNEGLYAQSIVTPLQTFTH-TTLVSVQIPTGRTHQIRIHLKSIKH 232

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           PI+GD  Y        +     +L LH +   L
Sbjct: 233 PIIGDIIY-----NKTSLIKAKRLMLHCQKTSL 260


>gi|120601628|ref|YP_966028.1| pseudouridine synthase [Desulfovibrio vulgaris DP4]
 gi|120561857|gb|ABM27601.1| pseudouridine synthase [Desulfovibrio vulgaris DP4]
          Length = 400

 Score =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 58/373 (15%), Positives = 116/373 (31%), Gaps = 83/373 (22%)

Query: 4   MTY-VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           MT+  + + +  D+   RLD       P +     +++   G V V+    +  + + +G
Sbjct: 1   MTHDARRITIAPDDAGRRLDAVLAPLCPGMGLRGRRRLCDEGLVLVNGHPRRPGHHVATG 60

Query: 63  QVVRI-------------------------------PPVINALNHIIKEQKILDSSVNLT 91
             V +                                    +      E    D+   L 
Sbjct: 61  DEVVLVDAADGTTGQGKAGPSTTGPSTTGTDTAEAAMAARTSAGTTSPEGTACDAEALLP 120

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGIS----------------VQGGSGIAYHIDGF--- 132
                       +        +P G +                    +G    +      
Sbjct: 121 APGPVADPTGHPKGEDPLAPLRPGGEAHAAGLRLILPLDGATDSPPPTGGVPRLVAVYKP 180

Query: 133 --LKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             L S   + G+ P         +L +RLD  TSGIL++A   A  +   ++      +K
Sbjct: 181 GGLHSAALAGGRAPNAENLLPALKLLNRLDGPTSGILMLAGDTAGERQWRKAEDEGGTRK 240

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI---SHFKV------ 232
            Y ++  G  + ++  +    L  +      V     +++  +  +   +HF++      
Sbjct: 241 TYLAVCTG--RLERGTVVRAALDTARRTVTRVRPCDTDDRLRHTEVVPLAHFRLGDLANP 298

Query: 233 -------IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
                  +    +    +  +   G  HQ+R H  H+G P++GD  Y A        P +
Sbjct: 299 ITDDSAGVPACDETVTLVCCRIRKGARHQIRAHMAHIGHPLLGDDVYAAPAS---PPPGR 355

Query: 286 NKLYLHARYMDLP 298
             L+LH   + LP
Sbjct: 356 MPLFLHHSRITLP 368


>gi|164657135|ref|XP_001729694.1| hypothetical protein MGL_3238 [Malassezia globosa CBS 7966]
 gi|159103587|gb|EDP42480.1| hypothetical protein MGL_3238 [Malassezia globosa CBS 7966]
          Length = 937

 Score =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 86/237 (36%), Gaps = 29/237 (12%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
            +  G   V+   V    +IQ+   +              E  + ++ V           
Sbjct: 52  AIHHGLCTVNGHPVTPTYQIQNNDFLVNRVHR-------HEPAVTNAPV----------- 93

Query: 100 ILLYEDS--KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
            +L+ D      V  KP  I V       +H    +     +K Q    ++RLD+ TSGI
Sbjct: 94  RILHRDDSQGRIVVVKPGSIPVHATGRYHHHTLVEMVKE-QAKLQNLYTSNRLDRLTSGI 152

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVV 216
           +V + T+ AA  L   F    + K Y   V G  P    +C    L      G + VH  
Sbjct: 153 MVCSTTKEAACELGNDFNAGLVNKAYVCRVVGRFPDGIVDCTEPILSVDRQSGLNIVH-- 210

Query: 217 KQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                      + F+ +   A      L  +P TGRTHQ+RVHA  +G  I  D  Y
Sbjct: 211 ----PKGKECRTLFQRLSYDAATDSSVLVCRPITGRTHQIRVHAQWLGHAISNDPLY 263


>gi|183233062|ref|XP_001913799.1| hypothetical protein [Entamoeba histolytica HM-1:IMSS]
 gi|169801746|gb|EDS89422.1| hypothetical protein, conserved [Entamoeba histolytica HM-1:IMSS]
          Length = 356

 Score =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 97/221 (43%), Gaps = 18/221 (8%)

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYED-SKIYVFNKPAGISVQGGSGIAYHIDG 131
            +N +I+E  IL S  +L +    +K I + E+ ++  V NKP+GI V       Y+ + 
Sbjct: 60  TINSVIEEHDILISKCHLHEPPVPIKEIQIIENTNEYLVINKPSGIPVHPTG--RYNQNC 117

Query: 132 FLKSWVDSKGQ-KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--------IQKI 182
            +   ++       +  +RLD+ TSGIL+ A+T+  A       + +         +QKI
Sbjct: 118 IINILLNEYHFSHLKPVYRLDKNTSGILLFAKTKIFASSFQSILKEKSSVISSTSSLQKI 177

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFC 241
           Y + V G   +  E   N  L     G +    + ++      A S FK +         
Sbjct: 178 YLARVVGYFPDSIEV--NLPLHLVRFGTESQSCICED---GIEARSSFKRLFFDKDSNTS 232

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
            +E  PHTGRTHQLR+H   +  PI  D  Y  N   N+  
Sbjct: 233 VIECVPHTGRTHQLRLHLKAIHHPIANDSAYLLNQIHNYRQ 273


>gi|224588366|gb|ACN58990.1| ribosomal large subunit pseudouridine synthase D [uncultured
           bacterium BLR19]
          Length = 171

 Score =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 41/162 (25%), Positives = 76/162 (46%), Gaps = 10/162 (6%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             +  HRLD+  SG+++ A+ RA  ++L+E F  R+++K Y +    +P + K  + +W 
Sbjct: 8   YAQHIHRLDRPVSGVVLFAKQRAVLKNLSEQFAGRKVKKFYQAFTEQMPASAKGRLEHWH 67

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            K+         +  +    A  A   ++V+   + +F W  ++ HTG+ HQ+R     +
Sbjct: 68  RKE----KKKAVLYDKEVPYAEKATLEYEVVPISSGRFVWT-IELHTGKYHQIRAQLASV 122

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           GCPI+GD  Y +       +     + L A  +   HP    
Sbjct: 123 GCPIIGDIVYGSTLPYKTDA-----IALCAWKLIFFHPVTNE 159


>gi|57242694|ref|ZP_00370631.1| ribosomal large subunit pseudouridine synthase, RluD subfamily,
           putative [Campylobacter upsaliensis RM3195]
 gi|57016623|gb|EAL53407.1| ribosomal large subunit pseudouridine synthase, RluD subfamily,
           putative [Campylobacter upsaliensis RM3195]
          Length = 250

 Score =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 54/221 (24%), Positives = 93/221 (42%), Gaps = 35/221 (15%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +L+ED KI   NKP                 ++   ++S+  K +L +RLD+ETSG+
Sbjct: 56  KPQILFEDEKILAINKPY---------------SYISEELESEF-KAKLLNRLDKETSGL 99

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++ +     +   E FR +R+ K Y +++ G+   +          K   G        
Sbjct: 100 ILLCKNEDFKKLCIEEFRKQRVYKSYIAVLDGVLAEELVVDEPIRTLKGKNG-----AFS 154

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +  K    A+S    +    +K    ++   TGRTHQ+RVH   +  PI+GD KY     
Sbjct: 155 KITKEGQSALSIINPLMIQGKK-TLAKICIQTGRTHQIRVHTAFVKHPIIGDEKYGK--- 210

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                   +++YLH+  + + H      +  A L     K 
Sbjct: 211 -----IAADRMYLHSYELKILH-----YEFKANLDESFAKC 241


>gi|325676842|ref|ZP_08156515.1| RNA pseudouridine synthase [Rhodococcus equi ATCC 33707]
 gi|325552390|gb|EGD22079.1| RNA pseudouridine synthase [Rhodococcus equi ATCC 33707]
          Length = 288

 Score =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 49/216 (22%), Positives = 85/216 (39%), Gaps = 8/216 (3%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
              +        +L+    + V +KP  +S     G        ++   D         H
Sbjct: 69  PAPEVPVPFDIDVLHHVGGLVVVDKPHFLSTIP-RGAHIRETVVVRLRRDLGLPDLVPVH 127

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ T+G+L+        +   E F  RR++K+Y ++        +  I      +S I
Sbjct: 128 RLDRMTAGVLLCTADPRLRRPYQEMFERRRVRKVYEAI-----APYRGDIDFPRTVRSRI 182

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
              +  +    E G   + +  ++++          + P TGRTHQLR+H   +G PIVG
Sbjct: 183 VKVHGELTAYEEAGEPNSETLIELVERRGD-LARYRLHPRTGRTHQLRLHLNAIGAPIVG 241

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           D+ Y   F+        + L L AR ++   P  G 
Sbjct: 242 DNFY-PQFRRRDRDDFTDPLRLLARSLEFDDPVTGE 276


>gi|114049531|emb|CAJ75876.1| hypothetical protein [Lactobacillus plantarum subsp. plantarum]
          Length = 122

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 39/125 (31%), Positives = 56/125 (44%), Gaps = 11/125 (8%)

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N  L +S        +V    K    A++HFKV+  + Q +  +  +  TGRTHQ+RVH
Sbjct: 1   INAPLGRSPKDRKKQAIV----KTGRPAVTHFKVLKRY-QHYTLISCRLETGRTHQIRVH 55

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVK 317
              +G P+VGD  Y         +   +  +LHA+ +   HP  G  L   APLP     
Sbjct: 56  LQSIGHPLVGDPLYGPK-----KTIKGHGQFLHAKLLGFKHPVTGDLLTFEAPLPPIFTT 110

Query: 318 TWDSL 322
           T   L
Sbjct: 111 TLAKL 115


>gi|307243831|ref|ZP_07525961.1| pseudouridine synthase, RluA family [Peptostreptococcus stomatis
           DSM 17678]
 gi|306492794|gb|EFM64817.1| pseudouridine synthase, RluA family [Peptostreptococcus stomatis
           DSM 17678]
          Length = 226

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 86/228 (37%), Gaps = 35/228 (15%)

Query: 19  MRLDRWFK---NHYPHINFVN--LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +R+DR  K        +NF    + K+ R   +  + +  K  +  + G +         
Sbjct: 17  IRVDRDLKIKDLLIDELNFSVRSISKMKRDKNIYKNGQPAKPTSMAKPGDI--------- 67

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                   +I  +          L   ++YED  + V +KP  + V        H DG L
Sbjct: 68  -------IEIEINEEKAGFEGQDLGIAIVYEDQDLIVADKPPFMVVHPTKS---HFDGTL 117

Query: 134 KSWVD------SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            + +        +  + R  +RLD  TSG++V+A+   A   L+      R+ K Y ++V
Sbjct: 118 ANAITYHIGRIGEDCRIRFVNRLDMNTSGLVVIAKNSYAHHKLSLDMGQDRVHKEYLAIV 177

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            GI       +   + +++      V      +     +I+H++V+  
Sbjct: 178 EGIISQDSGTLDFPIYRETEDSISRVV-----DPRGQRSITHYRVLQR 220


>gi|241949279|ref|XP_002417362.1| DRAP deaminase, putative; hydrolase, putative [Candida dubliniensis
           CD36]
 gi|223640700|emb|CAX45011.1| DRAP deaminase, putative [Candida dubliniensis CD36]
          Length = 405

 Score =  115 bits (289), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 50/227 (22%), Positives = 96/227 (42%), Gaps = 12/227 (5%)

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL---YEDSKIYVFNKPAG 116
           +      +  V       + E+ I+  + +  +      + ++   YED++I V +KP+G
Sbjct: 65  KPNDQSILTGVDKLTKRKLDEKDIICHTKHRHEPPIPWYNDIIKSIYEDNEILVVDKPSG 124

Query: 117 ISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           I     G+     +   +K   +         HRLD+ TSG+LV+A+T+      ++  R
Sbjct: 125 IPTHPTGNYYHNSLSEIIKQQYNMDSI--WTCHRLDKVTSGVLVLAKTKNGGVKFSKLMR 182

Query: 176 M--RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
              +  +K Y + V G      E I  +      +  +   +    E+    + + F+ I
Sbjct: 183 DSKQHTKKTYLARVSGKFP---EGIHQYRCPIFAVNMNGYLMSGNMEELPTDSTTVFEQI 239

Query: 234 DCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              A      ++  P TG+ HQ+R+H  ++G PIV D  Y  + + N
Sbjct: 240 KYNACLDQSLIKCIPITGKFHQIRIHLRNLGFPIVNDSFYQPDKQKN 286


>gi|221067233|ref|ZP_03543338.1| pseudouridine synthase [Comamonas testosteroni KF-1]
 gi|220712256|gb|EED67624.1| pseudouridine synthase [Comamonas testosteroni KF-1]
          Length = 305

 Score =  115 bits (289), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 54/303 (17%), Positives = 104/303 (34%), Gaps = 31/303 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV-RIP 68
           VV+ +    + +D +       +        LR               R+ +GQVV    
Sbjct: 21  VVLPSQGGGLLID-FLCERLSVVGRA---DWLR---------------RMAAGQVVSETG 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            +       +   +         +      + +++ D  + + +KP  + V       Y 
Sbjct: 62  EMAGPDAAFMPGLRYYYYRELEVEPEIPFAAEVIHRDEHLLIADKPHFLPVVPAG--QYL 119

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L          +    HR+D++T+G++V +  RA        FR R I K+Y ++ 
Sbjct: 120 QNTLLVRLKREFDLPELSPIHRIDRDTAGLVVFSLQRATRGIYQGMFRDRAIHKVYEAVA 179

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
               +     ++      S +             G   + +  ++I+     +    + P
Sbjct: 180 PYRAE-----LSFPREHVSRMEESGHFFRMHEVAGEPNSRTLMEIIE-HNNAWARYRLSP 233

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            +G+ HQLRVH   +G P+ GD  Y               L L AR +    P  G R +
Sbjct: 234 VSGKRHQLRVHMAALGLPLRGDAFY-PVVDDPEPGDYSRPLQLLARSLAFDDPLTGQRRE 292

Query: 307 ITA 309
            T+
Sbjct: 293 FTS 295


>gi|222150872|ref|YP_002560025.1| truncated ribosomal large subunit pseudouridine synthase
           [Macrococcus caseolyticus JCSC5402]
 gi|222119994|dbj|BAH17329.1| truncated ribosomal large subunit pseudouridine synthase
           [Macrococcus caseolyticus JCSC5402]
          Length = 235

 Score =  115 bits (289), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 48/255 (18%), Positives = 102/255 (40%), Gaps = 37/255 (14%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           + +NH    +  ++  I ++G + V+  +V     +     + +              ++
Sbjct: 10  FLQNH--QYSRKSISAIKQNGALLVNGHQVTVRYEMHKHDTLTV--------------QL 53

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
            D S + T     +  ++ Y+D  + + +KP  ++        +  D  +++        
Sbjct: 54  PDESRSKTLIPSHIPILIHYDDEYLIIVSKPPFMNTIPSK--QHPHDSLIEAVYGHLETH 111

Query: 144 -----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                     RLD++TSG++V ++ +     LT      +I+K Y  +  G  K+    +
Sbjct: 112 DDKSVLHPVSRLDRDTSGLVVFSKHQLTHHLLT-----GKIEKFYLLIAAGHVKDHGNYV 166

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRV 257
                ++  I    V+V         +A + + +ID  A+     + ++ HTGRTHQ+RV
Sbjct: 167 YPIDRREDSIITRTVNV------HGQHARTEYHLIDYDAEFDVSLVHVKLHTGRTHQIRV 220

Query: 258 HALHMGCPIVGDHKY 272
           H      P+  D  Y
Sbjct: 221 HFSAALHPL--DASY 233


>gi|307108910|gb|EFN57149.1| hypothetical protein CHLNCDRAFT_143494 [Chlorella variabilis]
          Length = 452

 Score =  115 bits (289), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 64/303 (21%), Positives = 111/303 (36%), Gaps = 49/303 (16%)

Query: 20  RLDRWFKNHYPHI--NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNH 76
           RLD   +   P    +  + ++ +R  ++RVD  +    +  +Q G++++      A   
Sbjct: 34  RLDEALQLLQPDRYPSITSAKRAVRRRELRVDGVQSTAPSIMLQGGELLQCMQRQGAAAL 93

Query: 77  IIKEQKILDSSVNLTKHSDFL----KSILLYEDSKIYVFNKPAGISV--QGGSGIAYHID 130
               Q    ++              +  + YEDS +    KP GI        G A   +
Sbjct: 94  QQCPQPAAGAAEAWMPSGAAAAGRYRLGVAYEDSHLACVVKPPGIPTDTPPHRGAARGAN 153

Query: 131 G-----------------------------------FLKSWVDSKGQ-----KPRLTHRL 150
                                                L + +   G+     +PR  HRL
Sbjct: 154 NATGSAATGASQPGAGAASGASSSSAAAQAVPSVYELLAAQLQPTGELGALRRPRHVHRL 213

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ T G++VVA+TR A   L+ +F  RR+ K Y +LVWG  + +         K+     
Sbjct: 214 DEPTGGLVVVAKTRLAQTQLSAAFMQRRVTKRYRALVWGRLEGRGLVRYCLDGKRCETEY 273

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                 + +        +        A     +++ PHTGR HQLR H   +G P++G+ 
Sbjct: 274 AAAQHTRVDLAALGLRPAAPLAAPQPAIWVTTVDLWPHTGRKHQLRRHMALLGHPLLGET 333

Query: 271 KYC 273
           +Y 
Sbjct: 334 RYS 336


>gi|293609404|ref|ZP_06691706.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292827856|gb|EFF86219.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 302

 Score =  115 bits (289), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 54/290 (18%), Positives = 109/290 (37%), Gaps = 29/290 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H+PHI     ++  + G +              +G  + +        HI   + +
Sbjct: 34  YLCGHFPHIKTEEWEQRFQDGLIYA-----------ANGDKLTLTSPYVGNTHIFYYRFL 82

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   KH       +L+E+  + V +KP  +++       Y  +  L       G +
Sbjct: 83  AYEPHVPFKHH------ILFENDDLLVVDKPHFLTISPTG--QYVQETLLVRLKKQTGNE 134

Query: 144 -PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIANW 201
                HRLD+ET+G+++  +   +     + F  R++ KIY ++  +    N  + +   
Sbjct: 135 FLTPIHRLDRETAGVVLFCKQVESRGIYQQLFAERQVNKIYHAIAPYKKDLNFPQTLHLH 194

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L K     G   + ++  E       ++ ++I+   Q +    + P TG+ HQLRVH  +
Sbjct: 195 LDK-----GLPFYTMQVIENAKANTQTYIELIE-HNQIWAKYRLTPTTGKQHQLRVHLNY 248

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           +  PI  D  Y    +          L L A+++    P     +   + 
Sbjct: 249 LEIPIKNDPFY-PVVQHKAEDDFSEPLQLLAKHISFTDPLTKEGMSFNSE 297


>gi|303284197|ref|XP_003061389.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226456719|gb|EEH54019.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 497

 Score =  115 bits (289), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 62/311 (19%), Positives = 103/311 (33%), Gaps = 55/311 (17%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG---QVVRIPPVINALNHIIKEQ 81
           F   +P       ++   SG +RV+  R K N            R   VI  L  +   +
Sbjct: 46  FAREFPARPREYYERAHASGALRVENVRAKSNGGNGGNGGNDNARTSDVIRPLRPLKAGE 105

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSK 140
           ++  +       +      ++     +   +KPA + V   G      + G+L +     
Sbjct: 106 RVRHALHRHEPPTLDRPVEVIAVADDLVAIHKPATMPVHPTGQYRKNTVLGYLAAHRRDL 165

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN------- 193
           G K    HRLD+  SG+LV+ART   A  +      R + K Y +LV     N       
Sbjct: 166 G-KLFPVHRLDKNVSGLLVMARTPTTANAMRTQVEGREVSKEYLALVTMKIFNAGGNAET 224

Query: 194 -----------KKECIANWLLKKSHIGGDYVHVVKQNE----KGANYAISHFKVIDCF-- 236
                      ++          + +  D    V   +     GA  A + F+++     
Sbjct: 225 VAAAALTAFAREEGTDVFAARCDAAVAYDERARVASCDVSVADGAKDASTAFELVARGEW 284

Query: 237 --------------------------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                                      ++   +  +P TGRTHQ+R H   +G PIV D 
Sbjct: 285 GVGGGDGGGDGGSACPFEDVVVRGGLPRRALLVRCRPTTGRTHQIRAHLSRLGWPIVNDV 344

Query: 271 KYCANFKGNFT 281
           KY      +  
Sbjct: 345 KYGGARAADLG 355


>gi|299532184|ref|ZP_07045578.1| pseudouridine synthase [Comamonas testosteroni S44]
 gi|298719846|gb|EFI60809.1| pseudouridine synthase [Comamonas testosteroni S44]
          Length = 305

 Score =  115 bits (289), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 56/303 (18%), Positives = 107/303 (35%), Gaps = 31/303 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV-RIP 68
           VV+ +    + +D +     P +        LR               R+ +GQVV    
Sbjct: 21  VVLPSQGGGLLID-FLCERLPAVGRT---DWLR---------------RMGAGQVVSETG 61

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            +       +   +         +      + +++ D+ + V +KP  + V       Y 
Sbjct: 62  EMAGPDAAFMPGLRYYYYRELEAEPEIPFAAEVIHRDAHLLVADKPHFLPVVPAGH--YL 119

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L          +    HR+D++T+G++V +  RA        FR R I K+Y ++ 
Sbjct: 120 QNTLLVRLRREFDLPELSPIHRIDRDTAGLVVFSVQRATRGIYQGLFRDRAIHKVYEAVA 179

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
               +     ++      S +             G   + +  ++I+  +  +    + P
Sbjct: 180 AYRAE-----LSFPREHASRMEESGHFFRMHEVAGEPNSRTLMEIIEHNS-AWARYRLSP 233

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            +G+ HQLRVH   +G P+ GD  Y               L L AR +    P  G R +
Sbjct: 234 VSGKRHQLRVHMAALGLPLRGDAFY-PMVNDPEPGDYSRPLQLLARSLAFDDPLTGQRRE 292

Query: 307 ITA 309
            T+
Sbjct: 293 FTS 295


>gi|281211459|gb|EFA85621.1| hypothetical protein PPL_00850 [Polysphondylium pallidum PN500]
          Length = 616

 Score =  115 bits (289), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 53/320 (16%), Positives = 112/320 (35%), Gaps = 93/320 (29%)

Query: 6   YVQYVVVENDEENM-RLDRWFKN---------HYPHINFVNLQKILRSGQVRVDKKRVKF 55
           Y    VV   ++   +L+++                +   ++QK++    V ++   +K 
Sbjct: 9   YTIEEVVPKQQQGADKLEKYLSGIWGTVKENGKLVQLTRSSVQKLMAQQLVSLNGNVIKE 68

Query: 56  NN-RIQSGQVVRI------------PPVINALNHIIKEQKILDS---------------- 86
              ++++  V+ +                      +K+Q I                   
Sbjct: 69  KTCKVRANDVIVLRLYSLDIFKQQENDTDRKAQQDLKKQHIAVPTSSSSSSSAKKQGASN 128

Query: 87  --------------SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-------GSGI 125
                          ++L  + D +   ++YED  + V NKPAG+ V          S  
Sbjct: 129 SESSSSSLSPFSSDDIDLVPNRD-IPIDVIYEDEWLAVVNKPAGLLVHPTPQRGGDDSNS 187

Query: 126 AYHIDGFLKSWVDSKG----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                  +   +   G          ++P + HRLD++T+GILV+A+T A  Q L +  +
Sbjct: 188 ENQTHTLVNGLLHKYGAKGLSTMGGLERPGIVHRLDKDTAGILVIAKTDAIHQQLKDMLQ 247

Query: 176 MR------------------RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
                               +IQK Y  LV G PK ++  I   + +  +     ++ + 
Sbjct: 248 EHTEDSISETKKSSSGGGSTKIQKKYRCLVAGKPKEQRGLIKRAIARHPND----MNKMI 303

Query: 218 QNEKGANYAISHFKVIDCFA 237
            +E+    +++ + V+  + 
Sbjct: 304 IDEEKGKPSLTEYTVVKAWN 323



 Score = 80.0 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 32/110 (29%), Positives = 54/110 (49%), Gaps = 6/110 (5%)

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           +  +  L++  HTGRTHQ+RVH+L  G PIVGD  Y     G  T  +   L L + Y+ 
Sbjct: 458 SSSYALLDITLHTGRTHQIRVHSLSEGMPIVGDPIYS----GKSTQFMVPYLLLASVYLC 513

Query: 297 LPHPEG-GRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQNI 345
             HP    + + T P P H  +  + L  + ++    +++   +E   ++
Sbjct: 514 FVHPVTKEKKEFTIPNPPHFQQFIELLD-QAEKQKKNQQIQFLEELGDDL 562


>gi|264678344|ref|YP_003278251.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
 gi|262208857|gb|ACY32955.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
          Length = 305

 Score =  115 bits (289), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 58/303 (19%), Positives = 106/303 (34%), Gaps = 31/303 (10%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VV+ +    + +D +     P +        LR               R+ +GQVV    
Sbjct: 21  VVLPSQGGGLLID-FLCERLPAVGRA---DWLR---------------RMAAGQVVSEAG 61

Query: 70  VINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
                N              L    +    + +++ D+ + V +KP  + V       Y 
Sbjct: 62  DKAGPNAAFMPGLRYYYYRELEAEPEIPFAAEVIHRDADLLVADKPHFLPVVPAGH--YL 119

Query: 129 IDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            +  L          +    HR+D++T+G++V +  RA        FR R I K+Y ++ 
Sbjct: 120 QNTLLVRLRREFDLPELSPIHRIDRDTAGLVVFSVQRATRGIYQGLFRDRAIHKVYEAVA 179

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
               +     ++      S +             G   + +  ++I+   + +    + P
Sbjct: 180 AYRAE-----LSFPREHASRMEESGHFFRMHEVAGEPNSRTLMEIIE-HNKAWARYRLSP 233

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQ 306
            +G+ HQLRVH   +G P+ GD  Y               L L AR +    P  G R +
Sbjct: 234 VSGKRHQLRVHMAALGLPLRGDAFY-PVVNDPEPGDYSRPLQLLARSLAFDDPLTGQRRE 292

Query: 307 ITA 309
            T+
Sbjct: 293 FTS 295


>gi|260779060|ref|ZP_05887952.1| pseudouridylate synthase LSU rRNA-specific [Vibrio coralliilyticus
           ATCC BAA-450]
 gi|260605224|gb|EEX31519.1| pseudouridylate synthase LSU rRNA-specific [Vibrio coralliilyticus
           ATCC BAA-450]
          Length = 231

 Score =  115 bits (289), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 56/199 (28%), Positives = 89/199 (44%), Gaps = 17/199 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +++  S   V NK   +SV    G    +       + +  ++  L HRLD+ TSG+L+
Sbjct: 3   DIVFSHSDFVVINKHPNVSVHKDDGETMLLHEV---ALVTGDEQLYLVHRLDKMTSGLLL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L+  F  RR++K Y ++    PK K+  ++        +        K  
Sbjct: 60  LARNAAAASELSTQFAQRRVEKFYLAIGSKKPKKKQGLVSG------DMERSRRSAWKLT 113

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              +N AI+ F +             +PHTG+THQ+RV    +G PIVGD  Y    K  
Sbjct: 114 SSHSNPAITQF-LSTSAEPGERLFLCKPHTGKTHQIRVALKSVGSPIVGDAIYTPASKS- 171

Query: 280 FTSPIQNKLYLHARYMDLP 298
                 ++ YLHA  ++  
Sbjct: 172 ------DRGYLHAFALEFE 184


>gi|57167720|ref|ZP_00366860.1| ribosomal large subunit pseudouridine synthase C, putative
           [Campylobacter coli RM2228]
 gi|57020842|gb|EAL57506.1| ribosomal large subunit pseudouridine synthase C, putative
           [Campylobacter coli RM2228]
          Length = 208

 Score =  115 bits (289), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 59/228 (25%), Positives = 101/228 (44%), Gaps = 39/228 (17%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I   NKP                 ++   ++ K    +L +RLD+ETSG+
Sbjct: 14  KPKVIFEDENIIAINKPY---------------AYISEELEKKFN-AKLLNRLDKETSGV 57

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++ +     +   E F+ +R+ K Y +++ GI   + E     L  K+  G      + 
Sbjct: 58  ILLCKNEDFRKICIEEFKKQRVYKSYIAVLDGILAEEIEIDEPILTIKTKNG-----ALS 112

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +  K    A+S F  I   A+K    ++   TGRTHQ+RVHA  +   I+GD KY     
Sbjct: 113 KISKEGLSAVSIFTPIMMQAKK-TLAKIIIKTGRTHQIRVHAKFIKHGIIGDEKY----- 166

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                   +++YLH+  + + +      Q  A L +   K    LGF+
Sbjct: 167 ---AKISSDRMYLHSHEIRILN-----YQFKAELDSSFSK----LGFE 202


>gi|46581082|ref|YP_011890.1| RNA pseudouridine synthase family protein [Desulfovibrio vulgaris
           str. Hildenborough]
 gi|46450503|gb|AAS97150.1| RNA pseudouridine synthase family protein [Desulfovibrio vulgaris
           str. Hildenborough]
 gi|311234759|gb|ADP87613.1| pseudouridine synthase [Desulfovibrio vulgaris RCH1]
          Length = 400

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 59/373 (15%), Positives = 116/373 (31%), Gaps = 83/373 (22%)

Query: 4   MTY-VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           MT+  + + +  D+   RLD       P +     +++   G V V+    +  + + +G
Sbjct: 1   MTHDARRITIAPDDAGRRLDAVLAPLCPGMGLRGRRRLCDEGLVLVNGHPRRPGHHVATG 60

Query: 63  QVVRI-------------------------------PPVINALNHIIKEQKILDSSVNLT 91
             V +                                    +      E    D+   L 
Sbjct: 61  DEVVLVDAADGTTGQGKAGPSTTGPSTTGTDTAEAAMAARTSAGTTSPEGTACDAEALLP 120

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGIS----------------VQGGSGIAYHIDGF--- 132
                       +        +P G +                    +G    +      
Sbjct: 121 APGPVADPTGHPKGEDPLAPLRPGGEAHAAGLRLILPLDGATDSPPPTGGVPRLVAVYKP 180

Query: 133 --LKSWVDSKGQKP---------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
             L S   + G+ P         +L +RLD  TSGIL++A   A  +   ++      +K
Sbjct: 181 GGLHSAALAGGRAPNAENLLPALKLLNRLDGPTSGILMLAGDTAGERQWRKAEDEGGTRK 240

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI---SHFKVID---- 234
            Y ++  G  + ++  +    L  +      V     +++  +  +   +HF++ D    
Sbjct: 241 TYLAVCTG--RLERGTVVRAALDTARRTVTRVRPCDTDDRLRHTEVVPLAHFRLGDLANL 298

Query: 235 ---------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
                       +    +  +   G  HQ+R H  H+G P++GD  Y A        P +
Sbjct: 299 ITDDTAGAPACDETVTLVCCRIRKGARHQIRAHMAHIGHPLLGDDVYAAPAS---PPPGR 355

Query: 286 NKLYLHARYMDLP 298
             L+LH   + LP
Sbjct: 356 MPLFLHHSRITLP 368


>gi|294790685|ref|ZP_06755843.1| RNA pseudouridine synthase [Scardovia inopinata F0304]
 gi|294458582|gb|EFG26935.1| RNA pseudouridine synthase [Scardovia inopinata F0304]
          Length = 252

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 56/245 (22%), Positives = 91/245 (37%), Gaps = 29/245 (11%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + +        +LYED  I   +KP  +      G+ Y     +     +        HR
Sbjct: 1   MDEPVIPADLPILYEDQAIIAVDKPHFLPTMP-RGMWYKSTAVMTMRERTGNDSLIPAHR 59

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW------------GIPKNKKEC 197
           LD+ T+G+L++ +     +     F+ R++ K Y  L              G   ++K  
Sbjct: 60  LDRMTAGVLILVKEPQYRKMYQMLFQSRQVHKTYQCLAPIRPASRPRLGLVGHVWSRKGE 119

Query: 198 IAN----------WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ- 246
             N           LL+ SHI      +    E  A  A+S   +    +       ++ 
Sbjct: 120 DNNLTVDVTNLSFPLLRSSHITKKRGILQAYEEAEAINAVSLITISSHQSSHALNKGLRA 179

Query: 247 ----PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
               P TG+THQLRVH   +G PI GD+ Y    +        + L L AR +    P  
Sbjct: 180 YTLHPLTGKTHQLRVHMTSLGLPIDGDNWY-PQVEERAYDDFSHPLQLIAREISFTDPLT 238

Query: 303 GRLQI 307
           G+ +I
Sbjct: 239 GQERI 243


>gi|149194110|ref|ZP_01871208.1| Pseudouridine synthase [Caminibacter mediatlanticus TB-2]
 gi|149136063|gb|EDM24541.1| Pseudouridine synthase [Caminibacter mediatlanticus TB-2]
          Length = 252

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 53/225 (23%), Positives = 86/225 (38%), Gaps = 35/225 (15%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K        +++ED+ + V +KP                 ++ S   SK  K  L HRLD
Sbjct: 51  KIEKIPNPKVIFEDNNLLVIDKPP----------------YITSEEISKRFKYPLLHRLD 94

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSGILV+ +     +   E F+ + + K Y + V GI     +      + K+  G  
Sbjct: 95  KETSGILVLTKNEDFRKKAIEEFKNKNVYKEYLAWVSGIVAEPMKIDFPIKVIKTKSG-- 152

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                 +       AI+  + I  F +    ++   HTG+THQ+R H   +  PI+GD K
Sbjct: 153 ---AFAKVSSDGEEAITEIEPILAF-RTKSKIKAIIHTGKTHQIRAHLKAIDHPIIGDEK 208

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           Y              ++ LH     +           +P P    
Sbjct: 209 YGGEPY--------KRVMLHHYKFKIFD-----YNFESPEPRDFK 240


>gi|329908268|ref|ZP_08274842.1| ribosomal large subunit pseudouridine synthase A-like protein
           [Oxalobacteraceae bacterium IMCC9480]
 gi|327546746|gb|EGF31689.1| ribosomal large subunit pseudouridine synthase A-like protein
           [Oxalobacteraceae bacterium IMCC9480]
          Length = 302

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 54/288 (18%), Positives = 101/288 (35%), Gaps = 32/288 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +  + +P I     Q                   R+  G V+    +      + + 
Sbjct: 21  LD-FLAHQFPAIGRDVWQA------------------RMAQGDVLDTAGMALDAQSLYRA 61

Query: 81  QKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVD 138
              +    +L   +      ++L+ D  + V +KP  + V   G  +   +   LK  + 
Sbjct: 62  HTKVFYFRSLPAEAAIPFDEVVLFRDDTLLVVDKPHFLPVTPAGRYLQQTLLVRLKRKLG 121

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + Q P   HR+D+ET+G+++     A        FR R + K Y ++   +P      +
Sbjct: 122 IETQAP--MHRIDRETAGLVLFTIQPATRAVYQGLFRDRAVTKHYEAIAPWLPA-----L 174

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +   S +      +  +   G   A +  ++++          + P TG+ HQLRV 
Sbjct: 175 QFPMQVSSRLVDAEHFMKMREVDGEPNAETRIELLEVQG-NLARYALHPSTGQRHQLRVQ 233

Query: 259 ALHMGCPIVGDHKYC---ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +G PI  D  Y                  L L A+ ++   P  G
Sbjct: 234 MEALGIPIRHDRIYPQLLPEAPSGMPPDYSKPLQLLAKSLEFTDPLSG 281


>gi|315126704|ref|YP_004068707.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
 gi|315015218|gb|ADT68556.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
          Length = 219

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 53/198 (26%), Positives = 87/198 (43%), Gaps = 20/198 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           + Y     Y+  KPAG++       +    GF+        +K    HRLD+ TSG++++
Sbjct: 4   VQYTHDDFYIITKPAGLNFH-----SEESPGFVFLAEQQLNEKLFAVHRLDKVTSGLIIL 58

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           AR + AA   T+ F    I K Y ++    PK K+  +   + K        ++      
Sbjct: 59  ARHKDAAAKFTQMFTEHTINKFYLAVSDSKPKKKQGWVKGDMAKSRRGTYKLLNSQ---- 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             +N AI+ F     F   F    ++P++G+THQLRV    +G  I+GD  Y  +     
Sbjct: 115 --SNPAITRFYSF-SFKSGFRAYLLKPYSGKTHQLRVALKSIGAAILGDASYSGS----- 166

Query: 281 TSPIQNKLYLHARYMDLP 298
                ++ YLHA  +D  
Sbjct: 167 ---AADRTYLHAFALDFE 181


>gi|68488811|ref|XP_711752.1| hypothetical protein CaO19.10304 [Candida albicans SC5314]
 gi|46433075|gb|EAK92530.1| hypothetical protein CaO19.10304 [Candida albicans SC5314]
          Length = 402

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 49/212 (23%), Positives = 91/212 (42%), Gaps = 12/212 (5%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILL---YEDSKIYVFNKPAGISVQG-GSGIAYHI 129
           +   + E+ I+  + +  +      + ++   YED +I V +KP+GI     G+     +
Sbjct: 79  IKRKLDEKDIICHTKHRHEPPIPWHNDIIKSVYEDDEILVVDKPSGIPTHPTGNYYFNSL 138

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--IQKIYWSLV 187
              +K  ++         HRLD+ TSG+LV+A+T+      ++  R  +   +K Y + V
Sbjct: 139 SEIIKQQLNMDSI--WTCHRLDKVTSGVLVLAKTKNGGVRFSKLMRDSKQYTEKTYLARV 196

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQ 246
            G      E I  +      +  +   +    E+    + + F+ I   A      ++  
Sbjct: 197 SGKFP---EGIHRYRCPIFAVNMNGYLMSGNMEELPTDSTTIFERIKYNASLDQSLVKCV 253

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           P TG+ HQ+RVH  ++G PIV D  Y      
Sbjct: 254 PITGKFHQIRVHLRNLGFPIVNDSFYQPEQDQ 285


>gi|305433225|ref|ZP_07402381.1| RNA pseudouridine synthase [Campylobacter coli JV20]
 gi|304443926|gb|EFM36583.1| RNA pseudouridine synthase [Campylobacter coli JV20]
          Length = 250

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 59/228 (25%), Positives = 101/228 (44%), Gaps = 39/228 (17%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +++ED  I   NKP                 ++   ++ K    +L +RLD+ETSG+
Sbjct: 56  KPKVIFEDENIIAINKPY---------------AYISEELEKKFN-AKLLNRLDKETSGV 99

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++ +     +   E F+ +R+ K Y +++ GI   + E     L  K+  G      + 
Sbjct: 100 ILLCKNEDFRKICIEEFKKQRVYKSYIAVLDGILAEEIEIDEPILTIKTKNG-----ALS 154

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +  K    A+S F  I   A+K    ++   TGRTHQ+RVHA  +   I+GD KY     
Sbjct: 155 KISKEGLSAVSIFTPIMMQAKK-TLAKIIIKTGRTHQIRVHAKFIKHGIIGDEKY----- 208

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                   +++YLH+  + + +      Q  A L +   K    LGF+
Sbjct: 209 ---AKISSDRMYLHSHEIRILN-----YQFKAELDSSFSK----LGFE 244


>gi|148548835|ref|YP_001268937.1| pseudouridine synthase [Pseudomonas putida F1]
 gi|148512893|gb|ABQ79753.1| pseudouridine synthase [Pseudomonas putida F1]
          Length = 301

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 53/254 (20%), Positives = 103/254 (40%), Gaps = 10/254 (3%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYV 110
           R ++ +R   G+V+       A +   K    L     +  +    ++ ++L+ D  + V
Sbjct: 45  RAQWLDRFARGRVLDAKGQAVAADLPYKRGMRLHYFREVPNERPIPVQEVVLHVDEHLVV 104

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
            +KP  + V   +G         +             HR+D+ T+G+++ +    +    
Sbjct: 105 ADKPHFLPVTP-TGEYVEQTLLRRLIRRLDNPHLVPLHRIDRHTAGLVLFSANPHSRSAY 163

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              F  RRI K Y ++   +P++    +     K   + G+    + + E  AN + +  
Sbjct: 164 QRLFPERRIDKRYQAIAAAMPQHTFPLVH----KSRLVHGEPFFRMHEVEGEAN-SETLA 218

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           +V++   +++ +  + P TG+THQLRVH   +G  I  D  Y      N     Q  L L
Sbjct: 219 EVLEKNGERWRYG-LSPVTGKTHQLRVHMAALGAGISNDPFYPQLL--NEEDDYQRPLKL 275

Query: 291 HARYMDLPHPEGGR 304
            A+ +    P  G 
Sbjct: 276 LAQSLRFEDPLSGE 289


>gi|149910060|ref|ZP_01898708.1| putative pseudouridylate synthase [Moritella sp. PE36]
 gi|149806928|gb|EDM66889.1| putative pseudouridylate synthase [Moritella sp. PE36]
          Length = 315

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 60/308 (19%), Positives = 120/308 (38%), Gaps = 32/308 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H+  I+    Q+ +  G+V             + G+++ +          +  +++
Sbjct: 27  FLIGHFKQIDATVWQQRIMDGKVH-----------WRDGRLITLDC------AFVPRERV 69

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +        ++YED  I V  KP  ++V              +  + +  + 
Sbjct: 70  YYYREVAVEKKVPFAENVIYEDDNIMVAYKPHFLAVSPSGQFVNECL-VNRLRIKTGIET 128

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKE 196
               HRLD+ T+G++++++         + F+   I K Y ++    P+        +  
Sbjct: 129 LVTAHRLDRATAGLMLLSKHPEQRHLYHDLFKYANITKHYQAIARLTPELYQQHQQGELA 188

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              +W +K   + G+    +K  +  AN + S  ++I    + F    + P TG+THQLR
Sbjct: 189 LPLHWTVKNRIVKGEPSFTMKIADGEAN-SHSEIELIAVKGE-FGLFRLSPITGKTHQLR 246

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG---RLQITA-PLP 312
           +H L +G P+V D  Y            +  L L A+ ++   P  G   ++   A  + 
Sbjct: 247 LHMLSLGLPLVNDRLY-PILLDRCDDNFKQPLQLLAQQLEFTDPVTGIEHKITTEALDID 305

Query: 313 AHMVKTWD 320
           A M KT D
Sbjct: 306 ALMDKTID 313


>gi|113971866|ref|YP_735659.1| pseudouridine synthase [Shewanella sp. MR-4]
 gi|113886550|gb|ABI40602.1| pseudouridine synthase [Shewanella sp. MR-4]
          Length = 308

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 55/288 (19%), Positives = 105/288 (36%), Gaps = 30/288 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   HY HI     ++ +  G+V             Q G ++ +             +++
Sbjct: 28  FLIEHYAHIGEAVWRQRILDGKVH-----------WQDGSLIGLDTAYRPTARAYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +      S +L++D  + +  KP  + V              +  + +    
Sbjct: 77  P------VEAQVPFASPILFQDGNLILAYKPHFLPVTPSGDYVNECL-VHRLRLSTGIDT 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKE 196
               HRLD+ET+G++++           + F    I+K Y ++    P+        +  
Sbjct: 130 IAPAHRLDRETAGVILMTTRPETRHIYHQLFVDDAIRKDYQAIAKLTPEIMAQYACGELT 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
              +W +K      +    +K  E  AN   +H ++ +     +F   E+ P TG+THQL
Sbjct: 190 LPLHWTVKNRMQRSEPSFTMKIVEGEAN---THSEISLVAVKGEFGLFELSPITGKTHQL 246

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH L +G P++ D  Y   +           L L A+ +    P  G
Sbjct: 247 RVHMLSLGMPLLNDRFYPTLYPKGLDDFT-KPLQLLAQRLRFVDPITG 293


>gi|68488860|ref|XP_711730.1| hypothetical protein CaO19.2788 [Candida albicans SC5314]
 gi|46433052|gb|EAK92508.1| hypothetical protein CaO19.2788 [Candida albicans SC5314]
          Length = 402

 Score =  115 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 48/212 (22%), Positives = 90/212 (42%), Gaps = 12/212 (5%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILL---YEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +   + E+ I+  + +  +      + ++   YED +I V +KP+GI         Y+  
Sbjct: 79  IKRKLDEKDIICHTKHRHEPPIPWHNDIIKSVYEDDEILVVDKPSGIPTHPTGNYYYNSL 138

Query: 131 G-FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--RRIQKIYWSLV 187
              +K  ++         HRLD+ TSG+LV+A+T+      ++  R   +  +K Y + V
Sbjct: 139 SEIIKQQLNMDSI--WTCHRLDKVTSGVLVLAKTKNGGVRFSKLMRDSKQHTEKTYLARV 196

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQ 246
            G      E I  +      +  +   +    E+    + + F+ I   A      ++  
Sbjct: 197 SGKFP---EGIHRYRCPIFAVNMNGYLMSGNMEELPTDSTTIFERIKYNASLDQSLVKCV 253

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           P TG+ HQ+R+H  ++G PIV D  Y      
Sbjct: 254 PITGKFHQIRIHLRNLGFPIVNDSFYQPEQDQ 285


>gi|307109077|gb|EFN57316.1| hypothetical protein CHLNCDRAFT_143940 [Chlorella variabilis]
          Length = 330

 Score =  115 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 75/331 (22%), Positives = 127/331 (38%), Gaps = 53/331 (16%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDK---KRV--KFNNRIQSG-------QVVRIPPVI 71
           W +   P +    L K+ R   VR+     +R+  + ++R Q G                
Sbjct: 17  WLRRRGPPLPESALHKLFRVSTVRLYDPATQRIHSRPSSRQQPGNDGAGSTTSGSTGGRS 76

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
           +    +   +          + +  L+S LL+ D  +    KPAG++ QGGSG+++ +D 
Sbjct: 77  SGDTSLAAARASPSRQRASERWAARLRSCLLHSDPDLLAVCKPAGLACQGGSGVSHSVDS 136

Query: 132 FLK----SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM---------RR 178
            +               RL HRLD++T+G L++AR   AA  L  +F+           R
Sbjct: 137 VMAAAFAHLPGPASHHLRLVHRLDRQTTGALLLARGPDAAAWLAAAFQESSGGGSSGGGR 196

Query: 179 IQKIYWSLV----WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
                 +++    W +    +   A+ L     I    V   +     A  A + ++V+ 
Sbjct: 197 GDSSSGAIIRKQYWAVVALPEGGAAHRLPAAGAISL-PVPGGRGGVAAAQPAPTRYRVLH 255

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                  WLE+ P TGR HQLR+H    +G  I+GD       +     P   +      
Sbjct: 256 R-GGGLAWLELAPATGRKHQLRLHCAQGLGAAILGD------GRLAVRKPGAGR------ 302

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
                    G++  TAPLPA      +  G+
Sbjct: 303 ---------GQVVATAPLPASWRALLEHQGW 324


>gi|126642162|ref|YP_001085146.1| putative pseudouridylate synthase [Acinetobacter baumannii ATCC
           17978]
          Length = 245

 Score =  115 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 86/223 (38%), Gaps = 10/223 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHR 149
            +     +  +L+E+  + V +KP  +++       Y  +  L       G +     HR
Sbjct: 27  NEVHVPFEHQILFENDDLLVVDKPHFLTISPTG--QYVQETLLVRLKKQTGNEFLTPIHR 84

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ET+G+++  +   +     + F  R++ KIY ++     + K        LK     
Sbjct: 85  LDRETAGVVLFCKRPQSRGIYQQLFADRQVNKIYHAIAAYKAELKF----PQNLKLYLDK 140

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           G   + ++          +  ++I+       +  + P TG+ HQLRVH  H+G PI  D
Sbjct: 141 GTPFYTMQVIAHTKTNTETKIELIEHNHSWAKYC-LTPTTGKQHQLRVHLNHLGIPIKND 199

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPL 311
             Y    +          L L A+ +    P     +   + L
Sbjct: 200 PFY-PIVQHKADDDFSQPLQLLAKQISFIDPLTKQEMVFNSQL 241


>gi|313499768|gb|ADR61134.1| Pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 294

 Score =  115 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 53/254 (20%), Positives = 103/254 (40%), Gaps = 10/254 (3%)

Query: 52  RVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYV 110
           R ++ +R   G+V+       A +   K    L     +  +    ++ ++L+ D  + V
Sbjct: 38  RAQWLDRFARGRVLDAEGQAVAADLPYKRGMRLHYFREVPNERPIPVQEVVLHVDEHLVV 97

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
            +KP  + V   +G         +             HR+D+ T+G+++ +    +    
Sbjct: 98  ADKPHFLPVTP-TGEYVEQTLLRRLIRRLDNPHLVPLHRIDRHTAGLVLFSANPHSRSAY 156

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              F  RRI K Y ++   +P++    +     K   + G+    + + E  AN + +  
Sbjct: 157 QRLFPERRIDKRYQAIAAAMPQHAFPLVH----KSRLVHGEPFFRMHEVEGEAN-SETLA 211

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           +V++   +++ +  + P TG+THQLRVH   +G  I  D  Y      N     Q  L L
Sbjct: 212 EVLEKNGERWRYG-LSPVTGKTHQLRVHMAALGAGISNDPFYPQLL--NEEDDYQRPLKL 268

Query: 291 HARYMDLPHPEGGR 304
            A+ +    P  G 
Sbjct: 269 LAQSLRFEDPLSGE 282


>gi|296119226|ref|ZP_06837795.1| RNA pseudouridine synthase [Corynebacterium ammoniagenes DSM 20306]
 gi|295967747|gb|EFG81003.1| RNA pseudouridine synthase [Corynebacterium ammoniagenes DSM 20306]
          Length = 326

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 52/271 (19%), Positives = 96/271 (35%), Gaps = 23/271 (8%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHII-KEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           D        R    +VV       + + ++  +Q +        +        ++YED+ 
Sbjct: 54  DDNEAALKERFAQREVVLFDATPISADTVLSADQDVFFYRTPAPEQPVPYDIPIVYEDAD 113

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I V +KP  ++    +         +K    +        HRLD+ TSG+L+  + R   
Sbjct: 114 ILVADKPPFMATMPRARHIVE-TATVKLRRSTGIDDLAPAHRLDRLTSGLLLFTKHREVR 172

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
                 F  R + K Y ++            +  L  +S +      +  + E+G   AI
Sbjct: 173 GAYQTLFARREVHKTYSAIA------DYADFSTPLTWQSRMEKTPGEIQGRIEEGEINAI 226

Query: 228 SHF--------------KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           +                + I           + P TG+THQLR+H    G PI+GD  Y 
Sbjct: 227 TTLVGVVPLTGEEQKALEKIHGEQSALARYTLAPETGKTHQLRLHMWAAGVPILGDPVYP 286

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             +  +    +   ++L A  ++   P  G+
Sbjct: 287 IIYPVDAED-MNIPMHLTAAGLEFIDPLSGK 316


>gi|322379039|ref|ZP_08053442.1| Pseudouridine synthase [Helicobacter suis HS1]
 gi|322380804|ref|ZP_08054910.1| pseudouridylate synthase [Helicobacter suis HS5]
 gi|321146808|gb|EFX41602.1| pseudouridylate synthase [Helicobacter suis HS5]
 gi|321148531|gb|EFX43028.1| Pseudouridine synthase [Helicobacter suis HS1]
          Length = 326

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 119/293 (40%), Gaps = 46/293 (15%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           ++  N   H +    Q  +  G+++ +D+  +K + +IQ   ++ +       + + K  
Sbjct: 51  KFVANIL-HCSVQKAQSHIDRGRLQALDQSPLKKSQKIQG--LIALTFFKALPSALHKP- 106

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
                                +       + KP  +     +  ++     L   V S  
Sbjct: 107 --------------------FFSTPFFQAYYKPKNLYSHPKNYHSFS----LYESVYSHN 142

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN---KKECI 198
           Q+ RL HRLD ETSGI++V++ +   ++L   F   +I K Y +LV G   N       I
Sbjct: 143 QEARLIHRLDYETSGIILVSQNKEHEKNLRALFSNHQIIKTYTALVQGDMHNYASGDFSI 202

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRV 257
              +L+ S++ GD   V  Q  K   ++ +  K++   A      L++ P TGRTHQ+R+
Sbjct: 203 ILPILEPSNLRGDLG-VRSQIHKQGKFSATTIKILCFDAFNNQTLLQISPLTGRTHQIRL 261

Query: 258 HALHMGCPIVGDHKYCANFKGNF------------TSPIQNKLYLHARYMDLP 298
           H   +G PIVG+  Y  +                  +P +  L L A  +D  
Sbjct: 262 HLSALGFPIVGEPLYTKDSNARAYLNAKKADFKGSYAPFKPHLALEASGLDFT 314


>gi|224438280|ref|ZP_03659207.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
 gi|313144719|ref|ZP_07806912.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
 gi|313129750|gb|EFR47367.1| ribosomal pseudouridine synthase [Helicobacter cinaedi CCUG 18818]
          Length = 245

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 60/297 (20%), Positives = 102/297 (34%), Gaps = 61/297 (20%)

Query: 22  DRW--FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           D+          I+    + ++  G V  + K++           + +P   N     IK
Sbjct: 4   DKAYKLLAKAKCISHNLAKSLIDKGLVSSNGKKITI-------ARLELPLSANFEVAEIK 56

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + K                  +++ED +I   +KP  I        +Y +    + W   
Sbjct: 57  KPK------------------VIFEDKQILALDKPPFI-------ESYDLSDMFEGW--- 88

Query: 140 KGQKPRLTHRLDQETSGI-LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                 L HRLD++TSG+ L++           E+F+ + + K Y  L+ GI  +     
Sbjct: 89  -----SLLHRLDKQTSGVILLIQENSPFHLKAKEAFKKQAVYKEYICLLHGILADSITIN 143

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                 K       +      +K    A +    +    +K    +    TGRTHQ+RVH
Sbjct: 144 KPISTIKKGFAKSRI------DKNGLSAHTQLTPLSIVGKK-TQAQAIITTGRTHQIRVH 196

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
              +  PIVGD  Y              +L LHA  + L        +  + LP   
Sbjct: 197 CQSINHPIVGDTLYGNTNDNA------KRLMLHAHKIRLLD-----YEFVSLLPQEF 242


>gi|262165841|ref|ZP_06033578.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus VM223]
 gi|262025557|gb|EEY44225.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus VM223]
          Length = 233

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 57/203 (28%), Positives = 88/203 (43%), Gaps = 17/203 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +        DS+     L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEVAAQSGDSQ---LYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L++ F  R ++K Y ++    PK K+  I   + +        V+     
Sbjct: 60  LARNAAAASELSQGFAKRTVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQH-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F      A        +PHTG+THQ+RV    +G  IVGD  Y A  +  
Sbjct: 118 ----NPAVTQFFS-ATAAPGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYNAADES- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEG 302
                 ++ YLHA  +   + + 
Sbjct: 172 ------DRGYLHAFALRFTYQDT 188


>gi|168010811|ref|XP_001758097.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162690553|gb|EDQ76919.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 361

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 52/211 (24%), Positives = 90/211 (42%), Gaps = 28/211 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQ---GGSGIAYHIDGFLKSWVDSK---GQKPRLTHRLDQETS 155
           LYED  I   +KP  + V      S +    + FLK+ V+++   GQK    HRLD+  S
Sbjct: 69  LYEDQYIIGVSKPGTLLVHNNKASSPLEKQRNAFLKNMVEAQLTAGQKVSPVHRLDRPAS 128

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G ++ +++  A +    S         + + +       +    ++ +    +       
Sbjct: 129 GAIIFSKSAVATRAAQAS-------LSHPACIKEYVVLARGTTPDFFICDEPVN------ 175

Query: 216 VKQNEKGA-NYAISHF-KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              +EKGA   A+S   K++D    +   L++   TGR HQ+R H  H    +VGD K+ 
Sbjct: 176 ---DEKGAPKSAVSQCEKILDLPESRCSLLKVVIKTGRWHQIRKHLNHRAHHVVGDVKHG 232

Query: 274 ANFKGNFTSP----IQNKLYLHARYMDLPHP 300
                 F       +  +++LHA  +  PHP
Sbjct: 233 KGKTNRFFRENHKMLSGRIFLHAARLTFPHP 263


>gi|158317482|ref|YP_001509990.1| pseudouridine synthase [Frankia sp. EAN1pec]
 gi|158112887|gb|ABW15084.1| pseudouridine synthase [Frankia sp. EAN1pec]
          Length = 285

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 55/268 (20%), Positives = 88/268 (32%), Gaps = 63/268 (23%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ED  +   +KP G+SV G        D  L S     G++    HR+D+ TSG+++ A
Sbjct: 13  IFEDEAVLALDKPVGVSVMG-----ERHDTDLVSMARDAGEELFPAHRIDKVTSGVVLFA 67

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL----LKKSHIGGDYVHVVK 217
           +       LT  F  R ++K Y +L           I   L      +  I  +   +V 
Sbjct: 68  KELRFHGDLTRQFNRRTVEKTYLALTRTRGLPALATIDLPLSVGRKNRVRIAANRADIVA 127

Query: 218 QNEKGAN----------------------------------------YAISHFKVIDCFA 237
                                                           +++    +   A
Sbjct: 128 WPGPAGTPTPDGPAGTPGSDGPAGSGARSPASWTVPAARTFPNVRSYPSVTRIARVWEGA 187

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +    +   P +GR HQ+RVH   +G PI GD          F      + +LH+  +  
Sbjct: 188 E-HTLVAAYPISGRRHQIRVHLAWVGHPIEGDPL--------FDRAPVTRTFLHSWRLSF 238

Query: 298 P--HPEGGRLQITAPLPAHMVKTWDSLG 323
                +G R    A   A     W SLG
Sbjct: 239 DAAWDDGRRTHTEATPGADF---WSSLG 263


>gi|260772679|ref|ZP_05881595.1| pseudouridylate synthase LSU rRNA-specific [Vibrio metschnikovii
           CIP 69.14]
 gi|260611818|gb|EEX37021.1| pseudouridylate synthase LSU rRNA-specific [Vibrio metschnikovii
           CIP 69.14]
          Length = 261

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 56/199 (28%), Positives = 87/199 (43%), Gaps = 19/199 (9%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ-KPRLTHRLDQETSGIL 158
            ++   +   V NK   +SV    G        L       G  +  L HRLD+ TSG+L
Sbjct: 32  DIVVTHTDFLVVNKHPNVSVHKDDGETM----LLHEVGQQSGDTQLYLVHRLDKMTSGLL 87

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++AR  AAA  L+ +F  R+++K Y ++    PK K+  I+  + +        V     
Sbjct: 88  LLARNAAAASELSRAFAKRKVEKYYLAIGAKKPKKKQGLISGDMQRSRRASWKLVPTYD- 146

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                N AI+ F  +     +      +PHTG+THQ+RV    +G PIVGD  Y    + 
Sbjct: 147 -----NPAITQFFSLPAEPGER-LFLCKPHTGKTHQIRVALKSIGSPIVGDPIYLPTSQA 200

Query: 279 NFTSPIQNKLYLHARYMDL 297
                  ++ YLHA  +  
Sbjct: 201 -------DRGYLHAFALRF 212


>gi|330881339|gb|EGH15488.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. glycinea
           str. race 4]
          Length = 126

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 40/121 (33%), Positives = 63/121 (52%), Gaps = 12/121 (9%)

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           +G   A+SH++V++ F +    + ++  TGRTHQ+RVH  H+  P+VGD  Y   F+   
Sbjct: 8   EGGKQAVSHYRVLERF-RSHTHVRVKLETGRTHQIRVHMAHINYPLVGDPAYGGRFRIPP 66

Query: 281 TSPIQ--------NKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLGFKYDRNLY 331
            + +          +  LHAR+++L HP  G R+   +PLP   V     L  K DR  +
Sbjct: 67  AASLTMVDSLKTFPRQALHARFLELDHPTTGKRMSWESPLPDDFVWLLSLL--KQDREAF 124

Query: 332 I 332
           I
Sbjct: 125 I 125


>gi|325274510|ref|ZP_08140575.1| pseudouridine synthase [Pseudomonas sp. TJI-51]
 gi|324100350|gb|EGB98131.1| pseudouridine synthase [Pseudomonas sp. TJI-51]
          Length = 294

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 46/215 (21%), Positives = 84/215 (39%), Gaps = 9/215 (4%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +    L+  +L+ D  + V +KP  + V        H     +             HR
Sbjct: 77  PNERPIPLQEHVLHVDEHLVVADKPHFLPVTPTGEYVEHTLLR-RLIRRLDNPHLVPLHR 135

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D+ T+G+++ +            F  RRI K Y ++   +P++    +     K   + 
Sbjct: 136 IDRHTAGLVLFSANPHTRSAYQRLFPERRIDKRYQAIAAALPQHAFPLVH----KSRLVH 191

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           G+    + + E  AN + +  +V++     + +  + P TG+THQLRVH   +G  I  D
Sbjct: 192 GEPFFRMHEVEGEAN-SETLAEVLEKRGALWRYG-LSPVTGKTHQLRVHMAALGAGISND 249

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             Y      +     Q  L L A+ +    P  G 
Sbjct: 250 PFYPQLL--DTADDYQRPLKLLAQSLRFTDPLSGE 282


>gi|294141810|ref|YP_003557788.1| ribosomal large subunit pseudouridine synthase family protein
           [Shewanella violacea DSS12]
 gi|293328279|dbj|BAJ03010.1| ribosomal large subunit pseudouridine synthase family protein
           [Shewanella violacea DSS12]
          Length = 287

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 50/309 (16%), Positives = 109/309 (35%), Gaps = 48/309 (15%)

Query: 21  LDRW-FKNHYPHINFVNLQKILRSGQVRVDKKRV-----KFNNRIQSGQVVRIPPVINAL 74
           LD          ++   +++ +  G V + + +      +    ++ G  + +      L
Sbjct: 20  LDAASLLAADTELSKQQIKQAMNKGAVWLTRGKQTQRLRRAKRALKLGDELHLYYNHQVL 79

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
            H +   +                  L+++  +  ++ KP G+  QG     +       
Sbjct: 80  AHKVDAAE------------------LIFDGGQYSIWYKPYGMLCQGSKWGDHTTINRYA 121

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               S  +   + HRLD+  +G++++  ++     L + F +R + K Y  +V G     
Sbjct: 122 ETHLSPDRPAFIIHRLDRAATGLVLIGHSKKTTAALAKLFELRLLDKYYQVIVEGQFNL- 180

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTH 253
                          G    V    +     A SH K++   A +    ++++  +GR H
Sbjct: 181 ---------------GQQESVTIGTDVDGKAACSHAKLLQYDAERGRSLVQVKIESGRKH 225

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           Q+R+H   +G P+VGD  +    +          L L + Y+    P    ++    LP 
Sbjct: 226 QIRIHMESIGYPVVGDRLHGVAKEDELN------LQLTSCYLKFTCPITDEIK-EFELPQ 278

Query: 314 HMVKTWDSL 322
            +     + 
Sbjct: 279 RLRPKLSAC 287


>gi|312130287|ref|YP_003997627.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
 gi|311906833|gb|ADQ17274.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
          Length = 206

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 49/224 (21%), Positives = 93/224 (41%), Gaps = 31/224 (13%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++E+    + +KP+GI+ Q   G     D  L ++         +  RLD+  SG++V+A
Sbjct: 3   IFENDNYIILDKPSGIASQDEPGK---NDSILSAF-----PGCHVLTRLDKRVSGLMVLA 54

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           ++   A   +     +     Y  +V      K+  + +W+ K+      + H V    +
Sbjct: 55  KSAEVAARWSPEKYSKT----YHCIVNLPGPGKEGVLKHWIKKQGLKAKVFDHAV----E 106

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
           GA  AI  ++ +   +Q++    ++  TGR HQ+R     +G P+VGD KY         
Sbjct: 107 GAKQAILRYQ-LRGNSQRYALYAVKIETGRFHQIRAQFSKVGFPLVGDLKYGYKRSTP-- 163

Query: 282 SPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                     + ++     +G   ++  PLP      W   GF+
Sbjct: 164 --------DGSIFLSCTQIKGPDFEVEIPLPF----LWAKYGFE 195


>gi|38233570|ref|NP_939337.1| putative RNA pseudouridylate synthase family protein
           [Corynebacterium diphtheriae NCTC 13129]
 gi|38199830|emb|CAE49493.1| Putative RNA pseudouridylate synthase family protein
           [Corynebacterium diphtheriae]
          Length = 243

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 88/244 (36%), Gaps = 16/244 (6%)

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAGISV 119
           +G     P    A   ++++       + + +         ++     + V +KP  +  
Sbjct: 5   AGDSPFSPGTPLAPGTLLEKPIPAWFWLGVPEEPSIPFDYTVIARTPDLLVVDKPCFLPA 64

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                I        ++ +          HRLD+ T+GIL+ +          + F+ R I
Sbjct: 65  TSNGRIVAETVQT-RARIRENNPHIVPLHRLDRLTTGILLCSTNPETRATYQQLFQHRAI 123

Query: 180 QKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            K Y + V G IP   +            +G   +      +       +  + ++    
Sbjct: 124 TKRYIAHVAGPIPFGPQWTEIA-------LGMRKMGPRVVVDPTGTLTRTRVRRLEEG-- 174

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
               +E+QP TG THQLRV    +GCPI+GD  Y  + +         KL L+A  ++  
Sbjct: 175 ---VVELQPATGHTHQLRVLLAWVGCPIIGDDTYPVDRRRRIYD-FSKKLELYATSLEFV 230

Query: 299 HPEG 302
            P  
Sbjct: 231 DPVS 234


>gi|238878813|gb|EEQ42451.1| conserved hypothetical protein [Candida albicans WO-1]
          Length = 402

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 55/241 (22%), Positives = 100/241 (41%), Gaps = 20/241 (8%)

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILL---YEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +   + E+ I+  + +  +      + ++   YED +I V +KP+GI         Y+  
Sbjct: 79  IKRKLDEKDIICHTKHRHEPPIPWHNDIIKSVYEDDEILVVDKPSGIPTHPTGNYYYNSL 138

Query: 131 G-FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR--IQKIYWSLV 187
              +K  ++         HRLD+ TSG+LV+A+T+      ++  R  +   +K Y + V
Sbjct: 139 SEIIKQQLNIDSI--WTCHRLDKVTSGVLVLAKTKNGGVRFSKLMRDSKQYTEKTYLARV 196

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQ 246
            G      E I  +      +  +   +    E+    + + F+ I   A      ++  
Sbjct: 197 SGKFP---EGIHRYRCPIFAVNMNGYLMSGNMEELPTDSTTIFERIKYNASLDESLIKCV 253

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFTSPIQNKLYLHARYMDLPHP 300
             TG+ HQ+R+H  ++G PIV D  Y            N    + NKL+  A+Y    H 
Sbjct: 254 SITGKFHQIRIHLRNLGFPIVNDSFYQPEQDQLTIQKCNIERQLYNKLF--AKYPQFKHF 311

Query: 301 E 301
           E
Sbjct: 312 E 312


>gi|127514276|ref|YP_001095473.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126639571|gb|ABO25214.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 313

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 64/299 (21%), Positives = 113/299 (37%), Gaps = 33/299 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +F   + +I+    ++    G+V             Q GQ + +            +QK+
Sbjct: 36  YFCQRFDNISAGVWRERFIQGKVH-----------WQDGQPLELT------TAYRPQQKV 78

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-Q 142
                   +        +LY D +I + NKP  +++  G  +       +    +  G +
Sbjct: 79  YYYREVAHEAPPPFSESILYLDEQIVLANKPHFMALHPGGEVINQC--LINRLRERTGCE 136

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKK 195
                HRLD+ T+GI+++ +   +       FR  +I K Y +L    P+        K 
Sbjct: 137 TLIAAHRLDRATAGIVLLVKQSDSRDAYHGLFRHGQITKEYQALARLTPELLAEYHAGKL 196

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                W +K     G     ++  +  AN + S   ++    +     E+ P TG+THQL
Sbjct: 197 SLPRRWTVKNRIDKGTPSFTMRIVDGEAN-SHSEIALVSVEGE-IGRFELMPITGKTHQL 254

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313
           R+H   +G PI+ D+ Y           +   + L AR +    P  GR L I   LP 
Sbjct: 255 RLHMNSLGMPILNDNFY-PTLLPRSAEDVAQPMKLLARRLAFTDPVTGRKLDIC--LPE 310


>gi|255528213|ref|ZP_05395034.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255508086|gb|EET84505.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 148

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 35/154 (22%), Positives = 67/154 (43%), Gaps = 11/154 (7%)

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           L         +K Y ++V G  K K+  I   + +      D  ++ +  ++    +I+ 
Sbjct: 3   LARDMHKEDFEKSYLAVVHGNLKEKEGIINLPIYR-----TDDGNIRRVVDERGQESITC 57

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           + V + F +    +++   TGRTHQ+RVH  H+G P+ GD  Y       +      +  
Sbjct: 58  YSVQESFNKGD-LVKLTLKTGRTHQIRVHMTHIGHPLYGDTLYGQIEDKEYIE----RQA 112

Query: 290 LHARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
           LHA  +  PHP    + ++   LP  + +  + +
Sbjct: 113 LHAYRLVFPHPRTREMLELEIGLPKDLQELIEKI 146


>gi|116327749|ref|YP_797469.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116120493|gb|ABJ78536.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
          Length = 277

 Score =  114 bits (285), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 57/277 (20%), Positives = 95/277 (34%), Gaps = 53/277 (19%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           L   + YE        KP GI V         +    L+  +  +    R  +RLD +TS
Sbjct: 6   LNIRIFYETESFLFAEKPPGIPVHATKDSKRENFADRLQEQLSLEY--LRTVNRLDLDTS 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++ + +     +        +   KIY  +  GI + +      ++        D    
Sbjct: 64  GLVFLCKNPDKNKEADRIL--KSSSKIYLCVADGIVEEEHFTETCYI-------KDGNKK 114

Query: 216 VKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V++   G + A++ F  +       +  L  + HTGR HQ+R+H    G  IVGD+ Y  
Sbjct: 115 VRKVFSGGDKAVTEFLTLKRNLKDHYSVLLAKLHTGRRHQIRLHLSEKGHSIVGDYVYGK 174

Query: 275 --------NFKGNFTSPIQNKL------------------------------YLHARYMD 296
                     K   TSP  N++                               LHA  + 
Sbjct: 175 SLDLNSTTKRKPMETSPSDNRISNIQKRNFLNKETITAPIRAKRQVSFAQRSLLHAIGVS 234

Query: 297 LPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
             +  G   +I  P P    K  +  G   D +++ K
Sbjct: 235 FRNEGGYEERIFCPPPIDFQKFLE--GISLDSSIFSK 269


>gi|315638653|ref|ZP_07893827.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
 gi|315481277|gb|EFU71907.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
          Length = 250

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 56/228 (24%), Positives = 96/228 (42%), Gaps = 39/228 (17%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +L+ED KI   NKP                 ++   ++S+  K +L +RLD+ETSG+
Sbjct: 56  KPQILFEDEKILAINKPY---------------SYISEGLESEF-KAKLLNRLDKETSGL 99

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++ +     +   E FR +R+ K Y +++ G+   +          K   G        
Sbjct: 100 ILLCKNEDFKKLCIEEFRKQRVYKSYIAVLDGVLAEELVVDEPIRTLKGKNG-----AFS 154

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +  K    A+S    +    +K    ++   TGRTHQ+RVH   +  PI+GD KY     
Sbjct: 155 KIAKEGQSALSIINPLMIQGKK-TLAKICIQTGRTHQIRVHTAFVKYPIIGDEKYGK--- 210

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                   +++YLH+  + + H      +  A L     K     GF+
Sbjct: 211 -----IAADRMYLHSYELKILH-----YEFKANLDESFAK----FGFE 244


>gi|116331588|ref|YP_801306.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116125277|gb|ABJ76548.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 277

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 57/277 (20%), Positives = 95/277 (34%), Gaps = 53/277 (19%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
           L   + YE        KP GI V         +    L+  +  +    R  +RLD +TS
Sbjct: 6   LNIRIFYETESFLFAEKPPGIPVHATKDSKRENFADRLQEQLSLEY--LRTVNRLDLDTS 63

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G++ + +     +        +   KIY  +  GI + +      ++        D    
Sbjct: 64  GLVFLCKNPDKNKEADRIL--KSSSKIYLCVADGIVEEEHFTETCYI-------KDGNKK 114

Query: 216 VKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           V++   G + A++ F  +       +  L  + HTGR HQ+R+H    G  IVGD+ Y  
Sbjct: 115 VRKVFSGGDKAVTEFLTLKRNLKDHYSVLLAKLHTGRRHQIRLHLSEKGHSIVGDYVYGK 174

Query: 275 --------NFKGNFTSPIQNKL------------------------------YLHARYMD 296
                     K   TSP  N++                               LHA  + 
Sbjct: 175 SLDLNSTTKRKPMETSPSDNRISNIQKRNFLNKETITAPIRAKRRVSFAQRSLLHAIGVS 234

Query: 297 LPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
             +  G   +I  P P    K  +  G   D +++ K
Sbjct: 235 FRNEGGYEERIFCPPPIDFQKFLE--GISLDSSIFSK 269


>gi|323447657|gb|EGB03570.1| hypothetical protein AURANDRAFT_15032 [Aureococcus anophagefferens]
          Length = 221

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 59/208 (28%), Positives = 93/208 (44%), Gaps = 17/208 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIA-----YHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +  ++ E S+  V +KP+G+                 D   +   D+   + RL HRLD 
Sbjct: 3   RLHVVGETSRWVVVDKPSGVPCHASDKGDGVLTLLRRDAVERGERDAAVAEYRLVHRLDD 62

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG L +A+ R  A  L  +FR RR +K Y  L    PK K+  +A  L+K +  G   
Sbjct: 63  GTSGCLAIAKDRETATLLGAAFRERRARKAYVGLTDKTPKKKQGVVAGDLVK-ARRGAFK 121

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM---QPHTGRTHQLRVHALHMGCPIVGD 269
           +   +     A  AI+    +   A      ++   +P TG+THQ+RV A  +G P++GD
Sbjct: 122 LARTRTVGACAVTAITRTAGLGAAAAGDAARKLLVARPVTGKTHQIRVAAKSLGAPLLGD 181

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDL 297
             Y             ++LYLHA  + +
Sbjct: 182 DLYGG--------AAADRLYLHAAALAI 201


>gi|149212744|ref|NP_439586.2| hypothetical protein HI1435 [Haemophilus influenzae Rd KW20]
 gi|262021233|gb|AAC23084.2| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
          Length = 182

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 39/162 (24%), Positives = 72/162 (44%), Gaps = 14/162 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDGFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVID----------CFAQKFCWLEMQPHTGRT 252
           K    AI+ ++ +               ++  +++ PHTG+ 
Sbjct: 120 KEPQEAITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGQK 161


>gi|91791846|ref|YP_561497.1| pseudouridine synthase [Shewanella denitrificans OS217]
 gi|91713848|gb|ABE53774.1| pseudouridine synthase [Shewanella denitrificans OS217]
          Length = 312

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 55/302 (18%), Positives = 109/302 (36%), Gaps = 27/302 (8%)

Query: 9   YVVVENDE-ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           YVV+  +E     +  +   H+  I     ++ L  G+V             + G+++  
Sbjct: 18  YVVLPKNELAPATVADFLMQHFSQIAPQVWRQRLSEGKVH-----------WKDGELINE 66

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                 +  +   +++        +       ++L++D    +  KP  + V        
Sbjct: 67  HTAYRPMARVYYYREVA------LETKVPFDEVILHQDEHAIIAYKPHFLPVTPSGNYVN 120

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                 +  + +        HRLD++T+GI+++             F   +I K Y +L 
Sbjct: 121 ECL-VHRLRIKTGIDTIAPAHRLDKDTAGIVLLTLNPEVRHQYHNLFTQGQISKHYHALA 179

Query: 188 WGIPK----NKKECIANWLL--KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
              P+    ++   +   L    K+ +G      + Q  +G   + S  ++I    +   
Sbjct: 180 KLTPEIHAAHQGGGLRLPLTWTVKNRLGPATPSFLMQLVEGEANSHSEIQLI-AIKEDMG 238

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
              + P TG+THQLRVH   +G PI+ D  Y    +          L L A+ +    P 
Sbjct: 239 LFALSPITGKTHQLRVHMQSLGVPILNDRFY-PQLQPKGVDNFDKPLKLLAQRLKFVDPI 297

Query: 302 GG 303
            G
Sbjct: 298 SG 299


>gi|229493866|ref|ZP_04387638.1| ribosomal pseudouridine synthase [Rhodococcus erythropolis SK121]
 gi|229319143|gb|EEN84992.1| ribosomal pseudouridine synthase [Rhodococcus erythropolis SK121]
          Length = 319

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 56/292 (19%), Positives = 107/292 (36%), Gaps = 31/292 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQ-VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +    + H++  NL +    G+ V +D   ++ +  + + + V     + A + +     
Sbjct: 32  YAVAKFDHLDAENLYRRFDDGEFVGIDGTSIRRSTELSAHRFVWYYRELPAEDPVP---- 87

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                             +L+ D  + V +KP  +     SG        ++  V     
Sbjct: 88  --------------FHEQILHTDDDLVVIDKPHFLPTTP-SGRYLRESALVRLRVRLDNP 132

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-----WGIPKNKKEC 197
                HRLD+ T+G+++ +   A        F  R++ K+Y ++      W         
Sbjct: 133 DLTPIHRLDRGTAGVVMFSARPATRGAYQSLFEKRQVTKVYEAVSARPTRWDQDAPGFAE 192

Query: 198 IANWLLKKSHI----GGDYVHVVKQNEKGANYAIS-HFKVIDCFAQKFCWLEMQPHTGRT 252
               L+ ++HI    G   V V    E  +   I      +    +      ++P +GR 
Sbjct: 193 SDGPLVYRNHIEARRGELRVLVDDSREPNSETMIEARGTGVSASGRAVLHTVLRPQSGRM 252

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           HQLRVH   +G  I+GD +Y  +   +        L L AR ++   P  G+
Sbjct: 253 HQLRVHLAALGAGILGDRRY-PDLLPDAPDDHSLPLQLLARELEFTDPLSGK 303


>gi|220905224|ref|YP_002480536.1| pseudouridine synthase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|219869523|gb|ACL49858.1| pseudouridine synthase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 493

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 56/331 (16%), Positives = 112/331 (33%), Gaps = 59/331 (17%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            Q   V++    +RLD+  ++  PH+     ++   +G V V+ +  K + R++ G VVR
Sbjct: 91  TQEFCVDHQHAGLRLDQALEHLLPHMGLRGRRRCAENGGVSVNGRAAKASRRMRQGDVVR 150

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +         +   +++  ++ +           +L    +   F+KPA +     +GI+
Sbjct: 151 LHNAEARKKKVALGREVSGTAFSCGSAVAACGLRMLGRQGEYCFFSKPARMHSASLAGIS 210

Query: 127 YHIDGFLK-----SWVDSKG-------QKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                 L       W +  G           L  RLD  TSG+L  A + +AA+    + 
Sbjct: 211 GVSVEALAPALAVRWTEKSGSGNEFDLAALTLMQRLDFGTSGLLCAALSTSAAEDFRAAE 270

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA-ISHFKVI 233
                +K Y +L+ G+       ++  ++ +  +        +     A++   + F  +
Sbjct: 271 AAGLCEKRYVALLSGV-------LSGPVVARQELDVSKRRKSRVLPALAHHTRWTEFWPL 323

Query: 234 DCF---------------------------------------AQKFCWLEMQPHTGRTHQ 254
             +                                       A        +   G  HQ
Sbjct: 324 HVWRPGDVSVQALQALLGPAGGGAPENDAPVVTPEAGGLPVPAAGLTLAACRIRRGARHQ 383

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           +R HA  +G P+ GD  Y    +    S   
Sbjct: 384 IRAHAAGLGHPLWGDSLYAEPEEHVAASGGL 414


>gi|258621886|ref|ZP_05716916.1| pseudouridine synthase Rlu family protein [Vibrio mimicus VM573]
 gi|258627415|ref|ZP_05722196.1| pseudouridine synthase Rlu family protein [Vibrio mimicus VM603]
 gi|258580221|gb|EEW05189.1| pseudouridine synthase Rlu family protein [Vibrio mimicus VM603]
 gi|258585824|gb|EEW10543.1| pseudouridine synthase Rlu family protein [Vibrio mimicus VM573]
          Length = 233

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 57/203 (28%), Positives = 88/203 (43%), Gaps = 17/203 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +        DS+     L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEVAAQSGDSQ---LYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L++ F  R ++K Y ++    PK K+  I   + +        V+     
Sbjct: 60  LARNAAAASELSQGFAKRTVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQH-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F      A        +PHTG+THQ+RV    +G  IVGD  Y A  +  
Sbjct: 118 ----NPAVTQFFS-ATAAPGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYNAADES- 171

Query: 280 FTSPIQNKLYLHARYMDLPHPEG 302
                 ++ YLHA  +   + + 
Sbjct: 172 ------DRGYLHAFALRFSYQDT 188


>gi|213023142|ref|ZP_03337589.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 150

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 42/154 (27%), Positives = 69/154 (44%), Gaps = 8/154 (5%)

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           +   K Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +
Sbjct: 1   KGNSKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERY 57

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHAR 293
           A     +   P TGRTHQ+RVH  + G PI  D +Y     + +         +L+LHA 
Sbjct: 58  A-FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAA 116

Query: 294 YMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKY 326
            +   HP  G  ++I AP+   + +  + L  K 
Sbjct: 117 ALKFTHPGTGDVMRIEAPMDKQLKRCLEVLRSKA 150


>gi|42522940|ref|NP_968320.1| putative pseudouridine synthase [Bdellovibrio bacteriovorus HD100]
 gi|39574136|emb|CAE79313.1| putative pseudouridine synthase [Bdellovibrio bacteriovorus HD100]
          Length = 225

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 49/212 (23%), Positives = 83/212 (39%), Gaps = 25/212 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILV 159
           +++E++   + +KPAG+               L  +    KG +    +RLD E SG++V
Sbjct: 4   IVFENTHFIICDKPAGVLSTPSRFEEDDARLCLGTALQKEKGFQIFPVNRLDFEVSGLVV 63

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-----IPKNKKECIANWLLKKSHIGGD--- 211
            A+T  A +     F  + ++K Y +L  G     IP N    + N  LK +   G+   
Sbjct: 64  YAKTAEAHRKANAWFEHKTVKKTYRALTTGQSYAHIPAN----VPNEKLKLTPEVGNTFE 119

Query: 212 ------YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                                ++   V       +   ++ P TGR+HQLR      G P
Sbjct: 120 WRCRLLRGKRRAYESPQGKECLT-VAVFRGMQGDYQVWDLNPVTGRSHQLRFDLSRHGFP 178

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           IVGD  Y +  +        N++ L +  +D 
Sbjct: 179 IVGDKLYGSTVE-----LADNRIALRSYRIDF 205


>gi|295396998|ref|ZP_06807115.1| ribosomal large subunit pseudouridine synthase [Aerococcus viridans
           ATCC 11563]
 gi|294974746|gb|EFG50456.1| ribosomal large subunit pseudouridine synthase [Aerococcus viridans
           ATCC 11563]
          Length = 156

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 43/157 (27%), Positives = 73/157 (46%), Gaps = 9/157 (5%)

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V A+T  AA  L++  R   +++ Y ++V   PK     + N+L K      + V +V 
Sbjct: 1   MVFAKTSKAASRLSDQVRRNAMERTYLAVVNEKPKQASSRLVNYLYKNRQ--KNKVSIVS 58

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           ++ K    A+  + VI         L ++  TGR HQ+RV    +G  I GD KY A + 
Sbjct: 59  EHHKEGKKAVLDYSVIASR-DGLSLLSVKLQTGRPHQIRVQLAGIGTSIWGDQKYGAQY- 116

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPA 313
               S +  ++ L A  + + HP     + + +PLP 
Sbjct: 117 ----SKVGQQIALWANSLTISHPVQKTPISVASPLPE 149


>gi|331005130|ref|ZP_08328531.1| Pseudouridylate synthase, 23S RNA-specific [gamma proteobacterium
           IMCC1989]
 gi|330421049|gb|EGG95314.1| Pseudouridylate synthase, 23S RNA-specific [gamma proteobacterium
           IMCC1989]
          Length = 227

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 48/170 (28%), Positives = 74/170 (43%), Gaps = 14/170 (8%)

Query: 131 GFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           G L       G ++    HRLD+ TSG+L+ A+T AAA  L++ F+ R+++K Y +L   
Sbjct: 2   GLLVHIKKDLGLEQLFPVHRLDKVTSGVLLCAKTSAAASELSQLFQNRQVEKYYLALSDQ 61

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
            PK K+  I+        +        K        AI+ F              ++P T
Sbjct: 62  KPKKKQGLISG------DMERGRRGAWKLCHSKNKPAITQFFSYG-LGDGNRLFLLKPKT 114

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           G+THQLRV    +G PI+GD  Y           +   + LHA  +   +
Sbjct: 115 GKTHQLRVALKSIGSPIIGDRLYGHPLS------LPEGILLHASVLSFEY 158


>gi|196005647|ref|XP_002112690.1| hypothetical protein TRIADDRAFT_25933 [Trichoplax adhaerens]
 gi|190584731|gb|EDV24800.1| hypothetical protein TRIADDRAFT_25933 [Trichoplax adhaerens]
          Length = 247

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 97/235 (41%), Gaps = 23/235 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGG-----SGIAYHIDGFLKSWVD-SKGQKPRLTHRLD 151
           K  ++++ +   + NKP  + +          +A  +   L + VD S     R  +RLD
Sbjct: 9   KVQIVHQTNSYVIINKPFDMHINSNEEDVKPTVATQLAELLPTLVDKSICFGFRFVNRLD 68

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI---ANWLLKKSHI 208
             TSG+L +A  + AA    + F    + K Y +LV GI       I       L +   
Sbjct: 69  YATSGLLCIAFDKRAANMARKLFEANHVSKKYLALVRGILSRDNGDILVRKAIGLDRRDP 128

Query: 209 GGDYVHVVKQNE---KGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            G  + +   N    +    A +  +++       +    + + P TGR HQLRVH L +
Sbjct: 129 RGFRMCIPDHNPHLCQSPKAAETLIRILGYGKYDGEDITKISLSPVTGRRHQLRVHCLTL 188

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA--P-LPAH 314
           G  IVGD+ Y              ++ LH+  + +P  +   +++T   P LP H
Sbjct: 189 GHCIVGDYTYSNEVDSKPY-----RMMLHSYSLKIPLQDCPAIEVTTYDPFLPDH 238


>gi|319949614|ref|ZP_08023655.1| pseudouridine synthase [Dietzia cinnamea P4]
 gi|319436720|gb|EFV91799.1| pseudouridine synthase [Dietzia cinnamea P4]
          Length = 329

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 51/260 (19%), Positives = 88/260 (33%), Gaps = 13/260 (5%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL-KSILLYEDSKIYVFNKP 114
             RI +G+ V            +   + +    +L        +  +LY D  + V +KP
Sbjct: 48  RRRISAGEFVGADGRAIGHGTPLGTHEFVWYHRDLPDEPVLPYREEILYRDDHLVVVDKP 107

Query: 115 AGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
             +     SG        ++             HRLD+ET+G+++ +            F
Sbjct: 108 HFLPTTP-SGHFLRETALVRLRTRLGNDDITPIHRLDRETAGVVMFSARADTRGAYQSMF 166

Query: 175 RMRRIQKIYWSLV-----WGIPKNKKECIANWLLKKSHIGGDYVH-VVKQNEKGANYAIS 228
             R + K+Y ++      W             +  ++HI        V  +      + +
Sbjct: 167 ERREVTKVYEAVSARPSGWDPAAPTLGGHPVPVTHRAHIRSRRGELRVTLHPDLPPNSET 226

Query: 229 HFKVIDC----FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
              V+        +      ++P TGR HQLRVH   +G  I+GD +Y          P 
Sbjct: 227 LVDVLRTGHSASGRLVVQTLLRPRTGRLHQLRVHLAALGIGILGDRRYPDLLPEAPDDPD 286

Query: 285 QNKLYLHARYMDLPHPEGGR 304
              L L AR +    P  G 
Sbjct: 287 L-PLQLLARELGFTDPVTGE 305


>gi|120554606|ref|YP_958957.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120324455|gb|ABM18770.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
          Length = 267

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 55/288 (19%), Positives = 95/288 (32%), Gaps = 61/288 (21%)

Query: 30  PHINFVNLQKILRSG---------QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
             +    ++  +  G         QVR+     K    ++ G  +++      L    + 
Sbjct: 23  SGLPKQRIKDAMAKGACWWTQKGKQVRL----RKAKRELKPGTRIQLFYDDQVLARKPET 78

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +L++                    +  V+ KP G+  QG     +     L+      
Sbjct: 79  PTLLENK------------------GRYSVWFKPHGLLSQGSQWGDHC--SLLRLAEIEL 118

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                L HRLD + +G++++A    AA  L+E F  R + KIY + V G        +  
Sbjct: 119 NTPCFLVHRLDADAAGLMLIAHDGKAAAALSELFAGRAMTKIYRARVAGNLMADDLRLDT 178

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHA 259
            L                       +IS    +          ++++  TGR HQ+R H 
Sbjct: 179 PL-------------------DGKDSISRVTTLSRDEDSDTTDVQVRIETGRKHQIRRHL 219

Query: 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
             +G PIVGD  Y               L L A  +    P   + Q+
Sbjct: 220 AGIGHPIVGDRLYGTASAAG--------LQLTAVELAFRCPVTRKAQV 259


>gi|320536302|ref|ZP_08036345.1| RNA pseudouridine synthase [Treponema phagedenis F0421]
 gi|320146862|gb|EFW38435.1| RNA pseudouridine synthase [Treponema phagedenis F0421]
          Length = 251

 Score =  113 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 95/247 (38%), Gaps = 32/247 (12%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-----------VDSKGQKP 144
             +  L+ E     V  KP+G+     + +       L +W           +  K  + 
Sbjct: 8   LPEPQLIKESEDFAVLYKPSGM---PTAPLRSDEKNTLIAWFIKREPAAAAVIGKKEIEK 64

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HRLD  TSG++++A+ + +   L ++ +  +I+K Y +       + K  I    + 
Sbjct: 65  GLIHRLDTATSGLVLIAKNQNSFDILQKAQQNGKIRKTYTAFCSPQLNSPKVKITLPFVV 124

Query: 205 KSH-----IGGDYVHVVKQNEKG-----ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           KS       G   V  + +  K        Y  +  ++++    +   +      G  HQ
Sbjct: 125 KSRFRNFGPGARKVAPIFEGGKNFTRNAKLYTTTLTEILEQ--GQTAMITCTLSLGYRHQ 182

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDLPHPE--GGRLQIT 308
           +R H   +G PI+GD  Y   ++  +   I N     L L A  +  P+P      +++ 
Sbjct: 183 VRAHLAWIGFPIIGDALYNPAYEKAYAQAIVNAHTYPLQLFATELSFPNPSVQAEEVRVL 242

Query: 309 APLPAHM 315
            P P  M
Sbjct: 243 LPPPDKM 249


>gi|23272995|gb|AAH38081.1| Rpusd3 protein [Mus musculus]
          Length = 331

 Score =  113 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 58/283 (20%), Positives = 106/283 (37%), Gaps = 44/283 (15%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQK 143
            ++ L + +  L++ ++ +   +   NKP G+ V G  G    +     L   +  + Q+
Sbjct: 48  ENLGLEELAHVLRAAVVDQKGPLVTLNKPQGLPVTGRPGELTLLSVLPQLSQALGLEHQE 107

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKECIA 199
            ++     +E SG+++++     A  L +    S R +R    Y ++  GIP+  +  + 
Sbjct: 108 LQVVRAPGKEASGLVLLSSCPQTASRLQKFFIHSRRAQRPTATYCAVTDGIPEPSEGTVC 167

Query: 200 NWLLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             L  +     D    V     K  ++G    +S F V+    +    +++QP T   +Q
Sbjct: 168 MPLKMEQMNDVDLAVPVMSPSRKDIQEGVKRTLSRFHVMAT-GRGCALVQLQPLTVFPNQ 226

Query: 255 LRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNK------LYLHAR------- 293
           L+VH     CPI+GDH Y           F     +    +      L  H R       
Sbjct: 227 LQVHMALQLCPILGDHTYAARVGTVLGQRFLWPAETTKPQRQVLDEALLRHLRLSPSQVA 286

Query: 294 -------YMDLPHPEGG----RLQITAPLPAHMVKTWDSLGFK 325
                     L  P  G      ++ APLP +  +T   L   
Sbjct: 287 QMPLHLHLHRLLLPGTGSRDPPSELLAPLPPYFSRTLQCLRLS 329


>gi|148667049|gb|EDK99465.1| mCG132976, isoform CRA_e [Mus musculus]
          Length = 331

 Score =  113 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 58/283 (20%), Positives = 106/283 (37%), Gaps = 44/283 (15%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQK 143
            ++ L + +  L++ ++ +   +   NKP G+ V G  G    +     L   +  + Q+
Sbjct: 48  ENLGLEELAHVLRAAVVDQKGPLVTLNKPQGLPVTGRPGELTLLSVLPQLSQALGLEHQE 107

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKECIA 199
            ++     +E SG+++++     A  L +    S R +R    Y ++  GIP+  +  + 
Sbjct: 108 LQVVRAPGKEASGLVLLSSCPQTASRLQKFFIHSRRAQRPTATYCAVTDGIPEPSEGTVC 167

Query: 200 NWLLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             L  +     D    V     K  ++G    +S F V+    +    +++QP T   +Q
Sbjct: 168 MPLKMEQMNDVDLAVPVMSPSRKDIQEGVKRTLSRFHVMAT-GRGCALVQLQPLTVFPNQ 226

Query: 255 LRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNK------LYLHAR------- 293
           L+VH     CPI+GDH Y           F     +    +      L  H R       
Sbjct: 227 LQVHMALQLCPILGDHTYAARVGTVLGQRFLWPAETTKPQRQVLDEALLRHLRLSPSQVA 286

Query: 294 -------YMDLPHPEGG----RLQITAPLPAHMVKTWDSLGFK 325
                     L  P  G      ++ APLP +  +T   L   
Sbjct: 287 QMPLHLHLHRLLLPGTGSRDPPSELLAPLPPYFSRTLQCLRLS 329


>gi|149247844|ref|XP_001528310.1| hypothetical protein LELG_00830 [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|146448264|gb|EDK42652.1| hypothetical protein LELG_00830 [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 430

 Score =  113 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 61/297 (20%), Positives = 107/297 (36%), Gaps = 38/297 (12%)

Query: 50  KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIY 109
              V    +IQ   V+      +    +  E  I                 +++ED  I 
Sbjct: 74  GIEVLSERKIQEKDVITCTQHRHEPKIVWPENPI----------------SVVFEDDDII 117

Query: 110 VFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
           V +KP+GI V   GS +   +   +K   +         HRLD+ TSG++++ + R AA 
Sbjct: 118 VIDKPSGIPVHPTGSYMFNSLSEIVKEMFN--FDNIWTCHRLDKVTSGVVILCKNRDAAV 175

Query: 169 HLTESFRMR--RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
                   +  +++KIY + V G   +        +L  +  G  Y+            +
Sbjct: 176 KFLNILLEKSDKVKKIYLARVNGKFPDGVYRYTCPILAVNMNG--YIQPSNLESLLTLTS 233

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
               +V          +  QP +G+ HQ+R+H  ++G PI  D  Y          P+  
Sbjct: 234 TIFERVNFDSLSNTSIVRCQPISGKFHQIRIHLRNLGFPISNDLFY-----KTQDVPLDT 288

Query: 287 KLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDECKQ 343
            L  +    DL      R+      P H  K      ++ +    + + Y QDE  +
Sbjct: 289 YLMKNELESDLY-----RIIFE-KYP-HFAKLQP---WRVESKYNVDQKYQQDEFYE 335


>gi|226494518|ref|NP_001028376.1| RNA pseudouridylate synthase domain-containing protein 3 [Mus
           musculus]
 gi|123796151|sp|Q14AI6|RUSD3_MOUSE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 3
 gi|109732980|gb|AAI16828.1| RNA pseudouridylate synthase domain containing 3 [Mus musculus]
 gi|109733482|gb|AAI16826.1| RNA pseudouridylate synthase domain containing 3 [Mus musculus]
          Length = 344

 Score =  113 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 58/283 (20%), Positives = 106/283 (37%), Gaps = 44/283 (15%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQK 143
            ++ L + +  L++ ++ +   +   NKP G+ V G  G    +     L   +  + Q+
Sbjct: 61  ENLGLEELAHVLRAAVVDQKGPLVTLNKPQGLPVTGRPGELTLLSVLPQLSQALGLEHQE 120

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKECIA 199
            ++     +E SG+++++     A  L +    S R +R    Y ++  GIP+  +  + 
Sbjct: 121 LQVVRAPGKEASGLVLLSSCPQTASRLQKFFIHSRRAQRPTATYCAVTDGIPEPSEGTVC 180

Query: 200 NWLLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             L  +     D    V     K  ++G    +S F V+    +    +++QP T   +Q
Sbjct: 181 MPLKMEQMNDVDLAVPVMSPSRKDIQEGVKRTLSRFHVMAT-GRGCALVQLQPLTVFPNQ 239

Query: 255 LRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNK------LYLHAR------- 293
           L+VH     CPI+GDH Y           F     +    +      L  H R       
Sbjct: 240 LQVHMALQLCPILGDHTYAARVGTVLGQRFLWPAETTKPQRQVLDEALLRHLRLSPSQVA 299

Query: 294 -------YMDLPHPEGG----RLQITAPLPAHMVKTWDSLGFK 325
                     L  P  G      ++ APLP +  +T   L   
Sbjct: 300 QMPLHLHLHRLLLPGTGSRDPPSELLAPLPPYFSRTLQCLRLS 342


>gi|317124662|ref|YP_004098774.1| pseudouridine synthase [Intrasporangium calvum DSM 43043]
 gi|315588750|gb|ADU48047.1| pseudouridine synthase [Intrasporangium calvum DSM 43043]
          Length = 321

 Score =  113 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 47/253 (18%), Positives = 98/253 (38%), Gaps = 10/253 (3%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVF 111
              + ++ +G  V         +     + +  +  +L    +   +  +L+ D ++ V 
Sbjct: 47  ADIDRKLAAGDFVDATGRPVPEDAPFVPRSVCWTHRDLPDEVEVPFEIDVLHRDERLVVI 106

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  +S     G         ++ V +   +    HRLD+ T+G+L+    +       
Sbjct: 107 DKPHFLSTMP-RGRHVVQSALARTRVLTGLDRLTPAHRLDRPTAGVLMFTTEQRWRGAYQ 165

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHF 230
             F   R+ K Y ++        ++ +   L++++H+  ++     +   G    A +  
Sbjct: 166 RVFAEGRVHKEYLAV-----APVRDGLGLPLVRRTHLVKEHGSHQAREVHGREPNAETLV 220

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           + ++  +       + P TGRTHQLR     +G PI+GD  Y    +          L L
Sbjct: 221 E-LEVESGGVGGYRLTPRTGRTHQLRCQLCGLGIPIIGDPLYPVE-REVADDDFSEPLQL 278

Query: 291 HARYMDLPHPEGG 303
            A  ++L  P  G
Sbjct: 279 LAAVLELDDPIDG 291


>gi|221134752|ref|ZP_03561055.1| 23S rRNA pseudouridylate synthase [Glaciecola sp. HTCC2999]
          Length = 240

 Score =  113 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 57/217 (26%), Positives = 96/217 (44%), Gaps = 22/217 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS------WVDSKGQKPRLTHRLDQET 154
           +LY+ S  ++  KP G+++   S     +    K+      + +++     L HRLD  T
Sbjct: 3   VLYDHSDFFIIAKPQGVTMHEASNGLPAVLPLFKAALANMAYPEAQYAHLHLVHRLDDHT 62

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L++A+   AA+   E F  +RIQK Y +L     K K   +   ++ K    G +V 
Sbjct: 63  SGCLIIAKHAVAAERFRELFSQQRIQKYYVALSHAKGKRKAGWVKGDMVNKRK--GQWVL 120

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
                      AIS+F              ++P +G+THQ+RV     G  I+GD +Y +
Sbjct: 121 TKSVE----RPAISYFFR-QGLGNGLYLFWVKPFSGKTHQVRVALKSNGSGILGDPQYSS 175

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
                       ++YLHA  +D  + +   +QI  P+
Sbjct: 176 EPAQ--------RMYLHAFALDFIY-DDEPIQIHCPV 203


>gi|152998983|ref|YP_001364664.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151363601|gb|ABS06601.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 305

 Score =  113 bits (282), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 49/288 (17%), Positives = 100/288 (34%), Gaps = 30/288 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H+  I     ++ +  G+V             + G ++ +         +   +++
Sbjct: 28  FLAQHFARIGEDVWRQRILDGKVH-----------WRDGSLIALDTEYRPAARVYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +     +  +L++D  + +  KP  + V              +  + +    
Sbjct: 77  P------VEAKIPFEEQILFQDDNVILAYKPHFLPVTPSGNYVNECL-VHRLRLRTGIDT 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKE 196
               HRLD+ET+G++++           + F    I+K Y ++    P+           
Sbjct: 130 IAPAHRLDRETAGVILMTVAPETRALYHQLFIDDAIRKDYQAIAKLTPEIIQQYQQGSLT 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
              +W +K      D    +K  E  AN   +H ++ +           + P TG+THQL
Sbjct: 190 LPLHWTVKNRMQPSDPSFTMKIVEGEAN---THSEISLVAIKGDLGLFHLSPITGKTHQL 246

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G P++ D  Y +             L L A+ +    P  G
Sbjct: 247 RVHMQSLGMPLLNDRFYPSLLPKG-PDKFATPLKLMAQRLRFIDPVSG 293


>gi|296131380|ref|YP_003638630.1| pseudouridine synthase [Cellulomonas flavigena DSM 20109]
 gi|296023195|gb|ADG76431.1| pseudouridine synthase [Cellulomonas flavigena DSM 20109]
          Length = 304

 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 53/216 (24%), Positives = 90/216 (41%), Gaps = 11/216 (5%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            +     +  +L+ D ++ V +KP  +S    G  I   +   L++ +D    +    HR
Sbjct: 85  AEPEVPGRIHVLHRDERLVVVDKPPFLSTIPRGRHIVQSVVVRLRAELDL--PELSPLHR 142

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ TSG+L++A  +        +F  R + K Y +L        ++ +      ++HI 
Sbjct: 143 LDRATSGVLLLATEQRWRAPYQTAFERRAVDKTYRAL-----APLRDDLELPADVRNHIR 197

Query: 210 GDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                   +   GA   A +H + ++          + P TGRTHQLR+H   +G PIVG
Sbjct: 198 KVRGTAHAEVVPGAPVNAETHVE-LEREVDGLGVYRLTPRTGRTHQLRLHLCGLGIPIVG 256

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           D  Y      +      + L L A  +    P  GR
Sbjct: 257 DRLYPVERDLDLDDFT-DPLQLLAVRIAFTDPVDGR 291


>gi|269218864|ref|ZP_06162718.1| RNA pseudouridylate synthase family protein [Actinomyces sp. oral
           taxon 848 str. F0332]
 gi|269211975|gb|EEZ78315.1| RNA pseudouridylate synthase family protein [Actinomyces sp. oral
           taxon 848 str. F0332]
          Length = 306

 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 51/245 (20%), Positives = 91/245 (37%), Gaps = 17/245 (6%)

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD-FLKSILLYEDSKIYVFNKPAGISV 119
           +G VV       A    +K    +     +    D  L+  ++    +    +KPAG++ 
Sbjct: 62  AGDVVDADANPLAPQQSVKHGSSVFVFRPIPDEPDAPLELDVVDGTDRWIAVDKPAGMAT 121

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
               G        + +       +    HRLD  T G+L++   +         F  R +
Sbjct: 122 MP-RGKHVAQTVTIAARRHFSNPEIVAAHRLDAATRGVLLLTLAKRWRAPYQMLFERREV 180

Query: 180 QKIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           +K Y ++     +  + + +A  L K     G    +V   +     A++  + +    +
Sbjct: 181 RKAYLAVAPADDRFVEAQTVALALAK---PRGSLKALVVDGQPN---AVTTVR-LADERR 233

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
                E++P TGRTHQ+RV   H+G PIVGD  Y     G     +  +L       +  
Sbjct: 234 GLGLYEIEPKTGRTHQIRVTMSHLGIPIVGDWLYPEVRDGGDLQLLAARL-------EFV 286

Query: 299 HPEGG 303
            P  G
Sbjct: 287 DPANG 291


>gi|196011042|ref|XP_002115385.1| expressed hypothetical protein [Trichoplax adhaerens]
 gi|190582156|gb|EDV22230.1| expressed hypothetical protein [Trichoplax adhaerens]
          Length = 267

 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 100/255 (39%), Gaps = 57/255 (22%)

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSGILVVARTRA 165
            +   NKP GI+     GI Y+     +   +D   Q   L+H LD+  +GIL+ ++   
Sbjct: 35  NVIAINKPYGIASHDNPGIGYNCHSIYRELNLDDDSQPVYLSHVLDRNCTGILIGSK--- 91

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
                              ++  GIPK  K  I   +++   +    V +  Q+E  +  
Sbjct: 92  -------------------AITVGIPKAIKGTIDIPIVEDKTL--KRVKLKMQDEGASKQ 130

Query: 226 AI------------SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKY 272
            I            +++KV+         +E +  T    Q+RVHA   +GCP++GDH+Y
Sbjct: 131 EIAYKYGGRVRLASTNYKVLSKSEIGCALIEFETKTYYKKQIRVHAADALGCPVLGDHQY 190

Query: 273 CANFKGNFT--SPIQN-------------KLYLHARYMDL-PHPEGGR---LQITAPLPA 313
            +   G+    SP                K++LH R + +   P  G+   L I A    
Sbjct: 191 SSKKIGHNQVVSPKIGQALNLIGGNTNTLKMHLHLRKVTISKWPASGKVINLAIVASPSY 250

Query: 314 HMVKTWDSLGFKYDR 328
             ++T + L  K  +
Sbjct: 251 EFMQTLEMLQLKSPK 265


>gi|262404083|ref|ZP_06080638.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. RC586]
 gi|262349115|gb|EEY98253.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. RC586]
          Length = 235

 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 56/200 (28%), Positives = 89/200 (44%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +   +    D +     L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEVVTQTGDGQ---LYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L++ F MR+++K Y ++    PK K+  I   + +        ++     
Sbjct: 60  LARNAAAASELSQGFAMRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLLNSQ--- 116

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              +N A++ F      A        +PHTG+THQ+RV    +G  IVGD  Y       
Sbjct: 117 ---SNPAVTQFFS-ATAALGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYN------ 166

Query: 280 FTSPIQNKLYLHARYMDLPH 299
            T    ++ YLHA  +   +
Sbjct: 167 -TIEGADRGYLHAFALRFTY 185


>gi|325116888|emb|CBZ52441.1| RNA pseudouridylate synthase domain-containing protein [Neospora
            caninum Liverpool]
          Length = 2211

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 43/170 (25%), Positives = 72/170 (42%), Gaps = 7/170 (4%)

Query: 135  SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            + +     +  + HRLD  TSG L+VA++ A    L       R +K+Y +LV+G    +
Sbjct: 1951 ALLFDATHQFGIGHRLDTPTSGPLLVAKSYAGLAFLRAQLASWRPKKVYLALVFGAVPLR 2010

Query: 195  KECIA-----NWLLKKSHIGGDYVHVVKQ-NEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
            +E +          +    G   + V    + K A   ++         + F    ++P 
Sbjct: 2011 RETVRLVHPLRPTFEARQAGKKEMEVASTIDAKIALLFLTALAQYSYAGRDFTLCRVEPV 2070

Query: 249  TGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNKLYLHARYMDL 297
            TGRTHQ+R    H+G PIV D  Y  +         + N+L+LH   +  
Sbjct: 2071 TGRTHQIRAQLAHIGHPIVADPIYVKDPADRALGRSLSNRLFLHCVSLSF 2120


>gi|297579243|ref|ZP_06941171.1| pseudouridine synthase Rlu family protein [Vibrio cholerae RC385]
 gi|297536837|gb|EFH75670.1| pseudouridine synthase Rlu family protein [Vibrio cholerae RC385]
          Length = 235

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 55/200 (27%), Positives = 88/200 (44%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +   +    D +     L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEVVTQTGDGQ---LYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L++ F  R+++K Y ++    PK K+  I   + +        ++     
Sbjct: 60  LARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLLNSQ--- 116

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
              +N A++ F      A        +PHTG+THQ+RV    +G  IVGD  Y       
Sbjct: 117 ---SNPAVTQFFS-ATAAPGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYN------ 166

Query: 280 FTSPIQNKLYLHARYMDLPH 299
            T    ++ YLHA  +   +
Sbjct: 167 -TIEGADRGYLHAFALRFTY 185


>gi|304411496|ref|ZP_07393109.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307306728|ref|ZP_07586470.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304350023|gb|EFM14428.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306910696|gb|EFN41125.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 305

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 48/288 (16%), Positives = 100/288 (34%), Gaps = 30/288 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H+  I     ++ +  G+V             + G ++ +         +   +++
Sbjct: 28  FLAQHFARIGEDVWRQRILDGKVH-----------WRDGSLIALDTEYRPAARVYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +     +  +L++D  + +  KP  + V              +  + +    
Sbjct: 77  P------VEAKIPFEEQILFQDDNVILAYKPHFLPVTPSGNYVNECL-VHRLRLRTSIDT 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKE 196
               HRLD+ET+G++++           + F    I+K Y ++    P+           
Sbjct: 130 IAPAHRLDRETAGVILMTVAPETRALYHQLFIDDAIRKDYQAIAKLTPEIIQQYQQGSLT 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
              +W ++      D    +K  E  AN   +H ++ +           + P TG+THQL
Sbjct: 190 LPLHWTVRNRMQPSDPSFTMKIVEGEAN---THSEISLVAIKGDLGLFHLSPITGKTHQL 246

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G P++ D  Y +             L L A+ +    P  G
Sbjct: 247 RVHMQSLGMPLLNDRFYPSLLPKG-PDKFATPLKLMAQRLRFIDPVSG 293


>gi|301112595|ref|XP_002998068.1| conserved hypothetical protein [Phytophthora infestans T30-4]
 gi|262112362|gb|EEY70414.1| conserved hypothetical protein [Phytophthora infestans T30-4]
          Length = 214

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 59/199 (29%), Positives = 108/199 (54%), Gaps = 18/199 (9%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV------DKKRVKFNNRI 59
           ++++VV   D+E +RLDRW ++ +P +    +Q  LR  ++R+      + +  + N+ +
Sbjct: 8   WMRHVVRAQDQE-LRLDRWLRHQFPTLPQSFVQTQLRKRKIRLQSATASNLEATRANSLL 66

Query: 60  QSGQVVRIPPVIN----ALNHIIKEQKILDSSVNLTKHSD----FLKSILLYEDSKIYVF 111
           + G VV I   +         + + ++ + +  +LT   D     LK  ++Y+D++  V 
Sbjct: 67  REGSVVAIDAHLFLSKLQPLVVQQVEQDIATRQHLTTAQDKRLLQLKRCVVYQDAQFVVL 126

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           NKP G++VQ GS +   +  +L    +   Q+ RL HRLD+ETSG+LV+AR+R AA   +
Sbjct: 127 NKPHGLAVQDGSTLTESLALYLPWIAE---QQLRLVHRLDKETSGVLVLARSRLAAAKFS 183

Query: 172 ESFRMRRIQKIYWSLVWGI 190
           +  R   + K Y +LV  +
Sbjct: 184 KLLRNGAVYKTYEALVEAL 202


>gi|26345624|dbj|BAC36463.1| unnamed protein product [Mus musculus]
          Length = 315

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 46/201 (22%), Positives = 88/201 (43%), Gaps = 12/201 (5%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQK 143
            ++ L + +  L++ ++ +   +   NKP G+ V G  G    +     L   +  + Q+
Sbjct: 61  ENLGLEELAHVLRAAVVDQKGPLVTLNKPQGLPVTGRPGELTLLSVLPQLSQALGLEHQE 120

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKECIA 199
            ++     +E SG+++++     A  L +    S R +R    Y ++  GIP+  +  + 
Sbjct: 121 LQVVRAPGKEASGLVLLSSCPQTASRLQKFFIHSRRAQRPTATYCAVTDGIPEPSEGTVC 180

Query: 200 NWLLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             L  +     D    V     K  ++G    +S F V+    +    +++QP T   +Q
Sbjct: 181 MPLKMEQMNDVDLAVPVMSPSRKDIQEGVKRTLSRFHVMAT-GRGCALVQLQPLTVFPNQ 239

Query: 255 LRVHALHMGCPIVGDHKYCAN 275
           L+VH     CPI+GDH Y A 
Sbjct: 240 LQVHMALQLCPILGDHTYAAR 260


>gi|262171321|ref|ZP_06038999.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus MB-451]
 gi|261892397|gb|EEY38383.1| pseudouridylate synthase LSU rRNA-specific [Vibrio mimicus MB-451]
          Length = 233

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 56/203 (27%), Positives = 88/203 (43%), Gaps = 17/203 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +        DS+     L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEVAAQSGDSQ---LYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L++ F  R ++K Y ++    PK K+  I   + +        V+     
Sbjct: 60  LARNAAAASELSQGFAKRTVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQN-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F        +      +PHTG+THQ+RV    +G  IVGD  Y       
Sbjct: 118 ----NPAVTQFFSATAVPGER-LFLCKPHTGKTHQIRVALKSIGSAIVGDPIYN------ 166

Query: 280 FTSPIQNKLYLHARYMDLPHPEG 302
            T+   ++ YLHA  +   + + 
Sbjct: 167 -TADESDRGYLHAFALRFSYQDT 188


>gi|118474954|ref|YP_892206.1| pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40]
 gi|118414180|gb|ABK82600.1| pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40]
          Length = 254

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 54/251 (21%), Positives = 101/251 (40%), Gaps = 46/251 (18%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                  I+    ++++ SG V    KR                        ++  + +L
Sbjct: 9   LLALQEGISNNEAKELIDSGLVSAGGKR------------------------LVLARGLL 44

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           + + +  K +   K +++YED  I   NKP  I+ +  + I                 K 
Sbjct: 45  NENTSF-KVTKLAKPVMIYEDDNIVAVNKPPFITSEKVAEI----------------FKF 87

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L +RLD+ETSG++++ +     +   + F   +++K Y ++V GI  ++          
Sbjct: 88  PLLNRLDKETSGVILLYKNEEFQKAAIKEFANNKVKKTYLAIVRGIVVDEFSVELPISTV 147

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           K+  G       K +      AI+H   +    +K   +++   TGRTHQ+R H  + G 
Sbjct: 148 KTKSG----AFSKIDLSRGKTAITHVSPLMVEGKK-SLIKVGIETGRTHQIRCHLAYSGY 202

Query: 265 PIVGDHKYCAN 275
            ++GD KY  N
Sbjct: 203 GVIGDEKYAKN 213


>gi|229515060|ref|ZP_04404520.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TMA 21]
 gi|229347765|gb|EEO12724.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae TMA 21]
          Length = 235

 Score =  112 bits (281), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 56/200 (28%), Positives = 88/200 (44%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +         +   +  L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEV---ATQTGDDQLYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L++ F  R+++K Y ++    PK K+  I   + +        V+  +  
Sbjct: 60  LARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A        +PHTG+THQ+RV    +G  IVGD  Y       
Sbjct: 118 ----NPAITQFFS-AAAATGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYN------ 166

Query: 280 FTSPIQNKLYLHARYMDLPH 299
            T+   ++ YLHA  +   +
Sbjct: 167 -TADESDRGYLHAFALRFTY 185


>gi|68535163|ref|YP_249868.1| putative pseudouridylate synthase [Corynebacterium jeikeium K411]
 gi|68262762|emb|CAI36250.1| putative pseudouridylate synthase [Corynebacterium jeikeium K411]
          Length = 338

 Score =  112 bits (280), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 51/281 (18%), Positives = 97/281 (34%), Gaps = 35/281 (12%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILD-SSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           +R  +G+V        A + +++    ++       +     +  +L++D+ I V +KP 
Sbjct: 52  DRFAAGEVCLDSGEALAPDDVLRPGSFINFYRRPAPERPVPGEIAVLHQDADIVVVDKPP 111

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            ++     G        +K+ V     +   +HRLD+ T G+L++             F 
Sbjct: 112 FLATLP-RGQHITETALVKARVQLGIPELSPSHRLDRLTRGVLLMTARPEIRGAYQTMFE 170

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLK------------------KSHIGGDYVHVVK 217
            R   K+Y +L   +P+         L                     S   G    ++ 
Sbjct: 171 RRVPHKVYEALT-PLPEEAPFAPIAPLADWRSWDPPTPERPWRLEHSMSKTRGHLSTILT 229

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                A   ++  +      +K     ++PHTG+THQLRV    +G PI+ D  Y     
Sbjct: 230 DGSPNALTLVTGLRTEWRGGRKILVWRLEPHTGKTHQLRVVLRSLGLPILNDPLYTELTD 289

Query: 278 GNF--------------TSPIQNKLYLHARYMDLPHPEGGR 304
                                 + + L A+ +  P P  G+
Sbjct: 290 AALFSIDAPTPRPVYVEDEDFSSPMGLIAKELRFPDPLSGQ 330


>gi|229529302|ref|ZP_04418692.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           12129(1)]
 gi|229333076|gb|EEN98562.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae
           12129(1)]
          Length = 235

 Score =  112 bits (280), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 56/200 (28%), Positives = 87/200 (43%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +         +   +  L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEV---ATQTGDDQLYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L++ F  R+++K Y ++    PK K+  I   + +        V+  +  
Sbjct: 60  LARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A        +PHTG+THQ+RV    +G  IVGD  Y    K  
Sbjct: 118 ----NPAITQFFS-ATAAPGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYNTADKS- 171

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +   +
Sbjct: 172 ------DRGYLHAFALRFTY 185


>gi|307191610|gb|EFN75107.1| RNA pseudouridylate synthase domain-containing protein 1
           [Harpegnathos saltator]
          Length = 269

 Score =  112 bits (280), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 45/212 (21%), Positives = 83/212 (39%), Gaps = 17/212 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-----LKSWVDSK-GQKPRLTHRLD 151
              +++      V NKP  + +   +    +         L   V+ K   +    HRLD
Sbjct: 18  PVKVVHRSENFLVVNKPYDMYINSNNPDRRNTLQLELKKMLPDLVNPKLCHEFHFVHRLD 77

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG++ +A  + AA+  + +F    +QK Y +LV G        I   +         
Sbjct: 78  YPTSGVICIALNKKAARAASVAFENHTVQKFYLALVHGHVHEPYIVIDKAIGDDIREKNS 137

Query: 212 YVHVVKQNE---KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              +   +    +    + +   V++     ++    + + P TGR HQLRVH  H+G  
Sbjct: 138 NHKMCTSDSIFCEKPRRSTTVLVVLEHGFWKSKPATKILLAPSTGRRHQLRVHCHHIGHT 197

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++GD+ Y             ++ YLH+  + L
Sbjct: 198 VIGDYTYSEGKDIE-----PHRTYLHSLRLIL 224


>gi|229523755|ref|ZP_04413160.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae bv.
           albensis VL426]
 gi|229337336|gb|EEO02353.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae bv.
           albensis VL426]
          Length = 235

 Score =  112 bits (280), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 56/200 (28%), Positives = 88/200 (44%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +         +   +  L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEV---ATQTGDDQLYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L++ F  R+++K Y ++    PK K+  I   + +        V+  +  
Sbjct: 60  LARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A        +PHTG+THQ+RV    +G  IVGD  Y       
Sbjct: 118 ----NPAITQFFS-ATAAPGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYN------ 166

Query: 280 FTSPIQNKLYLHARYMDLPH 299
            T+   ++ YLHA  +   +
Sbjct: 167 -TADESDRGYLHAFALRFTY 185


>gi|126176071|ref|YP_001052220.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125999276|gb|ABN63351.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 305

 Score =  112 bits (280), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 49/288 (17%), Positives = 99/288 (34%), Gaps = 30/288 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H+  I     ++ +  G+V             + G ++ +         +   +++
Sbjct: 28  FLAQHFARIGEDVWRQRILDGKVH-----------WRDGSLIAMDTEYRPAARVYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +     +  +L++D  + +  KP  + V              +  + +    
Sbjct: 77  P------VEAKIPFEEQILFQDDNVILAYKPHFLPVTPSGNYVNECL-VHRLRLRTGIDT 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKE 196
               HRLD+ET+G++++           + F    I+K Y ++    P            
Sbjct: 130 IAPAHRLDRETAGVILMTVAPETRALYHQLFIDDAIRKDYQAIAKLTPDIIEQYQQESLT 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
              +W +K      D    +K  E  AN   +H ++ +           + P TG+THQL
Sbjct: 190 LPLHWTVKNRMQPSDPSFTMKIVEGEAN---THSEISLVAIKGDLGLFHLSPITGKTHQL 246

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G P++ D  Y +             L L A+ +    P  G
Sbjct: 247 RVHMQSLGMPLLNDRFYPSLLPKG-PDKFATPLKLMAQRLRFIDPVSG 293


>gi|153828845|ref|ZP_01981512.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 623-39]
 gi|148875641|gb|EDL73776.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 623-39]
          Length = 235

 Score =  112 bits (280), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 56/200 (28%), Positives = 87/200 (43%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +         +   +  L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEV---ATQTGDDQLYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L++ F  R+++K Y ++    PK K+  I   + +        V+  +  
Sbjct: 60  LARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A        +PHTG+THQ+RV    +G  IVGD  Y    K  
Sbjct: 118 ----NPAITQFFS-ATAAPGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYNTADKS- 171

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +   +
Sbjct: 172 ------DRGYLHAFALRFTY 185


>gi|262191836|ref|ZP_06050006.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae CT
           5369-93]
 gi|262032263|gb|EEY50831.1| pseudouridylate synthase LSU rRNA-specific [Vibrio cholerae CT
           5369-93]
          Length = 235

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 56/200 (28%), Positives = 87/200 (43%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +         +   +  L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEV---ATQTGDDQLYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L++ F  R+++K Y ++    PK K+  I   + +        V+  +  
Sbjct: 60  LARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A        +PHTG+THQ+RV    +G  IVGD  Y    K  
Sbjct: 118 ----NPAITQFFS-ATAAPGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYNTADKS- 171

Query: 280 FTSPIQNKLYLHARYMDLPH 299
                 ++ YLHA  +   +
Sbjct: 172 ------DRGYLHAFALRFTY 185


>gi|160873570|ref|YP_001552886.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160859092|gb|ABX47626.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315265800|gb|ADT92653.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 303

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 49/288 (17%), Positives = 99/288 (34%), Gaps = 30/288 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H+  I     ++ +  G+V             + G ++ +         +   +++
Sbjct: 28  FLAQHFARIGEDVWRQRILDGKVH-----------WRDGSLIALDTEYRPAARVYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +     +  +L++D  + +  KP  + V              +  + +    
Sbjct: 77  P------VEAKIPFEEQILFQDDNVILAYKPHFLPVTPSGNYVNECL-VHRLRLRTGIDT 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKE 196
               HRLD+ET+G++++           + F    I+K Y ++    P            
Sbjct: 130 IAPAHRLDRETAGVILMTVAPETRALYHQLFIDDAIRKDYQAIAKLKPDIIEQYQQGNLT 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
              +W +K      D    +K  E  AN   +H ++ +           + P TG+THQL
Sbjct: 190 LPLHWTVKNRMQPSDPSFTMKIVEGEAN---THSEISLVAIKGDLGLFHLSPITGKTHQL 246

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G P++ D  Y +             L L A+ +    P  G
Sbjct: 247 RVHMQSLGMPLLNDRFYPSLLPKG-PDKFATPLKLMAQRLRFIDPVSG 293


>gi|221505297|gb|EEE30951.1| RNA pseudouridylate synthase domain-containing protein, putative
            [Toxoplasma gondii VEG]
          Length = 2273

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 44/190 (23%), Positives = 78/190 (41%), Gaps = 12/190 (6%)

Query: 117  ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            ++V          +    + +     +  + HRLD  TSG L+VA++ A    L      
Sbjct: 2008 LAVTQREREHRKREEERLALLFDASHQFGIGHRLDTPTSGPLLVAKSYAGLAFLRAQLAS 2067

Query: 177  RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYA------IS 228
             R +K+Y +LV+G    +++      L+ +   G      +   N   A  A      I+
Sbjct: 2068 WRPKKVYLALVFGAVPLREKVRLVHPLRPTFEAGKTGKKEMEVANTVDAKIALSFLSGIT 2127

Query: 229  HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNK 287
            H+       + F    ++P TGRTHQ+R    H+G PIV D  Y  +         + ++
Sbjct: 2128 HY---SYGGRDFTLCRVEPVTGRTHQIRAQLAHIGHPIVADPIYVNDPADRALGRSLSDR 2184

Query: 288  LYLHARYMDL 297
            ++LH   +  
Sbjct: 2185 VFLHCVSLSF 2194


>gi|304312830|ref|YP_003812428.1| Putative pseudouridine synthase A [gamma proteobacterium HdN1]
 gi|301798563|emb|CBL46793.1| Putative pseudouridine synthase A [gamma proteobacterium HdN1]
          Length = 301

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 62/334 (18%), Positives = 112/334 (33%), Gaps = 80/334 (23%)

Query: 4   MTYVQYVVVEN--DEENMRLDR--WFKNHYPHINFVNLQKILRSGQVR-------VDKKR 52
           M+ ++ + +E    E     D           +    ++  +  G +R         K++
Sbjct: 1   MSTIERICIEEKISESG---DACSLLAAR-TGLPKGRIKDAMNKGALRWRKGGRGAFKRQ 56

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
            +    +  G  +        L                      L   +  E     V+ 
Sbjct: 57  RRATAILAKGDEIAFFYDETLLTLKPP-----------------LPICISDEGQY-SVWY 98

Query: 113 KPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
           KPAG+  QG     ++          +  ++  L HR+D+ET+G+++VA    AA  L++
Sbjct: 99  KPAGLLSQGSEYGDHYSLLRQVELHSNPRREAFLVHRIDRETTGLILVAHNERAAAKLSQ 158

Query: 173 SFRMRRIQKIYWSLVWGIPKN--KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
            F  R ++K Y + V G       K  I   +                       A+SH 
Sbjct: 159 LFSGRDVEKHYLACVSGEIAEVGAKFTIDQAI-------------------DGKNAVSHI 199

Query: 231 KVIDCFA------------------QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            V+D  A                     C L+++  TGR HQ+R H    G P++GDH++
Sbjct: 200 TVLDSRAPASVQSEPSDRAQDLRKIDHGCLLDVRIETGRKHQIRKHLQGAGFPVIGDHRF 259

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
                     P    L L +  +    P   +++
Sbjct: 260 GG--------PQHPMLCLTSSMIAFRCPLSHKMR 285


>gi|221484026|gb|EEE22330.1| RNA pseudouridylate synthase domain-containing protein, putative
            [Toxoplasma gondii GT1]
          Length = 2255

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 44/190 (23%), Positives = 78/190 (41%), Gaps = 12/190 (6%)

Query: 117  ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            ++V          +    + +     +  + HRLD  TSG L+VA++ A    L      
Sbjct: 1990 LAVTQREREHRKREEERLALLFDASHQFGIGHRLDTPTSGPLLVAKSYAGLAFLRAQLAS 2049

Query: 177  RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYA------IS 228
             R +K+Y +LV+G    +++      L+ +   G      +   N   A  A      I+
Sbjct: 2050 WRPKKVYLALVFGAVPLREKVHLVHPLRPTFEAGKTGKKEMEVANTVDAKIALSFLSGIT 2109

Query: 229  HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNK 287
            H+       + F    ++P TGRTHQ+R    H+G PIV D  Y  +         + ++
Sbjct: 2110 HY---SYGGRDFTLCRVEPVTGRTHQIRAQLAHIGHPIVADPIYVNDPADRALGRSLSDR 2166

Query: 288  LYLHARYMDL 297
            ++LH   +  
Sbjct: 2167 VFLHCVSLSF 2176


>gi|260899347|ref|ZP_05907742.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus AQ4037]
 gi|308110268|gb|EFO47808.1| ribosomal large subunit pseudouridine synthase C [Vibrio
           parahaemolyticus AQ4037]
          Length = 109

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 38/115 (33%), Positives = 69/115 (60%), Gaps = 7/115 (6%)

Query: 1   MS-LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           MS + T VQ+V ++ D    R+D + +N    I    + +I+R G+VRV+KKR+K   ++
Sbjct: 1   MSEIRTQVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGEVRVNKKRIKAEYKL 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP 114
           ++G +VRIPP       + K+++ +  S  L K ++ L+ +++YED  + + NKP
Sbjct: 61  KAGDLVRIPP-----VTVEKKEEDVAPSTKLYKVAE-LEHMIIYEDDHMLILNKP 109


>gi|157962549|ref|YP_001502583.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157847549|gb|ABV88048.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 305

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 50/289 (17%), Positives = 111/289 (38%), Gaps = 50/289 (17%)

Query: 31  HINFVNLQKILRSGQVRVDKKRV-----KFNNRIQSGQVVRIPPVINALNHIIKEQKILD 85
            ++   +++ ++ G V     +      +    ++ G  +          H+   Q +LD
Sbjct: 52  GLSKQAIKQAMQKGAVWHGHGKQTNRLRRAKKALKVGDEL----------HLYYNQAVLD 101

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
            +V          + LL+++ +  V+ KP G+  QG     +           +  +   
Sbjct: 102 ETVT--------DAELLFDEEQYSVWYKPFGMRCQGSKWSDHTTINRFIETQLTPPRNAY 153

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           + HRLD   +G++V+  T+     + + F  R + K Y  +V G     +  I       
Sbjct: 154 IIHRLDLAATGLIVLGHTKKVTAAIAQLFETRALDKFYQVIVEGKFPEGQVTI------- 206

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGC 264
                         +     A+SH  +++  ++     ++++  +GR HQ+R+H   +G 
Sbjct: 207 ------------NTDVDNKKALSHAHILEYNSELNQSKVQVKIESGRKHQIRIHMASLGH 254

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313
           P++GD ++         S +   L L + ++    P  G  ++   LP 
Sbjct: 255 PVIGDRQHGNG------SDLTPNLQLTSCHLSFVCPVTGEDKVF-ELPQ 296


>gi|228469440|ref|ZP_04054448.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           uenonis 60-3]
 gi|228309015|gb|EEK17658.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           uenonis 60-3]
          Length = 133

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 29/122 (23%), Positives = 49/122 (40%), Gaps = 14/122 (11%)

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           + V     +    A++H+  ++        +  +  TGRTHQ+R H   +  P+ GD +Y
Sbjct: 1   MTVYPPTSEIGKPAVTHYTELERLG-FVTLIACELETGRTHQIRAHMKSIDHPLFGDERY 59

Query: 273 CANFKG------------NFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTW 319
             +               N    I  +  LHA  +   HP  G R+  +APLP  M +  
Sbjct: 60  GGDQILWGQRTSSYQQFVNNCLKICPRQALHAETLAFDHPTTGERMHFSAPLPDDMSQLI 119

Query: 320 DS 321
           + 
Sbjct: 120 EK 121


>gi|254285389|ref|ZP_04960354.1| pseudouridine synthase Rlu family protein [Vibrio cholerae
           AM-19226]
 gi|150424661|gb|EDN16597.1| pseudouridine synthase Rlu family protein [Vibrio cholerae
           AM-19226]
          Length = 235

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 56/200 (28%), Positives = 88/200 (44%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +         +   +  L HRLD+ TSGIL+
Sbjct: 3   DILFTYPDFLLINKHPNVSVHKDDGDTMLLQEV---ATQTGDDQLYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L++ F  R+++K Y ++    PK K+  I   + +        V+  +  
Sbjct: 60  LARNAAAASELSQGFAKRKVEKFYLAIGSKKPKKKQGLICGDMERSRRSSWKLVNSQE-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N AI+ F      A        +PHTG+THQ+RV    +G  IVGD  Y       
Sbjct: 118 ----NPAITQFFS-ATAAPGERMFLCKPHTGKTHQIRVALKSIGSSIVGDPIYN------ 166

Query: 280 FTSPIQNKLYLHARYMDLPH 299
            T+   ++ YLHA  +   +
Sbjct: 167 -TADESDRGYLHAFALRFTY 185


>gi|219119925|ref|XP_002180713.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217408186|gb|EEC48121.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 200

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 54/201 (26%), Positives = 79/201 (39%), Gaps = 5/201 (2%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           L Y+D  + V NKPAG+S     G   +             +K    HRLD  TSG L+ 
Sbjct: 1   LCYQDRWVCV-NKPAGMSTHRSGGNRSNQFVVSTLLKRQLSRKVFPVHRLDHRTSGALLF 59

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A        L ++ R +  +K Y  LV G   N  E     + K   + G          
Sbjct: 60  AFDSEMCASLHDALREQSARKTYVCLVRGFWDNFFESDTATVDKALTVDGTKRSATTVFT 119

Query: 221 KGANYAISHFKVI--DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           K A+  I +               +   P TGRTHQ+R HA  MG P++GD ++      
Sbjct: 120 KLASTIILNNSAYGEKNVPISCSLILAVPTTGRTHQIRRHASAMGMPVLGDTQHGETKVN 179

Query: 279 NFTSP--IQNKLYLHARYMDL 297
            +       ++L LH   ++L
Sbjct: 180 RWWRQKRGLDRLALHCLSLNL 200


>gi|321455306|gb|EFX66443.1| hypothetical protein DAPPUDRAFT_332203 [Daphnia pulex]
          Length = 309

 Score =  111 bits (278), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 49/209 (23%), Positives = 88/209 (42%), Gaps = 16/209 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWV-----DSKGQKPRLTHRLDQET 154
           +L++ S   V +K   + +     G+   ++  ++        D         HRLD  T
Sbjct: 47  VLHQSSDFLVVDKCYDVLINSDDPGVKITVEHQIRKIFPHFVNDKLAHGFHFVHRLDYST 106

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG+L +A  + AA   + +F  R+ +K Y +L+ G   ++   I+  +   S  G  +  
Sbjct: 107 SGVLCLATNKKAANLGSTAFSARKTRKYYLALLRGHVSHELIDISLPIGADSRPGHSHKM 166

Query: 215 VVKQNE--KGANYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                +  +    A +   V+            + M+P TGR HQLR+H   +G  IVGD
Sbjct: 167 CSSDKQFCQYPKAAFTRLLVLQKGFYDGFPVTKVMMKPVTGRRHQLRIHCSSLGHTIVGD 226

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLP 298
             Y      N    +  +++LH+  + LP
Sbjct: 227 FTYS-----NGKDVLPYRMFLHSHRLILP 250


>gi|260578643|ref|ZP_05846552.1| pseudouridylate synthase [Corynebacterium jeikeium ATCC 43734]
 gi|258603271|gb|EEW16539.1| pseudouridylate synthase [Corynebacterium jeikeium ATCC 43734]
          Length = 313

 Score =  111 bits (278), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 51/281 (18%), Positives = 97/281 (34%), Gaps = 35/281 (12%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILD-SSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           +R  +G+V        A + +++    ++       +     +  +L++D+ I V +KP 
Sbjct: 27  DRFAAGEVCLDSGEALAPDDVLRPGSFINFYRRPAPERPVPGEIAVLHQDADIVVVDKPP 86

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            ++     G        +K+ V     +   +HRLD+ T G+L++             F 
Sbjct: 87  FLATLP-RGQHITETALVKARVQLGIPELSPSHRLDRLTRGVLLMTARPEIRGAYQTMFE 145

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLK------------------KSHIGGDYVHVVK 217
            R   K+Y +L   +P+         L                     S   G    ++ 
Sbjct: 146 RRIPHKVYEALT-PLPEEAPFAPIAPLADWRSWDPPTPERPWRLEHSMSKTRGHLSTILT 204

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
                A   ++  +      +K     ++PHTG+THQLRV    +G PI+ D  Y     
Sbjct: 205 DGSPNALTLVTGLRTEWREGRKILVWRLEPHTGKTHQLRVVLRSLGLPILNDPLYTELTD 264

Query: 278 GNF--------------TSPIQNKLYLHARYMDLPHPEGGR 304
                                 + + L A+ +  P P  G+
Sbjct: 265 AALFSIDAPTPRPVYVEDEDFSSPMGLIAKELRFPDPLSGQ 305


>gi|217971665|ref|YP_002356416.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217496800|gb|ACK44993.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 305

 Score =  111 bits (278), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 48/288 (16%), Positives = 99/288 (34%), Gaps = 30/288 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H+  I     ++ +  G+V             + G ++ +         +   +++
Sbjct: 28  FLAQHFARIGEDVWRQRILDGKVH-----------WRDGSLIAMDTEYRPAARVYYYREV 76

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +     +  +L++D  + +  KP  + V              +  + +    
Sbjct: 77  P------VEAKIPFEEQILFQDDNVILAYKPHFLPVTPSGNYVNECL-VHRLRLRTGIDT 129

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKE 196
               HRLD+ET+G++++           + F    I+K Y ++    P            
Sbjct: 130 IAPAHRLDRETAGVILMTVAPETRALYHQLFIDDAIRKDYQAIAKLTPDIIEQYQQGSLT 189

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRTHQL 255
              +W ++      D    +K  E  AN   +H ++ +           + P TG+THQL
Sbjct: 190 LPLHWTVRNRMQPSDPSFTMKIVEGEAN---THSEISLVAIKGDLGLFHLSPITGKTHQL 246

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           RVH   +G P++ D  Y +             L L A+ +    P  G
Sbjct: 247 RVHMQSLGMPLLNDRFYPSLLPKG-PDKFATPLKLMAQRLRFIDPVSG 293


>gi|324999146|ref|ZP_08120258.1| RNA pseudouridylate synthase [Pseudonocardia sp. P1]
          Length = 308

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 52/258 (20%), Positives = 92/258 (35%), Gaps = 10/258 (3%)

Query: 47  RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
           RVD +R+     + +G++V     +   +       +        +        +L+ D 
Sbjct: 36  RVDPRRIDA--MLAAGEIVTAAGPLTPSSPFTPSTTLWLHREEPDEAEVPFPVEVLHADD 93

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
            + V +KP  ++     G        ++   +    +    HRLD+ T+G+L++      
Sbjct: 94  DVVVVDKPHLLATIP-RGSHVRQTVLVRLRHELGLPELSPAHRLDRATAGVLLLVARPEL 152

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
                  F   R+ K Y ++    P      +     + S I           E G   A
Sbjct: 153 RGAYQMLFAEGRVGKTYEAITRHDPS-----LTLPRTEVSRIVKRPGIFAAVTEPGTPNA 207

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
            +  + +D          + P TGRTHQLRVH   +G PI+GD  Y    +         
Sbjct: 208 ETRIE-LDTHRAGLARYRLFPRTGRTHQLRVHLNELGVPILGDDVY-PELRQRPDGDFTR 265

Query: 287 KLYLHARYMDLPHPEGGR 304
            L L +R ++   P  G 
Sbjct: 266 PLQLLSRSLEFDDPVSGE 283


>gi|237836503|ref|XP_002367549.1| RNA pseudouridylate synthase domain-containing protein [Toxoplasma
            gondii ME49]
 gi|211965213|gb|EEB00409.1| RNA pseudouridylate synthase domain-containing protein [Toxoplasma
            gondii ME49]
          Length = 2257

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 44/190 (23%), Positives = 78/190 (41%), Gaps = 12/190 (6%)

Query: 117  ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            ++V          +    + +     +  + HRLD  TSG L+VA++ A    L      
Sbjct: 1992 LAVTQREREHRKREEERLTLLFDASHQFGIGHRLDTPTSGPLLVAKSYAGLAFLRAQLAS 2051

Query: 177  RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYA------IS 228
             R +K+Y +LV+G    +++      L+ +   G      +   N   A  A      I+
Sbjct: 2052 WRPKKVYLALVFGAVPLREKVRLVHPLRPTFEAGKTGKKEMEVANTVDAKIALSFLSGIT 2111

Query: 229  HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNK 287
            H+       + F    ++P TGRTHQ+R    H+G PIV D  Y  +         + ++
Sbjct: 2112 HY---SYGGRDFTLCRVEPVTGRTHQIRAQLAHIGHPIVADPIYVNDPADRALGRSLSDR 2168

Query: 288  LYLHARYMDL 297
            ++LH   +  
Sbjct: 2169 VFLHCVSLSF 2178


>gi|209483640|gb|ACI47296.1| pseudouridine synthase 1 [Toxoplasma gondii]
          Length = 2117

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 44/190 (23%), Positives = 78/190 (41%), Gaps = 12/190 (6%)

Query: 117  ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
            ++V          +    + +     +  + HRLD  TSG L+VA++ A    L      
Sbjct: 1852 LAVTQREREHRKREEERLTLLFDASHQFGIGHRLDTPTSGPLLVAKSYAGLAFLRAQLAS 1911

Query: 177  RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD--YVHVVKQNEKGANYA------IS 228
             R +K+Y +LV+G    +++      L+ +   G      +   N   A  A      I+
Sbjct: 1912 WRPKKVYLALVFGAVPLREKVRLVHPLRPTFEAGKTGKKEMEVANTVDAKIALSFLSGIT 1971

Query: 229  HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN-FTSPIQNK 287
            H+       + F    ++P TGRTHQ+R    H+G PIV D  Y  +         + ++
Sbjct: 1972 HY---SYGGRDFTLCRVEPVTGRTHQIRAQLAHIGHPIVADPIYVNDPADRALGRSLSDR 2028

Query: 288  LYLHARYMDL 297
            ++LH   +  
Sbjct: 2029 VFLHCVSLSF 2038


>gi|224013728|ref|XP_002296528.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220968880|gb|EED87224.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 405

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 50/180 (27%), Positives = 85/180 (47%), Gaps = 20/180 (11%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN------- 200
             LD+ TSG+LVVA+T+ A   L+  F+ R+++K Y ++V G  + + E   +       
Sbjct: 179 RVLDRATSGLLVVAKTKPAMVDLSSQFKHRKVKKTYTAIVNGDIQERPESSISSREAKQL 238

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW------LEMQPHTGRTHQ 254
            +  ++    D+       E     A++ ++ +D  + ++ W      +E++P TGR HQ
Sbjct: 239 GVCIENTGSHDFRWQFVDEELDGQSAVTIWRTVDKSSLEYAWNNTIAMVELKPKTGRYHQ 298

Query: 255 LRVHALHM-GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE----GGRLQITA 309
           LR H   + GC IVGD  Y  +  G         LYL +  + L HP      GR +  +
Sbjct: 299 LRRHMAWVYGCSIVGDKSY--DGSGQAKLLRNEGLYLCSNKVTLQHPFYNTPSGRKEWES 356


>gi|157374654|ref|YP_001473254.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157317028|gb|ABV36126.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 282

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 50/290 (17%), Positives = 109/290 (37%), Gaps = 46/290 (15%)

Query: 33  NFVNLQKILRSGQVRVDKKR-----VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87
           +   +++ +  G V + + +      +    ++ G  + +      L H + + +     
Sbjct: 30  SKQLIKQAMNKGAVWLTRGKHTQRLRRAKRALKIGDELHLYYNQEVLEHEVADAE----- 84

Query: 88  VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT 147
                        L+ ++ +  ++ KP G+  QG     +           +  +   + 
Sbjct: 85  -------------LIADEGQYSLWYKPYGMLCQGSKWGDHTTINRYAETHLAPDRPAFII 131

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HRLD+  +G++++  ++     L + F +R + K Y  +V G   N    +   +   S 
Sbjct: 132 HRLDRAATGLVLIGHSKKTTAALAKLFELRLLDKYYQVIVEGHFSNHG--VDELVTIDSE 189

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           + G               A SH K +     Q    ++++  +GR HQ+R+H   +G P+
Sbjct: 190 VDG-------------KPARSHAKQLKYDPEQNRSLVQVKIESGRKHQIRIHMASIGYPV 236

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           VGD ++    +          L L + Y+  P P  G  +    LP  + 
Sbjct: 237 VGDRQHGIADESEVN------LQLTSCYLKFPCPITGE-EKEFELPQRLR 279


>gi|325122666|gb|ADY82189.1| putative pseudouridylate synthase [Acinetobacter calcoaceticus
           PHEA-2]
          Length = 292

 Score =  110 bits (276), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 53/290 (18%), Positives = 106/290 (36%), Gaps = 29/290 (10%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H+PHI     ++  + G +              +G  + +        HI   + +
Sbjct: 24  YLCGHFPHIRTDEWEQRFQDGLIYA-----------ANGDKLTLTSPYVGSTHIFYYRFL 72

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                   +H       +L+E+  + V +KP  +++       Y  +  L       G +
Sbjct: 73  AYEPHVPFEHH------ILFENDDLLVVDKPHFLTISPTG--QYVQETLLVRLKKQTGNE 124

Query: 144 -PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKECIANW 201
                HRLD+ET+G+++  +   +     + F  R++ KIY ++  +    N  + +   
Sbjct: 125 FLTPIHRLDRETAGVVLFCKRVESRGIYQQLFAERQVNKIYHAIAPYKKDLNFPQTLHLH 184

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
           L K        + V++  +     AI   +      Q +    + P TG+ HQLRVH  +
Sbjct: 185 LDKGHPFY--TMQVIENVKANTQTAIELIE----HNQIWAKYRLTPTTGKQHQLRVHLNY 238

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAP 310
           +  PI  D  Y    +          L L A+++    P     +   + 
Sbjct: 239 LEIPIKNDPFY-PVVQHKAEDDFSEPLQLLAKHISFTDPLTKEGMSFNSE 287


>gi|90021559|ref|YP_527386.1| copper-resistance protein CopA [Saccharophagus degradans 2-40]
 gi|89951159|gb|ABD81174.1| pseudouridine synthase [Saccharophagus degradans 2-40]
          Length = 209

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 46/166 (27%), Positives = 73/166 (43%), Gaps = 16/166 (9%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD+ TSG+ + A++  AA    + F  + + K Y ++    P  K+  I   ++
Sbjct: 23  LLPAHRLDKPTSGLCIFAKSSGAAAQFGQLFERKLVTKYYLAITSKKPAKKQGAIIGDMV 82

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           K +  G   +   K N      AI+HF      A     + ++P TG+THQLRV    +G
Sbjct: 83  K-TRNGSWKLTAAKTN-----PAITHFFSF-ALASGMRLILLKPSTGKTHQLRVALKALG 135

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
             I+GD +Y             ++LYLHA  ++     G R     
Sbjct: 136 AAIIGDERYGGEP--------SDRLYLHAYQLEFEF-NGERHSFKC 172


>gi|330793622|ref|XP_003284882.1| hypothetical protein DICPUDRAFT_28377 [Dictyostelium purpureum]
 gi|325085191|gb|EGC38603.1| hypothetical protein DICPUDRAFT_28377 [Dictyostelium purpureum]
          Length = 315

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 48/264 (18%), Positives = 94/264 (35%), Gaps = 58/264 (21%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           ++++     + NKP  +++   G      +  +L++         R  +R+D  TSGI+V
Sbjct: 51  VIFKSDDYCLVNKPYDVNIDDDGKDRNETVVKYLENEYPEVKGSIRFVNRIDYATSGIVV 110

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL-KKSHIGGDYVHVVKQ 218
            A  + +A    E F+ R   K Y ++V G  ++ +  I   +   KS +    + +  +
Sbjct: 111 TALNKKSANKGMELFQNRDTTKTYLAIVHGHIESDEGLIDKPIANDKSDLNSFKMCIGDK 170

Query: 219 NEKGANYAISHFKVIDC------------------------------------------- 235
            +     + +++KV++                                            
Sbjct: 171 IDNPGRSSQTNYKVLERGHIKRFKKFSDNLKLLSYNNSNNNGDNNSENNSDNNKNNDKND 230

Query: 236 -------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
                         + + P +GR HQLRVH   +G  IVGD  Y          P   ++
Sbjct: 231 NIQNEEIIEMPVTKVLLTPKSGRRHQLRVHLQSIGHIIVGDETYGPK------DPQSERM 284

Query: 289 YLHARYMDLPHPEGGRLQITAPLP 312
            LH+  + LP     ++ +    P
Sbjct: 285 MLHSWKLILPFKNEPQINVETDDP 308


>gi|56753585|gb|AAW24995.1| SJCHGC01427 protein [Schistosoma japonicum]
          Length = 567

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 73/393 (18%), Positives = 140/393 (35%), Gaps = 109/393 (27%)

Query: 51  KRVKFNNRIQ--SGQVVRIPPVINALNHIIKEQ----KILDSSVN-LTKHSDFLKSILLY 103
           K V+   R+   +G  + +       ++  K      ++ D  ++     ++   + +LY
Sbjct: 178 KIVRQRTRLNLYTGTTLDVSSSKVESSNPEKLDSHGYRVPDEDLHKFHLLTEEEAATVLY 237

Query: 104 ED-----SKIYVFNKPAGISVQGGSGIAYHIDGFL---KSWVDSKGQK-----------P 144
           +        + + NKP GI+ Q G+   ++I   L   +S +  +  +            
Sbjct: 238 KSIIEIRENVIIMNKPYGIASQPGADCKHNIVDLLPRIESMIRKRNHRASKVKEETVDEL 297

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRLD++++G +++AR R A+  L E+F  R I+K Y  +  GIP+++   I   L++
Sbjct: 298 STVHRLDKDSTGAMLIARNRDASLKLQEAFARRWIKKDYLCITVGIPRSEYGYIQLPLVE 357

Query: 205 KSHIGGDYVHVVKQNEKGANYA------------------------------------IS 228
           ++      + + K +      A                                    ++
Sbjct: 358 RNFKEFHKMCIPKLDRHLQELACKQTQLDENDETNEYDVTDAFSVLYNKMQTNNNNQPVT 417

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCA-------NFKGNF 280
            + ++D        +     TG  HQ+R H    +  PI+GDHKY             + 
Sbjct: 418 WYHLLDQRND-AGLMLCSTLTGIKHQVRAHLAFGLQTPILGDHKYSHGEYLAPQRLPKHL 476

Query: 281 TSPIQNK--------LYLHARYMDLP------------------------HPEGG----R 304
              +  +        L+LHA  + L                         H   G     
Sbjct: 477 LEALNVRQPKVRYLALHLHASSLHLRVSPSSSSSSCENFFDFVRSLENPLHTVTGSTRHP 536

Query: 305 LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
           L+  A LP H  +    +G K  +  Y+KRL+ 
Sbjct: 537 LKFHAQLPIHFRENLKRIGLKLPQ--YLKRLHW 567


>gi|224373533|ref|YP_002607905.1| ribosomal pseudouridine synthase [Nautilia profundicola AmH]
 gi|223589983|gb|ACM93719.1| ribosomal pseudouridine synthase [Nautilia profundicola AmH]
          Length = 253

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 52/225 (23%), Positives = 90/225 (40%), Gaps = 35/225 (15%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K   F K   ++ED  +   +KP                 ++ S   +K     L HRLD
Sbjct: 50  KVLKFPKPKKIFEDKNLLAVDKPP----------------YITSEEIAKNFGYELLHRLD 93

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG+L++ +     +   E F+ + + K Y + V GI     +      + K+  G  
Sbjct: 94  KETSGVLILVKNDEFKKKAIEEFKKQNVYKEYITWVSGIVAEPMKIDLPIKVIKTKSG-- 151

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               + +  K    A++  + I  F +    ++   HTGRTHQ+R H   +  PI+GD K
Sbjct: 152 ---ALAKISKDGEDAVTEIEPILAF-RTKSKVKAVIHTGRTHQIRAHLKAVEHPILGDEK 207

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           Y          P +  +  H ++    +        T+P P+   
Sbjct: 208 YGGE-------PFKRVMLHHHKFKIFDY------NFTSPEPSDFK 239


>gi|228469806|ref|ZP_04054764.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas uenonis 60-3]
 gi|228308645|gb|EEK17396.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas uenonis 60-3]
          Length = 341

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 55/289 (19%), Positives = 101/289 (34%), Gaps = 35/289 (12%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV--INALNHIIKEQKILDSSVN 89
           +   +++ LR+  V +       F+  +  G  + I  +     L H + E+        
Sbjct: 41  SRTTVKQFLRNRCVLLAGVTTTQFDAPVAIGDSIEIYNIGTAEELQHPLIEE-------- 92

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWVD-SKGQKPRL 146
                       LY D +  V +K  GI     GG+  +                +K  L
Sbjct: 93  ------------LYRDEQFIVLHKRPGIPTISVGGASKSSLFQVVTHHLKKVDPNEKIFL 140

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            +RLD++T GI++VAR R   Q L   +    +   + ++V G        +     K  
Sbjct: 141 LNRLDRDTEGIIIVARDRQLQQDLLAEWHSFVLFNSFEAVVLGALDTSSGELTTRPTKDK 200

Query: 207 HIGGDYVHVVKQNEKGANYA--ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             G D       + +    A   + ++V+         L +   T R + +R     +G 
Sbjct: 201 KRGSDKRRTSTSSGRDKKPASFRASYEVLST-GPYITRLSLSLLT-RNNSIRSTLASIGH 258

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           P++GDH        +    +   L L A  + + HP    ++  T   P
Sbjct: 259 PLLGDH----RANDSIAPDLSKYLALRATELAIFHPIKRQKMLFTIDKP 303


>gi|302695171|ref|XP_003037264.1| hypothetical protein SCHCODRAFT_47965 [Schizophyllum commune H4-8]
 gi|300110961|gb|EFJ02362.1| hypothetical protein SCHCODRAFT_47965 [Schizophyllum commune H4-8]
          Length = 263

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 48/202 (23%), Positives = 82/202 (40%), Gaps = 16/202 (7%)

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             ++  G      HRLD +T+G L++  T A  + L+  FR R ++K Y +LV G     
Sbjct: 20  RRLNHNGN-LYPVHRLDMDTTGALLLGLTEARTRDLSAQFRNRTVKKTYLALVHGGIDAF 78

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGA-NYAISHFKVIDCFA-QKFCWLEMQPHTGRT 252
                          G  VH  + N +     A + ++++   +      L+++  TG  
Sbjct: 79  SSISGQIREPIFLRDGQPVHHSRANARCEMKEAATDWELLGSSSIAPLSVLKLKLLTGYK 138

Query: 253 HQLRVHALH-MGCPIVGDHKYCANFK----GNFTSPIQNKLYLHARYMDLPH-----PEG 302
           HQLRVH  H +  PI GD  Y             +    +++LH+  + +       P  
Sbjct: 139 HQLRVHLAHRLKTPIFGDALYSPKTGSVELARVVTHSPERMFLHSAELGIHRYRSEGPTK 198

Query: 303 G---RLQITAPLPAHMVKTWDS 321
           G    L + APLP+  ++    
Sbjct: 199 GKRYELNVCAPLPSDFLQVCRQ 220


>gi|212636064|ref|YP_002312589.1| pseudouridine synthase [Shewanella piezotolerans WP3]
 gi|212557548|gb|ACJ30002.1| Pseudouridine synthase [Shewanella piezotolerans WP3]
          Length = 281

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 58/305 (19%), Positives = 118/305 (38%), Gaps = 46/305 (15%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRW--FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR 58
           MSL     ++ V + +    +D           ++   +++ ++ G V +   +     R
Sbjct: 1   MSLQKTECHIKVVDPQ----IDAVSLLAKQ-TGLSKQLVKQAMQKGAVWLTHGKQTNRLR 55

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
                 V+         H+   Q +LD SV          + LL+++ +  V+ KP G+ 
Sbjct: 56  -----RVKKVLSQGDELHLYYNQTVLDESVP--------NAELLFDEGQYSVWYKPFGMR 102

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
            QG     +              +   + HRLD   +G++V+  ++     + + F  R 
Sbjct: 103 CQGSKWSDHTTINRFAETHLEPARSAYIIHRLDLAATGLIVLGHSKKTTAAIAKLFETRA 162

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           + K Y  +V G   + K  I                     +     A+SH  +++  A+
Sbjct: 163 LDKYYQVIVEGEFPDSKVTID-------------------TDVDGKSALSHAHLLEYNAE 203

Query: 239 -KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                ++++  +GR HQ+R+H   +G P++GD  +     GN ++P    L L + Y++ 
Sbjct: 204 LNQSKVQVKIESGRKHQIRLHMASVGHPVIGDRLHG---NGNESTPN---LQLTSCYLNF 257

Query: 298 PHPEG 302
             P  
Sbjct: 258 ICPIT 262


>gi|227503769|ref|ZP_03933818.1| RNA pseudouridylate synthase family protein [Corynebacterium
           striatum ATCC 6940]
 gi|227199593|gb|EEI79641.1| RNA pseudouridylate synthase family protein [Corynebacterium
           striatum ATCC 6940]
          Length = 271

 Score =  110 bits (275), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 52/211 (24%), Positives = 85/211 (40%), Gaps = 18/211 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY D  + V +KP  +     G  +   +   L+  VD    +    HRLD+ T+G++V
Sbjct: 74  VLYADEHLLVVDKPHFLPTTSNGRIVRETLQTRLR--VDMDNDEIVPLHRLDRLTAGVVV 131

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            +            F+ R++ K Y + V   P   +  +    L+ +   G    VV   
Sbjct: 132 CSVNPRTRGLYQHMFQDRQMHKTYRARVTQ-PLQFEGMVT---LRMAKPHGSRQVVV--- 184

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           +       +  +           +E+QP TG THQLRV   H+G PI GD  Y  +   +
Sbjct: 185 DPAGTPTQTFVRASGKD------VELQPLTGHTHQLRVLLNHLGSPICGDDTYPVDKGLD 238

Query: 280 FTSPIQNKLYLHARYMDLPHPE-GGRLQITA 309
                +    +H R ++   P  G R Q  A
Sbjct: 239 LYDFSEPLQLVHER-LEFIDPICGARRQFFA 268


>gi|157116207|ref|XP_001652796.1| hypothetical protein AaeL_AAEL007487 [Aedes aegypti]
 gi|108876584|gb|EAT40809.1| conserved hypothetical protein [Aedes aegypti]
          Length = 300

 Score =  110 bits (275), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 50/226 (22%), Positives = 90/226 (39%), Gaps = 18/226 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQE 153
             +LY      V NK   + +         +   ++       Q          HRLD  
Sbjct: 52  VDVLYSSGNFLVINKKHDLLINSNDTKKKTVQTIMRKQFPEYVQDNLTHDFYFAHRLDFA 111

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH--IGGD 211
           TSGIL +   + A + + + F  +R +K Y +L+ G     +E I   + +         
Sbjct: 112 TSGILCIPLNKNACKEVCQVFEEQRARKYYLALLRGHTDFDEEVIDIAIGEDIRFKDTSK 171

Query: 212 YVHVVKQNE--KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +  + ++E  +    +I+   V+D      +    + ++P TGR HQLR+H   +G  I
Sbjct: 172 KMCTILEDELCQNPRRSITKVLVLDRGYYNGKPVTKVLLRPITGRRHQLRLHCSQIGHVI 231

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           VGD+ Y      +       +++LHA  + LP+     + I    P
Sbjct: 232 VGDYTYSLKIDTSPP-----RMFLHAFRLVLPNSF-ENIDIQTEDP 271


>gi|257457504|ref|ZP_05622672.1| ribosomal large subunit pseudouridine synthase family protein
           [Treponema vincentii ATCC 35580]
 gi|257445127|gb|EEV20202.1| ribosomal large subunit pseudouridine synthase family protein
           [Treponema vincentii ATCC 35580]
          Length = 276

 Score =  110 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 50/248 (20%), Positives = 89/248 (35%), Gaps = 41/248 (16%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             + +ED    V  K  G                  + +          +RLD   SGI+
Sbjct: 6   PRIYFEDDYCAVVYKLNG-----------ENAQTFFTPLFPHKPFIAPINRLDTPVSGII 54

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE------CIANWLLKKSHIGGDY 212
           ++A +  A   L+++F+   ++K YW++      +  E       + +WL   +     +
Sbjct: 55  LLAFSAQAQTLLSQAFKTGSVEKEYWAICERTAADTTEEEPGIHRLEHWLGFHTKTQKAF 114

Query: 213 VHVVKQNEKGANYA---ISH--------------FKVIDCFAQKFCWLEMQPHTGRTHQL 255
           V     +    N     I+               +  +     ++ ++ + P TGRTHQ+
Sbjct: 115 VGAAPIDITLTNTTAAGITKPKKHKKPALKKAVLYWTLCGKGDRYDFIRISPETGRTHQI 174

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAH 314
           RV     G PI GD KY A       S     + LH+  +   HP   + + + AP P  
Sbjct: 175 RVQMAAAGHPIKGDLKYGAR-----RSETGGGIRLHSYKLSFSHPVTHQDITVQAP-PIQ 228

Query: 315 MVKTWDSL 322
               W + 
Sbjct: 229 PDTLWKAC 236


>gi|255022733|ref|ZP_05294719.1| pseudouridine synthase, RluA family protein [Listeria monocytogenes
           FSL J1-208]
          Length = 124

 Score =  110 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 32/134 (23%), Positives = 64/134 (47%), Gaps = 13/134 (9%)

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+ + ++  I   + +K     +   + +       YA ++++V++ +   F  + +Q  
Sbjct: 1   GVLEAQEGSIEAPIGRK-----EVSIMERFVTPEGKYAKTNYEVLERYT-AFDHVAIQLE 54

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQI 307
           TGRTHQ+RVH  ++G P++GD  Y  +      + +  +  LH+ ++ L HP     +  
Sbjct: 55  TGRTHQIRVHFSYIGHPLIGDDMYGGD------TTLLKRQALHSCHLHLVHPVTEEYMAF 108

Query: 308 TAPLPAHMVKTWDS 321
             PLPA M +    
Sbjct: 109 DLPLPADMEEIIQK 122


>gi|328875057|gb|EGG23422.1| hypothetical protein DFA_05554 [Dictyostelium fasciculatum]
          Length = 637

 Score =  110 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 54/296 (18%), Positives = 108/296 (36%), Gaps = 63/296 (21%)

Query: 1   MSLMTYVQYVVVENDEEN-MRLDRWFKNH---YPH------INFVNLQKILRSGQVRVDK 50
           MS    ++ + V   ++   RL  +                +N  ++ K++  GQ+ ++ 
Sbjct: 1   MSNKCVIEEI-VPRQQKGVERLQVYLAAKKFTLKGQDKPVTLNKTSIVKLITQGQISIND 59

Query: 51  KRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSV---------NLTKHSDFLKSI 100
           K V+  N +I++   + I    +  +                       +   +  +   
Sbjct: 60  KVVQEKNAKIRANDRILITLPTSTTSTTSSSNNSESGQQSTTTTVIGKEINLVATKIDLN 119

Query: 101 LLYEDSKIYVFNKPAGISVQ----------GGSGIAYHIDGFLKSWVDSKG-------QK 143
           +L+ED  I V NKPAG+ V                   +   L     +KG        +
Sbjct: 120 ILFEDEYIVVINKPAGMIVHPPPPSPNHPLNEENQTRTLVNALLYRYGAKGLSIVGGVDR 179

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR---------------------RIQKI 182
           P + HRLD++T+GIL+VA+  +  + + +  +                        IQK 
Sbjct: 180 PGIVHRLDKDTAGILIVAKNDSVHEMVKKMLQDHTSTTIKGSMSAKANNNNNKPTTIQKT 239

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           Y+ LV G PK     I   + +   +  + + +   +E     +I+ +KVI  + +
Sbjct: 240 YYCLVTGKPKESHGIINKAISRH-PMDRNKMVI---DESKGKESITEYKVIKSWDK 291



 Score = 88.1 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 30/96 (31%), Positives = 43/96 (44%), Gaps = 5/96 (5%)

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           + +      A+ +  +E+  HTGR HQ+RVH    G PIVGD  Y       F  P    
Sbjct: 422 TKYVGKKIGARNYTLMEITLHTGRQHQIRVHMTSEGLPIVGDPIYSGK-SNQFMVPY--- 477

Query: 288 LYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSL 322
           L L +  +   HP    +++ T P P H+    D L
Sbjct: 478 LLLASVALRFQHPITKQQMEFTIPNPPHLQSFIDQL 513


>gi|261331318|emb|CBH14308.1| RNA pseudouridylate synthase protein, putative [Trypanosoma brucei
            gambiense DAL972]
          Length = 1279

 Score =  110 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 63/276 (22%), Positives = 103/276 (37%), Gaps = 57/276 (20%)

Query: 108  IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------RLTHRLDQETSGILVVA 161
            +   +KPAG+S     G   H+  FL   +  KG          L +R+D  TSG+++VA
Sbjct: 999  VAAVDKPAGMSTTLHVG-HPHLLDFLAGNLPWKGPSAPVLFQHGLVNRIDLGTSGLVLVA 1057

Query: 162  RTRAAAQHLTESFR-MRRIQKIYWSLVWGIPK-------------NKKECIANWLLKKSH 207
             T A+ +    +    R ++K+Y +LV   P              N    I   +L    
Sbjct: 1058 DTEASLEEARRASIVERCVEKVYRALVLHCPPPISRIDTSECWYLNPCGIIMCDVLANGA 1117

Query: 208  IGGDYVHVVKQNEKGA--------NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVH 258
                 +     ++ GA          A + ++V+  F +    +LE+  HTGR HQ+R H
Sbjct: 1118 DFSLQIAAYNSSKGGALPVGAMDRRSATTTYRVLQYFPRSGVYYLEIHLHTGRRHQIRQH 1177

Query: 259  ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP--H-----PE---------- 301
               +  P++GD +Y    +         +  LHA  + L   H     P           
Sbjct: 1178 FARLCHPLLGDGRYSRRAQVVGEEFGLQRPALHAVRVTLTPQHGASAKPRGGVVAPRVGD 1237

Query: 302  ----------GGRLQITAPLPAHMVKTWDSLGFKYD 327
                      GG+  +  P+P  M  T   L  + D
Sbjct: 1238 ADYDEYCGNGGGKTVVECPVPEDMRLTLKMLRERED 1273


>gi|126336397|ref|XP_001375428.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 3, [Monodelphis domestica]
          Length = 355

 Score =  110 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 61/287 (21%), Positives = 112/287 (39%), Gaps = 51/287 (17%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
            +++  + ++ +K+ +LY +  +   NKP G++V G  G        L S +   GQ   
Sbjct: 69  ETLSHKELTEVMKTAVLYHNGPLVALNKPPGLAVTGKPGEL-----TLLSVLPEIGQHLG 123

Query: 146 LTHRL------DQETSGILVVARTRAAAQHLT----ESFRMRRIQKIYWSLVWGIPKNKK 195
           L+  L       +E+SG+++++      +       +S R+++    YW++  G+P   K
Sbjct: 124 LSQELHIVRAPGKESSGLVLLSSCPRITKTFQNFFIQSRRVQKPTVTYWAVTVGVPATPK 183

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             I   L      G D    VK   +     G    ++ F V D        +++QP T 
Sbjct: 184 GEIQVALKLDQVRGADLAVPVKAPSRQTLKEGVKKTLTRFFVEDSTPDCA-LVKLQPITA 242

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFK------------------GNFTSPIQNKLYLHA 292
             +QL VH +   CP++GDH Y A                        +  + ++L++  
Sbjct: 243 FPNQLLVHMVLQLCPVLGDHLYSARVGSVLGESFLLPVETSVPQTQVLSELLLHRLHITP 302

Query: 293 RYMD------------LPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
           + M             LP        + APLP    +T  +LG +  
Sbjct: 303 KEMALLPLHLHLHQILLPQTSMAPTMLIAPLPPFFSQTLWNLGLQMS 349


>gi|261211789|ref|ZP_05926076.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. RC341]
 gi|260839139|gb|EEX65771.1| pseudouridylate synthase LSU rRNA-specific [Vibrio sp. RC341]
          Length = 235

 Score =  110 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 54/200 (27%), Positives = 87/200 (43%), Gaps = 17/200 (8%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            +L+      + NK   +SV    G    +         S   +  L HRLD+ TSGIL+
Sbjct: 3   DILFTHPDFLLINKHPNVSVHKDDGDTMLLQEVAA---QSGDHQLYLVHRLDKMTSGILL 59

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +AR  AAA  L++ F  R ++K Y ++    PK K+  ++  + +        ++     
Sbjct: 60  LARNAAAASELSQGFAKRSVEKFYLAIGSKKPKKKQGLVSGDMERSRRSSWKLLNSQH-- 117

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
               N A++ F      A        +PHTG+THQ+RV    +G  IVGD  Y       
Sbjct: 118 ----NPAVTQFFS-TTAAPGERLFLCKPHTGKTHQIRVALKSIGSAIVGDPIYN------ 166

Query: 280 FTSPIQNKLYLHARYMDLPH 299
            T+   ++ YLHA  +   +
Sbjct: 167 -TADEADRGYLHAFALRFTY 185


>gi|158292130|ref|XP_313685.4| AGAP004401-PA [Anopheles gambiae str. PEST]
 gi|157017288|gb|EAA09234.5| AGAP004401-PA [Anopheles gambiae str. PEST]
          Length = 300

 Score =  110 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 48/212 (22%), Positives = 86/212 (40%), Gaps = 17/212 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQE 153
             +LY      V NK   + +         +   ++       Q          HRLD  
Sbjct: 52  VDVLYTSGNFLVINKKHDLLINSNDTKKKTVQTIMRKQFPEYVQDNLTHDFYFAHRLDFA 111

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH--IGGD 211
           TSGIL +   + A + + + F  +R +K Y +L+ G     +E I   + +         
Sbjct: 112 TSGILCIPLNKNACKEVCQVFEEQRARKYYLALLRGHTDFDEEVIDIAIGEDVRFKDTSK 171

Query: 212 YVHVVKQNE--KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
            +  + ++E  +    +I+   V+D      +    + ++P TGR HQLR+H   +G  I
Sbjct: 172 KMCTILEDELCQNPRRSITKVLVLDRGYYNGKPVTKVLLRPITGRRHQLRLHCSQIGHVI 231

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           VGD+ Y      +       +++LHA  + LP
Sbjct: 232 VGDYTYSLKIDTSPP-----RMFLHAFRLVLP 258


>gi|71744882|ref|XP_827071.1| RNA pseudouridylate synthase protein [Trypanosoma brucei TREU927]
 gi|70831236|gb|EAN76741.1| RNA pseudouridylate synthase protein, putative [Trypanosoma brucei]
          Length = 1279

 Score =  110 bits (274), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 62/276 (22%), Positives = 102/276 (36%), Gaps = 57/276 (20%)

Query: 108  IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------RLTHRLDQETSGILVVA 161
            +   +KPAG+S     G   H+  FL   +  KG          L +R+D  TSG+++VA
Sbjct: 999  VAAVDKPAGMSTTLHVG-HPHLLDFLAGNLPWKGPSAPVLFQHGLVNRIDLGTSGLVLVA 1057

Query: 162  RTRAAAQHLTESFR-MRRIQKIYWSLVWGIPK-------------NKKECIANWLLKKSH 207
             T A+ +    +    R ++K+Y +LV   P              N    I   +L    
Sbjct: 1058 DTEASLEEARRASIVERCVEKVYRALVLHCPPPISRIDTSECWYLNPCGIIMCDVLANGA 1117

Query: 208  IGGDYVHVVKQNEKGA--------NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVH 258
                 +     ++ GA          A + ++V+  F +    +LE+  HTGR HQ+R H
Sbjct: 1118 DFSLQIAAYNSSKGGALPVGAMDRRSATTTYRVLQYFPRSGVYYLEIHLHTGRRHQIRQH 1177

Query: 259  ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP--HPE--------------- 301
               +  P++GD +Y    +         +  LHA  + L   H                 
Sbjct: 1178 FARLCHPLLGDGRYSRRAQVVGEEFGLQRPALHAVRVTLTPQHGTSAKPRGGVVAPRVGD 1237

Query: 302  ----------GGRLQITAPLPAHMVKTWDSLGFKYD 327
                      GG+  +  P+P  M  T   L  + D
Sbjct: 1238 ADYDEYCGNGGGKTVVECPVPEDMRLTLKMLRERED 1273


>gi|307171499|gb|EFN63340.1| RNA pseudouridylate synthase domain-containing protein 1
           [Camponotus floridanus]
          Length = 246

 Score =  110 bits (274), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 40/191 (20%), Positives = 75/191 (39%), Gaps = 12/191 (6%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPR----LTHRLDQ 152
             +++      V +KP  + +   +    +       K   D    K        HRLD 
Sbjct: 44  VKIVHRSENFLVIDKPYDMYINSNNPDRKNTVQLELRKMLPDLVNPKLCHEFYFVHRLDY 103

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSGI+ +A  + AA+  + +F  +++QK Y +LV G  +     I   +          
Sbjct: 104 PTSGIMCIALNKKAARAASFAFENQKVQKFYLALVHGHIREPHVIINKPIGDDIREKNGN 163

Query: 213 VHVVKQNE---KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             +   +    +    + +   V++      +    + + P TGR HQLRVH  ++G  +
Sbjct: 164 HKMCTNDSVFCEKPRNSYTVLMVLEHGFWKNKPATKILLAPGTGRRHQLRVHCHYIGHTV 223

Query: 267 VGDHKYCANFK 277
           +GD+ Y     
Sbjct: 224 IGDYTYSDGKD 234


>gi|315453301|ref|YP_004073571.1| ribosomal pseudouridine synthase [Helicobacter felis ATCC 49179]
 gi|315132353|emb|CBY82981.1| ribosomal pseudouridine synthase [Helicobacter felis ATCC 49179]
          Length = 302

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 56/224 (25%), Positives = 98/224 (43%), Gaps = 23/224 (10%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K S+      ++      ++ KP  +     +  ++     L   V +   + RL HRLD
Sbjct: 64  KASESANLHPIFSSPYFDIYYKPKNLYSHPKNYKSHS----LYESVYAHNPEARLIHRLD 119

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK----NKKECIANWLLKKSH 207
            ETSG+++V+  +     L E F  R+I+K Y + V G  +         I   L  K  
Sbjct: 120 YETSGLVMVSTQKRYENALRELFSARQIKKTYEAWVQGDVRAYAQGPFSVILRILEPKIK 179

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           I    + +  Q  K    + +  ++++     +   L++ P +GRTHQ+R+H   +G PI
Sbjct: 180 IKHADLAIRCQIAKEGKPSATTIEILNFCPHTQRTHLKITPLSGRTHQIRLHLSALGFPI 239

Query: 267 VGDHKYC-------------ANFKGNFTSPIQNKLYLHARYMDL 297
           VG+  Y              A+F+G+F S +Q +L L A  +  
Sbjct: 240 VGEPLYTDDAHARAYLDAKKADFQGSFKS-LQTQLALEAIELKF 282


>gi|301166303|emb|CBW25879.1| putative pseudouridylate synthase [Bacteriovorax marinus SJ]
          Length = 230

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 92/239 (38%), Gaps = 20/239 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++ ED    + NKP  +SV   S         +  +   +       HR+D+ETSG+L
Sbjct: 7   VEIIAEDQSWILINKPGAMSVHNDSKS-------VIEYFKQRNINLTPPHRIDKETSGLL 59

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ + +          +++   K Y ++  G  K         L  K+    +       
Sbjct: 60  LLTKEKNEVS--NHQQQLKNASKYYIAICRGQVKADNGKWEQPLSDKAEGHKNPA----G 113

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
            +      ++++  +    Q    +  +  TGRTHQ+R H    G  I+GD +Y      
Sbjct: 114 KKSDQKICLTNWWKVSSN-QYVTLILFKIETGRTHQIRKHCALNGHEILGDKRYGQGKYQ 172

Query: 279 NFTSP--IQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRL 335
                    + + LH+  +++   E   +   A +P +     D +G + +++L   ++
Sbjct: 173 KIIKDKYQLDSMLLHSYRLEILLREEPEV-FYAKMPQYFK---DIMGEEIEKSLQDFQI 227


>gi|270658450|ref|ZP_06222329.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae HK1212]
 gi|270317010|gb|EFA28676.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae HK1212]
          Length = 116

 Score =  109 bits (273), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 47/122 (38%), Positives = 78/122 (63%), Gaps = 8/122 (6%)

Query: 47  RVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
           RV+K R+K   ++Q+G VVRIPPV       + E+     S NL K +  L++ +L+ED 
Sbjct: 2   RVNKGRIKPEYKLQTGDVVRIPPVR------VAEKNDAPISKNLNKVA-ALENQILFEDD 54

Query: 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
            + + NKP+GI+V GGSG+ + +   L++ +  + +   L HRLD++TSGIL++A+ R+A
Sbjct: 55  CLIILNKPSGIAVHGGSGLNFGVIEALRA-LRPEARFLELVHRLDRDTSGILLIAKKRSA 113

Query: 167 AQ 168
            +
Sbjct: 114 LR 115


>gi|71279408|ref|YP_270347.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
 gi|71145148|gb|AAZ25621.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
          Length = 318

 Score =  109 bits (273), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 50/274 (18%), Positives = 103/274 (37%), Gaps = 31/274 (11%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           ++   L++ +  G + +     K   + Q  + ++   V     H     ++L S V   
Sbjct: 51  LSKAQLKQAITKGALWL--TPAKNKKQTQRLRRIKKQLVKGDELHFYFNSEVLSSPV--- 105

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
             +  +  ++ Y      V+ KP G+  QG     +              +   + HRLD
Sbjct: 106 PQALLIADLIDY-----SVWYKPYGMLSQGSKWSDHCTIARFAQQNLPNERPAFIVHRLD 160

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +  +G+++VA +++AA+ L+  F   +++K Y  +V G                 H    
Sbjct: 161 RAATGLIIVAHSKSAARALSHMFEHHQLEKHYQIIVHG----------------DHRKRA 204

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              ++  +  G     +   +          ++++  +GR HQ+R+HA  +  P+VGD  
Sbjct: 205 QPDIIDSDVDGKKARSTFTCLAYDEMTDQSLIKVKIDSGRKHQIRLHAASIAMPVVGDRL 264

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
           +    K       Q  L L A  +    P    +
Sbjct: 265 HGIADKDE-----QRNLQLCAVSLRFVCPLATEI 293


>gi|139436953|ref|ZP_01771113.1| Hypothetical protein COLAER_00086 [Collinsella aerofaciens ATCC
           25986]
 gi|133776600|gb|EBA40420.1| Hypothetical protein COLAER_00086 [Collinsella aerofaciens ATCC
           25986]
          Length = 154

 Score =  109 bits (273), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 35/136 (25%), Positives = 56/136 (41%), Gaps = 11/136 (8%)

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-----QKFCWLEMQPH 248
            +  I   + + +    D V +   ++  A  AI+ FKV++ F        +  +E    
Sbjct: 2   DEGTINTGIARST---RDRVKMAVSDDPFARQAITTFKVLERFDSTRFDDGYTLVECHLF 58

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQI 307
           TGRTHQ+RVH  H+    VGD  Y              + +LH+  +   HP  G R++ 
Sbjct: 59  TGRTHQIRVHMRHINHACVGDPLYGKC--DARADQGLTRQFLHSWRVAFEHPVTGERIEC 116

Query: 308 TAPLPAHMVKTWDSLG 323
              LP  +    D L 
Sbjct: 117 RDELPWDLAAVLDDLA 132


>gi|297171011|gb|ADI22025.1| pseudouridylate synthases, 23S RNA-specific [uncultured
           myxobacterium HF0200_05J13]
          Length = 154

 Score =  109 bits (273), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 36/152 (23%), Positives = 61/152 (40%), Gaps = 13/152 (8%)

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            + K Y ++V+G+P+  +  I     +       +   V +       A++ + V+    
Sbjct: 1   EVHKRYLAMVFGLPEPSRGIIETLYGRHPTDRKKFSGKVAR----GKKAVTSYGVMVSVG 56

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK-------LYL 290
                +++   TGRTHQ+RVH    G PIVGD  Y        +     +         L
Sbjct: 57  -GLSQVDLLLGTGRTHQIRVHLSERGHPIVGDPVYSGRQYARISDEGLRRIATEFDYQAL 115

Query: 291 HARYMDLPHPEGGR-LQITAPLPAHMVKTWDS 321
           HA  +   HP  G  L +TAP+P  +    + 
Sbjct: 116 HAWEIGFTHPVTGEKLSLTAPMPELLASLAER 147


>gi|260768225|ref|ZP_05877159.1| pseudouridylate synthase LSU rRNA-specific [Vibrio furnissii CIP
           102972]
 gi|260616255|gb|EEX41440.1| pseudouridylate synthase LSU rRNA-specific [Vibrio furnissii CIP
           102972]
          Length = 202

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 47/160 (29%), Positives = 75/160 (46%), Gaps = 14/160 (8%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            S   +  L HRLD+ TSGIL++AR   AA  L++ F  R+++K Y +L    PK K+  
Sbjct: 9   QSGDAQLYLVHRLDKMTSGILLLARNAKAASELSKGFAERQVEKFYLALGSKKPKKKQGL 68

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I+  + +        +          N A++ F  +     +      +P+TG+THQ+RV
Sbjct: 69  ISGDMERSRRASWKLLTSQT------NPAVTQFFSLAAEPGER-LFLCKPYTGKTHQIRV 121

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
               +G  IVGD  Y A  +        ++ YLHA  +  
Sbjct: 122 ALKSVGSGIVGDPIYNAGNQA-------DRGYLHAFALRF 154


>gi|307109346|gb|EFN57584.1| hypothetical protein CHLNCDRAFT_16942 [Chlorella variabilis]
          Length = 275

 Score =  109 bits (272), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 62/274 (22%), Positives = 103/274 (37%), Gaps = 42/274 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +P  +    Q+ L  G++RV+  +V     ++ GQ +R             E
Sbjct: 22  IDIF-TREFPARDRQYYQQALADGRLRVEGCQVTAETPLKDGQCIRHFIHR-------HE 73

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFL------ 133
             +   S+            ++ +        KP G+ V   G      + G L      
Sbjct: 74  APVPAGSI-----------QVVGQSEDAVAVCKPHGMPVHVAGQYRKNTVLGILTAEHTR 122

Query: 134 --------KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                   +S        P    RLD+  SG+L+ AR+ AAA  L        ++K+Y +
Sbjct: 123 LPVSPCLIRSDCSHHAPAPLPVCRLDKPVSGLLLFARSAAAAAALCGRIEGHAVEKVYVA 182

Query: 186 LVWGIPKNKKECIANWLLK-------KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
            V G       C A  L K        +          K ++  A  A + F+++     
Sbjct: 183 RVLGRFPATGVCTACKLRKQAKAERAAAAAAAAAAAAKKPSKGPAKPARTEFRLLAVAED 242

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
               + ++P TGRTHQ+RVH  H+G PI  D +Y
Sbjct: 243 GLTSV-VEPRTGRTHQIRVHLQHLGHPIANDTQY 275


>gi|224083169|ref|XP_002306957.1| predicted protein [Populus trichocarpa]
 gi|222856406|gb|EEE93953.1| predicted protein [Populus trichocarpa]
          Length = 192

 Score =  108 bits (271), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 44/184 (23%), Positives = 72/184 (39%), Gaps = 47/184 (25%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK--FNNRIQSGQVVRIP 68
            V++    +RLD W       I+   +Q I++SG V V+ K     F++ +++G  +   
Sbjct: 16  TVDSKSGKLRLDSWISCRISGISRARVQSIIKSGIVSVNGKITYKVFSHNVKAGDEMDC- 74

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY- 127
                         I+     L    + L   ++YED  + V NKPA + V    G A  
Sbjct: 75  --------------IILEWKPLRVEPENLPLDIVYEDENVLVVNKPAQMVVHPAPGNATG 120

Query: 128 -HIDGFLKSWV-----------------DSKGQ-----------KPRLTHRLDQETSGIL 158
             ++G L                     D  G+           +P + H LD+ TSG+L
Sbjct: 121 TLVNGILHHSSPTVSNQEVLSDAEDISDDGDGEGLCSSSYVASVRPGIVHWLDKGTSGLL 180

Query: 159 VVAR 162
           VVA+
Sbjct: 181 VVAK 184


>gi|23465740|ref|NP_696343.1| ribosomal pseudouridine synthase [Bifidobacterium longum NCC2705]
 gi|23326424|gb|AAN24979.1| possible ribosomal pseudouridine synthase [Bifidobacterium longum
           NCC2705]
          Length = 233

 Score =  108 bits (271), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 83/231 (35%), Gaps = 31/231 (13%)

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
            +KP  ++     G+ Y     ++             HRLD+ T+G+LV  R  A     
Sbjct: 2   VDKPHFLATMP-RGMWYRQTALIRLRERLGEPDITPAHRLDRMTAGVLVFVRDSACRGAY 60

Query: 171 TESFRMRRIQKIY--WSLVWGIPKNKKECIAN-------WLLKKSHIGGDYVHVVKQNEK 221
              F+ R+  KIY   +    I   +   I          LL++SHI  ++  +    E 
Sbjct: 61  QMLFQNRQAVKIYECLAPCRPISGPRFGTIMQVEPPRPFPLLRRSHITKEHGTMAAFEEP 120

Query: 222 GANYAISHFKVIDCF-------------------AQKFCWLEMQPHTGRTHQLRVHALHM 262
           G   A +  +  D                         C   + P TG+THQLRVH   +
Sbjct: 121 GLANAETLIERGDLCFPPAGGRWREAPEGGPHPGNHPICRYTLHPRTGKTHQLRVHMNSL 180

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLP 312
           G PIVGD  Y    +          L L AR +    P  G   +  + +P
Sbjct: 181 GLPIVGDDFY-PRIQTRPYDDFSQPLQLVARVLRFTDPITGEKREFVSRVP 230


>gi|270015056|gb|EFA11504.1| hypothetical protein TcasGA2_TC014218 [Tribolium castaneum]
          Length = 289

 Score =  108 bits (271), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 41/164 (25%), Positives = 76/164 (46%), Gaps = 9/164 (5%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    +    HRLD  TSG++ V   + A Q  +++ + R+ +K Y +LV G   +    
Sbjct: 91  NQLHHEYYFMHRLDYSTSGLMCVPVHKKACQVASQAIQQRKCKKYYIALVRGYLSSNLLD 150

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQ 254
           +   + + + I  D   +   ++  +  A +   V++           + ++P TGR HQ
Sbjct: 151 LNFPIGRDNSIT-DIEKMCVTHDSNSRSARTLIVVLENGLFENYPSSKVLIRPITGRRHQ 209

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +RVH  H+G  IVGD+ Y      N       ++YLH+  + +P
Sbjct: 210 IRVHCAHIGHTIVGDYTYS-----NKKDTTPERMYLHSLRLVIP 248


>gi|153827526|ref|ZP_01980193.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-2]
 gi|149738545|gb|EDM52900.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-2]
          Length = 172

 Score =  108 bits (271), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 38/168 (22%), Positives = 69/168 (41%), Gaps = 14/168 (8%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++Y+D  +   NKPAG+ V       +  +  +++  D  GQ     HRLD+ TSG+LV 
Sbjct: 4   IVYQDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVYPLHRLDRPTSGVLVF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  +   F    ++K Y ++V G  +           +   I   +       +
Sbjct: 64  ALSSQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQ----D 119

Query: 221 KGANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVH 258
           K A  A++ ++ +               ++C +EMQP   +T     H
Sbjct: 120 KEAQSAVTAYRPLAKVELPISTGKFATTRYCLIEMQPRRAQTSAASPH 167


>gi|311029949|ref|ZP_07708039.1| pseudouridine synthase [Bacillus sp. m3-13]
          Length = 105

 Score =  108 bits (271), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 34/108 (31%), Positives = 51/108 (47%), Gaps = 7/108 (6%)

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           +    + +  A++HF+VI+ F + F  +E Q  TGRTHQ+RVH  ++G P+ GD KY   
Sbjct: 1   MTVTNENSRNAVTHFRVIERF-KDFSHIECQLETGRTHQIRVHMKYIGYPLAGDPKYGPK 59

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
                 S       LHA  +   HP     ++  AP P    +    L
Sbjct: 60  -----KSLDIEGQALHAGILGFIHPRTEEYMEFEAPNPPEFERVLKHL 102


>gi|145630740|ref|ZP_01786518.1| hypothetical protein CGSHi22421_10087 [Haemophilus influenzae
           R3021]
 gi|144983622|gb|EDJ91082.1| hypothetical protein CGSHi22421_10087 [Haemophilus influenzae
           R3021]
          Length = 152

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 34/140 (24%), Positives = 63/140 (45%), Gaps = 4/140 (2%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A +   A  + E F  + +QK Y ++V G  + K+       ++   I   +     Q +
Sbjct: 64  ALSSEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKF----SQED 119

Query: 221 KGANYAISHFKVIDCFAQKF 240
           K    A++ ++ +      +
Sbjct: 120 KEPQEAVTDYEGLKIVEMPY 139


>gi|108798222|ref|YP_638419.1| pseudouridine synthase [Mycobacterium sp. MCS]
 gi|119867318|ref|YP_937270.1| pseudouridine synthase [Mycobacterium sp. KMS]
 gi|108768641|gb|ABG07363.1| pseudouridine synthase [Mycobacterium sp. MCS]
 gi|119693407|gb|ABL90480.1| pseudouridine synthase [Mycobacterium sp. KMS]
          Length = 287

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 56/281 (19%), Positives = 95/281 (33%), Gaps = 35/281 (12%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
             + +         K+   G V  D   V+    +  G  V +   +             
Sbjct: 31  LADRFGE---AVAAKVFDGGVVCADGTVVRPGTVLPPGTHVYLYRDLP------------ 75

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQK 143
                  +        +LY D  I V +KP  ++    G  +A      L+  +D    +
Sbjct: 76  ------VEVPVPFAMPVLYRDDNIVVVDKPHFLATMPRGRHVAETAVVRLRRALDL--PE 127

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
               HRLD+ T+G+L+    R         F    + K+Y +   G        +    +
Sbjct: 128 LSPAHRLDRLTAGVLLFTTRREIRGAYQTMFSDGAVAKVYLARSAGHAA-----VDLPTV 182

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            +S I  +   +      G   A +  + +           + P TGRTHQLRVH   +G
Sbjct: 183 VRSRIIKERGRLQAFEAPGEPNAETLVEHL-----GDDVYRLTPRTGRTHQLRVHMSSLG 237

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            P++GD  Y  +          + L L A  ++   P  GR
Sbjct: 238 LPLLGDPLY-PDVIDVAPDDFADPLQLLAHSIEFDDPLTGR 277


>gi|312374039|gb|EFR21691.1| hypothetical protein AND_16535 [Anopheles darlingi]
          Length = 912

 Score =  108 bits (269), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 43/171 (25%), Positives = 71/171 (41%), Gaps = 13/171 (7%)

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +V       ++   F+ +  +   +  R  HRLD+ TSG+L+  R+   A+ +    R R
Sbjct: 14  TVHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEHQIRNR 72

Query: 178 RIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           ++QK Y   V G  P    EC     +    IG      V +         + F+ +   
Sbjct: 73  QVQKEYICRVEGEFPDGVIECKEPIEVVSYKIG------VCKVSPKGKECTTTFQKLGFN 126

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
                 +  +P TGR HQ+RVH  ++G P+V D  Y     G    P + +
Sbjct: 127 GSS-SVVLCKPLTGRMHQIRVHLQYLGYPVVNDPLYNHEVFG----PAKGR 172


>gi|307109075|gb|EFN57314.1| hypothetical protein CHLNCDRAFT_12398 [Chlorella variabilis]
          Length = 198

 Score =  108 bits (269), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 61/198 (30%), Positives = 92/198 (46%), Gaps = 27/198 (13%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL----KSWVDSKGQKPRLTHRLDQ 152
           L+S LL+ D  +    KPAG++ QGGSG+A+ +D  +               RL HRLD+
Sbjct: 7   LRSCLLHSDPDLLAVCKPAGLACQGGSGVAHSVDSVMAAAFAHLPGPASHHLRLVHRLDR 66

Query: 153 ETSGILVVARTRAAAQHLTESFRMR----------------RIQKIYWSLVWGIPKNKKE 196
           +T+G L++AR   AA  L  +FR                   IQK YW++V  +P+    
Sbjct: 67  QTTGALLLARGPDAAAWLAAAFRESSGGSGGSGRGDSSSGASIQKQYWAVV-ALPEGGG- 124

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 L  +      V   +     A  A++ ++V+        WLE+ P TGR HQLR
Sbjct: 125 ---AHRLPAAGAISLPVPGGRGGAAAAQPALTRYRVLHR-GGGLAWLELAPATGRKHQLR 180

Query: 257 VHAL-HMGCPIVGDHKYC 273
           +H    +G  I+GD +Y 
Sbjct: 181 LHCAQGLGAAILGDGRYG 198


>gi|167949147|ref|ZP_02536221.1| Pseudouridylate synthase [Endoriftia persephone 'Hot96_1+Hot96_2']
          Length = 154

 Score =  108 bits (269), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 38/143 (26%), Positives = 65/143 (45%), Gaps = 4/143 (2%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
              ++Y+D  I   NKPAG+ V       Y     +K   D  G+     HRLD+ TSG+
Sbjct: 3   PLEIIYQDQAIVAINKPAGLLVHPSLVDRYETRSAMKLLRDQLGRWVYPVHRLDKPTSGV 62

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A     AQ L E F  R ++K Y ++V G P  ++  + ++ LK+  +         
Sbjct: 63  LLFALNSEVAQRLGEQFEGRGVEKRYLAVVRGHPDQQE--VIDYPLKE--LLDKMTDRRA 118

Query: 218 QNEKGANYAISHFKVIDCFAQKF 240
           +  K A  A++ ++ +      +
Sbjct: 119 RQNKPAQPAVTRYRCLATAELPY 141


>gi|146337531|ref|YP_001202579.1| putative RNA pseudouridine synthase [Bradyrhizobium sp. ORS278]
 gi|146190337|emb|CAL74333.1| putative RNA pseudouridine synthase (Uracil hydrolyase)
           [Bradyrhizobium sp. ORS278]
          Length = 300

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 40/144 (27%), Positives = 69/144 (47%), Gaps = 4/144 (2%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
              + + + +L+ D  + V +KPAGI V  G     +++    +      + P L HRLD
Sbjct: 6   PTDEEMLARVLHRDGLMLVIDKPAGIPVHKGPKGGPNLEASFDALRFGLPRPPVLAHRLD 65

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG LV+ R R A   L   F+  +I K YW++V G P+  +  I   L K +   G 
Sbjct: 66  KETSGCLVLGRHRKATASLGLLFKHGKISKTYWAVVEGGPEADEGVIELPLGKLNAERGW 125

Query: 212 YVHVVKQNEKGANYAISHFKVIDC 235
           +     + +     A++ ++V+  
Sbjct: 126 WQ----KPDPSGQPAVTKWRVLGR 145


>gi|282852229|ref|ZP_06261581.1| ribosomal large subunit pseudouridine synthase D family protein
           [Lactobacillus gasseri 224-1]
 gi|282556648|gb|EFB62258.1| ribosomal large subunit pseudouridine synthase D family protein
           [Lactobacillus gasseri 224-1]
          Length = 107

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 31/104 (29%), Positives = 52/104 (50%), Gaps = 7/104 (6%)

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                A++HF V++ F   +  ++    TGRTHQ+RVH  ++G P+ GD  Y        
Sbjct: 5   PKGKAAVTHFTVLEQFKD-YSLVKCILETGRTHQIRVHMKYIGHPLAGDPLYGPK----- 58

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            +   +  +LHA+ +    P   + L+ +APLPA   K  ++L 
Sbjct: 59  KTLAGHGQFLHAKTLGFYQPSTHKWLEFSAPLPAIFEKQLENLR 102


>gi|45657036|ref|YP_001122.1| pseudouridylate synthase, 23S RNA-specific [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
 gi|45600273|gb|AAS69759.1| pseudouridylate synthase, 23S RNA-specific [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
          Length = 292

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 43/183 (23%), Positives = 70/183 (38%), Gaps = 13/183 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            + YE        KP GI V         +    L+  +  +    R  +RLD +TSG++
Sbjct: 8   RIFYESESFLFAEKPPGIPVHATKDSKRENFTDQLQKQLSLEY--LRTVNRLDLDTSGLV 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
              +     +   +  +     KIY  +  G    K      ++      G   VH V  
Sbjct: 66  FFCKNPDKNKEADQILKN--SLKIYLCVTSGTILEKHFTETCYI----KDGNKKVHKVFS 119

Query: 219 NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              G + A++ F  +   + + +  L  + HTGR HQ+R H    G PI+GD  Y  N +
Sbjct: 120 ---GGDKAVTEFLTLKQNSKENYSVLLAKLHTGRRHQIRFHLSEKGYPILGDRVYGKNNE 176

Query: 278 GNF 280
              
Sbjct: 177 SKL 179


>gi|24215596|ref|NP_713077.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
 gi|24196749|gb|AAN50095.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
          Length = 292

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 43/183 (23%), Positives = 70/183 (38%), Gaps = 13/183 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
            + YE        KP GI V         +    L+  +  +    R  +RLD +TSG++
Sbjct: 8   RIFYESESFLFAEKPPGIPVHATKDSKRENFTDQLQKQLSLEY--LRTVNRLDLDTSGLV 65

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
              +     +   +  +     KIY  +  G    K      ++      G   VH V  
Sbjct: 66  FFCKNPDKNKEADQILKN--SLKIYLCVTSGTILEKHFTETCYI----KDGNKKVHKVFS 119

Query: 219 NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
              G + A++ F  +   + + +  L  + HTGR HQ+R H    G PI+GD  Y  N +
Sbjct: 120 ---GGDKAVTEFLTLKQNSKENYSVLLAKLHTGRRHQIRFHLSEKGYPILGDRVYGKNNE 176

Query: 278 GNF 280
              
Sbjct: 177 SKL 179


>gi|257068055|ref|YP_003154310.1| 23S RNA-specific pseudouridylate synthase [Brachybacterium faecium
           DSM 4810]
 gi|256558873|gb|ACU84720.1| 23S RNA-specific pseudouridylate synthase [Brachybacterium faecium
           DSM 4810]
          Length = 305

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 48/258 (18%), Positives = 91/258 (35%), Gaps = 8/258 (3%)

Query: 58  RIQSGQVVRIPPVINALNHIIKEQKILDSSVNL-TKHSDFLKSILLYEDSKIYVFNKPAG 116
           R  +G++V            +     +     L  +H    +  +L+ D+ + V +KP  
Sbjct: 37  RFAAGEIVDAEGRPWRAEEPVGPGDEMWFHRELRPEHVPAAELRILHRDAHLLVLDKPHD 96

Query: 117 ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           ++     G        ++    +        HRLD+ T+G+L             + F  
Sbjct: 97  MATMP-RGAHVLSSALVRLRRATGISTLVPLHRLDRRTAGVLAFGIRPEERSAYQQLFAR 155

Query: 177 RRIQKIYWSL-VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
           + + K Y +L V G   +    +    + +  +      +  +   G   A +  +V   
Sbjct: 156 QEVDKEYEALLVLGPGTSLPTAVGERAVLRDRLDKRRGELTTRVLDGPPNAETALEV-RA 214

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHA 292
             +    + + P TGRTHQLR      G PI+G+  Y         +        L L +
Sbjct: 215 AGEGLLQVRLHPRTGRTHQLRAQLAARGAPILGEDLYRPAQDPPPPADAGGPDLPLQLLS 274

Query: 293 RYMDLPHPEGG-RLQITA 309
           R +    P  G R + T+
Sbjct: 275 RTLRFADPHTGVRREFTS 292


>gi|242309086|ref|ZP_04808241.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pullorum MIT 98-5489]
 gi|239524510|gb|EEQ64376.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pullorum MIT 98-5489]
          Length = 257

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 110/292 (37%), Gaps = 60/292 (20%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                 +I+    + ++  G V +  K++K    +       + P        I E K  
Sbjct: 22  LLALQENISNNEAKSLIDRGLVSIQGKKLKIARAL-------LSPHTKFNIQKIPEIK-- 72

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
                           +L++D  I   +KPA ++                  +       
Sbjct: 73  ----------------ILFQDDNILALSKPAFLTS---------------EEIAKLYPNW 101

Query: 145 RLTHRLDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            L HRLD+ETSGIL++ +          E+F+  ++ K Y ++V GI + ++E  A  ++
Sbjct: 102 ALLHRLDKETSGILLLIKENSPFHLKAKEAFKKEQVFKQYIAIVEGIIEEEQEITAPLII 161

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +K +        V  ++K    A +    I+   +K    E+   TG+THQ+R H  H+ 
Sbjct: 162 QKGNFAK-----VLVSKKEGIRAYTKITPIEIIGKKTKL-EIIIKTGKTHQIRAHLAHIK 215

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
            PI+GD  Y             N++ LHA+ + L        +     P   
Sbjct: 216 HPIIGDTFYGGKPA--------NRILLHAQKISLL-----GYEFQDSPPKDF 254


>gi|302840471|ref|XP_002951791.1| hypothetical protein VOLCADRAFT_92295 [Volvox carteri f.
           nagariensis]
 gi|300263039|gb|EFJ47242.1| hypothetical protein VOLCADRAFT_92295 [Volvox carteri f.
           nagariensis]
          Length = 553

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 57/203 (28%), Positives = 82/203 (40%), Gaps = 32/203 (15%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-----QKPRLTHRLDQE 153
             + YED  + V  KP GI+ QG       + G LK  + +        +P+  HRLD  
Sbjct: 159 LPVAYEDDHLAVVIKPPGIATQGSGSG--TVQGRLKYCLRASPLVGALNRPQQVHRLDAP 216

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK-------- 205
           T G+L+VA+T AA + L      RR+ K Y +LV G  +     I   L  K        
Sbjct: 217 TGGLLLVAKTHAAQRRLAGDLHHRRMAKRYCTLVKGE-RYGSGTIDMPLSGKPCLTSFRV 275

Query: 206 -SHIGGDYVHVVKQNEKGANYAISHFKVID---------------CFAQKFCWLEMQPHT 249
            S  G  +   V  +        + +   +                       + + PHT
Sbjct: 276 VSKRGLSHTTEVVASAAIGARMAAAWTGGEKAVRCGPGPAAAAGRRHLDVLTKILLWPHT 335

Query: 250 GRTHQLRVHALHMGCPIVGDHKY 272
           GRTHQLR H  + G PI+GD +Y
Sbjct: 336 GRTHQLRKHMAYTGTPILGDPRY 358


>gi|303272579|ref|XP_003055651.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226463625|gb|EEH60903.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 547

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 59/364 (16%), Positives = 103/364 (28%), Gaps = 122/364 (33%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-----GSGIAYHIDGFLKSWVDSK 140
           +S+ +   +D  +  +++ED  I V NKP G+         G+ +     G ++     +
Sbjct: 183 ASLAVPLVADEERLEVIHEDDAILVVNKPPGLRFHPVHRFEGNSLLSRCIGHIRRRRRRR 242

Query: 141 GQK-------------------------------PRLTHRLDQETSGILVVARTRAAAQH 169
            +                                P + HRLD +TSG+ V  + ++    
Sbjct: 243 RRASDDGGEDGGEDADADGEEKVDDDEDAHADDMPHIVHRLDMDTSGVCVFVKDKSLVDG 302

Query: 170 LTESFR--MRRIQKIYWSLVWGIPK------------------------NKKECIANWLL 203
               FR     ++K Y +L  G                                +    +
Sbjct: 303 FARQFRGDDAGVKKEYVALAVGTVPRGDVVAFSSEAEEVRDDDDDAAAAAAAAAVGRAFV 362

Query: 204 KKSHIGGD-------------------YVHVVKQNEKGANYAISHFKVI----DCFAQKF 240
             +HIG                            +      A +   V            
Sbjct: 363 VDAHIGDHATMPEARAVHPPPLVASTTRATDPSADASAPKPATTACVVSSSAAARDGLVA 422

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN-------------- 286
             +   P TGRTHQ+R+H      PI+ D  Y  + +    +  +N              
Sbjct: 423 ALVRCAPRTGRTHQIRLHLALANLPILSDPLYGPHVRFGGAAMAENARGKAGGEEEDGGG 482

Query: 287 ----------------------KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDSLG 323
                                 +  LHA  + + HP+    +   APLP  M +   +LG
Sbjct: 483 GGDRGYFAAELEGYWGGDLWLGRQALHAASLTVRHPKTDVSMTFRAPLPEDMRRACVALG 542

Query: 324 FKYD 327
              D
Sbjct: 543 VDPD 546


>gi|254967063|gb|ACT97569.1| ribosomal large subunit pseudouridine synthase D [uncultured
           organism]
          Length = 133

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 31/123 (25%), Positives = 52/123 (42%), Gaps = 14/123 (11%)

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V  +     +A++H++V++        +E    TGRTHQ+RVH  H+G  +  D +
Sbjct: 1   MQMAVMSDPTVGKHAVTHYRVLERLG-YVTLVECILETGRTHQIRVHMKHIGHVLFNDER 59

Query: 272 YCAN--FKGNFTSPIQN----------KLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT 318
           Y  +   KG   S  +           +  LHA  +   HP  G  +  T+ LP  M + 
Sbjct: 60  YGGHEILKGTHFSKYKQFVNNCFDTCPRQALHAMTLGFVHPVTGEEMYFTSELPDDMTRL 119

Query: 319 WDS 321
            + 
Sbjct: 120 IEK 122


>gi|209880932|ref|XP_002141905.1| RNA pseudouridylate synthase family protein [Cryptosporidium muris
           RN66]
 gi|209557511|gb|EEA07556.1| RNA pseudouridylate synthase family protein [Cryptosporidium muris
           RN66]
          Length = 527

 Score =  106 bits (266), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 54/331 (16%), Positives = 109/331 (32%), Gaps = 92/331 (27%)

Query: 18  NMRL-DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALN 75
              L D +    +        QK +  G++ V+ K +   ++ I +G ++R         
Sbjct: 74  GKTLYDIF-SKEFRTRPINEYQKAVNCGKISVNGKPINSLDHHIFNGDIIRH-------- 124

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFL 133
                      S+ +   +     ++LY +       KP GI              +  +
Sbjct: 125 ----------ESLMIELPAPLDNVVILYNNKHFLAVYKPYGIPCHPQGRFHKLSLTNIVM 174

Query: 134 KSWVDSKGQ-----------------KPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
             +  S+ +                      +RLD+ TSG++++++   + + L++    
Sbjct: 175 SKYFRSETEVIIDNKAASRIINDDKLYAHPINRLDRVTSGLVILSKNCDSTRLLSKVIS- 233

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSH------------------------IGGDY 212
            +  K Y + V G   + +      L K +                         I  D 
Sbjct: 234 -KSHKYYLAHVEGDFSSLEHVDIGKLFKSTQLVKIQNLEMGLNINFGIKCEAPLEIIKDR 292

Query: 213 VH---VVKQNEKGANYAISH-----------------------FKVIDCFAQKFCWLEMQ 246
           V    + K + +    A++                        F+ I+   +   ++  +
Sbjct: 293 VGDSLMTKVSFENGKSALTWFFPLKIEYLSQEDRKKIKLDQVNFESINICHKPNSYVLCK 352

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           P TGRTHQ+R H  ++G P+  DH Y  N K
Sbjct: 353 PVTGRTHQIRAHLQYLGFPVTLDHLYSLNRK 383


>gi|126433880|ref|YP_001069571.1| pseudouridine synthase [Mycobacterium sp. JLS]
 gi|126233680|gb|ABN97080.1| pseudouridine synthase [Mycobacterium sp. JLS]
          Length = 287

 Score =  106 bits (266), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 57/271 (21%), Positives = 98/271 (36%), Gaps = 22/271 (8%)

Query: 41  LRSGQVRVD-----KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHS 94
           LR G V V+      + V    ++  G V+           ++     +    +L  +  
Sbjct: 22  LRGGAVLVELADRFGEAVAA--KVFDGGVLTADGSAVTPATVLPPGTHVYLYRDLPVEVP 79

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                 +L+ D  I V +KP  ++    G  +A      L+  +D    +    HRLD+ 
Sbjct: 80  VPFAMPVLHRDDNIVVVDKPHFLATMPRGRHVAETAVVRLRRALDL--PELSPAHRLDRL 137

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           T+G+L+    R         F    + K+Y +   G        +    + +S I  +  
Sbjct: 138 TAGVLLFTTRREIRGAYQTMFSDGAVAKVYLARSAGHA-----TVDLPTVVRSRIIKERG 192

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +      G   A +  + +           + P TGRTHQLRVH   +G P++GD  Y 
Sbjct: 193 RLQAFEAPGEPNAETLVEHL-----GDDVYRLTPRTGRTHQLRVHMASLGLPLLGDPLY- 246

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            +            L L A  ++   P  GR
Sbjct: 247 PDVIDVAPDDFSTPLQLLANSIEFDDPLTGR 277


>gi|308176219|ref|YP_003915625.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
 gi|307743682|emb|CBT74654.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
          Length = 350

 Score =  106 bits (266), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 53/272 (19%), Positives = 92/272 (33%), Gaps = 33/272 (12%)

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           Q+V +  V       + E + +    +L  +     ++ +L++D  + V +KP  +    
Sbjct: 53  QIVGLGGVPLTRQTPLGEHEFIWYYRSLPVETPIPFEARILHQDEHLLVVDKPHFLPTTP 112

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           G G        ++    +        HRLD+ T+G+++ A            F  R I K
Sbjct: 113 G-GRFIQESALVRLRNQTGIDDLVPMHRLDRATAGVILFAVNPQTRGDYQMLFERREIAK 171

Query: 182 IYWSLVWGIPKNKKEC------------------IANWLLKKSHIGGDYVHVVK-----Q 218
            Y ++V   P    E                   +   L        + +  VK      
Sbjct: 172 RYKAVVALQPGEGLETGRVLQPNGEHSQVKSQSELRELLAGMPLAFENRMTKVKGQLRSV 231

Query: 219 NEKGANYAISHFKVID-------CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            E G   A +   V             +   ++++P +G+THQLRVH   +G  I+ D  
Sbjct: 232 VEDGHPNAQTLINVEAIGTSSGFHAGLEVALMDLEPRSGKTHQLRVHLASLGLGIINDAF 291

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           Y            Q  L L A  +    P  G
Sbjct: 292 Y-PRLWDLAPDDYQRPLQLLAHTISFTDPLTG 322


>gi|308811949|ref|XP_003083282.1| pseudouridine synthase family protein (ISS) [Ostreococcus tauri]
 gi|116055161|emb|CAL57557.1| pseudouridine synthase family protein (ISS) [Ostreococcus tauri]
          Length = 267

 Score =  106 bits (265), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 57/256 (22%), Positives = 94/256 (36%), Gaps = 46/256 (17%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK---------GQKPRLTHRLDQE 153
           Y D  ++V  KP    V      A   DG ++   D++         G++ R  HRLD++
Sbjct: 8   YADDDVFVLVKPTRAYV-DDVIDAVRTDGVVRVIRDAREGGRETKLCGEEARCCHRLDRD 66

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY- 212
           TSG L+ AR   A + L   F    + K Y +L   +    +    +  L +   G    
Sbjct: 67  TSGALIFARNGNAVKSLAGQFARGTVTKRYVALCAVVDDADEGTWGSGDLVRVESGHGRA 126

Query: 213 ---------VHVVKQNEKG---ANYAISHFKV---IDCFAQKFC------------WLEM 245
                    V+ V ++  G       ++  +V   ++    ++C                
Sbjct: 127 RYGLYRLYDVNDVDRDLPGNNRVKRCVTTIRVERVVEGVELEYCEPERDGSNARLALARC 186

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-------GNFTSPIQNKLYLHARYMDLP 298
            P TGRTHQ+R+H   +G P+ GD +Y    +                   LHA  +   
Sbjct: 187 SPITGRTHQIRLHCASLGLPLAGDVRYGGPIRVKSCASASTSAIGDLPGALLHAEAITFR 246

Query: 299 HPEGGR-LQITAPLPA 313
           HP  G  + +T   P 
Sbjct: 247 HPRTGEDVTVTVDPPD 262


>gi|226941112|ref|YP_002796186.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
 gi|226716039|gb|ACO75177.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 236

 Score =  106 bits (265), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 52/199 (26%), Positives = 81/199 (40%), Gaps = 15/199 (7%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGIL 158
            L+ E +   V +K  G  V           G +    D  G     L HRLD  TSG+L
Sbjct: 3   RLVDEQAAFLVIDKAPGTHVHRDG----EATGLMDRLRDDTGCDTLHLVHRLDAMTSGLL 58

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           +VAR+  AA  L ++   R+++K Y +L    P+ K+  +   + +        +   + 
Sbjct: 59  LVARSADAAAALGQALAARQVEKFYLALSDRSPRKKQGWVIGDMERSRRASWKLLPTRQD 118

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                  A++ F              ++P TGRTHQLRV    +G PI GD  Y     G
Sbjct: 119 ------PAVTQFFS-AAAGDGRRLFLLRPRTGRTHQLRVALKSLGAPIWGDPLYHPQEPG 171

Query: 279 NFTSPIQNKLYLHARYMDL 297
                  ++ YLH+  +  
Sbjct: 172 R---EAPDRGYLHSYGIGF 187


>gi|282851241|ref|ZP_06260606.1| RNA pseudouridine synthase [Lactobacillus gasseri 224-1]
 gi|282557209|gb|EFB62806.1| RNA pseudouridine synthase [Lactobacillus gasseri 224-1]
          Length = 151

 Score =  106 bits (265), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 37/150 (24%), Positives = 62/150 (41%), Gaps = 13/150 (8%)

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGG 210
             T+G+L+VA+  A    L      + + + Y + V       +   I+  +        
Sbjct: 1   MLTNGLLLVAKNPAVVPILNRQLTNKTLHREYLAWVSKSNQLKQSGTISLSIGHDPDDQR 60

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
             +  +         AI+H++VI     K   +++   TGRTHQ+RVH   +G PI+GD 
Sbjct: 61  KRMVRL-----DGQKAITHYEVIKECENKE-LVKLTLETGRTHQIRVHLAALGAPIIGDP 114

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
            Y  N++         KL L A  +    P
Sbjct: 115 LYNPNYQNG------EKLQLTAYQLTFMGP 138


>gi|192288639|ref|YP_001989244.1| pseudouridine synthase [Rhodopseudomonas palustris TIE-1]
 gi|192282388|gb|ACE98768.1| pseudouridine synthase [Rhodopseudomonas palustris TIE-1]
          Length = 322

 Score =  106 bits (265), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 40/154 (25%), Positives = 69/154 (44%), Gaps = 4/154 (2%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
            D         D +++ +LY D  + V +KP G+ V  G     +++    +      + 
Sbjct: 6   PDQFEPPELTPDEIQARVLYRDGLMLVIDKPPGLPVHRGPKGGPNLEASFDALRYGLPRP 65

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P L HRLD++TSG LV+ R R A   L   F+  RI K YW++V G P   +  I   + 
Sbjct: 66  PVLAHRLDRDTSGCLVLGRHRKATATLGLLFKHSRISKTYWAIVEGGPTEDQGSIDLPIA 125

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           K +   G +  V    +     +++ ++V+    
Sbjct: 126 KLNAERGWWQKV----DPEGLPSLTKWRVMGRSG 155



 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 27/58 (46%), Positives = 36/58 (62%), Gaps = 5/58 (8%)

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            WL ++P TGRTHQLRVH   MG PI+GD+ Y      N     + +L+LHAR + +P
Sbjct: 240 TWLALEPITGRTHQLRVHCAAMGWPILGDNIYG-----NGPRFGEPRLHLHAREIVIP 292


>gi|222823998|ref|YP_002575572.1| ribosomal large subunit pseudouridine synthase [Campylobacter lari
           RM2100]
 gi|222539220|gb|ACM64321.1| putative ribosomal large subunit pseudouridine synthase
           [Campylobacter lari RM2100]
          Length = 250

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 57/263 (21%), Positives = 107/263 (40%), Gaps = 55/263 (20%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+    + ++  G V    K+V          V+    + +    ++++ K         
Sbjct: 15  ISNNAAKDLIDKGCVFAMGKKV----------VIARALMSSKTRFVVQKIK--------- 55

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                 K+ +L+ED KI   NKP G            I   L+   ++K     L +RLD
Sbjct: 56  ------KAKILFEDDKIIALNKPYG-----------EISENLEDVYNAK-----LINRLD 93

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +ETSG+L++++         + ++ + + K Y ++V G+   + E        K+  G  
Sbjct: 94  KETSGVLLLSKDEEFRLKCIQEYKKQNVYKSYLAIVDGVIAEELEICEKITTIKNKSG-- 151

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
                 + +K    A +    +   A+K   ++    TGRTHQ+RVH  H+   I+GD K
Sbjct: 152 ---AFSKIDKFGLEAHTQVVPLMVNAKK-TLIKAIIKTGRTHQIRVHLNHIKHGIIGDEK 207

Query: 272 YCANFKGNFTSPIQNKLYLHARY 294
           Y             ++++LH+  
Sbjct: 208 Y--------AKISSSRMFLHSYE 222


>gi|39933287|ref|NP_945563.1| pseudouridine synthase:pseudouridine synthase Rlu [Rhodopseudomonas
           palustris CGA009]
 gi|39652912|emb|CAE25654.1| Pseudouridine synthase:Pseudouridine synthase, Rlu
           [Rhodopseudomonas palustris CGA009]
          Length = 324

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 40/154 (25%), Positives = 69/154 (44%), Gaps = 4/154 (2%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
            D         D +++ +LY D  + V +KP G+ V  G     +++    +      + 
Sbjct: 6   PDQFEPPELTPDEIQARVLYRDGLMLVIDKPPGLPVHRGPKGGPNLEASFDALRYGLPRP 65

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           P L HRLD++TSG LV+ R R A   L   F+  RI K YW++V G P   +  I   + 
Sbjct: 66  PVLAHRLDRDTSGCLVLGRHRKATATLGLLFKHSRISKTYWAIVEGGPTEDQGSIDLPIA 125

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           K +   G +  V    +     +++ ++V+    
Sbjct: 126 KLNAERGWWQKV----DPEGLPSLTKWRVMGRSG 155



 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 27/58 (46%), Positives = 36/58 (62%), Gaps = 5/58 (8%)

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            WL ++P TGRTHQLRVH   MG PI+GD+ Y      N     + +L+LHAR + +P
Sbjct: 242 TWLALEPITGRTHQLRVHCAAMGWPILGDNIYG-----NGPRFGEPRLHLHAREIVIP 294


>gi|290976301|ref|XP_002670879.1| predicted protein [Naegleria gruberi]
 gi|284084442|gb|EFC38135.1| predicted protein [Naegleria gruberi]
          Length = 464

 Score =  106 bits (264), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 53/265 (20%), Positives = 97/265 (36%), Gaps = 52/265 (19%)

Query: 38  QKILRSGQVRVDKKRVKF----NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
           ++++  G + +  ++         +++S   +      N    + +E             
Sbjct: 107 KEMIEKGIITLTTQKPTSVSVLEYKLRSNDQIVTVDWKNEKPVLYRE------------- 153

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                  +LY D +  V +KP+ I V        +   +L     + G+K  L HRLD+ 
Sbjct: 154 ----FIRVLYHDDEFLVIDKPSSIPVHPAGRFVKNSLHYL--LESALGRKLFLIHRLDKV 207

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN------------------KK 195
           TSG+L+     A A+   ++ +   ++K Y + V+G                       K
Sbjct: 208 TSGVLIHTWNAALAKSYQDTMKEGNVRKCYLAQVYGEFPETENMSGEHVLLNGQSFHKDK 267

Query: 196 ECIANWLLKKSHIGGDYVHVVK----------QNEKGANYAISHFKVIDC-FAQKFCWLE 244
           E   +   K  +   D+  + +           + K  + A +  K I    A     + 
Sbjct: 268 EGFIHVKNKMVYKQNDWTFIWRADSSENGSDSTDPKNTDTAYTLVKRIYYDPASSRSIVI 327

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGD 269
             P TGRTHQ+R H   MG PI+ D
Sbjct: 328 AIPITGRTHQIREHLRVMGYPIIND 352


>gi|294877459|ref|XP_002767995.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239870127|gb|EER00713.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 439

 Score =  106 bits (264), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 56/289 (19%), Positives = 98/289 (33%), Gaps = 59/289 (20%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-------------------------- 126
             D     +L+E   + V  KPA   V   S IA                          
Sbjct: 112 EMDTTVPAVLHETKHLSVIWKPAHWHVSVTSAIAGAAEGEVDDATDEEAEAKDAAFKTMT 171

Query: 127 --YHIDGFLKSWVDS----------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                   L+ WV+           +     + HRLD  TSG L++A +          F
Sbjct: 172 SANGNASGLQEWVEEAYSGYPIARDRHHAHGILHRLDVGTSGPLLLAHSYKGFYMGRLVF 231

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIAN----WLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
              +I K Y +LV G      + I       +LK +   G               +++  
Sbjct: 232 CSHQIDKEYVALVKGHMGTVGKNIVISDRIKILKSTLDNGQSYSTTCVVAPDGKPSLTEV 291

Query: 231 KVIDCF----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPI 284
             +  +     +++  + ++ HTGRTHQ+RVH  ++G P+V D KY    + +       
Sbjct: 292 VPVAHYNDGSGEEYSLVLVKLHTGRTHQIRVHMAYIGHPLVCDPKYGNPTDPEAAKAVCA 351

Query: 285 QNKLYL-----HARYMDLPHP------EGGRLQITAPLPAHMVKTWDSL 322
            ++L+      H+  +    P      +   + +  P+P  +      L
Sbjct: 352 IDRLWCPRTFLHSYRLCYNQPMDVVDEKDATVDVYVPMPLDLRLALAKL 400


>gi|309808140|ref|ZP_07702052.1| RNA pseudouridine synthase [Lactobacillus iners LactinV 01V1-a]
 gi|308168609|gb|EFO70715.1| RNA pseudouridine synthase [Lactobacillus iners LactinV 01V1-a]
          Length = 194

 Score =  106 bits (264), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 40/195 (20%), Positives = 75/195 (38%), Gaps = 22/195 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              + V+ K +  N ++ +  ++ I      LNH+   Q+   +S N+          ++
Sbjct: 17  EKNILVNDKYLPLNFKVHTNDLITI-----KLNHVESLQQQYPASGNMPN--------II 63

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           YE+  + V NKPAG          Y  D  L       G  P + HRLD  T+G+L+VA+
Sbjct: 64  YENDDVLVINKPAGQKTHPN---LYETDTALNDCASYLGYSPYIVHRLDMLTNGLLLVAK 120

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEK 221
             A    L +    + + + Y++ +      +    I   +          +        
Sbjct: 121 NPAVVPILNKQLIDKTLSRSYFAWIEATNDISDNGTINLPIGDDPLDMRKRMVRA----- 175

Query: 222 GANYAISHFKVIDCF 236
               AI+H++V+   
Sbjct: 176 DGLKAITHYQVVKKQ 190


>gi|149002475|ref|ZP_01827409.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP14-BS69]
 gi|147759412|gb|EDK66404.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP14-BS69]
          Length = 127

 Score =  105 bits (263), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 29/125 (23%), Positives = 60/125 (48%), Gaps = 6/125 (4%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKSWVDSKGQ----KPRLT 147
           ++ L   ++Y+D  + V NKP G+ V   +G      ++  +    D  G     +P + 
Sbjct: 2   AEDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIV 61

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           HR+D++TSG+L++A+   A   L +  + ++  + YW++V G   N +  I   + +   
Sbjct: 62  HRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEK 121

Query: 208 IGGDY 212
              + 
Sbjct: 122 DRKNR 126


>gi|68171700|ref|ZP_00545058.1| Pseudouridine synthase [Ehrlichia chaffeensis str. Sapulpa]
 gi|67998881|gb|EAM85575.1| Pseudouridine synthase [Ehrlichia chaffeensis str. Sapulpa]
          Length = 146

 Score =  105 bits (263), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 46/149 (30%), Positives = 75/149 (50%), Gaps = 9/149 (6%)

Query: 174 FRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI 233
           F+ RR++K Y +L  GIPKN    I + ++K        + + K N+     A++ F V+
Sbjct: 3   FKNRRVEKKYLALTQGIPKNDIGQINHSIIKN----KRSLSLDKVNDSYLQEAVTSFSVL 58

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
                    LE++P TGR HQ+R+H  H+GC I+GD KY    +      +Q    LHA 
Sbjct: 59  KKLPYGIGLLELKPITGRKHQIRIHLSHIGCSIIGDKKYGKFCEHVLNDNLQ----LHAY 114

Query: 294 YMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           ++ +   E  ++  T P+P++M      L
Sbjct: 115 FLSINIGE-KKIDFTVPVPSYMKDAIMQL 142


>gi|42522740|ref|NP_968120.1| methyltransferase [Bdellovibrio bacteriovorus HD100]
 gi|39573936|emb|CAE79113.1| methyltransferase [Bdellovibrio bacteriovorus HD100]
          Length = 521

 Score =  105 bits (263), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 49/209 (23%), Positives = 91/209 (43%), Gaps = 20/209 (9%)

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           E +     +K AG++        Y   G ++ + +   +K    HRLD+ TSG LV A +
Sbjct: 11  EIAGCIFVDKIAGLNTH---TPEYGQRGCVEIYEEELDRKLYTVHRLDKATSGALVFATS 67

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
              A  LT++F   +++K Y  L        +    +++ K+ +     V V +  ++  
Sbjct: 68  SEIAAQLTQAFEQHKVEKKYLFLTDKKIARTEFTYESFIQKEKN-----VFVSRDTQEP- 121

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
             + + FK +      +   E  PHTG+ HQ+R+HA   G  ++GD  +           
Sbjct: 122 -NSKTSFKWVKALG-PYQLWEAVPHTGKPHQIRLHAEANGIAVLGDSDHNGTNHF----- 174

Query: 284 IQNKLYLHARYMDLPHPEGGRLQITAPLP 312
              +L LH++ +      G +++   PLP
Sbjct: 175 ---RLCLHSQVLGFE-LNGQKVRYETPLP 199


>gi|301167892|emb|CBW27477.1| putative ribosomal large subunit pseudouridine synthase
           [Bacteriovorax marinus SJ]
          Length = 291

 Score =  105 bits (263), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 50/288 (17%), Positives = 109/288 (37%), Gaps = 49/288 (17%)

Query: 32  INFVNLQKILRSGQVR--VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVN 89
            +   ++++L    ++  V+K           G  + +P  +     +            
Sbjct: 25  FSKSIVKRLLSKNFLKRGVNK-----------GDELSLPLDLLNYQWV------------ 61

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWV-------DSKG 141
                +    +++ ED      NK  GI            +  FL++         +SK 
Sbjct: 62  -NPSYEGESMMVIKEDDNFIAINKQHGIHGHPLNYSERNTVVNFLRNQFCLSAFLDESKR 120

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +  L +R+D+ETSG+++ A+  +  + + ++F     +K+Y ++V G     +E + + 
Sbjct: 121 GESNLLYRIDRETSGLMIFAKKNSIYESIRQNFNHMVKEKVYLAVVEGEF--NQEGVHSH 178

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
            L+     G  +      E+  +   S  +  +   +    + ++   G  HQ+R     
Sbjct: 179 YLESFGKKGAQMRAASSGEERVSIKTSLVEYNEQ--RGLSLIRIELGQGVRHQIRCQLSE 236

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           +G PIVGD  Y             ++L+LHA    +   +   +Q +A
Sbjct: 237 IGFPIVGDTLYGGCE--------SSRLFLHAYEYRIEVDD---IQFSA 273


>gi|255527012|ref|ZP_05393904.1| RNA-binding S4 domain protein [Clostridium carboxidivorans P7]
 gi|255509322|gb|EET85670.1| RNA-binding S4 domain protein [Clostridium carboxidivorans P7]
          Length = 173

 Score =  105 bits (263), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 37/158 (23%), Positives = 68/158 (43%), Gaps = 19/158 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+ +EE M+L  + K+     +   ++     G++ V+  RVK N  I+    +      
Sbjct: 32  VKGNEEGMKLRAYLKDVQKLSSR-LIKGAALDGRISVNNNRVKLNYVIKLDDEIAFDVEK 90

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HID 130
               +I  E+               +   ++YEDS + V NK  G+ V          + 
Sbjct: 91  KESQNIEPEK---------------MDIDVVYEDSDLIVVNKQPGMVVHPTKSYPNGTLA 135

Query: 131 GFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAA 166
             L  +   KG++   RL  RLD +TSG++++A+ + A
Sbjct: 136 NGLLYYFKEKGEQCIVRLVSRLDMDTSGLIIIAKNQFA 173


>gi|124506351|ref|XP_001351773.1| ribosomal large subunit pseudouridylate synthase, putative
           [Plasmodium falciparum 3D7]
 gi|23504702|emb|CAD51580.1| ribosomal large subunit pseudouridylate synthase, putative
           [Plasmodium falciparum 3D7]
          Length = 487

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 51/191 (26%), Positives = 80/191 (41%), Gaps = 6/191 (3%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
           +  L K        ++YE+    V NKP  I ++ G     +       +   K    R+
Sbjct: 52  TTPLYKSYKGHDLKIIYENDYFLVLNKPYDIKLEKGKLDDIYPSVETLLYQKRKLDVFRI 111

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
             +LD  TSG+L+VA+ + +   L  +   + I KIY ++++G        I   + K  
Sbjct: 112 CGQLDYATSGLLIVAKDKLSCNILNYNIESKNISKIYLAILYGHLPLDILHINTPISKN- 170

Query: 207 HIGGDYVHVVKQNE--KGANYAIS---HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH 261
             G         N+      Y  S    +K      +K    EM+  TGR HQLR+H+L 
Sbjct: 171 KEGFKMKLCYNYNDYYDNGKYCYSLIYPYKHSYINNEKVTLCEMRTVTGRRHQLRLHSLS 230

Query: 262 MGCPIVGDHKY 272
           +G  IVGD  Y
Sbjct: 231 LGSSIVGDETY 241


>gi|221056917|ref|XP_002259596.1| ribosomal large subunit pseudouridylate synthase [Plasmodium
           knowlesi strain H]
 gi|193809668|emb|CAQ40369.1| ribosomal large subunit pseudouridylate synthase, putative
           [Plasmodium knowlesi strain H]
          Length = 504

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 66/288 (22%), Positives = 114/288 (39%), Gaps = 32/288 (11%)

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +     D+     K        ++YE+    V NKP  I ++ G     +          
Sbjct: 46  ENPSPGDNPQPEYKSYKGHNLSIIYENEFFLVVNKPYDIKLEKGKLDDVYPSVETLLRQK 105

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +     R+  +LD  TSG+L++A+ + +   L  +   +RI KIY ++++G        +
Sbjct: 106 TNLDVFRICGQLDYATSGLLIIAKDKLSCNILNYNIESKRISKIYLAILYGHLPLGVLHV 165

Query: 199 ANWLLKKSHIGGDYVHVVKQN-------EKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
              +   S I  ++   +  N        K     I  +K      QK    E++  TGR
Sbjct: 166 NTPI---SKIKNNFKMKLCYNYNDYYDTGKYCYSLIYPYKQCYLKNQKVTLCELRTITGR 222

Query: 252 THQLRVHALHMGCPIVGDHKYCANF------KGNFTSPIQNK---LYLHARYMDLPHPEG 302
            HQLR+HAL +G  IVGD  Y  +        G+ ++P + +   L    +       + 
Sbjct: 223 RHQLRLHALCLGSGIVGDETYFEDMISNKYKIGSTSNPCEERIGLLAEEDQQDRFLDTQV 282

Query: 303 GRLQ-ITAPLPAHMVKTWDSLGFKYDR----------NLYIKRLYSQD 339
           GR+  I A     M+  W  L  K D+          N+  K+++ QD
Sbjct: 283 GRITKIDAE--RMMLHCWIILKNKADQKKELKKTEDINMLEKKIFDQD 328


>gi|293331663|ref|NP_001167875.1| hypothetical protein LOC100381582 [Zea mays]
 gi|223944581|gb|ACN26374.1| unknown [Zea mays]
          Length = 237

 Score =  105 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 53/194 (27%), Positives = 80/194 (41%), Gaps = 54/194 (27%)

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE---KGANYAISHFKVIDCFA 237
           + YW+LV G PK ++  I+  + K     G    V+  +     GA  AI+ ++V+    
Sbjct: 37  QKYWALVIGTPKEREGVISAPISKVLLDDGKAERVILAHPSGIDGAQEAITEYRVMGPTI 96

Query: 238 QKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYC------------ANFKGNFTSPI 284
               W+E+QP TGR HQLRVH    +G PIVGD+KY              +F+     P 
Sbjct: 97  NGCSWIELQPLTGRKHQLRVHCAEALGTPIVGDYKYGWFVHQTWKQNPQPDFEPFTGEPY 156

Query: 285 QNK------------------LYLHARYMDLPH----------------PEGGR----LQ 306
           + +                  L+LH R M +P+                P        L+
Sbjct: 157 KLRRPEGLEIQKGSVLSKVPLLHLHCREMVIPNIAKFLSSTGGWHENGTPWAKEKPNLLR 216

Query: 307 ITAPLPAHMVKTWD 320
             AP+P HM  +W+
Sbjct: 217 FVAPMPPHMKISWN 230


>gi|312376036|gb|EFR23246.1| hypothetical protein AND_13247 [Anopheles darlingi]
          Length = 327

 Score =  105 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 52/239 (21%), Positives = 89/239 (37%), Gaps = 44/239 (18%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----RLTHRLDQE 153
             +LY      V NK   + +         +   ++       Q          HRLD  
Sbjct: 52  VDVLYTSGNFLVINKKHDLLINSNDTKKKTVQTIMRKQFPEYVQDNLTHDFYFAHRLDFA 111

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH------ 207
           TSGIL +   + A + + + F  +R +K Y +L+ G     +E I   + K+S       
Sbjct: 112 TSGILCIPLNKNACKEVCQVFEEQRARKYYLALLRGHTDFDEEVIDIAIGKRSDGSSIGT 171

Query: 208 --------------IGGDYVHVVKQNEK-----------GANYAISHFKVIDC---FAQK 239
                         + G+ V     ++K               +I+   V+D      + 
Sbjct: 172 CVPERLTNFTILSSVPGEDVRFKDTSKKMCTILEEERCQNPRRSITKVLVLDRGYYNGKP 231

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
              + ++P TGR HQLR+H   +G  IVGD+ Y      +       +++LHA  + LP
Sbjct: 232 VTKVLLRPITGRRHQLRLHCAQIGHVIVGDYTYSLKIDTSPP-----RMFLHAFRLVLP 285


>gi|145353632|ref|XP_001421111.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|145357270|ref|XP_001422843.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144581347|gb|ABO99404.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144583087|gb|ABP01202.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 213

 Score =  105 bits (261), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/192 (26%), Positives = 82/192 (42%), Gaps = 36/192 (18%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +PR  HRLD+ T G+LV A+TR A   L+ +F  R ++K Y +++ G  ++KK  +   L
Sbjct: 42  RPRPVHRLDELTGGLLVCAKTRMAMTALSAAFEKREVRKRYRAVLRGRVESKKGVVDVPL 101

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVI-----DCFAQKFCWLEMQPHTGRTHQLRV 257
                              G   A++ + V+     + +      ++  P TGRTHQLR 
Sbjct: 102 -------------------GGLEALTEYSVVREYESEEYGGILTLIDFFPKTGRTHQLRR 142

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-------GRLQITAP 310
           HA  +  PI+GD KY    + +     ++ L+L A  + LP           G L +   
Sbjct: 143 HAKALCAPILGDVKYDYASRAH-----EDGLFLWATGIVLPPSATPWRGEDCGELIVDIE 197

Query: 311 LPAHMVKTWDSL 322
                 +     
Sbjct: 198 EGEKFARVLARC 209


>gi|307107653|gb|EFN55895.1| hypothetical protein CHLNCDRAFT_145520 [Chlorella variabilis]
          Length = 274

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 59/250 (23%), Positives = 99/250 (39%), Gaps = 25/250 (10%)

Query: 109 YVFNKPAG-ISVQGGSGIAYHIDG----FLKSWVDSKGQ-------KPRLTHRLDQETSG 156
            + + PAG + V    G+ +H  G     ++     +GQ            HRLD   SG
Sbjct: 15  LLHHSPAGCVIVHKPPGVPFHATGDQPGLMQLIRSQQGQAHLPYEGPLWPVHRLDLICSG 74

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH-----IGGD 211
            +V+A  + AA  L  +FR R++ K Y +L    P  K   +A  + +            
Sbjct: 75  CVVLATRQEAAGELIGAFRQRQVHKYYCALSDRRPSKKMGSVAGEMQRGRRGAWMLARSS 134

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE--MQPHTGRTHQLRVHALHMGCPIVGD 269
                         A++ F        +       ++P TGRTHQLRV    +G P++GD
Sbjct: 135 AAPAADAPAPPVYKAVTRFTSTAVLGSRPGLRAFLLKPETGRTHQLRVALKSLGSPVLGD 194

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRN 329
            +Y       +    + + YLH   +      G  +Q+  P P H  +  DS GF+   +
Sbjct: 195 ERYAQKEAAAW----EERAYLHCAALRFE-LGGAAVQVVCP-PEHGAEFADSPGFRAVFD 248

Query: 330 LYIKRLYSQD 339
            ++ +   Q+
Sbjct: 249 AWLPQSMEQE 258


>gi|322788452|gb|EFZ14121.1| hypothetical protein SINV_06605 [Solenopsis invicta]
          Length = 299

 Score =  104 bits (259), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 44/219 (20%), Positives = 85/219 (38%), Gaps = 17/219 (7%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-----GFLKSWVDSK-GQKP 144
            KH+      +++      + +KP  + +   +    +         L   V+ +   + 
Sbjct: 41  EKHTSARSVRIMHRSENFLIVDKPYDMYINSNNPDRKNTLQTELREMLPDLVNPRLCHEF 100

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRLD  TSG++ +A  + AA+  + +F   ++QK Y +LV G        I   +  
Sbjct: 101 HFVHRLDYPTSGVMCIALNKRAARAASFAFENHKVQKFYLALVHGHIHEPHIVIDRPIGA 160

Query: 205 KSHIGGDYVHVVKQNE---KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVH 258
                     +   +         + +   V++      +    + + P TGR HQLRVH
Sbjct: 161 DIREKTGNHKMCTSDSAFCDKPRKSYTTLVVLEHGYWKGKPATKILLAPGTGRRHQLRVH 220

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             H+G  ++GD+ Y             ++ YLH+  + L
Sbjct: 221 CHHIGHTVIGDYTYSEGKDVE-----PHRTYLHSLRLIL 254


>gi|149002476|ref|ZP_01827410.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP14-BS69]
 gi|147759413|gb|EDK66405.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP14-BS69]
          Length = 93

 Score =  104 bits (259), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 30/97 (30%), Positives = 50/97 (51%), Gaps = 7/97 (7%)

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           + F V++ F   +  +E+Q  TGRTHQ+RVH  ++G P+ GD  Y         +   + 
Sbjct: 2   TRFHVLERFGD-YSLVELQLETGRTHQIRVHMAYIGHPVAGDEVYGPR-----KTLKGHG 55

Query: 288 LYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG 323
            +LHA+ +   HP  G+ L+  A +P    +T + L 
Sbjct: 56  QFLHAKTLGFTHPRTGKTLEFKADIPEIFKETLERLR 92


>gi|242024726|ref|XP_002432777.1| Ribosomal large subunit pseudouridine synthase A, putative
           [Pediculus humanus corporis]
 gi|212518286|gb|EEB20039.1| Ribosomal large subunit pseudouridine synthase A, putative
           [Pediculus humanus corporis]
          Length = 227

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 39/157 (24%), Positives = 75/157 (47%), Gaps = 11/157 (7%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
              HRLD  TSG++ VA ++ +    + +F+ +  +K Y +L+ G    ++  +   + +
Sbjct: 37  YFPHRLDYSTSGVMCVALSKKSCAAASIAFQEKTTKKYYLALLRGHVSKREIELNAPIGE 96

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALH 261
               G   + ++    KGA  A S   V++     +     + ++P TGR HQLRVH   
Sbjct: 97  TIKKG---LKIMSSEVKGALPACSRLLVLERGIYDSYPATKVLLRPLTGRRHQLRVHCNI 153

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           +G  I+GD+ Y      +       +++LH+  + +P
Sbjct: 154 IGHTIIGDYTYSQKKDVSPP-----RMFLHSIRLIIP 185


>gi|148251982|ref|YP_001236567.1| putative RNA pseudouridine synthase [Bradyrhizobium sp. BTAi1]
 gi|146404155|gb|ABQ32661.1| putative RNA pseudouridine synthase (Uracil hydrolyase)
           [Bradyrhizobium sp. BTAi1]
          Length = 295

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 40/139 (28%), Positives = 67/139 (48%), Gaps = 4/139 (2%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           + + +L+ D  + V +KPAGI V  G     +++    +      + P L HRLD+ETSG
Sbjct: 1   MLARVLHRDGLMLVIDKPAGIPVHKGPKGGANLEASFDALRFGLPRPPVLAHRLDKETSG 60

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
            LV+ R R A   L   F+  +I K YW++V G P   +  I   L K +   G +    
Sbjct: 61  CLVLGRHRKATASLGLLFKHGKISKTYWAVVEGGPDADEGVIELPLGKLNAERGWWQ--- 117

Query: 217 KQNEKGANYAISHFKVIDC 235
            + +     A++ ++V+  
Sbjct: 118 -KPDPQGQPAVTKWRVLGR 135


>gi|82752903|ref|XP_727467.1| hypothetical protein [Plasmodium yoelii yoelii str. 17XNL]
 gi|23483320|gb|EAA19032.1| hypothetical protein [Plasmodium yoelii yoelii]
          Length = 588

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 58/267 (21%), Positives = 104/267 (38%), Gaps = 33/267 (12%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKF--------NNRIQSGQVVRIPPVINALNH 76
           F   + +I+  ++++I++        KR KF        N +            +   NH
Sbjct: 3   FSKIFNNISRHHIEQIIQL-------KRSKFRLTRRNFNNYK---------CENMKDQNH 46

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           ++KE      +  L K        + YE+    V NKP  I ++ G     +        
Sbjct: 47  VVKEN-----ATPLYKSYKGHDLKIEYENDYFLVVNKPYDIKLEKGKLDDIYPSVETLLR 101

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                   R+  +LD  TSG+L++A+ + ++  L  +   + I KIY ++++G       
Sbjct: 102 KKRNLNTFRMCGQLDYATSGLLIIAKDKLSSNILNYNIESKNISKIYLAILYGHLPLDVL 161

Query: 197 CIANWLLKKSHIGGDYVHV----VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            I   + K  +     +           K     I  +K      +K    E++  TGR 
Sbjct: 162 HINVPISKVKNEFKMKLCYNYNDYYDTGKYCYSLIYPYKHTYLKNEKVTLCELRTITGRR 221

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGN 279
           HQLR+H++ +G  IVGD  Y  +   N
Sbjct: 222 HQLRLHSICLGSGIVGDETYFEDMIEN 248


>gi|300121551|emb|CBK22070.2| unnamed protein product [Blastocystis hominis]
          Length = 260

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 54/257 (21%), Positives = 103/257 (40%), Gaps = 31/257 (12%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           +++G+ +  P  ++  ++ +K  + + +          +K  +LY D  I V +  +   
Sbjct: 3   MKAGERLLSPCTVHIPDYFVKMNEEMLNMNRPEHLPGDMKDRILYCDDHIIVTDLDS--- 59

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                  A  +   LKS   +    P   HRLD++T+G+L+VAR R  A+ L   F    
Sbjct: 60  -------ARSVISALKSMFSTSLLYP--VHRLDKDTTGVLLVARDRETARALGHEFACHE 110

Query: 179 IQKIYWS----------------LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
           + K+Y +                +V+   +       + +  K       +         
Sbjct: 111 VSKMYLAAGYDVSFSSSHFPRVGIVYSDFEQNAGHFYHAINSKVKPLPTNIFPAHIETSV 170

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYCANFKGNFT 281
           A  A + ++V+     +   L  + ++G+THQ+RVH    +G  ++ D KY    K N  
Sbjct: 171 ATPAATGYEVVK-QKDEIVLLRCRLYSGKTHQIRVHLKDVLGIELLNDSKYGKRRKMNRN 229

Query: 282 SPIQNK-LYLHARYMDL 297
             I  K  YLH   + +
Sbjct: 230 QLIDPKAFYLHCHKISI 246


>gi|297581272|ref|ZP_06943196.1| tRNA pseudouridine synthase C [Vibrio cholerae RC385]
 gi|297534588|gb|EFH73425.1| tRNA pseudouridine synthase C [Vibrio cholerae RC385]
          Length = 172

 Score =  103 bits (258), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 39/168 (23%), Positives = 62/168 (36%), Gaps = 17/168 (10%)

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV 232
            F    ++K Y ++V G  +           +   I   +       +K A  A++ ++ 
Sbjct: 3   MFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQ----DKEAQSAVTAYRP 58

Query: 233 I----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-- 280
           +               ++C +EMQP TGR HQLR H  H+  PIVGD  +          
Sbjct: 59  LAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDTTHGDGVHNRLFR 118

Query: 281 TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
                 +L LHA  +   HP   + L I A L           G++  
Sbjct: 119 EHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 166


>gi|312075546|ref|XP_003140465.1| hypothetical protein LOAG_04880 [Loa loa]
 gi|307764370|gb|EFO23604.1| hypothetical protein LOAG_04880 [Loa loa]
          Length = 479

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 50/297 (16%), Positives = 116/297 (39%), Gaps = 31/297 (10%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           IQS +++ +    +     I ++      ++     + + S ++YED ++  F+KP  ++
Sbjct: 180 IQSFEILDLKTYKDIGLKKIWDKIEPVWRMSDEDLVNVMTSRIIYEDEELIAFDKPYQVA 239

Query: 119 ---VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
                        I   L S +       R+   + +  +G+++ A+ + A + +   + 
Sbjct: 240 YSNAPSNQAELLRILPKLSSRIAPNMDCLRIVKSIGKSVTGVILFAKNQNAQEKIKVLYD 299

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV-----KQNEKGANYAISHF 230
              +++ Y  +    P +++  I   L+K +    +Y+ +       +       A +H+
Sbjct: 300 NGLMEQCYHVITNMAPAHQEAAINIPLVKCTRKNNNYMMLPLGANNSKEIPPFLEASTHY 359

Query: 231 KVIDCFAQKFC-WLEMQPHTGRTHQLRVHA-LHMGCPIVGDHK--YCANFKGNFTSPIQN 286
           +++    +    ++E   +     Q+R H  + + CPI+GD K  Y     G    P  +
Sbjct: 360 RLLKHDPKNHTSYMECFVNRDVPEQIRAHLGIGIACPIIGDVKYNYSRREAGRGIPPRLS 419

Query: 287 -----------------KLYLHARYM--DLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
                             +Y+H + M   L      ++ I APLP+  + T + L  
Sbjct: 420 DSALQDLNIAGNSFRRLPMYIHLKEMVISLSKRSSQKIHICAPLPSFFMYTLNKLRL 476


>gi|288576272|ref|ZP_06394280.1| RNA pseudouridine synthase [Neisseria mucosa ATCC 25996]
 gi|288565855|gb|EFC87415.1| RNA pseudouridine synthase [Neisseria mucosa ATCC 25996]
          Length = 169

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 36/159 (22%), Positives = 68/159 (42%), Gaps = 7/159 (4%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD++T+G+++++   A  +     F+ + + K Y ++        +  +A  L   
Sbjct: 8   PIHRLDKDTAGVMLLSHNPATRRDYQTMFQNKTVCKTYEAI-----APTRTDLAYPLNIS 62

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           S +            +G   A +  ++I+     F    + PHTG+ HQLRVH + +G P
Sbjct: 63  SRMVRGEKFFTTLEVEGEPNAHTTVELIENRG-AFSLYRLTPHTGKKHQLRVHMMSLGMP 121

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           ++ D  Y               L L A+ ++   P  G+
Sbjct: 122 LMNDALY-PVPSAAGDEDYGKPLKLLAKRIEFTDPVSGQ 159


>gi|320581259|gb|EFW95480.1| dolichyl-phosphate beta-glucosyltransferase [Pichia angusta DL-1]
          Length = 898

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 42/218 (19%), Positives = 82/218 (37%), Gaps = 58/218 (26%)

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
           + +++ G V+            + E  I+D+ +             +YED  + V NKPA
Sbjct: 657 SEKLKQGDVIVRHVH-------VHEPPIVDAKIQT-----------VYEDDDVLVVNKPA 698

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G+ +       Y+     K                                A+ +  + +
Sbjct: 699 GMPIHPVQNFYYNTMSVAK--------------------------------AKEIQAAIK 726

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC 235
            ++++K+Y + V G       C  + ++ ++  G         +      A + FK ++ 
Sbjct: 727 NKQVRKVYVARVAGKIPESLVCEDDVVIVETKRGLK-------DGIDRKSATTVFKRLNY 779

Query: 236 FA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            +      +E +P TGRTHQ+R+H  ++G PIV D  Y
Sbjct: 780 SSVLDESIVECRPLTGRTHQIRIHLRNLGFPIVNDQLY 817


>gi|71404491|ref|XP_804947.1| RNA pseudouridylate synthase [Trypanosoma cruzi strain CL Brener]
 gi|70868160|gb|EAN83096.1| RNA pseudouridylate synthase, putative [Trypanosoma cruzi]
          Length = 588

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 61/268 (22%), Positives = 104/268 (38%), Gaps = 50/268 (18%)

Query: 109 YVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVA 161
              NKPAG+S      +AY H+  +L   V  KG       +  L +R+D  TSG+++V 
Sbjct: 316 IAVNKPAGMST--TLHVAYPHLIQYLSRCVPWKGVDIPVLFQHGLVNRIDVGTSGLVLVT 373

Query: 162 RTRAAA-QHLTESFRMRRIQKIYWSLVWGIPK-------------NKKECI--------A 199
            T  +       S   RR++KIY +LV   P              N K  I        A
Sbjct: 374 DTGNSLVATRRASVVDRRVEKIYRALVLHCPPPESRAGSEEFWYLNPKGVINWNVFANGA 433

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVH 258
           ++ L+ +    +    +         A + ++V++ + +    +LE+Q  +GR HQ+R H
Sbjct: 434 DYSLQLAAHDPERKRGLPPAFMDRRPATTMYRVLNYYPSSGVYYLEVQLRSGRRHQIRQH 493

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH------------------P 300
              +  P+VGD +Y    +         +  LHA  + L                     
Sbjct: 494 FAQICHPLVGDGRYHERARSMGEQMGLYRPALHASRITLLPSSLDSATDAIDDASYTRKE 553

Query: 301 EGGRLQITAPLPAHMVKTWDSLGFKYDR 328
           +  +  +  PLP  + +    L  K +R
Sbjct: 554 DSEKTVVECPLPDDIRRALRWLQEKEER 581


>gi|325119975|emb|CBZ55528.1| hypothetical protein NCLIV_059530 [Neospora caninum Liverpool]
          Length = 830

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 63/313 (20%), Positives = 117/313 (37%), Gaps = 62/313 (19%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV------------------DKKRV 53
           VE  +  +R+  +   H    ++  +  +LR  ++ +                  D+   
Sbjct: 199 VEASQAGLRVGIFALRHVVG-SWPAVANLLRKKELFLVRKDAPFAQHVKFLRKQRDRPEA 257

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
             + R+ +G +V  P   +AL+H    ++I   S  L      L+  LLY+D+     +K
Sbjct: 258 SKDARVNAGDLVYFPRGSDALHHA---KEISRPSAGL-----DLRERLLYKDTDFLAIDK 309

Query: 114 PAGISV----------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           P G+                     +         S  + P+L HRL  E +G+L++ RT
Sbjct: 310 PFGLCTGQLRPRGRRAPKKDTEKASVLSLAHQLRFSLDETPKLLHRLGDEVTGVLLLGRT 369

Query: 164 RAAAQHLTESFRMRRI-QKIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +  A    + FR        + +LV G P   ++E +    L ++  G   V V    ++
Sbjct: 370 KQTAALALDRFRGGTFGTVTFLALVHGRPPGGRREGVIRIPLAENEAG---VMVPTAVQR 426

Query: 222 GANYAISHFKVID------------------CFAQKFCWLEMQP-HTGRTHQLRVHALH- 261
           G    ++ ++++                        F  +E++       HQ R H L+ 
Sbjct: 427 GGAAVVTRWRLLKVASAAGRHGCDRESDAHGSAGLGFSLIELEIDQQQCRHQARAHCLYG 486

Query: 262 MGCPIVGDHKYCA 274
           + CPIVGD  Y  
Sbjct: 487 LCCPIVGDRVYGP 499


>gi|192361858|ref|YP_001982092.1| putative pseudouridylate synthase [Cellvibrio japonicus Ueda107]
 gi|190688023|gb|ACE85701.1| putative pseudouridylate synthase [Cellvibrio japonicus Ueda107]
          Length = 291

 Score =  103 bits (257), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 62/305 (20%), Positives = 110/305 (36%), Gaps = 53/305 (17%)

Query: 21  LDR------WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           LDR          H+  ++   L+  +       +K    + ++   G+ +R+      L
Sbjct: 30  LDRPQTAIDALA-HHTGLSRQKLKDAM-------NKGACWWTSK---GKQLRLRRATKDL 78

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK-IYVFNKPAGISVQGGSGIAYHIDGFL 133
               + Q   D  V   K     +     ED     V+ KP G+  QG     +     L
Sbjct: 79  PAGTRLQLFYDEKVLALKPEAPQRL----EDVGRYSVWYKPHGLLAQGSQWGDHC--SLL 132

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +     + ++  L HRLD + +G++++A    AA  L++ F+ R ++K Y + V G  + 
Sbjct: 133 RWVEVVRQRECFLVHRLDADAAGLILIAHDAQAAAALSQLFQGRSLRKHYQAWVSGELQA 192

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTGRT 252
               +   L                       A++     +         ++++  TGR 
Sbjct: 193 TGLRLEQPL-------------------DGKDALTWVNTAVIDQPNNRSLVDVRIETGRK 233

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPL 311
           HQ+R H   +G PI+GD  Y            Q  L L A  +    P   R + I+ P 
Sbjct: 234 HQIRRHLAAIGHPIMGDKLYG--------QANQQPLQLLAWQLGFECPLLKRPITISLPE 285

Query: 312 PAHMV 316
           P    
Sbjct: 286 PLKFR 290


>gi|86151843|ref|ZP_01070057.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|86153369|ref|ZP_01071573.1| hypothetical RNA pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni HB93-13]
 gi|121612323|ref|YP_001000404.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|167005346|ref|ZP_02271104.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|315124210|ref|YP_004066214.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|85841472|gb|EAQ58720.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|85843095|gb|EAQ60306.1| hypothetical RNA pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni HB93-13]
 gi|87249488|gb|EAQ72448.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|315017932|gb|ADT66025.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
          Length = 250

 Score =  103 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 53/220 (24%), Positives = 90/220 (40%), Gaps = 35/220 (15%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED KI   NKP           AY  +         K    +L +RLD+ETSG++
Sbjct: 57  PQIIFEDDKIIAINKP----------YAYVSEDL------EKKFNAKLLNRLDKETSGVI 100

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ +     +   E F+  R+ K Y +++ G+   + E        K+  G      + +
Sbjct: 101 LLCKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKGG-----ALSK 155

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K    A+S    I   ++K    ++   TGRTHQ+RVHA  +   +VGD KY      
Sbjct: 156 VSKDGLSALSIITPIMMQSKK-TLTKIVIQTGRTHQIRVHAKFIKHGVVGDEKY------ 208

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                  +++YLH+  + +           A L     K 
Sbjct: 209 --AKISSDRMYLHSYEIKIFD-----YYFKAELDNSFAKV 241


>gi|188578461|ref|YP_001915390.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae PXO99A]
 gi|188522913|gb|ACD60858.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae PXO99A]
          Length = 206

 Score =  103 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 44/185 (23%), Positives = 77/185 (41%), Gaps = 9/185 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHR 149
            +        +L+ D+ + V  KP  + V      AY  +  L   V           HR
Sbjct: 29  DEPVIPYVETVLHADANLVVACKPHFLPVAPAG--AYVHETLLTRLVRRLDNPALVPLHR 86

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D+ET+G+++ +   A        FR RRI+K Y  +   +P+     ++   + +S + 
Sbjct: 87  IDRETAGLVLFSANPATRGIYQALFRERRIRKQYLVVAPPLPE-----LSFPYVHRSWLE 141

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                   +   G   + +   V+   A  + +  ++P TGR HQLRVH   +G PI+ D
Sbjct: 142 PGEPFFRMREGVGEPNSETVIDVVAPGADTWTY-RLEPVTGRKHQLRVHMAALGAPILHD 200

Query: 270 HKYCA 274
             Y  
Sbjct: 201 RFYPD 205


>gi|325970925|ref|YP_004247116.1| pseudouridine synthase [Spirochaeta sp. Buddy]
 gi|324026163|gb|ADY12922.1| pseudouridine synthase [Spirochaeta sp. Buddy]
          Length = 245

 Score =  103 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 76/244 (31%), Gaps = 44/244 (18%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL----------TH 148
             L+YED  I V +KP  +               L     S  +   +           H
Sbjct: 7   PTLVYEDPYILVVDKPGLLPTVPLKDDPPDKPTLLGMVARSFPEVLCVEGKNAWEGGVLH 66

Query: 149 RLDQETSGILVVARTRAAAQHLTE-----------SFRMRRIQKIYWSLVWGIPKNK--- 194
           RLD  TSG++V+ART+ A   L               +    Q I        P      
Sbjct: 67  RLDTPTSGLVVIARTKEAYASLQAIGKAELFVKEYQCQSSAPQSISLPAFPPFPYEDPVA 126

Query: 195 ---KECIANWLLKKSHIGGDYVHVVKQNEK-------GANYAISHFKVIDCFAQKFCWLE 244
              +E     L +        V  V  +            + ++         +      
Sbjct: 127 CGGREVTIGSLFRHYGDNRRQVRPVLADSPKQLLDKSTGAWYMTRVWY-AGEGKGAKLFT 185

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-G 303
            +  +G  HQ+RVH    G PI GD  Y    + N        L L A  ++ PHP    
Sbjct: 186 CRLTSGFRHQVRVHMAWSGHPIDGDAIYLGKQQPN--------LALRAVAVEFPHPVTSQ 237

Query: 304 RLQI 307
           +++I
Sbjct: 238 KMEI 241


>gi|157414995|ref|YP_001482251.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|157385959|gb|ABV52274.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|307747633|gb|ADN90903.1| Pseudouridine synthase [Campylobacter jejuni subsp. jejuni M1]
 gi|315931909|gb|EFV10864.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 250

 Score =  103 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 53/220 (24%), Positives = 90/220 (40%), Gaps = 35/220 (15%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED KI   NKP           AY  +         K    +L +RLD+ETSG++
Sbjct: 57  PQIIFEDDKIIAINKP----------YAYVSEDL------EKKFNAKLLNRLDKETSGVI 100

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ +     +   E F+  R+ K Y +++ G+   + E        K+  G      + +
Sbjct: 101 LLCKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKGG-----ALSK 155

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K    A+S    I   ++K    ++   TGRTHQ+RVHA  +   +VGD KY      
Sbjct: 156 VSKDGLSALSIITPIMMQSKK-TLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY------ 208

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                  +++YLH+  + +           A L     K 
Sbjct: 209 --AKISSDRMYLHSYEIKIFD-----YYFKAELDNSFAKV 241


>gi|57237010|ref|YP_178812.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
 gi|57165814|gb|AAW34593.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
          Length = 250

 Score =  103 bits (256), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 53/220 (24%), Positives = 90/220 (40%), Gaps = 35/220 (15%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED KI   NKP           AY  +         K    +L +RLD+ETSG++
Sbjct: 57  PQIIFEDDKIIAINKP----------YAYVSEDL------EKKFNAKLLNRLDKETSGVI 100

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ +     +   E F+  R+ K Y +++ G+   + E        K+  G      + +
Sbjct: 101 LLCKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKGG-----ALSK 155

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K    A+S    I   ++K    ++   TGRTHQ+RVHA  +   +VGD KY      
Sbjct: 156 VSKDGLSALSIITPIMMQSKK-TLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY------ 208

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                  +++YLH+  + +           A L     K 
Sbjct: 209 --AKISSDRMYLHSYEIKIFD-----YYFKAELDNSFAKV 241


>gi|315058171|gb|ADT72500.1| Ribosomal large subunit pseudouridine synthase D [Campylobacter
           jejuni subsp. jejuni S3]
          Length = 250

 Score =  103 bits (256), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 53/220 (24%), Positives = 90/220 (40%), Gaps = 35/220 (15%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED KI   NKP           AY  +         K    +L +RLD+ETSG++
Sbjct: 57  PQIIFEDDKIIAINKP----------YAYVSEDL------EKKFNAKLLNRLDKETSGVI 100

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ +     +   E F+  R+ K Y +++ G+   + E        K+  G      + +
Sbjct: 101 LLCKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKGG-----ALSK 155

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K    A+S    I   ++K    ++   TGRTHQ+RVHA  +   +VGD KY      
Sbjct: 156 VSKDGLSALSIITPIMMQSKK-TLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY------ 208

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                  +++YLH+  + +           A L     K 
Sbjct: 209 --AKISSDRMYLHSYEIKIFD-----YYFKAELDNSFAKV 241


>gi|257124830|ref|YP_003162944.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
 gi|257048769|gb|ACV37953.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
          Length = 380

 Score =  103 bits (256), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 30/121 (24%), Positives = 54/121 (44%), Gaps = 5/121 (4%)

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHAL 260
           ++ +  I  D  ++ +  +    YA +  KV+  + +     +E +  TGRTHQ+RVH  
Sbjct: 261 IIIERRIFRDGENLERIIDTRGQYAKTAIKVLKVYPEKNVTLVECELFTGRTHQIRVHLK 320

Query: 261 HMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GGRLQITAPLPAHMVKTW 319
            +G  IVGD  Y             N+ +LHA  +   HP     +++  P+   M +  
Sbjct: 321 SIGHTIVGDELYGNGLNKEL---GINRQFLHAYKVKFIHPALKKEIELEIPMFKDMKEFL 377

Query: 320 D 320
           +
Sbjct: 378 E 378



 Score = 87.7 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 78/193 (40%), Gaps = 28/193 (14%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +E + + M++ ++ +    +         LR+ +V ++ K+V+   ++       
Sbjct: 1   MKKFRIEKEHQRMKISQYLREVQNYSGRS-----LRNVEVFLNGKQVRLTKKL------- 48

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            P   N         ++++           L   +++ED  I V NK   +        A
Sbjct: 49  -PSHGNL--------RVVEKKKGTDIKPIKLPLDIIFEDEDILVVNKEPFLLTHPTQKKA 99

Query: 127 Y--HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +G +  + +  G+   PR  +RLD  TSG++++A+   A   L         +K 
Sbjct: 100 DFTLANGIVNHFFEKYGEVRVPRFYNRLDMNTSGLIIIAKNSFAQAFLQNFSI---FEKK 156

Query: 183 YWSLVWGIPKNKK 195
           Y ++V GI  +K 
Sbjct: 157 YLAIVNGIIDDKG 169


>gi|213420025|ref|ZP_03353091.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 183

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 37/164 (22%), Positives = 68/164 (41%), Gaps = 17/164 (10%)

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI- 233
               I+K Y ++V G   +        + ++  I   +       +K    A++ ++ + 
Sbjct: 1   EQHHIRKRYHAIVRGWLIDDAVLDYPLVEERDKIADKFAR----EDKAPQPAVTQYRGLA 56

Query: 234 ---------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTS 282
                         ++  +E++P TGR HQLR H  H+  PI+GD K+      +     
Sbjct: 57  TVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDSKHGDLRQNRSAAEH 116

Query: 283 PIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325
               +L LHA  ++L HP  G+ L I A L    ++     G++
Sbjct: 117 FACRRLMLHASRLELTHPFTGQPLIIQAGLDETWMQVLTQFGWR 160


>gi|290977304|ref|XP_002671378.1| predicted protein [Naegleria gruberi]
 gi|284084946|gb|EFC38634.1| predicted protein [Naegleria gruberi]
          Length = 272

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 91/237 (38%), Gaps = 41/237 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGG---------SGIAYHIDGFLKSWVDSKGQKP-----RL 146
           ++++   + V +KP  + + G          +     ++  L+      G  P     + 
Sbjct: 15  IIFKSRDVLVIDKPNDLHIDGDYELTVEKLINNYYPEMENPLEEIQHKPGHTPSRRKLKF 74

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            H+LD  TSGIL +A TR +   +T  F+ R  QK Y +++ G        I  ++ +  
Sbjct: 75  CHQLDYATSGILCLAFTRESCAKITYPFQQRTAQKQYLAVLRGHVLINDFEILTFIGEDP 134

Query: 207 HIGGDYVHVVK------------------QNEKGANYAISHFKVI-------DCFAQKFC 241
                +                       Q  K +  +++   V+       D       
Sbjct: 135 SDERKFRMRNFYLGREKTLLSELNTEEEIQEAKKSRESLTFGSVLCRGFYHKDNDTIPVT 194

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            + ++P TGR HQLR+H   +G PI+GD  Y     G       +++ LHA  + LP
Sbjct: 195 KVLLRPKTGRRHQLRLHTQLLGFPILGDATYS--LLGRDGEEGVHRMMLHAWNLTLP 249


>gi|86149810|ref|ZP_01068039.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|88597099|ref|ZP_01100335.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|218562347|ref|YP_002344126.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|85839628|gb|EAQ56888.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|88190788|gb|EAQ94761.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|112360053|emb|CAL34845.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|284925964|gb|ADC28316.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni IA3902]
 gi|315926823|gb|EFV06197.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni DFVF1099]
 gi|315929636|gb|EFV08817.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 250

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 55/227 (24%), Positives = 93/227 (40%), Gaps = 39/227 (17%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED KI   NKP           AY  +         K    +L +RLD+ETSG++
Sbjct: 57  PQIIFEDDKIIAINKP----------YAYVSEDL------EKKFNAKLLNRLDKETSGVI 100

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ +     +   E F+  R+ K Y +++ G+   + E        K   G      + +
Sbjct: 101 LLCKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKVKGG-----ALSK 155

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K    A+S    I   ++K    ++   TGRTHQ+RVHA  +   +VGD KY      
Sbjct: 156 VSKDGLSALSIITPIMMQSKK-TLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY------ 208

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                  +++YLH+  + + +         A L +   K     GF 
Sbjct: 209 --AKISSDRMYLHSYEIKIFN-----YHFRANLDSGFAK----FGFD 244


>gi|283956117|ref|ZP_06373604.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 1336]
 gi|283792437|gb|EFC31219.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 1336]
          Length = 250

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 53/220 (24%), Positives = 90/220 (40%), Gaps = 35/220 (15%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED KI   NKP           AY  +         K    +L +RLD+ETSG++
Sbjct: 57  PQIIFEDDKIIAINKP----------YAYVSEDL------EKKFNAKLLNRLDKETSGVI 100

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ +     +   E F+  R+ K Y +++ G+   + E        K+  G      + +
Sbjct: 101 LLCKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKCG-----ALSK 155

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K    A+S    I   ++K    ++   TGRTHQ+RVHA  +   +VGD KY      
Sbjct: 156 VSKDGLSALSIITPIMLQSKK-TLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY------ 208

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                  +++YLH+  + +           A L     K 
Sbjct: 209 --AKISSDRMYLHSYEIKIFD-----YYFKAELDNSFAKV 241


>gi|254443242|ref|ZP_05056718.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198257550|gb|EDY81858.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 244

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 88/229 (38%), Gaps = 24/229 (10%)

Query: 99  SILLYEDSK-IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-------------P 144
             +L  D   +    KPAG+               L +  D K Q               
Sbjct: 16  VTVLDCDQNGLLAIEKPAGVLSHPNKKGEK-AKALLDAGYDEKRQAYSVLDTESGETRLV 74

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L +RLD  TSGI+++A     A+   ++F  + ++K Y +LV+G P+       + L  
Sbjct: 75  YLLNRLDSATSGIVLLALEEGTAKAALKAFETKNVRKTYQALVFGAPRGGPPLWRDRLSV 134

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHM 262
           K   GG     V+ +  G   A +    ++          L + P TGRTHQLR+     
Sbjct: 135 KHAEGG-----VRASAGGGLSAETKLVKVELLPGVPLVSRLTLMPITGRTHQLRIQTSKR 189

Query: 263 GCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLPHPEGGR-LQITA 309
             PIVGD  Y    K    +     +L LH    +L +   GR  +  A
Sbjct: 190 RIPIVGDRTYGDFQKNKMAAKKGMKRLCLHCVGTELQYQLSGRSFRFKA 238


>gi|71403307|ref|XP_804468.1| RNA pseudouridylate synthase [Trypanosoma cruzi strain CL Brener]
 gi|70867455|gb|EAN82617.1| RNA pseudouridylate synthase, putative [Trypanosoma cruzi]
          Length = 474

 Score =  102 bits (254), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 61/402 (15%), Positives = 118/402 (29%), Gaps = 136/402 (33%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRV------DKKRVKFNNRIQSGQVVRIPPVINAL 74
           L  +  + + +++     K L +G + V      +         ++    +   P     
Sbjct: 37  LLEFLCSRFSYLSRDEWIKHLAAGHLSVVSASDSNAVTTSGEYVLRQNDEIYFNP----- 91

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFL 133
                  + L+  V+   H       ++++D  + V  K   + V +GG      + G L
Sbjct: 92  ------PRELEPDVDEYIH-------VVHDDDAVIVCVKNGNLPVAEGGRYSGNTLVGLL 138

Query: 134 KSW------------------------------VDSKGQKPRLTHRLDQETSGILVVART 163
           +                                V          HRLD+ET+G++V+A+ 
Sbjct: 139 ERRDAVSFVSEKYSAARQKMDQTREEDGDAGVSVHKVPASYYPIHRLDKETTGLVVLAKQ 198

Query: 164 RAAAQHLTESFR--------------------------------MRRIQKIYWSLVWGIP 191
            AAA+ L+  F                                  + + K+Y +++ G  
Sbjct: 199 LAAARALSRQFEKQSERITAQVSKRTDPAGDGLSTAVFEKLLAEEKVVTKVYVAVLAGAG 258

Query: 192 KNKKECI----ANWLLKKSHIGGD------------------YVHVVKQNEKGANYAISH 229
               + +       L       GD                   V++ +  ++    A S 
Sbjct: 259 PEGADFVMCDRIGLLFDSLWNEGDTEDAKKHNKLKKLKMACFPVNLKENPKRHGRPAASR 318

Query: 230 FKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG---------- 278
            +++    +       +   TGRTHQ+R+H   +G P++GD  Y     G          
Sbjct: 319 VRILSSDKKLGVSVARVDILTGRTHQIRIHCAQLGYPVLGDKLYETTTPGVVGGCCAVPD 378

Query: 279 ----------------NFTSPIQNKLYLHARYMDLPHPEGGR 304
                                   +  LHA  +   HP  G 
Sbjct: 379 DTYIARAKGNEGLVSAAAPRLRVKRHLLHAVVLSFLHPVSGE 420


>gi|66358534|ref|XP_626445.1| Yd1036cp-like RluD, S4+type 1 pseudouridine synthase
           [Cryptosporidium parvum Iowa II]
 gi|46227837|gb|EAK88757.1| Yd1036cp-like RluD, S4+type 1 pseudouridine synthase
           [Cryptosporidium parvum Iowa II]
          Length = 481

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 51/304 (16%), Positives = 112/304 (36%), Gaps = 69/304 (22%)

Query: 22  DRWFKNHYPHINFVN-LQ---KILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNH 76
           DR  ++ + +      ++   +++   ++ V+   V   +  +++G  ++          
Sbjct: 61  DRTLRDLFLNEFRTRPIEEYLRLIDQRRLSVNDTPVNSLDYIVRNGDKIKH--------- 111

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDG 131
                     S+ +       K  +LY+ S +    KP GI            +   I  
Sbjct: 112 ---------RSLFIELPVAIDKVKILYDSSTLLAVFKPCGIPCHPQGRFNKLSLTKLIQS 162

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR--------------MR 177
              S +++        +RLD+ TSG++++++  +  ++L+   +                
Sbjct: 163 EYLSKLNTNSTYIHPINRLDRVTSGLVLLSKDSSTTKNLSSKVQFAHKYYLAMINESTSN 222

Query: 178 RIQKIYWSLVWGIP-----KNKKECIANWLLK--------KSHIGGDYVHVVKQNEKGAN 224
            I  I  S + G+       ++   I + ++K        K   G   +  +  +E  + 
Sbjct: 223 FISHISQSSIEGVSIRELSLDESHGITSHVIKCEIGLKTLKDREGESLITRIDSSE-NSK 281

Query: 225 YAISHFKVIDCF-------------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y++++F  +                  K+  L  +P TGRTHQ+R H  ++G PIV D  
Sbjct: 282 YSLTYFFPLISCLDINEAKKQKINETDKYSILLCKPITGRTHQIRAHLKYIGFPIVRDIL 341

Query: 272 YCAN 275
           Y   
Sbjct: 342 YSDK 345


>gi|314922786|gb|EFS86617.1| RNA pseudouridine synthase [Propionibacterium acnes HL001PA1]
          Length = 209

 Score =  102 bits (254), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 49/199 (24%), Positives = 78/199 (39%), Gaps = 12/199 (6%)

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
            +KP  +S     G        ++        +  + HRLD+ T+G+L++ R R   +  
Sbjct: 2   VDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHRLDRVTAGVLLLTRERKWRRPY 60

Query: 171 TESFRMRRIQKIY--WSLVWGIPKNKKEC-IANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
            E F  R + K Y   + V   P  +      +    +S I  +   +  +   G    +
Sbjct: 61  QEIFERREVVKKYRLVAPVVHDPAGEGVTATKSGWQVRSRIIKERGILQAREVPGVPNTV 120

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK---GNFTSPI 284
           +   +I      +   E  P TGRTHQ+R+H   +G PIV D  Y         +FT P+
Sbjct: 121 TDIALIGEHG-GWGLYEASPRTGRTHQIRLHMQRLGAPIVNDPFYPVVLDIPVDDFTHPL 179

Query: 285 QNKLYLHARYMDLPHPEGG 303
           Q    L A  M    P  G
Sbjct: 180 Q----LQAWRMGFTDPVSG 194


>gi|325090610|gb|EGC43920.1| DRAP deaminase [Ajellomyces capsulatus H88]
          Length = 209

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 33/153 (21%), Positives = 58/153 (37%), Gaps = 19/153 (12%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           LD +    +        QK +  G V ++ K V  + +IQ+G V+              E
Sbjct: 66  LDVF-GTEFRDRPKEYYQKAVEDGAVCINGKAVSIDTKIQNGDVISHTLHR-------HE 117

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            +++ED  + V +KPAG+ V       Y+    +       
Sbjct: 118 PPVTSQPIG-----------IIHEDDDMIVIDKPAGVPVHPAGRYNYNSILEIMKAERGN 166

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           G  P   +RLD+ TSG++ +  T      L +S
Sbjct: 167 GWVPYPCNRLDRLTSGVMFIGSTPRVLSKLAKS 199


>gi|148926673|ref|ZP_01810354.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|145845192|gb|EDK22287.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
          Length = 251

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 53/220 (24%), Positives = 89/220 (40%), Gaps = 35/220 (15%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED KI   NKP           AY  +         K    +L +RLD+ETSG++
Sbjct: 58  PQIIFEDDKIIAINKP----------YAYVSEDL------EKKFNAKLLNRLDKETSGVI 101

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ +     +   E F+  R+ K Y +++ G+   + E        K   G      + +
Sbjct: 102 LLCKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKVKGG-----ALSK 156

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K    A+S    I   ++K    ++   TGRTHQ+RVHA  +   +VGD KY      
Sbjct: 157 VSKDGLSALSIITPIMMQSKK-TLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY------ 209

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKT 318
                  +++YLH+  + +           A L     K 
Sbjct: 210 --AKISSDRMYLHSYEIKIFD-----YYFKAELDNSFAKV 242


>gi|260809809|ref|XP_002599697.1| hypothetical protein BRAFLDRAFT_119379 [Branchiostoma floridae]
 gi|229284978|gb|EEN55709.1| hypothetical protein BRAFLDRAFT_119379 [Branchiostoma floridae]
          Length = 418

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 116/327 (35%), Gaps = 61/327 (18%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           L  G+V V K++V+      S     +  V    N I    + +     LTK     +  
Sbjct: 113 LDDGEVEVRKEKVQKQA--VSDDTGSVKKVSEKKNII--SGRTIPRVDKLTKKQLIGRIQ 168

Query: 101 ---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW-VDSKGQKPRLTHRLDQETSG 156
              ++Y+D  I   NK AG+ VQG +     I+  L       +     +   LD   SG
Sbjct: 169 NRGIVYDDGHIVAINKLAGLPVQGQTPEQLSINSLLPELGAALEASDLSIVKPLDWHLSG 228

Query: 157 ILVVARTRAAAQHLT----ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           I+++ART  A   +      + +  +  + YW +V G     ++C +   +K +      
Sbjct: 229 IVLLARTPEARAEVFNVTKAARQRDKFYRKYWGVVIGNLDPSEDCTS---VKPNP----- 280

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
                 +EK     +S            C + +        QL+VH     C I+GDH Y
Sbjct: 281 ----SCSEKEGGSELSDEIQGPQSGAGICPVFVD-------QLQVHLTTKLCSILGDHVY 329

Query: 273 CANFKGNFTSPI------------------------------QNKLYLHARYMDLPHPEG 302
            +        P                               +  ++LH   M LP   G
Sbjct: 330 SSRVGSVAGMPALMEPTNVGPRTQRVPKDILKKMNLRAIQMHKVPVHLHCGEMLLPGYRG 389

Query: 303 GRLQITAPLPAHMVKTWDSLGFKYDRN 329
             ++ITAPLP H + T   LG +   N
Sbjct: 390 RDVRITAPLPKHFLWTLQLLGLEDPTN 416


>gi|86747487|ref|YP_483983.1| pseudouridine synthase [Rhodopseudomonas palustris HaA2]
 gi|86570515|gb|ABD05072.1| Pseudouridine synthase [Rhodopseudomonas palustris HaA2]
          Length = 300

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 35/142 (24%), Positives = 68/142 (47%), Gaps = 4/142 (2%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           ++ ++S +L+ D  + V +KP G+ V  G     +++   +       + P L HRLD++
Sbjct: 16  AEDIQSRVLHRDGLMLVIDKPPGLPVHRGPKGGPNLETSFEFLRFGLPRPPVLAHRLDRD 75

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYV 213
           TSG LV+ R R A   L   F+  +I K YW++V G P   +  I   + + +   G + 
Sbjct: 76  TSGCLVLGRHRKATATLGLLFKHSKISKTYWAIVEGGPLEDQGTIDLPIGRLNAERGWWQ 135

Query: 214 HVVKQNEKGANYAISHFKVIDC 235
            +    +     +++ + V+  
Sbjct: 136 KI----DPEGLPSLTKWTVLGR 153



 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 28/58 (48%), Positives = 35/58 (60%), Gaps = 5/58 (8%)

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
            WL ++P TGRTHQLRVH   MG PI GD+ Y      N     + KL+LHAR + +P
Sbjct: 218 TWLALEPITGRTHQLRVHCAAMGWPIFGDNIYG-----NGPRFGEPKLHLHAREITIP 270


>gi|58580625|ref|YP_199641.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84622566|ref|YP_449938.1| putative pseudouridylate synthase [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
 gi|58425219|gb|AAW74256.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84366506|dbj|BAE67664.1| putative pseudouridylate synthase [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
          Length = 206

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 43/185 (23%), Positives = 76/185 (41%), Gaps = 9/185 (4%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHR 149
            +        +L+ D+ + V  K   + V      AY  +  L   V           HR
Sbjct: 29  DEPVIPYVETVLHADANLVVACKSHFLPVAPAG--AYVHETLLTRLVRRLDNPALVPLHR 86

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           +D+ET+G+++ +   A        FR RRI+K Y  +   +P+     ++   + +S + 
Sbjct: 87  IDRETAGLVLFSANPATRGIYQALFRERRIRKQYLVVAPPLPE-----LSFPYVHRSWLE 141

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                   +   G   + +   V+   A  + +  ++P TGR HQLRVH   +G PI+ D
Sbjct: 142 PGEPFFRMREGVGEPNSETVIDVVAPGADTWTY-RLEPVTGRKHQLRVHMAALGAPILHD 200

Query: 270 HKYCA 274
             Y  
Sbjct: 201 RFYPD 205


>gi|289706073|ref|ZP_06502446.1| RNA pseudouridine synthase [Micrococcus luteus SK58]
 gi|289557275|gb|EFD50593.1| RNA pseudouridine synthase [Micrococcus luteus SK58]
          Length = 348

 Score =  101 bits (252), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 62/314 (19%), Positives = 100/314 (31%), Gaps = 53/314 (16%)

Query: 42  RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS-I 100
           R G V  D  R     R   G+VV            +     L    ++   +    +  
Sbjct: 35  RFGHVDPDGIRA----RFARGEVVAADGTALTPATPLGVHDDLWYYRDVPDEAPLPVTHT 90

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           LL+ D  + V +KP  +    G    +  +  L    +  G       HRLD+ T+G+++
Sbjct: 91  LLHRDEHLVVIHKPHFLPTTPGG--RFVQETALVRLRNELGLDDLVPLHRLDRATAGVVM 148

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN-----------WLLKKSHI 208
            +   A        F  R + K Y ++                          L  +S I
Sbjct: 149 FSANPATRGAYHLLFERRAVAKTYEAVALLPDAPDDGARRPGAPADPVLGRFPLTVRSRI 208

Query: 209 GGD------------------------YVHVVKQNEKGANYAISHFKVIDCF-------A 237
             D                              +   GAN A S  +++           
Sbjct: 209 RKDKGVLRSVVEEIPPAASGRRAGAPVRTRRANRPHAGAN-AESRVELLGVGVSAGALAG 267

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++   L + P TGRTHQLR+H   +G  I  D  Y  +        +   L L +R +  
Sbjct: 268 RRVAHLRLTPRTGRTHQLRIHLAALGLGIAFDPFY-PDLLDLAPDDVTRPLQLLSRSLRF 326

Query: 298 PHP-EGGRLQITAP 310
             P  GG  + T+P
Sbjct: 327 TDPVTGGEREFTSP 340


>gi|323446696|gb|EGB02765.1| hypothetical protein AURANDRAFT_34908 [Aureococcus anophagefferens]
          Length = 237

 Score =  101 bits (252), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 49/215 (22%), Positives = 81/215 (37%), Gaps = 16/215 (7%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
              NKPAGISV                      +K    HRLD  TSG L+       A 
Sbjct: 1   VAVNKPAGISVHRNKDTGRRRVVT-TQLQRQFRRKVFPAHRLDHRTSGALLFGFDGPTAG 59

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
              ++      + +   L  G    +    A+ +++K          VK ++     A +
Sbjct: 60  KAHDALAAGTKEYLCL-LRGGDWPGEGG--ADVVVEKP---------VKGDDGAPRDART 107

Query: 229 HFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQ 285
            F+ +    +  C      P TGR HQ+R HA H+  P++GD K+  +    +       
Sbjct: 108 VFRYLASQEEPRCTLCIAAPATGRPHQIRRHAQHLSMPVIGDSKHGDSRVNRWWREERGL 167

Query: 286 NKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           ++L LH   + L   +G  + + APL   + +   
Sbjct: 168 DRLALHCLAISLDDVDGEAVSLLAPLEGELARALR 202


>gi|153952563|ref|YP_001398347.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
 gi|152940009|gb|ABS44750.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
          Length = 250

 Score =  101 bits (252), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 53/227 (23%), Positives = 93/227 (40%), Gaps = 39/227 (17%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED KI   NKP           AY  +         K    +L +RLD+ETSG++
Sbjct: 57  PQIIFEDDKIIAINKP----------YAYVSEDL------EKKFNAKLLNRLDKETSGVI 100

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ +     +   E F+  R+ K Y +++ G+   + E        K+  G      + +
Sbjct: 101 LLCKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKGG-----ALSK 155

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
             K    A+S    I   ++K    ++   TGRTHQ+R+HA  +   ++GD KY      
Sbjct: 156 VSKDGLSALSIITPIMMQSKK-TLAKIVIQTGRTHQIRIHAKFIKHGVIGDEKY------ 208

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                  +++YLH+  + +           A L     K     GF+
Sbjct: 209 --AKISSDRMYLHSYEIKIFD-----YYFKAELDNSFAK----FGFE 244


>gi|42526593|ref|NP_971691.1| RNA pseudouridylate synthase [Treponema denticola ATCC 35405]
 gi|41816786|gb|AAS11572.1| RNA pseudouridylate synthase [Treponema denticola ATCC 35405]
          Length = 261

 Score =  101 bits (252), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 85/231 (36%), Gaps = 30/231 (12%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----------DSKGQKPRL 146
           ++ +++E+    V  KP G+     + ++   +G L SW              K  +  L
Sbjct: 10  QAEVIFENEAYAVLYKPRGM---PTAPLSEDEEGTLVSWFLKRCPEAVSVKGKKDIEAGL 66

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  TSG++++A+ + +   L        I+K Y +      ++      + L    
Sbjct: 67  VHRLDTATSGLVLMAKNQESYDALNLMQGNDLIKKTYVAFTDIDNESDLNADFSRLNLPY 126

Query: 207 HIGGDYVHVVKQNEK-------------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            I   +     + +K              A    ++   I+        +      G  H
Sbjct: 127 RISSQFRSFGPKGKKVLPVFYGMRDFSSTAKIYTTNIIDINNLDDSVPRVTCTLTQGFRH 186

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPE 301
           Q+R H   +G PI GD  Y   FK      I++    L L+A  +  P P+
Sbjct: 187 QVRAHLASIGLPIYGDPLYNGKFKDFPQEKIEDHSYPLQLYAVGLSFPEPK 237


>gi|67595791|ref|XP_666024.1| N-terminal part related to RNA:pseudouridine (psi)-synthases
           C-terminal portion contains the deaminase domain
           implicated in Riboflavin synthesis; Rib2p
           [Cryptosporidium hominis TU502]
 gi|54656925|gb|EAL35796.1| N-terminal part related to RNA:pseudouridine (psi)-synthases
           C-terminal portion contains the deaminase domain
           implicated in Riboflavin synthesis; Rib2p
           [Cryptosporidium hominis]
          Length = 481

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 49/304 (16%), Positives = 111/304 (36%), Gaps = 69/304 (22%)

Query: 22  DRWFKNHYPHINFVN-LQ---KILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNH 76
           DR  ++ + +      ++   +++   ++ V+       +  +++G  ++          
Sbjct: 61  DRTLRDLFLNEFRTRPIEEYLRLIDQRRLSVNDTPANSLDYIVRNGDKIKH--------- 111

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG-----IAYHIDG 131
                     S+ +       K  +LY+ S +    KP GI            +   I  
Sbjct: 112 ---------RSLFIELPVATDKVKILYDSSTLLAVFKPCGIPCHPQGRFNKLSLTKLIQS 162

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR--------------MR 177
              S +++        +RLD+ TSG++++++  +  ++L+   +                
Sbjct: 163 EYLSKLNTNSTYIHPINRLDRVTSGLVLLSKDSSTTKNLSSKVQFAHKYYLAMINESASN 222

Query: 178 RIQKIYWSLVWGIP-----KNKKECIANWLLK--------KSHIGGDYVHVVKQNEKGAN 224
            I  +  S + G+       ++   I + ++K        K   G   +  +  +E  + 
Sbjct: 223 FISHVSQSSIEGVSIRELSLDESHGITSHVIKCEIGLKTLKDREGESLITRIDSSE-NSK 281

Query: 225 YAISHFKVIDCF-------------AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
           Y++++F  +                  K+  L  +P TGRTHQ+R H  ++G PIV D  
Sbjct: 282 YSLTYFFPLISCLDINEGKKQKINETDKYSILLCKPITGRTHQIRAHLKYIGFPIVRDIL 341

Query: 272 YCAN 275
           Y   
Sbjct: 342 YSDK 345


>gi|239916876|ref|YP_002956434.1| 23S RNA-specific pseudouridylate synthase [Micrococcus luteus NCTC
           2665]
 gi|281414672|ref|ZP_06246414.1| pseudouridine synthase [Micrococcus luteus NCTC 2665]
 gi|239838083|gb|ACS29880.1| 23S RNA-specific pseudouridylate synthase [Micrococcus luteus NCTC
           2665]
          Length = 348

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 65/314 (20%), Positives = 105/314 (33%), Gaps = 53/314 (16%)

Query: 42  RSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS-I 100
           R G V  D  R     R   G+VV            +     L    ++   +    +  
Sbjct: 35  RFGHVDPDGIRA----RFARGEVVAADGTALTPATPLGVHDDLWYYRDVPDEAPLPVTHT 90

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           LL+ D  + V +KP  +S   G    +  +  L    +  G       HRLD+ T+G+++
Sbjct: 91  LLHRDEHLVVIHKPHFLSTTPGG--RFVQETALVQLRNELGLDDLVPLHRLDRATAGVVM 148

Query: 160 VARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNK---KECIANW------LLKKSHI 208
            +   A        F  R + K Y   +L+   P +        A+       L  +S I
Sbjct: 149 FSANPATRGAYHLLFERRAVAKTYEAVALLPDAPDDGARGPGTPADPVLGRFPLTVRSRI 208

Query: 209 GGD------------------------YVHVVKQNEKGANYAISHFKVIDCF-------A 237
             D                              +   GAN A S  +++           
Sbjct: 209 RKDKGVLRSVVEEIPPAASGRRAGAPVRTRRSNRPHAGAN-AESRVELLGVGVSAGTLAG 267

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           ++   L + P TGRTHQLR+H   +G  I  D  Y  +        +   L L +R +  
Sbjct: 268 RRVAHLRLTPRTGRTHQLRIHLAALGLGIAFDPFY-PDLLDLAPDDVTQPLQLLSRSLRF 326

Query: 298 PHPEGG-RLQITAP 310
             P  G   + T+P
Sbjct: 327 TDPVTGEEREFTSP 340


>gi|332297939|ref|YP_004439861.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332181042|gb|AEE16730.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 265

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 89/255 (34%), Gaps = 50/255 (19%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-------KGQKP---RLTHRL 150
           ++Y D    V +KPAG+            +  L+  ++         G+KP    L HR+
Sbjct: 6   IIYADQDFIVIDKPAGVPSAPLRPDDT--ENALQQAIERFPDMAGVTGRKPVEHGLVHRI 63

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-------------WGIPKNKKEC 197
           D  T G+L++ART+ A           R  K Y +                 +P+N    
Sbjct: 64  DTATRGLLLIARTQNAYDAFQRIQAENRFFKEYEATCRQLTVCEETRSGFPPLPENVARS 123

Query: 198 IANWLLKKSHI-------------GGDYVHVVKQ------NEKGANYAISHFKVIDCFAQ 238
           IA   L    +             G   V  V +       +K  +   +   V+ C ++
Sbjct: 124 IARLRLGAEAVSFSVQSAFRFYGEGRTSVRPVTELASKFARKKSGDSIYTTEIVLSCISK 183

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
                + +   G  HQ+R H    G P+  D  Y           +   L  +A  ++ P
Sbjct: 184 DTVLAKCRISKGFRHQVRCHLAWCGVPVADDSLYAPALPETGAERL---LQFYATALEFP 240

Query: 299 HPEGG---RLQITAP 310
           HP  G   R+++  P
Sbjct: 241 HPSSGVPLRIELKQP 255


>gi|302822493|ref|XP_002992904.1| hypothetical protein SELMODRAFT_136149 [Selaginella moellendorffii]
 gi|300139249|gb|EFJ05993.1| hypothetical protein SELMODRAFT_136149 [Selaginella moellendorffii]
          Length = 415

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 59/278 (21%), Positives = 105/278 (37%), Gaps = 25/278 (8%)

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSD----FLKSILLYEDSKIYVFNKPAGISVQG 121
           R P  +   NH  +    +   V+  +         +S ++  +    V NKPAG+SV G
Sbjct: 92  RKPERVTDPNHYAEPGSYIRVHVHPKRFPRCYEVDWRSRIIANEESFVVLNKPAGVSVGG 151

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                  I     +   +  Q    TH+LD  T G L++A+    A       +  +++K
Sbjct: 152 SVDNVEEICSTFATRALNLEQPLVTTHQLDNCTEGCLLLAKNNEFASRFHRFLKENKVEK 211

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDY------------VHV--VKQNEKGANYAI 227
            Y +L            A+++    +                 +HV   KQ    +  A+
Sbjct: 212 FYLALAAAPVP--LGKTAHYMRSDKYPPRIMSNNERLGWQLCVMHVLECKQVPWPSEAAL 269

Query: 228 SHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           S ++V  C    ++      ++  TG THQLR     +G P++GD  Y         +P 
Sbjct: 270 SEYQVQPCGWTKSKFAYECRVKLLTGLTHQLRAQFSALGSPLIGDSLYMPAAAARLENPE 329

Query: 285 QNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
            +  +L  R  ++   E G ++ +      + K W SL
Sbjct: 330 LDP-FLDTRKKEIADEEAG-IEKSPAESKQLEKKWISL 365


>gi|283953926|ref|ZP_06371455.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
 gi|283794531|gb|EFC33271.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
          Length = 250

 Score =  100 bits (250), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 50/227 (22%), Positives = 92/227 (40%), Gaps = 39/227 (17%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +++ED KI   NKP     +                   K    +L +RLD+ETSG++
Sbjct: 57  PQIIFEDDKIIAINKPYSCVSED----------------LEKKINAKLLNRLDKETSGVI 100

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++ +     +   E F+  R+ K Y +++ G+   + E        K+  G   +  V +
Sbjct: 101 LLCKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEIEVNEPIFTIKAKGGA--LSKVSK 158

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           +   A+  I+          K    ++   TGRTHQ+RVH   +   +VGD KY      
Sbjct: 159 DGLNASSIITPI----MMQSKKTLAKIVIQTGRTHQIRVHTKFIKHGVVGDEKY------ 208

Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                  +++YLH+  + +           A L +    +++  GF+
Sbjct: 209 --AKISSDRMYLHSYEIKIFD-----YHFKANLDS----SFEKFGFE 244


>gi|156095414|ref|XP_001613742.1| ribosomal large subunit pseudouridylate synthase [Plasmodium vivax
           SaI-1]
 gi|148802616|gb|EDL44015.1| ribosomal large subunit pseudouridylate synthase, putative
           [Plasmodium vivax]
          Length = 460

 Score =  100 bits (250), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 59/265 (22%), Positives = 103/265 (38%), Gaps = 31/265 (11%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++YE+    V NKP  I ++ G     +          +     R+  +LD  TSG+L+V
Sbjct: 25  IVYENEFFLVVNKPYDIKLEKGKLDDMYPSVETLLRQKTNLDVFRICGQLDYATSGLLIV 84

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN- 219
           A+ + +   L  +   +RI KIY ++++G        +   +   S I   +   +  N 
Sbjct: 85  AKDKLSCNILNYNIESKRISKIYLAMLYGHLPLGVLHVNTPI---SKIKNKFKMKLCYNY 141

Query: 220 ------EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
                  K     +  +K      +K    E++  TGR HQLR+HAL +G  IVGD  Y 
Sbjct: 142 NDYYDSGKYCYSLVYPYKHCYLKNEKVTLCELRTITGRRHQLRLHALCLGSGIVGDETYF 201

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH----------MVKTW---- 319
            +   N     +       +   L   EG + +  +P P            M+  W    
Sbjct: 202 EDMISNKYKLGRTSNLCEEQTGVLA--EGDQQERFSPTPEGAIAKIDAERMMLHCWIMLK 259

Query: 320 -----DSLGFKYDRNLYIKRLYSQD 339
                  L    D N+  ++++ +D
Sbjct: 260 NEDQKKELKKTEDINMLEEKIFDRD 284


>gi|302796789|ref|XP_002980156.1| hypothetical protein SELMODRAFT_112010 [Selaginella moellendorffii]
 gi|300152383|gb|EFJ19026.1| hypothetical protein SELMODRAFT_112010 [Selaginella moellendorffii]
          Length = 415

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 59/278 (21%), Positives = 105/278 (37%), Gaps = 25/278 (8%)

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSD----FLKSILLYEDSKIYVFNKPAGISVQG 121
           R P  +   NH  +    +   V+  +         +S ++  +    V NKPAG+SV G
Sbjct: 92  RKPERVTDPNHYAEPGSYIRVHVHPKRFPRCYEVDWRSRIIANEESFVVLNKPAGVSVGG 151

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                  I     +   +  Q    TH+LD  T G L++A+    A       +  +++K
Sbjct: 152 SVDNVEEICSTFATRALNLEQPLVTTHQLDNCTEGCLLLAKNNEFASRFHRLLKENKVEK 211

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDY------------VHV--VKQNEKGANYAI 227
            Y +L            A+++    +                 +HV   KQ    +  A+
Sbjct: 212 FYLALAAAPVP--LGKTAHYMRSDKYPPRIMSNNERLGWQLCVMHVLECKQVPWPSEAAL 269

Query: 228 SHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
           S ++V  C    ++      ++  TG THQLR     +G P++GD  Y         +P 
Sbjct: 270 SEYQVQPCGWTKSKFAYECRVKLLTGLTHQLRAQFSALGSPLIGDSLYMPAAAARLENPE 329

Query: 285 QNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
            +  +L  R  ++   E G ++ +      + K W SL
Sbjct: 330 LDP-FLDTRKKEIADEEAG-IEKSPAESKQLEKKWISL 365


>gi|325473129|gb|EGC76325.1| pseudouridine synthase [Treponema denticola F0402]
          Length = 261

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 85/231 (36%), Gaps = 30/231 (12%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV-----------DSKGQKPRL 146
           ++ +++E+    V  KP G+     + ++   +G L SW              K  +  L
Sbjct: 10  QAEVIFENEAYAVLYKPRGM---PTAPLSEDEEGTLVSWFLKRCPEAVSVKGKKDIEAGL 66

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD  TSG++++A+ + +   L        I+K Y +      ++      + L    
Sbjct: 67  VHRLDTATSGLVLMAKNQESYDALNLMQGNDLIKKTYVAFTDIDNESDLNADFSRLNLPY 126

Query: 207 HIGGDYVHVVKQNEK-------------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            I   +     + +K              A    ++   I+        +      G  H
Sbjct: 127 RISSQFRSFGPKGKKVLPVFYGMRDFSSTAKIYTTNIIDINNLDDSVPRVTCTLTQGFRH 186

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN---KLYLHARYMDLPHPE 301
           Q+R H   +G PI GD  Y   FK      I++    L L+A  +  P P+
Sbjct: 187 QVRAHLASIGLPIYGDPLYNGKFKDFPQEKIEDHSYPLQLYAVGISFPEPK 237


>gi|257487594|ref|ZP_05641635.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 100

 Score =  100 bits (249), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 33/99 (33%), Positives = 50/99 (50%), Gaps = 6/99 (6%)

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
               + +G  +A++ +KV++     +C +E+ P TGR+HQLRVH L +G P++GD  Y  
Sbjct: 6   RHVVDHEGGKHALTFWKVVERH-DTYCRVELTPITGRSHQLRVHMLSIGHPLLGDGLYAH 64

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLP 312
                       +L LHA  +   HP  G RL    P P
Sbjct: 65  PE----ALAAYPRLCLHASMLSFTHPGTGERLTFECPAP 99


>gi|71417514|ref|XP_810586.1| RNA pseudouridylate synthase [Trypanosoma cruzi strain CL Brener]
 gi|70875140|gb|EAN88735.1| RNA pseudouridylate synthase, putative [Trypanosoma cruzi]
          Length = 474

 Score =  100 bits (249), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 60/402 (14%), Positives = 117/402 (29%), Gaps = 137/402 (34%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRV------DKKRVKFNNRIQSGQVVRIPPVINAL 74
           LD +    + +++     K + +G + V      +         ++    +   P     
Sbjct: 38  LD-FLCTRFSYLSRDEWIKHMAAGHLSVVSASDSNAVTTSGEYVLRQNDEIYFNP----- 91

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFL 133
                  + L+  V+   H       ++++D  + V  K   + V +GG      + G L
Sbjct: 92  ------PRELEPDVDEYIH-------VVHDDDAVIVCVKNGNLPVAEGGRYSGNTLVGLL 138

Query: 134 KSW------------------------------VDSKGQKPRLTHRLDQETSGILVVART 163
           +                                V          HRLD+ET+G++V+A+ 
Sbjct: 139 ERRDAVSFVSEKYSAARQKMDQTREEDGDAGVSVHKVPASYYPIHRLDKETTGLVVLAKQ 198

Query: 164 RAAAQHLTESFR--------------------------------MRRIQKIYWSLVWGIP 191
            AAA+ L+  F                                  + + K+Y +++ G  
Sbjct: 199 LAAARALSRQFEKQSERITAQVSKRTDPAGDGLSTAVFEKLLAEEKVVTKVYVAVLAGAG 258

Query: 192 KNKKECI----ANWLLKKSHIGGD------------------YVHVVKQNEKGANYAISH 229
               + +       L       GD                   V++ +  ++    A S 
Sbjct: 259 PEGADFVMCDRIGLLFDSLWNEGDTEDAKKHNKLKKLKMACFPVNLKENPKRHGRPAASR 318

Query: 230 FKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG---------- 278
            +++    +       +   TGRTHQ+R+H   +G P++GD  Y     G          
Sbjct: 319 VRILSSDKKLGVSVARVDILTGRTHQIRIHCAQLGYPVLGDKLYETTTPGVVGGCCAVPD 378

Query: 279 ----------------NFTSPIQNKLYLHARYMDLPHPEGGR 304
                                   +  LHA  +   HP    
Sbjct: 379 DTYIARAKGNEGLVSAAAPRLRVKRHLLHAAVLSFLHPISEE 420


>gi|319441171|ref|ZP_07990327.1| putative pseudouridylate synthase [Corynebacterium variabile DSM
           44702]
          Length = 328

 Score =  100 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 107/322 (33%), Gaps = 67/322 (20%)

Query: 35  VNLQKILRSGQVRV-DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
             L +  R G+VR+ +   ++  + +  G  +               ++ +  +++L   
Sbjct: 30  TALYERFRRGEVRLDNGTVLQPADTVAGGTFIWFY-------RRPAPERPVPGNMHL--- 79

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
                   LY D  I V +KP  +S     G        +++            HRLD+ 
Sbjct: 80  --------LYRDENILVADKPPFMSTLP-RGQHITETAVVRARRQFGIDDLSPVHRLDRL 130

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP---------------------- 191
           T G+L+    R       + F  R +QK Y ++    P                      
Sbjct: 131 TRGVLLFTVRREVRGAYQQLFERRLVQKTYDAVTPRPPGWTDLTQVEVPAGALHLGSPAS 190

Query: 192 -KNKKECIANWLLKKSHI--GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
                     W+L+   I   G     V + +  +  A+   +  D    K  W  +QPH
Sbjct: 191 ALAAPSAAEPWVLRHRLIKDRGHLATYVAEGDANSETAVVGIRPSDLDDSKLVWT-LQPH 249

Query: 249 TGRTHQLRVHALHMGCPIVGDHKY---CANFKGNFTSPIQ-----------NKLYLHARY 294
           +GRTHQLRV+      PIV D  Y         + T+P+              + L AR 
Sbjct: 250 SGRTHQLRVNMRLFKTPIVDDPIYTDISDRALYDQTAPLPFVPAVEDEDFNRPMGLTARE 309

Query: 295 MDLPHPEGGRLQITAPLPAHMV 316
           +    P  G        P H V
Sbjct: 310 LSFTDPLSGE-------PRHFV 324


>gi|269214112|ref|ZP_06158361.1| RNA pseudouridine synthase [Neisseria cinerea ATCC 14685]
 gi|269144501|gb|EEZ70919.1| RNA pseudouridine synthase [Neisseria cinerea ATCC 14685]
          Length = 169

 Score =  100 bits (248), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 36/158 (22%), Positives = 70/158 (44%), Gaps = 7/158 (4%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD++T+G+++++   A        F+ + + K Y +L       + +      +  
Sbjct: 8   PLHRLDKDTAGVMLLSHNPATRGTYQTMFQNKTVWKTYEALA----PTRTDLPYPIDVVS 63

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
             + G+      Q  +G   A +  ++I+   + F    + PHTG+ HQLRVH + +G P
Sbjct: 64  RLVRGEKFF-TTQEAEGEPNAHTTVELIENRGE-FSLYRLTPHTGKKHQLRVHMMGLGMP 121

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           ++ D  Y    +   +   +  L L A+ +    P  G
Sbjct: 122 LLNDALYPVPSEAG-SEDYRKPLKLLAKKIAFADPLSG 158


>gi|332017005|gb|EGI57804.1| RNA pseudouridylate synthase domain-containing protein 1
           [Acromyrmex echinatior]
          Length = 295

 Score =  100 bits (248), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 40/211 (18%), Positives = 81/211 (38%), Gaps = 17/211 (8%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVD-----SKGQKPRLTHRLDQ 152
             +++      + +KP  + +   +    +     L+  +          +    HRLD 
Sbjct: 45  VKIMHRSENFLIIDKPYDMYINSNNPDRKNTLQMELRQMLPDLVNPRLCHEFHFVHRLDY 104

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG++ +A  + AA+  + +F   ++QK Y +LV G        I   +          
Sbjct: 105 PTSGVMCIALNKRAARAASSAFENHKVQKFYLALVHGHIHEPHIVIDKPIGADIREKTGN 164

Query: 213 VHVVKQNE---KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             +   +         + +   V++      +    + + P TGR HQLRVH  ++G  +
Sbjct: 165 HKMCISDSIFCDKPRRSYTTLVVLEHGFWKGKPATKILLAPGTGRRHQLRVHCHYIGHTV 224

Query: 267 VGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           +GD+ Y             ++ YLH+  + L
Sbjct: 225 IGDYTYSEGKDIE-----PHRTYLHSLRLIL 250


>gi|253744794|gb|EET00944.1| Ribosomal large subunit pseudouridine synthase D [Giardia
           intestinalis ATCC 50581]
          Length = 196

 Score =  100 bits (248), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 39/153 (25%), Positives = 65/153 (42%), Gaps = 17/153 (11%)

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A  + AA      F+MR + K+Y +LV G      + I+  +         +   V 
Sbjct: 1   MILAANKKAAGSAGREFQMRAVTKVYVALVAGDV--NSQTISLPIADDVSDPHQFRMCV- 57

Query: 218 QNEKGANYAISHFKVIDCFAQK------------FCWLEMQPHTGRTHQLRVHALHMGCP 265
                   + +H K I   ++             +  + ++P TGR HQLRVH  H+G P
Sbjct: 58  --SSTGKRSETHVKRIASISKDICDALALSPCESYTLVVLRPVTGRRHQLRVHLAHVGHP 115

Query: 266 IVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           IVGD  Y    +       + +L LHA  + +P
Sbjct: 116 IVGDQLYGNAIEDIHHVNGEQRLCLHAFMLSIP 148


>gi|297670735|ref|XP_002813515.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           3-like isoform 2 [Pongo abelii]
          Length = 335

 Score = 99.7 bits (247), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 91/244 (37%), Gaps = 41/244 (16%)

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRM 176
            G    + +   L   +    Q+ ++     +E+SG+++++     A  L +    + R 
Sbjct: 90  PGELTLFSVLPELSQSLGLGKQELQVVRASGKESSGLVLLSSCPQTASRLQKFFTHARRA 149

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFK 231
           +R    Y ++  GIP   +  I   L  +   G +    VK   +     G    +SHF+
Sbjct: 150 QRPTATYCAVTDGIPAASEGKIQAALKLEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFR 209

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQN- 286
           V+         +++QP T  + QL+VH +   CP++GDH Y A         F  P +N 
Sbjct: 210 VVAT-GSGCALVQLQPLTVFSSQLQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAENK 268

Query: 287 --KLYLHARYMDLPHPE------------------------GGRLQITAPLPAHMVKTWD 320
             +  L    +   H                             +++ APLP +  +T  
Sbjct: 269 PQRQVLDEALLRCLHLTPSQAAQLPLHLHLHRLLLPGTRASDTPIELLAPLPPYFSRTLQ 328

Query: 321 SLGF 324
            LG 
Sbjct: 329 CLGL 332


>gi|224011685|ref|XP_002295617.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|209583648|gb|ACI64334.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 344

 Score = 99.3 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 62/270 (22%), Positives = 94/270 (34%), Gaps = 53/270 (19%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----------SKGQKPR 145
           +   ++YE+ ++    KP  IS              L                    +  
Sbjct: 55  INIPIIYENDQLLAVCKPPHISHHDDPASNQLGLLSLIRLQQQQQQQQDESSFPYPHRLH 114

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL-----------------VW 188
             HRLD+ TSG+L++A+  + A  L   FR   + K Y ++                 V 
Sbjct: 115 GVHRLDRVTSGVLLLAKDSSVANELITKFRQGEVSKYYMAISGKKPKKKKQGWVKGQMVM 174

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHV---VKQNEKGANYAISHFKVI-----------D 234
           G   + K    N  +     G D V     V Q +K   YA++ F               
Sbjct: 175 GRRGSYKLVNENRDVLDEGDGDDEVEDGGEVSQVKKKGGYAVTRFYTAGLGDLQLAPLPK 234

Query: 235 CFAQKFCWLEM---------QPHTGRTHQLRVHALHMGCPIVGDHKYCAN-FKGNFTSPI 284
           C   +    E+         QPHTG+THQLRV A   G PI+GD +Y          +  
Sbjct: 235 CDGDESNDDELLIPKTAILFQPHTGKTHQLRVAAKSAGIPILGDVRYGGGTVTQREENAN 294

Query: 285 QNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
            ++ YLHA  +         + I +P P  
Sbjct: 295 FDRTYLHASAIHFQ-LNDEDVTIWSPPPFD 323


>gi|256089816|ref|XP_002580951.1| ribosomal pseudouridine synthase [Schistosoma mansoni]
 gi|238666672|emb|CAZ37190.1| ribosomal pseudouridine synthase, putative [Schistosoma mansoni]
          Length = 370

 Score = 99.3 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 44/217 (20%), Positives = 78/217 (35%), Gaps = 42/217 (19%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR-----------L 146
              +++E+    V NK   + +             L   +     +PR            
Sbjct: 44  DLRVVHENQGFLVINKHPELLI----NCTTPWINCLTLQMQLFYNRPRYVNWKLKNMFHF 99

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-------------IPKN 193
            HRLD  TSG++ +A    AA  +  +F  + ++K Y ++VWG               K+
Sbjct: 100 VHRLDCPTSGLICIAYDTKAASMIRRAFENKEVKKYYLAIVWGYVGSFCDSGLSSSFVKH 159

Query: 194 KKECIANWLLKK-------SHIGGDYVHVVKQNEKG---ANYAISHFKVIDC---FAQKF 240
           + + + +  +          + G     +V            +++   V+D      +  
Sbjct: 160 ESKLVHHIQMSIGSFRYLWPNTGRKQKIIVPITHPECYRPRESLTTVIVLDYGKLMGEPA 219

Query: 241 CWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYCANF 276
             + + P TGR HQLRVH    +G PI GD  Y    
Sbjct: 220 THILLIPETGRRHQLRVHCAIGLGHPIAGDTTYVRRP 256


>gi|68067749|ref|XP_675809.1| ribosomal large subunit pseudouridylate synthase, [Plasmodium
           berghei strain ANKA]
 gi|56495204|emb|CAI05271.1| ribosomal large subunit pseudouridylate synthase, putative
           [Plasmodium berghei]
          Length = 523

 Score = 99.3 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 55/259 (21%), Positives = 100/259 (38%), Gaps = 15/259 (5%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
           F   + +I+  + ++I++        KR KF          R        N   +   + 
Sbjct: 3   FSKIFNNISRHHREQIIQLKL-----KRSKFRL------TRRNFNNYKCENMKNQNNVVK 51

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           +++  L K        + YE+    V NKP  I ++ G     +                
Sbjct: 52  ENATPLYKSYKGHDLKIEYENDFFLVVNKPYDIKLEKGKLDDIYPSVETLLRKKRNLNTF 111

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R+  +LD  TSG+L++A+ + ++  L  +   + I KIY ++++G        I   + K
Sbjct: 112 RMCGQLDYATSGLLIIAKDKLSSNILNYNIESKNISKIYLAILYGHLPLDVLHINVPISK 171

Query: 205 KSHIGGDYVHV----VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +     +           K     I  +K      +K    E++  TGR HQLR+H++
Sbjct: 172 VKNEFKMKLCYNYNDYYDTGKYCYSLIYPYKHTYLKNEKVTLCELRTITGRRHQLRLHSI 231

Query: 261 HMGCPIVGDHKYCANFKGN 279
            +G  IVGD  Y  +   N
Sbjct: 232 CLGSGIVGDETYFEDMIEN 250


>gi|325116689|emb|CBZ52242.1| YDL036Cp-like protein, related [Neospora caninum Liverpool]
          Length = 430

 Score = 98.9 bits (245), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 44/215 (20%), Positives = 79/215 (36%), Gaps = 35/215 (16%)

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +         ++ +   + + +  D        P+ + V               +  +  
Sbjct: 196 KAPPPPFQESSRDARDEEPVEVPTDPAADSIGGPSSMRV----------SSVQLALPEEI 245

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            +   + HRLD  TSG LV A+T AAA++L   +  R++ K Y  L        +E  A 
Sbjct: 246 SRPASIVHRLDIGTSGALVAAKTIAAAENLKYQWAERKVLKGYIGLCAPEIHKLQEVDAA 305

Query: 201 WLLKKSHIGGDYV-----------HVVKQNEK-----------GANYAISHFKVIDCFAQ 238
             +++  +    +           H    +EK           GA   +S F  +     
Sbjct: 306 --IRRHPVQRGRMEALINDSRSGFHETVCDEKVAQNCQSNSRLGAKPGVSVFAPLGGNGV 363

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              +  +   TGRTHQ+R H  ++G P++GD  Y 
Sbjct: 364 YGMFAALAL-TGRTHQIRAHLEYIGHPLLGDPVYG 397



 Score = 45.7 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 14/33 (42%), Positives = 17/33 (51%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           +LT   D     +LYED  I V NKPAG+    
Sbjct: 125 SLTLLPDEKHLDVLYEDDDIVVINKPAGLLTHP 157


>gi|157821169|ref|NP_001102111.1| RNA pseudouridylate synthase domain-containing protein 3 [Rattus
           norvegicus]
 gi|149036916|gb|EDL91534.1| RNA pseudouridylate synthase domain containing 3 (predicted),
           isoform CRA_c [Rattus norvegicus]
          Length = 320

 Score = 98.9 bits (245), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 85/246 (34%), Gaps = 42/246 (17%)

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRM 176
            G      +  +L   +  + Q+ ++     +E SG+++++       HL +    S R 
Sbjct: 74  PGELTLLSVLPWLSQALGLEHQELQVVRAPGKEASGLVLLSSCPQTTSHLQKFFTHSRRA 133

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV-----KQNEKGANYAISHFK 231
           +R    Y ++  G+P+  +  +   L  +   G D    V     K  ++G    +SHF 
Sbjct: 134 QRPTATYCAITDGVPEPSEGTVHIALRLERMDGIDLAVPVTSPSRKDIQEGVKRTLSHFH 193

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSP 283
           V          +++QP T    QL+VH     CPI+GDH Y           F     + 
Sbjct: 194 V-TATGCGCALVQLQPLTVFPSQLQVHMALQLCPILGDHTYAARVGSVLGQRFLWPAETT 252

Query: 284 IQNKLYLHARYMDLPH------------------------PEGGRLQITAPLPAHMVKTW 319
              +  L    +   H                        P     ++ APLP +  +T 
Sbjct: 253 KPQRQVLDEALLRYLHLSPSQVAQMPLHLHLHRLLLPGTRPRDPPSELLAPLPPYFSRTL 312

Query: 320 DSLGFK 325
             L   
Sbjct: 313 QCLRLS 318


>gi|330836753|ref|YP_004411394.1| pseudouridine synthase [Spirochaeta coccoides DSM 17374]
 gi|329748656|gb|AEC02012.1| pseudouridine synthase [Spirochaeta coccoides DSM 17374]
          Length = 256

 Score = 98.9 bits (245), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 81/238 (34%), Gaps = 40/238 (16%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQG---GSGIAYHIDGFLKSWVDSKGQKPR------ 145
             +   ++ E     V  KPAG+       G      +D     + D +  + R      
Sbjct: 11  PDIPFSIIAETPSYLVVAKPAGMPAVPLKTGGKGETLLDAVADLYPDVRSVQGRNEWEGG 70

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG------IPKNKKECIA 199
           + HRLD  TSG+ V+ART  A   L          K Y +  +G       P      I 
Sbjct: 71  VVHRLDTLTSGLTVIARTDEAWWALQAQQTAGLFAKTYAAWSFGRQDDEMFPPGFPSEIV 130

Query: 200 NWLLKKSH----------IGGDYVHVVKQNEKG---ANYAISHFKV----IDCFAQKFCW 242
            ++ K             +G   V  V ++  G   +    + ++      +    K   
Sbjct: 131 YYVTKDGLFLRSSFRPWGVGARAVRPVCEDATGHGASKATDTIYETTIVSHEKGPGKLNT 190

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
             +Q + G  HQ+R H    G P+VGD  Y             ++L L A  ++   P
Sbjct: 191 FHVQIYRGFRHQIRCHLAWYGFPLVGDSLYGGEPN--------DRLGLFAEKVEFEDP 240


>gi|15618318|ref|NP_224603.1| pseudouridine synthetase family protein [Chlamydophila pneumoniae
           CWL029]
 gi|15835936|ref|NP_300460.1| pseudouridine synthetase family protein [Chlamydophila pneumoniae
           J138]
 gi|33241749|ref|NP_876690.1| pseudouridine synthetase [Chlamydophila pneumoniae TW-183]
 gi|4376683|gb|AAD18547.1| predicted pseudouridine synthetase family [Chlamydophila pneumoniae
           CWL029]
 gi|8978775|dbj|BAA98611.1| pseudouridine synthetase family [Chlamydophila pneumoniae J138]
 gi|33236258|gb|AAP98347.1| pseudouridine synthetase [Chlamydophila pneumoniae TW-183]
          Length = 232

 Score = 98.5 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 76/183 (41%), Gaps = 39/183 (21%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHII 78
           RL  + ++  P+ +   +   +R  + RV+    +F + ++Q G  V +  + +      
Sbjct: 27  RLSSFLRSQLPNHSKQEILASIRQHRCRVNGFIERFESYKVQPGDRVSLSLIPSTKQQ-- 84

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                 +L+ED    ++ KP  ++ +  + +             
Sbjct: 85  --------------------PSILWEDDYSIIYEKPPHLTTEQMAHMT------------ 112

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +    HRLD+ TSG L++ +++ AA  L + F+ R+I K Y + V+G PK K   +
Sbjct: 113 ----RFFTVHRLDKGTSGCLLMGKSKQAATELMKLFKQRKIHKQYIAFVFGHPKKKFGTV 168

Query: 199 ANW 201
            ++
Sbjct: 169 KSY 171


>gi|38566140|gb|AAH62362.1| RPUSD3 protein [Homo sapiens]
 gi|119584410|gb|EAW64006.1| RNA pseudouridylate synthase domain containing 3, isoform CRA_a
           [Homo sapiens]
          Length = 328

 Score = 98.5 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 93/246 (37%), Gaps = 42/246 (17%)

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRM 176
            G    + +   L   +  + Q+ ++     +E+SG+++++     A  L +    + R 
Sbjct: 82  PGELTLFSVLPELSQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFTHARRA 141

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFK 231
           +R    Y ++  GIP   +  I   L  +   G +    VK   +     G    +SHF+
Sbjct: 142 QRPTATYCAVTDGIPAASEGKIQAALKLEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFR 201

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQN- 286
           V+         +++QP T  + QL+VH +   CP++GDH Y A         F  P +N 
Sbjct: 202 VVAT-GSGCALVQLQPLTVFSSQLQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAENN 260

Query: 287 ---KLYLHARYMDLPHPE------------------------GGRLQITAPLPAHMVKTW 319
              +  L    +   H                             +++ APLP +  +T 
Sbjct: 261 KPQRQVLDEALLRRLHLTPSQAAQLPLHLHLHRLLLPGTRARDTPVELLAPLPPYFSRTL 320

Query: 320 DSLGFK 325
             LG +
Sbjct: 321 QCLGLR 326


>gi|242208602|ref|XP_002470151.1| predicted protein [Postia placenta Mad-698-R]
 gi|220730753|gb|EED84605.1| predicted protein [Postia placenta Mad-698-R]
          Length = 348

 Score = 98.5 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 56/248 (22%), Positives = 83/248 (33%), Gaps = 41/248 (16%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF---------LKSWVDSKGQKPRL 146
             K  LLY D  + + NKP+G+  Q         +           LK  +         
Sbjct: 54  LAKHALLYVDRGLLLVNKPSGLVCQYNRKDDREQNAHSDFNDFTDDLKRQLSLDA-DLLP 112

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG---IPKNKKECIANWLL 203
            HRLD+ T+G L  A T + AQ L E F    ++K Y ++V G      N+   I   L 
Sbjct: 113 LHRLDKATTGALAFALTHSHAQDLAEQFNAHTVKKSYLAIVRGGTASFPNRTGNIRGVLY 172

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHM 262
             +  G        Q EK A    + ++V+          + + P TG  HQLRVH   +
Sbjct: 173 --TTNGRVSSEAQGQWEKRAIT-ETDWEVLASSPVAPLSLVRLSPFTGHKHQLRVHMAKI 229

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                                   +L               R+   A LP + V+  D +
Sbjct: 230 L---------KGKLTRYLPEGPNKRL---------------RMTFGASLPRYFVRLCDRI 265

Query: 323 GFKYDRNL 330
                  L
Sbjct: 266 KIPLSSEL 273


>gi|224066344|ref|XP_002187027.1| PREDICTED: similar to RNA pseudouridylate synthase
           domain-containing protein 3 [Taeniopygia guttata]
          Length = 270

 Score = 98.1 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 53/278 (19%), Positives = 110/278 (39%), Gaps = 51/278 (18%)

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           ++ +++++   +    L+  +++ +  +   +KP G+ + G  G    +D  L +     
Sbjct: 7   REQVEAALGPKETVRLLEGFVVHREGALLALSKPPGLPILGRPGDL-SLDSLLPALRRRL 65

Query: 141 GQ--KPRLTHRLDQETSGILVVA----RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           G   +  +     +E SG+++++     T+   Q  T + R  +    Y ++  G+P   
Sbjct: 66  GLAAELHVVKAPAREYSGLVLLSSCYHTTKKLHQFFTSARRRGQYPATYRAVTVGVPAEV 125

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  ++  L              +Q    A   ++H++V+         L++QP T    Q
Sbjct: 126 EGEVSTGL------------CWQQQGDRAMSTLTHYRVLSTTG-GCALLQLQPRTAFPEQ 172

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSP------------------IQNKLYLHARYM- 295
           L+VH   + CP +GDHK+ +        P                  + ++L L  R + 
Sbjct: 173 LQVHLTLLLCPALGDHKHSSRVGRVLGVPFCLPLETAPTRTQVLDEELLSRLGLSPRQLH 232

Query: 296 ---------DLPHPEGGRLQITAPLPAHMVKTWDSLGF 324
                    +L  PEG    + AP P + + T  SLG 
Sbjct: 233 HLPLHIHLQELVLPEGP---LCAPPPPYFLHTLHSLGL 267


>gi|216548152|ref|NP_001136019.1| RNA pseudouridylate synthase domain-containing protein 3 isoform 2
           [Homo sapiens]
          Length = 336

 Score = 98.1 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 93/246 (37%), Gaps = 42/246 (17%)

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRM 176
            G    + +   L   +  + Q+ ++     +E+SG+++++     A  L +    + R 
Sbjct: 90  PGELTLFSVLPELSQSLGLREQELQVVRASGKESSGLVLLSSCPQTASRLQKYFTHARRA 149

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFK 231
           +R    Y ++  GIP   +  I   L  +   G +    VK   +     G    +SHF+
Sbjct: 150 QRPTATYCAVTDGIPAASEGKIQAALKLEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFR 209

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQN- 286
           V+         +++QP T  + QL+VH +   CP++GDH Y A         F  P +N 
Sbjct: 210 VVAT-GSGCALVQLQPLTVFSSQLQVHMVLQLCPVLGDHMYSARVGTVLGQRFLLPAENN 268

Query: 287 ---KLYLHARYMDLPHPE------------------------GGRLQITAPLPAHMVKTW 319
              +  L    +   H                             +++ APLP +  +T 
Sbjct: 269 KPQRQVLDEALLRRLHLTPSQAAQLPLHLHLHRLLLPGTRARDTPVELLAPLPPYFSRTL 328

Query: 320 DSLGFK 325
             LG +
Sbjct: 329 QCLGLR 334


>gi|170055019|ref|XP_001863394.1| conserved hypothetical protein [Culex quinquefasciatus]
 gi|167875138|gb|EDS38521.1| conserved hypothetical protein [Culex quinquefasciatus]
          Length = 252

 Score = 98.1 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 43/168 (25%), Positives = 75/168 (44%), Gaps = 12/168 (7%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D+        HRLD  TSGIL +   + A + + + F  +R +K Y +L+ G      E 
Sbjct: 48  DNLTHDFYFAHRLDFATSGILCIPLNKNACKEVCQVFEEQRARKYYLALLRGHTDFDDEV 107

Query: 198 IANWLLKKSH--IGGDYVHVVKQNE--KGANYAISHFKVIDC---FAQKFCWLEMQPHTG 250
           I   + +          +  + ++E  +    +I+   V+D      +    + ++P TG
Sbjct: 108 IDIAIGEDIRFKDTSKKMCTILEDELCQNPRRSITKVLVLDRGYYNGKPVTKVLLRPITG 167

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLP 298
           R HQLR+H   +G  IVGD+ Y      +       +++LHA  + LP
Sbjct: 168 RRHQLRLHCSQIGHVIVGDYTYSLKIDTSPP-----RMFLHAFRLVLP 210


>gi|229829765|ref|ZP_04455834.1| hypothetical protein GCWU000342_01862 [Shuttleworthia satelles DSM
           14600]
 gi|229791754|gb|EEP27868.1| hypothetical protein GCWU000342_01862 [Shuttleworthia satelles DSM
           14600]
          Length = 312

 Score = 97.7 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 63/293 (21%), Positives = 99/293 (33%), Gaps = 92/293 (31%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--KPRLTHRLDQE 153
            +++ ++YED+ I+V  KPAG + Q  S +   +   LK++  S+G+     L  RLDQ 
Sbjct: 1   MMRTEIIYEDADIFVCYKPAGFATQTASALQADLVSELKNYRKSRGESDYIGLIGRLDQP 60

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK--------------------- 192
             G++V+A+   AA  L  +    RI K Y +L  G+PK                     
Sbjct: 61  VEGLMVIAKNPRAAGKLEAAQAKGRIDKYYLALTQGLPKGPDCGQEADSLHRKGEWIFLE 120

Query: 193 --------NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI-------SHFKVIDCFA 237
                    K   +     K +  G       K  + G   A+       +         
Sbjct: 121 NDMLPASRGKNGRLLAPEDKGTKNGHQPAPEDKGTKNGHQPAVKDKGAKKTRL-PAPGTG 179

Query: 238 QKFCWLEMQPHTG---------------RT----HQL---------------RVH----- 258
           +     ++ P TG               R     +Q+               RVH     
Sbjct: 180 EAKTACQLAPGTGEAKKACLLAPGIKGARKARLEYQILDHSKTKDGRALALLRVHLLTGR 239

Query: 259 -------ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
                     +G PI+GD +Y A+  G         L L A  +  PHP  G 
Sbjct: 240 RHQIRLQLSGLGSPILGDARYGADPNG-------QPLALCACQLSFPHPGTGE 285


>gi|260434982|ref|ZP_05788952.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp. WH
           8109]
 gi|260412856|gb|EEX06152.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp. WH
           8109]
          Length = 248

 Score = 97.7 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 98/240 (40%), Gaps = 35/240 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPP 69
           V   +  + +  W  + Y H +    Q+ + +G++  +   +  +  +  G+ +  R PP
Sbjct: 20  VPRADAGLLVSEWLADRYRHSDRAVWQQRIAAGELDWNGALLTGDRALHGGETLFWRRPP 79

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +        EQ I D                +++D  + V NKP+G+ V  G G   H 
Sbjct: 80  WL--------EQAIPDQWET------------IHDDGDLLVINKPSGLPVMPGGGFLRH- 118

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR----MRRIQKIYWS 185
              L + ++  G  P   HRL + TSG+ V ART       ++ FR     R++ + +  
Sbjct: 119 --TLTALLEHAGALP--VHRLGRFTSGLQVCARTPQTRALWSKQFRPDGGCRKVYQAWSQ 174

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE----KGANYAISHFKVIDCFAQKFC 241
            V G+   +   +++ ++++ H    ++   +  +    +    A S  ++++  A    
Sbjct: 175 QVPGLELGQCLTVSSDVVERPHPLLGWIWGPEPFDDVPIRKRLSAHSELELLERTAGTST 234


>gi|313835228|gb|EFS72942.1| RNA pseudouridine synthase [Propionibacterium acnes HL037PA2]
 gi|314970851|gb|EFT14949.1| RNA pseudouridine synthase [Propionibacterium acnes HL037PA3]
          Length = 174

 Score = 97.7 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 44/161 (27%), Positives = 65/161 (40%), Gaps = 5/161 (3%)

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE---CIANWL 202
           + HRLD+ T+G+L++ R R   +   E F  R + K Y  +   +     E      N  
Sbjct: 1   MAHRLDRVTAGVLLLTRERQWRRPYQELFERREVVKKYRLVAPAVHDPAGEGAVVTNNGW 60

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
             +S I  +   +  +   G   A++   V+          E  P TGRTHQ+R+H   +
Sbjct: 61  QVRSRIVKERGILQAREVPGEPNAVTDI-VLVSEHGGLGLYEASPRTGRTHQIRLHMQRL 119

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           G PIV D  Y     G       + L L A  M    P  G
Sbjct: 120 GAPIVNDPFY-PIVLGTQIDDFTHPLQLQAWQMGFTDPVSG 159


>gi|260494555|ref|ZP_05814685.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_33]
 gi|260197717|gb|EEW95234.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_33]
          Length = 95

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 29/101 (28%), Positives = 49/101 (48%), Gaps = 8/101 (7%)

Query: 222 GANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
           G   A +H KV++  + +   +LE + +TGRTHQ+R H   +G  +VGD  Y  N     
Sbjct: 1   GGKSAKTHIKVLERNYEKNITFLEARLYTGRTHQIRAHLSLIGHSLVGDELYGGNMN--- 57

Query: 281 TSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWD 320
              +  +  LHA  ++  +P+    L+I   +P  M +   
Sbjct: 58  ---LAKRQMLHAYKLEFQNPKTLENLKIEIDIPIDMKEVLK 95


>gi|167933175|ref|ZP_02520262.1| pseudouridine synthase, RluA family protein [candidate division TM7
           single-cell isolate TM7b]
          Length = 94

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 28/101 (27%), Positives = 47/101 (46%), Gaps = 9/101 (8%)

Query: 222 GANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
               A + ++V      +    +++QP TGRTHQLRVH  ++  PI+GD  Y        
Sbjct: 2   NGKSAQTSYEVERSIIKKNISLIKLQPKTGRTHQLRVHMQYLNTPILGDLVYGGKPAE-- 59

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
                 +++LHA  +++    G R    APLP   +  ++ 
Sbjct: 60  ------RMFLHAESLEVTLLSGERKVFKAPLPDDFINFFNQ 94


>gi|303277319|ref|XP_003057953.1| RNA pseudouridylate synthase [Micromonas pusilla CCMP1545]
 gi|226460610|gb|EEH57904.1| RNA pseudouridylate synthase [Micromonas pusilla CCMP1545]
          Length = 348

 Score = 97.0 bits (240), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 66/317 (20%), Positives = 103/317 (32%), Gaps = 59/317 (18%)

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
            G   R      A+    + + +  S V + +  D              V  KPAG+ V 
Sbjct: 25  PGDDAREIESRRAVRAKARGESLAASDVPVLRRDDADADADGDGGGAFVVVRKPAGVYVD 84

Query: 121 GG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              + +         +      ++  L HRLD++TSG LVVA +  A   LT +F   ++
Sbjct: 85  DVLAALERDASASASASPSPSPRRLHLAHRLDRDTSGCLVVATSTRACAALTRAFADGKV 144

Query: 180 QKIYWSLVWG-------IPKNKKECI------ANWLLKKSHIGGDY-----------VHV 215
           +K Y +            P+            A  L  ++  G              V  
Sbjct: 145 RKEYLAHCSSAAASSSSEPREPDPSPSPSLDGARPLTLRTGHGRSRNGLWRVYPLSDVGR 204

Query: 216 VKQNEKGANY-----AISHFKVIDCFA----------QKFCWLEMQPHTGRTHQLRVHAL 260
               + G        A +   V+   A           +  ++   P TGRTHQ+R+H  
Sbjct: 205 ALPRDPGRKTTLVKIAETSLVVVATAAARGGGGGGERSRCAYVRATPTTGRTHQIRLHCA 264

Query: 261 HMGCPIVGDHKYCANF-----------------KGNFTSPIQNKLYLHARYMDLPHP--E 301
           H G  IVGD KY                              +   LHA  +  PHP  E
Sbjct: 265 HAGAAIVGDVKYGGPRVVEEEEEEEEKEKETQEDDALIDTRFDGFRLHAAKIAFPHPTRE 324

Query: 302 GGRLQITAPLPAHMVKT 318
           G  +++  P P    + 
Sbjct: 325 GQTVEVECPPPGWWREA 341


>gi|255019167|ref|ZP_05291293.1| hypothetical protein LmonF_18021 [Listeria monocytogenes FSL
           F2-515]
          Length = 163

 Score = 96.2 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 75/174 (43%), Gaps = 27/174 (15%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQ--KILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           VE +E+ + L  + K+   HI+   L   K    G++ V+ +       ++ G  VR+  
Sbjct: 7   VETEEDGLLLRTFLKS--KHISKQLLTAVKFGADGKIEVNSEEQNVLXHVKVGDKVRLTF 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                N  +               +++    +++ED  + + NKPAG++        YH 
Sbjct: 65  PTEQQNERL--------------LAEYTNLDIVFEDDFLLIINKPAGMASIPSQ---YHP 107

Query: 130 DGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +G + ++V    +         +  RLD+ETSG++++A+ R A   L+     R
Sbjct: 108 NGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLSTFLXKR 161


>gi|297285309|ref|XP_001096088.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein 3
           isoform 2 [Macaca mulatta]
          Length = 336

 Score = 96.2 bits (238), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 52/248 (20%), Positives = 92/248 (37%), Gaps = 45/248 (18%)

Query: 122 GSGIAYHIDGFLKSWVDSKG---QKPRLTHRLDQETSGILVVARTRAAAQHLTE----SF 174
           G      +   L     S G   Q+ ++     +E+SG+++++     A  L +    S 
Sbjct: 88  GKSGELTLLSVLPELSQSLGLGEQELQVVRASGKESSGLVLLSSCPQTASRLQKFFTHSQ 147

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISH 229
           R +R    Y ++  GIP   +  I   L  +   G +    VK   +     G    +SH
Sbjct: 148 RAQRPTATYCAVTNGIPTASEGKIQAALKLEHIDGVNLTVPVKAPSRKDILQGVKKTLSH 207

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN----FKGNFTSPIQ 285
           F+V+         +++QP T  + QL+VH +   CP++GDH Y A         F  P +
Sbjct: 208 FRVVAT-GSGCALVQLQPLTVFSSQLQVHMVLQLCPVLGDHTYSARVGTVLGQRFLLPAE 266

Query: 286 N----KLYLHARYMDLPHPE------------------------GGRLQITAPLPAHMVK 317
           +    +  L    +   H                             +++ APLP +  +
Sbjct: 267 STKPQRQVLDEALLRRLHLTPSQAAQLPLHLHLHRLLLPGTRARDTPIELLAPLPPYFSR 326

Query: 318 TWDSLGFK 325
           T   LG +
Sbjct: 327 TLQCLGLR 334


>gi|300717274|ref|YP_003742077.1| Pseudouridine synthase [Erwinia billingiae Eb661]
 gi|299063110|emb|CAX60230.1| Pseudouridine synthase [Erwinia billingiae Eb661]
          Length = 205

 Score = 96.2 bits (238), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 43/178 (24%), Positives = 72/178 (40%), Gaps = 15/178 (8%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           KI+D+ +    H    +  +LY+D+ + + NKP G+    G          +   +    
Sbjct: 3   KIIDTFIAPPCHE---QIEILYQDAYLVLINKPTGLLSLSGKNPQN--LDSVHHRLVQLF 57

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
               L HRLD  TSG++V+AR +A    L   F  R + K+Y +L+ G        I   
Sbjct: 58  PGCTLIHRLDFGTSGLMVIARNKAINAALCHQFSQRTVTKVYSALLCGHLAEDDGVIDAA 117

Query: 202 LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           + K   +    + +   N      A S ++V++ F +K       P T      RV  
Sbjct: 118 IAKDPAL-FPLMSICAVN---GKPARSRYQVVERFYRKSEDGTSLPVT------RVQL 165


>gi|172039791|ref|YP_001799505.1| putative pseudouridylate synthase [Corynebacterium urealyticum DSM
           7109]
 gi|171851095|emb|CAQ04071.1| putative pseudouridylate synthase [Corynebacterium urealyticum DSM
           7109]
          Length = 422

 Score = 96.2 bits (238), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 53/319 (16%), Positives = 101/319 (31%), Gaps = 70/319 (21%)

Query: 57  NRIQSGQVVRIPPVINALNHIIKEQKILD-SSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
            R  +G+VV       + + +I+  + ++       +     +  LL++D+ + V +KP 
Sbjct: 100 ERFAAGEVVDDAGRPLSPSDVIRPGRYINFYRRPAPERPVPGQLRLLFQDANLLVVDKPP 159

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
            ++     G        +++       +    HRLD+ T G+L+              F 
Sbjct: 160 FMATLP-RGQHIVETALVRARRQFGIPELSPAHRLDRLTRGVLMFTVRPEVRGPYQRLFD 218

Query: 176 MRRIQKIYWSLV-------------------WGIPKNKK------------ECIANWLLK 204
            R  +K Y ++                    W  P  ++              +A +L++
Sbjct: 219 ERVPEKTYEAVTLPADEAPFPPIPRFRGWQEWPAPTPEQPWLLRHHMVKERGRLATYLVE 278

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHF--------KVIDCFAQKFCW-------------- 242
                 D           A+ +   F        KV+   +++                 
Sbjct: 279 PEAPAIDATAPTDSGAAAASPSHDMFLAPPNALTKVVGVRSERRALAIAGGPTPRERRVL 338

Query: 243 -LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ--------------NK 287
             E+ P TG+THQLRV    +G PI+ D  Y          P                  
Sbjct: 339 VWELVPETGKTHQLRVALRTLGLPILNDPLYEELSDEALRDPTAALPSPPFAGEEDFGRP 398

Query: 288 LYLHARYMDLPHPEGGRLQ 306
           + L A+ +    P  G L+
Sbjct: 399 MELTAQRLRFHDPLTGELR 417


>gi|302837881|ref|XP_002950499.1| hypothetical protein VOLCADRAFT_90941 [Volvox carteri f.
           nagariensis]
 gi|300264048|gb|EFJ48245.1| hypothetical protein VOLCADRAFT_90941 [Volvox carteri f.
           nagariensis]
          Length = 535

 Score = 96.2 bits (238), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 30/82 (36%), Positives = 41/82 (50%), Gaps = 7/82 (8%)

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
                   +   PHTGRTHQ+RVH  H+G PI+GD  Y        T P   +  LHA  
Sbjct: 403 SIPSGASLMLCAPHTGRTHQIRVHLHHVGHPILGDDIYG------VTGPWMGRQALHAAE 456

Query: 295 MDLPHPEGGR-LQITAPLPAHM 315
           +   HP  G+ ++++APL   M
Sbjct: 457 LRFTHPLTGQVMRLSAPLHDDM 478



 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 25/118 (21%), Positives = 41/118 (34%), Gaps = 19/118 (16%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI---SVQ----------------GGSGIA 126
           ++V L          +++ED      NKP G+    +                 G  G  
Sbjct: 172 AAVPLAADWGGEPLDVVHEDEHFLAVNKPPGMHTAPIHRFAAAAAATSSEEPWVGDDGSE 231

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                           +P + HRLD  TSG+L+ A+       +   FR R ++K+Y 
Sbjct: 232 TTAAAPASGRTVPYQLEPYVLHRLDMNTSGLLLFAKRPEVVAGMHRQFRERTLRKLYL 289


>gi|223995833|ref|XP_002287590.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220976706|gb|EED95033.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 614

 Score = 95.8 bits (237), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 51/273 (18%), Positives = 96/273 (35%), Gaps = 37/273 (13%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG---------FLK 134
           +   +   K  D  K  +L +     + +KPA + V   S      D           L+
Sbjct: 316 IPEELLQQKVEDDGKVEILDQGENYVIASKPASVIVHHSSWTGKRSDPKRRWKEATPMLQ 375

Query: 135 SWVDSKGQKPRLTHRLDQETSGILV--VARTRA----------AAQHLTESFRMRRIQKI 182
              D+ G++  L HRLD+  SG LV   A+               + + E+ +    +K 
Sbjct: 376 RVRDATGRRVNLVHRLDRGASGCLVFSFAQNEENDNGETPPCSVTKSMIEAMQHPDARKT 435

Query: 183 YWSLV--WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN-------YAISHFKVI 233
           Y +L    G           W    + +  ++  ++                  S     
Sbjct: 436 YLALCDGDGTWNGVDYLNKGWFTFNNPVKDEWGKLIDDCCTDIRFVASKVLPPTSDEDPD 495

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALH--MGCPIVGDHKYCANFKGNF----TSPIQNK 287
           +   +K   +  +P TGR HQ+R H     +G  ++GD  +  +            ++ +
Sbjct: 496 NMEGRKVSLILARPKTGRWHQVRQHLSSGTIGHALLGDSTHGKSRTNRIWKKDRHLMKER 555

Query: 288 LYLHARYMDLPHPE-GGRLQITAPLPAHMVKTW 319
             LH   + +P  E    + I+ PLP+ ++K  
Sbjct: 556 TCLHLSRVQIPATEYTPAIDISCPLPSDLIKML 588



 Score = 81.9 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 47/219 (21%), Positives = 76/219 (34%), Gaps = 41/219 (18%)

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRA------------AAQHLTESFRMRRIQ 180
           L     +K +K  L HRLD+  SG L++A                +   L ++       
Sbjct: 74  LPDEQKAKVRKVNLVHRLDRGASGCLLLAYADDDGAEVANASVSGSTAMLIDALASPEST 133

Query: 181 KIYWSLV--WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           K Y +LV   GI + +      W      I        K        A + F  +    +
Sbjct: 134 KTYVALVRGEGILREEDFKTKGWFNVTRPI--------KDESGEEKDATTWFNFVAGQPE 185

Query: 239 ---------KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--- 286
                    +   +  +P  GR HQ+R H   +  PI+GD  + A+         +N   
Sbjct: 186 TVEDGIERPRMSLVLARPMQGRWHQIRKHLNGISHPILGDTTHGASTVNREWKEKRNLPG 245

Query: 287 -KLYLHARYMDLPH----PEGGRLQITAPLPAHMVKTWD 320
            ++ LH   + LP     PEG  + +  PL   M+    
Sbjct: 246 ERICLHLARLQLPPTEAVPEG--IDVCCPLLDDMLDMLR 282


>gi|255088607|ref|XP_002506226.1| RNA pseudouridylate synthase [Micromonas sp. RCC299]
 gi|226521497|gb|ACO67484.1| RNA pseudouridylate synthase [Micromonas sp. RCC299]
          Length = 481

 Score = 95.8 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 61/348 (17%), Positives = 106/348 (30%), Gaps = 99/348 (28%)

Query: 31  HINFVNLQKILRSGQVRVD--------KKRVKFNNR-----IQSGQVVRIPPVINALNHI 77
            ++     ++L  G V  +         K  ++        +  G+V+R+        H 
Sbjct: 114 DVSRELAAELLDVGAVYAECWPEGEGEGKPTRWRRIADRKIVAKGEVIRVHKRPRRYRHA 173

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKS 135
                           +D  +  +++ED  I V NKP  +       +G+  H  G L+ 
Sbjct: 174 CW------------LGADAWRHRVVHEDDAILVVNKPHRLPSMAHESNGVE-HCAGCLER 220

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM----RRIQKIYWSLVWGIP 191
            +       R+THRLD  TSG+LV+ +T  A +   +S       + I K Y +LV+   
Sbjct: 221 SLGLSPSTLRVTHRLDSSTSGVLVLGKTATAVREFNDSVAKTPGSKEIVKSYAALVYAKH 280

Query: 192 KNKKECIANWL---------------------LKKSHIGGDYVHVVKQNEKGANYAISHF 230
                 + +W+                     L +S   G+          G  +     
Sbjct: 281 AVPLGLMTHWMYPGPFGPGAFHGRTLRRSRARLVRSSADGERGDDTGGQGTGKRWKRCEL 340

Query: 231 KVI---------------------------------------------DCFAQKFCWLEM 245
           +V+                                             D        + +
Sbjct: 341 RVVSCDRATQSQVDTWRTLFDRELERARKPFDGGADDPLVSGGDSPGGDSPGASVWAVRV 400

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHAR 293
           +  TGRTHQ+R      G P++GD  Y A   G        +    A 
Sbjct: 401 ELVTGRTHQVRAQLAAAGAPLLGDSLY-APMAGYLHDRDDERAAEEAW 447


>gi|254445393|ref|ZP_05058869.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198259701|gb|EDY84009.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 270

 Score = 95.8 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 52/248 (20%), Positives = 89/248 (35%), Gaps = 29/248 (11%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL----------T 147
           K  L+  D  ++  NKPAG++           D  +    +   +KP+L           
Sbjct: 21  KFPLIANDEGLFAINKPAGLASFQHEWSLGKPDISMALRRELLNEKPQLKKLGIEGLYRA 80

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
           + LD E SG LV A+     + L  +    ++   +  LV       +E + +  L   H
Sbjct: 81  YNLDSELSGALVFAKNEEFEKILKNAVGSSQLVFRFHLLVKAE-TEDREFVCDLPLMNHH 139

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                +     + +      + F+ +  F Q +   E +  + R HQ+RVHA   G  IV
Sbjct: 140 QAKRMI----VSHRSGKKCETRFRFLRGFGQ-YQLWEAETTSLRVHQVRVHAAERGLNIV 194

Query: 268 GDHKYCANFK-------------GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH 314
           G+  Y    +                  P+   L +H   ++   P+     I APLP+ 
Sbjct: 195 GEDFYSDGEEIYLSRIKRDYMSGRGREKPLYGSLCVHLVEVEFRIPDLKLESILAPLPSR 254

Query: 315 MVKTWDSL 322
                  L
Sbjct: 255 FETLLKRL 262


>gi|294952723|ref|XP_002787432.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Perkinsus marinus ATCC 50983]
 gi|239902404|gb|EER19228.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Perkinsus marinus ATCC 50983]
          Length = 602

 Score = 95.8 bits (237), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 52/241 (21%), Positives = 94/241 (39%), Gaps = 18/241 (7%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +   + A+    KE  + D    +  H          E       +KP  + V  G+   
Sbjct: 289 VERGLKAVVRQEKETLVEDRQKIMDLHQRNDSPDQQQEHDNNNNIDKPYDLRV-DGNDFD 347

Query: 127 YHIDGFLKSWVDSKG-------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             ++ F++    ++         K RL ++LD  TSG LV+   + A +  +  F+ R  
Sbjct: 348 CTVEKFVRDIPHARPGSLKIPMDKFRLANQLDFATSGALVLTLNKTADRETSALFQFRLT 407

Query: 180 QKIYWSLVWGIPKNKKECIANWLL--KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
           +K+Y ++  G   + +      +     S  GG     +       +        + C  
Sbjct: 408 KKVYIAVCEGWVGDDELMKPRIITTGISSEGGGKMSSTIAVPVSTGH--------LLCDD 459

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            K     ++  TGR HQLR+H  ++G PI+GD+ Y  +       P   ++ LHA  + L
Sbjct: 460 IKCTVYILRLLTGRRHQLRLHLSYIGHPILGDYTYSTHLPKGGRGPTLPRMLLHAWRLTL 519

Query: 298 P 298
           P
Sbjct: 520 P 520


>gi|311740710|ref|ZP_07714537.1| RNA pseudouridylate synthase [Corynebacterium pseudogenitalium ATCC
           33035]
 gi|311304230|gb|EFQ80306.1| RNA pseudouridylate synthase [Corynebacterium pseudogenitalium ATCC
           33035]
          Length = 287

 Score = 95.8 bits (237), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 49/246 (19%), Positives = 79/246 (32%), Gaps = 20/246 (8%)

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            + P   AL H +                D+    +++ D  + V +KP  +       +
Sbjct: 52  TVLPPGAALPHPVPAWYHPSVPPERPIPFDY---SVVHADRDLIVADKPHFLPTTTNGRL 108

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                   +  VD         HRLD+ T+G+++ +R  A        F      K Y  
Sbjct: 109 QRETLQT-RLRVDFGEDDIVPLHRLDRLTAGLVICSRNPATRAAYQRIFLEGSAVKKYR- 166

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
              G+ K          L+     G     V          ++   V     +   W   
Sbjct: 167 ---GVVKQPLFVDQEIALRMHKPRGSRQVFVAPEG-----TLTSTYVRAAGREVTMW--- 215

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP--EGG 303
            P TG THQLRV   H+G P++GD  Y    K +     +  L L    +    P     
Sbjct: 216 -PRTGHTHQLRVLLNHLGHPLLGDDTYPTPRKLDLYD-FRTPLALLHEAITFIDPLSHSE 273

Query: 304 RLQITA 309
           R   ++
Sbjct: 274 RQFFSS 279


>gi|148667045|gb|EDK99461.1| mCG132976, isoform CRA_a [Mus musculus]
          Length = 320

 Score = 95.4 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 87/246 (35%), Gaps = 42/246 (17%)

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRM 176
            G      +   L   +  + Q+ ++     +E SG+++++     A  L +    S R 
Sbjct: 74  PGELTLLSVLPQLSQALGLEHQELQVVRAPGKEASGLVLLSSCPQTASRLQKFFIHSRRA 133

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV-----KQNEKGANYAISHFK 231
           +R    Y ++  GIP+  +  +   L  +     D    V     K  ++G    +S F 
Sbjct: 134 QRPTATYCAVTDGIPEPSEGTVCMPLKMEQMNDVDLAVPVMSPSRKDIQEGVKRTLSRFH 193

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSP 283
           V+    +    +++QP T   +QL+VH     CPI+GDH Y           F     + 
Sbjct: 194 VMAT-GRGCALVQLQPLTVFPNQLQVHMALQLCPILGDHTYAARVGTVLGQRFLWPAETT 252

Query: 284 IQNK------LYLHAR--------------YMDLPHPEGG----RLQITAPLPAHMVKTW 319
              +      L  H R                 L  P  G      ++ APLP +  +T 
Sbjct: 253 KPQRQVLDEALLRHLRLSPSQVAQMPLHLHLHRLLLPGTGSRDPPSELLAPLPPYFSRTL 312

Query: 320 DSLGFK 325
             L   
Sbjct: 313 QCLRLS 318


>gi|301606985|ref|XP_002933094.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 3
           [Xenopus (Silurana) tropicalis]
          Length = 368

 Score = 95.4 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 65/361 (18%), Positives = 131/361 (36%), Gaps = 63/361 (17%)

Query: 21  LDRWFKN---HYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +DR++     H+ +++ V   K             +   ++   G+  R  P  + ++ +
Sbjct: 18  IDRFYFRASCHFSNVSRVPWYK-----------THLDVRDK---GRKPRSEPQSSRVSIL 63

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                 +   ++  +    L   ++Y    +   NKP G+S+  G      +   L    
Sbjct: 64  RDPGVFVVDKMSRERICQLLVENVVYLKGPLVAINKPQGLSI-TGKEQEVSVSSLLADLQ 122

Query: 138 DSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIP 191
              G      +     +E+SG+++++      + L +      + ++    Y +++ G+P
Sbjct: 123 QHLGLGSDLHIVKAAPKESSGLVLLSTCHMTTKRLEDYYALCRKAQKPTASYCAVMAGVP 182

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGA------NYAISHFKVIDCFAQKFCWLEM 245
              +  I   L  +       V  V    KG          ++ +KV+D  A     +++
Sbjct: 183 HPAEGEIKAALKLERIEDWQLVVPVTDPSKGRLERREIKRTLTRYKVLDS-ADGCALVQL 241

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCAN----------------------------FK 277
           QP +    QL VH+  M C I+GDH Y A                              +
Sbjct: 242 QPMSVFQAQLLVHSTLMFCRILGDHTYSARVGKVLGENIFVPMDIALPRTQVLEENVLRR 301

Query: 278 GNFTSPIQNK--LYLHARYMDLP--HPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIK 333
            +FT    ++  L+LH + + +P   P  G   + AP P    +T   LG   ++ L   
Sbjct: 302 MHFTQQQMHRMPLHLHFQQLMIPGESPAEGDTFLDAPPPPFFQRTLQLLGLYANKQLCSD 361

Query: 334 R 334
           R
Sbjct: 362 R 362


>gi|123445956|ref|XP_001311733.1| RNA pseudouridylate synthase family protein [Trichomonas vaginalis
           G3]
 gi|121893554|gb|EAX98803.1| RNA pseudouridylate synthase family protein [Trichomonas vaginalis
           G3]
          Length = 173

 Score = 95.4 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 29/115 (25%), Positives = 57/115 (49%), Gaps = 6/115 (5%)

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A++ +AA+  TE     +I+K Y + V G    +K+ +   +++ +      V      
Sbjct: 1   MAKSDSAAKRFTEMLNNNKIEKTYIARVLGQFPPEKKIVDLPIIESAESRAKMVC----- 55

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           ++G   + + F+++    ++   ++  P TGRTHQ+RVH   +G PI  D  Y  
Sbjct: 56  KEGGKPSQTEFELVTTNGKE-SIVKCHPITGRTHQIRVHLASIGFPISNDVFYGG 109


>gi|170575159|ref|XP_001893124.1| RNA pseudouridylate synthase family protein [Brugia malayi]
 gi|158601026|gb|EDP38041.1| RNA pseudouridylate synthase family protein [Brugia malayi]
          Length = 422

 Score = 95.4 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 45/274 (16%), Positives = 99/274 (36%), Gaps = 34/274 (12%)

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I E+      +N     + + + ++YED ++  FNKP  ++          +   L    
Sbjct: 153 IWEEIEPVWKMNNDDLVNIMTNRIIYEDEELIAFNKPYQVACSNAPSNQAELLRILPQLS 212

Query: 138 DSKGQK---PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                     R+   + +  +G+ + A+ +   + +   +    I++ Y  +    P ++
Sbjct: 213 SRITPHMNCLRIVKSIGKSVTGVTLFAKNQNVQEKIKTLYENGLIEQCYRVITNMAPAHQ 272

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFC-WLEMQPHTGRT 252
           +  I   L+         +     NE      A ++++V+    +    ++E   +    
Sbjct: 273 EATINIPLML-------PLSANSSNEITPFLEASTYYRVLRHDPKNHTSYMECVVNCDVP 325

Query: 253 HQLRVHA-LHMGCPIVGDHK--YCANFKGNFTSPIQN-----------------KLYLHA 292
            Q+R H  + + CPI+GD K  Y     G    P  +                  +Y+H 
Sbjct: 326 EQIRAHLGIGIACPIIGDIKYNYSRREAGRGIPPRLSDSALRDLNIAGNSFRRLPMYIHL 385

Query: 293 RYMDLPHP--EGGRLQITAPLPAHMVKTWDSLGF 324
           + + +P       ++ I AP+P+    T   L  
Sbjct: 386 KEVIIPLSKQSSNKIHICAPIPSFFTYTLRKLRL 419


>gi|255324437|ref|ZP_05365554.1| RNA pseudouridine synthase family protein [Corynebacterium
           tuberculostearicum SK141]
 gi|255298343|gb|EET77643.1| RNA pseudouridine synthase family protein [Corynebacterium
           tuberculostearicum SK141]
          Length = 279

 Score = 95.0 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 48/243 (19%), Positives = 76/243 (31%), Gaps = 20/243 (8%)

Query: 69  PVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH 128
           P   AL H +                D+    +++ D    V +KP  +       +   
Sbjct: 47  PPGAALPHPVPAWYHPAVPPERPIPFDY---SVVHADRDFIVADKPHFLPTTTNGRLQRE 103

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                +  VD         HRLD+ T+G+++ +R           F      K Y     
Sbjct: 104 TLQT-RLRVDFGEDDIVPLHRLDRLTAGLVICSRNPETRAAYQRIFLEGSAVKRYR---- 158

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G+ K          L+     G     V          ++   V     +   W    P 
Sbjct: 159 GVVKQPLFVDQEIALRMHKPRGSRQVFVAPEG-----TLTSTYVRAAGREVTMW----PR 209

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP--EGGRLQ 306
           TG THQLRV   H+G P++GD  Y    K +     +  L L    +    P     R  
Sbjct: 210 TGHTHQLRVLLNHLGHPLLGDDTYPTPRKLDLYD-FRTPLALLHEAITFIDPLSHSERQF 268

Query: 307 ITA 309
            ++
Sbjct: 269 FSS 271


>gi|229524488|ref|ZP_04413893.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           bv. albensis VL426]
 gi|229338069|gb|EEO03086.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           bv. albensis VL426]
          Length = 177

 Score = 95.0 bits (235), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 30/104 (28%), Positives = 52/104 (50%), Gaps = 2/104 (1%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++YED  I   NKP+G+    G  +  H D      VD      ++ HRLD  TSG+++
Sbjct: 15  DVIYEDEHIIAANKPSGLLSVPGRPVE-HYDSMWARLVD-YCPDVKVVHRLDMSTSGLIL 72

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            A+ +     L + F+ R   KIY++ VWG+ +  +  +   ++
Sbjct: 73  FAKGKHMESALKKQFQYRLTHKIYYARVWGVMEQDEGEVNLPIV 116


>gi|306835774|ref|ZP_07468775.1| RNA pseudouridine synthase [Corynebacterium accolens ATCC 49726]
 gi|304568348|gb|EFM43912.1| RNA pseudouridine synthase [Corynebacterium accolens ATCC 49726]
          Length = 262

 Score = 95.0 bits (235), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 49/222 (22%), Positives = 77/222 (34%), Gaps = 25/222 (11%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +        +++ D  I V +KP  +       +        +  VD    +    HR
Sbjct: 48  PPEDPIPFDYCVVHADEDIMVADKPHFLPTTTNGRLQRETLQT-RLRVDFGEDEIVPLHR 106

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+++ +R  A        F   R  K Y     GI K    C     L      
Sbjct: 107 LDRLTAGLVICSRNPATRAAYQRIFLEGRAVKRYR----GIVKQPLFCDEEIQLPMHKPR 162

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           G    +V  N        ++ +      ++       P TG THQLRV   H+G P++GD
Sbjct: 163 GSRQVLVADN---GTPTSTYVR---AAGREVTMW---PRTGHTHQLRVLLNHLGSPLIGD 213

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
             Y      +        LY  +R + L H     +    PL
Sbjct: 214 DTYPTPRPLD--------LYDFSRPLSLLH---ETISFIDPL 244


>gi|168054605|ref|XP_001779721.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162668919|gb|EDQ55517.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 401

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 46/200 (23%), Positives = 81/200 (40%), Gaps = 15/200 (7%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
           S ++ E     V +KPAG+SV G       +     S      +   LTH++D  T G +
Sbjct: 142 SRVIAETDSFVVVDKPAGVSVGGTVDNLEEMCATFVSRALKLKKPLILTHQIDTCTEGCV 201

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC------IANWLLKKSHIGGDY 212
           V A+T+A + H     R R+++K Y +L                      +  ++   D+
Sbjct: 202 VFAKTKAFSTHFHMLLRERKVRKEYTALAAAPVAPGHHVHYMRSDRYAPRMVSNNDYSDW 261

Query: 213 VHV------VKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHMG 263
           ++        +Q +  ++     F++  C     +      ++  TGRTHQ+RV    + 
Sbjct: 262 MNCELNVLGCRQVKWPSSSVEKQFRIAHCGWESREHAYECNVRLLTGRTHQIRVQFAALD 321

Query: 264 CPIVGDHKYCANFKGNFTSP 283
            P+VGD  Y  +      SP
Sbjct: 322 APLVGDSVYMPSVVARKKSP 341


>gi|219120675|ref|XP_002181071.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217407787|gb|EEC47723.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 607

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 60/307 (19%), Positives = 102/307 (33%), Gaps = 63/307 (20%)

Query: 50  KKRVKFNNR---IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
            K V+ +     +Q+G  +R+        H  +     D S ++   S     +++ ED+
Sbjct: 130 GKPVRLDQTAPALQAGDYLRVHHHPRRFPHAHR----YDWSKSIHDTSGDKPGVIVAEDT 185

Query: 107 K--IYVFNKPAGISVQGG-SGIAYHIDGFLKSWV-------DSKGQKPRLTHRLDQETSG 156
                V  KP+ + V         ++   LK          D++        RLDQ TSG
Sbjct: 186 DKGWLVIRKPSMVPVHMTVDNCRENVADCLKQARAWQSPTADARDVYITTPQRLDQNTSG 245

Query: 157 ILVVARTRAAAQHLTESFRMRRI----------QKIYWSLVWGI------PKNKKECIAN 200
           ++VVA  +  A +     R +                   V  +       +  K  + +
Sbjct: 246 LVVVATHKPFAAYFASLLRSKTARQLSGDGDDRNHESLGSVHKLYRCLPSIRAPKRFVEH 305

Query: 201 WL--------------------LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
                                 L  S  G D    + Q+  G        K I   A+  
Sbjct: 306 PPDDTQWPECLLKIVKVGNVCELVGSPAGQDLAEALWQDASG------QAKRIPPQAKAV 359

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP----IQNKLYLHARYMD 296
             +E++  TGRTHQ+R     +G P+VGD +Y      N T+        +L L    + 
Sbjct: 360 VEVEIELLTGRTHQIRGQLSTLGFPLVGDAQYGGAVPRNPTNEQFYIGTEQLALQCCELA 419

Query: 297 LPHPEGG 303
              P+  
Sbjct: 420 FRDPDRE 426


>gi|56807623|ref|ZP_00365522.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Streptococcus
           pyogenes M49 591]
          Length = 112

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 25/90 (27%), Positives = 45/90 (50%), Gaps = 5/90 (5%)

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            + +  +    YA + +KV+  +++    ++++ HTGRTHQ+RVH  H+G P++GD  Y 
Sbjct: 1   MITRAVDPMGKYAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGFPLLGDDLYG 60

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                  T     +  LH  Y++   P   
Sbjct: 61  GRLDLGIT-----RQALHCHYLNFKDPFTE 85


>gi|330805411|ref|XP_003290676.1| hypothetical protein DICPUDRAFT_81402 [Dictyostelium purpureum]
 gi|325079175|gb|EGC32788.1| hypothetical protein DICPUDRAFT_81402 [Dictyostelium purpureum]
          Length = 731

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 40/242 (16%), Positives = 77/242 (31%), Gaps = 67/242 (27%)

Query: 9   YVVVENDEENMRLDRWFKN---------HYPHINFVNLQKILRSGQVRVDKKRVK-FNNR 58
            V+V       + D++  +             +   ++ KI+    V V+  ++K  + +
Sbjct: 5   EVIVPKQHVPEKFDKYISSSRIKVKETGELVKLTKSSIPKIIGLKLVTVNNVQLKDKSTK 64

Query: 59  IQSGQVVRIP---------------------------------------PVINALNHIIK 79
           ++    + I                                        P  N      +
Sbjct: 65  VKPNDHIIIKLTNIDQYKVESKGNQEQKESNNISKQTAWWDKNAEQQGKPQTNKKPAPAQ 124

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-------YHIDGF 132
            + I   S      S  +K  +LYED  + V NKPAG+ V   +                
Sbjct: 125 AKPISTGSKGAQLASTDIKLEVLYEDDNLAVINKPAGMLVHPSNTTHTVVLNKEDQTHTL 184

Query: 133 LKSWVDSKG-----------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
           + + +   G           ++P + HRLD++T+GI+++AR     + L   F       
Sbjct: 185 VNALIHRYGGISKLSNLGGNERPGIVHRLDKDTAGIIIIARNNNTHKQLQALFEEHTSTM 244

Query: 182 IY 183
           I 
Sbjct: 245 IK 246



 Score = 78.5 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 29/93 (31%), Positives = 43/93 (46%), Gaps = 5/93 (5%)

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYL 290
           +     +  F  LE+  HTGR+HQ+RVH      PIVGD  Y +  K    S     L L
Sbjct: 528 RTKSIGSNTFSLLEITLHTGRSHQIRVHMASENLPIVGDPIYSSKSKQFLVSH----LLL 583

Query: 291 HARYMDLPHPEGGRL-QITAPLPAHMVKTWDSL 322
            +  +   HP   ++ + T   P+H  +  DS+
Sbjct: 584 ASVSLKFVHPILNQVKEFTIEHPSHFKQFIDSI 616



 Score = 36.5 bits (83), Expect = 6.8,   Method: Composition-based stats.
 Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 8/77 (10%)

Query: 166 AAQHLTESFRMRRI----QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
            A HL++    + I    QK Y  +V G PK     I   + +  H G     V+  +E+
Sbjct: 307 TANHLSKLMEGKTIPLTIQKKYHCIVLGKPKETHGFINKKIAR--HPGDKNKMVI--DER 362

Query: 222 GANYAISHFKVIDCFAQ 238
               A++ +K++  +  
Sbjct: 363 VGKEALTEYKILKVWDN 379


>gi|224015040|ref|XP_002297181.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220968156|gb|EED86506.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 590

 Score = 94.3 bits (233), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 47/220 (21%), Positives = 77/220 (35%), Gaps = 50/220 (22%)

Query: 101 LLYEDSKIYVFNKPAGISV-QGGSGIA--------------------------------- 126
           +LY+D  + + +KP G+         A                                 
Sbjct: 284 ILYQDDDLLIVSKPPGMVCYHNKKTSAGKITTSRKKKSRAANNGKDDGSNDGGDGKLMDI 343

Query: 127 YHIDGFLKSWVDSKGQKP---RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              D  +          P    + HRLD+ TSG +V+A+       L  SF +R+  K+Y
Sbjct: 344 SLEDALIDMAFPLSTVNPSARGIVHRLDRGTSGAIVLAKNDETHLRLVASFFLRKATKVY 403

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ----- 238
            +LV G      +   +  +      G    +    ++    A S ++V+  +       
Sbjct: 404 SALVPGSCLQNIDGDEDANVSAMLTIGSEGEIDLPVDR--RPAKSKYRVVKMYGHQEEQT 461

Query: 239 -----KFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKY 272
                +   LE+Q  TGR HQ+RVH    +G PI  D  Y
Sbjct: 462 QQPTPEAILLEVQTLTGRKHQVRVHCASGLGRPIFLDPLY 501


>gi|307069602|ref|YP_003878079.1| putative pseudouridine synthase, RluA family [Candidatus Zinderia
           insecticola CARI]
 gi|306482862|gb|ADM89733.1| putative pseudouridine synthase, RluA family [Candidatus Zinderia
           insecticola CARI]
          Length = 291

 Score = 93.9 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 35/175 (20%), Positives = 77/175 (44%), Gaps = 10/175 (5%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +++  + + NK     +   +        + FL    ++K  +  + +R+D+ T G++++
Sbjct: 67  FKNKNLLIINKNDNFLIHPNNNTHNGTIFNFFLYKKNNNKIPRLGIINRIDKNTFGLIII 126

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
            +   +  +    F+   I+K Y  LVWG  KN      N++           + +  N+
Sbjct: 127 IKNIYSYFYFIYQFKFNTIKKKYICLVWGKVKNN-----NFINFSIIKNKKKYNKMIVNK 181

Query: 221 KGANYAISHFKVIDCFAQK---FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +  I+ +K+I+           L ++  TG+ HQ+R+H  ++   I+GD  Y
Sbjct: 182 NKKSNIITKYKIINYNKFNNLYISLLNIKLITGKMHQIRIHMKNIKHSILGDILY 236


>gi|145354623|ref|XP_001421579.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144581817|gb|ABO99872.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 359

 Score = 93.9 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 41/208 (19%), Positives = 67/208 (32%), Gaps = 34/208 (16%)

Query: 99  SILLYEDS--KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS----------------- 139
             +++E     + V  KPAG+ V  G+   +   G L +   +                 
Sbjct: 46  PEIVFECEKTGLVVVEKPAGVPVLAGAAPGWQGYGNLAALTSALRRRRAAKDDAADETRR 105

Query: 140 --------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                      K    +R+D   SGI + A +   A           + K Y +LV G  
Sbjct: 106 TKRARATGDAGKVWAVNRIDAPVSGIWLAATSPKLAAKANVWMSKTSLGKTYLALVRGAQ 165

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPH-T 249
                 I + L K          +   +EK      +   V+    ++    +  +    
Sbjct: 166 IECGVRIDSPLAKD-----KESSLAVVSEKDGKPCATRVVVLQRRESEDVALVACRLESH 220

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFK 277
           GR HQ+R H   +G PIV D  Y     
Sbjct: 221 GRYHQIRAHLSSIGHPIVFDSAYGDEDP 248


>gi|237843373|ref|XP_002370984.1| RNA pseudouridylate synthase domain-containing protein [Toxoplasma
           gondii ME49]
 gi|211968648|gb|EEB03844.1| RNA pseudouridylate synthase domain-containing protein [Toxoplasma
           gondii ME49]
 gi|221502314|gb|EEE28047.1| RNA pseudouridylate synthase domain-containing protein, putative
           [Toxoplasma gondii VEG]
          Length = 685

 Score = 93.9 bits (232), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 54/280 (19%), Positives = 97/280 (34%), Gaps = 87/280 (31%)

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK-IYWSLVWG 189
             L     S  + P+L HRL +E +G+L++ RT+  AQ   +  R        +++L+ G
Sbjct: 288 SLLHQLRFSMDETPKLLHRLGKEVTGVLLLGRTKQTAQVAVDRLRGGTFGVLTFFALLHG 347

Query: 190 IPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-------------- 234
            P   ++E +    L ++  G   V V    ++G + +++ +K++               
Sbjct: 348 RPPGGRREGVIRIPLAENEAG---VMVPTAVQRGGSVSVTRWKLLKVASPQTRDVKGDAE 404

Query: 235 -CFAQKFCWLEMQP-HTGRTHQLRVHALH-MGCPIVGDHKYCA----------------- 274
              A  F  +E++  H    HQ R H L+ + CPIVGD  Y                   
Sbjct: 405 QSHACGFSLVELEIRHQQCRHQARAHCLYGLSCPIVGDRVYGPLTSRWRQLASTGAASFT 464

Query: 275 ---------------------------------NFKGNFTSPIQNKLYLHARYMDLPHPE 301
                                              +    S  + +L      + +  P 
Sbjct: 465 SEDRVSAAAGTARLSVRNDAGDASAHAATDEETRSRVAAKSEEKRRLAEARATLGVTAPS 524

Query: 302 ---------------GGRLQITAPLPAHMVKTWDSLGFKY 326
                          G  ++I APLP HM +    LG+++
Sbjct: 525 MLHLHSRAISFETFAGRPVRIQAPLPPHMRQAASRLGWEF 564



 Score = 46.5 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 26/126 (20%), Positives = 51/126 (40%), Gaps = 27/126 (21%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV------------------DKKRV 53
           VE  +  +R+D + + H    ++     +L+  ++ V                  D+ RV
Sbjct: 88  VEAGQAGLRVDAFARLHIVG-SWPAAAHLLKKKELFVVPRNASFAEHVKLLRKQRDRPRV 146

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
             + R+ +G  V  P   ++L H    ++I   S  L      L+  LL++D+     +K
Sbjct: 147 SKDARVNAGDFVYFPRGADSLLHA---KEISRPSAGL-----DLRERLLFKDTDFLAVDK 198

Query: 114 PAGISV 119
           P G+  
Sbjct: 199 PFGLPT 204


>gi|406497|gb|AAD12509.1| Homology to M62747 [Mycoplasma genitalium]
          Length = 119

 Score = 93.9 bits (232), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 37/122 (30%), Positives = 61/122 (50%), Gaps = 4/122 (3%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L HRLD++TSG +VV + +A+  +L    + R +++ Y +LV          I   L +
Sbjct: 1   YLVHRLDRDTSGAIVVCKNQASLLNLQNQLQNRTLKRYYVALVHFPFNALTGSINAPLAR 60

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              +  + V         A  AI+ FKVI+   +K   + ++  TGRTHQ+RVH   +  
Sbjct: 61  ---VNNNKVMFKIAQTAKAKQAITKFKVIN-QNEKAALISLELLTGRTHQIRVHLKFIQH 116

Query: 265 PI 266
           P+
Sbjct: 117 PV 118


>gi|227501609|ref|ZP_03931658.1| RNA pseudouridylate synthase family protein [Corynebacterium
           accolens ATCC 49725]
 gi|227077634|gb|EEI15597.1| RNA pseudouridylate synthase family protein [Corynebacterium
           accolens ATCC 49725]
          Length = 262

 Score = 93.5 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 48/222 (21%), Positives = 76/222 (34%), Gaps = 25/222 (11%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
             +        +++ D  I V +KP  +       +        +  VD    +    HR
Sbjct: 48  PPEDPIPFDYCVVHTDEDIMVADKPHFLPTTTNGRLQRETLQT-RLRVDFGEDEIVPLHR 106

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G+++ +R  A        F   R  K Y     GI K    C     L      
Sbjct: 107 LDRLTAGLVICSRNPATRADYQRIFLEGRAVKRYR----GIVKQPLFCDEEIRLPMHKPR 162

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           G    +V  N        ++ +      ++       P TG THQLRV   H+G P++GD
Sbjct: 163 GSRQVLVADN---GTPTSTYVR---AAGREVTMW---PRTGHTHQLRVLLNHLGSPLIGD 213

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
             Y      +        LY  +  + L H     +    PL
Sbjct: 214 DTYPTPRPLD--------LYDFSCPLSLLH---ETISFIDPL 244


>gi|255082538|ref|XP_002504255.1| predicted protein [Micromonas sp. RCC299]
 gi|226519523|gb|ACO65513.1| predicted protein [Micromonas sp. RCC299]
          Length = 498

 Score = 93.5 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 47/272 (17%), Positives = 97/272 (35%), Gaps = 28/272 (10%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV--RIPPVINALNHIIKEQKILDSSVNLT 91
             +  + L SG+VR+         R+ +G  +         +L+  +          ++ 
Sbjct: 54  REHWARELASGRVRL---ASDVRRRLPTGGEIPEEWFAAPVSLDAPVPPDSFFRVVRHVH 110

Query: 92  KHSDFLK-SILLYEDSKIYVFNKPAGISVQGGSGI---AYHIDGFLKSWVDSKGQ----- 142
           +     +   +L EDSK+   +KPAG+    G G      +    L +   ++       
Sbjct: 111 EPCVGCEVPRVLLEDSKLVFVDKPAGVPTLAGCGPKLQGENNATRLLNRTRAENATGADD 170

Query: 143 -KPRLTHRLDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            +    +R+D+  SG+ ++A+ +R AA+      +     K Y + V G        +  
Sbjct: 171 GELFAVNRIDKPVSGVWILAKGSRLAARCRAALAKPGHETKTYLARVRGA-------VVG 223

Query: 201 WLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQP-HTGRTHQL 255
            +   + +  G            A  A++    +  +         +  +   +GR HQ+
Sbjct: 224 PIRIDAPLSVGADGRATTSGGADAKPAVTLVHPVARYPPPWDDCTLVACRLERSGRFHQI 283

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           R H   +G PI  D  Y  +     T+    +
Sbjct: 284 RCHLASVGVPIANDATYNESGAEESTNDSSTR 315


>gi|254030277|gb|ACT53870.1| DRAP deaminase [Candida membranifaciens]
          Length = 357

 Score = 93.5 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 29/120 (24%), Positives = 49/120 (40%), Gaps = 7/120 (5%)

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVV 216
           + + +    A    +  R R ++K Y + V G    +   +   L      +G + V   
Sbjct: 1   MFLGKNAKGADKFVQQIRDRTVKKEYIARVVGKFPVQNITVDKPLSTISPKLGLNRV--- 57

Query: 217 KQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
             ++     A + FK I    +     ++  P TGRTHQ+RVH  ++G PI  D  Y   
Sbjct: 58  --DDIDGKSATTEFKRISYDKESNTSVVKCLPLTGRTHQIRVHLQYLGHPIANDPIYSNE 115


>gi|323448452|gb|EGB04350.1| hypothetical protein AURANDRAFT_6163 [Aureococcus anophagefferens]
          Length = 166

 Score = 93.1 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 43/179 (24%), Positives = 68/179 (37%), Gaps = 27/179 (15%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGI-------AYHIDGFLKSWVDSKGQK-PRLTHRLDQ 152
           +L+ED ++    KP G+                        +  D  G     + HRLD+
Sbjct: 7   VLHEDDRVIAVAKPNGVLSMAAGTTKRFATLPDAVALAAGVALSDLGGPNALGVVHRLDR 66

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           + SG +V+A+TRAA   L   F  RR++K Y ++  G             +     G   
Sbjct: 67  DASGAMVLAKTRAAHALLVREFAARRVRKTYLAVGRGAATWDG----ARAVDDDVQGKPA 122

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
              V     G +                  L+ +  TGR HQ+R+H   +G P+VGD +
Sbjct: 123 ATEVAALAAGGDR---------------VLLDCRARTGRKHQVRLHCAALGLPLVGDPR 166


>gi|303281636|ref|XP_003060110.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226458765|gb|EEH56062.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 334

 Score = 93.1 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 52/215 (24%), Positives = 83/215 (38%), Gaps = 21/215 (9%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ----------KPRLTH 148
             +++E+  +   +KPAG S  G   +A    G L      +                 H
Sbjct: 53  PFVVFENDDVLCVHKPAGASFHGDD-LATRRPGVLARIRQLQASGTLRGSDYDGPLHSVH 111

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+ TSG L+ A+    A  L  +F  RR+ K Y +L    P  K   +   + +    
Sbjct: 112 RLDKVTSGALLFAKRPDVAAALGAAFASRRVHKYYVALSARRPSKKMGTVRGVMARSRRG 171

Query: 209 GGDYVHV-VKQNEKGANYAISHFKVIDCFAQKFC-----WLEMQPHTGRTHQLRVHALHM 262
                    +     A  A + F                 +  +P TG+THQLRV A  +
Sbjct: 172 TWKLTRDERRGGGGAAAAAETRFVGRGIVGHGESKRPLRLIVFRPLTGKTHQLRVAAKSL 231

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           G P++GD    A + G   +  +++ YLHA  +  
Sbjct: 232 GSPVLGD----AAYAGKDAAASEDRAYLHAAALRF 262


>gi|255520401|ref|ZP_05387638.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J1-175]
          Length = 202

 Score = 93.1 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 43/213 (20%), Positives = 82/213 (38%), Gaps = 23/213 (10%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           MT+V  + +  D E + L    +  + H+      +I  S  V ++ K +  +N  +  G
Sbjct: 1   MTHV-TLPILEDWEGLSLTTILQEKF-HLGKKARHEIRMSQNVLLNNKPLDDWNTPLFVG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG- 121
             + +P  ++    + +                     ++YED  + V NKP  +     
Sbjct: 59  ASLSLPVFLHDKIPVYE-----------------YDLEIIYEDDFLLVVNKPVDMKTHPN 101

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S         ++ +++  GQ       HRLDQ TSG+++ A+ + A   L+     R I
Sbjct: 102 DSYETDTCANAVQYYLEKTGQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAI 161

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            + Y + V G      + I   + +  H G   
Sbjct: 162 HRTYLAAVDGTWGLVMQTINKPIGEDXHHGSRR 194


>gi|261328814|emb|CBH11792.1| hypothetical protein, conserved [Trypanosoma brucei gambiense
           DAL972]
          Length = 377

 Score = 93.1 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 57/313 (18%), Positives = 94/313 (30%), Gaps = 115/313 (36%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKP--------------- 144
           ++YE+ ++ V NKP  + + G G  +             + G K                
Sbjct: 10  VIYENDELVVVNKPNDVPMDGVGCELTVERWALAYRSRRNDGDKVDSERFNEEVMKDASQ 69

Query: 145 ----------------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                           +  H+LD  TSG+L +A ++  A  L   F MR  +K Y +++ 
Sbjct: 70  LPDFVTEKPKGKKKMVKFVHQLDYATSGVLCIAFSKEMAARLAHCFEMRTAKKAYVAVLH 129

Query: 189 GIPKNKKECIAN---WLLKKSHIGGDY--------------------------------- 212
           G        I N   +L + +  GG                                   
Sbjct: 130 GSVSPLSSTIPNSTSFLSRNATQGGFRLISIKEVSSCQFILDCVRIATGQTEPNNVVSEE 189

Query: 213 -----------------VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ--------- 246
                               +  N + A  ++++  V+            Q         
Sbjct: 190 KIIEINLPVGYDDDDPDRFRMAVNGRDAKESLTYMYVLQNGYLPCPSKNCQVSVTKVILI 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----------------ANFKGNFTSPIQ---- 285
           P TGR HQLR+H   +G PIVGD  Y                       +   PI+    
Sbjct: 250 PQTGRRHQLRLHCNALGFPIVGDVTYGISSFPSTVLHQNEALMEGRNTKDVEVPIRASDW 309

Query: 286 NKLYLHARYMDLP 298
           +++ LHA  +  P
Sbjct: 310 SRMMLHAWRLSFP 322


>gi|221481814|gb|EEE20184.1| conserved hypothetical protein [Toxoplasma gondii GT1]
          Length = 713

 Score = 93.1 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 54/280 (19%), Positives = 97/280 (34%), Gaps = 87/280 (31%)

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK-IYWSLVWG 189
             L     S  + P+L HRL +E +G+L++ RT+  AQ   +  R        +++L+ G
Sbjct: 267 SLLHQLRFSMDETPKLLHRLGKEVTGVLLLGRTKQTAQVAVDRLRGGTFGVLTFFALLHG 326

Query: 190 IPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-------------- 234
            P   ++E +    L ++  G   V V    ++G + +++ +K++               
Sbjct: 327 RPPGGRREGVIRIPLAENEAG---VMVPTAVQRGGSVSVTRWKLLKVASPQTRDVKGDAE 383

Query: 235 -CFAQKFCWLEMQP-HTGRTHQLRVHALH-MGCPIVGDHKYCA----------------- 274
              A  F  +E++  H    HQ R H L+ + CPIVGD  Y                   
Sbjct: 384 QSHACGFSLVELEIRHQQCRHQARAHCLYGLSCPIVGDRVYGPLTSRWRQLASTGAASFT 443

Query: 275 ---------------------------------NFKGNFTSPIQNKLYLHARYMDLPHPE 301
                                              +    S  + +L      + +  P 
Sbjct: 444 SEDRVSATAGTARLSVRNDAGDASAHAATDEETRNRVAAKSEEKRRLAEARATLGVTAPS 503

Query: 302 ---------------GGRLQITAPLPAHMVKTWDSLGFKY 326
                          G  ++I APLP HM +    LG+++
Sbjct: 504 MLHLHSRAISFETFAGRPVRIQAPLPPHMRQAASRLGWEF 543



 Score = 46.1 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 26/126 (20%), Positives = 51/126 (40%), Gaps = 27/126 (21%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRV------------------DKKRV 53
           VE  +  +R+D + + H    ++     +L+  ++ V                  D+ RV
Sbjct: 67  VEAGQAGLRVDAFARLHIVG-SWPAAAHLLKKKELFVVPRNASFAEHVKLLRKQRDRPRV 125

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
             + R+ +G  V  P   ++L H    ++I   S  L      L+  LL++D+     +K
Sbjct: 126 SKDARVNAGDFVYFPRGADSLLHA---KEISRPSAGL-----DLRERLLFKDTDFLAVDK 177

Query: 114 PAGISV 119
           P G+  
Sbjct: 178 PFGLPT 183


>gi|72390235|ref|XP_845412.1| hypothetical protein [Trypanosoma brucei TREU927]
 gi|62360582|gb|AAX80994.1| hypothetical protein, conserved [Trypanosoma brucei]
 gi|70801947|gb|AAZ11853.1| hypothetical protein, conserved [Trypanosoma brucei brucei strain
           927/4 GUTat10.1]
          Length = 377

 Score = 93.1 bits (230), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 57/313 (18%), Positives = 94/313 (30%), Gaps = 115/313 (36%)

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKP--------------- 144
           ++YE+ ++ V NKP  + + G G  +             + G K                
Sbjct: 10  VIYENDELVVVNKPNDVPMDGVGCELTVERWALAYRSRRNDGDKVDSERFNEEVMKDASQ 69

Query: 145 ----------------RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                           +  H+LD  TSG+L +A ++  A  L   F MR  +K Y +++ 
Sbjct: 70  LPDFVTEKPKGKKKMVKFVHQLDYATSGVLCIAFSKEMAARLAHCFEMRTAKKAYVAVLH 129

Query: 189 GIPKNKKECIAN---WLLKKSHIGGDY--------------------------------- 212
           G        I N   +L + +  GG                                   
Sbjct: 130 GSVSPLSSTIPNSTSFLSRNATQGGFRLISIKEVSSCQFILDCVRIATGQTEPNNVVSEE 189

Query: 213 -----------------VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ--------- 246
                               +  N + A  ++++  V+            Q         
Sbjct: 190 KIIEINLPVGYDDDDPDRFRMAVNGRDAKESLTYMYVLQNGYLPCPSKNCQVSVTKVILI 249

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYC-----------------ANFKGNFTSPIQ---- 285
           P TGR HQLR+H   +G PIVGD  Y                       +   PI+    
Sbjct: 250 PQTGRRHQLRLHCNALGFPIVGDVTYGISSFPSTVLHQNEALMEGRNTKDVEVPIRASDW 309

Query: 286 NKLYLHARYMDLP 298
           +++ LHA  +  P
Sbjct: 310 SRMMLHAWRLSFP 322


>gi|71397355|ref|XP_802483.1| RNA pseudouridylate synthase [Trypanosoma cruzi strain CL Brener]
 gi|70863383|gb|EAN81037.1| RNA pseudouridylate synthase, putative [Trypanosoma cruzi]
          Length = 268

 Score = 93.1 bits (230), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 102/263 (38%), Gaps = 50/263 (19%)

Query: 114 PAGISVQGGSGIAY-HIDGFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAA 166
           PAG+S      +AY H+  +L   V  KG       +  L +R+D  TSG+++V  T  +
Sbjct: 1   PAGMST--TLHVAYPHLIQYLARCVPWKGVDIPVLFQHGLVNRIDVGTSGLVLVTDTGNS 58

Query: 167 A-QHLTESFRMRRIQKIYWSLVWGIPK-------------NKKECI--------ANWLLK 204
                  S   RR++KIY +LV   P              N K  I        A++ L+
Sbjct: 59  LVATRRASVVDRRVEKIYRALVLYCPPPESRAGSEEFWYLNPKGAINWNVFANGADYSLQ 118

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMG 263
            +    +    +         A + ++V++ + +    +LE+Q  +GR HQ+R H   + 
Sbjct: 119 LAAQDPERKRGLPPAFMDRRPATTMYRVLNYYPSSGVYYLEVQLRSGRRHQIRQHFAQIC 178

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH------------------PEGGRL 305
            P+VGD +Y    +         +  LHA  + L                     +  + 
Sbjct: 179 HPLVGDGRYHERARSMGEQMGLYRPALHASRITLLPSSLDSATDAIDVASYTRKEDSEKT 238

Query: 306 QITAPLPAHMVKTWDSLGFKYDR 328
            +  PLP  + +    L  K +R
Sbjct: 239 VVECPLPDDIRRALRWLQEKEER 261


>gi|255067494|ref|ZP_05319349.1| ribosomal large subunit pseudouridine synthase C [Neisseria sicca
           ATCC 29256]
 gi|255048289|gb|EET43753.1| ribosomal large subunit pseudouridine synthase C [Neisseria sicca
           ATCC 29256]
          Length = 125

 Score = 92.7 bits (229), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 31/113 (27%), Positives = 51/113 (45%), Gaps = 11/113 (9%)

Query: 216 VKQNEKGANYAISHFKVIDCFAQ---------KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
           + +  +    A + F+V++ F+              ++    TGRTHQ+RVH     CPI
Sbjct: 1   MVRVSEEGQSAHTIFRVLNRFSDDLLHQVGLSHLTLVQATLKTGRTHQIRVHLQSQHCPI 60

Query: 267 VGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            GD +Y               +++LHA  + L HP  G +L + APLP  + +
Sbjct: 61  AGDERYGDYQANKRLQKLGLKRMFLHAAELHLDHPLTGEKLILKAPLPQDLAQ 113


>gi|302845024|ref|XP_002954051.1| pseudouridine synthase mitochondrial precursor [Volvox carteri f.
           nagariensis]
 gi|300260550|gb|EFJ44768.1| pseudouridine synthase mitochondrial precursor [Volvox carteri f.
           nagariensis]
          Length = 955

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 57/314 (18%), Positives = 99/314 (31%), Gaps = 82/314 (26%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-------GSGIAYH------------- 128
            L    + ++  +L     +   NKPAG+ V G       G G                 
Sbjct: 634 PLALSPERVRRWVLAVHPGLLFLNKPAGVRVHGMAAGDEAGRGAGRSGDRSGVGGGMRPP 693

Query: 129 -----IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                 D   +     +  +PRL HRLDQ  SG++ ++R R   +    +          
Sbjct: 694 APVTLNDVMQEGLRFGQWDEPRLVHRLDQAASGVMALSRERRGGEDRDPNDEDEEAGGFG 753

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGD------------------------YVHVVKQN 219
                   + +       L +   +G D                         V +    
Sbjct: 754 GRGGDPARRGRVGPGGLALNRDERVGRDGEMPAIHRTYWAFLAGDLQPRQSGRVSLPVVV 813

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGDHKYC----- 273
           +     A++ ++V         W+E+ P TGR HQLR+H    +G PI+GD +Y      
Sbjct: 814 DGVLCPAVTAYRV-KATGCGVSWVELTPETGRRHQLRIHCARKLGAPIIGDGRYGYRGLP 872

Query: 274 --------------------------ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQI 307
                                     +        P+   + LH+R + +  P    L  
Sbjct: 873 PRLALRDHLPPEWWALLGDDPRVVRRSREAAGEPDPLPAPVLLHSRELVVKRPGKAALGA 932

Query: 308 TAPLPAHMVKTWDS 321
            APLP ++ +  ++
Sbjct: 933 VAPLPLYIRQLIEA 946


>gi|225444351|ref|XP_002264641.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|302144082|emb|CBI23187.3| unnamed protein product [Vitis vinifera]
          Length = 472

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/205 (24%), Positives = 77/205 (37%), Gaps = 15/205 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           KS ++       V +KPAG SV G +           +         R TH++D  T G 
Sbjct: 211 KSRIIAVTESYVVLDKPAGTSVGGTTDNIEESCATFATRALGLTTPLRTTHQIDNCTEGC 270

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHIGG 210
           +V+ART+          R ++++K+Y +L              +   IA  L+ +  I G
Sbjct: 271 VVLARTKEYCSVFHGKIREKKVKKLYRALAAAPMPIGIVTHYMRPVNIAPRLISEDFIKG 330

Query: 211 DY-----VHVVKQNEKGANYAISHFKVIDCFA---QKFCWLEMQPHTGRTHQLRVHALHM 262
            Y     V   K+    +      + + D            ++   TGRTHQ+R      
Sbjct: 331 WYLCQLEVLECKEVPWPSTLIEEKYCIEDRGWPLKNSAFKCKINLLTGRTHQIRAQLAAC 390

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNK 287
           G PIVGD  Y        TSP  N 
Sbjct: 391 GAPIVGDSMYMPAAIAEITSPGLNP 415


>gi|435099|gb|AAA16215.1| ORFX homologue [Mycoplasma capricolum subsp. capricolum ATCC 27343]
          Length = 145

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 37/159 (23%), Positives = 72/159 (45%), Gaps = 24/159 (15%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV 65
           +   +V  +++N  L ++ K  +       + K +R+  ++++ KRV   N  ++   VV
Sbjct: 1   MTKFIVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRVNDKNYLLKINDVV 60

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +    ++   II++Q    S+VNL          ++YED+ I + NKP  + +   S  
Sbjct: 61  EVY---DSNKPIIRDQFNYISNVNLD---------IVYEDNNILIVNKPNNLEMH--SIY 106

Query: 126 AYHIDGFLKSWVDSKGQK---------PRLTHRLDQETS 155
              +D  +KS++  K +              HRLD+ TS
Sbjct: 107 NLCLDDMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTS 145


>gi|147861752|emb|CAN83167.1| hypothetical protein VITISV_021912 [Vitis vinifera]
          Length = 208

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 34/130 (26%), Positives = 53/130 (40%), Gaps = 17/130 (13%)

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
            HRLD+  SG+L++AR+ + A    +      +QK Y + V G+  + +           
Sbjct: 4   IHRLDRLVSGLLILARSASKADSFRQQIEAGMVQKQYIAKVTGVFPDDEVG--------- 54

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                  +           A + F  I         +  +P TGRTHQ+RVH  + G PI
Sbjct: 55  -------NCCGNTPLKGKSACTKFTRISTNG-THSIVLCEPITGRTHQIRVHLQYTGHPI 106

Query: 267 VGDHKYCANF 276
             D  Y + F
Sbjct: 107 ANDMLYLSEF 116


>gi|224076324|ref|XP_002304926.1| predicted protein [Populus trichocarpa]
 gi|222847890|gb|EEE85437.1| predicted protein [Populus trichocarpa]
          Length = 470

 Score = 91.6 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 49/212 (23%), Positives = 81/212 (38%), Gaps = 29/212 (13%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           KS +++      V +KPAG SV G +           +         R TH++D  T G 
Sbjct: 205 KSRIIHVTESFVVLDKPAGTSVGGTTDNIEESCATFATRALGLTAPLRTTHQIDNCTEGC 264

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+ARTR          R + ++K+Y +L           + +++     I      V +
Sbjct: 265 VVLARTREDCSVFHGKIREKTVKKLYIALAASPVPI--GVVNHYM---RPINMAPRLVSE 319

Query: 218 QNEKGANYAISHFKVIDC---------FAQKFCWLEM-------------QPHTGRTHQL 255
           +  KG  + +   +V++C           +K+C  +                 TGRTHQ+
Sbjct: 320 EFIKG--WHLCQLEVMECKRVPWPDAVMEEKYCVQDCGWPSKDHAYECKINLLTGRTHQI 377

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           R     +G P+VGD  Y         SP  N 
Sbjct: 378 RAQLAALGAPLVGDSMYMPAAVAEMVSPGCNP 409


>gi|153823687|ref|ZP_01976354.1| RNA pseudouridine synthase family protein [Vibrio cholerae B33]
 gi|126518790|gb|EAZ76013.1| RNA pseudouridine synthase family protein [Vibrio cholerae B33]
          Length = 124

 Score = 91.6 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 32/118 (27%), Positives = 47/118 (39%), Gaps = 13/118 (11%)

Query: 223 ANYAISHFKVI----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           A  A++ ++ +               ++C +EMQP TGR HQLR H  H+  PIVGD  +
Sbjct: 2   AQSAVTAYRPLAKVELPIATGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIVGDTTH 61

Query: 273 CANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
                           +L LHA  +   HP   + L I A L           G++  
Sbjct: 62  GDGVHNRLFREHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 119


>gi|318075730|ref|ZP_07983062.1| RNA pseudouridine synthase [Streptomyces sp. SA3_actF]
          Length = 282

 Score = 91.6 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 85/229 (37%), Gaps = 17/229 (7%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            + +      +++ D  + V +KP  ++     G         +   D         HRL
Sbjct: 42  PEPAVPFPLRVVHRDDHLLVVDKPHFLATTP-RGSHITETALARLRRDLGIPALSPAHRL 100

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ T+G+++              F  + ++K Y ++    P      ++     +SH+  
Sbjct: 101 DRLTAGLVLFVVRPGDRGAYQSLFARKEVRKEYEAVAAHAPA-----LSLPRTVRSHLVK 155

Query: 211 DYVHVVKQNEKGANY-AISHFKVIDCFAQKF--------CWLEMQPHTGRTHQLRVHALH 261
           +   +  +   GA   + +  +++                   + P TGRTHQLR H   
Sbjct: 156 ERGEMAAREVAGAEPNSETRVELLGVRTAPALAGTPPLLARYRLLPRTGRTHQLRAHMNG 215

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           +G P++GD  Y         +  +  L L AR ++   P  G R + T+
Sbjct: 216 LGLPLLGDPLY-PRVTDPDPTDYRRPLQLLARSVEFTDPLSGERRRFTS 263


>gi|237784731|ref|YP_002905436.1| putative pseudouridylate synthase [Corynebacterium kroppenstedtii
           DSM 44385]
 gi|237757643|gb|ACR16893.1| putative pseudouridylate synthase [Corynebacterium kroppenstedtii
           DSM 44385]
          Length = 364

 Score = 91.6 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 46/263 (17%), Positives = 82/263 (31%), Gaps = 49/263 (18%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++    I V +KP  ++     G        ++    +        HRLD+ TSG+L+  
Sbjct: 102 VFSSPGILVVDKPPFLATMP-RGRHITETATVRLRRATGNDNLVPAHRLDRPTSGLLLFT 160

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIP--------------KNKKECI---ANWLLK 204
                       F  R+++K Y ++    P                    I    + +  
Sbjct: 161 THPRYRGPYQTLFARRQVRKTYQAIAPYHPVLAESTDRAEIEHVAIDSGTISLEDDGIHV 220

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDC---------------------FAQKFCWL 243
              +   +  +  + E G   A +    I                          ++   
Sbjct: 221 HQRMEKTHGFIQARLEPGKPNAETVISSIRMLTDDDERALREGYHNWFGDPLCDTRYALY 280

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA------NFKGNFTSPIQNKLYLHARYMDL 297
            M P +G+THQLR+    +G PIVGD  Y        +   +        L L +  +  
Sbjct: 281 TMHPLSGKTHQLRMCLNSLGVPIVGDQVYPRILPEAIDAHQHVDEAWHQPLCLRSTQLSW 340

Query: 298 PHPEGGR-LQITAPLPAHMVKTW 319
             P   R + +TAP    +  T 
Sbjct: 341 TDPNLHRPITVTAP---DLTHTL 360


>gi|221502885|gb|EEE28599.1| RNA pseudouridylate synthase, putative [Toxoplasma gondii VEG]
          Length = 6535

 Score = 91.6 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 51/89 (57%), Gaps = 3/89 (3%)

Query: 235  CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
             ++Q+F +  ++ HTGRTHQ+RVH  H+G P+VGD KYC  +K         +++LH+  
Sbjct: 4923 SYSQEFSFCRVRIHTGRTHQIRVHFRHIGHPLVGDTKYCDLYKCTVDRSWCARMFLHSAV 4982

Query: 295  MDLPHP---EGGRLQITAPLPAHMVKTWD 320
            ++  +P   E   +++  PL   ++   +
Sbjct: 4983 LEFDNPDKTETQHVRVVCPLATELLAALE 5011



 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 29/109 (26%), Positives = 51/109 (46%), Gaps = 3/109 (2%)

Query: 132  FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             L++    +  +  L HR D ETSG L++A+TR A + + E FR R + K Y  L  G  
Sbjct: 4747 RLETVRRWEEMECGLCHRTDLETSGSLLIAKTRRARESIFEQFRKRLVHKEYLLLCHGRL 4806

Query: 192  KNKKECIANWLLKK---SHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
                  I + +  +   S     +   V   ++G + A++ ++V+  F 
Sbjct: 4807 DKLHARIDHPIATRDFDSSRSKSHFSEVVGPDEGGDEALTEYQVVRVFG 4855


>gi|221482222|gb|EEE20577.1| RNA pseudouridylate synthase, putative [Toxoplasma gondii GT1]
          Length = 6535

 Score = 91.6 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 51/89 (57%), Gaps = 3/89 (3%)

Query: 235  CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
             ++Q+F +  ++ HTGRTHQ+RVH  H+G P+VGD KYC  +K         +++LH+  
Sbjct: 4923 SYSQEFSFCRVRIHTGRTHQIRVHFRHIGHPLVGDTKYCDLYKCTVDRSWCARMFLHSAV 4982

Query: 295  MDLPHP---EGGRLQITAPLPAHMVKTWD 320
            ++  +P   E   +++  PL   ++   +
Sbjct: 4983 LEFDNPDKTETQHVRVVCPLATELLAALE 5011



 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 29/109 (26%), Positives = 51/109 (46%), Gaps = 3/109 (2%)

Query: 132  FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             L++    +  +  L HR D ETSG L++A+TR A + + E FR R + K Y  L  G  
Sbjct: 4747 RLETVRRWEEMECGLCHRTDLETSGSLLIAKTRRARESIFEQFRKRLVHKEYLLLCHGRL 4806

Query: 192  KNKKECIANWLLKK---SHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
                  I + +  +   S     +   V   ++G + A++ ++V+  F 
Sbjct: 4807 DKLHARIDHPIATRDFDSSRSKSHFSEVVGPDEGGDEALTEYQVVRVFG 4855


>gi|237842261|ref|XP_002370428.1| RNA pseudouridine synthase domain containing protein [Toxoplasma
            gondii ME49]
 gi|211968092|gb|EEB03288.1| RNA pseudouridine synthase domain containing protein [Toxoplasma
            gondii ME49]
          Length = 6535

 Score = 91.6 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 51/89 (57%), Gaps = 3/89 (3%)

Query: 235  CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
             ++Q+F +  ++ HTGRTHQ+RVH  H+G P+VGD KYC  +K         +++LH+  
Sbjct: 4923 SYSQEFSFCRVRIHTGRTHQIRVHFRHIGHPLVGDTKYCDLYKCTVDRSWCARMFLHSAV 4982

Query: 295  MDLPHP---EGGRLQITAPLPAHMVKTWD 320
            ++  +P   E   +++  PL   ++   +
Sbjct: 4983 LEFDNPDKTETQHVRVVCPLATELLAALE 5011



 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 29/109 (26%), Positives = 51/109 (46%), Gaps = 3/109 (2%)

Query: 132  FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             L++    +  +  L HR D ETSG L++A+TR A + + E FR R + K Y  L  G  
Sbjct: 4747 RLETVRRWEEMECGLCHRTDLETSGSLLIAKTRRARESIFEQFRKRLVHKEYLLLCHGRL 4806

Query: 192  KNKKECIANWLLKK---SHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
                  I + +  +   S     +   V   ++G + A++ ++V+  F 
Sbjct: 4807 DKLHARIDHPIATRDFDSSRSKSHFSEVVGPDEGGDEALTEYQVVRVFG 4855


>gi|146320633|ref|YP_001200344.1| YlyB [Streptococcus suis 98HAH33]
 gi|145691439|gb|ABP91944.1| YlyB [Streptococcus suis 98HAH33]
          Length = 86

 Score = 91.2 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
            E+   T RTHQ+RVH  ++G P+ GD  Y         +   +  +LHAR +   HP  
Sbjct: 7   WELTWETERTHQIRVHMAYIGHPVAGDEAYGPR-----KTLKGHGQFLHARTLGFTHPRT 61

Query: 303 GR-LQITAPLPAHMVKTWDSLG 323
           G  ++ TA  PA   +  + L 
Sbjct: 62  GEVVEFTAEAPAIFQEALEKLR 83


>gi|318059080|ref|ZP_07977803.1| ribosomal pseudouridine synthase [Streptomyces sp. SA3_actG]
          Length = 323

 Score = 90.8 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 85/229 (37%), Gaps = 17/229 (7%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            + +      +++ D  + V +KP  ++     G         +   D         HRL
Sbjct: 83  PEPAVPFPLRVVHRDDHLLVVDKPHFLATTP-RGSHITETALARLRRDLGIPALSPAHRL 141

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ T+G+++              F  + ++K Y ++    P      ++     +SH+  
Sbjct: 142 DRLTAGLVLFVVRPGDRGAYQSLFARKEVRKEYEAVAAHAPA-----LSLPRTVRSHLVK 196

Query: 211 DYVHVVKQNEKGANY-AISHFKVIDCFAQKF--------CWLEMQPHTGRTHQLRVHALH 261
           +   +  +   GA   + +  +++                   + P TGRTHQLR H   
Sbjct: 197 ERGEMAAREVAGAEPNSETRVELLGVRTAPALAGTPPLLARYRLLPRTGRTHQLRAHMNG 256

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           +G P++GD  Y         +  +  L L AR ++   P  G R + T+
Sbjct: 257 LGLPLLGDPLY-PRVTDPDPTDYRRPLQLLARSVEFTDPLSGERRRFTS 304


>gi|218507605|ref|ZP_03505483.1| putative ribosomal large subunit pseudouridine synthase C
          [Rhizobium etli Brasil 5]
          Length = 67

 Score = 90.8 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 39/66 (59%), Positives = 49/66 (74%)

Query: 4  MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
          M  ++++ VE DE  MRLDRWFK H+P + F  LQK+LRSGQVRVD  RVK + R+Q GQ
Sbjct: 1  MAGIEHIKVEPDEAGMRLDRWFKVHFPGLGFGPLQKLLRSGQVRVDGGRVKSDARVQPGQ 60

Query: 64 VVRIPP 69
           VR+PP
Sbjct: 61 TVRVPP 66


>gi|333028229|ref|ZP_08456293.1| putative ribosomal pseudouridine synthase [Streptomyces sp. Tu6071]
 gi|332748081|gb|EGJ78522.1| putative ribosomal pseudouridine synthase [Streptomyces sp. Tu6071]
          Length = 323

 Score = 90.8 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 85/229 (37%), Gaps = 17/229 (7%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            + +      +++ D  + V +KP  ++     G         +   D         HRL
Sbjct: 83  PEPAVPFPLRVVHRDDHLLVVDKPHFLATTP-RGSHITETALARLRRDLGIPALSPAHRL 141

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ T+G+++              F  + ++K Y ++    P      ++     +SH+  
Sbjct: 142 DRLTAGLVLFVVRPGDRGAYQSLFARKEVRKEYEAVAAHAPA-----LSLPRTVRSHLVK 196

Query: 211 DYVHVVKQNEKGANY-AISHFKVIDCFAQKF--------CWLEMQPHTGRTHQLRVHALH 261
           +   +  +   GA   + +  +++                   + P TGRTHQLR H   
Sbjct: 197 ERGEMAAREVAGAEPNSETRVELLGVRTAPALAGTPPLLARYRLLPRTGRTHQLRAHMNG 256

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           +G P++GD  Y         +  +  L L AR ++   P  G R + T+
Sbjct: 257 LGLPLLGDPLY-PRVTDPDPTDYRRPLQLLARSVEFTDPLSGERRRFTS 304


>gi|330840802|ref|XP_003292398.1| hypothetical protein DICPUDRAFT_83013 [Dictyostelium purpureum]
 gi|325077354|gb|EGC31072.1| hypothetical protein DICPUDRAFT_83013 [Dictyostelium purpureum]
          Length = 382

 Score = 90.8 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 52/293 (17%), Positives = 99/293 (33%), Gaps = 62/293 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   +Q ++ SG +        +   +   +     P     N  + +  IL        
Sbjct: 40  SEEYIQNLIESGCI-------YYRQPLSECKTTPPNPNRIFTNIDLAKDSILKVFFYPRP 92

Query: 93  HS------DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW------VDSK 140
           +S      +     +++E+    + +KP G+ V  G  +  +               D++
Sbjct: 93  YSMEHVRCEDPSKYIIFENQYFLIVDKPHGLDV--GPIVDNYHGNITAIIGDYIEKRDNR 150

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
             K    HR+D  T G++V+ +     +   +      + KIY +    +PK+  + I N
Sbjct: 151 KHKLYNPHRIDGPTRGLIVIIKDPDFLKKFNKMIIKNEVSKIYKAF---LPKSSNQNIIN 207

Query: 201 WLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVI-------------------------- 233
             L + ++  D V   V  NEK   Y     +V+                          
Sbjct: 208 PGLYRHYMSPDNVLPKVMVNEKLEKYHECLLQVLNVEEKEISIPIDIDEVSLDLLQTPIN 267

Query: 234 -----------DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                         +  F  +++   TGRTHQ+R     MG P++GD  Y   
Sbjct: 268 FEQVGKGDYRKQMKSIPFYVVDINLITGRTHQIRAQFSKMGYPLLGDRLYGGK 320


>gi|329900914|ref|ZP_08272646.1| 23S rRNA pseudouridylate synthase [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327549326|gb|EGF33898.1| 23S rRNA pseudouridylate synthase [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 112

 Score = 90.4 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 33/98 (33%), Positives = 48/98 (48%), Gaps = 7/98 (7%)

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF------KGNFTSPIQ 285
            +    + F +LE +  TGRTHQ+RVHA   G PI GD KY          K +      
Sbjct: 3   TLLRKYENFAFLEAELKTGRTHQIRVHAASSGFPIAGDDKYGDFALNRLLQKADGKRVAL 62

Query: 286 NKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            +++LHA  +   HPE G+ + + APL    ++   SL
Sbjct: 63  KRMFLHAHQITFVHPESGKPMTLNAPLTPECLRFLASL 100


>gi|302518092|ref|ZP_07270434.1| ribosomal pseudouridine synthase [Streptomyces sp. SPB78]
 gi|302426987|gb|EFK98802.1| ribosomal pseudouridine synthase [Streptomyces sp. SPB78]
          Length = 323

 Score = 90.4 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 85/229 (37%), Gaps = 17/229 (7%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            + +      +++ D  + V +KP  ++     G         +   D         HRL
Sbjct: 83  PEPAVPFPLRVVHRDDHLLVVDKPHFLATTP-RGSHITETALARLRRDLGIPALSPAHRL 141

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           D+ T+G+++              F  + ++K Y ++    P      ++     +SH+  
Sbjct: 142 DRLTAGLVLFVVRPGDRGAYQSLFARKEVRKEYEAVSAHAPA-----LSLPRTVRSHLVK 196

Query: 211 DYVHVVKQNEKGANY-AISHFKVIDCFAQKF--------CWLEMQPHTGRTHQLRVHALH 261
           +   +  +   GA   + +  +++                   + P TGRTHQLR H   
Sbjct: 197 ERGEMAAREVAGAEPNSETRVELLGVRTAPALAGTPPLLARYRLLPRTGRTHQLRAHMNG 256

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITA 309
           +G P++GD  Y         +  +  L L AR ++   P  G R + T+
Sbjct: 257 LGLPLLGDPLY-PRVTDPDPTDYRRPLQLLARSVEFTDPLSGERRRFTS 304


>gi|255024923|ref|ZP_05296909.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Listeria monocytogenes FSL J1-208]
          Length = 180

 Score = 90.4 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 68/188 (36%), Gaps = 26/188 (13%)

Query: 45  QVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
            V ++ K +  +N  +  G  + +P                   ++    +      ++Y
Sbjct: 15  NVLLNNKPLDDWNTPLFVGASLSLPVF-----------------LHDKIPTYEYDLEIIY 57

Query: 104 EDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVV 160
           ED  + V NKP  +      S         ++ +++  GQ       HRLDQ TSG+++ 
Sbjct: 58  EDDFLLVVNKPVDMKTHANDSYETDTCANAVQYYLEKTGQDANALAVHRLDQTTSGLVLF 117

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+ + A   L+     R I + Y + V G      + I   + +  H G        Q  
Sbjct: 118 AKNKLAIAGLSWQMENRAIHRTYLAAVDGTWGLVMQTINKPIGEDRHHGSRR-----QIS 172

Query: 221 KGANYAIS 228
                A++
Sbjct: 173 PYGQPAVT 180


>gi|307243145|ref|ZP_07525319.1| conserved domain protein [Peptostreptococcus stomatis DSM 17678]
 gi|306493505|gb|EFM65484.1| conserved domain protein [Peptostreptococcus stomatis DSM 17678]
          Length = 84

 Score = 90.4 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 30/84 (35%), Positives = 44/84 (52%), Gaps = 6/84 (7%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE-GG 303
           ++  TGRTHQ+RVH  H+G PI+GD  Y         S + ++  LHA  +    P  G 
Sbjct: 3   LRLETGRTHQIRVHLSHIGHPIMGDDLYG-----RPDSSLIDRQALHAYKLIFDQPRLGD 57

Query: 304 RLQITAPLPAHMVKTWDSLGFKYD 327
           R+++ + LP  MV   + LG   D
Sbjct: 58  RIELKSSLPKDMVGLLEKLGGIID 81


>gi|332231641|ref|XP_003265002.1| PREDICTED: LOW QUALITY PROTEIN: RNA pseudouridylate synthase
           domain-containing protein 3-like [Nomascus leucogenys]
          Length = 344

 Score = 90.4 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 52/280 (18%), Positives = 105/280 (37%), Gaps = 39/280 (13%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSK 140
           +L  +++  +  D L++ ++     +   NKP G+ V G  G          L   +  +
Sbjct: 65  LLPKNLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLR 124

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKE 196
            Q+ ++     +E+SG+++++     A  L +    + R +R    Y ++  GIP   + 
Sbjct: 125 EQELQVVRASGKESSGLVLLSSCPQTASRLQKFFTHARRAQRPTATYCAVTNGIPAASEG 184

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            I   L  +   G +    VK   +     G    +SHF+V+         +++QP T  
Sbjct: 185 KIQAALKVEHIDGVNLTVPVKAPSRKDILEGVKKTLSHFRVVAT-GSGCALVQLQPLTVF 243

Query: 252 THQLRVHALHMGCPI---VGDHKYCANFKGNFTSPIQNKLYLHA--RYMDLPHPEGGR-- 304
           + QL+        PI   +G              P+  ++   A  R + L   +  +  
Sbjct: 244 SSQLQXXXXXXXTPISLELGTQL-LGKCGAEHNVPLPLQVLDEAXLRRLHLTPSQAAQLP 302

Query: 305 -------------------LQITAPLPAHMVKTWDSLGFK 325
                              +++ APLP +  +T   LG +
Sbjct: 303 LHLSLHRLLLPGTRDRDTPIELLAPLPPYFSRTLQCLGLR 342


>gi|149372534|ref|ZP_01891646.1| ribosomal large subunit pseudouridine synthase D [unidentified
           eubacterium SCB49]
 gi|149354577|gb|EDM43141.1| ribosomal large subunit pseudouridine synthase D [unidentified
           eubacterium SCB49]
          Length = 130

 Score = 90.0 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 36/129 (27%), Positives = 55/129 (42%), Gaps = 9/129 (6%)

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V   P   K+ + ++L +       Y +  K     +  AI H++VI      +  L + 
Sbjct: 2   VKEKPPKDKDTLVHFLKRNPKQNKSYAYPKKV--PDSKQAILHYEVIKKL-DNYYLLSID 58

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRL 305
             TGR HQ+R     + CPI GD KY  +      S     ++LHAR +   HP +   +
Sbjct: 59  LETGRHHQIRSQLAAIKCPIKGDLKYGFDRSNKDGS-----IHLHARKITFTHPVKKEEM 113

Query: 306 QITAPLPAH 314
            I AP P  
Sbjct: 114 TILAPTPDE 122


>gi|325114924|emb|CBZ50481.1| hypothetical protein NCLIV_009500 [Neospora caninum Liverpool]
          Length = 914

 Score = 90.0 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 94/252 (37%), Gaps = 36/252 (14%)

Query: 5   TYVQYVVVE------NDEENMR-----LDRWFKNHYPHINFVNLQKILRSGQ-VRVDKKR 52
           +Y+   VV         +  +R     +       +        Q+ + SG+ + V+ + 
Sbjct: 58  SYITVKVVPPYWHTFETDVKLRWRDKEILAVVTREFRSRPESYYQRAIESGKFILVNNQA 117

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
            K +  +++G             H+      ++ ++  T         +LYED  +    
Sbjct: 118 CKCDTVLRNGD------------HLTHRTLEIEFAIPWTT-----PVHVLYEDDGLVAAF 160

Query: 113 KPAGISVQG-GSGIAYHIDGFLK--SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169
           KPAG+ V   G      + G LK               +RLD+ T+G++++A+    A+ 
Sbjct: 161 KPAGMPVHPQGRYTQGSLTGVLKRFHLRQLMSAYLHPVNRLDRVTAGVVILAKNSIQART 220

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           LT +       K+Y + V G   N  E IA    +++ +G          E+ A+  ++ 
Sbjct: 221 LTTAI--GSALKLYIARVEGNFSNIVEKIATA-SREARVGETRSDWKSVGERFADT-VAE 276

Query: 230 FKVIDCFAQKFC 241
              ++    + C
Sbjct: 277 EDPLEAEEARRC 288



 Score = 66.5 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 28/131 (21%), Positives = 45/131 (34%), Gaps = 8/131 (6%)

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-----ANWLLKK 205
           D   S ++     R     +  +         +       P+ +   +     A  L+  
Sbjct: 478 DAPCSSLVATLTERQTRNSMHSTRPESMSDHKHPESRARSPELQDGGVYIKVSARLLVSS 537

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGC 264
             +G      V  NE+    A + FK++          +   P TGRTHQ+R H   +G 
Sbjct: 538 CLVGRQL--AVGWNEEYGKEAETVFKLLHYDENSDTSLVACIPLTGRTHQIRKHLQILGT 595

Query: 265 PIVGDHKYCAN 275
            IVGD  Y   
Sbjct: 596 SIVGDALYPTK 606


>gi|255554955|ref|XP_002518515.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223542360|gb|EEF43902.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 476

 Score = 90.0 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 48/212 (22%), Positives = 84/212 (39%), Gaps = 15/212 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           KS ++       V +KPAG SV G +           +         + TH++D  T G 
Sbjct: 211 KSRIIAVTDCYVVLDKPAGTSVGGTADNIEESCATFATRALGLTTPLKTTHQIDNCTEGC 270

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVW-----GIPKN--KKECIANWLLKKSHIGG 210
           +V+AR++          R ++++K+Y +L       G+ KN  +   IA  LL +  + G
Sbjct: 271 VVLARSKEYCSVFHGKIREKKVKKLYLALAASPVPVGVIKNYMRPVNIAPRLLSEEFVNG 330

Query: 211 DYVHVVK----QNEKGANYAISHFKVIDCFAQK----FCWLEMQPHTGRTHQLRVHALHM 262
            ++  ++    +     + AI     ++             ++   TGRTHQ+R      
Sbjct: 331 WHLCQLEVLECRKVPWPDAAIEEKYSVEDCGWPSKDFAYECKINLLTGRTHQIRAQLAAS 390

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
           G P+VGD  Y         +P  N    H + 
Sbjct: 391 GAPLVGDSMYMPAAVAEMANPGLNPFGKHRKQ 422


>gi|323452498|gb|EGB08372.1| hypothetical protein AURANDRAFT_26183 [Aureococcus anophagefferens]
          Length = 91

 Score = 89.3 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 29/82 (35%), Positives = 42/82 (51%), Gaps = 8/82 (9%)

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
                 + F V+D  A      E++PHTGR HQLR H   +G PI+GD  Y A+ +G   
Sbjct: 6   DGKPCRTTFAVVDRGADTTTL-ELEPHTGRLHQLRAHCAAIGHPILGDDIYGADAEG--- 61

Query: 282 SPIQNKLYLHARYMDLPHPEGG 303
               ++L+LHA+ +    P  G
Sbjct: 62  ----SRLHLHAKALRFAEPSSG 79


>gi|294873272|ref|XP_002766565.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Perkinsus marinus ATCC 50983]
 gi|239867556|gb|EEQ99282.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Perkinsus marinus ATCC 50983]
          Length = 350

 Score = 89.3 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 49/285 (17%), Positives = 91/285 (31%), Gaps = 78/285 (27%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-------------------------- 126
             D     +L+E   + V  KPA   V   S IA                          
Sbjct: 60  EMDTTVPAVLHETKHLSVIWKPAHWHVSVTSAIAGAAEGEVDDATDEEAEAKDAAFKTMT 119

Query: 127 --YHIDGFLKSWVDS----------KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174
                   L+ WV+           +     + HRLD  TSG L++A +           
Sbjct: 120 SANGNASGLQEWVEEAYTGYPIARDRHHAHGILHRLDVGTSGPLLLAHS----------- 168

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
                         G    +    ++ +LK +   G               +++    + 
Sbjct: 169 ------------YKGFYMGRLVFCSHQILKSTLDNGQSYSTTCVVAPDGKPSLTEAVPVA 216

Query: 235 CF----AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--ANFKGNFTSPIQNKL 288
            +     +++  + ++ HTGRTHQ+RVH  ++G P+V D KY    + +        ++L
Sbjct: 217 HYNDGSGEEYSLVLVKLHTGRTHQIRVHMAYIGHPLVCDPKYGNPTDPEAAKAVCAIDRL 276

Query: 289 YL-----HARYMDLPHP------EGGRLQITAPLPAHMVKTWDSL 322
           +      H+  +    P      +   + +  P+P  +      L
Sbjct: 277 WCPRTFLHSYRLCYNQPMDVVDEKDATVDVYVPMPLDLRLALGKL 321


>gi|320197496|gb|EFW72110.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           WV_060327]
          Length = 132

 Score = 89.3 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 35/101 (34%), Positives = 51/101 (50%), Gaps = 2/101 (1%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                  ++LY+D  I V NKP+G+    G  +  H D  + + +     +    HRLD 
Sbjct: 8   PPQEPWLVILYQDDHIMVVNKPSGLLSVPGR-LEEHKDSVM-TRIQRDYPQAESVHRLDM 65

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            TSG++VVA T+AA + L   FR R  +K Y + VWG P  
Sbjct: 66  ATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSP 106


>gi|223999965|ref|XP_002289655.1| hypothetical protein THAPSDRAFT_268629 [Thalassiosira pseudonana
           CCMP1335]
 gi|220974863|gb|EED93192.1| hypothetical protein THAPSDRAFT_268629 [Thalassiosira pseudonana
           CCMP1335]
          Length = 404

 Score = 89.3 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 44/222 (19%), Positives = 81/222 (36%), Gaps = 31/222 (13%)

Query: 82  KILDSSVNLTKHSDFLKS-ILLYEDSKIYVFNKPAGISVQG--------GSGIAYHIDGF 132
           ++           DF     LLYED+   V +KP  +  Q           G    + G 
Sbjct: 119 RVYPHPRRFPSCYDFADPNRLLYEDTTFIVVDKPPMLPSQPEPSNYEECCPGCVNTLLGP 178

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV----- 187
            K+       +P + HR+D    G LV+++     +  ++  R R+I+K+Y ++      
Sbjct: 179 FKTIAGEDVARPLICHRVDSCVGGCLVLSKDGNGQRVFSDLQRQRKIKKLYLAVTTEPVP 238

Query: 188 --------WGIPKNKKEC-------IANWLLKKSHIGGDYVHVVKQNEKGANYAI--SHF 230
                   WG    + +        +++           ++  V +  K    AI     
Sbjct: 239 LGMHVHWMWGSLNARGQSGGTPCQFVSHTPPVSRKKAKSWIRCVLEVVKCEPIAINKEDG 298

Query: 231 KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              D   ++     ++  TGR HQ+R     +GCP++ D  Y
Sbjct: 299 HTYDPGDKQHYQSTIRLVTGRKHQVRAQLASLGCPLIRDTLY 340


>gi|153820593|ref|ZP_01973260.1| RNA pseudouridine synthase family protein [Vibrio cholerae NCTC
           8457]
 gi|126508864|gb|EAZ71458.1| RNA pseudouridine synthase family protein [Vibrio cholerae NCTC
           8457]
          Length = 115

 Score = 89.3 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 31/109 (28%), Positives = 42/109 (38%), Gaps = 13/109 (11%)

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF- 280
              +A + +          C +EMQP TGR HQLR H  H+  PIVGD  +         
Sbjct: 12  TGKFATTRY----------CLMEMQPKTGRKHQLRRHMAHLRHPIVGDTTHGDGVHNRLF 61

Query: 281 -TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYD 327
                  +L LHA  +   HP   + L I A L           G++  
Sbjct: 62  REHFSAQRLMLHASELRFMHPYTQQPLVIRAGLDEVWQGLLSEFGWQES 110


>gi|213027168|ref|ZP_03341615.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 119

 Score = 89.3 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 29/114 (25%), Positives = 50/114 (43%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
             +  A + L + F    I+K Y ++V G   +        + ++  I   +  
Sbjct: 64  GLSSEAGRRLAQQFEQHHIRKRYHAIVRGWLIDDAVLDYPLVEERDKIADKFAR 117


>gi|226505766|ref|NP_001140548.1| hypothetical protein LOC100272613 [Zea mays]
 gi|194699944|gb|ACF84056.1| unknown [Zea mays]
          Length = 205

 Score = 88.9 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 38/197 (19%), Positives = 69/197 (35%), Gaps = 43/197 (21%)

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +V+ +    A  L ++F   +++K Y +L  G P   ++        +S  G   V+ + 
Sbjct: 1   MVITKCNKVAGKLVKAFTDHKVKKTYLALCIGFPPAWEKIKICSGHGRSKHGAWRVYAMS 60

Query: 218 QNEKG------ANYAISHFKVIDCFAQK-------------------------------- 239
              +            + F+V+    +                                 
Sbjct: 61  DVGRSLPGGSVVRDMSTRFEVLGVNGKGQFREPYSLDTDDIEPITVQEKATDQTCGGDAN 120

Query: 240 --FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +   P +GRTHQ+R+H  ++G PI GD KY    + +          LHA  +  
Sbjct: 121 SSVILVRAYPQSGRTHQIRLHCQYLGLPIRGDVKYGGVIEWDGVE--CEGHALHAESLSF 178

Query: 298 PHPEGG-RLQITAPLPA 313
            HP  G  + + +PLP 
Sbjct: 179 VHPITGLPITLRSPLPP 195


>gi|260890825|ref|ZP_05902088.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           hofstadii F0254]
 gi|260859378|gb|EEX73878.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           hofstadii F0254]
          Length = 302

 Score = 88.9 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 38/225 (16%), Positives = 88/225 (39%), Gaps = 31/225 (13%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++   +E + + M++ ++ +    +         LR+ +V ++ K+V+   ++       
Sbjct: 1   MKKFRIEKEHQRMKISQYLREVQNYSGRS-----LRNVEVFLNGKQVRLTKKL------- 48

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
            P   N         ++++           L   +++ED  I V NK   +        A
Sbjct: 49  -PSHGNL--------RVVEKKKGTDIKPIKLPLDIIFEDEDILVVNKEPFLLTHPTQKKA 99

Query: 127 Y--HIDGFLKSWVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +G +  +++  G+   PR  +RLD  TSG++++A+   A   L         +K 
Sbjct: 100 DFTLANGIVNHFLEKYGEVRVPRFYNRLDMNTSGLIIIAKNSFAQAFLQNFSI---FEKK 156

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           Y ++V GI  +K+      + ++    G    +    ++     I
Sbjct: 157 YLAIVNGIIDDKE---IARINEELAKDGKKHKIQDLEKENLKPEI 198


>gi|325684334|gb|EGD26503.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 241

 Score = 88.5 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 87/247 (35%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           +RLD++  N     +   + +I+++GQV V+ K  +    +++    V +          
Sbjct: 2   LRLDKFLANMKVG-SRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQA------ 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  ++Y+    ++ NKPAG+           +   LK   
Sbjct: 55  -----------------------VIYQQYHYFLLNKPAGVLSATEDSRQKTVLDLLKD-- 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
             + QK     RLD++T+G+L++      A  L        + K Y++L+ G+   +  +
Sbjct: 90  QDRYQKIAPVGRLDKDTTGLLLLTNDGQLAHQL--LAPEYHVPKTYYALLAGVADEETAK 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            IA  L  K               K     I          Q+   +E+    G+ HQ++
Sbjct: 148 AIAAGLTLKDGT----------ELKPGQLKILR----QDKDQEQSEIEITITEGKYHQVK 193

Query: 257 VHALHMG 263
                 G
Sbjct: 194 RMFASQG 200


>gi|300811357|ref|ZP_07091854.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300497721|gb|EFK32746.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 241

 Score = 88.5 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 87/247 (35%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           +RLD++  N     +   + +I+++GQV V+ K  +    +++    V +          
Sbjct: 2   LRLDKFLANMKVG-SRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQA------ 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  ++Y+    ++ NKPAG+           +   LK   
Sbjct: 55  -----------------------VVYQQYHYFLLNKPAGVLSATEDSRQKTVLDLLKD-- 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
             + QK     RLD++T+G+L++      A  L        + K Y++L+ G+   +  +
Sbjct: 90  QDRYQKIAPVGRLDKDTTGLLLLTNDGQLAHQL--LAPEYHVPKTYYALLAGVADEETAK 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            IA  L  K               K     I          Q+   +E+    G+ HQ++
Sbjct: 148 AIAAGLTLKDGT----------ELKPGQLKILR----QDKDQEQSEIEITITEGKYHQVK 193

Query: 257 VHALHMG 263
                 G
Sbjct: 194 RMFASQG 200


>gi|227813198|ref|YP_002813207.1| ribosomal large subunit pseudouridine synthase, RluA family
          [Bacillus anthracis str. CDC 684]
 gi|227007575|gb|ACP17318.1| ribosomal large subunit pseudouridine synthase, RluA family
          [Bacillus anthracis str. CDC 684]
          Length = 88

 Score = 88.5 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 38/87 (43%)

Query: 4  MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
          M+ V  V V  +++N R+D++        +   +Q+ ++   V V+ K VK N +++   
Sbjct: 1  MSEVVQVTVAEEQKNERIDKFVAGINNEWSRTQVQQWIKDDVVTVNGKAVKGNYKVREND 60

Query: 64 VVRIPPVINALNHIIKEQKILDSSVNL 90
           + +         I  E   L+  + L
Sbjct: 61 EITVTIPEPEELDIQPEDMNLEKMMKL 87


>gi|284799465|ref|ZP_06390155.1| ribosomal large subunit pseudouridine synthase [Neisseria subflava
           NJ9703]
 gi|284797936|gb|EFC53283.1| ribosomal large subunit pseudouridine synthase [Neisseria subflava
           NJ9703]
          Length = 125

 Score = 88.5 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 31/113 (27%), Positives = 51/113 (45%), Gaps = 11/113 (9%)

Query: 216 VKQNEKGANYAISHFKVIDCFAQKF---------CWLEMQPHTGRTHQLRVHALHMGCPI 266
           + +  +    A + F+V++ F+             ++E    TGRTHQ+RVH     CPI
Sbjct: 1   MVRVSEDGQSAHTIFRVLNRFSDGLLHQVGLSDLTFVEATLKTGRTHQIRVHLQSQDCPI 60

Query: 267 VGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVK 317
            GD +Y               +++LHA  + L HP  G +L + A LP  + +
Sbjct: 61  AGDERYGDYQANKRLQKLGLKRMFLHASELHLAHPLTGEKLILKAHLPQELAQ 113


>gi|104773810|ref|YP_618790.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|116513816|ref|YP_812722.1| 16S rRNA uridine-516 pseudouridylate synthase related
           pseudouridylate synthase [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC BAA-365]
 gi|103422891|emb|CAI97553.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|116093131|gb|ABJ58284.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|325125474|gb|ADY84804.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           delbrueckii subsp. bulgaricus 2038]
          Length = 241

 Score = 88.1 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 91/249 (36%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           +RLD++  N     +   + +I+++GQV V+ K  +    +++    V +          
Sbjct: 2   LRLDKFLANMKVG-SRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQA------ 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  ++Y+    ++ NKPAG+           +   LK   
Sbjct: 55  -----------------------VVYQQYHYFLLNKPAGVLSATEDSRQKTVLDLLKD-- 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
             + QK     RLD++T+G+L++      A  L        + K Y++L+ G+   +  +
Sbjct: 90  QDRYQKIAPVGRLDKDTTGLLLLTNDGQLAHQL--LAPEYHVPKTYYALLAGVADEETAK 147

Query: 197 CIANWLLKKSHIGGDY--VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            IA  L  K         +++++Q++      I                E+    G+ HQ
Sbjct: 148 AIAAGLTLKDGTELKPGQLNILRQDKDQEQSEI----------------EITITEGKYHQ 191

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 192 VKRMFASQG 200


>gi|226327068|ref|ZP_03802586.1| hypothetical protein PROPEN_00929 [Proteus penneri ATCC 35198]
 gi|225204286|gb|EEG86640.1| hypothetical protein PROPEN_00929 [Proteus penneri ATCC 35198]
          Length = 193

 Score = 88.1 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 37/159 (23%), Positives = 65/159 (40%), Gaps = 17/159 (10%)

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI------ 233
           +KIY ++V G  +      +  + +   I   +     Q        ++H + +      
Sbjct: 16  KKIYHAVVRGYVEEALVIDSPLVEELDKIADKFATQPPQI----QECVTHCQPLGTVEKE 71

Query: 234 ----DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA--NFKGNFTSPIQNK 287
                    +F  LE++P TGR HQLR H  H+  PI+GD  +      +G       ++
Sbjct: 72  VAIGRYPTSRFSLLELRPETGRKHQLRRHMSHIRHPIIGDTAHGDLRQNRGVVNYFQSHR 131

Query: 288 LYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSLGFK 325
           L LHA +++L HP     L +TA          +  G++
Sbjct: 132 LMLHASHLNLIHPITLQPLNLTAKWDLPWQHLINQFGWR 170


>gi|254481932|ref|ZP_05095174.1| hypothetical protein GPB2148_3 [marine gamma proteobacterium
           HTCC2148]
 gi|214037622|gb|EEB78287.1| hypothetical protein GPB2148_3 [marine gamma proteobacterium
           HTCC2148]
          Length = 143

 Score = 88.1 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 36/143 (25%), Positives = 57/143 (39%), Gaps = 16/143 (11%)

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID----------CFAQKFCWLEMQP 247
           I + L  +     D      +  +    A++ F+ +D              ++  + +QP
Sbjct: 2   IDHALQDQPDKIADRNRTQARPTRD---AVTRFERLDTVEIPYAVDRYPQSRYSLVALQP 58

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPEGG-R 304
             GR HQLR H  H+G PI+GD K+       F +      +L L    MD  HP  G  
Sbjct: 59  EQGRKHQLRRHMKHLGYPIIGDAKHGKGVHNRFFAEKYGCGRLLLACTGMDFSHPVNGDT 118

Query: 305 LQITAPLPAHMVKTWDSLGFKYD 327
           + I A L A   +   + G+K  
Sbjct: 119 VHIRAGLDAAFQRVLSAFGWKEP 141


>gi|255519723|ref|ZP_05386960.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Listeria monocytogenes FSL J1-175]
          Length = 68

 Score = 88.1 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 39/74 (52%), Gaps = 8/74 (10%)

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EG 302
           E Q  TGRTHQ+RVH   +G PI+GD  Y         SP  N++ LHA  + L HP +G
Sbjct: 1   ECQIETGRTHQIRVHLSGIGHPIIGDTLYGG-------SPRANRIMLHAEKLHLNHPFKG 53

Query: 303 GRLQITAPLPAHMV 316
             +  +AP     V
Sbjct: 54  KEMNFSAPAGDDWV 67


>gi|294055802|ref|YP_003549460.1| Pseudouridylate synthase 23S RNA-specific-like protein
           [Coraliomargarita akajimensis DSM 45221]
 gi|293615135|gb|ADE55290.1| Pseudouridylate synthase 23S RNA-specific-like protein
           [Coraliomargarita akajimensis DSM 45221]
          Length = 267

 Score = 87.7 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 83/246 (33%), Gaps = 40/246 (16%)

Query: 108 IYVFNKPAGISV--QGGSGIAYHIDGFLKSWVDSKGQKPRL----------THRLDQETS 155
                KPAG+ V          ++D  L   +  +  KP L           + L+ E S
Sbjct: 33  WLALQKPAGVGVRAHPWDVGVPNLDQALN--LQLEAAKPELAAYDAELLGSIYYLEPEVS 90

Query: 156 GILVVARTRAAAQHLTESF---RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           G+ + A  R A + L  +F     R + +    L  G+ + +       LL       D+
Sbjct: 91  GVALFATNREALEALRNAFGSGEFRFVFRFVAQLQPGLEEGQLLESDAPLL-----PHDW 145

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              +  +      A +  + +   +  +   E      R HQ+R HA  +G P++GD  Y
Sbjct: 146 KLKMIPSTAKGKKAQTRVRCLSVSSSGWALCEALTCYPRMHQVRAHAAVLGLPVLGDSLY 205

Query: 273 CA------------NFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPAHMVKTW 319
                                + + + L LH   + +P     R+  + A LP       
Sbjct: 206 GGPDAPLLRDLMPKKRGPGMAASVFDGLALHLAEVSIP-----RIGSVVAGLPRPFEVLL 260

Query: 320 DSLGFK 325
             LG  
Sbjct: 261 KRLGLN 266


>gi|255554953|ref|XP_002518514.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
 gi|223542359|gb|EEF43901.1| ribosomal pseudouridine synthase, putative [Ricinus communis]
          Length = 395

 Score = 87.7 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 50/212 (23%), Positives = 77/212 (36%), Gaps = 15/212 (7%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           KS ++       V +KPAG SV G +           +         + TH++D  T G 
Sbjct: 134 KSRIIAVTESYVVLDKPAGTSVGGTTNNIEETCATFATRALGLTIPLKTTHQIDNCTEGC 193

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHIGG 210
           +V+ART           R  +++K+Y +L              +   I   L+ +  I G
Sbjct: 194 VVLARTNEYCPVFHGKIRENKVKKLYLALAACPVPVGVITHYMRPGNIPPRLVSEEFIEG 253

Query: 211 DY-----VHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQP--HTGRTHQLRVHALHM 262
            Y     V   ++           + V DC +  K    E +    TGRTHQ+R      
Sbjct: 254 WYLCQLEVLECRKVPWPDTVTEEKYSVEDCGWPSKDFAYECKINLLTGRTHQIRAQLAAC 313

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
           G P+VGD  Y         +P  N    H + 
Sbjct: 314 GAPLVGDSMYMPAAIAEMANPGVNPFGKHKKQ 345


>gi|291287096|ref|YP_003503912.1| pseudouridine synthase [Denitrovibrio acetiphilus DSM 12809]
 gi|290884256|gb|ADD67956.1| pseudouridine synthase [Denitrovibrio acetiphilus DSM 12809]
          Length = 248

 Score = 87.7 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 50/277 (18%), Positives = 89/277 (32%), Gaps = 52/277 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR  R     Y  ++    +K ++ G V +D                     I     + 
Sbjct: 1   MRYSRRLSEQY-GLSVRMAKKYIKDGMVALDG--------------------IVTTKDLD 39

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWV 137
            ++  L+ +    +        ++ E   I  F+KPA +            +   + ++ 
Sbjct: 40  SDEGFLELTAETKRPDVTPADYIVKEFDHIVFFDKPAFMHTDLQKPDDPITMTDVIMAY- 98

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD  T G++      AA +     F  R++   Y + V G        
Sbjct: 99  ---SNEFSFISRLDYTTDGVI------AAVRDDFFVFETRKV---YLAHVEGK------- 139

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I    +  + I  D    V+  EK   Y  +   V   F      +  +      HQLR 
Sbjct: 140 IEKPFVMDNLIDADKRRKVRVLEKPGGYKTTFTPV--SFENGLTLVRAEMENASRHQLRA 197

Query: 258 HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
           +  H G PI+GD  Y             +++ LH + 
Sbjct: 198 YLAHKGHPILGDELYGGT--------AADRIMLHCKE 226


>gi|221505078|gb|EEE30732.1| RNA pseudouridylate synthase, putative [Toxoplasma gondii VEG]
          Length = 493

 Score = 87.3 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 53/269 (19%), Positives = 97/269 (36%), Gaps = 70/269 (26%)

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           +  ++  +   + HRLD  TSG LV A+T AAA++L   +  R++ K Y  L    P+  
Sbjct: 224 ALPEAISRPVSIVHRLDIGTSGALVAAKTAAAAENLKLQWADRKVLKGYIGLC--TPEIH 281

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEK--------------------GANYAISHFKVID 234
                +  L++       +  +    +                    GA   +S F  + 
Sbjct: 282 SLHEVDAPLRRHPTQRGRMEALSNESRSSFHDVCDETAQKDHSSYRIGAKPGVSVFAPLG 341

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--------------------- 273
                  +  +   TGRTHQ+R H  ++G P++GD  Y                      
Sbjct: 342 GNGAYGMFAALAL-TGRTHQIRAHLEYIGHPLLGDLVYGNQTVNEELRRFVKNVVVNPRH 400

Query: 274 ------------------ANFKGNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITA 309
                              +   +  +P  N     + +LHA ++   HP  G  + I A
Sbjct: 401 HREEAATRMTRKEVQVSCCDAGPDVLAPAGNVKVHMRPFLHAYFLRFAHPRTGAAVNIKA 460

Query: 310 PLPAHMVKTWDSLGFKYD--RNLYIKRLY 336
            LPA + +    +G  ++   +   +R++
Sbjct: 461 LLPADICQIAGKIGVDWELRADAAFERIH 489



 Score = 47.3 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/41 (39%), Positives = 19/41 (46%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           LT   D     +LYED  I V NKPAG+          +ID
Sbjct: 90  LTLLPDEKPLDVLYEDDDIVVINKPAGLLTHPPQLTVENID 130


>gi|213419310|ref|ZP_03352376.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 95

 Score = 87.3 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 28/91 (30%), Positives = 43/91 (47%), Gaps = 5/91 (5%)

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGN 279
              + + FKV + +A     +   P TGRTHQ+RVH  + G PI  D +Y     + +  
Sbjct: 1   GKPSETRFKVEERYA-FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLT 59

Query: 280 FTSPIQNKLYLHARYMDLPHPEGGR-LQITA 309
                  +L+LHA  +   HP  G  ++I A
Sbjct: 60  EAGTGLKRLFLHAAALKFTHPGTGDVMRIEA 90


>gi|260890826|ref|ZP_05902089.1| ribosomal large subunit pseudouridine synthase C [Leptotrichia
           hofstadii F0254]
 gi|260859379|gb|EEX73879.1| ribosomal large subunit pseudouridine synthase C [Leptotrichia
           hofstadii F0254]
          Length = 78

 Score = 87.3 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 4/81 (4%)

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
            +E +  TGRTHQ+RVH   +G  IVGD  Y             N+ +LHA  +   HP 
Sbjct: 1   MVECELFTGRTHQIRVHLKSIGHTIVGDELYGNGLNKEL---GINRQFLHAYKVKFTHPA 57

Query: 302 G-GRLQITAPLPAHMVKTWDS 321
               +++  P+   M +  + 
Sbjct: 58  SKKEVELEIPMFTDMKEFLEK 78


>gi|313123424|ref|YP_004033683.1| pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
 gi|312279987|gb|ADQ60706.1| Pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
          Length = 241

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 86/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           +RLD++  N     +   + +I+++GQV V+ K  +    +++    V +          
Sbjct: 2   LRLDKFLANMKVG-SRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQA------ 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  ++Y+    ++ NKPAG+           +   LK   
Sbjct: 55  -----------------------VIYQQYHYFLLNKPAGVLSATEDSRQKTVLDLLKD-- 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
               QK     RLD++T+G+L++      A  L        + K Y++L+ G+   +  +
Sbjct: 90  QDSYQKIAPVGRLDKDTTGLLLLTNDGQLAHQL--LAPEYHVPKPYYALLAGVADEETAK 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            IA  L  K               K     I          Q+   +E+    G+ HQ++
Sbjct: 148 AIAAGLTLKDGT----------ELKPGQLKILR----QDKDQEQSEIEITITEGKYHQVK 193

Query: 257 VHALHMG 263
                 G
Sbjct: 194 RMFASQG 200


>gi|295108497|emb|CBL22450.1| ribosomal small subunit pseudouridine synthase A [Ruminococcus
           obeum A2-162]
          Length = 257

 Score = 86.6 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 50/254 (19%), Positives = 94/254 (37%), Gaps = 40/254 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +         ++KI++ GQV+V+    K                      ++
Sbjct: 5   VRLDKFLADAGKG-TRSEVKKIIQKGQVQVNGVPAKK-----------------PEMKVV 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  ++  S      +      LL         NKPAG      S      D  +  +V 
Sbjct: 47  PENDVVVLSGETVGAAPEFVYYLL---------NKPAGCV----SATEDRNDRTVMEYVP 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-----PKN 193
           S  +      RLD++T G+L++      A  L      + + K Y+  V G       +N
Sbjct: 94  SDRKGLFPVGRLDKDTEGLLLITDDGMLAHEL--LAPGKHVDKTYFVRVEGKLTVENIRN 151

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            +  +     K +      V +V  + +GA  + S    I+   + +  L +  H G+ H
Sbjct: 152 LENGVDIGEEKMTMPA--KVEIVGGSWEGAGDSQSGRVRIENLPEVYTELHLTIHEGKFH 209

Query: 254 QLRVHALHMGCPIV 267
           Q++     +G P++
Sbjct: 210 QVKRMMAAVGNPVI 223


>gi|215447607|ref|ZP_03434359.1| hypothetical protein MtubT_17270 [Mycobacterium tuberculosis T85]
 gi|289759444|ref|ZP_06518822.1| conserved hypothetical protein [Mycobacterium tuberculosis T85]
 gi|289715008|gb|EFD79020.1| conserved hypothetical protein [Mycobacterium tuberculosis T85]
          Length = 306

 Score = 86.6 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 48/258 (18%), Positives = 87/258 (33%), Gaps = 23/258 (8%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT-KHSDFLKSILLYEDSKIYVF 111
           V    ++ +G+VV     +     ++    ++    +L  +        +L++D+ I V 
Sbjct: 38  VAARAKVLAGEVVDDDGAVVDSGTVLPPGSVVHLYRDLPDEVPVPFDVPVLHQDADIVVV 97

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +KP  ++     G        ++   +    +    HRLD+ T+G+L+    R       
Sbjct: 98  DKPHFLATMP-RGRHVAQTALVRLRRELGLPELSPAHRLDRLTAGVLLFTTRREVRGSYQ 156

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG------ANY 225
             F    ++K Y +     P      +A   L +S I     H+    E G      A  
Sbjct: 157 TMFARGLVRKTYLARAPVAP-----GLALPRLVRSRIVKRRGHLQAVCEPGVPNAGDAGG 211

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           A S  + +               T R          +G PI+GD  Y  N          
Sbjct: 212 ADSARRSVSADTDHRGAPTSCECTWR---------ALGIPIMGDPLY-PNVISVAAHDFS 261

Query: 286 NKLYLHARYMDLPHPEGG 303
             L L A+ ++   P  G
Sbjct: 262 TPLQLLAQRIEFDDPLTG 279


>gi|153825805|ref|ZP_01978472.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-2]
 gi|149740528|gb|EDM54643.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-2]
          Length = 145

 Score = 86.6 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 40/158 (25%), Positives = 66/158 (41%), Gaps = 21/158 (13%)

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFCWLEMQ 246
           G+ +  +  +   L        D+ +  KQ    +    +++ ++V+    +K   + + 
Sbjct: 2   GVMEQDEGEVNLPLC------CDWPNRPKQKVCFEEGRDSLTRYQVVKR-EEKTTVVRLI 54

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
           P TGR+HQLRVH   +G PIVGD  Y       F     ++L LHA  +   HP    L+
Sbjct: 55  PITGRSHQLRVHMQSLGHPIVGDDLYAPPEAVEFA----DRLQLHAAELCFYHPRSHWLR 110

Query: 307 ITAPLPAHM-----VKTWDSLGFKYDRNLYIKRLYSQD 339
            T  +P         +      F  +R L   +  SQD
Sbjct: 111 -TLFVPCDFYPEAEEQILQH--FDPERKLPDYKKLSQD 145


>gi|254561887|ref|YP_003068982.1| hypothetical protein METDI3488 [Methylobacterium extorquens DM4]
 gi|254269165|emb|CAX25131.1| hypothetical protein METDI3488 [Methylobacterium extorquens DM4]
          Length = 135

 Score = 86.6 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 30/92 (32%), Positives = 45/92 (48%)

Query: 95  DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
             +   LLY D+ + V +KPAG+ V  G      +   L +      ++P   HRLD++T
Sbjct: 8   PEIGPPLLYRDALMLVIDKPAGLPVHPGPKGGPTLTDHLDALRFGLPRRPEAAHRLDRDT 67

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
           SG LV+ R   A   L   F   ++ K YW+L
Sbjct: 68  SGCLVLGRHAKALARLNRLFADGKVDKTYWAL 99


>gi|226327069|ref|ZP_03802587.1| hypothetical protein PROPEN_00930 [Proteus penneri ATCC 35198]
 gi|225204287|gb|EEG86641.1| hypothetical protein PROPEN_00930 [Proteus penneri ATCC 35198]
          Length = 94

 Score = 86.2 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 25/84 (29%), Positives = 43/84 (51%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             ++Y+D  +   NKPAG  V       +     +++  D  GQ     HRLD+ TSG+L
Sbjct: 2   LDIIYQDEYLVAVNKPAGWLVHRSWLDRHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVL 61

Query: 159 VVARTRAAAQHLTESFRMRRIQKI 182
           ++A +   A+ L++SF   + +K 
Sbjct: 62  LMALSSDVARALSQSFEQHKTEKN 85


>gi|328948138|ref|YP_004365475.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
 gi|328448462|gb|AEB14178.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
          Length = 242

 Score = 86.2 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 46/229 (20%), Positives = 77/229 (33%), Gaps = 33/229 (14%)

Query: 104 EDSKIYVFNKPAGISVQG---GSGIAYHIDGFLKSWV----DSKGQKPRLTHRLDQETSG 156
           +++   V  KP G+       G   A+     L  ++      K  +  L HR+D ET G
Sbjct: 15  KENPFVVIKKPRGLPSAPLFEGDECAFMQAAKLYPYLLEVSGKKAIEHGLVHRIDTETEG 74

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE-CIANWLLKKSHIGGDYVHV 215
           +L++A T+ +        R  +  K Y +    I K  +    A +LL+          V
Sbjct: 75  LLLIATTQESYNAFINFQREGKFLKGYSAKCQKIEKPLEGFPPAEFLLENKSDNIKKYTV 134

Query: 216 VKQ-----------------NEKGANYAISH--FKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             +                 + K A    S   +           + +     G  HQ+R
Sbjct: 135 SSRFRPFSLKSAQVRPVTGNSGKAAQKKCSEKIYTTEIILDTDKFFAKCSIKEGYRHQVR 194

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
            H   +G P+ GD  Y      N        +   A  +  PHP  G++
Sbjct: 195 SHLAWLGFPVRGDKLYNPLCSQNEE------MQFFADCLKFPHPLTGKI 237


>gi|302822543|ref|XP_002992929.1| hypothetical protein SELMODRAFT_136180 [Selaginella moellendorffii]
 gi|300139274|gb|EFJ06018.1| hypothetical protein SELMODRAFT_136180 [Selaginella moellendorffii]
          Length = 428

 Score = 85.8 bits (211), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 45/192 (23%), Positives = 74/192 (38%), Gaps = 19/192 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           KS +L E+    V +KPAG+SV G             S          +TH++D  T G 
Sbjct: 149 KSRILAENDLFVVLDKPAGVSVGGSVDNLEESCVTFASRALGMAFPLLVTHQIDNCTEGC 208

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS----------- 206
           +V+A+ +    +     R R++ K Y  LV          +++++               
Sbjct: 209 VVLAKDKDFVSNFNRLLRTRKVDKRY--LVLAAFPVPLGIVSHYMRPDHFAPHLLSQDKR 266

Query: 207 ---HIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHAL 260
              H+    V    Q E  +   +    V +C           E++  TG+THQ+R    
Sbjct: 267 QGWHLCSMEVLQCHQVEWPSEARLRENGVSNCELEHDGHAYECEVKLLTGKTHQVRAQFA 326

Query: 261 HMGCPIVGDHKY 272
            +G PI+GD  Y
Sbjct: 327 ALGAPILGDTIY 338


>gi|298245869|ref|ZP_06969675.1| pseudouridine synthase [Ktedonobacter racemifer DSM 44963]
 gi|297553350|gb|EFH87215.1| pseudouridine synthase [Ktedonobacter racemifer DSM 44963]
          Length = 277

 Score = 85.8 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 91/256 (35%), Gaps = 45/256 (17%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVIN 72
            + +  RL R+   H    +  + ++++  G+VRV+   +     RI  GQ         
Sbjct: 32  QEAQGERLARFLA-HAGVASRRHAEELIAQGRVRVNGTIITAQGTRILPGQ--------- 81

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDG 131
             + I+ + K + +                       + +KPAG +S          +  
Sbjct: 82  --DRIVVDGKEIQAKAP----------------HAYLLLHKPAGYVSTVSDPEGRATVLD 123

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L    + +  +     RLD++TSG+L++    A AQHLT     +         V GIP
Sbjct: 124 LLP--PELRSLRLYPVGRLDRDTSGLLLLTNDGAFAQHLTHPRYEKEKHYEVQ--VKGIP 179

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             +                D V   + + K    + +  + +    Q   WL +  H GR
Sbjct: 180 TERTL----------QALRDGVTFTEDDGKHYTSSPARTRKLSSTEQS-SWLTLTIHEGR 228

Query: 252 THQLRVHALHMGCPIV 267
             Q+R     +  P++
Sbjct: 229 KRQVRRMLQAVDHPVL 244


>gi|66814022|ref|XP_641190.1| hypothetical protein DDB_G0280463 [Dictyostelium discoideum AX4]
 gi|60469215|gb|EAL67210.1| hypothetical protein DDB_G0280463 [Dictyostelium discoideum AX4]
          Length = 746

 Score = 85.8 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 68/199 (34%), Gaps = 60/199 (30%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGS----------GIAYHIDGFLKSWVDSKG---- 141
            +K  ++YED  + + NKPAG+ V   +                   + + +   G    
Sbjct: 190 DIKLDIVYEDKDLAIINKPAGMLVHPTALTLGSNALVINKEDQTHTLVNALIHRYGGVEN 249

Query: 142 -------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR----------------- 177
                  ++P + HRLD++T+G++++AR     Q L   F                    
Sbjct: 250 LSSVGGVERPGIVHRLDKDTAGMIIIARNNDVHQKLQTLFEKHTSTMITHTTIDQYEDNG 309

Query: 178 ------------------RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
                              I K Y  +V G PK +   I   + +  H       V+ Q+
Sbjct: 310 SISNNQIERMLQGKKIPLTISKKYHCIVLGKPKEQHGFINKKISR--HPADKNKMVIDQD 367

Query: 220 EKGANYAISHFKVIDCFAQ 238
                 A++ FKV+  +  
Sbjct: 368 --NGKEALTEFKVLKVWEN 384



 Score = 73.5 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 27/87 (31%), Positives = 39/87 (44%), Gaps = 5/87 (5%)

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           +  F  LE+  HTGR+HQ+RVH      PIVGD  Y +  K    S     L L +  + 
Sbjct: 544 SNTFSLLEVTLHTGRSHQIRVHMASENIPIVGDPIYSSKSKQFLVSY----LLLASMNLK 599

Query: 297 LPHPEGGRL-QITAPLPAHMVKTWDSL 322
             HP    + + +   P+H      S+
Sbjct: 600 FVHPILNEIKEFSIQYPSHFKNFISSI 626



 Score = 40.7 bits (94), Expect = 0.37,   Method: Composition-based stats.
 Identities = 12/70 (17%), Positives = 26/70 (37%), Gaps = 10/70 (14%)

Query: 9  YVVVENDEENMRLDRWFKN---------HYPHINFVNLQKILRSGQVRVDKKRVK-FNNR 58
           VVV       + DR+  +          Y  +    + KIL    V ++   +K  + +
Sbjct: 5  EVVVPKQHVPEKFDRFIASSRIKVKETGEYVKLTRSAIPKILALKSVSINGLPLKDKSTK 64

Query: 59 IQSGQVVRIP 68
          ++   ++ I 
Sbjct: 65 VKPNDIITIQ 74


>gi|145344926|ref|XP_001416975.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144577201|gb|ABO95268.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 371

 Score = 85.4 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 41/197 (20%), Positives = 68/197 (34%), Gaps = 25/197 (12%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           K+ +L         +KPAG+SV      +       L+     K    +  HRLD  T G
Sbjct: 121 KACVLKVGEGYVCAHKPAGVSVVPTVDNVKESCLAMLERAAGLKEGTLKPIHRLDVGTEG 180

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +LV+  T A A+   +    R + K+Y  L           +     + +  G   + + 
Sbjct: 181 VLVLGTTSAFAKEFGDMLADRSVTKVYRVLTENAVP---RGVHIHDAEPATEGPRKMIMT 237

Query: 217 KQNEK---------------------GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           K +                       G    I      +  A      +++  TGRTHQ+
Sbjct: 238 KVDTDDIDGEIERSAERGGGERGGVSGPKRCILRVLKSENIAPARWETKVELLTGRTHQI 297

Query: 256 RVHALHMGCPIVGDHKY 272
           R     +  P+VG+  Y
Sbjct: 298 RAQFAALSAPLVGETLY 314


>gi|151941011|gb|EDN59391.1| pseudouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|190405237|gb|EDV08504.1| pseudouridylate synthase PUS5 [Saccharomyces cerevisiae RM11-1a]
 gi|207343014|gb|EDZ70609.1| YLR165Cp-like protein [Saccharomyces cerevisiae AWRI1631]
 gi|256274348|gb|EEU09253.1| Pus5p [Saccharomyces cerevisiae JAY291]
 gi|259148157|emb|CAY81404.1| Pus5p [Saccharomyces cerevisiae EC1118]
 gi|323332309|gb|EGA73718.1| Pus5p [Saccharomyces cerevisiae AWRI796]
          Length = 254

 Score = 85.4 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 47/260 (18%), Positives = 95/260 (36%), Gaps = 47/260 (18%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQG----GSGIAYHIDG---FLKS-----WVDSKGQKPR 145
           +  +++E++  ++ NKP GI  Q       G  +        L+      +   + +  R
Sbjct: 6   QIPIIFENTHYFIVNKPPGIPSQPPDCRTWGRTHPNLDPTPLLERFKAIYYSHREVELCR 65

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD   +G +++A+T+ A+   +   +            +                +
Sbjct: 66  TVHRLDHCVTGGMLIAKTKDASVKFSRFLQKGGNNGYKLQRKYVAIVESSGRFNKPNNYE 125

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC- 264
              G  Y  ++    +     I+ FK +D        + +Q  TG+ HQ+R H   +   
Sbjct: 126 IKYGPKYNFLISHGGRE----ITKFKEVDEN-----CIVLQLVTGKKHQIRNHVSQILNQ 176

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHA-------------RYMDLPHPEGGRL------ 305
           PI+ D KY +    NF     +++ LH+               + + H   G+L      
Sbjct: 177 PILNDKKYGSTV--NFPELFNDQIALHSACIITKIGLQTKTHLIPMEHNNTGQLWSRKYV 234

Query: 306 ----QITAPLPAHMVKTWDS 321
               + T P+   +++ WD 
Sbjct: 235 NEEGEFTLPIKEVLLENWDQ 254


>gi|297250655|ref|ZP_06934184.1| ribosomal large subunit pseudouridine synthase [Neisseria
           polysaccharea ATCC 43768]
 gi|296838354|gb|EFH22292.1| ribosomal large subunit pseudouridine synthase [Neisseria
           polysaccharea ATCC 43768]
          Length = 147

 Score = 85.0 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 36/132 (27%), Positives = 52/132 (39%), Gaps = 9/132 (6%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +L+        NKP GISV    G                 +K  L HRLD++T GIL+ 
Sbjct: 4   ILFRHQDFVAINKPQGISVHRSDGEVSLTATLAAQL---GVEKVWLLHRLDKQTGGILLF 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A    +A  L   F  R+++K Y +L    P  K+  I   + K          + K   
Sbjct: 61  ALNPQSAAVLAAQFAERKMKKTYLALSDRKPSKKQGWIKGGMEK------SRRGMWKLTR 114

Query: 221 KGANYAISHFKV 232
              N A++ F V
Sbjct: 115 NMENIAVTRFSV 126


>gi|302796533|ref|XP_002980028.1| hypothetical protein SELMODRAFT_111763 [Selaginella moellendorffii]
 gi|300152255|gb|EFJ18898.1| hypothetical protein SELMODRAFT_111763 [Selaginella moellendorffii]
          Length = 428

 Score = 85.0 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 45/192 (23%), Positives = 74/192 (38%), Gaps = 19/192 (9%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           KS +L E+    V +KPAG+SV G             S          +TH++D  T G 
Sbjct: 149 KSRILAENDLFVVLDKPAGVSVGGSVDNLEESCVTFASRALGMAFPLLVTHQIDNCTEGC 208

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS----------- 206
           +V+A+ +    +     R R++ K Y  LV          +++++               
Sbjct: 209 VVLAKDKDFVSNFNRLLRTRKVDKRY--LVLAASPVPLGIVSHYMRPDHFAPHLLSQDKR 266

Query: 207 ---HIGGDYVHVVKQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHAL 260
              H+    V    Q E  +   +    V +C           E++  TG+THQ+R    
Sbjct: 267 QGWHLCSMEVLQCHQVEWPSEARLRENGVSNCELEHDGHAYECEVKLLTGKTHQVRAQFA 326

Query: 261 HMGCPIVGDHKY 272
            +G PI+GD  Y
Sbjct: 327 ALGAPILGDTIY 338


>gi|153824295|ref|ZP_01976962.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
 gi|126518181|gb|EAZ75406.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
          Length = 95

 Score = 85.0 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 30/86 (34%), Positives = 45/86 (52%), Gaps = 2/86 (2%)

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-PIQNKLYLHARYMDLP 298
              ++  P TGRTHQ+RVH  +MG PI  D +Y       +T+     +L+LHA  +   
Sbjct: 8   ATLVQASPVTGRTHQIRVHTQYMGHPIAWDDRYGDRRFDAYTAQFGIERLFLHAANIQFV 67

Query: 299 HPEGG-RLQITAPLPAHMVKTWDSLG 323
           HP    +L+I APL AH+ +    + 
Sbjct: 68  HPASEKKLEIHAPLEAHLEQALTKMR 93


>gi|221482001|gb|EEE20367.1| RNA pseudouridylate synthase, putative [Toxoplasma gondii GT1]
          Length = 493

 Score = 85.0 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 52/269 (19%), Positives = 96/269 (35%), Gaps = 70/269 (26%)

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           +  ++  +   + HRLD  TSG LV A+T AAA++L   +  R++ K Y  L    P+  
Sbjct: 224 ALPEAISRPVSIVHRLDIGTSGALVAAKTAAAAENLKLQWADRKVLKGYIGLC--TPEIH 281

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEK--------------------GANYAISHFKVID 234
                +  L++       +  +    +                    GA   +S F  + 
Sbjct: 282 SLHEVDAPLRRHPTQRGRMEALSNESRSSFHDVCDETTQKDHSSYRIGAKPGVSVFAPLG 341

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--------------------- 273
                  +  +   TGRTHQ+R H  ++G P++GD  Y                      
Sbjct: 342 GNGAYGMFAALAL-TGRTHQIRAHLEYIGHPLLGDLVYGNQTVNEELRRFVKNVVVNPRH 400

Query: 274 ------------------ANFKGNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITA 309
                              +   +  +P  N     + +LHA ++   HP  G  + I A
Sbjct: 401 HREEAATRMTRKEVQVSCCDAGPDVLAPAGNVKVHMRPFLHAYFLRFAHPRTGAAVNIKA 460

Query: 310 PLPAHMVKTWDSLGFKYD--RNLYIKRLY 336
             PA + +    +G  ++   +   +R++
Sbjct: 461 LPPADICQIAGKIGVDWELRADAAFERIH 489



 Score = 47.3 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/41 (39%), Positives = 19/41 (46%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           LT   D     +LYED  I V NKPAG+          +ID
Sbjct: 90  LTLLPDEKPLDVLYEDDDIVVINKPAGLLTHPPQLTVENID 130


>gi|291278963|ref|YP_003495798.1| hypothetical protein DEFDS_0560 [Deferribacter desulfuricans SSM1]
 gi|290753665|dbj|BAI80042.1| conserved hypothetical protein [Deferribacter desulfuricans SSM1]
          Length = 278

 Score = 85.0 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 90/252 (35%), Gaps = 38/252 (15%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +    + +I+    +K ++  +V +D K  K N        + I  +         E   
Sbjct: 28  YLSQQF-NISKRLAKKYIKEKKVLIDGKFAKEN--------LEITNI---------ENHH 69

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           +  ++++ K    L   ++     +    KP  +  +            +   V    ++
Sbjct: 70  ISLNIDIKKIEYNLDEFIISNYENVIFLYKPPFMHTERHKLEDSL---TISDIVSEHFKE 126

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
            +L  RLD ET G++           + + ++   + K Y ++V G            ++
Sbjct: 127 YKLISRLDFETDGVI---------AAIKDGYKPENVLKKYLAVVIGNFPEDT------IV 171

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
               +      V    E    + +S+ KVI+   + +  LE+       HQ+R H   +G
Sbjct: 172 FNKIVYKKRKKVKVLEEIDLEH-LSNIKVINSD-KNYSLLEITIFKATRHQIRAHLSFLG 229

Query: 264 CPIVGDHKYCAN 275
            PI+GD  Y   
Sbjct: 230 FPILGDTLYGDK 241


>gi|66818229|ref|XP_642774.1| hypothetical protein DDB_G0277359 [Dictyostelium discoideum AX4]
 gi|60470894|gb|EAL68866.1| hypothetical protein DDB_G0277359 [Dictyostelium discoideum AX4]
          Length = 386

 Score = 85.0 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 54/326 (16%), Positives = 108/326 (33%), Gaps = 74/326 (22%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHIN-FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           V Y++V+ ++    +     NHY +      + ++L +G +                  +
Sbjct: 27  VSYLIVDRED---TISNILINHYNNKPTKEYINQLLENGCIY-------------HQDSI 70

Query: 66  RIP-----PVINALNHIIKEQKILD----SSVNLTKHSDF--LKSILLYEDSKIYVFNKP 114
            +      P    ++ +I +  +L       VN T H DF      +++E+    V +KP
Sbjct: 71  EVTKTKTIPKRVQIDKVINKGSLLKYFFYPRVNSTDHIDFKNFNKYIIFENQYFLVIDKP 130

Query: 115 AGISVQG-GSGIAYHIDGFLKSWVDSKGQK------PRLTHRLDQETSGILVVARTRAAA 167
            GI+V      +  +   F+K W+  +             H LD  T G+ V+A+     
Sbjct: 131 HGINVGPIVDHLHNNFTSFVKDWLKKRNNNNDNNLILYNPHNLDSPTRGLFVIAKDFNFL 190

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK--SHIGGDYVHVVKQNEKGANY 225
               +    +++ K Y + +      +   I   + K            +  +  +  + 
Sbjct: 191 SKFNKLLSDKKVSKKYKAFIPIKENEENIEIKPGIYKHFMEITNHSPKKLFDEQNQDNSL 250

Query: 226 AISHFKVIDCFAQK-------------------------------------FCWLEMQPH 248
                KV+    ++                                     F  +E+Q  
Sbjct: 251 KECLLKVLKVERKEIYVPLGLKDVSIDLLQDDLQFDDIGKGDFRKQTKKLLFNVVEIQLI 310

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCA 274
           TGRTHQ+R     +G P++ D  Y  
Sbjct: 311 TGRTHQIRAQLSKLGFPLLSDIMYGG 336


>gi|237836949|ref|XP_002367772.1| RNA pseudouridylate synthase, putative [Toxoplasma gondii ME49]
 gi|211965436|gb|EEB00632.1| RNA pseudouridylate synthase, putative [Toxoplasma gondii ME49]
          Length = 493

 Score = 85.0 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 52/269 (19%), Positives = 96/269 (35%), Gaps = 70/269 (26%)

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           +  ++  +   + HRLD  TSG LV A+T AAA++L   +  R++ K Y  L    P+  
Sbjct: 224 ALPEAISRPVSIVHRLDIGTSGALVAAKTAAAAENLKLQWAERKVLKGYIGLC--TPEIH 281

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEK--------------------GANYAISHFKVID 234
                +  L++       +  +    +                    GA   +S F  + 
Sbjct: 282 SLHEVDAPLRRHPTQRGRMEALSNESRSSFHDVCDETAQKDHSSYRIGAKPGVSVFAPLG 341

Query: 235 CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC--------------------- 273
                  +  +   TGRTHQ+R H  ++G P++GD  Y                      
Sbjct: 342 GNGAYGMFAALAL-TGRTHQIRAHLEYIGHPLLGDLVYGNQTVNEELRRFVKNVVVNPRH 400

Query: 274 ------------------ANFKGNFTSPIQN-----KLYLHARYMDLPHPEGG-RLQITA 309
                              +   +  +P  N     + +LHA ++   HP  G  + I A
Sbjct: 401 HREEAATRMTRKEVQVSCCDAGPDVLAPAGNVKVHMRPFLHAYFLRFAHPRTGAAVNIKA 460

Query: 310 PLPAHMVKTWDSLGFKYD--RNLYIKRLY 336
             PA + +    +G  ++   +   +R++
Sbjct: 461 LPPADICQIAGKIGVDWELRADAAFERIH 489



 Score = 47.3 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/41 (39%), Positives = 19/41 (46%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           LT   D     +LYED  I V NKPAG+          +ID
Sbjct: 90  LTLLPDEKPLDVLYEDDDIVVINKPAGLLTHPPQLTVENID 130


>gi|5420076|emb|CAB46588.1| hypothetical protein [Yersinia enterocolitica]
          Length = 125

 Score = 84.6 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 29/105 (27%), Positives = 47/105 (44%), Gaps = 2/105 (1%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           LY+D  + + NKP G+    G          +   +        L HRLD  TSG++V+A
Sbjct: 21  LYQDDHLVLINKPTGLLSLSGENPQN--LDSVHHRLVQIFPGCTLVHRLDFGTSGLMVIA 78

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
           R +A    L + F  R + K+Y +L+ G   + +  I   + K  
Sbjct: 79  RNKAINAALCQQFSQRTVTKVYSALLCGHLDDNEGVIDAAIAKDP 123


>gi|308234451|ref|ZP_07665188.1| ribosomal large subunit pseudouridine synthase B [Atopobium vaginae
           DSM 15829]
 gi|328944298|ref|ZP_08241762.1| RNA pseudouridine synthase [Atopobium vaginae DSM 15829]
 gi|327491217|gb|EGF22992.1| RNA pseudouridine synthase [Atopobium vaginae DSM 15829]
          Length = 285

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 45/260 (17%), Positives = 89/260 (34%), Gaps = 38/260 (14%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSG-QVVRIPPV 70
            +D   MRL R+        +    +K++ +G+V V+ K+V+    ++      V +   
Sbjct: 19  PSDHFTMRLQRFLARA-GVASRRGSEKLISAGRVCVNGKQVRVLGTKVMPQYDHVTV--- 74

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                                      K  +L  D    + NKP+ +         +   
Sbjct: 75  -------------------------DGKEYVLGNDHVYLLLNKPSQVLTTMSDPFGFPCV 109

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L    D  G       RLD +T+G+L+          L        + K Y +L+ G 
Sbjct: 110 ASLVPCDDYPG--LFPVGRLDSDTTGVLLFTTNGNMGNRL--LHPSHHVWKTYVALIEGK 165

Query: 191 PKNKK--ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQP 247
             + +  +     +L+       ++  + Q+E   +   +H    D          E++ 
Sbjct: 166 LTSSQMQKLSQGIMLEDGMTSPCFIRTITQDEPCTHLDKNHSLFDDMRLNAASSLCELKI 225

Query: 248 HTGRTHQLRVHALHMGCPIV 267
           H GR HQ++     +G P++
Sbjct: 226 HEGRNHQVKRMLQEIGHPVI 245


>gi|297799888|ref|XP_002867828.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297313664|gb|EFH44087.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 476

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 58/336 (17%), Positives = 115/336 (34%), Gaps = 61/336 (18%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVR-------------- 47
           +L   ++++VV  D+  + +  +       +  + +  ++R G V               
Sbjct: 90  NLPPRIEHMVVLEDD--VLVSEFISKQL-DLPPLYVSDLIRFGAVHYALVCPKPPPTATP 146

Query: 48  -------------VDKKR--VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
                        V KKR  +K     ++ +  R+             +  +    +   
Sbjct: 147 EQIELFEEVTCPSVLKKRSSIKGKTVREAQKTFRVTHTNQYAEAGTYLRVHVHPKRSPRC 206

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +    KS ++       + +KPAG +V G +           S      +  + TH++D 
Sbjct: 207 YEIDWKSRIVAVTDSYVILDKPAGTTVGGTTDNIEESCATFASRALDLPEPLKTTHQIDN 266

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G +V ART+          R + ++K+Y +L           I++++  K+      
Sbjct: 267 CTEGCVVFARTKEYCSVFHTKIRNKEVKKLYRALAAAPLPT--GIISHYMRPKNMAPR-- 322

Query: 213 VHVVKQNEKGANYAISHFKVIDC--------------------FAQKFCWLEMQP--HTG 250
             V + + KG  + +   +V++C                    +  K    E      TG
Sbjct: 323 -LVSEDSIKG--WHLCQLEVLECKKIPWPDAATEKKHDIEDCGWTSKEFAYECTINLLTG 379

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           +THQ+R      G P+VGD  Y         +P  N
Sbjct: 380 KTHQIRAQLAACGAPLVGDSMYMPAAIAEMVNPDTN 415


>gi|25028115|ref|NP_738169.1| hypothetical protein CE1559 [Corynebacterium efficiens YS-314]
 gi|259507172|ref|ZP_05750072.1| RNA pseudouridine synthase [Corynebacterium efficiens YS-314]
 gi|23493399|dbj|BAC18369.1| conserved hypothetical protein [Corynebacterium efficiens YS-314]
 gi|259165253|gb|EEW49807.1| RNA pseudouridine synthase [Corynebacterium efficiens YS-314]
          Length = 329

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 48/254 (18%), Positives = 84/254 (33%), Gaps = 53/254 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSG-QVVRIPPVINAL 74
           E +RL +         +  + + ++ +G+V V+ + V     R+     V+R+  V   +
Sbjct: 87  EGIRLQKVLAQA-GVASRRHAEILIDNGRVEVNGRIVTTQGTRVNPNSDVIRVDGVRINI 145

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           N                            ED + +V NKP G+       +     G L 
Sbjct: 146 N----------------------------EDLEYFVLNKPRGMHSTMSDDLGRPCVGDLV 177

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           S   + GQ+     RLD +T G+L++      A  L        ++K Y + V G     
Sbjct: 178 SEKTASGQRLFHVGRLDADTEGLLLLTNDGELANRL--MHPKYEVRKTYLATVRGEAGPN 235

Query: 195 KECI--ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                     L+      DYV ++                     Q    + ++ H GR 
Sbjct: 236 LVTTLRKGIELEDGPAKADYVQIID------------------TFQGKSLIRLEIHEGRK 277

Query: 253 HQLRVHALHMGCPI 266
           H +R      G P+
Sbjct: 278 HIVRRMLDEAGFPV 291


>gi|307069601|ref|YP_003878078.1| putative pseudouridine synthase, RluA family [Candidatus Zinderia
           insecticola CARI]
 gi|306482861|gb|ADM89732.1| putative pseudouridine synthase, RluA family [Candidatus Zinderia
           insecticola CARI]
          Length = 242

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 49/174 (28%), Positives = 89/174 (51%), Gaps = 7/174 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ++ED  I + NKP  +SV  G  I  ++  FLK   + K     L HR+D++ SGIL+++
Sbjct: 18  IFEDKYIIIINKPNYLSVHSGYKIKLNLIEFLKKKYNLKLIN--LIHRIDKDISGILLLS 75

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
           +++   + + + F+ ++I+K Y S+V G      + I  +  K ++      ++ + N K
Sbjct: 76  KSKKILKIINKKFKNKKIKKNYLSIVHGNLNFINKKIKLFFKKNNNFINKKNYINR-NGK 134

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
                IS  K+       F  + ++  TG+ HQ+R+H   +G PI+ D KY   
Sbjct: 135 KTYSIISLIKIYK----NFSLINIKLITGKMHQIRMHLNFLGFPIIFDKKYGNK 184


>gi|15234586|ref|NP_193908.1| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|75212600|sp|Q9SVS0|PUS6_ARATH RecName: Full=RNA pseudourine synthase 6, chloroplastic; AltName:
           Full=RNA pseudouridylate synthase 6; AltName:
           Full=RNA-uridine isomerase 6; Flags: Precursor
 gi|4455285|emb|CAB36821.1| hypothetical protein [Arabidopsis thaliana]
 gi|7268974|emb|CAB81284.1| hypothetical protein [Arabidopsis thaliana]
 gi|23296381|gb|AAN13057.1| unknown protein [Arabidopsis thaliana]
 gi|110741616|dbj|BAE98756.1| hypothetical protein [Arabidopsis thaliana]
 gi|332659101|gb|AEE84501.1| RNA pseudourine synthase 6 [Arabidopsis thaliana]
          Length = 472

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 56/332 (16%), Positives = 107/332 (32%), Gaps = 51/332 (15%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVR-------------- 47
           +L   ++++VV  D+  + +  +       +  + +  ++R G V               
Sbjct: 86  NLPPRIEHMVVLEDD--VLVSEFISKQL-DLPPLYVADLIRFGAVHYALVCPKPPPTATP 142

Query: 48  -------------VDKKR--VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
                        V KKR  +K     ++ +  R+             +  +    +   
Sbjct: 143 EEIILFEEVTSPSVLKKRSSIKGKTVREAQKTFRVTHTNQYAEAGTYLRVHVHPKRSPRC 202

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
           +    KS ++       + +KPAG +V G +           S      +  + TH++D 
Sbjct: 203 YEIDWKSRIVAVTDSYVILDKPAGTTVGGTTDNIEESCATFASRALDLPEPLKTTHQIDN 262

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G +V ART+          R + ++K+Y +L           I++++  K+      
Sbjct: 263 CTEGCVVFARTKEYCSVFHTKIRNKEVKKLYRALAAAPLPI--GIISHYMRPKNMAPRLV 320

Query: 213 VHVVKQNEKGANYAISHFKVI-----------DCFAQKFCWLEM------QPHTGRTHQL 255
                Q        +   K I           D     +   E          TG+THQ+
Sbjct: 321 AEDSIQGWHLCQLEVLECKKIPWPDAATEKKHDIEDCGWTSKEFAYECTINLLTGKTHQI 380

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           R      G P+VGD  Y         +P  N 
Sbjct: 381 RAQLAACGAPLVGDSMYMPAAIAEMGNPDTNP 412


>gi|295839820|ref|ZP_06826753.1| RNA pseudouridine synthase [Streptomyces sp. SPB74]
 gi|197697764|gb|EDY44697.1| RNA pseudouridine synthase [Streptomyces sp. SPB74]
          Length = 323

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 43/255 (16%), Positives = 84/255 (32%), Gaps = 16/255 (6%)

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           + +G+ V            +             +        +++ D ++ V +KP  ++
Sbjct: 51  LAAGEFVDAGGRPAHGGERLPGATYWFHRTRAPEPEVPFALRVVHRDERLLVCDKPHFLA 110

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                G         +   D         HRLD+ T+G+++              F  + 
Sbjct: 111 TTP-RGSHITETALARLRRDLGIPALSPAHRLDRLTAGLVLFVVRPEDRGAYQSLFARKE 169

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY-AISHFKVIDCFA 237
           ++K Y ++    P      +      +SH+  +   +  +   GA   + +   ++    
Sbjct: 170 VRKEYEAVAAYAPS-----LPLPRTVRSHLVKERGDLAAREVAGAAPNSETRVALLGVRT 224

Query: 238 QKFC--------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
                          + P TGRTHQLR H   +G P++GD  Y         +  +  L 
Sbjct: 225 APAHAGLPPLLARYRLLPRTGRTHQLRAHMNGLGLPLLGDPLY-PRVTDPDPTDYRRPLQ 283

Query: 290 LHARYMDLPHPEGGR 304
           L AR +    P  G 
Sbjct: 284 LLARTLAFTDPLSGE 298


>gi|34189548|gb|AAH12951.2| RPUSD1 protein [Homo sapiens]
          Length = 190

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 31/121 (25%), Positives = 56/121 (46%), Gaps = 11/121 (9%)

Query: 207 HIGGDYVHVVK--QNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALH 261
            +G   V  ++  Q  +    +++   V++           + ++P TGRTHQLRVH   
Sbjct: 1   RVGRPRVRCIEGSQGCENPKPSLTDLVVLEHGLYAGDPVSKVLLKPLTGRTHQLRVHCSA 60

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
           +G P+VGD  Y     G    P   ++ LHA Y+ +P  +   +++  P P   + + D+
Sbjct: 61  LGHPVVGDLTYG-EVSGREDRPF--RMMLHAFYLRIP-TDTECVEVCTPDP--FLPSLDA 114

Query: 322 L 322
            
Sbjct: 115 C 115


>gi|226486578|emb|CAX74366.1| pseudouridylate synthase [Schistosoma japonicum]
          Length = 258

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 68/180 (37%), Gaps = 21/180 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
             ++ + H++   + +   SG + V+  RV  +  +    ++       +      E  +
Sbjct: 98  VLQSEFSHMSNDVIAQKCNSGDILVNGARVDPDYVLNDNDLL-------SQQVHRHEFPV 150

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+  +             +++   + V NKP  I +       Y ++          G +
Sbjct: 151 LNLPIEF-----------IHDSHDMLVINKPPSIPIHPCG--RYTLNSITHILAKDYGLR 197

Query: 144 P-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           P R THRLD+ TSG+L++A+    +  L      + + K Y   V G  +  +      L
Sbjct: 198 PLRFTHRLDRMTSGLLLIAKDYDTSVRLQSQIASKEVTKHYICHVDGCFQPNQSITVLAL 257


>gi|188997597|ref|YP_001931848.1| RNA-binding S4 domain protein [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188932664|gb|ACD67294.1| RNA-binding S4 domain protein [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 244

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 49/250 (19%), Positives = 93/250 (37%), Gaps = 47/250 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++  N     +   +QK+++ G V+V+ + VK  +          I P+ + +   
Sbjct: 1   MRLDKFLSNQGFG-SRSQVQKLIKKGFVKVNDEIVKDPSY--------HIDPMKDKVELE 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +E                    +LY+++  ++ NKPAG            +        
Sbjct: 52  DEE--------------------ILYKENHYFMLNKPAGYITATEDEEYPTVLDLFSDL- 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                K     RLD +T G+L++         L+       I+K Y+++V G        
Sbjct: 91  -PIASKLFPVGRLDIDTEGLLILTTDGQFGHRLSHPKWN--IEKEYYAIVEGD------- 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I+N    +S   G Y+   K   K         KV++    K   + +    G+ H ++ 
Sbjct: 141 ISNIDFSESENKGIYLKKEKYQTKPFK-----VKVLNTSKDK-SEILITLTEGKYHIVKR 194

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 195 IMQELGYPVL 204


>gi|219115335|ref|XP_002178463.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217410198|gb|EEC50128.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 497

 Score = 83.9 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 38/226 (16%), Positives = 78/226 (34%), Gaps = 39/226 (17%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--------GIAYHIDGFL 133
           ++  +        +  +  LLYED+   V +KP  +  Q  S        G      G  
Sbjct: 213 RVYPNPRRFPACEELTRDRLLYEDTTFIVVDKPPLLPTQPDSSNYVECCPGCVQDNLGPF 272

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK- 192
                ++  +P L HR+D    G +V+++     +   E  R R+++K+Y ++       
Sbjct: 273 TDIQGNEVVRPLLCHRVDSCVGGCVVLSKDGNGQKVFQEMQRERKLRKLYLAVTTQPVPL 332

Query: 193 -------------------NKKECIANWLLKKSHIGGDY-------VHVVKQNEKGANYA 226
                                 + +++   +       +       V   +  + G   +
Sbjct: 333 GMHLHWMWAPQSARGKSGGPPCQLVSHAPPESRRKARQFWNRCVLEVVKCEPIKIGKEDS 392

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
            ++    D   +      ++  TGR HQ+R     +G PI+ D  Y
Sbjct: 393 HTY----DPAGKVHYQSTIRLVTGRKHQVRAQLASLGAPIIRDSLY 434


>gi|212704374|ref|ZP_03312502.1| hypothetical protein DESPIG_02429 [Desulfovibrio piger ATCC 29098]
 gi|212672199|gb|EEB32682.1| hypothetical protein DESPIG_02429 [Desulfovibrio piger ATCC 29098]
          Length = 347

 Score = 83.9 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 63/345 (18%), Positives = 109/345 (31%), Gaps = 67/345 (19%)

Query: 11  VVENDEENMRLDRWFKNHYPHIN------FVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           V +      RLD         +           +++L  G+VRV+ ++     R++ G  
Sbjct: 10  VADAALAGQRLDAALAVVLEALGQPVPGLRGR-RRLLEEGRVRVNGRQAPAAYRVRQGDG 68

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGS 123
           + + P              L    +     D      L    +   F KPAG  SV    
Sbjct: 69  ISLCP-------------ALPEVFSDPAADDGDAPRALSRQGRWQAFFKPAGWHSVSLAG 115

Query: 124 GIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGILVVARTR------AAAQHLTESFR 175
           G    ++  + S        P   L  RLD  TSGI+  A         A  +   ++  
Sbjct: 116 GGGRSLEAAIPSLWAEGAVPPAWALLQRLDARTSGIVCAAVAEDEDSLAATVRDFRQAEA 175

Query: 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA-ISHFKVID 234
             R  K Y +L+ G  + +        ++++        V   + + A+ A  + F+ + 
Sbjct: 176 GGRCCKGYLALLSGSLERE------ACVRRALDMAQRRVVRVLDSEAADAARWTWFRPLY 229

Query: 235 CFAQKFC-----------------------WLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
            +  + C                             H G  HQ+R HA  +G  +  D  
Sbjct: 230 HWQGEACHAFARELCRRFSLSVPSLPDSLTLAGCTIHRGARHQIRAHAAALGHALWLDGL 289

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMV 316
           Y ++      SP   +      +  L  PE   L     LP   +
Sbjct: 290 YASSLPQ---SPEDGQGAFFLHHGALHLPEARWL-----LPPDWL 326


>gi|296117982|ref|ZP_06836565.1| RNA pseudouridylate synthase [Corynebacterium ammoniagenes DSM
           20306]
 gi|295969213|gb|EFG82455.1| RNA pseudouridylate synthase [Corynebacterium ammoniagenes DSM
           20306]
          Length = 308

 Score = 83.9 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 47/257 (18%), Positives = 86/257 (33%), Gaps = 53/257 (20%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSG-QVVRIPPVI 71
            + E  RL +         +  + + ++ +G+V V+ K +K    R+     V+R+  V 
Sbjct: 63  PNTEGERLQKVLAKA-GVASRRHAEVLIDAGRVEVNGKIIKRQGVRVNPNADVIRVDGVR 121

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
             +N                            ED + ++ NKP G+       +     G
Sbjct: 122 VNVN----------------------------EDHEYFILNKPRGVQSTMQDDMGRPCVG 153

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            + +   + GQ+     RLD +T G+L++      A  L        + K Y + V G  
Sbjct: 154 DMVAEKTASGQRLFHVGRLDADTEGLLILTNDGELANRL--MHPKYEVSKTYLATVLGEA 211

Query: 192 KNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +       L       D+V +V +N                  Q    + ++ H 
Sbjct: 212 DKSLVRTLKDGIELDDGMANADFVQIVDKN------------------QGMSLIRLELHE 253

Query: 250 GRTHQLRVHALHMGCPI 266
           GR H +R      G P+
Sbjct: 254 GRKHIVRRMLKAAGYPV 270


>gi|148690494|gb|EDL22441.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_c
           [Mus musculus]
          Length = 177

 Score = 83.5 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 28/105 (26%), Positives = 47/105 (44%), Gaps = 9/105 (8%)

Query: 221 KGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +    +++   V++           + ++P TGRTHQLRVH   +G PIVGD  Y     
Sbjct: 10  ENPKPSLTELLVLEHGLYAGDPVSKVLLKPLTGRTHQLRVHCSALGHPIVGDLTYGQAED 69

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                    ++ LHA Y+ +P  +  R++   P P   +   D+ 
Sbjct: 70  QEDQPF---RMMLHAFYLRIP-TQAERVEACTPDP--FLPALDAC 108


>gi|257487593|ref|ZP_05641634.1| ribosomal large subunit pseudouridine synthase A [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 108

 Score = 83.5 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 29/102 (28%), Positives = 48/102 (47%), Gaps = 1/102 (0%)

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
            ++Y+D+ + V +KP  +    G       D  +    ++   + R+ HRLD ETSGI++
Sbjct: 7   RIIYQDAAVLVIDKPTLLLSVPGRADDN-KDCLITRLQENGFPEARIVHRLDWETSGIIL 65

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           +AR     + L+  F  R  +K Y +L WG P      I   
Sbjct: 66  LARDADTHRELSRQFHDRETEKAYTALCWGQPSLDSGSIDLP 107


>gi|115473865|ref|NP_001060531.1| Os07g0660400 [Oryza sativa Japonica Group]
 gi|34395182|dbj|BAC83571.1| unknown protein [Oryza sativa Japonica Group]
 gi|113612067|dbj|BAF22445.1| Os07g0660400 [Oryza sativa Japonica Group]
          Length = 400

 Score = 83.5 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 48/259 (18%), Positives = 88/259 (33%), Gaps = 44/259 (16%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYV 110
           +    N R+++G  +R+                         +    KS ++       V
Sbjct: 96  RVTDPNQRLEAGTYLRVHVHPKRFPR---------------CYEIDWKSRVIAVTDNYVV 140

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
            +KPA  SV G +           S           TH++D  + G +V+++T+      
Sbjct: 141 LDKPAATSVGGATDNIEESCVVFTSRALGLETPLMTTHQIDNCSEGCVVLSKTKEFCSVF 200

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
               R +++ K Y +L           I +++     I      V + + KG  + +   
Sbjct: 201 HGMIREKQVNKRYLALTTAPVST--GIITHYM---RPINRAPRLVSEDHIKG--WHVCQM 253

Query: 231 KVIDC--------------------FAQKFCWLEMQP--HTGRTHQLRVHALHMGCPIVG 268
           +++DC                    + Q+    E +    TG+THQ+R     +G PIVG
Sbjct: 254 EILDCKKVPWPSSLIRKVHKVDNCGWPQQEAAYECKINLLTGKTHQIRAQLAAIGTPIVG 313

Query: 269 DHKYCANFKGNFTSPIQNK 287
           D  Y         +P  N 
Sbjct: 314 DSAYMTAAMAAIVNPSINP 332


>gi|323347394|gb|EGA81665.1| Pus5p [Saccharomyces cerevisiae Lalvin QA23]
          Length = 254

 Score = 83.1 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 46/260 (17%), Positives = 94/260 (36%), Gaps = 47/260 (18%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQG----GSGIAYHIDG---FLKS-----WVDSKGQKPR 145
           +  +++E++  ++ NKP GI  Q       G  +        L+      +   + +  R
Sbjct: 6   QIPIIFENTHYFIVNKPPGIPSQPPDCRTWGRTHPNLDPTPLLERFKAIYYSHREVELCR 65

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD   +G +++A+T+ A+   +   +            +                +
Sbjct: 66  TVHRLDHCVTGGMLIAKTKDASVKFSRFLQKGGNNGYKLQRKYVAIVESSGRFNKPNNYE 125

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC- 264
                 Y  ++    +     I+ FK +D        + +Q  TG+ HQ+R H   +   
Sbjct: 126 IKYXPKYNFLISHGGRE----ITKFKEVDEN-----CIVLQLVTGKKHQIRNHVSQILNQ 176

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHA-------------RYMDLPHPEGGRL------ 305
           PI+ D KY +    NF     +++ LH+               + + H   G+L      
Sbjct: 177 PILNDKKYGSTV--NFPELFNDQIALHSACIITKIGLQTKTHLIPMEHNNTGQLWSRKYV 234

Query: 306 ----QITAPLPAHMVKTWDS 321
               + T P+   +++ WD 
Sbjct: 235 NEEGEFTLPIKEVLLENWDQ 254


>gi|325681054|ref|ZP_08160586.1| putative 16S pseudouridylate 516 synthase [Ruminococcus albus 8]
 gi|324107283|gb|EGC01567.1| putative 16S pseudouridylate 516 synthase [Ruminococcus albus 8]
          Length = 246

 Score = 83.1 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 40/289 (13%), Positives = 100/289 (34%), Gaps = 54/289 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD+   + +  ++  +++K+    ++ V+ K   + + ++ +   + +          
Sbjct: 5   MRLDKLVASQFSDVSRADVKKLCLKKKISVNGKLMARSDAKVDTDDEIFVN--------- 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  L+Y+     + NKPAG+      G +  +   +   +
Sbjct: 56  --------------------GERLVYKKHVYIMLNKPAGVVCSTKEGDSMTVLDLVPPEL 95

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              G       RLD++T G +++      + + L+   +    +  +  L         +
Sbjct: 96  MRNG--LFPAGRLDKDTEGFVLLTDDGELSHRMLSP--KTHVPKTYFVRLEKPYQPEYAD 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +A  +  K   GG+    +     G++             +  C   +  H G+ HQ++
Sbjct: 152 IMAAGMTIKGLDGGEDEKCLPAQFSGSD-------------ENDCECTLILHEGKFHQVK 198

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
                +G  +V    Y          P+  +L    + +++ H +  +L
Sbjct: 199 RMFAELGNKVV----YLKR-TAIGEMPLNGELAS-GKCLEILHKDVEKL 241


>gi|124506149|ref|XP_001351672.1| RNA pseudouridylate synthase, putative [Plasmodium falciparum 3D7]
 gi|74862473|sp|Q8I3Z1|MLRR1_PLAF7 RecName: Full=MATH and LRR domain-containing protein PFE0570w
 gi|23504600|emb|CAD51479.1| RNA pseudouridylate synthase, putative [Plasmodium falciparum 3D7]
          Length = 10061

 Score = 82.7 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 32/115 (27%), Positives = 54/115 (46%), Gaps = 13/115 (11%)

Query: 187  VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
              G P  KKE   +   + + I  DY              ++  K I+ + ++F    ++
Sbjct: 7353 TSGAPSIKKEVCHHLCFRCNSISEDYF-------------LTDPKEIENYTKEFTLCNVK 7399

Query: 247  PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPE 301
             HTGRTHQ+RVH  H+G P+V D KY      N       +++LH+  ++  +P+
Sbjct: 7400 IHTGRTHQIRVHMRHIGHPLVSDKKYLNPSLSNLDKFWCFRMFLHSLILEFNNPD 7454



 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/105 (26%), Positives = 46/105 (43%), Gaps = 1/105 (0%)

Query: 133  LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            L++       +  L HR+D ETSG L++A+T+ A + L + FR R + K Y  L  G  K
Sbjct: 7069 LETVKKWHKLECGLCHRIDLETSGSLIIAKTKEAREFLFDQFRKRNVYKEYILLCHGRIK 7128

Query: 193  NKKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVIDCF 236
             KK  I   +    +       H     + G   A + +  +  +
Sbjct: 7129 KKKGFINKSIQTHEYNNFHSKSHFSLVVKTGGTDAYTEYNCVKVY 7173


>gi|119606120|gb|EAW85714.1| RNA pseudouridylate synthase domain containing 1, isoform CRA_b
           [Homo sapiens]
          Length = 183

 Score = 82.7 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 29/108 (26%), Positives = 51/108 (47%), Gaps = 9/108 (8%)

Query: 218 QNEKGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           Q  +    +++   V++           + ++P TGRTHQLRVH   +G P+VGD  Y  
Sbjct: 7   QGCENPKPSLTDLVVLEHGLYAGDPVSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYG- 65

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
              G    P   ++ LHA Y+ +P  +   +++  P P   + + D+ 
Sbjct: 66  EVSGREDRPF--RMMLHAFYLRIP-TDTECVEVCTPDP--FLPSLDAC 108


>gi|295091825|emb|CBK77932.1| pseudouridine synthase family/haloacid dehalogenase superfamily,
           subfamily IA, variant 3 with third motif having DD or ED
           [Clostridium cf. saccharolyticum K10]
          Length = 471

 Score = 82.3 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 50/254 (19%), Positives = 97/254 (38%), Gaps = 43/254 (16%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E+ MRLDR+        +   ++K+++SG+V VD +  +                     
Sbjct: 2   EKAMRLDRYLVEMKKG-SRSEVKKMIKSGRVSVDGEICR--------------------- 39

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
              + ++ +  S +             YE    ++ NKPAG+      G    +   ++ 
Sbjct: 40  ---EAERKIQPSASEVSLDGTQVGYAAYE---YFMLNKPAGVVSATEDGRHKTVVSLIE- 92

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWG-IPKN 193
             D+K +      RLD +T G+L++    + A + L+     + + K Y++ V G +P+N
Sbjct: 93  --DAKRRDLFPVGRLDIDTEGLLLITNDGKLAHRLLS---PKKHVDKTYFARVEGRLPEN 147

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E     L  +         ++ Q E G                    +E+  H G+ H
Sbjct: 148 AIEQFKEGLTLEDGTRTLPARLLIQKEAGTAEE-------GKADSSLSEIELTIHEGKFH 200

Query: 254 QLRVHALHMGCPIV 267
           Q++     +GC +V
Sbjct: 201 QVKRMFEAVGCRVV 214


>gi|327266342|ref|XP_003217965.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           3-like [Anolis carolinensis]
          Length = 312

 Score = 82.3 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 54/265 (20%), Positives = 93/265 (35%), Gaps = 52/265 (19%)

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL------DQETSGILVVART----RAAA 167
            V          +  L S +    QK  L   L       +E+SG+++++      R   
Sbjct: 41  LVHKDGKPG---EVTLLSLLPFLSQKLGLPQNLQVIKAAGKESSGLVLLSGCADTVRRVH 97

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA---- 223
                S R +R    Y ++   IP+  +  I+  L        D V  V    +G+    
Sbjct: 98  DFYIRSQRAKRPTATYCAITTRIPEASEGEISTGLKLMQIEDFDLVVPVASPSRGSIERR 157

Query: 224 --NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFT 281
                ++H+KV+D   +    L++QP T    QL VH+  +  PI+GDH Y +       
Sbjct: 158 EVKKTLTHYKVLDSN-EDCALLQLQPLTAFPSQLLVHSTLILSPILGDHMYSSRVGAVLG 216

Query: 282 SP------------------IQNKLYLHARYMDLPHPEGGRLQ--------------ITA 309
            P                  +  KL+L  R++          +              +TA
Sbjct: 217 EPFLLSPESALPRTQILNDSLLTKLHLQQRHVHRLPLHLHLHRLLLPSTEGFSSCAALTA 276

Query: 310 PLPAHMVKTWDSLGFKYDRNLYIKR 334
           P PA  ++T   LG    +    ++
Sbjct: 277 PFPAFFLRTLSLLGLALPQEETKEQ 301


>gi|52424446|ref|YP_087583.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52306498|gb|AAU36998.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 246

 Score = 82.3 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 84/250 (33%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      KILR G V+V+ + VK  +                   I 
Sbjct: 17  MRLDKFLAEN-TGLTRSQAAKILRQGNVQVNGQVVKSGSL-----------------KIT 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++L    +L             ED    + NKP G       G    +  F    + 
Sbjct: 59  PQDEVLFEGESLEWL----------EDGVYIMLNKPQGYVCSHDDGEYPTVYQFFDYPLA 108

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +TSG++++                 +      S  +   K     +
Sbjct: 109 G---KLHTAGRLDADTSGLVLLT-------------DDGKWSHRVTSPKYHCQKTYLVTL 152

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ +        +   +++  ++    AI   ++ID +       E     GR HQ++  
Sbjct: 153 ADPVESNYRQACEQGILLRGEKEPTKPAI--LEIIDDYNVNLTISE-----GRYHQVKRM 205

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 206 FAALGNKVVG 215


>gi|221057129|ref|XP_002259702.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
            knowlesi strain H]
 gi|193809774|emb|CAQ40478.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
            knowlesi strain H]
          Length = 10549

 Score = 82.3 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 31/143 (21%), Positives = 62/143 (43%), Gaps = 14/143 (9%)

Query: 160  VARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            +++  A  + L+     R   +   +    G P  K+    +   + + I  +Y      
Sbjct: 7544 LSKREALLKILSMPKENRNSNRHNKYDSRLGYPAMKRNVCHHLCFRCNSISEEYFQ---- 7599

Query: 219  NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
                     +  K ++ + ++F    ++ HTGRTHQ+RVH  H+G P+V D KY      
Sbjct: 7600 ---------TDPKEVENYTKEFTLCNVKIHTGRTHQIRVHMRHIGHPLVADKKYLNPSLS 7650

Query: 279  NFTSPIQNKLYLHARYMDLPHPE 301
            N       +++LH+  ++  +P+
Sbjct: 7651 NLDKYWCFRMFLHSVILEFNNPD 7673



 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/103 (28%), Positives = 45/103 (43%), Gaps = 1/103 (0%)

Query: 133  LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            L++       +  L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K
Sbjct: 7267 LETVKKWHKLECGLCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYLLLCHGRIK 7326

Query: 193  NKKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVID 234
             KK CI   +    +       H     + G   A + +  + 
Sbjct: 7327 KKKGCINKSIQTHEYNNFHSKSHFSLVVKTGGTDAYTEYNCVK 7369


>gi|254385863|ref|ZP_05001182.1| pseudouridine synthase [Streptomyces sp. Mg1]
 gi|194344727|gb|EDX25693.1| pseudouridine synthase [Streptomyces sp. Mg1]
          Length = 260

 Score = 81.9 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 42/254 (16%), Positives = 87/254 (34%), Gaps = 52/254 (20%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72
            +EE  RL +         +    ++++   +V V+ + V +   R+Q    +++  +  
Sbjct: 20  AEEEGERLQKVLARAGMG-SRRACEELIEQARVEVNGEIVLEQGKRVQPKDEIKVDGLTV 78

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           A    +                              +  NKPAG+             G 
Sbjct: 79  ATQSYL-----------------------------FFALNKPAGVVSTMEDPDGRQCLG- 108

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              +V ++  +     RLD ET GI+++      A  LT   +    +    ++   +P+
Sbjct: 109 --DYVTNRETRLFHVGRLDTETEGIILLTNHGELAHRLTHP-KYGVKKTYVAAITGPLPR 165

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                    + K+   G +      + +        HF+V+D   + +  +E+  H GR 
Sbjct: 166 E--------IGKRLKDGIELEDGYARAD--------HFRVVDQVGKNY-LVEVTLHEGRK 208

Query: 253 HQLRVHALHMGCPI 266
           H +R      G P+
Sbjct: 209 HIVRRMMAEAGFPV 222


>gi|291087689|ref|ZP_06572058.1| ribosomal small subunit pseudouridine synthase A [Clostridium sp.
           M62/1]
 gi|291074338|gb|EFE11702.1| ribosomal small subunit pseudouridine synthase A [Clostridium sp.
           M62/1]
          Length = 477

 Score = 81.9 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 52/254 (20%), Positives = 99/254 (38%), Gaps = 42/254 (16%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E+ MRLDR+        +   ++K+++SG+V VD +  +                     
Sbjct: 7   EKAMRLDRYLVEMKKG-SRSEVKKMIKSGRVSVDGEICR--------------------- 44

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
              + ++ +  S +             YE    ++ NKPAG+      G    +   ++ 
Sbjct: 45  ---EAERKIQPSASEVSLDGTQVGYAAYE---YFMLNKPAGVVSATEDGRHKTVVSLIE- 97

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWG-IPKN 193
             D+K +      RLD +T G+L++    + A + L+     + + K Y++ V G +P+N
Sbjct: 98  --DAKRRDLFPVGRLDIDTEGLLLITNDGKLAHRLLS---PKKHVDKTYFARVEGRLPEN 152

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E     L  +         +V Q  K +  A    K           +E+  H G+ H
Sbjct: 153 AIEQFKEGLTLEDGTRTLPARLVIQ--KASETAEDDGK----ADSSLSEIELTIHEGKFH 206

Query: 254 QLRVHALHMGCPIV 267
           Q++     +GC +V
Sbjct: 207 QVKRMFEAVGCRVV 220


>gi|322488012|emb|CBZ23257.1| RNA pseudouridylate synthase-like protein [Leishmania mexicana
            MHOM/GT/2001/U1103]
          Length = 1455

 Score = 81.9 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 30/114 (26%), Positives = 53/114 (46%), Gaps = 14/114 (12%)

Query: 224  NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNF 280
              AI+ ++V++ FA     +++++  +GR HQ+R H   +G P+VGD +Y          
Sbjct: 1324 RNAITRYRVLEYFASAGVAYVQVELRSGRRHQIRQHFAQLGFPLVGDARYHAGVVAGRAG 1383

Query: 281  TSPIQNKLYLHARYMDLPHPEGG-----------RLQITAPLPAHMVKTWDSLG 323
            T+    +  LHA  +D+     G           R+ + A LPA M +   +L 
Sbjct: 1384 TTFGMQRAALHAYTIDILATTDGDGLASGEEVPDRVVVQAALPADMHRALLALR 1437


>gi|268563128|ref|XP_002646857.1| Hypothetical protein CBG19546 [Caenorhabditis briggsae]
          Length = 356

 Score = 81.9 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 35/200 (17%), Positives = 75/200 (37%), Gaps = 24/200 (12%)

Query: 40  ILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
             + G++ V+ ++    +  +++G   R+   ++   H +++                L 
Sbjct: 112 ACKMGRIYVNGEQMTDVDYVMKNGD--RVEHWVHRHEHPVRD----------------LP 153

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHID-GFLKSWVDSKGQKPRLTHRLDQETSGI 157
             ++ E   + V  KP  + V      A H   G L+   +  G   R+ HRLD+ TSG+
Sbjct: 154 IRIISETDDLLVIEKPPSLPVHTCGQYAIHTVLGQLRENEEKTG--LRVLHRLDRATSGV 211

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L+ A+          + +     K Y   V G+  ++++     +     +    +  V+
Sbjct: 212 LLFAKNYETDLEFKTTLKQGEWSKEYVCKVDGVFPDEEQVCEQPIG--PLVISMGIQCVR 269

Query: 218 QNEKGANYAISHFKVIDCFA 237
            + K A    S  K  +   
Sbjct: 270 PDGKEAKSTFSSAKTFETRT 289


>gi|301106528|ref|XP_002902347.1| RNA pseudouridylate synthase, putative [Phytophthora infestans
           T30-4]
 gi|262098967|gb|EEY57019.1| RNA pseudouridylate synthase, putative [Phytophthora infestans
           T30-4]
          Length = 335

 Score = 81.9 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 40/200 (20%), Positives = 74/200 (37%), Gaps = 20/200 (10%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+       L   F + +P ++        + G  RV+ +    +  I  G         
Sbjct: 92  VKGRWAGRSLRELFASEFPTLSADYCVGAAQLGHFRVNGEVADLDKVITGGDFFEHIKHR 151

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
               H  K    +D S+ L+       + +  E  ++ V +KP+GI V        +   
Sbjct: 152 ----HEPKIHLPVDDSIELSTLKSLSNTWIHEETDELMVVDKPSGIPVHPTGSFQLNSLT 207

Query: 132 FLKSW-------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR--------- 175
            +           +++  K    HRLD+ TSG+L++A++   A+ LT             
Sbjct: 208 HMLIRDRREALIEETEALKLFPVHRLDRLTSGLLILAKSADKARSLTAELTATSSEGGIG 267

Query: 176 MRRIQKIYWSLVWGIPKNKK 195
            R +QK Y + V G   + +
Sbjct: 268 SRSVQKYYVARVKGKFPDTE 287


>gi|149020773|ref|ZP_01835302.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP23-BS72]
 gi|147930414|gb|EDK81397.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP23-BS72]
          Length = 131

 Score = 81.9 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 27/137 (19%), Positives = 52/137 (37%), Gaps = 15/137 (10%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
              + ++++ V +N  +  G V ++                 D S       +      +
Sbjct: 4   KKHILINQEEVHWNEIVNPGDVCQLTFDEE------------DYSQKTIPWGNPDLVQEV 51

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           Y+D  + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A+
Sbjct: 52  YQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFAK 108

Query: 163 TRAAAQHLTESFRMRRI 179
                  L      +R 
Sbjct: 109 NPFILPILNRLLEKKRF 125


>gi|70947911|ref|XP_743527.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56523063|emb|CAH79456.1| conserved hypothetical protein [Plasmodium chabaudi chabaudi]
          Length = 1071

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 42/74 (56%)

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +  K I+ + ++F    ++ HTGRTHQ+RVH  H+G P+V D KY      N       +
Sbjct: 382 TDPKDIETYTKEFTLCNVKIHTGRTHQIRVHMRHIGHPLVSDKKYLDASLSNLDKFWCFR 441

Query: 288 LYLHARYMDLPHPE 301
           ++LH+  ++  +P+
Sbjct: 442 MFLHSIILEFNNPD 455



 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/103 (27%), Positives = 45/103 (43%), Gaps = 1/103 (0%)

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L++       +  L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K
Sbjct: 64  LETVKKWHKLECGLCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYILLCHGRIK 123

Query: 193 NKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            KK  I   +   + +      H     + G   A + +  + 
Sbjct: 124 KKKGFINKSIQTHEYNNSHSKSHFSLVVKTGGTDAYTEYNCVK 166


>gi|217031565|ref|ZP_03437070.1| hypothetical protein HPB128_21g123 [Helicobacter pylori B128]
 gi|216946765|gb|EEC25361.1| hypothetical protein HPB128_21g123 [Helicobacter pylori B128]
          Length = 147

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 33/149 (22%), Positives = 58/149 (38%), Gaps = 10/149 (6%)

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWL 243
           +L  G+  +K   I   +L   +I  D     K +      + +  + +          L
Sbjct: 2   ALAHGLV-DKNIVIDKPILTPQNIQKDLRIRSKIS-PLGKPSTTLVEPLSYNPFLDISLL 59

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK------LYLHARYMDL 297
           ++ P TGRTHQ+R+H   +G  IVG+  Y    +         +      L LHA  ++ 
Sbjct: 60  KITPITGRTHQIRLHLSSVGHRIVGEGLYGVIDENAREYLQLKRENNAPLLMLHASSLEF 119

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLGFKY 326
              +    +IT+P+P   +     L   Y
Sbjct: 120 EF-KKAFYEITSPMPKRFMPFLKDLALFY 147


>gi|227503690|ref|ZP_03933739.1| pseudouridine synthase B [Corynebacterium accolens ATCC 49725]
 gi|227075726|gb|EEI13689.1| pseudouridine synthase B [Corynebacterium accolens ATCC 49725]
          Length = 303

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 50/262 (19%), Positives = 95/262 (36%), Gaps = 53/262 (20%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVR 66
           ++V ++  +  RL +         +  + + ++ +G+V V+   + K   ++     V+R
Sbjct: 53  WLVDDDKPKGERLQKVLAKA-GVASRRHAEILIDAGRVEVNGNVILKQGVKVNPAVDVIR 111

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V   +N                            ED + ++ NKP G+       + 
Sbjct: 112 VDGVRVNVN----------------------------EDQEYFILNKPRGMQSTMSDDLG 143

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
               G + S   + GQ+     RLD +T G+L++      A  L        ++K Y + 
Sbjct: 144 RPCVGDVVSEKVASGQRLFHVGRLDADTEGLLILTNDGELANRL--MHPKYEVKKTYLAT 201

Query: 187 VWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           V G   NK  ++      L+      D+V VV +N                  Q F  + 
Sbjct: 202 VLGEADNKLVRQLKEGIELEDGLAKADFVQVVDKN------------------QGFSLVR 243

Query: 245 MQPHTGRTHQLRVHALHMGCPI 266
           ++ H GR H +R      G P+
Sbjct: 244 VELHEGRKHIVRRLLKEAGYPV 265


>gi|332240387|ref|XP_003269368.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like, partial [Nomascus leucogenys]
          Length = 182

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 28/105 (26%), Positives = 50/105 (47%), Gaps = 9/105 (8%)

Query: 221 KGANYAISHFKVIDCF---AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +    +++   V++           + ++P TGRTHQLRVH   +G P+VGD  Y     
Sbjct: 9   ENPKPSLTELVVLEHGLYAGDPVSKVLLKPLTGRTHQLRVHCSALGHPVVGDLTYG-EAS 67

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
           G    P   ++ LHA Y+ +P  +   +++  P P   + + D+ 
Sbjct: 68  GREDRPF--RMMLHAFYLRIP-TDAECVEVCTPDP--FLPSLDAC 107


>gi|116335030|ref|YP_802525.1| ribosomal large subunit pseudouridine synthase [Candidatus
           Carsonella ruddii PV]
 gi|116235311|dbj|BAF35159.1| ribosomal large subunit pseudouridine synthase [Candidatus
           Carsonella ruddii PV]
          Length = 204

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 54/220 (24%), Positives = 93/220 (42%), Gaps = 28/220 (12%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           + Y D+ I V NKP GI V+           F+K  ++ K     + +RLD+ TSG+++V
Sbjct: 6   INYFDNNIIVINKPIGIEVK-----NLLNVNFIK--LNDKIPNFGILNRLDKYTSGLILV 58

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A+      +  +      I+K Y S V    K     +  +  KKS I  +    +    
Sbjct: 59  AKNFYFYFYFKKLIVKNLIKKNYISFVNKKIKKGFVNVDIFKKKKSSIIKNNKKSI---- 114

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
                  +++K+I    + F +L +   TGRTHQ+R+H +H+   I  D  Y   +  N 
Sbjct: 115 -------TYYKIIK-EKKNFSFLNICIKTGRTHQIRLHMMHIEKKIFNDFYYNKTYLLNN 166

Query: 281 TSPIQNKLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTW 319
           T         H + M   +P    ++ +   L   + K +
Sbjct: 167 TL--------HFKKMMFYYPFIKKKINLFCSLNNDIKKIF 198


>gi|255075765|ref|XP_002501557.1| predicted protein [Micromonas sp. RCC299]
 gi|226516821|gb|ACO62815.1| predicted protein [Micromonas sp. RCC299]
          Length = 372

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 52/301 (17%), Positives = 104/301 (34%), Gaps = 85/301 (28%)

Query: 101 LLYEDSK--IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK------------------ 140
           +LY D +   +V NKPAG+ V+            ++   +                    
Sbjct: 58  VLYVDPRARFFVVNKPAGMYVENVLDFIERYMEEVRRAPERHSERSKRAKTCSDGATSIR 117

Query: 141 ---------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS--LVWG 189
                    G++ +L HRLD++T+G L +A  +   + L+ +F+  R++K Y +  +   
Sbjct: 118 EAFDSLAKVGERFQLLHRLDRDTTGCLGIACDKETNRILSRAFQEGRVKKHYVAHCINTK 177

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQ------------------------------- 218
              + ++   +W + +    G       Q                               
Sbjct: 178 FADDFQKKWKDWEVDEPFEDGSRAMTWPQRFCNFRLECHTGHGRSKHGLWRLYAKEDVGR 237

Query: 219 ---NEKGANYAISH-FKVIDCFAQKFCWLEMQ----------PHTGRTHQLRVHALHMGC 264
                     A ++ ++  D  +       ++          P TGRTHQ+R+H      
Sbjct: 238 ELPGGSKVKEARTNLYRGFDSDSDSKRLAHLRELQSFPVVAEPITGRTHQIRMHCSQY-F 296

Query: 265 PIVGDHKYCANFKGN-----FTSPIQNKLYLHARYMDLPHPEGGRLQ---ITAPLPAHMV 316
           PIVGD+KY  +   +            +L+  +  + +  P+G   +   + AP P+   
Sbjct: 297 PIVGDYKYGYDDTADDDVVQEEREKGYRLHSFSLELPIKIPDGNGFRDTLVLAPPPSWWN 356

Query: 317 K 317
           +
Sbjct: 357 E 357


>gi|270659692|ref|ZP_06222356.1| tRNA pseudouridine synthase C [Haemophilus influenzae HK1212]
 gi|270316970|gb|EFA28650.1| tRNA pseudouridine synthase C [Haemophilus influenzae HK1212]
          Length = 97

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 25/89 (28%), Positives = 40/89 (44%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG+ V       +     +++  D  GQ     HRLD+ TSG+L+ 
Sbjct: 4   ILYQDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLF 63

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           A +   A     +     +    W  V+G
Sbjct: 64  ALSSEIANSGITATVQADVWIRPWLSVFG 92


>gi|50288967|ref|XP_446913.1| hypothetical protein [Candida glabrata CBS 138]
 gi|74609881|sp|Q6FS81|PUS5_CANGA RecName: Full=Pseudouridylate synthase PUS5; AltName:
           Full=Pseudouridine synthase 5; AltName: Full=Uracil
           hydrolyase PUS5
 gi|49526222|emb|CAG59846.1| unnamed protein product [Candida glabrata]
          Length = 223

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 31/185 (16%), Positives = 63/185 (34%), Gaps = 37/185 (20%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETS 155
           +  ++Y+     +  K AG+  Q G          +        +   L    RLD   +
Sbjct: 4   RLKVVYDGMHYMIVYKSAGVLSQPGLASDSRPV-LMSELRGLLSETLDLYSVQRLDACVT 62

Query: 156 GILVVARTRAAAQHLTESFRMRR-----IQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           G  VVA+ + AA   +   +        + + Y + +   P   +  I +  +       
Sbjct: 63  GGTVVAKNKRAAMMFSRYLKQGGGSGYGLTRRYLARINAQPVCDEGTIESPGM------- 115

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGD 269
                           +++++ +         + ++  TG+ HQ+R H    + CPIV D
Sbjct: 116 ----------------VTYYRRVRDD-----CVVVELKTGKKHQIRKHLALNLNCPIVND 154

Query: 270 HKYCA 274
             Y  
Sbjct: 155 TYYGG 159


>gi|306836036|ref|ZP_07469026.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           accolens ATCC 49726]
 gi|304568063|gb|EFM43638.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           accolens ATCC 49726]
          Length = 303

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 51/262 (19%), Positives = 94/262 (35%), Gaps = 53/262 (20%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVR 66
           ++V ++  +  RL +         +  + + ++  G+V V+   V K   ++     V+R
Sbjct: 53  WLVDDDKPKGERLQKVLAKA-GVASRRHAEILIDGGRVEVNGNVVLKQGVKVNPAVDVIR 111

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V   +N                            ED + ++ NKP G+       + 
Sbjct: 112 VDGVRVNVN----------------------------EDQEYFILNKPRGMQSTMSDDLG 143

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
               G + S   + GQ+     RLD +T G+L++      A  L        ++K Y + 
Sbjct: 144 RPCVGDVVSEKVASGQRLFHVGRLDADTEGLLILTNDGELANRL--MHPKYEVKKTYLAT 201

Query: 187 VWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           V G   NK  ++      L+      D+V VV +N                  Q F  + 
Sbjct: 202 VLGEADNKLVRQLKEGIELEDGLAKADFVQVVDKN------------------QGFSLVR 243

Query: 245 MQPHTGRTHQLRVHALHMGCPI 266
           ++ H GR H +R      G P+
Sbjct: 244 VELHEGRKHIVRRLLKEAGYPV 265


>gi|82540405|ref|XP_724523.1| RNA pseudouridylate synthase [Plasmodium yoelii yoelii str. 17XNL]
 gi|23479192|gb|EAA16088.1| RNA pseudouridylate synthase, putative [Plasmodium yoelii yoelii]
          Length = 1254

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 42/74 (56%)

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +  K I+ + ++F    ++ HTGRTHQ+RVH  H+G P+V D KY      N       +
Sbjct: 519 TDPKDIETYTKEFTLCNVKIHTGRTHQIRVHMRHIGHPLVSDKKYLNTSLSNLDKFWCFR 578

Query: 288 LYLHARYMDLPHPE 301
           ++LH+  ++  +P+
Sbjct: 579 MFLHSIILEFNNPD 592



 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 1/103 (0%)

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L++       +  L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K
Sbjct: 152 LETVKKWHKLECGLCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYILLCHGRIK 211

Query: 193 NKKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVID 234
            KK  I   +    +       H     + G   A + +  + 
Sbjct: 212 KKKGFINKSIQTHEYNNFHSKSHFSLVVKTGGTDAYTEYNCVK 254


>gi|303281620|ref|XP_003060102.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226458757|gb|EEH56054.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 539

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 45/258 (17%), Positives = 83/258 (32%), Gaps = 46/258 (17%)

Query: 61  SGQVV-RIPPVINALNHIIKEQKILDSSVNLTKHSDFLK-SILLYEDSKIYVFNKPAGIS 118
            G V  R      +L+  +     L    ++ +     +  ++L ED ++ + +KP G+ 
Sbjct: 97  GGDVPERWWATPASLDERVPRDSRLRVRRHVHEPCVHAEAPVVLTEDERVVIVDKPPGLP 156

Query: 119 ----VQGGSGIAYHIDGFLKSWVDS------------------------KGQKPRLTHRL 150
               V  G     +    L+    S                                +R+
Sbjct: 157 TLAGVGPGVAGENNAVAVLRRLRASASASAKRKREESDDGGGGGGGGDDDDAPLFAVNRI 216

Query: 151 DQETSGILVVAR----TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK-K 205
           D+  SG+ ++A+    +  A   L +       +K Y +LV G  +              
Sbjct: 217 DKPVSGVWILAKGSRLSARARDALHKGAARGETRKTYVALVKGRVEVGGGGAGGGGFVVD 276

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFA----------QKFCWLEMQPH-TGRTHQ 254
           + +  D   +      GA  A +    +   A          +      +    +GR HQ
Sbjct: 277 APLRKDERGLAVVGGDGAKPAATRVVPLAVVAVPSKGGGGEKEALTLAAVALEKSGRYHQ 336

Query: 255 LRVHALHMGCPIVGDHKY 272
           +R H  H+G PIV D  Y
Sbjct: 337 IRAHLAHVGHPIVFDRDY 354


>gi|68066382|ref|XP_675174.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56494204|emb|CAH93561.1| conserved hypothetical protein [Plasmodium berghei]
          Length = 895

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 43/74 (58%)

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
           +  K I+ + ++F    ++ HTGRTHQ+RVH  H+G P+V D KY  +   N       +
Sbjct: 337 TDPKDIETYTKEFTLCNVKIHTGRTHQIRVHMRHIGHPLVSDKKYLNSSLSNLDKFWCFR 396

Query: 288 LYLHARYMDLPHPE 301
           ++LH+  ++  +P+
Sbjct: 397 MFLHSIILEFNNPD 410



 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 1/103 (0%)

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L++       +  L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K
Sbjct: 23  LETVKKWHKLECGLCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYILLCHGRIK 82

Query: 193 NKKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVID 234
            KK  I   +    +       H     + G   A + +  + 
Sbjct: 83  KKKGFINKSIQTHEYNNFHSKSHFSLVVKTGGTDAYTEYNCVK 125


>gi|295115835|emb|CBL36682.1| ribosomal small subunit pseudouridine synthase A
           [butyrate-producing bacterium SM4/1]
          Length = 346

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 52/254 (20%), Positives = 98/254 (38%), Gaps = 42/254 (16%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E+ MRLDR+        +   ++K+++SG+V VD +  +                     
Sbjct: 2   EKAMRLDRYLVEMKKG-SRSEVKKMIKSGRVSVDGETCR--------------------- 39

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
              + ++ +  S +             YE    ++ NKPAG+      G    +   ++ 
Sbjct: 40  ---EAERKIQPSASEVSLDGTQVGYAAYE---YFMLNKPAGVVSATEDGRHKTVVSLIE- 92

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWG-IPKN 193
             D+K +      RLD +T G+L++    + A + L+     + + K Y++ V G +P+N
Sbjct: 93  --DAKRRDLFPVGRLDIDTEGLLLITNDGKLAHRLLS---PKKHVDKTYFARVEGRLPEN 147

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E     L  +         +V Q   G   A    K           +E+  H G+ H
Sbjct: 148 AIEQFKEGLTLEDGTRTLPARLVIQKASG--TAEDDGK----ADSSLSEIELTIHEGKFH 201

Query: 254 QLRVHALHMGCPIV 267
           Q++     +GC +V
Sbjct: 202 QVKRMFEAVGCRVV 215


>gi|328467386|gb|EGF38463.1| pseudouridine synthase [Lactobacillus rhamnosus MTCC 5462]
          Length = 159

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 7/87 (8%)

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
           ++ +   +    +++ ++ +   +     L +  HTGRTHQ+RVH   +G P+ GD  Y 
Sbjct: 24  YMRRVVSETGKPSVTEYQTLAQNSHAAAVL-VTLHTGRTHQIRVHFAAIGHPLFGDDLYN 82

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHP 300
                        +  LH  ++    P
Sbjct: 83  RQADD------FKRQALHCAHLRFWQP 103


>gi|58337102|ref|YP_193687.1| 16s pseudouridylate synthase [Lactobacillus acidophilus NCFM]
 gi|227903674|ref|ZP_04021479.1| 16S pseudouridylate synthase [Lactobacillus acidophilus ATCC 4796]
 gi|58254419|gb|AAV42656.1| 16s pseudouridylate synthase [Lactobacillus acidophilus NCFM]
 gi|227868561|gb|EEJ75982.1| 16S pseudouridylate synthase [Lactobacillus acidophilus ATCC 4796]
          Length = 236

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 86/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   + ++++ G V V+ K VK    +I    VV +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHQLIKKGLVDVNGKTVKTPKEKINEDDVVTVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   LK   
Sbjct: 51  --------------------GEKVAYQKYHYFLLNKPTGVLSATEDRSQKTVISLLK--P 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + + Q      RLD++T+G+L++         L      + + K+Y + + G+     E 
Sbjct: 89  EDRYQGIAPVGRLDKDTTGLLLLTNDGQLNHEL--LAPNKHVAKVYRAQIAGV--ADDET 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLR 256
           +  +    +   G  +   K             +++    +     +E++   G+ HQ++
Sbjct: 145 VKTFASGMTLGDGTKLKPAK------------LRILKQDRENATSEIEIEISEGKYHQIK 192

Query: 257 VHALHMG 263
                +G
Sbjct: 193 RMFGAVG 199


>gi|299115647|emb|CBN75848.1| 23S RNA-specific pseudouridylate synthase [Ectocarpus siliculosus]
          Length = 245

 Score = 81.2 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 47/208 (22%), Positives = 79/208 (37%), Gaps = 54/208 (25%)

Query: 158 LVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKKECIANWLL------------- 203
           + VART  AA  L+ SFR R  ++KIY ++V G    +     + L+             
Sbjct: 1   MCVARTSKAAARLSASFRARDDVEKIYHAVVAGSLAGR-GIRQDLLVSPDASGAVARRGR 59

Query: 204 ----------KKSHIGGDYVHVVKQNEKGANYAISHFKVID------------CFAQKFC 241
                      +   GG  +     +      A   ++ I+                   
Sbjct: 60  GPRAGLSSVPARGGAGGRLLAAGPTSSPDGKLAQLEWEAINVSSSSAVRLRCPRTGNPRT 119

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS--------------PIQNK 287
            + ++  TGR HQ+RV    MG P+VGD +Y  +  G+ T               P++++
Sbjct: 120 LVRVRLITGRKHQIRVQLAEMGHPVVGDTRYGRSRGGDATDESAVPPPRRAGRIEPLEDR 179

Query: 288 -LYLHARYMDLPHPE--GGRLQITAPLP 312
            + LHA  + +PHP   G  ++  A  P
Sbjct: 180 SILLHASELIVPHPTRVGATVRAVAAPP 207


>gi|294943238|ref|XP_002783805.1| Ribosomal large subunit pseudouridine synthase A, putative
           [Perkinsus marinus ATCC 50983]
 gi|239896540|gb|EER15601.1| Ribosomal large subunit pseudouridine synthase A, putative
           [Perkinsus marinus ATCC 50983]
          Length = 142

 Score = 81.2 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 41/120 (34%), Positives = 55/120 (45%), Gaps = 5/120 (4%)

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSGI++VA T AA   L   F+ R I K Y  LV G        I   +   S   
Sbjct: 27  LDIFTSGIIMVAHTYAAYYQLRHQFKKRAILKKYICLVHGHMDEDSGIIDTNIQTYSSSS 86

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
                 +  +   ++Y       I    +K   LE++  TGRTHQ+R+H  H+G PIV D
Sbjct: 87  NSRSKHIPISSSSSSY-----STIINNNKKVSLLEVEIPTGRTHQIRLHMYHIGHPIVSD 141


>gi|149052130|gb|EDM03947.1| RNA pseudouridylate synthase domain containing 1 (predicted),
           isoform CRA_c [Rattus norvegicus]
          Length = 177

 Score = 81.2 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 27/105 (25%), Positives = 44/105 (41%), Gaps = 9/105 (8%)

Query: 221 KGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           +    +++   V++           + ++P TGRTHQLRVH   +G PIVGD  Y     
Sbjct: 10  ENPKPSLTELLVLEHGLYSGDPVSKVLLKPLTGRTHQLRVHCSALGHPIVGDLTYGQADD 69

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSL 322
                    ++ LHA Y+ +  P      + A  P   +   D+ 
Sbjct: 70  QEDQPF---RMMLHAFYLRI--PTRAE-CVEACTPDPFLPALDAC 108


>gi|254393249|ref|ZP_05008402.1| pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|294811815|ref|ZP_06770458.1| Pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|326440444|ref|ZP_08215178.1| pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|197706889|gb|EDY52701.1| pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|294324414|gb|EFG06057.1| Pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
          Length = 376

 Score = 81.2 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 44/278 (15%), Positives = 89/278 (32%), Gaps = 55/278 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           ++E  RL +         +    ++++ +G+V V+   V                 I   
Sbjct: 136 EQEGERLQKVLARAGVG-SRRACEELIEAGRVEVNGSIV-----------------IEQG 177

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +  E   +           +L           +  NKPAG+             G   
Sbjct: 178 VRVDPENDEIKVDGLTVATQSYL----------FFALNKPAGVVSTMEDPDGRQCLG--- 224

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +V ++  +     RLD ET GI+++      A  LT   R    +    ++   +P+  
Sbjct: 225 DYVTNRETRLFHVGRLDTETEGIILLTNHGELAHRLTHP-RYGVKKTYLAAIQGPLPREL 283

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + + + +  +                       HF+V++   + +  +E+  H GR H 
Sbjct: 284 GKRLKDGIALEDGYARAD----------------HFRVVENTGKNY-LVEVTLHEGRKHI 326

Query: 255 LRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
           +R      G P+  D      +     G+  S    +L
Sbjct: 327 VRRMLAEAGFPV--DRLVRTAFGPIGLGDQKSGWLRRL 362


>gi|45200963|ref|NP_986533.1| AGL134Cp [Ashbya gossypii ATCC 10895]
 gi|74692056|sp|Q750S3|PUS5_ASHGO RecName: Full=Pseudouridylate synthase PUS5; AltName:
           Full=Pseudouridine synthase 5; AltName: Full=Uracil
           hydrolyase PUS5
 gi|44985733|gb|AAS54357.1| AGL134Cp [Ashbya gossypii ATCC 10895]
          Length = 260

 Score = 81.2 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 41/188 (21%), Positives = 70/188 (37%), Gaps = 32/188 (17%)

Query: 99  SILLYEDSKIYVFNKPAGISVQG---GSGIAYHI-------DGFLKSWVDSKGQKPRLTH 148
             +L+E    Y+ NK  GI  Q     +   YH        D   K   +  G+  R  H
Sbjct: 6   VPILHEHKHYYIVNKVHGIVCQPPDLRTWYKYHDYEPPVLLDLLRKQHPNFGGEVWRTVH 65

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD+  +G ++V+R + AA   + S  +   +        G P  ++         K   
Sbjct: 66  RLDEPVTGGVLVSRNKRAAAMFSRSLALGGNR--------GFPLTRRYVALLAREAKGLP 117

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM-GCPIV 267
               + +           I+ +K ++        + +Q  TGR HQ+R     + G P+V
Sbjct: 118 SEGRITMGDM--------ITDYKRLEND-----LVLLQLQTGRKHQIRKQMAQVFGQPVV 164

Query: 268 GDHKYCAN 275
            D  Y  +
Sbjct: 165 NDKMYGGD 172


>gi|145295560|ref|YP_001138381.1| hypothetical protein cgR_1487 [Corynebacterium glutamicum R]
 gi|140845480|dbj|BAF54479.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 320

 Score = 80.8 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 90/253 (35%), Gaps = 45/253 (17%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ND + +RL +         +  + + ++  G+V V+ + V         Q VR+ P    
Sbjct: 75  NDSDGVRLQKVLAQA-GVASRRHAEILIDQGRVEVNDRIVTT-------QGVRVNPN--- 123

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
            N +I+   +                I + ED + +V NKP G+       +     G L
Sbjct: 124 -NDVIRVDGV---------------RIHINEDLEYFVLNKPRGMHSTMSDELGRPCVGDL 167

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            S   + GQ+     RLD +T G+L++      A  L        + K Y + V G   N
Sbjct: 168 VSEKTASGQRLFHVGRLDADTEGLLLLTNDGELANRL--MHPKYEVSKTYLATVRGEATN 225

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           K   ++          G               A + F  I    Q    L ++ H GR H
Sbjct: 226 K--LVSALRDGVELEDG--------------PAKADFAQIIDVFQGKSLLRIEIHEGRKH 269

Query: 254 QLRVHALHMGCPI 266
            +R     +G P+
Sbjct: 270 IVRRLFDELGFPV 282


>gi|226724674|sp|A3BN26|PUS6_ORYSJ RecName: Full=RNA pseudourine synthase 6, chloroplastic; AltName:
           Full=RNA pseudouridylate synthase 6; AltName:
           Full=RNA-uridine isomerase 6; Flags: Precursor
 gi|125601389|gb|EAZ40965.1| hypothetical protein OsJ_25447 [Oryza sativa Japonica Group]
          Length = 477

 Score = 80.8 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 48/259 (18%), Positives = 88/259 (33%), Gaps = 44/259 (16%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYV 110
           +    N R+++G  +R+                         +    KS ++       V
Sbjct: 173 RVTDPNQRLEAGTYLRVHVHPKRFPR---------------CYEIDWKSRVIAVTDNYVV 217

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
            +KPA  SV G +           S           TH++D  + G +V+++T+      
Sbjct: 218 LDKPAATSVGGATDNIEESCVVFTSRALGLETPLMTTHQIDNCSEGCVVLSKTKEFCSVF 277

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHF 230
               R +++ K Y +L           I +++     I      V + + KG  + +   
Sbjct: 278 HGMIREKQVNKRYLALTTAPVST--GIITHYM---RPINRAPRLVSEDHIKG--WHVCQM 330

Query: 231 KVIDC--------------------FAQKFCWLEMQP--HTGRTHQLRVHALHMGCPIVG 268
           +++DC                    + Q+    E +    TG+THQ+R     +G PIVG
Sbjct: 331 EILDCKKVPWPSSLIRKVHKVDNCGWPQQEAAYECKINLLTGKTHQIRAQLAAIGTPIVG 390

Query: 269 DHKYCANFKGNFTSPIQNK 287
           D  Y         +P  N 
Sbjct: 391 DSAYMTAAMAAIVNPSINP 409


>gi|219117904|ref|XP_002179738.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217408791|gb|EEC48724.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 311

 Score = 80.8 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 45/229 (19%), Positives = 74/229 (32%), Gaps = 39/229 (17%)

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG-----FLKSWVDSKGQKPRLTHRLDQE 153
             +L    +  V  KP  +            D        ++     G    L HRL+  
Sbjct: 89  VTILARTDRYVVVAKPPTVVCHHSEWTGSRSDPFQIPMLQRTREAMGGNCVNLVHRLNWG 148

Query: 154 TSGILVVARTRAAA----------QHLTESFRMRRIQKIYWSLV--WGIPKNKKECIANW 201
            SG L++      A            L  S +     K Y +LV   G+ + +      W
Sbjct: 149 CSGCLLLTYAADTADAEIYIPNTTATLIASMKETASLKTYLALVRGEGLLQGRDFKQEGW 208

Query: 202 LLKKSHIGGDYVHVVKQNEKGA-NYAISHFKVIDCFAQ--------KFCWLEMQPHTGRT 252
                 I         +NEKG  N A + F+ +             +   +  +P TGR 
Sbjct: 209 FKVDRPI---------KNEKGILNNATTWFRFVAGQDNDSGRINQPRASLVLARPETGRW 259

Query: 253 HQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN----KLYLHARYMDL 297
           HQ+R H   +  PI+GD  +  +        ++     +  LH   + L
Sbjct: 260 HQIRRHLNGLSHPILGDTSHGNSHVNREWRDLRGMPAQRTCLHLARLQL 308


>gi|78045168|ref|YP_360757.1| ribosomal large subunit pseudouridine synthase B [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77997283|gb|ABB16182.1| ribosomal large subunit pseudouridine synthase B [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 241

 Score = 80.8 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 51/253 (20%), Positives = 89/253 (35%), Gaps = 57/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL ++           + ++++ +G+V+V+ K VK    ++    VV +         I
Sbjct: 2   ERLQKYLARA-GVAARRDAEQLILAGRVKVNGKVVKELGFKVSDRDVVEVD------GRI 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
           +K +K++                         +  KPAG I+          +   L   
Sbjct: 55  VKPEKLV-----------------------YILMYKPAGYITTVDDPFGRPTVLSLLAGK 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNK 194
           V    ++     RLD  T G+L++      A  LT      ++ K Y +LV G P     
Sbjct: 92  VK---ERVFPVGRLDMNTEGLLILTNDGDLAMALT--HPKHQVPKTYLALVRGTPNRAKL 146

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           KE     LL+  +     V+  K   K                    W+E+  H GR  Q
Sbjct: 147 KELERGVLLEDGYTAPAKVNFKKPEGKN------------------SWIEITIHEGRKRQ 188

Query: 255 LRVHALHMGCPIV 267
           +R     +G P++
Sbjct: 189 VRRMFKKIGHPVL 201


>gi|71663022|ref|XP_818509.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70883765|gb|EAN96658.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 378

 Score = 80.8 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 54/317 (17%), Positives = 92/317 (29%), Gaps = 119/317 (37%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------------------------GSGIAYHIDGFLKSW 136
           ++Y + ++ V NKP  + + G                          G     D   ++ 
Sbjct: 10  VIYGNEELVVVNKPHDVPMDGEACPVTVEKWAWAYLAKGGCADNNAGGGVEKEDDTTRTA 69

Query: 137 VDSKGQK--PRLTHRLDQETSGILVVARTRAAAQ---HLTESFRMRR------------- 178
              +G+K   +  H+LD  TSG+L VA +R  A    H  E    R+             
Sbjct: 70  GRRRGEKKMVKFVHQLDYATSGVLCVAFSREMAARLAHCFEMRTTRKAYLAVLFGMMPTT 129

Query: 179 ------------------------IQKIYWSLVWGIPKNKKECIAN-------------- 200
                                   ++++    V G+   +K  I                
Sbjct: 130 SAMQKKLDTDTGVDFLRGSPYASHVRRVSMDDVPGVCFIRKCVIEASGHEEGENADCCAT 189

Query: 201 WLLKKSHIGGDYV----HVVKQNEKGANYAISHFKVIDC---------FAQKFCWLEMQP 247
            L     +G D        +  N + A  ++++  V+                  + + P
Sbjct: 190 LLEVNLPVGYDTTDHEGFRMTVNGRDARGSVTYLSVLQRGYMTHPTSGCPVPVTKVALFP 249

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--------------------- 286
            TGR HQLRVH   +G PI+GD  Y           +                       
Sbjct: 250 RTGRRHQLRVHCHAIGFPILGDVTYARIPTPRVAPKVTGAEEVATVGATESINAPNEIGA 309

Query: 287 -----KLYLHARYMDLP 298
                ++ LHA  +  P
Sbjct: 310 IEAWQRMMLHAWRLSFP 326


>gi|213420423|ref|ZP_03353489.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 101

 Score = 80.8 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 34/101 (33%), Positives = 60/101 (59%), Gaps = 1/101 (0%)

Query: 118 SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177
           +V GGSG+++ +   L++ +  + +   L HRLD++TSG+L+VA+ R+A + L E  R +
Sbjct: 2   AVHGGSGLSFGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREK 60

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            +QK Y +LV G  ++  + +   LLK     G+ +  V Q
Sbjct: 61  GMQKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQ 101


>gi|315930491|gb|EFV09543.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 144

 Score = 80.4 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 33/163 (20%), Positives = 68/163 (41%), Gaps = 27/163 (16%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           I+    QK++   ++  D   V+  N+I +G +V +                      + 
Sbjct: 6   ISINEAQKLIDKKRLFCDGILVEEKNKILNG-LVEL----------------------IV 42

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
             ++     +++E+    +  K +GI     G    Y +   +       G++  + HRL
Sbjct: 43  YENNPKGVEIVFENEDFAILEKESGILSHPNGRHCKYSLSDEIWHL---WGKEACVAHRL 99

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           D+ETSG++++A+ + A   L   F  + +QK Y +L  G  + 
Sbjct: 100 DKETSGLILIAKNKKAQIDLKSLFEKKLVQKEYLALAHGKIEE 142


>gi|19552642|ref|NP_600644.1| 16S rRNA uridine-516 pseudouridylate synthase [Corynebacterium
           glutamicum ATCC 13032]
 gi|62390310|ref|YP_225712.1| 16S rRNA uridine-516 pseudouridylate synthase or related
           pseudouridylate synthase [Corynebacterium glutamicum
           ATCC 13032]
 gi|41325647|emb|CAF21436.1| 16S rRNA uridine-516 pseudouridylate synthase or related
           pseudouridylate synthase [Corynebacterium glutamicum
           ATCC 13032]
          Length = 320

 Score = 80.4 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 90/253 (35%), Gaps = 45/253 (17%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ND + +RL +         +  + + ++  G+V V+ + V         Q VR+ P    
Sbjct: 75  NDSDGVRLQKVLAQA-GVASRRHAEILIDQGRVEVNDRIVTT-------QGVRVDPN--- 123

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
            N +I+   +                I + ED + +V NKP G+       +     G L
Sbjct: 124 -NDVIRVDGV---------------RIHINEDLEYFVLNKPRGMHSTMSDELGRPCVGDL 167

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            S   + GQ+     RLD +T G+L++      A  L        + K Y + V G   N
Sbjct: 168 VSEKTASGQRLFHVGRLDADTEGLLLLTNDGELANRL--MHPKYEVSKTYLATVRGEATN 225

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           K   ++          G               A + F  I    Q    L ++ H GR H
Sbjct: 226 K--LVSALRDGVELEDG--------------PAKADFAQIIDVFQGKSLLRIEIHEGRKH 269

Query: 254 QLRVHALHMGCPI 266
            +R     +G P+
Sbjct: 270 IVRRLFDELGFPV 282


>gi|326429138|gb|EGD74708.1| hypothetical protein PTSG_06069 [Salpingoeca sp. ATCC 50818]
          Length = 224

 Score = 80.4 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 81/233 (34%), Gaps = 44/233 (18%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L   +LY+D  +   NK   +SVQ        +   L         +PRL HRLDQ T+G
Sbjct: 13  LLRAVLYQDHNVIALNKWRSLSVQDELQSDNTLLNNLHLLQLKHNDEPRLLHRLDQNTTG 72

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++ R   A   ++  F+ R IQK Y ++V   P        N   + +       H  
Sbjct: 73  VLLIGRKPQATAAISTLFQHRLIQKTYLAVVVATPTMD----TNNPFRNASGTWSSPHPD 128

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA--LHMGCPIVGDHKYCA 274
           +   +GA    S                          +R       +G P         
Sbjct: 129 EDPVRGAEKTASR-------------------------IRRQLKRAGLGHP--------- 154

Query: 275 NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYD 327
                +   I   L+ H   +     +G  L I APLP+HM  T  +L    D
Sbjct: 155 ----PYQHGILQHLHAHELLIPSYFTDGTPLHIVAPLPSHMSLTLGTLFNAAD 203


>gi|262182363|ref|ZP_06041784.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
          Length = 286

 Score = 80.4 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 87/254 (34%), Gaps = 53/254 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVRIPPVINAL 74
           +  RL +         +  + + ++  G+V V+ + + K   R+     V+R+      +
Sbjct: 44  QGERLQKVLAKA-GVASRRHAEILIDEGRVEVNGQVIIKQGTRVDPNKDVIRVDGTRINV 102

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           N                            E+++ +V NKP G+       +     G + 
Sbjct: 103 N----------------------------EETQYFVLNKPRGMQSTMSDDMGRPCVGDVV 134

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           +     GQ+     RLD +T G+L++      A  L        + K Y + V G    K
Sbjct: 135 ADRVVAGQRLFHVGRLDADTEGLLLLTNDGELANRL--MHPKYEVTKTYLATVLGEADKK 192

Query: 195 --KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             ++      L+      DYV +V +N                  Q +  + ++ H GR 
Sbjct: 193 LIRQLREGIELEDGLAQADYVQIVDKN------------------QGYSLVRVELHEGRK 234

Query: 253 HQLRVHALHMGCPI 266
           H +R      G P+
Sbjct: 235 HIVRRMLKEAGYPV 248


>gi|156095610|ref|XP_001613840.1| hypothetical protein [Plasmodium vivax SaI-1]
 gi|148802714|gb|EDL44113.1| hypothetical protein, conserved [Plasmodium vivax]
          Length = 11429

 Score = 80.4 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 23/74 (31%), Positives = 42/74 (56%)

Query: 228  SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            +  K ++ + ++F    ++ HTGRTHQ+RVH  H+G P+V D KY      N       +
Sbjct: 8225 TDPKEVENYTKEFTLCNVKIHTGRTHQIRVHMRHIGHPLVSDKKYLNPSLSNLDKYWCFR 8284

Query: 288  LYLHARYMDLPHPE 301
            ++LH+  ++  +P+
Sbjct: 8285 MFLHSVILEFNNPD 8298



 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/103 (28%), Positives = 45/103 (43%), Gaps = 1/103 (0%)

Query: 133  LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            L++       +  L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K
Sbjct: 7893 LETVKKWHKLECGLCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYLLLCHGRIK 7952

Query: 193  NKKECIANWLLKKSHIG-GDYVHVVKQNEKGANYAISHFKVID 234
             KK CI   +    +       H     + G   A + +  + 
Sbjct: 7953 KKKGCINKSIQTHEYNNFHSKSHFSLVVKTGGTDAYTEYNCVK 7995


>gi|76363649|ref|XP_888536.1| RNA pseudouridylate synthase [Leishmania major strain Friedlin]
 gi|12311860|emb|CAC22676.1| RNA pseudouridylate synthase-like protein [Leishmania major strain
            Friedlin]
          Length = 1469

 Score = 80.4 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 31/114 (27%), Positives = 54/114 (47%), Gaps = 14/114 (12%)

Query: 224  NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-- 280
              AI+ ++V++ FA     +++++  +GR HQ+R H   +G P+VGD +Y A        
Sbjct: 1334 RNAITRYRVLEYFASAGVAYVQVELCSGRRHQIRQHFAQLGFPLVGDARYHAGVVAGHAG 1393

Query: 281  TSPIQNKLYLHARYMDLPHPEGG-----------RLQITAPLPAHMVKTWDSLG 323
            T+    +  LHA  +D+     G           R+ + A LPA M +   +L 
Sbjct: 1394 TTLGMRRAALHAYTVDILATTDGDDLASSEEVPDRVVVQAALPADMHRALLALR 1447



 Score = 38.4 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 146  LTHRLDQETSGILVVARTRAA-AQHLTESFRMRRIQKIYWSLVWGIPK 192
            L +R+D  TSG+++VART  A         R   ++K Y +LV   P 
Sbjct: 1169 LVNRVDVGTSGVVLVARTADALHGAADAMIREHHMRKTYRALVQRWPP 1216


>gi|71420763|ref|XP_811602.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70876281|gb|EAN89751.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 378

 Score = 80.0 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 55/317 (17%), Positives = 94/317 (29%), Gaps = 119/317 (37%)

Query: 101 LLYEDSKIYVFNKPAGISVQG------------------------GSGIAYHIDGFLKSW 136
           ++Y + ++ V NKP  + + G                          G     +   ++ 
Sbjct: 10  VIYGNEELVVVNKPHDVPMDGEACPVTVEKWAWAYLAKGGCADNSAGGGVEKEEDTTRTA 69

Query: 137 VDSKGQK--PRLTHRLDQETSGILVVARTRAAAQ---HLTESFRMRR------------- 178
              +G+K   +  H+LD  TSG+L VA +R  A    H  E    R+             
Sbjct: 70  GRGRGEKKMVKFVHQLDYATSGVLCVAFSREMAARLAHCFEMRTTRKAYLAVLLGMMPTT 129

Query: 179 ------------------------IQKIYWSLVWGIPKNKKECIAN-------------- 200
                                   +++I    V G+   +K  I                
Sbjct: 130 SAMQKKLDTDTGVDFLRGSPYASHVRRISMDDVPGVCFIRKCVIEASGHEEGENADCCAT 189

Query: 201 WLLKKSHIGGDYV----HVVKQNEKGANYAISHFKVIDC---------FAQKFCWLEMQP 247
            L     +G D        +  N + A  ++++  V+            +     + + P
Sbjct: 190 LLEVNLPVGYDTTDHEGFRMTVNGRDARGSVTYLSVLQRGHMTHPTSGCSVPVTKVALFP 249

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN--------------------- 286
            TGR HQLRVH   +G PI+GD  Y         S +                       
Sbjct: 250 RTGRRHQLRVHCHAIGFPILGDVTYARIPTPRVASKVTGAEEVATVGAAESINAPNEIDA 309

Query: 287 -----KLYLHARYMDLP 298
                ++ LHA  +  P
Sbjct: 310 IEAWQRMMLHAWRLSFP 326


>gi|297195213|ref|ZP_06912611.1| pseudouridine synthase [Streptomyces pristinaespiralis ATCC 25486]
 gi|297152696|gb|EFH31937.1| pseudouridine synthase [Streptomyces pristinaespiralis ATCC 25486]
          Length = 368

 Score = 80.0 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 51/278 (18%), Positives = 92/278 (33%), Gaps = 55/278 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D+E  RL +         +    ++++ +G+V V+ K V                 I   
Sbjct: 128 DQEGERLQKVLARAGMG-SRRACEELIDAGRVEVNGKIV-----------------IEQG 169

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +  EQ  +            L           +  NKPAG+             G   
Sbjct: 170 VRVDPEQDEIKVDGLTVATQSHL----------FFALNKPAGVVSTMEDPDGRQCLG--- 216

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +V ++  +     RLD ET GI+++      A  LT       ++K Y + + G    +
Sbjct: 217 DYVTNRETRLFHVGRLDTETEGIILLTNHGELAHRLT--HPKYGVKKTYLAAIQGPLPRE 274

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                  L K+   G        + +        HF+V++   + +  +E+  H GR H 
Sbjct: 275 -------LGKRLKEGIQLEDGYARAD--------HFRVVENTGKNY-LVEVTLHEGRKHI 318

Query: 255 LRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
           +R      G P+  D      +     G+  S    +L
Sbjct: 319 VRRMLSEAGFPV--DKLVRTAFGPIALGDQKSGWLRRL 354


>gi|21324194|dbj|BAB98819.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Corynebacterium glutamicum
           ATCC 13032]
          Length = 252

 Score = 80.0 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 90/253 (35%), Gaps = 45/253 (17%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ND + +RL +         +  + + ++  G+V V+ + V         Q VR+ P    
Sbjct: 7   NDSDGVRLQKVLAQA-GVASRRHAEILIDQGRVEVNDRIVTT-------QGVRVDPN--- 55

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
            N +I+   +                I + ED + +V NKP G+       +     G L
Sbjct: 56  -NDVIRVDGV---------------RIHINEDLEYFVLNKPRGMHSTMSDELGRPCVGDL 99

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            S   + GQ+     RLD +T G+L++      A  L        + K Y + V G   N
Sbjct: 100 VSEKTASGQRLFHVGRLDADTEGLLLLTNDGELANRL--MHPKYEVSKTYLATVRGEATN 157

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           K   ++          G               A + F  I    Q    L ++ H GR H
Sbjct: 158 K--LVSALRDGVELEDG--------------PAKADFAQIIDVFQGKSLLRIEIHEGRKH 201

Query: 254 QLRVHALHMGCPI 266
            +R     +G P+
Sbjct: 202 IVRRLFDELGFPV 214


>gi|261867974|ref|YP_003255896.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413306|gb|ACX82677.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 155

 Score = 80.0 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/128 (28%), Positives = 55/128 (42%), Gaps = 15/128 (11%)

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISH 229
           +++ F   +IQK Y +L    PK K+  I+  + K            K  +   N A++ 
Sbjct: 1   MSQKFAYHQIQKTYLALATHKPKKKQGRISGDMQKA------RRGAWKLTQSKENPAVTD 54

Query: 230 FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
           F V    A       +QP T +THQLRV    +G PI+GD  Y  +          ++ Y
Sbjct: 55  F-VSHSLAPNLRLFILQPKTDKTHQLRVAMKSLGSPILGDALYGGDSA--------DRTY 105

Query: 290 LHARYMDL 297
           LHA  +  
Sbjct: 106 LHAYQLSF 113


>gi|227833146|ref|YP_002834853.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454162|gb|ACP32915.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
          Length = 305

 Score = 79.6 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 87/254 (34%), Gaps = 53/254 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVRIPPVINAL 74
           +  RL +         +  + + ++  G+V V+ + + K   R+     V+R+      +
Sbjct: 63  QGERLQKVLAKA-GVASRRHAEILIDEGRVEVNGQVIIKQGTRVDPNKDVIRVDGTRINV 121

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           N                            E+++ +V NKP G+       +     G + 
Sbjct: 122 N----------------------------EETQYFVLNKPRGMQSTMSDDMGRPCVGDVV 153

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           +     GQ+     RLD +T G+L++      A  L        + K Y + V G    K
Sbjct: 154 ADRVVAGQRLFHVGRLDADTEGLLLLTNDGELANRL--MHPKYEVTKTYLATVLGEADKK 211

Query: 195 --KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             ++      L+      DYV +V +N                  Q +  + ++ H GR 
Sbjct: 212 LIRQLREGIELEDGLAQADYVQIVDKN------------------QGYSLVRVELHEGRK 253

Query: 253 HQLRVHALHMGCPI 266
           H +R      G P+
Sbjct: 254 HIVRRMLKEAGYPV 267


>gi|328867454|gb|EGG15836.1| hypothetical protein DFA_09505 [Dictyostelium fasciculatum]
          Length = 418

 Score = 79.6 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 51/313 (16%), Positives = 99/313 (31%), Gaps = 64/313 (20%)

Query: 25  FKNHYPH-INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
             +H+   I   +L  ++  G V    +       +     +R  P      H + +Q  
Sbjct: 44  LYDHFKQTIPRSHLVDVINIGGVYC--RHATPKPTVLPNGRIRYHPHTLPNPHRVTDQNY 101

Query: 84  LDSSVNLTKHSDFLK-------------------------SILLYEDSKIYVFNKPAGIS 118
                +L K   F +                           +++++    V +KP GI+
Sbjct: 102 SLEPQSLVKLYLFPRHNTTIHLNNNNNNNNNSNNNNNNNGLNIIHDNESFMVVDKPHGIN 161

Query: 119 VQG-GSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
           V      +  ++   ++         P    HR+D  T G+ ++ +         + F+ 
Sbjct: 162 VGPLIDNLKNNLSWMVRQQQQQSIDTPIYNPHRIDFPTRGLCLLVKKSDEIHRFNQLFKD 221

Query: 177 RRIQKIYWS-LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY---------- 225
           R I+K Y   +        KE   +   K+    G Y+H +K ++               
Sbjct: 222 RTIKKRYRVFIYENQNDKDKEIEKDGEEKEKLRVGRYIHYMKPSKSTIKQLSLDKVDGWH 281

Query: 226 -AISHFKVIDCFAQKFCWLE----------------------MQPHTGRTHQLRVHALHM 262
              +    +     K  +++                      ++  TGRTHQ+R     M
Sbjct: 282 DCGTEIDYLKTDFTKNVYMDDRDIGKGDKRRPHRRIQLKTVDVELITGRTHQIRSQMSFM 341

Query: 263 GCPIVGDHKYCAN 275
           G PI+GD  Y   
Sbjct: 342 GYPIIGDKMYGGK 354


>gi|296133130|ref|YP_003640377.1| pseudouridine synthase [Thermincola sp. JR]
 gi|296031708|gb|ADG82476.1| pseudouridine synthase [Thermincola potens JR]
          Length = 244

 Score = 79.6 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 89/251 (35%), Gaps = 52/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++   H    +    ++++ +G+V+V+ K V      + G  V             
Sbjct: 4   QRLQKFMA-HAGVASRRKCEELIAAGKVKVNGKVVT-----EMGYTV------------- 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                 D SV+  + +     I+++E  +  +  KPAG+     S         +   + 
Sbjct: 45  ------DPSVDRVEVAGL--GIIVHEKKEYILLYKPAGVLS---SASDDRGRKTVVDLIK 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE-- 196
           +   +     RLD +T G++++         L       ++ K Y ++V GIP   K   
Sbjct: 94  NAKTRLYPVGRLDYDTEGLILLTNDGRLTNLL--IHPRYKVDKTYRAVVQGIPGEDKLAA 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +L+        V ++KQ                        +E+  H GR  Q+R
Sbjct: 152 LRNGIMLEDGPTYPARVKMLKQINGNG------------------LVEITIHEGRNRQVR 193

Query: 257 VHALHMGCPIV 267
                +G P++
Sbjct: 194 RMFDAIGHPVL 204


>gi|255325636|ref|ZP_05366733.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           tuberculostearicum SK141]
 gi|255297246|gb|EET76566.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           tuberculostearicum SK141]
          Length = 303

 Score = 79.6 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 49/262 (18%), Positives = 92/262 (35%), Gaps = 53/262 (20%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVR 66
           ++V E+  +  RL +         +  + + ++ +G+V V+ K + K   ++     V+R
Sbjct: 53  WLVDEDKPKGERLQKVLAKA-GVASRRHAEILIDAGRVEVNGKIISKQGVKVNPSVDVIR 111

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V   +N                            E+ + +V NKP G+       + 
Sbjct: 112 VDGVRVNVN----------------------------EEHEYFVLNKPRGMQSTMSDDLG 143

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
               G + S   + GQ+     RLD +T G+L++      A  L        + K Y + 
Sbjct: 144 RPCVGDVVSEKVAAGQRLFHVGRLDADTEGLLILTNDGELANRL--MHPKYEVTKTYLAT 201

Query: 187 VWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           V G    K  ++      L+      D+  VV  N                  Q +  + 
Sbjct: 202 VLGEADRKLVRQLKEGIELEDGLAKADFAQVVDTN------------------QGYSLVR 243

Query: 245 MQPHTGRTHQLRVHALHMGCPI 266
           ++ H GR H +R      G P+
Sbjct: 244 LELHEGRKHIVRRMLKEAGFPV 265


>gi|311739374|ref|ZP_07713209.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           pseudogenitalium ATCC 33035]
 gi|311305190|gb|EFQ81258.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           pseudogenitalium ATCC 33035]
          Length = 303

 Score = 79.6 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 49/262 (18%), Positives = 92/262 (35%), Gaps = 53/262 (20%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVR 66
           ++V E+  +  RL +         +  + + ++ +G+V V+ K + K   ++     V+R
Sbjct: 53  WLVDEDKPKGERLQKVLAKA-GVASRRHAEILIDAGRVEVNGKIIAKQGVKVNPSVDVIR 111

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +  V   +N                            E+ + +V NKP G+       + 
Sbjct: 112 VDGVRVNVN----------------------------EEHEYFVLNKPRGMQSTMSDDLG 143

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
               G + S   + GQ+     RLD +T G+L++      A  L        + K Y + 
Sbjct: 144 RPCVGDVVSEKVAAGQRLFHVGRLDADTEGLLILTNDGELANRL--MHPKYEVTKTYLAT 201

Query: 187 VWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           V G    K  ++      L+      D+  VV  N                  Q +  + 
Sbjct: 202 VLGEADRKLVRQLKEGIELEDGLAKADFAQVVDTN------------------QGYSLVR 243

Query: 245 MQPHTGRTHQLRVHALHMGCPI 266
           ++ H GR H +R      G P+
Sbjct: 244 LELHEGRKHIVRRMLKEAGFPV 265


>gi|290986063|ref|XP_002675744.1| predicted protein [Naegleria gruberi]
 gi|284089342|gb|EFC43000.1| predicted protein [Naegleria gruberi]
          Length = 301

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 45/207 (21%), Positives = 77/207 (37%), Gaps = 57/207 (27%)

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK------ 195
           +K R  HRLD  TSG+L ++ TR +   L+ SF  +  +K Y +L+ G    ++      
Sbjct: 56  RKIRFPHRLDMATSGVLCLSMTRESCACLSTSFEDKTSRKFYLALLSGDVNLEELKMNEK 115

Query: 196 --------------ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
                         + I    + +   G +         +G     +  K I+  ++   
Sbjct: 116 LRNNVKVVNENDCSKIIITSFIGRDDGGNNENEEYDPTGRGFVMKQTLEKPIEDLSKYKT 175

Query: 242 WLE------------------------------MQPHTGRTHQLRVHALHMGCPIVGDHK 271
             E                              ++P +GR HQLR+H+L +G  I+GD  
Sbjct: 176 KQERQQHQFREGTSEMIILSYGQVENKPVTKVLLRPLSGRKHQLRLHSLLLGHAIIGDEM 235

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLP 298
           Y  N          ++L LHA  + +P
Sbjct: 236 YGEN-------DGFSRLMLHAYSLQIP 255


>gi|291412474|ref|XP_002722515.1| PREDICTED: RNA pseudouridylate synthase domain containing 3-like
           [Oryctolagus cuniculus]
          Length = 306

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 53/275 (19%), Positives = 94/275 (34%), Gaps = 45/275 (16%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSK 140
           +   +++  +  D L++ ++     +   NKP G+ V G  G          L   +   
Sbjct: 47  LPSETLSREQLVDVLRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLHSVLPELSRSLGLG 106

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKE 196
             + ++     +E SG+++++     A  L E    S R  R    YW++  GIP   + 
Sbjct: 107 ESEFQVVQAPGKEISGLVLLSSCAQTASRLHEFFTHSRRAHRPTATYWAVTDGIPATPEG 166

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            I   L  +   G D V  VK   +          +SHF+V+         +++QP T  
Sbjct: 167 EIQAALKLERVDGVDLVLPVKPPSRRDVLASVKRTLSHFRVVAT-GSGCALVQLQPLT-- 223

Query: 252 THQLRVHALHMGCPIVGD-----------HKYCANFKGNFTSPIQNKLYLHARYMDL--- 297
                          VGD               A  +    +P Q        ++     
Sbjct: 224 ---------------VGDWLLAPFSFCHAVLDGALLRRLQLTPSQAAQLPLHLHLRRLLL 268

Query: 298 --PHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
               P     Q+ AP P +  +T   LG    ++L
Sbjct: 269 PGTRPGDAPTQLLAPPPPYFSRTLQCLGLCQQQSL 303


>gi|218886233|ref|YP_002435554.1| pseudouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|218757187|gb|ACL08086.1| pseudouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
          Length = 463

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 62/360 (17%), Positives = 101/360 (28%), Gaps = 107/360 (29%)

Query: 46  VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK------- 98
           V +D +  +   R+++GQ V + P+      +                 D L+       
Sbjct: 74  VLLDGRPAQPGTRVRTGQRVALRPLDAMRATMQTAALPAGPQAGQNATQDTLRSGAAPTG 133

Query: 99  ---------SILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQK----- 143
                      +L E   +    KP G+     +G A   ++  L + +           
Sbjct: 134 NATGNVADAPHVLAETDGLVALYKPGGLHSAAVAGSAAPSVEALLPTLLGQPDMTALADH 193

Query: 144 ---------------------------------------PRLTHRLDQETSGILVVARTR 164
                                                  PRL +RLD  TSGIL+ AR  
Sbjct: 194 ADPADLPGLTDLADPAALTDLAAPDASRPSPVADDTTGFPRLLNRLDGPTSGILLAARAP 253

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC----------IANWLLKKSHIGGDYVH 214
            AAQ    +    +  K Y +LV G+     +               L + +     +  
Sbjct: 254 QAAQRFHAAENSGQATKTYIALVHGVLAQPMKVRRGLDTANRATTRVLPQDTPDALRHTM 313

Query: 215 VVK------------------------QNEKGANYAISHFK-VIDCFAQKFCWLEMQPHT 249
           V                          Q+   A+   +H              +      
Sbjct: 314 VTPLGIMQTTDIPDAAPCTPTLAGDAGQDSAPASACTTHAPGPACTSGTPCTLVRCVIRK 373

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS-----------PIQNKLYLHARYMDLP 298
           G  HQ+R H   +G PIVGD +Y        T+           P    L+LH   ++LP
Sbjct: 374 GARHQIRAHLAVLGHPIVGDTRYGTPDGAGATTMPQGAPHSARLPAPATLFLHHARIELP 433


>gi|302561440|ref|ZP_07313782.1| RNA pseudouridine synthase [Streptomyces griseoflavus Tu4000]
 gi|302479058|gb|EFL42151.1| RNA pseudouridine synthase [Streptomyces griseoflavus Tu4000]
          Length = 359

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 44/279 (15%), Positives = 95/279 (34%), Gaps = 55/279 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V V+ + V                    
Sbjct: 118 AEQEGERLQKVLARAGYG-SRRACEELIEQARVEVNGEIV-------------------- 156

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
               +++ K +D   +  K      +   Y+    +  NKPAG+             G  
Sbjct: 157 ----LEQGKRVDPEKDEVKVDGLTVATQSYQ---FFSLNKPAGVVSTMEDPEGRQCLG-- 207

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET G++++      A  LT   +    +    ++V  IP++
Sbjct: 208 -DYVTNRETRLFHVGRLDTETEGVILLTNHGELAHRLTHP-KYGVKKTYLAAIVGPIPRD 265

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + + + +  +                       HF+V++   + +  +E+  H GR H
Sbjct: 266 LGKRLKDGIQLEDGYARAD----------------HFRVVEQTGKNY-LVEVTLHEGRKH 308

Query: 254 QLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
            +R      G P+  D      +     G+  S    +L
Sbjct: 309 IVRRMLAEAGFPV--DKLVRTAFGPITLGDQKSGWLRRL 345


>gi|322493583|emb|CBZ28871.1| RNA pseudouridylate synthase-like protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 533

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 32/210 (15%), Positives = 66/210 (31%), Gaps = 68/210 (32%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR------------------- 178
                      RLD+ETSG++V+A+   +A+ L      +                    
Sbjct: 212 QRSPLNLFTVQRLDKETSGVVVLAKNSVSARTLASKLETQTRGCTAAVESRLRECGHAVA 271

Query: 179 ----------------IQKIYWSLVWGIPKNKKECIA----NWLLKKSHIGGDYVH---- 214
                           + K Y +++ G     +  +     + + K      +  H    
Sbjct: 272 LSSDAFDELLRLKAQSVHKTYTAVLRGAAPEDRTFVVANYMDCMAKHPTHSREAQHTQLN 331

Query: 215 ------------------------VVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHT 249
                                     +Q  +    A++  +V+    +     ++++  T
Sbjct: 332 KLKMCCEPMKEMLFSHAAASLPTPPKEQETQWGRLAVTRIRVLARNQKLGLTCVQVELLT 391

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           GR+HQ+R+H   +G P++GD  Y     G 
Sbjct: 392 GRSHQIRLHCAAVGYPVLGDKLYTTTTPGR 421



 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 21/126 (16%), Positives = 46/126 (36%), Gaps = 22/126 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           + DE    L  +    + ++     ++ + +G + V+   +   +  ++ G ++R  P  
Sbjct: 13  DPDES---LLAYLSKKFTYLADTQWRQHIAAGDIHVNGVTLTDGSYVLRQGDMLRFAP-- 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHID 130
                            +L    D     +LYEDS + V  K + + V +GG      + 
Sbjct: 68  ---------------PRSLEPPVDSKHIEVLYEDSTLIVVTKNSNLPVAEGGRYCENTLV 112

Query: 131 GFLKSW 136
             L+  
Sbjct: 113 EVLRRR 118


>gi|145641802|ref|ZP_01797377.1| conserved hypothetical pseudouridine synthase [Haemophilus
           influenzae R3021]
 gi|145273424|gb|EDK13295.1| conserved hypothetical pseudouridine synthase [Haemophilus
           influenzae 22.4-21]
          Length = 123

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 35/124 (28%), Positives = 55/124 (44%), Gaps = 4/124 (3%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           ++  ++Y+ S   + NK  GISV          +   K        K  L HRLD+ TSG
Sbjct: 1   MEIEVVYQHSDFIIINKSEGISVHKDQEEQGLTELVAKQL---NVPKVWLVHRLDKVTSG 57

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           +L++A    +A   +  F   +I K Y +L    PK K+  I   + KK+  G   +   
Sbjct: 58  LLILALNAESAAEFSRLFSEHKIHKTYLALSNQKPKKKQGLIIGDM-KKAREGAWKLCQT 116

Query: 217 KQNE 220
           K+N 
Sbjct: 117 KENP 120


>gi|237750207|ref|ZP_04580687.1| predicted protein [Helicobacter bilis ATCC 43879]
 gi|229374101|gb|EEO24492.1| predicted protein [Helicobacter bilis ATCC 43879]
          Length = 671

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 35/176 (19%), Positives = 71/176 (40%), Gaps = 2/176 (1%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
             +  + QK+L   +++ D + +   + ++ G V  +  + + +N I     +  +   L
Sbjct: 24  GYSKKDTQKLLDKNRIKQDSRIIHKKDFLEKGYVEILSFMPDDINLIPFFACVPPNHAIL 83

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            +    L+  +        VFNKP+ +     +         L S     G+     HRL
Sbjct: 84  QQDIANLEIKISQNPPYFCVFNKPSKLLTHPKN--LADSKSILDSLRYYFGKHANPCHRL 141

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS 206
           D ETSG+LV +  + +   L   F  + ++K Y +++ G  K      +  +  K 
Sbjct: 142 DYETSGLLVCSIDKQSEVMLKNLFLQKGVEKSYMAILHGEVKESLLIESGIIFPKD 197



 Score = 51.5 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/38 (36%), Positives = 23/38 (60%)

Query: 236 FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
             +KF  +++ P +G+THQLR+H   +   I+GD  Y 
Sbjct: 389 QNEKFTLVKLFPLSGKTHQLRIHTSSLQHKILGDTLYG 426


>gi|322504203|emb|CAM41506.2| RNA pseudouridylate synthase-like protein [Leishmania braziliensis
            MHOM/BR/75/M2904]
          Length = 1340

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 30/114 (26%), Positives = 53/114 (46%), Gaps = 14/114 (12%)

Query: 224  NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-- 280
              AI+ ++V++ FA     +++++  +GR HQ+R H   +G P+VGD +Y A        
Sbjct: 1206 RNAITCYRVLEYFASTGVAYVQVELRSGRRHQIRQHFAQLGFPLVGDARYHAGVAAGHSG 1265

Query: 281  TSPIQNKLYLHARYMDLPHPEGG-----------RLQITAPLPAHMVKTWDSLG 323
            T+    +  LHA  +++     G           R+ + A LPA M     +L 
Sbjct: 1266 TTFGMQRAALHAYAVNILATTSGDGQASNEEGPNRVVVQAALPADMHHALLALR 1319



 Score = 40.7 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 146  LTHRLDQETSGILVVARTRAAAQHLTE-SFRMRRIQKIYWSLVWGIPK 192
            L +R+D  TSG+++VAR  AA    T+   R   I+K Y +LV   P 
Sbjct: 1043 LVNRIDVGTSGVVLVARNAAALHGATDTMIREHHIRKTYRALVQRWPP 1090


>gi|328479571|gb|EGF48794.1| ribosomal large subunit 23S pseudouridine synthase D [Lactobacillus
           rhamnosus MTCC 5462]
          Length = 100

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 30/100 (30%), Positives = 46/100 (46%), Gaps = 9/100 (9%)

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              +       +A++H+  I   A     +E+   TGRTHQ+RVH   +G PI+GD  Y 
Sbjct: 6   KRKRMIRADGAFAVTHYHRIAETADTAT-IELNLETGRTHQIRVHLASIGFPIIGDPLYA 64

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLP 312
           A       +    ++ LHA  + L  P     L +T+P P
Sbjct: 65  A-------TETATRMQLHAFRVRLIRPLTIEPLTVTSPSP 97


>gi|154331794|ref|XP_001561714.1| RNA pseudouridylate synthase-like protein [Leishmania braziliensis
            MHOM/BR/75/M2904]
          Length = 1340

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 30/114 (26%), Positives = 53/114 (46%), Gaps = 14/114 (12%)

Query: 224  NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-- 280
              AI+ ++V++ FA     +++++  +GR HQ+R H   +G P+VGD +Y A        
Sbjct: 1206 RNAITCYRVLEYFASTGVAYVQVELRSGRRHQIRQHFAQLGFPLVGDARYHAGVAAGHSG 1265

Query: 281  TSPIQNKLYLHARYMDLPHPEGG-----------RLQITAPLPAHMVKTWDSLG 323
            T+    +  LHA  +++     G           R+ + A LPA M     +L 
Sbjct: 1266 TTFGMQRAALHAYAVNILATTSGDGQASNEEGPNRVVVQAALPADMHHALLALR 1319



 Score = 40.7 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 146  LTHRLDQETSGILVVARTRAAAQHLTE-SFRMRRIQKIYWSLVWGIPK 192
            L +R+D  TSG+++VAR  AA    T+   R   I+K Y +LV   P 
Sbjct: 1043 LVNRIDVGTSGVVLVARNAAALHGATDTMIREHHIRKTYRALVQRWPP 1090


>gi|307106309|gb|EFN54555.1| hypothetical protein CHLNCDRAFT_53041 [Chlorella variabilis]
          Length = 362

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312
           Q+RVH  H G  I+GD  Y A      T P   +  LHA  + + HP  G  L + APLP
Sbjct: 275 QIRVHLAHAGHAILGDDLYGA------TGPWIARHALHAAAVTIRHPRSGELLTVRAPLP 328

Query: 313 AHMVKTWDSLGFK 325
           A  +   + LG +
Sbjct: 329 ADFLAAMEQLGLQ 341


>gi|260435147|ref|ZP_05789117.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           WH 8109]
 gi|260413021|gb|EEX06317.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           WH 8109]
          Length = 120

 Score = 78.9 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 32/101 (31%), Positives = 53/101 (52%), Gaps = 2/101 (1%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           LL  D  +   +KPAG+  Q   G+       + + +  +    RL HRLD++TSG+L++
Sbjct: 3   LLLRDPWLMAVDKPAGLLSQP--GLGQEQGDSVITRLQQQDPSLRLVHRLDRDTSGVLLL 60

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           AR+  A + L+  F  RRI K+Y + V G    +   ++ W
Sbjct: 61  ARSADALRRLSALFTERRINKLYQADVEGELHGRGCIVSPW 101


>gi|88797990|ref|ZP_01113577.1| Pseudouridylate synthase, 23S RNA-specific [Reinekea sp. MED297]
 gi|88779187|gb|EAR10375.1| Pseudouridylate synthase, 23S RNA-specific [Reinekea sp. MED297]
          Length = 270

 Score = 78.9 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 59/305 (19%), Positives = 108/305 (35%), Gaps = 56/305 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNR-----IQSGQ 63
           + VE  +  + +D +  ++  +++   L+ ++  G V RVD +  +   R     I  G+
Sbjct: 7   LEVEAGDPQIAID-FLVDNI-NLSKTRLKDLMNKGGVWRVDLQDRRERLRRAMTDIFVGE 64

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + I      L+                     LK+ LL++  +  V+NKP G+ + G  
Sbjct: 65  RIEIFYDEELLSL------------------KPLKAELLHDAGQYSVWNKPNGMPLSGTD 106

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM---RRIQ 180
              ++             ++       D + +G+ V+A +R AA  LTE F     +   
Sbjct: 107 WGDFNSFERAVELATHGERECYWLTPFDYQAAGVQVLAHSRKAASQLTEQFDPEGLKGAT 166

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-K 239
             Y   V G   ++ EC  +                   E GA    + F  +   A+  
Sbjct: 167 LKYRCDVEGDFNDEGECTTDL------------------EDGAVS--TRFSKVRFDARPN 206

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              LE +  TGR  Q+R     +  P+VGD  Y  N +      ++         +    
Sbjct: 207 RSVLEAELITGRDDQIRRQLSALRYPVVGDEDYGQNAEEQGLLRLK------CVEVRFTC 260

Query: 300 PEGGR 304
           P    
Sbjct: 261 PMTHE 265


>gi|254571685|ref|XP_002492952.1| hypothetical protein [Pichia pastoris GS115]
 gi|238032750|emb|CAY70773.1| Hypothetical protein PAS_chr3_0724 [Pichia pastoris GS115]
          Length = 249

 Score = 78.9 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 82/242 (33%), Gaps = 24/242 (9%)

Query: 103 YEDSKIYVFNKPAGISVQGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +E     V NKP GI  Q  S   G     +  L           R   RLD ET+G LV
Sbjct: 6   FEGPGFLVINKPPGIYTQPPSFRQGNRDKSNELLPLLEKQLQTTLRQVQRLDYETTGGLV 65

Query: 160 VARTRAAAQHLTESFR---------MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           V+  +  A+    + +           R     + L         + + +   +      
Sbjct: 66  VSTNKYTARMFHRNMQALSNNILDGRHRSSNKGYILTKRYIALLNKPVTSIYEQLPKTSD 125

Query: 211 DYVHVVKQN----EKGANYAISHFKVIDCFAQKFCWLEM--QPHTGRTHQLRVHALHM-G 263
            +  +  Q+       +   +S  + I+          +  +  TGR HQ+R     + G
Sbjct: 126 GWRLLETQDIDESNSSSKLLLSKVRTIESCRPMHDKFPLMFELITGRKHQIRRQIKQVFG 185

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLG 323
             IV D KY A  +        N++ LH+ ++ L      + Q   PL  +  + W   G
Sbjct: 186 TTIVNDVKYGAQLE---FPQYHNQIALHSCFLSLKVGL-KKFQFDIPL-EYGKEMWKYAG 240

Query: 324 FK 325
             
Sbjct: 241 LS 242


>gi|20807779|ref|NP_622950.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Thermoanaerobacter tengcongensis MB4]
 gi|254478705|ref|ZP_05092076.1| conserved hypothetical protein, putative [Carboxydibrachium
           pacificum DSM 12653]
 gi|20516335|gb|AAM24554.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Thermoanaerobacter
           tengcongensis MB4]
 gi|214035392|gb|EEB76095.1| conserved hypothetical protein, putative [Carboxydibrachium
           pacificum DSM 12653]
          Length = 236

 Score = 78.9 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 48/251 (19%), Positives = 90/251 (35%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL ++        +    ++ +  G+V+V+ K VK                      I 
Sbjct: 2   VRLQKYLAE-CGIASRRKCEEYILQGRVKVNGKVVK-----------------ELGTKID 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            +  I++    + +  +    I+LY         KPAG I+          +   +K   
Sbjct: 44  PDVDIIEFDDKIVRREEKKVYIMLY---------KPAGYITSVKDPFGRPTVLDLVKV-- 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKE 196
               ++     RLD +TSG+L++      A  L        I K Y + + GIP K + E
Sbjct: 93  ---KERIYPVGRLDFDTSGLLLLTNDGELANIL--MHPKHEIVKTYVAKIKGIPTKEEME 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              N L+                  G   A +  ++++        +E+Q H GR  Q++
Sbjct: 148 RFENGLIID----------------GRKTAKAKIRILNVK-NGTSVVEIQIHEGRNRQVK 190

Query: 257 VHALHMGCPIV 267
                +G P++
Sbjct: 191 KMCKAIGHPVI 201


>gi|320197497|gb|EFW72111.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           WV_060327]
          Length = 79

 Score = 78.5 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 28/84 (33%), Positives = 41/84 (48%), Gaps = 7/84 (8%)

Query: 233 IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHA 292
           ++  A     + ++P TGR+HQLRVH L +G PI+GD  Y +            +L LHA
Sbjct: 2   VEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMA----PRLLLHA 57

Query: 293 RYMDLPHPE-GGRLQITAPLPAHM 315
             + + HP  G  +   A  PA  
Sbjct: 58  EMLTITHPAYGNSMTFKA--PADF 79


>gi|281206797|gb|EFA80981.1| hypothetical protein PPL_05814 [Polysphondylium pallidum PN500]
          Length = 702

 Score = 78.5 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 44/290 (15%), Positives = 93/290 (32%), Gaps = 67/290 (23%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSK 140
           KI     + +     L+ +++YE+ +  V +KP G+S+         +I+  +K+   S+
Sbjct: 389 KIFFYPRHYSTDHIDLQRLVVYENDQFMVIDKPHGVSIGPVIDNYHNNINHLIKTSRPSE 448

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR----RIQKIYWSLVWGIPKNKKE 196
                  HRLD +T G+ V+ +            R R    +  + ++  V  + ++K +
Sbjct: 449 LTTIYNPHRLDFQTRGLCVLVKDSDYISQFNLLLRNRDNISKKYRAFYKQVDNLQEDKDD 508

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL------------- 243
            I   L                + K  ++     +V++                      
Sbjct: 509 IIEPGLYTHYMRPTKSTFKEMSHSKIDSWHECILRVLNGGKCNVDLPISDDEHSYLNIDL 568

Query: 244 ----------------------------------EMQPHTGRTHQLRVHALHMGCPIVGD 269
                                             +++  TGRTHQ+R     +G P++GD
Sbjct: 569 INSDNNTNNNNSYIDTIGKGNSRKRMNNVNLNYVDIELITGRTHQIRAQLTAIGKPLIGD 628

Query: 270 HKYCANFKGNFTSPIQN--------KLYLH-------ARYMDLPHPEGGR 304
             Y         +P+ +        +   H       +  +    P+ G+
Sbjct: 629 KMYGGIPIQQLANPLFSSSDQPYPYRSSKHSSIIGLVSYELSFKCPKTGK 678


>gi|322496292|emb|CBZ31363.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 1468

 Score = 78.5 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 30/114 (26%), Positives = 53/114 (46%), Gaps = 14/114 (12%)

Query: 224  NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-- 280
              AI+ ++V++ FA     +++++  +GR HQ+R H   +G P+VGD +Y A        
Sbjct: 1334 RNAITRYRVLEYFASAGVAYVQVELRSGRRHQIRQHFAQLGFPLVGDARYHAGVVAGHAG 1393

Query: 281  TSPIQNKLYLHARYMDLPHPEG-----------GRLQITAPLPAHMVKTWDSLG 323
            T+    +  LHA  +D+                 R+ + A LPA M +   +L 
Sbjct: 1394 TTFGMQRAALHAYTVDILATTDSDGLASGEEVPDRVVVQAALPADMHRALLALR 1447


>gi|146076176|ref|XP_001462862.1| RNA pseudouridylate synthase-like protein [Leishmania infantum]
 gi|134066943|emb|CAM65048.1| RNA pseudouridylate synthase-like protein [Leishmania infantum JPCM5]
          Length = 1468

 Score = 78.5 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 30/114 (26%), Positives = 53/114 (46%), Gaps = 14/114 (12%)

Query: 224  NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF-- 280
              AI+ ++V++ FA     +++++  +GR HQ+R H   +G P+VGD +Y A        
Sbjct: 1334 RNAITRYRVLEYFASAGVAYVQVELRSGRRHQIRQHFAQLGFPLVGDARYHAGVVAGHAG 1393

Query: 281  TSPIQNKLYLHARYMDLPHPEG-----------GRLQITAPLPAHMVKTWDSLG 323
            T+    +  LHA  +D+                 R+ + A LPA M +   +L 
Sbjct: 1394 TTFGMQRAALHAYTVDILATTDSDGLASGEEVPDRVVVQAALPADMHRALLALR 1447


>gi|146093858|ref|XP_001467040.1| RNA pseudouridylate synthase-like protein [Leishmania infantum
           JPCM5]
 gi|134071404|emb|CAM70091.1| RNA pseudouridylate synthase-like protein [Leishmania infantum
           JPCM5]
          Length = 533

 Score = 78.5 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 73/210 (34%), Gaps = 68/210 (32%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR------------------- 178
                      RLD+ETSG++V+A+   +A+ L      +                    
Sbjct: 212 QRSPLDLFTVQRLDKETSGVVVLAKNSFSARTLASRLEAQTKGCTDAVESRLRERGHAVA 271

Query: 179 ----------------IQKIYWSLVWGI-PKNKKECIANWL-----------------LK 204
                           + K Y +++ G  P++    + N++                 LK
Sbjct: 272 LSSDTFDELVRLKAQSVHKTYTAVLRGAAPEDHTFVVVNYMDCMAKHPTHSWEAQHTQLK 331

Query: 205 KSHIGGDYVHVV--------------KQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHT 249
           K  +  + +  +              +Q  +    A++  +V+    +     ++++  T
Sbjct: 332 KLKMCCEPMKEMLFSHAAASLPKPPKEQQMRWGKLAVTRIRVLASNRKLGLTCVQVELLT 391

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           GR+HQ+R+H   +G P++GD  Y     G 
Sbjct: 392 GRSHQIRLHCAAVGYPVLGDKLYTTTTPGR 421



 Score = 51.9 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/126 (15%), Positives = 45/126 (35%), Gaps = 22/126 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           + DE    L  +    + ++     ++ + +G + V+ + +   +  ++ G ++R  P  
Sbjct: 13  DPDES---LLAYLSTKFTYLAETQWRQHIAAGDISVNGETLTDGSYVLRQGDMLRFAP-- 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHID 130
                            +     D     +LYEDS + V  K   + V +GG      + 
Sbjct: 68  ---------------PRSFEPPVDSKHIEVLYEDSTLMVVTKNGNLPVAEGGRYCENTLV 112

Query: 131 GFLKSW 136
             L+  
Sbjct: 113 EVLRRR 118


>gi|325187007|emb|CCA21551.1| RNA pseudouridylate synthaselike protein putative [Albugo laibachii
           Nc14]
          Length = 639

 Score = 78.5 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 32/136 (23%), Positives = 55/136 (40%), Gaps = 16/136 (11%)

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQN----EKGANYAISHFKVIDC---FAQKFCW 242
           + K +   + N+ + +       + +V       EK    A++   V+       Q    
Sbjct: 322 VGKERMAYVLNFPIHEPSPNSFEMEIVTNTTDGSEKRGKDAVTIAYVLGHGYLDTQPVTK 381

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           + ++P +GR HQLR+H  H+G PI+GD  Y +    N      +++ LHA  +     E 
Sbjct: 382 VLLRPLSGRRHQLRLHLKHIGFPILGDATYGS---ANPLFRPPSRMMLHAWKLWFNTSET 438

Query: 303 ------GRLQITAPLP 312
                 G L    P P
Sbjct: 439 PIAQDYGDLNFETPDP 454



 Score = 50.7 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 6/89 (6%)

Query: 110 VFNKPAGISVQG---GSGIAYHIDGFLKSWVDSKGQ---KPRLTHRLDQETSGILVVART 163
           V  K +G+ V        +  + D  ++  +        K R  H+LD  TSG+L V  T
Sbjct: 69  VIRKTSGLIVLNKGFDQRLDGNFDATIEKALHRDYPDIAKFRWIHQLDFATSGVLCVGTT 128

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           + A       FR R+++K Y ++V G   
Sbjct: 129 KEATSLGCRLFRERKVEKEYLAIVSGHLP 157


>gi|153825782|ref|ZP_01978449.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-2]
 gi|149740505|gb|EDM54620.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-2]
          Length = 87

 Score = 78.5 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 29/87 (33%), Positives = 44/87 (50%), Gaps = 2/87 (2%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +YED  I   NKP+G+    G  +  H D      VD      ++ HRLD  TSG+++ A
Sbjct: 2   IYEDEHIIAANKPSGLLSVPGRPVE-HYDSMWARLVD-YCPDVKVVHRLDMSTSGLILFA 59

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVW 188
           + +     L + F+ R   KIY++ VW
Sbjct: 60  KGKHMESALKKQFQYRLTHKIYYARVW 86


>gi|320093560|ref|ZP_08025451.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 178 str. F0338]
 gi|319979487|gb|EFW10958.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 178 str. F0338]
          Length = 249

 Score = 78.5 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 87/249 (34%), Gaps = 47/249 (18%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RL +         +    ++++  G+V VD + V+       GQ +R+ P    + H+
Sbjct: 10  GVRLQKVLAQA-GVASRRAAEQMIADGRVSVDGQVVR-------GQGMRVDPTAQVI-HV 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ ILD + ++                 +   NKP G+               +   V
Sbjct: 61  DGERLILDETKHV-----------------VLAINKPVGVVSTMSDPEGR---PTVADIV 100

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  LT       I K Y + + G        
Sbjct: 101 AGYPERLYHVGRLDIDTSGLLLLTNDGELANRLT--HPSYEISKTYVARLHGEV------ 152

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                      G     +     +    A+  F+V+D +      +E+  H GR   +R 
Sbjct: 153 ---------RPGVKRRLMAGIELEDGPIAVDGFRVVDTYGDITT-VEIVVHEGRNRLVRR 202

Query: 258 HALHMGCPI 266
               +G P+
Sbjct: 203 MMDAVGFPV 211


>gi|255656021|ref|ZP_05401430.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-23m63]
 gi|296450550|ref|ZP_06892304.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           difficile NAP08]
 gi|296879328|ref|ZP_06903323.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           difficile NAP07]
 gi|296260625|gb|EFH07466.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           difficile NAP08]
 gi|296429871|gb|EFH15723.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           difficile NAP07]
          Length = 238

 Score = 78.1 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 46/251 (18%), Positives = 90/251 (35%), Gaps = 48/251 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++  +     +    ++I+  G+++V+   VK                     ++ 
Sbjct: 1   MRINKYIAS-CGIASRRKAEEIILEGRIKVNGSIVK-----------------ELFFNVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
           +E+ I++      K S+      +Y      V NKP G I+          +   LK   
Sbjct: 43  EEKDIVEFDNKKVKPSENY----IY-----IVLNKPEGYITTVKDQFNRPSVIDILKDV- 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD ETSG+L++         LT       I K Y + V GI    +  
Sbjct: 93  ---KERVYPIGRLDYETSGLLILTNDGDLTYKLT--HPKHEIDKTYVASVKGIISGDE-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++K   G   + +       A   ++     +   + +   E+  H GR  Q+R 
Sbjct: 146 -----IRKFETG---LKIEDYTTAPAKIKVTK----ENKEKNYSVCEITIHEGRNRQVRK 193

Query: 258 HALHMGCPIVG 268
               +  P++ 
Sbjct: 194 MCKAINHPVLN 204


>gi|328868525|gb|EGG16903.1| hypothetical protein DFA_07884 [Dictyostelium fasciculatum]
          Length = 595

 Score = 78.1 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/130 (26%), Positives = 49/130 (37%), Gaps = 25/130 (19%)

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-- 276
           N+ G  YA S F+ +  F       E+  HTGRTHQ+RVH    G PIVGD  Y   F  
Sbjct: 466 NKFGPRYAKSEFE-LKGFGAGKALFEVALHTGRTHQIRVHMSESGFPIVGDPYYNPYFID 524

Query: 277 ---------------------KGNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAH 314
                                         ++LYL + Y++  HP   + + +T   P  
Sbjct: 525 RVIQSNIKNIKDKEKESQQLNNDEDDDSEISRLYLQSYYLEFIHPTSQQPEVVTLDFPDS 584

Query: 315 MVKTWDSLGF 324
                + +  
Sbjct: 585 WKPVIEKIKL 594


>gi|332799305|ref|YP_004460804.1| pseudouridine synthase Rsu [Tepidanaerobacter sp. Re1]
 gi|332697040|gb|AEE91497.1| pseudouridine synthase Rsu [Tepidanaerobacter sp. Re1]
          Length = 237

 Score = 78.1 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 88/251 (35%), Gaps = 52/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSG-QVVRIPPVINALNH 76
           MRL ++        +    + I+  G+V V+ K +K    ++     ++++   + +L +
Sbjct: 3   MRLQKYLSQAGVD-SRRACEDIILQGKVSVNGKTIKKLGTKVNPETDIIKVNGKVCSLKY 61

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                       D    + NKP GI       +       +   
Sbjct: 62  ----------------------------DFIYILINKPKGILTTVKDPLGR---PTVLDL 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +    ++     RLD+ET G+L++         LT      ++ K Y + V G       
Sbjct: 91  LPEFCERVFPVGRLDKETEGLLILTNDGEVTYKLT--HPKYKVIKTYVAHVRG------- 141

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                ++  + I      ++ ++   A    +  KV+    +    ++++ H GR  Q+R
Sbjct: 142 -----IVGNNKIKSLEKGIILEDGVTAPAKANILKVL----RNSTIIKLEIHEGRKRQVR 192

Query: 257 VHALHMGCPIV 267
                +G PI+
Sbjct: 193 RMCDSIGHPII 203


>gi|224014186|ref|XP_002296756.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220968611|gb|EED86957.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 332

 Score = 78.1 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 61/297 (20%), Positives = 97/297 (32%), Gaps = 78/297 (26%)

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
            A H    L  +     +KP L HRLD  TSG ++V     +A  L    R    +K+Y 
Sbjct: 22  TAIHSFTHLPFFRRQLSRKPYLVHRLDHRTSGAVIVGFDSKSAGVLHGRLRGGEARKLYV 81

Query: 185 SLVWGIPKNK----------KECIANWLLKK------------------------SHIGG 210
           +LV G  + +             ++  L ++                        + I  
Sbjct: 82  ALVRGDLRERFRQAAADGCCDGGLSAILPERNDVEEASKMKNVEKAQTYVASEYTTKITV 141

Query: 211 DYVHVVKQNEKG-ANYAISHFKVIDCF--------------------AQKFCWLEMQPHT 249
           D    VK +       A + F  I                        +    +   P T
Sbjct: 142 DLPINVKVDGVDVEKDATTDFYFIASMCLDEDDSGRANDDTAKVPFTNKAVSLILCHPIT 201

Query: 250 GRTHQLRVHA-LHMGCPIVGDHKYCANFKGNFTSP--IQNKLYLHARYMDLPHPE----- 301
           GRTHQ+R HA      P+VGD ++  +    F       ++L LH  Y+DLP  E     
Sbjct: 202 GRTHQIRRHARKAFSSPVVGDREHGDSRVNRFWREKVGLDRLTLHCWYLDLPQAEEDCVE 261

Query: 302 -------------GGRLQITAPLPAHMVKTW--DSLGFKYDRNLYIKRLYSQDECKQ 343
                          R+Q  APLP         + L   ++  L ++   + +   +
Sbjct: 262 DRRGVDAVMEEVSKTRIQCMAPLPPDFATALKHEKLKPLWEEVLRMEPRLAMEPYDE 318


>gi|318061409|ref|ZP_07980130.1| pseudouridine synthase [Streptomyces sp. SA3_actG]
 gi|318078007|ref|ZP_07985339.1| pseudouridine synthase [Streptomyces sp. SA3_actF]
          Length = 416

 Score = 78.1 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 46/280 (16%), Positives = 96/280 (34%), Gaps = 58/280 (20%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72
            ++E  RL +         +    ++++   +V V+ + V +   R++    +++  +  
Sbjct: 176 AEQEGERLQKVLARAGYG-SRRACEELIEQARVEVNGEIVLEQGLRVKPSDEIKVDGLTV 234

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           A                                 + +  NKPAG+             G 
Sbjct: 235 ATQSY-----------------------------QFFSLNKPAGVVATMEDPEGRQNLG- 264

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              +V+++  +     RLD ET G++++      A  LT       ++K Y + + G   
Sbjct: 265 --DYVNNRETRLFHVGRLDTETEGVILLTNHGELAHRLT--HPRYGVRKTYLAHIVG--- 317

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I   L K+   G +      + +        HF+V++   + +  +E+  H GR 
Sbjct: 318 ----PIPRDLGKRLKDGIELEDGWARAD--------HFRVVEQTGKNY-LVEVTLHEGRK 364

Query: 253 HQLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
           H +R      G P+  D      +     G+  S    +L
Sbjct: 365 HIVRRMLAEAGFPV--DKLVRTAFGPITLGDQKSGWLRRL 402


>gi|254579681|ref|XP_002495826.1| ZYRO0C03894p [Zygosaccharomyces rouxii]
 gi|238938717|emb|CAR26893.1| ZYRO0C03894p [Zygosaccharomyces rouxii]
          Length = 250

 Score = 78.1 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/220 (20%), Positives = 77/220 (35%), Gaps = 51/220 (23%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV------------------DSKGQ 142
           +++E +  ++ NKP  +  Q G+   +   G  K+                         
Sbjct: 8   IVHECNNYFLINKPPNVLSQPGNVHRWIYHGLYKNQHVNTPKVLLDELKSQSSTSKRDFD 67

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
             RL HRLD   SG L+VA  + AA++ + + +                           
Sbjct: 68  SWRLVHRLDSCVSGGLLVATNKNAAKYFSRNLKEGGN----------------------- 104

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM-------QPHTGRTHQL 255
            K   I   YV ++    KG    ++ + +ID       +          +  TG+ HQ+
Sbjct: 105 -KGYKIDRRYVAMIDNPGKGDPKYLNEYGIIDKMGMVSKYRRFDEKCILVELSTGQKHQI 163

Query: 256 RVHALHMG-CPIVGDHKYCANFKGNFTSPIQNKLYLHARY 294
           R H  H+   P++ D KY      + T P+Q  L+     
Sbjct: 164 RKHLSHILKQPVLNDVKYGGPLLPH-TDPLQIALHAACVK 202


>gi|226325127|ref|ZP_03800645.1| hypothetical protein COPCOM_02919 [Coprococcus comes ATCC 27758]
 gi|225206475|gb|EEG88829.1| hypothetical protein COPCOM_02919 [Coprococcus comes ATCC 27758]
          Length = 234

 Score = 78.1 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 47/246 (19%), Positives = 90/246 (36%), Gaps = 51/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++            ++K++RSG+V VD + VK                        
Sbjct: 2   MRIDKYLAEMGQG-TRSEIKKLIRSGRVMVDGETVKK----------------------- 37

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E KI +++  ++         + Y   + Y+  KPAG+     +         L    D
Sbjct: 38  PELKIDETTQKVSLEGK----QIGYAKKEYYMLYKPAGVIS---ATKDDRDKTVLDLITD 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K        RLD++T G+L++      A + L+     + + K+Y++ V G        
Sbjct: 91  KKRNDLFPVGRLDKDTEGLLLITNDGELAHRLLS---PKKHVDKVYYAKVQGKVDESD-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K    G D       ++  A  A    +++    +    +E+    GR HQ++ 
Sbjct: 146 -----VKAFADGVDI-----GDDTPAKSA--DLRILKSGEE--SEIELTITEGRFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFHAVG 197


>gi|322501137|emb|CBZ36215.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 533

 Score = 77.7 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 72/210 (34%), Gaps = 68/210 (32%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR------------------- 178
                      RLD+ETSG++V+A+   +A+ L      +                    
Sbjct: 212 QRSPLDLFTVQRLDKETSGVVVLAKNSFSARTLASRLEAQTKGCTDAVESRLRERGHAVA 271

Query: 179 ----------------IQKIYWSLVWGI-PKNKKECIANWL-----------------LK 204
                           + K Y +++ G  P++    + N++                 LK
Sbjct: 272 LSSDTFDELVRLKAQSVHKTYTAVLRGAAPEDHTFVVVNYMDCMAKHPTHSWEAQHTQLK 331

Query: 205 KSHIGGDYVH--------------VVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHT 249
           K  +  + +                 +Q  +    A++  +V+    +     ++++  T
Sbjct: 332 KLKMCCEPMKEILFSHAAASLPKPPKEQQMRWGKLAVTRIRVLASNRKLGLTCVQVELLT 391

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           GR+HQ+R+H   +G P++GD  Y     G 
Sbjct: 392 GRSHQIRLHCAAVGYPVLGDKLYTTVTPGR 421



 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/126 (15%), Positives = 45/126 (35%), Gaps = 22/126 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           + DE    L  +    + ++     ++ + +G + V+ + +   +  ++ G ++R  P  
Sbjct: 13  DPDES---LLAYLSTKFTYLAETQWRQHIAAGDISVNGETLTDGSYVLRQGDMLRFAP-- 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHID 130
                            +     D     +LYEDS + V  K   + V +GG      + 
Sbjct: 68  ---------------PRSFEPPVDSKHIEVLYEDSTLMVVTKNGNLPVAEGGRYCENTLV 112

Query: 131 GFLKSW 136
             L+  
Sbjct: 113 EVLRRR 118


>gi|299821620|ref|ZP_07053508.1| ribosomal large subunit pseudouridine synthase B [Listeria grayi
           DSM 20601]
 gi|299817285|gb|EFI84521.1| ribosomal large subunit pseudouridine synthase B [Listeria grayi
           DSM 20601]
          Length = 243

 Score = 77.7 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 87/250 (34%), Gaps = 52/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +   N     +    ++++ +G+V V+ + V+    ++     + +          
Sbjct: 2   ERLQKVIANS-GVTSRRKAEQLIAAGRVTVNGEVVRELGTKVSPNDRIEV---------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                     + LTK           E+ + ++F KP G+     +         +  + 
Sbjct: 51  --------EGIELTK-----------EEHRYFLFYKPRGVVS---AVTDDKGRKTVADYF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
               ++     RLD ETSG+L++      A  L        ++K Y + V GIP  ++  
Sbjct: 89  VDIPERLYPVGRLDYETSGLLLMTNDGDFANKL--MHPKHEVEKQYIARVKGIPTKEQLR 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +   ++            ++  +K    AI               +E+  H GR  Q+R
Sbjct: 147 RLERGVVIDGRKTAPAKVKLRSADKAKEKAI---------------IEITIHEGRNRQVR 191

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 192 KMFESIGFPV 201


>gi|315641868|ref|ZP_07896860.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           italicus DSM 15952]
 gi|315482436|gb|EFU72976.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           italicus DSM 15952]
          Length = 272

 Score = 77.7 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 95/247 (38%), Gaps = 49/247 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   +++ ++ G+V V+ +  +           +I    + ++   
Sbjct: 24  MRLDKFLATMQLG-SRKEVKQFIKKGKVTVNGEITRS-------DKAQINEYEDQIS--- 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                            F   ++ Y+    Y+ NKPAG+     + +  + +  +   VD
Sbjct: 73  -----------------FEGEVIQYQKDYYYLLNKPAGVIS---ATVDNYDETVMDLLVD 112

Query: 139 SKG-QKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               +      RLD++T G+LV+      A + L+     + ++K Y + V G+   +  
Sbjct: 113 EDFREDLFPVGRLDKDTEGLLVLTNDGQLAHRLLS---PKKHVEKEYHATVAGVMTAEDV 169

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + +  L           ++ Q E+     ++   V +  + +   + +  H G+ HQ++
Sbjct: 170 ALFSEGL-----------MIDQGEQCLPAKLTILSVDE--SAQTSQISLILHEGKFHQVK 216

Query: 257 VHALHMG 263
                +G
Sbjct: 217 RMVAAVG 223


>gi|157872508|ref|XP_001684798.1| RNA pseudouridylate synthase-like protein [Leishmania major]
          Length = 533

 Score = 77.7 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 79/236 (33%), Gaps = 68/236 (28%)

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +   GI   G +  A        +             RLD+ETSG++V+A+   +A+ L 
Sbjct: 186 DGSHGIFAVGSAPCASVPSPKASTVQQRSSLDLFTVQRLDKETSGVVVLAKNSVSARTLA 245

Query: 172 ESFRMRR-----------------------------------IQKIYWSLVWGI-PKNKK 195
                +                                    + K Y +++ G  P++  
Sbjct: 246 SQLEAQTKGCADAVESRLRERGHAVALSSDAFDELLRLKAQSVHKTYTAVLRGAAPEDHT 305

Query: 196 ECIANWL-----------------LKKSHIGGDYVHVV--------------KQNEKGAN 224
             + N +                 LKK  +  + V  +              +Q  +   
Sbjct: 306 FVVVNCMDCMAKHPTHSWEAQHTQLKKLKMCCEPVKEMLFSHAAAALPQSPKEQQTRWGR 365

Query: 225 YAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            A++  +V+    +     ++++  TGR+HQ+R+H   +G P++GD  Y     G 
Sbjct: 366 LAVTRIRVLASNKKLGLTCVQVELLTGRSHQIRLHCAAVGYPVLGDKLYTTMTPGR 421



 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 21/126 (16%), Positives = 46/126 (36%), Gaps = 22/126 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           + DE    L  +    + ++     ++ + +G + V+ + +   +  ++ G ++R  P  
Sbjct: 13  DPDES---LLAYLSTKFTYLADAQWRQHIAAGDISVNGETLTDGSYVLRQGDMLRFAP-- 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHID 130
                            +L    D     +LYEDS + V  K   + V +GG      + 
Sbjct: 68  ---------------PRSLEPPVDSEHIEVLYEDSTLLVVTKNGNLPVAEGGRYCENTLV 112

Query: 131 GFLKSW 136
             L+  
Sbjct: 113 EVLRRR 118


>gi|153810142|ref|ZP_01962810.1| hypothetical protein RUMOBE_00523 [Ruminococcus obeum ATCC 29174]
 gi|149833321|gb|EDM88402.1| hypothetical protein RUMOBE_00523 [Ruminococcus obeum ATCC 29174]
          Length = 257

 Score = 77.7 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 48/253 (18%), Positives = 92/253 (36%), Gaps = 38/253 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +         ++K ++ GQV+V+    K          +++ P  +      
Sbjct: 5   VRLDKFLADAGKG-TRSEVKKFIQKGQVQVNGAPAKKPE-------LKVDPEKD------ 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                   +V L+  +  +    +Y     Y+ NKPAG      S      D  +  +V 
Sbjct: 51  --------TVILSGETVGVAPEFVY-----YLLNKPAGCV----SATEDRNDRTVMEYVP 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK----NK 194
           S  +      RLD++T G+L++      A  L      + + K Y+  V G        K
Sbjct: 94  SDRKGIFPVGRLDKDTEGLLLITDDGMLAHEL--LAPGKHVDKTYFVRVEGKLTVEKIEK 151

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E   +   KK  +      V    E          +  +   + +  L +  H G+ HQ
Sbjct: 152 LENGVDIGEKKLTMPAKVEIVGGSWEGAGEPEPGRVRR-ENLPEVYTELHLTIHEGKFHQ 210

Query: 255 LRVHALHMGCPIV 267
           ++     +G P++
Sbjct: 211 VKRMMEAVGTPVI 223


>gi|294460586|gb|ADE75868.1| unknown [Picea sitchensis]
          Length = 422

 Score = 77.7 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 26/102 (25%), Positives = 43/102 (42%), Gaps = 4/102 (3%)

Query: 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK---GANYAISHFK 231
              ++QK Y + V GI   ++  +   +   +  G     V   +++       A + F 
Sbjct: 145 EAGKVQKEYVAKVKGIFPTEEVEVDANVAYDAREGRSTTQVGNGDKEQPINGKTACTRFT 204

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            +      F  ++  P TGRTHQ+RVH  H+G  I  D  Y 
Sbjct: 205 RLATDG-VFSVVKCLPLTGRTHQIRVHLQHLGHSIANDALYS 245


>gi|6323194|ref|NP_013266.1| Pus5p [Saccharomyces cerevisiae S288c]
 gi|74644954|sp|Q06244|PUS5_YEAST RecName: Full=Pseudouridylate synthase PUS5; AltName:
           Full=Pseudouridine synthase 5; AltName: Full=Uracil
           hydrolyase PUS5
 gi|1234853|gb|AAB67489.1| Ylr165cp [Saccharomyces cerevisiae]
 gi|45269776|gb|AAS56268.1| YLR165C [Saccharomyces cerevisiae]
 gi|285813591|tpg|DAA09487.1| TPA: Pus5p [Saccharomyces cerevisiae S288c]
          Length = 254

 Score = 77.7 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/260 (16%), Positives = 94/260 (36%), Gaps = 47/260 (18%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQG----GSGIAYHIDG---FLKS-----WVDSKGQKPR 145
           +  +++E++  ++ NKP GI  Q       G  +        L+      +   + +  R
Sbjct: 6   QIPIIFENTHYFIVNKPPGIPSQPPDCRTWGRTHPNLDPTPLLERFKAIYYSHREVELCR 65

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
             HRLD   +G +++A+T+  +   +   +            +                +
Sbjct: 66  TVHRLDHCVTGGMLIAKTKDGSVKFSRFLQKGGNNGYKLQRKYVAIVESSGRFNKPNNYE 125

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC- 264
              G  Y  ++    +     I+ FK +D        + +Q  TG+ HQ+R H   +   
Sbjct: 126 IKYGPKYNFLISHGGRE----ITKFKEVDEN-----CIVLQLVTGKKHQIRNHVSQILNQ 176

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHA-------------RYMDLPHPEGGRL------ 305
           PI+ D ++ +    NF     +++ LH+               + + H   G+L      
Sbjct: 177 PILNDKRHGSTV--NFPELFNDQIALHSACIITKIGLQTKTHLIPMEHNNTGQLWSRKYV 234

Query: 306 ----QITAPLPAHMVKTWDS 321
               + T P+   +++ WD 
Sbjct: 235 NEEGEFTLPIKEVLLENWDQ 254


>gi|226306743|ref|YP_002766703.1| pseudouridine synthase [Rhodococcus erythropolis PR4]
 gi|226185860|dbj|BAH33964.1| putative pseudouridine synthase [Rhodococcus erythropolis PR4]
          Length = 267

 Score = 77.7 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 85/251 (33%), Gaps = 45/251 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + +RL +         +    ++++  G+V VD + V     ++ G  V           
Sbjct: 25  DGVRLQKVLAQA-GVASRRAAEELIDQGRVEVDGRIV-----VEQGLRV----------- 67

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                   ++ V +      ++  L+Y        NKP G        +     G + S 
Sbjct: 68  -----DPENAVVRVDGVRVVVQKDLVY-----LAMNKPRGWQCTMSDDLGRPCVGDIVSE 117

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               GQ+     RLD +T G+L+       A  L        + K Y + V G+ +    
Sbjct: 118 RVQSGQRLFHVGRLDADTEGLLLFTNDGDLAHRL--MHPSFEVPKTYLATVHGVVE---- 171

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                       G      V  ++  A   +  F V++   +    +++  H GR H +R
Sbjct: 172 ---------RSTGKQLRDGVTLDDGPAK--VDAFTVLE-INEGKTLVKLVLHEGRKHIVR 219

Query: 257 VHALHMGCPIV 267
                +G P+V
Sbjct: 220 RLLDAVGHPVV 230


>gi|298707166|emb|CBJ29939.1| RNA pseudouridylate synthase domain containing 1 [Ectocarpus
           siliculosus]
          Length = 453

 Score = 77.7 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 31/96 (32%), Positives = 48/96 (50%), Gaps = 10/96 (10%)

Query: 206 SHIGGDYVHVVKQNEKG-ANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALH 261
           S + GD+   + +   G    + +  KV++      +    + M+PHTGR HQLR+HALH
Sbjct: 272 SEVPGDFRMRLDEEAGGKGKPSRTFVKVLEHGSYRGRSVTKVLMRPHTGRRHQLRLHALH 331

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           MG PI+GD  Y              ++ LHA+ + L
Sbjct: 332 MGHPILGDTTYGD------ADHTIPRMCLHAQSLTL 361



 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 30/92 (32%), Positives = 46/92 (50%), Gaps = 3/92 (3%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVART 163
           D    V NKPA   V+        +D  ++ W  + + ++ +  H+LD  TSG+L VA  
Sbjct: 50  DDDFVVINKPAD--VRMDGNFDVAVDKLIRYWCPTLEDKELKWVHQLDFATSGVLCVALH 107

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           R AA    E+FR RR +K Y ++V G    + 
Sbjct: 108 REAAARGCEAFRERRAKKSYLAVVQGAVDPES 139


>gi|149003851|ref|ZP_01828679.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS69]
 gi|147758185|gb|EDK65188.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS69]
          Length = 119

 Score = 77.7 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 27/131 (20%), Positives = 51/131 (38%), Gaps = 15/131 (11%)

Query: 48  VDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
           ++++ V +N  +  G V ++                 D S       +      +Y+D  
Sbjct: 2   INQEEVHWNEIVNPGDVCQLTFDEE------------DYSQKTIPWGNPDLVQEVYQDQH 49

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + + NKP G+   G       +   + ++V   GQ   + HRLD ETSG+++ A+     
Sbjct: 50  LIIVNKPEGMKTHGNQPNEIALLNHVSTYV---GQTCYVVHRLDMETSGLVLFAKNPFIL 106

Query: 168 QHLTESFRMRR 178
             L      +R
Sbjct: 107 PILNRLLEKKR 117


>gi|290995478|ref|XP_002680322.1| predicted protein [Naegleria gruberi]
 gi|284093942|gb|EFC47578.1| predicted protein [Naegleria gruberi]
          Length = 279

 Score = 77.7 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 32/179 (17%), Positives = 69/179 (38%), Gaps = 29/179 (16%)

Query: 35  VNLQKILRSGQVRVDKKRVKFN---NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
              +++     + +++K +  +    +++     ++  +                     
Sbjct: 82  STFRRMCEMNVITLNEKPITKSLLKYKLKDDDCFQVKDMRMDR----------------- 124

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK------PR 145
               F K  ++ E++   V  KP GI V       YH +                    +
Sbjct: 125 PIKHFDKLEIIKEENDFVVVTKPPGICVHPIK--RYHKNSLFYMLEHEYAHHFGNDLHCK 182

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE-CIANWLL 203
             HRLD+ET G+L+V +T   A++  +  + ++++K Y + V GI K K +  I + L+
Sbjct: 183 TIHRLDKETCGVLIVGKTSEGAKYFQKLLKEKQVEKQYIARVDGIVKGKPQFEINDPLV 241


>gi|321399797|emb|CAJ06368.2| RNA pseudouridylate synthase-like protein [Leishmania major strain
           Friedlin]
          Length = 507

 Score = 77.3 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 79/236 (33%), Gaps = 68/236 (28%)

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           +   GI   G +  A        +             RLD+ETSG++V+A+   +A+ L 
Sbjct: 186 DGSHGIFAVGSAPCASVPSPKASTVQQRSSLDLFTVQRLDKETSGVVVLAKNSVSARTLA 245

Query: 172 ESFRMRR-----------------------------------IQKIYWSLVWGI-PKNKK 195
                +                                    + K Y +++ G  P++  
Sbjct: 246 SQLEAQTKGCADAVESRLRERGHAVALSSDAFDELLRLKAQSVHKTYTAVLRGAAPEDHT 305

Query: 196 ECIANWL-----------------LKKSHIGGDYVHVV--------------KQNEKGAN 224
             + N +                 LKK  +  + V  +              +Q  +   
Sbjct: 306 FVVVNCMDCMAKHPTHSWEAQHTQLKKLKMCCEPVKEMLFSHAAAALPQSPKEQQTRWGR 365

Query: 225 YAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
            A++  +V+    +     ++++  TGR+HQ+R+H   +G P++GD  Y     G 
Sbjct: 366 LAVTRIRVLASNKKLGLTCVQVELLTGRSHQIRLHCAAVGYPVLGDKLYTTMTPGR 421



 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 21/126 (16%), Positives = 46/126 (36%), Gaps = 22/126 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           + DE    L  +    + ++     ++ + +G + V+ + +   +  ++ G ++R  P  
Sbjct: 13  DPDES---LLAYLSTKFTYLADAQWRQHIAAGDISVNGETLTDGSYVLRQGDMLRFAP-- 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHID 130
                            +L    D     +LYEDS + V  K   + V +GG      + 
Sbjct: 68  ---------------PRSLEPPVDSEHIEVLYEDSTLLVVTKNGNLPVAEGGRYCENTLV 112

Query: 131 GFLKSW 136
             L+  
Sbjct: 113 EVLRRR 118


>gi|300858398|ref|YP_003783381.1| hypothetical protein cpfrc_00980 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|300685852|gb|ADK28774.1| hypothetical protein cpfrc_00980 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|302206111|gb|ADL10453.1| Putative ribosomal large subunit pseudourinine synthase B
           [Corynebacterium pseudotuberculosis C231]
          Length = 373

 Score = 77.3 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 87/252 (34%), Gaps = 49/252 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +RL +         +  + + ++ +G++ V+ K V     +  G  VR+ P  + +  
Sbjct: 131 EGIRLQKVLAQA-GVASRRHAEILIDAGRIEVNGKIV-----LTQG--VRVNPHADII-- 180

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                ++    +N+             ED + +V NKP G+       +     G +   
Sbjct: 181 -----RVDGVRINVN------------EDMQYFVLNKPRGLQSTMSDDMGRPCVGDIVGE 223

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-- 194
             + GQ+     RLD  T G+L++      A  L        + K Y + V G    +  
Sbjct: 224 RIAAGQRLFHVGRLDAATEGLLLLTNDGELANRL--MHPKYEVTKTYLATVLGEADKRLI 281

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K+      L       D+V +V                     Q    + ++ H GR H 
Sbjct: 282 KQLRDGIELDDGPAKADFVQIVDA------------------HQGKSLIRIELHEGRKHI 323

Query: 255 LRVHALHMGCPI 266
           +R      G P+
Sbjct: 324 VRRMLKTAGFPV 335


>gi|256848777|ref|ZP_05554211.1| 16s pseudouridylate synthase [Lactobacillus crispatus MV-1A-US]
 gi|256714316|gb|EEU29303.1| 16s pseudouridylate synthase [Lactobacillus crispatus MV-1A-US]
          Length = 236

 Score = 77.3 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 82/247 (33%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   + ++++ G V V+ K VK    +I    VV +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHQLIKKGVVAVNGKTVKTLKEKINENDVVTVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   L    
Sbjct: 51  --------------------GEEIAYQKYHYFLLNKPKGVLSATEDRSQKTVISLLD--P 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-RRIQKIYWSLVWGIPKNKKE 196
             + Q      RLD++T+G+L++         L    +   ++ +   + V      K  
Sbjct: 89  QDRYQGIVPVGRLDKDTTGLLLLTNDGQLNHELVAPNKHVAKVYRAEIAGVADEETAKAF 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                L   + +    + ++KQ+ + A   I                E++   G+ HQ++
Sbjct: 149 ASGMMLGDGTKLKPAKLKILKQDRENATSEI----------------EIEISEGKYHQIK 192

Query: 257 VHALHMG 263
                +G
Sbjct: 193 RMFGAVG 199


>gi|227504286|ref|ZP_03934335.1| pseudouridine synthase B [Corynebacterium striatum ATCC 6940]
 gi|227199125|gb|EEI79173.1| pseudouridine synthase B [Corynebacterium striatum ATCC 6940]
          Length = 287

 Score = 77.3 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 50/260 (19%), Positives = 100/260 (38%), Gaps = 55/260 (21%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V ++ +  RL +         +  + + ++ +G+V V+ K V     +Q G  VR+ P +
Sbjct: 40  VGDNPKGERLQKVLAKA-GVASRRHAEIMIDAGRVEVNGKIV-----MQQG--VRVDPNV 91

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
           + +       ++    +N+             E+++ ++ NKP G+       +     G
Sbjct: 92  DVI-------RVDGVRINVN------------EETRYFILNKPRGLQSTMSDELGRPCIG 132

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV---- 187
            L     + GQ+     RLD +T G++++      A  L        ++K Y + V    
Sbjct: 133 DLIGDRVAAGQRLFHVGRLDADTEGLILITNDGELANRL--MHPKYEVRKTYLATVLGEA 190

Query: 188 -WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G+ +  KE +    L+      DYV +V +N                  Q +  + ++
Sbjct: 191 GNGLVRTLKEGVE---LEDGLAKADYVQIVDKN------------------QGYSLVRVE 229

Query: 247 PHTGRTHQLRVHALHMGCPI 266
            H GR H +R      G P+
Sbjct: 230 LHEGRKHIVRRMLKEAGFPV 249


>gi|294628596|ref|ZP_06707156.1| LOW QUALITY PROTEIN: pseudouridine synthase, Rsu [Streptomyces sp.
           e14]
 gi|292831929|gb|EFF90278.1| LOW QUALITY PROTEIN: pseudouridine synthase, Rsu [Streptomyces sp.
           e14]
          Length = 358

 Score = 77.3 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 44/279 (15%), Positives = 94/279 (33%), Gaps = 55/279 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V V+ + V                    
Sbjct: 117 AEQEGERLQKVLARAGYG-SRRACEELIEQARVEVNGEIV-------------------- 155

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
               +++ K +D   +  K      +   Y+    +  NKPAG+             G  
Sbjct: 156 ----LEQGKRVDPEKDEVKVDGLTVATQSYQ---FFSLNKPAGVVSTMEDPEGRQCLG-- 206

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET G++++      A  LT   +    +     +V  IP++
Sbjct: 207 -DYVTNRETRLFHVGRLDTETEGVILLTNHGELAHRLTHP-KYGVRKTYLAHIVGPIPRD 264

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + + + +  +                       HF+V++   + +  +E+  H GR H
Sbjct: 265 LGKRLKDGIQLEDGYARAD----------------HFRVVEQTGKNY-LVEVTLHEGRKH 307

Query: 254 QLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
            +R      G P+  D      +     G+  S    +L
Sbjct: 308 IVRRMLAEAGFPV--DKLVRTAFGPITLGDQKSGWLRRL 344


>gi|221110365|ref|XP_002168193.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 153

 Score = 77.3 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 33/151 (21%), Positives = 65/151 (43%), Gaps = 19/151 (12%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           K + +G+++V+   V  ++++ +  V++     +    I +E + + ++           
Sbjct: 9   KAISTGKIKVNNNIVSHDHKLTAKDVLKTQIHRHEPPVIHEEIEFIQNN----------- 57

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
                   ++ V NKPA I V       ++   F+    D         HR+D+ TSG+L
Sbjct: 58  -------EEVVVINKPASIPVHPCGRFRHNTIVFILG-KDYGLYNLHTIHRIDRLTSGVL 109

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           + A+T   A+ L    R R + K Y + V G
Sbjct: 110 MFAKTSKKARELEGLVRGRLVIKEYLARVIG 140


>gi|307637033|gb|ADN79483.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 908]
          Length = 147

 Score = 77.3 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 33/149 (22%), Positives = 60/149 (40%), Gaps = 10/149 (6%)

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA- 237
           ++K Y  L  G+  +K   I   +L   +I  D + +  Q       +I+  + +     
Sbjct: 1   MKKTYLVLTHGLV-DKSIIIDKPILTPENIQKD-LRIRSQISPLGKPSITLVEPLSYNPF 58

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK------LYLH 291
                L++ P TGRTHQ+R+H   +   IVG+  Y    +         +      L LH
Sbjct: 59  LDISLLKITPLTGRTHQIRLHLSSVNHRIVGEGLYGVADENAREYLQLKRENNAPTLMLH 118

Query: 292 ARYMDLPHPEGGRLQITAPLPAHMVKTWD 320
           A  ++    +G   +I +P+P   +    
Sbjct: 119 AASLEFEF-KGAHYKIASPMPKRFMPFLK 146


>gi|302389711|ref|YP_003825532.1| ribosomal large subunit pseudouridine synthase B
           [Thermosediminibacter oceani DSM 16646]
 gi|302200339|gb|ADL07909.1| ribosomal large subunit pseudouridine synthase B
           [Thermosediminibacter oceani DSM 16646]
          Length = 237

 Score = 77.3 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 90/250 (36%), Gaps = 50/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL ++        +    +K++  G+V+V+ K V+                       +
Sbjct: 3   IRLQKFLA-MAGIASRRACEKLILEGRVQVNGKTVR--------------------ELGV 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
           K    LD  V +  +   L +  +Y      + NKP G ++          +   LK   
Sbjct: 42  KVDPALDE-VRVDGNVCRLNNKPIY-----ILMNKPKGILTTVKDPFGRPTVIDLLKGVR 95

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD++T G+L++      +  LT       I+K Y + V G P      
Sbjct: 96  ----ERVFPVGRLDKDTEGLLILTNDGELSYRLT--HPKHEIEKTYVAKVVGTPDESDFI 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                            +V ++ + A   +   +++    + F  LE+  H GR  Q+R 
Sbjct: 150 ------------RLRRGIVLEDGRTAPAKV---RILKA-GRDFTVLEIIIHEGRKRQVRR 193

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 194 MCKAIGHPVI 203


>gi|111220539|ref|YP_711333.1| hypothetical protein FRAAL1074 [Frankia alni ACN14a]
 gi|111148071|emb|CAJ59739.1| hypothetical protein FRAAL1074 [Frankia alni ACN14a]
          Length = 303

 Score = 77.3 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 26/95 (27%), Positives = 40/95 (42%), Gaps = 11/95 (11%)

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
            +++ F  I     +   L   P TGR HQ+RVH   +G PI GD          F    
Sbjct: 201 PSVTTFVRI-WEGGEHTLLAATPQTGRRHQIRVHLAWIGHPIAGDPL--------FVKAP 251

Query: 285 QNKLYLHARYMDLPHPEGG--RLQITAPLPAHMVK 317
           Q + +LH+  +       G  R+++ AP  A  + 
Sbjct: 252 QTRAFLHSWRLAFDAAWAGGARVEVEAPPDADFLA 286



 Score = 76.2 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 32/109 (29%), Positives = 46/109 (42%), Gaps = 5/109 (4%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +D  +   +YED  +   +KP GISV G        D  L       G++    HR+D+ 
Sbjct: 10  ADIRRLHAIYEDEAVLALDKPVGISVMG-----ERHDTDLVRLAADAGEELFPVHRIDKV 64

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           TSGI++ AR       LT  F+ R + K Y +L           I   L
Sbjct: 65  TSGIVLFARELRYHGDLTRQFQRRTVGKCYLALTRTRGLPAAGTIDLPL 113


>gi|238916961|ref|YP_002930478.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           eligens ATCC 27750]
 gi|238872321|gb|ACR72031.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           eligens ATCC 27750]
          Length = 244

 Score = 77.3 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 92/248 (37%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQS-GQVVRIPPVINALNH 76
           +RLD++  +         +++++R  +V V+   V K  ++I + G  V +         
Sbjct: 3   IRLDKYLADMQVG-TRSEVKELIRKKRVTVNDNIVTKPESKINTDGDSVNVDGNAVG--- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                     Y + + ++ NKPAG+     +         +   
Sbjct: 59  --------------------------YHEYEYFMLNKPAGVVS---ATDDNTCTTVIDLI 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            +   +      RLD++T G+L++    A A  L      + + K Y++ V G       
Sbjct: 90  KNKNRKDLFPVGRLDKDTEGLLIITNDGAMAHDL--LSPKKHVDKTYYAKVKGK------ 141

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQL 255
            I++  +K+   G     +    E  A  AI   KV+   + K +  + +  H G+ HQ+
Sbjct: 142 -ISDMEVKQFADG-----LFVDEELTALPAI--LKVLSYNSDKDYSEIHVTIHEGKFHQV 193

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 194 KRMFTAIG 201


>gi|320011602|gb|ADW06452.1| pseudouridine synthase [Streptomyces flavogriseus ATCC 33331]
          Length = 389

 Score = 77.3 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 45/253 (17%), Positives = 89/253 (35%), Gaps = 49/253 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V V+ + V     ++ G  V        
Sbjct: 148 AEQEGERLQKILARAGMG-SRRACEELIEQARVEVNGEIV-----LEQGMRVD------- 194

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                ++ +I    + +   S              +  NKPAG+    G        G  
Sbjct: 195 ----PQKDEIKVDGLTVATQSYL-----------FFALNKPAGVVSTMGDPDGRQNLG-- 237

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V+++  +     RLD ET GI+++      A  LT       ++K Y + + G    
Sbjct: 238 -DYVNNRETRLFHVGRLDTETEGIILLTNHGELAHRLT--HPKYGVKKTYLAAIQGPLPR 294

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                   L K+   G        + +        HF+V++   + +  +E+  H GR H
Sbjct: 295 D-------LGKRLKDGIQLEDGYARAD--------HFRVVENTGKNY-LVEVTLHEGRKH 338

Query: 254 QLRVHALHMGCPI 266
            +R      G P+
Sbjct: 339 IVRRMLAEAGFPV 351


>gi|333028084|ref|ZP_08456148.1| putative pseudouridine synthase [Streptomyces sp. Tu6071]
 gi|332747936|gb|EGJ78377.1| putative pseudouridine synthase [Streptomyces sp. Tu6071]
          Length = 455

 Score = 77.3 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 46/280 (16%), Positives = 96/280 (34%), Gaps = 58/280 (20%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72
            ++E  RL +         +    ++++   +V V+ + V +   R++    +++  +  
Sbjct: 215 AEQEGERLQKVLARAGYG-SRRACEELIEQARVEVNGEIVLEQGLRVKPSDEIKVDGLTV 273

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           A                                 + +  NKPAG+             G 
Sbjct: 274 ATQSY-----------------------------QFFSLNKPAGVVATMEDPEGRQNLG- 303

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              +V+++  +     RLD ET G++++      A  LT       ++K Y + + G   
Sbjct: 304 --DYVNNRETRLFHVGRLDTETEGVILLTNHGELAHRLT--HPRYGVRKTYLAHIVG--- 356

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I   L K+   G +      + +        HF+V++   + +  +E+  H GR 
Sbjct: 357 ----PIPRDLGKRLKDGIELEDGWARAD--------HFRVVEQTGKNY-LVEVTLHEGRK 403

Query: 253 HQLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
           H +R      G P+  D      +     G+  S    +L
Sbjct: 404 HIVRRMLAEAGFPV--DKLVRTAFGPITLGDQKSGWLRRL 441


>gi|290993466|ref|XP_002679354.1| predicted protein [Naegleria gruberi]
 gi|284092970|gb|EFC46610.1| predicted protein [Naegleria gruberi]
          Length = 579

 Score = 77.3 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 80/210 (38%), Gaps = 36/210 (17%)

Query: 12  VENDE----ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR------IQS 61
           VE D     E +R+D+      P I+    Q +L +G V+ + K++  +N+      I  
Sbjct: 99  VEEDSPILSEKIRVDKLLSQTVP-ISREYAQFLLSNGYVKANNKKLNEDNKFIKFTDILK 157

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           G  + I       +  +   K ++               +LYED  + V NKP G +V  
Sbjct: 158 GLQIEIYLENRPFSANLTPMKHVE-----MYDGPIAPIHVLYEDKDVIVVNKPVGYAVHS 212

Query: 122 --GSGIAYHIDGFLKSWV------------------DSKGQKPRLTHRLDQETSGILVVA 161
                 +  +   ++++V                  ++      L HR++ + SG+L+  
Sbjct: 213 SKSKPESETMIYAIRNYVLSKEKEKEKSKKKSKQTTNTLPLNINLAHRMESQMSGVLICG 272

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           +   + Q L+E F      +  +  V  +P
Sbjct: 273 KNSHSIQKLSEQFLPNTNLQKQYITVCAVP 302



 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 34/91 (37%), Gaps = 7/91 (7%)

Query: 228 SHFKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ- 285
           +   V++           +   +G   Q+R H    G P++GD  Y           +  
Sbjct: 461 TVVNVLELNEDNRIALATVSIPSGSVQQVRSHLATNGIPMLGDFPYFDQVDNRIPIGLSK 520

Query: 286 ----NKLYLHARYMDLPHPEGGR-LQITAPL 311
               NK++ H   +   HP  G+ + + APL
Sbjct: 521 NLNVNKIFFHLYKIVFQHPTSGKNVIVKAPL 551


>gi|302518236|ref|ZP_07270578.1| pseudouridine synthase [Streptomyces sp. SPB78]
 gi|302427131|gb|EFK98946.1| pseudouridine synthase [Streptomyces sp. SPB78]
          Length = 447

 Score = 77.3 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 46/280 (16%), Positives = 96/280 (34%), Gaps = 58/280 (20%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN 72
            ++E  RL +         +    ++++   +V V+ + V +   R++    +++  +  
Sbjct: 207 AEQEGERLQKVLARAGYG-SRRACEELIEQARVEVNGEIVLEQGLRVKPSDEIKVDGLTV 265

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           A                                 + +  NKPAG+             G 
Sbjct: 266 ATQSY-----------------------------QFFSLNKPAGVVATMEDPEGRQNLG- 295

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              +V+++  +     RLD ET G++++      A  LT       ++K Y + + G   
Sbjct: 296 --DYVNNRETRLFHVGRLDTETEGVILLTNHGELAHRLT--HPRYGVRKTYLAHIVG--- 348

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I   L K+   G +      + +        HF+V++   + +  +E+  H GR 
Sbjct: 349 ----PIPRDLGKRLKDGIELEDGWARAD--------HFRVVEQTGKNY-LVEVTLHEGRK 395

Query: 253 HQLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
           H +R      G P+  D      +     G+  S    +L
Sbjct: 396 HIVRRMLAEAGFPV--DKLVRTAFGPITLGDQKSGWLRRL 433


>gi|229494843|ref|ZP_04388596.1| pseudouridine synthase, Rsu [Rhodococcus erythropolis SK121]
 gi|229318201|gb|EEN84069.1| pseudouridine synthase, Rsu [Rhodococcus erythropolis SK121]
          Length = 354

 Score = 77.3 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 85/251 (33%), Gaps = 45/251 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + +RL +         +    ++++  G+V VD + V     ++ G  V           
Sbjct: 112 DGVRLQKVLAQA-GVASRRAAEELIDQGRVEVDGRIV-----VEQGLRV----------- 154

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                   ++ V +      ++  L+Y        NKP G        +     G + S 
Sbjct: 155 -----DPENAVVRVDGVRVVVQKDLVY-----LAMNKPRGWQCTMSDDLGRPCVGDIVSE 204

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               GQ+     RLD +T G+L+       A  L        + K Y + V G+ +    
Sbjct: 205 RVQSGQRLFHVGRLDADTEGLLLFTNDGDLAHRL--MHPSFEVPKTYLATVHGVVE---- 258

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                       G      V  ++  A   +  F V++   +    +++  H GR H +R
Sbjct: 259 ---------RSTGKQLRDGVTLDDGPAK--VDAFTVLE-INEGKTLVKLVLHEGRKHIVR 306

Query: 257 VHALHMGCPIV 267
                +G P+V
Sbjct: 307 RLLDAVGHPVV 317


>gi|194374167|dbj|BAG62396.1| unnamed protein product [Homo sapiens]
          Length = 184

 Score = 76.9 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 38/134 (28%), Positives = 56/134 (41%), Gaps = 19/134 (14%)

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGCPIVG 268
            D   V  +  + A  A++ ++V+         +E+QP TG  HQLRVH    + CPI+G
Sbjct: 34  DDGKMVKVRRSRNAQVAVTQYQVLSS-TLSSALVELQPITGIKHQLRVHLSFGLDCPILG 92

Query: 269 DHKYC------------ANFKGNFTSPIQNK---LYLHARYMDLPHPEGG--RLQITAPL 311
           DHKY                K       + +   L+LHAR + LP    G   L +   L
Sbjct: 93  DHKYSDWNRLAPQKLSVGTLKKLGLEQSKARYIPLHLHARQLILPALGSGKEELNLVCKL 152

Query: 312 PAHMVKTWDSLGFK 325
           P   V +   L  +
Sbjct: 153 PRFFVHSLHRLRLE 166


>gi|169629456|ref|YP_001703105.1| l RNA pseudouridine synthase [Mycobacterium abscessus ATCC 19977]
 gi|169241423|emb|CAM62451.1| Probablel RNA pseudouridine synthase [Mycobacterium abscessus]
          Length = 263

 Score = 76.9 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 46/279 (16%), Positives = 87/279 (31%), Gaps = 52/279 (18%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
            EE +RL +         +    ++++  G+V VD + V                     
Sbjct: 19  SEEGIRLQKVLSQA-GIASRRVAERMIYDGRVEVDGEIVT-------------------- 57

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
               ++ + +D +VN+ +       +++  D      NKP G+             G L 
Sbjct: 58  ----EQGRRIDPAVNVVRVDGA--RVIMNTDLVYLALNKPFGMLSTMSDDRGRPCVGKLI 111

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  Q  R   RLD +T G++++         L        + K Y + V G     
Sbjct: 112 EERVRGNQGVRNVGRLDADTVGLILLTNDGELTHRL--MHPSYEVPKTYIATVAG----- 164

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I   L ++   G +               +  FK +         +++  H GR   
Sbjct: 165 --TIPRGLGRQLRDGVELA--------DGPAKVDEFKFLGT-TDGQSMVQLTLHEGRNRI 213

Query: 255 LRVHALHMGCPIV-------GDHKYCANFKGNFTSPIQN 286
           +R      G P+V       GD        G+  +  ++
Sbjct: 214 VRRMMDAAGHPVVELVRTKIGDVTLGNQRPGSLRALGRD 252


>gi|257461210|ref|ZP_05626308.1| RNA pseudouridine synthase family protein [Campylobacter gracilis
           RM3268]
 gi|257441584|gb|EEV16729.1| RNA pseudouridine synthase family protein [Campylobacter gracilis
           RM3268]
          Length = 470

 Score = 76.9 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 50/93 (53%), Gaps = 4/93 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           ++E      F+KP+GI     G    Y++   + S     GQ   + HRLD ETSGIL+V
Sbjct: 72  IFECDAFAAFDKPSGILSHPSGRNSPYNMYDEIWSLY---GQDACVAHRLDLETSGILIV 128

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           A+ + AA+ L E F  RR+ K Y +LV G  + 
Sbjct: 129 AKDKDAARELKECFEQRRVMKSYLALVQGDLRE 161



 Score = 73.9 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 28/132 (21%), Positives = 53/132 (40%), Gaps = 16/132 (12%)

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTG 250
           K+ +  + +  +  S    D    +K + + +  AI+  + +  F+      +E  P TG
Sbjct: 324 KDFEGFVIDAPIAPSGEFADLKIRMKIS-RDSKEAITLIRPLRYFSDIDASLIECYPLTG 382

Query: 251 RTHQLRVHALHMGCPIVGDHKYCANFKG-------------NFTSPIQNKLYLHARYMDL 297
           R HQ+R+H    G PI+G+  Y  + +                 +    +L LHA  +  
Sbjct: 383 RQHQIRLHLFAAGAPILGEPLYGLSREQAERILDKKMDETERVRTTGAPRLLLHANAICF 442

Query: 298 PHPEGGRLQITA 309
               G R +I +
Sbjct: 443 E-LGGERYEIKS 453


>gi|325119615|emb|CBZ55168.1| putative RNA pseudouridylate synthase family protein [Neospora
            caninum Liverpool]
          Length = 1215

 Score = 76.9 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 24/94 (25%), Positives = 37/94 (39%), Gaps = 16/94 (17%)

Query: 214  HVVKQNEKGANYAISHFKVIDC----------FAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                   +    A+S  +V+                   +++   TGR HQLRVH  H+G
Sbjct: 1024 RRPVSKARSGKRAVSRVQVLYKGYLRNLPEPLVGVPGALVKLSLLTGRRHQLRVHCEHLG 1083

Query: 264  CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
             PIVGD  Y    +  F      +++LHA  +  
Sbjct: 1084 HPIVGDATYGTGDQTPF------RMFLHATSLQF 1111



 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 25/87 (28%), Positives = 41/87 (47%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D +  K RL H+LD  TSG+L+VA  +  A+ +    + R IQK Y +LV+G P+  +  
Sbjct: 808 DKEPCKVRLCHQLDYATSGLLMVAHNQKTARIVQTLLQRREIQKEYLALVYGHPQWSEVE 867

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGAN 224
           +   +   S      +     +   A 
Sbjct: 868 VVTLVAPHSTHAFKMMREHMLDATDAQ 894


>gi|207109585|ref|ZP_03243747.1| hypothetical protein HpylH_10299 [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 144

 Score = 76.9 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 29/143 (20%), Positives = 59/143 (41%), Gaps = 12/143 (8%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---------RLTHRLDQETSGILV 159
            V NKP  + V     +    +  L  W+ SK  +           + HRLD++TSG +V
Sbjct: 1   MVLNKPPNLVVHKAPSV---KEPTLVDWLKSKNYELSNLGLKERYGIVHRLDKDTSGGIV 57

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +A+      HL+E  + + + + Y +L+    K +K  +  +L +  +     + +    
Sbjct: 58  IAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPNNRLKMIALKAAK 117

Query: 220 EKGANYAISHFKVIDCFAQKFCW 242
           ++ + Y+ S F  +         
Sbjct: 118 KEKSRYSKSEFTSLLTSQNNLNL 140


>gi|329939210|ref|ZP_08288584.1| pseudouridine synthase [Streptomyces griseoaurantiacus M045]
 gi|329302095|gb|EGG45988.1| pseudouridine synthase [Streptomyces griseoaurantiacus M045]
          Length = 364

 Score = 76.9 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 45/279 (16%), Positives = 94/279 (33%), Gaps = 55/279 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V V+ + V                    
Sbjct: 123 AEQEGERLQKVLARAGYG-SRRACEELIEDARVEVNGEIV-------------------- 161

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
               +++ K +D   +  K      +   Y+    +  NKPAG+             G  
Sbjct: 162 ----LEQGKRVDPEHDEIKVDGLTVATQSYQ---FFSLNKPAGVVSTMEDPEGRQCLG-- 212

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET G++++      A  LT   R    +     +V  IP++
Sbjct: 213 -DYVTNRETRLFHVGRLDTETEGVILLTNHGELAHRLTHP-RYGVRKTYLAHIVGPIPRD 270

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + + + +  +                       HF+V++   + +  +E+  H GR H
Sbjct: 271 LGKRLKDGIQLEDGYARAD----------------HFRVVEQTGKNY-LVEVTLHEGRKH 313

Query: 254 QLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
            +R      G P+  D      +     G+  S    +L
Sbjct: 314 IVRRMLAEAGFPV--DKLVRTAFGPITLGDQKSGWLRRL 350


>gi|255716616|ref|XP_002554589.1| KLTH0F08866p [Lachancea thermotolerans]
 gi|238935972|emb|CAR24152.1| KLTH0F08866p [Lachancea thermotolerans]
          Length = 234

 Score = 76.9 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 41/194 (21%), Positives = 73/194 (37%), Gaps = 41/194 (21%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHID--------GFLKSWVDSKGQKPRLT 147
           L   L+YE     + NKP G+  Q     + Y+            LKS   ++  + R  
Sbjct: 5   LSINLVYEAKNYVIANKPPGVFCQPPDRNVWYNAQYKEPPILLELLKSQASTRAAEWRPV 64

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMR-----RIQKIYWSLVWGIPKNKKECIANWL 202
           HRLD   +G ++VA+ + AA   +   +       ++ + Y +LV G      +      
Sbjct: 65  HRLDTNVTGGVLVAKNKNAAAMFSRHLKKGGNHGYKLTRRYVALVEGNTAELPDT----- 119

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH- 261
                       V+ +N + + +  +   V+           +Q  TG+ HQ+R      
Sbjct: 120 -----------GVISENGRLSKFKKAGLHVL----------VLQLCTGKKHQIRQQLSQC 158

Query: 262 MGCPIVGDHKYCAN 275
           +  PI+ D KY   
Sbjct: 159 LKLPILNDLKYGGR 172


>gi|302533645|ref|ZP_07285987.1| pseudouridine synthase [Streptomyces sp. C]
 gi|302442540|gb|EFL14356.1| pseudouridine synthase [Streptomyces sp. C]
          Length = 239

 Score = 76.9 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 47/277 (16%), Positives = 90/277 (32%), Gaps = 58/277 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALN 75
           E  RL +         +    ++++   +V V+ + V     R+Q    +++  +  A  
Sbjct: 2   EGERLQKVLARAGMG-SRRACEELIEQARVEVNGEIVTEQGKRVQPKDEIKVDGLTVATQ 60

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
             +                              +  NKPAG+             G    
Sbjct: 61  SFL-----------------------------FFALNKPAGVVSTMEDPDGRQCLG---D 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +V ++  +     RLD ET GI+++      A  LT       +QK Y + + G      
Sbjct: 89  YVTNRETRLFHVGRLDTETEGIILLTNHGELAHRLT--HPKYGVQKTYVAAITGSLPRD- 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 + K+   G +      + +         F+V+D   + +  +E+  H GR H +
Sbjct: 146 ------IGKRLKEGIELEDGYARADN--------FRVVDQVGKNY-LVEVTLHEGRKHIV 190

Query: 256 RVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
           R      G P+  D      +     G+  S    +L
Sbjct: 191 RRMLAEAGFPV--DKLVRTSFGPIELGDQKSGWLRRL 225


>gi|310828101|ref|YP_003960458.1| pseudouridine synthase [Eubacterium limosum KIST612]
 gi|308739835|gb|ADO37495.1| pseudouridine synthase [Eubacterium limosum KIST612]
          Length = 241

 Score = 76.9 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 91/250 (36%), Gaps = 47/250 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL ++        +    ++++ +G+V V+ + V     +  G  V             
Sbjct: 1   MRLQKYMA-QCGVASRRKSEEMIAAGRVCVNGEAV-----LTPGLQV------------- 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYV-FNKPAGISVQGGSGIAYHIDGFLKSWV 137
                     +    +  +    + ED KIYV  NKP G+          H D  +   +
Sbjct: 42  ----------DPEADTVTVDGKTIAEDKKIYVLLNKPKGVVSTSA---DRHADQTVMDRL 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             K ++     RLD++T G+L++         LT         KIY  LV GIP   +  
Sbjct: 89  PIK-ERLFTVGRLDKDTEGLLILTNDGDLTFRLT--HPSHEFNKIYEGLVKGIPSAGELR 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +            + V +   +      A +  +V+  + +    LEM  H GR  Q+R 
Sbjct: 146 LFA----------EGVQIEDDDHTLHTTAPASVQVLKTY-RSTALLEMTIHEGRKRQIRK 194

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 195 MCAAIGHPVI 204


>gi|224050701|ref|XP_002196850.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 2 [Taeniopygia guttata]
          Length = 479

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 43/217 (19%), Positives = 84/217 (38%), Gaps = 37/217 (17%)

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSI-LLYEDSKIYVFNKPAGISVQGGSGIAYH 128
            +  L+ ++K    L ++V+  +     + I +L ED ++ V +KP+ + V       ++
Sbjct: 152 PVRDLDIVLKNNDFLRNTVHRHEPPVTAQPIRILAEDEEVVVVDKPSSLPVHPCGRFRHN 211

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              F+    +   ++    HRLD+ TSG+L+ A+T A ++ + E  R R+      +   
Sbjct: 212 TVIFILG-KEHGLRELHTLHRLDRMTSGVLMFAKTAAVSKRIDEQVRQRQCGAKPPA--- 267

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
              +++    A  +L+  H  G       ++  G++ A+                     
Sbjct: 268 ---RDRALRGAGPVLRHPHHRGCERAGCARHRNGSSGAV--------------------- 303

Query: 249 TGRTHQLRVHALHMGCPIVGDH----KYCANFKGNFT 281
            G  H +R    H G P   D      Y AN      
Sbjct: 304 RGARHVVR----HKGAPCCPDPGAAVLYGANVSSRAR 336


>gi|302330665|gb|ADL20859.1| Putative pseudourin ine synthase B [Corynebacterium
           pseudotuberculosis 1002]
 gi|308276349|gb|ADO26248.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Corynebacterium pseudotuberculosis I19]
          Length = 286

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 87/252 (34%), Gaps = 49/252 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +RL +         +  + + ++ +G++ V+ K V     +  G  VR+ P  + +  
Sbjct: 44  EGIRLQKVLAQA-GVASRRHAEILIDAGRIEVNGKIV-----LTQG--VRVNPHADII-- 93

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                ++    +N+             ED + +V NKP G+       +     G +   
Sbjct: 94  -----RVDGVRINVN------------EDMQYFVLNKPRGLQSTMSDDMGRPCVGDIVGE 136

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-- 194
             + GQ+     RLD  T G+L++      A  L        + K Y + V G    +  
Sbjct: 137 RIAAGQRLFHVGRLDAATEGLLLLTNDGELANRL--MHPKYEVTKTYLATVLGEADKRLI 194

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K+      L       D+V +V                     Q    + ++ H GR H 
Sbjct: 195 KQLRDGIELDDGPAKADFVQIVDA------------------HQGKSLIRIELHEGRKHI 236

Query: 255 LRVHALHMGCPI 266
           +R      G P+
Sbjct: 237 VRRMLKTAGFPV 248


>gi|126699667|ref|YP_001088564.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile 630]
 gi|255101182|ref|ZP_05330159.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-63q42]
 gi|255307056|ref|ZP_05351227.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile ATCC 43255]
 gi|115251104|emb|CAJ68935.1| Ribosomal large subunit pseudouridine synthase B [Clostridium
           difficile]
          Length = 238

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 92/251 (36%), Gaps = 48/251 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++  +     +    ++I+  G+++V+   VK                     +I 
Sbjct: 1   MRINKYIAS-CGIASRRKAEEIILGGRIKVNGSVVK-----------------ELSFNID 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
           +E+ I++      K S+      +Y      V NKP G I+          +   LK   
Sbjct: 43  EEKDIVEFDNKKVKPSENY----IY-----IVLNKPEGYITTVKDQFNRPSVIDILKDVR 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD ETSG+L++         LT       I K Y + V GI       
Sbjct: 94  ----ERVYPIGRLDYETSGLLILTNDGDLTYKLT--HPKHEIDKTYVASVKGI------- 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I++  +++   G   + +       A   ++     +   + +   E+  H GR  Q+R 
Sbjct: 141 ISDDEIRQFETG---LKIEDYTTAPAKIRVTK----ENKEKNYSVCEITIHEGRNRQVRK 193

Query: 258 HALHMGCPIVG 268
               +  P++ 
Sbjct: 194 MCKAINHPVLN 204


>gi|328792457|ref|XP_003251726.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           4-like, partial [Apis mellifera]
          Length = 312

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 57/309 (18%), Positives = 112/309 (36%), Gaps = 60/309 (19%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-----------GIAYHIDGFLKSWV 137
           +L + S  L + L+Y +  + + NKP GI  +  +           G+ Y ++  L    
Sbjct: 12  SLLEFSSDLVNNLIYNEDGLIILNKPYGIRSRKSNSFQSLKNNVSNGVNYTLEDALPYIA 71

Query: 138 DS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR-IQKIYWSLVWGIPKNKK 195
                    +    +   SGI ++A        +  ++   +     YW +  GIPK   
Sbjct: 72  KELNYPNLNIIKSPEMYMSGITLLAANSNIQNAIELAYIHGQYFINTYWIVTVGIPKQSN 131

Query: 196 -------ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQP 247
                  + +++   K            K  EK      + +K++       C  +++  
Sbjct: 132 NYSRLGIKLVSHPQFKNKKQIL-ITSWSKNEEKKIKILKTEYKILSNSILNLCSLIQLVS 190

Query: 248 HTGRTHQLRVHAL-HMGCPIVGDHKYCANFKGNFTS-------------PIQNKL----- 288
            T   H +R+ A   + CPI+GD+ Y +  +    +              + +KL     
Sbjct: 191 STHHKHAIRLFASTFLYCPILGDNIYASQIQKIGNTYVRVHPFFTCSAPKLDDKLFKLLG 250

Query: 289 -----------YLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYS 337
                      ++H R + L +  G  L+I APLP +   T + L FK+        +  
Sbjct: 251 VKPNNENIIPTHIHLRSIVLRNFLGKTLKIEAPLPPYFDWTCNQLEFKH--------IIE 302

Query: 338 QDECKQNIL 346
            + CK +++
Sbjct: 303 TENCKSHLV 311


>gi|239932155|ref|ZP_04689108.1| pseudouridine synthase [Streptomyces ghanaensis ATCC 14672]
 gi|291440523|ref|ZP_06579913.1| pseudouridine synthase [Streptomyces ghanaensis ATCC 14672]
 gi|291343418|gb|EFE70374.1| pseudouridine synthase [Streptomyces ghanaensis ATCC 14672]
          Length = 347

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 44/279 (15%), Positives = 94/279 (33%), Gaps = 55/279 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V V+ + V                    
Sbjct: 106 AEQEGERLQKVLARAGYG-SRRACEELIEQARVEVNGEIV-------------------- 144

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
               +++ + +D   +  K      +   Y+    +  NKPAG+             G  
Sbjct: 145 ----LEQGRRVDPEKDEVKVDGLTVATQSYQ---FFSLNKPAGVVSTMEDPEGRQCLG-- 195

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET G++++      A  LT   R    +     +V  IP++
Sbjct: 196 -DYVTNRETRLFHVGRLDTETEGVILLTNHGELAHRLTHP-RYGVKKTYLAHIVGPIPRD 253

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + + + +  +                       HF+V++   + +  +E+  H GR H
Sbjct: 254 LGKRLKDGIQLEDGYARAD----------------HFRVVEQTGKNY-LVEVTLHEGRKH 296

Query: 254 QLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
            +R      G P+  D      +     G+  S    +L
Sbjct: 297 IVRRMLAEAGFPV--DKLVRTAFGPITLGDQKSGWLRRL 333


>gi|295692648|ref|YP_003601258.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|295030754|emb|CBL50233.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
          Length = 236

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 38/247 (15%), Positives = 85/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   + ++++ G V V+ K VK    +I    VV +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHQLIKKGVVAVNGKTVKTLKEKINENDVVTVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   L   +
Sbjct: 51  --------------------GEEIAYQKYHYFLVNKPKGVLSATEDRNQKTVISLLD--L 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAA-AQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             + Q      RLD++T+G+L++        + L  +  + ++ +   + V      K  
Sbjct: 89  QDQYQGIVPVGRLDKDTTGLLLLTNDGQLNHELLAPNKHVAKVYRAQIAGVADEETAKAF 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                L   + +    + ++KQ+ + A   I                E++   G+ +Q++
Sbjct: 149 ASGMMLGDGTKLKPAKLKILKQDRENATSEI----------------EIEISEGKYYQIK 192

Query: 257 VHALHMG 263
                +G
Sbjct: 193 RMFGAVG 199


>gi|226486580|emb|CAX74367.1| pseudouridylate synthase [Schistosoma japonicum]
          Length = 253

 Score = 76.6 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 28/161 (17%), Positives = 62/161 (38%), Gaps = 21/161 (13%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
             ++ + H++   + +   SG + V+  RV  +  +    ++       +      E  +
Sbjct: 98  VLQSEFSHMSNDVIAQKCNSGDILVNGARVDPDYVLNDNDLL-------SQQVHRHEFPV 150

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
           L+  +             +++   + V NKP  I +       Y ++            +
Sbjct: 151 LNLPIEF-----------IHDSHDMLVINKPPSIPIHPCG--RYTLNSITHILAKDYSLR 197

Query: 144 P-RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
           P R THRLD+ TSG+L++A+    +  L      + + K+ 
Sbjct: 198 PLRFTHRLDRMTSGLLLIAKDYDTSVRLQSQIASKEVTKVT 238


>gi|114672841|ref|XP_001135109.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           3-like [Pan troglodytes]
          Length = 260

 Score = 76.2 bits (186), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 37/182 (20%), Positives = 75/182 (41%), Gaps = 12/182 (6%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSK 140
           +L  +++  +  D L++ ++     +   NKP G+ V G  G          L   +  +
Sbjct: 57  LLPKNLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLR 116

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKE 196
            Q+ ++     +E+SG+++++     A  L +    + R +R   IY ++  GIP   + 
Sbjct: 117 EQELQVVRASGKESSGLVLLSSCPQTASRLQKYFIHARRAQRPTAIYCAVTDGIPAASEG 176

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            I   L  +     +    VK   +     G    +SHF+V+         +++QP TG 
Sbjct: 177 KIQAALKLEHIDAVNLTVPVKAPSRKDILEGVKKTLSHFRVVAT-GSGCALVQLQPLTGF 235

Query: 252 TH 253
             
Sbjct: 236 RS 237


>gi|328881450|emb|CCA54689.1| Ribosomal large subunit pseudouridine synthase B [Streptomyces
           venezuelae ATCC 10712]
          Length = 453

 Score = 76.2 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 36/253 (14%), Positives = 82/253 (32%), Gaps = 49/253 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V V+ + V                 +  
Sbjct: 212 AEQEGERLQKVLARAGMG-SRRACEELIEQARVEVNGEIV-----------------LEQ 253

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              +  E+  +           +L           +  NKP+G+             G  
Sbjct: 254 GKRVDPEKDEIKVDGLTVATQSYL----------FFALNKPSGVVSTMEDPDGRQCLG-- 301

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET GI+++      A  LT   +    +    ++   +P+ 
Sbjct: 302 -DYVTNRETRLFHVGRLDTETEGIILLTNHGELAHRLTHP-KYGVKKTYLAAITGPLPRE 359

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + + + +  +                       HF+V++   + +  +E+  H GR H
Sbjct: 360 VGKRLKDGIQLEDGYARAD----------------HFRVVEQTGKNY-LVEVTLHEGRKH 402

Query: 254 QLRVHALHMGCPI 266
            +R      G P+
Sbjct: 403 IVRRMLAEAGFPV 415


>gi|304403869|ref|ZP_07385531.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
 gi|304346847|gb|EFM12679.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
          Length = 260

 Score = 76.2 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 81/245 (33%), Gaps = 41/245 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   +     ++K ++ G+V VD + VK +     G  ++            
Sbjct: 15  MRLDKLLAN-MGYGTRSEIKKAVKQGKVTVDGRVVKDS-----GLQIK------------ 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                        +   F   +++Y D    + +KP G+           +   L +  D
Sbjct: 57  ----------PNEQQVAFSGELVVYRDVVYLMLHKPPGVVSATEDSRDETVIDLLDA--D 104

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD++T G+L++      A  L      + + K Y++ V G     +   
Sbjct: 105 DRILQPFPVGRLDKDTEGLLLLTNDGQLAHDL--LSPRKHVPKTYFARVLGEEPVGQADR 162

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +        G      +   + A                   + +    G+ HQ++  
Sbjct: 163 ERFAAGVELDDGYVTMPAELEVEQAE---------QSDDGWVSLIRITIQEGKFHQIKRM 213

Query: 259 ALHMG 263
              +G
Sbjct: 214 FQAVG 218


>gi|299469703|emb|CBN76557.1| Pseudouridine synthase [Ectocarpus siliculosus]
          Length = 615

 Score = 76.2 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 27/169 (15%), Positives = 63/169 (37%), Gaps = 20/169 (11%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           +D +    +      + +  +R G + V+  +V  +  +Q+  ++              E
Sbjct: 114 VDVF-SAEFGGEARSHYENAVRGGLLTVNGNKVGVDYELQNSDLICNKTHR-------HE 165

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             +    +            ++ E ++  V +KP  + +       ++   ++       
Sbjct: 166 PPVCGGDIP-----------IVSESAEELVVDKPCTVPIHPCGSYRFNTLFYIMHR-QRP 213

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
               R+ HRLD+ TSG+ + A+T   A  + +     R +K Y + V G
Sbjct: 214 DLTLRVCHRLDRLTSGLTIFAKTAERAGVIQKQIGSGRTRKTYLARVSG 262



 Score = 67.7 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 21/82 (25%), Positives = 31/82 (37%), Gaps = 3/82 (3%)

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           D  H V +       A +  + +    A     +E  P  GRTHQ+R+H    G PI  D
Sbjct: 409 DPKHGVYECHPSGKEAQTVVRKVGYDTASDTSVVECTPVHGRTHQIRLHLQWAGHPIAND 468

Query: 270 HKYCANFKGNFTSPIQNKLYLH 291
             Y      +F +P   +    
Sbjct: 469 PCYGGEL--HFGNPEAKRRAEE 488


>gi|160893004|ref|ZP_02073792.1| hypothetical protein CLOL250_00542 [Clostridium sp. L2-50]
 gi|156865087|gb|EDO58518.1| hypothetical protein CLOL250_00542 [Clostridium sp. L2-50]
          Length = 239

 Score = 76.2 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 89/246 (36%), Gaps = 47/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N     +   +++ ++ G + V+    K                        
Sbjct: 1   MRIDKFLANQDIG-SRSQVKQYIKKGMISVNGIVCKS----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQKI +++  ++ +      ++ Y+    Y+ NKP+G        +   +   LK+ V 
Sbjct: 37  PEQKIDENADQISYNGK----VIGYQKHHYYMLNKPSGCVSATNDNLHITVLDLLKASVP 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K        RLD +T G+L++      +   L+     + + K Y++ + G+   +   
Sbjct: 93  VKN--LFPVGRLDIDTEGLLLITDDGELSHNLLS---PSKHVAKTYFARIDGLATEEH-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K    G D       ++K         K  D   Q    + +    GR HQ++ 
Sbjct: 146 -----IKAFKEGLDI-----GDDKPTKPGTLVIKNTDLNTQ-TSEILLTITEGRYHQVKR 194

Query: 258 HALHMG 263
               +G
Sbjct: 195 SFEALG 200


>gi|183237397|ref|XP_001914609.1| hypothetical protein [Entamoeba histolytica HM-1:IMSS]
 gi|169799122|gb|EDS88615.1| hypothetical protein, conserved [Entamoeba histolytica HM-1:IMSS]
          Length = 220

 Score = 76.2 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 40/140 (28%), Positives = 58/140 (41%), Gaps = 14/140 (10%)

Query: 152 QETSGILVVARTRAAAQHLTESFRMRR--------IQKIYWSLVWGIPKNKKECIANWLL 203
           + TSGIL+ A+T+  A       + +         +QKIY + V G   +  E   N  L
Sbjct: 3   KNTSGILLFAKTKTFASSFQSILKEKSSVISSTSSLQKIYLARVVGYFPDTIEV--NLPL 60

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHM 262
                G +    + ++      A S FK +          +E  PHTGRTHQLR+H   +
Sbjct: 61  HLVRFGTESQSCICED---GIEARSSFKRLFFDKDSNTSVIECVPHTGRTHQLRLHLKAI 117

Query: 263 GCPIVGDHKYCANFKGNFTS 282
             PI  D  Y  N   N+  
Sbjct: 118 HHPIANDSAYLLNQIHNYRQ 137


>gi|257866937|ref|ZP_05646590.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257873270|ref|ZP_05652923.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257800993|gb|EEV29923.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257807434|gb|EEV36256.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
          Length = 257

 Score = 76.2 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 46/266 (17%), Positives = 103/266 (38%), Gaps = 52/266 (19%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSL+      V+   ++ MRLD++  +   + +   ++++++ G V V+ + +K +++ Q
Sbjct: 1   MSLLCETLAAVLYERKKPMRLDKFLAD-MGYGSRKEVKQLIKKGLVTVNGQVIK-SDKAQ 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
                    V    + +  E +                  + Y+    Y+ NKPAG+   
Sbjct: 59  ---------VQETQDTVCFEGEP-----------------IAYQSQFYYLLNKPAGVI-- 90

Query: 121 GGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMR 177
             S      +  +      +   +      RLD++T G L++      A Q L+     +
Sbjct: 91  --SATVDSYEETVLDLFSEEAFREDLFPVGRLDKDTEGFLLITNDGGLAHQLLS---PKK 145

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y++ V GI   + + I             +   +K + +    A      +D   
Sbjct: 146 HVEKEYYAQVEGIMTAEDQKI-------------FAKGIKLDGEWTLPAELQILNVD-EE 191

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMG 263
           +    +++  H G+ HQ++     +G
Sbjct: 192 EMRSEIKLILHEGKFHQVKRMVHAVG 217


>gi|242005446|ref|XP_002423576.1| Ribosomal large subunit pseudouridine synthase C, putative
           [Pediculus humanus corporis]
 gi|212506724|gb|EEB10838.1| Ribosomal large subunit pseudouridine synthase C, putative
           [Pediculus humanus corporis]
          Length = 291

 Score = 76.2 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 34/118 (28%), Positives = 50/118 (42%), Gaps = 6/118 (5%)

Query: 170 LTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
           +    R R +QK Y   V G  P  + EC     +    IG     V K + KG + + +
Sbjct: 1   MEHQIRNRLVQKEYVCRVEGEFPSGQIECSEPIEVVSYKIG-----VCKVSSKGKSCSTT 55

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
             K+    +     +  +PHTGR HQ+RVH  ++G P+V D  Y     G       N
Sbjct: 56  FEKLGYSSSTNTSIVLCKPHTGRMHQIRVHLQYLGYPVVNDPLYNHTVFGPEKGKGGN 113


>gi|296269471|ref|YP_003652103.1| pseudouridine synthase [Thermobispora bispora DSM 43833]
 gi|296092258|gb|ADG88210.1| pseudouridine synthase [Thermobispora bispora DSM 43833]
          Length = 426

 Score = 75.8 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 47/250 (18%), Positives = 80/250 (32%), Gaps = 48/250 (19%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RL +         +    ++++  G+V VD + V+                      +
Sbjct: 188 GERLQKVLARA-GVASRRACEELIGQGRVTVDGQVVR-----------------RYGARV 229

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E++I+         S  L           Y FNKPAG+               L  +V
Sbjct: 230 DPERQIIRVDGKRIPTSTGLA---------YYAFNKPAGVVSTMDDPEGRPC---LADYV 277

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD  T G+L+       A  LT       ++K Y + V G    K   
Sbjct: 278 QDLAPRLFHVGRLDTATEGLLLFTNDGELAHRLT--HPSYGVRKKYIAKVAGPVPRK--- 332

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               L +    G +         +     +  F VI    ++   +E+  H GR H +R 
Sbjct: 333 ----LARTLRAGVEL--------EDGKVTVDGFTVIQQHGRQA-LVEIVLHEGRKHIVRR 379

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 380 LMEAVGHPVL 389


>gi|120404251|ref|YP_954080.1| pseudouridine synthase [Mycobacterium vanbaalenii PYR-1]
 gi|119957069|gb|ABM14074.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           vanbaalenii PYR-1]
          Length = 247

 Score = 75.8 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 45/252 (17%), Positives = 77/252 (30%), Gaps = 45/252 (17%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +RL +         +    +K++R G+V VD + V                     
Sbjct: 3   DNDGIRLQKVLSQA-GIASRRVAEKMIRDGRVEVDGRIVT-------------------- 41

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +        S + +      +   L+Y        NKP G+             G L 
Sbjct: 42  -ELGTRVDPAASVIRVDGARITVDDTLVY-----LAINKPRGMHSTMSDDRGRPCVGDLV 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  +K     RLD +T G+L++      A  L        + K Y + V G     
Sbjct: 96  EHRVRGNKKLFHVGRLDADTEGLLLLTNDGELAHRL--MHPSFEVPKSYVATVLGSVPK- 152

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                  L +K   G +         +     +  F V+D        + +  H GR H 
Sbjct: 153 ------GLGRKLREGVEL--------EDGPVQVDDFAVVDTTP-GRTLVRVTLHEGRKHI 197

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 198 VRRLLAEVGFPV 209


>gi|86739288|ref|YP_479688.1| pseudouridine synthase [Frankia sp. CcI3]
 gi|86566150|gb|ABD09959.1| pseudouridine synthase [Frankia sp. CcI3]
          Length = 304

 Score = 75.8 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 31/101 (30%), Positives = 44/101 (43%), Gaps = 5/101 (4%)

Query: 102 LYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           +YED  I V +KP GISV G        D  L +     G++    HR+D+ TSG+++ A
Sbjct: 2   IYEDEAILVLDKPVGISVMG-----ERHDTDLVTLAGDDGEELFPVHRIDKVTSGLVLFA 56

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           R       LT  F+ R + K Y  L           +   L
Sbjct: 57  RQLRFHGDLTRQFQRRTVDKRYLVLTRTRGLPASGTVDLPL 97



 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 23/106 (21%), Positives = 42/106 (39%), Gaps = 12/106 (11%)

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
               V  + +      +  +V +    ++  L + P +GR HQ+RVH   +G PI GD  
Sbjct: 179 PPAAVFPHVRTYPSVTTFIRVWE--GGEYTLLAVTPVSGRRHQIRVHLAWIGHPIEGDPL 236

Query: 272 YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG--RLQITAPLPAHM 315
           +  +           +  LH+  +       G  R+++ AP  A  
Sbjct: 237 FGRDATA--------RTLLHSWRLAFDAAWAGGSRIEVEAPPGADF 274


>gi|209882431|ref|XP_002142652.1| hypothetical protein [Cryptosporidium muris RN66]
 gi|209558258|gb|EEA08303.1| hypothetical protein, conserved [Cryptosporidium muris RN66]
          Length = 2982

 Score = 75.8 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 56/287 (19%), Positives = 107/287 (37%), Gaps = 36/287 (12%)

Query: 66   RIPPVINALNHIIKEQKILDSSVNL---TKHSDFLKSILLYEDSK-IYVFNKPAGI--SV 119
            R   +I  ++++IK + I+D    L    K      + ++ EDS    V  KP      +
Sbjct: 2330 RFIDIITGIDNLIKFESIVDIPNTLKAVDKKGIIKDTPVIIEDSDSWSVILKPPFWNCLM 2389

Query: 120  QGG------------SGIAYHIDGFLK-SWVDSKGQKPRLTHRL----DQETSGILVVAR 162
            +              SG    I GF K         K  +   L    D E SG +++++
Sbjct: 2390 EPNRYEDLNLESICNSGNIESILGFAKLRLSHDNNIKLDIKEELIVTFDDEISGPVLISK 2449

Query: 163  TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
            +  + Q+L   +  + I   Y  L  G  +     I+   L  + I  + +        G
Sbjct: 2450 SDDSYQNLLNQYNEKEIMAEYVFLCHGQLEKHDGYISFENL--ATIVCNRIFAKSVTV-G 2506

Query: 223  ANYAISHFKVIDCFAQK--------FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
            ++  I+ +KV   +           +         G  +++R     +G PIV D K+  
Sbjct: 2507 SSNCIAKYKVCGIYKHVNSTRDSLLYSLCRCHSTAGSVNKIRAFMSEIGHPIVCDSKFLN 2566

Query: 275  NFKGNFTSPIQNKLYLHARYMDL--PHPEGGRLQITAPLPAHMVKTW 319
            N + N    +   ++ H  Y++   P  +  + Q+   LP+++  T 
Sbjct: 2567 NKQLNADRRLFPHIFFHCWYLEFLKPDKDASKFQVKYSLPSNLTDTL 2613


>gi|297198681|ref|ZP_06916078.1| pseudouridine synthase [Streptomyces sviceus ATCC 29083]
 gi|297147171|gb|EDY58604.2| pseudouridine synthase [Streptomyces sviceus ATCC 29083]
          Length = 314

 Score = 75.8 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 47/280 (16%), Positives = 98/280 (35%), Gaps = 57/280 (20%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +  + ++++   +V V+ + V                    
Sbjct: 73  AEQEGERLQKILARAGYG-SRRSCEELIEQARVEVNGEIV-------------------- 111

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
               +++ K +D   +  K      +   Y+    +  NKPAG+             G  
Sbjct: 112 ----LEQGKRVDPERDEVKVDGLTVATQSYQ---FFSLNKPAGVVSTMEDNEGRQCLG-- 162

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET G++++      A  LT   R    +     +V  IP++
Sbjct: 163 -DYVTNRETRLFHVGRLDTETEGVILLTNHGELAHRLTHP-RYGVKKVYLAHIVGPIPRD 220

Query: 194 KKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             + + + + L+  +   D                 HF+V++   + +  +E+  H GR 
Sbjct: 221 LGKQLKDGIQLEDGYAKAD-----------------HFRVVEQTGKNY-LVEVTLHEGRK 262

Query: 253 HQLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
           H +R      G P+  D      +     G+  S    +L
Sbjct: 263 HIVRRMLAEAGFPV--DKLVRVAFGPITLGDQKSGWLRRL 300


>gi|238881201|gb|EEQ44839.1| conserved hypothetical protein [Candida albicans WO-1]
          Length = 274

 Score = 75.8 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 45/195 (23%), Positives = 75/195 (38%), Gaps = 24/195 (12%)

Query: 97  LKSILLYEDSKIYVFNKPAGIS---VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +K  L+       V NKP+G+        + I    + F K        + RL  RLD+ 
Sbjct: 1   MKLDLVKRTFNYAVVNKPSGMVCDASHTNNIITALTNEFTKILPSVNSSQFRLVQRLDRF 60

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-----WGIPKNKKECIANWLLKKSHI 208
            +G LVVAR +  A  + +SF      ++    V       IP++ +  I   +     +
Sbjct: 61  VTGGLVVARNKKWADKVRKSFFQEGTLRLTRRYVGLIALDQIPESTQGTIDFPI---QAL 117

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDC------------FAQKFCWLEMQPHTGRTHQLR 256
             DY    K  E     A++H+K+I                     + ++  TGR +Q+R
Sbjct: 118 EKDYRGKNKSRELFTYSAVTHYKLIPSARRTIKGVFPVFQQGPILPIILELETGRKNQIR 177

Query: 257 VH-ALHMGCPIVGDH 270
            H     G P++ D 
Sbjct: 178 DHIIQKFGVPLLNDD 192


>gi|68481156|ref|XP_715493.1| potential pseudouridine synthase [Candida albicans SC5314]
 gi|68481297|ref|XP_715423.1| potential pseudouridine synthase [Candida albicans SC5314]
 gi|74585553|sp|Q5A0Y2|PUS5_CANAL RecName: Full=Pseudouridylate synthase PUS5; AltName:
           Full=Pseudouridine synthase 5; AltName: Full=Uracil
           hydrolyase PUS5
 gi|46437045|gb|EAK96398.1| potential pseudouridine synthase [Candida albicans SC5314]
 gi|46437117|gb|EAK96469.1| potential pseudouridine synthase [Candida albicans SC5314]
          Length = 247

 Score = 75.8 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 45/195 (23%), Positives = 75/195 (38%), Gaps = 24/195 (12%)

Query: 97  LKSILLYEDSKIYVFNKPAGIS---VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +K  L+       V NKP+G+        + I    + F K        + RL  RLD+ 
Sbjct: 1   MKLDLVKRTFNYAVVNKPSGMVCDASHTNNIITALTNEFTKILPSVNSSQFRLVQRLDRF 60

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-----WGIPKNKKECIANWLLKKSHI 208
            +G LVVAR +  A  + +SF      ++    V       IP++ +  I   +     +
Sbjct: 61  VTGGLVVARNKKWADKVRKSFFQEGTLRLTRRYVGLIALDQIPESTQGTIDFPI---QAL 117

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDC------------FAQKFCWLEMQPHTGRTHQLR 256
             DY    K  E     A++H+K+I                     + ++  TGR +Q+R
Sbjct: 118 EKDYRGKNKSRELFTYSAVTHYKLIPSARRTIKGVFPVFQQGPILPIILELETGRKNQIR 177

Query: 257 VH-ALHMGCPIVGDH 270
            H     G P++ D 
Sbjct: 178 DHIIQKFGVPLLNDD 192


>gi|282864458|ref|ZP_06273514.1| pseudouridine synthase [Streptomyces sp. ACTE]
 gi|282560945|gb|EFB66491.1| pseudouridine synthase [Streptomyces sp. ACTE]
          Length = 382

 Score = 75.8 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 45/253 (17%), Positives = 89/253 (35%), Gaps = 49/253 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V V+ + V     ++ G+ V        
Sbjct: 141 AEQEGERLQKILARAGMG-SRRACEELIEQARVEVNGEIV-----LEQGKRVD------- 187

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                ++ +I    + +   S              +  NKPAG+    G        G  
Sbjct: 188 ----PQKDEIKVDGLTVATQSYL-----------FFALNKPAGVVSTMGDPDGRQNLG-- 230

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET GI+++      A  LT       ++K Y + + G    
Sbjct: 231 -DYVTNRETRLFHVGRLDTETEGIILLTNHGELAHRLT--HPRYGVKKTYLAAIQGPLPR 287

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                   L K+   G        + +        HF+V++   + +  +E+  H GR H
Sbjct: 288 D-------LGKRLKDGIQLEDGYARAD--------HFRVVENTGKNY-LVEVTLHEGRKH 331

Query: 254 QLRVHALHMGCPI 266
            +R      G P+
Sbjct: 332 IVRRMLAEAGFPV 344


>gi|304406989|ref|ZP_07388643.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
 gi|304343976|gb|EFM09816.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
          Length = 445

 Score = 75.8 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 82/249 (32%), Gaps = 47/249 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++ SGQV V+   V                         
Sbjct: 5   ERLQKILAQA-GIASRRKCEELIISGQVEVNGVPVT-----------------TLGAKAD 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ ++                ++ E+    + NKP G+     S         +  ++ 
Sbjct: 47  PEEDVITVGGKP----------IVSENKLYIMLNKPKGVIT---SASDPQGRKVVSDFLT 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              Q+     RLD +T G+L++      A  LT       + K YW+ V G+P   K   
Sbjct: 94  GIKQRVYPIGRLDYDTEGLLLLTNDGEFANLLT--HPKHHVPKTYWATVKGVPHGDKL-- 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                            ++  +   + A   ++ I+  + K   + +  + GR  Q+R  
Sbjct: 150 -----------DKLRKGIELEDGMTSPAEVEYQDIE-PSDKESTIRITIYEGRNRQVRRM 197

Query: 259 ALHMGCPIV 267
              +G P++
Sbjct: 198 FDAIGHPVI 206


>gi|281211738|gb|EFA85900.1| Mrp/NBP35 family protein [Polysphondylium pallidum PN500]
          Length = 687

 Score = 75.8 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 66/357 (18%), Positives = 95/357 (26%), Gaps = 140/357 (39%)

Query: 106 SKIYVFNKPAGISVQ---------------------------------GGSGIAYHIDGF 132
            K  V NKPAG  VQ                                    G        
Sbjct: 329 DKFVVINKPAGYPVQSNENQSIEKMMIERMRREMLELQALNDSASADEPLKGRPKRRLKT 388

Query: 133 LKSWVDSKGQK---PRLTHRLDQETSGILVVARTR----AAAQHLTESFRMRRIQKIYWS 185
           L    D+   K       +RLD+ TSG+LVVA T       +Q + +  +  R+     S
Sbjct: 389 LVKLFDNNHPKGILLYFINRLDKWTSGLLVVAITSPVCAQMSQTMHKWHKSYRLITDTPS 448

Query: 186 L---------------------VWGIPK--------NKKECIANWLLKKSHI-------- 208
                                 + G P         N    I +++  + H         
Sbjct: 449 CLNNSNNNNNNNNNNCCFISPFIKGNPPIFDVSGKVNGNGTIQSYIGPRIHPVPLFKRDS 508

Query: 209 ------GGDYVHVVKQNEKG----------------------------ANYAISHFKVID 234
                  G+     + NE+G                            A  A + +K++ 
Sbjct: 509 NSNDNGDGNQYKCKECNERGIVREVGHPFLSSFLLFGSSPEKGKNKFEARNAETEYKLLS 568

Query: 235 -CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP---------- 283
                +    E    TGRTHQLR+H    G PIVGD  Y   F                 
Sbjct: 569 ISKEHRKAMFEASLITGRTHQLRIHFSESGFPIVGDPYYNHYFIDQLLDKNQQILCENTQ 628

Query: 284 -----------------IQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWDSL 322
                             +N++ L A  +   HP     L +T   P       + L
Sbjct: 629 QQQQSTSSSSSSSSSDDQENEMMLQAYKLTFIHPTTLSPLTLTIDPPKSWNNIINKL 685


>gi|213419331|ref|ZP_03352397.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 78

 Score = 75.8 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 36/75 (48%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVV 160
           +LY+D  +   NKPAG  V             +++  D  GQ     HRLD+ TSG+L++
Sbjct: 4   ILYQDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLM 63

Query: 161 ARTRAAAQHLTESFR 175
             +  A + L + F 
Sbjct: 64  GLSSEAGRRLAQQFE 78


>gi|290961534|ref|YP_003492716.1| pseudouridine synthase [Streptomyces scabiei 87.22]
 gi|260651060|emb|CBG74179.1| putative pseudouridine synthase [Streptomyces scabiei 87.22]
          Length = 313

 Score = 75.8 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/279 (15%), Positives = 94/279 (33%), Gaps = 55/279 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +  + ++++   +V V+ + V                    
Sbjct: 72  AEQEGERLQKILARAGYG-SRRSCEELIEQARVEVNGEIV-------------------- 110

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
               +++ K +D   +  K      +   Y+    +  NKPAG+             G  
Sbjct: 111 ----LEQGKRVDPEKDEVKVDGLTVATQSYQ---FFSLNKPAGVVSTMEDNEGRQCLG-- 161

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET G++++      A  LT   +    +     +V  IP++
Sbjct: 162 -DYVTNRETRLFHVGRLDTETEGVILLTNHGELAHRLTHP-KYGVKKVYLAHIVGPIPRD 219

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + + + +  +                       HF+V+    + +  +E+  H GR H
Sbjct: 220 LGKQLKDGIQLEDGYARAD----------------HFRVVQQTGKNY-LVEVTLHEGRKH 262

Query: 254 QLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
            +R      G P+  D      +     G+  S    +L
Sbjct: 263 IVRRMLAEAGFPV--DKLVRVAFGPITLGDQKSGWLRRL 299


>gi|309810348|ref|ZP_07704183.1| pseudouridylate synthase [Dermacoccus sp. Ellin185]
 gi|308435661|gb|EFP59458.1| pseudouridylate synthase [Dermacoccus sp. Ellin185]
          Length = 303

 Score = 75.8 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 87/252 (34%), Gaps = 48/252 (19%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           EE  RL +         +  + + ++  G+V VD + V                      
Sbjct: 63  EEGTRLQKVLAQAGVG-SRRHCENLIAEGRVEVDGQVVT-----------------ELGT 104

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
            I  E  +    +++      L   L+Y       FNKP G+             G    
Sbjct: 105 RIDPESAV----IHVDGDRIQLDDTLVY-----LAFNKPTGVVSTMQDEEGRPCVG---E 152

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +++ + ++     RLD +T G+L++      A  L        ++K+Y + + G      
Sbjct: 153 YLEGRTERLFHVGRLDYDTEGLLLLTNDGNLANRL--QHPRYGVEKVYLATIPG------ 204

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +   L K+   G +         +    A+  FKV+D        +E+  H GR   +
Sbjct: 205 -PVPRDLGKRMREGIEL--------EDGPAAVDSFKVVDSQP-GMALVEIVLHEGRNRIV 254

Query: 256 RVHALHMGCPIV 267
           R     +G P++
Sbjct: 255 RRMFEEVGHPVI 266


>gi|322493543|emb|CBZ28831.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 453

 Score = 75.8 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/118 (27%), Positives = 48/118 (40%), Gaps = 21/118 (17%)

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +L      GG+        +     +++++ V          + + PHTGR HQLRVH
Sbjct: 290 RTYLAAPPPAGGEAPQWDAITKDS--PSVTNYPV--------TLVLLAPHTGRRHQLRVH 339

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQ-----------NKLYLHARYMDLPHPEGGRL 305
              +G PIVGD  YC +       P+             ++YLHA  + LP     RL
Sbjct: 340 CRAIGFPIVGDTLYCTDLPWCAALPLGPPTSTWVTAGVRRMYLHAWRLLLPGTVTPRL 397



 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/104 (25%), Positives = 45/104 (43%), Gaps = 17/104 (16%)

Query: 108 IYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQ----------------KPRLTHRL 150
           + V +KP GI + G   I    ++  +   + ++G                 + +  H+L
Sbjct: 1   MLVVSKPPGIPMDGDETIYGLTVESLVCKHMKARGIFDDTHAQLQKEKKRKKQLKFVHQL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           D  TSG+L +A T+  A  L   F MR I+K Y +L+ G     
Sbjct: 61  DLGTSGVLCLAFTKDMAARLAHCFEMRTIRKYYVALLHGHLPGD 104


>gi|154341733|ref|XP_001566818.1| RNA pseudouridylate synthase-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
 gi|134064143|emb|CAM40338.1| RNA pseudouridylate synthase-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 533

 Score = 75.8 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 34/210 (16%), Positives = 64/210 (30%), Gaps = 68/210 (32%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM--------------------- 176
                      RLD+ETSG++V+A+    A+ L                           
Sbjct: 212 QRSPLNLFTIQRLDKETSGVVVLAKHSVTARKLAAQLEAQTKGCTDAVESWLRERGHTVP 271

Query: 177 --------------RRIQKIYWSLVWGI-PKNKKECIANWL----------LKKSHIGGD 211
                           + K Y +++ G  P+     + N +          L+  H    
Sbjct: 272 FCSDVFGELLQLEAHVVHKSYTAVLRGAAPEGHTFVVVNCMDCMAKHPTHSLEAQHTQLK 331

Query: 212 YVHVVKQNEKG---------------------ANYAISHFKVIDCFA-QKFCWLEMQPHT 249
            + +  +  +G                        A +  +V+          + ++  T
Sbjct: 332 RLKMCCEPLRGMSDAPTASSLPTQPTEQRSHWGKLAATRIRVLASNKVLGLTCVHVELLT 391

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           GR+HQ+R+H   +G P++GD  Y     G 
Sbjct: 392 GRSHQIRLHCAAIGYPVLGDKLYMTTTPGR 421



 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 21/118 (17%), Positives = 44/118 (37%), Gaps = 19/118 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIK 79
           L  +    + ++     ++ + +G + V+   +   +  ++ G V+R  P          
Sbjct: 18  LLAYLSKKFTYLADAEWREHIAAGHISVNGATLTNESYVLRQGDVLRFAP---------- 67

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSW 136
                    +L    D     +LYEDS++ V  K   + V +GG      + G L+  
Sbjct: 68  -------PRSLEPPVDKNHIEVLYEDSRLMVVTKNGNLPVAEGGRYCENTLVGVLQRR 118


>gi|239940238|ref|ZP_04692175.1| putative pseudouridine synthase [Streptomyces roseosporus NRRL
           15998]
 gi|239986727|ref|ZP_04707391.1| putative pseudouridine synthase [Streptomyces roseosporus NRRL
           11379]
 gi|291443668|ref|ZP_06583058.1| pseudouridine synthase [Streptomyces roseosporus NRRL 15998]
 gi|291346615|gb|EFE73519.1| pseudouridine synthase [Streptomyces roseosporus NRRL 15998]
          Length = 427

 Score = 75.8 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 88/253 (34%), Gaps = 49/253 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V V+ + V     ++ G  V +      
Sbjct: 186 AEQEGERLQKVLARAGMG-SRRACEELIEQARVEVNGEIV-----VEQGMRVDV------ 233

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                 + +I    + +   S              +  NKPAG+             G  
Sbjct: 234 -----HKDEIKVDGLTVAAQSYL-----------FFALNKPAGVVSSMEDPDGRQCLG-- 275

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V+++  +     RLD ET GI+++      A  LT       ++K Y + + G    
Sbjct: 276 -DYVNNRETRLFHVGRLDTETEGIIMLTNHGELAHRLT--HPKYGVKKTYLAAIQGPLPR 332

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                   L K+   G        + +        HF+V++   + +  +E+  H GR H
Sbjct: 333 D-------LGKRLKDGIQLEDGYARAD--------HFRVVENTGKNY-LVEVTLHEGRKH 376

Query: 254 QLRVHALHMGCPI 266
            +R      G P+
Sbjct: 377 IVRRMLAEAGFPV 389


>gi|294874650|ref|XP_002767032.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239868459|gb|EEQ99749.1| ribosomal pseudouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 64

 Score = 75.4 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 33/55 (60%), Gaps = 1/55 (1%)

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKY 272
           +   ++ A S ++V++ + +    + ++  TG THQ+RVH    +G PIVGD KY
Sbjct: 7   SGPASSSAHSEYRVLERYEEGCTLMSVRITTGVTHQIRVHMAQGLGHPIVGDKKY 61


>gi|29833054|ref|NP_827688.1| pseudouridine synthase [Streptomyces avermitilis MA-4680]
 gi|29610175|dbj|BAC74223.1| putative pseudouridine synthase [Streptomyces avermitilis MA-4680]
          Length = 356

 Score = 75.4 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 49/280 (17%), Positives = 101/280 (36%), Gaps = 57/280 (20%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +  + ++++   +V V+ + V     ++ G  +R+ P    
Sbjct: 115 AEQEGERLQKVLARAGYG-SRRSCEELIEQARVEVNGEIV-----LEQG--LRVDPE--- 163

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                K++  +D     T+   F               NKPAG+             G  
Sbjct: 164 -----KDEIKVDGLTVATQSYQFFSL------------NKPAGVVSTMEDTEGRQCLG-- 204

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET G++++      A  LT   +    +     +V  IP++
Sbjct: 205 -DYVTNRETRLFHVGRLDTETEGVILLTNHGELAHRLTHP-KYGVKKVYLAHIVGPIPRD 262

Query: 194 KKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             + + + + L+  +   D                 HF+V++   + +  +E+  H GR 
Sbjct: 263 LGKRLKDGIQLEDGYAKAD-----------------HFRVVEQTGKNY-LVEVTLHEGRK 304

Query: 253 HQLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
           H +R      G P+  D      +     G+  S    +L
Sbjct: 305 HIVRRMLAEAGFPV--DKLVRVAFGPITLGDQKSGWLRRL 342


>gi|311742416|ref|ZP_07716225.1| ribosomal large subunit pseudouridine synthase B [Aeromicrobium
           marinum DSM 15272]
 gi|311314044|gb|EFQ83952.1| ribosomal large subunit pseudouridine synthase B [Aeromicrobium
           marinum DSM 15272]
          Length = 247

 Score = 75.4 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/251 (17%), Positives = 86/251 (34%), Gaps = 48/251 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + +RL +         +    ++++  G V V+ +        Q G  +R+ P  + ++ 
Sbjct: 8   DGIRLQKVLAQAGLG-SRRRCEQLMAEGHVEVNGEITT-----QMG--IRVDPATDVIH- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            +  +++   S                 D    + NKP G+     S         L+S 
Sbjct: 59  -VDGRRLPPPS-----------------DHVYVLLNKPRGVVT---SMADERGRPDLRSL 97

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +  + ++     RLD +TSG+L++      A  L          K Y +LV G+      
Sbjct: 98  LADRTERLFHVGRLDTDTSGLLMMTNDGDLAHRLAHPSFE--FTKTYVALVEGVVDPAVG 155

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                   +   G +               +  F+ I   +Q    +E+  H GR   +R
Sbjct: 156 T-------RLKSGVEL--------DDGPATVDRFR-IKDTSQGRSLVELDLHMGRNRIVR 199

Query: 257 VHALHMGCPIV 267
                +G P+V
Sbjct: 200 RLLAEVGHPVV 210


>gi|257877013|ref|ZP_05656666.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|257811179|gb|EEV39999.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
          Length = 257

 Score = 75.4 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 46/266 (17%), Positives = 103/266 (38%), Gaps = 52/266 (19%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MSL+      V+   ++ MRLD++  +   + +   ++++++ G V V+ + +K +++ Q
Sbjct: 1   MSLLCETLAAVLYERKKPMRLDKFLAD-MGYGSRKEVKQLIKKGLVTVNGQVIK-SDKAQ 58

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
                    V    + +  E +                  + Y+    Y+ NKPAG+   
Sbjct: 59  ---------VQETQDTVCFEGEP-----------------IAYQSQFYYLLNKPAGVI-- 90

Query: 121 GGSGIAYHIDGFLKSWVDSKG--QKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMR 177
             S      +  +      +   +      RLD++T G L++      A Q L+     +
Sbjct: 91  --SATVDSYEETVLDLFSEEAFREDLFPVGRLDKDTEGFLLITNDGGLAHQLLS---PKK 145

Query: 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA 237
            ++K Y++ V GI   + + I             +   +K + +    A      +D   
Sbjct: 146 HVEKEYYAQVEGIMTAEDQKI-------------FAKGIKLDGEWTLPAELQILNVD-ED 191

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMG 263
           +    +++  H G+ HQ++     +G
Sbjct: 192 EMRSEIKLILHEGKFHQVKRMVHAVG 217


>gi|300119373|ref|ZP_07057027.1| RluA family pseudouridine synthase [Bacillus cereus SJ1]
 gi|298723245|gb|EFI64033.1| RluA family pseudouridine synthase [Bacillus cereus SJ1]
          Length = 162

 Score = 75.4 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 18/56 (32%), Positives = 33/56 (58%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           + V V+ D    RLD +   H   +   ++ +I+RSG+VR++K RV  + R+++G 
Sbjct: 107 RLVEVDQDSAGQRLDNFLIRHLKGVPKTHVYRIIRSGEVRINKGRVSADTRVEAGD 162


>gi|126650120|ref|ZP_01722353.1| RluB [Bacillus sp. B14905]
 gi|126593292|gb|EAZ87254.1| RluB [Bacillus sp. B14905]
          Length = 243

 Score = 75.4 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 50/255 (19%), Positives = 86/255 (33%), Gaps = 60/255 (23%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNH 76
            RL +     Y  I +    ++++  G+V+V+ K ++    ++ +   + +         
Sbjct: 2   ERLQKVIA--YAGIASRRKAEQLILEGKVKVNGKVIRELGTKVSNSDTIEV--------- 50

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLK 134
                      V L K           ED   ++  KP G   +V    G     D    
Sbjct: 51  ---------EGVKLEK-----------EDKVYFLLYKPRGTISAVTDDKGRKTVTD---- 86

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--K 192
                  Q+     RLD +TSG+L++      +  LT      +I K Y + V GIP  +
Sbjct: 87  -LFHHIPQRIFPVGRLDYDTSGLLLLTNDGEFSYMLT--HPKFKIDKTYIARVKGIPTIE 143

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             K+      L+        V +   +EK                      E+  H GR 
Sbjct: 144 GLKKLQRGIKLEDGKTAPAKVSMTSFDEKAGK----------------AICEITIHEGRN 187

Query: 253 HQLRVHALHMGCPIV 267
            Q+R     +G P+V
Sbjct: 188 RQVRRMFEAIGTPVV 202


>gi|115744559|ref|XP_794566.2| PREDICTED: hypothetical protein, partial [Strongylocentrotus
           purpuratus]
 gi|115963314|ref|XP_001191250.1| PREDICTED: hypothetical protein, partial [Strongylocentrotus
           purpuratus]
          Length = 143

 Score = 75.4 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/131 (24%), Positives = 53/131 (40%), Gaps = 13/131 (9%)

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY----AISHFKVI---DCFAQK 239
           V G        I   +         ++  V   E         A++  +V+   +  ++ 
Sbjct: 1   VRGHVTEDTMMIEKAIYPNPEEDLSHMMKVDDGECPTGTRLLSALTRLEVLQRGEYDSEP 60

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
              L +Q HTGR HQLR+H   +G PIVGD+ Y      +       ++ L A  + +P 
Sbjct: 61  ATKLLLQLHTGRRHQLRIHCQSIGHPIVGDYTYSMRKDVSPY-----RMMLLAHTLHIPI 115

Query: 300 PEGGRLQITAP 310
           P G  + +TA 
Sbjct: 116 P-GEGIDVTAE 125


>gi|291563383|emb|CBL42199.1| ribosomal small subunit pseudouridine synthase A
           [butyrate-producing bacterium SS3/4]
          Length = 265

 Score = 75.4 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/261 (16%), Positives = 91/261 (34%), Gaps = 58/261 (22%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINA 73
           E+ +RLD++  +         L++++R G++ V+   VK    +I+ G   + +      
Sbjct: 19  EKAIRLDKYLADMGKG-TRTELKEMIRRGRITVNGVIVKKPETKIKKGEDTICLD----- 72

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                                    + + Y + + Y+ NKP G+     S         +
Sbjct: 73  ------------------------NAPVEYVELEYYLLNKPQGVI----SATEDRRRETV 104

Query: 134 KSWVDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              +D K +K      RLD +T G+L++    A A  L        + K+Y +   G   
Sbjct: 105 VDLIDEKSRKDLFPVGRLDIDTEGLLLITNDGALAHRL--LAPGHHVDKVYEARCKGFVP 162

Query: 193 NK------KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           ++      +       L       + +    ++ +    A S              + + 
Sbjct: 163 DEAVQRFREGMTLADGLSCMPSELEILERKPEDPETGTAAES-------------LVRLT 209

Query: 247 PHTGRTHQLRVHALHMGCPIV 267
            H G+ HQ++      GCP++
Sbjct: 210 LHEGKFHQVKRMMEETGCPVL 230


>gi|322501097|emb|CBZ36174.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 453

 Score = 75.4 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 33/119 (27%), Positives = 49/119 (41%), Gaps = 21/119 (17%)

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +L +    GG+        +     +++ + V          + + PHTGR HQLRVH
Sbjct: 290 RTYLAEPPPAGGEAPQRDAIAKDS--PSVTSYPV--------TLVLLAPHTGRRHQLRVH 339

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPI-----------QNKLYLHARYMDLPHPEGGRLQ 306
              +G PIVGD  YCA+       P+             ++YLHA  + LP     RL 
Sbjct: 340 CRAIGFPIVGDTSYCADLPWCAALPLGSSTSTWAAAGARRMYLHAWRLLLPGTVTPRLD 398



 Score = 50.4 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/104 (25%), Positives = 46/104 (44%), Gaps = 17/104 (16%)

Query: 108 IYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQ----------------KPRLTHRL 150
           + V +KP GI + G   I    ++  +   + ++G                 + +  H+L
Sbjct: 1   MLVLSKPPGIRMDGDETIYGRTVESLVCEHMKARGIFDDTHEQLQKEKKRKKQLKFVHQL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           D  TSG+L +A T+  A  L   F MR ++K Y +L+ G   + 
Sbjct: 61  DFGTSGVLCLAFTKDMAARLAHCFEMRTVRKYYVALLHGHLPSD 104


>gi|146093778|ref|XP_001467000.1| hypothetical protein [Leishmania infantum JPCM5]
 gi|134071364|emb|CAM70050.1| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 453

 Score = 75.4 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 33/119 (27%), Positives = 49/119 (41%), Gaps = 21/119 (17%)

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +L +    GG+        +     +++ + V          + + PHTGR HQLRVH
Sbjct: 290 RTYLAEPPPAGGEAPQRDAIAKDS--PSVTSYPV--------TLVLLAPHTGRRHQLRVH 339

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPI-----------QNKLYLHARYMDLPHPEGGRLQ 306
              +G PIVGD  YCA+       P+             ++YLHA  + LP     RL 
Sbjct: 340 CRAIGFPIVGDTSYCADLPWCAALPLGSSTSTWAAAGARRMYLHAWRLLLPGTVTPRLD 398



 Score = 50.4 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/104 (25%), Positives = 46/104 (44%), Gaps = 17/104 (16%)

Query: 108 IYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQ----------------KPRLTHRL 150
           + V +KP GI + G   I    ++  +   + ++G                 + +  H+L
Sbjct: 1   MLVLSKPPGIRMDGDETIYGRTVESLVCEHMKARGIFDDTHEQLQKEKKRKKQLKFVHQL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           D  TSG+L +A T+  A  L   F MR ++K Y +L+ G   + 
Sbjct: 61  DFGTSGVLCLAFTKDMAARLAHCFEMRTVRKYYVALLHGHLPSD 104


>gi|322823471|gb|EFZ29216.1| hypothetical protein TCSYLVIO_4532 [Trypanosoma cruzi]
          Length = 346

 Score = 75.4 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 51/272 (18%), Positives = 81/272 (29%), Gaps = 95/272 (34%)

Query: 122 GSGIAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVVARTRAAAQ---HLTESFRM 176
             G     D   ++ V  +G+K   +  H+LD  TSG+L VA +R  A    H  E    
Sbjct: 23  AGGGVEKEDDTTRTAVRGRGEKKMVKFVHQLDYATSGVLCVAFSREMAARLAHCFEMRTT 82

Query: 177 RR-------------------------------------IQKIYWSLVWGIPKNKKECIA 199
           R+                                     +++I    V G+   +K  I 
Sbjct: 83  RKAYLAVLLGMMPTTSAMEKKLDTDTGVDFLRGSPYASHVRRISMDDVPGVCFIRKCVIE 142

Query: 200 N--------------WLLKKSHIGGDYV----HVVKQNEKGANYAISHFKVIDC------ 235
                           L     +G D        +  N + A  ++++  V+        
Sbjct: 143 ASGHEEGENADCCATLLEVNLPVGYDTTDHEGFRMTVNGRDARGSVTYLSVLQRGHMTHP 202

Query: 236 ---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQN------ 286
                     + + P TGR HQLRVH   +G PI+GD  Y         S +        
Sbjct: 203 TSGCPVPVTKVALFPRTGRRHQLRVHCHAIGFPILGDVTYARIPTPRVASKVTGAEEVAT 262

Query: 287 --------------------KLYLHARYMDLP 298
                               ++ LHA  +  P
Sbjct: 263 VGATESINAPNEIDAIEAWQRMMLHAWRLSFP 294


>gi|227549324|ref|ZP_03979373.1| 16S rRNA uridine-516 pseudouridylate synthase [Corynebacterium
           lipophiloflavum DSM 44291]
 gi|227078643|gb|EEI16606.1| 16S rRNA uridine-516 pseudouridylate synthase [Corynebacterium
           lipophiloflavum DSM 44291]
          Length = 295

 Score = 75.4 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 49/252 (19%), Positives = 83/252 (32%), Gaps = 49/252 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSG-QVVRIPPVINAL 74
           E +RL +         +  + + ++  G+V V+  RV     R+     V+R+      +
Sbjct: 53  EGVRLQKVLAQA-GVASRRHAEIMITQGRVEVNGTRVTTQGMRVDPSRDVIRVDGTRINV 111

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           N  ++                             +VFNKP G+       +     G   
Sbjct: 112 NEELE----------------------------YFVFNKPRGVQSTMKDEMDRTSVGSYL 143

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           S   + GQ+     RLD +T G+L++      A  L        I K Y + V G  K  
Sbjct: 144 SERTASGQRLFHVGRLDADTEGLLLLTNDGELANRL--MHPRYEIAKTYMATVLGEAK-- 199

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                  L+KK   G +              A + +  I         + ++ H GR H 
Sbjct: 200 -----PALVKKLREGIEL---------DDGPAKADYVQIVDTHNGQSIIRVELHEGRKHI 245

Query: 255 LRVHALHMGCPI 266
           +R      G P+
Sbjct: 246 VRRMLKAAGHPV 257


>gi|256752042|ref|ZP_05492910.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
 gi|256749052|gb|EEU62088.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
          Length = 236

 Score = 75.0 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 85/250 (34%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    ++ +  G+V+V+ K VK                      I 
Sbjct: 2   ERLQKYLAE-CGIASRRKCEEYILQGRVKVNGKVVK-----------------ELGVKIN 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            +  I++    + +       I+L         NKP G I+          +   +K   
Sbjct: 44  PDVDIIEFDDKIVRREKKKVYIIL---------NKPTGYITSVKDQFGRPTVMDLVKV-- 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  L        I K Y + + GIP  ++  
Sbjct: 93  ---KERIYPVGRLDYDTSGLLLLTNDGEIANIL--MHPRHEIVKTYIAKIKGIPTQEELE 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                 +   + GDY+    + E            I         +E++ H G+  Q+R 
Sbjct: 148 ----RFRNGLLIGDYLTSKAEIE------------ILAVKNGTSVVEIKIHEGKNRQVRR 191

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 192 MCEAIGHPVI 201


>gi|319651400|ref|ZP_08005529.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317396931|gb|EFV77640.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 241

 Score = 75.0 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 88/252 (34%), Gaps = 54/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++  G+V+V+ K VK    ++     + +  +       
Sbjct: 2   ERLQKVIA-HAGFASRRKAEELMAEGRVKVNGKTVKELGVKVSPSDRIEVDGIPVEREEP 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
           +                              ++  KP G+  +V    G        +  
Sbjct: 61  V-----------------------------YFLLYKPRGVISAVSDDKGRK-----VVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +   Q+     RLD +TSGIL++      A  L        I+K+Y + + GIP  + 
Sbjct: 87  FFEGIKQRIYPVGRLDYDTSGILILTNDGEFANLL--MHPSNEIEKVYVAKIKGIPSKEG 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                       +      VV ++ K A  A +    +D   Q    +E+  H GR  Q+
Sbjct: 145 ------------MRSLQRGVVLEDGKTA-PAKTKLLSMDKKKQ-TAIVEISIHEGRNRQV 190

Query: 256 RVHALHMGCPIV 267
           R     +G P++
Sbjct: 191 RRMFEAIGHPVL 202


>gi|312139846|ref|YP_004007182.1| pseudouridylate synthase [Rhodococcus equi 103S]
 gi|325674277|ref|ZP_08153966.1| ribosomal large subunit pseudouridine synthase B [Rhodococcus equi
           ATCC 33707]
 gi|311889185|emb|CBH48499.1| pseudouridylate synthase [Rhodococcus equi 103S]
 gi|325554957|gb|EGD24630.1| ribosomal large subunit pseudouridine synthase B [Rhodococcus equi
           ATCC 33707]
          Length = 321

 Score = 75.0 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 90/251 (35%), Gaps = 45/251 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + +RL +         +    ++++  G+V VD + V     ++ G  V      +  N 
Sbjct: 79  DGVRLQKVLAQA-GVASRRAAEELIDQGRVEVDGRIV-----LEQGLRV------DPENA 126

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           I++   I                +++ +D      NKP G        +     G + S 
Sbjct: 127 IVRVDGI---------------RVVVKKDLVHIALNKPRGWQSTMSDDLGRPCIGDIVSE 171

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             S GQ+     RLD +T G++++      A  L        + K Y + V G+      
Sbjct: 172 RVSAGQRLFHVGRLDADTEGLILLTNDGDLAHRL--MHPSYEVPKTYLATVQGVV----- 224

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                     ++G      V+ ++  A   +  F ++D    K   + +  H GR H +R
Sbjct: 225 --------DRNVGKTLKAGVELDDGPAK--VDAFTLLDVNGGK-SLVRVVLHEGRKHIVR 273

Query: 257 VHALHMGCPIV 267
                +G P+V
Sbjct: 274 RLLEAVGHPVV 284


>gi|219123231|ref|XP_002181932.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406533|gb|EEC46472.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 418

 Score = 75.0 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 8/92 (8%)

Query: 224 NYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             +++   ++       Q    + ++P TGR HQLRVH+  +G  IVGD  Y A    + 
Sbjct: 319 KPSLTRCVILKHAAIRGQPVTKVRLEPRTGRRHQLRVHSALLGHAIVGDQTYKAPGSPDL 378

Query: 281 TSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           T    +++ LH++ +++P  E   +++ AP P
Sbjct: 379 T----DRMCLHSQCLEIPLFE-ELIKVEAPDP 405



 Score = 68.5 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 63/177 (35%), Gaps = 40/177 (22%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK----------------------- 134
             +++YE       NKP  +         +H    LK                       
Sbjct: 52  DKVVVYETDHFLALNKPPDL-----RMDGHHPSTVLKLLTYWYPPPAFQNLQSKGLLEKV 106

Query: 135 ----SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG- 189
               ++ + +G + R  H+LD  TSGIL+VAR R AA     SF  R  +K Y +LV G 
Sbjct: 107 SEFENYRNIEGNELRPCHQLDYATSGILLVARNRQAADQARVSFEERSTRKTYLALVHGH 166

Query: 190 ------IPKNKKECIANWLLKKSHIGGDYVHVVKQNE-KGANYAISHFKVIDCFAQK 239
                 IP  ++  I   + +   I        +++  +G   A   F+ +      
Sbjct: 167 LSVPSNIPVMRRTDIDERMGRLEEIYRQSRRKHRKDTYRGYQPAHGLFQQLQQQHNH 223


>gi|255071535|ref|XP_002499442.1| predicted protein [Micromonas sp. RCC299]
 gi|226514704|gb|ACO60700.1| predicted protein [Micromonas sp. RCC299]
          Length = 474

 Score = 75.0 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 47/197 (23%), Positives = 77/197 (39%), Gaps = 48/197 (24%)

Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK------------NKK 195
           HRLD  TSG+LV+AR  + A    ++ R RR+ K Y  +                    +
Sbjct: 249 HRLDVATSGVLVLARRSSFAAEFNDALRRRRVTKTYECVTARAVPVGVLEHWTEESSGAR 308

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYA-ISH-------FKVIDC------------ 235
           E  A + +++   G      V  + K ++ A ++         +V+ C            
Sbjct: 309 EGPARFEMRELEPGDPRWRDVAADGKYSDDAFVTPDGRKLCVLRVLGCEETEGLTKRLTK 368

Query: 236 ----------FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTS 282
                      A +     ++  TGRTHQ+R     +GCPI+GD  Y     + +G  T 
Sbjct: 369 RLAGEAGEAGEASRAYVSTIELVTGRTHQIRAQLSAIGCPILGDVLYGGVDLSREGGATP 428

Query: 283 PIQ---NKLYLHARYMD 296
            +    ++L LHA  M 
Sbjct: 429 RVLRDDDRLCLHAAEMR 445


>gi|256379430|ref|YP_003103090.1| pseudouridine synthase [Actinosynnema mirum DSM 43827]
 gi|255923733|gb|ACU39244.1| pseudouridine synthase [Actinosynnema mirum DSM 43827]
          Length = 246

 Score = 75.0 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 86/254 (33%), Gaps = 48/254 (18%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           +   E +RL +         +    ++++  G+V+VD + V+   R       RI P   
Sbjct: 3   DPGSEGVRLQKVLAKA-GIASRRVAEELIELGRVQVDGEVVREQGR-------RIDP--- 51

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                           +          ++L ED    V NKP G+             G 
Sbjct: 52  ----------------DKAVVHVDGVRVVLQEDVVTLVLNKPRGMLSTMHDDAHRPCVG- 94

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
               + ++ ++     RLD +T G+L+V      A  L        + K Y + V G   
Sbjct: 95  --DLLVNRKERLFHVGRLDADTEGLLLVTNDGDLAHRL--MHPSYEVPKTYLAEVPG--- 147

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                I   L K+   G +         +     +  FK+I     +   +E+  H GR 
Sbjct: 148 ----PIPRDLGKRLRSGIEL--------EDGPVKVDSFKLISSLPGRA-LVEVVLHEGRK 194

Query: 253 HQLRVHALHMGCPI 266
           H +R     +G P+
Sbjct: 195 HIVRRLLEAVGHPV 208


>gi|254975638|ref|ZP_05272110.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-66c26]
 gi|255093025|ref|ZP_05322503.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile CIP 107932]
 gi|255314767|ref|ZP_05356350.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-76w55]
 gi|255517442|ref|ZP_05385118.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-97b34]
 gi|255650552|ref|ZP_05397454.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-37x79]
 gi|260683650|ref|YP_003214935.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile CD196]
 gi|260687310|ref|YP_003218444.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile R20291]
 gi|306520500|ref|ZP_07406847.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile QCD-32g58]
 gi|260209813|emb|CBA63664.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile CD196]
 gi|260213327|emb|CBE04906.1| putative 23S RNA and tRNA pseudouridine synthase [Clostridium
           difficile R20291]
          Length = 238

 Score = 75.0 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 92/251 (36%), Gaps = 48/251 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++  +     +    ++I+  G+++V+   VK                     +I 
Sbjct: 1   MRINKYIAS-CGIASRRKSEEIILGGRIKVNGSVVK-----------------ELSFNID 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
           +E+ I++      K S+      +Y      V NKP G I+          +   LK   
Sbjct: 43  EEKDIVEFDNKKVKPSENY----IY-----IVLNKPEGYITTVKDQFNRPSVIDILKDVR 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD ETSG+L++         LT       I K Y + V GI       
Sbjct: 94  ----ERVYPIGRLDYETSGLLILTNDGDLTYKLT--HPKHEIDKTYVASVKGI------- 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I++  +++   G   + +       A   ++     +   + +   E+  H GR  Q+R 
Sbjct: 141 ISDDEIRQFETG---LKIEDYTTAPAKIRVTK----ENKEKNYSVCEITIHEGRNRQVRK 193

Query: 258 HALHMGCPIVG 268
               +  P++ 
Sbjct: 194 MCKAINHPVLN 204


>gi|256788622|ref|ZP_05527053.1| pseudouridine synthase [Streptomyces lividans TK24]
 gi|289772517|ref|ZP_06531895.1| pseudouridine synthase [Streptomyces lividans TK24]
 gi|289702716|gb|EFD70145.1| pseudouridine synthase [Streptomyces lividans TK24]
          Length = 371

 Score = 74.6 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 43/279 (15%), Positives = 95/279 (34%), Gaps = 55/279 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V ++ + V                    
Sbjct: 130 AEQEGERLQKVLARAGYG-SRRACEELIEQARVEINGEIV-------------------- 168

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
               +++ + +D   +  K      +   Y+    +  NKPAG+             G  
Sbjct: 169 ----LEQGRRVDPEKDEVKVDGLTVATQSYQ---FFSLNKPAGVVSTMEDPEGRQCLG-- 219

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET G++++      A  LT   R    +     +V  IP++
Sbjct: 220 -DYVTNRETRLFHVGRLDTETEGVILLTNHGELAHRLTHP-RYGVKKTYLAHIVGPIPRD 277

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + + + +  +                       HF+V++   + +  +E+  H GR H
Sbjct: 278 LGKRLKDGIQLEDGYARAD----------------HFRVVEQTGKNY-LVEVTLHEGRKH 320

Query: 254 QLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
            +R      G P+  D+     +     G+  S    +L
Sbjct: 321 IVRRMLAEAGFPV--DNLVRTAFGPITLGDQKSGWLRRL 357


>gi|326780186|ref|ZP_08239451.1| pseudouridine synthase Rsu [Streptomyces cf. griseus XylebKG-1]
 gi|326660519|gb|EGE45365.1| pseudouridine synthase Rsu [Streptomyces cf. griseus XylebKG-1]
          Length = 433

 Score = 74.6 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 87/253 (34%), Gaps = 49/253 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V V+ + V     ++ G  V +      
Sbjct: 192 AEQEGERLQKVLARAGMG-SRRACEELIEQARVEVNGEIV-----VEQGMRVDV------ 239

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                 + +I    + +   S              +  NKPAG+             G  
Sbjct: 240 -----HKDEIKVDGLTVAAQSYL-----------FFALNKPAGVVSSMEDPDGRQCLG-- 281

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET GI+++      A  LT       ++K Y + + G    
Sbjct: 282 -DYVTNRETRLFHVGRLDTETEGIIMLTNHGELAHRLT--HPKYGVKKTYLAAIQGPLPR 338

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                   L K+   G        + +        HF+V++   + +  +E+  H GR H
Sbjct: 339 D-------LGKRLKDGIQLEDGYARAD--------HFRVVENTGKNY-LVEVTLHEGRKH 382

Query: 254 QLRVHALHMGCPI 266
            +R      G P+
Sbjct: 383 IVRRMLAEAGFPV 395


>gi|270643349|ref|ZP_06222148.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae HK1212]
 gi|270317303|gb|EFA28858.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae HK1212]
          Length = 99

 Score = 74.6 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 2/85 (2%)

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC- 273
            + +  +    + + F + + +      ++  P TGRTHQ+RVH  + G PI  D KY  
Sbjct: 6   RIVRVSEQGKPSETRFSIEERYI-NATLVKASPVTGRTHQIRVHTQYAGHPIALDDKYGD 64

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLP 298
            +F         N+L+LHA  +   
Sbjct: 65  KDFDKQMNELGLNRLFLHAFSIRFE 89


>gi|296140073|ref|YP_003647316.1| pseudouridine synthase [Tsukamurella paurometabola DSM 20162]
 gi|296028207|gb|ADG78977.1| pseudouridine synthase [Tsukamurella paurometabola DSM 20162]
          Length = 319

 Score = 74.6 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 48/253 (18%), Positives = 87/253 (34%), Gaps = 45/253 (17%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            D E +RL +         +    ++++  G+V VD + V         Q +R+ P +  
Sbjct: 74  PDGEKIRLQKVLAQA-GVASRRVAEEMIADGRVEVDGEIVTE-------QGLRVDPSVAV 125

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           +        + ++ V+L                     NKP G        +     G +
Sbjct: 126 VRVDGVRVVVNENLVHL-------------------ALNKPRGWHSTMSDDMGRPCVGDI 166

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            +   + GQ+     RLD +T G+L+V      A  L        + K Y + V G    
Sbjct: 167 VAERVAAGQRLFHVGRLDADTEGLLLVTNDGELAHRL--MHPSYEVPKTYLAWVAGE--- 221

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               +   L KK   G +         +     +  F V++  A+    + +  H GR H
Sbjct: 222 ----VPRNLGKKLRDGVEL--------EDGPVTVDRFSVLEA-AEGKSTVRVVLHEGRKH 268

Query: 254 QLRVHALHMGCPI 266
            +R     +G P+
Sbjct: 269 IVRRLLAEVGHPV 281


>gi|182439522|ref|YP_001827241.1| putative pseudouridine synthase [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178468038|dbj|BAG22558.1| putative pseudouridine synthase [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 434

 Score = 74.6 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 87/253 (34%), Gaps = 49/253 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V V+ + V     ++ G  V +      
Sbjct: 193 AEQEGERLQKVLARAGMG-SRRACEELIEQARVEVNGEIV-----VEQGMRVDV------ 240

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                 + +I    + +   S              +  NKPAG+             G  
Sbjct: 241 -----HKDEIKVDGLTVAAQSYL-----------FFALNKPAGVVSSMEDPDGRQCLG-- 282

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET GI+++      A  LT       ++K Y + + G    
Sbjct: 283 -DYVTNRETRLFHVGRLDTETEGIIMLTNHGELAHRLT--HPKYGVKKTYLAAIQGPLPR 339

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                   L K+   G        + +        HF+V++   + +  +E+  H GR H
Sbjct: 340 D-------LGKRLKDGIQLEDGYARAD--------HFRVVENTGKNY-LVEVTLHEGRKH 383

Query: 254 QLRVHALHMGCPI 266
            +R      G P+
Sbjct: 384 IVRRMLAEAGFPV 396


>gi|21220260|ref|NP_626039.1| pseudouridine synthase [Streptomyces coelicolor A3(2)]
 gi|5738484|emb|CAB52832.1| putative pseudouridine synthase [Streptomyces coelicolor A3(2)]
          Length = 371

 Score = 74.6 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 43/279 (15%), Positives = 95/279 (34%), Gaps = 55/279 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V ++ + V                    
Sbjct: 130 AEQEGERLQKVLARAGYG-SRRACEELIEQARVEINGEIV-------------------- 168

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
               +++ + +D   +  K      +   Y+    +  NKPAG+             G  
Sbjct: 169 ----LEQGRRVDPEKDEVKVDGLTVATQSYQ---FFSLNKPAGVVSTMEDPEGRQCLG-- 219

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET G++++      A  LT   R    +     +V  IP++
Sbjct: 220 -DYVTNRETRLFHVGRLDTETEGVILLTNHGELAHRLTHP-RYGVKKTYLAHIVGPIPRD 277

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + + + +  +                       HF+V++   + +  +E+  H GR H
Sbjct: 278 LGKRLKDGIQLEDGYARAD----------------HFRVVEQTGKNY-LVEVTLHEGRKH 320

Query: 254 QLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
            +R      G P+  D+     +     G+  S    +L
Sbjct: 321 IVRRMLAEAGFPV--DNLVRTAFGPITLGDQKSGWLRRL 357


>gi|328955498|ref|YP_004372831.1| ribosomal large subunit pseudouridine synthase B [Coriobacterium
           glomerans PW2]
 gi|328455822|gb|AEB07016.1| ribosomal large subunit pseudouridine synthase B [Coriobacterium
           glomerans PW2]
          Length = 257

 Score = 74.6 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 77/250 (30%), Gaps = 49/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRL R+        +    + ++ +G+VRV+         ++  G   V +  +      
Sbjct: 1   MRLQRFLARA-GVASRRGSEHLMSAGRVRVNGLVASELGTKVDVGADRVEVDGIEVVFGA 59

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                    +Y      V NKPAG                L   
Sbjct: 60  PP-----------------------VY-----IVLNKPAGYLTTMSDPAGRPCVAELVPI 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               G       RLD++T+G+L+       AQ+L      + + K Y + V G P +   
Sbjct: 92  RRFPG--LFPVGRLDKDTTGVLLFTTDGDLAQNL--LHPSKHVAKTYLARVEGTPDSADL 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +    ++              ++     A     V    +     +E+    GR +Q++
Sbjct: 148 DVLRAGIE-------------LDDGPCLPARCRL-VERRASGGSSLVELIIREGRKNQVK 193

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 194 RMLAAVGHPV 203


>gi|213965939|ref|ZP_03394129.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           amycolatum SK46]
 gi|213951353|gb|EEB62745.1| ribosomal large subunit pseudouridine synthase B [Corynebacterium
           amycolatum SK46]
          Length = 324

 Score = 74.6 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 89/254 (35%), Gaps = 45/254 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
               E +RL +         +    +K++  G+V VD K V         Q VR+ P  +
Sbjct: 78  SEAGEGVRLQKVLAQA-GVASRRMAEKLIDEGRVEVDGKIVTR-------QGVRVDPNTS 129

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
            +                         +++ ED + +V NKP G+       +     G 
Sbjct: 130 VIR-------------------VDGSRVIVNEDMQYFVLNKPRGVQSTMHDDMGRPCVGD 170

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +     S GQ+     RLD  T G+L++      A  L        + K Y + V G   
Sbjct: 171 IIGEKISAGQRLFHVGRLDAATEGLLLLTNDGELANRL--MHPSYEVTKTYMATVVGEV- 227

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                        S +  +    ++ ++  A   ++  ++ID + Q    + ++ H GR 
Sbjct: 228 ------------DSKVMRELEKGIELDDGIAKADMA--QIIDVW-QGRSIVRIELHEGRK 272

Query: 253 HQLRVHALHMGCPI 266
           H +R      G P+
Sbjct: 273 HIVRRMLKTAGFPV 286


>gi|88607964|ref|YP_506037.1| putative RNA pseudouridylate synthase, truncation [Neorickettsia
           sennetsu str. Miyayama]
 gi|88600133|gb|ABD45601.1| putative RNA pseudouridylate synthase, truncation [Neorickettsia
           sennetsu str. Miyayama]
          Length = 119

 Score = 74.6 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 27/97 (27%), Positives = 46/97 (47%), Gaps = 7/97 (7%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSK------GQK 143
            +H+      + YED  + V  KPAG+ V  G G     +   L+    ++        +
Sbjct: 17  PRHAFIQPLDVRYEDDCLLVIYKPAGLVVHPGIGNREQTLVNILEHHYPTEKLSSLDSSR 76

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
           P + HRLD++T+G L+VA+T  A   L++  +   I 
Sbjct: 77  PGIVHRLDKDTAGFLIVAKTNPAHLSLSQMIKEGVIH 113


>gi|94267153|ref|ZP_01290785.1| Pseudouridine synthase, Rsu [delta proteobacterium MLMS-1]
 gi|93452121|gb|EAT02795.1| Pseudouridine synthase, Rsu [delta proteobacterium MLMS-1]
          Length = 240

 Score = 74.6 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 56/291 (19%), Positives = 97/291 (33%), Gaps = 58/291 (19%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RL +         +    ++ + +G+V VD +RV      + G  +R+ P   A+   
Sbjct: 3   PERLQKVLARAGVG-SRRRAEEFIAAGRVTVDGRRVT-----EMG--LRVDPEKQAITFD 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +  +  ++ V                     + NKPAG            + G L   +
Sbjct: 55  GRPLRFPENKVT-------------------VLLNKPAGYVTTMADPQGRPMVGSL---L 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              G +     RLD +T G L++      A + L  SF    I++ Y + V G P  +  
Sbjct: 93  KEPGLRLFPVGRLDFDTEGALLLTNDGDLAHRLLHPSF---EIKRTYQATVEGTPGAQAL 149

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                L +   + G   H                K +    ++    E+  H GR  Q+R
Sbjct: 150 ---RALRQGIELEGRRTHPAMV------------KTLRRRGEQTVL-EIIIHEGRKRQVR 193

Query: 257 VHALHMGCPIVGDHK----YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                +G P++  H     Y     G        +L  +   + L HPE  
Sbjct: 194 KMLAAVGHPVL--HLKRVAYGDLRLGRLPLGSYRRL--NHEDIALLHPEKK 240


>gi|239978707|ref|ZP_04701231.1| pseudouridine synthase [Streptomyces albus J1074]
 gi|291450599|ref|ZP_06589989.1| pseudouridine synthase [Streptomyces albus J1074]
 gi|291353548|gb|EFE80450.1| pseudouridine synthase [Streptomyces albus J1074]
          Length = 351

 Score = 74.2 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 44/282 (15%), Positives = 92/282 (32%), Gaps = 61/282 (21%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
              E  RL +         +    ++++   +V V+ + V                    
Sbjct: 110 PGNEGERLQKVLARAGYG-SRRACEELIEDARVEVNGEIV-------------------- 148

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                     L+  + +   +D +K     +  +  + +  NKPAG+             
Sbjct: 149 ----------LEQGLRVDPENDEIKVDGLTVATQSYQFFSLNKPAGVVSTMEDPDGRQCL 198

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G    +V ++  +     RLD ET G++++      A  LT   R    +     +V  I
Sbjct: 199 G---DYVTNRETRLFHVGRLDTETEGVILLTNHGELAHRLTHP-RYGVKKTYLAHIVGPI 254

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P++  + + + +  +                       HF+V++   + +  +E+  H G
Sbjct: 255 PRDLGKRLKDGIQLEDGYARAD----------------HFRVVEQTGKNY-LVEVTLHEG 297

Query: 251 RTHQLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
           R H +R      G P+  D      +     G+  S    +L
Sbjct: 298 RKHIVRRMLAEAGFPV--DKLVRVAFGPITLGDQKSGWLRRL 337


>gi|94263642|ref|ZP_01287451.1| Pseudouridine synthase, Rsu [delta proteobacterium MLMS-1]
 gi|93455947|gb|EAT06102.1| Pseudouridine synthase, Rsu [delta proteobacterium MLMS-1]
          Length = 240

 Score = 74.2 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 55/291 (18%), Positives = 93/291 (31%), Gaps = 58/291 (19%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RL +         +    ++ + +G+V VD +RV                        
Sbjct: 3   PERLQKVLARAGVG-SRRRAEEFIAAGRVTVDGRRVT----------------------- 38

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
               ++      +T     L+   L E+    + NKPAG            + G L   +
Sbjct: 39  EMGLRVDPEKQAITFDGRPLR---LPENKVTVLLNKPAGYVTTMADPQGRPMVGSL---L 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              G +     RLD +T G L++      A + L  SF    I++ Y + V G P  +  
Sbjct: 93  KEPGLRLFPVGRLDFDTEGALLLTNDGDLAHRLLHPSF---EIKRTYQATVEGTPGAQAL 149

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                L +   + G   H                K +    ++    E+  H GR  Q+R
Sbjct: 150 ---RALRQGIELEGRRTHPAMV------------KTLRRRGEQTVL-EIIIHEGRKRQVR 193

Query: 257 VHALHMGCPIVGDHK----YCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
                +G P++  H     Y     G        +L  +   + L HPE  
Sbjct: 194 KMLAAVGHPVL--HLKRVAYGDLRLGRLPLGSYRRL--NHEDIALLHPEKK 240


>gi|311030759|ref|ZP_07708849.1| pseudouridine synthase [Bacillus sp. m3-13]
          Length = 242

 Score = 74.2 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 85/252 (33%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +++++ G+VRV+ K VK    ++     + +          
Sbjct: 2   ERLQKVIA-HAGIASRRKAEELIKEGKVRVNDKVVKELGVKVNPNDKIEVE--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                       +    +     LLY         KP G+  SV    G     D     
Sbjct: 52  -----------GIPVEREKPVYFLLY---------KPRGVISSVSDDKGRKVATD----- 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     ++     RLD +TSG+L++      A  L        ++K+Y + + GIP  + 
Sbjct: 87  FFPYIEERIYPVGRLDYDTSGLLLMTNDGEFANVL--MHPASEVEKVYVAKLKGIPSREA 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
                  +K    G           +    A +  K++     +     E+  H GR  Q
Sbjct: 145 -------IKSLERGIKL--------EDGKTAPARIKLLSMERTKNTSIFEISIHEGRNRQ 189

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 190 VRRMFEAIGHPV 201


>gi|310641380|ref|YP_003946138.1| ribosomal small subunit pseudouridine synthase a [Paenibacillus
           polymyxa SC2]
 gi|309246330|gb|ADO55897.1| Ribosomal small subunit pseudouridine synthase A [Paenibacillus
           polymyxa SC2]
          Length = 260

 Score = 74.2 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 89/246 (36%), Gaps = 42/246 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+    H  + +  +++K ++ G + V+ + +K +        +++ P  + +    
Sbjct: 9   QRLDKILT-HMGYGSRSDIKKQVKQGMITVNGRTIKDSG-------LQVHPYQDQI---- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                           +    ++++ +    + +KP G+           +   L +  +
Sbjct: 57  ----------------EVNGELVVFREFIYIMLHKPPGVISATEDTRERTVLDLLSA--E 98

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +  +P    RLD++T G+L++    + A + L+     R + K Y + V G    +   
Sbjct: 99  ERHFEPFPVGRLDKDTEGLLLLTNDGKLAHELLS---PRRHVPKTYEATVSGHVTEED-- 153

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I  +        G                + H +      +   ++ +  H G+ HQ++ 
Sbjct: 154 ILQFTAGVELDDG------YVTLPAQLTILRHEQPHQADGEVTSYISLVIHEGKFHQVKR 207

Query: 258 HALHMG 263
               +G
Sbjct: 208 MFEAIG 213


>gi|227550282|ref|ZP_03980331.1| pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|257889008|ref|ZP_05668661.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257897603|ref|ZP_05677256.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|227180583|gb|EEI61555.1| pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|257825071|gb|EEV51994.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257834168|gb|EEV60589.1| pseudouridine synthase [Enterococcus faecium Com12]
          Length = 255

 Score = 74.2 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 88/248 (35%), Gaps = 51/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++ +++ G + V+ + VK           ++    + + +  
Sbjct: 17  MRLDKFLADMGLG-SRKEVKGLIKKGTIEVNGQVVKS-------DKTQVNEFEDTVTY-- 66

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                             L  I+ Y+    Y+ +KPAG+           +   LK    
Sbjct: 67  ------------------LGEIIAYQKDFYYILHKPAGVISATQDNHDQTVIDLLKD--Q 106

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              +      RLD++T G+L++      A Q L+     + ++K Y + V GI   +   
Sbjct: 107 DYREDLFPVGRLDKDTEGLLILTNDGIFAHQLLS---PKKHVEKEYLAEVSGIMTEEDIR 163

Query: 198 I--ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           +     ++            + Q ++ +  +I               + +  H G+ HQ+
Sbjct: 164 LFAEGLIIDGDEQTLPAKLQIDQVDQESETSI---------------IRLILHEGKFHQV 208

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 209 KRMVKAVG 216


>gi|224129476|ref|XP_002328726.1| predicted protein [Populus trichocarpa]
 gi|222839024|gb|EEE77375.1| predicted protein [Populus trichocarpa]
          Length = 177

 Score = 74.2 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 36/151 (23%), Positives = 60/151 (39%), Gaps = 51/151 (33%)

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYC------ 273
           + +  A++ ++V+        W+E++P T R HQLRVH    +G PIVGD+KY       
Sbjct: 20  EPSRDAVTEYRVLGPTINGCSWIELRPLTSRKHQLRVHCAEALGTPIVGDYKYGWFVHRR 79

Query: 274 ------ANFKGNFTSPIQNK------------------LYLHARYMDLP----------- 298
                  + + +   P + +                  L+LH R + LP           
Sbjct: 80  WKQMPRVDIEPSSGKPYKLRWPEGVDIQKGSVLAKVPLLHLHCRELVLPNIAKFLDVLDG 139

Query: 299 -----HPEGGR----LQITAPLPAHMVKTWD 320
                HP        L+  A +P+HM  +W+
Sbjct: 140 KSENVHPALSTRPDLLRFVASMPSHMKISWN 170


>gi|291536218|emb|CBL09330.1| ribosomal small subunit pseudouridine synthase A [Roseburia
           intestinalis M50/1]
          Length = 235

 Score = 74.2 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 49/245 (20%), Positives = 89/245 (36%), Gaps = 49/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +   ++K +RSG V V+ + VK                        
Sbjct: 1   MRLDKLLTELGTG-SRSEVKKYIRSGLVTVNGEVVKK----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQK+ + +  +    + L     Y + + Y+F+KPAG      +         +    D
Sbjct: 37  PEQKVDEKNDTVCFRGNPLT----YTEYEYYLFHKPAGCVT---ATEDNLHRTVMDYLTD 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +         RLD +T G+L++    A A  L      + + K+Y++ + G    +    
Sbjct: 90  TARHDLFPVGRLDIDTEGLLLITNDGALAHDL--LSPAKHVSKVYYAKIDGRVTEE---- 143

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L K     G+        EK A  A+   +V+   +     + +    GR HQ++  
Sbjct: 144 DVNLFKNGVDIGE--------EKPAKPAL--LEVL--HSGDNSEIRLTITEGRFHQVKRM 191

Query: 259 ALHMG 263
              +G
Sbjct: 192 FEAVG 196


>gi|148667046|gb|EDK99462.1| mCG132976, isoform CRA_b [Mus musculus]
 gi|219519715|gb|AAI44734.1| Rpusd3 protein [Mus musculus]
          Length = 279

 Score = 74.2 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 36/180 (20%), Positives = 75/180 (41%), Gaps = 13/180 (7%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQK 143
            ++ L + +  L++ ++ +   +   NKP G+ V G  G    +     L   +  + Q+
Sbjct: 61  ENLGLEELAHVLRAAVVDQKGPLVTLNKPQGLPVTGRPGELTLLSVLPQLSQALGLEHQE 120

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKECIA 199
            ++     +E SG+++++     A  L +    S R +R    Y ++  GIP+  +  + 
Sbjct: 121 LQVVRAPGKEASGLVLLSSCPQTASRLQKFFIHSRRAQRPTATYCAVTDGIPEPSEGTVC 180

Query: 200 NWLLKKSHIGGDYVHVV-----KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR-TH 253
             L  +     D    V     K  ++G    +S F V+    +    +++QP T   TH
Sbjct: 181 MPLKMEQMNDVDLAVPVMSPSRKDIQEGVKRTLSRFHVMAT-GRGCALVQLQPLTAAGTH 239


>gi|325568269|ref|ZP_08144636.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158038|gb|EGC70191.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           casseliflavus ATCC 12755]
          Length = 250

 Score = 74.2 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 95/249 (38%), Gaps = 52/249 (20%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLD++  +   + +   ++++++ G V V+ + +K +                     
Sbjct: 11  PMRLDKFLAD-MGYGSRKEVKQLIKKGLVTVNGQVIKSD--------------------- 48

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             + ++L++   +    +     ++Y+    Y+ NKPAG+     S      +  +    
Sbjct: 49  --KAQVLETQDTVCFEGEP----IVYQSQFYYLLNKPAGVI----SATVDSYEETVLDLF 98

Query: 138 DSKG--QKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             +   +      RLD++T G L++      A Q L+     + ++K Y++ V GI   +
Sbjct: 99  SEEAFREDLFPVGRLDKDTEGFLLITNDGGLAHQLLS---PKKHVEKEYYAQVEGIMTAE 155

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            +               +   +K + +    A      +D   +    +++  H G+ HQ
Sbjct: 156 DQ-------------KTFAKGIKLDGEWTLPAELQILNVD-EDETRSEIKLILHEGKFHQ 201

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 202 VKRMVHAVG 210


>gi|154341671|ref|XP_001566787.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134064112|emb|CAM40306.1| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 452

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 38/159 (23%), Positives = 59/159 (37%), Gaps = 23/159 (14%)

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE 220
           A      + L+E+     +  +   +  G      E +   ++ +   G     +V +  
Sbjct: 233 AVEDLIYRTLSENAASHSVINVDLPV--GYDSTDPEHLRMAVMAEHSRGAKTSLLVLKRT 290

Query: 221 --KGANYAISHFKVIDCFAQKF--------CWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
                  A S  +  D   Q F          + + PHTGR HQLRVH   +G PIVGD 
Sbjct: 291 YLAAPPPAESEAQSCDTLTQGFASATRYPVTLVLLAPHTGRRHQLRVHCRAIGFPIVGDT 350

Query: 271 KYCANFKGNFTSPI-----------QNKLYLHARYMDLP 298
            YC +       P+             ++YLHA  + LP
Sbjct: 351 LYCTDLPWCAALPLGPSASTWTTVEARRMYLHAWRLLLP 389



 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/103 (28%), Positives = 41/103 (39%), Gaps = 19/103 (18%)

Query: 108 IYVFNKPAGISV------------------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + V NKP GI +                      GI       L+     K Q  +  H+
Sbjct: 1   MLVVNKPPGIPMGGDEAIYGRTIESLAYDYMKARGIFDEAHEQLQQARKRKKQ-LKFVHQ 59

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           LD  TSG+L +A T+  A  L   F MR ++K Y +L+ G   
Sbjct: 60  LDFGTSGVLCLAFTKDMAARLAHCFEMRTVRKYYIALLHGHVP 102


>gi|297161649|gb|ADI11361.1| putative pseudouridine synthase [Streptomyces bingchenggensis
           BCW-1]
          Length = 333

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 42/279 (15%), Positives = 88/279 (31%), Gaps = 55/279 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V V+ K V                    
Sbjct: 92  AEQEGERLQKVLARAGMG-SRRACEELIDQARVEVNGKIVT-----------------EQ 133

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              +  E+  +           +L           +  NKPAG+             G  
Sbjct: 134 GLRVDPEKDEIKVDGLTVATQSYL----------FFALNKPAGVVSTMEDPDGRQCLG-- 181

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET GI+++      +  LT   R    +    ++   +P++
Sbjct: 182 -DYVTNRETRLFHVGRLDTETEGIILLTNHGELSHRLTHP-RYGVTKTYLAAIQGPLPRD 239

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + + + +  +                       HF+V+    + +  +E+  H GR H
Sbjct: 240 LGKRLKDGIQLEDGYARAD----------------HFRVVQNTGKNY-LVEVSLHEGRKH 282

Query: 254 QLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
            +R      G P+  D      +     G+  S    +L
Sbjct: 283 IVRRMLAEAGFPV--DKLVRTAFGPIALGDQKSGWLRRL 319


>gi|225017146|ref|ZP_03706338.1| hypothetical protein CLOSTMETH_01071 [Clostridium methylpentosum
           DSM 5476]
 gi|224950065|gb|EEG31274.1| hypothetical protein CLOSTMETH_01071 [Clostridium methylpentosum
           DSM 5476]
          Length = 248

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 33/248 (13%), Positives = 80/248 (32%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQS-GQVVRIPPVINALNH 76
           +R+D++             +++LR+G+V V+   VK  + ++   G  +R+   +     
Sbjct: 3   IRIDKFLSTQAI-ATRSQAKEMLRAGRVLVNGTPVKAADLKVDPEGDEIRVDGRVYG--- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                     Y++    + NKP G+       +   +   +   
Sbjct: 59  --------------------------YQEHLYLMLNKPQGVVSATDDKVHRTVLDLVPPE 92

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +  +G       RLD++T G +++      A   L+                  +PK  +
Sbjct: 93  LRRRG--LFPAGRLDRDTVGFVLITDDGEFAHNILSPRHH--------------VPKTYE 136

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +   + +          V+    K     ++  +  +        +++    GR HQ+
Sbjct: 137 AGLDGPIGENELSVLAQGVVLGDGTKCRPAELTVLQSGERP-----LIQIVIVEGRYHQI 191

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 192 KRMFAAVG 199


>gi|293379060|ref|ZP_06625213.1| pseudouridylate synthase [Enterococcus faecium PC4.1]
 gi|292642339|gb|EFF60496.1| pseudouridylate synthase [Enterococcus faecium PC4.1]
          Length = 239

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 88/248 (35%), Gaps = 51/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++ +++ G + V+ + VK           ++    + + +  
Sbjct: 1   MRLDKFLADMGLG-SRKEVKGLIKKGTIEVNGQVVKS-------DKTQVNEFEDTVTY-- 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                             L  I+ Y+    Y+ +KPAG+           +   LK    
Sbjct: 51  ------------------LGEIIAYQKDFYYILHKPAGVISATQDNHDQTVIDLLKD--Q 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              +      RLD++T G+L++      A Q L+     + ++K Y + V GI   +   
Sbjct: 91  DYREDLFPVGRLDKDTEGLLILTNDGIFAHQLLS---PKKHVEKEYLAEVSGIMTEEDIR 147

Query: 198 I--ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           +     ++            + Q ++ +  +I               + +  H G+ HQ+
Sbjct: 148 LFAEGLIIDGDEQTLPAKLQIDQVDQESETSI---------------IRLILHEGKFHQV 192

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 193 KRMVKAVG 200


>gi|167720582|ref|ZP_02403818.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
          pseudomallei DM98]
          Length = 88

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 15/58 (25%), Positives = 28/58 (48%)

Query: 6  YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           V  + ++      R+D +       +   ++ +ILRSG+VRV+K R+    R+  G 
Sbjct: 16 QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGD 73


>gi|331697591|ref|YP_004333830.1| pseudouridine synthase Rsu [Pseudonocardia dioxanivorans CB1190]
 gi|326952280|gb|AEA25977.1| pseudouridine synthase Rsu [Pseudonocardia dioxanivorans CB1190]
          Length = 252

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 45/280 (16%), Positives = 93/280 (33%), Gaps = 55/280 (19%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
              + + +RL +         +    ++++ +G+V VD + V+                 
Sbjct: 2   TTQNSDGVRLQKVLAQA-GVASRRAAEELIAAGRVSVDGEIVR----------------- 43

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  +  + +D    +         I+L +D      NKP G+             G
Sbjct: 44  -------EMGRRVDPDTAVVHV--DGSRIVLRDDLVYLALNKPRGMLSTMSDDRGRECVG 94

Query: 132 FL---KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
            L   ++ + ++  +     RLD +T G+L++         L        +QK Y + V 
Sbjct: 95  DLVADRAELLNQAGRLFHVGRLDADTEGLLLLTNDGELGHRL--MHPSFEVQKTYVAEVA 152

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        +A  + K+   G +         +     +  F+++D        +E+  H
Sbjct: 153 GQ-------VARDVGKRLRTGVEL--------EDGPVVVHSFRLVDSSG-GRSMVEIVLH 196

Query: 249 TGRTHQLRVHALHMGCPIV-------GDHKYCANFKGNFT 281
            GR H +R     +G P++       GD +      G   
Sbjct: 197 EGRKHVVRRLMDEVGYPVLRLVRTAIGDVRLGDQRPGKLR 236


>gi|227892643|ref|ZP_04010448.1| pseudouridylate synthase [Lactobacillus ultunensis DSM 16047]
 gi|227865514|gb|EEJ72935.1| pseudouridylate synthase [Lactobacillus ultunensis DSM 16047]
          Length = 233

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 27/176 (15%), Positives = 62/176 (35%), Gaps = 35/176 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   + ++++ G V V+ + VK    ++     V +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHQLIKKGIVSVNGQTVKTPKEKVAETDEVTVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  ++Y+    ++ NKP G+           +   L   +
Sbjct: 51  --------------------GEKIVYQKYHYFLMNKPKGVLSATEDRSQRTVISLLD--L 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             + Q      RLD++T+G+L++         L      + + K+Y + + G+   
Sbjct: 89  KDQYQGIVPVGRLDKDTTGLLLLTNDGQLNHEL--LAPNKHVAKVYRAKIAGVADE 142


>gi|317055194|ref|YP_004103661.1| pseudouridine synthase [Ruminococcus albus 7]
 gi|315447463|gb|ADU21027.1| pseudouridine synthase [Ruminococcus albus 7]
          Length = 246

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 40/289 (13%), Positives = 95/289 (32%), Gaps = 53/289 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD+   + +  I+  +++K+    ++ V+ K   + + ++ +   + I          
Sbjct: 5   MRLDKLVASQFADISRADVKKLCLKKKIMVNGKLMARSDAKVDTDDEIIIDGRKLT---- 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                    Y+     + NKPAG+      G +  +   +   +
Sbjct: 61  -------------------------YKKHIYIMLNKPAGVVCSTKEGASTTVLDLVPDEL 95

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              G       RLD++T G +++      + + L+   +    +  +  L      + K+
Sbjct: 96  RRDG--LFPAGRLDKDTEGFVLITDDGELSHRVLSP--KTHVPKTYFVRLEKPWEDSYKD 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +A  +       GD       +E+    A           +  C   +  H G+ HQ++
Sbjct: 152 IMAAGMTIDGLHEGD-------SEEKCQPAQ-----FLASDENVCECTLIIHEGKFHQVK 199

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
                +G  +V    Y             ++       +++ H +  +L
Sbjct: 200 RMFEKLGNKVV----YLKRVA--IGEMPLDRGLELGECLEIMHKDVEKL 242


>gi|331091189|ref|ZP_08340030.1| hypothetical protein HMPREF9477_00673 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330404636|gb|EGG84175.1| hypothetical protein HMPREF9477_00673 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 234

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 49/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++K +R G++ VD K                         + 
Sbjct: 2   MRLDKYLCEMNVG-SRSEVKKYIRQGRITVDGKTA-----------------------VK 37

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+KI + S  +   S     ++ YE  + Y+  KP+G+     +         L    +
Sbjct: 38  PEEKIDEHSQKVCVDS----RVIGYEAFEYYMLYKPSGVVS---ATTDRKEKTVLDLIEE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K +      RLD++T G+L++      A  L      + + K+Y++ + G    ++  I
Sbjct: 91  KKRKDLFPVGRLDKDTEGLLLITNDGEMAHRL--LSPKKHVDKVYYAKIDGKVTEREVQI 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            +  L               N++ A    S  K++         +E+    G+ HQ++  
Sbjct: 149 FSEGL------------SIGNDEYAKP--SALKILK--EGNISEIELTIQEGKFHQVKRM 192

Query: 259 ALHMG 263
              +G
Sbjct: 193 FHAVG 197


>gi|210615570|ref|ZP_03290668.1| hypothetical protein CLONEX_02886 [Clostridium nexile DSM 1787]
 gi|210150237|gb|EEA81246.1| hypothetical protein CLONEX_02886 [Clostridium nexile DSM 1787]
          Length = 240

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 89/247 (36%), Gaps = 53/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +         ++K++R G+V VD    K   R      + I           
Sbjct: 8   IRLDKYLADMGVG-TRTEVKKLIRQGKVTVDGSIEKSPER-----KIDIS---------- 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                        +    +   + YE  + Y+ NKPAG+     +         ++    
Sbjct: 52  ------------HQKVCCMGEAVSYETHEYYMLNKPAGVVS---ATTDRQDKTVVELISS 96

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K +      RLD++T G+L++      A + L+     + + K+Y++ V GI     + 
Sbjct: 97  KKRRDLFPVGRLDKDTEGLLLITNDGELAHRLLS---PKKHVDKVYYAKVQGIVDEVDQE 153

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAI-SHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           I                 V  +      A+ S  +++  ++ +   + +    G+ HQ++
Sbjct: 154 I---------------FAVGMSIGNGETALPSKLEIL--YSGEISEIRVTIQEGKFHQVK 196

Query: 257 VHALHMG 263
                +G
Sbjct: 197 RMFHAVG 203


>gi|213621035|ref|ZP_03373818.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 80

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 4/80 (5%)

Query: 251 RTHQLRVHALHMGCPIVGDHKYCA---NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQ 306
           RTHQ+RVH  + G PI  D +Y     + +         +L+LHA  +   HP  G  ++
Sbjct: 1   RTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTEAGTGLKRLFLHAAALKFTHPGTGDVMR 60

Query: 307 ITAPLPAHMVKTWDSLGFKY 326
           I AP+   + +  + L  K 
Sbjct: 61  IEAPMDKQLKRCLEVLRSKA 80


>gi|313672604|ref|YP_004050715.1| pseudouridine synthase [Calditerrivibrio nitroreducens DSM 19672]
 gi|312939360|gb|ADR18552.1| pseudouridine synthase [Calditerrivibrio nitroreducens DSM 19672]
          Length = 254

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 50/251 (19%), Positives = 87/251 (34%), Gaps = 40/251 (15%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
               Y +I+    +K L+  +V    K VK +  +               +  + E    
Sbjct: 7   ISKQY-NISKRLAKKYLKERRVSYQGKIVKDDYIV-----------DQFDDKFVLEVSCP 54

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           D   NL       K  LL +   I  F KP  +  +            L   ++++ +  
Sbjct: 55  DIDFNL-------KDFLLDDLGDIIFFYKPPFMHTERHKPTDELC---LSDILNNEFKDF 104

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R   RLD ET G++   +T          ++  ++ K Y + V GI     E I   +  
Sbjct: 105 RFISRLDFETDGVIAAIKT---------GYQPVKVHKRYRAWVKGIL---NEII---IFD 149

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           K         V   +EKG N      K +  +   +  +++       HQ+R    ++  
Sbjct: 150 KKIDANKRKKVSIIDEKGDN--FLRIKPVKHYT-FYTLVDVGIDFAHRHQIRAALSYLNF 206

Query: 265 PIVGDHKYCAN 275
           PI+GD  Y   
Sbjct: 207 PILGDKLYGDG 217


>gi|331265615|ref|YP_004325245.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           oralis Uo5]
 gi|326682287|emb|CBY99904.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           oralis Uo5]
          Length = 240

 Score = 73.5 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 87/245 (35%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q                I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQ----------------ID 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E+  +           F   +L YE+   Y+ NKP G+           +   L  +  
Sbjct: 43  EERDEI----------RFDGQVLEYEEFVYYMMNKPQGVISATEDPKHRTVLDLLDDYAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +K  +     RLD +T G+L++      A  L      R + K Y + V GI   +    
Sbjct: 93  AK--EVFPVGRLDIDTHGLLLLTNDGQLAHAL--LSPKRHVDKTYLAQVEGIMSQEDVET 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     A   F  +D   +    + +    G+ HQ++  
Sbjct: 149 -------------FAKGIPLKDFTCQPAKLEFVSVD-PEKNQSLVRVTIAEGKFHQVKRM 194

Query: 259 ALHMG 263
               G
Sbjct: 195 VAFCG 199


>gi|225174838|ref|ZP_03728835.1| pseudouridine synthase [Dethiobacter alkaliphilus AHT 1]
 gi|225169478|gb|EEG78275.1| pseudouridine synthase [Dethiobacter alkaliphilus AHT 1]
          Length = 242

 Score = 73.5 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 80/250 (32%), Gaps = 50/250 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL ++       + +    +K++ SG+V V+  RV                       +
Sbjct: 3   IRLQKFLS--MAGVCSRRAGEKLIESGRVTVNGSRVTA-----------------MGVTV 43

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E  +++      K     + ILLY+        K                   +K  V
Sbjct: 44  DPENDVVEVDGRRVKVQQNNEYILLYKPVGYVTTLKDEF------------GRPTVKELV 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD +TSG+L++      A  LT       ++K Y + V   PK +   
Sbjct: 92  ADIKTRVYPVGRLDLDTSGLLLLTNDGELANQLTHPSFG--VEKEYLAKVHDTPKKEALE 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I    ++                     A +  +++    +    + +    GR  Q+R 
Sbjct: 150 ILAKGVRLD---------------DGMTAPAKVQLVKS-GRLTSVVSLIIKEGRNRQVRR 193

Query: 258 HALHMGCPIV 267
               +G P+V
Sbjct: 194 MLEAVGHPVV 203


>gi|295398834|ref|ZP_06808828.1| ribosomal small subunit pseudouridine synthase A [Aerococcus
           viridans ATCC 11563]
 gi|294972924|gb|EFG48757.1| ribosomal small subunit pseudouridine synthase A [Aerococcus
           viridans ATCC 11563]
          Length = 258

 Score = 73.5 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 83/249 (33%), Gaps = 44/249 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD++  +  P  +  +++ +++   + V+    K     +  Q V +           
Sbjct: 11  QRLDKFVSSMTP-YSRSDVKTLIKKSAIYVNGSVAK-----KPNQPVNVT---------- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E K+           +     L+YE     + +KP G+           +   L   + 
Sbjct: 55  -EDKV-----------EVDGQELVYEPYVYIMMHKPDGVISATEDNRWETVIDLLPEDLI 102

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              Q P    RLD++T+G+L++         L      + ++K Y  LV G         
Sbjct: 103 LTYQ-PFPVGRLDKDTTGLLLITNDGQFNHAL--MAPKKHVEKEYAVLVDG--------- 150

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              LL   HI      +     +    A      +D  A       +    G+ HQ++  
Sbjct: 151 ---LLSDKHIDQFEKGLDIGQGEKTKPAQLFIDQVDEEA-GQSLARVVIAEGKYHQVKRM 206

Query: 259 ALHMGCPIV 267
              + C +V
Sbjct: 207 FHAVDCEVV 215


>gi|167816775|ref|ZP_02448455.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
          pseudomallei 91]
          Length = 89

 Score = 73.5 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 15/58 (25%), Positives = 28/58 (48%)

Query: 6  YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           V  + ++      R+D +       +   ++ +ILRSG+VRV+K R+    R+  G 
Sbjct: 16 QVSLIEIDESAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRIDAQYRLAFGD 73


>gi|255016964|ref|ZP_05289090.1| hypothetical protein LmonF_02463 [Listeria monocytogenes FSL
           F2-515]
          Length = 133

 Score = 73.5 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 26/137 (18%), Positives = 53/137 (38%), Gaps = 21/137 (15%)

Query: 45  QVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY 103
            V ++ K +  +N  +  G  + +P  ++    + +                     ++Y
Sbjct: 4   NVLLNNKPLDDWNTPLFVGASLSLPIFLHDKIPVYE-----------------YDLEIIY 46

Query: 104 EDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRL--THRLDQETSGILVV 160
           ED  + V NKP  +      S         ++ +++  GQ       HRLDQ TSG+++ 
Sbjct: 47  EDDFLLVVNKPVDMKTHPNDSYETDTCANAVQYYLEKTGQDANALAVHRLDQTTSGLVLF 106

Query: 161 ARTRAAAQHLTESFRMR 177
           A+ + A   L+     +
Sbjct: 107 AKNKLAIAGLSWQMENK 123


>gi|315038031|ref|YP_004031599.1| 16S pseudouridylate synthase [Lactobacillus amylovorus GRL 1112]
 gi|325956483|ref|YP_004291895.1| 16S pseudouridylate synthase [Lactobacillus acidophilus 30SC]
 gi|312276164|gb|ADQ58804.1| 16S pseudouridylate synthase [Lactobacillus amylovorus GRL 1112]
 gi|325333048|gb|ADZ06956.1| 16S pseudouridylate synthase [Lactobacillus acidophilus 30SC]
 gi|327183311|gb|AEA31758.1| 16S pseudouridylate synthase [Lactobacillus amylovorus GRL 1118]
          Length = 236

 Score = 73.5 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 86/249 (34%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  +++ G V V+   VK    +++    V +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQE------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   LK   
Sbjct: 54  -----------------------INYQKYHYFLMNKPKGVLSATEDRSQRTVISLLKPQD 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +G  P    RLD++T+G+L++         L      + + KIY + + G+  ++   
Sbjct: 91  QYQGITP--VGRLDKDTTGLLLLTNDGQLNHKL--LAPNKHVDKIYRAKIAGVADDETVK 146

Query: 198 IANW---LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           I      L   + +    + ++ Q+E+                     +E++   G+ HQ
Sbjct: 147 IFASGMTLGDSTKLKPAELKILSQDEE----------------HDSSEIEIRIREGKYHQ 190

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 191 IKRMFGAVG 199


>gi|167563551|ref|ZP_02356467.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
          oklahomensis EO147]
          Length = 91

 Score = 73.5 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 16/58 (27%), Positives = 29/58 (50%)

Query: 6  YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           V  + +++     R+D +       +   ++ +ILRSG+VRV+K RV    R+  G 
Sbjct: 16 QVSLIEIDDGAAGQRIDNFLLRVCKGVPKSHIYRILRSGEVRVNKGRVDAQYRLAHGD 73


>gi|292558985|gb|ADE31986.1| Pseudouridine synthase, Rsu [Streptococcus suis GZ1]
          Length = 245

 Score = 73.5 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELGTVIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V G+   + 
Sbjct: 86  LLPTVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYLARVKGVANKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
             +   L +           V  + K    A+  +++I     +    +E+  H GR HQ
Sbjct: 143 --VLRPLTRG----------VVIDGKKTKPAV--YEIIKVDPVKNRSVVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|258591956|emb|CBE68261.1| Uncharacterized RNA pseudouridine synthase aq_1464 (RNA-uridine
           isomerase) (RNA pseudouridylate synthase) [NC10
           bacterium 'Dutch sediment']
          Length = 282

 Score = 73.5 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 81/251 (32%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVRIPPVINALNH 76
            RL R+        +  + ++++  G+VRV+ +   +   ++  G   V         + 
Sbjct: 25  ERLQRYLARAGLG-SRRSCEQLILDGRVRVNGRIASQLGTKVSPGLDTVTCDHKPVTSSQ 83

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            +                               + +KPAG+           + G L   
Sbjct: 84  SL----------------------------HYLILHKPAGVLTSLSDPRGRPVIGDL--L 113

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                 +     RLD +T G++++      A  L        ++K Y + V G P     
Sbjct: 114 PPRGLPRLFPVGRLDYQTEGLVLLTNDGVLAHGL--MHPSFEVEKEYLAKVRGCPTPDD- 170

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                      +      VV + EK      +H  ++        WL++  H GR H++R
Sbjct: 171 -----------LARLKAGVVSEGEK---LWATHAAIVK-PGIGSAWLKLIVHQGRYHEIR 215

Query: 257 VHALHMGCPIV 267
                +G P++
Sbjct: 216 RMCDAIGHPVL 226


>gi|322411180|gb|EFY02088.1| hypothetical protein SDD27957_02020 [Streptococcus dysgalactiae
           subsp. dysgalactiae ATCC 27957]
          Length = 240

 Score = 73.5 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 85/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +  +   ++SG VV I          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTLNGQVITDSATTVKSGDVVEIE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                S +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVLD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD  TSG+L++         +        I K+Y + V GI   + 
Sbjct: 86  LLPQVKERIYPVGRLDWNTSGVLILTNDGDFTDTM--IHPRNEIDKVYLARVKGIATKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                               V  + K    A   + +I   A      +E+  H GR HQ
Sbjct: 144 L-------------RPLTRGVVIDGKKTKPA--RYNIIRVEADKNRSIVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFESVG 197


>gi|38233785|ref|NP_939552.1| putative pseudouridine synthase B [Corynebacterium diphtheriae NCTC
           13129]
 gi|38200046|emb|CAE49722.1| Putative pseudouridine synthase B [Corynebacterium diphtheriae]
          Length = 321

 Score = 73.5 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 50/256 (19%), Positives = 91/256 (35%), Gaps = 49/256 (19%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVRIPPV 70
           +   E +RL +         +  + + ++ +G+V V+ K V     R+     V+R+  V
Sbjct: 75  DGSTEGIRLQKVLAQA-GVASRRHAEILIDAGRVEVNGKIVMTQGMRVNPNVDVIRVDGV 133

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
              +N                            E+ + +V NKP G+       +     
Sbjct: 134 RVNVN----------------------------ENLQYFVLNKPRGLQSTMSDDMGRPCV 165

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G +     S GQ+     RLD  T G+L++      A  L        + K Y + V G 
Sbjct: 166 GDIVGERISAGQRLFHVGRLDAATEGLLLLTNDGELANRL--MHPRYEVSKTYLATVLGE 223

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              +       L+K+   G +       ++  A   +   ++ID F Q    + ++ H G
Sbjct: 224 ADKR-------LVKQLRDGIEL------DDGPAKADL--VQIIDTF-QGKSLIRIELHEG 267

Query: 251 RTHQLRVHALHMGCPI 266
           R H +R      G P+
Sbjct: 268 RKHIVRRMLKTAGFPV 283


>gi|410137|gb|AAA67493.1| ORFX13 [Bacillus subtilis subsp. subtilis str. 168]
          Length = 229

 Score = 73.5 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 47/250 (18%), Positives = 84/250 (33%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +++++ G+V+V+ K V     ++     + +          
Sbjct: 2   ERLQKVIA-HAGVASRSKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKS 135
                       L    +     LLY         KP G+    Q   G        +  
Sbjct: 52  -----------GLKVEREEPVYFLLY---------KPRGVISAAQDDKGRK-----VVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +  +  Q+     RLD +TSG+L++      A  L        I K Y + V GIP  + 
Sbjct: 87  FFKNIPQRIYPIGRLDYDTSGLLLLTNDGEFANKL--MHPKYEIDKTYVAKVKGIPPKE- 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQ 254
                 LL+K   G           +    A +  K++    +K    +++  H GR  Q
Sbjct: 144 ------LLRKLERGIRL--------EEGKTAPAKAKLLSLDKKKQTSIIQLTIHEGRNRQ 189

Query: 255 LRVHALHMGC 264
           +R     +G 
Sbjct: 190 VRRMFEAIGH 199


>gi|254796538|ref|YP_003081374.1| ribosomal large subunit pseudouridine synthase D [Neorickettsia
           risticii str. Illinois]
 gi|254589775|gb|ACT69137.1| ribosomal large subunit pseudouridine synthase D [Neorickettsia
           risticii str. Illinois]
          Length = 126

 Score = 73.5 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 30/110 (27%), Positives = 53/110 (48%), Gaps = 8/110 (7%)

Query: 79  KEQKILDSSVNLTKHSDFLKS-ILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSW 136
           +E  +LD  +       F++   + YED  + V +KPAG+ V  G G     +   L+  
Sbjct: 11  EEYHLLDLPLEQKPRHAFVQPLDVRYEDDSLLVIHKPAGLVVHPGIGNKEQTLVNILEHH 70

Query: 137 VDSK------GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             ++        +P + HRLD++T+G L+VA+T  +   L+E  +   I 
Sbjct: 71  YPTEQLSNLDSSRPGIVHRLDKDTAGFLIVAKTNPSHVRLSEMIKEGVIH 120


>gi|195978740|ref|YP_002123984.1| ribosomal large subunit pseudouridine synthase B RluB
           [Streptococcus equi subsp. zooepidemicus MGCS10565]
 gi|195975445|gb|ACG62971.1| ribosomal large subunit pseudouridine synthase B RluB
           [Streptococcus equi subsp. zooepidemicus MGCS10565]
          Length = 266

 Score = 73.5 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 86/250 (34%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + V      ++SG +V I          
Sbjct: 27  MRINKYIA-HAGVASRRKAEELIKRGLVTLNGQVVTDLATTVKSGDLVEIE--------- 76

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                S +  E+   Y+ NKP G+  SV    G    ID     
Sbjct: 77  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDDKGRQTVID----- 111

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG+L++         +        I K+Y + V G+   + 
Sbjct: 112 LLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDKM--IHPRNEIDKVYLARVKGVVTKES 169

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                               V  + K    A   +++I          +E+  H GR HQ
Sbjct: 170 L-------------RPLTRGVVIDGKKTKPA--RYRIIRVEPDKNRSIVELTIHEGRHHQ 214

Query: 255 LRVHALHMGC 264
           ++     +G 
Sbjct: 215 VKKMFEAVGH 224


>gi|315172332|gb|EFU16349.1| conserved hypothetical protein [Enterococcus faecalis TX1346]
          Length = 238

 Score = 73.1 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 94/253 (37%), Gaps = 58/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++  G+V+V+ + VK    ++     V +  V       
Sbjct: 2   ERLQKAIA-HAGVTSRRKAEELIVKGRVKVNGQVVKELGTQVSKQDTVEVDGVP------ 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSK-IYVFNKPAGI--SVQGGSGIAYHIDGFLK 134
                                   +Y++    Y+F KP G+  +V    G        + 
Sbjct: 55  ------------------------IYQEEYGYYLFYKPRGVISAVSDDKGRK-----VVT 85

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +     ++     RLD +TSG+L++    + +Q LT       + K+Y + + G+P  +
Sbjct: 86  DYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQKLT--HPKHEVDKVYVAKIKGVPTKR 143

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTH 253
                  L+K   I G               A ++F+++    +     +E+  H GR H
Sbjct: 144 DLL---PLVKGIRIDGKR------------TAPANFQILSADIKTGSSVVELTIHEGRNH 188

Query: 254 QLRVHALHMGCPI 266
           Q++     +G P+
Sbjct: 189 QVKKMFQAVGFPV 201


>gi|109127127|ref|XP_001118548.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Macaca mulatta]
          Length = 213

 Score = 73.1 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 33/164 (20%), Positives = 66/164 (40%), Gaps = 17/164 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP---------RLTHRLD 151
           ++Y      V NK   + +      A+     L+  +  +  +          R  H+LD
Sbjct: 11  IVYRSRDFLVVNKHWDVRI---DSKAWRETLTLQKQLRHRFPELADPDTCYGFRFCHQLD 67

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG L VA  +AAA      F+ RR+ K Y +L+ G  +  +  I++ + +    G  
Sbjct: 68  FSTSGALCVALNKAAAGSAYRCFKERRVTKAYLALLRGHIQESRVTISHAIGRNGTEGRA 127

Query: 212 YVHVVK--QNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTG 250
           +   ++  Q  +    +++   V++           + ++P TG
Sbjct: 128 HTMCIEGTQGCENPKPSLTELVVLEHGLYAGDPVSKVLLKPLTG 171


>gi|307267525|ref|ZP_07549006.1| pseudouridine synthase [Thermoanaerobacter wiegelii Rt8.B1]
 gi|326391079|ref|ZP_08212626.1| pseudouridine synthase [Thermoanaerobacter ethanolicus JW 200]
 gi|306917457|gb|EFN47750.1| pseudouridine synthase [Thermoanaerobacter wiegelii Rt8.B1]
 gi|325992864|gb|EGD51309.1| pseudouridine synthase [Thermoanaerobacter ethanolicus JW 200]
          Length = 236

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 85/250 (34%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    ++ +  G+V+V+ K VK                      I 
Sbjct: 2   ERLQKYLAE-CGIASRRKCEEYILQGRVKVNGKVVK-----------------ELGVKIN 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            +  I++    + +       I+L         NKP G I+          +   +K   
Sbjct: 44  PDVDIIEFDDKIVRREKKKVYIML---------NKPTGYITSVKDQFGRPTVMDLVKV-- 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  L        I K Y + + GIP  ++  
Sbjct: 93  ---KERIYPVGRLDYDTSGLLLLTNDGEIANIL--MHPRHEIVKTYIAKIKGIPTQEELE 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                 +   + GDY+    + E            I         +E++ H G+  Q+R 
Sbjct: 148 ----RFRNGLLIGDYLTSKAEIE------------ILAVKNGTSVVEIKIHEGKNRQVRR 191

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 192 MCEAIGHPVI 201


>gi|302550431|ref|ZP_07302773.1| pseudouridine synthase [Streptomyces viridochromogenes DSM 40736]
 gi|302468049|gb|EFL31142.1| pseudouridine synthase [Streptomyces viridochromogenes DSM 40736]
          Length = 372

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 42/279 (15%), Positives = 93/279 (33%), Gaps = 55/279 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            ++E  RL +         +    ++++   +V ++ + V                    
Sbjct: 131 AEQEGERLQKVLARAGFG-SRRACEELIEEARVEINGEIV-------------------- 169

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
               +++ + +D   +  K      +   Y+    +  NKPAG+             G  
Sbjct: 170 ----LEQGRRVDPEKDEIKVDGLTVATQSYQ---FFSLNKPAGVVSTMEDPEGRQCLG-- 220

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +V ++  +     RLD ET G++++      A  LT   +    +     +V  IP++
Sbjct: 221 -DYVTNRETRLFHVGRLDTETEGVILLTNHGELAHRLTHP-KYGVKKTYLAHIVGPIPRD 278

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + + + +  +                       HF+V+    + +  +E+  H GR H
Sbjct: 279 LGKQLKDGIQLEDGYARAD----------------HFRVVQQTGKNY-LVEVTLHEGRKH 321

Query: 254 QLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
            +R      G P+  D      +     G+  S    +L
Sbjct: 322 IVRRMLAEAGFPV--DKLVRVAFGPITLGDQKSGWLRRL 358


>gi|303232224|ref|ZP_07318923.1| pseudouridylate synthase [Atopobium vaginae PB189-T1-4]
 gi|302481634|gb|EFL44695.1| pseudouridylate synthase [Atopobium vaginae PB189-T1-4]
          Length = 375

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 81/254 (31%), Gaps = 38/254 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL R+        +    +K++ +G+V V+                             
Sbjct: 79  MRLQRYLAR-CGVASRRGAEKLISAGRVTVNGVV-------------------------- 111

Query: 79  KEQKILDSSVNLTKHSDFLK--SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
             Q +L S V+       +     +L ++    + NKP G+         +     L   
Sbjct: 112 --QDVLGSKVDCAHDVVCVDGTPCVLGDEHTYLILNKPQGVLTTMSDPFGHPCVAALV-- 167

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNK 194
                       RLD +T+G+L+ +        L        + K Y  L+ G      +
Sbjct: 168 PKDTYPGLFAVGRLDGDTTGLLLFSTDGNMGNRL--LHPSHHVWKTYVCLLQGSLTRAAQ 225

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYA-ISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           K+  A  +L        ++  +   +     A   H       A+ +    +    GR H
Sbjct: 226 KQLEAGIMLDDGPCAPSHITRLAPTDALCTLAPQCHILDGIPSARGYTICSISIREGRYH 285

Query: 254 QLRVHALHMGCPIV 267
           Q++     +GCP+V
Sbjct: 286 QVKRMFDAVGCPVV 299


>gi|227513314|ref|ZP_03943363.1| pseudouridylate synthase [Lactobacillus buchneri ATCC 11577]
 gi|227083515|gb|EEI18827.1| pseudouridylate synthase [Lactobacillus buchneri ATCC 11577]
          Length = 241

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 51/276 (18%), Positives = 86/276 (31%), Gaps = 54/276 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +K++  G V+V+ K VK    ++     V +          
Sbjct: 3   ERLQKVMA-HAGVASRRKAEKLIVEGHVKVNGKVVKELGTKVTESDEVEVD--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       +    +     LLY         KP G+          H    +   +
Sbjct: 53  -----------EVPISKEVPVYYLLY---------KPRGVIT--AVTDDKHRKTVI-DLL 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++        HLT       + K Y + V G        
Sbjct: 90  SEVTERIYPVGRLDYDTSGLLLLTNDGDLDNHLT--HPKYEVDKTYVAKVKG-------T 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I N  +KK   G   +H+  +    A         I         + +  H GR HQ++ 
Sbjct: 141 ITNDDMKKLRTG---IHIDGRKTASAKA------TIIRNNNNSTIVSLTIHEGRNHQVKK 191

Query: 258 HALHMGCPI--VGDHKYCANFKGNFTSPIQNKLYLH 291
             L +G P+  +    Y              +L  H
Sbjct: 192 MFLALGHPVEKLSRQSYGFLNLDGLQPGDYRRLKPH 227


>gi|325002515|ref|ZP_08123627.1| ribosomal large subunit pseudouridine synthase B [Pseudonocardia
           sp. P1]
          Length = 253

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 47/255 (18%), Positives = 88/255 (34%), Gaps = 48/255 (18%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +RL +         +    ++++  G+V+VD + V+                    
Sbjct: 6   DPDGVRLQKVLARA-GVASRRAAEELIAQGRVQVDGETVR-----------------EMG 47

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             I  E  +L        H D  +   L +D      NKP G+       +     G L 
Sbjct: 48  RRIDPETAVL--------HVDGARVT-LRDDQVYLALNKPVGLHSTMSDDLGRPCVGDLL 98

Query: 135 S---WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           +    + +  Q+     RLD +T G+L++         L        + K Y + V G  
Sbjct: 99  ADRVELMNSAQRLFHVGRLDADTEGLLLLTNDGELGHRL--MHPSYEVPKTYLAEVEGK- 155

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 IA  L ++   G +         +     +  FK++D    +   +++  H GR
Sbjct: 156 ------IARDLGRRLRDGIEL--------EDGIARVDAFKLVDAVPGRST-VQLILHEGR 200

Query: 252 THQLRVHALHMGCPI 266
            H +R     +G P+
Sbjct: 201 KHIVRRMLSEVGHPV 215


>gi|167758122|ref|ZP_02430249.1| hypothetical protein CLOSCI_00460 [Clostridium scindens ATCC 35704]
 gi|167664019|gb|EDS08149.1| hypothetical protein CLOSCI_00460 [Clostridium scindens ATCC 35704]
          Length = 246

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 89/247 (36%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +         +++ +R G+V +D    K                        
Sbjct: 7   IRLDKYLADMGIG-TRQEVKRYIRQGRVSIDGIPAKS----------------------- 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E KI + +  +T    F    + Y D + Y+ NKP+G+     +         +    D
Sbjct: 43  PETKIEEKARKIT----FDGREVDYADYEYYMLNKPSGVVS---ATEDARCTTVVDLIRD 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K +      RLD++T G+L++      + + L+     + + K Y++ V G    +   
Sbjct: 96  KKRKDLFPVGRLDKDTEGLLLITNDGQLSHRLLS---PKKHVDKTYYAKVAGKVTKE--- 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLR 256
                   +    + V++            +   V+D   +++   + +    G+ HQ++
Sbjct: 150 -------DAKAFREGVNI----GTEEKEEWTRPGVLDILKSEEVSEIRLTIQEGKYHQVK 198

Query: 257 VHALHMG 263
                +G
Sbjct: 199 RMFQAVG 205


>gi|238924043|ref|YP_002937559.1| 16S pseudouridylate synthase [Eubacterium rectale ATCC 33656]
 gi|238875718|gb|ACR75425.1| 16S pseudouridylate synthase [Eubacterium rectale ATCC 33656]
          Length = 250

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 42/257 (16%), Positives = 91/257 (35%), Gaps = 53/257 (20%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSG-QVVR 66
            V VE +   +RLD++            ++K++++GQ+ ++     K   ++ +    V 
Sbjct: 2   TVYVERNINMIRLDKFLSEMGLG-TRSEVKKLIKTGQIAINGTVAAKPETKVDTDADEVS 60

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +                                I+ Y+  + Y+FNKP+G      +   
Sbjct: 61  VN-----------------------------GRIVKYQRYEYYLFNKPSGCVS---ATCD 88

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
              D  +    D+         RLD +T G+L++    A +  L      + + K Y++ 
Sbjct: 89  NVHDTVMDYITDAVHDDLFPVGRLDIDTEGLLLITNDGALSHEL--LSPSKHVAKTYYAR 146

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           + G     +  + + +  K  I           EK    A    +++   +     +E+ 
Sbjct: 147 IDG-----EVTLDDIIRFKEGID-------IGEEKPTKPA----ELVIKKSGSVSEIELT 190

Query: 247 PHTGRTHQLRVHALHMG 263
              G+ HQ++     +G
Sbjct: 191 ITEGKFHQVKRMFEALG 207


>gi|313815672|gb|EFS53386.1| conserved domain protein [Propionibacterium acnes HL059PA1]
 gi|315099394|gb|EFT71370.1| conserved domain protein [Propionibacterium acnes HL059PA2]
          Length = 113

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 27/99 (27%), Positives = 39/99 (39%), Gaps = 2/99 (2%)

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +S I  +   +  +   G   A++   +I      +   E  P TGRTHQ+R+H   +G 
Sbjct: 2   RSRIIKERGILQAREVPGVPNAVTDIALIGEHG-GWGLYEASPRTGRTHQIRLHMQRLGA 60

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
           PIV D  Y             + L L A  M    P  G
Sbjct: 61  PIVNDPFY-PVVLDTPVDDFTHPLQLQAWRMGFTDPVTG 98


>gi|66824235|ref|XP_645472.1| pseudouridine synthase family protein [Dictyostelium discoideum
           AX4]
 gi|60473647|gb|EAL71588.1| pseudouridine synthase family protein [Dictyostelium discoideum
           AX4]
          Length = 316

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 28/104 (26%), Positives = 42/104 (40%), Gaps = 14/104 (13%)

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLE--------MQPHTGRTHQLRVHALHMGCPIVG 268
           K     A  + + +KV++    K    E        + P TGR HQLRVH L +G  IVG
Sbjct: 204 KNKSNPAKASQTSYKVLERGYLKINNDEYIPITKVMLFPKTGRRHQLRVHLLSIGHVIVG 263

Query: 269 DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
           D  Y             +++ LH+  + LP      + +    P
Sbjct: 264 DETYGPK------DSTIHRMMLHSWKLILPFKHRSHINVQCNDP 301



 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 25/128 (19%), Positives = 53/128 (41%), Gaps = 1/128 (0%)

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLD 151
                K   +Y D +  V NKP  +++   +G     +  ++++         R  +R+D
Sbjct: 15  PPTDPKYETIYLDKEYIVVNKPFDVNIDDETGERLTTVVKYIETEYPEHFGNVRFVNRID 74

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             TSG++VV+  + +     E F+ R   K Y ++V G  +  +  I   +   +     
Sbjct: 75  YATSGLVVVSFNKKSTTVAMELFQSRETSKTYLAIVHGHMEFDESIIDKPIQYDTSDENS 134

Query: 212 YVHVVKQN 219
           +   V ++
Sbjct: 135 FKMCVVED 142


>gi|301103159|ref|XP_002900666.1| RNA pseudouridylate synthase-like protein [Phytophthora infestans
           T30-4]
 gi|262101929|gb|EEY59981.1| RNA pseudouridylate synthase-like protein [Phytophthora infestans
           T30-4]
          Length = 458

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 27/126 (21%), Positives = 49/126 (38%), Gaps = 15/126 (11%)

Query: 199 ANWLLKKSHIGGDYVHVV-KQNEKGANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQ 254
              +++     G +  +V  + +  A  + +   V+       +    + ++P  GR HQ
Sbjct: 306 DAPVIEPHRSTGVFRMLVGTETDTAAKQSTTMCFVLGHAIYKGEPVTKVLLRPLNGRRHQ 365

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL-----PHPEGGRLQITA 309
           LR+H  H G PI GD  Y +            ++ LHA  + L        + G L   +
Sbjct: 366 LRLHMAHHGFPIAGDVTYGSQEDEA------PRMMLHAWRIWLRGRPADQKKYGDLYFES 419

Query: 310 PLPAHM 315
           P P  +
Sbjct: 420 PDPFDL 425



 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 31/111 (27%), Positives = 46/111 (41%), Gaps = 9/111 (8%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG--- 141
           D+     K  D L   +L  D    V NK   + + G        D  L+  +       
Sbjct: 51  DNERGGPKTQDQLHLRVLSRDEHFVVLNKGPDVRMDGA------FDVTLEKALARDFPQV 104

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +K R  H+LD  TSG+LVV   + A       FR +++QK Y ++V G   
Sbjct: 105 EKFRWIHQLDFATSGVLVVGVNKDATATGCRLFREKQVQKEYLAVVRGHLP 155


>gi|257900337|ref|ZP_05679990.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|257838249|gb|EEV63323.1| pseudouridine synthase [Enterococcus faecium Com15]
          Length = 255

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 38/248 (15%), Positives = 88/248 (35%), Gaps = 51/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++ +++ G + V+ + VK           ++    + + +  
Sbjct: 17  MRLDKFLADMGLG-SRKEVKGLIKKGTIEVNGQVVKS-------DKAQVNEFEDTVTY-- 66

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                             L  I+ Y+    Y+ +KPAG+           +   L+    
Sbjct: 67  ------------------LGEIIAYQKDFYYILHKPAGVISATQDNHDQTVIDLLED--Q 106

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              +      RLD++T G+L++      A Q L+     + ++K Y + V GI   +   
Sbjct: 107 DYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLS---PKKHVEKEYLAEVSGIMTEEDIR 163

Query: 198 I--ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           +     ++            + Q ++ +  +I               + +  H G+ HQ+
Sbjct: 164 LFAEGLIIDGDEQTLPAKLQIDQVDQESETSI---------------IRLILHEGKFHQV 208

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 209 KRMVKAVG 216


>gi|167037554|ref|YP_001665132.1| pseudouridine synthase [Thermoanaerobacter pseudethanolicus ATCC
           33223]
 gi|167040216|ref|YP_001663201.1| pseudouridine synthase [Thermoanaerobacter sp. X514]
 gi|300914300|ref|ZP_07131616.1| pseudouridine synthase [Thermoanaerobacter sp. X561]
 gi|307724464|ref|YP_003904215.1| pseudouridine synthase [Thermoanaerobacter sp. X513]
 gi|320115969|ref|YP_004186128.1| pseudouridine synthase [Thermoanaerobacter brockii subsp. finnii
           Ako-1]
 gi|166854456|gb|ABY92865.1| pseudouridine synthase [Thermoanaerobacter sp. X514]
 gi|166856388|gb|ABY94796.1| pseudouridine synthase [Thermoanaerobacter pseudethanolicus ATCC
           33223]
 gi|300889235|gb|EFK84381.1| pseudouridine synthase [Thermoanaerobacter sp. X561]
 gi|307581525|gb|ADN54924.1| pseudouridine synthase [Thermoanaerobacter sp. X513]
 gi|319929060|gb|ADV79745.1| pseudouridine synthase [Thermoanaerobacter brockii subsp. finnii
           Ako-1]
          Length = 236

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 85/250 (34%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    ++ +  G+V+V+ K VK                      I 
Sbjct: 2   ERLQKYLAE-CGIASRRKCEEYILQGRVKVNGKVVK-----------------ELGVKIN 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            +  I++    + +       I+L         NKP G I+          +   +K   
Sbjct: 44  PDVDIIEFDDKIVRREKKKVYIML---------NKPTGYITSVKDQFGRPTVMDLVKV-- 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  L        I K Y + + GIP  ++  
Sbjct: 93  ---KERIYPVGRLDYDTSGLLLLTNDGEIANIL--MHPRHEIVKTYIAKIKGIPTQEELE 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                 +   + GDY+    + E            I         +E++ H G+  Q+R 
Sbjct: 148 ----RFRNGLLIGDYLTSKAEIE------------ILAVKNGTSVVEIKIHEGKNRQVRR 191

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 192 MCEAIGHPVI 201


>gi|158320609|ref|YP_001513116.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158140808|gb|ABW19120.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 234

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 46/251 (18%), Positives = 92/251 (36%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRL ++   +    +    ++++ SG+V+V+   +     ++                  
Sbjct: 1   MRLQKFLAAN-GVASRRKSEELISSGRVKVNGNIITEMGYKV------------------ 41

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                     +++ K S   K I+L E     + NKP G        ++   +    + +
Sbjct: 42  ---------DLDIDKISVDNKDIILQERKVYILLNKPTGYVT----TVSEQFNRKKVTDL 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
                +     RLD  TSG+L++         LT      +++K+Y + V GIP  +  E
Sbjct: 89  VDVPYRIFPVGRLDYNTSGLLILTNDGELTYKLT--HPKFKVEKVYIAKVKGIPTKEALE 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              N L  + +I                 A +  K++    Q    +E++   G+  Q+R
Sbjct: 147 AFENGLKIEDYI----------------TAPAKIKILKEINQ-HTLVEVRIREGKNRQVR 189

Query: 257 VHALHMGCPIV 267
                +G P+V
Sbjct: 190 KMCEAIGHPVV 200


>gi|295692663|ref|YP_003601273.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|295030769|emb|CBL50248.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
          Length = 234

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 79/247 (31%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  +++ G V V+   VK    +++    V +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHLLIKKGIVAVNGVTVKTPKQQVKESDQVTVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   L    
Sbjct: 51  --------------------GDAVAYQKYHYFLLNKPKGVLSATEDRSQPTVISLLA--P 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             + Q      RLD++T+G+L++         L      + + KIY + + G+     E 
Sbjct: 89  QDRYQGIVPVGRLDKDTTGLLLLTNDGQLNHEL--LAPNKHVDKIYRAKIAGV--ADDET 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLR 256
           +  +    +   G  +                 K++           E++   G+ HQ++
Sbjct: 145 VKTFAAGMTLGDGTKLQPA------------ELKILSQDEEHNRSTTEIKIREGKYHQIK 192

Query: 257 VHALHMG 263
                +G
Sbjct: 193 RMFGAVG 199


>gi|307274982|ref|ZP_07556145.1| hypothetical protein HMPREF9521_00595 [Enterococcus faecalis
           TX2134]
 gi|306508430|gb|EFM77537.1| hypothetical protein HMPREF9521_00595 [Enterococcus faecalis
           TX2134]
          Length = 238

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 94/253 (37%), Gaps = 58/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++  G+V+V+ + VK    ++     V +  V       
Sbjct: 2   ERLQKAIA-HAGVTSRRKAEELIVKGRVKVNGQVVKELGTQVSKQDTVEVDGVP------ 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSK-IYVFNKPAGI--SVQGGSGIAYHIDGFLK 134
                                   +Y++    Y+F KP G+  +V    G        + 
Sbjct: 55  ------------------------IYQEEYGYYLFYKPRGVISAVSDDKGRK-----VVT 85

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +     ++     RLD +TSG+L++    + +Q LT       + K+Y + + G+P  +
Sbjct: 86  DYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQKLT--HPKHEVDKVYVAKIKGVPTKR 143

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTH 253
           +      L K   I G               A ++F+++    +     +E+  H GR H
Sbjct: 144 ELL---PLAKGIRIDGKR------------TAPANFQILSADIKTGSSVVELTIHEGRNH 188

Query: 254 QLRVHALHMGCPI 266
           Q++     +G P+
Sbjct: 189 QVKKMFQAVGFPV 201


>gi|332637861|ref|ZP_08416724.1| ribosomal large subunit pseudouridine synthase B [Weissella cibaria
           KACC 11862]
          Length = 255

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 90/251 (35%), Gaps = 44/251 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    ++++  G+V V+ K V+    +++    + +          
Sbjct: 3   ERLQKVMAQA-GVASRRASEQLILDGKVTVNGKTVRELGTKVEPSDKIEVS--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
               + +DS   L                  ++ NKP G+               +   V
Sbjct: 53  ---GEPIDSREKLV----------------YFLLNKPRGVVTTTNDDKGRQ---TVMDIV 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
           D + ++     RLD +T+G+L++      A  L       RI K+Y + V GIP N++ E
Sbjct: 91  D-EPERVYPVGRLDYDTTGVLLLTNDGELANRL--MHPSYRIDKVYVAKVKGIPTNEQLE 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + + +  ++   G Y          A   I+              +++  H G+ HQ++
Sbjct: 148 QLRHGVTVRTKQNGRYTTF---KAAPARAEITS----TNTKNHTAIVKLTIHEGKYHQVK 200

Query: 257 VHALHMGCPIV 267
                +G  ++
Sbjct: 201 EMMKAVGHEVL 211


>gi|302335698|ref|YP_003800905.1| ribosomal large subunit pseudouridine synthase B [Olsenella uli DSM
           7084]
 gi|301319538|gb|ADK68025.1| ribosomal large subunit pseudouridine synthase B [Olsenella uli DSM
           7084]
          Length = 267

 Score = 73.1 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 85/252 (33%), Gaps = 40/252 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRL R+        +    + ++ +G+VRV+ + V    +++  G  VV +  V   L+ 
Sbjct: 12  MRLQRFLARA-GVASRRGSENLMSAGRVRVNGRVVSELGSKVTPGIDVVTVDGVECRLS- 69

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSK-IYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                                       D     + NKPAG                L  
Sbjct: 70  ----------------------------DEHAYLMLNKPAGYLTTMSDPQGRPCVAELV- 100

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              ++        RLD +T+G+L+ +     A  L      R + K Y +LV G P  ++
Sbjct: 101 -PTARYPGLFPVGRLDADTTGLLLFSTDGEVANAL--LHPSRHVWKRYVALVRGTPTTRQ 157

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 L     +          +  GA+  +S   V          + ++ H G+ HQ+
Sbjct: 158 L---AMLRAGVPLDDGVARPADAHLLGADDPLSASVVTGGADPGCAVVSIRIHEGKKHQV 214

Query: 256 RVHALHMGCPIV 267
           +     +G  +V
Sbjct: 215 KRMLKAVGHEVV 226


>gi|329115789|ref|ZP_08244506.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           parauberis NCFD 2020]
 gi|326906194|gb|EGE53108.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           parauberis NCFD 2020]
          Length = 241

 Score = 72.7 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 84/249 (33%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + V      ++SG  V I          
Sbjct: 1   MRINKFIA-HAGVASRRKAEELIKQGLVTINGQVVTELATTVKSGDQVEIE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                S +  E+   Y+ NKP G+  SV    G    ID     
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDDKGRKTVID----- 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG+L++         +        I K+Y + V GI     
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGLLLLTNDGDFTDMM--IHPRNEIDKVYLARVKGIATKDN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                               V  + K    A   + +I   A      +E+  H GR HQ
Sbjct: 144 L-------------RPLTRGVVIDGKKTKPA--RYNIIRVEADKNRSIVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFESVG 197


>gi|146319353|ref|YP_001199065.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis 05ZYH33]
 gi|146321558|ref|YP_001201269.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis 98HAH33]
 gi|253752382|ref|YP_003025523.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis SC84]
 gi|253754208|ref|YP_003027349.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis P1/7]
 gi|253756142|ref|YP_003029282.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis BM407]
 gi|145690159|gb|ABP90665.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Streptococcus suis 05ZYH33]
 gi|145692364|gb|ABP92869.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Streptococcus suis 98HAH33]
 gi|251816671|emb|CAZ52312.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis SC84]
 gi|251818606|emb|CAZ56440.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis BM407]
 gi|251820454|emb|CAR47153.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis P1/7]
 gi|319758787|gb|ADV70729.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis JS14]
          Length = 243

 Score = 72.7 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELGTVIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V G+   + 
Sbjct: 86  LLPTVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYLARVKGVANKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
             +   L +           V  + K    A+  +++I     +    +E+  H GR HQ
Sbjct: 143 --VLRPLTRG----------VVIDGKKTKPAV--YEIIKVDPVKNRSVVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|227524458|ref|ZP_03954507.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
 gi|227088377|gb|EEI23689.1| pseudouridylate synthase [Lactobacillus hilgardii ATCC 8290]
          Length = 241

 Score = 72.7 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 49/276 (17%), Positives = 86/276 (31%), Gaps = 54/276 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +K++  G V+V+ K VK    ++     V +          
Sbjct: 3   ERLQKVMA-HAGVASRRKAEKLIVEGHVKVNGKVVKELGTKVTESDEVEVD--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       +    +     LLY         KP G+          H    +   +
Sbjct: 53  -----------EVPISKEVPVYYLLY---------KPRGVIT--AVTDDKHRKTVI-DLL 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++        HLT       + K Y + V G        
Sbjct: 90  SEVTERIYPVGRLDYDTSGLLLLTNDGDLDNHLT--HPKYEVDKTYVAKVKG-------T 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I N  +K+   G   +H+  +    A   +               + +  H GR HQ++ 
Sbjct: 141 ITNDDMKRLRTG---IHIDGRKTASAKATV------IRNNNNSTIVSLTIHEGRNHQVKK 191

Query: 258 HALHMGCPI--VGDHKYCANFKGNFTSPIQNKLYLH 291
             L +G P+  +    Y              +L  H
Sbjct: 192 MFLALGHPVEKLSRQSYGFLNLDGLQPGDYRRLKPH 227


>gi|23099278|ref|NP_692744.1| ribosomal large subunit pseudouridylate synthase [Oceanobacillus
           iheyensis HTE831]
 gi|22777507|dbj|BAC13779.1| ribosomal large subunit pseudouridylate synthase [Oceanobacillus
           iheyensis HTE831]
          Length = 244

 Score = 72.7 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 88/252 (34%), Gaps = 54/252 (21%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RL +         +    ++++  G+V+V+ + V+                      +
Sbjct: 5   GERLQKVIAQS-GVTSRRKAEQMILDGKVKVNGETVQ-----------------EMGVKV 46

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
               +I+   V L K           E    ++  KP G+  SV+   G        +  
Sbjct: 47  TANDEIVVDGVPLEK-----------ETPVYFLLYKPRGVISSVKDDKGRK-----VVTD 90

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + ++  Q+     RLD +TSG+L++      A  L        I K+Y + V GIP  K+
Sbjct: 91  YFEAVEQRIFPIGRLDYDTSGVLLLTNDGDFANLL--MHPRHEIDKVYIAKVRGIPNKKE 148

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
             +    ++        V V               K++    Q K   +E+  H G+  Q
Sbjct: 149 LALLQKGIRSDKDVLKAVQV---------------KLLSTDHQKKTSIIELTLHEGKNRQ 193

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 194 VRRMLEELGYPV 205


>gi|297544608|ref|YP_003676910.1| pseudouridine synthase [Thermoanaerobacter mathranii subsp.
           mathranii str. A3]
 gi|296842383|gb|ADH60899.1| pseudouridine synthase [Thermoanaerobacter mathranii subsp.
           mathranii str. A3]
          Length = 236

 Score = 72.7 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 46/251 (18%), Positives = 90/251 (35%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL ++        +    ++ +  G+V+V+ K VK                      I 
Sbjct: 2   VRLQKYLAE-CGIASRRKCEEYILQGRVKVNGKEVK-----------------ELGVKIN 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            +  I++    + +       I+L         NKP G I+          +   +K   
Sbjct: 44  PDVDIIEFDDKIVRREKKKVYIML---------NKPTGYITSVKDQFGRPTVMDLVKV-- 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
               ++     RLD +TSG+L++      A  L        I K Y + + GIP  ++ E
Sbjct: 93  ---KERIYPVGRLDYDTSGLLLLTNDGEIANIL--MHPRHEIAKTYIAKIKGIPTEEELE 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              N LL + ++                 + +  KV+    +    +E++ H G+  Q+R
Sbjct: 148 RFRNGLLIEDYV----------------TSKAEIKVL-TVKKGTSVVEIKIHEGKNRQVR 190

Query: 257 VHALHMGCPIV 267
                +G P++
Sbjct: 191 KMCEAIGHPVI 201


>gi|291538915|emb|CBL12026.1| ribosomal small subunit pseudouridine synthase A [Roseburia
           intestinalis XB6B4]
          Length = 235

 Score = 72.7 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 48/245 (19%), Positives = 89/245 (36%), Gaps = 49/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +   ++K +RSG V V+ + VK                        
Sbjct: 1   MRLDKLLTELGTG-SRSEVKKYIRSGLVTVNGEVVKK----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQK+ + +  +    + L     Y + + Y+F+KPAG      +         +    D
Sbjct: 37  PEQKVDEKNDTVCFRGNPLT----YTEYEYYLFHKPAGCVT---ATEDNLHRTVMDYLTD 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +         RLD +T G+L++    A A  L      + + K+Y++ + G    +    
Sbjct: 90  TARHDLFPVGRLDIDTEGLLLITNDGALAHDL--LSPAKHVSKVYYAKIDGRVTEE---- 143

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L +     G+        EK A  A+   +V+   +     + +    GR HQ++  
Sbjct: 144 DVNLFENGVDIGE--------EKPAKPAL--LEVL--HSGDNSEIRLTITEGRFHQVKRM 191

Query: 259 ALHMG 263
              +G
Sbjct: 192 FEAVG 196


>gi|161507296|ref|YP_001577250.1| 16S pseudouridylate synthase [Lactobacillus helveticus DPC 4571]
 gi|160348285|gb|ABX26959.1| 16S Pseudouridylate synthase [Lactobacillus helveticus DPC 4571]
 gi|328468687|gb|EGF39674.1| 16S pseudouridylate synthase [Lactobacillus helveticus MTCC 5463]
          Length = 236

 Score = 72.7 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 82/246 (33%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  +++ G V V+   VK    +++    V +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQE------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   LK   
Sbjct: 54  -----------------------VNYQKYHYFLMNKPKGVLSATEDRSQRTVISLLKPQD 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +G  P    RLD++T+G+L++         L      + + KIY + + G+     E 
Sbjct: 91  QYQGITP--VGRLDKDTTGLLLLTNDGQLNHEL--LAPNKHVDKIYRAKIAGV--ADDET 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +  +    +   G  +            A     V D        +E++   G+ HQ++ 
Sbjct: 145 VKTFASGMTLGDGTKL----------KPAELKILVQD-EEHDSSEIEIKIREGKYHQIKR 193

Query: 258 HALHMG 263
               +G
Sbjct: 194 MFGAVG 199


>gi|295115838|emb|CBL36685.1| Pseudouridylate synthases, 23S RNA-specific [butyrate-producing
          bacterium SM4/1]
          Length = 88

 Score = 72.7 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 30/73 (41%)

Query: 7  VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
          ++ V V  +E   RLD+    +        + K+LR   + ++ K+   + R+  G  +R
Sbjct: 1  MRLVTVTKNEAGQRLDKLLFKYMNLAGKSFVYKMLRKKNITLNGKKCDGSERLLEGDEIR 60

Query: 67 IPPVINALNHIIK 79
          +      +    +
Sbjct: 61 LFLSEETIEKFSE 73


>gi|308801855|ref|XP_003078241.1| putative RNA pseudouridylate synthase (ISS) [Ostreococcus tauri]
 gi|116056692|emb|CAL52981.1| putative RNA pseudouridylate synthase (ISS) [Ostreococcus tauri]
          Length = 215

 Score = 72.7 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 42/186 (22%), Positives = 70/186 (37%), Gaps = 20/186 (10%)

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW-----SL 186
            L+  +  +    +  HRLD  T G+LV+A T A A+   +    R + K+Y      ++
Sbjct: 1   MLERAMGLREGTLKPVHRLDVGTEGVLVLATTSAFAKEFGDMLAKRSVTKLYRVLTSRAV 60

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-----------GANYAISHFKVIDC 235
             GI  +  E       K          V  + EK            +       +VI+C
Sbjct: 61  ETGIHIHDAEPATEGPRKMILTEVRTADVASEIEKVMVRGGGERGGVSVPKRCILRVIEC 120

Query: 236 FAQKFCWLE--MQPHTGRTHQLRVHALHMGCPIVGDHKY--CANFKGNFTSPIQNKLYLH 291
                 + E  ++  TGRTHQ+R     +G P+VG+  Y    +           +L L 
Sbjct: 121 KEVGSGYFETTVELLTGRTHQIRAQFAALGSPLVGETLYRAPDDDGDVRVQKPDERLGLQ 180

Query: 292 ARYMDL 297
           A  + +
Sbjct: 181 ASELHI 186


>gi|306830208|ref|ZP_07463392.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis ATCC 6249]
 gi|304427734|gb|EFM30830.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis ATCC 6249]
          Length = 240

 Score = 72.7 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 87/245 (35%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q         +    + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQ---------IDEERDQIR 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++L+                 YE+   Y+ NKP G+           +   L  +  
Sbjct: 50  FDGQVLE-----------------YEEFVYYMMNKPQGVISATEDNKHRTVLDLLDDYAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +K  +     RLD +T G+L++      A  L      R + K Y + V GI   +    
Sbjct: 93  AK--EVFPVGRLDIDTHGLLLLTNDGQLAHAL--LSPKRHVDKTYLAQVEGIMSQEDV-- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     A      +D   +    + +    G+ HQ++  
Sbjct: 147 -----------DTFAKGIPLKDFTCQPAKLELVSVD-PEKNQSLVRVTIAEGKFHQVKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VAYCG 199


>gi|229543960|ref|ZP_04433019.1| pseudouridine synthase [Bacillus coagulans 36D1]
 gi|229325099|gb|EEN90775.1| pseudouridine synthase [Bacillus coagulans 36D1]
          Length = 245

 Score = 72.7 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 85/253 (33%), Gaps = 58/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
            RL +         +    ++++  G+V+V+ + V+    ++     + +          
Sbjct: 2   ERLQKVIAQA-GVTSRRKAEQLILEGKVKVNGETVRTLGTKVSQSDKIEV---------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                     + L +           E+   Y+F KP G+  +V    G        +  
Sbjct: 51  --------EGIPLER-----------EEKVYYLFYKPRGVISAVSDDKGRK-----TVSD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KN 193
           +    G +     RLD +TSG+LVV      A  L        I K Y + + GIP  + 
Sbjct: 87  YFRDAGARVYPVGRLDYDTSGLLVVTNDGEFANLL--MHPRFEIDKTYIARLSGIPSRQE 144

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K+      LK          ++  +++     +                ++  H GR  
Sbjct: 145 LKQLEKGIRLKDGMTAPARAKLLSMDKRKKKAIV----------------QLTIHEGRNR 188

Query: 254 QLRVHALHMGCPI 266
           Q+R    H+G P+
Sbjct: 189 QVRRMFEHLGYPV 201


>gi|30024033|ref|NP_267431.2| pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 239

 Score = 72.7 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 41/275 (14%), Positives = 90/275 (32%), Gaps = 56/275 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++ +G+V V+         ++ +G +V +          
Sbjct: 1   MRINKYLA-HAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDIVEVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G IS          +   +   
Sbjct: 51  --------------------GVAVYNEEPVYYLLNKPRGYISSVSDDKGRQTVMDLM--- 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +T       + K+Y + V G    +  
Sbjct: 88  -PQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMMT--HPRHGVDKVYVAKVEGQANKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
                L     I G  V   +            +++I     +    + +  H G+ HQ+
Sbjct: 145 ---RPLTLGMTIEGKKVSPAR------------YEIIKQEKTKNHSIVSLTIHEGQNHQV 189

Query: 256 RVHALHMGCPI--VGDHKYCANFKGNFTSPIQNKL 288
           +      G P+  +   +Y +       +    +L
Sbjct: 190 KKMFAAAGLPVQKLSRIQYGSLTLDGLPTGQFRRL 224


>gi|315611910|ref|ZP_07886829.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis ATCC 49296]
 gi|315316088|gb|EFU64121.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis ATCC 49296]
          Length = 240

 Score = 72.3 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 89/246 (36%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q                I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQ----------------IN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E+  +           F   +L YE+   Y+ NKP G+           +   L  +  
Sbjct: 43  EERDEI----------RFDGQVLEYEEFVYYMMNKPQGVISATEDTKHRTVLDLLDDYAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +K  +     RLD +T G+L++    + A   L+     R + K Y + V GI   +   
Sbjct: 93  AK--EVFPVGRLDIDTHGLLLLTNDGKLAHALLS---PKRHVDKTYLAQVKGIMTQEDV- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   +   +     A      +D   +    + +    G+ HQ++ 
Sbjct: 147 ------------DAFAKGIPLKDFTCQPARLELVSVD-PEKNQSLVRVTIAEGKFHQVKR 193

Query: 258 HALHMG 263
              + G
Sbjct: 194 MVAYCG 199


>gi|168576293|ref|ZP_02722176.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           MLV-016]
 gi|183577841|gb|EDT98369.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           MLV-016]
          Length = 240

 Score = 72.3 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 90/247 (36%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q  + +         + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQIDEKI---------DEIR 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++L+                 YE+   Y+ NKP G+           +   L     
Sbjct: 50  FDGQVLE-----------------YEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLAQ 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KE 196
           SK  +     RLD +T G+L++      A  L      R + K Y + V GI   +  + 
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNNGQLAHVL--LSPKRHVDKTYQAQVKGIMTQEDVET 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I    LK        + ++  + +                +    + +    G+ HQ++
Sbjct: 149 FIKGIPLKDFTCQPARLEILSTDAE----------------KNQSQIRVTIAEGKFHQIK 192

Query: 257 VHALHMG 263
               + G
Sbjct: 193 RMVGYCG 199


>gi|254775517|ref|ZP_05217033.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           avium subsp. avium ATCC 25291]
          Length = 247

 Score = 72.3 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 41/253 (16%), Positives = 77/253 (30%), Gaps = 47/253 (18%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + + +RL +         +    +K++  G+V VD + V             +   ++  
Sbjct: 3   EAQGIRLQKVLSQA-GIASRRAAEKLIVDGRVEVDGQVVT-----------ELGTRVDPD 50

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +I+                    ++L E       NKP G+             G L 
Sbjct: 51  AAVIR---------------VDGARVVLDESQVYLALNKPRGVHSTMSDDRGRPCIGDLI 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKN 193
                  +      RLD ET G++++      A  L        + K Y + V G IP+ 
Sbjct: 96  ERRVRGNKNLFHVGRLDAETEGLILLTNDGELAHRL--MHPSHEVPKTYLATVTGSIPRG 153

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + +   +     +                  +  F V+D    K   + +  H GR  
Sbjct: 154 LGKTLRAGIELDDGMAR----------------VDEFAVVDATPGK-TLVRVTLHEGRNR 196

Query: 254 QLRVHALHMGCPI 266
            +R      G P+
Sbjct: 197 IVRRLLAAAGFPV 209


>gi|223934211|ref|ZP_03626147.1| pseudouridine synthase [Streptococcus suis 89/1591]
 gi|302024332|ref|ZP_07249543.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis 05HAS68]
 gi|330833322|ref|YP_004402147.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis ST3]
 gi|223897127|gb|EEF63552.1| pseudouridine synthase [Streptococcus suis 89/1591]
 gi|329307545|gb|AEB81961.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           suis ST3]
          Length = 243

 Score = 72.3 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELGTVIKSGDKVEVEGKP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V G+   + 
Sbjct: 86  LLPTVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYLARVKGVANKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
             +   L +           V  + K    A+  +++I     +    +E+  H GR HQ
Sbjct: 143 --VLRPLTRG----------VVIDGKKTKPAV--YEIIKVDPVKNRSVVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|326803723|ref|YP_004321541.1| pseudouridine synthase B, ribosomal large subunit [Aerococcus
           urinae ACS-120-V-Col10a]
 gi|326650759|gb|AEA00942.1| pseudouridine synthase B, ribosomal large subunit [Aerococcus
           urinae ACS-120-V-Col10a]
          Length = 240

 Score = 72.3 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 47/261 (18%), Positives = 89/261 (34%), Gaps = 58/261 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +  + +K++ +G+VRV+ + V     ++    +V +          
Sbjct: 2   ERLQKVIA-HAGVASRRDAEKLILAGRVRVNGQVVTELGTKVTKKDLVEVD--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                               +  +  E+   Y+FNKP G+  SV    G        +  
Sbjct: 52  --------------------QVPIYKEEPVYYLFNKPDGVISSVADDKGRK-----VVVD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD  T+G+L++      A  L        I K+Y + V G P    
Sbjct: 87  YFKEIPQRIYPIGRLDYHTTGVLLLTNDGEFANLL--MHPRYEIDKVYVAKVKGYPSPDA 144

Query: 196 -ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + +   L+            +++N+     A                +E+  H GR  Q
Sbjct: 145 LKRLEEGLVIDGQKTAKARARIRKNKAAKENAT---------------VELTIHEGRNRQ 189

Query: 255 LRVHALHMGCPI--VGDHKYC 273
           +R     +G P+  +   +Y 
Sbjct: 190 VRKMLEAVGHPVKRLNRERYG 210


>gi|12724251|gb|AAK05373.1|AE006360_2 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 257

 Score = 72.3 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 41/275 (14%), Positives = 90/275 (32%), Gaps = 56/275 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++ +G+V V+         ++ +G +V +          
Sbjct: 19  MRINKYLA-HAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDIVEVN--------- 68

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G IS          +   +   
Sbjct: 69  --------------------GVAVYNEEPVYYLLNKPRGYISSVSDDKGRQTVMDLM--- 105

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +T       + K+Y + V G    +  
Sbjct: 106 -PQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMMT--HPRHGVDKVYVAKVEGQANKENL 162

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
                L     I G  V   +            +++I     +    + +  H G+ HQ+
Sbjct: 163 ---RPLTLGMTIEGKKVSPAR------------YEIIKQEKTKNHSIVSLTIHEGQNHQV 207

Query: 256 RVHALHMGCPI--VGDHKYCANFKGNFTSPIQNKL 288
           +      G P+  +   +Y +       +    +L
Sbjct: 208 KKMFAAAGLPVQKLSRIQYGSLTLDGLPTGQFRRL 242


>gi|68535954|ref|YP_250659.1| putative pseudouridylate synthase [Corynebacterium jeikeium K411]
 gi|260578661|ref|ZP_05846569.1| RNA pseudouridylate synthase [Corynebacterium jeikeium ATCC 43734]
 gi|68263553|emb|CAI37041.1| putative pseudouridylate synthase [Corynebacterium jeikeium K411]
 gi|258603158|gb|EEW16427.1| RNA pseudouridylate synthase [Corynebacterium jeikeium ATCC 43734]
          Length = 290

 Score = 72.3 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 98/254 (38%), Gaps = 45/254 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           E+++  +RL +   +     +    +K++ +G+V V+ + V     ++ G  +       
Sbjct: 44  ESEKAQVRLQKVLASA-GVASRRMSEKLIAAGRVEVNGEVV-----VKMGTRI------- 90

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                       D SV++ +     + + + E+   +V NKP G+       +     G 
Sbjct: 91  ------------DPSVDIVRV--DGERVQVNEEMVYFVLNKPRGVHSTMSDDLGRPCVGD 136

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L      +GQ      RLD +T G+L++      A  L        ++K Y + V G   
Sbjct: 137 LVGTRLKEGQGLFHVGRLDAQTEGLLLLTNDGELANRL--MHPKYEVKKTYMATVLGEAS 194

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            K       L+++   G +    + + +          +++D + Q    ++++ H GR 
Sbjct: 195 RK-------LIRELKDGVELDDGIARADS--------VQIVDVW-QGKSLIKVELHEGRK 238

Query: 253 HQLRVHALHMGCPI 266
           H +R      G P+
Sbjct: 239 HIVRRMLKEAGFPV 252


>gi|406952|gb|AAA03374.1| unknown [Mycoplasma genitalium]
          Length = 119

 Score = 72.3 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 30/100 (30%), Positives = 48/100 (48%), Gaps = 8/100 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIA--YHIDGFLKSW------VDSKGQKPRLTHR 149
           K  +++ED  I V +KP GI  Q     +     +  LK         +     P+  HR
Sbjct: 7   KLKIIFEDENIIVVDKPTGIVCQPDKKHSIINLSNMLLKHCGYRQFDSNKLNFYPQFAHR 66

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           +D+ TSGI++ A+T  A + L + F+   + K Y  LV+G
Sbjct: 67  IDRNTSGIVIGAKTNKALKELNKVFKNNHLTKRYKGLVFG 106


>gi|288905991|ref|YP_003431213.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
 gi|306832010|ref|ZP_07465165.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325978958|ref|YP_004288674.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|288732717|emb|CBI14291.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
 gi|304425936|gb|EFM29053.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325178886|emb|CBZ48930.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 241

 Score = 72.3 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 42/248 (16%), Positives = 84/248 (33%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ K V      ++SG VV +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKKGLVTINGKVVTELATTVKSGDVVEVE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                S +  E+   Y+ NKP G+ S          +   L + 
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDEKGRKTVVDLLPNV 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +T+G+L++         +        I K+Y + V GI   +  
Sbjct: 91  T----ERIYPVGRLDWDTTGLLILTNDGDFTDEM--IHPRNEIDKVYLARVKGIATKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQL 255
                              V  + K    A   + ++    +     +E+  H GR HQ+
Sbjct: 145 -------------RPLTRGVVIDGKKTKPA--RYNIVKVDPEKNRSVVELTIHEGRNHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KKMFESVG 197


>gi|323340736|ref|ZP_08080988.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           ruminis ATCC 25644]
 gi|323091859|gb|EFZ34479.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           ruminis ATCC 25644]
          Length = 261

 Score = 72.3 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 46/258 (17%), Positives = 92/258 (35%), Gaps = 54/258 (20%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           E+    +RL +   +     +    +K++  G+V+V+   VK    +++    + +   +
Sbjct: 11  EDHMAEVRLQKAMADA-GVASRRASEKLILEGRVKVNGVVVKELGTKVKGDDAIEVNGTL 69

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHI 129
                                            +   Y+F KP G+  +V+   G     
Sbjct: 70  IERER----------------------------NKVYYLFYKPRGVISAVKDDKGRR--- 98

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +  + + +  +     RLD +TSGIL++      A  L       ++ K Y + V G
Sbjct: 99  --VVTDYFEGEKNRIYPIGRLDYDTSGILLLTNDGELANLL--MHPRYKVDKTYVAKVEG 154

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPH 248
           + ++         LK+   G          + G   A +  KVI    A+    + +  H
Sbjct: 155 LVQSDD-------LKRLRKGVKM-------KDGHYSARAKAKVISSDRAKNHSIVSLTIH 200

Query: 249 TGRTHQLRVHALHMGCPI 266
            GR HQ++     +G P+
Sbjct: 201 EGRNHQVKNMFEAIGHPV 218


>gi|295112967|emb|CBL31604.1| ribosomal large subunit pseudouridine synthase B [Enterococcus sp.
           7L76]
          Length = 238

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 93/253 (36%), Gaps = 58/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++  G+V+V+ + VK    ++     V +  V       
Sbjct: 2   ERLQKAIA-HAGVTSRRKAEELIVKGRVKVNGQVVKELGTQVSKQDTVEVDGVP------ 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSK-IYVFNKPAGI--SVQGGSGIAYHIDGFLK 134
                                   +Y++    Y+F KP G+  +V    G        + 
Sbjct: 55  ------------------------IYQEEYGYYLFYKPKGVISAVSDDKGRK-----VVT 85

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +     ++     RLD +TSG+L++    + +Q LT       + K+Y + + G+P  +
Sbjct: 86  DYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQKLT--HPKHEVDKVYVAKIKGVPTKR 143

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTH 253
                  L K   I G               A ++F+++    +     +E+  H GR H
Sbjct: 144 DLL---PLAKGIRIDGKR------------TAPANFQILSADIKTGSSVVELTIHEGRNH 188

Query: 254 QLRVHALHMGCPI 266
           Q++     +G P+
Sbjct: 189 QVKKMFQAVGFPV 201


>gi|227518731|ref|ZP_03948780.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|227553340|ref|ZP_03983389.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|229545844|ref|ZP_04434569.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|229550036|ref|ZP_04438761.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|255972817|ref|ZP_05423403.1| pseudouridine synthase [Enterococcus faecalis T1]
 gi|255975873|ref|ZP_05426459.1| pseudouridine synthase [Enterococcus faecalis T2]
 gi|256619043|ref|ZP_05475889.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256762469|ref|ZP_05503049.1| pseudouridine synthase [Enterococcus faecalis T3]
 gi|256853105|ref|ZP_05558475.1| pseudouridine synthase [Enterococcus faecalis T8]
 gi|256958960|ref|ZP_05563131.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256961947|ref|ZP_05566118.1| pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256965145|ref|ZP_05569316.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|257078991|ref|ZP_05573352.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|257082570|ref|ZP_05576931.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257085203|ref|ZP_05579564.1| pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|257086764|ref|ZP_05581125.1| pseudouridine synthase [Enterococcus faecalis D6]
 gi|257089865|ref|ZP_05584226.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|257416073|ref|ZP_05593067.1| pseudouridine synthase [Enterococcus faecalis AR01/DG]
 gi|257419276|ref|ZP_05596270.1| pseudouridine synthase [Enterococcus faecalis T11]
 gi|257422639|ref|ZP_05599629.1| pseudouridine synthase [Enterococcus faecalis X98]
 gi|293383015|ref|ZP_06628933.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecalis R712]
 gi|293389496|ref|ZP_06633953.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecalis S613]
 gi|294781343|ref|ZP_06746686.1| pseudouridylate synthase [Enterococcus faecalis PC1.1]
 gi|300860430|ref|ZP_07106517.1| pseudouridine synthase B, ribosomal large subunit [Enterococcus
           faecalis TUSoD Ef11]
 gi|307271038|ref|ZP_07552321.1| hypothetical protein HMPREF9498_03124 [Enterococcus faecalis
           TX4248]
 gi|307273245|ref|ZP_07554491.1| hypothetical protein HMPREF9514_02011 [Enterococcus faecalis
           TX0855]
 gi|307278094|ref|ZP_07559178.1| hypothetical protein HMPREF9515_00429 [Enterococcus faecalis
           TX0860]
 gi|307289085|ref|ZP_07569041.1| hypothetical protein HMPREF9505_02455 [Enterococcus faecalis
           TX0109]
 gi|307292016|ref|ZP_07571885.1| hypothetical protein HMPREF9509_02313 [Enterococcus faecalis
           TX0411]
 gi|312900740|ref|ZP_07760037.1| conserved hypothetical protein [Enterococcus faecalis TX0470]
 gi|312903287|ref|ZP_07762467.1| conserved hypothetical protein [Enterococcus faecalis TX0635]
 gi|312907514|ref|ZP_07766505.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 512]
 gi|312910132|ref|ZP_07768979.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 516]
 gi|312951473|ref|ZP_07770369.1| conserved hypothetical protein [Enterococcus faecalis TX0102]
 gi|227073812|gb|EEI11775.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|227177527|gb|EEI58499.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|229304842|gb|EEN70838.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|229309043|gb|EEN75030.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|255963835|gb|EET96311.1| pseudouridine synthase [Enterococcus faecalis T1]
 gi|255968745|gb|EET99367.1| pseudouridine synthase [Enterococcus faecalis T2]
 gi|256598570|gb|EEU17746.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256683720|gb|EEU23415.1| pseudouridine synthase [Enterococcus faecalis T3]
 gi|256711564|gb|EEU26602.1| pseudouridine synthase [Enterococcus faecalis T8]
 gi|256949456|gb|EEU66088.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256952443|gb|EEU69075.1| pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256955641|gb|EEU72273.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|256987021|gb|EEU74323.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|256990600|gb|EEU77902.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|256993233|gb|EEU80535.1| pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256994794|gb|EEU82096.1| pseudouridine synthase [Enterococcus faecalis D6]
 gi|256998677|gb|EEU85197.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|257157901|gb|EEU87861.1| pseudouridine synthase [Enterococcus faecalis ARO1/DG]
 gi|257161104|gb|EEU91064.1| pseudouridine synthase [Enterococcus faecalis T11]
 gi|257164463|gb|EEU94423.1| pseudouridine synthase [Enterococcus faecalis X98]
 gi|291079680|gb|EFE17044.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecalis R712]
 gi|291081113|gb|EFE18076.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecalis S613]
 gi|294451573|gb|EFG20032.1| pseudouridylate synthase [Enterococcus faecalis PC1.1]
 gi|300849469|gb|EFK77219.1| pseudouridine synthase B, ribosomal large subunit [Enterococcus
           faecalis TUSoD Ef11]
 gi|306497014|gb|EFM66562.1| hypothetical protein HMPREF9509_02313 [Enterococcus faecalis
           TX0411]
 gi|306499794|gb|EFM69155.1| hypothetical protein HMPREF9505_02455 [Enterococcus faecalis
           TX0109]
 gi|306505491|gb|EFM74677.1| hypothetical protein HMPREF9515_00429 [Enterococcus faecalis
           TX0860]
 gi|306510230|gb|EFM79254.1| hypothetical protein HMPREF9514_02011 [Enterococcus faecalis
           TX0855]
 gi|306512536|gb|EFM81185.1| hypothetical protein HMPREF9498_03124 [Enterococcus faecalis
           TX4248]
 gi|310626542|gb|EFQ09825.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 512]
 gi|310630439|gb|EFQ13722.1| conserved hypothetical protein [Enterococcus faecalis TX0102]
 gi|310633163|gb|EFQ16446.1| conserved hypothetical protein [Enterococcus faecalis TX0635]
 gi|311289405|gb|EFQ67961.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 516]
 gi|311292221|gb|EFQ70777.1| conserved hypothetical protein [Enterococcus faecalis TX0470]
 gi|315027286|gb|EFT39218.1| conserved hypothetical protein [Enterococcus faecalis TX2137]
 gi|315029405|gb|EFT41337.1| conserved hypothetical protein [Enterococcus faecalis TX4000]
 gi|315033949|gb|EFT45881.1| conserved hypothetical protein [Enterococcus faecalis TX0017]
 gi|315036958|gb|EFT48890.1| conserved hypothetical protein [Enterococcus faecalis TX0027]
 gi|315144437|gb|EFT88453.1| conserved hypothetical protein [Enterococcus faecalis TX2141]
 gi|315147244|gb|EFT91260.1| conserved hypothetical protein [Enterococcus faecalis TX4244]
 gi|315150557|gb|EFT94573.1| conserved hypothetical protein [Enterococcus faecalis TX0012]
 gi|315152504|gb|EFT96520.1| conserved hypothetical protein [Enterococcus faecalis TX0031]
 gi|315155782|gb|EFT99798.1| conserved hypothetical protein [Enterococcus faecalis TX0043]
 gi|315158051|gb|EFU02068.1| conserved hypothetical protein [Enterococcus faecalis TX0312]
 gi|315160465|gb|EFU04482.1| conserved hypothetical protein [Enterococcus faecalis TX0645]
 gi|315163994|gb|EFU08011.1| conserved hypothetical protein [Enterococcus faecalis TX1302]
 gi|315169055|gb|EFU13072.1| conserved hypothetical protein [Enterococcus faecalis TX1341]
 gi|315169707|gb|EFU13724.1| conserved hypothetical protein [Enterococcus faecalis TX1342]
 gi|315575887|gb|EFU88078.1| conserved hypothetical protein [Enterococcus faecalis TX0309B]
 gi|315577727|gb|EFU89918.1| conserved hypothetical protein [Enterococcus faecalis TX0630]
 gi|315580539|gb|EFU92730.1| conserved hypothetical protein [Enterococcus faecalis TX0309A]
 gi|323480703|gb|ADX80142.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecalis 62]
 gi|327535112|gb|AEA93946.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecalis OG1RF]
          Length = 238

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 93/253 (36%), Gaps = 58/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++  G+V+V+ + VK    ++     V +  V       
Sbjct: 2   ERLQKAIA-HAGVTSRRKAEELIVKGRVKVNGQVVKELGTQVSKQDTVEVDGVP------ 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSK-IYVFNKPAGI--SVQGGSGIAYHIDGFLK 134
                                   +Y++    Y+F KP G+  +V    G        + 
Sbjct: 55  ------------------------IYQEEYGYYLFYKPRGVISAVSDDKGRK-----VVT 85

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +     ++     RLD +TSG+L++    + +Q LT       + K+Y + + G+P  +
Sbjct: 86  DYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQKLT--HPKHEVDKVYVAKIKGVPTKR 143

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTH 253
                  L K   I G               A ++F+++    +     +E+  H GR H
Sbjct: 144 DLL---PLAKGIRIDGKR------------TAPANFQILSADIKTGSSVVELTIHEGRNH 188

Query: 254 QLRVHALHMGCPI 266
           Q++     +G P+
Sbjct: 189 QVKKMFQAVGFPV 201


>gi|226312000|ref|YP_002771894.1| ribosomal large subunit pseudouridine synthase B [Brevibacillus
           brevis NBRC 100599]
 gi|226094948|dbj|BAH43390.1| probable ribosomal large subunit pseudouridine synthase B
           [Brevibacillus brevis NBRC 100599]
          Length = 249

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 87/250 (34%), Gaps = 49/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +    H    +  + ++++  G+V+V+ + V+        Q +++ P+ + +    
Sbjct: 2   ERLQKVLA-HAGVASRRHCEELIAQGKVQVNGQVVRE-------QGIKVDPLKDKIV--- 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                 +  E     +  KP G+     S         +   + 
Sbjct: 51  -----------------VNGQQVKLEQHVYLLLYKPTGVIT---SVTDPQGRRVVIDLLK 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC- 197
              ++     RLD +TSG+L++      A  L        I K+Y + V GIP  +K   
Sbjct: 91  GIQERVYPVGRLDYDTSGLLLLTNDGELANRLA--HPSYEIDKVYRAWVKGIPSPEKVRK 148

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +A  +  +  +       + + E  +  A                +E+  H GR  Q+R 
Sbjct: 149 LATGIRLEDGMTSPGQSKLLKAESSSQRA---------------LVELTIHEGRNRQVRR 193

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 194 MCEAIGHPVL 203


>gi|69244107|ref|ZP_00602643.1| Pseudouridine synthase, Rsu [Enterococcus faecium DO]
 gi|258614116|ref|ZP_05711886.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecium DO]
 gi|293557176|ref|ZP_06675728.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1039]
 gi|293563963|ref|ZP_06678370.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1162]
 gi|293568184|ref|ZP_06679518.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1071]
 gi|294614323|ref|ZP_06694240.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1636]
 gi|294619970|ref|ZP_06699342.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1679]
 gi|294622171|ref|ZP_06701239.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium U0317]
 gi|314940301|ref|ZP_07847468.1| conserved hypothetical protein [Enterococcus faecium TX0133a04]
 gi|314941863|ref|ZP_07848734.1| conserved hypothetical protein [Enterococcus faecium TX0133C]
 gi|314949516|ref|ZP_07852851.1| conserved hypothetical protein [Enterococcus faecium TX0082]
 gi|314952902|ref|ZP_07855870.1| conserved hypothetical protein [Enterococcus faecium TX0133A]
 gi|314994523|ref|ZP_07859796.1| conserved hypothetical protein [Enterococcus faecium TX0133B]
 gi|314995270|ref|ZP_07860382.1| conserved hypothetical protein [Enterococcus faecium TX0133a01]
 gi|68196564|gb|EAN10990.1| Pseudouridine synthase, Rsu [Enterococcus faecium DO]
 gi|291589084|gb|EFF20898.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1071]
 gi|291592795|gb|EFF24387.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1636]
 gi|291593800|gb|EFF25302.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1679]
 gi|291598298|gb|EFF29389.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium U0317]
 gi|291600677|gb|EFF30977.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1039]
 gi|291604053|gb|EFF33580.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1162]
 gi|313590526|gb|EFR69371.1| conserved hypothetical protein [Enterococcus faecium TX0133a01]
 gi|313591101|gb|EFR69946.1| conserved hypothetical protein [Enterococcus faecium TX0133B]
 gi|313595024|gb|EFR73869.1| conserved hypothetical protein [Enterococcus faecium TX0133A]
 gi|313599347|gb|EFR78192.1| conserved hypothetical protein [Enterococcus faecium TX0133C]
 gi|313640477|gb|EFS05057.1| conserved hypothetical protein [Enterococcus faecium TX0133a04]
 gi|313644130|gb|EFS08710.1| conserved hypothetical protein [Enterococcus faecium TX0082]
          Length = 239

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 88/248 (35%), Gaps = 51/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++ +++ G + V+ + VK           ++    +A+ +  
Sbjct: 1   MRLDKFLADMGLG-SRKEVKGLIKKGTIEVNGQVVKS-------DKAQVNEFEDAVTY-- 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                             L  I+ Y+    Y+ +KPAG+           +   L+    
Sbjct: 51  ------------------LGEIITYQKDFYYILHKPAGVISATQDNHDQTVIDLLED--Q 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              +      RLD++T G+L++      A Q L+     + ++K Y + V GI   +   
Sbjct: 91  DYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLS---PKKHVEKEYLAEVSGIMTEEDIR 147

Query: 198 I--ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           +     ++            + Q ++    +I               + +  H G+ HQ+
Sbjct: 148 LFAEGLIIDGDEQTLPAKLQIDQVDQETETSI---------------IRLILHEGKFHQV 192

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 193 KRMVKAVG 200


>gi|168485953|ref|ZP_02710461.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           CDC1087-00]
 gi|183570820|gb|EDT91348.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           CDC1087-00]
          Length = 240

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 88/245 (35%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q  + +         + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQIDEKI---------DEIR 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++L+                 YE+   Y+ NKP G+           +   L     
Sbjct: 50  FDGQVLE-----------------YEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK  +     RLD +T G+L++      A  L      R + K Y + V GI   +    
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNNGQLAHVL--LSPKRHVDKTYLAQVKGIMTQEDVET 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     AI     ID   +    + +    G+ HQ++  
Sbjct: 149 -------------FAEGIPLKDFTCQPAILELVSIDT-EKNQSQIRVTIAEGKFHQIKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VGYCG 199


>gi|118465035|ref|YP_882249.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           avium 104]
 gi|118166322|gb|ABK67219.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           avium 104]
          Length = 248

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 41/253 (16%), Positives = 77/253 (30%), Gaps = 47/253 (18%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + + +RL +         +    +K++  G+V VD + V             +   ++  
Sbjct: 4   EAQGIRLQKVLSQA-GIASRRAAEKLIVDGRVEVDGQVVT-----------ELGTRVDPD 51

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +I+                    ++L E       NKP G+             G L 
Sbjct: 52  AAVIR---------------VDGARVVLDESQVYLALNKPRGVHSTMSDDRGRPCIGDLI 96

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKN 193
                  +      RLD ET G++++      A  L        + K Y + V G IP+ 
Sbjct: 97  ERRVRGNKNLFHVGRLDAETEGLILLTNDGELAHRL--MHPSHEVPKTYLATVTGSIPRG 154

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + +   +     +                  +  F V+D    K   + +  H GR  
Sbjct: 155 LGKTLRAGIELDDGMAR----------------VDEFAVVDAIPGK-TLVRVTLHEGRNR 197

Query: 254 QLRVHALHMGCPI 266
            +R      G P+
Sbjct: 198 IVRRLLAAAGFPV 210


>gi|253578262|ref|ZP_04855534.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850580|gb|EES78538.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 255

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 95/246 (38%), Gaps = 39/246 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +         ++K ++ G+V+V+    K +        +++           
Sbjct: 5   VRLDKFLADAGAG-TRSEVKKFIQKGKVQVNGVPAKKSE-------IKVS---------- 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E +++     +++  +F+           Y+ +KPAG      S      D  +   V 
Sbjct: 47  EEDEVVLDGNRISQAPEFV----------YYLLHKPAGYV----SATEDKRDKTVMELVA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKEC 197
           S  +      RLD++T G+L++    A A  L      + + K Y+++  G   K   + 
Sbjct: 93  SDRKDLFPVGRLDKDTEGLLLITDDGALAHEL--LSPKKHVDKTYYAVTDGCMTKEDVQR 150

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            A+ L     IG     +  + +  +   +   ++    +     +++    G+ HQ++ 
Sbjct: 151 FADGL----EIGEKNPTMPAKLKILSTRKVEETELEQYPSGWSSEIQLTIKEGKFHQVKR 206

Query: 258 HALHMG 263
               +G
Sbjct: 207 MTEAVG 212


>gi|307328933|ref|ZP_07608102.1| pseudouridine synthase [Streptomyces violaceusniger Tu 4113]
 gi|306885443|gb|EFN16460.1| pseudouridine synthase [Streptomyces violaceusniger Tu 4113]
          Length = 366

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/278 (16%), Positives = 88/278 (31%), Gaps = 55/278 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + E  RL +         +    ++++   +V V+ K V                     
Sbjct: 126 EVEGERLQKVLARAGMG-SRRACEELIDQARVEVNGKIVT-----------------EQG 167

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +  E+  +           +L           +  NKPAG+             G   
Sbjct: 168 LRVDPEKDEIKVDGLTVATQSYL----------FFALNKPAGVVSTMEDPDGRQCLG--- 214

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +V ++  +     RLD ET GI+++      A  LT       ++K Y + + G     
Sbjct: 215 DYVTNRETRLFHVGRLDTETEGIILLTNHGELAHRLT--HPRYGVKKTYLAAIQGPLPRD 272

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                  L K+   G +      + +        HF+V+    + +  +E+  H GR H 
Sbjct: 273 -------LGKRLKSGIELEDGYARAD--------HFRVVQNTGKNY-LVEVTLHEGRKHI 316

Query: 255 LRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
           +R      G P+  D      +     G+  S    ++
Sbjct: 317 VRRMLAEAGFPV--DKLVRTAFGPIALGDQKSGWLRRM 352


>gi|60599504|gb|AAX26297.1| unknown [Schistosoma japonicum]
          Length = 148

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 28/148 (18%), Positives = 57/148 (38%), Gaps = 21/148 (14%)

Query: 37  LQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDF 96
           + +   SG + V+  RV  +  +    ++       +      E  +L+  +        
Sbjct: 6   IAQKCNSGDILVNGARVDPDYVLNDNDLL-------SQQVHRHEFPVLNLPIEF------ 52

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-RLTHRLDQETS 155
                +++   + V NKP  I +       Y ++          G +P R THRLD+ TS
Sbjct: 53  -----IHDSHDMLVINKPPSIPIHPCG--RYTLNSITHILAKDYGLRPLRFTHRLDRMTS 105

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIY 183
           G+L++A+    +  L      + + K+ 
Sbjct: 106 GLLLIAKDYDTSVRLQSQIASKEVTKVT 133


>gi|302871660|ref|YP_003840296.1| pseudouridine synthase [Caldicellulosiruptor obsidiansis OB47]
 gi|302574519|gb|ADL42310.1| pseudouridine synthase [Caldicellulosiruptor obsidiansis OB47]
          Length = 236

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 48/250 (19%), Positives = 91/250 (36%), Gaps = 49/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL ++        +    ++I++ G+V+V+ K V                       I 
Sbjct: 1   MRLQKFMA-QCGVASRRKCEEIIQQGRVKVNGKTVN-----------------QLGFKID 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ I++    +      L+S  +Y      + NKP G+     +         +    D
Sbjct: 43  PEKDIVE----VDGERISLQSHKVY-----IMLNKPFGVIS--SAKDEKGRKTVVDLVKD 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-EC 197
               +     RLD +T+G++++      A  +T       I+K Y +L+ GIP  ++ E 
Sbjct: 92  KVNVRVFPVGRLDFDTTGLILLTNDGEFAYKVT--HPKHDIEKTYIALIKGIPSKEEIER 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               LL    +                 A + FKV+         +E++ H GR  Q+R 
Sbjct: 150 FEKGLLIDGKM----------------TAPAKFKVLKQINGNA-MVEIKIHEGRNRQIRK 192

Query: 258 HALHMGCPIV 267
               +G  ++
Sbjct: 193 MCDMIGHKVL 202


>gi|149001603|ref|ZP_01826576.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP14-BS69]
 gi|237649412|ref|ZP_04523664.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae CCRI 1974]
 gi|237821288|ref|ZP_04597133.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae CCRI 1974M2]
 gi|147760061|gb|EDK67050.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP14-BS69]
          Length = 240

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 89/245 (36%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q  + +         + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQIDEKI---------DEIR 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++L+                 YE+   Y+ NKP G+           +   L     
Sbjct: 50  FDGQVLE-----------------YEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK  +     RLD +T G+L++A     A  L      R + K Y + V GI   +    
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLANDGQLAHVL--LSPKRHVDKTYLAQVKGIMTQEDVET 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     AI     ID   +    + +    G+ HQ++  
Sbjct: 149 -------------FAEGIPLKDFTCQPAILELVSIDT-EKNQSQIRVTIAEGKFHQIKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VGYCG 199


>gi|148994694|ref|ZP_01823798.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP9-BS68]
 gi|168489757|ref|ZP_02713956.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           SP195]
 gi|147927094|gb|EDK78134.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP9-BS68]
 gi|183571795|gb|EDT92323.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           SP195]
 gi|332075138|gb|EGI85608.1| hypothetical protein SPAR50_0282 [Streptococcus pneumoniae GA17570]
          Length = 240

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 89/245 (36%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q  + +         + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQIDEKI---------DEIR 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++L+                 YE+   Y+ NKP G+           +   L     
Sbjct: 50  FDGQVLE-----------------YEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK  +     RLD +T G+L++      A  L      R + K Y + V GI   +   I
Sbjct: 93  SK--EIFPVGRLDIDTHGLLLLTNDGQLAHVL--LSPKRHVDKTYLAQVKGIMTQEDVEI 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     AI     ID   +    + +    G+ HQ++  
Sbjct: 149 -------------FAEGIPLKDFTCQPAILELVSIDT-EKNQSQIRVTIAEGKFHQIKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VGYCG 199


>gi|293572005|ref|ZP_06683018.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E980]
 gi|291607929|gb|EFF37238.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E980]
          Length = 239

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 38/248 (15%), Positives = 88/248 (35%), Gaps = 51/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++ +++ G + V+ + VK           ++    + + +  
Sbjct: 1   MRLDKFLADMGLG-SRKEVKGLIKKGTIEVNGQVVKS-------DKAQVNEFEDTVTY-- 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                             L  I+ Y+    Y+ +KPAG+           +   L+    
Sbjct: 51  ------------------LGEIIAYQKDFYYILHKPAGVISATQDNHDQTVIDLLED--Q 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              +      RLD++T G+L++      A Q L+     + ++K Y + V GI   +   
Sbjct: 91  DYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLS---PKKHVEKEYLAEVNGIMTEEDIR 147

Query: 198 I--ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           +     ++            + Q ++ +  +I               + +  H G+ HQ+
Sbjct: 148 LFAEGLIIDGDEQTLPAKLQIDQVDQESETSI---------------IRLILHEGKFHQV 192

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 193 KRMVKAVG 200


>gi|257880467|ref|ZP_05660120.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257883279|ref|ZP_05662932.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257886356|ref|ZP_05666009.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257891502|ref|ZP_05671155.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|257894555|ref|ZP_05674208.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|260562466|ref|ZP_05832976.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|261207204|ref|ZP_05921893.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289566697|ref|ZP_06447113.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecium D344SRF]
 gi|257814695|gb|EEV43453.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257818937|gb|EEV46265.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257822212|gb|EEV49342.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257827862|gb|EEV54488.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|257830934|gb|EEV57541.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|260073151|gb|EEW61496.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|260078832|gb|EEW66534.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289161514|gb|EFD09398.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecium D344SRF]
          Length = 245

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 88/248 (35%), Gaps = 51/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++ +++ G + V+ + VK           ++    +A+ +  
Sbjct: 7   MRLDKFLADMGLG-SRKEVKGLIKKGTIEVNGQVVKS-------DKAQVNEFEDAVTY-- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                             L  I+ Y+    Y+ +KPAG+           +   L+    
Sbjct: 57  ------------------LGEIITYQKDFYYILHKPAGVISATQDNHDQTVIDLLED--Q 96

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              +      RLD++T G+L++      A Q L+     + ++K Y + V GI   +   
Sbjct: 97  DYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLS---PKKHVEKEYLAEVSGIMTEEDIR 153

Query: 198 I--ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           +     ++            + Q ++    +I               + +  H G+ HQ+
Sbjct: 154 LFAEGLIIDGDEQTLPAKLQIDQVDQETETSI---------------IRLILHEGKFHQV 198

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 199 KRMVKAVG 206


>gi|255084041|ref|XP_002508595.1| rRNA/tRNA pseudouridine synthase [Micromonas sp. RCC299]
 gi|226523872|gb|ACO69853.1| rRNA/tRNA pseudouridine synthase [Micromonas sp. RCC299]
          Length = 730

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 23/105 (21%), Positives = 37/105 (35%), Gaps = 17/105 (16%)

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-----------------KFCWL 243
              ++S    D    V+        A + ++ +                          +
Sbjct: 472 PGTRRSAAADDGGRCVRAVTPDGKPARTEYQCLSSRLGVPTQVTMPDGVTRRTVVGTALV 531

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKL 288
             +P TGRTHQ+R+H  H G PIVGD  Y  ++     S    +L
Sbjct: 532 LARPLTGRTHQVRLHLAHAGFPIVGDGLYGVDYASVAASIGAFRL 576



 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/140 (19%), Positives = 47/140 (33%), Gaps = 40/140 (28%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--------AYHIDGFLKSWVDSK 140
           ++    D     ++YED  +   +KPAG+       +        A H      +    +
Sbjct: 243 DVPLQPDPSPLHVVYEDEWLMAVSKPAGVMTYPAHRLRGESVVSRAVHHLSVSAARRRGR 302

Query: 141 GQ--------------------------------KPRLTHRLDQETSGILVVARTRAAAQ 168
                                             +P   HRLD ETSG+L++A+ +  A 
Sbjct: 303 LPYSSEDLPEESGVGTPVGTPGGSFAGAWTSSQVEPIAVHRLDLETSGVLLLAKDKRVAS 362

Query: 169 HLTESFRMRRIQKIYWSLVW 188
            L   F  R ++K Y ++  
Sbjct: 363 ELQAKFEARGVRKTYLAVCA 382


>gi|125624024|ref|YP_001032507.1| pseudouridylate synthase [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|124492832|emb|CAL97787.1| pseudouridylate synthase [Lactococcus lactis subsp. cremoris
           MG1363]
          Length = 257

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 42/275 (15%), Positives = 89/275 (32%), Gaps = 56/275 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++ +G+V V+         ++ +G VV +          
Sbjct: 19  MRINKYLA-HAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDVVEVN--------- 68

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G IS          +   +   
Sbjct: 69  --------------------GVAVYNEEPVYYLLNKPRGYISSVSDDKGRQTVMDLM--- 105

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +T       + K+Y + V G    +  
Sbjct: 106 -PQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMMT--HPSHGVDKVYVAKVEGQANKENL 162

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
                L     I G  V   +            +++I     +    + +  H G+ HQ+
Sbjct: 163 ---RPLTLGMTIEGKKVSPAR------------YEIIKQEKTKNHSIVSLTIHEGQNHQV 207

Query: 256 RVHALHMGCPI--VGDHKYCANFKGNFTSPIQNKL 288
           +      G P+  +   +Y         +    +L
Sbjct: 208 KKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRL 242


>gi|300070794|gb|ADJ60194.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. cremoris NZ9000]
          Length = 239

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 42/275 (15%), Positives = 89/275 (32%), Gaps = 56/275 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++ +G+V V+         ++ +G VV +          
Sbjct: 1   MRINKYLA-HAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDVVEVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G IS          +   +   
Sbjct: 51  --------------------GVAVYNEEPVYYLLNKPRGYISSVSDDKGRQTVMDLM--- 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +T       + K+Y + V G    +  
Sbjct: 88  -PQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMMT--HPSHGVDKVYVAKVEGQANKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
                L     I G  V   +            +++I     +    + +  H G+ HQ+
Sbjct: 145 ---RPLTLGMTIEGKKVSPAR------------YEIIKQEKTKNHSIVSLTIHEGQNHQV 189

Query: 256 RVHALHMGCPI--VGDHKYCANFKGNFTSPIQNKL 288
           +      G P+  +   +Y         +    +L
Sbjct: 190 KKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRL 224


>gi|302386350|ref|YP_003822172.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
 gi|302196978|gb|ADL04549.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
          Length = 241

 Score = 72.3 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 84/251 (33%), Gaps = 50/251 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++            ++++ R G++ VD +  K                        
Sbjct: 4   LRLDKYLTEMGEG-TRSQIKEMARKGRIFVDGQPEK------------------------ 38

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K ++ +    N         S + YE    Y+ NKP G+     +      D  +     
Sbjct: 39  KTERKIHPEQNQVSVDGRPVSYVRYE---YYMLNKPQGVVS---ATEDSRYDTVISLIKS 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K        RLD +T G+L++      A Q L+     + + K+Y++ + G        
Sbjct: 93  RKRDDLFPVGRLDIDTEGLLLITNDGDLAHQLLS---PKKHVDKVYFARIQGELPPD--- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLR 256
                        + +        G     +H +V+    ++    + +    G+ HQ++
Sbjct: 147 -----------AKEQMEEGLVLSDGTPTMPAHLEVLKQGREESSLEILLTIREGKFHQVK 195

Query: 257 VHALHMGCPIV 267
                +GC ++
Sbjct: 196 RMFETLGCRVI 206


>gi|268319723|ref|YP_003293379.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           johnsonii FI9785]
 gi|262398098|emb|CAX67112.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           johnsonii FI9785]
          Length = 233

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 81/246 (32%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  +++   V V+ + VK    +++    V +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   LK   
Sbjct: 51  --------------------GEKVAYQQYHYFLLNKPKGVISATEDRSQKTVLSLLK--P 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             + +      RLD++T+G+L++    A A  L      + + K Y + + G+   +   
Sbjct: 89  KDRYKDIAPVGRLDKDTTGLLLLTNDGALAHEL--LAPNKHVTKKYRAKIAGVADEETVK 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I              + +   +      A     ++         +E++   G+ HQ++ 
Sbjct: 147 IFA------------IGMTLGDGTKLKPAELKI-LMQDKESDQSEIEIEIQEGKYHQIKR 193

Query: 258 HALHMG 263
               +G
Sbjct: 194 MFGAVG 199


>gi|152967064|ref|YP_001362848.1| pseudouridine synthase [Kineococcus radiotolerans SRS30216]
 gi|151361581|gb|ABS04584.1| pseudouridine synthase [Kineococcus radiotolerans SRS30216]
          Length = 322

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 92/255 (36%), Gaps = 52/255 (20%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D E +RL +         +    ++++ +G+V VD + V      + G  VRI P    +
Sbjct: 81  DPEGVRLQKVLAQAGAG-SRRACEEMIAAGRVTVDGEVVT-----ELG--VRIDPTRQVV 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL- 133
                             H D ++  +  E   I V NKP G+         Y  +G L 
Sbjct: 133 ------------------HVDGMRFSIDDELVYIMV-NKPKGVVS-----TMYDEEGRLN 168

Query: 134 -KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
               V  + ++     RLD ET G++++    A    L        +QK Y + V G   
Sbjct: 169 LADMVGPREERLFHVGRLDLETEGLILLTNDGALTHRL--QHPSFGVQKTYLAEVRG--- 223

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                +   L +    G +              ++  FK++D     +  +E+  H GR 
Sbjct: 224 ----PVKRDLGRNLRAGIEL--------DDGPVSVDSFKLVDSKP-GYALVEVVLHEGRK 270

Query: 253 HQLRVHALHMGCPIV 267
           H +R      G P++
Sbjct: 271 HIVRRMLEAEGYPVL 285


>gi|327468371|gb|EGF13856.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK330]
          Length = 242

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 87/250 (34%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQLLKKGLVLVNGRAEKS----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                      + + +D +      L+YE    Y+ NKP G+           +   L  
Sbjct: 37  -------PKTQIDEAADDIVVSGQRLIYEKFVYYLLNKPQGVISATEDDHHKTVLDLLDE 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+    
Sbjct: 90  TARQK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLMNQA 144

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTH 253
                   +++   G +      Q          H K+++   +K    +E+    G+ H
Sbjct: 145 D-------VERFAAGIELKDFTCQPA--------HLKILELDEEKEASLVEITLAEGKFH 189

Query: 254 QLRVHALHMG 263
           Q++      G
Sbjct: 190 QVKRMVAACG 199


>gi|322385923|ref|ZP_08059564.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           cristatus ATCC 51100]
 gi|321270038|gb|EFX52957.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           cristatus ATCC 51100]
          Length = 273

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 89/252 (35%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 31  MRINKYIA-HAGIASRRKAEELIKQGLVTVNGQVVRELATTIKSGDRVEVEGQP------ 83

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 84  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 115

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG L++         +        I K+Y + V G+   + 
Sbjct: 116 LLPQVKERIYPVGRLDWDTSGALILTNDGDFTDEM--IHPRNEIDKVYVARVKGVANKE- 172

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
             +   L +   I G               A+  ++++     +    +++  H GR HQ
Sbjct: 173 --VLRPLTRGLVIEGKKT----------KPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 218

Query: 255 LRVHALHMGCPI 266
           ++     +G P+
Sbjct: 219 VKKMFEAVGLPV 230


>gi|257413346|ref|ZP_04742734.2| ribosomal small subunit pseudouridine synthase A [Roseburia
           intestinalis L1-82]
 gi|257203834|gb|EEV02119.1| ribosomal small subunit pseudouridine synthase A [Roseburia
           intestinalis L1-82]
          Length = 239

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 47/245 (19%), Positives = 89/245 (36%), Gaps = 49/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +   ++K +RSG V V+ + VK                        
Sbjct: 5   MRLDKLLTELGTG-SRSEVKKYIRSGLVTVNGEVVKK----------------------- 40

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ++ + +  +    + L     Y + + Y+F+KPAG      +         +    D
Sbjct: 41  PEQRVDEKNDTVCFRGNPLT----YTEYEYYLFHKPAGCVT---ATEDNLHRTVMDYLTD 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +         RLD +T G+L++    A A  L      + + K+Y++ + G    +    
Sbjct: 94  TARHDLFPVGRLDIDTEGLLLITNDGALAHDL--LSPAKHVSKVYYAKIDGRVTEE---- 147

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L +     G+        EK A  A+   +V+   +     + +    GR HQ++  
Sbjct: 148 DVNLFENGVDIGE--------EKPAKPAL--LEVL--HSGDNSEIRLTITEGRFHQVKRM 195

Query: 259 ALHMG 263
              +G
Sbjct: 196 FEAVG 200


>gi|157872395|ref|XP_001684746.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|68127816|emb|CAJ06253.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 453

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 28/85 (32%), Positives = 40/85 (47%), Gaps = 19/85 (22%)

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
            +++ + V          + + PHTGR HQLRVH   +G PIVGD  YCA+       P+
Sbjct: 314 PSVTSYPV--------TLVLLAPHTGRRHQLRVHCRAIGFPIVGDTSYCADLPWCTALPL 365

Query: 285 -----------QNKLYLHARYMDLP 298
                        ++YLHA  + LP
Sbjct: 366 GSSPSTWVTAGARRMYLHAWRLLLP 390



 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/111 (24%), Positives = 48/111 (43%), Gaps = 17/111 (15%)

Query: 108 IYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQ----------------KPRLTHRL 150
           + V NKP GI + G   I    ++  +   + ++G                 + +  H+L
Sbjct: 1   MLVVNKPPGILMDGDESIYGRTVESLVCEHMKARGIFDETHEQLQKEKKRKKQLKFVHQL 60

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
           D  TSG+L +A T+  A  L   F MR ++K Y +L+ G   +    + + 
Sbjct: 61  DFGTSGVLCLAFTKDMAARLAHCFEMRLVRKYYVALLHGHLPSDTALLEDA 111


>gi|329667573|gb|AEB93521.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii DPC 6026]
          Length = 233

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 81/246 (32%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  +++   V V+ + VK    +++    V +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVD--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   LK   
Sbjct: 51  --------------------GEKVAYQQYHYFLLNKPKGVISATEDRSQKTVLSLLKPKD 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             KG  P    RLD++T+G+L++    A A  L      + + K Y + + G+   +   
Sbjct: 91  RYKGIAP--VGRLDKDTTGLLLLTNDGALAHEL--LAPNKHVTKKYRAKIAGVADEETVE 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I                +   +      A     +I         +E++   G+ HQ++ 
Sbjct: 147 IFA------------SGMTLGDGTKLKPAELKI-LIQDKEADRSEIEIEIQEGKYHQIKR 193

Query: 258 HALHMG 263
               +G
Sbjct: 194 MFGAVG 199


>gi|296875977|ref|ZP_06900036.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           parasanguinis ATCC 15912]
 gi|296433052|gb|EFH18840.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           parasanguinis ATCC 15912]
          Length = 243

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 83/248 (33%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I++G  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATIIKTGDQVEVEGTP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G+ S          +   L   
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRTTVVDLLSQV 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +        I K+Y + V GI   +  
Sbjct: 91  P----ERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGIANKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQL 255
                              V  + K    A   ++++     +    +++  H GR HQ+
Sbjct: 145 -------------RPLTRGVTIDGKKTKPAT--YEILKVDVEKNRSVVQLTIHEGRNHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KKMFEAVG 197


>gi|300361439|ref|ZP_07057616.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           gasseri JV-V03]
 gi|300354058|gb|EFJ69929.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           gasseri JV-V03]
          Length = 248

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 86/251 (34%), Gaps = 48/251 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72
             +  MR+D++  N     +   +  +++   V V+ + V     +++   +V +     
Sbjct: 11  EKDIEMRIDKYLANMNVG-SRKEVHSLIKKKVVTVNGELVTAPKQQVKEDDLVVVDGNE- 68

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                                       + Y+    ++ NKP G+           +   
Sbjct: 69  ----------------------------IAYQQYHYFLLNKPKGVISATEDRSQQTVISL 100

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           LK+    + Q      RLD+ T+G+L++    A A  L      + + K+Y + + G+  
Sbjct: 101 LKT--KDRYQGIAPVGRLDKNTTGLLLLTNDGALAHEL--LAPNKHVTKVYRAKISGV-- 154

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +E I  +    +   G  +       K A   I    +          +E+Q   G+ 
Sbjct: 155 ASEETIKTFASGITLGDGTKL-------KPAKLEI----LAQDKVHDLSQIEIQIQEGKY 203

Query: 253 HQLRVHALHMG 263
           HQ++     +G
Sbjct: 204 HQIKRMFGAVG 214


>gi|268316878|ref|YP_003290597.1| RNA-binding S4 domain-containing protein [Rhodothermus marinus DSM
           4252]
 gi|262334412|gb|ACY48209.1| RNA-binding S4 domain protein [Rhodothermus marinus DSM 4252]
          Length = 268

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 41/258 (15%), Positives = 81/258 (31%), Gaps = 48/258 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           + V +    +RL+R+        +     +++ SGQVRV+ +  +   R+    +V +  
Sbjct: 1   MTVSDKSSLIRLNRYLARAGVCPSRRKADELIASGQVRVNGQVAQLGMRVGPDDIVEVN- 59

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
                             V +   +  L            + NKP               
Sbjct: 60  -----------------GVRVVPQTQAL----------YILMNKPHDTITTCDDERGRRT 92

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L +    +        RLD+ T+G+L++      A  L       R++KIY +    
Sbjct: 93  VLDLINLPPEQKNGLFPVGRLDRNTTGVLLLTNDGELANRL--MHPRYRVEKIYVARTAR 150

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             K ++               + +    Q E G   A+     +         + +  + 
Sbjct: 151 PVKPEE--------------AEQLRRGVQLEDGPARAVQ----VAVNPADPHEIALMIYE 192

Query: 250 GRTHQLRVHALHMGCPIV 267
           GR  Q+R     +G  +V
Sbjct: 193 GRNRQVRRMLEAIGHEVV 210


>gi|227515180|ref|ZP_03945229.1| pseudouridylate synthase [Lactobacillus fermentum ATCC 14931]
 gi|227086512|gb|EEI21824.1| pseudouridylate synthase [Lactobacillus fermentum ATCC 14931]
          Length = 241

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/255 (18%), Positives = 91/255 (35%), Gaps = 54/255 (21%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
              RL +    H    +    + ++ +G+V+V+ + V     ++     V +        
Sbjct: 2   AKERLQKVIA-HAGVASRRAAEGLILAGKVKVNGQVVTELGTKVDGNDEVMVNGEPVEQ- 59

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFL 133
                                       E  + Y+ +KP G+  S     G    +D   
Sbjct: 60  ----------------------------EQHEYYLLDKPRGVISSAHDDKGRKTVVDILK 91

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              V +   +     RLD +T+G+LV+      A  L        + K+Y + V G+  N
Sbjct: 92  NEGVQT---RVYPVGRLDYDTTGLLVMTNDGELANRL--MHPRFEVDKVYIAKVKGLVSN 146

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRT 252
            +      LL++          VK + K +  A +  K+++    QK   +++  H G  
Sbjct: 147 DEMR----LLREG---------VKIDGKKSQPART--KLLEANQRQKTSVVKLTIHEGHY 191

Query: 253 HQLRVHALHMGCPIV 267
           HQ++     +G P++
Sbjct: 192 HQVKKMMEAVGHPVL 206


>gi|322375796|ref|ZP_08050307.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           C300]
 gi|321279064|gb|EFX56106.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           C300]
          Length = 240

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 88/247 (35%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q                I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQ----------------IN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E+  +           F   +L YE+   Y+ NKP G+           +   L     
Sbjct: 43  EERDEI----------RFDGQVLEYEEFVYYMMNKPQGVISATEDSKHRTVLDLLDDIAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KE 196
           +K  +     RLD +T G+L++      A  L      R + K Y + V GI   +  + 
Sbjct: 93  TK--EVFPVGRLDIDTHGLLLLTNDGQLAHAL--LSPKRHVDKTYLAHVEGIMTQEDVET 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +    LK        + +V  +                  +    + +    G+ HQ++
Sbjct: 149 FVKGIPLKDFTCQPAKLEIVSVDS----------------VKNQSLVRVTIAEGKFHQVK 192

Query: 257 VHALHMG 263
               + G
Sbjct: 193 RMVAYCG 199


>gi|322384180|ref|ZP_08057890.1| 16S pseudouridylate synthase-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151072|gb|EFX44389.1| 16S pseudouridylate synthase-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 256

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 85/251 (33%), Gaps = 59/251 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD+    H  +     L+K+ ++G V V+ K VK                        
Sbjct: 11  LRLDKMLS-HLGYGTRSELKKLAKNGGVTVNGKVVK------------------------ 45

Query: 79  KEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 DS   +    D+++     +++ +    + NKPAG+           +   L  
Sbjct: 46  ------DSGWKVYPDEDYIEVNGEQVIFREHVYVLLNKPAGVISATEDMRDRTVVDLLDD 99

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +   G       RLD++T G+L++    + A   L+     + + K Y++ V G    +
Sbjct: 100 HIRVFG--VFPVGRLDKDTEGLLLLTNDGKLAHNLLS---PRKHVPKTYYARVNGDVTEE 154

Query: 195 KECIANWLLKKSH----IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              I +  +        +    V +   N +    A                +E+  H G
Sbjct: 155 DVRIFSEGVVLDDGYMTMPAQLVVLDSGNPEEEKPAE---------------IELTIHEG 199

Query: 251 RTHQLRVHALH 261
           + HQ++     
Sbjct: 200 KFHQVKRMFEA 210


>gi|293192784|ref|ZP_06609679.1| ribosomal large subunit pseudouridine synthase B [Actinomyces
           odontolyticus F0309]
 gi|292820031|gb|EFF79029.1| ribosomal large subunit pseudouridine synthase B [Actinomyces
           odontolyticus F0309]
          Length = 249

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 49/252 (19%), Positives = 93/252 (36%), Gaps = 49/252 (19%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RL +         +    ++++  G+V VD   V+        Q VR+ P    + 
Sbjct: 8   EGGVRLQKVLAQA-GVASRRASEQMIADGRVSVDGTVVR-------NQGVRVDPTKQVI- 58

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLK 134
           H+  E+ ILD + ++                 +   NKP G +S          I   + 
Sbjct: 59  HVDGERLILDETKHI-----------------VLAVNKPIGTVSTMSDPEGRPTIADLIA 101

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +     ++     RLD +TSG+L++      A  LT       I+K Y + + G  K  
Sbjct: 102 DYP----ERLYHVGRLDIDTSGLLLLTNDGELANRLT--HPKYEIRKTYVARLHGEVK-- 153

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                   +K++ + G          +     +  F+++D +      +E+  H GR   
Sbjct: 154 ------PGVKRTLMNG-------IELEDGPIKVDSFRIVDTYGDITT-VEIVVHEGRNRL 199

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 200 VRRMMEAVGYPV 211


>gi|108759403|ref|YP_632021.1| ribosomal large subunit pseudouridine synthase B [Myxococcus
           xanthus DK 1622]
 gi|108463283|gb|ABF88468.1| ribosomal large subunit pseudouridine synthase B [Myxococcus
           xanthus DK 1622]
          Length = 745

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 88/253 (34%), Gaps = 52/253 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINAL 74
              RL ++        +  + ++++ +G+V V+ K V    +R++ G  +V +       
Sbjct: 2   AAERLQKYLARA-GVASRRHAEELITAGRVAVNNKTVTELGSRVEPGTDLVTVDGT---- 56

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                          L    D     LLY         KP G+     +         + 
Sbjct: 57  ---------------LVTPPDESSYFLLY---------KPVGVVT---TLSDPQGRPTVA 89

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           ++V+  G++     RLD +  G L+     A A  LT      ++ + Y + V G P   
Sbjct: 90  NYVEETGKRLFPVGRLDYDAEGALLFTDDGALAHKLT--HPSFQVPRTYLAKVKGAPDT- 146

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                      + +      V  ++      ++S F+  +       WL++    GR H 
Sbjct: 147 -----------ATLDKLRGGVRLEDGMATPVSVSVFEAAERN----TWLKIVVAEGRPHL 191

Query: 255 LRVHALHMGCPIV 267
           ++     +G P+V
Sbjct: 192 IKRLCAAVGHPVV 204


>gi|194467810|ref|ZP_03073796.1| pseudouridine synthase [Lactobacillus reuteri 100-23]
 gi|194452663|gb|EDX41561.1| pseudouridine synthase [Lactobacillus reuteri 100-23]
          Length = 238

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 94/261 (36%), Gaps = 54/261 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++  G+V V+ K V     ++     + +          
Sbjct: 2   ERLQKAMAEA-GVASRRASEKLILQGKVAVNGKIVTELGTKVGVHDEIVVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  + +E    Y+ NKP G+  S     G    +D    +
Sbjct: 52  --------------------GVPIHHEQHVYYLLNKPRGVISSAHDDKGRRTVVDIIHDA 91

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +D   ++     RLD +T+GIL++    A A  L        ++K Y + V GI KN +
Sbjct: 92  DID---ERIYPVGRLDYDTTGILLLTNDGALANKL--MHPKYEVEKTYVAKVEGIVKNDE 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                  LK+  +G      V  + +    A S    +D  A+K   +++  H GR HQ+
Sbjct: 147 -------LKQLRLG------VVIDGRKTKPAKSKLLNVDR-AKKTSLVQLTIHEGRNHQV 192

Query: 256 RVHALHMGCPI--VGDHKYCA 274
           +     +G P+  +    Y  
Sbjct: 193 KNMFKAVGHPVTKLHRETYGP 213


>gi|312868359|ref|ZP_07728559.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           parasanguinis F0405]
 gi|322390066|ref|ZP_08063601.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           parasanguinis ATCC 903]
 gi|311096104|gb|EFQ54348.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           parasanguinis F0405]
 gi|321143193|gb|EFX38636.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           parasanguinis ATCC 903]
          Length = 243

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 83/248 (33%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I++G  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATIIKTGDQVEVEGTP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G+ S          +   L   
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRTTVVDLLSQV 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +        I K+Y + V GI   +  
Sbjct: 91  P----ERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGIANKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQL 255
                              V  + K    A   ++++     +    +++  H GR HQ+
Sbjct: 145 -------------RPLTRGVTIDGKKTKPAT--YEILKVDVEKNRSVVQLTIHEGRNHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KKMFEAVG 197


>gi|312277674|gb|ADQ62331.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 255

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 89/256 (34%), Gaps = 54/256 (21%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
             E  E+ MR++++   H    +    +++++ G+V ++ K V +    +++G +V +  
Sbjct: 7   TAEAVEKRMRINKYIA-HAGVASRRKAEELIKEGRVTLNGKTVMELATIVKNGDIVEVN- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYH 128
                                        S +  E+   Y+ NKP G+ S          
Sbjct: 65  ----------------------------GSPIYNEEKVYYLLNKPRGVISSVSDEKNRKT 96

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +   +        ++     RLD +T+G+L++         +        I K+Y + V 
Sbjct: 97  VIDLMPHV----KERIYPVGRLDWDTTGLLILTNDGDFTDKM--IHPRNEIDKVYLARVK 150

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQP 247
           GI   +                     V  + K    A  H+ +I     +    +E+  
Sbjct: 151 GIATKENL-------------RPLTRGVVIDGKKTQPA--HYNIIKVDHEKNRSVVELTI 195

Query: 248 HTGRTHQLRVHALHMG 263
           H GR HQ++     +G
Sbjct: 196 HEGRNHQVKKMFESVG 211


>gi|296225812|ref|XP_002758673.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           3-like [Callithrix jacchus]
          Length = 399

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 55/274 (20%), Positives = 98/274 (35%), Gaps = 66/274 (24%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
           +L  + +  +  D L++ ++     +   NKP G+ V G  G        L S +    Q
Sbjct: 157 LLSKNFSREELVDALRTAVVDRKGPLVTLNKPQGLPVTGKPGEL-----TLLSVLPELSQ 211

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              L    D+E   + VV     A+          R +  +            + +   +
Sbjct: 212 SLGLG---DRE---LQVV----RASGXXXXXXXXXRPELEHI-----------DGVNLSV 250

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
           L K+    D +       +G    +SHF+V+         +++QP T  + QL+VH +  
Sbjct: 251 LVKAPSRKDIL-------EGVKKTLSHFRVLAT-GSGCALVQLQPLTVFSSQLQVHMVLQ 302

Query: 263 GCPIVGDHKYCAN----FKGNFTSPI-----QNKLYLHA--RYMDLPHPEGGRL------ 305
            CP++GDH Y A         F  P      Q ++   A  R + L   +  ++      
Sbjct: 303 LCPVLGDHTYSARVGTVLGQRFLLPAESTKPQTQVLDEALLRRLQLTPSQAAQMPLHLHL 362

Query: 306 ---------------QITAPLPAHMVKTWDSLGF 324
                          ++ APLP +  +T   LG 
Sbjct: 363 HRLLLPGTRARDTPIELLAPLPPYFSRTLQCLGL 396


>gi|55820359|ref|YP_138801.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           thermophilus LMG 18311]
 gi|55822249|ref|YP_140690.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           thermophilus CNRZ1066]
 gi|116627195|ref|YP_819814.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           thermophilus LMD-9]
 gi|55736344|gb|AAV59986.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           thermophilus LMG 18311]
 gi|55738234|gb|AAV61875.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           thermophilus CNRZ1066]
 gi|116100472|gb|ABJ65618.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           thermophilus LMD-9]
          Length = 255

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 89/256 (34%), Gaps = 54/256 (21%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69
             E  E+ MR++++   H    +    +++++ G+V ++ K V +    +++G +V +  
Sbjct: 7   TAEAVEKRMRINKYIA-HAGVASRRKAEELIKEGRVTLNGKTVMELATIVKNGDIVEVN- 64

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYH 128
                                        S +  E+   Y+ NKP G+ S          
Sbjct: 65  ----------------------------GSPIYNEEKVYYLLNKPRGVISSVSDEKNRKT 96

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +   +        ++     RLD +T+G+L++         +        I K+Y + V 
Sbjct: 97  VIDLMPHV----KERIYPVGRLDWDTTGLLILTNDGDFTDKM--IHPRNEIDKVYLARVK 150

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQP 247
           GI   +                     V  + K    A  H+ +I     +    +E+  
Sbjct: 151 GIATKENL-------------RPLTRGVVIDGKKTQPA--HYNIIKVDHEKNRSVVELTI 195

Query: 248 HTGRTHQLRVHALHMG 263
           H GR HQ++     +G
Sbjct: 196 HEGRNHQVKKMFESVG 211


>gi|227544893|ref|ZP_03974942.1| pseudouridylate synthase [Lactobacillus reuteri CF48-3A]
 gi|300910080|ref|ZP_07127540.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri SD2112]
 gi|227185105|gb|EEI65176.1| pseudouridylate synthase [Lactobacillus reuteri CF48-3A]
 gi|300892728|gb|EFK86088.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri SD2112]
          Length = 238

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 51/261 (19%), Positives = 94/261 (36%), Gaps = 54/261 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++  G+V V+ K V     ++     + +          
Sbjct: 2   ERLQKAMAEA-GVASRRASEKLILQGKVAVNGKIVTELGTKVGVHDEIVVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  + +E    Y+ NKP G+  S     G    +D    +
Sbjct: 52  --------------------GVPIHHEQHVYYLLNKPRGVISSAHDDKGRRTVVDIIHDA 91

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +D   ++     RLD +T+GIL++    A A  +        ++K Y + V GI KN +
Sbjct: 92  EID---ERIYPVGRLDYDTTGILLLTNDGALANKM--MHPKYEVEKTYVAKVEGIVKNDE 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                  LK+  +G      V  + +    A S    +D  A+K   +++  H GR HQ+
Sbjct: 147 -------LKQLRLG------VVIDGRKTKPAKSKLLNVDR-AKKTSLVQLTIHEGRNHQV 192

Query: 256 RVHALHMGCPI--VGDHKYCA 274
           +     +G P+  +    Y  
Sbjct: 193 KNMFKAVGHPVTKLHRETYGP 213


>gi|239623801|ref|ZP_04666832.1| pseudouridine synthase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521832|gb|EEQ61698.1| pseudouridine synthase [Clostridiales bacterium 1_7_47FAA]
          Length = 243

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 89/249 (35%), Gaps = 47/249 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++      +     +++++R G+V+V+ + +K                        
Sbjct: 1   MRLDKFLGE-MGYGTRTQIKEMVRKGRVQVNGQVIKA----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E K+       T      +S++ Y   + Y+ NKP  +           + G +   + 
Sbjct: 37  PESKLAPE----TDQVMVDQSVVGYARMEYYMLNKPKDVVSATTDSRYPTVVGLIGDALR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC 197
                     RLD +T G+L++      A +L      + + K+Y + + G +P N KE 
Sbjct: 93  K---DLFPVGRLDVDTEGLLIITNDGEMAHNL--LSPKKHVDKVYMARLSGRLPVNAKER 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            +  ++    +                 A+  ++      +    + +    G+ HQ++ 
Sbjct: 148 FSEGIVLDDGVK-------------TLPALLEYEGCGNGTEGLTEVLLTIREGKFHQVKR 194

Query: 258 HALHMGCPI 266
               +GC +
Sbjct: 195 MFEALGCHV 203


>gi|148910624|gb|ABR18382.1| unknown [Picea sitchensis]
          Length = 358

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 30/104 (28%), Positives = 43/104 (41%), Gaps = 3/104 (2%)

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           + V V +QN K            +        +   P +GRTHQ+R+H  +MG PI GD 
Sbjct: 251 EKVVVTEQNSKAPGQDRDIVSSPNIRKNDEVLIRASPLSGRTHQIRLHCQYMGLPIRGDV 310

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL-QITAPLPA 313
           KY         +   +   LHA  +   HP    + +  APLP 
Sbjct: 311 KYEGPHIWKGITYANH--ALHAESLCFEHPVTNNMVKFHAPLPQ 352



 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 37/201 (18%), Positives = 72/201 (35%), Gaps = 16/201 (7%)

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           +      L+  ++  + + +   +       ++  +YED  +   NKP+G+       + 
Sbjct: 30  LSQPPPELSRQVEYDRAMRAEAAVKAGPALSRNEFIYEDEWMIAVNKPSGVYC---EHVL 86

Query: 127 YHIDGFLKSWV-------DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             I   L S         D    +  L +RLD++TSG++V+ +    A  L ++F  R++
Sbjct: 87  SSIPELLASSPSSAGAANDVNPLELHLANRLDRDTSGVMVITKLHKIAGQLVKAFTDRKV 146

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE---KGA---NYAISHFKVI 233
           +K Y +L  G               +S  G   V+          G        +H KV+
Sbjct: 147 RKTYLALCIGPAPKWNNIYIESGHGRSKFGAWRVYSRTDVGRILPGGTVVREMATHLKVL 206

Query: 234 DCFAQKFCWLEMQPHTGRTHQ 254
              A      +       + Q
Sbjct: 207 AVNANHRMHRDSVDKAQNSSQ 227


>gi|148983686|ref|ZP_01817005.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP3-BS71]
 gi|148996705|ref|ZP_01824423.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP11-BS70]
 gi|168490791|ref|ZP_02714934.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           CDC0288-04]
 gi|182683261|ref|YP_001835008.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae CGSP14]
 gi|194398298|ref|YP_002036978.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae G54]
 gi|225853878|ref|YP_002735390.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           JJA]
 gi|303255185|ref|ZP_07341259.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS455]
 gi|303259389|ref|ZP_07345366.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP-BS293]
 gi|303261144|ref|ZP_07347093.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP14-BS292]
 gi|303263472|ref|ZP_07349395.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS397]
 gi|303265764|ref|ZP_07351662.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS457]
 gi|303267805|ref|ZP_07353607.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS458]
 gi|307066956|ref|YP_003875922.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Streptococcus pneumoniae AP200]
 gi|147757280|gb|EDK64319.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP11-BS70]
 gi|147923833|gb|EDK74945.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP3-BS71]
 gi|182628595|gb|ACB89543.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae CGSP14]
 gi|183574853|gb|EDT95381.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           CDC0288-04]
 gi|194357965|gb|ACF56413.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae G54]
 gi|225722369|gb|ACO18222.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           JJA]
 gi|301799421|emb|CBW31958.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus pneumoniae OXC141]
 gi|301801222|emb|CBW33896.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus pneumoniae INV200]
 gi|302597818|gb|EFL64890.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS455]
 gi|302637981|gb|EFL68467.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP14-BS292]
 gi|302639323|gb|EFL69781.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP-BS293]
 gi|302642501|gb|EFL72846.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS458]
 gi|302644672|gb|EFL74921.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS457]
 gi|302647245|gb|EFL77469.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae BS397]
 gi|306408493|gb|ADM83920.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Streptococcus pneumoniae AP200]
 gi|332077581|gb|EGI88042.1| hypothetical protein SPAR68_0323 [Streptococcus pneumoniae GA41301]
 gi|332202193|gb|EGJ16262.1| hypothetical protein SPAR69_0304 [Streptococcus pneumoniae GA41317]
 gi|332204287|gb|EGJ18352.1| hypothetical protein SPAR120_0252 [Streptococcus pneumoniae
           GA47901]
          Length = 240

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 90/247 (36%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q  + +         + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQIDEKI---------DEIR 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++L+                 YE+   Y+ NKP G+           +   L     
Sbjct: 50  FDGQVLE-----------------YEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KE 196
           SK  +     RLD +T G+L++      A  L      R + K Y + V GI   +  + 
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNNGQLAHVL--LSPKRHVDKTYQAQVKGIMTQEDVET 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I    LK        + ++  + +                +    + +    G+ HQ++
Sbjct: 149 FIKGIPLKDFTCQPARLEILSTDAE----------------KNQSQIRVTIAEGKFHQIK 192

Query: 257 VHALHMG 263
               + G
Sbjct: 193 RMVGYCG 199


>gi|116512118|ref|YP_809334.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. cremoris SK11]
 gi|116107772|gb|ABJ72912.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. cremoris SK11]
          Length = 239

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 42/275 (15%), Positives = 89/275 (32%), Gaps = 56/275 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++ +G+V V+         ++ +G VV +          
Sbjct: 1   MRINKYLA-HAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDVVEVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G IS          +   +   
Sbjct: 51  --------------------GVAVYNEEPVYYLLNKPRGYISSVRDDKGRQTVMDLM--- 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +T       + K+Y + V G    +  
Sbjct: 88  -PQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMMT--HPSHGVDKVYVAKVEGQANKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
                L     I G  V   +            +++I     +    + +  H G+ HQ+
Sbjct: 145 ---RPLTLGMTIEGKKVSPAR------------YEIIKQEKTKNHSIVSLTIHEGQNHQV 189

Query: 256 RVHALHMGCPI--VGDHKYCANFKGNFTSPIQNKL 288
           +      G P+  +   +Y         +    +L
Sbjct: 190 KKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRL 224


>gi|291522211|emb|CBK80504.1| ribosomal small subunit pseudouridine synthase A [Coprococcus catus
           GD/7]
          Length = 250

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 81/245 (33%), Gaps = 52/245 (21%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD++  +         ++ +++ G V V+ + + K   ++           I   + + 
Sbjct: 6   RLDKYLADMSVG-TRSEVKNLIKKGLVTVNGEVIRKPEYKV----------DIEKDDLVC 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + + +                   Y+    Y+ NKPAG+     +         L    D
Sbjct: 55  RGEPVA------------------YQTLVYYMLNKPAGVIS---ATNDPKQKTVLDLITD 93

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
              +      RLD++T G+L++      A Q L+     + + K+Y + + G +      
Sbjct: 94  KSRKDLFPVGRLDKDTEGLLLITNDGDLAHQLLS---PKKHVDKVYRARIEGQVTAEDAA 150

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             A  L      G       K N            ++    +    +E+    G+ HQ++
Sbjct: 151 LFAKGLGIDDEDGAWRAMPAKLN------------ILSSGPE--SEIEITIREGKFHQIK 196

Query: 257 VHALH 261
                
Sbjct: 197 RMFEA 201


>gi|322391362|ref|ZP_08064832.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           peroris ATCC 700780]
 gi|321145788|gb|EFX41179.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           peroris ATCC 700780]
          Length = 240

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V GI     
Sbjct: 86  LLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGIADKDN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                               V+ + K    A+  ++++     +    +++  H GR HQ
Sbjct: 144 L-------------RPLTRGVEIDGKKTKPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|167464456|ref|ZP_02329545.1| pseudouridine synthase [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 250

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 86/253 (33%), Gaps = 59/253 (23%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +RLD+    H  +     L+K+ ++G V V+ K VK                      
Sbjct: 3   ETLRLDKMLS-HLGYGTRSELKKLAKNGGVTVNGKVVK---------------------- 39

Query: 77  IIKEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                   DS   +    D+++     +++ +    + NKPAG+           +   L
Sbjct: 40  --------DSGWKVYPDEDYIEVNGEQVIFREHVYVLLNKPAGVISATEDMRDRTVVDLL 91

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              +   G       RLD++T G+L++    + A   L+     + + K Y++ V G   
Sbjct: 92  DDHIRVFG--VFPVGRLDKDTEGLLLLTNDGKLAHNLLS---PRKHVPKTYYARVNGDVT 146

Query: 193 NKKECIANWLLKKSH----IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
            +   I +  +        +    V +   N +    A                +E+  H
Sbjct: 147 EEDVRIFSEGVVLDDGYMTMPAQLVVLDSGNPEEEKPAE---------------IELTIH 191

Query: 249 TGRTHQLRVHALH 261
            G+ HQ++     
Sbjct: 192 EGKFHQVKRMFEA 204


>gi|149006033|ref|ZP_01829762.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP18-BS74]
 gi|307126496|ref|YP_003878527.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           670-6B]
 gi|147762389|gb|EDK69350.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP18-BS74]
 gi|306483558|gb|ADM90427.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           670-6B]
 gi|332076726|gb|EGI87188.1| hypothetical protein SPAR148_0259 [Streptococcus pneumoniae
           GA17545]
          Length = 240

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 85/245 (34%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q  + +             
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQIDEKID------------ 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                            F   +L YE+   Y+ NKP G+           +   L     
Sbjct: 47  --------------EIRFDGQVLEYEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK  +     RLD +T G+L++      A  L      R + K Y + V GI   +   I
Sbjct: 93  SK--EIFPVGRLDIDTHGLLLLTNDGQLAHVL--LSPKRHVDKTYLAQVKGIMTQEDVEI 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     AI     ID   +    + +    G+ HQ++  
Sbjct: 149 -------------FAEGIPLKDFTCQPAILELVSIDT-EKNQSQIRVTIAEGKFHQIKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VGYCG 199


>gi|289578329|ref|YP_003476956.1| pseudouridine synthase [Thermoanaerobacter italicus Ab9]
 gi|289528042|gb|ADD02394.1| pseudouridine synthase [Thermoanaerobacter italicus Ab9]
          Length = 236

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 86/250 (34%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL ++        +    ++ +  G+V+V+ K VK                      I 
Sbjct: 2   VRLQKYLAE-CGIASRRKCEEYILQGRVKVNGKEVK-----------------ELGVKIN 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            +  I++    + +       I+L         NKP G I+          +   +K   
Sbjct: 44  PDVDIIEFDDKIVRREKKKVYIML---------NKPTGYITSVKDQFGRPTVMDLVKV-- 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  L        I K Y + + GIP  ++  
Sbjct: 93  ---KERIYPVGRLDYDTSGLLLLTNDGEIANIL--MHPRHEIVKTYIAKIKGIPTQEELE 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                 +   + GDY+    + E            I         +E++ H G+  Q+R 
Sbjct: 148 ----RFRNGLLIGDYLTSKAEIE------------ILAVKNGTSVVEIKIHEGKNRQVRR 191

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 192 MCEAIGHPVI 201


>gi|226360073|ref|YP_002777851.1| pseudouridine synthase [Rhodococcus opacus B4]
 gi|226238558|dbj|BAH48906.1| pseudouridine synthase [Rhodococcus opacus B4]
          Length = 350

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 44/251 (17%), Positives = 80/251 (31%), Gaps = 45/251 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + MRL +         +    ++++  G+V VD + V                 I     
Sbjct: 108 DGMRLQKVLAQA-GVASRRAAEELISQGRVEVDGRIV-----------------IEQGLR 149

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           I  E  ++            L              NKP G        +     G + S 
Sbjct: 150 IDPENAVVRVDGVRVVVQKDLVH---------LALNKPRGWQSTMSDDLGRPCVGDIVSE 200

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             + GQ+     RLD +T G+L++      A  L        + K Y + V G  +    
Sbjct: 201 RVAAGQRLFHVGRLDADTEGLLLLTNDGDLAHRL--MHPSFEVSKTYLATVSGALE---- 254

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                      +G      V+ ++  A   +  F ++D   +    + +  H GR H +R
Sbjct: 255 ---------RGVGKKLKEGVELDDGPAK--VDTFTLLD-INEGKSLVRVTLHEGRKHIVR 302

Query: 257 VHALHMGCPIV 267
                +G P++
Sbjct: 303 RLFDAVGHPVI 313


>gi|326406814|gb|ADZ63885.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. lactis CV56]
          Length = 257

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 41/275 (14%), Positives = 89/275 (32%), Gaps = 56/275 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++ +G+V V+         ++ +G +V +          
Sbjct: 19  MRINKYLA-HAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDIVEVN--------- 68

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G IS          +   +   
Sbjct: 69  --------------------GVAVYNEEPVYYLLNKPRGYISSVSDDKGRQTVMDLM--- 105

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +T       + K+Y + V G    +  
Sbjct: 106 -PQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMMT--HPRHGVDKVYVAKVEGQANKENL 162

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
                L     I G  V   +            +++I     +    + +  H G+ HQ+
Sbjct: 163 ---RPLTLGMTIEGKKVSPAR------------YEIIKQEKTKNHSIVSLTIHEGQNHQV 207

Query: 256 RVHALHMGCPI--VGDHKYCANFKGNFTSPIQNKL 288
           +      G P+  +   +Y         +    +L
Sbjct: 208 KKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRL 242


>gi|154508819|ref|ZP_02044461.1| hypothetical protein ACTODO_01329 [Actinomyces odontolyticus ATCC
           17982]
 gi|153798453|gb|EDN80873.1| hypothetical protein ACTODO_01329 [Actinomyces odontolyticus ATCC
           17982]
          Length = 249

 Score = 71.9 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 49/252 (19%), Positives = 93/252 (36%), Gaps = 49/252 (19%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RL +         +    ++++  G+V VD   V+        Q VR+ P    + 
Sbjct: 8   EGGVRLQKVLAQA-GVASRRASEQMIADGRVSVDGTVVR-------NQGVRVDPAKQVI- 58

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLK 134
           H+  E+ ILD + ++                 +   NKP G +S          I   + 
Sbjct: 59  HVDGERLILDETKHI-----------------VLAVNKPIGTVSTMSDPEGRPTIADLIA 101

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +     ++     RLD +TSG+L++      A  LT       I+K Y + + G  K  
Sbjct: 102 DYP----ERLYHVGRLDIDTSGLLLLTNDGELANRLT--HPKYEIRKTYVARLHGEVK-- 153

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                   +K++ + G          +     +  F+++D +      +E+  H GR   
Sbjct: 154 ------PGVKRTLMNG-------IELEDGPIKVDSFRIVDTYGDITT-VEIVVHEGRNRL 199

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 200 VRRMMEAVGYPV 211


>gi|315604212|ref|ZP_07879278.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 180 str. F0310]
 gi|315313918|gb|EFU61969.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 180 str. F0310]
          Length = 249

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 49/252 (19%), Positives = 93/252 (36%), Gaps = 49/252 (19%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RL +         +    ++++  G+V VD   V+        Q VR+ P    + 
Sbjct: 8   EGGVRLQKVLAQA-GIASRRASEQMIADGRVSVDGTVVRT-------QGVRVDPATQVI- 58

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLK 134
           H+  E+ ILD + ++                 +   NKP G +S          I   + 
Sbjct: 59  HVDGERLILDEAKHI-----------------VLAVNKPIGTVSTMSDPEGRPTIADLIA 101

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +     ++     RLD +TSG+L++      A  LT       I+K Y + + G  K  
Sbjct: 102 DYP----ERLYHVGRLDIDTSGLLLLTNDGELANRLT--HPSYEIRKTYVARLHGEVK-- 153

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                   +++  + G          +    A+  F+++D +      +E+  H GR   
Sbjct: 154 ------PGVRRRLLAG-------IELEDGPIAVDSFRLVDTYGDITT-VEIVVHEGRNRL 199

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 200 VRRMMEAVGYPV 211


>gi|15615835|ref|NP_244139.1| 16S pseudouridylate synthase [Bacillus halodurans C-125]
 gi|10175896|dbj|BAB06992.1| 16S pseudouridylate synthase [Bacillus halodurans C-125]
          Length = 238

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 88/248 (35%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N     +  +++K+L++G VRV  + +K                        
Sbjct: 1   MRIDKFLANMGFG-SRKDVKKLLKTGAVRVQGQPIK------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 D S ++   S+ +      + Y+     + NKP G+           +   L  
Sbjct: 36  ------DPSTHVEPESESITVYGEEVEYKPYVYLMMNKPKGVICATEDLEHETVIDLL-- 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             + +  +P    RLD++T G+L++         L        + K Y +LV G    + 
Sbjct: 88  GEEERHYEPSPVGRLDKDTVGLLLITNDGKFNHWL--MSPKHHVPKTYRALVEGHVTEED 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                       +G     VV  +      A  H  +++  A+    +E+    G+ HQ+
Sbjct: 146 ------------VGAFSHGVVLDDGYVTKPATLH--ILEAGAR--SHIELILTEGKFHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KRMFQAVG 197


>gi|169350789|ref|ZP_02867727.1| hypothetical protein CLOSPI_01562 [Clostridium spiroforme DSM 1552]
 gi|169292497|gb|EDS74630.1| hypothetical protein CLOSPI_01562 [Clostridium spiroforme DSM 1552]
          Length = 112

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 29/109 (26%), Positives = 41/109 (37%), Gaps = 8/109 (7%)

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
            GA    +  K +      +  +E+   TGR HQ+RVH   +  PI+GD KY       F
Sbjct: 4   PGALTMETIVKPVKYNND-YSKVEVTLVTGRMHQIRVHLSSIDHPIIGDRKYGDFELNKF 62

Query: 281 --TSPIQNKLYLHARYMDLPHPEG-----GRLQITAPLPAHMVKTWDSL 322
                  N   LHA  +      G        +I  P+P    K  + L
Sbjct: 63  VKKEFGLNHQLLHAYKIRFVKSFGILAYLQDKEIVCPVPKLFEKIENRL 111


>gi|312869081|ref|ZP_07729255.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           oris PB013-T2-3]
 gi|311095327|gb|EFQ53597.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           oris PB013-T2-3]
          Length = 238

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 42/252 (16%), Positives = 89/252 (35%), Gaps = 52/252 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++ +G V+V+ + V     ++ +   + +          
Sbjct: 2   ERLQKVMAEA-GVASRRASEKLIATGHVQVNGQTVTTLGTKVTAKDKIEVD--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                     + L +           E    Y+ NKP G+  S     G    +   L+ 
Sbjct: 52  ---------GIPLHR-----------EKQVYYLLNKPRGVISSAHDEKG-RRTVVDILRE 90

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             D   ++     RLD +T+G+L++           +     ++    +++        K
Sbjct: 91  --DEIEERIYPVGRLDYDTTGLLLLT---------NDGTLANKMMHPKFAVDKTYVAKVK 139

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I+N  LK+   G      VK + +    A +  K  D   +K   +++  H G  HQ+
Sbjct: 140 GLISNDDLKQLRTG------VKVDGRRTKPAKTRLKGTDR-EKKTSIVQLTIHEGHYHQV 192

Query: 256 RVHALHMGCPIV 267
           +     +G P++
Sbjct: 193 KRMLAAVGHPVI 204


>gi|320547375|ref|ZP_08041664.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           equinus ATCC 9812]
 gi|320447971|gb|EFW88725.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           equinus ATCC 9812]
          Length = 241

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 83/248 (33%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ K V      ++SG +V +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIKKGLVSINGKVVTELATTVKSGDIVEVEGTP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G+ S          +   L + 
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRKTVVDLLPNV 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +T+G+L++         +        I K+Y + V GI   +  
Sbjct: 91  T----ERIYPVGRLDWDTTGLLILTNDGDFTDEM--IHPRNEIDKVYLARVKGIATKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQL 255
                              V  + K    A   + +I    +     +E+  H GR HQ+
Sbjct: 145 -------------RPLTRGVVIDGKKTKPA--RYNIIKVDPEKNRSVVELTIHEGRNHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KKMFESVG 197


>gi|41407511|ref|NP_960347.1| hypothetical protein MAP1413 [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41395864|gb|AAS03730.1| hypothetical protein MAP_1413 [Mycobacterium avium subsp.
           paratuberculosis K-10]
          Length = 247

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/253 (16%), Positives = 77/253 (30%), Gaps = 47/253 (18%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + + +RL +         +    +K++  G+V VD + V             +   ++  
Sbjct: 3   EAQGIRLQKVLSQA-GIASRRAAEKLIVDGRVEVDGQVVT-----------ELGTRVDPD 50

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +I+                    ++L E       NKP G+             G L 
Sbjct: 51  AAVIR---------------VDGARVVLDESQVYLALNKPRGVHSTMSDDRGRPCIGDLI 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKN 193
                  +      RLD ET G++++      A  L        + K Y + V G IP+ 
Sbjct: 96  ERRVRGNKNLFHVGRLDAETEGLILLTNDGELAHRL--MHPSHEVPKTYLATVTGSIPRG 153

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + +   +     +                  +  F V+D    K   + +  H GR  
Sbjct: 154 LGKTLRAGIELDDGMAR----------------VDEFAVVDPIPGK-TLVRVTLHEGRNR 196

Query: 254 QLRVHALHMGCPI 266
            +R      G P+
Sbjct: 197 IVRRLLAAAGFPV 209


>gi|205355550|ref|ZP_03222321.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|205346784|gb|EDZ33416.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8421]
          Length = 152

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/169 (21%), Positives = 68/169 (40%), Gaps = 23/169 (13%)

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVV 216
           ++++ +     +   E F+  R+ K Y +++ G+   + E        K   G      +
Sbjct: 1   MILLCKDEDFRKLCIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKVKGG-----AL 55

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF 276
            +  K    A+S    I   ++K    ++   TGRTHQ+RVHA  +   +VGD KY    
Sbjct: 56  SKVSKDGLSALSIITPIMMQSKK-TLAKIVIQTGRTHQIRVHAKFIKHGVVGDEKY---- 110

Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
                    +++YLH+  + + +         A L +   K     GF 
Sbjct: 111 ----AKISSDRMYLHSYEIKIFN-----YHFRANLDSGFAK----FGFD 146


>gi|242044020|ref|XP_002459881.1| hypothetical protein SORBIDRAFT_02g012960 [Sorghum bicolor]
 gi|241923258|gb|EER96402.1| hypothetical protein SORBIDRAFT_02g012960 [Sorghum bicolor]
          Length = 246

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 39/144 (27%), Positives = 65/144 (45%), Gaps = 23/144 (15%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDK-----------------KRVKFNNRIQSGQVV 65
           RW +   PH+    +QK+ R  +V+ +                  +RV   + +  G ++
Sbjct: 94  RWVRRCCPHLPASLVQKLFRLRKVKKNLVTADTSSTDSIAQQLRLRRVSAKDELVPGDIL 153

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +P  I   +  + E+K   +   +    DFL+S+ +Y+D  I V NKP G+ VQGG GI
Sbjct: 154 FLPDNIQESS--VTEKKKFGNKNEI----DFLRSLEIYKDRAIIVLNKPPGMPVQGGVGI 207

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHR 149
              ID     + D   + PRL  +
Sbjct: 208 KNSIDILAPMFEDGSSEAPRLLKK 231


>gi|251796174|ref|YP_003010905.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247543800|gb|ACT00819.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
          Length = 249

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 91/249 (36%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D+    H  +     ++K+++ G+V V  K VK +     GQ+V             
Sbjct: 5   MRIDKLLS-HTGYGTRSEIKKLVKQGKVTVAGKVVKDS-----GQLV------------- 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                      L + + F   ++LY +    + NKP G+           +   L+   +
Sbjct: 46  --------DPELDEVA-FDGELVLYREVIYLMMNKPPGVISATEDRRERTVIDLLEQ--E 94

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKEC 197
            +   P    RLD++T G+L++      A  L      + + K Y ++V G + +  +E 
Sbjct: 95  DQLMDPFPVGRLDKDTVGLLLLTNDGQLAHEL--LSPRKHVPKTYEAVVQGDVGEEDQEQ 152

Query: 198 IANWLLKKS---HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
               +        +  D   + K + +G   ++               + +    G+ HQ
Sbjct: 153 FKAGVTLDDGYVTMPSDLKILKKDSGEGGVTSV---------------ISLTIMEGKFHQ 197

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 198 VKRMFEAVG 206


>gi|225378037|ref|ZP_03755258.1| hypothetical protein ROSEINA2194_03697 [Roseburia inulinivorans DSM
           16841]
 gi|225210038|gb|EEG92392.1| hypothetical protein ROSEINA2194_03697 [Roseburia inulinivorans DSM
           16841]
          Length = 261

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 46/259 (17%), Positives = 93/259 (35%), Gaps = 50/259 (19%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           T +Q +    +E  MRLD++            ++KIL++ Q+ V+ + V           
Sbjct: 12  TSLQTIEKGKNEL-MRLDKFLTEMGLG-TRSEVKKILKTKQITVNGEIVTK--------- 60

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG 124
                          E K+   +  ++   +     + Y + + Y+F KPAG      + 
Sbjct: 61  --------------PETKVAPENDQISYKGEP----VTYCEYEYYLFYKPAGCVT---AT 99

Query: 125 IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
                   +    D+         RLD +T G+L++    A A  L      + ++K Y+
Sbjct: 100 EDQLHKTVMDYLTDTVRSDLFPVGRLDIDTEGLLLITNDGALAHDL--LSPAKHVEKTYY 157

Query: 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
           +++ G+   K           S   G  +   K  + G        +++    +    +E
Sbjct: 158 AVIDGVVTEKD--------VNSFENGVDIGEEKLTKPGK------LRILKSEPE--SEIE 201

Query: 245 MQPHTGRTHQLRVHALHMG 263
           +    GR HQ++     +G
Sbjct: 202 LTITEGRFHQVKRMFEAVG 220


>gi|150391402|ref|YP_001321451.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
 gi|149951264|gb|ABR49792.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
          Length = 243

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 85/245 (34%), Gaps = 52/245 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   H +  +++++ R G V V+   VK ++                  H+ 
Sbjct: 5   QRLDKILAN-LGHGSRSDIRRLCRQGVVTVNGAVVKSSS-----------------QHVE 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   +             +  + Y +    + NKP  +           +   L+S   
Sbjct: 47  PENDKITVG----------EEEIYYREFVYIMMNKPQDVISATEDFKEKTVVDLLES--K 94

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KKE 196
            +        RLD++T G+L++    + A Q L+     + + K Y++ + G+  +   E
Sbjct: 95  YQAFDVFPVGRLDKDTEGLLMLTNDGKLAHQLLS---PKKHVPKTYYAKIEGVVTDADVE 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +                 E+      S  K++   A +   +E+  + G+ HQ++
Sbjct: 152 AFEKGIFI---------------EENLQTMPSQLKILK--ADEISEVEVTIYEGKYHQVK 194

Query: 257 VHALH 261
                
Sbjct: 195 RMFQA 199


>gi|56421368|ref|YP_148686.1| 16S pseudouridylate synthase [Geobacillus kaustophilus HTA426]
 gi|56381210|dbj|BAD77118.1| 16S pseudouridylate synthase [Geobacillus kaustophilus HTA426]
          Length = 248

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 89/247 (36%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           +R+D+    H  +     ++K+L+SG V+VD   V+    +++  + + +      +   
Sbjct: 3   LRIDKLLA-HMGYGTRKEVKKLLKSGAVKVDGAPVRDAKTKVRPDEQI-VTVWGETVE-- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                    Y+     + NKP+G+       +   +   L+   
Sbjct: 59  -------------------------YKPFIYLMMNKPSGVVSATEDAVEETVVDLLEE-- 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           + +   P    RLD++T G+L++      A Q L+     + + K Y+++V G       
Sbjct: 92  EDRAFSPFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVPKTYFAVVDGEVTE--- 145

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                    + +      VV  +      A    K++   +     +E+    G+ HQ++
Sbjct: 146 ---------ADVAAFQRGVVLDDGYETKPA----KLVVLKSGLRSDVEVTITEGKFHQVK 192

Query: 257 VHALHMG 263
                +G
Sbjct: 193 RMFQAVG 199


>gi|251781834|ref|YP_002996136.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|242390463|dbj|BAH80922.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|323126647|gb|ADX23944.1| hypothetical protein SDE12394_02010 [Streptococcus dysgalactiae
           subsp. equisimilis ATCC 12394]
          Length = 240

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 85/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +      ++SG VV I          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTLNGQIITDLATTVKSGDVVEIE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                S +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVLD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG+L++         +        I K+Y + V GI   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM--IHPRNEIDKVYLARVKGIATKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                               V  + K    A   + +I   A      +E+  H GR HQ
Sbjct: 144 L-------------RPLTRGVVIDGKKTKPA--RYNIIRVEADKNRSIVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFESVG 197


>gi|212638876|ref|YP_002315396.1| Pseudouridine synthase [Anoxybacillus flavithermus WK1]
 gi|212560356|gb|ACJ33411.1| Pseudouridine synthase [Anoxybacillus flavithermus WK1]
          Length = 255

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 52/258 (20%), Positives = 91/258 (35%), Gaps = 66/258 (25%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++  G+V+V+ K V     ++     + +          
Sbjct: 12  ERLQKVIA-HAGVASRRKAEQLIVEGKVKVNGKVVTELGVKVSPQDRIEVD--------- 61

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                       +    +     LLY         KP G+  SV+   G        +  
Sbjct: 62  -----------GIPLEREEPVYYLLY---------KPRGVISSVKDEKGRK-----VVTD 96

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     ++     RLD +TSG+L++      A  L        I+K+Y + V GIP  +K
Sbjct: 97  FFKHVNKRIYPIGRLDYDTSGLLLLTNDGEFANIL--MHPRYEIEKVYIAKVKGIPAREK 154

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKG-----ANYAISHFKVIDCFAQKFC-WLEMQPHT 249
                               VKQ EKG        A +  KV+    +K    +E++ H 
Sbjct: 155 --------------------VKQLEKGVMLEDGVTAPAKAKVLSIDKRKQTAIVELRIHE 194

Query: 250 GRTHQLRVHALHMGCPIV 267
           GR  Q+R     +G P++
Sbjct: 195 GRNRQVRRMFEAIGHPVL 212


>gi|329116700|ref|ZP_08245417.1| putative 16S pseudouridylate 516 synthase [Streptococcus parauberis
           NCFD 2020]
 gi|326907105|gb|EGE54019.1| putative 16S pseudouridylate 516 synthase [Streptococcus parauberis
           NCFD 2020]
          Length = 238

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 85/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++ +L+  +V V+ +      R       +I      L    
Sbjct: 1   MRLDKFLVDAGIG-SRSQVKSLLKKKEVLVNGQVESSAKRQIDSDKDQIVFQGQKL---- 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  +YE+   Y+ NKPAG+       +   +   L     
Sbjct: 56  -----------------------VYEEFLYYMLNKPAGVVSATEDNLHQTVVDLLDDRAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKEC 197
            K  +     RLD++T G+L++      A  L      + + KIY + + G+  K  +E 
Sbjct: 93  QK--EVFPVGRLDKDTHGLLLLTNNGELAHQL--LTPKKHVDKIYLAHIEGMMTKKDQEA 148

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
             N +    H      H +              +V++    K  C +++    G+ HQ++
Sbjct: 149 FENGIQLSDH------HCLPAT----------LEVLETDEHKQTCKVKITLKEGKFHQVK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVKACG 199


>gi|306830112|ref|ZP_07463296.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis ATCC 6249]
 gi|304427638|gb|EFM30734.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis ATCC 6249]
          Length = 240

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 88/249 (35%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I++G  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATTIKAGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V G+   + 
Sbjct: 86  LLSNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGVANKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                           +   V+   K    A+  ++++     +    +++  H GR HQ
Sbjct: 144 L-------------RPFTRGVEIEGKKTKPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|260102596|ref|ZP_05752833.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           helveticus DSM 20075]
 gi|260083623|gb|EEW67743.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           helveticus DSM 20075]
          Length = 236

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 84/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  +++ G V V+   VK    +++    V +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQE------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   LK   
Sbjct: 54  -----------------------VNYQKYHYFLMNKPKGVLSATEDRSQRTVISLLKPQD 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +G  P    RLD++T+G+L++         L      + + KIY + + G+     E 
Sbjct: 91  QYQGITP--VGRLDKDTTGLLLLTNDGQLNHEL--LAPNKHVDKIYRAKIAGV--ADDET 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLR 256
           +  +    +   G  +            A    K++    +     +E++   G+ HQ++
Sbjct: 145 VKTFASGMTLGDGTKL----------KPA--ELKILAQDEEHDSSEIEIKIREGKYHQIK 192

Query: 257 VHALHMG 263
                +G
Sbjct: 193 RMFGAVG 199


>gi|297570484|ref|YP_003691828.1| pseudouridine synthase [Desulfurivibrio alkaliphilus AHT2]
 gi|296926399|gb|ADH87209.1| pseudouridine synthase [Desulfurivibrio alkaliphilus AHT2]
          Length = 240

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 46/281 (16%), Positives = 90/281 (32%), Gaps = 50/281 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    ++ +  G+V+VD + V      Q G  +             
Sbjct: 3   ERLQKFLARA-GIASRRKAEEYIAQGRVQVDGRPVA-----QMGLTI----DPERQQVTF 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q +L  S  LT                  + NKPAG                + S ++
Sbjct: 53  DGQPVLPPSRKLT-----------------VLLNKPAGYVTTMADPQGR---PIVTSLIN 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             G +     RLD +T G L++      AQ++      R+I + Y + V G P       
Sbjct: 93  EPGLRLFPVGRLDLDTEGALLLTNDGELAQNI--LHPSRQINRTYHATVKGRPN------ 144

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                +++        ++    +G     +  + +    +     E+  H GR  Q+R  
Sbjct: 145 -----REALQQLRRGIML----EGRRTWPARIRELRRNQESTTL-EVIIHEGRKRQVRKM 194

Query: 259 ALHMGCPIVGDHK--YCANFKGNFTSPIQNKLYLHARYMDL 297
              +  P++   +  Y     G+  +    +L      +  
Sbjct: 195 FAAINHPVLQLKRVAYGGLRLGSLPTGRYRRLSPEDLQLLF 235


>gi|227495415|ref|ZP_03925731.1| pseudouridylate synthase [Actinomyces coleocanis DSM 15436]
 gi|226830962|gb|EEH63345.1| pseudouridylate synthase [Actinomyces coleocanis DSM 15436]
          Length = 248

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/252 (17%), Positives = 91/252 (36%), Gaps = 48/252 (19%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E+ +RL +         +  + +K++ SG+V+VD   V+       G  +R+ P +  + 
Sbjct: 8   EDGVRLQKVISQA-GVASRRHAEKLIISGRVKVDGNIVRT-----LG--IRVDPSVQTI- 58

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           H+   Q +LD+                         NKPAG+               L  
Sbjct: 59  HVDGNQIMLDTKSLT------------------IALNKPAGVVSTMDDPDGRPC---LAE 97

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +V+   Q+     RLD +T+G++++      +  L        + K Y + V G      
Sbjct: 98  FVEQYNQRLYHVGRLDTDTAGLILLTNDGELSHRL--MHPSWEVPKTYVATVHGEVP--- 152

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                       +G      +   +      +  F++ D + +    +++  H GR   +
Sbjct: 153 ----------RGLGRKLARGITLEDGPVK--VEDFQITDHYGE-MTLVQLTLHEGRNRIV 199

Query: 256 RVHALHMGCPIV 267
           R    H+G P++
Sbjct: 200 RRIMDHVGFPVI 211


>gi|169827290|ref|YP_001697448.1| ribosomal large subunit pseudouridine synthase B [Lysinibacillus
           sphaericus C3-41]
 gi|168991778|gb|ACA39318.1| Ribosomal large subunit pseudouridine synthase B [Lysinibacillus
           sphaericus C3-41]
          Length = 243

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 83/254 (32%), Gaps = 58/254 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    +    +    ++++  G+V+V+   V+    ++ +   + +          
Sbjct: 2   ERLQKVIA-YAGVASRRKAEQLIVEGKVKVNGIVVRELGTKVSNSDTIEV---------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                     V L K           ED   ++  KP G   +V    G     D     
Sbjct: 51  --------EGVKLEK-----------EDKVYFLLYKPRGTISAVTDDKGRKTVTD----- 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KN 193
                 Q+     RLD +TSG+L++      +  LT      +I K Y + V GIP  + 
Sbjct: 87  LFHHIPQRIFPVGRLDYDTSGLLLLTNDGEFSYMLT--HPKFKIDKTYIARVKGIPTIEG 144

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K+      L+        V +   +E                       E+  H GR  
Sbjct: 145 LKKLQRGIKLEDGKTAPAKVSMTSFDENAGK----------------AICEITIHEGRNR 188

Query: 254 QLRVHALHMGCPIV 267
           Q+R     +G P+V
Sbjct: 189 QVRRMFEAIGTPVV 202


>gi|297529009|ref|YP_003670284.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|297252261|gb|ADI25707.1| pseudouridine synthase [Geobacillus sp. C56-T3]
          Length = 248

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 90/247 (36%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           +R+D+    H  +     ++K+L+SG V+VD   V+    +++  + + +      +   
Sbjct: 3   LRIDKLLA-HMGYGTRKEVKKLLKSGAVKVDGAPVRDAKTKVRPDEQI-VTVWGETVE-- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                    Y+     + NKP+G+       +   +  FL+   
Sbjct: 59  -------------------------YKPFIYLMMNKPSGVVSATEDAVEETVVDFLEE-- 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           + +   P    RLD++T G+L++      A Q L+     + + K Y+++V G       
Sbjct: 92  EDRAFSPFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVPKTYFAVVDGEVTE--- 145

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                    + +      VV  +      A    K++   +     +E+    G+ HQ++
Sbjct: 146 ---------ADVAAFQRGVVLDDGYETKPA----KLVVLKSGLRSDVEVTITEGKFHQVK 192

Query: 257 VHALHMG 263
                +G
Sbjct: 193 RMFQAVG 199


>gi|225166280|ref|ZP_03727976.1| pseudouridine synthase [Opitutaceae bacterium TAV2]
 gi|224799481|gb|EEG18014.1| pseudouridine synthase [Opitutaceae bacterium TAV2]
          Length = 98

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 26/99 (26%), Positives = 51/99 (51%), Gaps = 1/99 (1%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           +   ++YED  +  F+KP+G+ V             ++   +  G      HR+D +TSG
Sbjct: 1   MLPPIVYEDETMLAFDKPSGLLVAPDRWDKNRPY-LMRYVHERYGHDTANVHRIDADTSG 59

Query: 157 ILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +L+ +RT+ A  +L+  F+ +   KIY ++V  +P  ++
Sbjct: 60  LLLCSRTKPALDYLSGQFQSKTPTKIYHAIVVILPPGRE 98


>gi|222151389|ref|YP_002560545.1| ribosomal large subunit pseudouridine synthase B [Macrococcus
           caseolyticus JCSC5402]
 gi|222120514|dbj|BAH17849.1| ribosomal large subunit pseudouridine synthase B [Macrococcus
           caseolyticus JCSC5402]
          Length = 245

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 39/256 (15%), Positives = 87/256 (33%), Gaps = 54/256 (21%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINA 73
           +E+  RL +         +    + ++  G+V V+ + V     +++   ++ +      
Sbjct: 2   NEQLERLQKVIAKS-GVTSRRKAEVLITEGKVTVNGQTVTELGTKVKPSDIIEV------ 54

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                 E   L++   +                   +F+KP G+     S         +
Sbjct: 55  ------EGIPLENPEKI-----------------YILFHKPTGVIT---SVSDEKGRKVV 88

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-- 191
             +      +     RLD +TSG+L++      A  +T      +++K Y + + G    
Sbjct: 89  TDYFPGLNLRIFPVGRLDYDTSGLLLLTNDGDFANQMT--HPKYKMKKKYVAKLKGFLLR 146

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           +  K+     +L+        V V  Q+++                +    +E+  + GR
Sbjct: 147 EQVKQLEKGIMLEDGKTAPALVKVKSQDKE----------------KNTTLVEITIYEGR 190

Query: 252 THQLRVHALHMGCPIV 267
             Q+R    H G  +V
Sbjct: 191 NRQVRRMFAHFGHEVV 206


>gi|297617939|ref|YP_003703098.1| pseudouridine synthase [Syntrophothermus lipocalidus DSM 12680]
 gi|297145776|gb|ADI02533.1| pseudouridine synthase [Syntrophothermus lipocalidus DSM 12680]
          Length = 249

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 91/250 (36%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL R+        +    + ++++G+V+V+ + V+                        
Sbjct: 10  LRLARYLAAA-GITSRRKAETLIQAGRVKVNGRVVR------------------------ 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKI-YVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                L   +N  K    L   LL+ +  +  + NKP+G      +    H    +   +
Sbjct: 45  ----ELGFVINEEKDQVELDGWLLHREEPVYILLNKPSGYLC---TLADTHGRPTVVDLL 97

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               Q+     RLD +T G+L+++        +T       I+K+Y + V G        
Sbjct: 98  RGVTQRVYPVGRLDYDTEGLLLLSNDGDFTHLMTHPRFE--IEKVYEAWVQG-------- 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               ++ +  I      V+    K A   +   +V+     +   +E++ H GR  Q++ 
Sbjct: 148 ----MVSRKAIERLRAGVIIDAVKTAPAKV---RVLAKRKDR-TLMEIRIHEGRKRQVKK 199

Query: 258 HALHMGCPIV 267
               +G P+V
Sbjct: 200 MCASVGHPVV 209


>gi|319938699|ref|ZP_08013063.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319811749|gb|EFW08015.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 241

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIKQGLVTVNGQVVRELATTIKSGDRVEVSGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRP-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG L++         +        I K+Y + V G+   + 
Sbjct: 86  LLPNVTERIYPVGRLDWDTSGALILTNDGDFTDEM--IHPRNEIDKVYVARVKGVADKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
             +   L K           V+ + K    A+  ++++     +    +++  H GR HQ
Sbjct: 143 --VLRPLTKG----------VEVDGKKTKPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|229815391|ref|ZP_04445726.1| hypothetical protein COLINT_02438 [Collinsella intestinalis DSM
           13280]
 gi|229809171|gb|EEP44938.1| hypothetical protein COLINT_02438 [Collinsella intestinalis DSM
           13280]
          Length = 272

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 40/252 (15%), Positives = 78/252 (30%), Gaps = 40/252 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRL R+        +    + ++ +G+VRV+ +                          
Sbjct: 20  PMRLQRFLARA-GVASRRGSEGLMTAGRVRVNGE-------------------------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
           +K +          + +     ++L       + NKPAG ++          +   + S 
Sbjct: 53  VKTELGTKVDPRCDEVTVDGAPVVLGSGPAYIMLNKPAGFLTTMSDPHGRPTVAELVPS- 111

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKK 195
              K        RLD +T+G+L+        Q L        + K Y ++V G       
Sbjct: 112 --KKFPGLFPVGRLDMDTTGLLLFTTDGDLGQRL--LHPSHHVWKTYRAIVDGRCLDGDL 167

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E +   L             V +       A +H             +E+    GR +Q+
Sbjct: 168 EPLRRGLTLDDGPCQPARCRVLE------PADAHIPGFPRLVTGATAVEVIIREGRKNQV 221

Query: 256 RVHALHMGCPIV 267
           +     +G P++
Sbjct: 222 KRMLSKIGHPVI 233


>gi|319946464|ref|ZP_08020701.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           australis ATCC 700641]
 gi|319747432|gb|EFV99688.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           australis ATCC 700641]
          Length = 242

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 86/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ K V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGKVVRELATTIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G    ID     
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRPTVID----- 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG+L++         +        I K+Y + V G+   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGLANKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                               V  + K    A   ++++    +     +++  H GR HQ
Sbjct: 144 L-------------RPLTRGVTIDGKKTKPAT--YEILKVDPEKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|241955122|ref|XP_002420282.1| pseudouridine synthase, putative; pseudouridylate synthase,
           putative; uracil hydrolyase, putative [Candida
           dubliniensis CD36]
 gi|223643623|emb|CAX42506.1| pseudouridine synthase, putative [Candida dubliniensis CD36]
          Length = 271

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/195 (21%), Positives = 74/195 (37%), Gaps = 24/195 (12%)

Query: 97  LKSILLYEDSKIYVFNKPAGISV---QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
           +K  L+       + NKP+G+        + I    + F          + RL  RLD+ 
Sbjct: 1   MKLDLVKRTFNYVIVNKPSGMVCDTNHTNNIITALTNEFKAILPSVNSSQFRLVQRLDRF 60

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-----WGIPKNKKECIANWLLKKSHI 208
            +G LVVAR +  A  + +SF      ++    V       IP++ +  I   +     +
Sbjct: 61  VTGGLVVARNKKWADKVRKSFFQEGTLRLTRRYVGLIALDQIPESTQGTIDFPI---QAL 117

Query: 209 GGDYVHVVKQNEKGANYAISHFKVID------------CFAQKFCWLEMQPHTGRTHQLR 256
             DY    +  +     A++H+K+I                     + ++  TGR +Q+R
Sbjct: 118 EKDYRGKGESRKLLTYSAVTHYKLIPKARRAIEGIFPISQQGPVLPIILELETGRKNQIR 177

Query: 257 VH-ALHMGCPIVGDH 270
            H     G P++ D 
Sbjct: 178 DHIIQKFGVPLLNDD 192


>gi|157149683|ref|YP_001450946.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           gordonii str. Challis substr. CH1]
 gi|157074477|gb|ABV09160.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           gordonii str. Challis substr. CH1]
          Length = 242

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + V+     +++G  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTINGQVVRELATLVKTGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG+L++         +        I K+Y + V GI   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDEM--IHPRNEIDKVYVARVKGIANKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                               V+ N K    A+  +++I     +    +++  H GR HQ
Sbjct: 144 L-------------RPLTRGVEINGKKTKPAV--YEIIKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFQAVG 197


>gi|213964760|ref|ZP_03392960.1| RNA pseudouridine synthase family protein [Corynebacterium
           amycolatum SK46]
 gi|213952953|gb|EEB64335.1| RNA pseudouridine synthase family protein [Corynebacterium
           amycolatum SK46]
          Length = 317

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 55/269 (20%), Positives = 88/269 (32%), Gaps = 58/269 (21%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
           +     + +++    +  V +KP  +     G  +A  +   L+  +          HRL
Sbjct: 31  EEYIPFEPVIVAGTDEFLVVDKPPFLPATPNGRIVANTVQERLRRSLGESEIVA--VHRL 88

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL-VWGIPKNKKECIANWLLKKSHIG 209
           D  TSG+L+++R  A      + F+ + I K Y  L V     +  E     LL   +  
Sbjct: 89  DLLTSGLLLLSRNPATRARYQQLFQNQEITKEYECLTVMPDDWHVGETRDVTLLLDPNPA 148

Query: 210 GDYVHVVKQNE-----------KGANYAISHFKVIDC----------------------- 235
           G  V VV+ +            K A   ++    +                         
Sbjct: 149 GRGVKVVETDVSARAAAKNPKFKLARTTVTFLGPVAADIGDVLASSRGGGSGGGATSASI 208

Query: 236 ------FAQKFC-------WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
                      C       +  +QPHTGRTHQLRV    +G PI+G+  Y         S
Sbjct: 209 PLHAVGCGCGHCGSSMQVGYWRLQPHTGRTHQLRVTMDWLGYPILGEDTYGREAGAQGPS 268

Query: 283 PIQN-------KLYLHARYMDLPHPEGGR 304
                      +L L A  +    P  G 
Sbjct: 269 ASAGSAPTYTPQLRLTATALAFVDPVTGE 297


>gi|228476518|ref|ZP_04061208.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           salivarius SK126]
 gi|228251939|gb|EEK10985.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           salivarius SK126]
          Length = 241

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 84/248 (33%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G+V ++ K V      +++G +V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKEGRVTLNGKTVTELATIVKNGDIVEVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                S +  E+   Y+ NKP G+ S          +   +   
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDEKNRKTVIDLMPHV 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +T+G+L++         +        I K+Y + V GI   +  
Sbjct: 91  ----KERIYPVGRLDWDTTGLLILTNDGDFTDKM--IHPRNEIDKVYLARVKGIATKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
                              V  + K    A   + +I     +    +E+  H GR HQ+
Sbjct: 145 -------------RPLTRGVVIDGKKTKPA--RYNIIKVDHEKNRSVVELTIHEGRNHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KKMFESVG 197


>gi|332977338|gb|EGK14123.1| ribosomal large subunit pseudouridine synthase B [Desmospora sp.
           8437]
          Length = 236

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 83/249 (33%), Gaps = 49/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++ + SG+VRV+ K V                       + 
Sbjct: 2   ERLQKVMARA-GVASRRKSEEWILSGKVRVNGKTVT-----------------QLGTRVD 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+  ++    L +           E  + ++F KP G+     S         +  W  
Sbjct: 44  PERDRIEVEGRLIRP----------EQKRYFLFYKPKGVIT---SLSDPDGRPVVTDWFR 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD +T G+L++         L        + K+Y + V GIP  K    
Sbjct: 91  EVEERVYPVGRLDYDTEGLLLLTNDGELTHGLA--HPRHEVDKVYQATVKGIPAKKS--- 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               L++   G                A +  +++    ++ C  E+  H GR  Q+R  
Sbjct: 146 ----LRRLETGVKLT--------DGWTAPAKVRMLRSGKEQACL-ELTIHEGRNRQVRRM 192

Query: 259 ALHMGCPIV 267
              +G P+V
Sbjct: 193 CEAVGHPVV 201


>gi|317488196|ref|ZP_07946767.1| RNA pseudouridylate synthase [Eggerthella sp. 1_3_56FAA]
 gi|316912701|gb|EFV34239.1| RNA pseudouridylate synthase [Eggerthella sp. 1_3_56FAA]
          Length = 285

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 40/265 (15%), Positives = 84/265 (31%), Gaps = 46/265 (17%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRL ++        +    + ++ +G+V V+ K V                 + +    
Sbjct: 13  PMRLQKFLARA-GAASRRGSENLMTAGRVTVNGKVVT---------------ELGSKVDP 56

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + ++  +D +V   + +D   +I+L+         KPAG                L    
Sbjct: 57  LVDEVAVDGAV--VRLADGPVTIMLH---------KPAGFVTTMSDPQGRRTVAELV--P 103

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +        RLD +T+G+L+ +        L        + K Y + V G P  +   
Sbjct: 104 TERYPGLFPIGRLDFDTTGLLLFSTDGELGNGL--LHPKHHVTKRYLACVEGRPTERDLA 161

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---------------VIDCFAQKFCW 242
           +    ++          V       A +A    +               V +  A +   
Sbjct: 162 LLRRGIELDDGPTQPADVRVVEGGAARHAERLLEIPAAVPPRSSKEYAAVCEGRATRRSI 221

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIV 267
           + +    GR  Q++     +G P++
Sbjct: 222 VRLGIREGRKRQVKRMLAAVGHPVL 246


>gi|261418151|ref|YP_003251833.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|319767889|ref|YP_004133390.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
 gi|261374608|gb|ACX77351.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|317112755|gb|ADU95247.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
          Length = 248

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 89/247 (36%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           +R+D+    H  +     ++K+L+SG V+VD   V+    +++  + + +      +   
Sbjct: 3   LRIDKLLA-HMGYGTRKEVKKLLKSGAVKVDGAPVRDAKTKVRPDEQI-VTVWGETVE-- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                    Y+     + NKP+G+       +   +   L+   
Sbjct: 59  -------------------------YKPFIYLMMNKPSGVVSATEDAVEETVVDLLEE-- 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           + +   P    RLD++T G+L++      A Q L+     + + K Y+++V G       
Sbjct: 92  EDRAFCPFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVPKTYFAVVGGEVTE--- 145

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                    + +      VV  +      A    K++   +     +E+    G+ HQ++
Sbjct: 146 ---------ADVAAFQRGVVLDDGYETKPA----KLVVLKSGLRSDVEVTITEGKFHQVK 192

Query: 257 VHALHMG 263
                +G
Sbjct: 193 RMFQAVG 199


>gi|125973211|ref|YP_001037121.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           thermocellum ATCC 27405]
 gi|256003686|ref|ZP_05428674.1| pseudouridine synthase [Clostridium thermocellum DSM 2360]
 gi|281417410|ref|ZP_06248430.1| pseudouridine synthase [Clostridium thermocellum JW20]
 gi|125713436|gb|ABN51928.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           thermocellum ATCC 27405]
 gi|255992247|gb|EEU02341.1| pseudouridine synthase [Clostridium thermocellum DSM 2360]
 gi|281408812|gb|EFB39070.1| pseudouridine synthase [Clostridium thermocellum JW20]
 gi|316940559|gb|ADU74593.1| pseudouridine synthase [Clostridium thermocellum DSM 1313]
          Length = 239

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/251 (17%), Positives = 86/251 (34%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRL ++        +    ++++  G+V+V+ + V     ++    VV +   +  +   
Sbjct: 4   MRLQKYLAE-CGVASRRKAEELISQGRVKVNGETVTQMGKKVSQNDVVEVDGKLVKMEKR 62

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                   +Y        NKP G IS          +   +K  
Sbjct: 63  K-----------------------VY-----IALNKPVGYISSVKDQFGRKTVMDLVK-- 92

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++      A  LT       I+K+Y + + G+P     
Sbjct: 93  --DIKERIFPVGRLDYDTSGLLLLTNDGDFAYRLT--HPKHEIKKVYEADLLGVPSKDDI 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                  K      DY             + + F+++     K   + +  H G+  Q+R
Sbjct: 149 M----RFKNGLWIDDYF-----------TSPADFEILKSDG-KTTKVRITIHEGKNRQVR 192

Query: 257 VHALHMGCPIV 267
                +GCP++
Sbjct: 193 KMCNKIGCPVI 203


>gi|145224079|ref|YP_001134757.1| pseudouridine synthase [Mycobacterium gilvum PYR-GCK]
 gi|315444416|ref|YP_004077295.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           Spyr1]
 gi|145216565|gb|ABP45969.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           gilvum PYR-GCK]
 gi|315262719|gb|ADT99460.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           Spyr1]
          Length = 247

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 42/252 (16%), Positives = 78/252 (30%), Gaps = 45/252 (17%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +RL +         +    +K++R G+V VD + V                     
Sbjct: 3   DNDGVRLQKVLSQA-GIASRRVAEKMIRDGRVEVDDRIVT-------------------- 41

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +       +S + +      +   L++        NKP G+             G L 
Sbjct: 42  -ELGTRVDPAESVIRVDGARITVDDTLVH-----LAINKPRGMHSTMSDDRGRPCVGDLV 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  +K     RLD +T G+L++      A  L        + K Y + V G     
Sbjct: 96  EHRVRGNKKLFHVGRLDADTEGLLLLTNDGELAHRL--MHPSYEVPKSYVATVLGSVP-- 151

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                        +G      V+ ++      +  F ++D        + +  H GR H 
Sbjct: 152 -----------RGLGRKLREGVELDDGPVQ--VDDFALVDTTP-GRTLVRVTLHEGRKHI 197

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 198 VRRLLAEVGFPV 209


>gi|312135342|ref|YP_004002680.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
 gi|311775393|gb|ADQ04880.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
          Length = 236

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 89/250 (35%), Gaps = 49/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL ++        +    ++I+  G+V+V+ K V                       + 
Sbjct: 1   MRLQKFMA-QCGIASRRKCEEIILQGRVKVNGKTVN-----------------QLGFKVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ +++    +      L+   +Y      + NKP G+     +         +    +
Sbjct: 43  PEKDVVE----IDGKRISLQRQKVY-----IMLNKPFGVIS--SAKDEKGRKTVVDLVRE 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-EC 197
               +     RLD +T+G++++      A  +T       I+K Y +LV GIP  K+ E 
Sbjct: 92  KVNVRVFPVGRLDFDTTGLILLTNDGEFAYKVT--HPKHDIEKTYIALVKGIPSKKEIEM 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               LL    +                 A + FK++         +E++ H GR  Q+R 
Sbjct: 150 FERGLLIDGKM----------------TAPAKFKILKLINGNA-LVEIKIHEGRNRQIRK 192

Query: 258 HALHMGCPIV 267
               +G  ++
Sbjct: 193 MCDMIGHKVL 202


>gi|323466841|gb|ADX70528.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 246

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 84/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  +++ G V V+   VK    +++    V +          
Sbjct: 11  MRIDKYLANMNVG-SRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQE------ 63

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   LK   
Sbjct: 64  -----------------------VNYQKYHYFLMNKPKGVLSATEDRSQRTVISLLKPQD 100

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +G  P    RLD++T+G+L++         L      + + KIY + + G+     E 
Sbjct: 101 QYQGITP--VGRLDKDTTGLLLLTNDGQLNHEL--LAPNKHVDKIYRAKIAGV--ADDET 154

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW-LEMQPHTGRTHQLR 256
           +  +    +   G  +            A    K++    +     +E++   G+ HQ++
Sbjct: 155 VKTFASGMTLGDGTKL----------KPA--ELKILAQDEEHDSSEIEIKIREGKYHQIK 202

Query: 257 VHALHMG 263
                +G
Sbjct: 203 RMFGAVG 209


>gi|227510307|ref|ZP_03940356.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
 gi|227189959|gb|EEI70026.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
          Length = 241

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 49/276 (17%), Positives = 86/276 (31%), Gaps = 54/276 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +K++  G V+V+ K V+    ++     V +          
Sbjct: 3   ERLQKVMA-HAGVASRRKAEKLIVEGHVKVNGKVVRELGTKVTESDEVEVD--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       +    +     LLY         KP G+          H    +   +
Sbjct: 53  -----------EVPISKEVPVYYLLY---------KPRGVIT--AVTDDKHRKTVI-DLL 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++        HLT       + K Y + V G        
Sbjct: 90  SEVTERIYPVGRLDYDTSGLLLLTNDGDLDNHLT--HPKYEVDKTYVAKVKG-------T 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I N  +KK   G   +H+  +    A   +               + +  H GR HQ++ 
Sbjct: 141 ITNDDMKKLRTG---IHIDGRKTASAKATV------IRNNNNSTIVSLTIHEGRNHQVKK 191

Query: 258 HALHMGCPI--VGDHKYCANFKGNFTSPIQNKLYLH 291
             L +G P+  +    Y              +L  H
Sbjct: 192 MFLALGHPVEKLSRQSYGFLNLDGLQPGDYRRLKPH 227


>gi|332523615|ref|ZP_08399867.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           porcinus str. Jelinkova 176]
 gi|332314879|gb|EGJ27864.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           porcinus str. Jelinkova 176]
          Length = 240

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 46/249 (18%), Positives = 86/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +      ++SG VV +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTLNGQVITDLATIVKSGDVVEVE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                S +  E+   Y+ NKP G+  SV    G    ID     
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDDKGRKTVID----- 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG+L++         +        I K+Y + V GI   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDKM--IHPRNEIDKVYLARVKGIATKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                               V  + K    A   + +I   A      +E+  H GR HQ
Sbjct: 144 L-------------RPLTRGVVIDGKKTKPA--RYNIIRVEADKNRSIVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFESVG 197


>gi|315223141|ref|ZP_07865009.1| conserved hypothetical protein [Streptococcus anginosus F0211]
 gi|315187830|gb|EFU21577.1| conserved hypothetical protein [Streptococcus anginosus F0211]
          Length = 241

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HSGIASRRKAEELIKQGLVTVNGQVVRELATTIKSGDRVEVSGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRP-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG L++         +        I K+Y + V G+   + 
Sbjct: 86  LLPNVTERIYPVGRLDWDTSGALILTNDGDFTDEM--IHPRNEIDKVYVARVKGVADKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
             +   L K           V+ + K    A+  ++++     +    +++  H GR HQ
Sbjct: 143 --VLRPLTKG----------VEVDGKKTKPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|323705338|ref|ZP_08116913.1| pseudouridine synthase [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535240|gb|EGB25016.1| pseudouridine synthase [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 235

 Score = 71.2 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 89/250 (35%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    ++++  G+V+V+ + V+     + G  V++ P  + + +  
Sbjct: 2   ERLQKYLAE-CGIASRRKCEQLILDGKVKVNGETVR-----ELG--VKVDPNKDVVEYNG 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
           K    ++ ++                     + NKP G I+          +   +    
Sbjct: 54  KVVTKVNKNI-------------------YIMLNKPVGYITTVKDQFDRPSVIDLV---- 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            S   +     RLD +TSG+L++      A  L        I K+Y + + G+P   K  
Sbjct: 91  -SIDDRVYPIGRLDYDTSGLLLLTNDGDLANKL--MHPRHNINKVYIAQIKGVPDKMK-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               + +      +Y        K A   I   KV          +++  H GR  Q+R 
Sbjct: 146 --LDMFRNGLRIDNY--------KTAKAEIDILKV----TNGNSTVKIAIHEGRNRQIRK 191

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 192 MCELIGHPVL 201


>gi|118618582|ref|YP_906914.1| pseudouridylate synthase [Mycobacterium ulcerans Agy99]
 gi|183982541|ref|YP_001850832.1| pseudouridylate synthase [Mycobacterium marinum M]
 gi|118570692|gb|ABL05443.1| pseudouridylate synthase [Mycobacterium ulcerans Agy99]
 gi|183175867|gb|ACC40977.1| pseudouridylate synthase [Mycobacterium marinum M]
          Length = 253

 Score = 71.2 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 42/253 (16%), Positives = 78/253 (30%), Gaps = 45/253 (17%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
             E  +RL +         +    +K++  G+V VD + V             +   ++ 
Sbjct: 8   EQERGIRLQKVLSQA-GIASRRAAEKLIIDGRVEVDGQVVT-----------ELGTRVDP 55

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              +I+   +                ++L +       NKP G+             G L
Sbjct: 56  DTSLIRVDGV---------------RVILDDSLVYLALNKPRGMHSTMSDDRGRPCIGDL 100

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                   +      RLD +T G++++      A  L        + K Y + V G    
Sbjct: 101 IERKVRGNKNLFHVGRLDADTEGLILLTNDGELAHRL--MHPSHEVPKTYLATVAG---- 154

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               +   L KK   G +         +     +  F V+D    K   + +  H GR  
Sbjct: 155 ---TVPRGLGKKLRAGIEL--------EDGPVRVDGFAVVDAIPGK-TLVRVTLHEGRNR 202

Query: 254 QLRVHALHMGCPI 266
            +R     +G P+
Sbjct: 203 IVRRMLAAVGFPV 215


>gi|322392605|ref|ZP_08066065.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           peroris ATCC 700780]
 gi|321144597|gb|EFX39998.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           peroris ATCC 700780]
          Length = 240

 Score = 71.2 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 45/246 (18%), Positives = 90/246 (36%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++  L++G+V V+ K+ K + ++Q         +    + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNFLKAGRVTVNGKKEK-SAKLQ---------IDEETDEIC 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + K L+                 YE+   Y+ NKP G+     +     +   +  +  
Sbjct: 50  FDGKKLE-----------------YEEFVYYMMNKPQGVISATENPKHKTVLDLMDDYAC 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +K  +     RLD +T G+L++    + A   L+     R + K Y + V GI  ++   
Sbjct: 93  AK--EVFPVGRLDIDTHGLLLLTNDGKLAHALLS---PKRHVDKTYMAQVKGIMTDED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I             +   +   +     A      ID    K   + +    G+ HQ++ 
Sbjct: 146 IET-----------FAKGIPLKDFTCQPAKLELVSIDTEENK-SLVRVTIAEGKFHQVKR 193

Query: 258 HALHMG 263
              + G
Sbjct: 194 MVAYCG 199


>gi|184155350|ref|YP_001843690.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
 gi|260662137|ref|ZP_05863033.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
 gi|183226694|dbj|BAG27210.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
 gi|260553520|gb|EEX26412.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
          Length = 241

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 91/253 (35%), Gaps = 54/253 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    + ++ +G+V+V+ + V     ++     V +          
Sbjct: 4   ERLQKVIA-HAGVASRRAAEGLILAGKVKVNGQVVTELGTKVDGNDEVMVNGEPVEQ--- 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                     E  + Y+ +KP G+  S     G    +D     
Sbjct: 60  --------------------------EQHEYYLLDKPRGVISSAHDDKGRKTVVDILKNE 93

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            V +   +     RLD +T+G+LV+      A  L        + K+Y + V G+  N +
Sbjct: 94  GVQT---RVYPVGRLDYDTTGLLVMTNDGELANRL--MHPRFEVDKVYIAKVKGLVSNDE 148

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                 LL++          VK + K +  A +  K+++    QK   +++  H G  HQ
Sbjct: 149 MR----LLREG---------VKIDGKKSQPART--KLLEANQRQKTSVVKLTIHEGHYHQ 193

Query: 255 LRVHALHMGCPIV 267
           ++     +G P++
Sbjct: 194 VKKMMEAVGHPVL 206


>gi|116333418|ref|YP_794945.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus brevis ATCC 367]
 gi|116098765|gb|ABJ63914.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           brevis ATCC 367]
          Length = 240

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 82/250 (32%), Gaps = 52/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +K++ SG+V+V+   V     ++     + +  V  +    
Sbjct: 2   ERLQKVLA-HAGVASRRQSEKLIMSGRVKVNGAAVTELGTKVGVHDQILVDGVPISSEAP 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I                               +  KP G+               +   V
Sbjct: 61  I-----------------------------YIMLYKPRGVVSTANDDKGR---KTVVDLV 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           ++  Q+     RLD +TSG+L++      A  LT       ++K Y + V G+P N    
Sbjct: 89  ENVSQRVYPVGRLDYDTSGLLLLTNDGELANRLT--HPRYEVEKTYIARVTGVPTND--- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGRTHQLR 256
                                   G  YA +  KV+     +K   + +  H G+ HQ++
Sbjct: 144 ------------AMKQLRQGITVDGETYAPAKSKVLSAADDRKTAIISLTIHEGKNHQVK 191

Query: 257 VHALHMGCPI 266
                +GCP+
Sbjct: 192 KMLAAVGCPV 201


>gi|293115329|ref|ZP_05790945.2| ribosomal small subunit pseudouridine synthase A [Butyrivibrio
           crossotus DSM 2876]
 gi|292810441|gb|EFF69646.1| ribosomal small subunit pseudouridine synthase A [Butyrivibrio
           crossotus DSM 2876]
          Length = 241

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 43/245 (17%), Positives = 85/245 (34%), Gaps = 49/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D++  +     +   ++  +R G V ++  +VK      +G                
Sbjct: 6   IRIDKYLADMGAG-SRTEIKDDIRKGLVYINGNKVKS-----AG---------------- 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                 + +  L     + ++I+ Y + +  + NKPAG+     S      +  +   +D
Sbjct: 44  ------EKADTLNDEVAYKENIIKYIEFEYILLNKPAGVV----SATEDRKEKTVLDIID 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK +      RLD++T G+L++      A  L      + + K Y+    G         
Sbjct: 94  SKRKDLFPVGRLDKDTEGLLLLTNDGMLAHEL--LSPKKHVDKKYYVETDG--------- 142

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              LL   H       +   +E  A  A      I     K     +    G+ HQ++  
Sbjct: 143 ---LLTDEHRKLFKNGIKVDDEFTAKEAELQ---ILSSGDKGSKAYLTIREGKYHQVKRM 196

Query: 259 ALHMG 263
              +G
Sbjct: 197 MEAVG 201


>gi|257791082|ref|YP_003181688.1| pseudouridine synthase [Eggerthella lenta DSM 2243]
 gi|257474979|gb|ACV55299.1| pseudouridine synthase [Eggerthella lenta DSM 2243]
          Length = 282

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 40/265 (15%), Positives = 84/265 (31%), Gaps = 46/265 (17%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRL ++        +    + ++ +G+V V+ K V                 + +    
Sbjct: 10  PMRLQKFLARA-GAASRRGSENLMTAGRVTVNGKVVT---------------ELGSKVDP 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + ++  +D +V   + +D   +I+L+         KPAG                L    
Sbjct: 54  LVDEVAVDGAV--VRLADGPVTIMLH---------KPAGFVTTMSDPQGRRTVAELV--P 100

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +        RLD +T+G+L+ +        L        + K Y + V G P  +   
Sbjct: 101 TERYPGLFPIGRLDFDTTGLLLFSTDGELGNGL--LHPKHHVTKRYLACVEGRPTERDLA 158

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---------------VIDCFAQKFCW 242
           +    ++          V       A +A    +               V +  A +   
Sbjct: 159 LLRRGIELDDGPTQPADVRVVEGGAARHAERLLEIPAAVPPRSSKEYAAVCEGRATRRSI 218

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIV 267
           + +    GR  Q++     +G P++
Sbjct: 219 VRLGIREGRKRQVKRMLAAVGHPVL 243


>gi|88855489|ref|ZP_01130153.1| RNA pseudouridine synthase [marine actinobacterium PHSC20C1]
 gi|88815396|gb|EAR25254.1| RNA pseudouridine synthase [marine actinobacterium PHSC20C1]
          Length = 257

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 80/256 (31%), Gaps = 50/256 (19%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVI 71
            ++ E  RL +         +    + ++  G+V V+ + V+    R+     V +  V 
Sbjct: 9   PSNPEGERLQKVMAAA-GVASRRVCEDLIYQGRVAVNGEVVEAAGRRVLPTDRVTVDDVA 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
             L+   +                              + NKP G+     S        
Sbjct: 68  IQLDTTKQ----------------------------YVMLNKPVGVVS---SMADESGRP 96

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L+ +     ++     RLD  TSG+L++      A  L        + K Y + V GI 
Sbjct: 97  DLREFTRDYDERLFNVGRLDANTSGLLILTNDGELAHILAHPSFG--VSKTYIAKVEGIV 154

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             +   IA          G  V                 + +   +     +E+  H+GR
Sbjct: 155 SAQ--TIAKLTKGIELDDGPIVADKA-------------RALGRASGNETMVEITLHSGR 199

Query: 252 THQLRVHALHMGCPIV 267
            H +R     +G P++
Sbjct: 200 NHIVRRMLDAVGHPVI 215


>gi|332365802|gb|EGJ43559.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK355]
          Length = 242

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 87/247 (35%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQLLKKGLVLVNGRAEKS----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +  +D + +    S      L+YE    Y+ NKP G+           +   L     
Sbjct: 37  -PKTQIDETADEIIVSG---QRLIYEKFVYYLLNKPQGVISVTEDDRHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKE 196
            K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+  +   E
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLMNQADVE 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             A  +  K  I                 A      +D  A++   +E+    G+ HQ++
Sbjct: 148 RFAAGIELKDFI--------------CQPAQLKIVELD-EAKETSLVEITLAEGKFHQVK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVASCG 199


>gi|303242311|ref|ZP_07328797.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
 gi|302590150|gb|EFL59912.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
          Length = 237

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 84/250 (33%), Gaps = 53/250 (21%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHII 78
           RL ++  +     +    +++++ G V+V+   V     ++ S   V +   +       
Sbjct: 5   RLQKYIAD-CGVASRRKAEELIQQGSVKVNGIVVSEMGIKVSSSDRVEVNGSV------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
                           +  K  +L         NKP+G ++          +   LK   
Sbjct: 57  -------------IKPESKKVYIL--------LNKPSGYVTTVKDQFRRPTVIDLLK--- 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD ET+G+LV+         +T       I+K Y + + G P   +  
Sbjct: 93  -GVDERVFPVGRLDYETTGLLVLTNDGDFTHKMT--HPRHEIEKTYQATIAGTPTKDE-- 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +     G +    V    K           I    ++ C +E+  H GR  Q+R 
Sbjct: 148 -----IHSFESGLEIEDYVTSPAKLK---------IISTKERTCVIEVTIHEGRNRQVRK 193

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 194 MCEAIGHPVL 203


>gi|297250654|ref|ZP_06934183.1| ribosomal large subunit pseudouridine synthase [Neisseria
           polysaccharea ATCC 43768]
 gi|296838353|gb|EFH22291.1| ribosomal large subunit pseudouridine synthase [Neisseria
           polysaccharea ATCC 43768]
          Length = 108

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 47/106 (44%), Gaps = 14/106 (13%)

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           ++ + +   Y    F  I   ++K     ++PHTG+THQLRV    +G PI+GD  Y   
Sbjct: 1   MEADAQYGKYCRYPFFSI-RISEKMRLFILEPHTGKTHQLRVAMKSLGSPILGDRLYGGT 59

Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDS 321
                        +L+A  +   + +   ++ITAPL       W +
Sbjct: 60  ESETT--------FLYAWKIQFTY-QQQEIEITAPL----KNAWQA 92


>gi|169832770|ref|YP_001693807.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           Hungary19A-6]
 gi|168995272|gb|ACA35884.1| RNA pseudouridine synthase family protein [Streptococcus pneumoniae
           Hungary19A-6]
          Length = 240

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 88/245 (35%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q  + +         + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQIDEKI---------DEIR 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++L+                 YE+   Y+ NKP G+           +   L     
Sbjct: 50  FDGQVLE-----------------YEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK  +     RLD +T G+L++      A  L      R + K Y + V GI   +    
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNDGQLAHVL--LSPKRHVDKTYLAQVKGIMTQEDVET 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     AI     ID   +    + +    G+ HQ++  
Sbjct: 149 -------------FAEGIPLKDFTCQPAILELVSIDT-EKNQSQIRVTIAEGKFHQIKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VGYCG 199


>gi|327462777|gb|EGF09099.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1057]
          Length = 242

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 89/248 (35%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQLLKKGLVLVNGRAEKS----------------PKTQIDE 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              +I+ S   LT           YE    Y+ NKP G+     +    H    L    +
Sbjct: 44  TADEIIVSGQRLT-----------YEKFVYYLLNKPQGVIS---ATEDDHHKTVLDLLDE 89

Query: 139 SKGQK-PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +  QK      RLD +T G+L++    + A   L+     + ++KIY + V G+      
Sbjct: 90  TARQKEVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLMNQAD- 145

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQL 255
                 +++   G +      Q          H K+++   +K    +E+    G+ HQ+
Sbjct: 146 ------VERFAAGIELKDFTCQPA--------HLKILELDEEKEASLVEITLAEGKFHQV 191

Query: 256 RVHALHMG 263
           +      G
Sbjct: 192 KRMVAACG 199


>gi|271964497|ref|YP_003338693.1| pseudouridine synthase, Rsu [Streptosporangium roseum DSM 43021]
 gi|270507672|gb|ACZ85950.1| pseudouridine synthase, Rsu [Streptosporangium roseum DSM 43021]
          Length = 621

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 47/262 (17%), Positives = 88/262 (33%), Gaps = 48/262 (18%)

Query: 6   YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           YV         + +RL +         +    + ++  G+V VD + V+     + G  V
Sbjct: 371 YVDERDTTEVPDGVRLQKVLAQA-GVASRRACEDMIGDGRVTVDGQVVR-----RFGARV 424

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
                                 +++          L+Y        NKP G+        
Sbjct: 425 ----------------DPAKQVIHVDGKRLPTMPDLVY-----LAINKPIGVVSTMSDPD 463

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                  L  +V  + ++     RLD ET G++++      A  LT       +QK YW+
Sbjct: 464 GRPS---LADFVADRTERLFHVGRLDTETEGLILLTNDGELANRLT--HPSYGVQKKYWA 518

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G        I   L ++   G +    + + +         F ++    Q+   +E+
Sbjct: 519 KVPG-------RIERDLGRRLKKGIELEDGIAKADS--------FTLVQEHGQQA-LVEV 562

Query: 246 QPHTGRTHQLRVHALHMGCPIV 267
             H GR H +R     +G P++
Sbjct: 563 VLHEGRKHIVRRMLEEVGHPVI 584


>gi|260494554|ref|ZP_05814684.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_33]
 gi|260197716|gb|EEW95233.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_33]
          Length = 163

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 32/164 (19%), Positives = 63/164 (38%), Gaps = 22/164 (13%)

Query: 45  QVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           ++ ++ KR           +      I  LN I+    I++   +    +  +   + YE
Sbjct: 5   EIYLNGKR-----------IKNNAKKIKKLNRIV----IIEKEKSTGIKAMDIPIDIAYE 49

Query: 105 DSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKGQK--PRLTHRLDQETSGILVV 160
           D  + + NK   I V            +  +  +  + G+K  PR  +RLD  TSG++++
Sbjct: 50  DENLLIVNKEPYIIVHPTQKKVDKTLANAVVNYFEKTLGKKLIPRFYNRLDMNTSGLIII 109

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           A+       L +      ++K Y  +  GI +     I   + K
Sbjct: 110 AKNAYTQAFLQDKT---EVKKTYKVIASGIIEKDDFFIEIPIGK 150


>gi|222152585|ref|YP_002561760.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           uberis 0140J]
 gi|222113396|emb|CAR41051.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           uberis 0140J]
          Length = 240

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 46/249 (18%), Positives = 84/249 (33%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + V      ++SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTLNGQVVSDLATTVKSGDTVEVE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                S +  E+   Y+ NKP G+  SV    G    ID     
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDDKGRKTVID----- 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG+L++         +        I K+Y + V GI     
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDKM--IHPRNEIDKVYLARVKGIATKDN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                               V  + K    A   + +I   A      +E+  H GR HQ
Sbjct: 144 L-------------RPLTRGVVIDGKKTKPA--RYNIIRVEADKNRSIVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFESVG 197


>gi|210622938|ref|ZP_03293443.1| hypothetical protein CLOHIR_01391 [Clostridium hiranonis DSM 13275]
 gi|210153904|gb|EEA84910.1| hypothetical protein CLOHIR_01391 [Clostridium hiranonis DSM 13275]
          Length = 238

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 92/251 (36%), Gaps = 52/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++  +     +    ++++ SG+V ++ +                  +I  L+  +
Sbjct: 1   MRINKYIAS-CGVASRRKAEELIISGRVTINGE------------------LITELSTTV 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            E K +     +  + +  K  +L         NKP G I+          +   LK   
Sbjct: 42  DETKDIVEVDGVPINQEEKKVYIL--------LNKPEGYITTVKDQFDRPSVLDILKDV- 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKK 195
               ++     RLD ETSG+L++         LT       ++K Y ++V GI  P+ K+
Sbjct: 93  ---DERVYPVGRLDYETSGLLILTNDGDLTYKLT--HPKHEVEKTYLAMVNGIITPEEKR 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                  ++        + +VK NE+                + +   ++  H GR  Q+
Sbjct: 148 RFENGLQIEDYTTAKAKLKIVKVNEE----------------KNYSVCKITIHEGRNRQV 191

Query: 256 RVHALHMGCPI 266
           R     +  P+
Sbjct: 192 RKMCKAINHPV 202


>gi|218896501|ref|YP_002444912.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           G9842]
 gi|228900151|ref|ZP_04064384.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|228907203|ref|ZP_04071064.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228938683|ref|ZP_04101288.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228964544|ref|ZP_04125654.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228971565|ref|ZP_04132189.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228978176|ref|ZP_04138554.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|218545922|gb|ACK98316.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           G9842]
 gi|228781648|gb|EEM29848.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228788224|gb|EEM36179.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228795144|gb|EEM42640.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228821059|gb|EEM67079.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228852424|gb|EEM97217.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228859557|gb|EEN03984.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|326939191|gb|AEA15087.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis serovar chinensis CT-43]
          Length = 242

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 45/255 (17%), Positives = 90/255 (35%), Gaps = 60/255 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----SVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + + G      
Sbjct: 87  FFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANIL--MHPKYKVEKTYVAKIKG------ 138

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRT 252
                       + G+ + ++++    +    A +H K+I    +K    +++  H GR 
Sbjct: 139 -----------PLTGEKIRMLERGVALEDGKTAPAHVKIISWDKRKEMAIVQLTIHEGRN 187

Query: 253 HQLRVHALHMGCPIV 267
            Q+R     + C +V
Sbjct: 188 RQVRRMFEALDCKVV 202


>gi|116629857|ref|YP_815029.1| 16S rRNA uridine-516 pseudouridylate synthase related
           pseudouridylate synthase [Lactobacillus gasseri ATCC
           33323]
 gi|116095439|gb|ABJ60591.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           gasseri ATCC 33323]
          Length = 245

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 36/252 (14%), Positives = 85/252 (33%), Gaps = 50/252 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72
             +  MR+D++  N     +   +  +++   V V+ + V     +++   +V +     
Sbjct: 8   EKDIEMRIDKYLANMNVG-SRKEVHSLIKKKVVTVNGELVTIPKQQVKETDLVAVDGNK- 65

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                                       + Y+    ++ NKP G+           +   
Sbjct: 66  ----------------------------IAYQQYHYFLLNKPKGVISATEDRSQQTVISL 97

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           LK+    + Q      RLD++T+G+L++      A + L  +  + ++ +   + V    
Sbjct: 98  LKT--KDRYQGIAPVGRLDKDTTGLLLLTNDGALAHELLAPNKHVAKVYRAKIAGVPDPE 155

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             KK      L   + +    + ++KQ+                       +E+Q   G+
Sbjct: 156 TAKKFAQGLILGDGTKLKPAKLKILKQD----------------QDNNLSQIEIQIQEGK 199

Query: 252 THQLRVHALHMG 263
            HQ++     +G
Sbjct: 200 YHQIKRMFGAVG 211


>gi|321467115|gb|EFX78106.1| hypothetical protein DAPPUDRAFT_225451 [Daphnia pulex]
          Length = 347

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 36/237 (15%), Positives = 79/237 (33%), Gaps = 30/237 (12%)

Query: 69  PVINALNHIIKEQKILDSSVNLTKHS------DFLKSILLYEDSKIYVFNKPAGISVQGG 122
           P I   +  ++E K +    N           D + + ++Y    +   NKP G+ +   
Sbjct: 27  PKIQLESEEVREPKPVHVLRNPYPWKTKEQFVDHIAANVIYNKDGLVAINKPFGVPLMKS 86

Query: 123 SGIAYHIDGFLKS-------WVDSKGQKPRLTHRLDQETSGILVVA--------RTRAAA 167
                H +                  +K      +++  SGI +          + R   
Sbjct: 87  GLTTGHNESLFSIDEVLIPLASKLNVEKLLPAKSVERFASGISLFTCQDEKVVDKIRQCY 146

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA---- 223
               +  ++   + +  ++    P   K  +   L +   +      ++K+  K      
Sbjct: 147 NT-NKLRKIHTFKYLVVTIGEPKPSESKRTVGMGLFEHKDLTRKLPVIMKEYSKKKVAEN 205

Query: 224 ---NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
               Y +S +K +         +E+   + + H LRV+  H+  PI+GDH +    +
Sbjct: 206 LVQEYKVS-YKTLSHGDGPCSLVEIDVSSVKNHFLRVYFAHLFSPILGDHIFGNRVQ 261


>gi|312862494|ref|ZP_07722736.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           vestibularis F0396]
 gi|322517477|ref|ZP_08070350.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           vestibularis ATCC 49124]
 gi|311101899|gb|EFQ60100.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           vestibularis F0396]
 gi|322123959|gb|EFX95518.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           vestibularis ATCC 49124]
          Length = 241

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 85/248 (34%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G+V ++ K V      ++SG +V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKEGRVTLNGKTVTELATIVKSGDIVEVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                S +  E+   Y+ NKP G+ S          +   +   
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDEKNRKTVIDLMPHV 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +T+G+L++         +        I K+Y + V GI   +  
Sbjct: 91  ----KERIYPVGRLDWDTTGLLILTNDGDFTDKM--IHPRNEIDKVYLARVKGIATKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
                           +  V  + K    A   + +I     +    +E+  H GR HQ+
Sbjct: 145 -------------RPLIRGVVLDGKKTQPA--RYNIIKVDHEKNRSVVELTIHEGRNHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KKMFESVG 197


>gi|323350518|ref|ZP_08086180.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis VMC66]
 gi|322123200|gb|EFX94885.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis VMC66]
          Length = 242

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 86/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQLLKKGLVLVNGRVEKS----------------PKTQIDE 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              +I+ S   LT           YE    Y+ NKP G+           +   L     
Sbjct: 44  TADEIIVSGQRLT-----------YEKFVYYLLNKPQGVISATEDDRHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+ K     
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLMKQADV- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLR 256
                         +   ++  +     A    KV++   A++   +E+    G+ HQ++
Sbjct: 147 ------------DRFAAGIELKDFTCQPA--QLKVLELDEAKETSLVEITLAEGKFHQVK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVAACG 199


>gi|293375505|ref|ZP_06621784.1| pseudouridylate synthase [Turicibacter sanguinis PC909]
 gi|325844949|ref|ZP_08168314.1| pseudouridine synthase B, ribosomal large subunit [Turicibacter sp.
           HGF1]
 gi|292645905|gb|EFF63936.1| pseudouridylate synthase [Turicibacter sanguinis PC909]
 gi|325488999|gb|EGC91388.1| pseudouridine synthase B, ribosomal large subunit [Turicibacter sp.
           HGF1]
          Length = 255

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 81/248 (32%), Gaps = 47/248 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++  G+V V+ K V+                      + 
Sbjct: 2   ERLQKVIAQA-GIASRRKAEQLILDGKVTVNDKVVR-----------------ELGTKVT 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            ++KI    V L +           E    YV +KP G        +       L  + D
Sbjct: 44  GKEKIEVEGVPLQR-----------EKKVYYVLHKPRGYVSTVSDELGRR--TVLDFFAD 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD +TSG+L++      A  +        I K+Y + V GI   +    
Sbjct: 91  RVSERVYPVGRLDYDTSGVLLMTNDGEFANKM--MHPSGEIDKVYLARVKGIVLPE---- 144

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                      G  + +     K A+  +    V      +   + +  H GR HQ++  
Sbjct: 145 ------NLKPFGKGIEIDGYKTKPASATL----VSVDKKNQSSLVRLTIHEGRYHQVKKM 194

Query: 259 ALHMGCPI 266
              +G P+
Sbjct: 195 FDAIGFPV 202


>gi|324989740|gb|EGC21683.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK353]
          Length = 242

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 87/250 (34%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLTENGLG-SRAQVKQLLKKGLVLVNGRAEKS----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                      + + +D +      L+YE    Y+ NKP G+           +   L  
Sbjct: 37  -------PKTQIDEAADDIVVSGQRLIYEKFVYYLLNKPQGVISATEDDHHKTVLDLLDE 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+    
Sbjct: 90  TARQK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLMNQA 144

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTH 253
                   +++   G +      Q          H K+++   +K    +E+    G+ H
Sbjct: 145 D-------VERFAAGIELKDFTCQPA--------HLKILELDEEKEASLVEITLAEGKFH 189

Query: 254 QLRVHALHMG 263
           Q++      G
Sbjct: 190 QVKRMVAACG 199


>gi|254447469|ref|ZP_05060935.1| pseudouridylate synthase, 23S RNA-specific [gamma proteobacterium
           HTCC5015]
 gi|198262812|gb|EDY87091.1| pseudouridylate synthase, 23S RNA-specific [gamma proteobacterium
           HTCC5015]
          Length = 256

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 47/282 (16%), Positives = 88/282 (31%), Gaps = 49/282 (17%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H P ++   ++  + +G V +   R     R++            A   ++   ++
Sbjct: 12  FLDEHLP-LSKSRIKSAMNAGAVWL--LRGASQERLR-----------RAKAELLPGDRV 57

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
                        L   L+ + +   ++ KP G+  +G     +            + ++
Sbjct: 58  AVFYNEALIQMPLLGLELVADRTHYSLWQKPEGMMSEGDEWGDWQALDRQVWLHFERQRE 117

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             +   L QE  GI++VA  R AA  L+      +I + Y   V G          +   
Sbjct: 118 VLVLFALAQEVGGIVLVAHNRRAAADLSALEEAGKITRHYRLEVLGETPPSGSINEH--- 174

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHM 262
                                   S ++ ID   A     L +Q   G    LR     M
Sbjct: 175 ------------------------SEYRRIDYLTALNASVLAVQSTRGTEDPLRERLAAM 210

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           G P++GD  Y            ++ L+L    +    P  G 
Sbjct: 211 GHPVLGDDVYG-------RQDYRDHLHLKGVGLAFTCPFSGE 245


>gi|168484154|ref|ZP_02709106.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC1873-00]
 gi|172042547|gb|EDT50593.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC1873-00]
 gi|332203445|gb|EGJ17512.1| hypothetical protein SPAR93_0315 [Streptococcus pneumoniae GA47368]
          Length = 240

 Score = 70.4 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 86/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q  + +             
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQIDEKID------------ 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                            F   +L YE+   Y+ NKP G+           +   L     
Sbjct: 47  --------------EIRFDGQVLEYEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KE 196
           SK  +     RLD +T G+L++      A  L      R + K Y + V GI   +  + 
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNDGQLAHVL--LSPKRHVDKTYLAQVKGIMTQEDVET 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I    LK        + ++  + +                +    + +    G+ HQ++
Sbjct: 149 FIKGIPLKDFTCQPARLEILSTDAE----------------KNQSQIRVTIAEGKFHQIK 192

Query: 257 VHALHMG 263
               + G
Sbjct: 193 RMVGYCG 199


>gi|42518880|ref|NP_964810.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii NCC 533]
 gi|41583166|gb|AAS08776.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii NCC 533]
          Length = 233

 Score = 70.4 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 80/246 (32%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  +++   V V+ + VK    +++    V +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVD--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   LK   
Sbjct: 51  --------------------GEKVAYQQYHYFLLNKPKGVISATEDKSQKTVLSLLK--P 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             + +      RLD++T+G+L++    A A  L      + + K Y + + G+   +   
Sbjct: 89  KDRYKDIAPVGRLDKDTTGLLLLTNDGALAHEL--LAPNKHVTKKYRAKIAGVADEETVK 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +                +   +      A     ++         +E++   G+ HQ++ 
Sbjct: 147 VFA------------SGMTLGDGTKLKPAELKI-LMQDKESDQSEIEIEIQEGKYHQIKR 193

Query: 258 HALHMG 263
               +G
Sbjct: 194 MFGAVG 199


>gi|308068498|ref|YP_003870103.1| RNA pseudouridine synthase (RNA-uridine isomerase) [Paenibacillus
           polymyxa E681]
 gi|305857777|gb|ADM69565.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Paenibacillus polymyxa E681]
          Length = 260

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 85/246 (34%), Gaps = 42/246 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+    H  + +  ++++ ++ G + V+ K  K +        +++ P  + +    
Sbjct: 9   QRLDKVLT-HMGYGSRSDIKRQMKQGMITVNGKITKDSG-------LQVHPYQDQI---- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                           +     +++ +    + +KP G+           +   L +  +
Sbjct: 57  ----------------EVNGERVVFREYIYIMLHKPPGVISATEDSRERTVLDLLSA--E 98

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +  +P    RLD++T G+L++    + A + L+     R + K Y + V G    +   
Sbjct: 99  ERHFEPFPVGRLDKDTEGLLLLTNDGKLAHELLS---PRRHVPKTYEATVSGHVTEED-- 153

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I  +        G                + H            ++ +  H G+ HQ++ 
Sbjct: 154 IHQFTAGVELDDG------YVTLPAQLTILRHEHPYQADGGVISYISLVIHEGKFHQVKR 207

Query: 258 HALHMG 263
               +G
Sbjct: 208 MFEAVG 213


>gi|281491795|ref|YP_003353775.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. lactis KF147]
 gi|281375509|gb|ADA65019.1| Ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. lactis KF147]
          Length = 257

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 41/275 (14%), Positives = 89/275 (32%), Gaps = 56/275 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++ +G+V V+         ++ +G +V +          
Sbjct: 19  MRINKYLA-HAGVASRRKAEELILAGKVTVNNVSMTNLGYQVSTGDIVEVN--------- 68

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G IS          +   +   
Sbjct: 69  --------------------GVAVYNEEPVYYLLNKPRGYISSVSDDKGRQTVMDLM--- 105

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +T       + K+Y + V G    +  
Sbjct: 106 -PQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMMT--HPRHGVDKVYVAKVEGQANKENL 162

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
                L     I G  V   +            +++I     +    + +  H G+ HQ+
Sbjct: 163 ---RPLTLGMTIEGKKVSPAR------------YEIIKQEKTKNHSIVSLTIHEGQNHQV 207

Query: 256 RVHALHMGCPI--VGDHKYCANFKGNFTSPIQNKL 288
           +      G P+  +   +Y         +    +L
Sbjct: 208 KKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRL 242


>gi|322387120|ref|ZP_08060731.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           infantis ATCC 700779]
 gi|321142107|gb|EFX37601.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           infantis ATCC 700779]
          Length = 241

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 88/249 (35%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V GI   + 
Sbjct: 86  LLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGIANKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                 L +   I G               A+  ++++     +    +++  H GR HQ
Sbjct: 144 L---RPLTRGLEIDGKKT----------KPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|221314557|ref|ZP_03596362.1| pseudouridine synthase [Bacillus subtilis subsp. subtilis str. NCIB
           3610]
          Length = 229

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 83/248 (33%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +++++ G+V+V+ K V     ++     + +          
Sbjct: 2   ERLQKVIA-HAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       L    +     LLY         KP G+     +         +  + 
Sbjct: 52  -----------GLKVEREEPVYFLLY---------KPRGVIS---AAQDDKGRKVVTDFF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +  Q+     RLD +TSG+L++      A  L        I K Y + V GIP  +   
Sbjct: 89  KNIPQRIYPIGRLDYDTSGLLLLTNDGEFANKL--MHPKYEIDKTYVAKVKGIPPKE--- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
               LL+K   G           +    A +  K++    +K    +++  H GR  Q+R
Sbjct: 144 ----LLRKLERGIRL--------EEGKTAPAKAKLLSLDKKKQTSIIQLTIHEGRNRQVR 191

Query: 257 VHALHMGC 264
                +G 
Sbjct: 192 RMFEAIGH 199


>gi|238853950|ref|ZP_04644307.1| RNA pseudouridine synthase family protein [Lactobacillus gasseri
           202-4]
 gi|282851629|ref|ZP_06260994.1| pseudouridylate synthase [Lactobacillus gasseri 224-1]
 gi|238833395|gb|EEQ25675.1| RNA pseudouridine synthase family protein [Lactobacillus gasseri
           202-4]
 gi|282557597|gb|EFB63194.1| pseudouridylate synthase [Lactobacillus gasseri 224-1]
          Length = 233

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 84/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  +++   V V+ + V     +++   +V +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHSLIKKKVVTVNGELVTIPKQQVKETDLVAVDGNK------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   LK+  
Sbjct: 54  -----------------------IAYQQYHYFLLNKPKGVISATEDRSQQTVISLLKT-- 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             + Q      RLD++T+G+L++      A + L  +  + ++ +   + V      KK 
Sbjct: 89  KDRYQGIAPVGRLDKDTTGLLLLTNDGALAHELLAPNKHVAKVYRAKIAGVPDPETAKKF 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                L   + +    + ++KQ+                       +E+Q   G+ HQ++
Sbjct: 149 AQGLILGDGTKLKPAKLKILKQD----------------QDNNLSQIEIQIQEGKYHQIK 192

Query: 257 VHALHMG 263
                +G
Sbjct: 193 RMFGAVG 199


>gi|311110505|ref|ZP_07711902.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           gasseri MV-22]
 gi|311065659|gb|EFQ45999.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           gasseri MV-22]
          Length = 240

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 36/252 (14%), Positives = 85/252 (33%), Gaps = 50/252 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72
             +  MR+D++  N     +   +  +++   V V+ + V     +++   +V +     
Sbjct: 3   EKDIEMRIDKYLANMNVG-SRKEVHSLIKKKVVTVNGELVTIPKQQVKETDLVAVDGNK- 60

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                                       + Y+    ++ NKP G+           +   
Sbjct: 61  ----------------------------IAYQQYHYFLLNKPKGVISATEDRSQQTVISL 92

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           LK+    + Q      RLD++T+G+L++      A + L  +  + ++ +   + V    
Sbjct: 93  LKT--KDRYQGIAPVGRLDKDTTGLLLLTNDGALAHELLAPNKHVAKVYRAKIAGVPDPE 150

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             KK      L   + +    + ++KQ+                       +E+Q   G+
Sbjct: 151 TAKKFAQGLILGDGTKLKPAKLKILKQD----------------QDNNLSQIEIQIQEGK 194

Query: 252 THQLRVHALHMG 263
            HQ++     +G
Sbjct: 195 YHQIKRMFGAVG 206


>gi|300781239|ref|ZP_07091093.1| 16S rRNA uridine-516 pseudouridylate synthase [Corynebacterium
           genitalium ATCC 33030]
 gi|300532946|gb|EFK54007.1| 16S rRNA uridine-516 pseudouridylate synthase [Corynebacterium
           genitalium ATCC 33030]
          Length = 318

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 47/250 (18%), Positives = 90/250 (36%), Gaps = 45/250 (18%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + +RL +         +  + + ++  G+V V+ K V+        Q VR+ P ++ +  
Sbjct: 76  DGIRLQKVLAQA-GVASRRHSEVMIDEGRVEVNGKIVRQ-------QGVRVDPNVDII-- 125

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                ++    VN+             ED + +  NKP G+       +     G   + 
Sbjct: 126 -----RVDGVRVNVN------------EDQQYFALNKPRGVHTTMEDELGRPCVGDFVAD 168

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             + GQ+     RLD +T G+L++      +  L        ++K Y + V G  K    
Sbjct: 169 RVAAGQRLFHVGRLDADTEGLLLLTNDGELSNRL--MHPKYGVEKTYLATVLGEAK---- 222

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                L+++   G +    V         A + +  I    Q    + +  H GR H +R
Sbjct: 223 ---PALVRELKKGIELEDGV---------AKADYAQIVDTHQGQSLIRLVIHEGRKHVVR 270

Query: 257 VHALHMGCPI 266
                 G P+
Sbjct: 271 RMLKEAGYPV 280


>gi|323141768|ref|ZP_08076638.1| pseudouridylate synthase [Phascolarctobacterium sp. YIT 12067]
 gi|322413757|gb|EFY04606.1| pseudouridylate synthase [Phascolarctobacterium sp. YIT 12067]
          Length = 241

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 82/248 (33%), Gaps = 47/248 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    +KI+ +G+VRV+ K V           VRI      +    
Sbjct: 3   ERLQKILAAA-GVASRREAEKIITAGRVRVNGKVVTELGCKFDADKVRISVDGKPIAQEA 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K                             Y+F KP G+               +  +V 
Sbjct: 62  K---------------------------AYYMFYKPRGVVTTMSDPQNRRS---IADFVQ 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +  ++     RLD  T G+L++    A AQ L        + K Y+  V GI   +K   
Sbjct: 92  NLPERVFPVGRLDFNTEGLLLLTNDGALAQAL--MHPSHEVNKTYFVKVPGIVPQEK--- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                    +    + V  ++   A  AI + +  D   + F   ++  H GR  Q+R  
Sbjct: 147 ---------LDQLRLGVKLEDGPTA-PAIVNLRDYD-HERGFTLFDITIHEGRNRQIRRM 195

Query: 259 ALHMGCPI 266
              +G P+
Sbjct: 196 CDAIGFPV 203


>gi|15900214|ref|NP_344818.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae TIGR4]
 gi|111656756|ref|ZP_01407636.1| hypothetical protein SpneT_02001953 [Streptococcus pneumoniae
           TIGR4]
 gi|148988021|ref|ZP_01819484.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP6-BS73]
 gi|149011151|ref|ZP_01832456.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP19-BS75]
 gi|168493975|ref|ZP_02718118.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC3059-06]
 gi|225856037|ref|YP_002737548.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae P1031]
 gi|225858129|ref|YP_002739639.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae 70585]
 gi|225860315|ref|YP_002741824.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298229569|ref|ZP_06963250.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae str. Canada MDR_19F]
 gi|298254034|ref|ZP_06977620.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae str. Canada MDR_19A]
 gi|298502097|ref|YP_003724037.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|14971752|gb|AAK74458.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae TIGR4]
 gi|147764787|gb|EDK71717.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP19-BS75]
 gi|147926485|gb|EDK77558.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP6-BS73]
 gi|183576148|gb|EDT96676.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC3059-06]
 gi|225721053|gb|ACO16907.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae 70585]
 gi|225725053|gb|ACO20905.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae P1031]
 gi|225728111|gb|ACO23962.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298237692|gb|ADI68823.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
          Length = 240

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 88/245 (35%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q  + +         + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQIDEKI---------DEIR 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++L+                 YE+   Y+ NKP G+           +   L     
Sbjct: 50  FDGQVLE-----------------YEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK  +     RLD +T G+L++      A  L      R + K Y + V GI   +    
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNDGQLAHVL--LSPKRHVDKTYLAQVKGIMTQEDVET 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     AI     ID   +    + +    G+ HQ++  
Sbjct: 149 -------------FAEGIPLKDFTCQPAILELVSIDT-EKNQSQIRVTIAEGKFHQIKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VGYCG 199


>gi|116618395|ref|YP_818766.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
 gi|116097242|gb|ABJ62393.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
          Length = 249

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 92/253 (36%), Gaps = 49/253 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINA 73
            EE  RL +         +    ++++ +G+V+V+ + V     ++ +   V++      
Sbjct: 2   SEEAQRLQKIIAQA-GLASRRGAEELIINGRVQVNGQTVTELGTKVTANDKVQV------ 54

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                 +   ++    L                  Y+ NKP G+     +         +
Sbjct: 55  ------DGAPIEGREKLV----------------YYLLNKPRGVVT---TNDDEKGRRTV 89

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              ++   Q+     RLD +T+G+L++      A  L       ++ K Y + V GI   
Sbjct: 90  LDILEDVDQRVYPVGRLDYDTTGVLLLTNDGVVANQL--MHPKTKVDKTYVAKVEGIATE 147

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +K       LK+         VV +  K A   +S  ++     ++   + +  H GR H
Sbjct: 148 EK----LAPLKRG--------VVLKGRKTAPARVSIERI--EPTKRTSMVRLTIHEGRNH 193

Query: 254 QLRVHALHMGCPI 266
           Q++     +G P+
Sbjct: 194 QVKNMLAKVGLPV 206


>gi|254818897|ref|ZP_05223898.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           intracellulare ATCC 13950]
          Length = 247

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 76/253 (30%), Gaps = 47/253 (18%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + E +RL +         +    +K++  G+V VD + V             +   ++  
Sbjct: 3   EAEGIRLQKVLSQA-GIASRRAAEKLIIEGRVEVDGQVVT-----------ELGTRVDPD 50

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +I+                    I+L +       NKP G+             G L 
Sbjct: 51  VSVIR---------------VDGARIVLDDSQVYLALNKPRGVHSTMSDDRGRPCIGDLI 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKN 193
                  +      RLD +T G++++      A  L        + K Y + V G +P+ 
Sbjct: 96  ERRVRGNKNLFHVGRLDADTEGLILLTNDGELAHRL--MHPSHEVPKTYLATVTGSVPRG 153

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + +   +                        +  F V+D    K   + +  H GR  
Sbjct: 154 VGKALRAGIELDDGPAR----------------VDEFAVVDAIPGK-TLVRVTLHEGRNR 196

Query: 254 QLRVHALHMGCPI 266
            +R      G P+
Sbjct: 197 IVRRLLAAAGFPV 209


>gi|77414368|ref|ZP_00790523.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae 515]
 gi|77159558|gb|EAO70714.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae 515]
          Length = 240

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + V     ++++G +V I          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIKQGMVTINGQVVNELATKVKAGDLVEIE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                S +  E+   Y+ NKP G+  SV    G    ID     
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDDKGRKTVID----- 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +T+G+L++         +        I K+Y + V GI   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTTGLLILTNDGDFTDKM--IHPRNEIDKVYLARVKGIATKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
                               V  + K    A   + +I     +    +E+  H GR HQ
Sbjct: 144 L-------------RPLTRGVVIDGKKTKPA--RYNIIKVDHEKNRSVVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEQVG 197


>gi|213865434|ref|ZP_03387553.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
          enterica serovar Typhi str. M223]
          Length = 56

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 1  MSLMT-YVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF 55
          M   T  V+ V +  DE   R+D + +     +    + +ILR G+VRV+KKR+K 
Sbjct: 1  MKTETPSVKIVAIAADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKP 56


>gi|148543988|ref|YP_001271358.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri DSM 20016]
 gi|184153383|ref|YP_001841724.1| putative pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227364901|ref|ZP_03848946.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri MM2-3]
 gi|325682474|ref|ZP_08161991.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri MM4-1A]
 gi|148531022|gb|ABQ83021.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri DSM 20016]
 gi|183224727|dbj|BAG25244.1| putative pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227070048|gb|EEI08426.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri MM2-3]
 gi|324978313|gb|EGC15263.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           reuteri MM4-1A]
          Length = 238

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 51/261 (19%), Positives = 93/261 (35%), Gaps = 54/261 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++  G+V V+ K V     ++     + +          
Sbjct: 2   ERLQKAMAEA-GVASRRASEKLILQGKVAVNGKIVTELGTKVGVHDEIVVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  + +E    Y+ NKP G+  S     G    +D    +
Sbjct: 52  --------------------GVPIHHEQHVYYLLNKPRGVISSAHDDKGRRTVVDIIHDA 91

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +D   ++     RLD +T+GIL++      A  L        ++K Y + V GI KN +
Sbjct: 92  DID---ERIYPVGRLDYDTTGILLLTNDGTLANKL--MHPKYEVEKTYVAKVEGIVKNDE 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                  LK+  +G      V  + +    A S    +D  A+K   +++  H GR HQ+
Sbjct: 147 -------LKQLRLG------VIIDGRKTKPAKSKLLNVDR-AKKTSLVQLTIHEGRNHQV 192

Query: 256 RVHALHMGCPI--VGDHKYCA 274
           +     +G P+  +    Y  
Sbjct: 193 KNMFKAVGHPVTKLHRETYGP 213


>gi|295093016|emb|CBK82107.1| ribosomal small subunit pseudouridine synthase A [Coprococcus sp.
           ART55/1]
          Length = 241

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 45/246 (18%), Positives = 86/246 (34%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   +++ ++ G V V+   VK ++       V+I    + + +  
Sbjct: 1   MRLDKFLVEMGIG-SRSQVKQYVKKGTVTVNGAPVKSSD-------VKIDENNDTIKYNG 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +                    IL Y   + ++ NKPAG        +   +   LK    
Sbjct: 53  R--------------------ILNYSRYRYFLLNKPAGCVSATKDNVHQTVIDLLK---G 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              +      RLD +T G+L++    A   HL        I K Y++ + G   +    I
Sbjct: 90  ENTKDLSPVGRLDIDTEGLLLLTNDGALTHHL--LSPAHHIPKTYYAEIDGYVTDD--TI 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLRV 257
             +             V   +EK    A    +++   +      +E+    GR HQ++ 
Sbjct: 146 NLFATG----------VDIGDEKPTLPA--DLRILSSDSTAARSEIELIITEGRFHQVKR 193

Query: 258 HALHMG 263
               +G
Sbjct: 194 MFEAVG 199


>gi|325830888|ref|ZP_08164272.1| pseudouridine synthase B, ribosomal large subunit [Eggerthella sp.
           HGA1]
 gi|325487295|gb|EGC89738.1| pseudouridine synthase B, ribosomal large subunit [Eggerthella sp.
           HGA1]
          Length = 301

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 40/265 (15%), Positives = 84/265 (31%), Gaps = 46/265 (17%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRL ++        +    + ++ +G+V V+ K V                 + +    
Sbjct: 29  PMRLQKFLARA-GAASRRGSENLMTAGRVTVNGKVVT---------------ELGSKVDP 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + ++  +D +V   + +D   +I+L+         KPAG                L    
Sbjct: 73  LVDEVAVDGAV--VRLADGPVTIMLH---------KPAGFVTTMSDPQGRRTVAELV--P 119

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +        RLD +T+G+L+ +        L        + K Y + V G P  +   
Sbjct: 120 TERYPGLFPIGRLDFDTTGLLLFSTDGELGNGL--LHPKHHVTKRYLACVEGRPTERDLA 177

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK---------------VIDCFAQKFCW 242
           +    ++          V       A +A    +               V +  A +   
Sbjct: 178 LLRRGIELDDGPTQPADVRMVEGGAARHAERLLEIPAAVPPRSSKEYAAVCEGRATRRSI 237

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIV 267
           + +    GR  Q++     +G P++
Sbjct: 238 VRLGIREGRKRQVKRMLAAVGHPVL 262


>gi|309798849|ref|ZP_07693110.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           infantis SK1302]
 gi|308117498|gb|EFO54913.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           infantis SK1302]
          Length = 199

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 87/248 (35%), Gaps = 56/248 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V GI   + 
Sbjct: 86  LLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGIANKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                               V+ + K    A+  ++++     +    +++  H GR HQ
Sbjct: 144 L-------------RPLTRGVEIDGKKTKPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHM 262
           ++     +
Sbjct: 189 VKKCLKLL 196


>gi|322388650|ref|ZP_08062250.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           infantis ATCC 700779]
 gi|321140570|gb|EFX36075.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           infantis ATCC 700779]
          Length = 240

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 45/246 (18%), Positives = 84/246 (34%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++  L+SG+V V+ K+ K + ++Q  +               
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNFLKSGRVTVNGKKEK-SAKLQIDEE-------------- 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                       T    F    L YE+   Y+ NKP G+           +   L  +  
Sbjct: 45  ------------TDEICFDGQKLDYEEFVYYMMNKPQGVISATEDPKHKTVLDLLDDYAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +K  +     RLD +T G+L++    + A   L+     R + K Y + V GI  +    
Sbjct: 93  AK--EVFPVGRLDIDTHGLLLLTNDGKLAHALLS---PKRHVDKTYLAQVKGIMTDTDVE 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   +   +     A      ID    +   + +    G+ HQ++ 
Sbjct: 148 T-------------FAKGIPLKDFTCQPAKLELVSIDTEKDQ-SLVRVTIAEGKFHQVKR 193

Query: 258 HALHMG 263
              + G
Sbjct: 194 MVAYCG 199


>gi|197301684|ref|ZP_03166754.1| hypothetical protein RUMLAC_00410 [Ruminococcus lactaris ATCC
           29176]
 gi|197299124|gb|EDY33654.1| hypothetical protein RUMLAC_00410 [Ruminococcus lactaris ATCC
           29176]
          Length = 246

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 42/248 (16%), Positives = 90/248 (36%), Gaps = 55/248 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +         ++K +  GQV V+    K                 +A   I 
Sbjct: 3   LRLDKYLADMGLG-TRSQIKKDISKGQVLVNGTVSK-----------------DAGTRID 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+  +           +L   + Y + + Y+ NKPAG+     S      D  +   +D
Sbjct: 45  TEKDQVS----------YLGQTVTYAEYEYYMLNKPAGVV----SATEDRHDRTVLDLID 90

Query: 139 SKGQK-PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +K +K      RLD++T G+L++      A + L+       + K+Y++ + G    +  
Sbjct: 91  TKQRKDLFPVGRLDKDTEGLLLITNDGALAHRLLSPKSH---VDKVYFARIEGKVTAED- 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
                           V + ++       A++    ++   +     + +    G+ HQ+
Sbjct: 147 ----------------VFLFQKGVDIGEQALTLPARLEILSSDTVSEIRLTICEGKFHQV 190

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 191 KRMFESVG 198


>gi|120556507|ref|YP_960858.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120326356|gb|ABM20671.1| ribosomal small subunit pseudouridine synthase A [Marinobacter
           aquaeolei VT8]
          Length = 231

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 39/245 (15%), Positives = 81/245 (33%), Gaps = 52/245 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  N    ++    +K++ +G+V+VD +  +  NR                    
Sbjct: 1   MRLDQYLSNG-TELSRKEAKKVVSAGRVKVDGETCRQANR-------------------- 39

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q   + SV+L          +        + +KPAG+     +         L     
Sbjct: 40  --QVEAEQSVHLDGKPVNPPGDI------YLMMHKPAGVLS---ATTDSSQPTALDLLPR 88

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +  +  RLD++T+G+L++      +  +T   R  R     W L   IP+     +
Sbjct: 89  GLASRVHIAGRLDKDTTGLLLLTSDGQWSHAVTSPRRECRKSYRVW-LAEAIPEQACRAL 147

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              ++                        +  +  +        +++    GR HQ++  
Sbjct: 148 EKGVMLNGE-------------------TTETRPAEVRVHNNQLIDLTIGEGRYHQVKRM 188

Query: 259 ALHMG 263
              +G
Sbjct: 189 LAAVG 193


>gi|221310234|ref|ZP_03592081.1| pseudouridine synthase [Bacillus subtilis subsp. subtilis str. 168]
          Length = 245

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 83/248 (33%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +++++ G+V+V+ K V     ++     + +          
Sbjct: 18  ERLQKVIA-HAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVN--------- 67

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       L    +     LLY         KP G+     +         +  + 
Sbjct: 68  -----------GLKVEREEPVYFLLY---------KPRGVIS---AAQDDKGRKVVTDFF 104

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +  Q+     RLD +TSG+L++      A  L        I K Y + V GIP  +   
Sbjct: 105 KNIPQRIYPIGRLDYDTSGLLLLTNDGEFANKL--MHPKYEIDKTYVAKVKGIPPKE--- 159

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
               LL+K   G           +    A +  K++    +K    +++  H GR  Q+R
Sbjct: 160 ----LLRKLERGIRL--------EEGKTAPAKAKLLSLDKKKQTSIIQLTIHEGRNRQVR 207

Query: 257 VHALHMGC 264
                +G 
Sbjct: 208 RMFEAIGH 215


>gi|293364698|ref|ZP_06611415.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           oralis ATCC 35037]
 gi|307702946|ref|ZP_07639893.1| putative ribosomal large subunit pseudouridine synthase B
           [Streptococcus oralis ATCC 35037]
 gi|291316148|gb|EFE56584.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           oralis ATCC 35037]
 gi|307623339|gb|EFO02329.1| putative ribosomal large subunit pseudouridine synthase B
           [Streptococcus oralis ATCC 35037]
          Length = 240

 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 47/245 (19%), Positives = 86/245 (35%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q                I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQ----------------IN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E+  +           F   +L YE+   Y+ NKP G+           +   L     
Sbjct: 43  EERDEI----------RFDGQVLEYEEFVYYMMNKPQGVISATEDSKHRTVLDLLDDVAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SKG       RLD +T G+L++      A  L      R + K Y + V GI   +    
Sbjct: 93  SKG--VFPVGRLDIDTHGLLLLTNDGQLAHAL--LSPKRHVDKTYLAQVKGIMSQEDVET 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     A      ID   +    + +    G+ HQ++  
Sbjct: 149 -------------FAKGIPLKDFTCQPARLEIISIDT-EKNQSKIRVTIAEGKFHQVKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VAYCG 199


>gi|326692499|ref|ZP_08229504.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           argentinum KCTC 3773]
          Length = 249

 Score = 70.0 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 49/253 (19%), Positives = 92/253 (36%), Gaps = 49/253 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINA 73
            EE  RL +         +    ++++  G+V+V+ + VK    ++     V++      
Sbjct: 2   SEEAQRLQKVIAQA-GLASRRGAEELITQGRVQVNGETVKTLGIKVMPHDTVQV------ 54

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                 +   ++    L                  Y+ NKP G+               +
Sbjct: 55  ------DGAPIEGREKLV----------------YYLMNKPRGVVTTNSDDKGRQ---TV 89

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              ++   Q+     RLD +T+G+L++      A  L       R+ K+Y + V GI  +
Sbjct: 90  LDVLEDVPQRVYPVGRLDYDTTGVLLLTNDGVIANQL--MHPKSRVDKVYMAKVEGIATD 147

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +K       LK+         VV Q  K A   +S  +V     +K   + +  H GR H
Sbjct: 148 EK----LAPLKRG--------VVIQGRKTAPARVSVERV--DKDKKTSMVRVIIHEGRNH 193

Query: 254 QLRVHALHMGCPI 266
           Q++     +G P+
Sbjct: 194 QVKNMLQKVGLPV 206


>gi|257056522|ref|YP_003134354.1| ribosomal large subunit pseudouridine synthase B [Saccharomonospora
           viridis DSM 43017]
 gi|256586394|gb|ACU97527.1| ribosomal large subunit pseudouridine synthase B [Saccharomonospora
           viridis DSM 43017]
          Length = 247

 Score = 70.0 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 46/257 (17%), Positives = 84/257 (32%), Gaps = 48/257 (18%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
           +   +  E +RL +         +    ++++ +G+V VD   V+            +  
Sbjct: 1   MTTADSSEGVRLQKVLAKA-GVASRRASEELIAAGRVSVDGVVVR-----------ELGR 48

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            ++    +I              H D ++  +  +D      NKP G+            
Sbjct: 49  RVDPDTAVI--------------HVDGIRVQVR-DDLVYLALNKPRGVHSTMSDAQGRPC 93

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            G    +V  + ++     RLD +T G+L++      A  L        + K Y + V G
Sbjct: 94  VG---DYVADRPERLFHVGRLDADTEGLLLLTNDGDLAHKL--MHPSFHVTKTYLAEVEG 148

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   +A  L K+   G        Q   G   A      I         +E+  H 
Sbjct: 149 A-------VARGLGKRLRAG-------VQLSDGPVTA--DAFRIKDVRPNRSLVEIVLHE 192

Query: 250 GRTHQLRVHALHMGCPI 266
           GR H +R     +G P+
Sbjct: 193 GRKHIVRRLLAEVGHPV 209


>gi|1531665|gb|AAB07777.1| 44.9 kDa protein C18B11 homolog [Homo sapiens]
          Length = 189

 Score = 70.0 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +       + F+ +    Q    +  +P TGRTHQ+RVH   +G PI+ D  Y +
Sbjct: 5   DPRGKPCETVFQRLSYNGQS-SVVRCRPLTGRTHQIRVHLQFLGHPILNDPIYNS 58


>gi|329767586|ref|ZP_08259107.1| hypothetical protein HMPREF0428_00804 [Gemella haemolysans M341]
 gi|328839213|gb|EGF88797.1| hypothetical protein HMPREF0428_00804 [Gemella haemolysans M341]
          Length = 235

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 38/247 (15%), Positives = 85/247 (34%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++    +KI++ G V ++   VK  + ++                  
Sbjct: 1   MRLDKFISTT-TTLSRAEAKKIIKKG-VLINNILVKSPDYKV------------------ 40

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       L+         L+Y+     + NKP  +       +   +   L+   
Sbjct: 41  ----------DELSDQVIVNGERLVYQKYIYIMMNKPKNVVSATEDAVEKTVVDILEE-- 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
             +  K     RLD++T G++++      A  L      + ++K Y+  V G  K++  E
Sbjct: 89  KDRIHKVFPVGRLDKDTEGLMLLTNDGELAHKL--ISPKKDVEKKYYVEVSGKLKDEYIE 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + N ++                  G     +  ++++   +K     +    G+ HQ++
Sbjct: 147 LVENGIIIDG---------------GYKCKSARLEILESNEEK-SRASIFITEGKFHQVK 190

Query: 257 VHALHMG 263
                +G
Sbjct: 191 RMMKALG 197


>gi|300173429|ref|YP_003772595.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299887808|emb|CBL91776.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 249

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 90/254 (35%), Gaps = 49/254 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINA 73
            EE  RL +         +    ++++  G+V+V+ + +     +++    V +      
Sbjct: 2   SEEAQRLQKIIAQA-GLASRRGAEELIAKGRVQVNGQTITELGMKVEPNDHVEVDGSPIE 60

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                                   +  L+Y     Y+ NKP G+     +         +
Sbjct: 61  G-----------------------REKLVY-----YLLNKPRGVVT---TNNDEKGRQTV 89

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              +    Q+     RLD +T+G+L++      A  L       R+ K+Y + V GI  +
Sbjct: 90  IDLLGDVSQRVYPIGRLDYDTTGVLLLTNDGVVANQL--MHPKSRVDKVYVAKVEGIATD 147

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +K       LK          VV +  K A   ++  +V     +K   + +  H GR H
Sbjct: 148 EK----LAPLKHG--------VVIKGRKTAPARVTIERV--DKDKKTSMVRVIIHEGRNH 193

Query: 254 QLRVHALHMGCPIV 267
           Q++     +  P+V
Sbjct: 194 QIKNMLQKVHLPVV 207


>gi|322377564|ref|ZP_08052054.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           M334]
 gi|321281329|gb|EFX58339.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           M334]
          Length = 240

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 47/246 (19%), Positives = 89/246 (36%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q                I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQ----------------ID 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E+  +           F   +L YE+   Y+ NKP G+           +   L     
Sbjct: 43  EERDEI----------RFDGQVLEYEEFVYYMMNKPQGVISATEDPKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           SK  +     RLD +T G+L++    + A   L+     R + K Y + V GI   +   
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNDGKLAHALLS---PKRHVDKTYLAQVKGIMTQEDVE 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   +   +     AI     ID   +    + +    G+ HQ++ 
Sbjct: 148 T-------------FAKGISLKDFTCQPAILELVSID-PEKNQSQIRVTIAEGKFHQVKR 193

Query: 258 HALHMG 263
              + G
Sbjct: 194 MVTYCG 199


>gi|54023979|ref|YP_118221.1| putative pseudouridine synthase [Nocardia farcinica IFM 10152]
 gi|54015487|dbj|BAD56857.1| putative pseudouridine synthase [Nocardia farcinica IFM 10152]
          Length = 237

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 42/235 (17%), Positives = 79/235 (33%), Gaps = 43/235 (18%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
            +    ++++  G+V VD   V+        Q +RI P    +        + D  V   
Sbjct: 8   ASRRAAEEMIDQGRVEVDGVIVRE-------QGLRIDPQTAVVRVDGVRVVVRDEQV--- 57

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                               NKP G        +     G + +   + GQ+     RLD
Sbjct: 58  ----------------YVALNKPKGWQSTMSDDLGRPCVGDIVAERIAAGQRLFHVGRLD 101

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +T G+L++      A  L        + K Y + V G   +K       + K+   G +
Sbjct: 102 ADTEGLLLLTNDGDLAHRL--MHPSFEVSKTYLATVHGEVHHKV------IGKRLRDGIE 153

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                    +     +  F+V++   +    +++  H GR H +R     +G P+
Sbjct: 154 L--------EDGPAKVDRFQVLE-LGEGRSLVKIVLHEGRKHIVRRLLDAVGHPV 199


>gi|317124964|ref|YP_004099076.1| pseudouridine synthase [Intrasporangium calvum DSM 43043]
 gi|315589052|gb|ADU48349.1| pseudouridine synthase [Intrasporangium calvum DSM 43043]
          Length = 334

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 51/255 (20%), Positives = 93/255 (36%), Gaps = 52/255 (20%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +RL +         +    + ++  G+V VD + +      + G  VRI P    +
Sbjct: 93  DPDGVRLQKLMAAAGVG-SRRVCENLIEQGRVEVDGQVIT-----ELG--VRINPQSQVV 144

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                             H D ++   L E+     FNKP G+     +         L 
Sbjct: 145 ------------------HVDGVRVN-LDEERVYLAFNKPKGVVT---TMHDELGRISLA 182

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +V ++ Q+     RLD +T G+L++      A  L        + K Y + V G     
Sbjct: 183 DYVGNREQRLFHVGRLDADTEGLLLLTNDGDLAHRL--QHPAYGVLKTYLATVRG----- 235

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS--HFKVIDCFAQKFCWLEMQPHTGRT 252
                        +G D    +++  +  +  ++   FKV+D    K   +E+  H GR 
Sbjct: 236 ------------PVGRDVGKQLREGVELEDGPVTVDSFKVVDSQPGKA-LIEVVLHEGRK 282

Query: 253 HQLRVHALHMGCPIV 267
           H +R     +G P++
Sbjct: 283 HVVRRMLELVGHPVL 297


>gi|304384543|ref|ZP_07366889.1| ribosomal small subunit pseudouridine synthase A [Pediococcus
           acidilactici DSM 20284]
 gi|304328737|gb|EFL95957.1| ribosomal small subunit pseudouridine synthase A [Pediococcus
           acidilactici DSM 20284]
          Length = 239

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 87/249 (34%), Gaps = 53/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  +         ++K+++   V V+    K + R++   VV             
Sbjct: 1   MRVDKFLHDMNVG-TRSQIRKLIKEKAVFVNDVVAK-SGRVKVDPVVD------------ 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                              + ++ Y+    ++ NKP G+               +    +
Sbjct: 47  --------------QVRLGEQVITYQQYFYFMMNKPLGVVT----ATEDRKQKTVMDLFN 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               +       RLD++T G+L++      A Q L      R +QK Y ++V G      
Sbjct: 89  KVDFRKDLFPVGRLDKDTEGLLLITNNGPLAHQLLA---PERHVQKTYEAVVTGQ----- 140

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
             I +  +K+   G     +V ++      A     +++  A  +   + +    G+ HQ
Sbjct: 141 --ITDPAVKQFADG-----IVLKDGTQLKPA--DLTILNYSALDEQTLVHVTLKEGKYHQ 191

Query: 255 LRVHALHMG 263
           +R     +G
Sbjct: 192 VRRMFGSLG 200


>gi|149017975|ref|ZP_01834434.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP23-BS72]
 gi|147931539|gb|EDK82517.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP23-BS72]
          Length = 240

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 87/245 (35%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q  + +         + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQIDEKI---------DEIR 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++L+                 YE+   Y+ NKP G+           +   L     
Sbjct: 50  FDGQVLE-----------------YEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK  +     RLD  T G+L++      A  L      R + K Y + V GI   +    
Sbjct: 93  SK--EVFPVGRLDINTHGLLLLTNDGQLAHVL--LSPKRHVGKTYLAQVKGIMTQEDVET 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     AI     ID   +    + +    G+ HQ++  
Sbjct: 149 -------------FAEGIPLKDFTCKPAILELVSIDT-EKNQSQIRVTIAEGKFHQIKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VGYCG 199


>gi|291518121|emb|CBK73342.1| ribosomal small subunit pseudouridine synthase A [Butyrivibrio
           fibrisolvens 16/4]
          Length = 234

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 82/246 (33%), Gaps = 51/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+             ++ +L+ G + VD ++                          
Sbjct: 2   MRLDKLLVELNIG-TRSEVKALLKKGLIFVDGEKATK----------------------- 37

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQK+ ++SV +T           Y+    YV NKP G+           +     S   
Sbjct: 38  PEQKVDENSVVITYQGKEYT----YQKFSYYVINKPKGVITATEDAHEKTVMDVFYSLCP 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              +      RLD++T+G+L++      A   L+     + + K Y+  + G    +   
Sbjct: 94  DAPKGLAPVGRLDKDTTGLLLITNDGQLAHDMLS---PKKHVDKTYFVTLDGELSEED-- 148

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               L    HIG        + E  A   +           K C+  +  H G+ HQ++ 
Sbjct: 149 -VAALEAGVHIG--------EGEPTAPATV------KYEGGKTCY--ITIHEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFFAVG 197


>gi|229160522|ref|ZP_04288517.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228622932|gb|EEK79763.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 242

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 45/255 (17%), Positives = 89/255 (34%), Gaps = 60/255 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----SVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + V G      
Sbjct: 87  FFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANVL--MHPKYKVEKTYVAKVKG------ 138

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRT 252
                       + G+ + ++++    +    A +  K+I    +K    +++  H GR 
Sbjct: 139 -----------PLTGEKIRMLERGVALEDGKTAPARVKIISWDKRKEMAIVQLTIHEGRN 187

Query: 253 HQLRVHALHMGCPIV 267
            Q+R     + C +V
Sbjct: 188 RQVRRMFEALDCKVV 202


>gi|322373877|ref|ZP_08048412.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           C150]
 gi|321277249|gb|EFX54319.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           C150]
          Length = 241

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 83/248 (33%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G+V ++ K V      +++G  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKEGRVTLNGKTVTELATIVKNGDTVEVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                S +  E+   Y+ NKP G+ S          +   +   
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDEKDRKTVIDLMPHV 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +T+G+L++         +        I K+Y + V GI   +  
Sbjct: 91  ----KERIYPVGRLDWDTTGLLILTNDGDFTDKM--IHPRNEIDKVYLARVKGIATKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
                              V  + K    A   + ++     +    +E+  H GR HQ+
Sbjct: 145 -------------RPLTRGVVIDGKKTKPA--RYNIVKVDHEKNRSVVELTIHEGRNHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KKMFESVG 197


>gi|259503200|ref|ZP_05746102.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           antri DSM 16041]
 gi|259168857|gb|EEW53352.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           antri DSM 16041]
          Length = 238

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 91/253 (35%), Gaps = 54/253 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++ +G V+V+ + V     ++ +   + +  V       
Sbjct: 2   ERLQKAMAEA-GVASRRASEKLIATGHVQVNGQTVTTLGTKVAARDRIEVDGVP------ 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIY-VFNKPAGI--SVQGGSGIAYHIDGFLK 134
                                   L+ +  +Y + NKP G+  S     G    +   L+
Sbjct: 55  ------------------------LHREKHVYYLLNKPRGVISSAHDEKG-RRTVVDILR 89

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
              D   ++     RLD +T+G+L++    A A  L        + K Y + V G+  N 
Sbjct: 90  E--DEIEERIYPVGRLDYDTTGLLLLTNDGALANKL--MHPKFAVDKTYVAKVKGLVSND 145

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                   LK+   G      VK + +    A +  K  D   ++   +++  H G  HQ
Sbjct: 146 D-------LKRLRTG------VKVDGRRTQPAKARLKATDR-EKRTSIVQLTIHEGHYHQ 191

Query: 255 LRVHALHMGCPIV 267
           ++     +G P++
Sbjct: 192 VKRMLAAVGHPVI 204


>gi|242051172|ref|XP_002463330.1| hypothetical protein SORBIDRAFT_02g041930 [Sorghum bicolor]
 gi|241926707|gb|EER99851.1| hypothetical protein SORBIDRAFT_02g041930 [Sorghum bicolor]
          Length = 480

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 39/237 (16%), Positives = 82/237 (34%), Gaps = 34/237 (14%)

Query: 51  KRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYV 110
           +    + R+++G  +R+                           D+   ++   D  + V
Sbjct: 176 RVTDPDQRLEAGTYLRVHVH--------------PKRFPRCYEIDWKSRVIAVADEYV-V 220

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
            +KPA  SV G +           S           TH++D  + G +V+++T+      
Sbjct: 221 LDKPAATSVGGATDNIEESCAVFTSRALGMETPLLTTHQIDNCSEGCVVLSKTKEFCSVF 280

Query: 171 TESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG-------DYVHVVKQNEKGA 223
               R ++++K+Y +L           I +++   +           +  H+ +      
Sbjct: 281 HGLIREKQVKKLYLALTTAPVST--GTITHYMRPVNRAPRLVSEDCIERWHLCQMEVLDC 338

Query: 224 N----YAISHFKVIDCFAQKFCWLE------MQPHTGRTHQLRVHALHMGCPIVGDH 270
                 + S  K+ +     +   E      +   TG+THQ+R     +G PI+GD 
Sbjct: 339 RKVPWPSSSIRKIHNVNGCGWPQQEAAYECKINLLTGKTHQIRAQLAAIGAPIIGDS 395


>gi|324992460|gb|EGC24381.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK405]
 gi|327460692|gb|EGF07027.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1]
 gi|327472413|gb|EGF17844.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK408]
 gi|327488766|gb|EGF20565.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1058]
          Length = 242

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 89/248 (35%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQLLKKGLVLVNGRVEKS----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I +++  +      L     YE    Y+ NKP G+           +   L     
Sbjct: 37  PKTQIDETADEIVVSGQRLT----YEKFVYYLLNKPQGVISATEDDRHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKE 196
            K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+  +  +E
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLMNQTDEE 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQL 255
             A  +  K                    A    K+++   A++   +E+    G+ HQ+
Sbjct: 148 RFAAGIELKDF--------------TCQPA--QLKILELDEAKETSLVEITLAEGKFHQV 191

Query: 256 RVHALHMG 263
           +      G
Sbjct: 192 KRMVAACG 199


>gi|301793545|emb|CBW35921.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus pneumoniae INV104]
          Length = 240

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 88/245 (35%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q  + +         + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQIDEKI---------DEIR 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++L+                 YE+   Y+ NKP G+           +   L     
Sbjct: 50  FDGQVLE-----------------YEEFVYYMMNKPKGVISATEDPKHRTVMDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK  +     RLD +T G+L++      A  L      R + K Y + V GI   +    
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNDGQLAHVL--LSPKRHVDKTYLAQVKGIMTQEDVET 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     AI     ID   +    + +    G+ HQ++  
Sbjct: 149 -------------FAEGIPLKDFTCQPAILELVSIDT-EKNQSQIRVTIAEGKFHQIKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VGYCG 199


>gi|299115628|emb|CBN75829.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 505

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 34/139 (24%), Positives = 52/139 (37%), Gaps = 8/139 (5%)

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV------- 137
           D               +++++    V +KPAG+              F  S         
Sbjct: 159 DPRTFPASQVMDWSKRIVHKNEDFVVVDKPAGVPTVPTIDNGVQNCVFQASLAVAGMPPG 218

Query: 138 -DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             S         RLD  TSGI+V AR + AA+ L E FR RR++K Y +L+   P     
Sbjct: 219 SRSLPPPLHAVSRLDVCTSGIVVFARHKEAAKQLNELFRARRVKKRYLALLTPGPAVPTG 278

Query: 197 CIANWLLKKSHIGGDYVHV 215
            +A+    K+  G     +
Sbjct: 279 SMAHCCRSKAFDGSRRPRI 297



 Score = 49.2 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY----CANFKGNFTSPIQNKLYLHAR 293
                  M+  TGRTHQLR+    MG  IVGD +Y        +G       ++      
Sbjct: 417 HAPHLCAMELETGRTHQLRLQLAAMGSAIVGDTRYRGVVGRVHRGLRVDDDTSRFGQEPE 476

Query: 294 YMDLPHPEGGRLQIT 308
            + L      R++  
Sbjct: 477 AIALQ---AARIEFE 488


>gi|221319479|ref|ZP_03600773.1| RluB [Bacillus subtilis subsp. subtilis str. JH642]
 gi|221323755|ref|ZP_03605049.1| RluB [Bacillus subtilis subsp. subtilis str. SMY]
 gi|255767501|ref|NP_390197.2| pseudouridine synthase [Bacillus subtilis subsp. subtilis str. 168]
 gi|321311788|ref|YP_004204075.1| pseudouridine synthase [Bacillus subtilis BSn5]
 gi|251757325|sp|P35159|RLUB_BACSU RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|225185129|emb|CAB14248.2| pseudouridine synthase [Bacillus subtilis subsp. subtilis str. 168]
 gi|291484745|dbj|BAI85820.1| pseudouridine synthase [Bacillus subtilis subsp. natto BEST195]
 gi|320018062|gb|ADV93048.1| pseudouridine synthase [Bacillus subtilis BSn5]
          Length = 244

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 83/248 (33%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +++++ G+V+V+ K V     ++     + +          
Sbjct: 2   ERLQKVIA-HAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       L    +     LLY         KP G+     +         +  + 
Sbjct: 52  -----------GLKVEREEPVYFLLY---------KPRGVIS---AAQDDKGRKVVTDFF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +  Q+     RLD +TSG+L++      A  L        I K Y + V GIP  +   
Sbjct: 89  KNIPQRIYPIGRLDYDTSGLLLLTNDGEFANKL--MHPKYEIDKTYVAKVKGIPPKE--- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
               LL+K   G           +    A +  K++    +K    +++  H GR  Q+R
Sbjct: 144 ----LLRKLERGIRL--------EEGKTAPAKAKLLSLDKKKQTSIIQLTIHEGRNRQVR 191

Query: 257 VHALHMGC 264
                +G 
Sbjct: 192 RMFEAIGH 199


>gi|50913682|ref|YP_059654.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS10394]
 gi|50902756|gb|AAT86471.1| Ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS10394]
          Length = 248

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 86/247 (34%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +      ++SG VV I          
Sbjct: 9   MRINKYIA-HAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIE--------- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                S +  E+   Y+ NKP G IS          +   L   
Sbjct: 59  --------------------GSPIYNEEKVYYLLNKPRGAISSVSDDKGRKTVLDLL--- 95

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +        I K+Y + V GI   +  
Sbjct: 96  -PQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM--IHPRNEIDKVYLARVKGIATKENL 152

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                L +   I G          K A Y I H +      +    +E+  H GR HQ++
Sbjct: 153 ---RPLTRGIVIDGKK-------TKPARYNIVHVE----ADKNRSIVELTIHEGRNHQVK 198

Query: 257 VHALHMG 263
                +G
Sbjct: 199 KMFESVG 205


>gi|291528900|emb|CBK94486.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           rectale M104/1]
          Length = 240

 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 38/247 (15%), Positives = 87/247 (35%), Gaps = 53/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSG-QVVRIPPVINALNH 76
           +RLD++            ++K++++GQ+ ++     K   ++ +    V +         
Sbjct: 2   IRLDKFLSEMGLG-TRSEVKKLIKTGQIAINGTVAAKPETKVDTDADEVSVN-------- 52

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                  I+ Y+  + Y+FNKP+G      +      D  +   
Sbjct: 53  ---------------------GRIVKYQRYEYYLFNKPSGCVS---ATSDNVHDTVMDYI 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            D+         RLD +T G+L++    A +  L      + + K Y++ + G     + 
Sbjct: 89  TDAVHDDLFPVGRLDIDTEGLLLITNDGALSHEL--LSPSKHVAKTYYARIDG-----EV 141

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + + +  K  I           E+    A    +++   +     +E+    G+ HQ++
Sbjct: 142 TLDDIIRFKEGID-------IGEERPTKPA----ELVIKKSGSVSEIELTITEGKFHQVK 190

Query: 257 VHALHMG 263
                +G
Sbjct: 191 RMFEALG 197


>gi|295398585|ref|ZP_06808617.1| ribosomal large subunit pseudouridine synthase B [Aerococcus
           viridans ATCC 11563]
 gi|294973186|gb|EFG48981.1| ribosomal large subunit pseudouridine synthase B [Aerococcus
           viridans ATCC 11563]
          Length = 240

 Score = 70.0 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 86/250 (34%), Gaps = 52/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +K++ +G+V+V+ + V+    ++ +   + +          
Sbjct: 2   ERLQKVMA-HAGVASRRESEKLIAAGRVKVNGEVVRELGYKVSNNDRIEVD--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                               +  +  E+   YVF KP G+     +         +  + 
Sbjct: 52  --------------------QVPIYKEEPVYYVFYKPIGVIS---AVKDDKDRKVVTDFF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               Q+     RLD  TSG+L++      A  L        I K+Y + V G+   ++  
Sbjct: 89  PGIEQRIYPVGRLDYNTSGLLLLTNDGEFANTL--MHPRYEINKVYVAKVEGVITGEE-- 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
                 +K    G  +        G   A +  K++     K    +E+  H GR  Q+R
Sbjct: 145 ------RKQLERGVEID-------GVKTAPAQAKILSVDKDKKTTIIELVIHEGRNRQVR 191

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 192 KMLEAVGHPV 201


>gi|222153299|ref|YP_002562476.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           uberis 0140J]
 gi|222114112|emb|CAR42564.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus uberis 0140J]
          Length = 239

 Score = 70.0 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 89/247 (36%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ IL+  +V V+ K  +   ++Q      I P  + ++   
Sbjct: 1   MRLDKFLVEAGIG-SRTQVKSILKKKEVFVNGKP-ESQAKLQ------IKPNQDQVS--- 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                            F   +L+YE+   Y+ NKP G+       +   +   L     
Sbjct: 50  -----------------FGGQVLVYEEFLYYLLNKPQGVVSATEDKVHQTVLDLLDDTAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
            K        RLD++T G+L++      A + L+     + + K+Y + V GI   +  E
Sbjct: 93  RKS--VFPVGRLDKDTHGLLLLTNDGELAHRLLS---PKKHVDKVYMARVDGIMTEQDVE 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             A  +    H                  A    + +D   +  C + +    G+ HQ++
Sbjct: 148 AFAKGITLSDHQ--------------CLPAQLQIEEVD-VERTCCKVRITIREGKFHQIK 192

Query: 257 VHALHMG 263
              L  G
Sbjct: 193 RMVLACG 199


>gi|228990582|ref|ZP_04150547.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
 gi|228996683|ref|ZP_04156320.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|229004333|ref|ZP_04162121.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228756916|gb|EEM06173.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228763002|gb|EEM11912.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|228769108|gb|EEM17706.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
          Length = 244

 Score = 70.0 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 87/252 (34%), Gaps = 60/252 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K V     ++     V +          
Sbjct: 4   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKVVTELGTKVTPQDKVEVN--------- 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 54  -----------NIPLEKEEPIYFLLY---------KPTGVISSVSDDKGRK-----VVTD 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + V G      
Sbjct: 89  FFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANIL--MHPKYKVEKTYVAKVKG------ 140

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRT 252
                       + G+ + ++++    +    A +  K++    +K    +++  H GR 
Sbjct: 141 -----------PLTGEKIRMLEKGVVLEDGKTAPARVKILSWDKRKEMAIVQLTIHEGRN 189

Query: 253 HQLRVHALHMGC 264
            Q+R     +GC
Sbjct: 190 RQVRRMFEALGC 201


>gi|323691878|ref|ZP_08106132.1| hypothetical protein HMPREF9475_00994 [Clostridium symbiosum
           WAL-14673]
 gi|323504085|gb|EGB19893.1| hypothetical protein HMPREF9475_00994 [Clostridium symbiosum
           WAL-14673]
          Length = 244

 Score = 70.0 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 84/249 (33%), Gaps = 47/249 (18%)

Query: 17  ENM-RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
             M RLD++            +++ +R G+V VD    + ++     +V  +      ++
Sbjct: 2   AGMIRLDKFLAEMKKG-TRSQVKEAVRKGRVTVDGAVCRSSDFKFDPEVSGVCMDGEPVS 60

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           +   E                            ++ NKP G+     +         +  
Sbjct: 61  YARME---------------------------YFMLNKPQGVVS---ATEDNLHPTVISL 90

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             D+K +      RLD +T G+L++    + A + L+     + + K+Y++ V G  +  
Sbjct: 91  IGDAKRKDLFPVGRLDIDTEGLLLITNDGKLAHELLS---PKKHVDKVYFAKVKGTLRED 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                   + ++  GG  +              S +   +   +  C   +  H G+ HQ
Sbjct: 148 --------IVQAFAGGITLADQTTVLPAELLIESSY---EEAGEPVCEARLTIHEGKFHQ 196

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 197 VKRMFEAAG 205


>gi|293364213|ref|ZP_06610939.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           oralis ATCC 35037]
 gi|306824561|ref|ZP_07457907.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|307702434|ref|ZP_07639390.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           oralis ATCC 35037]
 gi|291317059|gb|EFE57486.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           oralis ATCC 35037]
 gi|304433348|gb|EFM36318.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|307624016|gb|EFO02997.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           oralis ATCC 35037]
          Length = 240

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I++G  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATTIKAGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V G+     
Sbjct: 86  LLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGVANKDN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                 L +   I G               A+  ++++     +    +++  H GR HQ
Sbjct: 144 L---RPLTRGLEIDGKKT----------KPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|262283235|ref|ZP_06061002.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           2_1_36FAA]
 gi|262261487|gb|EEY80186.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           2_1_36FAA]
          Length = 242

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + V+     +++G  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTINGQVVRELATLVKTGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG+L++         +        I K+Y + V GI   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDEM--IHPRNEIDKVYVARVKGIANKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                               V+ + K    A+  +++I     +    +++  H GR HQ
Sbjct: 144 LL-------------PLTRGVEIDGKKTKPAV--YEIIKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFQAVG 197


>gi|172058280|ref|YP_001814740.1| pseudouridine synthase [Exiguobacterium sibiricum 255-15]
 gi|171990801|gb|ACB61723.1| pseudouridine synthase [Exiguobacterium sibiricum 255-15]
          Length = 239

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 84/245 (34%), Gaps = 47/245 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N     +   ++++L+SG ++VD + V                  +   H+ 
Sbjct: 1   MRLDKLLSNMGAG-SRKEVKQLLKSGAIQVDGEIVY-----------------DPKQHVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E           +        + Y+     + NKP G+           +   L  + D
Sbjct: 43  TEN----------QQVLLYGEPVTYQKFIYLMMNKPPGVISATEDKRDQTVIDLL--FDD 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               KP    RLD++T G+L++    +    L      + ++K+Y++ V G    +    
Sbjct: 91  VTYFKPFPVGRLDKDTEGLLLLTNDGSFNHAL--MSPKKHVEKVYYAEVIGTLTEEDV-- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                       + V      E G         +++   +     E+    G+ HQ++  
Sbjct: 147 ------------EEVAEGVTLEDGYKTKPGKLIILEATDETSTL-ELTITEGKFHQVKRM 193

Query: 259 ALHMG 263
            L +G
Sbjct: 194 MLALG 198


>gi|331265750|ref|YP_004325380.1| ribosomal small subunit pseudouridine synthase A, 16S rRNA
           pseudouridylate synthase and related pseudouridylate
           synthases [Streptococcus oralis Uo5]
 gi|326682422|emb|CBZ00039.1| ribosomal small subunit pseudouridine synthase A, 16S rRNA
           pseudouridylate synthase and related pseudouridylate
           synthases [Streptococcus oralis Uo5]
          Length = 240

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V G+     
Sbjct: 86  LLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYIARVKGVANKDN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                 L +   I G               A+  ++++     +    +++  H GR HQ
Sbjct: 144 L---RPLTRGLEIDGKKT----------KPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|227877298|ref|ZP_03995371.1| pseudouridylate synthase [Lactobacillus crispatus JV-V01]
 gi|256842860|ref|ZP_05548348.1| 16S pseudouridylate synthase [Lactobacillus crispatus 125-2-CHN]
 gi|256848766|ref|ZP_05554200.1| 16S pseudouridylate synthase [Lactobacillus crispatus MV-1A-US]
 gi|262045826|ref|ZP_06018790.1| 16S pseudouridylate synthase [Lactobacillus crispatus MV-3A-US]
 gi|293381695|ref|ZP_06627676.1| pseudouridine synthase [Lactobacillus crispatus 214-1]
 gi|312977621|ref|ZP_07789368.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           crispatus CTV-05]
 gi|227863154|gb|EEJ70600.1| pseudouridylate synthase [Lactobacillus crispatus JV-V01]
 gi|256614280|gb|EEU19481.1| 16S pseudouridylate synthase [Lactobacillus crispatus 125-2-CHN]
 gi|256714305|gb|EEU29292.1| 16S pseudouridylate synthase [Lactobacillus crispatus MV-1A-US]
 gi|260573785|gb|EEX30341.1| 16S pseudouridylate synthase [Lactobacillus crispatus MV-3A-US]
 gi|290921742|gb|EFD98763.1| pseudouridine synthase [Lactobacillus crispatus 214-1]
 gi|310895360|gb|EFQ44427.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           crispatus CTV-05]
          Length = 234

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 83/247 (33%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   + ++++ G V V+   VK    +++    V +     A    
Sbjct: 1   MRIDKYLANMNVG-SRKEVHQLIKKGIVAVNDVIVKTPKQQVKESDQVTVNGDAVA---- 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                    Y+    ++ NKP G+           +   L    
Sbjct: 56  -------------------------YQKYHYFLLNKPKGVLSATEDRNQPTVISLLA--P 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             + Q      RLD++T+G+L++         L      + + K+Y + + G        
Sbjct: 89  QDRYQGIVPVGRLDKDTTGLLLLTNDGQLNHEL--LAPGKHVDKVYRAEIAG-------- 138

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
           +AN    K+   G    +   +      A    K++    +      E++   G+ HQ++
Sbjct: 139 VANDATVKTFASG----MTLGDGTKLQPA--ELKILSQDEEHDRSTTEIKICEGKYHQIK 192

Query: 257 VHALHMG 263
                +G
Sbjct: 193 RMFGAVG 199


>gi|139474355|ref|YP_001129071.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes str. Manfredo]
 gi|134272602|emb|CAM30869.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes str. Manfredo]
          Length = 240

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 83/247 (33%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +      ++SG VV I          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                S +  E+   Y+ NKP G IS          +   L   
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGAISSVSDDKGRKTVLDLL--- 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +        I K+Y + V GI   +  
Sbjct: 88  -PQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM--IHPRNEIDKVYLARVKGIATKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                              +  + K    A  +   ++   +    +E+  H GR HQ++
Sbjct: 145 -------------RPLTRGIVIDGKKTKPARYNIVRVEAD-KNRSIVELTIHEGRNHQVK 190

Query: 257 VHALHMG 263
                +G
Sbjct: 191 KMFESVG 197


>gi|323484805|ref|ZP_08090162.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323401911|gb|EGA94252.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 244

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 84/249 (33%), Gaps = 47/249 (18%)

Query: 17  ENM-RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
             M RLD++            +++ +R G+V VD    + ++     +V  +      ++
Sbjct: 2   AGMIRLDKFLAEMKKG-TRSQVKEAVRKGRVTVDGAVCRSSDFKFDPEVSGVCMDGEPVS 60

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           +   E                            ++ NKP G+     +         +  
Sbjct: 61  YARME---------------------------YFMLNKPQGVVS---ATEDNLHPTVISL 90

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             D+K +      RLD +T G+L++    + A + L+     + + K+Y++ V G  +  
Sbjct: 91  IGDAKRKDLFPVGRLDIDTEGLLLITNDGKLAHELLS---PKKHVDKVYFAKVKGTLRED 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                   + ++  GG  +              S +   +   +  C   +  H G+ HQ
Sbjct: 148 --------IVQAFAGGITLADQTTVLPAELLIESSY---EEAGEPVCEARLTIHEGKFHQ 196

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 197 VKRMFEAAG 205


>gi|218132204|ref|ZP_03461008.1| hypothetical protein BACPEC_00061 [Bacteroides pectinophilus ATCC
           43243]
 gi|217992897|gb|EEC58897.1| hypothetical protein BACPEC_00061 [Bacteroides pectinophilus ATCC
           43243]
          Length = 500

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 79/249 (31%), Gaps = 40/249 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
            N+RLD++  +         +++ +R   V V+   V                       
Sbjct: 2   ANIRLDKYLADMQVG-TRSQVKEQIRKKLVSVNGVTVTK--------------------- 39

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILL-YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                   D  V+  +    + S ++ Y   + ++ NKP G+        A  +   +  
Sbjct: 40  -------PDVKVDTDRDKIMVGSDIIGYTQFEYFMLNKPKGVLSAANDPKAQTVVDLI-- 90

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             D+  +      RLD++T G++++      A  L      + + K Y+    GI  +  
Sbjct: 91  -TDNICRDLFPVGRLDKDTEGLMLITNDGELAHKL--LSPRKHVDKSYYVRFEGIIADN- 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             + ++      I  +               I H K             +    G+ HQ+
Sbjct: 147 -TVESFAKG---IDINIAKCADDEVDNNPKEIYHTKPAKLRLMSADEAVITISEGKFHQI 202

Query: 256 RVHALHMGC 264
           +   +  GC
Sbjct: 203 KRMFMAAGC 211


>gi|319790172|ref|YP_004151805.1| pseudouridine synthase [Thermovibrio ammonificans HB-1]
 gi|317114674|gb|ADU97164.1| pseudouridine synthase [Thermovibrio ammonificans HB-1]
          Length = 238

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 42/248 (16%), Positives = 84/248 (33%), Gaps = 49/248 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+             ++++++ G V V+ + VK                 +     +
Sbjct: 1   MRLDKLLAEGGFG-TRSQVKRLIKKGHVEVNGEVVK---------------DPSFQVDPL 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K++  +D      +   +L            V NKPAG  V         +   +     
Sbjct: 45  KDEVTVDGEPVYYEEEYYL------------VLNKPAG-YVTSTKDRQMTVMELVADI-- 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  K     RLD++  G+L++      A  LT      ++ K Y   V G    +    
Sbjct: 90  PRFDKLFPVGRLDKDAEGLLLMTTDGELAHRLT--HPKWKVPKTYVVKVEGRLTEEAVE- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               L++     D+          A  A    +++   +++    E+    G+ HQ++  
Sbjct: 147 ---PLRRGIELKDFK---------AKPA--EVRIL-RSSEEESEAEITITEGKFHQVKRM 191

Query: 259 ALHMGCPI 266
              +G P+
Sbjct: 192 FAAIGHPV 199


>gi|315611769|ref|ZP_07886691.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis ATCC 49296]
 gi|322375935|ref|ZP_08050446.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           C300]
 gi|315316184|gb|EFU64214.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis ATCC 49296]
 gi|321279203|gb|EFX56245.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           C300]
          Length = 240

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 88/249 (35%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V G+   + 
Sbjct: 86  LLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGVANKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                 L +   I G               A+  ++++     +    +++  H GR HQ
Sbjct: 144 L---RPLTRGLEIDGKKT----------KPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|270292060|ref|ZP_06198275.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           M143]
 gi|270279588|gb|EFA25430.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           M143]
          Length = 240

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 87/247 (35%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q                I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQ----------------IN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E+  +           F   +L YE+   Y+ NKP G+           +   L     
Sbjct: 43  EERDEI----------RFDGQVLEYEEFVYYMMNKPQGVISATEDSKHRTVLDLLDDVAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK  +     RLD +T G+L++      A  L      R + K Y + V GI   +    
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNDGQLAHAL--LSPKRHVDKTYLAQVEGIMTQEDVET 148

Query: 199 --ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 LK        + +V  + +                +    + +    G+ HQ++
Sbjct: 149 FAEGIPLKDFTCQPARLELVSVDPE----------------KNQSLVRVTIAEGKFHQVK 192

Query: 257 VHALHMG 263
               + G
Sbjct: 193 RMVAYCG 199


>gi|328944867|gb|EGG39027.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1087]
          Length = 242

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 88/247 (35%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQLLKKGLVLVNGRAEKS----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I +++  +      L     YE    Y+ NKP G+           +   L     
Sbjct: 37  PKTQIDETADEIAVSGQRLT----YEKFVYYLLNKPRGVISATEDDRHQTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+       
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLMNQAD-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLR 256
                +++   G +      Q          H K+++   +K    +E+    G+ HQ++
Sbjct: 146 -----VERFAAGIELKDFTCQPA--------HLKILELDEEKEDSLVEITLAEGKFHQVK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVAACG 199


>gi|145641816|ref|ZP_01797391.1| hypothetical protein CGSHiR3021_01062 [Haemophilus influenzae
           R3021]
 gi|145273438|gb|EDK13309.1| hypothetical protein CGSHiR3021_01062 [Haemophilus influenzae
           22.4-21]
          Length = 128

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283
           N AI+ F+ + C         ++P TG+THQLRV    +G PI+GD  Y  N +      
Sbjct: 23  NPAITRFESVSCEP-NLRLFILKPQTGKTHQLRVAMKSLGSPILGDGLYGKNTEK----- 76

Query: 284 IQNKLYLHARYMDL 297
             ++ YLHA  ++ 
Sbjct: 77  -IDRTYLHATQLEF 89


>gi|13899137|gb|AAG12403.1| Ybc5 [Chlorobaculum tepidum]
          Length = 101

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 17/65 (26%), Positives = 29/65 (44%)

Query: 9   YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
            + V   +  MR+DR+      +     +QK +   +V V+ K VK N RI+S   + I 
Sbjct: 36  TLQVSKVQTPMRIDRYLTQQVENATRNKVQKAIEEQRVLVNGKPVKSNYRIKSCDHIHIT 95

Query: 69  PVINA 73
            +   
Sbjct: 96  FLRPP 100


>gi|290579936|ref|YP_003484328.1| putative pseudouridylate synthase B large subunit [Streptococcus
           mutans NN2025]
 gi|254996835|dbj|BAH87436.1| putative pseudouridylate synthase B large subunit [Streptococcus
           mutans NN2025]
          Length = 240

 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 85/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + V      ++SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTLNGQMVTELATTVKSGDRVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV+   G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVRDDKGRQ-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG+L++         +        I K+Y + V G+     
Sbjct: 86  LLPEVKERIYPVGRLDWDTSGLLILTNDGDFTDKM--LHPRHEIDKVYVARVKGLASKDN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
                 L K   I G      +            ++++     +    +E+  H GR HQ
Sbjct: 144 L---RPLTKGIVIDGKKTQPAR------------YRIVKTDREKNRSVVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|225867942|ref|YP_002743890.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           equi subsp. zooepidemicus]
 gi|225871142|ref|YP_002747089.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           equi subsp. equi 4047]
 gi|225700546|emb|CAW95028.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           equi subsp. equi 4047]
 gi|225701218|emb|CAW98156.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           equi subsp. zooepidemicus]
          Length = 240

 Score = 69.6 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 86/250 (34%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +      ++SG +V +  +       
Sbjct: 1   MRINKYIA-HAGLASRRKAEELIKRGLVTLNGQVITDLATTVKSGDLVEVEGIP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G    ID     
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRQTVID----- 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG+L++         +        I K+Y + V G+   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDKM--IHPRNEIDKVYLARVKGVVTKES 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                               V  + K    A   +++I          +E+  H GR HQ
Sbjct: 144 L-------------RPLTRGVVIDGKKTKPA--RYRIIRVEPDKNRSIVELTIHEGRHHQ 188

Query: 255 LRVHALHMGC 264
           ++     +G 
Sbjct: 189 VKKMFEVVGH 198


>gi|15901702|ref|NP_346306.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae TIGR4]
 gi|15903731|ref|NP_359281.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae R6]
 gi|111657282|ref|ZP_01408047.1| hypothetical protein SpneT_02001499 [Streptococcus pneumoniae
           TIGR4]
 gi|116515785|ref|YP_817104.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae D39]
 gi|148984326|ref|ZP_01817621.1| hypothetical protein CGSSp3BS71_03857 [Streptococcus pneumoniae
           SP3-BS71]
 gi|148989667|ref|ZP_01820999.1| hypothetical protein CGSSp6BS73_00460 [Streptococcus pneumoniae
           SP6-BS73]
 gi|148993332|ref|ZP_01822872.1| hypothetical protein CGSSp9BS68_07037 [Streptococcus pneumoniae
           SP9-BS68]
 gi|148998738|ref|ZP_01826176.1| hypothetical protein CGSSp11BS70_11759 [Streptococcus pneumoniae
           SP11-BS70]
 gi|149003915|ref|ZP_01828729.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP14-BS69]
 gi|149006471|ref|ZP_01830170.1| segregation and condensation protein B [Streptococcus pneumoniae
           SP18-BS74]
 gi|149011261|ref|ZP_01832508.1| segregation and condensation protein B [Streptococcus pneumoniae
           SP19-BS75]
 gi|149024998|ref|ZP_01836378.1| hypothetical protein CGSSp23BS72_10018 [Streptococcus pneumoniae
           SP23-BS72]
 gi|168483406|ref|ZP_02708358.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC1873-00]
 gi|168489848|ref|ZP_02714047.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP195]
 gi|168491811|ref|ZP_02715954.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC0288-04]
 gi|168494210|ref|ZP_02718353.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC3059-06]
 gi|168574937|ref|ZP_02720900.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae MLV-016]
 gi|169833469|ref|YP_001695240.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae Hungary19A-6]
 gi|182684817|ref|YP_001836564.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CGSP14]
 gi|194398119|ref|YP_002038463.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae G54]
 gi|221232609|ref|YP_002511763.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae ATCC 700669]
 gi|225855307|ref|YP_002736819.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae JJA]
 gi|225859636|ref|YP_002741146.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae 70585]
 gi|225861667|ref|YP_002743176.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae Taiwan19F-14]
 gi|237651140|ref|ZP_04525392.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CCRI 1974]
 gi|237820920|ref|ZP_04596765.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CCRI 1974M2]
 gi|270292159|ref|ZP_06198374.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           M143]
 gi|289167211|ref|YP_003445478.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis B6]
 gi|298230346|ref|ZP_06964027.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae str. Canada MDR_19F]
 gi|298254732|ref|ZP_06978318.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae str. Canada MDR_19A]
 gi|298503601|ref|YP_003725541.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|303254617|ref|ZP_07340719.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS455]
 gi|303258820|ref|ZP_07344800.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP-BS293]
 gi|303261983|ref|ZP_07347929.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP14-BS292]
 gi|303263846|ref|ZP_07349768.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS397]
 gi|303265619|ref|ZP_07351518.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS457]
 gi|303269887|ref|ZP_07355630.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS458]
 gi|307068487|ref|YP_003877453.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Streptococcus pneumoniae AP200]
 gi|307128069|ref|YP_003880100.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae 670-6B]
 gi|307705578|ref|ZP_07642430.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK597]
 gi|307707612|ref|ZP_07644093.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis NCTC 12261]
 gi|322377639|ref|ZP_08052129.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           M334]
 gi|14973377|gb|AAK75946.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae TIGR4]
 gi|15459364|gb|AAL00492.1| Ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae R6]
 gi|116076361|gb|ABJ54081.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae D39]
 gi|147755432|gb|EDK62481.1| hypothetical protein CGSSp11BS70_11759 [Streptococcus pneumoniae
           SP11-BS70]
 gi|147758055|gb|EDK65060.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP14-BS69]
 gi|147761769|gb|EDK68732.1| segregation and condensation protein B [Streptococcus pneumoniae
           SP18-BS74]
 gi|147764251|gb|EDK71182.1| segregation and condensation protein B [Streptococcus pneumoniae
           SP19-BS75]
 gi|147923615|gb|EDK74728.1| hypothetical protein CGSSp3BS71_03857 [Streptococcus pneumoniae
           SP3-BS71]
 gi|147924984|gb|EDK76066.1| hypothetical protein CGSSp6BS73_00460 [Streptococcus pneumoniae
           SP6-BS73]
 gi|147928099|gb|EDK79118.1| hypothetical protein CGSSp9BS68_07037 [Streptococcus pneumoniae
           SP9-BS68]
 gi|147929491|gb|EDK80486.1| hypothetical protein CGSSp23BS72_10018 [Streptococcus pneumoniae
           SP23-BS72]
 gi|168995971|gb|ACA36583.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae Hungary19A-6]
 gi|172043185|gb|EDT51231.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC1873-00]
 gi|182630151|gb|ACB91099.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CGSP14]
 gi|183571751|gb|EDT92279.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP195]
 gi|183573862|gb|EDT94390.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC0288-04]
 gi|183575773|gb|EDT96301.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC3059-06]
 gi|183578730|gb|EDT99258.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae MLV-016]
 gi|194357786|gb|ACF56234.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae G54]
 gi|220675071|emb|CAR69649.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae ATCC 700669]
 gi|225720104|gb|ACO15958.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae 70585]
 gi|225723654|gb|ACO19507.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae JJA]
 gi|225728206|gb|ACO24057.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae Taiwan19F-14]
 gi|270279687|gb|EFA25529.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           M143]
 gi|288906776|emb|CBJ21610.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis B6]
 gi|298239196|gb|ADI70327.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|301794836|emb|CBW37292.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae INV104]
 gi|301800653|emb|CBW33297.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae OXC141]
 gi|301802565|emb|CBW35326.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae INV200]
 gi|302598329|gb|EFL65373.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS455]
 gi|302637066|gb|EFL67555.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP14-BS292]
 gi|302640321|gb|EFL70776.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae SP-BS293]
 gi|302640590|gb|EFL70994.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS458]
 gi|302644746|gb|EFL74994.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS457]
 gi|302646884|gb|EFL77109.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae BS397]
 gi|306410024|gb|ADM85451.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Streptococcus pneumoniae AP200]
 gi|306485131|gb|ADM92000.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae 670-6B]
 gi|307616325|gb|EFN95517.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis NCTC 12261]
 gi|307620855|gb|EFN99939.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK597]
 gi|321281404|gb|EFX58414.1| ribosomal large subunit pseudouridine synthase B [Streptococcus sp.
           M334]
 gi|327390035|gb|EGE88380.1| hypothetical protein SPAR5_1727 [Streptococcus pneumoniae GA04375]
 gi|332072212|gb|EGI82697.1| hypothetical protein SPAR148_1785 [Streptococcus pneumoniae
           GA17545]
 gi|332072697|gb|EGI83180.1| hypothetical protein SPAR50_1869 [Streptococcus pneumoniae GA17570]
 gi|332073025|gb|EGI83505.1| hypothetical protein SPAR68_1901 [Streptococcus pneumoniae GA41301]
 gi|332199894|gb|EGJ13969.1| hypothetical protein SPAR69_1806 [Streptococcus pneumoniae GA41317]
 gi|332200429|gb|EGJ14502.1| hypothetical protein SPAR93_1907 [Streptococcus pneumoniae GA47368]
 gi|332201284|gb|EGJ15355.1| hypothetical protein SPAR120_1791 [Streptococcus pneumoniae
           GA47901]
          Length = 240

 Score = 69.6 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V G+     
Sbjct: 86  LLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGVANKDN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                 L +   I G               A+  ++++     +    +++  H GR HQ
Sbjct: 144 L---RPLTRGLEIDGKKT----------KPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|306824439|ref|ZP_07457785.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|304433226|gb|EFM36196.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
          Length = 240

 Score = 69.6 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 86/245 (35%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q                I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQ----------------IN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E+  +           F   +L YE+   Y+ NKP G+           +   L     
Sbjct: 43  EERDEI----------RFDGQVLEYEEFVYYIMNKPKGVISATEDSKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +K  +     RLD +T G+L++      A  L      R + K Y + V GI   +    
Sbjct: 93  TK--EVFPVGRLDIDTHGLLLLTNDGQLAHAL--LSPKRHVDKTYLAQVKGIMSQEDVET 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     A      +D   +    + +    G+ HQ++  
Sbjct: 149 -------------FAKGISLKDFTCQPAKLEILSVDS-GKDESQVRVTIAEGKFHQVKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VSYCG 199


>gi|322489796|emb|CBZ25056.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 1047

 Score = 69.6 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 31/118 (26%), Positives = 49/118 (41%), Gaps = 8/118 (6%)

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI----ANWLLKKSHIGG-DYVHV 215
            RT  A     +   MR++ +   +   G   +  + +    A    +++     D    
Sbjct: 813 GRTPEAVAA--KHEHMRQLTRGGRAASVGALASALQPVSDVGAAPPARETSTARSDTSSR 870

Query: 216 VKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+Q  +    A +  KV+    A     ++    TGRTHQLRVH   +G PIV D KY
Sbjct: 871 VQQYLQTLRSAKTALKVMHYDQATDQTVVKCTLGTGRTHQLRVHLASLGHPIVHDSKY 928


>gi|306834130|ref|ZP_07467250.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           bovis ATCC 700338]
 gi|304423703|gb|EFM26849.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           bovis ATCC 700338]
          Length = 241

 Score = 69.6 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 82/248 (33%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    + +++ G V ++ K V      +++G VV +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEDLIKRGLVTINGKVVTELATTVKAGDVVEVEGTP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G+ S          +   L + 
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRKTVVDLLPNV 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +T+G+L++         +        I K+Y + V G+   +  
Sbjct: 91  T----ERIYPVGRLDWDTTGLLILTNDGDFTDEM--IHPRNEIDKVYLARVKGLATKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQL 255
                              V  + K    A   + +I    +     +E+  H GR HQ+
Sbjct: 145 -------------RPLTRGVVIDGKKTKPA--RYNIIKVDPEKNRSVVELTIHEGRNHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KKMFESVG 197


>gi|325571145|ref|ZP_08146717.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           casseliflavus ATCC 12755]
 gi|325156230|gb|EGC68416.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           casseliflavus ATCC 12755]
          Length = 240

 Score = 69.6 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 88/250 (35%), Gaps = 52/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    + ++  G+VRV+ + +K    ++ S  VV +          
Sbjct: 4   ERLQKVIA-HAGITSRRKAEGLITEGRVRVNGQVIKELGVQVGSKDVVEVD--------- 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  +  E    Y+F KP G+     +         +  + 
Sbjct: 54  --------------------GVPIEQEPHVYYLFYKPRGVIS---AVTDDKKRKVVLDYF 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      +Q L        ++K+Y + V GI   K+  
Sbjct: 91  AEVPERVYPVGRLDYDTSGLLLLTNDGELSQTL--MHPKHEVEKVYVAKVKGIADKKQLL 148

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLR 256
               L K   I            +G   A + F+++      +   +++  H GR HQ++
Sbjct: 149 ---PLTKGIRI------------EGRKTAPARFEILSTDQTAQSSIVQLTIHEGRNHQVK 193

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 194 NMLKAVGLPV 203


>gi|300933182|ref|ZP_07148438.1| putative pseudouridylate synthase [Corynebacterium resistens DSM
           45100]
          Length = 402

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 32/178 (17%), Positives = 67/178 (37%), Gaps = 21/178 (11%)

Query: 26  KNHYPHINFVNLQKILRSGQVRVD-KKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
           ++ +P+ +   + +     +V +D  + V  +  +  G        +N       E+++ 
Sbjct: 40  RHRHPNDDEAAVYQRFLDKEVVLDSGEPVAPDYEVPPG------RFLNFYRRPAPEREVP 93

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
            +              LLYED+ + V +KP+ ++     G         K+ +     + 
Sbjct: 94  GT------------LGLLYEDNDLLVVDKPSFLATLP-RGQHIAQTALTKARIQFGIPEL 140

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
              HRLD+ T G+L+  +           F  R  QK Y ++   IP +    + + L
Sbjct: 141 SPCHRLDRLTRGVLMFTKRPEIRGAYQTLFDRREPQKTYEAIT-DIPNDPPLWLVDLL 197



 Score = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 34/133 (25%), Positives = 53/133 (39%), Gaps = 22/133 (16%)

Query: 199 ANWLLKKS--HIGGDYVHVVKQNEKGANYAISHFK-VIDCFAQKFCW----LEMQPHTGR 251
             W+L+     + G     +  +E  A  AI+  +  +D  +           ++PH+GR
Sbjct: 268 RPWVLRHHMVKVRGRLATYLTGDEPNAETAITGVRAFLDTSSGPAPATRLAWRLEPHSGR 327

Query: 252 THQLRVHALHMGCPIVGDHKYC-------ANFKGNFTSPI-------QNKLYLHARYMDL 297
           THQLRV    +G PIV D  Y            G+  SP           + L A+ +  
Sbjct: 328 THQLRVVMRSLGMPIVNDSLYGFISNDALQRPDGDLPSPAFVEDEDFTRPMGLTAKELSF 387

Query: 298 PHPEGGRL-QITA 309
             P  G+L Q T+
Sbjct: 388 RDPLTGKLRQFTS 400


>gi|257876560|ref|ZP_05656213.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|257810726|gb|EEV39546.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
          Length = 240

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 87/250 (34%), Gaps = 52/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    + ++  G+VRV+ + +K    ++ S  VV +  V       
Sbjct: 4   ERLQKVIA-HAGITSRRKAEGLITEGRVRVNGQVIKELGVQVSSKDVVEVDGVPIEQEQH 62

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +                              Y+F KP G+     +         +  + 
Sbjct: 63  V-----------------------------YYLFYKPRGVIS---AVTDDKKRKVVLDYF 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      +Q L        + K+Y + V GI   K+  
Sbjct: 91  AEVPERVYPVGRLDYDTSGLLLLTNDGELSQTL--MHPKHEVDKVYVAKVKGIADKKQLL 148

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLR 256
               L K   I            +G   A + F+++      +   +++  H GR HQ++
Sbjct: 149 ---PLTKGIRI------------EGRKTAPARFEILSTDQTTQSSIVQLTIHEGRNHQVK 193

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 194 NMLKAVGLPV 203


>gi|125718847|ref|YP_001035980.1| 16S rRNA uridine-516 pseudouridylate synthase [Streptococcus
           sanguinis SK36]
 gi|125498764|gb|ABN45430.1| 16S rRNA uridine-516 pseudouridylate synthase, putative
           [Streptococcus sanguinis SK36]
          Length = 242

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 86/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQLLKKGLVLVNGRAEKS----------------PKTQIDE 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              +I+ S   LT           YE    Y+ NKP G+           +   L     
Sbjct: 44  TADEIIVSGQRLT-----------YEKFVYYLLNKPQGVISATEDDQHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++    + A   L+     + ++K Y + V G+ K     
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKTYRAQVAGLMKQAD-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLR 256
                +++   G +      Q            K+++   A++   +E+    G+ HQ++
Sbjct: 146 -----VERFAAGIELKDFTCQPA--------QLKILELDEAKETSLVEITLAEGKFHQVK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVAACG 199


>gi|24380085|ref|NP_722040.1| putative pseudouridylate synthase B, large subunit [Streptococcus
           mutans UA159]
 gi|24378080|gb|AAN59346.1|AE015000_4 putative pseudouridylate synthase B, large subunit [Streptococcus
           mutans UA159]
          Length = 240

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 85/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + V      ++SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTLNGQMVTELATTVKSGDRVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV+   G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVRDDKGRQ-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG+L++         +        I K+Y + V G+     
Sbjct: 86  LLPEVKERIYPVGRLDWDTSGLLILTNDGDFTDKM--LHPRHEIDKVYVARVKGLASKDN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
                 L K   I G      +            ++++     +    +E+  H GR HQ
Sbjct: 144 L---RPLTKGIVIDGKKTQPAR------------YRIVKTDREKNRSVVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|21909805|ref|NP_664073.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28896502|ref|NP_802852.1| hypothetical protein SPs1590 [Streptococcus pyogenes SSI-1]
 gi|21903991|gb|AAM78876.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28811756|dbj|BAC64685.1| putative hypothetical protein [Streptococcus pyogenes SSI-1]
          Length = 240

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 83/247 (33%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +      ++SG VV I          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                S +  E+   Y+ NKP G IS          +   L   
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGAISSVSDDKGRKTVLDLL--- 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +        I K+Y + V GI   +  
Sbjct: 88  -PQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM--IHPRNEIDKVYLARVKGIATKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                              +  + K    A  +   ++   +    +E+  H GR HQ++
Sbjct: 145 -------------RPLTRGIVIDGKKTKPARYNIVRVEAD-KNRSIVELTIHEGRNHQVK 190

Query: 257 VHALHMG 263
                +G
Sbjct: 191 KMFESVG 197


>gi|304316801|ref|YP_003851946.1| pseudouridine synthase [Thermoanaerobacterium thermosaccharolyticum
           DSM 571]
 gi|302778303|gb|ADL68862.1| pseudouridine synthase [Thermoanaerobacterium thermosaccharolyticum
           DSM 571]
          Length = 235

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 87/250 (34%), Gaps = 53/250 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    ++++  G+++V+   +K          ++I P  + + +  
Sbjct: 2   ERLQKYLAE-CSIASRRKCEQLILDGKIKVNGTVIK-------NLGIKIDPDKDIVEYDG 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
           +    +  ++                     + NKP G I+          +   +K   
Sbjct: 54  RVVAKVQHNI-------------------YIMLNKPTGFITTVKDQFGRPSVLDIIK--- 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
                +     RLD +TSG+L++      A  L        I K+Y + + GIP +K  +
Sbjct: 92  --IKDRIYPVGRLDCDTSGLLLLTNDGDIANKL--MHPKHEIDKVYIAKIRGIPDDKDLD 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              N LL  + +                 A +  +++         +++  H GR  Q+R
Sbjct: 148 RFRNGLLLDNRL----------------TAKAKIEILKKINNDA-LVKIVIHEGRNRQIR 190

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 191 RMCELIGHPV 200


>gi|89099642|ref|ZP_01172516.1| 16S pseudouridylate synthase [Bacillus sp. NRRL B-14911]
 gi|89085585|gb|EAR64712.1| 16S pseudouridylate synthase [Bacillus sp. NRRL B-14911]
          Length = 239

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 94/246 (38%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D+   N   + +   ++K+L+ G V V+ +++K                 +A  H+ 
Sbjct: 1   MRIDKVLAN-LGYGSRKEVKKLLKDGSVTVNDEKIK-----------------DAKQHVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ ++  +    ++ +F+            + NKP G+           +   L++  +
Sbjct: 43  PEKDLIRINGETVEYREFI----------YLMMNKPPGVISATEDNRDETVIDLLEA--E 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +P    RLD++T G+L++      A + L+     + + K Y++++      +   
Sbjct: 91  DLIFEPFPVGRLDKDTEGLLLITNDGQLAHRLLS---PKKHVPKTYFAVIDQEVTEEDVT 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                 +K  I  D             YA    ++    + +   +E+    G+ HQ++ 
Sbjct: 148 ----AFRKGVILDDG------------YATKPGELNILKSGERSDIELTITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|307710771|ref|ZP_07647199.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK321]
 gi|307617377|gb|EFN96549.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK321]
          Length = 240

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V G+     
Sbjct: 86  LLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGVANKDN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                 L +   I G               A+  ++++     +    +++  H GR HQ
Sbjct: 144 L---RPLTRGLDIDGKKT----------KPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|111017942|ref|YP_700914.1| pseudouridylate synthase ribosomal large subunit [Rhodococcus
           jostii RHA1]
 gi|110817472|gb|ABG92756.1| pseudouridylate synthase ribosomal large subunit [Rhodococcus
           jostii RHA1]
          Length = 241

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 79/249 (31%), Gaps = 45/249 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL +         +    ++++  G+V VD + V                 I     I 
Sbjct: 1   MRLQKVLAQA-GVASRRAAEELISQGRVEVDGRIV-----------------IEQGLRID 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  ++            L              NKP G        +     G + S   
Sbjct: 43  PENAVVRVDGVRVVVQKDLVH---------LALNKPRGWQSTMSDDLGRPCVGDIVSERV 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           + GQ+     RLD +T G+L++      A  L        + K Y + V G  +      
Sbjct: 94  AAGQRLFHVGRLDADTEGLLLLTNDGDLAHRL--MHPSFEVSKTYLATVSGALE------ 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                    +G      V+ ++  A   +  F ++D   +    + +  H GR H +R  
Sbjct: 146 -------RGVGKKLKEGVELDDGPAK--VDTFTLLD-INEGKSLVRVTLHEGRKHIVRRL 195

Query: 259 ALHMGCPIV 267
              +G P++
Sbjct: 196 FDAVGHPVI 204


>gi|257870825|ref|ZP_05650478.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257804989|gb|EEV33811.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 241

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 42/248 (16%), Positives = 99/248 (39%), Gaps = 53/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +   + +   +++ ++ G V V+ ++VK +++ Q                 +
Sbjct: 1   MRLDKFLAD-MGYGSRKEVKQAIKKGVVAVNGQQVK-SDKFQ-----------------V 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ+             F   ++ Y+    Y+ NKPAG+     +     +     +  +
Sbjct: 42  AEQE---------DQVSFAGELVRYQKDFYYLLNKPAGVIS-ATTDPEKTVLDLFAA--E 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIP--KNKK 195
              +      RLD++T G+L++      A + L+     + ++K Y++ V GI   +++ 
Sbjct: 90  DYRRDLFPVGRLDKDTEGLLLITNDGQLAHRLLS---PKKHVEKEYYAEVRGIMTEEDRH 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           + +    L    +    + ++K +E+     I+                +  H G+ HQ+
Sbjct: 147 QFLQGIELDGETLMPAQLTILKVDEQAETSTIT----------------LILHEGKFHQV 190

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 191 KRMVQAVG 198


>gi|323703049|ref|ZP_08114704.1| pseudouridine synthase [Desulfotomaculum nigrificans DSM 574]
 gi|323531943|gb|EGB21827.1| pseudouridine synthase [Desulfotomaculum nigrificans DSM 574]
          Length = 238

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 36/251 (14%), Positives = 76/251 (30%), Gaps = 52/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRI-QSGQVVRIPPVINALNH 76
            RL +         +    ++++ +G+V+V+ K V     ++  +   + +       + 
Sbjct: 3   ERLQKVLARA-GIASRRRCEELIVAGKVKVNGKAVTALGTKVDAAKDKIEVNGQPVTASQ 61

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                           ++ NKP G      +         +   
Sbjct: 62  P----------------------------KVYFMLNKPRGYVT---TLHDERGRKTVIDL 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           ++   Q+     RLD ++ G+L++         LT      ++ K Y   V G+P+  K 
Sbjct: 91  LEGIEQRVYPVGRLDYDSEGLLLLTNDGELTNALT--HPKHKVPKTYLVRVEGVPEPAKL 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                                        A +  + +         LE+  H GR  Q+R
Sbjct: 149 ---------------KAMARGLVLADGPTAPAQVR-LAGVRDNRALLEITIHEGRNRQVR 192

Query: 257 VHALHMGCPIV 267
               H+G P++
Sbjct: 193 RMCEHIGHPVL 203


>gi|154686561|ref|YP_001421722.1| RluB [Bacillus amyloliquefaciens FZB42]
 gi|154352412|gb|ABS74491.1| RluB [Bacillus amyloliquefaciens FZB42]
          Length = 244

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 44/251 (17%), Positives = 84/251 (33%), Gaps = 52/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +++++ G+V+V+ K +     ++     + +          
Sbjct: 2   ERLQKVIA-HAGVASRRKAEELIKEGKVKVNGKVITELGVKVTGSDQIEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       L    +     LLY         KP G+     +         +  + 
Sbjct: 52  -----------GLKVEREEPVYFLLY---------KPRGVIS---AADDDKGRKVVTDFF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               Q+     RLD +TSG+L++      A  L        I K Y + V GIP  +   
Sbjct: 89  KEVPQRIYPIGRLDYDTSGLLLLTNDGEFANKL--MHPKYEIDKTYVAKVKGIPSKE--- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
               LL+K   G           +    A +  K++    +K    +++  H GR  Q+R
Sbjct: 144 ----LLRKLERGIQL--------EEGKTAPARAKLLSLDKRKQTSIIQLTIHEGRNRQVR 191

Query: 257 VHALHMGCPIV 267
                +G  ++
Sbjct: 192 RMFEAIGHDVL 202


>gi|325686573|gb|EGD28599.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK72]
          Length = 242

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 86/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQLLKKGLVLVNGRAEKS----------------PKTQIDE 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              +I+ S   LT           YE    Y+ NKP G+           +   L     
Sbjct: 44  TADEIIVSGQRLT-----------YEKFVYYLLNKPQGVISATEDDHHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+       
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLMNQAD-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLR 256
                +++   G +      Q          H K+++   +K    +E+    G+ HQ++
Sbjct: 146 -----VERFAAGIELKDFTCQPA--------HLKILELDEEKEDSLVEITLAEGKFHQVK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVAACG 199


>gi|309799641|ref|ZP_07693863.1| RNA pseudouridine synthase family protein [Streptococcus infantis
           SK1302]
 gi|308116732|gb|EFO54186.1| RNA pseudouridine synthase family protein [Streptococcus infantis
           SK1302]
          Length = 240

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 82/245 (33%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++  L++G+V V+ K+ K + ++Q  +               
Sbjct: 1   MRLDKYLVACAVG-SRTEVKNFLKAGRVMVNGKKEK-SAKLQINEE-------------- 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                       T    F    L YE+   Y+ NKP G+           +   L     
Sbjct: 45  ------------TDEICFDGQKLEYEEFVYYMMNKPQGVISATEDSKHKTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK  +     RLD +T G+L++      A  L      R + K Y + V GI   +    
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNDGQLAHAL--LSPKRHVDKTYLAQVGGIMTQEDVET 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     AI     ID   +    + +    G+ HQ++  
Sbjct: 149 -------------FAQGIPLKDFTCQPAILELVSIDR-EKNQSLVRVTIAEGKFHQVKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VAYCG 199


>gi|307111759|gb|EFN59993.1| hypothetical protein CHLNCDRAFT_56496 [Chlorella variabilis]
          Length = 476

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 44/289 (15%), Positives = 83/289 (28%), Gaps = 73/289 (25%)

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE----DSKIYVFNKPAGISVQGGS 123
            P   A +  +     +   ++  +         L        +  V +KPAG+      
Sbjct: 130 TPQRAAADAEVARHAYIRVHLHPKRFPAAYSVDWLDRLVASTEEYAVVSKPAGVPAAPTV 189

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-------- 175
                      +      Q   +THRLDQ T G+LV+ RT++      E  +        
Sbjct: 190 DNWLECAPACAAQALGLPQPLLITHRLDQCTEGLLVLGRTKSFVARFNELVKRSSNQSSG 249

Query: 176 ------------------------------------------MRRIQKIYWSLVWGIPKN 193
                                                      R ++K Y ++    P  
Sbjct: 250 GGGSSDSAGNSARRRSGGSSSGGEAEEEAQTEGGLGGGTAAAQRPLRKFYRAVTASPPP- 308

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-------------QKF 240
               + + L  +    G     +           +  +V+                 Q+ 
Sbjct: 309 -LGLLRHHLSIERQQQGLPQFTIAHEAPVGGSLPAELRVLQVQPVRLGEQAAGLWGCQEV 367

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLY 289
               ++  TGRTHQ+R      GCP++GD  Y    +   +  ++ +L+
Sbjct: 368 FECTVELLTGRTHQIRAQLSAAGCPLLGDSLY----QPLASPELRQRLF 412


>gi|294501116|ref|YP_003564816.1| pseudouridine synthase [Bacillus megaterium QM B1551]
 gi|295706463|ref|YP_003599538.1| pseudouridine synthase [Bacillus megaterium DSM 319]
 gi|294351053|gb|ADE71382.1| pseudouridine synthase [Bacillus megaterium QM B1551]
 gi|294804122|gb|ADF41188.1| pseudouridine synthase [Bacillus megaterium DSM 319]
          Length = 241

 Score = 69.2 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 37/253 (14%), Positives = 86/253 (33%), Gaps = 56/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++  G+V+V+ K V+    ++     + +          
Sbjct: 2   ERLQKVIA-HAGVASRRKAEELIGQGRVKVNGKVVRELGTKVGPNDKIEVD--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       +   S+     +LY         KP G+     +         +  + 
Sbjct: 52  -----------EVPVESEAPVYFMLY---------KPRGVIS---AANDDKGRKTVVDFF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  L        + K+Y + + GIP      
Sbjct: 89  PHVEERIYPIGRLDYDTSGLLLLTNDGEFANQL--MHPKFEVDKVYVAKIKGIP------ 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQ 254
                        + +  +++    +    A +  KV+    +++   +E+  H G+  Q
Sbjct: 141 -----------SREKIRQLQRGVMLEDGKTAPARAKVLSIDKSKQTAIVELTIHEGKNRQ 189

Query: 255 LRVHALHMGCPIV 267
           +R     +G  ++
Sbjct: 190 VRRMFDAIGHSVL 202


>gi|325295032|ref|YP_004281546.1| pseudouridine synthase Rsu [Desulfurobacterium thermolithotrophum
           DSM 11699]
 gi|325065480|gb|ADY73487.1| pseudouridine synthase Rsu [Desulfurobacterium thermolithotrophum
           DSM 11699]
          Length = 238

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 41/252 (16%), Positives = 83/252 (32%), Gaps = 57/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   +         ++++++ G V V+ + +K                        
Sbjct: 1   MRLDKLLADSGFG-TRSQVKRLIKKGFVTVNGETIK------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 D S N+    D +      + YE     + +KP G                ++ 
Sbjct: 36  ------DPSFNVDPQKDEVLVDGELVEYEKDYYLILHKPQGYIT----STKDRQMTVMEL 85

Query: 136 WVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             D  + ++     RLD++  G+L++      A  LT      ++ K+Y+ +V G    +
Sbjct: 86  IADIPRFERLFPVGRLDKDAEGLLLITNDGELAHRLT--HPKWKVPKVYFVVVEGKLNEE 143

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                   LKK     D+          A  A    +++     +          G+ HQ
Sbjct: 144 NLE----PLKKGIELKDFR---------AKPA--KVRILKAEESESEAEIEITE-GKYHQ 187

Query: 255 LRVHALHMGCPI 266
           ++     +G P+
Sbjct: 188 VKRMFEKIGHPV 199


>gi|168487318|ref|ZP_02711826.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC1087-00]
 gi|183569796|gb|EDT90324.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae CDC1087-00]
          Length = 240

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V G+     
Sbjct: 86  LLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGVANKDN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                 L +   I G               A+  ++++     +    +++  H GR HQ
Sbjct: 144 L---RPLTRGLEIDGKKT----------KPAV--YEILKVDPVKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|325687113|gb|EGD29136.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK72]
          Length = 242

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++R G+V ++ + V+     ++SG  V +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDCVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVVE 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++         +        I K+Y + V G+   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM--IHPRNEIDKVYVARVKGLANKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
             +   L +   I G               A+  +++I    A+    +++  H GR HQ
Sbjct: 143 --VLRPLTRGIEIEGRKT----------KPAV--YEIIKVDPAKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFQAVG 197


>gi|164688313|ref|ZP_02212341.1| hypothetical protein CLOBAR_01958 [Clostridium bartlettii DSM
           16795]
 gi|164602726|gb|EDQ96191.1| hypothetical protein CLOBAR_01958 [Clostridium bartlettii DSM
           16795]
          Length = 237

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 84/251 (33%), Gaps = 50/251 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALNHI 77
           MR++++        +    ++++ +G+V V+ +   + + ++                  
Sbjct: 1   MRINKYIA-LCGVASRRKAEELILAGRVTVNDEVMTELSYKV------------------ 41

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +E  I+     L K  + L  ILL +        K                   +   V
Sbjct: 42  DEENDIVKVDDKLIKEENKLVYILLNKPEGYITTVKDQF------------DRPSVLDLV 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD ETSG+L++         LT       + K Y + V G    ++  
Sbjct: 90  SDIKERVYPIGRLDYETSGLLLLTNDGDLTYKLT--HPKHEVDKTYVARVKGKLTKEE-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
                +++   G           K         KVI    Q+    LE++ H G+  Q+R
Sbjct: 146 -----IERFKTGLKIEDYTTAPAK--------LKVIKYDEQRDSSLLEIKIHEGKNRQVR 192

Query: 257 VHALHMGCPIV 267
                +  P++
Sbjct: 193 KMCKAINHPVL 203


>gi|153814849|ref|ZP_01967517.1| hypothetical protein RUMTOR_01064 [Ruminococcus torques ATCC 27756]
 gi|317500363|ref|ZP_07958587.1| hypothetical protein HMPREF1026_00530 [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|331089629|ref|ZP_08338528.1| hypothetical protein HMPREF1025_02111 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145847880|gb|EDK24798.1| hypothetical protein RUMTOR_01064 [Ruminococcus torques ATCC 27756]
 gi|316898118|gb|EFV20165.1| hypothetical protein HMPREF1026_00530 [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|330404997|gb|EGG84535.1| hypothetical protein HMPREF1025_02111 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 261

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 44/259 (16%), Positives = 90/259 (34%), Gaps = 51/259 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++            ++K +  G V V+ +  K                        
Sbjct: 3   LRLDKYLTEMGCG-TRSQVKKEILKGSVSVNGEIAKK----------------------- 38

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+K+      +    +     + Y   + ++ NKPAG+           +   +K   +
Sbjct: 39  AERKVDTEKDEIIFKGE----KIFYAGYEYFMLNKPAGVVSATEDKKERTVIDLIK---E 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           SK +      RLD++T G+L++      A + L+     + + KIY++ + GI   +   
Sbjct: 92  SKRKDLFPAGRLDKDTEGLLLITNDGQLAHRLLS---PKKHVDKIYYAKIKGIVTEED-- 146

Query: 198 IANWLLKKSHIGGDYVHVV------KQNEKGANYAISHFKVI-------DCFAQKFCWLE 244
                 K  HIG +   +          ++     I   K++       D     +  + 
Sbjct: 147 -VRLFEKGVHIGDEKPTMPAALEILSVQKERRKEKIKEQKILPETKNETDEKEDGYSEIY 205

Query: 245 MQPHTGRTHQLRVHALHMG 263
           +    GR HQ++     +G
Sbjct: 206 LTIKEGRFHQVKRMFRAVG 224


>gi|296332250|ref|ZP_06874712.1| pseudouridine synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305674952|ref|YP_003866624.1| pseudouridine synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
 gi|296150564|gb|EFG91451.1| pseudouridine synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305413196|gb|ADM38315.1| pseudouridine synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
          Length = 244

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 82/248 (33%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +++++ G+V+V+ K V     ++     + +          
Sbjct: 2   ERLQKVIA-HAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       L    +     LLY         KP G+     +         +  + 
Sbjct: 52  -----------GLKVEREEPVYFLLY---------KPRGVIS---AAQDDKGRKVVTDFF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               Q+     RLD +TSG+L++      A  L        I K Y + V GIP  +   
Sbjct: 89  KEVPQRIYPIGRLDYDTSGLLLLTNDGEFANKL--MHPKYEIDKTYVAKVKGIPPKE--- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
               LL+K   G           +    A +  K++    +K    +++  H GR  Q+R
Sbjct: 144 ----LLRKLERGIRL--------EEGKTAPAKAKLLSLDKKKQTSIIQLTIHEGRNRQVR 191

Query: 257 VHALHMGC 264
                +G 
Sbjct: 192 RMFEAIGH 199


>gi|25011682|ref|NP_736077.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae NEM316]
 gi|24413222|emb|CAD47301.1| Unknown [Streptococcus agalactiae NEM316]
          Length = 240

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + V     ++++G +V I          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIKQGMVTINGQVVNELATKVKAGDLVEIE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                S +  E+   Y+ NKP G+  SV    G    ID     
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDDKGRKTVID----- 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +T+G+L++         +        I K+Y + + GI   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTTGLLILTNDGDFTDKM--IHPRNEIDKVYLARIKGIATKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
                               V  + K    A   + +I     +    +E+  H GR HQ
Sbjct: 144 L-------------RPLTRGVVIDGKKTKPA--RYNIIKVDHEKNRSVVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEQVG 197


>gi|93569001|gb|ABF13466.1| putative pseudouridine synthase [Arcanobacterium pyogenes]
          Length = 186

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 30/171 (17%), Positives = 55/171 (32%), Gaps = 29/171 (16%)

Query: 163 TRAAAQHLTESFRMRRIQKIYWSL------------VWGIPKNKKECIANWLLKKSHIGG 210
                    + F  R++ KIY ++            + G+ K +   +  W+     +  
Sbjct: 1   DPRWRGPYQDMFAARKVTKIYEAVARCVDLGALAGNLPGVAKAEAGHLGEWVRVDLRLAR 60

Query: 211 DYVHVVKQNEKGANYAISHFKVID-----------------CFAQKFCWLEMQPHTGRTH 253
           +   +     +G   A+++ + +                           E++P TGR H
Sbjct: 61  EPGAIAVHVAEGEPNAVTYIRKVRQLRATPELVPAAADGEATAPPALALYELRPITGRLH 120

Query: 254 QLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           QLR    ++G PI GD  Y        T+       L A  +    P  G 
Sbjct: 121 QLRATLNYLGAPIAGDPLYPKVLSLEDTAARSFPTQLLAAQLSFVDPVDGE 171


>gi|328709568|ref|XP_003244000.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Acyrthosiphon pisum]
          Length = 127

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 8/79 (10%)

Query: 222 GANYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
           G   A +   V++     +     + +Q  TGR HQ+RVH   +G  IVGD+ Y      
Sbjct: 11  GPRDAHTRLVVLERGVFMSYPATKVLLQLITGRRHQIRVHCSTIGHTIVGDYTYSGR--- 67

Query: 279 NFTSPIQNKLYLHARYMDL 297
                  ++ +LH+  ++L
Sbjct: 68  --KDISPSRTFLHSYRLEL 84


>gi|306827950|ref|ZP_07461217.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes ATCC 10782]
 gi|304429869|gb|EFM32911.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes ATCC 10782]
          Length = 240

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 83/247 (33%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +      ++ G VV I          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIKQGLVTLNGQVITDLATTVKLGDVVEIE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                S +  E+   Y+ NKP G IS          +   L   
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGAISSVSDDKGRKTVLDLL--- 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +T       I K+Y + V GI   +  
Sbjct: 88  -PQVKERIYPVGRLDWDTSGVLILTNDGDFTDTMT--HPRNEIDKVYLARVKGIATKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                              +  + K    A  +   ++   +    +E+  H GR HQ++
Sbjct: 145 -------------RPLTRGIVIDGKKTKPARYNIVRVEAD-KNRSIVELTIHEGRNHQVK 190

Query: 257 VHALHMG 263
                +G
Sbjct: 191 KMFESVG 197


>gi|257867652|ref|ZP_05647305.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257873981|ref|ZP_05653634.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257801735|gb|EEV30638.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257808145|gb|EEV36967.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
          Length = 240

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 87/250 (34%), Gaps = 52/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    + ++  G+VRV+ + +K    ++ S  VV +  V       
Sbjct: 4   ERLQKVIA-HAGITSRRKAEGLITEGRVRVNGQVIKELGVQVSSKDVVEVDGVPIEQEQH 62

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +                              Y+F KP G+     +         +  + 
Sbjct: 63  V-----------------------------YYLFYKPRGVIS---AVTDDKKRKVVLDYF 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      +Q L        + K+Y + V GI   K+  
Sbjct: 91  AEVPERVYPVGRLDYDTSGLLLLTNDGELSQTL--MHPKHEVDKVYVAKVKGIADKKQLL 148

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLR 256
               L K   I            +G   A + F+++      +   +++  H GR HQ++
Sbjct: 149 ---PLTKGIRI------------EGRKTAPARFEILSTDQTAQSSIVQLTIHEGRNHQVK 193

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 194 NMLKAVGLPV 203


>gi|284991416|ref|YP_003409970.1| pseudouridine synthase [Geodermatophilus obscurus DSM 43160]
 gi|284064661|gb|ADB75599.1| pseudouridine synthase [Geodermatophilus obscurus DSM 43160]
          Length = 280

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 47/257 (18%), Positives = 82/257 (31%), Gaps = 52/257 (20%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
            +   E  RL +         +   ++ ++  G++ V+ K V         Q +R+ P  
Sbjct: 36  TDASAEGERLQKVLARAGVG-SRRVVENMVDQGRISVNGKTVAV-------QGMRVDPER 87

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
           +                   K +     I L +D   Y  NKP G+     +        
Sbjct: 88  D-------------------KIAVDGVRIELRDDRVTYALNKPPGVIT---AMSDDRNRP 125

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +   V           RLDQ+T G+L+V      A  L        ++K Y + V G  
Sbjct: 126 TVGDMVGDLAPGLVHVGRLDQDTEGLLLVTNDGELAHRLA--HPSYEVKKTYLAQVSGSV 183

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHT 249
                              D    ++   +       +  F+V+D  A     +E+  H 
Sbjct: 184 P-----------------RDMARRLRSGVELEDGPVKVDSFRVVDTHA-GQSVVEVVLHE 225

Query: 250 GRTHQLRVHALHMGCPI 266
           GR H +R     +G P+
Sbjct: 226 GRKHIVRRLLASVGLPV 242


>gi|324996011|gb|EGC27922.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK678]
          Length = 242

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 88/247 (35%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   +++IL+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQILKKGLVLVNGRAEKS----------------PKTQIDE 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  +I+ S   LT           YE    Y+ NKP G+           +   L     
Sbjct: 44  RADEIVVSGQRLT-----------YEKFVYYLLNKPQGVISATEDDRHQTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+ +     
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLMEQAD-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLR 256
                +++   G +      Q            K+++   A++   +E+    G+ HQ++
Sbjct: 146 -----VERFAAGIELKDFTCQPA--------QLKILELDEAKETSLVEITLAEGKFHQVK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVAACG 199


>gi|323489657|ref|ZP_08094884.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
 gi|323396788|gb|EGA89607.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
          Length = 243

 Score = 69.2 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 87/251 (34%), Gaps = 54/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++  G+VRV+ K +K    ++ +   + +         +
Sbjct: 2   ERLQKVLA-HAGVASRRKSEQLILDGKVRVNGKTIKELGVKVSNSDKIEV-----EGVQL 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            KEQK+                         ++  KP G+     +         +  + 
Sbjct: 56  EKEQKV------------------------YHLLYKPRGVIS---AVSDDKNRKVVTDFF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--K 195
           +   ++     RLD +TSG+L++      A  LT       I K Y + + GIP+    +
Sbjct: 89  EGIEKRIYPVGRLDYDTSGLLIMTNDGEFANMLT--HPKFEIDKTYVARLKGIPEKDDLR 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           +      L+        V ++  ++K     +                ++  H GR  Q+
Sbjct: 147 KLERGIKLEDGMTAPAKVKLLSGDKKTGKAIV----------------QITIHEGRNRQV 190

Query: 256 RVHALHMGCPI 266
           R     +G P+
Sbjct: 191 RRMFEAIGYPV 201


>gi|15674518|ref|NP_268692.1| hypothetical protein SPy_0369 [Streptococcus pyogenes M1 GAS]
 gi|13621621|gb|AAK33413.1| putative hypothetical protein [Streptococcus pyogenes M1 GAS]
          Length = 240

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 84/248 (33%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +      ++SG VV I          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                S +  E+   Y+ NKP G IS          +   L   
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGAISSVSDDKGRKTVLDLL--- 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +        I K+Y + V GI   +  
Sbjct: 88  -PQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM--IHPRNEIDKVYLARVKGIATKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQL 255
                              +  + K    A   + ++   A K    +E+  H GR HQ+
Sbjct: 145 -------------RPLTRGIVIDGKKTKPA--RYNIVRVEADKSRSIVELTIHEGRNHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KKMFESVG 197


>gi|52143877|ref|YP_082953.1| pseudouridylate synthase [Bacillus cereus E33L]
 gi|51977346|gb|AAU18896.1| pseudouridylate synthase [Bacillus cereus E33L]
          Length = 242

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/255 (17%), Positives = 89/255 (34%), Gaps = 60/255 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVAPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----SVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + + G      
Sbjct: 87  FFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANVL--MHPRYKVEKTYVAKIKG------ 138

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRT 252
                       + G+ + ++++    +    A +  K+I    +K    +++  H GR 
Sbjct: 139 -----------PLTGEKIRMLERGVMLEDGKTAPARVKIISWDKRKEMAIVQLTIHEGRN 187

Query: 253 HQLRVHALHMGCPIV 267
            Q+R     + C +V
Sbjct: 188 RQVRRMFEALDCKVV 202


>gi|291524779|emb|CBK90366.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           rectale DSM 17629]
          Length = 240

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/247 (15%), Positives = 86/247 (34%), Gaps = 53/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSG-QVVRIPPVINALNH 76
           +RLD++            ++K++++GQ+ ++     K   ++ +    V +         
Sbjct: 2   IRLDKFLSEMGLG-TRSEVKKLIKTGQIAINGTVAAKPETKVDTDADEVSVN-------- 52

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                  I+ Y+  + Y+FNKP+G      +      D  +   
Sbjct: 53  ---------------------GRIVKYQRYEYYLFNKPSGCVS---ATSDNVHDTVMDYI 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            D+         RLD +T G+L++    A +  L      + + K Y++ + G     + 
Sbjct: 89  TDAVHDDLFPVGRLDIDTEGLLLITNDGALSHEL--LSPSKHVAKTYYARIDG-----EV 141

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              + +  K  I           E+    A    +++   +     +E+    G+ HQ++
Sbjct: 142 TWDDIIRFKEGID-------IGEERPTKPA----ELVIKKSGSVSEIELTITEGKFHQVK 190

Query: 257 VHALHMG 263
                +G
Sbjct: 191 RMFEALG 197


>gi|19745526|ref|NP_606662.1| hypothetical protein spyM18_0418 [Streptococcus pyogenes MGAS8232]
 gi|71902965|ref|YP_279768.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS6180]
 gi|94987940|ref|YP_596041.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS9429]
 gi|94989814|ref|YP_597914.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS10270]
 gi|94993700|ref|YP_601798.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS10750]
 gi|19747645|gb|AAL97161.1| putative hypothetical protein [Streptococcus pyogenes MGAS8232]
 gi|71802060|gb|AAX71413.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS6180]
 gi|94541448|gb|ABF31497.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS9429]
 gi|94543322|gb|ABF33370.1| Ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS10270]
 gi|94547208|gb|ABF37254.1| Ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS10750]
          Length = 248

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 83/247 (33%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +      ++SG VV I          
Sbjct: 9   MRINKYIA-HAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIE--------- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                S +  E+   Y+ NKP G IS          +   L   
Sbjct: 59  --------------------GSPIYNEEKVYYLLNKPRGAISSVSDDKGRKTVLDLL--- 95

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +        I K+Y + V GI   +  
Sbjct: 96  -PQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM--IHPRNEIDKVYLARVKGIATKENL 152

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                              +  + K    A  +   ++   +    +E+  H GR HQ++
Sbjct: 153 -------------RPLTRGIVIDGKKTKPARYNIVRVEAD-KNRSIVELTIHEGRNHQVK 198

Query: 257 VHALHMG 263
                +G
Sbjct: 199 KMFESVG 205


>gi|315222342|ref|ZP_07864248.1| conserved hypothetical protein [Streptococcus anginosus F0211]
 gi|315188675|gb|EFU22384.1| conserved hypothetical protein [Streptococcus anginosus F0211]
          Length = 246

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 47/246 (19%), Positives = 95/246 (38%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++++L+  QV V+ K ++ + +IQ                I 
Sbjct: 5   MRLDKFLVEMGLG-SRTEVKRLLKKKQVLVNGK-IETSAKIQ----------------ID 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + Q  +  +            +L+YE    Y+ NKP G+           +   L    +
Sbjct: 47  ENQDEISVN----------NQVLIYERFVYYLLNKPKGVISATEDDKHRTVLDLLNE--N 94

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           ++ ++     RLD +T G+L++    A A   L+     + + K+Y + V GI   K   
Sbjct: 95  ARQKEVFPVGRLDIDTHGLLLLTNNGALAHAMLS---PKKHVAKVYRAKVDGIITEKD-- 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++    G +      Q  K     ++  +V +   Q+   +E+    G+ HQ++ 
Sbjct: 150 -----VEHFEAGIELKDFTCQPAK-----LTILEVNE--EQQTSLVEIIISEGKFHQVKR 197

Query: 258 HALHMG 263
                G
Sbjct: 198 MVQACG 203


>gi|295115167|emb|CBL36014.1| hypothetical protein [butyrate-producing bacterium SM4/1]
          Length = 65

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 5/66 (7%)

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVK 317
              +G P++GD  Y  +     +        LHA  + + HP  G  ++ +APLP +  +
Sbjct: 1   MASIGHPLLGDSVYGPSK----SPFKLQGQTLHAGVLGIVHPRTGNYMEFSAPLPEYFSE 56

Query: 318 TWDSLG 323
             D L 
Sbjct: 57  LLDKLR 62


>gi|332358327|gb|EGJ36153.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK355]
          Length = 242

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++R G+V ++ + V+     ++SG  V I          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEIEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVVE 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++         +        I K+Y + V G+   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM--IHPRNEIDKVYVARVKGLANKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
             +   L +   I G               A+  +++I    A+    +++  H GR HQ
Sbjct: 143 --VLRPLTRGIEIEGRKT----------KPAV--YEIIKVDPAKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFQAVG 197


>gi|330948563|gb|EGH48823.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. pisi str. 1704B]
          Length = 75

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/76 (39%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           NKPAGI+V GGSG+++ +    +  +    ++  L HRLD++TSG+L++A+ R+  +HL 
Sbjct: 1   NKPAGIAVHGGSGLSFGVIEAFRQ-LRPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLH 59

Query: 172 ESFRMRRIQKIYWSLV 187
           E+ R   + K Y +LV
Sbjct: 60  EALRGDGVDKRYMALV 75


>gi|188590260|ref|YP_001922453.1| RNA pseudouridine synthase family protein [Clostridium botulinum E3
           str. Alaska E43]
 gi|188500541|gb|ACD53677.1| RNA pseudouridine synthase family protein [Clostridium botulinum E3
           str. Alaska E43]
          Length = 254

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/253 (13%), Positives = 82/253 (32%), Gaps = 37/253 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQK-ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       I    + +  ++ G V+V+ K +                        
Sbjct: 1   MRLDKFLAE--SAIGRRKIVRTYIKDGMVKVNGKIIT----------------------- 35

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
              +  LD +  L    ++L   +++     Y+FNKPAG           ++   +  + 
Sbjct: 36  ---EPSLDINEKLD-DVEYLGKKVIHNGKVYYMFNKPAGCVT----ATRDNVHKTVFDYF 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                      RLD++T G+L++         +    +       +W+L     ++KK+ 
Sbjct: 88  HEDMNGVFHVGRLDKDTEGLLLLTNDGEFEHKVMYPEKHVEKTYFFWALGSFDDEDKKQL 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL---EMQPHTGRTHQ 254
                +  +        +                + +   +    +    +    G+ HQ
Sbjct: 148 EEGIFIGNNESLTKPAKIDVHKSGLYKEFKEEIPIKNLENKDHQLVVSGYLTISEGQKHQ 207

Query: 255 LRVHALHMGCPIV 267
           ++     +GC ++
Sbjct: 208 VKRMLKAVGCYVI 220


>gi|23003940|ref|ZP_00047527.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 114

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 29/101 (28%), Positives = 43/101 (42%), Gaps = 2/101 (1%)

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +S I      +  +   G   A S   V++   A+      ++PH+GRTHQLR+H   +G
Sbjct: 2   RSRIVKRRGVMRAEEVDGEPNAESRVDVVETDPARGLARYRLEPHSGRTHQLRLHMARLG 61

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
            PIV D+ Y               L L +R +    P  GR
Sbjct: 62  VPIVHDNFY-PEPYDVSPEDYSRPLQLVSRSLAFTDPFTGR 101


>gi|291613735|ref|YP_003523892.1| RNA-binding S4 domain protein [Sideroxydans lithotrophicus ES-1]
 gi|291583847|gb|ADE11505.1| RNA-binding S4 domain protein [Sideroxydans lithotrophicus ES-1]
          Length = 280

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 37/256 (14%), Positives = 75/256 (29%), Gaps = 47/256 (18%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           E  +   RL +         +   +++ + +G+V V+        R+  G  V++     
Sbjct: 6   ETSQPGERLQKVLAQAGIG-SRREMEEWISAGRVTVNGTVATLGMRVAEGDKVQVDGRNV 64

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
            L               L       + +L ++     V     G                
Sbjct: 65  RLQ--------------LQTEQTMPRILLYHKQEGEIVSRDDPG-----------ERASV 99

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
             +    +GQK     RLD  TSG+L+   +   A  L        +++ Y   V G   
Sbjct: 100 FDALPKLRGQKWIAIGRLDFNTSGLLIFTTSGELANRL--MHPRFEVEREYAVRVQGQMT 157

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI--DCFAQKFCWLEMQPHTG 250
                             +++  V +     +  +  F+ +  +       W  +    G
Sbjct: 158 P-----------------EHMRQVTKEGIELDDGVVRFEQLSDEGGEGFNHWYRLVLKEG 200

Query: 251 RTHQLRVHALHMGCPI 266
           R   +R     +G P+
Sbjct: 201 RNRVVRRTFEALGLPV 216


>gi|229084572|ref|ZP_04216842.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
 gi|228698722|gb|EEL51437.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
          Length = 242

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 87/252 (34%), Gaps = 60/252 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K V     ++     V +          
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKVVTELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPIYFLLY---------KPTGVISSVSDDKGRK-----VVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + V G      
Sbjct: 87  FFPEIRQRLFPIGRLDYDTSGVLLMTNDGDFANIL--MHPKYKVEKTYVAKVKG------ 138

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRT 252
                       + G+ + ++++    +    A +  K+I    +K    +++  H GR 
Sbjct: 139 -----------PLTGEKIRMLEKGVVLEDGKTAPARVKIISWDKRKEMAIVQLTIHEGRN 187

Query: 253 HQLRVHALHMGC 264
            Q+R     +GC
Sbjct: 188 RQVRRMFEALGC 199


>gi|255281792|ref|ZP_05346347.1| ribosomal small subunit pseudouridine synthase A [Bryantella
           formatexigens DSM 14469]
 gi|255267859|gb|EET61064.1| ribosomal small subunit pseudouridine synthase A [Bryantella
           formatexigens DSM 14469]
          Length = 250

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 39/282 (13%), Positives = 90/282 (31%), Gaps = 57/282 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINAL 74
           E +RLD+             ++  +R G+V V+    K  ++++ +   V+ +       
Sbjct: 2   ETIRLDKLLAATGAG-TRSEVKNAIRKGRVTVNGAVCKSADSKVDADKDVICLD------ 54

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                   + ++Y   + ++  KPAG      +         + 
Sbjct: 55  -----------------------GAPVVYTRYEYHMLYKPAGCVT---AVRDARYPTVMD 88

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               ++ +      RLD +T G+L++      A  L        + K Y++ V G    +
Sbjct: 89  YISSARKKDLFPVGRLDLDTEGLLLITNDGELAHRLLAPGWH--VDKTYYARVQGEVTAE 146

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                           D     +  + G        ++    A +   + +  H G+ HQ
Sbjct: 147 ----------------DIRRFQEGIDIGEKRPTMPAELEILAAGQESEVRVTIHEGKYHQ 190

Query: 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMD 296
           ++     +G P++    Y    +    +  +N     +R + 
Sbjct: 191 VKRMFAAIGKPVL----YLKRLRMGSLTLDENLQAGGSRLLT 228


>gi|313814271|gb|EFS51985.1| RNA pseudouridine synthase [Propionibacterium acnes HL025PA1]
          Length = 230

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 32/158 (20%), Positives = 58/158 (36%), Gaps = 4/158 (2%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            T+        +LY D +I V +KP  +S     G        ++        +  + HR
Sbjct: 53  PTETPVPAGIGILYSDERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHR 111

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIY--WSLVWGIPKNKKEC-IANWLLKKS 206
           LD+ T+G+L++ R R   +   E F  R + K Y   + V   P  +      +    +S
Sbjct: 112 LDRVTAGVLLLTRERKWRRPYQEIFERREVVKRYRLVAPVVHNPAGEGVTATKSGWQVRS 171

Query: 207 HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244
            I  +   +  +   G   A++   +I       C   
Sbjct: 172 RIIKERGILQAREVPGVPNAVTDIALIGEHGGGGCTRR 209


>gi|225857461|ref|YP_002738972.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae P1031]
 gi|225725990|gb|ACO21842.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pneumoniae P1031]
          Length = 240

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V G+     
Sbjct: 86  LLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGVANKDN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                 L +   I G               A+  ++++     +    +++  H GR HQ
Sbjct: 144 L---RPLTRGLEIDGKKT----------KPAV--YEILKVDPVKNRSVVQLIIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|224826317|ref|ZP_03699419.1| RNA-binding S4 domain protein [Lutiella nitroferrum 2002]
 gi|224601418|gb|EEG07599.1| RNA-binding S4 domain protein [Lutiella nitroferrum 2002]
          Length = 497

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 82/251 (32%), Gaps = 35/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +RL +         +   +++ + +G + V+ K+    +R+     V        L  
Sbjct: 246 EPVRLQKALAASGVG-SRREMEEWIEAGLILVNGKKATLGDRVGPQDRVTAKGNPIRL-- 302

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K  D L  ++LY        +K  G  V                 
Sbjct: 303 ---------------KWPDRLPRVILY--------HKQEGELV--TRDDPEGRVTIFDRL 337

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +K  +     RLD  TSG+L+V  +   A  L         +     L    P+  KE
Sbjct: 338 PQAKSSRWVAVGRLDVNTSGLLIVTTSGELANRLMHPSFEAEREYAVRVLGQLEPEQMKE 397

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
                 L+       +  +V+Q  +G N+    ++V+    +      +  H G T    
Sbjct: 398 MTRGIELEDGP--AHFQRIVEQGGEGVNH---WYRVVIKEGRNREVRRIFEHFGLTVSRL 452

Query: 255 LRVHALHMGCP 265
           +RV   ++G P
Sbjct: 453 IRVRFGNIGLP 463


>gi|167629967|ref|YP_001680466.1| pseudouridine synthase [Heliobacterium modesticaldum Ice1]
 gi|167592707|gb|ABZ84455.1| pseudouridine synthase [Heliobacterium modesticaldum Ice1]
          Length = 333

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/253 (15%), Positives = 86/253 (33%), Gaps = 48/253 (18%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +RL +    H    +    + ++R+G+VR++   V+                    
Sbjct: 2   DSQTVRLQKLLAAH-GVASRREAEAMIRAGRVRINGTVVR-----------------EQG 43

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +   + +++    + K  +      LY+   +    K                   + 
Sbjct: 44  VRVDGARDVIEVDGRILKRREAPLYYALYKPRGVVTTCKDP------------QGRQTVI 91

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             +    ++     RLD++T G+L++      A  LT       ++K Y + + G     
Sbjct: 92  GLLSGVNERVYPVGRLDRDTEGLLLLTNDGQLAFRLTHPRFG--VEKTYRARLRGD---- 145

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              ++   LK    G           +    A +  +++        W+E++ H GR  Q
Sbjct: 146 ---VSAGALKALAEGVQL--------EDGVTAPAQVRLLRREGD-ATWIEIKIHEGRKRQ 193

Query: 255 LRVHALHMGCPIV 267
           +R     +G P++
Sbjct: 194 IRRMGDAIGHPVI 206


>gi|302528005|ref|ZP_07280347.1| pseudouridylate synthase ribosomal large subunit [Streptomyces sp.
           AA4]
 gi|302436900|gb|EFL08716.1| pseudouridylate synthase ribosomal large subunit [Streptomyces sp.
           AA4]
          Length = 250

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 49/278 (17%), Positives = 88/278 (31%), Gaps = 54/278 (19%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           E   + +RL +         +    + ++ +G+V VD + V     R+   + V      
Sbjct: 4   EQHPDGIRLQKVLSQA-GVASRRAAEDLIAAGRVEVDGEVVTELGRRVHPDEAV------ 56

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                           +++      L+  L+Y       FNKP G+             G
Sbjct: 57  ----------------IHVDGTRVNLRDDLVY-----LAFNKPKGVHSTMSDDRGRPCVG 95

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                   +        RLD+ T G+L++         L       R+ K Y++ V G+ 
Sbjct: 96  DYLRGRWEETPGVVHVGRLDENTEGLLLLTNDGDLGHRL--MHPSYRVLKTYFAEVEGL- 152

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 +   L K+   G +               +  F+V D  +     +E+  H GR
Sbjct: 153 ------VPRGLGKELRAGWEL--------PDGIVKVDQFRVKDMHS-GRSMIELVIHEGR 197

Query: 252 THQLRVHALHMGCPI-------VGDHKYCANFKGNFTS 282
            H +R      G P+       VGD +     +G    
Sbjct: 198 KHIVRRLMAATGHPVRKLVRTAVGDVQLGNQRQGTIRR 235


>gi|315282990|ref|ZP_07871273.1| ribosomal large subunit pseudouridine synthase B [Listeria marthii
           FSL S4-120]
 gi|313613361|gb|EFR87222.1| ribosomal large subunit pseudouridine synthase B [Listeria marthii
           FSL S4-120]
          Length = 244

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 85/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   N     +    +K+++ G+V V+ K VK                      + 
Sbjct: 2   ERLQKVIANA-GITSRRKAEKLIQEGKVTVNGKVVK-----------------ELGVKVS 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             ++I    + LTK           E+ + ++F KP G      +         +  +  
Sbjct: 44  GTERIEVEGIQLTK-----------EEHRYFLFYKPRGTVS---AVTDDKGRTTVADYFA 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC- 197
              ++     RLD +TSG+L++      A  L        + K Y + + GIP+ +    
Sbjct: 90  DIPERLYPVGRLDYDTSGLLLMTNDGDFANLL--MHPKNEVSKTYIARIKGIPEREVIRQ 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   ++            V+ ++K  + AI               +E+  H GR  Q+R 
Sbjct: 148 LERGVVIDGRKTAPAKVKVRSSDKTKDKAI---------------VEITIHEGRNRQVRK 192

Query: 258 HALHMGC 264
               +G 
Sbjct: 193 MFEAVGF 199


>gi|307709770|ref|ZP_07646221.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK564]
 gi|307619472|gb|EFN98597.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK564]
          Length = 240

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V V+ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVTDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  ++     RLD +TSG+L++         +        I K+Y + V G+     
Sbjct: 86  LLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM--IHPRNEIDKVYVARVKGVANKDN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
                 L +   I G               A+  ++++     +    +++  H GR HQ
Sbjct: 144 L---RPLTRGLEIDGKKT----------KPAV--YEILKVDPVKNRAVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEAVG 197


>gi|256827115|ref|YP_003151074.1| pseudouridine synthase family protein [Cryptobacterium curtum DSM
           15641]
 gi|256583258|gb|ACU94392.1| pseudouridine synthase family protein [Cryptobacterium curtum DSM
           15641]
          Length = 296

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 85/251 (33%), Gaps = 49/251 (19%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RL ++        +    ++++ +G+V V+               + I  +   ++ +
Sbjct: 49  PLRLQKFLARA-GVASRRGSERLISAGRVAVNG--------------IVITELGTKVDPL 93

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + E  +  + V     +  L              NKPAGI                    
Sbjct: 94  VDEVCVDGAIVTWGAPAVTL------------ALNKPAGIITTMKDLRGRRCVA--DIMP 139

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
             +        RLDQ+T+G+L+ +        L        + K+Y + + G I +   E
Sbjct: 140 TEQYPGLFPIGRLDQDTTGLLLFSTDGNLGNAL--LHPSHGVSKVYRATIEGSIGQAALE 197

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +A+ +L    +       V Q  K                 K   +E++ H GR HQ++
Sbjct: 198 QLASGILLDDGMTAPARVSVVQAGK-----------------KHSVIELELHEGRKHQVK 240

Query: 257 VHALHMGCPIV 267
                +G P+V
Sbjct: 241 RMCQAVGHPVV 251


>gi|22537733|ref|NP_688584.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae 2603V/R]
 gi|76787925|ref|YP_330211.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae A909]
 gi|76799444|ref|ZP_00781590.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae 18RS21]
 gi|77406891|ref|ZP_00783916.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae H36B]
 gi|77409463|ref|ZP_00786156.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae COH1]
 gi|77412369|ref|ZP_00788680.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae CJB111]
 gi|22534623|gb|AAN00457.1|AE014264_12 ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae 2603V/R]
 gi|76562982|gb|ABA45566.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae A909]
 gi|76585200|gb|EAO61812.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae 18RS21]
 gi|77161589|gb|EAO72589.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae CJB111]
 gi|77171930|gb|EAO75106.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae COH1]
 gi|77174500|gb|EAO77344.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae H36B]
 gi|319745532|gb|EFV97834.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           agalactiae ATCC 13813]
          Length = 240

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 87/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + V     ++++G +V I          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIKQGMVTINGQVVNELATQVKAGDLVEIE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                S +  E+   Y+ NKP G+  SV    G    ID     
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDDKGRKTVID----- 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +T+G+L++         +        I K+Y + V GI   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTTGLLILTNDGDFTDKM--IHPRNEIDKVYLARVKGIATKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
                               V  + K    A   + +I     +    +E+  H GR HQ
Sbjct: 144 L-------------RPLTRGVVIDGKKTKPA--RYTIIKVDHEKNRSVVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFEQVG 197


>gi|294879761|ref|XP_002768778.1| hypothetical protein Pmar_PMAR026919 [Perkinsus marinus ATCC 50983]
 gi|239871649|gb|EER01496.1| hypothetical protein Pmar_PMAR026919 [Perkinsus marinus ATCC 50983]
          Length = 302

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 40/153 (26%), Positives = 54/153 (35%), Gaps = 66/153 (43%)

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  TSGI++VA T AA   L   F+ R                        +LKK  I 
Sbjct: 178 LDIFTSGIIMVAHTYAAYYQLRHQFKNR-----------------------AILKKYSIA 214

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
            + V                             LE++  TGRTHQ+R+H  H+G PIV D
Sbjct: 215 QEKV---------------------------SLLEVEIPTGRTHQIRLHMYHIGHPIVSD 247

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG 302
           +                +L+LHA  +    P  
Sbjct: 248 Y----------------RLFLHAYLLAFYPPSS 264


>gi|152974996|ref|YP_001374513.1| pseudouridine synthase [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152023748|gb|ABS21518.1| pseudouridine synthase [Bacillus cytotoxicus NVH 391-98]
          Length = 242

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 90/252 (35%), Gaps = 60/252 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K V     ++     V +       NHI
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVTELGTKVTPQDKVEV-------NHI 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
             E+                      E+   ++  KP G+  SV    G        +  
Sbjct: 54  PLEK----------------------EEPVYFLLYKPTGVISSVSDDKGRK-----VVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + V G      
Sbjct: 87  FFQDIPQRLFPIGRLDYDTSGVLLMTNDGDFANIL--MHPKYKVEKTYVAKVKG------ 138

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRT 252
                       + G+ + ++++    +    + +  K+I    +K    +++  H GR 
Sbjct: 139 -----------PLTGEKIRMLEKGVILEDGKTSPARVKIISWDKRKEMSIVQLTIHEGRN 187

Query: 253 HQLRVHALHMGC 264
            Q+R     +GC
Sbjct: 188 RQVRRMFEAIGC 199


>gi|30019620|ref|NP_831251.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           ATCC 14579]
 gi|49477247|ref|YP_035689.1| pseudouridylate synthase [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|118477028|ref|YP_894179.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis str. Al Hakam]
 gi|196036830|ref|ZP_03104219.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           W]
 gi|196039034|ref|ZP_03106341.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           NVH0597-99]
 gi|196047636|ref|ZP_03114843.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           03BB108]
 gi|206968047|ref|ZP_03229003.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           AH1134]
 gi|218232708|ref|YP_002366253.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           B4264]
 gi|218902682|ref|YP_002450516.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           AH820]
 gi|225863435|ref|YP_002748813.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           03BB102]
 gi|228914146|ref|ZP_04077764.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|228920281|ref|ZP_04083629.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228926603|ref|ZP_04089672.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228932858|ref|ZP_04095725.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228945172|ref|ZP_04107528.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|228951948|ref|ZP_04114046.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228957847|ref|ZP_04119587.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|229043313|ref|ZP_04191033.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|229069124|ref|ZP_04202416.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|229078754|ref|ZP_04211308.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|229090533|ref|ZP_04221769.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|229109026|ref|ZP_04238627.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
 gi|229121114|ref|ZP_04250351.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|229126886|ref|ZP_04255898.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|229144171|ref|ZP_04272585.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|229149770|ref|ZP_04278000.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|229177979|ref|ZP_04305351.1| Pseudouridine synthase [Bacillus cereus 172560W]
 gi|229183767|ref|ZP_04310984.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|229189653|ref|ZP_04316668.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|254721252|ref|ZP_05183042.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A1055]
 gi|296502142|ref|YP_003663842.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis BMB171]
 gi|29895164|gb|AAP08452.1| Ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           ATCC 14579]
 gi|49328803|gb|AAT59449.1| pseudouridylate synthase [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|118416253|gb|ABK84672.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis str. Al Hakam]
 gi|195990559|gb|EDX54538.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           W]
 gi|196021550|gb|EDX60250.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           03BB108]
 gi|196030179|gb|EDX68779.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           NVH0597-99]
 gi|206736967|gb|EDZ54114.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           AH1134]
 gi|218160665|gb|ACK60657.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           B4264]
 gi|218539452|gb|ACK91850.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           AH820]
 gi|225790880|gb|ACO31097.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           03BB102]
 gi|228593917|gb|EEK51721.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|228599616|gb|EEK57219.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|228605467|gb|EEK62916.1| Pseudouridine synthase [Bacillus cereus 172560W]
 gi|228633801|gb|EEK90400.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|228639179|gb|EEK95595.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|228656826|gb|EEL12652.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|228662233|gb|EEL17836.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|228674495|gb|EEL29738.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
 gi|228692800|gb|EEL46523.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|228704627|gb|EEL57059.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|228714069|gb|EEL65952.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|228726027|gb|EEL77264.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|228801763|gb|EEM48640.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|228807871|gb|EEM54392.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228814407|gb|EEM60672.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|228826779|gb|EEM72546.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228832979|gb|EEM78547.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228839480|gb|EEM84773.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228845479|gb|EEM90512.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|296323194|gb|ADH06122.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis BMB171]
          Length = 242

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 84/253 (33%), Gaps = 56/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----SVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + + G    +K
Sbjct: 87  FFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANVL--MHPRYKVEKTYVAKIKGPLTGEK 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQ 254
                            +       +    A +  K+I    +K    +++  H GR  Q
Sbjct: 145 I---------------RMLERGVTLEDGKTAPARVKIISWDKRKEMAIVQLTIHEGRNRQ 189

Query: 255 LRVHALHMGCPIV 267
           +R     + C +V
Sbjct: 190 VRRMFEALDCKVV 202


>gi|305680918|ref|ZP_07403725.1| putative pseudouridine synthase B, ribosomal large subunit
           [Corynebacterium matruchotii ATCC 14266]
 gi|305659123|gb|EFM48623.1| putative pseudouridine synthase B, ribosomal large subunit
           [Corynebacterium matruchotii ATCC 14266]
          Length = 285

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 85/252 (33%), Gaps = 49/252 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + +RL +         +  N + ++ SG+V V+   V     +Q G  VR+ P ++ +  
Sbjct: 43  DGVRLQKVLAQA-GVASRRNAEIMIDSGRVEVNGAVV-----MQQG--VRVNPKVDVI-- 92

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                ++    VN+  +  +             V NKP GI       +     G L S 
Sbjct: 93  -----RVDGVRVNVNNNHQYF------------VLNKPRGIHSTMSDDLGRPCIGDLVSE 135

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             S GQ      RLD +T G++++      A  L+       + K Y + V G       
Sbjct: 136 RISAGQGLFHVGRLDADTEGLILLTNDGELANRLS--HPKYEVSKTYIAEVLGEADRSLV 193

Query: 197 CI--ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                   L       DYV +V                     Q    + +Q H GR H 
Sbjct: 194 TTLKNGVELDDGPAAADYVQIVDV------------------HQGRSLVRVQLHEGRKHI 235

Query: 255 LRVHALHMGCPI 266
           +R      G P+
Sbjct: 236 VRRMLKAAGYPV 247


>gi|229029250|ref|ZP_04185341.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|229172210|ref|ZP_04299774.1| Pseudouridine synthase [Bacillus cereus MM3]
 gi|228611198|gb|EEK68456.1| Pseudouridine synthase [Bacillus cereus MM3]
 gi|228732063|gb|EEL82954.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 242

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/255 (17%), Positives = 89/255 (34%), Gaps = 60/255 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----SVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + + G      
Sbjct: 87  FFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANVL--MHPRYKVEKTYVAKIKG------ 138

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQKFC-WLEMQPHTGRT 252
                       + G+ + ++++    +    A +  K+I    +K    +++  H GR 
Sbjct: 139 -----------PLTGEKIRMLERGVALEDGKTAPAQVKIISWDKRKETAIVQLTIHEGRN 187

Query: 253 HQLRVHALHMGCPIV 267
            Q+R     + C +V
Sbjct: 188 RQVRRMFEALDCKVV 202


>gi|324993667|gb|EGC25586.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK405]
 gi|324995021|gb|EGC26934.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK678]
 gi|327462936|gb|EGF09257.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1]
          Length = 242

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++R G+V ++ + V+     ++SG  V +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVVE 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++         +        I K+Y + V G+   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM--IHPRNEIDKVYVARVKGLANKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
             +   L +   I G               A+  +++I    A+    +++  H GR HQ
Sbjct: 143 --VLRPLTRGIEIEGRKT----------KPAV--YEIIKVDPAKNRSVIQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFQAVG 197


>gi|49184399|ref|YP_027651.1| RNA pseudouridine [Bacillus anthracis str. Sterne]
 gi|165872651|ref|ZP_02217281.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0488]
 gi|167634452|ref|ZP_02392773.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0442]
 gi|167641611|ref|ZP_02399857.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0193]
 gi|170689224|ref|ZP_02880420.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0465]
 gi|170706366|ref|ZP_02896827.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0389]
 gi|177651473|ref|ZP_02934262.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0174]
 gi|190568102|ref|ZP_03021012.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis Tsiankovskii-I]
 gi|227815681|ref|YP_002815690.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. CDC 684]
 gi|229602768|ref|YP_002865978.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0248]
 gi|254682364|ref|ZP_05146225.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. CNEVA-9066]
 gi|254733779|ref|ZP_05191493.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. Western North America USA6153]
 gi|254740530|ref|ZP_05198221.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. Kruger B]
 gi|254753919|ref|ZP_05205954.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. Vollum]
 gi|254759015|ref|ZP_05211042.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. Australia 94]
 gi|270000599|ref|YP_003329038.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. Ames]
 gi|291612213|ref|YP_003541027.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. 'Ames Ancestor']
 gi|49178326|gb|AAT53702.1| RNA pseudouridine [Bacillus anthracis str. Sterne]
 gi|164711595|gb|EDR17142.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0488]
 gi|167510404|gb|EDR85804.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0193]
 gi|167530340|gb|EDR93066.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0442]
 gi|170128900|gb|EDS97766.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0389]
 gi|170666779|gb|EDT17546.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0465]
 gi|172082751|gb|EDT67814.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0174]
 gi|190560836|gb|EDV14811.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis Tsiankovskii-I]
 gi|224552864|gb|ACN55073.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. 'Ames Ancestor']
 gi|227004794|gb|ACP14537.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. CDC 684]
 gi|229267176|gb|ACQ48813.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. A0248]
 gi|269850258|gb|ACZ49988.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           anthracis str. Ames]
          Length = 242

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 84/253 (33%), Gaps = 56/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   KRLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----SVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + + G    +K
Sbjct: 87  FFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANVL--MHPRYKVEKTYVAKIKGPLTGEK 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQ 254
                            +       +    A +  K+I    +K    +++  H GR  Q
Sbjct: 145 I---------------RMLERGVTLEDGKTAPARVKIISWDKRKEMAIVQLTIHEGRNRQ 189

Query: 255 LRVHALHMGCPIV 267
           +R     + C +V
Sbjct: 190 VRRMFEALDCKVV 202


>gi|15614139|ref|NP_242442.1| pseudouridylate synthase [Bacillus halodurans C-125]
 gi|10174193|dbj|BAB05295.1| pseudouridylate synthase [Bacillus halodurans C-125]
          Length = 242

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 48/250 (19%), Positives = 90/250 (36%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++  G+V+V+ + VK     + G  +++ P         
Sbjct: 2   ERLQKVIAQA-GIASRRKAEQLILEGKVKVNGQVVK-----ELG--IKVNPN-------- 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSW 136
            +  I    V + K           E+   ++  KP G+  SV+   G     D      
Sbjct: 46  -QDDIEVEGVPVEK-----------EEPVYFLLYKPTGVISSVKDDKGRKVVTDFL---- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                Q+     RLD +TSG+L++      A  L       +I+K+Y + V GIP   + 
Sbjct: 90  --EIEQRVYPVGRLDYDTSGLLLLTNDGEFANLL--MHPRHKIEKVYVAKVKGIPTRDQL 145

Query: 197 CIANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            +    +K          V ++  + +    AI               +++  H GR  Q
Sbjct: 146 KLLARGVKLEDGPTAPAKVKMLSVDRR-KQTAI---------------VKLTIHEGRNRQ 189

Query: 255 LRVHALHMGC 264
           +R     +GC
Sbjct: 190 VRRMFETIGC 199


>gi|217963899|ref|YP_002349577.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes HCC23]
 gi|290892109|ref|ZP_06555105.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL J2-071]
 gi|217333169|gb|ACK38963.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes HCC23]
 gi|290558232|gb|EFD91750.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL J2-071]
 gi|307571531|emb|CAR84710.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes L99]
 gi|313607907|gb|EFR84057.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL F2-208]
          Length = 244

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 84/246 (34%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   N     +    +K+++ G+V V+ K V                       + 
Sbjct: 2   ERLQKVIANA-GITSRRKAEKLIQEGKVTVNGKVVT-----------------ELGVKVS 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             ++I    + LTK           E+ + ++F KP G      +         +  +  
Sbjct: 44  GTERIEVEGIQLTK-----------EEHRYFLFYKPRGTVS---AVTDDKGRTTVADYFA 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD +TSG+L++      A  L        + K Y + + GIP+ +   +
Sbjct: 90  DIPERLYPVGRLDYDTSGLLLMTNDGDFANLL--MHPKNEVSKTYIARIKGIPERE---V 144

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L +   I G      K   + ++ A           +    +E+  H GR  Q+R  
Sbjct: 145 IRQLERGVVIDGRKTAPAKVKVRSSDKA-----------KDKAIVEITIHEGRNRQVRKM 193

Query: 259 ALHMGC 264
              +G 
Sbjct: 194 FEAVGF 199


>gi|71910124|ref|YP_281674.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS5005]
 gi|71852906|gb|AAZ50929.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS5005]
          Length = 248

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 84/248 (33%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +      ++SG VV I          
Sbjct: 9   MRINKYIA-HAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIE--------- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                S +  E+   Y+ NKP G IS          +   L   
Sbjct: 59  --------------------GSPIYNEEKVYYLLNKPRGAISSVSDDKGRKTVLDLL--- 95

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +        I K+Y + V GI   +  
Sbjct: 96  -PQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM--IHPRNEIDKVYLARVKGIATKENL 152

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQL 255
                              +  + K    A   + ++   A K    +E+  H GR HQ+
Sbjct: 153 -------------RPLTRGIVIDGKKTKPA--RYNIVRVEADKSRSIVELTIHEGRNHQV 197

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 198 KKMFESVG 205


>gi|313884640|ref|ZP_07818398.1| 16S pseudouridylate 516 synthase [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620150|gb|EFR31581.1| 16S pseudouridylate 516 synthase [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 242

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 46/251 (18%), Positives = 91/251 (36%), Gaps = 50/251 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++K++ SGQ++V+   V                    +NH +
Sbjct: 2   MRLDKFLATLGLG-SRKEVKKLITSGQIQVNDVTVT------------------KVNHGV 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E               +L   L+Y+     + NKP G+       +   +  ++   +D
Sbjct: 43  DED---------HDQVAYLGQELVYQAYYYVMLNKPDGLVSATEDKMHETVIDWVA--LD 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                     RLD +T+G+L++      A Q L+     + + K Y +LV G        
Sbjct: 92  FDHVDLFPVGRLDIDTTGLLLLTNNGQLAHQLLS---PKKHVAKTYQALVTGQVSEVD-- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
           IA            +   ++  +  A  A    +++D    K     ++  H G+ HQ++
Sbjct: 147 IAA-----------FAAGIRLKDFTAQAA--ELEILDYDPDKDQSLTKVTIHEGKFHQVK 193

Query: 257 VHALHMGCPIV 267
              L     ++
Sbjct: 194 RMFLARDHEVL 204


>gi|171780251|ref|ZP_02921155.1| hypothetical protein STRINF_02039 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281599|gb|EDT47034.1| hypothetical protein STRINF_02039 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 241

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 82/248 (33%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    + +++ G V ++ K V      +++G VV +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEDLIKRGLVTINGKVVTELATTVKAGDVVEVEGTP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G+ S          +   L + 
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRKTVVDLLPNV 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +T+G+L++         +        I K+Y + V G+   +  
Sbjct: 91  T----ERIYPVGRLDWDTTGLLILTNDGDFTDEM--IHPRNEIDKVYLARVKGLATKENL 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQL 255
                              V  + K    A   + +I    +     +E+  H GR HQ+
Sbjct: 145 -------------RPLTRGVVIDGKKTKPA--RYNIIKVDPEKNRSVVELTIHEGRNHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KKMFELVG 197


>gi|156841774|ref|XP_001644258.1| hypothetical protein Kpol_1030p8 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156114897|gb|EDO16400.1| hypothetical protein Kpol_1030p8 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 262

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/211 (19%), Positives = 76/211 (36%), Gaps = 37/211 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--------LKSWVDSKGQK------PRL 146
           + Y +S   + NKP  +  Q G   ++   G         L   +     K       R 
Sbjct: 9   ICYRNSNYIIVNKPFNVLSQPGYIGSWKCVGLSSPVVPVLLDDLIKQNAGKDENVTEWRT 68

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQ-KIYWSLVWGIPKNKKECIANWLLKK 205
            HRLD+  +G +++A  + +A   +++ R    +   +      + +N        + + 
Sbjct: 69  VHRLDKLVTGGVLIATNKNSAIKFSKNLRYGGNKGYKFTRRYVALVENSLNVNTRKIPEF 128

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALH-MGC 264
             I  D +             IS++K  D              TG  HQ+R H    +G 
Sbjct: 129 GQINFDGM-------------ISNYKQFD-----ESCFIFDLVTGGKHQIRKHLSLCLGR 170

Query: 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYM 295
           PI+ D KY A          +N++ LH+  +
Sbjct: 171 PILNDVKYNATPITEID---RNQIALHSACI 198


>gi|125718577|ref|YP_001035710.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK36]
 gi|125498494|gb|ABN45160.1| Ribosomal large subunit pseudouridine synthase B, putative
           [Streptococcus sanguinis SK36]
 gi|325695058|gb|EGD36961.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK150]
 gi|328946852|gb|EGG40989.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1087]
 gi|332367409|gb|EGJ45142.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1059]
          Length = 242

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++R G+V ++ + V+     ++SG  V +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVVE 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++         +        I K+Y + V G+   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM--IHPRNEIDKVYVARVKGLANKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
             +   L +   I G               A+  +++I    A+    +++  H GR HQ
Sbjct: 143 --VLRPLTRGIEIEGRKT----------KPAV--YEIIKVDPAKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFQAVG 197


>gi|327390694|gb|EGE89034.1| hypothetical protein SPAR5_0271 [Streptococcus pneumoniae GA04375]
          Length = 240

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 86/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q                  
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQ------------------ 40

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
               I +    +      L+    YE+   Y+ NKP G+           +   L     
Sbjct: 41  ----INEERDQIHFDGQKLE----YEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKE 196
           SK  +     RLD +T G+L++    + A   L+     R + K Y + V G+  +   E
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNDGKLAHTLLS---PKRHVDKTYQAQVKGMMTREDVE 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             A  +                 +     A      ID   +    + +    G+ HQ++
Sbjct: 148 TFAEGI--------------PLKDFTCQPAKLELVSIDT-EKNQSQIRVTIAEGKFHQIK 192

Query: 257 VHALHMG 263
               + G
Sbjct: 193 RMVAYCG 199


>gi|288941903|ref|YP_003444143.1| pseudouridine synthase [Allochromatium vinosum DSM 180]
 gi|288897275|gb|ADC63111.1| pseudouridine synthase [Allochromatium vinosum DSM 180]
          Length = 299

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/239 (15%), Positives = 74/239 (30%), Gaps = 32/239 (13%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           + +E +RL +         +   ++  +  G+VRV+ +  K  ++      +R+      
Sbjct: 13  SGDEPVRLQKLLAEAGLG-SRRQIEGWISEGRVRVNGQLAKLGDQATRADRIRVDGR--- 68

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                         V L    D    I++Y        +KP G  V              
Sbjct: 69  -------------DVTLKPKRDSETQIIVY--------HKPEGELV--TRRDPEERPTVF 105

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +     K  +     RLD  TSG+++       A  L      R I++ Y   + G    
Sbjct: 106 RRLPRPKQGRWIAVGRLDINTSGLILFTTDGELANRL--MHPSREIEREYSVRILGEVAP 163

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           +        ++       +  +  Q   GAN+    + V+    +      +    G T
Sbjct: 164 ETLERLTAGIELDDGPAKFERITDQGGTGANH---WYNVVLREGRNREVRRLWEAAGCT 219


>gi|297584469|ref|YP_003700249.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297142926|gb|ADH99683.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 239

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 48/235 (20%), Positives = 83/235 (35%), Gaps = 49/235 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +    +K++  G+V V+  +VK                       ++  +I    V L K
Sbjct: 15  SRRKAEKLIEEGRVYVNGNQVK----------------EVGAKADLQTDEISVDGVPLQK 58

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                      E+   Y+  KP+G+     +G        +   +     +     RLD 
Sbjct: 59  -----------EEPVYYLLYKPSGVIS--SAGDDKGRKTVID--LVPGEFRVFPVGRLDF 103

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           +TSG++V+      A  L       RI K Y + V G+P           L++     D 
Sbjct: 104 DTSGLIVLTNDGEFANLL--MHPKYRIHKTYIAKVKGLP-----------LREDLKKLDR 150

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPI 266
             V+    +    A +  KVI    +K    +E+  H GR  Q+R     +G P+
Sbjct: 151 GIVL----EDGKTAPAKTKVIKTDKRKGTAVVEITIHEGRNRQVRRMFDAIGFPV 201


>gi|210633114|ref|ZP_03297681.1| hypothetical protein COLSTE_01590 [Collinsella stercoris DSM 13279]
 gi|210159268|gb|EEA90239.1| hypothetical protein COLSTE_01590 [Collinsella stercoris DSM 13279]
          Length = 282

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/279 (13%), Positives = 85/279 (30%), Gaps = 55/279 (19%)

Query: 1   MSLMTYVQY--VVVENDEE---NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF 55
           M     ++   + V  D+E    MRL R+        +    + ++ +G+V V+ +    
Sbjct: 5   MRSDRDIERTPLKVHPDDERVVPMRLQRFLARA-GVASRRGSEALMSAGRVSVNGE---- 59

Query: 56  NNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPA 115
                                 +K +        + + +     ++L   +   + NKPA
Sbjct: 60  ----------------------VKTELGTKVDPAIDQVAVDGVPVVLGVGAAYLMLNKPA 97

Query: 116 GISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175
           G+                               RLD +T+G+L+          L     
Sbjct: 98  GVLTTMSDPHGRPCVA--DIMPVRSYPGLFPVGRLDMDTTGLLLFTTDGDLGHAL--LHP 153

Query: 176 MRRIQKIYWSLVWGI-------PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
            R + K Y ++V G+       P  +   + +   + +         V+        A +
Sbjct: 154 SRHVWKTYVAVVDGVCREGDLEPLRRGIVLDDGPCQPARCALRDERDVRDIAPRGLRAGT 213

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                         + ++   GR +Q++     +G P++
Sbjct: 214 ------------TAVRIEIREGRKNQVKRMLSKIGHPVL 240


>gi|270291591|ref|ZP_06197811.1| ribosomal small subunit pseudouridine synthase A [Pediococcus
           acidilactici 7_4]
 gi|270279910|gb|EFA25748.1| ribosomal small subunit pseudouridine synthase A [Pediococcus
           acidilactici 7_4]
          Length = 239

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 87/249 (34%), Gaps = 53/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  +         ++K+++   V V+    K + R++   VV             
Sbjct: 1   MRVDKFLHDMNVG-TRSQIRKLIKEKVVFVNDVVAK-SGRVKVDPVVD------------ 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                              + ++ Y+    ++ NKP G+               +    +
Sbjct: 47  --------------QVRLGEQVITYQQYFYFMMNKPLGVVT----ATEDRKQKTVMDLFN 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               +       RLD++T G+L++      A Q L      R +QK Y ++V G      
Sbjct: 89  KVDFRKDLFPVGRLDKDTEGLLLITNNGPLAHQLLA---PERHVQKTYEAVVTGQ----- 140

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254
             I +  +K+   G     +V ++      A     +++  A  +   + +    G+ HQ
Sbjct: 141 --ITDPAVKQFADG-----IVLKDGTQLKPA--DLTILNYSALDEQTLVHVTLKEGKYHQ 191

Query: 255 LRVHALHMG 263
           +R     +G
Sbjct: 192 VRRMFGSLG 200


>gi|296164607|ref|ZP_06847174.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295900026|gb|EFG79465.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 247

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 77/252 (30%), Gaps = 45/252 (17%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D E +RL +         +    +K++  G+V VD + V             +   ++  
Sbjct: 3   DTEGIRLQKVLSQA-GIASRRAAEKLIIDGRVEVDGRVVT-----------ELGTRVDPD 50

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +I+                    ++L E       NKP G+             G L 
Sbjct: 51  ASVIR---------------VDGARVVLDESLVYLALNKPRGMHSTMSDDRGRPCIGDLV 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  +      RLD +T G++++      A  L        + K Y + V G     
Sbjct: 96  ERKVRGNKNLFHVGRLDADTEGLILLTNDGELAHRL--MHPSHEVPKTYLATVTGSVP-- 151

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                        IG      ++ ++  A   +  F V+D    K   + +  H GR   
Sbjct: 152 -----------RGIGKKLKAGIELDDGPAR--VDDFAVVDAIPGK-TLVRVVLHEGRNRI 197

Query: 255 LRVHALHMGCPI 266
           +R      G P+
Sbjct: 198 VRRLLGAAGFPV 209


>gi|256391653|ref|YP_003113217.1| pseudouridine synthase [Catenulispora acidiphila DSM 44928]
 gi|256357879|gb|ACU71376.1| pseudouridine synthase [Catenulispora acidiphila DSM 44928]
          Length = 332

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 93/256 (36%), Gaps = 49/256 (19%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           + +EE +RL +         +    + ++ +G+V V+ + V+                 +
Sbjct: 90  DANEEGIRLQKVLAQAGVG-SRRVSEDLIAAGRVEVNGEIVR-----------------H 131

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
               +  E  ++         ++     +++     + FNKP G+          +    
Sbjct: 132 QGMRVDPETAVIRVDGMRISTAEG----IVH-----FAFNKPMGVVSAMDDPDRPN---- 178

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L  +V  + ++     RLD +T G++++      A  L        I+K+Y + V+G   
Sbjct: 179 LGDYVRGRNERLFHIGRLDVDTEGLILLTNDGELAHRLA--HPSYEIRKVYRAQVYGTVP 236

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                    L ++   G D         +     + HF+++D   +    +E+  H GR 
Sbjct: 237 KD-------LGRRLREGVDL--------EDGLARVDHFRLLDSVGRNA-LVEITIHEGRN 280

Query: 253 HQLRVHALHMGCPIVG 268
             +R     +G P+ G
Sbjct: 281 RIVRRIMDAVGLPVRG 296


>gi|229058206|ref|ZP_04196594.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228720070|gb|EEL71654.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 242

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 87/252 (34%), Gaps = 60/252 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----NVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + + G      
Sbjct: 87  FFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANVL--MHPRYKVEKTYVAKIKG------ 138

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRT 252
                       + GD + ++++    +    A +  K+I    +K    +++  H GR 
Sbjct: 139 -----------PLTGDKIRMLERGVALEDGKTAPAQVKIISWDKRKEMAIVQLTIHEGRN 187

Query: 253 HQLRVHALHMGC 264
            Q+R     + C
Sbjct: 188 RQVRRMFEALDC 199


>gi|225028080|ref|ZP_03717272.1| hypothetical protein EUBHAL_02350 [Eubacterium hallii DSM 3353]
 gi|224954550|gb|EEG35759.1| hypothetical protein EUBHAL_02350 [Eubacterium hallii DSM 3353]
          Length = 242

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 89/252 (35%), Gaps = 55/252 (21%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
               + MRLD++       +     ++ ++ G V VD + VK    ++ S   + +    
Sbjct: 2   PETLKKMRLDKFLTQA-AELTRSEAKQKIKKGSVTVDGEVVKKAEMKVSSEDAICLD--- 57

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                                       ++ YE  +  + +KPAG+     S        
Sbjct: 58  --------------------------GEVVTYEKYRYIMLHKPAGVV----SATEDAQCQ 87

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +   +    +      RLD++T G+L++    A A +L      + + K Y++++ G  
Sbjct: 88  TVLDLITEGRKGLFPVGRLDKDTEGLLLLTNDGALAHNL--LSPRKHVDKTYFAILDGEV 145

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             K++ +    L+   IG +   +       A   I+          K   + +    GR
Sbjct: 146 GEKEQEL---FLQGLDIGDEKKTL------PAKLEIT---------DKANEVFITVQEGR 187

Query: 252 THQLRVHALHMG 263
            HQ++  A  +G
Sbjct: 188 FHQVKRMAEAVG 199


>gi|134299005|ref|YP_001112501.1| pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134051705|gb|ABO49676.1| ribosomal large subunit pseudouridine synthase B [Desulfotomaculum
           reducens MI-1]
          Length = 309

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 85/249 (34%), Gaps = 48/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +  + ++++ SGQV+V+ K V      + G  +++ P  + +    
Sbjct: 3   ERLQKILAKA-GVASRRHSEELIISGQVKVNGKTVT-----EMG--LKVDPTKDKIEVKG 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K    L+  V                     + NKP G      +         +   + 
Sbjct: 55  KPLPPLEKKV-------------------YLLMNKPRGYVT---TLSDERDRKTVVDLLK 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              Q+     RLD ++ G+L++       Q LT      +++K Y + V GIP+ ++   
Sbjct: 93  GVEQRVYPVGRLDYDSEGLLLLTNDGELTQALT--HPKHKVKKTYLAKVDGIPETEEL-- 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                                 +    A +  + +         LE+  H GR  Q+R  
Sbjct: 149 -------------KAMAKGLVLEDGPTAPADVR-LAGTGDNRALLEISIHEGRNRQVRRM 194

Query: 259 ALHMGCPIV 267
             H+G  ++
Sbjct: 195 CEHIGYKVL 203


>gi|207110740|ref|ZP_03244902.1| hypothetical protein HpylH_16920 [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 85

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 27/91 (29%), Positives = 45/91 (49%), Gaps = 7/91 (7%)

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           ++K Y +L+ GI + ++E  A  L  K+      +       K    A++    +    +
Sbjct: 2   VKKEYLALIQGIIEEEREINAPILTIKTTKAFSKI------SKKGQEAVTIITPLKIINK 55

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           K   L++   TGRTHQ+RVH  H+  PI+GD
Sbjct: 56  K-TLLKVGIKTGRTHQIRVHLKHINHPIIGD 85


>gi|251779869|ref|ZP_04822789.1| RNA pseudouridine synthase family protein [Clostridium botulinum E1
           str. 'BoNT E Beluga']
 gi|243084184|gb|EES50074.1| RNA pseudouridine synthase family protein [Clostridium botulinum E1
           str. 'BoNT E Beluga']
          Length = 254

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 39/256 (15%), Positives = 86/256 (33%), Gaps = 43/256 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQK-ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       +    + +  ++ G V+V+ K +                        
Sbjct: 1   MRLDKFLAE--SAVGRRKIVRTYIKDGMVKVNGKIIT----------------------- 35

Query: 78  IKEQKILDSSVNLTKHSDFLK---SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                  + S+N+ +  D ++     +++     Y+FNKPAG           +I   + 
Sbjct: 36  -------EPSININEKLDDVEYLGKKVIHNGKVYYIFNKPAGCIT----ATRDNIHKTVF 84

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            + D          RLD++T G+L++         +    +       +W+L     ++K
Sbjct: 85  DYFDEDMNGVFHVGRLDKDTEGLLLLTNDGEFEHKVMYPEKHVEKTYFFWALGSLDDEDK 144

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNE---KGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K+  A   +  +        +        K     I    + +   Q      +    G+
Sbjct: 145 KQLEAGIFIGNNESLTKPAKIDLYKSGLYKEFKEEIPIKNLENKDHQPVVSGYLTISEGQ 204

Query: 252 THQLRVHALHMGCPIV 267
            HQ++     +GC ++
Sbjct: 205 KHQVKRMLKAVGCYVI 220


>gi|297559952|ref|YP_003678926.1| pseudouridine synthase [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
 gi|296844400|gb|ADH66420.1| pseudouridine synthase [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
          Length = 694

 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/251 (17%), Positives = 90/251 (35%), Gaps = 48/251 (19%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E  +RL +         +    ++++ +G+V VD + V+     + G  V          
Sbjct: 454 ENGIRLQKALAAA-GVASRRASEEMIAAGRVSVDGQVVR-----RFGARVD--------- 498

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
              +  +I    + +    D L           +  NKP G+     +         L  
Sbjct: 499 --PESSEIRVDGMRVVTAPDKL----------YFALNKPRGVVS---TMWDPEGRPTLAD 543

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     ++     RLD ET G++++      A  LT      ++ K Y + V G   ++ 
Sbjct: 544 YTGQTEERIFHVGRLDTETEGLILLTNDGELANRLT--HPRYKVVKTYIAKVPGPVPHR- 600

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 ++++   G +         +     +  F+V+D    K   +E++ H GR H +
Sbjct: 601 ------VVREVQKGVEL--------EDGPVEVDSFRVVDNEPPKA-LVEIRLHEGRKHIV 645

Query: 256 RVHALHMGCPI 266
           R     +G P+
Sbjct: 646 RRLMEAVGHPV 656


>gi|42780671|ref|NP_977918.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           ATCC 10987]
 gi|47569145|ref|ZP_00239833.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           G9241]
 gi|206978260|ref|ZP_03239138.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           H3081.97]
 gi|217959048|ref|YP_002337596.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           AH187]
 gi|222095202|ref|YP_002529262.1| ribosomal large subunit pseudouridine synthase b [Bacillus cereus
           Q1]
 gi|228984651|ref|ZP_04144824.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
 gi|229138265|ref|ZP_04266860.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|229155139|ref|ZP_04283251.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|229195772|ref|ZP_04322532.1| Pseudouridine synthase [Bacillus cereus m1293]
 gi|300117500|ref|ZP_07055290.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           SJ1]
 gi|301053111|ref|YP_003791322.1| pseudouridylate synthase [Bacillus anthracis CI]
 gi|42736591|gb|AAS40526.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           ATCC 10987]
 gi|47554216|gb|EAL12579.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           G9241]
 gi|206743509|gb|EDZ54938.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           H3081.97]
 gi|217066494|gb|ACJ80744.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           AH187]
 gi|221239260|gb|ACM11970.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           Q1]
 gi|228587669|gb|EEK45727.1| Pseudouridine synthase [Bacillus cereus m1293]
 gi|228628266|gb|EEK84981.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|228645157|gb|EEL01394.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|228775045|gb|EEM23438.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
 gi|298725335|gb|EFI65987.1| ribosomal large subunit pseudouridine synthase B [Bacillus cereus
           SJ1]
 gi|300375280|gb|ADK04184.1| pseudouridylate synthase [Bacillus cereus biovar anthracis str. CI]
 gi|324325588|gb|ADY20848.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           thuringiensis serovar finitimus YBT-020]
          Length = 242

 Score = 68.5 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/255 (17%), Positives = 89/255 (34%), Gaps = 60/255 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----SVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + + G      
Sbjct: 87  FFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANVL--MHPRYKVEKTYVAKIKG------ 138

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRT 252
                       + G+ + ++++    +    A +  K+I    +K    +++  H GR 
Sbjct: 139 -----------PLTGEKIRMLERGVMLEDGKTAPARVKIISWDKRKEMAIVQLTIHEGRN 187

Query: 253 HQLRVHALHMGCPIV 267
            Q+R     + C +V
Sbjct: 188 RQVRRMFEALDCKVV 202


>gi|308174106|ref|YP_003920811.1| pseudouridine synthase [Bacillus amyloliquefaciens DSM 7]
 gi|307606970|emb|CBI43341.1| pseudouridine synthase [Bacillus amyloliquefaciens DSM 7]
 gi|328552765|gb|AEB23257.1| pseudouridine synthase [Bacillus amyloliquefaciens TA208]
 gi|328912437|gb|AEB64033.1| pseudouridine synthase [Bacillus amyloliquefaciens LL3]
          Length = 244

 Score = 68.5 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/251 (17%), Positives = 84/251 (33%), Gaps = 52/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +++++ G+V+V+ K +     ++     + +          
Sbjct: 2   ERLQKVIA-HAGVASRRKAEELIKEGKVKVNGKVITELGVKVTGSDQIEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       L    +     LLY         KP G+     +         +  + 
Sbjct: 52  -----------GLKVEREEPVYFLLY---------KPRGVIS---AADDDKGRKVVTDFF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               Q+     RLD +TSG+L++      A  L        I K Y + V GIP  +   
Sbjct: 89  KEVPQRIYPIGRLDYDTSGLLLLTNDGEFANKL--MHPKYEIDKTYVAKVKGIPSKE--- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
               LL+K   G           +    A +  K++    +K    +++  H GR  Q+R
Sbjct: 144 ----LLRKLERGIQL--------EEGKTAPARAKMLSLDKRKQTSIIQLTIHEGRNRQVR 191

Query: 257 VHALHMGCPIV 267
                +G  ++
Sbjct: 192 RMFEAIGHDVL 202


>gi|311899116|dbj|BAJ31524.1| putative ribosomal large subunit pseudouridine synthase B
           [Kitasatospora setae KM-6054]
          Length = 428

 Score = 68.5 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 49/280 (17%), Positives = 96/280 (34%), Gaps = 55/280 (19%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           E  E+  RL +         +    ++++  G+V V+ + V     ++ G+ V       
Sbjct: 186 EVGEDGERLQKVLARAGMG-SRRACEELIAQGRVDVNGETV-----LEQGRRV------- 232

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                +K++  +D     T+   F               NKPAG+             G 
Sbjct: 233 ---DPVKDEIKVDGLTVATQSYLFF------------ALNKPAGVVSTMEDPEGRQCLG- 276

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              +V ++  +     RLD ET GI+++      A  LT   +    +    ++   +P+
Sbjct: 277 --DYVTNRETRLFHVGRLDTETEGIILLTNHGELAHRLTHP-KYGVTKTYLAAIQGPLPR 333

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           +  + +A  +  +                        FKVI    + +  +E+  H GR 
Sbjct: 334 DLGKTLAKGVELEDGWARADS----------------FKVISNLGKNY-LVEVTLHEGRK 376

Query: 253 HQLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNKL 288
           H +R     +G P+  D      +     G+  S    +L
Sbjct: 377 HIVRRLLAEVGFPV--DKLVRTAFGPITLGDQKSGWLRRL 414


>gi|153853074|ref|ZP_01994483.1| hypothetical protein DORLON_00468 [Dorea longicatena DSM 13814]
 gi|149753860|gb|EDM63791.1| hypothetical protein DORLON_00468 [Dorea longicatena DSM 13814]
          Length = 237

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 45/246 (18%), Positives = 88/246 (35%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++            ++K +R G+V V+   VK                        
Sbjct: 2   MRLDKYLAEMGVG-TRQEVKKQIRQGKVTVNGTVVKA----------------------- 37

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                +D + +         S + YE    Y+ NKP G+           +   +K   D
Sbjct: 38  -ADTKIDETCDEVTIGGRNISYVSYE---YYMLNKPGGVVSATEDRRDTTVIDLIK---D 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K +      RLD++T G+L++      A + L      + + K+Y++ + G+   +   
Sbjct: 91  KKRKDLFPVGRLDKDTEGLLLITNDGDLAHRLLA---PKKHVDKVYYAKIDGMVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K+   G D     ++  + A   I         + +   + +  H G+ HQ++ 
Sbjct: 146 -----VKRFAEGIDIGAEEEEMTRPAKLDI-------MKSAEESEIRLTIHEGKFHQVKR 193

Query: 258 HALHMG 263
             L +G
Sbjct: 194 MFLAVG 199


>gi|323351021|ref|ZP_08086678.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis VMC66]
 gi|322122745|gb|EFX94454.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis VMC66]
 gi|324991310|gb|EGC23243.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK353]
 gi|325696344|gb|EGD38235.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK160]
 gi|327474540|gb|EGF19945.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK408]
 gi|332362256|gb|EGJ40056.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1056]
          Length = 242

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++R G+V ++ + V+     ++SG  V +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++         +        I K+Y + V G+   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM--IHPRNEIDKVYVARVKGLANKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
             +   L +   I G               A+  +++I    A+    +++  H GR HQ
Sbjct: 143 --VLRPLTRGIEIEGRKT----------KPAV--YEIIKVDPAKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFQAVG 197


>gi|297697698|ref|XP_002825984.1| PREDICTED: hypothetical protein LOC100448251 [Pongo abelii]
          Length = 295

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQIT 308
            GRTHQLRVH   +G P+VGD  Y     G    P   ++ LHA Y+ +P  +   +++ 
Sbjct: 153 QGRTHQLRVHCSALGHPVVGDLTYG-EASGREDRPF--RMMLHAFYLRIP-TDAECVEVC 208

Query: 309 APLPAHMVKTWDSL 322
            P P   + + D+ 
Sbjct: 209 TPDP--FLPSLDAC 220


>gi|145636895|ref|ZP_01792560.1| malic enzyme [Haemophilus influenzae PittHH]
 gi|145269976|gb|EDK09914.1| malic enzyme [Haemophilus influenzae PittHH]
          Length = 232

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 82/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +R   V+++ + VK                      I 
Sbjct: 1   MRLDKFIAENV-GLTRSQATKAIRQSAVKINGEIVKS-----------------GSVQIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E +I      LT            E+ + ++ +KP G       G    I  F    + 
Sbjct: 43  QEDEIYFEDELLTWV----------EEGQYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 93  G---KLHSAGRLDMDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + +          +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPVEENYAAACSEGILLRGEKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|251791839|ref|YP_003006559.1| ribosomal small subunit pseudouridine synthase A [Aggregatibacter
           aphrophilus NJ8700]
 gi|247533226|gb|ACS96472.1| ribosomal small subunit pseudouridine synthase A [Aggregatibacter
           aphrophilus NJ8700]
          Length = 233

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/255 (16%), Positives = 80/255 (31%), Gaps = 61/255 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHI 77
           MRLD++       +      K+LR   V ++ K  K    ++     +            
Sbjct: 1   MRLDKFLAE-MTDLTRSQATKVLRQSAVTINGKIEKSGAAKVGPNDEIC----------- 48

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQ--GGSGIAYHIDGF-L 133
                            D  +   + E   I + NKP G I     G     Y   G+ L
Sbjct: 49  ----------------YDGERLAWVAEGQYIML-NKPQGYICSHEDGDHPTIYQFFGYPL 91

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            + + S G       RLD +T+G++++                 +      S     PK 
Sbjct: 92  SARLHSAG-------RLDVDTTGLVLLT-------------DDGQWSHRITSPKHHQPKT 131

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               +A+ +            +++  +     A    +++D +       E     GR H
Sbjct: 132 YLVTLADPVEANYVQACTEGILLRGEKDPTKPAT--LEILDDYNVNLTISE-----GRYH 184

Query: 254 QLRVHALHMGCPIVG 268
           Q++     +G  +VG
Sbjct: 185 QIKRMFAALGNKVVG 199


>gi|253576375|ref|ZP_04853705.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251844268|gb|EES72286.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 256

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 51/298 (17%), Positives = 101/298 (33%), Gaps = 67/298 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-----KFNNRIQSGQVVRIPPVINA 73
            RL +         +    ++++ SG+V+V+ + V     K +  +    V+ +      
Sbjct: 10  ERLQKILAAA-GVASRRKCEELILSGKVQVNGETVTTLGTKADPSV---DVITV------ 59

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                 E K + +   L                   +FNKP G+     S         +
Sbjct: 60  ------EGKPIGAEKKL-----------------YLMFNKPKGVIT---SASDPQGRKIV 93

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             ++    ++     RLD +T G+L++      A  LT       + K Y + V G+P  
Sbjct: 94  TDYLKGIKERVYPVGRLDYDTEGLLLLTNDGEFAHLLT--HPKHHVPKTYLATVKGVPHG 151

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                       + +      V+ ++   A   + ++ +     +K+  + +  H GR  
Sbjct: 152 ------------TALDKLKQGVMLEDGMTAPAEVEYYDI--DPEEKYATISITIHEGRNR 197

Query: 254 QLRVHALHMGCPI-------VGDHKYCANFKG---NFTSPIQNKLYLHARYMDLPHPE 301
           Q+R     +  P+        GD       +G   + T    + LY  AR    P P+
Sbjct: 198 QVRRMFDAISHPVTRLKRISFGDLVLGNLKRGLYRHLTKEEVDSLYKLARTTTPPTPK 255


>gi|145630872|ref|ZP_01786649.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae R3021]
 gi|260582948|ref|ZP_05850732.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae NT127]
 gi|144983532|gb|EDJ91000.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae R3021]
 gi|260094048|gb|EEW77952.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae NT127]
          Length = 232

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 82/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +R   V+++ + VK                      I 
Sbjct: 1   MRLDKFIAEN-TGLTRSQATKAIRQSAVKINGEIVKS-----------------GAVQIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E +I      LT            E+ + ++ NKP G       G    I  F    + 
Sbjct: 43  QEDEIYFEDQLLTWV----------EEGQYFMLNKPQGCVCSNDDGDYPTIYQFFDYPLA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 93  G---KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + +          +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPVEENYATACAEGILLRGEKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|26450633|dbj|BAC42428.1| putative RNA pseudouridylate synthase [Arabidopsis thaliana]
          Length = 148

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +P + HRLD+ T+G+LVVA+   +  HL E F++  I+++Y SL  G+P   +  I   +
Sbjct: 61  RPGIVHRLDKGTTGLLVVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPSPPQGRIEIPI 120

Query: 203 LKKSHIGGDYVHVVKQNEKGAN 224
            + S      +  +    +G  
Sbjct: 121 GRDSS-NRIRMAAIPGGVRGGR 141


>gi|312864688|ref|ZP_07724919.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           downei F0415]
 gi|311099815|gb|EFQ58028.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           downei F0415]
          Length = 241

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 83/249 (33%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + V      +++G  V +          
Sbjct: 1   MRINKYIA-HAGLASRRKAEELIKQGLVTINGQVVTELATTVKNGDRVEVSGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVLD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +T+G+L++         +        I K+Y + + G+   + 
Sbjct: 86  LLPDVKERIYPVGRLDWDTTGVLILTNDGDFTDEM--IHPRNEIDKVYLARLKGLATKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                               V  + K    A   +K+I          +E+  H GR HQ
Sbjct: 144 L-------------RPLTRGVVIDGKKTGPA--RYKIIKVEPDKNRSLVELTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKNMFQAVG 197


>gi|116873391|ref|YP_850172.1| ribosomal large subunit pseudouridine synthase B [Listeria
           welshimeri serovar 6b str. SLCC5334]
 gi|116742269|emb|CAK21393.1| ribosomal large subunit pseudouridine synthase B [Listeria
           welshimeri serovar 6b str. SLCC5334]
          Length = 244

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 85/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +   N     +    +K+++ G+V V+ K V     ++   + + +          
Sbjct: 2   ERLQKVIANA-GITSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEV---------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                     + LTK           E+ + ++F KP G      +         +  + 
Sbjct: 51  --------EGIQLTK-----------EEHRYFLFYKPRGTVS---AVTDDKGRTTVADYF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  L        + K Y + + GIP+ +   
Sbjct: 89  TDIPERLYPVGRLDYDTSGLLLMTNDGDFANLL--MHPKNEVSKTYIARIKGIPERE--- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   L +   I G      K   + ++ A           +    +E+  H GR  Q+R 
Sbjct: 144 VIRELERGVVIDGRKTAPAKVKVRSSDKA-----------KNKAIVEITIHEGRNRQVRK 192

Query: 258 HALHMGC 264
               +G 
Sbjct: 193 MFEAVGF 199


>gi|327462027|gb|EGF08356.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1057]
          Length = 242

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++R G+V ++ + V +    ++SG  V +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIRQGKVSINGQVVCELATNVKSGDRVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVVE 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++         +        I K+Y + V G+   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM--IHPRNEIDKVYVARVKGLANKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
             +   L +   I G               A+  +++I    A+    +++  H GR HQ
Sbjct: 143 --VLRPLTRGIEIEGRKT----------KPAV--YEIIKVDPAKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFQAVG 197


>gi|160939069|ref|ZP_02086420.1| hypothetical protein CLOBOL_03963 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438032|gb|EDP15792.1| hypothetical protein CLOBOL_03963 [Clostridium bolteae ATCC
           BAA-613]
          Length = 262

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 88/250 (35%), Gaps = 51/250 (20%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLDR+      +     ++ +++ G+VR++ + VK  +R                  +
Sbjct: 16  PMRLDRFLAE-MGYGTRTQVKDMVKKGRVRMNGEAVKDADR-----------------KV 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E  I++            +S + Y   + Y+ NKP G+           + G ++  +
Sbjct: 58  NPESDIVEVD----------RSRVAYARMEYYMLNKPQGVVSATEDRKYPTVVGLIREAL 107

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                      RLD +T G+L++      A   L+     + + K+Y + V G       
Sbjct: 108 RK---DLFPVGRLDIDTEGLLLITNDGELAHNLLS---PKKHVDKVYLAHVSGGLPEDA- 160

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE--MQPHTGRTHQ 254
                 +K+   G          E G     +  K++     +    E  +    G+ HQ
Sbjct: 161 ------VKRFEEGIKL-------EDGTMTLPAELKILKGAGPEEDAQEVLVTIREGKFHQ 207

Query: 255 LRVHALHMGC 264
           ++     +GC
Sbjct: 208 IKRMFEALGC 217


>gi|326791171|ref|YP_004308992.1| pseudouridine synthase Rsu [Clostridium lentocellum DSM 5427]
 gi|326541935|gb|ADZ83794.1| pseudouridine synthase Rsu [Clostridium lentocellum DSM 5427]
          Length = 242

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 85/246 (34%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           +RLD++   H  +     +QKI+R  +V+VD + + K    + S                
Sbjct: 6   IRLDKYLV-HVGYGTRSTVQKIIRGKKVKVDGQVIIKPETAVNS---------------- 48

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       LT   +     + Y++   ++ NKP G       G    +   L+   
Sbjct: 49  ------------LTSVVEVNGERMDYQEFYHFILNKPRGYITATEDGRDQTVLDLLEER- 95

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             + ++     RLD++T G+L++      A  L      R + K+Y++ V G    +   
Sbjct: 96  -DQNKEVFPVGRLDKDTEGLLILTNDGKMAHGL--LSPKRHVDKVYYARVAGKMTEE--- 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                                   G  YA    ++I    +   +  +  H G+ HQ++ 
Sbjct: 150 -----------DIKMFAEGIALTDGTKYAPGKLEIIRSDEESEIY--VTIHEGKFHQVKR 196

Query: 258 HALHMG 263
               +G
Sbjct: 197 MVQAVG 202


>gi|327470426|gb|EGF15882.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK330]
          Length = 242

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++R G+V ++ + V+     I+SG  V +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIRQGKVSINGQVVRELATNIKSGDRVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVVE 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++         +        I K+Y + V G+   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM--IHPRNEIDKVYVARVKGLANKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
             +   L +   I G               A+  +++I    A+    +++  H GR HQ
Sbjct: 143 --VLRPLTRGIEIEGRKT----------KPAV--YEIIKVDPAKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFQAVG 197


>gi|313623106|gb|EFR93379.1| ribosomal large subunit pseudouridine synthase B [Listeria innocua
           FSL J1-023]
          Length = 244

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 84/246 (34%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   N     +    +K+++ G+V V+ K V                       + 
Sbjct: 2   ERLQKVIANA-GVTSRRKAEKLIQEGKVTVNGKVVT-----------------ELGVKVT 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             ++I    + LTK           E+ + ++F KP G      +         +  +  
Sbjct: 44  GTERIEVEGIQLTK-----------EEHRYFLFYKPRGTVS---AVTDDKGRTTVADYFT 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD +TSG+L++      A  L        + K Y + + GIP+ +   +
Sbjct: 90  DIPERLYPVGRLDYDTSGLLLMTNDGDFANLL--MHPKNEVSKTYIARIKGIPERE---V 144

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L +   I G      K   + ++ A           +    +E+  H GR  Q+R  
Sbjct: 145 IRELERGVVIDGRKTAPAKVKVRSSDKA-----------KDKAIVEITIHEGRNRQVRKM 193

Query: 259 ALHMGC 264
              +G 
Sbjct: 194 FEAVGF 199


>gi|313890958|ref|ZP_07824580.1| pseudouridylate synthase [Streptococcus pseudoporcinus SPIN 20026]
 gi|313120682|gb|EFR43799.1| pseudouridylate synthase [Streptococcus pseudoporcinus SPIN 20026]
          Length = 239

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 38/239 (15%), Positives = 81/239 (33%), Gaps = 41/239 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++ +V V+ K      +       +I P ++ +    
Sbjct: 1   MRLDKFLAEAGFG-SRSQVKNLLKTKKVCVNGKNESQAKK-------QINPNLDRVEVEG 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E                    +LYE+   Y+ NKP G+       +   +   L +   
Sbjct: 53  QE--------------------VLYEEFVYYMLNKPKGVVSATQDKVHQTVLDLLDATAK 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYW----------SLV 187
            K        RLD++T G+L++      A + L+    + ++               +  
Sbjct: 93  QKA--VFPVGRLDKDTHGLLLLTNNGDLAHRLLSPKKHVNKVYVAEVDGLMTSQDIEAFE 150

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
            GI  +  +C    L   +     +   VK   K   +      V+ C  +      ++
Sbjct: 151 KGIQLSDHQCQPAVLEILASDRDKFQSRVKIVIKEGKFHQVKRMVLACGKEVRDLQRLE 209


>gi|315658229|ref|ZP_07911101.1| pseudouridine synthase RluB [Staphylococcus lugdunensis M23590]
 gi|315496558|gb|EFU84881.1| pseudouridine synthase RluB [Staphylococcus lugdunensis M23590]
          Length = 247

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/235 (14%), Positives = 73/235 (31%), Gaps = 49/235 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+ + V     +++    V +  +                     
Sbjct: 21  SRRKAETLITEGKVKVNGEVVTELGTKVKPSDQVEVEGIKMEQ----------------- 63

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                       ED    +F+KPA +     S    H    +  +      +     RLD
Sbjct: 64  ------------EDKIYILFHKPAQVIT---SVSDDHGRTVVTDYFKDLDTRIYPVGRLD 108

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+L++        +L    R    +     L   + + + + +   +  +  +   
Sbjct: 109 YDTSGVLLLT-NDGEFTNLMTHPRYHIPKTYVAKLKGYLMREEVKTLEAGIELEDGLTQP 167

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               +K+ +K  N                  +E+    GR  Q+R    H G  +
Sbjct: 168 ATVKIKRQDKDKNT---------------TLVEITISEGRNRQVRRMFEHFGHSV 207


>gi|229822888|ref|ZP_04448958.1| hypothetical protein GCWU000282_00178 [Catonella morbi ATCC 51271]
 gi|229787701|gb|EEP23815.1| hypothetical protein GCWU000282_00178 [Catonella morbi ATCC 51271]
          Length = 290

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/250 (14%), Positives = 82/250 (32%), Gaps = 54/250 (21%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHII 78
           RL +    H    +    + ++  G+V V+ + V+    ++ S   + +           
Sbjct: 3   RLQKVMA-HAGIASRRKCESLITEGRVSVNGQTVRELGTQVSSKDRIEVD---------- 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                 +  E+ +  + NKP  +     +         +  ++ 
Sbjct: 52  -------------------GVPIYREEPRYILINKPRHVIS---AVSDDKNRQVILDYIQ 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE-C 197
              ++     RLD +T+G+L++    A A  L       +I K+Y + V GIP  K    
Sbjct: 90  GIEERIYPVGRLDYDTTGLLLLTNDGAFANQL--MHPRHQIDKVYVAKVKGIPSEKSLAR 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLR 256
           +   ++                  G   A +  +++          +E+    G  HQ++
Sbjct: 148 LEAGIVLD----------------GKKTAKAKAQLLSQNLDNQTAIVELTIREGWNHQVK 191

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 192 RMFEAVGHPV 201


>gi|225165626|ref|ZP_03727436.1| pseudouridine synthase, RluA family [Opitutaceae bacterium TAV2]
 gi|224800140|gb|EEG18559.1| pseudouridine synthase, RluA family [Opitutaceae bacterium TAV2]
          Length = 101

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 22/117 (18%), Positives = 46/117 (39%), Gaps = 16/117 (13%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS     +Y  V +     R D+     +P ++ V  Q+   +G VR   + +   + ++
Sbjct: 1   MSASNSSRYR-VPDAIRRERADKVLAAAFPELSRVAWQRSFDAGLVRRAGRVLDKKDEVR 59

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI 117
           +G+V+         + +                +  +   +L+ED  + V NK AG+
Sbjct: 60  AGEVLEFSHPETKPSEL---------------RAADIPLEILHEDEHLLVVNKAAGM 101


>gi|229074764|ref|ZP_04207783.1| Pseudouridine synthase [Bacillus cereus Rock4-18]
 gi|229096063|ref|ZP_04227037.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|229102175|ref|ZP_04232885.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
 gi|229115019|ref|ZP_04244430.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228668435|gb|EEL23866.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228681245|gb|EEL35412.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
 gi|228687355|gb|EEL41259.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|228708362|gb|EEL60516.1| Pseudouridine synthase [Bacillus cereus Rock4-18]
          Length = 242

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 85/253 (33%), Gaps = 56/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----NVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + + G    +K
Sbjct: 87  FFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANVL--MHPRYKVEKTYVAKIKGPLTGEK 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQ 254
                            +       +    A ++ K+I    +K    +++  H GR  Q
Sbjct: 145 I---------------RMLERGVTLEDGKTAPANVKIISWDKRKEMAIVQLTIHEGRNRQ 189

Query: 255 LRVHALHMGCPIV 267
           +R     + C +V
Sbjct: 190 VRRMFEALDCKVV 202


>gi|319949182|ref|ZP_08023271.1| pseudouridylate synthase [Dietzia cinnamea P4]
 gi|319437168|gb|EFV92199.1| pseudouridylate synthase [Dietzia cinnamea P4]
          Length = 252

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 81/252 (32%), Gaps = 45/252 (17%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D   +RL +         +    + ++  G+V VD K V+            +   ++  
Sbjct: 8   DGAPVRLQKILAQA-GVASRRASEDLIARGRVEVDGKIVR-----------EMGVKVDPA 55

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +I+                    I+L +       NKP G        +     G L 
Sbjct: 56  TAVIR---------------VDGTRIVLDDTLVHLALNKPRGYHTTMSDEMGRPCVGDLV 100

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           +     GQ+     RLD +T G+L+V      A  L        + K Y + V G+    
Sbjct: 101 ADRIDAGQRLFHVGRLDADTEGLLLVTNDGELAHRL--MHPSYEVSKTYMATVTGVVGKG 158

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                        IG      V+  +  A   +  F ++D        +++  H GR H 
Sbjct: 159 -------------IGKQLREGVELEDGPAK--VDQFSLLDVH-DGRSLVKVVLHEGRKHI 202

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 203 VRRLLAEVGHPV 214


>gi|16273162|ref|NP_439399.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae Rd KW20]
 gi|260581161|ref|ZP_05848981.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae RdAW]
 gi|1175857|sp|P45124|RSUA_HAEIN RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|1574175|gb|AAC22895.1| 16s pseudouridylate 516 synthase (rsuA) [Haemophilus influenzae Rd
           KW20]
 gi|260092189|gb|EEW76132.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae RdAW]
          Length = 232

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 82/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +R   V+++ + VK                      I 
Sbjct: 1   MRLDKFIAENV-GLTRSQATKAIRQSAVKINGEIVKS-----------------GSVQIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E +I      LT            E+ + ++ NKP G       G    I  F    + 
Sbjct: 43  QEDEIYFEDELLTWI----------EEGQYFMLNKPQGCVCSNDDGDYPTIYQFFDYPLA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 93  G---KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + +          +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPVEENYSAACAEGILLRGEKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|332359120|gb|EGJ36941.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK49]
          Length = 242

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 88/248 (35%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++R G+V ++ + V+     ++SG  V +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEDQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                  +  E+   Y+ NKP G+ S          +   L   
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDEKGRKTVVDLL--- 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSGIL++         +        I K+Y + V G+   +  
Sbjct: 88  -PQVKERIYPVGRLDWDTSGILILTNDGDFTDEM--IHPRNEIDKVYVARVKGLANKE-- 142

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
            +   L +   I G               A+  +++I    A+    +++  H GR HQ+
Sbjct: 143 -VLRPLTRGIEIEGRKT----------KPAV--YEIIKVDPAKNRSVVQLTIHEGRNHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KKMFQAVG 197


>gi|317506859|ref|ZP_07964631.1| RNA pseudouridylate synthase [Segniliparus rugosus ATCC BAA-974]
 gi|316254787|gb|EFV14085.1| RNA pseudouridylate synthase [Segniliparus rugosus ATCC BAA-974]
          Length = 278

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 46/257 (17%), Positives = 80/257 (31%), Gaps = 33/257 (12%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V   ++  RL +         +    ++++  G+V VD + V     ++ G  V      
Sbjct: 12  VGGGDKAQRLHKVLARA-GVASRRGAEQLIAEGRVVVDGRLV-----VEQGMQVD----- 60

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                      +++         D   + LL         NKP G+           +  
Sbjct: 61  -------PATAVVEVDGKRVAVDDRHATYLL---------NKPKGVVTAMSDQRERCVGD 104

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L+   D          RLD +T+G+L+V+     A  L        I K Y + V G  
Sbjct: 105 LLREQPDLPA-GLFHVGRLDADTTGLLLVSNDGELAHRLA--HPSYEIPKTYLATVRGAV 161

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA-ISHFKVIDCFAQKFCWLEMQPHTG 250
              K  +       S   G         +  A  A +   +           +E+  H G
Sbjct: 162 --GKGALDALRRGVSLEDGPARADAVAVKGEARPAPLRKAQTGHASGGARSVVEITLHEG 219

Query: 251 RTHQLRVHALHMGCPIV 267
           R   +R     +G P+V
Sbjct: 220 RNRIVRRMFDAVGHPVV 236


>gi|118470853|ref|YP_888039.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           smegmatis str. MC2 155]
 gi|118172140|gb|ABK73036.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           smegmatis str. MC2 155]
          Length = 247

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 42/253 (16%), Positives = 75/253 (29%), Gaps = 45/253 (17%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +E+ +RL +         +    ++++  G+V VD + V                    
Sbjct: 2   AEEQGVRLQKVLSQA-GIASRRVAERMIIDGRVEVDGQIVT------------------- 41

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                  +        +         I+L +       NKP G+             G L
Sbjct: 42  -------ELGTRVDPAVADIRVDGSRIILDDTMVYLAINKPRGMHSTMSDDRGRPCVGDL 94

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                   +K     RLD +T G+L++      A  L        + K Y + V G    
Sbjct: 95  VEHRVRGNKKLFHVGRLDADTEGLLLLTNDGELAHRL--MHPSFEVPKTYVATVMG---- 148

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               +   L KK   G +               +  F V+D    K   +++  H GR  
Sbjct: 149 ---TVPRGLGKKLKAGVEL--------DDGPAHVDDFAVVDTVPGK-TMVKVTLHEGRNR 196

Query: 254 QLRVHALHMGCPI 266
            +R     +  P+
Sbjct: 197 IVRRLLAAVDFPV 209


>gi|311068833|ref|YP_003973756.1| RluB protein [Bacillus atrophaeus 1942]
 gi|310869350|gb|ADP32825.1| RluB [Bacillus atrophaeus 1942]
          Length = 244

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 88/251 (35%), Gaps = 52/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +++++ G+V+V+ K +     ++     + +  +      I
Sbjct: 2   ERLQKVIA-HAGVASRRKAEELIKEGKVKVNGKIITELGVKVTGSDQIEVNGM-----KI 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +E+ +                         ++  KP G+     +         +  + 
Sbjct: 56  EREEPV------------------------YFLLYKPRGVIS---AADDDKGRKVVTDFF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               Q+     RLD +TSG+L++      A  L       +I K Y + V GIP  +   
Sbjct: 89  KEIPQRIYPIGRLDYDTSGLLLLTNDGDFANKL--MHPKYQIDKTYVAKVKGIPSKE--- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLR 256
               L++K   G           +    A +  K++    +K    +++  H GR  Q+R
Sbjct: 144 ----LVRKLERGVQL--------EEGKTAPAKAKLLSLDKRKQTSIIQLTIHEGRNRQVR 191

Query: 257 VHALHMGCPIV 267
                +G  ++
Sbjct: 192 RMFEAIGHEVL 202


>gi|221142152|ref|ZP_03566645.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus str.
           JKD6009]
          Length = 183

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/163 (18%), Positives = 63/163 (38%), Gaps = 19/163 (11%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           +   H    +   +  I  +G + V+ + V    ++ +  ++ I        H+ +E   
Sbjct: 16  FLARH--DFSKKTVSAIKNNGALIVNDEPVTVRKQLMTNDILEI--------HLPRE--- 62

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH---IDGFLKSWVDSK 140
              SVNL  ++  L+  +LYED+ I +  KP   +        +               +
Sbjct: 63  -IPSVNLIPYARKLE--VLYEDAFIIIVTKPNNQNCTPSREHPHESLIEQVLYHCQEHGE 119

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
              P +  RLD+ T+GI++ A+        ++    + I  +Y
Sbjct: 120 NINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKVNLKKYILALY 162


>gi|65318840|ref|ZP_00391799.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Bacillus anthracis str.
           A2012]
          Length = 242

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 84/253 (33%), Gaps = 56/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   KRLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----SVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + + G    +K
Sbjct: 87  FSPEITQRLFPIGRLDYDTSGVLLMTNDGDFANVL--MHPRYKVEKTYVAKIKGPLTGEK 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQ 254
                            +       +    A +  K+I    +K    +++  H GR  Q
Sbjct: 145 I---------------RMLERGVTLEDGKTAPARVKIISWDKRKEMAIVQLTIHEGRNRQ 189

Query: 255 LRVHALHMGCPIV 267
           +R     + C +V
Sbjct: 190 VRRMFEALDCKVV 202


>gi|172040768|ref|YP_001800482.1| putative pseudouridylate synthase [Corynebacterium urealyticum DSM
           7109]
 gi|171852072|emb|CAQ05048.1| putative pseudouridylate synthase [Corynebacterium urealyticum DSM
           7109]
          Length = 291

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 89/254 (35%), Gaps = 45/254 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
              E+ +RL +         +    +K++ +G+V V+ K V      + G  VRI P  +
Sbjct: 45  PAAEDKVRLQKVLAAA-GVASRRMSEKLIAAGRVEVNGKVVD-----RMG--VRIDPNKD 96

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
            +       ++ D                       Y+FNKP G+       +     G 
Sbjct: 97  VVRVDGVRVQVNDE-------------------MHYYIFNKPRGVQSTMSDDMGRPSVGN 137

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                  +GQ      RLD +T G+L++      A  L        + K Y + V G  +
Sbjct: 138 FIDERLKQGQGLFHVGRLDAQTEGLLLLTNDGELANRL--MHPSYEVSKTYMATVLG--E 193

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            KK  +           G    + K ++          +++D + Q    ++++ H GR 
Sbjct: 194 AKKGLVHELKKGIELDDG----IAKADD---------VQIVDVW-QGKSLIKLELHEGRK 239

Query: 253 HQLRVHALHMGCPI 266
           H +R      G P+
Sbjct: 240 HIVRRLLKAAGFPV 253


>gi|328467476|gb|EGF38547.1| pseudouridine synthase [Lactobacillus rhamnosus MTCC 5462]
          Length = 135

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 52/135 (38%), Gaps = 21/135 (15%)

Query: 24  WFKNHYPHINFVNLQKI-LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           + K      +   L+K+  + G + V+K++      +++G  + +              +
Sbjct: 17  FLKQQ--GFSRAQLKKLRYQGGFIFVNKRQRHTAYPLRNGDRILV--------------Q 60

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWV---D 138
                   +      +  + YED    V NKPAG++     G     +   +K+++    
Sbjct: 61  TAPEQAAASVVPYEHEFPICYEDDDYLVVNKPAGVASIPAVGRRNDSMANMVKAYLIKTH 120

Query: 139 SKGQKPRLTHRLDQE 153
           ++ Q   +  RLD++
Sbjct: 121 AESQAVHVVTRLDRD 135


>gi|226324970|ref|ZP_03800488.1| hypothetical protein COPCOM_02762 [Coprococcus comes ATCC 27758]
 gi|225206318|gb|EEG88672.1| hypothetical protein COPCOM_02762 [Coprococcus comes ATCC 27758]
          Length = 95

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 7/81 (8%)

Query: 89  NLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSG--IAYHIDGFLKSWVDSKG----- 141
                 + +   +LYED  I V NKP G+ V   +G      ++  +    D        
Sbjct: 3   EPDILPENIPLDILYEDDDILVVNKPKGMVVHPAAGHYTGTLVNAIMYHCKDRLSGINGV 62

Query: 142 QKPRLTHRLDQETSGILVVAR 162
            +P + HR+D +T+G L+V +
Sbjct: 63  MRPGIVHRIDMDTTGSLLVCK 83


>gi|325688986|gb|EGD30994.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK115]
          Length = 242

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 86/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQLLKKGLVLVNGRAEKS----------------PKTQIDE 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              +I+ S   LT           YE    Y+ NKP G+           +   L     
Sbjct: 44  TADEIIVSGQRLT-----------YEKFVYYLLNKPQGVISATEDDRHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+     E 
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHVMLS---PKKHVEKIYRAQVAGLMNQADE- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLR 256
                         +   ++  +     A    K+++   A++   +E+    G+ HQ++
Sbjct: 147 ------------ERFAAGIELKDFTCQPA--QLKILELDEAKETSLVEITLAEGKFHQVK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVASCG 199


>gi|16801129|ref|NP_471397.1| hypothetical protein lin2063 [Listeria innocua Clip11262]
 gi|16414564|emb|CAC97293.1| lin2063 [Listeria innocua Clip11262]
 gi|313618115|gb|EFR90216.1| ribosomal large subunit pseudouridine synthase B [Listeria innocua
           FSL S4-378]
          Length = 244

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 84/246 (34%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   N     +    +K+++ G+V V+ K V                       + 
Sbjct: 2   ERLQKVIANA-GVTSRRKAEKLIQEGKVTVNGKVVT-----------------ELGVKVS 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             ++I    + LTK           E+ + ++F KP G      +         +  +  
Sbjct: 44  GTERIEVEGIQLTK-----------EEHRYFLFYKPRGTVS---AVTDDKGRTTVADYFT 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD +TSG+L++      A  L        + K Y + + GIP+ +   +
Sbjct: 90  DIPERLYPVGRLDYDTSGLLLMTNDGDFANLL--MHPKNEVSKTYIARIKGIPERE---V 144

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L +   I G      K   + ++ A           +    +E+  H GR  Q+R  
Sbjct: 145 IRELERGVVIDGRKTAPAKVKVRSSDKA-----------KDKAIVEITIHEGRNRQVRKM 193

Query: 259 ALHMGC 264
              +G 
Sbjct: 194 FEAVGF 199


>gi|83590199|ref|YP_430208.1| ribosomal large subunit pseudouridine synthase B [Moorella
           thermoacetica ATCC 39073]
 gi|83573113|gb|ABC19665.1| ribosomal large subunit pseudouridine synthase B [Moorella
           thermoacetica ATCC 39073]
          Length = 240

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 79/250 (31%), Gaps = 50/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRL ++        +    + ++R+G+VRV+ + +K    +++ GQ              
Sbjct: 1   MRLQKYLA-LAGVASRRRAEDLIRAGRVRVNGRVIKVMGVQVEPGQ-------------- 45

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                         K +   + +   E     +  KPAG                    V
Sbjct: 46  -------------DKVTVDGQPVTGPERKYYLLLFKPAGYVTTVSDPRGRPKVT---DLV 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD  T G+L++         LT       + K Y +LV GIP      
Sbjct: 90  HGIPARLYPVGRLDYATEGLLLLTNDGELTLRLT--HPRYGVTKTYLALVRGIPDA---- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                   + I      V  ++   A   +     +    +    LE+    GR  ++R 
Sbjct: 144 --------NTIQHLRCGVKLEDGPTAPARV----NLCRAGKDSALLELTLREGRNREVRR 191

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 192 MLAAVGHPVL 201


>gi|309775612|ref|ZP_07670612.1| ribosomal small subunit pseudouridine synthase A
           [Erysipelotrichaceae bacterium 3_1_53]
 gi|308916706|gb|EFP62446.1| ribosomal small subunit pseudouridine synthase A
           [Erysipelotrichaceae bacterium 3_1_53]
          Length = 233

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 38/248 (15%), Positives = 87/248 (35%), Gaps = 58/248 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVRIPPVINALNH 76
           MRLD++   H  + +   +++ +R G VR+++    K + RIQ G  VV +         
Sbjct: 1   MRLDKYLA-HAGYGSRKEVKQAIRKGLVRINEVECRKDDTRIQEGIDVVCVN-------- 51

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   ++YE     + NKP  +           +   + + 
Sbjct: 52  ---------------------GEEVVYEAVVYIMLNKPQDVVSATSDPTHETVLDCIDAI 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +           RLD +T G+L++    + A + L+   +   ++  +  L   + +  K
Sbjct: 91  LPRDC---FPVGRLDIDTEGLLLITNDGKLAHRLLSP--KNHVVKTYFVQLAKPLQEADK 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           + + +  +               +E+    A    ++++        + +    GR HQ+
Sbjct: 146 KRLEDGSI-------------VLDEEPVQCA--RVELLE-----ETQILLHIQEGRFHQV 185

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 186 KRMLHAVG 193


>gi|225021516|ref|ZP_03710708.1| hypothetical protein CORMATOL_01537 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945898|gb|EEG27107.1| hypothetical protein CORMATOL_01537 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 241

 Score = 67.7 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 54/250 (21%), Positives = 87/250 (34%), Gaps = 49/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL +         +  N + ++ SG+V V+   V     +Q G  VR+ P ++ +    
Sbjct: 1   MRLQKVLAQA-GVASRRNAEIMIDSGRVEVNGAVV-----MQQG--VRVNPEVDVI---- 48

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              ++    VN+  +  +             V NKP GI       +     G L S   
Sbjct: 49  ---RVDGVRVNVNNNHQYF------------VLNKPRGIHSTMSDDLGRPCIGDLVSERI 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-EC 197
           S GQ      RLD +T G++++      A  L+       + K Y + V G         
Sbjct: 94  SAGQGLFHVGRLDADTEGLILLTNDGELANRLS--HPKYEVSKTYIAEVLGEADRSLVTT 151

Query: 198 IANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           + N + L       DYV +V                     Q    + +Q H GR H +R
Sbjct: 152 LKNGVELDDGPAAADYVQIVDV------------------HQGRSLVRVQLHEGRKHIVR 193

Query: 257 VHALHMGCPI 266
                 G P+
Sbjct: 194 RMLKAAGYPV 203


>gi|240173130|ref|ZP_04751788.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           kansasii ATCC 12478]
          Length = 250

 Score = 67.7 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 74/249 (29%), Gaps = 45/249 (18%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RL +         +    +K++  G+V VD K V             +   ++    +
Sbjct: 9   GIRLQKVLSQA-GIASRRAAEKMIIDGRVEVDGKLVT-----------ELGTRVDPDVSV 56

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I+                    ++L E       NKP G+             G L    
Sbjct: 57  IR---------------VDGARVVLDESLVYLALNKPRGMHSTMADDRGRPCIGDLIERK 101

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +      RLD +T G++++      A  L        + K Y + V G        
Sbjct: 102 VRGNKNLFHVGRLDADTEGLILLTNDGELAHRL--MHPSHEVPKTYLATVAG-------T 152

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   L KK   G +               +  F V+D    K   + +  H GR   +R 
Sbjct: 153 VPRGLGKKLRTGIEL--------DDGLARVDGFAVVDAIPGK-TLVRVTLHEGRNRIVRR 203

Query: 258 HALHMGCPI 266
                G P+
Sbjct: 204 LLAAAGFPV 212


>gi|315929948|gb|EFV09105.1| Ribosomal large subunit pseudouridine synthase C [Campylobacter
           jejuni subsp. jejuni 305]
          Length = 112

 Score = 67.7 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 14/86 (16%)

Query: 228 SHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC------------- 273
           + F++++ F +     L  +P TGR HQ+RVH  +    I+GD  Y              
Sbjct: 5   TEFEILEYFPKINATLLLCKPLTGRQHQIRVHLHYKNHTILGDPLYGLSKQQIESILDEK 64

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPH 299
            N K         +L LH+  +   +
Sbjct: 65  LNPKERLKLTGALRLCLHSYRLKFQY 90


>gi|325690957|gb|EGD32957.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK115]
          Length = 242

 Score = 67.7 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    ++++R G+V ++ + V+     ++SG  V +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++         +        I K+Y + V G+   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM--IHPRNEIDKVYVARVKGLANKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
             +   L +   I G               A+  +++I    A+    +++  H GR HQ
Sbjct: 143 --VLRPLTRGIEIEGRKT----------QPAV--YEIIKVDPAKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFQAVG 197


>gi|331701399|ref|YP_004398358.1| pseudouridine synthase Rsu [Lactobacillus buchneri NRRL B-30929]
 gi|329128742|gb|AEB73295.1| pseudouridine synthase Rsu [Lactobacillus buchneri NRRL B-30929]
          Length = 242

 Score = 67.7 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 46/249 (18%), Positives = 86/249 (34%), Gaps = 52/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++  G V+V+ + VK    ++     V++          
Sbjct: 4   ERLQKVIA-HAGVASRRKAEELIAKGHVKVNGEVVKELGTKVTPNDEVKVD--------- 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       +    +     LLY         KP G+          H    +   +
Sbjct: 54  -----------EVPISKEAPVYYLLY---------KPRGVIT--AVTDDKHRKTVV-DIL 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +   ++     RLD +TSG+L++         LT       ++K Y + V GI  N    
Sbjct: 91  EEVPERIYPVGRLDYDTSGLLLLTNDGDLDNKLT--HPKYEVEKTYVAKVKGIVTNDD-- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                LK    G     VV ++ K A  A +    +    +    +++  H GR HQ++ 
Sbjct: 147 -----LKHLRTG-----VVIEHRKTAK-AKTK---LIRTNKDSSIVQLTIHEGRNHQVKN 192

Query: 258 HALHMGCPI 266
               +G P+
Sbjct: 193 MFEKIGYPV 201


>gi|220931567|ref|YP_002508475.1| ribosomal large subunit pseudouridine synthase B [Halothermothrix
           orenii H 168]
 gi|219992877|gb|ACL69480.1| ribosomal large subunit pseudouridine synthase B [Halothermothrix
           orenii H 168]
          Length = 237

 Score = 67.7 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 50/253 (19%), Positives = 84/253 (33%), Gaps = 55/253 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++   H    +    +KI+  G+V+V+ K V                       I 
Sbjct: 2   ERLQKYMA-HAGVASRRKSEKIITQGRVKVNGKIVT-----------------ELGTKID 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            ++ I++    +     ++            + NKP G I+          + G +K   
Sbjct: 44  PDKDIVEVDGRVISKEKYV----------YILLNKPVGYITSVSDPHGRKTVTGLIK--- 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--K 195
               Q+     RLD +TSG+L++         LT       ++K Y   V G P ++  K
Sbjct: 91  -GVSQRIYPVGRLDYDTSGLLILTNDGELTYVLT--HPSHMVEKTYRVEVKGFPSDEVLK 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           +      LK        V  VK+ EK                       +  H GR  Q+
Sbjct: 148 KLETGVKLKDGLTAPARVSAVKRKEKN------------------TIFNLTIHEGRNRQV 189

Query: 256 RVHALHMGCPIVG 268
           R     +G P+V 
Sbjct: 190 RRMCDKIGFPVVN 202


>gi|329770321|ref|ZP_08261705.1| hypothetical protein HMPREF0433_01469 [Gemella sanguinis M325]
 gi|328836745|gb|EGF86399.1| hypothetical protein HMPREF0433_01469 [Gemella sanguinis M325]
          Length = 143

 Score = 67.7 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 27/143 (18%), Positives = 59/143 (41%), Gaps = 17/143 (11%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
            + K    +++ + +Q    +  + V+    K N  +    V+ +   ++  N++  +  
Sbjct: 18  NFLKISKKNLHTIRMQTHQDNNTILVNNDIAKLNTSLAKNDVLELNIELSKSNYLTNK-- 75

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
               S+++TK          YED  + + +KP GI            D  L +++ S  Q
Sbjct: 76  ----SISITKE---------YEDPYLLIVSKPFGIKTHPNDISIE--DDTLVNYLISDYQ 120

Query: 143 KPRLTHRLDQETSGILVVARTRA 165
                HRLD +T G+++ ++   
Sbjct: 121 YLEPIHRLDIDTCGLVIFSKNNH 143


>gi|260186664|ref|ZP_05764138.1| hypothetical protein MtubCP_11646 [Mycobacterium tuberculosis
           CPHL_A]
 gi|289447326|ref|ZP_06437070.1| conserved hypothetical protein [Mycobacterium tuberculosis CPHL_A]
 gi|289420284|gb|EFD17485.1| conserved hypothetical protein [Mycobacterium tuberculosis CPHL_A]
          Length = 254

 Score = 67.7 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 73/250 (29%), Gaps = 47/250 (18%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RL +         +    +K++  G+V VD   V             +   ++    +
Sbjct: 13  GIRLQKVLSQA-GIASRRAAEKMIVDGRVEVDGHVVT-----------ELGTRVDPPVAV 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           ++                    ++L +       NKP G+             G L    
Sbjct: 61  VR---------------VDGARVVLDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERK 105

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
               +K     RLD +T G++++      A  L        + K Y + V G +P+    
Sbjct: 106 VRGTKKLFHVGRLDADTEGLMLLTNDGELAHRL--MHPSHEVPKTYLATVTGSVPRGLGR 163

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +   +                        +  F V+D    K   + +  H GR   +R
Sbjct: 164 TLRAGIELDD----------------GPAFVDDFAVVDAIPGK-TLVRVTLHEGRNRIVR 206

Query: 257 VHALHMGCPI 266
                 G P+
Sbjct: 207 RLLAAAGFPV 216


>gi|121533339|ref|ZP_01665167.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
 gi|121307898|gb|EAX48812.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
          Length = 245

 Score = 67.7 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 50/300 (16%), Positives = 98/300 (32%), Gaps = 82/300 (27%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+    H  + +   ++K++++ +V V+   V+                 +   H+ 
Sbjct: 7   QRLDKVLA-HLGYGSRREIKKMVKAERVIVNGAVVR-----------------DPELHVF 48

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q  ++               + Y +    + NKP G+           +   L+   +
Sbjct: 49  PWQDRIEVDGEP----------IHYREYIYLMMNKPQGVLSATEDAAGKVVVDLLR--PE 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K   P    RLD++T G+L++      A  L      + + K Y++ V G         
Sbjct: 97  HKAFAPFPVGRLDKDTEGLLLLTNDGQLAHRL--LAPKKHVPKRYYARVKG--------- 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYA-ISH---FKVIDC-----FAQKFCWLEMQPHT 249
                           VV   +KGA  A I+    ++ +        A     +E+  + 
Sbjct: 146 ----------------VVTDEDKGAFQAGITLDDGYRTLPAELTILHAGPVSEVELVIYE 189

Query: 250 GRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITA 309
           G+ HQ++      G                 T     +L + A  +D     G   ++TA
Sbjct: 190 GKFHQVKRMFAARG----------------KTVTYLKRLAMGALVLDEKLAPGEYRELTA 233


>gi|40890007|pdb|1VIO|A Chain A, Crystal Structure Of Pseudouridylate Synthase
 gi|40890008|pdb|1VIO|B Chain B, Crystal Structure Of Pseudouridylate Synthase
          Length = 243

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 82/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++   +   +      K +R   V+++ + VK                      I 
Sbjct: 3   LRLDKFIAENV-GLTRSQATKAIRQSAVKINGEIVKS-----------------GSVQIS 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E +I      LT            E+ + ++ NKP G       G    I  F    + 
Sbjct: 45  QEDEIYFEDELLTWI----------EEGQYFMLNKPQGCVCSNDDGDYPTIYQFFDYPLA 94

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 95  G---KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 138

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + +          +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 139 ADPVEENYSAACAEGILLRGEKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 191

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 192 FAALGNKVVG 201


>gi|229166414|ref|ZP_04294170.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228616988|gb|EEK74057.1| Pseudouridine synthase [Bacillus cereus AH621]
          Length = 242

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 44/255 (17%), Positives = 89/255 (34%), Gaps = 60/255 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----NVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + + G      
Sbjct: 87  FFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANVL--MHPRYKVEKTYVAKIKG------ 138

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRT 252
                       + G+ + ++++    +    A +  K+I    +K    +++  H GR 
Sbjct: 139 -----------PLTGEKIRMLERGVALEDGKTAPAQAKIISWDKRKEMAIVQLTIHEGRN 187

Query: 253 HQLRVHALHMGCPIV 267
            Q+R     + C +V
Sbjct: 188 RQVRRMFEALDCKVV 202


>gi|319955817|ref|YP_004167080.1| RNA-binding s4 domain protein [Nitratifractor salsuginis DSM 16511]
 gi|319418221|gb|ADV45331.1| RNA-binding S4 domain protein [Nitratifractor salsuginis DSM 16511]
          Length = 263

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 46/255 (18%), Positives = 92/255 (36%), Gaps = 37/255 (14%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72
            +EE MRL+++  ++ P  +  +  K++  G V V++  VK F  +++    V +     
Sbjct: 3   QNEEGMRLNKYISHNTP-YSRRDADKLIEEGLVTVNRLPVKDFGYKVRPEDKVAV---RG 58

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
            L H  K  ++                        + V+NKP G+ V   +         
Sbjct: 59  KLIHPRKRGEVT-----------------------MVVYNKPRGVLV---TKRDDRGRTT 92

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   +  K +      RLD  + G+L++      A  L  S   R         +   P+
Sbjct: 93  IYHKLPGKFRHFIPVGRLDYASEGLLLLTDNPEVADVLMGSKLPRTYNLKIDKPL--TPE 150

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +K      +L+ +  GG     + + E      +  ++     + K   L +    G+ 
Sbjct: 151 MEKAMKEGLILEDAREGGHKESEITRMEFAPFLEV-QYR---GQSGKNTKLRVTIAEGKN 206

Query: 253 HQLRVHALHMGCPIV 267
            +LR    H G  ++
Sbjct: 207 RELRRFFGHFGAKVL 221


>gi|291550320|emb|CBL26582.1| ribosomal small subunit pseudouridine synthase A [Ruminococcus
           torques L2-14]
          Length = 241

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 97/247 (39%), Gaps = 53/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +         ++K +  GQVRV+++ VK                        
Sbjct: 3   LRLDKYLADMGIG-TRTEVKKAITKGQVRVNEETVK------------------------ 37

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + +  +D+  +   +   + +   YE    Y+ NKPAG+     S      D  +   +D
Sbjct: 38  RPEIKIDTEKDHVFYQGQMVAYAEYE---YYMLNKPAGVV----SATEDKNDSTVLDLID 90

Query: 139 SKGQK-PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            K +K      RLD++T G+L++      A Q L+     + + K+Y++ + G    +  
Sbjct: 91  EKQRKDLFPVGRLDKDTEGLLLITNDGELAHQLLS---PKKHVDKVYFARIDGKVTEED- 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 +++   G +        EK    A  H +++    ++   + +    G+ HQ++
Sbjct: 147 ------VRRFAEGLEI-----GEEKPTLPA--HLEILKR--EEISEIRLTIREGKFHQVK 191

Query: 257 VHALHMG 263
                +G
Sbjct: 192 RMFHAVG 198


>gi|307705665|ref|ZP_07642514.1| conserved hypothetical protein [Streptococcus mitis SK597]
 gi|307620791|gb|EFN99878.1| conserved hypothetical protein [Streptococcus mitis SK597]
          Length = 240

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 85/246 (34%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q  + +             
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQIDEKID------------ 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                            F   +L YE+   Y+ NKP G+           +   L     
Sbjct: 47  --------------EIRFDGQVLEYEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDIAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           SK  +     RLD +T G+L++    + A   L+     R + K Y + V GI   +   
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNDGKLAHDLLS---PKRHVDKTYLAQVKGIMTQEDVE 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   +   +     A      ID   +    + +    G+ HQ++ 
Sbjct: 148 T-------------FAKGIPLKDFTCKPARLELVSIDA-EKNQSQIRVTIAEGKFHQVKR 193

Query: 258 HALHMG 263
              + G
Sbjct: 194 MVGYCG 199


>gi|72161610|ref|YP_289267.1| pseudouridine synthase, Rsu [Thermobifida fusca YX]
 gi|71915342|gb|AAZ55244.1| pseudouridine synthase, Rsu [Thermobifida fusca YX]
          Length = 375

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 87/251 (34%), Gaps = 49/251 (19%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RL +         +    ++++ +G+V VD + V+     + G  V            
Sbjct: 134 GIRLQKALAQA-GVASRRACEELIAAGRVSVDGQIVR-----RFGARV------------ 175

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                        ++       ++  ++ + Y  NKP G+             G   + +
Sbjct: 176 ---------DPEKSEIRVDGMRVVTSQNLRYYALNKPRGVVSTMFDPEGRPTIGDYAAQI 226

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +T G++++      A  LT      ++ K Y + V G        
Sbjct: 227 GPIEERLFHVGRLDTDTEGLILLTNDGELANRLT--HPRYKVTKTYLAKVPG-------- 276

Query: 198 IANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                     +  D +  +++  +       +  F+VID   +    +E++ H GR H +
Sbjct: 277 ---------PVPRDVIRQIRKGVELDDGFVKVDSFRVIDNI-EPKALVEIRLHEGRKHIV 326

Query: 256 RVHALHMGCPI 266
           R     +G P+
Sbjct: 327 RRLMKAVGHPV 337


>gi|299535393|ref|ZP_07048715.1| putative RNA pseudouridine synthase ytzF [Lysinibacillus fusiformis
           ZC1]
 gi|298729154|gb|EFI69707.1| putative RNA pseudouridine synthase ytzF [Lysinibacillus fusiformis
           ZC1]
          Length = 237

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 94/248 (37%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++++L+   V VD   VK                 +A  H+ 
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKQLLKQKAVTVDGAYVK-----------------DAALHVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ+I+                ++Y +   ++ NKP G+     S      D  +   ++
Sbjct: 43  PEQQIVS----------VFGERVVYTEFVYFIMNKPPGVI----SATEDLRDETVIDLLE 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              Q   P    RLD++T G+L++      A   L+     + + K+Y++ + G+   + 
Sbjct: 89  PLHQHFQPFPVGRLDKDTEGLLLLTNDGHLAHNLLS---PKKHVPKVYYAQIEGVVTEE- 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
               +     + I  D  +V K             K++   + +   +E+    G+ HQ+
Sbjct: 145 ----DAEKFANGIELDDGYVTKPG-----------KLVILKSAQQSEIELTIQEGKFHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KRMFEAVG 197


>gi|312127407|ref|YP_003992281.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
 gi|311777426|gb|ADQ06912.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
          Length = 240

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 88/250 (35%), Gaps = 49/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL ++        +    ++I+  G+V+V+ K V                       + 
Sbjct: 5   VRLQKFMA-QCGVASRRKCEEIILQGRVKVNGKLVN-----------------QLGFKVD 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ +++           L+   +Y      + NKP G+     +         +    D
Sbjct: 47  PEKDVVEVDGKRI----SLQRQKVY-----IMLNKPFGVIS--SAKDEKGRKTVVDLVKD 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-EC 197
               +     RLD +T+G++++      A  +T       I+K Y +L+ GIP  ++ E 
Sbjct: 96  KVNVRVFPVGRLDFDTTGLILLTNDGEFAYKVT--HPKHDIEKTYIALIKGIPSKEEIER 153

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               LL    +                 A + FK++         +E++ H GR  Q+R 
Sbjct: 154 FEKGLLIDGKM----------------TAPAKFKILKLINGNA-LVEIKIHEGRNRQIRK 196

Query: 258 HALHMGCPIV 267
               +G  ++
Sbjct: 197 MCDQIGHKVL 206


>gi|312793758|ref|YP_004026681.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312180898|gb|ADQ41068.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 240

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 88/250 (35%), Gaps = 49/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL ++        +    ++I+  G+V+V+ K V                       + 
Sbjct: 5   VRLQKYMA-QCGIASRRKCEEIILQGRVKVNGKTVN-----------------QLGFKVD 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ +++           L+   +Y      + NKP G+     +         +    D
Sbjct: 47  PEKDVVEVDGKRI----TLQMQKVY-----IMLNKPFGVIS--SAKDEKGRKTVVDLVKD 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-EC 197
               +     RLD +T+G++++      A  +T       I+K Y +L+ GIP  ++ E 
Sbjct: 96  KVNVRVFPVGRLDFDTTGLILLTNDGEFAYKVT--HPKHDIEKTYIALIRGIPSKEEIER 153

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               LL    +                 A + FK++         +E++ H GR  Q+R 
Sbjct: 154 FEKGLLIDGKM----------------TAPAKFKILKLINGNA-LVEIKIHEGRNRQIRK 196

Query: 258 HALHMGCPIV 267
               +G  ++
Sbjct: 197 MCDQIGHEVL 206


>gi|227890506|ref|ZP_04008311.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           salivarius ATCC 11741]
 gi|227867444|gb|EEJ74865.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           salivarius ATCC 11741]
          Length = 238

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 87/245 (35%), Gaps = 52/245 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG---QVVRIPPVINALN 75
           MRLD++             +K++++ +VR++ + VK + +I+       + +   + ALN
Sbjct: 1   MRLDKFLSQTGK-FTRAEAKKVIKAKRVRLNGEVVK-DGKIKINEDSDKIFLDGELLALN 58

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           +                                Y+ NKPAG+           +   +  
Sbjct: 59  N----------------------------KEVYYMLNKPAGVVSATRDDKDKTVIDLIN- 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               + +      RLD++T+G+L++    + A   ++     + + K Y ++V G    K
Sbjct: 90  -FPGRKEDLFPVGRLDKDTTGLLIITNDGKFAHNIIS---PKKHVSKTYEAVVTGKISEK 145

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I +  ++ ++        +           S  +VI              H G+ HQ
Sbjct: 146 EVKIFSQGMELANGDKLQPAQLDIISYSEKDDTSKVRVI-------------IHEGKYHQ 192

Query: 255 LRVHA 259
           +R   
Sbjct: 193 VRRMF 197


>gi|288556014|ref|YP_003427949.1| pseudouridylate synthase [Bacillus pseudofirmus OF4]
 gi|288547174|gb|ADC51057.1| pseudouridylate synthase [Bacillus pseudofirmus OF4]
          Length = 242

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 93/252 (36%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    + ++  G+V+V+ + V+     + G  V++ P         
Sbjct: 2   ERLQKVIAQA-GITSRRKAETMITEGKVKVNGQVVR-----ELG--VKVNPN-------- 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSW 136
            + +I    V + K           E+   Y+  KP G+  SV+   G     D      
Sbjct: 46  -KDEIEVEGVPIDK-----------EEPVYYLMYKPQGVISSVKDEKGRKVVTDFL---- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-- 194
                Q+     RLD +TSG++++      A  L       +I K+Y + V GIP  +  
Sbjct: 90  --EIEQRVFPIGRLDYDTSGLILLTNDGEFANQL--MHPKFKIDKVYVAKVKGIPARESL 145

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K+     +L+        V +V  ++K    AI               +++  H GR  Q
Sbjct: 146 KKLQHGVVLEDGKTAPAKVKLVSMDKK-KQTAI---------------VQLTIHEGRNRQ 189

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 190 VRRMFEAIGHPV 201


>gi|169334035|ref|ZP_02861228.1| hypothetical protein ANASTE_00428 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258752|gb|EDS72718.1| hypothetical protein ANASTE_00428 [Anaerofustis stercorihominis DSM
           17244]
          Length = 238

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 93/252 (36%), Gaps = 48/252 (19%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           EE MR++++  +     +    ++I+  G+V V+ + V+     + G ++ +   +  + 
Sbjct: 2   EEKMRINKYLAS-CGVASRRKCEEIISRGKVTVNGEVVR-----ELGTIINVEKDLVKV- 54

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                               + K + L      Y+ NKP G+     S      +  +  
Sbjct: 55  --------------------YGKEVSLDTKKVYYMLNKPQGVISASKSKYG---EETVVD 91

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  K  +     RLD++T+G++++      A  LT     +  +K Y +LV G   +K 
Sbjct: 92  LLGKKEHRLFPVGRLDKDTTGLIILTNDGDFAYKLTHPKYEK--EKTYEALVKGKVDSKS 149

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                       +      VV   +K +   +   K+I         +E+    GR  Q+
Sbjct: 150 ------------LDKLKQGVVIDGKKTSRAKVRLVKMIGVN----SLVEITLIEGRKRQV 193

Query: 256 RVHALHMGCPIV 267
           +     +G  ++
Sbjct: 194 KKMCEKVGHKVI 205


>gi|50954353|ref|YP_061641.1| RNA pseudouridine synthase [Leifsonia xyli subsp. xyli str. CTCB07]
 gi|50950835|gb|AAT88536.1| RNA pseudouridine synthase [Leifsonia xyli subsp. xyli str. CTCB07]
          Length = 260

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 46/257 (17%), Positives = 84/257 (32%), Gaps = 51/257 (19%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             + +  RL +         +    ++++ +G+V V+   V    R       R+ PV+ 
Sbjct: 2   SAEPQGERLQKVMAAA-GVASRRVSEELIAAGRVSVNGTVVTELGR-------RVDPVV- 52

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
             +H+  +   +     L                +  + NKP G+     S         
Sbjct: 53  --DHVAVDGAAVQLDTTL----------------RYVMLNKPVGVVS---SLRDEQGRPD 91

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-- 190
           L  +V    ++     RLD ETSG+L++      A  L        + K Y + V G   
Sbjct: 92  LSRFVADYEERLFNVGRLDAETSGLLILTNDGELAHVLAHPRFG--VTKTYIARVRGAVT 149

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P+          L+   I  D                   K++         +E+  H+G
Sbjct: 150 PQTIGRLTRGVELEDGPIAADRA-----------------KLLQSDPGGGSLVEVTLHSG 192

Query: 251 RTHQLRVHALHMGCPIV 267
           R   +R     +G P+V
Sbjct: 193 RNRIVRRMLAEVGHPVV 209


>gi|108758119|ref|YP_629838.1| RsuA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108461999|gb|ABF87184.1| pseudouridine synthase, RsuA family [Myxococcus xanthus DK 1622]
          Length = 266

 Score = 67.3 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 76/249 (30%), Gaps = 55/249 (22%)

Query: 24  WFKNHYPH---INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           W          +     +  +R G+V +D                R+     A      E
Sbjct: 30  WLARALGKAGVMPRAQAEAAIREGRVTLDG---------------RVEHEPFAPVRPEME 74

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVD 138
            ++     NL      L            +F+KPAG+ V G    G+    +   +    
Sbjct: 75  VRVDGLVRNLEAPVLTL------------MFHKPAGLVVHGSDAEGVGTVFECLRERLTQ 122

Query: 139 S-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +  +     RLD++T+G+L+        QH   S      ++    +V   P++    
Sbjct: 123 PLRDYEWLAVGRLDRDTTGLLLFTNDERLVQH-GTSPERHLPKRYVAGVVGPPPEDALRR 181

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   L+ +          ++  +                      +E+    GR HQ++ 
Sbjct: 182 LREGLVLEDGPTRPAGARLRAPD---------------------VVELTLTEGRNHQVKR 220

Query: 258 HALHMGCPI 266
               +G P+
Sbjct: 221 MLAAVGHPV 229


>gi|261328132|emb|CBH11109.1| hypothetical protein, conserved [Trypanosoma brucei gambiense
           DAL972]
          Length = 727

 Score = 67.3 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 33/127 (25%), Positives = 49/127 (38%), Gaps = 30/127 (23%)

Query: 217 KQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--- 272
           +Q  +    A +  +            +E    TGRTHQ+RVH   +G PIV DHKY   
Sbjct: 588 RQLRETLKRATTLVRRWSYDEDLDESVVECVLLTGRTHQVRVHLASVGHPIVDDHKYIYH 647

Query: 273 ---CANFKGNFTSPIQNKL----------------------YLHARYMDLPHPEGGRLQ- 306
                 F GN+   ++++L                      +LHA    L +      + 
Sbjct: 648 LSRNTPFTGNYRKEVKSRLPPYPSTIPHVASNCSSVTTQGIFLHAWRYTLQYKNSETPET 707

Query: 307 ITAPLPA 313
           + APLPA
Sbjct: 708 LEAPLPA 714


>gi|221053087|ref|XP_002257918.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
           knowlesi strain H]
 gi|193807750|emb|CAQ38455.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
           knowlesi strain H]
          Length = 392

 Score = 67.3 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 47/261 (18%), Positives = 90/261 (34%), Gaps = 42/261 (16%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            LK  +LY+D    V NK  G+S  G +     I   L+       +   + ++L     
Sbjct: 17  DLKKSVLYQDDDYLVVNKAYGVSTFGRAPQKESIIKSLEELNLEGHESANVLYKLHNHVG 76

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L++ + +          +       + +LV+G  +N +       LK     G  +  
Sbjct: 77  GCLLICKNKF--------IKNHTYGNTFLALVYGQVENAQNVKVKLGLKYLPNSGIMIPS 128

Query: 216 VKQNEKGANYAISHFKVIDCF--AQKFCWLEMQPHTGRTHQ--LRVH-ALHMGCPIVGDH 270
             QN      +I  + VI      +   +  ++ HT       ++      +   IVGD+
Sbjct: 129 NDQNHLRDLKSI-KYDVISNTISYETHKFSLLKIHTAAKDAKFIKPLVFYSLYTCIVGDN 187

Query: 271 KYCANFKGNFTSPI------------QNK----------------LYLHARYMDLPHPEG 302
           +Y   ++    +               N+                L+LH   +       
Sbjct: 188 EYVGGWRKLIKNGFFAYRDVGGQVERANRLLLKKLPHMGKNNELMLHLHCLTVTFQSACS 247

Query: 303 GRLQITAPLPAHMVKTWDSLG 323
             + +++PLP HM +T + LG
Sbjct: 248 RVVSVSSPLPRHMRETLNFLG 268


>gi|84496363|ref|ZP_00995217.1| pseudouridine synthase, Rsu [Janibacter sp. HTCC2649]
 gi|84383131|gb|EAP99012.1| pseudouridine synthase, Rsu [Janibacter sp. HTCC2649]
          Length = 306

 Score = 67.3 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 82/254 (32%), Gaps = 51/254 (20%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINA 73
           D + +RL +   +     +    + ++  G+V VD + V     RI S QVV +  V   
Sbjct: 66  DPDGIRLQKLLASAGVG-SRRVCENMITEGRVEVDGQIVTELGVRINSEQVVHVDGVRVT 124

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                                       L E      FNKP  +       +     G  
Sbjct: 125 ----------------------------LDETRVYLAFNKPLNVVTSMNDDLGRIDIG-- 154

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +   + ++     RLD +T G+L++      A  L             + ++      
Sbjct: 155 -DYFGDRKERLFHVGRLDSDTEGLLLLTNDGDLAHRLQ---------HPKYGVLKTYLAQ 204

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            +  +   L KK   G +         +     +  F+V+D    K   +E+  H GR H
Sbjct: 205 IRGPVPRDLGKKLREGIEL--------EDGPVKVDSFRVVDSQPGKA-IVEVILHEGRKH 255

Query: 254 QLRVHALHMGCPIV 267
            +R      G P++
Sbjct: 256 IVRRMLAEAGHPVL 269


>gi|295100099|emb|CBK89188.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           cylindroides T2-87]
          Length = 230

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 89/248 (35%), Gaps = 59/248 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++   H  +     ++ I+++G V ++ K + K +++++  Q+V +          
Sbjct: 1   MRLDKFLS-HMGYGTRNKVKNIIKNGWVTIEGKTIKKADHQVKEDQIVYVD--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                            D   S + YE    Y+ NKP+G      S    ++   +   +
Sbjct: 51  -----------------DTPVSYIQYE---YYILNKPSGYV----SATEDNVHPTIMELI 86

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
            S  +      RLD +T G+L+V         L      + +QK Y+    G +P+N  E
Sbjct: 87  PSIRKDLYPVGRLDIDTEGLLLVCNDGQLTHDL--LSPKKHVQKKYYVEFEGTLPENAVE 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +     I                   S  +++D         E     G+ HQ++
Sbjct: 145 IFNQPMDLDDFIAKP----------------STLEILDTNKAYLTISE-----GKFHQVK 183

Query: 257 VHALHMGC 264
                +GC
Sbjct: 184 RMFQKIGC 191


>gi|293400568|ref|ZP_06644713.1| ribosomal small subunit pseudouridine synthase A
           [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305594|gb|EFE46838.1| ribosomal small subunit pseudouridine synthase A
           [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 232

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 84/247 (34%), Gaps = 57/247 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++  +         +++++R   VRV+ +  VK +  ++   +V++          
Sbjct: 1   MRLDKYLSHAGVG-TRKEVKQLIRKKHVRVNGELVVKDDMHVEEDDLVQLD--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + YE     + NKP+G+     +      +  L  + 
Sbjct: 51  --------------------GEHIYYEPFVYLMLNKPSGVIC---ATQDSEHETVLDCFD 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               +      RLD +T G+++++   + A   L+    +R+   +   L       K  
Sbjct: 88  VMLPKGCFPVGRLDMDTEGLVLISNDGKLAHHLLSPKHHVRKTYYVEHQLCLDETAIKTL 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C  + +L               +EK    A      ++   +  C+       GR HQ++
Sbjct: 148 CNGSIIL---------------DEKTVLCA-----ALEVINETSCF--FHIEEGRYHQIK 185

Query: 257 VHALHMG 263
                +G
Sbjct: 186 RMFSAVG 192


>gi|331085062|ref|ZP_08334149.1| hypothetical protein HMPREF0987_00452 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330408762|gb|EGG88227.1| hypothetical protein HMPREF0987_00452 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 241

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 82/245 (33%), Gaps = 49/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +         +++++R G V VD   VK                        
Sbjct: 6   LRLDKYLADMQVG-TRSEVKQMIRKGLVTVDGLIVK------------------------ 40

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K ++ +D    +   S  + S   YE    Y+ NKPAG+     +         +    D
Sbjct: 41  KPEEKVDCEKQVVVCSGAIVSYHQYE---YYMLNKPAGVVS---ATEDPRDKTVIDLIED 94

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + +      RLD++T G+L++    A A  L      + + K Y++ + G    +   +
Sbjct: 95  RRRKDLFPAGRLDKDTEGLLLITNDGALAHDL--LSPKKHVDKKYYAKIEGTVTEEDVEL 152

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +           V+     G    I+                +    G+ HQ++  
Sbjct: 153 FGKGIDIGEKRVTLPAVLTILSSGEESEIT----------------LTIREGKFHQVKRM 196

Query: 259 ALHMG 263
              +G
Sbjct: 197 FEAVG 201


>gi|256847151|ref|ZP_05552597.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           coleohominis 101-4-CHN]
 gi|256715815|gb|EEU30790.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           coleohominis 101-4-CHN]
          Length = 240

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 45/253 (17%), Positives = 84/253 (33%), Gaps = 54/253 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++ +G V V+ + V     ++     V +          
Sbjct: 2   ERLQKVMAEA-GVASRRASEKLIAAGHVAVNGQVVTELGTKVTKSDQVTVD--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKS 135
                                  +  E  K Y+ NKP G+        G    +   LK 
Sbjct: 52  --------------------GVPIKREPLKYYLLNKPRGVVSTAHDDKG-RRTVVDILKD 90

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             D   ++     RLD +T+GIL++    A A  L        ++K Y + V G+  N  
Sbjct: 91  --DDVEERVYPVGRLDYDTTGILLLTNDGALANKL--MHPKFEVEKTYIAKVKGVLSN-- 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQ 254
                      H        V  + +    A S  K+++    ++   + +  H G  HQ
Sbjct: 145 -----------HDLQKLRQGVIVDGRKTREAKS--KLLEVADNRQSSRVRLTIHEGHYHQ 191

Query: 255 LRVHALHMGCPIV 267
           ++     +G P++
Sbjct: 192 VKRMLKAVGHPVI 204


>gi|262202716|ref|YP_003273924.1| pseudouridine synthase [Gordonia bronchialis DSM 43247]
 gi|262086063|gb|ACY22031.1| pseudouridine synthase [Gordonia bronchialis DSM 43247]
          Length = 329

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 76/251 (30%), Gaps = 45/251 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + +RL +         +    ++++ +G+V +D + V         Q +RI P    +  
Sbjct: 87  DGVRLQKVLAQA-GVASRRGAEEMIAAGRVEIDGEIVTE-------QGLRIDPDTAIIR- 137

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                  +++ E  +    NKP G              G + + 
Sbjct: 138 ------------------VDGARVIIDETRQYLALNKPRGWQSTMADDQGRPCVGDIVAE 179

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               GQ+     RLD +T G+L++      A  L        + K Y + V G       
Sbjct: 180 RVMAGQRLFHVGRLDADTEGLLLLTNDGELAHRL--MHPSYEVPKTYLATVRGEV----- 232

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                           +            A+    ++D   +    L +  H GR   +R
Sbjct: 233 ----------PRSLSRMLRDGVELDDGPVAVDKLTIVDVH-EGQSLLRITLHEGRNRIVR 281

Query: 257 VHALHMGCPIV 267
                +G P+V
Sbjct: 282 RMMDEVGFPVV 292


>gi|300934025|ref|ZP_07149281.1| putative pseudouridylate synthase [Corynebacterium resistens DSM
           45100]
          Length = 335

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 89/253 (35%), Gaps = 45/253 (17%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +++ +RL +   +     +    +K++ +G+V V+ + V+     Q G  +RI P ++ 
Sbjct: 90  KEKQQVRLQKVLSSA-GVASRRMSEKLIAAGRVEVNGEVVQ-----QMG--LRIDPSVDV 141

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           +                         + + E+   +  NKP G+       +     G L
Sbjct: 142 VR-------------------VDGTRVQVNEEMVYFALNKPRGVHSTMHDDLGRPHVGEL 182

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                ++GQ      RLD  T G+L++      A  L        + K Y + V G    
Sbjct: 183 IEAKFNQGQGLFHVGRLDAATEGLLLLTNDGELANRL--MHPKYEVSKTYMATVLGEA-- 238

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                   L++    G D    +         A + +  I    Q    ++++ H GR H
Sbjct: 239 -----DRGLIRTLKDGVDLEDGM---------ARADYVQIVDVWQGKSLIKVELHEGRKH 284

Query: 254 QLRVHALHMGCPI 266
            +R      G P+
Sbjct: 285 IVRRMLKAAGFPV 297


>gi|289167140|ref|YP_003445407.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis B6]
 gi|288906705|emb|CBJ21539.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           mitis B6]
          Length = 240

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 88/246 (35%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L+SG+V V+ K+ K + ++Q                I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKSGRVTVNGKKEK-SAKLQ----------------ID 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E+  +           F   +L YE+   Y+ NKP G+           +   L     
Sbjct: 43  EERDEI----------RFDGQVLEYEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDIAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           SK  +     RLD +T G+L++    + A   L+     R + K Y + V GI   +   
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNDGKLAHALLS---PKRHVDKTYLAQVKGIMTQED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   +   +     A      +D   +    + +    G+ HQ++ 
Sbjct: 146 -----------AETFAKGIPLKDFTCQPARLELVSVDTK-KNQSQIRVTIAEGKFHQVKR 193

Query: 258 HALHMG 263
              + G
Sbjct: 194 MVGYCG 199


>gi|322412052|gb|EFY02960.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           dysgalactiae subsp. dysgalactiae ATCC 27957]
          Length = 243

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 45/246 (18%), Positives = 84/246 (34%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L+   + V+ + V+ + ++Q      I    + + ++ 
Sbjct: 1   MRLDKFLVETGVG-SRSQVKSLLKKKAILVN-QEVETSPKVQ------INEHKDVVTYLG 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K                     L YE    YV NKPAG            +   L     
Sbjct: 53  KP--------------------LTYEAFVYYVLNKPAGFLSATKDRAQATVIDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K        RLD++T G+L++      A  L      + + K Y + V GI        
Sbjct: 93  QK--DVFPVGRLDKDTRGLLLLTNNGQLAHDL--LSPKKHVTKEYLAKVAGIMTEAD--- 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRV 257
                       D+   +   +     A    +V+D   +Q+ C + +    G+ HQ++ 
Sbjct: 146 ----------KDDFAKGISLKDYQCLPA--KLEVLDKDVSQETCVVSITIQEGKFHQVKR 193

Query: 258 HALHMG 263
                G
Sbjct: 194 MVAACG 199


>gi|332359960|gb|EGJ37774.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1056]
          Length = 242

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 84/246 (34%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   +++ L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQFLKKGLVLVNGRAEKS----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I +++  +      L     YE    Y+ NKP G+           +   L     
Sbjct: 37  PKTQIDETADEIVVSGQRLT----YEKFVYYLLNKPQGVISATEDDRHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+       
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLM------ 141

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   ++  +     A      +D  A++   +E+    G+ HQ++ 
Sbjct: 142 -------NQADVERFAAGIELKDFTCQPAQLKIVELD-EAKETSLVEITLAEGKFHQVKR 193

Query: 258 HALHMG 263
                G
Sbjct: 194 MVASCG 199


>gi|313890897|ref|ZP_07824521.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           pseudoporcinus SPIN 20026]
 gi|313120795|gb|EFR43910.1| pseudouridine synthase B, ribosomal large subunit [Streptococcus
           pseudoporcinus SPIN 20026]
          Length = 240

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 85/249 (34%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +      ++S  VV +          
Sbjct: 1   MRINKYIA-HAGVASRRKAEELIKQGLVTLNGQVITDLATLVKSSDVVEVE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                S +  E+   Y+ NKP G+  SV    G    ID     
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGVISSVSDDKGRKTVID----- 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSG+L++         +        I K+Y + V GI   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDKM--IHPRNEIDKVYLARVKGIATKEN 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                               V  + K    A   + +I   A      +E+  H GR HQ
Sbjct: 144 L-------------RPLTRGVVIDGKKTKPA--RYNIIRVEADKNRSIVELTIHEGRHHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFESVG 197


>gi|257063679|ref|YP_003143351.1| ribosomal large subunit pseudouridine synthase B [Slackia
           heliotrinireducens DSM 20476]
 gi|256791332|gb|ACV22002.1| ribosomal large subunit pseudouridine synthase B [Slackia
           heliotrinireducens DSM 20476]
          Length = 249

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 89/264 (33%), Gaps = 52/264 (19%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M   +  +V      MR+ ++        +    + ++ +G+V V+ + V      + G 
Sbjct: 1   MPQQEERIVP-----MRVQKFLARA-GVASRRRSEDLMTAGRVCVNGEVVT-----ELGA 49

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
             ++ P ++ +    +E ++ D  V                     + NKP G       
Sbjct: 50  --KVDPRVDTVTVDGREVRLTDGPVT-------------------IMLNKPCGFITTMSD 88

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                    L               RLD +TSG+L+ +        L        + K Y
Sbjct: 89  PYGRACVAELV--PSDDYPGLFPVGRLDTDTSGLLLFSTDGELGNSL--LHPRHHVDKTY 144

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            + V G        I++  L+    G +       +   +  A++    +   +++   +
Sbjct: 145 EACVQG-------RISDEALQTLRDGVEL-----DDGVTSPAAVT----LVSRSKEKSRI 188

Query: 244 EMQPHTGRTHQLRVHALHMGCPIV 267
            +  H GRT Q+R     +G P++
Sbjct: 189 TLVIHEGRTRQVRRMCQKVGHPVL 212


>gi|15608849|ref|NP_216227.1| hypothetical protein Rv1711 [Mycobacterium tuberculosis H37Rv]
 gi|15841171|ref|NP_336208.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis CDC1551]
 gi|31792898|ref|NP_855391.1| hypothetical protein Mb1738 [Mycobacterium bovis AF2122/97]
 gi|121637619|ref|YP_977842.1| hypothetical protein BCG_1750 [Mycobacterium bovis BCG str. Pasteur
           1173P2]
 gi|148661509|ref|YP_001283032.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis H37Ra]
 gi|148822917|ref|YP_001287671.1| hypothetical protein TBFG_11726 [Mycobacterium tuberculosis F11]
 gi|167967185|ref|ZP_02549462.1| hypothetical protein MtubH3_03737 [Mycobacterium tuberculosis
           H37Ra]
 gi|215403985|ref|ZP_03416166.1| hypothetical protein Mtub0_09916 [Mycobacterium tuberculosis
           02_1987]
 gi|215411359|ref|ZP_03420167.1| hypothetical protein Mtub9_08567 [Mycobacterium tuberculosis
           94_M4241A]
 gi|215427035|ref|ZP_03424954.1| hypothetical protein MtubT9_11867 [Mycobacterium tuberculosis T92]
 gi|215430604|ref|ZP_03428523.1| hypothetical protein MtubE_08018 [Mycobacterium tuberculosis
           EAS054]
 gi|215445897|ref|ZP_03432649.1| hypothetical protein MtubT_08146 [Mycobacterium tuberculosis T85]
 gi|218753419|ref|ZP_03532215.1| hypothetical protein MtubG1_08264 [Mycobacterium tuberculosis GM
           1503]
 gi|219557635|ref|ZP_03536711.1| hypothetical protein MtubT1_10192 [Mycobacterium tuberculosis T17]
 gi|224990094|ref|YP_002644781.1| hypothetical protein JTY_1725 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253799250|ref|YP_003032251.1| hypothetical protein TBMG_02284 [Mycobacterium tuberculosis KZN
           1435]
 gi|254550722|ref|ZP_05141169.1| hypothetical protein Mtube_09734 [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260200774|ref|ZP_05768265.1| hypothetical protein MtubT4_11812 [Mycobacterium tuberculosis T46]
 gi|260204981|ref|ZP_05772472.1| hypothetical protein MtubK8_11835 [Mycobacterium tuberculosis K85]
 gi|289443169|ref|ZP_06432913.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           tuberculosis T46]
 gi|289569762|ref|ZP_06449989.1| conserved hypothetical protein [Mycobacterium tuberculosis T17]
 gi|289574379|ref|ZP_06454606.1| RNA pseudouridine synthase [Mycobacterium tuberculosis K85]
 gi|289745851|ref|ZP_06505229.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis 02_1987]
 gi|289750268|ref|ZP_06509646.1| conserved hypothetical protein [Mycobacterium tuberculosis T92]
 gi|289753802|ref|ZP_06513180.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis EAS054]
 gi|289757820|ref|ZP_06517198.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis T85]
 gi|289761867|ref|ZP_06521245.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis GM 1503]
 gi|294993179|ref|ZP_06798870.1| hypothetical protein Mtub2_01388 [Mycobacterium tuberculosis 210]
 gi|297634264|ref|ZP_06952044.1| hypothetical protein MtubK4_09092 [Mycobacterium tuberculosis KZN
           4207]
 gi|297731251|ref|ZP_06960369.1| hypothetical protein MtubKR_09182 [Mycobacterium tuberculosis KZN
           R506]
 gi|306972006|ref|ZP_07484667.1| hypothetical protein TMJG_03142 [Mycobacterium tuberculosis
           SUMu010]
 gi|313658583|ref|ZP_07815463.1| hypothetical protein MtubKV_09197 [Mycobacterium tuberculosis KZN
           V2475]
 gi|54040263|sp|P65843|Y1738_MYCBO RecName: Full=Uncharacterized RNA pseudouridine synthase Mb1738;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|54042595|sp|P65842|Y1711_MYCTU RecName: Full=Uncharacterized RNA pseudouridine synthase
           Rv1711/MT1751.1; AltName: Full=RNA pseudouridylate
           synthase; AltName: Full=RNA-uridine isomerase
 gi|2326754|emb|CAB10968.1| CONSERVED HYPOTHETICAL PROTEIN [Mycobacterium tuberculosis H37Rv]
 gi|13881392|gb|AAK46022.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis CDC1551]
 gi|31618489|emb|CAD94441.1| CONSERVED HYPOTHETICAL PROTEIN [Mycobacterium bovis AF2122/97]
 gi|121493266|emb|CAL71737.1| Conserved hypothetical protein [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148505661|gb|ABQ73470.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis H37Ra]
 gi|148721444|gb|ABR06069.1| conserved hypothetical protein [Mycobacterium tuberculosis F11]
 gi|224773207|dbj|BAH26013.1| hypothetical protein JTY_1725 [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253320753|gb|ACT25356.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN
           1435]
 gi|289416088|gb|EFD13328.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           tuberculosis T46]
 gi|289538810|gb|EFD43388.1| RNA pseudouridine synthase [Mycobacterium tuberculosis K85]
 gi|289543516|gb|EFD47164.1| conserved hypothetical protein [Mycobacterium tuberculosis T17]
 gi|289686379|gb|EFD53867.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis 02_1987]
 gi|289690855|gb|EFD58284.1| conserved hypothetical protein [Mycobacterium tuberculosis T92]
 gi|289694389|gb|EFD61818.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis EAS054]
 gi|289709373|gb|EFD73389.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis GM 1503]
 gi|289713384|gb|EFD77396.1| RNA pseudouridylate synthase [Mycobacterium tuberculosis T85]
 gi|308358526|gb|EFP47377.1| hypothetical protein TMJG_03142 [Mycobacterium tuberculosis
           SUMu010]
 gi|323719802|gb|EGB28916.1| hypothetical protein TMMG_00962 [Mycobacterium tuberculosis
           CDC1551A]
 gi|326903326|gb|EGE50259.1| hypothetical protein TBPG_01194 [Mycobacterium tuberculosis W-148]
          Length = 254

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 73/250 (29%), Gaps = 47/250 (18%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RL +         +    +K++  G+V VD   V             +   ++    +
Sbjct: 13  GIRLQKVLSQA-GIASRRAAEKMIVDGRVEVDGHVVT-----------ELGTRVDPQVAV 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           ++                    ++L +       NKP G+             G L    
Sbjct: 61  VR---------------VDGARVVLDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERK 105

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
               +K     RLD +T G++++      A  L        + K Y + V G +P+    
Sbjct: 106 VRGTKKLFHVGRLDADTEGLMLLTNDGELAHRL--MHPSHEVPKTYLATVTGSVPRGLGR 163

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +   +                        +  F V+D    K   + +  H GR   +R
Sbjct: 164 TLRAGIELDD----------------GPAFVDDFAVVDAIPGK-TLVRVTLHEGRNRIVR 206

Query: 257 VHALHMGCPI 266
                 G P+
Sbjct: 207 RLLAAAGFPV 216


>gi|254231907|ref|ZP_04925234.1| conserved hypothetical protein [Mycobacterium tuberculosis C]
 gi|254364550|ref|ZP_04980596.1| conserved hypothetical protein [Mycobacterium tuberculosis str.
           Haarlem]
 gi|289554516|ref|ZP_06443726.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN 605]
 gi|298525209|ref|ZP_07012618.1| conserved hypothetical protein [Mycobacterium tuberculosis
           94_M4241A]
 gi|308231906|ref|ZP_07414234.2| hypothetical protein TMAG_01544 [Mycobacterium tuberculosis
           SUMu001]
 gi|308369503|ref|ZP_07418052.2| hypothetical protein TMBG_00254 [Mycobacterium tuberculosis
           SUMu002]
 gi|308370796|ref|ZP_07422771.2| hypothetical protein TMCG_03412 [Mycobacterium tuberculosis
           SUMu003]
 gi|308372033|ref|ZP_07427137.2| hypothetical protein TMDG_03429 [Mycobacterium tuberculosis
           SUMu004]
 gi|308373217|ref|ZP_07431453.2| hypothetical protein TMEG_01610 [Mycobacterium tuberculosis
           SUMu005]
 gi|308374378|ref|ZP_07435832.2| hypothetical protein TMFG_00797 [Mycobacterium tuberculosis
           SUMu006]
 gi|308375655|ref|ZP_07444660.2| hypothetical protein TMGG_00259 [Mycobacterium tuberculosis
           SUMu007]
 gi|308376799|ref|ZP_07440079.2| hypothetical protein TMHG_00891 [Mycobacterium tuberculosis
           SUMu008]
 gi|308377802|ref|ZP_07480471.2| hypothetical protein TMIG_01963 [Mycobacterium tuberculosis
           SUMu009]
 gi|308380151|ref|ZP_07488888.2| hypothetical protein TMKG_02217 [Mycobacterium tuberculosis
           SUMu011]
 gi|308401397|ref|ZP_07493409.2| hypothetical protein TMLG_00694 [Mycobacterium tuberculosis
           SUMu012]
 gi|124600966|gb|EAY59976.1| conserved hypothetical protein [Mycobacterium tuberculosis C]
 gi|134150064|gb|EBA42109.1| conserved hypothetical protein [Mycobacterium tuberculosis str.
           Haarlem]
 gi|289439148|gb|EFD21641.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN 605]
 gi|298495003|gb|EFI30297.1| conserved hypothetical protein [Mycobacterium tuberculosis
           94_M4241A]
 gi|308215647|gb|EFO75046.1| hypothetical protein TMAG_01544 [Mycobacterium tuberculosis
           SUMu001]
 gi|308327365|gb|EFP16216.1| hypothetical protein TMBG_00254 [Mycobacterium tuberculosis
           SUMu002]
 gi|308330808|gb|EFP19659.1| hypothetical protein TMCG_03412 [Mycobacterium tuberculosis
           SUMu003]
 gi|308334631|gb|EFP23482.1| hypothetical protein TMDG_03429 [Mycobacterium tuberculosis
           SUMu004]
 gi|308338418|gb|EFP27269.1| hypothetical protein TMEG_01610 [Mycobacterium tuberculosis
           SUMu005]
 gi|308342141|gb|EFP30992.1| hypothetical protein TMFG_00797 [Mycobacterium tuberculosis
           SUMu006]
 gi|308345612|gb|EFP34463.1| hypothetical protein TMGG_00259 [Mycobacterium tuberculosis
           SUMu007]
 gi|308349928|gb|EFP38779.1| hypothetical protein TMHG_00891 [Mycobacterium tuberculosis
           SUMu008]
 gi|308354549|gb|EFP43400.1| hypothetical protein TMIG_01963 [Mycobacterium tuberculosis
           SUMu009]
 gi|308362465|gb|EFP51316.1| hypothetical protein TMKG_02217 [Mycobacterium tuberculosis
           SUMu011]
 gi|308366085|gb|EFP54936.1| hypothetical protein TMLG_00694 [Mycobacterium tuberculosis
           SUMu012]
 gi|328459002|gb|AEB04425.1| conserved hypothetical protein [Mycobacterium tuberculosis KZN
           4207]
          Length = 253

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 73/250 (29%), Gaps = 47/250 (18%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            +RL +         +    +K++  G+V VD   V             +   ++    +
Sbjct: 12  GIRLQKVLSQA-GIASRRAAEKMIVDGRVEVDGHVVT-----------ELGTRVDPQVAV 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           ++                    ++L +       NKP G+             G L    
Sbjct: 60  VR---------------VDGARVVLDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERK 104

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
               +K     RLD +T G++++      A  L        + K Y + V G +P+    
Sbjct: 105 VRGTKKLFHVGRLDADTEGLMLLTNDGELAHRL--MHPSHEVPKTYLATVTGSVPRGLGR 162

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +   +                        +  F V+D    K   + +  H GR   +R
Sbjct: 163 TLRAGIELDD----------------GPAFVDDFAVVDAIPGK-TLVRVTLHEGRNRIVR 205

Query: 257 VHALHMGCPI 266
                 G P+
Sbjct: 206 RLLAAAGFPV 215


>gi|163791509|ref|ZP_02185915.1| RluB [Carnobacterium sp. AT7]
 gi|159873232|gb|EDP67330.1| RluB [Carnobacterium sp. AT7]
          Length = 244

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 88/252 (34%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++  G V+V+ K VK    +I +  VV +          
Sbjct: 2   ERLQKVLA-HAGVASRRKSEELISKGHVKVNGKVVKEMGIQIGNSDVVEVD--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   ++ NKP  +  +V    G        +  
Sbjct: 52  --------------------GVPIYREEPVYFLLNKPRNMITAVSDDKGRP-----VVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              +  Q+     RLD +T+G L++      +Q L       +I K Y + V G+     
Sbjct: 87  LFPNIEQRIYPVGRLDYDTTGALMLTNDGELSQLL--MHPKYQINKTYVAKVKGLVD--- 141

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
                   +K+    +   VV    +G   A +  K++    A+    +E+  H GR  Q
Sbjct: 142 --------RKALNKLEKGVVV----EGKKTAPAKAKILSADRAKDITMVELTIHEGRNRQ 189

Query: 255 LRVHALHMGCPI 266
           ++     +G P+
Sbjct: 190 VKNMFQAIGHPV 201


>gi|31789454|gb|AAP58568.1| pseudouridylate synthase [uncultured Acidobacteria bacterium]
          Length = 317

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 82/238 (34%), Gaps = 47/238 (19%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN-HIIKEQKILDSSVNL 90
            +  + ++++ +G+V V+ K V             +    +A N HI    K+++ ++  
Sbjct: 69  ASRRHAEQLITAGEVTVNGKVVT-----------ELGTKADAQNDHIKVRGKLINPTLKR 117

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            +                 + NKP G +S          +   L + +     +     R
Sbjct: 118 VEK-------------NYILLNKPRGYLSSVSDPEGRPTVLELLPASLG----RVYPVGR 160

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD  T G+L++         +T      ++ K+Y + V G+P                  
Sbjct: 161 LDFNTEGLLLLTNDGDFTNFIT--SARNKVDKVYEAKVKGVPTEASV------------- 205

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            + +      + G   A +  +++        W E+  H G+  Q+R     +G  +V
Sbjct: 206 -ERLRRGVTLDDGVRTAPAKIRLLGETESNA-WFEVLLHEGKNQQIRRMFDLIGHSVV 261


>gi|16803988|ref|NP_465473.1| hypothetical protein lmo1949 [Listeria monocytogenes EGD-e]
 gi|46908183|ref|YP_014572.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|47093378|ref|ZP_00231145.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes str. 4b H7858]
 gi|47097092|ref|ZP_00234662.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes str. 1/2a F6854]
 gi|224498601|ref|ZP_03666950.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes Finland 1988]
 gi|224501251|ref|ZP_03669558.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL R2-561]
 gi|226224554|ref|YP_002758661.1| hypothetical protein Lm4b_01968 [Listeria monocytogenes Clip81459]
 gi|254825555|ref|ZP_05230556.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL J1-194]
 gi|254827166|ref|ZP_05231853.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL N3-165]
 gi|254831450|ref|ZP_05236105.1| hypothetical protein Lmon1_08853 [Listeria monocytogenes 10403S]
 gi|254852851|ref|ZP_05242199.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL R2-503]
 gi|254899354|ref|ZP_05259278.1| hypothetical protein LmonJ_06059 [Listeria monocytogenes J0161]
 gi|254912507|ref|ZP_05262519.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes J2818]
 gi|254931879|ref|ZP_05265238.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes HPB2262]
 gi|254936834|ref|ZP_05268531.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes F6900]
 gi|254992999|ref|ZP_05275189.1| hypothetical protein LmonocytoFSL_08071 [Listeria monocytogenes FSL
           J2-064]
 gi|255026085|ref|ZP_05298071.1| hypothetical protein LmonocytFSL_06510 [Listeria monocytogenes FSL
           J2-003]
 gi|255520090|ref|ZP_05387327.1| hypothetical protein LmonocFSL_02452 [Listeria monocytogenes FSL
           J1-175]
 gi|284802394|ref|YP_003414259.1| hypothetical protein LM5578_2150 [Listeria monocytogenes 08-5578]
 gi|284995536|ref|YP_003417304.1| hypothetical protein LM5923_2101 [Listeria monocytogenes 08-5923]
 gi|300763739|ref|ZP_07073736.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL N1-017]
 gi|16411402|emb|CAD00027.1| lmo1949 [Listeria monocytogenes EGD-e]
 gi|46881453|gb|AAT04749.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|47014537|gb|EAL05500.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes str. 1/2a F6854]
 gi|47018249|gb|EAL09015.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes str. 4b H7858]
 gi|225877016|emb|CAS05725.1| Hypothetical protein of unknown function [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|258599548|gb|EEW12873.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL N3-165]
 gi|258606184|gb|EEW18792.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL R2-503]
 gi|258609430|gb|EEW22038.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes F6900]
 gi|284057956|gb|ADB68897.1| hypothetical protein LM5578_2150 [Listeria monocytogenes 08-5578]
 gi|284061003|gb|ADB71942.1| hypothetical protein LM5923_2101 [Listeria monocytogenes 08-5923]
 gi|293583430|gb|EFF95462.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes HPB2262]
 gi|293590492|gb|EFF98826.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes J2818]
 gi|293594796|gb|EFG02557.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL J1-194]
 gi|300515475|gb|EFK42525.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes FSL N1-017]
 gi|328466297|gb|EGF37454.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes 1816]
 gi|328472791|gb|EGF43640.1| ribosomal large subunit pseudouridine synthase B [Listeria
           monocytogenes 220]
 gi|332312390|gb|EGJ25485.1| Pseudouridine synthase [Listeria monocytogenes str. Scott A]
          Length = 244

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 84/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   N     +    +K+++ G+V V+ K V                       + 
Sbjct: 2   ERLQKVIANA-GITSRRKAEKLIQEGKVTVNGKVVT-----------------ELGVKVS 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             ++I    + LTK           E+ + ++F KP G      +         +  +  
Sbjct: 44  GTERIEVEGIQLTK-----------EEHRYFLFYKPRGTVS---AVTDDKGRTTVADYFA 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC- 197
              ++     RLD +TSG+L++      A  L        + K Y + + GIP+ +    
Sbjct: 90  DIPERLYPVGRLDYDTSGLLLMTNDGDFANLL--MHPKNEVSKTYIARIKGIPEREVIRQ 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   ++            V+ ++K  + AI               +E+  H GR  Q+R 
Sbjct: 148 LERGVVIDGRKTAPAKVKVRSSDKTKDKAI---------------VEITIHEGRNRQVRK 192

Query: 258 HALHMGC 264
               +G 
Sbjct: 193 MFEAVGF 199


>gi|119478215|ref|ZP_01618271.1| putative pseudouridine synthase [marine gamma proteobacterium
           HTCC2143]
 gi|119448724|gb|EAW29968.1| putative pseudouridine synthase [marine gamma proteobacterium
           HTCC2143]
          Length = 307

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 34/249 (13%), Positives = 77/249 (30%), Gaps = 56/249 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR K  +++ +G  V++   I       
Sbjct: 8   RLNKYISE--SGICSRREADRFVEKGSVFINGKRAKVGDQVSAGDTVKVNGQIIDPRD-- 63

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E++++                       +   NKP G+          +I  ++     
Sbjct: 64  -EERLV-----------------------LIALNKPVGVVCTTEGSEKNNIVDYVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             G++     RLD+++ G++ +         +  +      + +       + K   +  
Sbjct: 97  --GERIFPIGRLDKDSQGLIFLTNNGDLVNKILRAGNRHEKEYLVT-----VDKPITDTF 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + K   I G+     K  ++                       +    G   Q+R  
Sbjct: 150 IRDMAKGVPILGEVTRKCKIVKETP-----------------TLFRITLVQGLNRQIRRM 192

Query: 259 ALHMGCPIV 267
             H G  IV
Sbjct: 193 CDHFGYDIV 201


>gi|332359298|gb|EGJ37119.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK49]
          Length = 242

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 43/245 (17%), Positives = 86/245 (35%), Gaps = 50/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQLLKKGLVLVNGRAEKS----------------PKTQIDE 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  +I+ S   LT           YE    Y+ NKP G+           +   L     
Sbjct: 44  RADEIVVSGQRLT-----------YEKFVYYLLNKPQGVISATEDDRHQTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+ +     
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLMEQAD-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQLR 256
                +++   G +      Q            K+++   +K    +E+    G+ HQ++
Sbjct: 146 -----VERFAAGIELKDFTCQPA--------QLKILELDEEKESSLVEITLAEGKFHQVK 192

Query: 257 VHALH 261
                
Sbjct: 193 RMVAA 197


>gi|47210854|emb|CAF89720.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 220

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 23/79 (29%), Positives = 32/79 (40%)

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
            LL+  H       +  +  K     ++  +      +      +QP TGRTHQLRVH  
Sbjct: 90  PLLQGPHRHQSLPRLSCEKPKTCRSELAVLEYGLYDGEPVTKALLQPLTGRTHQLRVHCS 149

Query: 261 HMGCPIVGDHKYCANFKGN 279
            +G PIVGD  Y       
Sbjct: 150 AIGHPIVGDVTYSCGADAG 168


>gi|239828089|ref|YP_002950713.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239808382|gb|ACS25447.1| pseudouridine synthase [Geobacillus sp. WCH70]
          Length = 240

 Score = 66.9 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 91/248 (36%), Gaps = 52/248 (20%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNH 76
            +R+D+   N   +     ++K+L+SG V++D   VK    ++   + V           
Sbjct: 2   GLRIDKMLAN-MGYGTRKEVKKLLKSGVVKIDGVVVKDPKTQVNPTEQVV---------- 50

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            ++ +++                   Y++    + NKP G+       +   +   L+  
Sbjct: 51  TVRGKEVE------------------YKEFIYLMMNKPPGVVSATEDVVEETVVDLLEE- 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +   P    RLD++T G+L++      A Q L+     + + K Y++++ G    + 
Sbjct: 92  -EDRVFSPFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVPKTYFAVIDGEVTEED 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                       I      +V  +      A    +++   +     +E+    G+ HQ+
Sbjct: 148 ------------IASFRRGIVLDDGYETKPA----ELVVLKSGLRSDVEVTITEGKFHQV 191

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 192 KRMFRAIG 199


>gi|302878407|ref|YP_003846971.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
 gi|302581196|gb|ADL55207.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
          Length = 302

 Score = 66.9 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 42/252 (16%), Positives = 79/252 (31%), Gaps = 47/252 (18%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   +L +         +  N+++ + +G+V V+ +      R+  G +V+         
Sbjct: 13  EAGEKLQKVLAQAGFG-SRRNMEEWIAAGRVSVNGEPATLGMRVVPGDLVK--------- 62

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                    +         D    +LLY        +KP G  V                
Sbjct: 63  --------TERRTIRVGERDHTARVLLY--------HKPEGEIV--SRDDPEKRASVFDK 104

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               +GQK     RLD  TSG+L+   +   A  L        +++ Y   V G     +
Sbjct: 105 LPKLRGQKWIAVGRLDFNTSGLLIFTTSGELANRL--MHPRFEVEREYAVRVQGSMTEDQ 162

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF-CWLEMQPHTGRTHQ 254
                              V+K+     +  ++  K+ D   + F  W ++    GR   
Sbjct: 163 IT----------------QVLKEGVMLEDGPVTFDKLEDNGGEGFNHWYKVMLKEGRNRI 206

Query: 255 LRVHALHMGCPI 266
           +R     +  P+
Sbjct: 207 VRRTFDALALPV 218


>gi|325661183|ref|ZP_08149810.1| hypothetical protein HMPREF0490_00543 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325472690|gb|EGC75901.1| hypothetical protein HMPREF0490_00543 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 237

 Score = 66.9 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 82/245 (33%), Gaps = 49/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +         +++++R G V VD   VK                        
Sbjct: 2   LRLDKYLADMQVG-TRSEVKQMIRKGLVTVDGLIVK------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K ++ +D    +   S  + S   YE    Y+ NKPAG+     +         +    D
Sbjct: 37  KPEEKVDCEKQVVVCSGAIVSYHQYE---YYMLNKPAGVVS---ATEDPRDKTVIDLIED 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + +      RLD++T G+L++    A A  L      + + K Y++ + G    +   +
Sbjct: 91  RRRKDLFPAGRLDKDTEGLLLITNDGALAHDL--LSPKKHVDKKYYAKIEGTVTEEDVEL 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +           V+     G    I+                +    G+ HQ++  
Sbjct: 149 FGKGVDIGEKRVTLPAVLTILSSGEESEIT----------------LTIREGKFHQVKRM 192

Query: 259 ALHMG 263
              +G
Sbjct: 193 FEAVG 197


>gi|163939386|ref|YP_001644270.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
 gi|229132378|ref|ZP_04261232.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
 gi|163861583|gb|ABY42642.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
 gi|228651084|gb|EEL07065.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
          Length = 242

 Score = 66.9 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 87/252 (34%), Gaps = 60/252 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----NVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +++K Y + + G      
Sbjct: 87  FFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANVL--MHPRYKVEKTYVAKIKG------ 138

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRT 252
                       + G+ + ++++    +    A +  K+I    +K    +++  H GR 
Sbjct: 139 -----------PLTGEKIRMLERGVALEDGKTAPAQAKIISWDKRKEMAIVQLTIHEGRN 187

Query: 253 HQLRVHALHMGC 264
            Q+R     + C
Sbjct: 188 RQVRRMFEALDC 199


>gi|332365597|gb|EGJ43357.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1059]
          Length = 242

 Score = 66.5 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 87/247 (35%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   +++ L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQFLKKGLVLVNGRAEKS----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I +++  +      L     YE    Y+ NKP G+           +   L     
Sbjct: 37  PKTQIDETADEIAVSGQRLT----YEKFVYYLLNKPQGVISATEDDRHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+       
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLMNQAD-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLR 256
                +++   G +      Q            K+++   A++   +E+    G+ HQ++
Sbjct: 146 -----VERFAAGIELKAFTCQPA--------QLKILELDEAKETSLVEITLAEGKFHQVK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVAACG 199


>gi|89099078|ref|ZP_01171957.1| ribosomal large subunit pseudouridine synthaseB (pseudouridylate
           synthase) (uracil hydrolyase) [Bacillus sp. NRRL
           B-14911]
 gi|89086208|gb|EAR65330.1| ribosomal large subunit pseudouridine synthaseB (pseudouridylate
           synthase) (uracil hydrolyase) [Bacillus sp. NRRL
           B-14911]
          Length = 224

 Score = 66.5 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 42/223 (18%), Positives = 73/223 (32%), Gaps = 51/223 (22%)

Query: 46  VRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYE 104
           V+V+ K VK    ++ S   V +  +       +                          
Sbjct: 6   VKVNGKVVKELGLKVSSSDRVEVDGIPVEREEPV-------------------------- 39

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
                +  KP G+     S         +   +    ++     RLD +TSG+L++    
Sbjct: 40  ---YILLYKPRGVIS---SVTDEKGRKVVTDLLPQIKERVYPVGRLDFDTSGLLLMTNDG 93

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
             A  L        ++K+Y + + GIP  +K       LK    G           +   
Sbjct: 94  EFANLL--MHPKNEVEKVYVAKIKGIPAREK-------LKSLERGVRL--------EDGK 136

Query: 225 YAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPI 266
            A +  KV+    QK    +E+  H GR  Q+R     +G P+
Sbjct: 137 TAPARVKVLSIDKQKNTAIVELVIHEGRNRQVRRMLEAIGHPV 179


>gi|322386947|ref|ZP_08060571.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           cristatus ATCC 51100]
 gi|321269229|gb|EFX52165.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           cristatus ATCC 51100]
          Length = 242

 Score = 66.5 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 86/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++++L+ GQV V+   V  + + Q  +               
Sbjct: 1   MRLDKFLVESGLG-SRSQVKQLLKKGQVWVNGAAVT-SAKTQINER-------------- 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +Q ++D               L+YE    Y+ NKP G+           +   L     
Sbjct: 45  SDQIVVDGQ------------TLVYEKFVYYLLNKPKGVISATEDDRHKTVLDLLDDTAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++      +   L+     R + K+Y + V G+       
Sbjct: 93  QK--EVFPVGRLDVDTHGLLLLTNNGQLSHAMLS---PKRHVAKVYQAQVAGLMDQAD-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLR 256
                +++   G +      Q            ++++     K   + +    G+ HQ++
Sbjct: 146 -----VERFAQGIELKDFTCQPA--------QLEILERDEGAKTSLVRITLSEGKFHQVK 192

Query: 257 VHALHMG 263
              L  G
Sbjct: 193 RMVLACG 199


>gi|312793399|ref|YP_004026322.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312877026|ref|ZP_07736999.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796167|gb|EFR12523.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
 gi|312180539|gb|ADQ40709.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 232

 Score = 66.5 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 86/245 (35%), Gaps = 51/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   H    +   ++K++R G V V+ KR           +V +   IN      
Sbjct: 1   MRLDKFLT-HCGFGSRSQVKKLIREGIVTVNGKR-----------IVEVDFKIN------ 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ +++    + K S  +            + NKP G         +  +   +    D
Sbjct: 43  PEEDVVEVDGRVAKFSRQI----------YIMMNKPKGYVCSNDDPASLTVFSLISD--D 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K +      RLD++  G+L++        H   S + R  ++    L   + + K +  
Sbjct: 91  LKYRDLHTVGRLDKDAEGLLIIT-DDGEYTHRVISPKKRIEKEYLVRLEKEVDEEKLKEF 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N ++                  G     + + +ID    K C  E     G+ HQ++  
Sbjct: 150 ENGIILDD---------------GYKTLPAKYTIIDSTTVKLCIYE-----GKYHQVKRM 189

Query: 259 ALHMG 263
              +G
Sbjct: 190 FEAIG 194


>gi|256617552|ref|ZP_05474398.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256597079|gb|EEU16255.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
          Length = 244

 Score = 66.5 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 88/251 (35%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 1   MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +           F+  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 43  EETDQI----------AFMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 89  DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G+ HQ+
Sbjct: 146 CQLFA------------QGFALKDGEMVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 192

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 193 KRMLATVGKPV 203


>gi|256825344|ref|YP_003149304.1| pseudouridine synthase family protein [Kytococcus sedentarius DSM
           20547]
 gi|256688737|gb|ACV06539.1| pseudouridine synthase family protein [Kytococcus sedentarius DSM
           20547]
          Length = 284

 Score = 66.5 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 56/288 (19%), Positives = 97/288 (33%), Gaps = 55/288 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +  RL +         +    ++++  G+V VD   V      + G  VRI P       
Sbjct: 45  QGERLQKVLAAAGLG-SRRACEQMIADGRVEVDGVPVT-----ELG--VRIDPSRQ---- 92

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +     + L +     VFNKP G+             G    +
Sbjct: 93  ---------------KVAVDGLPVQLDDSKVYLVFNKPVGVISTMEDEEGRLSVG---DY 134

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             ++ ++     RLDQ+TSG+L++      A  L        + K Y + V G  K    
Sbjct: 135 TYTRKERLFHVGRLDQDTSGLLLLTNDGELAHRL--QHPSYSVPKTYVAKVPGPVKKGLG 192

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                LL++     D V  V             F V+      +  +++  H GR H +R
Sbjct: 193 ----NLLREGVELEDGVVKVDD-----------FSVVASQP-GWAMVQLVIHEGRKHVVR 236

Query: 257 VHALHMGCPI-------VGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
                +G P+       VG+ +      GN  +   ++L    + + L
Sbjct: 237 RLLEEVGYPVEELVRTQVGEIRMGDLRPGNLRAVTPDELARTMKLVGL 284


>gi|218132474|ref|ZP_03461278.1| hypothetical protein BACPEC_00333 [Bacteroides pectinophilus ATCC
           43243]
 gi|217992584|gb|EEC58586.1| hypothetical protein BACPEC_00333 [Bacteroides pectinophilus ATCC
           43243]
          Length = 62

 Score = 66.5 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 7/67 (10%)

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQ-NKLYLHARYMDLPHPEGGR-LQITAPLPAHMV 316
              +G P++GD  Y      N  SP +     LHAR +   HP   + ++  APLP +  
Sbjct: 1   MASIGHPLLGDDVYS-----NAVSPYKLQGQTLHARVLGFIHPRTNQYIEFEAPLPEYFS 55

Query: 317 KTWDSLG 323
              D L 
Sbjct: 56  HLLDILR 62


>gi|194016715|ref|ZP_03055328.1| ribosomal large subunit pseudouridine synthase B [Bacillus pumilus
           ATCC 7061]
 gi|194011321|gb|EDW20890.1| ribosomal large subunit pseudouridine synthase B [Bacillus pumilus
           ATCC 7061]
          Length = 290

 Score = 66.5 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 39/268 (14%), Positives = 91/268 (33%), Gaps = 54/268 (20%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQS 61
           +++    +V E  ++  RL +    H    +    +++++ G+V V+ + V     ++ S
Sbjct: 32  VLSQASKIVHEVKDKMERLQKVIA-HAGVASRRKAEELIKEGRVTVNGQTVTELGVKVGS 90

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              + +                      L    +     +LY         KP G+    
Sbjct: 91  SDKIEVN--------------------GLKLEREEPVYFMLY---------KPRGVIS-- 119

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            +         +  + D   Q+     RLD +TSG++++      A  L        I K
Sbjct: 120 -AAEDDKGRKVVTDFFDDVPQRLYPIGRLDYDTSGLILITNDGEFAHKL--MHPKYEIDK 176

Query: 182 IYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
            Y + + GIP  +  ++     +L           ++  +++                ++
Sbjct: 177 TYAAKLKGIPSKELLRKLEKGIMLDHKKTARARAKMLSIDKR----------------KQ 220

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              +++  H GR  Q+R     +G  ++
Sbjct: 221 TSIVQLTIHEGRNRQVRRMFEAIGHDVL 248


>gi|163816624|ref|ZP_02207987.1| hypothetical protein COPEUT_02814 [Coprococcus eutactus ATCC 27759]
 gi|158447881|gb|EDP24876.1| hypothetical protein COPEUT_02814 [Coprococcus eutactus ATCC 27759]
          Length = 239

 Score = 66.5 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 80/248 (32%), Gaps = 56/248 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   +++ ++ G V V+      ++                     
Sbjct: 1   MRLDKFLVEMNIG-SRSQVKQYIKKGMVSVNGTNAASSD--------------------- 38

Query: 79  KEQKILDSSVNLTKHSDFLK---SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                    + + + +D +K     L Y   + ++ NKPAG        +   +   L  
Sbjct: 39  ---------MKINEDTDTIKYNGKQLCYSKYRYFLLNKPAGCVSATKDNVHQTVIDLLN- 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                 +      RLD +T G+L++    R A   L+       I K Y++ + G     
Sbjct: 89  --GENTKDLFPVGRLDLDTEGLLIITNDGRLAHHLLS---PAHHIAKTYYADIDGY---- 139

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTH 253
                   +    I      +   ++     A    K+I+   +     +E+    GR H
Sbjct: 140 --------VDDQTISLFKQGIDIGDDTPTLPA--SLKIIEADRSTGSSRIELTITEGRFH 189

Query: 254 QLRVHALH 261
           Q++     
Sbjct: 190 QVKRMFQA 197


>gi|125625272|ref|YP_001033755.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. cremoris MG1363]
 gi|124494080|emb|CAL99081.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. cremoris MG1363]
          Length = 328

 Score = 66.5 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 43/244 (17%), Positives = 84/244 (34%), Gaps = 41/244 (16%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRLD++        +   ++ +L+ G+V V            +G++ R        N  
Sbjct: 86  GMRLDKFLAESGLG-SRSEVKVLLKKGRVTV------------AGEIQRDGRFQVDKN-- 130

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                        ++   F   IL Y++   Y+ NKP G+       +   +   L    
Sbjct: 131 -------------SRQVAFDGQILDYQEYYYYLLNKPQGVVSATKDNVFKTVVQLLSEKD 177

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             K   P    RLD+ T G+L++    A    LT+    + ++K Y++ + G   +  E 
Sbjct: 178 FRKDIFP--VGRLDKNTEGLLILTNDGALGHDLTQ--PKKHVEKEYFARIDGKVTD--EI 231

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I  +    +   G+               +      D  +     + +  H G+ HQ++ 
Sbjct: 232 INKFAEGLTLKNGEKAR-------PGELFVEKTYKGDSQSGWVSEIRVIIHEGKFHQVKR 284

Query: 258 HALH 261
               
Sbjct: 285 MFEA 288


>gi|315170764|gb|EFU14781.1| conserved hypothetical protein [Enterococcus faecalis TX1342]
          Length = 257

 Score = 66.5 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 14  MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGNVVK-----------------EAKTQVN 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 56  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 101

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 102 DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 158

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G+ HQ+
Sbjct: 159 CQLFA------------QGFALKDGEIVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 205

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 206 KRMLATVGKPV 216


>gi|296877269|ref|ZP_06901309.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 15912]
 gi|296431789|gb|EFH17596.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 15912]
          Length = 242

 Score = 66.5 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 91/248 (36%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+  ++ V+ K+     ++Q      I P  + +    
Sbjct: 1   MRLDKFLVDCGVG-SRTEVKQLLKQKKIAVNGKKETAG-KLQ------IDPGKDRVT--- 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                            F+   L++E    Y+ NKPAG+           +   L     
Sbjct: 50  -----------------FMGEDLVHETFVYYLLNKPAGVISATEDDHHQTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-- 195
            K  +     RLD +T G+L++    + A   L+     + + KIY + V GI       
Sbjct: 93  HK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVSKIYRAQVAGIMDEADVA 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
              A   LK        + +++ NE  A+                 ++E++   G+ HQ+
Sbjct: 148 RFEAGIALKDFTTLPARLQILEVNEANAS----------------SYVEIEIAEGKFHQV 191

Query: 256 RVHALHMG 263
           +      G
Sbjct: 192 KRMVAACG 199


>gi|255099545|ref|ZP_05328522.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-63q42]
          Length = 240

 Score = 66.5 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 85/246 (34%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D+   N   + +   ++K  + G V V+   V        G  V             
Sbjct: 5   QRIDKILSN-LGYGSRSEIKKYCKQGSVVVNGSEVS-----NPGTQVD-----------T 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  +IL +              ++Y +    + NKPAG            +   +   + 
Sbjct: 48  ENDEILFNGEE-----------VIYREYIYLMMNKPAGYISATTDKYDPTVLDLID--LS 94

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +P    RLD++T G+LV+    + + + L+     + + K Y++ + G+   +   
Sbjct: 95  YLVFEPFPVGRLDKDTEGLLVLTNDGKLSHRVLS---PKKHVPKTYYAKIDGVVTEED-- 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +  +L                 + G     S   ++   +     +E+  H G+ HQ++ 
Sbjct: 150 VEAFLEG------------VVLDDGYKTMPSQLNILK--SDDESEIELTIHEGKFHQVKR 195

Query: 258 HALHMG 263
               +G
Sbjct: 196 MFESVG 201


>gi|312622236|ref|YP_004023849.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202703|gb|ADQ46030.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
          Length = 240

 Score = 66.5 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 86/250 (34%), Gaps = 49/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL ++        +    ++I+  G+V+V+ + V                       + 
Sbjct: 5   VRLQKFMA-QCGVASRRKCEEIILQGRVKVNGELVN-----------------QLGFKVD 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ +++              I+L         NKP G+     +         +    D
Sbjct: 47  PEKDVVEVDGKRISPQMQKVYIML---------NKPFGVIS--SAKDEKGRKTVVDLVKD 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-EC 197
               +     RLD +T+G++++      A  +T       I+K Y +L+ GIP  K+ E 
Sbjct: 96  KVNVRVFPVGRLDFDTTGLILLTNDGEFAYKVT--HPKHDIEKTYIALIKGIPSKKEIER 153

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               LL    +                 A + FK++         +E++ H GR  Q+R 
Sbjct: 154 FEKGLLIDGKM----------------TAPAKFKILKLINGNA-LVEIKIHEGRNRQIRK 196

Query: 258 HALHMGCPIV 267
               +G  ++
Sbjct: 197 MCDQIGHKVL 206


>gi|295696969|ref|YP_003590207.1| pseudouridine synthase [Bacillus tusciae DSM 2912]
 gi|295412571|gb|ADG07063.1| pseudouridine synthase [Bacillus tusciae DSM 2912]
          Length = 250

 Score = 66.5 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 86/252 (34%), Gaps = 50/252 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLDR         +  +++K+ RSG + VD + V+                 +A  H
Sbjct: 2   AKQRLDRILAEMGVG-SRRDIKKMARSGLIEVDGRVVR-----------------DASLH 43

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +   Q++L  + +           + Y+    ++ NKP G+           +   L   
Sbjct: 44  VDPGQQVLCVAGHP----------VHYQPFHYWMMNKPPGVVSAVIDPRHRTVIDLLDE- 92

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              +  +     RLD +T G +++      A   L+     R + K Y + V G   +  
Sbjct: 93  -SDRTPRLFPAGRLDIDTEGFVLITDDGQLAHAILS---PKRHVSKTYRATVQGRVSDA- 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                    +  + GD           A  A    +     A +   +E+    G+ HQ+
Sbjct: 148 ---DVAAFARGLVLGDGYR--------ALPAHLQIR----DAGERSEVEIVLREGKFHQI 192

Query: 256 RVHALHMGCPIV 267
           +     +G P++
Sbjct: 193 KRMFAALGKPVL 204


>gi|221231179|ref|YP_002510331.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           pneumoniae ATCC 700669]
 gi|220673639|emb|CAR68127.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus pneumoniae ATCC 700669]
          Length = 240

 Score = 66.5 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 88/246 (35%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L+SG+V V+ K+ K + ++Q                I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNMLKSGRVTVNGKKEK-SAKLQ----------------ID 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E+  +           F   +L YE+   Y+ NKP G+           +   L     
Sbjct: 43  EERDEI----------RFDGQVLEYEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDIAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           SK  +     RLD +T G+L++    + A   L+     R + K Y + V GI   +   
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNDGKLAHALLS---PKRHVDKTYLAQVKGIMTQED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   +   +     A      +D   +    + +    G+ HQ++ 
Sbjct: 146 -----------AETFAKGIPLKDFTCQPARLELVSVDTK-KNQSQIRVTIAEGKFHQVKR 193

Query: 258 HALHMG 263
              + G
Sbjct: 194 MVGYCG 199


>gi|251782725|ref|YP_002997028.1| ribosomal small subunit pseudouridine synthaseA [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|242391355|dbj|BAH81814.1| ribosomal small subunit pseudouridine synthaseA [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
          Length = 245

 Score = 66.5 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 85/246 (34%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L+   + V+ + V+ + ++Q      I    + + ++ 
Sbjct: 3   MRLDKFLVETGVG-SRSQVKSLLKKKAILVN-QEVETSPKVQ------INEHKDVVTYLG 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K                     L YE    Y+ NKPAG            +   L     
Sbjct: 55  KP--------------------LTYEAFVYYILNKPAGFLSATKDRAQATVIDLLDETAR 94

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K        RLD++T G+L++      A  L      + + K Y + V GI  +     
Sbjct: 95  QK--DVFPVGRLDKDTRGLLLLTNNGQLAHDL--LSPKKHVTKEYLAKVAGIMTDAD--- 147

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRV 257
                       D+   +   +     A    +V+D   +Q+ C + +    G+ HQ++ 
Sbjct: 148 ----------KDDFAKGISLKDHQCLPA--KLEVLDKDLSQETCVVSITIQEGKFHQVKR 195

Query: 258 HALHMG 263
                G
Sbjct: 196 MVAACG 201


>gi|108799895|ref|YP_640092.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           MCS]
 gi|119869005|ref|YP_938957.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           KMS]
 gi|126435523|ref|YP_001071214.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           JLS]
 gi|108770314|gb|ABG09036.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           MCS]
 gi|119695094|gb|ABL92167.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           KMS]
 gi|126235323|gb|ABN98723.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium sp.
           JLS]
          Length = 247

 Score = 66.5 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 40/252 (15%), Positives = 73/252 (28%), Gaps = 45/252 (17%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + + +RL +         +    +K++  G+V VD   V                     
Sbjct: 3   EPDGVRLQKVLSQA-GIASRRVAEKMILDGRVEVDGHIVT-------------------- 41

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +        + + +      L   L++        NKP G+             G L 
Sbjct: 42  -ELGTRVDPTAADIRVDGTRVLLDDTLVH-----LAINKPRGMHSTMSDDRGRPCIGDLV 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  +      RLD +T G++++      A  L        + K Y + V G     
Sbjct: 96  EHRVRGNKGLFHVGRLDADTEGLMLLTNDGELAHRL--MHPSYEVPKTYVATVLG----- 148

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              +   L KK   G +               +  F V+D        + +  H GR   
Sbjct: 149 --TVPRGLGKKLRAGVEL--------DDGPARVDDFAVVDAMP-GRSMVRVTLHEGRKRI 197

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 198 VRRLLAAVGFPV 209


>gi|157692817|ref|YP_001487279.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
 gi|157681575|gb|ABV62719.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
          Length = 281

 Score = 66.5 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 48/266 (18%), Positives = 94/266 (35%), Gaps = 50/266 (18%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQS 61
           +++    +V E  ++  RL +    H    +    +++++ G+V V+ + V     ++ S
Sbjct: 23  VLSQASKIVHEVKDKMERLQKVIA-HAGVASRRKAEELIKEGRVTVNGQTVTELGVKVGS 81

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              + +                      L    +     +LY         KP G+    
Sbjct: 82  SDKIEVN--------------------GLKLEREEPVYFMLY---------KPRGVIS-- 110

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            +         +  + D   Q+     RLD +TSG++++      A  L        I K
Sbjct: 111 -AAEDDKGRKVVTDFFDDVPQRLYPIGRLDYDTSGLILITNDGEFAHKL--MHPKYEIDK 167

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y + + GIP  +       LL+K   G      +  + K    A +    ID   Q  C
Sbjct: 168 TYAAKLKGIPSKE-------LLRKLEKG------IMLDHKKTAPARAKMLSIDKRKQ-TC 213

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIV 267
            +++  H GR  Q+R     +G  ++
Sbjct: 214 IVQLTIHEGRNRQVRRMFEAIGHDVL 239


>gi|138896374|ref|YP_001126827.1| ribosomal small subunit pseudouridine synthase A [Geobacillus
           thermodenitrificans NG80-2]
 gi|196250000|ref|ZP_03148695.1| pseudouridine synthase [Geobacillus sp. G11MC16]
 gi|134267887|gb|ABO68082.1| Ribosomal small subunit pseudouridine synthase A [Geobacillus
           thermodenitrificans NG80-2]
 gi|196210514|gb|EDY05278.1| pseudouridine synthase [Geobacillus sp. G11MC16]
          Length = 248

 Score = 66.5 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 83/247 (33%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVRIPPVINALNH 76
           +R+D+    H  +     ++K+L+SG V+VD   V     +++   Q V +         
Sbjct: 3   LRIDKLLA-HMGYGTRKEVKKLLKSGLVKVDGAAVYDPKTKVRPDEQTVTVWGETVEYKQ 61

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            I                               + NKP G+       +   +   L+  
Sbjct: 62  FI-----------------------------YLMMNKPPGVISATEDAVEETVVDLLEE- 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            + +   P    RLD++T G+L++      A  L      + + K Y++++ G       
Sbjct: 92  -EDRLFDPFPVGRLDKDTEGLLLLTNDGQLAHQL--LAPKKHVPKTYFAVIDGEVTEDD- 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +  +             VV  +      A    +++   +     +E+    G+ HQ++
Sbjct: 148 -VEAF----------RRGVVLDDGYETKPA----ELVVLKSGLRSDVEVTITEGKFHQVK 192

Query: 257 VHALHMG 263
                +G
Sbjct: 193 RMFQAVG 199


>gi|134101741|ref|YP_001107402.1| pseudouridylate synthase ribosomal large subunit [Saccharopolyspora
           erythraea NRRL 2338]
 gi|291003087|ref|ZP_06561060.1| pseudouridylate synthase ribosomal large subunit [Saccharopolyspora
           erythraea NRRL 2338]
 gi|133914364|emb|CAM04477.1| pseudouridylate synthase ribosomal large subunit [Saccharopolyspora
           erythraea NRRL 2338]
          Length = 253

 Score = 66.5 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 49/266 (18%), Positives = 89/266 (33%), Gaps = 52/266 (19%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M+  +        E +RL +         +    ++++  G+V V+ + V          
Sbjct: 1   MSEHRSPTNSPSAEGVRLQKVLSQA-GVASRRAAEQMIVEGRVEVNGEIV---------- 49

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                  +     +  +  ++    N    +  L  +LL         NKP GI      
Sbjct: 50  -------LELGTRVDPDTAVIHVDGNRIMVNADLTHLLL---------NKPKGILCTMSD 93

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                  G    ++  +  +     RLD ++ G+L++      A  L       RI K Y
Sbjct: 94  DQGRPCIG---DYLRERQGRLYHVGRLDVDSEGLLLITNDGELAHRL--MHPSYRILKTY 148

Query: 184 WSLVWG-IPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            + V G IPKN    + N + L+   +  D   +V  NE                     
Sbjct: 149 LAEVPGPIPKNLGRELRNGIELEDGPVKVDSFKLVDVNE------------------GRA 190

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIV 267
            +E+  H GR H +R     +G P++
Sbjct: 191 LVEVVLHEGRKHVVRRLLKQVGHPVL 216


>gi|307707699|ref|ZP_07644178.1| RNA pseudouridine synthase family protein [Streptococcus mitis NCTC
           12261]
 gi|307616197|gb|EFN95391.1| RNA pseudouridine synthase family protein [Streptococcus mitis NCTC
           12261]
          Length = 240

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 85/245 (34%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + ++Q         +    + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKLQ---------IDEERDEIR 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + K+L+                 YE+   Y+ NKP G+           +   L     
Sbjct: 50  FDGKVLE-----------------YEEFVYYMMNKPQGVISATEDPKHRTVLDLLDDIAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK  +     RLD +T G+L++      A  L      R + K Y   V GI       I
Sbjct: 93  SK--EVFPVGRLDIDTHGLLLLTNDGQLAHAL--LSPKRHVNKTYLVQVKGIMTQGDVDI 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +   +     A      ID   +    + +    G+ HQ++  
Sbjct: 149 -------------FAEGIPLKDFTCQPARLELVSIDT-EKNQSQIRVTIAEGKFHQVKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 VGYCG 199


>gi|229010875|ref|ZP_04168072.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
 gi|228750549|gb|EEM00378.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
          Length = 242

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 87/252 (34%), Gaps = 60/252 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +++++ G+V+V+ K VK    ++     V +          
Sbjct: 2   ERLQKVIAQA-GIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                      N+    +     LLY         KP G+  SV    G        +  
Sbjct: 52  -----------NIPLEKEEPVYFLLY---------KPTGVISSVSDDKGR-----NVVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     Q+     RLD +TSG+L++      A  L       +I+K Y + + G      
Sbjct: 87  FFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANVL--MHPRYKIEKTYVAKIKG------ 138

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNE--KGANYAISHFKVIDCFAQK-FCWLEMQPHTGRT 252
                       + G+ + ++++    +    A +  K+I    +K    +++  H GR 
Sbjct: 139 -----------PLTGEKIRMLERGVALEDGKTAPAQAKIISWDKRKEMAIVQLTIHEGRN 187

Query: 253 HQLRVHALHMGC 264
            Q+R     + C
Sbjct: 188 RQVRRMFEALDC 199


>gi|289435297|ref|YP_003465169.1| ribosomal large subunit pseudouridine synthase B [Listeria
           seeligeri serovar 1/2b str. SLCC3954]
 gi|289171541|emb|CBH28087.1| ribosomal large subunit pseudouridine synthase B [Listeria
           seeligeri serovar 1/2b str. SLCC3954]
 gi|313632602|gb|EFR99592.1| ribosomal large subunit pseudouridine synthase B [Listeria
           seeligeri FSL N1-067]
 gi|313637139|gb|EFS02679.1| ribosomal large subunit pseudouridine synthase B [Listeria
           seeligeri FSL S4-171]
          Length = 243

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 84/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +   N     +    + +++ G+V V+ K V     ++   + + +          
Sbjct: 2   ERLQKVIANA-GITSRRKAETLIKEGKVTVNGKVVTELGVKVSGSERIEV---------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                     + LTK           E+ + ++F KP G      +         +  + 
Sbjct: 51  --------EGIQLTK-----------EEHRYFLFYKPRGTVS---AVTDDKGRTTVADYF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  L        + K Y + + GIP+ +   
Sbjct: 89  TDIPERLYPVGRLDYDTSGLLLMTNDGDFANLL--MHPKNEVSKTYIARIKGIPERE--- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   L +   I G      K   + ++ A           +    +E+  H GR  Q+R 
Sbjct: 144 VIRELERGVVIDGRKTAPAKVKIRSSDKA-----------KDKAIVEITIHEGRNRQVRK 192

Query: 258 HALHMGC 264
               +G 
Sbjct: 193 MFEAVGF 199


>gi|225389037|ref|ZP_03758761.1| hypothetical protein CLOSTASPAR_02782 [Clostridium asparagiforme
           DSM 15981]
 gi|225044895|gb|EEG55141.1| hypothetical protein CLOSTASPAR_02782 [Clostridium asparagiforme
           DSM 15981]
          Length = 247

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 90/250 (36%), Gaps = 56/250 (22%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             +RLD++            +++++R G++ V+ + V+  +       ++I P  + +  
Sbjct: 7   AMIRLDKFLTEMGRG-TRSQVKEMVRKGRITVNGQAVRQAD-------LKINPEADQIC- 57

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                 + + Y  ++ Y+ NKP G+      G    +   +   
Sbjct: 58  -------------------LDGAAVAYARTEYYMLNKPQGVVSATEDGRYQTVTELITGA 98

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
           +           RLD +T G+L++      A   L+     + + K+Y++ + G +P++ 
Sbjct: 99  LRG---DIFPVGRLDIDTEGLLLLTNDGSLAHNLLS---PRKHVDKVYFARIEGQLPEDA 152

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
               A  L+                E G     +  ++++        + +    G+ HQ
Sbjct: 153 VGRAAAGLVL---------------EDGTKTLPARLEILEPGQ-----VRLTIREGKFHQ 192

Query: 255 LRVHALHMGC 264
           ++     MGC
Sbjct: 193 VKRMFEAMGC 202


>gi|145629302|ref|ZP_01785101.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae 22.1-21]
 gi|144978805|gb|EDJ88528.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae 22.1-21]
          Length = 232

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 82/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +R   V+++ + VK                      I 
Sbjct: 1   MRLDKFIAENV-GLTRSQATKAIRQSAVKINGEIVKS-----------------GSVQIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E +I      LT            E+ + ++ +KP G       G    I  F    + 
Sbjct: 43  QEDEIYFEDELLTWI----------EEGQYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 93  G---KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + +          +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPVEENYAAACSEGILLRGEKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|23099754|ref|NP_693220.1| 16S pseudouridine synthase [Oceanobacillus iheyensis HTE831]
 gi|22777984|dbj|BAC14255.1| 16S pseudouridine synthase [Oceanobacillus iheyensis HTE831]
          Length = 237

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 91/249 (36%), Gaps = 55/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N     +   ++++L+S ++ V++  VK                        
Sbjct: 2   MRLDKLLSNMGVG-SRKEVKQLLKSKRITVNEVIVK------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFL---KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 DS +++    D +     ++ Y+     + +KP G+           +   L +
Sbjct: 37  ------DSGMHVDPEYDQIFVDDQLISYQKHIYLMMHKPPGVVSATVDNRDRTVIDLLSA 90

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             D K  +P    RLD++T G+L++      A  LT     + ++K+Y + + G      
Sbjct: 91  --DEKKFEPFPVGRLDKDTEGLLLITNDGELAHRLT--SPKKHVEKVYIAHISGEFPEN- 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +  +    +   G          K A         ++   ++   +++    G+ HQ+
Sbjct: 146 -IVEQFQEGLTLEDG-------YQTKPAK--------LEILNKQSKEVKVTITEGKYHQI 189

Query: 256 RVHALHMGC 264
           +   + +GC
Sbjct: 190 KRMFIAVGC 198


>gi|319776127|ref|YP_004138615.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae F3047]
 gi|329123291|ref|ZP_08251859.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           aegyptius ATCC 11116]
 gi|317450718|emb|CBY86938.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae F3047]
 gi|327471500|gb|EGF16948.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           aegyptius ATCC 11116]
          Length = 232

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 82/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +R   V+++ + VK                      I 
Sbjct: 1   MRLDKFIAEN-TGLTRSQATKAIRQSAVKINGEIVKS-----------------GAVQIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E KI      LT            E+ + ++ +KP G       G    I  F    + 
Sbjct: 43  QEDKIYFEDELLTWV----------EEGQYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 93  G---KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + +          +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPVEENYAAACSEGILLRGEKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|257869547|ref|ZP_05649200.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257803711|gb|EEV32533.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 238

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 88/250 (35%), Gaps = 52/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++ +G+V V+ + VK    ++ +   V +          
Sbjct: 2   ERLQKVIA-HAGITSRRKAEELIVAGRVSVNGQIVKELGVQVSAKDRVEVD--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       +    +     +LY         KP G+     +         +  + 
Sbjct: 52  -----------GVPIEQESPVYYMLY---------KPRGVIS---AVTDDKKRKVVLDFF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      +Q L        + K+Y + V GI   K+  
Sbjct: 89  TEVPERLYPIGRLDYDTSGLLLLTNDGDLSQKL--MHPKHEVDKVYVAKVKGIADKKQLL 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLR 256
               L +   I            +G   A + F+++    A +   +++  H GR HQ++
Sbjct: 147 ---PLSRGIRI------------EGKKTAPARFEILSTDAATQTSIVQLTIHEGRNHQVK 191

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 192 NMLKAVGLPV 201


>gi|317128531|ref|YP_004094813.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
 gi|315473479|gb|ADU30082.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
          Length = 242

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 83/252 (32%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++  G+V V+  +V      + G  V +           
Sbjct: 5   ERLQKVIAQA-GVTSRRKAEQLILEGKVIVNGNKVT-----ELGTKVDLQH--------- 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSW 136
              +++   V L K                ++  KP G+  SV    G     D      
Sbjct: 50  --DEVIVEGVPLEKEEPI-----------YFLLYKPTGVISSVDDEKGRKVVTDFI---- 92

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNK 194
                ++     RLD +TSG++++      A  L        I K Y + V G+P  ++ 
Sbjct: 93  --PTDKRIFPIGRLDYDTSGLILLTNDGDFANLL--MHPKHEIYKTYIAKVEGVPLREDI 148

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K+      L+        V V + ++K     I                E+  H GR  Q
Sbjct: 149 KKLEKGIHLEDGRTAPAKVKVSRSDKKKGTSII----------------EISIHEGRNRQ 192

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 193 VRRMFEAIGHPV 204


>gi|225574967|ref|ZP_03783577.1| hypothetical protein RUMHYD_03046 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037814|gb|EEG48060.1| hypothetical protein RUMHYD_03046 [Blautia hydrogenotrophica DSM
           10507]
          Length = 246

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 85/248 (34%), Gaps = 51/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +         ++K +   QV+V+ K V                       + 
Sbjct: 4   IRLDKYLADAGAG-TRSEVKKYISKAQVQVNGKTV-----------------------LN 39

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSK-IYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +KI    V +          +++ D    Y+ +KPAG      S      +  +  +V
Sbjct: 40  PAEKIEPEEVEVCCLGQ-----VVHVDRYEYYLLHKPAGCV----SATEDVRERTVMEFV 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            S+ +      RLD++T G+L++      A  L      R + K Y++ + G    +   
Sbjct: 91  PSRRKDLFPVGRLDKDTEGLLLITNDGELAHRL--LAPRRHVPKQYFAQIKGKMTQED-- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKF-CWLEMQPHTGRTHQL 255
                         +   V+  EK     A      ++   + +   + +    G+ HQ+
Sbjct: 147 -----------AQKFRQGVEIGEKNPTLPAKLEILSVENGEEGWISCINLTIEEGKFHQI 195

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 196 KRMVQAVG 203


>gi|115380386|ref|ZP_01467383.1| ribosomal large subunit pseudouridine synthase B [Stigmatella
           aurantiaca DW4/3-1]
 gi|310821617|ref|YP_003953975.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115362608|gb|EAU61846.1| ribosomal large subunit pseudouridine synthase B [Stigmatella
           aurantiaca DW4/3-1]
 gi|309394689|gb|ADO72148.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 648

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 91/250 (36%), Gaps = 50/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL ++        +  + ++++ +G+V V+ ++V    +R++ G               
Sbjct: 3   ERLQKYLARA-GVASRRHAEELITAGRVMVNNQKVTELGSRVEPG--------------- 46

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                ++     L    +     LLY         KPAG+     +         + S+V
Sbjct: 47  ---TDLVSVDGELVSLPETSSYYLLY---------KPAGVVT---TLSDPQGRPTVASYV 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           ++ G++     RLD +  G L+       A  LT      ++ + Y + V G P      
Sbjct: 92  EATGKRLFPVGRLDYDAEGALLFTDDGTLAHKLT--HPSFQVPRTYLAKVKGSPD----- 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                  ++ +      V  ++      ++  F+     A++  WL++    GR H ++ 
Sbjct: 145 -------RATLEKLRGGVRLEDGMATPLSVDLFE----QAERNTWLKIVVAEGRPHLIKR 193

Query: 258 HALHMGCPIV 267
               +G P+V
Sbjct: 194 LCAAVGHPVV 203


>gi|325697447|gb|EGD39333.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK160]
          Length = 242

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 84/246 (34%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   +++ L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQFLKKGLVLVNGRAEKS----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I +++  +      L     YE    Y+ NKP G+           +   L     
Sbjct: 37  PKTQIDETADEIVVSGQRLT----YEKFVYYLLNKPQGVISATEDDRHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+       
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLM------ 141

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   ++  +     A      +D  A++   +E+    G+ HQ++ 
Sbjct: 142 -------NQADVERFAAGIELKDFTCQPAQLKIVELD-EAKETSLVEITLAEGKFHQVKR 193

Query: 258 HALHMG 263
                G
Sbjct: 194 MVASCG 199


>gi|226941109|ref|YP_002796183.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
 gi|226716036|gb|ACO75174.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 703

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 77/246 (31%), Gaps = 46/246 (18%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           MRL +        + +  ++ +++ +G+V ++    +   R++ G  VR+          
Sbjct: 453 MRLQKALA--LAGLGSRRDMDELVAAGRVSINGAVAELGARVRPGDKVRV---------- 500

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                  DS   L +  D L  +++Y        +K  G  V                  
Sbjct: 501 -------DSKPVLIRWPDRLPRVIVY--------HKQEGEIVTRDDPEGRT--TVFDRLP 543

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            ++  K     RLD  TSG+L+   +   A  +T        +     L    P+  KE 
Sbjct: 544 QTRSSKWVAIGRLDVNTSGLLIFTTSGDLANRMTHPSFEVEREYAVRVLGKLTPEQMKET 603

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            A   L        ++      E   N+                W  +    GR  ++R 
Sbjct: 604 TAGVQLDDGPASFQFIREDDDKEDSVNH----------------WYRVGIREGRNREVRR 647

Query: 258 HALHMG 263
              H G
Sbjct: 648 MFEHFG 653


>gi|313901058|ref|ZP_07834546.1| 16S pseudouridylate 516 synthase [Clostridium sp. HGF2]
 gi|312954016|gb|EFR35696.1| 16S pseudouridylate 516 synthase [Clostridium sp. HGF2]
          Length = 233

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 37/248 (14%), Positives = 81/248 (32%), Gaps = 58/248 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSG-QVVRIPPVINALNH 76
           MRLD++  +         ++  +R G+V V+ +  + ++R IQ G  VV +         
Sbjct: 1   MRLDKYLAHAGLG-TRKEVKLAIRKGRVSVNGEVCRKDDRKIQEGVDVVCLD-------- 51

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                K  + YE     + NKP  +           +   + ++
Sbjct: 52  ---------------------KEEIYYEAVVYIMLNKPQDVVSATSDPTYETVLDCIDAF 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +           RLD +T G+L++    + A + L+    + +   +  +        KK
Sbjct: 91  LPKDC---FPVGRLDMDTEGLLLITNDGKLAHRLLSPKHHVEKTYLVDLAQPLQEGDQKK 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
               + +L +  +    V +++                         + +    GR HQ+
Sbjct: 148 LENGSIVLDEEPVLPARVEILED----------------------TQILLHIQEGRFHQV 185

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 186 KRMLHAIG 193


>gi|145630739|ref|ZP_01786517.1| tRNA pseudouridine synthase C [Haemophilus influenzae R3021]
 gi|144983621|gb|EDJ91081.1| tRNA pseudouridine synthase C [Haemophilus influenzae R3021]
          Length = 72

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 259 ALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             H+  PI+GD +Y      +   +    ++L+LH+  +   HP     + ITA L    
Sbjct: 1   MKHIFHPILGDTQYGDLHQNRALMSHLGCSRLFLHSDSLSFIHPITKEQITITAGLDEQW 60

Query: 316 VKTWDSLGFK 325
            +  +  G++
Sbjct: 61  QQLMNQFGWE 70


>gi|94499453|ref|ZP_01305990.1| Hypothetical protein yjbC [Oceanobacter sp. RED65]
 gi|94428207|gb|EAT13180.1| Hypothetical protein yjbC [Oceanobacter sp. RED65]
          Length = 376

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 36/254 (14%), Positives = 80/254 (31%), Gaps = 56/254 (22%)

Query: 15  DEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ++   RL+++       I +     + +  G V ++ KR +  +R+  G  V++      
Sbjct: 3   NDSTTRLNKYISE--SGICSRREADRYIEQGNVYINGKRAEVGDRVAPGDTVKVN----- 55

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              II+ Q+                     ED      NKP GI     S    +I  F+
Sbjct: 56  -GQIIEPQEP--------------------EDFVFIALNKPVGIVSTTESSERNNIVRFV 94

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                    +     RLD+++ G++ +         +  +      + +           
Sbjct: 95  -----GHSTRIFPIGRLDKDSQGLIFLTNNGDLVNKILRAGNDHEKEYLV---------E 140

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             + I +  ++    G   +  + +  K    + + F++                 G   
Sbjct: 141 VNKPIRDNFIEGMANGVPILGTMTKKCKVKKESPTVFRI-------------TLVEGLNR 187

Query: 254 QLRVHALHMGCPIV 267
           Q+R    + G  +V
Sbjct: 188 QIRRMCEYFGYDVV 201


>gi|302871978|ref|YP_003840614.1| RNA-binding S4 domain protein [Caldicellulosiruptor obsidiansis
           OB47]
 gi|302574837|gb|ADL42628.1| RNA-binding S4 domain protein [Caldicellulosiruptor obsidiansis
           OB47]
          Length = 233

 Score = 66.2 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 88/245 (35%), Gaps = 51/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   H    +   ++K++R G V V+ K           Q+V +   IN      
Sbjct: 1   MRLDKFLT-HCGFGSRTQVKKLIREGIVTVNGK-----------QIVEVDFKIN------ 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ +++    + K S ++            + NKP G        ++  +   +    D
Sbjct: 43  PEEDVVEVDGRVVKFSRWI----------YIMMNKPKGYVCSNEDPMSLTVFSLISD--D 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K +      RLD++  G+L++        H   S + R  ++    L   + + + +  
Sbjct: 91  LKHRDLHTVGRLDKDAEGLLIITDNGE-YTHRVISPKKRIEKEYLVRLEKEVDEERLKEF 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N ++                  G     + + +ID    K C  E     G+ HQ++  
Sbjct: 150 ENGIILDD---------------GYKTLPAKYTIIDSTTVKLCIYE-----GKYHQVKRM 189

Query: 259 ALHMG 263
              +G
Sbjct: 190 FEAIG 194


>gi|223999175|ref|XP_002289260.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220974468|gb|EED92797.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 571

 Score = 66.2 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 31/144 (21%), Positives = 48/144 (33%), Gaps = 13/144 (9%)

Query: 181 KIYWSLVWGIPKNKK--ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
             Y     G PK+ K    +    ++ S  G       K        +++   V      
Sbjct: 407 TFYMCASIGEPKDGKFRVIVEPSRIQTSPDGMSPSDAAKTELPEMRPSLTKCSVAWRGNM 466

Query: 239 KFCWLE---------MQPHTGRTHQLRVHALHM-GCPIVGDHKYCANFKGNFTSPIQNKL 288
                +         ++P TGR HQLRVH   + G PI+GD  Y            + ++
Sbjct: 467 NTSSSKKNIPVTKVFLKPWTGRRHQLRVHLALVAGFPILGDVAYSKEETKQRVMTCE-RM 525

Query: 289 YLHARYMDLPHPEGGRLQITAPLP 312
            LHA  + +P          A  P
Sbjct: 526 CLHAHMLSIPLLGEETKMFVAADP 549



 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/146 (19%), Positives = 44/146 (30%), Gaps = 49/146 (33%)

Query: 101 LLYEDSKIYVFNKPAGI--------SVQ--------------GGSG-------------- 124
           ++Y+D    V NKP  +        SV                                 
Sbjct: 69  VVYQDDNYLVINKPPDLRMDGPYLASVHKLLLYLFPPPSLRGPSQEGGGGDVEGDSTDIN 128

Query: 125 -------IAYHIDGFLKSWVDSKGQ------KPRLTHRLDQETSGILVVARTRAAAQHLT 171
                     H    L++               R+ H+LD  TSG+L+ A+ R AA    
Sbjct: 129 TTSNLQLDHRHHTQLLQAIAPLSKHSSLRDDPFRIVHQLDYATSGVLLYAKNRKAAGKAC 188

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKEC 197
            SF+ R+  K Y ++V        E 
Sbjct: 189 ISFQERKTDKQYVAIVTNQDPAASET 214


>gi|322824625|gb|EFZ29968.1| hypothetical protein TCSYLVIO_3750 [Trypanosoma cruzi]
          Length = 681

 Score = 66.2 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 30/115 (26%), Positives = 47/115 (40%), Gaps = 25/115 (21%)

Query: 224 NYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             AI+  +++   A      +E    TGRTHQ+RVH   +G PI GD KY      + + 
Sbjct: 547 KQAITLIRLLAYDAACDESVVECLLLTGRTHQVRVHLASLGHPIRGDKKYIRLAADSPSI 606

Query: 283 PIQ-----------------------NKLYLHARYMDLPHPEGGRLQI-TAPLPA 313
           P++                       + ++LHA    L +  G   ++  AP PA
Sbjct: 607 PLRTDVRDEEEEDEEEEEELKGYLSSHGIFLHAWRYTLRYAAGEAPEVLEAPPPA 661



 Score = 36.9 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 13/42 (30%), Positives = 20/42 (47%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
            S G K  + HRLD  TSG+L+      +A+   E    + +
Sbjct: 324 PSHGLKVFVVHRLDAATSGVLLFGLDSRSARMTAELMAQKGV 365


>gi|282934173|ref|ZP_06339451.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 208-1]
 gi|297205793|ref|ZP_06923188.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii JV-V16]
 gi|281301787|gb|EFA94053.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 208-1]
 gi|297148919|gb|EFH29217.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii JV-V16]
          Length = 234

 Score = 66.2 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 23/144 (15%), Positives = 54/144 (37%), Gaps = 33/144 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  ++++ +V V+ + VK    ++    +V++          
Sbjct: 1   MRIDKYLANMKVG-SRKEVHDLIKAKKVTVNGQLVKQAKQQVADTDIVKV---------- 49

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + YE    ++ NKPAG+           +   ++   
Sbjct: 50  -------------------ADETIAYEQFHYFMLNKPAGVITATEDPQQKTVLDLIEH-- 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVA 161
             + Q      RLD++T+G+L++ 
Sbjct: 89  KDRYQGLSPVGRLDKDTTGLLLLT 112


>gi|152996949|ref|YP_001341784.1| 23S rRNA pseudouridine synthase F [Marinomonas sp. MWYL1]
 gi|150837873|gb|ABR71849.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 355

 Score = 66.2 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 73/249 (29%), Gaps = 56/249 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +  +  + +  G V ++ KR    +++ +G  VR+         II
Sbjct: 8   RLNKYISE--SGICSRRDADRFIEQGNVFINGKRASVGDQVVAGDTVRVN------GQII 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + Q                      +D    V NKP GI     S    +I  F+     
Sbjct: 60  EPQDA--------------------DDFVFIVLNKPVGIVSTTESSEKNNIVDFVSH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             G +     RLD+++ G++ +         +  +      + +                
Sbjct: 97  --GVRIFPIGRLDKDSQGLIFLTNNGDLVNKVLRAGNNHEKEYL--------------VT 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N  +    I G    V           ++                +    G   Q+R  
Sbjct: 141 VNKPITDDFIAGLAGGVPILGTMTKKCPVTKVSP--------TVFNITLVQGLNRQIRRM 192

Query: 259 ALHMGCPIV 267
             + G  +V
Sbjct: 193 CEYFGYEVV 201


>gi|325289798|ref|YP_004265979.1| ribosomal large subunit pseudouridine synthase B [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965199|gb|ADY55978.1| ribosomal large subunit pseudouridine synthase B [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 270

 Score = 66.2 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 45/280 (16%), Positives = 88/280 (31%), Gaps = 50/280 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           E ++  MRL +        + +    ++++  G+V+V+   V     ++     + +   
Sbjct: 19  EENQIRMRLQKAIA--LSGLASRRRAEEMMTEGRVKVNGVVVTELGMKVCGTDTIEVDGK 76

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                 +  +                       E+   Y+ NKP G+     S       
Sbjct: 77  TVQSLEVKGK-----------------------ENKVYYMLNKPVGVIT---SLRDPQGR 110

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             ++  +    ++     RLD +TSGIL++      A  LT             +     
Sbjct: 111 KTVRDLLGDVKERVYPVGRLDYDTSGILLLTNDGDLAYRLTHPKFGVSKIYRVQTGSRIP 170

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           PK+ ++     LL+        VH + Q                   Q    +E+  H G
Sbjct: 171 PKSIEQLEKGLLLEDGWTAPAKVHRLPQ------------------GQNDHIVEITIHEG 212

Query: 251 RTHQLRVHALHMGCPI--VGDHKYCANFKGNFTSPIQNKL 288
           R  Q+R     +G P+  +    +   F G        +L
Sbjct: 213 RNRQIRRMFERIGYPVQRLHRKSFGPLFTGELAPGGHRRL 252


>gi|312196764|ref|YP_004016825.1| pseudouridine synthase [Frankia sp. EuI1c]
 gi|311228100|gb|ADP80955.1| pseudouridine synthase [Frankia sp. EuI1c]
          Length = 285

 Score = 66.2 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 83/256 (32%), Gaps = 48/256 (18%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
              +E +RL +   +     +  + ++++ +G+VRVD K V+   R              
Sbjct: 40  TASQEGIRLQKVLASAGVG-SRRHNEELIDAGRVRVDGKVVREQGR-------------- 84

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDG 131
               +  E  +++           L              NKP G +S          I  
Sbjct: 85  ---RVDPETAVIEVDGERVVTRTGLVH---------LALNKPRGVVSTMSDPEDRPTISD 132

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L  +  S G       RLD ++ G+L+V      A  LT                  +P
Sbjct: 133 LLTEFGASAG--LFHVGRLDVDSEGLLLVTNNGDLAHRLTHPSYQ-------------VP 177

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K  +  I   L K++          +         +   ++ID    +   LE+  H GR
Sbjct: 178 KTYQVQINGPLRKETM----RRLHTRVELSDGPVRVDSARIIDQVGSQI-LLEIVLHEGR 232

Query: 252 THQLRVHALHMGCPIV 267
              +R     +G P+V
Sbjct: 233 NRIVRRMMEEVGHPVV 248


>gi|222529211|ref|YP_002573093.1| pseudouridine synthase [Caldicellulosiruptor bescii DSM 6725]
 gi|222456058|gb|ACM60320.1| pseudouridine synthase [Caldicellulosiruptor bescii DSM 6725]
          Length = 233

 Score = 66.2 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 85/245 (34%), Gaps = 51/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   H    +   ++K++R G V V+ K           Q+V +   IN      
Sbjct: 1   MRLDKFLT-HCGFGSRSQVKKLIREGIVTVNGK-----------QIVEVDFKIN------ 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ I++    + K S  +            + NKP G         +  +   +    D
Sbjct: 43  PEEDIIEVDGRVAKFSKQI----------YIMMNKPKGYVCSNEELASLTVFSLISD--D 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K +      RLD++  G+L++        H   S + R  ++    L   + + K    
Sbjct: 91  LKYRDLHTVGRLDKDAEGLLIIT-DDGEYTHRVISPKKRIEKEYLVRLEKEVDEEKLNEF 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N ++                  G     + + +ID    K C  E     G+ HQ++  
Sbjct: 150 ENGIILDD---------------GYKTLPAKYTIIDSTTVKLCIYE-----GKYHQVKRM 189

Query: 259 ALHMG 263
              +G
Sbjct: 190 FEAIG 194


>gi|72389112|ref|XP_844851.1| hypothetical protein [Trypanosoma brucei TREU927]
 gi|62358662|gb|AAX79120.1| hypothetical protein, conserved [Trypanosoma brucei]
 gi|70801385|gb|AAZ11292.1| hypothetical protein, conserved [Trypanosoma brucei brucei strain
           927/4 GUTat10.1]
          Length = 700

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 32/127 (25%), Positives = 49/127 (38%), Gaps = 30/127 (23%)

Query: 217 KQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--- 272
           +Q  +    A +  +            +E    TGRTHQ+RVH   +G PIV DHKY   
Sbjct: 561 RQLRETLKRATTLVRRWSYDEDLDESVVECVLLTGRTHQVRVHLASVGHPIVDDHKYIHH 620

Query: 273 ---CANFKGNFTSPIQNK----------------------LYLHARYMDLPHPEGGRLQ- 306
                 F GN+   ++++                      ++LHA    L +      + 
Sbjct: 621 LSRNTPFTGNYRKEVKSRSPPYPSTIPHVASNCSSVTTQGIFLHAWRYTLQYKNSETPET 680

Query: 307 ITAPLPA 313
           + APLPA
Sbjct: 681 LEAPLPA 687


>gi|270291299|ref|ZP_06197521.1| ribosomal large subunit pseudouridine synthase B [Pediococcus
           acidilactici 7_4]
 gi|304385048|ref|ZP_07367394.1| ribosomal large subunit pseudouridine synthase B [Pediococcus
           acidilactici DSM 20284]
 gi|270280145|gb|EFA25981.1| ribosomal large subunit pseudouridine synthase B [Pediococcus
           acidilactici 7_4]
 gi|304329242|gb|EFL96462.1| ribosomal large subunit pseudouridine synthase B [Pediococcus
           acidilactici DSM 20284]
          Length = 237

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 84/251 (33%), Gaps = 50/251 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
              RL +         +    +K++  G V+V+ + VK    +++    + +        
Sbjct: 2   AEERLQKVMAEA-GVASRRKSEKLIAEGHVKVNGRVVKELGTKVEQHDRIEVD------- 53

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                                 +  +  E +  ++ NKP G+     S         +  
Sbjct: 54  ----------------------EVPIQREQNVYFLLNKPRGVIT---SVSDDKNRKTVMD 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     ++     RLD +TSG +++      A  L       + +K Y + V G+     
Sbjct: 89  FFPDVTERIYPVGRLDYDTSGAVLMTNDGELANRL--MHPKFKFEKTYTAKVKGL----- 141

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +    LK+   G    H      K A    +  +      +K   +++  H GR HQ+
Sbjct: 142 --VNGSALKRLEEGVVIDHRKTAKAK-AKLISTDLE------KKTSIVQLTIHEGRNHQV 192

Query: 256 RVHALHMGCPI 266
           +   + +G P+
Sbjct: 193 KKMFMAVGHPV 203


>gi|224013634|ref|XP_002296481.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220968833|gb|EED87177.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 536

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 48/291 (16%), Positives = 96/291 (32%), Gaps = 73/291 (25%)

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKI--YVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-- 139
           + + V +TK  D    +L+Y D  +   V NKP GI     S I+ H +  +  +  S  
Sbjct: 212 VKAHVPMTKLPDKKDGVLVYVDDDLGFTVLNKPGGIPTH--STISNHAEDVVSMYRASLK 269

Query: 140 -----KGQKPRLTHRLDQETS--GILVVARTRAAAQHLTESFRMRR-------------- 178
                +   P ++  +  E    G+ + +  +    ++T+     +              
Sbjct: 270 EERGDEAHTPHVSIPIRMEPEMYGLTLASTKKEFCAYITKQLAASKELHDENSSNGNSIP 329

Query: 179 IQKIYWSLVWGIPKNKKECIANWLLKK-----SHIGGDYVHVVKQNEKGANYAI------ 227
           ++K Y  LV     +  + I   + K        +       V+   K +N+        
Sbjct: 330 VKKSYRVLVCIKNPDDIDRIEKMVGKTLEHYVDPVSPTPKKFVRNKPKSSNHDWQQCLML 389

Query: 228 ------SHFK------------------VIDCFAQKF----------CWLEMQPHTGRTH 253
                 + F+                   + C                 LE++  T + H
Sbjct: 390 ITSVGDTKFRAACVSSKYTDSNDFTLAHRLWCPDMDHPAEDLGVSYVMQLELELLTAKPH 449

Query: 254 QLRVHALHMGCPIVGDHKYCANF-KGNFTSPIQNKLYLHARYMDLPHPEGG 303
           Q+R     +GCPIVGD  Y     +      + +++ +    ++ P P+  
Sbjct: 450 QIRGQLAALGCPIVGDTPYGGGTCEMRMHRHMWSRVAVQVCNLEFPLPQWE 500


>gi|69248060|ref|ZP_00604605.1| Pseudouridine synthase, Rsu [Enterococcus faecium DO]
 gi|257877984|ref|ZP_05657637.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257881230|ref|ZP_05660883.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257884895|ref|ZP_05664548.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257889817|ref|ZP_05669470.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|257892245|ref|ZP_05671898.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|258616531|ref|ZP_05714301.1| ribosomal large subunit pseudouridine synthase B, putative
           [Enterococcus faecium DO]
 gi|260559035|ref|ZP_05831221.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|261207569|ref|ZP_05922254.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289565081|ref|ZP_06445534.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium D344SRF]
 gi|293556726|ref|ZP_06675289.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1039]
 gi|293563384|ref|ZP_06677833.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1162]
 gi|293568042|ref|ZP_06679380.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1071]
 gi|294614860|ref|ZP_06694755.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1636]
 gi|294618690|ref|ZP_06698224.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1679]
 gi|294622981|ref|ZP_06701871.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium U0317]
 gi|314939485|ref|ZP_07846719.1| conserved hypothetical protein [Enterococcus faecium TX0133a04]
 gi|314941116|ref|ZP_07848014.1| conserved hypothetical protein [Enterococcus faecium TX0133C]
 gi|314948728|ref|ZP_07852100.1| conserved hypothetical protein [Enterococcus faecium TX0082]
 gi|314951701|ref|ZP_07854744.1| conserved hypothetical protein [Enterococcus faecium TX0133A]
 gi|314993952|ref|ZP_07859279.1| conserved hypothetical protein [Enterococcus faecium TX0133B]
 gi|314997516|ref|ZP_07862461.1| conserved hypothetical protein [Enterococcus faecium TX0133a01]
 gi|68194579|gb|EAN09070.1| Pseudouridine synthase, Rsu [Enterococcus faecium DO]
 gi|257812212|gb|EEV40970.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257816888|gb|EEV44216.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257820733|gb|EEV47881.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257826177|gb|EEV52803.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|257828624|gb|EEV55231.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|260074792|gb|EEW63108.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|260077952|gb|EEW65658.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289163088|gb|EFD10935.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium D344SRF]
 gi|291589263|gb|EFF21073.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1071]
 gi|291592322|gb|EFF23936.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1636]
 gi|291595073|gb|EFF26416.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1679]
 gi|291597609|gb|EFF28770.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium U0317]
 gi|291601058|gb|EFF31347.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1039]
 gi|291604645|gb|EFF34130.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E1162]
 gi|313588427|gb|EFR67272.1| conserved hypothetical protein [Enterococcus faecium TX0133a01]
 gi|313591554|gb|EFR70399.1| conserved hypothetical protein [Enterococcus faecium TX0133B]
 gi|313596165|gb|EFR75010.1| conserved hypothetical protein [Enterococcus faecium TX0133A]
 gi|313600117|gb|EFR78960.1| conserved hypothetical protein [Enterococcus faecium TX0133C]
 gi|313641287|gb|EFS05867.1| conserved hypothetical protein [Enterococcus faecium TX0133a04]
 gi|313644794|gb|EFS09374.1| conserved hypothetical protein [Enterococcus faecium TX0082]
          Length = 238

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 86/252 (34%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++ + +G+V+V+ + V+    ++     V +          
Sbjct: 2   ERLQKVIA-HAGITSRRKAEEFILAGRVKVNGQVVRELGIKVGKHDTVEVD--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                               +  +  E+   Y+  KP G+  +V    G        +  
Sbjct: 52  --------------------EVPIYQEEYGYYLLYKPKGVISAVADDKGRK-----VVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++      AQ LT       + K+Y + V GI     
Sbjct: 87  LLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQRLT--HPKHEVDKVYVAKVKGIATKSM 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                 L K   I G      K            F+++    +     +E+  H GR HQ
Sbjct: 145 L---APLTKGIKIEGRKTSPAK------------FQILSVDPKTNHSIVELTIHEGRNHQ 189

Query: 255 LRVHALHMGCPI 266
           ++     +G P+
Sbjct: 190 VKNMLQAVGLPV 201


>gi|238924577|ref|YP_002938093.1| pseudouridylate synthase [Eubacterium rectale ATCC 33656]
 gi|238876252|gb|ACR75959.1| pseudouridylate synthase [Eubacterium rectale ATCC 33656]
 gi|291525250|emb|CBK90837.1| ribosomal large subunit pseudouridine synthase F [Eubacterium
           rectale DSM 17629]
 gi|291529291|emb|CBK94877.1| ribosomal large subunit pseudouridine synthase F [Eubacterium
           rectale M104/1]
          Length = 272

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 38/253 (15%), Positives = 84/253 (33%), Gaps = 54/253 (21%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E  +R++++        +     + + +G+V +D    K  +R+  GQ V     +   
Sbjct: 2   EENGVRINKFLSEA-GVCSRREADRQIEAGKVGIDGVTAKTGDRVLKGQTVTYNGQV--- 57

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             + KE++++                       +   NKPAGI          ++  +L 
Sbjct: 58  --VSKEEEMI-----------------------LIALNKPAGIVCTAEKREKNNVIDYL- 91

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               +  ++     RLD+++ G+L++         +  S      + I            
Sbjct: 92  ----NYPKRIYPIGRLDKDSEGLLLLTNNGEIVNKMMRSGNRHEKEYIV---------TV 138

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I++  ++    G      V   E G      H K +          ++    G   Q
Sbjct: 139 NKTISDSFIRGLAGG------VPLVELGVTTRKCHVKKLSSKQ-----FKIILTQGYNRQ 187

Query: 255 LRVHALHMGCPIV 267
           +R    + G  +V
Sbjct: 188 IRRMCEYFGYRVV 200


>gi|315025675|gb|EFT37607.1| conserved hypothetical protein [Enterococcus faecalis TX2137]
 gi|315173996|gb|EFU18013.1| conserved hypothetical protein [Enterococcus faecalis TX1346]
          Length = 257

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 14  MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 56  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 101

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 102 DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 158

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G+ HQ+
Sbjct: 159 CQLFA------------QGFALKDGEMVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 205

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 206 KRMLATVGKPV 216


>gi|312865980|ref|ZP_07726201.1| putative 16S pseudouridylate 516 synthase [Streptococcus downei
           F0415]
 gi|311098384|gb|EFQ56607.1| putative 16S pseudouridylate 516 synthase [Streptococcus downei
           F0415]
          Length = 242

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 90/247 (36%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++ IL+  +V+V+ +                           
Sbjct: 1   MRLDKFLVDCTVG-SRSQVKAILKKKEVQVNGQI-----------------------ESS 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +++I +    +T     LK    +E    Y+ NKP G+           +   L     
Sbjct: 37  PKRQIDEKKDRVTLAGQLLK----HETFVYYLLNKPQGVVSATEDSQHQTVLDLLDEPAH 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T+G+L++      A   L+     + + K+Y + V G+  ++   
Sbjct: 93  QK--QVFPVGRLDIDTTGLLLLTNNGPLAHAMLS---PKKHVAKVYQAKVEGLMTDEDVV 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLR 256
                ++      D+V    Q            ++++   AQ  C ++++   G+ HQ++
Sbjct: 148 AFGQGIRL----KDFVCRPAQ-----------LQILESDQAQGSCLVQIEIAEGKFHQVK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVASRG 199


>gi|28378541|ref|NP_785433.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|254556755|ref|YP_003063172.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|300767486|ref|ZP_07077398.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308180698|ref|YP_003924826.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28271377|emb|CAD64282.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|254045682|gb|ACT62475.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|300495305|gb|EFK30461.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308046189|gb|ADN98732.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 238

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 89/252 (35%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
            RL +         +    + ++ SG V+V+ K V     +++    V +          
Sbjct: 3   ERLQKVMAEA-GIASRRKSEVLITSGHVKVNGKTVTTLGVKVEPSDHVEVD--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS--VQGGSGIAYHIDGFLKS 135
                       +  +++ L   L Y         KP G+   V    G        +  
Sbjct: 53  -----------GVPLNAEKLVYYLFY---------KPRGVVTTVHDEKGRK-----TVLD 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +   ++     RLD +TSG+L++    A A  LT       ++K Y + V G+P N  
Sbjct: 88  FFEDVPERIYPVGRLDYDTSGLLIMTNDGALANRLT--HPKYEVKKTYLAKVEGVPTNAD 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
                  LK+  +G +          G   A +   ++D    +    +++  H G  HQ
Sbjct: 146 -------LKQLRLGVEI--------DGRKTAPAKSNLLDSDHKKNNALVQLTIHEGHNHQ 190

Query: 255 LRVHALHMGCPI 266
           ++     +G P+
Sbjct: 191 VKKMLAAVGHPV 202


>gi|56963596|ref|YP_175327.1| ribosomal large subunit pseudouridine synthase B [Bacillus clausii
           KSM-K16]
 gi|56909839|dbj|BAD64366.1| ribosomal large subunit pseudouridine synthase B [Bacillus clausii
           KSM-K16]
          Length = 242

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 92/252 (36%), Gaps = 54/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++ +  G+V+V+ + V                         
Sbjct: 2   ERLQKVIAKA-GVASRRKAEEYIVEGRVKVNGETVT------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKI-YVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                L + VN +K +  +  + L ++  + ++  KP G+               +  ++
Sbjct: 37  ----ELGTKVNPSKDAVEVDGVPLDKEEPVYHLLYKPTGVVSTSNDEKGR---KVVTDFI 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--K 195
           +S+ Q+     RLD +TSG+L++      A  L       +I+K Y + V GIP+ K  K
Sbjct: 90  ESE-QRIYPIGRLDYDTSGLLLLTNDGEFAHLL--MHPRYKIEKEYIAKVKGIPERKRIK 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E     +L+          V+  ++K    AI               + +  H G+  Q+
Sbjct: 147 ELETGIVLEDGKTAPAKAKVLSIDKK-KQTAI---------------VRLIIHEGKNRQV 190

Query: 256 RVHALHMGCPIV 267
           R     +G P+V
Sbjct: 191 RRMFEAIGHPVV 202


>gi|83590579|ref|YP_430588.1| ribosomal small subunit pseudouridine synthase A [Moorella
           thermoacetica ATCC 39073]
 gi|83573493|gb|ABC20045.1| ribosomal small subunit pseudouridine synthase A [Moorella
           thermoacetica ATCC 39073]
          Length = 243

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 66/176 (37%), Gaps = 34/176 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLDR    H        ++K+++  +V+V+ +                    +   H+I
Sbjct: 7   QRLDRVLA-HMGFGTRKMIKKLIKEKRVQVNGRPA-----------------EDPGLHVI 48

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +  ++ +             L+YE+    + NKP G+        A  +   L     
Sbjct: 49  PGRDYIEVNGEP----------LVYEEYIYLMLNKPQGVLSATEDRYAKVVVDLLP--PR 96

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            +   P    RLD++  G+L++      A + L+     + + K+Y+++V GI   
Sbjct: 97  YRAFHPFPVGRLDKDAEGLLLLTNDGELAHRLLS---PKKHVSKMYYAVVDGIVTE 149


>gi|312622542|ref|YP_004024155.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203009|gb|ADQ46336.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
          Length = 233

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 86/245 (35%), Gaps = 51/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   H    +   ++K++R G V V+ K           Q+V +   IN      
Sbjct: 1   MRLDKFLT-HCGFGSRSQVKKLIREGIVTVNGK-----------QIVEVDFKIN------ 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ I++    + K S  +            + NKP G         +  +   +    D
Sbjct: 43  PEEDIVEVDGRVVKFSKQI----------YIMMNKPKGYVCSNEELASLTVFSLISD--D 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K +      RLD++  G+L++        H   S + R  ++    L   + + K +  
Sbjct: 91  LKYRDLHTVGRLDKDAEGLLIIT-DDGEYTHRVISPKKRIEKEYLVRLEKEVDEEKLKEF 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N ++                  G     + + +ID    K C  E     G+ HQ++  
Sbjct: 150 ENGIILDD---------------GYKTLPAKYTIIDSTTVKLCIYE-----GKYHQVKRM 189

Query: 259 ALHMG 263
              +G
Sbjct: 190 FEAIG 194


>gi|157866798|ref|XP_001681954.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|68125405|emb|CAJ03264.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 1067

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 31/118 (26%), Positives = 47/118 (39%), Gaps = 8/118 (6%)

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI-----ANWLLKKSHIGGDYVHV 215
            RT  A +   +  RMR++ +   +   G      + +     A           D    
Sbjct: 833 GRTPEAVEA--KHERMRQLTRGGGASSLGAWAAALQPVSGVGAAQPARGTLPALSDSSRR 890

Query: 216 VKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+Q  +    A +  +V+   A      ++    TGRTHQLRVH   +G PIV D KY
Sbjct: 891 VQQYLETLRSAQTALQVMHYDAATDQTVVKCTLGTGRTHQLRVHLASLGHPIVHDSKY 948


>gi|145641141|ref|ZP_01796722.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae R3021]
 gi|145274302|gb|EDK14167.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae 22.4-21]
          Length = 232

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 82/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +R   V+++ + VK                      I 
Sbjct: 1   MRLDKFIAEN-TGLTRSQATKAIRQSAVKINGEIVKS-----------------GAVQIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E KI      LT            E+ + ++ +KP G       G    I  F    + 
Sbjct: 43  QEDKIYFEDELLTWL----------EEGQYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 93  G---KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + +          +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPVEENYAAACSEGILLRGEKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|152989816|ref|YP_001355538.1| RNA pseudouridine synthase [Nitratiruptor sp. SB155-2]
 gi|151421677|dbj|BAF69181.1| RNA pseudouridine synthase [Nitratiruptor sp. SB155-2]
          Length = 260

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 49/246 (19%), Positives = 88/246 (35%), Gaps = 39/246 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRL+++   H    +     ++++ G V+V+++ VK     +Q G  V +          
Sbjct: 1   MRLNKYIS-HNTTYSRREADRLIQEGFVKVNRQIVKEPFYDVQEGDKVFV---------- 49

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                              +K  + Y    + V+NKP G  V   +         +   +
Sbjct: 50  ---------------KGKLIKPKVDYT---VIVYNKPKGELV---TKKDDRGRKTIYDSL 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             K        RLD  + G+L++  +   AQ L ES   R         V   PK ++  
Sbjct: 89  PKKFAHYIPVGRLDFASEGLLLLTDSPKIAQALMESDIPRVYNVKIKGEV--TPKMEEAM 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                L+ +  GG     V   +    +A   ++ ID  A  F  L++    G+  ++R 
Sbjct: 147 REGLELEDATAGGHEKSRVTSMKFAPFFA---YR-IDKNAPTFSKLKVALTEGKNREIRR 202

Query: 258 HALHMG 263
              H G
Sbjct: 203 FFAHFG 208


>gi|22298198|ref|NP_681445.1| pseudouridylate synthase [Thermosynechococcus elongatus BP-1]
 gi|22294377|dbj|BAC08207.1| pseudouridylate synthase [Thermosynechococcus elongatus BP-1]
          Length = 250

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 85/251 (33%), Gaps = 48/251 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +    H+   +  + + ++RSGQV V+ +R K  +++      RI      LN   
Sbjct: 4   ERLQKVLA-HWGVASRRHAETLIRSGQVFVNGQRAKLGDKVDP-ARDRIEYKGERLNPPR 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS--VQGGSGIAYHIDGFLKSW 136
             Q++                          + +KP G+        G    +D     +
Sbjct: 62  PPQRL------------------------YLLLHKPKGVLCTCHDPQGRTTVLDLLPPMY 97

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               G  P    RLD ++SG L++    A   +L+       I K Y   V G P     
Sbjct: 98  QRVGGLHP--VGRLDADSSGALLLTNDGAFTYYLS--HPRHHIPKTYRVWVQGQPPEN-- 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +  W   +  I  D V  +    K                     LE+  H GR  Q+R
Sbjct: 152 VLQRW---RQGIPLDGVMTLPATVKRLRS-----------EGDRALLEIILHEGRNRQIR 197

Query: 257 VHALHMGCPIV 267
             A  +G P++
Sbjct: 198 RVADQLGYPVL 208


>gi|312868136|ref|ZP_07728340.1| pseudouridylate synthase [Streptococcus parasanguinis F0405]
 gi|311096540|gb|EFQ54780.1| pseudouridylate synthase [Streptococcus parasanguinis F0405]
          Length = 242

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 89/248 (35%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+  ++ V+ K+     ++Q      I P  + +    
Sbjct: 1   MRLDKFLVDCGVG-SRTEVKQLLKQKKIAVNGKKETAG-KLQ------IDPDKDQVT--- 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                            F+   L++E    Y+ NKPAG+           +   L     
Sbjct: 50  -----------------FMGEDLVHETFVYYLLNKPAGVISATEDDHHQTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-- 195
            K  +     RLD +T G+L++    + A   L+     + + K Y + V GI       
Sbjct: 93  HK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVSKNYRAQVAGIMDEADVA 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                  LK        + +++ NE  A+                 ++E++   G+ HQ+
Sbjct: 148 RFEEGIALKDFTTLPARLQILEVNEASAS----------------SYVEIEIAEGKFHQV 191

Query: 256 RVHALHMG 263
           +      G
Sbjct: 192 KRMVAACG 199


>gi|145633297|ref|ZP_01789028.1| malic enzyme [Haemophilus influenzae 3655]
 gi|145634426|ref|ZP_01790136.1| malic enzyme [Haemophilus influenzae PittAA]
 gi|148825838|ref|YP_001290591.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae PittEE]
 gi|229845029|ref|ZP_04465165.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae 6P18H1]
 gi|229846853|ref|ZP_04466960.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae 7P49H1]
 gi|144986143|gb|EDJ92733.1| malic enzyme [Haemophilus influenzae 3655]
 gi|145268406|gb|EDK08400.1| malic enzyme [Haemophilus influenzae PittAA]
 gi|148715998|gb|ABQ98208.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae PittEE]
 gi|229810342|gb|EEP46061.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae 7P49H1]
 gi|229812001|gb|EEP47694.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae 6P18H1]
 gi|309972980|gb|ADO96181.1| 16S rRNA U516 pseudouridine synthase [Haemophilus influenzae R2846]
          Length = 232

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 82/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +R   V+++ + VK                      I 
Sbjct: 1   MRLDKFIAENV-GLTRSQATKAIRQSAVKINGEIVKS-----------------GSVQIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E +I      LT            E+ + ++ +KP G       G    I  F    + 
Sbjct: 43  QEDEIYFEDELLTWV----------EEGQYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 93  G---KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + +          +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPVEENYAAACAEGILLRGEKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|322390862|ref|ZP_08064371.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 903]
 gi|321142447|gb|EFX37916.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 903]
          Length = 242

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 91/248 (36%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+  ++ V+ K+     ++Q      I P  + +    
Sbjct: 1   MRLDKFLVDCGMG-SRTEVKQLLKQKKIAVNGKKETAG-KLQ------IDPGKDRVT--- 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                            F+   L++E    Y+ NKPAG+           +   L     
Sbjct: 50  -----------------FMGEDLVHETFVYYLLNKPAGVISATEDDHHQTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-- 195
            K  +     RLD +T G+L++    + A   L+     + + KIY + V GI       
Sbjct: 93  HK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVSKIYRAQVAGIMDEADVA 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
              A   LK        + +++ NE  A+                 ++E++   G+ HQ+
Sbjct: 148 RFEAGIALKDFTTLPARLQILEVNEANAS----------------SYVEIEIAEGKFHQV 191

Query: 256 RVHALHMG 263
           +      G
Sbjct: 192 KRMVAACG 199


>gi|328957343|ref|YP_004374729.1| ribosomal large subunit pseudouridine synthase B [Carnobacterium
           sp. 17-4]
 gi|328673667|gb|AEB29713.1| ribosomal large subunit pseudouridine synthase B [Carnobacterium
           sp. 17-4]
          Length = 251

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 46/257 (17%), Positives = 89/257 (34%), Gaps = 56/257 (21%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72
             E   RL +    H    +    ++++  G V+V+ K VK    +I +  VV +     
Sbjct: 3   EGEIMERLQKVLA-HAGVASRRKSEELISKGHVKVNGKVVKEMGIQIGNSDVVEVD---- 57

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHID 130
                                       +  E+   ++ NKP  +  +V    G      
Sbjct: 58  -------------------------GVPIYREEPVYFLLNKPRNMITAVSDDKGRP---- 88

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             +     +  Q+     RLD +T+G L++      +Q L       +I K Y + V G+
Sbjct: 89  -VVTDLFTNIEQRIYPVGRLDYDTTGALMLTNDGELSQLL--MHPKYQIDKTYVAKVKGL 145

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHT 249
                        +K+    +   V+    +G   A +  K++    A+    +E+  H 
Sbjct: 146 VD-----------RKALNKLEKGIVI----EGKKTAPAKAKILSADRAKDITMVELTIHE 190

Query: 250 GRTHQLRVHALHMGCPI 266
           GR  Q++     +G P+
Sbjct: 191 GRNRQVKNMFQAIGHPV 207


>gi|145639224|ref|ZP_01794831.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae PittII]
 gi|145271786|gb|EDK11696.1| 16S pseudouridylate 516 synthase [Haemophilus influenzae PittII]
 gi|309750799|gb|ADO80783.1| 16S RNA U516 pseudouridine synthase [Haemophilus influenzae R2866]
          Length = 232

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 82/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +R   V+++ + VK                      I 
Sbjct: 1   MRLDKFIAEN-TGLTRSQATKAIRQSAVKINGEIVKS-----------------GSVQIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E +I      LT            E+ + ++ +KP G       G    I  F    + 
Sbjct: 43  QEDEIYFEDELLTWI----------EEGQYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 93  G---KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + +          +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPVEENYAAACSEGILLRGEKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|319896936|ref|YP_004135131.1| ribosomal small subunit pseudouridine synthase a [Haemophilus
           influenzae F3031]
 gi|317432440|emb|CBY80795.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae F3031]
          Length = 232

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 79/250 (31%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +    V+++ + VK                      I 
Sbjct: 1   MRLDKFIAEN-TGLTRSQATKAIHQSAVKINGEIVKS-----------------GAVQIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E KI      LT          + ED    +  KP G       G    I  F    + 
Sbjct: 43  QEDKIYFEDELLT---------WVEEDQYFMLH-KPQGCVCSNDDGDYPTIYQFFDYPLA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 93  G---KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + +          +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPVEENYAAACSEGILLRGEKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|315166874|gb|EFU10891.1| conserved hypothetical protein [Enterococcus faecalis TX1341]
          Length = 257

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 86/250 (34%), Gaps = 49/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 14  MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     +      +  +    D
Sbjct: 56  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVIS---ATEDQRNETVIDLLTD 102

Query: 139 SKGQ-KPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +       RLD++T G+L++      A Q L+     + + K Y + V G+   +  
Sbjct: 103 QDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAEDC 159

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +                   ++ +    +    + I+   +    + +    G+ HQ++
Sbjct: 160 QLFA------------QGFALKDGEMVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQVK 206

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 207 RMLATVGKPV 216


>gi|284048580|ref|YP_003398919.1| pseudouridine synthase [Acidaminococcus fermentans DSM 20731]
 gi|283952801|gb|ADB47604.1| pseudouridine synthase [Acidaminococcus fermentans DSM 20731]
          Length = 244

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 48/253 (18%), Positives = 79/253 (31%), Gaps = 49/253 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINA 73
           ++   RL +         +    +KI+ +G+V+V+ K V     R+     + +      
Sbjct: 2   EQTKERLQKVMAAA-GVASRRECEKIILAGRVQVNGKPVTELGTRVGKADRITVDG---- 56

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                                    + LLY+   +    K      QG   +A  + G  
Sbjct: 57  ---------------KALHRKSARHTYLLYKPGGVVTTMKDP----QGRRTVADLMAGL- 96

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                   Q+     RLD  T G+L++      AQHLT       + K Y   V G    
Sbjct: 97  -------HQRLYPVGRLDYLTEGLLLMTNDGELAQHLT--HPSHHVDKTYEVEVHGRVPE 147

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +K  +   L      G     VV   +      ++ F V               H GR  
Sbjct: 148 EKLDVLR-LGVPLEDGLTAPAVVYVKKWDPEKNLTRFTV-------------TIHEGRNR 193

Query: 254 QLRVHALHMGCPI 266
           Q+R     +G P+
Sbjct: 194 QVRRMCDFIGFPV 206


>gi|221501569|gb|EEE27342.1| RNA pseudouridylate synthase, putative [Toxoplasma gondii VEG]
          Length = 382

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               V  NE     A + FK++          +   P TGRTHQ+R H   +G  IVGD 
Sbjct: 90  RQLAVGWNEDHGKEAETVFKMLHYDEDSDTSLVACIPLTGRTHQIRKHLQILGTSIVGDA 149

Query: 271 KYCANFKGNFTS 282
            Y    +   TS
Sbjct: 150 LYPPKSRMPHTS 161


>gi|221480824|gb|EEE19248.1| conserved hypothetical protein [Toxoplasma gondii GT1]
          Length = 435

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               V  NE     A + FK++          +   P TGRTHQ+R H   +G  IVGD 
Sbjct: 90  RQLAVGWNEDHGKEAETVFKMLHYDEDSDTSLVACIPLTGRTHQIRKHLQILGTSIVGDA 149

Query: 271 KYCANFKGNFTS 282
            Y    +   TS
Sbjct: 150 LYPPKSRMPHTS 161


>gi|237844937|ref|XP_002371766.1| RNA pseudouridylate synthase, putative [Toxoplasma gondii ME49]
 gi|211969430|gb|EEB04626.1| RNA pseudouridylate synthase, putative [Toxoplasma gondii ME49]
          Length = 435

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
               V  NE     A + FK++          +   P TGRTHQ+R H   +G  IVGD 
Sbjct: 90  RQLAVGWNEDHGKEAETVFKMLHYDEDSDTSLVACIPLTGRTHQIRKHLQILGTSIVGDA 149

Query: 271 KYCANFKGNFTS 282
            Y    +   TS
Sbjct: 150 LYPPKSRMPHTS 161


>gi|68250225|ref|YP_249337.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae 86-028NP]
 gi|68058424|gb|AAX88677.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           influenzae 86-028NP]
          Length = 232

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 82/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +R   V+++ + VK                      I 
Sbjct: 1   MRLDKFIAENV-GLTRSQATKAIRQSAVKINGEIVKS-----------------GAVQIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E KI      LT            E+ + ++ +KP G       G    I  F    + 
Sbjct: 43  QEDKIYFEDELLTWV----------EEGQYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G +++      +  +T          +               +
Sbjct: 93  G---KLHSAGRLDVDTTGFVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + +          ++++ ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPVEENYAAACSEGILLRREKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|227889739|ref|ZP_04007544.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
 gi|227849603|gb|EEJ59689.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
          Length = 233

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/181 (16%), Positives = 63/181 (34%), Gaps = 35/181 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  +++   V V+ + VK    +++    V +          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVD--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   LK   
Sbjct: 51  --------------------GEKVAYQQYHYFLLNKPKGVISATEDRSQKTVLSLLK--P 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             + +      RLD++T+G+L++    A A  L      + + K Y + + G+   +   
Sbjct: 89  KDRYKDIAPVGRLDKDTTGLLLLTNDGALAHEL--LAPNKHVTKKYRAKIAGVADEETVK 146

Query: 198 I 198
           I
Sbjct: 147 I 147


>gi|153956083|ref|YP_001396848.1| hypothetical protein CKL_3486 [Clostridium kluyveri DSM 555]
 gi|219856417|ref|YP_002473539.1| hypothetical protein CKR_3074 [Clostridium kluyveri NBRC 12016]
 gi|146348941|gb|EDK35477.1| RsuA [Clostridium kluyveri DSM 555]
 gi|219570141|dbj|BAH08125.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 238

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 42/244 (17%), Positives = 88/244 (36%), Gaps = 47/244 (19%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLD+   N   +     ++ I++SG V++D   VK N+       ++I P    +     
Sbjct: 3   RLDKVLAN-LGYGTRKEVKAIVKSGAVKIDGLVVKDNS-------MKIDPDECKI----- 49

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                          +  ++++ Y+ +   + NKP G+           +   L+     
Sbjct: 50  ---------------EVEETVVEYKKNIYILMNKPEGVVCATFDNYQETVIDILE--PKY 92

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +  KP    RLD++T G+L++         L        + K+Y++ +            
Sbjct: 93  QAFKPFPVGRLDKDTKGLLLITNDGELNHRL--ISPKNHVDKVYYAEIDKKVDMDD---- 146

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
                   I    + +V ++E     A    K+I+        +E+    G+ HQ++   
Sbjct: 147 --------IRKFKMGIVLKDEYTCMPA--ELKIIESDENGA-RVEVTVQEGKFHQIKRMF 195

Query: 260 LHMG 263
             +G
Sbjct: 196 NSLG 199


>gi|312876843|ref|ZP_07736820.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796358|gb|EFR12710.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
          Length = 230

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 83/236 (35%), Gaps = 46/236 (19%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
            +    ++I+  G+V+V+ K V                       +  E+ +++      
Sbjct: 7   ASRRKCEEIILQGRVKVNGKTVN-----------------QLGFKVDPEKDVVEVDGKRI 49

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                L+   +Y      + NKP G+     +         +    D    +     RLD
Sbjct: 50  ----SLQMQKVY-----IMLNKPFGVIS--SAKDEKGRKTVVDLVKDKVNVRVFPVGRLD 98

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +T+G++++      A  +T       I+K Y +L+ GIP  ++    +   K   I G 
Sbjct: 99  FDTTGLILLTNDGEFAYKVT--HPKHDIEKTYIALIRGIPSKEE---IDRFEKGLLIDGK 153

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                         A + FK++         +E++ H GR  Q+R     +G  ++
Sbjct: 154 M------------TAPAKFKILKLINGNA-LVEIKIHEGRNRQIRKMCAQIGHEVL 196


>gi|293570237|ref|ZP_06681306.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E980]
 gi|291609644|gb|EFF38905.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           faecium E980]
          Length = 238

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 86/252 (34%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++ + +G+V+V+ + V+    ++     V +          
Sbjct: 2   ERLQKVIA-HAGITSRRKAEEFILAGRVKVNGQVVRELGIKVGKQDTVEVD--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                               +  +  E+   Y+  KP G+  +V    G        +  
Sbjct: 52  --------------------EVPIYQEEYGYYLLYKPKGVISAVADDKGRK-----VVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++      AQ LT       + K+Y + V GI     
Sbjct: 87  LLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQRLT--HPKHEVDKVYVAKVKGIATKSM 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                 L K   I G      K            F+++    +     +E+  H GR HQ
Sbjct: 145 L---APLAKGIKIEGRKTSPAK------------FQILSVDPKTNHSIVELTIHEGRNHQ 189

Query: 255 LRVHALHMGCPI 266
           ++     +G P+
Sbjct: 190 VKNMLQAVGLPV 201


>gi|253573324|ref|ZP_04850667.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251846852|gb|EES74857.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 257

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 38/252 (15%), Positives = 88/252 (34%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+    H  +     ++K ++ G+V ++   VK +        ++  P ++ +    
Sbjct: 8   QRLDKIL-GHLGYGTRSEIKKYVKQGRVTINGVVVKDSG-------IQCNPDVDVV---- 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                           +     + Y +    + +KP G+           +   L   VD
Sbjct: 56  ----------------ELDGEQIFYREFVYLMLHKPPGVISATEDMREKTVIDLLP--VD 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +   P    RLD++T G+L++      A  L      + + K Y ++V G         
Sbjct: 98  FQVFSPFPVGRLDKDTEGLLLLTNDGQLAHDL--LSPRKHVPKTYEAVVLG--------- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAIS---HFKVIDC----FAQKFCWLEMQPHTGR 251
                   H+G +     ++  +  +  ++     KV++        +   +++    G+
Sbjct: 147 --------HVGDEEAARFREGVELDDGYVTLPAELKVLEHGIDADGTRISRVQLTISEGK 198

Query: 252 THQLRVHALHMG 263
            HQ++     +G
Sbjct: 199 FHQVKRMFEAVG 210


>gi|326803925|ref|YP_004321743.1| pseudouridylate synthase [Aerococcus urinae ACS-120-V-Col10a]
 gi|326650643|gb|AEA00826.1| pseudouridylate synthase [Aerococcus urinae ACS-120-V-Col10a]
          Length = 243

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 88/246 (35%), Gaps = 46/246 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  N +   +   ++K++++ ++ V+                             
Sbjct: 1   MRLDKFIAN-FTLYSRKEVKKLIKAKRITVNDSIAS-----------------------R 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E +I + +  ++    ++     YE    Y+ NKP         G    +  FL +   
Sbjct: 37  PEMQIDEETDTISLDGQWIG----YEPYIYYLLNKPQNCLSTTRPGPTSIVTDFLPANEV 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              Q P    RLD++T G+L++      A   L+     + + K Y++ + GI   +   
Sbjct: 93  EIYQ-PFPVGRLDKDTEGLLLLTNDGDFAHDLLS---PKKLVSKEYYAEIEGIVTEED-- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +  +    +   GD+    + +    + A           +    + +    G+ HQ++ 
Sbjct: 147 VKAFAKGLTIDQGDHCAPSQLDILATDPA-----------KNRSEITVTLTEGKYHQVKR 195

Query: 258 HALHMG 263
               +G
Sbjct: 196 MFQAVG 201


>gi|90961915|ref|YP_535831.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           salivarius UCC118]
 gi|301299322|ref|ZP_07205607.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           salivarius ACS-116-V-Col5a]
 gi|90821109|gb|ABD99748.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           salivarius UCC118]
 gi|300214638|gb|ADJ79054.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
 gi|300853062|gb|EFK80661.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           salivarius ACS-116-V-Col5a]
          Length = 242

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 85/248 (34%), Gaps = 51/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +   N     +    +K+++ G+V V+   V     +++S   + +          
Sbjct: 3   ERLQKVMANA-GVASRRASEKLIQEGRVMVNGVVVTELGTKVESDDSISVDG-------- 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       L K  +     LLY         KP G+     +         +  ++
Sbjct: 54  -----------KLLKKDEKKVYYLLY---------KPRGVIS---AAKDNKGREVVTDYL 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  +       ++ K Y + V G+       
Sbjct: 91  KDVPERLYPVGRLDYDTSGLLILTNDGDFANQM--MHPRYKVDKTYVAKVEGL------- 141

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLR 256
           I    +KK   G      V  + K  + A    K++   A +    + +  H GR HQ++
Sbjct: 142 ITPDSIKKLRNG------VVIDGKPTSRA--RAKILSRDAKKNTSIVSLTIHEGRYHQVK 193

Query: 257 VHALHMGC 264
                +G 
Sbjct: 194 KMFDAVGH 201


>gi|227517632|ref|ZP_03947681.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|227554784|ref|ZP_03984831.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|293384990|ref|ZP_06630824.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis R712]
 gi|293389260|ref|ZP_06633722.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis S613]
 gi|307270257|ref|ZP_07551569.1| hypothetical protein HMPREF9498_02370 [Enterococcus faecalis
           TX4248]
 gi|307272482|ref|ZP_07553735.1| hypothetical protein HMPREF9514_01246 [Enterococcus faecalis
           TX0855]
 gi|307278240|ref|ZP_07559319.1| hypothetical protein HMPREF9515_00573 [Enterococcus faecalis
           TX0860]
 gi|307289637|ref|ZP_07569581.1| hypothetical protein HMPREF9505_02998 [Enterococcus faecalis
           TX0109]
 gi|312900258|ref|ZP_07759570.1| conserved hypothetical protein [Enterococcus faecalis TX0470]
 gi|312905979|ref|ZP_07764992.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 512]
 gi|312909325|ref|ZP_07768181.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 516]
 gi|227074938|gb|EEI12901.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|227176083|gb|EEI57055.1| pseudouridylate synthase [Enterococcus faecalis HH22]
 gi|291077668|gb|EFE15032.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis R712]
 gi|291081424|gb|EFE18387.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis S613]
 gi|306499451|gb|EFM68824.1| hypothetical protein HMPREF9505_02998 [Enterococcus faecalis
           TX0109]
 gi|306504991|gb|EFM74182.1| hypothetical protein HMPREF9515_00573 [Enterococcus faecalis
           TX0860]
 gi|306510767|gb|EFM79784.1| hypothetical protein HMPREF9514_01246 [Enterococcus faecalis
           TX0855]
 gi|306513400|gb|EFM82020.1| hypothetical protein HMPREF9498_02370 [Enterococcus faecalis
           TX4248]
 gi|310627974|gb|EFQ11257.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 512]
 gi|311290349|gb|EFQ68905.1| conserved hypothetical protein [Enterococcus faecalis DAPTO 516]
 gi|311292619|gb|EFQ71175.1| conserved hypothetical protein [Enterococcus faecalis TX0470]
 gi|315031424|gb|EFT43356.1| conserved hypothetical protein [Enterococcus faecalis TX0017]
 gi|315034401|gb|EFT46333.1| conserved hypothetical protein [Enterococcus faecalis TX0027]
 gi|315164553|gb|EFU08570.1| conserved hypothetical protein [Enterococcus faecalis TX1302]
 gi|315575298|gb|EFU87489.1| conserved hypothetical protein [Enterococcus faecalis TX0309B]
 gi|315581464|gb|EFU93655.1| conserved hypothetical protein [Enterococcus faecalis TX0309A]
          Length = 257

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 14  MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 56  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 101

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 102 DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 158

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G+ HQ+
Sbjct: 159 CQLFA------------QGFALKDGEMVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 205

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 206 KRMLATVGKPV 216


>gi|71418712|ref|XP_810945.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70875553|gb|EAN89094.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 682

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 224 NYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             AI+  +++   A      +E    TGRTHQ+RVH   +G PI GD KY      + + 
Sbjct: 547 KQAITLIRLLAYDAACDESVVECLLLTGRTHQVRVHLASLGHPIRGDKKYIRLAADSPSI 606

Query: 283 PIQ 285
           P++
Sbjct: 607 PLR 609



 Score = 36.5 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 12/41 (29%), Positives = 19/41 (46%)

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
             G K  + HRLD  TSG+L+      +A+   E    + +
Sbjct: 325 PHGLKVFVVHRLDAATSGVLLFGLDSRSARMTAELMAQKGV 365


>gi|170740346|ref|YP_001769001.1| pseudouridine synthase [Methylobacterium sp. 4-46]
 gi|168194620|gb|ACA16567.1| pseudouridine synthase [Methylobacterium sp. 4-46]
          Length = 244

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 87/249 (34%), Gaps = 47/249 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLDR   N   + +   +Q + R+G++R+D + ++       G   RI    +    + 
Sbjct: 7   IRLDRLLAN-LGYGSRREIQALARAGRIRLDGEALRE----ADG---RIAATADLPARLT 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              + LD    L        +++L++ + +   +K AG  V           G L     
Sbjct: 59  VSGEPLDPPAPL--------ALMLHKPTGVTCSHKEAGPLV----------YGLLPERWR 100

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++TSG+L+V                        +L+  I   K +  
Sbjct: 101 RREPALSTVGRLDKDTSGLLLV--------------------TDDGALLHRIISPKAKIE 140

Query: 199 ANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             + ++    + GD   ++           +    +   AQ      +    GR HQ+R 
Sbjct: 141 KQYRVELDRPLRGDEGAILVSGTLMLEGEEAPLLPVGFTAQGPRQARVVLTEGRYHQVRR 200

Query: 258 HALHMGCPI 266
               +G  +
Sbjct: 201 MFAALGNHV 209


>gi|295399574|ref|ZP_06809556.1| pseudouridine synthase [Geobacillus thermoglucosidasius C56-YS93]
 gi|312109871|ref|YP_003988187.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
 gi|294979040|gb|EFG54636.1| pseudouridine synthase [Geobacillus thermoglucosidasius C56-YS93]
 gi|311214972|gb|ADP73576.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
          Length = 240

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 89/248 (35%), Gaps = 52/248 (20%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNH 76
            +R+D+   N         ++K+L+SG V++D   VK    ++   + V           
Sbjct: 2   GLRIDKMLANMGFG-TRKEVKKLLKSGVVKIDGMIVKDPKTQVNPSEQVV---------- 50

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            ++ +++                   Y++    + NKP G+           +   L+  
Sbjct: 51  TVRGEEVE------------------YKEFIYLMMNKPPGVISATEDMAEETVIDLLEE- 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +   P    RLD++T G+L++      A Q L+     + + K Y++++ G    + 
Sbjct: 92  -EDRVFAPFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVPKTYFAVIDGEVTEED 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                       I      +V  +      A    ++I   +     +E+    G+ HQ+
Sbjct: 148 ------------IESFRHGIVLDDGYKTKPA----ELIILKSGLRSDVEVTITEGKFHQI 191

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 192 KRMFRALG 199


>gi|241889378|ref|ZP_04776679.1| ribosomal small subunit pseudouridine synthase A [Gemella
           haemolysans ATCC 10379]
 gi|241863921|gb|EER68302.1| ribosomal small subunit pseudouridine synthase A [Gemella
           haemolysans ATCC 10379]
          Length = 235

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 85/246 (34%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++    +K+++ G + ++ K +K  + ++                  
Sbjct: 1   MRLDKFISTT-TTLSRAEAKKVIKKG-ILINDKLIKSPDYKV----------------DE 42

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I +Q ILD               L+Y+     + NKP          I   +   LK   
Sbjct: 43  INDQVILDGK------------RLVYQKYVYIMMNKPQDTISATEDAIEKTVVDILKE-- 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + +  K     RLD++T G++++      A  L      + + K Y+  V G  K +   
Sbjct: 89  EDRIHKVFPVGRLDKDTEGLMLLTNDGELAHRL--ISPKKDVVKKYYVEVSGELKEEHLP 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I    +                E G     +  ++++    +     +    G+ HQ++ 
Sbjct: 147 IIEAGV--------------TLEDGYKCKAAKLEILESNEDE-SKANIYITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MMKSLG 197


>gi|282917118|ref|ZP_06324876.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           D139]
 gi|282319605|gb|EFB49957.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           D139]
          Length = 144

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 27/125 (21%), Positives = 52/125 (41%), Gaps = 19/125 (15%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           S  + ++ K  +  +++ +G  V +P +    N++                  +  + + 
Sbjct: 34  SKDITINDKPARLMDKVHTGDDVFVPTIDEKSNYV----------------PSYRYAQIK 77

Query: 103 YEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           YED  + +  KP G+         +  +   +   VDS   +P   HRLDQET G+L+VA
Sbjct: 78  YEDDDMAIVMKPKGVKTHPNDLKESNTLMNHVIYTVDSDYVEP--IHRLDQETVGLLIVA 135

Query: 162 RTRAA 166
           +    
Sbjct: 136 KNPLM 140


>gi|118586875|ref|ZP_01544309.1| ribosomal pseudouridine synthase B, large subunit [Oenococcus oeni
           ATCC BAA-1163]
 gi|118432707|gb|EAV39439.1| ribosomal pseudouridine synthase B, large subunit [Oenococcus oeni
           ATCC BAA-1163]
          Length = 237

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 95/239 (39%), Gaps = 54/239 (22%)

Query: 32  INFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
            +    ++++ +GQV+V+ K + K   ++ S  +V +             +KI + S   
Sbjct: 17  ASRRKAEEMIVNGQVKVNGKIITKLGKKVSSDDIVYVD-----------NKKINEESFE- 64

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
                             Y+ NKPAG      S  +Y     +   + +K  +     RL
Sbjct: 65  -----------------YYLLNKPAGYVS---SNRSYPNQPSVIELIKTKT-RIFSVGRL 103

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKECIANWLLKKSHI- 208
           DQ+T+G+L++       Q LT      RI++ Y + V GI  +++ E +   +     I 
Sbjct: 104 DQDTTGVLLLTNDGELTQKLT--HPKHRIKRTYAAWVKGIVNEDELEQLTKPIRFDGEIY 161

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                 ++K ++K                ++   +E+    G+TH+++     +G P++
Sbjct: 162 FPQAARILKVDQK----------------RQESLIEITIAEGKTHEIKKILDFIGHPVI 204


>gi|227890935|ref|ZP_04008740.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           salivarius ATCC 11741]
 gi|227867344|gb|EEJ74765.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           salivarius ATCC 11741]
          Length = 242

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 85/248 (34%), Gaps = 51/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +   N     +    +K+++ G+V V+   V     +++S   + +          
Sbjct: 3   ERLQKVMANA-GVASRRASEKLIQEGRVMVNGVVVTELGTKVESDDSISVDG-------- 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       L K  +     LLY         KP G+     +         +  ++
Sbjct: 54  -----------KLLKKDEKKVYYLLY---------KPRGVIS---AAKDNKGREVVTDYL 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  +       ++ K Y + V G+       
Sbjct: 91  KDVPERLYPVGRLDYDTSGLLILTNDGDFANQM--MHPRYKVDKTYVAKVEGL------- 141

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLR 256
           I    +KK   G      V  + K  + A    K+I   A +    + +  H GR HQ++
Sbjct: 142 ITPDSIKKLRNG------VVIDGKPTSRA--RAKIISRDAKKNTSIVSLTIHEGRYHQVK 193

Query: 257 VHALHMGC 264
                +G 
Sbjct: 194 KMFDAVGH 201


>gi|259046491|ref|ZP_05736892.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           adiacens ATCC 49175]
 gi|259036656|gb|EEW37911.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           adiacens ATCC 49175]
          Length = 238

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 84/246 (34%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D+   +         ++ +L+S ++ V+ K V  N ++Q                  
Sbjct: 1   MRIDKCLADCGLG-TRSEVKSLLKSKKITVNGKVVT-NGKVQVN---------------P 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  +IL           F    + YE+    + NKP G+       +   +   +     
Sbjct: 44  ETDEIL-----------FDGEKIQYEEFVYIMMNKPKGVVSATEDNLHKTVLDLINPLYF 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            KG       RLD +T G+L++      A + L+     + + KIY + V G+   +   
Sbjct: 93  KKG--VFPVGRLDIDTHGLLLLTNDGELAHRLLS---PKKHVTKIYQARVEGVMTPE--- 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                 ++         +V  +      A      I    Q    +++    G+ HQ++ 
Sbjct: 145 -DAAAFERG--------IVLSDGTECMPARLD---ILSTTQDESIVQIHLKEGKFHQVKR 192

Query: 258 HALHMG 263
                G
Sbjct: 193 MVKACG 198


>gi|257086025|ref|ZP_05580386.1| pseudouridine synthase [Enterococcus faecalis D6]
 gi|256994055|gb|EEU81357.1| pseudouridine synthase [Enterococcus faecalis D6]
          Length = 244

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 1   MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 43  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 89  DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G+ HQ+
Sbjct: 146 CQLFA------------QGFALKDGEMVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 192

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 193 KRMLATVGKPV 203


>gi|229548610|ref|ZP_04437335.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|312953045|ref|ZP_07771898.1| conserved hypothetical protein [Enterococcus faecalis TX0102]
 gi|229306241|gb|EEN72237.1| pseudouridylate synthase [Enterococcus faecalis ATCC 29200]
 gi|310629074|gb|EFQ12357.1| conserved hypothetical protein [Enterococcus faecalis TX0102]
 gi|315144498|gb|EFT88514.1| conserved hypothetical protein [Enterococcus faecalis TX2141]
 gi|315153886|gb|EFT97902.1| conserved hypothetical protein [Enterococcus faecalis TX0031]
 gi|315156684|gb|EFU00701.1| conserved hypothetical protein [Enterococcus faecalis TX0043]
 gi|327534254|gb|AEA93088.1| ribosomal small subunit pseudouridine synthase A [Enterococcus
           faecalis OG1RF]
          Length = 257

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 14  MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 56  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 101

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 102 DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 158

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G+ HQ+
Sbjct: 159 CQLFA------------QGFALKDGEIVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 205

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 206 KRMLATVGKPV 216


>gi|315149408|gb|EFT93424.1| conserved hypothetical protein [Enterococcus faecalis TX0012]
          Length = 257

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 14  MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 56  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 101

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 102 DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 158

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G+ HQ+
Sbjct: 159 CQLFA------------QGFALKDGEMVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 205

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 206 KRMLATVGKPV 216


>gi|312135036|ref|YP_004002374.1| RNA-binding S4 domain-containing protein [Caldicellulosiruptor
           owensensis OL]
 gi|311775087|gb|ADQ04574.1| RNA-binding S4 domain protein [Caldicellulosiruptor owensensis OL]
          Length = 233

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 49/276 (17%), Positives = 96/276 (34%), Gaps = 55/276 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   H    +   ++K++R G V V+ K           Q+V +   IN      
Sbjct: 1   MRLDKFLT-HCGFGSRTQVKKLIREGIVTVNGK-----------QIVEVDFKIN------ 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ +++    + K S ++            + NKP G        ++  +   +    D
Sbjct: 43  PEEDVVEVDGRIVKFSRWI----------YIMMNKPKGYVCSNEDPMSLTVFSLISD--D 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K +      RLD++  G+L++        H   S + R  ++    L   + + + +  
Sbjct: 91  LKHRDLHTVGRLDKDAEGLLIIT-DDGEYTHRVISPKKRIEKEYLVRLEKEVDEERLKEF 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N ++                  G     + + +ID    K C  E     G+ HQ++  
Sbjct: 150 ENGIILDD---------------GYKTLPAKYTIIDSTTVKLCIYE-----GKYHQVKRM 189

Query: 259 ALHMGCPIVGDHKY---CANFKGNFTSPIQNKLYLH 291
              +G  +V D K              P + +L   
Sbjct: 190 FEAIGNKVV-DLKRRRIGGLNLDESLKPGEYRLMKE 224


>gi|227551154|ref|ZP_03981203.1| pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|257896222|ref|ZP_05675875.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|257898859|ref|ZP_05678512.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|293379537|ref|ZP_06625679.1| pseudouridylate synthase [Enterococcus faecium PC4.1]
 gi|227179716|gb|EEI60688.1| pseudouridylate synthase [Enterococcus faecium TX1330]
 gi|257832787|gb|EEV59208.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|257836771|gb|EEV61845.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|292641846|gb|EFF60014.1| pseudouridylate synthase [Enterococcus faecium PC4.1]
          Length = 238

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 86/252 (34%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++ + +G+V+V+ + V+    ++     V +          
Sbjct: 2   ERLQKVIA-HAGITSRRKAEEFILAGRVKVNGQVVRELGIKVGKHDTVEVD--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                               +  +  E+   Y+  KP G+  +V    G        +  
Sbjct: 52  --------------------EVPIYQEEYGYYLLYKPKGVISAVADDKGRK-----VVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++      AQ LT       + K+Y + V GI     
Sbjct: 87  LLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQRLT--HPKHEVDKVYVAKVKGIATKSM 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                 L K   I G      K            F+++    +     +E+  H GR HQ
Sbjct: 145 L---APLAKGIKIEGRKTSPAK------------FQILSVDPKTNHSIVELTIHEGRNHQ 189

Query: 255 LRVHALHMGCPI 266
           ++     +G P+
Sbjct: 190 VKNMLQAVGLPV 201


>gi|296112011|ref|YP_003622393.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
 gi|295833543|gb|ADG41424.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
          Length = 249

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 43/253 (16%), Positives = 89/253 (35%), Gaps = 49/253 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINA 73
            EE  R+ +         +    ++++  G+V+V+ + +     +++    V +  +   
Sbjct: 2   SEEAQRVQKVIAQA-GLASRRGAEELIIKGRVQVNGQTITALGVKVEPTDTVTVDSIPLE 60

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                                   +  L+Y     Y+ NKP G+               +
Sbjct: 61  G-----------------------REKLVY-----YLLNKPRGVVTTNNDEKGRR---TV 89

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              +    ++     RLD +T+G+L++      A  L       R+ K+Y + V GI  +
Sbjct: 90  LDILSDVNERVYPIGRLDYDTTGVLLLTNDGVIANQL--MHPKSRVDKVYIAKVAGIATD 147

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K       LK          VV +  K A   ++  ++     +K   + +  H GR H
Sbjct: 148 DK----LAPLKHG--------VVIKGRKTAPARVTIERI--DKDKKTSMVRVILHEGRNH 193

Query: 254 QLRVHALHMGCPI 266
           Q++     +G P+
Sbjct: 194 QVKNMLQKVGLPV 206


>gi|15902300|ref|NP_357850.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae R6]
 gi|116516048|ref|YP_815778.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae D39]
 gi|15457806|gb|AAK99060.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae R6]
 gi|116076624|gb|ABJ54344.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae D39]
          Length = 240

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 86/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++G+V V+ K+ K + + Q  + +         + I 
Sbjct: 1   MRLDKFLVACAVG-SRTEVKNLLKAGRVTVNGKKEK-SAKFQIDEKI---------DEIR 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++L+                 YE+   Y+ NKP G+           +   L     
Sbjct: 50  FDGQVLE-----------------YEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           SK  +     RLD  T G+L++      A  L      R + K Y + V GI   +    
Sbjct: 93  SK--EVFPVGRLDINTHGLLLLTNDGQLAHVL--LSPKRHVDKTYLAQVKGIMTQEDVET 148

Query: 199 --ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 LK        + ++  + +                +    + +    G+ HQ++
Sbjct: 149 FAEGIPLKDFTCQPARLEILSTDAE----------------KNQSQIRVTIAEGKFHQIK 192

Query: 257 VHALHMG 263
               + G
Sbjct: 193 RMVGYCG 199


>gi|255971130|ref|ZP_05421716.1| pseudouridine synthase [Enterococcus faecalis T1]
 gi|255973742|ref|ZP_05424328.1| pseudouridine synthase [Enterococcus faecalis T2]
 gi|256761441|ref|ZP_05502021.1| pseudouridine synthase [Enterococcus faecalis T3]
 gi|256957465|ref|ZP_05561636.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256959802|ref|ZP_05563973.1| pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256964546|ref|ZP_05568717.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|257077544|ref|ZP_05571905.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|257418285|ref|ZP_05595279.1| pseudouridine synthase [Enterococcus faecalis T11]
 gi|294780454|ref|ZP_06745819.1| pseudouridylate synthase [Enterococcus faecalis PC1.1]
 gi|255962148|gb|EET94624.1| pseudouridine synthase [Enterococcus faecalis T1]
 gi|255966614|gb|EET97236.1| pseudouridine synthase [Enterococcus faecalis T2]
 gi|256682692|gb|EEU22387.1| pseudouridine synthase [Enterococcus faecalis T3]
 gi|256947961|gb|EEU64593.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256950298|gb|EEU66930.1| pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256955042|gb|EEU71674.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|256985574|gb|EEU72876.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|257160113|gb|EEU90073.1| pseudouridine synthase [Enterococcus faecalis T11]
 gi|294452453|gb|EFG20890.1| pseudouridylate synthase [Enterococcus faecalis PC1.1]
 gi|295114108|emb|CBL32745.1| ribosomal small subunit pseudouridine synthase A [Enterococcus sp.
           7L76]
          Length = 244

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 1   MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 43  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 89  DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G+ HQ+
Sbjct: 146 CQLFA------------QGFALKDGEMVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 192

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 193 KRMLATVGKPV 203


>gi|227529187|ref|ZP_03959236.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           vaginalis ATCC 49540]
 gi|227350912|gb|EEJ41203.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           vaginalis ATCC 49540]
          Length = 240

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 87/250 (34%), Gaps = 48/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++ SG V+V+ K V     ++     V +  V       
Sbjct: 2   ERLQKVMAEA-GVASRRASEKLIASGHVQVNGKTVTEMGIKVSEHDEVVVDGVPLHREAH 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +        SV  + H D  +  ++          K  G++                   
Sbjct: 61  VYYLLNKPRSVITSAHDDKGRRTVVD-------ILKEEGVA------------------- 94

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +T+GIL++      A  L        ++K Y + V GI  N    
Sbjct: 95  ----ERVYPVGRLDYDTTGILLLTNDGELANRL--MHPKFEVEKTYIAKVRGIVNNND-- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                LK+  IG      V+ N +    A S   +     ++   +++  H GR HQ+++
Sbjct: 147 -----LKQLRIG------VEVNGRLTKKAKSRL-IETDHKKQTSLVKLTIHEGRYHQVKL 194

Query: 258 HALHMGCPIV 267
               +  P++
Sbjct: 195 MFDAIHHPVI 204


>gi|52786201|ref|YP_092030.1| RluB [Bacillus licheniformis ATCC 14580]
 gi|163119522|ref|YP_079621.2| pseudouridine synthase [Bacillus licheniformis ATCC 14580]
 gi|319645211|ref|ZP_07999444.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
 gi|52348703|gb|AAU41337.1| RluB [Bacillus licheniformis ATCC 14580]
 gi|145903029|gb|AAU23983.2| pseudouridine synthase [Bacillus licheniformis ATCC 14580]
 gi|317393020|gb|EFV73814.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
          Length = 244

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 88/253 (34%), Gaps = 56/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +++++ G+V V+ K V+    ++ S   + +          
Sbjct: 2   ERLQKVIA-HAGIASRRKAEELIKEGRVTVNGKTVRELGVKVSSSDRIEVN--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                       +   S+     LLY         KP G+  +V+   G        +  
Sbjct: 52  -----------GVQLESEEPVYFLLY---------KPRGVISAVKDDKGRK-----VVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     ++     RLD +TSG+L++      A  L        I K Y + + GIP  + 
Sbjct: 87  FFTEVEERIYPIGRLDYDTSGLLLLTNDGDFANKL--MHPKYEINKTYVAKLKGIPLKEN 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQ 254
                  LKK   G           +    A +  K++    +K    +++  H GR  Q
Sbjct: 145 -------LKKLERGVRL--------EDGKTAPAKVKLLSLDKKKQTSIVQITIHEGRNRQ 189

Query: 255 LRVHALHMGCPIV 267
           +R     +G  ++
Sbjct: 190 VRRMFEAIGHEVL 202


>gi|332686546|ref|YP_004456320.1| ribosomal large subunit pseudouridine synthase B [Melissococcus
           plutonius ATCC 35311]
 gi|332370555|dbj|BAK21511.1| ribosomal large subunit pseudouridine synthase B [Melissococcus
           plutonius ATCC 35311]
          Length = 236

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 54/278 (19%), Positives = 100/278 (35%), Gaps = 57/278 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RL +    H    +    ++I+  G+V+V+ + +      + G+ V     I   N  I 
Sbjct: 3   RLQKVLA-HAGIASRRKAEQIILEGRVKVNGEIIN-----ELGRQVSKQDKIEVDNVPIY 56

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           ++  +                        Y+F KP GI     S         +  +   
Sbjct: 57  QEAPV-----------------------YYLFYKPRGIIT---SVSDDKKRKTVADYFLH 90

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             ++     RLD +T+G+L+V    +  Q LT       I K+Y + V GI   K     
Sbjct: 91  SNERVYPVGRLDYDTTGLLIVTNDGSLTQQLT--HPSHEIDKVYVAKVKGIALRKTLL-- 146

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTHQLRVH 258
             L K   I            KG   A ++F+++    +K    +++  H GR HQ++  
Sbjct: 147 -PLTKGIKI------------KGRKTAPANFQILSVDTKKQTSLVQLTIHEGRNHQVKDM 193

Query: 259 ALHMGCPI-------VGDHKYCANFKGNFTSPIQNKLY 289
              +G P+       +GD        G +    + +++
Sbjct: 194 LDTVGYPVQKLKRERIGDLTLEGLHPGEYRRLTKKEIH 231


>gi|229546498|ref|ZP_04435223.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|307277044|ref|ZP_07558150.1| hypothetical protein HMPREF9521_02651 [Enterococcus faecalis
           TX2134]
 gi|307289941|ref|ZP_07569870.1| hypothetical protein HMPREF9509_00254 [Enterococcus faecalis
           TX0411]
 gi|312904312|ref|ZP_07763474.1| conserved hypothetical protein [Enterococcus faecalis TX0635]
 gi|229308398|gb|EEN74385.1| pseudouridylate synthase [Enterococcus faecalis TX1322]
 gi|306499007|gb|EFM68496.1| hypothetical protein HMPREF9509_00254 [Enterococcus faecalis
           TX0411]
 gi|306506288|gb|EFM75452.1| hypothetical protein HMPREF9521_02651 [Enterococcus faecalis
           TX2134]
 gi|310632408|gb|EFQ15691.1| conserved hypothetical protein [Enterococcus faecalis TX0635]
 gi|315030592|gb|EFT42524.1| conserved hypothetical protein [Enterococcus faecalis TX4000]
 gi|315159713|gb|EFU03730.1| conserved hypothetical protein [Enterococcus faecalis TX0312]
 gi|315162686|gb|EFU06703.1| conserved hypothetical protein [Enterococcus faecalis TX0645]
 gi|315578753|gb|EFU90944.1| conserved hypothetical protein [Enterococcus faecalis TX0630]
          Length = 257

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 14  MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 56  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 101

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+     
Sbjct: 102 DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLV---- 154

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             + +  L               + +    +    + I+   +    + +    G+ HQ+
Sbjct: 155 -TVEDCQLFAQGFALK-------DGEMVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 205

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 206 KRMLATVGKPV 216


>gi|239631549|ref|ZP_04674580.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           paracasei subsp. paracasei 8700:2]
 gi|301066420|ref|YP_003788443.1| 16S rRNA uridine-516 pseudouridylate synthase-like protein
           [Lactobacillus casei str. Zhang]
 gi|239526014|gb|EEQ65015.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           paracasei subsp. paracasei 8700:2]
 gi|300438827|gb|ADK18593.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus casei str. Zhang]
          Length = 247

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 87/252 (34%), Gaps = 54/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   N     +  + + ++ +G V+V+ +       I++   ++I P        +
Sbjct: 6   ERLQKIIANA-GIASRRHAETLIATGHVKVNGQ-------IETEMGIKIGPHDEVEVDGV 57

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSW 136
              K                     E  + ++F KP G+  +VQ   G        +  +
Sbjct: 58  PIGK---------------------EAKRYFLFYKPRGVISAVQDNKGR-----DVVTDY 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKK 195
                ++     RLD +TSG+LV+      A HL        ++K Y + V G+P +   
Sbjct: 92  FKDIAERLYPVGRLDYDTSGLLVMTNDGDLANHL--MHPRYALEKKYVAKVQGVPNRPAL 149

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +   +     +       +   +K    AI               + +  H G  HQ+
Sbjct: 150 APLKTGVEVDGKMTAPAKVDIISTDKAKKTAI---------------VSLTIHQGMNHQV 194

Query: 256 RVHALHMGCPIV 267
           +     +G P++
Sbjct: 195 KKMFKAVGFPVL 206


>gi|257080911|ref|ZP_05575272.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257415240|ref|ZP_05592234.1| pseudouridine synthase [Enterococcus faecalis AR01/DG]
 gi|256988941|gb|EEU76243.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257157068|gb|EEU87028.1| pseudouridine synthase [Enterococcus faecalis ARO1/DG]
          Length = 244

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 1   MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 43  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 89  DQDYRVDLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G+ HQ+
Sbjct: 146 CQLFA------------QGFALKDGEMVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 192

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 193 KRMLATVGKPV 203


>gi|81429040|ref|YP_396040.1| pseudouridylate synthase, 16S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610682|emb|CAI55733.1| Pseudouridylate synthase, 16S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 239

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 92/248 (37%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+DR+  +         L+ +L++G+VRV  K +K    ++    VV +          
Sbjct: 1   MRIDRFLSHMNVG-TRKTLKPLLKAGRVRVADKVIKEAKYQVTPETVVYVD--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+ +  ++ NKPAG+           +D F  +  
Sbjct: 51  --------------------DEPIRYQTNFYWLLNKPAGVISATTDPQKTVMDLFAPADY 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               +      RLD++T+G+L++      A   L+     + + K Y + + G+     +
Sbjct: 91  R---EDLFPVGRLDKDTTGLLLITNDGDLAHDLLS---PKKHVAKTYRAKIAGVVTAADQ 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYA-ISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                          +   +K  +  A  A ++  +     A++   +E++ H G+ HQ+
Sbjct: 145 -------------AQFAAGLKLRDFDAQPAQLTILRT--DTARQESLIEVEIHEGKFHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KRMFHAVG 197


>gi|116492417|ref|YP_804152.1| ribosomal small subunit pseudouridine synthase A [Pediococcus
           pentosaceus ATCC 25745]
 gi|116102567|gb|ABJ67710.1| ribosomal small subunit pseudouridine synthase A [Pediococcus
           pentosaceus ATCC 25745]
          Length = 239

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 89/247 (36%), Gaps = 49/247 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  +         ++K+++   + V+   VK   R++             ++ ++
Sbjct: 1   MRVDKFLHDMNMG-TRTQIRKMIKDKLIFVNDTVVKTG-RVK-------------VDPVV 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E ++ D              ++ Y+    ++ NKP G+               +    +
Sbjct: 46  DEVRLKDQ-------------VIEYQQYFYFMMNKPLGVLT----ATEDRKQKTVMDLFN 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               +       RLD++T G+L++      A  L      R + K Y ++V G   ++  
Sbjct: 89  KVDLRNDLFPVGRLDKDTQGLLLITNNGQLAHDL--LAPERHVDKTYEAVVTGKITDQ-- 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +  +    +   G  +       K A   I H+  +D        +++    G+ HQ+R
Sbjct: 145 AVEEFQKGITLRDGTTL-------KPAQLIIEHYSELD----DQTVVKVVLKEGKYHQVR 193

Query: 257 VHALHMG 263
                +G
Sbjct: 194 RMFGSLG 200


>gi|315146884|gb|EFT90900.1| conserved hypothetical protein [Enterococcus faecalis TX4244]
          Length = 257

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 14  MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 56  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 101

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 102 DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 158

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G+ HQ+
Sbjct: 159 CQLFA------------QGFALKDGEIVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 205

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 206 KRMLATVGKPV 216


>gi|325283294|ref|YP_004255835.1| pseudouridine synthase Rsu [Deinococcus proteolyticus MRP]
 gi|324315103|gb|ADY26218.1| pseudouridine synthase Rsu [Deinococcus proteolyticus MRP]
          Length = 252

 Score = 65.0 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 37/251 (14%), Positives = 72/251 (28%), Gaps = 57/251 (22%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +   RL +         +    ++++ +G+V V+        R+Q G  V +        
Sbjct: 3   DSGERLQKVLARA-GVASRRAAEELITAGRVAVNGIPAGLGVRVQPGDRVTVD------- 54

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                + +   + ++T                 Y+ +KPAG        +       L +
Sbjct: 55  ----GEPVAAPTPHVT-----------------YMLHKPAGFVTTAQDELGRR--TVLDA 91

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                G  P    RLD+++ G+L++         LT            W           
Sbjct: 92  MPPVPGLHP--VGRLDKDSEGLLILTTDGDLTLRLTHPRFEHEKVYRVWCF-----PEPG 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E     L +   +   +     +   G   A+                      GR  Q+
Sbjct: 145 EQELAALRRGVELEEGFARAEVEPAPGGALAL-------------------LREGRKRQV 185

Query: 256 RVHALHMGCPI 266
           R     +GCP+
Sbjct: 186 RRMFAEVGCPV 196


>gi|327490097|gb|EGF21885.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1058]
          Length = 242

 Score = 65.0 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 90/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G+V ++ + V+     ++SG  V +          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIKQGKVSINGQVVRELAINVKSGDRVEVEGQP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                                  +  E+   Y+ NKP G+  SV    G        +  
Sbjct: 54  -----------------------IYNEEKVYYLLNKPRGVISSVSDDKGRK-----TVVD 85

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++         +        I K+Y + V G+   + 
Sbjct: 86  LLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM--IHPRNEIDKVYVARVKGLANKE- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQ 254
             +   L +   I G               A+  +++I    A+    +++  H GR HQ
Sbjct: 143 --VLRPLTRGIEIEGRKT----------QPAV--YEIIKVDPAKNRSVVQLTIHEGRNHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKKMFQAVG 197


>gi|319892477|ref|YP_004149352.1| Ribosomal large subunit pseudouridine synthase B [Staphylococcus
           pseudintermedius HKU10-03]
 gi|317162173|gb|ADV05716.1| Ribosomal large subunit pseudouridine synthase B [Staphylococcus
           pseudintermedius HKU10-03]
 gi|323464420|gb|ADX76573.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           pseudintermedius ED99]
          Length = 248

 Score = 65.0 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 77/237 (32%), Gaps = 53/237 (22%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+ K V     +++    V +                    + L 
Sbjct: 19  SRRKAETLIEEGKVQVNGKTVTELGTKVRPSDEVTV------------------EGIPLE 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +           ED    +F KPA +     S         +  + D    +     RLD
Sbjct: 61  Q-----------EDKLYILFYKPAQVIT---SVSDDRGRKVVTDYFDDLVTRIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIG 209
            +TSG+L++         +T      +I K Y + + G    +  K+      L+     
Sbjct: 107 YDTSGLLLLTNDGEFTNLMT--HPRYKIPKTYVAKIEGYILREQVKQLEKGIQLEDGLTQ 164

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              V V KQN++                +    +E+    GR  Q+R    H G  +
Sbjct: 165 PAKVKVKKQNKE----------------KNTSLVEITITEGRNRQVRRMFEHFGFSV 205


>gi|325695507|gb|EGD37407.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK150]
          Length = 242

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 83/246 (33%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+   V V+ +  K                        
Sbjct: 1   MRLDKFLAENGLG-SRAQVKQLLKKELVLVNGRAEKS----------------PKTQIDE 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              +I+ S   LT           YE    Y+ NKP G+           +   L     
Sbjct: 44  TADEIIVSGQRLT-----------YEKFVYYLLNKPQGVISATEDDRHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+     E 
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLMNQADE- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   ++  +     A      +D  A++   +E+    G+ HQ++ 
Sbjct: 147 ------------ERFAAGIELKDFTCQPAQLKILELDA-AKETSLVEITLAEGKFHQVKR 193

Query: 258 HALHMG 263
                G
Sbjct: 194 MVAACG 199


>gi|256850915|ref|ZP_05556304.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 27-2-CHN]
 gi|260661129|ref|ZP_05862043.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 115-3-CHN]
 gi|256615977|gb|EEU21165.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 27-2-CHN]
 gi|260548066|gb|EEX24042.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 115-3-CHN]
          Length = 234

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 23/144 (15%), Positives = 54/144 (37%), Gaps = 33/144 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  ++++ +V V+ + VK    ++    +V++          
Sbjct: 1   MRIDKYLANMKVG-SRKEVHDLIKAKKVTVNGQLVKQAKQQVADTDIVKV---------- 49

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + YE    ++ NKPAG+           +   ++   
Sbjct: 50  -------------------ADETIAYEQFYYFMLNKPAGVITATEDPQQKTVLDLIEH-- 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVA 161
             + Q      RLD++T+G+L++ 
Sbjct: 89  KDRYQGLSPVGRLDKDTTGLLLLT 112


>gi|254496468|ref|ZP_05109345.1| pseudouridine synthase [Legionella drancourtii LLAP12]
 gi|254354324|gb|EET12982.1| pseudouridine synthase [Legionella drancourtii LLAP12]
          Length = 252

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/233 (14%), Positives = 78/233 (33%), Gaps = 34/233 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +   +++ + +G V+V+ K VK  +       + +           
Sbjct: 4   ERLQKILSQAGLG-SRREMERWIENGWVQVNGKPVKLGDSASGDDKITV----------- 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            + K++ + + + +++            +I +++KP G IS +        +   L    
Sbjct: 52  -KGKLIPNPLKIKQNT------------RILLYHKPVGEISSRHDPKFEKTVFDRLPHLR 98

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +  +     RLD  TSG+L+       A  L        +++ Y   V G    +   
Sbjct: 99  QGRWVQ---VGRLDLNTSGLLIFTNNGELANQL--MHPRYGLEREYAVRVHGQVTQEMLT 153

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           +   L K   +        +   +G + A + + V     +      +    G
Sbjct: 154 V---LQKGVELDDGPAKFSRLESRGGDGANTWYHVTLNEGRNREVRRLWESQG 203


>gi|257420928|ref|ZP_05597918.1| pseudouridine synthase [Enterococcus faecalis X98]
 gi|300861842|ref|ZP_07107922.1| pseudouridylate synthase [Enterococcus faecalis TUSoD Ef11]
 gi|257162752|gb|EEU92712.1| pseudouridine synthase [Enterococcus faecalis X98]
 gi|300848367|gb|EFK76124.1| pseudouridylate synthase [Enterococcus faecalis TUSoD Ef11]
          Length = 244

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 1   MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 43  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 89  DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G+ HQ+
Sbjct: 146 CQLFA------------QGFALKDGEIVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 192

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 193 KRMLATVGKPV 203


>gi|108707582|gb|ABF95377.1| pseudouridine synthase family protein, putative, expressed [Oryza
           sativa Japonica Group]
          Length = 208

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/149 (22%), Positives = 53/149 (35%), Gaps = 29/149 (19%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           K++   +   +        +LYED  +   NKP+G+ V                  D K 
Sbjct: 8   KLVYHRLPWQEPFAPHLLDVLYEDDDMIALNKPSGLQVLPKGLFQQRTVLAQLQLKDWKM 67

Query: 142 Q------------KPRLTHRLDQETSGILVVARTRAAAQHL-----------------TE 172
                         P   HRL + TSG+L+ A+T+ A   L                 T+
Sbjct: 68  PSSFCSKRKDAQSHPVPVHRLGRGTSGLLLCAKTKLAKAQLAAYFAEGATNAGKSRDETD 127

Query: 173 SFRMRRIQKIYWSLVWGIPKNKKECIANW 201
             + R+I K Y +LV GI +N +      
Sbjct: 128 ICKARKISKFYRALVTGILENDEVLTFPP 156


>gi|150017514|ref|YP_001309768.1| pseudouridine synthase [Clostridium beijerinckii NCIMB 8052]
 gi|149903979|gb|ABR34812.1| pseudouridine synthase [Clostridium beijerinckii NCIMB 8052]
          Length = 261

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 49/266 (18%), Positives = 92/266 (34%), Gaps = 58/266 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +  N++  ++ G V+V+K+ V                         
Sbjct: 1   MRLDKFLAEAAVG-SRKNVRIYIKEGMVKVNKELVT------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +    +D + ++    ++L  I+ Y     Y+FNKPAG        I   +  FL    +
Sbjct: 36  EPAIEIDENCDVI---EYLNEIVSYAGKLYYMFNKPAGCITAKTDEIHKTVFDFL---GE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +  +      RLD++T G+L+          +   +  + ++K Y+    G    +    
Sbjct: 90  AGTKGIFHVGRLDKDTEGLLLFTNDGEFEHKI--MYPEKHVEKTYFFWALGSLSEED--- 144

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-----------------CFAQKFC 241
                KK    G Y+   K   K A   +  F + +                    Q   
Sbjct: 145 -----KKQLEQGTYIGQCKILTKPAKIEVDKFGIYEELKHEMATDNVNNINSNHGTQPVV 199

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIV 267
              +    GR HQ++     +GC +V
Sbjct: 200 SGYLTISEGRKHQVKRMLKSVGCYVV 225


>gi|256854470|ref|ZP_05559834.1| pseudouridine synthase [Enterococcus faecalis T8]
 gi|257089099|ref|ZP_05583460.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|256710030|gb|EEU25074.1| pseudouridine synthase [Enterococcus faecalis T8]
 gi|256997911|gb|EEU84431.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|323479852|gb|ADX79291.1| S4 domain pseudouridine synthase family protein [Enterococcus
           faecalis 62]
          Length = 244

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 1   MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 43  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+     
Sbjct: 89  DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLV---- 141

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             + +  L               + +    +    + I+   +    + +    G+ HQ+
Sbjct: 142 -TVEDCQLFAQGFALK-------DGEMVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 192

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 193 KRMLATVGKPV 203


>gi|149200710|ref|ZP_01877696.1| Pseudouridylate synthase, 23S RNA-specific [Lentisphaera araneosa
           HTCC2155]
 gi|149136200|gb|EDM24667.1| Pseudouridylate synthase, 23S RNA-specific [Lentisphaera araneosa
           HTCC2155]
          Length = 134

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/102 (30%), Positives = 40/102 (39%), Gaps = 8/102 (7%)

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
              K  E   N A++ F       Q      ++P TG+THQLRV    +G PI GD  Y 
Sbjct: 12  RRWKLCESRKNPAVTQFFS-YSIGQGKRVYLLRPRTGKTHQLRVAMKAIGAPICGDPNYY 70

Query: 274 ANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
                      + + YLHA  +     E    Q T  L  HM
Sbjct: 71  P----GLIKGHEERCYLHAYVIRFTLKE-REYQFT--LKPHM 105


>gi|312863597|ref|ZP_07723835.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
 gi|311101133|gb|EFQ59338.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
          Length = 243

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 81/246 (32%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++  L+  QV V+ +                  +  +    I
Sbjct: 1   MRLDKFLVDCGVG-SRSQVKNFLKKKQVTVNGQ------------------LETSPKTQI 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E K             +L   L +E    Y+ NKP G+     +     +   L     
Sbjct: 42  DENK---------DRIAYLDQELTHETFVYYLLNKPQGVISATENPRHKTVLDLLDDTAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++      A   L+     + + KIY + V G+   +   
Sbjct: 93  HK--QVFPVGRLDIDTHGLLLLTNNGDLAHAMLS---PKKHVDKIYQAKVAGVMDEEDIL 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   +K  +     A      +D   +   W+++    G+ HQ++ 
Sbjct: 148 -------------AFEKGIKLKDHTCQPAKLEIVSVDRN-ESTSWVQITIAEGKFHQVKR 193

Query: 258 HALHMG 263
                G
Sbjct: 194 MVAACG 199


>gi|296449151|ref|ZP_06890938.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           difficile NAP08]
 gi|296880870|ref|ZP_06904818.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           difficile NAP07]
 gi|296261970|gb|EFH08778.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           difficile NAP08]
 gi|296428157|gb|EFH14056.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           difficile NAP07]
          Length = 240

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 38/246 (15%), Positives = 84/246 (34%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D+   N   + +   ++K  + G V V+   V        G  V             
Sbjct: 5   QRIDKILSN-LGYGSRSEIKKYCKQGSVVVNGSEVS-----NPGTQVD-----------T 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  +IL +              ++Y +    + NKP G            +   +   + 
Sbjct: 48  ENDEILFNGEE-----------VIYREYIYLMMNKPDGYVSATTDKYDPTVLDLID--LS 94

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +P    RLD++T G+LV+    + + + L+     + + K Y++ + G+   +   
Sbjct: 95  YLAFEPFPVGRLDKDTEGLLVLTNDGKLSHRVLS---PKKHVPKTYYAKIDGVVTEED-- 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +  +L                 + G     S   ++   +     +E+  H G+ HQ++ 
Sbjct: 150 VEAFLEG------------VVLDDGYKTMPSQLNILK--SDDESEIELTIHEGKFHQVKR 195

Query: 258 HALHMG 263
               +G
Sbjct: 196 MFESVG 201


>gi|168186328|ref|ZP_02620963.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum C str. Eklund]
 gi|169295670|gb|EDS77803.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum C str. Eklund]
          Length = 236

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 89/250 (35%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++  +     +    ++I+ S +V+V+   V                         
Sbjct: 3   ERLQKYMAS-CGVASRRKCEEIITSNRVQVNGTVV------------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
             +       +  K     K I L E +     NKP G +S          I   +    
Sbjct: 37  -NELGFKVDPSKDKVYVDSKLIFLEEKNVYIALNKPEGYVSTVKDERDRKTIMDLV---- 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD  TSG+L++         +      + I K+Y +++ GIP N+   
Sbjct: 92  -EVEERIFPIGRLDYNTSGLLLMTNDGDVYNKI--IHPRKEIDKVYIAIIKGIPSNEA-- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++K   G D    +         + ++F+VID  ++    +++  H G+  Q+R 
Sbjct: 147 -----IRKFCNGLDIGDYI--------TSKANFEVIDT-SENKSKVKITIHEGKNRQVRR 192

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 193 MCDKIGHPVI 202


>gi|220929165|ref|YP_002506074.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|219999493|gb|ACL76094.1| pseudouridine synthase [Clostridium cellulolyticum H10]
          Length = 235

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 86/251 (34%), Gaps = 51/251 (20%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNH 76
            +RL ++   H    +    +++++ G+V V+   V+     + +   V +         
Sbjct: 3   GIRLQKFIA-HAGVASRRTAEEMIKQGRVAVNNTVVQDMGFTVSNDDFVTVDGKPVK--- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            I+E+K+                          + +KP G                +   
Sbjct: 59  -IEEEKV------------------------YIMLHKPVGYVSTSQDQFGR---PTVVDL 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           V   G++     RLD +TSG++++         LT       I K+Y +++ G P+  + 
Sbjct: 91  VKDAGKRLYPVGRLDYDTSGLILLTNDGDFTYRLT--HPKHEINKVYEAVISGFPEKNE- 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                   KS   G  +       +    + + F V++        + +  H G+  Q+R
Sbjct: 148 -------IKSFESGLKI-------ENYQTSPAEFVVLEKQGIN-TLVRITIHEGKNRQVR 192

Query: 257 VHALHMGCPIV 267
                +G  ++
Sbjct: 193 KMCEAIGHKVL 203


>gi|110833959|ref|YP_692818.1| ribosomal small subunit pseudouridine synthase A [Alcanivorax
           borkumensis SK2]
 gi|110647070|emb|CAL16546.1| Ribosomal small subunit pseudouridine synthase A [Alcanivorax
           borkumensis SK2]
          Length = 248

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 37/240 (15%), Positives = 82/240 (34%), Gaps = 52/240 (21%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+       ++  NL+ +L +G+VRV+ +  +   R            I   + ++ 
Sbjct: 14  RLDRFLSARL-QMSRSNLRLLLAAGRVRVNGQVERDRQR-----------RIGLFDAVVC 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + +IL ++                      + NKPAG+     +    H    L+     
Sbjct: 62  DGEILQANRPR-----------------YLMINKPAGVVS---ATRDEHHPTVLELLPRG 101

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +   L  RLD  ++G++++    A ++ L+                 G+ K+ +  + 
Sbjct: 102 QREGLHLAGRLDFNSTGLVLLTNDGAWSRRLSLPET-------------GLWKHYRVSVD 148

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L  +  +           +     A    +            ++  H G+ HQ++   
Sbjct: 149 KPLSDEDVVSFSQRMWFDFEQIYTQPARLTIR-------SSFEADVWLHEGKYHQIKRMF 201


>gi|315646387|ref|ZP_07899505.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315278030|gb|EFU41350.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 251

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 41/275 (14%), Positives = 89/275 (32%), Gaps = 62/275 (22%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
            +    ++++  G+V+V+ + V                               +      
Sbjct: 14  ASRRKCEELILEGKVQVNGETVT------------------------------ELGTKAD 43

Query: 92  KHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH 148
              D +      + +E     + NKP G+     S         +  ++    ++     
Sbjct: 44  PAQDMITVSGKPIKHEKKVYVMLNKPKGVIT---SASDPEGRKIVSDYLKGIKERVYPIG 100

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           RLD +T G+L++      A  L+       + K Y + V G+P              + +
Sbjct: 101 RLDYDTEGLLLLTNDGEFANLLS--HPKYHVPKTYLATVKGVPHG------------TEL 146

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV- 267
                 ++ ++   +  A   +K +D    K   + +  H GR  Q+R     +  P++ 
Sbjct: 147 DKLRQGIMLEDGMTS-PAEVEYKDVD-PDNKQSVISITIHEGRNRQVRRMFEAISHPVLR 204

Query: 268 ------GDHKYCANFKG---NFTSPIQNKLYLHAR 293
                 GD       +G   + T+   N+L   A+
Sbjct: 205 LKRISYGDLLLQNLKRGLYRHLTADEINQLMQMAK 239


>gi|317473625|ref|ZP_07932914.1| RNA pseudouridylate synthase [Anaerostipes sp. 3_2_56FAA]
 gi|316898915|gb|EFV20940.1| RNA pseudouridylate synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 238

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 83/248 (33%), Gaps = 55/248 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           +RLD++  +          +K++R G+V    + +K    ++                  
Sbjct: 4   LRLDKFLCDVL-GCTRSEARKMIRQGRVLAGDEIIKKPEYKVNP---------------- 46

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +E +I      L            YE     + NKP G+      G    +   L    
Sbjct: 47  -EEDEITADGQRLNFRK--------YE---YLMMNKPKGVVTATKDGRDKTVMDLLTGRH 94

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKK 195
                      RLD++T G+L++      A + L+       + K Y   V G I + ++
Sbjct: 95  RKG---LFPAGRLDKDTEGLLLITNDGELAHRLLS---PKHHVTKCYSVTVTGEIGREQQ 148

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E   + +     IG D         K    A    K++   + +    E+    GR HQ+
Sbjct: 149 EIFESGM----DIGDD---------KPLKPA----KLVILTSGEVSQAEVFITEGRFHQI 191

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 192 KRMFEAVG 199


>gi|187933363|ref|YP_001887508.1| RNA pseudouridine synthase family protein [Clostridium botulinum B
           str. Eklund 17B]
 gi|187721516|gb|ACD22737.1| RNA pseudouridine synthase family protein [Clostridium botulinum B
           str. Eklund 17B]
          Length = 264

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 38/261 (14%), Positives = 87/261 (33%), Gaps = 53/261 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQK-ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       +    + +  ++ G V+V+ + +                        
Sbjct: 1   MRLDKFLAE--SAVGRRKIVRTYIKDGMVKVNGEIIT----------------------- 35

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
              +  +D +  L    ++L+  +++     Y+FNKP+G           +I   +  + 
Sbjct: 36  ---EPSIDINEKLD-DVEYLEKKVVHTGKVYYMFNKPSGCIT----ATKDNIHRTVFDYF 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS-----------L 186
           D          RLD++T G+L++         +    +       +W+           L
Sbjct: 88  DEDMNGVFHVGRLDKDTEGLLLLTNDGEFEHKVMHPEKHVEKTYFFWALGSLDDEDKKQL 147

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G+     E +        H  G Y+   ++    +     H  V+  +        + 
Sbjct: 148 QEGVFIGSNEALTKPAKIDIHKSGSYIEFKEEIPINSLKNKDHQPVVSGY--------LT 199

Query: 247 PHTGRTHQLRVHALHMGCPIV 267
              G+ HQ++     +GC ++
Sbjct: 200 ISEGQKHQVKRMLKAVGCYVI 220


>gi|126664623|ref|ZP_01735607.1| 16S rRNA pseudouridylate 516 synthase [Marinobacter sp. ELB17]
 gi|126630949|gb|EBA01563.1| 16S rRNA pseudouridylate 516 synthase [Marinobacter sp. ELB17]
          Length = 230

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 81/249 (32%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++    ++ + +G V+V+    K +   + +   V +   + AL   
Sbjct: 1   MRLDQFIATS-SELSRKEAKRAIAAGDVQVNGDVWKNSATAVPANAEVMLQGELVALPA- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                        +  + NKPAG                L + +
Sbjct: 59  ----------------------------ERYLMLNKPAGFISATRDSDQPTALDLLPAEL 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                   +  RLD +T+G+L++          ++     R+           PK  +  
Sbjct: 91  TRN---LHIAGRLDADTTGLLLLT---------SDGQWSHRVTSPRVEC----PKTYQVA 134

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           ++  + + +    +   +++ + K    A     V+         +E+    GR HQ++ 
Sbjct: 135 LSVPISQAAIAALETGVMLRNDTKPTKPA--QVTVLQSQ-----LVELTISEGRYHQVKR 187

Query: 258 HALHMGCPI 266
               +G  +
Sbjct: 188 MLAAVGNHV 196


>gi|90961422|ref|YP_535338.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           salivarius UCC118]
 gi|90820616|gb|ABD99255.1| Ribosomal small subunit pseudouridine synthase A [Lactobacillus
           salivarius UCC118]
          Length = 240

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/242 (18%), Positives = 87/242 (35%), Gaps = 46/242 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++             +K++++ +VR++ + VK       G++              
Sbjct: 3   MRLDKFLSQTGK-FTRAEAKKVIKAKRVRLNDEVVK------DGKI-------------- 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              KI + S  +    + L    L      Y+ NKPAG+           +   +     
Sbjct: 42  ---KINEESDKIFLDGELLA---LNNKEVYYMLNKPAGVVSATRDDKDKTVIDLIN--FP 93

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            + +      RLD+ET+G+L++    + A   ++     + + K Y ++V G    K+  
Sbjct: 94  GRKEDLFPVGRLDKETTGLLIITNDGKFAHDIIS---PKKHVSKTYEAVVTGKISEKEVK 150

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I +  ++ S+        +           S  +VI              H G+ HQ+R 
Sbjct: 151 IFSQGMELSNGDKLQPAQLDIISYSEKDDTSKVRVI-------------IHEGKYHQVRR 197

Query: 258 HA 259
             
Sbjct: 198 MF 199


>gi|282882075|ref|ZP_06290716.1| ribosomal large subunit pseudouridine synthase B [Peptoniphilus
           lacrimalis 315-B]
 gi|300814964|ref|ZP_07095192.1| putative pseudouridine synthase B, ribosomal large subunit
           [Peptoniphilus sp. oral taxon 836 str. F0141]
 gi|281298105|gb|EFA90560.1| ribosomal large subunit pseudouridine synthase B [Peptoniphilus
           lacrimalis 315-B]
 gi|300510934|gb|EFK38206.1| putative pseudouridine synthase B, ribosomal large subunit
           [Peptoniphilus sp. oral taxon 836 str. F0141]
          Length = 235

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 85/246 (34%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL ++   H    +    +++++ G+V+V+   V                         
Sbjct: 1   MRLQKFMA-HAGAASRRKSEELIKEGRVKVNNNIVT------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +  L+   N  +     K + L  ++   + NKP G+               L     
Sbjct: 36  --EMGLEVDPNKDRVYLDGKRLNLENENIYIILNKPIGVVTTSSDEKGRINVVDLV---- 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            + ++     RLD +T+G++++      A  L        I K Y + V G P  ++   
Sbjct: 90  DETKRVYPVGRLDIDTTGLVLLTNDGTLANIL--MHPKNNIYKTYIATVEGKPNARE--- 144

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              LL+      D              + +  K++  F  K   +E+  H G+ HQ++  
Sbjct: 145 -LNLLRNGLSLRDL-----------KTSKAKVKILKNF-DKDSIIEISIHEGKNHQVKRM 191

Query: 259 ALHMGC 264
             ++G 
Sbjct: 192 FSYIGH 197


>gi|257083600|ref|ZP_05577961.1| pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256991630|gb|EEU78932.1| pseudouridine synthase [Enterococcus faecalis Fly1]
          Length = 244

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 87/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 1   MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 43  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 89  DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G+ HQ+
Sbjct: 146 CQLFA------------QGFALKDGEVVKPSRLVIETIN-EEEGTSVVRLVIQEGKFHQV 192

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 193 KRMLATVGKPV 203


>gi|15895126|ref|NP_348475.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|15024828|gb|AAK79815.1|AE007694_1 Predicted pseudouridylate synthase [Clostridium acetobutylicum ATCC
           824]
 gi|325509265|gb|ADZ20901.1| pseudouridylate synthase [Clostridium acetobutylicum EA 2018]
          Length = 236

 Score = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 86/254 (33%), Gaps = 61/254 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-----KFNNRIQSGQVVRIPPVINA 73
            RL ++        +    +K+++ G+V+V+   V     K + +      + +      
Sbjct: 3   ERLQKYMAE-CGVASRRKCEKMIQDGRVKVNGTIVTELGFKVDYK---KDTIELDNKE-- 56

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF-NKPAGISVQGGSGIAYHIDGF 132
                                      +  ED K+Y   NKP G      +   Y     
Sbjct: 57  ---------------------------IKLEDKKVYAILNKPKGYLT---AASDYRGRKT 86

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   ++ K ++     RLD  T+G+L+V         +      + + K Y + V G P+
Sbjct: 87  VIDLLNFK-ERVFPVGRLDFNTTGLLIVTNDGEIFNRI--MHPRQNVNKCYLATVKGKPQ 143

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            K     + L K   IGG          K A  ++  F        K   L++  H G+ 
Sbjct: 144 FKHL---DALRKGIDIGG-------YITKEAEVSVVSF------DGKNSILKIVIHEGKK 187

Query: 253 HQLRVHALHMGCPI 266
            Q+R     +G P+
Sbjct: 188 RQVRRMCAAVGFPV 201


>gi|326407871|gb|ADZ64942.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. lactis CV56]
          Length = 273

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 84/243 (34%), Gaps = 41/243 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L+ G+V V            +G+V R        N   
Sbjct: 32  MRLDKFLAESGLG-SRSEVKILLKKGRVTV------------AGEVQRDGRFQVDKN--- 75

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                       ++   F   IL Y++   Y+ NKP G+       +   +   L     
Sbjct: 76  ------------SRQVAFDGEILDYQEYYYYLLNKPQGLVSATKDNLFKTVVQLLSE--K 121

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              +      RLD+ T G+L++    A    LT+    R ++K Y++ + G   +  E +
Sbjct: 122 DFREDIFPVGRLDKNTEGLLILTNDGALGHDLTQ--PKRHVEKEYFARIDGKVTD--EIV 177

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +    +   G+               I +    +  +     + +  H G+ HQ++  
Sbjct: 178 NKFAEGLTLKNGEKAR-------PGELFIENIYKGESQSGWISEIRVIIHEGKFHQVKRM 230

Query: 259 ALH 261
              
Sbjct: 231 FEA 233


>gi|148827048|ref|YP_001291801.1| malic enzyme [Haemophilus influenzae PittGG]
 gi|148718290|gb|ABQ99417.1| malic enzyme [Haemophilus influenzae PittGG]
          Length = 232

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 82/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +R   V+++ + VK                      I 
Sbjct: 1   MRLDKFIAEN-TGLTRSQATKAIRQSAVKINGEIVKS-----------------GAVQIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           ++ +I      LT            E+ + ++ +KP G       G    I  F    + 
Sbjct: 43  QKDEIYFEDELLTWV----------EEGQYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 93  G---KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + K          +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPVEKNYAEACAEGILLRGEKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|292493543|ref|YP_003528982.1| RNA-binding S4 domain protein [Nitrosococcus halophilus Nc4]
 gi|291582138|gb|ADE16595.1| RNA-binding S4 domain protein [Nitrosococcus halophilus Nc4]
          Length = 266

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/236 (14%), Positives = 73/236 (30%), Gaps = 36/236 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +   ++  +++G+VRV+    +  +++     V I     +   + 
Sbjct: 3   ERLQKILARGGLG-SRREIEAWIKAGRVRVNGVPAQLGDKVSVKDRVTIDGRPISPKRLQ 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                      S++ +++KPAG                 +S   
Sbjct: 62  PPS------------------------SQVIIYHKPAGEVC--SRKDPEGRPNVFQSLPR 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +     RLD  TSG+L++      A  L       ++++ Y   V G        I
Sbjct: 96  PQQGRWISVGRLDINTSGLLLLTTDGELANRL--MHPSTQVEREYAVRVLGTVAED--VI 151

Query: 199 ANWLLKKSHIGG--DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                  +   G   +  ++    +GAN+    + VI    +      +    G  
Sbjct: 152 ERLQGGVTLEDGLARFEQILDAGGEGANH---WYHVILREGRNREVRRLWESQGVR 204


>gi|255729054|ref|XP_002549452.1| hypothetical protein CTRG_03749 [Candida tropicalis MYA-3404]
 gi|240132521|gb|EER32078.1| hypothetical protein CTRG_03749 [Candida tropicalis MYA-3404]
          Length = 271

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/198 (21%), Positives = 79/198 (39%), Gaps = 30/198 (15%)

Query: 97  LKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQE 153
           +K  ++       V NKP+G+  + +G + I   +    K ++ +    + R+  RLD+ 
Sbjct: 1   MKLEIVKRTFNYAVINKPSGLICAARGPNNIVDAVSEEFKQFLPTVSSSQFRIVQRLDRF 60

Query: 154 TSGILVVARTRAAAQHLTESFRMRRI-----QKIYWSLVWGIPKNKKECIAN---WLLKK 205
            +G L++AR +  A  + +SF          + +    +  IPK  K  I +    L K 
Sbjct: 61  VTGGLLIARNKKWADKVRKSFYGGGNLKLIRRYVGLIPLTNIPKKTKGVIEHEIEALEKD 120

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK------------FCWLEMQPHTGRTH 253
                +   V+K        A +H++++   A+K                  Q  TGR +
Sbjct: 121 YRGKHEPRKVLKY------TAKTHYQLLPALARKLEGDYPVFQQSQVVPAIFQLETGRKN 174

Query: 254 QLRVH-ALHMGCPIVGDH 270
           Q+R H     G  ++ D 
Sbjct: 175 QIRDHVLQEFGVTLLNDD 192


>gi|332533576|ref|ZP_08409438.1| ribosomal large subunit pseudouridine synthase B [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332036978|gb|EGI73437.1| ribosomal large subunit pseudouridine synthase B [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 289

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/211 (16%), Positives = 71/211 (33%), Gaps = 33/211 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +  +L +         +   ++K + + +V V+ K  K  +R++   ++R+         
Sbjct: 4   QGEKLQKVLARAGVG-SRREMEKYIDANRVSVNGKVAKLGDRVEETDLIRVDGH------ 56

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                     +V + + +D +  +++Y        NKP G                    
Sbjct: 57  ----------TVKIEEKADRICRVIMY--------NKPEGELSTRKDPEGRR--TVFDRL 96

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               G +     RLD  TSG+++       A  L        +++ Y + V+G   N  E
Sbjct: 97  PRIDGDRWIAVGRLDVNTSGLMLFTNDGELANRL--MHPSYEVEREYSARVFGEVTN--E 152

Query: 197 CIANWLLKKSHIGG--DYVHVVKQNEKGANY 225
            + N L       G   +  V     +G N 
Sbjct: 153 TVKNLLRGVELEDGPAKFTTVTPMGGEGVNR 183


>gi|257784526|ref|YP_003179743.1| pseudouridine synthase [Atopobium parvulum DSM 20469]
 gi|257473033|gb|ACV51152.1| pseudouridine synthase [Atopobium parvulum DSM 20469]
          Length = 279

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 41/253 (16%), Positives = 80/253 (31%), Gaps = 35/253 (13%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRL R+        +    ++++ SG+V V+ + V                       +
Sbjct: 8   PMRLQRFLARA-GVASRRGSERLMTSGRVTVNGQVVT---------------------EL 45

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
             +   L   V +      +    +Y      + NKPAG ++          I   + + 
Sbjct: 46  GSKVDPLVDVVAVDGVVCSIAEKPVY-----LMLNKPAGYLTTMKDPQGRPTIVDMVPT- 99

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK- 195
                       RLD +T+G+L        AQ L      + + K Y + V G P  ++ 
Sbjct: 100 --DTYPGLFPVGRLDMDTTGLLFFTTDGQMAQEL--LHPSKHVWKHYVAHVVGTPTEEQL 155

Query: 196 -ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                   L+        V ++  + K  N             +    + +    GR HQ
Sbjct: 156 NRLREGIELEDGPAAPAEVEIISDDVKMKNLLAPQGLGKTGGGEPNALVSVTIREGRKHQ 215

Query: 255 LRVHALHMGCPIV 267
           ++   L +   ++
Sbjct: 216 VKKMLLAIHHRVL 228


>gi|310658498|ref|YP_003936219.1| ribosomal small subunit pseudouridine synthase a [Clostridium
           sticklandii DSM 519]
 gi|308825276|emb|CBH21314.1| Ribosomal small subunit pseudouridine synthase A [Clostridium
           sticklandii]
          Length = 243

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 38/248 (15%), Positives = 81/248 (32%), Gaps = 51/248 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E MR+D++  N     +   +++ +++ +V V+   +  N  I                 
Sbjct: 6   EKMRIDKYLANMGVG-SRSEIKRYIKNKRVMVNGVYITDNGLI----------------- 47

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                      +NL     F +  + Y      + NKP G+           +   L   
Sbjct: 48  -----------INLDDDIIFDEEKISYRKFVYIMMNKPQGVISATEDKYQNTVLDLLD-- 94

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                       RLD++T G L++    + A   L+     + ++K Y+  V G   N+ 
Sbjct: 95  PSYLHFDLFPAGRLDKDTEGFLLLTNDGKLAHNMLS---PKKHVEKKYYVEVIGHLVNED 151

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                       I     +++  +      A    +++D  +       +    G+ HQ+
Sbjct: 152 ------------IDAFSGNIIIDDGYECMPA--KLEILD--SNDISKAYVTIKEGKFHQI 195

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 196 KRMFEAIG 203


>gi|257887727|ref|ZP_05667380.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257823781|gb|EEV50713.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
          Length = 238

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 45/252 (17%), Positives = 86/252 (34%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++ + +G+V+V+ + ++    ++     V +          
Sbjct: 2   ERLQKVIA-HAGITSRRKAEEFILAGRVKVNGQVIRELGIKVGKHDTVEVD--------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                               +  +  E+   Y+  KP G+  +V    G        +  
Sbjct: 52  --------------------EVPIYQEEYGYYLLYKPKGVISAVADDKGRK-----VVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    ++     RLD +TSGIL++      AQ LT       + K+Y + V GI     
Sbjct: 87  LLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQRLT--HPKHEVDKVYVAKVKGIATKSM 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                 L K   I G      K            F+++    +     +E+  H GR HQ
Sbjct: 145 L---APLAKGIKIEGRKTSPAK------------FQILSVDPKTNHSIVELTIHEGRNHQ 189

Query: 255 LRVHALHMGCPI 266
           ++     +G P+
Sbjct: 190 VKNMLQAVGLPV 201


>gi|332704996|ref|ZP_08425081.1| ribosomal large subunit pseudouridine synthase B [Lyngbya majuscula
           3L]
 gi|332356173|gb|EGJ35628.1| ribosomal large subunit pseudouridine synthase B [Lyngbya majuscula
           3L]
          Length = 251

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 80/250 (32%), Gaps = 46/250 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+ +     +   +    +K++ +GQVR++   V    +                    
Sbjct: 3   ERVQKILS-QWGIASRRRAEKMIAAGQVRLNGTTVHLGQK------------------AD 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWV 137
            E  +++            +SI         + NKPAG+      S     +   L   +
Sbjct: 44  PETDVIEVDGKPINPYQRPQSI-------YLLLNKPAGVVSTCRDSRNRPTVIDLLPDKL 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +KGQ      RLD +++G L++         LT       I K Y   V G P      
Sbjct: 97  -TKGQGIHPVGRLDADSTGALLLTNDGELTFRLT--HPSHHIPKTYQVWVRGNPPES--V 151

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +  W                 N  G     +  +V+    Q    LE+    GR  Q+R 
Sbjct: 152 LQTW-------------REGVNLLGKKTLPAQVRVLKRKGQS-TLLEVVLTEGRNRQIRR 197

Query: 258 HALHMGCPIV 267
            A  +  P++
Sbjct: 198 VAQLLSYPVI 207


>gi|323341451|ref|ZP_08081692.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           ruminis ATCC 25644]
 gi|323091062|gb|EFZ33693.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           ruminis ATCC 25644]
          Length = 240

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 85/251 (33%), Gaps = 49/251 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++            ++ +L+S +V V+                            +
Sbjct: 1   MRLDKFLAECNQG-TRSEVKVLLKSKRVTVNG---------------------------V 32

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E         ++      +  L Y+    Y+ NKP  +       +   +   +     
Sbjct: 33  TENSGKRQINEVSDVVCLDEKKLTYQSFAYYMLNKPKDVITATEDSVQKTVLDLIDKKDR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            KG       RLD++T+G++++    A A +L      + ++K+Y + + GI    +  +
Sbjct: 93  IKG--LFPVGRLDKDTTGLVLLTNDGALAHNL--LAPKKHVEKVYEAKIEGIVTEAEVEL 148

Query: 199 --ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 LK   +      VVK+ ++ A                   +E+    G+ HQ++
Sbjct: 149 FSKPIELKNGEVTKPSRLVVKKADEDA---------------GMSEIEITISEGKYHQIK 193

Query: 257 VHALHMGCPIV 267
                 G  ++
Sbjct: 194 RMFASTGMHVL 204


>gi|167747171|ref|ZP_02419298.1| hypothetical protein ANACAC_01885 [Anaerostipes caccae DSM 14662]
 gi|167654131|gb|EDR98260.1| hypothetical protein ANACAC_01885 [Anaerostipes caccae DSM 14662]
          Length = 243

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 80/247 (32%), Gaps = 53/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           +RLD++  +          +K++R G+V    + +K    ++                  
Sbjct: 9   LRLDKFLCDVL-GCTRSEARKMIRQGRVLAGDEIIKKPEYKVNP---------------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +E +I      L            YE     + NKP G+      G    +   L    
Sbjct: 52  -EEDEITADGQRLNFRK--------YE---YLMMNKPKGVVTATKDGRDKTVMDLLTGRH 99

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                      RLD++T G+L++      A + L+       + K Y   V G    +++
Sbjct: 100 RKG---LFPAGRLDKDTEGLLLITNDGELAHRLLS---PKHHVTKCYSVTVTGEIGREQQ 153

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I                +   ++K    A    K++   + +    E+    GR HQ++
Sbjct: 154 EIFE------------SGMDIGDDKPLKPA----KLVILTSGEVSQAEVFITEGRFHQIK 197

Query: 257 VHALHMG 263
                +G
Sbjct: 198 RMFEAVG 204


>gi|149036914|gb|EDL91532.1| RNA pseudouridylate synthase domain containing 3 (predicted),
           isoform CRA_a [Rattus norvegicus]
          Length = 157

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/142 (21%), Positives = 45/142 (31%), Gaps = 33/142 (23%)

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY--- 272
            K  ++G    +SHF V          +++QP T    QL+VH     CPI+GDH Y   
Sbjct: 15  RKDIQEGVKRTLSHFHV-TATGCGCALVQLQPLTVFPSQLQVHMALQLCPILGDHTYAAR 73

Query: 273 -----CANFKGNFTSPIQNKLYLHARYMDLPH------------------------PEGG 303
                   F     +    +  L    +   H                        P   
Sbjct: 74  VGSVLGQRFLWPAETTKPQRQVLDEALLRYLHLSPSQVAQMPLHLHLHRLLLPGTRPRDP 133

Query: 304 RLQITAPLPAHMVKTWDSLGFK 325
             ++ APLP +  +T   L   
Sbjct: 134 PSELLAPLPPYFSRTLQCLRLS 155


>gi|329667453|gb|AEB93401.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii DPC 6026]
          Length = 239

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 87/250 (34%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++ +GQV V+ K+V     +++    + +       N +
Sbjct: 3   ERLQKVIAQA-GVASRRKAEKMISAGQVTVNGKKVTELGTKVEPSDKIEV-------NGV 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
             E++ L                        Y+F KP G+  SV    G        +  
Sbjct: 55  PIEKEAL----------------------HTYLFCKPRGVISSVSDDKGRK-----TVVD 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +    +     RLD +TSG+L++      A  L        + K+Y + + GI   ++
Sbjct: 88  FFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANKL--MHPRNEVPKVYVAKIKGILSPEE 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQ 254
                             H V+ + +    A +  K++    +K    +++  H G  HQ
Sbjct: 146 I-------------RSLTHGVRIDGR--KSAPAKLKILKTDEKKKTQIVQLTIHEGHYHQ 190

Query: 255 LRVHALHMGC 264
           ++     +  
Sbjct: 191 VKRMFEAVHH 200


>gi|312127717|ref|YP_003992591.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
 gi|311777736|gb|ADQ07222.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
          Length = 233

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 86/245 (35%), Gaps = 51/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   H    +   ++K++R G V V+ KR           +V +   IN      
Sbjct: 1   MRLDKFLT-HCGFGSRSQVKKLIRGGIVTVNGKR-----------IVEVDFKIN------ 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ +++    + K S  +            + NKP G         +  +   +    +
Sbjct: 43  PEEDVVEVDGRIVKFSRRI----------YIMMNKPKGYVCSNDDPASLTVFSLISD--N 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K +      RLD++  G+L++        H   S R R  ++    L   + + + +  
Sbjct: 91  LKYRDLHTVGRLDKDAEGLLIIT-DDGEYTHRVISPRKRIEKEYLVRLEKEVDEERLKEF 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N ++                  G     + + +ID    K C  E     G+ HQ++  
Sbjct: 150 ENGIILDD---------------GYKTLPAKYTIIDSTTVKLCIYE-----GKYHQVKRM 189

Query: 259 ALHMG 263
              +G
Sbjct: 190 FEAIG 194


>gi|116494858|ref|YP_806592.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus casei ATCC 334]
 gi|227535145|ref|ZP_03965194.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|116105008|gb|ABJ70150.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           casei ATCC 334]
 gi|227187190|gb|EEI67257.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
          Length = 247

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 87/252 (34%), Gaps = 54/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   N     +  + + ++ +G V+V+ +       I++   ++I P        +
Sbjct: 6   ERLQKIIANA-GIASRRHAETLIATGHVKVNGQ-------IETEMGIKIGPHDEVEVDGV 57

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSW 136
              K                     E  + ++F KP G+  +VQ   G        +  +
Sbjct: 58  PIGK---------------------EAKRYFLFYKPRGVISAVQDNKGR-----DVVTDY 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKK 195
                ++     RLD +TSG+LV+      A HL        ++K Y + V G+P +   
Sbjct: 92  FKDITERLYPVGRLDYDTSGLLVMTNDGDLANHL--MHPRYALEKKYVAKVQGVPNRPAL 149

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +   +     +       +   +K    AI               + +  H G  HQ+
Sbjct: 150 APLKTGVEVDGKMTAPAKVDIISTDKAKKTAI---------------VSLTIHQGMNHQV 194

Query: 256 RVHALHMGCPIV 267
           +     +G P++
Sbjct: 195 KKMFKAVGFPVL 206


>gi|191638365|ref|YP_001987531.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|190712667|emb|CAQ66673.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|327382393|gb|AEA53869.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           casei LC2W]
 gi|327385594|gb|AEA57068.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           casei BD-II]
          Length = 247

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 87/252 (34%), Gaps = 54/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   N     +  + + ++ +G V+V+ +       I++   ++I P        +
Sbjct: 6   ERLQKIIANA-GIASRRHAETLIATGHVKVNGQ-------IETEMGIKIGPHDEVEVDGV 57

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSW 136
              K                     E  + ++F KP G+  +VQ   G        +  +
Sbjct: 58  PIGK---------------------EAKRYFLFYKPRGVISAVQDNKGR-----DVVTDY 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKK 195
                ++     RLD +TSG+LV+      A HL        ++K Y + V G+P +   
Sbjct: 92  FKDITERLYPVGRLDYDTSGLLVMTNDGDLANHL--MHPRYALEKKYVAKVQGVPNRPAL 149

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +   +     +       +   +K    AI               + +  H G  HQ+
Sbjct: 150 APLKTGVEVDGKMTAPAKVDIISTDKAKKTAI---------------VSLTIHQGMNHQV 194

Query: 256 RVHALHMGCPIV 267
           +     +G P++
Sbjct: 195 KKMFKAVGFPVL 206


>gi|58337261|ref|YP_193846.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           acidophilus NCFM]
 gi|227903846|ref|ZP_04021651.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           acidophilus ATCC 4796]
 gi|58254578|gb|AAV42815.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           acidophilus NCFM]
 gi|227868733|gb|EEJ76154.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           acidophilus ATCC 4796]
          Length = 238

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 82/247 (33%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    +K++ +G+V+VD + V      + G  V     I   +  I
Sbjct: 3   ERLQKVIAEA-GIASRRKAEKMITAGRVKVDGQVVT-----KLGTKVDTFSNITVDDEPI 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + + +                         Y+F KP G+               +  + +
Sbjct: 57  ERESL-----------------------HTYIFYKPRGVVSTADDDKGR---KTVVDYFE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD +TSG+L++      A  L        + K+Y + + GI   ++   
Sbjct: 91  DIPYRVYPIGRLDYDTSGLLLMTNDGELANLL--MHPRNEVSKVYVAKIKGILTPEE--- 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRV 257
              L K   +G                A +  KV+    +K    +++  H G  HQ++ 
Sbjct: 146 IKSLTKGVKLGR------------FKSAPAKVKVLKTDKRKNTQIVQITIHEGHYHQVKR 193

Query: 258 HALHMGC 264
               +G 
Sbjct: 194 MFKAVGH 200


>gi|300855314|ref|YP_003780298.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           ljungdahlii DSM 13528]
 gi|300435429|gb|ADK15196.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           ljungdahlii DSM 13528]
          Length = 229

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 85/243 (34%), Gaps = 60/243 (24%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKF-----NNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
            +    + I+  G+V+V+ + +K      ++++     + +         I KE K +  
Sbjct: 7   ASRRKCESIILQGRVKVNGETIKSLGTKIDDKV---DKITVDD-----VKIEKENKKV-- 56

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
                                  + NKP G +S          I   +K       ++  
Sbjct: 57  ---------------------YILLNKPTGYVSTVKDDRGRNTILDIVKV-----KERIY 90

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
              RLD  TSGI+++         +      +   K+Y +++ GIP  +        + K
Sbjct: 91  PIGRLDYNTSGIIILTNDGEVYNKVAHPKMEK--NKVYVAVIKGIPSKED-------IDK 141

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              G         N  G   A + F +++   ++    + ++ H G+  Q+R     +G 
Sbjct: 142 FKNG--------VNIDGYITAKADFNILNINKSKNNSKVRIKIHEGKNRQIRKMCDAIGH 193

Query: 265 PIV 267
           P++
Sbjct: 194 PVI 196


>gi|55823410|ref|YP_141851.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus CNRZ1066]
 gi|55739395|gb|AAV63036.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus CNRZ1066]
          Length = 243

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 78/246 (31%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++  L+  QV V+ +                     +    I
Sbjct: 1   MRLDKFLVDCGVG-SRSQVKTFLKKKQVTVNGQV------------------ETSPKTQI 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E K             +L   L +E    Y+ NKP G+           +   L     
Sbjct: 42  DEDK---------DQIAYLGQELTHETFVYYLLNKPQGVISATEDSRHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++      A   L+     R + KIY + V GI   +   
Sbjct: 93  HK--QVFPVGRLDIDTHGLLLLTNNGDLAHAMLS---PKRHVDKIYQAKVAGIMDEEDIL 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   +K  +     A      +D  A     +++    G+ HQ++ 
Sbjct: 148 -------------AFEKGIKLKDHTCQPAKLEIVSVDRNAS-TSLVQITIAEGKFHQVKR 193

Query: 258 HALHMG 263
                G
Sbjct: 194 MVAACG 199


>gi|74228830|dbj|BAE21901.1| unnamed protein product [Mus musculus]
          Length = 288

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 26/146 (17%), Positives = 58/146 (39%), Gaps = 6/146 (4%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSKGQK 143
            ++ L + +  L++ ++ +   +   NKP G+ V G  G    +     L   +  + Q+
Sbjct: 61  ENLGLEELAHVLRAAVVDQKGPLVTLNKPQGLPVTGRPGELTLLSVLPQLSQALGLEHQE 120

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKECIA 199
            ++     +E SG+++++     A  L +    S R +R    Y ++  GIP+  +  + 
Sbjct: 121 LQVVRAPGKEASGLVLLSSCPQTASRLQKFFIHSRRAQRPTATYCAVTDGIPEPSEGTVC 180

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANY 225
             L  +     D    V       + 
Sbjct: 181 MPLKMEQMNDVDLAVPVDVPISKGHP 206


>gi|313837519|gb|EFS75233.1| conserved hypothetical protein [Propionibacterium acnes HL037PA2]
 gi|314927273|gb|EFS91104.1| conserved hypothetical protein [Propionibacterium acnes HL044PA1]
 gi|314972725|gb|EFT16822.1| conserved hypothetical protein [Propionibacterium acnes HL037PA3]
 gi|328907871|gb|EGG27634.1| pseudouridylate synthase [Propionibacterium sp. P08]
          Length = 245

 Score = 64.2 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/255 (15%), Positives = 86/255 (33%), Gaps = 51/255 (20%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +DE+ +RL +         +    ++++ +G+V V+ + +                 +  
Sbjct: 2   SDEQGIRLQKVLAQA-GLASRRAAEEMIAAGRVEVNGELI-----------------VEQ 43

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              +  E   +    +    +   +  + Y      V NKP G+        +      L
Sbjct: 44  GRRVDPEHDEIRVDGSRIPTA---RRHVYY------VLNKPRGVVSTMDDPESRPCLSDL 94

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +     +G +     RLD ETSG++++      A  +T      ++ K Y + V G   +
Sbjct: 95  EGV--PRGIRLFHVGRLDTETSGLILLTNDGEFANRMT--HPSYKVLKTYLADVEGRVDD 150

Query: 194 K--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K  +       L+   +  D V +V+                     +   +E+  H GR
Sbjct: 151 KVIRRLSKGLTLEDGPVKPDAVRLVQA------------------GDEHSLVEVSLHEGR 192

Query: 252 THQLRVHALHMGCPI 266
              +R     +  P+
Sbjct: 193 NRIVRRMMDSVAHPV 207


>gi|220921089|ref|YP_002496390.1| pseudouridine synthase [Methylobacterium nodulans ORS 2060]
 gi|219945695|gb|ACL56087.1| pseudouridine synthase [Methylobacterium nodulans ORS 2060]
          Length = 247

 Score = 64.2 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 84/247 (34%), Gaps = 45/247 (18%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR   N   + +   +Q + R+G + +D  R++  +        RIP   +    +  
Sbjct: 8   RLDRLLAN-LGYGSRREIQALARAGAIILDGARLRAADE-------RIPVTRDLPERLTV 59

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
               LD    L         ++L++ + +   +K AG  V           G L      
Sbjct: 60  GGVALDPPPGLV--------LMLHKPTGVTCSHKEAGPLV----------YGLLPERWRR 101

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +        RLD+ETSG+L++     A  H   S + +  ++    L   +  ++    A
Sbjct: 102 RDPPLSTVGRLDKETSGLLLLT-DDGALLHRIISPKAKVAKRYRVELARPLAGDEGALFA 160

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +  L         + V    E     +++                     GR HQ+R   
Sbjct: 161 SGTLMLEGEDKPLLPVELVAEGPTRASVT------------------LTEGRYHQVRRMF 202

Query: 260 LHMGCPI 266
             +G  +
Sbjct: 203 AAVGNHV 209


>gi|241896291|ref|ZP_04783587.1| pseudouridylate synthase [Weissella paramesenteroides ATCC 33313]
 gi|241870452|gb|EER74203.1| pseudouridylate synthase [Weissella paramesenteroides ATCC 33313]
          Length = 255

 Score = 64.2 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 89/248 (35%), Gaps = 44/248 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++  GQV V+ + ++    +++    + +          
Sbjct: 3   ERLQKVMAQA-GVASRRASEKMITEGQVTVNGQVIRELGTKVEPTDHIEVN--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                 +DS   L                  ++ +KP G+               +   V
Sbjct: 53  ---GTPIDSKEKLV----------------YFLLDKPRGVVTTNSDDKGRQ---TVMDIV 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D + ++     RLD +T+G L++      A  L       RI K+Y + V GIP N++  
Sbjct: 91  D-EPERVYPVGRLDYDTTGALLLTNDGDLANKL--MHPKYRIDKVYVAKVKGIPTNEE-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLR 256
                L+K   G     V        N A +H +++    +K    +++  H G+ HQ++
Sbjct: 146 -----LEKLRHGVTVKTVQNGRHYTFNAAPAHAEILSTDKKKHTAIVKLTIHEGKYHQVK 200

Query: 257 VHALHMGC 264
                +G 
Sbjct: 201 EMLKSVGH 208


>gi|326384757|ref|ZP_08206434.1| pseudouridine synthase [Gordonia neofelifaecis NRRL B-59395]
 gi|326196565|gb|EGD53762.1| pseudouridine synthase [Gordonia neofelifaecis NRRL B-59395]
          Length = 362

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 40/252 (15%), Positives = 82/252 (32%), Gaps = 45/252 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + MRL +         +    ++++ +G+                        V      
Sbjct: 120 DGMRLQKVLAAA-GVASRRGAEELIAAGR------------------------VEVDGEV 154

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           ++++   +D    + K       +++ E  +    NKP G              G + + 
Sbjct: 155 VVEQGLRIDPDTAIIKVDGA--RVVIDESKQYLALNKPKGWHSTMSDDQGRPCIGDIIAE 212

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               GQ+     RLD +T G+L++      A  L        + K Y + V G       
Sbjct: 213 RVMAGQRLFHVGRLDADTEGLLLLTNDGELAHRL--MHPSYEVPKTYLATVRGE------ 264

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +   L ++   G +         +    A+  F +++   Q    + +  H GR   +R
Sbjct: 265 -VNRGLGRELRQGVEL--------EDGPVAVDSFALLE-VNQGKSLVRLTLHEGRKRVVR 314

Query: 257 VHALHMGCPIVG 268
                +G P+VG
Sbjct: 315 RLLAEVGFPVVG 326


>gi|319946247|ref|ZP_08020487.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           australis ATCC 700641]
 gi|319747629|gb|EFV99882.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           australis ATCC 700641]
          Length = 247

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 97/251 (38%), Gaps = 52/251 (20%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E +MRLD++  +     +   ++++L+  +++V+ K       +++   + I P  + + 
Sbjct: 3   EASMRLDKYLVDCGVG-SRTEVKQVLKKKKIQVNGK-------VETSPKIHIDPDKDQVT 54

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           +                    L   L +E+   Y+ NKP G+     +    H    L  
Sbjct: 55  Y--------------------LGESLFHEEFVYYLLNKPKGVIS---ATEDDHHQTVLDL 91

Query: 136 WVD-SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             D ++ ++     RLD +T G+L++    + A   L+     + + K+Y + V GI   
Sbjct: 92  LDDTARHKEVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVDKVYRAQVAGIMTQ 148

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRT 252
           +        + +   G +         +         ++++   +   C ++++   G+ 
Sbjct: 149 ED-------IDRFKEGIELKDFTTLPAE--------LEMLEVDQEANSCLVQIRIAEGKF 193

Query: 253 HQLRVHALHMG 263
           HQ++      G
Sbjct: 194 HQVKRMVAACG 204


>gi|213620477|ref|ZP_03373303.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 79

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 4/82 (4%)

Query: 177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF 236
           + +QK Y +LV G  ++  + +   LLK     G+ +  V Q       + + FKV + +
Sbjct: 1   KGMQKDYLALVRGQWQSHVKTVQAPLLKNILQSGERIVRVSQE---GKPSETRFKVEERY 57

Query: 237 AQKFCWLEMQPHTGRTHQLRVH 258
           A     +   P TGRTHQ+RVH
Sbjct: 58  A-FATLVRCSPVTGRTHQIRVH 78


>gi|116491036|ref|YP_810580.1| ribosomal large subunit pseudouridine synthase B [Oenococcus oeni
           PSU-1]
 gi|116091761|gb|ABJ56915.1| ribosomal large subunit pseudouridine synthase B [Oenococcus oeni
           PSU-1]
          Length = 237

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 89/238 (37%), Gaps = 52/238 (21%)

Query: 32  INFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
            +    ++++ +GQV+V+ K + K   ++ S  +V +             +KI + S   
Sbjct: 17  ASRRKAEEMIVNGQVKVNGKIITKLGKKVSSDDIVYVD-----------NKKINEESFE- 64

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
                             Y+ NKPAG      S  +Y     +   + +K  +     RL
Sbjct: 65  -----------------YYLLNKPAGYVS---SNRSYPNQPSVIELIKTKT-RIFSVGRL 103

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
           DQ+T+G+L++       Q LT      RI++ Y + V GI    +      L K     G
Sbjct: 104 DQDTTGVLLLTNDGELTQKLT--HPKHRIKRTYAAWVKGIVNEDE---IEQLTKPIRFDG 158

Query: 211 DYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +                   +++     ++   +E+    G+ H+++     +G P++
Sbjct: 159 EIYFPQAA------------RILKVDQKRQESLIEITIAEGKNHEIKKILDFIGHPVI 204


>gi|290890516|ref|ZP_06553591.1| hypothetical protein AWRIB429_0981 [Oenococcus oeni AWRIB429]
 gi|290479912|gb|EFD88561.1| hypothetical protein AWRIB429_0981 [Oenococcus oeni AWRIB429]
          Length = 237

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 94/239 (39%), Gaps = 54/239 (22%)

Query: 32  INFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
            +    ++++ +GQV+V+ K + K   ++ S  +V +             +KI + S   
Sbjct: 17  ASRRKAEEMIVNGQVKVNGKIITKLGKKVSSDDIVYVD-----------NKKINEESFE- 64

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
                             Y+ NKPAG      S  +Y     +   + +K  +     RL
Sbjct: 65  -----------------YYLLNKPAGYVS---SNRSYPNQPSVIELIKTKT-RIFSVGRL 103

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKECIANWLLKKSHI- 208
           DQ+T+G+L++       Q LT      RI++ Y + V GI  +++ E +   +     I 
Sbjct: 104 DQDTTGVLLLTNDGELTQKLT--HPKHRIKRTYAAWVKGIVNEDELEQLTKPIRFDGEIY 161

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                 ++K ++K                ++   +E+    G+ H+++     +G P++
Sbjct: 162 FPQAARILKVDQK----------------RQESLIEITIAEGKNHEIKKILDFIGHPVI 204


>gi|330719107|ref|ZP_08313707.1| 16S rRNA uridine-516 pseudouridylate synthase [Leuconostoc fallax
           KCTC 3537]
          Length = 252

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 44/264 (16%), Positives = 90/264 (34%), Gaps = 57/264 (21%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M+ +Q     N+E   RL +         +    + ++  G+V V+ ++VK    +++  
Sbjct: 1   MSEIQ-----NEE---RLQKVIAQA-GLASRRGAEALIVEGRVSVNGQQVKELGTKVRRS 51

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             V +                              +  L+Y     Y+ NKP G+     
Sbjct: 52  DTVAVDG-----------------------VPIEGRERLVY-----YLLNKPRGVVT--- 80

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +         +   +D   Q+     RLD +T+G L++      A  L       ++ K+
Sbjct: 81  TTQDEKGRATVLDILDDVSQRVYPVGRLDYDTTGALLLTNDGTIANEL--MHPKSKVDKV 138

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y + V G+           L K   I G      + + +  +             +K   
Sbjct: 139 YIAKVKGMATENDLL---PLKKGVMIEGHKTQPARVSVESVD-----------KTKKTSM 184

Query: 243 LEMQPHTGRTHQLRVHALHMGCPI 266
           +++  H G+ HQ++     +G P+
Sbjct: 185 VKLIIHEGKNHQVKNMLAKVGFPV 208


>gi|51892921|ref|YP_075612.1| ribosomal large subunit pseudouridine synthase B [Symbiobacterium
           thermophilum IAM 14863]
 gi|51856610|dbj|BAD40768.1| ribosomal large subunit pseudouridine synthase B [Symbiobacterium
           thermophilum IAM 14863]
          Length = 254

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 44/251 (17%), Positives = 79/251 (31%), Gaps = 56/251 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
            RL +         +  + + ++++G+V V+ + V     ++  G  V+ +         
Sbjct: 3   ERLQKVMARA-GVASRRHCEALIQAGRVTVNGQVVTQLGTKVVPGKDVIEVDGRPLGTP- 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG---FL 133
                                      E     + NKP G          Y   G    +
Sbjct: 61  ---------------------------ETKVYVMLNKPKGYVS-----TLYDPQGRPKVI 88

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
               D   Q+     RLD +T G+L++      A  L      R ++K Y   V G+P  
Sbjct: 89  DLLGDEVAQRVYPVGRLDFDTEGLLLLTNDGDLAHGL--MHPSRMVKKTYIVKVRGVPGP 146

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K       L+    G +         +    A +  K++D        L ++ H GR  
Sbjct: 147 AK-------LRALQEGIEL--------EDGPTAPAEVKMLDVRPPNSATLSVRIHEGRNR 191

Query: 254 QLRVHALHMGC 264
           Q+R     +G 
Sbjct: 192 QVRRMFAALGH 202


>gi|289550733|ref|YP_003471637.1| Ribosomal large subunit pseudouridine synthase B [Staphylococcus
           lugdunensis HKU09-01]
 gi|289180265|gb|ADC87510.1| Ribosomal large subunit pseudouridine synthase B [Staphylococcus
           lugdunensis HKU09-01]
          Length = 245

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/235 (13%), Positives = 72/235 (30%), Gaps = 49/235 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+ + V     +++    V +  +                     
Sbjct: 19  SRRKAETLITEGKVKVNGEVVTELGTKVKPSDQVEVEGIKMEQ----------------- 61

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                       ED    +F+KPA +     S         +  +      +     RLD
Sbjct: 62  ------------EDKIYILFHKPAQVIT---SVSDDRGRTVVTDYFKDLDTRIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+L++        +L    R    +     L   + + + + +   +  +  +   
Sbjct: 107 YDTSGVLLLT-NDGEFTNLMTHPRYHIPKTYVAKLKGYLMREEVKALEAGIELEDGLTQP 165

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               +K+ +K  N                  +E+    GR  Q+R    H G  +
Sbjct: 166 ATVKIKRQDKDKNT---------------TLVEITISEGRNRQVRRMFEHFGHSV 205


>gi|42519012|ref|NP_964942.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii NCC 533]
 gi|41583299|gb|AAS08908.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii NCC 533]
          Length = 239

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 87/250 (34%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++ +GQV V+ K+V     +++    + +       N +
Sbjct: 3   ERLQKVIAQA-GVASRRKAEKMISAGQVTVNGKKVTELGTKVEPSDKIEV-------NGV 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
             E++ L                        Y+F KP G+  SV    G        +  
Sbjct: 55  PIEKEAL----------------------HTYLFYKPRGVISSVSDDKGRK-----TVVD 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +    +     RLD +TSG+L++      A  L        + K+Y + + GI   ++
Sbjct: 88  FFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANKL--MHPRNEVPKVYVAKIKGILSPEE 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQ 254
                             H V+ + +    A +  K++    +K    +++  H G  HQ
Sbjct: 146 I-------------RSLTHGVRIDGR--KSAPAKLKILKTDEKKKTQIVQLTIHEGHYHQ 190

Query: 255 LRVHALHMGC 264
           ++     +  
Sbjct: 191 VKRMFEAVHH 200


>gi|269127043|ref|YP_003300413.1| pseudouridine synthase [Thermomonospora curvata DSM 43183]
 gi|268312001|gb|ACY98375.1| pseudouridine synthase [Thermomonospora curvata DSM 43183]
          Length = 250

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 45/255 (17%), Positives = 87/255 (34%), Gaps = 49/255 (19%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
               +E +RL +         +    ++++  G+V+VD + V +      G  V      
Sbjct: 7   TAEHKEGVRLQKVLAEAGLG-SRRQCERLIVEGRVKVDGEVVSW-----LGARVD----- 55

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                                H D L+     E  + Y  NKP G+              
Sbjct: 56  ---------------PAKAVIHVDGLRVETRPE-MRYYALNKPRGVVSTMA---DERGRK 96

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L  +VD   ++     RLD +T G++++      A  LT       ++K+Y + + G  
Sbjct: 97  SLADYVDVP-ERLFHVGRLDTDTEGLILLTNDGDLAHRLTHPSFG--VEKVYLAEIVG-- 151

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 I   L ++   G +         +        F++++   ++   +E+  H GR
Sbjct: 152 -----PIRRDLGRRLRAGIEL--------EDGLAKADRFRLVEQVGKRA-LVEITLHEGR 197

Query: 252 THQLRVHALHMGCPI 266
            H +R      G P+
Sbjct: 198 KHIVRRMLKEAGHPV 212


>gi|146321792|ref|YP_001201503.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis 98HAH33]
 gi|253752593|ref|YP_003025734.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           suis SC84]
 gi|253754419|ref|YP_003027560.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           suis P1/7]
 gi|253756353|ref|YP_003029493.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           suis BM407]
 gi|145692598|gb|ABP93103.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Streptococcus suis 98HAH33]
 gi|251816882|emb|CAZ52530.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus suis SC84]
 gi|251818817|emb|CAZ56658.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus suis BM407]
 gi|251820665|emb|CAR47426.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus suis P1/7]
 gi|319759007|gb|ADV70949.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Streptococcus suis JS14]
          Length = 242

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 89/247 (36%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++K+L++ QV V+ +                           
Sbjct: 1   MRLDKFLVDCGVG-SRTEVKKLLKNKQVTVNGQV-------------------------- 33

Query: 79  KEQKILDSSVNLTKHSDFLKSILL-YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +      +N  K    +   +L +E    Y+ NKP G+           +   L +  
Sbjct: 34  --ETSPKQQINEKKDQIAVAGQVLSHETFVYYLLNKPKGVISATEDDHHRTVLDLLDNTA 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVA-RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             K  +     RLD +T G+L++  + + A   L+     + + K+Y + V GI   +  
Sbjct: 92  RQK--EVFPVGRLDIDTHGLLLLTNKGQLAHAMLS---PKKHVDKLYRAQVDGIMTQED- 145

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 +++   G +      Q  +     ++     +  A++   +++    G+ HQ++
Sbjct: 146 ------VERFAAGIELKDFTCQPAQ-----LTILSTDE--AKQTSLVDITIREGKFHQIK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVQACG 199


>gi|329576942|gb|EGG58425.1| pseudouridylate synthase [Enterococcus faecalis TX1467]
          Length = 257

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 86/251 (34%), Gaps = 51/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   V V+   VK                  A   + 
Sbjct: 14  MRLDKFLADVGIG-SRKEIKQLLKKKVVTVNGDVVK-----------------EAKTQVN 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E   +            +  IL Y+    Y+ +KP G+     S      D  +   + 
Sbjct: 56  EETDQI----------ALMGEILTYQKFFYYMLHKPQGVI----SATEDQRDETVIDLLT 101

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  +       RLD++T G+L++      A Q L+     + + K Y + V G+   + 
Sbjct: 102 DQDYRADLFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVDKEYLAEVEGLVTAED 158

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +                   ++ +    +    + I+   +    + +    G  HQ+
Sbjct: 159 CQLFA------------QGFALKDGEMVKPSRLVIETIN-EEEGTSVVRLVIQEGEFHQV 205

Query: 256 RVHALHMGCPI 266
           +     +G P+
Sbjct: 206 KRMLATVGKPV 216


>gi|146296790|ref|YP_001180561.1| pseudouridine synthase [Caldicellulosiruptor saccharolyticus DSM
           8903]
 gi|145410366|gb|ABP67370.1| ribosomal small subunit pseudouridine synthase A
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 232

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 38/251 (15%), Positives = 84/251 (33%), Gaps = 63/251 (25%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI-QSGQVVRIPPVINALNH 76
           MRLDR+  +         ++++++ G V+V+ K+ K  + +I +   VV++   I  L  
Sbjct: 1   MRLDRFLAHSGFG-TRSEVKRLIKKGLVKVNGKQAKSPDLKIDEDKDVVQVGEEIVELQK 59

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            +                               + NKP G        ++  I   +   
Sbjct: 60  RV-----------------------------YIMMNKPQGYVCSNDDPLSPTIFSLIPE- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            + K +      RLD++  G+L++                             +   KK 
Sbjct: 90  -NLKYRNLHTVGRLDKDAEGLLIITNNGE--------------------YTHKVISPKKH 128

Query: 197 CIANWLLK-KSHIGGDYVHVVKQN---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
               +++K +  +  + + V +     + G     + + ++D F       E     G+ 
Sbjct: 129 IEKEYIVKLEKELNREKIKVFEDGVVLDDGYKTLPAKYTILDDFTVSLTIYE-----GKY 183

Query: 253 HQLRVHALHMG 263
           HQ++     +G
Sbjct: 184 HQIKRMFESIG 194


>gi|319892809|ref|YP_004149684.1| Ribosomal small subunit pseudouridine synthase A [Staphylococcus
           pseudintermedius HKU10-03]
 gi|317162505|gb|ADV06048.1| Ribosomal small subunit pseudouridine synthase A [Staphylococcus
           pseudintermedius HKU10-03]
 gi|323464159|gb|ADX76312.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           pseudintermedius ED99]
          Length = 232

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 78/250 (31%), Gaps = 52/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++            ++ +L+ G V  +  ++K +                    I 
Sbjct: 1   MRIDKFLAQMGVG-TRTEVKALLKKGHVLHNGAKIKSS-----------------KTQID 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +++              ++ YE     + NKP  +     + +       +     
Sbjct: 43  PEHDVVEVK----------GRVIAYEPFVYLMMNKPQNVIS---ATVDDQHQTVIDIIEG 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++T G+L++         L      + + K YW             +
Sbjct: 90  YRHLDLFPVGRLDKDTEGLLLITNDGQFNHAL--MNPNKHVSKTYW-------------V 134

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                 K++    +   +   E     A  H +++D     F    +    G+ HQ++  
Sbjct: 135 KAKYALKTNDPKRFEEGITLKEGRLQPA--HLEILDDSMTAF----VTIQEGKYHQVKRM 188

Query: 259 ALHMGCPIVG 268
              +   +VG
Sbjct: 189 FHAIDNEVVG 198


>gi|227893487|ref|ZP_04011292.1| pseudouridylate synthase [Lactobacillus ultunensis DSM 16047]
 gi|227864712|gb|EEJ72133.1| pseudouridylate synthase [Lactobacillus ultunensis DSM 16047]
          Length = 238

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 83/248 (33%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    +K++ +G+V+VD K +      + G  V     I   +  I
Sbjct: 3   ERLQKVIAEA-GIASRRKAEKMITAGRVKVDGKVIT-----KLGTKVDTFSNITVDDEPI 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + + +                         Y+F KP G+               +  + +
Sbjct: 57  ERESL-----------------------HTYLFYKPRGVVSTASDDKGRR---TVVDYFE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKE 196
               +     RLD +TSG+L++      A  L        +QK+Y + + GI  P+  + 
Sbjct: 91  DIPYRLYPVGRLDYDTSGLLLMTNDGKLANLL--MHPRNEVQKVYVAKIKGILTPEEIEG 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 L +       V ++K +++                +    +++  H G  HQ++
Sbjct: 149 LTHGVKLDRFKAAPAKVKILKTDKR----------------KDTQIVQLTIHEGHYHQVK 192

Query: 257 VHALHMGC 264
                +G 
Sbjct: 193 RMFKAVGH 200


>gi|281492918|ref|YP_003354898.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. lactis KF147]
 gi|281376570|gb|ADA66056.1| Ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. lactis KF147]
          Length = 273

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 84/243 (34%), Gaps = 41/243 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L+ G+V V            +G+V R        N   
Sbjct: 32  MRLDKFLAESGLG-SRSEVKILLKKGRVTV------------AGEVQRDGRFQVDKN--- 75

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                       ++   F   IL Y++   Y+ NKP G+       +   +   L     
Sbjct: 76  ------------SRQVAFDGEILDYQEYYYYLLNKPQGLVSATKDNLFKTVVQLLSE--K 121

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              +      RLD+ T G+L++    A    LT+    + ++K Y++ + G   +  E +
Sbjct: 122 DFREDIFPVGRLDKNTEGLLILTNDGALGHDLTQ--PKKHVEKEYFARIDGKVTD--EIV 177

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +    +   G+               I +    +  +     + +  H G+ HQ++  
Sbjct: 178 NKFAEGLTLKNGEKAR-------PGELFIENIYKGESQSGWISEIRVIIHEGKFHQVKRM 230

Query: 259 ALH 261
              
Sbjct: 231 FEA 233


>gi|289674870|ref|ZP_06495760.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
          synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
          syringae FF5]
          Length = 65

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 10/55 (18%), Positives = 24/55 (43%)

Query: 12 VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
          V ++    RLD+     +   +   L   ++ G++ VD   ++  + +  G V+ 
Sbjct: 11 VPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGGVLRPRDIVHGGAVLE 65


>gi|255305403|ref|ZP_05349575.1| putative RNA pseudouridine synthase [Clostridium difficile ATCC
           43255]
          Length = 240

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 38/246 (15%), Positives = 84/246 (34%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D+   N   + +   ++K  + G V V+   V        G  V             
Sbjct: 5   QRIDKILSN-LGYGSRSEIKKYCKQGSVVVNGSEVS-----NPGTQVD-----------T 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  +IL +              ++Y +    + NKP G            +   +   + 
Sbjct: 48  ENDEILFNGEE-----------VIYREYIYLMMNKPDGYISATTDKYDPTVLDLID--LS 94

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +P    RLD++T G+LV+    + + + L+     + + K Y++ + G+   +   
Sbjct: 95  YLAFEPFPVGRLDKDTEGLLVLTNDGKLSHRVLS---PKKHVSKTYYAKIDGVVTEED-- 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +  +L                 + G     S   ++   +     +E+  H G+ HQ++ 
Sbjct: 150 VEAFLEG------------VVLDDGYKTMPSQLNILK--SDDESEIELTIHEGKFHQVKR 195

Query: 258 HALHMG 263
               +G
Sbjct: 196 MFESVG 201


>gi|146296765|ref|YP_001180536.1| pseudouridine synthase [Caldicellulosiruptor saccharolyticus DSM
           8903]
 gi|145410341|gb|ABP67345.1| ribosomal large subunit pseudouridine synthase B
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 237

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 88/249 (35%), Gaps = 47/249 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL ++  +     +    ++I+  G+V+V+ + +                         
Sbjct: 2   VRLQKFMAD-CGVASRRKCEEIILQGRVKVNGRTIT----------------ELGFKVDP 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           ++ K+L     L      +            + NKP G+     +         +    D
Sbjct: 45  QKDKVLVDGKKLVPVQKKI----------YIMLNKPFGVIS--SAKDEKGRKTVVDLVKD 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD +T+G++++      A  +T       I+K Y +L+ G+P  ++   
Sbjct: 93  KVDVRVFPVGRLDFDTTGLILLTNDGEFAYKVT--HPKHDIEKTYIALIEGVPTKEEI-- 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +  + K  + A   F+++  F +    +E++ H GR  Q+R  
Sbjct: 149 -----------EQFKKGLFIDGKLTSPA--KFRILKVF-KGMSLVEIKIHEGRNRQVRKM 194

Query: 259 ALHMGCPIV 267
              +G  ++
Sbjct: 195 CDAIGHRVL 203


>gi|315633718|ref|ZP_07889008.1| ribosomal small subunit pseudouridine synthase A [Aggregatibacter
           segnis ATCC 33393]
 gi|315477760|gb|EFU68502.1| ribosomal small subunit pseudouridine synthase A [Aggregatibacter
           segnis ATCC 33393]
          Length = 234

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 40/255 (15%), Positives = 82/255 (32%), Gaps = 61/255 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++       +      K+LR   V ++ K  K    ++     +            
Sbjct: 1   MRLDKFLAET-TGLTRSQAAKVLRQSAVTINGKIEKSGAAKVSPDDEI------------ 47

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQ--GGSGIAYHIDGF-L 133
                          + D  +   + E+ +  + +KP G I     G     Y    + L
Sbjct: 48  ---------------YYDGERLTWV-ENGQYIMLHKPQGYICSHEDGDHPTIYQFFDYPL 91

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            + + S G       RLD +T+G++++                 +      S     PK 
Sbjct: 92  STCLHSAG-------RLDVDTTGLVLLT-------------DDGQWSHRITSPKHHYPKT 131

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               +A+ +            +++  ++    A    +++D +       E     GR H
Sbjct: 132 YLVTLADPVEANYAQACAEGILLRGEKEPTKPA--ELEILDDYNVNLTISE-----GRYH 184

Query: 254 QLRVHALHMGCPIVG 268
           Q++     +G  +VG
Sbjct: 185 QVKRMFAALGNKVVG 199


>gi|308812959|ref|XP_003083786.1| pseudouridine synthase family 1 protein (ISS) [Ostreococcus tauri]
 gi|116055668|emb|CAL57753.1| pseudouridine synthase family 1 protein (ISS) [Ostreococcus tauri]
          Length = 391

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/237 (15%), Positives = 78/237 (32%), Gaps = 30/237 (12%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                PH+        + +G+V V+ + V+ + R+  G VV +             + + 
Sbjct: 97  LVRCMPHLKRREADDAVSAGRVLVNGELVRPSRRVVHGDVVTLD-----------GKAMD 145

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
                 +  S+   +  +Y       +NKP G+           +   L     + G+  
Sbjct: 146 WEPYAQSVESELGDARFVY-----LKYNKPRGVVCTMSDTERTSMFHALHHERKALGKDV 200

Query: 145 RL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           RL    RLD+++SG++++      +  L +  R +  +     +   + +     +A  +
Sbjct: 201 RLFPVGRLDKDSSGLVLLTNDGRVSDALLDPER-KAEKTYDVDVDRIVSEADARTLARGV 259

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +  +    D    V         A    +V     +           GR  Q+R   
Sbjct: 260 VISTTQQRDLKETV--------AATLPCEVTKTGEKSL---RFVLKEGRNRQIRKMC 305


>gi|284032996|ref|YP_003382927.1| pseudouridine synthase [Kribbella flavida DSM 17836]
 gi|283812289|gb|ADB34128.1| pseudouridine synthase [Kribbella flavida DSM 17836]
          Length = 244

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 90/252 (35%), Gaps = 48/252 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E+ +RL +         +  N + ++  G+V VD   V      + G   R+ P ++ +
Sbjct: 3   EEDGIRLQKALAQA-GVASRRNAELLIEQGRVEVDGAVVT-----EFG--TRVDPAVSVI 54

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
              +  ++I   + ++                   V NKP G+               + 
Sbjct: 55  R--VDGERIPPVTAHV-----------------YLVLNKPRGVVTTMSDPQGRPC---IA 92

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +V  + ++     RLD +T G+L++      A  L        + K Y + V G  K  
Sbjct: 93  DYVQERPERLFHIGRLDTDTEGLLLLTNHGEFAHRLA--HPSYEVSKTYVAEVDGNVK-- 148

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                  ++ +  + G       + E G   A +  KV+    +    +++  H GR   
Sbjct: 149 ------PIVLRRLLDG------VELEDGFAQADT-VKVMSEI-KGRTLIQITLHEGRNRI 194

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 195 VRRMFDAVGHPV 206


>gi|322516330|ref|ZP_08069256.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           vestibularis ATCC 49124]
 gi|322125168|gb|EFX96557.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           vestibularis ATCC 49124]
          Length = 243

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 82/246 (33%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++  L+  QV V+ +                           
Sbjct: 1   MRLDKFLVDCGVG-SRSQVKNFLKKKQVIVNGQV-----------------------ETS 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I ++   +T    +L   L +E    Y+ NKP G+           +   L     
Sbjct: 37  PKTQIDENKDRIT----YLDQELTHETFVYYLLNKPQGVISATEDPRHKTVLDLLDDTAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++      A   L+     + + KIY + V G+   +   
Sbjct: 93  HK--RVFPVGRLDIDTHGLLLLTNNGDLAHAMLS---PKKHVDKIYQAKVAGVMDEEDIL 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   +K  +     A      +D   +   W+++    G+ HQ++ 
Sbjct: 148 -------------AFEKGIKLKDHTCQPAKLEIVSVDRN-ESTSWVQITIAEGKFHQVKR 193

Query: 258 HALHMG 263
                G
Sbjct: 194 MVAACG 199


>gi|326202112|ref|ZP_08191982.1| pseudouridine synthase [Clostridium papyrosolvens DSM 2782]
 gi|325987907|gb|EGD48733.1| pseudouridine synthase [Clostridium papyrosolvens DSM 2782]
          Length = 235

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/250 (14%), Positives = 80/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           +RL ++   H    +    +++++ G+V V+   +      +    VV +          
Sbjct: 4   IRLQKYLA-HAGVASRRKAEEMIKQGRVAVNNVIIENMGATVTCNDVVTVDGKPVTTE-- 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     E     + NKP G                +   V
Sbjct: 61  --------------------------EAKVYIMLNKPVGYVSTSKDQFGR---PAVIDLV 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              G++     RLD +TSG++++         LT       + K+Y +++ G P   +  
Sbjct: 92  KDAGKRLYPVGRLDYDTSGLILLTNDGDFTYRLT--HPKHEVNKVYEAVISGFPDKNEIT 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   +K ++   + A   F+V++        + +  H G+  Q+R 
Sbjct: 150 -------------RFETGLKIDDYQTSPA--EFEVLNKKGIN-TLVRITIHEGKNRQVRK 193

Query: 258 HALHMGCPIV 267
               +G  ++
Sbjct: 194 MCEAIGHKVL 203


>gi|223998336|ref|XP_002288841.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220975949|gb|EED94277.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 438

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 28/111 (25%), Positives = 44/111 (39%), Gaps = 13/111 (11%)

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG-------FLKSWVDS---- 139
           T         ++Y ++ + V NKPAG   Q G G               L    +     
Sbjct: 122 TSSPKLEPPEIIYSNNHLLVVNKPAGWKSQPGDGGGTGSMSNAVDPKCLLTHLQNQSLGG 181

Query: 140 --KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             +      THRLDQ  +G L+ A+   AA  +  ++  R ++K YW +V 
Sbjct: 182 GSQKNFISPTHRLDQPCTGALIFAKNGKAASRVQVAWAKRNVKKCYWVVVE 232



 Score = 50.7 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/97 (25%), Positives = 37/97 (38%), Gaps = 14/97 (14%)

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHM-GCPIVGDHKYCANF------KGNFTSPIQNK-L 288
                 L +   TG  HQ+R       G PI GD +Y  N        G  + P+ +  +
Sbjct: 332 PSNRHLLSVTTDTGAKHQIRAMLALAGGAPISGDLRYGNNVSNINQSGGRVSQPLPDGSV 391

Query: 289 YLHARYMDLPHPEGGRLQ------ITAPLPAHMVKTW 319
            LHAR + LP    G ++        AP+P      +
Sbjct: 392 ALHARSVFLPTVSLGGMEFLKEEPFVAPIPTRWRDFF 428


>gi|15827715|ref|NP_301978.1| pseudouridine synthase [Mycobacterium leprae TN]
 gi|221230192|ref|YP_002503608.1| putative pseudouridine synthase [Mycobacterium leprae Br4923]
 gi|13093266|emb|CAC31751.1| possible pseudouridine synthase [Mycobacterium leprae]
 gi|219933299|emb|CAR71465.1| possible pseudouridine synthase [Mycobacterium leprae Br4923]
          Length = 257

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 45/264 (17%), Positives = 80/264 (30%), Gaps = 45/264 (17%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +M  +    ++     +RL +         +    +K++  G+V VD + V+        
Sbjct: 1   MMVEIHDSRMDRGAGAVRLQKILSRA-GIASRRAAEKLIIEGRVEVDGQLVR-------- 51

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
                         +        S V +      +   L+Y        NKP G+     
Sbjct: 52  -------------ELGTRVDPDVSVVRVDGVKVVVDDSLVY-----LALNKPRGMYSTMS 93

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                   G L        +K     RLD +T G++++      A  L        + K 
Sbjct: 94  DDRGRPCVGDLIERRVRGNKKLFHVGRLDADTEGLILLTNDGELAHRL--MHPSHEVSKT 151

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y + V G        +   L KK  +G +               +  F V+D    K   
Sbjct: 152 YLATVKGA-------VPRGLGKKLSVGLEL--------DDGPAHVDDFAVVDAIPGK-TL 195

Query: 243 LEMQPHTGRTHQLRVHALHMGCPI 266
           + +  H GR   +R      G P+
Sbjct: 196 VRLTLHEGRKRIVRRLLTAAGFPV 219


>gi|321445061|gb|EFX60583.1| hypothetical protein DAPPUDRAFT_9799 [Daphnia pulex]
          Length = 107

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 8/78 (10%)

Query: 224 NYAISHFKVID---CFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             A +   V+            + M+P TGR HQLR+H   +G  IVGD  Y      N 
Sbjct: 20  KAAFTRLLVLQKGFYDGFPVTKVMMKPVTGRRHQLRIHCSSLGHTIVGDFTYS-----NG 74

Query: 281 TSPIQNKLYLHARYMDLP 298
              +  +++LH+  + LP
Sbjct: 75  KDVLPYRMFLHSHRLILP 92


>gi|314933904|ref|ZP_07841269.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           caprae C87]
 gi|313654054|gb|EFS17811.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           caprae C87]
          Length = 230

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 38/244 (15%), Positives = 80/244 (32%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N         ++++L+ G V V++K++K                        
Sbjct: 1   MRIDKFLANMGLG-TRTEVKQLLKKGLVEVNEKKIKT----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I   +  +    +     + Y D+   + NKP G      +         L    +
Sbjct: 37  PKSQIDPETDKVVVDGE----EISYVDNVYMMLNKPKGYIS---ATEDNAHQTVLDLIPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                     RLD++T G+L++         L      + + K Y            E I
Sbjct: 90  FSHLGIFPVGRLDKDTEGLLLLTNDGQFNHEL--MSPKKHVSKTY------------EVI 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           + + +K+S I    + V   + K         K  +          +  + G+ HQ++  
Sbjct: 136 SKYPIKQSDIEAFKLGVELSDGK--------VKPAELIKGNDRLSYVTIYEGKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|301169983|emb|CBW29587.1| 16S rRNA pseudouridylate 516 synthase [Haemophilus influenzae
           10810]
          Length = 232

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 81/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +    V+++ + VK                      I 
Sbjct: 1   MRLDKFIAENV-GLTRSQATKAIHQSAVKINGEIVKS-----------------GSVQIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E +I      LT            E+ + ++ +KP G       G    I  F    + 
Sbjct: 43  QEDEIYFEDELLTWV----------EEGQYFMLHKPQGCVCSNDDGDYPTIYQFFDYPLA 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 93  G---KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + +          +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPVEENYAAACSEGILLRGEKEPTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|154334484|ref|XP_001563489.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
          Length = 1015

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/115 (27%), Positives = 46/115 (40%), Gaps = 6/115 (5%)

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+     + LT   R   +  +  S     P  +         K S +  D    V+Q
Sbjct: 790 VAAKNERM-RLLTRGGRRDSVGAVALSP----PPVRNGPATLLAHKASAVLSDTSRRVQQ 844

Query: 219 NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +    A +  +V+   A      ++    TGRTHQLRVH   +G PIV D KY
Sbjct: 845 YLETLRSAKTALQVMRYDAATDQTVVKCTLGTGRTHQLRVHLASLGHPIVRDRKY 899


>gi|322504491|emb|CAM42057.2| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 1015

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/115 (27%), Positives = 46/115 (40%), Gaps = 6/115 (5%)

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V A+     + LT   R   +  +  S     P  +         K S +  D    V+Q
Sbjct: 790 VAAKNERM-RLLTRGGRRDSVGAVALSP----PPVRNGPATLLAHKASAVLSDTSRRVQQ 844

Query: 219 NEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +    A +  +V+   A      ++    TGRTHQLRVH   +G PIV D KY
Sbjct: 845 YLETLRSAKTALQVMRYDAATDQTVVKCTLGTGRTHQLRVHLASLGHPIVRDRKY 899


>gi|55821481|ref|YP_139923.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMG 18311]
 gi|55737466|gb|AAV61108.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMG 18311]
 gi|312278820|gb|ADQ63477.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 243

 Score = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 78/246 (31%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++  L+  QV V+ +                     +    I
Sbjct: 1   MRLDKFLVDCGVG-SRSQVKTFLKKKQVTVNGQV------------------ETSPKTQI 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E K             +L   L +E    Y+ NKP G+           +   L     
Sbjct: 42  DEDK---------DQIAYLGQELTHETFVYYLLNKPQGVISATEDSRHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++      A   L+     + + KIY + V GI   +   
Sbjct: 93  HK--QVFPVGRLDIDTHGLLLLTNNGDLAHAMLS---PKKHVDKIYQAKVAGIMDEEDIL 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   +K  +     A      +D  A     +++    G+ HQ++ 
Sbjct: 148 -------------AFEKGIKLKDHTCQPAKLEIVSVDRNAS-TSLVQITIAEGKFHQVKR 193

Query: 258 HALHMG 263
                G
Sbjct: 194 MVAACG 199


>gi|237785455|ref|YP_002906160.1| putative pseudouridylate synthase [Corynebacterium kroppenstedtii
           DSM 44385]
 gi|237758367|gb|ACR17617.1| putative pseudouridylate synthase [Corynebacterium kroppenstedtii
           DSM 44385]
          Length = 278

 Score = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 79/250 (31%), Gaps = 45/250 (18%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +RL +         +    +K++  G+V V+   V         Q VR+ P  + +  
Sbjct: 36  EGIRLQKVLAAA-GVASRRMSEKLIDEGRVEVNGDIVTR-------QGVRVDPDYDVIR- 86

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                  +++ E  + +  NKP G+       +     G +   
Sbjct: 87  ------------------VDGSRVVVDESMQYFALNKPRGVQSTMHDDMGRPCVGDIVGE 128

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               GQ+     RLD  T G+L++      A  L        I+K Y + V G    K  
Sbjct: 129 KVDAGQRLFHVGRLDAATQGLLLLTNDGELANRL--IHPKYGIKKTYLATVLGEVDKK-- 184

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                         D   + +  E     A +    I    Q    +++  H GR H +R
Sbjct: 185 --------------DLRRLTQGIELDDGTARADDADIIDVWQGRSLVKVVLHEGRKHIVR 230

Query: 257 VHALHMGCPI 266
                 G P+
Sbjct: 231 RMLKAAGFPV 240


>gi|34498841|ref|NP_903056.1| hypothetical protein CV_3386 [Chromobacterium violaceum ATCC 12472]
 gi|34104693|gb|AAQ61050.1| conserved hypothetical protein [Chromobacterium violaceum ATCC
           12472]
          Length = 479

 Score = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 44/261 (16%), Positives = 84/261 (32%), Gaps = 49/261 (18%)

Query: 6   YVQYVVVENDE-ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
            ++ V V++ E E +RL +   +     +   +++ + +G V V+ K+    +++     
Sbjct: 198 KLKEVRVDHAEIEPVRLQKALSSSGVG-SRREMEEWIEAGLVTVNGKKASLGDKVGPQDK 256

Query: 65  VRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLY--EDSKIYVFNKPAGISVQGG 122
           V +      L                 K  D L  +++Y  E+ +I   + P G      
Sbjct: 257 VLVKGDQIKL-----------------KWPDRLPRVIMYHKEEGEIVTRDDPEG------ 293

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                           +K  +     RLD  TSG+L++  +   A  +         +  
Sbjct: 294 ------RVTVFDRLPQAKSSRWVAIGRLDVNTSGLLLITTSGELANRMMHPSFEVEREYS 347

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
              L    P+  KE      L+      D +      E+ AN                 W
Sbjct: 348 VRVLGELTPEIMKEMTKGVELEDGEARFDRIFQTGGQEESANQ----------------W 391

Query: 243 LEMQPHTGRTHQLRVHALHMG 263
             +    GR  ++R    H G
Sbjct: 392 YNVVIKEGRNREVRRMFEHFG 412


>gi|118444952|ref|YP_878908.1| RNA pseudouridylate synthase family protein [Clostridium novyi NT]
 gi|118135408|gb|ABK62452.1| RNA pseudouridylate synthase family protein [Clostridium novyi NT]
          Length = 238

 Score = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 66/179 (36%), Gaps = 36/179 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   + +   ++  ++ G++ VD K VK N        +++ P  + +    
Sbjct: 2   ERLDKVLSN-LGYGSRKEIKAFVKKGEIEVDGKVVKDNG-------IKVDPNKSIIKVNG 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E                    + Y      + NKPAG+     S    + D  +   +D
Sbjct: 54  EE--------------------INYRKYIYIMMNKPAGVV----SATFDNYDETVIDLLD 89

Query: 139 SKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +     P    RLD++T G+L++         LT       + K Y++ +  +   K 
Sbjct: 90  YEYTVFDPFPVGRLDKDTEGLLLITNDGELNHRLT--SPKWHVDKTYYAEIDKMVDEKD 146


>gi|114566930|ref|YP_754084.1| ribosomal large subunit pseudouridine synthaseB [Syntrophomonas
           wolfei subsp. wolfei str. Goettingen]
 gi|114337865|gb|ABI68713.1| ribosomal large subunit pseudouridine synthase B [Syntrophomonas
           wolfei subsp. wolfei str. Goettingen]
          Length = 239

 Score = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 84/249 (33%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHIN-FVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNH 76
           MRL ++       I+     ++++  G+V+V+ K +      ++ G  V           
Sbjct: 1   MRLAKYLAE--SGISSRRQAERLITQGKVKVNDKTITELAFTLKPGDRV----------- 47

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKS 135
                             +F   I+   D    + +KPAG IS          +   L +
Sbjct: 48  ------------------EFAGKIIEQTDKIYLLLHKPAGYISSLADPQGRPRVIDLLSA 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                  +     RLD +T G+L+++     +  +T       I K Y + V G      
Sbjct: 90  V----NTRVFPVGRLDYDTEGLLLLSNDGEFSNLMT--HPRYLIPKKYEAWVQG------ 137

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 L+K   I      V  ++   A   +     +    +    LE++ H G+  Q+
Sbjct: 138 ------LVKPDTIRQLEQGVALEDGITAPARV----RLLSSKKGQSLLELEIHEGKKRQI 187

Query: 256 RVHALHMGC 264
           +   L +G 
Sbjct: 188 KRMCLAVGH 196


>gi|329768850|ref|ZP_08260278.1| hypothetical protein HMPREF0433_00042 [Gemella sanguinis M325]
 gi|328837213|gb|EGF86850.1| hypothetical protein HMPREF0433_00042 [Gemella sanguinis M325]
          Length = 235

 Score = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 79/247 (31%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI-QSGQVVRIPPVINALNH 76
           MRLD++  +     +    +KI++ G V V+   VK  + ++ +    V I         
Sbjct: 1   MRLDKYISS-ITVYSRAETKKIIKKG-VLVNNVLVKQPDYQVDEENDQVVID-------- 50

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   L Y+     + NKP  I           +   L   
Sbjct: 51  ---------------------GKSLFYQKHVYIMMNKPGNIISATEDKKDTTVIDILNE- 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +  KP    RLD++T G++++      A  L      + + K Y+  V G  K +  
Sbjct: 89  -KDRLFKPFPVGRLDKDTEGLMLLTNDGELAHKL--ISPKKDVIKKYYVEVDGELKVEHV 145

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I    +                E G     +  +++    +K     +    G+ HQ++
Sbjct: 146 TIIRDGVVL--------------EDGYKTKCAALEILTSNTEK-SRAYISITEGKFHQVK 190

Query: 257 VHALHMG 263
                +G
Sbjct: 191 RMMKSLG 197


>gi|15674222|ref|NP_268397.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. lactis Il1403]
 gi|12725309|gb|AAK06338.1|AE006453_2 ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. lactis Il1403]
          Length = 273

 Score = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 84/243 (34%), Gaps = 41/243 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L+ G+V V            +G+V R        N   
Sbjct: 32  MRLDKFLAESGLG-SRSEVKILLKKGRVTV------------AGEVQRDGRFQVDKN--- 75

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                       ++   F   IL Y++   Y+ NKP G+       +   +   L     
Sbjct: 76  ------------SRQVAFDGEILDYQEYYYYLLNKPQGLVSATKDNLFKTVVQLLSE--K 121

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              +      RLD+ T G+L++    A    LT+    + ++K Y++ + G   +  E +
Sbjct: 122 DFREDIFPVGRLDKNTEGLLILTNDGALGHDLTQ--PKKHVEKEYFARIDGKVTD--EIV 177

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +    +   G+               I +    +  +     + +  H G+ HQ++  
Sbjct: 178 NKFAEGLTLKNGEKAR-------PGELFIENIYEGESQSGWISEIRVIIHEGKFHQVKRM 230

Query: 259 ALH 261
              
Sbjct: 231 FEA 233


>gi|28211988|ref|NP_782932.1| putative ribosomal small subunit pseudouridine synthase A
           [Clostridium tetani E88]
 gi|28204431|gb|AAO36869.1| putative ribosomal small subunit pseudouridine synthase A
           [Clostridium tetani E88]
          Length = 238

 Score = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 39/252 (15%), Positives = 89/252 (35%), Gaps = 63/252 (25%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D+   N   + +   ++K++++  V V+ ++VK                        
Sbjct: 2   ERIDKILAN-MGYGSRKEVKKLIKNNLVEVNGEKVK------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFL---KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 D S+N+    D +     ++ Y      + NKP G+     S    + D  +  
Sbjct: 37  ------DPSINIDPEKDKILVGDKVVNYRKFIYIMMNKPEGVV----SATFDNYDETVID 86

Query: 136 WVDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS-LVWGIPK 192
            ++ + Q   P    RLD++T G+L++         L       ++ K+Y++ +   + +
Sbjct: 87  LLEEEYQVFNPFPVGRLDKDTVGLLLITNDGELNHKL--ISPKWKVDKVYYAEINKEVNE 144

Query: 193 NKKECIANWLLKKS--HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              E   N ++           + ++K +E GA   ++                     G
Sbjct: 145 KDIEAFQNGIVISDGYKCMPGKLEIIKSDENGAEVYVT------------------IQEG 186

Query: 251 RTHQLRVHALHM 262
           + HQ++     +
Sbjct: 187 KFHQVKRMFEAL 198


>gi|315648476|ref|ZP_07901575.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315276170|gb|EFU39516.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 253

 Score = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 78/248 (31%), Gaps = 48/248 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N     +   L+K+ + G + V+   +K                 +   H+ 
Sbjct: 9   QRLDKVLSNLGFG-SRAELKKMAKQGSIVVNGTVMK-----------------DPGKHVD 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
               I++          F    + Y +    + +KP G+           +   L    D
Sbjct: 51  PYTDIIE----------FEGETIQYREYVYIMLHKPPGVVSATEDLRDRTVLDLLDK--D 98

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +P    RLD++T G+L++    + A + L+     + I K Y ++V G    +   
Sbjct: 99  YLVFEPFPVGRLDKDTEGLLLLTNDGKLAHELLS---PRKHIPKTYEAIVEGRVGEEDAR 155

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE--MQPHTGRTHQL 255
           +                V   +      A       +            +  H G+ HQ+
Sbjct: 156 LFAA------------GVTLDDGYATMPAELVIHSHEERDDGVILSRISLTIHEGKFHQV 203

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 204 KRMFEAVG 211


>gi|297715439|ref|XP_002834085.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like, partial [Pongo abelii]
          Length = 142

 Score = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 29/131 (22%), Positives = 53/131 (40%), Gaps = 6/131 (4%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP------RLTHRLDQET 154
           ++Y      V NK   + +   +            +   +   P      R  H+LD  T
Sbjct: 11  IVYRSRDFLVVNKHWDVRIDSKAWRETLTLQKQLRYRFPELADPDTCYGFRFCHQLDFST 70

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
           SG L VA  +AAA      F+ RR+ K Y +L+ G  +  +  I++ + + S  G  +  
Sbjct: 71  SGALCVALNKAAAGSAYRCFKERRVTKAYLALLRGHIQESRVTISHAIGRNSTEGRAHTM 130

Query: 215 VVKQNEKGANY 225
            ++ ++   N 
Sbjct: 131 CIEGSQGCENP 141


>gi|154504970|ref|ZP_02041708.1| hypothetical protein RUMGNA_02480 [Ruminococcus gnavus ATCC 29149]
 gi|153794853|gb|EDN77273.1| hypothetical protein RUMGNA_02480 [Ruminococcus gnavus ATCC 29149]
          Length = 241

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 87/246 (35%), Gaps = 51/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +         +++ +  G+V VD   VK                        
Sbjct: 3   IRLDKYLADMGVG-TRTEVKRAISKGRVSVDGACVKK----------------------- 38

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E KI      +     F   I+ Y   + Y+ +KPAG+     +         +   V 
Sbjct: 39  PETKIDTEETTVV----FDGQIVEYTKKEYYMLHKPAGVIS---ATEDAREKTVIDLIVS 91

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K +      RLD++T G+L++      A + L+     + + K Y++ V GI   +   
Sbjct: 92  RKRKDLFPVGRLDKDTEGLLLITNDGELAHRLLS---PKKHVDKTYYAKVQGIVTQEDV- 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   V  +EK    A +  +V+   + +   + +    G+ HQ++ 
Sbjct: 148 ------------RKFAEGVDIHEK-KLTAPAVLEVVK--SGEVSEILLTICEGKFHQVKR 192

Query: 258 HALHMG 263
               +G
Sbjct: 193 MFEAVG 198


>gi|322515146|ref|ZP_08068149.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           ureae ATCC 25976]
 gi|322118860|gb|EFX91050.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           ureae ATCC 25976]
          Length = 232

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 38/179 (21%), Positives = 69/179 (38%), Gaps = 22/179 (12%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            LK  L +ED+ + +FNKP  +  Q            LK ++     +     RLD+++ 
Sbjct: 30  PLKPQLSFEDTVVVLFNKPFDVLTQ---FTDEQGRQTLKDFIPI--PQVYPVGRLDRDSE 84

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHI 208
           G+L++         L      ++  K Y + V GIP+        K   + + L K +  
Sbjct: 85  GLLLLTNNGEIQHRLANPKFEKQ--KTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAK- 141

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   K          +  K+ +       W+E++ H G+  Q+R    H+G P +
Sbjct: 142 -------AKAISAPNYEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTL 193


>gi|260424785|ref|ZP_05733291.2| ribosomal small subunit pseudouridine synthase A [Dialister invisus
           DSM 15470]
 gi|260403192|gb|EEW96739.1| ribosomal small subunit pseudouridine synthase A [Dialister invisus
           DSM 15470]
          Length = 277

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 43/267 (16%), Positives = 87/267 (32%), Gaps = 61/267 (22%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72
           ++E+ MRLD++  +         L++ +R G V+V+ +++      +     +       
Sbjct: 13  DEEDVMRLDKFLSDMNMG-TRTELKRDIRKGAVQVNGEKITDPGFMVNENDEIIFAGEPV 71

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                                         YE    Y+ NKPAG+     +    +    
Sbjct: 72  PYFR--------------------------YE---YYMLNKPAGVIT---ATEDRYQKTV 99

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L  + + + +      RLD++T G+L+V         L      + I K Y++ + G   
Sbjct: 100 LDFFGERRRKDLSPVGRLDKDTVGLLLVTNDGGFHHRL--LSPKKHIDKEYYARIDGRVD 157

Query: 193 N------KKEC----IANWLLKKSHIGGDYVHVVKQ------NEKGANYAISHFKVIDCF 236
                  +K      I   L  K  I G   + ++       N +    A+         
Sbjct: 158 EADREKFEKGIYVDEIFTALPAKLMIDGYRENALESDFMDLANSRAPKSAL--------- 208

Query: 237 AQKFCWLEMQPHTGRTHQLRVHALHMG 263
                 + +    G+ HQ++     +G
Sbjct: 209 ENGVSEIRVVVQEGKFHQIKRMFHALG 235


>gi|221054544|ref|XP_002258411.1| pseudouridylate synthase [Plasmodium knowlesi strain H]
 gi|193808480|emb|CAQ39183.1| pseudouridylate synthase, putative [Plasmodium knowlesi strain H]
          Length = 795

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 17/128 (13%), Positives = 48/128 (37%), Gaps = 20/128 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             R+     + +   +   +++ +R G ++V+K+ V  +  ++S  +++          +
Sbjct: 68  GKRISDVLTSEFCAYDLSYIKESIRKGYIKVNKENVSCDYLLKSNDLIQ-------HKLL 120

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + E+ ++ + +           ++LYED       K A +         Y  +  L+   
Sbjct: 121 LFEKPVICNKI-----------LILYEDQNFICVYKSASMPTHPVG--FYQYNSLLRILQ 167

Query: 138 DSKGQKPR 145
           +      R
Sbjct: 168 NYISSTLR 175



 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 224 NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             +I+ F  +    +     +  QP TGRTHQ+R H   +  PI  D +Y  NF   +  
Sbjct: 591 KPSITRFMFLAYNPELNESLVLCQPITGRTHQIRAHLKSLSFPISNDPQYNDNFAKEYMD 650



 Score = 42.7 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 7/85 (8%)

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-------PRLTHRLDQETSGILVVARTR 164
           +K A   V+  S          KS+ + +  K           HRLD+ TSGI++  + +
Sbjct: 342 DKSAKPPVEPISENVQRRVKQHKSYNNERKDKQEKDDSYIYTLHRLDKLTSGIVMFGKNK 401

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWG 189
             +   +++     I+K Y + V G
Sbjct: 402 NFSTFFSQNISNNSIKKSYITRVEG 426


>gi|319651915|ref|ZP_08006038.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317396407|gb|EFV77122.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 239

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 37/246 (15%), Positives = 87/246 (35%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D+   N   + +  +++K+L+ G V V+ ++VK                 +  + + 
Sbjct: 1   MRIDKMLAN-LGYGSRKDVKKLLKDGAVTVNDEKVK-----------------DPKHQVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ  +  +    ++ +F+            + NKP G+           +   L+  + 
Sbjct: 43  PEQDAVIINGEKVEYKEFI----------YLMMNKPPGVISATEDSQFETVVDLLE--MR 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD++T G+L++      A + L+     + + K Y+++           
Sbjct: 91  DLVFSPFPVGRLDKDTEGLLLLTNDGQLAHRLLS---PKKHVPKTYFAV----------- 136

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   +            ++    +     +   K     +     +E+    G+ HQ++ 
Sbjct: 137 IDREVTADDVAAFKKGVILDDGYETKPGELEILK-----SGITSDIELTITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|253998637|ref|YP_003050700.1| pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|313200711|ref|YP_004039369.1| pseudouridine synthase [Methylovorus sp. MP688]
 gi|253985316|gb|ACT50173.1| pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|312440027|gb|ADQ84133.1| pseudouridine synthase [Methylovorus sp. MP688]
          Length = 362

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/235 (13%), Positives = 74/235 (31%), Gaps = 35/235 (14%)

Query: 12  VENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
            + D    RL +        + +   +++++ SG++ ++ K  +    +  G VVR    
Sbjct: 22  TDPDAVPQRLHKLLA--LAGLGSRREMEELILSGRITINGKVAEVGAAVVPGDVVRFDSR 79

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                            V+L   ++  + ++ ++     V                    
Sbjct: 80  ----------------PVHLPFEAELAQVLIYHKPEGEIVSQDDP-----------EKRA 112

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                    +G K     RLD  TSG+L+   +   A           +++ Y   ++G 
Sbjct: 113 TVFDKLPRVRGAKWIAIGRLDINTSGLLIFTTSGELANRF--MHPRYEVEREYAVRIFGE 170

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
               +       ++       +  +  Q  +GAN+    ++VI    +      +
Sbjct: 171 LTEGEMLQLTQGIELEDGPASFDSIRPQGGEGANH---WYQVILREGRNREVRRL 222


>gi|239827574|ref|YP_002950198.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239807867|gb|ACS24932.1| pseudouridine synthase [Geobacillus sp. WCH70]
          Length = 243

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 87/251 (34%), Gaps = 58/251 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++  G+V+V+ K V     ++     V +  +       
Sbjct: 2   ERLQKVIA-HAGIASRRKAEQLILQGKVKVNGKVVTELGVKVGPQDKVEVDGIPVEREEP 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
           +                              Y+F KP G+  SV+   G        +  
Sbjct: 61  V-----------------------------YYLFYKPRGVISSVKDDKGRK-----VVTD 86

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KN 193
           +     ++     RLD +TSGIL++      A  L        I+K+Y + V GIP  + 
Sbjct: 87  FFKDVDKRIYPIGRLDYDTSGILLLTNDGDFANLL--MHPRYEIEKVYIAKVKGIPTREQ 144

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K+     +L+        V ++  N K    AI               +E++ H GR  
Sbjct: 145 LKQLERGIMLEDGMTAPAKVKLLSHN-KQKQTAI---------------IEIRIHEGRNR 188

Query: 254 QLRVHALHMGC 264
           Q+R     +GC
Sbjct: 189 QVRRMFEAIGC 199


>gi|82702976|ref|YP_412542.1| pseudouridine synthase, Rsu [Nitrosospira multiformis ATCC 25196]
 gi|82411041|gb|ABB75150.1| ribosomal large subunit pseudouridine synthase B [Nitrosospira
           multiformis ATCC 25196]
          Length = 315

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 39/245 (15%), Positives = 82/245 (33%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            +L +         +   +++++ SGQV ++ K  +  +RI +  VVR+   +       
Sbjct: 73  QKLHKVLAQAGLG-SRREMEELIASGQVTINGKTAQVGDRIAARDVVRVGKRVVHF---- 127

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                        + +  L  ++LY        +KP G  V                   
Sbjct: 128 -------------RSARRLPRVMLY--------HKPEGEIV--SQDDPQGRTSVFDKLPQ 164

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  K     RLD  TSG+LV       A  L        +++ Y   + G    ++  +
Sbjct: 165 LRSSKWIAIGRLDYNTSGLLVFTTDGELANRL--MHPRFEVEREYAVRIIGRLTPEQATL 222

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               ++       + ++  +  +G+N+    ++VI                GR  ++R  
Sbjct: 223 LTSGVELEDGAAKFDYLSDEGGEGSNH---WYRVI-------------LKEGRNREVRRM 266

Query: 259 ALHMG 263
              +G
Sbjct: 267 FEAVG 271


>gi|303256973|ref|ZP_07342987.1| ribosomal large subunit pseudouridine synthase B [Burkholderiales
           bacterium 1_1_47]
 gi|302860464|gb|EFL83541.1| ribosomal large subunit pseudouridine synthase B [Burkholderiales
           bacterium 1_1_47]
          Length = 355

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 46/299 (15%), Positives = 88/299 (29%), Gaps = 47/299 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
            N +L +   +     +  ++++ +  G++ V+ +      R+    V+R    I   + 
Sbjct: 52  ANEKLHKVLADAGIG-SRRDMEERIAEGRISVNGEPAHVGQRVTPSDVIRFDGRIVRRSA 110

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +                ++ +  +L+Y        +KPAG  V                 
Sbjct: 111 L---------------ENNDVPKVLIY--------HKPAGEIV--SKDDPEGRPTVFDHL 145

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               G +     RLD  T G+L+   +   A  L        I++ Y   V G    +  
Sbjct: 146 PRIGGARWIAVGRLDFNTEGLLLFTDSGNLANFL--MHPRHEIEREYAVRVQGTMSPEA- 202

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              + LLK   +           E G                   W  +    GR  ++R
Sbjct: 203 --KDKLLKGIKLDDGIAKFTTLEEGGGK-------------GFNRWYNVTLSEGRNREVR 247

Query: 257 VHALHMGCPI--VGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                +G P+  +   KY       +       ++        L      +   TAP P
Sbjct: 248 RMFEAVGLPVSRLIRVKYGNLELPSDLPRGKTRRMSTEETEKWLDSISYKKGMSTAPAP 306


>gi|71065415|ref|YP_264142.1| 23S rRNA pseudouridine synthase F [Psychrobacter arcticus 273-4]
 gi|71038400|gb|AAZ18708.1| ribosomal large subunit pseudouridine synthase F [Psychrobacter
           arcticus 273-4]
          Length = 332

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 72/249 (28%), Gaps = 56/249 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +  +  + +  G V ++ KR    +++ +G  V++   +       
Sbjct: 8   RLNKYISE--SGICSRRDADRFIEQGNVYLNGKRAAVGDQVVAGDTVKVNGQLIEPKEA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D    V NKP GI     S    +I  F++  V 
Sbjct: 65  -------------------------DDFVFIVLNKPVGIVSTTESSEKNNIVDFVRHSV- 98

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++ +         +  +        +                
Sbjct: 99  ----RIFPIGRLDKDSQGLIFLTNNGDLVNKVLRAGNNHEKDYV--------------VT 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N  +  S I G    V    +      ++                +    G   Q+R  
Sbjct: 141 VNKPITDSFIEGLAGGVPMLGKMTKKCPVTKVAP--------NVFNITLVQGLNRQIRRM 192

Query: 259 ALHMGCPIV 267
             H G  +V
Sbjct: 193 CEHFGYEVV 201


>gi|307243938|ref|ZP_07526063.1| pseudouridylate synthase [Peptostreptococcus stomatis DSM 17678]
 gi|306492760|gb|EFM64788.1| pseudouridylate synthase [Peptostreptococcus stomatis DSM 17678]
          Length = 243

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 91/252 (36%), Gaps = 49/252 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++  +     +    + ++  G+++V+ + +                  +    + 
Sbjct: 1   MRINKYIASA-GIASRRKAENLVSEGRIKVNGQIIY-----------------DLGYQVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +++ I++      K  D     L+Y      + NKP G      S   +     +   V 
Sbjct: 43  EDKDIVEYD---GKKIDINSEKLVY-----ILLNKPEGYIT--SSKDQFGRKDVM-DLVT 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-EC 197
              ++     RLD ETSG+L++         +T       I K Y + V GIP +++ E 
Sbjct: 92  DIKERIYPVGRLDYETSGLLLMTNDGDLTYKIT--HPKHEITKTYIASVKGIPTSEELER 149

Query: 198 IANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             N L ++        + V+K + K                + +    +  H GR  Q+R
Sbjct: 150 FENGLEIEDYVTSKAKIRVLKTDVK----------------KNYSVCRVSIHEGRNRQVR 193

Query: 257 VHALHMGCPIVG 268
                +  P++ 
Sbjct: 194 KMFNAINHPVMN 205


>gi|326791357|ref|YP_004309178.1| pseudouridine synthase Rsu [Clostridium lentocellum DSM 5427]
 gi|326542121|gb|ADZ83980.1| pseudouridine synthase Rsu [Clostridium lentocellum DSM 5427]
          Length = 240

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 83/250 (33%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRL ++  +     +    ++++  G+V V+ + ++    +++    V        L   
Sbjct: 1   MRLQKYLAS-CGIASRRKCEELILEGKVSVNGQIIQTLGTQVEEDDEVYYNHKRVQLE-- 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     E    Y+ NKPAG      +         +   +
Sbjct: 58  --------------------------EKHVYYMLNKPAGYVT---TVQDEKQRATVLDLM 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD  TSG+L++    A    LT       + K Y   + G    +   
Sbjct: 89  KGVKTRIFPVGRLDYNTSGLLLLTSDGALTYGLT--HPKHHVNKTYEVKLSGKVTERS-- 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               +L+K          V  + +    A    +V+   A K  WL++  H GR  Q+R 
Sbjct: 145 --LDMLRKG---------VMIDHRKTYPA--EVEVVKQNA-KHTWLKITIHEGRNRQIRK 190

Query: 258 HALHMGCPIV 267
               +G P+V
Sbjct: 191 MCEAVGYPVV 200


>gi|328952678|ref|YP_004370012.1| pseudouridine synthase Rsu [Desulfobacca acetoxidans DSM 11109]
 gi|328453002|gb|AEB08831.1| pseudouridine synthase Rsu [Desulfobacca acetoxidans DSM 11109]
          Length = 242

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 83/251 (33%), Gaps = 52/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    ++++R+G+V VD + V        GQ++           ++
Sbjct: 4   ERLQKYLARA-GVASRRQGEELIRAGRVSVDGRIVTT-----LGQLI----DSEKAEVMV 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +K+L      T                  V NKP G                +   + 
Sbjct: 54  DGRKVLPPPHCRT-----------------IVLNKPYGCVTTMADPQGRRK---VIDLLP 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKE 196
            + ++     RLD + +G+L++      A  L       ++ K Y + V G   P  ++ 
Sbjct: 94  DQEERLYPVGRLDYDATGLLLLTNDGELAHRL--MHPRYKVAKTYRATVAGQFSPAARRR 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 L       + V +VK + +                     LE+    GR H ++
Sbjct: 152 LREGITLDGRLTIPEQVRLVKTSSE------------------RSVLELTIREGRYHLVK 193

Query: 257 VHALHMGCPIV 267
                +GCP++
Sbjct: 194 RLCAAVGCPVL 204


>gi|261406009|ref|YP_003242250.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|329929803|ref|ZP_08283479.1| pseudouridine synthase B, ribosomal large subunit [Paenibacillus
           sp. HGF5]
 gi|261282472|gb|ACX64443.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|328935781|gb|EGG32242.1| pseudouridine synthase B, ribosomal large subunit [Paenibacillus
           sp. HGF5]
          Length = 251

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 37/236 (15%), Positives = 78/236 (33%), Gaps = 46/236 (19%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
            +    ++++  G+V+V+ + V                           Q I+  S    
Sbjct: 14  ASRRKCEELILEGKVQVNGETVT-----------------ELGTKADPAQDIITVSGKPI 56

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           K+          E     + NKP G+     S         +  ++    ++     RLD
Sbjct: 57  KN----------EKKVYVMLNKPKGVIT---SASDPEGRKIVSDYLKGIKERVYPIGRLD 103

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +T G+L++      A  L+       + K Y + V G+P              + +   
Sbjct: 104 YDTEGLLLLTNDGEFANLLS--HPKYHVPKTYLATVKGVPHG------------TELDKL 149

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              ++ ++   +  A   +K +D    K   + +  H GR  Q+R     +  P++
Sbjct: 150 RQGIMLEDGMTS-PAEVEYKDVD-PDNKQSVISITIHEGRNRQVRRMFEAISHPVL 203


>gi|290968302|ref|ZP_06559844.1| pseudouridylate synthase [Megasphaera genomosp. type_1 str. 28L]
 gi|290781661|gb|EFD94247.1| pseudouridylate synthase [Megasphaera genomosp. type_1 str. 28L]
          Length = 238

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 89/249 (35%), Gaps = 59/249 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSG-QVVRIPPVINALNH 76
           +RLD+W  +     +   ++ + R G+V V+ +  +     +++G   V++         
Sbjct: 5   LRLDKWLSHSGQG-SRKEVRDLCRQGRVLVNGEICRDGAQLVETGVDRVQVD-------- 55

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                +  + YE+    + +KP G+           +  FL   
Sbjct: 56  ---------------------RQPVCYEEFYYIMLHKPRGVISATTDAACRTVLDFLPPP 94

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
             + G       RLD++T+G+L++      A + L+     +   K+Y + V G IP++ 
Sbjct: 95  CRTGG--VFPVGRLDKDTTGLLLLTNDGVWAHRILS---PKKHCYKVYEATVSGSIPEDL 149

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
               A+ ++            ++ + +     I+ ++                  GR HQ
Sbjct: 150 TVRFASRIVLADGTVCLPARALRIDGQTVE--ITVYE------------------GRYHQ 189

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 190 VKRMCAAVG 198


>gi|291297121|ref|YP_003508519.1| RNA-binding S4 domain-containing protein [Meiothermus ruber DSM
           1279]
 gi|290472080|gb|ADD29499.1| RNA-binding S4 domain protein [Meiothermus ruber DSM 1279]
          Length = 295

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 59/171 (34%), Gaps = 35/171 (20%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            MRL ++        +    + ++R+G+V ++++       +Q G +VR+      +   
Sbjct: 3   GMRLQQFLARA-GIASRRKAEDLIRAGRVTINEQVASIGAVVQPGDIVRLDGERVRMPQK 61

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                +       T H D     ++YE     +  K  G+                    
Sbjct: 62  KVVIALHKPKGYTTTHEDEHAEKIVYE-----LVPKHPGL-------------------- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                      RLD++T G+L++       QHLT      ++ K+Y +   
Sbjct: 97  -------HAVGRLDKDTEGLLLLTNDGHLTQHLT--HPRNQVPKLYRAWCK 138


>gi|268608512|ref|ZP_06142239.1| 16s pseudouridylate synthase [Ruminococcus flavefaciens FD-1]
          Length = 255

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 39/311 (12%), Positives = 90/311 (28%), Gaps = 74/311 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSG-QVVRIPPVINALNH 76
           +RLD++            ++ +   G V V+   VK ++ +I +G   V +     +   
Sbjct: 4   IRLDKFISER-TEYTRSQIKSLCAKGSVTVNGSPVKRSDTKIDTGADDVTVCGNAISSER 62

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                         +  + NKP G            +   +   
Sbjct: 63  F-----------------------------RYILLNKPKGYVSSTDDKDGETVIKLVPPE 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + SKG       RLD++++G L++      A +  + +  + +I     S        ++
Sbjct: 94  MRSKG--LFPAGRLDKDSTGALLITDDGALAHRICSPNNHISKIYAAELSR-----PFEQ 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E +  +        G+     K               +           ++ H G  HQ+
Sbjct: 147 EYVEKFAKGIVLANGEACSPCK---------------VQKAENADNLAFVELHEGMYHQV 191

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM 315
           +     +G  +                    ++ +    +    P G  + +   LP  +
Sbjct: 192 KRMFAAVGNHV----------------ENLKRISIGGLILPKDLPLGKCMYL---LPKDI 232

Query: 316 VKTWDSLGFKY 326
            + +  + F  
Sbjct: 233 EQMFTKIDFDA 243


>gi|167038569|ref|YP_001666147.1| pseudouridine synthase [Thermoanaerobacter pseudethanolicus ATCC
           33223]
 gi|307266602|ref|ZP_07548133.1| pseudouridine synthase [Thermoanaerobacter wiegelii Rt8.B1]
 gi|320116965|ref|YP_004187124.1| pseudouridine synthase [Thermoanaerobacter brockii subsp. finnii
           Ako-1]
 gi|166857403|gb|ABY95811.1| pseudouridine synthase [Thermoanaerobacter pseudethanolicus ATCC
           33223]
 gi|306918399|gb|EFN48642.1| pseudouridine synthase [Thermoanaerobacter wiegelii Rt8.B1]
 gi|319930056|gb|ADV80741.1| pseudouridine synthase [Thermoanaerobacter brockii subsp. finnii
           Ako-1]
          Length = 241

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 42/254 (16%), Positives = 82/254 (32%), Gaps = 61/254 (24%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             MR+D+   N         ++K ++ G V V+   VK      +G +V           
Sbjct: 2   AKMRIDKLLSNIGIG-TRKEVKKFIKEGLVLVNGNTVKD-----AGLIVD---------- 45

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
             +  +IL           F    + Y++    + NKP G+       +   +   L   
Sbjct: 46  -TESDEIL-----------FDGEKINYKEFIYIMINKPKGVISATYDEVEKTVIDLLPQE 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK- 194
           +  K + P    RLD++T G+L++      A Q L+     + + K Y++ + G      
Sbjct: 94  L--KARNPFPVGRLDKDTEGLLLITNDGDLAHQLLS---PKKNVIKKYYAEILGFVNESD 148

Query: 195 -----KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I     K      + +       K                     + +    
Sbjct: 149 IKAFNEGIILEDGYKTLPANLEILFSSSDVSK---------------------VYVYIRE 187

Query: 250 GRTHQLRVHALHMG 263
           G+ HQ++     +G
Sbjct: 188 GKYHQIKRMFESVG 201


>gi|91776224|ref|YP_545980.1| ribosomal large subunit pseudouridine synthase B [Methylobacillus
           flagellatus KT]
 gi|91710211|gb|ABE50139.1| ribosomal large subunit pseudouridine synthase B [Methylobacillus
           flagellatus KT]
          Length = 383

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/243 (15%), Positives = 78/243 (32%), Gaps = 37/243 (15%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           +  + V  + D    RL +          +   ++ ++ SG++ ++ K  +    +    
Sbjct: 15  SPAKPVAADPDAVPQRLHKLLA--LAGFGSRREMETLIASGRITINGKTAEVGASVVPSD 72

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGG 122
           VVR                 LDS          L  +LLY        +KP G I     
Sbjct: 73  VVR-----------------LDSRPLRLPFEPELPQVLLY--------HKPEGEIVSHDD 107

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +           +  K     RLD  TSG+L+   +   A           +++ 
Sbjct: 108 P---ENRASVFDKLPRIRNGKWIAIGRLDMNTSGLLIFTTSGELANRF--MHPRYEVERE 162

Query: 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           Y   ++G     +     + ++      ++  +  Q  +GAN+    ++VI    +    
Sbjct: 163 YAVRIFGELTEGEMAQLTYGIELDDGPANFDSIRPQGGEGANH---WYEVILREGRNREV 219

Query: 243 LEM 245
             +
Sbjct: 220 RRL 222


>gi|223933741|ref|ZP_03625714.1| pseudouridine synthase [Streptococcus suis 89/1591]
 gi|302024514|ref|ZP_07249725.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           suis 05HAS68]
 gi|330833556|ref|YP_004402381.1| pseudouridine synthase [Streptococcus suis ST3]
 gi|223897583|gb|EEF63971.1| pseudouridine synthase [Streptococcus suis 89/1591]
 gi|329307779|gb|AEB82195.1| pseudouridine synthase [Streptococcus suis ST3]
          Length = 242

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 82/246 (33%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++K+L++ QV V+ +                           
Sbjct: 1   MRLDKFLVDCGVG-SRTEVKKLLKNKQVTVNGQV-----------------------ETS 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +Q+I + S  +      L     +E    YV NKP G+           +   L +   
Sbjct: 37  PKQQIDEKSDQIAVAGQVLS----HETFVYYVLNKPKGVISATEDDRHRTVLDLLDNTAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++      A   L+     + + K+Y + V GI   +   
Sbjct: 93  QK--EVFPVGRLDIDTHGLLLLTNNGQLAHVMLS---PKKHVDKLYRAQVDGIMTQEDVE 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                ++   +      +   +   A               +   +++    G+ HQ++ 
Sbjct: 148 RFAAGIELKDLTCQPAQLTILSTDEAK--------------QTSLVDITIREGKFHQVKR 193

Query: 258 HALHMG 263
                G
Sbjct: 194 MVQACG 199


>gi|284045196|ref|YP_003395536.1| pseudouridine synthase [Conexibacter woesei DSM 14684]
 gi|283949417|gb|ADB52161.1| pseudouridine synthase [Conexibacter woesei DSM 14684]
          Length = 233

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/248 (15%), Positives = 81/248 (32%), Gaps = 53/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL ++   H    +    ++++  G++ V  + V                        +
Sbjct: 1   MRLAKFLA-HAGVASRRASEQLIAEGRIAVGGEIV------------------------L 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              + +D+S  +T   + ++     E   +Y  +KPAG+               L     
Sbjct: 36  DPARDVDASSGVTYDGEPVRGE---EPRVVYALHKPAGVVSTAADTHGRRTVTELV---- 88

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +G++     RLD +++G++++      A  LT                  +PK  +  +
Sbjct: 89  PQGRRLYPVGRLDADSTGLILLTNDGELANRLTHPRFE-------------VPKTYRATV 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +    +      V  ++   A   +               LE+  H GR  Q+R  
Sbjct: 136 GGPQIGDRTLRQLREGVRLEDGMTAPARVRRL--------SAHVLELTIHEGRKRQVRRM 187

Query: 259 ALHMGCPI 266
              +G P+
Sbjct: 188 CEEVGHPV 195


>gi|300361572|ref|ZP_07057749.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri JV-V03]
 gi|300354191|gb|EFJ70062.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri JV-V03]
          Length = 244

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 86/250 (34%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++ +GQV V+ KR+     +++    + +       N +
Sbjct: 8   ERLQKVIAQA-GVASRRKAEKMITAGQVTVNGKRITELGTKVEPSDKIEV-------NGV 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
             E++ L                        Y+F KP G+  SV+   G        +  
Sbjct: 60  PIEKETL----------------------HTYLFYKPRGVISSVKDDKGRK-----TVVD 92

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +    +     RLD +TSG+L++      A  L        + K+Y + + G+   + 
Sbjct: 93  YFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANKL--MHPRNEVPKVYVAKIKGLLSPED 150

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQ 254
               + L     I G               A +  K++    +K    +++  H G  HQ
Sbjct: 151 ---IHSLTHGVRIDGR------------KSAPAKLKILKTDEKKNTQIVQLTIHEGHYHQ 195

Query: 255 LRVHALHMGC 264
           ++     +  
Sbjct: 196 VKRMFEAVHH 205


>gi|261408369|ref|YP_003244610.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261284832|gb|ACX66803.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
          Length = 253

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 85/248 (34%), Gaps = 48/248 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N     +   L+K  + G + V+    K                 +   H+ 
Sbjct: 9   QRLDKVLSNLGFG-SRAELKKKAKQGSIVVNGTVTK-----------------DPGKHVD 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
               I++          F    + Y +    + +KP G+     S      D  +   +D
Sbjct: 51  PYADIIE----------FEGETIQYREYVYLMLHKPPGVV----SATEDLRDRTVLDLLD 96

Query: 139 SKGQ--KPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           ++ +  +P    RLD++T G+L++    + A + L+     + I K Y + V G    + 
Sbjct: 97  AEYRVFEPFPVGRLDKDTEGLLLLTNDGKLAHELLS---PRKHIPKTYEATVEGRVDEED 153

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                    +    G  +        G     SH +  D    +   + +  H G+ HQ+
Sbjct: 154 --------VRRFAAGVTLDDGYVTLPGELAIHSHEERED--GVQLSRISLTIHEGKFHQV 203

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 204 KRMFEAVG 211


>gi|170032599|ref|XP_001844168.1| ribosomal pseudouridine synthase [Culex quinquefasciatus]
 gi|167872799|gb|EDS36182.1| ribosomal pseudouridine synthase [Culex quinquefasciatus]
          Length = 493

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           V +         + F+ +         +  +P TGR HQ+RVH  ++G P+V D  Y   
Sbjct: 223 VCKVSPKGKECTTTFQKLGYNGSS-SVVLCKPLTGRMHQIRVHLQYLGYPVVNDPLYNHE 281

Query: 276 FKG 278
             G
Sbjct: 282 VFG 284



 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           V       ++   F+ +  +   +  R  HRLD+ TSG+L+  R+   A+ +    R R+
Sbjct: 12  VHPCGRYRHNTVVFILA-KEYNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEHQIRNRQ 70

Query: 179 IQKIYWSLVWGIPKNKKEC 197
           +QK Y   V G        
Sbjct: 71  VQKEYICRVEGEFPESSPV 89


>gi|315126449|ref|YP_004068452.1| pseudouridine synthase [Pseudoalteromonas sp. SM9913]
 gi|315014963|gb|ADT68301.1| pseudouridine synthase [Pseudoalteromonas sp. SM9913]
          Length = 289

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 27/178 (15%), Positives = 62/178 (34%), Gaps = 29/178 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +  +L +         +   ++K + + +V V+ K  K  +R++   ++R+         
Sbjct: 4   QGEKLQKVLARAGVG-SRREMEKYIDANRVSVNGKVAKLGDRVEETDLIRVDGH------ 56

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                     +V + + +D +  +++Y        NKP G                    
Sbjct: 57  ----------TVKIEEKADRICRVIMY--------NKPEGELSTRKDPEGRR--TVFDRL 96

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               G +     RLD  TSG+++       A  L        +++ Y + V+G   ++
Sbjct: 97  PRIDGDRWIAVGRLDVNTSGLMLFTNDGELANRL--MHPSYEVEREYSARVFGEVTDE 152


>gi|310642601|ref|YP_003947359.1| pseudouridine synthase [Paenibacillus polymyxa SC2]
 gi|309247551|gb|ADO57118.1| Pseudouridine synthase [Paenibacillus polymyxa SC2]
          Length = 252

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 34/253 (13%), Positives = 77/253 (30%), Gaps = 55/253 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++++G V V+   V                         
Sbjct: 2   ERLQKILAQA-GVASRRKCEELIQAGSVEVNGVTVT------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 +         D +      +  E     + NKP G+     S         +  
Sbjct: 37  ------ELGTKADPDQDMITVKGRPIKTEKKIYLMMNKPKGVIT---SASDPEGRKIVSD 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NK 194
           ++    ++     RLD +T G+L++      A  LT       + K Y + V G+P   +
Sbjct: 88  YLKGVKERVYPVGRLDYDTEGLLLLTNDGEFANLLT--HPKHHVPKTYVATVKGVPHGTE 145

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + +   ++ +  I        K  +     ++               +++  + GR  Q
Sbjct: 146 LDKLKKGIVLEDGITAPAEVEYKDVDPDGKESV---------------IQITIYEGRNRQ 190

Query: 255 LRVHALHMGCPIV 267
           +R     +  P++
Sbjct: 191 VRRMFEAISHPVI 203


>gi|194366464|ref|YP_002029074.1| RNA-binding S4 domain-containing protein [Stenotrophomonas
           maltophilia R551-3]
 gi|194349268|gb|ACF52391.1| RNA-binding S4 domain protein [Stenotrophomonas maltophilia R551-3]
          Length = 549

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 37/246 (15%), Positives = 75/246 (30%), Gaps = 41/246 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +   L++ +  G V+V+ +  +    ++SG  + +         + 
Sbjct: 28  ERLHKVLAQAGLG-SRRALEQRIAEGLVKVNGEVAQTGMSVKSGDKIELDGRGFVATALA 86

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    E S++ V+NKP G                 +S   
Sbjct: 87  -------------------------EPSRVLVYNKPEGEVT--TREDPEGRPTVFESLPP 119

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            KG +     RLD  T+G+L+       A  +        +++ Y   V       +E +
Sbjct: 120 LKGARWIAVGRLDINTTGLLLATTDGELANAM--MHPSFEVEREYVVRVRA--PEGEEKV 175

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           ++ ++ +   G     V  ++       I              W  +    GR  ++R  
Sbjct: 176 SDAIIDRLGRG-----VALEDGPAKFDEIERI----GGTDSHDWFRVVVKEGRNREVRRL 226

Query: 259 ALHMGC 264
               GC
Sbjct: 227 WESQGC 232


>gi|88798249|ref|ZP_01113835.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Reinekea sp. MED297]
 gi|88779025|gb|EAR10214.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Reinekea sp. MED297]
          Length = 282

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 61/176 (34%), Gaps = 31/176 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+ +         +   +++ + SG+V+V+ +  K  +++     +R+           
Sbjct: 6   ERIQKVLAKAGQG-SRREMERAIESGRVQVNGEVAKLGDKVSEKDELRLD---------- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                      ++  ++ ++ +L+Y        NKP G           H          
Sbjct: 55  --------GKKISVEAEKVRRVLIY--------NKPEGEICTRKDPEGRH--TVFDRLPR 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             G++     RLD  TSG+L+       A  L       +I++ Y   V G  + +
Sbjct: 97  IPGERWIAVGRLDINTSGLLLFTNDGELANRL--MHPSHQIEREYAVRVLGDVQQE 150


>gi|303249716|ref|ZP_07335920.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|307251902|ref|ZP_07533803.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|302651283|gb|EFL81435.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|306860594|gb|EFM92606.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
          Length = 230

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 39/282 (13%), Positives = 85/282 (30%), Gaps = 70/282 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      + L+SG V V+ K  K  + ++ G                
Sbjct: 1   MRLDKFIAEN-TGLTRSQAARALKSGLVTVNGKLEKSGS-VKIGDT-------------- 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKI-YVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                 + YE  ++ +V      +  +    +  H DG   +  
Sbjct: 45  --------------------DEICYEGERLEWVDEGQYFMLYKPQGYVCSHDDGEYPTVF 84

Query: 138 DSKGQ----KPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              G     K     RLD +T+G++++    + + +  +      +   +  +       
Sbjct: 85  QFFGYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHRITSPKHHCEKTYLVTLA------- 137

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + ++  KK   G       +         I  + V            +    GR 
Sbjct: 138 ---DPVEDFYAKKLAEGILLRGEREPCLPAKMEVIDDYNV-----------NLTISEGRY 183

Query: 253 HQLRVHALHMGCPI-------VGDHKYCANFKGNFTSPIQNK 287
           HQ++     +G  +       +GD     N +     P+  +
Sbjct: 184 HQVKRMFAALGNKVEALHRWRIGDVVLDENLEEGEYRPLSEQ 225


>gi|255533735|ref|YP_003094107.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
 gi|255346719|gb|ACU06045.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
          Length = 348

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 30/246 (12%), Positives = 72/246 (29%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       + +     + +  G V ++ K+ K  +++  G +V +         + 
Sbjct: 7   RLNKYISE--SGLCSRRAADRYIEQGNVYINGKKAKVGDKVFFGDIVTVNGQTIDPKEV- 63

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    E+S +  +NKP GI+    +G+  +I   +     
Sbjct: 64  -------------------------ENSVLIAYNKPVGITSTTEAGVKGNIVDHVNH--- 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD+++ G++ +         +  +      + +                
Sbjct: 96  --SERVFPIGRLDKDSQGLIFLTNNGDLVNKILRAGNNHEKEYV--------------VT 139

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N  L    I G    V           +          +     ++    G   Q+R  
Sbjct: 140 VNKPLTDQFITGMAKGVPVLGVMTKKCKV--------VKESPLIFKITLIQGLNRQIRRM 191

Query: 259 ALHMGC 264
             + G 
Sbjct: 192 CEYFGY 197


>gi|146081861|ref|XP_001464379.1| hypothetical protein [Leishmania infantum JPCM5]
 gi|134068471|emb|CAM66761.1| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 516

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 31/118 (26%), Positives = 48/118 (40%), Gaps = 8/118 (6%)

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-----GDYVHV 215
            RT  A     +  RMR++ +   +   G      + ++     +   G      D    
Sbjct: 282 GRTPEAVAA--KHKRMRQLTRGGGTASVGALAAALQPVSGAGAAQPARGTSTALSDSSRR 339

Query: 216 VKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+Q  +    A +  +V+   A      ++    TGRTHQLRVH   +G PIV D KY
Sbjct: 340 VQQYLETLRSAETALQVMHYDAATDQTVVKCTLGTGRTHQLRVHLASLGHPIVHDSKY 397


>gi|33602225|ref|NP_889785.1| hypothetical protein BB3249 [Bordetella bronchiseptica RB50]
 gi|33576663|emb|CAE33741.1| conserved hypothetical protein [Bordetella bronchiseptica RB50]
          Length = 593

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 40/258 (15%), Positives = 78/258 (30%), Gaps = 59/258 (22%)

Query: 19  MRLDRWFKNH--YPHI----------NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            RL ++  +    P +          +   +++++ +G+V V+ +      R+     VR
Sbjct: 111 QRLGKYLNSEAVMPKLHKVLADAGIGSRREMEELIVAGRVSVNGEPAHIGQRVAPNDQVR 170

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGI 125
           +     A  +  K  ++                 +LY        +KPAG I      G 
Sbjct: 171 VNGKPIARPNAKKPPRV-----------------ILY--------HKPAGEIVSHDDPGG 205

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                         +  K     RLD  T G+L+   +   A  +         ++ Y  
Sbjct: 206 R---ASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSGDMANRI--MHPRYGTEREYAV 260

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G   + +        +KS   G          +    A   F+ +        W  +
Sbjct: 261 RVLGEMDDAQ--------RKSLTEG-------IELEDGKAAFGSFEYLGGDGSNR-WYRV 304

Query: 246 QPHTGRTHQLRVHALHMG 263
               GR  ++R     +G
Sbjct: 305 TLQEGRNREVRRMFEAVG 322


>gi|33596480|ref|NP_884123.1| hypothetical protein BPP1859 [Bordetella parapertussis 12822]
 gi|33566249|emb|CAE37160.1| conserved hypothetical protein [Bordetella parapertussis]
          Length = 592

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 40/258 (15%), Positives = 78/258 (30%), Gaps = 59/258 (22%)

Query: 19  MRLDRWFKNH--YPHI----------NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            RL ++  +    P +          +   +++++ +G+V V+ +      R+     VR
Sbjct: 111 QRLGKYLNSEAVMPKLHKVLADAGIGSRREMEELIVAGRVSVNGEPAHIGQRVAPNDQVR 170

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGI 125
           +     A  +  K  ++                 +LY        +KPAG I      G 
Sbjct: 171 VNGKPIARPNAKKPPRV-----------------ILY--------HKPAGEIVSHDDPGG 205

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                         +  K     RLD  T G+L+   +   A  +         ++ Y  
Sbjct: 206 R---ASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSGDMANRI--MHPRYGTEREYAV 260

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G   + +        +KS   G          +    A   F+ +        W  +
Sbjct: 261 RVLGEMDDAQ--------RKSLTEG-------IELEDGKAAFGSFEYLGGDGSNR-WYRV 304

Query: 246 QPHTGRTHQLRVHALHMG 263
               GR  ++R     +G
Sbjct: 305 TLQEGRNREVRRMFEAVG 322


>gi|93005736|ref|YP_580173.1| 23S rRNA pseudouridine synthase F [Psychrobacter cryohalolentis K5]
 gi|92393414|gb|ABE74689.1| ribosomal large subunit pseudouridine synthase F [Psychrobacter
           cryohalolentis K5]
          Length = 328

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 73/249 (29%), Gaps = 56/249 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +  +  + +  G V ++ KR    +++ +G  V++   +       
Sbjct: 8   RLNKYISE--SGICSRRDADRFIEQGNVYLNGKRAAVGDQVVAGDTVKVNGQLIEPKEA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D    V NKP GI     S    +I  F++  V 
Sbjct: 65  -------------------------DDFVFIVLNKPVGIVSTTESSEKNNIVDFVRHSV- 98

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++ +         +  +      + +                
Sbjct: 99  ----RIFPIGRLDKDSQGLIFLTSNGDLVNKVLRAGNNHEKEYL--------------VT 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N  L  S I G    V    +      ++                +    G   Q+R  
Sbjct: 141 VNKPLTDSVIEGLAGGVPMLGKMTKKCPVTKVAP--------NVFNITLVQGLNRQIRRM 192

Query: 259 ALHMGCPIV 267
             H G  +V
Sbjct: 193 CEHFGYEVV 201


>gi|295426293|ref|ZP_06818953.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           amylolyticus DSM 11664]
 gi|295064032|gb|EFG54980.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           amylolyticus DSM 11664]
          Length = 239

 Score = 63.1 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 44/254 (17%), Positives = 86/254 (33%), Gaps = 60/254 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++ +G+VRVD K V K   ++ +   + +          
Sbjct: 4   ERLQKVIAEA-GIASRRKAEKMIVAGRVRVDGKLVTKLGTKVDTFSTITVD--------- 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKS 135
                  D  +               E    Y+F KP G+        G        +  
Sbjct: 54  -------DEPIER-------------ESLHTYLFYKPRGVVSTAHDDKGRK-----TVVD 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + D    +     RLD +TSG+L++      A  L        + K+Y + + GI +   
Sbjct: 89  YFDDLPYRLYPVGRLDYDTSGLLLMTNDGKLANLL--MHPKNEVPKVYVAKIEGILEP-- 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDC-FAQKFCWLEMQPHTGRT 252
                          D +  +K+  K  G   A +  K++     +    +++  H G  
Sbjct: 145 ---------------DQIMTLKKGVKVDGRKCAPAKVKILKTNQKKNNQIVQLTIHEGHY 189

Query: 253 HQLRVHALHMGCPI 266
           H+++     +G P+
Sbjct: 190 HEVKRMFKAVGHPV 203


>gi|268319598|ref|YP_003293254.1| hypothetical protein FI9785_1123 [Lactobacillus johnsonii FI9785]
 gi|262397973|emb|CAX66987.1| conserved hypothetical protein [Lactobacillus johnsonii FI9785]
          Length = 239

 Score = 63.1 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 87/250 (34%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++ +GQV V+ K+V     +++    + +       N +
Sbjct: 3   ERLQKVIAQA-GVASRRKAEKMISAGQVTVNGKKVTELGTKVEPRDKIEV-------NGV 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
             E++ L                        Y+F KP G+  SV    G        +  
Sbjct: 55  PIEKEAL----------------------HTYLFYKPRGVISSVSDDKGRK-----TVVD 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +    +     RLD +TSG+L++      A  L        + K+Y + + GI   ++
Sbjct: 88  FFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANKL--MHPRNEVPKVYVAKIKGILSTEE 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQ 254
                             H V+ + +    A +  K++    +K    +++  H G  HQ
Sbjct: 146 I-------------RSLTHGVRIDGR--KSAPAKLKILKTDEKKKTQIVQLTIHEGHYHQ 190

Query: 255 LRVHALHMGC 264
           ++     +  
Sbjct: 191 VKRMFEAVHH 200


>gi|227889866|ref|ZP_04007671.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
 gi|227849730|gb|EEJ59816.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
          Length = 244

 Score = 63.1 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 87/250 (34%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++ +GQV V+ K+V     +++    + +       N +
Sbjct: 8   ERLQKVIAQA-GIASRRKAEKMITAGQVTVNGKKVTELGTKVEPSDKIEV-------NGV 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
             E++ L                        Y+F KP G+  SV    G        +  
Sbjct: 60  PIEKEAL----------------------HTYLFYKPRGVISSVSDDKGRK-----TVVD 92

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +    +     RLD +TSG+L++      A  L        + K+Y + + GI   ++
Sbjct: 93  FFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANKL--MHPRNEVPKVYVAKIKGILSPEE 150

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQ 254
                             H V+ + +    A +  K++    +K    +++  H G  HQ
Sbjct: 151 I-------------RSLTHGVRIDGR--KSAPAKLKILKTDEKKKTQIVQLTIHEGHYHQ 195

Query: 255 LRVHALHMGC 264
           ++     +  
Sbjct: 196 VKRMFEAVHH 205


>gi|313682886|ref|YP_004060624.1| ribosomal small subunit pseudouridine synthase a [Sulfuricurvum
           kujiense DSM 16994]
 gi|313155746|gb|ADR34424.1| ribosomal small subunit pseudouridine synthase A [Sulfuricurvum
           kujiense DSM 16994]
          Length = 234

 Score = 63.1 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 85/251 (33%), Gaps = 51/251 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVR-VDKKRVKFNNRIQSGQVVRIPPVINALN 75
             +RLD+   +   + +   +  ++R G +       +K + ++             + +
Sbjct: 3   SKLRLDKLLSS-LGYCSRREVALLIREGIITHAHNLPLKSDTKV-------------SHD 48

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
            I+ E + LD    +                 + + +KPAG+      G    +   L  
Sbjct: 49  EILCEGEPLDPPQGI-----------------VILMHKPAGLVCSHDDGEGKLVYDLLPE 91

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               +  K     RLD++TSG+L++    A    LT      ++ K+Y + +    K  +
Sbjct: 92  RWRLRDPKISTVGRLDKDTSGLLLLTDDGALLHRLT--SPKHKVPKVYEARLDRALKGDE 149

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I                 +  N +      +   VID        + ++   GR HQ+
Sbjct: 150 AEIFA------------SGTLMLNGEKTPCLPAKLTVIDD-----THVTLEIVEGRYHQV 192

Query: 256 RVHALHMGCPI 266
           R     +G  +
Sbjct: 193 RRMFAAVGNHV 203


>gi|126207576|ref|YP_001052801.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           pleuropneumoniae L20]
 gi|126096368|gb|ABN73196.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
          Length = 231

 Score = 63.1 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 39/179 (21%), Positives = 69/179 (38%), Gaps = 22/179 (12%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            LK  L +ED+ + +FNKP  +  Q            LK ++      P    RLD+++ 
Sbjct: 29  PLKPQLSFEDTVVVLFNKPFDVLTQ---FTDEQGRQTLKDFIPIPQIYP--VGRLDRDSE 83

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHI 208
           G+L++         L      ++  K Y + V GIP+        K   + + L K +  
Sbjct: 84  GLLLLTNNGEVQHRLANPKFEKQ--KTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAK- 140

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   K          +  K+ +       W+E++ H G+  Q+R    H+G P +
Sbjct: 141 -------AKAISAPNYEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTL 192


>gi|302546514|ref|ZP_07298856.1| pseudouridine synthase RluB [Streptomyces hygroscopicus ATCC 53653]
 gi|302464132|gb|EFL27225.1| pseudouridine synthase RluB [Streptomyces himastatinicus ATCC
           53653]
          Length = 226

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 41/234 (17%), Positives = 75/234 (32%), Gaps = 48/234 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +    + ++   +V V+ K V                       +  E+  +        
Sbjct: 3   SRRACEDLIDQARVEVNGKIVT-----------------EQGLRVDPEKDEIKVDGLTVA 45

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
              +L           +  NKPAG+             G    +V ++  +     RLD 
Sbjct: 46  TQSYL----------FFALNKPAGVVSTMEDPDGRQCLG---DYVTNRETRLFHVGRLDT 92

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
           ET GI+++      A  LT       ++K Y + + G            L K+   G + 
Sbjct: 93  ETEGIILLTNHGELAHRLT--HPRYGVKKTYLAAIQGPLPRD-------LGKQLKNGIEL 143

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                + +        HFKV+    + +  +E+  H GR H +R      G P+
Sbjct: 144 EDGYARAD--------HFKVVQNTGKNY-LVEVSLHEGRKHIVRRMLSEAGFPV 188


>gi|212550926|ref|YP_002309243.1| ribosomal large subunit pseudouridine synthase B [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
 gi|212549164|dbj|BAG83832.1| putative ribosomal large subunit pseudouridine synthase B
           [Candidatus Azobacteroides pseudotrichonymphae
           genomovar. CFP2]
          Length = 290

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 46/285 (16%), Positives = 91/285 (31%), Gaps = 58/285 (20%)

Query: 6   YVQYVVVENDEEN-MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
            ++Y  VE +    +RL+R+  N    + +     K +++G V+ +   V  F  R+   
Sbjct: 41  KIKYYKVEPNSNGPIRLNRYLAN--SGLCSRRKADKYIQTGLVKKNGIPVTEFGTRVNRT 98

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             +     +    H +                               + NKP        
Sbjct: 99  DNITFCNSLVRSEHKV-----------------------------YLLLNKPKNCVT--T 127

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +         +     +  ++     RLD+ T+G+L++      +  LT    M++    
Sbjct: 128 TNDPQGRLTVMDLIKTACKEQIFPVGRLDRNTTGVLLLTNDGKLSAKLTHPRHMKKKIYH 187

Query: 183 YWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            W L  GI     + ++  + L+   I  D +  V   +K                    
Sbjct: 188 VW-LNRGIDAADIKKLSKGIQLEDGGIWADDISYVNDKDK-------------------T 227

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVG-DHKYCANFKGNFTSPIQ 285
            + ++ H+GR H +R     +G  +V  D  Y A          Q
Sbjct: 228 QINIEIHSGRNHIIRRMFESLGYHVVKLDRVYFAGLTKKKLKKGQ 272


>gi|304311685|ref|YP_003811283.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium HdN1]
 gi|301797418|emb|CBL45638.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium HdN1]
          Length = 248

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 38/261 (14%), Positives = 82/261 (31%), Gaps = 54/261 (20%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
             ++E  RLDR+       ++    +K + +G+V ++    +  + +I     V      
Sbjct: 9   TPNQERQRLDRFLSQS-GRLSRSMARKAILAGEVTINGTLCRDASTKIGPNDTVHHHH-- 65

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                                       I++       + +KP G+      G    +  
Sbjct: 66  ---------------------------DIVVAPSHHYLMLHKPEGVVCATEDGRHRTVID 98

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L    +       +  RLD +T+G++++      +  +T     +  +           
Sbjct: 99  LL---GEPWRSDLHIAGRLDIDTTGLVLLTSDGDWSHRVTSPRHNKAKRYHV-------- 147

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                  A+ +        +   ++    K    A    +++D F    C  E     GR
Sbjct: 148 -----TTADPIASSWCASFEQGVMLDGETKLTRPA--QLEILDEFHANLCLQE-----GR 195

Query: 252 THQLRVHALHMGCPIVGDHKY 272
            HQ++     MG  +V  H+Y
Sbjct: 196 YHQVKRMFAAMGTRVVKLHRY 216


>gi|322497782|emb|CBZ32858.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 516

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 31/118 (26%), Positives = 48/118 (40%), Gaps = 8/118 (6%)

Query: 161 ARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG-----GDYVHV 215
            RT  A     +  RMR++ +   +   G      + ++     +   G      D    
Sbjct: 282 GRTPEAVAA--KHKRMRQLTRGGGTASVGALAAALQAVSGAGAAQPARGTSTALSDSSRR 339

Query: 216 VKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           V+Q  +    A +  +V+   A      ++    TGRTHQLRVH   +G PIV D KY
Sbjct: 340 VQQYLETLRSAKTALQVMHYDAATDQTVVKCTLGTGRTHQLRVHLASLGHPIVHDSKY 397


>gi|308069544|ref|YP_003871149.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) [Paenibacillus polymyxa E681]
 gi|305858823|gb|ADM70611.1| Ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) [Paenibacillus polymyxa E681]
          Length = 252

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 34/253 (13%), Positives = 77/253 (30%), Gaps = 55/253 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++++G V V+   V                         
Sbjct: 2   ERLQKILAQA-GVASRRKCEELIQAGSVEVNGVIVT------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 +         D +      +  E     + NKP G+     S         +  
Sbjct: 37  ------ELGTKADPDQDMITVKGRPIKTEKKIYLMMNKPKGVIT---SASDPEGRKIVSD 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-NK 194
           ++    ++     RLD +T G+L++      A  LT       + K Y + V G+P   +
Sbjct: 88  YLKGVKERVYPVGRLDYDTEGLLLLTNDGEFANLLT--HPKHHVPKTYVATVKGVPHGTE 145

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + +   ++ +  I        K  +     ++               +++  + GR  Q
Sbjct: 146 LDKLKKGIVLEDGITAPAEVEYKDVDPNGKESV---------------IQITIYEGRNRQ 190

Query: 255 LRVHALHMGCPIV 267
           +R     +  P++
Sbjct: 191 VRRMFEAISHPVI 203


>gi|46143311|ref|ZP_00135512.2| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
          Length = 232

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 39/179 (21%), Positives = 69/179 (38%), Gaps = 22/179 (12%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            LK  L +ED+ + +FNKP  +  Q            LK ++      P    RLD+++ 
Sbjct: 30  PLKPQLSFEDTVVVLFNKPFDVLTQ---FTDEQGRQTLKDFIPIPQIYP--VGRLDRDSE 84

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHI 208
           G+L++         L      ++  K Y + V GIP+        K   + + L K +  
Sbjct: 85  GLLLLTNNGEVQHRLANPKFEKQ--KTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAK- 141

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   K          +  K+ +       W+E++ H G+  Q+R    H+G P +
Sbjct: 142 -------AKAISAPNYEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTL 193


>gi|325978633|ref|YP_004288349.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|325178561|emb|CBZ48605.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 242

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 84/248 (33%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++++L+  QV V+ K                         I 
Sbjct: 1   MRLDKFLVEAGIG-SRTEVKQLLKKKQVLVNGKV-----------------------EIS 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I + +  ++     L     YE    Y+ NKP G+     +    H    L     
Sbjct: 37  PKTQIDEKADRISCQGQTLS----YEKYVYYMLNKPKGVIS---ATEDNHHKTVLDLLDK 89

Query: 139 SKGQK-PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +   K      RLD +T G+L++    + A   L+     + + K Y + V G+      
Sbjct: 90  TAWDKEVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVDKTYRAKVAGLMTTADV 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQL 255
                          + + +   +     A     +++   A++   +E+    G+ HQ+
Sbjct: 147 -------------AAFANGIDLKDFTCQPA--QLVILETNEAERTSVVEITIKEGKFHQV 191

Query: 256 RVHALHMG 263
           +      G
Sbjct: 192 KRMVQACG 199


>gi|56420818|ref|YP_148136.1| ribosomal large subunit pseudouridine synthase B [Geobacillus
           kaustophilus HTA426]
 gi|261417880|ref|YP_003251562.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|297529548|ref|YP_003670823.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|319767308|ref|YP_004132809.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
 gi|56380660|dbj|BAD76568.1| ribosomal large subunit pseudouridine synthaseB (pseudouridylate
           synthase) (uracil hydrolyase) [Geobacillus kaustophilus
           HTA426]
 gi|261374337|gb|ACX77080.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|297252800|gb|ADI26246.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|317112174|gb|ADU94666.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
          Length = 243

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 48/252 (19%), Positives = 95/252 (37%), Gaps = 54/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++  G+V+V+ + VK     + G  V++ P  +     I
Sbjct: 2   ERLQKVIARA-GIASRRKAEELILQGRVKVNGRVVK-----ELG--VKVGPRDDVEVDGI 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSW 136
             ++                     E+   Y+  KP G+  SV+   G        +  +
Sbjct: 54  PIER---------------------EEPVYYLLYKPRGVISSVKDDRGRK-----VVTDF 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++      A  L        I+K+Y + V GIP +++ 
Sbjct: 88  FKDLDKRIYPIGRLDYDTSGLLLLTNDGDFANLL--MHPRYEIEKVYIAKVKGIPTHEQ- 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQL 255
                 LK+   G           +    A +  K++     +    +E++ H GR  Q+
Sbjct: 145 ------LKRLEQGVQL--------EDGMTAPAKVKLLSADRKKGTAIVEIRIHEGRNRQV 190

Query: 256 RVHALHMGCPIV 267
           R     +GC ++
Sbjct: 191 RRMFEAIGCEVL 202


>gi|330999160|ref|ZP_08322879.1| pseudouridine synthase B, ribosomal large subunit [Parasutterella
           excrementihominis YIT 11859]
 gi|329575360|gb|EGG56904.1| pseudouridine synthase B, ribosomal large subunit [Parasutterella
           excrementihominis YIT 11859]
          Length = 313

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 46/299 (15%), Positives = 88/299 (29%), Gaps = 47/299 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
            N +L +   +     +  ++++ +  G++ V+ +      R+    V+R    I   + 
Sbjct: 10  ANEKLHKVLADAGIG-SRRDMEERIAEGRISVNGEPAHVGQRVTPSDVIRFDGRIVRRSA 68

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +                ++ +  +L+Y        +KPAG  V                 
Sbjct: 69  L---------------ENNDVPKVLIY--------HKPAGEIV--SKDDPEGRPTVFDHL 103

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               G +     RLD  T G+L+   +   A  L        I++ Y   V G    +  
Sbjct: 104 PRIGGARWIAVGRLDFNTEGLLLFTDSGNLANFL--MHPRHEIEREYAVRVQGTMSPEA- 160

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              + LLK   +           E G                   W  +    GR  ++R
Sbjct: 161 --KDKLLKGIKLDDGIAKFTTLEEGGGK-------------GFNRWYNVTLSEGRNREVR 205

Query: 257 VHALHMGCPI--VGDHKYCA-NFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLP 312
                +G P+  +   KY       +       ++        L      +   TAP P
Sbjct: 206 RMFEAVGLPVSRLIRVKYGNLELPSDLPRGKTRRMSTEETEKWLDSISYKKGMSTAPAP 264


>gi|170017037|ref|YP_001727956.1| 16S rRNA uridine-516 pseudouridylate synthase [Leuconostoc citreum
           KM20]
 gi|169803894|gb|ACA82512.1| 16S rRNA uridine-516 pseudouridylate synthase [Leuconostoc citreum
           KM20]
          Length = 249

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 49/252 (19%), Positives = 90/252 (35%), Gaps = 47/252 (18%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
            EE MRL +         +    + ++  G+V+V+ + V        G  V I   +   
Sbjct: 2   SEEEMRLQKVVAQA-GLASRRGAETMITEGRVKVNGETVTT-----LGVKVGIHDTVEVD 55

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
              I+ ++ L                 +Y     Y+ NKP G+     +         + 
Sbjct: 56  GAPIEGREKL-----------------VY-----YLLNKPRGVVT---TTSDEKGRKTVL 90

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             ++   Q+     RLD +T+G L++      A  L       R+ KIY + V GI   +
Sbjct: 91  DLLEDIDQRVYPVGRLDYDTTGALLLTNDGTIANQL--MHPKSRVDKIYLAKVSGIATVE 148

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K            +      V+ +  K A   ++  +V     +K   + +  H GR HQ
Sbjct: 149 K------------LAPLKQGVIIKGRKTAPARVTIERV--DKDKKTSMVRIIIHEGRNHQ 194

Query: 255 LRVHALHMGCPI 266
           ++     +G P+
Sbjct: 195 VKDMLQKVGLPV 206


>gi|33592372|ref|NP_880016.1| hypothetical protein BP1244 [Bordetella pertussis Tohama I]
 gi|33572017|emb|CAE41540.1| conserved hypothetical protein [Bordetella pertussis Tohama I]
 gi|332381788|gb|AEE66635.1| hypothetical protein BPTD_1234 [Bordetella pertussis CS]
          Length = 588

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 40/258 (15%), Positives = 78/258 (30%), Gaps = 59/258 (22%)

Query: 19  MRLDRWFKNH--YPHI----------NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            RL ++  +    P +          +   +++++ +G+V V+ +      R+     VR
Sbjct: 104 QRLGKYLNSEAVMPKLHKVLADAGIGSRREMEELIVAGRVSVNGEPAHIGQRVAPNDQVR 163

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGI 125
           +     A  +  K  ++                 +LY        +KPAG I      G 
Sbjct: 164 VNGKPIARPNAKKPPRV-----------------ILY--------HKPAGEIVSHDDPGG 198

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                         +  K     RLD  T G+L+   +   A  +         ++ Y  
Sbjct: 199 R---ASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSGDMANRI--MHPRYGTEREYAV 253

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G   + +        +KS   G          +    A   F+ +        W  +
Sbjct: 254 RVLGEMDDAQ--------RKSLTEG-------IELEDGKAAFGSFEYLGGDGSNR-WYRV 297

Query: 246 QPHTGRTHQLRVHALHMG 263
               GR  ++R     +G
Sbjct: 298 TLQEGRNREVRRMFEAVG 315


>gi|326390305|ref|ZP_08211864.1| pseudouridine synthase [Thermoanaerobacter ethanolicus JW 200]
 gi|325993582|gb|EGD52015.1| pseudouridine synthase [Thermoanaerobacter ethanolicus JW 200]
          Length = 241

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 42/254 (16%), Positives = 82/254 (32%), Gaps = 61/254 (24%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             MR+D+   N         ++K ++ G V V+   VK      +G +V           
Sbjct: 2   AKMRIDKLLSNIGIG-TRKEVKKFIKEGLVLVNGNTVKD-----AGLIVD---------- 45

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
             +  +IL           F    + Y++    + NKP G+       +   +   L   
Sbjct: 46  -TESDEIL-----------FDGEKINYKEFIYIMINKPKGVISATYDEVEKTVIDLLPQE 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK- 194
           +  K + P    RLD++T G+L++      A Q L+     + + K Y++ + G      
Sbjct: 94  L--KARNPFPVGRLDKDTEGLLLITNDGDLAHQLLS---PKKNVIKKYYAEILGFVNESD 148

Query: 195 -----KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                +  I     K      + +       K                     + +    
Sbjct: 149 IKAFNEGIILEDGYKTLPANLEILFSSSDVSK---------------------VYVYIRE 187

Query: 250 GRTHQLRVHALHMG 263
           G+ HQ++     +G
Sbjct: 188 GKYHQIKRMFESVG 201


>gi|294507508|ref|YP_003571566.1| ribosomal large subunit pseudouridine synthase B [Salinibacter
           ruber M8]
 gi|294343836|emb|CBH24614.1| ribosomal large subunit pseudouridine synthase B [Salinibacter
           ruber M8]
          Length = 261

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 52/284 (18%), Positives = 103/284 (36%), Gaps = 62/284 (21%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV-----R 66
            +D E MR++++   H    +  +   ++  G+V +D +RV +   R++ GQ V      
Sbjct: 17  SSDREGMRINKYIA-HAGVCSRRDADDLVEQGRVHIDGERVDQHGTRVREGQTVTVDGEE 75

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P+      + K +  + ++ +       L +I + ED+       P+G+         
Sbjct: 76  VYPLEFEYLLLNKPKDTISTTDDPKDRRTVLDAIGVPEDN-------PSGL--------- 119

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                                 RLD+ T+G+L+V+     A  L        I KIY+  
Sbjct: 120 ------------------FPVGRLDRNTTGVLLVSNDGDLAHRL--MHPRYEIPKIYYVR 159

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           +    K  +                 +  +K+  + ++ A +  +V     Q+   + ++
Sbjct: 160 LQDDVKPHQ-----------------LDQLKRGVELSDGAAAADQVAYLDPQRKTDIALE 202

Query: 247 PHTGRTHQLRVHALHMGCPIVG--DHKYCANFKGNFTSPIQNKL 288
            H GR  Q+R     +G  IV     KY     G        +L
Sbjct: 203 LHEGRNRQIRRMMEALGHTIVQLERAKYATLTTGRLQRGEWRRL 246


>gi|149002474|ref|ZP_01827408.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
          pneumoniae SP14-BS69]
 gi|147759411|gb|EDK66403.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
          pneumoniae SP14-BS69]
          Length = 64

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 12 VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
          ++ +   +RLD+   +    ++     + ++SGQV V+ +  K    +Q G VV 
Sbjct: 3  IKIETGGLRLDKALSD-LTELSRSLANEQIKSGQVLVNGQVKKAKYTVQEGDVVT 56


>gi|126697974|ref|YP_001086871.1| putative RNA pseudouridine synthase [Clostridium difficile 630]
 gi|115249411|emb|CAJ67226.1| Ribosomal small subunit pseudouridine synthase A [Clostridium
           difficile]
          Length = 240

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 37/246 (15%), Positives = 82/246 (33%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D+   N   + +   ++K  + G V V+   V        G  V             
Sbjct: 5   QRIDKILSN-LGYGSRSEIKKYCKQGSVVVNGSEVS-----NPGTQVD-----------T 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  +IL +              ++Y +    + NKP G            +   +   + 
Sbjct: 48  ENDEILFNGEE-----------VIYREYIYLMMNKPDGYISATTDKYDPTVLDLID--LS 94

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +P    RLD++T G+LV+    + + + L+     + + K Y++ + G+   +   
Sbjct: 95  YLAFEPFPVGRLDKDTEGLLVLTNDGKLSHRVLS---PKKHVPKTYYAKIDGVVTEED-- 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +  +L                         S   ++   +     +E+  H G+ HQ++ 
Sbjct: 150 VEAFLEGVVLDDRYKTMP------------SQLNILK--SDDESEIELTIHEGKFHQVKR 195

Query: 258 HALHMG 263
               +G
Sbjct: 196 MFESVG 201


>gi|170749852|ref|YP_001756112.1| pseudouridine synthase [Methylobacterium radiotolerans JCM 2831]
 gi|170656374|gb|ACB25429.1| pseudouridine synthase [Methylobacterium radiotolerans JCM 2831]
          Length = 246

 Score = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 86/248 (34%), Gaps = 45/248 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD+   N   + +   +Q + R+G +R+D   +       +G  V + P  +    + 
Sbjct: 7   VRLDKLLAN-LGYGSRREIQALARAGAIRLDGAELAD-----AGDRVALAP--DLPERLT 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + + LD    L         ++L++   +   +K AG  V           G L     
Sbjct: 59  VDGESLDPLPGL--------CLMLHKPLGVTCSHKEAGPLV----------YGLLPERWR 100

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD+ETSG+L++     A  H   S + +  ++   +L   +   + E  
Sbjct: 101 RRDPPLSTVGRLDKETSGLLLLT-DDGALLHRIISPKAQVAKRYRVTLDRPLTGREAEVF 159

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A   L         + V    E     A++                     GR HQ+R  
Sbjct: 160 AAGTLVLEGEERPLLPVRLDVEDATRCAVT------------------LTEGRYHQVRRM 201

Query: 259 ALHMGCPI 266
              +G  +
Sbjct: 202 FAAVGNHV 209


>gi|145298479|ref|YP_001141320.1| 16S rRNA uridine-516 pseudouridylate synthase [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142851251|gb|ABO89572.1| 16S rRNA uridine-516 pseudouridylate synthase [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 230

 Score = 63.1 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 94/251 (37%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +    +      K++R G+V VD   VK                     HI 
Sbjct: 1   MRLDKFLCD-CSDLTRSLAGKLIRQGEVTVDGIVVK-----------------QPAFHIN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           ++ ++    V LT          L + ++ ++ +KP G      +    H   F      
Sbjct: 43  EQSQVEFDGVMLT----------LDQRNRYFMLHKPEGYVC--SNEDPDHPTVFFLMDEP 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + G K  +  RLD +T+G+++V    + + +  +      +   ++ +         ++ 
Sbjct: 91  AMG-KLHVVGRLDLDTTGLVLVTDDGKWSHRITSPRHECAKTYHVWLA-----DPVHQDA 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I+ +         D V +  + EK      +    ++  A+  C   +  H G+ HQ++ 
Sbjct: 145 ISLF--------ADGVFLRNETEK------TRPAQLEILAE--CEARLTIHEGKYHQVKR 188

Query: 258 HALHMGCPIVG 268
               +G  +VG
Sbjct: 189 MFASIGNKVVG 199


>gi|253578001|ref|ZP_04855273.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850319|gb|EES78277.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 323

 Score = 63.1 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 34/249 (13%), Positives = 81/249 (32%), Gaps = 55/249 (22%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E +R++++        +     +++  G++ V+ K+       +SGQ V +   I A N
Sbjct: 11  DEKIRINKYLSEA-GICSRREADRMIEEGRITVNGKKA------ESGQKVSLEDEICADN 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
             + +                       E   + +FNKP GI     S      +  +  
Sbjct: 64  IPVHKN----------------------EKKVLLLFNKPRGIVC---STKQQFDETTVTD 98

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           ++D    +     RLD+E+ G+L++         +  +      +               
Sbjct: 99  YLD-YPLRVYPVGRLDKESQGLLLLTNEGDLVNKIMRAGNYHEKEY-------------- 143

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                ++     +  ++V  + +     +      +V+       C   +    G   Q+
Sbjct: 144 -----FVTVNKPVDREFVRRMSKGVPVLDTVTRPCRVVQT---GECSFRIILTQGLNRQI 195

Query: 256 RVHALHMGC 264
           R    ++G 
Sbjct: 196 RRMCRYLGY 204


>gi|254468122|ref|ZP_05081528.1| ribosomal large subunit pseudouridine synthase B [beta
           proteobacterium KB13]
 gi|207086932|gb|EDZ64215.1| ribosomal large subunit pseudouridine synthase B [beta
           proteobacterium KB13]
          Length = 257

 Score = 63.1 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 35/234 (14%), Positives = 82/234 (35%), Gaps = 34/234 (14%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           ++  +  R+ ++  N     +  +++++++  ++ V++K +   + +   +++ I     
Sbjct: 9   DSGNKKERIQKFLANMGMG-SRRSIEELIKQKKITVNQKPIDLGHMVYGNEIIHINGRRI 67

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDG 131
              +  K +                        S++ +++KP G I          H   
Sbjct: 68  YFKNAEKRE------------------------SRLIIYHKPEGEIVSHSDPK---HQKT 100

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             +     K  K     RLD  TSG+L++      A H+      ++I + Y   + G  
Sbjct: 101 VFQKLPKVKNGKWISIGRLDINTSGLLLITNDGKLANHM--MHPSQQIDREYSVRILGEV 158

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
             +   I N + K   +     HV      G   A   F++I    +      +
Sbjct: 159 TEE---IINNIRKGVKLDDGVAHVDTFEHTGGEGANQWFRIILKEGRNREIRRL 209


>gi|307260542|ref|ZP_07542235.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 12
           str. 1096]
 gi|306869771|gb|EFN01555.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 12
           str. 1096]
          Length = 231

 Score = 63.1 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 39/179 (21%), Positives = 69/179 (38%), Gaps = 22/179 (12%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            LK  L +ED+ + +FNKP  +  Q            LK ++      P    RLD+++ 
Sbjct: 29  PLKPQLSFEDTVVVLFNKPFDVLTQ---FTDEQRRQTLKDFIPIPQIYP--VGRLDRDSE 83

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHI 208
           G+L++         L      ++  K Y + V GIP+        K   + + L K +  
Sbjct: 84  GLLLLTNNGEIQHRLANPKFEKQ--KTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAK- 140

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   K          +  K+ +       W+E++ H G+  Q+R    H+G P +
Sbjct: 141 -------AKAISAPNYEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTL 192


>gi|218663826|ref|ZP_03519756.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli IE4771]
          Length = 267

 Score = 63.1 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 35/253 (13%), Positives = 73/253 (28%), Gaps = 50/253 (19%)

Query: 13  ENDEENMR--LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
             D    R  L R       + +    ++++  G+V VD + V                 
Sbjct: 17  TADAAGKRVTLPRALSK-LGYCSRTQAERLIAEGRVSVDGRTVN---------------D 60

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
            +A   ++  +  +D              ++  E     + NKP G+             
Sbjct: 61  PSAWVDLVTAEIRVDG------------LVIAAEAKIYLMLNKPRGLVT--TRHDPEGRP 106

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                  D +        RLD+ + G+L+       AQ L +       +  +  +    
Sbjct: 107 TVYDCLKDFEIPHLSPVGRLDKASEGLLLFTNDTEFAQILLDPI-THVTKTYHVQI---- 161

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                    + ++    I      +    E     A+   +       +  W+E++   G
Sbjct: 162 ---------DRIMDDEAIAAMTSGIRHDGELLTATAVRRLR----QGDRNSWIEVELDEG 208

Query: 251 RTHQLRVHALHMG 263
           R  Q+R     +G
Sbjct: 209 RNRQIRRMLEALG 221


>gi|329946750|ref|ZP_08294162.1| pseudouridylate synthase [Actinomyces sp. oral taxon 170 str.
           F0386]
 gi|328526561|gb|EGF53574.1| pseudouridylate synthase [Actinomyces sp. oral taxon 170 str.
           F0386]
          Length = 324

 Score = 63.1 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 42/258 (16%), Positives = 85/258 (32%), Gaps = 55/258 (21%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RL +    H    +    ++++  G+V VD               + +      ++ 
Sbjct: 76  SGQRLQKVLA-HAGVASRRACEQLIADGRVSVDG--------------ITVTEPGVRVDP 120

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDG 131
           + +E ++  S +        L            + +KPAG+       +G   +A +   
Sbjct: 121 LTQEIRVDGSRILTNPELITL------------MLHKPAGVVTTMEDPEGRPTVAQYGLD 168

Query: 132 FLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG- 189
           +L    +     +     RLD ET G+L+++     +  L        I K Y ++V G 
Sbjct: 169 YLAEHPELPDSLRLVHVGRLDTETEGLLLLSNDGELSHRL--MHPSFEIAKTYVAIVEGQ 226

Query: 190 -IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
             P   ++      L+      D V V     +G                    +E+  H
Sbjct: 227 VEPWVPRKLRRGIALEDGETRADRVTVKDSGPRG------------------SIVEITLH 268

Query: 249 TGRTHQLRVHALHMGCPI 266
           +G+   +R     +G P+
Sbjct: 269 SGKNRIVRRMLDAVGHPV 286


>gi|306831693|ref|ZP_07464850.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|304426118|gb|EFM29233.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
          Length = 253

 Score = 63.1 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 84/248 (33%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++++L+  QV V+ K                         I 
Sbjct: 12  MRLDKFLVEAGIG-SRTEVKQLLKKKQVLVNGKV-----------------------EIS 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I + +  ++     L     YE    Y+ NKP G+     +    H    L     
Sbjct: 48  PKTQIDEKADRISCQGQTLS----YEKYVYYMLNKPKGVIS---ATEDNHHKTVLDLLDK 100

Query: 139 SKGQK-PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +   K      RLD +T G+L++    + A   L+     + + K Y + V G+      
Sbjct: 101 TAWDKEVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVDKTYRAKVAGLMTTADV 157

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQL 255
                          + + +   +     A     +++   A++   +E+    G+ HQ+
Sbjct: 158 -------------AAFANGIDLKDFTCQPA--QLVILETNEAERTSVVEITIKEGKFHQV 202

Query: 256 RVHALHMG 263
           +      G
Sbjct: 203 KRMVQACG 210


>gi|288905607|ref|YP_003430829.1| ribosomal small subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
 gi|288732333|emb|CBI13903.1| ribosomal small subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
          Length = 242

 Score = 63.1 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 83/247 (33%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++++L+  QV V+ K                         I 
Sbjct: 1   MRLDKFLVEAGIG-SRTEVKQLLKKKQVLVNGKV-----------------------EIS 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I + +  ++     L     YE    Y+ NKP G+           +   L     
Sbjct: 37  PKTQIDEKADRISCQGQTLS----YEKYVYYMLNKPKGVISATEDNHHKTVLDLLDKIAW 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++    + A   L+     + + K Y + V G+       
Sbjct: 93  DK--EAFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVDKTYRAKVAGLMTTADV- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLR 256
                         + + +   +     A     +++   A++   +E+    G+ HQ++
Sbjct: 147 ------------AAFANGIDLKDFTCQPA--QLVILETNEAERTSVVEITIKEGKFHQVK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVQACG 199


>gi|212696243|ref|ZP_03304371.1| hypothetical protein ANHYDRO_00779 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676872|gb|EEB36479.1| hypothetical protein ANHYDRO_00779 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 115

 Score = 63.1 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 2/82 (2%)

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
           + +  KG    I+ F  ++     F  LE +  TG+THQ+R        PI+GD KY   
Sbjct: 1   MVKGNKGGKRIITKFYPLESK-NNFTLLECELITGKTHQIRYSLHKNSTPIIGDRKYS-K 58

Query: 276 FKGNFTSPIQNKLYLHARYMDL 297
            K N+     N   L A  +  
Sbjct: 59  SKINYKKINLNSQALLAYKLVF 80


>gi|217978386|ref|YP_002362533.1| pseudouridine synthase [Methylocella silvestris BL2]
 gi|217503762|gb|ACK51171.1| pseudouridine synthase [Methylocella silvestris BL2]
          Length = 255

 Score = 63.1 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 78/249 (31%), Gaps = 45/249 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLDR   N   +     +Q +  +G++++D   ++          +R+         + 
Sbjct: 11  LRLDRLLAN-LGYGTRTQMQAMAHAGRIKLDGAALRDPA-------LRVAATPEFCARLS 62

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              + LD    +                 +   NKP G++           D  L     
Sbjct: 63  INGEALDPPPGM-----------------VIALNKPRGVTCSRKEAGPLVFD-LLPPRFR 104

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++TSG+L++    A    L        I K Y + +    +  +  I
Sbjct: 105 LREPALSTVGRLDKDTSGLLLITDDGALLHRL--ISPKHNIAKRYCAKLARPLRGDEAEI 162

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                           ++    K    A+   +V+     +    E     GR HQ+R  
Sbjct: 163 FA----------SGEMMLDDEAKPLLPAV--LRVLSPTEAEVSVTE-----GRYHQIRRM 205

Query: 259 ALHMGCPIV 267
               G  ++
Sbjct: 206 FAATGNHVL 214


>gi|313680897|ref|YP_004058636.1| ribosomal large subunit pseudouridine synthase b [Oceanithermus
           profundus DSM 14977]
 gi|313153612|gb|ADR37463.1| ribosomal large subunit pseudouridine synthase B [Oceanithermus
           profundus DSM 14977]
          Length = 252

 Score = 63.1 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 79/251 (31%), Gaps = 55/251 (21%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + +RL ++        +    + ++R+G+V V+   V    R+  G  VR+      L  
Sbjct: 5   DGIRLQKYLVLAGAAPSRRKAEDLIRAGRVSVNGAVVGLGARVYPGDEVRVGGRRAEL-- 62

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKS 135
              E+++                        +   +KP G  + +     A  +   L  
Sbjct: 63  --PERRV------------------------VLALHKPKGYETTRQSRSGAPTVYELLPD 96

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                        RLD+++ G+L+     A  Q LT      +     WS     P +  
Sbjct: 97  L-----PGLHPVGRLDRDSEGLLLFTNDGALTQRLTHPRYGVKKVYRVWSRKGTPPPDLL 151

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +   L+ KS   G  V  +K   K     I+                     G+  ++
Sbjct: 152 RKLERGLVLKS---GVRVQALKARPKDGGAVIT------------------LTEGKKREV 190

Query: 256 RVHALHMGCPI 266
           R     +G P+
Sbjct: 191 RYMMAAIGYPV 201


>gi|257469264|ref|ZP_05633358.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           ulcerans ATCC 49185]
 gi|317063511|ref|ZP_07927996.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           ulcerans ATCC 49185]
 gi|313689187|gb|EFS26022.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           ulcerans ATCC 49185]
          Length = 236

 Score = 63.1 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 85/251 (33%), Gaps = 50/251 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E MR++++  +     +   + K++  G ++V+ ++     ++     + I         
Sbjct: 2   EEMRINKYLAS-LGIASRREVDKMIEEGAIKVNGEKAAPGIKVSDEDEIYI--------- 51

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
             K +KI  ++                E    Y+ NKP  + V   S         +   
Sbjct: 52  --KGKKIEKNT----------------EKKVYYILNKP--LEVLSSSKDDRGRKTVVD-- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +    ++     RLD  TSG++++         +        I K Y++ V+G  K +  
Sbjct: 90  LIKCKERIFPIGRLDYNTSGLIILTNDGELFNRIIHPKAE--IFKEYYAKVFGEIKEEN- 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                LL+K     D + +    +            I    +    L +    GR  Q+R
Sbjct: 147 ---AELLRKGVELDDGMTLPANVK------------ILRRERGKTELLVAIREGRNRQVR 191

Query: 257 VHALHMGCPIV 267
                +  P++
Sbjct: 192 RMLDKINHPVI 202


>gi|271500910|ref|YP_003333935.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270344465|gb|ACZ77230.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 232

 Score = 62.7 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 83/249 (33%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + LR+ +V V+ + VK      SG    +P    A +  +
Sbjct: 1   MRLDKFLSQQL-GISRSLIVRELRAQRVTVNGEVVK------SGAFKLLPEHEVAFDGNV 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ+                          ++ NKP G      S         L    +
Sbjct: 54  LEQQNGPR---------------------YFMLNKPQGYVC---STDDPDHPTILYFIDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +TSG++++           +     RI               ++ +
Sbjct: 90  PVAHKLHAAGRLDIDTSGLVLLT---------DDGQWSHRITSPKHHCEKTYLVTLEQPL 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A    +K   G     V   NEK     ++    ++  ++    + +    GR HQ++  
Sbjct: 141 AADTAEKFQAG-----VQLHNEKN----LTRPATLEVLSEHQ--VRLTITEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAIGNHVV 198


>gi|289422766|ref|ZP_06424605.1| RNA pseudouridine synthase family protein [Peptostreptococcus
           anaerobius 653-L]
 gi|289156821|gb|EFD05447.1| RNA pseudouridine synthase family protein [Peptostreptococcus
           anaerobius 653-L]
          Length = 244

 Score = 62.7 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 87/246 (35%), Gaps = 44/246 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   +     ++K  + G VRV+    K ++                  H+ 
Sbjct: 1   MRLDKLLGN-LGYGTRSEIKKYCKQGFVRVNGAEAKKSD-----------------VHVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   +  +  L  + +F+            + NKPAG      +   Y          +
Sbjct: 43  PENDEIVFNGELVNYREFV----------YLLLNKPAGYVS--ATFDKYDPTVIDLIGEE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +P    RLD++T G+LV+    + + + L+       + K Y+++   I K   + 
Sbjct: 91  YLPFEPFPVGRLDKDTEGLLVITNDGKLSHRVLS---PKNHVPKKYYAI---IDKEVDDM 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                 K  +IG DY        K +   + +    +  +     + +    G+ HQ++ 
Sbjct: 145 DVRIFEKGVYIGEDY------TTKPSKLEVLNPFEFEDGSLG-SEVHVTISEGKFHQVKR 197

Query: 258 HALHMG 263
               +G
Sbjct: 198 MFEAVG 203


>gi|165975545|ref|YP_001651138.1| pseudouridylate synthase [Actinobacillus pleuropneumoniae serovar 3
           str. JL03]
 gi|303250222|ref|ZP_07336423.1| pseudouridylate synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|303251911|ref|ZP_07338082.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|307244890|ref|ZP_07526988.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|307247067|ref|ZP_07529120.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|307251610|ref|ZP_07533516.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|165875646|gb|ABY68694.1| probable pseudouridylate synthase [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|302649341|gb|EFL79526.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|302650933|gb|EFL81088.1| pseudouridylate synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
 gi|306854212|gb|EFM86419.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 1
           str. 4074]
 gi|306856436|gb|EFM88586.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 2
           str. S1536]
 gi|306860921|gb|EFM92928.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 6
           str. Femo]
          Length = 231

 Score = 62.7 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 39/179 (21%), Positives = 69/179 (38%), Gaps = 22/179 (12%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            LK  L +ED+ + +FNKP  +  Q            LK ++      P    RLD+++ 
Sbjct: 29  PLKPQLSFEDTVVVLFNKPFDVLTQ---FTDEQGRQTLKDFIPIPQIYP--VGRLDRDSE 83

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHI 208
           G+L++         L      ++  K Y + V GIP+        K   + + L K +  
Sbjct: 84  GLLLLTNNGEIQHRLANPKFEKQ--KTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAK- 140

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   K          +  K+ +       W+E++ H G+  Q+R    H+G P +
Sbjct: 141 -------AKAISAPNYEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTL 192


>gi|302037904|ref|YP_003798226.1| pseudouridine synthase, rsuA family [Candidatus Nitrospira
           defluvii]
 gi|300605968|emb|CBK42301.1| Pseudouridine synthase, rsuA family [Candidatus Nitrospira
           defluvii]
          Length = 255

 Score = 62.7 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 80/247 (32%), Gaps = 51/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           M LDR         +    Q+ +R+G+VR++++ V+  +       +  P     L+   
Sbjct: 1   MTLDRLLSK-LGIASRSQAQEWIRAGRVRINRRLVRMPDT-----WIDWPGDAVTLDDRP 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWV 137
            EQ+                           +F+KP G+            I   L   +
Sbjct: 55  IEQRPPQ----------------------FILFHKPKGVVTTHQDEKGRPTIFDVLPPEL 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                      RLDQ TSG+L++      +  LT+  +  ++ ++Y   V G    +   
Sbjct: 93  KG----LHAVGRLDQATSGLLLLTNDSTLSSFLTDPKQ--QVPRLYLVTVRGEVSEETGR 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            A   +      G+ +H                  I   + +   L +    G+  ++R 
Sbjct: 147 AALDGVDDQ---GERLHCASV-------------TIQKRSGRESHLVVTLTEGKNREIRR 190

Query: 258 HALHMGC 264
               +G 
Sbjct: 191 LFKALGH 197


>gi|225389448|ref|ZP_03759172.1| hypothetical protein CLOSTASPAR_03196 [Clostridium asparagiforme
           DSM 15981]
 gi|225044495|gb|EEG54741.1| hypothetical protein CLOSTASPAR_03196 [Clostridium asparagiforme
           DSM 15981]
          Length = 121

 Score = 62.7 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 23/134 (17%), Positives = 47/134 (35%), Gaps = 20/134 (14%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRS-GQVRVDKKRVKFNNRIQS 61
           ++  V    +  D+    ++ + +      +   +  + ++ G +    + V    R+  
Sbjct: 1   MIKRVLSYAIPADQGGRTVEEFLRGL--GYSHRLVVHLKQTPGGILAGGESVFSTYRLHP 58

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           GQV+ +               + +   +       L   ++YED  I V NK AGI V  
Sbjct: 59  GQVLTVT--------------LTEEEPSRNIPPADLPLAVVYEDPDILVVNKEAGIPVHP 104

Query: 122 GSGIAYHIDGFLKS 135
             G   H    L +
Sbjct: 105 SQG---HHGNTLAN 115


>gi|307253844|ref|ZP_07535697.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
 gi|307258300|ref|ZP_07540042.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 11
           str. 56153]
 gi|306863204|gb|EFM95145.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 9
           str. CVJ13261]
 gi|306867639|gb|EFM99485.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 11
           str. 56153]
          Length = 232

 Score = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 68/177 (38%), Gaps = 22/177 (12%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            LK  L +ED+ + +FNKP  +  Q            LK ++      P    RLD+++ 
Sbjct: 30  PLKPQLSFEDTVVVLFNKPFDVLTQ---FTDEQGRQTLKDFIPIPQIYP--VGRLDRDSE 84

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHI 208
           G+L++         L      ++  K Y + V GIP+        K   + + L K +  
Sbjct: 85  GLLLLTNNGEIQHRLANPKFEKQ--KTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAK- 141

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
                   K          +  K+ +       W+E++ H G+  Q+R    H+G P
Sbjct: 142 -------AKAISAPNYEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFP 191


>gi|300787858|ref|YP_003768149.1| ribosomal large subunit pseudouridine synthase B [Amycolatopsis
           mediterranei U32]
 gi|299797372|gb|ADJ47747.1| ribosomal large subunit pseudouridine synthase B [Amycolatopsis
           mediterranei U32]
          Length = 250

 Score = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 41/255 (16%), Positives = 80/255 (31%), Gaps = 45/255 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
               + +RL +         +    + ++ +G+V VD + V                   
Sbjct: 4   SEHPDGVRLQKVLSQA-GVASRRAAEDLIVAGRVEVDGEVVT------------------ 44

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
               + +      + +++      L+  L+Y        NKP G+             G 
Sbjct: 45  ---ELGRRVDPDAAIIHVDGTRVNLRDDLIY-----LALNKPKGVHSTMSDDRGRPCVGD 96

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                  +        RLD+ T G+L++         L       R+ K Y + V G+  
Sbjct: 97  YLRGRYEETPGVVHVGRLDENTEGLLLLTNDGDLGHRL--MHPSYRVLKTYLAEVDGL-- 152

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                +   L K+   G +               +  F+V D  + K   +E+  H G+ 
Sbjct: 153 -----VPRGLGKELRNGWEL--------PDGIVKVDQFRVKDMHSGK-SLVELVIHEGKK 198

Query: 253 HQLRVHALHMGCPIV 267
           H +R      G P++
Sbjct: 199 HIVRRLLKDTGHPVL 213


>gi|187779593|ref|ZP_02996066.1| hypothetical protein CLOSPO_03189 [Clostridium sporogenes ATCC
           15579]
 gi|187773218|gb|EDU37020.1| hypothetical protein CLOSPO_03189 [Clostridium sporogenes ATCC
           15579]
          Length = 236

 Score = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 85/252 (33%), Gaps = 55/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
            RL ++  +     +    + I+  G+V V+  ++K    +I SG  ++++   I     
Sbjct: 3   ERLQKYMAS-CGVASRRKCEDIILEGRVEVNGIKIKEVGTKIISGKDIIKVDGNIIKPE- 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKS 135
                                      E+    + NKP G +           I   +K 
Sbjct: 61  ---------------------------ENKIYILLNKPKGYLCTAKDEKGRKTILDLVKV 93

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 ++     RLD +TSGI+++         +      +   K Y + V G  K   
Sbjct: 94  -----KERIYPIGRLDMDTSGIIILTNDGEIYNKIIHPKFEK--IKTYKAKVKGTMKKDH 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 L KK    GDY+         A  A+  FK      +    + ++ H G+  Q+
Sbjct: 147 IE----LFKKGIDIGDYI--------TAPAALEIFKT----NKDTSEIIIKIHEGKNRQV 190

Query: 256 RVHALHMGCPIV 267
           R     +G P++
Sbjct: 191 RRMCKSIGHPVI 202


>gi|169829656|ref|YP_001699814.1| putative RNA pseudouridine synthase ytzF [Lysinibacillus sphaericus
           C3-41]
 gi|168994144|gb|ACA41684.1| Hypothetical RNA pseudouridine synthase ytzF [Lysinibacillus
           sphaericus C3-41]
          Length = 237

 Score = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 90/248 (36%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++++L+   V VD   VK                 +A  H+ 
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKQLLKQKAVTVDGASVK-----------------DAAMHVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ          ++       ++Y +   ++ NKP G+     S      D  +   ++
Sbjct: 43  PEQ----------QNVSVYGERVIYTEFVYFMMNKPPGVI----SATEDLRDETVIDLLE 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              Q   P    RLD++T G+LV+      A   L+     + + K+Y++ + G+   + 
Sbjct: 89  PVDQHFQPFPVGRLDKDTEGLLVLTNDGILAHNLLS---PKKHVPKVYYAHIEGVVTEED 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                    +    G  +      + G        K++   +     +E+    G+ HQ+
Sbjct: 146 --------VEKFANGVELDDGYMTKPG--------KLVILKSAPQSEIELTIQEGKFHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KRMFEAVG 197


>gi|116492846|ref|YP_804581.1| ribosomal large subunit pseudouridine synthase B [Pediococcus
           pentosaceus ATCC 25745]
 gi|116102996|gb|ABJ68139.1| ribosomal large subunit pseudouridine synthase B [Pediococcus
           pentosaceus ATCC 25745]
          Length = 241

 Score = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 40/252 (15%), Positives = 82/252 (32%), Gaps = 52/252 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           E  RL +         +    +K++  G VRV+ K +K    ++ +   + +  V     
Sbjct: 2   EEERLQKVMAEA-GVASRRKSEKLITEGHVRVNGKVIKQLGTKVTAHDKIEVDGVPLQRE 60

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
            ++                              ++ NKP G+     S         +  
Sbjct: 61  KMV-----------------------------YFLLNKPRGVIT---SVSDDKKRKTVMD 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-K 194
           +     ++     RLD +TSG +++      A  LT      + +K Y + V GI  +  
Sbjct: 89  FFPDVVERIYPVGRLDYDTSGAVLMTNDGTLANGLT--HPKFKFEKTYTAKVKGIVNSLD 146

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + + N L+            +   +     +I               + +  H GR HQ
Sbjct: 147 LKKLENGLVIDHKKTAKAKAHLISTDDEKKTSI---------------VSLTIHEGRNHQ 191

Query: 255 LRVHALHMGCPI 266
           ++   + +G P+
Sbjct: 192 VKNMFMAVGHPV 203


>gi|332799735|ref|YP_004461234.1| pseudouridine synthase Rsu [Tepidanaerobacter sp. Re1]
 gi|332697470|gb|AEE91927.1| pseudouridine synthase Rsu [Tepidanaerobacter sp. Re1]
          Length = 242

 Score = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 36/250 (14%), Positives = 81/250 (32%), Gaps = 48/250 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
             ++  R+D+   +   + +  +++K+++SGQV ++               V I      
Sbjct: 2   KSQKPARIDKILAS-CGYGSRKDVKKLIKSGQVSING--------------VIINDAGTL 46

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
           +N  + E  +                 + YED+   + NKP  +           +   L
Sbjct: 47  VNPSLDEIIVAGE-------------CIFYEDNVYIMMNKPQDVVSSTYDDFETTVIDLL 93

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +     +  K     RLD++  G++ +      A  L       R+ K Y+  V+G    
Sbjct: 94  EGEYFHR--KLFPVGRLDKDAEGLIFLTDDGKMAHRL--LSPKNRVPKTYYVEVYGRL-- 147

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                             +   ++  +  A  A     +++          +  + G+ H
Sbjct: 148 -----------NESDVKAFAAGMELEDFTALPA--ELDILEKNNNISSAY-VTIYEGKFH 193

Query: 254 QLRVHALHMG 263
           Q++      G
Sbjct: 194 QIKRMMKARG 203


>gi|297583540|ref|YP_003699320.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297141997|gb|ADH98754.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 236

 Score = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 85/250 (34%), Gaps = 49/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D+    H  + +  +++++L+ G   V+ + VK                  A  H+ 
Sbjct: 1   MRVDKLLA-HVGYGSRKDVKQLLKKGLFTVNGEVVKS-----------------AKAHVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   L           F    +LY +    + +KPAG+           +   L+   +
Sbjct: 43  PETDDL----------AFGGEPILYREHLYVMMHKPAGVLSATEDVSERTVVDLLEE--E 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD++T+G+L++      A  +T     R+I K Y            E +
Sbjct: 91  DRLFQPFPVGRLDKDTTGLLLLTNDGKWAHGIT--SPARKIPKTY------------EVL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +           V   +      A      +    +    L +    G+ HQ++  
Sbjct: 137 TAEPVTDEMADQLQQGVTLDDGYETRPA-----GVAFPDESRSRLYLTIDEGKYHQVKRM 191

Query: 259 ALHMGCPIVG 268
              +G  + G
Sbjct: 192 LAAVGNHVDG 201


>gi|239637925|ref|ZP_04678886.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           warneri L37603]
 gi|239596488|gb|EEQ79024.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           warneri L37603]
          Length = 230

 Score = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 24/160 (15%), Positives = 54/160 (33%), Gaps = 35/160 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD++  N         +++ L+ G V+V+ + +K    +I     ++ +         
Sbjct: 1   MRLDKFLANMGVG-TRNEVKQSLKKGYVKVNNEVIKSPKTQIDPNEDIITVN-------- 51

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   ++Y D    + NKP+G+           +   +  +
Sbjct: 52  ---------------------DEKIIYIDKVYIMLNKPSGVVSATEDDKHQTVIDLIPEY 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              +  +     RLD++T G+L++         L    + 
Sbjct: 91  ---QHLEIFPVGRLDKDTEGLLLITNDGQFNHDLMSPNKH 127


>gi|209558865|ref|YP_002285337.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
 gi|209540066|gb|ACI60642.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
          Length = 240

 Score = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 83/247 (33%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MR++++   H    +    +++++ G V ++ + +      ++SG VV I          
Sbjct: 1   MRINKYIA-HAGIASRRKAEELIKQGLVTLNGQVIMDLATTVKSGDVVEIE--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                S +  E+   Y+ NKP G IS          +   L   
Sbjct: 51  --------------------GSPIYNEEKVYYLLNKPRGAISSVSDDKGRKTVLDLL--- 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD +TSG+L++         +        I K+ W +          
Sbjct: 88  -PQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM--IHPRNEIDKVIWRVSK-------- 136

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +L++          +  + K    A  +   ++   +    +E+  H GR HQ++
Sbjct: 137 -----VLQRKKNLRPLTRGIVIDGKKTKPARYNIVRVEAD-KNRSIVELTIHEGRNHQVK 190

Query: 257 VHALHMG 263
                +G
Sbjct: 191 KMFESVG 197


>gi|126651298|ref|ZP_01723505.1| pseudouridylate synthase (ribosomal small subunit pseudouridine
           synthase A) [Bacillus sp. B14905]
 gi|126591827|gb|EAZ85910.1| pseudouridylate synthase (ribosomal small subunit pseudouridine
           synthase A) [Bacillus sp. B14905]
          Length = 237

 Score = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 91/248 (36%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++++L+   V VD   VK                 +A  H+ 
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKQLLKQKAVTVDGASVK-----------------DAAMHVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ          ++       ++Y +   ++ NKP G+     S      D  +   ++
Sbjct: 43  PEQ----------QNVSVYGERVVYTEFVYFMMNKPPGVI----SATEDLRDETVIDLLE 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              Q   P    RLD++T G+LV+      A + L+     + + K+Y++ + G+   + 
Sbjct: 89  PLDQHFQPFPVGRLDKDTEGLLVLTNDGILAHKLLS---PKKHVPKVYYAHIEGVVTEED 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +  +        G         + G        K++   +     +E+    G+ HQ+
Sbjct: 146 --VEKFAEGVELDDG------YMTKPG--------KLVILKSAPQSEIELTIQEGKFHQV 189

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 190 KRMFESVG 197


>gi|3915542|sp|O05668|Y1370_MYCLE RecName: Full=Uncharacterized RNA pseudouridine synthase ML1370;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2065214|emb|CAB08276.1| unnamed protein product [Mycobacterium leprae]
          Length = 256

 Score = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 45/263 (17%), Positives = 79/263 (30%), Gaps = 45/263 (17%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M  +    ++     +RL +         +    +K++  G+V VD + V+         
Sbjct: 1   MVEIHDSRMDRGAGAVRLQKILSRA-GIASRRAAEKLIIEGRVEVDGQLVR--------- 50

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                        +        S V +      +   L+Y        NKP G+      
Sbjct: 51  ------------ELGTRVDPDVSVVRVDGVKVVVDDSLVY-----LALNKPRGMYSTMSD 93

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                  G L        +K     RLD +T G++++      A  L        + K Y
Sbjct: 94  DRGRPCVGDLIERRVRGNKKLFHVGRLDADTEGLILLTNDGELAHRL--MHPSHEVSKTY 151

Query: 184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243
            + V G        +   L KK  +G +               +  F V+D    K   +
Sbjct: 152 LATVKGA-------VPRGLGKKLSVGLEL--------DDGPAHVDDFAVVDAIPGK-TLV 195

Query: 244 EMQPHTGRTHQLRVHALHMGCPI 266
            +  H GR   +R      G P+
Sbjct: 196 RLTLHEGRKRIVRRLLTAAGFPV 218


>gi|332670389|ref|YP_004453397.1| pseudouridine synthase [Cellulomonas fimi ATCC 484]
 gi|332339427|gb|AEE46010.1| pseudouridine synthase [Cellulomonas fimi ATCC 484]
          Length = 248

 Score = 62.7 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 91/252 (36%), Gaps = 48/252 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +RL +   +     +    ++++ +G+V VD   V+     + G  VR+ P     
Sbjct: 7   DPDGVRLQKVLASAGLG-SRRACEELIATGRVTVDGSTVR-----ELG--VRVDP----- 53

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                    L + +++      L S ++         NKP G+     +         + 
Sbjct: 54  ---------LTAVIHVDGMRVQLDSSVV-----TLALNKPKGVVS---TMHDPEGRPSVA 96

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +V  + ++     RLD ET G+L++      A  L+       + K Y + V G     
Sbjct: 97  QFVADRSERLFHVGRLDSETEGLLLLTNDGELANRLS--HPSHGVAKTYLAHVEG----- 149

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              +A  L  +   G +         +     +  F+V+    Q    +E+  H GR   
Sbjct: 150 --RVAGSLAGRLARGVEL--------EDGVVTVDRFQVVQTTPQ-ASLVEVVLHEGRNRV 198

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 199 VRRLLEEVGHPV 210


>gi|222529534|ref|YP_002573416.1| pseudouridine synthase [Caldicellulosiruptor bescii DSM 6725]
 gi|222456381|gb|ACM60643.1| pseudouridine synthase [Caldicellulosiruptor bescii DSM 6725]
          Length = 230

 Score = 62.7 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 82/237 (34%), Gaps = 48/237 (20%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
            +    ++I+  G+V+V+ K V                       +  E+ +++      
Sbjct: 7   ASRRKCEEIILQGRVKVNGKTVN-----------------QLGFKVDPEKDVVEVDGKRI 49

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                L+   +Y      + NKP G+     +         +    D    +     RLD
Sbjct: 50  ----SLQMQKVY-----IMLNKPFGVIS--SAKDEKGRKTVVDLVKDKVNVRVFPVGRLD 98

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-ECIANWLLKKSHIGG 210
            +T+G++++      A  +T       I+K Y  L+ GIP  ++ E     LL    +  
Sbjct: 99  FDTTGLIILTNDGEFAYKVT--HPKHDIEKTYIVLIKGIPSKEEIERFEKGLLIDGKM-- 154

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                          A + FK++         +E++ H GR  Q+R     +G  ++
Sbjct: 155 --------------TAPAKFKILKLINGNA-LVEIKIHEGRNRQIRKMCDQIGHKVL 196


>gi|301301292|ref|ZP_07207445.1| putative 16S pseudouridylate 516 synthase [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300851107|gb|EFK78838.1| putative 16S pseudouridylate 516 synthase [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 238

 Score = 62.7 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 85/245 (34%), Gaps = 52/245 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG---QVVRIPPVINALN 75
           MRLD++             +K++++ +VR++ + VK + +I+       + +   + ALN
Sbjct: 1   MRLDKFLSQTGK-FTRAEAKKVIKAKRVRLNGEVVK-DGKIKINEDSDKIFLDGELLALN 58

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           +                                Y+ NKP G+           +   +  
Sbjct: 59  N----------------------------KEVYYMLNKPIGVLSATRDDKDKTVIDLIN- 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               + +      RLD+ET+G+L++    + A   ++     + + K Y ++V G    K
Sbjct: 90  -FPGRKEDLFPVGRLDKETTGLLIITNDGKFAHDIIS---PKKHVSKTYEAVVTGKISEK 145

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  +  +        GD +   + +            +          + +  H G+ HQ
Sbjct: 146 E--VKTFSQGMELANGDKLQPAQLDI-----------ISYSEKDDTSKVRVIIHEGKYHQ 192

Query: 255 LRVHA 259
           +R   
Sbjct: 193 VRRMF 197


>gi|289423805|ref|ZP_06425600.1| ribosomal large subunit pseudouridine synthase B
           [Peptostreptococcus anaerobius 653-L]
 gi|289155844|gb|EFD04514.1| ribosomal large subunit pseudouridine synthase B
           [Peptostreptococcus anaerobius 653-L]
          Length = 238

 Score = 62.7 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 37/251 (14%), Positives = 77/251 (30%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MR++++        +    + ++  G++RV+ K +K  + ++      V           
Sbjct: 1   MRINKFIAAS-GVASRRKAETLILEGRIRVNNKVIKELSYQVDEDLDQVTF--------- 50

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKS 135
                             D     +  E     + NKP G I+              +  
Sbjct: 51  ------------------DNKPISVKDEKLVYIMLNKPEGYITSVKDQFDRPS----VSD 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 ++     RLD ETSG+L++         +T       + K Y + V GI   ++
Sbjct: 89  LTSDIKERIYPVGRLDYETSGLLLMTNDGDLTYKIT--HPKHEMNKTYIASVRGIVTQEE 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQ 254
                           Y        +    A ++ K++       +   ++  H G+  Q
Sbjct: 147 ---------------KYAFENGLKIEDYTTAKANLKILKTDTNKNYSVCKVTIHEGKNRQ 191

Query: 255 LRVHALHMGCP 265
           +R     +  P
Sbjct: 192 VRKMFQAINHP 202


>gi|227431698|ref|ZP_03913728.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
 gi|227352522|gb|EEJ42718.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
          Length = 224

 Score = 62.7 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 40/228 (17%), Positives = 84/228 (36%), Gaps = 48/228 (21%)

Query: 40  ILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           ++ +G+V+V+ + V     ++ +   V++            +   ++    L        
Sbjct: 1   MIINGRVQVNGQTVTELGTKVTANDKVQV------------DGAPIEGREKLV------- 41

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
                     Y+ NKP G+     +         +   ++   Q+     RLD +T+G+L
Sbjct: 42  ---------YYLLNKPRGVVT---TNDDEKGRRTVLDILEDVDQRVYPVGRLDYDTTGVL 89

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++      A  L       ++ K Y + V GI   +K       LK+         VV +
Sbjct: 90  LLTNDGVVANQL--MHPKTKVDKTYVAKVEGIATEEK----LAPLKRG--------VVLK 135

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             K A   +S  ++     ++   + +  H GR HQ++     +G P+
Sbjct: 136 GRKTAPARVSIERI--EPTKRTSMVRLTIHEGRNHQVKNMLAKVGLPV 181


>gi|289208914|ref|YP_003460980.1| RNA-binding S4 domain protein [Thioalkalivibrio sp. K90mix]
 gi|288944545|gb|ADC72244.1| RNA-binding S4 domain protein [Thioalkalivibrio sp. K90mix]
          Length = 318

 Score = 62.7 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 37/234 (15%), Positives = 76/234 (32%), Gaps = 35/234 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+ +         +   ++  +  G+V+V+++  K  +++    V+R+   +       
Sbjct: 3   ERVQKVLAARGLG-SRREIEGWIERGEVKVNQRTAKLGDQVGPNDVIRVRGRV------- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ +H+            +  V++KP G                  S   
Sbjct: 55  ---------IHMAEHA-----------HRWLVYHKPVGEIC--SRSDPEGRKPVFASLPR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            KGQ+     RLD  TSG+L+       A  L        +++ Y   V G   +     
Sbjct: 93  LKGQRWVAVGRLDLNTSGLLLFTTDGELANRL--MHPSHSLEREYAVRVLGEVPDDT--- 147

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              LL+   +           E+G + A   F V+    +      +    G T
Sbjct: 148 RRMLLEGVELEDGPARFDVLEERGGDGANHWFHVVVSEGRNRLVRRLWDAVGVT 201


>gi|116628203|ref|YP_820822.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMD-9]
 gi|116101480|gb|ABJ66626.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMD-9]
          Length = 243

 Score = 62.7 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 78/246 (31%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++  L+  QV V+ +                     +    I
Sbjct: 1   MRLDKFLVDCGVG-SRSQVKTFLKKKQVTVNGQV------------------ETSPKTQI 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E K             +L   L +E    Y+ NKP G+           +   L     
Sbjct: 42  DEDK---------DQIAYLGQELTHETFVYYLLNKPQGVISATEDSRHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++      A   L+     + + KIY + V GI   +   
Sbjct: 93  HK--QVFPVGRLDIDTHGLLLLTNNGDLAHAMLS---PKKHVDKIYQAKVAGIMDEEDIL 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   +K  +     A      +D  A     +++    G+ HQ++ 
Sbjct: 148 -------------AFEKGIKLKDHTCQPAKLEIVSVDRNAS-TSLVQITVAEGKFHQVKR 193

Query: 258 HALHMG 263
                G
Sbjct: 194 MVAACG 199


>gi|328951588|ref|YP_004368923.1| pseudouridine synthase Rsu [Marinithermus hydrothermalis DSM 14884]
 gi|328451912|gb|AEB12813.1| pseudouridine synthase Rsu [Marinithermus hydrothermalis DSM 14884]
          Length = 240

 Score = 62.7 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 36/250 (14%), Positives = 80/250 (32%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL ++        +    + ++R+G+V ++ +      ++  G  V +     A     
Sbjct: 4   IRLQKYLAQAGVASSRRKAEALIRAGRVTINGQVAALGAKVTPGDEVCVDGRPVAPTAR- 62

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                        +   +KP G++       A      L   + 
Sbjct: 63  ---------------------------RVVLALHKPPGVTTTRRDRFAERTVFELVPAIP 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-RRIQKIYWSLVWGIPKNKKEC 197
                     RLD+++ G+L++       Q LT       ++ +++ +         K  
Sbjct: 96  G----LHTVGRLDRDSEGLLLLTNDGRLTQRLTHPRYGVPKVYRVWTA---------KGE 142

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +  ++LK+   G      V+  +  A    +  KV  C         +    GR  ++R 
Sbjct: 143 VPPFILKRLEKG------VRLEDGPARALKARPKVGGCV--------LTLAEGRKREVRR 188

Query: 258 HALHMGCPIV 267
               +G P+V
Sbjct: 189 MLRAVGYPVV 198


>gi|298707966|emb|CBJ30337.1| pseudouridine synthase [Ectocarpus siliculosus]
          Length = 468

 Score = 62.7 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 37/247 (14%), Positives = 83/247 (33%), Gaps = 42/247 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++  +     +    ++++  G+VRV+ K VK     + G  V++ P  + ++   
Sbjct: 35  ERLQKFLSHAGLD-SRRQCEQMILDGRVRVNGKMVK-----ELG--VKVNPRRDQVH--- 83

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    V+  + S    S + +        NKP G+       +       + S   
Sbjct: 84  ---------VDGNRVSMRPDSEIKW-----VALNKPKGVICTVSDELG--RPTAVASIPR 127

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-EC 197
               +     RLD+++ G+L++    +    LT        +    +L  G P  ++ + 
Sbjct: 128 GLEMRLVPVGRLDRDSCGLLLLTNENSWINPLTHPSYGHE-KTYRVALTSGYPTTEEWDV 186

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   +L           +V+         ++   +I                G+  Q+R 
Sbjct: 187 LTQGMLLDGDPNPTRPCIVEVVNYDRRTRVTTVDII-------------IREGKNRQIRR 233

Query: 258 HALHMGC 264
               +G 
Sbjct: 234 MFEGIGH 240


>gi|225870791|ref|YP_002746738.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           equi subsp. equi 4047]
 gi|225700195|emb|CAW94370.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus equi subsp. equi 4047]
          Length = 237

 Score = 62.7 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 79/248 (31%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++  +     +   ++ +L+  QV V+   +     ++                  
Sbjct: 1   MRLDKFLVDAGLG-SRSQVKLLLKKKQVSVNGVSQTSPKYQVN----------------- 42

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       +T    +    L YE    Y+ NKP G+           +   L    
Sbjct: 43  -----------EMTDEVSYQGQRLNYEAFVYYMLNKPKGVISATEDSSHKTVLDLLDDTA 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             K        RLD++T G+L+V    + A   L+     + + K Y ++V G+   +  
Sbjct: 92  RQKA--VFPVGRLDKDTHGLLLVTNDGKLAHALLS---PKKHVAKQYLAVVDGMMTQEDV 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQL 255
                                   K      +H  +++   + K   +++    G+ HQ+
Sbjct: 147 ---------------KHFAQGITLKDHQCMPAHLDILEINESLKTSLVKITIEEGKFHQV 191

Query: 256 RVHALHMG 263
           +      G
Sbjct: 192 KRMVAACG 199


>gi|27262400|gb|AAN87481.1| Ribosomal large subunit pseudouridine synthase B [Heliobacillus
           mobilis]
          Length = 253

 Score = 62.7 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 48/267 (17%), Positives = 91/267 (34%), Gaps = 59/267 (22%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG 62
           M  V            RL +    H    +    +  +R+G+V+V+   V     R++ G
Sbjct: 1   MKEVLSTTTAE-----RLQKVLAAH-GLASRREAEDWIRAGRVQVNGTVVTELGLRVEEG 54

Query: 63  -QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQ 120
             V+++                              K + + E  + ++  KP G ++ +
Sbjct: 55  KDVIQV----------------------------DGKPLTVRERHQYFLLYKPRGFVTTR 86

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                   +   LK        +     RLDQ+T G+L++      A  LT       ++
Sbjct: 87  KDPEGRPTVIDLLKDVPA----RIYPVGRLDQDTEGLLLLTNDGELAYRLT--HPKYGVE 140

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
           K Y + + G        + + ++K                +    A +  KV+D      
Sbjct: 141 KTYHARMRGN-------VPDPVIK--------AFAEGVMLEDGLTAPAKVKVLDREG-GA 184

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIV 267
            W+E+  H GR  Q+R     +G P+V
Sbjct: 185 TWIELTIHEGRNRQVRRMGDAVGYPVV 211


>gi|225166146|ref|ZP_03727870.1| pseudouridine synthase, RluA family [Opitutaceae bacterium TAV2]
 gi|224799614|gb|EEG18119.1| pseudouridine synthase, RluA family [Opitutaceae bacterium TAV2]
          Length = 72

 Score = 62.3 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 3/68 (4%)

Query: 259 ALHMGCPIVGDHKYC--ANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
              +G  ++GD  Y    + +      +  ++ LHA ++   HP  GR L + APLP   
Sbjct: 1   MKSIGHVLLGDATYGWKPDPRLEALDAMPRRVMLHAEHIRFQHPVTGRELVVRAPLPEDF 60

Query: 316 VKTWDSLG 323
            +   +L 
Sbjct: 61  EEMLRALR 68


>gi|77164554|ref|YP_343079.1| pseudouridine synthase, Rsu [Nitrosococcus oceani ATCC 19707]
 gi|254433620|ref|ZP_05047128.1| conserved hypothetical protein, putative [Nitrosococcus oceani
           AFC27]
 gi|76882868|gb|ABA57549.1| ribosomal large subunit pseudouridine synthase B [Nitrosococcus
           oceani ATCC 19707]
 gi|207089953|gb|EDZ67224.1| conserved hypothetical protein, putative [Nitrosococcus oceani
           AFC27]
          Length = 268

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/232 (14%), Positives = 71/232 (30%), Gaps = 32/232 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +   +++ +++G+VR++    +  +++     V +     +   + 
Sbjct: 3   ERLQKILARGGLG-SRREVEEWIKAGRVRINGIPARLGDKVSDEDQVTVNGRPLSPRRLQ 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                ++LY        +KPAG                 +S   
Sbjct: 62  APS----------------SQVILY--------HKPAGEIC--SRKDPEGRPTVFRSLPR 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +     RLD  TSG+L+       A  L       ++++ Y   V G      E I
Sbjct: 96  PRQGRWVSVGRLDINTSGLLLFTTDGELANRL--MHPSTQVEREYAVRVLGTVT---EVI 150

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              L +   +        +  + G   A   + VI    +K     +    G
Sbjct: 151 LERLQRGVQLEDGLASFKRILDAGGEGANHWYHVILWEGRKREVRRLWESQG 202


>gi|119716723|ref|YP_923688.1| ribosomal large subunit pseudouridine synthase B [Nocardioides sp.
           JS614]
 gi|119537384|gb|ABL82001.1| ribosomal large subunit pseudouridine synthase B [Nocardioides sp.
           JS614]
          Length = 251

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 87/256 (33%), Gaps = 49/256 (19%)

Query: 12  VENDEENM-RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           +E+D++ + RL +         +    ++++  G V VD + V            R+   
Sbjct: 6   IESDDDGLVRLQKLLAQS-GVASRRKCEELMLEGHVVVDGEVVT-----------RLGTK 53

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           ++    +I+          L   S+ +            V NKP G+             
Sbjct: 54  VDPRTAVIRVD-----GKRLPPVSEKV----------YLVLNKPRGVVSTMSDPEGRR-- 96

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             L   V  + ++     RLD +TSG+L++      A  +        + K Y + V G 
Sbjct: 97  -TLSDLVADRPERLFHVGRLDTDTSGLLLLTNDGDFAHRMA--HPSYEVDKTYVAEVEGE 153

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
               +  I   L   +   G                +S  ++++  A K   +E+  H G
Sbjct: 154 VY--RRTIKQLLEGVTLDDGPV-------------TVSKARIVEATAAK-SIVELVIHEG 197

Query: 251 RTHQLRVHALHMGCPI 266
           R   +R     +G P+
Sbjct: 198 RNRIVRRLLDQVGHPV 213


>gi|156093775|ref|XP_001612926.1| hypothetical protein [Plasmodium vivax SaI-1]
 gi|148801800|gb|EDL43199.1| hypothetical protein, conserved [Plasmodium vivax]
          Length = 403

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 41/266 (15%), Positives = 87/266 (32%), Gaps = 48/266 (18%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            LK  LLY+D    V +K  G+S  G +     I   L+     + +   + ++L     
Sbjct: 17  DLKKSLLYQDDDYLVVDKAYGVSTFGRAPQKESIIKSLQGLNLEEPEDANVVYKLHNHVG 76

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G L++ + +          +       + +LV+G  +  +       LK        V V
Sbjct: 77  GCLLICKNKF--------IKNHTYGNTFLALVYGKVEKAQNVEVKLGLKYLPNS--TVMV 126

Query: 216 VKQNEKGANYAIS-HFKVIDC--FAQKFCWLEMQPHTGRTHQ--LRVHALH-MGCPIVGD 269
               ++      +  + V+    + +   +  ++  +       ++    + +   IVGD
Sbjct: 127 PSNGQEHLRDLKTIRYNVVSNSIWYETHNFSLLKIDSTAKDARFIKPLLFYSLYTCIVGD 186

Query: 270 HKYCANFK-----------------GNFTSPIQNK---------------LYLHARYMDL 297
            +Y   +K                       +  +               L+LH   +  
Sbjct: 187 TEYVGGWKKLRENGFFSYRDVGGQVERANRLLLKRVSKRVSPGGKNNELMLHLHCSGVTF 246

Query: 298 PHPEGGRLQITAPLPAHMVKTWDSLG 323
                  + + +PLP HM +T + LG
Sbjct: 247 QSACSRVVYVASPLPRHMRETLNLLG 272


>gi|238852693|ref|ZP_04643103.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri 202-4]
 gi|282852074|ref|ZP_06261432.1| pseudouridylate synthase [Lactobacillus gasseri 224-1]
 gi|311110814|ref|ZP_07712211.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri MV-22]
 gi|238834839|gb|EEQ27066.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri 202-4]
 gi|282556834|gb|EFB62438.1| pseudouridylate synthase [Lactobacillus gasseri 224-1]
 gi|311065968|gb|EFQ46308.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri MV-22]
          Length = 239

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 87/250 (34%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++ +GQV V+ K++     +++    + +       N +
Sbjct: 3   ERLQKVIAQA-GVASRRKAEKMISAGQVTVNGKKITELGTKVEPSDKIEV-------NGV 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
             E++ L                        Y+F KP G+  SV+   G        +  
Sbjct: 55  PIEKETL----------------------HTYLFYKPRGVISSVKDDKGRK-----TVVD 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +    +     RLD +TSG+L++      A  L        + K+Y + + G+   + 
Sbjct: 88  FFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANKL--MHPRNEVPKVYVAKIKGLLSPED 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQ 254
                             H V+ + +    A +  K++    +K    +++  H G  HQ
Sbjct: 146 I-------------RSLTHGVRIDGR--KSAPAKLKILKTDEKKNTQIVQLTIHEGHYHQ 190

Query: 255 LRVHALHMGC 264
           ++     +  
Sbjct: 191 VKRMFEAVHH 200


>gi|317496566|ref|ZP_07954915.1| RNA pseudouridylate synthase [Gemella moribillum M424]
 gi|316913369|gb|EFV34866.1| RNA pseudouridylate synthase [Gemella moribillum M424]
          Length = 235

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 88/248 (35%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI-QSGQVVRIPPVINALNH 76
           MRLD++   H   ++    +KI++ G V V+   VK  + +I +    V +         
Sbjct: 1   MRLDKYI-GHTTLLSRAESKKIIKKG-VLVNGNIVKAPDFKIDELNDEVIVN-------- 50

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                +  L+Y+     + NKP G+       I+  +   L+  
Sbjct: 51  ---------------------EKKLIYQKYIYIMMNKPKGVISATEDSISRTVIDLLEE- 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                 +P    RLD++T G++++         LT     + ++K Y+  V G+ K    
Sbjct: 89  -KDCIFEPFPVGRLDKDTEGLMLLTNDGNLGHQLT--SPKKDVEKQYYVEVNGVLK---- 141

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + +    K  I  +  +      K A   I    V    A  +         G+ HQ++
Sbjct: 142 -VEHIPYLKEGIILEDGYKC----KSAKLDILTSDVSKSTAYIYVTE------GKFHQVK 190

Query: 257 VHALHMGC 264
                +GC
Sbjct: 191 RMMKALGC 198


>gi|319941976|ref|ZP_08016297.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
 gi|319804629|gb|EFW01499.1| pseudouridine synthase [Sutterella wadsworthensis 3_1_45B]
          Length = 400

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/193 (16%), Positives = 67/193 (34%), Gaps = 27/193 (13%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   +++++ SG V V+    K  +R+ +  V+R+   +                  L+ 
Sbjct: 54  SRREMERLIESGIVTVNGNPAKLGDRVSAEDVIRVEGRLVR---------------RLSP 98

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
            +     +LLY        +KPAG  V                     G +     RLD 
Sbjct: 99  EAADTPRVLLY--------HKPAGEIV--SRDDPEGRPSVFNHLPRVPGGRWIAVGRLDF 148

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L+   + + A  L         +    ++    P+++ + +A   L+       +
Sbjct: 149 NTEGLLLFTTSGSLANRLMHPRYEMEREYAVRTVGELTPEDEAKLLAGVELEDGP--AKF 206

Query: 213 VHVVKQNEKGANY 225
             +  +  KG N+
Sbjct: 207 ETLTDEGGKGLNH 219


>gi|319442276|ref|ZP_07991432.1| putative pseudouridylate synthase [Corynebacterium variabile DSM
           44702]
          Length = 282

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 49/255 (19%), Positives = 85/255 (33%), Gaps = 49/255 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQS-GQVVRIPPVI 71
           +D E  RL +         +    +K++ +G+V V+   V     R+     V+R+  V 
Sbjct: 37  SDNEKTRLQKVLAAA-GVASRRMSEKLIEAGRVEVNGSIVTEQGMRVDPENDVIRVDGVR 95

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                                       ++  E+   +  NKP GI              
Sbjct: 96  ----------------------------VIADEEIVTFALNKPRGIHSTMHDEFGRPCLS 127

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L       GQ+     RLD +T G+L++      A  L        I+K Y + V G  
Sbjct: 128 DLVGERVEAGQRLFHVGRLDAQTEGLLLLTNDGELANRL--MHPRYGIKKTYLATVLG-- 183

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           +  +  +   L       G    +V  +E          ++ID + Q    +++  H GR
Sbjct: 184 EADRRLVRQLLDGIELDDG----IVIADE---------VQIIDAW-QGKSLIKVVIHEGR 229

Query: 252 THQLRVHALHMGCPI 266
            H +R      G P+
Sbjct: 230 KHVVRRMLKEAGFPV 244


>gi|254426889|ref|ZP_05040596.1| conserved hypothetical protein, putative [Alcanivorax sp. DG881]
 gi|196193058|gb|EDX88017.1| conserved hypothetical protein, putative [Alcanivorax sp. DG881]
          Length = 241

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 73/241 (30%), Gaps = 54/241 (22%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHII 78
           RLDR+       ++   L+ +L +G+VRV+   V+    RI     V +           
Sbjct: 7   RLDRFLSQVL-QVSRSGLRPVLAAGRVRVNGVPVRDRQQRIGPFDRVELDGQPLQS---- 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    E  +  + NKPAG+     +         +     
Sbjct: 62  -------------------------EAPRYLMVNKPAGVVS---ATSDDQHTTVMDLLPA 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           S+ Q   L  RLD  ++G++++    A ++ L++                 + K+ +  +
Sbjct: 94  SQRQGLHLAGRLDFNSTGLVLLTNDGAWSRQLSQPQSQ-------------VRKHYRVTV 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L +                     A    K+   +       E     GR HQ++  
Sbjct: 141 EQPLTEAYVAAFSEGMWFAFEGIKTRPA--EIKIRSAYEADVWLCE-----GRYHQIKRM 193

Query: 259 A 259
            
Sbjct: 194 F 194


>gi|227488999|ref|ZP_03919315.1| pseudouridine synthase B [Corynebacterium glucuronolyticum ATCC
           51867]
 gi|227091075|gb|EEI26387.1| pseudouridine synthase B [Corynebacterium glucuronolyticum ATCC
           51867]
          Length = 349

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 82/248 (33%), Gaps = 45/248 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL +         +    ++++  G+V V+ + V     ++ G  VR+ P         
Sbjct: 109 VRLQKVLAQA-GVASRRMSEELIAQGRVEVNGEIV-----MRQG--VRVDPDTA------ 154

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                           D ++  +  ED      NKP G+       +     G +     
Sbjct: 155 ------------VIRVDGVRVKV-NEDLVYIALNKPLGVQSTMKDDMGRPCVGDIVGEKV 201

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             G       RLD +T G+L++      A  L        + K Y + V G    +    
Sbjct: 202 DAGLHLFHVGRLDAKTEGLLLLTNDGELANRL--MHPKYHVSKTYLATVLGEADRE---- 255

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L+KK   G D    +         A + +  I    +    + ++ H GR H +R  
Sbjct: 256 ---LVKKLREGVDLEDGI---------AKADYVQIVDTYEGRSLIRVELHEGRKHIVRRM 303

Query: 259 ALHMGCPI 266
              +G P+
Sbjct: 304 LKELGFPV 311


>gi|116629543|ref|YP_814715.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus gasseri ATCC 33323]
 gi|116095125|gb|ABJ60277.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           gasseri ATCC 33323]
          Length = 245

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 87/250 (34%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++ +GQV V+ K++     +++    + +       N +
Sbjct: 9   ERLQKVIAQA-GVASRRKAEKMISAGQVTVNGKKITELGTKVEPSDKIEV-------NGV 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
             E++ L                        Y+F KP G+  SV+   G        +  
Sbjct: 61  PIEKETL----------------------HTYLFYKPRGVISSVKDDKGRK-----TVVD 93

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +    +     RLD +TSG+L++      A  L        + K+Y + + G+   + 
Sbjct: 94  FFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANKL--MHPRNEVPKVYVAKIKGLLSPED 151

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQ 254
                             H V+ + +    A +  K++    +K    +++  H G  HQ
Sbjct: 152 I-------------RSLTHGVRIDGR--KSAPAKLKILKTDEKKNTQIVQLTIHEGHYHQ 196

Query: 255 LRVHALHMGC 264
           ++     +  
Sbjct: 197 VKRMFEAVHH 206


>gi|240138865|ref|YP_002963340.1| 16S rRNA pseudouridylate 516 synthase [Methylobacterium extorquens
           AM1]
 gi|240008837|gb|ACS40063.1| 16S rRNA pseudouridylate 516 synthase [Methylobacterium extorquens
           AM1]
          Length = 242

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 84/260 (32%), Gaps = 47/260 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLDR   N   + +   ++ + R+G VR+D + ++  ++       RIP   +    + 
Sbjct: 4   LRLDRLLAN-LGYGSRREVEGLARAGLVRLDGQALRDASQ-------RIPLEPDLSARMT 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + + LD    +         ++L++   +   +K  G  V             L     
Sbjct: 56  VQGEALDPLPGV--------CLMLHKPLGVTCSHKEVGPLV----------YSLLPERWR 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD+ETSG+L++    A    L      +      + +    P    E  
Sbjct: 98  RRDPALSTVGRLDKETSGLLLMTDDGA---LLHRIISPKAKVSKRYRVTLARPLQGDETA 154

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                +    G D   +                 ++          +  H GR HQ+R  
Sbjct: 155 ILASGEMMLEGEDKPLL----------------PVEMETDDPTHCTVTLHEGRYHQVRRM 198

Query: 259 ALHMGCPIVGDHKYCANFKG 278
              +G  +  D  +     G
Sbjct: 199 FAALGNHV--DALHRDRVGG 216


>gi|323488402|ref|ZP_08093649.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
 gi|323397909|gb|EGA90708.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
          Length = 237

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 46/249 (18%), Positives = 91/249 (36%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  N   H +   ++ +L+S  V V+ + V+                        
Sbjct: 1   MRLDKYLSN-MGHGSRKEVKVLLKSKAVEVNGEIVR------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 D  V++ +H+D +      + Y +    + NKP G+           +   L  
Sbjct: 36  ------DPKVHVNEHTDLVSVGGEAVTYTEFIYLLMNKPQGVISATEDKYDKTVIDLL-- 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             D +  +P    RLD++T G L++    + A + L+     + + K Y++ V G+   +
Sbjct: 88  GKDEQHFEPFPVGRLDKDTEGFLLLTNDGKLAHELLS---PKKHVDKTYFAHVEGVVTEE 144

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                    KK         VV  +      A     ++D  +     +E+    G+ HQ
Sbjct: 145 ----DTEAFKKG--------VVLDDGYETKPA--SLNILD--SAVVSKIELTITEGKFHQ 188

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 189 VKRMFESVG 197


>gi|307249289|ref|ZP_07531284.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
 gi|306858688|gb|EFM90749.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 4
           str. M62]
          Length = 232

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/179 (21%), Positives = 69/179 (38%), Gaps = 22/179 (12%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            LK  L +ED+ + +FNKP  +  Q            LK ++     +     RLD+++ 
Sbjct: 30  PLKPQLSFEDTVVVLFNKPFDVLTQ---FTDEQGRQTLKDFIPI--PQVYPVGRLDRDSE 84

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHI 208
           G+L++         L      ++  K Y + V GIP+        K   + + L K +  
Sbjct: 85  GLLLLTNNGEIQHRLANPKFEKQ--KTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAK- 141

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   K          +  K+ +       W+E++ H G+  Q+R    H+G P +
Sbjct: 142 -------AKAISAPNYEWQTAPKIRERKIIPTSWIELKIHEGKNRQVRRMTAHIGFPTL 193


>gi|227872023|ref|ZP_03990406.1| pseudouridylate synthase [Oribacterium sinus F0268]
 gi|227842134|gb|EEJ52381.1| pseudouridylate synthase [Oribacterium sinus F0268]
          Length = 239

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 88/245 (35%), Gaps = 50/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++  +     +   L++ +R G V+++ + VK  +  +Q G            + I
Sbjct: 1   MRLDKYLSDMGVE-SRSVLKREIRKGLVKINGEIVKDPSMEVQPG-----------NSEI 48

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + + +                  + YE+   Y+ NKP G+     S         L  + 
Sbjct: 49  VYKDEP-----------------IHYEEFSYYMMNKPVGVLS---STEDRKQKTVLDLFS 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D   +      RLD+++ G+L++    A A  L        I+K Y   + G    ++  
Sbjct: 89  DKHRKDLFPVGRLDKDSEGLLLIMNDGALAHKL--LSPKMHIEKKYLVEIPGKISEEE-- 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                     +      +    +  A  A +  + +    +    +E+    G+ HQ++ 
Sbjct: 145 ----------LDRLRQGIQYDTDLIAMPAKA--RCLSSTEEG-SRVEVIIMEGKFHQIKK 191

Query: 258 HALHM 262
             L +
Sbjct: 192 MFLAL 196


>gi|306833833|ref|ZP_07466958.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           bovis ATCC 700338]
 gi|304424027|gb|EFM27168.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           bovis ATCC 700338]
          Length = 242

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 80/247 (32%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++++L+  QV V+ K                         I 
Sbjct: 1   MRLDKFLVEAGIG-SRTEVKQLLKKKQVLVNGKV-----------------------EIS 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I + +  +      L     YE    Y+ NKP G+     +    H    L     
Sbjct: 37  PKTQIDEKADQIRCQGQTLS----YEKYVYYMLNKPKGVIS---ATEDNHHKTVLDLLDK 89

Query: 139 SKGQKP-RLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +   K      RLD +T G+L++    + A   L+     + + K Y + V G+      
Sbjct: 90  TAWDKETFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVDKTYRAKVAGLM----T 142

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                         D+        + A   I         A++   +E+    G+ HQ++
Sbjct: 143 TTDVAAFANGIDLKDFTC------QPAQLVILEI----NEAERTSVVEITIKEGKFHQIK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVQACG 199


>gi|255636627|gb|ACU18651.1| unknown [Glycine max]
          Length = 160

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
              A + F  I         +  +P TGRTHQ+RVH  + G PI  D  Y
Sbjct: 17  GKAASTKFTRISTNG-TQSIVLCEPITGRTHQIRVHLQYSGHPIANDMLY 65


>gi|254561472|ref|YP_003068567.1| 16S rRNA pseudouridylate 516 synthase [Methylobacterium extorquens
           DM4]
 gi|254268750|emb|CAX24711.1| 16S rRNA pseudouridylate 516 synthase [Methylobacterium extorquens
           DM4]
          Length = 242

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 84/260 (32%), Gaps = 47/260 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLDR   N   + +   ++ + R+G VR+D + ++  ++       RIP   +    + 
Sbjct: 4   LRLDRLLAN-LGYGSRREVEGLARAGLVRLDGQALRDASQ-------RIPLEPDLSARMT 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + + LD    +         ++L++   +   +K  G  V             L     
Sbjct: 56  VQGEALDPLPGV--------CLMLHKPLGVTCSHKEVGPLV----------YSLLPERWR 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD+ETSG+L++    A    L      +      + +    P    E  
Sbjct: 98  RRDPALSTVGRLDKETSGLLLMTDDGA---LLHRIISPKAKVSKRYRVTLARPLQGDETA 154

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                +    G D   +                 ++          +  H GR HQ+R  
Sbjct: 155 ILASGEMMLEGEDKPLL----------------PVEMETDDPTHCTVTLHEGRYHQVRRM 198

Query: 259 ALHMGCPIVGDHKYCANFKG 278
              +G  +  D  +     G
Sbjct: 199 FAALGNHV--DALHRDRVGG 216


>gi|258654177|ref|YP_003203333.1| pseudouridine synthase [Nakamurella multipartita DSM 44233]
 gi|258557402|gb|ACV80344.1| pseudouridine synthase [Nakamurella multipartita DSM 44233]
          Length = 249

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 88/254 (34%), Gaps = 48/254 (18%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           E  ++ +RL +   +     +    ++++R G+V+VD   V+                  
Sbjct: 6   EAADDGVRLQKVLASA-GVASRRKAEELIRDGRVKVDGIVVR-----------------E 47

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
               I  E  +    V++  +    ++ L+Y        NK  G+       +     G 
Sbjct: 48  MGTRIDPENAV----VHVDGNRITTRTDLVY-----LALNKERGVLSTMSDELGRPHIG- 97

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
               ++ + ++     RLD E+ G+L++      A  LT       + K Y + V G   
Sbjct: 98  --QMLEDRSERLFHVGRLDMESEGLLLLTNDGDLAHRLT--HPSYGVAKTYVAEVPGPIP 153

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                    L ++   G +         +     +  F V+D    +   +E+  H GR 
Sbjct: 154 KD-------LGRRLKAGVEL--------EDGPAKVDSFDVMDLHHNRAV-VEVVIHEGRK 197

Query: 253 HQLRVHALHMGCPI 266
           H +R     +  P+
Sbjct: 198 HIVRRLLEAVDRPV 211


>gi|218530506|ref|YP_002421322.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
 gi|218522809|gb|ACK83394.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
          Length = 242

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 84/260 (32%), Gaps = 47/260 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLDR   N   + +   ++ + R+G VR+D + ++  ++       RIP   +    + 
Sbjct: 4   LRLDRLLAN-LGYGSRREVEGLARAGLVRLDGQALRDASQ-------RIPLEPDLSARMT 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + + LD    +         ++L++   +   +K  G  V             L     
Sbjct: 56  VQGEALDPLPGV--------CLMLHKPLGVTCSHKEVGPLV----------YSLLPERWR 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD+ETSG+L++    A    L      +      + +    P    E  
Sbjct: 98  RRDPALSTVGRLDKETSGLLLMTDDGA---LLHRIISPKAKVSKRYRVTLARPLQGDETA 154

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                +    G D   +                 ++          +  H GR HQ+R  
Sbjct: 155 ILASGEMMLEGEDKPLL----------------PVEMETDDPTHCTVTLHEGRYHQVRRM 198

Query: 259 ALHMGCPIVGDHKYCANFKG 278
              +G  +  D  +     G
Sbjct: 199 FAALGNHV--DALHRDRVGG 216


>gi|83815539|ref|YP_445618.1| ribosomal large subunit pseudouridine synthase B [Salinibacter
           ruber DSM 13855]
 gi|83756933|gb|ABC45046.1| ribosomal large subunit pseudouridine synthase B [Salinibacter
           ruber DSM 13855]
          Length = 249

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 52/284 (18%), Positives = 102/284 (35%), Gaps = 62/284 (21%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVV-----R 66
            +D E MR++++   H    +  +   ++  G+V +D +RV +    ++ GQ V      
Sbjct: 5   SSDREGMRINKYIA-HAGVCSRRDADDLVEQGRVHIDGERVDQHGTCVREGQTVTVDGEE 63

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           + P+      + K +  + ++ +       L +I + ED+       P+G+         
Sbjct: 64  VYPLEFEYLLLNKPKDTISTTDDPKDRRTVLDAIGVPEDN-------PSGL--------- 107

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                                 RLD+ T+G+L+V+     A  L        I KIY+  
Sbjct: 108 ------------------FPVGRLDRNTTGVLLVSNDGDLAHRL--MHPRYEIPKIYYVR 147

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V    K  +                 +  +K+  + ++ A +  +V     Q+   + ++
Sbjct: 148 VQDDVKPHQ-----------------LDQLKRGVELSDGAAAADQVAYLDPQRKTDIALE 190

Query: 247 PHTGRTHQLRVHALHMGCPIVG--DHKYCANFKGNFTSPIQNKL 288
            H GR  Q+R     +G  IV     KY     G        +L
Sbjct: 191 LHEGRNRQIRRMMEALGHTIVQLERAKYATLTTGRLQRGEWRRL 234


>gi|332830030|gb|EGK02658.1| hypothetical protein HMPREF9455_00908 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 342

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/244 (13%), Positives = 79/244 (32%), Gaps = 60/244 (24%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++  N      +     + +  G+V ++ KR +   R+  GQ V++           
Sbjct: 4   RLNKYISN--SGFCSRREADRFIEEGRVTINGKRAQVGMRVLPGQKVKVN---------- 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              +++ + +                      FNKP GI          +I  F++    
Sbjct: 52  --GELIVNKIEPV----------------YIAFNKPVGIVSTTDPQERDNIINFIRH--- 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              Q+     RLD+++ G++++         +  +    +                    
Sbjct: 91  --EQRIFPIGRLDKDSQGLILLTNDGDIVNKILRAGNNHK-------------------- 128

Query: 199 ANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            ++L+K    I  D++  + Q     +      ++++     F    +    G   Q+R 
Sbjct: 129 KDYLVKVNRPITKDFLTRMAQGVPILDRVTRRCEIVEINPYMF---RISLIQGLNRQIRR 185

Query: 258 HALH 261
              +
Sbjct: 186 MCEY 189


>gi|146329607|ref|YP_001209391.1| ribosomal large subunit pseudouridine synthase, RluB [Dichelobacter
           nodosus VCS1703A]
 gi|146233077|gb|ABQ14055.1| ribosomal large subunit pseudouridine synthase, RluB [Dichelobacter
           nodosus VCS1703A]
          Length = 266

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/295 (12%), Positives = 88/295 (29%), Gaps = 46/295 (15%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +++  R+ ++        +   ++  ++ G+++VD +  +   +I   + + +      
Sbjct: 4   KNDDAQRIQKYLAARGVG-SRRQIETWIKEGRLKVDGRVAELGQKISGNERLSL------ 56

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF-NKPAGISVQGGSGIAYHIDGF 132
                                  L+  + +++  + +  +KPAG                
Sbjct: 57  -------------------DGKPLRIAVEHKNPHMILMYHKPAGEIC--TRKDPEGRVSV 95

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +        +     RLD  TSG+L+     A A  L        I++ YW  V G   
Sbjct: 96  FQHLPKISHGRWVAIGRLDLNTSGLLLFTNDGALANQL--MHPSAEIEREYWVRVAGEVT 153

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVI-DCFAQKFCWLEMQPHTGR 251
            +                    +   +       I   K + +   Q   +  +    GR
Sbjct: 154 EEMLT------------ALRQGIPLDDGLARFTEICPLKTLHEDDTQFNRYFSVTLKEGR 201

Query: 252 THQLRVHALHMGCPI--VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             ++R     +GC +  +   +Y         S  +++L        L      +
Sbjct: 202 NREVRRLWEAVGCKVSRLKRIRYGTISLPPSLSAGRHRLLTAGEQASLISLVSEK 256


>gi|299822093|ref|ZP_07053979.1| ribosomal small subunit pseudouridine synthase A [Listeria grayi
           DSM 20601]
 gi|299815622|gb|EFI82860.1| ribosomal small subunit pseudouridine synthase A [Listeria grayi
           DSM 20601]
          Length = 242

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 91/245 (37%), Gaps = 52/245 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK--FNNRIQSGQVVRIPPVINALNH 76
           MRLD++   H+ + +   +++ L+  +V V+ KRV+      + +  +VR+         
Sbjct: 1   MRLDKFLA-HHGYGSRKEVKQFLKKTEVTVNGKRVQDGKQAIVPTSDIVRVQ-------- 51

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                  ++LY++   ++ +KP+G         A  +   LK  
Sbjct: 52  ---------------------DEVILYQEYVYWMLHKPSGYIS-ATEDQAKTVLDLLK-- 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               G+      RLD++T G+L++      A  L      + + K+Y + + G+      
Sbjct: 88  PKDAGRAVFPVGRLDKDTEGLLLLTDDGQLAHEL--LSPKKHVNKVYEATIEGVVTGD-- 143

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                  KK         +V +++     A    +++     K   + +    G+ HQ++
Sbjct: 144 --DVHAFKKG--------IVLEDDYQCKPA--KLEILQVNGVK-TDIRITIQEGKYHQIK 190

Query: 257 VHALH 261
              L 
Sbjct: 191 RMFLA 195


>gi|332981538|ref|YP_004462979.1| pseudouridine synthase [Mahella australiensis 50-1 BON]
 gi|332699216|gb|AEE96157.1| pseudouridine synthase [Mahella australiensis 50-1 BON]
          Length = 244

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 46/249 (18%), Positives = 87/249 (34%), Gaps = 47/249 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL ++        +    +++++SG V V+   VK          + I P  +      
Sbjct: 8   IRLHKYMA-QCGVASRRKSEELIKSGAVSVNGHVVK-------DMGILIDPQKDE----- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    V +      LKS ++Y        NKP G          +     L     
Sbjct: 55  ---------VRVYGRIIRLKSDMIY-----IAVNKPRGYVS--TVKDQFGRPTVLDLVPV 98

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +   +     RLD +T+G++++         LT       I+KIY + + GIP N+    
Sbjct: 99  ADEYRLYPVGRLDYDTTGLILLTNDGDLTYRLT--HPKHEIEKIYVAGLRGIPDNQDI-- 154

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +        +G   A + F++I    Q+   +++    GR  Q+R  
Sbjct: 155 -------------FRFEHGLVLEGRLTAPAGFELIKAD-QRLSVVKITLREGRNRQIRKM 200

Query: 259 ALHMGCPIV 267
              +G P++
Sbjct: 201 CDMIGHPVI 209


>gi|296131694|ref|YP_003638941.1| pseudouridine synthase [Thermincola sp. JR]
 gi|296030272|gb|ADG81040.1| pseudouridine synthase [Thermincola potens JR]
          Length = 244

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/252 (15%), Positives = 85/252 (33%), Gaps = 52/252 (20%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72
            ++E  RLD+    H         +K+++  +V V+ +  +     ++ GQ         
Sbjct: 2   AEKERQRLDKVLA-HMGLGTRKEAKKLIKERKVEVNGELAQDPGLHVRPGQ--------- 51

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
             + I+   + ++                 Y      + NKP G+    G      +   
Sbjct: 52  --DRIVVNGEPVE-----------------YRQFVYLMLNKPQGVLSATGDESGQVVVDL 92

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           L    + +   P    RLD++T G+L++      A + L+     + + K Y++ V G  
Sbjct: 93  LS--PNYQSFHPFPVGRLDKDTEGLLLLTNDGHLAHRLLS---PKKHVPKTYYATVSGTV 147

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             +                +        + G        K++    +    +E+  + G+
Sbjct: 148 TQEDV--------------EMFRQGVILDDGYRTLPGCLKILRSGPE--SEVELTIYEGK 191

Query: 252 THQLRVHALHMG 263
            HQ++     +G
Sbjct: 192 YHQVKRMFQAVG 203


>gi|17566858|ref|NP_505498.1| hypothetical protein ZK287.7 [Caenorhabditis elegans]
 gi|14530707|emb|CAA94803.2| C. elegans protein ZK287.7, partially confirmed by transcript
           evidence [Caenorhabditis elegans]
          Length = 387

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 53/348 (15%), Positives = 96/348 (27%), Gaps = 79/348 (22%)

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILL-YEDSKIYVFNKPAGISVQG-------- 121
              LN  +++     +  N  + + +L   +L +   +  V  KP G+S  G        
Sbjct: 26  PAPLNPKVQKALTPATFSNPNQLARYLSKKVLAHAPGRFVVLEKPYGLSCVGQLQENGGV 85

Query: 122 ------GSGIAYHIDGFLKSWVDS-----------------KGQKPRLTHRLDQETSGIL 158
                          G +K+                     +  +      L +  SG +
Sbjct: 86  FGNSVRDERKTEKWAGTIKARTQEQMGVTISDCIKDLRKLLREPQLSFCTGLKRYLSGAI 145

Query: 159 VVARTRAAAQHLTESFRMRRIQ------KIYWSLVWGIPKNKKECIANWLL-KKSHIGGD 211
           V+      +  L E  R               ++  G P+     I  +   +      +
Sbjct: 146 VLPCNEKDSNILKECIRSTSSNVEPPFMYNALAITIGRPEKSSGVITGFATFRNVGKHKE 205

Query: 212 YV---HVVKQNEKGANYAIS---HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           Y+       +  K   YA+     ++V+D        ++   +    H  R+    M CP
Sbjct: 206 YIFEERKTTKRAKTGKYAVEGHMSYRVLDTK-NGISLIDFSVNKFARHLPRLMLTQMSCP 264

Query: 266 IVGDHKYCANFKGNFTSP-----------------------IQNK-------LYLHARYM 295
           I+GD  Y          P                         N+       +Y H    
Sbjct: 265 ILGDTIYWRRLADVDGVPELISAGNMGHRIFIPPHLCSTLETSNRSLLTSLPIYCHVYNT 324

Query: 296 DLPHPEGGR---LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
                 G     L   A  PAH +   D LG ++    ++ R     E
Sbjct: 325 IFEDVGGHEAHGLVAAAKPPAHFIAMLDLLGLRHAYKDFMNRSEKPSE 372


>gi|77360285|ref|YP_339860.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Pseudoalteromonas haloplanktis TAC125]
 gi|76875196|emb|CAI86417.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 290

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 26/178 (14%), Positives = 61/178 (34%), Gaps = 29/178 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +  +L +         +   ++K + + +V V+ K  K  +R++    +R+         
Sbjct: 5   QGEKLQKVLARAGVG-SRREMEKYIDANRVSVNGKVAKLGDRVEETDSIRVDGH------ 57

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                     +V + + +D +  +++Y        NKP G                    
Sbjct: 58  ----------TVKIEEKADRICRVIMY--------NKPEGELSTRKDPEGRR--TVFDRL 97

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               G++     RLD  T+G+++       A  L        +++ Y + V+G    +
Sbjct: 98  PRIDGERWIAVGRLDINTAGLMLFTNDGELANRL--MHPSYEVEREYSARVFGEVTKE 153


>gi|223985762|ref|ZP_03635806.1| hypothetical protein HOLDEFILI_03112 [Holdemania filiformis DSM
           12042]
 gi|223962272|gb|EEF66740.1| hypothetical protein HOLDEFILI_03112 [Holdemania filiformis DSM
           12042]
          Length = 237

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/172 (18%), Positives = 63/172 (36%), Gaps = 33/172 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +         +++++R G+V V+ +RVK ++                     
Sbjct: 2   MRLDKFLAHAGFG-TRKAVKELVRKGRVEVNGQRVKKDD--------------------- 39

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             QKI +    +         I+ YE     + NKP G+     S         +   ++
Sbjct: 40  --QKIDERQDQIQVDG----RIVTYETEVYIMLNKPQGVV----SATEDSRYETVLDCLE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWG 189
           +         RLD +T G+L++      A   L+    + +  +++    W 
Sbjct: 90  TNRSDLFPVGRLDIDTEGLLLITNDGALAHDLLSPKKHVDKTYEVHLERPWD 141


>gi|300214283|gb|ADJ78699.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 240

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 86/245 (35%), Gaps = 52/245 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG---QVVRIPPVINALN 75
           MRLD++             +K++++ +VR++ + VK + +I+       + +   + ALN
Sbjct: 3   MRLDKFLSQTGK-FTRAEAKKVIKAKRVRLNGEVVK-DGKIKINEDSDKIFLDGELLALN 60

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
           +                                Y+ NKP G+           +   +  
Sbjct: 61  N----------------------------KEVYYMLNKPIGVVSATRDDKDKTVIDLIN- 91

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               + +      RLD+ET+G+L++    + A   ++     + + K Y ++V G    K
Sbjct: 92  -FPGRKEDLFPVGRLDKETTGLLIITNDGKFAHDIIS---PKKHVSKTYEAVVTGKISEK 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  I +  ++ ++        +           S  +VI              H G+ HQ
Sbjct: 148 EVKIFSQGMELANGDKLQPAQLDIISYSEKDDTSKVRVI-------------IHEGKYHQ 194

Query: 255 LRVHA 259
           +R   
Sbjct: 195 VRRMF 199


>gi|225874153|ref|YP_002755612.1| pseudouridine synthase rsuA family protein [Acidobacterium
           capsulatum ATCC 51196]
 gi|225791360|gb|ACO31450.1| pseudouridine synthase rsuA family protein [Acidobacterium
           capsulatum ATCC 51196]
          Length = 406

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 44/254 (17%), Positives = 85/254 (33%), Gaps = 43/254 (16%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           E      RL +   +     +    ++++ +G+V+V+ + V      + G          
Sbjct: 18  EEPRGGERLQKILASA-GVASRRKAEELILAGRVQVNGQVVT-----EMG-----FKADA 66

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           A +HI  + K+L     L                + ++ NKP G           H    
Sbjct: 67  ASDHIRVDGKLLQGPEKL----------------RYFMLNKPKGYVTTVSDPEGRHTVME 110

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                   G++     RLD  + G+L++    A A  LT++     ++K+Y   V G P 
Sbjct: 111 FFHGRGKGGERLYPVGRLDYASEGLLLMTNDGALANTLTKASSH--VEKVYLVKVSGRPT 168

Query: 193 NK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            +  ++  A  ++ +   G   V       +    A            +  W E+    G
Sbjct: 169 EEQLEQIRAGIMIDRGRPGEGRVMTAPAGVRMVRDA------------ENPWFELTLIEG 216

Query: 251 RTHQLRVHALHMGC 264
           R  ++R      G 
Sbjct: 217 RNREIRKMFEETGH 230


>gi|119469277|ref|ZP_01612216.1| pseudouridine synthase [Alteromonadales bacterium TW-7]
 gi|119447141|gb|EAW28410.1| pseudouridine synthase [Alteromonadales bacterium TW-7]
          Length = 289

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 62/178 (34%), Gaps = 29/178 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +  +L +         +   ++K + + +V V+ K  K  +R++   ++R+         
Sbjct: 4   QGEKLQKVLARAGVG-SRREMEKYIDANRVSVNGKVAKLGDRVEETDLIRVDGH------ 56

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                     +V + + +D +  +++Y        NKP G                    
Sbjct: 57  ----------TVKIEEKADRICRVIMY--------NKPEGELSTRKDPEGRR--TVFDRL 96

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               G +     RLD  TSG+++       A  L        +++ Y S V+G   N+
Sbjct: 97  PRIDGDRWIAVGRLDVNTSGLMLFTNDGELANRL--MHPSYEVEREYSSRVFGEVTNE 152


>gi|221066029|ref|ZP_03542134.1| pseudouridine synthase [Comamonas testosteroni KF-1]
 gi|220711052|gb|EED66420.1| pseudouridine synthase [Comamonas testosteroni KF-1]
          Length = 529

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/232 (14%), Positives = 77/232 (33%), Gaps = 45/232 (19%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      RIQ G +V++                         
Sbjct: 176 SRLEMEQLILEGRISVNNEPAHVGQRIQFGDIVKVN------------------------ 211

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
               ++  +    +++  ++KP G  V        +     +     +  K +   RLD 
Sbjct: 212 -GQPIRFRIDPPPARVIAYHKPVGEVV--THDDPQNRPTVFRKLPKLQHGKWQSVGRLDL 268

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L+   +   A  L        +++ Y + V G    +++      ++       +
Sbjct: 269 NTEGLLLFTSSGELANSL--MHPRFGLEREYAARVLGALSKEEKQRLLDGVQLEDGEASF 326

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             V     +GAN                CW  +    GR  ++R     +G 
Sbjct: 327 GAVEDGGGEGAN----------------CWYRVTISEGRNREVRRMFEAVGH 362


>gi|264679428|ref|YP_003279335.1| Pseudouridine synthase, Rsu [Comamonas testosteroni CNB-2]
 gi|262209941|gb|ACY34039.1| Pseudouridine synthase, Rsu [Comamonas testosteroni CNB-2]
          Length = 529

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/232 (14%), Positives = 77/232 (33%), Gaps = 45/232 (19%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      RIQ G +V++                         
Sbjct: 176 SRLEMEQLILEGRISVNNEPAHVGQRIQFGDIVKVN------------------------ 211

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
               ++  +    +++  ++KP G  V        +     +     +  K +   RLD 
Sbjct: 212 -GQPIRFRIDPPPARVIAYHKPVGEVV--THDDPQNRPTVFRKLPKLQHGKWQSVGRLDL 268

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L+   +   A  L        +++ Y + V G    +++      ++       +
Sbjct: 269 NTEGLLLFTSSGELANSL--MHPRFGLEREYAARVLGALSKEEKQRLLDGVQLEDGEASF 326

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             V     +GAN                CW  +    GR  ++R     +G 
Sbjct: 327 GAVEDGGGEGAN----------------CWYRVTISEGRNREVRRMFEAVGH 362


>gi|217031566|ref|ZP_03437071.1| hypothetical protein HPB128_21g124 [Helicobacter pylori B128]
 gi|216946766|gb|EEC25362.1| hypothetical protein HPB128_21g124 [Helicobacter pylori B128]
          Length = 159

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/149 (24%), Positives = 62/149 (41%), Gaps = 19/149 (12%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N      Q VR   +I  +  +I               
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----QAVRKSQMIQGVVSLI------------HFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +     L++E     VF+KP  +      G  YH +  L       G+     HRLD E
Sbjct: 64  PNEKTQALVFETKDFGVFDKPPQVYTHP-KGYFYH-ESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRRIQKI 182
           TSG+++  +T  +A+ L   F  ++++K 
Sbjct: 122 TSGLVLAGKTLQSAKDLKALFMQKKVEKN 150


>gi|28897989|ref|NP_797594.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|153838627|ref|ZP_01991294.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ3810]
 gi|260364226|ref|ZP_05776929.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
 gi|260877145|ref|ZP_05889500.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|260898993|ref|ZP_05907434.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|260902058|ref|ZP_05910453.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
 gi|34098481|sp|Q87QD4|RSUA_VIBPA RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|28806203|dbj|BAC59478.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|149747999|gb|EDM58859.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ3810]
 gi|308088663|gb|EFO38358.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|308093845|gb|EFO43540.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|308109089|gb|EFO46629.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
 gi|308111860|gb|EFO49400.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
 gi|328473055|gb|EGF43903.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 10329]
          Length = 233

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 87/247 (35%), Gaps = 54/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRLD++  +           KI++SG+V VD +  K  + ++  G VV            
Sbjct: 1   MRLDKYLCDAL-GATRKQATKIIKSGEVLVDGEVQKSGSFKVPEGGVVEWDGREVG---- 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                           +   + I+LY+ +                    Y+   F+    
Sbjct: 56  ----------------APGPRYIMLYKPADFVC-----------SHEDGYNPTAFVL-LD 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           + K +      RLD +T+G++++      + +  +   + ++  +++ +          +
Sbjct: 88  EPKVENLHFAGRLDVDTTGLVLITDDGQWSHRITSPKHKCKKTYRVWLA----------D 137

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I    ++K   G +      +NE+ A    +    ++   +    + +    G+ HQ++
Sbjct: 138 AIQPDYVEKFAQGIEL-----RNEREA----TLPAHLEIVNEAENEVLLTIVEGKYHQVK 188

Query: 257 VHALHMG 263
                +G
Sbjct: 189 RMFAALG 195


>gi|163783757|ref|ZP_02178743.1| hypothetical protein HG1285_01633 [Hydrogenivirga sp. 128-5-R1-1]
 gi|159881003|gb|EDP74521.1| hypothetical protein HG1285_01633 [Hydrogenivirga sp. 128-5-R1-1]
          Length = 244

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 79/249 (31%), Gaps = 48/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL+R+        +     K++  G+V+V+ + V+                 +    I 
Sbjct: 3   VRLNRYLS-MCGVTSRRKADKLIEEGRVKVNGEVVR-----------------DLGVKID 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   ++      K    +            + NKP     Q G   +      ++  + 
Sbjct: 45  PEVDRVEVDGKEVKPPRKI----------YIILNKPCCYLTQLGK--SQSGKKTIEELIK 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD  T G+L++      A  +       ++ K+Y +LV G         
Sbjct: 93  DVPERVFPVGRLDYNTEGLLLLTNDGELANRV--LHPRYKLPKVYLALVKGKVSK----- 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                   +      H  +  +  A       +++         LE+  H GR H ++  
Sbjct: 146 --------NTLRKMKHGAELEDGFAKPD--DVRIVRYEGDN-TLLEIVFHEGRKHIVKRF 194

Query: 259 ALHMGCPIV 267
               G P++
Sbjct: 195 LASFGHPVI 203


>gi|190149356|ref|YP_001967881.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|307262671|ref|ZP_07544300.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 13
           str. N273]
 gi|189914487|gb|ACE60739.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|306871999|gb|EFN03714.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 13
           str. N273]
          Length = 232

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/179 (21%), Positives = 69/179 (38%), Gaps = 22/179 (12%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            LK  L +ED+ + +FNKP  +  Q            LK ++      P    RLD+++ 
Sbjct: 30  PLKLQLSFEDTVVVLFNKPFDVLTQ---FTDEQGRQTLKDFIPIPQIYP--VGRLDRDSE 84

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHI 208
           G+L++         L      ++  K Y + V GIP+        K   + + L K +  
Sbjct: 85  GLLLLTNNGEIQHRLANPKFEKQ--KTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAK- 141

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   K          +  K+ +       W+E++ H G+  Q+R    H+G P +
Sbjct: 142 -------AKAISAPNYEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTL 193


>gi|258545095|ref|ZP_05705329.1| ribosomal large subunit pseudouridine synthase D [Cardiobacterium
           hominis ATCC 15826]
 gi|258519672|gb|EEV88531.1| ribosomal large subunit pseudouridine synthase D [Cardiobacterium
           hominis ATCC 15826]
          Length = 80

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 18/74 (24%), Positives = 26/74 (35%), Gaps = 9/74 (12%)

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQ--------NKLYLHARYMDLPHP-EGGRLQITA 309
                 P+VGD  Y          P +         +  LHA  + L HP +   +   +
Sbjct: 1   MAAQHYPLVGDPLYGLATPSGKGLPPEVRQTLLAFPRQALHATALTLSHPADDDEITFAS 60

Query: 310 PLPAHMVKTWDSLG 323
           PLPA M     +L 
Sbjct: 61  PLPADMQTLLAALR 74


>gi|190575146|ref|YP_001972991.1| ribosomal large subunit pseudouridine synthase B [Stenotrophomonas
           maltophilia K279a]
 gi|190013068|emb|CAQ46700.1| ribosomal large subunit pseudouridine synthase B [Stenotrophomonas
           maltophilia K279a]
          Length = 542

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/246 (15%), Positives = 75/246 (30%), Gaps = 41/246 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +   L++ +  G V+V+ +  +    ++SG  + +         + 
Sbjct: 24  ERLHKVLAQAGLG-SRRALEQRIAEGLVKVNGEVAQTGMSVKSGDKIELDGRGFVATALA 82

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    E S++ V+NKP G                 +S   
Sbjct: 83  -------------------------EPSRVLVYNKPEGEVT--TREDPEGRPTVFESLPP 115

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            KG +     RLD  T+G+L+       A  +        +++ Y   V       +E +
Sbjct: 116 LKGARWIAIGRLDINTTGLLLATTDGELANAM--MHPSFEVEREYVVRVRA--PEGEEKV 171

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           ++ ++ +   G     V  ++       I              W  +    GR  ++R  
Sbjct: 172 SDAIVDRLARG-----VALEDGPAKFDEIERI----GGTDSHDWFRVVVKEGRNREVRRL 222

Query: 259 ALHMGC 264
               GC
Sbjct: 223 WESQGC 228


>gi|166031891|ref|ZP_02234720.1| hypothetical protein DORFOR_01592 [Dorea formicigenerans ATCC
           27755]
 gi|166028344|gb|EDR47101.1| hypothetical protein DORFOR_01592 [Dorea formicigenerans ATCC
           27755]
          Length = 243

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 80/246 (32%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++            +++ +R G+V VD +  K                        
Sbjct: 7   IRLDKFLSEMGVG-TRQEVKQYIRKGKVEVDGEIAK-----------------------R 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E K+ ++  N+T   +     + Y     Y+ NKP+G+           +   +K    
Sbjct: 43  PELKVDETKANVTLDGE----RIGYASYVYYMLNKPSGVVSATEDKREKTVIDLIK---G 95

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K +      RLD++T G+L++      A + L+       + K Y++ V G        
Sbjct: 96  QKRKDLFPVGRLDKDTVGLLLITNDGNLAHRLLS---PKHHVDKCYFAKVQGNVTKDD-- 150

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                         +   V    +         K+    +     + +    G+ HQ++ 
Sbjct: 151 -----------AEKFAEGVNIGTEDEPEITMPGKLDIIKSDDLSEIRLTIQEGKFHQVKR 199

Query: 258 HALHMG 263
               +G
Sbjct: 200 MFQAVG 205


>gi|299530511|ref|ZP_07043931.1| Pseudouridine synthase, Rsu [Comamonas testosteroni S44]
 gi|298721487|gb|EFI62424.1| Pseudouridine synthase, Rsu [Comamonas testosteroni S44]
          Length = 529

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/232 (14%), Positives = 77/232 (33%), Gaps = 45/232 (19%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      RIQ G +V++                         
Sbjct: 176 SRLEMEQLILEGRISVNNEPAHVGQRIQFGDIVKVN------------------------ 211

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
               ++  +    +++  ++KP G  V        +     +     +  K +   RLD 
Sbjct: 212 -GQPIRFRIDPPPARVIAYHKPVGEVV--THDDPQNRPTVFRKLPKLQHGKWQSVGRLDL 268

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L+   +   A  L        +++ Y + V G    +++      ++       +
Sbjct: 269 NTEGLLLFTSSGELANSL--MHPRFGLEREYAARVLGALSKEEKQRLLDGVQLEDGEASF 326

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             V     +GAN                CW  +    GR  ++R     +G 
Sbjct: 327 GAVEDGGGEGAN----------------CWYRVTISEGRNREVRRMFEAVGH 362


>gi|74317276|ref|YP_315016.1| ribosomal large subunit pseudouridine synthase B [Thiobacillus
           denitrificans ATCC 25259]
 gi|74056771|gb|AAZ97211.1| pseudouridine synthase, Rsu [Thiobacillus denitrificans ATCC 25259]
          Length = 296

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/252 (13%), Positives = 72/252 (28%), Gaps = 46/252 (18%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
              +  + RL +   +     +   +++ +  G+V+V+ +     +++    VV++    
Sbjct: 27  TAPEAASERLHKALASAGLG-SRREMEEWIAEGRVQVNGETATVGSKVGPRDVVKVSGRR 85

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
             L    K  +IL                + ++     V     G               
Sbjct: 86  VYLRFDEKRTRIL----------------IYHKSEGEIVSRDDPG-----------GRAT 118

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
              +    +G K     RLD  T G+++   +   A  L        +++ Y   V G  
Sbjct: 119 VFDALPRLRGSKWIAVGRLDYNTDGLMIFTTSGDLANRL--MHPRFEVEREYAVRVLGEL 176

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                      ++                +GAN                 W  +    GR
Sbjct: 177 TEDMIAELLAGVELDDGPAQLQSCFAAGGEGANR----------------WYRVVIKEGR 220

Query: 252 THQLRVHALHMG 263
             ++R    H+G
Sbjct: 221 KREVRRLFEHLG 232


>gi|116513179|ref|YP_812086.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. cremoris SK11]
 gi|116108833|gb|ABJ73973.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. cremoris SK11]
          Length = 242

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 85/243 (34%), Gaps = 41/243 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L+ G+V V            +G++ R        N   
Sbjct: 1   MRLDKFLAESGLG-SRSEVKVLLKKGRVTV------------AGEIQRDGRFQVDKN--- 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                       ++   F   IL Y++   Y+ NKP G+       +   +   L     
Sbjct: 45  ------------SRQVAFDGQILDYQEYYYYLLNKPQGVVSATKDNVFKTVVQLLSEKDF 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K   P    RLD+ T G+L+++   A    LT+    + ++K Y++ + G   +  E I
Sbjct: 93  RKDIFP--VGRLDKNTEGLLILSNDGALGHDLTQ--PKKHVEKEYFARIDGKVTD--EII 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +    +   G+               +      D  +     + +  H G+ HQ++  
Sbjct: 147 NKFAEGLTLKNGEKAR-------PGELFVEKTYKGDSQSGWVSEIRVIIHEGKFHQVKRM 199

Query: 259 ALH 261
              
Sbjct: 200 FEA 202


>gi|327439180|dbj|BAK15545.1| 16S rRNA uridine-516 pseudouridylate synthase [Solibacillus
           silvestris StLB046]
          Length = 240

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 88/248 (35%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++ +L+   V VD   VK                 ++  H+ 
Sbjct: 5   MRLDKLLAN-MGYGSRKEVKLLLKQKAVTVDGVTVK-----------------DSAMHVN 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E++ +       ++ +F+            + NKP G+     S      D  +   +D
Sbjct: 47  PEKQNVSVFGERVEYVEFI----------YLMMNKPPGVI----SATEDRYDQTVIDLLD 92

Query: 139 SKGQK--PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + Q   P    RLD++T G+L++      A   L+     + + K Y++ + G+     
Sbjct: 93  PEYQHFEPFPVGRLDKDTEGLLLITNDGNLAHNLLS---PKKHVPKWYYAKIDGVVTEAD 149

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I  +    +   G        + K     I         + +   +E+    G+ HQ+
Sbjct: 150 --IEAFAQGVTLEDG-------YHTKPGELKI-------LVSGEQSEIELMIQEGKFHQV 193

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 194 KRMFEAVG 201


>gi|269215383|ref|ZP_06159237.1| ribosomal large subunit pseudouridine synthase B [Slackia exigua
           ATCC 700122]
 gi|269130870|gb|EEZ61945.1| ribosomal large subunit pseudouridine synthase B [Slackia exigua
           ATCC 700122]
          Length = 256

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 84/252 (33%), Gaps = 51/252 (20%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQS-GQVVRIPPVINALN 75
            MR+ ++        +    + ++ +G+V V+ + V    +R+     VVR+   +  L+
Sbjct: 17  PMRVQKFLARA-GVASRRGSENLMTTGRVSVNGRVVTELGSRVDPRCDVVRVDGHVVHLS 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                                       + S   + NKPAG                L  
Sbjct: 76  ----------------------------DGSTTLMLNKPAGYITTMSDPFGRACVAELVP 107

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                G       RLD +T+GIL+ +        L      + + K Y +LV G    ++
Sbjct: 108 IDAYPG--LFPIGRLDADTTGILLFSTDGELGNGL--LHPRKHVDKTYQALVEGSVSEEE 163

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                  L++   G +    +    +           + C ++    L++  H GR  Q+
Sbjct: 164 -------LERLRSGVELEDGMTAPAEA---------RLTCVSEDESRLDITIHEGRKRQV 207

Query: 256 RVHALHMGCPIV 267
           R     +G P+V
Sbjct: 208 RRMCATVGHPVV 219


>gi|254525039|ref|ZP_05137094.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219722630|gb|EED41155.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 546

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/246 (15%), Positives = 76/246 (30%), Gaps = 41/246 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +   L++ +  G V+V+ +  +    ++SG  + +           
Sbjct: 24  ERLHKVLAQAGLG-SRRALEQRIAEGLVKVNGEVAQTGMSVKSGDKIEL----------- 71

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                               +  L E S++ V+NKP G                 +S   
Sbjct: 72  --------------DGRGFVATALAEPSRVLVYNKPEGEVT--TREDPEGRPTVFESLPP 115

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            KG +     RLD  T+G+L+       A  +        +++ Y   V       +E +
Sbjct: 116 LKGARWIAIGRLDINTTGLLLATTDGELANAM--MHPSFEVEREYVVRVRA--PEGEEKV 171

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           ++ ++ +   G     V  ++       I              W  +    GR  ++R  
Sbjct: 172 SDAIVDRLSRG-----VALEDGPAKFDEIERI----GGTDSHDWFRVVVKEGRNREVRRL 222

Query: 259 ALHMGC 264
               GC
Sbjct: 223 WESQGC 228


>gi|315038194|ref|YP_004031762.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           amylovorus GRL 1112]
 gi|325956646|ref|YP_004292058.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           acidophilus 30SC]
 gi|312276327|gb|ADQ58967.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           amylovorus GRL 1112]
 gi|325333211|gb|ADZ07119.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           acidophilus 30SC]
 gi|327183471|gb|AEA31918.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           amylovorus GRL 1118]
          Length = 238

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 83/247 (33%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    +K++ +G+V+VD K +      + G  V     I   +  I
Sbjct: 3   ERLQKIIAEA-GIASRRKAEKMITAGRVKVDGKVIT-----KLGTKVDTFSNITVDDEPI 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + + +                         Y+F KP G+               +  + +
Sbjct: 57  ERESL-----------------------HTYLFYKPRGVVSTASDDKDR---KTVVDYFE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD +TSG+L++      A  L        + K+Y + + GI   ++   
Sbjct: 91  DVPYRLYPVGRLDYDTSGLLLMTNDGKLANLL--MHPRNEVSKVYVAKIKGILTPEEI-- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRV 257
                          H VK ++  A  A    KV+    +K    +++  H G  HQ++ 
Sbjct: 147 -----------KTLTHGVKLDDFKAAPA--KVKVLKTDKRKDTQIVQLTIHEGHYHQVKR 193

Query: 258 HALHMGC 264
               +G 
Sbjct: 194 MFKAVGH 200


>gi|317498387|ref|ZP_07956682.1| RNA pseudouridylate synthase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316894281|gb|EFV16468.1| RNA pseudouridylate synthase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 242

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 36/245 (14%), Positives = 87/245 (35%), Gaps = 50/245 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHII 78
           RLD++  +   ++     ++ ++ G+V V+ + +K    ++ +                 
Sbjct: 6   RLDKFLCDSL-NMTRKEAKESVKKGKVVVNGEAIKKPEYKVDA----------------- 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ  ++    L          + +E     + +KP G+     +   +H    L    +
Sbjct: 48  -EQDQVEFDHKL----------IQFEQFHYLMLHKPQGVVS---ATKDHHDQTVLDLIHE 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD++T G+L++      A  L      + + K+Y++ V G     +   
Sbjct: 94  DYKDRLFPVGRLDKDTEGLLLLTDDGMLAHEL--LSPRKHVDKVYFAKVSGQFGENE--- 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               + +   G D          G     +  +++    Q+   + +    G+ HQ++  
Sbjct: 149 ----IARFKEGLDI-------GNGEKSKQARLQILKADVQE-SEVLITIMEGKFHQVKRM 196

Query: 259 ALHMG 263
              +G
Sbjct: 197 VKAVG 201


>gi|238855198|ref|ZP_04645517.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 269-3]
 gi|260664561|ref|ZP_05865413.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii SJ-7A-US]
 gi|282932508|ref|ZP_06337933.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 208-1]
 gi|313471973|ref|ZP_07812465.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 1153]
 gi|238832090|gb|EEQ24408.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 269-3]
 gi|239529095|gb|EEQ68096.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 1153]
 gi|260561626|gb|EEX27598.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii SJ-7A-US]
 gi|281303457|gb|EFA95634.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 208-1]
          Length = 237

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 81/250 (32%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++  G+V V+ K V     +++S   + +          
Sbjct: 3   ERLQKLIAQA-GIASRRKAEKLITEGRVAVNGKIVTELGTKVESSASIEVD--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                       L    +   + LLY         KP G+  SV+   G        +  
Sbjct: 53  -----------GLPIQKESKHTYLLY---------KPRGVISSVKDDKGRK-----TVLD 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +    +     RLD +TSG+L++      A  L        + K+Y + + G    ++
Sbjct: 88  FFEESPYRLYPVGRLDYDTSGLLLITNDGELANKL--MHPRHMVDKVYVAKIKGFLTPEE 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQ 254
                  ++                 G   A +  K+I     +    +++  H G  HQ
Sbjct: 146 IHSLKHGVRID---------------GKKSAPAKVKIISTNREKGTSIVQLTIHEGHYHQ 190

Query: 255 LRVHALHMGC 264
           ++     +G 
Sbjct: 191 VKRMFKAVGH 200


>gi|218551308|ref|YP_002385100.1| 23S rRNA pseudouridine synthase F [Escherichia fergusonii ATCC
           35469]
 gi|218358850|emb|CAQ91507.1| 23S rRNA pseudouridine synthase [Escherichia fergusonii ATCC 35469]
 gi|325499580|gb|EGC97439.1| 23S rRNA pseudouridine synthase F [Escherichia fergusonii ECD227]
          Length = 290

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSIRLNKYISE--SGICSRREADRFIEQGNVFINGKRATIGDQVKPGDVVKVNGRLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|199598710|ref|ZP_03212124.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus rhamnosus HN001]
 gi|229552173|ref|ZP_04440898.1| pseudouridylate synthase [Lactobacillus rhamnosus LMS2-1]
 gi|258508377|ref|YP_003171128.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           rhamnosus GG]
 gi|258539588|ref|YP_003174087.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           rhamnosus Lc 705]
 gi|199590398|gb|EDY98490.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus rhamnosus HN001]
 gi|229314475|gb|EEN80448.1| pseudouridylate synthase [Lactobacillus rhamnosus LMS2-1]
 gi|257148304|emb|CAR87277.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           rhamnosus GG]
 gi|257151264|emb|CAR90236.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           rhamnosus Lc 705]
 gi|259649691|dbj|BAI41853.1| pseudouridylate synthase [Lactobacillus rhamnosus GG]
          Length = 248

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 87/253 (34%), Gaps = 54/253 (21%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N RL +   N     +  + + ++ SG V+V+         + +   ++I P        
Sbjct: 5   NERLQKVIANA-GIASRRHAETLIASGHVKVNG-------HVTTEMGIKIGPHDTVEVDG 56

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
           +   K                     E  + ++F KP G+  +V+   G        +  
Sbjct: 57  VPIGK---------------------EAKRYFLFYKPRGVISAVEDNKGRK-----VVTD 90

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNK 194
           + +   ++     RLD +TSG+LV+      A HL        ++K Y + V GIP +  
Sbjct: 91  YFEDVQERLYPVGRLDYDTSGLLVMTNDGELANHL--MHPRYALEKKYVAKVEGIPNRPA 148

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              +   +     +       +   +K    AI               + +  H G  HQ
Sbjct: 149 LAPLKTGVSIDGKMTAPAKVEILSTDKAKKTAI---------------VALTIHQGMNHQ 193

Query: 255 LRVHALHMGCPIV 267
           ++     +G P++
Sbjct: 194 VKKMFKAVGFPVI 206


>gi|92112979|ref|YP_572907.1| ribosomal large subunit pseudouridine synthase B [Chromohalobacter
           salexigens DSM 3043]
 gi|91796069|gb|ABE58208.1| ribosomal large subunit pseudouridine synthase B [Chromohalobacter
           salexigens DSM 3043]
          Length = 286

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/220 (15%), Positives = 71/220 (32%), Gaps = 31/220 (14%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++  +  G+V+V+ +     +RI++   V                   +  VNL  
Sbjct: 19  SRREMETAIADGRVKVNGQVATLGDRIETRDRVTFD----------------ERPVNLRD 62

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
             +  + +++Y        NKP G                 +     KG++     RLD 
Sbjct: 63  AEEVPRRVIMY--------NKPEGELC--TRRDPEGRRTVFERLPRLKGERWIAVGRLDI 112

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+L+       A  L       ++++ Y   V G  + +     N +++   +    
Sbjct: 113 NTSGLLLFTTDGELANRL--MHPATQVEREYAVRVMGNVRQEH---VNAMVEGVMLEDGP 167

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                  E G     + F V+    +      +    G T
Sbjct: 168 ARFTDVQEFGGEGINTWFHVVILEGRNREVRRLWESQGLT 207


>gi|325068740|ref|ZP_08127413.1| pseudouridine synthase family protein [Actinomyces oris K20]
          Length = 303

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 44/256 (17%), Positives = 94/256 (36%), Gaps = 51/256 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RL +    H    +    ++++  G+V VD   V      ++G  VR+ P+   +  
Sbjct: 76  SGQRLQKVLA-HAGVASRRACEQLIADGRVSVDGVTVT-----EAG--VRVDPLTQEIR- 126

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDG 131
            +   +IL +   +T                  + +KPAG+       +G   +A +   
Sbjct: 127 -VDGSRILTNPELIT-----------------LMLHKPAGVVTTMEDPEGRPTVAQYGRD 168

Query: 132 FLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           +L    +     +     RLD ET G+L+++     +  L        I K Y ++V G 
Sbjct: 169 YLAEHPELPDSLRLVHVGRLDTETEGLLLLSNDGELSHRL--MHPSFEIAKTYVAIVEGQ 226

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                  +  W+ +K   G +      ++ +     ++    +     +   +E+  H+G
Sbjct: 227 -------VEAWVPRKLRRGIEL-----EDGEAKADRVT----VKDSGPRGSIVEITLHSG 270

Query: 251 RTHQLRVHALHMGCPI 266
           +   +R     +G P+
Sbjct: 271 KNRIVRRMLDAVGHPV 286


>gi|220912302|ref|YP_002487611.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
 gi|219859180|gb|ACL39522.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
          Length = 403

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 86/252 (34%), Gaps = 45/252 (17%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +RL +   +     +    ++++  G+V VD + V      + G  VRI P     
Sbjct: 159 DADGVRLQKVMASA-GVASRRVCEEMIAEGRVEVDGQVVT-----ELG--VRIDP----- 205

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                             H D L+   L E+    VFNKP G+                 
Sbjct: 206 -------------ATAVIHVDGLRIQ-LDENLVYMVFNKPKGVVSTMEDPDGRPCISDFL 251

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               + G++     RLD  T G+L++      A  LT       + K Y   V G     
Sbjct: 252 KNNKNTGERLFHVGRLDVATEGLLLLTNDGELANRLT--HPSYEVPKTYLVQVRGPFPQG 309

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                        IG      V+  +  A  A+  F+++D        +E+  H+G+   
Sbjct: 310 -------------IGAQLKAGVELEDGPA--AVDSFRLVDSTP-GHVLIEVVLHSGKNRI 353

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 354 VRRMFDAVGFPV 365


>gi|289428195|ref|ZP_06429891.1| pseudouridylate synthase [Propionibacterium acnes J165]
 gi|295130922|ref|YP_003581585.1| pseudouridylate synthase [Propionibacterium acnes SK137]
 gi|289158576|gb|EFD06783.1| pseudouridylate synthase [Propionibacterium acnes J165]
 gi|291375273|gb|ADD99127.1| pseudouridylate synthase [Propionibacterium acnes SK137]
 gi|313764054|gb|EFS35418.1| conserved hypothetical protein [Propionibacterium acnes HL013PA1]
 gi|313771915|gb|EFS37881.1| conserved hypothetical protein [Propionibacterium acnes HL074PA1]
 gi|313807148|gb|EFS45643.1| conserved hypothetical protein [Propionibacterium acnes HL087PA2]
 gi|313809640|gb|EFS47376.1| conserved hypothetical protein [Propionibacterium acnes HL083PA1]
 gi|313816404|gb|EFS54118.1| conserved hypothetical protein [Propionibacterium acnes HL059PA1]
 gi|313819344|gb|EFS57058.1| conserved hypothetical protein [Propionibacterium acnes HL046PA2]
 gi|313819993|gb|EFS57707.1| conserved hypothetical protein [Propionibacterium acnes HL036PA1]
 gi|313823215|gb|EFS60929.1| conserved hypothetical protein [Propionibacterium acnes HL036PA2]
 gi|313824997|gb|EFS62711.1| conserved hypothetical protein [Propionibacterium acnes HL063PA1]
 gi|313827299|gb|EFS65013.1| conserved hypothetical protein [Propionibacterium acnes HL063PA2]
 gi|313829960|gb|EFS67674.1| conserved hypothetical protein [Propionibacterium acnes HL007PA1]
 gi|313833036|gb|EFS70750.1| conserved hypothetical protein [Propionibacterium acnes HL056PA1]
 gi|314914915|gb|EFS78746.1| conserved hypothetical protein [Propionibacterium acnes HL005PA4]
 gi|314917860|gb|EFS81691.1| conserved hypothetical protein [Propionibacterium acnes HL050PA1]
 gi|314919749|gb|EFS83580.1| conserved hypothetical protein [Propionibacterium acnes HL050PA3]
 gi|314924832|gb|EFS88663.1| conserved hypothetical protein [Propionibacterium acnes HL036PA3]
 gi|314930009|gb|EFS93840.1| conserved hypothetical protein [Propionibacterium acnes HL067PA1]
 gi|314956415|gb|EFT00727.1| conserved hypothetical protein [Propionibacterium acnes HL027PA1]
 gi|314957284|gb|EFT01387.1| conserved hypothetical protein [Propionibacterium acnes HL002PA1]
 gi|314960611|gb|EFT04713.1| conserved hypothetical protein [Propionibacterium acnes HL002PA2]
 gi|314967733|gb|EFT11832.1| conserved hypothetical protein [Propionibacterium acnes HL037PA1]
 gi|314972874|gb|EFT16971.1| conserved hypothetical protein [Propionibacterium acnes HL053PA1]
 gi|314975703|gb|EFT19798.1| conserved hypothetical protein [Propionibacterium acnes HL045PA1]
 gi|314978089|gb|EFT22183.1| conserved hypothetical protein [Propionibacterium acnes HL072PA2]
 gi|314984113|gb|EFT28205.1| conserved hypothetical protein [Propionibacterium acnes HL005PA1]
 gi|314986250|gb|EFT30342.1| conserved hypothetical protein [Propionibacterium acnes HL005PA2]
 gi|314989536|gb|EFT33627.1| conserved hypothetical protein [Propionibacterium acnes HL005PA3]
 gi|315080909|gb|EFT52885.1| conserved hypothetical protein [Propionibacterium acnes HL078PA1]
 gi|315084832|gb|EFT56808.1| conserved hypothetical protein [Propionibacterium acnes HL027PA2]
 gi|315086005|gb|EFT57981.1| conserved hypothetical protein [Propionibacterium acnes HL002PA3]
 gi|315088276|gb|EFT60252.1| conserved hypothetical protein [Propionibacterium acnes HL072PA1]
 gi|315095697|gb|EFT67673.1| conserved hypothetical protein [Propionibacterium acnes HL038PA1]
 gi|315098205|gb|EFT70181.1| conserved hypothetical protein [Propionibacterium acnes HL059PA2]
 gi|315101641|gb|EFT73617.1| conserved hypothetical protein [Propionibacterium acnes HL046PA1]
 gi|315109460|gb|EFT81436.1| conserved hypothetical protein [Propionibacterium acnes HL030PA2]
 gi|327327900|gb|EGE69674.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes HL096PA3]
 gi|327330039|gb|EGE71792.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes HL096PA2]
 gi|327442730|gb|EGE89384.1| hypothetical protein HMPREF9570_02678 [Propionibacterium acnes
           HL043PA1]
 gi|327443872|gb|EGE90526.1| hypothetical protein HMPREF9571_02471 [Propionibacterium acnes
           HL043PA2]
 gi|327443940|gb|EGE90594.1| hypothetical protein HMPREF9568_01854 [Propionibacterium acnes
           HL013PA2]
 gi|327452345|gb|EGE98999.1| hypothetical protein HMPREF9581_01384 [Propionibacterium acnes
           HL087PA3]
 gi|327452780|gb|EGE99434.1| hypothetical protein HMPREF9586_02253 [Propionibacterium acnes
           HL083PA2]
 gi|328752647|gb|EGF66263.1| hypothetical protein HMPREF9588_02444 [Propionibacterium acnes
           HL025PA2]
 gi|328753801|gb|EGF67417.1| hypothetical protein HMPREF9579_01456 [Propionibacterium acnes
           HL087PA1]
 gi|328755029|gb|EGF68645.1| hypothetical protein HMPREF9563_01406 [Propionibacterium acnes
           HL020PA1]
 gi|328761441|gb|EGF74967.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes HL099PA1]
 gi|332675803|gb|AEE72619.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes 266]
          Length = 245

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 47/294 (15%), Positives = 97/294 (32%), Gaps = 58/294 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ++E+ +RL +         +    + ++ +G+V V+ + +                 +  
Sbjct: 2   SNEQGIRLQKVLAQA-GLASRRAAEDMIAAGRVEVNGELI-----------------VEQ 43

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              +  E+  +    +    +   +  + Y      V NKP G+               L
Sbjct: 44  GRRVDPERDEIRVDGSRIPTA---RRHVYY------VLNKPQGVVSTMDDPEGRPCLSDL 94

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +     +G +     RLD ETSG++++      A  +T      ++ K Y + V G   +
Sbjct: 95  EGV--PRGIRLFHVGRLDTETSGLILLTNDGEFANRMT--HPSYKVLKTYLADVEGRVDD 150

Query: 194 K--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K  +       L+   +  D V +V+  E+                     +E+  H GR
Sbjct: 151 KVIRRLSKGLTLEDGPVKPDAVRLVQAGEE------------------HSLVEVSLHEGR 192

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              +R     +  P+                P++ K        +L H E G+L
Sbjct: 193 NRIVRRIMDSVAHPV-------RRLSRTAIGPVRLKRLGRGDMRELTHEELGQL 239


>gi|163851700|ref|YP_001639743.1| pseudouridine synthase [Methylobacterium extorquens PA1]
 gi|163663305|gb|ABY30672.1| pseudouridine synthase [Methylobacterium extorquens PA1]
          Length = 242

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 42/260 (16%), Positives = 84/260 (32%), Gaps = 47/260 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLDR   N   + +   ++ + R+G VR+D + ++  ++       R+P   +    + 
Sbjct: 4   LRLDRLLAN-LGYGSRREVEGLARAGLVRLDGQALRDASQ-------RVPLEPDLSARMT 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + + LD    +         ++L++   +   +K  G  V             L     
Sbjct: 56  VQGEALDPLPGV--------CLMLHKPLGVTCSHKEVGPLV----------YSLLPERWR 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD+ETSG+L++    A    L      +      + +    P    E  
Sbjct: 98  RRDPALSTVGRLDKETSGLLLMTDDGA---LLHRIISPKAKVSKRYRVTLARPLQGDETA 154

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                +    G D   +                 ++          +  H GR HQ+R  
Sbjct: 155 ILASGEMMLEGEDKPLL----------------PVEMETDDPTHCTVTLHEGRYHQVRRM 198

Query: 259 ALHMGCPIVGDHKYCANFKG 278
              +G  +  D  +     G
Sbjct: 199 FAALGNHV--DALHRDRVGG 216


>gi|332687173|ref|YP_004456947.1| ribosomal small subunit pseudouridine synthaseA [Melissococcus
           plutonius ATCC 35311]
 gi|332371182|dbj|BAK22138.1| ribosomal small subunit pseudouridine synthaseA [Melissococcus
           plutonius ATCC 35311]
          Length = 243

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 88/248 (35%), Gaps = 51/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++++L+   ++V+    K   +       +I  + + + H  
Sbjct: 1   MRLDKFLSDSGLG-SRKEVKQLLKQKCIKVNGTLAKDGKQ-------QISQIDDYVTHAG 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           ++                    ++Y+    YV NKP  +       I   +   L     
Sbjct: 53  EK--------------------IVYQKYFYYVLNKPKNVISSTKDPIERTVVDLLAKKHY 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K   P    RLD++T G+L++      A Q L+     + + K Y + + GI   +   
Sbjct: 93  RKDIFP--VGRLDKDTEGLLLLTNDGDLAHQLLS---PKKHVDKEYLAEIDGIVTEQDIK 147

Query: 198 I--ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           +    + LK          ++ Q ++G                +   + +    G+ HQ+
Sbjct: 148 LFAKGFTLKNGEAVKPARLIIDQMDEG---------------HQMTIVHLTIQEGKFHQV 192

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 193 KRVFETIG 200


>gi|221041208|dbj|BAH12281.1| unnamed protein product [Homo sapiens]
          Length = 230

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/175 (19%), Positives = 66/175 (37%), Gaps = 7/175 (4%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSK 140
           +L  +++  +  D L++ ++     +   NKP G+ V G  G          L   +   
Sbjct: 57  LLPKNLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLW 116

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKE 196
            Q+ ++     +E+SG+++++     A  L +    + R +R    Y ++  GIP   + 
Sbjct: 117 EQELQVVRASGKESSGLVLLSSCPQTASRLQKYFTHARRAQRPTATYCAVTDGIPAASEG 176

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
            I   L K  HI G  +        G    I   +             + P TG+
Sbjct: 177 KIQAAL-KLEHIDGVNLVSPGLGRGGVLLDIVPLQRGVRGMDLGWLALLSPKTGK 230


>gi|52081501|ref|YP_080292.1| putative pseudouridine synthase YtzF [Bacillus licheniformis ATCC
           14580]
 gi|52786879|ref|YP_092708.1| hypothetical protein BLi03154 [Bacillus licheniformis ATCC 14580]
 gi|319647410|ref|ZP_08001631.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
 gi|52004712|gb|AAU24654.1| putative Pseudouridine synthase YtzF [Bacillus licheniformis ATCC
           14580]
 gi|52349381|gb|AAU42015.1| putative protein [Bacillus licheniformis ATCC 14580]
 gi|317390456|gb|EFV71262.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
          Length = 240

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 49/263 (18%), Positives = 88/263 (33%), Gaps = 59/263 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N     +   ++K+L++G VRV+ + VK                        
Sbjct: 1   MRLDKLLSNSGYG-SRKEVKKMLKNGAVRVNDQLVK------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSI---LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 D+  ++   SD +      ++Y +    + NKP G+           +   L  
Sbjct: 36  ------DAKKHVDPESDDITVYGAPVMYREFIYLMMNKPQGVLSATEDSRQETVVDLLD- 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             +    +P    RLD++T G+L++      A Q L+   +    +     +   I +  
Sbjct: 89  -PELLRFEPFPVGRLDKDTEGLLLLTNDGQLAHQLLSP--KKHVPKTYEVHVNKPIDQAA 145

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                + L K   IG  YV       K A  +      +         L +    G+ HQ
Sbjct: 146 L----DQLEKGVDIGEGYV------TKPAEAS------LLASENGVERLLLTITEGKFHQ 189

Query: 255 LRVHALHMGCPIVGDHKYCANFK 277
           ++     +G     D  Y    K
Sbjct: 190 VKRMLKAVGH----DVIYLKRLK 208


>gi|256822107|ref|YP_003146070.1| RNA-binding S4 domain-containing protein [Kangiella koreensis DSM
           16069]
 gi|256795646|gb|ACV26302.1| RNA-binding S4 domain protein [Kangiella koreensis DSM 16069]
          Length = 267

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/218 (17%), Positives = 70/218 (32%), Gaps = 31/218 (14%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++K +  G+V V+    K   R      +R+   I ++  I  E+           
Sbjct: 16  SRREIEKWIEGGRVSVNGSIAKLGERATDKDTIRVDGRIISI--ISAEETYT-------- 65

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                         ++  +NKP G                  +  ++   +     RLD 
Sbjct: 66  --------------RVLAYNKPLGEVS--TKKDPEGRATVFDNLPNTSFGRWISIGRLDI 109

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T+G+L+       A  L       ++++ Y   V G      E I+N L K   I GD 
Sbjct: 110 NTTGLLLFTNNGELAHRL--MHPSYQVERKYAVRVHGEVTP--EMISN-LTKGVLIEGDT 164

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                  +KG   A   ++V     +     ++    G
Sbjct: 165 CQFTYVQDKGGEGANHWYEVGLAEGKNREVRKLWESQG 202


>gi|320534116|ref|ZP_08034657.1| hypothetical protein HMPREF9057_02553 [Actinomyces sp. oral taxon
           171 str. F0337]
 gi|320133695|gb|EFW26102.1| hypothetical protein HMPREF9057_02553 [Actinomyces sp. oral taxon
           171 str. F0337]
          Length = 324

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 46/257 (17%), Positives = 92/257 (35%), Gaps = 53/257 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RL +    H    +    ++++  G+V VD   V      ++G  VR+ P       
Sbjct: 76  SGQRLQKVLA-HAGVASRRACEQLIADGRVSVDGITVT-----EAG--VRVDP------- 120

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKI-YVFNKPAGISV-----QGGSGIAYHID 130
                        LT+      S +L     I  + +KPAG+       +G   +A +  
Sbjct: 121 -------------LTQEIRLDGSRILTNPELITLMLHKPAGVVTTMDDPEGRPTVAQYGR 167

Query: 131 GFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
            +L    +     +     RLD ET G+L+++     +  L        I K Y ++V G
Sbjct: 168 DYLAEHPELPDSLRLVHVGRLDTETEGLLLLSNDGELSHRL--MHPSFEIAKTYVAIVEG 225

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   +  W+ +K   G +      ++ +     ++    +     +   +E+  H+
Sbjct: 226 Q-------VEPWVPRKLRRGIEL-----EDGEAKADRVT----VKDSGPRGSIVEITLHS 269

Query: 250 GRTHQLRVHALHMGCPI 266
           G+   +R     +G P+
Sbjct: 270 GKNRIVRRMLDAVGHPV 286


>gi|300072082|gb|ADJ61482.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. cremoris NZ9000]
          Length = 242

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 84/243 (34%), Gaps = 41/243 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L+ G+V V            +G++ R        N   
Sbjct: 1   MRLDKFLAESGLG-SRSEVKVLLKKGRVTV------------AGEIQRDGRFQVDKN--- 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                       ++   F   IL Y++   Y+ NKP G+       +   +   L     
Sbjct: 45  ------------SRQVAFDGQILDYQEYYYYLLNKPQGVVSATKDNVFKTVVQLLSEKDF 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K   P    RLD+ T G+L++    A    LT+    + ++K Y++ + G   +  E I
Sbjct: 93  RKDIFP--VGRLDKNTEGLLILTNDGALGHDLTQ--PKKHVEKEYFARIDGKVTD--EII 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +    +   G+               +      D  +     + +  H G+ HQ++  
Sbjct: 147 NKFAEGLTLKNGEKAR-------PGELFVEKTYKGDSQSGWVSEIRVIIHEGKFHQVKRM 199

Query: 259 ALH 261
              
Sbjct: 200 FEA 202


>gi|260893153|ref|YP_003239250.1| pseudouridine synthase [Ammonifex degensii KC4]
 gi|260865294|gb|ACX52400.1| pseudouridine synthase [Ammonifex degensii KC4]
          Length = 251

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 86/251 (34%), Gaps = 52/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++ +G+V+V+ + V   +++     V++ P  +      
Sbjct: 4   ERLQKVLARA-GIASRRKAEELIVAGRVKVNGQVV---DKLG----VKVDPERD------ 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSW 136
                   S+ +      L   L+Y       F+KP G+        G        +  +
Sbjct: 50  --------SIEVDGKPVKLPERLVY-----LAFHKPRGVVTTLHDPQGRPK-----VADF 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +    ++     RLD ++ G+L++      A  L        + K Y   V G    +K 
Sbjct: 92  LKGIKERVFPVGRLDYDSEGLLLLTNDGELAHRL--LHPRFHVPKTYLVWVKGEVGKEKL 149

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +    +K                +      +  +V+   A+    L++    GR  Q+R
Sbjct: 150 NLLRRGIKL---------------EDGPTLPAEVRVL-RRARGETVLQLTIREGRKRQIR 193

Query: 257 VHALHMGCPIV 267
                +GC ++
Sbjct: 194 RMLKALGCEVL 204


>gi|330685968|gb|EGG97591.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           epidermidis VCU121]
          Length = 246

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 36/233 (15%), Positives = 72/233 (30%), Gaps = 49/233 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+ + V     ++ +   V +                    + L 
Sbjct: 19  SRRKAETLITDGKVKVNGQVVTELGTKVSNSDTVEV------------------EGIKLE 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +           ED    +FNKPA +     S         +  +      +     RLD
Sbjct: 61  Q-----------EDKIYILFNKPAQVIT---SVSDDRGRKVVTDYFKDIETRIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+L++        +L    R    +K    L   + + + + +   +  +      
Sbjct: 107 YDTSGLLLLT-NDGEFTNLMTHPRYHIKKKYVAKLKGYLMREEVKALEKGIELEDGFTQP 165

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               VK  +K  N                  +E+    GR  Q+R    H G 
Sbjct: 166 AQVKVKNQDKDKNT---------------TLVEITISEGRNRQVRRMFEHFGH 203


>gi|307256109|ref|ZP_07537896.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 10
           str. D13039]
 gi|306865290|gb|EFM97186.1| Pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 10
           str. D13039]
          Length = 231

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/179 (21%), Positives = 69/179 (38%), Gaps = 22/179 (12%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            LK  L +ED+ + +FNKP  +  Q            LK ++      P    RLD+++ 
Sbjct: 29  PLKPQLSFEDTVVVLFNKPFDVLTQ---FTDEQGRQTLKDFIPIPQIYP--VGRLDRDSE 83

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKECIANWLLKKSHI 208
           G+L++         L      ++  K Y + V GIP+        K   + + L K +  
Sbjct: 84  GLLLLTNNGEIQHRLANPKFEKQ--KTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAK- 140

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                   K          +  K+ +       W+E++ H G+  Q+R    H+G P +
Sbjct: 141 -------AKAISAPNYEWQTAPKIRERKIIPTSWIELKIHEGKNRQVRRMTAHIGFPTL 192


>gi|325090611|gb|EGC43921.1| DRAP deaminase [Ajellomyces capsulatus H88]
          Length = 243

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 22/85 (25%), Positives = 30/85 (35%), Gaps = 9/85 (10%)

Query: 238 QKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANF-------KGNFTSPIQNKLYL 290
           + +  +   P TGRTHQLRVH  ++G PI  D  Y           K + T     ++  
Sbjct: 6   EGYSIVHCLPLTGRTHQLRVHLQYLGHPITNDPIYSNRRVFGHSLGKADATGENDEQIIY 65

Query: 291 HARYMDLPHPEG--GRLQITAPLPA 313
               M    P           P P 
Sbjct: 66  RLSKMGKTEPVDSLSYQTFQTPPPE 90


>gi|301156469|emb|CBW15940.1| 16S rRNA pseudouridylate 516 synthase [Haemophilus parainfluenzae
           T3T1]
          Length = 232

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/245 (15%), Positives = 78/245 (31%), Gaps = 51/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +R   V+++ + VK                 N    + 
Sbjct: 1   MRLDKFIAEN-TGLTRSQATKAIRQSAVKINGEIVK-----------------NGATKVS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E +I      L             E+ + ++ +KP G       G    I  F +    
Sbjct: 43  LEDEIYFEDELLPWV----------EEGQYFMLHKPQGYVCSHDDGDYPTIYQFFE---P 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PLSGKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHQCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ +        +   +++  ++    A    +V+D +       E     GR HQ++  
Sbjct: 137 ADPVENHYASACEEGILLRGEKEPTKPA--KLEVLDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMG 263
              +G
Sbjct: 190 FAALG 194


>gi|288918462|ref|ZP_06412813.1| pseudouridine synthase [Frankia sp. EUN1f]
 gi|288350102|gb|EFC84328.1| pseudouridine synthase [Frankia sp. EUN1f]
          Length = 308

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 80/253 (31%), Gaps = 48/253 (18%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            + E +RL +         +    ++++ +G+VRVD + V+   R               
Sbjct: 66  PEAEGIRLQKVLAAAGIG-SRRASEELIDAGRVRVDGEVVREQGR--------------- 109

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              +  E+ +++           L  + L+         KP G+               +
Sbjct: 110 --RVDPERAVIEVDGERVVTRTGLVHLALH---------KPRGVLSTMA---DDRGRPTI 155

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              +   G +     RLD ++ G+L+V      A  L                 +G+ K 
Sbjct: 156 ADLLTEFGTRLFHVGRLDADSEGLLLVTNDGDLAHRLMH-------------PSYGVQKT 202

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               I   + K                +     +   ++ID  A +   +E+  H GR H
Sbjct: 203 YLVEITGPVRKDLP----RRLRSGVELEDGPVKVDSARIIDMAASRV-MMEIVLHEGRNH 257

Query: 254 QLRVHALHMGCPI 266
            +R     +G P+
Sbjct: 258 VVRRVMESVGHPV 270


>gi|326773388|ref|ZP_08232671.1| ribosomal large subunit pseudouridine synthase B [Actinomyces
           viscosus C505]
 gi|326636618|gb|EGE37521.1| ribosomal large subunit pseudouridine synthase B [Actinomyces
           viscosus C505]
          Length = 324

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 44/256 (17%), Positives = 94/256 (36%), Gaps = 51/256 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RL +    H    +    ++++  G+V VD   V      ++G  VR+ P+   +  
Sbjct: 76  SGQRLQKVLA-HAGVASRRACEQLIADGRVSVDGVTVT-----EAG--VRVDPLTQEIR- 126

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDG 131
            +   +IL +   +T                  + +KPAG+       +G   +A +   
Sbjct: 127 -VDGSRILTNPELIT-----------------LMLHKPAGVVTTMEDPEGRPTVAQYGRD 168

Query: 132 FLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           +L    +     +     RLD ET G+L+++     +  L        I K Y ++V G 
Sbjct: 169 YLTEHPELPDSLRLVHVGRLDTETEGLLLLSNDGELSHRL--MHPSFEIAKTYVAIVEGQ 226

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                  +  W+ +K   G +      ++ +     ++    +     +   +E+  H+G
Sbjct: 227 -------VEPWVPRKLRRGIEL-----EDGEAKADRVT----VKDSGPRGSIVEITLHSG 270

Query: 251 RTHQLRVHALHMGCPI 266
           +   +R     +G P+
Sbjct: 271 KNRIVRRMLDAVGHPV 286


>gi|255505461|ref|ZP_05346261.3| ribosomal large subunit pseudouridine synthase F [Bryantella
           formatexigens DSM 14469]
 gi|255267773|gb|EET60978.1| ribosomal large subunit pseudouridine synthase F [Bryantella
           formatexigens DSM 14469]
          Length = 267

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/258 (12%), Positives = 76/258 (29%), Gaps = 63/258 (24%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           + +  E +R++++        +     +++  G+V VD        ++   Q +R+    
Sbjct: 22  ITDTAEPVRINKYLAQA-GICSRREADRLIAEGKVLVDGAAAVAGQKVLPSQDIRV---- 76

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                 ++ Q+ +                       + V NKP G+              
Sbjct: 77  -EGEQAVRSQERI-----------------------LLVVNKPRGVVCTTDKTWGDTTLE 112

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L  +      +     RLD+++ G++++         +  +      + +         
Sbjct: 113 ELVDYPS----RVFYAGRLDKDSEGLILMTNDGELQDKIMRAANRHEKEYLV-------- 160

Query: 192 KNKKECIANWLLKKSHIGG-----DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                 + +  LKK   G      D V    + EK    A   F+++             
Sbjct: 161 -KVDRTVDDTFLKKMAKGVYLRELDTVTRPCRVEKTGRRA---FRIV------------- 203

Query: 247 PHTGRTHQLRVHALHMGC 264
              G   Q+R     +G 
Sbjct: 204 LTQGLNRQIRRMCAALGY 221


>gi|83647424|ref|YP_435859.1| 16S rRNA uridine-516 pseudouridylate synthase-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83635467|gb|ABC31434.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Hahella chejuensis KCTC 2396]
          Length = 323

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 27/184 (14%), Positives = 54/184 (29%), Gaps = 31/184 (16%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
              +  +L +         +    ++ +  G+VRV+ K     +R+ +   + +     A
Sbjct: 7   EKAQGEKLQKVIARQ-GLASRREAEEWISGGRVRVNGKVAHLGDRVTAEDKISVDGHKIA 65

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                                     ++  E++ + V+NKP G                 
Sbjct: 66  --------------------------MVDAEETMVLVYNKPEGEVT--SRKDPEGRPTVF 97

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 K  +     RLD  T+G+L+       A  L       +I + Y   V G    
Sbjct: 98  ARLPKLKSGRWVAVGRLDINTTGLLIFTTDGELANRL--MHPSSQIDREYAVRVHGEVTE 155

Query: 194 KKEC 197
           +   
Sbjct: 156 EMVT 159


>gi|149277497|ref|ZP_01883638.1| 23S rRNA pseudouridine synthase [Pedobacter sp. BAL39]
 gi|149231730|gb|EDM37108.1| 23S rRNA pseudouridine synthase [Pedobacter sp. BAL39]
          Length = 329

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/246 (12%), Positives = 75/246 (30%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       + +     + +  G V ++ K+ K  +++  G +V +         + 
Sbjct: 7   RLNKYISE--SGLCSRRAADRYIEQGNVYINGKKAKVGDKVFFGDLVMVNGQTIEPKEV- 63

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    E S +  +NKP GI+    +G+  +I   +     
Sbjct: 64  -------------------------EHSVLIAYNKPVGITSTTEAGVKGNIVDHVNH--- 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD+++ G++ +         +  +      + +   +    P  ++   
Sbjct: 96  --SERVFPIGRLDKDSQGLIFLTNNGDLVNKILRAGNNHEKEYL---VTVNKPLTEQFIT 150

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + K   I G      K  ++                      ++    G   Q+R  
Sbjct: 151 N--MSKGVPILGIMTKKCKVTKESP-----------------FVFKITLIQGLNRQIRRM 191

Query: 259 ALHMGC 264
             H G 
Sbjct: 192 CEHFGF 197


>gi|320547064|ref|ZP_08041362.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           equinus ATCC 9812]
 gi|320448301|gb|EFW89046.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           equinus ATCC 9812]
          Length = 242

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 48/249 (19%), Positives = 87/249 (34%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++++L+  QV V+ K             +   P       + 
Sbjct: 1   MRLDKFLVEAGVG-SRTEVKQLLKKKQVLVNGK-------------LETSPKTQIDEKL- 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              KI+    NL+           YE    Y+ NKP G+     +    H    L     
Sbjct: 46  --DKIVCQGQNLS-----------YEKFVYYMLNKPKGVIS---ATEDDHHKTVLDLLDK 89

Query: 139 SKGQK-PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-- 194
           +   K      RLD +T G+L++    + A   L+     + + K+Y + V GI  ++  
Sbjct: 90  TAWDKEVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVDKLYCAKVAGIMTDEDV 146

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K       LK        ++++  +EK                     +E+    G+ HQ
Sbjct: 147 KAFADGIELKDFTCQPAQLNIINADEK----------------SNTSLVEIVIKEGKFHQ 190

Query: 255 LRVHALHMG 263
           ++   L  G
Sbjct: 191 VKRMVLACG 199


>gi|145355123|ref|XP_001421818.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582057|gb|ABP00112.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 238

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 36/221 (16%), Positives = 77/221 (34%), Gaps = 26/221 (11%)

Query: 43  SGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILL 102
           +G+V V+ + V+ + R+++G VV +   +     ++ E         +   +      LL
Sbjct: 10  AGRVLVNGELVRPSQRVKAGDVVTLDGKV-----MLWEAYARRVEEEIANDATSSFVYLL 64

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFL-KSWVDSKGQKPRLTHRLDQETSGILVVA 161
           Y        NKP G+           +   L +     K  +     RLD+++SG++++ 
Sbjct: 65  Y--------NKPRGVVCTMEPHQRTSLHFALERERARMKKIRIFPVGRLDKDSSGLVLLT 116

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK 221
                +  L +  R +  ++    +   +     E +A  ++  +             E 
Sbjct: 117 NDGRVSDALLDPSR-KAEKEYDVDVDRDVSAADVERLAAGVVITTLQQR------TMTET 169

Query: 222 GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
            A       + I     +F   E     GR  Q+R     +
Sbjct: 170 TAPTQPCEVRKIGPRTLRFVLKE-----GRNRQIRKMCEAL 205


>gi|114586115|ref|XP_001171216.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 3 [Pan troglodytes]
          Length = 209

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 30/134 (22%), Positives = 59/134 (44%), Gaps = 7/134 (5%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF--LKSWVDSK 140
           +L  +++  +  D L++ ++     +   NKP G+ V G  G          L   +  +
Sbjct: 65  LLPKNLSREELVDALRAAVVDRKGPLVTLNKPQGLPVTGKPGELTLFSVLPELSQSLGLR 124

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNKKE 196
            Q+ ++     +E+SG+++++     A  L +    + R +R   IY ++  GIP   + 
Sbjct: 125 EQELQVVRASGKESSGLVLLSSCPQTASRLQKYFIHARRAQRPTAIYCAVTDGIPAASEG 184

Query: 197 CIANWLLKKSHIGG 210
            I   L K  HI G
Sbjct: 185 KIQAAL-KLEHIDG 197


>gi|297623666|ref|YP_003705100.1| RNA-binding S4 domain-containing protein [Truepera radiovictrix DSM
           17093]
 gi|297164846|gb|ADI14557.1| RNA-binding S4 domain protein [Truepera radiovictrix DSM 17093]
          Length = 241

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/248 (14%), Positives = 70/248 (28%), Gaps = 57/248 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    + ++ SG V V+  R +   R+ +G  VR+           
Sbjct: 3   ERLQKFLARA-GVASRRKAEALILSGAVTVNGVRAELGQRVAAGDEVRV----------- 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + +++   + ++T                 Y   KP G+     +         +   V 
Sbjct: 51  RGERVAPPAAHVT-----------------YALYKPKGVIS---AVTDDRGRVTVLQLVP 90

Query: 139 SKGQKP--RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              + P      RLD ++ G+L++         LT               VW  P    E
Sbjct: 91  PSARVPGLHPVGRLDADSEGLLLLTTDGELTLTLTHPRYGHEKTYR----VWCEPVPGPE 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +       +   G       +   G                      +    GR  Q+R
Sbjct: 147 ALRRLERGVALEDGPARARRARAAPGG-------------------CTLVLSEGRNRQVR 187

Query: 257 VHALHMGC 264
                +GC
Sbjct: 188 RMLAALGC 195


>gi|295399019|ref|ZP_06809001.1| pseudouridine synthase [Geobacillus thermoglucosidasius C56-YS93]
 gi|312110375|ref|YP_003988691.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
 gi|294978485|gb|EFG54081.1| pseudouridine synthase [Geobacillus thermoglucosidasius C56-YS93]
 gi|311215476|gb|ADP74080.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
          Length = 243

 Score = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 90/250 (36%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++  G+V+V+ K V      + G  V++ P        I
Sbjct: 2   ERLQKVIARA-GIASRRKAEQLILQGKVKVNGKIVT-----ELG--VKVGPRDKVEVDGI 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSW 136
             +K                     E+   Y+F KP G+  SV+   G        +  +
Sbjct: 54  PVEK---------------------EEPVYYLFYKPRGVISSVKDDKGRK-----VVTDF 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNK 194
                ++     RLD +TSGIL++      A  L        I+K+Y + V  IP  +  
Sbjct: 88  FKDIDKRIYPVGRLDYDTSGILLLTNDGDFANLL--MHPRYEIEKVYIAKVKKIPTREQL 145

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K+     +L+        V ++  + K    AI               +E++ H GR  Q
Sbjct: 146 KQLEKGIMLEDGMTAPAKVKLLSHD-KQKQTAI---------------IEIRIHEGRNRQ 189

Query: 255 LRVHALHMGC 264
           +R     +GC
Sbjct: 190 VRRMFEAIGC 199


>gi|260913145|ref|ZP_05919627.1| ribosomal small subunit pseudouridine synthase A [Pasteurella
           dagmatis ATCC 43325]
 gi|260632732|gb|EEX50901.1| ribosomal small subunit pseudouridine synthase A [Pasteurella
           dagmatis ATCC 43325]
          Length = 233

 Score = 61.9 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 78/250 (31%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       +      K+L+   V ++ K  K N  ++      I      L  I 
Sbjct: 1   MRLDKFLAES-TGLTRSQANKVLKQSAVTMNGKVEK-NGSVKVNSEDEICFDGELLTWI- 57

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    E+ +  +  KP G       G    I  F    + 
Sbjct: 58  -------------------------EEGQYIMLYKPQGYVCSHDDGDYPTIYQFFDYPLS 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +   K     RLD +T+G++++      +  +T          +               +
Sbjct: 93  T---KLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ +        +   +++  ++    A    +++D +       E     GR HQ++  
Sbjct: 137 ADPIESNYQQACEAGILLRGEKELTKPA--KLEILDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAALGNKVVG 199


>gi|332652688|ref|ZP_08418433.1| ribosomal small subunit pseudouridine synthase A [Ruminococcaceae
           bacterium D16]
 gi|332517834|gb|EGJ47437.1| ribosomal small subunit pseudouridine synthase A [Ruminococcaceae
           bacterium D16]
          Length = 239

 Score = 61.9 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/253 (14%), Positives = 81/253 (32%), Gaps = 54/253 (21%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RLD+   +     +   +++++  G+V VD +                         
Sbjct: 2   AMERLDKLLAST-GRWSRKEVKELIARGRVLVDGRPA----------------------- 37

Query: 77  IIKEQKILDSSVNLTKHSDFLK-SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
              E K    S  +    + +  +  +Y      + +KPAG+           +   L  
Sbjct: 38  GRPEDKCEPQSACIQVDGEIVDCAPCVY-----IMLHKPAGLLSATQDKKQSTVLDLLPE 92

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +  +G       RLD++T G+L++          L+     + + K+Y++ V G     
Sbjct: 93  HLRRRG--LFPVGRLDKDTEGLLLLTDDGPLGHDLLS---PRKHVDKVYYARVDG----- 142

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                        I  + V V+ Q     +  +     ++          +    G+ HQ
Sbjct: 143 ------------QIDKEDVQVLAQGMTLGDGLVCLPAGLEPLGDG-SECLVTLREGKYHQ 189

Query: 255 LRVHALHMGCPIV 267
           ++      G P++
Sbjct: 190 VKRMLAARGKPVL 202


>gi|121607089|ref|YP_994896.1| pseudouridine synthase [Verminephrobacter eiseniae EF01-2]
 gi|121551729|gb|ABM55878.1| ribosomal large subunit pseudouridine synthase B [Verminephrobacter
           eiseniae EF01-2]
          Length = 520

 Score = 61.9 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/233 (15%), Positives = 77/233 (33%), Gaps = 47/233 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      RIQ G  V++                         
Sbjct: 184 SRLEMEQLILEGRISVNNEPAHIGQRIQFGDQVKVN------------------------ 219

Query: 93  HSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
               ++  +    +++  ++KP G +           +   L   V  K Q      RLD
Sbjct: 220 -GKPIRYRIDPPPARVIAYHKPVGEVVSHDDPHNRPTVFRRLPRLVQGKWQS---VGRLD 275

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             T G+L++  +   A  L        +++ Y   V G   N+++      ++       
Sbjct: 276 LNTEGLLLLTSSGELANQL--MHPRFGLEREYAVRVLGALSNEEKQKLLDGVRLDDGIAS 333

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +  +     +GAN                CW  +    GR  ++R     +G 
Sbjct: 334 FGTIEDGGGEGAN----------------CWYRVTIAEGRNREVRRMLEAVGH 370


>gi|225868275|ref|YP_002744223.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           equi subsp. zooepidemicus]
 gi|225701551|emb|CAW98765.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus equi subsp. zooepidemicus]
          Length = 237

 Score = 61.9 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 82/249 (32%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDK-KRVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++  +     +   ++ +L+  QV V+   +     ++                  
Sbjct: 1   MRLDKFLVDAGLG-SRSQVKLLLKKKQVSVNGVSQTSPKYQVN----------------- 42

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       LT +  +    L YE    Y+ NKP G+           +   L    
Sbjct: 43  -----------ELTDNVTYQGQRLNYETFVYYMLNKPKGVISATEDPSHKTVLDLLDDTA 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-- 194
             K        RLD++T G+L++    + A   L+     + + K Y + V G    +  
Sbjct: 92  RQKA--VFPVGRLDKDTHGLLLLTNDGKLAHALLS---PKKHVAKQYLAKVDGTMTQEDV 146

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K       LK       Y+ +++ NE                + K   +++    G+ HQ
Sbjct: 147 KHFAQGITLKDHQCMPAYLDILEINE----------------SLKTSLVKITIEEGKFHQ 190

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 191 VKRMVAACG 199


>gi|217966542|ref|YP_002352048.1| RNA-binding S4 domain protein [Dictyoglomus turgidum DSM 6724]
 gi|217335641|gb|ACK41434.1| RNA-binding S4 domain protein [Dictyoglomus turgidum DSM 6724]
          Length = 243

 Score = 61.9 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 91/246 (36%), Gaps = 45/246 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  N     +   +QK++++G V V+                   PV +   HI 
Sbjct: 1   MRLDKFLVNQGFG-SRKEVQKLIKAGIVYVNN-----------------FPVEDPSFHIN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ +++               + Y+++  ++ NKP G      +    +         +
Sbjct: 43  PEKDVVEIE----------GQEIEYKENYYFMLNKPKGYIT--ATYDENYPTVMDLFASE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T G+L++      A  L+       ++K Y+ +V G   +     
Sbjct: 91  PIVSKLFPVGRLDVDTEGLLIITSDGVLAHRLSHPKWN--VEKEYFVIVEGDISD----- 143

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +  S    + +++ K+  K   + +   KV+    ++   L +    G+ H ++  
Sbjct: 144 ----IDFSKYEKEGMYLKKEKYKTKPFKV---KVLKTSFEESELL-ITITEGKYHIVKKI 195

Query: 259 ALHMGC 264
              +G 
Sbjct: 196 MYAVGH 201


>gi|322832033|ref|YP_004212060.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321167234|gb|ADW72933.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 235

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 36/250 (14%), Positives = 75/250 (30%), Gaps = 53/250 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++   + + LR+ +V VD + VK  + +I   Q V     +      
Sbjct: 1   MRLDKFLSQQL-GVSRALVLRELRNKRVTVDGEIVKTGSMKISPEQRVEFDGNVLDQITG 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                             ++ NKP G      S         L    
Sbjct: 60  PR----------------------------YFMLNKPQGYVC---STDDPDHPTVLYFLE 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    K     RLD +T+G++++      +  +T          +               
Sbjct: 89  EPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------T 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + L   +    +    +   +     A      ++      C + +    GR HQ++ 
Sbjct: 136 LEHPLADDTAAQFEAGVQLHNEDSLTKPAQ-----LEKIED--CLVRLTLSEGRYHQVKR 188

Query: 258 HALHMGCPIV 267
               +G  +V
Sbjct: 189 MFAAVGNRVV 198


>gi|165975813|ref|YP_001651406.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|190149629|ref|YP_001968154.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|303252597|ref|ZP_07338760.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|307247349|ref|ZP_07529397.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|307249573|ref|ZP_07531560.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|307256398|ref|ZP_07538180.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|307260827|ref|ZP_07542513.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|307262953|ref|ZP_07544575.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
 gi|165875914|gb|ABY68962.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|189914760|gb|ACE61012.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|302648565|gb|EFL78758.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|306856193|gb|EFM88348.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|306858428|gb|EFM90497.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|306865028|gb|EFM96929.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|306869394|gb|EFN01185.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|306871579|gb|EFN03301.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
          Length = 230

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 39/277 (14%), Positives = 82/277 (29%), Gaps = 60/277 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      + L+SG V V+ K  K  + ++ G    I      L    
Sbjct: 1   MRLDKFIAEN-TGLTRSQAARALKSGLVTVNGKLEKSGS-VKIGDTDEICYEGERLE--- 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  + E     ++ KP G      S          + +  
Sbjct: 56  ----------------------WVDEGQYFMLY-KPQGYVC---SHDDGEYPTVFQFFDY 89

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               K     RLD +T+G++++    + + +  +      +   +  +          + 
Sbjct: 90  PLMTKLHTAGRLDVDTTGLVLLTDDGKWSHRITSPKHHCEKTYLVTLA----------DP 139

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + ++  KK   G       +         I  + V            +    GR HQ++ 
Sbjct: 140 VEDFYAKKLAEGILLRGEREPCLPAKMEVIDDYNV-----------NLTISEGRYHQVKR 188

Query: 258 HALHMGCPI-------VGDHKYCANFKGNFTSPIQNK 287
               +G  +       +GD     N +     P+  +
Sbjct: 189 MFAALGNKVEALHRWRIGDVVLDENLEEGEYRPLSEQ 225


>gi|308496136|ref|XP_003110256.1| hypothetical protein CRE_06624 [Caenorhabditis remanei]
 gi|308245093|gb|EFO89045.1| hypothetical protein CRE_06624 [Caenorhabditis remanei]
          Length = 787

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 17/39 (43%), Positives = 24/39 (61%)

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
              +++   TGRTHQ+RVH+  +G PIVGD  Y +   G
Sbjct: 637 HSVVQVHIETGRTHQIRVHSQFLGHPIVGDQLYNSTVWG 675


>gi|307824285|ref|ZP_07654511.1| RNA-binding S4 domain protein [Methylobacter tundripaludum SV96]
 gi|307734665|gb|EFO05516.1| RNA-binding S4 domain protein [Methylobacter tundripaludum SV96]
          Length = 279

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/156 (14%), Positives = 53/156 (33%), Gaps = 27/156 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +  R+ +         +   +++ +  G+++++ K V   +R+++G  + I       + 
Sbjct: 15  DGERIQKVLARGGVG-SRREIERWIDEGRLKINGKPVGLGDRLKAGDHLLIN------DR 67

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           ++  +K ++                      + +++KP G  V                 
Sbjct: 68  VVHWEKFVEQPTR------------------VLLYHKPVGEVV--TRRDPEGRPVVFTQL 107

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
                 +     RLD  TSG+L+V      A  L  
Sbjct: 108 PKLAISRWIAVGRLDINTSGLLLVTNNGELANRLMH 143


>gi|261885552|ref|ZP_06009591.1| pseudouridine synthase [Campylobacter fetus subsp. venerealis str.
           Azul-94]
          Length = 155

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/185 (18%), Positives = 71/185 (38%), Gaps = 41/185 (22%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKIL 84
                  I+    ++++ SG V    KR                        ++  + +L
Sbjct: 9   LLALQEGISNNEAKELIDSGLVSAGGKR------------------------LVLARGLL 44

Query: 85  DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP 144
           + + +  K +   K +++YED  I   NKP  I+ +  + I                 K 
Sbjct: 45  NENTSF-KVTKLAKPVMIYEDDNIVAVNKPPFITSEKVAEI----------------FKF 87

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
            L +RLD+ETSG++++ +     +   + F   +++K Y ++V GI  ++          
Sbjct: 88  PLLNRLDKETSGVILLYKNEEFQKAAIKEFANTKVKKTYLAIVRGIVVDEFSVELPISTV 147

Query: 205 KSHIG 209
           K+  G
Sbjct: 148 KTKSG 152


>gi|157150331|ref|YP_001449642.1| pseudouridine synthase rRNA-specific [Streptococcus gordonii str.
           Challis substr. CH1]
 gi|157075125|gb|ABV09808.1| pseudouridine synthase rRNA-specific [Streptococcus gordonii str.
           Challis substr. CH1]
          Length = 242

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 84/250 (33%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +    +   ++++L+ G V V+ +  K                        
Sbjct: 1   MRLDKFLVENGLG-SRSQVKEVLKKGLVLVNGRAEKS----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                     ++ + +D +      L YE    Y+ NKP G            +   L  
Sbjct: 37  -------PKTHINETADEIVVSGQKLTYEKFVYYLLNKPKGYISATEDERHKTVLDLLDE 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               K  +     RLD +T G+L++    + A   L+     + ++KIY + V G+    
Sbjct: 90  TARQK--EVFPVGRLDIDTHGLLLLTNNGKLAHAMLS---PKKHVEKIYRAQVAGLM--- 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK-FCWLEMQPHTGRTH 253
                            +   ++  +     A    K+++   +K    +E+    G+ H
Sbjct: 142 ----------NQSDVEQFARGIELKDFTCQPA--QLKIVELDEEKETSLVEITLAEGKFH 189

Query: 254 QLRVHALHMG 263
           Q++      G
Sbjct: 190 QVKRMVAACG 199


>gi|226496591|ref|NP_001140345.1| hypothetical protein LOC100272393 [Zea mays]
 gi|194699086|gb|ACF83627.1| unknown [Zea mays]
          Length = 116

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/97 (25%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
           E    R+I K Y +LV GI  + +  +   +    + G         +      A+S   
Sbjct: 6   EFSEERKISKFYRALVTGILDDDEVVVTQPIGLVHYPGVAEGLYAACSS--GKPAMSKVC 63

Query: 232 VIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           V++  A Q    ++++ H+GR HQ+R+H  ++G P+V
Sbjct: 64  VLERLAHQNHTLVQVEIHSGRPHQIRIHLAYIGHPLV 100


>gi|70949961|ref|XP_744344.1| pseudouridylate synthase [Plasmodium chabaudi chabaudi]
 gi|56524260|emb|CAH74473.1| pseudouridylate synthase, putative [Plasmodium chabaudi chabaudi]
          Length = 736

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 27/122 (22%), Positives = 52/122 (42%), Gaps = 9/122 (7%)

Query: 224 NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             +++ F  +    Q     L  QP TGRTHQ+R H   +  PI  D  Y  N +  + +
Sbjct: 558 KPSVTKFMFLSYNNQLNESLLLCQPMTGRTHQIRTHLKSLSFPISNDSHYNPNVEKEYMT 617

Query: 283 PIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWD-SLGFKYDRNLYIKRLYSQDEC 341
             + KL+   +    P+ E   ++  +  P  +V   + S  + YD  + +  + +++  
Sbjct: 618 KTE-KLHFENQ----PNEESKNIEKYSYYP--LVPFLNTSFNWLYDDTINLNNIDNEENL 670

Query: 342 KQ 343
             
Sbjct: 671 NN 672



 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 18/101 (17%), Positives = 39/101 (38%), Gaps = 18/101 (17%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           ++ G ++V+ K +  +  I+S   +           ++ E+ +L           + K I
Sbjct: 94  IKKGYIKVNNKNITNDYIIKSNDFIE-------HKLLLFEKPVL-----------YNKII 135

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           +LYED      NK A +         Y+    + +++   G
Sbjct: 136 ILYEDENFICVNKVASMPTHPVGSYQYNSLLRILNYISQSG 176



 Score = 45.0 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              HRLD+ TSGI++  + +  +   +E     +I K Y + V G  +N
Sbjct: 351 YTLHRLDKLTSGIVLFGKNKKFSTLFSEYVCNNKITKSYITRVEGDFRN 399


>gi|158316819|ref|YP_001509327.1| pseudouridine synthase [Frankia sp. EAN1pec]
 gi|158112224|gb|ABW14421.1| pseudouridine synthase [Frankia sp. EAN1pec]
          Length = 259

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 43/255 (16%), Positives = 82/255 (32%), Gaps = 49/255 (19%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           +   E +RL +   +     +  + ++++ SG+VRVD + V+   R              
Sbjct: 15  DPASEGIRLQKVLASAGIG-SRRHNEELIDSGRVRVDGEVVREQGR-------------- 59

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDG 131
               +  E  +++           L              NKP G+            I  
Sbjct: 60  ---RVDPETAVIEVDGERVVTRTGLVH---------LALNKPRGVLSAMSDDRGRPTIAD 107

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           FL  +            RLD ++ G+L+V      A  LT                 G+P
Sbjct: 108 FLTEF---GSVGLFHVGRLDGDSEGLLLVTNDGDLAHRLTHPSF-------------GVP 151

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K     I+  + +                +    ++   +++D  A +   +E+  H GR
Sbjct: 152 KTYLVEISGPVRRDVP----RRLRSGVTLEDGPVSVDAARIVDVAASRV-MMELTLHEGR 206

Query: 252 THQLRVHALHMGCPI 266
            H +R     +G P+
Sbjct: 207 KHVVRRMMEAVGHPV 221


>gi|289425044|ref|ZP_06426821.1| pseudouridylate synthase [Propionibacterium acnes SK187]
 gi|289154022|gb|EFD02710.1| pseudouridylate synthase [Propionibacterium acnes SK187]
 gi|313792449|gb|EFS40542.1| conserved hypothetical protein [Propionibacterium acnes HL110PA1]
 gi|313801506|gb|EFS42755.1| conserved hypothetical protein [Propionibacterium acnes HL110PA2]
 gi|313838267|gb|EFS75981.1| conserved hypothetical protein [Propionibacterium acnes HL086PA1]
 gi|314963143|gb|EFT07243.1| conserved hypothetical protein [Propionibacterium acnes HL082PA1]
 gi|315078206|gb|EFT50249.1| conserved hypothetical protein [Propionibacterium acnes HL053PA2]
 gi|327453532|gb|EGF00187.1| hypothetical protein HMPREF9584_01968 [Propionibacterium acnes
           HL092PA1]
          Length = 245

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/255 (15%), Positives = 86/255 (33%), Gaps = 51/255 (20%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ++E+ +RL +         +    + ++ +G+V V+ + +                 +  
Sbjct: 2   SNEQGIRLQKVLAQA-GLASRRAAEDMIAAGRVEVNGELI-----------------VEQ 43

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              +  E+  +    +    +   +  + Y      V NKP G+               L
Sbjct: 44  GRRVDPERDEIRVDGSRIPTA---RRHVYY------VLNKPQGVVSTMDDPEGRPCLSDL 94

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +     +G +     RLD ETSG++++      A  +T      ++ K Y + V G   +
Sbjct: 95  EGV--PRGIRLFHVGRLDTETSGLILLTNDGEFANRMT--HPSYKVLKTYLADVEGRVDD 150

Query: 194 K--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K  +       L+   +  D V +V+  E+                     +E+  H GR
Sbjct: 151 KVIRRLSKGLTLEDGPVKPDAVRLVQAGEE------------------HSLVEVSLHEGR 192

Query: 252 THQLRVHALHMGCPI 266
              +R     +  P+
Sbjct: 193 NRIVRRIMDSVAHPV 207


>gi|269218469|ref|ZP_06162323.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 848 str. F0332]
 gi|269211580|gb|EEZ77920.1| ribosomal large subunit pseudouridine synthase B [Actinomyces sp.
           oral taxon 848 str. F0332]
          Length = 247

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 79/253 (31%), Gaps = 56/253 (22%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RL +    +    +    + ++  G+V VD                          H+
Sbjct: 9   GERLQKVLARNGVG-SRRACEGLIAQGRVSVDG-------------------------HV 42

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIY--VFNKPAGISVQGGSGIAYHIDGFLKS 135
           ++E       V    H D ++      DS +      KP G+     +         L  
Sbjct: 43  VRELGTRVDPVASVIHVDGIRVQ---TDSSLLTLALYKPPGVVS---TMYDDMGRPGLAQ 96

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +V+ + ++     RLDQ+T G+++++        LT       + K Y + V G      
Sbjct: 97  YVEDRPERLYHVGRLDQDTEGLILLSNDGELTHRLT--HPKYEVPKTYIARVEGSVTRGL 154

Query: 196 ECI--ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             +      L+      D                    ++   A +   +E+  H+GR  
Sbjct: 155 GRVLERGITLEDGPARVDRF------------------ILRESAPRNSIVEITLHSGRNR 196

Query: 254 QLRVHALHMGCPI 266
            +R     +G P+
Sbjct: 197 IVRRMMAEVGHPV 209


>gi|227496094|ref|ZP_03926400.1| possible pseudouridine synthase Rsu [Actinomyces urogenitalis DSM
           15434]
 gi|226834328|gb|EEH66711.1| possible pseudouridine synthase Rsu [Actinomyces urogenitalis DSM
           15434]
          Length = 325

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 57/282 (20%), Positives = 98/282 (34%), Gaps = 56/282 (19%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RL +    H    +    ++I+ +G+V VD   V      + G  VR+ P    +   
Sbjct: 75  GERLQKVLA-HAGVASRRACEEIIAAGRVSVDGVVVT-----EPG--VRVDPSRQEIR-- 124

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-----QGGSGIAYHIDGF 132
                 +D S  LT             D    + +KPAG+       QG   +A   + F
Sbjct: 125 ------VDGSRVLTDP-----------DVITVLLHKPAGVVTTMEDPQGRPTVADLAEQF 167

Query: 133 LKSWV--DSKGQKPRLTH--RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           +          +  RL H  RLD ET G+L+++     A  L        I K Y ++V 
Sbjct: 168 ISEHRTELEHPESVRLVHVGRLDTETEGLLLLSNDGDLAHRL--MHPSFEISKTYVAIVE 225

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G        +  W+ +K   G +    + Q ++          V+         +E+  H
Sbjct: 226 GQ-------VEGWVPRKLRRGIELDDGLAQADR---------VVVKDAGPSGSIVEITLH 269

Query: 249 TGRTHQLRVHALHMGCPI--VGDHKYCANFKGNFTSPIQNKL 288
           +G+   +R     +G P+  +   K      G        +L
Sbjct: 270 SGKNRIVRRMLDAVGHPVTRLARTKLGPLGIGGLRPGQMRRL 311


>gi|255086821|ref|XP_002509377.1| predicted protein [Micromonas sp. RCC299]
 gi|226524655|gb|ACO70635.1| predicted protein [Micromonas sp. RCC299]
          Length = 179

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/130 (23%), Positives = 50/130 (38%), Gaps = 20/130 (15%)

Query: 49  DKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKI 108
           D + V+    + +G+ VR             E  +LD  V++   +D            +
Sbjct: 69  DDETVEPLRPLAAGERVRHWLHR-------HEPPVLDHPVDVVAVTD-----------DL 110

Query: 109 YVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
              +KPA + V   G      + G L +     G +    HRLD+  SG+L++AR    A
Sbjct: 111 VAVHKPATMPVHPTGQYRKNTVLGVLAATRRDLG-RLSPAHRLDRNVSGLLLMARNARTA 169

Query: 168 QHLTESFRMR 177
             L E+    
Sbjct: 170 SALREALAEG 179


>gi|253581558|ref|ZP_04858783.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           varium ATCC 27725]
 gi|251836628|gb|EES65163.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           varium ATCC 27725]
          Length = 236

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/251 (13%), Positives = 82/251 (32%), Gaps = 50/251 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E MR++++  +     +   + K++  G ++++ ++     ++     + I         
Sbjct: 2   EEMRINKYLAS-LGIASRREVDKMIEEGSIKINGEKATPGIKVSDKDEIYI--------- 51

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                        + KH++     +L         NKP  + V   S         +   
Sbjct: 52  ---------RGKKIEKHTEKKVYYIL---------NKP--LEVLSSSKDDRGRKTVVD-- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           + +  ++     RLD  TSG++++         +         ++ Y  ++  I +N  E
Sbjct: 90  LINCKERIFPIGRLDYNTSGLIILTNDGELFNRIIHPKAE-IFKEYYVKVLGEIKENNVE 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + N +     I       + + EKG                    L +    GR  Q+R
Sbjct: 149 LLKNGVELDDGITLPANVRILRREKGK-----------------TELLVAIREGRNRQVR 191

Query: 257 VHALHMGCPIV 267
                +  P++
Sbjct: 192 RMMDKINHPVI 202


>gi|327438231|dbj|BAK14596.1| 16S rRNA uridine-516 pseudouridylate synthase [Solibacillus
           silvestris StLB046]
          Length = 234

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 81/248 (32%), Gaps = 56/248 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++       ++     K +  G+V+++       +++++G  V +          +
Sbjct: 1   MRINKFLAET-GIVSRRGADKWVEDGRVKINGVVATNGSQVETGDEVLVD------GKPV 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K Q+ L                 +Y      V NKP GI+      I  ++  F+   + 
Sbjct: 54  KRQEEL-----------------VY-----IVLNKPVGITSTTEKQIEGNVVDFVNHRL- 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G+L++         +  +      + +                
Sbjct: 91  ----RIFHIGRLDKDSEGLLLLTNDGDIVNEILRAENHHEKEYVVQ-------------- 132

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                    I   ++H +    +  +      +V    ++ F   ++    G   Q+R  
Sbjct: 133 -----VDKPITDQFIHDMSSGVEILDTTTLPCRVEKVSSKVF---KIILEQGLNRQIRRM 184

Query: 259 ALHMGCPI 266
              +G  +
Sbjct: 185 CSALGYSV 192


>gi|159489452|ref|XP_001702711.1| pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158280733|gb|EDP06490.1| pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 301

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 79/239 (33%), Gaps = 73/239 (30%)

Query: 24  WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83
           W +   P +    L ++ R  QV           R+  G  V                  
Sbjct: 91  WLRRRGPEVPHAVLYRLFRQRQV-----------RLYDGDKVV----------------- 122

Query: 84  LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-----------GIAYHIDGF 132
                      + ++  +L     +   NKPAG+ V G +           G    +D  
Sbjct: 123 ------RLLTPERVRRWVLGVQPGLVFINKPAGVRVHGRAAGDVDSAGGRDGGGPTLDSV 176

Query: 133 L-KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
           + ++    +  +P+L HRLD + SG++VVAR   AA  L+ +FR +              
Sbjct: 177 MGEALRFGEQDEPKLVHRLDAQASGVMVVARNADAAAWLSAAFRGKS------------- 223

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                       ++    G     V  +      A+S ++V         W+E+ P TG
Sbjct: 224 ------------RQPRQSGRIRFPVAVDGSF-YPAVSSYRV-RGTGCGVTWVELTPETG 268


>gi|229820641|ref|YP_002882167.1| pseudouridine synthase [Beutenbergia cavernae DSM 12333]
 gi|229566554|gb|ACQ80405.1| pseudouridine synthase [Beutenbergia cavernae DSM 12333]
          Length = 245

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 77/252 (30%), Gaps = 52/252 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +RL +         +    + ++ +G+V VD + V+                      
Sbjct: 6   EGVRLQKVLAGAGLG-SRRACEDLISAGRVSVDGEVVR---------------------- 42

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKI--YVFNKPAGISVQGGSGIAYHIDGFLK 134
              E            H D L+  L   D  +     NKP G  V             L 
Sbjct: 43  ---ELGTRVDPTAAVIHVDGLRLQL---DPGVVTLALNKPRG--VHSTMHDDRGRPA-LA 93

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             V  + ++     RLD +T G+L++      A  L        + K Y + V G     
Sbjct: 94  ELVADRPERLFHVGRLDADTEGLLLLTNDGELAHRLA--HPSYEVPKTYVARVTG----- 146

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              +A  L ++   G +               +  F +++        +E+  H GR   
Sbjct: 147 --RVARGLGRRLKDGIEL--------DDGPARVDRFTILEQGPDSAV-VELVLHEGRNRI 195

Query: 255 LRVHALHMGCPI 266
           +R      G P+
Sbjct: 196 VRRLLDAAGHPV 207


>gi|161507454|ref|YP_001577408.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           helveticus DPC 4571]
 gi|260101634|ref|ZP_05751871.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           helveticus DSM 20075]
 gi|160348443|gb|ABX27117.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           helveticus DPC 4571]
 gi|260084567|gb|EEW68687.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           helveticus DSM 20075]
          Length = 238

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 79/247 (31%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    +K++ +G+V+VD K V      + G  V     I   +  I
Sbjct: 3   ERLQKVIAEA-GIASRRKAEKMIVAGRVKVDGKVVT-----KLGTKVETFSNITVDDEPI 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + + +                         Y+F KP G+               +  + +
Sbjct: 57  ERESL-----------------------HTYLFYKPRGVVSTADDDKGR---KTVVDYFE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD +TSG+L++      A  L        + K+Y + + GI    +   
Sbjct: 91  DVPYRLYPVGRLDYDTSGLLLMTNDGKLANLL--MHPRNEVSKVYVAKIKGILTPDEIKT 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRV 257
               +K                     A +  K++    +K    +++  H G  HQ++ 
Sbjct: 149 LTTGVKLDRF---------------KAAPAKVKILKTDKRKDTQIIQLTIHEGHYHQVKR 193

Query: 258 HALHMGC 264
               +G 
Sbjct: 194 MFKAVGH 200


>gi|323445870|gb|EGB02271.1| hypothetical protein AURANDRAFT_69035 [Aureococcus anophagefferens]
          Length = 542

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/94 (26%), Positives = 45/94 (47%), Gaps = 2/94 (2%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
              L++   +    +KP  + + GG        +   L++ V +  ++ R  H+LD  TS
Sbjct: 426 DVTLIHVCDRYVAVDKPFDMRIDGGREGRDEATLIDVLRARVPAHARELRHCHQLDYATS 485

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
           G+++ A +R AA   +  F  R  +K Y +LV G
Sbjct: 486 GVMLYALSRKAAGEASVCFERRTARKTYVALVVG 519


>gi|260587785|ref|ZP_05853698.1| ribosomal small subunit pseudouridine synthase A [Blautia hansenii
           DSM 20583]
 gi|331083787|ref|ZP_08332896.1| hypothetical protein HMPREF0992_01820 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260542050|gb|EEX22619.1| ribosomal small subunit pseudouridine synthase A [Blautia hansenii
           DSM 20583]
 gi|330403212|gb|EGG82772.1| hypothetical protein HMPREF0992_01820 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 238

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 89/247 (36%), Gaps = 54/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           +RLD++  +         +++ ++ G++ V+ + VK    +I               + +
Sbjct: 4   IRLDKYLADMGLG-TRTEVKRDIKKGRISVNGEIVKSPEYKI-----------DIQTDVV 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + + K                  + YE+   Y+ NKP G+     +         L    
Sbjct: 52  LADGK-----------------EIAYEELVYYMLNKPQGVVS---ATEDRRDKTVLDLIS 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           + K +      RLD++T G+L++      A   L+   +    +K +  L   + +  K+
Sbjct: 92  EKKRKDLFPVGRLDKDTEGLLLITNDGELAHNLLSP--KKHVDKKYFVRLRDALSEEDKK 149

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +   +     IG D + +            SH  V++    +    E+    G+ HQ++
Sbjct: 150 HLEEGV----DIGEDKLTLP-----------SHVFVLNEKRDEA---EIVIREGKFHQIK 191

Query: 257 VHALHMG 263
                +G
Sbjct: 192 RMFHAVG 198


>gi|220905836|ref|YP_002481147.1| pseudouridine synthase [Cyanothece sp. PCC 7425]
 gi|219862447|gb|ACL42786.1| pseudouridine synthase [Cyanothece sp. PCC 7425]
          Length = 261

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 44/255 (17%), Positives = 81/255 (31%), Gaps = 49/255 (19%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +   RL +     +   +    ++++  G+V ++ +      +                +
Sbjct: 2   DSGERLQKILA-QWGIASRRQAEQMILDGRVWLNGEPATLGQK-----------ADPHCD 49

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLK 134
            I  + + L S           +  LLY      +  KP G+ S          I   L 
Sbjct: 50  RIQVDGRTLQSD----------RPDLLY-----LLLYKPTGVISTCSDPQGRPTILDLLP 94

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               + G  P    RLD ET+G L++         LT      ++ K+Y   V G P   
Sbjct: 95  PHYRNLGLHP--VGRLDSETTGALLITNDGWLTHALTHPC--HQVSKVYQVWVSGHPPES 150

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--FAQKFCWLEMQPHTGRT 252
                        +   +   V    +    A    ++++          LE+    GR 
Sbjct: 151 -------------VLQQWRDGVMLAGRLTLPA--QVRLLERTEIPSALTCLEVILWEGRN 195

Query: 253 HQLRVHALHMGCPIV 267
            Q+R  A  +G P+V
Sbjct: 196 RQIRRVAKKLGYPVV 210


>gi|326791990|ref|YP_004309811.1| pseudouridine synthase Rsu [Clostridium lentocellum DSM 5427]
 gi|326542754|gb|ADZ84613.1| pseudouridine synthase Rsu [Clostridium lentocellum DSM 5427]
          Length = 240

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/251 (14%), Positives = 81/251 (32%), Gaps = 60/251 (23%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           MR+++   N    I +     +++ +G+V+V+ +          GQ V     I   +  
Sbjct: 1   MRINKLLSN--KGICSRSQAHQLIVAGRVKVNGQLC------IPGQWVEETDEILLDDRP 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +KE++ L                         + NKP GI      G+  +I  ++    
Sbjct: 53  VKEKERL-----------------------YIILNKPVGIVCTAAEGVKDNIIRYM---- 85

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +         RLD+++ G++++                         L   I + +K  
Sbjct: 86  -NYPAYLFPVGRLDKDSQGLILL--------------------TNDGDLASDILEAEKGH 124

Query: 198 IANWLL-KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              +++        D++H + Q     +  I+    +    +      +    G   Q+R
Sbjct: 125 EKEYMVQVDRPYEEDFLHKMSQGVNLGDGVITRICQVSAINEDT--FRIILTQGMNRQIR 182

Query: 257 VHALHMGCPIV 267
                 G  +V
Sbjct: 183 RMTKAFGYNVV 193


>gi|270262758|ref|ZP_06191029.1| ribosomal small subunit pseudouridine synthase A [Serratia
           odorifera 4Rx13]
 gi|270043442|gb|EFA16535.1| ribosomal small subunit pseudouridine synthase A [Serratia
           odorifera 4Rx13]
          Length = 237

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 74/249 (29%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V VD + VK                      + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTVDGEVVKS-----------------GAVKLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ++      L + S            + ++ NKP G      S         L    +
Sbjct: 43  PEQEVAFDGNPLQQLSGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G+++                  +      S      K     +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVL-------------MTDDGQWSHRVTSPKHHCEKTYLVTL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L + +         +   +     A      ++        + +    GR HQ++  
Sbjct: 137 EHPLAEDTAQQFAEGVQLHNEKDLTRPAQ-----LEKIED--TLVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNRVV 198


>gi|121591505|ref|ZP_01678772.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 2740-80]
 gi|121546635|gb|EAX56823.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 2740-80]
          Length = 134

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 26/92 (28%), Positives = 37/92 (40%), Gaps = 8/92 (8%)

Query: 208 IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +        K      N AI+ F      A        +PHTG+THQ+RV    +G  IV
Sbjct: 1   MERSRRSSWKLVNSQENPAITQFFS-AAAATGERLFLCKPHTGKTHQIRVALKSIGSAIV 59

Query: 268 GDHKYCANFKGNFTSPIQNKLYLHARYMDLPH 299
           GD  Y        T+   ++ YLHA  +   +
Sbjct: 60  GDPIYN-------TADESDRGYLHAFALRFTY 84


>gi|311693777|gb|ADP96650.1| pseudouridine synthase family 1 protein [marine bacterium HP15]
          Length = 312

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/245 (11%), Positives = 70/245 (28%), Gaps = 54/245 (22%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RL+++        +     + +  G V ++ KR    +++  G  V++            
Sbjct: 8   RLNKYISES-GMCSRREADRYIEQGNVYINGKRATVGDQVLPGDTVKVN----------- 55

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             ++++                  ED      NKP GI     S   ++I  F+      
Sbjct: 56  -GQVIEPRAE--------------EDLVFIALNKPVGIVSTTDSAEKHNIQRFV-----G 95

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             ++     RLD+++ G++ +         +  +      + +                 
Sbjct: 96  HSERIFPIGRLDKDSQGLIFMTSNGDLVNKILRAGNNHEKEYL--------------VTV 141

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +  + +  + G    V           +S         +      +    G   Q+R   
Sbjct: 142 DKPVTREFVEGMANGVPILGTMTKKCKVSR--------ESRFVFRITLVQGLNRQIRRMC 193

Query: 260 LHMGC 264
            + G 
Sbjct: 194 EYFGY 198


>gi|261346079|ref|ZP_05973723.1| ribosomal small subunit pseudouridine synthase A [Providencia
           rustigianii DSM 4541]
 gi|282565731|gb|EFB71266.1| ribosomal small subunit pseudouridine synthase A [Providencia
           rustigianii DSM 4541]
          Length = 234

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 78/250 (31%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + LR+G + VD K VK  +             I+A N + 
Sbjct: 1   MRLDKFLSQQL-GISRNLVARELRAGNITVDDKVVKSGS-----------MQISADNEVS 48

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +  +L             +  +L++                            L    +
Sbjct: 49  YDGNVLIQITGP-------RYFMLHKPEGYVCSTDD---PTHPT---------ILYFIDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              QK     RLD +T+G++++           +     RI                E I
Sbjct: 90  PVTQKLHAAGRLDIDTTGLVLLT---------DDGQWSHRITSPKHHCEKTYRVQLSEDI 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +++K  IG          +      IS  +V+           +    GR HQ++  
Sbjct: 141 TDDVIQKFEIGVMLNGEKSPTKPAQLEIISPREVL-----------LTISEGRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  + G
Sbjct: 190 FAAVGNHVCG 199


>gi|164687721|ref|ZP_02211749.1| hypothetical protein CLOBAR_01363 [Clostridium bartlettii DSM
           16795]
 gi|164603495|gb|EDQ96960.1| hypothetical protein CLOBAR_01363 [Clostridium bartlettii DSM
           16795]
          Length = 258

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 88/246 (35%), Gaps = 54/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D+   N   + +   L+K  ++G V+V+ K +        G  V +           
Sbjct: 22  QRIDKILSN-LGYGSRSELKKFCKNGLVKVNGKVIN-----NPGVQVDV----------- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  +I+           F    + Y++    + NKP G      S      D  +   +D
Sbjct: 65  ENDEII-----------FDGEKVTYKEFIYLMLNKPDGYI----SATFDKRDPIVLDLID 109

Query: 139 SKG--QKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    +P    RLD++T G+LV+      A + L+     + + K Y++ + GI   + 
Sbjct: 110 KEDLVFEPFPVGRLDKDTEGLLVLTNDGQLAHRVLS---PKKHVPKTYYAKIEGIVTEED 166

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I  +    +   G                    ++I   + +   +E+  H G+ HQ+
Sbjct: 167 --IKAFAKGVTLDDGYETMPA--------------ELIILKSDEISEIELTIHEGKFHQV 210

Query: 256 RVHALH 261
           +     
Sbjct: 211 KRMFES 216


>gi|87120132|ref|ZP_01076028.1| putative pseudouridine synthase [Marinomonas sp. MED121]
 gi|86164834|gb|EAQ66103.1| putative pseudouridine synthase [Marinomonas sp. MED121]
          Length = 376

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 36/245 (14%), Positives = 69/245 (28%), Gaps = 54/245 (22%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RL+++        +     + +  G V ++KKR +  +++  G VVR+            
Sbjct: 8   RLNKYISES-GMCSRREADRFIEQGNVFINKKRAEVGDQVNPGDVVRVN----------- 55

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             KI                    ED      NKP GI          ++  F+      
Sbjct: 56  GAKIEPPEA---------------EDLVFIALNKPVGIVSTTEMEEPDNMVSFVNH---- 96

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +     RLD+++ G++ +         +  +      + +               + 
Sbjct: 97  -SSRIFPIGRLDKDSQGLIFLTSNGDLVNKILRAGNNHEKEYVV-------------TVD 142

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L + + I      V     K         KV+      F    +    G   Q+R   
Sbjct: 143 KPLTEDA-INTMASGVPMLGTKTKKC-----KVVQEAPNVF---RIFLVQGLNRQIRRMC 193

Query: 260 LHMGC 264
              G 
Sbjct: 194 EFCGY 198


>gi|294142202|ref|YP_003558180.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293328671|dbj|BAJ03402.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 229

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/251 (15%), Positives = 87/251 (34%), Gaps = 54/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHI 77
           MRLD++       +     +K L  G V  D + VK ++ ++++GQ++ +   + ++   
Sbjct: 1   MRLDKFICES-TELTRSFAKKALHRGDVTCDGEVVKSSSFKVKAGQIICLDGKVISV--- 56

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                +    + L K +D + +                   V         +   L    
Sbjct: 57  -----VGPRFLMLNKPADTICAT---------------FDIVHP------TVIDLLDI-- 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             K     +  RLD +T+G++++          T+     +I                + 
Sbjct: 89  -EKADTLHIAGRLDIDTTGLVLIT---------TDGQWSHKITSPKKDCGKCYLVTLTDE 138

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   L++    G +    ++  +     A+   ++ID    +    E     G+ HQ++ 
Sbjct: 139 LDASLVETFAQGVE----LRNEDGLTKPAV--LEIIDSHHARLTITE-----GKYHQVKR 187

Query: 258 HALHMGCPIVG 268
               +G  +VG
Sbjct: 188 MFAAVGNKVVG 198


>gi|282917013|ref|ZP_06324771.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus D139]
 gi|283770831|ref|ZP_06343723.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus H19]
 gi|282319500|gb|EFB49852.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus D139]
 gi|283460978|gb|EFC08068.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus H19]
 gi|302333417|gb|ADL23610.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus JKD6159]
          Length = 231

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 79/244 (32%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N         ++++L+ G V V+++ +K                     HI 
Sbjct: 1   MRIDKFLANMGVG-TRNEVKQLLKKGLVNVNEQVIKS-----------------PKTHIE 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   +     L          + Y ++   + NKP G      +   +H    +    +
Sbjct: 43  PENDKISVRGEL----------IEYVENVYIMLNKPKGYIS---ATEDHHSKTVIDLIPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++T G+L++         L      + + K Y            E I
Sbjct: 90  YQHLNIFPVGRLDKDTEGLLLITNDGDFNHEL--MSPNKHVSKKY------------EVI 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +   + +  I      V   + K    AI  +  ID         E     G+ HQ++  
Sbjct: 136 SANPITEDDIQAFKEGVTLSDGK-VKPAILTY--IDNQTSHVTIYE-----GKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|50842867|ref|YP_056094.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes KPA171202]
 gi|282853641|ref|ZP_06262978.1| pseudouridylate synthase [Propionibacterium acnes J139]
 gi|50840469|gb|AAT83136.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes KPA171202]
 gi|282583094|gb|EFB88474.1| pseudouridylate synthase [Propionibacterium acnes J139]
 gi|313813285|gb|EFS50999.1| conserved hypothetical protein [Propionibacterium acnes HL025PA1]
 gi|314923703|gb|EFS87534.1| conserved hypothetical protein [Propionibacterium acnes HL001PA1]
 gi|314967055|gb|EFT11154.1| conserved hypothetical protein [Propionibacterium acnes HL082PA2]
 gi|314983150|gb|EFT27242.1| conserved hypothetical protein [Propionibacterium acnes HL110PA3]
 gi|315092372|gb|EFT64348.1| conserved hypothetical protein [Propionibacterium acnes HL110PA4]
 gi|315092741|gb|EFT64717.1| conserved hypothetical protein [Propionibacterium acnes HL060PA1]
 gi|315105956|gb|EFT77932.1| conserved hypothetical protein [Propionibacterium acnes HL030PA1]
 gi|327327189|gb|EGE68965.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes HL103PA1]
          Length = 245

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 47/294 (15%), Positives = 96/294 (32%), Gaps = 58/294 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ++E+ +RL +         +    + ++ +G+V V+ + +                 +  
Sbjct: 2   SNEQGIRLQKVLAQA-GLASRRAAEDMIAAGRVEVNGELI-----------------VEQ 43

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              +  E+  +    +    +   +  + Y      V NKP G+               L
Sbjct: 44  GRRVDPERDEIRVDGSRIPTA---RRHVYY------VLNKPQGVVSTMDDPEGRPCLSDL 94

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +     +G +     RLD ETSG++++      A  +T      ++ K Y + V G   +
Sbjct: 95  EGV--PRGIRLFHVGRLDTETSGLILLTNDGEFANRMT--HPSYKVLKTYLADVEGRVDD 150

Query: 194 K--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K          L+   +  D V +V+  E+                     +E+  H GR
Sbjct: 151 KVIHRLSKGLTLEDGPVKPDAVRLVQAGEE------------------HSLVEVSLHEGR 192

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              +R     +  P+                P++ K        +L H E G+L
Sbjct: 193 NRIVRRIMDSVAHPV-------RRLSRTAIGPVRLKRLGRGDMRELTHEELGQL 239


>gi|82751342|ref|YP_417083.1| 16S RNA pseudouridylate synthase [Staphylococcus aureus RF122]
 gi|82656873|emb|CAI81302.1| 16S RNA pseudouridylate synthase [Staphylococcus aureus RF122]
          Length = 231

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 79/244 (32%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N         ++++L+ G V V+++ +K                     HI 
Sbjct: 1   MRIDKFLANMGVG-TRNEVKQLLKKGLVNVNEQVIKS-----------------PKTHIE 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  ++     L          + Y ++   + NKP G          +H    +    +
Sbjct: 43  PENDMISVRGEL----------IEYVENVYIMLNKPKGYIS---GTEDHHSKTVIDLIPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++T G+L++         L      + + K Y            E I
Sbjct: 90  YQHLNIFPVGRLDKDTEGLLLITNDGDFNHEL--MSPNKHVSKKY------------EVI 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +   + +  I      V   + K    AI  +  ID         E     G+ HQ++  
Sbjct: 136 SANPITEDDIQAFKEGVTLSDGK-VKPAILTY--IDNQTSHVTIYE-----GKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|315924794|ref|ZP_07921011.1| ribosomal large subunit pseudouridine synthase B [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315621693|gb|EFV01657.1| ribosomal large subunit pseudouridine synthase B [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 246

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 82/253 (32%), Gaps = 52/253 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MRL ++        +    + ++  G+V V+   V     ++  G VV +   + A    
Sbjct: 1   MRLQKYMA-QCGVASRRGSEAMIADGRVMVNGSVVDTPGVQVTPGDVVFVDGKLIAPERK 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +                               + NKP G+     +    H +  +   V
Sbjct: 60  V-----------------------------YLLLNKPRGVVT---TSEDVHAERRILDLV 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            ++  +     RLD++T G+L++         LT       + K+Y ++V G        
Sbjct: 88  AAEV-RLYAIGRLDKDTEGLLILTNDGDLTFRLT--HPSYHLDKVYEAVVKGQ------- 137

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAIS---HFKVIDCFAQKFCWLEMQPHTGRTHQ 254
               L   +        V+  ++ G     +      V+    +    L +    G+  Q
Sbjct: 138 ----LTAPALAALREGVVIPLDDAGTKTYRTQPAEVTVLRRK-RGSTRLSITLCEGKKRQ 192

Query: 255 LRVHALHMGCPIV 267
           +R     +G P+V
Sbjct: 193 IRKMCAAVGYPVV 205


>gi|82779348|ref|YP_405697.1| 23S rRNA pseudouridine synthase F [Shigella dysenteriae Sd197]
 gi|309784076|ref|ZP_07678718.1| ribosomal large subunit pseudouridine synthase F [Shigella
           dysenteriae 1617]
 gi|81243496|gb|ABB64206.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
 gi|308928069|gb|EFP73534.1| ribosomal large subunit pseudouridine synthase F [Shigella
           dysenteriae 1617]
          Length = 290

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|327330001|gb|EGE71755.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes HL097PA1]
          Length = 245

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 47/294 (15%), Positives = 97/294 (32%), Gaps = 58/294 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ++E+ +RL +         +    + ++ +G+V V+ + +                 ++ 
Sbjct: 2   SNEQGIRLQKVLAQA-GLASRRAAEDMIAAGRVEVNGELI-----------------VDQ 43

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              +  E+  +    +    +   +  + Y      V NKP G+               L
Sbjct: 44  GRRVDPERDEIRVDGSRIPTA---RRHVYY------VLNKPQGVVSTMDDPEGRPCLSDL 94

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +     +G +     RLD ETSG++++      A  +T      ++ K Y + V G   +
Sbjct: 95  EGV--PRGIRLFHVGRLDTETSGLILLTNDGEFANRMT--HPSYKVLKTYLADVEGRVDD 150

Query: 194 K--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K          L+   +  D V +V+  E+                     +E+  H GR
Sbjct: 151 KVIHRLSKGLTLEDGPVKPDAVRLVQAGEE------------------HSLVEVSLHEGR 192

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              +R     +  P+                P++ K        +L H E G+L
Sbjct: 193 NRIVRRIMDSVAHPV-------RRLSRTAIGPVRLKRLGRGDMRELTHEELGQL 239


>gi|212633763|ref|YP_002310288.1| pseudouridine synthase Rsu [Shewanella piezotolerans WP3]
 gi|212555247|gb|ACJ27701.1| Pseudouridine synthase, Rsu [Shewanella piezotolerans WP3]
          Length = 233

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 86/249 (34%), Gaps = 52/249 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+       ++  +++ +L  G V+VD +  +            I  +++  +HI  
Sbjct: 7   RLDRFISAT-KRVSRKHVRVLLAKGLVKVDGEIAR-----------DIDQIVDEFSHITL 54

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E ++L ++  +                   + +KP G+     + +       +      
Sbjct: 55  EGEVLQANTPI-----------------YLMLHKPVGVVS---ATVDDKHKTVIDLLSHP 94

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             Q+  +  RLD  TSG+L++      ++ L       ++ K+Y           +  + 
Sbjct: 95  DKQQLHIVGRLDLNTSGLLLLTNDGRWSKRL--MSPEHKVAKLY-----------RVSLE 141

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           N +              +  +     A    +++D        +E     GR HQ++   
Sbjct: 142 NPIDASYIQAFHEGMYFEFEDITTLPA--KLEIVDPHTALVTLME-----GRYHQIKRMF 194

Query: 260 LHMGCPIVG 268
                P++G
Sbjct: 195 GRFRNPVIG 203


>gi|37526757|ref|NP_930101.1| 16S rRNA pseudouridylate synthase A [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|36786189|emb|CAE15241.1| ribosomal small subunit pseudouridine synthase A (16S
           pseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (uracil hydrolyase) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 233

 Score = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 79/247 (31%), Gaps = 55/247 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++       I+  ++ + LR+G++ VD + VK    ++   Q V     +      
Sbjct: 1   MRLDKFLSQQL-GISRNDVGRELRAGRITVDDEIVKTGAYKLTPEQQVMFDGSLLEQQQG 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +   +      +    D +   +LY        ++PA                      
Sbjct: 60  PRYFMLNKPQGYVCSTDDPINPTVLY------FIDEPA---------------------- 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                K     RLD +T+G++++      + +  +     ++   +             E
Sbjct: 92  ---AHKLHTAGRLDMDTTGLVLLTDDGQWSHRITSPKHHCKKTYLVTL-----------E 137

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C          + G  ++  K   K A       ++++          +    GR HQ++
Sbjct: 138 CPVAAETADKFLAGVQLNGEKTVTKPAQ-----LEILEPQ-----IARLTISEGRYHQVK 187

Query: 257 VHALHMG 263
                +G
Sbjct: 188 RMFAAVG 194


>gi|219122723|ref|XP_002181690.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406966|gb|EEC46904.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 217

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/236 (14%), Positives = 80/236 (33%), Gaps = 38/236 (16%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +     K++ +G+V V+   VK       G    +P         I      D+++N   
Sbjct: 1   SRREADKLIEAGRVSVNDIPVKSK-----GGFKVVPFHDKITLDGIPVTGTSDATINF-- 53

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                             + KP G++      IA +I   L+       ++     RLD+
Sbjct: 54  --------------DYVKYWKPVGVTCTTDRKIAGNIIDALEEAGFDSSKRIFPVGRLDK 99

Query: 153 ETSGILVVART----RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHI 208
           ETSG++++        A  +   +  ++ ++      L   + + +   I   + ++   
Sbjct: 100 ETSGLILLTSDGRVPNAVLRGRHKQPKIYQVWVDRPVLAKDVAQLRDGVIITTVAQRDGN 159

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             + +       +  + A+   +V+     +   +E     GR  Q+R     +  
Sbjct: 160 RAEPL-----TARTKSCAV---QVLGREKLQLTLVE-----GRNRQIRKMLGALNY 202


>gi|222110298|ref|YP_002552562.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221729742|gb|ACM32562.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 435

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 33/232 (14%), Positives = 72/232 (31%), Gaps = 45/232 (19%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      R+Q G  +++              +I    V    
Sbjct: 124 SRLEMEQLILEGRISVNNEPAHIGQRVQFGDQIKVNGKPIRF-------RIAPPPVR--- 173

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                          +  ++KP G  V        +     +     +  K +   RLD 
Sbjct: 174 ---------------VIAYHKPVGEVV--THDDPQNRPTVFRKLPRLQQGKWQSVGRLDL 216

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L+   +   A  L        +++ Y + V G    ++      LL+   +    
Sbjct: 217 NTEGLLLFTSSGELANKL--MHPRFGLEREYAARVLGALSTEE---KQRLLEGVPLEDGM 271

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                  + G   A              CW  +    GR  ++R     +G 
Sbjct: 272 ASFGSVEDGGGEGA-------------NCWYRVTISEGRNREVRRMFEAVGH 310


>gi|238786255|ref|ZP_04630200.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           bercovieri ATCC 43970]
 gi|238712846|gb|EEQ04913.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           bercovieri ATCC 43970]
          Length = 290

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 76/247 (30%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR     ++ +G VV++   I    + 
Sbjct: 7   IRLNKYISE--SGICSRRDADRYIEQGNVFINGKRATVGVQVSAGDVVKVNGQIIEPRNE 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     ED  +   NKP G+      G   +I  F+    
Sbjct: 65  --------------------------EDLILIALNKPVGVISTTEDGEQNNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD+++ G++++         +  +      + +   +    P   +  
Sbjct: 97  ---SKRVFPIGRLDKDSQGLILLTNHGDLVNKILRAGNDHEKEYV---VTVNKPVTDEFI 150

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +          G   +  V +  K    A   F++                 G   Q+R 
Sbjct: 151 LGLG------AGVPMLGTVTKKCKVKREATFVFRI-------------TLVQGLNRQIRR 191

Query: 258 HALHMGC 264
              H G 
Sbjct: 192 MCKHFGY 198


>gi|121535833|ref|ZP_01667633.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
 gi|121305605|gb|EAX46547.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
          Length = 241

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 81/250 (32%), Gaps = 49/250 (19%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RL +         +    +K++  G+V V+ K +      + G  V  P     ++  
Sbjct: 2   PERLQKILSQA-GIASRRAAEKLILDGRVAVNGKIIT-----ELGAKVDWPRDRVTVD-- 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  +  E     + NKP G+     S         +   +
Sbjct: 54  --------------------GKPIAAEAPVYILLNKPKGVIT---SLKDPRGRKTVIDLL 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD  T G+L++         LT       I+K Y S + G+P  ++  
Sbjct: 91  KDVPERVYPVGRLDYNTEGLLLLTNDGDLTHALT--HPSHEIKKTYVSKIAGLPNEEQ-- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLR 256
                     +      +   +   +  A+   +++D    ++   +E+  H GR  Q+R
Sbjct: 147 ----------LDRLRAGIKLSDGMTSPAAV---RLLDFDPVKQVAVVEITIHEGRNRQVR 193

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 194 RMFEAIGHPV 203


>gi|315103786|gb|EFT75762.1| conserved hypothetical protein [Propionibacterium acnes HL050PA2]
          Length = 245

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 47/294 (15%), Positives = 97/294 (32%), Gaps = 58/294 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ++E+ +RL +         +    + ++ +G+V V+ + +                 +  
Sbjct: 2   SNEQGIRLQKVLAQA-GLASRRAAEDMIAAGRVEVNGELI-----------------VEQ 43

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
              +  E+  +    +    +   +  + Y      V NKP G+               L
Sbjct: 44  GRRVDPERDEIRVDGSRIPTA---RRHVYY------VLNKPQGVVSTMDDPEGRPCLSDL 94

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +     +G +     RLD ETSG++++      A  +T      ++ K Y + V G   +
Sbjct: 95  EGV--PRGIRLFHVGRLDTETSGLILLTNDGEFANRMT--HPSYKVLKTYLADVEGRVDD 150

Query: 194 K--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K          L+   +  D V +V+ +E+                     +E+  H GR
Sbjct: 151 KVIHRLSKGLTLEDGPVKPDAVRLVQASEE------------------HSLVEVSLHEGR 192

Query: 252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRL 305
              +R     +  P+                P++ K        +L H E G+L
Sbjct: 193 NRIVRRIMDSVAHPV-------RRLSRTAIGPVRLKRLGRGDMRELTHEELGQL 239


>gi|167646666|ref|YP_001684329.1| pseudouridine synthase [Caulobacter sp. K31]
 gi|167349096|gb|ABZ71831.1| pseudouridine synthase [Caulobacter sp. K31]
          Length = 245

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 81/250 (32%), Gaps = 47/250 (18%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR   N   + +  ++Q ++ +G+V +D   +K      +GQ + +   +     I  
Sbjct: 8   RLDRLLAN-LGYGSRRDVQALVSTGKVTLDGVAIKD-----AGQKIAVTADLPLRMRI-- 59

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVD 138
               +D    L                 + + +KP G+       G    I   L     
Sbjct: 60  RGVPVDPPAPL-----------------VLLMHKPLGVVCSHREDG--ERIYDLLPKRWQ 100

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++TSG+L++                        S    +PK  +  +
Sbjct: 101 IRDPALSSVGRLDKDTSGLLLIT-------------DDGDFLHRVISPKRHVPKVYRATL 147

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L            ++ + E+      +   V+     +    E     GR HQ+R  
Sbjct: 148 DRPLNGTEGAAFASGALMLEGEEKPLLPAT-LDVLGDHEARLTITE-----GRYHQVRRM 201

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 202 FAAVGNHVVG 211


>gi|237808158|ref|YP_002892598.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
 gi|237500419|gb|ACQ93012.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
          Length = 231

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/248 (15%), Positives = 81/248 (32%), Gaps = 50/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+        I+     ++L++G++ V+   +K                     H+ 
Sbjct: 1   MRLDKHLHQCL-GISRSQASQLLKAGRISVNSLIIKS-----------------GAQHVT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           ++  +L     L    + L   +L++       N   G +   G    + +         
Sbjct: 43  EQDSVLLDDKPLDTPGEKLYYFMLHKPQGYVCAN---GDASHPGITRLFDL--------- 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD +T+G+++V      +  +T   +        W L   I    +E  
Sbjct: 91  PCASELHAAGRLDADTTGLVLVTNDGQWSHRVTSPRKQCDKTYRVW-LAEPISPETEEIF 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A  +L +S          +         I+  +V+           +  H G+ HQ++  
Sbjct: 150 AKGILLRSE--------TQVTRPAQLETITPQEVL-----------LTIHEGKYHQVKRM 190

Query: 259 ALHMGCPI 266
              +G  +
Sbjct: 191 FAAVGNHV 198


>gi|115452369|ref|NP_001049785.1| Os03g0288500 [Oryza sativa Japonica Group]
 gi|113548256|dbj|BAF11699.1| Os03g0288500 [Oryza sativa Japonica Group]
          Length = 162

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/152 (19%), Positives = 49/152 (32%), Gaps = 37/152 (24%)

Query: 36  NLQKILRSGQVRVDKKRVK-FNNRIQSGQVV---RIPPVINALNHIIKEQKILDSSVNLT 91
              K +R GQ+ VD +     +  ++ G  +   R+P       H++             
Sbjct: 8   RWIKRIRDGQITVDGEVATDPDMILREGSKLVYHRLPWQEPFAPHLL------------- 54

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ--------- 142
                    +LYED  +   NKP+G+ V                  D K           
Sbjct: 55  --------DVLYEDDDMIALNKPSGLQVLPKGLFQQRTVLAQLQLKDWKMPSSFCSKRKD 106

Query: 143 ---KPRLTHRLDQETSGILVVARTRAAAQHLT 171
               P   HRL + TSG+ +   +  A +  +
Sbjct: 107 AQSHPVPVHRLGRGTSGLFLCFCSVHAQKPWS 138


>gi|295839696|ref|ZP_06826629.1| RNA pseudouridylate synthase [Streptomyces sp. SPB74]
 gi|295827612|gb|EFG65503.1| RNA pseudouridylate synthase [Streptomyces sp. SPB74]
          Length = 196

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/181 (20%), Positives = 68/181 (37%), Gaps = 27/181 (14%)

Query: 112 NKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           NKPAG+             G    +V+++  +     RLD ET G++++      A  LT
Sbjct: 25  NKPAGVVATMEDPEGRQNLG---DYVNNRETRLFHVGRLDTETEGVILLTNHGELAHRLT 81

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK 231
                  ++K Y + + G        I   L K+   G +      + +        HF+
Sbjct: 82  --HPRYGVRKTYLAHIVG-------PIPRDLGKRLKDGIELEDGWARAD--------HFR 124

Query: 232 VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK----YCANFKGNFTSPIQNK 287
           V++   + +  +E+  H GR H +R      G P+  D      +     G+  S    +
Sbjct: 125 VVEQTGKNY-LVEVTLHEGRKHIVRRMLAEAGFPV--DKLVRTAFGPITLGDQKSGWLRR 181

Query: 288 L 288
           L
Sbjct: 182 L 182


>gi|298695021|gb|ADI98243.1| pseudouridine synthase, family 1 [Staphylococcus aureus subsp.
           aureus ED133]
 gi|323439591|gb|EGA97311.1| 16S RNA pseudouridylate synthase [Staphylococcus aureus O11]
 gi|323441503|gb|EGA99155.1| 16S RNA pseudouridylate synthase [Staphylococcus aureus O46]
          Length = 231

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 81/244 (33%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N         ++++L+ G V V+++ +K                     HI 
Sbjct: 1   MRIDKFLANMGVG-TRNEVKQLLKKGLVNVNEQVIKS-----------------PKTHIE 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   +     L          + Y ++   + NKP G      +   +H    +    +
Sbjct: 43  PENDKISVRGEL----------IEYVENVYIMLNKPKGYIS---ATEDHHSKTVIDLIPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++T G+L++         L      + + K Y            E I
Sbjct: 90  YQHLNIFPVGRLDKDTEGLLLITNDGDFNHEL--MSPNKHVSKKY------------EVI 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +   + +  I   +   VK ++     AI  +  ID         E     G+ HQ++  
Sbjct: 136 SANPITEDDIQA-FKEGVKLSDGKVKPAILTY--IDNQTSHVTIYE-----GKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|260685750|ref|YP_003216883.1| pseudouridine synthase [Clostridium difficile R20291]
 gi|260211766|emb|CBE02116.1| pseudouridine synthase [Clostridium difficile R20291]
          Length = 258

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 84/246 (34%), Gaps = 32/246 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D+   N   + +   ++K  + G V V+   V        G  V         N   
Sbjct: 5   QRIDKILSN-LGYGSRSEIKKYCKQGSVVVNGSEVS-----NPGTQVDTENDEILFNG-- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+ I    + L   +   +    +   +    NKP G            +   +   + 
Sbjct: 57  -EEVIYREYIYLIMQNSVKQEPCDFSHGRFR-MNKPDGYISATTDKYDPTVLDLID--LS 112

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +P    RLD++T G+LV+    + + + L+     + + K Y++ + G+   +   
Sbjct: 113 YLAFEPFPVGRLDKDTEGLLVLTNDGKLSHRVLS---PKKHVPKTYYAKIDGVVTEED-- 167

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +  +L                 + G     S   ++   +     +E+  H G+ HQ++ 
Sbjct: 168 VEAFLEG------------VVLDDGYKTMPSQLNILK--SDDESEIELTIHEGKFHQVKR 213

Query: 258 HALHMG 263
               +G
Sbjct: 214 MFESVG 219


>gi|77918905|ref|YP_356720.1| ribosomal large subunit pseudouridine synthase B [Pelobacter
           carbinolicus DSM 2380]
 gi|77544988|gb|ABA88550.1| ribosomal large subunit pseudouridine synthase B [Pelobacter
           carbinolicus DSM 2380]
          Length = 236

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 79/250 (31%), Gaps = 53/250 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++ + +G+V V+ +  +   +                + I+
Sbjct: 3   QRLQKLIAAA-GLTSRRRAEEWIANGRVTVNGRVAELGAQ-----------ADPDKDRIL 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + + L  +                E+    + +KP G      S         +   + 
Sbjct: 51  VDNRPLPQA----------------EEPVCVLLHKPVGYVT---SRRDPQGRPVVTDLLG 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKE 196
               +     RLD  T G+L++      A  L+       + K Y   V G    + +++
Sbjct: 92  KFRARLFPVGRLDLNTEGLLLLTNDGDLAWRLS--HPSHEVCKTYLVRVQGSLSCEARRQ 149

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                LL++       V  V+Q                  A    W+E+  H GR  Q+R
Sbjct: 150 LQEGVLLEEGVTAPAKVARVRQ------------------AGSHTWMELSIHEGRNRQVR 191

Query: 257 VHALHMGCPI 266
                +GCP+
Sbjct: 192 RMCEAVGCPV 201


>gi|329117728|ref|ZP_08246445.1| pseudouridylate synthase [Streptococcus parauberis NCFD 2020]
 gi|326908133|gb|EGE55047.1| pseudouridylate synthase [Streptococcus parauberis NCFD 2020]
          Length = 238

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 85/246 (34%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D+  +      +   ++ +++S QV+V++K +                         
Sbjct: 1   MRIDKLLEEEGIG-SRNQVKTLIKSQQVKVNEKVIT------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +  +D S+ +   S    + +  E    ++ NKP G+      G+   +   L   V+
Sbjct: 36  DGKTNVDPSLQVITASG---TPIQAEGHHYFILNKPNGVVSARSDGLHQTVIDCLS--VE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +  K     RLD++T G++++        + L        + K Y   V G  K+    
Sbjct: 91  DRYAKLYPIGRLDRDTEGLVLLTDNGPLGFRMLH---PSHHVSKTYLVRVNGQLKDDALV 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                            +V  +      A  H +++    +K     +    G+ HQ++ 
Sbjct: 148 FFE------------EGIVFHDGTKCKPA--HLQILKKD-EKCSEAVVTISEGKFHQVKK 192

Query: 258 HALHMG 263
             L  G
Sbjct: 193 MFLAYG 198


>gi|307245181|ref|ZP_07527272.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307254128|ref|ZP_07535973.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|307258592|ref|ZP_07540327.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|306853825|gb|EFM86039.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|306862828|gb|EFM94777.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|306867249|gb|EFM99102.1| Ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
          Length = 230

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 73/246 (29%), Gaps = 53/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      + L+SG V V+ K  K  + ++ G    I      L    
Sbjct: 1   MRLDKFIAEN-TGLTRSQAARALKSGLVTVNGKLEKSGS-VKIGDTDEICYEGERLE--- 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  + E     ++ KP G      S          + +  
Sbjct: 56  ----------------------WVDEGQYFMLY-KPQGYVC---SHDDGEYPTVFQFFDY 89

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               K     RLD +T+G++++    + + +  +      +   +  +          + 
Sbjct: 90  PLMTKLHTAGRLDVDTTGLVLLTDDGKWSHRITSPKHHCEKTYLVTLA----------DP 139

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + ++  KK   G       +         I  + V            +    GR HQ++ 
Sbjct: 140 VEDFYAKKLAEGILLRGEREPCLPAQMEIIDDYNV-----------NLTISEGRYHQVKR 188

Query: 258 HALHMG 263
               +G
Sbjct: 189 MFAALG 194


>gi|291561019|emb|CBL39819.1| ribosomal small subunit pseudouridine synthase A
           [butyrate-producing bacterium SSC/2]
          Length = 242

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 36/245 (14%), Positives = 87/245 (35%), Gaps = 50/245 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHII 78
           RLD++  +   ++     ++ ++ G+V V+ + +K    ++ +                 
Sbjct: 6   RLDKFLCDSL-NMTRKEAKESVKKGKVVVNGEAIKKPEYKVDA----------------- 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ  ++    L          + +E     + +KP G+     +   +H    L    +
Sbjct: 48  -EQDQVEFDHKL----------IQFEQFHYLMLHKPQGVVS---ATKDHHDQTVLDLIHE 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD++T G+L++      A  L      + + K+Y++ V G     +   
Sbjct: 94  DYKDRLFPVGRLDKDTEGLLLLTDDGMLAHEL--LSPRKHVDKVYFAKVSGQFGENE--- 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               + +   G D          G     +  +++    Q+   + +    G+ HQ++  
Sbjct: 149 ----IARFKEGLDI-------GNGERSKQARLQILKADVQE-SEVLITIMEGKFHQVKRM 196

Query: 259 ALHMG 263
              +G
Sbjct: 197 VKAVG 201


>gi|325962913|ref|YP_004240819.1| pseudouridine synthase family protein [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323469000|gb|ADX72685.1| pseudouridine synthase family protein [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 400

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 87/253 (34%), Gaps = 45/253 (17%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +RL +   +     +    ++++  G+V VD + V      + G  VR+ P     
Sbjct: 156 DADGVRLQKVMASA-GVASRRVCEEMIAEGRVEVDGQVVT-----ELG--VRVDPKTA-- 205

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                             H D ++   L E+    VFNKP G+                 
Sbjct: 206 ----------------VIHVDGIRIQ-LDENMVYMVFNKPKGVVSTMEDPEGRPCISDFL 248

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               +KG++     RLD  T G+L++      A  LT       + K Y   V G     
Sbjct: 249 KNAKNKGERLFHVGRLDVATEGLLLLTNDGELANRLT--HPSYEVPKTYLVQVRGPFPQ- 305

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                  +  +   G +         +    ++  F+++D        +E+  H+G+   
Sbjct: 306 ------GIGAQLKEGVEL--------EDGFASVDSFRLVDSTP-GHVLIEVVLHSGKNRI 350

Query: 255 LRVHALHMGCPIV 267
           +R     +G P++
Sbjct: 351 VRRLFDAVGFPVL 363


>gi|283471019|emb|CAQ50230.1| RNA pseudouridine synthase family protein [Staphylococcus aureus
           subsp. aureus ST398]
          Length = 231

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 79/244 (32%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N         ++++L+ G V V+++ +K                     HI 
Sbjct: 1   MRIDKFLANMGVG-TRNEVKQLLKKGLVNVNEQVIKS-----------------PKTHIE 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   +     L          + Y ++   + NKP G      +   +H    +    +
Sbjct: 43  PENDKISVRGEL----------IEYVENVYIMLNKPKGYIS---ATEDHHSKTVIDLIPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++T G+L++         L      + + K Y            E I
Sbjct: 90  YQHLNIFPVGRLDKDTEGLLLITNDGDFNHEL--MSPNKHVSKKY------------EVI 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +   + +  I      V   + K    AI  +  ID         E     G+ HQ++  
Sbjct: 136 SANPITEEDIQAFKEGVTLSDGK-VKPAILTY--IDNQTSHVTIYE-----GKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|156097284|ref|XP_001614675.1| pseudouridylate synthase [Plasmodium vivax SaI-1]
 gi|148803549|gb|EDL44948.1| pseudouridylate synthase, putative [Plasmodium vivax]
          Length = 805

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 224 NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             +I+ F  +    + K   +  QP TGRTHQ+R H   +  PI  D +Y  NF   +
Sbjct: 600 KPSITRFMFLAYNPELKESLVLCQPITGRTHQIRAHLKSLSFPISNDAQYNDNFAKEY 657



 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 20/139 (14%), Positives = 47/139 (33%), Gaps = 20/139 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             R+     + +   +    Q+ ++ G V+V+++ V  +  ++S  +++   ++      
Sbjct: 68  GKRIADVLSSEFCAYDLSYFQESIKKGYVKVNEENVSCDYLMKSNDLIQHKLLL------ 121

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                         K     K ++LYED       K A +         Y  +  L+   
Sbjct: 122 ------------FEKPVMCNKILILYEDKNFICVYKSASLPTHPVG--FYQYNSLLRLLQ 167

Query: 138 DSKGQKPRLTHRLDQETSG 156
           +         H    ++SG
Sbjct: 168 NYISSTLAKGHPSGGDSSG 186



 Score = 43.4 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 7/67 (10%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK-------NKKEC 197
              HRLD+ TSGI++  + ++ +   +++     I K Y + V G  +       ++K+ 
Sbjct: 383 YTLHRLDKLTSGIVLFGKNKSFSTFFSQNISNNSITKSYVTRVEGDFRALIRTLLDQKKV 442

Query: 198 IANWLLK 204
           I +W  K
Sbjct: 443 IDDWDNK 449


>gi|193063125|ref|ZP_03044217.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           E22]
 gi|193067850|ref|ZP_03048816.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           E110019]
 gi|194426901|ref|ZP_03059454.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           B171]
 gi|260846816|ref|YP_003224594.1| 23S rRNA pseudouridine synthase [Escherichia coli O103:H2 str.
           12009]
 gi|192931384|gb|EDV83986.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           E22]
 gi|192958825|gb|EDV89262.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           E110019]
 gi|194415237|gb|EDX31506.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           B171]
 gi|257761963|dbj|BAI33460.1| 23S rRNA pseudouridine synthase [Escherichia coli O103:H2 str.
           12009]
 gi|323161320|gb|EFZ47228.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           E128010]
          Length = 290

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|315617385|gb|EFU97991.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           3431]
          Length = 290

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/168 (14%), Positives = 57/168 (33%), Gaps = 34/168 (20%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGGRDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  ++     RLD+++ G++ +         +  +      + +
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|94992201|ref|YP_600300.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
          pyogenes MGAS2096]
 gi|94545709|gb|ABF35756.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
          pyogenes MGAS2096]
          Length = 64

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
             RLD+   +  P ++       ++ G V V+ ++ K    +Q+G V+
Sbjct: 8  SGQRLDKALADLSP-LSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVI 55


>gi|258511697|ref|YP_003185131.1| pseudouridine synthase [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
 gi|257478423|gb|ACV58742.1| pseudouridine synthase [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
          Length = 273

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 47/250 (18%), Positives = 85/250 (34%), Gaps = 48/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +    H    +    ++++ +G+V VD + V      Q G  V       A++ + 
Sbjct: 2   ERLQKVLA-HAGVASRRKCEELILAGRVSVDGEIVT-----QLGAKVDPSRQRIAVDGVP 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP-AGISVQGGSGIAYHIDGFLKSWV 137
            E                       E   + V NKP A +S              +   +
Sbjct: 56  IEL----------------------EQPVVLVLNKPVAYLSTVSDPLGRRT----VMQLL 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L+        Q L      R I+K+Y   V G        
Sbjct: 90  PPIRERVYPVGRLDYDTSGLLLFTNDGELTQRL--LHPSREIEKVYRVSVRG-------- 139

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I +   +++ + G    V  ++   A   +   +  D        + +  H GR  Q+R 
Sbjct: 140 IVDRETRRALMEG----VELEDGVTAPAKVEVLRQADR-EDGVAVVHLAIHEGRNRQVRR 194

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 195 MFERLGLPVL 204


>gi|167768019|ref|ZP_02440072.1| hypothetical protein CLOSS21_02562 [Clostridium sp. SS2/1]
 gi|167710348|gb|EDS20927.1| hypothetical protein CLOSS21_02562 [Clostridium sp. SS2/1]
          Length = 245

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 36/245 (14%), Positives = 87/245 (35%), Gaps = 50/245 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHII 78
           RLD++  +   ++     ++ ++ G+V V+ + +K    ++ +                 
Sbjct: 9   RLDKFLCDSL-NMTRKEAKESVKKGKVVVNGEAIKKPEYKVDA----------------- 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ  ++    L          + +E     + +KP G+     +   +H    L    +
Sbjct: 51  -EQDQVEFDHKL----------IQFEQFHYLMLHKPQGVVS---ATKDHHDQTVLDLIHE 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD++T G+L++      A  L      + + K+Y++ V G     +   
Sbjct: 97  DYKDRLFPVGRLDKDTEGLLLLTDDGMLAHEL--LSPRKHVDKVYFAKVSGQFGENE--- 151

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               + +   G D          G     +  +++    Q+   + +    G+ HQ++  
Sbjct: 152 ----IARFKEGLDI-------GNGERSKQARLQILKADVQE-SEVLITIMEGKFHQVKRM 199

Query: 259 ALHMG 263
              +G
Sbjct: 200 VKAVG 204


>gi|126655906|ref|ZP_01727345.1| pseudouridine synthase, RluD [Cyanothece sp. CCY0110]
 gi|126623385|gb|EAZ94090.1| pseudouridine synthase, RluD [Cyanothece sp. CCY0110]
          Length = 64

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/63 (34%), Positives = 28/63 (44%), Gaps = 4/63 (6%)

Query: 262 MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPLPAHMVKTWD 320
           MG PIVGD  Y AN          +   LHA  + L HP    +++  APLP    K  +
Sbjct: 1   MGNPIVGDPLYSANRSLKMK---LSGQALHAYKLTLTHPITSEKIEAIAPLPHEFTKLLN 57

Query: 321 SLG 323
            L 
Sbjct: 58  YLR 60


>gi|145299656|ref|YP_001142497.1| 23S rRNA pseudouridine synthase F [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142852428|gb|ABO90749.1| ribosomal large subunit pseudouridine synthase F [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 344

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 80/249 (32%), Gaps = 56/249 (22%)

Query: 17  ENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E+MRL+++       I +     + +  GQV ++ KR    +++ +G +V++   +    
Sbjct: 5   ESMRLNKYISE--SGICSRREADRFIEQGQVFINGKRAGIGDQVFAGDLVKVNGQVIE-- 60

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                           + +D L            V NKP GI     +G   +I  F+  
Sbjct: 61  ---------------AREADSLV---------FIVLNKPVGIVSTTEAGEKDNIVDFVNH 96

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                  +     RLD+++ G++ +         +  +      + +             
Sbjct: 97  -----STRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TVD 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           + + +  +K    G   +  V +  K    A   F++                 G   Q+
Sbjct: 143 KPVTDDFIKGMGAGVPILGAVTKKCKVKKEAPFVFRI-------------TLVQGLNRQI 189

Query: 256 RVHALHMGC 264
           R    H G 
Sbjct: 190 RRMCEHFGF 198


>gi|218707643|ref|YP_002415162.1| 23S rRNA pseudouridine synthase F [Escherichia coli UMN026]
 gi|293402661|ref|ZP_06646758.1| 23S rRNA pseudouridine synthase F [Escherichia coli FVEC1412]
 gi|298378190|ref|ZP_06988074.1| 23S rRNA pseudouridine synthase F [Escherichia coli FVEC1302]
 gi|300899867|ref|ZP_07118079.1| conserved hypothetical protein [Escherichia coli MS 198-1]
 gi|218434740|emb|CAR15672.1| 23S rRNA pseudouridine synthase [Escherichia coli UMN026]
 gi|291429576|gb|EFF02590.1| 23S rRNA pseudouridine synthase F [Escherichia coli FVEC1412]
 gi|298280524|gb|EFI22025.1| 23S rRNA pseudouridine synthase F [Escherichia coli FVEC1302]
 gi|300356569|gb|EFJ72439.1| conserved hypothetical protein [Escherichia coli MS 198-1]
          Length = 290

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 24/168 (14%), Positives = 57/168 (33%), Gaps = 34/168 (20%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  ++     RLD+++ G++ +         +  +      + +
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|218289586|ref|ZP_03493806.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
 gi|218240236|gb|EED07419.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
          Length = 273

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 47/250 (18%), Positives = 85/250 (34%), Gaps = 48/250 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +    H    +    ++++ +G+V VD + V      Q G  V       A++ + 
Sbjct: 2   ERLQKVLA-HAGVASRRKCEELILAGRVSVDGEIVT-----QLGAKVDPSRQRIAVDGVP 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKP-AGISVQGGSGIAYHIDGFLKSWV 137
            E                       E   + V NKP A +S              +   +
Sbjct: 56  IEL----------------------EQPVVLVLNKPVAYLSTVSDPLGRRT----VMQLL 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L+        Q L      R I+K+Y   V G        
Sbjct: 90  PPIRERVYPVGRLDYDTSGLLLFTNDGELTQRL--LHPSREIEKVYRVSVRG-------- 139

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I +   +++ + G    V  ++   A   +   +  D        + +  H GR  Q+R 
Sbjct: 140 IVDRETRRALMEG----VELEDGVTAPAKVEVLRQADR-EDGVAVVHLAIHEGRNRQVRR 194

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 195 MFERLGLPVL 204


>gi|15804615|ref|NP_290656.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 EDL933]
 gi|15834259|ref|NP_313032.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           Sakai]
 gi|168750850|ref|ZP_02775872.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4113]
 gi|168755170|ref|ZP_02780177.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4401]
 gi|168760865|ref|ZP_02785872.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4501]
 gi|168766260|ref|ZP_02791267.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4486]
 gi|168774357|ref|ZP_02799364.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4196]
 gi|168780412|ref|ZP_02805419.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4076]
 gi|168784615|ref|ZP_02809622.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC869]
 gi|168798338|ref|ZP_02823345.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC508]
 gi|195935788|ref|ZP_03081170.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           EC4024]
 gi|208808749|ref|ZP_03251086.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4206]
 gi|208811969|ref|ZP_03253298.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4045]
 gi|208821132|ref|ZP_03261452.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4042]
 gi|209400390|ref|YP_002273541.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4115]
 gi|209921498|ref|YP_002295582.1| 23S rRNA pseudouridine synthase F [Escherichia coli SE11]
 gi|217325648|ref|ZP_03441732.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. TW14588]
 gi|254796022|ref|YP_003080859.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           TW14359]
 gi|261223462|ref|ZP_05937743.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261256997|ref|ZP_05949530.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291285439|ref|YP_003502257.1| Ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O55:H7 str. CB9615]
 gi|293417527|ref|ZP_06660149.1| 23S rRNA pseudouridine synthase F [Escherichia coli B185]
 gi|331655840|ref|ZP_08356828.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli M718]
 gi|34098615|sp|Q8X4L9|RLUF_ECO57 RecName: Full=Ribosomal large subunit pseudouridine synthase F;
           AltName: Full=rRNA pseudouridylate synthase F; AltName:
           Full=rRNA-uridine isomerase F
 gi|12518965|gb|AAG59221.1|AE005635_1 orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]
 gi|13364481|dbj|BAB38428.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|187769953|gb|EDU33797.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4196]
 gi|188015005|gb|EDU53127.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4113]
 gi|189001699|gb|EDU70685.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4076]
 gi|189357499|gb|EDU75918.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4401]
 gi|189364343|gb|EDU82762.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4486]
 gi|189368503|gb|EDU86919.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4501]
 gi|189374896|gb|EDU93312.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC869]
 gi|189379218|gb|EDU97634.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC508]
 gi|208728550|gb|EDZ78151.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4206]
 gi|208733246|gb|EDZ81933.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4045]
 gi|208741255|gb|EDZ88937.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4042]
 gi|209161790|gb|ACI39223.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. EC4115]
 gi|209751528|gb|ACI74071.1| hypothetical protein ECs5005 [Escherichia coli]
 gi|209751530|gb|ACI74072.1| hypothetical protein ECs5005 [Escherichia coli]
 gi|209751532|gb|ACI74073.1| hypothetical protein ECs5005 [Escherichia coli]
 gi|209751534|gb|ACI74074.1| hypothetical protein ECs5005 [Escherichia coli]
 gi|209751536|gb|ACI74075.1| hypothetical protein ECs5005 [Escherichia coli]
 gi|209914757|dbj|BAG79831.1| putative pseudouridine synthase [Escherichia coli SE11]
 gi|217321869|gb|EEC30293.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O157:H7 str. TW14588]
 gi|254595422|gb|ACT74783.1| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str.
           TW14359]
 gi|290765312|gb|ADD59273.1| Ribosomal large subunit pseudouridine synthase F [Escherichia coli
           O55:H7 str. CB9615]
 gi|291430245|gb|EFF03243.1| 23S rRNA pseudouridine synthase F [Escherichia coli B185]
 gi|320190877|gb|EFW65527.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           EC1212]
 gi|320638776|gb|EFX08422.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           G5101]
 gi|320644144|gb|EFX13209.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H- str.
           493-89]
 gi|320649463|gb|EFX17987.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H- str. H
           2687]
 gi|320654859|gb|EFX22820.1| 23S rRNA pseudouridine synthase F [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320660707|gb|EFX28164.1| 23S rRNA pseudouridine synthase F [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|320665636|gb|EFX32673.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           LSU-61]
 gi|324017076|gb|EGB86295.1| hypothetical protein HMPREF9542_04288 [Escherichia coli MS 117-3]
 gi|326340567|gb|EGD64365.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           1125]
 gi|326342524|gb|EGD66299.1| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str.
           1044]
 gi|331046194|gb|EGI18284.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli M718]
          Length = 290

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|157156860|ref|YP_001465515.1| 23S rRNA pseudouridine synthase F [Escherichia coli E24377A]
 gi|170021980|ref|YP_001726934.1| 23S rRNA pseudouridine synthase F [Escherichia coli ATCC 8739]
 gi|188492339|ref|ZP_02999609.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           53638]
 gi|191167475|ref|ZP_03029289.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           B7A]
 gi|218556572|ref|YP_002389486.1| 23S rRNA pseudouridine synthase F [Escherichia coli IAI1]
 gi|218697724|ref|YP_002405391.1| 23S rRNA pseudouridine synthase F [Escherichia coli 55989]
 gi|293476325|ref|ZP_06664733.1| 23S rRNA pseudouridine synthase F [Escherichia coli B088]
 gi|300817929|ref|ZP_07098142.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300823552|ref|ZP_07103680.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300924275|ref|ZP_07140255.1| hypothetical protein HMPREF9548_02431 [Escherichia coli MS 182-1]
 gi|301330618|ref|ZP_07223223.1| conserved hypothetical protein [Escherichia coli MS 78-1]
 gi|307312141|ref|ZP_07591778.1| pseudouridine synthase [Escherichia coli W]
 gi|309795820|ref|ZP_07690234.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|312974192|ref|ZP_07788363.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           1827-70]
 gi|331670876|ref|ZP_08371710.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA271]
 gi|331680144|ref|ZP_08380803.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli H591]
 gi|157078890|gb|ABV18598.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           E24377A]
 gi|169756908|gb|ACA79607.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|188487538|gb|EDU62641.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           53638]
 gi|190902517|gb|EDV62252.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           B7A]
 gi|218354456|emb|CAV01282.1| 23S rRNA pseudouridine synthase [Escherichia coli 55989]
 gi|218363341|emb|CAR00994.1| 23S rRNA pseudouridine synthase [Escherichia coli IAI1]
 gi|291320778|gb|EFE60220.1| 23S rRNA pseudouridine synthase F [Escherichia coli B088]
 gi|300419503|gb|EFK02814.1| hypothetical protein HMPREF9548_02431 [Escherichia coli MS 182-1]
 gi|300523884|gb|EFK44953.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300529339|gb|EFK50401.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300843430|gb|EFK71190.1| conserved hypothetical protein [Escherichia coli MS 78-1]
 gi|306907948|gb|EFN38449.1| pseudouridine synthase [Escherichia coli W]
 gi|308120481|gb|EFO57743.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|310331726|gb|EFP98982.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           1827-70]
 gi|315063343|gb|ADT77670.1| 23S rRNA pseudouridine synthase [Escherichia coli W]
 gi|320200854|gb|EFW75440.1| 23S rRNA pseudouridine synthase F [Escherichia coli EC4100B]
 gi|323182119|gb|EFZ67529.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           1357]
 gi|323380593|gb|ADX52861.1| pseudouridine synthase [Escherichia coli KO11]
 gi|323946150|gb|EGB42184.1| RNA pseudouridylate synthase [Escherichia coli H120]
 gi|324118589|gb|EGC12481.1| RNA pseudouridylate synthase [Escherichia coli E1167]
 gi|331061790|gb|EGI33715.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA271]
 gi|331071607|gb|EGI42943.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli H591]
          Length = 290

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|169824529|ref|YP_001692140.1| ribosomal large subunit pseudouridine synthase B [Finegoldia magna
           ATCC 29328]
 gi|167831334|dbj|BAG08250.1| ribosomal large subunit pseudouridine synthase B [Finegoldia magna
           ATCC 29328]
          Length = 242

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 82/253 (32%), Gaps = 58/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MR++++      + +  N  +++++ +V V+   +   + ++    +V +      L   
Sbjct: 1   MRINKFIAQS-GYCSRRNADELIKNSKVYVNGTILLDLSYQVNDTDIVEVEGKKINLK-- 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                     ED      NKP G  S          +   +KS 
Sbjct: 58  --------------------------EDKIYIAINKPIGYASTVKDKFADKKVVDLIKS- 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-- 194
                 +     RLD+++ G+L++         LT      +  KIY  LV G P     
Sbjct: 91  ----DTRVYPVGRLDKDSHGLLILTNDGEFTYELTHPKFEHK--KIYEVLVKGKPNKTEI 144

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K+     LL    +    +  ++  +    Y ++ F+                  GR  Q
Sbjct: 145 KQLKDGILLDGYKLKKSKIEFIENVKNDTKYRVTIFE------------------GRNRQ 186

Query: 255 LRVHALHMGCPIV 267
           +R     +  P++
Sbjct: 187 IRRMFDFINHPVL 199


>gi|117619273|ref|YP_856164.1| 23S rRNA pseudouridine synthase F [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117560680|gb|ABK37628.1| ribosomal large subunit pseudouridine synthase F [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 344

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 79/250 (31%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E+MRL+++       I +     + +  G V ++ KR    +++ +G +V++       
Sbjct: 4   DESMRLNKYISE--SGICSRREADRFIEQGNVFINGKRAGVGDQVFAGDLVKVNGQ---- 57

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
              + E +  DS V                     V NKP GI     +G   +I  F+ 
Sbjct: 58  ---VIEPREADSLV-------------------FIVLNKPVGIVSTTEAGEKDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                   +     RLD+++ G++ +                      +  LV  I +  
Sbjct: 96  H-----STRIFPIGRLDKDSQGLIFL--------------------TNHGDLVNKILRAG 130

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            +    +L+       D              A++  K      +      +    G   Q
Sbjct: 131 NDHEKEYLVTVDKPVTDEFIRGMGAGVPILGAVT--KKCKVKKEAPFVFRITLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGF 198


>gi|332752067|gb|EGJ82460.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           4343-70]
          Length = 290

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G +V++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDIVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|325261871|ref|ZP_08128609.1| ribosomal large subunit pseudouridine synthase F [Clostridium sp.
           D5]
 gi|324033325|gb|EGB94602.1| ribosomal large subunit pseudouridine synthase F [Clostridium sp.
           D5]
          Length = 256

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 77/251 (30%), Gaps = 62/251 (24%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +RL+++        +     +++ SG+V+VD K      ++  GQ VRI   I + + 
Sbjct: 14  EPVRLNKYLSEA-GVCSRREADRLIESGKVKVDGKAAGMGMKVSPGQEVRIGRKIVSRS- 71

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                      E+  +   NKPAGI     +     I  FL   
Sbjct: 72  ---------------------------EEMIVLAVNKPAGIVCTEETRERKSIVRFL--- 101

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK---IYWSLVWGIPKN 193
             +   +     RLD+++ G+L++         +  +      +    +  +L     + 
Sbjct: 102 --NYPVRVTYVGRLDKDSRGLLLMTNNGDIINKMMRAGNRHEKEYKVTVDKALTPEFLEK 159

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
               +A             V    + +K   Y  +                +    G   
Sbjct: 160 MSSGVAILGT---------VTRPCRVQKIGKYTFT----------------IILTQGLNR 194

Query: 254 QLRVHALHMGC 264
           Q+R     +G 
Sbjct: 195 QIRRMCEVLGY 205


>gi|157163487|ref|YP_001460805.1| 23S rRNA pseudouridine synthase F [Escherichia coli HS]
 gi|300916198|ref|ZP_07132950.1| conserved hypothetical protein [Escherichia coli MS 115-1]
 gi|157069167|gb|ABV08422.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           HS]
 gi|300416478|gb|EFJ99788.1| conserved hypothetical protein [Escherichia coli MS 115-1]
          Length = 290

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|323965683|gb|EGB61135.1| RNA pseudouridylate synthase [Escherichia coli M863]
 gi|327250364|gb|EGE62077.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           STEC_7v]
          Length = 290

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 74/250 (29%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +   +    P   
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL---VTVDKPVTD 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E I         +G        + E    + I+                     G   Q
Sbjct: 148 -EFIRGMGAGVPILGTVTKKCKVKKEAPFVFRIT------------------LVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|315657981|ref|ZP_07910855.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           lugdunensis M23590]
 gi|315497017|gb|EFU85338.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           lugdunensis M23590]
          Length = 230

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 79/246 (32%), Gaps = 57/246 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD++   H        +++ L+ G V V+ K  K    +I     VV+I         
Sbjct: 2   MRLDKFLA-HMGQGTRTEVKQSLKKGNVTVNGKVEKSAKTQINPHHDVVQIHGH------ 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   + Y ++   + NKP G            +   +K +
Sbjct: 55  -----------------------QIDYVETVYLMLNKPKGYISATEDPKQATVIDLIKDY 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              K        RLD++T G+L++      + +L      + + K Y             
Sbjct: 92  ---KYLDLFPVGRLDKDTEGLLLITNDGQFSHNL--MNPNKHVAKTYL------------ 134

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             + + + K +       V+  +       ++   +ID +  K    E     GR HQ++
Sbjct: 135 VTSKYPVTKDNQYMFKQGVMLSDGLTKPAELT---IIDDYHSKVTIYE-----GRYHQIK 186

Query: 257 VHALHM 262
                +
Sbjct: 187 RMFHSI 192


>gi|167761342|ref|ZP_02433469.1| hypothetical protein CLOSCI_03750 [Clostridium scindens ATCC 35704]
 gi|167661008|gb|EDS05138.1| hypothetical protein CLOSCI_03750 [Clostridium scindens ATCC 35704]
          Length = 247

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 77/249 (30%), Gaps = 56/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL+++  +     +     +++ SGQV VD +R     ++  GQ V++           
Sbjct: 2   VRLNKYLSDA-GVCSRREADRLIESGQVSVDGQRAVPGMKVADGQEVKV----------- 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +K++ S+                    +   NKPAGI          +I  +LK    
Sbjct: 50  -GKKVIRSNTEKI----------------VLAVNKPAGIVCTEDVREKKNIIRYLK---- 88

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY---WSLVWGIPKNKK 195
               +     RLD+++ G+L++         +  +      +        +        K
Sbjct: 89  -YPIRVTYAGRLDKDSEGLLIMTNDGDLINGMMRARHGHEKEYKVTVNKPVTQDFISKMK 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E I    +       D      + EK   Y  S                +    G   Q+
Sbjct: 148 EGIR---IVDKEKRLDVATRPCKAEKLGKYTFS----------------ITLTQGLNRQI 188

Query: 256 RVHALHMGC 264
           R     +G 
Sbjct: 189 RRMCEALGY 197


>gi|89901090|ref|YP_523561.1| pseudouridine synthase Rsu [Rhodoferax ferrireducens T118]
 gi|89345827|gb|ABD70030.1| ribosomal large subunit pseudouridine synthase B [Rhodoferax
           ferrireducens T118]
          Length = 466

 Score = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/233 (14%), Positives = 74/233 (31%), Gaps = 47/233 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      RIQ G  V++                         
Sbjct: 110 SRLEMEQLIMEGRITVNNEPAHIGQRIQFGDHVKVN------------------------ 145

Query: 93  HSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
               ++  +    +++  ++KP G +           +   L      K Q      RLD
Sbjct: 146 -GKPIRFRIDAPPARVIAYHKPVGEVVTHDDPQNRPTVFRRLPKLFQGKWQS---VGRLD 201

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             T G+L+   +   A +L        +++ Y   V G     ++      +K       
Sbjct: 202 LNTEGLLLFTSSGELANNL--MHPRFGLEREYAVRVLGALNKDEKQRLLDGVKLDDGVAQ 259

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +  +     +GAN                CW  +    GR  ++R     +G 
Sbjct: 260 FGSIEAGGGEGAN----------------CWYRVTIAEGRNREVRRMFEAVGH 296


>gi|323975348|gb|EGB70451.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
          Length = 290

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|170682433|ref|YP_001746411.1| 23S rRNA pseudouridine synthase F [Escherichia coli SMS-3-5]
 gi|218702664|ref|YP_002410293.1| 23S rRNA pseudouridine synthase F [Escherichia coli IAI39]
 gi|300939713|ref|ZP_07154358.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|331660590|ref|ZP_08361522.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA206]
 gi|170520151|gb|ACB18329.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           SMS-3-5]
 gi|218372650|emb|CAR20525.1| 23S rRNA pseudouridine synthase [Escherichia coli IAI39]
 gi|284924116|emb|CBG37215.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           042]
 gi|300455410|gb|EFK18903.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|315300783|gb|EFU60008.1| conserved hypothetical protein [Escherichia coli MS 16-3]
 gi|323190114|gb|EFZ75392.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           RN587/1]
 gi|331051632|gb|EGI23671.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA206]
          Length = 290

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|147677969|ref|YP_001212184.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Pelotomaculum
           thermopropionicum SI]
 gi|146274066|dbj|BAF59815.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Pelotomaculum
           thermopropionicum SI]
          Length = 252

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 78/249 (31%), Gaps = 48/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +  + ++++ +G V+V+ K V      + G  V             
Sbjct: 14  ERLQKVMARA-GVASRRHCERLIAAGAVKVNGKVVT-----EVGCKV------------- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                        K     ++I L+      +  KP G                L   V 
Sbjct: 55  --------DPARDKIQVGNRTISLFPRRYYILLYKPRGYVTTLSDEKGRKKVTDLLKGVA 106

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD ++ G+L++         LT      R+ K Y   V G+P  +    
Sbjct: 107 G---RVYPVGRLDYDSEGLLLLTNDGELTYALT--HPKHRVPKTYVVSVKGLPGRE---- 157

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                K   + G  +       +    A +  ++I    +    LE+    GR  Q+R  
Sbjct: 158 -----KLEKMAGGLML------EDGPTAPARVRLIGRRGKNV-LLEITISEGRNRQIRRM 205

Query: 259 ALHMGCPIV 267
              +G P+V
Sbjct: 206 CDSIGHPVV 214


>gi|311281430|ref|YP_003943661.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308750625|gb|ADO50377.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 292

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 67/246 (27%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++  G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRATIGDQVAPGDVVKVNGQLIEPRDA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    ED      NKP GI      G   +I  F+     
Sbjct: 65  -------------------------EDLVFIALNKPVGIVSTTEDGERNNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++ +         +  +      +      V  + K   +  
Sbjct: 97  --SSRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEY-----VVTVNKPVTDEF 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +     I G      K  ++                       +    G   Q+R  
Sbjct: 150 IRAMGAGVPILGTVTKKCKVKKEAPFA-----------------FRITLIQGLNRQIRRM 192

Query: 259 ALHMGC 264
             H G 
Sbjct: 193 CEHFGY 198


>gi|303233760|ref|ZP_07320414.1| putative pseudouridine synthase B, ribosomal large subunit
           [Finegoldia magna BVS033A4]
 gi|302495194|gb|EFL54946.1| putative pseudouridine synthase B, ribosomal large subunit
           [Finegoldia magna BVS033A4]
          Length = 242

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 82/253 (32%), Gaps = 58/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MR++++      + +  N  +++++ +V V+   +   + ++    +V +      L   
Sbjct: 1   MRINKFIAQS-GYCSRRNADELIKNSKVYVNGTILLDLSYQVNDTDIVEVEGKKINLK-- 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                     ED      NKP G  S          +   +KS 
Sbjct: 58  --------------------------EDKIYIAINKPIGYASTVKDKFADKKVVDLIKS- 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-- 194
                 +     RLD+++ G+L++         LT      +  KIY  LV G P     
Sbjct: 91  ----DTRVYPVGRLDKDSHGLLILTNDGEFTYELTHPKFEHK--KIYEVLVKGKPNKTEI 144

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K+     LL    +    +  ++  +    Y ++ F+                  GR  Q
Sbjct: 145 KQLKDGILLDGYKLKKSKIEFIENVKNDTKYRVTIFE------------------GRNRQ 186

Query: 255 LRVHALHMGCPIV 267
           +R     +  P++
Sbjct: 187 IRRMFDFINHPVL 199


>gi|16131848|ref|NP_418446.1| 23S rRNA U2604 pseudouridine synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|89110743|ref|AP_004523.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           W3110]
 gi|170083479|ref|YP_001732799.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|194437171|ref|ZP_03069269.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           101-1]
 gi|238903075|ref|YP_002928871.1| 23S rRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|253775354|ref|YP_003038185.1| 23S rRNA pseudouridine synthase F [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254037014|ref|ZP_04871091.1| ribosomal large subunit pseudouridine synthase F [Escherichia sp.
           1_1_43]
 gi|254163958|ref|YP_003047066.1| 23S rRNA pseudouridine synthase F [Escherichia coli B str. REL606]
 gi|256024891|ref|ZP_05438756.1| 23S rRNA pseudouridine synthase F [Escherichia sp. 4_1_40B]
 gi|300929753|ref|ZP_07145207.1| conserved hypothetical protein [Escherichia coli MS 187-1]
 gi|300946586|ref|ZP_07160846.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300957575|ref|ZP_07169780.1| hypothetical protein HMPREF9547_03329 [Escherichia coli MS 175-1]
 gi|301019105|ref|ZP_07183310.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|301645001|ref|ZP_07244966.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|418534|sp|P32684|RLUF_ECOLI RecName: Full=Ribosomal large subunit pseudouridine synthase F;
           AltName: Full=rRNA pseudouridylate synthase F; AltName:
           Full=rRNA-uridine isomerase F
 gi|228312012|pdb|3DH3|A Chain A, Crystal Structure Of Rluf In Complex With A 22 Nucleotide
           Rna Substrate
 gi|228312014|pdb|3DH3|B Chain B, Crystal Structure Of Rluf In Complex With A 22 Nucleotide
           Rna Substrate
 gi|228312016|pdb|3DH3|C Chain C, Crystal Structure Of Rluf In Complex With A 22 Nucleotide
           Rna Substrate
 gi|228312018|pdb|3DH3|D Chain D, Crystal Structure Of Rluf In Complex With A 22 Nucleotide
           Rna Substrate
 gi|396357|gb|AAC43116.1| ORF_o290a [Escherichia coli str. K-12 substr. MG1655]
 gi|1790453|gb|AAC76992.1| 23S rRNA U2604 pseudouridine synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|85676774|dbj|BAE78024.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K12 substr.
           W3110]
 gi|169891314|gb|ACB05021.1| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|194423727|gb|EDX39716.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           101-1]
 gi|226840120|gb|EEH72122.1| ribosomal large subunit pseudouridine synthase F [Escherichia sp.
           1_1_43]
 gi|238859759|gb|ACR61757.1| 23S rRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|242379552|emb|CAQ34371.1| 23S rRNA pseudouridine 2604 synthase [Escherichia coli BL21(DE3)]
 gi|253326398|gb|ACT31000.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253975859|gb|ACT41530.1| 23S rRNA pseudouridine synthase [Escherichia coli B str. REL606]
 gi|253980015|gb|ACT45685.1| 23S rRNA pseudouridine synthase [Escherichia coli BL21(DE3)]
 gi|260451153|gb|ACX41575.1| pseudouridine synthase [Escherichia coli DH1]
 gi|299882399|gb|EFI90610.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|300315689|gb|EFJ65473.1| hypothetical protein HMPREF9547_03329 [Escherichia coli MS 175-1]
 gi|300453742|gb|EFK17362.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300462326|gb|EFK25819.1| conserved hypothetical protein [Escherichia coli MS 187-1]
 gi|301076689|gb|EFK91495.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|309704434|emb|CBJ03783.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           ETEC H10407]
 gi|315138575|dbj|BAJ45734.1| 23S rRNA pseudouridine synthase F [Escherichia coli DH1]
 gi|323935584|gb|EGB31911.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323940200|gb|EGB36393.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323960493|gb|EGB56124.1| RNA pseudouridylate synthase [Escherichia coli H489]
          Length = 290

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 24/168 (14%), Positives = 57/168 (33%), Gaps = 34/168 (20%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  ++     RLD+++ G++ +         +  +      + +
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|293407757|ref|ZP_06651597.1| 23S rRNA pseudouridine synthase F [Escherichia coli B354]
 gi|301021535|ref|ZP_07185540.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|331665691|ref|ZP_08366585.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA143]
 gi|331675512|ref|ZP_08376260.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA280]
 gi|331685769|ref|ZP_08386350.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli H299]
 gi|291472008|gb|EFF14490.1| 23S rRNA pseudouridine synthase F [Escherichia coli B354]
 gi|300398018|gb|EFJ81556.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|331056742|gb|EGI28736.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA143]
 gi|331067286|gb|EGI38693.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli TA280]
 gi|331076966|gb|EGI48183.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli H299]
          Length = 290

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|157871141|ref|XP_001684120.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|68127188|emb|CAJ05143.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 977

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 5/67 (7%)

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY-----CANFKGNFT 281
           + H +       +   +   P+TGR HQ+R+H   +GCPIVGD  Y      A+  G  +
Sbjct: 623 VQHAETSAAGVSEEAVVLCTPYTGRLHQIRMHLSSLGCPIVGDVVYAPTSGSADVPGTPS 682

Query: 282 SPIQNKL 288
           +P+Q  L
Sbjct: 683 TPVQPPL 689



 Score = 38.4 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 13/44 (29%), Positives = 25/44 (56%), Gaps = 2/44 (4%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTE--SFRMRRIQKIYWS 185
           PR  HRLD+ TSG+L++A  + AA+ +      +   +++   +
Sbjct: 366 PRPCHRLDKVTSGVLLLAVRQDAARRIGSVLMRKANEVEEAVTA 409


>gi|256019605|ref|ZP_05433470.1| 23S rRNA pseudouridine synthase F [Shigella sp. D9]
 gi|332280733|ref|ZP_08393146.1| 23S rRNA pseudouridine synthase F [Shigella sp. D9]
 gi|332103085|gb|EGJ06431.1| 23S rRNA pseudouridine synthase F [Shigella sp. D9]
          Length = 290

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G +V++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDIVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|212712415|ref|ZP_03320543.1| hypothetical protein PROVALCAL_03504 [Providencia alcalifaciens DSM
           30120]
 gi|212685161|gb|EEB44689.1| hypothetical protein PROVALCAL_03504 [Providencia alcalifaciens DSM
           30120]
          Length = 235

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 77/250 (30%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + LR+G V VD + VK  + +Q G    +    N L  + 
Sbjct: 1   MRLDKFLSQQL-GISRSLVARELRAGNVTVDDEVVKSGS-MQVGLDNEVAYDGNVLVQVT 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +                           ++ NKP G      S         L    +
Sbjct: 59  GPR--------------------------YFMLNKPEGYVC---STDDPTHPTILYFIDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              Q      RLD +T+G++++      +  +T                          +
Sbjct: 90  PIAQNLHAAGRLDIDTTGLVLLTDDGQWSHRITSPKHHCEKTYRVQ-------------L 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +  +     I  +   ++   +     A      ++  + +     +    GR HQ++  
Sbjct: 137 SEDIADDVTIQFEQGVMLNGEKSPTKPAQ-----LEIISPREVL--LTISEGRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  + G
Sbjct: 190 FAAVGNHVCG 199


>gi|307244534|ref|ZP_07526639.1| pseudouridylate synthase [Peptostreptococcus stomatis DSM 17678]
 gi|306492061|gb|EFM64109.1| pseudouridylate synthase [Peptostreptococcus stomatis DSM 17678]
          Length = 244

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 86/251 (34%), Gaps = 46/251 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   +     ++K+ R G V V+ + VK                    +HI 
Sbjct: 1   MRLDKMLSN-LGYGTRSEIKKMCRQGMVTVNGQEVKK-----------------PDHHID 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +Q  +  +    ++ +++            + NKPAG      +   Y          +
Sbjct: 43  PDQDQVCLNGQAVRYREYI----------YLMMNKPAGCVS--ATYDKYDQTVIDLIDPE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +P    RLD++T G+LV+      + + L+     + + KIY++            
Sbjct: 91  YLAFEPFPVGRLDKDTEGLLVITNDGQLSHRVLS---PKKHVPKIYYA-----------E 136

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEMQPHTGRTHQLR 256
           I + +L +          +  +       +   K  +         + +    G+ HQ++
Sbjct: 137 IDHEVLARDIEAFSKGVYIGDDYTTKPAKLEVIKSFEAEDGAIHSEIYVTISEGKFHQVK 196

Query: 257 VHALHMGCPIV 267
                +G  ++
Sbjct: 197 RMFEAVGKSVL 207


>gi|118444164|ref|YP_878165.1| ribosomal large subunit pseudouridine synthase B [Clostridium novyi
           NT]
 gi|118134620|gb|ABK61664.1| ribosomal large subunit pseudouridine synthase B [Clostridium novyi
           NT]
          Length = 236

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 85/250 (34%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++  +     +    ++I+ S +V+V+   V                         
Sbjct: 3   ERLQKYMAS-CGVASRRKCEEIIISNRVKVNGTIV------------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
             +       +  K     K I L E       NKP G +S          I   +    
Sbjct: 37  -NELGFKVDPSKDKVYVDSKLIFLEEKKVYIALNKPEGYVSTVKDERNRKTIMDLV---- 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD  TSG+L++         +      + I K+Y +++ G+P +++  
Sbjct: 92  -EVEERIFPIGRLDYNTSGLLLMTNDGDIYNKI--IHPRKEIDKVYIAIIKGVPSDEEI- 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                       GDY+            + ++F+VID    K   + +  H G+  Q+R 
Sbjct: 148 ---HKFCNGLDIGDYI-----------TSKANFEVIDKLEDK-SKVRITIHEGKNRQVRR 192

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 193 MCDKIGHPVI 202


>gi|117618383|ref|YP_857355.1| ribosomal small subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117559790|gb|ABK36738.1| ribosomal small subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 230

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 84/250 (33%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +    +      K++R G+V VD   VK                     HI 
Sbjct: 1   MRLDKFLCD-CSDLTRSLAGKLIRQGEVMVDGIVVK-----------------QPAFHIN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           ++ ++    V LT          L + ++ ++ +KP G      +    H   F      
Sbjct: 43  EQSQVEFDGVTLT----------LDQRNRYFMLHKPEGYVC--SNEDPDHPTVFFLMDEP 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           + G K  +  RLD +T+G+++V      +  +T            W             +
Sbjct: 91  AMG-KLHVVGRLDLDTTGLVLVTDDGQWSHRITSPRHECAKTYHVW-------------L 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ +   +        +++   +    A              C   +  H G+ HQ++  
Sbjct: 137 ADPVSPDAIALFAEGVLLRSETEKTRPAQLEI-------LGECEARLTIHEGKYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAAIGNKVVG 199


>gi|24115303|ref|NP_709813.1| 23S rRNA pseudouridine synthase F [Shigella flexneri 2a str. 301]
 gi|30064697|ref|NP_838868.1| 23S rRNA pseudouridine synthase F [Shigella flexneri 2a str. 2457T]
 gi|74314515|ref|YP_312934.1| 23S rRNA pseudouridine synthase F [Shigella sonnei Ss046]
 gi|82546365|ref|YP_410312.1| 23S rRNA pseudouridine synthase F [Shigella boydii Sb227]
 gi|110807871|ref|YP_691391.1| 23S rRNA pseudouridine synthase F [Shigella flexneri 5 str. 8401]
 gi|187733719|ref|YP_001882708.1| 23S rRNA pseudouridine synthase F [Shigella boydii CDC 3083-94]
 gi|194432289|ref|ZP_03064577.1| ribosomal large subunit pseudouridine synthase F [Shigella
           dysenteriae 1012]
 gi|34098456|sp|Q83IR6|RLUF_SHIFL RecName: Full=Ribosomal large subunit pseudouridine synthase F;
           AltName: Full=rRNA pseudouridylate synthase F; AltName:
           Full=rRNA-uridine isomerase F
 gi|24054601|gb|AAN45520.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
 gi|30042957|gb|AAP18679.1| hypothetical protein S3635 [Shigella flexneri 2a str. 2457T]
 gi|73857992|gb|AAZ90699.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|81247776|gb|ABB68484.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|110617419|gb|ABF06086.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|187430711|gb|ACD09985.1| ribosomal large subunit pseudouridine synthase F [Shigella boydii
           CDC 3083-94]
 gi|194419492|gb|EDX35573.1| ribosomal large subunit pseudouridine synthase F [Shigella
           dysenteriae 1012]
 gi|281603406|gb|ADA76390.1| Ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           2002017]
 gi|313648678|gb|EFS13118.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           2a str. 2457T]
 gi|320187140|gb|EFW61842.1| 23S rRNA pseudouridine synthase F [Shigella flexneri CDC 796-83]
 gi|332083850|gb|EGI89067.1| ribosomal large subunit pseudouridine synthase F [Shigella boydii
           5216-82]
 gi|332084289|gb|EGI89492.1| ribosomal large subunit pseudouridine synthase F [Shigella
           dysenteriae 155-74]
 gi|332087766|gb|EGI92892.1| ribosomal large subunit pseudouridine synthase F [Shigella boydii
           3594-74]
 gi|332752238|gb|EGJ82630.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           K-671]
 gi|332753238|gb|EGJ83619.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           2747-71]
 gi|332764829|gb|EGJ95058.1| 23S rRNA pseudouridine synthase [Shigella flexneri 2930-71]
 gi|332998087|gb|EGK17691.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           VA-6]
 gi|332999015|gb|EGK18604.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           K-272]
 gi|333014244|gb|EGK33600.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           K-304]
 gi|333014452|gb|EGK33803.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           K-227]
          Length = 290

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G +V++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDIVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|331644758|ref|ZP_08345875.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli H736]
 gi|331035733|gb|EGI07971.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli H736]
          Length = 227

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 24/168 (14%), Positives = 57/168 (33%), Gaps = 34/168 (20%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  ++     RLD+++ G++ +         +  +      + +
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|331649882|ref|ZP_08350959.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli M605]
 gi|281181089|dbj|BAI57419.1| putative pseudouridine synthase [Escherichia coli SE15]
 gi|330908342|gb|EGH36861.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           AA86]
 gi|331041262|gb|EGI13415.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Escherichia coli M605]
          Length = 290

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/250 (14%), Positives = 78/250 (31%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++SG VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKSGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|260858132|ref|YP_003232023.1| 23S rRNA pseudouridine synthase [Escherichia coli O26:H11 str.
           11368]
 gi|260870735|ref|YP_003237137.1| 23S rRNA pseudouridine synthase [Escherichia coli O111:H- str.
           11128]
 gi|257756781|dbj|BAI28283.1| 23S rRNA pseudouridine synthase [Escherichia coli O26:H11 str.
           11368]
 gi|257767091|dbj|BAI38586.1| 23S rRNA pseudouridine synthase [Escherichia coli O111:H- str.
           11128]
 gi|323155588|gb|EFZ41764.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           EPECa14]
 gi|323174457|gb|EFZ60082.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           LT-68]
 gi|323177584|gb|EFZ63169.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           1180]
          Length = 290

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G +V++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDIVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|291086679|ref|ZP_06356433.2| ribosomal large subunit pseudouridine synthase F [Citrobacter
           youngae ATCC 29220]
 gi|291067434|gb|EFE05543.1| ribosomal large subunit pseudouridine synthase F [Citrobacter
           youngae ATCC 29220]
          Length = 318

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 75/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 31  DSSIRLNKYISE--SGICSRREADRFIEQGNVFLNGKRATIGDQVKPGDVVKVNGRLIEP 88

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED      NKP GI          +I  F+ 
Sbjct: 89  REA--------------------------EDLVFIALNKPVGIVSTTEDSERDNIVDFVN 122

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 123 H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 168

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 169 DKPITDDFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLIQGLNRQ 215

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 216 IRRMCEHFGY 225


>gi|229917541|ref|YP_002886187.1| RNA-binding S4 domain protein [Exiguobacterium sp. AT1b]
 gi|229468970|gb|ACQ70742.1| RNA-binding S4 domain protein [Exiguobacterium sp. AT1b]
          Length = 236

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 28/249 (11%), Positives = 79/249 (31%), Gaps = 62/249 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++        +     +++  G+V ++ K+ K  ++++ G  V +   +       
Sbjct: 1   MRINKFISESGK-ASRRQADRLVEEGRVTINGKKAKIGDQVKPGDEVLVNGSVAR----- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  +  ++     +KP GI+      +  ++   +   + 
Sbjct: 55  -----------------------VARNNVYIAVHKPVGITSTTEKKVKGNLVDMVNHPL- 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++++                         +V  I + + E  
Sbjct: 91  ----RIFNIGRLDKDSEGLILM--------------------TNDGDIVNEILRAEGEHE 126

Query: 199 ANWLL-KKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +++     I  ++V  ++   K  G        + +  F       +     G   Q+
Sbjct: 127 KEYIVSVDKPITPEFVEQMEAGVKILGQKTLPCKVRPLSKFDFNITLTQ-----GLNRQI 181

Query: 256 RVHALHMGC 264
           R     +G 
Sbjct: 182 RRMCEALGY 190


>gi|294933367|ref|XP_002780699.1| Sulfopyruvate decarboxylase subunit alpha, putative [Perkinsus
           marinus ATCC 50983]
 gi|239890697|gb|EER12494.1| Sulfopyruvate decarboxylase subunit alpha, putative [Perkinsus
           marinus ATCC 50983]
          Length = 372

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/138 (25%), Positives = 51/138 (36%), Gaps = 42/138 (30%)

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
           A+   G  +    S+G +    HRLD+ TSGI+V A+T  AA+    + R   + K Y +
Sbjct: 264 AFLHYGIREILEASRGYQLYPLHRLDRVTSGIVVFAKTADAARKFEANQRSWPVTKTYIA 323

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
            V G                           + +   AN +I               +E 
Sbjct: 324 RVTG---------------------------RCSVSEANESI---------------VEC 341

Query: 246 QPHTGRTHQLRVHALHMG 263
            P TGR HQ+RV     G
Sbjct: 342 IPITGRKHQIRVAIAKSG 359


>gi|303274711|ref|XP_003056671.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226461023|gb|EEH58316.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 548

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 44/225 (19%), Positives = 82/225 (36%), Gaps = 33/225 (14%)

Query: 31  HINFVNLQKILRSGQVRVD----KKRVKFNN---------RIQSGQVVR--IPPVINALN 75
            ++     ++L +G V VD     +R   ++         R++ G V+R  +  V     
Sbjct: 120 DVSDALASELLDAGAVYVDWWPEGRRAGGDDDDESAARWRRLR-GDVIRRRLAVVPTPFP 178

Query: 76  HIIKEQKILDSSVNLTKH------SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
           H    +++                    +  ++YED +    NKP  +  Q     A   
Sbjct: 179 HARAGERVRVHRTPRRYRDACWLGEAGWRKRVVYEDEETLAVNKPHALPTQAHESNAAEC 238

Query: 130 D-GFLKSWVDSKG------QKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQK 181
             G +   +   G          +THRLD  TSG++V+ +T  A +    S    +R+ K
Sbjct: 239 VPGCVARALGFTGGVTDGDDALLVTHRLDASTSGVVVLGKTLGAVRAFNASIAGGKRVTK 298

Query: 182 IYWSLVWGI--PKNKKECIANWLLKKSHIG-GDYVHVVKQNEKGA 223
            Y +LV      + +   + +       +  G +VH +     GA
Sbjct: 299 TYVALVENASNVRRRGVTVEDATTPPPPVPLGRFVHYMYPGPFGA 343



 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 14/31 (45%), Positives = 19/31 (61%)

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           E++  TGRTHQ+R     +G PI+GD  Y  
Sbjct: 436 EIELVTGRTHQVRAQLAALGFPILGDTLYAP 466


>gi|49484000|ref|YP_041224.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257425866|ref|ZP_05602290.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257428533|ref|ZP_05604931.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257431166|ref|ZP_05607543.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257433848|ref|ZP_05610206.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257436765|ref|ZP_05612809.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           M876]
 gi|282904328|ref|ZP_06312216.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus C160]
 gi|282906153|ref|ZP_06314008.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282909070|ref|ZP_06316888.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282911378|ref|ZP_06319180.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282914547|ref|ZP_06322333.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus M899]
 gi|282919515|ref|ZP_06327250.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus C427]
 gi|282924893|ref|ZP_06332559.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus C101]
 gi|283958507|ref|ZP_06375958.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus A017934/97]
 gi|293503625|ref|ZP_06667472.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|293510641|ref|ZP_06669346.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus M809]
 gi|293537182|ref|ZP_06671862.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus M1015]
 gi|295428329|ref|ZP_06820958.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297590707|ref|ZP_06949345.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus MN8]
 gi|49242129|emb|CAG40829.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257271560|gb|EEV03706.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257275374|gb|EEV06861.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257278114|gb|EEV08762.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257281941|gb|EEV12078.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257284116|gb|EEV14239.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           M876]
 gi|282313259|gb|EFB43655.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus C101]
 gi|282317325|gb|EFB47699.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus C427]
 gi|282321728|gb|EFB52053.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus M899]
 gi|282325073|gb|EFB55383.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282327334|gb|EFB57629.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282331445|gb|EFB60959.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282595946|gb|EFC00910.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus C160]
 gi|283790656|gb|EFC29473.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus A017934/97]
 gi|290920027|gb|EFD97095.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus M1015]
 gi|291095291|gb|EFE25556.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|291466532|gb|EFF09053.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus M809]
 gi|295127729|gb|EFG57366.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297575593|gb|EFH94309.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus MN8]
 gi|312437790|gb|ADQ76861.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|315195667|gb|EFU26054.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           CGS00]
          Length = 231

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 79/244 (32%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N         ++++L+ G V V+++ +K                     HI 
Sbjct: 1   MRIDKFLANMGVG-TRNEVKQLLKKGLVNVNEQVIKS-----------------PKTHIE 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   +     L          + Y ++   + NKP G      +   +H    +    +
Sbjct: 43  PENDKISVRGEL----------IEYVENVYIMLNKPKGYIS---ATEDHHSKTVIDLIPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++T G+L++         L      + + K Y            E I
Sbjct: 90  YQHLNIFPVGRLDKDTEGLLLITNDGDFNHEL--MSPNKHVSKKY------------EVI 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +   + +  I      +   + K    AI  +  ID         E     G+ HQ++  
Sbjct: 136 SANPITEEDIQAFKEGITLSDGK-VKPAILTY--IDNQTSHVTIYE-----GKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|26250800|ref|NP_756840.1| 23S rRNA pseudouridine synthase F [Escherichia coli CFT073]
 gi|91213543|ref|YP_543529.1| 23S rRNA pseudouridine synthase F [Escherichia coli UTI89]
 gi|117626291|ref|YP_859614.1| 23S rRNA pseudouridine synthase F [Escherichia coli APEC O1]
 gi|191171992|ref|ZP_03033537.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           F11]
 gi|215489360|ref|YP_002331791.1| 23S rRNA pseudouridine synthase F [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218561092|ref|YP_002394005.1| 23S rRNA pseudouridine synthase F [Escherichia coli S88]
 gi|218692307|ref|YP_002400519.1| 23S rRNA pseudouridine synthase F [Escherichia coli ED1a]
 gi|227886973|ref|ZP_04004778.1| RluF protein [Escherichia coli 83972]
 gi|300980609|ref|ZP_07175103.1| hypothetical protein HMPREF9553_01625 [Escherichia coli MS 200-1]
 gi|300992903|ref|ZP_07180085.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|306815865|ref|ZP_07450010.1| 23S rRNA pseudouridine synthase F [Escherichia coli NC101]
 gi|312965319|ref|ZP_07779552.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           2362-75]
 gi|34098551|sp|Q8FB47|RLUF_ECOL6 RecName: Full=Ribosomal large subunit pseudouridine synthase F;
           AltName: Full=rRNA pseudouridylate synthase F; AltName:
           Full=rRNA-uridine isomerase F
 gi|26111231|gb|AAN83414.1|AE016770_214 Hypothetical protein yjbC [Escherichia coli CFT073]
 gi|91075117|gb|ABE09998.1| putative 23S rRNA pseudouridine synthase subunit yjbC [Escherichia
           coli UTI89]
 gi|115515415|gb|ABJ03490.1| conserved hypothetical protein [Escherichia coli APEC O1]
 gi|190907757|gb|EDV67351.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           F11]
 gi|215267432|emb|CAS11885.1| 23S rRNA pseudouridine synthase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218367861|emb|CAR05656.1| 23S rRNA pseudouridine synthase [Escherichia coli S88]
 gi|218429871|emb|CAR10842.2| 23S rRNA pseudouridine synthase [Escherichia coli ED1a]
 gi|222035737|emb|CAP78482.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           LF82]
 gi|227836114|gb|EEJ46580.1| RluF protein [Escherichia coli 83972]
 gi|294492958|gb|ADE91714.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           IHE3034]
 gi|300307733|gb|EFJ62253.1| hypothetical protein HMPREF9553_01625 [Escherichia coli MS 200-1]
 gi|300406779|gb|EFJ90317.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|305850840|gb|EFM51296.1| 23S rRNA pseudouridine synthase F [Escherichia coli NC101]
 gi|307556168|gb|ADN48943.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           ABU 83972]
 gi|307629071|gb|ADN73375.1| 23S rRNA pseudouridine synthase F [Escherichia coli UM146]
 gi|312289993|gb|EFR17880.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           2362-75]
 gi|312948600|gb|ADR29427.1| 23S rRNA pseudouridine synthase F [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315287806|gb|EFU47208.1| conserved hypothetical protein [Escherichia coli MS 110-3]
 gi|315291492|gb|EFU50852.1| conserved hypothetical protein [Escherichia coli MS 153-1]
 gi|320193592|gb|EFW68228.1| 23S rRNA pseudouridine synthase F [Escherichia coli WV_060327]
 gi|323950434|gb|EGB46315.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323954517|gb|EGB50301.1| RNA pseudouridylate synthase [Escherichia coli H263]
 gi|324014259|gb|EGB83478.1| hypothetical protein HMPREF9533_01657 [Escherichia coli MS 60-1]
          Length = 290

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  RES--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|325578607|ref|ZP_08148707.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325159843|gb|EGC71973.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 232

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/245 (14%), Positives = 79/245 (32%), Gaps = 51/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K +R   V+++ + VK                 N    + 
Sbjct: 1   MRLDKFIAEN-TGLTRSQATKAIRQSAVKINDEIVK-----------------NGATKVS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E +I      L+            E+ + ++ +KP G      S          + +  
Sbjct: 43  QEDEIYFEDELLSWV----------EEGQYFMLHKPQGYVC---SHDDDDYPTIYQFFEP 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PLSGKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHQCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ +        +   +++  ++    A    +V+D +       E     GR HQ++  
Sbjct: 137 ADPVENHYASACEEGILLRGEKEPTKPA--KLEVLDDYNVNLTISE-----GRYHQVKRM 189

Query: 259 ALHMG 263
              +G
Sbjct: 190 FAALG 194


>gi|113475036|ref|YP_721097.1| ribosomal large subunit pseudouridine synthase B [Trichodesmium
           erythraeum IMS101]
 gi|110166084|gb|ABG50624.1| ribosomal large subunit pseudouridine synthase B [Trichodesmium
           erythraeum IMS101]
          Length = 254

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 79/250 (31%), Gaps = 45/250 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIPPVINALNHI 77
            RL +     +   +    ++++ +G+V+V+ K V+   + Q     + +          
Sbjct: 3   ERLQKILS-QWGIASRRQAEQMIIAGRVKVNGKIVQLGEKAQPDLDNIEVD--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       L    +   S +        + NKP G+               + +  
Sbjct: 53  -----------GLPIRPEARPSPI------YLLLNKPMGVISTCSEPRKRSKVLDILNAE 95

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              G+      RLD +++G L++         LT       + K Y  LV G P+     
Sbjct: 96  LRNGKGIHPVGRLDADSTGALLLTNDGRVTYCLTHPKYC--LSKTYQVLVEGHPQES--- 150

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                     I   +   +  + K    A    KV+         LE+    GR  Q+R 
Sbjct: 151 ----------ILKLWRQGIILSGKKTLPA--EVKVLKECNSSQTLLEVVISEGRNRQIRR 198

Query: 258 HALHMGCPIV 267
            A  +G  ++
Sbjct: 199 VADKLGHRVL 208


>gi|110644361|ref|YP_672091.1| 23S rRNA pseudouridine synthase F [Escherichia coli 536]
 gi|110345953|gb|ABG72190.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           536]
          Length = 290

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 76/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  RES--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +         + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRPGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGPGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|311031252|ref|ZP_07709342.1| ribosomal small subunit pseudouridine synthase A [Bacillus sp.
           m3-13]
          Length = 236

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 89/246 (36%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N         ++K+L++G V+VD   VK                 +A  H+ 
Sbjct: 1   MRLDKMLANSGFG-TRKEVKKLLKTGVVKVDGNVVK-----------------DAKVHVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E + +    ++ ++ +F+            + +KP G+           +   L+   +
Sbjct: 43  PEVQEVTVHDDIVEYREFI----------YLMMHKPPGLLSATEDHRQETVVDILQE--E 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +P    RLD++T G+L++      A Q L+     + + K Y++ + G    +   
Sbjct: 91  DKMFEPFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVPKTYYAKIDGEVTTE--- 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                        D     K       Y     +++   A     +E+    G+ HQ++ 
Sbjct: 145 -------------DMEAFKKGVTLDDGYETLPAELVILEAGPESQIEITIVEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFQAVG 197


>gi|92114073|ref|YP_574001.1| ribosomal small subunit pseudouridine synthase A [Chromohalobacter
           salexigens DSM 3043]
 gi|91797163|gb|ABE59302.1| ribosomal small subunit pseudouridine synthase A [Chromohalobacter
           salexigens DSM 3043]
          Length = 232

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 39/244 (15%), Positives = 74/244 (30%), Gaps = 49/244 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+       +     +K L  G+V V+   VK N   + G    +  +   L  I 
Sbjct: 1   MRLDRFLSES-TELTRSLAKKALHRGEVEVNGDVVK-NAAFKLGDEHVVRWLGEPLARI- 57

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                       +  + NKPAG       G    +   L     
Sbjct: 58  --------------------------GVRYLMLNKPAGYECTTRPGRYPSVIELLDVAKR 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +  +  RLD +T+G++++      +  LT   R      +               +
Sbjct: 92  G---RLHIAGRLDVDTTGLVLITEDGQWSHRLTSPRRRCDKHYLV-------------TL 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A  L + +        +++  +K    A    ++          + +    GR HQ++  
Sbjct: 136 ARPLAEGAETALAEGLMLEGEDKPTLPA----RLERLDDADGVRVRLVIQEGRFHQIKRM 191

Query: 259 ALHM 262
              +
Sbjct: 192 FAAL 195


>gi|302380740|ref|ZP_07269205.1| putative pseudouridine synthase B, ribosomal large subunit
           [Finegoldia magna ACS-171-V-Col3]
 gi|302311683|gb|EFK93699.1| putative pseudouridine synthase B, ribosomal large subunit
           [Finegoldia magna ACS-171-V-Col3]
          Length = 242

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 82/253 (32%), Gaps = 58/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MR++++      + +  N  +++++ +V V+   +   + ++    +V +      L   
Sbjct: 1   MRINKFIAQS-GYCSRRNADELIKNSKVYVNGTILLDLSYQVNDTDIVEVEGKKINLK-- 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                                     ED      NKP G  S          +   +KS 
Sbjct: 58  --------------------------EDKIYIAINKPIGYASTVKDKFADKKVVDLIKS- 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-- 194
                 +     RLD+++ G+L++         LT      +  KIY  LV G P     
Sbjct: 91  ----DTRVYPVGRLDKDSHGLLILTNDGEFTYELTHPKFEHK--KIYEVLVKGKPNKTEI 144

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K+     LL    +    +  ++  +    Y ++ F+                  GR  Q
Sbjct: 145 KQLKDGILLDGYKLKKSKIEFIENIKNDTKYRVTIFE------------------GRNRQ 186

Query: 255 LRVHALHMGCPIV 267
           +R     +  P++
Sbjct: 187 IRRMFDFINHPVL 199


>gi|332999092|gb|EGK18679.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           K-218]
          Length = 291

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G +V++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDIVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|326331280|ref|ZP_08197572.1| ribosomal large subunit pseudouridine synthase B [Nocardioidaceae
           bacterium Broad-1]
 gi|325950913|gb|EGD42961.1| ribosomal large subunit pseudouridine synthase B [Nocardioidaceae
           bacterium Broad-1]
          Length = 255

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 42/255 (16%), Positives = 87/255 (34%), Gaps = 52/255 (20%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVRIPPVI 71
           +DE  +RL +         +    + ++ +G+V V+ + V +   ++  G  VVR+    
Sbjct: 13  DDEGLIRLQKLLA-LAGIASRRGSEILMLNGEVEVNGEVVTRLGTKVDPGKDVVRVG--- 68

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                    +++   S  +                   V NKP G+              
Sbjct: 69  --------GKRLPPISGKV-----------------YLVLNKPRGVVSTMSDPEGRRN-- 101

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L   V  + ++     RLD +T G++++      A  L        + K Y + V G  
Sbjct: 102 -LSDLVADRPERLFHVGRLDTDTEGLIILTNDGDFAHRLA--HPSYEVDKTYVAEVKGE- 157

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                      ++K  + G          +     ++  ++++    K   +E+  H GR
Sbjct: 158 -------IFPNVRKRLLAG-------VTLEDGPVTVTKARIMETRKDK-SIIELVIHEGR 202

Query: 252 THQLRVHALHMGCPI 266
              +R    H+G P+
Sbjct: 203 NRIVRRLLDHLGHPV 217


>gi|304440267|ref|ZP_07400157.1| ribosomal large subunit pseudouridine synthase B [Peptoniphilus
           duerdenii ATCC BAA-1640]
 gi|304371316|gb|EFM24932.1| ribosomal large subunit pseudouridine synthase B [Peptoniphilus
           duerdenii ATCC BAA-1640]
          Length = 234

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 43/257 (16%), Positives = 87/257 (33%), Gaps = 67/257 (26%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL ++   H    +    ++++ +G+V+V+ + V                         
Sbjct: 1   MRLQKYLA-HAGVASRRTSEELILNGRVKVNGEVVT------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKI--------YVFNKPAGISVQGGSGIAYHID 130
                      L    D LK  + ++D K+         + NKP GI     +    +  
Sbjct: 36  ----------ELGYKVDPLKDKVYFDDKKLKLVREYTYVMINKPIGIVS--TAKDEKNRK 83

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
             +   +    ++     RLD +T+G+L++      A  L      + I K+Y + V G 
Sbjct: 84  TVVD--LVPNDERIYPIGRLDIDTTGLLILTNDGELANKL--MHPRKEIDKVYIATVEGT 139

Query: 191 PKNKK-ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           P     + + N +                   G   + S  K++  +      + +  H 
Sbjct: 140 PSKSGLDKLRNGITID----------------GYKLSKSEIKILKSYESD-SIVRVTIHE 182

Query: 250 GRTHQLRVHALHMGCPI 266
           GR  Q++     +G P+
Sbjct: 183 GRNRQVKKMFERIGNPV 199


>gi|254785989|ref|YP_003073418.1| ribosomal small subunit pseudouridine synthase A [Teredinibacter
           turnerae T7901]
 gi|237683937|gb|ACR11201.1| ribosomal small subunit pseudouridine synthase A [Teredinibacter
           turnerae T7901]
          Length = 238

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 33/251 (13%), Positives = 81/251 (32%), Gaps = 58/251 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++  ++    +   ++ +L++ ++RV+ +     +  ++S   V +          
Sbjct: 1   MRLDKFVADN-TSYSRSQVRGLLKAKRIRVNGQTALAPSAALKSDDEVTLD--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID-----GF 132
                       L   SD              + +KPAG      +  A H       GF
Sbjct: 51  ---------DAPLQARSDV-----------YLMLHKPAGYVC--ANTDAEHPTVFDLPGF 88

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              + ++   + ++  RLD +T+G++++         +T   +  R              
Sbjct: 89  SARYSNADIARLQIAGRLDLDTTGLVLITSDGQWNHRITSPRQKCRKAYYVEC------- 141

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                 A  +  ++        ++   ++    A    +++           +    G  
Sbjct: 142 ------AAPIAAETKSAFAEGVLLHGEKRPTLPA--ELELLSANTAN-----LYIEQGIY 188

Query: 253 HQLRVHALHMG 263
           HQ++      G
Sbjct: 189 HQVKRMFASTG 199


>gi|225028067|ref|ZP_03717259.1| hypothetical protein EUBHAL_02337 [Eubacterium hallii DSM 3353]
 gi|224954615|gb|EEG35824.1| hypothetical protein EUBHAL_02337 [Eubacterium hallii DSM 3353]
          Length = 273

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 81/248 (32%), Gaps = 56/248 (22%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E MRL+++  +     +     + +  G++ VD +  +   ++ +GQ +R+     +++ 
Sbjct: 34  EPMRLNKFLSDA-GVCSRRQADRYVEQGRILVDGEPAQMGQKVHAGQDIRVDGKRVSVSR 92

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                          +   NKP GI          +I  F+   
Sbjct: 93  ----------------------------KQIVLAVNKPKGIVCTTEKREKDNIVDFI--- 121

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD+++ G++++         + E  + R   +  + +    P     
Sbjct: 122 --GYPERIYPVGRLDKDSEGLILMTNDGE---LMNEILKARNYHEKEYEVTINRP----- 171

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + N  LK+   G + +  V +  K     +  F++I                G   Q+R
Sbjct: 172 -VTNVFLKQMSEGVEILDTVTRPCKVKRTGVYTFRII-------------LTQGLNRQIR 217

Query: 257 VHALHMGC 264
                 G 
Sbjct: 218 RMCEACGY 225


>gi|158319769|ref|YP_001512276.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158139968|gb|ABW18280.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 242

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 91/251 (36%), Gaps = 64/251 (25%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D+   N   + +  ++++I ++G V+VD K VK                 ++  H+ 
Sbjct: 5   QRIDKILSN-LGYGSRKDIRQICKNGLVKVDGKVVK-----------------DSSAHVD 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   +     +  + +F+            + +KP G+     S    + D  +   +D
Sbjct: 47  PENSQIIIGNEVVNYREFV----------YLMMHKPQGVI----SATEDNRDQTVVDLLD 92

Query: 139 SKGQK--PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +          RLD++T G+L++    + A   L+     + + K Y++ V G      
Sbjct: 93  EEYLPFSVFPVGRLDKDTEGLLLLTNDGKLAHNLLS---PKKNVPKTYYAKVLGTVT--- 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC-----FAQKFCWLEMQPHTG 250
                    +S I         ++ K   +    +K +        + +   +E+  + G
Sbjct: 147 ---------RSDI---------ESFKEGVFIEEDYKTLPAELNILKSDEISEIELTIYEG 188

Query: 251 RTHQLRVHALH 261
           + HQ++     
Sbjct: 189 KFHQVKRMFEA 199


>gi|257438815|ref|ZP_05614570.1| ribosomal small subunit pseudouridine synthase A [Faecalibacterium
           prausnitzii A2-165]
 gi|257198724|gb|EEU97008.1| ribosomal small subunit pseudouridine synthase A [Faecalibacterium
           prausnitzii A2-165]
          Length = 235

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 67/242 (27%), Gaps = 52/242 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRLD++             + +L  G+V V+    K  + +++ G  V +     A    
Sbjct: 1   MRLDKYLAET-AQCTRSEAKTLLNRGRVTVNGAVCKKGDTQLREGDSVAVDGAPLAYRQF 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +                               + NKP G+           +   +    
Sbjct: 60  V-----------------------------YLMLNKPEGVVSASTDKRDTTVVDLIGDAY 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +  +     RLD+ ++G +++                        +    + K     
Sbjct: 91  PRR--ELFPVGRLDKTSTGFVLLT-------------DDGGFAHEILAPKRHVSKTYTVV 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   L ++   G      +         A+S  +V          ++++   G  HQ++ 
Sbjct: 136 IDTPLTEEMRRGFAEGVTLADG-----TALSPAEVEALTPDGLT-VKVRLRQGVYHQIKR 189

Query: 258 HA 259
             
Sbjct: 190 MF 191


>gi|310659128|ref|YP_003936849.1| pseudouridylate synthase [Clostridium sticklandii DSM 519]
 gi|308825906|emb|CBH21944.1| pseudouridylate synthase [Clostridium sticklandii]
          Length = 236

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 33/247 (13%), Positives = 74/247 (29%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           MRL+ +  +    + +     +++++ +V+V+ K      ++  G +V +   I      
Sbjct: 1   MRLNNYISS--SGLCSRRKADELIKNNKVKVNSKIADLGYQVSEGDIVEVDGTIIKPK-- 56

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     ED       KP GI+         HI+G +  +V
Sbjct: 57  --------------------------EDKVYIALYKPVGITC----TTEEHIEGNIVDYV 86

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + K ++     RLD+++ G++++         +         + I               
Sbjct: 87  NYK-ERIFPIGRLDKDSEGLILLTNDGDIVNRILREENHHEKEYIV-------------T 132

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   L  K+      +    +         +  K            ++    G   Q+R 
Sbjct: 133 VDKPLDSKTL---KQMSQGVRIYNPVKNTYTTTKPCKIHKISEKSFKIVLSQGLNRQIRR 189

Query: 258 HALHMGC 264
              H G 
Sbjct: 190 MCQHFGY 196


>gi|302387646|ref|YP_003823468.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
 gi|302198274|gb|ADL05845.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
          Length = 262

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 31/252 (12%), Positives = 71/252 (28%), Gaps = 50/252 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + E +RL+++        +     + + +G+V ++ K      ++  GQ V I       
Sbjct: 2   ETEGIRLNKFLSEA-GICSRREADRFIEAGKVSINGKAAATGQKVLPGQSVTINGRTVQA 60

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
               +  K                     E+      +KP GI                 
Sbjct: 61  GKGDQSHK---------------------EEPVFLAVHKPRGIVC------TTSHKDRAP 93

Query: 135 SWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           + VD      R+    RLD+++ G++++    +    +  S      + +          
Sbjct: 94  NIVDMVDYPVRIYPVGRLDKDSEGLILMTNQGSLVNKMMRSGNAHEKEYLV--------- 144

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                          +  D++  +K+        ++  K             +    G  
Sbjct: 145 ----------KVNRPVTDDFIRTMKKGVFLPELNVTT-KPCFVTKAGEKAFRIVLTQGLN 193

Query: 253 HQLRVHALHMGC 264
            Q+R     +G 
Sbjct: 194 RQIRRMCSQLGF 205


>gi|224476606|ref|YP_002634212.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           carnosus subsp. carnosus TM300]
 gi|222421213|emb|CAL28027.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           carnosus subsp. carnosus TM300]
          Length = 245

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 73/233 (31%), Gaps = 49/233 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+ + V     +++    V +                    V L 
Sbjct: 19  SRRKAETLIVEGKVKVNGETVTELGTKVKPSDNVEV------------------EGVKLE 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +           ED    +F KPA +     S         +  + D    +     RLD
Sbjct: 61  Q-----------EDKLYILFYKPAQVIT---SVSDDRGRTVVTDYFDDLETRIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+L++         +T      +I+K Y + + G     +      L K   +   
Sbjct: 107 YDTSGLLLLTNDGEFTNLMT--HPRYKIKKKYVAKLKGYLMRDE---VKALEKGIQLEDG 161

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             H  +   K  N             +    +E+    GR  Q+R    H G 
Sbjct: 162 KTHPAEVKIKNQN-----------KEKNTTVVEITISEGRNRQVRRMFEHFGH 203


>gi|55731469|emb|CAH92446.1| hypothetical protein [Pongo abelii]
          Length = 208

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 32/136 (23%), Positives = 59/136 (43%), Gaps = 9/136 (6%)

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYV-FNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
           +L  +++  +  D L++ ++       V  NKP G+ V GG      +   L     S G
Sbjct: 59  LLPKNLSREELVDALRAAVVDRKGGPLVTLNKPQGLPVTGGKPGELTLFSVLPELSQSLG 118

Query: 142 ---QKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIPKNK 194
              Q+ ++     +E+SG+++++     A  L +    + R +R    Y ++  GIP   
Sbjct: 119 LGKQELQVVRASGKESSGLVLLSSCPQTASRLQKFFTHARRAQRPTATYCAVTDGIPAAS 178

Query: 195 KECIANWLLKKSHIGG 210
           +  I   L K  HI G
Sbjct: 179 EGKIQAAL-KLEHIDG 193


>gi|294497295|ref|YP_003560995.1| pseudouridine synthase F (ribosomal large subunit) [Bacillus
           megaterium QM B1551]
 gi|294347232|gb|ADE67561.1| pseudouridine synthase F (ribosomal large subunit) [Bacillus
           megaterium QM B1551]
          Length = 238

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 75/248 (30%), Gaps = 60/248 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL+++        +     K++  G+V V+ K  K  ++++ G  +R+           
Sbjct: 4   LRLNKFISESGK-ASRRGADKLISEGRVTVNGKVAKVGDQVKPGDDIRVSGQQLR----- 57

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  +  ++     NKP GI+      +  +I   +   + 
Sbjct: 58  -----------------------IARNNVYIALNKPVGITSTSEKKVKGNIIDLVNHPL- 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++++         +  +      + I                
Sbjct: 94  ----RIHHVGRLDKDSDGLILLTNDGDIINEILRAENKHEKEYIVA-------------- 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TGRTHQLR 256
                    I  +++  + +  K     I   K + C   +    E Q     G   Q+R
Sbjct: 136 -----VDKPITPEFIKNMSEGVK-----ILGTKTLPCEVTQLSKYEFQIILTQGLNRQIR 185

Query: 257 VHALHMGC 264
                +G 
Sbjct: 186 RMCEVLGY 193


>gi|332346017|gb|AEE59351.1| 23S rRNA pseudouridylate synthase F YjbC [Escherichia coli UMNK88]
          Length = 277

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|295702668|ref|YP_003595743.1| pseudouridine synthase F [Bacillus megaterium DSM 319]
 gi|294800327|gb|ADF37393.1| pseudouridine synthase F (ribosomal large subunit) [Bacillus
           megaterium DSM 319]
          Length = 238

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 75/248 (30%), Gaps = 60/248 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL+++        +     K++  G+V V+ K  K  ++++ G  +R+           
Sbjct: 4   LRLNKFISESGK-ASRRGADKLISEGRVTVNGKVAKVGDQVKPGDDIRVSGQQLR----- 57

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  +  ++     NKP GI+      +  +I   +   + 
Sbjct: 58  -----------------------IARNNVYIALNKPVGITSTSEKKVKGNIIDLVNHPL- 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++++         +  +      + I                
Sbjct: 94  ----RIHHVGRLDKDSDGLILLTNDGDIINEILRAENKHEKEYIVA-------------- 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TGRTHQLR 256
                    I  +++  + +  K     I   K + C   +    E Q     G   Q+R
Sbjct: 136 -----VDKPITPEFIKNMSEGVK-----ILGTKTLPCKVTQLSKYEFQIILTQGLNRQIR 185

Query: 257 VHALHMGC 264
                +G 
Sbjct: 186 RMCEVLGY 193


>gi|241764490|ref|ZP_04762511.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241366074|gb|EER60671.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 504

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 31/232 (13%), Positives = 76/232 (32%), Gaps = 45/232 (19%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      R+Q G  V++                         
Sbjct: 170 SRLEMEQLILEGRISVNNEPAHIGQRVQFGDQVKVN------------------------ 205

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
               ++  +    +++  ++KP G  V        +     +     +  K +   RLD 
Sbjct: 206 -GKPIRYRIDPPPARVIAYHKPVGEVV--SHDDPQNRPTVFRKLPRLQQGKWQSVGRLDL 262

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L+   +   A  L        +++ Y   V G   N+++      ++       +
Sbjct: 263 NTEGLLLFTSSGELANKL--MHPRFGLEREYAVRVLGALSNEEKQQLLDGVRLDDGMAAF 320

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             +     +G+N                CW  +    GR  ++R     +G 
Sbjct: 321 GSIEDGGGEGSN----------------CWYRVTISEGRNREVRRMLEAVGH 356


>gi|145355350|ref|XP_001421926.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582165|gb|ABP00220.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 287

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 38/258 (14%), Positives = 72/258 (27%), Gaps = 60/258 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD          +  +  + +    V  D  R                          
Sbjct: 48  ERLDALLSR-LGLTSRADAARFIAERVVTTDGARAT---------------------ERA 85

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              K+   + ++    + L+ +    D  + V +K  G+           +   L     
Sbjct: 86  TSGKLKARAADVRVDGETLEDV----DGLLIVMHKARGVVCSHDVREGTSVYDALPERWR 141

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++TSG+L++                        +LV  +   KKE  
Sbjct: 142 RRKPSIESVGRLDKDTSGLLLL--------------------TDDGALVHALTTPKKEIG 181

Query: 199 ANWLLK-KSHIGGDYVHVVKQNE-------KGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             + +K    I  D V V    E       +    A+                 ++   G
Sbjct: 182 KWYRVKTDRPIPRDAVEVFASGELTLDGETRACKPAVCEL------MDDETEARLRLTEG 235

Query: 251 RTHQLRVHALHMGCPIVG 268
           + HQ++      GC ++G
Sbjct: 236 KFHQVKRMFAFFGCTVIG 253


>gi|238757900|ref|ZP_04619082.1| Ribosomal small subunit pseudouridine synthase A [Yersinia aldovae
           ATCC 35236]
 gi|238703885|gb|EEP96420.1| Ribosomal small subunit pseudouridine synthase A [Yersinia aldovae
           ATCC 35236]
          Length = 236

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 78/249 (31%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK      SG +            + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEVVK------SGAI-----------KLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEQDVRFDGNPLQQTVGP----------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L   +         +   E     A    +VI+        + +    GR HQ++  
Sbjct: 137 EHPLADDTAQQFTDGVQLHNEESLTKPA--RLEVIEPQ-----LVRLTLSEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  ++
Sbjct: 190 FAAVGNRVL 198


>gi|167756918|ref|ZP_02429045.1| hypothetical protein CLORAM_02467 [Clostridium ramosum DSM 1402]
 gi|167703093|gb|EDS17672.1| hypothetical protein CLORAM_02467 [Clostridium ramosum DSM 1402]
          Length = 239

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 64/177 (36%), Gaps = 33/177 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N+        ++ ++R G V+V+   +K ++                ++H I
Sbjct: 3   MRLDKLLANYGIG-TRKEVKSLIRKGFVKVNGMIIKKDD--------------FKVDHEI 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E    D              ++ Y      + NKPAG        +   +   ++ +  
Sbjct: 48  DEIVFDDE-------------LIEYRPYVYIMLNKPAGYISATKDNLHPTVLELIEGY-- 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +        RLD +T G+L++      +  L    R     KIY++ + G+   + 
Sbjct: 93  -ENYDLFPVGRLDLDTEGLLLITNDGDFSHKLLAPSRNHS--KIYFANIAGVMDEQD 146


>gi|227879091|ref|ZP_03996980.1| pseudouridylate synthase [Lactobacillus crispatus JV-V01]
 gi|256843080|ref|ZP_05548568.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus 125-2-CHN]
 gi|256850268|ref|ZP_05555697.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus MV-1A-US]
 gi|262046340|ref|ZP_06019302.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus MV-3A-US]
 gi|293379763|ref|ZP_06625895.1| pseudouridine synthase [Lactobacillus crispatus 214-1]
 gi|295692876|ref|YP_003601486.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|312977265|ref|ZP_07789013.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus CTV-05]
 gi|227861332|gb|EEJ68962.1| pseudouridylate synthase [Lactobacillus crispatus JV-V01]
 gi|256614500|gb|EEU19701.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus 125-2-CHN]
 gi|256712905|gb|EEU27897.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus MV-1A-US]
 gi|260573211|gb|EEX29769.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus MV-3A-US]
 gi|290923672|gb|EFE00543.1| pseudouridine synthase [Lactobacillus crispatus 214-1]
 gi|295030982|emb|CBL50461.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|310895696|gb|EFQ44762.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           crispatus CTV-05]
          Length = 238

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 80/247 (32%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    +K++ +G+V+VD   V      + G  V     I   +  I
Sbjct: 3   ERLQKVIAEA-GIASRRKAEKMIVAGRVKVDGHVVT-----KLGTKVDTFSNITVDDEPI 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + + +                         Y+F KP G+     +         +  + +
Sbjct: 57  ERESL-----------------------HTYLFYKPRGVVS---TAEDDRGRKTVVDYFE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD +TSG+L++      A  L        + K+Y + + GI    +   
Sbjct: 91  DLPYRLYPVGRLDYDTSGLLLMTNDGKLANLL--MHPKNEVAKVYVAKIKGILTPDEIKT 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRV 257
               +K  H                  A +  KV+    +K    +++  H G  HQ++ 
Sbjct: 149 LTQGVKLDHF---------------KAAPAKVKVLKTDHKKDTQIVQITIHEGHYHQVKR 193

Query: 258 HALHMGC 264
               +G 
Sbjct: 194 MFKAVGH 200


>gi|296327880|ref|ZP_06870416.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
 gi|296155014|gb|EFG95795.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
          Length = 226

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 37/211 (17%), Positives = 84/211 (39%), Gaps = 38/211 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++K++ +G++ V+                        +++I+
Sbjct: 1   MRLDKFLVECGIG-SRKEVKKLISNGEITVNG-----------------------MSYIL 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +  I ++S  +  + + L+    Y++ + Y+ NK AG            +   L  WV 
Sbjct: 37  AKDNIDENSDTIEYNGERLE----YKEFRYYIMNKKAGYITATEDFKEDTVMDLLPEWVI 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYW---SLVWGIPKNK 194
            K   P    RLD++T G+L+     +   + L+    + ++  +      L   I K +
Sbjct: 93  KKDLAP--VGRLDKDTEGLLLFTNDGKLNHKLLSPKNHIDKVYYVEIEKNILDEDILKLE 150

Query: 195 KEC-IANWLL---KKSHIGGDYVHVVKQNEK 221
           +   I N++    K   I  + +++  +  K
Sbjct: 151 QGVDIGNYITQPAKVEKISDNKIYLTIKEGK 181


>gi|160900456|ref|YP_001566038.1| pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160366040|gb|ABX37653.1| pseudouridine synthase [Delftia acidovorans SPH-1]
          Length = 467

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 33/233 (14%), Positives = 80/233 (34%), Gaps = 47/233 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      RIQ G  +++                         
Sbjct: 126 SRLEMEQLILEGRISVNNEPAHVGQRIQFGDQIKVN------------------------ 161

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
               ++  +    +++  ++KP G  V        +     +     +  K +   RLD 
Sbjct: 162 -GQPIRFRIDPPPARVIAYHKPVGEVV--THDDPQNRPTVFRKLPRLQHGKWQSVGRLDL 218

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKECIANWLLKKSHIGGD 211
            T G+L+   +   A  L        +++ Y + V G   K +K+ + + +  +  +   
Sbjct: 219 NTEGLLLFTSSGELANSL--MHPRFGLEREYAARVLGALSKEEKQRLTDGVQLEDGVAA- 275

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +  +     +GAN                CW  +    GR  ++R     +G 
Sbjct: 276 FGSIEDGGGEGAN----------------CWYRVTISEGRNREVRRMFEAVGH 312


>gi|251796373|ref|YP_003011104.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247543999|gb|ACT01018.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
          Length = 250

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 85/249 (34%), Gaps = 47/249 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++ +G V V+ ++V                        +
Sbjct: 5   ERLQKILAQA-GVASRRKCEELILAGAVEVNGEKVT--------------------TLGV 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K     D    +T +   ++S    E     + NKP G+     S         +  ++ 
Sbjct: 44  KADPATDE---ITVNGKPIRS----EKKIYLMLNKPKGVIT---SAKDPQGRKVVADFLP 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD +T G+L++      A  LT       + K Y++ V G+P       
Sbjct: 94  GIRERVYPVGRLDYDTEGLLLLTNDGEFANLLT--HPSHHVPKTYYATVKGVPHG----- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                  S +      V+ ++   A  A   ++ ID   +    + +  + GR  Q+R  
Sbjct: 147 -------SLLDQLKKGVMLEDGLTA-PAEVEYQDID-EEKNMSTIRITIYEGRNRQVRRM 197

Query: 259 ALHMGCPIV 267
              +  P++
Sbjct: 198 FDAIKHPVL 206


>gi|167855378|ref|ZP_02478145.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           parasuis 29755]
 gi|219871231|ref|YP_002475606.1| pseudouridylate synthase [Haemophilus parasuis SH0165]
 gi|167853526|gb|EDS24773.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           parasuis 29755]
 gi|219691435|gb|ACL32658.1| pseudouridylate synthase [Haemophilus parasuis SH0165]
          Length = 220

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 32/167 (19%), Positives = 64/167 (38%), Gaps = 12/167 (7%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           ++++ + + NKP G+  Q            LK ++           RLD+++ G+L++  
Sbjct: 22  FDETIVVLVNKPYGVLSQ---FTNNQACKTLKEFISI--PNVYPIGRLDKDSEGLLLLTN 76

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSHIGGDYVHVVKQNE 220
                  L      +   K YW  + GIP+ +      +  +LK        V ++    
Sbjct: 77  NGQIQHRLANPKFEKE--KTYWVQIEGIPQPEDLNRLASGVILKDGLTKPAKVKIIPDPH 134

Query: 221 KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                A    K+ +       W+E++   G+  Q+R    H+G P +
Sbjct: 135 FKWQSAP---KIRERKNIPTSWIELKIVEGKNRQVRRMTAHIGFPTL 178


>gi|51595406|ref|YP_069597.1| 23S rRNA pseudouridine synthase F [Yersinia pseudotuberculosis IP
           32953]
 gi|170025288|ref|YP_001721793.1| 23S rRNA pseudouridine synthase F [Yersinia pseudotuberculosis
           YPIII]
 gi|186894432|ref|YP_001871544.1| 23S rRNA pseudouridine synthase F [Yersinia pseudotuberculosis
           PB1/+]
 gi|51588688|emb|CAH20298.1| conserved hypothetical protein [Yersinia pseudotuberculosis IP
           32953]
 gi|169751822|gb|ACA69340.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186697458|gb|ACC88087.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
          Length = 290

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 70/247 (28%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR    +++ +G VV++   I      
Sbjct: 7   IRLNKYISE--SGICSRRDGDRYIEQGNVFINGKRATVGDQVFAGDVVKVNGQIIEPRDE 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     ED      NKPAGI      G   +I  F+    
Sbjct: 65  --------------------------EDLVFIALNKPAGIITTMEEGERDNISDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD+++ G++ +         +  +      + +               
Sbjct: 97  ---SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNNHEKEYV--------------V 139

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             N  +    I G    V           +          +      +    G   Q+R 
Sbjct: 140 TVNKPVTDEFIQGMSAGVPILGTVTKKCKV--------QKEAPLVFRITLVQGLNRQIRR 191

Query: 258 HALHMGC 264
              H G 
Sbjct: 192 MCKHFGY 198


>gi|324112367|gb|EGC06345.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
          Length = 290

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 76/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSIRLNKYISE--SGICSRREADRFIEQGNVFINGKRATIGDQVKPGDVVKVNGRLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NK  GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKSVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|134301050|ref|YP_001114546.1| pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134053750|gb|ABO51721.1| ribosomal small subunit pseudouridine synthase A [Desulfotomaculum
           reducens MI-1]
          Length = 249

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 92/256 (35%), Gaps = 60/256 (23%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            + E +RLDR   NH        ++K++++ QV V+                        
Sbjct: 2   AENEKLRLDRLL-NHMGLGTRKEIKKLIKAKQVMVNG----------------------- 37

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                  +  +D  +++    D ++    ++ Y +    + NKP  +     S      D
Sbjct: 38  -------ELAMDPGLHIFPQRDHIEVQGEVIEYREYIYLMLNKPQDVL----SATEDASD 86

Query: 131 GFLKSWVDSKGQ--KPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLV 187
             +   +D       P    RLD++T G+L++    + A Q L+     + + K Y++LV
Sbjct: 87  KVVIDLLDPTYHSFNPFPVGRLDKDTEGLLLLTNNGKLAHQLLS---PKKHVPKTYYALV 143

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G+   +         +   +   Y  +  Q            K+I    Q    +E+  
Sbjct: 144 QGLVTEED---VAAFARGVELDDGYRTLPGQ-----------LKIIRSAPQ--SEIELTI 187

Query: 248 HTGRTHQLRVHALHMG 263
           + G+ HQ++     +G
Sbjct: 188 YEGKYHQVKRMFEAVG 203


>gi|330467060|ref|YP_004404803.1| pseudouridine synthase [Verrucosispora maris AB-18-032]
 gi|328810031|gb|AEB44203.1| pseudouridine synthase [Verrucosispora maris AB-18-032]
          Length = 256

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 86/251 (34%), Gaps = 52/251 (20%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RL +         +    + ++   +V V+ +  +  +++                  
Sbjct: 18  PERLQKVLAAAGVG-SRRACEDLIFRRKVTVNGRVAQLGDKV------------------ 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSW 136
                   + +++        + L+Y        NKP G+ S          +  FL + 
Sbjct: 59  ----DPATAVIHVNGERLQADTRLVY-----LAMNKPRGVVSTMADERGRTALADFLNNR 109

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKK 195
           V+   Q+     RLD ++ G+L++      A  L        +QK Y   V G IP+N  
Sbjct: 110 VE---QRVYHVGRLDADSEGLLLLTNDGTLAHRL--MHPSYGVQKTYLCEVAGPIPRNLG 164

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           + +A  +                  +    ++  F+V+D   +    +E+  H GR H +
Sbjct: 165 KRLAAGI----------------ELEDGPVSVDAFRVVDSLGR-TAQVELSLHEGRKHIV 207

Query: 256 RVHALHMGCPI 266
           R     +G P+
Sbjct: 208 RRLLAEVGHPV 218


>gi|317133055|ref|YP_004092369.1| pseudouridine synthase [Ethanoligenens harbinense YUAN-3]
 gi|315471034|gb|ADU27638.1| pseudouridine synthase [Ethanoligenens harbinense YUAN-3]
          Length = 243

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 76/246 (30%), Gaps = 52/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIPPVINALNHI 77
           MRL ++        +    +  + +G+V+V+ +  +    +     +V +     A +  
Sbjct: 6   MRLQKYLSE-CGETSRRKAEIWITAGRVQVNGRPARLGQSVHPSKDLVTVDGRAVAPSPK 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +                                 NKP G        +       L   V
Sbjct: 65  V-----------------------------YIALNKPRGYVTTLHDELDRRCVTDLLKGV 95

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           ++   +     RLD+++ G+L++    A A  LT   R    +  + S+   + + +   
Sbjct: 96  ET---RVYPIGRLDRDSEGLLLLTDDGAFANALTHP-RHHVPKIYHVSVRPRVTEEQVAR 151

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + N +     +              A   ++  +           LE+  + GR  Q+R 
Sbjct: 152 LQNGIELDGRM-------------TAPAKVTVLR----SGSDRSVLELVLYEGRNRQIRR 194

Query: 258 HALHMG 263
               +G
Sbjct: 195 MCEALG 200


>gi|237732602|ref|ZP_04563083.1| RNA pseudouridine synthase [Mollicutes bacterium D7]
 gi|229384319|gb|EEO34410.1| RNA pseudouridine synthase [Coprobacillus sp. D7]
          Length = 155

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 64/177 (36%), Gaps = 33/177 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N+        ++ ++R G V+V+   +K ++                ++H I
Sbjct: 3   MRLDKLLANYGIG-TRKEVKSLIRKGFVKVNGMIIKKDD--------------FKVDHEI 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E    D              ++ Y      + NKPAG        +   +   ++ +  
Sbjct: 48  DEIVFDDE-------------LIEYRPYVYIMLNKPAGYISATKDNLHPTVLELIEGY-- 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +        RLD +T G+L++      +  L    R     KIY++ + G+   + 
Sbjct: 93  -ENYDLFPVGRLDLDTEGLLLITNDGDFSHKLLAPSRNHS--KIYFANIAGVMDEQD 146


>gi|46143798|ref|ZP_00204573.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|126207838|ref|YP_001053063.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae L20]
 gi|126096630|gb|ABN73458.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
          Length = 230

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 38/277 (13%), Positives = 82/277 (29%), Gaps = 60/277 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      + L+SG V ++ K  K  + ++ G    I      L    
Sbjct: 1   MRLDKFIAEN-TGLTRSQAARALKSGLVTINGKLEKSGS-VKIGDTDEICYEGERLE--- 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  + E     ++ KP G      S          + +  
Sbjct: 56  ----------------------WVDEGQYFMLY-KPQGYVC---SHDDGEYPTVFQFFDY 89

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               K     RLD +T+G++++    + + +  +      +   +  +          + 
Sbjct: 90  PLMTKLHTAGRLDVDTTGLVLLTDDGKWSHRITSPKHHCEKTYLVTLA----------DP 139

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + ++  KK   G       +         I  + V            +    GR HQ++ 
Sbjct: 140 VEDFYAKKLAEGILLRGEREPCLPAKMEVIDDYNV-----------NLTISEGRYHQVKR 188

Query: 258 HALHMGCPI-------VGDHKYCANFKGNFTSPIQNK 287
               +G  +       +GD     N +     P+  +
Sbjct: 189 MFAALGNKVEALHRWRIGDVVLDENLEEGEYRPLSEQ 225


>gi|320179014|gb|EFW53973.1| 23S rRNA pseudouridine synthase F [Shigella boydii ATCC 9905]
          Length = 290

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 76/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G +V++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDIVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +         + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRVGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|222099396|ref|YP_002533964.1| Pseudouridine synthase [Thermotoga neapolitana DSM 4359]
 gi|221571786|gb|ACM22598.1| Pseudouridine synthase [Thermotoga neapolitana DSM 4359]
          Length = 240

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 88/247 (35%), Gaps = 59/247 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MRLDR+  N         ++ +++ G+V V+ + V     ++    VV++          
Sbjct: 1   MRLDRYLSNRGIG-TRKEVRALIKHGRVTVNDRTVLDPAYKLSDKDVVKV---------- 49

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             + K++D    +                   +F KPAG      S    H +  ++   
Sbjct: 50  --DGKVIDLPEKV-----------------YILFYKPAGYVT---STRDPHSETIMEFLP 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           D KG  P    RLD++  G+L+V      A + ++      +++K Y   V G     K 
Sbjct: 88  DIKGIFP--VGRLDKDAEGLLLVTNDGEFAHRVIS---PRWKVEKEYVVKVEGEITEDKL 142

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                L +   +   +    K  EK +N  +                ++    G+ HQ++
Sbjct: 143 ---EKLRRGVSLRDGFFAKAKHVEKISNDTV----------------KIVITEGKYHQVK 183

Query: 257 VHALHMG 263
                +G
Sbjct: 184 RMMAAVG 190


>gi|149181685|ref|ZP_01860178.1| RluB [Bacillus sp. SG-1]
 gi|148850663|gb|EDL64820.1| RluB [Bacillus sp. SG-1]
          Length = 243

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 84/249 (33%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++++  G+V+V+ K  K    ++     + +  +      I
Sbjct: 2   ERLQKVIA-HAGVASRRKAEELILEGKVKVNGKTEKELGTKVSGTDKIEVNGI-----QI 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +E K+                 LLY         KP G+     +         +  + 
Sbjct: 56  ERENKVY---------------YLLY---------KPRGVIS---AVTDDKDRKVVTDFF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--K 195
               ++     RLD +TSG++++      A  LT       I K Y + + GIP     K
Sbjct: 89  PYIQERIYPVGRLDYDTSGLILLTNDGEFANLLTHPRYN--IDKTYVARLKGIPPKFKLK 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E     +L+        V V+K  +K                Q    +E+  H G+  Q+
Sbjct: 147 ELEKGIMLEDGKTAPAKVKVLKIEKK----------------QDKSIVEITIHEGKNRQV 190

Query: 256 RVHALHMGC 264
           +     +G 
Sbjct: 191 KRMFEAIGY 199


>gi|270160115|ref|ZP_06188771.1| ribosomal large subunit pseudouridine synthase B [Legionella
           longbeachae D-4968]
 gi|289165108|ref|YP_003455246.1| ribosomal large subunit pseudouridine synthase B (Pseudouridylate
           synthase) [Legionella longbeachae NSW150]
 gi|269988454|gb|EEZ94709.1| ribosomal large subunit pseudouridine synthase B [Legionella
           longbeachae D-4968]
 gi|288858281|emb|CBJ12149.1| putative ribosomal large subunit pseudouridine synthase B
           (Pseudouridylate synthase) [Legionella longbeachae
           NSW150]
          Length = 246

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 38/235 (16%), Positives = 78/235 (33%), Gaps = 34/235 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
            N RL +         +   +++ + +G V+V+ K VK  +       + +         
Sbjct: 2   SNERLQKILSQAGLG-SRREMERWIENGWVQVNGKPVKLGDSASEEDKITV--------- 51

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKS 135
              + K++ + + + K+             +I +++KP G IS +        +   L  
Sbjct: 52  ---KGKLIPNPLKVKKN------------VRILLYHKPVGEISSRHDPKFEKTVFDHLPH 96

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               +  +     RLD  TSG+L+   +   A  L         ++ Y   V G    + 
Sbjct: 97  LRQGRWVQ---VGRLDLNTSGLLIFTNSGELANQL--MHPKYGFEREYAVRVRGQVSQE- 150

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             + N L K   +        +   +G   A S + V     +      +    G
Sbjct: 151 --VLNNLTKGVELDDGMAKFTRLEFRGGEGANSWYHVTLNEGRNREVRRLWESQG 203


>gi|163731747|ref|ZP_02139194.1| RNA pseudouridylate synthase [Roseobacter litoralis Och 149]
 gi|161395201|gb|EDQ19523.1| RNA pseudouridylate synthase [Roseobacter litoralis Och 149]
          Length = 187

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 31/161 (19%), Positives = 60/161 (37%), Gaps = 6/161 (3%)

Query: 108 IYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           + +FNKP G+  Q    G        L +++D  G  P    RLD+++ G++V+      
Sbjct: 4   VILFNKPYGVLSQFTDKGSEGSPRPTLSAYIDQPGFYP--AGRLDRDSEGLMVLTDDGKL 61

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
              ++      ++ K Y   V G P+ ++  +    ++                    + 
Sbjct: 62  QARIS--NPKHKMAKTYLVQVEGTPEPQQLEVLRAGVRLKDGMTKPAKATLACPPENLWE 119

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +   V         WL++    GR  Q+R    H+G P +
Sbjct: 120 RTP-PVRYRKTVPDSWLQISISEGRNRQVRRMTAHVGLPCL 159


>gi|149920284|ref|ZP_01908755.1| ribosomal large subunit pseudouridine synthase B [Plesiocystis
           pacifica SIR-1]
 gi|149818871|gb|EDM78311.1| ribosomal large subunit pseudouridine synthase B [Plesiocystis
           pacifica SIR-1]
          Length = 300

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 38/273 (13%), Positives = 89/273 (32%), Gaps = 51/273 (18%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + +RL ++  +     +    ++++ +G VRV+ + V+                      
Sbjct: 29  DGVRLQKFMASA-GVASRRKAEELITAGVVRVNGQVVR-----------------ELGTR 70

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +  E+      V +       +S + Y      V NKP G+       +       + S 
Sbjct: 71  VFPERD----RVTVRGEPIQAESKVYY------VLNKPDGVVSSAAGSVDERGRPTVISL 120

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +    ++     RLD  + G+L++      A+ LT   R   ++  +      + + +++
Sbjct: 121 LHGVSERLYPVGRLDFHSRGVLLLTNDGGLAEALTHP-RHGVVKTYHVKFQGKLTEEQEQ 179

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + + +          V  +    + A                  W ++    G   Q+R
Sbjct: 180 LLRDGVELDDGAITRPVAELFAFRETAT---------------NVWYQIGIREGLNRQIR 224

Query: 257 VHALHMGCPIV-------GDHKYCANFKGNFTS 282
                +G P++       GD       +G F +
Sbjct: 225 RMGEAIGHPVLKLIRVAIGDITADGVPEGEFRA 257


>gi|297517087|ref|ZP_06935473.1| 23S rRNA pseudouridine synthase F [Escherichia coli OP50]
          Length = 147

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 24/168 (14%), Positives = 57/168 (33%), Gaps = 34/168 (20%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  ++     RLD+++ G++ +         +  +      + +
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|282897729|ref|ZP_06305728.1| Pseudouridine synthase, Rsu [Raphidiopsis brookii D9]
 gi|281197408|gb|EFA72305.1| Pseudouridine synthase, Rsu [Raphidiopsis brookii D9]
          Length = 252

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 78/236 (33%), Gaps = 43/236 (18%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
            +    ++++   +VRV+    +   ++                    + K+   S++  
Sbjct: 15  ASRRQAEEMIGQSRVRVNGNLARLGQKV--------------------DPKVDMISIDGK 54

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
             +      L+Y      + NKPAG+               L      +G       RLD
Sbjct: 55  PVTQGSPPALVY-----LLLNKPAGVVSTCNDPQGRTTVLDLLPTKLRQGTGICPVGRLD 109

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +++G L++         LT       + K Y  +V G P              +++   
Sbjct: 110 ADSTGALILTNDGDVTFALT--HPSHDVPKTYHVVVEGHPP-------------TNVLRM 154

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +   V  + +    A    K+I+        LE+    GR  Q+R  A  +G P+V
Sbjct: 155 WSQGVMLDGRKTRTA--QVKLIE-QGFTQSKLEIILQEGRNRQIRRVAQQLGYPVV 207


>gi|153950805|ref|YP_001401950.1| 23S rRNA pseudouridine synthase F [Yersinia pseudotuberculosis IP
           31758]
 gi|152962300|gb|ABS49761.1| RNA pseudouridine synthase family protein [Yersinia
           pseudotuberculosis IP 31758]
          Length = 290

 Score = 60.4 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 70/247 (28%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR    +++ +G VV++   I      
Sbjct: 7   IRLNKYISE--SGICSRRDGDRYIEQGNVFINGKRATVGDQVFAGDVVKVNGQIIEPRDE 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     ED      NKPAGI      G   +I  F+    
Sbjct: 65  --------------------------EDLVFIALNKPAGIITTMEEGERDNISDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD+++ G++ +         +  +      + +               
Sbjct: 97  ---SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNNHEKEYV--------------V 139

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             N  +    I G    V           +          +      +    G   Q+R 
Sbjct: 140 TVNKPVTDEFIQGMSAGVPILGTVTKKCKV--------QKEAPLVFRITLVQGLNRQIRR 191

Query: 258 HALHMGC 264
              H G 
Sbjct: 192 MCKHFGY 198


>gi|300856844|ref|YP_003781828.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           ljungdahlii DSM 13528]
 gi|300436959|gb|ADK16726.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           ljungdahlii DSM 13528]
          Length = 244

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 39/254 (15%), Positives = 91/254 (35%), Gaps = 67/254 (26%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+D+   N         ++ ++++G+V+++   +K                         
Sbjct: 9   RIDKILANLGFG-TRKEIKAVVKNGEVKINGTVIK------------------------- 42

Query: 80  EQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                DSS+ +      ++    ++ Y+ +   + NKP G+     S    + D  +   
Sbjct: 43  -----DSSMKIDPDKSTIEVGGNVVEYKKNIYLLMNKPQGVV----SATFDNYDETVIDI 93

Query: 137 VDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           ++ + Q  KP    RLD++T G+L++         +        + K+Y++ +      +
Sbjct: 94  LEPEYQAFKPFPVGRLDKDTEGLLLITNDGELNHRM--ISPKNHVDKVYYAEIDKYLDER 151

Query: 195 -----KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                K+ I      K   G   +H+++ +E GA   ++                     
Sbjct: 152 DVNRFKKGIQLKDGYKCLPG--KLHIIESDEDGAKVEVT------------------IQE 191

Query: 250 GRTHQLRVHALHMG 263
           G+ HQ++     +G
Sbjct: 192 GKFHQVKRMFNALG 205


>gi|223043526|ref|ZP_03613571.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Staphylococcus capitis
           SK14]
 gi|222443014|gb|EEE49114.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Staphylococcus capitis
           SK14]
          Length = 230

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 37/244 (15%), Positives = 79/244 (32%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N         ++++L+ G V V++K++K                        
Sbjct: 1   MRIDKFLANMGLG-TRTEVKQLLKKGLVEVNEKKIKT----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I   +  +    +     + Y D+   + NKP        +         L    +
Sbjct: 37  PKSQIDPETDKVVVDGE----EISYVDNVYMMLNKPKDYIS---ATEDNAHQTVLDLIPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                     RLD++T G+L++         L      + + K Y            E I
Sbjct: 90  FSHLGIFPVGRLDKDTEGLLLLTNDGQFNHEL--MSPKKHVSKTY------------EVI 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           + + +K+S I    + V   + K         K  +          +  + G+ HQ++  
Sbjct: 136 SKYPIKQSDIEAFKLGVELSDGK--------VKPAELIKGNDRLSYVTIYEGKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|169830079|ref|YP_001700237.1| ribosomal large subunit pseudouridine synthase F [Lysinibacillus
           sphaericus C3-41]
 gi|168994567|gb|ACA42107.1| Ribosomal large subunit pseudouridine synthase F [Lysinibacillus
           sphaericus C3-41]
          Length = 233

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 33/248 (13%), Positives = 78/248 (31%), Gaps = 56/248 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++       I+     K +  G+V ++ +     +++Q G +V I         + 
Sbjct: 1   MRINKYLSET-GIISRRGADKWIAEGKVTINGEPATVGSQVQDGDIVCID-----GKEVK 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           KEQ+++                           NKP GI+      I  ++  F+     
Sbjct: 55  KEQQLV-----------------------YIALNKPVGITSTTERHIKGNVVDFVNH--- 88

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+E+ G+L++                         +V  I + +    
Sbjct: 89  --PLRIFHIGRLDKESEGLLLL--------------------TNDGDIVNKILRAENHHE 126

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             ++++      +                +    ++  + K    ++    G   Q+R  
Sbjct: 127 KEYIVQVDKPITEQFINKMSAGVDILDTTTLPCYVEKISDKV--FKIILEQGLNRQIRRM 184

Query: 259 ALHMGCPI 266
              +G  +
Sbjct: 185 CSALGYSV 192


>gi|259046873|ref|ZP_05737274.1| ribosomal large subunit pseudouridine synthase B [Granulicatella
           adiacens ATCC 49175]
 gi|259036496|gb|EEW37751.1| ribosomal large subunit pseudouridine synthase B [Granulicatella
           adiacens ATCC 49175]
          Length = 241

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 37/250 (14%), Positives = 85/250 (34%), Gaps = 52/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +  ++ G+V+V+ + V+    ++ +   + +          
Sbjct: 2   ERLQKVMA-HAGVASRRKCEAFIQEGRVKVNGEVVRELGFKVGANDKIEV---------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIY-VFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                 I +Y++  +Y +F KP G+               +  +
Sbjct: 51  --------------------DGIPIYKEEPVYFMFYKPKGVLSSASDDKGRT---VVTDY 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                Q+     RLD +T+G+L++      +  +T       ++K Y + V GIP  ++ 
Sbjct: 88  FKDVEQRVYPVGRLDYDTTGLLLLTNDGEFSNLMT--HPKHHVEKKYIAKVKGIPTPRQM 145

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                              +  + K  + AI+    +D   +    + +  H G  HQ++
Sbjct: 146 -------------RQLERGIVLDGKKTSNAIAQILSVDTD-KGTGIVALTIHEGWNHQVK 191

Query: 257 VHALHMGCPI 266
                +  P+
Sbjct: 192 RMFEAVELPV 201


>gi|149908393|ref|ZP_01897056.1| pseudouridine synthase family 1 protein [Moritella sp. PE36]
 gi|149808556|gb|EDM68491.1| pseudouridine synthase family 1 protein [Moritella sp. PE36]
          Length = 239

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 35/160 (21%), Positives = 58/160 (36%), Gaps = 9/160 (5%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           +YVFNKP  +  Q            LK ++  K        RLD+++ G+L++       
Sbjct: 60  VYVFNKPYMVLTQ---FTDADNRETLKDYI--KVPDIYAAGRLDRDSEGLLLLTNNGRLQ 114

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             LT+     + +K YW  V G P  +K     + +           V    E      +
Sbjct: 115 AKLTQPGE--KTEKTYWVQVEGEPSPEKLSDLRYGIILKDGPTLPAKVEIMTEPSVWPRV 172

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              +  +       WL +    GR  Q+R    H+G P +
Sbjct: 173 PPIR--ERQNIPTTWLAITIIEGRNRQIRRMTAHIGHPTL 210


>gi|152988322|ref|YP_001350132.1| putative pseudouridylate synthase [Pseudomonas aeruginosa PA7]
 gi|150963480|gb|ABR85505.1| probable pseudouridylate synthase [Pseudomonas aeruginosa PA7]
          Length = 230

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 78/243 (32%), Gaps = 51/243 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+  N  P ++  + Q+++  G++RVD + V+          VR+   +     ++
Sbjct: 1   MRLDRFLAN-LPELSRRDAQRLIAGGRLRVDGQVVRDGTH-----EVRVFSRVELDERLL 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  K                       ++ Y+ +KP G      +         L+    
Sbjct: 55  QAGKP----------------------ARYYMLHKPMGCVS---ATRDPEHPTVLELLPP 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                  +  RLD  T+G++++      ++ LT     R         V       +  +
Sbjct: 90  DHRDDLHIGGRLDYNTTGLMLLTNDGRWSRRLTLPGSRRDKVYY----VETEEPIDQRYV 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +         D V +  Q E     +                  +  H GR HQ++  
Sbjct: 146 DAFAAGIHFRFEDLVTLPAQLEPLGPRS----------------ARLTLHEGRYHQVKRM 189

Query: 259 ALH 261
             H
Sbjct: 190 FGH 192


>gi|304310662|ref|YP_003810260.1| Ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium HdN1]
 gi|301796395|emb|CBL44603.1| Ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium HdN1]
          Length = 282

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 27/174 (15%), Positives = 58/174 (33%), Gaps = 29/174 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +         +  +++  + SG+V V+ K+ K  +R++ G V+R+             
Sbjct: 5   LQKVLARAGIG-SRRSMEDWIASGRVSVNGKKAKVGDRVERGDVLRVDGR---------- 53

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                 S++ +      + +++Y         KP G                        
Sbjct: 54  ------SMDYSGEDSDSRRMIIY--------YKPEGEVC--TRTDPEGRPTVFDRLPRLD 97

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            ++     RLD  T G+L+       A  L        I++ Y + ++G    +
Sbjct: 98  NERWVAVGRLDVNTQGLLLFTTDGDLANRL--MHPSSEIEREYAARIFGEVTPE 149


>gi|253989148|ref|YP_003040504.1| 16S rRNA pseudouridylate synthase A [Photorhabdus asymbiotica
           subsp. asymbiotica ATCC 43949]
 gi|253780598|emb|CAQ83760.1| ribosomal small subunit pseudouridine synthase A [Photorhabdus
           asymbiotica]
          Length = 233

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 37/247 (14%), Positives = 78/247 (31%), Gaps = 55/247 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++       I+   + + LR+G++ VD + +K    +I   Q +     +      
Sbjct: 1   MRLDKFLSQQL-GISRNEVGRELRAGRITVDDEIIKTGAYKITPEQQIMFDGSLLEQQQG 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                             ++ NKP+G        +   +  F+    
Sbjct: 60  PR----------------------------YFMLNKPSGYVCSTDDPVNPTVLYFID--- 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +    K     RLD +T+G++++      + +  +     ++   +             E
Sbjct: 89  EPAAHKLHTAGRLDMDTTGLVLLTDDGQWSHRITSPKHHCKKTYLVTL-----------E 137

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           C          + G  +H  K   K A   +   +V            +    GR HQ++
Sbjct: 138 CPVAAETADKFLAGVQLHGEKTLTKPAQLEMLEPQV----------TRLTISEGRYHQVK 187

Query: 257 VHALHMG 263
                +G
Sbjct: 188 RMFAAVG 194


>gi|256851006|ref|ZP_05556395.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 27-2-CHN]
 gi|260661218|ref|ZP_05862132.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 115-3-CHN]
 gi|282932041|ref|ZP_06337499.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 208-1]
 gi|256616068|gb|EEU21256.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 27-2-CHN]
 gi|260548155|gb|EEX24131.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 115-3-CHN]
 gi|281303808|gb|EFA95952.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii 208-1]
          Length = 237

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 80/250 (32%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++  G+V V+ + V     +++    + +          
Sbjct: 3   ERLQKLIAQA-GVASRRKAEKMITEGRVAVNGRIVTELGTKVEPSANIEVD--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                       L    +   + LLY         KP G+  SV+   G        +  
Sbjct: 53  -----------GLPIQKESKHTYLLY---------KPRGVISSVKDDKGRK-----TVLD 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +    +     RLD +TSG+L++      A  L        + K+Y + + G    ++
Sbjct: 88  FFEESPYRLYPVGRLDYDTSGLLLITNDGELANKL--MHPRHMVDKVYVAKIKGFLTPEE 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQ 254
                  ++                 G   A +  K+I     +    +++  H G  HQ
Sbjct: 146 IHSLKHGVRID---------------GKKSAPAKVKIISTNREKGTSIVQLTIHEGHYHQ 190

Query: 255 LRVHALHMGC 264
           ++     +G 
Sbjct: 191 VKRMFKAVGH 200


>gi|297205889|ref|ZP_06923284.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii JV-V16]
 gi|297149015|gb|EFH29313.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii JV-V16]
          Length = 237

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 80/250 (32%), Gaps = 56/250 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    +K++  G+V V+ + V     +++    + +          
Sbjct: 3   ERLQKLIAQA-GIASRRKAEKMITEGRVAVNGRIVTELGTKVEPSANIEVD--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKS 135
                       L    +   + LLY         KP G+  SV+   G        +  
Sbjct: 53  -----------GLPIQKESKHTYLLY---------KPRGVISSVKDDKGRK-----TVLD 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           + +    +     RLD +TSG+L++      A  L        + K+Y + + G    ++
Sbjct: 88  FFEESPYRLYPVGRLDYDTSGLLLITNDGELANKL--MHPRHMVDKVYVAKIKGFLTPEE 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQ 254
                  ++                 G   A +  K+I     +    +++  H G  HQ
Sbjct: 146 IYSLKHGVRID---------------GKKSAPAKVKIISTNREKGTSIVQLTIHEGHYHQ 190

Query: 255 LRVHALHMGC 264
           ++     +G 
Sbjct: 191 VKRMFKAVGH 200


>gi|196248745|ref|ZP_03147445.1| pseudouridine synthase [Geobacillus sp. G11MC16]
 gi|196211621|gb|EDY06380.1| pseudouridine synthase [Geobacillus sp. G11MC16]
          Length = 243

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 50/253 (19%), Positives = 92/253 (36%), Gaps = 56/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++  G+V+V+ + V      + G  V++ P  +     I
Sbjct: 2   ERLQKVIARA-GIASRRKAEEMILQGRVKVNGRVVT-----ELG--VKVGPRDDVEVDGI 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSW 136
             ++                     E+   Y+  KP G+  SV+   G        +  +
Sbjct: 54  PVER---------------------EEPVYYLLYKPRGVISSVKDEKGRK-----VVTDF 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNK 194
                Q+     RLD +TSG+L++      A  L        I+K+Y + V GIP  +  
Sbjct: 88  FKDIHQRIYPIGRLDYDTSGLLLLTNDGDFANLL--MHPRYEIEKVYVAKVKGIPTREQL 145

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K+     LL+        V ++  + K    AI               +E+  H GR  Q
Sbjct: 146 KQLEKGVLLEDGITAPAKVKLLSADRK-KRTAI---------------VEISIHEGRNRQ 189

Query: 255 LRVHALHMGCPIV 267
           +R     +GC ++
Sbjct: 190 VRRMFEAIGCEVL 202


>gi|170769533|ref|ZP_02903986.1| ribosomal large subunit pseudouridine synthase F [Escherichia
           albertii TW07627]
 gi|170121590|gb|EDS90521.1| ribosomal large subunit pseudouridine synthase F [Escherichia
           albertii TW07627]
          Length = 290

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 24/168 (14%), Positives = 56/168 (33%), Gaps = 34/168 (20%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    +++  G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVNPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  ++     RLD+++ G++ +         +  +      + +
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|299541884|ref|ZP_07052207.1| ribosomal large subunit pseudouridine synthase F [Lysinibacillus
           fusiformis ZC1]
 gi|298725622|gb|EFI66263.1| ribosomal large subunit pseudouridine synthase F [Lysinibacillus
           fusiformis ZC1]
          Length = 233

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 79/248 (31%), Gaps = 56/248 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++       I+     K +  G+V ++ +     +++++G +V +         + 
Sbjct: 1   MRINKYLSET-GIISRRGADKWIAEGKVTINGEVATVGSQVEAGDIVCVD-----GKEVK 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           KEQ+++                           NKP GI+      I  ++  F+     
Sbjct: 55  KEQQLV-----------------------YIALNKPVGITSTTERHIKGNVVDFVNH--- 88

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+E+ G+L++         +  +      + I             + I
Sbjct: 89  --PLRIFHIGRLDKESEGLLLLTNDGDIVNKILRAENHHEKEYIV---------QVDKPI 137

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               ++K   G D +            +   FK+I                G   Q+R  
Sbjct: 138 TAQFIQKMGAGVDILDTTTLPCHVEKISEKVFKII-------------LEQGLNRQIRRM 184

Query: 259 ALHMGCPI 266
              +G  +
Sbjct: 185 CSALGYSV 192


>gi|239906975|ref|YP_002953716.1| pseudouridine synthase [Desulfovibrio magneticus RS-1]
 gi|239796841|dbj|BAH75830.1| pseudouridine synthase [Desulfovibrio magneticus RS-1]
          Length = 322

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 86/246 (34%), Gaps = 47/246 (19%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R+++   +     +  +   ++ +G+V V+   V      ++G  +RI P  +AL     
Sbjct: 10  RINKALASA-GVCSRRHADDLIAAGRVTVNGAVVT-----EAG--LRIDPARDAL----- 56

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS--GIAYHIDGFLKSWV 137
              +  + VNL                     +K  G+        G     DG  + W 
Sbjct: 57  --AVDGAPVNLAPEIPIT-----------LALHKKPGVVTTASDPEGRPTVFDGLPEVW- 102

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +G++     RLD  + G+L++      A  LT                W +PK  +  
Sbjct: 103 --RGKRLFPVGRLDFFSEGLLLLTTDGELALRLTHPR-------------WHVPKRYRVT 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   +             + + E+ A  A    +V++  AQ    LEM+ H G   Q+R 
Sbjct: 148 VRGQVTPDMLGTMARGMRLAEGERLAPVAA---RVVEGPAQDRSILEMELHQGVNRQIRR 204

Query: 258 HALHMG 263
               +G
Sbjct: 205 MCRDLG 210


>gi|119486449|ref|ZP_01620507.1| hypothetical protein L8106_00605 [Lyngbya sp. PCC 8106]
 gi|119456351|gb|EAW37482.1| hypothetical protein L8106_00605 [Lyngbya sp. PCC 8106]
          Length = 250

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 75/251 (29%), Gaps = 47/251 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIPPVINALNHI 77
            RL +     +   +    ++++ + +VRV+        +       + +       +H 
Sbjct: 3   ERLQKIMAT-WGIASRRQAEQMILAKRVRVNGNIAHLGQKANPSSDDIEVDGKPIKPSH- 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSW 136
                               + + +Y      + NKP G+       G   ++   L   
Sbjct: 61  --------------------RPVPIY-----LLLNKPIGVVSTCADPGGRRNVLDLLPRR 95

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +  KGQ      RLD +++G L++         LT       + K Y   V G P     
Sbjct: 96  LQ-KGQGVHPVGRLDVDSTGALLLTNDGELTFRLT--HPRHHVPKTYQVWVQGHPPES-- 150

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +  W           +                 + +         LE+    GR  Q+R
Sbjct: 151 VLQAWRQGVILSSRKTLSA-------------EVRRLQQSIDSQTLLEVILFEGRNRQIR 197

Query: 257 VHALHMGCPIV 267
             A  +G P+V
Sbjct: 198 KVAEQLGYPVV 208


>gi|238794236|ref|ZP_04637850.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           intermedia ATCC 29909]
 gi|238726418|gb|EEQ17958.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           intermedia ATCC 29909]
          Length = 235

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 42/273 (15%), Positives = 84/273 (30%), Gaps = 58/273 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK      SG +            + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEVVK------SGAI-----------KLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEQDVRFDGNPLQQTVGP----------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L   +         +   +     A    +VI+        + +    GR HQ++  
Sbjct: 137 EHPLADDTAQQFTEGVQLHNEKSLTKPA--QLEVIEPQ-----LVRLTLSEGRYHQVKRM 189

Query: 259 ALHMGCPIV-------GDHKYCANFKGNFTSPI 284
              +G  +V       GD K   +       P+
Sbjct: 190 FAAVGNRVVELHRERIGDIKLDDDLAPGEYRPL 222


>gi|302836900|ref|XP_002950010.1| hypothetical protein VOLCADRAFT_90418 [Volvox carteri f.
           nagariensis]
 gi|300264919|gb|EFJ49113.1| hypothetical protein VOLCADRAFT_90418 [Volvox carteri f.
           nagariensis]
          Length = 421

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 41/228 (17%), Positives = 71/228 (31%), Gaps = 14/228 (6%)

Query: 31  HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90
                   ++L+ G V V     K  + I   + + +P    A          +      
Sbjct: 72  EFGRARALELLQLGAVYV-GVPQKGLDFINWMRSLELPVAPTAAVVPRGHYVRVHPRPKR 130

Query: 91  TK--HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-----QK 143
               +       +L+ DS   V NKPAG+          H    L+      G     + 
Sbjct: 131 YPACYCADWPRRVLHCDSDYVVVNKPAGLPCMR------HESNALEELASCVGRALGMEG 184

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
             + HRLDQ T+G++V++RT+ A +    S + R    I               + +++ 
Sbjct: 185 LEVCHRLDQWTTGVVVLSRTKEANKAFKRSLQDREAGLIKTYKGLTYSPVPLGTLEHYMY 244

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                 G  V             +S          +    E + HTG 
Sbjct: 245 DGPFNEGAPVLGGGNLRPRGPRLLSRTAHARWRLCRLDVRECREHTGA 292



 Score = 50.7 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/30 (46%), Positives = 18/30 (60%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           +  HTGRTHQ+R     +G P+VGD  Y  
Sbjct: 390 IDLHTGRTHQIRAQLASIGRPLVGDVMYAP 419


>gi|311113298|ref|YP_003984520.1| pseudouridine synthase [Rothia dentocariosa ATCC 17931]
 gi|310944792|gb|ADP41086.1| pseudouridine synthase [Rothia dentocariosa ATCC 17931]
          Length = 357

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 52/254 (20%), Positives = 90/254 (35%), Gaps = 51/254 (20%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINA 73
           D E +RL +         +    ++++  G+V V+ + V     R+    V+        
Sbjct: 115 DHEGVRLQK-LMAQAGVASRRVCEEMITEGRVTVNGEVVTELGVRVNPADVI-------- 165

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGF 132
                         V +   +      L+Y       FNKPAG+ S          I  F
Sbjct: 166 --------------VQVDGMTVQTNEKLIY-----MAFNKPAGVVSTMEDPDGRPCIKDF 206

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L+   DS  ++     RLD ET G+L++      A  LT       + K Y   V G  +
Sbjct: 207 LR---DSMNERVFHVGRLDVETEGLLLLTNDGELANRLT--HPSYEVPKTYLVQVRGPVE 261

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                        S IG +    ++   +     +  FK++D  A     +E+  H+G+ 
Sbjct: 262 -------------SGIGAELKKGIRL--EDGVSRVDSFKLVDS-APGHVLIEVTIHSGKN 305

Query: 253 HQLRVHALHMGCPI 266
             +R     +G P+
Sbjct: 306 RIVRRLFEAVGYPV 319


>gi|255326184|ref|ZP_05367270.1| ribosomal large subunit pseudouridine synthase B [Rothia
           mucilaginosa ATCC 25296]
 gi|255296638|gb|EET75969.1| ribosomal large subunit pseudouridine synthase B [Rothia
           mucilaginosa ATCC 25296]
          Length = 386

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 91/253 (35%), Gaps = 49/253 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +RL +         +    ++++  G+V V+ + V      + G  VR+ P     
Sbjct: 144 DHDGVRLQKLLAQA-GVASRRVCEEMITEGRVTVNGEVVT-----ELG--VRVDPSKV-- 193

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFL 133
                       +V +   +      L+Y       FNKPAG +S          I  FL
Sbjct: 194 ------------TVQVDGMTVQTNDKLVY-----MAFNKPAGVVSTMEDPEGRPCISDFL 236

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +S   S  ++     RLD ET G+L++      A  LT       + K Y   V G  + 
Sbjct: 237 RS---SMSERVFHVGRLDVETEGLLLLTNDGELANRLT--HPSYEVPKTYLVQVPGPMEP 291

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                    +KK     D V  V +           FK++D        +E+  H+G+  
Sbjct: 292 GVG----AAMKKGIRLEDGVTRVDE-----------FKLVDSTP-GHVLVEVTIHSGKNR 335

Query: 254 QLRVHALHMGCPI 266
            +R     +G P+
Sbjct: 336 IVRRLFDAVGYPV 348


>gi|120556720|ref|YP_961071.1| 23S rRNA pseudouridine synthase F [Marinobacter aquaeolei VT8]
 gi|120326569|gb|ABM20884.1| ribosomal large subunit pseudouridine synthase F [Marinobacter
           aquaeolei VT8]
          Length = 332

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/247 (11%), Positives = 72/247 (29%), Gaps = 58/247 (23%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RL+++        +  +  + +  G V ++ +R +  +++  G VV++   +        
Sbjct: 8   RLNKYISES-GMCSRRDADRFIEQGNVHINGRRAQVGDQVLPGDVVKVNGQVVEPRDE-- 64

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                                   ED      NKP GI     S    +I  F+      
Sbjct: 65  ------------------------EDLVFIALNKPVGIVSTTDSAEKDNIQRFV-----G 95

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             ++     RLD+++ G++ +         +  +      + +               + 
Sbjct: 96  HSERIFPIGRLDKDSQGLIFLTSNGDLVNKILRAGNNHEKEYLV-------------TVD 142

Query: 200 NWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             + ++    +      +    ++     +S F              +    G   Q+R 
Sbjct: 143 KPVTREFVEGMSNGVPILGTMTKRCKVEKVSRF-----------VFRITLVQGLNRQIRR 191

Query: 258 HALHMGC 264
            A + G 
Sbjct: 192 MAEYFGY 198


>gi|330830315|ref|YP_004393267.1| Pseudouridine synthase [Aeromonas veronii B565]
 gi|328805451|gb|AEB50650.1| Pseudouridine synthase [Aeromonas veronii B565]
          Length = 230

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 78/250 (31%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +    +      K++R G+V VD   VK                       I
Sbjct: 1   MRLDKFLCD-CSDLTRSLAGKLIRQGEVMVDGIVVK------------------QPAFHI 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ  ++    L       +  +L++       N+              H   F      
Sbjct: 42  NEQSQIEFDGVLLTLEQRNRYFMLHKPEGYVCSNEDP-----------DHPTVFFLMDEP 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           + G K  +  RLD +T+G+++V      +  +T               VW       + I
Sbjct: 91  AMG-KLHVVGRLDLDTTGLVLVTDDGQWSHRITSPRHECAKTYH----VWLADPVSPDAI 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A +        G Y+       + A   I             C   +  H G+ HQ++  
Sbjct: 146 ALF------AEGVYLRNETDKTRPAQLEI----------LGECEARLTIHEGKYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FASIGNKVVG 199


>gi|302023694|ref|ZP_07248905.1| RNA pseudouridylate synthase [Streptococcus suis 05HAS68]
          Length = 54

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 18 NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           +RLD+   +    ++     + +++GQV V+ +  K    +Q G V
Sbjct: 9  GIRLDKALSD-LTDLSRSFANEQIKAGQVLVNGQPKKAKYSVQVGDV 54


>gi|160880922|ref|YP_001559890.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
 gi|160429588|gb|ABX43151.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
          Length = 240

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 38/244 (15%), Positives = 83/244 (34%), Gaps = 54/244 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++  +         +++++R G+V V+                             
Sbjct: 8   LRLDKYLADLSVG-TRTEVKQMIRKGRVMVNG-----------------------NTETS 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E K+  +   +   S  L  + L    + ++ NKPAG+           +   +    +
Sbjct: 44  PETKVDSNHDKIFVDSRELSYVTL----EYFMLNKPAGVVSASNDKKQTTVVDLID---E 96

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +K +      RLD++T G+L++      A Q L+   +    +  +  L   + K  +E 
Sbjct: 97  AKRKDLFPVGRLDKDTEGLLIITNDGDLAHQLLSP--KKHVDKVYFAKLRDPLKKEDEEA 154

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            A  L                 E  A  A      ++  +++  +  +    G+ HQ++ 
Sbjct: 155 FAAGLKID-------------EEFTALPAK-----LERISEQEAY--VTIREGKFHQIKR 194

Query: 258 HALH 261
               
Sbjct: 195 MFEA 198


>gi|239636840|ref|ZP_04677839.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           warneri L37603]
 gi|239597514|gb|EEQ80012.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           warneri L37603]
          Length = 246

 Score = 60.0 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 36/233 (15%), Positives = 71/233 (30%), Gaps = 49/233 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+   V     ++ +   V +                    + L 
Sbjct: 19  SRRKAETLITDGKVKVNGHVVTELGTKVSNSDTVEV------------------EGIKLE 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +           ED    +FNKPA +     S         +  +      +     RLD
Sbjct: 61  Q-----------EDKIYILFNKPAQVIT---SVSDDRGRKVVTDYFKDIETRIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+L++        +L    R    +K    L   + + + + +   +  +      
Sbjct: 107 YDTSGLLLLT-NDGEFTNLMTHPRYHIKKKYVAKLKGYLMREEVKALEKGIELEDGFTQP 165

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               VK  +K  N                  +E+    GR  Q+R    H G 
Sbjct: 166 AQVKVKNQDKDKNT---------------TLVEITISEGRNRQVRRMFEHFGH 203


>gi|260905260|ref|ZP_05913582.1| pseudouridine synthase, Rsu [Brevibacterium linens BL2]
          Length = 238

 Score = 60.0 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 81/248 (32%), Gaps = 48/248 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL +         +    ++++  G+V VD   V      + G  +             
Sbjct: 1   MRLQKILAEAGLG-SRRACEQLILDGRVEVDGSIVT-----ELGTRID-----------T 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + Q +   +V ++  +  +            V NKPAG+               L  +V 
Sbjct: 44  ETQAVYVDAVRISTQTQKV----------YLVLNKPAGVVSTMSDPDGRPC---LADYVK 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           ++  +     RLD ET G++++      +  L        I K Y + V G         
Sbjct: 91  NRVDRLFHVGRLDTETEGLILLTNDGELSNRLA--HPRYEIPKTYLAQVRGQLAKDVGS- 147

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                 +   G D               +  FK++D    K   +E+  H+GR   +R  
Sbjct: 148 ------RLKAGMDL--------DDGFVKVDSFKLVDSTPGK-SVVELTLHSGRNRIVRRL 192

Query: 259 ALHMGCPI 266
              +G P+
Sbjct: 193 LKEVGHPV 200


>gi|328554622|gb|AEB25114.1| 16S pseudouridylate synthase [Bacillus amyloliquefaciens TA208]
          Length = 239

 Score = 60.0 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 43/245 (17%), Positives = 86/245 (35%), Gaps = 47/245 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N     +  +++KI+++G V +D +  K          V+I    +  +  +
Sbjct: 1   MRLDKLLANSGFG-SRKDVKKIVKAGAVMIDGEPAKD---------VKIHVDPDKQDITV 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +                     Y +    + NKP G+           +   L    +
Sbjct: 51  YGEPAE------------------YREFIYVMMNKPQGVLSATEDSRQQTVVDLLT--PE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD++T G L++      A  L              S    +PK  +  +
Sbjct: 91  EQRFEPFPAGRLDKDTEGFLLLTNDGQLAHRL-------------LSPKKHVPKTYEVRL 137

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L  +  I  +   V++   K    A+   K I   +     + +    G+ HQ+++ 
Sbjct: 138 TSPLSPEDIIDLERGVVIEGGYKTKPAAV---KTI-TESPDETVIHLTITEGKYHQVKLM 193

Query: 259 ALHMG 263
           A  +G
Sbjct: 194 AKAVG 198


>gi|68064484|ref|XP_674226.1| pseudouridylate synthase [Plasmodium berghei strain ANKA]
 gi|56492648|emb|CAH96681.1| pseudouridylate synthase, putative [Plasmodium berghei]
          Length = 490

 Score = 60.0 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 224 NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             +++ F  +    Q     +  QP TGRTHQ+R H   +  PI  D  Y  NF+  + +
Sbjct: 313 KPSVTRFMFLSYNYQFNESLILCQPMTGRTHQIRTHLKSLSFPISNDSHYNPNFEKKYMT 372

Query: 283 PIQN 286
             + 
Sbjct: 373 KTEK 376



 Score = 47.3 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              HRLD+ TSGI++  + +  +   +E     +I K Y + V G  ++
Sbjct: 95  YTLHRLDKLTSGIVLFGKNKKFSTIFSEYVCNNKITKSYIARVEGDFRD 143


>gi|260583963|ref|ZP_05851711.1| ribosomal large subunit pseudouridine synthase B [Granulicatella
           elegans ATCC 700633]
 gi|260158589|gb|EEW93657.1| ribosomal large subunit pseudouridine synthase B [Granulicatella
           elegans ATCC 700633]
          Length = 241

 Score = 60.0 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 81/250 (32%), Gaps = 52/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    +  +  G+V+V+   V+    ++     + +          
Sbjct: 2   ERLQKVMA-HAGIASRRKCEAFIEEGRVKVNGTVVRELGYKVSQSDKIEV---------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIY-VFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                 I +Y++  +Y +F KP  +     S         +  +
Sbjct: 51  --------------------DGIPIYKEEPVYFMFYKPKSVLS---SVTDDRGRTVISDY 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                Q+     RLD +T+G++++      A  +T       ++K Y + V G+P  +  
Sbjct: 88  FKDIPQRVYPVGRLDYDTTGLILLTNDGEFANLMT--HPKHHVEKKYIAKVKGVPTPRHM 145

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                              +  + K  + A++    +D   +    + +  H G  HQ++
Sbjct: 146 -------------RQLERGIWIDGKKTSKAVARILSVDT-EKNTGIVSLTIHEGWNHQVK 191

Query: 257 VHALHMGCPI 266
                +  P+
Sbjct: 192 KMFEAVELPV 201


>gi|307130686|ref|YP_003882702.1| 16S rRNA pseudouridylate 516 synthase [Dickeya dadantii 3937]
 gi|306528215|gb|ADM98145.1| 16S rRNA pseudouridylate 516 synthase [Dickeya dadantii 3937]
          Length = 232

 Score = 60.0 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 77/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + LR+ +V V+ + +K      SG    +P    A +  +
Sbjct: 1   MRLDKFLSQQL-GISRALVARELRAQRVTVNGEVIK------SGAFKLLPEHEVAFDGNV 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ+                          ++ NKP G      S         L    +
Sbjct: 54  LEQQNGPR---------------------YFMLNKPQGYVC---STDDPDHPTILYFIDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +TSG++++      +  +T          +               +
Sbjct: 90  PVAHKLHAAGRLDIDTSGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L   +         +   +     A      ++  ++    + +    GR HQ++  
Sbjct: 137 EQPLAPDTADNFQAGVQLHGEKNLTRPA-----TLEQISEHQ--VRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|221502237|gb|EEE27975.1| conserved hypothetical protein [Toxoplasma gondii VEG]
          Length = 231

 Score = 60.0 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 21/109 (19%), Positives = 34/109 (31%), Gaps = 4/109 (3%)

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
               G     +         A S F+ I      A     +E++   G     R+HA  +
Sbjct: 14  RPSPGSREWRLAGERTEGKAAYSIFRPIVQAALEAHPVTLVEIRLVQGPPIVPRLHAASL 73

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           G  ++GD  Y               L LH   + +  P     + + AP
Sbjct: 74  GHSVIGDPTYGPEVHRRRHHRCDKPLMLHCWILKIAPPYAQEEVCVEAP 122


>gi|308174693|ref|YP_003921398.1| 16S pseudouridylate synthase [Bacillus amyloliquefaciens DSM 7]
 gi|307607557|emb|CBI43928.1| putative 16S pseudouridylate synthase [Bacillus amyloliquefaciens
           DSM 7]
 gi|328913028|gb|AEB64624.1| putative 16S pseudouridylate synthase [Bacillus amyloliquefaciens
           LL3]
          Length = 240

 Score = 60.0 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 43/245 (17%), Positives = 86/245 (35%), Gaps = 47/245 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N     +  +++KI+++G V +D +  K          V+I    +  +  +
Sbjct: 2   MRLDKLLANSGFG-SRKDVKKIVKAGAVMIDGEPAKD---------VKIHVDPDKQDITV 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +                     Y +    + NKP G+           +   L    +
Sbjct: 52  YGEPAE------------------YREFIYVMMNKPQGVLSATEDSRQQTVVDLLT--PE 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD++T G L++      A  L              S    +PK  +  +
Sbjct: 92  EQRFEPFPAGRLDKDTEGFLLLTNDGQLAHRL-------------LSPKKHVPKTYEVRL 138

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L  +  I  +   V++   K    A+   K I   +     + +    G+ HQ+++ 
Sbjct: 139 TSPLSPEDIIDLERGVVIEGGYKTKPAAV---KTI-TESPDETVIHLTITEGKYHQVKLM 194

Query: 259 ALHMG 263
           A  +G
Sbjct: 195 AKAVG 199


>gi|253681692|ref|ZP_04862489.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum D str. 1873]
 gi|253561404|gb|EES90856.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum D str. 1873]
          Length = 236

 Score = 60.0 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 88/250 (35%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    ++I+   +V+V+ + V             +   ++     +
Sbjct: 3   ERLQKYMAA-CGVASRRKCEEIILQDRVKVNGEIVN-----------ELGFKVDPAKDRV 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
               +L S               L E       NKP G +S          I   +K   
Sbjct: 51  HVDSVLIS---------------LEEKKVYIALNKPEGYVSTVKDERGRKTILDIVKV-- 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD  TSG++++         +        I K+Y +++ G+P N +  
Sbjct: 94  ---NERIFPIGRLDYNTSGLIILTNDGDVYNKI--IHPREEIDKVYIAVIKGVPSNDE-- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K    G D    V         + ++F++I+    K C +++  H G+  Q+R 
Sbjct: 147 -----IKNFCNGVDIGGYV--------TSKANFEIIEKLDDK-CKVKIVIHEGKNRQVRR 192

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 193 MCEKIGHPVI 202


>gi|219870596|ref|YP_002474971.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           parasuis SH0165]
 gi|219690800|gb|ACL32023.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           parasuis SH0165]
          Length = 230

 Score = 60.0 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 71/246 (28%), Gaps = 53/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++   +   +      K LR+GQV V+    K +  +I     +            
Sbjct: 1   MRLDKFIAEN-TGLTRSQASKALRAGQVTVNGVVEKNSATKISEQDEICF---------- 49

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                            D      + E     ++ KP         G    +  F     
Sbjct: 50  -----------------DGEPLAWVDEGQYFMLY-KPQNCVCSHDDGDYPTVFQFFDY-- 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                K     RLD +T+G++++      +  +T          +               
Sbjct: 90  -PLTTKLHCAGRLDADTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------T 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +A+ +            +++  +     A    +++D +       E     GR HQ++ 
Sbjct: 136 LADPVEDFYATQFAEGILLRGEKTATKPA--QLEILDDYNVNLTISE-----GRYHQVKR 188

Query: 258 HALHMG 263
               +G
Sbjct: 189 MFAALG 194


>gi|169350449|ref|ZP_02867387.1| hypothetical protein CLOSPI_01217 [Clostridium spiroforme DSM 1552]
 gi|169292769|gb|EDS74902.1| hypothetical protein CLOSPI_01217 [Clostridium spiroforme DSM 1552]
          Length = 239

 Score = 60.0 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 83/238 (34%), Gaps = 50/238 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD+   N+        ++  +R G V V+ + +K +  ++                  
Sbjct: 3   MRLDKLLANYGIG-TRKEVKSYIRKGFVEVNGEIIKKDDYKV----------------DY 45

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            K++ I D  +            + Y      + NKP G        +   +   +  + 
Sbjct: 46  QKDEIIFDGEL------------IEYRPYVYLMLNKPKGYVSATKDNVHPTVIDLIVGY- 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +        RLD +T G+L+++     A  L      R   K+Y + + GI       
Sbjct: 93  --ENYDLFPVGRLDIDTEGLLLISNDGDFAHRL--MSPNRNHAKVYVARIAGIMNEF--- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             + L  K  +  D  +  K           + K+++ F    C +E++   G+ HQ+
Sbjct: 146 --DILAFKDGVILDNGYKCKPA---------NLKILEVF-DDSCEVEIEIFEGKFHQV 191


>gi|325181852|emb|CCA16307.1| RNA pseudouridylate synthase putative [Albugo laibachii Nc14]
          Length = 226

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 29/101 (28%), Positives = 41/101 (40%), Gaps = 11/101 (10%)

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFK-----VIDCFAQKFCWLEMQP 247
            K+  +   L   SH  G     V +  K    + + F+     V        C L   P
Sbjct: 50  KKQIRVKCPLKCLSHKNG-----VWECHKDGKESETIFERDQLTVPVENRDVSCVLRCFP 104

Query: 248 HTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNK 287
            TGRTHQ+R+H   +G PI  D  Y      G+ T+P+  K
Sbjct: 105 VTGRTHQIRLHLQLIGLPIANDPCYGGELHFGSKTTPLDTK 145


>gi|313123532|ref|YP_004033791.1| pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
 gi|312280095|gb|ADQ60814.1| Pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
 gi|325684293|gb|EGD26466.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 239

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 82/252 (32%), Gaps = 56/252 (22%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
              RL +         +    +K++ +G+VRVD + V K   ++ S + V +        
Sbjct: 2   AEERLQKVIAQA-GIASRREAEKMILAGRVRVDGQVVTKLGTKVSSIEQVVVDNQP---- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFL 133
                                    +  E    Y+F KP G+  +V+   G        +
Sbjct: 57  -------------------------IERESHHTYLFYKPRGVISAVKDNKGRK-----TV 86

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +      +     RLD +TSG+L++      A  L        + K+Y + + GI + 
Sbjct: 87  ADYFTDLPYRLYPVGRLDYDTSGLLLMTNDGELANLL--MHPRNEVDKVYVAKIKGILQP 144

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRT 252
            +      L K   IG       +             KV+    +     +++  H G  
Sbjct: 145 DE---IKALKKGVQIGRYKTKPAR------------VKVLKTNPRAQTQIVQLTIHEGHY 189

Query: 253 HQLRVHALHMGC 264
           HQ++     +  
Sbjct: 190 HQVKEMFKAVNH 201


>gi|289550491|ref|YP_003471395.1| Ribosomal small subunit pseudouridine synthase A [Staphylococcus
           lugdunensis HKU09-01]
 gi|289180023|gb|ADC87268.1| Ribosomal small subunit pseudouridine synthase A [Staphylococcus
           lugdunensis HKU09-01]
          Length = 230

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 79/246 (32%), Gaps = 57/246 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD++   H        +++ L+ G V V+ K  K    +I     VV+I         
Sbjct: 2   MRLDKFLA-HMGQGTRTEVKQSLKKGNVTVNGKVEKSAKTQIDPHHDVVQIHGH------ 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   + Y ++   + NKP G            +   +K +
Sbjct: 55  -----------------------QIDYVETVYLMLNKPKGYISATEDPKQATVIDLIKDY 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              K        RLD++T G+L++      + +L      + + K Y             
Sbjct: 92  ---KYLDLFPVGRLDKDTEGLLLITNDGQFSHNL--MNPNKHVAKTYL------------ 134

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             + + + K +       V+  +       ++   +ID +  K    E     GR HQ++
Sbjct: 135 VTSKYPVTKDNQYMFKQGVMLSDGLTKPAELT---IIDDYHSKVTIYE-----GRYHQIK 186

Query: 257 VHALHM 262
                +
Sbjct: 187 RMFHSI 192


>gi|89094110|ref|ZP_01167053.1| ribosomal large subunit pseudouridine synthase B [Oceanospirillum
           sp. MED92]
 gi|89081585|gb|EAR60814.1| ribosomal large subunit pseudouridine synthase B [Oceanospirillum
           sp. MED92]
          Length = 276

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 54/177 (30%), Gaps = 29/177 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
            + +L +         +   +++ ++ G+V+V+ +     +RI  G  V +         
Sbjct: 2   ADEKLHKVLARSGVG-SRREMERWIKEGRVQVNGQVATLGDRISEGDQVEVDGR------ 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                        L   +   + +L+Y        NKP G                 +  
Sbjct: 55  ----------KTPLIFDNQAERRVLIY--------NKPVGEIC--TRHDPEGRPTVFRHL 94

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              K  +     RLD  TSG+L+       A  L       +I + Y   V G    
Sbjct: 95  PPLKEGRWIAIGRLDINTSGLLLFTTDGELANAL--MHPSAQIDREYAVRVLGDVDE 149


>gi|253734463|ref|ZP_04868628.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|253727517|gb|EES96246.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|329733199|gb|EGG69536.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           21193]
          Length = 231

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 79/244 (32%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N         ++++L+ G V V+++ +K                     HI 
Sbjct: 1   MRIDKFLANMGVG-TRNEVKQLLKKGLVNVNEQVIKS-----------------PKTHIE 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   +     L          + Y ++   + NKP G      +   +H    +    +
Sbjct: 43  PENDKITVRGEL----------IEYIENVYIMLNKPKGYIS---ATEDHHSKTVIDLIPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++T G+L++         L      + + K Y            E I
Sbjct: 90  YQHLNIFPVGRLDKDTEGLLLITNDGDFNHEL--MSPNKHVSKKY------------EVI 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +   + +  I      V   + K    AI  +  ID         E     G+ HQ++  
Sbjct: 136 SANPITEDDIQAFKEGVTLSDGK-VKPAILTY--IDNQTSHVTIYE-----GKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|253680889|ref|ZP_04861692.1| RNA pseudouridine synthase family protein [Clostridium botulinum D
           str. 1873]
 gi|253562738|gb|EES92184.1| RNA pseudouridine synthase family protein [Clostridium botulinum D
           str. 1873]
          Length = 238

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 67/179 (37%), Gaps = 36/179 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   + +   ++ +++ G++ +D K +K N        +++ P  + +    
Sbjct: 2   ERLDKILSN-LGYGSRKEIKALVKKGEIEIDGKIIKDNG-------IKVDPNKSTIKVSG 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E                    + Y      + NKPAG+     S    + D  +   +D
Sbjct: 54  EE--------------------INYRKYIYLMMNKPAGVV----SATFDNYDETVIDLLD 89

Query: 139 SKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +     P    RLD++T G L++         LT       + KIY++ +  I   K 
Sbjct: 90  YEYTVFDPFPVGRLDKDTEGFLLITNDGDLNHRLT--SPKWHVDKIYYAEIDKIVDEKD 146


>gi|255084639|ref|XP_002508894.1| predicted protein [Micromonas sp. RCC299]
 gi|226524171|gb|ACO70152.1| predicted protein [Micromonas sp. RCC299]
          Length = 248

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 40/226 (17%), Positives = 74/226 (32%), Gaps = 28/226 (12%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           + + +G+VRV+   VK + R++SG VV +                 + S+     S+   
Sbjct: 6   EAVSAGRVRVNGALVKPSFRVRSGDVVTLDGKALDWEPFAA---ATEGSIGAHAGSNGF- 61

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
                       +NKP G++    S          K        +     RLD+++SG++
Sbjct: 62  --------FYLKYNKPRGVTCTMESSQRT------KPAKGVGSARVFPVGRLDRDSSGLV 107

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-ECIANWLLKKSHIGGDYVHVVK 217
           ++       + L      R+  K Y   V   P     E + + ++  +    D V    
Sbjct: 108 LLTDDGRVPEAL--LDPSRKAPKTYEVDVRPAPTPDAIEALRDGVVITTTQQRDGVTTTS 165

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                   A     +I            +   GR  Q+R     +G
Sbjct: 166 P------TAPCPVDLIKKSETSATL-RFELREGRNRQIRKMCEAVG 204


>gi|225569254|ref|ZP_03778279.1| hypothetical protein CLOHYLEM_05336 [Clostridium hylemonae DSM
           15053]
 gi|225162053|gb|EEG74672.1| hypothetical protein CLOHYLEM_05336 [Clostridium hylemonae DSM
           15053]
          Length = 247

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 33/246 (13%), Positives = 72/246 (29%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL+++        +     +++  G+V VD K+     ++     VR+           
Sbjct: 1   MRLNKFLSEA-GVCSRREADRLIEEGRVTVDGKKAVPGMQVDPSSEVRVGKKRIRSK--- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +   +   +KPAGI       +  +I  FLK    
Sbjct: 57  -------------------------DKKTVLAVHKPAGIVCTEDKRVKNNIIRFLK---- 87

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD+E+ G+L++         +  S      +   W              
Sbjct: 88  -YPERITYAGRLDKESEGLLIMTDDGELINGMMRSRYGHEKEYKVW-------------- 132

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N  + +  +      V   +++     ++  +  +          +    G   Q+R  
Sbjct: 133 VNKPVTEEFVNRMSSGVRLVDKEKGLDEVT--RPCEVRQCGTYIFTIILTQGLNRQIRRM 190

Query: 259 ALHMGC 264
              +G 
Sbjct: 191 CEALGY 196


>gi|237832285|ref|XP_002365440.1| hypothetical protein TGME49_063400 [Toxoplasma gondii ME49]
 gi|211963104|gb|EEA98299.1| hypothetical protein TGME49_063400 [Toxoplasma gondii ME49]
          Length = 231

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 21/109 (19%), Positives = 34/109 (31%), Gaps = 4/109 (3%)

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
               G     +         A S F+ I      A     +E++   G     R+HA  +
Sbjct: 14  RPSPGSREWRLAGERTEGKAAYSIFRPIVQAALEAHPVTLVEIRLVQGPPIVPRLHAASL 73

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           G  ++GD  Y               L LH   + +  P     + + AP
Sbjct: 74  GHSVIGDPTYGPEVHRRRHHRCDKPLMLHCWILKIAPPYAQEEVCVEAP 122


>gi|300812160|ref|ZP_07092604.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
 gi|300496845|gb|EFK31923.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
          Length = 239

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 82/252 (32%), Gaps = 56/252 (22%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
              RL +         +    +K++ +G+VRVD + V K   ++ S + V +        
Sbjct: 2   AEERLQKVIAQA-GIASRREAEKMILAGRVRVDGQVVTKLGTKVSSIEQVVVDNQP---- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFL 133
                                    +  E    Y+F KP G+  +V+   G        +
Sbjct: 57  -------------------------IERESHHTYLFYKPRGVISAVKDNKGRK-----TV 86

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +      +     RLD +TSG+L++      A  L        + K+Y + + GI + 
Sbjct: 87  ADYFTDLPYRLYPVGRLDYDTSGLLLMTNDGELANLL--MHPRNEVDKVYVAKIKGILQP 144

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRT 252
            +      L K   IG                A    KV+    +     +++  H G  
Sbjct: 145 DE---IKALKKGVQIGRYKT----------KPA--QVKVLKTNPRAQTQIVQLTIHEGHY 189

Query: 253 HQLRVHALHMGC 264
           HQ++     +  
Sbjct: 190 HQVKEMFKAVNH 201


>gi|238855289|ref|ZP_04645608.1| putative ribosomal small subunit pseudouridine synthase A
           [Lactobacillus jensenii 269-3]
 gi|282932418|ref|ZP_06337843.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 208-1]
 gi|313471899|ref|ZP_07812391.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 1153]
 gi|238832181|gb|EEQ24499.1| putative ribosomal small subunit pseudouridine synthase A
           [Lactobacillus jensenii 269-3]
 gi|239529181|gb|EEQ68182.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 1153]
 gi|281303367|gb|EFA95544.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           jensenii 208-1]
          Length = 234

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 21/144 (14%), Positives = 53/144 (36%), Gaps = 33/144 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  ++++ +V +++K VK    ++    +V++          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHNLIKAKKVTINEKLVKQAKQQVTENDMVKVDNQ------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   + S  
Sbjct: 53  ----------------------TITYQQFHYFMLNKPTGVITATEDPQQKTVLDLIAS-- 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVA 161
             +        RLD++T+G+L++ 
Sbjct: 89  KDRYPDLAPVGRLDKDTTGLLLIT 112


>gi|86607697|ref|YP_476459.1| RNA pseudouridine synthase family protein [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86556239|gb|ABD01196.1| RNA pseudouridine synthase family protein [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 274

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 77/251 (30%), Gaps = 36/251 (14%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   ++  + +G+VRV+ K V                     + 
Sbjct: 3   EPQRLQKLLAQQ-GLASRRQVEAWILAGRVRVNGKVVT-----------------ELGSK 44

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
              E+  ++ +  +   +      +L       + +KP G+               L   
Sbjct: 45  ADPERDCIEVNGQVIPLAKDPARYVL-------LLHKPVGVLSTCADPWGRKTVLDLLPP 97

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +  +     RLD ++SG L++         LT       + K Y   V G P   + 
Sbjct: 98  SWKRQTRLYPVGRLDADSSGALLLTNDGDLTLKLT--HPRYHLPKTYRVQVQGHP--SQA 153

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + +W       G D         +        F+          WL +    GR  Q+R
Sbjct: 154 TLQHW-----RDGVDLEGYTTLPAEVEFCPAPDFR--QREHPNCSWLRVVLFEGRNRQIR 206

Query: 257 VHALHMGCPIV 267
             A  +G P++
Sbjct: 207 RVAERLGHPVL 217


>gi|254491124|ref|ZP_05104305.1| conserved hypothetical protein, putative [Methylophaga thiooxidans
           DMS010]
 gi|224463637|gb|EEF79905.1| conserved hypothetical protein, putative [Methylophaga thiooxydans
           DMS010]
          Length = 293

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 74/249 (29%), Gaps = 34/249 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+ +         +   ++  ++ G+V  + +     ++I  G  +++   + +   + 
Sbjct: 3   ERIQKVLARAGYG-SRRQVETWIKEGKVSCNGETATLGDQISEGDRLKLDNKLLSPKRLW 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           ++                 + ++LY        NKP G                 ++   
Sbjct: 62  QQP----------------QQVILY--------NKPVGEVCTRSDPEGRR--TIFQALPT 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +     RLD  TSG++++      A  L        + + Y   V G    +   I
Sbjct: 96  PEQGRWVSVGRLDLNTSGLIILTTDGELANRL--MHPSNEMDREYAVRVLGEVTPE---I 150

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L     +     H     E G   A   + V+    +      +    G   Q+   
Sbjct: 151 MQNLRDGVMLEDGEAHFADIQESGGEGANHWYHVVIQEGRNREVRRLWESQGV--QVSRL 208

Query: 259 ALHMGCPIV 267
                 PI+
Sbjct: 209 MRVRYGPII 217


>gi|15924743|ref|NP_372277.1| 16S psudouridylate synthase [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|15927330|ref|NP_374863.1| hypothetical protein SA1574 [Staphylococcus aureus subsp. aureus
           N315]
 gi|57652051|ref|YP_186636.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus COL]
 gi|87160516|ref|YP_494393.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus USA300_FPR3757]
 gi|88195567|ref|YP_500373.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus NCTC 8325]
 gi|148268231|ref|YP_001247174.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH9]
 gi|150394299|ref|YP_001316974.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1]
 gi|151221858|ref|YP_001332680.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus str. Newman]
 gi|156980070|ref|YP_001442329.1| hypothetical protein SAHV_1739 [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|161509971|ref|YP_001575630.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|221141491|ref|ZP_03565984.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus str.
           JKD6009]
 gi|253315873|ref|ZP_04839086.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus str. CF-Marseille]
 gi|255006539|ref|ZP_05145140.2| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus Mu50-omega]
 gi|257794136|ref|ZP_05643115.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9781]
 gi|258415840|ref|ZP_05682111.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9763]
 gi|258420669|ref|ZP_05683608.1| pseudouridine synthase, family 1 [Staphylococcus aureus A9719]
 gi|258438319|ref|ZP_05689603.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9299]
 gi|258443777|ref|ZP_05692116.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8115]
 gi|258445988|ref|ZP_05694164.1| pseudouridylate synthase [Staphylococcus aureus A6300]
 gi|258448285|ref|ZP_05696412.1| pseudouridylate synthase [Staphylococcus aureus A6224]
 gi|258452304|ref|ZP_05700317.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A5948]
 gi|258454188|ref|ZP_05702159.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           A5937]
 gi|262049062|ref|ZP_06021940.1| hypothetical protein SAD30_2267 [Staphylococcus aureus D30]
 gi|262053064|ref|ZP_06025237.1| hypothetical protein SA930_1121 [Staphylococcus aureus 930918-3]
 gi|269203391|ref|YP_003282660.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus ED98]
 gi|282893247|ref|ZP_06301481.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8117]
 gi|282925640|ref|ZP_06333289.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9765]
 gi|282927882|ref|ZP_06335493.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A10102]
 gi|284024800|ref|ZP_06379198.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus 132]
 gi|294849914|ref|ZP_06790653.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9754]
 gi|295406064|ref|ZP_06815872.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8819]
 gi|296276053|ref|ZP_06858560.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus MR1]
 gi|297245011|ref|ZP_06928888.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8796]
 gi|304380652|ref|ZP_07363323.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|7328274|emb|CAB82472.1| hypothetical protein [Staphylococcus aureus subsp. aureus COL]
 gi|13701549|dbj|BAB42842.1| SA1574 [Staphylococcus aureus subsp. aureus N315]
 gi|14247525|dbj|BAB57915.1| similar to 16S psudouridylate synthase [Staphylococcus aureus
           subsp. aureus Mu50]
 gi|57286237|gb|AAW38331.1| pseudouridine synthase, family 1 [Staphylococcus aureus subsp.
           aureus COL]
 gi|87126490|gb|ABD21004.1| pseudouridine synthase, family 1 [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|87203125|gb|ABD30935.1| ribosomal small subunit pseudouridine synthase A, putative
           [Staphylococcus aureus subsp. aureus NCTC 8325]
 gi|147741300|gb|ABQ49598.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149946751|gb|ABR52687.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1]
 gi|150374658|dbj|BAF67918.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus str. Newman]
 gi|156722205|dbj|BAF78622.1| hypothetical protein [Staphylococcus aureus subsp. aureus Mu3]
 gi|160368780|gb|ABX29751.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|257788108|gb|EEV26448.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9781]
 gi|257839433|gb|EEV63906.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9763]
 gi|257843273|gb|EEV67683.1| pseudouridine synthase, family 1 [Staphylococcus aureus A9719]
 gi|257848363|gb|EEV72354.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9299]
 gi|257851183|gb|EEV75126.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8115]
 gi|257855230|gb|EEV78169.1| pseudouridylate synthase [Staphylococcus aureus A6300]
 gi|257858524|gb|EEV81400.1| pseudouridylate synthase [Staphylococcus aureus A6224]
 gi|257860029|gb|EEV82864.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A5948]
 gi|257863640|gb|EEV86397.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           A5937]
 gi|259159041|gb|EEW44112.1| hypothetical protein SA930_1121 [Staphylococcus aureus 930918-3]
 gi|259162879|gb|EEW47443.1| hypothetical protein SAD30_2267 [Staphylococcus aureus D30]
 gi|262075681|gb|ACY11654.1| pseudouridine synthase family 1 protein [Staphylococcus aureus
           subsp. aureus ED98]
 gi|269941231|emb|CBI49619.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           TW20]
 gi|282590392|gb|EFB95471.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A10102]
 gi|282592420|gb|EFB97434.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9765]
 gi|282764565|gb|EFC04691.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8117]
 gi|285817435|gb|ADC37922.1| 16S pseudouridine synthase A [Staphylococcus aureus 04-02981]
 gi|294823253|gb|EFG39683.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A9754]
 gi|294969061|gb|EFG45082.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8819]
 gi|297178091|gb|EFH37339.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus A8796]
 gi|302751580|gb|ADL65757.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus str. JKD6008]
 gi|304340759|gb|EFM06688.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|312830131|emb|CBX34973.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           ECT-R 2]
 gi|315130607|gb|EFT86593.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS03]
 gi|315197223|gb|EFU27562.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320140780|gb|EFW32631.1| hypothetical protein HMPREF9528_00946 [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320143781|gb|EFW35555.1| hypothetical protein HMPREF9529_00791 [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|329314428|gb|AEB88841.1| Pseudouridine synthase [Staphylococcus aureus subsp. aureus T0131]
 gi|329726944|gb|EGG63401.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           21189]
 gi|329727428|gb|EGG63884.1| putative 16S pseudouridylate 516 synthase [Staphylococcus aureus
           subsp. aureus 21172]
          Length = 231

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 79/244 (32%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N         ++++L+ G V V+++ +K                     HI 
Sbjct: 1   MRIDKFLANMGVG-TRNEVKQLLKKGLVNVNEQVIKS-----------------PKTHIE 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   +     L          + Y ++   + NKP G      +   +H    +    +
Sbjct: 43  PENDKITVRGEL----------IEYIENVYIMLNKPKGYIS---ATEDHHSKTVIDLIPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++T G+L++         L      + + K Y            E I
Sbjct: 90  YQHLNIFPVGRLDKDTEGLLLITNDGDFNHEL--MSPNKHVSKKY------------EVI 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +   + +  I      V   + K    AI  +  ID         E     G+ HQ++  
Sbjct: 136 SANPITEDDIQAFKEGVTLTDGK-VKPAILTY--IDNQTSHVTIYE-----GKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|30248452|ref|NP_840522.1| pseudouridylate synthase family protein 1 [Nitrosomonas europaea
           ATCC 19718]
 gi|30138338|emb|CAD84346.1| possible pseudouridylate synthase family 1 [Nitrosomonas europaea
           ATCC 19718]
          Length = 292

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 36/244 (14%), Positives = 78/244 (31%), Gaps = 46/244 (18%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RL +    +    +   ++ ++ +G+V ++    K  +R   G ++RI            
Sbjct: 35  RLQKLLARNGLG-SRREIEDMIAAGRVSINGVTAKPGDRAGPGDMIRI------------ 81

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                D  +   + +  L  +++Y        +KP G  V                    
Sbjct: 82  -----DGKIIRFRLAALLPRVIIY--------HKPEGEIV--SVRDPQGRPSVFDKLPHI 126

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +  K     RLD  TSG+L+       A HL       ++++ Y   + G    ++    
Sbjct: 127 RSSKWIAIGRLDFNTSGLLIFTTDGTLANHL--MHPRYQMEREYAVRIVGELTPEQITRL 184

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              ++       +  ++ +   G N+                W  +    GR  ++R   
Sbjct: 185 TTGIELEDGLAKFDQLLDEGGTGTNH----------------WYRIMLKEGRNREVRRMF 228

Query: 260 LHMG 263
             +G
Sbjct: 229 EALG 232


>gi|94991824|ref|YP_599923.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS2096]
 gi|94545332|gb|ABF35379.1| Ribosomal large subunit pseudouridine synthase B [Streptococcus
           pyogenes MGAS2096]
          Length = 220

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 39/226 (17%), Positives = 73/226 (32%), Gaps = 51/226 (22%)

Query: 40  ILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           +++ G V ++ + +      ++SG VV I                               
Sbjct: 1   MIKQGLVTLNGQVITDLATTVKSGDVVEIE-----------------------------G 31

Query: 99  SILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           S +  E+   Y+ NKP G IS          +   L        ++     RLD +TSG+
Sbjct: 32  SPIYNEEKVYYLLNKPRGAISSVSDDKGRKTVLDLL----PQVKERIYPVGRLDWDTSGV 87

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++         +        I K+Y + V GI   +                     + 
Sbjct: 88  LILTNDGDFTDTM--IHPRNEIDKVYLARVKGIATKENL-------------RPLTRGIV 132

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
            + K    A  +   ++   +    +E+  H GR HQ++     +G
Sbjct: 133 IDGKKTKPARYNIVRVEAD-KNRSIVELTIHEGRNHQVKKMFESVG 177


>gi|296393714|ref|YP_003658598.1| pseudouridine synthase [Segniliparus rotundus DSM 44985]
 gi|296180861|gb|ADG97767.1| pseudouridine synthase [Segniliparus rotundus DSM 44985]
          Length = 272

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 42/258 (16%), Positives = 79/258 (30%), Gaps = 55/258 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++  G+VRVD +                         ++
Sbjct: 19  QRLHKVLARA-GVASRRGSEQLIAEGRVRVDGR-------------------------LV 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKI-YVFNKPAGISVQGGSGIAYHIDGFLKSW- 136
            EQ +L          D  +  +  +D    Y  NKP G+           +   L+   
Sbjct: 53  TEQGVLVDPHTAVVEVDGKRIAV--DDRHATYALNKPKGVLTAMSDTRERCVGDLLREAG 110

Query: 137 -------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                              RLD +T+G+L+V+     A  L        I K Y + V G
Sbjct: 111 PDFAADGRAGLPAGLFHVGRLDADTTGLLLVSNDGELAHRLA--HPSYEIPKTYIATVRG 168

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
           +            + K  +      VV ++       +     +    +    +E+  H 
Sbjct: 169 V------------VAKRAVEQLRAGVVLEDGPAKADEV----CLRGSQRDRTVVEITLHE 212

Query: 250 GRTHQLRVHALHMGCPIV 267
           GR   +R     +G P++
Sbjct: 213 GRNRIVRRMFDEVGHPVI 230


>gi|257068695|ref|YP_003154950.1| pseudouridine synthase family protein [Brachybacterium faecium DSM
           4810]
 gi|256559513|gb|ACU85360.1| pseudouridine synthase family protein [Brachybacterium faecium DSM
           4810]
          Length = 306

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 78/250 (31%), Gaps = 50/250 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +  RL +         +    + ++ +G+VRVD   V+        Q VRI P    ++ 
Sbjct: 65  DGERLQKVLARAGFG-SRRACETLISTGRVRVDGAVVQE-------QGVRIDPAAQVVH- 115

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                + + L E     V NKP G+               L  +
Sbjct: 116 ------------------VDGRRLQLDETKLTLVLNKPRGVVSAMSDPEGRRD---LSEF 154

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-RRIQKIYWSLVWGIPKNKK 195
             +  Q+     RLD ET G+L++      A  LT       +     +    G P+   
Sbjct: 155 TAAHSQRLYHVGRLDYETEGLLLLTNDGELAHRLTHPSFEVAKTYVCRFDAPGGPPRGLV 214

Query: 196 ECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
             + + + L+      D   V+ Q+ + A                   +E+  H GR   
Sbjct: 215 RTLRDGVELEDGPARADRARVLAQDGREA------------------VVEVTLHEGRNRI 256

Query: 255 LRVHALHMGC 264
           +R      G 
Sbjct: 257 VRRMFASRGF 266


>gi|226314668|ref|YP_002774564.1| hypothetical protein BBR47_50830 [Brevibacillus brevis NBRC 100599]
 gi|226097618|dbj|BAH46060.1| conserved hypothetical protein [Brevibacillus brevis NBRC 100599]
          Length = 167

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 7   VQYVVV--ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQV 64
           VQ V +  E+ E   RLD+         +   + + ++ GQ+ ++++  K +  + +  +
Sbjct: 102 VQEVTIRIESTEARFRLDKLLSEQIEGWSRSQIARKIKDGQILLNEQETKPSVVLSAADI 161

Query: 65  VRI 67
           ++I
Sbjct: 162 IQI 164


>gi|327188988|gb|EGE56177.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli CNPAF512]
          Length = 267

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 38/254 (14%), Positives = 72/254 (28%), Gaps = 52/254 (20%)

Query: 13  ENDEENMR--LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
             D    R  L R       + +    ++++   +V +D + V   +  +    +V    
Sbjct: 17  TADAAGKRVTLPRALSK-LGYCSRTQAERLIAESRVSIDGRTVNDPSAWV---DLVTAKI 72

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            ++ L  I  E KI                          + NKP G+            
Sbjct: 73  RVDGLV-IAAEAKI------------------------YLILNKPRGLVT--TRHDPEGR 105

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                   D          RLD+ + G+L+       AQ L +       +  +  +   
Sbjct: 106 PTVYDCLRDFDIPHLSPVGRLDKASEGLLLFTNDTEFAQILLDPV-THVTKTYHVQI--- 161

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                     + LL    I      +    E     A+   +       +  W+E++   
Sbjct: 162 ----------DRLLDDEEIAAMTSGIRHDGELLTATAVRRLR----QGDRNSWIEVELDE 207

Query: 250 GRTHQLRVHALHMG 263
           GR  Q+R     +G
Sbjct: 208 GRNRQIRRMLEALG 221


>gi|221481694|gb|EEE20070.1| conserved hypothetical protein [Toxoplasma gondii GT1]
          Length = 231

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 21/109 (19%), Positives = 34/109 (31%), Gaps = 4/109 (3%)

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVI---DCFAQKFCWLEMQPHTGRTHQLRVHALHM 262
               G     +         A S F+ I      A     +E++   G     R+HA  +
Sbjct: 14  RPSPGSREWRLAGERTEGKAAYSIFRPIVQAALEAHPITLVEIRLVQGPPIVPRLHAASL 73

Query: 263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP-EGGRLQITAP 310
           G  ++GD  Y               L LH   + +  P     + + AP
Sbjct: 74  GHSVIGDPTYGPEVHRRRHHRCDKPLMLHCWILKIAPPYAQEEVCVEAP 122


>gi|205374450|ref|ZP_03227246.1| pseudouridylate synthase (ribosomal small subunit pseudouridine
           synthase A) [Bacillus coahuilensis m4-4]
          Length = 236

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 87/246 (35%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D+   N   + +   ++ +L+SG V V+    K                 +   H+ 
Sbjct: 1   MRIDKLLAN-MGYGSRKEVKSLLKSGNVVVNGTGCK-----------------DGKQHVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q  +                ++Y +    + NKP G+           +   L+   D
Sbjct: 43  PSQDEVFVH----------GEKVVYREFIYLLMNKPQGVISATEDLRDETVIDLLE--PD 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +   P    RLD++T G+L++      + Q L+     + + K Y++ V G+   +   
Sbjct: 91  HRVFNPFPVGRLDKDTEGLLIITNDGQLSHQLLS---PKKHVPKTYYAEVKGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +A +    +   G        + K  +  I         + +   +E+    G+ HQ++ 
Sbjct: 146 VAAFSEGVTLDDG-------YHTKPGDLVI-------LSSGEMSEIELTITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFESVG 197


>gi|213021537|ref|ZP_03335984.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 93

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 259 ALHMGCPIVGDHKYCA--NFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHM 315
             H+  PI+GD K+      +         +L LHA  ++L HP  G+ L I A L    
Sbjct: 1   MAHLRHPIIGDSKHGDLRQNRSAAEHFACRRLMLHASRLELTHPFTGQPLIIQAGLDETW 60

Query: 316 VKTWDSLGFK 325
           ++     G++
Sbjct: 61  MQVLTQFGWR 70


>gi|329119926|ref|ZP_08248600.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327464082|gb|EGF10393.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 369

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 41/252 (16%), Positives = 80/252 (31%), Gaps = 34/252 (13%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +E  RL +         +   +++ + +G V+V+ K  +  +++     V +      L 
Sbjct: 115 QEPERLQKVLAASGAG-SRREMEEWIAAGLVQVNGKTAQLGDKVTPDDQVTVKGSPIKL- 172

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                           K +D L  I+LY         K  G  V                
Sbjct: 173 ----------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDR 206

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++
Sbjct: 207 LPQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGELTAEQ 264

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--H 253
             +     +   +      V +  E+G   A   + V+    +      +  H G T   
Sbjct: 265 --MRELTTEGVMLDDGLAKVERIFEQGGEGANKWYSVVIKEGRNREVRRIFEHFGLTVSR 322

Query: 254 QLRVHALHMGCP 265
            +RV    +G P
Sbjct: 323 LVRVGFGPIGLP 334


>gi|295105192|emb|CBL02736.1| ribosomal small subunit pseudouridine synthase A [Faecalibacterium
           prausnitzii SL3/3]
          Length = 233

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 28/243 (11%), Positives = 68/243 (27%), Gaps = 54/243 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRLD++             + +L  G+V+V+    K  + +++    V +          
Sbjct: 1   MRLDKYLAET-AQCTRSEAKTMLAKGRVQVNGAVCKKGDTQLKDNDTVTVDGAPLR---- 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                    Y+     + NKP G+           +   +    
Sbjct: 56  -------------------------YQKFVYLMLNKPEGVVSASTDKRDTTVVDLVGDAY 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +  +     RLD+ ++G +++      A   L+    + +   +              
Sbjct: 91  PRR--ELFPAGRLDKTSTGFVLLTDDGGFAHDILSPRHHVSKTYTV-------------- 134

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I   L ++   G      +      +   ++        +   C + +    G  HQ++
Sbjct: 135 TIDTPLTQEMRTGFAAGVTLADGTALSPAEVT------ALSPDGCTVRVVLRQGVYHQIK 188

Query: 257 VHA 259
              
Sbjct: 189 RMF 191


>gi|3805993|gb|AAC69259.1| hypothetical protein [Helicobacter pylori]
          Length = 83

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 7/83 (8%)

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK------LYLHARYMDL 297
           ++ P TGRTHQ+R+H   +   IVG+  Y    +         +      L LHA  ++ 
Sbjct: 1   KITPLTGRTHQIRLHLSSVDHRIVGEGLYGVADENAREYLQLKRENNAPTLMLHAASLEF 60

Query: 298 PHPEGGRLQITAPLPAHMVKTWD 320
              +G   +I +P+P   +    
Sbjct: 61  EF-KGAHYKIASPMPKRFMPFLK 82


>gi|78222432|ref|YP_384179.1| ribosomal large subunit pseudouridine synthase B [Geobacter
           metallireducens GS-15]
 gi|78193687|gb|ABB31454.1| ribosomal large subunit pseudouridine synthase B [Geobacter
           metallireducens GS-15]
          Length = 258

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 75/249 (30%), Gaps = 48/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++  G+V V+ K V           + +    ++    I
Sbjct: 3   ERLQKILSQA-GIASRREAERMITDGRVAVNGKPV-----------IELGAKADSSRDAI 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                          +   K + + E     + NKP G      +         +   + 
Sbjct: 51  ---------------TVDGKPVTVDEKRVYILLNKPVGYVT---TLKDPEGRPIVTELLK 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             G +     RLD  T G+L++      A  L        + K Y   V G         
Sbjct: 93  GLGVRVFPVGRLDYNTEGLLLLTNDGEWANRLA--HPRHEVDKEYLVRVRGT-------- 142

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               + +  I      +  ++ K A   +S    +   +    W+ +  H GR  Q+R  
Sbjct: 143 ----VAREQITRLEQGIELEDGKAAPARVS----VTKQSDNNTWVSITIHEGRYRQVRRM 194

Query: 259 ALHMGCPIV 267
              +   +V
Sbjct: 195 CEAVSLSVV 203


>gi|323491918|ref|ZP_08097088.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio brasiliensis
           LMG 20546]
 gi|323313839|gb|EGA66933.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio brasiliensis
           LMG 20546]
          Length = 342

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 76/249 (30%), Gaps = 55/249 (22%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           +   RL+++        +     +++  G+V ++ K  +   ++QSG  VR+        
Sbjct: 4   DTGKRLNKFISET-GFCSRREADRLIEQGRVTINGKIPEMGTKVQSGDDVRVD------- 55

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                           K         +Y        NKP GI+      I  +I  F+  
Sbjct: 56  ---------------DKPIAAASDKPIY-----IALNKPTGITCTTERDIPGNIVDFV-- 93

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 ++     RLD+ + G++ +         +  +      + +             
Sbjct: 94  ---GHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVR---------VD 141

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           + I++  +KK   G + +  V    K        F+++                G   Q+
Sbjct: 142 KPISDDFIKKMSSGVNILDTVTLPCKVEKETKYSFRIV-------------LTQGLNRQI 188

Query: 256 RVHALHMGC 264
           R     +G 
Sbjct: 189 RRMCEALGY 197


>gi|283458425|ref|YP_003363049.1| 16S rRNA uridine-516 pseudouridylate synthase [Rothia mucilaginosa
           DY-18]
 gi|283134464|dbj|BAI65229.1| 16S rRNA uridine-516 pseudouridylate synthase [Rothia mucilaginosa
           DY-18]
          Length = 378

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 91/253 (35%), Gaps = 49/253 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +RL +         +    ++++  G+V V+ + V      + G  VR+ P     
Sbjct: 136 DHDGVRLQKLLAQA-GVASRRVCEEMITEGRVTVNGEVVT-----ELG--VRVDPSKV-- 185

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFL 133
                       +V +   +      L+Y       FNKPAG +S          I  FL
Sbjct: 186 ------------TVQVDGMTVQTNDKLVY-----MAFNKPAGVVSTMEDPEGRPCISDFL 228

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +S   S  ++     RLD ET G+L++      A  LT       + K Y   V G  + 
Sbjct: 229 RS---SMSERVFHVGRLDVETEGLLLLTNDGELANRLT--HPSYEVPKTYLVQVPGPMEP 283

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                    +KK     D V  V +           FK++D        +E+  H+G+  
Sbjct: 284 GVG----AAMKKGIRLEDGVTRVDE-----------FKLVDSTP-GHVLVEVTIHSGKNR 327

Query: 254 QLRVHALHMGCPI 266
            +R     +G P+
Sbjct: 328 IVRRLFDAVGYPV 340


>gi|138895852|ref|YP_001126305.1| pseudouridylate synthase [Geobacillus thermodenitrificans NG80-2]
 gi|134267365|gb|ABO67560.1| Pseudouridylate synthase [Geobacillus thermodenitrificans NG80-2]
          Length = 243

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 48/253 (18%), Positives = 92/253 (36%), Gaps = 56/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++  G+V+V+ + V      + G  V++ P  +     I
Sbjct: 2   ERLQKVIARA-GIASRRKAEEMILQGRVKVNGRVVT-----ELG--VKVGPRDDVEVDGI 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSW 136
             ++                     E+   Y+  KP G+  SV+   G        +  +
Sbjct: 54  PVER---------------------EEPVYYLLYKPRGVISSVKDEKGRK-----VVTDF 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNK 194
                Q+     RLD +TSG+L++      A  L        I+K+Y + V GIP  +  
Sbjct: 88  FKDIHQRIYPIGRLDYDTSGLLLLTNDGDFANLL--MHPRYEIEKVYVAKVKGIPTREQL 145

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K+     LL+        V ++  + K                ++   +E+  H GR  Q
Sbjct: 146 KQPEKGVLLEDGITAPAKVKLLSADRK----------------KRAAIVEISIHEGRNRQ 189

Query: 255 LRVHALHMGCPIV 267
           +R     +GC ++
Sbjct: 190 VRRMFEAIGCEVL 202


>gi|315126735|ref|YP_004068738.1| ribosomal large subunit pseudouridine synthase E [Pseudoalteromonas
           sp. SM9913]
 gi|315015249|gb|ADT68587.1| ribosomal large subunit pseudouridine synthase E [Pseudoalteromonas
           sp. SM9913]
          Length = 225

 Score = 59.6 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 39/182 (21%), Positives = 71/182 (39%), Gaps = 9/182 (4%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           S+V  +     +K  +   D K+ +FNKP  +  Q            L +++  K     
Sbjct: 24  SAVKKSPIKRAIKPQIAQSDKKVILFNKPYDVLCQ---FTDEQNRQTLANFIPIK--DVY 78

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
              RLD+++ G+L++         LT     ++  K YW  V G+P       A     +
Sbjct: 79  AAGRLDRDSEGLLLLTNCGKLQNTLTA--PGKKTNKTYWVQVEGVPTEAS-IDALSQGVE 135

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
              G      VK  ++ A +  +   V +  +    WL +  + G+  Q+R    H+G P
Sbjct: 136 LKDGLTLPAQVKLIDEPALWPRTP-PVRERKSIPTSWLSITINEGKNRQVRRMTAHIGHP 194

Query: 266 IV 267
            +
Sbjct: 195 TL 196


>gi|293400699|ref|ZP_06644844.1| ribosomal large subunit pseudouridine synthase B
           [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305725|gb|EFE46969.1| ribosomal large subunit pseudouridine synthase B
           [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 245

 Score = 59.6 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 74/249 (29%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    ++++  G+V V+   +     +++ G VV +        + 
Sbjct: 2   ERLQKVIAQA-GIASRRKAEEMIAQGRVCVNGDIITEMGYKVKRGDVVEVDGNPIEKENK 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +            T + +F ++ ++       +  K                        
Sbjct: 61  VYFLMNKPKKTMCTSNDEFDRTTVID-----LIPCK------------------------ 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  +                   IPK     
Sbjct: 92  ----ERIFTVGRLDYDTSGVLLLTNDGEFANEIIHPRYH-------------IPKVYNLT 134

Query: 198 IANWLLKKSHIGGDYVHVVKQNEK--GANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           I   L  +  I      V+   +K   A   ++         +  C  ++  + GR  Q+
Sbjct: 135 INGILTPEEMIQIKKGIVLDDGKKTLPAKLKLTE----KDVTKNQCSFDLTIYEGRNRQI 190

Query: 256 RVHALHMGC 264
           +     +G 
Sbjct: 191 KRMMEALGY 199


>gi|218281417|ref|ZP_03487881.1| hypothetical protein EUBIFOR_00446 [Eubacterium biforme DSM 3989]
 gi|218217429|gb|EEC90967.1| hypothetical protein EUBIFOR_00446 [Eubacterium biforme DSM 3989]
          Length = 227

 Score = 59.6 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 86/248 (34%), Gaps = 59/248 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++   H       +++K++++G V ++ + + K +  ++    V +          
Sbjct: 1   MRLDKYLS-HMGFGTRNDVKKLIKNGWVTINDETIKKADYNVKEDDKVFVD--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                            D   S + +E    Y+ NKP G      S     +   +   +
Sbjct: 51  -----------------DEPVSYVEFE---YYILNKPQGYV----SATEDMLYPTVMELI 86

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            S+        RLD +T G+L+++   +   + L+     + + K Y+    G       
Sbjct: 87  QSQRHDLYPVGRLDVDTEGLLLISNDGKLTHEVLS---PKKHVDKKYYVEFDGTLPE--- 140

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                         D+ +   + E+    A S  +++D          +  H G+ HQ++
Sbjct: 141 -----------NAVDFFNQPMEFEEF-TSAPSKLEILDTNKAY-----LTIHEGKFHQVK 183

Query: 257 VHALHMGC 264
                  C
Sbjct: 184 RMFEKANC 191


>gi|242373794|ref|ZP_04819368.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
 gi|242348531|gb|EES40133.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
          Length = 245

 Score = 59.6 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 38/235 (16%), Positives = 74/235 (31%), Gaps = 53/235 (22%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V V+ + V     ++ +   V +                    + + 
Sbjct: 19  SRRKAETLITEGKVSVNGQVVTELGTKVSNSDTVEV------------------EGIKIE 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +           ED    +F KP  +     S         +  + D    +     RLD
Sbjct: 61  Q-----------EDKMYILFYKPTQVIT---SVSDDRGRTVVTDYFDDIETRIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIG 209
            +TSGIL++         +T       I+K Y + + G    +  KE      L+     
Sbjct: 107 YDTSGILLLTNDGEFTNLMT--HPRYHIKKKYVAKLKGYLMREEVKELEKGIQLEDGFTQ 164

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              V + KQ+++                +    +E+    GR  Q+R    H G 
Sbjct: 165 PAQVKIKKQDKE----------------KNTTLVEITISEGRNRQVRRMFEHFGH 203


>gi|332828688|gb|EGK01380.1| hypothetical protein HMPREF9455_02213 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 86

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 15/76 (19%), Positives = 26/76 (34%), Gaps = 13/76 (17%)

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLHARYMDLPHPEGG-RL 305
             ++G  +  D +Y  N     T   +             +  LHA+ +    P  G  L
Sbjct: 1   MKYIGHTLFNDERYGGNEVLKGTHFAKYKQFVQNCFNICPRQALHAQTLGFIQPRTGKEL 60

Query: 306 QITAPLPAHMVKTWDS 321
              AP+P  M +  + 
Sbjct: 61  MFEAPIPDDMSQLLEK 76


>gi|218768378|ref|YP_002342890.1| putative pseudouridine synthase [Neisseria meningitidis Z2491]
 gi|121052386|emb|CAM08718.1| putative pseudouridine synthase [Neisseria meningitidis Z2491]
          Length = 256

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 2   EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 59  ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 94  PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 152 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 209

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 210 VRVGFGPIGLP 220


>gi|304315594|ref|YP_003850739.1| RNA-binding S4 domain protein [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302777096|gb|ADL67655.1| RNA-binding S4 domain protein [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 241

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 84/249 (33%), Gaps = 52/249 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             MR+D+   N         ++  ++ G V V+ + V        G ++           
Sbjct: 2   AKMRIDKLLSNTGFG-TRKEVKGFIKEGLVTVNGRTVND-----PGLIIE---------- 45

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
              +  I+           F    + Y      + NKP G+           +   L   
Sbjct: 46  -TDKDDII-----------FNDEKIFYRKYIYIMMNKPRGVISATYDPSEKTVLDLLPD- 92

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWG-IPKNK 194
            D K +K     RLD++T G+L++      A + L+     + + K Y++ + G I ++ 
Sbjct: 93  -DIKARKVFPAGRLDKDTEGLLLLTNDGILAHKLLS---PKKHVYKKYYAEISGFIDEDD 148

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
               +N ++                  G     ++ ++I   +     + +    G+ HQ
Sbjct: 149 ISLFSNGIVLDD---------------GYKTMPAYLEIISSGS--ISKVYVSIKEGKYHQ 191

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 192 IKRMFESLG 200


>gi|237703577|ref|ZP_04534058.1| 23S rRNA pseudouridine synthase F [Escherichia sp. 3_2_53FAA]
 gi|226901489|gb|EEH87748.1| 23S rRNA pseudouridine synthase F [Escherichia sp. 3_2_53FAA]
          Length = 290

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 76/250 (30%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  RES--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD++  G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDFQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|37523966|ref|NP_927343.1| hypothetical protein glr4397 [Gloeobacter violaceus PCC 7421]
 gi|35214972|dbj|BAC92338.1| glr4397 [Gloeobacter violaceus PCC 7421]
          Length = 248

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 90/251 (35%), Gaps = 47/251 (18%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             +RL +    H    +    + ++ SGQV V+   V   +R+ +    R+ P I+    
Sbjct: 3   AAIRLQKLLAEH-GIASRRKAEALIVSGQVCVNGTVV---DRLGT----RVDPQIDL--- 51

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKS 135
                      + +          LLY      + +KP G +S          +   L +
Sbjct: 52  -----------IEVFGQPLHCMPPLLY-----VLLHKPVGWLSTCFDPRGRRTVLDLLPA 95

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              + GQ      RLD ++SG L+V+        LT      ++ K Y   V G P    
Sbjct: 96  EWRT-GQGLHPVGRLDCDSSGALIVSNDGEFTFRLT--HPRHQLPKTYRVWVRGRPTA-- 150

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                     + +G     VV + +K    A++   V+   A+     E+    GR  Q+
Sbjct: 151 ----------AVLGRWRAGVVLEGQKTLPAAVT---VVSRAAEATEL-EVVLVEGRNRQI 196

Query: 256 RVHALHMGCPI 266
           R  A  +G P+
Sbjct: 197 RKVAELLGHPV 207


>gi|293376750|ref|ZP_06622972.1| pseudouridylate synthase [Turicibacter sanguinis PC909]
 gi|325845685|ref|ZP_08168968.1| ribosomal large subunit pseudouridine synthase F [Turicibacter sp.
           HGF1]
 gi|292644616|gb|EFF62704.1| pseudouridylate synthase [Turicibacter sanguinis PC909]
 gi|325488286|gb|EGC90712.1| ribosomal large subunit pseudouridine synthase F [Turicibacter sp.
           HGF1]
          Length = 235

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 31/246 (12%), Positives = 73/246 (29%), Gaps = 56/246 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL+++  +     +     K++  G+V+V+ +  K  ++++ G  V +   I  L    
Sbjct: 1   MRLNKFISDSGK-ASRRGADKLIAEGRVKVNGRIAKIGDQVKPGDEVMVNGNIIRLAR-- 57

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                     +      NKP GI+     G+  +I   +   + 
Sbjct: 58  --------------------------NHVYLALNKPVGITCTTEKGVKGNIVDLVNHPL- 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++++         +  +      + I                
Sbjct: 91  ----RVFNIGRLDKDSDGLILLTNDGDIVNEILRAENNHEKEYIVS-------------- 132

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            +  +    I      V    +K     ++     +          +    G   Q+R  
Sbjct: 133 VDKPITPEFIEKMSKGVRILGQKTLPCKVTQISKYE--------FNIILTQGLNRQIRRM 184

Query: 259 ALHMGC 264
              +G 
Sbjct: 185 CEVLGY 190


>gi|259419278|ref|ZP_05743195.1| ribosomal large subunit pseudouridine synthase E [Silicibacter sp.
           TrichCH4B]
 gi|259345500|gb|EEW57354.1| ribosomal large subunit pseudouridine synthase E [Silicibacter sp.
           TrichCH4B]
          Length = 227

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 33/161 (20%), Positives = 64/161 (39%), Gaps = 6/161 (3%)

Query: 108 IYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           +  FNKP  +  Q    G        L  +VD  G  P    RLD+++ G++++      
Sbjct: 4   LIRFNKPFDVLPQFTDRGSEGSPRATLSDYVDCPGVYP--AGRLDRDSEGLMLLTDNGRL 61

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
              +++     +++K YW+ V GIP      +    ++              NE    +A
Sbjct: 62  QAWISD--PKHKLEKTYWAQVEGIPDEDALNLLRQGVELKDGMTRPAKARLINEPAQLWA 119

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +   + +  +    WLE++   G+  Q+R     +G P +
Sbjct: 120 RTP-PIRERKSVPTAWLELKITEGKNRQVRRMTAAVGHPTL 159


>gi|157371489|ref|YP_001479478.1| 16S rRNA pseudouridylate synthase A [Serratia proteamaculans 568]
 gi|157323253|gb|ABV42350.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 237

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 76/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V VD + VK                      + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTVDGEVVKS-----------------GALKLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ++      L + +            + ++ NKP G      S         L    +
Sbjct: 43  PEQEVTFDGNPLQRQNGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L   +         +   +     A      ++    K   + +    GR HQ++  
Sbjct: 137 EHPLAADTAQQFAEGVQLHNEKDLTRPAQ-----LEQIEDK--LVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  ++
Sbjct: 190 FAAVGNRVL 198


>gi|104773906|ref|YP_618886.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|116513914|ref|YP_812820.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus delbrueckii subsp. bulgaricus ATCC
           BAA-365]
 gi|103422987|emb|CAI97669.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|116093229|gb|ABJ58382.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|325125580|gb|ADY84910.1| Ribosomal large subunit pseudouridine synthase B [Lactobacillus
           delbrueckii subsp. bulgaricus 2038]
          Length = 239

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 82/252 (32%), Gaps = 56/252 (22%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALN 75
              RL +         +    +K++ +G+VRVD + V K   ++ S + V +        
Sbjct: 2   AEERLQKVIAQA-GIASRREAEKMILAGRVRVDGQVVTKLGTKVSSIEQVVVDNQP---- 56

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFL 133
                                    +  E    Y+F KP G+  +V+   G        +
Sbjct: 57  -------------------------IERESHHTYLFYKPRGVISAVKDNKGRK-----TV 86

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +      +     RLD +TSG+L++      A  L        + K+Y + + GI + 
Sbjct: 87  ADYFTDLPYRLYPVGRLDYDTSGLLLMTNDGELANLL--MHPRNEVDKVYVAKIKGILQP 144

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRT 252
            +      L K   IG                A    KV+    +     +++  H G  
Sbjct: 145 DE---IKALKKGVQIGRYKT----------KPA--QVKVLKTNPRAQTQIVQLTIHEGHY 189

Query: 253 HQLRVHALHMGC 264
           HQ++     +  
Sbjct: 190 HQVKEMFKAVNH 201


>gi|333030055|ref|ZP_08458116.1| pseudouridine synthase Rsu [Bacteroides coprosuis DSM 18011]
 gi|332740652|gb|EGJ71134.1| pseudouridine synthase Rsu [Bacteroides coprosuis DSM 18011]
          Length = 321

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 32/242 (13%), Positives = 77/242 (31%), Gaps = 56/242 (23%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RL+++  N   + +     K++ +GQV+V+ K+    +R+   Q V +            
Sbjct: 4   RLNKYISNS-GYCSRREADKLIEAGQVKVNGKKASIGDRVYPKQKVTVN----------- 51

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             +++ + +                      FNKP GI          +I  ++      
Sbjct: 52  -GELIVNDIEPV----------------YIAFNKPVGIVSTTDPNEKANIVKYISH---- 90

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             Q+     RLD+++ G++++         +  +    +   I             + I 
Sbjct: 91  -EQRIFPIGRLDKDSQGLILLTNDGDIVNKILRAGNNHKKVYIV---------QVDKPIT 140

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           +  ++K   G   +  V              +  +         +++   G   Q+R   
Sbjct: 141 DEFIEKMKTGVPILDRVT-------------RKCEVEKINPYTFKIELIQGLNRQIRRMC 187

Query: 260 LH 261
            +
Sbjct: 188 AY 189


>gi|297571446|ref|YP_003697220.1| pseudouridine synthase [Arcanobacterium haemolyticum DSM 20595]
 gi|296931793|gb|ADH92601.1| pseudouridine synthase [Arcanobacterium haemolyticum DSM 20595]
          Length = 251

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 42/254 (16%), Positives = 86/254 (33%), Gaps = 52/254 (20%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + +  RL +    H    +    + +++ G+V V+   V+     Q G  +R+ P     
Sbjct: 10  NPQGERLQKVLA-HAGVASRRAAEDMIQQGRVSVEGTIVR-----QLG--IRVDPQS--- 58

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                   ++    N  +    L ++ LY         KP G+     +         L 
Sbjct: 59  -------AVIHVDGNRVQLDQELITVALY---------KPPGVVS---TMSDDQGRKTLA 99

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +V+   Q+     RLD +T G+++++        LT       + K Y + V G     
Sbjct: 100 DFVEDYPQRLVHVGRLDVDTEGLILLSNDGELVHRLT--HPSYEVPKTYIARVEGTVTRG 157

Query: 195 KECI--ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            + +      L+   +  D   + +  +K                     +E+  H+GR 
Sbjct: 158 LQRVMEKGITLEDGPVHADRFIIREVAKKN------------------SIVEITLHSGRN 199

Query: 253 HQLRVHALHMGCPI 266
             +R     +G P+
Sbjct: 200 RIVRRMMEEVGHPV 213


>gi|229076216|ref|ZP_04209183.1| Pseudouridine synthase [Bacillus cereus Rock4-18]
 gi|229099186|ref|ZP_04230119.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|229118198|ref|ZP_04247556.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228665245|gb|EEL20729.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228684239|gb|EEL38184.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|228706865|gb|EEL59071.1| Pseudouridine synthase [Bacillus cereus Rock4-18]
          Length = 242

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 95/246 (38%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGTPVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMLHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K+   G     ++    +    A++  K     +     +E+    G+ HQ++ 
Sbjct: 146 -----VKEFAKG----VILDDGYETKPGALTILK-----SDDVSEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|150016762|ref|YP_001309016.1| pseudouridine synthase [Clostridium beijerinckii NCIMB 8052]
 gi|149903227|gb|ABR34060.1| pseudouridine synthase [Clostridium beijerinckii NCIMB 8052]
          Length = 236

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 88/250 (35%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++  N     +    ++++ SG+V+V+   V      + G  +++ P+ + + +  
Sbjct: 3   ERLQKYLAN-CGVASRRKCEELIISGKVKVNGVIVN-----EVG--IKVDPLKDMIEYDG 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
           KE K                     ED    + NKP G IS          I   +K   
Sbjct: 55  KEIKKK-------------------EDKVYIMLNKPEGYISSVKDEKGRDTILDIVKV-- 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD ++SG+L++         +        I K Y ++V G   +K   
Sbjct: 94  ---NERIYPIGRLDYDSSGLLLLTNDGEIYNKI--IHPRVEIIKRYVAVVKGEITDKD-- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                             +  +  G   A +  KVI  + +    +E+  H G+  Q+R 
Sbjct: 147 -------------KMKFEIGIDIGGYITAPAELKVI-SYDKGVSTIEIGIHEGKNRQIRK 192

Query: 258 HALHMGCPIV 267
               +   ++
Sbjct: 193 MCAAIHHDVL 202


>gi|209524582|ref|ZP_03273130.1| pseudouridine synthase [Arthrospira maxima CS-328]
 gi|209495040|gb|EDZ95347.1| pseudouridine synthase [Arthrospira maxima CS-328]
          Length = 257

 Score = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 47/250 (18%), Positives = 81/250 (32%), Gaps = 43/250 (17%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N RL +    H+   +  + ++++ SG+V+V+  R     +                + I
Sbjct: 2   NERLQKIIS-HWGVASRRHAEEMILSGRVKVNGDRAYLGQK-----------ADPKCDRI 49

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             + + L  S              LY      + NKP G+               L    
Sbjct: 50  EIDGRALHPSSQPQP---------LY-----LLLNKPLGVVCTCAEPQGRKAVLDLLPRQ 95

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              GQ      RLD +++G L++         LT       + K Y  LV G P      
Sbjct: 96  MRVGQGLHPVGRLDSDSTGALLITNDGELTFLLT--HPRYHVAKTYQVLVQGCPPES--- 150

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                     +   +   +  + K    A    + I   ++    LE+    GR  Q+R 
Sbjct: 151 ----------VLEQWRQGILLSGKNTLPA--QVRPIGKPSRSQTLLEVVLREGRNRQIRR 198

Query: 258 HALHMGCPIV 267
            A  +G P+V
Sbjct: 199 VAEALGYPVV 208


>gi|258424167|ref|ZP_05687049.1| RNA pseudouridine synthase [Staphylococcus aureus A9635]
 gi|257845788|gb|EEV69820.1| RNA pseudouridine synthase [Staphylococcus aureus A9635]
          Length = 231

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 79/244 (32%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N         ++++L+ G V V+++ +K                     HI 
Sbjct: 1   MRIDKFLANMGVG-TRNEVKQLLKKGLVNVNEQVIKS-----------------PKAHIE 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +   +     L          + Y ++   + NKP G      +   +H    +    +
Sbjct: 43  PKNDKISVRGEL----------IEYVENVYIMLNKPKGYIS---ATEDHHSKTVIDLIPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++T G+L++         L      + + K Y            E I
Sbjct: 90  YQHLNIFPVGRLDKDTEGLLLITNDGDFNHEL--MSPNKHVSKKY------------EVI 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +   + +  I      V   + K    AI  +  ID         E     G+ HQ++  
Sbjct: 136 SANPITEEDIQAFKEGVTLSDGK-VKPAILTY--IDNQTSHVTIYE-----GKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|323167301|gb|EFZ53010.1| ribosomal large subunit pseudouridine synthase F [Shigella sonnei
           53G]
          Length = 291

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 23/168 (13%), Positives = 57/168 (33%), Gaps = 34/168 (20%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    ++++ G +V++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDIVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------EDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  ++     RLD+++ G++ +         +  +      + +
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|229007288|ref|ZP_04164889.1| hypothetical protein bmyco0002_41700 [Bacillus mycoides Rock1-4]
 gi|228754042|gb|EEM03479.1| hypothetical protein bmyco0002_41700 [Bacillus mycoides Rock1-4]
          Length = 166

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 12/74 (16%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 1   MSLMTYVQY------VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK 54
           +S+M Y +       +V+E    + R+D+    +    +   +   +++G ++++ +++K
Sbjct: 92  ISIMQYKEAGTTELAIVLETVFGSHRMDKALATYISDWSRTAIVDRIKNGHIQLNGQKMK 151

Query: 55  FNNRIQSGQVVRIP 68
            N  +  G ++ I 
Sbjct: 152 PNTTLSEGDLISIC 165


>gi|291294585|ref|YP_003505983.1| pseudouridine synthase [Meiothermus ruber DSM 1279]
 gi|290469544|gb|ADD26963.1| pseudouridine synthase [Meiothermus ruber DSM 1279]
          Length = 257

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 69/245 (28%), Gaps = 50/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+    H    +   + ++ R+G + ++ K V                  +A     
Sbjct: 19  ERLDKVL-GHLGVGSRKEIHRLARAGLITINGKIV-----------------ADAGFKFD 60

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q           H +     L+Y+     + NKPAG            I   L     
Sbjct: 61  PSQA----------HIEVAGEPLVYQKFFYLLLNKPAGYITSTKDPSGTPITALLPEEFW 110

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                P    RLD++T G+L++         LT     +  ++ Y  L            
Sbjct: 111 RNDWMP--VGRLDKDTEGLLLLTTDGELLHRLTHPRW-KVTKRYYVELASPATPEDVAVF 167

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A   L+                +    A  +             +E+    GR HQ++  
Sbjct: 168 AAGTLE-------------LEGEPLQPAELYL------GPDPRKVELVLREGRFHQVKRM 208

Query: 259 ALHMG 263
               G
Sbjct: 209 FAARG 213


>gi|187478887|ref|YP_786911.1| ribosomal large subunit pseudouridine synthase B [Bordetella avium
           197N]
 gi|115423473|emb|CAJ50007.1| ribosomal large subunit pseudouridine synthase B [Bordetella avium
           197N]
          Length = 457

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 34/232 (14%), Positives = 69/232 (29%), Gaps = 47/232 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   +++++ +G+V V+ +      R+ +   VR+   + +  +  K  ++         
Sbjct: 15  SRREMEELIVAGRVSVNGEPAHIGQRVAANDQVRVNGKLISRPNAKKPPRV--------- 65

Query: 93  HSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                   +LY        +KPAG I          ++   L      K        RLD
Sbjct: 66  --------ILY--------HKPAGEIVSHDDPNGRANVFTRLPKLRTGKWLS---VGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             T G+L+   +   A  +         ++ Y   V G     +                
Sbjct: 107 LNTEGLLIFTTSGDMANRI--MHPRYGTEREYAVRVLGEMDEAQRT-------------- 150

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
              V   +      A   F  +        W  +    GR  ++R     +G
Sbjct: 151 -SLVEGIDLDDGKAAFGSFDYLGGDGSNR-WYRVTLQEGRNREVRRMFEAVG 200


>gi|30022777|ref|NP_834408.1| ribosomal small subunit pseudouridine synthase A [Bacillus cereus
           ATCC 14579]
 gi|206969480|ref|ZP_03230434.1| RNA pseudouridine synthase family protein [Bacillus cereus AH1134]
 gi|218233459|ref|YP_002369504.1| RNA pseudouridine synthase family protein [Bacillus cereus B4264]
 gi|228923463|ref|ZP_04086748.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228954985|ref|ZP_04117002.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228960980|ref|ZP_04122610.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|229048415|ref|ZP_04193982.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|229072210|ref|ZP_04205418.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|229081964|ref|ZP_04214455.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|229129987|ref|ZP_04258951.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|229147277|ref|ZP_04275628.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|229152907|ref|ZP_04281089.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|229181024|ref|ZP_04308359.1| Pseudouridine synthase [Bacillus cereus 172560W]
 gi|229192993|ref|ZP_04319949.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|296505173|ref|YP_003666873.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           thuringiensis BMB171]
 gi|29898336|gb|AAP11609.1| Ribosomal small subunit pseudouridine synthase A [Bacillus cereus
           ATCC 14579]
 gi|206735168|gb|EDZ52336.1| RNA pseudouridine synthase family protein [Bacillus cereus AH1134]
 gi|218161416|gb|ACK61408.1| RNA pseudouridine synthase family protein [Bacillus cereus B4264]
 gi|228590440|gb|EEK48303.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|228602581|gb|EEK60067.1| Pseudouridine synthase [Bacillus cereus 172560W]
 gi|228630520|gb|EEK87167.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|228636178|gb|EEK92657.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|228653431|gb|EEL09305.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|228701341|gb|EEL53836.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|228710948|gb|EEL62915.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|228722930|gb|EEL74308.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|228798697|gb|EEM45680.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|228804712|gb|EEM51314.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228836189|gb|EEM81545.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|296326225|gb|ADH09153.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           thuringiensis BMB171]
          Length = 242

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 95/246 (38%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGTPVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K+   G     ++    +    A++  K     +     +E+    G+ HQ++ 
Sbjct: 146 -----VKEFAKG----VILDDGYETKPGALTILK-----SDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|171779572|ref|ZP_02920528.1| hypothetical protein STRINF_01409 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281674|gb|EDT47108.1| hypothetical protein STRINF_01409 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 238

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 48/271 (17%), Positives = 91/271 (33%), Gaps = 54/271 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +   ++K++RS QV VD        R+     + + P   +L  I+
Sbjct: 1   MRLDKLLGQAGFG-SRNQVKKLIRSRQVYVDG-------RLAEADNLNVEP---SLQEIM 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              K L+ S                   K ++ NKPAG+          H          
Sbjct: 50  VSGKRLEQST-----------------EKYFILNKPAGVVS--AVSDKEHQTVIDLIAEA 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +     RLD++T G+L++                  + K Y+  V G+        
Sbjct: 91  DRVPRLYPVGRLDRDTEGLLLITNN--GLLGFRMLHPKYHVTKTYYVEVNGLLAE----- 143

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                 ++ +  D   V K           + ++I+  ++K     +    G+ HQ++  
Sbjct: 144 DAPAFFENGVTFDDGTVCKPA---------NLEIIEASSEKSSAY-ISIAEGKFHQVKKM 193

Query: 259 ALHMGCPIV-------GDHKYCANFKGNFTS 282
            L  G  ++       GD +     +G +  
Sbjct: 194 FLAYGVKVIYLKRMTFGDFELGDLPRGQYRE 224


>gi|19746315|ref|NP_607451.1| 16S pseudouridylate synthase [Streptococcus pyogenes MGAS8232]
 gi|21910554|ref|NP_664822.1| putative 16S pseudouridylate synthase [Streptococcus pyogenes
           MGAS315]
 gi|19748507|gb|AAL97950.1| putative 16S pseudouridylate synthase [Streptococcus pyogenes
           MGAS8232]
 gi|21904754|gb|AAM79625.1| putative 16S pseudouridylate synthase [Streptococcus pyogenes
           MGAS315]
          Length = 243

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 88/249 (35%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++            ++ +L+   + V+ ++V+ + +            I+    ++
Sbjct: 1   MRLDKFLVATGVG-TRSQVKLLLKKKAIFVN-QKVETSAK----------AHIDEYKDLV 48

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q                 + L+YE    Y+ NKP+G      S         +   +D
Sbjct: 49  TYQ----------------GTPLVYESFVYYLLNKPSGYV----SATQDRQQATVMELLD 88

Query: 139 --SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KK 195
             ++ +      RLD++T G+L++      A  L      + + K Y + V GI     K
Sbjct: 89  DTARQKTVFPVGRLDKDTRGLLLLTNNGQLAHDL--LSPKKHVTKEYLAKVAGIMTEADK 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQ 254
           +  A  +  K H                    +H +V+     Q+   +++    G+ HQ
Sbjct: 147 DYFARGISLKDHQCLP----------------AHLEVLASDLQQQTSLVKITIQEGKFHQ 190

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 191 VKRMVAACG 199


>gi|171779942|ref|ZP_02920846.1| hypothetical protein STRINF_01729 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281290|gb|EDT46725.1| hypothetical protein STRINF_01729 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 242

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 84/247 (34%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +  +++++L+  QV V+ +             +   P       I 
Sbjct: 1   MRLDKFLVGAGIG-SRNDVKQLLKKKQVTVNGE-------------IETSPKTQIDEKI- 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              KI+    NL+           YE    Y+ NKP G+     +    H    L     
Sbjct: 46  --DKIVCQGENLS-----------YEKYVYYMLNKPKGVIS---ATEDNHHKTVLDLLDK 89

Query: 139 SKGQK-PRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +   K      RLD +T G+L +    + A   L+     + + K+Y + V GI   +  
Sbjct: 90  TAWDKEVFPVGRLDIDTHGLLFLTNNGKLAHAMLS---PKKHVDKLYRAKVAGIMTAEDV 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                          +   ++  +     A      ID  A K   + +    G+ HQ++
Sbjct: 147 -------------EHFAKGIELKDFTCQPAQLEILEID-EAAKTSLVAITIKEGKFHQVK 192

Query: 257 VHALHMG 263
              L  G
Sbjct: 193 RMVLACG 199


>gi|168487228|ref|ZP_02711736.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC1087-00]
 gi|183569856|gb|EDT90384.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC1087-00]
          Length = 241

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 78/248 (31%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD         I+   +++ L  G + VD    +                        
Sbjct: 1   MRLDNLLAQ--EKISRKAMKQALLKGDILVDGCPARS----------------------- 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILL--YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                L  +++        +  ++  YE + + +  KPAG+           +   L S 
Sbjct: 36  -----LAQNIDTGLQELLFQDRIIQGYEHTYLMLH-KPAGVVTANKDKELPTVMDLLPS- 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            D +  K     RLD++T+G+L++        Q L   + + +  ++             
Sbjct: 89  -DIQSDKLYAVGRLDRDTTGLLLLTDNGPLGFQLLHPQYHVDKTYQVE------------ 135

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
               N LL   HI      +V  +      A      I   +       +    G+ HQ+
Sbjct: 136 ---VNGLLTPDHIQTFQKGIVFLDGTICKPARLE---ILSASPSLSQASITISEGKFHQI 189

Query: 256 RVHALHMG 263
           +   L +G
Sbjct: 190 KKMFLSVG 197


>gi|325130402|gb|EGC53166.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis OX99.30304]
 gi|325204354|gb|ADY99807.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M01-240355]
          Length = 256

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 2   EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 59  ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 94  PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 152 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 209

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 210 VRVGFGPIGLP 220


>gi|315635284|ref|ZP_07890561.1| pseudouridylate synthase [Aggregatibacter segnis ATCC 33393]
 gi|315476030|gb|EFU66785.1| pseudouridylate synthase [Aggregatibacter segnis ATCC 33393]
          Length = 233

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 40/192 (20%), Positives = 77/192 (40%), Gaps = 14/192 (7%)

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K QK    + +      F +S + +  +++ +FNKP  +  Q       +    LK ++D
Sbjct: 14  KPQKWRKPTQSAVHFCGFSRSKIAFSQTQVILFNKPFDVLCQFS---DENGRSTLKDFID 70

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G+L++         L E     +++K YW  V G+P       
Sbjct: 71  I--AEVYPVGRLDRDSEGLLLLTNNGEIQHRLAEPKF--KMEKTYWMQVEGVPDE----T 122

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV---IDCFAQKFCWLEMQPHTGRTHQL 255
           A   L++     D +    +    +       +V    +       WLE++ + GR  Q+
Sbjct: 123 ALEQLRRGVQLKDGMTKPAKVRLISEPDCLWQRVPPIRERKNIPTSWLEIKIYEGRNRQV 182

Query: 256 RVHALHMGCPIV 267
           R    H+G P +
Sbjct: 183 RRMTAHIGFPTL 194


>gi|168186069|ref|ZP_02620704.1| RNA pseudouridine synthase family protein [Clostridium botulinum C
           str. Eklund]
 gi|169295997|gb|EDS78130.1| RNA pseudouridine synthase family protein [Clostridium botulinum C
           str. Eklund]
          Length = 238

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 33/179 (18%), Positives = 66/179 (36%), Gaps = 36/179 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   + +   ++ +++ G++ +D K +K N                      
Sbjct: 2   ERLDKVLSN-LGYGSRKEIKALVKKGEIEIDGKVIKDN---------------------- 38

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                +D + ++ K +      + Y      + NKPAG+     S    + D  +   +D
Sbjct: 39  --GLKVDPNKSIIKVNG---EKINYRKYIYIMMNKPAGVV----SATFDNYDETVIDLLD 89

Query: 139 SKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +     P    RLD++T G+L++         LT       + KIY++ +      K 
Sbjct: 90  YEYTVFDPFPVGRLDKDTEGLLIITNDGELNHRLT--SPKWHVDKIYYAEIDKRVDEKD 146


>gi|330828860|ref|YP_004391812.1| ribosomal large subunit pseudouridine synthase E [Aeromonas veronii
           B565]
 gi|328803996|gb|AEB49195.1| ribosomal large subunit pseudouridine synthase E [Aeromonas veronii
           B565]
          Length = 307

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 39/182 (21%), Positives = 67/182 (36%), Gaps = 9/182 (4%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
           +     +H+   K  L  ED K+ + NKP  +  Q            LK ++   G    
Sbjct: 23  AKPAAPRHASPRKPELAPEDRKLLLLNKPYMVLCQ---FTDEAGRETLKDYIKEPGIYA- 78

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
              RLD+++ G+L++         LT+     +  K YW  V GIP  +K       ++ 
Sbjct: 79  -AGRLDRDSEGLLLLTNDGKLQARLTQPGE--KTPKTYWVQVEGIPSEEKLAALRAGVEL 135

Query: 206 SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
           +            +E          +  +       WLE++   GR  Q+R    H+G P
Sbjct: 136 NDGMTLPAGARIMDEPAVWPRNPPIR--ERKEIPTSWLEIKIIEGRNRQVRRMTAHIGHP 193

Query: 266 IV 267
            +
Sbjct: 194 TL 195


>gi|302874254|ref|YP_003842887.1| pseudouridine synthase [Clostridium cellulovorans 743B]
 gi|307689482|ref|ZP_07631928.1| pseudouridine synthase [Clostridium cellulovorans 743B]
 gi|302577111|gb|ADL51123.1| pseudouridine synthase [Clostridium cellulovorans 743B]
          Length = 241

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 34/251 (13%), Positives = 83/251 (33%), Gaps = 59/251 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSG-QVVRIPPVINALNH 76
            RLD+   N   +     ++ +++ G V ++  + K ++ ++ +   ++++         
Sbjct: 2   ERLDKVLAN-LGYGTRKEVKVLVKKGAVEINGVQAKNSDVKVDTNEDIIKVN-------- 52

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   + Y      + NKPAG+     S    + D  +   
Sbjct: 53  ---------------------GETINYRKFIYLMMNKPAGVV----SATFDNYDETVIDL 87

Query: 137 VDSKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           +D + Q  +P    RLD++T G+L++         L    +    +  Y  +   +    
Sbjct: 88  LDPEEQIFEPFPVGRLDKDTVGLLLLTNDGELNHKLISP-KYHVDKVYYAEIDKPVDDKD 146

Query: 195 KECIANWLLKKS--HIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +C    ++           + ++K  E G+   ++                     G+ 
Sbjct: 147 VKCFEKGIVLDDGYKTMPGKLEILKATEHGSEVYVT------------------IQEGKF 188

Query: 253 HQLRVHALHMG 263
           HQ++     +G
Sbjct: 189 HQVKRMFESLG 199


>gi|28895754|ref|NP_802104.1| 16S pseudouridylate synthase [Streptococcus pyogenes SSI-1]
 gi|50914410|ref|YP_060382.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10394]
 gi|94994587|ref|YP_602685.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10750]
 gi|28811003|dbj|BAC63937.1| putative 16S pseudouridylate synthase [Streptococcus pyogenes
           SSI-1]
 gi|50903484|gb|AAT87199.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10394]
 gi|94548095|gb|ABF38141.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10750]
          Length = 244

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 88/249 (35%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++            ++ +L+   + V+ ++V+ + +            I+    ++
Sbjct: 2   MRLDKFLVATGVG-TRSQVKLLLKKKAIFVN-QKVETSAK----------AHIDEYKDLV 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q                 + L+YE    Y+ NKP+G      S         +   +D
Sbjct: 50  TYQ----------------GTPLVYESFVYYLLNKPSGYV----SATQDRQQATVMELLD 89

Query: 139 --SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KK 195
             ++ +      RLD++T G+L++      A  L      + + K Y + V GI     K
Sbjct: 90  DTARQKTVFPVGRLDKDTRGLLLLTNNGQLAHDL--LSPKKHVTKEYLAKVAGIMTEADK 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQ 254
           +  A  +  K H                    +H +V+     Q+   +++    G+ HQ
Sbjct: 148 DYFARGISLKDHQCLP----------------AHLEVLASDLQQQTSLVKITIQEGKFHQ 191

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 192 VKRMVAACG 200


>gi|209559583|ref|YP_002286055.1| Putative 16S pseudouridylate synthase [Streptococcus pyogenes
           NZ131]
 gi|209540784|gb|ACI61360.1| Putative 16S pseudouridylate synthase [Streptococcus pyogenes
           NZ131]
          Length = 243

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 87/249 (34%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++            ++ +L+   + V+ ++V+ + +            I+    ++
Sbjct: 1   MRLDKFLVATGVG-TRSQVKLLLKKKAIFVN-QKVETSAK----------AHIDEYKDLV 48

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q                 + L+YE    Y+ NKP+G      S         +   +D
Sbjct: 49  TYQ----------------GTPLVYESFVYYLLNKPSGYV----SATQDRQQATVMELLD 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KK 195
              ++       RLD++T G+L++      A  L      + + K Y + V GI     K
Sbjct: 89  DTARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDL--LSPKKHVTKEYLAKVAGIMTEADK 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQ 254
           +  A  +  K H                    +H +V+     Q+   +++    G+ HQ
Sbjct: 147 DYFARGISLKDHQCLP----------------AHLEVLASDLQQQTSLVKITIQEGKFHQ 190

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 191 VKRMVAACG 199


>gi|139439675|ref|ZP_01773088.1| Hypothetical protein COLAER_02116 [Collinsella aerofaciens ATCC
           25986]
 gi|133775016|gb|EBA38836.1| Hypothetical protein COLAER_02116 [Collinsella aerofaciens ATCC
           25986]
          Length = 321

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 39/260 (15%), Positives = 82/260 (31%), Gaps = 58/260 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL R+        +    + ++ +G+V V+          + G  V +           
Sbjct: 30  MRLQRFLARA-GVASRRGSEDLMTAGRVTVNGLVAT-----ELGTKVDV----------- 72

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            ++  ++      K +     ++LY         KP G                L     
Sbjct: 73  -DRDHIEVDGVPVKLNQGAVYLMLY---------KPTGYLTTMSDPQERPCVADLV--PR 120

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---- 194
           ++        RLD++T+G+L+       +Q L      + + K Y +LV G   ++    
Sbjct: 121 NRFPGLFPVGRLDRDTTGLLLFTTDGDLSQDL--LHPSKHVHKTYQALVDGQLTDRDLDQ 178

Query: 195 -------KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                   + +    + +     + V V  Q  K    A+                E+  
Sbjct: 179 LRRGIELDDGLCQPAICRVINAREAVAVAPQGVKPGTTAV----------------EVII 222

Query: 248 HTGRTHQLRVHALHMGCPIV 267
             GR +Q++     +  P++
Sbjct: 223 REGRKNQVKRMLGKIHHPVI 242


>gi|15675276|ref|NP_269450.1| putative 16S pseudouridylate synthase [Streptococcus pyogenes M1
           GAS]
 gi|71910905|ref|YP_282455.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS5005]
 gi|94988765|ref|YP_596866.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS9429]
 gi|94992591|ref|YP_600690.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS2096]
 gi|139473614|ref|YP_001128330.1| ribosomal small subunit pseudouridine synthase B [Streptococcus
           pyogenes str. Manfredo]
 gi|13622451|gb|AAK34171.1| putative 16S pseudouridylate synthase [Streptococcus pyogenes M1
           GAS]
 gi|71853687|gb|AAZ51710.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS5005]
 gi|94542273|gb|ABF32322.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS9429]
 gi|94546099|gb|ABF36146.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS2096]
 gi|134271861|emb|CAM30097.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus pyogenes str. Manfredo]
          Length = 244

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 87/249 (34%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++            ++ +L+   + V+ ++V+ + +            I+    ++
Sbjct: 2   MRLDKFLVATGVG-TRSQVKLLLKKKAIFVN-QKVETSAK----------AHIDEYKDLV 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q                 + L+YE    Y+ NKP+G      S         +   +D
Sbjct: 50  TYQ----------------GTPLVYESFVYYLLNKPSGYV----SATQDRQQATVMELLD 89

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KK 195
              ++       RLD++T G+L++      A  L      + + K Y + V GI     K
Sbjct: 90  DTARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDL--LSPKKHVTKEYLAKVAGIMTEADK 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQ 254
           +  A  +  K H                    +H +V+     Q+   +++    G+ HQ
Sbjct: 148 DYFARGISLKDHQCLP----------------AHLEVLASDLQQQTSLVKITIQEGKFHQ 191

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 192 VKRMVAACG 200


>gi|253996068|ref|YP_003048132.1| pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253982747|gb|ACT47605.1| pseudouridine synthase [Methylotenera mobilis JLW8]
          Length = 374

 Score = 59.2 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 30/228 (13%), Positives = 72/228 (31%), Gaps = 35/228 (15%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            RL +        + +  ++++++ SG+V V+ K  +    +    VVR+          
Sbjct: 37  QRLHKLLA--LAGLGSRRDMEELIASGRVTVNGKVAEVGAGVTEHDVVRLDSR------- 87

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                     + L    +  + ++ ++     V                           
Sbjct: 88  ---------PLRLPFEPELPQVLIYHKPEGEIVSQDDP-----------EGRASVFDKLP 127

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             K  K     RLD  TSG+L+   +   A           +++ Y   ++G     +  
Sbjct: 128 KVKHGKWIAIGRLDMNTSGLLIFTTSGELANRF--MHPRYEVEREYAVRIFGELTEGQIA 185

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
                ++      ++  ++ Q  +GAN+    ++VI    +      +
Sbjct: 186 QLKEGIELEDGPANFDSIIPQGGEGANH---WYQVILREGRNREVRRL 230


>gi|313678967|ref|YP_004056706.1| ribosomal small subunit pseudouridine synthase a [Oceanithermus
           profundus DSM 14977]
 gi|313151682|gb|ADR35533.1| ribosomal small subunit pseudouridine synthase A [Oceanithermus
           profundus DSM 14977]
          Length = 233

 Score = 59.2 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 80/249 (32%), Gaps = 58/249 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
            RLDR    H        + K++R+G VRVD   V+    ++                  
Sbjct: 3   ERLDRVLA-HLGLGTRKEVGKLIRAGAVRVDGAVVRDRGYKL------------------ 43

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                    +  +    + ++    Y      + +KPAG+     S     +   L   +
Sbjct: 44  ------DPEAARIEVRGEPVR----YARHFYVLLHKPAGVLTATRSERETTVLDLLPDAL 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +P    RLD++T G+L++         LT     +  +  +  L   +P++    
Sbjct: 94  WRDDLRP--VGRLDRDTEGLLLLTNHGELLHRLTHPRW-KVAKVYFAELASELPEDAARR 150

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            A  +L                     +A +  + +   A +    E     G+  Q+R 
Sbjct: 151 FAEGVLD--------------------FAPAELEALGPRAARVTLYE-----GKHRQVRR 185

Query: 258 HALHMGCPI 266
               +G P+
Sbjct: 186 MFAALGAPV 194


>gi|166030628|ref|ZP_02233457.1| hypothetical protein DORFOR_00294 [Dorea formicigenerans ATCC
           27755]
 gi|166029630|gb|EDR48387.1| hypothetical protein DORFOR_00294 [Dorea formicigenerans ATCC
           27755]
          Length = 246

 Score = 59.2 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 79/246 (32%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL+++        +     +++ +G+V VD  R     ++   Q + +   +       
Sbjct: 2   IRLNKYLSEA-GVCSRREADRLIEAGRVTVDGVRAVPGMKVSEEQKICVGKKVIQG---- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQK+                        +   NKPAGI   G   +  +I  FL     
Sbjct: 57  AEQKV------------------------VLAVNKPAGIVCTGDMKVKNNIIRFLH---- 88

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G+L++         +  +      +           +  KE  
Sbjct: 89  -YPVRVTYAGRLDKDSEGLLIMTNDGELINSMMRARYHHEKEY--------HVRVDKEIT 139

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           + ++ + S        V  Q+ +    A++  +  +          +    G   Q+R  
Sbjct: 140 SEFVRQMSE------GVHIQDVEKNLDAVT--RPCEVKQIGKYTFSIILTQGLNRQIRRM 191

Query: 259 ALHMGC 264
              +G 
Sbjct: 192 CEALGY 197


>gi|94990658|ref|YP_598758.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10270]
 gi|306827141|ref|ZP_07460432.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes ATCC 10782]
 gi|94544166|gb|ABF34214.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10270]
 gi|304430668|gb|EFM33686.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes ATCC 10782]
          Length = 244

 Score = 59.2 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 87/249 (34%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++            ++ +L+   + V+ ++V+ + +            I+    ++
Sbjct: 2   MRLDKFLVATGVG-TRSQVKLLLKKKAIFVN-QKVETSAK----------AHIDEYKDLV 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q                 + L+YE    Y+ NKP+G      S         +   +D
Sbjct: 50  TYQ----------------GTPLVYESFVYYLLNKPSGYV----SATQDRQQATVMELLD 89

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KK 195
              ++       RLD++T G+L++      A  L      + + K Y + V GI     K
Sbjct: 90  DTARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDL--LSPKKHVTKEYLAKVAGIMTEADK 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQ 254
           +  A  +  K H                    +H +V+     Q+   +++    G+ HQ
Sbjct: 148 DYFARGISLKDHQCLP----------------AHLEVLASDLQQQTSLVKITIQEGKFHQ 191

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 192 VKRMVAACG 200


>gi|52140796|ref|YP_086033.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
 gi|229198871|ref|ZP_04325562.1| Pseudouridine synthase [Bacillus cereus m1293]
 gi|51974265|gb|AAU15815.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
 gi|228584574|gb|EEK42701.1| Pseudouridine synthase [Bacillus cereus m1293]
          Length = 242

 Score = 59.2 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 95/246 (38%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGIPVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K+   G     ++    +    A++  K     +     +E+    G+ HQ++ 
Sbjct: 146 -----VKEFAKG----VILDDGYETKPGALTILK-----SDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|325128449|gb|EGC51330.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis N1568]
          Length = 256

 Score = 59.2 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 2   EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 59  ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 94  PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQI 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 152 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 209

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 210 VRVGFGPIGLP 220


>gi|300741224|ref|ZP_07071245.1| ribosomal large subunit pseudouridine synthase B [Rothia
           dentocariosa M567]
 gi|300380409|gb|EFJ76971.1| ribosomal large subunit pseudouridine synthase B [Rothia
           dentocariosa M567]
          Length = 357

 Score = 59.2 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 51/254 (20%), Positives = 90/254 (35%), Gaps = 51/254 (20%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINA 73
           D + +RL +         +    ++++  G+V V+ + V     R+    V+        
Sbjct: 115 DHDGVRLQK-LMAQAGVASRRVCEEMITEGRVTVNGEVVTELGVRVNPADVI-------- 165

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGF 132
                         V +   +      L+Y       FNKPAG+ S          I  F
Sbjct: 166 --------------VQVDGMTVQTNEKLIY-----MAFNKPAGVVSTMEDPDGRPCIKDF 206

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L+   DS  ++     RLD ET G+L++      A  LT       + K Y   V G  +
Sbjct: 207 LR---DSMNERVFHVGRLDVETEGLLLLTNDGELANRLT--HPSYEVPKTYLVQVRGPVE 261

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                        S IG +    ++   +     +  FK++D  A     +E+  H+G+ 
Sbjct: 262 -------------SGIGAELKKGIRL--EDGVSRVDSFKLVDS-APGHVLIEVTIHSGKN 305

Query: 253 HQLRVHALHMGCPI 266
             +R     +G P+
Sbjct: 306 RIVRRLFEAVGYPV 319


>gi|148997238|ref|ZP_01824892.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP11-BS70]
 gi|168575350|ref|ZP_02721286.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae MLV-016]
 gi|307067298|ref|YP_003876264.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Streptococcus pneumoniae AP200]
 gi|147756938|gb|EDK63978.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP11-BS70]
 gi|183578472|gb|EDT99000.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae MLV-016]
 gi|306408835|gb|ADM84262.1| 16S rRNA uridine-516 pseudouridylate synthase-like pseudouridylate
           synthase [Streptococcus pneumoniae AP200]
          Length = 241

 Score = 59.2 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 78/248 (31%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD         I+   +++ L  G + VD    +                        
Sbjct: 1   MRLDNLLAQ--EKISRKAMKQALLKGDILVDGCPARS----------------------- 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILL--YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                L  +++        +  ++  YE + + +  KPAG+           +   L S 
Sbjct: 36  -----LAQNIDTGLQELLFQDRIIQGYEHTYLMLH-KPAGVVTANKDKELPTVMDLLPS- 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            D +  K     RLD++T+G+L++        Q L   + + +  ++             
Sbjct: 89  -DIQSDKLYAVGRLDRDTTGLLLLTDNGPLGFQLLHPQYHVDKTYQVE------------ 135

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
               N LL   HI      +V  +      A      I   +       +    G+ HQ+
Sbjct: 136 ---VNGLLTPDHIQTFQKGIVFLDGTICKPARLE---ILSASPSLSQASITISEGKFHQI 189

Query: 256 RVHALHMG 263
           +   L +G
Sbjct: 190 KKMFLSVG 197


>gi|325201930|gb|ADY97384.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M01-240149]
          Length = 256

 Score = 59.2 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 2   EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 59  ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 94  PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 152 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 209

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 210 VRVGFGPIGLP 220


>gi|229105336|ref|ZP_04235984.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
 gi|228678093|gb|EEL32322.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
          Length = 242

 Score = 59.2 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 95/246 (38%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGTPVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMLHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K+   G     ++    +    A++  K     +     +E+    G+ HQ++ 
Sbjct: 146 -----VKEFAKG----VILDDGYETKPGALTILK-----SDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|218899863|ref|YP_002448274.1| RNA pseudouridine synthase family protein [Bacillus cereus G9842]
 gi|228910563|ref|ZP_04074377.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228941890|ref|ZP_04104435.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228974817|ref|ZP_04135381.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981409|ref|ZP_04141709.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|218544778|gb|ACK97172.1| RNA pseudouridine synthase family protein [Bacillus cereus G9842]
 gi|228778609|gb|EEM26876.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228784915|gb|EEM32930.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228817795|gb|EEM63875.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228849127|gb|EEM93967.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|326942491|gb|AEA18387.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           thuringiensis serovar chinensis CT-43]
          Length = 242

 Score = 59.2 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 95/246 (38%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGTPVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K+   G     ++    +    A++  K     +     +E+    G+ HQ++ 
Sbjct: 146 -----VKEFAKG----VILDDGYETKPGALTILK-----SDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|149634122|ref|XP_001506727.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 3 [Ornithorhynchus anatinus]
          Length = 258

 Score = 59.2 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/260 (16%), Positives = 87/260 (33%), Gaps = 38/260 (14%)

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           A +++     + D  ++  + +D L+  ++  +  +   NKP G++V G  G    +   
Sbjct: 31  AASYLQASNGLQDEKMSRMELTDVLEEAVVQREGHLVTLNKPQGLAVIGKPGDV-TVHSV 89

Query: 133 LKSWVDSKG--QKPRLTHRLDQETSGILVVARTRAA----AQHLTESFRMRRIQKIYWSL 186
           L       G  Q   +    ++E+SG+++++           +   S R +R    Y ++
Sbjct: 90  LPELSQRLGFDQPLEVVKSAEKESSGLVLLSGCPKTSENLRNYFIWSHRAKRPAVTYRAI 149

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             GIP   +  +   L  +   G  +       ++            D   QK    E  
Sbjct: 150 TVGIPNPFEGEVKTALKLEQKWGEKWFVGTALGQR-------FLLSPDTMPQKQVLDERL 202

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQ 306
            H       R+H       +V       +   +     +  L      +           
Sbjct: 203 LH-------RLHLTQQQMSLV-----PIHLHLHQLLLPKKGLKPGHNVL----------- 239

Query: 307 ITAPLPAHMVKTWDSLGFKY 326
            TAP P   V+T + L  ++
Sbjct: 240 -TAPPPPFFVQTLERLQLRF 258


>gi|188533404|ref|YP_001907201.1| 16S rRNA pseudouridylate synthase A [Erwinia tasmaniensis Et1/99]
 gi|188028446|emb|CAO96308.1| Ribosomal small subunit pseudouridine synthase A [Erwinia
           tasmaniensis Et1/99]
          Length = 234

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/250 (12%), Positives = 73/250 (29%), Gaps = 53/250 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++     + LR+ +V VD + V+  + ++ +   +            
Sbjct: 1   MRLDKFLSQQL-EVSRAIAARELRAKKVTVDGEVVRDGSYKLSADSAIEYDGNALQQQLG 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                             ++ NKP G      S         L    
Sbjct: 60  PR----------------------------YFMLNKPVGYVC---STDDPDHPTILYFLE 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    K     RLD +T+G++++      +  +T          +               
Sbjct: 89  EPSAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------T 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + +   +         +   +     A    +VI+        + +    GR HQ++ 
Sbjct: 136 LESPIGHDTAQQFADGVQLHNEKTLTKPAA--LEVIEPN-----LVRLTISEGRYHQVKR 188

Query: 258 HALHMGCPIV 267
               +G  +V
Sbjct: 189 MFAAVGNRVV 198


>gi|149180996|ref|ZP_01859497.1| tRNA pseudouridine synthase A [Bacillus sp. SG-1]
 gi|148851280|gb|EDL65429.1| tRNA pseudouridine synthase A [Bacillus sp. SG-1]
          Length = 238

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/248 (10%), Positives = 77/248 (31%), Gaps = 60/248 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R++++        +     +++  G+V ++ K+ K  ++++ G  +R+           
Sbjct: 4   LRINKFISEAGK-ASRRGADRLIEEGRVTINGKKAKIGDQVEPGDDIRVSGQQIR----- 57

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  +  ++     NKP GI+      +  +I   +   + 
Sbjct: 58  -----------------------VARNNVYLALNKPVGITSTTEKNVKGNIVDLVNHPL- 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++++         +  +      + I                
Sbjct: 94  ----RVFNIGRLDKDSDGLILLTNDGDIVNEILRAENQHEKEYIVS-------------- 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TGRTHQLR 256
                    I  +++  + +  K     I   K + C  ++    + +     G   Q+R
Sbjct: 136 -----VDKPITPEFLTQMSEGVK-----ILGTKTLPCKVEQLSKFDFKIILTQGLNRQIR 185

Query: 257 VHALHMGC 264
                +G 
Sbjct: 186 RMCEALGY 193


>gi|303286517|ref|XP_003062548.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226456065|gb|EEH53367.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 230

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 81/244 (33%), Gaps = 46/244 (18%)

Query: 27  NHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILD 85
             +    +  N  +++ SG V V+   V     +  G VV +                  
Sbjct: 4   KCFKDFTSRRNADRLVASGAVTVNGAVVAAGAMVFPGDVVELR----------------- 46

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
                          + +E      + KP G++    +    +I   + ++ D+   +  
Sbjct: 47  ------------GERVRWETLNYVKYWKPRGVTCTTDARDRTNIVDAV-NYPDA---RLF 90

Query: 146 LTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-ECIANWLLK 204
              RLD++++G++++  T             R+  K Y  +V  + + +    + + ++ 
Sbjct: 91  PVGRLDKDSTGLILL--TSDGRLPNAALRSGRKRDKKYLVVVDAVVRPEDVRMLRDGVVI 148

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            + +  D V  V         A +     +        LE+    GR  Q+R     +G 
Sbjct: 149 STPVQRDRVDRV-------LTARTL--PCEIDVVGARTLEITLREGRNRQIRRMLDAVGY 199

Query: 265 PIVG 268
            ++ 
Sbjct: 200 RVIN 203


>gi|160872807|ref|ZP_02062939.1| RNA pseudouridine synthase family protein [Rickettsiella grylli]
 gi|159121606|gb|EDP46944.1| RNA pseudouridine synthase family protein [Rickettsiella grylli]
          Length = 245

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/230 (16%), Positives = 72/230 (31%), Gaps = 32/230 (13%)

Query: 23  RWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQK 82
           +    H+   +   +++ +  G+V ++ +  K   RI     V I               
Sbjct: 7   KILA-HFGLGSRREIERWIHDGRVHINGQPAKLGMRIHLKAKVTIDNQR----------- 54

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                + LT +  F + +L+Y        +KP G           H     +     + Q
Sbjct: 55  -----IRLTTNKPFERRVLIY--------HKPLGEIC--SRSDPRHHVTVFEHLPRLRDQ 99

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWL 202
           +  +  RLD  TSG+L+       A  L+      +I++ Y   V G          + L
Sbjct: 100 RWVMIGRLDMNTSGLLIFTNEGEFAYRLS--HPSYQIEREYVVRVLGKVNKSML---DRL 154

Query: 203 LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            K   +             G + A   + V+    +      +    G T
Sbjct: 155 KKGVMLKEKRAAFTSIQASGGSGANRWYHVVLKEGRNREVRRLWETQGVT 204


>gi|182417073|ref|ZP_02948451.1| RNA pseudouridine synthase family protein [Clostridium butyricum
           5521]
 gi|237667148|ref|ZP_04527132.1| RNA pseudouridine synthase family protein [Clostridium butyricum E4
           str. BoNT E BL5262]
 gi|182379082|gb|EDT76586.1| RNA pseudouridine synthase family protein [Clostridium butyricum
           5521]
 gi|237655496|gb|EEP53052.1| RNA pseudouridine synthase family protein [Clostridium butyricum E4
           str. BoNT E BL5262]
          Length = 258

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/257 (15%), Positives = 88/257 (34%), Gaps = 40/257 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++            +++ ++ G V+++   +                   A   I 
Sbjct: 1   MRLDKFLAQSQIG-TRKIVRQYVKDGLVKINGITI-----------------FEAAVEIN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + + I++ +  +T+          Y++   Y+FNKP+G            +  + K    
Sbjct: 43  EIEDIIEYNGQITE----------YKEKVYYMFNKPSGCITARKDADDKTVFDYFKEI-- 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                     RLD++T G+L+          L         +  + +L     KNKK   
Sbjct: 91  -NMDGVFHVGRLDKDTEGLLLFTNDGDFNNKLMSPKFHVDKKYFFIALGSIDEKNKKNLE 149

Query: 199 AN-------WLLKKSHIGGDYVHVVKQNEKGANYAISHFKV-IDCFAQKFCWLEMQPHTG 250
           +         + K + I  +  +   +  K       ++ V  + + Q      +    G
Sbjct: 150 SGVSIGENEPITKPAKIE-NLKNGTYEELKDKLNLKKYYHVNSEYYIQPVVCGHITISEG 208

Query: 251 RTHQLRVHALHMGCPIV 267
           R HQ++     +GC ++
Sbjct: 209 RRHQVKRMLKSIGCHVI 225


>gi|163791560|ref|ZP_02185963.1| hypothetical protein CAT7_05483 [Carnobacterium sp. AT7]
 gi|159873165|gb|EDP67266.1| hypothetical protein CAT7_05483 [Carnobacterium sp. AT7]
          Length = 239

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 66/178 (37%), Gaps = 34/178 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N         ++ +L++ +V V+    K                 +   H+ 
Sbjct: 1   MRLDKLLANMGFG-TRKTVKNVLKAKEVTVNGLVEK-----------------DGKTHVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   ++ S            ++ Y++   ++ +KP G+       +   +   L+    
Sbjct: 43  PETDKIEVS----------GEVIQYQEFMYFMLHKPQGVVSATTDHVHKTVIDLLQ--PQ 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +   P    RLD++T G+L++      A   L+     + + K Y +++ G+   + 
Sbjct: 91  DQVMDPFPVGRLDKDTEGLLILTNDGTLAHNLLS---PKKHVDKCYEAIIEGVVDEQD 145


>gi|89095132|ref|ZP_01168058.1| 16S rRNA uridine-516 pseudouridylate synthase [Oceanospirillum sp.
           MED92]
 gi|89080627|gb|EAR59873.1| 16S rRNA uridine-516 pseudouridylate synthase [Oceanospirillum sp.
           MED92]
          Length = 230

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 84/246 (34%), Gaps = 54/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   +++ +++G+V V+   +K                 +   HI 
Sbjct: 1   MRLDKYLAQS-TGFSRKEVRRFMKAGEVVVNDLEIK-----------------DPALHIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +  S   +    +  K ++L++       N     S              L     
Sbjct: 43  DEDDVYLSGYPVEAPGE--KYLMLHKPLGCVCSNDD---STHPT---------VLSLLDL 88

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            + ++  +  RLD +T+G++++    + A +  +   +  +  ++  +            
Sbjct: 89  PRAEELTICGRLDVDTTGLVLITSNGKWAHKVTSPKHKTGKRYQVTTA---------DPI 139

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             + + K +  G   ++  ++ +      I  ++            E+    GR HQ++ 
Sbjct: 140 PQDAITKFAK-GLMLINEKERTKPAELTIIGEYE-----------AEVVLTEGRYHQVKR 187

Query: 258 HALHMG 263
               +G
Sbjct: 188 MFAAIG 193


>gi|78213141|ref|YP_381920.1| ribosomal large subunit pseudouridine synthase B [Synechococcus sp.
           CC9605]
 gi|78197600|gb|ABB35365.1| Pseudouridine synthase, Rsu [Synechococcus sp. CC9605]
          Length = 250

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 71/249 (28%), Gaps = 48/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++ L++G+V VD +              R+    +     I
Sbjct: 4   QRLQKLIAAA-GLCSRRRAEEWLQAGRVTVDGQVA------------RVGDQADPQQQTI 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                   S  + +               + + NKP G+               L     
Sbjct: 51  HVDGQPLPSPGMAR---------------VLLMNKPVGVICSCDDPQGRR--TVLDLLPP 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                     RLD ++ G L++         LT            W  V G+P       
Sbjct: 94  EHRAGLHPVGRLDADSHGALLLTDLGELTLKLTHPRYSHAKTYRVW--VQGVPSE----- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                    +   +   V  + +    A    + +  +  +   LE++   GR  Q+R  
Sbjct: 147 --------PVLDRWRRGVPLDGRLTRPA--RVRQLRTWGDR-SLLEIELREGRNRQIRRM 195

Query: 259 ALHMGCPIV 267
           A  +G P+V
Sbjct: 196 AEALGYPVV 204


>gi|320540531|ref|ZP_08040181.1| putative 23S rRNA pseudouridylate synthase [Serratia symbiotica
           str. Tucson]
 gi|320029462|gb|EFW11491.1| putative 23S rRNA pseudouridylate synthase [Serratia symbiotica
           str. Tucson]
          Length = 299

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/176 (16%), Positives = 61/176 (34%), Gaps = 29/176 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ ++ +G+V VD K  K  +R++    ++I    + ++    E
Sbjct: 5   LQKVLARA-GHGSRREIEAMIDAGRVSVDGKIAKLGDRVEVNPAMKIRMDGHVVSVKESE 63

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDS 139
           + +                       ++  + KP G +           +   L      
Sbjct: 64  EAVC----------------------RVLAYYKPEGELCTHSDPEGRPTVFDRLPKL--- 98

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +  
Sbjct: 99  RGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPNREVEREYAVRVFGQTDDDS 152


>gi|221234852|ref|YP_002517288.1| ribosomal small subunit pseudouridine synthase A [Caulobacter
           crescentus NA1000]
 gi|220964024|gb|ACL95380.1| ribosomal small subunit pseudouridine synthase A [Caulobacter
           crescentus NA1000]
          Length = 246

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 80/249 (32%), Gaps = 47/249 (18%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR   N   + +   +Q ++  G+V +D   +K      +G  + +   +     +  
Sbjct: 8   RLDRLLAN-LGYGSRKEVQALVAGGKVVLDGAILKD-----AGARIAVDATL--PERMTI 59

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVD 138
               +D    L                 + + +KP G+       G    I   L     
Sbjct: 60  RGAPVDPPAPL-----------------VLIMHKPLGVVCSHKEDGEK--IYDLLPRRWR 100

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++TSG++++         +      R + K Y + +       +  +
Sbjct: 101 LRDPGLSTVGRLDKDTSGLILITDDGDFLHRV--ISPKRHVPKTYLATLDRPLNGSEGEV 158

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                           ++   EK    A     V++  A +    E     GR HQ+R  
Sbjct: 159 FAAGT----------LMLDSEEKPLLPA--RLDVVNAHAARLTITE-----GRYHQVRRM 201

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 202 FAAVGNHVV 210


>gi|163789367|ref|ZP_02183806.1| ribosomal small subunit pseudouridine synthase A [Carnobacterium
           sp. AT7]
 gi|159875221|gb|EDP69286.1| ribosomal small subunit pseudouridine synthase A [Carnobacterium
           sp. AT7]
          Length = 239

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 39/245 (15%), Positives = 90/245 (36%), Gaps = 47/245 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +   ++++L+S QV+V+ + +                ++++LN   
Sbjct: 1   MRLDKLLFETGFG-SRRTVKRLLKSKQVQVNGQTI----------------MVDSLNVDP 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + Q++  + V            + Y+    Y+ +KPAG+       +   +   ++    
Sbjct: 44  QLQEVTVAGVP-----------IDYQPHVYYMLHKPAGVVSAVSDAVNQTVIDLIE--PS 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++T G+L++                + + K Y  +V     N++   
Sbjct: 91  QRVPGLFPVGRLDKDTEGLLLLTNN--GQLGYQLLIPKKEVTKCYEVVV-----NERVTD 143

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L   + I  D   + K  +            I   +     + ++   G+ HQ++  
Sbjct: 144 DDQLAFTAGIVFDGGVICKPAQL----------TILSQSDTESRVLLEISEGKFHQVKKM 193

Query: 259 ALHMG 263
            L +G
Sbjct: 194 FLSVG 198


>gi|71903738|ref|YP_280541.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS6180]
 gi|71802833|gb|AAX72186.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS6180]
          Length = 244

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 87/249 (34%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++            ++ +L+   + V+ ++V+ + +            I+    ++
Sbjct: 2   MRLDKFLVATGVG-TRSQVKLLLKKKAIFVN-QKVETSAK----------AHIDEYKDLV 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q                 + L+YE    Y+ NKP+G      S         +   +D
Sbjct: 50  TYQ----------------GTPLVYESFVYYLLNKPSGYV----SATQDRQQATVMELLD 89

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KK 195
              ++       RLD++T G+L++      A  L      + + K Y + V GI     K
Sbjct: 90  DTARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDL--LSPKKHVTKEYLAKVVGIMTEADK 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQ 254
           +  A  +  K H                    +H +V+     Q+   +++    G+ HQ
Sbjct: 148 DYFARGISLKDHQCLP----------------AHLEVLASDLQQRTSLVKITIQEGKFHQ 191

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 192 VKRMVAACG 200


>gi|309807638|ref|ZP_07701581.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 01V1-a]
 gi|312875457|ref|ZP_07735460.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 2053A-b]
 gi|325911995|ref|ZP_08174397.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners UPII 143-D]
 gi|325912892|ref|ZP_08175270.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners UPII 60-B]
 gi|329921334|ref|ZP_08277772.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners SPIN 1401G]
 gi|308169119|gb|EFO71194.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 01V1-a]
 gi|311088968|gb|EFQ47409.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 2053A-b]
 gi|325476180|gb|EGC79344.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners UPII 143-D]
 gi|325477885|gb|EGC81019.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners UPII 60-B]
 gi|328934626|gb|EGG31130.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners SPIN 1401G]
          Length = 239

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 79/248 (31%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           +RL +         +    + ++ SGQV V+   V     ++     + +          
Sbjct: 3   LRLQKVIAEA-GIASRRKAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVN--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       +  H + L + LLY+   +        +S    +     +  F K   
Sbjct: 53  -----------GVPIHKEQLHTYLLYKPRNV--------VSTVSDNKGRKTVTDFFKDLP 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD +TSG+L++      A  L        I+K+Y + + G     +  
Sbjct: 94  ----YRLYPVGRLDYDTSGLLLMTNDGELANRL--MHPKNEIEKVYVAKISGFLTASEIY 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLR 256
                        D  H V  + +    A +  K+I     +    +++  H G  HQ++
Sbjct: 148 -------------DLKHGVTIDGR--KTAPAKVKIIKTDKNRNIQLVQLTIHEGHYHQVK 192

Query: 257 VHALHMGC 264
                +  
Sbjct: 193 NMFKAVNH 200


>gi|260664647|ref|ZP_05865499.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii SJ-7A-US]
 gi|260561712|gb|EEX27684.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           jensenii SJ-7A-US]
          Length = 234

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 21/144 (14%), Positives = 53/144 (36%), Gaps = 33/144 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MR+D++  N     +   +  ++++ +V +++K VK    ++    +V++          
Sbjct: 1   MRIDKYLANMNVG-SRKEVHNLIKAKKVTINEKLVKQAKQQVTENDMVKVDNQ------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + Y+    ++ NKP G+           +   + S  
Sbjct: 53  ----------------------TITYQQFHYFMLNKPTGVITATEDPQQKTVLDLIAS-- 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVA 161
             +        RLD++T+G+L++ 
Sbjct: 89  KDRYSDLAPVGRLDKDTTGLLLIT 112


>gi|259500661|ref|ZP_05743563.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           iners DSM 13335]
 gi|302191350|ref|ZP_07267604.1| 16S rRNA uridine-516 pseudouridylate synthase related enzyme
           [Lactobacillus iners AB-1]
 gi|312871408|ref|ZP_07731503.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 3008A-a]
 gi|315653504|ref|ZP_07906425.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           iners ATCC 55195]
 gi|259168045|gb|EEW52540.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           iners DSM 13335]
 gi|311093061|gb|EFQ51410.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 3008A-a]
 gi|315489195|gb|EFU78836.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           iners ATCC 55195]
          Length = 239

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 79/248 (31%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           +RL +         +    + ++ SGQV V+   V     ++     + +          
Sbjct: 3   LRLQKVIAEA-GIASRRKAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVN--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       +  H + L + LLY+   +        +S    +     +  F K   
Sbjct: 53  -----------GVPIHKEQLHTYLLYKPRNV--------VSTVSDNKGRKTVTDFFKDLP 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD +TSG+L++      A  L        I+K+Y + + G     +  
Sbjct: 94  ----YRLYPVGRLDYDTSGLLLMTNDGELANRL--MHPKNEIEKVYVAKISGFLTASEIY 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLR 256
                        D  H V  + +    A +  K+I     +    +++  H G  HQ++
Sbjct: 148 -------------DLKHGVTIDGR--KTAPAKVKIIKTDKNRNIQLVQLTIHEGHYHQVK 192

Query: 257 VHALHMGC 264
                +  
Sbjct: 193 NMFKAVNH 200


>gi|290475237|ref|YP_003468123.1| Ribosomal large subunit pseudouridine synthase F [Xenorhabdus
           bovienii SS-2004]
 gi|289174556|emb|CBJ81350.1| Ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) (rRNA pseudouridylate synthase F)
           [Xenorhabdus bovienii SS-2004]
          Length = 290

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/247 (12%), Positives = 69/247 (27%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR    +++ +G +V++   +      
Sbjct: 7   IRLNKYISE--SGICSRRDADRYIEQGNVFINGKRAAVGDQVFAGDIVKVNGQLIEPRDE 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     ED  +   NKP GI          +I  F+    
Sbjct: 65  --------------------------EDLVLIALNKPVGIITTMEDSERDNISDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD+++ G++ +         +  +      + +               
Sbjct: 97  ---SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNNHEKEYV--------------V 139

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             N  +    I G    V           +          +      +    G   Q+R 
Sbjct: 140 TVNKPVTDEFIQGMSAGVPMLGTVTKKCKV--------QKEASFVFRITLVQGLNRQIRR 191

Query: 258 HALHMGC 264
              H G 
Sbjct: 192 MCKHFGY 198


>gi|227357716|ref|ZP_03842065.1| ribosomal small subunit pseudouridine synthase A [Proteus mirabilis
           ATCC 29906]
 gi|227162045|gb|EEI47059.1| ribosomal small subunit pseudouridine synthase A [Proteus mirabilis
           ATCC 29906]
          Length = 244

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 84/249 (33%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + LR+G V +D + VK                      I 
Sbjct: 11  MRLDKFLSQQL-GISRNLVARELRAGLVTIDGEMVK-----------------TGATKIT 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ++      LT+        +L    + ++ NKP G        +   I  F+    +
Sbjct: 53  PEQEVAYDGNVLTQ--------IL--GPRYFMLNKPIGYVCSTDDPVNPTILYFID---E 99

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +            ++ I
Sbjct: 100 PLAHKLHAAGRLDIDTTGLVLLTDNGQWSHRITAPKHHCEKTYVV---------TLEQPI 150

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A  + +K   G       +  +      I+  +V           ++    G+ HQ++  
Sbjct: 151 ATDVAEKFKTGVQLNGEKELTKPATLEVITPTEV-----------KLTISEGKYHQVKRM 199

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 200 FAAVGNHVV 208


>gi|304387322|ref|ZP_07369514.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis ATCC 13091]
 gi|304338573|gb|EFM04691.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis ATCC 13091]
          Length = 350

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 96  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 152

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 153 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 187

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 188 PQAASSRWGAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 245

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 246 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 303

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 304 VRVGFGPIGLP 314


>gi|296129772|ref|YP_003637022.1| pseudouridine synthase [Cellulomonas flavigena DSM 20109]
 gi|296021587|gb|ADG74823.1| pseudouridine synthase [Cellulomonas flavigena DSM 20109]
          Length = 306

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 88/252 (34%), Gaps = 48/252 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D E +RL +   +     +    ++++ +G+V V  + V      + G  VR+ P     
Sbjct: 65  DPEGVRLQKVLASAGLG-SRRACEELIAAGRVTVAGQVVT-----ELG--VRVDPRTAV- 115

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                        ++L      L S ++         NKP G+     +         L 
Sbjct: 116 -------------IHLDGMRVQLDSSVV-----TLALNKPVGVVS---TMHDPEGRPSLA 154

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +V ++ ++     RLD ++ G+L++      A  L        + K Y   V G     
Sbjct: 155 QYVANREERLFHVGRLDADSEGLLLLTNDGELANRLA--HPSHGVPKTYLVEVQG----- 207

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              + + L K+   G +         +     +  FKV+   A     +E+  H GR   
Sbjct: 208 --RVRDALGKQLKEGVEL--------EDGTVRVDEFKVVQ-VASHASLVEVVLHEGRNRV 256

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 257 VRRLFDEVGHPV 268


>gi|218282361|ref|ZP_03488643.1| hypothetical protein EUBIFOR_01225 [Eubacterium biforme DSM 3989]
 gi|218216647|gb|EEC90185.1| hypothetical protein EUBIFOR_01225 [Eubacterium biforme DSM 3989]
          Length = 242

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/253 (16%), Positives = 78/253 (30%), Gaps = 63/253 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
            RL +         +    ++++  G+V+V+ +       ++    ++ +       N I
Sbjct: 2   ERLQKVIAQA-GICSRRKAEELILDGKVKVNGEICDVLGTKVSKQDIIEVN-----GNMI 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            KE+K+                         Y+ NKP G      S         L    
Sbjct: 56  SKEEKV------------------------YYIMNKPKGCLC--TSSDDKGRKTVLDYM- 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             K ++     RLD +TSG+L++        H+        ++K Y   + GI       
Sbjct: 89  -PKNERIFSVGRLDYDTSGVLLLTNDGEFCNHM--IHPRYHLEKTYVVNLQGILSEDD-- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF------AQKFCWLEMQPHTGR 251
                             +KQ  KG       ++    F       +     E+    G+
Sbjct: 144 ------------------IKQLRKGLKTKTEKYQPAKVFVLQKDLTRNRTQFELTISEGK 185

Query: 252 THQLRVHALHMGC 264
            HQ++   L +G 
Sbjct: 186 NHQVKNMMLALGH 198


>gi|30023005|ref|NP_834636.1| putative cytoplasmic protein [Bacillus cereus ATCC 14579]
 gi|217962429|ref|YP_002341001.1| hypothetical protein BCAH187_A5106 [Bacillus cereus AH187]
 gi|228961212|ref|ZP_04122832.1| hypothetical protein bthur0005_46600 [Bacillus thuringiensis
           serovar pakistani str. T13001]
 gi|229049658|ref|ZP_04194215.1| hypothetical protein bcere0027_46160 [Bacillus cereus AH676]
 gi|229112410|ref|ZP_04241948.1| hypothetical protein bcere0018_46500 [Bacillus cereus Rock1-15]
 gi|229130224|ref|ZP_04259183.1| hypothetical protein bcere0015_46600 [Bacillus cereus BDRD-Cer4]
 gi|229141682|ref|ZP_04270212.1| hypothetical protein bcere0013_47720 [Bacillus cereus BDRD-ST26]
 gi|229147514|ref|ZP_04275861.1| hypothetical protein bcere0012_46430 [Bacillus cereus BDRD-ST24]
 gi|29898565|gb|AAP11837.1| hypothetical Cytosolic Protein [Bacillus cereus ATCC 14579]
 gi|217064433|gb|ACJ78683.1| conserved hypothetical protein [Bacillus cereus AH187]
 gi|228635940|gb|EEK92423.1| hypothetical protein bcere0012_46430 [Bacillus cereus BDRD-ST24]
 gi|228641750|gb|EEK98051.1| hypothetical protein bcere0013_47720 [Bacillus cereus BDRD-ST26]
 gi|228653157|gb|EEL09036.1| hypothetical protein bcere0015_46600 [Bacillus cereus BDRD-Cer4]
 gi|228671058|gb|EEL26364.1| hypothetical protein bcere0018_46500 [Bacillus cereus Rock1-15]
 gi|228722571|gb|EEL73959.1| hypothetical protein bcere0027_46160 [Bacillus cereus AH676]
 gi|228798418|gb|EEM45411.1| hypothetical protein bthur0005_46600 [Bacillus thuringiensis
           serovar pakistani str. T13001]
          Length = 165

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RIDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNTILSEGDHISIC 164


>gi|207111256|ref|ZP_03245418.1| hypothetical protein HpylH_19513 [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 58

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 3/58 (5%)

Query: 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
             TGRTHQ+R H  ++   I+GD+ Y  N         + ++ LHA  ++  HP   +
Sbjct: 1   LFTGRTHQIRAHLEYLNRHIIGDNLYGLN---GALPKEEIRIMLHAYLIEFKHPRSEQ 55


>gi|16126081|ref|NP_420645.1| ribosomal small subunit pseudouridine synthase A [Caulobacter
           crescentus CB15]
 gi|13423277|gb|AAK23813.1| ribosomal small subunit pseudouridine synthase A [Caulobacter
           crescentus CB15]
          Length = 241

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 80/249 (32%), Gaps = 47/249 (18%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR   N   + +   +Q ++  G+V +D   +K      +G  + +   +     +  
Sbjct: 3   RLDRLLAN-LGYGSRKEVQALVAGGKVVLDGAILKD-----AGARIAVDATL--PERMTI 54

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVD 138
               +D    L                 + + +KP G+       G    I   L     
Sbjct: 55  RGAPVDPPAPL-----------------VLIMHKPLGVVCSHKEDGEK--IYDLLPRRWR 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++TSG++++         +      R + K Y + +       +  +
Sbjct: 96  LRDPGLSTVGRLDKDTSGLILITDDGDFLHRV--ISPKRHVPKTYLATLDRPLNGSEGEV 153

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                           ++   EK    A     V++  A +    E     GR HQ+R  
Sbjct: 154 FAAGT----------LMLDSEEKPLLPA--RLDVVNAHAARLTITE-----GRYHQVRRM 196

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 197 FAAVGNHVV 205


>gi|318606383|emb|CBY27881.1| ribosomal small subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica Y11]
          Length = 235

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/273 (14%), Positives = 82/273 (30%), Gaps = 58/273 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK      SG +            + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEVVK------SGAI-----------KLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEQDVRFDGNPLQQTVGP----------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +   +         +   +     A    +VI+        + +    GR HQ++  
Sbjct: 137 EQPIADDTAQQFTDGVQLHNEKSLTKPA--QLEVIEPQ-----LVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV-------GDHKYCANFKGNFTSPI 284
               G  ++       GD K   +       P+
Sbjct: 190 FAAAGNRVLELHRERIGDIKLDDDLAPGEYRPL 222


>gi|332161874|ref|YP_004298451.1| 23S rRNA pseudouridylate synthase B [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|318605612|emb|CBY27110.1| ribosomal large subunit pseudouridine synthase B; LSU Psi2605
           [Yersinia enterocolitica subsp. palearctica Y11]
 gi|325666104|gb|ADZ42748.1| 23S rRNA pseudouridylate synthase B [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330860992|emb|CBX71265.1| ribosomal large subunit pseudouridine synthase B [Yersinia
           enterocolitica W22703]
          Length = 349

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/178 (17%), Positives = 61/178 (34%), Gaps = 27/178 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +       H +   ++ I++ G+V VD K  K  +R++  Q  +I    + L+  
Sbjct: 34  GEKLQKILARA-GHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLLSIK 92

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ +                       ++  + KP G                     
Sbjct: 93  ESEEAVC----------------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLP 128

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 129 KLRGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDEK 184


>gi|332162312|ref|YP_004298889.1| 16S rRNA pseudouridylate synthase A [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|325666542|gb|ADZ43186.1| 16S rRNA pseudouridylate synthase A [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859689|emb|CBX70026.1| ribosomal small subunit pseudouridine synthase A [Yersinia
           enterocolitica W22703]
          Length = 235

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/273 (14%), Positives = 83/273 (30%), Gaps = 58/273 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK      SG +            + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEVVK------SGAI-----------KLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEQDVRFDGNPLQQTVGP----------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +   +         +   +     A    +VI+        + +    GR HQ++  
Sbjct: 137 EQPIADDTAQQFTDGVQLHNEKSLTKPA--QLEVIEPQ-----LVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV-------GDHKYCANFKGNFTSPI 284
              +G  ++       GD K   +       P+
Sbjct: 190 FAAVGNRVLELHRERIGDIKLDDDLAPGEYRPL 222


>gi|322514615|ref|ZP_08067646.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           ureae ATCC 25976]
 gi|322119449|gb|EFX91548.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           ureae ATCC 25976]
          Length = 230

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 76/247 (30%), Gaps = 55/247 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRLD++   +   +      K L+SG V V+ K  K  + +I     +            
Sbjct: 1   MRLDKFIAEN-TGLTRSQAGKALKSGLVTVNGKIEKSGSAKISETDEI------------ 47

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E + L+                + E     ++ KP G      S          + + 
Sbjct: 48  CYEGECLE---------------WVDEGQYFMLY-KPQGYVC---SHDDGEYPTVFQFFD 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                K     RLD +T+G++++    + + +  +      +   +  +          +
Sbjct: 89  YPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHRITSPKHHCEKTYLVTLA----------D 138

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + ++ ++K   G       +         I  + V            +    GR HQ++
Sbjct: 139 PVEDFYVEKLAEGILLRGEREPCLPAQMEIIDDYNV-----------NLTISEGRYHQVK 187

Query: 257 VHALHMG 263
                +G
Sbjct: 188 RMFAALG 194


>gi|85703587|ref|ZP_01034691.1| RNA pseudouridylate synthase [Roseovarius sp. 217]
 gi|85672515|gb|EAQ27372.1| RNA pseudouridylate synthase [Roseovarius sp. 217]
          Length = 180

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/162 (22%), Positives = 65/162 (40%), Gaps = 9/162 (5%)

Query: 108 IYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           + +FNKP  +  Q  G G A      L  ++D    +     RLD+++ G+LV+      
Sbjct: 4   LILFNKPYDVLSQFTGRGSADSPRATLSDFID--VPRVYPAGRLDRDSEGLLVLTDDGQL 61

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD-YVHVVKQNEKGANY 225
              +       + +K Y++ V G+P +    +A      +   G      V + E    +
Sbjct: 62  QARIA--NPRFKTEKTYFAQVEGLPDDA--TLAALRQGVTLNDGPTRPARVDRMEPPTLW 117

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             +   V    +   CWL++    GR  Q+R    H+G P +
Sbjct: 118 PRTP-PVRFRKSVPDCWLKLTISEGRNRQVRRMTAHIGHPTL 158


>gi|240948999|ref|ZP_04753353.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           minor NM305]
 gi|240296586|gb|EER47204.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           minor NM305]
          Length = 230

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 76/248 (30%), Gaps = 57/248 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRLD++   +   +      K L+SG V V++K  K  + +I +   +R           
Sbjct: 1   MRLDKFIAEN-TGLTRSQAAKALKSGLVTVNQKVEKSGSVKISAQDEIRYDG-------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       L +  D  +  +LY         KP G      S          + + 
Sbjct: 52  -----------ELLEWMDEGQYFMLY---------KPQGYVC---SHDDGEYPTVFQFFD 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKK 195
                K     RLD +T+G++++      +  +T  +    +         V      + 
Sbjct: 89  YPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHRITSPKHHCEKTYLVTLADPVEDFYAQRF 148

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E     LL+          +               +V+D +       E     GR HQ+
Sbjct: 149 E--EGILLRGEREPCLPAKM---------------EVLDDYNVNLTISE-----GRYHQV 186

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 187 KRMFAALG 194


>gi|220935178|ref|YP_002514077.1| ribosomal large subunit pseudouridine synthase B [Thioalkalivibrio
           sp. HL-EbGR7]
 gi|219996488|gb|ACL73090.1| ribosomal large subunit pseudouridine synthase B [Thioalkalivibrio
           sp. HL-EbGR7]
          Length = 268

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/176 (14%), Positives = 49/176 (27%), Gaps = 31/176 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +       H +   +++ +  G V V+ K     ++      V I   +  L+   
Sbjct: 3   ERLQKLLAR-LGHGSRREIERWIEEGLVTVNGKVASLGDQAGPDDKVAIRGRVVPLDVAP 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K +                          +  ++KP G                 +    
Sbjct: 62  KPR--------------------------VIAYHKPDGELT--TRKDPEGRPTVFEHLPR 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +  +     RLD  TSG+L+       A  L        +++ Y   + G     
Sbjct: 94  LRNGRWIAVGRLDYNTSGLLLFTTDGELAAKL--MHPSGEVEREYAVRILGEVSPD 147


>gi|149374978|ref|ZP_01892751.1| putative pseudouridine synthase [Marinobacter algicola DG893]
 gi|149360867|gb|EDM49318.1| putative pseudouridine synthase [Marinobacter algicola DG893]
          Length = 324

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 23/176 (13%), Positives = 57/176 (32%), Gaps = 29/176 (16%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             R+ +         +   ++  + +G++ ++ K V+   ++     + +          
Sbjct: 22  PERIQKLLARAGVG-SRREVESWIEAGRLSINGKPVEPGQKVTVNDRIDLDGKR------ 74

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                     +++   ++ ++ +L+Y        NKP G                  S  
Sbjct: 75  ----------LDIAAGAEVVRRVLIY--------NKPEGEVT--TRRDPEGRPTVFDSLP 114

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             +  +     RLD  T+G+++       A  L      R+I + Y   V+G    
Sbjct: 115 RLRDHRWIAIGRLDINTTGLVLFTTDGELANRL--MHPSRQIDREYAVRVFGEVDE 168


>gi|184201169|ref|YP_001855376.1| pseudouridine synthase [Kocuria rhizophila DC2201]
 gi|183581399|dbj|BAG29870.1| pseudouridine synthase [Kocuria rhizophila DC2201]
          Length = 368

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 50/252 (19%), Positives = 86/252 (34%), Gaps = 47/252 (18%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           DE  +RL +         +    +++++ G+V VD + V      + G  VR+ P + A 
Sbjct: 126 DENGVRLQK-LMAQAGVASRRVCEEMIQDGRVSVDGEIVT-----ELG--VRVDPALQA- 176

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                        V++          L+Y     Y FNKPAG+                 
Sbjct: 177 -------------VHVDGMRIQTDEKLVY-----YAFNKPAGVVSTMEDPDGRRCVSDFL 218

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                K Q+     RLD ET G+L++         LT       + K Y   V G  +  
Sbjct: 219 D--PRKHQRVFHVGRLDVETEGLLLLTNDGELTNRLT--HPSYEVPKTYLVQVHGPVEKG 274

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                        IG      ++  +  A   +  F+++D        +E+  H+GR   
Sbjct: 275 -------------IGNQMKQGIRLEDGIAK--VDDFRLVDSTP-GHVLIEVVLHSGRNRI 318

Query: 255 LRVHALHMGCPI 266
           +R     +  P+
Sbjct: 319 VRRMFDAVDHPV 330


>gi|229087263|ref|ZP_04219407.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
 gi|228696053|gb|EEL48894.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
          Length = 242

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/244 (17%), Positives = 87/244 (35%), Gaps = 50/244 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK                    +  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGTPVK----------------DAKFHVNV 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               I+ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEIVEYKEFVYLMMHKPQGVISATEDDNHETVVDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + A Q L+     + + K Y++ V GI   K   
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLLTNDGKLAHQLLS---PKKHVPKKYYAHVAGIVTEKDVE 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                            ++    +    A++  K     +     +E+    G+ HQ++ 
Sbjct: 148 EFA-----------KGVILDDGYETKPGALTILK-----SDDVSEIELVITEGKFHQVKR 191

Query: 258 HALH 261
               
Sbjct: 192 MFEA 195


>gi|309804173|ref|ZP_07698251.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 11V1-d]
 gi|308163756|gb|EFO66025.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 11V1-d]
          Length = 239

 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 80/248 (32%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           +RL +         +  N + ++ SGQV V+   V     ++     + +          
Sbjct: 3   LRLQKVIAEA-GIASRRNAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVN--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       +  H + L + LLY+   +        +S    +     +  F K   
Sbjct: 53  -----------GVPIHKEQLHTYLLYKPRNV--------VSTVSDNKGRKTVTDFFKDLP 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD +TSG+L++      A  L        I+K+Y + + G     +  
Sbjct: 94  ----YRLYPVGRLDYDTSGLLLMTNDGELANRL--MHPKNEIEKVYVAKISGFLTASEIY 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLR 256
                        D  H V  + +    A +  K+I     +    +++  H G  HQ++
Sbjct: 148 -------------DLKHGVTIDGR--KTAPAKVKIIKTDKNRNIQLVQLTIHEGHYHQVK 192

Query: 257 VHALHMGC 264
                +  
Sbjct: 193 NMFKAVNH 200


>gi|108804279|ref|YP_644216.1| ribosomal large subunit pseudouridine synthase B [Rubrobacter
           xylanophilus DSM 9941]
 gi|108765522|gb|ABG04404.1| ribosomal large subunit pseudouridine synthase B [Rubrobacter
           xylanophilus DSM 9941]
          Length = 236

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 75/246 (30%), Gaps = 51/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL  +        +    ++++R+G+VRV+ +      R+             + + + 
Sbjct: 4   VRLQAFLARSGAAPSRRKAEEMIRAGRVRVNGRVASLGERV-----------DPSSDRVS 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + + ++                       Y  +KP G                L   + 
Sbjct: 53  LDGRRVEPPSGYA----------------YYALHKPRGYLTTMRDDFGRRTVASLMPRIP 96

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                     RLD++TSG+L++    R A +    +    R++K Y  +V G P  +   
Sbjct: 97  G----LVPVGRLDRDTSGLLLLTNDGRLAHRI---AHPSSRVEKEYELVVRGDPPQEA-- 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                     +         ++       +SH +       +     +  H GR   +R 
Sbjct: 148 ----------LRRLAAGPTLEDGPMLPPRLSHLR----RGPRATTFHLTIHEGRKRIIRR 193

Query: 258 HALHMG 263
                G
Sbjct: 194 ACAATG 199


>gi|82541066|ref|XP_724803.1| hypothetical protein [Plasmodium yoelii yoelii str. 17XNL]
 gi|23479575|gb|EAA16368.1| 1st euk. member [Plasmodium yoelii yoelii]
          Length = 318

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 93/253 (36%), Gaps = 24/253 (9%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL+++      +I+     K +++G ++++ K +     I  G  V I       + I 
Sbjct: 46  IRLNKFIS-INNNISRRKSDKFIQNGNIKINNKTI-----INPGTHVDI-----TKDQIK 94

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              K ++        +++  +   Y+     V +KP G+     +            + +
Sbjct: 95  VNDKKINIQNIKNILNNYNINNNSYK---WIVLHKPKGLIC--TNQDEKDRKSVFSIFPE 149

Query: 139 SKGQKPRLTH--RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              QK R+    RLD+ TSGIL+     A    LT     R ++K    +   +  +  +
Sbjct: 150 DLLQKYRIVSVGRLDRNTSGILLFTNEYAWVNKLTHPKYER-VRKYMIHIEGPVRMDALK 208

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--KFCWLEMQPHTGRTHQ 254
            +AN +        D      +  + A   +   + +    Q  K   L +    GR  Q
Sbjct: 209 MLANGVY---LKDEDNDKKKNKKTQPALIEVLREENVKIQNQIKKISVLNISIKEGRNRQ 265

Query: 255 LRVHALHMGCPIV 267
           +R     +  PI+
Sbjct: 266 IRKMFQQINQPII 278


>gi|293604235|ref|ZP_06686643.1| pseudouridine synthase [Achromobacter piechaudii ATCC 43553]
 gi|292817460|gb|EFF76533.1| pseudouridine synthase [Achromobacter piechaudii ATCC 43553]
          Length = 614

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/190 (15%), Positives = 58/190 (30%), Gaps = 43/190 (22%)

Query: 19  MRLDRWFKN--HYPHI----------NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            RL ++  +    P +          +   +++++ +G+V V+ +      R+     VR
Sbjct: 102 QRLGKYLNSDSVMPKLHKVLADAGIGSRREMEELIVAGRVSVNGEPAHIGQRVAPNDQVR 161

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGI 125
           +        +  K  ++                 +LY        +KPAG I      G 
Sbjct: 162 VNGKPIMRTNTKKPPRV-----------------ILY--------HKPAGEIVSHDDPGG 196

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                         +  K     RLD  T G+L+   +   A  +         ++ Y  
Sbjct: 197 R---ASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSGDMANRI--MHPRYGTEREYAV 251

Query: 186 LVWGIPKNKK 195
            V G     +
Sbjct: 252 RVLGEMDEAQ 261


>gi|212638279|ref|YP_002314799.1| RNA pseudouridine synthase [Anoxybacillus flavithermus WK1]
 gi|212559759|gb|ACJ32814.1| RNA pseudouridine synthase [Anoxybacillus flavithermus WK1]
          Length = 240

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 87/246 (35%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R+D+   N   +     ++K+L++G V+VD   +K                 +A  H+ 
Sbjct: 2   LRIDKLLAN-MGYGTRKEVKKLLKAGVVKVDGTIIK-----------------DAKTHVD 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +++       ++  F+            + NKP G+       +   +   L+   +
Sbjct: 44  PKAQVVTVWGEEVEYKPFI----------YLMMNKPKGVISATEDAVEETVVDLLEE--E 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +   P    RLD++T G+L++      A Q L+     + + KIY +++ G        
Sbjct: 92  DRIFDPFPVGRLDKDTEGLLLLTNDGQLAHQLLS---PKKHVPKIYEAIIDGEVTEDDVV 148

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                            VV  +      A    +++         + +    G+ HQ++ 
Sbjct: 149 ------------AFQRGVVLDDGYETKPA----ELVVIRTGLRSDVRITITEGKFHQIKR 192

Query: 258 HALHMG 263
               +G
Sbjct: 193 MFQAVG 198


>gi|18311246|ref|NP_563180.1| 16S pseudouridylate synthase [Clostridium perfringens str. 13]
 gi|110800371|ref|YP_696936.1| 16S pseudouridylate synthase [Clostridium perfringens ATCC 13124]
 gi|168205092|ref|ZP_02631097.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           E str. JGS1987]
 gi|168216772|ref|ZP_02642397.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           NCTC 8239]
 gi|182625568|ref|ZP_02953339.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           D str. JGS1721]
 gi|18145929|dbj|BAB81970.1| 16S pseudouridylate synthase [Clostridium perfringens str. 13]
 gi|110675018|gb|ABG84005.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           ATCC 13124]
 gi|170663292|gb|EDT15975.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           E str. JGS1987]
 gi|177909256|gb|EDT71721.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           D str. JGS1721]
 gi|182381141|gb|EDT78620.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           NCTC 8239]
          Length = 239

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 85/248 (34%), Gaps = 53/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     ++++++ G V V+ ++VK                        
Sbjct: 2   ERLDKVLSN-LGYGTRKEIKQVVKKGFVTVNDEKVK------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFLK---SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 DS + +    D +      + Y+     + NKPAG+           +   L  
Sbjct: 37  ------DSGLQIDPEKDTIVINGEKVEYKKYIYLMMNKPAGVISATYDKRDETVIDLL-- 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +++ +  +P    RLD++T G+L++         L        + K+Y++          
Sbjct: 89  YMEDQVFEPFPVGRLDKDTVGLLLLTNDGDLNHKL--ISPKYHVDKVYYA---------- 136

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   + +K     +    +   + G     +  KVI+        +E+    G+ HQ+
Sbjct: 137 -EINAPITEKDIKAFENGVTL---DDGYKCMSAKLKVIENLEDS-SRVEVTVQEGKYHQV 191

Query: 256 RVHALHMG 263
           +      G
Sbjct: 192 KRMFEARG 199


>gi|328719931|ref|XP_001942830.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Acyrthosiphon pisum]
          Length = 176

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 26/117 (22%), Positives = 50/117 (42%), Gaps = 5/117 (4%)

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK----SWVDSKGQK-PRLTH 148
           S+ +   ++Y+ +   + NKP  +     +     +D  L+      V+S  +      H
Sbjct: 50  SNNINVEIVYKSNDFIIVNKPEDVFTNNHNKARPSLDVLLRKKYPHLVNSNLEHSFYFVH 109

Query: 149 RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKK 205
           RLD  TSG+L +A  + A    + + + R  +K Y +LV G        + + +  K
Sbjct: 110 RLDFVTSGVLCIALNKRACAKASCAMQKRISRKYYIALVRGHVSQDHLDLTDSIGNK 166


>gi|154507970|ref|ZP_02043612.1| hypothetical protein ACTODO_00456 [Actinomyces odontolyticus ATCC
           17982]
 gi|293190470|ref|ZP_06608857.1| heat shock protein 15 [Actinomyces odontolyticus F0309]
 gi|153797604|gb|EDN80024.1| hypothetical protein ACTODO_00456 [Actinomyces odontolyticus ATCC
           17982]
 gi|292820881|gb|EFF79837.1| heat shock protein 15 [Actinomyces odontolyticus F0309]
          Length = 140

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 23/106 (21%), Positives = 46/106 (43%), Gaps = 12/106 (11%)

Query: 4   MTYV-QYVVVENDE---ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI 59
           M+ + + VV+         +R+D W        +       +R+G VRV+ + VK   ++
Sbjct: 1   MSEIPEEVVIPAGALASSAVRVDTWLWATRQLKSRSQATAAVRAGHVRVNGEPVKAAYKV 60

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYED 105
           + G  VR+         I    +IL  ++ L K   + ++ + Y+D
Sbjct: 61  RVGDEVRL--------RIEGFDRILGVNLLLNKRVSYPQARIAYDD 98


>gi|113460886|ref|YP_718953.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           somnus 129PT]
 gi|112822929|gb|ABI25018.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           somnus 129PT]
          Length = 325

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 58/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI--QSGQVVRIPPVINAL 74
           E  RL +         +   ++ ++ + ++ +D K     +R+   SG  +RI   I   
Sbjct: 43  EGERLQKVLARAGQG-SRRTIEAMISANRISIDGKMATLGDRVDIHSGVKIRIDGHI--- 98

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                        VNLT+    +  +LLY         KP G                  
Sbjct: 99  -------------VNLTQAQKEVCRVLLY--------YKPEGELC--TRHDPEGRATVFD 135

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L        +++ Y   V+G   +
Sbjct: 136 RLPRLNGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPRHEVEREYAVRVFGEVDD 192


>gi|254229618|ref|ZP_04923030.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. Ex25]
 gi|262394552|ref|YP_003286406.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. Ex25]
 gi|151937901|gb|EDN56747.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. Ex25]
 gi|262338146|gb|ACY51941.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. Ex25]
          Length = 233

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 77/246 (31%), Gaps = 52/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++  +           KI++SG + VD +  K    ++  G              +
Sbjct: 1   MRLDKYLCDAL-GATRKQATKIIKSGDITVDGEVQKSGAFKVPEG------------VEV 47

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + E +++ +           + I+LY         KPA        G        L    
Sbjct: 48  MWEDRVIGAPGP--------RYIMLY---------KPADFVCSHEDGYNQTAFALLD--- 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + K +      RLD +T+G++++      +  +T            W +    P   ++ 
Sbjct: 88  EPKIENLHFAGRLDVDTTGLVLITDDGKWSHRITSPKHKCEKTYRVWLVDAIQPDYAEKL 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               +L+                       +    ++   +    + +    G+ HQ++ 
Sbjct: 148 EQGIILRNESEA------------------TLPARLEIVNEAENEVLLTIVEGKYHQVKR 189

Query: 258 HALHMG 263
               +G
Sbjct: 190 MFAALG 195


>gi|116048646|ref|YP_792554.1| putative pseudouridylate synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|115583867|gb|ABJ09882.1| putative pseudouridylate synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
          Length = 230

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 39/243 (16%), Positives = 77/243 (31%), Gaps = 51/243 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+  N  P ++  + Q ++  G++RVD + V+          VR+   +     ++
Sbjct: 1   MRLDRFLAN-LPELSRRDAQMLIAGGRLRVDGQVVRDGTH-----EVRVFSRVELDEQLL 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  K                       ++ Y+ +KP G      +         L    +
Sbjct: 55  QAGKP----------------------ARYYMLHKPMGCVS---ATRDPQHPTVLDLLPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +     +  RLD  T+G++++      ++ LT     R         V       +  +
Sbjct: 90  DQRDDLHIGGRLDYNTTGLMLLTNDGQWSRRLTLPGSRRDKVYY----VETEAPIDQRYV 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +         D + +  Q E                        +  H GR HQ++  
Sbjct: 146 DAFAAGLHFRFEDLITLPAQLEPIGPR----------------CARLTLHEGRYHQVKRM 189

Query: 259 ALH 261
             H
Sbjct: 190 FGH 192


>gi|242239776|ref|YP_002987957.1| 16S rRNA pseudouridylate synthase A [Dickeya dadantii Ech703]
 gi|242131833|gb|ACS86135.1| pseudouridine synthase [Dickeya dadantii Ech703]
          Length = 232

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/248 (14%), Positives = 77/248 (31%), Gaps = 51/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + LR+ +V VD            G V++     N    + 
Sbjct: 1   MRLDKFLSQQL-GISRSLIARELRAQRVTVD------------GDVIK-----NGAFKLA 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E ++      L + +            + ++ +KP G      S         L    +
Sbjct: 43  PEHQVAFDGNPLVQQTGP----------RYFMLHKPQGYVC---STDDPDHPTILYFIDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +TSG++++      +  +T          +                
Sbjct: 90  PVAHKLHAAGRLDIDTSGLVLLTDDGQWSHRITSPKHHCEKTYLVA-------------- 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               L +    G   H     +      ++   V++   ++     +    GR HQ++  
Sbjct: 136 ----LDRPIEPGTAEHFAAGIQLNGEKELTKPAVLEVLDEQ--LARLTISEGRYHQVKRM 189

Query: 259 ALHMGCPI 266
              +G  +
Sbjct: 190 FAAVGNHV 197


>gi|152978349|ref|YP_001343978.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150840072|gb|ABR74043.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 231

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/246 (15%), Positives = 72/246 (29%), Gaps = 53/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHI 77
           MRLD++       +      K +R G V V+    K    ++     +            
Sbjct: 1   MRLDKFIAQQ-TGLTRSQATKSIRQGVVEVNGNMEKSGALKVSPQDEIVF---------- 49

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                            D      L E  + ++ NKP G       G    +  F    +
Sbjct: 50  -----------------DGEPLPWL-EGLQYFMLNKPQGYVCSHEDGDYPTVYQFFDYPL 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                K     RLD +T+G++++                 +      S      K     
Sbjct: 92  AG---KLHTAGRLDADTTGLVLLT-------------DDGQWSHRVTSPKHYCEKTYLVT 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +A+ +        +   +++  ++    A    ++ID +       E     GR HQ++ 
Sbjct: 136 LADPVESNYQSACEQGILLRGEKEATKPA--KLEIIDDYNVNLTITE-----GRYHQVKR 188

Query: 258 HALHMG 263
               +G
Sbjct: 189 MFAALG 194


>gi|110802628|ref|YP_699525.1| 16S pseudouridylate synthase [Clostridium perfringens SM101]
 gi|110683129|gb|ABG86499.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           SM101]
          Length = 239

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 85/248 (34%), Gaps = 53/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     ++++++ G V V+ ++VK                        
Sbjct: 2   ERLDKVLSN-LGYGTRKEIKQVVKKGFVTVNDEKVK------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFLK---SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 DS + +    D +      + Y+     + NKPAG+           +   L  
Sbjct: 37  ------DSGLQIDPEKDTIVINGEKVEYKKYIYLMMNKPAGVISATYDKRDETVIDLL-- 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +++ +  +P    RLD++T G+L++         L        + K+Y++          
Sbjct: 89  YMEDQVFEPFPVGRLDKDTVGLLLLTNDGDLNHKL--ISPKYHVDKVYYA---------- 136

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   + +K     +    +   + G     +  KVI+        +E+    G+ HQ+
Sbjct: 137 -EINAPITEKDIKAFENGVTL---DDGYKCMSAKLKVIENLEDS-SRVEVTVQEGKYHQV 191

Query: 256 RVHALHMG 263
           +      G
Sbjct: 192 KRMFEARG 199


>gi|37679411|ref|NP_934020.1| pseudouridine synthase family 1 protein [Vibrio vulnificus YJ016]
 gi|320156837|ref|YP_004189216.1| ribosomal large subunit pseudouridine synthase B [Vibrio vulnificus
           MO6-24/O]
 gi|37198154|dbj|BAC93991.1| pseudouridine synthase family 1 protein [Vibrio vulnificus YJ016]
 gi|319932149|gb|ADV87013.1| ribosomal large subunit pseudouridine synthase B [Vibrio vulnificus
           MO6-24/O]
          Length = 320

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/235 (17%), Positives = 82/235 (34%), Gaps = 34/235 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ-VVRIPPVINALNH 76
           N +L +       H +   L+ +++SG+V V+    K   R++  Q VVRI   + +   
Sbjct: 2   NEKLQKVLARA-GHGSRRELEALIKSGRVSVNGIVAKLGERLEDEQAVVRIDGHVVS--- 57

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +  +++++                      ++  + KP G                    
Sbjct: 58  VKAQEEVI---------------------CRVLAYYKPEGELC--TRHDPEGRRTVFDRL 94

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +G +     RLD  TSG+L+       A  L      R++++ Y   V+G     K 
Sbjct: 95  PKIRGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVNEHKV 152

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
                 ++       +  VV    +G N+  + + VI+     +     E Q  T
Sbjct: 153 RNLVNGVELDDGLARFEDVVYTGGEGMNH--TFYVVINEGRNREVRRLWESQDCT 205


>gi|239624076|ref|ZP_04667107.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239522107|gb|EEQ61973.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 294

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 74/247 (29%), Gaps = 48/247 (19%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L++W        +     +++ +G+V VD        +++ GQ V               
Sbjct: 36  LNKWLS-QMGVCSRREADRLIEAGKVWVDGSPAAMGQKVKPGQKVVCD------------ 82

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVDS 139
                  VN    +D  K   +     + V NKP GI         A +I  +L      
Sbjct: 83  ----GVPVNGGSGADSRKPKPV-----LLVVNKPRGIVCTTSDKDRAMNIVEYL-----D 128

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             ++     RLD+++ G+L++         +  S      + I               + 
Sbjct: 129 YPERIYPVGRLDKDSEGLLLMTNQGDLVNKIMRSGNAHEKEYIV-------------TVD 175

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L   +         +++ E          KV     + F    +    G   Q+R   
Sbjct: 176 RPLTDDAMDRMAKGIYLRELETVTRPC----KVKRVDGKTFS---IILTQGLNRQIRRMC 228

Query: 260 LHMGCPI 266
              GC +
Sbjct: 229 EACGCHV 235


>gi|149365868|ref|ZP_01887903.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           pestis CA88-4125]
 gi|153947333|ref|YP_001400903.1| 23S rRNA pseudouridylate synthase B [Yersinia pseudotuberculosis IP
           31758]
 gi|229894897|ref|ZP_04510075.1| 23S rRNA pseudouridylate synthase [Yersinia pestis Pestoides A]
 gi|229897640|ref|ZP_04512796.1| 23S rRNA pseudouridylate synthase [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229898285|ref|ZP_04513432.1| 23S rRNA pseudouridylate synthase [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229902144|ref|ZP_04517265.1| 23S rRNA pseudouridylate synthase [Yersinia pestis Nepal516]
 gi|34098644|sp|Q8ZEG0|RLUB_YERPE RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|115347920|emb|CAL20842.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           pestis CO92]
 gi|149292281|gb|EDM42355.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           pestis CA88-4125]
 gi|152958828|gb|ABS46289.1| ribosomal large subunit pseudouridine synthase B [Yersinia
           pseudotuberculosis IP 31758]
 gi|229681040|gb|EEO77135.1| 23S rRNA pseudouridylate synthase [Yersinia pestis Nepal516]
 gi|229688575|gb|EEO80644.1| 23S rRNA pseudouridylate synthase [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229693977|gb|EEO84026.1| 23S rRNA pseudouridylate synthase [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229701992|gb|EEO90013.1| 23S rRNA pseudouridylate synthase [Yersinia pestis Pestoides A]
 gi|320014878|gb|ADV98449.1| 23S rRNA pseudouridylate synthase [Yersinia pestis biovar
           Medievalis str. Harbin 35]
          Length = 318

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/178 (17%), Positives = 60/178 (33%), Gaps = 27/178 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +       H +   ++ I++ G+V VD K  K  +R++  Q  +I    + L+  
Sbjct: 2   GEKLQKILARA-GHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLSIK 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ +                       ++  + KP G                     
Sbjct: 61  ESEENVC----------------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLP 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   + K
Sbjct: 97  KLRGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDDK 152


>gi|123966487|ref|YP_001011568.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. MIT 9515]
 gi|123200853|gb|ABM72461.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. MIT 9515]
          Length = 240

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/245 (13%), Positives = 73/245 (29%), Gaps = 53/245 (21%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R++++      + +     +++  G+V ++ K  +   +++    V +            
Sbjct: 4   RINKYLSE-VGYCSRRVADRLIEEGKVTINGKISEIGTKVKEDDQVEV------------ 50

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E  I+D            K   +Y       FNKP GI       +         ++   
Sbjct: 51  EGIIIDKPT---------KQKYIY-----LAFNKPVGIVCTTDRRVEPDNIIDFINY--- 93

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +     RLD+ + G++ +         +  +      + I                 
Sbjct: 94  -STRIFPIGRLDKNSEGLIFLTNDGDIVNKILRARNNHEKEYIVS--------------- 137

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
                   I  D++H +    K  +    +  V     +KF   ++    G   Q+R   
Sbjct: 138 ----VNRPINRDFIHNMSNGVKILDTITKNCFVKQLGVKKF---KIILTQGLNRQIRRMC 190

Query: 260 LHMGC 264
             +G 
Sbjct: 191 ESLGY 195


>gi|197284712|ref|YP_002150584.1| 16S rRNA pseudouridylate synthase A [Proteus mirabilis HI4320]
 gi|194682199|emb|CAR41885.1| ribosomal small subunit pseudouridine synthase A [Proteus mirabilis
           HI4320]
          Length = 234

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 84/249 (33%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + LR+G V +D + VK                      I 
Sbjct: 1   MRLDKFLSQQL-GISRNLVARELRAGLVTIDGEMVK-----------------TGATKIT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ++      LT+        +L    + ++ NKP G        +   I  F+    +
Sbjct: 43  PEQEVAYDGNVLTQ--------IL--GPRYFMLNKPIGYVCSTDDPVNPTILYFID---E 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +            ++ I
Sbjct: 90  PLAHKLHAAGRLDIDTTGLVLLTDNGQWSHRITAPKHHCEKTYVV---------TLEQPI 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A  + +K   G       +  +      I+  +V           ++    G+ HQ++  
Sbjct: 141 ATDVAEKFKTGVQLNGEKELTKPATLEVITPTEV-----------KLTISEGKYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|183599526|ref|ZP_02961019.1| hypothetical protein PROSTU_03005 [Providencia stuartii ATCC 25827]
 gi|188021773|gb|EDU59813.1| hypothetical protein PROSTU_03005 [Providencia stuartii ATCC 25827]
          Length = 234

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 77/250 (30%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + LR+G+V VD + VK                      + 
Sbjct: 1   MRLDKFLSQQL-GISRSLVARELRAGKVTVDDEIVKS-----------------GAVQVS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ +      L   +            + ++ +KP G      S         L    +
Sbjct: 43  PEQVVAYEGSVLVHVTGP----------RYFMLHKPQGYVC---STDDPAHPTILYFIDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++           +     RI               +  I
Sbjct: 90  PLADKLHSAGRLDIDTTGLVLLT---------DDGQWSHRITSPKHHCEKTYRVELENDI 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+ + K+   G          +      IS  +V+           +    GR HQ++  
Sbjct: 141 ADDVAKRFAEGVMLNGEKYPTKPAQLEVISPKEVL-----------LTISEGRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  + G
Sbjct: 190 FAAVGNHVCG 199


>gi|152993935|ref|YP_001359656.1| RNA pseudouridine synthase [Sulfurovum sp. NBC37-1]
 gi|151425796|dbj|BAF73299.1| RNA pseudouridine synthase [Sulfurovum sp. NBC37-1]
          Length = 281

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/240 (15%), Positives = 82/240 (34%), Gaps = 39/240 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRL+++  +H    +     +++  G+V ++KK ++ F   +Q G  + +       ++ 
Sbjct: 1   MRLNKYIAHHTK-YSRREADRLIEEGEVTLNKKVLRDFAYDVQEGDHIYVKSRPIKPSNE 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I                             + V+NKP G+ V   +         +   +
Sbjct: 60  IT----------------------------VIVYNKPKGVLV---TKKDDRGRATIYHKL 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             K +      RLD  + G+L++  +      L  S   R        +   + +     
Sbjct: 89  PGKFRHFVPVGRLDYASEGLLILTDSVEVVTALMGSDLERTYN---LKIDKPVTQEMVAA 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   L+      G +        + A +A  HF+ I    + +  L +    G+  +LR 
Sbjct: 146 MNEGLVLDDARAGGHEKSKIYGMEFAPFA--HFE-IRSEGKSYTKLRVTITEGKNRELRR 202


>gi|22125944|ref|NP_669367.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis KIM 10]
 gi|45441810|ref|NP_993349.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108807566|ref|YP_651482.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis Antiqua]
 gi|108811842|ref|YP_647609.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis Nepal516]
 gi|145598219|ref|YP_001162295.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis Pestoides F]
 gi|165927423|ref|ZP_02223255.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165938234|ref|ZP_02226793.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166010649|ref|ZP_02231547.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166210657|ref|ZP_02236692.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167400806|ref|ZP_02306312.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167420205|ref|ZP_02311958.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167424996|ref|ZP_02316749.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|167470517|ref|ZP_02335221.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           FV-1]
 gi|218929309|ref|YP_002347184.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis CO92]
 gi|270490618|ref|ZP_06207692.1| pseudouridylate synthase [Yersinia pestis KIM D27]
 gi|294503749|ref|YP_003567811.1| hypothetical protein YPZ3_1639 [Yersinia pestis Z176003]
 gi|21958885|gb|AAM85618.1|AE013808_1 hypothetical protein y2054 [Yersinia pestis KIM 10]
 gi|45436672|gb|AAS62226.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108775490|gb|ABG18009.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           Nepal516]
 gi|108779479|gb|ABG13537.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           Antiqua]
 gi|145209915|gb|ABP39322.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           Pestoides F]
 gi|165913895|gb|EDR32513.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|165920689|gb|EDR37937.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165990351|gb|EDR42652.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166207837|gb|EDR52317.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166961900|gb|EDR57921.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167049659|gb|EDR61067.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167056183|gb|EDR65961.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|262362131|gb|ACY58852.1| hypothetical protein YPD4_1945 [Yersinia pestis D106004]
 gi|270339122|gb|EFA49899.1| pseudouridylate synthase [Yersinia pestis KIM D27]
 gi|294354208|gb|ADE64549.1| hypothetical protein YPZ3_1639 [Yersinia pestis Z176003]
          Length = 344

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/178 (17%), Positives = 60/178 (33%), Gaps = 27/178 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +       H +   ++ I++ G+V VD K  K  +R++  Q  +I    + L+  
Sbjct: 28  GEKLQKILARA-GHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLSIK 86

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ +                       ++  + KP G                     
Sbjct: 87  ESEENVC----------------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLP 122

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   + K
Sbjct: 123 KLRGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDDK 178


>gi|121635067|ref|YP_975312.1| putative pseudouridine synthase [Neisseria meningitidis FAM18]
 gi|120866773|emb|CAM10526.1| putative pseudouridine synthase [Neisseria meningitidis FAM18]
 gi|325138220|gb|EGC60789.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis ES14902]
          Length = 256

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G + V+ K  +  +++     V +   I  L  
Sbjct: 2   EPERLQKVLAASGVG-SRREMEEWITNGWITVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 59  ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 94  PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 152 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 209

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 210 VRVGFGPIGLP 220


>gi|116670095|ref|YP_831028.1| pseudouridine synthase, Rsu [Arthrobacter sp. FB24]
 gi|116610204|gb|ABK02928.1| Pseudouridine synthase, Rsu [Arthrobacter sp. FB24]
          Length = 406

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 53/254 (20%), Positives = 92/254 (36%), Gaps = 49/254 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +RL +   +     +    ++++  G+V VD K V      + G  VR+ P     
Sbjct: 164 DADGIRLQKVMASA-GVASRRVCEEMISEGRVEVDGKVVT-----ELG--VRVDPKTA-- 213

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFL 133
                             H D L+   L E+    VFNKP G+ S          I  F+
Sbjct: 214 ----------------VIHVDGLRIQ-LDENMVYMVFNKPKGVVSTMEDPDGRPCISDFV 256

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           ++   + G++     RLD  T G+L++      A  LT       + K Y   V G    
Sbjct: 257 RN---THGERLFHVGRLDVATEGLLLLTNDGELANRLT--HPSYEVPKTYLVQVRGPFPQ 311

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                         IG      V+   +    ++  FK++D        +E+  H+G+  
Sbjct: 312 G-------------IGAQLKAGVEL--EDGMASVDSFKLVDSTP-GHVLIEVVLHSGKNR 355

Query: 254 QLRVHALHMGCPIV 267
            +R     +G P++
Sbjct: 356 IVRRLFDAVGFPVL 369


>gi|117928443|ref|YP_872994.1| ribosomal large subunit pseudouridine synthase B [Acidothermus
           cellulolyticus 11B]
 gi|117648906|gb|ABK53008.1| ribosomal large subunit pseudouridine synthase B [Acidothermus
           cellulolyticus 11B]
          Length = 269

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 83/253 (32%), Gaps = 50/253 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D+  +RL +         +    ++++ +G+V VD   V            R+   ++  
Sbjct: 28  DDGAVRLQKVLAAAGVG-SRRACEELIAAGRVEVDGVPVT-----------RLGVRVDPQ 75

Query: 75  NHIIK-EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
             +I+ + K +  +                     +  NKP G+             G  
Sbjct: 76  TAVIRVDGKRIPPATPFA----------------YFALNKPRGVVTTMSDPRGRPCVG-- 117

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              V     +     RLD ++ G+L++         LT       + K Y + V G    
Sbjct: 118 -DLVADLPVRVFHVGRLDTDSEGLLLLTNDGRLTHRLT--HPSHAVPKTYVADVEGR--- 171

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                    L ++ +      V   +      A+   ++++ +      +E+  H GRTH
Sbjct: 172 ---------LGRTGVHLLRSGVDLADGPAQADAV---RILERYG-ARTLVEVVVHEGRTH 218

Query: 254 QLRVHALHMGCPI 266
            +R     +G P+
Sbjct: 219 LVRRMLAAVGHPV 231


>gi|319744819|gb|EFV97158.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae ATCC 13813]
          Length = 239

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 82/246 (33%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +  +++K++RS QV VD + V                         
Sbjct: 1   MRLDKLLGQAGFG-SRNHVKKLIRSRQVSVDGQIVT------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K+  I+DSS+         K  +  ++S  Y+  KP+G+        + H          
Sbjct: 36  KDNVIVDSSLQSIFVG---KERVCLKESSYYLLYKPSGVVS--AVRDSEHKTVIDLISEK 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K +      RLD++T G+L++        + L        + K Y+  V G        
Sbjct: 91  DKVEGLYPIGRLDRDTEGLLIITNNGPLGYRMLH---PKHHVAKTYYVEVNGF------- 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                L++  I      VV  +      A      ID          +    G+ HQ++ 
Sbjct: 141 -----LERDAITFFEEGVVFDDGTKCKPAEL---TIDTANNDKSTARITITEGKFHQVKK 192

Query: 258 HALHMG 263
             L  G
Sbjct: 193 MFLAYG 198


>gi|295095390|emb|CBK84480.1| ribosomal large subunit pseudouridine synthase F [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 290

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 71/246 (28%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++  G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVVPGDVVKVNGQVIEPRDA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    ED      NKP GI      G   +I  F+     
Sbjct: 65  -------------------------EDLVFIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++ +         +  +      + I             + +
Sbjct: 97  --SSRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYIV---------TVNKPV 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            +  ++    G   +  V +  K    A   F++                 G   Q+R  
Sbjct: 146 TDEFIRGMGAGVPILGTVTKKCKVRKEAPFAFRI-------------TLVQGLNRQIRRM 192

Query: 259 ALHMGC 264
             + G 
Sbjct: 193 CEYFGY 198


>gi|170760151|ref|YP_001788590.1| RNA pseudouridine synthase family protein [Clostridium botulinum A3
           str. Loch Maree]
 gi|169407140|gb|ACA55551.1| RNA pseudouridine synthase family protein [Clostridium botulinum A3
           str. Loch Maree]
          Length = 238

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 88/243 (36%), Gaps = 47/243 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     ++ +++ GQV VD + VK N        ++I P  N +    
Sbjct: 2   ERLDKILAN-LGYGTRKEVKALIKKGQVDVDGEVVKDNG-------MQIDPEKNKIFVFG 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           KE                    L+Y+     + NKP G+           +   L+   +
Sbjct: 54  KE--------------------LVYKKYIYLIMNKPQGVVSATFDNYDETVVDLLED--E 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD+ T G+L++         L        + KIY++ +     ++    
Sbjct: 92  DRIFEPFPVGRLDKNTVGLLLLTNDGELNHRL--ISPKWHVDKIYYAKINKKVTDED--- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +KK   G     ++  +      A    ++I  F ++   + +  H G+ HQ++  
Sbjct: 147 ----IKKFKKG-----IILDDGYECFPA--KLEIIKSFNEE-SEVRVTIHEGKFHQVKRM 194

Query: 259 ALH 261
              
Sbjct: 195 FES 197


>gi|152977062|ref|YP_001376579.1| pseudouridine synthase [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025814|gb|ABS23584.1| pseudouridine synthase [Bacillus cytotoxicus NVH 391-98]
          Length = 242

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 86/247 (34%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G VR+D K VK                        
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVRIDGKPVKD----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILL-YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                    VN+ K    +   ++ Y++    + +KP G+           +   L+   
Sbjct: 37  -----AKFHVNIEKQEVTIYGEVVEYKEFVYLMMHKPQGVISATEDDHHETVVDLLE--F 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +     P    RLD +T G+L++    +   Q L+     + + K Y++ + G+   K  
Sbjct: 90  EDAIFNPFPVGRLDIDTEGLLLLTNDGKLTHQLLS---PKKHVPKKYYAHIEGVVTEKD- 145

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                   +    G  +    + + G    +         +     +E+    G+ HQ++
Sbjct: 146 -------VEDFAKGVVLDDGYETKPGELTIL--------NSDDISEIELVITEGKFHQVK 190

Query: 257 VHALHMG 263
                +G
Sbjct: 191 RMFEAVG 197


>gi|302392426|ref|YP_003828246.1| ribosomal large subunit pseudouridine synthase B [Acetohalobium
           arabaticum DSM 5501]
 gi|302204503|gb|ADL13181.1| ribosomal large subunit pseudouridine synthase B [Acetohalobium
           arabaticum DSM 5501]
          Length = 244

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 75/235 (31%), Gaps = 48/235 (20%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
            +    + I+ +G+V V+ + V                       +  EQ  +       
Sbjct: 14  ASRRKSEDIITAGRVEVNGEVVT-----------------ELGTKVDPEQDTIKVD---- 52

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                 +  L+Y      + NKP G      +    H    +   +    Q      RLD
Sbjct: 53  -GQQIKREKLVY-----LLLNKPQGYIT---TVDDPHNRRTVIDLIQDVSQAVHPVGRLD 103

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           ++T G+L++         LT       I K Y + V G+P N+ +  A     K   G  
Sbjct: 104 KDTEGLLLLTNDGDLTYALT--HPSHGIDKTYMATVKGVP-NQSKIEALEKGIKLKDGWT 160

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                K   + A  A+               + +  H GR HQ++     +G P+
Sbjct: 161 APAEAKLVAELAERAV---------------VSLTIHEGRKHQVKRMLKSVGHPV 200


>gi|254000317|ref|YP_003052380.1| RNA-binding S4 domain-containing protein [Methylovorus sp. SIP3-4]
 gi|253986996|gb|ACT51853.1| RNA-binding S4 domain protein [Methylovorus sp. SIP3-4]
          Length = 455

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 78/252 (30%), Gaps = 50/252 (19%)

Query: 25  FKNHYPHI---NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
                  +   +     + + +G VRV+ + V                  + L   ++  
Sbjct: 218 LSKRMAELGLCSRREADEWIVNGWVRVNGQVV------------------DELGSRVEPD 259

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-----ISVQGGSGIAYHIDGFLKSW 136
             ++ S    KH   + +ILL++           G     + V   +  A   D   K +
Sbjct: 260 ANIEVSKEAEKHQSEIVTILLHKPVGYVSGQAEDGYEPAVVLVHPDNHWAE--DPVQKEF 317

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                +      RLD +++G+LV+ +    A+ L       + +K Y   V G   ++  
Sbjct: 318 RRGFLKGLAPAGRLDIDSTGLLVLTQDGRVARQL--IGEDSQTEKEYLVRVEGTLSDEGL 375

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              N  L    +      V  QNE                      L      GR  Q+R
Sbjct: 376 RKLNHGLSLDGVQLKPAKVSWQNED--------------------QLRFVLREGRKRQIR 415

Query: 257 VHALHMGCPIVG 268
                +G  +VG
Sbjct: 416 RMCELVGLHVVG 427


>gi|167856142|ref|ZP_02478882.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           parasuis 29755]
 gi|167852738|gb|EDS24012.1| ribosomal small subunit pseudouridine synthase A [Haemophilus
           parasuis 29755]
          Length = 230

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 71/246 (28%), Gaps = 53/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++   +   +      K LR+GQV V+    K +  +I     +            
Sbjct: 1   MRLDKFIAEN-TGLTRSQASKALRAGQVTVNGVVEKNSATKISEQDEICF---------- 49

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                            D      + E     ++ KP         G    +  F     
Sbjct: 50  -----------------DGEPLAWVDEGQYFMLY-KPQNCVCSHDDGDYPTVFQFFDY-- 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                K     RLD +T+G++++      +  +T          +               
Sbjct: 90  -PLTTKLHCAGRLDADTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------T 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +A+ +            +++  +     A    +++D +       E     GR HQ++ 
Sbjct: 136 LADPVEDFYATQFAEGILLRGEKTLTKPAT--LEILDDYNVNLTISE-----GRYHQVKR 188

Query: 258 HALHMG 263
               +G
Sbjct: 189 MFAALG 194


>gi|49081896|gb|AAT50348.1| PA0733 [synthetic construct]
          Length = 231

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 76/243 (31%), Gaps = 51/243 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+  N  P ++  + Q ++  G +RVD + V+          VR+   +     ++
Sbjct: 1   MRLDRFLAN-LPELSRRDAQMLIAGGHLRVDGQVVRDGTH-----EVRVFSRVELDERLL 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  K                       ++ Y+ +KP G      +         L  + +
Sbjct: 55  QAGKP----------------------ARYYMLHKPMGCVS---ATRDPQHPTVLDLFPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                  +  RLD  T+G++++      ++ LT     R         V       +  +
Sbjct: 90  DLRDDLHIGGRLDYNTTGLMLLTNDGQWSRRLTLPGSRRDKVYY----VETEAPIDQRYV 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +         D V +  Q E                        +  H GR HQ++  
Sbjct: 146 DAFAAGLHFRFEDLVTLPAQLEPIGPR----------------CARLTLHEGRYHQVKRM 189

Query: 259 ALH 261
             H
Sbjct: 190 FGH 192


>gi|51596461|ref|YP_070652.1| 23S rRNA pseudouridylate synthase B [Yersinia pseudotuberculosis IP
           32953]
 gi|170024274|ref|YP_001720779.1| 23S rRNA pseudouridylate synthase B [Yersinia pseudotuberculosis
           YPIII]
 gi|186895510|ref|YP_001872622.1| 23S rRNA pseudouridylate synthase B [Yersinia pseudotuberculosis
           PB1/+]
 gi|51589743|emb|CAH21373.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           pseudotuberculosis IP 32953]
 gi|169750808|gb|ACA68326.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186698536|gb|ACC89165.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
          Length = 344

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/178 (17%), Positives = 60/178 (33%), Gaps = 27/178 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +       H +   ++ I++ G+V VD K  K  +R++  Q  +I    + L+  
Sbjct: 28  GEKLQKILARA-GHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLSIK 86

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ +                       ++  + KP G                     
Sbjct: 87  ESEENVC----------------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLP 122

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   + K
Sbjct: 123 KLRGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDDK 178


>gi|219669430|ref|YP_002459865.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
 gi|219539690|gb|ACL21429.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
          Length = 255

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/250 (14%), Positives = 78/250 (31%), Gaps = 50/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
            RL +         +  + ++I+  G+V+V+ + ++    ++ S   + +   + ++   
Sbjct: 14  ERLQKVLAQA-GIASRRHAEEIILQGRVKVNGEVIRTLGTKVVSTDRIVVDGRLLSIPQN 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                      D   Y+ +KP G      S         +   +
Sbjct: 73  ---------------------------DYAYYLLHKPTGYIT---SVTDPQGRKTVMELM 102

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  L         +     +   IP+   + 
Sbjct: 103 PKIPRRVYPVGRLDYDTSGLLLLTNDGDLAHRLMHPSY-GVEKTYRVEVGEKIPEQALKR 161

Query: 198 IANW-LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           +    LL+        +  V    +G+                    E+  H GR  Q+R
Sbjct: 162 LEKGVLLEDGKTAPARIREVSPKGRGSLPT----------------YEITIHEGRNRQVR 205

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 206 RMFKAVGFPL 215


>gi|257465344|ref|ZP_05629715.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           minor 202]
 gi|257451004|gb|EEV25047.1| ribosomal small subunit pseudouridine synthase A [Actinobacillus
           minor 202]
          Length = 230

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 44/276 (15%), Positives = 84/276 (30%), Gaps = 64/276 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRLD++   +   +      K L+SG V V++K  K  + +I +   +R           
Sbjct: 1   MRLDKFIAEN-TGLTRSQAAKALKSGLVTVNQKVEKSGSVKISAQDEIRYDG-------- 51

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       L +  D  +  +LY         KP G      S          + + 
Sbjct: 52  -----------ELLEWMDEGQYFMLY---------KPQGYVC---SHDDGEYPTVFQFFD 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLT--ESFRMRRIQKIYWSLVWGIPKNKK 195
                K     RLD +T+G++++      +  +T  +    +         V      + 
Sbjct: 89  YPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHRITSPKHHCEKTYLVTLADPVEDFYAQRF 148

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E     LL+          +               +V+D +       E     GR HQ+
Sbjct: 149 E--EGILLRGEREPCLPAKM---------------EVLDDYNVNLTISE-----GRYHQV 186

Query: 256 RVHALHMGCPI-------VGDHKYCANFKGNFTSPI 284
           +     +G  +       +GD     + +     P+
Sbjct: 187 KRMFAALGNKVEALHRWRIGDVVLDEDLQEGEFRPL 222


>gi|229175424|ref|ZP_04302937.1| Pseudouridine synthase [Bacillus cereus MM3]
 gi|228608032|gb|EEK65341.1| Pseudouridine synthase [Bacillus cereus MM3]
          Length = 242

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 96/246 (39%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGTPVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFIYLMLHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K+   G     ++    +    A++  K     + +   +E+    G+ HQ++ 
Sbjct: 146 -----VKEFAKG----VILDDGYETKPGALTILK-----SDEISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|168183575|ref|ZP_02618239.1| RNA pseudouridine synthase family protein [Clostridium botulinum
           Bf]
 gi|237796714|ref|YP_002864266.1| RNA pseudouridine synthase family protein [Clostridium botulinum
           Ba4 str. 657]
 gi|182673348|gb|EDT85309.1| RNA pseudouridine synthase family protein [Clostridium botulinum
           Bf]
 gi|229261203|gb|ACQ52236.1| RNA pseudouridine synthase family protein [Clostridium botulinum
           Ba4 str. 657]
          Length = 238

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 88/243 (36%), Gaps = 47/243 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     ++ +++ GQV VD + VK N        ++I P  N +    
Sbjct: 2   ERLDKILAN-LGYGTRKEVKALIKKGQVDVDGEVVKDNG-------MQIDPEKNKIFVFG 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           KE                    L+Y+     + NKP G+           +   L+   +
Sbjct: 54  KE--------------------LVYKKYIYLIMNKPQGVVSATFDNYDETVVDLLED--E 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD+ T G+L++         L        + KIY++ +     ++    
Sbjct: 92  DRIFEPFPVGRLDKNTVGLLLLTNDGELNHRL--ISPKWHVDKIYYAKINKKVTDED--- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +KK   G     ++  +      A    ++I  F ++   + +  H G+ HQ++  
Sbjct: 147 ----IKKFKKG-----IILDDGYECFPA--KLEIIKSFNEE-SEVRVTIHEGKFHQVKRM 194

Query: 259 ALH 261
              
Sbjct: 195 FES 197


>gi|154499812|ref|ZP_02037850.1| hypothetical protein BACCAP_03469 [Bacteroides capillosus ATCC
           29799]
 gi|150271410|gb|EDM98667.1| hypothetical protein BACCAP_03469 [Bacteroides capillosus ATCC
           29799]
          Length = 238

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 82/248 (33%), Gaps = 50/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   +     +   +++++R+G+V  +   V+                        
Sbjct: 2   ERLDKILAST-GRWSRREVKELVRAGRVTANGAVVRS----------------------- 37

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+K     ++L          +L E     + +KPAG+           +   L   + 
Sbjct: 38  PEEKYQREGLDLRVDGQS----VLCERYTYLMLHKPAGLVSATEDPRQATVLELLPEHLR 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             G       RLD++T G+L++    A A  L      + + K Y+  V G        +
Sbjct: 94  KIG--LFPAGRLDRDTEGLLLLTNDGALAHDL--LSPRKHVDKTYFVQVEGQLDQSD--V 147

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +    +   GD +  +              K+++   +      +    G+ HQ++  
Sbjct: 148 EAFQGGMTL--GDGLVCLPAG----------LKLLEAPDEAL----VTLREGKYHQIKRM 191

Query: 259 ALHMGCPI 266
               G P+
Sbjct: 192 LAARGKPV 199


>gi|89895026|ref|YP_518513.1| hypothetical protein DSY2280 [Desulfitobacterium hafniense Y51]
 gi|89334474|dbj|BAE84069.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 257

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/250 (14%), Positives = 78/250 (31%), Gaps = 50/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
            RL +         +  + ++I+  G+V+V+ + ++    ++ S   + +   + ++   
Sbjct: 16  ERLQKVLAQA-GIASRRHAEEIILQGRVKVNGEVIRTLGTKVVSTDRIVVDGRLLSIPQN 74

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                      D   Y+ +KP G      S         +   +
Sbjct: 75  ---------------------------DYAYYLLHKPTGYIT---SVTDPQGRKTVMELM 104

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG+L++      A  L         +     +   IP+   + 
Sbjct: 105 PKIPRRVYPVGRLDYDTSGLLLLTNDGDLAHRLMHPSY-GVEKTYRVEVGEKIPEQALKR 163

Query: 198 IANW-LLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           +    LL+        +  V    +G+                    E+  H GR  Q+R
Sbjct: 164 LEKGVLLEDGKTAPARIREVSPKGRGSLPT----------------YEITIHEGRNRQVR 207

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 208 RMFKAVGFPL 217


>gi|27366329|ref|NP_761857.1| ribosomal large subunit pseudouridine synthase B [Vibrio vulnificus
           CMCP6]
 gi|34098527|sp|Q8D8C0|RLUB_VIBVU RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|27362530|gb|AAO11384.1| Ribosomal large subunit pseudouridine synthase B [Vibrio vulnificus
           CMCP6]
          Length = 320

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/235 (17%), Positives = 82/235 (34%), Gaps = 34/235 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ-VVRIPPVINALNH 76
           N +L +       H +   L+ +++SG+V V+    K   R++  Q VVRI   + +   
Sbjct: 2   NEKLQKVLARA-GHGSRRELEALIKSGRVSVNGIVAKLGERLEDEQAVVRIDGHVVS--- 57

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +  +++++                      ++  + KP G                    
Sbjct: 58  VKAQEEVI---------------------CRVLAYYKPEGELC--TRHDPEGRRTVFDRL 94

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +G +     RLD  TSG+L+       A  L      R++++ Y   V+G     K 
Sbjct: 95  PKIRGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVNEHKV 152

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
                 ++       +  VV    +G N+  + + VI+     +     E Q  T
Sbjct: 153 RNLVNGVELDDGLARFEDVVYTGGEGMNH--TFYVVINEGRNREVRRLWESQDCT 205


>gi|238790412|ref|ZP_04634183.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           frederiksenii ATCC 33641]
 gi|238721519|gb|EEQ13188.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           frederiksenii ATCC 33641]
          Length = 342

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/178 (17%), Positives = 61/178 (34%), Gaps = 27/178 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +       H +   ++ I++ G+V VD K  K  +R++  Q  +I    + L+  
Sbjct: 27  GEKLQKILARA-GHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLLSIK 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ +                       ++  + KP G                     
Sbjct: 86  ESEEAVC----------------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLP 121

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 122 KLRGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDEK 177


>gi|309805712|ref|ZP_07699752.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 09V1-c]
 gi|309809248|ref|ZP_07703117.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners SPIN 2503V10-D]
 gi|312872332|ref|ZP_07732402.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 2062A-h1]
 gi|312873963|ref|ZP_07733999.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 2052A-d]
 gi|308164965|gb|EFO67208.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 09V1-c]
 gi|308170361|gb|EFO72385.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners SPIN 2503V10-D]
 gi|311090512|gb|EFQ48920.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 2052A-d]
 gi|311092155|gb|EFQ50529.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LEAF 2062A-h1]
          Length = 239

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 79/248 (31%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           +RL +         +    + ++ SGQV V+   V     ++     + +          
Sbjct: 3   LRLQKVIAEA-GIASRRKAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVN--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       +  H + L + LLY+   +        +S    +     +  F K   
Sbjct: 53  -----------GVPIHKEQLHTYLLYKPRNV--------VSTVSDNKGRKTVTDFFKDLP 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD +TSG+L++      A  L        I+K+Y + + G     +  
Sbjct: 94  ----YRLYPVGRLDYDTSGLLLMTNDGELANRL--MHPKNEIEKVYVAKIRGFLTASEIY 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLR 256
                        D  H V  + +    A +  K+I     +    +++  H G  HQ++
Sbjct: 148 -------------DLKHGVTIDGR--KTAPAKVKIIKTDKNRNIQLVQLTIHEGHYHQVK 192

Query: 257 VHALHMGC 264
                +  
Sbjct: 193 NMFKAVNH 200


>gi|149175162|ref|ZP_01853785.1| ribosomal large subunit pseudouridine synthase B [Planctomyces
           maris DSM 8797]
 gi|148846140|gb|EDL60480.1| ribosomal large subunit pseudouridine synthase B [Planctomyces
           maris DSM 8797]
          Length = 352

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 89/256 (34%), Gaps = 49/256 (19%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           V+++   +RL ++        +  + ++ + +G+V VD            G V+      
Sbjct: 16  VDDESHLIRLQKFLAATGLG-SRRHCEEYIETGRVSVD------------GDVIT----- 57

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                I  E + ++      +           +  + Y+ NKP+G               
Sbjct: 58  ELGAKIDPETQFIEVDGERVRL----------QPRRYYLLNKPSGFLCTNNDPAGRR--- 104

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +     + GQ+     RLD+ + G+++V      AQ L    R R  +  +  +V   P
Sbjct: 105 RVVDLFPNDGQRLFTVGRLDENSEGLILVTNDGELAQRLAHP-RYRVARTYHVQVVGNPP 163

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           + K + +      +   G   V  +K  +K    A               +LE+  H G+
Sbjct: 164 REKLDELRK--GVRFKEGVFRVSGLKYLKKQGKSA---------------FLELTLHEGQ 206

Query: 252 THQLRVHALHMGCPIV 267
             ++R     +G  ++
Sbjct: 207 NREIRRMMARIGHKVI 222


>gi|228477053|ref|ZP_04061691.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus salivarius SK126]
 gi|228251072|gb|EEK10243.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus salivarius SK126]
          Length = 243

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 78/246 (31%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++  L+  QV V+ +                           
Sbjct: 1   MRLDKFLVDCGVG-SRSQVKTFLKKKQVAVNGQV-----------------------ETS 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I ++   +      L     +E    Y+ NKP G+           +   L     
Sbjct: 37  PKTQIDENQDQIAFQGQVLT----HETFVYYLLNKPQGVISATEDARHKTVLDLLDDTAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G+L++      A   L+     + + KIY + V GI   +   
Sbjct: 93  HK--QVFPVGRLDIDTHGLLLLTNNGDLAHAMLS---PKKHVDKIYQAKVDGIMNQE--- 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                 +K     DY             A      +D  A     +++    G+ HQ++ 
Sbjct: 145 -DILAFEKGIELKDY---------TCQPAKLEIISVDR-ATGTSLVQITIAEGKFHQVKR 193

Query: 258 HALHMG 263
                G
Sbjct: 194 MVAACG 199


>gi|308389478|gb|ADO31798.1| putative pseudouridine synthase [Neisseria meningitidis alpha710]
          Length = 349

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 79/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q  T       +++ Y   V G    ++ 
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFTHPSFE--VEREYAVRVLGGLTGEQM 244

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 245 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 302

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 303 VRVGFGPIGLP 313


>gi|261392364|emb|CAX49904.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B; rRNA pseudouridylate synthase B) [Neisseria
           meningitidis 8013]
          Length = 350

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 96  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 152

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 153 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 187

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 188 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 245

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 246 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 303

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 304 VRVGFGPIGLP 314


>gi|170717435|ref|YP_001784534.1| pseudouridine synthase [Haemophilus somnus 2336]
 gi|168825564|gb|ACA30935.1| pseudouridine synthase [Haemophilus somnus 2336]
          Length = 348

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 58/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRI--QSGQVVRIPPVINAL 74
           E  RL +         +   ++ ++ + ++ +D K     +R+   SG  +RI   I   
Sbjct: 66  EGERLQKVLARVGQG-SRRTIEAMISANRISIDGKMATLGDRVDIHSGVKIRIDGHI--- 121

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                        VNLT+    +  +LLY         KP G                  
Sbjct: 122 -------------VNLTQAQKEVCRVLLY--------YKPEGELC--TRHDPEGRATVFD 158

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L        +++ Y   V+G   +
Sbjct: 159 RLPRLNGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPRHEVEREYAVRVFGEVDD 215


>gi|261329116|emb|CBH12095.1| hypothetical protein, conserved [Trypanosoma brucei gambiense
           DAL972]
          Length = 638

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 17/46 (36%), Positives = 23/46 (50%)

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           D        +   P +GR HQ+R+H    G PIVGD  Y  N +G+
Sbjct: 470 DAGTNTESLVHCVPFSGRMHQIRIHLSDWGHPIVGDVTYNTNERGH 515



 Score = 47.3 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 39/254 (15%), Positives = 72/254 (28%), Gaps = 86/254 (33%)

Query: 21  LDRWFKNHYPHINFV---------NLQKILRSG-QVRVDKKR------------------ 52
           +D +    + H +            LQKI RS   VR +  +                  
Sbjct: 80  VDVY-SEEHVHHSRSYYEACVEKGRLQKISRSRCNVRRNHMKRSHTAGEPSGADASAEDS 138

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
              N  +Q G VV      +           +   +  T     + + +   +  I V +
Sbjct: 139 SNANGPLQHGDVVLHSVHRHE----------IPVRMGATGVEPIVLAAVRICEYGILVVH 188

Query: 113 KPAGISVQGGSG---------------------------------------IAYHIDGFL 133
           KPAG+                                                   D  L
Sbjct: 189 KPAGLPTHASGRYFMNSCTAMLEYVLAPRRLHAWLVEKDPLLQSLVSTIHLTGRERDELL 248

Query: 134 KSWVDSKGQK--------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             ++    ++        PR  HRLD+ TSG+L++  ++ AA+ + E+   +  Q     
Sbjct: 249 AYYLTDSMEEDTVPIERLPRPCHRLDKVTSGVLLLGISKVAARRVGEALMSKTRQMEEIL 308

Query: 186 LVWGIPKNKKECIA 199
                 ++ +  I 
Sbjct: 309 PRRSRFESDEGTIT 322


>gi|72390816|ref|XP_845702.1| hypothetical protein [Trypanosoma brucei TREU927]
 gi|62176177|gb|AAX70294.1| hypothetical protein, conserved [Trypanosoma brucei]
 gi|70802238|gb|AAZ12143.1| hypothetical protein, conserved [Trypanosoma brucei brucei strain
           927/4 GUTat10.1]
          Length = 638

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 17/46 (36%), Positives = 23/46 (50%)

Query: 234 DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN 279
           D        +   P +GR HQ+R+H    G PIVGD  Y  N +G+
Sbjct: 470 DAGTNTESLVHCVPFSGRMHQIRIHLSDWGHPIVGDVTYNTNERGH 515



 Score = 47.3 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 39/254 (15%), Positives = 72/254 (28%), Gaps = 86/254 (33%)

Query: 21  LDRWFKNHYPHINFV---------NLQKILRSG-QVRVDKKR------------------ 52
           +D +    + H +            LQKI RS   VR +  +                  
Sbjct: 80  VDVY-SEEHVHHSRSYYEACVEKGRLQKISRSRCNVRRNHMKRSHTAGEPSGADASAGDS 138

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
              N  +Q G VV      +           +   +  T     + + +   +  I V +
Sbjct: 139 SNANGPLQHGDVVLHSVHRHE----------IPVRMGATGVEPIVLAAVRICEYGILVVH 188

Query: 113 KPAGISVQGGSG---------------------------------------IAYHIDGFL 133
           KPAG+                                                   D  L
Sbjct: 189 KPAGLPTHASGRYFMNSCTAMLEYVLAPRRLHAWLVEKDPLLQSLVSTIHLTGRERDELL 248

Query: 134 KSWVDSKGQK--------PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             ++    ++        PR  HRLD+ TSG+L++  ++ AA+ + E+   +  Q     
Sbjct: 249 AYYLTDSMEEDTVPIERLPRPCHRLDKVTSGVLLLGISKVAARRVGEALMSKTRQMEEIL 308

Query: 186 LVWGIPKNKKECIA 199
                 ++ +  I 
Sbjct: 309 PRRSRFESDEGTIT 322


>gi|229169439|ref|ZP_04297147.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228614044|gb|EEK71161.1| Pseudouridine synthase [Bacillus cereus AH621]
          Length = 248

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 90/247 (36%), Gaps = 50/247 (20%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           NMRLD+   N   H +   ++K+L+ G V++D   VK                    +  
Sbjct: 6   NMRLDKLLAN-MGHGSRKEVKKLLKDGVVKIDGVPVK----------------DAKFHVN 48

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           ++EQ+++               ++ Y++    + +KP G+           +   L+  +
Sbjct: 49  VEEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--L 95

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +     P    RLD +T G L++    +   Q L+     + + K Y++ + G+   +  
Sbjct: 96  EDAIFDPFPVGRLDIDTEGFLLITNDGKLTHQLLS---PKKHVPKKYYAHISGVVTEEDV 152

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                      I      +++   +     ++  K     +     +E+    G+ HQ++
Sbjct: 153 -----------IEFAKGVILEDGYETKPGELTILK-----SDDISEIELVITEGKFHQVK 196

Query: 257 VHALHMG 263
                +G
Sbjct: 197 RMFEAVG 203


>gi|91227384|ref|ZP_01261773.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio alginolyticus
           12G01]
 gi|91188648|gb|EAS74938.1| 23S rRNA ribosomal pseudouridine synthase [Vibrio alginolyticus
           12G01]
          Length = 104

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 12/44 (27%), Positives = 23/44 (52%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQ 45
            + T VQ+V ++ D    R+D + +N    I    + +I+R G+
Sbjct: 57  EIRTKVQFVDIDEDMAGQRIDNFLRNQLKDIPKSMIYRIVRKGR 100


>gi|15595930|ref|NP_249424.1| pseudouridylate synthase [Pseudomonas aeruginosa PAO1]
 gi|34098724|sp|Q9I5J6|RSUA_PSEAE RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|9946618|gb|AAG04122.1|AE004508_7 probable pseudouridylate synthase [Pseudomonas aeruginosa PAO1]
          Length = 230

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 76/243 (31%), Gaps = 51/243 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+  N  P ++  + Q ++  G +RVD + V+          VR+   +     ++
Sbjct: 1   MRLDRFLAN-LPELSRRDAQMLIAGGHLRVDGQVVRDGTH-----EVRVFSRVELDERLL 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  K                       ++ Y+ +KP G      +         L  + +
Sbjct: 55  QAGKP----------------------ARYYMLHKPMGCVS---ATRDPQHPTVLDLFPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                  +  RLD  T+G++++      ++ LT     R         V       +  +
Sbjct: 90  DLRDDLHIGGRLDYNTTGLMLLTNDGQWSRRLTLPGSRRDKVYY----VETEAPIDQRYV 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +         D V +  Q E                        +  H GR HQ++  
Sbjct: 146 DAFAAGLHFRFEDLVTLPAQLEPIGPR----------------CARLTLHEGRYHQVKRM 189

Query: 259 ALH 261
             H
Sbjct: 190 FGH 192


>gi|160935783|ref|ZP_02083158.1| hypothetical protein CLOBOL_00673 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441527|gb|EDP19237.1| hypothetical protein CLOBOL_00673 [Clostridium bolteae ATCC
           BAA-613]
          Length = 251

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 70/247 (28%), Gaps = 51/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL++W        +     +++ +G+V VD +      ++  GQ V     +  ++   
Sbjct: 3   ERLNKWLS-QMGVCSRREADRLIEAGKVLVDNRPASMGQKVTPGQKVVCNGKMVRVDRSQ 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWV 137
           + + +                        +   NKP GI         A +I  FL    
Sbjct: 62  RPRPV------------------------LLAVNKPKGIVCTTTDKDRAENIVDFL---- 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD+++ G+L++         +  S      + I   +    P  ++  
Sbjct: 94  -GYPERIYPVGRLDKDSEGLLLMTNQGDLVNKIMRSGNAHEKEYI---VTIDKPVTERFL 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                  +           K  +   N                    +    G   Q+R 
Sbjct: 150 EQMAGGIRLPELDQVTRPCKVKKVERNT-----------------FSIILTQGLNRQIRR 192

Query: 258 HALHMGC 264
                GC
Sbjct: 193 MCEACGC 199


>gi|269968137|ref|ZP_06182172.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
 gi|269827268|gb|EEZ81567.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
          Length = 233

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 77/246 (31%), Gaps = 52/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++  +           KI++SG + VD +  K    ++  G  V            
Sbjct: 1   MRLDKYLCDAL-GATRKQATKIIKSGDITVDGEVQKSGAFKVPKGAEV------------ 47

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + E +++ +           + I+LY         KPA        G        L    
Sbjct: 48  MWEDRVIGAPGP--------RYIMLY---------KPADFVCSHEDGYNQTAFALLD--- 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + K +      RLD +T+G++++      +  +T            W +    P   ++ 
Sbjct: 88  EPKIENLHFAGRLDVDTTGLVLITDDGKWSHRITSPKHKCEKTYRVWLVDAIQPDYAEKL 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               +L+                       +    ++   +    + +    G+ HQ++ 
Sbjct: 148 EQGIILRNESEA------------------TLPARLEIVNEAENEVLLTIVEGKYHQVKR 189

Query: 258 HALHMG 263
               +G
Sbjct: 190 MFAALG 195


>gi|115376490|ref|ZP_01463724.1| ribosomal large subunit pseudouridine synthase B [Stigmatella
           aurantiaca DW4/3-1]
 gi|310819631|ref|YP_003951989.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115366493|gb|EAU65494.1| ribosomal large subunit pseudouridine synthase B [Stigmatella
           aurantiaca DW4/3-1]
 gi|309392703|gb|ADO70162.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 264

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/258 (15%), Positives = 86/258 (33%), Gaps = 58/258 (22%)

Query: 16  EENMRLDRWFKNHYPH---INFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVI 71
           E + R D W          +     ++ +R G+V+V+ +  ++    ++ G  V +    
Sbjct: 21  EGDERAD-WLARALGRAGVMPQQEAEQAIRDGRVKVEGRLELEPFAPVRLGSNVFVDGWA 79

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID- 130
           + L   +                             + +F+KP G+ V G          
Sbjct: 80  HRLEAPL----------------------------HVLMFHKPEGVIVAGTDPEGRGTVF 111

Query: 131 GFLKSWV--DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
             L++ +  D +  +     RLD++T+G+L+        QH T     + + K Y + V 
Sbjct: 112 ERLRAVLPPDMRNFEWYAVGRLDRDTTGLLLFTNDERVVQHGT--SPDKHLPKRYVAQVA 169

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           G P  +             +      +V ++           +           +E+   
Sbjct: 170 GKPSEE------------TLARLREGIVLEDGPT--------RPAGARLLAPECVELVLT 209

Query: 249 TGRTHQLRVHALHMGCPI 266
            GR HQ++     +G P+
Sbjct: 210 EGRHHQVKRMLAAVGHPV 227


>gi|168213173|ref|ZP_02638798.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           CPE str. F4969]
 gi|170715238|gb|EDT27420.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           CPE str. F4969]
          Length = 239

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 85/248 (34%), Gaps = 53/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     ++++++ G V V+ ++VK                        
Sbjct: 2   ERLDKVLSN-LGYGTRKEIKQVVKKGFVTVNDEKVK------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFLK---SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 DS + +    D +      + Y+     + NKPAG+           +   L  
Sbjct: 37  ------DSGLQIDPEKDTIVINGEKVEYKKYIYLMMNKPAGVISATYDKRDETVIDLL-- 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +++ +  +P    RLD++T G+L++         L        + K+Y++          
Sbjct: 89  YMEDQVFEPFTVGRLDKDTVGLLLLTNDGDLNHKL--ISPKYHVDKVYYA---------- 136

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   + +K     +    +   + G     +  KVI+        +E+    G+ HQ+
Sbjct: 137 -EINAPITEKDIKAFENGVTL---DDGYKCMSAKLKVIENLEDS-SRVEVTVQEGKYHQV 191

Query: 256 RVHALHMG 263
           +      G
Sbjct: 192 KRMFEARG 199


>gi|83314457|ref|XP_730367.1| RNA pseudouridylate synthase [Plasmodium yoelii yoelii str. 17XNL]
 gi|23490071|gb|EAA21932.1| RNA pseudouridylate synthase, putative [Plasmodium yoelii yoelii]
          Length = 745

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 224 NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTS 282
             +++ F  +    +     L  QP TGRTHQ+R H   +  PI  D  Y  NF+  + +
Sbjct: 568 KPSVTKFMFLSYNYKLNESLLLCQPMTGRTHQIRTHLKSLSFPISNDSHYNPNFEKEYMT 627

Query: 283 PIQN 286
             + 
Sbjct: 628 KTEK 631



 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 20/102 (19%), Positives = 41/102 (40%), Gaps = 19/102 (18%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           ++ G ++V+ K +  +  I+S   +           ++ E+ +L           + K I
Sbjct: 71  IKKGYIKVNNKNITNDYIIKSNDFIE-------HKLLLFEKPVL-----------YNKII 112

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
           +LYED      NK A +     GS     +   L++++   G
Sbjct: 113 ILYEDENFICVNKVASMPTHPVGSYQYNSLLRILQNYISQSG 154



 Score = 51.5 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN--KKECIANWL 202
              HRLD+ TSGI++  + +  +   +E     +I K Y + V G  +N  KK  I N +
Sbjct: 349 YTLHRLDKLTSGIVLFGKNKKFSTIFSEYVCDNKITKSYIARVEGDFRNLIKKLIIENKI 408

Query: 203 LKKS 206
           LK  
Sbjct: 409 LKSD 412


>gi|238751905|ref|ZP_04613391.1| Ribosomal large subunit pseudouridine synthase B [Yersinia rohdei
           ATCC 43380]
 gi|238709885|gb|EEQ02117.1| Ribosomal large subunit pseudouridine synthase B [Yersinia rohdei
           ATCC 43380]
          Length = 346

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/178 (17%), Positives = 61/178 (34%), Gaps = 27/178 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +       H +   ++ I++ G+V VD K  K  +R++  Q  +I    + L+  
Sbjct: 31  GEKLQKILARA-GHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLLSIK 89

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ +                       ++  + KP G                     
Sbjct: 90  ESEETVC----------------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLP 125

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 126 KLRGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDEK 181


>gi|188581487|ref|YP_001924932.1| pseudouridine synthase [Methylobacterium populi BJ001]
 gi|179344985|gb|ACB80397.1| pseudouridine synthase [Methylobacterium populi BJ001]
          Length = 242

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 44/260 (16%), Positives = 86/260 (33%), Gaps = 47/260 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLDR   N   + +   ++ + R+G VR D + ++      + Q + + P ++A   + 
Sbjct: 4   VRLDRLLAN-LGYGSRREVEGLARAGLVRRDGEALRD-----ASQRIALEPDLSA--RMT 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +   LD    +         ++L++   +   +K AG            I   L     
Sbjct: 56  VQGAPLDPLPGV--------CLMLHKPLGVTCSHKEAG----------PLIYSLLPERWR 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD+ETSG+L++    A    L      +      + +    P    E  
Sbjct: 98  RRDPALSTVGRLDKETSGLLLMTDDGA---LLHRIIAPKAKVAKRYRVTLARPLQGDEAA 154

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                +    G D   +                 ++   +      +  H GR HQ+R  
Sbjct: 155 ILASGELMLEGEDKPLL----------------PVEMEGEDATHCTVTLHEGRYHQVRRM 198

Query: 259 ALHMGCPIVGDHKYCANFKG 278
              +G  +  D  +     G
Sbjct: 199 FAALGNHV--DALHRDRVGG 216


>gi|254805154|ref|YP_003083375.1| putative pseudouridine synthase [Neisseria meningitidis alpha14]
 gi|254668696|emb|CBA06445.1| putative pseudouridine synthase [Neisseria meningitidis alpha14]
          Length = 349

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 244

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 245 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 302

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 303 VRVGFGPIGLP 313


>gi|119962911|ref|YP_947435.1| RNA pseudouridine synthase [Arthrobacter aurescens TC1]
 gi|119949770|gb|ABM08681.1| putative RNA pseudouridine synthase [Arthrobacter aurescens TC1]
          Length = 404

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 79/252 (31%), Gaps = 45/252 (17%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D + +RL +         +    ++++  G+V VD                 +   ++  
Sbjct: 160 DVDGVRLQKVMAQA-GVASRRVCEEMILEGRVEVDGVVTT-----------ELGMRVDPT 207

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           + +I    I                I L E     VFNKP G+                 
Sbjct: 208 SAVIHVDGI---------------RIQLDETLVYMVFNKPKGVVSTMEDPEGRPCISDFL 252

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               +KG++     RLD  T G+L++      A  LT       + K Y   V G     
Sbjct: 253 KNNKNKGERLFHVGRLDVATEGLLLLTNDGELANRLT--HPSYEVPKTYLVQVRGPFPQG 310

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                     K   G +         +    A+  F+++D        +E+  H+G+   
Sbjct: 311 VGA-------KLKNGVEL--------EDGVAAVDSFRLVDSTP-GHVLIEVVLHSGKNRI 354

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 355 VRRMFDAVGFPV 366


>gi|330685516|gb|EGG97168.1| putative 16S pseudouridylate 516 synthase [Staphylococcus
           epidermidis VCU121]
          Length = 230

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/160 (15%), Positives = 52/160 (32%), Gaps = 35/160 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD++  N         +++ L+ G V+V+ K  K    +I     ++ +         
Sbjct: 1   MRLDKFLANMGIG-TRNEVKQSLKKGYVKVNDKVNKSPKTQINPDEDIITVN-------- 51

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   ++Y D    + NKP+ +           +   +  +
Sbjct: 52  ---------------------GEKIIYIDKVYIMLNKPSDVVSATEDDKHQTVIDLIPEY 90

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM 176
              K        RLD++T G+L++        +L    + 
Sbjct: 91  ---KHLGIFPVGRLDKDTEGLLLITNDGQFNHNLMSPNKH 127


>gi|123441748|ref|YP_001005732.1| 16S rRNA pseudouridylate synthase A [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122088709|emb|CAL11514.1| ribosomal small subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. enterocolitica 8081]
          Length = 235

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 77/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK      SG +            + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEVVK------SGAI-----------KLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEQDVRFDGNPLQQTVGP----------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +   +         +   +     A    +VI+        + +    GR HQ++  
Sbjct: 137 EQPIADDTAQQFTDGVQLHNEKSLTKPA--QLEVIEPQ-----LVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  ++
Sbjct: 190 FAAVGNRVL 198


>gi|121593577|ref|YP_985473.1| ribosomal large subunit pseudouridine synthase B [Acidovorax sp.
           JS42]
 gi|120605657|gb|ABM41397.1| ribosomal large subunit pseudouridine synthase B [Acidovorax sp.
           JS42]
          Length = 447

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/232 (14%), Positives = 71/232 (30%), Gaps = 45/232 (19%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      R+Q G  +++              +I    V    
Sbjct: 136 SRLEMEQLILEGRISVNNEPAHIGQRVQFGDQIKVNGKPIRF-------RIAPPPVR--- 185

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                          +  ++KP G  V        +     +     +  K +   RLD 
Sbjct: 186 ---------------VIAYHKPVGEVV--THDDPQNRPTVFRKLPRLQQGKWQSVGRLDL 228

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L+   +   A  L        +++ Y   V G    ++      LL+   +    
Sbjct: 229 NTEGLLLFTSSGELANKL--MHPRFGLEREYAVRVLGALSTEE---KQRLLEGVPLEDGM 283

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                  + G   A              CW  +    GR  ++R     +G 
Sbjct: 284 ASFGSVEDGGGEGA-------------NCWYRVTISEGRNREVRRMFEAVGH 322


>gi|168211270|ref|ZP_02636895.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           B str. ATCC 3626]
 gi|169347003|ref|ZP_02865945.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           C str. JGS1495]
 gi|169296686|gb|EDS78815.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           C str. JGS1495]
 gi|170710722|gb|EDT22904.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           B str. ATCC 3626]
          Length = 239

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 85/248 (34%), Gaps = 53/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     ++++++ G V V+ ++VK                        
Sbjct: 2   ERLDKVLSN-LGYGTRKEIKQVVKKGFVTVNDEKVK------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFLK---SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 DS + +    D +      + Y+     + NKPAG+           +   L  
Sbjct: 37  ------DSGLQIDPEKDTIVINGEKVEYKKYIYLMMNKPAGVISATYDKRDETVIDLL-- 88

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +++ +  +P    RLD++T G+L++         L        + K+Y++          
Sbjct: 89  YMEDQVFEPFPVGRLDKDTVGLLLLTNDGDLNHKL--ISPKYHVDKVYYA---------- 136

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   + +K     +    +   + G     +  KVI+        +E+    G+ HQ+
Sbjct: 137 -EINAPITEKDIKAFENGVTL---DDGYKCMSAKLKVIENLEDSA-RVEVTVQEGKYHQV 191

Query: 256 RVHALHMG 263
           +      G
Sbjct: 192 KRMFEARG 199


>gi|251790037|ref|YP_003004758.1| 16S rRNA pseudouridylate synthase A [Dickeya zeae Ech1591]
 gi|247538658|gb|ACT07279.1| pseudouridine synthase [Dickeya zeae Ech1591]
          Length = 232

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 78/249 (31%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + LR+ +V VD + +K                 N    ++
Sbjct: 1   MRLDKFLSQQL-GISRSLVARELRAQRVTVDGEVIK-----------------NGAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E ++      L + +            + ++ NKP G      S         L    +
Sbjct: 43  PEHEVAFDDNVLVQQNGP----------RYFMLNKPLGYVC---STDDPDHPTILYFIDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +TSG++++      +  +T          +               +
Sbjct: 90  PVAHKLHAAGRLDIDTSGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L   +             +     +++    ++  ++    + +    GR HQ++  
Sbjct: 137 DQPLAPDTAE-----KFQAGVQLHGEQSLTRPATLEIISEHQ--VRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|226330601|ref|ZP_03806119.1| hypothetical protein PROPEN_04519 [Proteus penneri ATCC 35198]
 gi|225201396|gb|EEG83750.1| hypothetical protein PROPEN_04519 [Proteus penneri ATCC 35198]
          Length = 244

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/258 (16%), Positives = 86/258 (33%), Gaps = 58/258 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + LR+G V +D + VK                      I 
Sbjct: 11  MRLDKFLSQQL-GISRSLILRELRAGLVTIDGEMVKS-----------------GSTKIA 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ++      LT+        +L    + ++ NKP G        +   I  F+    +
Sbjct: 53  PEQEVAYDGKVLTQ--------IL--GPRYFMLNKPIGYVCSTDDPVNPTILYFID---E 99

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +       + +   E +
Sbjct: 100 PLAHKLHAAGRLDIDTTGLVLLTDNGQWSHRITAPKHHCEKTYLVT-----LEEPIGEGV 154

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A    K   + G+        +      ++  +V           ++    G+ HQ++  
Sbjct: 155 AEQFQKGVQLNGEK----DLTKPAKLEILTPTEV-----------KLTISEGKYHQVKRM 199

Query: 259 ALHMGCPI-------VGD 269
              +G  +       +GD
Sbjct: 200 FAAVGNHVSALHRERIGD 217


>gi|210623378|ref|ZP_03293775.1| hypothetical protein CLOHIR_01725 [Clostridium hiranonis DSM 13275]
 gi|210153639|gb|EEA84645.1| hypothetical protein CLOHIR_01725 [Clostridium hiranonis DSM 13275]
          Length = 241

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 85/248 (34%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D+   N   + +   L+K  + G V V+ K V                     N  +
Sbjct: 5   QRVDKVLSN-LGYGSRAELKKFCKQGLVFVNGKAV--------------------SNPGL 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +    +D  V       F    + Y +    + NKP G      S      D  +   +D
Sbjct: 44  QVDTDIDEIV-------FNGEKINYREFIYLMMNKPDGYI----SATFDKHDPIVLDLID 92

Query: 139 SKG--QKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    +P    RLD++T G+LV+      A + L+     + + K Y++ + G    + 
Sbjct: 93  DEYLVFEPFPVGRLDKDTEGLLVLTNDGQLAHRVLS---PKKHVPKTYYAKIDGKVTEED 149

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                       I      VV  +      +    +++   +     +E+  H G+ HQ+
Sbjct: 150 ------------IEAFKQGVVLDDGYETMPS----ELVILKSDDISEIELTIHEGKFHQV 193

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 194 KRMFESVG 201


>gi|188532201|ref|YP_001905998.1| 23S rRNA pseudouridine synthase F [Erwinia tasmaniensis Et1/99]
 gi|188027243|emb|CAO95082.1| Ribosomal large subunit pseudouridine synthase F [Erwinia
           tasmaniensis Et1/99]
          Length = 293

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/165 (15%), Positives = 57/165 (34%), Gaps = 34/165 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR    +R+ +G VV++   +    + 
Sbjct: 7   IRLNKYIGE--SGICSRRDADRYIEQGNVFINGKRASVGDRVLAGDVVKVNGQLIEPRNE 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     ED  +   NKP GI      G   +I  F+    
Sbjct: 65  --------------------------EDLVVIALNKPVGIVSTTEEGERDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  ---SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|15606629|ref|NP_214009.1| hypothetical protein aq_1464 [Aquifex aeolicus VF5]
 gi|3915445|sp|O67444|Y1464_AQUAE RecName: Full=Uncharacterized RNA pseudouridine synthase aq_1464;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2983856|gb|AAC07410.1| hypothetical protein aq_1464 [Aquifex aeolicus VF5]
          Length = 249

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 78/248 (31%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R++++        +    +K++  G+V+V+ + V+                      + 
Sbjct: 4   VRINKFLSEA-GVASRRKAEKLILEGRVKVNGEVVRS-----------------LGVKVN 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  I++      K              +  + NKP     Q G          ++  + 
Sbjct: 46  PEVDIVEVDGKPVKPQR----------KRYIILNKPCCYLTQLGRSPDGRK--TIEELIK 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KE 196
              ++     RLD  T G+L++      A  +       ++ K+Y +LV G    K  K 
Sbjct: 94  DIPERVFPVGRLDYNTEGLLILTNDGELANRI--LHPRYKLPKVYLALVEGKVDQKTLKR 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 L+      D + +V+   K                     LE+  H GR H ++
Sbjct: 152 MKQGIELEDGFAKPDNIRIVRYEGKN------------------TLLEITFHEGRKHLVK 193

Query: 257 VHALHMGC 264
                 G 
Sbjct: 194 RFLGAFGH 201


>gi|121604769|ref|YP_982098.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120593738|gb|ABM37177.1| ribosomal large subunit pseudouridine synthase B [Polaromonas
           naphthalenivorans CJ2]
          Length = 527

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/235 (16%), Positives = 79/235 (33%), Gaps = 51/235 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      RIQ G  V++                         
Sbjct: 109 SRLEMEQLILEGRISVNAEPAHIGQRIQFGDTVKVN------------------------ 144

Query: 93  HSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
               ++  +     ++  ++KPAG +           +   L      K Q      RLD
Sbjct: 145 -GKPIRVQIDPPPPRVIAYHKPAGEVVTHDDPQNRPTVFRRLPKLFQGKWQS---VGRLD 200

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             T G+L++  +   A  L        +++ Y   V G   N++        KK  + G 
Sbjct: 201 LNTEGLLLLTSSGELANKL--MHPRFGLEREYAVRVLGALNNEE--------KKRLLDG- 249

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGC 264
              V   +       ++ F  I+    +   CW  +    GR  ++R     +G 
Sbjct: 250 ---VTLDDG------VAQFGSIEAGGGEGANCWYRVTISEGRNREVRRMFEAVGH 295


>gi|183599733|ref|ZP_02961226.1| hypothetical protein PROSTU_03236 [Providencia stuartii ATCC 25827]
 gi|188021992|gb|EDU60032.1| hypothetical protein PROSTU_03236 [Providencia stuartii ATCC 25827]
          Length = 291

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 77/246 (31%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +  +  + +  G V ++ KR    +++ SG VV++   +    +  
Sbjct: 8   RLNKYISE--SGICSRRDADRYIEQGNVFINGKRAAIGDQVFSGDVVKVNGQLIEPRNE- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    ED  +   NKP GI     SG   +I  ++     
Sbjct: 65  -------------------------EDLVLIALNKPVGIVSTTESGERDNIVDYVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD+++ G++ +         +  +      + +             + I
Sbjct: 97  --SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNEHEKEYLV---------TVNKPI 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            +  ++    G   +  V +  K    A   F++                 G   Q+R  
Sbjct: 146 TDDFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLVQGLNRQIRRM 192

Query: 259 ALHMGC 264
             + G 
Sbjct: 193 CEYFGF 198


>gi|168179079|ref|ZP_02613743.1| RNA pseudouridine synthase family protein [Clostridium botulinum
           NCTC 2916]
 gi|226950699|ref|YP_002805790.1| RNA pseudouridine synthase family protein [Clostridium botulinum A2
           str. Kyoto]
 gi|182669965|gb|EDT81941.1| RNA pseudouridine synthase family protein [Clostridium botulinum
           NCTC 2916]
 gi|226843144|gb|ACO85810.1| RNA pseudouridine synthase family protein [Clostridium botulinum A2
           str. Kyoto]
          Length = 238

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 87/243 (35%), Gaps = 47/243 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     ++ +++ GQV VD + VK N        ++I P  N +    
Sbjct: 2   ERLDKILAN-LGYGTRKEVKALIKKGQVDVDGEVVKDNG-------MQIDPEKNKIFVFG 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           KE                    L+Y+     + NKP G+           +   L+   +
Sbjct: 54  KE--------------------LVYKKYIYLMMNKPQGVVSATFDNYDETVIDLLED--E 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD+ T G+L+          L        + KIY++ +     ++    
Sbjct: 92  DRIFEPFPVGRLDKNTVGLLLFTNDGELNHRL--ISPKWHVDKIYYAKINKKVTDED--- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +KK   G     ++  +      A    ++I  F ++   + +  H G+ HQ++  
Sbjct: 147 ----IKKFKKG-----IILDDGYECFPA--KLEIIKSFNEE-SEVRVTIHEGKFHQVKRM 194

Query: 259 ALH 261
              
Sbjct: 195 FES 197


>gi|110679964|ref|YP_682971.1| RNA pseudouridylate synthase [Roseobacter denitrificans OCh 114]
 gi|109456080|gb|ABG32285.1| RNA pseudouridylate synthase [Roseobacter denitrificans OCh 114]
          Length = 187

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/161 (20%), Positives = 60/161 (37%), Gaps = 6/161 (3%)

Query: 108 IYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           + +FNKP G+  Q    G        L +++D+ G  P    RLD+++ G++V+      
Sbjct: 4   VILFNKPFGVLSQFTDKGSEGSPRPTLSAFIDAPGFYP--AGRLDRDSEGLMVLTDDGKL 61

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
              ++      ++ K Y + + G P+ +    A     +   G      V          
Sbjct: 62  QARIS--NPKHKMTKTYLAQIEGTPEPQH-IEALRAGVRLKDGMTRPAQVSVATPPDTLW 118

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                V         WL++    GR  Q+R    H+G P +
Sbjct: 119 ERSPPVRFRKTVPDAWLQISISEGRNRQVRRMCAHVGLPCL 159


>gi|269978223|ref|ZP_06185173.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           mulieris 28-1]
 gi|306818599|ref|ZP_07452322.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           mulieris ATCC 35239]
 gi|269933732|gb|EEZ90316.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           mulieris 28-1]
 gi|304648772|gb|EFM46074.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           mulieris ATCC 35239]
          Length = 278

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/256 (15%), Positives = 81/256 (31%), Gaps = 51/256 (19%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           VE  EE +RL +         +    + +++ G+V+VD + V     ++     + +   
Sbjct: 35  VEIPEEPVRLQKLLSQA-GVASRRASEDLIKRGRVQVDGETVTEMGLKVLPSARITVNGQ 93

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
               +  ++                            ++ FNKP G              
Sbjct: 94  RIHTDAALQ----------------------------VWAFNKPVGTVSTMQPEDDRPCL 125

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G    W     Q+     RLD  TSG++++      A  L        + K Y ++V G 
Sbjct: 126 G---DWATKLPQRVFHVGRLDVATSGLILLTNNGDLANRL--VHPRYEVPKTYVAMVQGQ 180

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K                    V       +     +  FK+++   +    +++  H+G
Sbjct: 181 VKPGLG---------------KVLRRGVELEDGVTKVDTFKLVEVR-RGSSIVQLTLHSG 224

Query: 251 RTHQLRVHALHMGCPI 266
           +   +R     +G P+
Sbjct: 225 KNRVVRRLLSEVGHPV 240


>gi|229088058|ref|ZP_04220113.1| hypothetical protein bcere0022_45680 [Bacillus cereus Rock3-44]
 gi|228695260|gb|EEL48190.1| hypothetical protein bcere0022_45680 [Bacillus cereus Rock3-44]
          Length = 166

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 12/74 (16%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 1   MSLMTYVQY------VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK 54
           +S+M Y +       +++E    + R+D+    +    +   + + ++ G ++++ K++K
Sbjct: 92  ISIMQYKEIGTTELNIILETVLGSHRMDKALAAYISDWSRTAIVERIKIGHIQLNGKQMK 151

Query: 55  FNNRIQSGQVVRIP 68
            N  +  G ++ I 
Sbjct: 152 PNTTLSEGDLISIC 165


>gi|319425419|gb|ADV53493.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 236

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 86/249 (34%), Gaps = 52/249 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+       +    ++ +L SG+V+VD + VK            +   ++  +HI  
Sbjct: 7   RLDRYLSAKM-QMPRKLVRDLLLSGRVQVDGQIVK-----------EMDRQVDEFSHIQL 54

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + ++L ++  +                   + +KP G+           +   L +    
Sbjct: 55  DDQVLQANTPV-----------------YMMLHKPVGVVSATKDNQHKTVIDLLDNEYR- 96

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +  +  RLD  +SG+L++      ++ L       ++ K+Y           +  +A
Sbjct: 97  --HELHIAGRLDLNSSGLLLLTNDSRWSEAL--MSPTEKVDKVY-----------RVTLA 141

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           N L        DYV    +        I+  +            E+    G+ HQ++   
Sbjct: 142 NPLT------HDYVTAFAEGMYFGFEDITT-QPAKLVILDSHLAEVTLKEGKYHQIKRMF 194

Query: 260 LHMGCPIVG 268
                P++G
Sbjct: 195 GRFRNPVIG 203


>gi|313105549|ref|ZP_07791817.1| putative pseudouridylate synthase [Pseudomonas aeruginosa 39016]
 gi|310878319|gb|EFQ36913.1| putative pseudouridylate synthase [Pseudomonas aeruginosa 39016]
          Length = 230

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/243 (16%), Positives = 78/243 (32%), Gaps = 51/243 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+  N  P ++  + Q ++  G++RVD + V+          VR+   +     ++
Sbjct: 1   MRLDRFLAN-LPELSRRDAQMLIAGGRLRVDGQVVRDGTH-----EVRVFSRVELDEQLL 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  K                       ++ Y+ +KP G      +         L  + +
Sbjct: 55  QAGKP----------------------ARYYMLHKPMGCVS---ATRDPQHPTVLDLFPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +     +  RLD  T+G++++      ++ LT     R         V       +  +
Sbjct: 90  DQRDDLHIGGRLDYNTTGLMLLTNDGQWSRRLTLPGSRRDKVYY----VETEAPIDQRYV 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +         D + +  Q E                        +  H GR HQ++  
Sbjct: 146 DAFAAGLHFRFEDLITLPAQLEPIGPR----------------CARLTLHEGRYHQVKRM 189

Query: 259 ALH 261
             H
Sbjct: 190 FGH 192


>gi|238786125|ref|ZP_04630080.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           bercovieri ATCC 43970]
 gi|238712977|gb|EEQ05034.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           bercovieri ATCC 43970]
          Length = 342

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/178 (17%), Positives = 60/178 (33%), Gaps = 27/178 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +       H +   ++ I++ G+V VD K     +R++  Q  +I    + L+  
Sbjct: 27  GEKLQKVLARA-GHGSRREIEAIIQQGRVSVDGKISTLGDRVEVTQATKIRLDGHLLSIT 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ +                       ++  + KP G                     
Sbjct: 86  ESEEAVC----------------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLP 121

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 122 KLRGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDEK 177


>gi|238751859|ref|ZP_04613346.1| Ribosomal small subunit pseudouridine synthase A [Yersinia rohdei
           ATCC 43380]
 gi|238709988|gb|EEQ02219.1| Ribosomal small subunit pseudouridine synthase A [Yersinia rohdei
           ATCC 43380]
          Length = 235

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 79/249 (31%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK      SG +            + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEVVK------SGAI-----------KLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ +      L +             S+ ++ NKP G      S         L    +
Sbjct: 43  PEQDVRFDGNPLQQMVG----------SRYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L   +         +   +     A    +VI+        + +    GR HQ++  
Sbjct: 137 EHPLADDTAQQFADGVQLHNEKSLTKPA--QLEVIEPQ-----LVRLTLSEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  ++
Sbjct: 190 FAAVGNRVL 198


>gi|228993695|ref|ZP_04153602.1| hypothetical protein bpmyx0001_44210 [Bacillus pseudomycoides DSM
           12442]
 gi|228766124|gb|EEM14771.1| hypothetical protein bpmyx0001_44210 [Bacillus pseudomycoides DSM
           12442]
          Length = 166

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 12/74 (16%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 1   MSLMTYVQY------VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK 54
           +S+M Y +       +V+E    + R+D+    +    +   +   +++G ++++ +++K
Sbjct: 92  ISIMQYKEAGTTELAIVLETVFGSHRMDKALATYISDWSRTAIVDKIKNGHIQLNGQKMK 151

Query: 55  FNNRIQSGQVVRIP 68
            N  +  G ++ I 
Sbjct: 152 PNTTLSEGDLISIC 165


>gi|110834248|ref|YP_693107.1| S4 domain-containing protein [Alcanivorax borkumensis SK2]
 gi|110647359|emb|CAL16835.1| S4 domain protein [Alcanivorax borkumensis SK2]
          Length = 280

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/295 (14%), Positives = 87/295 (29%), Gaps = 65/295 (22%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   L+  +  G+V V+       +R+ S   +R+   I                + +  
Sbjct: 16  SRRELETWISDGRVSVNGTVATLGDRVGSEDTLRVDGRI----------------IKVKT 59

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
             D ++ +++Y        +KP G                  +    +G +     RLD 
Sbjct: 60  EEDTVQRVIMY--------HKPPGEVC--SRNDPEGRPTVFDNLPRLQGMRWVQVGRLDI 109

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKECIANWLLKKSHIGG 210
            T+G+++       A  L          + Y   V G+  P+ ++  +   LL+      
Sbjct: 110 NTTGMMLFTTDGELAHRL--MHPSNGFVREYAVRVRGVMTPEKRQAMLDGVLLEDGVSKF 167

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDH 270
           D +      E+GAN+                W +     G+  ++R            D 
Sbjct: 168 DSIEDAGGAEEGANH----------------WYKATLTGGKYREVRRLFQSQ------DL 205

Query: 271 KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           +     +  F            R+M+L              P  M    + +  K
Sbjct: 206 EVARLMRIRFGDLTLPPQLRQGRWMELE-------------PEQMKALIEKVDLK 247


>gi|295099584|emb|CBK88673.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           cylindroides T2-87]
          Length = 241

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/248 (14%), Positives = 74/248 (29%), Gaps = 53/248 (21%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNH 76
            RL +        I +    ++++  G+V V+ +       ++     + +   +  L  
Sbjct: 2   ERLQKVIAR--SGICSRRKAEELILEGKVYVNGELCTTLGTKVSGNDEIEVDGKLLEL-- 57

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                      ED   YV NK  G      S         +  +
Sbjct: 58  ---------------------------EDKVYYVINKTKGCIC---SSNDDRDRRTVLDY 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +D   Q+     RLD +TSG+L++           +     ++    + L      N + 
Sbjct: 88  LD-IPQRVYTVGRLDYDTSGVLLLT---------NDGDFCNQMIHPRYHLPKTYVVNLQG 137

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +    ++    G      +K N      A     + +   +     E+    G+ HQ++
Sbjct: 138 TLTQDDIRLLRKG------LKTNIGDFQPAKVKI-ISNDVTRDRTIFELTIMEGKNHQVK 190

Query: 257 VHALHMGC 264
                +G 
Sbjct: 191 NMMEALGH 198


>gi|308050759|ref|YP_003914325.1| ribosomal small subunit pseudouridine synthase A [Ferrimonas
           balearica DSM 9799]
 gi|307632949|gb|ADN77251.1| ribosomal small subunit pseudouridine synthase A [Ferrimonas
           balearica DSM 9799]
          Length = 232

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/245 (14%), Positives = 80/245 (32%), Gaps = 52/245 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +    +     +K+L  G+V+ D + VK                 +    + 
Sbjct: 1   MRLDKYLCS-CTDLTRSMAKKLLHKGEVQCDGEVVK-----------------DPGFKVT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +++   V L   +   + I+L++ ++    N            +       L     
Sbjct: 43  DDTQVVLEGVPLGPVA--TRYIMLHKPAEFLCSN------------VDELYPSVLNLIEL 88

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K +  R+  RLD +T+G+++++        +T   R    +   W             +
Sbjct: 89  PKRETLRIAGRLDVDTTGLVLLSEDGQWCHQITSPRRQCSKRYRAW-------------L 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A  L+  +         +   E     A       +        + +    G+ HQ++  
Sbjct: 136 AEPLVADAEQQLAQGVQLHNEEGLTRPA-------ELVRISDTEVLLTIEEGKYHQVKRM 188

Query: 259 ALHMG 263
              +G
Sbjct: 189 FAALG 193


>gi|107100191|ref|ZP_01364109.1| hypothetical protein PaerPA_01001214 [Pseudomonas aeruginosa PACS2]
 gi|254239095|ref|ZP_04932418.1| hypothetical protein PACG_05277 [Pseudomonas aeruginosa C3719]
 gi|254244988|ref|ZP_04938310.1| hypothetical protein PA2G_05867 [Pseudomonas aeruginosa 2192]
 gi|126171026|gb|EAZ56537.1| hypothetical protein PACG_05277 [Pseudomonas aeruginosa C3719]
 gi|126198366|gb|EAZ62429.1| hypothetical protein PA2G_05867 [Pseudomonas aeruginosa 2192]
          Length = 230

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 77/243 (31%), Gaps = 51/243 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+  N  P ++  + Q ++  G++RVD + V+          VR+   +     ++
Sbjct: 1   MRLDRFLAN-LPELSRRDAQMLIAGGRLRVDGQVVRDGTH-----EVRVFSRVELDERLL 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  K                       ++ Y+ +KP G      +         L  + +
Sbjct: 55  QAGKP----------------------ARYYMLHKPMGCVS---ATRDPQHPTVLDLFPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                  +  RLD  T+G++++      ++ LT     R         V       +  +
Sbjct: 90  DLRDDLHIGGRLDYNTTGLMLLTNDGQWSRRLTLPGSRRDKVYY----VETEAPIDQRYV 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +         D V +  Q E                        +  H GR HQ++  
Sbjct: 146 DAFAAGLHFRFEDLVTLPAQLEPIGPR----------------CARLTLHEGRYHQVKRM 189

Query: 259 ALH 261
             H
Sbjct: 190 FGH 192


>gi|190893225|ref|YP_001979767.1| RNA-pseudouridine synthase, ribosomal large subunit B [Rhizobium
           etli CIAT 652]
 gi|190698504|gb|ACE92589.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli CIAT 652]
          Length = 267

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/254 (14%), Positives = 72/254 (28%), Gaps = 52/254 (20%)

Query: 13  ENDEENMR--LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
             D    R  L R       + +    ++++   +V +D + V   +  +    +V    
Sbjct: 17  TADAAGKRVTLPRALSK-LGYCSRTQAERLIAESRVSIDGRTVNDPSAWV---DLVTAKI 72

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            ++ L  I  E KI                          + NKP G+            
Sbjct: 73  RVDGLV-IAAEAKI------------------------YLILNKPRGLVT--TRHDPEGR 105

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                   D          RLD+ + G+L+       AQ L +       +  +  +   
Sbjct: 106 PTVYDCLRDFDIPHLSPVGRLDKASEGLLLFTNDTEFAQILLDPV-THVTKTYHVQI--- 161

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                     + +L    I      +    E     A+   +       +  W+E++   
Sbjct: 162 ----------DRVLDDEEIAAMTSGIRHDGELLTATAVRRLR----QGDRNSWIEVELDE 207

Query: 250 GRTHQLRVHALHMG 263
           GR  Q+R     +G
Sbjct: 208 GRNRQIRRMLEALG 221


>gi|81428635|ref|YP_395635.1| pseudouridylate synthase, 16SrRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610277|emb|CAI55326.1| Pseudouridylate synthase, 16SrRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 256

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 86/250 (34%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   N     +    + ++ +G V ++ K VK            +   +++ +  I
Sbjct: 2   ERLQKVIANA-GVASRRKAETLIATGHVTLNGKVVK-----------EMGIKVDSTSAHI 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +   +  +      ++ +    ++                    +         +  +++
Sbjct: 50  EVDGVPLTREKKVYYALYKPRQVI-------------------SAVTDDKKRRVVTEYLE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KE 196
              ++     RLD +TSG+L++      A  +       ++ K Y + V G+P  +  ++
Sbjct: 91  DIQERVYPIGRLDYDTSGLLLLTNDGDFANMM--MHPKYKVDKTYVAKVSGLPTAEMLRQ 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +L+K       V ++  + +  N AI               L +  H G  HQ++
Sbjct: 149 LRKGIMLEKRKTAPAKVKIISTDRR-KNTAI---------------LSITIHEGMNHQVK 192

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 193 NMLAAVGLPV 202


>gi|254670545|emb|CBA06380.1| conserved hypothetical protein [Neisseria meningitidis alpha153]
          Length = 349

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 244

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 245 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 302

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 303 VRVGFGPIGLP 313


>gi|163750152|ref|ZP_02157395.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           benthica KT99]
 gi|161330209|gb|EDQ01191.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           benthica KT99]
          Length = 241

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/269 (14%), Positives = 91/269 (33%), Gaps = 60/269 (22%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRI 59
           MS + Y++   +      +RLD++       +     +K L  G V  D + VK +  ++
Sbjct: 1   MSPILYLKLRSI------VRLDKFICES-TELTRSFAKKALHRGDVTCDGEVVKNSGFKV 53

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
           + GQ + +   + ++        +    + L K +D + +                   V
Sbjct: 54  KVGQTICLDGKVISV--------VGPRFLMLNKPADTICAT---------------FDIV 90

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   L      K     +  RLD +T+G++++          T+     +I
Sbjct: 91  HP------TVIDLLDI---EKADTLHIAGRLDIDTTGLVLIT---------TDGQWSHKI 132

Query: 180 QKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK 239
                           + +   L++    G +    ++  +     A+   ++ID    +
Sbjct: 133 TSPKKDCSKCYLVKLTDELDASLVETFAQGVE----LRNEDGLTKPAV--LEIIDTHTAR 186

Query: 240 FCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               E     G+ HQ++     +G  +VG
Sbjct: 187 LTITE-----GKYHQVKRMFAAVGNKVVG 210


>gi|228942133|ref|ZP_04104673.1| hypothetical protein bthur0008_47640 [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|228975063|ref|ZP_04135622.1| hypothetical protein bthur0003_48110 [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228981702|ref|ZP_04141997.1| hypothetical protein bthur0002_48610 [Bacillus thuringiensis Bt407]
 gi|228777814|gb|EEM26086.1| hypothetical protein bthur0002_48610 [Bacillus thuringiensis Bt407]
 gi|228784584|gb|EEM32604.1| hypothetical protein bthur0003_48110 [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228817467|gb|EEM63552.1| hypothetical protein bthur0008_47640 [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|326942784|gb|AEA18680.1| putative cytoplasmic protein [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 165

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RIDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNAILSEGDSISIC 164


>gi|187776810|ref|ZP_02993283.1| hypothetical protein CLOSPO_00326 [Clostridium sporogenes ATCC
           15579]
 gi|187775469|gb|EDU39271.1| hypothetical protein CLOSPO_00326 [Clostridium sporogenes ATCC
           15579]
          Length = 238

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 85/243 (34%), Gaps = 47/243 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     ++ +++ GQV VD + VK N        ++I P  N +    
Sbjct: 2   ERLDKILAN-LGYGTRKEVKALIKKGQVDVDGEVVKDNG-------MQIDPEKNKIFVFG 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           KE                    L+Y+     + NKP G+           I   L+   +
Sbjct: 54  KE--------------------LVYKKYIYLMMNKPQGVVSATFDNYDETIVDLLED--E 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD+ T G+L++         L        + KIY++ +     ++    
Sbjct: 92  DRIFEPFPVGRLDKNTVGLLLLTNDGELNHRL--ISPKWHVDKIYYAKINKKVTDED--- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                    I      +V  +      A    ++I  F ++   + +  H G+ HQ++  
Sbjct: 147 ---------IEKFKKGIVLDDGYECFPA--KLEIIKSFNEE-SEVRVTIHEGKFHQVKRM 194

Query: 259 ALH 261
              
Sbjct: 195 FES 197


>gi|268559230|ref|XP_002637606.1| Hypothetical protein CBG19344 [Caenorhabditis briggsae]
 gi|187024570|emb|CAP36614.1| hypothetical protein CBG_19344 [Caenorhabditis briggsae AF16]
          Length = 384

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/186 (18%), Positives = 59/186 (31%), Gaps = 16/186 (8%)

Query: 113 KPAG-ISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
           K AG I ++    +   I   LK      K  +      L +  SG +V+      +  L
Sbjct: 92  KWAGTIKMRSDEQVGVTITDSLKLLRKILKEPQLSFCTGLKRYLSGAIVLPCNEHDSNIL 151

Query: 171 TESFRMRR------IQKIYWSLVWGIPKNKKECIANWLL-KKSHIGGDYV---HVVKQNE 220
               R               ++  G P+     I  +   +      +Y+     V +  
Sbjct: 152 KNCIRRMSSDVEPPFMYNALAITVGRPEKSSGLITGFATFRNVGKHKEYIFEERKVSKRA 211

Query: 221 KGANYAIS---HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK 277
           K   YA+     ++V+D        ++        H  R+   HM  PI+GD  Y     
Sbjct: 212 KSGKYAVEGHMSYRVLDTK-NGVSLVDFSIDKFARHLPRLMLTHMLSPILGDRIYWRRLM 270

Query: 278 GNFTSP 283
               +P
Sbjct: 271 EVDGAP 276


>gi|229824809|ref|ZP_04450878.1| hypothetical protein GCWU000182_00158 [Abiotrophia defectiva ATCC
           49176]
 gi|229790812|gb|EEP26926.1| hypothetical protein GCWU000182_00158 [Abiotrophia defectiva ATCC
           49176]
          Length = 242

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/171 (14%), Positives = 54/171 (31%), Gaps = 36/171 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI-QSGQVVRIPPVINALNH 76
           +RLD++  +         +++ +R G+V  +   +K    ++      + I         
Sbjct: 5   IRLDKYLSDMTSE-TRSKVKEYIRKGRVTANGVVIKSPETKVDTDNDEICIDGKPVG--- 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                     Y +   Y+ NKP G+      G    +    K  
Sbjct: 61  --------------------------YVEYYYYMMNKPQGVITSTEKGRTKTVMDVFKET 94

Query: 137 V--DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                +  +     RLD++T G+L++         L        + K+Y++
Sbjct: 95  GTGCPRFNELSPVGRLDKDTEGLLLITNDGELNHKL--LSPKNHVDKVYYA 143


>gi|268593179|ref|ZP_06127400.1| ribosomal large subunit pseudouridine synthase F [Providencia
           rettgeri DSM 1131]
 gi|291311225|gb|EFE51678.1| ribosomal large subunit pseudouridine synthase F [Providencia
           rettgeri DSM 1131]
          Length = 289

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 75/246 (30%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ SG VV++   +    +  
Sbjct: 8   RLNKYISE--SGICSRREADRYIEQGNVFINGKRAGIGDQVFSGDVVKVNGQLIEPRNE- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    ED  +   NKP GI     SG   +I  ++     
Sbjct: 65  -------------------------EDLVLIALNKPVGIVSTTESGEKDNIVDYVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++ +         +  +      + +             + +
Sbjct: 97  --STRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNSHEKEYLV---------TVNKPV 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            +  ++    G   +  + +  K    A   F++                 G   Q+R  
Sbjct: 146 TDEFIRGMGAGVPILGTMTKKCKVKKEAPFVFRI-------------TLVQGLNRQIRRM 192

Query: 259 ALHMGC 264
             H G 
Sbjct: 193 CEHFGF 198


>gi|332535580|ref|ZP_08411350.1| ribosomal large subunit pseudouridine synthase E [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332034998|gb|EGI71518.1| ribosomal large subunit pseudouridine synthase E [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 228

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/172 (23%), Positives = 70/172 (40%), Gaps = 11/172 (6%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-PRLTHRLDQETS 155
           +K  +  +D KI +FNKP  +  Q      +  D   K+  +    K      RLD+++ 
Sbjct: 38  IKPQIASKDRKIVLFNKPFDVLCQ------FTDDADRKTLAEFIPIKEVYAAGRLDRDSE 91

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++         LT     ++  K YW+ V G P ++          +   G      
Sbjct: 92  GLLLLTNCGKLQNSLTA--PDKKTNKTYWAQVEGEPTSES-INDLCNGVELKDGLTLPAN 148

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           VK  ++   +A +   V +  A    WL +  + GR  Q+R    H+G P +
Sbjct: 149 VKIIDEPTIWARNP-PVRERKAIPTTWLSITINEGRNRQVRRMTAHIGHPTL 199


>gi|270262113|ref|ZP_06190385.1| ribosomal large subunit pseudouridine synthase B [Serratia
           odorifera 4Rx13]
 gi|270043989|gb|EFA17081.1| ribosomal large subunit pseudouridine synthase B [Serratia
           odorifera 4Rx13]
          Length = 298

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/175 (17%), Positives = 60/175 (34%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ I+ +G+V VD K  K  +R++    ++I    + L+    E
Sbjct: 5   LQKVLARA-GHGSRREIETIIEAGRVSVDGKVAKLGDRVEVTASMKIRLDGHVLSIKESE 63

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           + +                       ++  + KP G                       +
Sbjct: 64  ETVC----------------------RVLAYYKPEGELC--TRSDPEGRPTVFDRLPKLR 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 100 GSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDEK 152


>gi|154687141|ref|YP_001422302.1| YtzF [Bacillus amyloliquefaciens FZB42]
 gi|154352992|gb|ABS75071.1| YtzF [Bacillus amyloliquefaciens FZB42]
          Length = 239

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/245 (16%), Positives = 87/245 (35%), Gaps = 47/245 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N     +  +++KI+++G V +D +  K                 +   H+ 
Sbjct: 1   MRLDKLLANSGFG-SRKDVKKIVKAGAVMIDGEPAK-----------------DVKTHVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E++ +        + +F+            + NKP G+           +   L    +
Sbjct: 43  PEKQDITVYGEPADYREFI----------YVMMNKPQGVLSATEDSRQQTVVDLLT--PE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD++T G L++      A  L              S    +PK  +  +
Sbjct: 91  EQRFEPFPAGRLDKDTEGFLLLTNDGQLAHRL-------------LSPKKHVPKTYEVRL 137

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L  +  +  +   V++   K    A+     I   +     + +    G+ HQ+++ 
Sbjct: 138 TSPLSPEDIVHLERGVVIEGGYKTKPAAVE----IITESPDETVIHLTITEGKYHQVKLM 193

Query: 259 ALHMG 263
           A  +G
Sbjct: 194 AKAVG 198


>gi|325136137|gb|EGC58745.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M0579]
 gi|325136446|gb|EGC59053.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M0579]
 gi|325208319|gb|ADZ03771.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis NZ-05/33]
          Length = 349

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 244

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 245 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 302

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 303 VRVGFGPIGLP 313


>gi|317502014|ref|ZP_07960198.1| pseudouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|316896694|gb|EFV18781.1| pseudouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 249

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 76/250 (30%), Gaps = 60/250 (24%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E++RL+++        +     +++ SG+V VD    +   R+ +GQ+V++         
Sbjct: 19  ESVRLNKYLSEA-GVCSRREADRLIESGKVTVDGVTAQMGMRVTAGQIVKV--------- 68

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                        ++K  + +          +   NKP GI           I  FL   
Sbjct: 69  ---------GKKTVSKQDEMI----------VLAVNKPKGIVCTEDQRERDSIVRFL--- 106

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD+++ G+L++         +  +      +              KE
Sbjct: 107 --NYPVRVTYAGRLDKDSRGLLLMTNNGDIINQMMRAANRHEKEY--------KVTVDKE 156

Query: 197 CIANWLLKKSH--IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
               ++ K S      D V      +K   Y  S                +    G   Q
Sbjct: 157 ITEQFIKKMSEGVPILDTVTRPCTVKKIGKYTFS----------------IILTQGLNRQ 200

Query: 255 LRVHALHMGC 264
           +R      G 
Sbjct: 201 IRRMCAAFGY 210


>gi|298346749|ref|YP_003719436.1| pseudouridylate synthase [Mobiluncus curtisii ATCC 43063]
 gi|304389546|ref|ZP_07371509.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           curtisii subsp. curtisii ATCC 35241]
 gi|298236810|gb|ADI67942.1| pseudouridylate synthase [Mobiluncus curtisii ATCC 43063]
 gi|304327356|gb|EFL94591.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           curtisii subsp. curtisii ATCC 35241]
          Length = 278

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/255 (14%), Positives = 83/255 (32%), Gaps = 51/255 (20%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           E+  E  RL +         +    + ++  G+V+++ + V+    ++     + +    
Sbjct: 36  ESTSEPERLQKVLSRA-GVASRRASEDLIARGRVQINGETVREMGVKVLPTDRITVDGQR 94

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              + +++                            ++ F+KP G              G
Sbjct: 95  IHTDTVLQ----------------------------VWAFHKPVGTVSSMQPEDDRPCIG 126

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
               WV    ++     RLD  T+G+L++      A  +        + K Y ++V G  
Sbjct: 127 ---DWVTKLPERVYNVGRLDAATAGLLLLTNNGELANRI--MHPSYEVPKTYVAVVQGQV 181

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K               +G   V       +     +  FK+I+   +    +++  H+G+
Sbjct: 182 K---------------MGLGKVLRRGVELEDGKVKVDKFKLIEVR-RGSSIVQLTLHSGK 225

Query: 252 THQLRVHALHMGCPI 266
              +R     +G P+
Sbjct: 226 NRVVRRLLSAVGHPV 240


>gi|218893324|ref|YP_002442193.1| putative pseudouridylate synthase [Pseudomonas aeruginosa LESB58]
 gi|218773552|emb|CAW29366.1| probable pseudouridylate synthase [Pseudomonas aeruginosa LESB58]
          Length = 230

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 77/243 (31%), Gaps = 51/243 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+  N  P ++  + Q ++  G++RVD + V+          VR+   +     ++
Sbjct: 1   MRLDRFLAN-LPELSRRDAQMLIAGGRLRVDGQVVRDGTH-----EVRVFSRVELDEQLL 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  K                       ++ Y+ +KP G      +         L  + +
Sbjct: 55  QAGKP----------------------ARYYMLHKPMGCVS---ATRDPQHPTVLDLFPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                  +  RLD  T+G++++      ++ LT     R         V       +  +
Sbjct: 90  DLRDDLHIGGRLDYNTTGLMLLTNDGQWSRRLTLPGSRRDKVYY----VETEAPIDQRYV 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +         D V +  Q E                        +  H GR HQ++  
Sbjct: 146 DAFAAGLHFRFEDLVTLPAQLEPIGPR----------------CARLTLHEGRYHQVKRM 189

Query: 259 ALH 261
             H
Sbjct: 190 FGH 192


>gi|229032362|ref|ZP_04188334.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|228728970|gb|EEL79974.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 242

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 96/246 (39%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGTPVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ + G+   +   
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHIAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K+   G     ++    +    A++  K     + +   +E+    G+ HQ++ 
Sbjct: 146 -----VKEFAKG----VILDDGYETKPGALTILK-----SDEISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|323144920|ref|ZP_08079483.1| pseudouridine synthase B, ribosomal large subunit [Succinatimonas
           hippei YIT 12066]
 gi|322415318|gb|EFY06089.1| pseudouridine synthase B, ribosomal large subunit [Succinatimonas
           hippei YIT 12066]
          Length = 340

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 58/177 (32%), Gaps = 33/177 (18%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +         +   L  ++ +G+V V+ K     +R++    V+I             
Sbjct: 5   LQKVLARQGLG-SRRELDALIAAGRVEVNGKVAAVGDRVEGPLTVKI------------- 50

Query: 81  QKILDSSVNLTKHSDFLKSILL--YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
               D  V LT  S+  K  +L  Y+        K                         
Sbjct: 51  ----DGKVVLTPLSEKPKCRVLMYYKPEGEVTTYKDP-----------EDRPTVFDHLPR 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             G +     RLD  TSG+L+       A  L      + I+++Y + ++G   +K+
Sbjct: 96  PDGGRWIYVGRLDLNTSGLLLFTTDGELANAL--MHPSKEIERVYAARIYGEVTDKQ 150


>gi|283832379|ref|ZP_06352120.1| ribosomal small subunit pseudouridine synthase A [Citrobacter
           youngae ATCC 29220]
 gi|291072028|gb|EFE10137.1| ribosomal small subunit pseudouridine synthase A [Citrobacter
           youngae ATCC 29220]
          Length = 235

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 79/249 (31%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R+ +V VD + VK                 N+   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRANRVTVDGEIVK-----------------NSAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +     +L + +            + ++ NKP G      S         L    +
Sbjct: 43  PEHDVEYDGNSLIQQNGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + + + +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVAEDTAEQFARGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|227817496|ref|YP_002817505.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           CDC 684]
 gi|227006383|gb|ACP16126.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           CDC 684]
          Length = 214

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 95/246 (38%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGISVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K+   G     ++    +    A++  K     +     +E+    G+ HQ++ 
Sbjct: 146 -----VKEFAKG----VILDDGYETKPGALTILK-----SDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|120599941|ref|YP_964515.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|146292123|ref|YP_001182547.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|120560034|gb|ABM25961.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|145563813|gb|ABP74748.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
          Length = 236

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 86/249 (34%), Gaps = 52/249 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+       +    ++ +L SG+V+VD + VK            +   ++  +HI  
Sbjct: 7   RLDRYLSAKM-QMPRKLVRDLLLSGRVQVDGQIVK-----------EMDRQVDEFSHIQL 54

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + ++L ++  +                   + +KP G+           +   L +    
Sbjct: 55  DDQVLQANTPV-----------------YMMLHKPVGVVSATKDNQHKTVIDLLDNEYR- 96

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +  +  RLD  +SG+L++      ++ L       ++ K+Y           +  +A
Sbjct: 97  --HELHIAGRLDLNSSGLLLLTNDSRWSEAL--MSPTEKVDKVY-----------RVTLA 141

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           N L        DYV    +        I+  +            E+    G+ HQ++   
Sbjct: 142 NPLT------HDYVTAFAEGMYFGFEDITT-QPAKLVILDSHLAEVTLKEGKYHQIKRMF 194

Query: 260 LHMGCPIVG 268
                P++G
Sbjct: 195 GRFRNPVIG 203


>gi|331088168|ref|ZP_08337088.1| hypothetical protein HMPREF1025_00671 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330408824|gb|EGG88287.1| hypothetical protein HMPREF1025_00671 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 244

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 76/250 (30%), Gaps = 60/250 (24%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E++RL+++        +     +++ SG+V VD    +   R+ +GQ+V++         
Sbjct: 14  ESVRLNKYLSEA-GVCSRREADRLIESGKVTVDGVTAQMGMRVTAGQIVKV--------- 63

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                        ++K  + +          +   NKP GI           I  FL   
Sbjct: 64  ---------GKKTVSKQDEMI----------VLAVNKPKGIVCTEDQRERDSIVRFL--- 101

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD+++ G+L++         +  +      +              KE
Sbjct: 102 --NYPVRVTYAGRLDKDSRGLLLMTNNGDIINQMMRAANRHEKEY--------KVTVDKE 151

Query: 197 CIANWLLKKSH--IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
               ++ K S      D V      +K   Y  S                +    G   Q
Sbjct: 152 ITEQFIKKMSEGVPILDTVTRPCTVKKIGKYTFS----------------IILTQGLNRQ 195

Query: 255 LRVHALHMGC 264
           +R      G 
Sbjct: 196 IRRMCAAFGY 205


>gi|313202274|ref|YP_004040932.1| RNA-binding s4 domain-containing protein [Methylovorus sp. MP688]
 gi|312441590|gb|ADQ85696.1| RNA-binding S4 domain protein [Methylovorus sp. MP688]
          Length = 425

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 78/252 (30%), Gaps = 50/252 (19%)

Query: 25  FKNHYPHI---NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
                  +   +     + + +G VRV+ + V                  + L   ++  
Sbjct: 188 LSKRMAELGLCSRREADEWIVNGWVRVNGQVV------------------DELGSRVEPD 229

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-----ISVQGGSGIAYHIDGFLKSW 136
             ++ S    KH   + +ILL++           G     + V   +  A   D   K +
Sbjct: 230 ANIEVSKEAEKHQSEIVTILLHKPVGYVSGQAEDGYEPAVVLVHPDNHWAE--DPVQKEF 287

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                +      RLD +++G+LV+ +    A+ L       + +K Y   V G   ++  
Sbjct: 288 RRGFLKGLAPAGRLDIDSTGLLVLTQDGRVARQL--IGEDSQTEKEYLVRVEGTLSDEGL 345

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              N  L    +      V  QNE                      L      GR  Q+R
Sbjct: 346 RKLNHGLSLDGVQLKPAKVSWQNED--------------------QLRFVLREGRKRQIR 385

Query: 257 VHALHMGCPIVG 268
                +G  +VG
Sbjct: 386 RMCELVGLHVVG 397


>gi|311104985|ref|YP_003977838.1| ribosomal large subunit pseudouridine synthase B [Achromobacter
           xylosoxidans A8]
 gi|310759674|gb|ADP15123.1| ribosomal large subunit pseudouridine synthase B [Achromobacter
           xylosoxidans A8]
          Length = 604

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/190 (15%), Positives = 58/190 (30%), Gaps = 43/190 (22%)

Query: 19  MRLDRWFKN--HYPHI----------NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            RL ++  +    P +          +   +++++ +G+V V+ +      R+     VR
Sbjct: 97  QRLGKYLNSDSVMPKLHKVLADAGIGSRREMEELIVAGRVSVNGEPAHIGQRVAPNDQVR 156

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGI 125
           +        +  K  ++                 +LY        +KPAG I      G 
Sbjct: 157 VNGKPIMRVNTKKPPRV-----------------ILY--------HKPAGEIVSHDDPGG 191

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                         +  K     RLD  T G+L+   +   A  +         ++ Y  
Sbjct: 192 R---ASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSGDMANRI--MHPRYGTEREYAV 246

Query: 186 LVWGIPKNKK 195
            V G     +
Sbjct: 247 RVLGEMDEAQ 256


>gi|312899113|ref|ZP_07758491.1| conserved hypothetical protein [Megasphaera micronuciformis F0359]
 gi|310619780|gb|EFQ03362.1| conserved hypothetical protein [Megasphaera micronuciformis F0359]
          Length = 237

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 85/247 (34%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHI 77
           +RLD+    H  +     ++ + +SG V V+ + V+ ++ ++  G  V +          
Sbjct: 2   IRLDKLL-GHSGYGTRKEIKSLCKSGDVTVNGEIVRDSSVKVDEGATVIV---------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  + YE     + +KPAG+           +   L S  
Sbjct: 51  -------------------AGEKVEYEAVSYLMLHKPAGVVSATQDSRVRTVLDILPSRY 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKE 196
            +   +     RLD +T+G+L+++     A  +      + + K+Y + V G IP +  E
Sbjct: 92  AAS--RVAPVGRLDIDTTGLLLLSNDGTWAHKV--ISPKKHVPKVYEAQVEGVIPADVGE 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             A  ++ +  +        K  E      I+  +                  G+ HQ++
Sbjct: 148 RFAAGIVLEDGVECLPARAEKTAE--GRLQITVCE------------------GKFHQVK 187

Query: 257 VHALHMG 263
                +G
Sbjct: 188 RMCSVVG 194


>gi|323308009|gb|EGA61263.1| Pus5p [Saccharomyces cerevisiae FostersO]
          Length = 177

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/188 (17%), Positives = 66/188 (35%), Gaps = 35/188 (18%)

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+T+ A+   +   +            +                +   G  Y  ++ 
Sbjct: 1   MLIAKTKDASVKFSRFLQKGGNNGYKLQRKYVAIVESSGRFNKPNNXEIKYGPKYNFLIS 60

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC-PIVGDHKYCANF 276
              +     I+ FK +D        + +Q  TG+ HQ+R H   +   PI+ D KY +  
Sbjct: 61  HGGRE----ITKFKEVDXN-----CIVLQLVTGKKHQIRNHVSQILNQPILNDKKYGSTV 111

Query: 277 KGNFTSPIQNKLYLHA-------------RYMDLPHPEGGRL----------QITAPLPA 313
             NF     +++ LH+               + + H   G+L          + T P+  
Sbjct: 112 --NFPELFNDQIALHSACIITKIGLQTKTHLIPMEHNNTGQLWSRKYVNEEGEFTLPIKE 169

Query: 314 HMVKTWDS 321
            +++ WD 
Sbjct: 170 VLLENWDQ 177


>gi|161870231|ref|YP_001599401.1| pseudouridine synthase [Neisseria meningitidis 053442]
 gi|161595784|gb|ABX73444.1| pseudouridine synthase [Neisseria meningitidis 053442]
          Length = 416

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 162 EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 218

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 219 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 253

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 254 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 311

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 312 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 369

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 370 VRVGFGPIGLP 380


>gi|146309893|ref|YP_001174967.1| 23S rRNA pseudouridine synthase F [Enterobacter sp. 638]
 gi|145316769|gb|ABP58916.1| ribosomal large subunit pseudouridine synthase F [Enterobacter sp.
           638]
          Length = 289

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 72/246 (29%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++  G VV++   +    +  
Sbjct: 8   RLNKYISE--SGICSRREADRYIEQGNVFINGKRAAIGDQVAPGDVVKVNGQLIEPRNE- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    ED      NKP GI      G   +I  F+     
Sbjct: 65  -------------------------EDLVFIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++ +         +  +      + +             + I
Sbjct: 97  --SSRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYVV---------TVNKPI 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            +  ++    G   +  V +  K    A   F++                 G   Q+R  
Sbjct: 146 TDDFIRGMGAGVPILGTVTKKCKVKKEAPFAFRI-------------TLVQGLNRQIRRM 192

Query: 259 ALHMGC 264
             H G 
Sbjct: 193 CEHFGF 198


>gi|197294800|ref|YP_001799341.1| 16S rRNA pseudouridylate synthase [Candidatus Phytoplasma
           australiense]
 gi|171854127|emb|CAM12116.1| 16S rRNA pseudouridylate synthase [Candidatus Phytoplasma
           australiense]
          Length = 243

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 87/251 (34%), Gaps = 49/251 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            RL ++  +    ++   ++ ++   +V+V+ + V +   ++++  VV +  V+     +
Sbjct: 2   ERLQKFIASANL-VSRRKVEILILQKRVKVNNQVVSQLGTKVKASDVVTLDDVLIKKTTL 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
                                          Y+ NKP G +S          +   +K  
Sbjct: 61  F-----------------------------YYLLNKPQGYLSTTKDDKKRPTVLDLIK-- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            +S+ Q+     RLD  T+G++++       Q LT                 GIPK    
Sbjct: 90  -ESQNQRLYSVGRLDFNTTGLILITNDGEMTQKLTHPCF-------------GIPKEYHV 135

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            I  +L KK         ++  N       I+  K      +   WL++    G+  Q+R
Sbjct: 136 KINVFLTKKDLSLLLKGVIIDHNYLSIPKEINILK-QRYLPKPSTWLKIVITEGKNRQIR 194

Query: 257 VHALHMGCPIV 267
                +G  ++
Sbjct: 195 KMMEALGYQVL 205


>gi|114777044|ref|ZP_01452064.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Mariprofundus ferrooxydans
           PV-1]
 gi|114552565|gb|EAU55025.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Mariprofundus ferrooxydans
           PV-1]
          Length = 249

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/253 (16%), Positives = 86/253 (33%), Gaps = 50/253 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +D+++ RLD+   N        +++  +++G + V  +  +             P     
Sbjct: 2   SDQKSERLDKLLSNLGYGA-RKDVRHWIKAGWITVQGEAAES------------PAQKVF 48

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
            + ++ E + LD    LT         ++Y        +KP         G     D   
Sbjct: 49  ASDVLLEGEPLDHPDGLT---------IIY--------HKPLDTVCSRKEGGRLIYDDLP 91

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             W+D K        RLD++TSG+L+V         LT   +    +    +L   +   
Sbjct: 92  ARWLDRK-PPFSPVGRLDKDTSGLLIVTDDGQLNHCLTSP-KQHISKTYSVTLAEPLQGR 149

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           + E +A   L           +++ +++    A       +          +  H GR H
Sbjct: 150 EAEIMAAGTL-----------LLENDDRPCLPA-------ELIVHSPTQASLTLHEGRYH 191

Query: 254 QLRVHALHMGCPI 266
           Q R   + +G  +
Sbjct: 192 QARRMFVALGNHV 204


>gi|91788475|ref|YP_549427.1| ribosomal large subunit pseudouridine synthase B [Polaromonas sp.
           JS666]
 gi|91697700|gb|ABE44529.1| ribosomal large subunit pseudouridine synthase B [Polaromonas sp.
           JS666]
          Length = 544

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 77/235 (32%), Gaps = 51/235 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      RIQ G  V++                         
Sbjct: 110 SRLEMEQLILEGRISVNAEPAHIGQRIQFGDTVKVN------------------------ 145

Query: 93  HSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
               ++  +     ++  ++KP+G +           +   L      K Q      RLD
Sbjct: 146 -GKPIRVRIDPPPPRVIAYHKPSGEVVTHDDPQNRPTVFRRLPKLFQGKWQS---VGRLD 201

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             T G+L++  +   A  L        +++ Y   V G   N+++     L   +   G 
Sbjct: 202 LNTEGLLLLTSSGELANKL--MHPRFGLEREYAVRVLGALSNEEK--KRLLEGVTLDDG- 256

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRVHALHMGC 264
                          ++ F  I+    +   CW  +    GR  ++R     +G 
Sbjct: 257 ---------------VAQFSSIEAGGGEGANCWYRVTISEGRNREVRRMFEAVGH 296


>gi|77408873|ref|ZP_00785599.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae COH1]
 gi|77172512|gb|EAO75655.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae COH1]
          Length = 239

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 47/246 (19%), Positives = 80/246 (32%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +   ++K++RS QV VD + V                         
Sbjct: 1   MRLDKLLGQAGFG-SRNQVKKLIRSRQVSVDGQIVT------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K+  I+DS +         K  +  ++S  Y+  KP+G+        + H          
Sbjct: 36  KDNVIVDSGLQSIFVG---KERVCLKESSYYLLYKPSGVVS--AVRDSEHKTVIDLISEK 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K +      RLD++T G+L++        + L        + K Y+  V G        
Sbjct: 91  DKVEGLYPIGRLDRDTEGLLIITNNGPLGYRMLH---PKHHVAKTYYVEVNGF------- 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                L++  I      VV  +      A      ID          +    G+ HQ++ 
Sbjct: 141 -----LERDAITFFEEGVVFDDGTKCKPAEL---TIDTANNDKSTARITITEGKFHQVKK 192

Query: 258 HALHMG 263
             L  G
Sbjct: 193 MFLAYG 198


>gi|238798380|ref|ZP_04641862.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           mollaretii ATCC 43969]
 gi|238717765|gb|EEQ09599.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           mollaretii ATCC 43969]
          Length = 342

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/178 (17%), Positives = 60/178 (33%), Gaps = 27/178 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +       H +   ++ I++ G+V VD K     +R++  Q  +I    + L+  
Sbjct: 27  GEKLQKVLARA-GHGSRREIETIIQQGRVSVDGKISTLGDRVEVTQATKIRLDGHLLSIT 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ +                       ++  + KP G                     
Sbjct: 86  ESEEAVC----------------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLP 121

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 122 KLRGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDEK 177


>gi|157370902|ref|YP_001478891.1| 23S rRNA pseudouridylate synthase B [Serratia proteamaculans 568]
 gi|157322666|gb|ABV41763.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 299

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 61/175 (34%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ I+ +G+V VD K  K  +R++    ++I    + ++    E
Sbjct: 5   LQKVLARA-GHGSRREIETIIEAGRVSVDGKIAKLGDRVEVTASMKIRLDGHVVSIKESE 63

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +++                       ++  + KP G                       +
Sbjct: 64  EEVC----------------------RVLAYYKPEGELC--TRSDPEGRPTVFDRLPKLR 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 100 GSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDEK 152


>gi|91226537|ref|ZP_01261286.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
 gi|91189169|gb|EAS75450.1| ribosomal small subunit pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
          Length = 233

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 77/246 (31%), Gaps = 52/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++  +           KI++SG + VD +  K    ++  G  V            
Sbjct: 1   MRLDKYLCDAL-GATRKQATKIIKSGDITVDGEVQKSGAFKVPKGAEV------------ 47

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + E +++ +           + I+LY         KPA        G        L    
Sbjct: 48  MWEDRVIGAPGP--------RYIMLY---------KPADFVCSHEDGYNQTAFALLD--- 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + K +      RLD +T+G++++      +  +T            W +    P   ++ 
Sbjct: 88  EPKIENLHFAGRLDVDTTGLVLITDDGKWSHRITSPKHKCEKTYRVWLVDAIQPDYAEKL 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               +L+                       +    ++   +    + +    G+ HQ++ 
Sbjct: 148 EQGIILRNESEA------------------TLPARLEIVNEAENEVLLTIVEGKYHQVKR 189

Query: 258 HALHMG 263
               +G
Sbjct: 190 MFAALG 195


>gi|325134403|gb|EGC57048.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M13399]
 gi|325142531|gb|EGC64931.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis 961-5945]
 gi|325198505|gb|ADY93961.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis G2136]
 gi|325200018|gb|ADY95473.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis H44/76]
          Length = 256

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/236 (15%), Positives = 72/236 (30%), Gaps = 32/236 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G + V+ K  +  +++     V +   I  L  
Sbjct: 2   EPERLQKVLAASGVG-SRREMEEWITNGWITVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 58

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 59  ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 94  PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +          G   V  ++  E+G   A   + V+    +      +    G T
Sbjct: 152 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLT 205


>gi|254672143|emb|CBA04924.1| conserved hypothetical protein [Neisseria meningitidis alpha275]
          Length = 349

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/236 (16%), Positives = 72/236 (30%), Gaps = 32/236 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 244

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +          G   V  ++  E+G   A   + V+    +      +    G T
Sbjct: 245 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLT 298


>gi|238763121|ref|ZP_04624087.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           kristensenii ATCC 33638]
 gi|238698620|gb|EEP91371.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           kristensenii ATCC 33638]
          Length = 324

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/178 (17%), Positives = 61/178 (34%), Gaps = 27/178 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +       H +   ++ I++ G+V VD K  K  +R++  Q  +I    + L+  
Sbjct: 9   GEKLQKILARA-GHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLLSIK 67

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ +                       ++  + KP G                     
Sbjct: 68  ESEEAVC----------------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLP 103

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 104 KLRGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDEK 159


>gi|237728101|ref|ZP_04558582.1| 23S rRNA pseudouridine synthase F [Citrobacter sp. 30_2]
 gi|226910112|gb|EEH96030.1| 23S rRNA pseudouridine synthase F [Citrobacter sp. 30_2]
          Length = 291

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/250 (13%), Positives = 74/250 (29%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    +++  G VV++   +   
Sbjct: 4   DSSIRLNKYISE--SGICSRREADRFIEQGNVFLNGKRATIGDQVMPGDVVKVNGRLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED      NKP GI          +I  F+ 
Sbjct: 62  REA--------------------------EDLVFIALNKPVGIVSTTEDSERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + + +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPVTDDFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLIQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|34762584|ref|ZP_00143579.1| Ribosomal small subunit pseudouridine synthase A [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
 gi|237741688|ref|ZP_04572169.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           4_1_13]
 gi|256845012|ref|ZP_05550470.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           3_1_36A2]
 gi|294785701|ref|ZP_06750989.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           3_1_27]
 gi|27887750|gb|EAA24824.1| Ribosomal small subunit pseudouridine synthase A [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
 gi|229429336|gb|EEO39548.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           4_1_13]
 gi|256718571|gb|EEU32126.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           3_1_36A2]
 gi|294487415|gb|EFG34777.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           3_1_27]
          Length = 226

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 82/211 (38%), Gaps = 38/211 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++K++ + ++ V+                        ++ I+
Sbjct: 1   MRLDKFLVECGIG-SRKEVKKLISNDEITVNG-----------------------MSDIL 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +  I ++S  +  + + L+    Y++ + Y+ NK AG            +   L  WV 
Sbjct: 37  PKDNIDENSDIIEYNGERLE----YKEFRYYIMNKKAGYITATEDFKENTVMDLLPEWVI 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYW---SLVWGIPKNK 194
            K   P    RLD++T G+L+     +   + L+    + ++  +      L   I K +
Sbjct: 93  RKDLAP--VGRLDKDTEGLLLFTNDGKLNHRLLSPKNHIDKVYYVEIENNILDEDILKLE 150

Query: 195 KEC-IANWLL---KKSHIGGDYVHVVKQNEK 221
           +   I N++    K   I  + +++  +  K
Sbjct: 151 QGVNIGNYITQPAKVEKISDNKIYLTIKEGK 181


>gi|329571723|gb|EGG53404.1| pseudouridine synthase B, ribosomal large subunit [Enterococcus
           faecalis TX1467]
          Length = 205

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/188 (20%), Positives = 75/188 (39%), Gaps = 25/188 (13%)

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSWVDS 139
           K L + V+     +     +  E+   Y+F KP G+  +V    G        +  +   
Sbjct: 3   KELGTQVSKQDTVEVDGVPIYQEEYGYYLFYKPRGVISAVSDDKGRK-----VVTDYFTD 57

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             ++     RLD +TSG+L++    + +Q LT       + K+Y + + G+P  +     
Sbjct: 58  VTERIYPVGRLDYDTSGLLLLTNDGSFSQKLT--HPKHEVDKVYVAKIKGVPTKRDLL-- 113

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVH 258
             L K   I G               A ++F+++    +     +E+  H GR HQ++  
Sbjct: 114 -PLAKGIRIDGKR------------TAPANFQILSADIKTGSSVVELTIHEGRNHQVKKM 160

Query: 259 ALHMGCPI 266
              +G P+
Sbjct: 161 FQAVGFPV 168


>gi|300114572|ref|YP_003761147.1| RNA-binding S4 domain-containing protein [Nitrosococcus watsonii
           C-113]
 gi|299540509|gb|ADJ28826.1| RNA-binding S4 domain protein [Nitrosococcus watsonii C-113]
          Length = 268

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 70/232 (30%), Gaps = 32/232 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +   ++  +++G+VR++    +  +++     V I     +   + 
Sbjct: 3   ERLQKILARGGLG-SRREVEAWIKAGRVRINGIPAQLGDKVSDEDQVTINGRPLSPRRLQ 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                ++LY        +K AG                 +S   
Sbjct: 62  APS----------------SQVILY--------HKSAGEIC--SRKDPEGRPTVFRSLPR 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +     RLD  TSG+L+       A  L       ++++ Y   V G         
Sbjct: 96  PRQGRWVSVGRLDISTSGLLLFTTDGELANRL--MHPSTQVEREYAVRVLGAVTEATLER 153

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
               ++       +  ++    +GAN+    + VI    +K     +    G
Sbjct: 154 LQRGVQLEDGLASFKRILDAGGEGANH---WYHVILREGRKREVRRLWESQG 202


>gi|293395935|ref|ZP_06640216.1| ribosomal large subunit pseudouridine synthase B [Serratia
           odorifera DSM 4582]
 gi|291421433|gb|EFE94681.1| ribosomal large subunit pseudouridine synthase B [Serratia
           odorifera DSM 4582]
          Length = 297

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 60/177 (33%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS--GQVVRIPPVINALNHII 78
           L +       H +   ++ ++ +G+V VD K  K  +R++   G  +R+   + ++    
Sbjct: 5   LQKVLARA-GHGSRREIETMIEAGRVSVDGKIAKLGDRVEVVQGMKIRLDGHVVSI---- 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                        K S+     +L        + KP G                      
Sbjct: 60  -------------KESEEAVCRVL-------AYYKPEGELC--TRSDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDDK 152


>gi|238757070|ref|ZP_04618258.1| Ribosomal large subunit pseudouridine synthase B [Yersinia aldovae
           ATCC 35236]
 gi|238704900|gb|EEP97429.1| Ribosomal large subunit pseudouridine synthase B [Yersinia aldovae
           ATCC 35236]
          Length = 349

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/178 (17%), Positives = 61/178 (34%), Gaps = 27/178 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +       H +   ++ I++ G+V VD K     +R++  Q  +I    + L+  
Sbjct: 34  GEKLQKVLARA-GHGSRREIETIIQQGRVSVDGKISTLGDRVEVTQATKIRLDGHLLSIK 92

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ +                       ++  + KP G                     
Sbjct: 93  ESEETVC----------------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLP 128

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G +     RLD  TSG+L+       A  L      R +++ Y   V+G+  ++K
Sbjct: 129 KLRGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGLIDDEK 184


>gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudouridine synthase A [Herbaspirillum
           seropedicae SmR1]
 gi|300073839|gb|ADJ63238.1| ribosomal small subunit pseudouridine synthase A protein
           [Herbaspirillum seropedicae SmR1]
          Length = 240

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 85/248 (34%), Gaps = 52/248 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             + LDR  ++     +    ++++  G+V ++ + V            R  P    L  
Sbjct: 2   AKLTLDRILQSQGFG-SRKYCRELIEDGEVVINGEVV---------DDYRATPDTKDLVL 51

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            I E++                    Y +      NKP  I     S    H  G L   
Sbjct: 52  TIFEEEWE------------------YREHVYIAINKPPNI---ECSRKPSHHPGVLTLL 90

Query: 137 VDSKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +    +  +   RLD +T+G+L+++   A      +S   R + K+Y +          
Sbjct: 91  PEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFIHA--QSSPKRHVPKVYAATTA------- 141

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E +   L+ +   G      V+ +++ A  A +  + +         LE+    G+ HQ+
Sbjct: 142 EPVTEALIAQLKAG------VQLHDEPAPLAATRCRQL-----GENLLEIVLEQGKYHQV 190

Query: 256 RVHALHMG 263
           +      G
Sbjct: 191 KRMLAAAG 198


>gi|326797290|ref|YP_004315110.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
 gi|326548054|gb|ADZ93274.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
          Length = 355

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 76/247 (30%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +R++++       + +     + +  G V ++ KR    +++  G +V++         I
Sbjct: 7   IRINKYISE--SGLCSRREADRFIDQGSVFINGKRAGTGDQVSPGDLVKVN------GQI 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I+ Q+                     ED      NKP GI     S    +I  F+K   
Sbjct: 59  IEPQEA--------------------EDLIFIALNKPVGIVSTTESSEPANIVSFVKH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              G +     RLD+++ G++ +         +  +      + +               
Sbjct: 97  ---GARIFPIGRLDKDSQGLIFLTNNGDLVNKILRAANNHEKEYL--------------V 139

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             N  + ++ I G    V    +      +          +      +    G   Q+R 
Sbjct: 140 TVNKPITQAFIDGMSGGVPILGQVTKKCKV--------VKESTYVFNITLVQGLNRQIRR 191

Query: 258 HALHMGC 264
            A H G 
Sbjct: 192 MAEHFGY 198


>gi|325132446|gb|EGC55139.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M6190]
          Length = 349

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G + V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWITNGWITVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 244

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 245 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 302

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 303 VRVGFGPIGLP 313


>gi|324117539|gb|EGC11445.1| RNA pseudouridylate synthase [Escherichia coli E1167]
          Length = 299

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 62/177 (35%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 14  LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 65

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L+Y         KP G                      
Sbjct: 66  ---------ISVRESAEQICRVLVY--------YKPEGELC--TRNDPEGRPTVFDRLPK 106

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 107 LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 161


>gi|254756822|ref|ZP_05208850.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Australia 94]
          Length = 57

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 17/61 (27%), Positives = 23/61 (37%), Gaps = 6/61 (9%)

Query: 264 CPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSL 322
            P+ GD KY      +      N   LHA  +   HP  G  +Q  AP+P       + L
Sbjct: 1   YPLAGDPKYGPKKTLDM-----NGQALHAGILGFDHPRTGEYIQFEAPIPEVFEDALNIL 55

Query: 323 G 323
            
Sbjct: 56  R 56


>gi|222087732|ref|YP_002546269.1| heat shock protein (ribosome-associated) [Agrobacterium radiobacter
           K84]
 gi|221725180|gb|ACM28336.1| heat shock protein (ribosome-associated) [Agrobacterium radiobacter
           K84]
          Length = 134

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/141 (17%), Positives = 50/141 (35%), Gaps = 24/141 (17%)

Query: 19  MRLDRWF--KNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
            R+D+W          +    Q  ++ G VRV+ +R+   ++ +++G  + +        
Sbjct: 13  QRIDKWLFFARMLK--SRSLAQVYVQKGNVRVNGERITQPSHGVKAGDRIELS------- 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
            + +   IL   +   +   F ++ LLYED           ++        +        
Sbjct: 64  -LERRDVILIVRLPGDRRGPFEEARLLYED-----------LTPTPDPTKRFTPFEQALR 111

Query: 136 WVDSKGQKPRLTHRLDQETSG 156
              S     R    +D+ TSG
Sbjct: 112 SPGSGRPTKRERRAIDRLTSG 132


>gi|330004789|ref|ZP_08305026.1| ribosomal large subunit pseudouridine synthase F [Klebsiella sp. MS
           92-3]
 gi|328536522|gb|EGF62861.1| ribosomal large subunit pseudouridine synthase F [Klebsiella sp. MS
           92-3]
          Length = 284

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/250 (13%), Positives = 73/250 (29%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + + RL+++       I +     + +  G V ++ KR    ++++ G +V++   +   
Sbjct: 4   DSSTRLNKYISE--SGICSRREADRFIEQGNVFINGKRATIGDQVKPGDLVKVNGRLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        +D  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +   +    P   
Sbjct: 96  H-----SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL---VTVDKPVTD 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E I         +G        + E    + I+                     G   Q
Sbjct: 148 -EFIRGMGAGVPILGTVTKKCKVKKEAPFVFRIT------------------LVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|315655295|ref|ZP_07908195.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           curtisii ATCC 51333]
 gi|315490235|gb|EFU79860.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           curtisii ATCC 51333]
          Length = 278

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/255 (14%), Positives = 82/255 (32%), Gaps = 51/255 (20%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           E   E  RL +         +    + ++  G+V+++ + V+    ++     + +    
Sbjct: 36  EATSEPERLQKVLSRA-GVASRRASEDLIARGRVQINGETVREMGVKVLPTDRITVDGQR 94

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              + +++                            ++ F+KP G              G
Sbjct: 95  IHTDTVLQ----------------------------VWAFHKPVGTVSSMQPEDDRPCIG 126

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
               WV    ++     RLD  T+G+L++      A  +        + K Y ++V G  
Sbjct: 127 ---DWVTKLPERVYNVGRLDAATAGLLLLTNNGELANRI--MHPSYEVPKTYVAVVQGQV 181

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K               +G   V       +     +  FK+I+   +    +++  H+G+
Sbjct: 182 K---------------MGLGKVLRRGVELEDGKVKVDKFKLIEVR-RGSSIVQLTLHSGK 225

Query: 252 THQLRVHALHMGCPI 266
              +R     +G P+
Sbjct: 226 NRVVRRLLSAVGHPV 240


>gi|89095415|ref|ZP_01168328.1| putative ribosomal small subunit pseudouridine synthase A
           [Oceanospirillum sp. MED92]
 gi|89080322|gb|EAR59581.1| putative ribosomal small subunit pseudouridine synthase A
           [Oceanospirillum sp. MED92]
          Length = 237

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/240 (16%), Positives = 82/240 (34%), Gaps = 53/240 (22%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+   H    +  +++ ++  G+V V++              V +  +I   + +I 
Sbjct: 7   RLDRFIAKH-TDHSKNDVRILIAKGRVYVNQTVA-----------VSVDQIIKQFDEVIL 54

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + ++L  +  +                   + NKPAG+           +   L    D 
Sbjct: 55  DDEVLQKNTPI-----------------YLMLNKPAGVVSATSDPQHTTVIDLL----DD 93

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             +   +  RLD+ ++G+L++      +  L+      R+ K Y      I + K+    
Sbjct: 94  HYKDLHIAGRLDRFSTGLLLLTNDGEWSNSLS--HPDNRVAKRY------IVELKEPITD 145

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            +    +   G +        + A       +V           E+  H GR HQ++   
Sbjct: 146 AY--GDAFAKGMHFAYEDITTQPAQLKQLEPRV----------AEVTLHEGRYHQIKRMF 193


>gi|296100644|ref|YP_003610790.1| 23S rRNA pseudouridine synthase F [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295055103|gb|ADF59841.1| 23S rRNA pseudouridine synthase F [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 289

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/165 (15%), Positives = 52/165 (31%), Gaps = 34/165 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +     + +  G V ++ KR    +++  G VV++   +      
Sbjct: 7   IRLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVMPGDVVKVNGQLIEPRDA 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     ED      NKP GI      G   +I  F+    
Sbjct: 65  --------------------------EDLVFIALNKPVGIVSTTEDGERDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +     RLD+++ G++ +         +  +      + I
Sbjct: 97  ---SSRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYI 138


>gi|259906718|ref|YP_002647074.1| 23S rRNA pseudouridine synthase F [Erwinia pyrifoliae Ep1/96]
 gi|224962340|emb|CAX53795.1| Ribosomal large subunit pseudouridine synthase F [Erwinia
           pyrifoliae Ep1/96]
 gi|283476501|emb|CAY72316.1| putative pseudouridylate synthase [Erwinia pyrifoliae DSM 12163]
          Length = 292

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/165 (15%), Positives = 57/165 (34%), Gaps = 34/165 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR    +R+ +G VV++   +    + 
Sbjct: 7   IRLNKYIGE--SGICSRRDADRYIEQGNVFINGKRASVGDRVFAGDVVKVNGQLIEPRNE 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     ED  +   NKP GI      G   +I  F+    
Sbjct: 65  --------------------------EDLVVIALNKPVGIISTTEEGERDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  ---SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|112280311|gb|ABI14689.1| pseudouridylate synthase [Plasmodium chabaudi chabaudi]
 gi|112280313|gb|ABI14690.1| pseudouridylate synthase [Plasmodium chabaudi chabaudi]
          Length = 157

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 20/102 (19%), Positives = 41/102 (40%), Gaps = 19/102 (18%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           ++ G ++V+ K +  +  I+S   +           ++ E+ +L           + K I
Sbjct: 74  IKKGYIKVNNKNITNDYIIKSNDFIE-------HKLLLFEKPVL-----------YNKII 115

Query: 101 LLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKSWVDSKG 141
           +LYED      NK A +     GS     +   L++++   G
Sbjct: 116 ILYEDENFICVNKVASMPTHPVGSYQYNSLLRILQNYISQSG 157


>gi|157960717|ref|YP_001500751.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157845717|gb|ABV86216.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 234

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 46/249 (18%), Positives = 88/249 (35%), Gaps = 52/249 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+       IN  +++ +L  GQV VD +  +            I  +I+  +H+  
Sbjct: 7   RLDRFISAK-TGINKKHVRLLLAKGQVLVDGEVAR-----------DIDQIIDEFSHVCL 54

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + K+L ++            ++LY         KP G+     + +       +      
Sbjct: 55  DGKVLQANAP--------SYVMLY---------KPVGVVS---ATVDDKHRTVIDLLERD 94

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                 +  RLD  TSG+L++      ++ L       ++ K+Y   +       +  IA
Sbjct: 95  DKHSLHIVGRLDLNTSGLLLLTNDGRWSKKL--MSPDHKVGKVYRVTLKN--PIDESYIA 150

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
            +       GG Y        + A       +++D        +E     GR HQ++   
Sbjct: 151 AF------AGGMYFAFEDITTQPAK-----LEIVDEHTALVTLVE-----GRYHQIKRMF 194

Query: 260 LHMGCPIVG 268
                P++G
Sbjct: 195 GRFRNPVIG 203


>gi|262045577|ref|ZP_06018597.1| ribosomal large subunit pseudouridine synthase F [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|259037074|gb|EEW38325.1| ribosomal large subunit pseudouridine synthase F [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
          Length = 291

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/250 (13%), Positives = 73/250 (29%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + + RL+++       I +     + +  G V ++ KR    ++++ G +V++   +   
Sbjct: 4   DSSTRLNKYISE--SGICSRREADRFIEQGNVFINGKRATIGDQVKPGDLVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        +D  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +   +    P   
Sbjct: 96  H-----SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL---VTVDKPVTD 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E I         +G        + E    + I+                     G   Q
Sbjct: 148 -EFIRGMGAGVPILGTVTKKCKVKKEAPFVFRIT------------------LVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|124506829|ref|XP_001352012.1| pseudouridylate synthase, putative [Plasmodium falciparum 3D7]
 gi|23505040|emb|CAD51823.1| pseudouridylate synthase, putative [Plasmodium falciparum 3D7]
          Length = 955

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 224 NYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNF 280
             +I+ F  +   +      +  QP TGRTHQ+R H   +  PI  D  Y   F+  +
Sbjct: 738 KPSITKFMFLSYNSSIDESLILCQPITGRTHQIRAHLKSLSYPISNDAHYNKTFEQEY 795



 Score = 51.9 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/96 (18%), Positives = 37/96 (38%), Gaps = 20/96 (20%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           ++ G V+V+K+ V  +  IQS   +           ++ E+ +L + +           I
Sbjct: 92  IKKGYVKVNKQMVSTDYIIQSNDFIE-------HKLLLFEKPVLCNKI-----------I 133

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +LYED       K + +        +Y  +  L+  
Sbjct: 134 ILYEDQNFICVYKHSSLPTHPVG--SYQYNSLLRIL 167



 Score = 43.8 bits (102), Expect = 0.040,   Method: Composition-based stats.
 Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
           V   +    H D  LK+            HRLD+ TSGI+   + +  + + +++    +
Sbjct: 490 VPKYNSYNNHFDKDLKT---QDKSYIYTLHRLDKLTSGIVFFGKNKKFSTYFSQNLSDNK 546

Query: 179 IQKIYWSLVWGIPKN 193
           I+K Y + V G  + 
Sbjct: 547 IKKTYITRVQGDFRK 561


>gi|331269561|ref|YP_004396053.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum BKT015925]
 gi|329126111|gb|AEB76056.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum BKT015925]
          Length = 237

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 84/250 (33%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    ++I+   +V+V+ + V                         
Sbjct: 4   ERLQKYMAA-CGVASRRKCEEIISQDRVKVNCEIV------------------------- 37

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
             +        + K       I L E       NKP G +S          I   +K   
Sbjct: 38  -NELGFKVDPEIDKVYVDSVLITLEEQKVYIALNKPEGYVSTVKDERGRKTILDIVKV-- 94

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD  TSG++++         +        I K+Y +++ GIP + +  
Sbjct: 95  ---NERIFPIGRLDYNTSGLILLTNDGDVYNKI--IHPREEIDKVYIAVIKGIPSHDE-- 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K    G D    V         + + F++++    K C +++  H G+  Q+R 
Sbjct: 148 -----IKNFCNGIDIGGYV--------TSKASFEILEKLNDK-CKVKIIIHEGKNRQVRR 193

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 194 MCEKIGHPVI 203


>gi|170725411|ref|YP_001759437.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169810758|gb|ACA85342.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 236

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 80/249 (32%), Gaps = 52/249 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+   H   IN  N++ +L  GQVRVD +  +            I  +++  +HI  
Sbjct: 7   RLDRFISQHLK-INRKNVRLMLAKGQVRVDGELAR-----------DIDLIVDEFSHICV 54

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
             +++ +                   +   + +KP G+     + +       ++     
Sbjct: 55  NDEVIQAKQ-----------------ASYIMLHKPVGVVS---ATVDDKHKTVIELLKCD 94

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                 +  RLD  TSG+L++          ++       +      V          + 
Sbjct: 95  DRNSLHIVGRLDLNTSGLLLLTND----GRWSKQLMDPEYKVGKLYRVE---------LQ 141

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           N L  +           +  +     A    +++D         E     GR HQ++   
Sbjct: 142 NPLTVEYISAFAKGMYFEFEDITTLPA--ELEIVDSHTALVTLYE-----GRYHQIKRMF 194

Query: 260 LHMGCPIVG 268
                P+VG
Sbjct: 195 GRFRNPVVG 203


>gi|322499928|emb|CBZ35002.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 757

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 5/49 (10%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY-----CANFKGNFTSPIQNKL 288
             P+TGR HQ+R+H   +GCPIVGD  Y      A+  G  ++ +Q +L
Sbjct: 422 CTPYTGRLHQIRMHLSSLGCPIVGDVVYAHTSGNADVPGTSSTQVQPQL 470



 Score = 39.2 bits (90), Expect = 0.90,   Method: Composition-based stats.
 Identities = 13/44 (29%), Positives = 25/44 (56%), Gaps = 2/44 (4%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTE--SFRMRRIQKIYWS 185
           PR  HRLD+ TSG+L++A  + AA+ +      + + + +   +
Sbjct: 147 PRPCHRLDKVTSGVLLLAVRQDAARRIGSVLMRKAKEVDEAVTA 190


>gi|146089719|ref|XP_001470456.1| hypothetical protein [Leishmania infantum JPCM5]
 gi|134070489|emb|CAM68832.1| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 757

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 5/49 (10%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY-----CANFKGNFTSPIQNKL 288
             P+TGR HQ+R+H   +GCPIVGD  Y      A+  G  ++ +Q +L
Sbjct: 422 CTPYTGRLHQIRMHLSSLGCPIVGDVVYAHTSGNADVPGTSSTQVQPQL 470



 Score = 39.2 bits (90), Expect = 0.90,   Method: Composition-based stats.
 Identities = 13/44 (29%), Positives = 25/44 (56%), Gaps = 2/44 (4%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTE--SFRMRRIQKIYWS 185
           PR  HRLD+ TSG+L++A  + AA+ +      + + + +   +
Sbjct: 147 PRPCHRLDKVTSGVLLLAVRQDAARRIGSVLMRKAKEVDEAVTA 190


>gi|15902641|ref|NP_358191.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae R6]
 gi|116516226|ref|YP_816091.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae D39]
 gi|15458178|gb|AAK99401.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae R6]
 gi|116076802|gb|ABJ54522.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae D39]
          Length = 241

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 79/248 (31%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD         I+   +++ L  G++ VD    +                        
Sbjct: 1   MRLDNLLAQ--EKISRKAMKQALLRGKILVDGCPARS----------------------- 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILL--YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                L  +++        +  ++  YE + + +  KPAG+           +   L S 
Sbjct: 36  -----LAQNIDTGLQELLFQDRIIQGYEHTYLMLH-KPAGVVTANKDKELPTVMDLLPS- 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            D +  K     RLD++T+G+L++        Q L   + + +  ++             
Sbjct: 89  -DIQSDKLYAVGRLDRDTTGLLLLTDNGPLGFQLLHPQYHVDKTYQVE------------ 135

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
               N LL   HI      +V  +      A      I   +       +    G+ HQ+
Sbjct: 136 ---VNGLLTPDHIQAFQKGIVFLDGTVCKPAKLE---ILSASPSISQASITISEGKFHQI 189

Query: 256 RVHALHMG 263
           +   L +G
Sbjct: 190 KKMFLSVG 197


>gi|192361094|ref|YP_001982433.1| ribosomal small subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
 gi|190687259|gb|ACE84937.1| ribosomal small subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
          Length = 234

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/246 (13%), Positives = 82/246 (33%), Gaps = 54/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            RLD +  N+        +Q+++++G+V +D K V +   ++   + VR+   +      
Sbjct: 3   QRLDAFISNN-SDFTRSQIQRLIKAGRVHIDDKPVSQGAQKLNGTESVRVDGEL------ 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                              L+ ++L++       N  +                 L    
Sbjct: 56  --------------IEPLSLRYLMLHKPQGYVCANTDSE---HPT---------VLDLID 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             + Q  ++  RLD +T+G++++         +T   R    +              +  
Sbjct: 90  LPRKQTLQIAGRLDLDTTGLVLLTDDGQWNHRITSPRRECSKRY-------------RVT 136

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            A  +   +     +   ++ + +      +H ++ID +        +  H G+ HQ++ 
Sbjct: 137 TAEPIAADT--AHYFTDGIQLHGEKHKTRPAHLELIDDYNAW-----LDIHEGKYHQVKR 189

Query: 258 HALHMG 263
                G
Sbjct: 190 MFAATG 195


>gi|188995083|ref|YP_001929335.1| ribosomal large subunit pseudouridine synthase B [Porphyromonas
           gingivalis ATCC 33277]
 gi|188594763|dbj|BAG33738.1| ribosomal large subunit pseudouridine synthase B [Porphyromonas
           gingivalis ATCC 33277]
          Length = 439

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 44/282 (15%), Positives = 94/282 (33%), Gaps = 54/282 (19%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V+ + +E  +RL+++  N     +      ++  G++ V+ + V             +
Sbjct: 194 REVLADPNE-PIRLNKFLSNA-GVCSRREADLLIEKGEITVNGEVVT-----------EL 240

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
              I   + +I + K ++                  E     + NKP        S    
Sbjct: 241 GRRITRQDEVIYKDKRVEI-----------------ESKVYVLLNKPKNCVT--TSDDPE 281

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                +     +  ++     RLD+ T+G+L++      A  LT     ++     W L 
Sbjct: 282 CRTTVMDIVRYACPERIYPVGRLDRNTTGVLLITNDGDLASKLTHPSFKKKKIYHVW-LN 340

Query: 188 WGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             +     + IA+ + L    I  D +  VK+++                      + ++
Sbjct: 341 KDVSIEDMQKIADGVELDDGEIHADAISYVKEDD-------------------LSQVGIE 381

Query: 247 PHTGRTHQLRVHALHMGCPIVG-DHKYCANFKGNFTSPIQNK 287
            H+GR   +R    H+G  +V  D  Y A          + +
Sbjct: 382 IHSGRNRIVRRLFEHLGYRVVKLDRVYFAGLTKKNLPRGKWR 423


>gi|156974936|ref|YP_001445843.1| ribosomal small subunit pseudouridine synthase A [Vibrio harveyi
           ATCC BAA-1116]
 gi|156526530|gb|ABU71616.1| hypothetical protein VIBHAR_02655 [Vibrio harveyi ATCC BAA-1116]
          Length = 233

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 73/249 (29%), Gaps = 58/249 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++  +           KI++SG++ VD +  K    ++  G VV            
Sbjct: 1   MRLDKYLCDGL-GATRKQATKIIKSGEITVDGEVQKSGAFKVPEGGVVEWEGREVG---- 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                           +   + I+LY+ +                S    H         
Sbjct: 56  ----------------APGPRYIMLYKPADFVC------------SHEDGHNPTAFVLLD 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW---SLVWGIPKNK 194
           + K +      RLD +T+G++++      +  +T            W   ++     +  
Sbjct: 88  EPKVENLHFAGRLDVDTTGLVLITDDGQWSHRITSPKHKCEKTYRVWLVDAIQPDYVEKF 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E I     ++  +                        ++   +    + +    G+ HQ
Sbjct: 148 AEGIELRNEREPTLPAH---------------------LEIVNEAENEVLLTIVEGKYHQ 186

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 187 VKRMFAALG 195


>gi|168482908|ref|ZP_02707860.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC1873-00]
 gi|172043870|gb|EDT51916.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC1873-00]
 gi|332203838|gb|EGJ17905.1| hypothetical protein SPAR93_0709 [Streptococcus pneumoniae GA47368]
          Length = 241

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 79/248 (31%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD         I+   +++ L  G++ VD    +                        
Sbjct: 1   MRLDNLLAQ--EKISRKAMKQALLRGKILVDGCPARS----------------------- 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILL--YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                L  +++        +  ++  YE + + +  KPAG+           +   L S 
Sbjct: 36  -----LAQNIDTGLQELLFQDRIIQGYEHTYLMLH-KPAGVVTANKDKELPTVMDLLPS- 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            D +  K     RLD++T+G+L++        Q L   + + +  ++             
Sbjct: 89  -DIQSDKLYAVGRLDRDTTGLLLLTDNGPLGFQLLHPQYHVDKTYQVE------------ 135

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
               N LL   HI      +V  +      A      I   +       +    G+ HQ+
Sbjct: 136 ---VNGLLTPDHIQAFQKGIVFLDGTVCKPAKLE---ILSASPSISQASITISEGKFHQI 189

Query: 256 RVHALHMG 263
           +   L +G
Sbjct: 190 KKMFLSVG 197


>gi|238926990|ref|ZP_04658750.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
 gi|238885224|gb|EEQ48862.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
          Length = 290

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 74/247 (29%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   N     +    + ++R+G+V VD   V                +    +   
Sbjct: 3   ERLQKIISNA-GAASRRAAEALIRAGRVTVDGLPVTA--------------LGGKYDAAR 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +  + +   +                 + +KP G      +         +   + 
Sbjct: 48  HEIAVDGTPIRRNERR------------FYILLHKPRGCLS---TAYDDRGRRTVLDLLP 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC- 197
               +     RLD +T G+L++    A  Q L        I K+Y + V G         
Sbjct: 93  HFPARLYPVGRLDADTEGLLIITNDGAMTQGL--LHPRFEIDKVYRAEVTGNVTEDGLTA 150

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + N +L                      A +  +V+    ++   +E   H GR  Q+R 
Sbjct: 151 LRNGILLDD----------------GRTAPARLRVLHREGER-TVVETIIHEGRKRQVRR 193

Query: 258 HALHMGC 264
               +GC
Sbjct: 194 MFAAIGC 200


>gi|149190891|ref|ZP_01869154.1| pseudouridine synthase family 1 protein [Vibrio shilonii AK1]
 gi|148835246|gb|EDL52220.1| pseudouridine synthase family 1 protein [Vibrio shilonii AK1]
          Length = 310

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/232 (17%), Positives = 77/232 (33%), Gaps = 34/232 (14%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   L+ +++SG+V V+ +  +   R++    V+RI     +      
Sbjct: 5   LQKVLARA-GHGSRRELEALIKSGRVSVNGQVARLGERLEDENAVIRIDGHTVS------ 57

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                       K  + +   +L        + KP G                       
Sbjct: 58  -----------AKAQEEVVCRVL-------AYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    KK    
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEINEKKVRNV 155

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
              ++       +  VV    +G N+  + + VI+     +     E Q  T
Sbjct: 156 VNGVELEDGMARFEDVVYAGGEGMNH--TFYVVINEGRNREVRRLWESQETT 205


>gi|165869849|ref|ZP_02214507.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0488]
 gi|167633985|ref|ZP_02392308.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0442]
 gi|167637988|ref|ZP_02396266.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0193]
 gi|170685858|ref|ZP_02877081.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0465]
 gi|170705568|ref|ZP_02896032.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0389]
 gi|177651245|ref|ZP_02934076.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0174]
 gi|190568332|ref|ZP_03021240.1| RNA pseudouridine synthase family protein [Bacillus anthracis
           Tsiankovskii-I]
 gi|196033247|ref|ZP_03100660.1| RNA pseudouridine synthase family protein [Bacillus cereus W]
 gi|196040819|ref|ZP_03108117.1| RNA pseudouridine synthase family protein [Bacillus cereus
           NVH0597-99]
 gi|196043991|ref|ZP_03111228.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB108]
 gi|225866694|ref|YP_002752072.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB102]
 gi|228917358|ref|ZP_04080911.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|228929759|ref|ZP_04092776.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228936016|ref|ZP_04098826.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228948455|ref|ZP_04110737.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|229186962|ref|ZP_04314116.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|229600897|ref|YP_002868983.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0248]
 gi|254687515|ref|ZP_05151371.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           anthracis str. CNEVA-9066]
 gi|254725079|ref|ZP_05186862.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           anthracis str. A1055]
 gi|254736817|ref|ZP_05194523.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           anthracis str. Western North America USA6153]
 gi|254741853|ref|ZP_05199540.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           anthracis str. Kruger B]
 gi|254754548|ref|ZP_05206583.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           anthracis str. Vollum]
 gi|254757380|ref|ZP_05209407.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           anthracis str. Australia 94]
 gi|270000608|ref|YP_003329047.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           Ames]
 gi|291612224|ref|YP_003541038.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           'Ames Ancestor']
 gi|301056214|ref|YP_003794425.1| RNA pseudouridylate synthase [Bacillus anthracis CI]
 gi|164714678|gb|EDR20197.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0488]
 gi|167513805|gb|EDR89173.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0193]
 gi|167530786|gb|EDR93488.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0442]
 gi|170129693|gb|EDS98556.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0389]
 gi|170670322|gb|EDT21062.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0465]
 gi|172083071|gb|EDT68133.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0174]
 gi|190560588|gb|EDV14565.1| RNA pseudouridine synthase family protein [Bacillus anthracis
           Tsiankovskii-I]
 gi|195994676|gb|EDX58631.1| RNA pseudouridine synthase family protein [Bacillus cereus W]
 gi|196025327|gb|EDX63997.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB108]
 gi|196028273|gb|EDX66882.1| RNA pseudouridine synthase family protein [Bacillus cereus
           NVH0597-99]
 gi|224552861|gb|ACN55070.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           'Ames Ancestor']
 gi|225786978|gb|ACO27195.1| RNA pseudouridine synthase family protein [Bacillus cereus 03BB102]
 gi|228596516|gb|EEK54182.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|228811214|gb|EEM57553.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|228823784|gb|EEM69606.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228829938|gb|EEM75558.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228842285|gb|EEM87380.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|229265305|gb|ACQ46942.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           A0248]
 gi|269850291|gb|ACZ49996.1| RNA pseudouridine synthase family protein [Bacillus anthracis str.
           Ames]
 gi|300378383|gb|ADK07287.1| RNA pseudouridylate synthase [Bacillus cereus biovar anthracis str.
           CI]
          Length = 242

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 95/246 (38%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGISVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K+   G     ++    +    A++  K     +     +E+    G+ HQ++ 
Sbjct: 146 -----VKEFAKG----VILDDGYETKPGALTILK-----SDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|149194803|ref|ZP_01871897.1| Pseudouridine synthase, Rsu [Caminibacter mediatlanticus TB-2]
 gi|149134962|gb|EDM23444.1| Pseudouridine synthase, Rsu [Caminibacter mediatlanticus TB-2]
          Length = 256

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 84/246 (34%), Gaps = 41/246 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRL+++   H+   +     K++  G+V+V+ K V      +  G  V +          
Sbjct: 1   MRLNKFIS-HHTSFSRREADKLIFDGKVKVNGKVVTNPAYEVLDGDKVAVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
               K +  S   T         ++Y        NKP G  V   +         +   +
Sbjct: 51  ---GKPVKKSTKYT--------CIIY--------NKPRGELV---TKKDDRGRKTIYDSL 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             K +      RLD  + G+L++  +   A  L +S   R  +      + G    +   
Sbjct: 89  PKKYKHFIPIGRLDFASEGLLILTDSPKVADALMKSDLPRVYKLR----IKGNITPE--- 141

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I   + +   IG +  H   + EK        +++I    +     ++    G+  +LR 
Sbjct: 142 IEKAMQEGVEIGVEGAHEKTKQEKIKLKPFYSYQIIKNDPKYSTL-KVAITEGKNRELRR 200

Query: 258 HALHMG 263
              H G
Sbjct: 201 FFAHFG 206


>gi|189425784|ref|YP_001952961.1| pseudouridine synthase [Geobacter lovleyi SZ]
 gi|189422043|gb|ACD96441.1| pseudouridine synthase [Geobacter lovleyi SZ]
          Length = 274

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 45/278 (16%), Positives = 86/278 (30%), Gaps = 56/278 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +    ++++ +G+V V+ + V                     +     + ++       K
Sbjct: 16  SRRAAEEMILAGRVTVNGQVVT-----------------ELGSKADPAKDLIALDGQPVK 58

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
            ++    +LL+         KPAG      S         +   V   G++     RLD 
Sbjct: 59  PAETFYYVLLH---------KPAGYVT---SLKDPQGRQLVTELVKDVGERLFPVGRLDY 106

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            + G+L++    A A  L       ++ K Y   V G        I    +KK   G + 
Sbjct: 107 NSEGLLLLTNDGAWANRL--MHPRHQVDKEYHVRVRGK-------IDPQQIKKLADGVEL 157

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK- 271
                   +      +  +++           +    GR  Q+R     +G  +V     
Sbjct: 158 --------EDGPTGATTVRLLKNDQSNDWLS-VTIREGRNRQVRRMCAAVGLFVV--RLR 206

Query: 272 ---YCANFKGNFTSPIQNKLY--LHARYMDLPHPEGGR 304
              Y     G    P + +L     A+ +D P P   R
Sbjct: 207 RIRYGNLTLGGL-QPGEYRLLSREEAQALDAPPPVKQR 243


>gi|325205871|gb|ADZ01324.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M04-240196]
          Length = 349

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G + V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWITNGWITVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 244

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + V+    +      +    G T    
Sbjct: 245 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 302

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 303 VRVGFGPIGLP 313


>gi|94984870|ref|YP_604234.1| pseudouridine synthase, Rsu [Deinococcus geothermalis DSM 11300]
 gi|94555151|gb|ABF45065.1| Pseudouridine synthase, Rsu [Deinococcus geothermalis DSM 11300]
          Length = 253

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 47/297 (15%), Positives = 86/297 (28%), Gaps = 78/297 (26%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RL +         +    + ++ +G+V V+ +       +     VR+   +    
Sbjct: 3   EGGERLQKRLARA-GVASRRAAEDLITAGRVTVNGQIATLGRTVMPDDEVRVDGRL---- 57

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                         +   +    + LLY         KPAG      +   Y     L +
Sbjct: 58  --------------IEAPAQESVTFLLY---------KPAGYVT--TARDEYGRRNVLSA 92

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                G  P    RLD+++ G+L++         LT        +K Y +   G P   +
Sbjct: 93  MPPIPGLHP--VGRLDKDSEGLLLLTTDGQLTLTLTHPRYGH--EKAYRAWTAGQPVAAE 148

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +    ++ +  G       +    GA   ++                     GR  Q+
Sbjct: 149 LRVLETGIELA-DGPARALSARPARGGALVTLTE--------------------GRNRQV 187

Query: 256 RVHALHMGCPI------------VGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP 300
           R     +G P+            +GD             P + +L       DL HP
Sbjct: 188 RRMLDAIGYPVHRLLRYRVGGLWLGD-----------LEPGEYRLLSPRDLHDLLHP 233


>gi|50307743|ref|XP_453865.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|74606197|sp|Q6CQC4|PUS5_KLULA RecName: Full=Pseudouridylate synthase PUS5; AltName:
           Full=Pseudouridine synthase 5; AltName: Full=Uracil
           hydrolyase PUS5
 gi|49642999|emb|CAH00961.1| KLLA0D18172p [Kluyveromyces lactis]
          Length = 299

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 53/250 (21%), Positives = 83/250 (33%), Gaps = 44/250 (17%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGF----LKSWVDSKG--------- 141
            LK   L+ D    +FNKP     Q       Y+   +    L   V S           
Sbjct: 36  PLKVQELWRDKHHVIFNKPPLALSQLPDKRTWYNTHDYDPPVLLDIVQSSSGSILKDGTY 95

Query: 142 -QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
                  HR+D   SG +V A  + +AQ  + + R    +    +  +     K +    
Sbjct: 96  EPSYYPIHRIDTPVSGGIVYAVNKQSAQQFSRNLRYGGNKGFSLTRKYVAKVGKSKT--- 152

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
                        +  K+     N AI++F+ +D        L +Q  TG+ HQ+R    
Sbjct: 153 ------------ANECKEGLIKWNGAITYFQRVDNE-----HLILQLVTGKKHQIRKLTQ 195

Query: 261 H-MGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTW 319
             +  PI  D KY    K  F S  Q  L+       +      ++    P+P      W
Sbjct: 196 QVLDSPIYNDLKYGG--KKVFDSDFQIALHSAYIRTKIGFNIHEQI---IPVPDGFRMIW 250

Query: 320 DSLGFKYDRN 329
              G   D+N
Sbjct: 251 ---GESVDQN 257


>gi|163942437|ref|YP_001647321.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
 gi|229013913|ref|ZP_04171040.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
 gi|229135547|ref|ZP_04264331.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
 gi|163864634|gb|ABY45693.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
 gi|228647927|gb|EEL03978.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
 gi|228747383|gb|EEL97259.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
          Length = 242

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 89/246 (36%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   H +   ++K+L+ G V++D   VK                    +  +
Sbjct: 1   MRLDKLLAN-MGHGSRKEVKKLLKDGVVKIDGTPVK----------------DAKFHVNV 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    +   Q L+     + + K Y++ + G+   +   
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLITNDGKLTHQLLS---PKKHVPKKYYAHISGVVTEEDV- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                     I      +++   +     ++  K     +     +E+    G+ HQ++ 
Sbjct: 147 ----------IEFAKGVILEDGYETKPGELTILK-----SDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|162419712|ref|YP_001606744.1| 23S rRNA pseudouridylate synthase B [Yersinia pestis Angola]
 gi|162352527|gb|ABX86475.1| ribosomal large subunit pseudouridine synthase B [Yersinia pestis
           Angola]
          Length = 344

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/178 (17%), Positives = 60/178 (33%), Gaps = 27/178 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +       H +   ++ I++ G+V VD K  K  +R++  Q  +I    + L+  
Sbjct: 28  GEKLQKILARA-GHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLSIK 86

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ +                       ++  + KP G                     
Sbjct: 87  ESEENVC----------------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLP 122

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   + K
Sbjct: 123 KLRGSRWVAVGRLDVNTSGLLLFTTDGELANCL--MHPSREVEREYAVRVFGQIDDDK 178


>gi|296390923|ref|ZP_06880398.1| putative pseudouridylate synthase [Pseudomonas aeruginosa PAb1]
          Length = 230

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/243 (16%), Positives = 77/243 (31%), Gaps = 51/243 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+  N  P ++  + Q ++  G++RVD + V+          VR+   +     ++
Sbjct: 1   MRLDRFLAN-LPELSRRDAQMLIAGGRLRVDGQVVRDGTH-----EVRVFSRVELDERLL 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  K                       ++ Y+ +KP G      +         L  + +
Sbjct: 55  QAGKP----------------------ARYYMLHKPMGCVS---ATRDPQHPTVLDLFPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +     +  RLD  T+G++++      ++ LT     R         V       +  +
Sbjct: 90  DQRDDLHIGGRLDYNTTGLMLLTNDGQWSRRLTLPGSRRDKVYY----VETEAPIDQRYV 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
             +         D   +  Q E                        +  H GR HQ++  
Sbjct: 146 DAFAAGLHFRFEDLTTLPAQLEPIGPR----------------CARLTLHEGRYHQVKRM 189

Query: 259 ALH 261
             H
Sbjct: 190 FGH 192


>gi|221231495|ref|YP_002510647.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae ATCC 700669]
 gi|225854205|ref|YP_002735717.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae JJA]
 gi|220673955|emb|CAR68464.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae ATCC 700669]
 gi|225723188|gb|ACO19041.1| ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus pneumoniae JJA]
          Length = 241

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 79/248 (31%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD         I+   +++ L  G++ VD    +                        
Sbjct: 1   MRLDNLLAQ--EKISRKAMKQALLRGKILVDGCPARS----------------------- 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILL--YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                L  +++        +  ++  YE + + +  KPAG+           +   L S 
Sbjct: 36  -----LAQNIDTGLQELLFQDRIIQGYEHTYLMLH-KPAGVVTANKDKELPTVMDLLPS- 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            D +  K     RLD++T+G+L++        Q L   + + +  ++             
Sbjct: 89  -DIQSDKLYAVGRLDRDTTGLLLLTDNGPLGFQLLHPQYHVDKTYQVE------------ 135

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
               N LL   HI      +V  +      A      I   +       +    G+ HQ+
Sbjct: 136 ---VNGLLTPDHIQAFQKGIVFLDGTVCKPAKLE---ILSASPSISQASITISEGKFHQI 189

Query: 256 RVHALHMG 263
           +   L +G
Sbjct: 190 KKMFLSVG 197


>gi|241889716|ref|ZP_04777014.1| ribosomal large subunit pseudouridine synthase B [Gemella
           haemolysans ATCC 10379]
 gi|241863338|gb|EER67722.1| ribosomal large subunit pseudouridine synthase B [Gemella
           haemolysans ATCC 10379]
          Length = 243

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 84/249 (33%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +       + +    ++++  G+V V+ + VK    + +   ++ +         +
Sbjct: 3   ERLQKLIAAS-GYTSRRKAEQLILDGKVSVNGEVVKELGVKAEPSDIIIV-----EGVRL 56

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +KE K               +  L Y+  K+              S         +K + 
Sbjct: 57  LKENK---------------RYYLFYKPEKVI------------TSMSDEKDRTCVKDFF 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           ++  ++     RLD +TSG L+++        +T      +I+K Y + + G  ++    
Sbjct: 90  ENVNERVVPVGRLDYDTSGALIMSNDGEFINLIT--HPKHKIKKTYVAKINGKLEDNHLR 147

Query: 198 IANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           I    ++          V+VVK   K  N                  + +  H G+  Q+
Sbjct: 148 ILRNGVRIDNYKTAKAEVNVVKNKNKSGN----------------TLVRLTIHEGKNRQV 191

Query: 256 RVHALHMGC 264
           R     +G 
Sbjct: 192 RRMFEALGY 200


>gi|282600611|ref|ZP_05979218.2| ribosomal small subunit pseudouridine synthase A [Subdoligranulum
           variabile DSM 15176]
 gi|282571938|gb|EFB77473.1| ribosomal small subunit pseudouridine synthase A [Subdoligranulum
           variabile DSM 15176]
          Length = 237

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 72/242 (29%), Gaps = 50/242 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       +     +K +  G+V V+     K + ++     + +     A +  
Sbjct: 2   MRLDKYLSER-TGLTRSESRKAITKGRVAVNGMVCRKADTQVAEDAAIAVDGTPLAGS-- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                    Y+     + NKP G+           +   + +  
Sbjct: 59  -------------------------YQKYVYIMLNKPEGVVSASRDKRDTTVVDLVAADF 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +        RLD+ ++G +++    A A  L              S    + K     
Sbjct: 94  PRRA--LFPAGRLDKTSTGFVLLTDDGALAHDL-------------LSPAHHVDKQYLVT 138

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   L   +   G    V   + +    A +     +   +  C +++  H G  HQ++ 
Sbjct: 139 LDTPLT-DAMRAGFAAGVTLADGETMAPAEA-----EPAGEDPCVVKVTLHQGVYHQIKR 192

Query: 258 HA 259
             
Sbjct: 193 MF 194


>gi|168492837|ref|ZP_02716980.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC3059-06]
 gi|183576842|gb|EDT97370.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae CDC3059-06]
          Length = 241

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 79/248 (31%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD         ++   +++ L  G++ VD    +                        
Sbjct: 1   MRLDNLLAQ--EKVSRKAMKQALLRGKILVDGCPARS----------------------- 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILL--YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                L  +++        +  ++  YE + + +  KPAG+           +   L S 
Sbjct: 36  -----LAQNIDTGLQELLFQDRIIQGYEHTYLMLH-KPAGVVTANKDKELPTVMDLLPS- 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            D +  K     RLD++T+G+L++        Q L   + + +  ++             
Sbjct: 89  -DIQSDKLYAVGRLDRDTTGLLLLTDNGPLGFQLLHPQYHVDKTYQVE------------ 135

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
               N LL   HI      +V  +      A      I   +       +    G+ HQ+
Sbjct: 136 ---VNGLLTPDHIQAFQKGIVFLDGTVCKPAKLE---ILSASPSISQASITISEGKFHQI 189

Query: 256 RVHALHMG 263
           +   L +G
Sbjct: 190 KKMFLSVG 197


>gi|42783894|ref|NP_981141.1| RNA pseudouridylate synthase family protein [Bacillus cereus ATCC
           10987]
 gi|49478734|ref|YP_038752.1| pseudouridylate synthase (ribosomal small subunit pseudouridine
           synthase A) [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|206977314|ref|ZP_03238211.1| RNA pseudouridine synthase family protein [Bacillus cereus
           H3081.97]
 gi|217962194|ref|YP_002340764.1| RNA pseudouridine synthase family protein [Bacillus cereus AH187]
 gi|228987961|ref|ZP_04148067.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
 gi|229141441|ref|ZP_04269978.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|229158317|ref|ZP_04286384.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|42739824|gb|AAS43749.1| RNA pseudouridylate synthase family protein [Bacillus cereus ATCC
           10987]
 gi|49330290|gb|AAT60936.1| pseudouridylate synthase (ribosomal small subunit pseudouridine
           synthase A) [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|206744465|gb|EDZ55875.1| RNA pseudouridine synthase family protein [Bacillus cereus
           H3081.97]
 gi|217065826|gb|ACJ80076.1| RNA pseudouridine synthase family protein [Bacillus cereus AH187]
 gi|228625275|gb|EEK82035.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|228642004|gb|EEK98298.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|228771765|gb|EEM20225.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
          Length = 242

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 95/246 (38%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGISVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K+   G     ++    +    A++  K     +     +E+    G+ HQ++ 
Sbjct: 146 -----VKEFAKG----VILDDGYETKPGALTILK-----SDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|238789715|ref|ZP_04633498.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           frederiksenii ATCC 33641]
 gi|238722268|gb|EEQ13925.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           frederiksenii ATCC 33641]
          Length = 235

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 79/249 (31%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK      SG +            + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEVVK------SGAI-----------KLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEQDVRFDGNPLQQTVGP----------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L + +         +   +     A    +VI+        + +    GR HQ++  
Sbjct: 137 EHPLAEDTAQQFADGVQLHNEQSLTKPA--QLEVIEPQ-----VVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  ++
Sbjct: 190 FAAVGNRVL 198


>gi|300724003|ref|YP_003713317.1| 16S rRNA pseudouridylate 516 synthase [Xenorhabdus nematophila ATCC
           19061]
 gi|297630534|emb|CBJ91199.1| 16S rRNA pseudouridylate 516 synthase [Xenorhabdus nematophila ATCC
           19061]
          Length = 235

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 79/250 (31%), Gaps = 53/250 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++       I+  ++ + LR+G V VD + +K    +++  Q V     I    + 
Sbjct: 1   MRLDKFLSQQL-GISRNDVGRELRAGLVTVDNEVIKTGAYKLKLDQQVAYDGTIFQQLNG 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                             ++ NKP G      S         L    
Sbjct: 60  PR----------------------------YFMLNKPQGYVC---STDDPSNPTVLYFID 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    K     RLD +T+G++++      +  +T              LV       +E 
Sbjct: 89  EPVAHKLHSAGRLDIDTTGLVLLTDDGQWSHRITSPKHHCEKTY----LVTLEQPISEET 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
              +L      G   +       K A       ++I+        + +    GR HQ++ 
Sbjct: 145 EEKFLAGIQLNGEKTL------TKPAK-----LEIIEPQ-----IVRLTISEGRYHQVKR 188

Query: 258 HALHMGCPIV 267
               +G  +V
Sbjct: 189 MFAAVGNHVV 198


>gi|281412320|ref|YP_003346399.1| pseudouridine synthase [Thermotoga naphthophila RKU-10]
 gi|281373423|gb|ADA66985.1| pseudouridine synthase [Thermotoga naphthophila RKU-10]
          Length = 239

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 84/246 (34%), Gaps = 57/246 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MRLDR+  N         ++K+++ G+V V+ + V    + +    VV +       +  
Sbjct: 1   MRLDRYLSNSGVG-TRKEVKKLIKQGRVTVNGRVVLDPGHSVSENDVVVLDGETVNFHR- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                               K  +L+        +KP+G      S    H +  ++   
Sbjct: 59  --------------------KVYILF--------HKPSGYVT---STKDPHSETIMEFLP 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             KG  P    RLD++  G+L++           +     R+    WS+        +  
Sbjct: 88  PLKGIFP--VGRLDKDAEGLLIIT---------NDGDFAHRVTSPKWSVEKEYIVKVEGE 136

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I    ++K   G     V  ++   A       K ++  +     L++    GR HQ++ 
Sbjct: 137 ITEDKIEKLKNG-----VTLRDGFFAKA-----KCVEKLSNDT--LKIVITEGRYHQVKR 184

Query: 258 HALHMG 263
               +G
Sbjct: 185 MTAAVG 190


>gi|149182614|ref|ZP_01861084.1| 16S pseudouridylate synthase [Bacillus sp. SG-1]
 gi|148849692|gb|EDL63872.1| 16S pseudouridylate synthase [Bacillus sp. SG-1]
          Length = 239

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 31/178 (17%), Positives = 69/178 (38%), Gaps = 34/178 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D+   N   + +   ++K L+ G   V+ + VK                        
Sbjct: 1   MRIDKLLSN-MGYGSRKEVKKHLKGGGTVVNGEVVKD----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + ++   S  +T H +     ++Y +    + NKP G+           +   L+  ++
Sbjct: 37  PKFQVDPESDTVTVHGE----EVVYREFIYLMMNKPPGVLSATEDAEGETVIDLLE--ME 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +   P    RLD++T G+L++      + Q L+     + + K Y++++ G    + 
Sbjct: 91  DQIFNPFPVGRLDKDTEGLLLITNDGQLSHQLLS---PKKHVPKTYFAVIEGEVTEED 145


>gi|229193246|ref|ZP_04320197.1| hypothetical protein bcere0002_48930 [Bacillus cereus ATCC 10876]
 gi|228590223|gb|EEK48091.1| hypothetical protein bcere0002_48930 [Bacillus cereus ATCC 10876]
          Length = 164

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 8/49 (16%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ K++K N  +  G  + I 
Sbjct: 115 RIDKALSTYISDWSRTLIVDKIKNGDIQLNGKQMKPNTILSEGDHISIC 163


>gi|237830323|ref|XP_002364459.1| RNA pseudouridylate synthase family protein [Toxoplasma gondii
           ME49]
 gi|211962123|gb|EEA97318.1| RNA pseudouridylate synthase family protein [Toxoplasma gondii
           ME49]
 gi|221507328|gb|EEE32932.1| ribosomal pseudouridine synthase, putative [Toxoplasma gondii VEG]
          Length = 254

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 40/76 (52%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D+   K RL H+LD  TSG+L++A  + AA+ +    + R IQK Y +LV+G P+  +  
Sbjct: 144 DADACKVRLCHQLDYATSGLLMLAHNQKAARIVQTLLQRREIQKEYLALVYGHPRWSEVE 203

Query: 198 IANWLLKKSHIGGDYV 213
           +   +   S      +
Sbjct: 204 VETLVAPHSTHAFKMM 219


>gi|119470121|ref|ZP_01612887.1| ribosomal large subunit pseudouridine synthase E [Alteromonadales
           bacterium TW-7]
 gi|119446542|gb|EAW27816.1| ribosomal large subunit pseudouridine synthase E [Alteromonadales
           bacterium TW-7]
          Length = 227

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 40/183 (21%), Positives = 72/183 (39%), Gaps = 11/183 (6%)

Query: 86  SSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK-P 144
           S++    +   +K  +  +D KI +FNKP  +  Q      +  D   K+  +    K  
Sbjct: 26  SAIKKPTNKREIKPQIDAKDKKIVLFNKPFDVLCQ------FTDDADRKTLAEFIPIKDV 79

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
               RLD+++ G+L++         LT     ++  K YW  V G P  +    A     
Sbjct: 80  YAAGRLDRDSEGLLLLTNCGKLQNTLTA--PNKKTNKTYWVQVEGEPSTES-IQALCKGV 136

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +   G      VK  E+   +  +   V +  +    WL +  + G+  Q+R    H+G 
Sbjct: 137 ELKDGLTLPANVKMIEEPNIWQRTP-PVRERKSIPTSWLSITINEGKNRQVRRMTAHIGH 195

Query: 265 PIV 267
           P +
Sbjct: 196 PTL 198


>gi|228903228|ref|ZP_04067361.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|228967810|ref|ZP_04128824.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228791860|gb|EEM39448.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228856402|gb|EEN00929.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
          Length = 242

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 91/246 (36%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGTPVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                  K    G  +    + + G    +         +     +E+    G+ HQ++ 
Sbjct: 146 ------VKEFAKGVILDDGYETKPGTLTIL--------KSDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|218905935|ref|YP_002453769.1| RNA pseudouridine synthase family protein [Bacillus cereus AH820]
 gi|218539238|gb|ACK91636.1| RNA pseudouridine synthase family protein [Bacillus cereus AH820]
          Length = 242

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 91/246 (36%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGISVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                  K    G  +    + + GA             +     +E+    G+ HQ++ 
Sbjct: 146 ------VKEFAKGVILDDGYETKPGALTI--------SKSDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|310765941|gb|ADP10891.1| 23S rRNA pseudouridine synthase F [Erwinia sp. Ejp617]
          Length = 292

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/247 (13%), Positives = 73/247 (29%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR    +R+ +G VV++   +    + 
Sbjct: 7   IRLNKYIGE--SGICSRRDADRYIEQGNVFINGKRASVGDRVFAGDVVKVNGQLIEPRNE 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     +D  +   NKP GI      G   +I  F+    
Sbjct: 65  --------------------------DDLVVIALNKPVGIISTTEEGERDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD+++ G++ +         +  +      + +               
Sbjct: 97  ---SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL--------------V 139

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             N  + +  I G    V           +          +      +    G   Q+R 
Sbjct: 140 TVNKPVTEEFIRGLGAGVPMLGTVTKKCKV--------NKESTFVFRITLVQGLNRQIRR 191

Query: 258 HALHMGC 264
            + H G 
Sbjct: 192 MSEHFGY 198


>gi|229019939|ref|ZP_04176733.1| Pseudouridine synthase [Bacillus cereus AH1273]
 gi|229026174|ref|ZP_04182538.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228735102|gb|EEL85733.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228741357|gb|EEL91563.1| Pseudouridine synthase [Bacillus cereus AH1273]
          Length = 242

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 69/178 (38%), Gaps = 34/178 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   H +   ++K+L+ G V++D   VK                    +  +
Sbjct: 1   MRLDKLLAN-MGHGSRKEVKKLLKDGVVKIDGTPVK----------------DPKFHVNV 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                P    RLD +T G L++    +   Q L+     + + K Y++ V G+   + 
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLITNDGKLTHQLLS---PKKHVPKKYYAHVSGVVTEED 145


>gi|163857448|ref|YP_001631746.1| pseudouridine synthase [Bordetella petrii DSM 12804]
 gi|163261176|emb|CAP43478.1| pseudouridine synthase [Bordetella petrii]
          Length = 588

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/258 (13%), Positives = 71/258 (27%), Gaps = 59/258 (22%)

Query: 19  MRLDRWFKN--HYPHI----------NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            RL ++  +    P +          +   +++++ +G+V V+ +      R+     VR
Sbjct: 110 QRLGKYLNSDAAMPKLHKVLADAGIGSRREMEELITAGRVSVNGEPAHIGQRVAPSDQVR 169

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGI 125
           +     A  +  K  ++                 +LY        +KPAG I      G 
Sbjct: 170 VNGKPVARPNTKKPPRV-----------------ILY--------HKPAGEIVSHDDPGG 204

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                         +  K     RLD  T G+L+   +   A  +         +     
Sbjct: 205 R---ASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSGDMANRIMHPRYGTEREYAVRV 261

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           L       +K  +    L+                     A      +        W  +
Sbjct: 262 LGEMDDATRKSLVEGIELED-----------------GQAAFGALDYLGGDGSNR-WYRV 303

Query: 246 QPHTGRTHQLRVHALHMG 263
               GR  ++R     +G
Sbjct: 304 TLQEGRNREVRRMFESVG 321


>gi|150014984|ref|YP_001307238.1| RNA-binding S4 domain-containing protein [Clostridium beijerinckii
           NCIMB 8052]
 gi|149901449|gb|ABR32282.1| RNA-binding S4 domain protein [Clostridium beijerinckii NCIMB 8052]
          Length = 86

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 6/88 (6%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++ K           ++I  SG++ ++ K  K + +I+ G ++ I      L   I
Sbjct: 1   MRLDKYLKVSRIIKRRTVAKEICESGRILINGKVAKPSTKIKEGDIIEITFANKVLKAEI 60

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDS 106
                  S V   +  +  +  ++ E  
Sbjct: 61  A------SVVEHVRKEEAKEMYIILEGE 82


>gi|19704052|ref|NP_603614.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
 gi|19714248|gb|AAL94913.1| Ribosomal small subunit pseudouridine synthase A [Fusobacterium
           nucleatum subsp. nucleatum ATCC 25586]
          Length = 226

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/211 (17%), Positives = 83/211 (39%), Gaps = 38/211 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++K++ +G++ V+                        ++ I+
Sbjct: 1   MRLDKFLVECGIG-SRKEVKKLISNGEIAVNG-----------------------MSDIL 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +  I ++S  +  + + L+    Y++ + Y+ NK AG            +   L  WV 
Sbjct: 37  AKDNIDENSDTIEYNGERLE----YKEFRYYIMNKKAGYITATEDFKEDTVMDLLPEWVI 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYW---SLVWGIPKNK 194
            K   P    RLD++T G+L+     +   + L+    + ++  +      L   I K +
Sbjct: 93  KKDLAP--VGRLDKDTEGLLLFTNDGKLNHKLLSPKNHIDKVYYVEIEKNILDEDILKLE 150

Query: 195 KEC-IANWLL---KKSHIGGDYVHVVKQNEK 221
           +   I N++    K   I  + +++  +  K
Sbjct: 151 QGVDIGNYITQPAKVEKISDNKIYLTIKEGK 181


>gi|315656791|ref|ZP_07909678.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           curtisii subsp. holmesii ATCC 35242]
 gi|315492746|gb|EFU82350.1| ribosomal large subunit pseudouridine synthase B [Mobiluncus
           curtisii subsp. holmesii ATCC 35242]
          Length = 278

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 35/251 (13%), Positives = 81/251 (32%), Gaps = 51/251 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           E  RL +         +    + ++  G+V+++ + V+    ++     + +       +
Sbjct: 40  EPERLQKVLSRA-GVASRRASEDLIARGRVQINGETVREMGVKVLPTDRITVDGQRIHTD 98

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
            +++                            ++ F+KP G              G    
Sbjct: 99  TVLQ----------------------------VWAFHKPVGTVSSMQPEDDRPCIG---D 127

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           WV    ++     RLD  T+G+L++      A  +        + K Y ++V G  K   
Sbjct: 128 WVTKLPERVYNVGRLDAATAGLLLLTNNGELANRI--MHPSYEVPKTYVAVVQGQVK--- 182

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                       +G   V       +     +  FK+I+   +    +++  H+G+   +
Sbjct: 183 ------------MGLGKVLRRGVELEDGKVKVDKFKLIEVR-RGSSIVQLTLHSGKNRVV 229

Query: 256 RVHALHMGCPI 266
           R     +G P+
Sbjct: 230 RRLLSAVGHPV 240


>gi|57158194|dbj|BAD84160.1| putative ribosomal pseudouridine synthase [Corynebacterium
           glutamicum]
          Length = 74

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           + P TG+THQLR+H      PI+GD  Y               ++L AR +    P+   
Sbjct: 3   LAPSTGKTHQLRIHMRDFAAPILGDPLY-PVLHAVDDEDYTTPMHLIARTLTFVDPQTNE 61


>gi|152972885|ref|YP_001338031.1| 23S rRNA pseudouridine synthase F [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238892493|ref|YP_002917227.1| 23S rRNA pseudouridine synthase F [Klebsiella pneumoniae
           NTUH-K2044]
 gi|288937681|ref|YP_003441740.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|150957734|gb|ABR79764.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae MGH
           78578]
 gi|238544809|dbj|BAH61160.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae
           NTUH-K2044]
 gi|288892390|gb|ADC60708.1| pseudouridine synthase [Klebsiella variicola At-22]
          Length = 291

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/250 (13%), Positives = 73/250 (29%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + + RL+++       I +     + +  G V ++ KR    ++++ G +V++   +   
Sbjct: 4   DSSTRLNKYISE--SGICSRREADRFIEQGNVFINGKRATIGDQVKPGDLVKVNGRLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        +D  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +   +    P   
Sbjct: 96  H-----SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL---VTVDKPVTD 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E I         +G        + E    + I+                     G   Q
Sbjct: 148 -EFIRGMGAGVPILGTVTKKCKVKKEAPFVFRIT------------------LVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|46200149|ref|YP_005816.1| ribosomal small subunit pseudouridine synthase A [Thermus
           thermophilus HB27]
 gi|55980117|ref|YP_143414.1| ribosomal large subunit pseudouridine synthase B [Thermus
           thermophilus HB8]
 gi|46197777|gb|AAS82189.1| ribosomal small subunit pseudouridine synthase A [Thermus
           thermophilus HB27]
 gi|55771530|dbj|BAD69971.1| ribosomal large subunit pseudouridine synthase B [Thermus
           thermophilus HB8]
          Length = 243

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/251 (15%), Positives = 73/251 (29%), Gaps = 57/251 (22%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNH 76
             RLD+         +   + +++R G+VRV  + VK    R+  G  + +         
Sbjct: 3   GERLDKVLARLGLG-SRKEVARLVRQGKVRVLGQVVKDPGFRVPEGAALEV--------- 52

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
              E + L+   +L                 + +  KP G       G            
Sbjct: 53  ---EGRPLEVRRHL----------------HVLLH-KPPGFVTSRTEGP-----SVYALL 87

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                +      RLD++  G+L+          LT   R +  ++    L   +    +E
Sbjct: 88  QGFPTRDLSPVGRLDKDAEGLLLFTTDGLLLHRLTHP-RHKVAKRYLVHLERPVGPKDQE 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +L                  G     +    ++       W E+    GR HQ++
Sbjct: 147 AFREGILLD----------------GKKTLPAELTPLE----DPTWAEVVLKEGRFHQIK 186

Query: 257 VHALHMGCPIV 267
                 G  ++
Sbjct: 187 RMFRARGNRVL 197


>gi|221487535|gb|EEE25767.1| ribosomal pseudouridine synthase, putative [Toxoplasma gondii GT1]
          Length = 254

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 40/76 (52%)

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D+   K RL H+LD  TSG+L++A  + AA+ +    + R IQK Y +LV+G P+  +  
Sbjct: 144 DADACKVRLCHQLDYATSGLLMLAHNQKAARIVQTLLQRREIQKEYLALVYGHPRWSEVE 203

Query: 198 IANWLLKKSHIGGDYV 213
           +   +   S      +
Sbjct: 204 VETLVAPHSTHAFKMM 219


>gi|15603470|ref|NP_246544.1| hypothetical protein PM1605 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|34098696|sp|Q9CKK7|RLUE_PASMU RecName: Full=Ribosomal large subunit pseudouridine synthase E;
           AltName: Full=rRNA pseudouridylate synthase E; AltName:
           Full=rRNA-uridine isomerase E
 gi|12722002|gb|AAK03689.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 241

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/223 (18%), Positives = 83/223 (37%), Gaps = 31/223 (13%)

Query: 54  KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK 113
           K N +    Q  +  P      +  K  +I      L+      K  + + ++++ +FNK
Sbjct: 2   KPNTK--FNQKTKPRPSSLRSVNKRKAAEIKPQKRPLSFRQ---KKTVNFAETQVILFNK 56

Query: 114 PAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES 173
           P  +  Q            LK+++           RLD+++ G++++         L   
Sbjct: 57  PYDVLTQFS---DEEGRATLKAFIPI--PHVYPAGRLDRDSEGLVLLTNNGEIQHRLAVP 111

Query: 174 FRMRRIQKIYWSLVWGIPKN------KKECIANW---LLKKSHIGGDYVHVVKQNEKGAN 224
                 +K Y++ V GIP+       ++  + N    L  K  +  +   + ++N     
Sbjct: 112 KFN--TEKTYFAQVEGIPQETDLAQLRQGVVLNDGKTLPAKVRLVPEPNWLWQRNPP--- 166

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  + +       WLE++ H GR  Q+R    H+G P +
Sbjct: 167 -------IRERKQIPTSWLEIKIHEGRNRQVRRMTAHIGFPTL 202


>gi|212710610|ref|ZP_03318738.1| hypothetical protein PROVALCAL_01676 [Providencia alcalifaciens DSM
           30120]
 gi|212686691|gb|EEB46219.1| hypothetical protein PROVALCAL_01676 [Providencia alcalifaciens DSM
           30120]
          Length = 292

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 75/246 (30%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G VV++   +    +  
Sbjct: 8   RLNKYISE--SGICSRREADRYIEQGHVFINGKRAGIGDQVSAGDVVKVNGQLIEPRNE- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    ED  +   NKP GI     SG   +I  ++     
Sbjct: 65  -------------------------EDLVLIALNKPVGIVSTTESGEKDNIVDYVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++ +         +  +      + I             + +
Sbjct: 97  --STRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYIV---------TVNKPV 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            +  ++    G   +  + +  K    A   F++                 G   Q+R  
Sbjct: 146 TDEFIRGMGAGVPILGTMTKKCKVKKEAPFVFRI-------------TLVQGLNRQIRRM 192

Query: 259 ALHMGC 264
             H G 
Sbjct: 193 TEHFGY 198


>gi|114561788|ref|YP_749301.1| 23S rRNA pseudouridine synthase F [Shewanella frigidimarina NCIMB
           400]
 gi|114333081|gb|ABI70463.1| ribosomal large subunit pseudouridine synthase F [Shewanella
           frigidimarina NCIMB 400]
          Length = 293

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 31/251 (12%), Positives = 67/251 (26%), Gaps = 56/251 (22%)

Query: 15  DEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            E   RL+++       I +     + +  G V ++ KR K  + ++ G  V++     A
Sbjct: 2   SESATRLNKYISE--SGICSRREADRYIEQGNVFINGKRAKIGDSVEFGDKVKVNGHDIA 59

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                                          D      NKP GI     +    +I  F+
Sbjct: 60  PRDEA--------------------------DLVFIALNKPVGIVSTTENTERDNIVDFV 93

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                   ++     RLD+++ G++ +         +  +      + +           
Sbjct: 94  NH-----SERVFPIGRLDKDSQGLIFLTSNGDLVNKILRAGNNHDKEYV----------- 137

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                 N  + ++ + G    V           +                ++    G   
Sbjct: 138 ---VTVNKPITEAFLQGMRAGVPMLGVITKKCKVEQVST--------FVFKIILVQGLNR 186

Query: 254 QLRVHALHMGC 264
           Q+R    H   
Sbjct: 187 QIRRMCEHFNF 197


>gi|317402968|gb|EFV83508.1| pseudouridine synthase [Achromobacter xylosoxidans C54]
          Length = 469

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 29/190 (15%), Positives = 58/190 (30%), Gaps = 43/190 (22%)

Query: 19  MRLDRWFKNH--YPHI----------NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
            RL ++  +    P +          +   +++++ +G+V V+ +      R+     VR
Sbjct: 100 QRLGKYLNSEAVMPKLHKVLADAGIGSRREMEELIVAGRVSVNGEPAHIGQRVAPNDQVR 159

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGI 125
           +        +  K  ++                 +LY        +KPAG I      G 
Sbjct: 160 VNGKPIMRANTKKPPRV-----------------ILY--------HKPAGEIVSHDDPGG 194

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                         +  K     RLD  T G+L+   +   A  +         ++ Y  
Sbjct: 195 R---ASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSGDMANRI--MHPRYGTEREYAV 249

Query: 186 LVWGIPKNKK 195
            V G     +
Sbjct: 250 RVLGEMDEAQ 259


>gi|157374135|ref|YP_001472735.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157316509|gb|ABV35607.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 247

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 88/249 (35%), Gaps = 52/249 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+       IN  +++ +L  G+VRVD +  +            I  V++  +HI  
Sbjct: 21  RLDRFIS-VNTGINRKHVRLMLAKGRVRVDGELAR-----------DIDQVVDEFSHICL 68

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + K+L ++                 ++   + +KP G+     + I       +      
Sbjct: 69  DDKVLQAN-----------------EASYVMLHKPVGVVS---ATIDDKHRTVIDLLEQD 108

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             +   +  RLD  TSG+L++      ++ L       ++ K+Y           +  + 
Sbjct: 109 DKESLHIVGRLDLNTSGLLLLTNDGRWSKRL--MDPEHKVGKLY-----------RVHLQ 155

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           N L      G       +  +     A    ++ID +       E     GR HQ++   
Sbjct: 156 NPLTPDYISGFAQGMYFEFEDITTLPA--ELEIIDSYTALVTLYE-----GRYHQIKRMF 208

Query: 260 LHMGCPIVG 268
                P++G
Sbjct: 209 GRFRNPVIG 217


>gi|206578740|ref|YP_002241036.1| ribosomal large subunit pseudouridine synthase F [Klebsiella
           pneumoniae 342]
 gi|290512420|ref|ZP_06551787.1| ribosomal large subunit pseudouridine synthase F [Klebsiella sp.
           1_1_55]
 gi|206567798|gb|ACI09574.1| ribosomal large subunit pseudouridine synthase F [Klebsiella
           pneumoniae 342]
 gi|289775415|gb|EFD83416.1| ribosomal large subunit pseudouridine synthase F [Klebsiella sp.
           1_1_55]
          Length = 291

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/250 (13%), Positives = 73/250 (29%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + + RL+++       I +     + +  G V ++ KR    ++++ G +V++   +   
Sbjct: 4   DSSTRLNKYISE--SGICSRREADRFIEQGNVFINGKRATIGDQVKPGDLVKVNGRLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        +D  +   NKP GI      G   +I  F+ 
Sbjct: 62  REA--------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +   +    P   
Sbjct: 96  H-----SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL---VTVDKPVTD 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E I         +G        + E    + I+                     G   Q
Sbjct: 148 -EFIRGMGAGVPILGTVTKKCKVKKEAPFVFRIT------------------LVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|124801447|ref|XP_001349696.1| pseudouridine synthase, putative [Plasmodium falciparum 3D7]
 gi|3845303|gb|AAC71967.1| pseudouridine synthase, putative [Plasmodium falciparum 3D7]
          Length = 338

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 51/284 (17%), Positives = 92/284 (32%), Gaps = 44/284 (15%)

Query: 10  VVVENDEENM-RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVR 66
           +   N++ N+ RL++       +I+     + ++ G+V+++ K +      +  G   +R
Sbjct: 36  LTKTNEDANIIRLNKLISMK-RNISRRKSDEFIKDGKVKINNKIITNPGTHVHIGKDSLR 94

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           I      L +II    I  +   L K                 V +KP G+         
Sbjct: 95  IYDKKIKLTNII--NMIKQNENKLHK---------------WIVLHKPKGLLCTSNDEKN 137

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS- 185
                 L      +  +     RLD+ TSG+L++    A    LT     R         
Sbjct: 138 RKSIYTLFPEEMLQKYRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIE 197

Query: 186 ----------LVWGIPKNKKECIANWLL-------KKSHIGGDYVHVVKQNEKGANYAIS 228
                     L  GI   + E      +       +KS+I       + + +K  N A  
Sbjct: 198 GPVKMNALKELARGIYLEEDEKTQPKKIYNYKESREKSNIDDKKKKKMSKMKKKTNPAFI 257

Query: 229 HFKV-----IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                    I    +K   L +    GR  Q+R     +  P++
Sbjct: 258 EILREEKIKIKEDTKKITVLNISIKEGRNRQIRKMFQQINQPVI 301


>gi|309807073|ref|ZP_07701052.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 03V1-b]
 gi|308166503|gb|EFO68703.1| pseudouridine synthase B, ribosomal large subunit [Lactobacillus
           iners LactinV 03V1-b]
          Length = 239

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 79/248 (31%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           +RL +         +    + ++ SGQV V+   V     ++     + +          
Sbjct: 3   LRLQKVIAEA-GIASRRKAEILITSGQVTVNGDLVTTLGTKVDDNDKIEVN--------- 52

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                       +  H + L + LLY+   +        +S    +     +  F K   
Sbjct: 53  -----------GVPIHKEQLHTYLLYKPRNV--------VSTVSDNKGRKTVTDFFKDLP 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD +TSG+L++      A  L        I+K+Y + + G     +  
Sbjct: 94  ----YRLYPVGRLDYDTSGLLLMTNDGELANRL--MHPKNEIEKVYVAKIRGFLTASEIY 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQLR 256
                        D  H V  + +    A +  K+I     +    +++  H G  HQ++
Sbjct: 148 -------------DLKHGVTIDGR--KTAPAKVKIIKTDKNRNIQLVQLTIHEGHYHQVK 192

Query: 257 VHALHMGC 264
                +  
Sbjct: 193 NMFKAVNH 200


>gi|295706927|ref|YP_003600002.1| RNA pseudouridylate synthase [Bacillus megaterium DSM 319]
 gi|294804586|gb|ADF41652.1| RNA pseudouridylate synthase [Bacillus megaterium DSM 319]
          Length = 238

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 91/246 (36%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+       + +   ++ +L++G V+VD   VK                 +A  H+ 
Sbjct: 1   MRLDKLLST-IGYGSRKEVKGLLKTGAVKVDGSAVK-----------------DAKVHVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +++       +T H + +     Y +   ++ +KP G+       +   +   L+  +D
Sbjct: 43  PDEQ------EITVHGEAVS----YREFVYFMLHKPQGVISATEDSLHETVLDLLE--LD 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD++T G+L++      A Q L+   +    +  +  +   + +   E 
Sbjct: 91  DAVYDPFPVGRLDKDTEGLLLLTNDGQLAHQLLSP--KKHVPKTYFAKINAPVTEEDAEA 148

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                  +  +  D  +V K  E          K++   +     +E+    G+ HQ++ 
Sbjct: 149 F------RQGVTLDDGYVTKSAE---------LKIL--TSGVESEIELTIVEGKFHQVKR 191

Query: 258 HALHMG 263
                G
Sbjct: 192 MFEARG 197


>gi|149203717|ref|ZP_01880686.1| RNA pseudouridylate synthase [Roseovarius sp. TM1035]
 gi|149142834|gb|EDM30876.1| RNA pseudouridylate synthase [Roseovarius sp. TM1035]
          Length = 180

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/161 (20%), Positives = 63/161 (39%), Gaps = 7/161 (4%)

Query: 108 IYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           + +FNKP  +  Q    G        L  ++D    +     RLD+++ G+L++      
Sbjct: 4   LILFNKPYDVLSQFTDRGSEGSPRATLSDFIDI--PRVYPAGRLDRDSEGLLLLTDDGQL 61

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
              +       + +K Y++ V G+P +         +  S  G      V++ E    + 
Sbjct: 62  QARIA--NPRFKTEKTYYAQVEGLPDDTALAALRAGVTLS-DGPTRPARVERTEPPTLWP 118

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +   V    +   CWL++    GR  Q+R    H+G P +
Sbjct: 119 RTP-PVRFRKSVPDCWLKLTISEGRNRQVRRMTAHIGHPTL 158


>gi|322807584|emb|CBZ05159.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           botulinum H04402 065]
          Length = 238

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 88/243 (36%), Gaps = 47/243 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     ++ +++ GQV VD + VK N        ++I P  N +    
Sbjct: 2   ERLDKILAN-LGYGTRKEVKALIKKGQVDVDGEVVKDNG-------MQIDPEKNKIFVFG 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           KE                    L+Y+     + NKP G+           +   L+   +
Sbjct: 54  KE--------------------LVYKKYIYLMMNKPQGVVSATFDNYDETVVDLLED--E 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD+ T G+L++         L        + KIY++ +     ++    
Sbjct: 92  DRIFEPFPVGRLDKNTVGLLLLTNDGELNHRL--ISPKWHVDKIYYAKINKKVTDED--- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +KK   G     ++  +      A    ++I  F ++   + +  H G+ HQ++  
Sbjct: 147 ----IKKFKKG-----IILDDGYECFPA--KLEIIKSFNEE-SEVRVTIHEGKFHQVKRM 194

Query: 259 ALH 261
              
Sbjct: 195 FES 197


>gi|319638171|ref|ZP_07992934.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317400444|gb|EFV81102.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 352

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 77/251 (30%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ +  +  +++     V +   I  L  
Sbjct: 98  EPERLQKVLAASGVG-SRREMEEWISNGWVTVNGRVAQLGDKVTPDDHVTVKGSIIKL-- 154

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 155 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRISIFDRL 189

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 190 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGELTTEQM 247

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  +   E+G   A   + V+    +      +    G T    
Sbjct: 248 RVLTEEGVMLEDGLAKVERIY--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 305

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 306 VRVGFGPIGLP 316


>gi|260776099|ref|ZP_05884994.1| ribosomal large subunit pseudouridine synthase B [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260607322|gb|EEX33587.1| ribosomal large subunit pseudouridine synthase B [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 314

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 77/235 (32%), Gaps = 34/235 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNH 76
           N +L +       H +   L+ ++++G+V V+    K   R++    VVRI     +   
Sbjct: 2   NEKLQKVLARA-GHGSRRELEALIKAGRVSVNGVVAKLGERLEDENAVVRIDGHTVS--- 57

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K  + +   +L        + KP G                    
Sbjct: 58  --------------AKAQEEVVCRVL-------AYYKPEGELC--TRHDPEGRRTVFDRL 94

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    KK 
Sbjct: 95  PKIRGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGDVDEKKI 152

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
                 ++       +  VV     G N+  + + VI+     +     E Q  T
Sbjct: 153 RNLVGGVELEDGLARFEDVVYAGGDGMNH--TFYVVINEGRNREVRRLWESQDCT 205


>gi|324328601|gb|ADY23861.1| RNA pseudouridine synthase family protein [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 242

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 95/246 (38%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGISVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +K+   G     ++    +    A++  K     +     +E+    G+ HQ++ 
Sbjct: 146 -----VKEFAKG----VILDDGYETKPGALTILK-----SDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|257094536|ref|YP_003168177.1| RNA-binding S4 domain-containing protein [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257047060|gb|ACV36248.1| RNA-binding S4 domain protein [Candidatus Accumulibacter phosphatis
           clade IIA str. UW-1]
          Length = 322

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 77/246 (31%), Gaps = 46/246 (18%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RL +         +   +++++ +G++ ++ +         +G  V++   +  L   
Sbjct: 66  PERLHKLLAQSGIG-SRREMEELIAAGRISINGETASVGQTASAGDRVKVNGKLVQL--- 121

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                         + SD L  ++LY        +KP G  V        H      S  
Sbjct: 122 --------------RFSDRLPRVILY--------HKPEGEIV--SRNDPEHRPNVFTSMP 157

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD  TSG+L++  +   A  L       ++ + Y   + G    +   
Sbjct: 158 RISAGRWVAVGRLDFNTSGLLLLTTSGDLANRL--MHPRYQLVREYAVRILGELTEE--- 212

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   LL    +           E G   A   ++V               H GR  ++R 
Sbjct: 213 VRRQLLDGIDLDDGPAQFASFQEAGGEGANRWYRV-------------SLHEGRNREVRR 259

Query: 258 HALHMG 263
               +G
Sbjct: 260 MFEAVG 265


>gi|255994193|ref|ZP_05427328.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           saphenum ATCC 49989]
 gi|255993861|gb|EEU03950.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           saphenum ATCC 49989]
          Length = 250

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 39/252 (15%), Positives = 85/252 (33%), Gaps = 45/252 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++        +     ++++ G+V V    +     ++ G  V             
Sbjct: 1   MRINKYIAK-CGICSRRKADELIKEGRVTVGGIPL-----LECGVNVD------------ 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                 D+ + +      ++   +Y        NKP G        +       +   + 
Sbjct: 43  -----EDAVIAIDGRPIEIQKKTVY-----IAMNKPCGYVCTVSDELGRR---TVYDLLT 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP------K 192
              ++     RLD+++ G++++      AQ L      R+I+K Y  +V G+P      K
Sbjct: 90  DIDERLFTIGRLDKDSEGLILLTNDGDLAQKL--LSPKRKIEKNYEVVVRGVPGANDIKK 147

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                  +  + ++        +VK + K A      F++          L M    G+ 
Sbjct: 148 LSGGITIDVEISQTKQNKPVKSIVKYHTKPAKI----FEIGQKQGDMK--LSMIIKEGKK 201

Query: 253 HQLRVHALHMGC 264
            Q+R     +G 
Sbjct: 202 RQIRKMFDVIGH 213


>gi|256832502|ref|YP_003161229.1| pseudouridine synthase [Jonesia denitrificans DSM 20603]
 gi|256686033|gb|ACV08926.1| pseudouridine synthase [Jonesia denitrificans DSM 20603]
          Length = 265

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 88/250 (35%), Gaps = 48/250 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           + +RL +   +     +    + ++R G+V VD + V           + +   ++   H
Sbjct: 26  DGIRLQKVMADAGVG-SRRECENLIRQGRVEVDGQIV-----------MELGVRVDPTAH 73

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           ++           L   +D  K  +          NKP  +     +         +   
Sbjct: 74  VVTVD-------GLRIMADASKITI--------AVNKPQKMV---ATMHDPEGRATVADL 115

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           V  + ++     RLD E+ G+L++      A  L+       ++K Y   V G   N   
Sbjct: 116 VSKRTERLFHVGRLDYESEGLLLLTNDGELANRLSHPRYN--VRKTYVVTVKGRVAN--- 170

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + + LL+   +            +    A+  ++VID        +E+Q H+GR   +R
Sbjct: 171 GVGSQLLRGITL------------EDGEVALDSYRVID-QTDTETMIEVQLHSGRNRIVR 217

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 218 RIFDSLGHPV 227


>gi|25010876|ref|NP_735271.1| hypothetical protein gbs0821 [Streptococcus agalactiae NEM316]
 gi|77414995|ref|ZP_00791079.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 515]
 gi|23095255|emb|CAD46465.1| Unknown [Streptococcus agalactiae NEM316]
 gi|77158953|gb|EAO70180.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 515]
          Length = 239

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 80/246 (32%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +   ++K++RS QV VD + V                         
Sbjct: 1   MRLDKLLGQAGFG-SRNQVKKLIRSRQVSVDGQIVT------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K+  I+DS +         K  +  ++S  Y+  KP+G+        + H          
Sbjct: 36  KDNVIVDSGLQSIFVG---KERVCLKESSYYLLYKPSGVVS--AVRDSEHKTVIDLISEK 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            + +      RLD++T G+L++        + L        + K Y+  V G        
Sbjct: 91  DRVEGLYPIGRLDRDTEGLLIITNNGPLGYRMLH---PKHHVAKTYYVEVNGF------- 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                L++  I      VV  +      A      ID          +    G+ HQ++ 
Sbjct: 141 -----LERDAITFFEEGVVFDDGTKCKPAEL---TIDTANNDKSTARITITEGKFHQVKK 192

Query: 258 HALHMG 263
             L  G
Sbjct: 193 MFLAYG 198


>gi|319410624|emb|CBY90993.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B; rRNA pseudouridylate synthase B) [Neisseria
           meningitidis WUE 2594]
          Length = 349

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 77/251 (30%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 244

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  +   E+G   A   + V+    +      +    G T    
Sbjct: 245 RVLTEEGVMLEDGLAKVERIY--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 302

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 303 VRVGFGPIGLP 313


>gi|189501858|ref|YP_001957575.1| hypothetical protein Aasi_0430 [Candidatus Amoebophilus asiaticus
           5a2]
 gi|189497299|gb|ACE05846.1| hypothetical protein Aasi_0430 [Candidatus Amoebophilus asiaticus
           5a2]
          Length = 252

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 42/260 (16%), Positives = 97/260 (37%), Gaps = 56/260 (21%)

Query: 12  VENDEEN-MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPP 69
           V +D+ N +RL++W  N     +     +++++G++ V+ +++     ++++  +V+   
Sbjct: 11  VASDQINYVRLNKWISNA-GICSRREADELIQAGRITVNGEKITTLGYQVKNTDIVKFRD 69

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +   N  +                               + NKP        +      
Sbjct: 70  KVLKPNKHV-----------------------------YILLNKPRNCIT--TAFDPERR 98

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE-SFRMRRIQKIYWSLVW 188
              L     +  ++     RLD+ T+G+LV+      AQ L   S+++++I ++  +   
Sbjct: 99  RTVLDFVKGACQERVYPVGRLDRNTTGLLVLTNDGDLAQKLAHPSYQIKKIYQVELASPI 158

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
             PK+     A   LK   +  D + +V+ +E                      L ++ H
Sbjct: 159 Q-PKDLAAIKAGICLKDGIVQVDSISIVQGDE--------------------SKLGIEIH 197

Query: 249 TGRTHQLRVHALHMGCPIVG 268
           +G+   +R    H+G  I+ 
Sbjct: 198 SGKNRIIRRLFEHLGYQIIN 217


>gi|194246524|ref|YP_002004163.1| 16S rRNA pseudouridylate synthase [Candidatus Phytoplasma mali]
 gi|193806881|emb|CAP18310.1| 16S rRNA pseudouridylate synthase [Candidatus Phytoplasma mali]
          Length = 242

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 89/256 (34%), Gaps = 59/256 (23%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNH 76
            RL +     Y ++ +    +K++   +V+V+ K V K   ++    ++ +   I   + 
Sbjct: 2   ERLQKILS--YSNVASRRKSEKLILEKRVKVNGKLVTKLGVKVSKKDIILVDDQIIKNSE 59

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKS 135
                                        +  Y+ NKP+G IS          +   +K 
Sbjct: 60  -----------------------------NCYYLINKPSGCISTVKDEKNRPTVIDLIK- 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYWSLVWGIP 191
             D++ ++     RLD  T+G+L++       + LT       +   ++  Y      + 
Sbjct: 90  --DTEKKRIYPVGRLDFNTTGLLLITNDGQLTKKLTHPSSLIEKEYHVKINYCLSSLELK 147

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K ++  I         I  +Y+ V K+ +                 +   WL++    G+
Sbjct: 148 KLQQGVI---------IDENYLSVPKKIKI---------LKKRLLPKPSTWLQIIITEGK 189

Query: 252 THQLRVHALHMGCPIV 267
            HQ+R     +G  I+
Sbjct: 190 NHQIRKMMEKLGFHIL 205


>gi|65322075|ref|ZP_00395034.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Bacillus anthracis str.
           A2012]
 gi|118479842|ref|YP_896993.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           thuringiensis str. Al Hakam]
 gi|118419067|gb|ABK87486.1| ribosomal small subunit pseudouridine synthase A [Bacillus
           thuringiensis str. Al Hakam]
          Length = 245

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 96/247 (38%), Gaps = 50/247 (20%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N+RLD+   N   + +   ++K+L+ G V++D   VK + ++                  
Sbjct: 3   NVRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGISVK-DAKVHVN--------------- 45

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           ++EQ+++               ++ Y++    + +KP G+           +   L+  +
Sbjct: 46  VEEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--L 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +     P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +  
Sbjct: 93  EDAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED- 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 +K+   G     ++    +    A++  K     +     +E+    G+ HQ++
Sbjct: 149 ------VKEFAKG----VILDDGYETKPGALTILK-----SDDISEIELVITEGKFHQVK 193

Query: 257 VHALHMG 263
                +G
Sbjct: 194 RMFEAVG 200


>gi|313815673|gb|EFS53387.1| RNA pseudouridine synthase [Propionibacterium acnes HL059PA1]
 gi|315099393|gb|EFT71369.1| RNA pseudouridine synthase [Propionibacterium acnes HL059PA2]
          Length = 168

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 22/90 (24%), Positives = 38/90 (42%), Gaps = 1/90 (1%)

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
            T+        +LY D +I V +KP  +S     G        ++        +  + HR
Sbjct: 53  PTETPVPAGIGILYSDERILVVDKPHFLSSIP-RGRHVLESVVVRLRTQLGLPELTVAHR 111

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRI 179
           LD+ T+G+L++ R R   +   E F  R +
Sbjct: 112 LDRVTAGVLLLTRERKWRRPYQEIFERREV 141


>gi|299538371|ref|ZP_07051654.1| ribosomal large subunit pseudouridine synthase B [Lysinibacillus
           fusiformis ZC1]
 gi|298725958|gb|EFI66550.1| ribosomal large subunit pseudouridine synthase B [Lysinibacillus
           fusiformis ZC1]
          Length = 243

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 38/168 (22%), Positives = 59/168 (35%), Gaps = 27/168 (16%)

Query: 104 EDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVA 161
           ED   ++  KP G   +V    G     D           Q+     RLD +TSG+L++ 
Sbjct: 58  EDKVYFLLYKPRGTISAVTDDKGRKTVTD-----LFHHIPQRIFPVGRLDYDTSGLLLLT 112

Query: 162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIGGDYVHVVKQN 219
                +  LT      +I K Y + V G+P  +  K+      L+        V +   +
Sbjct: 113 NDGEFSYMLT--HPKFKIDKTYIARVKGVPTIEGLKKLQRGIKLEDGKTAPAKVSMTSFD 170

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           EK                      E+  H GR  Q+R     +G P+V
Sbjct: 171 EKAGK----------------AICEITIHEGRNRQVRRMFEAIGTPVV 202


>gi|229163701|ref|ZP_04291648.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228619763|gb|EEK76642.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 242

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 91/246 (36%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK + ++                  +
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGTPVK-DAKVHVN---------------V 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    + + Q L+     + + K Y++ V G+   +   
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLITNDGKLSHQLLS---PKKHVPKKYYAHVAGVVTEED-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                  K    G  +    + + G    +         +     +E+    G+ HQ++ 
Sbjct: 146 ------VKEFAKGVILDDGYETKPGVLTIL--------KSDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|221194614|ref|ZP_03567671.1| ribosomal large subunit pseudouridine synthase B [Atopobium rimae
           ATCC 49626]
 gi|221185518|gb|EEE17908.1| ribosomal large subunit pseudouridine synthase B [Atopobium rimae
           ATCC 49626]
          Length = 269

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 32/162 (19%), Positives = 60/162 (37%), Gaps = 9/162 (5%)

Query: 108 IYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
             + NKP G ++          I   + +    +        RLD +TSG+L+       
Sbjct: 71  YLMLNKPEGYLTTMSDPQGRPTIKTMVPT---KRYPGLFPVGRLDMDTSGLLLFTTDGTM 127

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKK-ECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
           AQ L      R + K Y +LV G+P   + E +   ++    +      V  +++    +
Sbjct: 128 AQEL--LHPSRHVWKHYLALVLGVPTEAELERLRRGIMLDDGMA-QPAKVELRDDLLELH 184

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             S +       Q      +  H GR HQ++     +G  ++
Sbjct: 185 GTSRYPQNPNKPQNAIVG-IWIHEGRKHQVKKMMSAIGHRVL 225


>gi|114046295|ref|YP_736845.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           MR-7]
 gi|113887737|gb|ABI41788.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           MR-7]
          Length = 235

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/252 (14%), Positives = 79/252 (31%), Gaps = 54/252 (21%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNH 76
            +RLD++       +     +K L  G++  D   VK +  ++  G  V +     +L  
Sbjct: 6   PVRLDKFICES-TSLTRSLAKKALHRGEITCDGVVVKDSGFKVLEGMQVCLDGEPISLV- 63

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                         +  + NKP        S I       L   
Sbjct: 64  ----------------------------GERYLMLNKPVDTIC---STIDEAYPSVLSLL 92

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              K +   +  RLD +T+G++++      +  +T   +    ++   +L   + ++   
Sbjct: 93  DIEKPETLHIAGRLDADTTGLVLITSDGQWSHRITSPKKDCG-KRYLVALADPVDESLVG 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             A  +  ++  G     V++  E                      + +    G+ HQ++
Sbjct: 152 IFAAGVELRNEDGLTKPAVLEIIEP-------------------QLVRLTITEGKYHQVK 192

Query: 257 VHALHMGCPIVG 268
                +G  +VG
Sbjct: 193 RMFAAVGNHVVG 204


>gi|316984168|gb|EFV63146.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis H44/76]
 gi|325140419|gb|EGC62940.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis CU385]
 gi|325144504|gb|EGC66803.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M01-240013]
          Length = 349

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/236 (15%), Positives = 72/236 (30%), Gaps = 32/236 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G + V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWITNGWITVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 244

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +          G   V  ++  E+G   A   + V+    +      +    G T
Sbjct: 245 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLT 298


>gi|70925735|ref|XP_735515.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56509243|emb|CAH81272.1| hypothetical protein PC000519.04.0 [Plasmodium chabaudi chabaudi]
          Length = 248

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/103 (27%), Positives = 45/103 (43%), Gaps = 1/103 (0%)

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L++       +  L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K
Sbjct: 144 LETVKKWHKLECGLCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYILLCHGRIK 203

Query: 193 NKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            KK  I   +   + +      H     + G   A + +  + 
Sbjct: 204 KKKGFINKSIQTHEYNNSHSKSHFSLVVKTGGTDAYTEYNCVK 246


>gi|70938677|ref|XP_739983.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56517373|emb|CAH87667.1| hypothetical protein PC302577.00.0 [Plasmodium chabaudi chabaudi]
          Length = 310

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/103 (27%), Positives = 45/103 (43%), Gaps = 1/103 (0%)

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L++       +  L HR+D ETSG L++A+T+ A   L + FR R + K Y  L  G  K
Sbjct: 175 LETVKKWHKLECGLCHRIDLETSGSLIIAKTKDARDFLFDQFRKRNVYKEYILLCHGRIK 234

Query: 193 NKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVID 234
            KK  I   +   + +      H     + G   A + +  + 
Sbjct: 235 KKKGFINKSIQTHEYNNSHSKSHFSLVVKTGGTDAYTEYNCVK 277


>gi|269959632|ref|ZP_06174012.1| pseudouridine synthase family 1 protein [Vibrio harveyi 1DA3]
 gi|269835555|gb|EEZ89634.1| pseudouridine synthase family 1 protein [Vibrio harveyi 1DA3]
          Length = 312

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 43/232 (18%), Positives = 78/232 (33%), Gaps = 34/232 (14%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   ++ +++SG+V V+    K   R++    VVRI   I +     +
Sbjct: 5   LQKVLARA-GHGSRREIESLIKSGRVSVNGIVAKLGERLEDENSVVRIDGHIVSAK--AQ 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E+ I                       ++  + KP G                       
Sbjct: 62  EEVIC----------------------RVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    KK    
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVNEKKVRNL 155

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
              ++       +  VV    +G N+  + + VI+     +     E Q  T
Sbjct: 156 VSGVELEDGMARFEDVVHAGGEGMNH--TFYVVINEGRNREVRRLWESQECT 205


>gi|332288671|ref|YP_004419523.1| 16S rRNA pseudouridylate synthase A [Gallibacterium anatis UMN179]
 gi|330431567|gb|AEC16626.1| 16S rRNA pseudouridylate synthase A [Gallibacterium anatis UMN179]
          Length = 234

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/247 (14%), Positives = 84/247 (34%), Gaps = 55/247 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHI 77
            RLD++    Y  ++     K LR   V+V+++ VK    ++    VV            
Sbjct: 3   QRLDKFLSE-YTGLSRSQATKALRQNLVKVNQQLVKDGALKVSPEDVVEFDG-------- 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                         +     +  LLY         KP G       G    +  F    +
Sbjct: 54  -----------ETLEWVSGNQYFLLY---------KPEGYVCSHDDGEYPTVYQFFDYPL 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            S   +     RLD +T+G++++      + +  +  +  ++   +  +           
Sbjct: 94  SS---RLHTAGRLDVDTTGLVLLTDDGQWSHRITSPKYHYKKTYLVTLAA---------- 140

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + ++ L++   G     +++  ++    A    ++ID +      +E     G+ HQ++
Sbjct: 141 PVEDFYLEQCAQG----ILLRGEKQPTKPA--QIEIIDDYNLNLTIVE-----GKYHQVK 189

Query: 257 VHALHMG 263
                +G
Sbjct: 190 RMFAALG 196


>gi|127513903|ref|YP_001095100.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126639198|gb|ABO24841.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           loihica PV-4]
          Length = 230

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/252 (14%), Positives = 80/252 (31%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       +     +K L  G+V VD + +K  + ++   Q V +     +L   
Sbjct: 1   MRLDKFISES-TQLTRSLAKKALHRGEVTVDGQVIKDGSFKLNESQQVCLDGEPISL--- 56

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                I    + L K +D L                         S +       L    
Sbjct: 57  -----IGPRFIMLHKPADTL------------------------CSTVDEVYPSVLNLLD 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               +   +  RLD +T+G++++      + +  +      +   +  +        K E
Sbjct: 88  LPHKEDLHIAGRLDADTTGLVLITSDGQWSHRVTSPKRECGKTYLVQLA-----DPLKAE 142

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +  +    +         ++  E     A    +++     +    E     G+ HQ++
Sbjct: 143 WVEQFATGLA---------LRSEEGLTKPAT--LELLGSHEARLTITE-----GKYHQVK 186

Query: 257 VHALHMGCPIVG 268
                +G  +VG
Sbjct: 187 RMFAAVGNKVVG 198


>gi|15677226|ref|NP_274379.1| hypothetical protein NMB1361 [Neisseria meningitidis MC58]
 gi|7226606|gb|AAF41735.1| conserved hypothetical protein [Neisseria meningitidis MC58]
          Length = 350

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/236 (15%), Positives = 72/236 (30%), Gaps = 32/236 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G + V+ K  +  +++     V +   I  L  
Sbjct: 96  EPERLQKVLAASGVG-SRREMEEWITNGWITVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 152

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 153 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 187

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 188 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 245

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +          G   V  ++  E+G   A   + V+    +      +    G T
Sbjct: 246 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLT 299


>gi|239997156|ref|ZP_04717680.1| RNA pseudouridine synthase family protein [Alteromonas macleodii
           ATCC 27126]
          Length = 252

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 26/252 (10%), Positives = 75/252 (29%), Gaps = 54/252 (21%)

Query: 14  NDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           +++   RL+++  +    + +     K++   +V V+ +  +   ++  G  V++   + 
Sbjct: 2   SEQAPKRLNKYISD--TGLCSRREADKLIEQNRVTVNNQPPELGTKVGPGDTVKVDGKVV 59

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                 K  ++                          V+NKP GI+      +  +I   
Sbjct: 60  GAVASDKSDRV------------------------YIVYNKPIGITCTTERHVKGNIIDA 95

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +        ++     RLD+ + G++++         +  +      +            
Sbjct: 96  I-----GHKERIFPVGRLDKPSEGLIILTSDGDIVNKILRAENAHDKEYEV--------- 141

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                          I   +V+ + +        ++   V+    +      +    G  
Sbjct: 142 ----------TVNQPISERFVNRMSRGVPILGT-VTKPCVVKPTGKNT--FTIILTQGLN 188

Query: 253 HQLRVHALHMGC 264
            Q+R     +G 
Sbjct: 189 RQIRRMCEFLGY 200


>gi|254518907|ref|ZP_05130963.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
 gi|226912656|gb|EEH97857.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
          Length = 242

 Score = 57.3 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 48/280 (17%), Positives = 103/280 (36%), Gaps = 56/280 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    ++I+ S +V+++ K V      + G  V+I P  + + +  
Sbjct: 3   ERLQKYMAR-CGVASRRKCEEIILSSKVKINDKVVN-----ELG--VKIDPYKDKVFYNG 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVF-NKPAG-ISVQGGSGIAYHIDGFLKSW 136
           K                     +L E++K+Y+  NKP G I+          I   +K  
Sbjct: 55  K--------------------RILPEENKLYIMLNKPEGYITSVKDEKGRKTILDLVKV- 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK- 195
                ++     RLD ++SG++++         +        ++K Y +L  G+  +++ 
Sbjct: 94  ----NERIYPIGRLDYDSSGLILLTNDGDIYNKI--IHPRVEVEKKYIALCKGVFSDEEI 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           +   N +    +I  +    +   EK                     +E+  H G+  Q+
Sbjct: 148 KKFENGIDIGGYITANAKIKLIDKEKDKKT-----------NTVNSLVEIIIHEGKNRQI 196

Query: 256 RVHALHMGCPI-------VGDHKYCANFKGNFTSPIQNKL 288
           R     +G  +       VGD K     +G + +  +++L
Sbjct: 197 RKMCSALGHEVITLKRVAVGDIKLGYLKRGEWRNLTEDEL 236


>gi|114330607|ref|YP_746829.1| pseudouridine synthase, Rsu [Nitrosomonas eutropha C91]
 gi|114307621|gb|ABI58864.1| ribosomal large subunit pseudouridine synthase B [Nitrosomonas
           eutropha C91]
          Length = 272

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 38/244 (15%), Positives = 77/244 (31%), Gaps = 46/244 (18%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RL +    +    +   ++ ++ +G+V ++    K  +R   G  +RI   I  L+    
Sbjct: 34  RLQKLLARNGLG-SRREIEAMIAAGRVSINNTTAKLGDRAGLGDKIRIDGRIIRLS---- 88

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                            L  I++Y        +KP G  V   +                
Sbjct: 89  -------------MPALLPRIIIY--------HKPEGEIV--SARDPQGRLSVFDKLPHI 125

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +  K     RLD  TSG+L+     A A  L       ++++ Y   + G    ++    
Sbjct: 126 QSSKWIAIGRLDFNTSGLLIFTTDGALANRL--MHPRYQMEREYAVRIVGELSPEQITHL 183

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
              ++       +  ++ +   G N+                W  +    GR  ++R   
Sbjct: 184 TTGIELEDGSAKFDQLLDEGGLGTNH----------------WYRIVLKEGRNREVRRMF 227

Query: 260 LHMG 263
             +G
Sbjct: 228 EALG 231


>gi|254967056|gb|ACT97565.1| ribosomal large subunit pseudouridine synthase D [uncultured
           organism]
          Length = 87

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 16/76 (21%), Positives = 26/76 (34%), Gaps = 13/76 (17%)

Query: 259 ALHMGCPIVGDHKYCANFKGNFTSPIQ------------NKLYLHARYMDLPHPEGGR-L 305
             H+G  +  D +Y  +     T   +             +  LHA  +   HP  G  +
Sbjct: 1   MKHIGHILFNDERYGGHEILKGTHFAKYKQFVNNCFDICPRQALHAMTLGFVHPVTGEEM 60

Query: 306 QITAPLPAHMVKTWDS 321
             T+ LP  M +  D 
Sbjct: 61  YFTSELPDDMNRLLDK 76


>gi|227823780|ref|YP_002827753.1| RNA-binding S4 domain protein [Sinorhizobium fredii NGR234]
 gi|227342782|gb|ACP27000.1| RNA-binding S4 domain protein [Sinorhizobium fredii NGR234]
          Length = 136

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 19/90 (21%), Positives = 36/90 (40%), Gaps = 13/90 (14%)

Query: 19  MRLDRWF--KNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
            RLD+W          +    QK + +G V V+  R    +  +++G  + +      L 
Sbjct: 13  QRLDKWLFFARLIK--SRSLAQKAIEAGHVAVNGARATQSSATVKAGDTLELSLERRDL- 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYED 105
                  ++   +  T+   F ++ LLYED
Sbjct: 70  -------VVRVLLPGTRRGPFEEARLLYED 92


>gi|148381218|ref|YP_001255759.1| RNA pseudouridine synthase family protein [Clostridium botulinum A
           str. ATCC 3502]
 gi|153932230|ref|YP_001385593.1| RNA pseudouridine synthase family protein [Clostridium botulinum A
           str. ATCC 19397]
 gi|153934698|ref|YP_001388999.1| RNA pseudouridine synthase family protein [Clostridium botulinum A
           str. Hall]
 gi|148290702|emb|CAL84832.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. ATCC 3502]
 gi|152928274|gb|ABS33774.1| RNA pseudouridine synthase family protein [Clostridium botulinum A
           str. ATCC 19397]
 gi|152930612|gb|ABS36111.1| RNA pseudouridine synthase family protein [Clostridium botulinum A
           str. Hall]
          Length = 238

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 88/243 (36%), Gaps = 47/243 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     ++ +++ GQV VD + VK N        ++I P  N +    
Sbjct: 2   ERLDKILAN-LGYGTRKEVKALIKKGQVDVDGEVVKDNG-------MQIDPEKNKIFVFG 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           KE                    L+Y+     + NKP G+           +   L+   +
Sbjct: 54  KE--------------------LVYKKYIYLMMNKPQGVVSATFDNYDETVIDLLED--E 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD+ T G+L++         L        + KIY++ +     ++    
Sbjct: 92  DRIFEPFPVGRLDKNTVGLLLLTNDGELNHRL--ISPKWHVDKIYYAKINKKVTDED--- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +KK   G     ++  +      A    ++I  F ++   + +  H G+ HQ++  
Sbjct: 147 ----IKKFKKG-----IILDDGYECFPA--KLEIIKSFNEE-SEVRVTIHEGKFHQVKRM 194

Query: 259 ALH 261
              
Sbjct: 195 FES 197


>gi|126667221|ref|ZP_01738195.1| 23S rRNA pseudouridine synthase [Marinobacter sp. ELB17]
 gi|126628377|gb|EAZ99000.1| 23S rRNA pseudouridine synthase [Marinobacter sp. ELB17]
          Length = 317

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 71/246 (28%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G VR++ KR    +++     V +           
Sbjct: 8   RLNKYISE--SGICSRREADRYIEQGNVRINGKRASVGDQVLPTDTVMVN---------- 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              +I++                  ED      NKP GI     S    +I  F+   V 
Sbjct: 56  --GQIIEPRAE--------------EDQVFIALNKPVGIVSTTDSAERDNIQRFVGHTV- 98

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++ +         +  +      + +               +
Sbjct: 99  ----RIFPIGRLDKDSQGLIFMTSNGDLVNKILRAGNNHEKEYLV-------------TV 141

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              + K + I G    V           +S         +      +    G   Q+R  
Sbjct: 142 DKPITK-TFIDGMAGGVPILGTVTKKCRVSQ--------ESRFVFRIVLVQGLNRQIRRM 192

Query: 259 ALHMGC 264
           A H G 
Sbjct: 193 AEHFGF 198


>gi|163801131|ref|ZP_02195031.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. AND4]
 gi|159175480|gb|EDP60277.1| ribosomal small subunit pseudouridine synthase A [Vibrio sp. AND4]
          Length = 233

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 76/249 (30%), Gaps = 58/249 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRLD++  +           KI++SG V VD +  K  + ++    VV     +      
Sbjct: 1   MRLDKYLCDGL-GATRKQATKIIKSGDVTVDGEVQKSGSFKVPEAGVVEWEGRLVG---- 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                           +   + I+LY+ +                S    H         
Sbjct: 56  ----------------APGPRYIMLYKPADFVC------------SHEDGHNPTAFVLLD 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW---SLVWGIPKNK 194
           + K +K     RLD +T+G++++      +  +T            W   ++     +  
Sbjct: 88  EPKVEKLHFAGRLDVDTTGLVLITDDGQWSHRITSPKHKCEKTYRVWLADAIQPDYIEKF 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E I                   +NE G     +    ++   +    + +    G+ HQ
Sbjct: 148 AEGIEL-----------------RNESGP----TLPAHLEIVNEAENEVLLTIVEGKYHQ 186

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 187 VKRMFAALG 195


>gi|153939754|ref|YP_001392619.1| RNA pseudouridine synthase family protein [Clostridium botulinum F
           str. Langeland]
 gi|170754583|ref|YP_001782897.1| RNA pseudouridine synthase family protein [Clostridium botulinum B1
           str. Okra]
 gi|152935650|gb|ABS41148.1| RNA pseudouridine synthase family protein [Clostridium botulinum F
           str. Langeland]
 gi|169119795|gb|ACA43631.1| RNA pseudouridine synthase family protein [Clostridium botulinum B1
           str. Okra]
 gi|295320605|gb|ADG00983.1| RNA pseudouridine synthase family protein [Clostridium botulinum F
           str. 230613]
          Length = 238

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 88/243 (36%), Gaps = 47/243 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     ++ +++ GQV VD + VK N        ++I P  N +    
Sbjct: 2   ERLDKILAN-LGYGTRKEVKALIKKGQVDVDGEVVKDNG-------MQIDPEKNKIFVFG 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           KE                    L+Y+     + NKP G+           +   L+   +
Sbjct: 54  KE--------------------LVYKKYIYLMMNKPQGVVSATFDNYDETVIDLLED--E 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD+ T G+L++         L        + KIY++ +     ++    
Sbjct: 92  DRIFEPFPVGRLDKNTVGLLLLTNDGELNHRL--ISPKWHVDKIYYAKINKKVTDED--- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +KK   G     ++  +      A    ++I  F ++   + +  H G+ HQ++  
Sbjct: 147 ----IKKFKKG-----IILDDGYECFPA--KLEIIKSFNEE-SEVRVTIHEGKFHQVKRM 194

Query: 259 ALH 261
              
Sbjct: 195 FES 197


>gi|152997397|ref|YP_001342232.1| RNA-binding S4 domain-containing protein [Marinomonas sp. MWYL1]
 gi|150838321|gb|ABR72297.1| RNA-binding S4 domain protein [Marinomonas sp. MWYL1]
          Length = 300

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 26/174 (14%), Positives = 51/174 (29%), Gaps = 30/174 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +         +   ++  +R G+V V+ +     +R+     + I             
Sbjct: 5   LQKVLARAGQG-SRREMETRIREGRVLVNGEVATLGDRVSVKDTITIDGYSI-------- 55

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                    +   +   + +++Y        NKP G                       +
Sbjct: 56  ---------IATEAGENRRVIIY--------NKPEGEVC--TRKDPEGRPTVFDKLPKLR 96

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           G++     RLD  TSG+L+       A  L        I + Y   V G   ++
Sbjct: 97  GERWIAVGRLDINTSGLLLFTTDGELANRL--MHPSTEIDREYLVRVMGEVTDE 148


>gi|331092461|ref|ZP_08341285.1| hypothetical protein HMPREF9477_01928 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330401201|gb|EGG80793.1| hypothetical protein HMPREF9477_01928 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 243

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 78/249 (31%), Gaps = 56/249 (22%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           EE +RL+++        +     +++ +G+V VD +R +   R+   Q +++   +    
Sbjct: 3   EELIRLNKFLSEA-GVCSRREADRLIEAGKVFVDGRRAETGMRVSPAQEIKVGKKV---- 57

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                         + K ++ +          +   NKPAGI         ++I  FL  
Sbjct: 58  --------------IHKGNEMV----------LLAVNKPAGIVCTEEKKEKHNIIRFL-- 91

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              +   +     RLD+++ G+L++         +  +      +               
Sbjct: 92  ---NYPTRITYIGRLDKDSEGLLLMTNNGDIINKMMRAGNRHEKEYKV------------ 136

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                       +  +++  + Q     +   +  +     A       +    G   Q+
Sbjct: 137 -------TVNKPVTREFIEKMGQGVPILD---TVTRPCKVKAIGKYKFNIVLTQGLNRQI 186

Query: 256 RVHALHMGC 264
           R    + G 
Sbjct: 187 RRMCEYFGY 195


>gi|237744301|ref|ZP_04574782.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           7_1]
 gi|256027971|ref|ZP_05441805.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           D11]
 gi|289765917|ref|ZP_06525295.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           D11]
 gi|229431530|gb|EEO41742.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           7_1]
 gi|289717472|gb|EFD81484.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           D11]
          Length = 226

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 89/246 (36%), Gaps = 54/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++K++ + ++ V+                        +++I 
Sbjct: 1   MRLDKFLVECGIG-SRKEVKKLISNNEITVNG-----------------------ISNIS 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +  I ++S  +  + + L+    Y+  + Y+ NK +G            +   L  WV 
Sbjct: 37  AKDNIDENSDIIEYNEEKLE----YKKFRYYIMNKKSGYITATEDFKENTVMDLLPEWVI 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K   P    RLD++T G+L+     +   + L+    + ++  +               
Sbjct: 93  KKDLAP--VGRLDKDTEGLLLFTNDGKLNHKLLSPKNHVDKVYYVEI------------- 137

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                  K++I  + +  ++Q     NY I+    ++  +    +  +    G+ HQ++ 
Sbjct: 138 -------KNNISDEDIFKLEQGVDIGNY-ITQPAKVEKISDNEIY--LTIKEGKFHQIKK 187

Query: 258 HALHMG 263
               + 
Sbjct: 188 MLEAIN 193


>gi|291301885|ref|YP_003513163.1| pseudouridine synthase [Stackebrandtia nassauensis DSM 44728]
 gi|290571105|gb|ADD44070.1| pseudouridine synthase [Stackebrandtia nassauensis DSM 44728]
          Length = 244

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 54/292 (18%), Positives = 99/292 (33%), Gaps = 56/292 (19%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             + E +RL +         +    + ++ +G+V V+ K+ +  NR+            +
Sbjct: 2   TAEPEGVRLQKVMAAAGIG-SRRACENLIAAGRVTVNGKKAQLGNRV---------DPQH 51

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           A+ H+  E+ I D+              L++     +  NKP G        +       
Sbjct: 52  AVIHVDGERVITDTK-------------LVH-----FALNKPRGYVSTMDDELKRPD--- 90

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L  +     ++     RLD E+ G+L++         LT       I K Y   V G   
Sbjct: 91  LNEFTAGISERVFHVGRLDTESEGLLLLTNDGELGNRLT--HPSYEIAKTYRCQVTGY-- 146

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                 A   + +    G          +     +  FKVID  A +   +E+  H GR 
Sbjct: 147 ------AGPAIARRLAAG-------VVLEDGPVTVDDFKVIDEHADQA-LVEIVVHEGRK 192

Query: 253 HQLRVHALHMGCPI-------VGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
           H +R     +G P+       +GD +      G       +++    R + L
Sbjct: 193 HVVRRLLAEVGLPVNRLVRTAIGDIRLANLKPGTLRKLRPDEIASLYRTVGL 244


>gi|317492524|ref|ZP_07950952.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316919516|gb|EFV40847.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 240

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 74/249 (29%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + LR+ +V VD + VK                    + + 
Sbjct: 1   MRLDKFLSQQL-GISRALIARELRAKRVTVDGEIVKS-----------------GAHKLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ++      L +         ++      +  KP G      S         L    +
Sbjct: 43  PEQEVAFDGQVLEQ---------IHGPRYFMLH-KPEGYVC---STDDPDHSTILYFIDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              +K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PLAEKLHAAGRLDLDTTGLVLLTDDGQWSHRITSPKHECDKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L   +     +   +   +     A                + +    GR HQ++  
Sbjct: 137 EHPLADDTAEQFAHGVQLHGEKDLTKPATLE-------QLDANVVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNRVV 198


>gi|227542008|ref|ZP_03972057.1| pseudouridine synthase B [Corynebacterium glucuronolyticum ATCC
           51866]
 gi|227182223|gb|EEI63195.1| pseudouridine synthase B [Corynebacterium glucuronolyticum ATCC
           51866]
          Length = 225

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 43/228 (18%), Positives = 76/228 (33%), Gaps = 44/228 (19%)

Query: 39  KILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK 98
           +++  G+V V+ + V     ++ G  VR+ P                         D ++
Sbjct: 4   ELIAQGRVEVNGEIV-----MRQG--VRVDPDTA------------------VIRVDGVR 38

Query: 99  SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
             +  ED      NKP G+       +     G +       G       RLD +T G+L
Sbjct: 39  VKV-NEDLVYIALNKPLGVQSTMKDDMGRPCVGDIVGEKVDAGLHLFHVGRLDAKTEGLL 97

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           ++      A  L        + K Y + V G    +       L+KK   G D    +  
Sbjct: 98  LLTNDGELANRL--MHPKYHVSKTYLATVLGEADRE-------LVKKLREGVDLEDGI-- 146

Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                  A + +  I    +    + ++ H GR H +R     +G P+
Sbjct: 147 -------AKADYVQIVDTYEGRSLIRVELHEGRKHIVRRMLKELGFPV 187


>gi|40062484|gb|AAR37436.1| RNA pseudouridylate synthase, putative [uncultured marine bacterium
           105]
          Length = 255

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 34/249 (13%), Positives = 84/249 (33%), Gaps = 44/249 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL +   +     +    ++++  G+V V+ + V    ++ +                 
Sbjct: 6   VRLQKVLASAGIS-SRRAAERLIEVGRVTVNGRSV---TKLGA----------------K 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +  + D  V+  K       I         +  KP G      +         + + + 
Sbjct: 46  ADPDLDDIRVDGRKVKTGRPRI-------YLLVCKPRGYVT---TRFDPEGRRTILNLIS 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +  +      RLD ++ G++++      A  LT       ++++Y   V G+P       
Sbjct: 96  NVREYVYPVGRLDYDSEGLVILTNDGTLAARLT--HPRYGVERVYEVRVRGVPSQ----- 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                  + I      V+    + A+ ++   + +   + +   L +    GR  Q+R  
Sbjct: 149 -------AAIDSLRHGVLINGRRTASSSVKFLRRLKAKSSENALLRVAIREGRNRQVRKM 201

Query: 259 ALHMGCPIV 267
              +G P++
Sbjct: 202 CEAIGHPVI 210


>gi|311032169|ref|ZP_07710259.1| pseudouridine synthase F (ribosomal large subunit) [Bacillus sp.
           m3-13]
          Length = 235

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/251 (14%), Positives = 83/251 (33%), Gaps = 60/251 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++  +     +     K++  G+V+++ K  +   ++  G  V +   I       
Sbjct: 1   MRINKFISDS-GVASRRGADKLIEEGKVKINGKVAQIGGQVNPGDEVLVNGQIIR----- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  +  D+     NKP GI+      +  +I   +   + 
Sbjct: 55  -----------------------IARDNVYIALNKPIGITSTTEKKVKGNIIDLVNHPL- 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+E+ G++++                         ++    K++KE I
Sbjct: 91  ----RLSHIGRLDKESEGLILLTNDGDIINE----------------ILRPENKHEKEYI 130

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TGRTHQLR 256
            +       I  D+V  + +  K     I   K + C  ++    + +     G   Q+R
Sbjct: 131 VS---VDKPITPDFVKQMSEGVK-----ILGTKTLPCEVEQLSKFDFKIILTQGLNRQIR 182

Query: 257 VHALHMGCPIV 267
                +G  ++
Sbjct: 183 RMCAELGYEVL 193


>gi|306830930|ref|ZP_07464092.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325977819|ref|YP_004287535.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|304426953|gb|EFM30063.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325177747|emb|CBZ47791.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 238

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 82/246 (33%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +   ++K++RS QV VD        R+     + + P +  +   +
Sbjct: 1   MRLDKLLGQAGFG-SRNQVKKLIRSRQVYVDG-------RLAEADNLNVEPSLQKI--TV 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +++  SS                   K ++ NKPAG+           +   +K    
Sbjct: 51  SGKQVKQSS------------------EKYFLLNKPAGVVSAVSDKEHQTVIDLIKE--A 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +  K     RLD+ T G+L+V        + L          K + +  + +  N    
Sbjct: 91  DRVPKLYPVGRLDRSTEGLLLVTNNGPLGYRMLH--------PKYHVAKTYYVEVNAFLA 142

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                  ++ +  D   + K  +          ++I    +      +    G+ HQ++ 
Sbjct: 143 DDAPAFFENGVSFDDGTICKPAK---------LEIITASPETSSAY-VTISEGKFHQIKK 192

Query: 258 HALHMG 263
             L  G
Sbjct: 193 MFLAYG 198


>gi|207110310|ref|ZP_03244472.1| hypothetical protein HpylH_14560 [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 80

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 7/78 (8%)

Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK------LYLHARYMDLPHPEG 302
            GRTHQ+R+H   +   IVG+  Y    +         +      L LHA  ++    +G
Sbjct: 3   NGRTHQIRLHLSSINHRIVGEGLYGVIDENAREYLQLKRENNAPLLMLHAASLEFEF-KG 61

Query: 303 GRLQITAPLPAHMVKTWD 320
              +I +P+P   +    
Sbjct: 62  AIYKIASPMPERFMPFLK 79


>gi|89069156|ref|ZP_01156529.1| RNA pseudouridine synthase family protein [Oceanicola granulosus
           HTCC2516]
 gi|89045329|gb|EAR51395.1| RNA pseudouridine synthase family protein [Oceanicola granulosus
           HTCC2516]
          Length = 180

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/163 (22%), Positives = 62/163 (38%), Gaps = 12/163 (7%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + +FNKP G+  Q     +      L  +VD          RLD+++ G+LV+       
Sbjct: 4   VILFNKPFGVLSQFTDTRSPTERPTLSRYVD--VPAVYPAGRLDRDSEGLLVLTDDGRLQ 61

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS---HIGGDYVHVVKQNEKGAN 224
             +       R +K+Y + V G P +     A   L++      G     V +  E  A 
Sbjct: 62  ARIASPKA--RTEKVYLAQVEGDPDDD----ALAPLRRGLELKDGPTRPAVARLIEPPAL 115

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +      V    +    W+E+    GR  Q+R     +G P++
Sbjct: 116 WERDP-PVRFRKSVPDRWVEVTITEGRNRQVRRMCAAIGFPVL 157


>gi|258515325|ref|YP_003191547.1| pseudouridine synthase [Desulfotomaculum acetoxidans DSM 771]
 gi|257779030|gb|ACV62924.1| pseudouridine synthase [Desulfotomaculum acetoxidans DSM 771]
          Length = 264

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 83/249 (33%), Gaps = 48/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++  G V+V+ + VK        Q +++ P     + I+
Sbjct: 12  ERLQKVMARA-GIASRRKCEELIAEGVVKVNGRLVKE-------QGIKVDPQK---DRIM 60

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + KI++                  ED    +  KP G      +         +   + 
Sbjct: 61  VQGKIINR----------------LEDKIYLLMYKPRGYVT---TLHDPEGRKTIVDLLK 101

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +  ++     RLD ++ G+L+V      A  LT       ++K Y   V GIP  K    
Sbjct: 102 NIKERVFPVGRLDYDSEGLLLVTNDGELANALT--HPRHEVKKTYLVTVAGIPLPKSLE- 158

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                                 +    A +   +++    +   LE+  H G+   +R  
Sbjct: 159 --------------QMSKGLELEDGMTAPTQVALVELLEDR-SLLEITVHEGKNRLVRRM 203

Query: 259 ALHMGCPIV 267
              +G P++
Sbjct: 204 CEKIGHPVL 212


>gi|217967848|ref|YP_002353354.1| pseudouridine synthase [Dictyoglomus turgidum DSM 6724]
 gi|217336947|gb|ACK42740.1| pseudouridine synthase [Dictyoglomus turgidum DSM 6724]
          Length = 241

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 46/251 (18%), Positives = 85/251 (33%), Gaps = 50/251 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    ++++  G+V+V+ K ++                      I 
Sbjct: 3   ERLQKFISRS-GVTSRRKAEELILEGRVKVNGKVIR-----------------TLGVKID 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            E+ +++    + K    L               KP G +S          I   LK   
Sbjct: 45  PEKDVVEVDNKIIKPEKKL----------YIALYKPVGYLSSLYDPFGRRTIKDLLK--- 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D    +     RLD ++ G+L+       A  +       +I KIY  LV GIPK ++  
Sbjct: 92  DKLSSRVYPVGRLDFDSEGLLLCTNDGEIANFV--IHPRYKIPKIYEVLVNGIPKEEE-- 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLR 256
                LKK   G           +      + F+V+   ++ K   L++  + G   Q+R
Sbjct: 148 -----LKKFREG--------VILEEGKTLPAEFEVVWKNSKTKRSLLKVVLYQGWKRQIR 194

Query: 257 VHALHMGCPIV 267
                 G  ++
Sbjct: 195 RMLALFGYEVL 205


>gi|317129994|ref|YP_004096276.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
 gi|315474942|gb|ADU31545.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
          Length = 237

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/245 (15%), Positives = 78/245 (31%), Gaps = 50/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D+   N     +   ++ +L+ G V V+      +  I+ G                
Sbjct: 1   MRIDKLLSNTGFG-SRKEVKGLLKKGGVTVN------SELIKDG---------------- 37

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             ++ +D S +   H +    ++ Y+     + NKP G+           +   L +  +
Sbjct: 38  --KRQIDPSED---HIEVFGEVIEYKPFIYLMMNKPKGVISATEDVTDKTVVDLLAT--E 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                P    RLD++T+G +++      A  LT   +              + K  +  I
Sbjct: 91  HALYDPFPVGRLDKDTTGFMLLTNDGKLAHQLTSPKKK-------------VDKTYRVHI 137

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L   +        V   +      A   +            + +    G+ HQ++  
Sbjct: 138 DAPLT-SADEASLIAGVELDDGYITKPAKLTY------GNDNTVIFLTITEGKFHQVKRM 190

Query: 259 ALHMG 263
              +G
Sbjct: 191 FQALG 195


>gi|71908073|ref|YP_285660.1| ribosomal large subunit pseudouridine synthase B [Dechloromonas
           aromatica RCB]
 gi|71847694|gb|AAZ47190.1| ribosomal large subunit pseudouridine synthase B [Dechloromonas
           aromatica RCB]
          Length = 340

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 35/251 (13%), Positives = 77/251 (30%), Gaps = 44/251 (17%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            + + +RL +         +   +++ + +G+V V+         + +   V+I   +  
Sbjct: 81  AEAKPVRLQKVLAEAGVG-SRREMEEWIAAGKVSVNGVVATVGQSVVNSDKVKIGGRL-- 137

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                         +N+          +L       +++KP G  V              
Sbjct: 138 --------------INIRFTGSSRPPRVL-------MYHKPEGEIV--SRDDPDGRPSVF 174

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            +    +G +     RLD  TSG+L+   +   A  L        + + Y   V G    
Sbjct: 175 AALPRMRGGRWINVGRLDFNTSGLLLFTTSGELANKL--MHPSSELVREYAVRVLGELTL 232

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             +      ++      ++  +     +GAN+                W  +    GR  
Sbjct: 233 DAQQKLLHGVELEDGRANFGSLHDGGGEGANH----------------WYRVTISEGRNR 276

Query: 254 QLRVHALHMGC 264
           ++R     +GC
Sbjct: 277 EVRRMFEAVGC 287


>gi|254448673|ref|ZP_05062131.1| ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium HTCC5015]
 gi|198261681|gb|EDY85968.1| ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium HTCC5015]
          Length = 298

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 27/176 (15%), Positives = 56/176 (31%), Gaps = 29/176 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+ +         +   ++  +R G++ V+ K  +  + ++    V +           
Sbjct: 3   ERIQKRLA-QLGMGSRRQIEHWIRDGKITVNGKVAQLGDTLEWSDRVTLD---------- 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                   +++L +     K +LLY        +KP G                 +    
Sbjct: 52  ------GKAIDLEQVDTIPKEVLLY--------HKPEGEVCTRSDPQGRT--TVFERLPR 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +  +     RLD  T+G+L+       A  L      R I + Y   V G   ++
Sbjct: 96  LRAGRWISVGRLDVNTAGLLLFTTDGELANRL--MHPSREIDREYAVRVLGDVSDE 149


>gi|294501579|ref|YP_003565279.1| RNA pseudouridylate synthase [Bacillus megaterium QM B1551]
 gi|294351516|gb|ADE71845.1| RNA pseudouridylate synthase [Bacillus megaterium QM B1551]
          Length = 238

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 91/246 (36%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+       + +   ++ +L++G V+VD   VK                 +A  H+ 
Sbjct: 1   MRLDKLLST-IGYGSRKEVKGLLKTGAVKVDGTAVK-----------------DAKVHVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +++       +T H + +     Y +   ++ +KP G+       +   +   L+  +D
Sbjct: 43  PDEQ------EITVHGEAVS----YREFVYFMLHKPQGVISATEDSLHETVLDLLE--LD 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD++T G+L++      A Q L+   +    +  +  +   + +   E 
Sbjct: 91  DAVYDPFPVGRLDKDTEGLLLLTNDGQLAHQLLSP--KKHVPKTYFAKINAPVTEEDAEA 148

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                  +  +  D  +V K  E          K++   +     +E+    G+ HQ++ 
Sbjct: 149 F------RQGVTLDDGYVTKSAE---------LKIL--TSGVESEIELTIVEGKFHQVKR 191

Query: 258 HALHMG 263
                G
Sbjct: 192 MFEARG 197


>gi|225024981|ref|ZP_03714173.1| hypothetical protein EIKCOROL_01870 [Eikenella corrodens ATCC
           23834]
 gi|224942211|gb|EEG23420.1| hypothetical protein EIKCOROL_01870 [Eikenella corrodens ATCC
           23834]
          Length = 325

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 50/156 (32%), Gaps = 28/156 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +RL +         +   +++ +++G V V+ K  +  +++Q    V +   +  L  
Sbjct: 72  EPVRLQKALAASGVG-SRREMEEWIQNGWVTVNGKVAQLGDKVQPEDQVLVKGSVIKL-- 128

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K  D L  I+LY         K  G  V                 
Sbjct: 129 ---------------KWPDRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 163

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
             +   +     RLD  TSG+L++  +   A     
Sbjct: 164 PQAASSRWVAIGRLDINTSGLLILTTSGELANRFAH 199


>gi|323336439|gb|EGA77706.1| Pus5p [Saccharomyces cerevisiae Vin13]
 gi|323353758|gb|EGA85613.1| Pus5p [Saccharomyces cerevisiae VL3]
          Length = 177

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 32/188 (17%), Positives = 66/188 (35%), Gaps = 35/188 (18%)

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           +++A+T+ A+   +   +            +                +   G  Y  ++ 
Sbjct: 1   MLIAKTKDASVKFSRFLQKGGNNGYKLQRKYVAIVESSGRFNKPNNYEIKYGPKYNFLIS 60

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC-PIVGDHKYCANF 276
              +     I+ FK +D        + +Q  TG+ HQ+R H   +   PI+ D KY +  
Sbjct: 61  HGGRE----ITKFKEVDEN-----CIVLQLVTGKKHQIRNHVSQILNQPILNDKKYGSTV 111

Query: 277 KGNFTSPIQNKLYLHA-------------RYMDLPHPEGGRL----------QITAPLPA 313
             NF     +++ LH+               + + H   G+L          + T P+  
Sbjct: 112 --NFPELFNDQIALHSACIITKIGLQTKTHLIPMEHNNTGQLWSRKYVNEEGEFTLPIKE 169

Query: 314 HMVKTWDS 321
            +++ WD 
Sbjct: 170 VLLENWDQ 177


>gi|303242956|ref|ZP_07329414.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
 gi|302589505|gb|EFL59295.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
          Length = 250

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 93/248 (37%), Gaps = 50/248 (20%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  R+DR   N +       +++++++G+V+VD + +K                 ++  H
Sbjct: 3   ETQRVDRILSN-FGFGTRREIKQLVKNGEVKVDGEVIK-----------------DSGMH 44

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +  +   ++ S  +  +  F+            + NKPAG+     +      +  +   
Sbjct: 45  VDPKTSKIEISGQVLNYRQFI----------YVMMNKPAGVIS---ATFDNRHETVVDIL 91

Query: 137 VDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  K   P    RLD +T G+L++      A  L      + + K Y++ + G      
Sbjct: 92  PEEYKCFDPFPVGRLDIDTEGLLLMTNDGQLAHEL--LSPRKHVPKKYFAYIEGE----- 144

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             ++   +K    G     ++  +      A  H  +++    +   +E+    G+ HQ+
Sbjct: 145 --VSAGDVKMFEEG-----ILLDDGYKTLPAELH--ILEQ--GESSSVEVIIFEGKFHQV 193

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 194 KRMFEAVG 201


>gi|154502351|ref|ZP_02039411.1| hypothetical protein RUMGNA_00164 [Ruminococcus gnavus ATCC 29149]
 gi|153796976|gb|EDN79396.1| hypothetical protein RUMGNA_00164 [Ruminococcus gnavus ATCC 29149]
          Length = 252

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 76/250 (30%), Gaps = 60/250 (24%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +RL+++        +     +++ SG+V VD KR +   +I  GQVV++   + +   
Sbjct: 14  EEVRLNKYLSEA-GVCSRREADRLIESGRVSVDGKRAQTGMKIVPGQVVKVGKKVVSKQD 72

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            +                             +   NKPAGI           I  FL   
Sbjct: 73  EM----------------------------VVLAVNKPAGIVCTEERRERNSIVRFL--- 101

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                 +     RLD+++ G+L++         +  +      +              KE
Sbjct: 102 --DYPIRITYVGRLDKDSKGLLLMTNNGDIINKMMRAGNRHEKEY--------KVTVDKE 151

Query: 197 CIANWLLKKSH--IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
               +L K +      D V    + EK   Y  S                +    G   Q
Sbjct: 152 ITQEFLEKMASGVPILDTVTRPCKVEKIGKYTFS----------------IILTQGLNRQ 195

Query: 255 LRVHALHMGC 264
           +R     +G 
Sbjct: 196 IRRMCEALGY 205


>gi|229542673|ref|ZP_04431733.1| RNA-binding S4 domain protein [Bacillus coagulans 36D1]
 gi|229327093|gb|EEN92768.1| RNA-binding S4 domain protein [Bacillus coagulans 36D1]
          Length = 168

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 9/52 (17%), Positives = 27/52 (51%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           +E +R+D+   N    I+   +  +++ G++ ++K  +K +  ++    + I
Sbjct: 115 DEPVRIDKLLGNQLIDISRNQICSLIKEGKILLNKNTIKNHTAVKEKDTIEI 166


>gi|261341580|ref|ZP_05969438.1| ribosomal large subunit pseudouridine synthase F [Enterobacter
           cancerogenus ATCC 35316]
 gi|288316382|gb|EFC55320.1| ribosomal large subunit pseudouridine synthase F [Enterobacter
           cancerogenus ATCC 35316]
          Length = 290

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 25/164 (15%), Positives = 51/164 (31%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++  G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRYIEQGNVFLNGKRATIGDQVVPGDVVKVNGQLIEPRDA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    ED      NKP GI      G   +I  F+     
Sbjct: 65  -------------------------EDLVFIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               +     RLD+++ G++ +         +  +      + I
Sbjct: 97  --SSRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYI 138


>gi|158337477|ref|YP_001518652.1| pseudouridine synthase family 1 protein [Acaryochloris marina
           MBIC11017]
 gi|158307718|gb|ABW29335.1| pseudouridine synthase family [Acaryochloris marina MBIC11017]
          Length = 269

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 76/249 (30%), Gaps = 43/249 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL +     +   +    ++++ +GQV+++    +   +                    
Sbjct: 3   IRLQKLLS-QWGVASRRQAEQLILAGQVQLNGHTAELGQK-------------------- 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +      ++N    +   +   LY      + NKP G+               L     
Sbjct: 42  ADPDQDQITLNGQILNPTDRPQPLY-----LLVNKPKGVVSTCQDPQHRRTVLELLPKTY 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +GQ      RLD  ++G L++         LT       I K Y   + G P  +    
Sbjct: 97  QQGQGLHPVGRLDVASTGALLLTNDGQLTFALTHPRFH--IAKTYQVWIEGCPPPE---- 150

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYA-ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                    I   +   +  + +    A +   K         C  E+    GR  Q+R 
Sbjct: 151 ---------ILDRWRQGIHLDGRTTLPAQVEILKPYQSHTNSICL-EVILQEGRNRQIRR 200

Query: 258 HALHMGCPI 266
            A  +G P+
Sbjct: 201 IAEQLGYPV 209


>gi|311278834|ref|YP_003941065.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308748029|gb|ADO47781.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 235

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 80/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R+ +V VD   VK                 +    + 
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRASRVTVDGDIVK-----------------DTAFKLQ 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +     +L + +            + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNSLVQQTGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G+++                  +      S      K  +  +
Sbjct: 90  PVAHKLHAAGRLDIDTTGLVL-------------MTDDGQWSHRITSPRHHCEKTYRVTL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L + +     + H ++ + + A    +  +VI         + +    GR HQ++  
Sbjct: 137 ESPLAEDT--AEQFAHGIQLHNEKALTKPAQLEVI-----TATEVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAAVGNHVVG 199


>gi|258512547|ref|YP_003185981.1| pseudouridine synthase [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
 gi|257479273|gb|ACV59592.1| pseudouridine synthase [Alicyclobacillus acidocaldarius subsp.
           acidocaldarius DSM 446]
          Length = 245

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 88/250 (35%), Gaps = 54/250 (21%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
            ++R+D+W             +K+ R+G+VR++ + VK                 +A  H
Sbjct: 2   ASIRVDKWLTTAGYG-TRSEAKKLCRAGRVRLNGETVK-----------------DAAKH 43

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                 +L+    L            YE    ++  KP G      S      D  +   
Sbjct: 44  ADPAVDVLEVDGELVP----------YEPLVYFMMYKPPGYV----SSTEDPRDPVVIEL 89

Query: 137 VDSKG--QKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +D +   +      RLD++  G+L++      A + L      R + K Y+  V G    
Sbjct: 90  LDEEDIWRDVFPVGRLDKDAEGLLLLTNDGPLAHRLLA---PKRHVPKRYFVRVRGAL-- 144

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E  A  L +          VV  +   A  A    +++   A+    +++  + G+ H
Sbjct: 145 -GEGDARALAE---------GVVLDDGYKAMPA--ELEILRSGAESEAIIQV--YEGKYH 190

Query: 254 QLRVHALHMG 263
           Q++     +G
Sbjct: 191 QVKRMFASLG 200


>gi|157148091|ref|YP_001455410.1| 23S rRNA pseudouridine synthase F [Citrobacter koseri ATCC BAA-895]
 gi|157085296|gb|ABV14974.1| hypothetical protein CKO_03898 [Citrobacter koseri ATCC BAA-895]
          Length = 291

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 33/250 (13%), Positives = 74/250 (29%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    +++  G VV++   +   
Sbjct: 4   DSSVRLNKYISE--SGICSRREADRYIEQGNVFINGKRATIGDQVMPGDVVKVNGRLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        ED      NKP GI          +I  F+ 
Sbjct: 62  REA--------------------------EDLVFIALNKPVGIVSTTEDSERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +            
Sbjct: 96  H-----SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TV 141

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + + +  ++    G   +  V +  K    A   F++                 G   Q
Sbjct: 142 DKPVTDDFIRGMGAGVPILGTVTKKCKVKKEAPFVFRI-------------TLIQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCEHFGY 198


>gi|90021367|ref|YP_527194.1| ribosomal large subunit pseudouridine synthase B [Saccharophagus
           degradans 2-40]
 gi|89950967|gb|ABD80982.1| ribosomal large subunit pseudouridine synthase B [Saccharophagus
           degradans 2-40]
          Length = 398

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 27/184 (14%), Positives = 55/184 (29%), Gaps = 29/184 (15%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
             ++  ++ +L +         +   +++ +  G+V+V+       +R+     +++   
Sbjct: 3   TTDSSPQDEKLQKVLARAGQG-SRREMERAITEGRVKVNGVVATLGDRVTESDKIQVD-- 59

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                         D  + + K       ++LY        NKP G              
Sbjct: 60  --------------DQYIRVKKGEADTTRVILY--------NKPEGQIC--SRNDPEGRP 95

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
               +    K  +     RLD  TSG+L+       A  L        I + Y   V G 
Sbjct: 96  TVYDNLPRLKSGRWISVGRLDFNTSGLLLFTNDGELAHKL--MHPSSNIDREYLVRVQGE 153

Query: 191 PKNK 194
               
Sbjct: 154 VDGD 157


>gi|302333165|gb|ADL23358.1| ribosomal large subunit pseudouridine synthase B, RluB
           [Staphylococcus aureus subsp. aureus JKD6159]
          Length = 245

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 33/233 (14%), Positives = 71/233 (30%), Gaps = 49/233 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+   V     +++    + +  +   L                 
Sbjct: 19  SRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIEL----------------- 61

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                       ED    +F+KP  +     S         +  +      +     RLD
Sbjct: 62  ------------EDKIYILFHKPTQVIT---SVSDDRGRTVVTDYFKDIDARIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+L++         +T      +I+K Y + + G    ++       +K    G +
Sbjct: 107 YDTSGLLLLTNDGEFTNLMT--HPRYQIKKKYVAKLKGYLMREE-------VKALEKGIE 157

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               + Q  +                +    +E+    GR  Q+R    H G 
Sbjct: 158 LEDGMTQPAEVKVK-------KQDKDKNTTLVEITITEGRNRQVRRMFEHFGH 203


>gi|292486534|ref|YP_003529400.1| putative pseudouridylate synthase [Erwinia amylovora CFBP1430]
 gi|292897771|ref|YP_003537140.1| ribosomal large subunit pseudouridine synthase F [Erwinia amylovora
           ATCC 49946]
 gi|291197619|emb|CBJ44713.1| ribosomal large subunit pseudouridine synthase F [Erwinia amylovora
           ATCC 49946]
 gi|291551947|emb|CBA18984.1| putative pseudouridylate synthase [Erwinia amylovora CFBP1430]
 gi|312170602|emb|CBX78865.1| putative pseudouridylate synthase [Erwinia amylovora ATCC BAA-2158]
          Length = 288

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 25/165 (15%), Positives = 57/165 (34%), Gaps = 34/165 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR    +R+ +G VV++   +    + 
Sbjct: 7   IRLNKYIGE--SGICSRRDADRYIEQGNVFINGKRAAVGDRVFAGDVVKVNGQLIEPRNE 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     +D  I   NKP GI      G   +I  F+    
Sbjct: 65  --------------------------DDLVIIALNKPVGIVSTTEGGERDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  ---SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|296103839|ref|YP_003613985.1| 16S rRNA pseudouridylate synthase A [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295058298|gb|ADF63036.1| 16S rRNA pseudouridylate synthase A [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 235

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 35/251 (13%), Positives = 74/251 (29%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++     + +R+ +V VD   V+ +  ++Q    V          H 
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRASRVTVDGDIVRDSAFKLQPDHQVEYDGNPLTQQHG 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                             ++ NKP G      S         L    
Sbjct: 60  PR----------------------------YFMLNKPEGYVC---STDDPDHPTVLYFLD 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    K     RLD +T+G++++      +  +T          +               
Sbjct: 89  EPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------T 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + +   +         +   +     A+   +VI         + +    GR HQ++ 
Sbjct: 136 LESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTEVRLTISEGRYHQVKR 188

Query: 258 HALHMGCPIVG 268
               +G  +VG
Sbjct: 189 MFAAVGNHVVG 199


>gi|146311853|ref|YP_001176927.1| 23S rRNA pseudouridylate synthase B [Enterobacter sp. 638]
 gi|145318729|gb|ABP60876.1| ribosomal large subunit pseudouridine synthase B [Enterobacter sp.
           638]
          Length = 291

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++  +G  +R+   +       
Sbjct: 5   LQKVLARA-GHGSRREIETIIEAGRVSVDGKIAKLGDRVEVVAGMKIRLDGHV------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVKESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+++       A  L      R +++ Y   V+G     K
Sbjct: 98  LRGARWIAVGRLDVNTCGLMLFTTDGELANRL--MHPSREVEREYAVRVFGEVDEHK 152


>gi|15895934|ref|NP_349283.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|15025707|gb|AAK80623.1|AE007765_5 Predicted pseudouridylate synthase [Clostridium acetobutylicum ATCC
           824]
 gi|325510086|gb|ADZ21722.1| pseudouridylate synthase [Clostridium acetobutylicum EA 2018]
          Length = 242

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 33/167 (19%), Positives = 67/167 (40%), Gaps = 32/167 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   + +  +++KI++ G+V+VD + VK NN+       ++ P  + +    
Sbjct: 2   ERLDKIISN-MGYGSRKDVKKIIKDGRVKVDGEVVKDNNK-------QLDPQKSKIIVNG 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E                    + Y+     + NKP G+           +   L+  V+
Sbjct: 54  EE--------------------ISYKKYIYLMMNKPDGVISATSDDYDKTVIDLLE--VE 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
            +  +P    RLD++T G+L +         L        + K+Y++
Sbjct: 92  DQVFEPFPIGRLDKDTVGLLFLTNDGDFNHRL--ISPKWHVDKVYYA 136


>gi|77405184|ref|ZP_00782282.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae H36B]
 gi|77411049|ref|ZP_00787403.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae CJB111]
 gi|77162872|gb|EAO73829.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae CJB111]
 gi|77176186|gb|EAO78957.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae H36B]
          Length = 240

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 81/249 (32%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ IL+  Q+ V+                             
Sbjct: 1   MRLDKFLVECGLG-SRTQVKLILKKKQISVNG---------------------------- 31

Query: 79  KEQKILDSSVNLTKHSDFLK---SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                    V + ++ D +K   +++ YE    Y+ +KP G+           +   L  
Sbjct: 32  --NSETSPKVQVDEYRDEIKYNGTLVSYEKFVYYMLHKPKGVISATDDPSHKTVLDLLDK 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               K        RLD +T+G+L++      A + L+     + + K Y + + GI    
Sbjct: 90  TARDKA--VFPVGRLDIDTTGLLLITNNGELAHKMLS---PKKHVDKCYEAKISGIMTED 144

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                     K  I  D+  +          A+    V     +K   +++    G+ HQ
Sbjct: 145 ----DILAFDKGIILKDFTCL---------PALLEI-VEVNQVKKQSLVKITIKEGKFHQ 190

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 191 VKRMVAACG 199


>gi|329929427|ref|ZP_08283175.1| pseudouridylate synthase [Paenibacillus sp. HGF5]
 gi|328936514|gb|EGG32959.1| pseudouridylate synthase [Paenibacillus sp. HGF5]
          Length = 243

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/245 (16%), Positives = 83/245 (33%), Gaps = 48/245 (19%)

Query: 22  DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
           D+   N     +   L+K  + G + V+    K                 +   H+    
Sbjct: 2   DKVLSNLGFG-SRAELKKKAKQGSIVVNGTITK-----------------DPGKHVDPYA 43

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG 141
            I++          F    + Y +    + +KP G+     S      D  +   +D++ 
Sbjct: 44  DIIE----------FEGETIQYREYVYLMLHKPPGVV----SATEDLRDRTVLDLLDAEY 89

Query: 142 Q--KPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +  +P    RLD++T G+L++    + A + L+     + I K Y + V G    +    
Sbjct: 90  RVFEPFPVGRLDKDTEGLLLLTNDGKLAHELLS---PRKHIPKTYEATVEGRVDEED--- 143

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                 +    G  +        G     SH +  D    +   + +  H G+ HQ++  
Sbjct: 144 -----VRRFAAGVTLDDGYVTLPGELAIHSHEERED--GDQLSRISLTIHEGKFHQVKRM 196

Query: 259 ALHMG 263
              +G
Sbjct: 197 FEAVG 201


>gi|228955231|ref|ZP_04117239.1| hypothetical protein bthur0006_45890 [Bacillus thuringiensis
           serovar kurstaki str. T03a001]
 gi|228804364|gb|EEM50975.1| hypothetical protein bthur0006_45890 [Bacillus thuringiensis
           serovar kurstaki str. T03a001]
          Length = 165

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RIDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDSISIC 164


>gi|78779587|ref|YP_397699.1| ribosomal large subunit pseudouridine synthase F [Prochlorococcus
           marinus str. MIT 9312]
 gi|78713086|gb|ABB50263.1| ribosomal large subunit pseudouridine synthase F [Prochlorococcus
           marinus str. MIT 9312]
          Length = 240

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 30/246 (12%), Positives = 74/246 (30%), Gaps = 55/246 (22%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R++++      + +     +++  G+V ++ K  +   +++ G  V +       +   K
Sbjct: 4   RINKYLSE-VGYCSRRKADRLIEEGKVTINGKIPEIGAKVEDGDQVEVEGQRIKKSTKQK 62

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVD 138
                                 +Y       FNKP G+      G+   +I  F+K    
Sbjct: 63  N---------------------IY-----LAFNKPIGVVCTTDRGVEPDNIIDFIK---- 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD+ + G++ +         +  +      + I                
Sbjct: 93  -YPKRIFPIGRLDKSSEGLIFLTNDGDIVNKILRARNNHEKEYIVS-------------- 137

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                    I  +++  +    +       +  V     +KF   ++    G   Q+R  
Sbjct: 138 -----VNRPINREFIQTMSNGVEILETKTKNCFVKKLGPKKF---KIILTQGLNRQIRRM 189

Query: 259 ALHMGC 264
              +G 
Sbjct: 190 CESLGY 195


>gi|197301581|ref|ZP_03166654.1| hypothetical protein RUMLAC_00307 [Ruminococcus lactaris ATCC
           29176]
 gi|197299311|gb|EDY33838.1| hypothetical protein RUMLAC_00307 [Ruminococcus lactaris ATCC
           29176]
          Length = 266

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 84/264 (31%), Gaps = 61/264 (23%)

Query: 3   LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG 62
           +   ++   ++  E  +RL+++        +     +++ +G+V VD KR     +I  G
Sbjct: 1   MSNRIREEFIQKKE-PVRLNKYLSEA-GVCSRREADRLIETGKVSVDGKRAGMGMKIYPG 58

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
           Q V++                   +  +++  + +          +   NKP GI     
Sbjct: 59  QTVKV------------------GNKTVSRQDEMI----------VLAVNKPKGIVCTEE 90

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                 I  FL     +   +     RLD+++ G+L++         +  +      +  
Sbjct: 91  RRERDSIVRFL-----NYPVRVTYIGRLDKDSRGLLLMTNNGDIINKIMRAANYHEKEY- 144

Query: 183 YWSLVWGIPKNKKECIANWLLKKSH--IGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
                        E   ++L K S      D V    + EK   Y    FK+I       
Sbjct: 145 -------KVTVDHEITEDFLKKMSRGVAILDTVTRPCKVEKLGKYT---FKII------- 187

Query: 241 CWLEMQPHTGRTHQLRVHALHMGC 264
                    G   Q+R     +G 
Sbjct: 188 ------LTQGLNRQIRRMCEALGY 205


>gi|313888050|ref|ZP_07821728.1| pseudouridine synthase B, ribosomal large subunit [Peptoniphilus
           harei ACS-146-V-Sch2b]
 gi|312846005|gb|EFR33388.1| pseudouridine synthase B, ribosomal large subunit [Peptoniphilus
           harei ACS-146-V-Sch2b]
          Length = 235

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 80/246 (32%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL ++   H    +    ++ ++ G V+V+ K V                         
Sbjct: 1   MRLQKYMA-HCGAASRRKCEEFIQEGLVKVNDKVVT------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +       N+ +     K + L       + NKP G+               L     
Sbjct: 36  --ELGTKIDPNVDRVYLDGKRLTLEGKKVYMILNKPIGVVTSASDEKDRPTVTDLV---- 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD +T+G++ +      A  +       +I K Y   V G P  ++  I
Sbjct: 90  PDDYRVYPVGRLDIDTTGLVFLTNDGQLANIM--MHPRYKIGKKYIVTVDGTPNARELSI 147

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               L++     D              + ++ +++  F Q    LE++   G+ HQ++  
Sbjct: 148 ----LREGLDIRDL-----------KTSPANVRILKSFKQD-SILEIEIFEGQNHQVKRM 191

Query: 259 ALHMGC 264
             ++G 
Sbjct: 192 FDYIGH 197


>gi|68068373|ref|XP_676096.1| pseudouridine synthetase [Plasmodium berghei strain ANKA]
 gi|56495631|emb|CAH95418.1| pseudouridine synthetase, putative [Plasmodium berghei]
          Length = 318

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 47/262 (17%), Positives = 91/262 (34%), Gaps = 29/262 (11%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +E  +RL++   +   +I+     K +++  ++++ K V     +  G  V I      
Sbjct: 41  KNENIIRLNK-LISINNNISRRKSDKFIQNANIKINNKVV-----LNPGTHVDITKDQI- 93

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK----IYVFNKPAGISVQGGSGIAYHI 129
                   K+ D  +++      L +  +   +       V +KP G+     +      
Sbjct: 94  --------KVHDKKIDIENIKKILNNYNISNTNHNSYKWIVMHKPKGLIC--TNQDEKDR 143

Query: 130 DGFLKSWVDSKGQKPRLTH--RLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                 + D   QK R+    RLD+ TSG+L+          LT     R ++K    + 
Sbjct: 144 KSIFSIFPDDLLQKYRIVSVGRLDRNTSGVLLFTNEYTWVNKLTHPKYER-VRKYMIHIE 202

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--KFCWLEM 245
             +  +  + +AN +  K            Q    A   +   + +    Q  K   L +
Sbjct: 203 GPVRMDALKMLANGVYLKDEDNNKKKKKKTQ---PAFIEVLREENVKIQNQIKKITVLNI 259

Query: 246 QPHTGRTHQLRVHALHMGCPIV 267
               GR  Q+R     +  PIV
Sbjct: 260 SIKEGRNRQIRKMFQQINQPIV 281


>gi|293398946|ref|ZP_06643111.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           gonorrhoeae F62]
 gi|291610360|gb|EFF39470.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           gonorrhoeae F62]
          Length = 399

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 78/251 (31%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 145 EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 201

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 202 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 236

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 237 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTGEQM 294

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  ++  E+G   A   + ++    +      +    G T    
Sbjct: 295 RVLTEEGVMLEDGLAKVERIR--EQGGEGANKWYNIVIKEGRNREVRRIFESQGLTVSRL 352

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 353 VRVAFGPIGLP 363


>gi|237732236|ref|ZP_04562717.1| 16S rRNA pseudouridylate synthase A [Citrobacter sp. 30_2]
 gi|226907775|gb|EEH93693.1| 16S rRNA pseudouridylate synthase A [Citrobacter sp. 30_2]
          Length = 235

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 79/249 (31%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R+ +V VD + VK                 N+   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRANRVTVDGEIVK-----------------NSAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +     +L + +            + ++ NKP G      S         L    +
Sbjct: 43  PEHDVEYDGNSLVQQNGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +     +   +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAHGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|225076444|ref|ZP_03719643.1| hypothetical protein NEIFLAOT_01490 [Neisseria flavescens
           NRL30031/H210]
 gi|224952123|gb|EEG33332.1| hypothetical protein NEIFLAOT_01490 [Neisseria flavescens
           NRL30031/H210]
          Length = 352

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 76/251 (30%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ +  +   ++     V +   I  L  
Sbjct: 98  EPERLQKVLAASGVG-SRREMEEWISNGWVTVNGRVAQLGEKVTPDDHVTVKGSIIKL-- 154

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 155 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 189

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 190 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGELTTEQM 247

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  +   E+G   A   + V+    +      +    G T    
Sbjct: 248 RVLTEEGVMLEDGLAKVERIY--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 305

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 306 VRVGFGPIGLP 316


>gi|303229867|ref|ZP_07316643.1| pseudouridine synthase B, ribosomal large subunit [Veillonella
           atypica ACS-134-V-Col7a]
 gi|303232045|ref|ZP_07318748.1| pseudouridine synthase B, ribosomal large subunit [Veillonella
           atypica ACS-049-V-Sch6]
 gi|302513151|gb|EFL55190.1| pseudouridine synthase B, ribosomal large subunit [Veillonella
           atypica ACS-049-V-Sch6]
 gi|302515423|gb|EFL57389.1| pseudouridine synthase B, ribosomal large subunit [Veillonella
           atypica ACS-134-V-Col7a]
          Length = 241

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 86/248 (34%), Gaps = 47/248 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++  +     +    ++++ SG+VRV+ ++V                 +      +
Sbjct: 2   ERLQKFIAS-CGVASRRKAEELIASGKVRVNGRKVT---------------ELGVKVDPM 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K++ ++D  +   +   +            Y+ NKP G+     S         +  ++ 
Sbjct: 46  KDKVMVDGQLLAVEKPVY------------YLMNKPKGVIT---SVTDPQGRETVMDYIK 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           ++ ++     RLD  T G+L++      AQ+LT     + ++K Y   + G   +    +
Sbjct: 91  NEKRRIYPIGRLDLHTEGLLLLTNDGELAQNLT--HPSKGVEKTYEVRIKGRVNDTDLQV 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               +                E G     +   +          +E+  H GR  Q+R  
Sbjct: 149 IADGV--------------PLEDGVTAPATLVDLGFDDHNGVHEVEITIHEGRNRQVRRM 194

Query: 259 ALHMGCPI 266
             H G  I
Sbjct: 195 FEHFGYRI 202


>gi|298694777|gb|ADI97999.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus ED133]
          Length = 245

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 33/233 (14%), Positives = 71/233 (30%), Gaps = 49/233 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+   V     +++    + +  +   L                 
Sbjct: 19  SRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIEL----------------- 61

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                       ED    +F+KP  +     S         +  +      +     RLD
Sbjct: 62  ------------EDKIYILFHKPTQVIT---SVSDDRGRTVVTDYFKDIDARIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+L++         +T      +I+K Y + + G    ++       +K    G +
Sbjct: 107 YDTSGLLLLTNDGEFTNLMT--HPRYQIKKKYVAKLKGYLMREE-------VKALEKGIE 157

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               + Q  +                +    +E+    GR  Q+R    H G 
Sbjct: 158 LEDGMTQPAEVKVK-------KQDKDKNTTLVEITITEGRNRQVRRMFEHFGH 203


>gi|241760499|ref|ZP_04758592.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           flavescens SK114]
 gi|261380706|ref|ZP_05985279.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           subflava NJ9703]
 gi|241319003|gb|EER55505.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           flavescens SK114]
 gi|284796417|gb|EFC51764.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           subflava NJ9703]
          Length = 352

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 76/251 (30%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ +  +   ++     V +   I  L  
Sbjct: 98  EPERLQKVLAASGVG-SRREMEEWISNGWVTVNGRVAQLGEKVTPDDHVTVKGSIIKL-- 154

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 155 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 189

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++ 
Sbjct: 190 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGELTTEQM 247

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT--HQ 254
            +          G   V  +   E+G   A   + V+    +      +    G T    
Sbjct: 248 RVLTEEGVMLEDGLAKVERIY--EQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRL 305

Query: 255 LRVHALHMGCP 265
           +RV    +G P
Sbjct: 306 VRVGFGPIGLP 316


>gi|332140787|ref|YP_004426525.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Alteromonas macleodii str. 'Deep ecotype']
 gi|327550809|gb|AEA97527.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Alteromonas macleodii str. 'Deep ecotype']
          Length = 298

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 35/243 (14%), Positives = 68/243 (27%), Gaps = 40/243 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +   N     +   +++ +  G+V V+       +R+     +R+   + +      E
Sbjct: 5   LQKVLANQGLG-SRREMERWIEEGRVSVNGSVATLGDRVDHTAQIRVDGHLLSRQT---E 60

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           Q I                       ++ ++NKP G             D         +
Sbjct: 61  QPIC----------------------RVLMYNKPEGELC--SRHDPEGRDTVFDRLPAIR 96

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
             +     RLD  TSG+L+       A  L        +++ Y   V+G    K   +  
Sbjct: 97  LGRWITVGRLDMNTSGLLLFTNDGELANRL--MHPKCEVEREYAVRVFGEVSTK--TLNT 152

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
                    G+   +         +A               W  +    GR  ++R    
Sbjct: 153 LQKGVELDDGEAKFLTISGTPTPQHAEEE--------SMNRWFNVTLKEGRNREVRRLWE 204

Query: 261 HMG 263
             G
Sbjct: 205 SQG 207


>gi|320546398|ref|ZP_08040713.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           equinus ATCC 9812]
 gi|320448783|gb|EFW89511.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           equinus ATCC 9812]
          Length = 238

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 35/177 (19%), Positives = 61/177 (34%), Gaps = 34/177 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +   ++K++RS QV VD        R+     + + P        +
Sbjct: 1   MRLDKLLGQAGFG-SRNQVKKLIRSRQVYVDG-------RLAEADNLNVEPS-------L 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E  +    V L+               K ++ NKPAG+          H          
Sbjct: 46  QEITVSGKQVTLST-------------EKYFILNKPAGVVS--AVSDKEHQTVIDLIVES 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +  K     RLD++T G L++        + L   +    + K Y+  V G   + 
Sbjct: 91  DRVPKLYPVGRLDRDTEGFLLITNNGPLGYRMLHPKYH---VTKTYYVEVNGRLADD 144


>gi|322492659|emb|CBZ27936.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 969

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 16/28 (57%), Positives = 19/28 (67%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             P+TGR HQ+R H   +GCPIVGD  Y
Sbjct: 634 CTPYTGRLHQIRRHLGSLGCPIVGDVVY 661



 Score = 39.6 bits (91), Expect = 0.81,   Method: Composition-based stats.
 Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 19/85 (22%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
           PR  HRLD+ TSG+L++A  + AA+ +      +              K  +E +   LL
Sbjct: 359 PRPCHRLDKVTSGVLLLAVRQDAAKRIGSVLMRK-------------AKEVEEAVTTELL 405

Query: 204 KKSHIGGDYVHVVKQNEKGANYAIS 228
           ++       V      ++G   A++
Sbjct: 406 RR------RVEPYASRDRGVETAVT 424


>gi|302875017|ref|YP_003843650.1| pseudouridine synthase [Clostridium cellulovorans 743B]
 gi|307690365|ref|ZP_07632811.1| pseudouridine synthase [Clostridium cellulovorans 743B]
 gi|302577874|gb|ADL51886.1| pseudouridine synthase [Clostridium cellulovorans 743B]
          Length = 235

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 37/251 (14%), Positives = 87/251 (34%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQS-GQVVRIPPVINALNH 76
            RL ++        +    ++++  G+V V+   +     +++    ++++       N+
Sbjct: 2   ERLQKYMAK-CGVASRRKCEELILQGKVSVNNTIITELGYKVEEENDIIKV-------NN 53

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +I   +     + L K   ++ S +  E  +  V +                        
Sbjct: 54  VIIYPEAQKVYIALNKPVKYISS-VKDEKGRKNVID------------------------ 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +    ++     RLD ++SG+L++        +L      + + K Y   V GIP  ++ 
Sbjct: 89  LIDVKERIYPIGRLDYDSSGLLLLTNDGDIYNNL--MHPSKEVYKTYLVTVNGIPTIEE- 145

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 +KK   G D    +    K           I+        L++Q + G+  Q+R
Sbjct: 146 ------IKKLETGIDIGGYITAPAKVK---------IEKLDYNKASLKIQIYEGKNRQIR 190

Query: 257 VHALHMGCPIV 267
                +G  ++
Sbjct: 191 KMCDSIGHSVI 201


>gi|257126419|ref|YP_003164533.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
 gi|257050358|gb|ACV39542.1| pseudouridine synthase [Leptotrichia buccalis C-1013-b]
          Length = 252

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 87/245 (35%), Gaps = 31/245 (12%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  N         +++IL++ +V V+      N  ++ G++           H+ 
Sbjct: 1   MRLDKFLANSGIG-TRKEVKEILKNKKVSVN------NVFVKDGKI-----------HVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E+ I+           +   I+ Y+     + NKPAG+           +   L     
Sbjct: 43  EEKDIVK----------YENKIINYKPFVYIMMNKPAGVISATEDSHHKTVIDLLNDEYR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +    P    RLD +T G++++        H   S +    +K Y  +   + ++  + +
Sbjct: 93  TYDIFP--VGRLDIDTEGLILLT-NDGILSHNLLSPKKHVDKKYYVKITKSLSEDDIKTL 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N +  + +       V          +       +   +    + +    G+ HQ++  
Sbjct: 150 ENGIKLEENFITKNAKVEIICNNSEKESEDFDFGENENNKNENSVYITISEGKFHQVKRM 209

Query: 259 ALHMG 263
              +G
Sbjct: 210 FKAVG 214


>gi|91228669|ref|ZP_01262584.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus
           12G01]
 gi|269967050|ref|ZP_06181118.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus 40B]
 gi|91187790|gb|EAS74107.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus
           12G01]
 gi|269828309|gb|EEZ82575.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus 40B]
          Length = 312

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 37/231 (16%), Positives = 75/231 (32%), Gaps = 32/231 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ +++SG+V V+    K   R+                    E
Sbjct: 5   LQKVLARA-GHGSRREIESLIKSGRVSVNGVVAKLGERL--------------------E 43

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            +     ++    S  ++  ++     +  + KP G                       +
Sbjct: 44  DESSVVRIDGHIVSAKIQEEVICR---VLAYYKPEGELC--TRHDPEGRRTVFDRLPKIR 98

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K     
Sbjct: 99  GSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVTEQKVRNLV 156

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
             ++       +  VV    +G N+  + + VI+     +     E Q  T
Sbjct: 157 KGVELEDGLARFEDVVYAGGEGMNH--TFYVVINEGRNREVRRLWESQECT 205


>gi|302866907|ref|YP_003835544.1| pseudouridine synthase [Micromonospora aurantiaca ATCC 27029]
 gi|302569766|gb|ADL45968.1| pseudouridine synthase [Micromonospora aurantiaca ATCC 27029]
          Length = 256

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 84/252 (33%), Gaps = 50/252 (19%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RL +         +    + ++   +V V+ +  +  ++              A +
Sbjct: 16  EGAERLQKVLAAAGVG-SRRACEDLIFRRRVTVNGRVAQLGDK-----------ADPARD 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLK 134
            I+ + + L + V L                     NKP G+            +  F+ 
Sbjct: 64  VIVVDGERLQADVRLV----------------YVAMNKPRGVVTTMADEKGRTELADFIG 107

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           + ++   Q+     RLD ++ G+L++      A  L        + K Y + V G     
Sbjct: 108 ARLE---QRVYHVGRLDADSEGLLLLTNDGTLAHKL--MHPSYEVLKTYLAEVAG----- 157

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              I   L K+   G +         +     +  FKV+D    K   +E+  H GR H 
Sbjct: 158 --PIPRNLGKRLTAGVEL--------EDGPVKVDGFKVVDTLG-KTAQVELTLHEGRKHI 206

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 207 VRRLMAEVGHPV 218


>gi|254230520|ref|ZP_04923892.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. Ex25]
 gi|262393864|ref|YP_003285718.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. Ex25]
 gi|151936968|gb|EDN55854.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. Ex25]
 gi|262337458|gb|ACY51253.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. Ex25]
          Length = 312

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/231 (16%), Positives = 75/231 (32%), Gaps = 32/231 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ +++SG+V V+    K   R+                    E
Sbjct: 5   LQKVLARA-GHGSRREIESLIKSGRVSVNGVVAKLGERL--------------------E 43

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            +     ++    S  ++  ++     +  + KP G                       +
Sbjct: 44  DESSVVRIDGHIVSAKIQEEVICR---VLAYYKPEGELC--TRHDPEGRRTVFDRLPKIR 98

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K     
Sbjct: 99  GSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVTEQKVRNLV 156

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
             ++       +  VV    +G N+  + + VI+     +     E Q  T
Sbjct: 157 KGVELEDGLARFEDVVYAGGEGMNH--TFYVVINEGRNREVRRLWESQECT 205


>gi|301308375|ref|ZP_07214329.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           20_3]
 gi|300833845|gb|EFK64461.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           20_3]
          Length = 495

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 47/290 (16%), Positives = 88/290 (30%), Gaps = 55/290 (18%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M         V+ +  E +RL+++  N     +     + ++ G V+V+   V     +I
Sbjct: 242 MRPKQIKYKEVLADPNEPIRLNKFLSNA-GVCSRREADEFIQKGAVKVNDVVVTELGTKI 300

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
               VV        +                             E     V NKP     
Sbjct: 301 TRQDVVTFNEKPVQI-----------------------------ESKVYIVLNKPKNCVT 331

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              S         +    ++  ++     RLD+ T+G+L++      A  LT     ++ 
Sbjct: 332 --TSDDPQERLTVMDLVKNACQERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPSFKKKK 389

Query: 180 QKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
               W L   +     E IAN L L+   I  D +    +++K                 
Sbjct: 390 IYHVW-LDKNVAIEDMEKIANGLELEDGEIHADAISYASEDDK----------------- 431

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVG-DHKYCANFKGNFTSPIQNK 287
               + ++ H+GR   +R     +G  +   D  Y A          + +
Sbjct: 432 --SQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWR 479


>gi|298374690|ref|ZP_06984648.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           3_1_19]
 gi|298269058|gb|EFI10713.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           3_1_19]
          Length = 495

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 47/290 (16%), Positives = 88/290 (30%), Gaps = 55/290 (18%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M         V+ +  E +RL+++  N     +     + ++ G V+V+   V     +I
Sbjct: 242 MRPKQIKYKEVLADPNEPIRLNKFLSNA-GVCSRREADEFIQKGAVKVNDVVVTELGTKI 300

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
               VV        +                             E     V NKP     
Sbjct: 301 TRQDVVTFNEKPVQI-----------------------------ESKVYIVLNKPKNCVT 331

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              S         +    ++  ++     RLD+ T+G+L++      A  LT     ++ 
Sbjct: 332 --TSDDPQERLTVMDLVKNACQERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPSFKKKK 389

Query: 180 QKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
               W L   +     E IAN L L+   I  D +    +++K                 
Sbjct: 390 IYHVW-LDKNVAIEDMEKIANGLELEDGEIHADAISYASEDDK----------------- 431

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVG-DHKYCANFKGNFTSPIQNK 287
               + ++ H+GR   +R     +G  +   D  Y A          + +
Sbjct: 432 --SQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWR 479


>gi|255012441|ref|ZP_05284567.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_1_7]
          Length = 495

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 47/290 (16%), Positives = 88/290 (30%), Gaps = 55/290 (18%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M         V+ +  E +RL+++  N     +     + ++ G V+V+   V     +I
Sbjct: 242 MRPKQIKYKEVLADPNEPIRLNKFLSNA-GVCSRREADEFIQKGAVKVNDVVVTELGTKI 300

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
               VV        +                             E     V NKP     
Sbjct: 301 TRQDVVTFNEKPVQI-----------------------------ESKVYIVLNKPKNCVT 331

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              S         +    ++  ++     RLD+ T+G+L++      A  LT     ++ 
Sbjct: 332 --TSDDPQERLTVMDLVKNACQERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPSFKKKK 389

Query: 180 QKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
               W L   +     E IAN L L+   I  D +    +++K                 
Sbjct: 390 IYHVW-LDKNVAIEDMEKIANGLELEDGEIHADAISYASEDDK----------------- 431

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVG-DHKYCANFKGNFTSPIQNK 287
               + ++ H+GR   +R     +G  +   D  Y A          + +
Sbjct: 432 --SQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWR 479


>gi|254506983|ref|ZP_05119121.1| ribosomal large subunit pseudouridine synthase B [Vibrio
           parahaemolyticus 16]
 gi|219549978|gb|EED26965.1| ribosomal large subunit pseudouridine synthase B [Vibrio
           parahaemolyticus 16]
          Length = 322

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/179 (18%), Positives = 61/179 (34%), Gaps = 30/179 (16%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNH 76
           N +L +       H +   L+ ++++G+V V+    K   R++    +VRI         
Sbjct: 2   NEKLQKVLARA-GHGSRRELEALIKAGRVSVNGVVAKLGERLEDENAIVRIDGH------ 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                     +V+     + +  +L Y         KP G                    
Sbjct: 55  ----------TVSAKAQEEVICRVLAY--------YKPEGELC--TRHDPEGRRTVFDRL 94

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K
Sbjct: 95  PKIRGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVTEQK 151


>gi|150010293|ref|YP_001305036.1| ribosomal large subunit pseudouridine synthase B [Parabacteroides
           distasonis ATCC 8503]
 gi|256839144|ref|ZP_05544654.1| ribosomal large subunit pseudouridine synthase B [Parabacteroides
           sp. D13]
 gi|149938717|gb|ABR45414.1| ribosomal large subunit pseudouridine synthase B [Parabacteroides
           distasonis ATCC 8503]
 gi|256740063|gb|EEU53387.1| ribosomal large subunit pseudouridine synthase B [Parabacteroides
           sp. D13]
          Length = 495

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 47/290 (16%), Positives = 88/290 (30%), Gaps = 55/290 (18%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRI 59
           M         V+ +  E +RL+++  N     +     + ++ G V+V+   V     +I
Sbjct: 242 MRPKQIKYKEVLADPNEPIRLNKFLSNA-GVCSRREADEFIQKGAVKVNDVVVTELGTKI 300

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
               VV        +                             E     V NKP     
Sbjct: 301 TRQDVVTFNEKPVQI-----------------------------ESKVYIVLNKPKNCVT 331

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
              S         +    ++  ++     RLD+ T+G+L++      A  LT     ++ 
Sbjct: 332 --TSDDPQERLTVMDLVKNACQERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPSFKKKK 389

Query: 180 QKIYWSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
               W L   +     E IAN L L+   I  D +    +++K                 
Sbjct: 390 IYHVW-LDKNVAIEDMEKIANGLELEDGEIHADAISYASEDDK----------------- 431

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPIVG-DHKYCANFKGNFTSPIQNK 287
               + ++ H+GR   +R     +G  +   D  Y A          + +
Sbjct: 432 --SQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWR 479


>gi|28898725|ref|NP_798330.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|153839754|ref|ZP_01992421.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|260363727|ref|ZP_05776503.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus K5030]
 gi|260877279|ref|ZP_05889634.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus AN-5034]
 gi|260897774|ref|ZP_05906270.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus Peru-466]
 gi|260903494|ref|ZP_05911889.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus AQ4037]
 gi|34098479|sp|Q87NB7|RLUB_VIBPA RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|28806943|dbj|BAC60214.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|149746721|gb|EDM57709.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|308087596|gb|EFO37291.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus Peru-466]
 gi|308090332|gb|EFO40027.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus AN-5034]
 gi|308106753|gb|EFO44293.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus AQ4037]
 gi|308114915|gb|EFO52455.1| pseudouridine synthase B, ribosomal large subunit [Vibrio
           parahaemolyticus K5030]
 gi|328474711|gb|EGF45516.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           10329]
          Length = 312

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 42/232 (18%), Positives = 79/232 (34%), Gaps = 34/232 (14%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   ++ +++SG+V V+    K   R++    VVRI   I +    ++
Sbjct: 5   LQKVLARA-GHGSRREIESLIKSGRVSVNGVVAKLGERLEDESSVVRIDGHIVSAK--VQ 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E+ I                       ++  + KP G                       
Sbjct: 62  EEVIC----------------------RVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K    
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVTEQKVRNL 155

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
              ++       +  VV    +G N+  + + VI+     +     E Q  T
Sbjct: 156 VKGVELEDGLARFEDVVYAGGEGMNH--TFYVVINEGRNREVRRLWESQECT 205


>gi|299143841|ref|ZP_07036921.1| ribosomal large subunit pseudouridine synthase B [Peptoniphilus sp.
           oral taxon 386 str. F0131]
 gi|298518326|gb|EFI42065.1| ribosomal large subunit pseudouridine synthase B [Peptoniphilus sp.
           oral taxon 386 str. F0131]
          Length = 235

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 50/270 (18%), Positives = 96/270 (35%), Gaps = 56/270 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL ++   H    +    ++ +  G+V+V+ K V                    L +++
Sbjct: 1   MRLQKYMA-HSGAASRRKSEEYILDGRVKVNGKIVT------------------ELGYVV 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E K          + D  +  ++ E++     NKP GI     S +    D      + 
Sbjct: 42  DENK-------DKVYLDDKRLKIIKENTY-IALNKPMGIV----STVKDEKDRKTVVDLI 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD +T+G++++    A    LT       I K Y + V G P       
Sbjct: 90  DGSTRLYPIGRLDIDTTGLIILTDDGAITNKLT--HPKNEINKTYIATVEGKPTK---TE 144

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + + K   +G +     K             K++  F +    +E+  H G+ H++++ 
Sbjct: 145 LDMIRKGIKVGAEKFSPAK------------VKILKSF-EADSIIEVIIHEGKNHEVKLM 191

Query: 259 ALHMGCPI-------VGDHKYCANFKGNFT 281
              +  P+       +GD +      GNF 
Sbjct: 192 FDKINHPVKKLKRISIGDIELGDLEIGNFR 221


>gi|326204454|ref|ZP_08194312.1| pseudouridine synthase [Clostridium papyrosolvens DSM 2782]
 gi|325985486|gb|EGD46324.1| pseudouridine synthase [Clostridium papyrosolvens DSM 2782]
          Length = 247

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/246 (15%), Positives = 84/246 (34%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N +   +  +++  ++ G V VD   VK                 ++  H+ 
Sbjct: 5   QRLDKVISN-FGFGSRNDIKSAVKKGLVTVDGAIVK-----------------DSGIHVD 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  I++ +     +  F+            + NKP G+           +   L    +
Sbjct: 47  PEASIIEINGERLNYRKFI----------YIMMNKPQGVISATSDRKQRTVFDILPE--E 94

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K  +     RLD +T G++++      + + L+     + + K Y++ V G    +   
Sbjct: 95  YKCFELFPAGRLDIDTEGLVLMTNDGQLSHEILS---PKKHVPKQYYAKVLGRVNQED-- 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                            V   +      A+   +V+   + +   +++    G+ HQ++ 
Sbjct: 150 ----------ADAFRQGVTLDDGYSTLPAV--LEVLK--SDELSEIKLTIVEGKFHQVKR 195

Query: 258 HALHMG 263
               +G
Sbjct: 196 MFEAVG 201


>gi|229062392|ref|ZP_04199708.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228716863|gb|EEL68550.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 242

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 88/246 (35%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   H +   ++K+L+ G V++D   VK                    +  I
Sbjct: 1   MRLDKLLAN-MGHGSRKEVKKLLKDGVVKIDGTPVK----------------DAKFHVNI 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +EQ+++               ++ Y++    + +KP G+           +   L+  ++
Sbjct: 44  EEQEVM-----------IHGEVVEYKEFVYLMMHKPQGVISATEDDNHETVIDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    +   Q L+     + + K Y++ + G+   +   
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLITNDGKLTHQLLS---PKKHVPKKYYAHISGVVTEEDV- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                            +++   +     ++  K     +     +E+    G+ HQ++ 
Sbjct: 147 ----------KEFSKGVILEDGYETKPGELTILK-----SDDISEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|294946256|ref|XP_002784994.1| hypothetical protein Pmar_PMAR020318 [Perkinsus marinus ATCC 50983]
 gi|239898369|gb|EER16790.1| hypothetical protein Pmar_PMAR020318 [Perkinsus marinus ATCC 50983]
          Length = 262

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 12/72 (16%)

Query: 97  LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSG 156
           L+  +LY D+     NKP G+SV  G  I Y              + P L HRLD  T+G
Sbjct: 194 LEDAVLYRDADFIAINKPWGLSVTDGPKIKYS------------SEVPILIHRLDTATAG 241

Query: 157 ILVVARTRAAAQ 168
           + ++AR ++AA 
Sbjct: 242 VQLLARHKSAAT 253


>gi|148241876|ref|YP_001227033.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. RCC307]
 gi|147850186|emb|CAK27680.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. RCC307]
          Length = 254

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 86/251 (34%), Gaps = 52/251 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++R G+V ++ +     ++   G  +R            
Sbjct: 6   QRLQKVLSQA-GVCSRRRAEELMRQGRVLLNGRPASPGDQ---GDPLR------------ 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG---GSGIAYHIDGFLKS 135
              +IL     ++  ++ L  +L          +KP G  V            +   L +
Sbjct: 50  --DRILVDGELVSPPAEELTVLL----------HKPRG--VHSTCFDPRGRRTVLDLLPA 95

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + ++GQ      RLD ++ G L+++   A    LT      R     W  V G P    
Sbjct: 96  EL-AEGQGLHPVGRLDCDSRGALLLSNNGALTLALTHPRFSHRKSYRIW--VSGHP---- 148

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                     S +   + H V  + +    A    + +   A+    LE+    GR  Q+
Sbjct: 149 ---------SSAVLQQWRHGVLLDGRPTRSA--DVRELQQDAE-HSQLELVMREGRNRQI 196

Query: 256 RVHALHMGCPI 266
           R  A  +G P+
Sbjct: 197 RRVAEQLGHPV 207


>gi|86740160|ref|YP_480560.1| ribosomal large subunit pseudouridine synthase B [Frankia sp. CcI3]
 gi|86567022|gb|ABD10831.1| ribosomal large subunit pseudouridine synthase B [Frankia sp. CcI3]
          Length = 252

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 76/251 (30%), Gaps = 48/251 (19%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           ++ +RL +         +  + ++++ +G+VRVD   V+   R                 
Sbjct: 12  DQGIRLQKVLAAAGVG-SRRHGEELIAAGRVRVDGTVVREQGR----------------- 53

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
            +  E  +++           L              NKP G+     +         +  
Sbjct: 54  RVDPETALIEVDGERIVTRTGLVH---------LALNKPRGVLS---AMSDDRGRPTIAD 101

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +   G       RLD ++ G+L+V      A  LT                  +PK   
Sbjct: 102 LLTEFGGGLFHVGRLDADSEGLLLVTNDGELAHRLTHPSF-------------AVPKTYL 148

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             ++  L +           +      A+ A      I   A     +E+  H GR H +
Sbjct: 149 VEVSGPLRRDVLRQLRAEVELDDGPVRADSAR-----IVDNANGRVMVEVVVHEGRKHVV 203

Query: 256 RVHALHMGCPI 266
           R     +G P+
Sbjct: 204 RRMMDAVGHPV 214


>gi|224014790|ref|XP_002297057.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220968437|gb|EED86785.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 686

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 29/158 (18%), Positives = 57/158 (36%), Gaps = 26/158 (16%)

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECI----------ANWLLKKSHIGGDYVHVVK 217
           + L +  R R + + +       PK     +          A  LL+ +++    +  V 
Sbjct: 440 ERLRKYSRERTVVRHFLEPSIRAPKAFFSTVPKDVYNPESWAECLLRITNVSD--ICTVV 497

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQ--PHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
            N+     A+S +       +    +E++    TGRTHQ+R      G P+VGD +Y   
Sbjct: 498 GNKPSDELAVSLWGESGKPDECVAVVELEVELLTGRTHQIRGQLAAEGFPLVGDAQYGGA 557

Query: 276 FKGNFTSPIQN------------KLYLHARYMDLPHPE 301
              + +   +             +L L    ++  +P 
Sbjct: 558 VPDDCSVWKEKCKGRAESYLDSEQLALQCCSLEFLNPR 595


>gi|149592489|ref|XP_001521009.1| PREDICTED: hypothetical protein, partial [Ornithorhynchus anatinus]
          Length = 152

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 36/76 (47%)

Query: 145 RLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK 204
           R  H+LD  TSG L VA  RAAA      F+ R + K Y +LV G     +  I + + K
Sbjct: 41  RFCHQLDFSTSGALCVALNRAAAGRAYRCFKERIVTKAYVALVRGHVGEDRMTINHAIGK 100

Query: 205 KSHIGGDYVHVVKQNE 220
            +  G  +   ++  E
Sbjct: 101 NTTEGLTHTMCIQGTE 116


>gi|331270360|ref|YP_004396852.1| pseudouridine synthase [Clostridium botulinum BKT015925]
 gi|329126910|gb|AEB76855.1| pseudouridine synthase [Clostridium botulinum BKT015925]
          Length = 240

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 68/179 (37%), Gaps = 36/179 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   + +   ++ +++ G++ +D +++K N        V++ P  + +    
Sbjct: 4   ERLDKILSN-LGYGSRKEIKVLVKKGEIEIDGEKIKDNG-------VKVDPNKSIIKVSG 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E                    + Y      + NKPAG+     S    + D  +   +D
Sbjct: 56  EE--------------------INYRKYIYLMMNKPAGVV----SATFDNYDETVIDLLD 91

Query: 139 SKG--QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +     P    RLD++T G L++         LT       + KIY++ +  I   K 
Sbjct: 92  YEYTVFDPFPVGRLDKDTEGFLLITNDGDLNHRLT--SPKWHVDKIYYAEIDKIVDEKD 148


>gi|324328895|gb|ADY24155.1| hypothetical protein YBT020_24640 [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 165

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNTILSEGDHISIC 164


>gi|260584045|ref|ZP_05851793.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           elegans ATCC 700633]
 gi|260158671|gb|EEW93739.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           elegans ATCC 700633]
          Length = 243

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 82/246 (33%), Gaps = 47/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +         ++ IL+  +VR +++ V  N ++Q                  
Sbjct: 1   MRLDKFLADS-GIATRSQVKLILKQKRVRKNQETVT-NGKVQ------------------ 40

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                +D  ++     D     + YE    YV NKP G+           +   +     
Sbjct: 41  -----IDEKLDEIYLDD---ERVYYEKYLYYVMNKPKGVVSATEDTKHATVLDLIGELAQ 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +G       RLD +T G L++      +   L+     + ++K Y + + GI   + + 
Sbjct: 93  KRG--VFPVGRLDIDTHGFLLLTNNGALSHAMLS---PKKHVEKTYVAKIEGIMTQEDQV 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                            +   +      A      +D   Q    ++++   G+ HQ++ 
Sbjct: 148 SFE------------KGITLDDGYECMPAHLEILSVDKNHQ-ASLVQIKIKEGKFHQVKR 194

Query: 258 HALHMG 263
                G
Sbjct: 195 MVKACG 200


>gi|229175663|ref|ZP_04303171.1| hypothetical protein bcere0006_47400 [Bacillus cereus MM3]
 gi|228607804|gb|EEK65118.1| hypothetical protein bcere0006_47400 [Bacillus cereus MM3]
          Length = 165

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNTILSEGDHISIC 164


>gi|15924483|ref|NP_372017.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Mu50]
 gi|15927074|ref|NP_374607.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus N315]
 gi|21283176|ref|NP_646264.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MW2]
 gi|49483743|ref|YP_040967.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MRSA252]
 gi|49486331|ref|YP_043552.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MSSA476]
 gi|57650449|ref|YP_186378.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus COL]
 gi|82751087|ref|YP_416828.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus RF122]
 gi|87160582|ref|YP_494139.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus USA300_FPR3757]
 gi|88195298|ref|YP_500102.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus NCTC 8325]
 gi|148267977|ref|YP_001246920.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus JH9]
 gi|150394042|ref|YP_001316717.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus JH1]
 gi|151221613|ref|YP_001332435.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus str. Newman]
 gi|156979812|ref|YP_001442071.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Mu3]
 gi|161509722|ref|YP_001575381.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus USA300_TCH1516]
 gi|221140086|ref|ZP_03564579.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus str. JKD6009]
 gi|253314861|ref|ZP_04838074.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus str. CF-Marseille]
 gi|253733259|ref|ZP_04867424.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus TCH130]
 gi|255006279|ref|ZP_05144880.2| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Mu50-omega]
 gi|257425616|ref|ZP_05602040.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 55/2053]
 gi|257428277|ref|ZP_05604675.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 65-1322]
 gi|257430914|ref|ZP_05607294.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 68-397]
 gi|257433603|ref|ZP_05609961.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus E1410]
 gi|257436516|ref|ZP_05612560.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus M876]
 gi|257793570|ref|ZP_05642549.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9781]
 gi|258407188|ref|ZP_05680336.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9763]
 gi|258437324|ref|ZP_05689308.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9299]
 gi|258443529|ref|ZP_05691868.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8115]
 gi|258446736|ref|ZP_05694890.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A6300]
 gi|258448651|ref|ZP_05696763.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A6224]
 gi|258451151|ref|ZP_05699186.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A5948]
 gi|258454267|ref|ZP_05702237.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A5937]
 gi|262049080|ref|ZP_06021957.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus D30]
 gi|262053234|ref|ZP_06025385.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus 930918-3]
 gi|269203120|ref|YP_003282389.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282892992|ref|ZP_06301226.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8117]
 gi|282904073|ref|ZP_06311961.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus C160]
 gi|282905900|ref|ZP_06313755.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282908810|ref|ZP_06316628.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus WW2703/97]
 gi|282911129|ref|ZP_06318931.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus WBG10049]
 gi|282914298|ref|ZP_06322084.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus M899]
 gi|282916759|ref|ZP_06324517.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus D139]
 gi|282919267|ref|ZP_06327002.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus C427]
 gi|282924592|ref|ZP_06332260.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus C101]
 gi|282924742|ref|ZP_06332409.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9765]
 gi|282928963|ref|ZP_06336550.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A10102]
 gi|283958255|ref|ZP_06375706.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|284024553|ref|ZP_06378951.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 132]
 gi|293503375|ref|ZP_06667222.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|293510390|ref|ZP_06669096.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus M809]
 gi|293530929|ref|ZP_06671611.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M1015]
 gi|294848523|ref|ZP_06789269.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9754]
 gi|295406613|ref|ZP_06816418.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8819]
 gi|295428069|ref|ZP_06820701.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|296276357|ref|ZP_06858864.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MR1]
 gi|297207787|ref|ZP_06924222.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|297245803|ref|ZP_06929668.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8796]
 gi|297590963|ref|ZP_06949601.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus MN8]
 gi|300911868|ref|ZP_07129311.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH70]
 gi|304380920|ref|ZP_07363580.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus ATCC
           BAA-39]
 gi|13701292|dbj|BAB42586.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus N315]
 gi|14247264|dbj|BAB57655.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Mu50]
 gi|21204616|dbj|BAB95312.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MW2]
 gi|49241872|emb|CAG40565.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MRSA252]
 gi|49244774|emb|CAG43210.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus MSSA476]
 gi|57284635|gb|AAW36729.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus COL]
 gi|82656618|emb|CAI81043.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus RF122]
 gi|87126556|gb|ABD21070.1| ribosomal large subunit pseudouridine synthase B, RluB
           [Staphylococcus aureus subsp. aureus USA300_FPR3757]
 gi|87202856|gb|ABD30666.1| ribosomal large subunit pseudouridine synthase B, putative
           [Staphylococcus aureus subsp. aureus NCTC 8325]
 gi|147741046|gb|ABQ49344.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149946494|gb|ABR52430.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1]
 gi|150374413|dbj|BAF67673.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus str. Newman]
 gi|156721947|dbj|BAF78364.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Mu3]
 gi|160368531|gb|ABX29502.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|253728799|gb|EES97528.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus TCH130]
 gi|257271310|gb|EEV03456.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 55/2053]
 gi|257275118|gb|EEV06605.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 65-1322]
 gi|257278344|gb|EEV08980.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 68-397]
 gi|257281696|gb|EEV11833.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus E1410]
 gi|257283867|gb|EEV13990.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus M876]
 gi|257787542|gb|EEV25882.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9781]
 gi|257841215|gb|EEV65661.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9763]
 gi|257848529|gb|EEV72517.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9299]
 gi|257850935|gb|EEV74878.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8115]
 gi|257854311|gb|EEV77260.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A6300]
 gi|257857929|gb|EEV80818.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A6224]
 gi|257861206|gb|EEV84019.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A5948]
 gi|257863546|gb|EEV86304.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A5937]
 gi|259158873|gb|EEW43966.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus 930918-3]
 gi|259162749|gb|EEW47314.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus D30]
 gi|262075410|gb|ACY11383.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus ED98]
 gi|269940985|emb|CBI49369.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus TW20]
 gi|282313427|gb|EFB43822.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus C101]
 gi|282317077|gb|EFB47451.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus C427]
 gi|282319246|gb|EFB49598.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus D139]
 gi|282321479|gb|EFB51804.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus M899]
 gi|282324824|gb|EFB55134.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus WBG10049]
 gi|282327074|gb|EFB57369.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus WW2703/97]
 gi|282331192|gb|EFB60706.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282589370|gb|EFB94461.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A10102]
 gi|282592749|gb|EFB97755.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9765]
 gi|282595691|gb|EFC00655.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus C160]
 gi|282764310|gb|EFC04436.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8117]
 gi|283470772|emb|CAQ49983.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus ST398]
 gi|283790404|gb|EFC29221.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|285817174|gb|ADC37661.1| Ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus 04-02981]
 gi|290920197|gb|EFD97263.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M1015]
 gi|291095041|gb|EFE25306.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus 58-424]
 gi|291466754|gb|EFF09274.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus M809]
 gi|294824549|gb|EFG40972.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9754]
 gi|294968360|gb|EFG44384.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8819]
 gi|295128427|gb|EFG58061.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|296887804|gb|EFH26702.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|297177454|gb|EFH36706.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A8796]
 gi|297575849|gb|EFH94565.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus MN8]
 gi|300886114|gb|EFK81316.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH70]
 gi|302751325|gb|ADL65502.1| ribosomal large subunit pseudouridine synthase B, RluB
           [Staphylococcus aureus subsp. aureus str. JKD6008]
 gi|304340647|gb|EFM06581.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus ATCC
           BAA-39]
 gi|312438039|gb|ADQ77110.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH60]
 gi|312829882|emb|CBX34724.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Staphylococcus aureus subsp. aureus ECT-R 2]
 gi|315129766|gb|EFT85756.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS03]
 gi|315195390|gb|EFU25777.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS00]
 gi|315198816|gb|EFU29144.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320140623|gb|EFW32477.1| hypothetical protein HMPREF9528_01247 [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320144159|gb|EFW35928.1| hypothetical protein HMPREF9529_00596 [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|323441527|gb|EGA99178.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus O46]
 gi|329314171|gb|AEB88584.1| Pseudouridine synthase [Staphylococcus aureus subsp. aureus T0131]
 gi|329725278|gb|EGG61765.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           aureus subsp. aureus 21189]
 gi|329727675|gb|EGG64131.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           aureus subsp. aureus 21172]
 gi|329730831|gb|EGG67209.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           aureus subsp. aureus 21193]
          Length = 245

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/233 (14%), Positives = 71/233 (30%), Gaps = 49/233 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+   V     +++    + +  +   L                 
Sbjct: 19  SRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIEL----------------- 61

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                       ED    +F+KP  +     S         +  +      +     RLD
Sbjct: 62  ------------EDKIYILFHKPTQVIT---SVSDDRGRTVVTDYFKDIEARIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+L++         +T      +I+K Y + + G    ++       +K    G +
Sbjct: 107 YDTSGLLLLTNDGEFTNLMT--HPRYQIKKKYVAKLKGYLMREE-------VKALEKGIE 157

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               + Q  +                +    +E+    GR  Q+R    H G 
Sbjct: 158 LEDGMTQPAEVKVK-------KQDKDKNTTLVEITITEGRNRQVRRMFEHFGH 203


>gi|52140565|ref|YP_086262.1| group-specific protein [Bacillus cereus E33L]
 gi|51974034|gb|AAU15584.1| group-specific protein [Bacillus cereus E33L]
          Length = 165

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNTILSEGDCISIC 164


>gi|262276079|ref|ZP_06053888.1| ribosomal large subunit pseudouridine synthase B [Grimontia
           hollisae CIP 101886]
 gi|262219887|gb|EEY71203.1| ribosomal large subunit pseudouridine synthase B [Grimontia
           hollisae CIP 101886]
          Length = 331

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 78/235 (33%), Gaps = 37/235 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIPPVINALNHIIK 79
           L +         +   ++ ++++G+V V+    K  +R++     +R+     +++   +
Sbjct: 5   LQKVLARAGLG-SRREIESMIQAGRVSVNGVVAKLGDRLEDLNAAIRVDGHHVSVSASSE 63

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                                   +  ++  +NKP G                       
Sbjct: 64  ------------------------QVCRVLAYNKPEGELCTRSDPEGRR--TVFDRLPRL 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
            G +     RLD  TSG+L+       A  L      R++Q+ Y   V+G     ++ + 
Sbjct: 98  NGARWVAVGRLDANTSGLLLFTTDGELANRL--MHPSRQVQREYMVRVFGEV--NEQMVK 153

Query: 200 NWLLKKSHIGGD--YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           N +       G+  +  VV    +GAN+    F V+    +      +    G T
Sbjct: 154 NLVRGVELEDGEARFEDVVYAGGEGANHT---FYVVITEGRNREVRRLWETQGVT 205


>gi|228999731|ref|ZP_04159307.1| hypothetical protein bmyco0003_42850 [Bacillus mycoides Rock3-17]
 gi|228760093|gb|EEM09063.1| hypothetical protein bmyco0003_42850 [Bacillus mycoides Rock3-17]
          Length = 166

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 11/74 (14%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 1   MSLMTYVQY------VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK 54
           +S+M Y +       +V+E    + R+D+    +    +   +   +++G ++++ +++K
Sbjct: 92  ISIMQYKEAGTTELAIVLETVFGSHRMDKALATYISDWSRTAIVDRIKNGHIQLNGQKMK 151

Query: 55  FNNRIQSGQVVRIP 68
            +  +  G ++ I 
Sbjct: 152 PHTTLSEGDLISIC 165


>gi|253732136|ref|ZP_04866301.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus USA300_TCH959]
 gi|253724091|gb|EES92820.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus subsp. aureus USA300_TCH959]
          Length = 245

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/233 (14%), Positives = 71/233 (30%), Gaps = 49/233 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+   V     +++    + +  +   L                 
Sbjct: 19  SRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIEL----------------- 61

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                       ED    +F+KP  +     S         +  +      +     RLD
Sbjct: 62  ------------EDKIYILFHKPTQVIT---SVSDDRGRTVVTDYFKDIEARIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+L++         +T      +I+K Y + + G    ++       +K    G +
Sbjct: 107 YDTSGLLLLTNDGEFTNLMT--HPRYQIKKKYVAKLKGYIMREE-------VKALEKGIE 157

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               + Q  +                +    +E+    GR  Q+R    H G 
Sbjct: 158 LEDGMTQPAEVKVK-------KQDKDKNTTLVEITITEGRNRQVRRMFEHFGH 203


>gi|309378850|emb|CBX22555.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 349

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 30/179 (16%), Positives = 56/179 (31%), Gaps = 30/179 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTTEQ 243


>gi|296314446|ref|ZP_06864387.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           polysaccharea ATCC 43768]
 gi|296838734|gb|EFH22672.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           polysaccharea ATCC 43768]
          Length = 349

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 30/179 (16%), Positives = 56/179 (31%), Gaps = 30/179 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTTEQ 243


>gi|261253105|ref|ZP_05945678.1| ribosomal small subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
 gi|260936496|gb|EEX92485.1| ribosomal small subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
          Length = 233

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 88/249 (35%), Gaps = 58/249 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRLD++  +           +I++SG V V+    K  + ++  G  V            
Sbjct: 1   MRLDKYLCDAL-GATRREATRIIKSGDVTVNDVVQKSGSVKVTDGCTVEWQGREL----- 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
              QK     + L K   F+ S   +ED     FN+ A +                    
Sbjct: 55  ---QKPGPRYIMLFKPDGFVCS---HEDG----FNQTAFML-----------------LD 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWS--LVWGIPKNK 194
           + K ++     RLD +T+G++++    + + +  +   +  +  +++ +  +     +  
Sbjct: 88  EVKIEELHFAGRLDVDTTGLVLITDDGKWSHRITSPKHKCEKTYRVWLADPIQADYVEKF 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E I                   +NEKG    ++    ++   ++   + +    G+ HQ
Sbjct: 148 AEGIQL-----------------RNEKG----LTLPAQLEIVDEEENEVLLTITEGKYHQ 186

Query: 255 LRVHALHMG 263
           ++     +G
Sbjct: 187 VKRMFAALG 195


>gi|260598642|ref|YP_003211213.1| 16S rRNA pseudouridylate synthase A [Cronobacter turicensis z3032]
 gi|260217819|emb|CBA32307.1| Ribosomal small subunit pseudouridine synthase A [Cronobacter
           turicensis z3032]
          Length = 235

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 77/250 (30%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R+ +V V+   VK                 +    ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRASRVTVNGDIVK-----------------DTAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + +I      LT+ +            + ++ NKP G      S         L    +
Sbjct: 43  PDHEIEYDGNPLTQQNGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A    +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAALFAKGVQLNNEKDLTKPA--QLEVI-----TPTEVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAAVGNHVVG 199


>gi|148985263|ref|ZP_01818486.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP3-BS71]
 gi|147922461|gb|EDK73580.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pneumoniae SP3-BS71]
 gi|301799717|emb|CBW32282.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pneumoniae OXC141]
          Length = 241

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 78/248 (31%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD         I+   +++ L  G + VD    +                        
Sbjct: 1   MRLDNLLAQ--EKISRKAMKQALLKGDILVDSCPARS----------------------- 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILL--YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                L  +++        +  ++  YE + + +  KPAG+           +   L S 
Sbjct: 36  -----LAQNIDTGLQELLFQDRIIQGYEHTYLMLH-KPAGVVTANKDKELPTVMDLLPS- 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            D +  K     RLD++T+G+L++        Q L   + + +  ++             
Sbjct: 89  -DIQSDKLYAVGRLDRDTTGLLLLTDNGPLGFQLLHPQYHVDKTYQVE------------ 135

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
               N LL   HI      +V  +      A      I   +       +    G+ HQ+
Sbjct: 136 ---VNGLLTPDHIQAFQKGIVFLDGTICKPARLE---ILSASPSLSQASITISEGKFHQI 189

Query: 256 RVHALHMG 263
           +   L +G
Sbjct: 190 KKMFLSVG 197


>gi|227875336|ref|ZP_03993478.1| possible pseudouridine synthase [Mobiluncus mulieris ATCC 35243]
 gi|307700863|ref|ZP_07637888.1| putative pseudouridine synthase B, ribosomal large subunit
           [Mobiluncus mulieris FB024-16]
 gi|227844241|gb|EEJ54408.1| possible pseudouridine synthase [Mobiluncus mulieris ATCC 35243]
 gi|307613858|gb|EFN93102.1| putative pseudouridine synthase B, ribosomal large subunit
           [Mobiluncus mulieris FB024-16]
          Length = 278

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 39/256 (15%), Positives = 81/256 (31%), Gaps = 51/256 (19%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
           VE  EE +RL +         +    + +++ G+V+VD + V     ++     + +   
Sbjct: 35  VEIPEEPVRLQKLLSQA-GVASRRASEDLIKRGRVQVDGETVTEMGLKVLPSARITVNGQ 93

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
               +  ++                            ++ FNKP G              
Sbjct: 94  RIHTDAALQ----------------------------VWAFNKPVGTVSTMQPEDDRPCL 125

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
           G    W     Q+     RLD  T+G++++      A  L        + K Y ++V G 
Sbjct: 126 G---DWATKLPQRVFHVGRLDVATAGLILLTNNGDLANRL--VHPRYEVPKTYVAMVQGQ 180

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
            K                    V       +     +  FK+++   +    +++  H+G
Sbjct: 181 VKPGLG---------------KVLRRGVELEDGVTKVDTFKLVEVR-RGSSIVQLTLHSG 224

Query: 251 RTHQLRVHALHMGCPI 266
           +   +R     +G P+
Sbjct: 225 KNRVVRRLLSEVGHPV 240


>gi|260890235|ref|ZP_05901498.1| ribosomal small subunit pseudouridine synthase A [Leptotrichia
           hofstadii F0254]
 gi|260859855|gb|EEX74355.1| ribosomal small subunit pseudouridine synthase A [Leptotrichia
           hofstadii F0254]
          Length = 238

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 35/184 (19%), Positives = 70/184 (38%), Gaps = 31/184 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  N         +++IL++ ++ V+   VK + +IQ                  
Sbjct: 1   MRLDKFLANSGIG-TRKEVKEILKNKKISVNDAFVK-DGKIQ------------------ 40

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                +D   ++ K+ D   +I+ Y+     + NKPAG+           +   L     
Sbjct: 41  -----IDEEKDIVKYED---NIIYYKPFVYIMMNKPAGVISATEDNHHRTVIDLLNDEYR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +    P    RLD +T G+L++        H   S +    +K Y  +   + +   + +
Sbjct: 93  TYDIFP--VGRLDIDTEGLLLLT-NDGILSHNLLSPKKHVDKKYYVKISNPLTEEDIKTL 149

Query: 199 ANWL 202
            N +
Sbjct: 150 ENGI 153


>gi|242243012|ref|ZP_04797457.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242233613|gb|EES35925.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 230

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 27/146 (18%), Positives = 53/146 (36%), Gaps = 37/146 (25%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  N         ++++L+ G V+V++ +VK                        
Sbjct: 1   MRLDKFLANMGVG-TRSEVKQLLKKGAVKVNQNKVKS----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFL---KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                    +++  +SD +     ++ Y D    + NKP G        +   I   +  
Sbjct: 37  -------PKLHVNPNSDEIMVNDEVVSYIDKVYIMLNKPKGYISATEDELHPTIIDLIPE 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVA 161
           +            RLD++T G+L+V 
Sbjct: 90  YAHLN---IFPVGRLDKDTEGLLLVT 112


>gi|161505323|ref|YP_001572435.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160866670|gb|ABX23293.1| hypothetical protein SARI_03464 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 309

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 72/247 (29%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +     + +  G V ++ KR    +++ +G VV++   +      
Sbjct: 25  IRLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA 82

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     +D  +   NKP GI      G   +I  F+    
Sbjct: 83  --------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH-- 114

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD+++ G++ +         +  +      + +   +    P    E 
Sbjct: 115 ---SKRIFPVGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL---VTVDKPVTD-EF 167

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I         +G        + E    + I+                     G   Q+R 
Sbjct: 168 IRGMGAGVPILGTVTKKCKVKKEAPFVFRIT------------------LVQGLNRQIRR 209

Query: 258 HALHMGC 264
              H G 
Sbjct: 210 MCEHFGY 216


>gi|25011583|ref|NP_735978.1| hypothetical protein gbs1541 [Streptococcus agalactiae NEM316]
 gi|77414111|ref|ZP_00790278.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 515]
 gi|24413122|emb|CAD47200.1| unknown [Streptococcus agalactiae NEM316]
 gi|77159822|gb|EAO70966.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 515]
          Length = 240

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 81/249 (32%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ IL+  Q+ V+                             
Sbjct: 1   MRLDKFLVECGLG-SRTQVKLILKKKQISVNG---------------------------- 31

Query: 79  KEQKILDSSVNLTKHSDFLK---SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                    V + ++ D +K   +++ YE    Y+ +KP G+           +   L  
Sbjct: 32  --NSETSPKVQVDEYRDEIKYNGTLVSYEKFVYYMLHKPKGVISATDDPSHKTVLDLLDK 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               K        RLD +T+G+L++      A + L+     + + K Y + + GI    
Sbjct: 90  TARDKA--VFPVGRLDIDTTGLLLITNNGELAHKMLS---PKKHVDKCYEAKISGIMTED 144

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                     K  I  D+  +          A+    V     +K   +++    G+ HQ
Sbjct: 145 ----DILAFDKGIILKDFTCL---------PALLEI-VEVNQVKKQSLVKITIKEGKFHQ 190

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 191 VKRMVAACG 199


>gi|253732405|ref|ZP_04866570.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|297207533|ref|ZP_06923969.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|253723857|gb|EES92586.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|296887869|gb|EFH26766.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus ATCC 51811]
          Length = 231

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 78/244 (31%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N         ++++L+ G V V+++ +K                     HI 
Sbjct: 1   MRIDKFLANMGVG-TRNEVKQLLKKGLVNVNEQVIKS-----------------PKTHIE 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   +     L          + Y ++   + NKP        +   +H    +    +
Sbjct: 43  PENDKITVRGEL----------IEYIENVYIMLNKPKDYIS---ATEDHHSKTVIDLIPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++T G+L++         L      + + K Y            E I
Sbjct: 90  YQHLNIFPVGRLDKDTEGLLLITNDGDFNHEL--MSPNKHVSKKY------------EVI 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +   + +  I      V   + K    AI  +  ID         E     G+ HQ++  
Sbjct: 136 SANPITEDDIQAFKEGVTLSDGK-VKPAILTY--IDNQTSHVTIYE-----GKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|238764926|ref|ZP_04625865.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           kristensenii ATCC 33638]
 gi|238696867|gb|EEP89645.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           kristensenii ATCC 33638]
          Length = 256

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/247 (14%), Positives = 75/247 (30%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR    +++  G VV++          
Sbjct: 7   IRLNKYISE--SGICSRRDADRYIEQGNVFINGKRAAVGDQVYVGDVVKVN--------- 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
              Q I     N               D  +   NKP GI      G + +I  F+    
Sbjct: 56  --GQLIEPRDEN---------------DLVLIALNKPVGIISTTEDGESDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD+++ G++ +         +  +      + +   +    P    E 
Sbjct: 97  ---SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYV---VTVNKPVTD-EF 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I         +G        + E    ++I+                     G   Q+R 
Sbjct: 150 ILGLGAGVPMLGTVTKKCKVKKEAAFVFSIT------------------LVQGLNRQIRR 191

Query: 258 HALHMGC 264
              H G 
Sbjct: 192 MCKHFGY 198


>gi|116791102|gb|ABK25858.1| unknown [Picea sitchensis]
          Length = 326

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 3/72 (4%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            RLD      +P  +   +Q  +  G+V VD +   K    +    +V I        ++
Sbjct: 82  QRLDEVCVERFPQYSRSMIQSWILQGKVLVDGRVAGKAGMAVTDKAIVEIT--AETPKYV 139

Query: 78  IKEQKILDSSVN 89
            +    L++++ 
Sbjct: 140 CRAGYKLEAALE 151


>gi|33863340|ref|NP_894900.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. MIT 9313]
 gi|33640789|emb|CAE21244.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. MIT 9313]
          Length = 244

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 83/250 (33%), Gaps = 50/250 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            RL +        + +  + +++L   +V ++    K  ++               L+ I
Sbjct: 4   QRLQKLIAA--SGLCSRRHAEQLLLQERVTLNGHLAKLGDK-----------ADPELDKI 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             + ++L+S+                   ++ +FNKPAG+         +          
Sbjct: 51  SVDGRVLNSNTET----------------RVLLFNKPAGVIT--SCHDPHGRVTVFSMLP 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D   +      RLD ++ G L++         LT         K Y  LV G P      
Sbjct: 93  DKLCKGLHPVGRLDADSRGALLITNQGELTLRLTHPRYAH--DKTYQVLVEGKP------ 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                   + +   + H V  + K    A    +++     +   L++    GR  Q+R 
Sbjct: 145 -------SALVLSSWRHGVMLDGKTTLPA--ELELLQSHPSQ-SLLKVVLREGRNRQIRR 194

Query: 258 HALHMGCPIV 267
            A  +G P++
Sbjct: 195 VAEQLGHPVL 204


>gi|315640594|ref|ZP_07895700.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           italicus DSM 15952]
 gi|315483622|gb|EFU74112.1| ribosomal large subunit pseudouridine synthase B [Enterococcus
           italicus DSM 15952]
          Length = 236

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 83/249 (33%), Gaps = 52/249 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHII 78
           RL +         +    +  +  G+V+V+   V     ++ S   + +           
Sbjct: 3   RLQKVIAQA-GITSRRKAEVYILDGRVKVNGVVVNELGTKVSSKDTIEVD---------- 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                 +  E S  Y+F KP G+     +         +  +  
Sbjct: 52  -------------------NVPISQEGSVYYLFYKPRGVIS---AVSDDKKRKVVTDFFT 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD  TSG+L++      +Q LT       I+K Y + V G+        
Sbjct: 90  EVSERIYPIGRLDYNTSGLLLLTNDGEFSQLLT--HPKNEIEKKYVAKVKGVAL------ 141

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGRTHQLRV 257
               LK    G  Y        KG  YA + + ++    + +   +++  H G+ HQ++ 
Sbjct: 142 -PHALKPLTRGLKY--------KGEKYAPAKYDILSTDTRAETSIVQLTIHEGKNHQVKN 192

Query: 258 HALHMGCPI 266
               +G P+
Sbjct: 193 MLEAVGLPV 201


>gi|298713714|emb|CBJ48905.1| putative RNA pseudouridylate synthase [Ectocarpus siliculosus]
          Length = 555

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/176 (18%), Positives = 62/176 (35%), Gaps = 17/176 (9%)

Query: 53  VKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFN 112
            K    +   + V I   +     I  E +   + + +   S      ++Y+ + + + N
Sbjct: 95  AKPKRELDPDREVEIGEYL----RIFPEPRRYPAFLGVDWESK-----IVYDCAGVMLVN 145

Query: 113 KPAGISVQGGSGIAYHIDGFLKSWVD-SKGQKPRLTHRLDQETSGILVVARTRAAAQHLT 171
           KPAG+     + +    +  L             L HRLD +TSG+++V       Q L 
Sbjct: 146 KPAGVPAH--ATVDNFAENMLAGIRSVRPDLDLLLPHRLDIDTSGLVIVVTRNLGVQELG 203

Query: 172 ESFRMRRIQKIYWSLVWGIPKNKKECIANW-LLKKSHIG--GDYVHVVKQNEKGAN 224
                 R +    +   G  ++  E I    L+ ++ I    D     K   + A 
Sbjct: 204 --LARNRTKHAGRAKGAGTLRSINEIIKRPGLILRTGIDSPRDRRRKNKALRRAAK 257



 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 17/42 (40%), Positives = 22/42 (52%)

Query: 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQ 285
           E+Q  TGRTHQ+R      GCPI GD+ Y    +      +Q
Sbjct: 450 EVQLLTGRTHQIRGQLAAEGCPIYGDYLYGPAEESVRQPGLQ 491


>gi|291619766|ref|YP_003522508.1| RluF [Pantoea ananatis LMG 20103]
 gi|291154796|gb|ADD79380.1| RluF [Pantoea ananatis LMG 20103]
          Length = 297

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 74/250 (29%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + + RL+++       I +  +  + +  G V ++ KR     ++ +G VV++   +   
Sbjct: 11  QSSTRLNKYISE--SGICSRRDADRFIEQGNVFINGKRAAVGAQVFAGDVVKVNGQLIEP 68

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        +D  +   NKP GI      G   +I  F+ 
Sbjct: 69  RDE--------------------------DDLVLIALNKPTGIITTMEEGERDNISDFVN 102

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +   +    P   
Sbjct: 103 H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNNHEKEYV---VTVDKPVTD 154

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E IA        +G        + E    + I+                     G   Q
Sbjct: 155 -EFIAGMASGVPMLGTVTKKCKVKKEAPYVFRIT------------------LVQGLNRQ 195

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 196 IRRMCKHFGY 205


>gi|257462340|ref|ZP_05626755.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           D12]
 gi|317060006|ref|ZP_07924491.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           D12]
 gi|313685682|gb|EFS22517.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           D12]
          Length = 239

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 81/249 (32%), Gaps = 50/249 (20%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E  +R++++  +     +   +   +  G++ V+        ++               
Sbjct: 2   EENKIRINKFLASK-GLASRRQVDLWIEEGRISVNGSLATSGQKVS-------------- 46

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
               +E  I+ +  ++++        LLY++ ++         +V+   G    +D  L 
Sbjct: 47  ----EEDDIVVNGKSISQKKQKKVYYLLYKEEEVLS-------AVKDDRGRRTVVDCVLS 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +      +     RLD  TSG++++         +        I K Y  L  G    +
Sbjct: 96  PY------RIFPVGRLDYRTSGLILLTNDGDLFNRM--MHPRAEIFKSYEVLAKGHLTKE 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +               + V + +     A  A   ++      +   + E+    G+  Q
Sbjct: 148 QL----------KTLEEGVELEEGKTLAALIAKVKYE------KGNTFFEISIREGKNRQ 191

Query: 255 LRVHALHMG 263
           +R     +G
Sbjct: 192 IRRMVEAVG 200


>gi|323492456|ref|ZP_08097604.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio brasiliensis
           LMG 20546]
 gi|323313243|gb|EGA66359.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio brasiliensis
           LMG 20546]
          Length = 312

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 61/179 (34%), Gaps = 30/179 (16%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNH 76
           N +L +       H +   L+ ++++G+V V+    K   R++    VVRI         
Sbjct: 2   NEKLQKVLARA-GHGSRRELEALIKAGRVSVNGIVAKLGERLEDENAVVRIDGH------ 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                     +V+     + +  +L Y         KP G                    
Sbjct: 55  ----------TVSAKAQEEVICRVLAY--------YKPEGELC--TRHDPEGRRTVFDRL 94

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K
Sbjct: 95  PKIRGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVTEQK 151


>gi|467162|gb|AAA50926.1| u0247g [Mycobacterium leprae]
          Length = 186

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 50/159 (31%), Gaps = 18/159 (11%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
               NKP G+             G L        +K     RLD +T G++++      A
Sbjct: 8   YLALNKPRGMYSTMSDDRGRPCVGDLIERRVRGNKKLFHVGRLDADTEGLILLTNDGELA 67

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             L        + K Y + V G        +   L KK  +G +               +
Sbjct: 68  HRL--MHPSHEVSKTYLATVKGA-------VPRGLGKKLSVGLEL--------DDGPAHV 110

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
             F V+D    K   + +  H GR   +R      G P+
Sbjct: 111 DDFAVVDAIPGK-TLVRLTLHEGRKRIVRRLLTAAGFPV 148


>gi|237737269|ref|ZP_04567750.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           mortiferum ATCC 9817]
 gi|229421131|gb|EEO36178.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium
           mortiferum ATCC 9817]
          Length = 230

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 84/247 (34%), Gaps = 54/247 (21%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E+ MRLD++        +   ++K+L +G++RV+              ++   P  N   
Sbjct: 2   EDKMRLDKFLTECGLG-SRREVKKLLDNGKIRVN-------------DIIVKNPQANIKE 47

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
            I K               ++  + L Y++ + Y+ NK  G            +   L  
Sbjct: 48  SIDK--------------IEYDGNKLEYKEFRYYIMNKKGGYITATEDPKEKTVMELLPE 93

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           WV  K   P    RLD++T G+L+     +     L+     + + K Y++ +    K  
Sbjct: 94  WVIKKDLAP--VGRLDKDTEGLLLFTNDGKLGHSLLS---PKKHVDKTYYAKLE---KEI 145

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E     L +   IGG      K    G                    +E+    G+ HQ
Sbjct: 146 GEVEIKKLEEGVDIGGYITQPAKAKIVGEKE-----------------IELTIREGKFHQ 188

Query: 255 LRVHALH 261
           ++     
Sbjct: 189 VKKMLEA 195


>gi|296112282|ref|YP_003626220.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis RH4]
 gi|295919976|gb|ADG60327.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis RH4]
 gi|326561792|gb|EGE12127.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis 7169]
 gi|326562268|gb|EGE12594.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis 103P14B1]
 gi|326563228|gb|EGE13495.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis 46P47B1]
 gi|326564754|gb|EGE14967.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis 12P80B1]
 gi|326568983|gb|EGE19052.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis BC1]
 gi|326569283|gb|EGE19344.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis BC7]
 gi|326571959|gb|EGE21964.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis BC8]
 gi|326575471|gb|EGE25396.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis 101P30B1]
 gi|326576441|gb|EGE26349.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis CO72]
 gi|326577913|gb|EGE27777.1| ribosomal small subunit pseudouridine synthase A [Moraxella
           catarrhalis O35E]
          Length = 234

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 91/249 (36%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++  + +K+L +G++ V+   +K +                + +  +
Sbjct: 1   MRLDKFLSKA-TELSRKDAKKVLHAGEITVNGTIIKDS----------------SHHVDL 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              +IL +   L+  +D  + ILLY+        KP            Y +   L +   
Sbjct: 44  ANDEILWAGEALS-VADGNRYILLYKPDGFECTLKP----------KEYPMVTDLIAV-- 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +    R+  RLD +T+G L+++   A    +T   R +             PK  +  +
Sbjct: 91  PEVANLRIAGRLDVDTTGALLLSDDGAWLHRVTSPKRHQ-------------PKQYQLTL 137

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKG----ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           A+ + K +       + +KQ   G         +   V+    +      +    G+ HQ
Sbjct: 138 ADAMDKDAQ-----AYAIKQIANGILLEGETEKTRPAVLSFIDETHAV--LTLTEGKYHQ 190

Query: 255 LRVHALHMG 263
           ++    + G
Sbjct: 191 VKRMMAYFG 199


>gi|150398308|ref|YP_001328775.1| RNA-binding S4 domain-containing protein [Sinorhizobium medicae
           WSM419]
 gi|150029823|gb|ABR61940.1| RNA-binding S4 domain protein [Sinorhizobium medicae WSM419]
          Length = 137

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 13/90 (14%)

Query: 19  MRLDRWF--KNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALN 75
            RLD+W          +    QK + +G V V+ KR  + + +I++G ++ +      L 
Sbjct: 13  QRLDKWLFFARLIK--SRSLAQKAIEAGHVVVNGKRETQSSAQIKAGDMLEVSLERRDL- 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYED 105
                  +L   +  ++   + ++ LLYED
Sbjct: 70  -------VLRVLLPGSRRGPYEEARLLYED 92


>gi|328870986|gb|EGG19358.1| hypothetical protein DFA_02145 [Dictyostelium fasciculatum]
          Length = 534

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 31/247 (12%), Positives = 76/247 (30%), Gaps = 49/247 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD+   N         +Q+ + + +V    ++V    ++     +R+         ++
Sbjct: 5   VRLDKLLSN-LGLCTRSKVQQFINANKVTYQGQKVSPKAKVDVED-IRVMGRKVDHPELL 62

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID--GFLKSW 136
                                            +KP G           H      L   
Sbjct: 63  T-----------------------------IAVHKPIGYVCSNSREDGDHKIIYDLLPKE 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +     +  RLD+  +G++V+++     + +    +  ++ K+Y  +          
Sbjct: 94  FADRSPTLSIAGRLDKWVTGLVVMSQNGKIVERIITP-KDDKMGKVYEVVCESKFNG--- 149

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                  +   +    V +  ++      A  HF+V+D   +      +  + G+ HQ+R
Sbjct: 150 ------TEADEMASGRVQLRSEDGPC-KPA--HFEVVDQENKMA---RLTLYEGKYHQVR 197

Query: 257 VHALHMG 263
                +G
Sbjct: 198 RMMSAVG 204


>gi|315506751|ref|YP_004085638.1| pseudouridine synthase [Micromonospora sp. L5]
 gi|315413370|gb|ADU11487.1| pseudouridine synthase [Micromonospora sp. L5]
          Length = 256

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 44/254 (17%), Positives = 85/254 (33%), Gaps = 54/254 (21%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E   RL +         +    + ++   +V V+ +  +  ++              A +
Sbjct: 16  EGAERLQKVLAAAGVG-SRRACEDLIFRRRVTVNGRVAQLGDK-----------ADPARD 63

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLK 134
            I+ + + L + V L                     NKP G+            +  F+ 
Sbjct: 64  VIVVDGERLQADVRLV----------------YVAMNKPRGVVTTMADEKGRTELADFIG 107

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKN 193
           + ++   Q+     RLD ++ G+L++      A  L        + K Y + V G IP+N
Sbjct: 108 ARLE---QRVYHVGRLDADSEGLLLLTNDGTLAHKL--MHPSYEVLKTYLAEVAGPIPRN 162

Query: 194 KKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             + +   + L+   +  D   VV    K A                   +E+  H GR 
Sbjct: 163 LSKRLTAGVELEDGPVKVDGFKVVDTLGKTAQ------------------VELTLHEGRK 204

Query: 253 HQLRVHALHMGCPI 266
           H +R     +G P+
Sbjct: 205 HIVRRLMAEVGHPV 218


>gi|313668495|ref|YP_004048779.1| pseudouridine synthase [Neisseria lactamica ST-640]
 gi|313005957|emb|CBN87414.1| putative pseudouridine synthase [Neisseria lactamica 020-06]
          Length = 350

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 48/156 (30%), Gaps = 28/156 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 96  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 152

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 153 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 187

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
             +   +     RLD  TSG+L++  +    Q    
Sbjct: 188 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAH 223


>gi|284053272|ref|ZP_06383482.1| pseudouridine synthase [Arthrospira platensis str. Paraca]
 gi|291565993|dbj|BAI88265.1| putative pseudouridylate synthase [Arthrospira platensis NIES-39]
          Length = 257

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 79/250 (31%), Gaps = 43/250 (17%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N RL +    H+   +  + ++++ SG+V+V+  +     +                + I
Sbjct: 2   NERLQKIIS-HWGVASRRHAEEMILSGRVKVNGDQAYLGQK-----------ADPKCDRI 49

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             + + L  S              LY      + NKP G+               L    
Sbjct: 50  EIDGRALHPSSQPQP---------LY-----LLLNKPLGVVSTCAEPQGRKTVLDLLPRQ 95

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              GQ      RLD +++G L++         LT       + K Y  LV G P      
Sbjct: 96  LQVGQGLHPVGRLDTDSTGALLITNDGELTFLLT--HPRYHVAKTYQVLVQGCPPES--- 150

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                     +   +   +  + K    A    + I         LE+    GR  Q+R 
Sbjct: 151 ----------VLEQWRQGILLSGKNTLPA--KVRRIGKPRGSQTLLEVVLREGRNRQIRR 198

Query: 258 HALHMGCPIV 267
            A  +G P+V
Sbjct: 199 VAEALGYPVV 208


>gi|289810128|ref|ZP_06540757.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 256

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 23/164 (14%), Positives = 54/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  --SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|222098414|ref|YP_002532472.1| hypothetical protein BCQ_4782 [Bacillus cereus Q1]
 gi|221242473|gb|ACM15183.1| conserved hypothetical protein [Bacillus cereus Q1]
          Length = 165

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNTILSEGDRISIC 164


>gi|147833193|emb|CAN68642.1| hypothetical protein VITISV_030809 [Vitis vinifera]
          Length = 400

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 18/45 (40%), Positives = 21/45 (46%)

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNK 287
            ++   TGRTHQ+R      G PIVGD  Y        TSP  N 
Sbjct: 299 CKINLLTGRTHQIRAQLAACGAPIVGDSMYMPAAIAEITSPGLNP 343


>gi|239917903|ref|YP_002957461.1| pseudouridine synthase family protein [Micrococcus luteus NCTC
           2665]
 gi|281413596|ref|ZP_06245338.1| pseudouridine synthase family protein [Micrococcus luteus NCTC
           2665]
 gi|289706509|ref|ZP_06502862.1| pseudouridylate synthase [Micrococcus luteus SK58]
 gi|239839110|gb|ACS30907.1| pseudouridine synthase family protein [Micrococcus luteus NCTC
           2665]
 gi|289556767|gb|EFD50105.1| pseudouridylate synthase [Micrococcus luteus SK58]
          Length = 318

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 45/252 (17%), Positives = 81/252 (32%), Gaps = 48/252 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           DE   RL +         +    + ++  G+V VD   V      + G  VR+ P    +
Sbjct: 77  DESGERLQKVLAAA-GVASRRVSEDLIAEGRVEVDGVVVT-----EPG--VRVDPATAVI 128

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                    +    ++TK                +VFNKP G+     + +       + 
Sbjct: 129 RV-----DGISVQTDVTKQ--------------YFVFNKPRGVIS---TMVDPEGRPSIA 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           +++    +      RLD ET G+L++      A  LT                  +PK  
Sbjct: 167 TYLKPGQEHLFHVGRLDNETEGLLILTNDGELANRLTHPSYE-------------VPKTY 213

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                  L K    G           +     +  FK++D        +E+  H+G+   
Sbjct: 214 VVQTRGPLAK----GVSNRLREGVELEDGVAQVDSFKLVDSTP-GHVLVEVVLHSGKNRI 268

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 269 VRRMFQEIGHPV 280


>gi|257466391|ref|ZP_05630702.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|315917547|ref|ZP_07913787.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|313691422|gb|EFS28257.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           gonidiaformans ATCC 25563]
          Length = 238

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 76/249 (30%), Gaps = 50/249 (20%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E  +R++++  +     +   +   +  G++ V+        ++ +             
Sbjct: 2   EENKIRINKFLASK-GVASRRQIDLWIEEGKILVNGILATSGQKVSA------------- 47

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                E KIL +   +++  +     +LY++ ++    K                   + 
Sbjct: 48  -----EDKILVNGKMISEKEEKKVYYILYKEEEVLSAVK------------DERGRKTVV 90

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             + +K  +     RLD  TSG++++         +        I K Y  L  G    +
Sbjct: 91  DCIPTKA-RIFPVGRLDYRTSGLILLTNDGELFNRV--MHPRAEIFKTYEVLAKGHLTRE 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +       ++          V K   +  N                 + E+    GR  Q
Sbjct: 148 QLKTLEEGVELEEGKTLEALVAKVKYEKGN----------------TFFEISIREGRNRQ 191

Query: 255 LRVHALHMG 263
           +R     +G
Sbjct: 192 IRRMVEAVG 200


>gi|228988206|ref|ZP_04148303.1| hypothetical protein bthur0001_48640 [Bacillus thuringiensis
           serovar tochigiensis BGSC 4Y1]
 gi|228771503|gb|EEM19972.1| hypothetical protein bthur0001_48640 [Bacillus thuringiensis
           serovar tochigiensis BGSC 4Y1]
          Length = 165

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNTLLSEGDHISIC 164


>gi|332665442|ref|YP_004448230.1| pseudouridine synthase Rsu [Haliscomenobacter hydrossis DSM 1100]
 gi|332334256|gb|AEE51357.1| pseudouridine synthase Rsu [Haliscomenobacter hydrossis DSM 1100]
          Length = 274

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 45/293 (15%), Positives = 90/293 (30%), Gaps = 52/293 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
               E MRL+++   H    +     +I++ G + V+         +I++G +V+     
Sbjct: 32  PESTEGMRLNKYVA-HCGVASRREAAEIVKQGHITVNSVVETEPFYQIKTGDIVK----- 85

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                   + +++   V                    Y+ NKP  +     +        
Sbjct: 86  -------YKGQVIRPEVRRV----------------YYLMNKPKNVIT--TTSDEKGRKT 120

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L    D   ++     RLD++T+G+L++      A  +T     +  +  + +L   + 
Sbjct: 121 VLDLVADRVEERVFPVGRLDRDTTGLLLLTNDGELALKMTHPSY-KIKKIYHATLNKTVS 179

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           K   E I   L  +                 A+Y I               + +  H GR
Sbjct: 180 KEDLEKIRAGLELEDGPA---------PVDAADYIIER---------PHSEVGLTVHIGR 221

Query: 252 THQLRVHALHMGCPIVG-DHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGG 303
              +R    H+G  ++  D  Y              +       + L H  G 
Sbjct: 222 NRIVRRIFEHLGYEVLKLDRVYLGGLTKKDLPRGFVRRLTSQELIMLKHFTGK 274


>gi|240950257|ref|ZP_04754536.1| pseudouridylate synthase [Actinobacillus minor NM305]
 gi|240295234|gb|EER46035.1| pseudouridylate synthase [Actinobacillus minor NM305]
          Length = 224

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 37/164 (22%), Positives = 61/164 (37%), Gaps = 8/164 (4%)

Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           E++ I +FNKP  +  Q            LK ++D    K     RLD+++ G+L++   
Sbjct: 29  EETIIVLFNKPYDVLTQ---FTDEQGRKTLKDFIDI--PKIYPVGRLDRDSEGLLLLTNN 83

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA 223
                 L      +   K YW  V GIP             +   G       KQ E   
Sbjct: 84  GEIQHRLAHPKFEKE--KTYWVQVEGIPSQADLA-KLEKGVELKDGLTQPAKAKQIEAPD 140

Query: 224 NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               +  K+ +       W+E++   G+  Q+R    H+G P +
Sbjct: 141 FDWQTAPKIRERKTIPTSWIELKITEGKNRQVRRMTAHIGFPTL 184


>gi|238761999|ref|ZP_04622972.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           kristensenii ATCC 33638]
 gi|238699727|gb|EEP92471.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           kristensenii ATCC 33638]
          Length = 246

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 40/273 (14%), Positives = 84/273 (30%), Gaps = 58/273 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK      SG +            + 
Sbjct: 12  MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEIVK------SGAI-----------KLT 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ +      L +              + ++ NKP G      S         L    +
Sbjct: 54  PEQDVRFDGNPLQQTVGP----------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 100

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 101 PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 147

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A    +VI+        + +    GR HQ++  
Sbjct: 148 EHPVADDTAQQFTDGVQLHNEKSLTKPA--QLEVIEPQ-----LVRLTISEGRYHQVKRM 200

Query: 259 ALHMGCPIV-------GDHKYCANFKGNFTSPI 284
              +G  ++       GD K   +       P+
Sbjct: 201 FGAVGNRVLELHRERIGDIKLDDDLAPGEYRPL 233


>gi|167823890|ref|ZP_02455361.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei 9]
          Length = 74

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           +  LHA  + L HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 6   RQALHAWRLGLVHPASGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 60


>gi|16762895|ref|NP_458512.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|29144382|ref|NP_807724.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|213420596|ref|ZP_03353662.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
 gi|213581144|ref|ZP_03362970.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213647413|ref|ZP_03377466.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213855503|ref|ZP_03383743.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|289827405|ref|ZP_06546017.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|34098634|sp|Q8Z1V3|RLUF_SALTI RecName: Full=Ribosomal large subunit pseudouridine synthase F;
           AltName: Full=rRNA pseudouridylate synthase F; AltName:
           Full=rRNA-uridine isomerase F
 gi|25324020|pir||AE1012 probable pseudouridine synthase STY4410 [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16505202|emb|CAD09198.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhi]
 gi|29140020|gb|AAO71584.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
          Length = 289

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 23/164 (14%), Positives = 54/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  --SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|205354985|ref|YP_002228786.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205274766|emb|CAR39823.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|326630136|gb|EGE36479.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 289

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 23/165 (13%), Positives = 55/165 (33%), Gaps = 34/165 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +     + +  G V ++ KR    +++ +G VV++   +      
Sbjct: 7   IRLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     +D  +   NKP GI      G   +I  F+    
Sbjct: 65  --------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  ---SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|206976421|ref|ZP_03237328.1| conserved hypothetical protein [Bacillus cereus H3081.97]
 gi|206745345|gb|EDZ56745.1| conserved hypothetical protein [Bacillus cereus H3081.97]
          Length = 165

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNTILSEGDRISIC 164


>gi|238794709|ref|ZP_04638313.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           intermedia ATCC 29909]
 gi|238725940|gb|EEQ17490.1| Ribosomal large subunit pseudouridine synthase B [Yersinia
           intermedia ATCC 29909]
          Length = 342

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 31/178 (17%), Positives = 60/178 (33%), Gaps = 27/178 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +       H +   ++ I++ G+V VD K     +R++  Q  +I    + L+  
Sbjct: 27  GEKLQKILARA-GHGSRREIETIIQQGRVSVDGKISTLGDRVEVTQATKIRLDGHLLSIK 85

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E+ +                       ++  + KP G                     
Sbjct: 86  ESEEAVC----------------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLP 121

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 122 KLRGSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDEK 177


>gi|332530537|ref|ZP_08406476.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
 gi|332040012|gb|EGI76399.1| pseudouridine synthase [Hylemonella gracilis ATCC 19624]
          Length = 444

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 70/235 (29%), Gaps = 51/235 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      RIQ G  +++                         
Sbjct: 96  SRLEMEQLIMEGRISVNNEPAHIGQRIQFGDQIKVN------------------------ 131

Query: 93  HSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
               ++  +    +++  ++KP G +           +   L      K Q      RLD
Sbjct: 132 -GKPIRFRIAPPPARVIAYHKPVGEVVTHDDPQNRPTVFRRLPKLPQGKWQS---VGRLD 187

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIG 209
             T G+L+   +   A  L        +++ Y + V G    + K+  +    L  +   
Sbjct: 188 LNTEGLLLFTNSGDLANRL--MHPRFGLEREYAARVLGALSNEEKQRLLDGVPLDDTKAQ 245

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              +                            W  +    GR  ++R     +G 
Sbjct: 246 FGSIEEGGGEGSN------------------LWYRVTISEGRNREVRRMFEAVGH 282


>gi|255526472|ref|ZP_05393383.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|296184845|ref|ZP_06853256.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255509854|gb|EET86183.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|296050627|gb|EFG90050.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 238

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 38/246 (15%), Positives = 77/246 (31%), Gaps = 51/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     ++ +++ G V +D + VK +     G  +             
Sbjct: 2   ERLDKILSN-LGYGTRKEIKALVKQGLVEIDNEVVKDS-----GMKID------------ 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                        K       ++ Y  +   + NKP G+     S    + D  +   +D
Sbjct: 44  ----------PDDKEIRVSGEMVNYRQNIYLIMNKPNGVV----SATFDNYDETVVDLLD 89

Query: 139 SKGQ--KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            + Q  KP    RLD++T G+L++         L         +  Y  +   + +N  E
Sbjct: 90  PEHQAFKPFPVGRLDKDTVGLLLLTNDGELNHRLISPKW-HVDKIYYAEIDKPVDQNDVE 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +                   G        K+++        +E+    G+ HQ++
Sbjct: 149 KFKIGITLDD---------------GYKCLPGKLKILESDENG-SKVEVTIQEGKFHQVK 192

Query: 257 VHALHM 262
                +
Sbjct: 193 RMFNAL 198


>gi|84394229|ref|ZP_00992957.1| pseudouridine synthase family 1 protein [Vibrio splendidus 12B01]
 gi|218709944|ref|YP_002417565.1| ribosomal large subunit pseudouridine synthase B [Vibrio splendidus
           LGP32]
 gi|84375143|gb|EAP92062.1| pseudouridine synthase family 1 protein [Vibrio splendidus 12B01]
 gi|218322963|emb|CAV19140.1| Ribosomal large subunit pseudouridine synthase B [Vibrio splendidus
           LGP32]
          Length = 342

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 33/176 (18%), Positives = 59/176 (33%), Gaps = 30/176 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   L+ +++SG+V V+ +  K   R++    V+RI            
Sbjct: 5   LQKVLARA-GHGSRRELEGLIKSGRVSVNGQVAKLGERLEDENSVIRIDGHTITG----- 58

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                       K S+ +   +L        + KP G                       
Sbjct: 59  ------------KASEEVVCRVL-------AYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVTEQK 151


>gi|269214394|ref|ZP_05986473.2| ribosomal large subunit pseudouridine synthase B [Neisseria
           lactamica ATCC 23970]
 gi|269209982|gb|EEZ76437.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           lactamica ATCC 23970]
          Length = 350

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 30/179 (16%), Positives = 56/179 (31%), Gaps = 30/179 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 96  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 152

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 153 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 187

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++
Sbjct: 188 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTTEQ 244


>gi|118369895|ref|XP_001018150.1| conserved hypothetical protein [Tetrahymena thermophila]
 gi|89299917|gb|EAR97905.1| conserved hypothetical protein [Tetrahymena thermophila SB210]
          Length = 484

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 29/179 (16%), Positives = 60/179 (33%), Gaps = 30/179 (16%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            RL ++       + +    +K+++ G ++VD K    N  +     + I          
Sbjct: 176 ERLSKYLSR--SGVCSRRQAEKMIKDGLIKVDGKVATSNLPVTPKNNIEIFTQRGEKFAP 233

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSW 136
           +K                        +++KI++F KP G+            +  ++ + 
Sbjct: 234 VK------------------------QNAKIWIFYKPRGMICSHDDPLKRPSVFNYIYNN 269

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              K        RLD  + G++++      AQ L +      I + Y   V G    +K
Sbjct: 270 TKIKEPHIIAVGRLDYNSEGLILLTNDGDIAQCLEQPESN--IYRQYRVRVQGELDERK 326


>gi|332305273|ref|YP_004433124.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332172602|gb|AEE21856.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 269

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 42/248 (16%), Positives = 75/248 (30%), Gaps = 50/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   + +    + +L+  +V V  +  K                        
Sbjct: 40  KRLDQLLSN-LGYCSRKEARYLLKDNRVTVAGEYAKS----------------------- 75

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             QK+  ++V +          +L       + NKP G      SG    I   L    +
Sbjct: 76  PAQKVDAATVRVDGEPLDFPEGIL------VMLNKPLGYVCSHDSGEGMRIYDLLPERWE 129

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  K     RLD++T+G+++V         LT       + K+Y           K  +
Sbjct: 130 FRNPKIVSVGRLDKDTTGLILVTDDTKLVHQLT--SPKHHVDKLY-----------KVTV 176

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L            V+    +    A    ++I          E     G+ HQ+R  
Sbjct: 177 NSPLQPDIIEAFAKGVVLGDGAEQCLPA--KVEIISENMANVTLNE-----GKYHQVRRM 229

Query: 259 ALHMGCPI 266
               G  +
Sbjct: 230 FAACGYHV 237


>gi|288818043|ref|YP_003432390.1| ribosomal protein S4 [Hydrogenobacter thermophilus TK-6]
 gi|288787442|dbj|BAI69189.1| ribosomal protein S4 [Hydrogenobacter thermophilus TK-6]
 gi|308751644|gb|ADO45127.1| ribosomal protein S4 [Hydrogenobacter thermophilus TK-6]
          Length = 209

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 14/88 (15%), Positives = 35/88 (39%), Gaps = 4/88 (4%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHII 78
           RLD         +     ++++  G + V+ K+V   + R+Q G ++ + P    +   I
Sbjct: 99  RLDNVVYRLGMAVTRRQARQMIAHGHILVNGKKVDIPSYRVQVGDIIELKPASRDVPQFI 158

Query: 79  KEQKILDS---SVNLTKHSDFLKSILLY 103
           +  + +D       L    +  +  ++ 
Sbjct: 159 ENIQSIDPRSIPPWLELDKENFRGKVID 186


>gi|297585561|ref|YP_003701341.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297144018|gb|ADI00776.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 237

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 77/249 (30%), Gaps = 60/249 (24%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N+R++++        +     K+++ G+V ++ K  +  ++++ G  V +        HI
Sbjct: 2   NVRINKYVSETGKT-SRRGADKLIQEGKVTINGKPAQLGDQVEPGDDVIVN---GEPVHI 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +KE                     +Y        NKP GI+      +  +I   +    
Sbjct: 58  VKEN--------------------VY-----IALNKPVGITSTTERKVKGNIIDLVNH-- 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD+++ G++++         +  +      + I               
Sbjct: 91  ---PLRIFHIGRLDKDSEGLILLTNDGDIVNEILRAENKHEKEYIV-------------- 133

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM--QPHTGRTHQL 255
                     I  +++  + +        I     + C  +K    E       G   Q+
Sbjct: 134 -----TVNKPITPEFLKQMSEGVD-----ILDTTTLPCKVKKLSKYEFNITLTQGLNRQI 183

Query: 256 RVHALHMGC 264
           R     +G 
Sbjct: 184 RRMCDALGY 192


>gi|327396520|dbj|BAK13941.1| ribosomal large subunit pseudouridine synthase F [Pantoea ananatis
           AJ13355]
          Length = 290

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 74/250 (29%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + + RL+++       I +  +  + +  G V ++ KR     ++ +G VV++   +   
Sbjct: 4   QSSTRLNKYISE--SGICSRRDADRFIEQGNVFINGKRAAVGAQVFAGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        +D  +   NKP GI      G   +I  F+ 
Sbjct: 62  RDE--------------------------DDLVLIALNKPTGIITTMEEGERDNISDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +   +    P   
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNNHEKEYV---VTVDKPVTD 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E IA        +G        + E    + I+                     G   Q
Sbjct: 148 -EFIAGMASGVPMLGTVTKKCKVKKEAPYVFRIT------------------LVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCKHFGY 198


>gi|168821347|ref|ZP_02833347.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|238913060|ref|ZP_04656897.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|205342140|gb|EDZ28904.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|320088621|emb|CBY98379.1| pseudouridylate synthase [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
          Length = 289

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 23/165 (13%), Positives = 55/165 (33%), Gaps = 34/165 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +     + +  G V ++ KR    +++ +G VV++   +      
Sbjct: 7   IRLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     +D  +   NKP GI      G   +I  F+    
Sbjct: 65  --------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  ---SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|62182642|ref|YP_219059.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|62130275|gb|AAX67978.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|322717140|gb|EFZ08711.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 289

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 23/165 (13%), Positives = 55/165 (33%), Gaps = 34/165 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +     + +  G V ++ KR    +++ +G VV++   +      
Sbjct: 7   IRLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     +D  +   NKP GI      G   +I  F+    
Sbjct: 65  --------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  ---SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|223041724|ref|ZP_03611918.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           minor 202]
 gi|223017462|gb|EEF15879.1| ribosomal large subunit pseudouridine synthase E [Actinobacillus
           minor 202]
          Length = 224

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 39/176 (22%), Positives = 64/176 (36%), Gaps = 8/176 (4%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                L + L  E++ I +FNKP  +  Q            LK ++D    K     RLD
Sbjct: 17  PQKRPLATRLNLEETIIVLFNKPYDVLTQ---FTDEQGRKTLKDFIDI--PKIYPVGRLD 71

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
           +++ G+L++         L      +   K YW  V GIP             +   G  
Sbjct: 72  RDSEGLLLLTNNGEIQHRLAHPKFEKE--KTYWVQVEGIPSQADLA-KLEKGVELKDGLT 128

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                KQ E       +  K+ +       W+E++   G+  Q+R    H+G P +
Sbjct: 129 QPAKAKQIEAPDFDWQTAPKIRERKTVPTSWIELKITEGKNRQVRRMTAHIGFPTL 184


>gi|198242968|ref|YP_002218105.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|207859366|ref|YP_002246017.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|197937484|gb|ACH74817.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|206711169|emb|CAR35544.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|326625901|gb|EGE32246.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Dublin str. 3246]
          Length = 289

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 23/165 (13%), Positives = 55/165 (33%), Gaps = 34/165 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +     + +  G V ++ KR    +++ +G VV++   +      
Sbjct: 7   IRLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     +D  +   NKP GI      G   +I  F+    
Sbjct: 65  --------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  ---SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|123442126|ref|YP_001006108.1| 23S rRNA pseudouridine synthase F [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122089087|emb|CAL11923.1| conserved hypothetical protein [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 290

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 74/247 (29%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR     ++ +G VV++          
Sbjct: 7   IRLNKYISE--SGICSRRDADRYIEQGNVFINGKRATVGEQVYAGDVVKVN--------- 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
              Q I     N               D  +   NKP GI      G   +I  F+    
Sbjct: 56  --GQLIEPRDQN---------------DLVLIALNKPVGIICTTEDGEGDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD+++ G++ +         +  +      + +   +    P    E 
Sbjct: 97  ---SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYV---VTVNKPLTD-EF 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I         +G        + E    ++I+                     G   Q+R 
Sbjct: 150 ILGLGAGVPMLGTVTKKCKVRKEAPFVFSIT------------------LVQGLNRQIRR 191

Query: 258 HALHMGC 264
              + G 
Sbjct: 192 MCKYFGY 198


>gi|168180387|ref|ZP_02615051.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum NCTC 2916]
 gi|168184870|ref|ZP_02619534.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum Bf]
 gi|226949054|ref|YP_002804145.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A2 str. Kyoto]
 gi|182668845|gb|EDT80823.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum NCTC 2916]
 gi|182672066|gb|EDT84027.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum Bf]
 gi|226841110|gb|ACO83776.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A2 str. Kyoto]
          Length = 236

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 84/252 (33%), Gaps = 55/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
            RL ++  +     +    + I+  G+V V+  R+K    +I SG  ++++   I     
Sbjct: 3   ERLQKYMAS-CGVASRRKCEDIILEGRVEVNGIRIKELGTKIISGEDIIKVDGNIIEPE- 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKS 135
                                      E+    + NKP G             I   +K 
Sbjct: 61  ---------------------------ENKIYILLNKPKGYVCTAKDEKDRKTILDLVKV 93

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 ++     RLD +TSGI+++         +      +   K Y + V G  K   
Sbjct: 94  -----KERIYPIGRLDMDTSGIIILTNDGEIYNKIIHPKFEK--IKTYKAKVKGTIKKDH 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 L KK    GDY+            A +  +++   ++    + ++ H G+  Q+
Sbjct: 147 IE----LFKKGIDIGDYI-----------TAPATLEILK-ISKDTSEIIIKIHEGKNRQV 190

Query: 256 RVHALHMGCPIV 267
           R     +G  ++
Sbjct: 191 RRMCKSIGHAVI 202


>gi|313893433|ref|ZP_07827005.1| pseudouridine synthase B, ribosomal large subunit [Veillonella sp.
           oral taxon 158 str. F0412]
 gi|313442074|gb|EFR60494.1| pseudouridine synthase B, ribosomal large subunit [Veillonella sp.
           oral taxon 158 str. F0412]
          Length = 242

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 87/249 (34%), Gaps = 49/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++  +     +    ++++  G+V+V+ ++V                         
Sbjct: 2   ERLQKYIAS-CGIASRRKAEELITEGKVQVNGRKVT------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIY-VFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                L   +N  K    +   LL ++  +Y + NKP G+     S         +  ++
Sbjct: 37  ----ELGVKINPQKDKVKVNGQLLAQEKPVYYLLNKPKGVIT---SVSDPQGRETVLDYI 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            ++ ++     RLD  T G+L++      AQ+LT     + ++K Y   + G  +++   
Sbjct: 90  KNESKRIYPVGRLDLYTEGLLLLTNDGELAQNLT--HPSKGVEKTYEVRIKGRVRDEDLQ 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +    +K               E G     +   +          +E+  H GR  Q+R 
Sbjct: 148 VIANGVKL--------------EDGMTAPATIVDLGFDDHNGVHEVEITIHEGRNRQVRR 193

Query: 258 HALHMGCPI 266
              H G  I
Sbjct: 194 MFEHFGYRI 202


>gi|310767747|gb|ADP12697.1| 23S rRNA pseudouridylate synthase B [Erwinia sp. Ejp617]
          Length = 295

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 61/175 (34%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ ++ +G+V VD K     +R++ G  ++I    +        
Sbjct: 5   LQKVLARA-GHGSRREIETLISAGRVSVDGKLATLGDRVEPGASLKIRIDGH-------- 55

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             ++  S +++            E  +I  + KP G                       +
Sbjct: 56  --VVPVSESIS------------EVCRILAYYKPEGELC--TRSDPEGRPTVFDRLPKLR 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  T G+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 100 GARWVAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGAVDDEK 152


>gi|298717565|ref|YP_003730207.1| pseudouridylate synthase [Pantoea vagans C9-1]
 gi|298361754|gb|ADI78535.1| pseudouridylate synthase [Pantoea vagans C9-1]
          Length = 292

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 72/246 (29%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +  +  + +  G V ++ KR     ++ +G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRRDADRYIEQGNVFINGKRASVGAQVFAGDVVKVNGQLIEPRDE- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIITTMEEGERDNISDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD+++ G++ +         +  +      + +   +    P    E I
Sbjct: 97  --SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNNHEKEYV---VTVDKPITD-EFI 150

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A        +G        + E    + I+                     G   Q+R  
Sbjct: 151 AGMSAGVPMLGTVTKKCKVKKEAPFVFRIT------------------LVQGLNRQIRRM 192

Query: 259 ALHMGC 264
             H G 
Sbjct: 193 CKHFGF 198


>gi|157736321|ref|YP_001489004.1| ribosomal large subunit pseudouridine synthase B [Arcobacter
           butzleri RM4018]
 gi|157698175|gb|ABV66335.1| ribosomal large subunit pseudouridine synthase B [Arcobacter
           butzleri RM4018]
          Length = 275

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 90/244 (36%), Gaps = 37/244 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           +RL+++   H  + +     K++  G++RV+ K V     +++S   V I         +
Sbjct: 20  IRLNKFLS-HNSNYSRREADKLIEEGKIRVNNKVVTDLATKVKSTDKVEI------GKKL 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           IKE+K            + L ++++Y        NKP G  V   S         +   +
Sbjct: 73  IKEEK------------NKLYTVIVY--------NKPKGEIV---SKKDPQGRKTIYDGL 109

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + K +      RLD  + G+L+++ +      L  S   R  +     L+   P  ++  
Sbjct: 110 EHKYKHFLSVGRLDYSSEGLLLLSDSVDIVNALMHSDLERVYKIKLNGLI--TPAVEQAM 167

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            +   ++ +  G      +K        A      I     K   +++  + G+  +LR 
Sbjct: 168 QSGITIEDATSGAYKGTKIKSMSFAPFLA----YDIQTNGTKHSKIKVVINEGKNRELRR 223

Query: 258 HALH 261
              H
Sbjct: 224 FFAH 227


>gi|148269796|ref|YP_001244256.1| pseudouridine synthase [Thermotoga petrophila RKU-1]
 gi|147735340|gb|ABQ46680.1| ribosomal small subunit pseudouridine synthase A [Thermotoga
           petrophila RKU-1]
          Length = 239

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 65/179 (36%), Gaps = 40/179 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MRLDR+  N         ++K+++ G+V V+ + V    + +    VV +       +  
Sbjct: 1   MRLDRYLSNSGVG-TRKEVKKLIKQGRVTVNGRVVLDPGHSVSENDVVVLDGETVNFHR- 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                               K  +L+        +KP+G      S    H +  ++   
Sbjct: 59  --------------------KVYILF--------HKPSGYVT---STKDPHSETIMEFLP 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             KG  P    RLD++  G+L++      A + ++  +    ++K Y   V G     K
Sbjct: 88  PLKGIFP--VGRLDKDAEGLLIITSDGDFAHRVISPKW---SVEKEYIVKVEGEVTEDK 141


>gi|21283425|ref|NP_646513.1| hypothetical protein MW1696 [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49486578|ref|YP_043799.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|300911616|ref|ZP_07129060.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|21204866|dbj|BAB95561.1| MW1696 [Staphylococcus aureus subsp. aureus MW2]
 gi|49245021|emb|CAG43482.1| RNA pseudouridine synthase [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|300887037|gb|EFK82238.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           aureus subsp. aureus TCH70]
          Length = 231

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 78/244 (31%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++  N         ++++L+ G V V+++ +K                     HI 
Sbjct: 1   MRIDKFLANMGVG-TRNEVKQLLKKGLVNVNEQVIKS-----------------PKTHIE 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   +     L          + Y ++   + NKP        +   +H    +    +
Sbjct: 43  PENDKITVRGEL----------IEYIENVYIMLNKPKDYIS---ATEDHHSKTVIDLIPE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD++T G+L++         L      + + K Y            E I
Sbjct: 90  YQHLNIFTVGRLDKDTEGLLLITNDGDFNHEL--MSPNKHVSKKY------------EVI 135

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           +   + +  I      V   + K    AI  +  ID         E     G+ HQ++  
Sbjct: 136 SANPITEDDIQAFKEGVTLSDGK-VKPAILTY--IDNQTSHVTIYE-----GKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|329766937|ref|ZP_08258465.1| hypothetical protein HMPREF0428_00162 [Gemella haemolysans M341]
 gi|328837662|gb|EGF87287.1| hypothetical protein HMPREF0428_00162 [Gemella haemolysans M341]
          Length = 243

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 83/249 (33%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +       + +    ++++  G+V V+ + VK    + +   ++ +         +
Sbjct: 3   ERLQKLIAAS-GYTSRRKAEQLILDGKVSVNGEVVKELGVKAEPSDIIIV-----EGVRL 56

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +KE K               +  L Y+  K+              S         +K + 
Sbjct: 57  LKENK---------------RYYLFYKPEKVI------------TSMSDEKDRTCVKDFF 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +   ++     RLD +TSG L+++        +T      +I+K Y + + G  ++    
Sbjct: 90  EDVNERVVPVGRLDYDTSGALIMSNDGEFINLIT--HPKHKIRKTYVAKINGKLEDNHLR 147

Query: 198 IANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           I    ++          V++VK   K  N                  + +  H G+  Q+
Sbjct: 148 ILRNGVRIDNYKTAKAEVNIVKNKNKSGN----------------TLVRLTIHEGKNRQV 191

Query: 256 RVHALHMGC 264
           R     +G 
Sbjct: 192 RRMFEALGY 200


>gi|257452524|ref|ZP_05617823.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           3_1_5R]
 gi|317059065|ref|ZP_07923550.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           3_1_5R]
 gi|313684741|gb|EFS21576.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium sp.
           3_1_5R]
          Length = 238

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 76/249 (30%), Gaps = 50/249 (20%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E  +R++++  +     +   +   +  G++ V+        ++ +             
Sbjct: 2   EENKIRINKFLASK-GVASRRQIDLWIEEGKILVNGILATSGQKVSA------------- 47

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                E KIL +   +++  +     +LY++ ++    K                   + 
Sbjct: 48  -----EDKILVNGKMISEKEEKKVYYILYKEEEVLSAVK------------DERGRKTVV 90

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             + +K  +     RLD  TSG++++         +        I K Y  L  G    +
Sbjct: 91  DCIPTKA-RIFPVGRLDYRTSGLILLTNDGELFNRV--MHPRAEIFKTYEVLAKGHLTRE 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +       ++          V K   +  N                 + E+    GR  Q
Sbjct: 148 QLKTLEEGVELEEGKTLEALVAKVKYEKGN----------------TFFEISIREGRNRQ 191

Query: 255 LRVHALHMG 263
           +R     +G
Sbjct: 192 IRRMVEAVG 200


>gi|213163156|ref|ZP_03348866.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
          Length = 289

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 23/164 (14%), Positives = 54/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  --SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|28211002|ref|NP_781946.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           tetani E88]
 gi|28203441|gb|AAO35883.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           tetani E88]
          Length = 234

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 42/257 (16%), Positives = 82/257 (31%), Gaps = 65/257 (25%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++  +     +    + I+ +G+V+V+ + +K                      + 
Sbjct: 2   ERLQKYMASCGVD-SRRKCEDIILNGRVKVNGESIK-----------------ELGVKVD 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            E+ I+     + K           E+ K    NKP G IS          I   +    
Sbjct: 44  PEKDIVTIDNRIIKKE---------ENKKYIALNKPTGYISSVKDDKGRKTILDLI---- 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK----- 192
               ++     RLD +TSG++++         +      +  +K+Y + + GIP      
Sbjct: 91  -DVKERIYPIGRLDYDTSGLILLTNDGDFYNKVIHPREEK--EKVYVATIKGIPNSSELQ 147

Query: 193 --NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
              K   I ++L   S I      ++      A   I+                     G
Sbjct: 148 DFKKGLVIDDYLTSPSKI-----KIISVKNNNAEVIIT------------------IMEG 184

Query: 251 RTHQLRVHALHMGCPIV 267
           R  Q+R     +  P++
Sbjct: 185 RNRQVRKMCEKINHPVI 201


>gi|33861215|ref|NP_892776.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus subsp. pastoris str.
           CCMP1986]
 gi|33639947|emb|CAE19117.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus subsp. pastoris str.
           CCMP1986]
          Length = 240

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 33/246 (13%), Positives = 76/246 (30%), Gaps = 55/246 (22%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R++++      + +      ++  G+V ++ +  +   +++ G  V +            
Sbjct: 4   RINKYLSE-VGYCSRRVADSLIEEGKVTINGEIPEMGTKVEEGDQVEV------------ 50

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGFLKSWVD 138
           E + ++ S+   K         +Y      VFNKP GI       +   +I  F+K    
Sbjct: 51  EGQRIEKSMKHEK---------IY-----LVFNKPVGIVCTTDRRVESDNIIDFIK---- 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+ + G++ +         +  +      + I                
Sbjct: 93  -YPTRIFPIGRLDKPSEGLIFLTNDGDIVNKILRARNNHEKEYIVS-------------- 137

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                    I  D++  +    +       +  V     +KF    +    G   Q+R  
Sbjct: 138 -----VNRPINRDFIQSMSNGVEILGTITKNCFVKQLGPKKF---RIILTQGLNRQIRRM 189

Query: 259 ALHMGC 264
              +G 
Sbjct: 190 CESLGF 195


>gi|294635983|ref|ZP_06714424.1| ribosomal large subunit pseudouridine synthase B [Edwardsiella
           tarda ATCC 23685]
 gi|291090692|gb|EFE23253.1| ribosomal large subunit pseudouridine synthase B [Edwardsiella
           tarda ATCC 23685]
          Length = 291

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 57/175 (32%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ +++ G+V VD K     +R++    ++I      ++    E
Sbjct: 5   LQKVLARA-GHGSRREIEALIKEGRVSVDGKLATLGDRVEVTANMKIRVDGRVVSIRESE 63

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           Q+I                       ++  + KP G                       +
Sbjct: 64  QEIC----------------------RVLAYYKPEGELC--TRRDPEGRPTVFDRLPRLR 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G     K
Sbjct: 100 GSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDEDK 152


>gi|297538013|ref|YP_003673782.1| pseudouridine synthase [Methylotenera sp. 301]
 gi|297257360|gb|ADI29205.1| pseudouridine synthase [Methylotenera sp. 301]
          Length = 374

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 35/228 (15%), Positives = 71/228 (31%), Gaps = 35/228 (15%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            RL +        + +  +++ ++ SG+V V+         +     VR+      L  I
Sbjct: 37  QRLHKLLA--LAGLGSRRDMETLISSGRVTVNGAPATQGQGVTQFDTVRLDSRPVKLPFI 94

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                 L  +L+Y        +KP G  V                  
Sbjct: 95  AE-----------------LPQVLIY--------HKPEGEIV--SQDDPEGRASVFDKLP 127

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             K  K     RLD  TSG+L+   +   A           +++ Y   ++G     +  
Sbjct: 128 KVKNGKWIAIGRLDMNTSGLLIFTTSGELANRF--MHPRYEVEREYAVRIFGELTEGQMT 185

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
                ++      ++  +  Q  +GAN+    ++VI    +      +
Sbjct: 186 QLKEGIELEDGPANFDSISAQGGEGANH---WYQVILREGRNREVRRL 230


>gi|229199112|ref|ZP_04325795.1| hypothetical protein bcere0001_46250 [Bacillus cereus m1293]
 gi|228584383|gb|EEK42518.1| hypothetical protein bcere0001_46250 [Bacillus cereus m1293]
          Length = 165

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNTILSEGDHISIC 164


>gi|119505054|ref|ZP_01627130.1| 16S rRNA uridine-516 pseudouridylate synthase [marine gamma
           proteobacterium HTCC2080]
 gi|119459036|gb|EAW40135.1| 16S rRNA uridine-516 pseudouridylate synthase [marine gamma
           proteobacterium HTCC2080]
          Length = 305

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 32/235 (13%), Positives = 70/235 (29%), Gaps = 34/235 (14%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   +++ +  G++ +  ++ K  +R+  G+ V +      L+  
Sbjct: 22  GDKLQKALAKTGLG-SRREIERWIEQGRLTIGGRKAKLGDRVMLGERVTLDGKPVELDET 80

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     E  +  +++KP G                  S  
Sbjct: 81  --------------------------ERVRCLLYHKPVGEVC--SRKDPEGRRTVFDSLP 112

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + +G +  +  RLD  TSG+L+       A  +        I++ Y   V G   ++   
Sbjct: 113 ELQGGRWIVVGRLDFNTSGLLLFTTDGELAHKM--MHPSSTIEREYLVRVMGNATDEILD 170

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                +        +  +V     G N     F V+    +      +    G T
Sbjct: 171 TLRAGVILDDGPARFTDIVDGGGDGINR---WFYVVLMEGRNREVRRLWESQGLT 222


>gi|119356331|ref|YP_910975.1| ribosomal large subunit pseudouridine synthase B [Chlorobium
           phaeobacteroides DSM 266]
 gi|119353680|gb|ABL64551.1| ribosomal large subunit pseudouridine synthase B [Chlorobium
           phaeobacteroides DSM 266]
          Length = 243

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 88/254 (34%), Gaps = 53/254 (20%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             DE  +R++R+        +     K++  G+V V+ K        + G  +RI P   
Sbjct: 4   TEDEGGIRINRYLA-MCGIASRRAADKLVADGRVTVNGKIAD-----EPG--LRILPF-- 53

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                 K++ I+D    +   +  +            + NKP  +     S      +  
Sbjct: 54  ------KDEVIVDGRKFVVPEAKKV----------YILLNKPRNVIT--TSHDEKDRETI 95

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           L   + S  ++     RLD++T+G++++      A  L       + + +          
Sbjct: 96  LD--LVSVEERVYPVGRLDRKTTGVILLTNDGILAHRLMHPSSNVKKEYVAE-------- 145

Query: 193 NKKECIANWLLKKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                    L K+   G     V  +K  + G   +    K++D   + +    +  H G
Sbjct: 146 ---------LDKRFPQGLLSQLVGGMKLKDTGEKVSPCQAKLLDDGMRIW----ISIHEG 192

Query: 251 RTHQLRVHALHMGC 264
           + HQ+R     +G 
Sbjct: 193 KNHQVRRMLETLGF 206


>gi|47567000|ref|ZP_00237717.1| hypothetical protein cytosolic protein [Bacillus cereus G9241]
 gi|47556318|gb|EAL14652.1| hypothetical protein cytosolic protein [Bacillus cereus G9241]
          Length = 165

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNTLLSEGDHISIC 164


>gi|168231182|ref|ZP_02656240.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|194472572|ref|ZP_03078556.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194458936|gb|EDX47775.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|205334218|gb|EDZ20982.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
          Length = 289

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 23/166 (13%), Positives = 54/166 (32%), Gaps = 34/166 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184
              ++     RLD+++ G++ +         +  +      + +  
Sbjct: 97  --SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVA 140


>gi|323447017|gb|EGB02989.1| hypothetical protein AURANDRAFT_34656 [Aureococcus anophagefferens]
          Length = 273

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 45/259 (17%), Positives = 83/259 (32%), Gaps = 47/259 (18%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              R+       +P ++       + +G+VRV+ +  K + R++SG  + +         
Sbjct: 24  AGFRV----VRCFPELSRRAADAAVAAGRVRVNGETAKPSLRLRSGDTLALDGKKRDWEA 79

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLK 134
           +  +   L+    L                  Y ++KP G++    +           LK
Sbjct: 80  LAAK---LEGGGGLE----------------YYAYHKPEGVACTTDANDRRSLRRAPALK 120

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAA-QHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G++     RLD ++ G++V+    AAA   L  S ++ ++ ++           
Sbjct: 121 KLFAG-GKRIFPAGRLDVDSCGLVVLTNDGAAADAALQPSSKLAKVYEVELDRRAADDDV 179

Query: 194 KKEC----IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                   IA  L + S             EK            D         E     
Sbjct: 180 AALAAGVEIATPLQRGSK-----------AEKTGKTLPCDVARGDGRGLVITLAE----- 223

Query: 250 GRTHQLRVHALHMGCPIVG 268
           GR  QLR  A  +G  + G
Sbjct: 224 GRNRQLRRMAEALGYEVTG 242


>gi|260913991|ref|ZP_05920465.1| ribosomal large subunit pseudouridine synthase B [Pasteurella
           dagmatis ATCC 43325]
 gi|260632078|gb|EEX50255.1| ribosomal large subunit pseudouridine synthase B [Pasteurella
           dagmatis ATCC 43325]
          Length = 358

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 36/191 (18%), Positives = 62/191 (32%), Gaps = 31/191 (16%)

Query: 5   TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSG 62
           + V+  V +   E  +L +         +   ++ ++   +V VD K     +R  ++SG
Sbjct: 63  SSVKNTVKKPKVEGEKLQKVLARAGQG-SRREIEAMIAENRVSVDGKMATLGDRIDVRSG 121

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
             VRI   I  L H  KE                          ++ ++ KP G      
Sbjct: 122 VKVRIDGHIVNLMHAQKEV------------------------CRVLMYYKPEGELC--T 155

Query: 123 SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                             G +     RLD  TSG+L+       A  L      R +++ 
Sbjct: 156 RHDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVERE 213

Query: 183 YWSLVWGIPKN 193
           Y   V+G   +
Sbjct: 214 YSVRVFGQVDD 224


>gi|167552572|ref|ZP_02346325.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|168263493|ref|ZP_02685466.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|200389083|ref|ZP_03215695.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|199606181|gb|EDZ04726.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|205322854|gb|EDZ10693.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|205348000|gb|EDZ34631.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
          Length = 289

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 23/164 (14%), Positives = 54/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  --SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|148981773|ref|ZP_01816521.1| pseudouridine synthase family 1 protein [Vibrionales bacterium
           SWAT-3]
 gi|145960740|gb|EDK26079.1| pseudouridine synthase family 1 protein [Vibrionales bacterium
           SWAT-3]
          Length = 305

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 33/176 (18%), Positives = 60/176 (34%), Gaps = 30/176 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   L+ +++SG+V V+ +  K   R++    V+RI     +      
Sbjct: 5   LQKVLARA-GHGSRRELEGLIKSGRVSVNGQVAKLGERLEDENSVIRIDGHTVSG----- 58

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                       K S+ +   +L        + KP G                       
Sbjct: 59  ------------KASEEVVCRVL-------AYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVTEQK 151


>gi|325497996|gb|EGC95855.1| 16S rRNA pseudouridylate synthase A [Escherichia fergusonii ECD227]
          Length = 231

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 76/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGETVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E ++      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHEVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|319947493|ref|ZP_08021725.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           australis ATCC 700641]
 gi|319746433|gb|EFV98694.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           australis ATCC 700641]
          Length = 240

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 86/248 (34%), Gaps = 54/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVRIPPVINALNH 76
           MRLD+   ++   I    +++ L   Q+ VD     K +  + +G Q VR          
Sbjct: 1   MRLDQLLAHY--QIPRKEIKQSLAKRQILVDGLAATKLSQNVDTGLQEVRW--------- 49

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
             K+Q + D S                     ++ +KP G+           +   L++ 
Sbjct: 50  --KDQVLTDCSH------------------HYFLLHKPQGLVTATKDAQHSTVLDLLRT- 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            + +  K     RLD++T+G+L++        Q L   +    I+K Y + V G      
Sbjct: 89  -EDRTPKTYPIGRLDRDTTGLLLLTDNGPLGFQLLHPQYH---IEKEYAATVNG------ 138

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                  L+ +HI      +   +      A      I   +       +    G+ HQ+
Sbjct: 139 ------PLEPAHIEKFQEGITFLDGTTCKPAKLE---ILSSSLTESQALVTLSEGKFHQV 189

Query: 256 RVHALHMG 263
           +   L +G
Sbjct: 190 KKMLLSVG 197


>gi|315635454|ref|ZP_07890720.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
 gi|315480212|gb|EFU70879.1| RNA pseudouridine synthase [Arcobacter butzleri JV22]
          Length = 275

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 43/244 (17%), Positives = 90/244 (36%), Gaps = 37/244 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           +RL+++   H  + +     K++  G++RV+ K V     +++S   V I         +
Sbjct: 20  IRLNKFLS-HNSNYSRREADKLIEEGKIRVNNKVVTDLATKVKSTDKVEI------GKKL 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           IKE+K            + L ++++Y        NKP G  V   S         +   +
Sbjct: 73  IKEEK------------NKLYTVIVY--------NKPKGEIV---SKKDPQGRKTIYDGL 109

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           + K +      RLD  + G+L+++ +      L  S   R  +     ++   P  ++  
Sbjct: 110 EHKYKHFLSVGRLDYSSEGLLLLSDSVDIVNALMHSDLERVYKIKLNGVI--TPAVEQAM 167

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            +   ++ +  G      +K        A      I     K   +++  + G+  +LR 
Sbjct: 168 QSGITIEDATSGAYKGTKIKSMSFAPFLA----YDIQTNGTKHSKIKVVINEGKNRELRR 223

Query: 258 HALH 261
              H
Sbjct: 224 FFAH 227


>gi|168239322|ref|ZP_02664380.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|168466867|ref|ZP_02700715.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|194442736|ref|YP_002043438.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194735254|ref|YP_002117092.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|204927294|ref|ZP_03218496.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|194401399|gb|ACF61621.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194710756|gb|ACF89977.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|195630602|gb|EDX49214.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197287935|gb|EDY27323.1| ribosomal large subunit pseudouridine synthase F (rRNA-uridine
           isomerase F) [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|204323959|gb|EDZ09154.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
          Length = 289

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 23/164 (14%), Positives = 54/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  --SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|327480926|gb|AEA84236.1| pseudouridine synthase [Pseudomonas stutzeri DSM 4166]
          Length = 375

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 28/191 (14%), Positives = 58/191 (30%), Gaps = 30/191 (15%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           MT  +   +       +L +         +  +++K +  G+V+V+        R+ S  
Sbjct: 1   MTEHEETTIHAT-HGEKLQKVLAR-LGIASRRDVEKWIVEGRVKVNGAVATLGQRVDSHD 58

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
            + +   +                +   + S  ++ +L+Y        NKP G       
Sbjct: 59  AIAVDGRL----------------LKREETSQVVRRVLIY--------NKPDGEIC--TR 92

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                           K  +     RLD  T+G+L+       A  L        + + Y
Sbjct: 93  NDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLLFTTDGELANRL--MHPSYEMDREY 150

Query: 184 WSLVWGIPKNK 194
              V G   ++
Sbjct: 151 AVRVRGEVDDE 161


>gi|254303709|ref|ZP_04971067.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148323901|gb|EDK89151.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 226

 Score = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 38/211 (18%), Positives = 80/211 (37%), Gaps = 38/211 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++K++ + ++ V+                         N I 
Sbjct: 1   MRLDKFLVECGIG-SRKEVKKLISNDEITVNG-----------------------FNDIS 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +  I ++S  +  + + L+    Y++ + Y+ NK AG            +   L  WV 
Sbjct: 37  AKDNIDENSDIIEYNGEKLE----YKEFRYYIMNKKAGYITATEDFKENTVMDLLPEWVI 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYW---SLVWGIPKNK 194
            K   P    RLD++T G+L+     +   + L+    + ++  I      L   I K +
Sbjct: 93  RKDLAP--VGRLDKDTEGLLLFTNDGKLNHRLLSPKNHIDKVYYIEIENNILDKDILKLE 150

Query: 195 KEC-IANWLL---KKSHIGGDYVHVVKQNEK 221
           +   I N++    K   I  + +++  +  K
Sbjct: 151 QGVDIGNYITQPAKVEKISDNKIYLTIKEGK 181


>gi|320539063|ref|ZP_08038735.1| putative 23S rRNA U2604 pseudouridine synthase [Serratia symbiotica
           str. Tucson]
 gi|320030873|gb|EFW12880.1| putative 23S rRNA U2604 pseudouridine synthase [Serratia symbiotica
           str. Tucson]
          Length = 288

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 26/144 (18%), Positives = 53/144 (36%), Gaps = 34/144 (23%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KRV   +R+  G VV++          
Sbjct: 7   LRLNKYISE--SGICSRRDADRYIEQGNVFINGKRVTLGDRVFPGDVVKVNGQ------- 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + E +  D+ +                       NKP GI      G   +I  F+    
Sbjct: 58  VIEPRNEDNLI-------------------FIALNKPVGIVSTTEDGEKDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVA 161
                +     RLD+++ G++ + 
Sbjct: 97  ---STRIFPIGRLDKDSQGLIFLT 117


>gi|319400836|gb|EFV89055.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           epidermidis FRI909]
          Length = 245

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 38/251 (15%), Positives = 80/251 (31%), Gaps = 54/251 (21%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           E  RL +       + +    + ++  G+V+V+ + V    +++    +V +        
Sbjct: 4   EKERLQKRIAKS-GYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVD------- 55

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                                    +  ED    +F KP  +     S         +  
Sbjct: 56  ----------------------GIKIEQEDKIYILFYKPTQVIT---SVSDDRGRRVVTD 90

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KN 193
           + D    +     RLD +TSG+L++         +T       I+K Y + + G    + 
Sbjct: 91  YFDDLESRIYPVGRLDYDTSGVLLLTNDGEFTNLMT--HPRYHIKKKYVAKLKGYLMREE 148

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K+      L+  +     V + KQ+++                +    +E+    GR  
Sbjct: 149 IKQLEKGIELEDGYTQPAQVKIKKQDKE----------------KNTTLVEITISEGRNR 192

Query: 254 QLRVHALHMGC 264
           Q+R    + G 
Sbjct: 193 QVRRMFEYFGH 203


>gi|317491810|ref|ZP_07950245.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316920244|gb|EFV41568.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 293

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 23/164 (14%), Positives = 55/164 (33%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +  +  + +  G V ++ KR    +++ +G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRRDADRYIEQGHVFINGKRAGIGDQVFAGDVVKVNGQLIEPRDA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI     +G   +I  ++     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTENGEKDNIVDYVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               +     RLD+++ GI+ +         +  +      + +
Sbjct: 97  --STRVFPIGRLDKDSQGIIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|293414601|ref|ZP_06657250.1| 23S rRNA pseudouridylate synthase B [Escherichia coli B185]
 gi|291434659|gb|EFF07632.1| 23S rRNA pseudouridylate synthase B [Escherichia coli B185]
          Length = 311

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 26  LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 77

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 78  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 118

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 119 LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 173


>gi|229099423|ref|ZP_04230353.1| hypothetical protein bcere0020_46420 [Bacillus cereus Rock3-29]
 gi|228684047|gb|EEL37995.1| hypothetical protein bcere0020_46420 [Bacillus cereus Rock3-29]
          Length = 165

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 8/49 (16%), Positives = 25/49 (51%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   ++SG ++++ +++K N ++  G  + I 
Sbjct: 116 RIDKVLSTYISDWSRTTIVDKIKSGDIQLNGQQMKPNKQLSEGDYISIC 164


>gi|229105582|ref|ZP_04236216.1| hypothetical protein bcere0019_47110 [Bacillus cereus Rock3-28]
 gi|229118436|ref|ZP_04247790.1| hypothetical protein bcere0017_47030 [Bacillus cereus Rock1-3]
 gi|228665006|gb|EEL20494.1| hypothetical protein bcere0017_47030 [Bacillus cereus Rock1-3]
 gi|228677852|gb|EEL32095.1| hypothetical protein bcere0019_47110 [Bacillus cereus Rock3-28]
          Length = 165

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 8/49 (16%), Positives = 25/49 (51%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   ++SG ++++ +++K N ++  G  + I 
Sbjct: 116 RIDKVLSTYISDWSRTTIVDKIKSGDIQLNGQQMKPNKQLSEGDYISIC 164


>gi|156933241|ref|YP_001437158.1| 16S rRNA pseudouridylate synthase A [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156531495|gb|ABU76321.1| hypothetical protein ESA_01053 [Cronobacter sakazakii ATCC BAA-894]
          Length = 235

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 77/250 (30%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R+ +V VD + VK                 ++   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRASRVTVDGEIVK-----------------DSAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +  +      L + +            + ++ NKP G      S         L    +
Sbjct: 43  ADNDVEYDGNPLIQQNGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A    +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAALFAKGVQLNNEKDLTKPA--QLEVI-----TPTEVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAAVGNHVVG 199


>gi|171059554|ref|YP_001791903.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170776999|gb|ACB35138.1| pseudouridine synthase [Leptothrix cholodnii SP-6]
          Length = 736

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 33/220 (15%), Positives = 67/220 (30%), Gaps = 32/220 (14%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +  +++++++ GQV V+ +      RI  G  ++I                         
Sbjct: 303 SRRDMEQLIQEGQVSVNGEVAHIGMRIAQGDQIKI------------------------- 337

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
               +K  +    +++  ++KP G  V              +        K     RLD 
Sbjct: 338 AGRPIKVRIAPPPARVLAYHKPVGEVV--THHDPEGRPTVFRRLPRLPVGKWLSVGRLDI 395

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L+   +   A  L        +++ Y   V G            LL+   I G  
Sbjct: 396 NTEGLLLFTNSGELANQL--MHPRFGVEREYAVRVLGSLDEAA---RARLLEGVEIEGQR 450

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                 ++ G       ++V+    +      +    G T
Sbjct: 451 AMFKSIDDGGGEGINHWYRVVITEGRNREVRRLFDAVGLT 490


>gi|304395011|ref|ZP_07376895.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304357264|gb|EFM21627.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 292

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 74/250 (29%), Gaps = 56/250 (22%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + + RL+++       I +  +  + +  G V ++ KR     ++ +G VV++   +   
Sbjct: 4   DSSTRLNKYISE--SGICSRRDADRYIEQGNVFINGKRASVGAQVFAGDVVKVNGQLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        +D  +   NKP GI      G   +I  F+ 
Sbjct: 62  RDE--------------------------DDLVLIALNKPVGIITTMEEGERDNISDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+++ G++ +         +  +      + +   +    P   
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNNHEKEYV---VTVDKPITD 147

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E IA        +G        + E    + I+                     G   Q
Sbjct: 148 -EFIAGMSAGVPMLGTVTKKCKVKKEAPFVFRIT------------------LVQGLNRQ 188

Query: 255 LRVHALHMGC 264
           +R    H G 
Sbjct: 189 IRRMCKHFGF 198


>gi|228923698|ref|ZP_04086976.1| hypothetical protein bthur0011_46730 [Bacillus thuringiensis
           serovar huazhongensis BGSC 4BD1]
 gi|228835827|gb|EEM81190.1| hypothetical protein bthur0011_46730 [Bacillus thuringiensis
           serovar huazhongensis BGSC 4BD1]
          Length = 165

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RIDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDYISIC 164


>gi|228968077|ref|ZP_04129083.1| hypothetical protein bthur0004_48610 [Bacillus thuringiensis
           serovar sotto str. T04001]
 gi|228791632|gb|EEM39228.1| hypothetical protein bthur0004_48610 [Bacillus thuringiensis
           serovar sotto str. T04001]
          Length = 165

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RIDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDYISIC 164


>gi|261377503|ref|ZP_05982076.1| ribosomal large subunit pseudouridine synthase B [Neisseria cinerea
           ATCC 14685]
 gi|269146237|gb|EEZ72655.1| ribosomal large subunit pseudouridine synthase B [Neisseria cinerea
           ATCC 14685]
          Length = 349

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 30/179 (16%), Positives = 56/179 (31%), Gaps = 30/179 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTTEQ 243


>gi|213424484|ref|ZP_03357281.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
          Length = 267

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 23/164 (14%), Positives = 54/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  --SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|221134960|ref|ZP_03561263.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Glaciecola sp. HTCC2999]
          Length = 331

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 22/174 (12%), Positives = 52/174 (29%), Gaps = 30/174 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +   N     +   ++  +  G++ V+       +R++    +R+   +   +     
Sbjct: 5   LQKVLANQGVG-SRREMETWIEQGRISVNGTIATLGDRVEPSDQIRVDGHLLKRDQKAPV 63

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            +                         + ++NKP G                     + +
Sbjct: 64  CR-------------------------VLMYNKPEGELC--SRTDPLGRQTVFDRLPNIQ 96

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             +     RLD  T+G+L+       A  L        +++ Y   V+G  + K
Sbjct: 97  SGRWIAVGRLDLNTAGLLLFTNDGELANRL--MHPRHEVEREYAVRVFGEVEPK 148


>gi|261253231|ref|ZP_05945804.1| ribosomal large subunit pseudouridine synthase B [Vibrio orientalis
           CIP 102891]
 gi|260936622|gb|EEX92611.1| ribosomal large subunit pseudouridine synthase B [Vibrio orientalis
           CIP 102891]
          Length = 312

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 32/179 (17%), Positives = 60/179 (33%), Gaps = 30/179 (16%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNH 76
           N +L +       H +   L+ ++++G+V V+    K   R++    +VRI     +   
Sbjct: 2   NEKLQKVLARA-GHGSRRELEALIKAGRVSVNGVVAKLGERLEDENAIVRIDGHTVS--- 57

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K  + +   +L        + KP G                    
Sbjct: 58  --------------AKAQEEVVCRVL-------AYYKPEGELC--TRHDPEGRRTVFDRL 94

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K
Sbjct: 95  PKIRGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVTEQK 151


>gi|150390402|ref|YP_001320451.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
 gi|149950264|gb|ABR48792.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
          Length = 234

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 48/250 (19%), Positives = 88/250 (35%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRL ++  N     +    + +++ G V V+ K V     ++    VV         +H+
Sbjct: 1   MRLQKYIAN-CGVASRRKSETLIQQGLVTVNDKVVTEMGFKL---DVVE--------DHV 48

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
               K++  +  +                   + NKP G        ++   D    + +
Sbjct: 49  KVRGKLIKPTEEMI----------------YILLNKPTGFVT----TVSDQFDRKTVTDL 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD  TSG L++         LT      ++ K+Y + V G P + K  
Sbjct: 89  VGVSERIFPVGRLDYHTSGFLLLTNDGNLTFKLT--HPKFKVSKVYIAKVKGKPSSSKLS 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
               L +K     DYV         A   IS  K++         +++    G+  Q+R 
Sbjct: 147 ----LFEKGLEIEDYV--------TAPAKISIIKILPHE----VIVKITLREGKNRQVRK 190

Query: 258 HALHMGCPIV 267
               +G P+V
Sbjct: 191 MCDAIGHPVV 200


>gi|288904878|ref|YP_003430100.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus UCN34]
 gi|288731604|emb|CBI13159.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           gallolyticus UCN34]
          Length = 238

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 30/165 (18%), Positives = 59/165 (35%), Gaps = 31/165 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +   ++K++RS QV VD        R+     + + P +  +   +
Sbjct: 1   MRLDKLLGQAGFG-SRNQVKKLIRSRQVYVDG-------RLAEADNLNVEPSLQKI--TV 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +++  SS                   K ++ NKPAG+           +   +K    
Sbjct: 51  SGKQVKQSS------------------EKYFLLNKPAGVVSAVSDKEHQTVIDLIKE--A 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKI 182
               K     RLD+ T G+L++        + L   + + +   +
Sbjct: 91  DCVPKLYPVGRLDRSTEGLLLITNNGPLGYRMLHPKYHVAKTYYV 135


>gi|197247683|ref|YP_002149101.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197211386|gb|ACH48783.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
          Length = 289

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 23/164 (14%), Positives = 54/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  --SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|314936380|ref|ZP_07843727.1| pseudouridylate synthase [Staphylococcus hominis subsp. hominis
           C80]
 gi|313654999|gb|EFS18744.1| pseudouridylate synthase [Staphylococcus hominis subsp. hominis
           C80]
          Length = 245

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 73/235 (31%), Gaps = 53/235 (22%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+ + V     +++S   V +                    + + 
Sbjct: 19  SRRKAETLITEGKVKVNGQVVTELGTKVKSSDTVEV------------------EGIKIE 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +           ED    +F KP  +     S         +  +  +   +     RLD
Sbjct: 61  Q-----------EDKIYILFYKPTQVIT---SVSDDRGRTVVTDYFKNLEARIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIG 209
            +TSG+L++         +T       IQK Y + + G    +  K       L+     
Sbjct: 107 YDTSGLLLLTNDGEFTNLMT--HPRYHIQKKYVAKLKGYLMREEVKALEQGIELEDGFTQ 164

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              V +  QN++                +    +E+    GR  Q+R    H   
Sbjct: 165 PAQVKIKNQNKE----------------KNTTLVEITISEGRNRQVRRMFEHFNH 203


>gi|218659525|ref|ZP_03515455.1| pseudouridine synthase, RluA family protein [Rhizobium etli IE4771]
          Length = 45

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 22/36 (61%), Positives = 31/36 (86%)

Query: 290 LHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
           +HAR++D+PHP GGRL+++APLP HMV+TW+ LG  
Sbjct: 1   MHARHIDIPHPSGGRLRVSAPLPPHMVQTWNLLGLD 36


>gi|310768104|gb|ADP13054.1| 16S rRNA pseudouridylate synthase A [Erwinia sp. Ejp617]
          Length = 234

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 33/251 (13%), Positives = 75/251 (29%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++     + LR+ +V VD + V+  + ++ +   V     +      
Sbjct: 1   MRLDKFISQQL-EVSRAIAARELRARKVTVDGEVVREGSYKLNADSTVEYDGNVLEQQLG 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                             ++ NKP G      S         L    
Sbjct: 60  PR----------------------------YFMLNKPVGYVC---STDDPDHPTILYFLE 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    +     RLD +T+G++++      +  +T          +               
Sbjct: 89  EPGAYRLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------T 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + +   +         +   +     A    +VI+        + +    GR HQ++ 
Sbjct: 136 LESAISDDNAQQFADGVQLHNEKTLTKPAA--LEVIEPN-----VVRLTISEGRYHQVKR 188

Query: 258 HALHMGCPIVG 268
               +G  +VG
Sbjct: 189 MFAAVGNRVVG 199


>gi|51595642|ref|YP_069833.1| 16S rRNA pseudouridylate synthase A [Yersinia pseudotuberculosis IP
           32953]
 gi|186894712|ref|YP_001871824.1| 16S rRNA pseudouridylate synthase A [Yersinia pseudotuberculosis
           PB1/+]
 gi|51588924|emb|CAH20541.1| ribosomal small subunit pseudouridine synthase A [Yersinia
           pseudotuberculosis IP 32953]
 gi|186697738|gb|ACC88367.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
          Length = 235

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 73/245 (29%), Gaps = 51/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK      SG +            + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEVVK------SGAI-----------KLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEQDVRFDGNPLQQMVGP----------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G+++                  +      S      K     +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVL-------------MTDDGQWSHRVTSPRHHCEKTYLVTL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L   +         +   +     A     VI+        + +    GR HQ++  
Sbjct: 137 EHPLSDDTAQQFADGVQLHNEKSLTKPA--QLDVIEPQ-----RVRLTIREGRYHQVKRM 189

Query: 259 ALHMG 263
              +G
Sbjct: 190 FAAVG 194


>gi|260768728|ref|ZP_05877662.1| ribosomal large subunit pseudouridine synthase B [Vibrio furnissii
           CIP 102972]
 gi|260616758|gb|EEX41943.1| ribosomal large subunit pseudouridine synthase B [Vibrio furnissii
           CIP 102972]
          Length = 314

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 80/234 (34%), Gaps = 38/234 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   L+ ++R+G+V V+ K      R++    VVRI     A++   +
Sbjct: 5   LQKVLARA-GHGSRRELEALIRAGRVSVNGKVAVLGERLEDENAVVRIDGH--AVSAKAQ 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E+ I                       ++  + KP G                       
Sbjct: 62  EEVIC----------------------RVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G     K  I 
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGDVTEDK--IR 153

Query: 200 NWLLKKSHIGG--DYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
           N +       G   +  VV    +G N+  + + VI+     +     E Q  T
Sbjct: 154 NLVRGVQLEDGLARFEDVVYAGGEGMNH--TFYVVINEGRNREVRRLWESQETT 205


>gi|90420204|ref|ZP_01228112.1| ribosomal small subunit pseudouridine synthase A [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90335538|gb|EAS49288.1| ribosomal small subunit pseudouridine synthase A [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 251

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 88/248 (35%), Gaps = 47/248 (18%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR   N   + +   +Q + R+G++++D       ++       RI    +    ++ 
Sbjct: 8   RLDRLLAN-MGYASRREIQMLARNGRIQLDGAAFHDADK-------RIALTPDLETRLVV 59

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + + LD             +++L++   +   +K AG  V             L      
Sbjct: 60  DGEALDPLPGF--------ALMLHKPLGVTCSHKEAGPLV----------YDLLPQRWRR 101

Query: 140 KGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +        RLD+ETSG+L++    +   + ++    + +  +++ +             
Sbjct: 102 RDPAISTVGRLDKETSGLLLMTDDGKLLHRIISPKRHVAKRYRVHLAR-------SMTGD 154

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L     +      +++  EK    A      ++    +   LE+  H GR HQ+R  
Sbjct: 155 EAALFAAGTL------MLEGEEKPLAPAE-----LEVVGPQEALLEV--HEGRYHQVRRM 201

Query: 259 ALHMGCPI 266
               G  +
Sbjct: 202 FAATGNHV 209


>gi|315180431|gb|ADT87345.1| pseudouridine synthase family 1 protein [Vibrio furnissii NCTC
           11218]
          Length = 315

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 80/234 (34%), Gaps = 38/234 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   L+ ++R+G+V V+ K      R++    VVRI     A++   +
Sbjct: 5   LQKVLARA-GHGSRRELEALIRAGRVSVNGKVAVLGERLEDENAVVRIDGH--AVSAKAQ 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E+ I                       ++  + KP G                       
Sbjct: 62  EEVIC----------------------RVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G     K  I 
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGDVTEDK--IR 153

Query: 200 NWLLKKSHIGG--DYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
           N +       G   +  VV    +G N+  + + VI+     +     E Q  T
Sbjct: 154 NLVRGVQLEDGLARFEDVVYAGGEGMNH--TFYVVINEGRNREVRRLWESQETT 205


>gi|313884122|ref|ZP_07817888.1| pseudouridine synthase B, ribosomal large subunit [Eremococcus
           coleocola ACS-139-V-Col8]
 gi|312620569|gb|EFR31992.1| pseudouridine synthase B, ribosomal large subunit [Eremococcus
           coleocola ACS-139-V-Col8]
          Length = 236

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 36/252 (14%), Positives = 80/252 (31%), Gaps = 54/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +    H    +    ++I+  G+V V+ + V     +++    + +  V   L   
Sbjct: 2   ERLQKVMA-HAGIASRRKCEEIISQGRVTVNGQTVTELGFKVKQSDKIEVDQVPIYLEEP 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                    +V      D  + ++L                                 + 
Sbjct: 61  RYFLFYKPRNVISAVSDDKGRPVVLD--------------------------------YF 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               Q+     RLD +T+G+L++      A  L       ++ K+Y + +  I   +   
Sbjct: 89  KHIDQRIYPIGRLDFDTTGLLLLTNDGEFANQL--MHPRYQVDKVYVAKLDKILDKEALR 146

Query: 198 -IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF-AQKFCWLEMQPHTGRTHQL 255
            +   ++                  G   + +  KV+D    +K   +++  H G  HQ+
Sbjct: 147 KLERGIIID----------------GKKTSKARAKVLDTNLEKKMSVVQLTIHEGWNHQV 190

Query: 256 RVHALHMGCPIV 267
           +     +G  +V
Sbjct: 191 KKMFEAVGAHVV 202


>gi|260435028|ref|ZP_05788998.1| pseudouridine synthase [Synechococcus sp. WH 8109]
 gi|260412902|gb|EEX06198.1| pseudouridine synthase [Synechococcus sp. WH 8109]
          Length = 250

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 69/250 (27%), Gaps = 50/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ-VVRIPPVINALNHI 77
            RL +         +    ++ L++G+V VD       ++    Q  + +         +
Sbjct: 4   QRLQKLIAAA-GLCSRRRAEEWLQAGRVTVDGLVASVGDQADPQQQTIHVDGQPLPSRGV 62

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                            + + NKP G+               L    
Sbjct: 63  AR----------------------------VLLMNKPVGVICSCDDPQGRR--TVLDLLP 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                      RLD ++ G L++         LT            W  V G+P      
Sbjct: 93  PEHRAGLHPVGRLDADSHGALLLTDLGELTLKLTHPRYSHAKTYRVW--VKGVPPE---- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                     +   +   +  +      A    + +  +  +   LE++   GR  Q+R 
Sbjct: 147 ---------PVLDRWRRGLPLDGCLTRPA--RVRRLRTWGDR-SLLEIELREGRNRQIRR 194

Query: 258 HALHMGCPIV 267
            A  +G P++
Sbjct: 195 MAEALGHPVL 204


>gi|254361758|ref|ZP_04977893.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|153093293|gb|EDN74289.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
          Length = 355

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 83/246 (33%), Gaps = 43/246 (17%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   L++I+ +G+V VD K     +R+Q     +I    + +N +
Sbjct: 77  GEKLQKILARAGQG-SRRELEEIIAAGRVSVDGKMATLGDRVQVSSSTKIRIDGHLVNLM 135

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 136 PAQKEIC----------------------RVLMYYKPEGELCTRSDPEGRS--TVFDRLP 171

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              G +     RLD  TSG+L+       A  L      R +++ Y   V+G        
Sbjct: 172 RLSGARWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGN------- 222

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I + +L++   G      V+  +  AN+     KV+        W ++    GR  ++R 
Sbjct: 223 IDDAMLQRLRKG------VQLEDGPANFK--QIKVVGGTGLNQ-WFDVTLTEGRNREVRR 273

Query: 258 HALHMG 263
                G
Sbjct: 274 LWESQG 279


>gi|58699467|ref|ZP_00374204.1| ribosomal large subunit pseudouridine synthase D [Wolbachia
           endosymbiont of Drosophila ananassae]
 gi|58534014|gb|EAL58276.1| ribosomal large subunit pseudouridine synthase D [Wolbachia
           endosymbiont of Drosophila ananassae]
          Length = 98

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 25/106 (23%), Positives = 53/106 (50%), Gaps = 14/106 (13%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++++GQV++    +  N+ I       + P    + H+++     D S ++  + D +K 
Sbjct: 1   MIQNGQVKLLGIPIINNDHI-------VKPGEEYIVHLVQ----PDISTSIEPNYD-IKL 48

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR 145
            ++YED  I V +K +G++V  G+G   + D  L + +   G+ P 
Sbjct: 49  DIVYEDEDIIVLSKQSGLTVHPGAGT--NNDTLLNAVIAHLGKIPY 92


>gi|258544383|ref|ZP_05704617.1| ribosomal large subunit pseudouridine synthase B [Cardiobacterium
           hominis ATCC 15826]
 gi|258520387|gb|EEV89246.1| ribosomal large subunit pseudouridine synthase B [Cardiobacterium
           hominis ATCC 15826]
          Length = 260

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 56/176 (31%), Gaps = 29/176 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+ +W        +   ++  +R G++RV+ K  +   RI   + + +           
Sbjct: 6   ERIQKWLAARGLG-SRREIEGWIREGRLRVNGKLAELGQRISGYERLSLD---------- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    + ++   +  + IL+Y        +KP G                 +    
Sbjct: 55  ------GKPLRVSPEREAPRQILMY--------HKPPGEIC--SRNDPDGRPTVFRHLPK 98

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            +  +     RLD  T+G+L+       A  L        I++ YW  V G     
Sbjct: 99  LRQGRWVSIGRLDLNTAGLLLFTNDGELANRL--MHPSAEIEREYWVRVAGEVNED 152


>gi|239999104|ref|ZP_04719028.1| Pseudouridine synthase [Neisseria gonorrhoeae 35/02]
 gi|240013989|ref|ZP_04720902.1| Pseudouridine synthase [Neisseria gonorrhoeae DGI18]
 gi|240016430|ref|ZP_04722970.1| Pseudouridine synthase [Neisseria gonorrhoeae FA6140]
 gi|240113081|ref|ZP_04727571.1| Pseudouridine synthase [Neisseria gonorrhoeae MS11]
 gi|240115837|ref|ZP_04729899.1| Pseudouridine synthase [Neisseria gonorrhoeae PID18]
 gi|240121555|ref|ZP_04734517.1| Pseudouridine synthase [Neisseria gonorrhoeae PID24-1]
 gi|240125874|ref|ZP_04738760.1| Pseudouridine synthase [Neisseria gonorrhoeae SK-92-679]
 gi|240128384|ref|ZP_04741045.1| Pseudouridine synthase [Neisseria gonorrhoeae SK-93-1035]
 gi|268599167|ref|ZP_06133334.1| pseudouridine synthase [Neisseria gonorrhoeae MS11]
 gi|268601513|ref|ZP_06135680.1| pseudouridine synthase [Neisseria gonorrhoeae PID18]
 gi|268684473|ref|ZP_06151335.1| pseudouridine synthase [Neisseria gonorrhoeae SK-92-679]
 gi|268686783|ref|ZP_06153645.1| pseudouridine synthase [Neisseria gonorrhoeae SK-93-1035]
 gi|268583298|gb|EEZ47974.1| pseudouridine synthase [Neisseria gonorrhoeae MS11]
 gi|268585644|gb|EEZ50320.1| pseudouridine synthase [Neisseria gonorrhoeae PID18]
 gi|268624757|gb|EEZ57157.1| pseudouridine synthase [Neisseria gonorrhoeae SK-92-679]
 gi|268627067|gb|EEZ59467.1| pseudouridine synthase [Neisseria gonorrhoeae SK-93-1035]
          Length = 349

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/179 (16%), Positives = 56/179 (31%), Gaps = 30/179 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTTEQ 243


>gi|110835398|ref|YP_694257.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
 gi|110648509|emb|CAL17985.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
          Length = 229

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/251 (12%), Positives = 76/251 (30%), Gaps = 54/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD +   H   +     ++++  G V V+ + + K N +++  Q V +          
Sbjct: 1   MRLDYFLA-HSAGLTRKEAKQLISRGAVTVEGEAKPKANLQLRPDQAVTVHGERV----- 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                               + ++L++   +    +  G                L    
Sbjct: 55  ---------------QPPGHRYLMLHKPVDVVCSTEDPG------------HRTVLDLLP 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD++T+G++++      +  LT        +                 
Sbjct: 88  PELRAQVHPAGRLDRDTTGLVLLTSDGQWSHRLTSPNHACGKRYRVQC------------ 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
            A+ +  +         +++  +K    A      ++   +      +    GR HQ++ 
Sbjct: 136 -ADPVSDEDMQALREGVLLRGEDKPTLPAQ-----VERLDEACLL--LTIREGRYHQVKR 187

Query: 258 HALHMGCPIVG 268
                G  ++G
Sbjct: 188 MLAACGNKVLG 198


>gi|87119433|ref|ZP_01075330.1| ribosomal large subunit pseudouridine synthase B [Marinomonas sp.
           MED121]
 gi|86164909|gb|EAQ66177.1| ribosomal large subunit pseudouridine synthase B [Marinomonas sp.
           MED121]
          Length = 296

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/233 (15%), Positives = 72/233 (30%), Gaps = 35/233 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +         +   ++  +R G+V V+       +R++    +++            E
Sbjct: 5   LQKVLARAGQG-SRREMENRIREGRVLVNGDVATLGDRVKVTDTIKLDGY---------E 54

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            K+ ++  +        + +++Y        NKP G                       +
Sbjct: 55  VKVTEAGAS--------RRVIIY--------NKPEGEVC--TRKDPEGRPTVFDKLPKLR 96

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-ECIA 199
           G++     RLD  TSG+L+       A  L        I + Y   V G   +   E + 
Sbjct: 97  GERWIAVGRLDINTSGLLLFTTDGELANKL--MHPSTEIDREYLVRVMGEINDDHIETLK 154

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +L    +  ++  +V    +G N     F V     +      +    G  
Sbjct: 155 KGVLLDDGMA-NFTDIVDGGGEGINR---WFYVCVMEGRNREVRRLWESQGVK 203


>gi|59801084|ref|YP_207796.1| hypothetical protein NGO0657 [Neisseria gonorrhoeae FA 1090]
 gi|59717979|gb|AAW89384.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
          Length = 350

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/179 (16%), Positives = 56/179 (31%), Gaps = 30/179 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 96  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 152

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 153 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 187

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++
Sbjct: 188 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTTEQ 244


>gi|16767443|ref|NP_463058.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|161617332|ref|YP_001591297.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167991374|ref|ZP_02572473.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|168243582|ref|ZP_02668514.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|194448614|ref|YP_002048178.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|197263699|ref|ZP_03163773.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|34098651|sp|Q8ZKL1|RLUF_SALTY RecName: Full=Ribosomal large subunit pseudouridine synthase F;
           AltName: Full=rRNA pseudouridylate synthase F; AltName:
           Full=rRNA-uridine isomerase F
 gi|16422749|gb|AAL23017.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|161366696|gb|ABX70464.1| hypothetical protein SPAB_05187 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194406918|gb|ACF67137.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|197241954|gb|EDY24574.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|205330127|gb|EDZ16891.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|205337314|gb|EDZ24078.1| ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|261249293|emb|CBG27155.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. D23580]
 gi|267996496|gb|ACY91381.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301160685|emb|CBW20216.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. SL1344]
 gi|312915294|dbj|BAJ39268.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|321223059|gb|EFX48129.1| Ribosomal large subunit pseudouridine synthase F [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|323132528|gb|ADX19958.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|332991008|gb|AEF09991.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 289

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/164 (13%), Positives = 54/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G +V++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDIVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  --SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|305664746|ref|YP_003861033.1| pseudouridine synthase, Rsu [Maribacter sp. HTCC2170]
 gi|88707868|gb|EAR00107.1| pseudouridine synthase, Rsu [Maribacter sp. HTCC2170]
          Length = 245

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/245 (13%), Positives = 72/245 (29%), Gaps = 54/245 (22%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R++++      + +     K++  G+V ++ K  +   +I SG  VR+         +I 
Sbjct: 7   RINKYLSE-VGYCSRRAADKLIDQGRVTINGKVPEMGTKIISGDEVRVD------GELIS 59

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E K                     E      FNKP GI     + +         ++   
Sbjct: 60  EPK---------------------EKPVYLAFNKPIGIVCTTDTRVEKDNIIDFINYPK- 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
              +     RLD+ + G++ +         +  +      + +               + 
Sbjct: 98  ---RIFPIGRLDKPSQGLIFLTNDGDIVNKILRARNHHEKEYLV-------------TVD 141

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             + KK          + Q   G     +  +  +         ++    G   Q+R   
Sbjct: 142 KPINKK---------FLDQMASGVPILDTVTRKCEITEVNKYQFKIILTQGLNRQIRRMC 192

Query: 260 LHMGC 264
            ++G 
Sbjct: 193 EYLGY 197


>gi|238754970|ref|ZP_04616319.1| Ribosomal large subunit pseudouridine synthase B [Yersinia ruckeri
           ATCC 29473]
 gi|238706829|gb|EEP99197.1| Ribosomal large subunit pseudouridine synthase B [Yersinia ruckeri
           ATCC 29473]
          Length = 321

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/175 (18%), Positives = 56/175 (32%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ I++ G+V VD K          G  V + P           
Sbjct: 5   LQKVLARA-GHGSRREIEAIIQQGRVSVDGKVATL------GDRVDVTPST--------- 48

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +  LD  +     S+     +L        + KP G                       +
Sbjct: 49  KIRLDGRILPITESEEAVCRVL-------AYYKPEGELCTRSDPDG--RPTVFDRLPKLR 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 100 GSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDEK 152


>gi|261365463|ref|ZP_05978346.1| ribosomal large subunit pseudouridine synthase B [Neisseria mucosa
           ATCC 25996]
 gi|288566133|gb|EFC87693.1| ribosomal large subunit pseudouridine synthase B [Neisseria mucosa
           ATCC 25996]
          Length = 348

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/179 (16%), Positives = 56/179 (31%), Gaps = 30/179 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 94  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 150

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 151 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 185

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++
Sbjct: 186 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTTEQ 242


>gi|322795953|gb|EFZ18579.1| hypothetical protein SINV_04957 [Solenopsis invicta]
          Length = 363

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 56/298 (18%), Positives = 97/298 (32%), Gaps = 59/298 (19%)

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISV-QGGSGIAYHIDGFLKSWVDSKGQK-----PR 145
           + +D L   ++Y    I   NKP GIS+      +  H        V +         P 
Sbjct: 54  EFTDDLLKNVIYNADGIIAINKPYGISIANRKPNLNNHRMQLNHKIVGAVDYAVEDTLPY 113

Query: 146 LTHRLD-----------QETSGILVVARTRAAAQHLT-ESFRMRRIQKIYWSLVWGIPKN 193
           L   LD           +  SG+ V        Q L     R     + YW++   +P  
Sbjct: 114 LAKELDVPILIPCLGAEKYMSGVYVFGINDQVCQQLAIARNRTYGKYRKYWAITSRVPNE 173

Query: 194 KKECIANWLLKKSHIGGDY--VHVVKQNEKGANYAIS-----HFKVIDCFAQKF-CWLEM 245
            K      ++ K+ + GD   V V   +        +      +KVI          +E+
Sbjct: 174 IKGKYHLAMILKTSVLGDKKPVIVTSWSNNSVKRNETKIMNIDYKVISNSTHNLSSLIEI 233

Query: 246 QPHTGRTHQLRVHALHMGC-PIVGDHKYCANFKGNFTSPIQ-----------NKL----- 288
              + + + +R+ A  M   PI+GD+ + +  +    + ++            KL     
Sbjct: 234 IASSRKWNGIRLFASTMLYAPILGDNIHGSRVQEIMGTWLRVDPFSDSCWDLPKLNQELL 293

Query: 289 ---------------YLHARYMDLPH-PEGGRLQITAPLPAHMVKTWDSLGFKYDRNL 330
                          ++H + + L +  E   L I APL      T   L FK    +
Sbjct: 294 KLLDITPKQQEIIPAHIHLKSVHLVYGKEKKDLIIEAPLTEWFDWTCKQLKFKISNEV 351


>gi|228476152|ref|ZP_04060860.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           hominis SK119]
 gi|228269975|gb|EEK11455.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           hominis SK119]
          Length = 245

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 72/235 (30%), Gaps = 53/235 (22%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+ + V     +++S   V +                    + + 
Sbjct: 19  SRRKAETLITEGKVKVNGQVVTELGTKVKSSDTVEV------------------EGIKIE 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +           ED    +F KP  +     S         +  +      +     RLD
Sbjct: 61  Q-----------EDKIYILFYKPTQVIT---SVSDDRGRTVVTDYFKDLEARIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIG 209
            +TSG+L++         +T       IQK Y + + G    +  K       L+     
Sbjct: 107 YDTSGLLLLTNDGEFTNLMT--HPRYHIQKKYVAKLKGYLMREEVKSLEQGIELEDGFTQ 164

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              V +  QN++                +    +E+    GR  Q+R    H   
Sbjct: 165 PAQVKIKNQNKE----------------KNTTLVEITISEGRNRQVRRMFEHFNH 203


>gi|332522623|ref|ZP_08398875.1| pseudouridylate synthase [Streptococcus porcinus str. Jelinkova
           176]
 gi|332313887|gb|EGJ26872.1| pseudouridylate synthase [Streptococcus porcinus str. Jelinkova
           176]
          Length = 239

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 92/245 (37%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ +L++ +V V+ K+     +       +I P ++ +    
Sbjct: 1   MRLDKFLAETGFG-SRTQVKSLLKTKKVCVNGKKESQAKK-------QINPNLDRVEVEG 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E                    +LYE+   Y+ NKP G+       +   +   L +   
Sbjct: 53  QE--------------------VLYEEFVYYMLNKPKGVVSATQDKVHQTVLDLLDATAK 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K  +     RLD++T G+L++      A  L      + + K+Y + V G+  N+   I
Sbjct: 93  QK--EVFPVGRLDKDTHGLLLLTNNGNLAHRL--LSPKKHVNKVYVADVDGLMTNQD--I 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                        +   +  ++     A+     +D + +    +++    G+ HQ++  
Sbjct: 147 EA-----------FKKGIHLSDHQCQPALLEILALD-YEKSQSRVKIVIKEGKFHQVKRM 194

Query: 259 ALHMG 263
            L  G
Sbjct: 195 VLACG 199


>gi|294139593|ref|YP_003555571.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293326062|dbj|BAJ00793.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 236

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/254 (15%), Positives = 86/254 (33%), Gaps = 52/254 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+  +    I   +++ +L   +VRVD    K            I  +++  +H+  
Sbjct: 7   RLDRFLSSELK-IKRKDIRLMLAQNRVRVDGIVAK-----------DIQQLVDEFSHVSV 54

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +  +L ++                      + NKP G+           +   L     S
Sbjct: 55  DDAVLKNNRPS-----------------YVMLNKPVGVVSATKDDKHKTVIDLLDHPAKS 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +     +  RLD  TSG++++      ++ L       +++K Y           +  + 
Sbjct: 98  E---LHIVGRLDLNTSGLMLLTNDGRWSRKL--MSPESKVEKRY-----------RVTLQ 141

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           N L  +           +  +     A      ++  ++     E+    G+ HQ++   
Sbjct: 142 NPLSTEYIDAFAKGFYFEFEDITTQAAK-----LEIISEHIA--EVTLTEGKYHQIKRMF 194

Query: 260 LHMGCPIVGDHKYC 273
                P++G H+Y 
Sbjct: 195 GRFRNPVIGLHRYS 208


>gi|170768335|ref|ZP_02902788.1| ribosomal large subunit pseudouridine synthase B [Escherichia
           albertii TW07627]
 gi|170123101|gb|EDS92032.1| ribosomal large subunit pseudouridine synthase B [Escherichia
           albertii TW07627]
          Length = 291

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   + ++   +
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLVSVRESV 63

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +                        +  ++  + KP G                      
Sbjct: 64  E------------------------QICRVLAYYKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDTK 152


>gi|50121219|ref|YP_050386.1| 23S rRNA pseudouridylate synthase B [Pectobacterium atrosepticum
           SCRI1043]
 gi|49611745|emb|CAG75194.1| putative RNA pseudouridylate synthase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 294

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 59/175 (33%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ I+++G+V VD K     +R++    V     I    H++  
Sbjct: 5   LQKVLARA-GHGSRREIESIIQAGRVSVDGKIATLGDRVE----VTKATKIRIDGHVVTV 59

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           ++  ++                     + V+ KP G                       +
Sbjct: 60  KETEETVCR------------------VLVYYKPEGELC--TRNDPDGRPTVFDRLPKIQ 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L        +++ Y   V+G   ++K
Sbjct: 100 GSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSHEVEREYAVRVFGEVDDEK 152


>gi|260494116|ref|ZP_05814247.1| pseudouridylate synthase [Fusobacterium sp. 3_1_33]
 gi|260198262|gb|EEW95778.1| pseudouridylate synthase [Fusobacterium sp. 3_1_33]
          Length = 226

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/246 (15%), Positives = 87/246 (35%), Gaps = 54/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++K++ + ++ V+                     I+A ++I 
Sbjct: 1   MRLDKFLVECGIG-SRKEVKKLISNNEITVNG-----------------MSNISAKDNID 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +   I++ +    +          Y+  + Y+ NK +G            +   L  WV 
Sbjct: 43  ENSDIIEYNEEKLE----------YKKFRYYIMNKKSGYITATEDFKENTVMDLLPEWVI 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K   P    RLD++T G+L+     +   + L+    + ++  +               
Sbjct: 93  KKDLAP--VGRLDKDTEGLLLFTNDGKLNHKLLSPKNHVDKVYYVEI------------- 137

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                  K++I  + +  ++Q     NY IS    ++  +    +  +    G+ HQ++ 
Sbjct: 138 -------KNNISDEDIFKLEQGVDIGNY-ISQPAKVEKISDNKIY--LTIKEGKFHQIKK 187

Query: 258 HALHMG 263
               + 
Sbjct: 188 MLEAIN 193


>gi|56416014|ref|YP_153089.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197364941|ref|YP_002144578.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|56130271|gb|AAV79777.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197096418|emb|CAR62024.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
          Length = 289

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/164 (13%), Positives = 54/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G +V++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDIVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  --SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|238019398|ref|ZP_04599824.1| hypothetical protein VEIDISOL_01262 [Veillonella dispar ATCC 17748]
 gi|237864097|gb|EEP65387.1| hypothetical protein VEIDISOL_01262 [Veillonella dispar ATCC 17748]
          Length = 242

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 86/251 (34%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++  +     +    ++++  G+V+V+ ++V                         
Sbjct: 2   ERLQKFIAS-CGVASRRKAEELITEGKVQVNGRKVT------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 +  V +    D +K    +L  E    Y+ NKP G+     S         +  
Sbjct: 37  ------ELGVKIDPQKDKVKVNGQLLAQEKPVYYLLNKPKGVIT---SVSDPQGRETVLD 87

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           ++ ++ ++     RLD  T G+L++      AQ+LT     + ++K Y   + G  +++ 
Sbjct: 88  YIKNESKRIYPIGRLDLYTEGLLLLTNDGELAQNLT--HPSKGVEKTYEVRIKGRVRDED 145

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +    +K               E G     +   +          +E+  H GR  Q+
Sbjct: 146 LQVIANGVKL--------------EDGMTAPATIVDLGFDDHNGVHEVEITIHEGRNRQV 191

Query: 256 RVHALHMGCPI 266
           R    H G  I
Sbjct: 192 RRMFEHFGYRI 202


>gi|229020203|ref|ZP_04176976.1| hypothetical protein bcere0030_46950 [Bacillus cereus AH1273]
 gi|229026429|ref|ZP_04182786.1| hypothetical protein bcere0029_47060 [Bacillus cereus AH1272]
 gi|228734892|gb|EEL85530.1| hypothetical protein bcere0029_47060 [Bacillus cereus AH1272]
 gi|228741099|gb|EEL91324.1| hypothetical protein bcere0030_46950 [Bacillus cereus AH1273]
          Length = 165

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNAILSEGDSISIC 164


>gi|19746361|ref|NP_607497.1| 16S pseudouridylate synthetase [Streptococcus pyogenes MGAS8232]
 gi|19748557|gb|AAL97996.1| putative 16S pseudouridylate synthetase [Streptococcus pyogenes
           MGAS8232]
          Length = 254

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/180 (15%), Positives = 56/180 (31%), Gaps = 38/180 (21%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALN 75
           NMRLD+         +   ++K++++  V VD    +     +  G Q++ +        
Sbjct: 16  NMRLDKLL-EGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQR---- 70

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                                    + +      + NKP+G+           I   L  
Sbjct: 71  -------------------------VTHPKHSYIILNKPSGVVSAKKDTNYLTIIDQLAE 105

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             + K        RLD++T G++++        + L        + K Y   V G+    
Sbjct: 106 --EDKSPDLYPVGRLDRDTEGLVLLTDNGPLGFRMLH---PSHHVSKTYLVTVNGLLAED 160


>gi|242242766|ref|ZP_04797211.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242233902|gb|EES36214.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 245

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 38/251 (15%), Positives = 80/251 (31%), Gaps = 54/251 (21%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
           E  RL +       + +    + ++  G+V+V+ + V    +++    +V +        
Sbjct: 4   EQERLQKRIAKS-GYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVD------- 55

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                                    +  ED    +F KP  +     S         +  
Sbjct: 56  ----------------------GIKIEQEDKIYILFYKPTQVIT---SVSDDRGRRVVTD 90

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KN 193
           + D    +     RLD +TSG+L++         +T       I+K Y + + G    + 
Sbjct: 91  YFDDLESRIYPVGRLDYDTSGVLLLTNDGEFTNLMT--HPRYHIKKKYIAKLKGYLMREE 148

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
            K+      L+  +     V + KQ+++                +    +E+    GR  
Sbjct: 149 IKQLEKGIELEDGYTQPAQVKIKKQDKE----------------KNTTLVEITISEGRNR 192

Query: 254 QLRVHALHMGC 264
           Q+R    + G 
Sbjct: 193 QVRRMFEYFGH 203


>gi|283787307|ref|YP_003367172.1| ribosomal large subunit pseudouridine synthase F [Citrobacter
           rodentium ICC168]
 gi|282950761|emb|CBG90437.1| ribosomal large subunit pseudouridine synthase F [Citrobacter
           rodentium ICC168]
          Length = 291

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/168 (13%), Positives = 54/168 (32%), Gaps = 34/168 (20%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           + ++RL+++       I +     + +  G V ++ KR    +++  G VV++   +   
Sbjct: 4   DASIRLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVMPGDVVKVNGRLIEP 61

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                                        E+      NKP GI          +I  F+ 
Sbjct: 62  REA--------------------------EELVFIALNKPVGIVSTTEDSERDNIVDFVN 95

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  ++     RLD+++ G++ +         +  +      + +
Sbjct: 96  H-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|266622691|ref|ZP_06115626.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           hathewayi DSM 13479]
 gi|288865556|gb|EFC97854.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           hathewayi DSM 13479]
          Length = 266

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/251 (11%), Positives = 71/251 (28%), Gaps = 48/251 (19%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
            E+ +RL+++        +     +++  G+V V  +      +I+ G+ V       A 
Sbjct: 2   GEDGIRLNKFLSGA-GICSRREADRLIEEGKVTVGGRTAVPGQKIKKGETVVCNGRTIAA 60

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFL 133
                E+K                         +   +KP GI         A +I   +
Sbjct: 61  GSRGAEKKPERV---------------------LLAVHKPCGIVCTTSDKDRAPNIVDMV 99

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                    +     RLD+E+ G++++         +         + + W         
Sbjct: 100 -----DCPVRIYPAGRLDKESEGLILMTNQGDLVNRMMRGSSGHEKEYLVW--------- 145

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                         +  +++  +++        ++  K             +    G   
Sbjct: 146 ----------IDRPVKPEFIQKMRKGVFLPELDVTT-KPCFAEKTGEKSFRIVLTQGLNR 194

Query: 254 QLRVHALHMGC 264
           Q+R     +GC
Sbjct: 195 QIRRMCEQLGC 205


>gi|240080549|ref|ZP_04725092.1| Pseudouridine synthase [Neisseria gonorrhoeae FA19]
 gi|240118135|ref|ZP_04732197.1| Pseudouridine synthase [Neisseria gonorrhoeae PID1]
 gi|240123684|ref|ZP_04736640.1| Pseudouridine synthase [Neisseria gonorrhoeae PID332]
 gi|260440347|ref|ZP_05794163.1| Pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|268603851|ref|ZP_06138018.1| pseudouridine synthase [Neisseria gonorrhoeae PID1]
 gi|268682316|ref|ZP_06149178.1| pseudouridine synthase [Neisseria gonorrhoeae PID332]
 gi|268587982|gb|EEZ52658.1| pseudouridine synthase [Neisseria gonorrhoeae PID1]
 gi|268622600|gb|EEZ55000.1| pseudouridine synthase [Neisseria gonorrhoeae PID332]
          Length = 349

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/179 (16%), Positives = 56/179 (31%), Gaps = 30/179 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGGLTTEQ 243


>gi|123442465|ref|YP_001006444.1| 23S rRNA pseudouridylate synthase B [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122089426|emb|CAL12274.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           enterocolitica subsp. enterocolitica 8081]
          Length = 309

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/163 (18%), Positives = 57/163 (34%), Gaps = 26/163 (15%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++ I++ G+V VD K  K  +R++  Q  +I    + L+    E+ +         
Sbjct: 8   SRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLLSIKESEEAVC-------- 59

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                         ++  + KP G                       +G +     RLD 
Sbjct: 60  --------------RVLAYYKPEGELC--TRNDPEGRPTVFDRLPKLRGSRWVAVGRLDV 103

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 104 NTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQIDDEK 144


>gi|602963|gb|AAB59990.1| ORF4 [Escherichia coli str. K-12 substr. W3110]
          Length = 243

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|325111054|ref|YP_004272122.1| pseudouridine synthase Rsu [Planctomyces brasiliensis DSM 5305]
 gi|324971322|gb|ADY62100.1| pseudouridine synthase Rsu [Planctomyces brasiliensis DSM 5305]
          Length = 368

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 88/248 (35%), Gaps = 55/248 (22%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RL ++  +     +    ++++R+G+V VD   V+       G  + + P          
Sbjct: 31  RLQKFLASAGLG-SRRQCEELIRTGRVTVDGLPVE-----NPG--INVNP---------- 72

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKSWV 137
                     L +  ++    L  E  K +V NKP G+       +G    ID F K  V
Sbjct: 73  ----------LKQVVEYDGERLKPERLKYFVLNKPKGVLCTNHDPAGRTRVIDLFAKERV 122

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
                +     RLD+++ G+L+V      A  L       RI + Y   V G P N+K +
Sbjct: 123 -----RLFPVGRLDEDSEGLLIVTNDGDLANQLA--HPRYRIYRTYRVQVAGFPTNEKLQ 175

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + + +  +   G   V   K   K    A               +LE+    G   ++R
Sbjct: 176 QLRDGIFFRE--GKFQVISAKFAGKQGKSA---------------FLEIVLGQGHNREIR 218

Query: 257 VHALHMGC 264
                +G 
Sbjct: 219 RLFARIGH 226


>gi|253688397|ref|YP_003017587.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251754975|gb|ACT13051.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 294

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/175 (17%), Positives = 60/175 (34%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ I+++G+V VD K     +R++    V     I    H++  
Sbjct: 5   LQKVLARA-GHGSRREIEGIIQAGRVSVDGKVATLGDRVE----VTKATKIRIDGHVVTV 59

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           ++  ++                     + V+ KP G                       +
Sbjct: 60  KETEETVCR------------------VLVYYKPEGELC--TRNDPDGRPTVFDRLPKIQ 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 100 GSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGEVDDEK 152


>gi|330830231|ref|YP_004393183.1| 23S rRNA pseudouridine synthase F [Aeromonas veronii B565]
 gi|328805367|gb|AEB50566.1| 23S rRNA pseudouridine synthase F [Aeromonas veronii B565]
          Length = 338

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/167 (16%), Positives = 60/167 (35%), Gaps = 34/167 (20%)

Query: 17  ENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E+MRL+++       I +     + +  G V ++ KR    +++Q G +V++        
Sbjct: 5   ESMRLNKYISE--SGICSRREADRFIEQGHVFINGKRAGIGDQVQVGDLVKVNGQ----- 57

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
             + E +  DS V                   +   NKP GI     +G   +I  F+  
Sbjct: 58  --VIEPREADSLV-------------------LIALNKPVGIVSTTEAGEKDNIVDFVNH 96

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                  +     RLD+++ G++ +         +  +      + +
Sbjct: 97  -----STRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|124022690|ref|YP_001016997.1| pseudouridylate synthase specific to ribosomal small subunit
           [Prochlorococcus marinus str. MIT 9303]
 gi|123962976|gb|ABM77732.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Prochlorococcus marinus str. MIT 9303]
          Length = 244

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 82/250 (32%), Gaps = 50/250 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            RL +        + +  + +++L   +V ++    K  ++               L+ I
Sbjct: 4   QRLQKLIAA--SGLCSRRHAEQLLLQERVTLNGHLAKLGDK-----------ADPELDKI 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             + ++L+S+                   ++ +FNKPAG+         +          
Sbjct: 51  SVDGRVLNSNTET----------------RVLLFNKPAGVIT--SCHDPHGRVTVFSLLP 92

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           D   +      RLD ++ G L++         LT         K Y  LV G P      
Sbjct: 93  DKLCKGLHPVGRLDADSRGALLITNRGELTLRLTHPRYAH--DKTYQVLVEGKP------ 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                     +   + H V  + K    A    +++     +   L++    GR  Q+R 
Sbjct: 145 -------SPLVLSSWRHGVMLDGKTTLPA--ELELLQSHPSQ-SLLKVVLREGRNRQIRR 194

Query: 258 HALHMGCPIV 267
            A  +G P++
Sbjct: 195 VAEQLGHPVL 204


>gi|223999397|ref|XP_002289371.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220974579|gb|EED92908.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 543

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/199 (15%), Positives = 74/199 (37%), Gaps = 14/199 (7%)

Query: 11  VVENDEEN-MRLDRWFKNH----YPHI--NFVNLQKILRSGQVRVDKKRVKFNNR-IQSG 62
            V  +  +  RL +W              +    +  +++G+V V++  V  ++R ++  
Sbjct: 186 TVGEEFADSKRL-KWLCRQQNFALSKFIRSKSQCEDAIKNGRVFVNRCVVMDSSRIVREN 244

Query: 63  QVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG 122
            V+ +      ++         D+  N ++    +K +L+ +D  + V +KP G+   G 
Sbjct: 245 DVITLVEEYALVSTSTNNINANDNDSNSSEKVKVVKELLINKDVTLVVVHKPVGMRCVGS 304

Query: 123 SGIAYHIDGFLKSW---VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                      + +       G    +  +LD  ++G+ ++  + +            + 
Sbjct: 305 FSHTTLEMITKRQYETIRGVNGLSCNVISKLDTGSAGLCLLTVSSSTVD--NGILDSVKA 362

Query: 180 QKIYWSLVWGIPKNKKECI 198
              +  LV G P+N K  +
Sbjct: 363 VYTFTVLVHGCPENWKSGV 381


>gi|332093194|gb|EGI98254.1| ribosomal small subunit pseudouridine synthase A [Shigella boydii
           5216-82]
          Length = 231

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTNDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|55822523|ref|YP_140964.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus CNRZ1066]
 gi|55738508|gb|AAV62149.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus CNRZ1066]
          Length = 239

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 79/247 (31%), Gaps = 51/247 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD+          +   ++K++RS QV VD                 +    + LN  
Sbjct: 1   MRLDKLLGQ--SGYGSRNQVKKLIRSRQVYVDG----------------VLADRDNLNVD 42

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
              Q I+ S   L    +             Y+ NKP+G+          H         
Sbjct: 43  ASLQTIMVSGKELEHAPEV-----------YYLMNKPSGVVS--ARKDKEHQTVIDLIRP 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           + + +      RLD++T G++++          L          + + +  + +  N   
Sbjct: 90  EDRREGLYPVGRLDRDTEGLVLITNNGPLGFAMLH--------PRYHVAKTYYVEVNDIL 141

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                   +S        VV ++      A    +V+   + K C   +    G+ HQ++
Sbjct: 142 GPDAPAFFESG-------VVFEDGTVCKSA--QLEVLSSASDKSC-ARVTISEGKFHQVK 191

Query: 257 VHALHMG 263
              L  G
Sbjct: 192 KMFLAYG 198


>gi|323455461|gb|EGB11329.1| hypothetical protein AURANDRAFT_61729 [Aureococcus anophagefferens]
          Length = 294

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 81/249 (32%), Gaps = 43/249 (17%)

Query: 27  NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDS 86
             +P ++       + +G+VRV+ +  K + R++SG  + +         +  +   L+ 
Sbjct: 30  RCFPELSRRAADAAVAAGRVRVNGETAKPSLRLRSGDTLALDGKKRDWEALAAK---LEG 86

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY--HIDGFLKSWVDSKGQKP 144
              L                  Y ++KP G++    +           LK      G++ 
Sbjct: 87  GGGLE----------------YYAYHKPEGVACTTDANDRRSLRRAPALKKLFAG-GKRI 129

Query: 145 RLTHRLDQETSGILVVARTRAAA-QHLTESFRMRRIQKIYWSLVWGIPKNKKEC----IA 199
               RLD ++ G++V+    AAA   L  S ++ ++ ++                   IA
Sbjct: 130 FPAGRLDVDSCGLVVLTNDGAAADAALQPSSKLAKVYEVELDRRAADDDVAALAAGVEIA 189

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L + S             EK            D         E     GR  QLR  A
Sbjct: 190 TPLQRGSK-----------AEKTGKTLPCDVARGDGRGLVITLAE-----GRNRQLRRMA 233

Query: 260 LHMGCPIVG 268
             +G  + G
Sbjct: 234 EALGYEVTG 242


>gi|254467319|ref|ZP_05080730.1| ribosomal large subunit pseudouridine synthase E [Rhodobacterales
           bacterium Y4I]
 gi|206688227|gb|EDZ48709.1| ribosomal large subunit pseudouridine synthase E [Rhodobacterales
           bacterium Y4I]
          Length = 217

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/162 (20%), Positives = 59/162 (36%), Gaps = 8/162 (4%)

Query: 108 IYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           +  FNKP  +  Q   SG        L  ++D  G       RLD+++ G+L++      
Sbjct: 4   LIRFNKPYDVLPQFTDSGSQDSPRATLSKYIDCPG--VYAAGRLDRDSEGLLLLTDNGRL 61

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
              +T+     ++ K YW  V GIP  +        ++          V    E    +A
Sbjct: 62  QAWITD--PKHKMDKTYWVQVEGIPDQEALKNLAEGVELKDGITRPAKVRLMPEPTGLWA 119

Query: 227 ISH-FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +   +V         W+ +    GR  Q+R     +G P +
Sbjct: 120 RTPPVRVRKTVPD--SWIALTLREGRNRQVRRMTAAVGHPTL 159


>gi|59711487|ref|YP_204263.1| 16S rRNA pseudouridylate 516 synthase [Vibrio fischeri ES114]
 gi|197335138|ref|YP_002155642.1| ribosomal small subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
 gi|59479588|gb|AAW85375.1| 16S rRNA pseudouridylate 516 synthase [Vibrio fischeri ES114]
 gi|197316628|gb|ACH66075.1| ribosomal small subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
          Length = 234

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 75/246 (30%), Gaps = 52/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRLD++              +I++SG V VD  + K  + ++     V         +  
Sbjct: 1   MRLDKFLCETL-GATRKEATRIIKSGTVTVDGVKTKVTSVKVTDDSTVEWDGRELKFHGP 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                               + I+L++       ++    S    +              
Sbjct: 60  --------------------RYIMLFKPDGYVCSHED---STHPSALSLLDEVNL----- 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +K     RLD +T+G++++      +  +T   R        W             
Sbjct: 92  ----EKLHFAGRLDVDTTGLVLITDDGQWSHKITSPKRKCAKTYRVW------------- 134

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +A+ +        +    +K  +     A     V++   ++   L +  H G+ HQ++ 
Sbjct: 135 LADPIGADYAEKLEAGIQLKSEKDLTMPA-----VMEIVDEEEHELLLTIHEGKYHQVKR 189

Query: 258 HALHMG 263
               +G
Sbjct: 190 MFAALG 195


>gi|238795690|ref|ZP_04639204.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           mollaretii ATCC 43969]
 gi|238720416|gb|EEQ12218.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           mollaretii ATCC 43969]
          Length = 290

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/165 (13%), Positives = 55/165 (33%), Gaps = 34/165 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR     ++  G VV++        + 
Sbjct: 7   IRLNKYISE--SGICSRRDADRYIEQGNVFINGKRAAVGVQVFPGDVVKVNGQTIEPRNE 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     ED  +   NKP G+      G   +I  F+    
Sbjct: 65  --------------------------EDLVLIALNKPVGVISTTEDGEQNNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               ++     RLD+++ G++++         +  +      + +
Sbjct: 97  ---SKRVFPIGRLDKDSQGLILLTNHGDLVNKILRAGNDHEKEYV 138


>gi|298368371|ref|ZP_06979689.1| ribosomal large subunit pseudouridine synthase B [Neisseria sp.
           oral taxon 014 str. F0314]
 gi|298282374|gb|EFI23861.1| ribosomal large subunit pseudouridine synthase B [Neisseria sp.
           oral taxon 014 str. F0314]
          Length = 348

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 48/156 (30%), Gaps = 28/156 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 95  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 151

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 152 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 186

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
             +   +     RLD  TSG+L++  +    Q    
Sbjct: 187 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAH 222


>gi|296271690|ref|YP_003654321.1| RNA-binding S4 domain-containing protein [Arcobacter nitrofigilis
           DSM 7299]
 gi|296095865|gb|ADG91815.1| RNA-binding S4 domain protein [Arcobacter nitrofigilis DSM 7299]
          Length = 266

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 46/255 (18%), Positives = 82/255 (32%), Gaps = 43/255 (16%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           E  EEN RL+++   H    +      I+  G+V+V+KK +   + ++    +V I    
Sbjct: 6   EAKEENTRLNKFIS-HNSKYSRREADAIIAEGRVKVNKKTITDLSTKVLDSDIVAIDNKP 64

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK---IYVFNKPAGISVQGGSGIAYH 128
                                        + +E +K   + V+NKP G  V         
Sbjct: 65  -----------------------------IKFEKNKMYTVLVYNKPKGELVTKNDPQGRR 95

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
               +   + +K +      RLD  + G+L++  +   A  L  S   R  +      + 
Sbjct: 96  ---IIFDTLGAKYKHFLPIGRLDYASEGVLLLTDSVDVANGLMHSDLQRVYKIKVSGPI- 151

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
                 K+     L                  K  ++A      ID     F  L++   
Sbjct: 152 -----NKQVEDAMLHGLELEDATKGAWKDSKVKSMSFAPFLGYKIDSVKDTFSKLKVAIT 206

Query: 249 TGRTHQLRVHALHMG 263
            G+  +LR    H G
Sbjct: 207 EGKNRELRRFFAHFG 221


>gi|163841326|ref|YP_001625731.1| ribosomal large subunit pseudouridine synthase B [Renibacterium
           salmoninarum ATCC 33209]
 gi|162954802|gb|ABY24317.1| ribosomal large subunit pseudouridine synthase B [Renibacterium
           salmoninarum ATCC 33209]
          Length = 345

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 50/253 (19%), Positives = 86/253 (33%), Gaps = 48/253 (18%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           D E +RL +         +    ++++  G+V VD   V      + G  V +   + ++
Sbjct: 102 DPEGVRLQKVMAAA-GVASRRVCEEMIEDGRVEVDGSIVT-----ELGLRVNVETAVISV 155

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFL 133
           + I                   LK  ++Y      VFNKP G +S         +I  FL
Sbjct: 156 DGI----------------RLQLKENMIY-----LVFNKPRGVVSTMDDPEGRRNISDFL 194

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           K+      ++     RLDQ T G+L++      A  LT       + K Y     G  + 
Sbjct: 195 KNKYAH--ERLFHVGRLDQATEGLLLLTNDGELANRLT--HPSYEVPKTYLVQTKGPMET 250

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                          G           +     I  FK++D        +E+  H+G+  
Sbjct: 251 ---------------GVSNQMRKGIELEDGVTKIDAFKLVDSTP-GHVLVEVVLHSGKNR 294

Query: 254 QLRVHALHMGCPI 266
            +R     +G P+
Sbjct: 295 IVRRLFDAVGYPV 307


>gi|238791770|ref|ZP_04635407.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           intermedia ATCC 29909]
 gi|238728874|gb|EEQ20391.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           intermedia ATCC 29909]
          Length = 290

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/246 (15%), Positives = 73/246 (29%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +  +  + +  G V ++ KR    +++ SG VV++           
Sbjct: 8   RLNKYIGE--SGICSRRDADRYIEQGHVFINGKRAAVGDQVYSGDVVKVN---------- 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q I   + N               D  +   NKP GI      G + +I  F+     
Sbjct: 56  -GQLIEPRNEN---------------DLVLIALNKPVGIISTTEEGESDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD+++ G++ +         +  +      + +                
Sbjct: 97  --SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL--------------VT 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N  + +  I G    V           +S                +    G   Q+R  
Sbjct: 141 VNKPVTEEFILGLGAGVPMMGTVTKKCKVSKV--------ATFVFNITLVQGLNRQIRRM 192

Query: 259 ALHMGC 264
             H G 
Sbjct: 193 CKHFGY 198


>gi|261821582|ref|YP_003259688.1| 23S rRNA pseudouridylate synthase B [Pectobacterium wasabiae
           WPP163]
 gi|261605595|gb|ACX88081.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
          Length = 294

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/175 (17%), Positives = 60/175 (34%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ I+++G+V VD K     +R++    V     I    H++  
Sbjct: 5   LQKVLARA-GHGSRREIEGIIQAGRVSVDGKVATLGDRVE----VTKATKIRIDGHVVTV 59

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           ++  ++                     + V+ KP G                       +
Sbjct: 60  KETEETVCR------------------VLVYYKPEGELC--TRNDPDGRPTVFDRLPKIQ 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 100 GSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGEVDDEK 152


>gi|153939039|ref|YP_001391068.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum F str. Langeland]
 gi|152934935|gb|ABS40433.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum F str. Langeland]
 gi|295319117|gb|ADF99494.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum F str. 230613]
          Length = 236

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/252 (16%), Positives = 83/252 (32%), Gaps = 55/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
            RL ++  +     +    + I+  G+V V+  ++K    +I SG  ++++   I     
Sbjct: 3   ERLQKYMAS-CGVASRRKCEDIILEGRVEVNGIKIKELGTKIISGKDIIKVDGNIIEPE- 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKS 135
                                      E+    + NKP G             I   +K 
Sbjct: 61  ---------------------------ENKIYILLNKPKGYVCTAKDEKGRKTILDLVK- 92

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 ++     RLD +TSGI+++         +      +   K Y + V G  K   
Sbjct: 93  ----IKERIYPIGRLDMDTSGIIILTNDGEIYNKIIHPKFEK--IKTYKAKVKGTIKKDH 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 L KK    GDY+            A +  +++    +    + ++ H G+  Q+
Sbjct: 147 IE----LFKKGIDIGDYI-----------TAPATLEILK-INKDTSEIIIKIHEGKNRQV 190

Query: 256 RVHALHMGCPIV 267
           R     +G  ++
Sbjct: 191 RRMCKSIGHAVI 202


>gi|229163944|ref|ZP_04291884.1| hypothetical protein bcere0009_47070 [Bacillus cereus R309803]
 gi|228619565|gb|EEK76451.1| hypothetical protein bcere0009_47070 [Bacillus cereus R309803]
          Length = 165

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNAILSEGDSISIC 164


>gi|255654429|ref|ZP_05399838.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-23m63]
          Length = 141

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/154 (16%), Positives = 53/154 (34%), Gaps = 31/154 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D+   N   + +   ++K  + G V V+   V        G  V             
Sbjct: 5   QRIDKILSN-LGYGSRSEIKKYCKQGSVVVNGSEVS-----NPGTQVD-----------T 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  +IL +              ++Y +    + NKP G            +   +   + 
Sbjct: 48  ENDEILFNGEE-----------VIYREYIYLMMNKPDGYVSATTDKYDPTVLDLID--LS 94

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLT 171
               +P    RLD++T G+LV+    + + + L+
Sbjct: 95  YLAFEPFPVGRLDKDTEGLLVLTNDGKLSHRVLS 128


>gi|323497601|ref|ZP_08102618.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio sinaloensis
           DSM 21326]
 gi|323317350|gb|EGA70344.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio sinaloensis
           DSM 21326]
          Length = 321

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 61/179 (34%), Gaps = 30/179 (16%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNH 76
           N +L +       H +   L+ ++++G+V V+    K   R++    VVRI         
Sbjct: 2   NEKLQKVLARA-GHGSRRELEALIKAGRVSVNGIVAKLGERLEDENAVVRIDGH------ 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                     +V+     + +  +L Y         KP G                    
Sbjct: 55  ----------TVSAKAQEEVICRVLAY--------YKPEGELC--TRHDPEGRRTVFDRL 94

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K
Sbjct: 95  PKIRGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGDVTEQK 151


>gi|255525211|ref|ZP_05392153.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255511074|gb|EET87372.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 234

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 48/271 (17%), Positives = 88/271 (32%), Gaps = 58/271 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++        +    ++I+   +V+V+ K V                       I 
Sbjct: 3   ERLQKYMAA-CGIASRRKCEEIILQARVKVNGKIVN-----------------ELGVKID 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
           +E+ ++     L K           ++      NKP G +S          I   +    
Sbjct: 45  EEKDLVTLDGKLIKKE---------KNKVYIALNKPKGYVSTVKDERGRKTILDLV---- 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +TSG++++         +    + +   KIY +L+ GIP      
Sbjct: 92  -DVTERIYPIGRLDYDTSGLILLTNDGDIYNKIIHPKQEK--NKIYIALIKGIPTEND-- 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                +KK  IG +    V    K           I    + +C +E+  H GR  Q+R 
Sbjct: 147 -----IKKFEIGINIDGYVTAPAK---------FKIIKKFKDYCEVEIIIHEGRNRQIRK 192

Query: 258 HALHMGCPIV-------GDHKYCANFKGNFT 281
               +   ++       GD K      G + 
Sbjct: 193 MCDFINHQVLELKRIQIGDIKLGNLPLGKWR 223


>gi|229014151|ref|ZP_04171272.1| hypothetical protein bmyco0001_45560 [Bacillus mycoides DSM 2048]
 gi|228747105|gb|EEL96987.1| hypothetical protein bmyco0001_45560 [Bacillus mycoides DSM 2048]
          Length = 165

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RIDKVLSTYISDWSRALIVDKIKNGHIQLNGQQMKPNKTLSEGDYISIC 164


>gi|224585957|ref|YP_002639756.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|224470485|gb|ACN48315.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
          Length = 289

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/165 (13%), Positives = 55/165 (33%), Gaps = 34/165 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +     + +  G V ++ KR    +++ +G VV++   +      
Sbjct: 7   IRLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIESREA 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     +D  +   NKP GI      G   +I  F+    
Sbjct: 65  --------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  ---SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|170727048|ref|YP_001761074.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169812395|gb|ACA86979.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 235

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/162 (24%), Positives = 65/162 (40%), Gaps = 13/162 (8%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I +FNKP  +  Q            LK ++   G       RLD+++ G+L++       
Sbjct: 53  IVLFNKPFDVLCQ---FTDEQGRQTLKDFIPIPG--VYAAGRLDRDSEGLLLLTNDGKLQ 107

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             LTE    ++  K YW+ V G P   +      LL+K     D + +  +    +   +
Sbjct: 108 SKLTE--PKKKTFKTYWAQVEGAPDEAQ----LDLLRKGVELKDGMTLPAKISIMSQPTV 161

Query: 228 SHF--KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                 + +  A    WLE+Q   GR  Q+R    H+G P +
Sbjct: 162 WERVPPIRERKAIPTTWLEIQICEGRNRQVRRMTAHIGFPTL 203


>gi|229181265|ref|ZP_04308595.1| hypothetical protein bcere0005_46070 [Bacillus cereus 172560W]
 gi|228602158|gb|EEK59649.1| hypothetical protein bcere0005_46070 [Bacillus cereus 172560W]
          Length = 165

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNTILSEGDYISIC 164


>gi|218289710|ref|ZP_03493918.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
 gi|218240167|gb|EED07351.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
          Length = 242

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 86/250 (34%), Gaps = 54/250 (21%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             +R+D+W             +K+ R+G+VR++ + VK                 +A  H
Sbjct: 2   ATIRVDKWLTTAGYG-TRSEAKKLCRAGRVRLNGETVK-----------------DAAKH 43

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                 +L+    +            YE    ++  KP G      S      D  +   
Sbjct: 44  ADPAVDVLEVDGEIVP----------YEPLVYFMMYKPPGYV----SSTEDPRDPVVIEL 89

Query: 137 VDSKG--QKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           +D +   +      RLD++  G+L++      A + L      R + K Y+  V G    
Sbjct: 90  LDEEDIWRDVFPVGRLDKDAEGLLLLTNDGPLAHRLLA---PKRHVPKRYFVRVRGALGE 146

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                A  L +          VV  +   A  A    +++   A+    +++  + G+ H
Sbjct: 147 DD---ARALAE---------GVVLDDGYKAMPA--ELEILRSGAESEAIIQV--YEGKYH 190

Query: 254 QLRVHALHMG 263
           Q++     +G
Sbjct: 191 QVKRMFASLG 200


>gi|322373412|ref|ZP_08047948.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           C150]
 gi|321278454|gb|EFX55523.1| ribosomal small subunit pseudouridine synthase A [Streptococcus sp.
           C150]
          Length = 243

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 78/247 (31%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +     +   ++  L+  QV V+ +                           
Sbjct: 1   MRLDKFLVDCGLG-SRSQVKIYLKKKQVTVNGQVETS----------------PKTQIDE 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K+ +I   S  LT           +E    Y+ NKP G+           +   L     
Sbjct: 44  KKDQIAYQSQELT-----------HETFVYYLLNKPKGVISATEDARHKTVLDLLDETAR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKN-KKE 196
            K  +     RLD +T G+L++      A   L+     + + KIY + V G+      +
Sbjct: 93  HK--QVFPVGRLDIDTHGLLLLTNNGDLAHAMLS---PRKHVDKIYQAKVAGVMDEADMQ 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                +  K H                  A      +D  A K   +++    G+ HQ++
Sbjct: 148 AFEKGIELKDH--------------TCQPAKLEILSVD-QAVKTSTVQVTIAEGKFHQVK 192

Query: 257 VHALHMG 263
                 G
Sbjct: 193 RMVAACG 199


>gi|218553820|ref|YP_002386733.1| 23S rRNA pseudouridylate synthase B [Escherichia coli IAI1]
 gi|218694839|ref|YP_002402506.1| 23S rRNA pseudouridylate synthase B [Escherichia coli 55989]
 gi|218351571|emb|CAU97283.1| 23S rRNA pseudouridylate synthase [Escherichia coli 55989]
 gi|218360588|emb|CAQ98146.1| 23S rRNA pseudouridylate synthase [Escherichia coli IAI1]
 gi|323947451|gb|EGB43455.1| RNA pseudouridylate synthase [Escherichia coli H120]
          Length = 299

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 14  LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 65

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 66  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 106

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 107 LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 161


>gi|331677046|ref|ZP_08377742.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli H591]
 gi|331075735|gb|EGI47033.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli H591]
          Length = 299

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 14  LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 65

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 66  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 106

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 107 LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 161


>gi|307709844|ref|ZP_07646293.1| conserved hypothetical protein [Streptococcus mitis SK564]
 gi|307619393|gb|EFN98520.1| conserved hypothetical protein [Streptococcus mitis SK564]
          Length = 220

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/224 (18%), Positives = 79/224 (35%), Gaps = 45/224 (20%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +L++G+V V+ K+ K + ++Q         +    + II + ++L+              
Sbjct: 1   MLKAGRVTVNGKKEK-SAKLQ---------IDEERDEIIFDGQVLE-------------- 36

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
              YE+   Y+ NKP G+           +   L     SK  +     RLD +T G+L+
Sbjct: 37  ---YEEFVYYMMNKPKGVISATEDPKHRTVLDLLDDLARSK--EVFPVGRLDIDTHGLLL 91

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +      A  L      R + K Y + V GI   +   I             +   +   
Sbjct: 92  LTNDGQLAHAL--LSPKRHVDKTYQAQVKGIMTQEDVEI-------------FAKGIPLK 136

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +     A      ID   +    + +    G+ HQ++    + G
Sbjct: 137 DFTCQPAKLEIVSIDT-EKIQSQIRVTIAEGKFHQVKRMVAYCG 179


>gi|15967012|ref|NP_387365.1| HEAT shock-like protein [Sinorhizobium meliloti 1021]
 gi|307302480|ref|ZP_07582237.1| RNA-binding S4 domain protein [Sinorhizobium meliloti BL225C]
 gi|307316190|ref|ZP_07595634.1| RNA-binding S4 domain protein [Sinorhizobium meliloti AK83]
 gi|15076285|emb|CAC47838.1| Heat shock protein 15 (HSP15) [Sinorhizobium meliloti 1021]
 gi|306898030|gb|EFN28772.1| RNA-binding S4 domain protein [Sinorhizobium meliloti AK83]
 gi|306903150|gb|EFN33740.1| RNA-binding S4 domain protein [Sinorhizobium meliloti BL225C]
          Length = 143

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 19/90 (21%), Positives = 40/90 (44%), Gaps = 13/90 (14%)

Query: 19  MRLDRWF--KNHYPHINFVNLQKILRSGQVRVDKKR-VKFNNRIQSGQVVRIPPVINALN 75
            RLD+W          +    QK + +G V V+ KR  + + +I++G ++ +      L 
Sbjct: 13  QRLDKWLFFARLIK--SRSLAQKAIEAGHVAVNGKRETQSSAQIKAGDMLEVSLERRDL- 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYED 105
                  ++   +  ++   + ++ LLYED
Sbjct: 70  -------VVRVLLPGSRRGPYEEARLLYED 92


>gi|260433638|ref|ZP_05787609.1| ribosomal large subunit pseudouridine synthase E [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260417466|gb|EEX10725.1| ribosomal large subunit pseudouridine synthase E [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 205

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/162 (19%), Positives = 59/162 (36%), Gaps = 6/162 (3%)

Query: 107 KIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
               FNKP  +  Q             L  ++D  G  P    RLD+++ G++++     
Sbjct: 7   WFIRFNKPFDVLPQFTDRQNTDSPRSTLSDFIDLPGVYP--AGRLDRDSEGLMLLTDNGR 64

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
              H+++     ++ K YW  V GIP           ++ +            +E    +
Sbjct: 65  LQSHISD--PKHKMPKTYWVQVEGIPDAAAIRALRDGVELNDGMTRPAKARLIDEPEGLW 122

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             +   + +      CWLE+    GR  Q+R     +G P +
Sbjct: 123 PRTP-PIRERKTVPDCWLELTLREGRNRQVRRMTAAVGHPTL 163


>gi|145631249|ref|ZP_01787022.1| predicted methyltransferase [Haemophilus influenzae R3021]
 gi|144983176|gb|EDJ90671.1| predicted methyltransferase [Haemophilus influenzae R3021]
          Length = 357

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/194 (19%), Positives = 66/194 (34%), Gaps = 34/194 (17%)

Query: 5   TYVQYVVVENDE---ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--I 59
             V+ VV  +++   E  +L +         +   ++ ++ +G+V V+ K     +R  +
Sbjct: 59  PKVKSVVKASNQPKVEGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDV 117

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            SG  VRI   I  L+H  KE                          ++ ++ KP G   
Sbjct: 118 HSGVKVRIDGQIINLSHAQKEI------------------------CRVLMYYKPEGELC 153

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                                G +     RLD  TSG+L+       A  L      R +
Sbjct: 154 --TRSDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREV 209

Query: 180 QKIYWSLVWGIPKN 193
           ++ Y   V+G   +
Sbjct: 210 EREYSVRVFGQVDD 223


>gi|312883597|ref|ZP_07743322.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio
           caribbenthicus ATCC BAA-2122]
 gi|309368820|gb|EFP96347.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio
           caribbenthicus ATCC BAA-2122]
          Length = 311

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/179 (17%), Positives = 63/179 (35%), Gaps = 30/179 (16%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNH 76
           N +L +       H +   L+ ++++G+V V+    +   R++    VVRI   I +   
Sbjct: 2   NEKLQKVLARA-GHGSRRELEALIKAGRVSVNGVVARLGERLEDENAVVRIDGHIVSAK- 59

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
              +++++                      ++  + KP G                    
Sbjct: 60  --AQEEVI---------------------CRVLAYYKPEGELC--TRHDPEGRRTVFDRL 94

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K
Sbjct: 95  PKIRGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVTEQK 151


>gi|71894432|ref|YP_278540.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Mycoplasma synoviae 53]
          Length = 232

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 86/249 (34%), Gaps = 57/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++  +         ++K++  G V+V+   +K +  I              L+ I 
Sbjct: 1   MRIEKFIADS-TLYTRNEIKKLISKGLVKVNDLIIKKSQSI-----------DPKLDKIY 48

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +L++    +                  + NKPAG      +   ++     +  +D
Sbjct: 49  LEGILLEAREEFS----------------YIMMNKPAGYIC---ANFDWNKQVVFELLLD 89

Query: 139 SKGQ--KPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +          RLD +T G+L++    + +   L+   +    +  Y  L   + KN K
Sbjct: 90  LEMNLKDFFTIGRLDIDTEGLLIITNDGKLSHNLLSP--KKHIPKTYYVELDKPLEKNIK 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E +   LL        Y   +  N     + I+ F+                  G+ HQ+
Sbjct: 148 ELLEKELLIDE---IKYKKSILNNISNNKWEITIFE------------------GKFHQI 186

Query: 256 RVHALHMGC 264
           ++   H G 
Sbjct: 187 KIIFAHFGY 195


>gi|329769599|ref|ZP_08261003.1| hypothetical protein HMPREF0433_00767 [Gemella sanguinis M325]
 gi|328838354|gb|EGF87963.1| hypothetical protein HMPREF0433_00767 [Gemella sanguinis M325]
          Length = 243

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 38/252 (15%), Positives = 86/252 (34%), Gaps = 54/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            RL +       + +    ++++  G+V V+   V +   + +   ++ +         +
Sbjct: 3   ERLQKLIAAS-GYTSRRKAEQLILDGKVTVNGTVVNQLGVKAEPSDIIIV-----EGVRL 56

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +KE K               +  L Y+  K+              S         +K + 
Sbjct: 57  LKENK---------------RYYLFYKPEKVI------------TSMSDEKDRTCVKDFF 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +S  ++     RLD +TSG L+++        +T      +I+K Y + + G   ++   
Sbjct: 90  ESVNERVVPVGRLDYDTSGALIMSNDGEFINLIT--HPRHKIKKTYVAKISGKLDDRHLK 147

Query: 198 IANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           I    ++          V++VK   K +N                  + +  H G+  Q+
Sbjct: 148 ILRSGVRIDNYKTAPAEVNIVKNKNKSSN----------------TLVRLTIHEGKNRQI 191

Query: 256 RVHALHMGCPIV 267
           R     +G  ++
Sbjct: 192 RRMFETLGYEVL 203


>gi|110806162|ref|YP_689682.1| 16S rRNA pseudouridylate synthase A [Shigella flexneri 5 str. 8401]
 gi|26108971|gb|AAN81174.1|AE016763_133 Ribosomal small subunit pseudouridine synthase A [Escherichia coli
           CFT073]
 gi|91073047|gb|ABE07928.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           UTI89]
 gi|110615710|gb|ABF04377.1| 16S pseudouridylate 516 synthase [Shigella flexneri 5 str. 8401]
 gi|281601638|gb|ADA74622.1| Ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           2002017]
          Length = 263

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 33  MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 74

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 75  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 121

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 122 PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 168

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 169 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 221

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 222 FAAVGNHVV 230


>gi|302389211|ref|YP_003825032.1| ribosomal small subunit pseudouridine synthase A
           [Thermosediminibacter oceani DSM 16646]
 gi|302199839|gb|ADL07409.1| ribosomal small subunit pseudouridine synthase A
           [Thermosediminibacter oceani DSM 16646]
          Length = 243

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 85/250 (34%), Gaps = 53/250 (21%)

Query: 16  EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           E+  RLD+          +  +++KI++ G+V V+ + V                  +A 
Sbjct: 3   EKTERLDKVLS--MAGYGSRKDVKKIIKRGEVEVNGRVVT-----------------DAG 43

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +      +  S  L          L++++    + NKP G+           +   L+
Sbjct: 44  TPVAPAVDSISVSGEL----------LIFKEHIYIMMNKPQGVISATHDRRETTVIDLLE 93

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                +        RLD++  G+L++      A + L+     ++++K+Y+  V G    
Sbjct: 94  DEFSHRN--LFPVGRLDKDAEGLLLLTDDGQLAHRLLS---PRKKVEKVYYVEVKGRLVE 148

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
           +                  V   K+     +Y     K+    A +     +  + G+ H
Sbjct: 149 ED-----------------VKAFKEGVFLGDYRALPAKLEILEAGEVSSALVTIYEGKFH 191

Query: 254 QLRVHALHMG 263
           Q++      G
Sbjct: 192 QIKRMMKARG 201


>gi|300902164|ref|ZP_07120164.1| hypothetical protein HMPREF9536_00353 [Escherichia coli MS 84-1]
 gi|301306200|ref|ZP_07212275.1| hypothetical protein HMPREF9347_04814 [Escherichia coli MS 124-1]
 gi|300405683|gb|EFJ89221.1| hypothetical protein HMPREF9536_00353 [Escherichia coli MS 84-1]
 gi|300838566|gb|EFK66326.1| hypothetical protein HMPREF9347_04814 [Escherichia coli MS 124-1]
 gi|315255301|gb|EFU35269.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           MS 85-1]
          Length = 268

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 38  MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 79

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 80  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 126

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 127 PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 173

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 174 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 226

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 227 FAAVGNHVV 235


>gi|319745443|gb|EFV97749.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae ATCC 13813]
          Length = 240

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 79/249 (31%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ IL+  Q+ V+                             
Sbjct: 1   MRLDKFLVECGLG-SRTQVKLILKKKQISVNG---------------------------- 31

Query: 79  KEQKILDSSVNLTKHSDFLK---SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                    V + ++ D +K   +++ YE    Y+ +KP G+           +   L  
Sbjct: 32  --NSETSPKVQVDEYRDEIKYNGTLVSYEKFVYYMLHKPKGVISATDDPSHKTVLDLLDK 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               K        RLD +T+G L++      A + L+     + + K Y + + GI    
Sbjct: 90  TARDKA--VFPVGRLDIDTTGFLLLTNNGELAHKILS---PKKHVDKCYEAKISGIMTED 144

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                     K  I  D+  +          A+    V     +    +++    G+ HQ
Sbjct: 145 ----DILAFDKGIILKDFTCL---------PALLEI-VEVNQVKNQSLVKITIKEGKFHQ 190

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 191 VKRMVAACG 199


>gi|119477504|ref|ZP_01617695.1| ribosomal small subunit pseudouridine synthase A [marine gamma
           proteobacterium HTCC2143]
 gi|119449430|gb|EAW30669.1| ribosomal small subunit pseudouridine synthase A [marine gamma
           proteobacterium HTCC2143]
          Length = 229

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/246 (13%), Positives = 77/246 (31%), Gaps = 54/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++        +    ++++RSG+VRV    V      + +  V+ +          
Sbjct: 1   MRLDKYLS-QVTDYSRSEGKRLIRSGRVRVAGHVVIDPRENVDNNAVIVVNGQQL----- 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                           S   +  +L++        K                   L+ + 
Sbjct: 55  ---------------RSASPRYFMLHKPDGYISATK------------DRQHLTALELFD 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    +  +  RLD +T+G+L+V+        +T      +      ++           
Sbjct: 88  EDNVDQLHIAGRLDIDTTGLLLVSDDGQWCHRVTSPKSDCKKTYRVEAV----------- 136

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             + +  ++    +    + Q +K    A     ++D    +    E     G+ HQ++ 
Sbjct: 137 --DPITPEAIKNIEQGIHLSQEKKPTLPA--DLDLLDEHTARLTITE-----GKYHQVKR 187

Query: 258 HALHMG 263
               +G
Sbjct: 188 MFAAVG 193


>gi|20806585|ref|NP_621756.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Thermoanaerobacter tengcongensis MB4]
 gi|254478969|ref|ZP_05092328.1| conserved hypothetical protein, putative [Carboxydibrachium
           pacificum DSM 12653]
 gi|20515028|gb|AAM23360.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Thermoanaerobacter
           tengcongensis MB4]
 gi|214035085|gb|EEB75800.1| conserved hypothetical protein, putative [Carboxydibrachium
           pacificum DSM 12653]
          Length = 240

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/254 (16%), Positives = 80/254 (31%), Gaps = 62/254 (24%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
             MRLD+   N         ++K ++ G V V+ + V                       
Sbjct: 2   AKMRLDKLLSNMGIG-TRKEVKKYIKDGLVEVNGEIV----------------------- 37

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKI-------YVFNKPAGISVQGGSGIAYHI 129
                      ++ +K  D  K  +L++  K+        + NKP G+           +
Sbjct: 38  -----------LDPSKTVDTEKDEVLFDGEKVEYKEFIYVMMNKPQGVISATHDKSEETV 86

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              L   +  +  K     RLD++T G+L++      A  L                +  
Sbjct: 87  IDLLPEEIALR--KVFPVGRLDKDTEGLLIITNDGELAHKL----------------LSP 128

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
             K  K+  A  L K +    +        E G     S  ++I+  +     + +    
Sbjct: 129 KKKVVKKYYAEVLGKITEKDAEKFKEGVILEDGYRTMPSQLEIIE--SSDISKVYVYLTE 186

Query: 250 GRTHQLRVHALHMG 263
           G+ HQ++     +G
Sbjct: 187 GKYHQVKRMFEAIG 200


>gi|194436993|ref|ZP_03069092.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           101-1]
 gi|194423976|gb|EDX39964.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           101-1]
          Length = 291

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|261494040|ref|ZP_05990543.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261496199|ref|ZP_05992605.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261308151|gb|EEY09448.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261310206|gb|EEY11406.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 355

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 83/246 (33%), Gaps = 43/246 (17%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   L++I+ +G+V VD K     +R+Q     +I    + +N +
Sbjct: 77  GEKLQKILARAGQG-SRRELEEIIAAGRVSVDGKMATLGDRVQVSSSTKIRIDGHLVNLM 135

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 136 PAQKEIC----------------------RVLMYYKPEGELC--TRSDPEGRATVFDRLP 171

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              G +     RLD  TSG+L+       A  L      R +++ Y   V+G        
Sbjct: 172 RLSGARWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGN------- 222

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I + +L++   G      V+  +  AN+     KV+        W ++    GR  ++R 
Sbjct: 223 IDDAMLQRLRKG------VQLEDGPANFK--QIKVVGGTGLNQ-WFDVTLTEGRNREVRR 273

Query: 258 HALHMG 263
                G
Sbjct: 274 LWESQG 279


>gi|94499317|ref|ZP_01305855.1| hypothetical protein RED65_11024 [Oceanobacter sp. RED65]
 gi|94428949|gb|EAT13921.1| hypothetical protein RED65_11024 [Oceanobacter sp. RED65]
          Length = 290

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/162 (13%), Positives = 50/162 (30%), Gaps = 29/162 (17%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   +++ +  G+V ++    K   R ++   +++            + K+++      +
Sbjct: 16  SRREMERWIEQGRVELNGSPAKLGERAEAKDQIKV------------DGKVIEHGQRKAR 63

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                          +  +NKP G                        G++     RLD 
Sbjct: 64  R--------------VLAYNKPEGEVC--TRHDPEGRPTVFDRLPKLHGERWIAVGRLDI 107

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            TSG+L+       A  L        + + Y   V G   ++
Sbjct: 108 NTSGLLLFTTDGELANKLMHPS-TNTVDREYAVRVAGEVTDE 148


>gi|332974446|gb|EGK11370.1| ribosomal large subunit pseudouridine synthase B [Kingella kingae
           ATCC 23330]
          Length = 390

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/179 (15%), Positives = 54/179 (30%), Gaps = 30/179 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V+V+ +      ++     V +      L  
Sbjct: 138 EPERLQKVLAASGVG-SRREMEEWINNGWVQVNGRVATLGEKVSPDDQVTVKGSAIKL-- 194

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 195 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 229

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++
Sbjct: 230 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGELSPEQ 286


>gi|237795222|ref|YP_002862774.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum Ba4 str. 657]
 gi|229261861|gb|ACQ52894.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum Ba4 str. 657]
          Length = 236

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/252 (16%), Positives = 84/252 (33%), Gaps = 55/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
            RL ++  +     +    + I+  G+V V+  ++K    +I SG  ++++   I     
Sbjct: 3   ERLQKYMAS-CGVASRRKCEDIILEGRVEVNGIKIKELGTKIISGEDIIKVDGNIIEPE- 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKS 135
                                      E+    + NKP G             I   +K 
Sbjct: 61  ---------------------------ENKIYILLNKPKGYVCTAKDEKDRKTILDLVKV 93

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 ++     RLD +TSGI+++         +      +   K Y + V G  K   
Sbjct: 94  -----KERIYPIGRLDMDTSGIIILTNDGEIYNKIIHPKFEK--IKTYKAKVKGTIKKDH 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 L KK    GDY+            A +  +++   ++    + ++ H G+  Q+
Sbjct: 147 IE----LFKKGIDIGDYI-----------TAPATLEILK-ISKDTSEIIIKIHEGKNRQV 190

Query: 256 RVHALHMGCPIV 267
           R     +G  ++
Sbjct: 191 RRMCKSIGHAVI 202


>gi|218549599|ref|YP_002383390.1| 16S rRNA pseudouridylate synthase A [Escherichia fergusonii ATCC
           35469]
 gi|218357140|emb|CAQ89774.1| 16S rRNA pseudouridylate 516 synthase [Escherichia fergusonii ATCC
           35469]
 gi|324114400|gb|EGC08369.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
          Length = 231

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 76/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E ++      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHEVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|320667979|gb|EFX34882.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 231

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTADQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|254517670|ref|ZP_05129726.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
 gi|226911419|gb|EEH96620.1| pseudouridine synthase [Clostridium sp. 7_2_43FAA]
          Length = 238

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 89/243 (36%), Gaps = 47/243 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   +     +++++R G + V+ + VK N     G  +             
Sbjct: 2   ERLDKVLSN-LGYGTRKEIKQVVRKGLIEVNGEIVKDN-----GMQID-----------P 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  KIL +              + Y      + NKP G+           +   L+  ++
Sbjct: 45  EVDKILVNGEE-----------IFYRKYIYLMMNKPDGVVSATFDNRDETVIDLLE--IE 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  +P    RLD++T G+L++         L       ++ K+Y++ +     +KK   
Sbjct: 92  HQVFEPFPVGRLDKDTVGLLLLTNDGELNHRL--ISPKWKVDKVYYAKI-----DKKVTE 144

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+    K+ I  D  +  K+ +          ++++  +     + +    G+ HQ++  
Sbjct: 145 ADIKKFKNGITLDDGYTCKEAK---------LEILES-SDSGSEVMITIQEGKFHQVKRM 194

Query: 259 ALH 261
              
Sbjct: 195 FEA 197


>gi|145298401|ref|YP_001141242.1| ribosomal large subunit pseudouridine synthase E [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142851173|gb|ABO89494.1| ribosomal large subunit pseudouridine synthase E [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 321

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/197 (19%), Positives = 73/197 (37%), Gaps = 17/197 (8%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K  +   D K+ + NKP  +  Q            LK ++   G       RLD+++ G+
Sbjct: 49  KPQVAPADRKLLLLNKPYMVLCQ---FTDEAGRETLKDYIKEPGIYA--AGRLDRDSEGL 103

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVK 217
           L++         LT+     +  K YW  V GIP  ++       ++ +           
Sbjct: 104 LLLTNDGKLQARLTQPGE--KTPKTYWVQVEGIPSEEELAALRAGVELNDGLTLPAEARL 161

Query: 218 QNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV-------GDH 270
            +E          +  +       WLE++   GR  Q+R    H+G P +       GD 
Sbjct: 162 MDEPNVWPRNPPIR--ERKEVPTRWLEIKIVEGRNRQVRRMTAHIGHPTLRLIRYAIGDW 219

Query: 271 KYCANFKGNFTSPIQNK 287
               N++ +  +P +++
Sbjct: 220 T-LGNWQEDGLAPGESR 235


>gi|320663977|gb|EFX31164.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 290

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|16129230|ref|NP_415785.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|89108115|ref|AP_001895.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12
           substr. W3110]
 gi|157160774|ref|YP_001458092.1| 23S rRNA pseudouridylate synthase B [Escherichia coli HS]
 gi|170020367|ref|YP_001725321.1| 23S rRNA pseudouridylate synthase B [Escherichia coli ATCC 8739]
 gi|170080946|ref|YP_001730266.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12
           substr. DH10B]
 gi|170682451|ref|YP_001743918.1| 23S rRNA pseudouridylate synthase B [Escherichia coli SMS-3-5]
 gi|188492201|ref|ZP_02999471.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           53638]
 gi|194435058|ref|ZP_03067297.1| ribosomal large subunit pseudouridine synthase B [Shigella
           dysenteriae 1012]
 gi|218699976|ref|YP_002407605.1| 23S rRNA pseudouridylate synthase B [Escherichia coli IAI39]
 gi|238900502|ref|YP_002926298.1| 23S rRNA pseudouridylate synthase [Escherichia coli BW2952]
 gi|253773734|ref|YP_003036565.1| 23S rRNA pseudouridylate synthase B [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254161349|ref|YP_003044457.1| 23S rRNA pseudouridylate synthase B [Escherichia coli B str.
           REL606]
 gi|256023023|ref|ZP_05436888.1| 23S rRNA pseudouridylate synthase B [Escherichia sp. 4_1_40B]
 gi|300927775|ref|ZP_07143339.1| conserved hypothetical protein [Escherichia coli MS 187-1]
 gi|300940072|ref|ZP_07154682.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|300951921|ref|ZP_07165725.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300955866|ref|ZP_07168205.1| hypothetical protein HMPREF9547_01723 [Escherichia coli MS 175-1]
 gi|301019493|ref|ZP_07183662.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|301022795|ref|ZP_07186637.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|301647237|ref|ZP_07247056.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|307137906|ref|ZP_07497262.1| 23S rRNA pseudouridylate synthase B [Escherichia coli H736]
 gi|312971458|ref|ZP_07785633.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           1827-70]
 gi|331641827|ref|ZP_08342962.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli H736]
 gi|331652309|ref|ZP_08353328.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli M718]
 gi|1175678|sp|P37765|RLUB_ECOLI RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|1742064|dbj|BAA14806.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K12
           substr. W3110]
 gi|1787524|gb|AAC74351.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|157066454|gb|ABV05709.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           HS]
 gi|169755295|gb|ACA77994.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|169888781|gb|ACB02488.1| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12
           substr. DH10B]
 gi|170520169|gb|ACB18347.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           SMS-3-5]
 gi|188487400|gb|EDU62503.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           53638]
 gi|194416715|gb|EDX32845.1| ribosomal large subunit pseudouridine synthase B [Shigella
           dysenteriae 1012]
 gi|218369962|emb|CAR17736.1| 23S rRNA pseudouridylate synthase [Escherichia coli IAI39]
 gi|238859761|gb|ACR61759.1| 23S rRNA pseudouridylate synthase [Escherichia coli BW2952]
 gi|242377048|emb|CAQ31772.1| 23S rRNA pseudouridine 2605 synthase [Escherichia coli BL21(DE3)]
 gi|253324778|gb|ACT29380.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253973250|gb|ACT38921.1| 23S rRNA pseudouridylate synthase [Escherichia coli B str. REL606]
 gi|253977464|gb|ACT43134.1| 23S rRNA pseudouridylate synthase [Escherichia coli BL21(DE3)]
 gi|260449601|gb|ACX40023.1| pseudouridine synthase [Escherichia coli DH1]
 gi|299881096|gb|EFI89307.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|300317268|gb|EFJ67052.1| hypothetical protein HMPREF9547_01723 [Escherichia coli MS 175-1]
 gi|300399234|gb|EFJ82772.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|300448865|gb|EFK12485.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300455107|gb|EFK18600.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|300464168|gb|EFK27661.1| conserved hypothetical protein [Escherichia coli MS 187-1]
 gi|301074599|gb|EFK89405.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|309701567|emb|CBJ00874.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           ETEC H10407]
 gi|310336055|gb|EFQ01255.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           1827-70]
 gi|315135905|dbj|BAJ43064.1| 23S rRNA pseudouridylate synthase B [Escherichia coli DH1]
 gi|315297258|gb|EFU56538.1| conserved hypothetical protein [Escherichia coli MS 16-3]
 gi|315619347|gb|EFU99891.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           3431]
 gi|320181709|gb|EFW56620.1| 23S rRNA pseudouridylate synthase B [Shigella boydii ATCC 9905]
 gi|320195718|gb|EFW70343.1| 23S rRNA pseudouridylate synthase B [Escherichia coli WV_060327]
 gi|323937590|gb|EGB33858.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323942383|gb|EGB38553.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323962569|gb|EGB58149.1| RNA pseudouridylate synthase [Escherichia coli H489]
 gi|323973491|gb|EGB68677.1| RNA pseudouridylate synthase [Escherichia coli TA007]
 gi|331038625|gb|EGI10845.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli H736]
 gi|331050587|gb|EGI22645.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli M718]
 gi|332091659|gb|EGI96739.1| ribosomal large subunit pseudouridine synthase B [Shigella boydii
           5216-82]
 gi|332097910|gb|EGJ02883.1| ribosomal large subunit pseudouridine synthase B [Shigella
           dysenteriae 155-74]
 gi|332342861|gb|AEE56195.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli UMNK88]
          Length = 291

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|330911132|gb|EGH39642.1| ribosomal large subunit pseudouridine synthase B LSU [Escherichia
           coli AA86]
          Length = 291

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|229169688|ref|ZP_04297388.1| hypothetical protein bcere0007_46320 [Bacillus cereus AH621]
 gi|228613727|gb|EEK70852.1| hypothetical protein bcere0007_46320 [Bacillus cereus AH621]
          Length = 165

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RIDKVLSTYISDWSRTIIVDKIKNGHIQLNGQQMKPNAILSEGDHISIC 164


>gi|223043161|ref|ZP_03613208.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           capitis SK14]
 gi|222443372|gb|EEE49470.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           capitis SK14]
          Length = 245

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/235 (14%), Positives = 74/235 (31%), Gaps = 53/235 (22%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+ + V     ++     V +                    + + 
Sbjct: 19  SRRKAETLITEGKVKVNGQVVTELGTKVSHSDTVEV------------------EGIKIE 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +           ED    +F KP  +     S         +  + +    +     RLD
Sbjct: 61  Q-----------EDKMYILFYKPTQVIT---SVSDDRGRKVVTDYFEDIETRIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIG 209
            +TSG+L++         +T       I+K Y + + G    +  KE      L+     
Sbjct: 107 YDTSGVLLLTNDGEFTNLMT--HPRYHIKKKYVAKLKGYLMREQVKELEQGIELEDGFTQ 164

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              V + +Q+++                +    +E+    GR  Q+R    + G 
Sbjct: 165 PAQVKIKRQDKE----------------KNTTLVEITISEGRNRQVRRMFEYFGH 203


>gi|154248798|ref|YP_001409623.1| RNA-binding S4 domain-containing protein [Fervidobacterium nodosum
           Rt17-B1]
 gi|154152734|gb|ABS59966.1| RNA-binding S4 domain protein [Fervidobacterium nodosum Rt17-B1]
          Length = 245

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/252 (13%), Positives = 89/252 (35%), Gaps = 54/252 (21%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           E++ +++RLD++  N +       ++KI++ G+V V+ + ++  +  ++   ++ +    
Sbjct: 9   ESEIKSIRLDKFLSNAHIG-TRNEVKKIIKEGRVSVNFEIIRNPDFHVKLDDIIELDGNR 67

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
              +  +                               +F+KP+G      S  +     
Sbjct: 68  IEPHKNV-----------------------------YIIFHKPSGFV----STTSDREPS 94

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            L         +  +  RLD++  G+L++        +L      + I+K YW       
Sbjct: 95  VLNLIDHPYLNELHIAGRLDKDVEGLLILTNDGEFTHNL--ISPKKHIEKEYWIYTK--- 149

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                       +   +  + V +V +  +      +    I   ++K   + +    G+
Sbjct: 150 ------------ENVEVTQNMVKMVSEGIELEKGTKTLPGKIRKVSEK--IISLTIVEGK 195

Query: 252 THQLRVHALHMG 263
            HQ++   + +G
Sbjct: 196 YHQVKKMCISLG 207


>gi|229525790|ref|ZP_04415195.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           bv. albensis VL426]
 gi|229339371|gb|EEO04388.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           bv. albensis VL426]
          Length = 322

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/232 (16%), Positives = 79/232 (34%), Gaps = 34/232 (14%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIPPVINALNHIIK 79
           L +       H +   L+ ++R+G+V V+ K      R++    VVRI   + +   +  
Sbjct: 5   LQKVLARA-GHGSRRELEALIRAGRVSVNGKVAILGERLEEDNAVVRIDGHVVS---VKA 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +++++                      ++  + KP G                       
Sbjct: 61  QEEVI---------------------CRVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G     K    
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGDVTEDKVRNL 155

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
              ++       +  V+    +G N+  + + VI+     +     E Q  T
Sbjct: 156 VRGVQLEDGMARFEDVMYAGGEGINH--TFYVVINEGRNREVRRLWESQGTT 205


>gi|259908330|ref|YP_002648686.1| 23S rRNA pseudouridylate synthase B [Erwinia pyrifoliae Ep1/96]
 gi|224963952|emb|CAX55457.1| Ribosomal large subunit pseudouridine synthase B [Erwinia
           pyrifoliae Ep1/96]
 gi|283478269|emb|CAY74185.1| ribosomal large subunit pseudouridine synthase B [Erwinia
           pyrifoliae DSM 12163]
          Length = 295

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/175 (16%), Positives = 61/175 (34%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ ++ +G+V VD K     +R++ G  ++I    +        
Sbjct: 5   LQKVLARA-GHGSRREIETMISAGRVSVDGKLATLGDRVEPGASLKIRIDGH-------- 55

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             ++  S +++            E  ++  + KP G                       +
Sbjct: 56  --VVPVSESIS------------EVCRVLAYYKPEGELC--TRSDPEGRPTVFDRLPKLR 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  T G+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 100 GARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGAVDDEK 152


>gi|167719293|ref|ZP_02402529.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei DM98]
          Length = 69

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 287 KLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFKYDRNLYIKRLYSQDE 340
           +  LHA  + L HP  GR +Q  APLPA +    D+LGF  D   +       D+
Sbjct: 1   RQALHAWRLGLVHPASGRSMQWRAPLPADLAALVDALGFGADDAEFGDDDAVYDD 55


>gi|326796385|ref|YP_004314205.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
 gi|326547149|gb|ADZ92369.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
          Length = 228

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 81/246 (32%), Gaps = 54/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD +   H    +    ++ +  G++RV+            G VV  P          
Sbjct: 1   MRLDYFLA-HTTSWSRKEAKRFIAKGKIRVN------------GDVVTKPN--------- 38

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                  +SV      +    ++L+   K +   KPA       S +       L   ++
Sbjct: 39  -------ASVTEDCKVESHGEVILWRKEKYFALYKPADYV----SALEDSESPVLIDLIE 87

Query: 139 SKGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            + +K  ++  RLD++T+G++ +       Q L      +      + +    P ++  C
Sbjct: 88  PEERKNLKIVGRLDKDTTGLIFLTTDG---QWLHRITSPKHDCYKTYRVYCADPISEANC 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                  KS   G  ++        A         ++  +       +    G+ HQ++ 
Sbjct: 145 -------KSLETGVMLNGEDLPTSPAK--------VERVSDTEIL--LSIKEGKYHQVKR 187

Query: 258 HALHMG 263
               +G
Sbjct: 188 MLAAVG 193


>gi|323356708|ref|YP_004223104.1| 16S rRNA uridine-516 pseudouridylate synthase [Microbacterium
           testaceum StLB037]
 gi|323273079|dbj|BAJ73224.1| 16S rRNA uridine-516 pseudouridylate synthase [Microbacterium
           testaceum StLB037]
          Length = 245

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/234 (17%), Positives = 81/234 (34%), Gaps = 36/234 (15%)

Query: 36  NLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95
            LQK+L +  V         + R+    +V     +N +       +I   +  +     
Sbjct: 2   RLQKVLANAGV--------ASRRVSEEMIVAGRVRVNGVVVTELGSRIHPETDLVDVDGT 53

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
            ++   L    +  + NKP G+     S         L+ +     ++     RLD +TS
Sbjct: 54  AIQ---LDTSKRYVILNKPTGVVS---SMSDDRGRPDLRQYTKDWDERLFNVGRLDADTS 107

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG--IPKNKKECIANWLLKKSHIGGDYV 213
           G+LV+      A  L        + K+Y + V G  +P+  +  +    L+   I  D  
Sbjct: 108 GLLVLTNDGDLAHVLAHPSFG--VTKVYIAKVEGQVLPQTIQHLLKGVDLEDGRIAADKA 165

Query: 214 HVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                              +   ++    +E+  H+G+   +R     +G P++
Sbjct: 166 R------------------LLDSSRGESLVELTLHSGKNRIVRRLMAEVGHPVI 201


>gi|319937384|ref|ZP_08011791.1| pseudouridine synthase [Coprobacillus sp. 29_1]
 gi|319807750|gb|EFW04343.1| pseudouridine synthase [Coprobacillus sp. 29_1]
          Length = 234

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 87/247 (35%), Gaps = 53/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   +         ++  ++ G V V+ +       I     +++ P  + +    
Sbjct: 1   MRLDKLLAHSGFG-TRKEVKDFIKKGIVTVNGE-------IAEKDKMQVDPQTDEVC--- 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                ++ YE+   Y+ NKPAG        +   +   +  +  
Sbjct: 50  -----------------VNGEVITYEEFVYYMLNKPAGYVSATEDNLYPTVVDLIDDYYR 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-E 196
                     RLD +T G+L+++     A Q L+     +   K+Y++ + GI  N+  E
Sbjct: 93  D---DLFPVGRLDVDTEGLLLISNDGVLAHQLLS---PKKHCPKVYYAKINGIVTNQDVE 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              N +        DY     + +  +  A +              +E+  + G+ HQ++
Sbjct: 147 AFFNGITID-----DYQCQSAELKILSTSATT------------SEIEVTIYEGKFHQVK 189

Query: 257 VHALHMG 263
              + +G
Sbjct: 190 KMFIAVG 196


>gi|213028620|ref|ZP_03343067.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 122

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/145 (15%), Positives = 50/145 (34%), Gaps = 34/145 (23%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVART 163
              ++     RLD+++ G++ +   
Sbjct: 97  --SKRIFPIGRLDKDSQGLIFLTNH 119


>gi|147673214|ref|YP_001216750.1| pseudouridine synthase family 1 protein [Vibrio cholerae O395]
 gi|262169496|ref|ZP_06037188.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           RC27]
 gi|262191635|ref|ZP_06049813.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           CT 5369-93]
 gi|146315097|gb|ABQ19636.1| pseudouridine synthase family 1 protein [Vibrio cholerae O395]
 gi|227013096|gb|ACP09306.1| pseudouridine synthase family 1 protein [Vibrio cholerae O395]
 gi|262022309|gb|EEY41018.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           RC27]
 gi|262032477|gb|EEY51037.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           CT 5369-93]
          Length = 321

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/232 (16%), Positives = 80/232 (34%), Gaps = 34/232 (14%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   L+ ++R+G+V V+ K      R++    VVRI   + +   +  
Sbjct: 5   LQKVLARA-GHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNAVVRIDGHVVS---VKA 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +++++                      ++  + KP G                       
Sbjct: 61  QEEVI---------------------CRVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K    
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGDVTEEKVRNL 155

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
              ++       +  V+    +G N+  + + VI+     +     E Q  T
Sbjct: 156 VRGVQLEDGMARFEDVMYAGGEGINH--TFYVVINEGRNREVRRLWESQGTT 205


>gi|26247598|ref|NP_753638.1| 23S rRNA pseudouridylate synthase B [Escherichia coli CFT073]
 gi|91210560|ref|YP_540546.1| 23S rRNA pseudouridylate synthase B [Escherichia coli UTI89]
 gi|110641498|ref|YP_669228.1| 23S rRNA pseudouridylate synthase B [Escherichia coli 536]
 gi|191171000|ref|ZP_03032551.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           F11]
 gi|215486564|ref|YP_002328995.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218549040|ref|YP_002382831.1| 23S rRNA pseudouridylate synthase B [Escherichia fergusonii ATCC
           35469]
 gi|218558254|ref|YP_002391167.1| 23S rRNA pseudouridylate synthase B [Escherichia coli S88]
 gi|218704792|ref|YP_002412311.1| 23S rRNA pseudouridylate synthase B [Escherichia coli UMN026]
 gi|227886303|ref|ZP_04004108.1| 23S rRNA pseudouridylate synthase [Escherichia coli 83972]
 gi|237705292|ref|ZP_04535773.1| ribosomal large subunit pseudouridine synthase B [Escherichia sp.
           3_2_53FAA]
 gi|293404810|ref|ZP_06648802.1| 23S rRNA pseudouridylate synthase B [Escherichia coli FVEC1412]
 gi|298380451|ref|ZP_06990050.1| 23S rRNA pseudouridylate synthase B [Escherichia coli FVEC1302]
 gi|300897321|ref|ZP_07115752.1| conserved hypothetical protein [Escherichia coli MS 198-1]
 gi|300971792|ref|ZP_07171626.1| hypothetical protein HMPREF9553_00034 [Escherichia coli MS 200-1]
 gi|300982412|ref|ZP_07176109.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|301046931|ref|ZP_07194045.1| conserved hypothetical protein [Escherichia coli MS 185-1]
 gi|306813708|ref|ZP_07447889.1| 23S rRNA pseudouridylate synthase B [Escherichia coli NC101]
 gi|312966803|ref|ZP_07781021.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           2362-75]
 gi|331646590|ref|ZP_08347693.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli M605]
 gi|331662681|ref|ZP_08363604.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA143]
 gi|331672793|ref|ZP_08373579.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA280]
 gi|331682754|ref|ZP_08383373.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli H299]
 gi|34098555|sp|Q8FHV4|RLUB_ECOL6 RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|26108000|gb|AAN80200.1|AE016760_59 Hypothetical protein yciL [Escherichia coli CFT073]
 gi|91072134|gb|ABE07015.1| hypothetical protein YciL [Escherichia coli UTI89]
 gi|110343090|gb|ABG69327.1| putative ribosomal large subunit pseudouridine synthase
           [Escherichia coli 536]
 gi|190908732|gb|EDV68320.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           F11]
 gi|215264636|emb|CAS09007.1| 23S rRNA pseudouridy late synthase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218356581|emb|CAQ89204.1| 23S rRNA pseudouridylate synthase [Escherichia fergusonii ATCC
           35469]
 gi|218365023|emb|CAR02726.1| 23S rRNA pseudouridylate synthase [Escherichia coli S88]
 gi|218431889|emb|CAR12774.1| 23S rRNA pseudouridylate synthase [Escherichia coli UMN026]
 gi|222033073|emb|CAP75813.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           LF82]
 gi|226900049|gb|EEH86308.1| ribosomal large subunit pseudouridine synthase B [Escherichia sp.
           3_2_53FAA]
 gi|227836507|gb|EEJ46973.1| 23S rRNA pseudouridylate synthase [Escherichia coli 83972]
 gi|281178457|dbj|BAI54787.1| putative pseudouridine synthase [Escherichia coli SE15]
 gi|284921150|emb|CBG34216.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           042]
 gi|291427018|gb|EFF00045.1| 23S rRNA pseudouridylate synthase B [Escherichia coli FVEC1412]
 gi|294492436|gb|ADE91192.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           IHE3034]
 gi|298277893|gb|EFI19407.1| 23S rRNA pseudouridylate synthase B [Escherichia coli FVEC1302]
 gi|300301157|gb|EFJ57542.1| conserved hypothetical protein [Escherichia coli MS 185-1]
 gi|300309298|gb|EFJ63818.1| hypothetical protein HMPREF9553_00034 [Escherichia coli MS 200-1]
 gi|300358900|gb|EFJ74770.1| conserved hypothetical protein [Escherichia coli MS 198-1]
 gi|300408750|gb|EFJ92288.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|305852982|gb|EFM53427.1| 23S rRNA pseudouridylate synthase B [Escherichia coli NC101]
 gi|307553327|gb|ADN46102.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           ABU 83972]
 gi|307627157|gb|ADN71461.1| 23S rRNA pseudouridylate synthase B [Escherichia coli UM146]
 gi|312288267|gb|EFR16169.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           2362-75]
 gi|312945903|gb|ADR26730.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O83:H1 str.
           NRG 857C]
 gi|315289107|gb|EFU48505.1| conserved hypothetical protein [Escherichia coli MS 110-3]
 gi|315294756|gb|EFU54099.1| conserved hypothetical protein [Escherichia coli MS 153-1]
 gi|323187500|gb|EFZ72809.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           RN587/1]
 gi|323949128|gb|EGB45020.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323953860|gb|EGB49661.1| RNA pseudouridylate synthase [Escherichia coli H263]
 gi|323964605|gb|EGB60078.1| RNA pseudouridylate synthase [Escherichia coli M863]
 gi|323977101|gb|EGB72188.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
 gi|324006121|gb|EGB75340.1| hypothetical protein HMPREF9532_04240 [Escherichia coli MS 57-2]
 gi|324011320|gb|EGB80539.1| hypothetical protein HMPREF9533_04708 [Escherichia coli MS 60-1]
 gi|327253958|gb|EGE65587.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           STEC_7v]
 gi|331045342|gb|EGI17469.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli M605]
 gi|331061103|gb|EGI33067.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA143]
 gi|331070014|gb|EGI41383.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA280]
 gi|331080385|gb|EGI51564.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli H299]
          Length = 291

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|313636574|gb|EFS02285.1| ribosomal small subunit pseudouridine synthase A [Listeria
           seeligeri FSL S4-171]
          Length = 233

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/249 (13%), Positives = 83/249 (33%), Gaps = 59/249 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG---QVVRIPPVINALN 75
           MRLD+   +     +   ++ +L+SG V V+   ++ ++++Q       + +        
Sbjct: 1   MRLDKLLSHTGFG-SRREVKPLLKSGSVVVNG-VIQKDSKLQVNPEKDQITVHGNP---- 54

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                                    ++Y++   ++ +KP  +       ++  +   L  
Sbjct: 55  -------------------------VIYQEFVYFMLHKPQNVVSATEDNLSETVIDLLAQ 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             +     P    RLD++T G+L++      A   L+     + I K Y++ + G     
Sbjct: 90  --EDTLTNPFPVGRLDKDTEGLLIITNDGTLAHNLLS---PKKHIDKTYYAKIEGDVTA- 143

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                      + +      +   +      A  H +++     +    E     G+ HQ
Sbjct: 144 -----------TDVEAFRTGITLDDGYTCKPA--HLEIMAPNEIRVTIQE-----GKFHQ 185

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 186 VKRMFAATG 194


>gi|169835682|ref|ZP_02868870.1| hypothetical protein cdivTM_00929 [candidate division TM7
           single-cell isolate TM7a]
          Length = 56

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 7/56 (12%)

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297
            L+++  TGR HQ+R      G  IVGD KY             ++ +L   ++  
Sbjct: 1   LLDIELITGRKHQIRAQLADKGLFIVGDKKYG-------IKDGSDRFFLCCYFLSF 49


>gi|150392376|ref|YP_001322425.1| RNA-binding S4 domain-containing protein [Alkaliphilus
           metalliredigens QYMF]
 gi|149952238|gb|ABR50766.1| RNA-binding S4 domain protein [Alkaliphilus metalliredigens QYMF]
          Length = 235

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/253 (12%), Positives = 70/253 (27%), Gaps = 58/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL+ +  +     +     ++++  +V V+ K      ++  G  V +        +  
Sbjct: 1   MRLNNFISSTGK-CSRREADELIKQKKVTVNGKIATLGCKVDPGDQVMLKGKPLQAKN-- 57

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                     +      NKP GI+      I  +I  F+     
Sbjct: 58  --------------------------NDVYIALNKPVGITCTTERHIRGNIIDFINH--- 88

Query: 139 SKGQKPRLTHRLDQETSGILVVART----RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
              ++     RLD+++ G++++               +  +   +          I    
Sbjct: 89  --PERIFPIGRLDKDSEGLILLTNDGSIVNEILAEENKHEKDYIVTVNKKITPSFIEGMS 146

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K       +K          +V+ N++                      ++    G   Q
Sbjct: 147 KGVKIYNPVKNKDTMTKRCKLVRINDRT--------------------FKITLCQGLNRQ 186

Query: 255 LRVHALHMGCPIV 267
           +R    H G  +V
Sbjct: 187 IRRMCTHFGYRVV 199


>gi|320451314|ref|YP_004203410.1| ribosomal large subunit pseudouridine synthase B [Thermus
           scotoductus SA-01]
 gi|320151483|gb|ADW22861.1| ribosomal large subunit pseudouridine synthase B [Thermus
           scotoductus SA-01]
          Length = 236

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 38/252 (15%), Positives = 80/252 (31%), Gaps = 57/252 (22%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           E+ +RL  +        +    ++++R G+VRV+ K      ++  G VV +        
Sbjct: 2   EKPLRLQAFLARAGVG-SRRKAEELIRQGRVRVNGKVAVLGQKVNPGDVVEVD------- 53

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                           K  +  +  ++         +KP G +        +        
Sbjct: 54  ---------------GKPVEPPRERIV------LALHKPRGYTT--TRHDPHAQKTVFDL 90

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM-RRIQKIYWSLVWGIPKNK 194
             D  G  P    RLD+++ G+L++         LT      R++ ++Y          +
Sbjct: 91  LPDIPGLHP--IGRLDRDSEGLLLLTNDGHLTLRLTHPRYGVRKVYRVY---------TE 139

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  +   + ++   G D        E G   A+                 +    GR  +
Sbjct: 140 RGTLPLAICQRLLEGVDL-------EDGPARAL-------ACRPAPGGALLTLAEGRKRE 185

Query: 255 LRVHALHMGCPI 266
           +R     +G P+
Sbjct: 186 VRRMLKAVGYPV 197


>gi|260582128|ref|ZP_05849922.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae NT127]
 gi|260094760|gb|EEW78654.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae NT127]
          Length = 357

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/194 (19%), Positives = 66/194 (34%), Gaps = 34/194 (17%)

Query: 5   TYVQYVVVENDE---ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--I 59
             V+ VV  +++   E  +L +         +   ++ ++ +G+V V+ K     +R  +
Sbjct: 59  PKVKSVVKASNQPKVEGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDV 117

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            SG  VRI   I  L+H  KE                          ++ ++ KP G   
Sbjct: 118 HSGVKVRIDGQIINLSHAQKEI------------------------CRVLMYYKPEGELC 153

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                                G +     RLD  TSG+L+       A  L      R +
Sbjct: 154 --TRSDPEGRATVFDRLPHLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREV 209

Query: 180 QKIYWSLVWGIPKN 193
           ++ Y   V+G   +
Sbjct: 210 EREYSVRVFGQVDD 223


>gi|193068120|ref|ZP_03049084.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           E110019]
 gi|331683863|ref|ZP_08384459.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli H299]
 gi|192958399|gb|EDV88838.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           E110019]
 gi|323945000|gb|EGB41065.1| RNA pseudouridylate synthase [Escherichia coli H120]
 gi|331078815|gb|EGI50017.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli H299]
          Length = 231

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLVQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|307544267|ref|YP_003896746.1| RNA-binding S4 domain protein [Halomonas elongata DSM 2581]
 gi|307216291|emb|CBV41561.1| RNA-binding S4 domain protein [Halomonas elongata DSM 2581]
          Length = 287

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/213 (15%), Positives = 63/213 (29%), Gaps = 31/213 (14%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++  +  G+V+V+ +     +R++    V                   D  V L  
Sbjct: 19  SRREMETAIADGRVKVNGQVATLGDRVELRDKV----------------AFDDRPVALRG 62

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
             +  + +++Y        NKP G                       KG++     RLD 
Sbjct: 63  ADEVPRRVIMY--------NKPEGELCTRKDPEGRR--TVFDRLPRLKGERWIAIGRLDI 112

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+L+       A  L       +I++ Y   V G            +++   +    
Sbjct: 113 NTSGLLLFTTDGELANRL--MHPSTQIEREYAVRVMGEVTMDH---IKAMVEGVMLDDGP 167

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
                  E G     + F V+    +      +
Sbjct: 168 ARFTDVQEFGGEGINTWFHVVIMEGRNREVRRL 200


>gi|260773017|ref|ZP_05881933.1| ribosomal large subunit pseudouridine synthase B [Vibrio
           metschnikovii CIP 69.14]
 gi|260612156|gb|EEX37359.1| ribosomal large subunit pseudouridine synthase B [Vibrio
           metschnikovii CIP 69.14]
          Length = 346

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/233 (17%), Positives = 75/233 (32%), Gaps = 36/233 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   L+ ++R+G+V V+ K      R+                    E
Sbjct: 5   LQKVLARA-GHGSRRELEALIRAGRVSVNGKVAILGERL--------------------E 43

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            +     ++    S      ++     +  + KP G                       +
Sbjct: 44  DETAVVRIDGHAVSAKAPEEVICR---VLAYYKPEGELC--TRHDPEGRRTVFDRLPKIR 98

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K  I N
Sbjct: 99  GSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEINEEK--IRN 154

Query: 201 WLLKKSHIGG--DYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
            +       G   +  V+    +G N+  + + VI+     +     E Q  T
Sbjct: 155 LVRGVQLEDGMARFEDVMYAGGEGMNH--TFYVVINEGRNREVRRLWESQGTT 205


>gi|327398210|ref|YP_004339079.1| RNA-binding S4 domain-containing protein [Hippea maritima DSM
          10411]
 gi|327180839|gb|AEA33020.1| RNA-binding S4 domain protein [Hippea maritima DSM 10411]
          Length = 86

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 12/61 (19%), Positives = 28/61 (45%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
          MRLD++ K           +++   G V ++ K+ K +  ++ G ++ I      + + I
Sbjct: 1  MRLDQFLKETRIIKRRTLAKQMCDEGFVLINSKKAKASYEVKIGDIIDIYFKQKKIKYRI 60

Query: 79 K 79
          +
Sbjct: 61 E 61


>gi|32266018|ref|NP_860050.1| hypothetical protein HH0519 [Helicobacter hepaticus ATCC 51449]
 gi|32262067|gb|AAP77116.1| conserved hypothetical protein [Helicobacter hepaticus ATCC
          51449]
          Length = 241

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 3/51 (5%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
           RLD + K      +    Q+ + SG VRV+ K V K +  ++S   V I 
Sbjct: 2  QRLDIYLKTLLS--SRTKAQEAIESGCVRVNGKVVYKSSLPLKSSDEVDID 50


>gi|27468095|ref|NP_764732.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           epidermidis ATCC 12228]
 gi|57866960|ref|YP_188633.1| pseudouridine synthase RluB [Staphylococcus epidermidis RP62A]
 gi|251810910|ref|ZP_04825383.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|293366546|ref|ZP_06613223.1| pseudouridine synthase RluB [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|27315641|gb|AAO04776.1|AE016748_10 ribosomal large subunit pseudouridine synthase B [Staphylococcus
           epidermidis ATCC 12228]
 gi|57637618|gb|AAW54406.1| pseudouridine synthase RluB [Staphylococcus epidermidis RP62A]
 gi|251805590|gb|EES58247.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|291319315|gb|EFE59684.1| pseudouridine synthase RluB [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|329725404|gb|EGG61887.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           epidermidis VCU144]
 gi|329735190|gb|EGG71482.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           epidermidis VCU045]
          Length = 245

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 75/235 (31%), Gaps = 53/235 (22%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+ + V    +++    +V +                        
Sbjct: 19  SRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVD----------------------- 55

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                    +  ED    +F KP  +     S         +  + D    +     RLD
Sbjct: 56  ------GIKIEQEDKIYILFYKPTQVIT---SVSDDRGRRVVTDYFDDLESRIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIG 209
            +TSG+L++         +T       I+K Y + + G    +  K+      L+  +  
Sbjct: 107 YDTSGVLLLTNDGEFTNLMT--HPRYHIKKKYVAKLKGYLMREEIKQLEKGIELEDGYTQ 164

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              V + KQ+++                +    +E+    GR  Q+R    + G 
Sbjct: 165 PAQVKIKKQDKE----------------KNTTLVEITISEGRNRQVRRMFEYFGH 203


>gi|325295025|ref|YP_004281539.1| pseudouridine synthase Rsu [Desulfurobacterium thermolithotrophum
           DSM 11699]
 gi|325065473|gb|ADY73480.1| pseudouridine synthase Rsu [Desulfurobacterium thermolithotrophum
           DSM 11699]
          Length = 252

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/211 (15%), Positives = 62/211 (29%), Gaps = 32/211 (15%)

Query: 19  MRLDRWFKNHYPHIN-FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           MRL+++    Y  +     ++++++ G+V V+ + V                      + 
Sbjct: 1   MRLNKFLA--YAGLGARRKVEELIKQGRVTVNGEVV---------------------ENP 37

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E       V +      L    +Y       FNKP G+               +  + 
Sbjct: 38  AVEVDPKKDEVRVDGERVRLPKRFIY-----LAFNKPQGVLTAMEREPGD-KRPIVADYF 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD  T G+L++      A+ L        I K Y + V G     +  
Sbjct: 92  RKYPVRLFPVGRLDYNTEGLLLMTNDGELAERLA--HPRYHIPKTYIAKVKGRVTPAEIE 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAIS 228
                 K     G        + K    + +
Sbjct: 150 RMKKGAKLVDDKGKPFFAKPIDIKLLKPSRT 180


>gi|182415600|ref|YP_001820666.1| RNA-binding S4 domain-containing protein [Opitutus terrae PB90-1]
 gi|177842814|gb|ACB77066.1| RNA-binding S4 domain protein [Opitutus terrae PB90-1]
          Length = 266

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/252 (14%), Positives = 90/252 (35%), Gaps = 48/252 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +RL ++  +     +    + ++ SG+V V+    +   ++  G           ++ 
Sbjct: 5   EPIRLQKYLADA-GVCSRRAAEALIASGEVWVNGAPAQVGQKVTPG-----------VDR 52

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +    K + ++                        +KP G+     +    H    + S 
Sbjct: 53  VTTGGKPVRTTAQPRVT---------------LAMHKPRGLVC---TNEDPHNPETIFSV 94

Query: 137 VDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
           +  +  K R     RLD+++ G++++      A  L        +++ + +L    P  +
Sbjct: 95  LPREFAKLRFFCAGRLDKDSEGLVILTTDGDLAHRLMHPS-NLVVKRYHVTLEKPFPAKR 153

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                  L+K     G+ + V +      N ++SH         +   L++  H G+  +
Sbjct: 154 L----PLLVKGVIAQGERLKVER--AALINPSVSH---------EATNLDVHMHHGKKRE 198

Query: 255 LRVHALHMGCPI 266
           +R+    +G P+
Sbjct: 199 IRLLFTELGYPV 210


>gi|153835311|ref|ZP_01987978.1| RNA pseudouridine synthase family protein [Vibrio harveyi HY01]
 gi|156975027|ref|YP_001445934.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio harveyi ATCC
           BAA-1116]
 gi|148868176|gb|EDL67329.1| RNA pseudouridine synthase family protein [Vibrio harveyi HY01]
 gi|156526621|gb|ABU71707.1| hypothetical protein VIBHAR_02753 [Vibrio harveyi ATCC BAA-1116]
          Length = 312

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 60/176 (34%), Gaps = 30/176 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   ++ +++SG+V V+    K   R++    VVRI   + +     +
Sbjct: 5   LQKVLARA-GHGSRREIESLIKSGRVSVNGIVAKLGERLEDENSVVRIDGHVVSAK--AQ 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E+ I                       ++  + KP G                       
Sbjct: 62  EEVIC----------------------RVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVTEQK 151


>gi|270263002|ref|ZP_06191272.1| ribosomal large subunit pseudouridine synthase F [Serratia
           odorifera 4Rx13]
 gi|270042690|gb|EFA15784.1| ribosomal large subunit pseudouridine synthase F [Serratia
           odorifera 4Rx13]
          Length = 287

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/247 (14%), Positives = 76/247 (30%), Gaps = 58/247 (23%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +  +  + +  G V ++ KRV   +R+  G VV++   +    +  
Sbjct: 8   RLNKYISE--SGICSRRDADRYIEQGNVFINGKRVALGDRVFPGDVVKVNGQLIEPRN-- 63

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKI-YVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                    ED+ I    NKP GI      G   +I  F+    
Sbjct: 64  -------------------------EDNLIFIALNKPVGIVSTTEEGEKDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD+++ G++ +         +  +      +               + 
Sbjct: 97  ---STRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYRV---------TVNKP 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + +  ++    G   +  V +  K    A   F+++                G   Q+R 
Sbjct: 145 VTDDFIRGLGAGVPMLGTVTKKCKVKKEAPFVFRIV-------------LVQGLNRQIRR 191

Query: 258 HALHMGC 264
              H G 
Sbjct: 192 MCEHFGY 198


>gi|194098813|ref|YP_002001876.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|254493881|ref|ZP_05107052.1| pseudouridine synthase [Neisseria gonorrhoeae 1291]
 gi|268594941|ref|ZP_06129108.1| pseudouridine synthase [Neisseria gonorrhoeae 35/02]
 gi|193934103|gb|ACF29927.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|226512921|gb|EEH62266.1| pseudouridine synthase [Neisseria gonorrhoeae 1291]
 gi|268548330|gb|EEZ43748.1| pseudouridine synthase [Neisseria gonorrhoeae 35/02]
 gi|317164395|gb|ADV07936.1| Pseudouridine synthase [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 416

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 48/156 (30%), Gaps = 28/156 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 162 EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 218

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 219 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 253

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
             +   +     RLD  TSG+L++  +    Q    
Sbjct: 254 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAH 289


>gi|324113141|gb|EGC07116.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
 gi|325497457|gb|EGC95316.1| 23S rRNA pseudouridylate synthase B [Escherichia fergusonii ECD227]
          Length = 290

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|15643034|ref|NP_228077.1| 16S pseudouridylate synthase [Thermotoga maritima MSB8]
 gi|4980760|gb|AAD35352.1|AE001708_20 16S pseudouridylate synthase [Thermotoga maritima MSB8]
          Length = 239

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 81/248 (32%), Gaps = 61/248 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MRLDR+  N         ++K+++ G+V V+ + V    + +     V +          
Sbjct: 1   MRLDRYLSNSGVG-TRKEVKKLIKQGRVTVNGRVVLDPGHPVLENDAVALD--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                 ++ +      +F KP+G      S    H +  ++   
Sbjct: 51  --------------------GEVVRFHKKVYILFYKPSGYVT---STKDPHSETIMEFLP 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK- 195
             KG  P    RLD++  G+L++      A + ++  +    ++K Y   V G     K 
Sbjct: 88  PLKGIFP--VGRLDKDAEGLLIITNDGDFAHRVISPKW---SVEKEYIVKVEGEVTEDKI 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E + N +  +         V K +       I+                     G+ HQ+
Sbjct: 143 EKLKNGVTLRDGFFAKAKRVEKLSNDTLKIVITE--------------------GKYHQI 182

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 183 KRMTAAVG 190


>gi|30062791|ref|NP_836962.1| 23S rRNA pseudouridylate synthase B [Shigella flexneri 2a str.
           2457T]
 gi|110805271|ref|YP_688791.1| 23S rRNA pseudouridylate synthase B [Shigella flexneri 5 str. 8401]
 gi|34098404|sp|P59815|RLUB_SHIFL RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|30041039|gb|AAP16769.1| hypothetical protein S1356 [Shigella flexneri 2a str. 2457T]
 gi|110614819|gb|ABF03486.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|281600690|gb|ADA73674.1| Ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           2002017]
 gi|313649457|gb|EFS13888.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           2a str. 2457T]
 gi|332757920|gb|EGJ88247.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           4343-70]
 gi|332759264|gb|EGJ89572.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           2747-71]
 gi|332760363|gb|EGJ90653.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           K-671]
 gi|332767503|gb|EGJ97697.1| 23S rRNA pseudouridine synthase [Shigella flexneri 2930-71]
 gi|333005742|gb|EGK25260.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           K-218]
 gi|333019134|gb|EGK38424.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           K-304]
          Length = 290

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|328951538|ref|YP_004368873.1| pseudouridine synthase Rsu [Marinithermus hydrothermalis DSM 14884]
 gi|328451862|gb|AEB12763.1| pseudouridine synthase Rsu [Marinithermus hydrothermalis DSM 14884]
          Length = 243

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 65/180 (36%), Gaps = 38/180 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+D+    H        ++++LR+G VRVD + V+                        
Sbjct: 6   ERIDKILA-HLGFGTRKEVKRLLRAGGVRVDGRVVR------------------------ 40

Query: 79  KEQKILDSSVNLTKHSDFLKS---ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                 D  + L      L+    +++++     +  KPAG+           +   L +
Sbjct: 41  ------DPGMKLDPARARLEVAGEVVVWQRHHHVMLYKPAGVVTATRDARHATVLDCLPA 94

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +  K        RLD++T G+L++    A    LT      ++ K+Y++ +    + + 
Sbjct: 95  SLARK--DLLPVGRLDRDTEGLLLLTTDGALLHRLT--HPRWKVPKVYYAELEQPARPED 150


>gi|312277957|gb|ADQ62614.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 239

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 81/247 (32%), Gaps = 51/247 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD+          +   ++K++RS QV VD                 +    + LN  
Sbjct: 1   MRLDKLLGQ--SGYGSRNQVKKLIRSRQVYVDG----------------VLADRDNLNVD 42

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
              Q I+ S   L    +             Y+ NKP+G+           +   ++   
Sbjct: 43  ASLQTIMVSGKELEHAPEV-----------YYLMNKPSGVVSARKDKEHQTVIDLIRPED 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
             +G  P    RLD++T G++++          L          + + +  + +  N   
Sbjct: 92  QREGLYP--VGRLDRDTEGLVLITNNGPLGFAMLH--------PRYHVAKTYYVEVNDIL 141

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                   +S        VV ++      A    +V+   + K C   +    G+ HQ++
Sbjct: 142 GPDAPAFFESG-------VVFEDGTVCQSA--QLEVLSSASDKSC-ARVTISEGKFHQVK 191

Query: 257 VHALHMG 263
              L  G
Sbjct: 192 KMFLAYG 198


>gi|295135656|ref|YP_003586332.1| ribosomal large subunit pseudouridine synthase F [Zunongwangia
           profunda SM-A87]
 gi|294983671|gb|ADF54136.1| ribosomal large subunit pseudouridine synthase F [Zunongwangia
           profunda SM-A87]
          Length = 278

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/252 (11%), Positives = 79/252 (31%), Gaps = 54/252 (21%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +E   R++++      + +     K++  G+V ++    +   +I  G  V++   + A
Sbjct: 2   AEENLTRINKFLSEA-GYCSRRAADKLIDQGRVTINGVVPEMGTKIAPGDEVKVDGELIA 60

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                K                      +Y       FNKP GI     +      +  +
Sbjct: 61  TEEKEKPN--------------------VY-----IAFNKPIGIVC--TTDTKREKNNII 93

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                +  ++     RLD+ + G++ +                         +V  I + 
Sbjct: 94  DYI--NYPERIFPIGRLDKPSEGLIFL--------------------TSDGDIVNKILRA 131

Query: 194 KKECIANWLLK-KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           +      +++K    +  D+V  + +     +  ++    ++   +      +    G  
Sbjct: 132 RNNHEKEYIVKVNKPLQPDFVKKMSKGIPILDT-VTRECFVEQTGENE--FRIILTQGLN 188

Query: 253 HQLRVHALHMGC 264
            Q+R    ++G 
Sbjct: 189 RQIRRMCEYLGY 200


>gi|283769551|ref|ZP_06342447.1| pseudouridylate synthase [Bulleidia extructa W1219]
 gi|283103819|gb|EFC05205.1| pseudouridylate synthase [Bulleidia extructa W1219]
          Length = 231

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/169 (15%), Positives = 60/169 (35%), Gaps = 34/169 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR   N     +   ++ ++++G+V V+ K    ++ +                   
Sbjct: 1   MRLDRVLANASVG-SRTQVKNMVKNGRVSVNGKIALASSMM------------------- 40

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                +D + ++ +  D +     Y+     +  KPAG            +   + ++  
Sbjct: 41  -----VDPNQDVIRIDDEILQYAKYQ---YLMLYKPAGYISATEGRYDPTVLELVPNYKG 92

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSL 186
                     RLD++T G+L++    R A   L+    + +   +   L
Sbjct: 93  -----LFPCGRLDKDTEGLLLMTNDGRLAHNLLSPKKHVEKEYYVEHQL 136


>gi|220929584|ref|YP_002506493.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|219999912|gb|ACL76513.1| pseudouridine synthase [Clostridium cellulolyticum H10]
          Length = 245

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/246 (13%), Positives = 81/246 (32%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N +   +   ++  ++ G V VD + +K                 ++  H+ 
Sbjct: 5   QRLDKVLSN-FGFGSRNYIKGAVKKGLVTVDGRIIK-----------------DSGIHVD 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  I++       +  ++            + NKP G+           +   L    +
Sbjct: 47  PEVSIIEIDGERLNYRKYI----------YIMLNKPQGVISATSDRKQKTVFDILPE--E 94

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K        RLD +T G++++      + + L+     + + K Y++ V G    +   
Sbjct: 95  YKCFDLFPAGRLDIDTEGLVLMTNDGQLSHEILS---PKKHVPKQYYAKVMGRVNQE--- 148

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                        +        + G     +  +++   +     +++    G+ HQ++ 
Sbjct: 149 -----------DAEAFSRGVTLDDGYQTLPAVLEILK--SDDLSEIKLTIVEGKFHQVKR 195

Query: 258 HALHMG 263
               +G
Sbjct: 196 MFEAVG 201


>gi|78188520|ref|YP_378858.1| pseudouridine synthase, Rsu [Chlorobium chlorochromatii CaD3]
 gi|78170719|gb|ABB27815.1| ribosomal large subunit pseudouridine synthase B [Chlorobium
           chlorochromatii CaD3]
          Length = 251

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 90/251 (35%), Gaps = 49/251 (19%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ++ + MR++R+        +     ++++ G+V ++ K V        G  V++ P    
Sbjct: 8   SNNDGMRINRFLA-MCGIASRRAADQLVQEGRVCINGKIVTT-----PG--VKVNPS--- 56

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                +++ I+D         +  K  +L         NKP  +               +
Sbjct: 57  -----RDEVIIDG--KRFAQPENRKVYIL--------LNKPRNVITTSS---DERQREMV 98

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
             ++D   ++     RLD++T+G++++      A  L        ++K Y +        
Sbjct: 99  LDFIDVP-ERIFPVGRLDRKTTGVILLTNDGELAHKL--MHPSSGVKKEYIA-------E 148

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
             E     +L K   G      ++  + G   +    K++D        + +  H G+ H
Sbjct: 149 LSERFPAAMLGKLTNG------MRLKDTGEKVSPCRAKLLD----DGMRVLLSIHEGKNH 198

Query: 254 QLRVHALHMGC 264
           Q+R     +G 
Sbjct: 199 QVRRMFDTLGF 209


>gi|15801910|ref|NP_287930.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7
           EDL933]
 gi|15831095|ref|NP_309868.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           Sakai]
 gi|74312362|ref|YP_310781.1| 23S rRNA pseudouridylate synthase B [Shigella sonnei Ss046]
 gi|82544277|ref|YP_408224.1| 23S rRNA pseudouridylate synthase B [Shigella boydii Sb227]
 gi|157154729|ref|YP_001462565.1| 23S rRNA pseudouridylate synthase B [Escherichia coli E24377A]
 gi|168751157|ref|ZP_02776179.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4113]
 gi|168758353|ref|ZP_02783360.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4401]
 gi|168763584|ref|ZP_02788591.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4501]
 gi|168771267|ref|ZP_02796274.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4486]
 gi|168775077|ref|ZP_02800084.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4196]
 gi|168783771|ref|ZP_02808778.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4076]
 gi|168790068|ref|ZP_02815075.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC869]
 gi|168801615|ref|ZP_02826622.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC508]
 gi|191166646|ref|ZP_03028474.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           B7A]
 gi|193062722|ref|ZP_03043816.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           E22]
 gi|193069992|ref|ZP_03050940.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           E110019]
 gi|194426137|ref|ZP_03058693.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           B171]
 gi|195939202|ref|ZP_03084584.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           EC4024]
 gi|208810912|ref|ZP_03252745.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4206]
 gi|208815453|ref|ZP_03256632.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4045]
 gi|208820806|ref|ZP_03261126.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4042]
 gi|209396722|ref|YP_002270323.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4115]
 gi|209918508|ref|YP_002292592.1| 23S rRNA pseudouridylate synthase B [Escherichia coli SE11]
 gi|217329090|ref|ZP_03445170.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. TW14588]
 gi|254792857|ref|YP_003077694.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           TW14359]
 gi|256018485|ref|ZP_05432350.1| 23S rRNA pseudouridylate synthase B [Shigella sp. D9]
 gi|260843616|ref|YP_003221394.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli O103:H2
           str. 12009]
 gi|260854966|ref|YP_003228857.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli O26:H11
           str. 11368]
 gi|260867717|ref|YP_003234119.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli O111:H-
           str. 11128]
 gi|261224251|ref|ZP_05938532.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261257493|ref|ZP_05950026.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291282356|ref|YP_003499174.1| Ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O55:H7 str. CB9615]
 gi|300820147|ref|ZP_07100316.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300822569|ref|ZP_07102708.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300904135|ref|ZP_07122008.1| hypothetical protein HMPREF9536_02226 [Escherichia coli MS 84-1]
 gi|300919449|ref|ZP_07135950.1| conserved hypothetical protein [Escherichia coli MS 115-1]
 gi|301304781|ref|ZP_07210887.1| hypothetical protein HMPREF9347_03390 [Escherichia coli MS 124-1]
 gi|307309978|ref|ZP_07589628.1| pseudouridine synthase [Escherichia coli W]
 gi|309793259|ref|ZP_07687686.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|331667653|ref|ZP_08368517.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA271]
 gi|332279541|ref|ZP_08391954.1| ribosomal large subunit pseudouridine synthase B [Shigella sp. D9]
 gi|34098616|sp|Q8X4Q8|RLUB_ECO57 RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|12515528|gb|AAG56546.1|AE005380_5 orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]
 gi|13361306|dbj|BAB35264.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|73855839|gb|AAZ88546.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|81245688|gb|ABB66396.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|157076759|gb|ABV16467.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           E24377A]
 gi|187769333|gb|EDU33177.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4196]
 gi|188014796|gb|EDU52918.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4113]
 gi|188998981|gb|EDU67967.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4076]
 gi|189354811|gb|EDU73230.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4401]
 gi|189359963|gb|EDU78382.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4486]
 gi|189366282|gb|EDU84698.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4501]
 gi|189370413|gb|EDU88829.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC869]
 gi|189376287|gb|EDU94703.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC508]
 gi|190903295|gb|EDV63016.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           B7A]
 gi|192931844|gb|EDV84444.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           E22]
 gi|192956745|gb|EDV87200.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           E110019]
 gi|194416192|gb|EDX32458.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           B171]
 gi|208724418|gb|EDZ74126.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4206]
 gi|208732101|gb|EDZ80789.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4045]
 gi|208740929|gb|EDZ88611.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4042]
 gi|209158122|gb|ACI35555.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. EC4115]
 gi|209772018|gb|ACI84321.1| hypothetical protein ECs1841 [Escherichia coli]
 gi|209772020|gb|ACI84322.1| hypothetical protein ECs1841 [Escherichia coli]
 gi|209772022|gb|ACI84323.1| hypothetical protein ECs1841 [Escherichia coli]
 gi|209772024|gb|ACI84324.1| hypothetical protein ECs1841 [Escherichia coli]
 gi|209772026|gb|ACI84325.1| hypothetical protein ECs1841 [Escherichia coli]
 gi|209911767|dbj|BAG76841.1| putative pseudouridine synthase [Escherichia coli SE11]
 gi|217317529|gb|EEC25957.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O157:H7 str. TW14588]
 gi|254592257|gb|ACT71618.1| 23S rRNA pseudouridylate synthase [Escherichia coli O157:H7 str.
           TW14359]
 gi|257753615|dbj|BAI25117.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli O26:H11
           str. 11368]
 gi|257758763|dbj|BAI30260.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli O103:H2
           str. 12009]
 gi|257764073|dbj|BAI35568.1| 23S rRNA pseudouridylate synthase RluB [Escherichia coli O111:H-
           str. 11128]
 gi|290762229|gb|ADD56190.1| Ribosomal large subunit pseudouridine synthase B [Escherichia coli
           O55:H7 str. CB9615]
 gi|300403900|gb|EFJ87438.1| hypothetical protein HMPREF9536_02226 [Escherichia coli MS 84-1]
 gi|300413471|gb|EFJ96781.1| conserved hypothetical protein [Escherichia coli MS 115-1]
 gi|300524985|gb|EFK46054.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300527302|gb|EFK48364.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300839902|gb|EFK67662.1| hypothetical protein HMPREF9347_03390 [Escherichia coli MS 124-1]
 gi|306909696|gb|EFN40190.1| pseudouridine synthase [Escherichia coli W]
 gi|308122846|gb|EFO60108.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|315060519|gb|ADT74846.1| 23S rRNA pseudouridylate synthase [Escherichia coli W]
 gi|315254773|gb|EFU34741.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           MS 85-1]
 gi|320176684|gb|EFW51722.1| 23S rRNA pseudouridylate synthase B [Shigella dysenteriae CDC
           74-1112]
 gi|320187507|gb|EFW62193.1| 23S rRNA pseudouridylate synthase B [Shigella flexneri CDC 796-83]
 gi|320189980|gb|EFW64632.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           EC1212]
 gi|320199303|gb|EFW73894.1| 23S rRNA pseudouridylate synthase B [Escherichia coli EC4100B]
 gi|320637163|gb|EFX06989.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           G5101]
 gi|320642529|gb|EFX11777.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H- str.
           493-89]
 gi|320647882|gb|EFX16590.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H- str.
           H 2687]
 gi|320653484|gb|EFX21589.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320659184|gb|EFX26773.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|323153300|gb|EFZ39558.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           EPECa14]
 gi|323162371|gb|EFZ48226.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           E128010]
 gi|323168243|gb|EFZ53928.1| ribosomal large subunit pseudouridine synthase B [Shigella sonnei
           53G]
 gi|323172376|gb|EFZ58013.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           LT-68]
 gi|323179780|gb|EFZ65341.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           1180]
 gi|323185573|gb|EFZ70934.1| ribosomal large subunit pseudouridine synthase B [Escherichia coli
           1357]
 gi|323378918|gb|ADX51186.1| pseudouridine synthase [Escherichia coli KO11]
 gi|326341071|gb|EGD64864.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           1125]
 gi|326343312|gb|EGD67079.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           1044]
 gi|331065238|gb|EGI37133.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA271]
 gi|332094735|gb|EGI99779.1| ribosomal large subunit pseudouridine synthase B [Shigella boydii
           3594-74]
 gi|332101893|gb|EGJ05239.1| ribosomal large subunit pseudouridine synthase B [Shigella sp. D9]
 gi|333004583|gb|EGK24107.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           VA-6]
 gi|333007605|gb|EGK27083.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           K-272]
 gi|333019539|gb|EGK38819.1| ribosomal large subunit pseudouridine synthase B [Shigella flexneri
           K-227]
          Length = 290

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|224825900|ref|ZP_03699004.1| RNA-binding S4 domain protein [Lutiella nitroferrum 2002]
 gi|224602124|gb|EEG08303.1| RNA-binding S4 domain protein [Lutiella nitroferrum 2002]
          Length = 242

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 45/252 (17%), Positives = 75/252 (29%), Gaps = 39/252 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +RL +         +       +  G V+VD +      ++   Q + + P       
Sbjct: 2   EPVRLSKRLAE-LGICSRREADSYIEQGWVKVDGQVAVLGFKVLPHQHIELDPRAKKAQ- 59

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                        L + +  L   + Y   +     KPA +     +       G   S 
Sbjct: 60  -------------LERVTILLNKPVGYVSGQAEKGYKPAAMLAVPANHWEGDKSGIRFSP 106

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              KG  P    RLD ++ G+LV+ +    A+ L        ++K Y   V G    +  
Sbjct: 107 NHLKGLAP--AGRLDIDSVGLLVLTQDGVVAKRL--IGENSTVEKEYLVRVTGELSPEGL 162

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + N  L           V  QNE                      L      G+  Q+R
Sbjct: 163 KLLNHGLSLDGQPLRPAKVSWQNED--------------------QLRFILREGKKRQIR 202

Query: 257 VHALHMGCPIVG 268
                +G  +VG
Sbjct: 203 RMCEQVGLYVVG 214


>gi|153949734|ref|YP_001401683.1| 16S rRNA pseudouridylate synthase A [Yersinia pseudotuberculosis IP
           31758]
 gi|170025018|ref|YP_001721523.1| 16S rRNA pseudouridylate synthase A [Yersinia pseudotuberculosis
           YPIII]
 gi|152961229|gb|ABS48690.1| ribosomal small subunit pseudouridine synthase A [Yersinia
           pseudotuberculosis IP 31758]
 gi|169751552|gb|ACA69070.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
          Length = 235

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 73/245 (29%), Gaps = 51/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK      SG +            + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEVVK------SGAI-----------KLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEQDVRFDGNPLQQMVGP----------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G+++                  +      S      K     +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVL-------------MTDDGQWSHRVTSPRHHCEKTYLVTL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L   +         +   +     A     VI+        + +    GR HQ++  
Sbjct: 137 EHPLSDDTAQQFADGVQLHNEKSLTKPA--QLDVIEPQ-----RVRLTISEGRYHQVKRM 189

Query: 259 ALHMG 263
              +G
Sbjct: 190 FAAVG 194


>gi|218690332|ref|YP_002398544.1| 16S rRNA pseudouridylate synthase A [Escherichia coli ED1a]
 gi|218427896|emb|CAR08815.2| 16S rRNA pseudouridylate 516 synthase [Escherichia coli ED1a]
          Length = 231

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|330015788|ref|ZP_08308280.1| 16S pseudouridylate 516 synthase [Klebsiella sp. MS 92-3]
 gi|328530489|gb|EGF57362.1| 16S pseudouridylate 516 synthase [Klebsiella sp. MS 92-3]
          Length = 239

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 79/251 (31%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++     + +R  +V VD   VK  + ++Q                 
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGSRVTVDGDIVKDASFKLQ----------------- 42

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E ++      LT+ +            + ++ NKP G      S         L    
Sbjct: 43  -PEHEVEYDGNTLTQQNGP----------RYFMLNKPQGYVC---STDDPDHPTILYFLD 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    K     RLD +T+G++++      +  +T          +               
Sbjct: 89  EPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVA------------- 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + N L + +         +   +     A+   +VI         + +    GR HQ++ 
Sbjct: 136 LENPLAEGTAELFAKGVQLHNEKDLTKPAL--LEVI-----TPTEVRLTISEGRYHQVKR 188

Query: 258 HALHMGCPIVG 268
               +G  +VG
Sbjct: 189 MFAAVGNHVVG 199


>gi|167622881|ref|YP_001673175.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167352903|gb|ABZ75516.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 234

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 85/249 (34%), Gaps = 52/249 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+       IN   ++ +L  GQV VD +  +            I  +I+  +H+  
Sbjct: 7   RLDRFISVK-TGINKKYVRLLLAKGQVLVDGEIAR-----------DIDLIIDQFSHVSL 54

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + ++L ++            ++LY         KP G+     + I       +      
Sbjct: 55  DGQVLQANAP--------SYVMLY---------KPVGVVS---ATIDDKHKTVIDLLDRE 94

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                 +  RLD  TSG+L++      ++ L       ++ K+Y           +  + 
Sbjct: 95  DKHSLHIVGRLDLNTSGLLLLTNDGRWSKKL--MSPQHKVDKVY-----------RVTLK 141

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           N + +   +           +     A    +++D        +E     GR HQ++   
Sbjct: 142 NPIDESYIVAFAAGMYFAFEDITTQPA--KLEIVDDHTALVTLVE-----GRYHQIKRMF 194

Query: 260 LHMGCPIVG 268
                P++G
Sbjct: 195 GRFRNPVIG 203


>gi|70726424|ref|YP_253338.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           haemolyticus JCSC1435]
 gi|68447148|dbj|BAE04732.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           haemolyticus JCSC1435]
          Length = 245

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/234 (14%), Positives = 73/234 (31%), Gaps = 51/234 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+ + V     +++S   V +                    + + 
Sbjct: 19  SRRKAETLITEGKVKVNGQTVTELGTKVKSSDTVEV------------------EGIKIE 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +           ED    +F KP  +     S         +  +      +     RLD
Sbjct: 61  Q-----------EDKMYILFYKPTQVIT---SVSDDRGRTVVTDYFKDLETRIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGG 210
            +TSG+L++         +T       IQK Y + + G + + + + + N +        
Sbjct: 107 YDTSGLLLLTNDGEFTNLMT--HPRYHIQKKYVAKLKGYLMREEVKALENGI-------- 156

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                  + E G               +    +E+    GR  Q+R    H G 
Sbjct: 157 -------ELEDGFTQPAQVKVKKQDKDKNITLVEITISEGRNRQVRRMFEHFGH 203


>gi|33151571|ref|NP_872924.1| pseudouridylate synthase [Haemophilus ducreyi 35000HP]
 gi|33147791|gb|AAP95313.1| probable pseudouridylate synthase [Haemophilus ducreyi 35000HP]
          Length = 229

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/172 (17%), Positives = 61/172 (35%), Gaps = 8/172 (4%)

Query: 96  FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETS 155
             K  + + ++ + +FNKP  +  Q            LK ++  +   P    RLD+++ 
Sbjct: 27  PPKPKVSFAETIVLLFNKPYNVLSQFS---DQQGRATLKDFIPIENVYP--VGRLDRDSE 81

Query: 156 GILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV 215
           G+L++         L      +   K Y + + G P+            +   G      
Sbjct: 82  GLLLLTNNGEIQHRLAHPKFEKV--KTYLAQLEGQPQAVDLA-KLTCGVELKDGLTRPAK 138

Query: 216 VKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           V           +   + +       WLE++ + G+  Q+R    H+G P +
Sbjct: 139 VSVIAPPNYNWHTAPNIRERKTIPTSWLELKIYEGKNRQVRRMTAHIGFPTL 190


>gi|312128212|ref|YP_003993086.1| RNA-binding S4 domain-containing protein [Caldicellulosiruptor
          hydrothermalis 108]
 gi|311778231|gb|ADQ07717.1| RNA-binding S4 domain protein [Caldicellulosiruptor
          hydrothermalis 108]
          Length = 80

 Score = 55.0 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 24/50 (48%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          MR+D++ K           Q+   +G+V V+ K  K +  ++ G V+ + 
Sbjct: 1  MRIDKYLKVSRIIKRRTLAQQACEAGRVFVNGKVAKPSTDVKVGDVIEVH 50


>gi|52425093|ref|YP_088230.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52307145|gb|AAU37645.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 402

 Score = 55.0 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/177 (15%), Positives = 57/177 (32%), Gaps = 27/177 (15%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  +L +         +   ++ I+  G+V VD K     +R+     ++I    + +N 
Sbjct: 118 EGEKLQKVLARAGQG-SRREIESIIEQGRVSVDGKIATLGDRVTVHDGLKIRIDGHLVNL 176

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
              ++++                       ++ ++ KP G                    
Sbjct: 177 TAAQREVC----------------------RVLMYYKPEGELC--TRHDPEGRATVFDRL 212

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
               G +     RLD  TSG+L+       A  L      + +++ Y   V+G   +
Sbjct: 213 PRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSQEVEREYSVRVFGQVDD 267


>gi|293409653|ref|ZP_06653229.1| conserved hypothetical protein [Escherichia coli B354]
 gi|291470121|gb|EFF12605.1| conserved hypothetical protein [Escherichia coli B354]
          Length = 291

 Score = 55.0 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDTK 152


>gi|15802739|ref|NP_288766.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7
           EDL933]
 gi|15832329|ref|NP_311102.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           Sakai]
 gi|16130121|ref|NP_416688.1| 16S rRNA U516 pseudouridine synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|24113572|ref|NP_708082.1| 16S rRNA pseudouridylate synthase A [Shigella flexneri 2a str. 301]
 gi|30063626|ref|NP_837797.1| 16S rRNA pseudouridylate synthase A [Shigella flexneri 2a str.
           2457T]
 gi|82544599|ref|YP_408546.1| 16S rRNA pseudouridylate synthase A [Shigella boydii Sb227]
 gi|89109001|ref|AP_002781.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli str. K-12
           substr. W3110]
 gi|110642394|ref|YP_670124.1| 16S rRNA pseudouridylate synthase A [Escherichia coli 536]
 gi|117624381|ref|YP_853294.1| 16S rRNA pseudouridylate synthase A [Escherichia coli APEC O1]
 gi|157155587|ref|YP_001463536.1| 16S rRNA pseudouridylate synthase A [Escherichia coli E24377A]
 gi|157161665|ref|YP_001458983.1| 16S rRNA pseudouridylate synthase A [Escherichia coli HS]
 gi|161486177|ref|NP_754606.2| 16S rRNA pseudouridylate synthase A [Escherichia coli CFT073]
 gi|162138407|ref|YP_541459.2| 16S rRNA pseudouridylate synthase A [Escherichia coli UTI89]
 gi|168749590|ref|ZP_02774612.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4113]
 gi|168759074|ref|ZP_02784081.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4401]
 gi|168767807|ref|ZP_02792814.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4486]
 gi|168773096|ref|ZP_02798103.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4196]
 gi|168780036|ref|ZP_02805043.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4076]
 gi|168789002|ref|ZP_02814009.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC869]
 gi|170019500|ref|YP_001724454.1| 16S rRNA pseudouridylate synthase A [Escherichia coli ATCC 8739]
 gi|170081805|ref|YP_001731125.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli str. K-12
           substr. DH10B]
 gi|170681582|ref|YP_001744379.1| 16S rRNA pseudouridylate synthase A [Escherichia coli SMS-3-5]
 gi|188495180|ref|ZP_03002450.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           53638]
 gi|191165380|ref|ZP_03027222.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           B7A]
 gi|191170122|ref|ZP_03031676.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           F11]
 gi|193062338|ref|ZP_03043433.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           E22]
 gi|194427231|ref|ZP_03059782.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           B171]
 gi|194434188|ref|ZP_03066455.1| ribosomal small subunit pseudouridine synthase A [Shigella
           dysenteriae 1012]
 gi|194436203|ref|ZP_03068305.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           101-1]
 gi|195935565|ref|ZP_03080947.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           EC4024]
 gi|208805677|ref|ZP_03248014.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4206]
 gi|208814565|ref|ZP_03255894.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4045]
 gi|208818354|ref|ZP_03258674.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4042]
 gi|209400555|ref|YP_002271597.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4115]
 gi|209919643|ref|YP_002293727.1| 16S rRNA pseudouridylate synthase A [Escherichia coli SE11]
 gi|215487405|ref|YP_002329836.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217327530|ref|ZP_03443613.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. TW14588]
 gi|218559104|ref|YP_002392017.1| 16S rRNA pseudouridylate synthase A [Escherichia coli S88]
 gi|218695798|ref|YP_002403465.1| 16S rRNA pseudouridylate synthase A [Escherichia coli 55989]
 gi|218700655|ref|YP_002408284.1| 16S rRNA pseudouridylate synthase A [Escherichia coli IAI39]
 gi|218705715|ref|YP_002413234.1| 16S rRNA pseudouridylate synthase A [Escherichia coli UMN026]
 gi|227887240|ref|ZP_04005045.1| 16S rRNA pseudouridylate synthase A [Escherichia coli 83972]
 gi|237704656|ref|ZP_04535137.1| ribosomal small subunit pseudouridine synthase A [Escherichia sp.
           3_2_53FAA]
 gi|238901360|ref|YP_002927156.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli BW2952]
 gi|253772890|ref|YP_003035721.1| 16S rRNA pseudouridylate synthase A [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254162198|ref|YP_003045306.1| 16S rRNA pseudouridylate synthase A [Escherichia coli B str.
           REL606]
 gi|254794084|ref|YP_003078921.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           TW14359]
 gi|256017648|ref|ZP_05431513.1| 16S rRNA pseudouridylate synthase A [Shigella sp. D9]
 gi|256022132|ref|ZP_05435997.1| 16S rRNA pseudouridylate synthase A [Escherichia sp. 4_1_40B]
 gi|260844789|ref|YP_003222567.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O103:H2 str. 12009]
 gi|260856157|ref|YP_003230048.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O26:H11 str. 11368]
 gi|260868884|ref|YP_003235286.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O111:H- str. 11128]
 gi|261223356|ref|ZP_05937637.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli O157:H7
           str. FRIK2000]
 gi|261259093|ref|ZP_05951626.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O157:H7 str. FRIK966]
 gi|291283437|ref|YP_003500255.1| Pseudouridine synthase [Escherichia coli O55:H7 str. CB9615]
 gi|293405651|ref|ZP_06649643.1| 16S rRNA pseudouridylate synthase A [Escherichia coli FVEC1412]
 gi|293410547|ref|ZP_06654123.1| 16S rRNA pseudouridylate synthase A [Escherichia coli B354]
 gi|293415469|ref|ZP_06658112.1| 16S rRNA pseudouridylate synthase A [Escherichia coli B185]
 gi|293446535|ref|ZP_06662957.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           B088]
 gi|298381333|ref|ZP_06990932.1| 16S rRNA pseudouridylate synthase A [Escherichia coli FVEC1302]
 gi|300819120|ref|ZP_07099322.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300822636|ref|ZP_07102774.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300897756|ref|ZP_07116149.1| conserved hypothetical protein [Escherichia coli MS 198-1]
 gi|300918831|ref|ZP_07135400.1| conserved hypothetical protein [Escherichia coli MS 115-1]
 gi|300926291|ref|ZP_07142094.1| hypothetical protein HMPREF9548_04311 [Escherichia coli MS 182-1]
 gi|300930419|ref|ZP_07145828.1| conserved hypothetical protein [Escherichia coli MS 187-1]
 gi|300935111|ref|ZP_07150142.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|300950052|ref|ZP_07163999.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300956858|ref|ZP_07169118.1| hypothetical protein HMPREF9547_02661 [Escherichia coli MS 175-1]
 gi|300981435|ref|ZP_07175516.1| hypothetical protein HMPREF9553_01804 [Escherichia coli MS 200-1]
 gi|300982903|ref|ZP_07176367.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|301021043|ref|ZP_07185086.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|301024319|ref|ZP_07188008.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|301048923|ref|ZP_07195916.1| conserved hypothetical protein [Escherichia coli MS 185-1]
 gi|301328667|ref|ZP_07221728.1| conserved hypothetical protein [Escherichia coli MS 78-1]
 gi|301644209|ref|ZP_07244217.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|307138843|ref|ZP_07498199.1| 16S rRNA pseudouridylate synthase A [Escherichia coli H736]
 gi|307311237|ref|ZP_07590881.1| pseudouridine synthase [Escherichia coli W]
 gi|309793067|ref|ZP_07687495.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|312967483|ref|ZP_07781698.1| conserved hypothetical protein [Escherichia coli 2362-75]
 gi|331642812|ref|ZP_08343947.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli H736]
 gi|331647839|ref|ZP_08348931.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli M605]
 gi|331653617|ref|ZP_08354618.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli M718]
 gi|331658264|ref|ZP_08359226.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA206]
 gi|331663688|ref|ZP_08364598.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA143]
 gi|331668887|ref|ZP_08369735.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA271]
 gi|331673705|ref|ZP_08374468.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA280]
 gi|331678137|ref|ZP_08378812.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli H591]
 gi|332278659|ref|ZP_08391072.1| 16S rRNA pseudouridylate 516 synthase [Shigella sp. D9]
 gi|76364197|sp|P0AA43|RSUA_ECOLI RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|88941974|sp|P0AA45|RSUA_ECO57 RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|88941975|sp|P0AA44|RSUA_ECOL6 RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|88941976|sp|P0AA46|RSUA_SHIFL RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|12516515|gb|AAG57321.1|AE005451_2 16S pseudouridylate 516 synthase [Escherichia coli O157:H7 str.
           EDL933]
 gi|405907|gb|AAA16377.1| yejD [Escherichia coli]
 gi|1042177|gb|AAB34905.1| 16S RNA pseudouridine 516 synthase, 16S RNA psi 516 synthase=rsuA
           gene product [Escherichia coli, Peptide, 231 aa]
 gi|1788510|gb|AAC75244.1| 16S rRNA U516 pseudouridine synthase [Escherichia coli str. K-12
           substr. MG1655]
 gi|13362544|dbj|BAB36498.1| 16S pseudouridylate 516 synthase [Escherichia coli O157:H7 str.
           Sakai]
 gi|24052623|gb|AAN43789.1| 16S pseudouridylate 516 synthase [Shigella flexneri 2a str. 301]
 gi|30041879|gb|AAP17606.1| 16S pseudouridylate 516 synthase [Shigella flexneri 2a str. 2457T]
 gi|81246010|gb|ABB66718.1| 16S pseudouridylate 516 synthase [Shigella boydii Sb227]
 gi|85675292|dbj|BAE76648.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli str. K12
           substr. W3110]
 gi|110343986|gb|ABG70223.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           536]
 gi|115513505|gb|ABJ01580.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli APEC O1]
 gi|157067345|gb|ABV06600.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           HS]
 gi|157077617|gb|ABV17325.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           E24377A]
 gi|169754428|gb|ACA77127.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|169889640|gb|ACB03347.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli str. K-12
           substr. DH10B]
 gi|170519300|gb|ACB17478.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           SMS-3-5]
 gi|187771075|gb|EDU34919.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4196]
 gi|188016070|gb|EDU54192.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4113]
 gi|188490379|gb|EDU65482.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           53638]
 gi|189002071|gb|EDU71057.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4076]
 gi|189354270|gb|EDU72689.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4401]
 gi|189363003|gb|EDU81422.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4486]
 gi|189371377|gb|EDU89793.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC869]
 gi|190904543|gb|EDV64250.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           B7A]
 gi|190909638|gb|EDV69223.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           F11]
 gi|192932004|gb|EDV84603.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           E22]
 gi|194414852|gb|EDX31123.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           B171]
 gi|194417517|gb|EDX33619.1| ribosomal small subunit pseudouridine synthase A [Shigella
           dysenteriae 1012]
 gi|194424931|gb|EDX40916.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           101-1]
 gi|208725478|gb|EDZ75079.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4206]
 gi|208735842|gb|EDZ84529.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4045]
 gi|208738477|gb|EDZ86159.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4042]
 gi|209161955|gb|ACI39388.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. EC4115]
 gi|209765918|gb|ACI81271.1| 16S pseudouridylate 516 synthase [Escherichia coli]
 gi|209765920|gb|ACI81272.1| 16S pseudouridylate 516 synthase [Escherichia coli]
 gi|209765922|gb|ACI81273.1| 16S pseudouridylate 516 synthase [Escherichia coli]
 gi|209765924|gb|ACI81274.1| 16S pseudouridylate 516 synthase [Escherichia coli]
 gi|209765926|gb|ACI81275.1| 16S pseudouridylate 516 synthase [Escherichia coli]
 gi|209912902|dbj|BAG77976.1| ribosomal small subunit pseudouridine synthase [Escherichia coli
           SE11]
 gi|215265477|emb|CAS09878.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli O127:H6
           str. E2348/69]
 gi|217319897|gb|EEC28322.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           O157:H7 str. TW14588]
 gi|218352530|emb|CAU98307.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli 55989]
 gi|218365873|emb|CAR03614.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli S88]
 gi|218370641|emb|CAR18450.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli IAI39]
 gi|218432812|emb|CAR13706.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli UMN026]
 gi|222033944|emb|CAP76685.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           LF82]
 gi|226901022|gb|EEH87281.1| ribosomal small subunit pseudouridine synthase A [Escherichia sp.
           3_2_53FAA]
 gi|227835590|gb|EEJ46056.1| 16S rRNA pseudouridylate synthase A [Escherichia coli 83972]
 gi|238859736|gb|ACR61734.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli BW2952]
 gi|242377823|emb|CAQ32589.1| 16S rRNA pseudouridine 516 synthase [Escherichia coli BL21(DE3)]
 gi|253323934|gb|ACT28536.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253974099|gb|ACT39770.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli B str.
           REL606]
 gi|253978266|gb|ACT43936.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli BL21(DE3)]
 gi|254593484|gb|ACT72845.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli O157:H7
           str. TW14359]
 gi|257754806|dbj|BAI26308.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O26:H11 str. 11368]
 gi|257759936|dbj|BAI31433.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O103:H2 str. 12009]
 gi|257765240|dbj|BAI36735.1| 16S rRNA pseudouridylate 516 synthase RsuA [Escherichia coli
           O111:H- str. 11128]
 gi|260448722|gb|ACX39144.1| pseudouridine synthase [Escherichia coli DH1]
 gi|281179275|dbj|BAI55605.1| ribosomal small subunit pseudouridine synthase [Escherichia coli
           SE15]
 gi|284922167|emb|CBG35249.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           042]
 gi|290763310|gb|ADD57271.1| Pseudouridine synthase [Escherichia coli O55:H7 str. CB9615]
 gi|291323365|gb|EFE62793.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           B088]
 gi|291427859|gb|EFF00886.1| 16S rRNA pseudouridylate synthase A [Escherichia coli FVEC1412]
 gi|291433117|gb|EFF06096.1| 16S rRNA pseudouridylate synthase A [Escherichia coli B185]
 gi|291471015|gb|EFF13499.1| 16S rRNA pseudouridylate synthase A [Escherichia coli B354]
 gi|294489663|gb|ADE88419.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           IHE3034]
 gi|298278775|gb|EFI20289.1| 16S rRNA pseudouridylate synthase A [Escherichia coli FVEC1302]
 gi|299880416|gb|EFI88627.1| conserved hypothetical protein [Escherichia coli MS 196-1]
 gi|300299299|gb|EFJ55684.1| conserved hypothetical protein [Escherichia coli MS 185-1]
 gi|300307508|gb|EFJ62028.1| hypothetical protein HMPREF9553_01804 [Escherichia coli MS 200-1]
 gi|300316339|gb|EFJ66123.1| hypothetical protein HMPREF9547_02661 [Escherichia coli MS 175-1]
 gi|300358471|gb|EFJ74341.1| conserved hypothetical protein [Escherichia coli MS 198-1]
 gi|300398295|gb|EFJ81833.1| conserved hypothetical protein [Escherichia coli MS 69-1]
 gi|300408703|gb|EFJ92241.1| conserved hypothetical protein [Escherichia coli MS 45-1]
 gi|300414074|gb|EFJ97384.1| conserved hypothetical protein [Escherichia coli MS 115-1]
 gi|300417720|gb|EFK01031.1| hypothetical protein HMPREF9548_04311 [Escherichia coli MS 182-1]
 gi|300450542|gb|EFK14162.1| conserved hypothetical protein [Escherichia coli MS 116-1]
 gi|300459692|gb|EFK23185.1| conserved hypothetical protein [Escherichia coli MS 21-1]
 gi|300461741|gb|EFK25234.1| conserved hypothetical protein [Escherichia coli MS 187-1]
 gi|300524836|gb|EFK45905.1| conserved hypothetical protein [Escherichia coli MS 119-7]
 gi|300528273|gb|EFK49335.1| conserved hypothetical protein [Escherichia coli MS 107-1]
 gi|300845059|gb|EFK72819.1| conserved hypothetical protein [Escherichia coli MS 78-1]
 gi|301077507|gb|EFK92313.1| conserved hypothetical protein [Escherichia coli MS 146-1]
 gi|306908743|gb|EFN39240.1| pseudouridine synthase [Escherichia coli W]
 gi|307554252|gb|ADN47027.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           ABU 83972]
 gi|307626276|gb|ADN70580.1| 16S rRNA pseudouridylate synthase A [Escherichia coli UM146]
 gi|308123353|gb|EFO60615.1| conserved hypothetical protein [Escherichia coli MS 145-7]
 gi|309702498|emb|CBJ01824.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           ETEC H10407]
 gi|312287680|gb|EFR15585.1| conserved hypothetical protein [Escherichia coli 2362-75]
 gi|312946803|gb|ADR27630.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O83:H1 str.
           NRG 857C]
 gi|313651297|gb|EFS15695.1| hypothetical protein SF2457T_0264 [Shigella flexneri 2a str. 2457T]
 gi|315061493|gb|ADT75820.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli W]
 gi|315136817|dbj|BAJ43976.1| pseudouridine synthase [Escherichia coli DH1]
 gi|315285741|gb|EFU45181.1| conserved hypothetical protein [Escherichia coli MS 110-3]
 gi|315294447|gb|EFU53795.1| conserved hypothetical protein [Escherichia coli MS 153-1]
 gi|315297949|gb|EFU57219.1| conserved hypothetical protein [Escherichia coli MS 16-3]
 gi|315615429|gb|EFU96061.1| RNA pseudouridylate synthase family protein [Escherichia coli 3431]
 gi|320174783|gb|EFW49909.1| 16S rRNA pseudouridylate synthase A [Shigella dysenteriae CDC
           74-1112]
 gi|320178861|gb|EFW53824.1| 16S rRNA pseudouridylate synthase A [Shigella boydii ATCC 9905]
 gi|320184699|gb|EFW59492.1| 16S rRNA pseudouridylate synthase A [Shigella flexneri CDC 796-83]
 gi|320192188|gb|EFW66833.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           EC1212]
 gi|320199781|gb|EFW74370.1| 16S rRNA pseudouridylate synthase A [Escherichia coli EC4100B]
 gi|320641254|gb|EFX10732.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           G5101]
 gi|320646643|gb|EFX15554.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H- str.
           493-89]
 gi|320651898|gb|EFX20273.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H- str.
           H 2687]
 gi|320657623|gb|EFX25421.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320663228|gb|EFX30537.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|323152225|gb|EFZ38515.1| RNA pseudouridylate synthase [Escherichia coli EPECa14]
 gi|323161735|gb|EFZ47617.1| RNA pseudouridylate synthase [Escherichia coli E128010]
 gi|323171836|gb|EFZ57480.1| RNA pseudouridylate synthase [Escherichia coli LT-68]
 gi|323176916|gb|EFZ62506.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           1180]
 gi|323184191|gb|EFZ69568.1| RNA pseudouridylate synthase [Escherichia coli 1357]
 gi|323188090|gb|EFZ73385.1| RNA pseudouridylate synthase [Escherichia coli RN587/1]
 gi|323377926|gb|ADX50194.1| pseudouridine synthase [Escherichia coli KO11]
 gi|323936800|gb|EGB33085.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323940746|gb|EGB36934.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323951979|gb|EGB47853.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323955953|gb|EGB51706.1| RNA pseudouridylate synthase [Escherichia coli H263]
 gi|323961577|gb|EGB57184.1| RNA pseudouridylate synthase [Escherichia coli H489]
 gi|323972934|gb|EGB68131.1| RNA pseudouridylate synthase [Escherichia coli TA007]
 gi|324006506|gb|EGB75725.1| hypothetical protein HMPREF9532_03776 [Escherichia coli MS 57-2]
 gi|324013929|gb|EGB83148.1| hypothetical protein HMPREF9533_01960 [Escherichia coli MS 60-1]
 gi|324020657|gb|EGB89876.1| hypothetical protein HMPREF9542_00685 [Escherichia coli MS 117-3]
 gi|324117976|gb|EGC11875.1| RNA pseudouridylate synthase [Escherichia coli E1167]
 gi|326339539|gb|EGD63350.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           1125]
 gi|326344000|gb|EGD67761.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           1044]
 gi|330912016|gb|EGH40526.1| ribosomal small subunit pseudouridine synthase A [Escherichia coli
           AA86]
 gi|331039610|gb|EGI11830.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli H736]
 gi|331043563|gb|EGI15701.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli M605]
 gi|331048466|gb|EGI20542.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli M718]
 gi|331056512|gb|EGI28521.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA206]
 gi|331059487|gb|EGI31464.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA143]
 gi|331064081|gb|EGI35992.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA271]
 gi|331068978|gb|EGI40370.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli TA280]
 gi|331074597|gb|EGI45917.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Escherichia coli H591]
 gi|332093691|gb|EGI98749.1| ribosomal small subunit pseudouridine synthase A [Shigella boydii
           3594-74]
 gi|332096238|gb|EGJ01241.1| ribosomal small subunit pseudouridine synthase A [Shigella
           dysenteriae 155-74]
 gi|332101011|gb|EGJ04357.1| 16S rRNA pseudouridylate 516 synthase [Shigella sp. D9]
 gi|332343965|gb|AEE57299.1| conserved hypothetical protein [Escherichia coli UMNK88]
 gi|332754826|gb|EGJ85191.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           4343-70]
 gi|332755230|gb|EGJ85594.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           K-671]
 gi|332756177|gb|EGJ86528.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           2747-71]
 gi|332765997|gb|EGJ96207.1| 16S rRNA pseudouridine synthase [Shigella flexneri 2930-71]
 gi|333001324|gb|EGK20892.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           VA-6]
 gi|333001796|gb|EGK21362.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           K-218]
 gi|333002908|gb|EGK22464.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           K-272]
 gi|333016616|gb|EGK35945.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           K-304]
 gi|333016912|gb|EGK36236.1| ribosomal small subunit pseudouridine synthase A [Shigella flexneri
           K-227]
          Length = 231

 Score = 55.0 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|313904278|ref|ZP_07837656.1| pseudouridine synthase [Eubacterium cellulosolvens 6]
 gi|313470828|gb|EFR66152.1| pseudouridine synthase [Eubacterium cellulosolvens 6]
          Length = 256

 Score = 55.0 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 72/248 (29%), Gaps = 41/248 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  +         L+  +R G   V+  R+                         
Sbjct: 1   MRLDKYLSDMNVG-TRKELKTKIRKGAATVNGIRITD----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                   S+   +   F    + Y + + Y+ NKPAG+     +         L     
Sbjct: 37  -----PGFSIKGDEDVTFDGKPIRYNEYEYYMLNKPAGVIT---ATEDRKQQTVLDLLGK 88

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN----- 193
            + +      RLD+ T G+L++         L      +   K Y++ + G   +     
Sbjct: 89  DRRKDLFPVGRLDKNTVGLLLITNDGDLNHKL--LSPKKHTDKKYYAKIDGRVTDADVEA 146

Query: 194 --KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             K   I + L                 +      ++        +     + +  H G+
Sbjct: 147 FAKGLRIDDELTALPAKLEILSFRETATDADREDLLTAEHPESSLSSGVSEICVTIHEGK 206

Query: 252 THQLRVHA 259
            HQ++   
Sbjct: 207 FHQIKRMF 214


>gi|306814702|ref|ZP_07448864.1| 16S rRNA pseudouridylate synthase A [Escherichia coli NC101]
 gi|305852096|gb|EFM52548.1| 16S rRNA pseudouridylate synthase A [Escherichia coli NC101]
 gi|320196056|gb|EFW70680.1| 16S rRNA pseudouridylate synthase A [Escherichia coli WV_060327]
          Length = 231

 Score = 55.0 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|197284775|ref|YP_002150647.1| ribosomal large subunit pseudouridine synthase E [Proteus mirabilis
           HI4320]
 gi|227357781|ref|ZP_03842130.1| RluE protein [Proteus mirabilis ATCC 29906]
 gi|194682262|emb|CAR41996.1| ribosomal large subunit pseudouridine synthase E [Proteus mirabilis
           HI4320]
 gi|227162110|gb|EEI47124.1| RluE protein [Proteus mirabilis ATCC 29906]
          Length = 209

 Score = 55.0 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/164 (22%), Positives = 67/164 (40%), Gaps = 16/164 (9%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAA 166
           + +FNKP  + VQ      +  D   K+  D           RLD+++ G+LV+      
Sbjct: 32  VIIFNKPFDVLVQ------FTDDSGRKTLKDFIPIPDIYAAGRLDRDSEGLLVLTNDGKL 85

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
              LT+    ++  K+Y++ V GIP      IA    ++     D   +  + E+     
Sbjct: 86  QAKLTQ--PNKKTGKVYYAQVEGIPTE----IALQQFREGLNLKDGKTLPAKIERVEQPT 139

Query: 227 I--SHFKVI-DCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              + F  I +  +    WL++    G+  Q+R    H+G P +
Sbjct: 140 WVWTRFPPIRERQSIPTSWLKITLFEGKNRQVRRMTAHIGYPTL 183


>gi|76157234|gb|AAX28220.2| SJCHGC03415 protein [Schistosoma japonicum]
          Length = 184

 Score = 55.0 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 4/57 (7%)

Query: 224 NYAISHFKVIDC---FAQKFCWLEMQPHTGRTHQLRVHAL-HMGCPIVGDHKYCANF 276
             +++   V+       +    + + P TGR HQLRVH    +G PI GD  Y    
Sbjct: 29  RESLTTIIVLGYGKLMGEPATRVLLIPKTGRRHQLRVHCAVGLGHPIAGDITYVRRP 85


>gi|322615369|gb|EFY12289.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322618430|gb|EFY15319.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322622159|gb|EFY19009.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322627229|gb|EFY24021.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322631190|gb|EFY27954.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322637592|gb|EFY34293.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322642558|gb|EFY39155.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322643574|gb|EFY40129.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322648310|gb|EFY44769.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322654619|gb|EFY50939.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322659579|gb|EFY55822.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322662213|gb|EFY58429.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322666043|gb|EFY62221.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322672462|gb|EFY68573.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322675891|gb|EFY71962.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322680375|gb|EFY76413.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322684730|gb|EFY80734.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323195994|gb|EFZ81160.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323197076|gb|EFZ82217.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323202220|gb|EFZ87270.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323206320|gb|EFZ91282.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323213332|gb|EFZ98134.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323215701|gb|EGA00445.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323222124|gb|EGA06510.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323226535|gb|EGA10741.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323229161|gb|EGA13290.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323236230|gb|EGA20306.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323237651|gb|EGA21712.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323241684|gb|EGA25713.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323248169|gb|EGA32106.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323258439|gb|EGA42116.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323259719|gb|EGA43353.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323265992|gb|EGA49488.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323270434|gb|EGA53882.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
          Length = 289

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/164 (14%), Positives = 54/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ SG VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVSGDVVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFV----- 94

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  ++     RLD+++ G++ +         +         + +
Sbjct: 95  NYSKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRVGNDHEKEYL 138


>gi|268596680|ref|ZP_06130847.1| pseudouridine synthase [Neisseria gonorrhoeae FA19]
 gi|268550468|gb|EEZ45487.1| pseudouridine synthase [Neisseria gonorrhoeae FA19]
          Length = 416

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 48/156 (30%), Gaps = 28/156 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 162 EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 218

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 219 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 253

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
             +   +     RLD  TSG+L++  +    Q    
Sbjct: 254 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAH 289


>gi|319763718|ref|YP_004127655.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|330824019|ref|YP_004387322.1| pseudouridine synthase Rsu [Alicycliphilus denitrificans K601]
 gi|317118279|gb|ADV00768.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|329309391|gb|AEB83806.1| pseudouridine synthase Rsu [Alicycliphilus denitrificans K601]
          Length = 451

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/232 (12%), Positives = 68/232 (29%), Gaps = 45/232 (19%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      R+Q G  +++              +          
Sbjct: 144 SRLEMEQLILEGRISVNNEPAHIGQRVQFGDQIKVNGKPIRFRVAPPPTR---------- 193

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                          +  ++KP G  V        +     +     +  K +   RLD 
Sbjct: 194 ---------------VIAYHKPVGEVV--THDDPQNRPTVFRKLPRLQQGKWQSVGRLDL 236

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L+   +   A  L         +     L     + ++  +    L+       +
Sbjct: 237 NTEGLLLFTSSGELANKLMHPRFGLEREYAVRVLGALSDEERQRLLDGVSLEDGMAA--F 294

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
             +     +GAN                CW  +    GR  ++R     +G 
Sbjct: 295 GSIEDGGGEGAN----------------CWYRVTISEGRNREVRRMFEAVGH 330


>gi|269797888|ref|YP_003311788.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269094517|gb|ACZ24508.1| pseudouridine synthase [Veillonella parvula DSM 2008]
          Length = 242

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 86/249 (34%), Gaps = 49/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++  +     +    ++++  G+V+V+ ++V                         
Sbjct: 2   ERLQKYIAS-CGIASRRKAEELITEGKVQVNGRKVT------------------------ 36

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIY-VFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                L   +N  K    +   LL ++  +Y + NKP G+     S         +  ++
Sbjct: 37  ----ELGVKINPQKDKVKVNGQLLAQEKPVYYLLNKPKGVIT---SVSDPQGRETVLDYI 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            ++ ++     RLD  T G+L++      AQ+LT     + ++K Y   + G  ++    
Sbjct: 90  KNETKRIYPIGRLDLYTEGLLLLTNDGEFAQNLT--HPSKGVEKTYEVRIKGRVRDDDLQ 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I    ++               E G     +   +          +E+  H GR  Q+R 
Sbjct: 148 IIANGVEL--------------EDGITAPATIVDLGFDDHNGVHEVEITIHEGRNRQVRR 193

Query: 258 HALHMGCPI 266
              H G  I
Sbjct: 194 MFEHFGYRI 202


>gi|187731466|ref|YP_001880099.1| 23S rRNA pseudouridylate synthase B [Shigella boydii CDC 3083-94]
 gi|187428458|gb|ACD07732.1| ribosomal large subunit pseudouridine synthase B [Shigella boydii
           CDC 3083-94]
          Length = 290

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|311069499|ref|YP_003974422.1| putative 16S pseudouridylate synthase [Bacillus atrophaeus 1942]
 gi|310870016|gb|ADP33491.1| putative 16S pseudouridylate synthase [Bacillus atrophaeus 1942]
          Length = 239

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/237 (16%), Positives = 79/237 (33%), Gaps = 47/237 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N     +   ++KI+++G V +D K+ K            +   ++   H  
Sbjct: 1   MRLDKLLANSGIG-SRKEVKKIVKAGAVSIDGKQAK-----------DVKTHVDPSEH-- 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +    +              Y +    + NKP G+           +   L    D
Sbjct: 47  -EVTVYGEPIE-------------YREFIYLMMNKPQGVLSATEDSRQKTVIDLLA--PD 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +P    RLD++T G+L++      A  L              S    +PK  +  +
Sbjct: 91  DMRFEPFPAGRLDKDTVGLLLLTNDGQLAHRL-------------LSPKKHVPKTYEVHL 137

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
            + L ++     +    ++   K     +         +++   + +    G+ HQ+
Sbjct: 138 RSGLSEEDIANLESGVFIEGGYKTKPAKVETI----ANSEEHTEIRLTITEGKYHQV 190


>gi|222528664|ref|YP_002572546.1| RNA-binding S4 domain-containing protein [Caldicellulosiruptor
          bescii DSM 6725]
 gi|222455511|gb|ACM59773.1| RNA-binding S4 domain protein [Caldicellulosiruptor bescii DSM
          6725]
          Length = 80

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 24/50 (48%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          MR+D++ K           Q+   +G+V V+ K  K +  ++ G V+ + 
Sbjct: 1  MRIDKYLKVSRIIKRRTLAQQACEAGRVFVNGKVAKPSTDVKVGDVIEVH 50


>gi|145633070|ref|ZP_01788802.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 3655]
 gi|144986296|gb|EDJ92875.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 3655]
          Length = 357

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELC--TRSDPEGRATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPHLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|82776214|ref|YP_402563.1| 16S rRNA pseudouridylate synthase A [Shigella dysenteriae Sd197]
 gi|309786649|ref|ZP_07681269.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
 gi|81240362|gb|ABB61072.1| 16S pseudouridylate 516 synthase [Shigella dysenteriae Sd197]
 gi|308925342|gb|EFP70829.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
          Length = 231

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|319776559|ref|YP_004139047.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae F3047]
 gi|317451150|emb|CBY87383.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae F3047]
          Length = 357

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/194 (18%), Positives = 65/194 (33%), Gaps = 34/194 (17%)

Query: 5   TYVQYVVVENDE---ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--I 59
             V+ VV  +++   E  +L +         +   ++ ++ +G+V V+ K     +R  +
Sbjct: 59  PKVKSVVKASNQPKVEGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDV 117

Query: 60  QSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV 119
            SG  VRI   I  L+H  KE                          ++ ++ KP G   
Sbjct: 118 HSGVKVRIDGQIINLSHAQKEI------------------------CRVLMYYKPEGELC 153

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                                G +     RLD  TSG+L+       A  L        +
Sbjct: 154 --TRSDPEGRATVFDRLPHLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSHEV 209

Query: 180 QKIYWSLVWGIPKN 193
           ++ Y   V+G   +
Sbjct: 210 EREYSVRVFGQVDD 223


>gi|261345329|ref|ZP_05972973.1| ribosomal large subunit pseudouridine synthase F [Providencia
           rustigianii DSM 4541]
 gi|282566663|gb|EFB72198.1| ribosomal large subunit pseudouridine synthase F [Providencia
           rustigianii DSM 4541]
          Length = 291

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/164 (13%), Positives = 55/164 (33%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G +V++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRYIEQGNVFINGKRAGIGDQVSAGDIVKVNGQLIEPRDE- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI     SG   +I  ++     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTESGEKGNIVDYVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  --SKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYV 138


>gi|197286701|ref|YP_002152573.1| ribosomal large subunit pseudouridine synthase F [Proteus mirabilis
           HI4320]
 gi|227355108|ref|ZP_03839519.1| RluF protein [Proteus mirabilis ATCC 29906]
 gi|194684188|emb|CAR45657.1| ribosomal large subunit pseudouridine synthase F [Proteus mirabilis
           HI4320]
 gi|227164895|gb|EEI49742.1| RluF protein [Proteus mirabilis ATCC 29906]
          Length = 292

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 71/246 (28%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +R+ +G  V++           
Sbjct: 8   RLNKYISE--SGICSRREADRYIEQGLVLINGKRAGIGDRVTAGDEVKVNG--------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                      L +  D  + +       +   NKP GI      G   +I  ++     
Sbjct: 57  ----------RLIEAQDNSELV-------LIALNKPVGIVSTTDEGEKDNIVDYVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++ +         +  +      + +   +    P   +   
Sbjct: 97  --STRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNSHEKEYL---VTVDKPITDEFI- 150

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +     I G      K  ++ A                     +    G   Q+R  
Sbjct: 151 -RGMGAGVPILGQKTKKCKVKKEAA-----------------MVFRITLVQGLNRQIRRM 192

Query: 259 ALHMGC 264
             + G 
Sbjct: 193 CEYFGY 198


>gi|311745139|ref|ZP_07718924.1| RNA pseudouridine synthase family protein [Algoriphagus sp. PR1]
 gi|126577657|gb|EAZ81877.1| RNA pseudouridine synthase family protein [Algoriphagus sp. PR1]
          Length = 243

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/252 (13%), Positives = 81/252 (32%), Gaps = 56/252 (22%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            +++ +R++++        +     K+L +G++ ++ K  +   ++    VV +      
Sbjct: 2   EEKQGIRINKYLSE-VGFCSRREGDKLLEAGRITLNGKIPEIGTKVMPKDVVCV------ 54

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA-YHIDGF 132
                 + K +   +               +D     FNKP GI     +     ++  +
Sbjct: 55  ------DGKPVGKPI---------------QDHVYIAFNKPVGIVSTTDTKAEKNNMIDY 93

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +        Q+     RLD+++ G++ +         +  S      + I          
Sbjct: 94  I-----GHQQRIFPIGRLDKDSEGLIFLTSEGDIVNKILRSKNNHEKEYIV--------- 139

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + I +  ++K   G   +  V    K    +   F++I                G  
Sbjct: 140 TVDKPITDRFIQKMGAGIPILDTVTDPCKVEKISKVKFRII-------------LTQGLN 186

Query: 253 HQLRVHALHMGC 264
            Q+R    ++G 
Sbjct: 187 RQIRRMCEYLGY 198


>gi|146312421|ref|YP_001177495.1| 16S rRNA pseudouridylate synthase A [Enterobacter sp. 638]
 gi|145319297|gb|ABP61444.1| ribosomal small subunit pseudouridine synthase A [Enterobacter sp.
           638]
          Length = 235

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 80/250 (32%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R+ +V VD            G +VR     ++   ++
Sbjct: 1   MRLDKFIAQQLS-VSRAIAGREIRASRVTVD------------GDIVR-----DSAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      LT+             S+ ++ NKP G      S         L    +
Sbjct: 43  PEHDVEFDGNTLTQQIG----------SRYFMLNKPQGYVC---STDDPDHPTVLYFLEE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVM-------------L 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFTKGVQLHNEKDLTKPAV--LEVI-----TPTEVRLTIIEGRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  +VG
Sbjct: 190 FAAVGNRVVG 199


>gi|332527071|ref|ZP_08403153.1| RNA-binding S4 domain-containing protein [Rubrivivax
           benzoatilyticus JA2]
 gi|332111503|gb|EGJ11486.1| RNA-binding S4 domain-containing protein [Rubrivivax
           benzoatilyticus JA2]
          Length = 255

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 46/257 (17%), Positives = 85/257 (33%), Gaps = 35/257 (13%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           +    E +R+ +         +       + +G V+VD K      R  +   + I P  
Sbjct: 5   ISGAAEGVRVSKLITER-GLASRREADAWIEAGWVKVDGKMAVLGQRAAADCRIEIDPR- 62

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                  + ++    +V L K   F+      ED       KPA   V   +        
Sbjct: 63  ------ARNEQARRVTVLLHKPMGFVSGQ--AEDGY-----KPAATLVIPANRWKDDPTR 109

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
                   +G  P    RLD +++G+LV+ +    A+ L       +++K Y   V    
Sbjct: 110 LAFHPGQLRGLAP--AGRLDIDSTGLLVLTQDGRIAKTL--IGDETKVEKEYLVRVQ--- 162

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
             K   + +  L++   G +       + +    A   ++  D        L      GR
Sbjct: 163 YTKPGRLPDADLERLRHGLEL------DGRPLRPARVSWQNEDQ-------LRFVLREGR 209

Query: 252 THQLRVHALHMGCPIVG 268
             Q+R     +G  +VG
Sbjct: 210 KRQIRRMCELVGLKVVG 226


>gi|311696250|gb|ADP99123.1| pseudouridine synthase, Rsu [marine bacterium HP15]
          Length = 230

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 75/249 (30%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++  N    ++    ++ +  G+V ++++  K  N R+   + V +     +L   
Sbjct: 1   MRLDQFIANS-TELSRKEAKRAIGRGEVTINEQICKGANTRLAGDERVALSGTPLSLP-- 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                        +  + NKPAG+               L +  
Sbjct: 58  ---------------------------GERYLMMNKPAGVVSATTDSDHPTALDLLPA-- 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +   +  RLD         A T       T+     R+           PK  +  
Sbjct: 89  -EITRHLHIAGRLD---------ADTTGLLLLTTDGQWSHRVTS----PRTDCPKTYRVT 134

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   L   +    +    +  + +    A  HF        +   +E+    GR HQ++ 
Sbjct: 135 LNEPLSDAAAQQLERGVDLHNDPRPTRPARVHF-------LEDRIIELTISEGRYHQVKR 187

Query: 258 HALHMGCPI 266
               +G  +
Sbjct: 188 MMAAVGNHV 196


>gi|257465549|ref|ZP_05629920.1| pseudouridine synthase [Actinobacillus minor 202]
 gi|257451209|gb|EEV25252.1| pseudouridine synthase [Actinobacillus minor 202]
          Length = 340

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/176 (17%), Positives = 58/176 (32%), Gaps = 27/176 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   L++I+ +G+V VD K     +R+Q     +I    + +N I
Sbjct: 60  GEKLQKILARAGQG-SRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGHLINLI 118

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 119 PTQKEIC----------------------RVLMYYKPEGELC--TRSDPEGRATVFDRLP 154

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              G +     RLD  TSG+L+       A  L      R +++ Y   V+G    
Sbjct: 155 RLTGARWVAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGNVDE 208


>gi|157363887|ref|YP_001470654.1| RNA-binding S4 domain-containing protein [Thermotoga lettingae TMO]
 gi|157314491|gb|ABV33590.1| RNA-binding S4 domain protein [Thermotoga lettingae TMO]
          Length = 234

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/168 (17%), Positives = 58/168 (34%), Gaps = 36/168 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLDR+  N         ++KI++ G++ V+ + VK  +  I    +V            
Sbjct: 1   MRLDRFLANAKIG-TRSEVRKIIKKGEISVNGEIVKNISFHINETDIVEYMGKTVVPYRK 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I                               +FNKPAG      +      D     ++
Sbjct: 60  I-----------------------------YLIFNKPAGFVSDKTNAQPSVFDLIDHPFI 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYW 184
           D       +  RLD++  G+L++        + ++  F + +   I++
Sbjct: 91  DQM----HVAGRLDRDVEGLLILTNDGLFTHRLISPKFHVEKEYMIWF 134


>gi|239993811|ref|ZP_04714335.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Alteromonas macleodii ATCC 27126]
          Length = 298

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 69/243 (28%), Gaps = 40/243 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +   N     +   +++ +  G+V VD  +    +R+     +R+   + +      E
Sbjct: 5   LQKVLANQGLG-SRREMERWIEEGRVSVDGTKATLGDRVDHTAQIRVDGHLLSRQT---E 60

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           Q I                       ++ ++NKP G             D         +
Sbjct: 61  QPIC----------------------RVLMYNKPEGELC--SRHDPEGRDTVFDRLPAIR 96

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
             +     RLD  TSG+L+       A  L        +++ Y   V+G    K   +  
Sbjct: 97  LGRWITVGRLDMNTSGLLLFTNDGELANRL--MHPKCEVEREYAVRVFGEVTGK--TLHT 152

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
                    G+   +         +A               W  +    GR  ++R    
Sbjct: 153 LQKGVELEDGEAKFLTISGAPTPQHAE--------DESMNRWYNVTLKEGRNREVRRLWE 204

Query: 261 HMG 263
             G
Sbjct: 205 SQG 207


>gi|90416540|ref|ZP_01224471.1| probable pseudouridine synthase [marine gamma proteobacterium
           HTCC2207]
 gi|90331739|gb|EAS46967.1| probable pseudouridine synthase [marine gamma proteobacterium
           HTCC2207]
          Length = 278

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/227 (14%), Positives = 74/227 (32%), Gaps = 44/227 (19%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   L+K + +G+V V+    K  +R  +   + +                         
Sbjct: 16  SRRELEKWISAGRVSVNGSIAKLGDRAAADDRILVDGR---------------------- 53

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
               L  I+  +  ++ +++KP G                          +     RLD 
Sbjct: 54  ----LIKIVTDDSPRVLMYSKPEGEVCTTSDPDG--RPTVFDRLPRLSRGRWIAIGRLDI 107

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+L+       A  L        +Q+ Y + + G        +   ++K+   G   
Sbjct: 108 NTSGLLLFTNHGELANRL--MHPSYEVQREYMARIHGE-------VDEAMIKRLTDG--- 155

Query: 213 VHVVKQNEKGANYAI--SHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             VV ++   +  ++   H +  +    +  W ++    GRT ++R 
Sbjct: 156 --VVLEDGLASFKSVKAQHARSSEDLGGRNRWFKVILAEGRTREVRR 200


>gi|75763968|ref|ZP_00743593.1| Ribosomal large subunit pseudouridine synthase F [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|74488543|gb|EAO52134.1| Ribosomal large subunit pseudouridine synthase F [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
          Length = 254

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/254 (13%), Positives = 74/254 (29%), Gaps = 60/254 (23%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           E D  N+R++++        +     K++   +V ++ K  K  +++  G  VR+     
Sbjct: 14  EKDVPNLRINKFISEAGK-ASRRGADKLINERRVIINGKVAKIGDQVNPGDDVRVNGEQL 72

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                                        +  D      NKP GI+      +  +I   
Sbjct: 73  R----------------------------IARDHVYIALNKPVGITCTSEKAVKGNIIDL 104

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   +     +     RLD+++ G++++         +  +      + I          
Sbjct: 105 VNHPL-----RISHIGRLDKDSDGLILLTNDGDIVNEILRAENKHEKEYIVS-------- 151

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TG 250
                          I  D++  +    K     I   K + C   +    E Q     G
Sbjct: 152 -----------VDKPITPDFLEKMAAGVK-----ILGTKTLPCEITQLSKYEFQIILTQG 195

Query: 251 RTHQLRVHALHMGC 264
              Q+R     +G 
Sbjct: 196 LNRQIRRMCEALGY 209


>gi|312973563|ref|ZP_07787735.1| conserved hypothetical protein [Escherichia coli 1827-70]
 gi|310332158|gb|EFP99393.1| conserved hypothetical protein [Escherichia coli 1827-70]
          Length = 231

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKSYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|15641192|ref|NP_230824.1| pseudouridine synthase family 1 protein [Vibrio cholerae O1 biovar
           El Tor str. N16961]
 gi|121587810|ref|ZP_01677569.1| pseudouridine synthase family 1 protein [Vibrio cholerae 2740-80]
 gi|121728227|ref|ZP_01681260.1| pseudouridine synthase family 1 protein [Vibrio cholerae V52]
 gi|153215349|ref|ZP_01949962.1| pseudouridine synthase family 1 protein [Vibrio cholerae 1587]
 gi|153819079|ref|ZP_01971746.1| pseudouridine synthase family 1 protein [Vibrio cholerae NCTC 8457]
 gi|153823509|ref|ZP_01976176.1| pseudouridine synthase family 1 protein [Vibrio cholerae B33]
 gi|153826657|ref|ZP_01979324.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-2]
 gi|183179584|ref|ZP_02957795.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-3]
 gi|227081351|ref|YP_002809902.1| pseudouridine synthase family 1 protein [Vibrio cholerae M66-2]
 gi|229505227|ref|ZP_04394737.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           BX 330286]
 gi|229511103|ref|ZP_04400582.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           B33]
 gi|229515560|ref|ZP_04405019.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           TMA 21]
 gi|229518222|ref|ZP_04407666.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           RC9]
 gi|229520392|ref|ZP_04409817.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           TM 11079-80]
 gi|229529733|ref|ZP_04419123.1| LSU pseudouridine synthase B [Vibrio cholerae 12129(1)]
 gi|229608246|ref|YP_002878894.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           MJ-1236]
 gi|254226705|ref|ZP_04920282.1| pseudouridine synthase family 1 protein [Vibrio cholerae V51]
 gi|254291998|ref|ZP_04962777.1| pseudouridine synthase family 1 protein [Vibrio cholerae AM-19226]
 gi|254848305|ref|ZP_05237655.1| pseudouridine synthase family 1 protein [Vibrio cholerae MO10]
 gi|255745589|ref|ZP_05419537.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholera
           CIRS 101]
 gi|262158338|ref|ZP_06029454.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           INDRE 91/1]
 gi|297578779|ref|ZP_06940707.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           RC385]
 gi|298498719|ref|ZP_07008526.1| pseudouridine synthase family 1 protein [Vibrio cholerae MAK 757]
 gi|34098735|sp|Q9KSS7|RLUB_VIBCH RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|9655656|gb|AAF94338.1| pseudouridine synthase family 1 protein [Vibrio cholerae O1 biovar
           El Tor str. N16961]
 gi|121547974|gb|EAX58055.1| pseudouridine synthase family 1 protein [Vibrio cholerae 2740-80]
 gi|121629478|gb|EAX61904.1| pseudouridine synthase family 1 protein [Vibrio cholerae V52]
 gi|124114792|gb|EAY33612.1| pseudouridine synthase family 1 protein [Vibrio cholerae 1587]
 gi|125620766|gb|EAZ49123.1| pseudouridine synthase family 1 protein [Vibrio cholerae V51]
 gi|126510362|gb|EAZ72956.1| pseudouridine synthase family 1 protein [Vibrio cholerae NCTC 8457]
 gi|126518977|gb|EAZ76200.1| pseudouridine synthase family 1 protein [Vibrio cholerae B33]
 gi|149739519|gb|EDM53747.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-2]
 gi|150422075|gb|EDN14043.1| pseudouridine synthase family 1 protein [Vibrio cholerae AM-19226]
 gi|183012995|gb|EDT88295.1| pseudouridine synthase family 1 protein [Vibrio cholerae MZO-3]
 gi|227009239|gb|ACP05451.1| pseudouridine synthase family 1 protein [Vibrio cholerae M66-2]
 gi|229333507|gb|EEN98993.1| LSU pseudouridine synthase B [Vibrio cholerae 12129(1)]
 gi|229342490|gb|EEO07483.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           TM 11079-80]
 gi|229344937|gb|EEO09911.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           RC9]
 gi|229347329|gb|EEO12289.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           TMA 21]
 gi|229351068|gb|EEO16009.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           B33]
 gi|229357450|gb|EEO22367.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           BX 330286]
 gi|229370901|gb|ACQ61324.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           MJ-1236]
 gi|254844010|gb|EET22424.1| pseudouridine synthase family 1 protein [Vibrio cholerae MO10]
 gi|255736664|gb|EET92061.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholera
           CIRS 101]
 gi|262029779|gb|EEY48427.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           INDRE 91/1]
 gi|297536373|gb|EFH75206.1| ribosomal large subunit pseudouridine synthase B [Vibrio cholerae
           RC385]
 gi|297543052|gb|EFH79102.1| pseudouridine synthase family 1 protein [Vibrio cholerae MAK 757]
 gi|327483880|gb|AEA78287.1| Ribosomal large subunit pseudouridine synthase B LSU Psi2605
           [Vibrio cholerae LMA3894-4]
          Length = 321

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/232 (16%), Positives = 80/232 (34%), Gaps = 34/232 (14%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   L+ ++R+G+V V+ K      R++    VVRI   + +   +  
Sbjct: 5   LQKVLARA-GHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNAVVRIDGHVVS---VKA 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +++++                      ++  + KP G                       
Sbjct: 61  QEEVI---------------------CRVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K    
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGDVTEEKVRNL 155

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
              ++       +  V+    +G N+  + + VI+     +     E Q  T
Sbjct: 156 VRGVQLEDGMARFEDVMYAGGEGINH--TFYVVINEGRNREVRRLWESQGTT 205


>gi|22126794|ref|NP_670217.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis KIM 10]
 gi|45441149|ref|NP_992688.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108806980|ref|YP_650896.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis Antiqua]
 gi|108812871|ref|YP_648638.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis Nepal516]
 gi|145599700|ref|YP_001163776.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis Pestoides F]
 gi|149366750|ref|ZP_01888784.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           CA88-4125]
 gi|162418753|ref|YP_001606002.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis Angola]
 gi|165924511|ref|ZP_02220343.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165936140|ref|ZP_02224709.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166009884|ref|ZP_02230782.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166211428|ref|ZP_02237463.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167400432|ref|ZP_02305945.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167419607|ref|ZP_02311360.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167424159|ref|ZP_02315912.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|218928420|ref|YP_002346295.1| 16S rRNA pseudouridylate synthase A [Yersinia pestis CO92]
 gi|229841215|ref|ZP_04461374.1| 16S rRNA pseudouridylate 516 synthase [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229843320|ref|ZP_04463466.1| 16S rRNA pseudouridylate 516 synthase [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229903299|ref|ZP_04518412.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|270487103|ref|ZP_06204177.1| pseudouridylate synthase [Yersinia pestis KIM D27]
 gi|294503270|ref|YP_003567332.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Z176003]
 gi|34098649|sp|Q8ZGM2|RSUA_YERPE RecName: Full=Ribosomal small subunit pseudouridine synthase A;
           AltName: Full=16S pseudouridine 516 synthase; AltName:
           Full=16S pseudouridylate 516 synthase; AltName:
           Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|21959821|gb|AAM86468.1|AE013894_3 16S pseudouridylate 516 synthase [Yersinia pestis KIM 10]
 gi|45436008|gb|AAS61565.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Microtus str. 91001]
 gi|108776519|gb|ABG19038.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|108778893|gb|ABG12951.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Antiqua]
 gi|115347031|emb|CAL19923.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           CO92]
 gi|145211396|gb|ABP40803.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Pestoides F]
 gi|149291124|gb|EDM41199.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           CA88-4125]
 gi|162351568|gb|ABX85516.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Angola]
 gi|165915754|gb|EDR34362.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|165923571|gb|EDR40703.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165991280|gb|EDR43581.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166207199|gb|EDR51679.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166962348|gb|EDR58369.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167050381|gb|EDR61789.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167057008|gb|EDR66771.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|229679069|gb|EEO75172.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|229689667|gb|EEO81728.1| 16S rRNA pseudouridylate 516 synthase [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229697581|gb|EEO87628.1| 16S rRNA pseudouridylate 516 synthase [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|262361308|gb|ACY58029.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           D106004]
 gi|262365154|gb|ACY61711.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           D182038]
 gi|270335607|gb|EFA46384.1| pseudouridylate synthase [Yersinia pestis KIM D27]
 gi|294353729|gb|ADE64070.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           Z176003]
 gi|320015889|gb|ADV99460.1| Ribosomal small subunit pseudouridine synthaseA [Yersinia pestis
           biovar Medievalis str. Harbin 35]
          Length = 235

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 73/245 (29%), Gaps = 51/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK      SG +            + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEVVK------SGAI-----------KLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEQDVRFDGNPLQQMVGP----------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G+++                  +      S      K     +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVL-------------MTDDGQWSHRVTSPRHHCEKTYLVTL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + L   +         +   +     A     VI+        + +    GR HQ++  
Sbjct: 137 EHPLSDDTAQQFADGVQLYNEKSLTKPA--QLDVIEPQ-----RVRLTISEGRYHQVKRM 189

Query: 259 ALHMG 263
              +G
Sbjct: 190 FAAVG 194


>gi|312623027|ref|YP_004024640.1| RNA-binding S4 domain-containing protein [Caldicellulosiruptor
          kronotskyensis 2002]
 gi|312203494|gb|ADQ46821.1| RNA-binding S4 domain protein [Caldicellulosiruptor
          kronotskyensis 2002]
          Length = 80

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 24/50 (48%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          MR+D++ K           Q+   +G+V V+ K  K +  ++ G V+ + 
Sbjct: 1  MRIDKYLKVSRIIKRRTLAQQACEAGRVFVNGKVAKPSTDVKVGDVIEVH 50


>gi|291278664|ref|YP_003495499.1| RNA-binding S4 protein [Deferribacter desulfuricans SSM1]
 gi|290753366|dbj|BAI79743.1| RNA-binding S4 protein [Deferribacter desulfuricans SSM1]
          Length = 93

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 16/93 (17%), Positives = 34/93 (36%), Gaps = 3/93 (3%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV---INALN 75
           MRLD++ K            +    G + V+ ++ K + +I+ G  + +           
Sbjct: 1   MRLDKFLKVTMLIKRRSVANEAADEGFIYVNGRKAKASTKIKVGDKILLDMWNYKKEVFV 60

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKI 108
             + E K      ++ K+ + L     + D  I
Sbjct: 61  KALPETKGGIPKKDVDKYIEVLSYEPKHTDDFI 93


>gi|262275813|ref|ZP_06053622.1| ribosomal small subunit pseudouridine synthase A [Grimontia
           hollisae CIP 101886]
 gi|262219621|gb|EEY70937.1| ribosomal small subunit pseudouridine synthase A [Grimontia
           hollisae CIP 101886]
          Length = 234

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 86/251 (34%), Gaps = 54/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD++       +      KIL+  +V VD   +K      +G +            I 
Sbjct: 2   IRLDKFLCETV-GVTRKQAAKILKEERVTVDGNIIK------NGAI-----------KIA 43

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E  +    ++L                + Y+ NKPAG          Y+   F+   +D
Sbjct: 44  EEADVEFDGMSLRLAGP-----------RYYMMNKPAGYVC--SHDDPYNPTVFV--LLD 88

Query: 139 SKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             G +K  +  RLD +T+G+L++      +  +T            W      P+ ++  
Sbjct: 89  EIGAEKLHIAGRLDCDTTGLLLLTDDGQWSHRVTSPKHKCDKVYRVWLDDPVSPETEQCF 148

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                L+          + +  EK         +V+           +  H G+ HQ++ 
Sbjct: 149 AEGIKLRGERTETLPAQMQRVGEK---------EVL-----------LTIHEGKYHQVKR 188

Query: 258 HALHMGCPIVG 268
               +G  +VG
Sbjct: 189 MFAAVGNKVVG 199


>gi|237807721|ref|YP_002892161.1| RNA-binding S4 domain-containing protein [Tolumonas auensis DSM
           9187]
 gi|237499982|gb|ACQ92575.1| RNA-binding S4 domain protein [Tolumonas auensis DSM 9187]
          Length = 348

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 53/161 (32%), Gaps = 28/161 (17%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++ ++  G+V V+ K     +R+++  V+R+                    +++  
Sbjct: 16  SRREMETVISEGRVSVNGKVATLGDRVEAKDVIRVDGH----------------QISVPT 59

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
            +D +  +L Y        +KP G                       K  +     RLD 
Sbjct: 60  LNDVICRVLAY--------HKPEGEVC--TRHDPEGRPTVFDRLPRIKDSRWVAVGRLDV 109

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            TSG+L+       A  L        +++ Y   V+G    
Sbjct: 110 NTSGLLLFTTDGELANRL--MHPSHEVEREYAVRVFGEVTE 148


>gi|109899133|ref|YP_662388.1| pseudouridine synthase, Rsu [Pseudoalteromonas atlantica T6c]
 gi|109701414|gb|ABG41334.1| ribosomal large subunit pseudouridine synthase B [Pseudoalteromonas
           atlantica T6c]
          Length = 289

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/162 (16%), Positives = 53/162 (32%), Gaps = 29/162 (17%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++K + SG++ V+ K     +R++    +R+   +                     
Sbjct: 16  SRREMEKWIASGRISVNGKVATLGDRVEPLDQLRVDGNL--------------------- 54

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
            +   KS +     ++ ++NKP G                       +  +     RLD 
Sbjct: 55  ITAAAKSTIC----RVLMYNKPEGELC--SRKDPQGRPTVFDRLPKIQNGRWIAVGRLDI 108

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            TSG+L+       A  L        I++ Y   V+G   + 
Sbjct: 109 NTSGLLLFTNDGELANRL--MHPKHEIEREYAVRVFGEVDDD 148


>gi|292559208|gb|ADE32209.1| Pseudouridine synthase, Rsu [Streptococcus suis GZ1]
          Length = 235

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/233 (15%), Positives = 82/233 (35%), Gaps = 49/233 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++K+L++ QV V+ +                             +      +N  K
Sbjct: 7   SRTEVKKLLKNKQVTVNGQV----------------------------ETSPKQQINEKK 38

Query: 93  HSDFLKSILL-YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
               +   +L +E    Y+ NKP G+           +   L +    K  +     RLD
Sbjct: 39  DQIAVAGQVLSHETFVYYLLNKPKGVISATEDDHHRTVLDLLDNTARQK--EVFPVGRLD 96

Query: 152 QETSGILVVA-RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGG 210
            +T G+L++  + + A   L+     + + K+Y + V GI   +        +++   G 
Sbjct: 97  IDTHGLLLLTNKGQLAHAMLS---PKKHVDKLYRAQVDGIMTQED-------VERFAAGI 146

Query: 211 DYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +      Q  +     ++     +  A++   +++    G+ HQ++      G
Sbjct: 147 ELKDFTCQPAQ-----LTILSTDE--AKQTSLVDITIREGKFHQIKRMVQACG 192


>gi|145641201|ref|ZP_01796781.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae R3021]
 gi|145274038|gb|EDK13904.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 22.4-21]
          Length = 357

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELC--TRSDPEGRATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|282163383|ref|YP_003355768.1| hypothetical protein MCP_0713 [Methanocella paludicola SANAE]
 gi|282155697|dbj|BAI60785.1| conserved hypothetical protein [Methanocella paludicola SANAE]
          Length = 215

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
          MRLD +  +     +    ++++  GQV+VD K V K + +++ G+ V I 
Sbjct: 1  MRLDEYLVSEGLVPSRSRAKRLIEKGQVKVDGKAVLKPSQKVEYGRKVAIE 51


>gi|291043642|ref|ZP_06569358.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|291012105|gb|EFE04094.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
          Length = 399

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 48/156 (30%), Gaps = 28/156 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  +++     V +   I  L  
Sbjct: 145 EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKVTPDDHVTVKGSIIKL-- 201

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 202 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 236

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
             +   +     RLD  TSG+L++  +    Q    
Sbjct: 237 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAH 272


>gi|290978734|ref|XP_002672090.1| predicted protein [Naegleria gruberi]
 gi|284085664|gb|EFC39346.1| predicted protein [Naegleria gruberi]
          Length = 133

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/122 (19%), Positives = 48/122 (39%), Gaps = 18/122 (14%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-PKNKKECIANWL 202
               HR+D+ TSG+L++ ++   A+  + S + +++ K Y ++  GI P      +   L
Sbjct: 7   LFPLHRIDRLTSGVLILGKSSEVARDFSASLKSKQVGKQYIAVAEGICPTEGLFKVDYPL 66

Query: 203 LKKSH----------------IGGDYVHVVKQNEKGANYAISHFKVIDC-FAQKFCWLEM 245
           ++                   I   Y+H    +      A + F+V+   +A        
Sbjct: 67  MEIDPLLGIWRAVHSEESKEFIKKHYLHHTPLDWNNVKEAETLFQVLYRDYASNRTVFLC 126

Query: 246 QP 247
           QP
Sbjct: 127 QP 128


>gi|254416564|ref|ZP_05030315.1| conserved hypothetical protein, putative [Microcoleus
           chthonoplastes PCC 7420]
 gi|196176530|gb|EDX71543.1| conserved hypothetical protein, putative [Microcoleus
           chthonoplastes PCC 7420]
          Length = 255

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 81/244 (33%), Gaps = 52/244 (21%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
            +    +K++ +G+VR++   V+   +                     E  +++ +    
Sbjct: 15  ASRRQAEKMIVAGRVRLNGTVVQLGQK------------------ANPETDLIEVNGQRL 56

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI--------AYHIDGFLKSWVDSKGQK 143
           K S+  ++I         + NKP G+     +             +   L S +   GQ 
Sbjct: 57  KPSNRPQAI-------YLLLNKPVGVVSTCRNYRVCNTILEKRRTVLDLLPSTIRQ-GQG 108

Query: 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLL 203
                RLD E++G L++         LT       + K Y   V G P            
Sbjct: 109 IHPVGRLDMESTGALILTNDGTLTYKLT--HPRHHVPKTYRVWVKGHPPES--------- 157

Query: 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
               I   +   V  + +    A    +V+     K   LE+    GR  Q+R  A  +G
Sbjct: 158 ----ILSAWRQGVDLSGRTTLPA--QVRVLKQQPDK-TLLEIVLTEGRNRQIRRVADLLG 210

Query: 264 CPIV 267
            P++
Sbjct: 211 YPVI 214


>gi|323254500|gb|EGA38311.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
          Length = 289

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/164 (14%), Positives = 54/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ SG VV++   +       
Sbjct: 8   RLNKYISE--SGICSRREADRFIEQGNVFINGKRAAIGDQVVSGDVVKVNGRLIEPREA- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIVSTTEDGERDNIVDFV----- 94

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +  ++     RLD+++ G++ +         +         + +
Sbjct: 95  NYSKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRVGNDHEKEYL 138


>gi|291551160|emb|CBL27422.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog) [Ruminococcus
          torques L2-14]
          Length = 79

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 14/62 (22%), Positives = 27/62 (43%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
          MRLD++ K            +   +G+V V+ K  K + +++ G V+ I      +   +
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNGKTAKASVKVKPGDVIEIQFGTRTVKVEV 60

Query: 79 KE 80
           E
Sbjct: 61 LE 62


>gi|320106004|ref|YP_004181594.1| pseudouridine synthase [Terriglobus saanensis SP1PR4]
 gi|319924525|gb|ADV81600.1| pseudouridine synthase [Terriglobus saanensis SP1PR4]
          Length = 301

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 81/251 (32%), Gaps = 34/251 (13%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +RL +   +     +    ++++  G+V+V+ K V                       
Sbjct: 12  EGVRLQKILADA-GIASRRKSEEVILEGRVQVNGKVVT-----------------ELGTR 53

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKS 135
              E+  +     L +           E+ + Y+ NKP G ++          I   L  
Sbjct: 54  ANPEKDHIRVDGKLLQGP---------EEHRYYLVNKPRGYVTTMHDPEKRPTIVDLLIK 104

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                  +     RLD  + G+L++      A  L+++     ++K Y   V G P  + 
Sbjct: 105 DGKMPDVRLYPVGRLDYNSEGLLLMTNDGELANALSKA--SNSVEKTYLVKVAGQPSEQA 162

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
               + L +   I    +   +   +      +  KV    A    W E+    GR  QL
Sbjct: 163 ---IDQLRRGVMIERGRLQETQGARRN-RVMTAPAKVKLVRAGLNPWFEVSLTEGRNRQL 218

Query: 256 RVHALHMGCPI 266
           R     +   +
Sbjct: 219 RKMFEEIDHHV 229


>gi|295396784|ref|ZP_06806919.1| ribosomal large subunit pseudouridine synthase B [Brevibacterium
           mcbrellneri ATCC 49030]
 gi|294970368|gb|EFG46308.1| ribosomal large subunit pseudouridine synthase B [Brevibacterium
           mcbrellneri ATCC 49030]
          Length = 271

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 88/252 (34%), Gaps = 48/252 (19%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
              +RL +   +     +    ++++  G+V VD   V     I+ G  +          
Sbjct: 31  HSGVRLQKVMADAGLG-SRRACEQMILDGRVEVDGHIV-----IELGTRID--------- 75

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
               +Q+++  S+ +   ++ +           +  NKPA +    G          L  
Sbjct: 76  --PTKQRLVVDSMPIETSTEKV----------YFALNKPAKVVSSMGDPEGRRN---LDE 120

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +V  + ++     RLD ET G+L++      A  LT       I K Y + V G      
Sbjct: 121 FVRDRTERLFHVGRLDYETEGLLLLTNDGDMANRLT--HPRYEIPKKYLAQVKGPVAKDV 178

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                  L++     D +  V             FK+ID        +E+  H+G+   +
Sbjct: 179 G----ARLREGIELDDGISRVDS-----------FKLIDSQP-GVALVEVILHSGKNRIV 222

Query: 256 RVHALHMGCPIV 267
           R     +G P++
Sbjct: 223 RRLLSAVGNPVL 234


>gi|145639281|ref|ZP_01794887.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae PittII]
 gi|145271584|gb|EDK11495.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae PittII]
 gi|309751158|gb|ADO81142.1| 23S rRNA pseudouridylate synthase RluB [Haemophilus influenzae
           R2866]
          Length = 357

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELC--TRSDPEGRATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|255528344|ref|ZP_05395151.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|296188339|ref|ZP_06856731.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255507968|gb|EET84401.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|296047465|gb|EFG86907.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 258

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/255 (12%), Positives = 84/255 (32%), Gaps = 56/255 (21%)

Query: 14  NDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
            + ++MR++++       I +      +++  +V ++    +  +R++S   V++     
Sbjct: 10  ENSDSMRINKFISE--KGICSRREADTLIQEKRVTINGITAELGSRVKSTDEVKLD---- 63

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
               ++ E++                     +D      NKP GI       I  +I  F
Sbjct: 64  --GKLLTEKEK--------------------DDKVYIALNKPVGIICTTEKKIKNNIVDF 101

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +     +  ++     RLD+++ G++ +         +  +      + I          
Sbjct: 102 V-----NYPKRIFHIGRLDKDSEGLIFLTNDGDIVNKILRAGNNHEKEYIV--------- 147

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              +CI N  LK+   G   ++             +  K    + +      +    G  
Sbjct: 148 TVDKCITNSFLKEMASGVSILN-------------TVTKPCKVYKEGSHIFRIILTQGLN 194

Query: 253 HQLRVHALHMGCPIV 267
            Q+R     +G  ++
Sbjct: 195 RQIRRMCEALGYNVL 209


>gi|297520148|ref|ZP_06938534.1| 23S rRNA pseudouridylate synthase B [Escherichia coli OP50]
          Length = 281

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|295689516|ref|YP_003593209.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
 gi|295431419|gb|ADG10591.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
          Length = 246

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 81/248 (32%), Gaps = 47/248 (18%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR   N   + +   +Q ++ +G+V +D K +K      +G  +RI         +  
Sbjct: 8   RLDRLLAN-LGYGSRKEVQALVAAGKVVLDGKPLKD-----AG--LRIAVDATLPERMTI 59

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS-VQGGSGIAYHIDGFLKSWVD 138
               +D    L                 + + +KP G+       G    I   L     
Sbjct: 60  RGVAVDPPAPL-----------------VLMMHKPLGVVCSHKEDGEK--IYDLLPRRWR 100

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD+ETSG++++         +      R + K Y + +       +   
Sbjct: 101 LRDPALSTVGRLDKETSGLILITDDGDFLHRV--ISPKRHVPKTYLARLDRPLSGSEGET 158

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                           +++  EK    A    +++D    +    E     GR HQ+R  
Sbjct: 159 FAAGT----------LMLEGEEKPLLPA--RLEIVDERTARLTITE-----GRYHQVRRM 201

Query: 259 ALHMGCPI 266
              +G  +
Sbjct: 202 FAAVGNHV 209


>gi|227498494|ref|ZP_03928640.1| pseudouridine synthase [Acidaminococcus sp. D21]
 gi|226903952|gb|EEH89870.1| pseudouridine synthase [Acidaminococcus sp. D21]
          Length = 246

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 41/235 (17%), Positives = 79/235 (33%), Gaps = 47/235 (20%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
            +    +KI+  G+V V+ K V           + +   ++  + I+ + + L    +  
Sbjct: 19  ASRRECEKIILQGRVTVNGKPV-----------IELGTKVSPTDRILIDGRPLRKERHR- 66

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                            ++ NKP  +               +   +D + ++     RLD
Sbjct: 67  ----------------YFLLNKPPAVMTTMKDPRGRR---TVAELMDKERERVYPVGRLD 107

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             T G+L++    A AQ +T       I K Y  +V G  + +K            +   
Sbjct: 108 FMTEGLLIMTNDGALAQGMT--HPSYHINKTYEVVVDGHVEEEK------------LDKL 153

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
              +   +   A  A+   K  D   +     E+  H GR  Q+R     +G P+
Sbjct: 154 RTGIRLCDGMTA-PALVEVKRYDSR-RDQSIFEVTIHEGRNRQVRRMCEAIGYPV 206


>gi|194017854|ref|ZP_03056463.1| RNA pseudouridine synthase family protein [Bacillus pumilus ATCC
           7061]
 gi|194010506|gb|EDW20079.1| RNA pseudouridine synthase family protein [Bacillus pumilus ATCC
           7061]
          Length = 238

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 85/246 (34%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   +     +  +++K++++  V V+ +  K                    +H+ 
Sbjct: 1   MRLDKLLASSGFG-SRKDVKKLVKARAVTVNGELAK-----------------QVKDHVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                +       ++ +F+            + NKP G+           +   L+   +
Sbjct: 43  PSNDEVLVHGERVEYKEFI----------YLMMNKPDGVISATEDLRDETVVDLLE--PE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              ++P    RLD++T G+L++      A Q L+    + +  +++              
Sbjct: 91  DIAREPFPVGRLDKDTVGLLLLTNDGQLAHQLLSPKKHVPKTYEVHL------------- 137

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
              + L    I      VV  ++     A      +D    +   + +    G+ HQ+++
Sbjct: 138 --KYPLGDQDIKRLEEGVVILDDYRTKPAKVE---VDANESEDTRIRLTITEGKYHQVKL 192

Query: 258 HALHMG 263
            A  +G
Sbjct: 193 MAQAVG 198


>gi|238919603|ref|YP_002933118.1| 23S rRNA pseudouridylate synthase B [Edwardsiella ictaluri 93-146]
 gi|269138896|ref|YP_003295597.1| 23S rRNA pseudouridylate synthase/pseudouridine synthase
           [Edwardsiella tarda EIB202]
 gi|238869172|gb|ACR68883.1| RNA pseudouridine synthase family protein [Edwardsiella ictaluri
           93-146]
 gi|267984557|gb|ACY84386.1| 23S rRNA pseudouridylate synthase/pseudouridine synthase
           [Edwardsiella tarda EIB202]
 gi|304558882|gb|ADM41546.1| Ribosomal large subunit pseudouridine synthase B [Edwardsiella
           tarda FL6-60]
          Length = 291

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 57/175 (32%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ +++ G+V VD K     +R++    ++I      ++    E
Sbjct: 5   LQKVLARA-GHGSRREIEALIKEGRVSVDGKLATLGDRVEVMPNMKIRVDGRVVSIRESE 63

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           Q+I                       ++  + KP G                       +
Sbjct: 64  QEIC----------------------RVLAYYKPEGELC--TRRDPEGRPTVFDRLPRLR 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G     K
Sbjct: 100 GSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDEDK 152


>gi|293394546|ref|ZP_06638842.1| ribosomal large subunit pseudouridine synthase F [Serratia
           odorifera DSM 4582]
 gi|291423011|gb|EFE96244.1| ribosomal large subunit pseudouridine synthase F [Serratia
           odorifera DSM 4582]
          Length = 289

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/165 (15%), Positives = 57/165 (34%), Gaps = 34/165 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KRV   +R+  G VV++          
Sbjct: 7   IRLNKYISE--SGICSRRDADRYIEQGNVFINGKRVALGDRVFPGDVVKVNGQ------- 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           + E +  D+ +                       NKP G+      G   +I  F+    
Sbjct: 58  LIEPRNEDNLI-------------------FIALNKPVGVVSTTEDGEKDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                +     RLD+++ G++ +         +  +      + +
Sbjct: 97  ---STRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 138


>gi|224373114|ref|YP_002607486.1| hemolysin A [Nautilia profundicola AmH]
 gi|223589777|gb|ACM93513.1| hemolysin A [Nautilia profundicola AmH]
          Length = 236

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
          MRLD++   +    +    Q+I++SG V+V+ K + K + +I     V +
Sbjct: 1  MRLDQYLVTNEYTFSRNKAQEIIKSGYVKVNDKIIKKPSFKIAETDSVEV 50


>gi|170767473|ref|ZP_02901926.1| ribosomal small subunit pseudouridine synthase A [Escherichia
           albertii TW07627]
 gi|170123807|gb|EDS92738.1| ribosomal small subunit pseudouridine synthase A [Escherichia
           albertii TW07627]
          Length = 231

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 76/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R+ +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRANRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHNVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|153829628|ref|ZP_01982295.1| pseudouridine synthase family 1 protein [Vibrio cholerae 623-39]
 gi|148874904|gb|EDL73039.1| pseudouridine synthase family 1 protein [Vibrio cholerae 623-39]
          Length = 321

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/232 (16%), Positives = 80/232 (34%), Gaps = 34/232 (14%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   L+ ++R+G+V V+ K      R++    VVRI   + +   +  
Sbjct: 5   LQKVLARA-GHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNAVVRIDGHVVS---VKA 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +++++                      ++  + KP G                       
Sbjct: 61  QEEVI---------------------CRVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K    
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGDVTEEKVRNL 155

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT 249
              ++       +  V+    +G N+  + + VI+     +     E Q  T
Sbjct: 156 VRGVQLEDGMARFEDVMYAGGEGINH--TFYVVINEGRNREVRRLWESQGTT 205


>gi|314933670|ref|ZP_07841035.1| pseudouridine synthase RluB [Staphylococcus caprae C87]
 gi|313653820|gb|EFS17577.1| pseudouridine synthase RluB [Staphylococcus caprae C87]
          Length = 245

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/235 (14%), Positives = 74/235 (31%), Gaps = 53/235 (22%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+ + V     ++     V +                    + + 
Sbjct: 19  SRRKAETLITEGKVKVNGQVVTELGTKVSHSDTVEV------------------EGIKIE 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +           ED    +F KP  +     S         +  + +    +     RLD
Sbjct: 61  Q-----------EDKMYILFYKPTQVIT---SVSDDLGRKVVTDYFEDIETRIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP--KNKKECIANWLLKKSHIG 209
            +TSG+L++         +T       I+K Y + + G    +  KE      L+     
Sbjct: 107 YDTSGVLLLTNDGEFTNLMT--HPRYHIKKKYVAKLKGYLMREQVKELEQGIELEDGFTQ 164

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              V + +Q+++                +    +E+    GR  Q+R    + G 
Sbjct: 165 PAQVKIKRQDKE----------------KNTTLVEITISEGRNRQVRRMFEYFGH 203


>gi|260913461|ref|ZP_05919939.1| ribosomal large subunit pseudouridine synthase E [Pasteurella
           dagmatis ATCC 43325]
 gi|260632401|gb|EEX50574.1| ribosomal large subunit pseudouridine synthase E [Pasteurella
           dagmatis ATCC 43325]
          Length = 241

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 73/179 (40%), Gaps = 26/179 (14%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGI 157
           K ++ + ++K+ +FNKP  +  Q       +    LK ++     +     RLD+++ G+
Sbjct: 41  KKVISFAETKVILFNKPYDVLTQFS---DENGRATLKDFIPVS--QVYPAGRLDRDSEGL 95

Query: 158 LVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN------KKECIANW---LLKKSHI 208
           +++         L E     + +K Y++ V  IP+       ++  + N    L  K  +
Sbjct: 96  VLLTNNGEIQHRLAEPKF--KTEKTYFAQVEAIPQEVDLEQLRQGVVLNDGKTLPAKVRL 153

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
             +   + ++N            + +       WLE++   GR  Q+R    H+G P +
Sbjct: 154 VSEPNWLWERNPP----------IRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTL 202


>gi|170761840|ref|YP_001787134.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A3 str. Loch Maree]
 gi|169408829|gb|ACA57240.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A3 str. Loch Maree]
          Length = 236

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/252 (16%), Positives = 83/252 (32%), Gaps = 55/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
            RL ++  +     +    + I+  G+V V+  ++K    +I SG  ++++   I     
Sbjct: 3   ERLQKYMAS-CGVASRRKCEDIILEGRVEVNGIKIKELGTKIISGKDIIKVDGNIIEPE- 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKS 135
                                      E+    + NKP G             I   +K 
Sbjct: 61  ---------------------------ENKIYILLNKPKGYVCTAKDEKGRKTILDLVKV 93

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 ++     RLD +TSGI+++         +      +   K Y + V G  K   
Sbjct: 94  -----KERIYPIGRLDMDTSGIIILTNDGEIYNKIIHPKFEK--IKTYKAKVKGTIKKDH 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 L KK    GDY+            A +  +++    +    + ++ H G+  Q+
Sbjct: 147 IE----LFKKGIDIGDYI-----------TAPATLEILK-INKDTSEIIIKIHEGKNRQV 190

Query: 256 RVHALHMGCPIV 267
           R     +G  ++
Sbjct: 191 RRMCKSIGHAVI 202


>gi|229082214|ref|ZP_04214678.1| hypothetical protein bcere0023_48320 [Bacillus cereus Rock4-2]
 gi|228701132|gb|EEL53654.1| hypothetical protein bcere0023_48320 [Bacillus cereus Rock4-2]
          Length = 165

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQQMKPNTILSQGDYISIC 164


>gi|254480346|ref|ZP_05093594.1| conserved hypothetical protein, putative [marine gamma
           proteobacterium HTCC2148]
 gi|214039908|gb|EEB80567.1| conserved hypothetical protein, putative [marine gamma
           proteobacterium HTCC2148]
          Length = 313

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/164 (14%), Positives = 58/164 (35%), Gaps = 30/164 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RL+++      H +     K++ S +V+++  R +   +++SG VV +       +   
Sbjct: 7   IRLNKFISES-GHCSRREADKLIASNRVKINGTRPELGTKVESGDVVTVDGQEIMGSAPG 65

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K  ++                           +NKP GI+      +  +I   +     
Sbjct: 66  KSDRV------------------------YIAYNKPVGITCTTERSVQGNIVDAIDHH-- 99

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              Q+     RLD+ + G++++         +  +      + +
Sbjct: 100 ---QRIFPIGRLDKPSEGLILLTSDGDIVNKILRAENAHEKEYL 140


>gi|222150708|ref|YP_002559861.1| tRNA pseudouridine synthase A homolog [Macrococcus caseolyticus
           JCSC5402]
 gi|222119830|dbj|BAH17165.1| tRNA pseudouridine synthase A homolog [Macrococcus caseolyticus
           JCSC5402]
          Length = 236

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/247 (12%), Positives = 79/247 (31%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++        +     K + +G+++++  + +  +++  G  V +   +  LN   
Sbjct: 1   MRINKFLSEA-GICSRRGADKWIEAGRIKINGVKAELGSKVTEGDSVEVDNKVVTLNT-- 57

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +       NKP GI+      I  +I  F+     
Sbjct: 58  ------------------------DKGYVYIKLNKPRGITSTTERHIKGNIVDFV----- 88

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD+++ G++++                         +V  I + +    
Sbjct: 89  GHSERIFHIGRLDKDSEGLILL--------------------TNDGDIVNEILRKEGRHE 128

Query: 199 ANWLL-KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             +++     I  D+V  + +     +      +V     + F   ++    G   Q+R 
Sbjct: 129 KEYIVTVDKPITDDFVKQMSEGVAILDTVTLPAEVEKLNTKTF---KIILTQGLNRQIRR 185

Query: 258 HALHMGC 264
               +G 
Sbjct: 186 MTEALGY 192


>gi|322515424|ref|ZP_08068415.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           ureae ATCC 25976]
 gi|322118547|gb|EFX90780.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           ureae ATCC 25976]
          Length = 347

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/176 (17%), Positives = 58/176 (32%), Gaps = 27/176 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   L++I+ +G+V VD K     +R+Q     +I    N ++ I
Sbjct: 67  GEKLQKILARAGQG-SRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNLISLI 125

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 126 PAQKEIC----------------------RVLMYYKPEGELC--TRSDPEGRATVFDRLP 161

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              G +     RLD  TSG+L+       A  L      R +++ Y   V+G    
Sbjct: 162 RLTGARWVAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGNIDE 215


>gi|297521296|ref|ZP_06939682.1| 16S rRNA pseudouridylate synthase A [Escherichia coli OP50]
          Length = 207

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|149377823|ref|ZP_01895554.1| 23S rRNA pseudouridine synthase [Marinobacter algicola DG893]
 gi|149357881|gb|EDM46372.1| 23S rRNA pseudouridine synthase [Marinobacter algicola DG893]
          Length = 318

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 19/163 (11%), Positives = 49/163 (30%), Gaps = 32/163 (19%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RL+++        +     + + +G V ++ K  +  +++  G  V +   +        
Sbjct: 8   RLNKYISES-GMCSRREADRYIENGNVAINGKAAQVGDQVLPGDKVTVNGQLIEPRDE-- 64

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                                   ED      NKP G+          +I   +      
Sbjct: 65  ------------------------EDLIFIALNKPVGVVSTTDPAERRNIVNHV-----G 95

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
            G++     RLD+++ G++ +         +  +      + +
Sbjct: 96  HGERIFPIGRLDKDSQGLIFLTSNGDLVNKILRAGNNHEKEYL 138


>gi|325662260|ref|ZP_08150875.1| hypothetical protein HMPREF0490_01613 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|331086071|ref|ZP_08335154.1| hypothetical protein HMPREF0987_01457 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325471512|gb|EGC74733.1| hypothetical protein HMPREF0490_01613 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|330406994|gb|EGG86499.1| hypothetical protein HMPREF0987_01457 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 255

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/266 (16%), Positives = 87/266 (32%), Gaps = 63/266 (23%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           MS     ++   +  +E++RL+++        +     +++ SG+V VD +R +   R+ 
Sbjct: 1   MSNQIEREF---DAPKESVRLNKFLSEA-GVCSRREADRLIESGRVTVDGRRAEMGMRVT 56

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
             Q V +   +     I K+ +++                       +   NKP GI   
Sbjct: 57  KDQEVCVGKKV-----IQKKDRMV-----------------------LLAVNKPTGIVCT 88

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                  +I  FL     +   +     RLD+++ G+L++         +  +      +
Sbjct: 89  EEKREKKNIIRFL-----NYPTRITYIGRLDKDSEGLLLMTNNGDIINKMMRAGNCHEKE 143

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSH--IGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
                         KE    ++ K S      D V    + EK   Y    F++I     
Sbjct: 144 Y--------KVTVNKEVTKEFVRKMSEGVPILDTVTRPCKVEKTGKY---KFRII----- 187

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGC 264
                      G   Q+R    + G 
Sbjct: 188 --------LTQGLNRQIRRMCEYFGY 205


>gi|320451356|ref|YP_004203452.1| ribosomal small subunit pseudouridine synthase A [Thermus
           scotoductus SA-01]
 gi|320151525|gb|ADW22903.1| ribosomal small subunit pseudouridine synthase A [Thermus
           scotoductus SA-01]
          Length = 238

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 75/251 (29%), Gaps = 57/251 (22%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RLD+         +   + +++RSGQV+V             GQVVR P         
Sbjct: 3   GERLDKLLARLGLG-SRKEVARLVRSGQVQV------------EGQVVRDPAFHVPPGAR 49

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           ++                  + ++L     I +  KPAG       G             
Sbjct: 50  LE---------------VDGEPLVLRCHHHILLH-KPAGYVTSRREGP-----SVYALLE 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +      RLD++T G+L+          LT   R +  ++    L     +  +E 
Sbjct: 89  GFPTRDLSPVGRLDKDTEGLLLFTTDGELLHRLTHP-RHKVEKRYLVHLERPATREDQEA 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID-CFAQKFCWLEMQPHTGRTHQLR 256
               L+ +                      +     +  + Q    +E+    GR HQ++
Sbjct: 148 FREGLVLEG---------------------TRLLPAELSWDQDPTRVELVLREGRFHQVK 186

Query: 257 VHALHMGCPIV 267
                 G  ++
Sbjct: 187 RMFQARGNRVL 197


>gi|317054344|ref|YP_004118369.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316952339|gb|ADU71813.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 290

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/164 (14%), Positives = 53/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +  +  + +  G V ++ KR     ++ +G  V++   +       
Sbjct: 8   RLNKYISE--SGICSRRDADRYIEQGNVFINGKRASVGAQVFAGDEVKVNGQLIEPRDE- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    ED  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------EDLVLIALNKPVGIITTMEEGERDNISDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
              ++     RLD+++ G++ +         +  +      + +
Sbjct: 97  --SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNNHEKEYV 138


>gi|254427640|ref|ZP_05041347.1| conserved hypothetical protein, putative [Alcanivorax sp. DG881]
 gi|196193809|gb|EDX88768.1| conserved hypothetical protein, putative [Alcanivorax sp. DG881]
          Length = 280

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/293 (13%), Positives = 83/293 (28%), Gaps = 61/293 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   L+  +  G+V V+       +R+ S   +R+   +                + +  
Sbjct: 16  SRRELETWISDGRVSVNGTVATLGDRVGSEDTLRVDGRM----------------IKVKA 59

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
             D ++ +++Y        +KP G                  +    +G +     RLD 
Sbjct: 60  EEDTVQRVIMY--------HKPPGEVC--SRNDPEGRPTVFDNLPRLQGMRWVQVGRLDI 109

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T+G+++       A  L         +           + ++  +   LL+      D 
Sbjct: 110 NTTGMMLFTTDGELAHRLMHPSNGFVREYAVRVRGGMTQEKRQAMLDGVLLEDGVSKFDS 169

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
           +      E+GAN+                W ++    G+  ++R            D + 
Sbjct: 170 IEDAGGAEEGANH----------------WYKVTLTGGKYREVRRLFQSQ------DLEV 207

Query: 273 CANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVKTWDSLGFK 325
               +  F            R+M+L              P  M    D +  K
Sbjct: 208 ARLMRIRFGDLNLPPQLRQGRWMELE-------------PEQMKALIDKVELK 247


>gi|16273119|ref|NP_439355.1| hypothetical protein HI1199 [Haemophilus influenzae Rd KW20]
 gi|260581101|ref|ZP_05848922.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae RdAW]
 gi|1175679|sp|P45104|RLUB_HAEIN RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|1574128|gb|AAC22853.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|260092230|gb|EEW76172.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae RdAW]
          Length = 357

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHTQKEI------------------------CRVLMYYKPEGELC--TRSDPEGRATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|317492193|ref|ZP_07950623.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316919898|gb|EFV41227.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 317

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/175 (18%), Positives = 61/175 (34%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +   N   H +   ++ +++ G+V VD K          G  V + P          +
Sbjct: 5   LQKVLANA-GHGSRREIEAMIKEGRVSVDGKLATL------GDRVEVTP--------AMK 49

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            ++    V++ + ++ +  +L Y         KP G                       +
Sbjct: 50  IRVDGRVVSIRESTESVCRVLAY--------YKPEGELC--TRRDPEGRPTVFDRLPKLR 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 100 GSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDEK 152


>gi|291287278|ref|YP_003504094.1| pseudouridine synthase [Denitrovibrio acetiphilus DSM 12809]
 gi|290884438|gb|ADD68138.1| pseudouridine synthase [Denitrovibrio acetiphilus DSM 12809]
          Length = 229

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/240 (15%), Positives = 79/240 (32%), Gaps = 54/240 (22%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R++++       ++  +  K +  G+VRV+ K       +  G  V++            
Sbjct: 3   RINKYLAAR-SQLSRRDADKAIEEGRVRVNGK-------LPEGPWVQLS----------- 43

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
                     +T   + +      ED   + F KP  +    G G   H    L+ +   
Sbjct: 44  ------EKDKVTLDGNDISGA---EDYFYWAFYKPKSVLTAYGDG---HGKDTLEIYPFL 91

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +KP  + RLD ++ G+++ +      + L  +                  + +     
Sbjct: 92  REKKPAYSGRLDYDSEGLIIFSNDGDFIRRLQRAEEK--------------VEKEYIVTV 137

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
           N +LKK  +      +V +           ++            ++  H G+  Q+R H 
Sbjct: 138 NRVLKKGEMDDLRKGIVYEGI--------RYRECIVEQHSHDRYQVVLHEGKKRQIR-HM 188


>gi|261855955|ref|YP_003263238.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261836424|gb|ACX96191.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
          Length = 369

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/248 (13%), Positives = 77/248 (31%), Gaps = 48/248 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RL +         +   ++  + +G+V+++    +  +  ++G V+ +      ++ 
Sbjct: 2   SKQRLQKILATQGLG-SRRMIEGWISAGEVKLNGVVAQLGDVAEAGDVLDVRGQKITVSD 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKS 135
                               ++ +++Y        +KP G I+          + G L +
Sbjct: 61  ETP-----------------IRRVIIY--------HKPEGEITSTSDPEGRPTVFGSLPA 95

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
               +        RLD  TSG+L+       A  L       +I++ Y   V G     +
Sbjct: 96  IRQGRWIT---VGRLDFNTSGLLLATNDGELANRL--MHPSHQIERTYAVRVLGGLTEDQ 150

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 L  +  +     H  + ++ G                   W  +    GR  ++
Sbjct: 151 ---VKQLTTEVQLDDGPAHFDQLSDAGG-------------TGVNRWYHVTLREGRNREI 194

Query: 256 RVHALHMG 263
           R     +G
Sbjct: 195 RRMIEAVG 202


>gi|74312704|ref|YP_311123.1| 16S rRNA pseudouridylate synthase A [Shigella sonnei Ss046]
 gi|73856181|gb|AAZ88888.1| 16S pseudouridylate 516 synthase [Shigella sonnei Ss046]
 gi|323168668|gb|EFZ54348.1| RNA pseudouridylate synthase [Shigella sonnei 53G]
          Length = 231

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 VSPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|254515164|ref|ZP_05127225.1| ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium NOR5-3]
 gi|219677407|gb|EED33772.1| ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium NOR5-3]
          Length = 327

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/178 (14%), Positives = 53/178 (29%), Gaps = 31/178 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +  +L +         +   +++ +   +V +D K     +R+ +GQ + +     A   
Sbjct: 18  DGEKLQKVLARSGLG-SRREMERWIEQDRVTIDGKPASLGDRVVAGQRIEVDGRPLAAGD 76

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                      E ++  +++KP G                 +  
Sbjct: 77  G--------------------------EKTRCLLYHKPTGEVC--SRKDPEGRRTVFERL 108

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
              K  +     RLD  TSG+L+       A  L        I++ Y   V G    +
Sbjct: 109 PKVKSGRWISIGRLDYNTSGLLLFTTDGELANALMHPSAN--IEREYMVRVMGDVTEE 164


>gi|170288482|ref|YP_001738720.1| pseudouridine synthase [Thermotoga sp. RQ2]
 gi|170175985|gb|ACB09037.1| pseudouridine synthase [Thermotoga sp. RQ2]
          Length = 239

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 81/248 (32%), Gaps = 61/248 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           MRLDR+  N         ++K+++ G+V V+ + V    + +     V +          
Sbjct: 1   MRLDRYLSNSGVG-TRKEVKKLIKQGRVTVNGRVVLDPGHPVLENDAVALD--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                 ++ +      +F KP+G      S    H +  ++   
Sbjct: 51  --------------------GEVVRFHKKVYILFYKPSGYVT---STKDPHSETIMEFLP 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK- 195
             KG  P    RLD++  G+L++      A + ++  +    ++K Y   V G     K 
Sbjct: 88  PLKGIFP--VGRLDKDAEGLLIITNDGDFAHRVISPKW---SVEKEYIVKVEGEVTEDKI 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E + N +  +         V K +       I+                     G+ HQ+
Sbjct: 143 EKLKNGVTLRDGFFAKAKCVEKLSNDTLKIVITE--------------------GKYHQI 182

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 183 KRMTAAVG 190


>gi|258423147|ref|ZP_05686040.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9635]
 gi|257846597|gb|EEV70618.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus A9635]
          Length = 245

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/233 (13%), Positives = 72/233 (30%), Gaps = 49/233 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+   V     +++    + +                    + + 
Sbjct: 19  SRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEV------------------EGIKIE 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +           ED    +F+KP  +     S         +  +      +     RLD
Sbjct: 61  Q-----------EDKIYILFHKPTQVIT---SVSDDRGRTVVTDYFKDIDARIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+L++         +T      +I+K Y + + G           +L+++     +
Sbjct: 107 YDTSGLLLLTNDGEFTNLMT--HPRYQIKKKYVAKLKG-----------YLMREEVKALE 153

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                 + E G               +    +E+    GR  Q+R    H G 
Sbjct: 154 KGI---ELEDGLTQPADVKVKKQDKDKNTTLVEITITEGRNRQVRRMFEHFGH 203


>gi|154339315|ref|XP_001562349.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134062932|emb|CAM39380.1| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 957

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 15/32 (46%), Positives = 20/32 (62%)

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272
             +   P+TGR HQ+R+H   + CPIVGD  Y
Sbjct: 635 ALVLCTPYTGRLHQIRMHLSSLDCPIVGDVVY 666



 Score = 42.7 bits (99), Expect = 0.097,   Method: Composition-based stats.
 Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 144 PRLTHRLDQETSGILVVARTRAAAQH--LTESFRMRRIQKIYWSLVWGIPKNKK 195
           PR  HRLD+ TSG+L++A  + AA+   L    + + ++K   + + G      
Sbjct: 364 PRPCHRLDKVTSGVLLLAVRQDAAKRIGLVLMRKAKEVEKAVAAELLGHGTEPP 417


>gi|3915395|sp|P72581|Y612_SYNY3 RecName: Full=Uncharacterized RNA pseudouridine synthase slr0612;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
          Length = 261

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/162 (19%), Positives = 61/162 (37%), Gaps = 13/162 (8%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQ 168
            VF KP G+  Q     A H    LK +++          RLDQ++ G+L++        
Sbjct: 42  IVFYKPYGVLCQFTDNSA-HPRPTLKDYINL--PDLYPVGRLDQDSEGLLLLTSNGKLQH 98

Query: 169 HLTESFRMRRIQKIYWSLVWGIPKNKK-ECIANWLLKKSHIGGDYVH--VVKQNEKGANY 225
            L       +  + Y++ V G P ++  E +   +    +     +   + + +    N 
Sbjct: 99  RLAHREFAHQ--RTYFAQVEGSPTDEDLEPLRRGITFADYPTRPAIAKIITEPDFPPRNP 156

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            I  ++     +    WL +    GR  Q+R     +G P +
Sbjct: 157 PI-RYR----ASIPTSWLSITLTEGRNRQVRRMTAAVGFPTL 193


>gi|329915247|ref|ZP_08276235.1| Ribosomal large subunit pseudouridine synthase B [Oxalobacteraceae
           bacterium IMCC9480]
 gi|327544952|gb|EGF30293.1| Ribosomal large subunit pseudouridine synthase B [Oxalobacteraceae
           bacterium IMCC9480]
          Length = 621

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/252 (15%), Positives = 74/252 (29%), Gaps = 48/252 (19%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             D++  +L +         +  ++++++ SG+V V+ +      RI +   VRI   + 
Sbjct: 201 TADDDAPKLHKVLAEAGLG-SRRDMEELIISGRVSVNGEPAHIGQRILAQDQVRINGKLI 259

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDG 131
                 K  +                         + V++KPAG I              
Sbjct: 260 QRRVSKKPPR-------------------------VLVYHKPAGEIVSHDDPDGRP---S 291

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             +   + K  K     RLD  T G+L+   +   A  L        I + Y     G  
Sbjct: 292 VFERLPNMKAGKWLAVGRLDFNTEGLLLFTTSGDLANRL--MHPRYNIDREYAVRTLGEL 349

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           +          ++       +  V     +G N                 W  +    GR
Sbjct: 350 EEGMRQKLLAGVELDDGVAQFSRVADGGGEGVNK----------------WYRVTIGEGR 393

Query: 252 THQLRVHALHMG 263
             ++R     +G
Sbjct: 394 NREVRRMFEAIG 405


>gi|307637034|gb|ADN79484.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 908]
          Length = 146

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/145 (21%), Positives = 54/145 (37%), Gaps = 19/145 (13%)

Query: 34  FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
              L+  L+  Q  +DK+R+K N                    + K Q I      +   
Sbjct: 21  RDVLKCSLKEAQRHLDKQRLKQNQ-----------------QAVRKSQIIQGVVSLIYFK 63

Query: 94  SDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQE 153
            +  +  L++E      F+KPA I         +  +  L       G+     HRLD E
Sbjct: 64  PNEKQERLVFEAKDFGAFDKPAQIYTHPKGYFDH--ESLLDCIQSHFGKNAHPAHRLDYE 121

Query: 154 TSGILVVARTRAAAQHLTESFRMRR 178
           TSG+++  +T  + + L   F  ++
Sbjct: 122 TSGLVLAGKTLQSTKDLKALFMQKK 146


>gi|309775550|ref|ZP_07670550.1| pseudouridine synthase RluB [Erysipelotrichaceae bacterium 3_1_53]
 gi|308916644|gb|EFP62384.1| pseudouridine synthase RluB [Erysipelotrichaceae bacterium 3_1_53]
          Length = 245

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/247 (12%), Positives = 71/247 (28%), Gaps = 50/247 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +         +    + ++  G+V V+ K V     +++ G ++ +     A    
Sbjct: 2   ERLQKVIAAA-GITSRRKAEVLISEGRVAVNGKTVTELGYKVKRGDLIEVDGKPIAKEDK 60

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +            T   +F +  ++                                  +
Sbjct: 61  VYFLMNKPKRTMCTSEDEFGRQTVVD---------------------------------L 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               Q+     RLD +TSG++++      A  +    R    +    ++   +     + 
Sbjct: 88  IDCEQRIFTVGRLDYDTSGLIILTNDGDFANEIIHP-RYHIPKVYNLTINGILTSEDMKK 146

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I + ++    I              A Y I+         +  C  ++    GR  Q++ 
Sbjct: 147 IKSGIVLDDGI----------KTLPAKYRITE----KDPQKNQCSFDLTIVEGRNRQIKR 192

Query: 258 HALHMGC 264
               +G 
Sbjct: 193 MMEALGY 199


>gi|262375673|ref|ZP_06068905.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           lwoffii SH145]
 gi|262309276|gb|EEY90407.1| 16S rRNA uridine-516 pseudouridylate synthase [Acinetobacter
           lwoffii SH145]
          Length = 350

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/220 (15%), Positives = 71/220 (32%), Gaps = 31/220 (14%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   +++++ +G+V V+ +  +   RI+ G  +RI                    V    
Sbjct: 16  SRRYMEEVIAAGRVSVNGQIAQVGERIEPGDELRIDGR----------------KVAFQI 59

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
             +  + +++Y         KP G           +     +      G +  +  RLD 
Sbjct: 60  EDEIRRRVIIY--------YKPEGEIC--SRSDPENRPTVFEQLPAIPGDRWVMVGRLDI 109

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            ++G+L+       A  L        I++ Y   V G    +   I N +LK   +    
Sbjct: 110 NSTGLLLFTNDGELANRL--MHPSNEIEREYAVRVMGEVTPQ---IRNNMLKGVVLDDGP 164

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                 +E G +     F+V+    +      +    G  
Sbjct: 165 AKFESFSELGGDGINRWFQVVVKEGRNREVRRIFESQGLK 204


>gi|271500649|ref|YP_003333674.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270344204|gb|ACZ76969.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 296

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/243 (15%), Positives = 78/243 (32%), Gaps = 43/243 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ ++ +G++ VD K     +R++  +  +I    + ++    E
Sbjct: 5   LQKVLARA-GHGSRREIESMIEAGRISVDGKIATLGDRVEVTRATKIRIDGHVVSVRETE 63

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           + +                       ++ ++ KP G                       +
Sbjct: 64  EAVC----------------------RVLMYYKPEGELC--TRSDPEGRPTVFDRLPRIQ 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G           
Sbjct: 100 GYRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGE---------- 147

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
             +    I      V  ++   A  AI  ++  +   Q   W  +    GR  ++R    
Sbjct: 148 --VGDDKIRQLSKGVQLEDGPAAFRAI-RYQGGEGLNQ---WYNVTLTEGRNREVRRLWE 201

Query: 261 HMG 263
            +G
Sbjct: 202 AVG 204


>gi|228993454|ref|ZP_04153364.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
 gi|228999492|ref|ZP_04159070.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|229007048|ref|ZP_04164675.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228754197|gb|EEM03615.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228760203|gb|EEM09171.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|228766276|gb|EEM14920.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
          Length = 244

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 89/246 (36%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N   + +   ++K+L+ G V++D   VK                 +A  H+ 
Sbjct: 1   MRLDKLLAN-MGYGSRKEVKKLLKDGVVKIDGISVK-----------------DAKFHVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E++ +     + ++ +F+            + +KP G+           +   L+  ++
Sbjct: 43  VEEQEVTIHGEIVEYKEFV----------YLMMHKPQGVISATEDDNHETVVDLLE--LE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD +T G L++    +   Q L+     + + K Y++ V G+   K   
Sbjct: 91  DAIFDPFPVGRLDIDTEGFLLLTNDGKLTHQLLS---PKKHVPKKYYAHVAGVVTEKD-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                  +    G  +    + + G    +         +     +E+    G+ HQ++ 
Sbjct: 146 ------VEEFAKGVILDDGYETKPGELTIL--------KSDDVSEIELVITEGKFHQVKR 191

Query: 258 HALHMG 263
               +G
Sbjct: 192 MFEAVG 197


>gi|254361964|ref|ZP_04978095.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261493683|ref|ZP_05990202.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261494350|ref|ZP_05990844.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|153093511|gb|EDN74491.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261309999|gb|EEY11208.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261310683|gb|EEY11867.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 233

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/251 (14%), Positives = 83/251 (33%), Gaps = 63/251 (25%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++   +   +      K+L+SG V V+    K                      I 
Sbjct: 1   MRLDKFIAEN-TGLTRSQAAKVLKSGVVTVNGNIEKS-----------------GAAKIS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKI-YVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +E +                  + YED K+ +V      +  +    I  H DG   +  
Sbjct: 43  QEDE------------------IYYEDQKLEWVEEGQYFMLYKPQGYICSHDDGEYPTVF 84

Query: 138 DSKGQ----KPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                    K     RLD +T+G++++    + + +  +      +   +  +       
Sbjct: 85  QFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHRITSPKHHCEKTYLVTLA------- 137

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              + + ++  ++   G     +++  ++    A    +++D +       E     GR 
Sbjct: 138 ---DPVEDFYAQRLAEG----ILLRGEKEPTLPA--QLEILDDYNVNLTISE-----GRY 183

Query: 253 HQLRVHALHMG 263
           HQ++     +G
Sbjct: 184 HQVKRMFAALG 194


>gi|103487783|ref|YP_617344.1| pseudouridine synthase, Rsu [Sphingopyxis alaskensis RB2256]
 gi|98977860|gb|ABF54011.1| ribosomal large subunit pseudouridine synthase E [Sphingopyxis
           alaskensis RB2256]
          Length = 185

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/171 (19%), Positives = 64/171 (37%), Gaps = 24/171 (14%)

Query: 108 IYVFNKPAGISVQ----GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
           + +FNKP G+  Q    GG+         L  ++D  G  P    RLD+++ G+LV+   
Sbjct: 4   LILFNKPYGVLSQFTDRGGADGTGGGRATLSDYIDVPGVYP--AGRLDKDSEGLLVLTDD 61

Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKN-------KKECIANWLLKKSHIGGDYVHVV 216
            A    ++      ++ K Y + V G P +       +   + +   + + +       +
Sbjct: 62  GALQARIS--SPKHKMPKTYLAQVEGEPDDAALDALARGVTLNDGPTRPATVRRIGAPKL 119

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              +    Y           +    WLE+    GR  Q+R     +G P +
Sbjct: 120 WDRDPPVRY---------RKSVPDSWLELTITEGRNRQVRRMTAAVGHPTL 161


>gi|229844846|ref|ZP_04464984.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 6P18H1]
 gi|229812227|gb|EEP47918.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 6P18H1]
          Length = 357

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELC--TRSDPEGRATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|259907987|ref|YP_002648343.1| 16S rRNA pseudouridylate synthase A [Erwinia pyrifoliae Ep1/96]
 gi|224963609|emb|CAX55102.1| Ribosomal small subunit pseudouridine synthase A [Erwinia
           pyrifoliae Ep1/96]
 gi|283477874|emb|CAY73790.1| putative 16S pseudouridylate 516 synthase [Erwinia pyrifoliae DSM
           12163]
          Length = 234

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/251 (13%), Positives = 75/251 (29%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++     + LR+ +V VD + V+    ++ +   V     +      
Sbjct: 1   MRLDKFISQQL-EVSRAIAARELRARKVTVDGEVVREGAYKLSADSTVEYDGNVLEQQLG 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                             ++ NKP G      S         L    
Sbjct: 60  PR----------------------------YFMLNKPVGYVC---STDDPDHPTILYFLE 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    +     RLD +T+G++++      +  +T          +               
Sbjct: 89  EPGAYRLHAAGRLDNDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------T 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + +   +         +   +     A+   +VI+        + +    GR HQ++ 
Sbjct: 136 LESAISDDNAQQFADGVQLHNEKTLTKPAM--LEVIEPN-----VVRLTISEGRYHQVKR 188

Query: 258 HALHMGCPIVG 268
               +G  +VG
Sbjct: 189 MFAAVGNRVVG 199


>gi|229846229|ref|ZP_04466341.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 7P49H1]
 gi|229811233|gb|EEP46950.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 7P49H1]
          Length = 357

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELCTRSDPKG--RATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|206576604|ref|YP_002237397.1| ribosomal small subunit pseudouridine synthase A [Klebsiella
           pneumoniae 342]
 gi|288934323|ref|YP_003438382.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|290508526|ref|ZP_06547897.1| ribosomal small subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
 gi|206565662|gb|ACI07438.1| ribosomal small subunit pseudouridine synthase A [Klebsiella
           pneumoniae 342]
 gi|288889052|gb|ADC57370.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|289777920|gb|EFD85917.1| ribosomal small subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
          Length = 239

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/251 (15%), Positives = 79/251 (31%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++     + +R  +V VD   VK  + ++Q                 
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGSRVTVDGDIVKDASFKLQ----------------- 42

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E ++      LT+ +            + ++ NKP G      S         L    
Sbjct: 43  -PEHEVEYDGNTLTQQNGP----------RYFMLNKPQGYVC---STDDPDHPTILYFLD 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    K     RLD +T+G++++      +  +T          +               
Sbjct: 89  EPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVE------------- 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + L + +         +   +     A+   +VI         + +    GR HQ++ 
Sbjct: 136 LESPLAEGTAELFAKGVQLHNEKDLTKPAV--LEVI-----TPTEVRLTISEGRYHQVKR 188

Query: 258 HALHMGCPIVG 268
               +G  +VG
Sbjct: 189 MFAAVGNHVVG 199


>gi|154491797|ref|ZP_02031423.1| hypothetical protein PARMER_01414 [Parabacteroides merdae ATCC
           43184]
 gi|154088038|gb|EDN87083.1| hypothetical protein PARMER_01414 [Parabacteroides merdae ATCC
           43184]
          Length = 249

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 48/286 (16%), Positives = 93/286 (32%), Gaps = 55/286 (19%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M Y +  V+ +  E +RL+++  N     +     + ++ G V+V+ + V          
Sbjct: 1   MKYKE--VLADPNEPIRLNKFLSNA-GVCSRREADEFIQEGVVQVNGQIVT--------- 48

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                        I ++  +L     +   S               V NKP        S
Sbjct: 49  --------ELGTKITRQDTVLFKDQPVQIESKV-----------YIVLNKPKNCVT--TS 87

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                    +    ++  ++     RLD+ T+G+L++      A  LT     ++     
Sbjct: 88  DDPQERLTVMDLVKNACQERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPSFKKKKIYHV 147

Query: 184 WSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           W L   +     E IAN L L+   I  D +    +++K                     
Sbjct: 148 W-LDKNVSIEDMEKIANGLELEDGEIHADAISYASEDDK-------------------SQ 187

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVG-DHKYCANFKGNFTSPIQNK 287
           + ++ H+GR   +R     +G  +V  D  Y A          + +
Sbjct: 188 VGIEIHSGRNRIVRRIFESLGYHVVKLDRVYFAGLTKKNLGRGKWR 233


>gi|187733584|ref|YP_001879484.1| 16S rRNA pseudouridylate synthase A [Shigella boydii CDC 3083-94]
 gi|187430576|gb|ACD09850.1| ribosomal small subunit pseudouridine synthase A [Shigella boydii
           CDC 3083-94]
          Length = 231

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRYHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|261821191|ref|YP_003259297.1| 16S rRNA pseudouridylate synthase A [Pectobacterium wasabiae
           WPP163]
 gi|261605204|gb|ACX87690.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
          Length = 231

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/253 (14%), Positives = 72/253 (28%), Gaps = 59/253 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + L + +V VD + VK                      + 
Sbjct: 1   MRLDKFLSQQL-EISRSLVARELHAQRVTVDGEVVKS-----------------GAFKLS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L + S            + ++ NKP G      S         L     
Sbjct: 43  PEHNVEFDGNPLKQQSGP----------RYFMLNKPQGYVC---STDDPDHPTILYFMDV 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLLTDDGQWSHRITSPKHECEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYA----ISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              L + +         +   +     A    ++ + V            +    GR HQ
Sbjct: 137 EQPLAEDTAAQFTAGVQLHSEKNLTKPASLEKVTDYVV-----------RLTISEGRYHQ 185

Query: 255 LRVHALHMGCPIV 267
           ++     +G  +V
Sbjct: 186 VKRMFAAVGNRVV 198


>gi|157144864|ref|YP_001452183.1| 16S rRNA pseudouridylate synthase A [Citrobacter koseri ATCC
           BAA-895]
 gi|157082069|gb|ABV11747.1| hypothetical protein CKO_00593 [Citrobacter koseri ATCC BAA-895]
          Length = 245

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 77/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +RS +V VD + ++                 NA   ++
Sbjct: 14  MRLDKFIAQQL-GVSRAIAGREIRSNRVTVDGEIIR-----------------NAAFKLL 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L + +            + ++ NKP G      S         L    +
Sbjct: 56  PEHNVEYDGNTLVQQNGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 102

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 103 PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 150 ESPVAADTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLTISEGRYHQVKRM 202

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 203 FAAVGNHVV 211


>gi|117623529|ref|YP_852442.1| 23S rRNA pseudouridylate synthase B [Escherichia coli APEC O1]
 gi|115512653|gb|ABJ00728.1| 23S rRNA pseudouridylate synthase [Escherichia coli APEC O1]
          Length = 291

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/173 (17%), Positives = 59/173 (34%), Gaps = 30/173 (17%)

Query: 25  FKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHIIKEQK 82
                 H +   ++ I+ +G+V VD K  K  +R++   G  +RI   +           
Sbjct: 8   LLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHL----------- 56

Query: 83  ILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQ 142
                +++ + ++ +  +L Y         KP G                       +G 
Sbjct: 57  -----ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPKLRGA 101

Query: 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 102 RWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|297626538|ref|YP_003688301.1| Pseudouridine synthase [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
 gi|296922303|emb|CBL56875.1| Pseudouridine synthase [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
          Length = 275

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/268 (14%), Positives = 80/268 (29%), Gaps = 56/268 (20%)

Query: 4   MTYVQYVVVENDEE---NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M+      ++        +RL +         +    + ++  G+V V+   V       
Sbjct: 21  MSETHEPPIDQSAAKPEGIRLQKVLAQA-GIASRRASEGLITEGRVEVNGHIV------- 72

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQ 120
               V +   ++  +  I+                              + NKP G+   
Sbjct: 73  ----VELGTRVDPEHDSIRVDGARIPPPRRHM---------------YLLLNKPRGVVS- 112

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
             +         L  +V  + Q+     RLD ET G++++         L+       ++
Sbjct: 113 --TMDDPEGRPTLAEYV-PRHQRLFHVGRLDTETEGLIILTNDGEFGHRLS--HPSYEVR 167

Query: 181 KIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ 238
           K Y     G+  N+  +       L+   I  D V +V +                    
Sbjct: 168 KTYLVDAEGLMDNRTIRRLEKGLTLEDGPIKPDRVKLVSR------------------GP 209

Query: 239 KFCWLEMQPHTGRTHQLRVHALHMGCPI 266
               L++  H+GR   +R     +G P+
Sbjct: 210 VHTMLQITLHSGRNRIVRRMMDSVGHPV 237


>gi|148826192|ref|YP_001290945.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae PittEE]
 gi|148716352|gb|ABQ98562.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae PittEE]
          Length = 357

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELCTRSDPKG--RATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|309973338|gb|ADO96539.1| 23S rRNA pseudouridylate synthase RluB [Haemophilus influenzae
           R2846]
          Length = 357

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELCTRSDPKG--RATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|227325901|ref|ZP_03829925.1| 16S rRNA pseudouridylate synthase A [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 231

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/253 (14%), Positives = 72/253 (28%), Gaps = 59/253 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + L + +V VD + VK                      + 
Sbjct: 1   MRLDKFLSQQL-EISRSLVARELHAQRVTVDGEVVKS-----------------GAFKLS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L + +            + ++ NKP G      S         L     
Sbjct: 43  PEHNVEFDGEPLKQQNGP----------RYFMLNKPQGYVC---STDDPDHPTILYFMDV 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLLTDDGQWSHRITSPKHQCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYA----ISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              L + +         +   +     A    I+ + V            +    GR HQ
Sbjct: 137 EQPLAEDTAAQFTAGVQLHNEKNLTKPATLEKITDYVV-----------RLTISEGRYHQ 185

Query: 255 LRVHALHMGCPIV 267
           ++     +G  +V
Sbjct: 186 VKRMFAAVGNRVV 198


>gi|187735933|ref|YP_001878045.1| pseudouridine synthase [Akkermansia muciniphila ATCC BAA-835]
 gi|187425985|gb|ACD05264.1| pseudouridine synthase [Akkermansia muciniphila ATCC BAA-835]
          Length = 230

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 76/251 (30%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD      Y + +       ++   +    K      +++Q+                
Sbjct: 1   MRLDALLSR-YGYCSRREAPGWIKRHSITFKGKPCSSPTDKVQA---------------- 43

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E  +LD               + + D       KP G +     G    I   L    
Sbjct: 44  --EGILLDGEP------------VEFPDGLYAALYKPEGYTCSHDDGEGNLIYDLLPFQW 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGIPKNKKE 196
             +        RLD+ETSG+L++         +T       + K+Y ++    IP    E
Sbjct: 90  RHRNPAVSSVGRLDKETSGLLLLTDDGKFIHRMT--SPRHHVAKVYEAVTEEDIPTEAVE 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             A+  L               N +    A +  ++ +         E     G+ HQ+R
Sbjct: 148 LFASGTL-------------TLNGETRPCAPALLEIREPRRALLTLTE-----GKYHQVR 189

Query: 257 VHALHMGCPIV 267
                +G P++
Sbjct: 190 RMLAAVGAPVL 200


>gi|218689259|ref|YP_002397471.1| 23S rRNA pseudouridylate synthase B [Escherichia coli ED1a]
 gi|218426823|emb|CAR07673.2| 23S rRNA pseudouridylate synthase [Escherichia coli ED1a]
          Length = 291

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/175 (18%), Positives = 59/175 (33%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ I+ +G+V VD K  K       G  V I P +         
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKL------GDRVEITPRLKI------- 50

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
            +I    +++ + ++ +  +L Y         KP G                       +
Sbjct: 51  -RIDGHLISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPKLR 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 100 GARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|225419695|ref|ZP_03761998.1| hypothetical protein CLOSTASPAR_06033 [Clostridium asparagiforme
           DSM 15981]
 gi|225041659|gb|EEG51905.1| hypothetical protein CLOSTASPAR_06033 [Clostridium asparagiforme
           DSM 15981]
          Length = 300

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/304 (11%), Positives = 84/304 (27%), Gaps = 51/304 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL++         +     +++ SG+V VD    K   +++  Q V     +       
Sbjct: 4   ERLNKLLSA-MGVCSRREADRLIESGKVLVDGVPAKMGQKVRMDQTVVCRGKVVGRGEAA 62

Query: 79  KEQKI-----------LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                            D +         L   +      +   NKP G+          
Sbjct: 63  AGAGNGKTARRVGSGRADGTAAQDARPASLPRSMKKPRPVLLAVNKPKGVVCTASDKDKA 122

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
                +  +      +     RLD+++ G++++         +  S      +       
Sbjct: 123 PNIVDMIQYP----VRVYYVGRLDKDSEGLVLMTNQGDLVNKIMRSGNAHEKEY------ 172

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
                  +  +   +  +     +    +K+ ++         KV     ++F    +  
Sbjct: 173 -------QVVVDRPVTAEFLARMEKGVRLKELDRTTLPC----KVRKTGDKRFS---IVL 218

Query: 248 HTGRTHQLRVHALHMGCPI------------VGDHKYCANFKGNFTSPIQN--KLYLHAR 293
             G   Q+R      GC +            +GD K    ++    +  +   KL  H+ 
Sbjct: 219 TQGLNRQIRRMCEACGCHVRSLKRVRVMNICLGDLK-SGEYRQVEGAEYREFMKLLEHST 277

Query: 294 YMDL 297
            +  
Sbjct: 278 NLSF 281


>gi|145635048|ref|ZP_01790754.1| predicted methyltransferase [Haemophilus influenzae PittAA]
 gi|145267656|gb|EDK07654.1| predicted methyltransferase [Haemophilus influenzae PittAA]
          Length = 357

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELC--TRSDPEGRATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|68249745|ref|YP_248857.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 86-028NP]
 gi|68057944|gb|AAX88197.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 86-028NP]
          Length = 357

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELC--TRSDPEGRATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|284039270|ref|YP_003389200.1| RNA-binding S4 domain protein [Spirosoma linguale DSM 74]
 gi|283818563|gb|ADB40401.1| RNA-binding S4 domain protein [Spirosoma linguale DSM 74]
          Length = 638

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/211 (16%), Positives = 70/211 (33%), Gaps = 37/211 (17%)

Query: 12  VENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
              ++   RL+R+  N    + +     +++  G + V+ K V     +++ G  V+   
Sbjct: 398 TPANDGTTRLNRFIAN--SGVCSRREADELIAHGDISVNGKIVTEMGYKVKEGDTVKYGT 455

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            +      +         V L K  D++ +    E+                        
Sbjct: 456 KVLNPERFVY--------VLLNKPKDYITTTEDPEE-----------------------R 484

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              ++   D+   +     RLD+ T+G+L++      A  LT      R +     L   
Sbjct: 485 KTVMELVADAGKFRMYPVGRLDRNTTGLLLITNDGELADKLTHPSNNIR-KIYQVELDKP 543

Query: 190 IPKNKKECIANWL-LKKSHIGGDYVHVVKQN 219
           I     E I   + L+   I  D + +V  +
Sbjct: 544 ITDEHFEAIKKGIELEDGPIKPDAISIVTPD 574


>gi|240948952|ref|ZP_04753308.1| pseudouridine synthase [Actinobacillus minor NM305]
 gi|240296767|gb|EER47378.1| pseudouridine synthase [Actinobacillus minor NM305]
          Length = 340

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/176 (17%), Positives = 58/176 (32%), Gaps = 27/176 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   L++I+ +G+V VD K     +R+Q     +I    + +N I
Sbjct: 60  GEKLQKILARAGQG-SRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGHLINLI 118

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 119 PTQKEIC----------------------RVLMYYKPEGELC--TRSDPEGRATVFDRLP 154

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              G +     RLD  TSG+L+       A  L      R +++ Y   V+G    
Sbjct: 155 RLTGSRWVAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGNVDE 208


>gi|163803033|ref|ZP_02196919.1| anthranilate synthase component II [Vibrio sp. AND4]
 gi|159173207|gb|EDP58036.1| anthranilate synthase component II [Vibrio sp. AND4]
          Length = 312

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/176 (18%), Positives = 60/176 (34%), Gaps = 30/176 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   ++  ++SG+V V+    K   R++    VVRI   + +    I+
Sbjct: 5   LQKVLARA-GHGSRREIESFIKSGRVSVNGIVAKLGERLEDENSVVRIDGHVVSAK--IQ 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E+ I                       ++  + KP G                       
Sbjct: 62  EEVIC----------------------RVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGEVTEQK 151


>gi|148828349|ref|YP_001293102.1| methyltransferase [Haemophilus influenzae PittGG]
 gi|148719591|gb|ABR00719.1| predicted methyltransferase [Haemophilus influenzae PittGG]
          Length = 357

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELCTRSDPKG--RATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPHLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|312134570|ref|YP_004001908.1| RNA-binding S4 domain-containing protein [Caldicellulosiruptor
          owensensis OL]
 gi|311774621|gb|ADQ04108.1| RNA-binding S4 domain protein [Caldicellulosiruptor owensensis
          OL]
          Length = 80

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 24/50 (48%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          MR+D++ K           Q+   +G+V V+ K  K +  ++ G V+ + 
Sbjct: 1  MRIDKYLKVSRIIKRRTLAQEACEAGRVFVNGKVAKPSTDVKVGDVIEVH 50


>gi|319897335|ref|YP_004135531.1| ribosomal large subunit pseudouridine synthase b [Haemophilus
           influenzae F3031]
 gi|301169940|emb|CBW29544.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 10810]
 gi|317432840|emb|CBY81205.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae F3031]
          Length = 357

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELC--TRSDPEGRATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|145637046|ref|ZP_01792709.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae PittHH]
 gi|145269700|gb|EDK09640.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae PittHH]
          Length = 357

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELCTRSDPKG--RATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|218554753|ref|YP_002387666.1| 16S rRNA pseudouridylate synthase A [Escherichia coli IAI1]
 gi|218361521|emb|CAQ99110.1| 16S rRNA pseudouridylate 516 synthase [Escherichia coli IAI1]
          Length = 231

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAV--LEVI-----TPTQVRLIISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|205374821|ref|ZP_03227614.1| tRNA pseudouridine synthase A [Bacillus coahuilensis m4-4]
          Length = 235

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 74/248 (29%), Gaps = 60/248 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++  +     +     K++  G+V ++ +R K  +++  G  V +      L    
Sbjct: 1   MRINKYISDAGK-ASRRGADKLIEEGRVYINGRRAKIGDQVNPGDDVLVNGNHVRLAR-- 57

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                     ++     NKP GI+     G+  +I   +     
Sbjct: 58  --------------------------NNVYIALNKPVGITSTTEKGVKGNIIDLVNH--- 88

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+E+ G++++         +  +      +                  
Sbjct: 89  --PLRIFNIGRLDKESDGLILLTNDGDIVNEILRAENKHEKEYFVS-------------- 132

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP--HTGRTHQLR 256
                    I  +++  +    K     I   K + C  ++    + Q     G   Q+R
Sbjct: 133 -----VDKPITQEFLDNMASGVK-----ILGTKTLPCKIEQISKYDFQITLTQGLNRQIR 182

Query: 257 VHALHMGC 264
                +G 
Sbjct: 183 RMCEALGY 190


>gi|157693404|ref|YP_001487866.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
 gi|157682162|gb|ABV63306.1| pseudouridylate synthase [Bacillus pumilus SAFR-032]
          Length = 238

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 85/246 (34%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   +     +  +++K++++  V V+ +  K                    +H+ 
Sbjct: 1   MRLDKLLASSGFG-SRKDVKKLVKARAVTVNGELAK-----------------QVKDHVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                +       ++ +F+            + NKP G+           +   L+   +
Sbjct: 43  PSNDEVLVHGERVEYKEFI----------YLMMNKPDGVISATEDVRDETVVDLLE--PE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              ++P    RLD++T G+L++      A Q L+    + +  +++              
Sbjct: 91  DIAREPFPVGRLDKDTVGLLLLTNDGQLAHQLLSPKKHVPKTYEVHL------------- 137

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
              + L    I      V+  ++     A      +D    +   + +    G+ HQ+++
Sbjct: 138 --KYPLGDQDINRLEEGVIILDDYRTKPAKVE---VDANESEDTRIRLTITEGKYHQVKL 192

Query: 258 HALHMG 263
            A  +G
Sbjct: 193 MAQAVG 198


>gi|88810635|ref|ZP_01125892.1| Pseudouridine synthase, Rsu [Nitrococcus mobilis Nb-231]
 gi|88792265|gb|EAR23375.1| Pseudouridine synthase, Rsu [Nitrococcus mobilis Nb-231]
          Length = 267

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/231 (14%), Positives = 67/231 (29%), Gaps = 44/231 (19%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++  +R G++RV+ +  +   R+     + +         +               
Sbjct: 18  SRRQMEHWIRDGRIRVNGRIARLGERVAPRMQITVDGRPLRRRSL--------------- 62

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
               L  +LLY        +KP G+                +     K  +     RLD 
Sbjct: 63  --SGLPRMLLY--------HKPVGVVTTRSDPAG--RPTVFQHLPRIKKGRWIAVGRLDI 110

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L+       A  L       R+ + Y   V+G        +   ++ +   G + 
Sbjct: 111 NTCGLLLFTTDGELANRL--MHPSFRLVREYAVRVYGE-------VTAEMITRLQQGVEL 161

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
                   +    A    +V+        W  +    GR  ++R      G
Sbjct: 162 --------EDGRGAFDRIEVLCEAQAANGWYRVSLAEGRRREVRRLWESQG 204


>gi|90023354|ref|YP_529181.1| pseudouridine synthase, Rsu [Saccharophagus degradans 2-40]
 gi|89952954|gb|ABD82969.1| Pseudouridine synthase, Rsu [Saccharophagus degradans 2-40]
          Length = 249

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/242 (15%), Positives = 81/242 (33%), Gaps = 52/242 (21%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+      ++N  +++  +   ++ V+ K               I  V++   HI  
Sbjct: 7   RLDRFIS-LNSNLNRRDVRLAIAQKRILVNGKHAS-----------TIHQVVSQFCHITF 54

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + + L ++  +                   + NKPAG            + G L   + +
Sbjct: 55  DNQTLQANAPV-----------------YIMLNKPAGRVSATKDSTHPTVVGCLPQQLQA 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                 +  RLD  ++G++++    A ++HLT                   P+NK   I 
Sbjct: 98  N---IHIVGRLDFNSTGLMLLTNNGAWSRHLTS------------------PENKVNKIY 136

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQK--FCWLEMQPHTGRTHQLRV 257
              L+++    ++   +     G  +A           ++       +    GR HQ++ 
Sbjct: 137 EVELERTINDDEWPQYISAFASGMYFAFEDLTTQPAKLERLTATRARVTLVEGRYHQIKR 196

Query: 258 HA 259
             
Sbjct: 197 MF 198


>gi|315634119|ref|ZP_07889408.1| ribosomal large subunit pseudouridine synthase B [Aggregatibacter
           segnis ATCC 33393]
 gi|315477369|gb|EFU68112.1| ribosomal large subunit pseudouridine synthase B [Aggregatibacter
           segnis ATCC 33393]
          Length = 328

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 58/181 (32%), Gaps = 27/181 (14%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
               E  +L +         +   ++ I+   +V VD K     +RI     V++     
Sbjct: 41  TTSAEGEKLQKVLARAGQG-SRREIESIIAENRVSVDGKIATLGDRINVNSGVKV----- 94

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                    +I  + +NLT+    +  +L+Y         KP G                
Sbjct: 95  ---------RIDGNLINLTQAQKEVCRVLMY--------YKPEGELC--TRHDPEGRATV 135

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
                   G +     RLD  TSG+L+       A  L      R +++ Y   V+G   
Sbjct: 136 FDRLPRLTGARWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGAVD 193

Query: 193 N 193
           +
Sbjct: 194 D 194


>gi|167855222|ref|ZP_02477992.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           parasuis 29755]
 gi|167853675|gb|EDS24919.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           parasuis 29755]
          Length = 339

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/172 (17%), Positives = 58/172 (33%), Gaps = 27/172 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   +++++ +G+V VD K     +R+Q     +I    N +N I
Sbjct: 60  GEKLQKILARAGQG-SRREIEEVIAAGRVSVDGKIATLGDRVQVSSSTKIRIDGNLVNLI 118

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 119 PTQKEIC----------------------RVLMYYKPEGELC--TRSDPEGRATVFDRLP 154

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              G +     RLD  TSG+L+       A  L      R +++ Y   V+G
Sbjct: 155 RLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFG 204


>gi|114776453|ref|ZP_01451498.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Mariprofundus ferrooxydans
           PV-1]
 gi|114553283|gb|EAU55681.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthase [Mariprofundus ferrooxydans
           PV-1]
          Length = 289

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/250 (15%), Positives = 89/250 (35%), Gaps = 50/250 (20%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNH 76
             R++R+   H    +     + +++G+V ++ + ++     ++SG  V +   +     
Sbjct: 42  PERINRYLA-HCGLCSRREADRWIQAGRVSINGQLIEAPGVIVKSGDTVMVDDKLVEPQQ 100

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                 + +LY        NKP G      S +       +  +
Sbjct: 101 --------------------GHTYILY--------NKPKGQLC---SRLDKKKRPLIYDF 129

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +D      +   RLD +T G+L++    A  + LT      ++ + Y + V GI + +  
Sbjct: 130 IDV-APNVQSIGRLDMDTEGLLMLTDDGALTRALTHPAA--KVPREYRARVAGIVELETL 186

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                    + +    + + + +   A + ++    +D  +    WL +    GR  ++R
Sbjct: 187 ---------AKLRRGGMDIGRGDTSDA-WEVT----VDSESAGHTWLNIIILRGRWREVR 232

Query: 257 VHALHMGCPI 266
                 G P+
Sbjct: 233 RTLEECGHPV 242


>gi|78485572|ref|YP_391497.1| pseudouridine synthase, Rsu [Thiomicrospira crunogena XCL-2]
 gi|78363858|gb|ABB41823.1| ribosomal large subunit pseudouridine synthase B [Thiomicrospira
           crunogena XCL-2]
          Length = 317

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 28/178 (15%), Positives = 59/178 (33%), Gaps = 29/178 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              +L +         +   ++K++  G V+V+ K     +R      +++       + 
Sbjct: 16  AGEKLQKILARGGFG-SRREVEKLISQGLVKVNGKVATLGDRAFPTDTLKVN------DQ 68

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           ++KE ++                ++LY        NKP G             +    S 
Sbjct: 69  LVKETRLEKQPT----------QVILY--------NKPEGQVC--SRKDEKGRETIFTSL 108

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                 +     RLD  TSG+L++      A  L        +++ Y   V+G   ++
Sbjct: 109 PRIINSRWISVGRLDINTSGLLILTNNGELANRL--MHPSYEMEREYSVRVFGEVSDE 164


>gi|295098123|emb|CBK87213.1| ribosomal small subunit pseudouridine synthase A [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 235

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/251 (13%), Positives = 70/251 (27%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++     + +R+ +V VD   VK +  ++Q    V          + 
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRASRVTVDGDIVKDSAFKLQPEHQVEYDGNPLTQQNG 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                             ++ NKP G      S         L    
Sbjct: 60  PR----------------------------YFMLNKPEGYVC---STDDPDHPTVLYFLD 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    K     RLD +T+G+++                  +      S      K  +  
Sbjct: 89  EPVAHKLHAAGRLDIDTTGLVL-------------MTDDGQWSHRITSPRHHCDKTYRVM 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + +   +         +   +     A+               + +    GR HQ++ 
Sbjct: 136 LESPVSDDTAEQFAKGVQLHNEKDLTKPAVLEI-------LTPTDVRLTISEGRYHQVKR 188

Query: 258 HALHMGCPIVG 268
               +G  +VG
Sbjct: 189 MFAAVGNHVVG 199


>gi|113971512|ref|YP_735305.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           MR-4]
 gi|113886196|gb|ABI40248.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           MR-4]
          Length = 235

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/252 (14%), Positives = 78/252 (30%), Gaps = 54/252 (21%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNH 76
            +RLD++       +     +K L  G++  D   VK +  ++  G  V +     +L  
Sbjct: 6   PVRLDKFICES-TSLTRSLAKKALHRGEITCDGIVVKDSGFKVLEGMQVCLEGEPISLV- 63

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                         +  + NKP        S I       L   
Sbjct: 64  ----------------------------GERYLMLNKPVDTIC---STIDEAYPSVLSLL 92

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              K +   +  RLD +T+G++++          ++     RI                +
Sbjct: 93  DIEKPETLHIAGRLDADTTGLVLIT---------SDGQWSHRITSPKKDCGKRYLVTLAD 143

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +   L+     G +    ++  +     A+   ++I+        + +    G+ HQ++
Sbjct: 144 PVDGSLVGIFAAGVE----LRNEDGLTKPAV--LEIIEPQ-----LVRLTITEGKYHQVK 192

Query: 257 VHALHMGCPIVG 268
                +G  +VG
Sbjct: 193 RMFAAVGNHVVG 204


>gi|329124070|ref|ZP_08252617.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           aegyptius ATCC 11116]
 gi|327467495|gb|EGF12993.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           aegyptius ATCC 11116]
          Length = 357

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/179 (18%), Positives = 58/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ +G+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELCTRSDPKG--RATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L        +++ Y   V+G   +
Sbjct: 167 RLPHLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSHEVEREYSVRVFGQVDD 223


>gi|295136030|ref|YP_003586706.1| ribosomal large subunit pseudouridine synthase [Zunongwangia
           profunda SM-A87]
 gi|294984045|gb|ADF54510.1| putative ribosomal large subunit pseudouridine synthase
           [Zunongwangia profunda SM-A87]
          Length = 284

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/212 (18%), Positives = 72/212 (33%), Gaps = 35/212 (16%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVI 71
           E  E+ MRL+++  N     +  +    + SG V V+ + V     ++Q    V+     
Sbjct: 46  EKREDGMRLNKYIANA-GICSRRDADIYIASGNVSVNGEVVTEMGYKVQLTDEVK----- 99

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                                   F    +  +  + +V NK  G+ V G   +      
Sbjct: 100 ------------------------FDGRSITPDKPEYFVLNKSKGVFVTGS--VHKGGLT 133

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            +     +   K     +LD +T+G+LV     A A+ L    +    Q  +  L   + 
Sbjct: 134 VMDIMAKASKSKLDPIGKLDTQTTGLLVFTNDGALAKKLANP-KNGIRQIYHIKLDHALS 192

Query: 192 KNKKECIANWL-LKKSHIGGDYVHVVKQNEKG 222
           ++  E I   + ++   I    V  VK   K 
Sbjct: 193 QDDLEKIREGVYIESKKINVTDVSYVKDRPKT 224


>gi|294340472|emb|CAZ88853.1| putative Pseudouridine synthase [Thiomonas sp. 3As]
          Length = 562

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/262 (14%), Positives = 76/262 (29%), Gaps = 47/262 (17%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
                V+ V+   ++    L +         +   ++ ++ +G+V V+ +      RI  
Sbjct: 159 ETAEIVRRVLAPAEDAPK-LHKVLAQSGVG-SRREMEDLILAGRVSVNGEPAHLGQRILP 216

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              +R+   I        + +                         +  ++KP G  V  
Sbjct: 217 TDQIRVNGKIIKRRLRPAQAR-------------------------VLAYHKPTGEVV-- 249

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                       +     +G K     RLD  T G+L+   +   A  L         ++
Sbjct: 250 SFKDPEGRPTVFQHLPKLQGAKWTAVGRLDINTEGLLLFTTSGDLANRL--MHPSYGAER 307

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y   V G          + LL+   +G      +   E G   A   ++V+        
Sbjct: 308 EYAVRVLGELDAAA---RDELLEGVQLGDGPARFLSLEEAGGEGANRWWRVV-------- 356

Query: 242 WLEMQPHTGRTHQLRVHALHMG 263
                   GR  ++R     +G
Sbjct: 357 -----ISEGRNREVRRMFEAVG 373


>gi|237736761|ref|ZP_04567242.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           mortiferum ATCC 9817]
 gi|229420623|gb|EEO35670.1| ribosomal large subunit pseudouridine synthase B [Fusobacterium
           mortiferum ATCC 9817]
          Length = 236

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/251 (13%), Positives = 85/251 (33%), Gaps = 50/251 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +R++++  +     +   + K++  G++RV+ + +    ++    ++ +         
Sbjct: 2   EEIRINKYLASLGVG-SRREIDKLIEEGKIRVNGEVISAGVKVTDKDIIEV--------- 51

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K S  ++  + Y      + NKP  + V   +         +   
Sbjct: 52  ------------KGKKISKDIEKKVYY------MLNKP--LEVLSSAKDDRGRKTVVD-- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +    ++     RLD  T+G++++         +        + K Y+  V G  K+   
Sbjct: 90  IVKCKERIFPIGRLDYNTTGLILLTNDGELFNRV--IHPRSEVYKEYYVKVLGEIKDSS- 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 +KK   G +         +      ++ K+I     K   + +    GR  Q+R
Sbjct: 147 ------IKKLEDGVEL--------EDGITLPAYVKLISRERGKSELM-VSIREGRNRQVR 191

Query: 257 VHALHMGCPIV 267
                +  P++
Sbjct: 192 RMLEAVNTPVL 202


>gi|261337851|ref|ZP_05965735.1| cytotoxin/hemolysin [Bifidobacterium gallicum DSM 20093]
 gi|270277318|gb|EFA23172.1| cytotoxin/hemolysin [Bifidobacterium gallicum DSM 20093]
          Length = 285

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 11/87 (12%)

Query: 1  MSLMTYVQYVVVENDEEN----------MRLDRWFKNHYPHINFVNLQKILRSGQVRVDK 50
          MS+    Q   + + +            +RLD+         +    Q+++  G+V VD 
Sbjct: 1  MSMGVGRQPADIGSGQAGGRASQGSGHQLRLDQALVRRGLVQSRSRAQRLIDEGRVFVDG 60

Query: 51 KRV-KFNNRIQSGQVVRIPPVINALNH 76
          K V K ++++     +R+    + ++ 
Sbjct: 61 KCVSKSSSKVDGAADIRVDKGDDYVSR 87


>gi|238755438|ref|ZP_04616779.1| Ribosomal small subunit pseudouridine synthase A [Yersinia ruckeri
           ATCC 29473]
 gi|238706375|gb|EEP98751.1| Ribosomal small subunit pseudouridine synthase A [Yersinia ruckeri
           ATCC 29473]
          Length = 235

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 76/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V VD + VK                      + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTVDGEIVK-----------------TGALKLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ+++     L +              + ++ NKP G      S         L    +
Sbjct: 43  PEQEVMFDGNLLQQQVGP----------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPKHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +         A    +VI+    +    E     GR HQ++  
Sbjct: 137 EHPVADDTAEQFAVGVQLHNEPTLTKPA--QLEVIEPQQVRLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FGAVGNRVV 198


>gi|73662568|ref|YP_301349.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
 gi|72495083|dbj|BAE18404.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
          Length = 245

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/233 (14%), Positives = 72/233 (30%), Gaps = 49/233 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+V+V+         +++    + +                    + L 
Sbjct: 19  SRRKAETLITEGKVKVNGTVETELGTKVKPSDSIEV------------------EGIKLE 60

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           +           ED    +F KPA +     S         +  +      +     RLD
Sbjct: 61  Q-----------EDKLYILFYKPAQVIT---SVSDDRGRKVVTDYFKQIKTRIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+L++        +L    R +  +K    L   + + + + +   +  +  +   
Sbjct: 107 YDTSGLLLLT-NDGEFTNLMTHPRYKIKKKYVVKLKGYLMREEVKSLEQGVQLEDGVTQP 165

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
            +  VK  +K  N                  +E+    GR  Q+R    H G 
Sbjct: 166 AIIKVKNQDKDKNT---------------TLVEITITEGRNRQVRRMFEHFGH 203


>gi|253998302|ref|YP_003050365.1| pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|313200376|ref|YP_004039034.1| pseudouridine synthase [Methylovorus sp. MP688]
 gi|253984981|gb|ACT49838.1| pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|312439692|gb|ADQ83798.1| pseudouridine synthase [Methylovorus sp. MP688]
          Length = 178

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/163 (23%), Positives = 67/163 (41%), Gaps = 14/163 (8%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + +FNKP G+  Q     A+     LK ++           RLD ++ G+L++       
Sbjct: 2   LILFNKPFGVVCQFS---AHENHPTLKDYIAM--PDVYAAGRLDTDSEGLLILTDDGRLQ 56

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             +       +  KIYW+ V G P ++    A   L++    GD+V    Q +  A  A 
Sbjct: 57  HRIA--HPKHKEIKIYWAQVEGAPDDE----ALSPLRRGVDLGDFVTQPAQVKIIAEPAN 110

Query: 228 SHFKV---IDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              +V    +  A    WLE++   G+  Q+R     +G P +
Sbjct: 111 LWARVPPIRERKAIPTTWLEIRISEGKNRQVRRMTAKIGFPTL 153


>gi|148379772|ref|YP_001254313.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. ATCC 3502]
 gi|153931029|ref|YP_001384070.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. ATCC 19397]
 gi|153937131|ref|YP_001387610.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. Hall]
 gi|148289256|emb|CAL83352.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. ATCC 3502]
 gi|152927073|gb|ABS32573.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. ATCC 19397]
 gi|152933045|gb|ABS38544.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum A str. Hall]
          Length = 236

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/252 (16%), Positives = 83/252 (32%), Gaps = 55/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
            RL ++  +     +    + I+  G+V V+  ++K    +I SG  ++++   I     
Sbjct: 3   ERLQKYMAS-CGVASRRKCEDIILEGRVEVNGIKIKELGTKIISGKDIIKVDGNIIEPE- 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKS 135
                                      E+    + NKP G             I   +K 
Sbjct: 61  ---------------------------ENKIYILLNKPKGYVCTAKDEKDRKTILDLVKV 93

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 ++     RLD +TSGI+++         +      +   K Y + V G  K   
Sbjct: 94  -----KERIYPIGRLDMDTSGIIILTNDGEIYNKIIHPKFEK--IKTYKAKVKGTIKKDH 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 L KK    GDY+            A +  +++    +    + ++ H G+  Q+
Sbjct: 147 IE----LFKKGIDIGDYL-----------TAPATLEILK-INKDTSEIIIKIHEGKNRQV 190

Query: 256 RVHALHMGCPIV 267
           R     +G  ++
Sbjct: 191 RRMCKSIGHAVI 202


>gi|15602526|ref|NP_245598.1| hypothetical protein PM0661 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|34098697|sp|Q9CMY9|RLUB_PASMU RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|12720938|gb|AAK02745.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 345

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/179 (17%), Positives = 55/179 (30%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++   +V VD K     +R  + +G  +RI   +  L
Sbjct: 62  EGEKLQKVLARAGQG-SRREIEAMIAENRVSVDGKIATLGDRIDVHAGVKIRIDGHLINL 120

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
            H  KE                          ++ ++ KP G                  
Sbjct: 121 LHAQKEV------------------------CRVLMYYKPEGELC--TRHDPEGRPTVFD 154

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G    
Sbjct: 155 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDE 211


>gi|320104277|ref|YP_004179868.1| pseudouridine synthase [Isosphaera pallida ATCC 43644]
 gi|319751559|gb|ADV63319.1| pseudouridine synthase [Isosphaera pallida ATCC 43644]
          Length = 655

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/252 (15%), Positives = 79/252 (31%), Gaps = 49/252 (19%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           E  ++  RL +    H    +    ++++  G+V V+ + V+                  
Sbjct: 120 EPSDQPQRLQKILA-HAGIASRRACEELILQGRVTVNGETVR------------------ 160

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
               +       +S + +      L+ ++ +        NKP G      S         
Sbjct: 161 ---ELGARYNPYESKIAIDGEPIKLEKLVYF------AVNKPKGYIC---SNEDPDNRPR 208

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   +    Q+     RLD+ ++G++++      A  LT       ++K Y  +V G P 
Sbjct: 209 VVDLLPEIPQRVYTIGRLDEASTGLILLTNDGELANKLT--HPKFGVEKRYEVVVAGHPD 266

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                +   L+    +    V   K  E G                    LE+    G+ 
Sbjct: 267 RD---VLRKLIDGVWLSDGKVRAKKVRELGRR-------------GDSSILELVLAEGKN 310

Query: 253 HQLRVHALHMGC 264
            ++R     +G 
Sbjct: 311 REIRRMLARLGH 322


>gi|170756858|ref|YP_001781361.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum B1 str. Okra]
 gi|169122070|gb|ACA45906.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum B1 str. Okra]
 gi|322806051|emb|CBZ03618.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum H04402 065]
          Length = 236

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/252 (16%), Positives = 83/252 (32%), Gaps = 55/252 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
            RL ++  +     +    + I+  G+V V+  ++K    +I SG  ++++   I     
Sbjct: 3   ERLQKYMAS-CGVASRRKCEDIILEGRVEVNGIKIKELGTKIISGKDIIKVDGNIIEPE- 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFLKS 135
                                      E+    + NKP G             I   +K 
Sbjct: 61  ---------------------------ENKIYILLNKPKGYVCTAKDEKGRKTILDLVKV 93

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                 ++     RLD +TSGI+++         +      +   K Y + V G  K   
Sbjct: 94  -----KERIYPIGRLDMDTSGIIILTNDGEIYNKIIHPKFEK--IKTYKAKVKGTIKKDH 146

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                 L KK    GDY+            A +  +++    +    + ++ H G+  Q+
Sbjct: 147 IE----LFKKGIDIGDYL-----------TAPATLEILK-INKDTSEIIIKIHEGKNRQV 190

Query: 256 RVHALHMGCPIV 267
           R     +G  ++
Sbjct: 191 RRMCKSIGHAVI 202


>gi|222150212|ref|YP_002551169.1| hypothetical protein Avi_4348 [Agrobacterium vitis S4]
 gi|221737194|gb|ACM38157.1| conserved hypothetical protein [Agrobacterium vitis S4]
          Length = 133

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 20/91 (21%), Positives = 41/91 (45%), Gaps = 13/91 (14%)

Query: 19  MRLDRWF--KNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
            R+D+W      +   +    Q+ + SG+VRV+ K  K  +  ++ G V+ I    + + 
Sbjct: 12  QRIDKWLFFARIFK--SRTLAQQQIVSGRVRVNGKPGKQPSIIVRPGDVLDITLPNHDMK 69

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
            ++++          T    + ++ LLYED 
Sbjct: 70  LVVRQ--------PGTHRGPYEQAKLLYEDQ 92


>gi|126735443|ref|ZP_01751189.1| Pseudouridine synthase, Rsu [Roseobacter sp. CCS2]
 gi|126715998|gb|EBA12863.1| Pseudouridine synthase, Rsu [Roseobacter sp. CCS2]
          Length = 180

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/168 (19%), Positives = 63/168 (37%), Gaps = 22/168 (13%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + +FNKP G+  Q     +      L +++D  G  P    RLD+++ G+LV+       
Sbjct: 4   VILFNKPFGVLSQFTDAKSPTPRPTLSAFIDVPGVYP--AGRLDRDSEGLLVLTDDGKLQ 61

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNK-------KECIANWLLKKSHIG-GDYVHVVKQN 219
             +       ++ K Y+  V G P  K          + +   + + +   D   +  ++
Sbjct: 62  ARIAA--PKNKMSKTYFVQVEGEPTEKDLSLLRDGVTLKDGPTRPAKLRLIDPPQLWDRD 119

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                       V    +    W+E+    GR  Q+R    H+G P +
Sbjct: 120 PP----------VRFRKSVPDTWIEITISEGRNRQVRRMTAHIGFPTL 157


>gi|300717592|ref|YP_003742395.1| ribosomal small subunit pseudouridine synthase A [Erwinia
           billingiae Eb661]
 gi|299063428|emb|CAX60548.1| Ribosomal small subunit pseudouridine synthase A [Erwinia
           billingiae Eb661]
          Length = 234

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 74/250 (29%), Gaps = 53/250 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++       I+     + LR+ +V VD + V+    +++    V        L   
Sbjct: 1   MRLDKFLSQQL-EISRAIALRELRAHKVTVDGEVVRQGAFKLKPENQVEYDGNPLHLQFG 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                             ++ NKP G      S         L    
Sbjct: 60  PR----------------------------YFMLNKPQGYVC---STDDPDHPTVLYFLE 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    K     RLD +T+G++++      +  +T          +               
Sbjct: 89  EPTAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------T 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + L   +         +   +     A      ++  ++  C + +    GR HQ++ 
Sbjct: 136 LESPLADDTAAQFTAGVQLHNEKYLTKPA-----TLEVVSE--CQVRLTISEGRYHQVKR 188

Query: 258 HALHMGCPIV 267
               +G  +V
Sbjct: 189 MFAAVGNHVV 198


>gi|300741214|ref|ZP_07071235.1| ribosomal RNA large subunit methyltransferase J [Rothia
          dentocariosa M567]
 gi|300380399|gb|EFJ76961.1| ribosomal RNA large subunit methyltransferase J [Rothia
          dentocariosa M567]
          Length = 244

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
          MRLD++   H    +     K++ +G V V+ K V K +  +     V + 
Sbjct: 1  MRLDKFLAEHGLAASRTLAAKLIDAGCVSVNGKIVYKASQPVHRDDDVLVQ 51


>gi|193782973|gb|ACF20459.1| pseudouridine synthase [Serratia symbiotica]
          Length = 300

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 28/163 (17%), Positives = 58/163 (35%), Gaps = 25/163 (15%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++ ++ + +V ++ K  K       G  + I P++          +I  + +++ K
Sbjct: 16  SRREIEAMINACRVSINGKIAKL------GDRIEIHPMMKI--------RIDGNIISIKK 61

Query: 93  HSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
             + +  +L Y         KP G +                      +  +     RLD
Sbjct: 62  AEETICRVLAY--------YKPEGELCTISNPSNPEGRLTVFDHLPKLRNLRWVSVGRLD 113

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             TSG+L+       A  L      R+I++ Y   V+G P  +
Sbjct: 114 INTSGLLLFTTNGELANRL--MHPSRKIEREYAVRVFGKPSAE 154


>gi|197302368|ref|ZP_03167425.1| hypothetical protein RUMLAC_01097 [Ruminococcus lactaris ATCC
          29176]
 gi|197298547|gb|EDY33090.1| hypothetical protein RUMLAC_01097 [Ruminococcus lactaris ATCC
          29176]
          Length = 79

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          MRLD++ K            +   +G+V V+ K  K + +++ G V+ I 
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNGKTAKASVKVKPGDVIEIQ 50


>gi|238784264|ref|ZP_04628276.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           bercovieri ATCC 43970]
 gi|238714831|gb|EEQ06831.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           bercovieri ATCC 43970]
          Length = 235

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 77/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK          +++ P  +      
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEVVKSGA-------IKLTPESDVRFDGN 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             Q+ L                      + ++ NKP G      S         L    +
Sbjct: 53  PLQQTLGP--------------------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + + + +         +         A    ++I+        + +    GR HQ++  
Sbjct: 137 EHPVAEDTAQRFADGVQLHNETSLTKPA--QLEIIEPQ-----LVRLTLSEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  ++
Sbjct: 190 FGAVGNRVL 198


>gi|322389007|ref|ZP_08062577.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 903]
 gi|321144312|gb|EFX39720.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           parasanguinis ATCC 903]
          Length = 251

 Score = 54.2 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 45/257 (17%), Positives = 87/257 (33%), Gaps = 54/257 (21%)

Query: 10  VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVRI 67
           + +   E +MRLD+   NH       +++++L   Q+ VD     K +  I  G Q ++I
Sbjct: 2   IRISEKEPSMRLDQLMANH--QYTRKDIKQLLARRQILVDHLPAQKLSQNIDPGLQQIQI 59

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY 127
                    II+E +                          Y+ +KP G         A+
Sbjct: 60  G------ERIIQEPR-----------------------HHYYMLHKPIGAVT--AKRDAH 88

Query: 128 HIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSL 186
           H           +        RLD++TSG+L++        Q L   + + ++       
Sbjct: 89  HPTVIDLVDPQQEYPDLYPLGRLDRDTSGLLLLTDNGPLGFQLLHPQYHVEKVY------ 142

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
                    E   N  L  +HI      +   +      A     +++     +   +++
Sbjct: 143 ---------EVEVNGPLYAAHIEQFQNGISFTDGPICKPA--SLTILESTPS-YSKAQVR 190

Query: 247 PHTGRTHQLRVHALHMG 263
              G+ HQ++   L +G
Sbjct: 191 ISEGKYHQVKKMFLAIG 207


>gi|229085292|ref|ZP_04217534.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
 gi|228698011|gb|EEL50754.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
          Length = 238

 Score = 54.2 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 73/249 (29%), Gaps = 60/249 (24%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N+R++++        +     K++   +V ++ K  K  +++Q G  VR+          
Sbjct: 3   NLRINKFISESGK-ASRRGADKLINERRVIINGKVAKIGDQVQPGDDVRVNGEQLR---- 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                   +  D      NKP GI+      +  +I   +   +
Sbjct: 58  ------------------------IARDHVYIALNKPVGITCTSEKAVKGNIIDLVNHPL 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD+++ G++++         +  +      + I               
Sbjct: 94  -----RVNHVGRLDKDSDGLILLTNDGDIINEILRAENKHEKEYIVS------------- 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TGRTHQL 255
                     I  +++  +    K     I   K + C   +    E Q     G   Q+
Sbjct: 136 ------VDKPITPEFLKQMAAGVK-----ILGTKTLPCEITQLSKYEFQIILTQGLNRQI 184

Query: 256 RVHALHMGC 264
           R     +G 
Sbjct: 185 RRMCEALGY 193


>gi|209551387|ref|YP_002283304.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv. trifolii
           WSM2304]
 gi|209537143|gb|ACI57078.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv. trifolii
           WSM2304]
          Length = 134

 Score = 54.2 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 17/90 (18%), Positives = 38/90 (42%), Gaps = 13/90 (14%)

Query: 19  MRLDRWF--KNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN 75
            R+D+W          +    Q  ++SG VRV+ +R K  +  ++ G  + +      + 
Sbjct: 13  QRIDKWLFFARMVK--SRSLAQSHVQSGHVRVNGERCKHPSQMVKPGDRIELTLERRDVV 70

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYED 105
            +++        +   +   + ++ LLYED
Sbjct: 71  LVMR--------LAGERRGPYEEARLLYED 92


>gi|118580486|ref|YP_901736.1| pseudouridine synthase [Pelobacter propionicus DSM 2379]
 gi|118503196|gb|ABK99678.1| ribosomal large subunit pseudouridine synthase B [Pelobacter
           propionicus DSM 2379]
          Length = 271

 Score = 54.2 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 50/281 (17%), Positives = 88/281 (31%), Gaps = 50/281 (17%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
            +    ++++ +G+V V+   V                       +  +      S+ + 
Sbjct: 15  ASRRAAEEMILAGRVTVNGLVVT---------------------ELGSKADPTVDSIAVD 53

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                  S  LY      + NKPAG      +         +   +    ++     RLD
Sbjct: 54  GRPVKPASQHLY-----ILLNKPAGFMT---TLDDPEGRQVVTDLLPEIKERVYPVGRLD 105

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             T G+L++      A  L        I+K Y   V G     +       + +   G D
Sbjct: 106 YNTEGLLLLTNDGDWANKL--MHPRHEIEKEYHVRVRGKVHQSQ-------IDQLKNGVD 156

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV--GD 269
                     G   A +  ++I    ++  WL +  H GR  Q+R     +   +V    
Sbjct: 157 L--------DGRPTAPAQVRLIK-DGEQNDWLSITIHEGRNRQVRRMCEAVSLSVVRLKR 207

Query: 270 HKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
            +Y A  +     P Q++L   A    L  P  G     AP
Sbjct: 208 VRYGA-LEMRGLKPGQHRLLTEAEARALLTPGAGLRSAEAP 247


>gi|312792842|ref|YP_004025765.1| RNA-binding S4 domain-containing protein [Caldicellulosiruptor
          kristjanssonii 177R1B]
 gi|312876108|ref|ZP_07736096.1| RNA-binding S4 domain protein [Caldicellulosiruptor lactoaceticus
          6A]
 gi|311797094|gb|EFR13435.1| RNA-binding S4 domain protein [Caldicellulosiruptor lactoaceticus
          6A]
 gi|312179982|gb|ADQ40152.1| RNA-binding S4 domain protein [Caldicellulosiruptor
          kristjanssonii 177R1B]
          Length = 80

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 24/50 (48%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          MR+D++ K           Q+   +G+V V+ K  K +  ++ G ++ + 
Sbjct: 1  MRIDKYLKVSRIIKRRTLAQEACEAGRVFVNGKVAKPSTDVKVGDIIEVH 50


>gi|307252799|ref|ZP_07534689.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|307255057|ref|ZP_07536875.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|307261643|ref|ZP_07543310.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|307263831|ref|ZP_07545436.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
 gi|306859698|gb|EFM91721.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|306861930|gb|EFM93906.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|306868635|gb|EFN00445.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|306870820|gb|EFN02559.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
          Length = 373

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/176 (17%), Positives = 58/176 (32%), Gaps = 27/176 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   L++I+ +G+V VD K     +R+Q     +I    N ++ I
Sbjct: 93  GEKLQKILARAGQG-SRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNLISLI 151

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 152 PVQKEIC----------------------RVLMYYKPEGELC--TRSDPEGRATVFDRLP 187

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              G +     RLD  TSG+L+       A  L      R +++ Y   V+G    
Sbjct: 188 RLTGARWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGNIDE 241


>gi|289523408|ref|ZP_06440262.1| S4 RNA-binding domain protein [Anaerobaculum hydrogeniformans
          ATCC BAA-1850]
 gi|289503100|gb|EFD24264.1| S4 RNA-binding domain protein [Anaerobaculum hydrogeniformans
          ATCC BAA-1850]
          Length = 89

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 30/57 (52%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
          MR+D++ K  +        Q+++ +G VR++ + VK ++ ++ G +V +      L 
Sbjct: 1  MRIDKYLKISHIVKRRSVAQEMIAAGVVRLNGRPVKASSMVKVGDIVEVAFPRRTLK 57


>gi|312978410|ref|ZP_07790152.1| S4 domain protein [Lactobacillus crispatus CTV-05]
 gi|310894753|gb|EFQ43825.1| S4 domain protein [Lactobacillus crispatus CTV-05]
          Length = 90

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 11/85 (12%), Positives = 35/85 (41%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++ K           +++   G+++V+ + VK +  ++   ++ +      +   +
Sbjct: 1   MRIDKFLKVSRLVKRRTVAKEMADQGRIKVNGRVVKSSYDVKIDDIIEVGYGAKTIKAKV 60

Query: 79  KEQKILDSSVNLTKHSDFLKSILLY 103
              +        ++  +  K I+ Y
Sbjct: 61  LNIRETTKKAEASELYELAKCIIFY 85


>gi|257455144|ref|ZP_05620382.1| ribosomal small subunit pseudouridine synthase A [Enhydrobacter
           aerosaccus SK60]
 gi|257447477|gb|EEV22482.1| ribosomal small subunit pseudouridine synthase A [Enhydrobacter
           aerosaccus SK60]
          Length = 234

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/245 (15%), Positives = 83/245 (33%), Gaps = 46/245 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++  + +KIL +G+V V+ + VK                 +A  HI 
Sbjct: 1   MRLDKFLSKA-TELSRKDCKKILHAGEVTVNGEVVK-----------------DASLHID 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +    ++ +      +   + +LLY+        KP    +         +         
Sbjct: 43  EVGDDIEWAGEPLSVAMGNRYLLLYKPEGFECTLKPKEWPIVTDLIDVPQLGSL------ 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                 R+  RLD +T+G L+++        +T   +    +    +L   + + ++   
Sbjct: 97  ------RIAGRLDVDTTGALLLSDDGGFLHRVTSP-KHHVAKVYELTLADPMTEAQQAFA 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L K   +  +Y        K A  + S               ++    G+ HQ++  
Sbjct: 150 IKELAKGIMLEDEY-----DKTKPAELSFS----------DATHAKLVLTEGKYHQVKRM 194

Query: 259 ALHMG 263
             + G
Sbjct: 195 MGYFG 199


>gi|302144209|emb|CBI23336.3| unnamed protein product [Vitis vinifera]
          Length = 300

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 3/71 (4%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD      +   +   +Q  +  G+V VD K V K    +    VV I  +     ++ 
Sbjct: 61  RLDEVCLERFQQYSRTFIQSWILQGKVFVDGKVVNKAGTPVSDKAVVEI--MAEVPKYVC 118

Query: 79  KEQKILDSSVN 89
           +    L++++ 
Sbjct: 119 RAGYKLEAAIE 129


>gi|296136237|ref|YP_003643479.1| RNA-binding S4 domain protein [Thiomonas intermedia K12]
 gi|295796359|gb|ADG31149.1| RNA-binding S4 domain protein [Thiomonas intermedia K12]
          Length = 562

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/262 (14%), Positives = 76/262 (29%), Gaps = 47/262 (17%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
                V+ V+   ++    L +         +   ++ ++ +G+V V+ +      RI  
Sbjct: 156 ETAEIVRRVLAPAEDAPK-LHKVLAQSGVG-SRREMEDLILAGRVSVNGEPAHLGQRILP 213

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
              +R+   I        + +                         +  ++KP G  V  
Sbjct: 214 TDQIRVNGKIIKRRLRPAQAR-------------------------VLAYHKPTGEVV-- 246

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
                       +     +G K     RLD  T G+L+   +   A  L         ++
Sbjct: 247 SFKDPEGRPTVFQHLPKLQGAKWTAVGRLDINTEGLLLFTTSGDLANRL--MHPSYGAER 304

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
            Y   V G          + LL+   +G      +   E G   A   ++V+        
Sbjct: 305 EYAVRVLGELDAAA---RDELLEGVQLGDGPARFLSLEEAGGEGANRWWRVV-------- 353

Query: 242 WLEMQPHTGRTHQLRVHALHMG 263
                   GR  ++R     +G
Sbjct: 354 -----ISEGRNREVRRMFEAVG 370


>gi|225469571|ref|XP_002271057.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 316

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 3/71 (4%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD      +   +   +Q  +  G+V VD K V K    +    VV I  +     ++ 
Sbjct: 77  RLDEVCLERFQQYSRTFIQSWILQGKVFVDGKVVNKAGTPVSDKAVVEI--MAEVPKYVC 134

Query: 79  KEQKILDSSVN 89
           +    L++++ 
Sbjct: 135 RAGYKLEAAIE 145


>gi|254462214|ref|ZP_05075630.1| ribosomal large subunit pseudouridine synthase E [Rhodobacterales
           bacterium HTCC2083]
 gi|206678803|gb|EDZ43290.1| ribosomal large subunit pseudouridine synthase E [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 181

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/163 (22%), Positives = 59/163 (36%), Gaps = 11/163 (6%)

Query: 108 IYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           + + NKP G+  Q    G+       L ++VD    +     RLD+++ G+LV+      
Sbjct: 4   VILLNKPFGVLSQFTDKGLEGTTRPTLSAYVD--VPQVYPAGRLDRDSEGLLVLTDDGRL 61

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNK--KECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
              + +    +   K Y  LV  IP     +       LK        V  V+  E    
Sbjct: 62  QAQIADPKFKK--PKTYLVLVERIPSEDALQSLRKGITLKDGMTRPAQVERVEPPELWER 119

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                F+     +   CWL+     GR  Q+R     +G P +
Sbjct: 120 DPPVRFR----KSVPDCWLKFTIREGRNRQVRRMTAAVGHPTL 158


>gi|293390209|ref|ZP_06634543.1| ribosomal large subunit pseudouridine synthase B [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290950743|gb|EFE00862.1| ribosomal large subunit pseudouridine synthase B [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 322

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 34/183 (18%), Positives = 59/183 (32%), Gaps = 31/183 (16%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPV 70
            +  E  +L +         +   ++ I+   +V VD K     +R  + +G  VRI   
Sbjct: 35  TSAAEGEKLQKVLARAGQG-SRREIEAIIAENRVSVDGKIATLGDRINVYAGVKVRIDGH 93

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +                +NLT+    +  +L+Y         KP G              
Sbjct: 94  L----------------INLTQAQKEVCRVLMY--------YKPEGELC--TRHDPEGRA 127

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                     G +     RLD  TSG+L+       A  L      R +++ Y   V+G 
Sbjct: 128 TVFDRLPRLTGARWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQ 185

Query: 191 PKN 193
             +
Sbjct: 186 VDD 188


>gi|154707706|ref|YP_001424364.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           Dugway 5J108-111]
 gi|154356992|gb|ABS78454.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           Dugway 5J108-111]
          Length = 244

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 30/234 (12%), Positives = 72/234 (30%), Gaps = 34/234 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+ +         +   ++K++  G+++V+++  +  +RI    +V I   +++L+   
Sbjct: 3   ERIQKVLARSGYG-SRREIEKMIAEGRIKVNQRLAQLGDRITEQDLVYIDGQLSSLSA-- 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                           + ++ +L ++        K                    ++   
Sbjct: 60  ---------------PEQVRVLLYHKPEGEICTRKDP-----------EGRTTVFETLPR 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K  +  +  RLD  TSG+L+       A  L       ++++ Y   V G         
Sbjct: 94  LKDGRWVIIGRLDINTSGLLLFTNEGELANRL--MHPSAQVEREYAVRVLGAVDADMTQK 151

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
               +        +  +V     G N     F V+    +      +    G  
Sbjct: 152 LAHGVGLEDGKARFEDIVDVGGDGKNR---WFHVVVVEGRHRFVRRLWESQGVK 202


>gi|52841050|ref|YP_094849.1| pseudouridine synthase [Legionella pneumophila subsp. pneumophila
           str. Philadelphia 1]
 gi|52628161|gb|AAU26902.1| pseudouridine synthase [Legionella pneumophila subsp. pneumophila
           str. Philadelphia 1]
          Length = 222

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/165 (21%), Positives = 63/165 (38%), Gaps = 9/165 (5%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           ++  ++ +FNKP GI  Q         +  L +++   G       RLD+++ G+L++  
Sbjct: 21  HKMPQLILFNKPYGILTQ---FTGELPEQTLSAFIKLPGFYA--AGRLDKQSEGLLILTD 75

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  LT     ++  K YW  V G+P +K        L    I          +E  
Sbjct: 76  DGKLQHRLTHPKFEKK--KHYWVQVEGVPTDKDLQPLRKGLVIKDITFLPAEARLISEPK 133

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               I   +  +       WLE+    G+ HQ+R     +G P +
Sbjct: 134 IWPRIPPIR--ERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTL 176


>gi|307257215|ref|ZP_07538986.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|306864257|gb|EFM96169.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
          Length = 349

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/176 (17%), Positives = 58/176 (32%), Gaps = 27/176 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   L++I+ +G+V VD K     +R+Q     +I    N ++ I
Sbjct: 69  GEKLQKILARAGQG-SRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNLISLI 127

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 128 PVQKEIC----------------------RVLMYYKPEGELC--TRSDPEGRATVFDRLP 163

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              G +     RLD  TSG+L+       A  L      R +++ Y   V+G    
Sbjct: 164 RLTGARWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGNIDE 217


>gi|223985880|ref|ZP_03635918.1| hypothetical protein HOLDEFILI_03224 [Holdemania filiformis DSM
           12042]
 gi|223962146|gb|EEF66620.1| hypothetical protein HOLDEFILI_03224 [Holdemania filiformis DSM
           12042]
          Length = 244

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 73/233 (31%), Gaps = 48/233 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    ++ +  G+V+VD + V     + + G ++ +     A                  
Sbjct: 15  SRRKAEEWILQGRVKVDGQVVTELGVKPRKGALIEVDGKAIAR----------------- 57

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                       ED   YV NKP  +     +    H    +   +    Q+     RLD
Sbjct: 58  ------------EDKVYYVMNKPKKVLC---TLNDEHDRRTVVDLMMDVPQRVFPVGRLD 102

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +T+G+L++      A  +          + + + V+       E   N +LK   I   
Sbjct: 103 YDTTGVLIMTNDGEFANEIIH-------PRYHIAKVY-------EVTINGILKTEEIKQL 148

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
              VV  +      A   +     FA +    E+    GR  Q++      G 
Sbjct: 149 EQGVVLDDGIKTLPAK-LWVTNKDFAHEQTMFELTIQEGRNRQIKRMLEVFGY 200


>gi|33865483|ref|NP_897042.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Synechococcus sp. WH 8102]
 gi|33632652|emb|CAE07464.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Synechococcus sp. WH 8102]
          Length = 250

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 68/249 (27%), Gaps = 48/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    +  + +G+V+VD +          G                
Sbjct: 4   QRLQKLIAAA-GLCSRRTAEDWIDAGRVKVDGRISSL------GDQ-----------ADP 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           + Q I      L+   +            + + NKPAG+               L     
Sbjct: 46  ESQLIHVDGRPLSFRGEPT----------VLLINKPAGVIS--TCRDPRGRSTVLDLLPQ 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              Q      RLD ++ G L++         LT            W  V G P +     
Sbjct: 94  QLRQGLHPVGRLDADSRGALLLTDYGDLTLRLTHPRYDHAKTYRVW--VEGTPLDTSL-- 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                                  G     +  +V+   + +   LE+    GR  Q+R  
Sbjct: 150 -------------QRWRQGVTLDGTRTRSAEVRVLQRRSDR-TLLEVVLLEGRNRQIRRV 195

Query: 259 ALHMGCPIV 267
           A  +G P+V
Sbjct: 196 AELLGHPVV 204


>gi|190150487|ref|YP_001969012.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|189915618|gb|ACE61870.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
          Length = 349

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/176 (17%), Positives = 58/176 (32%), Gaps = 27/176 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   L++I+ +G+V VD K     +R+Q     +I    N ++ I
Sbjct: 69  GEKLQKILARAGQG-SRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNLISLI 127

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 128 PVQKEIC----------------------RVLMYYKPEGELC--TRSDPEGRATVFDRLP 163

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              G +     RLD  TSG+L+       A  L      R +++ Y   V+G    
Sbjct: 164 RLTGARWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGNIDE 217


>gi|165976586|ref|YP_001652179.1| pseudouridine synthase [Actinobacillus pleuropneumoniae serovar 3
           str. JL03]
 gi|303250091|ref|ZP_07336293.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|303253264|ref|ZP_07339413.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|307246075|ref|ZP_07528157.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307248183|ref|ZP_07530211.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|307259493|ref|ZP_07541218.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|165876687|gb|ABY69735.1| probable pseudouridine synthase [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|302647946|gb|EFL78153.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|302651154|gb|EFL81308.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|306853010|gb|EFM85233.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|306855360|gb|EFM87535.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|306866429|gb|EFM98292.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
          Length = 349

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/176 (17%), Positives = 58/176 (32%), Gaps = 27/176 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   L++I+ +G+V VD K     +R+Q     +I    N ++ I
Sbjct: 69  GEKLQKILARAGQG-SRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNLISLI 127

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 128 PVQKEIC----------------------RVLMYYKPEGELC--TRSDPEGRATVFDRLP 163

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              G +     RLD  TSG+L+       A  L      R +++ Y   V+G    
Sbjct: 164 RLTGARWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGNIDE 217


>gi|53729057|ref|ZP_00348305.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|126208628|ref|YP_001053853.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae L20]
 gi|126097420|gb|ABN74248.1| ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
          Length = 349

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/176 (17%), Positives = 58/176 (32%), Gaps = 27/176 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   L++I+ +G+V VD K     +R+Q     +I    N ++ I
Sbjct: 69  GEKLQKILARAGQG-SRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNLISLI 127

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 128 PVQKEIC----------------------RVLMYYKPEGELC--TRSDPEGRATVFDRLP 163

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              G +     RLD  TSG+L+       A  L      R +++ Y   V+G    
Sbjct: 164 RLTGARWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGNIDE 217


>gi|228475940|ref|ZP_04060649.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           hominis SK119]
 gi|228270011|gb|EEK11485.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           hominis SK119]
          Length = 228

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/244 (13%), Positives = 76/244 (31%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  N         ++++L+   V+V+ K  K                    + + 
Sbjct: 1   MRLDKFLSNMGVG-TRTEVKQLLKKNSVKVNDKVEKS-----------------PKSQVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ  +               I+ Y +    + NKP G        I   +   +  +  
Sbjct: 43  PEQDEITVDGK----------IIEYINHVYIMLNKPKGYVSATYDDINQTVIDLIADYRH 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                     RLD++T G+L++        +L    +        + +    P   ++ I
Sbjct: 93  L---DLFPVGRLDKDTEGLLLITNDGQFNHNLMSPSKH---VSKTYKVTSKYPIKNEDII 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A            + + ++ ++     A      ++          +  + G+ HQ++  
Sbjct: 147 A------------FKNGIELSDGKVKPAQ-----LEKLDHNVSL--VTIYEGKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|114047181|ref|YP_737731.1| ribosomal large subunit pseudouridine synthase E [Shewanella sp.
           MR-7]
 gi|113888623|gb|ABI42674.1| ribosomal large subunit pseudouridine synthase E [Shewanella sp.
           MR-7]
          Length = 265

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 41/168 (24%), Positives = 63/168 (37%), Gaps = 19/168 (11%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  I +FNKP  +  Q            LK ++   G       RLD+++ G+L++    
Sbjct: 82  DPMIVLFNKPFDVLCQ---FTDEQGRKTLKDYIPIPG--VYAAGRLDRDSEGLLLLTNDG 136

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
                LTE    ++  K YW  V G P           L K   G +    +    K + 
Sbjct: 137 QLQAKLTE--PKKKTFKTYWVQVEGEPTEAD-------LAKLRQGVELKDGMTLPAKVSL 187

Query: 225 YAISHFK-----VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            A  +       + +       WLE+Q H GR  Q+R    H+G P +
Sbjct: 188 MATPNVWPRNPPIRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTL 235


>gi|90021564|ref|YP_527391.1| ribosomal small subunit pseudouridine synthase A [Saccharophagus
           degradans 2-40]
 gi|89951164|gb|ABD81179.1| ribosomal small subunit pseudouridine synthase A [Saccharophagus
           degradans 2-40]
          Length = 242

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/259 (15%), Positives = 88/259 (33%), Gaps = 60/259 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++  N+    +   +++++++  V VDKK     +  + +   VRI          
Sbjct: 1   MRLDKFIANN-SSYSRTEVKRLIKNKTVCVDKKITTDPSFTVTNLNTVRI---------- 49

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW- 136
             + +I+++   L                   + NKP G        I   +   +    
Sbjct: 50  --DGEIIEAIKPL-----------------YIMLNKPTGYVCANKDNIHSPVVDLITEQH 90

Query: 137 --------VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                      + Q  ++  RLD +T+G++++                 R+     +   
Sbjct: 91  ARQSDQTPPKYRAQSLQIAGRLDVDTTGLVLLTDNGE---------WNHRVTSPNKACFK 141

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
                 ++ + +  +K    G     V+   EK A    +    ++  +       +   
Sbjct: 142 RYRVKLEKPLDDAAIKLLSEG-----VMLHGEKAATLPAT----VELISNTEVL--LSIQ 190

Query: 249 TGRTHQLRVHALHMGCPIV 267
            GR HQ++   + +G  +V
Sbjct: 191 EGRFHQVKRMFVKVGTCVV 209


>gi|319790166|ref|YP_004151799.1| pseudouridine synthase [Thermovibrio ammonificans HB-1]
 gi|317114668|gb|ADU97158.1| pseudouridine synthase [Thermovibrio ammonificans HB-1]
          Length = 251

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/255 (14%), Positives = 80/255 (31%), Gaps = 51/255 (20%)

Query: 19  MRLDRWFKNHYPHIN-FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           MRL+++    Y        ++++++ G+V V+ + V                     +  
Sbjct: 1   MRLNKFLA--YAGFGARRKVEELIKQGRVEVNGQVV---------------------DSP 37

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISV--QGGSGIAYHIDGFLKS 135
             E       V +      L +  +Y       FNKP G+    +   G        +  
Sbjct: 38  AVEVDPKKDVVKVDGERVRLPNKFVY-----IAFNKPQGVLTAMERAPGDKR---PIVAD 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           +  +   +     RLD  T G+L++      A  L        + K Y + V G      
Sbjct: 90  YFRNYPVRLFPVGRLDYNTEGLLIMTNDGELADRLA--HPRYHVPKTYIAKVKGR----- 142

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKV---IDCFAQKFCWLEMQPHTGRT 252
                  +K + I       +  ++KG  + I    V         +  ++++    G+ 
Sbjct: 143 -------VKPAEIERMKKGALLVDDKGKKFFIKPLDVKLLHPSKTGRNTYVQITIDQGKN 195

Query: 253 HQLRVHALHMGCPIV 267
             +R         ++
Sbjct: 196 RVVRRFFDRFDHGVL 210


>gi|307250415|ref|ZP_07532362.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|306857544|gb|EFM89653.1| Ribosomal large subunit pseudouridine synthase B [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
          Length = 349

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/176 (17%), Positives = 58/176 (32%), Gaps = 27/176 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   L++I+ +G+V VD K     +R+Q     +I    N ++ I
Sbjct: 69  GEKLQKILARAGQG-SRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNLISLI 127

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 128 PVQKEIC----------------------RVLMYYKPEGELC--TRSDPEGRATVFDRLP 163

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              G +     RLD  TSG+L+       A  L      R +++ Y   V+G    
Sbjct: 164 RLTGARWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGNIDE 217


>gi|49480754|ref|YP_038984.1| hypothetical protein BT9727_4674 [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|49332310|gb|AAT62956.1| hypothetical protein BT9727_4674 [Bacillus thuringiensis serovar
           konkukian str. 97-27]
          Length = 165

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDSISIC 164


>gi|62180286|ref|YP_216703.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|62127919|gb|AAX65622.1| putative ribosomal large subunit pseudouridine synthase [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|322714760|gb|EFZ06331.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 291

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K     +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVKESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G     K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDESK 152


>gi|228910806|ref|ZP_04074615.1| hypothetical protein bthur0013_49480 [Bacillus thuringiensis IBL
           200]
 gi|228848757|gb|EEM93602.1| hypothetical protein bthur0013_49480 [Bacillus thuringiensis IBL
           200]
          Length = 165

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 8/49 (16%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ K++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGKQMKPNAILSEGDHISIC 164


>gi|55820632|ref|YP_139074.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMG 18311]
 gi|55736617|gb|AAV60259.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           thermophilus LMG 18311]
          Length = 239

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/146 (19%), Positives = 50/146 (34%), Gaps = 32/146 (21%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD+          +   ++K++RS QV VD                 +    + LN  
Sbjct: 1   MRLDKLLGQ--SGYGSRNQVKKLIRSRQVYVDG----------------VLADRDNLNVD 42

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
              Q I+ S   L    +             Y+ NKP+G+          H         
Sbjct: 43  ASLQTIMVSGKELEHAPEV-----------YYLMNKPSGVVS--ARKDKEHQTVIDLIRP 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVART 163
           + + +      RLD++T G++++   
Sbjct: 90  EDRREGLYPVGRLDRDTEGLVLITNN 115


>gi|299139090|ref|ZP_07032266.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX8]
 gi|298598770|gb|EFI54932.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX8]
          Length = 307

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 46/259 (17%), Positives = 87/259 (33%), Gaps = 45/259 (17%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RL +         +    + I+  G+V+V+ + V                        
Sbjct: 12  GDRLQKILAQA-GIASRRAAETIILEGRVQVNGQVVT----------------------- 47

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLY--EDSKIYVFNKPAGISV------QGGSGIAYHI 129
                 L +  + T+    +   LL+  E  + ++ NKP G            + +    
Sbjct: 48  -----ELGTRADATRDHIRVDGKLLHGPEPQRYFMVNKPRGYVTTLDDPEHRPTVMQLLG 102

Query: 130 DGFLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
               K  V    + PRL    RLD  + G+L++      A  L+++     ++K Y   V
Sbjct: 103 QDAQKKSVGEHNKLPRLYPVGRLDYLSEGLLLMTNDGELANKLSKAAAG--VEKTYLVKV 160

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
            G P ++     + L +   I    ++ V+   +      S  K+      +  W E+  
Sbjct: 161 SGSPTDEA---IDQLRRGIMIDRGRLNEVRSGRRD-RVLTSPAKIEQVRRGENPWFEVTL 216

Query: 248 HTGRTHQLRVHALHMGCPI 266
             GR  QLR     +G  +
Sbjct: 217 TEGRNRQLRKMFEEIGHHV 235


>gi|225848372|ref|YP_002728535.1| ribosomal large subunit pseudouridine synthase B
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225643927|gb|ACN98977.1| ribosomal large subunit pseudouridine synthase B
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 247

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 82/250 (32%), Gaps = 53/250 (21%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
            RL+++       I +     +++  G+V+V+ K VK                 N    I
Sbjct: 2   ERLNKYIAK--SGICSRRKADELILEGKVKVNGKTVK-----------------NLGLKI 42

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIY-VFNKPAGISVQGGSGIAYHIDGFLKSW 136
             ++ +++    + K ++    + +Y+         K        G          LK  
Sbjct: 43  DPKKDVVEVEGKIVKPTEKKIYLAIYKPVGYLSAVGKDRF-----GRKTLTDFLNELK-- 95

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK-- 194
                 K     RLD  + G+L++      A  +        I+K+Y   V G    +  
Sbjct: 96  ---IPYKLFPVGRLDYNSEGLLILTNDGEFANKVA--HPRNEIKKVYKVKVAGEVSQETL 150

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           K+     +L+      D + ++K+ E G                   WL ++ H+G+   
Sbjct: 151 KKMEEGTILEDGFFKPDKIKMLKREEDG------------------TWLLVEIHSGKKRI 192

Query: 255 LRVHALHMGC 264
           +R      G 
Sbjct: 193 IRRFMDSFGH 202


>gi|161502618|ref|YP_001569730.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160863965|gb|ABX20588.1| hypothetical protein SARI_00665 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 231

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 34/253 (13%), Positives = 76/253 (30%), Gaps = 59/253 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD            G +++     NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVD------------GDIIK-----NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHAVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYA----ISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + +   +         +   ++    A    ++  +V            +    GR HQ
Sbjct: 137 ESPVTDDTAAQFAKGVQLHNEKELTKPATLEVVTPVQV-----------RLTISEGRYHQ 185

Query: 255 LRVHALHMGCPIV 267
           ++     +G  +V
Sbjct: 186 VKRMFAAVGNHVV 198


>gi|152971155|ref|YP_001336264.1| 16S rRNA pseudouridylate synthase A [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238895743|ref|YP_002920479.1| 16S rRNA pseudouridylate synthase A [Klebsiella pneumoniae
           NTUH-K2044]
 gi|262040199|ref|ZP_06013451.1| ribosomal small subunit pseudouridine synthase A [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|150956004|gb|ABR78034.1| 16S pseudouridylate 516 synthase [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238548061|dbj|BAH64412.1| 16S pseudouridylate 516 synthase [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|259042436|gb|EEW43455.1| ribosomal small subunit pseudouridine synthase A [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
          Length = 239

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/251 (15%), Positives = 79/251 (31%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       ++     + +R  +V VD   VK  + ++Q                 
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGSRVTVDGDIVKDASFKLQ----------------- 42

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E ++      LT+ +            + ++ NKP G      S         L    
Sbjct: 43  -PEHEVEYDGNTLTQQNGP----------RYFMLNKPQGYVC---STDDPDHPTILYFLD 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    K     RLD +T+G++++      +  +T          +               
Sbjct: 89  EPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVA------------- 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + L + +         +   +     A+   +VI         + +    GR HQ++ 
Sbjct: 136 LESPLAEGTAELFAKGVQLHNEKDLTKPAL--LEVI-----TPTEVRLTISEGRYHQVKR 188

Query: 258 HALHMGCPIVG 268
               +G  +VG
Sbjct: 189 MFAAVGNHVVG 199


>gi|227112086|ref|ZP_03825742.1| 16S rRNA pseudouridylate synthase A [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 231

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/253 (14%), Positives = 72/253 (28%), Gaps = 59/253 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + L + +V VD + VK                      + 
Sbjct: 1   MRLDKFLSQQL-EISRSLVARELHAQRVTVDGEVVKS-----------------GAFKLS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L + +            + ++ NKP G      S         L     
Sbjct: 43  PEHNVEFDGNPLKQQNGP----------RYFMLNKPQGYVC---STDDPDHPTILYFMDV 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLLTDDGQWSHRITSPKHQCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYA----ISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
              L + +         +   +     A    I+ + V            +    GR HQ
Sbjct: 137 EQPLAEDTAAQFTAGVQLHNEKNLTKPATLEKITDYVV-----------RLTISEGRYHQ 185

Query: 255 LRVHALHMGCPIV 267
           ++     +G  +V
Sbjct: 186 VKRMFAAVGNRVV 198


>gi|295090937|emb|CBK77044.1| ribosomal large subunit pseudouridine synthase F [Clostridium cf.
           saccharolyticum K10]
          Length = 271

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/256 (14%), Positives = 86/256 (33%), Gaps = 63/256 (24%)

Query: 13  ENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           E + + +RL+++         +     +++ +G+V VD        +I+ GQ +      
Sbjct: 7   EKERQEIRLNKFLSE--SGFCSRREADRLIEAGKVLVDGAVASMGMKIREGQQIE----- 59

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                            + T  S   + ++L       + NKP GI              
Sbjct: 60  ----------------ADGTLISGKDRPVVL-------LVNKPRGIVC------TTSDRD 90

Query: 132 FLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             ++ VD  G   R+    RLD+++ G++++                         LV  
Sbjct: 91  RAENIVDFIGYPLRVYPVGRLDKDSEGLILM--------------------TNQGELVNR 130

Query: 190 IPKNKKECIANWLL-KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           I K +      +L+     I   +++ +++  K  +  ++    ++   +K     +   
Sbjct: 131 ILKGRYGHEKEYLVSVDREITEQFLNRMRKGVKILDT-VTRPCTVEKTGEKS--FRIILT 187

Query: 249 TGRTHQLRVHALHMGC 264
            G   Q+R     +G 
Sbjct: 188 QGLNRQIRRMCEALGY 203


>gi|228903471|ref|ZP_04067596.1| hypothetical protein bthur0014_46320 [Bacillus thuringiensis IBL
           4222]
 gi|228856156|gb|EEN00691.1| hypothetical protein bthur0014_46320 [Bacillus thuringiensis IBL
           4222]
          Length = 165

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDHISIC 164


>gi|187933805|ref|YP_001885871.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum B str. Eklund 17B]
 gi|187721958|gb|ACD23179.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum B str. Eklund 17B]
          Length = 236

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 87/250 (34%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL ++  +     +    ++I+ +G+V+V+               V I  +   +N + 
Sbjct: 3   ERLQKYMAS-CGVASRRKCEEIILNGEVKVNG--------------VVITELGTRVNPV- 46

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            E K+      +TK           E+    + NKP G I+          +   +K   
Sbjct: 47  -EDKVEYKGSLITKE----------ENKVYIILNKPEGYITSAKDEKGRKTVLDLVKV-- 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD ++SG++++         +        + K Y ++V G    K   
Sbjct: 94  ---NERIYPIGRLDYDSSGLILLTNDGDVYNKI--IHPREELNKKYIAVVKGKVSKKDID 148

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I N  +               +  G   A +  +V+    +K   +E+  H G+  Q+R 
Sbjct: 149 IFNKGI---------------DIGGYITAPASLEVLSYANEKST-VEVCIHEGKNRQIRK 192

Query: 258 HALHMGCPIV 267
               +   ++
Sbjct: 193 MCTAINHEVL 202


>gi|154147941|ref|YP_001407262.1| RNA pseudouridine synthase [Campylobacter hominis ATCC BAA-381]
 gi|153803950|gb|ABS50957.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           (RNA pseudouridylate synthase) [Campylobacter hominis
           ATCC BAA-381]
          Length = 253

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/234 (16%), Positives = 74/234 (31%), Gaps = 39/234 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL+++   H    +     +++++G+V V+ + +     I     +RI   +  L    
Sbjct: 1   MRLNKFIS-HNTGYSRREADELIKNGKVSVNGRIISDFIEINESDKIRINKHLIKLK--- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  + ++NKP G  V   S         +   + 
Sbjct: 57  -------------------------KDFTMIIYNKPKGELV---SKKDDRGRKTIYDSLP 88

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN--KKE 196
               K     RLD  + G+L++    A A  L +S   R         +    K   K  
Sbjct: 89  KGFSKFVSIGRLDYASEGLLLLTDAPAIATALMQSNIEREYYLKVKGEITDEIKTAMKDG 148

Query: 197 CIANWLLKKSHIGGDYVHV-----VKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
             A    K +H   +   +     V  +  G++   +  +V+    Q       
Sbjct: 149 FFAKDATKGAHPKTEIKSMNFAPFVAFDIFGSSGGYTKLRVLIKEGQNRELRRF 202


>gi|153853144|ref|ZP_01994553.1| hypothetical protein DORLON_00538 [Dorea longicatena DSM 13814]
 gi|149753930|gb|EDM63861.1| hypothetical protein DORLON_00538 [Dorea longicatena DSM 13814]
          Length = 251

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 25/50 (50%), Gaps = 2/50 (4%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRI 67
           +RLD      YP ++   +   + +G+V V+ K +  N  R++   ++ +
Sbjct: 175 IRLDSVLALAYP-LSRSKITAQIEAGKVFVNGKLITSNGYRLKDNDIISV 223


>gi|320355051|ref|YP_004196390.1| ribosomal large subunit pseudouridine synthase B [Desulfobulbus
           propionicus DSM 2032]
 gi|320123553|gb|ADW19099.1| ribosomal large subunit pseudouridine synthase B [Desulfobulbus
           propionicus DSM 2032]
          Length = 247

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 76/249 (30%), Gaps = 49/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++  G++R++   V                       + 
Sbjct: 3   ERLQKILAKA-GIASRRKAEQLILEGRIRINGHVVTG---------------------MG 40

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +      ++    H       L++E+    + NKPAG      +         +   + 
Sbjct: 41  SKADPNRDTITCDGHP------LVFEEKIYVLLNKPAGYVT---TLSDPQGRPMVSDLLA 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD +T G L++         +        + K Y + V G P   K   
Sbjct: 92  DIPLRLFPVGRLDLDTEGALLMTNDGELGNAI--LHPRYEVNKTYEAEVSGSPSVDK--- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               LK+   G +   V+         A+     +    +    +E+  H G+  Q+R  
Sbjct: 147 ----LKRLESGIEIDGVMT------RPAVVR---LLRRHKGTTLVEITIHEGKKRQVRKM 193

Query: 259 ALHMGCPIV 267
              +   ++
Sbjct: 194 FQAINHRVL 202


>gi|15805921|ref|NP_294620.1| ribosomal large subunit pseudouridine synthase B [Deinococcus
           radiodurans R1]
 gi|6458615|gb|AAF10472.1|AE001942_4 ribosomal large subunit pseudouridine synthase B [Deinococcus
           radiodurans R1]
          Length = 257

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 69/248 (27%), Gaps = 53/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++R+G+V V+ +       +     VR+   +  L    
Sbjct: 4   ERLHKRLARA-GIASRRAAEELIRAGRVTVNGQTAGLGQGVNDTDDVRVDGRLVELTR-- 60

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                 + Y         KP G      +   Y     L +  D
Sbjct: 61  -------------------PETVTY------ALYKPVGFVT--TAHDEYGRRNVLDAMPD 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             G  P    RLD+++ G+L++         LT         K Y +   G     +  +
Sbjct: 94  VPGLHP--VGRLDKDSEGLLLLTNDGDLTLTLTHPRYGHE--KAYRAWTEGREPPTQAEL 149

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +   +   G    +     +   Y +                      GR  Q+R  
Sbjct: 150 DVLVRGIAMDDGPAQALSAAPAEDGAYVV-------------------LGEGRNRQVRRM 190

Query: 259 ALHMGCPI 266
              +G P+
Sbjct: 191 LEALGHPV 198


>gi|294669327|ref|ZP_06734406.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           elongata subsp. glycolytica ATCC 29315]
 gi|291308737|gb|EFE49980.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           elongata subsp. glycolytica ATCC 29315]
          Length = 345

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/156 (17%), Positives = 48/156 (30%), Gaps = 28/156 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G V V+ K  +  ++I     V +   I  L  
Sbjct: 93  EPERLQKVLAASGVG-SRREMEEWINNGWVTVNGKTAQLGDKITPDDQVLVKGNIIKL-- 149

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 150 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRVSIFDRL 184

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
             +   +     RLD  TSG+L++  +    Q    
Sbjct: 185 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAH 220


>gi|206889194|ref|YP_002248392.1| ribosomal large subunit pseudouridine synthase B
           [Thermodesulfovibrio yellowstonii DSM 11347]
 gi|206741132|gb|ACI20189.1| ribosomal large subunit pseudouridine synthase B
           [Thermodesulfovibrio yellowstonii DSM 11347]
          Length = 237

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 81/249 (32%), Gaps = 49/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   + Y   +  + +++++ G+V V+ +      +                    
Sbjct: 3   ERLQKILSD-YGIASRRHAEELIKEGRVTVNGQIAVIGQK-------------------- 41

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                  +           K ++  E    Y F KP  +     + +       ++ ++ 
Sbjct: 42  -------ADPEKDYIKVDGKLLIKPEPKVYYAFYKPRKVIT---ALLDPQGRPTIRDFIK 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD ++ G+L++      A          +I+K Y   V GI +   E I
Sbjct: 92  GIKFRIYPVGRLDFDSEGLLLLTNDGELA--YKVMHPSSQIEKTYMVKVDGIVEP--ETI 147

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L K   I G     V  +             +    +   W+++  H GR  Q+R  
Sbjct: 148 EK-LRKGIKIEGKLAVPVSVH-------------LVKKLKANSWIKITLHEGRKRQIRKM 193

Query: 259 ALHMGCPIV 267
              +G P++
Sbjct: 194 LERVGHPVI 202


>gi|290475891|ref|YP_003468784.1| 16S rRNA pseudouridylate 516 synthase [Xenorhabdus bovienii
           SS-2004]
 gi|289175217|emb|CBJ82020.1| 16S rRNA pseudouridylate 516 synthase [Xenorhabdus bovienii
           SS-2004]
          Length = 235

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 37/250 (14%), Positives = 84/250 (33%), Gaps = 53/250 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFN-NRIQSGQVVRIPPVINALNHI 77
           MRLD++       I+  ++ + LR+ +V VD + +K    +++              + I
Sbjct: 1   MRLDKFLSQQL-GISRNDVGRELRASRVTVDDEVIKSGAYKLKPD------------HQI 47

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             E  +L+                    S+ ++ NKP G      S         L    
Sbjct: 48  AYEGSVLEQLGG----------------SRYFMLNKPQGYVC---STDDPTNPTILYFID 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +    K     RLD +T+G++++      +  +T          +               
Sbjct: 89  EPVAHKLHSAGRLDIDTTGLVLLTDDGQWSHRITSPKHHCEKTYLV-------------T 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   +   + +   ++  V+ N +      +  ++I+        + +    GR HQ++ 
Sbjct: 136 LEYPISDDTEM--KFLAGVQLNGEKTLTKPAKLEIIEPH-----RVRLSIREGRYHQVKR 188

Query: 258 HALHMGCPIV 267
               +G  +V
Sbjct: 189 MFAAVGNHVV 198


>gi|187931629|ref|YP_001891613.1| 16S rRNA pseudouridine synthase [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|187712538|gb|ACD30835.1| 16S rRNA pseudouridine synthase [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 271

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/184 (14%), Positives = 58/184 (31%), Gaps = 29/184 (15%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ND+   RL +    +    +   +++ +  G+V+V+ K     ++      +        
Sbjct: 8   NDKNPERLQKLLAKYGIG-SRRKIEEYIEQGRVKVNGKVATLGDKASEADKISFD----- 61

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                        +++          +++Y        +K AG      S          
Sbjct: 62  -----------GKALHSYGQPMTRPRVVIY--------HKRAGEVC--TSKDEKDRQTVF 100

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            S       +  +  RLD  T+G+L+       A  L       +I++ Y   V+G   +
Sbjct: 101 DSLPKLAKSRWIMVGRLDINTTGLLLFTTDGDLANRL--MHPSYQIEREYAVRVFGQQLS 158

Query: 194 KKEC 197
            +  
Sbjct: 159 DETI 162


>gi|303272809|ref|XP_003055766.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226463740|gb|EEH61018.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 483

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 37/184 (20%), Positives = 66/184 (35%), Gaps = 31/184 (16%)

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSD----FLKSILLYEDSKIYVFNKPAGISV---- 119
           P  + + N ++     L   V+  +         +  ++       V +KPAG++V    
Sbjct: 124 PQRVKSANRVVHPGGYLRVHVHPKRFPAARATDWRRAIIAAGDAFVVVDKPAGVNVGFTV 183

Query: 120 ---------------------QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
                                 G    +        SW  +      +THRLD  TSG+L
Sbjct: 184 DNAKECVAQCVARALGDAFAENGSDSSSTDSSTECSSWGWADATPLIVTHRLDAATSGVL 243

Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
           V+AR    A+H  ++ R R++QK Y  +           + +W   +    G   HV++ 
Sbjct: 244 VLARDVEFARHFNDALRERKVQKTYACVSEARVP--VGVMEHWTDPEDATRGPRRHVMRP 301

Query: 219 NEKG 222
             +G
Sbjct: 302 PREG 305



 Score = 50.0 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCA 274
           ++  TGRTHQ+R      G P++GD  Y  
Sbjct: 394 VELVTGRTHQIRAQFAASGAPLLGDVLYGG 423


>gi|302871273|ref|YP_003839909.1| RNA-binding S4 domain protein [Caldicellulosiruptor obsidiansis
          OB47]
 gi|302574132|gb|ADL41923.1| RNA-binding S4 domain protein [Caldicellulosiruptor obsidiansis
          OB47]
          Length = 80

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          MR+D++ K           Q+   +G+V V+ K  K +  I+ G V+ + 
Sbjct: 1  MRIDKYLKVSRIIKRRTLAQEACEAGRVFVNGKVAKPSTDIKVGDVIEVH 50


>gi|251811134|ref|ZP_04825607.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|282875829|ref|ZP_06284696.1| pseudouridylate synthase [Staphylococcus epidermidis SK135]
 gi|293366306|ref|ZP_06612986.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|251805354|gb|EES58011.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|281294854|gb|EFA87381.1| pseudouridylate synthase [Staphylococcus epidermidis SK135]
 gi|291319544|gb|EFE59910.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|329737233|gb|EGG73487.1| putative 16S pseudouridylate 516 synthase [Staphylococcus
           epidermidis VCU028]
 gi|329737517|gb|EGG73770.1| putative 16S pseudouridylate 516 synthase [Staphylococcus
           epidermidis VCU045]
          Length = 230

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/146 (18%), Positives = 52/146 (35%), Gaps = 37/146 (25%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  N         ++++L+ G V+V++  VK                        
Sbjct: 1   MRLDKFLANMGVG-TRSEVKQLLKKGSVKVNQNIVKL----------------------- 36

Query: 79  KEQKILDSSVNLTKHSDFL---KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                    +++  +SD +     ++ Y D    + NKP G        +   I   +  
Sbjct: 37  -------PKLHVNPNSDEIMVNDEVVSYIDKVYIMLNKPKGYISATEDEVHPTIIDLIPE 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVA 161
           +            RLD++T G+L+V 
Sbjct: 90  YAHLN---IFPVGRLDKDTEGLLLVT 112


>gi|148360539|ref|YP_001251746.1| pseudouridine synthase [Legionella pneumophila str. Corby]
 gi|148282312|gb|ABQ56400.1| pseudouridine synthase [Legionella pneumophila str. Corby]
          Length = 219

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 67/167 (40%), Gaps = 13/167 (7%)

Query: 103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVAR 162
           ++  ++ +FNKP G+  Q         +  L +++   G       RLD+++ G+LV+  
Sbjct: 18  HKMPQLILFNKPYGVLTQ---FTGELPEQTLSAFIKFPGFYA--AGRLDKQSEGLLVLTD 72

Query: 163 TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKG 222
                  LT     ++  K YW  V G P +K        L+K  +  D   +  + +  
Sbjct: 73  DGKLQHRLTHPKFEKK--KHYWVQVEGAPTDK----DLQPLRKGLVIKDITFLPAEAKLI 126

Query: 223 ANYAISHF--KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +   I      + +       WLE+    G+ HQ+R     +G P +
Sbjct: 127 SEPKIWPRIPPIRERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTL 173


>gi|75761951|ref|ZP_00741871.1| Hypothetical cytosolic protein [Bacillus thuringiensis serovar
          israelensis ATCC 35646]
 gi|74490556|gb|EAO53852.1| Hypothetical cytosolic protein [Bacillus thuringiensis serovar
          israelensis ATCC 35646]
          Length = 87

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20 RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 38 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDHISIC 86


>gi|152979359|ref|YP_001344988.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150841082|gb|ABR75053.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 373

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 37/195 (18%), Positives = 62/195 (31%), Gaps = 31/195 (15%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-- 58
           M      Q V  +      +L +         +   ++ ++  G+V VD K     +R  
Sbjct: 74  MRRPKPAQPVERKAAVAGEKLQKVLARAGQG-SRREIEAVIAEGRVSVDGKIAALGDRVI 132

Query: 59  IQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGIS 118
           + SG  +RI   +                VNLT     +  +L+Y         KP G  
Sbjct: 133 VHSGLKIRIDGHL----------------VNLTGVQKDVCRVLMY--------YKPEGEL 168

Query: 119 VQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178
                          +      G +     RLD  TSG+L+       A  L      R 
Sbjct: 169 C--TRHDPEGRATVFERLPRLTGSRWVAVGRLDINTSGLLLFTTDGELANRL--MHPSRE 224

Query: 179 IQKIYWSLVWGIPKN 193
           +++ Y   V+G   +
Sbjct: 225 VEREYSVRVFGNVDD 239


>gi|327405122|ref|YP_004345960.1| ribosomal large subunit pseudouridine synthase F [Fluviicola
           taffensis DSM 16823]
 gi|327320630|gb|AEA45122.1| ribosomal large subunit pseudouridine synthase F [Fluviicola
           taffensis DSM 16823]
          Length = 305

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 23/167 (13%), Positives = 58/167 (34%), Gaps = 32/167 (19%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
            E++RL+++  +   + +     K +  G V ++  R K   ++     V +      L 
Sbjct: 2   HESIRLNKFISDS-GYCSRREADKYIEQGSVFINGVRAKIGTQVTRRDKVVVNGH--TLQ 58

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
              +E++I                            NKP G++     G+  +I  ++  
Sbjct: 59  QKSQEEEI------------------------YIALNKPPGVTSTTEKGVVDNIVDYV-- 92

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
                 Q+     RLD+++ G++ +         +  +    + + +
Sbjct: 93  ---GHPQRIFPIGRLDKDSQGLIFLTSNGDIVNKILRAGNEHQKEYL 136


>gi|84516902|ref|ZP_01004260.1| RNA pseudouridine synthase family protein [Loktanella vestfoldensis
           SKA53]
 gi|84509370|gb|EAQ05829.1| RNA pseudouridine synthase family protein [Loktanella vestfoldensis
           SKA53]
          Length = 183

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/162 (24%), Positives = 63/162 (38%), Gaps = 10/162 (6%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I + NKP G+  Q     +      L  +V   G  P    RLD+++ G+LV+    A  
Sbjct: 4   ILLLNKPYGVLSQFTDARSPSPRPTLSGFVTVPGVYP--AGRLDRDSEGLLVLTDDGALQ 61

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             + +     ++ K Y   V G P +        LL+      D      Q ++ A  A+
Sbjct: 62  ARIAD--PRHKLPKTYLVQVEGAPTDA----DLALLRHGVTLNDGPTRPAQVQRIAPPAL 115

Query: 228 SHF--KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                 V    +    W+E+  H GR  Q+R    H+G P +
Sbjct: 116 WERDPPVRFRKSVPDQWIEITIHEGRNRQVRRMTAHIGFPTL 157


>gi|320539364|ref|ZP_08039033.1| putative 16S rRNA pseudouridylate 516 synthase [Serratia symbiotica
           str. Tucson]
 gi|320030489|gb|EFW12499.1| putative 16S rRNA pseudouridylate 516 synthase [Serratia symbiotica
           str. Tucson]
          Length = 239

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 73/246 (29%), Gaps = 53/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHI 77
           MRLD++       I+   + + LR+ ++ VD + VK    ++   Q V+    + A  + 
Sbjct: 1   MRLDKFLSQQL-GISRALVARELRARRITVDGEVVKNGAVKLAVEQEVKFDGNLLAQQNG 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                             ++ NKP G      S         L    
Sbjct: 60  PR----------------------------YFMLNKPQGYVC---STDDPDHPTVLYFLD 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           +          RLD +T+G+++                  +      S      K     
Sbjct: 89  EPVAYNLHAAGRLDIDTTGLVL-------------MTDDGQWSHRVTSPKHHCEKTYLVT 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + L   +        V   NEK     +   K+ D        + +    GR HQ++ 
Sbjct: 136 LEHSLAANTAQ-RFAAGVQLHNEKSLTRPVQLEKINDRQ------VRLAISEGRYHQVKR 188

Query: 258 HALHMG 263
               +G
Sbjct: 189 MFAAIG 194


>gi|317495282|ref|ZP_07953652.1| RNA pseudouridylate synthase [Gemella moribillum M424]
 gi|316914704|gb|EFV36180.1| RNA pseudouridylate synthase [Gemella moribillum M424]
          Length = 243

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 84/249 (33%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL +       + +    ++++  G+V V+ + +K    + +   V+ +  +      +
Sbjct: 3   ERLQKLIAAS-GYTSRRKAEQLILEGKVSVNGEVIKQLGVKAEPSDVIIVEGL-----RL 56

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +KE K               K  L Y+  K+              S         +K + 
Sbjct: 57  LKENK---------------KYYLFYKPEKVI------------TSMSDEKDRVCVKDFF 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
           ++  ++     RLD +TSG L+++        +T      +I+K Y + + G  +     
Sbjct: 90  EAVNERVVPVGRLDYDTSGALIMSNDGEFINLIT--HPKHKIKKTYVAKINGKLEEHHLK 147

Query: 198 IANWLLK--KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           I    ++          V++VK   K  N                  + +  H G+  Q+
Sbjct: 148 ILRSGVRIDNYKTSPAEVNIVKNKNKSGN----------------TLVRLTIHEGKNRQV 191

Query: 256 RVHALHMGC 264
           R     +G 
Sbjct: 192 RRMFEALGY 200


>gi|224543302|ref|ZP_03683841.1| hypothetical protein CATMIT_02502 [Catenibacterium mitsuokai DSM
           15897]
 gi|224523835|gb|EEF92940.1| hypothetical protein CATMIT_02502 [Catenibacterium mitsuokai DSM
           15897]
          Length = 231

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 83/246 (33%), Gaps = 53/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D+    H  + +  +++++L+ G V  + K+++ +                   H+ 
Sbjct: 1   MRIDKLLA-HCGYGSRKDVKQLLKDGLVTSNGKKIRSS-----------------GAHVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+  +                + Y     Y+ NKP G        +   +   +K +  
Sbjct: 43  PEKDEIYVG----------DEKINYSKYVYYMLNKPDGYVSATEDNVYPTVIDLIKEYHP 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                     RLD +T G+L++      A + L+       + K Y+  V G        
Sbjct: 93  G----LFPVGRLDVDTEGLLLITNDGQLAHRLLSPRTH---VPKTYYVKVKGRL-----G 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I +       I  +    +           S+ K+I   + +    E+  + G+ HQ++ 
Sbjct: 141 IGDINAFTKGIPLEDFTCMP----------SYLKIIK--SDEISECEVTIYEGKFHQVKR 188

Query: 258 HALHMG 263
                G
Sbjct: 189 MFQACG 194


>gi|15606155|ref|NP_213532.1| hemolysin [Aquifex aeolicus VF5]
 gi|2983347|gb|AAC06935.1| hemolysin [Aquifex aeolicus VF5]
          Length = 258

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNH 76
          MRLD++  +     +    Q ++ +GQV V+ K V K   R++  + V +  +   ++ 
Sbjct: 1  MRLDKYLTDKGIVPSREKAQAVIMAGQVLVNGKVVDKPGYRLKGNEKVEVKELPKYVSR 59


>gi|16760161|ref|NP_455778.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|34098636|sp|Q8Z7D5|RLUB_SALTI RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|25324005|pir||AI0653 probable pseudouridine synthase STY1331 [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16502455|emb|CAD08412.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhi]
          Length = 291

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K     +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVKESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G     K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDESK 152


>gi|113969946|ref|YP_733739.1| ribosomal large subunit pseudouridine synthase E [Shewanella sp.
           MR-4]
 gi|113884630|gb|ABI38682.1| ribosomal large subunit pseudouridine synthase E [Shewanella sp.
           MR-4]
          Length = 261

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 41/168 (24%), Positives = 63/168 (37%), Gaps = 19/168 (11%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D  I +FNKP  +  Q            LK ++   G       RLD+++ G+L++    
Sbjct: 82  DPMIVLFNKPFDVLCQ---FTDEQGRKTLKDYIPIPG--VYAAGRLDRDSEGLLLLTNDG 136

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
                LTE    ++  K YW  V G P           L K   G +    +    K + 
Sbjct: 137 QLQAKLTE--PKKKTFKTYWVQVEGKPTEAD-------LAKLRQGVELKDGMTLPAKVSI 187

Query: 225 YAISHFK-----VIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            A  +       + +       WLE+Q H GR  Q+R    H+G P +
Sbjct: 188 MATPNVWPRNPPIRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTL 235


>gi|314936152|ref|ZP_07843499.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           hominis subsp. hominis C80]
 gi|313654771|gb|EFS18516.1| ribosomal small subunit pseudouridine synthase A [Staphylococcus
           hominis subsp. hominis C80]
          Length = 228

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/244 (13%), Positives = 76/244 (31%), Gaps = 53/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  N         ++++L+   V+V+ K  K                    + + 
Sbjct: 1   MRLDKFLSNMGVG-TRTEVKQLLKKNSVKVNDKVEKS-----------------PKSQVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            EQ  +               I+ Y +    + NKP G        I   +   +  +  
Sbjct: 43  PEQDEITVDGK----------IIEYINHVYIMLNKPKGYVSATYDDINQTVIDLIADYCH 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                     RLD++T G+L++        +L    +        + +    P   ++ I
Sbjct: 93  L---DLFPVGRLDKDTEGLLLITNDGQFNHNLMSPSKH---VSKTYKVTSKYPIKNEDII 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A            + + ++ ++     A      ++          +  + G+ HQ++  
Sbjct: 147 A------------FKNGIELSDGKVKPAQ-----LEKLDHNVSL--VTIYEGKYHQVKRM 187

Query: 259 ALHM 262
              +
Sbjct: 188 FHSI 191


>gi|311279823|ref|YP_003942054.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308749018|gb|ADO48770.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 299

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 58/177 (32%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ ++ +G+V VD K     +R++   G  +RI   + ++   +
Sbjct: 5   LQKVLARA-GHGSRREIESMIEAGRVSVDGKIATLGDRVEITPGLKIRIDGHLISVKESV 63

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +                        +  ++  + KP G                      
Sbjct: 64  E------------------------QICRVLAYYKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDNK 152


>gi|73540741|ref|YP_295261.1| RNA-binding S4 [Ralstonia eutropha JMP134]
 gi|72118154|gb|AAZ60417.1| RNA-binding S4 [Ralstonia eutropha JMP134]
          Length = 131

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 10/81 (12%), Positives = 29/81 (35%), Gaps = 4/81 (4%)

Query: 14 NDEENMRLDRWF--KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
            +  +R+D+W      +         + +  G+V V+ +  K +  ++ G  + +    
Sbjct: 6  EPDARLRIDKWLWCARFFK--TRSLAAEAVERGKVTVNGQPCKNSREVKPGDTIVLEAHQ 63

Query: 72 NALNHIIKEQKILDSSVNLTK 92
               ++K       S  + +
Sbjct: 64 QRWELVVKGIAPARGSAPVAQ 84


>gi|328786669|ref|XP_003250827.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           1-like [Apis mellifera]
          Length = 138

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 18/79 (22%), Positives = 31/79 (39%)

Query: 142 QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW 201
            +    HRLD  TSG++ +A  + AAQ  + +F  R  +K Y +L+ G        I   
Sbjct: 41  HEFHFVHRLDYVTSGVICIALNKKAAQIASNAFEARTAKKFYLALLHGHIDEPHLIINKA 100

Query: 202 LLKKSHIGGDYVHVVKQNE 220
           +            +   + 
Sbjct: 101 IGIDIKENKGNHKMCVSDS 119


>gi|300863940|ref|ZP_07108855.1| ribosomal large subunit pseudouridine synthase B [Oscillatoria sp.
           PCC 6506]
 gi|300338060|emb|CBN54001.1| ribosomal large subunit pseudouridine synthase B [Oscillatoria sp.
           PCC 6506]
          Length = 263

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 75/250 (30%), Gaps = 46/250 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHI 77
            RL +     +   +    ++++ +G+VRV+   V+   +   +   + +  V       
Sbjct: 3   ERLQKILA-QWGIASRRQAEEMILAGRVRVNGNTVQLGQKANPASDRIEVDGVRVKSERR 61

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
            +                      +Y      + NKPAG+               L    
Sbjct: 62  PQP---------------------VY-----LLLNKPAGVVSTCSDPAQRTTVLDLLPPK 95

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              G       RLD E++G L++         LT       + K Y   V G P      
Sbjct: 96  LRAGCGIHPVGRLDVESTGALLLTNDGNLTFALT--HPRHCVPKTYQVWVEGDPPKSVLQ 153

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
             +  +  S        V  Q   G+                   LE+  + GR  Q+R 
Sbjct: 154 TWSQGVLLSRRMTLPAQVRVQERNGSQ----------------TLLEVILYEGRNRQVRR 197

Query: 258 HALHMGCPIV 267
            A  +G P++
Sbjct: 198 VAEQLGYPVI 207


>gi|229030086|ref|ZP_04186150.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|228731256|gb|EEL82174.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 248

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 34/254 (13%), Positives = 73/254 (28%), Gaps = 60/254 (23%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           E D  N+R++++        +     K++   +V ++ K  K  +++  G  VR+     
Sbjct: 8   EKDVPNLRINKFISEAGK-ASRRGADKLINERRVIINGKVAKIGDQVNPGDDVRVNGEQL 66

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                                        +  D      NKP GI+      +  +I   
Sbjct: 67  R----------------------------IARDHVYIALNKPVGITCTSEKAVKGNIIDL 98

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   +     +     RLD+++ G++++         +  +      + I          
Sbjct: 99  VNHPL-----RISHIGRLDKDSDGLILLTNDGDIVNEILRAENKHEKEYIVS-------- 145

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TG 250
                          I  D++  +    K     I   K + C   +    E       G
Sbjct: 146 -----------VDKPITPDFLEKMAAGVK-----ILGTKTLPCEITQLSKYEFNIILTQG 189

Query: 251 RTHQLRVHALHMGC 264
              Q+R     +G 
Sbjct: 190 LNRQIRRMCEALGY 203


>gi|217077200|ref|YP_002334918.1| RNA pseudouridine synthase family protein [Thermosipho africanus
           TCF52B]
 gi|217037055|gb|ACJ75577.1| RNA pseudouridine synthase family protein [Thermosipho africanus
           TCF52B]
          Length = 225

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/200 (14%), Positives = 68/200 (34%), Gaps = 39/200 (19%)

Query: 33  NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +   ++K+++  +V+V+   V K    +     V +                        
Sbjct: 8   SRKQVKKLIKEKRVKVNGSIVTKPEFNVDENDEVFVD----------------------- 44

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                    ++   +   VFNKP+G +           +     ++D       +  RLD
Sbjct: 45  ------DIEIIPHHNVYIVFNKPSGFTSSKSEYERNIFEFIDHPYLDE----LHIVGRLD 94

Query: 152 QETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA-NWLLKKSHIG 209
           ++  G++++        + ++       I+K Y   + GI   +   IA N +   + I 
Sbjct: 95  KDVEGLILITNDGNFTHKVIS---PKSNIEKEYIVKIEGILTKEMIEIASNGITLNNGIK 151

Query: 210 GDYVHVVKQNEKGANYAISH 229
                + K +++  +  I+ 
Sbjct: 152 FKPAKITKIDDETISLVITE 171


>gi|189219451|ref|YP_001940092.1| ribosomal protein S4 [Methylacidiphilum infernorum V4]
 gi|189186309|gb|ACD83494.1| Ribosomal protein S4 [Methylacidiphilum infernorum V4]
          Length = 228

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 16/87 (18%), Positives = 35/87 (40%), Gaps = 4/87 (4%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALN-- 75
            RLD          + +  ++++  G + V+ K+V   + R + G V+ + P   +    
Sbjct: 118 ERLDNVVYRLCFATSRMEARQLVNHGHIYVNGKKVNIPSYRTKPGDVIEVCPKPQSRKLA 177

Query: 76  -HIIKEQKILDSSVNLTKHSDFLKSIL 101
              ++  K +     L    D LK ++
Sbjct: 178 LRNLEAMKGVKIPDWLALEPDNLKGVV 204


>gi|165918548|ref|ZP_02218634.1| RNA pseudouridine synthase family protein [Coxiella burnetii RSA
           334]
 gi|165917794|gb|EDR36398.1| RNA pseudouridine synthase family protein [Coxiella burnetii RSA
           334]
          Length = 244

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/234 (14%), Positives = 73/234 (31%), Gaps = 34/234 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+ +         +   ++K++  G+++V+++  +  +RI    +V I   +++L+   
Sbjct: 3   ERIQKVLARSGYG-SRREIEKMIAEGRIKVNQRLAQLGDRITEQDLVYIDGQLSSLSAP- 60

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    E  +I +++KP G                 ++   
Sbjct: 61  -------------------------EQVRILLYHKPEGEIC--TRKDPEGRTTVFETLPR 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K  +  +  RLD  TSG+L+       A  L       ++++ Y   V G         
Sbjct: 94  LKDGRWVIIGRLDINTSGLLLFTNEGELANRL--MHPSAQVEREYAVRVLGAVDADMTQK 151

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
               +        +  +V     G N     F V+    +      +    G  
Sbjct: 152 LAHGVGLEDGKARFEDIVDVGGDGKNR---WFHVVVVEGRHRFVRRLWESQGVK 202


>gi|42784147|ref|NP_981394.1| hypothetical protein BCE_5101 [Bacillus cereus ATCC 10987]
 gi|42740078|gb|AAS44002.1| hypothetical protein BCE_5101 [Bacillus cereus ATCC 10987]
          Length = 165

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKTLSTYISDWSRTRIVNKIKNGDIQLNGQQMKPNTILSEGDRISIC 164


>gi|307172417|gb|EFN63879.1| RNA pseudouridylate synthase domain-containing protein 4
           [Camponotus floridanus]
          Length = 364

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 45/263 (17%), Positives = 89/263 (33%), Gaps = 28/263 (10%)

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
               +++   + +    +  +  + L   ++Y    I   NKP GI +            
Sbjct: 33  EYTKNLVHPYRRIHPWKSENEFVNDLLKNVIYNADGIVAINKPYGIPIHNKRLYDESSSK 92

Query: 132 FLKSWVDSKGQK-----PRLTHRLD-----------QETSGILVVARTRAAAQHLTESFR 175
                V+          P L   LD           +  +GI +        Q L ++ R
Sbjct: 93  ICHKIVNPVNYSVHDVLPHLAKELDVPALIPSMGSEKYMTGIYIFGINDNVCQQLEKARR 152

Query: 176 MRRIQ--KIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHVVKQNEKGANYAISH-- 229
                  + YW++   +    K    +A  L K S      + + K +            
Sbjct: 153 RFHTHKFRKYWAITTRVSNEIKGNYNLAMILQKSSLGIKKPIIITKWSNNAVKKDEVQIL 212

Query: 230 ---FKVIDCFAQKF-CWLEMQPHTGRTHQLRVHALHMGC-PIVGDHKYCANFKGNFTSPI 284
              +KVI          +E++  T + H +R+ A  M   PI+GD+ + +  +    + I
Sbjct: 213 NINYKVISNSTHNLSSLIEIEASTRKWHSIRLFASTMLYSPILGDNYHGSRVQNIMGTWI 272

Query: 285 QNKLYLHARYMDLPHPEGGRLQI 307
           +   +  + + D+PH     LQ+
Sbjct: 273 KVNPFAESCW-DMPHISKELLQL 294


>gi|52841677|ref|YP_095476.1| pseudouridine synthase [Legionella pneumophila subsp. pneumophila
           str. Philadelphia 1]
 gi|52628788|gb|AAU27529.1| pseudouridine synthase [Legionella pneumophila subsp. pneumophila
           str. Philadelphia 1]
          Length = 248

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 34/233 (14%), Positives = 74/233 (31%), Gaps = 34/233 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +   +++ + +G V+V+ K  K  +       + +           
Sbjct: 4   ERLQKILSQAGLG-SRREMERWIDNGWVQVNGKPAKLGDSAGPSDKISV----------- 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            + K++ + +               ++ ++ +++KP G +S +        +   L    
Sbjct: 52  -KGKLIPNPLKSK------------QNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLR 98

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +  +     RLD  TSG+L+       A  L        +++ Y   V G    +   
Sbjct: 99  QGRWVQ---VGRLDLNTSGLLIFTNNGELANQL--MHPKYGLEREYAVRVHGQVSQESL- 152

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N LLK   +        K   +G     S + V     +      +    G
Sbjct: 153 --NNLLKGVMLDDGLAKFTKIQFRGGEGTNSWYHVTLNEGRNREVRRLWESQG 203


>gi|157372205|ref|YP_001480194.1| 23S rRNA pseudouridine synthase F [Serratia proteamaculans 568]
 gi|157323969|gb|ABV43066.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 286

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 77/246 (31%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +  +  + +  G V ++ KRV   +++  G VV++          +
Sbjct: 8   RLNKYISE--SGICSRRDADRYIEQGNVFINGKRVTLGDQVFPGDVVKVNGQ-------L 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E +  D+ +                       NKP GI      G   +I  F+     
Sbjct: 59  IEPRNEDNLI-------------------FIALNKPVGIVSTTEEGEKDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++ +         +  +      + +             + +
Sbjct: 97  --STRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLV---------TVNKPV 145

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            +  ++    G   +  V +  K    A   F+++                G   Q+R  
Sbjct: 146 TDDFIRGLGAGVPMLGTVTKKCKVKKEAPFVFRIV-------------LVQGLNRQIRRM 192

Query: 259 ALHMGC 264
             H G 
Sbjct: 193 CEHFGY 198


>gi|56478942|ref|YP_160531.1| pseudouridylate synthase [Aromatoleum aromaticum EbN1]
 gi|56314985|emb|CAI09630.1| pseudouridylate synthase [Aromatoleum aromaticum EbN1]
          Length = 317

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 32/247 (12%), Positives = 76/247 (30%), Gaps = 46/247 (18%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G++ V+    +   +I  G  V+    +  L  
Sbjct: 53  EPERLQKVLAQIGLG-SRREIEEWVVAGRISVNGLPAELGQKIGPGDRVKYNGKLIPLRF 111

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            ++  +                         + +++KP G  V              +  
Sbjct: 112 TVRTPR-------------------------VLIYHKPEGEIV--SREDPEGRPTVFERL 144

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +  +     RLD  TSG+L+       A  L         ++    L+  +   + E
Sbjct: 145 PILRKGRWIAVGRLDFNTSGLLLFTNDGTLANRLMHPRYELE-REYAVRLLGQLDDEQLE 203

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +   +  +  +   +  +  +  +GAN+                W  +    GR  ++R
Sbjct: 204 SLKTGIQLEDGLAR-FTSISDEGGEGANH----------------WYRVTLSEGRNREVR 246

Query: 257 VHALHMG 263
                +G
Sbjct: 247 RMFEAVG 253


>gi|150025290|ref|YP_001296116.1| pseudouridylate synthase [Flavobacterium psychrophilum JIP02/86]
 gi|149771831|emb|CAL43305.1| Pseudouridylate synthase [Flavobacterium psychrophilum JIP02/86]
          Length = 266

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 80/250 (32%), Gaps = 55/250 (22%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   R++++      H +     K+L  G++ ++    +   ++     VR+       
Sbjct: 2   EENLTRINKFLSET-GHCSRREADKLLDEGRITINGIVPEMGTKVSHHDEVRVD------ 54

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             +++E+                      E      FNKP GI       + Y+I  F+ 
Sbjct: 55  GKLVREKT---------------------EKPVYLAFNKPVGIECTTNLDVRYNIVDFI- 92

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               +  ++     RLD+ + G++ +         +  +      +              
Sbjct: 93  ----NYPKRIFPIGRLDKASEGLIFMTNDGDIVNKILRARNNHEKEYTV---------TV 139

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I +  ++K   G   +  V +  K    + + FK++                G   Q
Sbjct: 140 NKLITDRFIQKMSNGIPILDTVTKKCKVEQISKTTFKIV-------------LTQGLNRQ 186

Query: 255 LRVHALHMGC 264
           +R    ++G 
Sbjct: 187 IRRMCEYLGY 196


>gi|320529017|ref|ZP_08030109.1| hypothetical protein HMPREF9555_00165 [Selenomonas artemidis F0399]
 gi|320138647|gb|EFW30537.1| hypothetical protein HMPREF9555_00165 [Selenomonas artemidis F0399]
          Length = 244

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 81/248 (32%), Gaps = 52/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   N     +  + ++++R+G+V VD               V +  +    +  +
Sbjct: 4   ERLQKILANA-GIASRRSAEEMIRAGRVTVDG--------------VCVTELGRKYDAAL 48

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  I    + + K ++ +            + NKP G      +         +   + 
Sbjct: 49  HE--IAVDGIPVQKETERV----------YLLLNKPVGYLS---TARDDRGRKTVLDLLP 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI--PKNKKE 196
               +     RLD +T G+L++    A  Q L        I K+Y + + G   P+  + 
Sbjct: 94  HTSARLYPVGRLDADTEGLLLITNDGAMTQGL--LHPRYEIDKVYRAEIEGALTPEKLRH 151

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                LL+        + ++  +                       +E+  H GR  Q+R
Sbjct: 152 LRGGILLEDGITAPARMRILSAD------------------DTVTTIEIVIHEGRNRQVR 193

Query: 257 VHALHMGC 264
                +GC
Sbjct: 194 RMFAAVGC 201


>gi|167549772|ref|ZP_02343530.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|204927933|ref|ZP_03219134.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|204323275|gb|EDZ08471.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205324943|gb|EDZ12782.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
          Length = 291

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K     +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVKESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G     K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDESK 152


>gi|153206799|ref|ZP_01945640.1| RNA pseudouridine synthase family protein [Coxiella burnetii 'MSU
           Goat Q177']
 gi|212218389|ref|YP_002305176.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           CbuK_Q154]
 gi|120577162|gb|EAX33786.1| RNA pseudouridine synthase family protein [Coxiella burnetii 'MSU
           Goat Q177']
 gi|212012651|gb|ACJ20031.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           CbuK_Q154]
          Length = 244

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/234 (14%), Positives = 73/234 (31%), Gaps = 34/234 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+ +         +   ++K++  G+++V+++  +  +RI    +V I   +++L+   
Sbjct: 3   ERIQKVLARSGYG-SRREIEKMIAEGRIKVNQRLAQLGDRITEQDLVYIDGQLSSLSAP- 60

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    E  +I +++KP G                 ++   
Sbjct: 61  -------------------------EQVRILLYHKPEGEIC--TRKDPEGRTTVFETLPR 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K  +  +  RLD  TSG+L+       A  L       ++++ Y   V G         
Sbjct: 94  LKDGRWVIIGRLDINTSGLLLFTNEGELANRL--MHPSAQVEREYAVRVLGAVDADMTQK 151

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
               +        +  +V     G N     F V+    +      +    G  
Sbjct: 152 LAHGVGLEDGKARFEDIVDVGGDGKNR---WFHVVVVEGRHRFVRRLWESQGVK 202


>gi|269960959|ref|ZP_06175328.1| pseudouridine synthase family 1 protein [Vibrio harveyi 1DA3]
 gi|269834178|gb|EEZ88268.1| pseudouridine synthase family 1 protein [Vibrio harveyi 1DA3]
          Length = 236

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 42/183 (22%), Positives = 67/183 (36%), Gaps = 13/183 (7%)

Query: 87  SVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRL 146
               T+ S  +K  +  ED K+ +FNKP     Q   G        L  ++  K      
Sbjct: 38  PSRPTRSSKPIKPRIAPEDRKVIIFNKPYDTLSQFTDGDGR---KTLADYIPVK--DVYA 92

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK--KECIANWLLK 204
             RLD+++ G++V+         LT+     +  K YW  V G P  +  ++      LK
Sbjct: 93  AGRLDRDSEGLMVLTNDGILQAKLTQ--PQSKSPKTYWVQVDGAPTEEDLEKLRKGVELK 150

Query: 205 KSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
                   V V+ + E         F+          WL +    GR  Q+R    H+G 
Sbjct: 151 DGMTLPAKVEVMPEPEIWDRTPPVRFR----ANIPTTWLAITITEGRNRQVRRMTAHIGF 206

Query: 265 PIV 267
           P +
Sbjct: 207 PTL 209


>gi|262382422|ref|ZP_06075559.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_1_33B]
 gi|262295300|gb|EEY83231.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_1_33B]
          Length = 334

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 46/280 (16%), Positives = 87/280 (31%), Gaps = 55/280 (19%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69
           V+ +  E +RL+++  N     +     + ++ G V+V+   V     +I    VV    
Sbjct: 91  VLADPNEPIRLNKFLSNA-GVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVVTFNE 149

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
               +                             E     V NKP        S      
Sbjct: 150 KPVQI-----------------------------ESKVYIVLNKPKNCVT--TSDDPQER 178

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +    ++  ++     RLD+ T+G+L++      A  LT     ++     W L   
Sbjct: 179 LTVMDLVKNACQERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPSFKKKKIYHVW-LDKN 237

Query: 190 IPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           +     E IAN L L+   I  D +    +++K                     + ++ H
Sbjct: 238 VAIEDMEKIANGLELEDGEIHADAISYASEDDK-------------------SQVGIEIH 278

Query: 249 TGRTHQLRVHALHMGCPIVG-DHKYCANFKGNFTSPIQNK 287
           +GR   +R     +G  +   D  Y A          + +
Sbjct: 279 SGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWR 318


>gi|154505534|ref|ZP_02042272.1| hypothetical protein RUMGNA_03071 [Ruminococcus gnavus ATCC
          29149]
 gi|153794192|gb|EDN76612.1| hypothetical protein RUMGNA_03071 [Ruminococcus gnavus ATCC
          29149]
          Length = 79

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          MRLD++ K            +   +G+V V+ K  K + +++ G V+ I 
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNGKPAKASVKVKVGDVIEIQ 50


>gi|144575100|gb|AAZ43829.2| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Mycoplasma synoviae 53]
          Length = 234

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 86/249 (34%), Gaps = 57/249 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R++++  +         ++K++  G V+V+   +K +  I              L+ I 
Sbjct: 3   IRIEKFIADS-TLYTRNEIKKLISKGLVKVNDLIIKKSQSI-----------DPKLDKIY 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +L++    +                  + NKPAG      +   ++     +  +D
Sbjct: 51  LEGILLEAREEFS----------------YIMMNKPAGYIC---ANFDWNKQVVFELLLD 91

Query: 139 SKGQ--KPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +          RLD +T G+L++    + +   L+   +    +  Y  L   + KN K
Sbjct: 92  LEMNLKDFFTIGRLDIDTEGLLIITNDGKLSHNLLSP--KKHIPKTYYVELDKPLEKNIK 149

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           E +   LL        Y   +  N     + I+ F+                  G+ HQ+
Sbjct: 150 ELLEKELLIDE---IKYKKSILNNISNNKWEITIFE------------------GKFHQI 188

Query: 256 RVHALHMGC 264
           ++   H G 
Sbjct: 189 KIIFAHFGY 197


>gi|260887142|ref|ZP_05898405.1| ribosomal large subunit pseudouridine synthase B [Selenomonas
           sputigena ATCC 35185]
 gi|330839088|ref|YP_004413668.1| pseudouridine synthase Rsu [Selenomonas sputigena ATCC 35185]
 gi|260863204|gb|EEX77704.1| ribosomal large subunit pseudouridine synthase B [Selenomonas
           sputigena ATCC 35185]
 gi|329746852|gb|AEC00209.1| pseudouridine synthase Rsu [Selenomonas sputigena ATCC 35185]
          Length = 242

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 77/247 (31%), Gaps = 49/247 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++++ +G+V VD   V+                        
Sbjct: 3   ERLQKIISRA-GVASRRKAEELIAAGRVTVDGAVVR---------------------EPG 40

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            +     + + +       +  L+Y     ++ NKP G +S          +   L    
Sbjct: 41  TKADASTARIEVDGKRIPAEERLVY-----FLLNKPKGCVSTVSDERGRRTVLDLL---- 91

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             K  +     RLDQ T G++++       Q L        + K Y + V G    +   
Sbjct: 92  PVKNVRVYPVGRLDQNTEGLILLTNDGTLTQAL--LHPRFLVHKTYRAKVAGELTPEA-- 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                LKK   G +              A +  +V     +    +E+  H GR  Q+R 
Sbjct: 148 -----LKKLRSGIELA--------DGMTAPAEVRVYGVTEKGLSDVEVTLHEGRNRQVRR 194

Query: 258 HALHMGC 264
               +GC
Sbjct: 195 MFEAVGC 201


>gi|183220850|ref|YP_001838846.1| putative ribosomal subunit pseudouridine synthase [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
 gi|189910947|ref|YP_001962502.1| pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167775623|gb|ABZ93924.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167779272|gb|ABZ97570.1| Putative ribosomal subunit pseudouridine synthase [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 247

 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/242 (15%), Positives = 80/242 (33%), Gaps = 38/242 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++ +        +   +++++ +G+V+++   +                  +    + 
Sbjct: 1   MRINAFLAKLGLG-SRRKVEELVLAGRVKINGSTIT-----------------DLSFQVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E  IL     +TK              KI  FNKP G      S    H +  + + + 
Sbjct: 43  EEDSILFDGKPVTKEEGSDSR------PKIIAFNKPPGFLT---SHEDKHHENTIFTLLP 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              QK     RLD ++ G+++++      Q +T      +I K Y   +      KK   
Sbjct: 94  ESFQKYNYAGRLDLDSRGLILLSIDGNFIQKVT--HPKNKIDKEYIISLKQPVSWKKIAE 151

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L  +   GG+ +  +           +             +L +    G+  Q+R  
Sbjct: 152 EFMLGVRE--GGETLRALAVKPANVFPEKT-------PPGFTSYLSIVLKEGKKRQIRRM 202

Query: 259 AL 260
             
Sbjct: 203 CK 204


>gi|261867973|ref|YP_003255895.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413305|gb|ACX82676.1| pseudouridine synthase Rlu family protein [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 67

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 5/66 (7%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILV 159
           ++++     V NKP GISV           G  +      G  +  L HRLD+ TSG+L+
Sbjct: 5   IVFQHPDFIVINKPNGISVHKDDAD----IGLTRLVAQQLGVPQVWLVHRLDKVTSGLLM 60

Query: 160 VARTRA 165
           +A    
Sbjct: 61  LALNEQ 66


>gi|327479891|gb|AEA83201.1| pseudouridylate synthase [Pseudomonas stutzeri DSM 4166]
          Length = 230

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 81/246 (32%), Gaps = 53/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+  +    ++  ++++++  G+ RV+ +  +  +R      VRI   +     ++
Sbjct: 1   MRLDRYLGSR-AQLSRQDVRRLVSDGRARVNGEVTRTLDR-----EVRIFDCVELDGQVL 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  K+                      ++  + +KP G            +   +    +
Sbjct: 55  QPGKV----------------------ARYLMLHKPPGCVSATRDAAHRTVIDLID---E 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQKIYWSLVWGIPKNKKEC 197
                  +  RLD  T+G++++      ++ LT+      ++      LV    +    C
Sbjct: 90  PDKDDLHIAGRLDFNTTGLMLLTNDGQWSRRLTQPTSLQGKVY-----LVETEDEIDPGC 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +  +        G Y          A          +          +  H GR HQ++ 
Sbjct: 145 VEAF------ARGLYFRFEDLTTLPA----------ELVLLGPRRARLTLHEGRYHQVKR 188

Query: 258 HALHMG 263
              H G
Sbjct: 189 MFGHFG 194


>gi|322835106|ref|YP_004215133.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321170307|gb|ADW76006.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 290

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 25/165 (15%), Positives = 56/165 (33%), Gaps = 34/165 (20%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ +R     ++ +G VV++   I      
Sbjct: 7   IRLNKYISE--SGICSRRDADRYIEQGNVFINGRRAAVGAQVFAGDVVKVNGQIIEPRDE 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     ED  +   NKP GI      G   +I  F+    
Sbjct: 65  --------------------------EDLVLIALNKPVGIITTMEEGERDNIRDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               ++     RLD+++ G++++         +  +      + I
Sbjct: 97  ---SKRVFPIGRLDKDSQGLILLTNHGDLVNKILRAGNDHEKEYI 138


>gi|222624207|gb|EEE58339.1| hypothetical protein OsJ_09447 [Oryza sativa Japonica Group]
          Length = 1194

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 72/247 (29%), Gaps = 44/247 (17%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQ-SGQVVRIPPVI 71
            + E  RL +         +    ++++  G+V V+         ++  S   + +    
Sbjct: 73  KEHEPQRLAKVLAAA-GVASRRTCEELIFQGKVTVNGSVCTAPQTKVDISKDSIYVNGNR 131

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK-PAGISVQGGSGIAYHID 130
            +     K    ++            KSI+   D  +  +NK   G+             
Sbjct: 132 ISKKLPPKLYFAVNKPKGYICSCGEPKSIISLFDDYLKGWNKIQPGVP------------ 179

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                       +     RLD  TSG++++      AQ L+                  I
Sbjct: 180 ----------KPRLFTVGRLDVATSGLIIITNDGEFAQKLSHPSSN-------------I 216

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHT 249
            K     I   + +   I       +     G        + +D  +  K   + +  H 
Sbjct: 217 MKEYVVTIDGPVHRNHLIAISEGTKID----GVKCIPDLVEPLDVQSNTKRTRIRIAVHE 272

Query: 250 GRTHQLR 256
           GR H++R
Sbjct: 273 GRNHEVR 279


>gi|206896167|ref|YP_002246897.1| heat shock protein 15 [Coprothermobacter proteolyticus DSM 5265]
 gi|206738784|gb|ACI17862.1| heat shock protein 15 [Coprothermobacter proteolyticus DSM 5265]
          Length = 82

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 31/60 (51%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
          MRLD++ K           Q+I+++G V+++ K  K ++ ++   ++ +   +    +++
Sbjct: 1  MRLDKFLKESGIIKRRTLAQRIIQAGYVKINGKLAKQSDPVKVDDMIEVDTPVAYTRYVV 60


>gi|16765063|ref|NP_460678.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|29142068|ref|NP_805410.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|56413355|ref|YP_150430.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|161613791|ref|YP_001587756.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167993774|ref|ZP_02574867.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|168230158|ref|ZP_02655216.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|168237772|ref|ZP_02662830.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           SL480]
 gi|168241298|ref|ZP_02666230.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|168260059|ref|ZP_02682032.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|168462806|ref|ZP_02696737.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|168819542|ref|ZP_02831542.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|194444498|ref|YP_002040973.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194451051|ref|YP_002045766.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194471762|ref|ZP_03077746.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194733904|ref|YP_002114751.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197249960|ref|YP_002146307.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197265930|ref|ZP_03166004.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197362279|ref|YP_002141916.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|198242127|ref|YP_002215422.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200389338|ref|ZP_03215949.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|205352607|ref|YP_002226408.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|207856768|ref|YP_002243419.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|213163149|ref|ZP_03348859.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213421199|ref|ZP_03354265.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
 gi|213424436|ref|ZP_03357249.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
 gi|213582563|ref|ZP_03364389.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
 gi|213649101|ref|ZP_03379154.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213855225|ref|ZP_03383465.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|224583789|ref|YP_002637587.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|238911889|ref|ZP_04655726.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|289829089|ref|ZP_06546769.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|34098653|sp|Q8ZP51|RLUB_SALTY RecName: Full=Ribosomal large subunit pseudouridine synthase B;
           AltName: Full=rRNA pseudouridylate synthase B; AltName:
           Full=rRNA-uridine isomerase B
 gi|16420249|gb|AAL20637.1| putative ribosomal large subunit pseudouridine synthase [Salmonella
           enterica subsp. enterica serovar Typhimurium str. LT2]
 gi|29137697|gb|AAO69259.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|56127612|gb|AAV77118.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|161363155|gb|ABX66923.1| hypothetical protein SPAB_01525 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194403161|gb|ACF63383.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194409355|gb|ACF69574.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|194458126|gb|EDX46965.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|194709406|gb|ACF88627.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|195634468|gb|EDX52820.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197093756|emb|CAR59230.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|197213663|gb|ACH51060.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
 gi|197244185|gb|EDY26805.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197289238|gb|EDY28605.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           SL480]
 gi|197936643|gb|ACH73976.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|199601783|gb|EDZ00329.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|205272388|emb|CAR37268.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205328271|gb|EDZ15035.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|205335319|gb|EDZ22083.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|205339577|gb|EDZ26341.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|205343695|gb|EDZ30459.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|205350643|gb|EDZ37274.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|206708571|emb|CAR32892.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|224468316|gb|ACN46146.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|261246909|emb|CBG24726.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. D23580]
 gi|267993665|gb|ACY88550.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301158247|emb|CBW17746.1| putative pseudouridine synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. SL1344]
 gi|312912712|dbj|BAJ36686.1| 23S rRNA pseudouridine synthase B [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320085782|emb|CBY95558.1| ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           2007-60-3289-1]
 gi|321224350|gb|EFX49413.1| Ribosomal large subunit pseudouridine synthase B [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|322614978|gb|EFY11903.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322621428|gb|EFY18282.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322623230|gb|EFY20072.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322628520|gb|EFY25308.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322633684|gb|EFY30424.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322638508|gb|EFY35203.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322640822|gb|EFY37471.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322645314|gb|EFY41842.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322651803|gb|EFY48175.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322654300|gb|EFY50622.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322659265|gb|EFY55513.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322662733|gb|EFY58940.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322667656|gb|EFY63816.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322671930|gb|EFY68051.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322677024|gb|EFY73088.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322680314|gb|EFY76353.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322685257|gb|EFY81253.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323129991|gb|ADX17421.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323195433|gb|EFZ80612.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323199316|gb|EFZ84410.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323204774|gb|EFZ89770.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323205930|gb|EFZ90893.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323217255|gb|EGA01976.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323220712|gb|EGA05157.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323227964|gb|EGA12116.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323232119|gb|EGA16226.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323234646|gb|EGA18733.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323238098|gb|EGA22157.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323243298|gb|EGA27317.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323248445|gb|EGA32380.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323252551|gb|EGA36394.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323255424|gb|EGA39190.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323260826|gb|EGA44428.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323267587|gb|EGA51070.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323270947|gb|EGA54383.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326623169|gb|EGE29514.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|326627671|gb|EGE34014.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
 gi|332988608|gb|AEF07591.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 291

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K     +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVKESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G     K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDESK 152


>gi|167758166|ref|ZP_02430293.1| hypothetical protein CLOSCI_00504 [Clostridium scindens ATCC 35704]
 gi|167664063|gb|EDS08193.1| hypothetical protein CLOSCI_00504 [Clostridium scindens ATCC 35704]
          Length = 251

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 21/87 (24%)

Query: 1   MSLMTYVQYVVVE---------------NDEEN----MRLDRWFKNHYPHINFVNLQKIL 41
           M  +T +++  V+                + +     +RLD      YP ++   +  ++
Sbjct: 138 MEHLTRIRHTTVKTSILSAFEDSYEPRYEELKGTVASVRLDTVLSLAYP-LSRSKITGLI 196

Query: 42  RSGQVRVDKKRVKFN-NRIQSGQVVRI 67
              +V V+ K V  N  R++ G ++ +
Sbjct: 197 EGARVFVNGKLVTSNGYRLKEGDILSV 223


>gi|251789770|ref|YP_003004491.1| 23S rRNA pseudouridylate synthase B [Dickeya zeae Ech1591]
 gi|247538391|gb|ACT07012.1| pseudouridine synthase [Dickeya zeae Ech1591]
          Length = 301

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/175 (15%), Positives = 59/175 (33%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ ++ +G++ VD K     +R++  +  +I    + ++    E
Sbjct: 5   LQKVLARA-GHGSRREIESMIEAGRISVDGKIATLGDRVEVTRATKIRIDGHVVSVRETE 63

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           + +                       ++ ++ KP G                       +
Sbjct: 64  EAVC----------------------RVLMYYKPEGELC--TRSDPEGRPTVFDRLPRIQ 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G   + K
Sbjct: 100 GYRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGEVGDDK 152


>gi|212212525|ref|YP_002303461.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           CbuG_Q212]
 gi|212010935|gb|ACJ18316.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           CbuG_Q212]
          Length = 244

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 32/228 (14%), Positives = 71/228 (31%), Gaps = 31/228 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+ +         +   ++K++  G+++V+++  +  +RI    +V I   +++L+   
Sbjct: 3   ERIQKVLARSGYG-SRREIEKMIAEGRIKVNQRLAQLGDRITEQDLVYIDGQLSSLS--- 58

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  + E  ++ +++KP G                 ++   
Sbjct: 59  -----------------------VPEQVRVLLYHKPEGEIC--TRKDPEWRTTVFETLPR 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K  +  +  RLD  TSG+L+       A  L       ++++ Y   V G         
Sbjct: 94  LKDGRWVIIGRLDINTSGLLLFTNEGELANRL--MHPSAQVEREYAVRVLGAVDADMTQK 151

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
               +        +  +V     G N       V           E Q
Sbjct: 152 LAHGVGLEDGKARFEDIVDVGGDGKNRWFHVVVVEGRHRLVRRLWESQ 199


>gi|119945902|ref|YP_943582.1| pseudouridine synthase [Psychromonas ingrahamii 37]
 gi|119864506|gb|ABM03983.1| ribosomal large subunit pseudouridine synthase F [Psychromonas
           ingrahamii 37]
          Length = 318

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 35/262 (13%), Positives = 89/262 (33%), Gaps = 55/262 (20%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           +Q  +V+N+ E +RL+++  +      +     K++   +V+++    +   ++Q G +V
Sbjct: 12  IQDNIVDNNSE-IRLNKFISD--SGFCSRREADKLIEQNRVKINGDIPELGTKVQLGDLV 68

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            +                    +N +      +  ++Y        NKP GI+       
Sbjct: 69  LVDGKR----------------INASAQDKLDRIYIVY--------NKPIGITC----TT 100

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             HI G + + +  K ++     RLD+ + G++ +         +  +      + +   
Sbjct: 101 ERHIHGNIINAIGHK-KRIFPIGRLDKPSEGLIFLTSDGDIVNKILRAENAHDKEYLV-- 157

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
                       +   L ++          V++ ++G     +  K             +
Sbjct: 158 -----------TVDKPLSER---------FVERMQRGVPILDTITKPCKVTVDSRFIFRI 197

Query: 246 QPHTGRTHQLRVHALHMGCPIV 267
               G   Q+R    H+G  ++
Sbjct: 198 VLTQGLNRQIRRMCEHLGYEVL 219


>gi|307130978|ref|YP_003882994.1| 23S rRNA pseudouridylate synthase [Dickeya dadantii 3937]
 gi|306528507|gb|ADM98437.1| 23S rRNA pseudouridylate synthase [Dickeya dadantii 3937]
          Length = 296

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 29/175 (16%), Positives = 58/175 (33%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ ++ +G++ VD K     +R++    V     I    H++  
Sbjct: 5   LQKVLARA-GHGSRREIESMIEAGRISVDGKIATLGDRVE----VTRATKIRIDGHVVSV 59

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           ++  +S                     + ++ KP G                       +
Sbjct: 60  RETEESVCR------------------VLMYYKPEGELC--TRSDPEGRPTVFDRLPRIQ 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G   + K
Sbjct: 100 GYRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGEVGDDK 152


>gi|229032605|ref|ZP_04188569.1| hypothetical protein bcere0028_46420 [Bacillus cereus AH1271]
 gi|228728690|gb|EEL79702.1| hypothetical protein bcere0028_46420 [Bacillus cereus AH1271]
          Length = 165

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 23/49 (46%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ + +K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTRIVDKIKNGDIQLNGQLMKPNAILSEGDYISIC 164


>gi|291087005|ref|ZP_06345121.2| ribosomal large subunit pseudouridine synthase B [Clostridium sp.
           M62/1]
 gi|291076613|gb|EFE13977.1| ribosomal large subunit pseudouridine synthase B [Clostridium sp.
           M62/1]
          Length = 283

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 38/256 (14%), Positives = 85/256 (33%), Gaps = 63/256 (24%)

Query: 13  ENDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
           E   + +RL+++         +     +++ +G+V VD        +I+ GQ +      
Sbjct: 19  EKGTQEIRLNKFLSE--SGFCSRREADRLIEAGEVLVDGAVASMGMKIREGQQIE----- 71

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                            + T  S   + ++L       + NKP GI              
Sbjct: 72  ----------------ADGTLISGKDRPVVL-------LVNKPRGIVC------TTSDRD 102

Query: 132 FLKSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             ++ VD  G   R+    RLD+++ G++++                         LV  
Sbjct: 103 RAENIVDFIGYPLRVYPVGRLDKDSEGLILM--------------------TNQGELVNR 142

Query: 190 IPKNKKECIANWLL-KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
           I K +      +L+     I   +++ +++  K  +  ++    ++   +K     +   
Sbjct: 143 ILKGRYGHEKEYLVSVDREITEQFLNRMRKGVKILDT-VTRPCTVEKTGEKS--FRIILT 199

Query: 249 TGRTHQLRVHALHMGC 264
            G   Q+R     +G 
Sbjct: 200 QGLNRQIRRMCEALGY 215


>gi|54296835|ref|YP_123204.1| hypothetical protein lpp0876 [Legionella pneumophila str. Paris]
 gi|53750620|emb|CAH12027.1| hypothetical protein lpp0876 [Legionella pneumophila str. Paris]
          Length = 200

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/160 (22%), Positives = 60/160 (37%), Gaps = 9/160 (5%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + +FNKP GI  Q         +  L +++   G       RLD+++ G+L++       
Sbjct: 4   LILFNKPYGILTQ---FTGELPEQTLSAFIKLPGFYA--AGRLDKQSEGLLILTDDGKLQ 58

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             LT     ++  K YW  V G+P +K        L    I          +E      I
Sbjct: 59  HRLTHPKFEKK--KHYWVQVEGVPTDKDLQPLRKGLVIKDITFLPAEARLISEPKIWPRI 116

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              +  +       WLE+    G+ HQ+R     +G P +
Sbjct: 117 PPIR--ERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTL 154


>gi|331657316|ref|ZP_08358278.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA206]
 gi|331055564|gb|EGI27573.1| ribosomal large subunit pseudouridine synthase B (rRNA-uridine
           isomerase B) (rRNA pseudouridylate synthase B)
           [Escherichia coli TA206]
          Length = 291

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 33/177 (18%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ IL +G+V VD K  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESILEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|298368975|ref|ZP_06980293.1| ribosomal large subunit pseudouridine synthase E [Neisseria sp.
           oral taxon 014 str. F0314]
 gi|298282978|gb|EFI24465.1| ribosomal large subunit pseudouridine synthase E [Neisseria sp.
           oral taxon 014 str. F0314]
          Length = 186

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/173 (20%), Positives = 59/173 (34%), Gaps = 28/173 (16%)

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
             +  FNKP G+  Q      +     LK +VD  G  P    RLD ++ G+L++     
Sbjct: 2   DDLIAFNKPCGVICQFSEHEKHPC---LKDYVDRPGFYP--AGRLDTDSEGLLLLTDNGV 56

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKK-----------ECIANWLLKKSHIGGDYVH 214
               + +    R   K YW+ V G P  +K             +      +    G+   
Sbjct: 57  LQAQIADPKFKRE--KTYWAQVEGSPDEEKLDLLCNGMDLGGFVTRPAKVRLLEAGEADI 114

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +  +N            V         WLE++   G+  Q+R      G P +
Sbjct: 115 LWPRNPP----------VRMRKTVPDFWLEIRIAEGKNRQVRRMTAKAGYPCL 157


>gi|291522303|emb|CBK80596.1| ribosomal large subunit pseudouridine synthase F [Coprococcus catus
           GD/7]
          Length = 261

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/170 (15%), Positives = 65/170 (38%), Gaps = 35/170 (20%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
            D+ ++RL+R+  +     +     +++ +G+V VD  + +   R++ GQVV++   +  
Sbjct: 13  EDKSDVRLNRFLSDA-GFCSRREADRLIEAGRVTVDGTKAELGTRVRPGQVVKVGSKVVR 71

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGF 132
            N  +                             +  FNKP GI           +I  +
Sbjct: 72  QNDRM----------------------------VLIAFNKPRGIVCTTDRVREKNNIIDY 103

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +        ++     RLD+++ G++++        H+ ++ +    + I
Sbjct: 104 IH-----YPERIYPIGRLDKDSEGLILLTNDGTIVNHILKASQYHEKEYI 148


>gi|76157412|gb|ABA40473.1| SJCHGC01105 protein [Schistosoma japonicum]
          Length = 230

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/104 (20%), Positives = 37/104 (35%), Gaps = 15/104 (14%)

Query: 98  KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKP-----------RL 146
              +++E+    V NK   + +             L   +     +P             
Sbjct: 119 DLRVVHEEQGFVVINKHPELLI----NCTNPWVNCLTLQMQLFYNRPQYVNWKLKNMFHF 174

Query: 147 THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
            HRLD  TSG++ +A     A  +  +F  R + K Y ++V G 
Sbjct: 175 VHRLDCPTSGLICIAYDTKVASMIRRAFEKREVTKYYLAIVRGY 218


>gi|295095683|emb|CBK84773.1| ribosomal large subunit pseudouridine synthase B [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 291

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K     +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIEAIIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVKESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G     K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDENK 152


>gi|283785437|ref|YP_003365302.1| ribosomal large subunit pseudouridine synthase B [Citrobacter
           rodentium ICC168]
 gi|282948891|emb|CBG88493.1| ribosomal large subunit pseudouridine synthase B [Citrobacter
           rodentium ICC168]
          Length = 291

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K  +  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIARLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVKESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|301107450|ref|XP_002902807.1| conserved hypothetical protein [Phytophthora infestans T30-4]
 gi|262097925|gb|EEY55977.1| conserved hypothetical protein [Phytophthora infestans T30-4]
          Length = 263

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/102 (30%), Positives = 47/102 (46%), Gaps = 6/102 (5%)

Query: 99  SILLYEDSKIYVFNKPAGISVQG-GSGIAYHIDGFL--KSWVDSKGQK---PRLTHRLDQ 152
             ++YE S + +  KP GI V+G G          L  K  VD+   +   P   HRLD 
Sbjct: 111 LRVVYECSILALVVKPVGIHVKGRGKRTVEQALPLLLRKQHVDAGDFELPLPHAVHRLDY 170

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
              G+L+VA+TR     L+  F    + K Y +++ G   +K
Sbjct: 171 RVGGLLLVAKTRKMEVKLSAQFERHSVAKQYRAILVGNVFDK 212


>gi|117620907|ref|YP_857421.1| ribosomal large subunit pseudouridine synthase B [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117562314|gb|ABK39262.1| ribosomal large subunit pseudouridine synthase B [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 307

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 29/173 (16%), Positives = 55/173 (31%), Gaps = 29/173 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ ++ +G+V VD K     +R++   V+R+        H IK 
Sbjct: 5   LQKVLARA-GHGSRREMEALITAGRVSVDGKVATLGDRVEVNAVIRVD------GHQIKT 57

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +   +                      +  ++KP G                       +
Sbjct: 58  RAAEEVICR------------------VLAYHKPEGEMC--TRHDPEGRPTVFDRLPKME 97

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           G +     RLD  TSG+L+       A  L        +++ Y   V+G    
Sbjct: 98  GARWIAVGRLDVNTSGLLLFTTDGELANRL--MHPSHEVEREYAVRVFGEITE 148


>gi|50121666|ref|YP_050833.1| 16S rRNA pseudouridylate synthase A [Pectobacterium atrosepticum
           SCRI1043]
 gi|49612192|emb|CAG75642.1| ribosomal small subunit pseudouridine synthase [Pectobacterium
           atrosepticum SCRI1043]
          Length = 231

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/249 (13%), Positives = 71/249 (28%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + L + +V VD + VK                      + 
Sbjct: 1   MRLDKFLSQQL-EISRSLVARELHAQRVTVDGEVVKS-----------------GAFKLS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L + +            + ++ NKP G      S         L     
Sbjct: 43  PEHNVEFDGNPLKQQNGP----------RYFMLNKPQGYVC---STDDPDHPTILYFMDV 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLLTDDGQWSHRITSPKHECEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L + +         +   +     A      ++        + +    GR HQ++  
Sbjct: 137 ELPLAEDTAEQFTVGVQLHNEKNLTKPA-----TLEKITDHV--VRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNRVV 198


>gi|261340036|ref|ZP_05967894.1| ribosomal large subunit pseudouridine synthase B [Enterobacter
           cancerogenus ATCC 35316]
 gi|288317956|gb|EFC56894.1| ribosomal large subunit pseudouridine synthase B [Enterobacter
           cancerogenus ATCC 35316]
          Length = 291

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K     +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIEAIIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVKESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G     K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDENK 152


>gi|221052937|ref|XP_002257843.1| pseudouridine synthetase [Plasmodium knowlesi strain H]
 gi|193807675|emb|CAQ38379.1| pseudouridine synthetase, putative [Plasmodium knowlesi strain H]
          Length = 328

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 91/256 (35%), Gaps = 27/256 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI----NAL 74
           +RL++        I+     + ++ G V+++ K VK       G  + +          L
Sbjct: 56  VRLNKIIS-MEKKISRRKSDEFIKDGNVKLNNKVVK-----NPGTHIDVSKDKIKISGKL 109

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
            +I++ QK+++ +      ++F K  +L+         KP G                L 
Sbjct: 110 VNIVRTQKMINRN-----DNNFYKWFVLH---------KPKGFLCTSNDEKDRASIYSLF 155

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-RIQKIYWSLVWGIPKN 193
                   +     RLD+ TSG+L++    A    LT     R R  +++      +   
Sbjct: 156 PQDIMDNYRLVSVGRLDRNTSGVLLLTNEYAWVNKLTHPKYQRIRTYRVHIEGPAQMKVL 215

Query: 194 KKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ--KFCWLEMQPHTGR 251
           K+     +L   +    +   V K+  + A   I   + I    Q  K   L +    GR
Sbjct: 216 KQLATGIYLQDDNRGKENKKIVKKKRTQPAFIEILREETIKVKDQVKKVSVLNISVREGR 275

Query: 252 THQLRVHALHMGCPIV 267
             Q+R     +  P++
Sbjct: 276 NRQIRKMFEQINQPVI 291


>gi|83942369|ref|ZP_00954830.1| RNA pseudouridylate synthase [Sulfitobacter sp. EE-36]
 gi|83846462|gb|EAP84338.1| RNA pseudouridylate synthase [Sulfitobacter sp. EE-36]
          Length = 187

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 37/165 (22%), Positives = 66/165 (40%), Gaps = 10/165 (6%)

Query: 106 SKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           +++ +FNKP G+  Q    G        L +++D KG  P    RLD+++ G++V+  + 
Sbjct: 2   NRVILFNKPFGVLSQFTDKGTEGSPRPTLSAYIDEKGFYP--AGRLDRDSEGLMVLTDSG 59

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHVVKQNEKG 222
                ++      ++ K YW  V G P  +      +   LK          ++   E  
Sbjct: 60  PLQARIS--HPKYKLAKTYWVQVEGTPDEQALAALRSGVTLKDGKTAPAKARLMDPPEPL 117

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +       V    +    WLE+    GR  Q+R    H+G P +
Sbjct: 118 WDR---DPPVRFRKSVPDAWLEITITEGRNRQVRRMTAHVGLPTL 159


>gi|296102094|ref|YP_003612240.1| 23S rRNA pseudouridylate synthase B [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295056553|gb|ADF61291.1| 23S rRNA pseudouridylate synthase B [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 291

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K     +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIEAIIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVKESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G     K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDENK 152


>gi|257870927|ref|ZP_05650580.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257805091|gb|EEV33913.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 237

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 89/247 (36%), Gaps = 52/247 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D+  +      +   ++++ + G+V VD             Q +   P  N  + + 
Sbjct: 1   MRIDKLIEERLAT-SRKEMKRLFQQGKVLVD-------------QQIERNPSRNVDSRL- 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                         H   +  +LL      Y+ NKPAG+          H    +   + 
Sbjct: 46  --------------HEIKVAGVLLQTRDVYYLLNKPAGVVT----ANIDHQHATVIDLLQ 87

Query: 139 SKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            + ++  L    RLD++T G++++         L      +++ K Y  +V G    +  
Sbjct: 88  PEDRQATLYAVGRLDRDTEGLVLLTTNGQLGYEL--LHPNKKVPKRYDVIVNGPVTAED- 144

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +A +       GG    VV Q  K           I+  + +  ++ ++   G+ HQ++
Sbjct: 145 -VAAFAQGIVFHGG----VVCQPAKL---------TIEMTSGRRSFVHLEIAEGKFHQVK 190

Query: 257 VHALHMG 263
              L  G
Sbjct: 191 KMFLARG 197


>gi|161829731|ref|YP_001596671.1| RNA pseudouridine synthase family protein [Coxiella burnetii RSA
           331]
 gi|161761598|gb|ABX77240.1| RNA pseudouridine synthase family protein [Coxiella burnetii RSA
           331]
          Length = 244

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 30/228 (13%), Positives = 69/228 (30%), Gaps = 31/228 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+ +         +   ++K++  G+++V+++  +  +RI    +V I   +++L+   
Sbjct: 3   ERIQKVLARSGYG-SRREIEKMIAEGRIKVNQRLAQLGDRITEQDLVYIDGQLSSLSA-- 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                           + ++ +L ++        K                    ++   
Sbjct: 60  ---------------PEQVRVLLYHKPEGEICTRKDP-----------EWRTTVFETLPR 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K  +  +  RLD  TSG+L+       A  L       ++++ Y   V G         
Sbjct: 94  LKDGRWVIIGRLDINTSGLLLFTNEGELANRL--MHPSAQVEREYAVRVLGAVDADMTQK 151

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
               +        +  +V     G N       V           E Q
Sbjct: 152 LAHGVGLEDGKARFEDIVDVGGDGKNRWFHVVVVEGRHRLVRRLWESQ 199


>gi|77358718|ref|YP_338282.1| RNA pseudouridine synthase family protein [Coxiella burnetii RSA
           493]
 gi|71066708|gb|AAZ22630.1| ribosomal large subunit pseudouridine synthase B [Coxiella burnetii
           RSA 493]
          Length = 244

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 30/228 (13%), Positives = 69/228 (30%), Gaps = 31/228 (13%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            R+ +         +   ++K++  G+++V+++  +  +RI    +V I   +++L+   
Sbjct: 3   ERIQKVLARSGYG-SRREIEKMIAEGRIKVNQRLAQLGDRITEQDLVYIDGQLSSLSA-- 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                           + ++ +L ++        K                    ++   
Sbjct: 60  ---------------PEQVRVLLYHKPEGEICTRKDP-----------EWRTTVFETLPR 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K  +  +  RLD  TSG+L+       A  L       ++++ Y   V G         
Sbjct: 94  LKDGRWVIIGRLDINTSGLLLFTNEGELANRL--MHPSAQVEREYAVRVLGAVDADMTQK 151

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
               +        +  +V     G N       V           E Q
Sbjct: 152 LAHGVGLEDGKARFEDIVDVGGDGKNRWFHVVVVEGRHRLVRRLWESQ 199


>gi|238796852|ref|ZP_04640357.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           mollaretii ATCC 43969]
 gi|238719340|gb|EEQ11151.1| Ribosomal small subunit pseudouridine synthase A [Yersinia
           mollaretii ATCC 43969]
          Length = 235

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 39/285 (13%), Positives = 82/285 (28%), Gaps = 63/285 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++   + + LR+ +V +D + VK                      + 
Sbjct: 1   MRLDKFLSQQL-GVSRALVARELRAKRVTIDGEVVKS-----------------GATKLT 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PESDVRFDGNPLQQTLGP----------RYFMLNKPQGYVC---STEDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL--- 255
            + + + +         +         A    ++I+        + +    GR HQ+   
Sbjct: 137 EHPVAEDTAQRFADGVQLHNETSLTKPA--QLEIIEPQ-----LVRLTLSEGRYHQVKRM 189

Query: 256 ------RV---HALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLH 291
                 RV   H   +G  I+ D      ++      I +    H
Sbjct: 190 FGAVGNRVLALHRERIGAMILDDDLAPGEYRPLTAEEIASVGAPH 234


>gi|331002924|ref|ZP_08326437.1| hypothetical protein HMPREF0491_01299 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330413217|gb|EGG92591.1| hypothetical protein HMPREF0491_01299 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 242

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 37/245 (15%), Positives = 81/245 (33%), Gaps = 48/245 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL+++  +     +     K + +G+V ++ +  +    +    +V +     A    +
Sbjct: 1   MRLNKFLAS-IGVCSRREADKAIEAGRVMINGEVAELGAMVGEEDLVSLDGRYIATGKDV 59

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           ++ K +                       I  FNKP GI               +  ++ 
Sbjct: 60  EKVKPI-----------------------IIAFNKPEGIVCTTSDNDGATN---VVDYIG 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            K ++     RLD+++SG+L++    +    L  +      +         I K  K+  
Sbjct: 94  MK-ERIYPVGRLDKDSSGLLLLTNQGSLTNSLLRAANYHEKEY--------IVKVNKDID 144

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            +++ K S   G Y++ +K          +  +             +    G   Q+R  
Sbjct: 145 DDFINKMS--NGIYLYELK----------TKTRKCKVKKLNKNTFSIVLTQGLNRQIRRM 192

Query: 259 ALHMG 263
            L  G
Sbjct: 193 CLACG 197


>gi|222084363|ref|YP_002542892.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221721811|gb|ACM24967.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 278

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/256 (14%), Positives = 74/256 (28%), Gaps = 58/256 (22%)

Query: 14  NDEENMR--LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71
            + +  R  L R       + +    + ++ +G+V VD + +            RI    
Sbjct: 18  QESDGKRVTLPRALSK-LGYCSRTQAEALIAAGRVTVDGREITDPTAWIDLDRARIAVDG 76

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
            A   I  E+K+                         ++ NKP G+              
Sbjct: 77  EA---IAAEKKL------------------------YFMLNKPRGLVT--TRDDPEGRPT 107

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL----TESFRMRRIQKIYWSLV 187
                 D   +      RLD+ + G+L+       AQ L    +   ++  +Q       
Sbjct: 108 VYDCLRDIDARHLAPVGRLDKASEGLLLFTNDTVLAQALLDPISHVGKIYHVQVNTIMEQ 167

Query: 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQP 247
             + + ++  I +  L  +                          +     +  W+E++ 
Sbjct: 168 ELLDRMERGVIDDGELLTATAAR----------------------LLRSGDRNGWIEVEL 205

Query: 248 HTGRTHQLRVHALHMG 263
             GR  Q+R     +G
Sbjct: 206 KEGRNRQIRRMLEVLG 221


>gi|161503173|ref|YP_001570285.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160864520|gb|ABX21143.1| hypothetical protein SARI_01241 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 291

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K     +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVKESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G     K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDESK 152


>gi|19879252|gb|AAK38326.1| hypothetical pseudouridine synthase [Flavobacterium johnsoniae
           UW101]
          Length = 304

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 30/252 (11%), Positives = 76/252 (30%), Gaps = 59/252 (23%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RL+++      + +     K++  G+V ++    +   ++ S   +RI       
Sbjct: 2   EENLKRLNKFIGET-GYCSRREADKLIEEGRVTINGAAAEMGTKVSSDDEIRI------- 53

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                               D    +  +E      FNKP GI       +  +I  ++ 
Sbjct: 54  --------------------DGKLIVEKHEKLVYLAFNKPVGIECTTNLEVKNNIVDYI- 92

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               +  ++     RLD+ + G++ +         +  +      +              
Sbjct: 93  ----NYPKRIFPIGRLDKASEGLIFMTNDGDIVNKILRARNNHEKEYTV----------- 137

Query: 195 KECIANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              +   + ++    +G     +    +K     IS +             ++    G  
Sbjct: 138 --TVNKPITERFIQRMGNGVPILDTVTKKCKVEQISKYT-----------FKIILTQGLN 184

Query: 253 HQLRVHALHMGC 264
            Q+R  + ++G 
Sbjct: 185 RQIRRMSEYLGY 196


>gi|332527848|ref|ZP_08403885.1| ribosomal large subunit pseudouridine synthase B [Rubrivivax
           benzoatilyticus JA2]
 gi|332112425|gb|EGJ12218.1| ribosomal large subunit pseudouridine synthase B [Rubrivivax
           benzoatilyticus JA2]
          Length = 487

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/258 (13%), Positives = 71/258 (27%), Gaps = 49/258 (18%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V+    +    L +         +  ++++++  G++ V+ +      RI +G  + +
Sbjct: 44  KRVLAPEPDAPK-LHKVLAQAGIG-SRRDMEQMILEGRITVNGEPAHIGQRIAAGDRIAV 101

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIA 126
                         +                         +  ++KPAG +         
Sbjct: 102 GGKPVRYRIAPPPTR-------------------------VIAYHKPAGEVVTHDDPQQR 136

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
             +   L      K Q      RLD  T G+L+   +   A  L         +    SL
Sbjct: 137 PTVFRRLPRLHQGKWQS---VGRLDINTEGLLLFTNSGELANQLMHPRFGIEREYAVRSL 193

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
             G+    ++     LL+   I G           G   A               W    
Sbjct: 194 -GGLDDASRQK----LLEGVEIDGQRCAFKSIENGGGEGA-------------NQWYRCV 235

Query: 247 PHTGRTHQLRVHALHMGC 264
              GR  ++R     +G 
Sbjct: 236 ITEGRNREVRKLFDAVGH 253


>gi|307710882|ref|ZP_07647309.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK321]
 gi|307617327|gb|EFN96500.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           mitis SK321]
          Length = 220

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 40/224 (17%), Positives = 78/224 (34%), Gaps = 45/224 (20%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           +L++G+V V+ K+ K + ++Q         +    + I  + ++L+              
Sbjct: 1   MLKAGRVTVNGKKEK-SAKLQ---------IDEERDEIRLDGQVLE-------------- 36

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
              YE+   Y+ NKP G+           +   L     +K  +     RLD +T G+L+
Sbjct: 37  ---YEEFVYYMMNKPQGVISATEDPKHRTVLDLLDDLARTK--EVFPVGRLDIDTHGLLL 91

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +      A  L      R + K Y + V GI   +                 +   +   
Sbjct: 92  LTNDGQLAHAL--LSPKRHVDKTYLAQVKGIMTQEDVET-------------FAKGIPLK 136

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           +     A      ID  A+    + +    G+ HQ++    + G
Sbjct: 137 DFTCQPARLELVSIDT-AKNQSQIRVTIAEGKFHQVKRMVAYCG 179


>gi|206970431|ref|ZP_03231384.1| conserved hypothetical protein [Bacillus cereus AH1134]
 gi|206735008|gb|EDZ52177.1| conserved hypothetical protein [Bacillus cereus AH1134]
          Length = 165

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDYISIC 164


>gi|224476843|ref|YP_002634449.1| RNA pseudouridine synthase [Staphylococcus carnosus subsp. carnosus
           TM300]
 gi|222421450|emb|CAL28264.1| RNA pseudouridine synthase [Staphylococcus carnosus subsp. carnosus
           TM300]
          Length = 231

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 79/244 (32%), Gaps = 52/244 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++  N         ++++L+  +V+V+ K  K                  +  HI 
Sbjct: 1   MRLDKYLANMGVG-TRSEVKQLLKKNKVQVNGKNEK-----------------QSKAHIN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            +   +    NL          + Y D    + NKPAG      +         +    D
Sbjct: 43  PDTDEITVDGNL----------IEYVDKVYIMLNKPAGYIS---ATEDEEQSTIVSLIKD 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  K     R+ ++T G++++         +      + + KIY           K  I
Sbjct: 90  FQHMKIFPVGRVGKDTEGLILLTNDGQFNHDI--MSPNKHVSKIYR-------VEAKNPI 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            +  +K+   G   V +     K A    +  + +           +    GR HQ++  
Sbjct: 141 TDDDIKQFAEG---VELSDGKTKPAQLERTENEKVAF---------VSIREGRYHQVKRM 188

Query: 259 ALHM 262
              +
Sbjct: 189 FHAI 192


>gi|148358978|ref|YP_001250185.1| pseudouridine synthase [Legionella pneumophila str. Corby]
 gi|296107027|ref|YP_003618727.1| ribosomal large subunit pseudouridine synthase B [Legionella
           pneumophila 2300/99 Alcoy]
 gi|148280751|gb|ABQ54839.1| pseudouridine synthase [Legionella pneumophila str. Corby]
 gi|295648928|gb|ADG24775.1| ribosomal large subunit pseudouridine synthase B [Legionella
           pneumophila 2300/99 Alcoy]
          Length = 248

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/233 (14%), Positives = 74/233 (31%), Gaps = 34/233 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +   +++ + +G V+V+ K  K  +       + +           
Sbjct: 4   ERLQKILSQAGLG-SRREMERWIDNGWVQVNGKPAKLGDSAGPSDKISV----------- 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            + K++ + +               ++ ++ +++KP G +S +        +   L    
Sbjct: 52  -KGKLIPNPLKGK------------QNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLR 98

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +  +     RLD  TSG+L+       A  L        +++ Y   V G    +   
Sbjct: 99  QGRWVQ---VGRLDLNTSGLLIFTNNGELANQL--MHPKYGLEREYAVRVHGQVSQESL- 152

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N LLK   +        K   +G     S + V     +      +    G
Sbjct: 153 --NNLLKGVMLDDGLAKFTKIQFRGGEGTNSWYHVTLNEGRNREVRRLWESQG 203


>gi|300714626|ref|YP_003739429.1| Pseudouridine synthase [Erwinia billingiae Eb661]
 gi|299060462|emb|CAX57569.1| Pseudouridine synthase [Erwinia billingiae Eb661]
          Length = 292

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 74/247 (29%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR    +++ +G VV++   +    + 
Sbjct: 7   IRLNKYIGE--SGICSRRDADRYIEQGNVFINGKRAAVGDQVYAGDVVKVNGQLIEPRNE 64

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     +D  +   NKP GI      G   +I  F+    
Sbjct: 65  --------------------------DDLVLIALNKPVGIISTTEEGERDNIVNFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD+E+ G++ +         +  +      +     +V        E 
Sbjct: 97  ---SKRVFPIGRLDKESQGLIFLTNHGDLVNKILRAGNDHEKEY----VVTVNKLVTDEF 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           IA        +G        + E    + I+                     G   Q+R 
Sbjct: 150 IAGLGAGVPMLGTVTKKCKVKKEAPFVFRIT------------------LVQGLNRQIRR 191

Query: 258 HALHMGC 264
              H G 
Sbjct: 192 MCKHFGY 198


>gi|229062633|ref|ZP_04199942.1| hypothetical protein bcere0026_46990 [Bacillus cereus AH603]
 gi|228716603|gb|EEL68300.1| hypothetical protein bcere0026_46990 [Bacillus cereus AH603]
          Length = 87

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20 RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 38 RIDKVLSTYISDWSRTIIVDKIKNGAIQLNGQQMKPNKMLSEGDYISIC 86


>gi|158321656|ref|YP_001514163.1| RNA-binding S4 domain-containing protein [Alkaliphilus oremlandii
          OhILAs]
 gi|158141855|gb|ABW20167.1| RNA-binding S4 domain protein [Alkaliphilus oremlandii OhILAs]
          Length = 80

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 25/60 (41%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
          MRLD++ KN          ++    G+V ++ K  K +  +  G ++ I      L   I
Sbjct: 1  MRLDKYLKNSRIIKRRTVAKEACEGGRVSINGKVAKPSTEVALGDIIEIQFGDKTLKAEI 60


>gi|329119600|ref|ZP_08248281.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327464197|gb|EGF10501.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 186

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 39/167 (23%), Positives = 70/167 (41%), Gaps = 16/167 (9%)

Query: 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
             + VFNKP G+  Q G+   +     LK ++D+ G  P    RLD ++ G+L++     
Sbjct: 2   DDLIVFNKPCGVVCQFGAHEKHRS---LKDFIDAPGFYP--AGRLDTDSEGLLLLTCNGR 56

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHV---VKQNEKG 222
               +       +++K YW+ + G P+  K       L++    GD+V     ++  + G
Sbjct: 57  MQARIA--HPKFKLEKTYWAQLEGSPQADK----LAALQRPMDLGDFVARPAKIRLPDAG 110

Query: 223 ANYAISHF--KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              A+      V         WLE++   G+  Q+R      G P +
Sbjct: 111 ETDALWPRVPPVRLRKTVPDFWLEIKIAEGKNRQVRRMTAKAGYPCL 157


>gi|296106395|ref|YP_003618095.1| ribosomal large subunit pseudouridine synthase E [Legionella
           pneumophila 2300/99 Alcoy]
 gi|295648296|gb|ADG24143.1| ribosomal large subunit pseudouridine synthase E [Legionella
           pneumophila 2300/99 Alcoy]
 gi|307609608|emb|CBW99110.1| hypothetical protein LPW_08951 [Legionella pneumophila 130b]
          Length = 200

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/162 (22%), Positives = 64/162 (39%), Gaps = 13/162 (8%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + +FNKP G+  Q         +  L +++   G       RLD+++ G+LV+       
Sbjct: 4   LILFNKPYGVLTQ---FTGELPEQTLSAFIKFPGFYA--AGRLDKQSEGLLVLTDDGKLQ 58

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             LT     ++  K YW  V G P +K        L+K  +  D   +  + +  +   I
Sbjct: 59  HRLTHPKFEKK--KHYWVQVEGAPTDK----DLQPLRKGLVIKDITFLPAEAKLISEPKI 112

Query: 228 SHF--KVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                 + +       WLE+    G+ HQ+R     +G P +
Sbjct: 113 WPRIPPIRERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTL 154


>gi|238752726|ref|ZP_04614196.1| Ribosomal large subunit pseudouridine synthase F [Yersinia rohdei
           ATCC 43380]
 gi|238709057|gb|EEQ01305.1| Ribosomal large subunit pseudouridine synthase F [Yersinia rohdei
           ATCC 43380]
          Length = 290

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 72/246 (29%), Gaps = 56/246 (22%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +  +  + +  G V ++ KR    +++ +G VV++   +       
Sbjct: 8   RLNKYISE--SGICSRRDADRYVEQGNVFINGKRAAVGDQVYAGDVVKVNGQLIEPRDE- 64

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                    +D  +   NKP GI      G   +I  F+     
Sbjct: 65  -------------------------DDLVLIALNKPVGIISTTEDGEHDNIVDFVNH--- 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD+++ G++ +         +  +      + +   +    P    E I
Sbjct: 97  --SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYV---VTVNKPVTD-EFI 150

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                    +G        + E    + I+                     G   Q+R  
Sbjct: 151 LGLGAGVPMLGTVTKKCKVKKESTFVFRIT------------------LVQGLNRQIRRM 192

Query: 259 ALHMGC 264
             H G 
Sbjct: 193 CKHFGY 198


>gi|224541350|ref|ZP_03681889.1| hypothetical protein CATMIT_00510 [Catenibacterium mitsuokai DSM
           15897]
 gi|224525684|gb|EEF94789.1| hypothetical protein CATMIT_00510 [Catenibacterium mitsuokai DSM
           15897]
          Length = 247

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 78/249 (31%), Gaps = 50/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
            RL +       + +    +++++ G+V V+ + V     ++     + +   +      
Sbjct: 3   ERLQKVIAQS-GYTSRRKAEELIQQGKVTVNGEVVTVLGTKVTKKDTICVNGKL------ 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  +  ED   Y+F KP        +    H    +  + 
Sbjct: 56  -----------------------INKEDKVYYLFYKPEKCVC---TMSDEHDRTCVADYF 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD +T+G L +      A  +        ++K+Y   V G+    +  
Sbjct: 90  ADSNERVYPVGRLDYDTTGALFMTNDGEFANLI--MHPSSHLEKVYEVSVKGLLTKAE-- 145

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                 K     G Y+  VK        AI+     +        L ++   G+  Q++ 
Sbjct: 146 ------KNQLEKGIYLEGVK--TLPCEIAIT----GNDEEHGTTMLLIRLVEGKNRQIKK 193

Query: 258 HALHMGCPI 266
               +G P+
Sbjct: 194 MFEEVGHPV 202


>gi|77409420|ref|ZP_00786117.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae COH1]
 gi|77171978|gb|EAO75150.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae COH1]
          Length = 240

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 81/249 (32%), Gaps = 54/249 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++        +   ++ IL+  Q+ V+                             
Sbjct: 1   MRLDKFLVECGLG-SRTQVKLILKKKQISVN----------------------------- 30

Query: 79  KEQKILDSSVNLTKHSDFLK---SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
                    V + ++ D +K   +++ YE    Y+ +KP G+           +   L  
Sbjct: 31  -SNSETSPKVQVDEYRDEIKYNGTLVSYEKFVYYMLHKPKGVISATDDPSHKTVLDLLDK 89

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               K        RLD +T+G+L++      A + L+     + + K Y + + GI    
Sbjct: 90  TARDKA--VFPVGRLDIDTTGLLLITNNGELAHKMLS---PKKHVDKCYEAKISGIMTED 144

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
                     K  I  D+  +          A+    V     +K   +++    G+ HQ
Sbjct: 145 ----DILAFDKGIILKDFTCL---------PALLEI-VEVNQVKKQSLVKITIKEGKFHQ 190

Query: 255 LRVHALHMG 263
           ++      G
Sbjct: 191 VKRMVAACG 199


>gi|313632172|gb|EFR99245.1| ribosomal small subunit pseudouridine synthase A [Listeria
           seeligeri FSL N1-067]
          Length = 233

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 83/246 (33%), Gaps = 53/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   +     +   ++ +L+SG V V+    K                 ++ + + 
Sbjct: 1   MRLDKLLSHTGFG-SRREVKPLLKSGSVVVNGVIQK-----------------DSKSQVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+  +    N           ++Y++   ++ +KP  +       ++  +   L    +
Sbjct: 43  PEKDQITVHGNP----------VIYQEFVYFMLHKPQNVVSATEDNLSETVIDLLAQ--E 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD++T G+L++      A   L+     + I K Y++ + G        
Sbjct: 91  DTLTNPFPVGRLDKDTEGLLIITNDGTLAHNLLS---PKKHIDKTYYAKIEGDVTA---- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                   + +      +   +      A  H +++     +    E     G+ HQ++ 
Sbjct: 144 --------TDVEAFRTGITLDDGYTCKPA--HLEIMAPNEIRVTIQE-----GKFHQVKR 188

Query: 258 HALHMG 263
                G
Sbjct: 189 MFAATG 194


>gi|218232678|ref|YP_002369767.1| hypothetical protein BCB4264_A5107 [Bacillus cereus B4264]
 gi|229153157|ref|ZP_04281336.1| hypothetical protein bcere0011_46870 [Bacillus cereus m1550]
 gi|218160635|gb|ACK60627.1| conserved hypothetical protein [Bacillus cereus B4264]
 gi|228630256|gb|EEK86906.1| hypothetical protein bcere0011_46870 [Bacillus cereus m1550]
          Length = 165

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGRQMKPNTILSEGDSISIC 164


>gi|91776879|ref|YP_546635.1| pseudouridine synthase, Rsu [Methylobacillus flagellatus KT]
 gi|91710866|gb|ABE50794.1| Pseudouridine synthase, Rsu [Methylobacillus flagellatus KT]
          Length = 380

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 40/252 (15%), Positives = 74/252 (29%), Gaps = 50/252 (19%)

Query: 25  FKNHYPHI---NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQ 81
                  +   +     + + +G V+V+ + V                  + L   +   
Sbjct: 143 LSKRMAELGLCSRREADEFIANGWVKVNGEVV------------------DVLGTRVAPD 184

Query: 82  KILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-----ISVQGGSGIAYHIDGFLKSW 136
             ++ S    +H     +ILL++           G     + V   +         +   
Sbjct: 185 AKIEVSKEAHQHQAETVTILLHKPVGYVSGQAEDGYEPAVVLVHPDNQWKEDPSQTVFKR 244

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +G  P    RLD +++G+LV+ +    A+ L        ++K Y   V G    +  
Sbjct: 245 GHLRGLAP--AGRLDIDSTGLLVLTQDGRVARRL--IGEDSTVEKEYLVRVTGTLSEEGL 300

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              N  L    +      V  QNE                      L      GR  Q+R
Sbjct: 301 RKLNHGLSLDGVKLKPAKVSWQNED--------------------QLRFVLREGRKRQIR 340

Query: 257 VHALHMGCPIVG 268
                +G  +VG
Sbjct: 341 RMCELVGLTVVG 352


>gi|332161503|ref|YP_004298080.1| 23S rRNA pseudouridine synthase F [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|325665733|gb|ADZ42377.1| 23S rRNA pseudouridine synthase F [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
          Length = 290

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 76/247 (30%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR    +++  G VV++   +      
Sbjct: 7   IRLNKYISE--SGICSRRDADRYVEQGNVFINGKRAAVGDQVYVGDVVKVNGQL------ 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                     +     SD +          +   NKP GI      G + +I  F+    
Sbjct: 59  ----------IEPRDESDLI----------LIALNKPVGIISTTEDGESDNIVDFVNH-- 96

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD+++ G++ +         +  +      + +   +    P    E 
Sbjct: 97  ---SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYV---VTVNKPVTD-EF 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I         +G        + E    ++I+                     G   Q+R 
Sbjct: 150 ILGLGAGVPMLGTVTKKCKVRKEAPFVFSIT------------------LVQGLNRQIRR 191

Query: 258 HALHMGC 264
              H G 
Sbjct: 192 MCKHFGY 198


>gi|261840134|gb|ACX99899.1| pseudouridylate synthase [Helicobacter pylori 52]
          Length = 257

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 28/175 (16%), Positives = 64/175 (36%), Gaps = 30/175 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++   HY   +    +K++  G+V+++ +  K  + ++    V +      L   +
Sbjct: 1   MRINQFLA-HYTKHSRREAEKLVLEGRVKINHEHAKLASVVKENDKVFLD---KRLIKPL 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K +K                         + V++KP G  V     +  H    +   ++
Sbjct: 57  KNKKFS-----------------------VLVYHKPKGELVSKNDPLKRH---VIYESLE 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            K        RLD  + G+L+++ ++A    L  +   +         V    +N
Sbjct: 91  KKYAHFVPVGRLDFASEGVLLLSDSKAVVSALMHANLEKEYLVKIQGFVTREMEN 145


>gi|253742037|gb|EES98891.1| DRAP deaminase [Giardia intestinalis ATCC 50581]
          Length = 568

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 23/112 (20%), Positives = 49/112 (43%), Gaps = 5/112 (4%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           N I+++  ++   ++  +     + +L  E   ++   KPA + V       YH    L 
Sbjct: 119 NFILRDSDLILHVMHRHEPPILAQPVLRDEGEHVF-CEKPASMPVHPCGKYCYHSVNELV 177

Query: 135 SWVDSK---GQKPRLTHRLDQETSGILVVA-RTRAAAQHLTESFRMRRIQKI 182
           +  D+K    +  R  +R+D+  SG++V+A  ++ A Q   E      ++  
Sbjct: 178 ASPDTKLTTKKGLRACNRIDKLVSGLIVMADSSKEAEQKRNEIVERGNVKVY 229



 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/109 (23%), Positives = 37/109 (33%), Gaps = 13/109 (11%)

Query: 224 NYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFK 277
             AI+  + +   A          P TGRTHQLR+H    G PI  D  +         +
Sbjct: 353 QAAITVIEYVHTDAATETVLAMCVPVTGRTHQLRLHLQAAGTPIHNDPSHGGLQANLAIR 412

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSLGFK 325
               SP   +  L    + +       L+ I A       K+  SL   
Sbjct: 413 CTLPSPSVLQQMLRYEPLSMKAYASKVLERIKA------QKSLQSLDLN 455


>gi|323439505|gb|EGA97226.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus O11]
          Length = 245

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 32/233 (13%), Positives = 70/233 (30%), Gaps = 49/233 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +    + ++  G+ +V+   V     +++    + +  +   L                 
Sbjct: 19  SRRKAETLISEGKAKVNGTTVTELGTKVKPSDTIEVEGIKIEL----------------- 61

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                       ED    +F+KP  +     S         +  +      +     RLD
Sbjct: 62  ------------EDKIYILFHKPTQVIT---SVSDDRGRTVVTDYFKDIEARIYPVGRLD 106

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
            +TSG+L++         +T      +I+K Y + + G    ++       +K    G +
Sbjct: 107 YDTSGLLLLTNDGEFTNLMT--HPRYQIKKKYVAKLKGYLMREE-------VKALEKGIE 157

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
               + Q  +                +    +E+    GR  Q+R    H G 
Sbjct: 158 LEDGMTQPAEVKVK-------KQDKDKNTTLVEITITEGRNRQVRRMLEHFGH 203


>gi|317131163|ref|YP_004090477.1| pseudouridine synthase [Ethanoligenens harbinense YUAN-3]
 gi|315469142|gb|ADU25746.1| pseudouridine synthase [Ethanoligenens harbinense YUAN-3]
          Length = 237

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 76/247 (30%), Gaps = 55/247 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +RLD+         +   +  +LR G+V+VD + V       +GQ V        L+   
Sbjct: 4   LRLDKLLAGQGQG-SRKEVHTLLRGGRVQVDGQTVTD-----AGQKVDPDRQRVTLD--- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                 LL+      + NKPAG+        A  +   L + + 
Sbjct: 55  -------------------GHALLWRAHLYLMMNKPAGVISASRDPKARTVLDLLPADLC 95

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWS-LVWGIPKNKKE 196
             G       RLD++T G L++      A   L      R ++KIY + L         +
Sbjct: 96  RPG--LFPAGRLDKDTEGFLLITDDGAFAHDILA---PRRHVEKIYLATLDRPADTADTD 150

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
             A  L  +  +      +       A  A+                      G+ HQ+R
Sbjct: 151 AFATGLTLEDGLHCLPARLWLGEGTDAYAAV--------------------REGKFHQVR 190

Query: 257 VHALHMG 263
                 G
Sbjct: 191 RMFAARG 197


>gi|300778899|ref|ZP_07088757.1| ribosomal large subunit pseudouridine synthase F [Chryseobacterium
           gleum ATCC 35910]
 gi|300504409|gb|EFK35549.1| ribosomal large subunit pseudouridine synthase F [Chryseobacterium
           gleum ATCC 35910]
          Length = 240

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/248 (12%), Positives = 75/248 (30%), Gaps = 54/248 (21%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  R++++      + +     K+L  G+++++ K  +   ++    +V +         
Sbjct: 2   EKTRINKYLSE-VGYCSRRAADKLLEEGRIKINGKIPELGTKVSDEDLVEVD------GK 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
            I+E +                     E     VFNKP GI     +      +  +   
Sbjct: 55  PIREPQ---------------------EKPVYIVFNKPVGIVC--TTDTKREKNNIVDYI 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              K  +     RLD+ + G++++                         +V  I + +  
Sbjct: 92  NHPK--RIFPIGRLDKPSEGLILL--------------------TSDGDIVNKILRARNN 129

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
               +L++             +N       I+    ++   +      +    G   Q+R
Sbjct: 130 HEKEYLVRVDKPITPKFLEKMRNGVPILDTITRKCKVEKIDEMN--FRIILTQGLNRQIR 187

Query: 257 VHALHMGC 264
               ++G 
Sbjct: 188 RMCEYLGY 195


>gi|167747373|ref|ZP_02419500.1| hypothetical protein ANACAC_02092 [Anaerostipes caccae DSM 14662]
 gi|167653351|gb|EDR97480.1| hypothetical protein ANACAC_02092 [Anaerostipes caccae DSM 14662]
          Length = 91

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 5/73 (6%)

Query: 18 NMRLDRWFK--NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP-VINAL 74
           MRLD++ K              +   +G+V V+ K  K    ++ G  +RI      A 
Sbjct: 12 GMRLDKFLKVSRLIKR--RTVANEACSAGRVTVNGKTAKAGTDVKPGDEIRIQFGNKEAA 69

Query: 75 NHIIKEQKILDSS 87
            +++ ++ +   
Sbjct: 70 VEVLRVEETVKKD 82


>gi|150020759|ref|YP_001306113.1| RNA-binding S4 domain-containing protein [Thermosipho melanesiensis
           BI429]
 gi|149793280|gb|ABR30728.1| RNA-binding S4 domain protein [Thermosipho melanesiensis BI429]
          Length = 230

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 32/238 (13%), Positives = 81/238 (34%), Gaps = 56/238 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++  N     +   ++++++ G V+++ + +   + +++   +V +        H 
Sbjct: 1   MRLDKFLSNAKVG-SRKEVKRLIKFGIVKINGEIITNVDFKVKENDIVTVNNTPITPYHN 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +                               +FNKP G +           +     +V
Sbjct: 60  V-----------------------------YIIFNKPTGYTSSKSEFERNIFEFIDHPYV 90

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               +   +  RLD++  G+L++           +     +I      +         + 
Sbjct: 91  ----ENLHIAGRLDKDVEGLLLIT---------NDGIFTHKITSPKSKIEKEYIVKVDKE 137

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
           I++ +++K+  G     +V +N      AI     I      F  + +    G+ H++
Sbjct: 138 ISDEMIQKAKDG-----IVLKNGTRFKPAI-----IKRLKDNF--ISITITEGKYHEI 183


>gi|187934882|ref|YP_001884642.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum B str. Eklund 17B]
 gi|187723035|gb|ACD24256.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum B str. Eklund 17B]
          Length = 238

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/178 (17%), Positives = 62/178 (34%), Gaps = 32/178 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   + +    + + R G + VD K +K ++       V I P  + +    
Sbjct: 2   ERLDKIISN-LGYGSRKEAKVLARKGLIEVDGKIIKDSS-------VTIDPEKSIVKING 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +E                    + Y      + NKP G+           +   L+  +D
Sbjct: 54  EE--------------------IFYRKYIYLMMNKPTGVISATHDSKDETVIDLLE--LD 91

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            +   P    RLD++T G+L++         +        + K+Y++ +      K +
Sbjct: 92  HQIFNPFPVGRLDKDTVGLLLLTNDGEFNHRM--ISPKWHVDKVYYAKIDKEVNEKDQ 147


>gi|15675319|ref|NP_269493.1| putative 16S pseudouridylate synthetase [Streptococcus pyogenes M1
           GAS]
 gi|13622499|gb|AAK34214.1| putative 16S pseudouridylate synthetase [Streptococcus pyogenes M1
           GAS]
          Length = 194

 Score = 53.4 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/179 (14%), Positives = 55/179 (30%), Gaps = 38/179 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD+         +   ++K++++  V VD    +     +  G Q++ +         
Sbjct: 1   MRLDKLL-EGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQR----- 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   + +      + NKP+G+           +   L   
Sbjct: 55  ------------------------VTHPKHSYIILNKPSGVVSAKKDTNYLTVIDQLAE- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            + K        RLD++T G++++        + L        + K Y   V G+    
Sbjct: 90  -EDKSPDLYPVGRLDRDTEGLVLLTDNGPLGFRMLH---PSHHVSKTYLVTVNGLLAED 144


>gi|330830517|ref|YP_004393469.1| ribosomal large subunit pseudouridine synthase B [Aeromonas veronii
           B565]
 gi|328805653|gb|AEB50852.1| Ribosomal large subunit pseudouridine synthase B [Aeromonas veronii
           B565]
          Length = 307

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 28/173 (16%), Positives = 54/173 (31%), Gaps = 29/173 (16%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ ++ +G+V VD K     +R++   V+R+            E
Sbjct: 5   LQKVLARA-GHGSRREMEALITAGRVSVDGKVATLGDRVEVNAVIRVDGHQVKTR--AAE 61

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           + I                       ++  ++KP G                       +
Sbjct: 62  EVIC----------------------RVLAYHKPEGEMC--TRHDPEGRPTVFDRLPKME 97

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
           G +     RLD  TSG+L+       A  L        +++ Y   V+G    
Sbjct: 98  GARWIAVGRLDVNTSGLLLFTTDGELANRL--MHPSHEVEREYAVRVFGEITE 148


>gi|227111426|ref|ZP_03825082.1| 23S rRNA pseudouridylate synthase B [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 294

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/175 (17%), Positives = 60/175 (34%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ I+++G+V VD K     +R++    V     I    H++  
Sbjct: 5   LQKVLARA-GHGSRREIEGIIQAGRVSVDGKIATLGDRVE----VTKATKIRIDGHVVTV 59

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           ++  +S                     + ++ KP G                       +
Sbjct: 60  KETEESVCR------------------VLMYYKPEGELC--TRNDPDGRPTVFDRLPKIQ 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 100 GSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGEVDDEK 152


>gi|14596127|gb|AAK68791.1| hemolysin-like [Arabidopsis thaliana]
 gi|18377474|gb|AAL66903.1| hemolysin-like [Arabidopsis thaliana]
          Length = 125

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINA 73
            RLD      +   +   +Q  +  G+V VD +RV K    + +   ++I   +  
Sbjct: 55  QRLDEACVERFNEYSRTLIQSWIMQGKVLVDGRRVIKAGMPVSTTAAIKITAEVPK 110


>gi|323968113|gb|EGB63523.1| RNA pseudouridylate synthase [Escherichia coli M863]
 gi|323977618|gb|EGB72704.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
 gi|327252432|gb|EGE64091.1| RNA pseudouridylate synthase [Escherichia coli STEC_7v]
          Length = 231

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 75/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD + V+                 NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVR-----------------NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHDVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            + +   +         +   +     A+   +VI         + +    GR HQ++  
Sbjct: 137 ESPVADDTAEQFAKGVQLHNEKDLTKPAM--LEVI-----TPTQVRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNHVV 198


>gi|317406580|gb|EFV86770.1| RNA pseudouridylate synthase [Achromobacter xylosoxidans C54]
          Length = 241

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 40/219 (18%), Positives = 74/219 (33%), Gaps = 49/219 (22%)

Query: 25  FKNHY---PHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKE 80
                      +  + ++ +  G V VD K V+    R+  GQVV + P        ++E
Sbjct: 7   LAKRLAAEQSCSRGDAERYIEGGWVAVDGKVVEEPGFRVSPGQVVVLLPGAR-----LEE 61

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL------- 133
            + +                         + +KPAG+S    S  A+   G +       
Sbjct: 62  MRPVS-----------------------ILVHKPAGLS---ASDPAHSALGLVVPENLMP 95

Query: 134 -----KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
                + ++       +L   L++  SG++V  +  A A+ L E    R +++ Y + V 
Sbjct: 96  GDRSGQRYLKRMFNGLKLATPLERAASGLVVYTQEYAVARKLVE--EGRHVEQEYIAQVR 153

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
           G             L         + V  QNE    +A+
Sbjct: 154 GTLDAVGLARLQRGLAYEGRPATPMKVSWQNETHLRFAL 192


>gi|71910951|ref|YP_282501.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS5005]
 gi|139473571|ref|YP_001128287.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes str. Manfredo]
 gi|71853733|gb|AAZ51756.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS5005]
 gi|134271818|emb|CAM30052.1| putative ribosomal small subunit pseudouridine synthase A
           [Streptococcus pyogenes str. Manfredo]
          Length = 238

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 26/179 (14%), Positives = 55/179 (30%), Gaps = 38/179 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD+         +   ++K++++  V VD    +     +  G Q++ +         
Sbjct: 1   MRLDKLL-EGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQR----- 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   + +      + NKP+G+           +   L   
Sbjct: 55  ------------------------VTHPKHSYIILNKPSGVVSAKKDTNYLTVIDQLAE- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            + K        RLD++T G++++        + L        + K Y   V G+    
Sbjct: 90  -EDKSPDLYPVGRLDRDTEGLVLLTDNGPLGFRMLH---PSHHVSKTYLVTVNGLLAED 144


>gi|332993044|gb|AEF03099.1| RNA pseudouridine synthase family protein [Alteromonas sp. SN2]
          Length = 246

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 33/252 (13%), Positives = 78/252 (30%), Gaps = 54/252 (21%)

Query: 14  NDEENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           + E   RL+++  +    + +     K++   +V ++ K  +   ++  G  V++   + 
Sbjct: 2   SSEVTKRLNKYISD--TGLCSRREADKLIEQNRVTINDKLPELGTKVAQGDKVKVDGKLV 59

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                 K  +I                          V+NKP GI+      +  +I   
Sbjct: 60  KAVAEDKSDRI------------------------YLVYNKPIGITCTTERHVKGNIIDA 95

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +K       Q+     RLD+ + G++++         +  +                  K
Sbjct: 96  IKH-----KQRIFPVGRLDKPSEGLIILTSDGDIVNKILRAENSH-------------DK 137

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
             +  +   + ++          V++  KG     +  K     A+      +    G  
Sbjct: 138 EYEVTVNQPISER---------FVQKMAKGVPILGTVTKPCKVNARGKFQFSIILTQGLN 188

Query: 253 HQLRVHALHMGC 264
            Q+R     +G 
Sbjct: 189 RQIRRMCEFLGY 200


>gi|254362527|ref|ZP_04978630.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261494150|ref|ZP_05990653.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|153094127|gb|EDN75026.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261310316|gb|EEY11516.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 227

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 32/162 (19%), Positives = 60/162 (37%), Gaps = 12/162 (7%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + + NKP  +  Q            LK ++      P    RLD+++ G+L++       
Sbjct: 36  LVLLNKPYDVLTQ---FTDEQGRKTLKDFITMPNIYP--VGRLDRDSEGLLLLTNNGEIQ 90

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
             L      ++  K YW  V G+P+ +   +      LK        V  +   +   N 
Sbjct: 91  HRLAHPKFDKQ--KTYWVQVEGVPQPEDLAKLAKGVELKDGLTKPAKVRAIATPDFAWNI 148

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           A    ++ +       W+E+    G+  Q+R    H+G P +
Sbjct: 149 AP---QIRERKTIPTSWIELIISEGKNRQVRRMTAHIGFPTL 187


>gi|150376249|ref|YP_001312845.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
 gi|150030796|gb|ABR62912.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
          Length = 260

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 79/253 (31%), Gaps = 52/253 (20%)

Query: 15  DEENMR--LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           +    R  L R       +      +K++  G+V V  +RV                 + 
Sbjct: 17  ERAGKRVTLARALSK-LGYCTRTQAEKLIAEGRVSVGGRRVT---------------DLA 60

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
               I  ++  +D +V            +  +     + NKP G+               
Sbjct: 61  HWVDIEADRIAVDGTV------------IAAQPKVYLMLNKPRGLVTTRDDPEGRPTVFT 108

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVAR-TRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
               VD+    P    RLD+ + G+L+    T  A + L     + +   +    V G  
Sbjct: 109 CLETVDAPSLSP--VGRLDKASEGLLLFTNDTVLAQRLLDPQTHLGKRYHVQ---VRGFL 163

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
               E +A  +++    GG+ +   +               +     +  W+E++   GR
Sbjct: 164 ---GEAMAARMVEGVTEGGELLRAARVA-------------LLRGGDRNSWIEVELTEGR 207

Query: 252 THQLRVHALHMGC 264
             Q+R     +G 
Sbjct: 208 NRQIRRMLDALGF 220


>gi|18404536|ref|NP_566765.1| bacterial hemolysin-related [Arabidopsis thaliana]
 gi|9279726|dbj|BAB01316.1| hemolysin-like [Arabidopsis thaliana]
 gi|21593347|gb|AAM65296.1| hemolysin, putative [Arabidopsis thaliana]
 gi|332643493|gb|AEE77014.1| putative hemolysin [Arabidopsis thaliana]
          Length = 301

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINA 73
            RLD      +   +   +Q  +  G+V VD +RV K    + +   ++I   +  
Sbjct: 55  QRLDEACVERFNEYSRTLIQSWIMQGKVLVDGRRVIKAGMPVSTTAAIKITAEVPK 110


>gi|238027587|ref|YP_002911818.1| hypothetical protein bglu_1g20050 [Burkholderia glumae BGR1]
 gi|237876781|gb|ACR29114.1| Hypothetical protein bglu_1g20050 [Burkholderia glumae BGR1]
          Length = 571

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 38/257 (14%), Positives = 74/257 (28%), Gaps = 49/257 (19%)

Query: 8   QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
           + V+   D+    L +         +   +++++ +G+V V+ +      RI     VRI
Sbjct: 174 KRVLAPEDDAPK-LHKVLAEAGMG-SRREMEELIVAGRVSVNGEPAHIGQRILPTDQVRI 231

Query: 68  PPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIA 126
                      K  ++L                 LY        +KP G I         
Sbjct: 232 NGKPVKRKLPNKPPRVL-----------------LY--------HKPTGEIVSHADP--- 263

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
                        K  K     RLD  T G+L++  +   A           +++ Y   
Sbjct: 264 EGRASVFDRLPPMKTAKWLAVGRLDFNTEGLLMLTTSGDLANRF--MHPRYSVEREYAVR 321

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246
           V G             ++      +++ +     +G N+                W  + 
Sbjct: 322 VVGELSEASRQKLLHGVELDDGPANFLRIRDGGGEGTNH----------------WYHVA 365

Query: 247 PHTGRTHQLRVHALHMG 263
              GR  ++R     +G
Sbjct: 366 LAEGRNREVRRMFEAVG 382


>gi|254517600|ref|ZP_05129656.1| ribosomal large subunit pseudouridine synthase f [Clostridium sp.
           7_2_43FAA]
 gi|226911349|gb|EEH96550.1| ribosomal large subunit pseudouridine synthase f [Clostridium sp.
           7_2_43FAA]
          Length = 258

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 33/266 (12%), Positives = 79/266 (29%), Gaps = 67/266 (25%)

Query: 8   QYVVVENDEEN-MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           ++V++ ND    +RL+++        +     K++ +G+V VD  +     +++      
Sbjct: 9   KFVIIHNDRGPEIRLNKFISET-GFCSRREADKLIENGRVTVDGIKAVMGTKVKE----- 62

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
                              + V +   S      L+Y        NKP GI+      + 
Sbjct: 63  ------------------SADVKVDGKSIKKVDELVY-----IALNKPVGITCTTEKKVK 99

Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            +I  F+        ++     RLD+++ G++++         +  +      + I    
Sbjct: 100 GNIVDFVNH-----KKRIFPIGRLDKDSQGLILLTNDGDVVNKILRAGNNHEKEYIV--- 151

Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEK-----GANYAISHFKVIDCFAQKFC 241
                                I   ++  +    K          ++         +   
Sbjct: 152 ----------------TVDKPIDEKFIKSMSSGVKILGTITKKCIVTK--------ENKN 187

Query: 242 WLEMQPHTGRTHQLRVHALHMGCPIV 267
              +    G   Q+R     +G  +V
Sbjct: 188 TFRIILTQGMNRQIRRMCEALGYNVV 213


>gi|217970106|ref|YP_002355340.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|217507433|gb|ACK54444.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 379

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 32/247 (12%), Positives = 74/247 (29%), Gaps = 46/247 (18%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  RL +         +   +++ + +G++ V+        +I  G  V++   +  L  
Sbjct: 115 EPERLQKVLAQA-GVASRREIEEWVVAGRISVNGLPASLGQKIGPGDRVKVNGKLVPLRF 173

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
             +  +                         + +++KP G  V              +  
Sbjct: 174 TQRSPR-------------------------VLIYHKPEGEIV--SRDDPEGRPTVFERL 206

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
              +  +     RLD  TSG+L+       A  L        +++ Y   + G    ++ 
Sbjct: 207 PILRKGRWLAVGRLDFNTSGLLLFTNDGDLANKL--MHPRYELEREYAVRILGELTEEQV 264

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 ++       +  +  +  +GAN+                W  +    GR  ++R
Sbjct: 265 KSLTDGIQLEDGPAKFNLLRDEGGEGANH----------------WYRVTISEGRNREVR 308

Query: 257 VHALHMG 263
                +G
Sbjct: 309 RMFEAVG 315


>gi|254509192|ref|ZP_05121290.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           parahaemolyticus 16]
 gi|219547897|gb|EED24924.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           parahaemolyticus 16]
          Length = 345

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/246 (12%), Positives = 75/246 (30%), Gaps = 55/246 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL+++        +     +++  G+V ++ +  +   ++  G  VR+           
Sbjct: 7   KRLNKFISET-GFCSRREADRLIEQGRVTINGQVPEMGTKVMPGDDVRVD---------- 55

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                        K  + +    +Y        NKP GI+      I  +I  F+     
Sbjct: 56  ------------DKPINAVTDKPVY-----IALNKPTGITCTTERDIPGNIVDFV----- 93

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD+ + G++ +         +  +      + +             + I
Sbjct: 94  GHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVR---------VDKPI 144

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           ++  +KK   G + +  +    K        F+++                G   Q+R  
Sbjct: 145 SDDFIKKMSSGVNILDTITLPCKVTKETKFSFRIV-------------LTQGLNRQIRRM 191

Query: 259 ALHMGC 264
              +G 
Sbjct: 192 CEALGY 197


>gi|196040466|ref|ZP_03107766.1| conserved hypothetical protein [Bacillus cereus NVH0597-99]
 gi|228936261|ref|ZP_04099060.1| hypothetical protein bthur0009_46990 [Bacillus thuringiensis
           serovar andalousiensis BGSC 4AW1]
 gi|196028598|gb|EDX67205.1| conserved hypothetical protein [Bacillus cereus NVH0597-99]
 gi|228823377|gb|EEM69210.1| hypothetical protein bthur0009_46990 [Bacillus thuringiensis
           serovar andalousiensis BGSC 4AW1]
          Length = 165

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDYISIC 164


>gi|116328224|ref|YP_797944.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116330948|ref|YP_800666.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116120968|gb|ABJ79011.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116124637|gb|ABJ75908.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 244

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 42/253 (16%), Positives = 83/253 (32%), Gaps = 56/253 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           +RL+R+  +     +    ++++  GQ+ ++ KRV     +I+ G  VV     +     
Sbjct: 13  IRLNRFLADCGLG-SRRKTEELILRGQITINGKRVTDLGTKIKPGSDVVSYLGNVVEPTR 71

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
             K                           +I + NKP G       G  +H      S 
Sbjct: 72  KPK---------------------------RILILNKPVGYLC--SHGDRFHEKTVF-SL 101

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           +    +  ++  RLD  + G+L++      AQ ++                         
Sbjct: 102 LPLTYKNFKIAGRLDLNSRGLLILTNDGELAQKISH--------------------PSNG 141

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYA--ISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
               +L+  +H  G+   +    +KG   A  I   K++     K C   +    G+  Q
Sbjct: 142 SEKEYLVTLNHDPGEK-WIQAAFQKGILDAGEILRAKMVKLVPGKNCVYRVILAEGKKRQ 200

Query: 255 LRVHALHMGCPIV 267
           +R      G  ++
Sbjct: 201 IRRMFHASGASVI 213


>gi|311113288|ref|YP_003984510.1| ribosomal RNA large subunit methyltransferase J [Rothia
          dentocariosa ATCC 17931]
 gi|310944782|gb|ADP41076.1| ribosomal RNA large subunit methyltransferase J [Rothia
          dentocariosa ATCC 17931]
          Length = 244

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
          MRLD++   H    +     K++ +G V V+ K V K +  +     V + 
Sbjct: 1  MRLDKFLAEHGLVASRTLAAKLIDAGCVSVNGKIVYKASQPVHRDDDVLVQ 51


>gi|260776566|ref|ZP_05885461.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260607789|gb|EEX34054.1| ribosomal large subunit pseudouridine synthase F [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 344

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/250 (12%), Positives = 72/250 (28%), Gaps = 55/250 (22%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
            ++  RL+++        +     +++  G+V ++ K  +   ++  G  V +       
Sbjct: 2   SQDAKRLNKFISET-GFCSRREADRLIEQGRVTINGKVPEMGTKVLPGDDVCV------- 53

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                               D      + +       NKP GI+      I  +I  F+ 
Sbjct: 54  --------------------DDKPISAVTDKPVYIALNKPTGITCTTERDIPGNIVDFI- 92

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
                  ++     RLD+ + G++ +         +  +      + +            
Sbjct: 93  ----GHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVR---------V 139

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + I    +KK   G D +       K +      F+++                G   Q
Sbjct: 140 DKPITEQFIKKMSSGVDILDTTTLPCKVSKETKFSFRIV-------------LTQGLNRQ 186

Query: 255 LRVHALHMGC 264
           +R     +G 
Sbjct: 187 IRRMCEALGY 196


>gi|260584747|ref|ZP_05852492.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           elegans ATCC 700633]
 gi|260157404|gb|EEW92475.1| ribosomal small subunit pseudouridine synthase A [Granulicatella
           elegans ATCC 700633]
          Length = 237

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 80/246 (32%), Gaps = 50/246 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL+     H+  I+   ++K++ SG+V +D               V            +
Sbjct: 1   MRLEHLLMKHF-DISRKQMKKLISSGEVLIDSTPAT---------HVSNNVDPQIQVITV 50

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  ++ D+S                     Y+ NKP G+           +    K+   
Sbjct: 51  QGSRMEDNSQK------------------YYLLNKPKGVITATTDSQLPTVIDLFKN--- 89

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
              +      RLD++T G+L++        + L        I+K Y+  V G        
Sbjct: 90  ENIEGLYPIGRLDRDTEGLLIITNNGPLGYRLLNPIQH---IEKEYYVEVNG-------- 138

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                L  S I   Y  ++  +      A     +++     F    +    G+ HQ++ 
Sbjct: 139 ----PLDNSCIQRFYDGIMFHDGTICKPA--KLSILESSPS-FSKATVTISEGKFHQIKK 191

Query: 258 HALHMG 263
             L +G
Sbjct: 192 MFLCVG 197


>gi|118480049|ref|YP_897200.1| hypothetical protein BALH_4497 [Bacillus thuringiensis str. Al
           Hakam]
 gi|196043994|ref|ZP_03111231.1| conserved hypothetical protein [Bacillus cereus 03BB108]
 gi|225866934|ref|YP_002752312.1| hypothetical protein BCA_5096 [Bacillus cereus 03BB102]
 gi|229187200|ref|ZP_04314345.1| hypothetical protein bcere0004_47360 [Bacillus cereus BGSC 6E1]
 gi|118419274|gb|ABK87693.1| conserved hypothetical protein [Bacillus thuringiensis str. Al
           Hakam]
 gi|196025330|gb|EDX64000.1| conserved hypothetical protein [Bacillus cereus 03BB108]
 gi|225789296|gb|ACO29513.1| conserved hypothetical protein [Bacillus cereus 03BB102]
 gi|228596210|gb|EEK53885.1| hypothetical protein bcere0004_47360 [Bacillus cereus BGSC 6E1]
          Length = 165

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDYISIC 164


>gi|325287412|ref|YP_004263202.1| pseudouridine synthase Rsu [Cellulophaga lytica DSM 7489]
 gi|324322866|gb|ADY30331.1| pseudouridine synthase Rsu [Cellulophaga lytica DSM 7489]
          Length = 245

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 79/250 (31%), Gaps = 58/250 (23%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           R++++      + +     K++  G+V ++ K  +   +I     VR+         +I 
Sbjct: 8   RINKYLSE-VGYCSRRAADKLIDQGRVTINGKIPEMGTKIIPTDEVRVD------GELIS 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E K                     ED     FNKP GI     + +    D  +     +
Sbjct: 61  ESK---------------------EDFVYLAFNKPVGIVCTTDTRVE--KDNIIDYI--N 95

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
             ++     RLD+ + G++ +                         +V  I + +     
Sbjct: 96  YPKRIFPIGRLDKPSEGLIFL--------------------TNDGDIVNKILRARNHHEK 135

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TGRTHQLRV 257
            +++K  +I  D       N       I+      C  +K    E +     G   Q+R 
Sbjct: 136 EYIVKVDNIITDDFVHQMSNGIPILDTITR----KCKVEKLSKYEFRIILTQGLNRQIRR 191

Query: 258 HALHMGCPIV 267
              ++G  +V
Sbjct: 192 MTEYLGYNVV 201


>gi|229060031|ref|ZP_04197402.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228719250|gb|EEL70858.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 227

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/248 (12%), Positives = 71/248 (28%), Gaps = 60/248 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++        +     K++   +V ++ K  K  +++  G  VR+           
Sbjct: 1   MRINKFISEAGK-ASRRGADKLINERKVIINGKVAKIGDQVNPGDDVRVNGEQLR----- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  +  D      NKP GI+      +  +I   +   + 
Sbjct: 55  -----------------------IARDHVYIALNKPVGITCTSEKAVKGNIIDLVNHPL- 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++++         +  +      + I                
Sbjct: 91  ----RINHIGRLDKDSDGLILLTNDGDIVNEILRAENKHEKEYIVS-------------- 132

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TGRTHQLR 256
                    I  +++  +    K     I   K + C   +    E +     G   Q+R
Sbjct: 133 -----VDKPITPEFLEKMAAGVK-----ILDTKTLPCEITQLSKYEFEIILTQGLNRQIR 182

Query: 257 VHALHMGC 264
                +G 
Sbjct: 183 RMCEALGY 190


>gi|229072456|ref|ZP_04205658.1| hypothetical protein bcere0025_46170 [Bacillus cereus F65185]
 gi|228710432|gb|EEL62405.1| hypothetical protein bcere0025_46170 [Bacillus cereus F65185]
          Length = 165

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDYISIC 164


>gi|330502861|ref|YP_004379730.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           mendocina NK-01]
 gi|328917147|gb|AEB57978.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           mendocina NK-01]
          Length = 385

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 26/178 (14%), Positives = 55/178 (30%), Gaps = 29/178 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              +L +         +   ++  +  G+V+V+        R+ +   + +         
Sbjct: 10  AGEKLQKVLAR-LGLASRREIETWIAEGRVKVNGAAATLGQRVDANDAIALD------GR 62

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           ++K ++I  S          ++ +L+Y        NKP G                    
Sbjct: 63  LLKREEITGS----------VRRVLIY--------NKPDGEIC--TRDDPEGRPTVFDRL 102

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
              K  +     RLD  T+G+L+       A  L       ++ + Y   V G    +
Sbjct: 103 PRPKEGRWINIGRLDINTTGLLLFTTDGELANRL--MHPSYQMDREYAVRVRGEVTEE 158


>gi|153854752|ref|ZP_01995986.1| hypothetical protein DORLON_01984 [Dorea longicatena DSM 13814]
 gi|149752659|gb|EDM62590.1| hypothetical protein DORLON_01984 [Dorea longicatena DSM 13814]
          Length = 85

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 27/55 (49%)

Query: 14 NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           + ++MRLD++ K            +   +G+V V+ K  K + +++ G ++ I 
Sbjct: 2  QENKDMRLDKFLKVSRLIKRRTVANEACDAGRVLVNDKPAKASVKVKPGDIIEIQ 56


>gi|110803415|ref|YP_699574.1| ribosomal large subunit pseudouridine synthase f [Clostridium
           perfringens SM101]
 gi|110683916|gb|ABG87286.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           SM101]
          Length = 298

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 40/259 (15%), Positives = 84/259 (32%), Gaps = 59/259 (22%)

Query: 9   YVVVENDEE---NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVV 65
            ++V N  E    +RL+++        +     K++  G+V++D  +     ++  GQ V
Sbjct: 47  TIIVSNKNEIRDEVRLNKYISET-GFCSRREADKLIEQGRVKIDGVKATTGMKVSKGQSV 105

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125
            I                             +++ L+Y      V NKP GI+    S I
Sbjct: 106 FIDGKPLK-----------------------VENELVY-----IVLNKPVGITCTTESKI 137

Query: 126 AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
             +I  F+        ++     RLD+++ G++ +         +  +      + I   
Sbjct: 138 KGNIVDFINH-----EKRIFPIGRLDKDSQGLIFMTNDGDIVNKILRAGNNHEKEYIV-- 190

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
                     + I +  +K    G   +  V +       + + F++I            
Sbjct: 191 -------TVNKPITDEFIKGMSNGVPILGTVTKKCLVKKESKNSFRII------------ 231

Query: 246 QPHTGRTHQLRVHALHMGC 264
               G   Q+R    + G 
Sbjct: 232 -LTQGLNRQIRRMCEYFGY 249


>gi|284007248|emb|CBA72545.1| ribosomal small subunit pseudouridine synthase A [Arsenophonus
           nasoniae]
          Length = 231

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 45/271 (16%), Positives = 89/271 (32%), Gaps = 59/271 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRLD++       I+   + + LR+G+V VD + +K  + +I    +V        L HI
Sbjct: 2   MRLDKFLSQQL-TISRGLVIRELRAGKVMVDNEIIKTGSYQITPEMIVS--YDGVVLQHI 58

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I  +                           ++ NKP G            ++  + S++
Sbjct: 59  IGPR--------------------------YFMLNKPQGYVC----STVDSVNLTILSFI 88

Query: 138 DSKGQ-KPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D     K  +  RLD +T+G++++    +   + ++      +   +  +         K
Sbjct: 89  DEPAITKLHIAGRLDIDTTGLVIITDDGKWTHKMISPKHHCEKTYLVTLAQPVSTELADK 148

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                WL  +           K   K A  +I   K +           +    GR HQ+
Sbjct: 149 FLAGIWLKGE-----------KLPTKPAKLSIVSSKQV----------RLTISEGRYHQV 187

Query: 256 RVHALHMGCPIVGDHKYCANFKGNFTSPIQN 286
           +     +G  +     +     G +  P   
Sbjct: 188 KRMFAAVGNHVC--ALHRERIGGIYLDPALR 216


>gi|229135792|ref|ZP_04264562.1| hypothetical protein bcere0014_46750 [Bacillus cereus BDRD-ST196]
 gi|228647658|gb|EEL03723.1| hypothetical protein bcere0014_46750 [Bacillus cereus BDRD-ST196]
          Length = 165

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RIDKVLSTYISDWSRTIIVDKIKNGAIQLNGQQMKPNKMLSEGDYISIC 164


>gi|83953590|ref|ZP_00962311.1| RNA pseudouridylate synthase [Sulfitobacter sp. NAS-14.1]
 gi|83841535|gb|EAP80704.1| RNA pseudouridylate synthase [Sulfitobacter sp. NAS-14.1]
          Length = 187

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 36/165 (21%), Positives = 66/165 (40%), Gaps = 10/165 (6%)

Query: 106 SKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           +++ +FNKP G+  Q    G        L +++D KG  P    RLD+++ G++V+  + 
Sbjct: 2   NRVILFNKPFGVLSQFTDKGTEGSPRPTLSAYIDEKGFYP--AGRLDRDSEGLMVLTDSG 59

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE--CIANWLLKKSHIGGDYVHVVKQNEKG 222
                ++      ++ K YW  V G P  +      +   LK          ++   +  
Sbjct: 60  PLQARIS--HPKYKLAKTYWVQVEGTPDEQALAALRSGVTLKDGKTAPARARLMDPPDPL 117

Query: 223 ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +       V    +    WLE+    GR  Q+R    H+G P +
Sbjct: 118 WDR---DPPVRFRKSVPDAWLEITITEGRNRQVRRMTAHVGLPTL 159


>gi|262369297|ref|ZP_06062625.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           johnsonii SH046]
 gi|262315365|gb|EEY96404.1| ribosomal large subunit pseudouridine synthase B [Acinetobacter
           johnsonii SH046]
          Length = 368

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 32/220 (14%), Positives = 68/220 (30%), Gaps = 31/220 (14%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   +++++ +G+V V+ +  +   RI+ G  +RI                    V+   
Sbjct: 16  SRRYMEEVIAAGRVSVNGQVAQVGERIEPGDELRIDGR----------------KVSFQI 59

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
             +  + +L+Y         KP G                          +  +  RLD 
Sbjct: 60  EDEIRRRVLIY--------YKPEGEIC--SRNDPESRPTVFDQLPAIANDRWVMVGRLDI 109

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            ++G+L+       A  L        +++ Y   V G    +   I N +LK   +    
Sbjct: 110 NSTGLLLFTNDGELANRL--MHPSNEVEREYAVRVMGEVTPQ---IKNNMLKGVVLDDGP 164

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                 +E G       ++V+    +      +    G  
Sbjct: 165 AKFESFSEIGGEGINRWYQVVVKEGRNREVRRIFESQGLK 204


>gi|289435619|ref|YP_003465491.1| ribosomal small subunit pseudouridine synthase A [Listeria
           seeligeri serovar 1/2b str. SLCC3954]
 gi|289171863|emb|CBH28409.1| ribosomal small subunit pseudouridine synthase A [Listeria
           seeligeri serovar 1/2b str. SLCC3954]
          Length = 233

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 83/246 (33%), Gaps = 53/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   +     +   ++ +L+SG V V+    K                 ++ + + 
Sbjct: 1   MRLDKLLSHTGFG-SRREVKPLLKSGSVVVNGVIQK-----------------DSKSQVN 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+  +    N           ++Y++   ++ +KP  +       ++  +   L    +
Sbjct: 43  PEKDQITVHGNP----------VIYQEFVYFMLHKPQNVVSATEDNLSETVIDLLAQ--E 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                P    RLD++T G+L++      A   L+     + I K Y++ + G        
Sbjct: 91  DTLTNPFPVGRLDKDTEGLLIITNDGTLAHNLLS---PKKHIDKTYYAKIEGDVTA---- 143

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                   + +      +   +      A  H +++     +    E     G+ HQ++ 
Sbjct: 144 --------TDVEAFRTGITLDDGYTCKPA--HLEIMAPNEIRVTIQE-----GKFHQVKR 188

Query: 258 HALHMG 263
                G
Sbjct: 189 MFAATG 194


>gi|270159867|ref|ZP_06188523.1| ribosomal large subunit pseudouridine synthase E [Legionella
           longbeachae D-4968]
 gi|289165378|ref|YP_003455516.1| 23S rRNA pseudouridine synthase [Legionella longbeachae NSW150]
 gi|269988206|gb|EEZ94461.1| ribosomal large subunit pseudouridine synthase E [Legionella
           longbeachae D-4968]
 gi|288858551|emb|CBJ12432.1| 23S rRNA pseudouridine synthase [Legionella longbeachae NSW150]
          Length = 183

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 39/160 (24%), Positives = 59/160 (36%), Gaps = 9/160 (5%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I +FNKP G+  Q       H    L +++D          RLD+ + G+L++  + A  
Sbjct: 4   IVLFNKPYGVVSQFSGEEHEH---TLAAFIDIPNFYA--AGRLDKNSEGLLLLTDSGALQ 58

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             LT     +R  K YW  V G P N+   I    L    I          +E       
Sbjct: 59  HRLTAPKFNKR--KYYWVQVEGTPCNQDLDILRNGLVLKDISFLPAGARLIDEPHLWPRN 116

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              +          WLE+    G+ HQ+R     +G P +
Sbjct: 117 PPIRF--RKNIPTSWLEIILSEGKNHQIRKMTAAIGFPTL 154


>gi|56750544|ref|YP_171245.1| ribosomal large subunit pseudouridine synthase B [Synechococcus
           elongatus PCC 6301]
 gi|81299819|ref|YP_400027.1| ribosomal large subunit pseudouridine synthase B [Synechococcus
           elongatus PCC 7942]
 gi|56685503|dbj|BAD78725.1| probable ribosomal large subunit pseudouridine synthase B
           [Synechococcus elongatus PCC 6301]
 gi|81168700|gb|ABB57040.1| ribosomal large subunit pseudouridine synthase B [Synechococcus
           elongatus PCC 7942]
          Length = 243

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 82/249 (32%), Gaps = 46/249 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++ ++ G+V ++ +                   I     + 
Sbjct: 3   ERLQKILS-QLGVASRRQAEQWIQQGRVTINGRVA----------------EIGQQADLK 45

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +++  LD      KH    + +LL+         KP G+               L     
Sbjct: 46  RDRIHLDGKRLRPKHRPEARYLLLH---------KPVGVVSTCRDPQRRRTVIDLVDPEF 96

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
             G  P    RLD ++SG+L++            S     I+K Y   V G P      +
Sbjct: 97  RPGLHP--VGRLDTDSSGLLLLCNDGEL--TYQISHPRFHIEKTYRVWVEGHPPAS--VL 150

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            +W        G ++   +    G        +++   A+    LE+  H GR  Q+R  
Sbjct: 151 EHW------RSGVWLDDYQTLPAG-------VRILHDRAES-TLLEVILHEGRNRQIRRV 196

Query: 259 ALHMGCPIV 267
           A  +G P++
Sbjct: 197 AEQLGHPVL 205


>gi|261210662|ref|ZP_05924954.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. RC341]
 gi|260840147|gb|EEX66727.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. RC341]
          Length = 319

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 48/294 (16%), Positives = 97/294 (32%), Gaps = 45/294 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   L+ ++R+G+V V+ K      R++    +VR+   + +   +  
Sbjct: 5   LQKVLARA-GHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNALVRVDGHVVS---VKA 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +++++                      ++  + KP G                       
Sbjct: 61  QEEVI---------------------CRVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K    
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGDVNEEKVRNL 155

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT-GRTHQLR 256
              ++       +  V+    +G N+  + + VI+     +     E Q  T  R  ++R
Sbjct: 156 VRGVQLEDGMARFEDVMYAGGEGINH--TFYVVINEGRNREVRRLWESQGTTVSRLKRVR 213

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                      GD              +  K   + R +    PE   +  TAP
Sbjct: 214 ----------YGDIFLDKKLPRGGWMELDLKQVNYLRELVELRPEKETVLNTAP 257


>gi|160931609|ref|ZP_02079004.1| hypothetical protein CLOLEP_00441 [Clostridium leptum DSM 753]
 gi|156869480|gb|EDO62852.1| hypothetical protein CLOLEP_00441 [Clostridium leptum DSM 753]
          Length = 242

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/249 (12%), Positives = 78/249 (31%), Gaps = 51/249 (20%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIPPVINAL 74
           ++ +RL +   +     +    +++++ G+V+V+    +  +++      V +     A 
Sbjct: 3   DQKIRLQKMLAD-CGVASRRKAEELIQQGKVKVNGHVAQIGDKVNPKTDHVTV-----AG 56

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             I+  ++                           + +KP G        +       + 
Sbjct: 57  RRIVASRQY-----------------------YYIMLHKPRGYVSTMSDEMGRKC---VA 90

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
             V     +     RLD+++ G+L++      A  +    +              +PK  
Sbjct: 91  ELVKDIPARVYPVGRLDRDSEGLLLMTNDGEFANLIMHPSKH-------------VPKTY 137

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
           +  +   + ++       +  V     G   A +   VI     +    E+    GR  Q
Sbjct: 138 RVTVRPDISEEQLA----LMNVGMEIDGVRTAPADAWVISREPGRVVL-EIILREGRNRQ 192

Query: 255 LRVHALHMG 263
           +R     +G
Sbjct: 193 IRKMCEQLG 201


>gi|78066108|ref|YP_368877.1| ribosomal large subunit pseudouridine synthase B [Burkholderia sp.
           383]
 gi|77966853|gb|ABB08233.1| ribosomal large subunit pseudouridine synthase B [Burkholderia sp.
           383]
          Length = 588

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 38/254 (14%), Positives = 75/254 (29%), Gaps = 48/254 (18%)

Query: 11  VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           V+  D++  +L +         +   +++++ +G+V V+ +      RI     VRI   
Sbjct: 178 VLSPDDDAPKLHKVLAEAGMG-SRREMEELIVAGRVSVNGEPAHIGQRIMPTDQVRINGK 236

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHI 129
                   K  ++L                 LY        +KP G I            
Sbjct: 237 PVKRKLPNKPPRVL-----------------LY--------HKPTGEIVSHADPEGRP-- 269

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
                     K  K     RLD  T G+L++  +   A           +++ Y   V G
Sbjct: 270 -SVFDRLPPMKTAKWLAVGRLDFNTEGLLMLTTSGDLANRF--MHPRYSVEREYAVRVVG 326

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
                        ++      +++ +     +G N+                W  +    
Sbjct: 327 ELAEGMRQKLLHGVELDDGPANFLRIRDGGGEGTNH----------------WYHVALAE 370

Query: 250 GRTHQLRVHALHMG 263
           GR  ++R     +G
Sbjct: 371 GRNREVRRMFEAVG 384


>gi|88859932|ref|ZP_01134571.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
 gi|88817926|gb|EAR27742.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
          Length = 293

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/230 (13%), Positives = 72/230 (31%), Gaps = 32/230 (13%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +         +   ++K + + +V VD    +  +R++  Q++R+   I         
Sbjct: 5   LQKVLARAGKG-SRREIEKFIEAHRVSVDGNVARLGDRVEPHQLIRLDGHI--------- 54

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
                  V + +  + +  +L+Y        +KP G                    +   
Sbjct: 55  -------VKIEEPEERVCRVLMY--------HKPEGELC--TRKDPEGRPTVFDRLMRLD 97

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
             +     RLD  TSG+L+       A  L        +++ Y   V+G    +      
Sbjct: 98  DDRWIAVGRLDVNTSGLLLFTNDGELANRL--MHPRYEVEREYAVRVFGEVTTETLKTLT 155

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             ++       ++ ++    +G N     + V+    +      +    G
Sbjct: 156 KGVELEDGPAKFLKIMPHGGEGINK---WYNVLLTEGRNREVRRLWQSQG 202


>gi|15612417|ref|NP_224070.1| hypothetical protein jhp1352 [Helicobacter pylori J99]
 gi|11136000|sp|Q9ZJG0|YE59_HELPJ RecName: Full=Uncharacterized RNA pseudouridine synthase jhp_1352;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|4155973|gb|AAD06937.1| putative [Helicobacter pylori J99]
          Length = 262

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/175 (15%), Positives = 64/175 (36%), Gaps = 30/175 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R++++   HY   +    +K++  G+V+++ +  K  + ++    V +      L   +
Sbjct: 6   LRINQFLA-HYTKHSRREAEKLVLEGRVKINHEHAKLASVVKENDKVFLD---KRLIKPL 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K +K                         + V++KP G  V     +  H    +   ++
Sbjct: 62  KNKKFS-----------------------VLVYHKPKGELVSKADPLKRH---VIYESLE 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            K        RLD  + G+L+++ ++A    L  +   +         V    +N
Sbjct: 96  KKYAHFAPVGRLDFASEGVLLLSDSKAVVSALMHANLEKEYLVKIQGFVTREMEN 150


>gi|308187008|ref|YP_003931139.1| ribosomal large subunit pseudouridine synthase B [Pantoea vagans
           C9-1]
 gi|308057518|gb|ADO09690.1| ribosomal large subunit pseudouridine synthase B [Pantoea vagans
           C9-1]
          Length = 296

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 28/175 (16%), Positives = 61/175 (34%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ ++ +G+V VD K     +R++S + ++I    + ++     
Sbjct: 5   LQKVLARA-GHGSRREIESMIAAGRVSVDGKIATLGDRVESSKSLKIRIDGHLVS----- 58

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             I +S+  + +               +  + KP G                       +
Sbjct: 59  --IAESATEVCR---------------VLAYYKPEGELC--TRSDPEGRPTVFDRLPRLR 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  T G+++       A  L      R +++ Y   V+G   + K
Sbjct: 100 GSRWIAVGRLDVNTCGLMLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDDK 152


>gi|262165448|ref|ZP_06033185.1| ribosomal large subunit pseudouridine synthase B [Vibrio mimicus
           VM223]
 gi|262402464|ref|ZP_06079025.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. RC586]
 gi|262025164|gb|EEY43832.1| ribosomal large subunit pseudouridine synthase B [Vibrio mimicus
           VM223]
 gi|262351246|gb|EEZ00379.1| ribosomal large subunit pseudouridine synthase B [Vibrio sp. RC586]
          Length = 319

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 48/294 (16%), Positives = 97/294 (32%), Gaps = 45/294 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   L+ ++R+G+V V+ K      R++    +VR+   + +   +  
Sbjct: 5   LQKVLARA-GHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNALVRVDGHVVS---VKA 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +++++                      ++  + KP G                       
Sbjct: 61  QEEVI---------------------CRVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K    
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGDVNEEKVRNL 155

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT-GRTHQLR 256
              ++       +  V+    +G N+  + + VI+     +     E Q  T  R  ++R
Sbjct: 156 VRGVQLEDGMARFEDVMYAGGEGINH--TFYVVINEGRNREVRRLWESQGTTVSRLKRVR 213

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                      GD              +  K   + R +    PE   +  TAP
Sbjct: 214 ----------YGDIFLDKKLPRGGWMELDLKQVNYLRELVELRPEKETVLNTAP 257


>gi|163803577|ref|ZP_02197444.1| pseudouridine synthase family 1 protein [Vibrio sp. AND4]
 gi|159172619|gb|EDP57476.1| pseudouridine synthase family 1 protein [Vibrio sp. AND4]
          Length = 383

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 72/246 (29%), Gaps = 56/246 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL+++        +     +++  G+V ++ ++ +   ++Q G  V +     A     
Sbjct: 7   KRLNKFISET-GFCSRREADRLIEQGRVTINGQQPEMGTKVQPGDDVCVDGNPVA----A 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           KE+ I                            NKP GI+      I  +I  F+     
Sbjct: 62  KEKPI------------------------YIALNKPTGITCTTERDIPGNIVDFI----- 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD+ + G++ +         +  +      + +                
Sbjct: 93  GHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVV--------------- 137

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                    I G+++  +    K  +      KV     +      +    G   Q+R  
Sbjct: 138 ----RVDKPITGEFLKQMSSGVKILDTVTLPCKVEK---ETKFSFRIVLTQGLNRQIRRM 190

Query: 259 ALHMGC 264
              +G 
Sbjct: 191 CEALGY 196


>gi|304396082|ref|ZP_07377964.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304356451|gb|EFM20816.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 296

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 28/175 (16%), Positives = 61/175 (34%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ ++ +G+V VD K     +R++S + ++I    + ++     
Sbjct: 5   LQKVLARA-GHGSRREIESMIAAGRVSVDGKIATLGDRVESSKSLKIRIDGHLVS----- 58

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             I +S+  + +               +  + KP G                       +
Sbjct: 59  --IAESATEVCR---------------VLAYYKPEGELC--TRSDPEGRPTVFDRLPRLR 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  T G+++       A  L      R +++ Y   V+G   + K
Sbjct: 100 GSRWIAVGRLDVNTCGLMLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDDK 152


>gi|258621657|ref|ZP_05716688.1| pseudouridine synthase family 1 protein [Vibrio mimicus VM573]
 gi|258626398|ref|ZP_05721245.1| pseudouridine synthase family 1 protein [Vibrio mimicus VM603]
 gi|258581450|gb|EEW06352.1| pseudouridine synthase family 1 protein [Vibrio mimicus VM603]
 gi|258585888|gb|EEW10606.1| pseudouridine synthase family 1 protein [Vibrio mimicus VM573]
          Length = 319

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 48/294 (16%), Positives = 97/294 (32%), Gaps = 45/294 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   L+ ++R+G+V V+ K      R++    +VR+   + +   +  
Sbjct: 5   LQKVLARA-GHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNALVRVDGHVVS---VKA 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +++++                      ++  + KP G                       
Sbjct: 61  QEEVI---------------------CRVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K    
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGDVNEEKVRNL 155

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT-GRTHQLR 256
              ++       +  V+    +G N+  + + VI+     +     E Q  T  R  ++R
Sbjct: 156 VRGVQLEDGMARFEDVMYAGGEGINH--TFYVVINEGRNREVRRLWESQGTTVSRLKRVR 213

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                      GD              +  K   + R +    PE   +  TAP
Sbjct: 214 ----------YGDIFLDKKLPRGGWMELDLKQVNYLRELVELRPEKETVLNTAP 257


>gi|213618826|ref|ZP_03372652.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 276

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 20/150 (13%), Positives = 48/150 (32%), Gaps = 31/150 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +     + +  G V ++ KR    +++ +G VV++   +                     
Sbjct: 7   SRREADRFIEQGNVFINGKRAAIGDQVVAGDVVKVNGRLIEPREA--------------- 51

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                      +D  +   NKP GI      G   +I  F+        ++     RLD+
Sbjct: 52  -----------DDLVLIALNKPVGIVSTTEDGERDNIVDFVNH-----SKRIFPIGRLDK 95

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           ++ G++ +         +  +      + +
Sbjct: 96  DSQGLIFLTNHGDLVNKILRAGNDHEKEYL 125


>gi|304409066|ref|ZP_07390687.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307303069|ref|ZP_07582824.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304352887|gb|EFM17284.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306913429|gb|EFN43851.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 282

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 37/162 (22%), Positives = 60/162 (37%), Gaps = 13/162 (8%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I +FNKP  +  Q            LK ++           RLD+++ G+L++       
Sbjct: 103 IVLFNKPFDVLCQ---FTDEQGRKTLKDYIPI--ADVYAAGRLDRDSEGLLLLTNDGQLQ 157

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANY 225
             LTE    ++  K YW  V G+P           ++          V ++   + G   
Sbjct: 158 ARLTE--PKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSPDIGPRN 215

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                 V +       WLE+Q H GR  Q+R    H+G P +
Sbjct: 216 P----PVRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTL 253


>gi|229823649|ref|ZP_04449718.1| hypothetical protein GCWU000282_00950 [Catonella morbi ATCC 51271]
 gi|229786886|gb|EEP23000.1| hypothetical protein GCWU000282_00950 [Catonella morbi ATCC 51271]
          Length = 238

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 77/248 (31%), Gaps = 53/248 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD+         +   ++++L+S QV+VD +  +  N  +  G Q +++   I     
Sbjct: 1   MRLDQVMNQAGLG-SRNQVKRLLKSCQVQVDGQVERRPNRNVDPGLQEIKVQGRILTQPA 59

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                           ++ +KP G+           +   L   
Sbjct: 60  -----------------------------ETYWLLHKPQGVLTAVTDDRFTTVIDCLA-- 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
              +        RLD+ T+G++ +        + L   +               + K  +
Sbjct: 89  PQDQAPGLYPVGRLDRSTTGLVFLTTNGPLGYRMLHPQYH--------------VEKEYQ 134

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             +   L +          ++ QN   A   +    VI+    +     +    G+ HQ+
Sbjct: 135 VVVNGPLTQDHVASFAQGILIDQNRPCAPAHL----VIEASGPQESRARLTIREGKFHQV 190

Query: 256 RVHALHMG 263
           +   L +G
Sbjct: 191 KKMFLSVG 198


>gi|196033136|ref|ZP_03100549.1| conserved hypothetical protein [Bacillus cereus W]
 gi|218906156|ref|YP_002453990.1| hypothetical protein BCAH820_5068 [Bacillus cereus AH820]
 gi|228929988|ref|ZP_04092999.1| hypothetical protein bthur0010_46700 [Bacillus thuringiensis
           serovar pondicheriensis BGSC 4BA1]
 gi|228948687|ref|ZP_04110965.1| hypothetical protein bthur0007_48110 [Bacillus thuringiensis
           serovar monterrey BGSC 4AJ1]
 gi|229124500|ref|ZP_04253685.1| hypothetical protein bcere0016_47840 [Bacillus cereus 95/8201]
 gi|195994565|gb|EDX58520.1| conserved hypothetical protein [Bacillus cereus W]
 gi|218534831|gb|ACK87229.1| conserved hypothetical protein [Bacillus cereus AH820]
 gi|228658840|gb|EEL14495.1| hypothetical protein bcere0016_47840 [Bacillus cereus 95/8201]
 gi|228810994|gb|EEM57337.1| hypothetical protein bthur0007_48110 [Bacillus thuringiensis
           serovar monterrey BGSC 4AJ1]
 gi|228829668|gb|EEM75294.1| hypothetical protein bthur0010_46700 [Bacillus thuringiensis
           serovar pondicheriensis BGSC 4BA1]
          Length = 165

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDYISIC 164


>gi|306827091|ref|ZP_07460388.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes ATCC 10782]
 gi|304430725|gb|EFM33737.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes ATCC 10782]
          Length = 238

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 26/179 (14%), Positives = 55/179 (30%), Gaps = 38/179 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD+         +   ++K++++  V VD    +     +  G Q++ +         
Sbjct: 1   MRLDKLL-EGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQ------ 53

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   + +      + NKP+G+           +   L   
Sbjct: 54  -----------------------QVTHPKHSYIILNKPSGVVSAKKDTNYLTVIDQLAE- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            + K        RLD++T G++++        + L        + K Y   V G+    
Sbjct: 90  -EDKSPDLYPVGRLDRDTEGLVLLTDNGPLGFRMLH---PSHHVSKTYLVTVNGLLAED 144


>gi|217973052|ref|YP_002357803.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217498187|gb|ACK46380.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 282

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 37/162 (22%), Positives = 60/162 (37%), Gaps = 13/162 (8%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I +FNKP  +  Q            LK ++           RLD+++ G+L++       
Sbjct: 103 IVLFNKPFDVLCQ---FTDEQGRKTLKDYIPI--ADVYAAGRLDRDSEGLLLLTNDGQLQ 157

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLK--KSHIGGDYVHVVKQNEKGANY 225
             LTE    ++  K YW  V G+P           ++          V ++   + G   
Sbjct: 158 ARLTE--PKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSPDIGPRN 215

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                 V +       WLE+Q H GR  Q+R    H+G P +
Sbjct: 216 P----PVRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTL 253


>gi|332307254|ref|YP_004435105.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332174583|gb|AEE23837.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 289

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/162 (16%), Positives = 54/162 (33%), Gaps = 29/162 (17%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++K + SG++ V+ K     +R++    +R+                 D ++  + 
Sbjct: 16  SRREMEKWIASGRISVNGKVATLGDRVEPVDQLRV-----------------DGNLITSA 58

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
               +  +L+Y        NKP G                       +  +     RLD 
Sbjct: 59  AKSTMCRVLMY--------NKPEGELC--SRKDPQGRPTVFDRLPKIQNGRWIAVGRLDI 108

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            TSG+L+       A  L        I++ Y   V+G  ++ 
Sbjct: 109 NTSGLLLFTNDGELANRL--MHPKHEIEREYAVRVFGEVEDD 148


>gi|323466661|gb|ADX70348.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 216

 Score = 53.4 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 37/226 (16%), Positives = 73/226 (32%), Gaps = 49/226 (21%)

Query: 40  ILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKS 99
           ++ +G+V+VD K V      + G  V     I   +  I+ + +                
Sbjct: 1   MIVAGRVKVDGKVVT-----KLGTKVETFSNITVDDEPIERESL---------------- 39

Query: 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
                    Y+F KP G+               +  + +    +     RLD +TSG+L+
Sbjct: 40  -------HTYLFYKPRGVVSTADDDKGR---KTVVDYFEDVPCRLYPVGRLDYDTSGLLL 89

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
           +      A  L        + K+Y + + GI    +       +K               
Sbjct: 90  MTNDGKLANLL--MHPRNEVSKVYVAKIKGILTPDEIKTLTTGVKLDRF----------- 136

Query: 220 EKGANYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGC 264
                 A +  K++    +K    +++  H G  HQ++     +G 
Sbjct: 137 ----KAAPAKVKILKTDKRKDTQIIQLTIHEGHYHQVKRMFKAVGH 178


>gi|268591199|ref|ZP_06125420.1| ribosomal small subunit pseudouridine synthase A [Providencia
           rettgeri DSM 1131]
 gi|291313360|gb|EFE53813.1| ribosomal small subunit pseudouridine synthase A [Providencia
           rettgeri DSM 1131]
          Length = 235

 Score = 53.4 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 74/250 (29%), Gaps = 51/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + LR+G V VD + VK          V I   +    +++
Sbjct: 1   MRLDKFLSQQL-GISRSLVARELRAGLVTVDDEIVKSGAF-----QVTIDHEVAYDGNVL 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                              +  +L++                            L    +
Sbjct: 55  -------------VQVTGPRYFMLHKPQGYICSTDD---PTHPT---------ILFFIDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              QK     RLD +T+G++++           +     RI                + I
Sbjct: 90  PLAQKLHSAGRLDIDTTGLVLLT---------DDGQWSHRITSPKHHCEKTYRVQLSDDI 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           AN       +   +   V  N +      +  ++I     +    E     GR HQ++  
Sbjct: 141 AN------DVAEQFAQGVMLNGEKYLTKPAKLEIISPRDVRLTISE-----GRYHQVKRM 189

Query: 259 ALHMGCPIVG 268
              +G  + G
Sbjct: 190 FAAVGNHVCG 199


>gi|228917590|ref|ZP_04081134.1| hypothetical protein bthur0012_47960 [Bacillus thuringiensis
           serovar pulsiensis BGSC 4CC1]
 gi|228842070|gb|EEM87173.1| hypothetical protein bthur0012_47960 [Bacillus thuringiensis
           serovar pulsiensis BGSC 4CC1]
          Length = 165

 Score = 53.4 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDYISIC 164


>gi|291544370|emb|CBL17479.1| ribosomal large subunit pseudouridine synthase B [Ruminococcus sp.
           18P13]
          Length = 242

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 79/247 (31%), Gaps = 48/247 (19%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E  R+ +   +   + +    +  + +GQV+ + + VK  ++  S  ++ +     A+  
Sbjct: 2   EKTRIQKIIADS-GYCSRRKAESFIAAGQVKCNGRPVKLGDKAGSRDLITVNGERIAIPK 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
             K+QK+                          + NKP G        +       +   
Sbjct: 61  --KKQKL------------------------YLMLNKPRGYVTTMSDELDRRC---VMDL 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           ++   ++     RLD+ + G+L++      A   +     R + K Y   V     +++ 
Sbjct: 92  LEDVPERVYPVGRLDRNSEGLLLLTNDGDFAN--SIMHPSRHVSKTYRVTVRPDITDQQL 149

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                              V+ + K    A     V+     +   L +    GR  Q+R
Sbjct: 150 V-------------QLSEGVEIDGKPTLPAT--VNVLTKEPGRVVLL-ITIREGRNRQIR 193

Query: 257 VHALHMG 263
                +G
Sbjct: 194 RMCEAVG 200


>gi|262171789|ref|ZP_06039467.1| ribosomal large subunit pseudouridine synthase B [Vibrio mimicus
           MB-451]
 gi|261892865|gb|EEY38851.1| ribosomal large subunit pseudouridine synthase B [Vibrio mimicus
           MB-451]
          Length = 319

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 48/294 (16%), Positives = 97/294 (32%), Gaps = 45/294 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ-SGQVVRIPPVINALNHIIK 79
           L +       H +   L+ ++R+G+V V+ K      R++    +VR+   + +   +  
Sbjct: 5   LQKVLARA-GHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNALVRVDGHVVS---VKA 60

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           +++++                      ++  + KP G                       
Sbjct: 61  QEEVI---------------------CRVLAYYKPEGELC--TRHDPEGRRTVFDRLPKI 97

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           +G +     RLD  TSG+L+       A  L      R++++ Y   V+G    +K    
Sbjct: 98  RGSRWISVGRLDANTSGLLLFTTDGELANRL--MHPSRQVEREYLVRVFGDVNEEKVRNL 155

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVID--CFAQKFCWLEMQPHT-GRTHQLR 256
              ++       +  V+    +G N+  + + VI+     +     E Q  T  R  ++R
Sbjct: 156 VRGVQLEDGMARFEDVMYAGGEGINH--TFYVVINEGRNREVRRLWESQGTTVSRLKRVR 213

Query: 257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP 310
                      GD              +  K   + R +    PE   +  TAP
Sbjct: 214 ----------YGDIFLDKKLPRGGWMELDLKQVNYLRELVELRPEKETVLNTAP 257


>gi|50914459|ref|YP_060431.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10394]
 gi|50903533|gb|AAT87248.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10394]
          Length = 238

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 26/179 (14%), Positives = 55/179 (30%), Gaps = 38/179 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD+         +   ++K++++  V VD    +     +  G Q++ +         
Sbjct: 1   MRLDKLL-EGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQR----- 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   + +      + NKP+G+           +   L   
Sbjct: 55  ------------------------VTHPKHSYIILNKPSGVVSAKKDTNYLTVIDQLAE- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            + K        RLD++T G++++        + L        + K Y   V G+    
Sbjct: 90  -EDKSPDLYPVGRLDRDTEGLVLLTDNGPLGFRMLH---PSHHVSKTYLVTVNGLLAED 144


>gi|56412865|ref|YP_149940.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|168261760|ref|ZP_02683733.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|197361796|ref|YP_002141432.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|56127122|gb|AAV76628.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. ATCC 9150]
 gi|197093272|emb|CAR58718.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. AKU_12601]
 gi|205349524|gb|EDZ36155.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
          Length = 231

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 35/253 (13%), Positives = 75/253 (29%), Gaps = 59/253 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD            G +++     NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVD------------GDIIK-----NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHAVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYA----ISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + +   +         +   +     A    I+  +V            +    GR HQ
Sbjct: 137 ESPVADDTAAQFAKGVQLHNEKDLTKPATLEVITPVQV-----------RLTISEGRYHQ 185

Query: 255 LRVHALHMGCPIV 267
           ++     +G  +V
Sbjct: 186 VKRMFAAVGNHVV 198


>gi|301056451|ref|YP_003794662.1| hypothetical protein BACI_c49690 [Bacillus anthracis CI]
 gi|300378620|gb|ADK07524.1| conserved hypothetical protein [Bacillus cereus biovar anthracis
           str. CI]
          Length = 165

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDYISIC 164


>gi|22536965|ref|NP_687816.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae 2603V/R]
 gi|22533819|gb|AAM99688.1|AE014228_9 ribosomal small subunit pseudouridine synthase A, putative
           [Streptococcus agalactiae 2603V/R]
          Length = 239

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 47/246 (19%), Positives = 79/246 (32%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +   ++K++ S QV VD + V                         
Sbjct: 1   MRLDKLLGQAGFG-SRNQVKKLICSRQVSVDGQIVT------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K+  I+DS +         K  +  ++S  Y+  KP+G+        + H          
Sbjct: 36  KDNVIVDSGLQSIFVG---KERVCLKESSYYLLYKPSGVVS--AVRDSEHKTVIDLISEK 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K +      RLD++T G+L+V        + L        + K Y+  V G        
Sbjct: 91  DKVEGLYPIGRLDRDTEGLLIVTNNGPLGYRMLH---PKHHVAKTYYVEVNGF------- 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                L++  I      VV  +      A      ID          +    G+ HQ++ 
Sbjct: 141 -----LERDAITFFEEGVVFDDGTKCKPAEL---TIDTANNDKSTARITITEGKFHQVKK 192

Query: 258 HALHMG 263
             L  G
Sbjct: 193 MFLAYG 198


>gi|51892979|ref|YP_075670.1| putative rRNA methylase [Symbiobacterium thermophilum IAM 14863]
 gi|51856668|dbj|BAD40826.1| putative rRNA methylase [Symbiobacterium thermophilum IAM 14863]
          Length = 257

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 5/55 (9%)

Query: 17 ENMRLDRWF--KNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68
             RLD     + H+P  +    Q+ + +G VRV+ + + K   ++  G  + + 
Sbjct: 2  AGERLDVALVSRGHFP--SRERAQEAIAAGMVRVNGRVITKPARKVDPGDAIEVT 54


>gi|76787803|ref|YP_329548.1| RNA pseudouridine synthase family protein [Streptococcus agalactiae
           A909]
 gi|77406572|ref|ZP_00783621.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae H36B]
 gi|77411336|ref|ZP_00787684.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae CJB111]
 gi|76562860|gb|ABA45444.1| RNA pseudouridine synthase family protein [Streptococcus agalactiae
           A909]
 gi|77162596|gb|EAO73559.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae CJB111]
 gi|77174825|gb|EAO77645.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae H36B]
          Length = 239

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 79/246 (32%), Gaps = 49/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+         +   ++K++ S QV VD + V                         
Sbjct: 1   MRLDKLLGQAGFG-SRNQVKKLICSRQVSVDGQIVT------------------------ 35

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K+  I+DS +         K  +  ++S  Y+  KP+G+        + H          
Sbjct: 36  KDNVIVDSGLQSIFVG---KERVCLKESSYYLLYKPSGVVS--AVRDSEHKTVIDLISEK 90

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            K +      RLD++T G+L++        + L        + K Y+  V G        
Sbjct: 91  DKVEGLYPIGRLDRDTEGLLIITNNGPLGYRMLH---PKHHVAKTYYVEVNGF------- 140

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
                L++  I      VV  +      A      ID          +    G+ HQ++ 
Sbjct: 141 -----LERDAITFFEEGVVFDDGTKCKPAEL---TIDTANNDKSTARITITEGKFHQVKK 192

Query: 258 HALHMG 263
             L  G
Sbjct: 193 MFLAYG 198


>gi|253688026|ref|YP_003017216.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251754604|gb|ACT12680.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 231

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 34/249 (13%), Positives = 71/249 (28%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       I+   + + L + +V VD + VK                      + 
Sbjct: 1   MRLDKFLSQQL-EISRSLVARELHAQRVTVDGEVVKS-----------------GAFKLS 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L + +            + ++ NKP G      S         L     
Sbjct: 43  PEHNVEFDGNPLKQQNGP----------RYFMLNKPQGYVC---STDDPDHPTILYFMDV 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLLTDDGKWSHRITSPKHQCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              L + +         +   +     A      ++        + +    GR HQ++  
Sbjct: 137 EQPLAEDTAAQFTAGVQLHNEKNLTKPA-----TLEKITDHV--VRLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNRVV 198


>gi|229094067|ref|ZP_04225151.1| hypothetical protein bcere0021_47820 [Bacillus cereus Rock3-42]
 gi|228689279|gb|EEL43098.1| hypothetical protein bcere0021_47820 [Bacillus cereus Rock3-42]
          Length = 165

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RMDKALSTYISDWSRTLIVDKIKNGDIQLNGQQMKPNTILSEGDYISIC 164


>gi|94990717|ref|YP_598817.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10270]
 gi|94544225|gb|ABF34273.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10270]
          Length = 238

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 26/179 (14%), Positives = 55/179 (30%), Gaps = 38/179 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD+         +   ++K++++  V VD    +     +  G Q++ +         
Sbjct: 1   MRLDKLL-EGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQ------ 53

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   + +      + NKP+G+           +   L   
Sbjct: 54  -----------------------QVTHPKHSYIILNKPSGVVSAKKDTNYLTVIDQLAE- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            + K        RLD++T G++++        + L        + K Y   V G+    
Sbjct: 90  -EDKSPDLYPVGRLDRDTEGLVLLTDNGPLGFRMLH---PSHHVSKTYLVTVNGLLAED 144


>gi|317051704|ref|YP_004112820.1| pseudouridine synthase [Desulfurispirillum indicum S5]
 gi|316946788|gb|ADU66264.1| pseudouridine synthase [Desulfurispirillum indicum S5]
          Length = 251

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 36/244 (14%), Positives = 70/244 (28%), Gaps = 44/244 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL +         +    ++ +R G+V V+ K V                         
Sbjct: 3   MRLQKILAQA-GVASRRKAEEYIRQGRVMVNGKVVT------------------------ 37

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             +    +  +    +   K I ++ +    + +KP G                +   + 
Sbjct: 38  --ELGTQADPDEDFVAVDGKRIQIFHNHAYIILHKPTGYITSRSDDKER---PVVMDLLP 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
           +  +      RLD +TSG+L++      A  LT        +     L   +     +  
Sbjct: 93  NIREPLIPVGRLDWDTSGLLLLTNDGDLAYVLTHP-AFHVAKTYLVRLDKPMTAEHMQVF 151

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
              +L +   G      V++   G   A               W E+    GR  Q+R  
Sbjct: 152 EKGILLED--GKTKPARVRRVNTGKQTAT-----------PNLWYEVTITEGRNRQIRKM 198

Query: 259 ALHM 262
              +
Sbjct: 199 FEAL 202


>gi|294874652|ref|XP_002767033.1| hypothetical protein Pmar_PMAR027662 [Perkinsus marinus ATCC 50983]
 gi|239868460|gb|EEQ99750.1| hypothetical protein Pmar_PMAR027662 [Perkinsus marinus ATCC 50983]
          Length = 122

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 40/86 (46%)

Query: 129 IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
           ++  L   +   G    + HRLD++TSG +++AR   + + +   F+  ++ K Y  LV 
Sbjct: 37  MNEELNPALSGGGGFGPMCHRLDKQTSGPVLIARKLESWKFIRRQFQKEQVTKRYVCLVD 96

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVH 214
           GI  N    I + +  +     ++  
Sbjct: 97  GICANDSGMIDSPIRVRRTEKREFHR 122


>gi|229133216|ref|ZP_04262048.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
 gi|229167200|ref|ZP_04294941.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228616238|gb|EEK73322.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228650235|gb|EEL06238.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
          Length = 238

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 72/249 (28%), Gaps = 60/249 (24%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N+R++++        +     K++   +V ++ K  K  +++  G  VR+          
Sbjct: 3   NLRINKFISEAGK-ASRRGADKLINERKVIINGKVAKIGDQVNPGDDVRVNGEQLR---- 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                   +  D      NKP GI+      +  +I   +   +
Sbjct: 58  ------------------------IARDHVYIALNKPVGITCTSEKAVKGNIIDLVNHPL 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD+++ G++++         +  +      + I               
Sbjct: 94  -----RINHIGRLDKDSDGLILLTNDGDIVNEILRAENKHEKEYIVS------------- 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TGRTHQL 255
                     I  +++  +    K     I   K + C   +    E Q     G   Q+
Sbjct: 136 ------VDKPITPEFLEKMAAGVK-----ILDTKTLPCEVTQLSKYEFQIILTQGLNRQI 184

Query: 256 RVHALHMGC 264
           R     +G 
Sbjct: 185 RRMCEALGY 193


>gi|332288598|ref|YP_004419450.1| 23S rRNA pseudouridine synthase E [Gallibacterium anatis UMN179]
 gi|330431494|gb|AEC16553.1| 23S rRNA pseudouridine synthase E [Gallibacterium anatis UMN179]
          Length = 223

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 37/160 (23%), Positives = 62/160 (38%), Gaps = 8/160 (5%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + +FNKP  +  Q            LK+++      P    RLD+++ G+L++       
Sbjct: 28  VVLFNKPYDVLTQ---FTDEQGRKTLKNFIHIPDIYP--CGRLDRDSEGLLLLTNCGEIQ 82

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             LT      + +K YW  V G+P  +++  A         G     +VK      N   
Sbjct: 83  HRLT--TPAFKSKKTYWVQVEGVPS-EQDLEALRQGVILKDGKTLPALVKFIPPPQNLWQ 139

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
               + +       WLE+  H GR  Q+R    H+G P +
Sbjct: 140 RDPPIRERKTIPTSWLEIAIHEGRNRQVRRMTAHIGYPTL 179


>gi|288560866|ref|YP_003424352.1| rRNA methylase [Methanobrevibacter ruminantium M1]
 gi|288543576|gb|ADC47460.1| rRNA methylase [Methanobrevibacter ruminantium M1]
          Length = 264

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67
           RLD++  N+    +    +++++S  V+V+ K + K +  ++ G  V I
Sbjct: 3  ERLDKYLVNNNLIASRTKSKEMIKSKNVKVNDKIITKASYTVRDGDKVEI 52


>gi|163942681|ref|YP_001647565.1| RNA-binding S4 domain-containing protein [Bacillus
           weihenstephanensis KBAB4]
 gi|163864878|gb|ABY45937.1| RNA-binding S4 domain protein [Bacillus weihenstephanensis KBAB4]
          Length = 165

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   +++G ++++ +++K N  +  G  + I 
Sbjct: 116 RIDKVLSTYISDWSRTIIVDKIKNGAIQLNGQQMKPNKMLSEGDYISIC 164


>gi|303228803|ref|ZP_07315617.1| putative 16S pseudouridylate 516 synthase [Veillonella atypica
           ACS-134-V-Col7a]
 gi|303232129|ref|ZP_07318832.1| putative 16S pseudouridylate 516 synthase [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302513235|gb|EFL55274.1| putative 16S pseudouridylate 516 synthase [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302516515|gb|EFL58443.1| putative 16S pseudouridylate 516 synthase [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 232

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 31/187 (16%), Positives = 64/187 (34%), Gaps = 35/187 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD+   N     +   + +I+R G+V V+   +     ++  Q + I   I A++ + 
Sbjct: 1   MRLDKLLANKAFG-SRKEVHQIIRDGRVTVNGAVI-----LKKDQSIHIDDDIIAVDGV- 53

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                 +  +      F+KPAG        +       +   + 
Sbjct: 54  ---------------------QISTKQQYYIKFHKPAGYIT----AVEDPTHPVVMDLLP 88

Query: 139 SKGQK--PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            + +K       RLD++T G+L++        H   +      +  Y      + K+  E
Sbjct: 89  PEFKKMGVFPVGRLDKDTEGLLLLT-NDGIWAHSIINGHKHVPKVYYVEFNGKLTKDGLE 147

Query: 197 CIANWLL 203
            I   ++
Sbjct: 148 RIETGIV 154


>gi|260893899|ref|YP_003239996.1| RNA-binding S4 domain protein [Ammonifex degensii KC4]
 gi|260866040|gb|ACX53146.1| RNA-binding S4 domain protein [Ammonifex degensii KC4]
          Length = 81

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 23/50 (46%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          MR+D++ K            + LR G V ++ +  K   R++ G ++ + 
Sbjct: 1  MRIDKFLKEARLITRRTVANQALREGLVTINGRTAKPATRVKKGDIITLN 50


>gi|148264550|ref|YP_001231256.1| pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146398050|gb|ABQ26683.1| ribosomal large subunit pseudouridine synthase B [Geobacter
           uraniireducens Rf4]
          Length = 239

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 76/249 (30%), Gaps = 48/249 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +    ++I+  G+V V+ + V                         
Sbjct: 3   ERLQKILSQA-GIASRREAERIITDGRVAVNGQVVT-----------------ELGTKAD 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E+  +       +       +LLY+        K                   +   + 
Sbjct: 45  AEKDRITVDGRPIRVEANKLYVLLYKPVGYMTTMKDP------------EGRPIVTDLLK 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
              ++     RLD  T G+L++    A A  L        + K Y   V G        +
Sbjct: 93  GIKERVYPVGRLDYNTEGLLLLTNDGALANRLA--HPSHEVDKGYLVRVRGK-------V 143

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
               LK   +G D      ++ + A   +S  +     +++ CW+ +  H GR  Q+R  
Sbjct: 144 TPAQLKHLAVGVDL-----EDGRTAPAVVSLVR----ESEQNCWISITIHEGRYRQVRRM 194

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 195 CEAVGLTVV 203


>gi|116073056|ref|ZP_01470318.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Synechococcus sp. RS9916]
 gi|116068361|gb|EAU74113.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [Synechococcus sp. RS9916]
          Length = 249

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 80/238 (33%), Gaps = 53/238 (22%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSG-QVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +  + +++LR+G+V+V+ +  +  +R + G   + I       N   +            
Sbjct: 26  SRRHAEELLRAGRVKVNDRMAQLGDRAEPGLDRITIDGTPLPANDPPR------------ 73

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGI--SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
                           + + NKP G+  S Q   G    +D   K              R
Sbjct: 74  ----------------LLLLNKPRGVISSCQDPQGRPIVLDLVPKHLRRG----LHPVGR 113

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD E+ G L++         LT            W  V G P +    + +W        
Sbjct: 114 LDAESRGALLLTNQGELTLQLTHPRYSHAKTYRVW--VQGRPSH--GALEHW-------- 161

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                 ++ +++    A    + +   A +   LE+    GR  Q+R  A  +G P++
Sbjct: 162 ---RRGLRLDQRLTQPA--EVRELHHNANR-TLLEVVLREGRNRQIRRVAELLGHPVL 213


>gi|33152184|ref|NP_873537.1| pseudouridine synthase [Haemophilus ducreyi 35000HP]
 gi|33148406|gb|AAP95926.1| probable pseudouridine synthase [Haemophilus ducreyi 35000HP]
          Length = 354

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 27/176 (15%), Positives = 56/176 (31%), Gaps = 27/176 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             +L +         +   L++++ +G+V VD K     +R+      +I      +N +
Sbjct: 74  GEKLQKILARAGQG-SRRELEEVIAAGRVSVDGKIASLGDRVHVNATTKIRIDGTLINLV 132

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             +++I                       ++ ++ KP G                     
Sbjct: 133 TAQKEIC----------------------RVLMYYKPEGELCTRADPEG--RATVFDRLP 168

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
              G +     RLD  TSG+L+       A  L        +++ Y   V+G   +
Sbjct: 169 RLSGSRWIAVGRLDINTSGLLLFTTDGDLANRL--MHPSHEVEREYSVRVFGQVDD 222


>gi|289641301|ref|ZP_06473467.1| pseudouridine synthase [Frankia symbiont of Datisca glomerata]
 gi|289508899|gb|EFD29832.1| pseudouridine synthase [Frankia symbiont of Datisca glomerata]
          Length = 248

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 40/256 (15%), Positives = 87/256 (33%), Gaps = 52/256 (20%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           + + E +RL +         +  + ++++ +G+VRVD + V+        Q +R+ P   
Sbjct: 5   DANAEGVRLQKVLAAAGVG-SRRHSEELIAAGRVRVDGRVVET-------QGMRVDPQT- 55

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                        + + +       ++ L++        NKP G+     +         
Sbjct: 56  -------------AIIEVDGERVVTRAGLVH-----LALNKPVGVLS---AMSDDRGRPT 94

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +   V   G       RLD ++ G+L+V      A  L+       + K Y   V G   
Sbjct: 95  VADLVTDAGPGLFHVGRLDVDSEGLLLVTNDGELAHRLSHPSFE--VAKTYLVEVAG--- 149

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAIS--HFKVIDCFAQKFCWLEMQPHTG 250
                          +G D    +++  + A+  +     +++     +    E+  H G
Sbjct: 150 --------------PVGRDVPRRLREGVELADGPVRADAVRIVGSAGSRVML-EITLHEG 194

Query: 251 RTHQLRVHALHMGCPI 266
           R   +R     +  P+
Sbjct: 195 RNRVVRRLMEAVDHPV 210


>gi|225573958|ref|ZP_03782603.1| hypothetical protein RUMHYD_02052 [Blautia hydrogenotrophica DSM
          10507]
 gi|225038796|gb|EEG49042.1| hypothetical protein RUMHYD_02052 [Blautia hydrogenotrophica DSM
          10507]
          Length = 79

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 25/50 (50%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          MRLD++ K            +   +G+V V++K  K + +++ G V+ I 
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNEKPAKASAKVKPGDVIEIQ 50


>gi|213859463|ref|ZP_03385167.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
          Length = 231

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 76/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD            G +++     NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVD------------GDIIK-----NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHAVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +            +  +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV---------TLESPV 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+    +   G    +     +      I+  +V            +    GR HQ++  
Sbjct: 141 ADDTAAQFAKGVQLHNRKSLTKPATLEVITPVQV-----------RLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNRVV 198


>gi|170727748|ref|YP_001761774.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169813095|gb|ACA87679.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 239

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 37/248 (14%), Positives = 85/248 (34%), Gaps = 49/248 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK-RVKFNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       +      +++ +G+V V+ +  V  + ++     +R           
Sbjct: 1   MRLDKFLCKS-TQLTRHEACELILAGKVLVNGESVVSPSAQVHENNHIR----------- 48

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                 L+    LT  +   + I+L++ +     N      V G     ++         
Sbjct: 49  ------LEGGQRLTARAS--RYIMLHKPADTLSSN------VDGDHPSVFNFINL----- 89

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWS-LVWGIPKNKK 195
                +  +  RLD +T+G+L++    R +       +   ++ ++Y    + G    + 
Sbjct: 90  -EHTSELHIAGRLDADTTGLLLITDDGRWSFNVFNPKYHCEKVYRVYLRDSIEGEIAGE- 147

Query: 196 ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
             I   L  +   G D              A++    ++  + K     +    GR HQ+
Sbjct: 148 --IDAELKARFKQGLDLQ---------GEQALTLPAKLEFVSPKEVL--LTITEGRYHQM 194

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 195 KRMFARVG 202


>gi|251779623|ref|ZP_04822543.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum E1 str. 'BoNT E Beluga']
 gi|243083938|gb|EES49828.1| ribosomal large subunit pseudouridine synthase B [Clostridium
           botulinum E1 str. 'BoNT E Beluga']
          Length = 236

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 84/251 (33%), Gaps = 53/251 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RL ++  +     +    ++I+ SG+V+V+   V     R+       +   +     +
Sbjct: 3   ERLQKYMAS-CGLASRRKCEEIILSGEVKVNGVVVTELGTRVNP-----VEDKVEYKGCL 56

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSW 136
           IK++                      E+    + NKP G I+          +   +K  
Sbjct: 57  IKKE----------------------ENKVYIILNKPEGYITSAKDEKGRKTVLDLVKV- 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                ++     RLD ++SG++++         +        + K Y ++V G    K  
Sbjct: 94  ----NERIYPIGRLDYDSSGLILLTNDGDIYNKI--IHPREELNKKYIAVVKGEVSKKD- 146

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
              +   K   IG            G   A +  +V+  +      +E+  H G+  Q+R
Sbjct: 147 --IDAFNKGIDIG------------GYVTAPASLEVL-SYENGKSTVEVCIHEGKNRQIR 191

Query: 257 VHALHMGCPIV 267
                +   ++
Sbjct: 192 KMCTAINHEVL 202


>gi|229011635|ref|ZP_04168818.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
 gi|228749593|gb|EEL99435.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
          Length = 235

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 32/248 (12%), Positives = 71/248 (28%), Gaps = 60/248 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++        +     K++   +V ++ K  K  +++  G  VR+           
Sbjct: 1   MRINKFISEAGK-ASRRGADKLINERKVIINGKVAKIGDQVNPGDDVRVNGEQLR----- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  +  D      NKP GI+      +  +I   +   + 
Sbjct: 55  -----------------------IARDHVYIALNKPVGITCTSEKAVKGNIIDLVNHPL- 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++++         +  +      + I                
Sbjct: 91  ----RINHIGRLDKDSDGLILLTNDGDIVNEILRAENKHEKEYIVS-------------- 132

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TGRTHQLR 256
                    I  +++  +    K     I   K + C   +    E Q     G   Q+R
Sbjct: 133 -----VDKPITPEFLEKMAAGVK-----ILDTKTLPCEVTQLSKYEFQIILTQGLNRQIR 182

Query: 257 VHALHMGC 264
                +G 
Sbjct: 183 RMCEALGY 190


>gi|324018876|gb|EGB88095.1| hypothetical protein HMPREF9542_02380 [Escherichia coli MS 117-3]
          Length = 277

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 30/166 (18%), Positives = 57/166 (34%), Gaps = 30/166 (18%)

Query: 32  INFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHIIKEQKILDSSVN 89
                ++ I+ +G+V VD K  K  +R++   G  +RI   +                ++
Sbjct: 2   APRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL----------------IS 45

Query: 90  LTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHR 149
           + + ++ +  +L Y         KP G                       +G +     R
Sbjct: 46  VRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPKLRGARWIAVGR 95

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           LD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 96  LDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 139


>gi|212710702|ref|ZP_03318830.1| hypothetical protein PROVALCAL_01769 [Providencia alcalifaciens DSM
           30120]
 gi|212686399|gb|EEB45927.1| hypothetical protein PROVALCAL_01769 [Providencia alcalifaciens DSM
           30120]
          Length = 313

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 30/180 (16%), Positives = 58/180 (32%), Gaps = 27/180 (15%)

Query: 16  EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
           ++  +L +       H +   ++ +L+ G++ VD K     +R++     +I      L 
Sbjct: 14  QQTEKLQKILARS-GHGSRREIEGLLKEGRISVDGKMATLGDRVEVKATTKIRLDGRLLA 72

Query: 76  HIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKS 135
               E++I                       ++  + KP G                   
Sbjct: 73  IKEPEKEIC----------------------RVMAYYKPEGELC--TRHDPEGRPTVFNR 108

Query: 136 WVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
                G +     RLD  TSG+L+       A  L      R +++ Y   V+G   + K
Sbjct: 109 LPRLTGARWIAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGEITDAK 166


>gi|110597201|ref|ZP_01385490.1| Pseudouridine synthase, Rsu [Chlorobium ferrooxidans DSM 13031]
 gi|110341392|gb|EAT59857.1| Pseudouridine synthase, Rsu [Chlorobium ferrooxidans DSM 13031]
          Length = 247

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 37/252 (14%), Positives = 80/252 (31%), Gaps = 53/252 (21%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVIN 72
           + E +R++R+        +     +++  G+V V+   +     ++      V +     
Sbjct: 6   NSEEVRINRFLA-LCGIASRRAADQLVLEGRVMVNGTVITQPGTKVNPDKDEVIVDGQKY 64

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
           A                     +  K  +L+        NKP  +               
Sbjct: 65  A-------------------QPESRKVYILF--------NKPRNVISTSS---DEKNREM 94

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +  ++D K ++     RLD++T+G++++      A  L        ++K Y + V G   
Sbjct: 95  VLDYIDVK-ERVFPVGRLDRKTTGLILLTNDGTLANKL--MHPSSNVKKEYIA-VLGEKF 150

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                       +    G+ V   +             K++D   Q      +  H G+ 
Sbjct: 151 PASMLPQLTGGMRLKDTGEKVRPCRA------------KLLDEGMQVL----LSIHEGKN 194

Query: 253 HQLRVHALHMGC 264
           HQ+R     +G 
Sbjct: 195 HQVRRMFETLGY 206


>gi|297831472|ref|XP_002883618.1| hypothetical protein ARALYDRAFT_899194 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297329458|gb|EFH59877.1| hypothetical protein ARALYDRAFT_899194 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 302

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 5/61 (8%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD      +   +   +Q  +  G+V VD +RV     I++G  V     I     + 
Sbjct: 55  QRLDEACVERFNEYSRTLIQSWIIQGKVLVDGRRV-----IKAGMPVSNTAAIKITAEVP 109

Query: 79  K 79
           K
Sbjct: 110 K 110


>gi|291459824|ref|ZP_06599214.1| ribosomal small subunit pseudouridine synthase A [Oribacterium sp.
           oral taxon 078 str. F0262]
 gi|291417614|gb|EFE91333.1| ribosomal small subunit pseudouridine synthase A [Oribacterium sp.
           oral taxon 078 str. F0262]
          Length = 249

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 77/245 (31%), Gaps = 49/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+        +   L+K +R GQV ++ +  +                 +    + 
Sbjct: 1   MRLDRFLSE-MGISSRSELKKEIRRGQVLLNGEEAR-----------------DPSLFVD 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E   +        H         YE    Y+ NKPAGI           +   ++    
Sbjct: 43  PENPPVVLYRGREFH---------YEAFSYYMMNKPAGILSASRDKKQSTVLDLIQEDRR 93

Query: 139 SKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                     RLD++  G+L+++     + + L        + K+Y+  V G        
Sbjct: 94  R---DLFPVGRLDKDCEGLLLISNDGPLSHRLL---RPKSHVPKLYFVRVSGRLTESDAE 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +    L+               +  A  A       +    + C   ++   G+ HQ++ 
Sbjct: 148 LFRRGLRYD------------EDLTALPAELTILSAEDIISEAC---VRITEGKFHQIKK 192

Query: 258 HALHM 262
             L +
Sbjct: 193 MFLAL 197


>gi|168205142|ref|ZP_02631147.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           E str. JGS1987]
 gi|169347063|ref|ZP_02866005.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           C str. JGS1495]
 gi|169296746|gb|EDS78875.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           C str. JGS1495]
 gi|170663342|gb|EDT16025.1| RNA pseudouridine synthase family protein [Clostridium perfringens
           E str. JGS1987]
          Length = 301

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 39/263 (14%), Positives = 85/263 (32%), Gaps = 59/263 (22%)

Query: 5   TYVQYVVVENDEE---NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
           +    ++V N  E    +RL+++        +     K++  G+V++D  +     ++ +
Sbjct: 46  SAKNTIIVSNKNEIRDEVRLNKYISET-GFCSRREADKLIEQGRVKIDGVKATTGMKVSN 104

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQG 121
           GQ V I                             +++ L+Y        NKP GI+   
Sbjct: 105 GQSVSIDGKPLK-----------------------VENELVY-----IALNKPVGITCTT 136

Query: 122 GSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQK 181
            S I  +I  F+        ++     RLD+++ G++ +         +  +      + 
Sbjct: 137 ESKIKGNIVDFINH-----EKRIFPIGRLDKDSQGLIFMTNDGDIVNKILRAGNNHEKEY 191

Query: 182 IYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC 241
           I             + I +  +K    G   +  V +       + + F++I        
Sbjct: 192 IV---------TVNKPITDEFIKGMSNGVPILGTVTKKCLVKKESKNSFRII-------- 234

Query: 242 WLEMQPHTGRTHQLRVHALHMGC 264
                   G   Q+R    + G 
Sbjct: 235 -----LTQGLNRQIRRMCEYFGY 252


>gi|54297357|ref|YP_123726.1| hypothetical protein lpp1402 [Legionella pneumophila str. Paris]
 gi|53751142|emb|CAH12553.1| hypothetical protein lpp1402 [Legionella pneumophila str. Paris]
          Length = 248

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 34/233 (14%), Positives = 74/233 (31%), Gaps = 34/233 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +   +++ + +G V+V+ K  K  +       + +           
Sbjct: 4   ERLQKILSQAGLG-SRREMERWIDNGWVQVNGKPAKLGDSAGPSDKISV----------- 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            + K++ + +               ++ ++ +++KP G +S +        +   L    
Sbjct: 52  -KGKLIPNPLKGK------------QNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLR 98

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +  +     RLD  TSG+L+       A  L        +++ Y   V G    +   
Sbjct: 99  QGRWVQ---VGRLDLNTSGLLIFTNNGELANQL--MHPKYGLEREYAVRVHGQVSQESL- 152

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N LLK   +        K   +G     S + V     +      +    G
Sbjct: 153 --NNLLKGVMLDDGLGKFTKIQFRGGEGTNSWYHVTLNEGRNREVRRLWESQG 203


>gi|126668319|ref|ZP_01739278.1| Pseudouridine synthase, Rsu [Marinobacter sp. ELB17]
 gi|126627236|gb|EAZ97874.1| Pseudouridine synthase, Rsu [Marinobacter sp. ELB17]
          Length = 367

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 32/246 (13%), Positives = 72/246 (29%), Gaps = 45/246 (18%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             R+ +         +   ++  + +G++ V+ K V    +     V  +          
Sbjct: 56  PERIQKLLARAGVG-SRREIEGWMDAGRLLVNGKPVTPGQKATVSDVFELDGKR------ 108

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                     + +   ++ L+ +L+Y        NKP G                     
Sbjct: 109 ----------LEVAAAAEVLRRVLIY--------NKPEGEVT--TRKDPEGRPTVFDRLP 148

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +  +     RLD  T+G+++       A  L        I + Y   ++G        
Sbjct: 149 RLREHRWISIGRLDLNTTGLVMFTTDGELANRL--MHPSSEIDREYAVRIFGE------- 199

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + ++++   G     V  ++ +     IS             W  +    GR  ++R 
Sbjct: 200 VDDAMIERLRTG-----VTLEDGEAKFSDIS----AAGGTGMNRWFHVTLLEGRNREVRR 250

Query: 258 HALHMG 263
                G
Sbjct: 251 LWESQG 256


>gi|117617574|ref|YP_855956.1| ribosomal large subunit pseudouridine synthase E [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117558981|gb|ABK35929.1| ribosomal large subunit pseudouridine synthase E [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 313

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 38/163 (23%), Positives = 66/163 (40%), Gaps = 9/163 (5%)

Query: 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           D K+ + NKP  +  Q            LK ++   G       RLD+++ G+L++    
Sbjct: 56  DRKLLLLNKPYMVLCQ---FTDEAGRETLKDYITEPGIYA--AGRLDRDSEGLLLLTNDG 110

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
                LT+     +  K YW  V G+P  +K   A     + + G       +  E+ A 
Sbjct: 111 KLQARLTQPGE--KTPKTYWVQVEGVPSEEKLA-ALCAGVELNDGMTLPAGARIMEEPAV 167

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +  +   + +      CWLE++   GR  Q+R    H+G P +
Sbjct: 168 WPRNP-PIRERKEIPTCWLEIKIVEGRNRQVRRMTAHIGHPTL 209


>gi|300926650|ref|ZP_07142426.1| hypothetical protein HMPREF9548_04653 [Escherichia coli MS 182-1]
 gi|300417316|gb|EFK00627.1| hypothetical protein HMPREF9548_04653 [Escherichia coli MS 182-1]
          Length = 276

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 30/165 (18%), Positives = 57/165 (34%), Gaps = 30/165 (18%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHIIKEQKILDSSVNL 90
               ++ I+ +G+V VD K  K  +R++   G  +RI   +                +++
Sbjct: 2   PRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHL----------------ISV 45

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRL 150
            + ++ +  +L Y         KP G                       +G +     RL
Sbjct: 46  RESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPKLRGARWIAVGRL 95

Query: 151 DQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           D  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 96  DVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 138


>gi|256424973|ref|YP_003125626.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
 gi|256039881|gb|ACU63425.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
          Length = 389

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 80/248 (32%), Gaps = 54/248 (21%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L+++  +   + +      ++ SG+V ++ +     NR + G  V +   +  +    KE
Sbjct: 7   LNKFISDT-GYCSRREADNLITSGRVLLNDRPAALGNRYKPGDTVEVDGSL--ITAAKKE 63

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           +++                            NKP GI+      I  +I  F+     + 
Sbjct: 64  KRV------------------------YLALNKPPGITTTTELHIKDNIISFV-----NY 94

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIAN 200
            Q+     RLD+++ G++ +         +  +      + +                  
Sbjct: 95  PQRIFPIGRLDKDSEGLIFLTNDGDIINKILRAANNHEKEYVV----------------- 137

Query: 201 WLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHAL 260
                  I  +++H + Q     +      KV     Q F    +    G   Q+R    
Sbjct: 138 --RVNKPIDTNFLHQMSQGVPILDTRTLPCKVQMTGRQTF---RITLTQGLNRQIRRMCE 192

Query: 261 HMGCPIVG 268
           ++G  +VG
Sbjct: 193 YLGYTVVG 200


>gi|115450787|ref|NP_001048994.1| Os03g0152700 [Oryza sativa Japonica Group]
 gi|108706231|gb|ABF94026.1| RNA pseudouridylate synthase family protein, expressed [Oryza
           sativa Japonica Group]
 gi|113547465|dbj|BAF10908.1| Os03g0152700 [Oryza sativa Japonica Group]
          Length = 415

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 72/247 (29%), Gaps = 44/247 (17%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQ-SGQVVRIPPVI 71
            + E  RL +         +    ++++  G+V V+         ++  S   + +    
Sbjct: 168 KEHEPQRLAKVLAAA-GVASRRTCEELIFQGKVTVNGSVCTAPQTKVDISKDSIYVNGNR 226

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK-PAGISVQGGSGIAYHID 130
            +     K    ++            KSI+   D  +  +NK   G+             
Sbjct: 227 ISKKLPPKLYFAVNKPKGYICSCGEPKSIISLFDDYLKGWNKIQPGVP------------ 274

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                       +     RLD  TSG++++      AQ L+                  I
Sbjct: 275 ----------KPRLFTVGRLDVATSGLIIITNDGEFAQKLSHPSSN-------------I 311

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHT 249
            K     I   + +   I       +     G        + +D  +  K   + +  H 
Sbjct: 312 MKEYVVTIDGPVHRNHLIAISEGTKID----GVKCIPDLVEPLDVQSNTKRTRIRIAVHE 367

Query: 250 GRTHQLR 256
           GR H++R
Sbjct: 368 GRNHEVR 374


>gi|120610106|ref|YP_969784.1| ribosomal large subunit pseudouridine synthase B [Acidovorax
           citrulli AAC00-1]
 gi|120588570|gb|ABM32010.1| ribosomal large subunit pseudouridine synthase B [Acidovorax
           citrulli AAC00-1]
          Length = 483

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 33/232 (14%), Positives = 67/232 (28%), Gaps = 45/232 (19%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      R+Q G  V++              +          
Sbjct: 162 SRLEMEQLILEGRISVNNEPAHIGQRVQYGDQVKVNGRPIRYRIDPPAPR---------- 211

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                          +  ++KP G  V        +     +        K +   RLD 
Sbjct: 212 ---------------VIAYHKPVGEVV--THDDPQNRPTVFRKLPRLAHGKWQSVGRLDL 254

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L+       A  L        +++ Y   V G   N+++      L       D 
Sbjct: 255 NTEGLLLFTSAGELANKL--MHPRFGLEREYAVRVLGALSNEEKQ----RLLDGVQLEDG 308

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +      E G                  CW  +    GR  ++R     +G 
Sbjct: 309 MAAFGSIEDGG------------GEGSNCWYRVTISEGRNREVRRMLESVGH 348


>gi|163940156|ref|YP_001645040.1| RNA-binding S4 domain-containing protein [Bacillus
           weihenstephanensis KBAB4]
 gi|163862353|gb|ABY43412.1| RNA-binding S4 domain protein [Bacillus weihenstephanensis KBAB4]
          Length = 235

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 31/248 (12%), Positives = 71/248 (28%), Gaps = 60/248 (24%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++        +     K++   +V ++ K  K  +++  G  VR+           
Sbjct: 1   MRINKFISEAGK-ASRRGADKLINERKVIINGKVAKIGDQVNPGDDVRVNGEQLR----- 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                  +  D      NKP GI+      +  +I   +   + 
Sbjct: 55  -----------------------IARDHVYIALNKPVGITCTSEKAVKGNIIDLVNHPL- 90

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD+++ G++++         +  +      + I                
Sbjct: 91  ----RINHIGRLDKDSDGLILLTNDGDIVNEILRAENKHEKEYIVS-------------- 132

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TGRTHQLR 256
                    I  +++  +    K     I   K + C   +    E +     G   Q+R
Sbjct: 133 -----VDKPITPEFLEKMAAGVK-----ILDTKTLPCEVTQLSKYEFEIILTQGLNRQIR 182

Query: 257 VHALHMGC 264
                +G 
Sbjct: 183 RMCEALGY 190


>gi|224373604|ref|YP_002607976.1| ribosomal large subunit pseudouridine synthase B [Nautilia
           profundicola AmH]
 gi|223588928|gb|ACM92664.1| ribosomal large subunit pseudouridine synthase B [Nautilia
           profundicola AmH]
          Length = 253

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 30/165 (18%), Positives = 57/165 (34%), Gaps = 33/165 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRL+++   H+   +     K++  G+V+V+ + +K     ++ G  V +          
Sbjct: 1   MRLNKFIS-HHTTYSRREADKLIFDGRVKVNGRVIKEPGFEVEEGDKVAVN--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
               K +  S   T                  V+NKP G  V   +         +   +
Sbjct: 51  ---GKPVKKSTKYT----------------CIVYNKPRGELV---TKKDDRGRKTIYDSL 88

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             K +      RLD  + G+L++  +   A  L  S   R  +  
Sbjct: 89  PKKYRHFIPVGRLDFNSEGLLILTDSPKVAHALMNSDLPRVYKLK 133


>gi|134095614|ref|YP_001100689.1| putative pseudouridine synthase (Uracil hydrolyase) [Herminiimonas
           arsenicoxydans]
 gi|133739517|emb|CAL62568.1| Pseudouridine synthase [Herminiimonas arsenicoxydans]
          Length = 538

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 26/160 (16%), Positives = 54/160 (33%), Gaps = 28/160 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             D++  +L +         +  ++++++ +G+V V+ +      RI     VRI     
Sbjct: 171 TADDDAPKLHKVLAEAGLG-SRRDMEELIIAGRVSVNGEPAHIGQRILPADQVRIN---- 225

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                                   ++  +  +  ++ V++KPAG  V   +         
Sbjct: 226 ---------------------GKLIQRKVSNKPPRVLVYHKPAGEIV--STNDPEGRPSV 262

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172
            +     K  K     RLD  T G+L+   +   A  L  
Sbjct: 263 FERLPTMKAAKWLAVGRLDFNTEGLLLFTTSGDLANRLMH 302


>gi|197105762|ref|YP_002131139.1| ribosomal small subunit pseudouridine synthase A [Phenylobacterium
           zucineum HLK1]
 gi|196479182|gb|ACG78710.1| ribosomal small subunit pseudouridine synthase A [Phenylobacterium
           zucineum HLK1]
          Length = 242

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 43/274 (15%), Positives = 92/274 (33%), Gaps = 49/274 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
           +RLD+   N   + +   +Q + R+G + +D   V K + RI            +    +
Sbjct: 5   VRLDKLLAN-MGYGSRREVQALARAGAITLDGAPVPKADTRIA--------LTPDLPARM 55

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             + + LD    +        +++L++ + +   +K  G  V             L S  
Sbjct: 56  QVDGRPLDPLPGM--------ALMLHKPTGVTCSHKETGELV----------YSLLPSRW 97

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +        RLD+ETSG+L++         +      R + K Y + +    +  +  
Sbjct: 98  RMREPPLSTVGRLDKETSGLLLLTDDGDLLHRI--ISPRRHVAKRYVATLARPLRGDEGA 155

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           I           G+ +  ++  +K    A+                 +    GR HQ+R 
Sbjct: 156 IFA--------AGELM--LEGEDKPLAPAVLE-------PLSPTLARLTITEGRYHQVRR 198

Query: 258 HALHMGCPI--VGDHKYCANFKGNFTSPIQNKLY 289
               +G  +  +   +          +P + +L 
Sbjct: 199 MFAAVGNHVEALHRDRIGGLDLPADLAPGRYRLM 232


>gi|304440182|ref|ZP_07400072.1| S4 RNA-binding domain protein [Peptoniphilus duerdenii ATCC
          BAA-1640]
 gi|304371231|gb|EFM24847.1| S4 RNA-binding domain protein [Peptoniphilus duerdenii ATCC
          BAA-1640]
          Length = 81

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
          MRLD++ KN          ++   +G++ V+ +  K +  + +G ++ I
Sbjct: 1  MRLDKFLKNSRVIKRRTLAKEACDAGRITVNGRVAKASTEVNTGDILEI 49


>gi|258624941|ref|ZP_05719868.1| ribosomal small subunit pseudouridine synthase A [Vibrio mimicus
           VM603]
 gi|258582797|gb|EEW07619.1| ribosomal small subunit pseudouridine synthase A [Vibrio mimicus
           VM603]
          Length = 257

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 40/280 (14%), Positives = 90/280 (32%), Gaps = 68/280 (24%)

Query: 1   MSLMTYVQYVVV---------ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK 51
           M  M  +++V+V         + DE +MRLD++  +            +L+SG+V VD  
Sbjct: 1   MRDM-QLRWVIVVTGLYNSRLQADEVSMRLDKFLCDAL-GTTRKEATMLLKSGEVTVDDL 58

Query: 52  RVKFN-NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYV 110
             K    +++                              T   ++    +     +  +
Sbjct: 59  VQKSGAFKLKE-----------------------------TSRVEWQGREITAHGPRYIM 89

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA-AAQH 169
            +KP G+      G        L    +   Q      RLD +T+G+L++      + + 
Sbjct: 90  MHKPDGVVCSHEDGFNQTAFILLD---EVNIQDLHFAGRLDVDTTGLLLITDDGQWSHRV 146

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAIS 228
            +   +  +  +++ +                      I  DY        E      ++
Sbjct: 147 TSPKHKCEKTYRVWLA--------------------DPIQADYAEQFTNGIELRGERELT 186

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               ++  ++      +  H G+ HQ++     +G  ++G
Sbjct: 187 LPAQLEVVSETEVL--LTIHEGKYHQVKRMFAALGNKVIG 224


>gi|163750086|ref|ZP_02157329.1| putative ribosomal small subunit pseudouridine synthase A
           [Shewanella benthica KT99]
 gi|161330143|gb|EDQ01125.1| putative ribosomal small subunit pseudouridine synthase A
           [Shewanella benthica KT99]
          Length = 233

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 82/249 (32%), Gaps = 52/249 (20%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+       IN  N++ +L  G V VD    +            I  +I+  + +  
Sbjct: 7   RLDRFISVK-TGINRKNVRLLLAKGLVEVDGDIAR-----------NIDQIIDEFSDVSL 54

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           E ++L S+                      + +KP G+     + +       +    D 
Sbjct: 55  EGEVLQSNSPS-----------------YVMLHKPVGVVS---ATVDDKHKTVIDLLTDK 94

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
                 +  RLD  TSG+L++      ++ L       ++ K+Y   +     +      
Sbjct: 95  SKHDLHIVGRLDLNTSGLLLLTNDGRWSKKL--MSPHHKVGKLYRVTLQNPIDDS----- 147

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
                K+   G Y        K A  A+     +D        +E     GR HQ++   
Sbjct: 148 ---YVKAFAEGIYFEFEDIITKPAQLAL-----VDSHTALVTLVE-----GRYHQIKRMF 194

Query: 260 LHMGCPIVG 268
                P++G
Sbjct: 195 GRFRNPVIG 203


>gi|325972637|ref|YP_004248828.1| ribosomal protein S4 [Spirochaeta sp. Buddy]
 gi|324027875|gb|ADY14634.1| ribosomal protein S4 [Spirochaeta sp. Buddy]
          Length = 213

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRI 67
            RLD      +   +     + +  G + V+ KRV   + R++ G VV +
Sbjct: 101 QRLDNVVFRLHFAASRNQAAQFVNHGHIFVNGKRVSIPSYRLRPGDVVSV 150


>gi|229076341|ref|ZP_04209306.1| hypothetical protein bcere0024_46450 [Bacillus cereus Rock4-18]
 gi|228706776|gb|EEL58984.1| hypothetical protein bcere0024_46450 [Bacillus cereus Rock4-18]
          Length = 165

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 7/49 (14%), Positives = 24/49 (48%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
           R+D+    +    +   +   ++SG ++++ +++K N ++     + I 
Sbjct: 116 RIDKVLSTYISDWSRTTIVDKIKSGDIQLNGQQMKPNKQLSEDDYISIC 164


>gi|225571162|ref|ZP_03780160.1| hypothetical protein CLOHYLEM_07250 [Clostridium hylemonae DSM
          15053]
 gi|225159993|gb|EEG72612.1| hypothetical protein CLOHYLEM_07250 [Clostridium hylemonae DSM
          15053]
          Length = 79

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 23/50 (46%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          MRLD++ K            +   +G+V V+    K + +++ G ++ I 
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVTVNGSVAKASVKVKPGDIIEIQ 50


>gi|218264461|ref|ZP_03478294.1| hypothetical protein PRABACTJOHN_03990 [Parabacteroides johnsonii
           DSM 18315]
 gi|218221954|gb|EEC94604.1| hypothetical protein PRABACTJOHN_03990 [Parabacteroides johnsonii
           DSM 18315]
          Length = 249

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 49/286 (17%), Positives = 95/286 (33%), Gaps = 55/286 (19%)

Query: 4   MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQ 63
           M Y +  V+ +  E +RL+++  N     +     + +++G V+V+ + V          
Sbjct: 1   MKYKE--VLADPNEPIRLNKFLSNA-GVCSRREADEFIQAGVVQVNDQVVT--------- 48

Query: 64  VVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGS 123
                        I ++ K+L     +   S               V NKP        S
Sbjct: 49  --------ELGTKITRQDKVLFKDQQVQIESKV-----------YIVLNKPKNCVT--TS 87

Query: 124 GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183
                    +    ++  ++     RLD+ T+G+L++      A  LT     ++     
Sbjct: 88  DDPQERLTVMDLVKNACQERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPSFKKKKIYHV 147

Query: 184 WSLVWGIPKNKKECIANWL-LKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCW 242
           W L   +     E IAN L L+   I  D +    +++K                     
Sbjct: 148 W-LDKNVSIEDMEKIANGLELEDGEIHADAISYASEDDK-------------------SQ 187

Query: 243 LEMQPHTGRTHQLRVHALHMGCPIVG-DHKYCANFKGNFTSPIQNK 287
           + ++ H+GR   +R     +G  +V  D  Y A          + +
Sbjct: 188 VGIEIHSGRNRIVRRIFESLGYHVVKLDRVYFAGLTKKNLGRGKWR 233


>gi|28895711|ref|NP_802061.1| 16S pseudouridylate synthetase [Streptococcus pyogenes SSI-1]
 gi|28810960|dbj|BAC63894.1| putative 16S pseudouridylate synthetase [Streptococcus pyogenes
           SSI-1]
          Length = 238

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 26/179 (14%), Positives = 55/179 (30%), Gaps = 38/179 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD+         +   ++K++++  V VD    +     +  G Q++ +         
Sbjct: 1   MRLDKLL-EGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQR----- 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   + +      + NKP+G+           +   L   
Sbjct: 55  ------------------------VTHPKHSYIILNKPSGVVSAKKDTNYLTVIDQLAE- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            + K        RLD++T G++++        + L        + K Y   V G+    
Sbjct: 90  -EDKSPDLYPVGRLDRDTEGLVLLTDNGPLGFRML---DPSHHVSKTYLVTVNGLLAED 144


>gi|189499452|ref|YP_001958922.1| pseudouridine synthase [Chlorobium phaeobacteroides BS1]
 gi|189494893|gb|ACE03441.1| pseudouridine synthase [Chlorobium phaeobacteroides BS1]
          Length = 254

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 39/255 (15%), Positives = 81/255 (31%), Gaps = 53/255 (20%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG-QVVRIPP 69
           VE     +R++++        +     +++ SG+V V+ + + K    ++ G   V +  
Sbjct: 10  VETPGAAVRINKYLA-LCGIASRRAADRLVESGEVMVNGRIMMKKGATVRPGVDEVVVSN 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
            + AL                             E     + NKP               
Sbjct: 69  RLLALPE---------------------------EKKVYILLNKPRNYITTSSDEKER-- 99

Query: 130 DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
              +   VD + ++     RLD++T+G+L++    A A  L        ++K Y + +  
Sbjct: 100 -ETVLDLVDVR-ERVFPVGRLDRKTTGMLLLTNDGALAHRL--MHPSSEVEKEYLAELET 155

Query: 190 IPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHT 249
               K        ++    G        +  +G        +V+           +  H 
Sbjct: 156 PFSEKDLPSLTGGMRLKDTGEKTSPCKGKIMQGG------LRVL-----------VTIHE 198

Query: 250 GRTHQLRVHALHMGC 264
           G+ HQ+R     +G 
Sbjct: 199 GKNHQVRRMFRSLGY 213


>gi|302847122|ref|XP_002955096.1| pseudouridine synthase mitochondrial precursor [Volvox carteri f.
           nagariensis]
 gi|300259624|gb|EFJ43850.1| pseudouridine synthase mitochondrial precursor [Volvox carteri f.
           nagariensis]
          Length = 564

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 76/250 (30%), Gaps = 44/250 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQV-RVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +R++R   N   +      Q +++ G+V R D  ++K  +++  G VV     ++  + +
Sbjct: 79  LRVERLLAN-LGYGKRRECQVLVKKGRVTRRDGGKLKVGDKVCWGDVVLDEEDLDPPSPL 137

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +         V  +   + +   ++Y+                            L    
Sbjct: 138 LLALHKPGGYVVTSPDDENITDPVVYD---------------------------LLPYRF 170

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +        RLD++TSG+L++    A    +    R             GI K  +  
Sbjct: 171 ARRRPFLAPVGRLDKDTSGLLLLTDDGALLHRINSPRR-------------GIWKVYEAT 217

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +A  +                     ++  +                +    G+ HQ+R 
Sbjct: 218 LAEPMSTNQAAAAARRFASGSLVLEGDH--TPLLPAKLDLIGARTARVAICEGKYHQVRR 275

Query: 258 HALHMGCPIV 267
               +G  +V
Sbjct: 276 MFAAVGSHVV 285


>gi|241206829|ref|YP_002977925.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv. trifolii
           WSM1325]
 gi|240860719|gb|ACS58386.1| RNA-binding S4 domain protein [Rhizobium leguminosarum bv. trifolii
           WSM1325]
          Length = 134

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 14/89 (15%), Positives = 38/89 (42%), Gaps = 9/89 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            R+D+W        +    Q  ++SG VR++ +R  + +  ++ G  + +      +  +
Sbjct: 13  QRIDKWLFFARMAKSRSVAQSHIQSGHVRINGERCSQPSQMVKPGDRIELTLERRDVVLV 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDS 106
           ++        +   +   + ++ LLY+D 
Sbjct: 73  VR--------LAGERRGPYEQARLLYDDQ 93


>gi|225377123|ref|ZP_03754344.1| hypothetical protein ROSEINA2194_02768 [Roseburia inulinivorans DSM
           16841]
 gi|225211028|gb|EEG93382.1| hypothetical protein ROSEINA2194_02768 [Roseburia inulinivorans DSM
           16841]
          Length = 260

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 31/251 (12%), Positives = 79/251 (31%), Gaps = 56/251 (22%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E  +R++++        +     + +  G + +D K  +   R+  GQ V     +   
Sbjct: 2   EENGIRINKFLSEA-GVCSRREADRQVELGNITIDGKVAETGARVLPGQTV-----LFQG 55

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
             + KE++++                       +  F+KP GI          ++  ++ 
Sbjct: 56  KKVSKEEEMI-----------------------LIAFHKPVGIVCTAEKREKNNVIDYI- 91

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               +  ++     RLD+++ G+L++         +  S  M   + I            
Sbjct: 92  ----NYPKRIYPIGRLDKDSEGLLLLTNNGDIVNKMMRSGNMHEKEYIV----------- 136

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGAN-YAISHFKVIDCFAQKFCWLEMQPHTGRTH 253
                        +   ++H +      A    ++    +    +K    ++    G   
Sbjct: 137 --------TVNRPVTESFIHGLANGVPLAELNTMTRKCHVKQIGKKQ--FKIILTQGLNR 186

Query: 254 QLRVHALHMGC 264
           Q+R    + G 
Sbjct: 187 QIRRMCEYFGY 197


>gi|221632463|ref|YP_002521684.1| putative pseudouridine synthase [Thermomicrobium roseum DSM 5159]
 gi|221155848|gb|ACM04975.1| possible pseudouridine synthase [Thermomicrobium roseum DSM 5159]
          Length = 282

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 83/250 (33%), Gaps = 52/250 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL R    H    +    ++++ +G+V VD   V+                        
Sbjct: 8   QRLQRVLAAH-GVASRRKAEELILAGRVTVDGVVVR------------------------ 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLY-EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                L   V+  +    +    L+ E  +  V +KP G      +   Y     L   +
Sbjct: 43  ----ELGRKVDPERQEICVDGKPLHSEPRRYIVLHKPVGYIT--TTADEYGRKTVLD--L 94

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
               ++     RLD+++SG+L++         +T       ++K Y  LV G P  +   
Sbjct: 95  VQVPERVVPVGRLDRDSSGLLLLTNDGDLIYRIT--HPRYELEKEYEVLVDGFPPPE--- 149

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +   L +   + G  V + +          + ++V+              H GR   +R 
Sbjct: 150 VEEALRRGVPVDGRPVRIRRLEAIRVEPQGTVYRVV-------------IHEGRNRIIRR 196

Query: 258 HALHMGCPIV 267
               +G P++
Sbjct: 197 VFERVGYPVL 206


>gi|56696990|ref|YP_167352.1| RNA pseudouridylate synthase [Ruegeria pomeroyi DSS-3]
 gi|56678727|gb|AAV95393.1| RNA pseudouridylate synthase [Ruegeria pomeroyi DSS-3]
          Length = 200

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/163 (19%), Positives = 57/163 (34%), Gaps = 8/163 (4%)

Query: 107 KIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165
               FNKP  +  Q    G A      L   +D  G  P    RLD+++ G++++     
Sbjct: 3   WFIRFNKPYDVLSQFTDRGSADSPRATLSDHIDLPGVYP--AGRLDRDSEGLMLLTDVGR 60

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKK-ECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
               + +     ++ K YW  V G+P       +A  +  K  +             G  
Sbjct: 61  LQARIAD--PRHKLAKTYWVQVEGVPDAAALRALAEGVELKDGLTRPARARAMPEPPGLW 118

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                 +  +  +    W+E+    GR  Q+R     +G P +
Sbjct: 119 PRNPPIR--ERKSVPDSWIELTIREGRNRQVRRMTAAVGHPTL 159


>gi|157145597|ref|YP_001452916.1| 23S rRNA pseudouridylate synthase B [Citrobacter koseri ATCC
           BAA-895]
 gi|157082802|gb|ABV12480.1| hypothetical protein CKO_01343 [Citrobacter koseri ATCC BAA-895]
          Length = 291

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 60/177 (33%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K     +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIATLGDRVEITPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVKESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|116254343|ref|YP_770181.1| heat shock protein 15 [Rhizobium leguminosarum bv. viciae 3841]
 gi|115258991|emb|CAK10100.1| putative heat shock protein 15 [Rhizobium leguminosarum bv. viciae
           3841]
          Length = 134

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 14/89 (15%), Positives = 37/89 (41%), Gaps = 9/89 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHI 77
            R+D+W        +    Q  ++SG VR++ +R    +  ++ G  + +      +  +
Sbjct: 13  QRIDKWLFFARMAKSRSVAQSHIQSGHVRINGERCSYPSQMVKPGDRIELTLERRDVVLV 72

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDS 106
           ++        +   +   + ++ LLY+D 
Sbjct: 73  VR--------LAGERRGPYEEARLLYDDQ 93


>gi|254519947|ref|ZP_05132003.1| RNA pseudouridine synthase [Clostridium sp. 7_2_43FAA]
 gi|226913696|gb|EEH98897.1| RNA pseudouridine synthase [Clostridium sp. 7_2_43FAA]
          Length = 227

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 22/164 (13%), Positives = 52/164 (31%), Gaps = 35/164 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+++   N Y + +   + + +   ++ V+ K  +    ++    + +           
Sbjct: 1   MRINKLLSN-YGYCSRKEVSRWIEDKRIIVNGKLCEQGQWVEESDEILLD---------- 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                                 +  ++      NKP GI       I  +I  FL     
Sbjct: 50  -------------------GEKIKPKEKVYIALNKPPGIVCTSAREIDNNIIDFL----- 85

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
           +         RLD+++ G++++      A  +  S      + I
Sbjct: 86  NYKDYVFPVGRLDKDSQGLILMTNDGELANKILSSDSYHEKEYI 129


>gi|297538421|ref|YP_003674190.1| RNA-binding S4 domain-containing protein [Methylotenera sp. 301]
 gi|297257768|gb|ADI29613.1| RNA-binding S4 domain protein [Methylotenera sp. 301]
          Length = 138

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 4/58 (6%)

Query: 12 VENDEENMRLDRWF--KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
          +END+   RLD+W      +           + +G+V VD  RVK    +  GQV+ I
Sbjct: 5  IENDDAKCRLDKWLWSARFFK--TRSLATAAIETGKVHVDGDRVKPAKEVHIGQVIHI 60


>gi|226355753|ref|YP_002785493.1| RNA pseudouridylate synthase [Deinococcus deserti VCD115]
 gi|226317743|gb|ACO45739.1| putative RNA pseudouridylate synthase [Deinococcus deserti VCD115]
          Length = 253

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 68/250 (27%), Gaps = 53/250 (21%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
              RL +         +    ++++ +G+V V+         +     VR+   +     
Sbjct: 2   SGERLQKRLARA-GIASRRAAEEMITAGRVTVNGVVAHLGQTVTDADDVRVDGSLVDSTA 60

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +                       + Y         KP G      +   Y     L + 
Sbjct: 61  VPA---------------------VTY------ALYKPRGYVT--TARDEYGRRNVLDAM 91

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
            +  G  P    RLD+++ G+L++         LT +      +K Y +   G     + 
Sbjct: 92  PEIPGLHP--VGRLDRDSEGLLLLTTD--GQLTLTMTHPRYGHEKAYRAWTEGPHDPTQG 147

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            +   +       G    V      G  + +                      GR  Q+R
Sbjct: 148 ELDTLVSGVELEDGPARAVSASPAYGGAFVV-------------------LGEGRNRQVR 188

Query: 257 VHALHMGCPI 266
                +G P+
Sbjct: 189 RMLEAVGHPV 198


>gi|225024022|ref|ZP_03713214.1| hypothetical protein EIKCOROL_00889 [Eikenella corrodens ATCC
          23834]
 gi|224943047|gb|EEG24256.1| hypothetical protein EIKCOROL_00889 [Eikenella corrodens ATCC
          23834]
          Length = 136

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 4/56 (7%)

Query: 15 DEENMRLDRWF--KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP 68
          DE +MRLD+W      +        QK +  G+V V+  +VK +  I+ G  + + 
Sbjct: 8  DEHHMRLDKWLWAARFFK--TRGMAQKHIELGRVLVNGAKVKNSKNIEPGDTIDLT 61


>gi|145627819|ref|ZP_01783620.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 22.1-21]
 gi|144979594|gb|EDJ89253.1| ribosomal large subunit pseudouridine synthase B [Haemophilus
           influenzae 22.1-21]
          Length = 357

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 35/179 (19%), Positives = 59/179 (32%), Gaps = 31/179 (17%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPVINAL 74
           E  +L +         +   ++ ++ SG+V V+ K     +R  + SG  VRI   I  L
Sbjct: 74  EGEKLQKVLARAGQG-SRREIETMIASGRVSVEGKIAILGDRIDVHSGVKVRIDGQIINL 132

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           +H  KE                          ++ ++ KP G                  
Sbjct: 133 SHAQKEI------------------------CRVLMYYKPEGELC--TRSDPEGRATVFD 166

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
                 G +     RLD  TSG+L+       A  L      R +++ Y   V+G   +
Sbjct: 167 RLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQVDD 223


>gi|94500050|ref|ZP_01306585.1| ribosomal small subunit pseudouridine synthase [Oceanobacter sp.
           RED65]
 gi|94427908|gb|EAT12883.1| ribosomal small subunit pseudouridine synthase [Oceanobacter sp.
           RED65]
          Length = 236

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 41/255 (16%), Positives = 82/255 (32%), Gaps = 64/255 (25%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF-NNRIQSGQVVRIPPVINALNHI 77
           MRLD++  N Y  ++     K L+  +V V+   VK  ++++ +   V +      +N  
Sbjct: 1   MRLDKFLAN-YSSLSRTEATKALKQKRVLVNGDLVKTGSHKVANDDQVWLDGRRIEMNTA 59

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           +                              ++ NKPA                      
Sbjct: 60  V-----------------------------YFMMNKPANYL-----------------CA 73

Query: 138 DSKGQKPRLTHRLDQETSGIL-VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           ++  Q   +   +D+ ++ +L  V R       L       +      S    IPK  + 
Sbjct: 74  NADPQHALVFDLIDEASTYVLHTVGRLDLDTTGLLLITDDGQWSHRLTSPKHHIPKTYRV 133

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYA----ISHFKVIDCFAQKFCWLEMQPHTGRT 252
            +   L+  + I  +   +++   K    A    I+  +V+           +    GR 
Sbjct: 134 WLDEPLVADAEIQCEQGLLLRSESKPTLPAELNRITDTEVL-----------ITISEGRY 182

Query: 253 HQLRVHALHMGCPIV 267
           HQ++     MG  +V
Sbjct: 183 HQVKRMFAAMGNRVV 197


>gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum
           seropedicae SmR1]
 gi|300075686|gb|ADJ65085.1| 16S rRNA uridine-516 pseudouridylate synthase protein
           [Herbaspirillum seropedicae SmR1]
          Length = 560

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 30/187 (16%), Positives = 59/187 (31%), Gaps = 32/187 (17%)

Query: 1   MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ 60
           M      + +  E+D     L +   +     +  ++++++ +G+V V+ +      RI 
Sbjct: 181 MRGKNGRRDLTAEDDAPK--LHKVLADAGLG-SRRDMEELIVAGRVSVNGEPAHIGQRIL 237

Query: 61  SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISV 119
               VRI   +       +  +                         + V++KPAG I  
Sbjct: 238 PTDAVRINGKLIQRKVSKRPPR-------------------------VLVYHKPAGEIVS 272

Query: 120 QGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRI 179
                    +   L +    K  K     RLD  T G+L+   +   A  L         
Sbjct: 273 HADPEGRNSVFDRLPTM---KAGKWLAVGRLDYNTEGLLLFTTSGDLANRLMHPRYNIER 329

Query: 180 QKIYWSL 186
           +    +L
Sbjct: 330 EYAVRTL 336


>gi|153815230|ref|ZP_01967898.1| hypothetical protein RUMTOR_01464 [Ruminococcus torques ATCC
          27756]
 gi|317502313|ref|ZP_07960482.1| S4 RNA-binding domain-containing protein [Lachnospiraceae
          bacterium 8_1_57FAA]
 gi|331089917|ref|ZP_08338809.1| hypothetical protein HMPREF1025_02392 [Lachnospiraceae bacterium
          3_1_46FAA]
 gi|145847489|gb|EDK24407.1| hypothetical protein RUMTOR_01464 [Ruminococcus torques ATCC
          27756]
 gi|316896269|gb|EFV18371.1| S4 RNA-binding domain-containing protein [Lachnospiraceae
          bacterium 8_1_57FAA]
 gi|330403149|gb|EGG82710.1| hypothetical protein HMPREF1025_02392 [Lachnospiraceae bacterium
          3_1_46FAA]
          Length = 79

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 26/60 (43%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
          MRLD++ K            +   +G+V V+ K  K + +++ G V+ I      +   +
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVSVNGKPAKASVQVKPGDVIEIYFGTREVKAEV 60


>gi|54294518|ref|YP_126933.1| hypothetical protein lpl1594 [Legionella pneumophila str. Lens]
 gi|53754350|emb|CAH15834.1| hypothetical protein lpl1594 [Legionella pneumophila str. Lens]
 gi|307610150|emb|CBW99696.1| hypothetical protein LPW_14641 [Legionella pneumophila 130b]
          Length = 248

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 34/233 (14%), Positives = 74/233 (31%), Gaps = 34/233 (14%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +   +++ + +G V+V+ K  K  +       + +           
Sbjct: 4   ERLQKILSQAGLG-SRREMERWIDNGWVQVNGKPAKLGDSAGPSDKISV----------- 51

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWV 137
            + K++ + +               ++ ++ +++KP G +S +        +   L    
Sbjct: 52  -KGKLIPNPLKGK------------QNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLR 98

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             +  +     RLD  TSG+L+       A  L        +++ Y   V G    +   
Sbjct: 99  QGRWVQ---VGRLDLNTSGLLIFTNNGELANQL--MHPKYGLEREYAVRVHGQVSQEAL- 152

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
             N LLK   +        K   +G     S + V     +      +    G
Sbjct: 153 --NNLLKGVMLDDGLAKFTKIQFRGGEGTNSWYHVTLNEGRNREVRRLWESQG 203


>gi|297586934|ref|ZP_06945579.1| ribosomal small subunit pseudouridine synthase A [Finegoldia magna
           ATCC 53516]
 gi|297574915|gb|EFH93634.1| ribosomal small subunit pseudouridine synthase A [Finegoldia magna
           ATCC 53516]
          Length = 235

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 25/152 (16%), Positives = 54/152 (35%), Gaps = 31/152 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR             ++++++ G + V+   VK ++                     
Sbjct: 1   MRLDRMLSE-MKIATRKEIKQMVKKGIITVNDVTVKKSS--------------------- 38

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              + +D + ++ K  D    ++ Y     +V NK  G++      +       +    +
Sbjct: 39  ---EHIDENKDVVKIYD---EVIEYRKYLYFVMNKRKGVTSHSKDPMHRT---VIDDMGE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHL 170
                     RLD +T+G+L++      A +L
Sbjct: 90  LCVFDLNPVGRLDLDTTGLLIITNDGKFAHNL 121


>gi|196233446|ref|ZP_03132289.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
 gi|196222442|gb|EDY16969.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
          Length = 237

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 81/247 (32%), Gaps = 56/247 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRL+R+  +     +   +++++ SGQVR++ + V   + ++     V++   +     +
Sbjct: 1   MRLNRFLASAGLG-SRRGVEELITSGQVRINGQVVTDLSTQVGPTDAVKVGSRL-----L 54

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
             EQKI                          + NKPAG                +   +
Sbjct: 55  RTEQKIT------------------------VLLNKPAGYVCTAS---DERDRKTIFDLL 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
            +   +     RLD+++ G+L+V      +  LT        +          P+++++ 
Sbjct: 88  PANWPRVYHVGRLDKDSEGLLLVTNDGDLSLALTHPRYKIEKEYEVLLDKPFNPQDREKL 147

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +  + +       + V ++                          L +    G   Q+R+
Sbjct: 148 LKGFHIIGGRAKAERVEIL----------------------NPTHLSLTLTQGIKRQIRL 185

Query: 258 HALHMGC 264
               +G 
Sbjct: 186 MLYDLGY 192


>gi|167623648|ref|YP_001673942.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167353670|gb|ABZ76283.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 239

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 35/160 (21%), Positives = 62/160 (38%), Gaps = 9/160 (5%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           I +FNKP  +  Q            LK ++   G       RLD+++ G+L++       
Sbjct: 63  IVLFNKPFDVLCQ---FTDEQGRKTLKDYIPVPG--VYAAGRLDRDSEGLLLLTNDGKLQ 117

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             +TE    ++  K YW+ V G P +  +        +   G      +   +  A +  
Sbjct: 118 SQITE--PKKKTYKTYWAQVEGAP-DDSDLEKLRQGVELKDGMTLPAKISIMDNPAIWPR 174

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +   + +       WLE+Q   GR  Q+R    H+G P +
Sbjct: 175 TP-PIRERANIPTTWLEIQICEGRNRQVRRMTAHIGFPTL 213


>gi|260425703|ref|ZP_05779683.1| ribosomal large subunit pseudouridine synthase E [Citreicella sp.
           SE45]
 gi|260423643|gb|EEX16893.1| ribosomal large subunit pseudouridine synthase E [Citreicella sp.
           SE45]
          Length = 179

 Score = 52.7 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/161 (19%), Positives = 58/161 (36%), Gaps = 7/161 (4%)

Query: 108 IYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           + + NKP G+  Q    G A      L  +V  +  +     RLD+++ G+L++     A
Sbjct: 2   LILLNKPYGVLSQFTDKGNADSPRATLSDYV--EVPRVYPAGRLDRDSEGLLLLT-DDGA 58

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
            Q      + R+ +  Y   V G P + +       +  +        V +         
Sbjct: 59  LQARIAHPKFRKPK-TYLVQVEGDPTDDQLAQLRRGVSLNDGPTRPATVRRLPPPDLWPR 117

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +   +          WLE+    GR  Q+R    H+G P +
Sbjct: 118 VPPVRFRKSVPD--AWLELTITEGRNRQVRRMTAHVGLPCL 156


>gi|283796887|ref|ZP_06346040.1| S4 RNA-binding domain protein [Clostridium sp. M62/1]
 gi|291075297|gb|EFE12661.1| S4 RNA-binding domain protein [Clostridium sp. M62/1]
 gi|295089875|emb|CBK75982.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog) [Clostridium
          cf. saccharolyticum K10]
 gi|295114738|emb|CBL35585.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog)
          [butyrate-producing bacterium SM4/1]
          Length = 79

 Score = 52.7 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 28/57 (49%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALN 75
          MRLD++ K            +   +G+V V+ K VK +  +++G ++ I   + ++ 
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNDKAVKASYAVKTGDIIEIQFGVKSVK 57


>gi|90408508|ref|ZP_01216666.1| probable pseudouridine synthase [Psychromonas sp. CNPT3]
 gi|90310387|gb|EAS38514.1| probable pseudouridine synthase [Psychromonas sp. CNPT3]
          Length = 295

 Score = 52.7 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 36/231 (15%), Positives = 74/231 (32%), Gaps = 40/231 (17%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++ +++ G+V VD + V    R+   Q++R+      + +I +E  I         
Sbjct: 16  SRRKMETVIQEGRVSVDGQVVGLGTRVTVEQILRVDGH--TVKYITEENTIC-------- 65

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                         +I  +NKP G                 +      G +     RLD 
Sbjct: 66  --------------RILAYNKPEGEVC--TRSDEAGRKTVFERLPRLNGARWISIGRLDI 109

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+L+       A  +      R +++ Y   ++G             +  + +    
Sbjct: 110 NTSGLLLFTTDGEFANRM--MHPSREVEREYAVRIFGN------------VDDAMLNRLR 155

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG 263
           + V  ++ +    +I              W  +    GRT ++R      G
Sbjct: 156 MGVKLEDGEAKFLSIKESGKEAGGEGINRWYHVVLTEGRTREVRRLWESQG 206


>gi|313895603|ref|ZP_07829159.1| pseudouridine synthase B, ribosomal large subunit [Selenomonas sp.
           oral taxon 137 str. F0430]
 gi|312975729|gb|EFR41188.1| pseudouridine synthase B, ribosomal large subunit [Selenomonas sp.
           oral taxon 137 str. F0430]
          Length = 243

 Score = 52.7 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 83/246 (33%), Gaps = 48/246 (19%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +   N     +  + ++++R+G+V VD               V +  +    +  +
Sbjct: 3   ERLQKILANA-GIASRRSAEEMIRAGRVTVDG--------------VCVTGLGRKYDAAL 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  I    + + K ++ +            + NKP G      +         +   + 
Sbjct: 48  HE--IAVDGIPVQKETERV----------YLLLNKPVGYLS---TARDDRGRKTVLDLLP 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               +     RLD +T G+L++    A  Q L        I K+Y + + G    +    
Sbjct: 93  HTSTRLYPVGRLDADTEGLLLITNDGAMTQGL--LHPRYEIDKVYRAEIEGALTPE---- 146

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                K  H+ G  +       +    A +  ++    +     +E+  H GR  Q+R  
Sbjct: 147 -----KLRHLRGGILL------EDGITAPARVRIFAADSTVTT-VEIVIHEGRNRQVRRM 194

Query: 259 ALHMGC 264
              +GC
Sbjct: 195 FAAVGC 200


>gi|127511849|ref|YP_001093046.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126637144|gb|ABO22787.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 236

 Score = 52.7 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 38/240 (15%), Positives = 74/240 (30%), Gaps = 52/240 (21%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR+   H   I    ++ IL  G+V VD + V+        Q+ +   V+     + +
Sbjct: 7   RLDRFISQHC-QIPRKQVRLILAKGRVSVDGQVVRD----ADCQIDQFSQVMLDGQALRQ 61

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           EQ I                          + +KP G+     +         +    D 
Sbjct: 62  EQPI------------------------YLMLHKPVGVVS---ATKDDEHKTVMDLLPDY 94

Query: 140 KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIA 199
           + +   +  RLD  TSG+L++      ++ +       ++ K Y              + 
Sbjct: 95  QDKGLHIVGRLDLNTSGLLLLTNDSRWSKRI--MSPEHKVAKQYL-----------VTLK 141

Query: 200 NWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHA 259
             L +                     A    ++++          +  H GR HQ++   
Sbjct: 142 APLTQAYVKAFAEGFYFAFENITTQPA--QLEILEPH-----LARVTLHEGRYHQIKRMF 194


>gi|159111355|ref|XP_001705909.1| DRAP deaminase [Giardia lamblia ATCC 50803]
 gi|157434000|gb|EDO78235.1| DRAP deaminase [Giardia lamblia ATCC 50803]
          Length = 568

 Score = 52.7 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 22/112 (19%), Positives = 48/112 (42%), Gaps = 5/112 (4%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           N  +++  ++   ++  +     + +L  E   ++   KPA + V       YH    L 
Sbjct: 119 NFTLRDSDLILHVMHRHEPPILAQPVLRDEGDHVF-CEKPASMPVHPCGKYCYHSVNELV 177

Query: 135 SWVDSK---GQKPRLTHRLDQETSGILVVA-RTRAAAQHLTESFRMRRIQKI 182
           +  D+K    +  R  +R+D+  SG++V+A  ++ A Q   E      ++  
Sbjct: 178 ASPDTKLTTKKSLRACNRIDKLVSGLIVMADSSKEAEQKRNEIVERGNVKVY 229



 Score = 51.9 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/108 (23%), Positives = 37/108 (34%), Gaps = 13/108 (12%)

Query: 224 NYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFK 277
             AI+  + +   +          P TGRTHQLR+H    G PI  D  +         +
Sbjct: 353 QAAITVIEYVHVDSSTQTALAMCVPITGRTHQLRLHLQAAGTPIHNDPSHGGLQANLAVR 412

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSLGF 324
               SP   +  L    + +       L+ I A       K+  SL  
Sbjct: 413 CTLPSPSVLQQMLRYEPLSMKAYASKVLERIKA------QKSLQSLDL 454


>gi|326516230|dbj|BAJ88138.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 318

 Score = 52.7 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 1/55 (1%)

Query: 20 RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINA 73
          RLD      Y   +   +Q  +  G+V V+ + V K   ++    V+ I   I  
Sbjct: 43 RLDEACLERYQQYSRTYIQSWILQGKVHVNGRVVNKAGTQVSDKSVIEIKAEIPK 97


>gi|259501959|ref|ZP_05744861.1| S4 domain protein [Lactobacillus antri DSM 16041]
 gi|259170136|gb|EEW54631.1| S4 domain protein [Lactobacillus antri DSM 16041]
          Length = 87

 Score = 52.7 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
          MRLD++ K           ++I   G++ V+    K + ++++G  + I
Sbjct: 1  MRLDKFLKVSRIIKRRSVAKEIADQGRILVNNLPAKSSTKVKAGDTLTI 49


>gi|24214991|ref|NP_712472.1| pseudouridylate synthase [Leptospira interrogans serovar Lai str.
           56601]
 gi|24196034|gb|AAN49490.1| pseudouridylate synthase [Leptospira interrogans serovar Lai str.
           56601]
          Length = 246

 Score = 52.7 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 51/267 (19%), Positives = 96/267 (35%), Gaps = 57/267 (21%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            +  ++Q++ +       RL+R+  +     +    +++++ G + ++ KRV        
Sbjct: 5   EMEEFMQHLEI-------RLNRFLADCGLG-SRRKTEELIQKGHIEINGKRVT-----NL 51

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQ 120
           G   RI P I+ ++++                 D +K I+  E  KI +FNKP G +   
Sbjct: 52  G--TRIDPEIDVVSYL----------------GDVVKPIV--ESKKILIFNKPIGYLCSH 91

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                   I   L     S  +  ++  RLD  + G+L++    A AQ +T        +
Sbjct: 92  ADRFHEKTIFSLL----PSDYKNFKIAGRLDLNSRGLLILTNDGALAQKITHPSNGSEKE 147

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
                LV       ++ I     K     G+               I H K++     K 
Sbjct: 148 Y----LVTLKHDPGEKLIQAAFQKGILDAGE---------------ILHAKMVKLVPGKK 188

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIV 267
           C   +    G+  Q+R      G  +V
Sbjct: 189 CVYRVILEEGKKRQIRRMFRWFGVSVV 215


>gi|146281644|ref|YP_001171797.1| pseudouridylate synthase [Pseudomonas stutzeri A1501]
 gi|145569849|gb|ABP78955.1| probable pseudouridylate synthase [Pseudomonas stutzeri A1501]
          Length = 230

 Score = 52.7 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 81/246 (32%), Gaps = 53/246 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLDR+  +    ++  ++++++  G+ RV+ +  +  +R      VRI   +     ++
Sbjct: 1   MRLDRYLGSR-AQLSRQDVRRLVSDGRARVNGEVTRTLDR-----EVRIFDCVELDGQVL 54

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           +  K+                      ++  + +KP G            +   +    +
Sbjct: 55  QPGKV----------------------ARYVMLHKPPGCVSATRDAAHRTVIDLID---E 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR-MRRIQKIYWSLVWGIPKNKKEC 197
                  +  RLD  T+G++++      ++ LT+      ++      LV    +    C
Sbjct: 90  PDKDDLHIAGRLDFNTTGLMLLTNDGQWSRRLTQPTSLQGKVY-----LVETEDEIDPGC 144

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           +  +        G Y          A          +          +  H GR HQ++ 
Sbjct: 145 VGAF------ARGLYFRFEDLTTLPA----------ELVLLGPRRARLTLHEGRYHQVKR 188

Query: 258 HALHMG 263
              H G
Sbjct: 189 MFGHFG 194


>gi|294788878|ref|ZP_06754119.1| ribosomal large subunit pseudouridine synthase B [Simonsiella
           muelleri ATCC 29453]
 gi|294483360|gb|EFG31046.1| ribosomal large subunit pseudouridine synthase B [Simonsiella
           muelleri ATCC 29453]
          Length = 353

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 29/179 (16%), Positives = 54/179 (30%), Gaps = 30/179 (16%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           +  RL +         +   +++ + +G V+V+    +   +I     V I      L  
Sbjct: 101 QPERLQKVLAASGVG-SRREMEEWINNGWVQVNGHVARLGEKITPNDQVTIKGNAIKL-- 157

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                          K +D L  I+LY         K  G  V                 
Sbjct: 158 ---------------KWADRLPRIILY--------YKQEGEIV--SRDDPQGRISIFDRL 192

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
             +   +     RLD  TSG+L++  +    Q          +++ Y   V G    ++
Sbjct: 193 PQAASSRWVAIGRLDINTSGLLILTTSGELVQRFAHPSFE--VEREYAVRVLGELTPEQ 249


>gi|255264737|ref|ZP_05344079.1| ribosomal large subunit pseudouridine synthase E [Thalassiobium sp.
           R2A62]
 gi|255107072|gb|EET49746.1| ribosomal large subunit pseudouridine synthase E [Thalassiobium sp.
           R2A62]
          Length = 178

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 32/160 (20%), Positives = 53/160 (33%), Gaps = 8/160 (5%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + + NKP G+  Q       H    LK +V   G       RLD+++ G+LV+       
Sbjct: 4   VILLNKPFGVLSQFTDEGTNHP--TLKDYVKIPG--VYAAGRLDRDSEGLLVLTDDGRLQ 59

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             +      +   K YW+ V G P +         +K              +        
Sbjct: 60  NRIASPKFKQ--PKTYWAQVEGTPDDAALEALRAGVKLKDGMTKPARARIIDAPDVWERD 117

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
              +V         W+E+    GR  Q+R     +G P +
Sbjct: 118 PPIRVRKAIPD--TWIELVLTEGRNRQVRRMTAAVGHPTL 155


>gi|256371242|ref|YP_003109066.1| ribosomal protein S4 [Acidimicrobium ferrooxidans DSM 10331]
 gi|256007826|gb|ACU53393.1| ribosomal protein S4 [Acidimicrobium ferrooxidans DSM 10331]
          Length = 208

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 22  DRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKE 80
           D          +    ++++R G V VD +RV   + R++ GQVV + P    L+ I   
Sbjct: 102 DNVVFRALWGSSRAQARQLVRHGHVLVDGQRVDIPSYRLRPGQVVTLNPKARDLDIIAFN 161

Query: 81  QKILDSSVN 89
           ++ L   V 
Sbjct: 162 REHLTREVP 170


>gi|308162188|gb|EFO64597.1| DRAP deaminase [Giardia lamblia P15]
          Length = 568

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 23/112 (20%), Positives = 48/112 (42%), Gaps = 5/112 (4%)

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
           N  +++  ++   ++  +     + +L  E   ++   KPA + V       YH    L 
Sbjct: 119 NFTLRDSDLILHVMHRHEPPILAQPVLRDEGEHVF-CEKPASMPVHPCGKYCYHSVNELV 177

Query: 135 SWVDSK---GQKPRLTHRLDQETSGILVVA-RTRAAAQHLTESFRMRRIQKI 182
           +  D+K    +  R  +R+D+  SG++V+A  ++ A Q   E      I+  
Sbjct: 178 ASPDTKLTTKKSLRACNRIDKLVSGLVVMADSSKEAEQKRNEIVERGNIKVY 229



 Score = 51.9 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/108 (23%), Positives = 37/108 (34%), Gaps = 13/108 (12%)

Query: 224 NYAISHFKVIDCFAQKFC-WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCA-----NFK 277
             AI+  + +   +          P TGRTHQLR+H    G PI  D  +         +
Sbjct: 353 QAAITVIEYVHIDSSTRTALAMCAPITGRTHQLRLHLQAAGTPIHNDPSHGGLQANLAVR 412

Query: 278 GNFTSPIQNKLYLHARYMDLPHPEGGRLQ-ITAPLPAHMVKTWDSLGF 324
               SP   +  L    + +       L+ I A       K+  SL  
Sbjct: 413 CTLPSPSVLQQMLRYEPLSMKAYASKVLERIKA------QKSLQSLDL 454


>gi|115484941|ref|NP_001067614.1| Os11g0247400 [Oryza sativa Japonica Group]
 gi|62734664|gb|AAX96773.1| hemolysin A, putative [Oryza sativa Japonica Group]
 gi|77549558|gb|ABA92355.1| hemolysin A family protein, expressed [Oryza sativa Japonica
          Group]
 gi|113644836|dbj|BAF27977.1| Os11g0247400 [Oryza sativa Japonica Group]
          Length = 295

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 1/55 (1%)

Query: 20 RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINA 73
          RLD      +   +   +Q  +  G+V VD + V K   ++    ++ I   I  
Sbjct: 45 RLDEVCLERFQQYSRTYIQSWILQGKVLVDGRVVNKAGTQVSDKSIIEIKAEIPK 99


>gi|315185198|gb|EFU18998.1| pseudouridine synthase [Spirochaeta thermophila DSM 6578]
          Length = 86

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 4/59 (6%)

Query: 132 FLKSWVDSKG----QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
            L+      G     +  L +RLD+ TSGI++ AR R AA   ++ FR R + K+YW++
Sbjct: 28  LLEHLRRRDGAGAPPRLHLVNRLDRPTSGIVLFARHRKAAGKFSDLFRRRGVYKLYWAV 86


>gi|254457105|ref|ZP_05070533.1| RNA pseudouridylate synthase family protein [Campylobacterales
           bacterium GD 1]
 gi|207085897|gb|EDZ63181.1| RNA pseudouridylate synthase family protein [Campylobacterales
           bacterium GD 1]
          Length = 263

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 75/249 (30%), Gaps = 44/249 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL+++   H+   +     K +  G VR++ +                    N    + 
Sbjct: 3   MRLNKYIA-HHSSYSRREADKAILDGYVRINGE-----------------IQDNPATQVD 44

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           ++  I+  S       D            + V+NKP G  V             +   ++
Sbjct: 45  EKDDIVYVSGKQITPKDKYT---------VIVYNKPKGELVTKSDPKGRR---TIYDGLE 92

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR----RIQKIYWSLVWGIPKNK 194
            K +      RLD  T G+L++      A  L  S   R    +I+      +     N 
Sbjct: 93  KKYKHYIPVGRLDYATEGVLLLTDASKIASALMNSNLERIYKVKIKGEVTPEIEAAMMNG 152

Query: 195 KECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            E +       SH     +                +K I      +  L++    G+  +
Sbjct: 153 LELLDATAGGHSHSKVTSMTFAPFLG---------YK-IQKNEHNYSVLKIAISEGQNRE 202

Query: 255 LRVHALHMG 263
           +R    H G
Sbjct: 203 IRRFFAHFG 211


>gi|45657519|ref|YP_001605.1| pseudouridylate synthase [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|45600758|gb|AAS70242.1| pseudouridylate synthase [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 246

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 51/267 (19%), Positives = 96/267 (35%), Gaps = 57/267 (21%)

Query: 2   SLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS 61
            +  ++Q++ +       RL+R+  +     +    +++++ G + ++ KRV        
Sbjct: 5   EMEEFMQHLEI-------RLNRFLADCGLG-SRRKTEELIQKGHIEINGKRVT-----NL 51

Query: 62  GQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAG-ISVQ 120
           G   RI P I+ ++++                 D +K I+  E  KI +FNKP G +   
Sbjct: 52  G--TRIDPEIDVVSYL----------------GDVVKPIV--ESKKILIFNKPIGYLCSH 91

Query: 121 GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQ 180
                   I   L     S  +  ++  RLD  + G+L++    A AQ +T        +
Sbjct: 92  ADRFHEKTIFSLL----PSDYKNFKIAGRLDLNSRGLLILTNDGALAQKITHPSNGSEKE 147

Query: 181 KIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKF 240
                LV       ++ I     K     G+               I H K++     K 
Sbjct: 148 Y----LVTLKHDPGEKLIQAAFQKGILDAGE---------------ILHAKMVKLVPGKK 188

Query: 241 CWLEMQPHTGRTHQLRVHALHMGCPIV 267
           C   +    G+  Q+R      G  +V
Sbjct: 189 CVYRVILEEGKKRQIRRMFRWFGVSVV 215


>gi|317014873|gb|ADU82309.1| hypothetical protein HPGAM_07680 [Helicobacter pylori Gambia94/24]
          Length = 257

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 38/251 (15%), Positives = 86/251 (34%), Gaps = 40/251 (15%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR++++   HY   +    +K++  G+V+++ +  K  + ++    V +   +       
Sbjct: 1   MRINQFLA-HYTKHSRREAEKLVLEGRVKINHEHAKLASVVKENDKVFLDKRLIKPLKNK 59

Query: 79  KEQKIL--DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           K   ++       L   +D LK  ++YE                                
Sbjct: 60  KFSVLIYHKPKGELVSKADPLKRRVIYE-------------------------------S 88

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           ++ K        RLD  + G+L+++ ++A    L  +   +         V    +N  +
Sbjct: 89  LEKKYAHFAPVGRLDFASEGVLLLSDSKAVVSALMHANLEKEYLVKIQGFVTREMENAMQ 148

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                 LK +  G      +K  E         +++I   A K+  L +  + G+  +LR
Sbjct: 149 --EGLKLKNATKGAHQKTPIKSMEFAPFIG---YEIIKNHA-KYSKLRVIINEGKNRELR 202

Query: 257 VHALHMGCPIV 267
                    ++
Sbjct: 203 RFFAFFNAGVL 213


>gi|328353035|emb|CCA39433.1| Ribosomal large subunit pseudouridine synthase D [Pichia pastoris
           CBS 7435]
          Length = 200

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 30/76 (39%), Gaps = 3/76 (3%)

Query: 103 YEDSKIYVFNKPAGISVQGGS---GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +E     V NKP GI  Q  S   G     +  L           R   RLD ET+G LV
Sbjct: 22  FEGPGFLVINKPPGIYTQPPSFRQGNRDKSNELLPLLEKQLQTTLRQVQRLDYETTGGLV 81

Query: 160 VARTRAAAQHLTESFR 175
           V+  +  A+    + +
Sbjct: 82  VSTNKYTARMFHRNMQ 97


>gi|326316275|ref|YP_004233947.1| pseudouridine synthase Rsu [Acidovorax avenae subsp. avenae ATCC
           19860]
 gi|323373111|gb|ADX45380.1| pseudouridine synthase Rsu [Acidovorax avenae subsp. avenae ATCC
           19860]
          Length = 485

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 34/232 (14%), Positives = 68/232 (29%), Gaps = 45/232 (19%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           + + +++++  G++ V+ +      R+Q G  V++                +D       
Sbjct: 164 SRLEMEQLILEGRISVNNEPAHIGQRVQYGDQVKVNGRPIRYR--------IDPPAPR-- 213

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                          +  ++KP G  V        +     +        K +   RLD 
Sbjct: 214 ---------------VIAYHKPVGEVV--THDDPQNRPTVFRKLPRLAHGKWQSVGRLDL 256

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            T G+L+       A  L        +++ Y   V G   N+++      L       D 
Sbjct: 257 NTEGLLLFTSAGELANKL--MHPRFGLEREYAVRVLGALSNEEKQ----RLLDGVQLEDG 310

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264
           +      E G                  CW  +    GR  ++R     +G 
Sbjct: 311 MAAFGSIEDGG------------GEGSNCWYRVTISEGRNREVRRMLESVGH 350


>gi|225075257|ref|ZP_03718456.1| hypothetical protein NEIFLAOT_00260 [Neisseria flavescens
           NRL30031/H210]
 gi|241758831|ref|ZP_04756944.1| RNA-binding S4 domain protein [Neisseria flavescens SK114]
 gi|261380145|ref|ZP_05984718.1| heat shock protein 15 [Neisseria subflava NJ9703]
 gi|224953432|gb|EEG34641.1| hypothetical protein NEIFLAOT_00260 [Neisseria flavescens
           NRL30031/H210]
 gi|241321039|gb|EER57252.1| RNA-binding S4 domain protein [Neisseria flavescens SK114]
 gi|284796982|gb|EFC52329.1| heat shock protein 15 [Neisseria subflava NJ9703]
          Length = 133

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 22/96 (22%), Positives = 42/96 (43%), Gaps = 12/96 (12%)

Query: 13  ENDEENMRLDRWF--KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70
           ++D  +MRLD+W      +        QK +  G+V V+  +VK +  I +G  + +   
Sbjct: 4   DHDNSSMRLDKWLWAARFFK--TRALAQKHIELGRVLVNGSKVKNSKNISAGDTIDM--- 58

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
              LN +  + K+   +       +   + LLYE+ 
Sbjct: 59  --TLNSLPYKFKVAALNHQRRPAPE---ARLLYEED 89


>gi|167551196|ref|ZP_02344951.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|168466080|ref|ZP_02699950.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|205353355|ref|YP_002227156.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|207857656|ref|YP_002244307.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|195631355|gb|EDX49915.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|205273136|emb|CAR38093.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Gallinarum str. 287/91]
 gi|205324100|gb|EDZ11939.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|206709459|emb|CAR33800.1| ribosomal small subunit pseudouridine synthase [Salmonella enterica
           subsp. enterica serovar Enteritidis str. P125109]
 gi|326628444|gb|EGE34787.1| ribosomal small subunit pseudouridine synthase A [Salmonella
           enterica subsp. enterica serovar Gallinarum str. 9]
          Length = 231

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 77/249 (30%), Gaps = 51/249 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD            G +++     NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVD------------GDIIK-----NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHAVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +            +  +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV---------TLESPV 140

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+  + +   G    +     +      I+  +V            +    GR HQ++  
Sbjct: 141 ADDTVAQFAKGVQLHNEKDLTKPATLEVITPVQV-----------RLTISEGRYHQVKRM 189

Query: 259 ALHMGCPIV 267
              +G  +V
Sbjct: 190 FAAVGNRVV 198


>gi|121308590|dbj|BAF43685.1| hypothetical protein [Vibrio fischeri]
          Length = 354

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 38/221 (17%), Positives = 79/221 (35%), Gaps = 32/221 (14%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +   L+ ++++G+V VD +R K  +R+++    +RI   +                V++ 
Sbjct: 16  SRRELETMIQAGRVSVDGQRAKLGDRLENVDAKIRIDGHV----------------VSVK 59

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           + +D +  +L Y        +KP G                       +  +     RLD
Sbjct: 60  ESTDVICRVLAY--------HKPEGELC--TRHDPEGRRTVFDRLPKIRDSRWVSVGRLD 109

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             T+G+L+       A  L      R++++ Y   V+G    K        +K       
Sbjct: 110 ANTAGLLLFTTDGELANRL--MHPSRKVEREYMCRVFGEINEKMIRNLVSGVKLEDGEAR 167

Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           +  V+    +G N+  + + VI+   +      +    G T
Sbjct: 168 FEDVMYAGGEGMNH--TFYVVIN-EGRNREVRRLWDSQGVT 205


>gi|116628946|ref|YP_814118.1| ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit S4-like protein
          [Lactobacillus gasseri ATCC 33323]
 gi|116094528|gb|ABJ59680.1| Ribosome-associated heat shock protein implicated in the
          recycling of the 50S subunit (S4 paralog)
          [Lactobacillus gasseri ATCC 33323]
          Length = 91

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 29/53 (54%)

Query: 15 DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
          +E  MR+D++ K           +++   G+V+V+++ VK +  ++ G V+ I
Sbjct: 8  EENKMRIDKFLKVSRLVKRRTVAKEMADQGRVKVNERVVKSSYDVKVGDVIEI 60


>gi|258621922|ref|ZP_05716952.1| ribosomal small subunit pseudouridine synthase A [Vibrio mimicus
           VM573]
 gi|258585860|gb|EEW10579.1| ribosomal small subunit pseudouridine synthase A [Vibrio mimicus
           VM573]
          Length = 257

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 40/280 (14%), Positives = 90/280 (32%), Gaps = 68/280 (24%)

Query: 1   MSLMTYVQYVVV---------ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKK 51
           M  M  +++V+V         + DE +MRLD++  +            +L+SG+V VD  
Sbjct: 1   MRDM-QLRWVIVVTGLYNSRLQADEVSMRLDKFLCDAL-GTTRKEATMLLKSGEVTVDDL 58

Query: 52  RVKFN-NRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYV 110
             K    +++                              T   ++    +     +  +
Sbjct: 59  VQKSGAFKLKE-----------------------------TSCVEWQGREITAHGPRYIM 89

Query: 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA-AAQH 169
            +KP G+      G        L    +   Q      RLD +T+G+L++      + + 
Sbjct: 90  MHKPDGVVCSHEDGFNQTAFILLD---EVNIQDLHFAGRLDVDTTGLLLITDDGQWSHRV 146

Query: 170 LTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN-EKGANYAIS 228
            +   +  +  +++ +                      I  DY        E      ++
Sbjct: 147 TSPKHKCEKTYRVWLA--------------------DPIQADYAEQFTNGIELRGERELT 186

Query: 229 HFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
               ++  ++      +  H G+ HQ++     +G  ++G
Sbjct: 187 LPAQLEIVSETEVL--LTIHEGKYHQVKRMFAALGNKVIG 224


>gi|226327594|ref|ZP_03803112.1| hypothetical protein PROPEN_01465 [Proteus penneri ATCC 35198]
 gi|225204120|gb|EEG86474.1| hypothetical protein PROPEN_01465 [Proteus penneri ATCC 35198]
          Length = 303

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 22/164 (13%), Positives = 54/164 (32%), Gaps = 34/164 (20%)

Query: 20  RLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           RL+++       I +     + +  G V ++ KR    +++ +G  V++           
Sbjct: 18  RLNKYISE--SGICSRREADRYIEQGLVLINGKRASIGDQVFAGDEVKVNG--------- 66

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                      L +  D  + +       +   NKP GI      G   +I  ++     
Sbjct: 67  ----------RLIEAQDNSELV-------LIALNKPVGIVSTTDDGEKDNIVDYVNH--- 106

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
               +     RLD+++ G++ +         +  +      + +
Sbjct: 107 --STRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYL 148


>gi|71280205|ref|YP_271062.1| putative ribosomal small subunit pseudouridine synthase A
           [Colwellia psychrerythraea 34H]
 gi|71145945|gb|AAZ26418.1| putative ribosomal small subunit pseudouridine synthase A
           [Colwellia psychrerythraea 34H]
          Length = 240

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 44/255 (17%), Positives = 81/255 (31%), Gaps = 50/255 (19%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIK 79
           RLDR   +    IN   ++ IL   +V VD                 I  +++  +H++ 
Sbjct: 7   RLDRLISDS-RQINRKKVRLILAQKRVYVDGVLAT-----------DIAQLVDQFSHVVM 54

Query: 80  EQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS 139
           + ++L ++                      + NKP G+           +   L    D 
Sbjct: 55  DNEVLQANQT-----------------HYIMLNKPIGVVCATKDKKHKTVIDLLAEQFDQ 97

Query: 140 KGQK-PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
                  +  RLD  TSG++++      ++ LT      ++ K Y           +  +
Sbjct: 98  DVLDSLHIVGRLDLNTSGLVLLTNDSRWSERLT--SPEHKVSKGY-----------QVTL 144

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
            N L                       AI H  ++  F  +    E     GR HQ++  
Sbjct: 145 ENALTTDYIDAFAKGMYFPYENITTKPAILH--IVSLFEAQVSLTE-----GRYHQIKRM 197

Query: 259 ALHMGCPIVGDHKYC 273
                 P++  H+Y 
Sbjct: 198 FGRFRNPVIALHRYS 212


>gi|59711645|ref|YP_204421.1| 23S rRNA pseudouridylate synthase [Vibrio fischeri ES114]
 gi|59479746|gb|AAW85533.1| 23S rRNA pseudouridylate synthase [Vibrio fischeri ES114]
          Length = 354

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 36/202 (17%), Positives = 71/202 (35%), Gaps = 31/202 (15%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +   L+ ++++G+V VD +R K  +R+++    +RI   +                V++ 
Sbjct: 16  SRRELETMIQAGRVSVDGQRAKLGDRLENVDAKIRIDGHV----------------VSVK 59

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           + +D +  +L Y        +KP G                       +  +     RLD
Sbjct: 60  ESTDVICRVLAY--------HKPEGELC--TRHDPEGRRTVFDRLPKIRDSRWVSVGRLD 109

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             T+G+L+       A  L      R++++ Y   V+G    K   I N +       G+
Sbjct: 110 ANTAGLLLFTTDGELANRL--MHPSRKVEREYMCRVFGEINEK--MIRNLVTGVKLEDGE 165

Query: 212 YVHVVKQNEKGANYAISHFKVI 233
                     G     + + VI
Sbjct: 166 ARFEDVMYAGGEGMNHTFYVVI 187


>gi|319638355|ref|ZP_07993117.1| hsp15-like protein [Neisseria mucosa C102]
 gi|317400104|gb|EFV80763.1| hsp15-like protein [Neisseria mucosa C102]
          Length = 133

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 22/94 (23%), Positives = 40/94 (42%), Gaps = 12/94 (12%)

Query: 15  DEENMRLDRWF--KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           D  +MRLD+W      +        QK +  G+V V+  +VK +  I +G  + +     
Sbjct: 6   DNSSMRLDKWLWAARFFK--TRALAQKHIELGRVLVNGSKVKNSKNISAGDTIDM----- 58

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDS 106
            LN +  + K+   +       +   + LLYE+ 
Sbjct: 59  TLNSLPYKFKVAALNHQRRPAPE---ARLLYEED 89


>gi|146298001|ref|YP_001192592.1| pseudouridine synthase [Flavobacterium johnsoniae UW101]
 gi|146152419|gb|ABQ03273.1| ribosomal large subunit pseudouridine synthase F [Flavobacterium
           johnsoniae UW101]
          Length = 272

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 30/252 (11%), Positives = 76/252 (30%), Gaps = 59/252 (23%)

Query: 15  DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
           +E   RL+++      + +     K++  G+V ++    +   ++ S   +RI       
Sbjct: 2   EENLKRLNKFIGET-GYCSRREADKLIEEGRVTINGAAAEMGTKVSSDDEIRI------- 53

Query: 75  NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLK 134
                               D    +  +E      FNKP GI       +  +I  ++ 
Sbjct: 54  --------------------DGKLIVEKHEKLVYLAFNKPVGIECTTNLEVKNNIVDYI- 92

Query: 135 SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
               +  ++     RLD+ + G++ +         +  +      +              
Sbjct: 93  ----NYPKRIFPIGRLDKASEGLIFMTNDGDIVNKILRARNNHEKEYTV----------- 137

Query: 195 KECIANWLLKK--SHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
              +   + ++    +G     +    +K     IS +             ++    G  
Sbjct: 138 --TVNKPITERFIQRMGNGVPILDTVTKKCKVEQISKYT-----------FKIILTQGLN 184

Query: 253 HQLRVHALHMGC 264
            Q+R  + ++G 
Sbjct: 185 RQIRRMSEYLGY 196


>gi|197334991|ref|YP_002155841.1| ribosomal large subunit pseudouridine synthase B [Vibrio fischeri
           MJ11]
 gi|197316481|gb|ACH65928.1| ribosomal large subunit pseudouridine synthase B [Vibrio fischeri
           MJ11]
          Length = 354

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 36/202 (17%), Positives = 71/202 (35%), Gaps = 31/202 (15%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIPPVINALNHIIKEQKILDSSVNLT 91
           +   L+ ++++G+V VD +R K  +R+++    +RI   +                V++ 
Sbjct: 16  SRRELETMIQAGRVSVDGQRAKLGDRLENVDAKIRIDGHV----------------VSVK 59

Query: 92  KHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
           + +D +  +L Y        +KP G                       +  +     RLD
Sbjct: 60  ESTDVICRVLAY--------HKPEGELC--TRHDPEGRRTVFDRLPKIRDSRWVSVGRLD 109

Query: 152 QETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGD 211
             T+G+L+       A  L      R++++ Y   V+G    K   I N +       G+
Sbjct: 110 ANTAGLLLFTTDGELANRL--MHPSRKVEREYMCRVFGEINEK--MIRNLVTGVKLEDGE 165

Query: 212 YVHVVKQNEKGANYAISHFKVI 233
                     G     + + VI
Sbjct: 166 ARFEDVMYAGGEGMNHTFYVVI 187


>gi|290954061|ref|ZP_06558682.1| RNA pseudouridine synthase B [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295312554|ref|ZP_06803314.1| RNA pseudouridine synthase B [Francisella tularensis subsp.
           holarctica URFT1]
          Length = 198

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 25/184 (13%), Positives = 57/184 (30%), Gaps = 29/184 (15%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           ND+   RL +    +    +   +++ +  G+V+V+ K     ++      +        
Sbjct: 8   NDKNPERLQKLLAKYGIG-SRRKIEEYIEQGRVKVNGKVATLGDKASEADKISFD----- 61

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                        +++          +++Y        +K  G      S          
Sbjct: 62  -----------SKALHSYGQPMTRPRVVIY--------HKREGEVC--TSKDEKDRQTVF 100

Query: 134 KSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            S       +  +  RLD  T+G+L+       A  L       +I++ Y   V+G   +
Sbjct: 101 DSLPKLAKSRWIMVGRLDINTTGLLLFTTDGDLANRL--MHPSYQIEREYAVRVFGQQLS 158

Query: 194 KKEC 197
            +  
Sbjct: 159 DETI 162


>gi|238786961|ref|ZP_04630761.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           frederiksenii ATCC 33641]
 gi|238724749|gb|EEQ16389.1| Ribosomal large subunit pseudouridine synthase F [Yersinia
           frederiksenii ATCC 33641]
          Length = 289

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 23/144 (15%), Positives = 52/144 (36%), Gaps = 34/144 (23%)

Query: 19  MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           +RL+++       I +  +  + +  G V ++ KR    +++ +G VV++   +      
Sbjct: 6   IRLNKYISE--SGICSRRDADRYIEQGNVFINGKRAVIGDQVYAGDVVKVNGQLIDARDE 63

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     +D  + V NKP GI          +I  F+    
Sbjct: 64  --------------------------DDLVLIVLNKPVGIISTTEDSEHNNIVDFVNH-- 95

Query: 138 DSKGQKPRLTHRLDQETSGILVVA 161
               ++     RLD+++ G++ + 
Sbjct: 96  ---SKRIFPIGRLDKDSQGLIFLT 116


>gi|329297659|ref|ZP_08254995.1| 23S rRNA pseudouridylate synthase B [Plautia stali symbiont]
          Length = 292

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 27/175 (15%), Positives = 62/175 (35%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ ++ +G++ VD K     +RI++ + ++I    + ++     
Sbjct: 5   LQKVLARA-GHGSRREIEAMISAGRISVDGKLATLGDRIENDKTLKIRIDGHLVS----- 58

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
             I +S+  + +               +  + KP G                       +
Sbjct: 59  --IAESATEVCR---------------VLAYYKPEGELC--TRNDPEGRPTVFDRLPRLR 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  T G+++       A  L      R +++ Y   V+G   ++K
Sbjct: 100 GSRWIAVGRLDVNTCGLMLFTTDGELANRL--MHPSRAVEREYAVRVFGEVDDEK 152


>gi|229017689|ref|ZP_04174580.1| Pseudouridine synthase [Bacillus cereus AH1273]
 gi|229023908|ref|ZP_04180391.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228737421|gb|EEL87933.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228743615|gb|EEL93724.1| Pseudouridine synthase [Bacillus cereus AH1273]
          Length = 238

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 31/249 (12%), Positives = 72/249 (28%), Gaps = 60/249 (24%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
           N+R++++        +     K++   +V ++ K  K  +++  G  VR+          
Sbjct: 3   NLRINKFISEAGK-ASRRGADKLINERRVIINGKVAKIGDQVNPGDDVRVNGEQLR---- 57

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                   +  D      NKP GI+      +  +I   +   +
Sbjct: 58  ------------------------IARDHVYIALNKPVGITCTSEKAVKGNIIDLVNHPL 93

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
                +     RLD+++ G++++         +  +      + I               
Sbjct: 94  -----RINHIGRLDKDSDGLILLTNDGDIVNEILRAENKHEKEYIVS------------- 135

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH--TGRTHQL 255
                     I  +++  +    K     I   K + C   +    E +     G   Q+
Sbjct: 136 ------VDKPITPEFLEKMAAGVK-----ILDTKTLPCEITQLSKYEFKIILTQGLNRQI 184

Query: 256 RVHALHMGC 264
           R     +G 
Sbjct: 185 RRMCEALGY 193


>gi|218283273|ref|ZP_03489328.1| hypothetical protein EUBIFOR_01917 [Eubacterium biforme DSM 3989]
 gi|218215963|gb|EEC89501.1| hypothetical protein EUBIFOR_01917 [Eubacterium biforme DSM 3989]
          Length = 89

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 40/87 (45%), Gaps = 5/87 (5%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++ K           +++   G++ V+ +  K +  ++ G  +RI      L    
Sbjct: 1   MRLDKYLKTARILKRREAAKELALQGRIWVNDRVAKPSTELKIGDTIRIRFGARLL---- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYED 105
            E ++LD    ++K +  L   +++E+
Sbjct: 57  -EIRVLDIQKQVSKQNAQLLFEIIHEE 82


>gi|313682076|ref|YP_004059814.1| RNA-binding s4 domain protein [Sulfuricurvum kujiense DSM 16994]
 gi|313154936|gb|ADR33614.1| RNA-binding S4 domain protein [Sulfuricurvum kujiense DSM 16994]
          Length = 82

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 12/75 (16%), Positives = 32/75 (42%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
          MR+D++  +          Q ++  G V ++ K VK +  +  G ++ +  +   + + +
Sbjct: 1  MRIDKFLNSVNLTKRRTVAQDMIGEGVVYINGKAVKPSKNVAVGDIITLIYLDKEMKYEV 60

Query: 79 KEQKILDSSVNLTKH 93
               + S+    +H
Sbjct: 61 LAIPTIKSTPKSQQH 75


>gi|261367125|ref|ZP_05980008.1| heat shock protein 15 [Subdoligranulum variabile DSM 15176]
 gi|282571248|gb|EFB76783.1| heat shock protein 15 [Subdoligranulum variabile DSM 15176]
          Length = 83

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
          MRLD++ K            ++  +G+V V+ K  K +  +++G V+ I      +   +
Sbjct: 1  MRLDKYLKVSRLIKRRTLANEVADAGRVLVNDKPAKASYAVKTGDVIEITFGNRPIKVRV 60

Query: 79 ---KEQKILDSSVNLTKHSDF 96
             +E K  D +  L +  D 
Sbjct: 61 LSTEEPKGKDVARELFEVMDL 81


>gi|124267222|ref|YP_001021226.1| putative arginine/proline rich protein [Methylibium petroleiphilum
           PM1]
 gi|124259997|gb|ABM94991.1| putative arginine/proline rich protein [Methylibium petroleiphilum
           PM1]
          Length = 421

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 83/252 (32%), Gaps = 29/252 (11%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVI 71
             +E N RL +         +     + +  G VRVD + V +   R++  Q + I P  
Sbjct: 164 PPEELNPRLSKRMSE-LGLASRREADEWIEQGYVRVDGEVVDQLGARVRPEQQITIDPQA 222

Query: 72  NALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDG 131
                    ++    ++ L K   ++      ED        PA   V   +  A   DG
Sbjct: 223 RL-------EQAQRVTILLHKPLGYVSGQ--AEDGHA-----PAFTLVTAANRWAT--DG 266

Query: 132 FLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
             + +  S+ +      RLD +++G+LV+ +    A+ L        ++K Y   V    
Sbjct: 267 SKQRFNASQLKHLVPAGRLDLDSTGLLVLTQDGRVAKLL--IGEDSPVEKEYVVRVQWTA 324

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
           + +   +               H +  + +    A           Q    L      G+
Sbjct: 325 RPELTDLKQHF--PPEALARLRHGLALDGEKLKPA-------KVSWQNEQHLRFVLREGK 375

Query: 252 THQLRVHALHMG 263
             Q+R     +G
Sbjct: 376 KRQIRRMCELVG 387


>gi|152992058|ref|YP_001357779.1| hemolysin A [Sulfurovum sp. NBC37-1]
 gi|151423919|dbj|BAF71422.1| hemolysin A [Sulfurovum sp. NBC37-1]
          Length = 237

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
          MRLD++        +     + +++GQV VD K+ K + +I +   V +
Sbjct: 1  MRLDKYLVEEGYFESRNRALEAIKAGQVTVDGKKAKPSVKIDTNSYVEV 49


>gi|149913759|ref|ZP_01902291.1| Pseudouridine synthase, Rsu [Roseobacter sp. AzwK-3b]
 gi|149812043|gb|EDM71874.1| Pseudouridine synthase, Rsu [Roseobacter sp. AzwK-3b]
          Length = 195

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 33/168 (19%), Positives = 64/168 (38%), Gaps = 21/168 (12%)

Query: 108 IYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           + +FNKP G+  Q    G+A      L   +D  G  P    RLD+++ G+L++      
Sbjct: 4   LILFNKPYGVLSQFTDKGMADSKRATLSDHIDLPGVYP--AGRLDRDSEGLLLLTDDGKL 61

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKN-------KKECIANWLLKKSHIGGDYVHVVKQN 219
            + +       + +KIY   V  IP +       +   + +   + + +       + + 
Sbjct: 62  QERIASPRF--KTEKIYLVQVERIPDDAAIEALCRGVTLKDGPTRPARVSRIAPPDLWER 119

Query: 220 EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           +    +           +   CWL +    GR  Q+R    H+G P +
Sbjct: 120 DPPVRF---------RKSVPDCWLSITISEGRNRQVRRMTAHVGHPTL 158


>gi|170781661|ref|YP_001709993.1| putative RNA pseudouridine synthase [Clavibacter michiganensis
           subsp. sepedonicus]
 gi|169156229|emb|CAQ01371.1| putative RNA pseudouridine synthase [Clavibacter michiganensis
           subsp. sepedonicus]
          Length = 291

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 40/256 (15%), Positives = 84/256 (32%), Gaps = 52/256 (20%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
           +     +RL +         +    + ++ +G+V V+ + V      + G+ +       
Sbjct: 19  DEPVAGVRLQKVMAAA-GVASRRVCEDMIAAGRVTVNGETVT-----EPGRRI------- 65

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                           ++ + +   +++ L    +  + NKP GI     S         
Sbjct: 66  --------------DPDVDEVAVDDQAVQLDTSKRYLMLNKPVGIYS---SLRDERGRPD 108

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI-- 190
           L+ + +   ++     RLD ETSG+L++      A  L        + K Y + V G   
Sbjct: 109 LREFTEEFEERLFNVGRLDAETSGLLILTNDGDLAHVLAHPSFG--VLKTYIAKVTGRVT 166

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
           P+  +       L+   I  D   ++                          +E+  H+G
Sbjct: 167 PQTIQRLTQGVDLEDGPIQADRARIL------------------SGGGDQTLVEITLHSG 208

Query: 251 RTHQLRVHALHMGCPI 266
           R   +R     +G P+
Sbjct: 209 RNRIVRRMLDEVGHPV 224


>gi|109899770|ref|YP_663025.1| pseudouridine synthase, Rsu [Pseudoalteromonas atlantica T6c]
 gi|109702051|gb|ABG41971.1| ribosomal small subunit pseudouridine synthase A [Pseudoalteromonas
           atlantica T6c]
          Length = 241

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 74/248 (29%), Gaps = 50/248 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RLD+   N   + +    + +L+  +V V  +  K                        
Sbjct: 14  KRLDQLLSN-LGYCSRKEARYLLKGKRVTVKGEFAKS----------------------- 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
              K+  ++V +   +      +L       + NKP G      +     I   L    +
Sbjct: 50  PALKVDPATVRVDGEALDAPDGIL------VMLNKPLGYVCSHDNNEGMRIYDLLPERWE 103

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +  K     RLD++TSG+++V         LT       + K+Y   V    +      
Sbjct: 104 FRNPKIVSVGRLDKDTSGLILVTDDTKLVHQLT--SPKHHVDKVYQVSVDCPLQ------ 155

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
                  S I   +   V   E       +  +++          E     G+ HQ+R  
Sbjct: 156 -------SDIIDSFAKGVVLGEGAEQCLPAKIEIVSENVANVTLNE-----GKYHQVRRM 203

Query: 259 ALHMGCPI 266
               G  +
Sbjct: 204 FAACGYHV 211


>gi|331092507|ref|ZP_08341329.1| hypothetical protein HMPREF9477_01972 [Lachnospiraceae bacterium
          2_1_46FAA]
 gi|330400728|gb|EGG80331.1| hypothetical protein HMPREF9477_01972 [Lachnospiraceae bacterium
          2_1_46FAA]
          Length = 79

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 26/60 (43%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
          MRLD++ K            +   +G+V V+    K + +++ G ++ I     ++   +
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVLVNGLVAKASQKVKVGDIIEIQFGTKSVKAEV 60


>gi|329894510|ref|ZP_08270324.1| Ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium IMCC3088]
 gi|328923035|gb|EGG30360.1| Ribosomal large subunit pseudouridine synthase B [gamma
           proteobacterium IMCC3088]
          Length = 303

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 28/182 (15%), Positives = 55/182 (30%), Gaps = 31/182 (17%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
              +++ +L +         +   ++K +  G+V++D +  +  +R+     + +     
Sbjct: 26  SKSQKDEKLQKVLARAGLG-SRREMEKWISDGRVKLDGRIAELGDRVCDNAAIEVDGQA- 83

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                            L++        LLY        +KP G                
Sbjct: 84  -----------------LSRAPAEAVRCLLY--------HKPTGEVCTRKDPEGRR--TV 116

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
            +     KG +     RLD  TSG+L+       A  L        I++ Y   V G   
Sbjct: 117 FERLPKVKGGRWISIGRLDYNTSGLLLFTTDGELANAL--MHPSAVIEREYMVRVMGEWD 174

Query: 193 NK 194
             
Sbjct: 175 TD 176


>gi|289548515|ref|YP_003473503.1| ribosomal protein S4 [Thermocrinis albus DSM 14484]
 gi|289182132|gb|ADC89376.1| ribosomal protein S4 [Thermocrinis albus DSM 14484]
          Length = 209

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 16/93 (17%), Positives = 34/93 (36%), Gaps = 4/93 (4%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHII 78
           RLD               ++ +  G + V+ K+V   +  ++ G V+ + P    +  II
Sbjct: 99  RLDNVVYRLGIACTRRQARQFVAHGHILVNGKKVNIPSYLVEPGDVIEVKPSSRDIPQII 158

Query: 79  KEQKILDS---SVNLTKHSDFLKSILLYEDSKI 108
           +  + +D       L    +  +  +L     I
Sbjct: 159 ENLENMDPRSVPPWLELDKENFRGKVLDYPKDI 191


>gi|148981998|ref|ZP_01816586.1| pseudouridine synthase family 1 protein [Vibrionales bacterium
           SWAT-3]
 gi|145960686|gb|EDK26030.1| pseudouridine synthase family 1 protein [Vibrionales bacterium
           SWAT-3]
          Length = 381

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 32/252 (12%), Positives = 71/252 (28%), Gaps = 56/252 (22%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVIN 72
             + +  RL+++        +     K++ +G+V ++ K  +   ++  G  V I     
Sbjct: 2   SQESQAKRLNKYISET-GFCSRREADKLIDAGRVTINGKIPEMGTKVMPGDDVEIDNKPV 60

Query: 73  ALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF 132
                 KE+ I                            NKP GI+      I  +I  F
Sbjct: 61  RS----KEKPI------------------------YIALNKPTGITCTTERDIPGNIVDF 92

Query: 133 LKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
           +        ++     RLD+ + G++ +         +  +      + +          
Sbjct: 93  I-----GHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVV--------- 138

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
                          I G+++  +       +      KV     +      +    G  
Sbjct: 139 ----------RVDKPITGEFLQKMAAGVPILDTVTLPCKVEK---ETKFSFRITLTQGLN 185

Query: 253 HQLRVHALHMGC 264
            Q+R     +G 
Sbjct: 186 RQIRRMCEALGY 197


>gi|295692139|ref|YP_003600749.1| RNA-binding s4 domain protein [Lactobacillus crispatus ST1]
 gi|295030245|emb|CBL49724.1| RNA-binding S4 domain protein [Lactobacillus crispatus ST1]
          Length = 90

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 10/83 (12%), Positives = 34/83 (40%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MR+D++ K           +++   G+++V+ + VK +  ++   ++ +      +   +
Sbjct: 1   MRIDKFLKVSRLVKRRTVAKEMADQGRIKVNGRVVKSSYDVKIDDIIEVGYGAKTIKAKV 60

Query: 79  KEQKILDSSVNLTKHSDFLKSIL 101
              +        ++  +  K I+
Sbjct: 61  LNIRETTKKAEASELYELAKCII 83


>gi|160915077|ref|ZP_02077290.1| hypothetical protein EUBDOL_01085 [Eubacterium dolichum DSM 3991]
 gi|158432876|gb|EDP11165.1| hypothetical protein EUBDOL_01085 [Eubacterium dolichum DSM 3991]
          Length = 230

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 81/247 (32%), Gaps = 57/247 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR-IQSGQVVRIPPVINALNHI 77
           MRLD++  +         ++K++RS +VRV+ +     +R +Q    V +          
Sbjct: 1   MRLDKYLAHAQLG-TRKEVKKLIRSKRVRVNDEICTKEDRQLQKEDCVYVD--------- 50

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                 +L+Y++    +  KP G+     +         +  + 
Sbjct: 51  --------------------DELLVYDELVYLMLYKPQGVIS---ATEDRVHTTVMDIFD 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRA-AAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
               +      RLD ++ G+L++      A Q L+     + + K Y+        ++  
Sbjct: 88  APLPKNCFPVGRLDIDSEGLLLITNDGQLAHQLLS---PKKHVDKTYYVECEKTLSSE-- 142

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
                LL+   I  D  HV+    K           I   +      E     G+ HQ++
Sbjct: 143 --DLQLLESGTIQLDKEHVLPAQAK----------RISANSLYLTIQE-----GKFHQVK 185

Query: 257 VHALHMG 263
                 G
Sbjct: 186 RMLQACG 192


>gi|83859466|ref|ZP_00952987.1| RNA pseudouridylate synthase family protein [Oceanicaulis
           alexandrii HTCC2633]
 gi|83852913|gb|EAP90766.1| RNA pseudouridylate synthase family protein [Oceanicaulis
           alexandrii HTCC2633]
          Length = 354

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 24/197 (12%), Positives = 65/197 (32%), Gaps = 37/197 (18%)

Query: 12  VENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70
              +E   R+ +    H    +    ++++  G+V V+ + ++    ++ +G  VR+   
Sbjct: 10  TPEEEGGERIAKVLA-HAGIASRREAERLIEKGRVSVNGEILRTPAFKVMAGDDVRVDGE 68

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
                   +                            ++ ++KP G+            D
Sbjct: 69  SIGQRPPTR----------------------------VWRYHKPVGLLTTHSDPQG--RD 98

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHL----TESFRMRRIQKIYWSL 186
              ++     G +     RLD  + G+L++      A+ L    T   R  R++    + 
Sbjct: 99  TVFQTLPQDMG-RVISVGRLDLNSEGLLLLTNDGELARVLELPSTGWTRRYRVRAYGNAS 157

Query: 187 VWGIPKNKKECIANWLL 203
              + + +   + + ++
Sbjct: 158 DKALAELENGTVVDGVV 174


>gi|332283699|ref|YP_004415610.1| pseudouridylate synthase [Pusillimonas sp. T7-7]
 gi|330427652|gb|AEC18986.1| pseudouridylate synthase [Pusillimonas sp. T7-7]
          Length = 598

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 24/141 (17%), Positives = 46/141 (32%), Gaps = 29/141 (20%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   +++++ +G+V V+ +      R+ +   VR+        +  K  +I         
Sbjct: 166 SRREMEELIVAGRVSVNGEPAHIGQRVGANDQVRVNGRPIVRPNAKKPPRI--------- 216

Query: 93  HSDFLKSILLYEDSKIYVFNKPAG-ISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLD 151
                   +LY        +KPAG I                      +  K     RLD
Sbjct: 217 --------ILY--------HKPAGEIVSHDDP---EGRATVFARLPKMRVGKWLSVGRLD 257

Query: 152 QETSGILVVARTRAAAQHLTE 172
             T G+L++  +   A  L  
Sbjct: 258 LNTEGLLILTTSGDLANRLMH 278


>gi|226940953|ref|YP_002796027.1| ribosome-associated heat shock protein HSP15 [Laribacter
          hongkongensis HLHK9]
 gi|226715880|gb|ACO75018.1| probable ribosome-associated heat shock protein HSP15 [Laribacter
          hongkongensis HLHK9]
          Length = 131

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 10/53 (18%), Positives = 27/53 (50%), Gaps = 2/53 (3%)

Query: 16 EENMRLDRWF-KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
          ++ +RLD+W     + +      Q  + +G V ++ +R K +  +++G  + +
Sbjct: 5  QDRVRLDKWLWAARF-YKTRGLAQDAIEAGHVSLNGERAKPSRLVKAGDRIEL 56


>gi|82776628|ref|YP_402977.1| 23S rRNA pseudouridylate synthase B [Shigella dysenteriae Sd197]
 gi|309789069|ref|ZP_07683664.1| ribosomal large subunit pseudouridine synthase B [Shigella
           dysenteriae 1617]
 gi|81240776|gb|ABB61486.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
 gi|308923340|gb|EFP68852.1| ribosomal large subunit pseudouridine synthase B [Shigella
           dysenteriae 1617]
          Length = 290

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 61/177 (34%), Gaps = 31/177 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V +D +  K  +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSIDGRIAKLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVRESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G   + K
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDDAK 152


>gi|71903794|ref|YP_280597.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS6180]
 gi|94988815|ref|YP_596916.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS9429]
 gi|94992701|ref|YP_600800.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS2096]
 gi|71802889|gb|AAX72242.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS6180]
 gi|94542323|gb|ABF32372.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS9429]
 gi|94546209|gb|ABF36256.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS2096]
          Length = 238

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 26/179 (14%), Positives = 56/179 (31%), Gaps = 38/179 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD+         +   ++K++++  V VD    +     +  G Q++ +         
Sbjct: 1   MRLDKLL-EGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQR----- 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   + +      + NKP+G+           +   L   
Sbjct: 55  ------------------------VTHPKHSYIILNKPSGVVSAKKDTNYLTVIDQLAE- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            + K        RLD++T G++++        + L     +  + K Y   V G+    
Sbjct: 90  -EDKSPDLYPVGRLDRDTEGLVLLTDNGPLGFRMLH---PIHHVSKTYLVTVNGLLAED 144


>gi|323209958|gb|EFZ94867.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
          Length = 150

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 58/175 (33%), Gaps = 31/175 (17%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHII 78
           L +       H +   ++ I+ +G+V VD K     +R++   G  +RI   +       
Sbjct: 5   LQKVLARA-GHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHL------- 56

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
                    +++ + ++ +  +L Y         KP G                      
Sbjct: 57  ---------ISVKESAEQICRVLAY--------YKPEGELC--TRNDPEGRPTVFDRLPK 97

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKN 193
            +G +     RLD  T G+L+       A  L      R +++ Y   V+G    
Sbjct: 98  LRGARWIAVGRLDVNTCGLLLFTTDGELANRL--MHPSREVEREYAVRVFGQVDE 150


>gi|73748599|ref|YP_307838.1| RsuA family pseudouridine synthase [Dehalococcoides sp. CBDB1]
 gi|147669359|ref|YP_001214177.1| ribosomal large subunit pseudouridine synthase B [Dehalococcoides
           sp. BAV1]
 gi|289432625|ref|YP_003462498.1| pseudouridine synthase [Dehalococcoides sp. GT]
 gi|73660315|emb|CAI82922.1| pseudouridine synthase, RsuA family [Dehalococcoides sp. CBDB1]
 gi|146270307|gb|ABQ17299.1| ribosomal large subunit pseudouridine synthase B [Dehalococcoides
           sp. BAV1]
 gi|288946345|gb|ADC74042.1| pseudouridine synthase [Dehalococcoides sp. GT]
          Length = 249

 Score = 52.7 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 31/237 (13%), Positives = 73/237 (30%), Gaps = 51/237 (21%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKF-NNRIQS-GQVVRIPPVINALNHIIKEQKILDSSVNL 90
           +   + + ++ G V ++ ++ +  +  + +    V     +  L+ + +           
Sbjct: 22  SRRKMAEAIKQGLVTLNGQKAESYSQPVNTQKDKVTFEGKLVVLSRVRR----------- 70

Query: 91  TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAY-HIDGFLKSWVDSKGQKPRLTHR 149
                      +Y      + NKP  I       +    +   L    +  G       R
Sbjct: 71  -----------IY-----LMLNKPPEIVSTTSDELGRKTVMDLLHRRYEGAG--LFPVGR 112

Query: 150 LDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIG 209
           LD+ T+G++++         LT        + +  S+   + +  KE +   +L    + 
Sbjct: 113 LDEATTGLILLTNDGEMTNRLTHPSYEIEKEYL-ISIDAALTQADKESLEKGILLDDGLT 171

Query: 210 GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266
                    +E   NY                  ++  H G+   +R     +G PI
Sbjct: 172 SPARLSRVTDEPPYNY------------------KLIIHEGKKRIVRRMFARLGHPI 210


>gi|291276387|ref|YP_003516159.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
 gi|290963581|emb|CBG39413.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
          Length = 273

 Score = 52.3 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 86/245 (35%), Gaps = 40/245 (16%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRL+++   H+   +      ++  G+V V+KK+      ++ GQ V +           
Sbjct: 1   MRLNQYIA-HHSKYSRREADGLIAQGRVNVEKKKAVLGQELKEGQRVFVD---------- 49

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGG--SGIAYHIDGFLKSW 136
                      L +  D   ++++Y        +KP G  V      G     D   + +
Sbjct: 50  --------GKQLREKKDGPSTVIVY--------HKPKGELVTRSDDRGRRSIFDSLGRRY 93

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
                       RLD  + G+L+++  +  A  L +S   R        +   + +  KE
Sbjct: 94  A-----HFTPVGRLDFASEGLLLLSDDKKIAHFLMQSDLERE---YILKISGAVTEKMKE 145

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
            + N L  +    G +     Q      +A   F  I    + F  L+++   G+  +LR
Sbjct: 146 AMENGLELEDARAGGHEKSKIQKMSFKPFA---FYQIQKNDRNFSKLKVRITEGKNRELR 202

Query: 257 VHALH 261
               H
Sbjct: 203 RFFAH 207


>gi|322715286|gb|EFZ06857.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 231

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/253 (13%), Positives = 75/253 (29%), Gaps = 59/253 (23%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           MRLD++       ++     + +R  +V VD            G +++     NA   ++
Sbjct: 1   MRLDKFIAQQL-GVSRAIAGREIRGNRVTVD------------GDIIK-----NAAFKLL 42

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            E  +      L +              + ++ NKP G      S         L    +
Sbjct: 43  PEHAVAYDGNPLAQQHGP----------RYFMLNKPQGYVC---STDDPDHPTVLYFLDE 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
               K     RLD +T+G++++      +  +T          +               +
Sbjct: 90  PVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLV-------------TL 136

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYA----ISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254
            + +   +         +   +     A    I+  +V            +    GR HQ
Sbjct: 137 ESPVADDTAAQFAKGVQLHNEKDLTKPATLEVITPVQV-----------RLTISEGRYHQ 185

Query: 255 LRVHALHMGCPIV 267
           ++     +G  +V
Sbjct: 186 VKRMFAAVGNCVV 198


>gi|254474543|ref|ZP_05087929.1| ribosomal large subunit pseudouridine synthase E [Ruegeria sp. R11]
 gi|214028786|gb|EEB69621.1| ribosomal large subunit pseudouridine synthase E [Ruegeria sp. R11]
          Length = 251

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 34/162 (20%), Positives = 56/162 (34%), Gaps = 8/162 (4%)

Query: 108 IYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA 166
           +  FNKP  +  Q    G        L  W+D  G  P    RLD+++ G++++  T   
Sbjct: 4   LIRFNKPYDVLPQFTDRGSTDSPRATLSDWIDLPGVYP--AGRLDRDSEGLMLL--TDQG 59

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
                 S    ++ K YW  V G P           ++               E    +A
Sbjct: 60  RLQAWISDPQHKMPKTYWVQVEGTPDAAAITALAEGVELKDGLTRPAKARLIAEPEGLWA 119

Query: 227 ISH-FKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +   +V         W+E+    GR  Q+R     +G P +
Sbjct: 120 RNPPIRVRKSVPD--SWIELTIREGRNRQVRRMTAAVGHPTL 159


>gi|167759630|ref|ZP_02431757.1| hypothetical protein CLOSCI_01988 [Clostridium scindens ATCC
          35704]
 gi|167662756|gb|EDS06886.1| hypothetical protein CLOSCI_01988 [Clostridium scindens ATCC
          35704]
          Length = 79

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 23/49 (46%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI 67
          MRLD++ K            +   +G+V V+    K + +++ G ++ I
Sbjct: 1  MRLDKFLKVSRLIKRRTVANEACDAGRVTVNGSVAKASVKVKPGDIIEI 49


>gi|120437125|ref|YP_862811.1| ribosomal large subunit pseudouridine synthase F [Gramella forsetii
           KT0803]
 gi|117579275|emb|CAL67744.1| ribosomal large subunit pseudouridine synthase F [Gramella forsetii
           KT0803]
          Length = 266

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/166 (11%), Positives = 56/166 (33%), Gaps = 30/166 (18%)

Query: 17  ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNH 76
           E +R++++      + +     K++  G++ ++ K  +   ++  G +V++     +   
Sbjct: 3   EEVRINKYLS-QLGYCSRRAADKLIDQGRITINDKVPEMGTKVTPGDLVKVDGKPVSKEE 61

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
           +                          E +    FNKP GI     + +    D  +   
Sbjct: 62  LK-------------------------EPNVYIAFNKPVGIVCTTDTRVE--KDNIIDYI 94

Query: 137 VDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182
             +  ++     RLD+ + G++ +         +  +      + +
Sbjct: 95  --NYPKRIFPIGRLDKPSEGLIFLTNDGDIVNKILRARNNHEKEYV 138


>gi|322434202|ref|YP_004216414.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX9]
 gi|321161929|gb|ADW67634.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX9]
          Length = 312

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 75/254 (29%), Gaps = 40/254 (15%)

Query: 18  NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHI 77
             RL +         +    ++I+  G+V+V+   V             +    +A    
Sbjct: 23  GERLQKILAQA-GLASRRKAEEIILDGRVQVNGTVVT-----------ELGTRADATKDH 70

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
           I+    L                   E  K Y+ NKP G           H    ++   
Sbjct: 71  IRVDGKLIKGP---------------EQQKYYMVNKPRGYVT--TLDDPQHRPTVMQLMT 113

Query: 138 DSKGQK-----PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPK 192
              G            RLD  + G+L++      A  L+++     ++K Y     G+P 
Sbjct: 114 PKSGPHETQVRLYPVGRLDYLSEGLLLMTNDGDLANALSKASTG--VEKTYLVKTSGVPP 171

Query: 193 NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           +         +       D V   +++      A    KV         W E+    GR 
Sbjct: 172 DSALDQIRRGIMIDRGRLDEVRAGRRDRILTAPA----KVELVRRGDNPWYEVTLTEGRN 227

Query: 253 HQLRVHALHMGCPI 266
            QLR     +G  +
Sbjct: 228 RQLRKMFEEVGHHV 241


>gi|325576785|ref|ZP_08147400.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325160991|gb|EGC73109.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 230

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/160 (19%), Positives = 63/160 (39%), Gaps = 8/160 (5%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + +FNKP  +  Q       +    LK ++           RLD+++ G+L++       
Sbjct: 38  VILFNKPFDVLTQ---FTDENGRATLKDFI--IIPNVYAAGRLDRDSEGLLILTNNGEVQ 92

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI 227
             L +     + +K Y++ V GIP+ + +        +   G      V+   +      
Sbjct: 93  HRLADPKF--KTEKTYFAQVEGIPE-ESDLDKLRQGVELKDGMTKPAKVRLISEPDFLWP 149

Query: 228 SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +  + +  +    WLE++   GR  Q+R    H+G P +
Sbjct: 150 RNPPIRERQSIPTSWLEIKISEGRNRQVRRMTAHIGFPTL 189


>gi|261838734|gb|ACX98500.1| pseudouridine synthase B [Helicobacter pylori 51]
          Length = 262

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/169 (15%), Positives = 63/169 (37%), Gaps = 30/169 (17%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           +R++++   HY   +    +K++  G+V+++ +  K ++ ++    V +      L   +
Sbjct: 6   LRINQFLA-HYTMHSRREAEKLVLEGRVKINHEHAKLSSVVKENDKVFLD---KRLIKPL 61

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
           K +K                         + V++KP G  V     +       +   ++
Sbjct: 62  KNKKFS-----------------------VLVYHKPKGELVSKNDPLKRR---VIYESLE 95

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187
            K        RLD  + G+L+++ ++A    L  +   +       S V
Sbjct: 96  KKYAHFAPVGRLDFASEGVLLLSDSKAVVSALMHANLEKEYLVKIQSFV 144


>gi|94994641|ref|YP_602739.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10750]
 gi|94548149|gb|ABF38195.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           pyogenes MGAS10750]
          Length = 238

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/179 (14%), Positives = 56/179 (31%), Gaps = 38/179 (21%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG-QVVRIPPVINALNH 76
           MRLD+         +   ++K++++  V VD    +     +  G Q++ +         
Sbjct: 1   MRLDKLL-EGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQR----- 54

Query: 77  IIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSW 136
                                   + +      + NKP+G+           +   L   
Sbjct: 55  ------------------------VTHPKHSYIILNKPSGVVSAKKDTNYLTVIDQLAE- 89

Query: 137 VDSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNK 194
            + K        RLD++T G++++        + L     +  + K Y   V G+    
Sbjct: 90  -EDKSPDLYPVGRLDRDTEGLVLLTDNGPLGFRMLH---PIHHVSKTYLVTVNGLLAED 144


>gi|15890001|ref|NP_355682.1| hypothetical protein Atu2752 [Agrobacterium tumefaciens str. C58]
 gi|15157972|gb|AAK88467.1| conserved hypothetical protein [Agrobacterium tumefaciens str. C58]
          Length = 138

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 17/89 (19%), Positives = 37/89 (41%), Gaps = 9/89 (10%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
            RLD+W        +    Q  ++SG V+V+   ++  ++ +++G  + I          
Sbjct: 13  QRLDKWLFFARMAKSRSLAQSYIQSGHVKVNGATIRQPSHMLKAGDRLDIGFERM----- 67

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDS 106
               K+L       +   + ++ LLY+D 
Sbjct: 68  ---DKVLVVKSGGARRGPYEEARLLYDDQ 93


>gi|326796234|ref|YP_004314054.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
 gi|326546998|gb|ADZ92218.1| pseudouridine synthase Rsu [Marinomonas mediterranea MMB-1]
          Length = 298

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/220 (15%), Positives = 68/220 (30%), Gaps = 40/220 (18%)

Query: 33  NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTK 92
           +   ++  +R G+V V+ +     +R+     + +     +++   + ++          
Sbjct: 16  SRREMENRIREGRVVVNGEVATLGDRVGLEDQIELDGYPVSVSGAGQNRR---------- 65

Query: 93  HSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQ 152
                          + ++NKP G                       +G++     RLD 
Sbjct: 66  ---------------VIIYNKPEGEVC--TRKDPEGRPTVFDRLPKLRGERWIAVGRLDI 108

Query: 153 ETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDY 212
            TSG+L+       A  L        I + Y   V G   ++        LKK  +  D 
Sbjct: 109 NTSGLLLFTTDGELANRL--MHPSTEIDREYLVRVMGQVTDEHI----ATLKKGVLLDDG 162

Query: 213 VHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRT 252
           +        G    I+H+  +       C +E +    R 
Sbjct: 163 MASFSDVVDGGGEGINHWFYV-------CLMEGRNREVRR 195


>gi|320156638|ref|YP_004189017.1| ribosomal small subunit pseudouridine synthase A [Vibrio vulnificus
           MO6-24/O]
 gi|319931950|gb|ADV86814.1| ribosomal small subunit pseudouridine synthase A [Vibrio vulnificus
           MO6-24/O]
          Length = 233

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/248 (14%), Positives = 81/248 (32%), Gaps = 56/248 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHI 77
           MRLD++  +           KIL+SG+V V+++  K    ++    V+       A+   
Sbjct: 1   MRLDKFLCDAL-GATRKEATKILKSGEVTVNEQVQKSGAVKVTEECVIEWQGRELAM--- 56

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                     +  +  +  KP G       G  +     L    
Sbjct: 57  --------------------------QGPRYIMLYKPEGFVCSHEDGFNHTAFVLLD--- 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVART-RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKE 196
           + K  +     RLD +T+G++++    + + +  +   +  +  +++ +           
Sbjct: 88  EVKMDELHFAGRLDVDTTGLVLITDDGKWSHRITSPKHKCDKTYRVWLA----------- 136

Query: 197 CIANWLLKKSHIGGDYVHVVKQNEKGANYA-ISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255
                      IG DY   + +  +  N   ++    +         + +  H G+ HQ+
Sbjct: 137 ---------DPIGSDYAEKLAEGVQLRNEKELTLPAQMSIVNADENEVLLTIHEGKYHQV 187

Query: 256 RVHALHMG 263
           +     +G
Sbjct: 188 KRMFAALG 195


>gi|255572704|ref|XP_002527285.1| Hemolysin A, putative [Ricinus communis]
 gi|223533378|gb|EEF35129.1| Hemolysin A, putative [Ricinus communis]
          Length = 312

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 3/71 (4%)

Query: 20  RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHII 78
           RLD      +   +   +Q  +  G+V VD K V K    +    VV I  +     ++ 
Sbjct: 69  RLDEICLERFQQYSRTFIQSWILQGKVFVDGKMVNKAGTPVSDKAVVEI--MAEVPKYVC 126

Query: 79  KEQKILDSSVN 89
           +    L++++ 
Sbjct: 127 RAGHKLEAAIE 137


>gi|194364580|ref|YP_002027190.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
 gi|194347384|gb|ACF50507.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
          Length = 268

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/253 (15%), Positives = 69/253 (27%), Gaps = 54/253 (21%)

Query: 13  ENDEENMRLDRWFKNHYPHI---NFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69
            N    +R               +     + +  G+VRV            SG++VR P 
Sbjct: 23  PNASSGVR--HGLARVLSKAGVCSRSEAARWIAEGRVRV------------SGRIVRDPE 68

Query: 70  VINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHI 129
              A      E      +              LY      + NKP G+     +      
Sbjct: 69  FPIASPAPPIEVDGQPMAAPQR----------LY-----LMLNKPRGVVT---TAQDERG 110

Query: 130 DGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188
              +    D  G        RLD+ + G+L+ +     A HLT+                
Sbjct: 111 RDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAHLTD---------------- 154

Query: 189 GIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
             P+   +   +  + +         +    E    + ++    +     K  WLE+   
Sbjct: 155 --PETGPQKTYHVQVDRLPDEDTLAALRAGVEDEGEFLVALAVRVLRSGDKTAWLEVVLD 212

Query: 249 TGRTHQLRVHALH 261
            GR   +R     
Sbjct: 213 EGRNRHIRRLLAA 225


>gi|120600175|ref|YP_964749.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|146291897|ref|YP_001182321.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|120560268|gb|ABM26195.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           W3-18-1]
 gi|145563587|gb|ABP74522.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           putrefaciens CN-32]
 gi|319425188|gb|ADV53262.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 229

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/252 (15%), Positives = 79/252 (31%), Gaps = 56/252 (22%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHI 77
           MRLD++       +     +K L  G +  D   +K    ++  G  + +          
Sbjct: 1   MRLDKFICES-TSLTRSLAKKALHRGDITCDGVVIKDAGFKVTEGMQICLEGEP------ 53

Query: 78  IKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWV 137
                                  ++    +  + NKP        S I       L    
Sbjct: 54  -----------------------IVLVGERYVMLNKPVDTIC---STIDEAYPSVLSLLD 87

Query: 138 DSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC 197
             K +   +  RLD +T+G++++          ++     +I                + 
Sbjct: 88  IPKPETLHIAGRLDADTTGLVLIT---------SDGQWSHKITSPKKECGKRYLVQLADP 138

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKG-ANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR 256
           + + L++    G     V  +NE G    A+   ++ID    +    E     G+ HQ++
Sbjct: 139 VDDGLIEVFAKG-----VALRNEDGLTKPAV--LEIIDPQQVRLTITE-----GKYHQVK 186

Query: 257 VHALHMGCPIVG 268
                +G  +VG
Sbjct: 187 RMFAAVGNLVVG 198


>gi|317121959|ref|YP_004101962.1| ribosomal large subunit pseudouridine synthase B [Thermaerobacter
           marianensis DSM 12885]
 gi|315591939|gb|ADU51235.1| ribosomal large subunit pseudouridine synthase B [Thermaerobacter
           marianensis DSM 12885]
          Length = 320

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 34/246 (13%), Positives = 72/246 (29%), Gaps = 46/246 (18%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
            RL +         +   ++  + +G++ V+ +      R                   +
Sbjct: 4   QRLQKLLSRA-GIASRRQVENWIAAGRITVNGRPAVLGTR----------ADPERDVIAV 52

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
             + + D    L +              +  + +KP G+             G       
Sbjct: 53  DGRPLADLRQRLARK-------------RYVMLHKPRGMVTTLRDPQGRPSVGDFCRRAG 99

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK-EC 197
            +G  P    RLD ++ G+L++         LT       + K+Y  LV G  + ++   
Sbjct: 100 LRGLHP--VGRLDFDSEGLLLLTDDGELTFALT--HPRHEVDKVYHVLVRGPLEPQRLRR 155

Query: 198 IANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257
           + + +L            + +   G                   W+E+    GR  Q+R 
Sbjct: 156 LRDGVLLDDGPARARSARILRPRPGG-----------------GWVEVVLREGRKRQVRR 198

Query: 258 HALHMG 263
               +G
Sbjct: 199 MCRAVG 204


>gi|261867923|ref|YP_003255845.1| ribosomal large subunit pseudouridine synthase B [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413255|gb|ACX82626.1| ribosomal large subunit pseudouridine synthase B [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 328

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 43/253 (16%), Positives = 81/253 (32%), Gaps = 47/253 (18%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNR--IQSGQVVRIPPV 70
            +  E  +L +         +   ++ I+   +V VD K     +R  + +G  +RI   
Sbjct: 35  TSAAEGEKLQKVLARAGQG-SRREIEAIIAENRVSVDGKIATLGDRINVYAGVKLRIDGH 93

Query: 71  INALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHID 130
           +                +NLT+    +  +++Y         K  G              
Sbjct: 94  L----------------INLTQAQKEVCRVVMY--------YKAEGELC--TRHDPEGRA 127

Query: 131 GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190
                     G +     RLD  TSG+L+       A  L      R +++ Y   V+G 
Sbjct: 128 TVFDRLPRLTGARWIAVGRLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFGQ 185

Query: 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTG 250
                  + + +L +   G      V+  +  AN+     KV+        W ++    G
Sbjct: 186 -------VDDAMLNRLKKG------VQLEDGPANFK--EIKVVGGVGMNQ-WFDVTLMEG 229

Query: 251 RTHQLRVHALHMG 263
           R  ++R      G
Sbjct: 230 RNREVRRLWESQG 242


>gi|261496009|ref|ZP_05992419.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|261308259|gb|EEY09552.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
          Length = 227

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/162 (19%), Positives = 60/162 (37%), Gaps = 12/162 (7%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
           + + NKP  +  Q            LK ++      P    RLD+++ G+L++       
Sbjct: 36  LVLLNKPYDVLTQ---FTDEQGRKTLKDFITMPNIYP--VGRLDRDSEGLLLLTNNGEIQ 90

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKK--ECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
             L      ++  K YW  V G+P+ +   +      LK        V  +   +   + 
Sbjct: 91  HRLAHPKFDKQ--KTYWVQVEGVPQPEDLAKLAKGVELKDGLTKPAKVRAIATPDFAWHI 148

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           A    ++ +       W+E+    G+  Q+R    H+G P +
Sbjct: 149 AP---QIRERKTIPTSWIELIISEGKNRQVRRMTAHIGFPTL 187


>gi|332141187|ref|YP_004426925.1| RNA pseudouridine synthase family protein [Alteromonas macleodii
           str. 'Deep ecotype']
 gi|327551209|gb|AEA97927.1| RNA pseudouridine synthase family protein [Alteromonas macleodii
           str. 'Deep ecotype']
          Length = 248

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/253 (13%), Positives = 77/253 (30%), Gaps = 56/253 (22%)

Query: 14  NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA 73
           +D+   RL+++  +     +     K++   +V V+    +   +I    +V++   I  
Sbjct: 2   SDQAPKRLNKYISDT-GLCSRREADKLIEQKRVSVNNHPPELGTKIGPNDIVKVDGKIVG 60

Query: 74  LNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFL 133
                K  ++                          V+NKP GI+         H+ G  
Sbjct: 61  AVAKDKSDRV------------------------YIVYNKPIGITC----TTERHVKG-- 90

Query: 134 KSWVDSKGQKPRL--THRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIP 191
            + +D+ G K R+    RLD+ + G++++         +  +      +           
Sbjct: 91  -NIIDAIGHKARIFPVGRLDKPSEGLIILTSDGDIVNKILRAENAHDKEYEV-------- 141

Query: 192 KNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGR 251
                           I   +V  + +        ++   V+    +      +    G 
Sbjct: 142 -----------TVNQPISERFVKRMARGVPILGT-VTKPCVVKPTGKNT--FTIILTQGL 187

Query: 252 THQLRVHALHMGC 264
             Q+R     +G 
Sbjct: 188 NRQIRRMCEFLGY 200


>gi|71901117|ref|ZP_00683224.1| Pseudouridine synthase, Rsu [Xylella fastidiosa Ann-1]
 gi|71729122|gb|EAO31246.1| Pseudouridine synthase, Rsu [Xylella fastidiosa Ann-1]
          Length = 236

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 83/245 (33%), Gaps = 50/245 (20%)

Query: 19  MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHII 78
           M+L ++  N   + +   + +I R G++  +            G+V+     +     + 
Sbjct: 1   MKLLKYIAN-LGYGSRKEVARIFRDGRIT-NG----------EGEVLYADDHVQ-HTAVR 47

Query: 79  KEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD 138
            + + LD    L         ++L++ S      K AG  V             L +   
Sbjct: 48  FDGEPLDPPPGL--------MVMLHKPSGYICSTKDAGRLV----------YDLLPARFR 89

Query: 139 SKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECI 198
            +        RLD +TSG+L++     A  H   S +    +    +LV  +  ++    
Sbjct: 90  LRSPLLSTVGRLDGDTSGLLLLT-DDGALLHRMISPKTHLPKVYEATLVQALRGDEATLF 148

Query: 199 ANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258
           A+  L           ++  + K    A+   +V+     +    E     GR HQ+R  
Sbjct: 149 ASGTL-----------LLDGDTKPLQPAV--LEVLGPCQVRLTLYE-----GRYHQVRRM 190

Query: 259 ALHMG 263
               G
Sbjct: 191 FGATG 195


>gi|227326052|ref|ZP_03830076.1| 23S rRNA pseudouridylate synthase B [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 294

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/175 (17%), Positives = 60/175 (34%), Gaps = 27/175 (15%)

Query: 21  LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKE 80
           L +       H +   ++ I+++G+V VD K     +R++    V     I    H++  
Sbjct: 5   LQKVLARA-GHGSRREIEVIIQAGRVSVDGKIATLGDRVE----VTKATKIRIDGHVVTV 59

Query: 81  QKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK 140
           ++  +S                     + ++ KP G                       +
Sbjct: 60  KETEESVCR------------------VLMYYKPEGELC--TRNDPDGRPTVFDRLPKIQ 99

Query: 141 GQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK 195
           G +     RLD  TSG+L+       A  L      R +++ Y   V+G   ++K
Sbjct: 100 GSRWVAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGEVDDEK 152


  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
   0.311    0.142    0.405 

Lambda     K      H
   0.267   0.0439    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,706,315,934
Number of Sequences: 14124377
Number of extensions: 295714886
Number of successful extensions: 825362
Number of sequences better than 10.0: 10000
Number of HSP's better than 10.0 without gapping: 16511
Number of HSP's successfully gapped in prelim test: 7462
Number of HSP's that attempted gapping in prelim test: 749550
Number of HSP's gapped (non-prelim): 27225
length of query: 346
length of database: 4,842,793,630
effective HSP length: 140
effective length of query: 206
effective length of database: 2,865,380,850
effective search space: 590268455100
effective search space used: 590268455100
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.2 bits)
S2: 82 (36.1 bits)